Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network representation that
offers unmatched efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop, simulated annealing, stochastic
gradient) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon),
but it is first and foremost an efficient computational engine. Users can
easily implement their algorithms by taking advantage of fast gradient computing
routines, as well as network reconstruction functionality (removing weights
and redundant neurons, reordering inputs, merging networks). Networks can be
exported to C functions in order to integrate them into virtually any software
solution.
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.5.0 dated 2015-10-12 and 0.6.0 dated 2015-12-31
FCNN4R-0.5.0/FCNN4R/man/mlp_net-single-weight-access.Rd |only FCNN4R-0.5.0/FCNN4R/man/mlp_net-weight-indexing.Rd |only FCNN4R-0.6.0/FCNN4R/DESCRIPTION | 27 FCNN4R-0.6.0/FCNN4R/MD5 | 107 - FCNN4R-0.6.0/FCNN4R/NAMESPACE | 7 FCNN4R-0.6.0/FCNN4R/R/dataset.R |only FCNN4R-0.6.0/FCNN4R/R/fcnn4r.R |only FCNN4R-0.6.0/FCNN4R/R/mlp_gteach.R | 7 FCNN4R-0.6.0/FCNN4R/R/mlp_net.R | 595 +++++----- FCNN4R-0.6.0/FCNN4R/R/mlp_plot.R | 14 FCNN4R-0.6.0/FCNN4R/R/mlp_prune.R | 16 FCNN4R-0.6.0/FCNN4R/R/mlp_teach.R | 183 ++- FCNN4R-0.6.0/FCNN4R/man/FCNN4R-package.Rd | 46 FCNN4R-0.6.0/FCNN4R/man/is.mlp_net.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_actvfunc2str.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_check_inout.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_check_w.Rd | 14 FCNN4R-0.6.0/FCNN4R/man/mlp_eval.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_export_C.Rd | 14 FCNN4R-0.6.0/FCNN4R/man/mlp_net-MSE-gradients.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_net-absolute-weight-indices.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-accessing-individual-weights.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-class.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_net-combining-two-networks.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_net-export-import.Rd | 38 FCNN4R-0.6.0/FCNN4R/man/mlp_net-general-information.Rd | 5 FCNN4R-0.6.0/FCNN4R/man/mlp_net-manipulating-network-inputs.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-names.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_net-weights-access.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_net.Rd | 4 FCNN4R-0.6.0/FCNN4R/man/mlp_plot.Rd | 11 FCNN4R-0.6.0/FCNN4R/man/mlp_prune_mag.Rd | 12 FCNN4R-0.6.0/FCNN4R/man/mlp_prune_obs.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_rm_neurons.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_rnd_weights.Rd | 4 FCNN4R-0.6.0/FCNN4R/man/mlp_set_activation.Rd | 19 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_bp.Rd | 22 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_grprop.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_rprop.Rd | 20 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_sa.Rd | 12 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_sgd.Rd |only FCNN4R-0.6.0/FCNN4R/man/read-write-fcnndataset.Rd |only FCNN4R-0.6.0/FCNN4R/src/Makevars | 2 FCNN4R-0.6.0/FCNN4R/src/Makevars.win | 2 FCNN4R-0.6.0/FCNN4R/src/dataset.cpp |only FCNN4R-0.6.0/FCNN4R/src/fcnn/activation.h | 58 FCNN4R-0.6.0/FCNN4R/src/fcnn/error.h | 3 FCNN4R-0.6.0/FCNN4R/src/fcnn/export.cpp | 455 ++++--- FCNN4R-0.6.0/FCNN4R/src/fcnn/export.h | 27 FCNN4R-0.6.0/FCNN4R/src/fcnn/level1.h | 2 FCNN4R-0.6.0/FCNN4R/src/fcnn/level2.cpp | 68 - FCNN4R-0.6.0/FCNN4R/src/fcnn/level2.h | 8 FCNN4R-0.6.0/FCNN4R/src/fcnn/level3.cpp | 56 FCNN4R-0.6.0/FCNN4R/src/fcnn/level3.h | 12 FCNN4R-0.6.0/FCNN4R/src/fcnn/struct.cpp | 245 +++- FCNN4R-0.6.0/FCNN4R/src/fcnn/struct.h | 46 FCNN4R-0.6.0/FCNN4R/src/fcnn/utils.cpp | 32 FCNN4R-0.6.0/FCNN4R/src/fcnn/utils.h | 7 FCNN4R-0.6.0/FCNN4R/src/fcnn/version.h |only FCNN4R-0.6.0/FCNN4R/src/interface.cpp | 316 +++-- 60 files changed, 1655 insertions(+), 933 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
is more familiar to experienced R users. Also, implements various functions
related to topic modeling. It works well with with the "lda" package by J.
Chang.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 1.5.0 dated 2015-12-30 and 1.5.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/CalcLikelihoodC.cpp | 13 +++++++------ src/CalcSumSquares.cpp | 2 +- src/HellingerMat.cpp | 8 +++++--- src/Hellinger_cpp.cpp | 6 +++--- src/JSD_cpp.cpp | 6 +++--- src/JSDmat.cpp | 6 +++--- 8 files changed, 33 insertions(+), 30 deletions(-)
Title: Interface to 'Sunlight' Foundation 'APIs'
Description: Interface to three 'Sunlight' Foundation 'APIs' (http://
sunlightfoundation.com/api/) for government data, including the
Congress 'API' 'v3', the Capitol Words 'API', and the Open States
'API'. 'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that collects and
provides data on government activities, and those that influence government.
Functions are provided to interact with each of the three 'APIs'.
Author: Scott Chamberlain [aut, cre],
Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rsunlight versions 0.4.0 dated 2015-07-01 and 0.4.2 dated 2015-12-31
rsunlight-0.4.0/rsunlight/R/ie_contr.R |only rsunlight-0.4.0/rsunlight/R/ie_contr_bundled.R |only rsunlight-0.4.0/rsunlight/R/ie_earmarks.R |only rsunlight-0.4.0/rsunlight/R/ie_entities.R |only rsunlight-0.4.0/rsunlight/R/ie_epa.R |only rsunlight-0.4.0/rsunlight/R/ie_faca.R |only rsunlight-0.4.0/rsunlight/R/ie_getcontracts.R |only rsunlight-0.4.0/rsunlight/R/ie_getgrants.R |only rsunlight-0.4.0/rsunlight/R/ie_getlobbying.R |only rsunlight-0.4.0/rsunlight/R/ie_individuals.R |only rsunlight-0.4.0/rsunlight/R/ie_industries.R |only rsunlight-0.4.0/rsunlight/R/ie_misconduct.R |only rsunlight-0.4.0/rsunlight/R/ie_organizations.R |only rsunlight-0.4.0/rsunlight/R/ie_politicians.R |only rsunlight-0.4.0/rsunlight/data/ie_sectors.rda |only rsunlight-0.4.0/rsunlight/man/ie_contr.Rd |only rsunlight-0.4.0/rsunlight/man/ie_contr_bundled.Rd |only rsunlight-0.4.0/rsunlight/man/ie_contracts.Rd |only rsunlight-0.4.0/rsunlight/man/ie_earmarks.Rd |only rsunlight-0.4.0/rsunlight/man/ie_entities.Rd |only rsunlight-0.4.0/rsunlight/man/ie_epa.Rd |only rsunlight-0.4.0/rsunlight/man/ie_faca.Rd |only rsunlight-0.4.0/rsunlight/man/ie_grants.Rd |only rsunlight-0.4.0/rsunlight/man/ie_individuals.Rd |only rsunlight-0.4.0/rsunlight/man/ie_industries.Rd |only rsunlight-0.4.0/rsunlight/man/ie_lobbying.Rd |only rsunlight-0.4.0/rsunlight/man/ie_misconduct.Rd |only rsunlight-0.4.0/rsunlight/man/ie_organizations.Rd |only rsunlight-0.4.0/rsunlight/man/ie_politicians.Rd |only rsunlight-0.4.0/rsunlight/man/ie_sectors.Rd |only rsunlight-0.4.2/rsunlight/DESCRIPTION | 20 - rsunlight-0.4.2/rsunlight/MD5 | 127 ++++------ rsunlight-0.4.2/rsunlight/NAMESPACE | 11 rsunlight-0.4.2/rsunlight/R/cg_bills.R | 14 + rsunlight-0.4.2/rsunlight/R/cg_committees.R | 4 rsunlight-0.4.2/rsunlight/R/cg_legislators.R | 12 rsunlight-0.4.2/rsunlight/R/cw_timeseries.R | 4 rsunlight-0.4.2/rsunlight/R/defunct.R |only rsunlight-0.4.2/rsunlight/R/query.R | 8 rsunlight-0.4.2/rsunlight/R/rsunlight-package.R | 17 - rsunlight-0.4.2/rsunlight/R/tbldf.R | 7 rsunlight-0.4.2/rsunlight/R/zzz.R | 12 rsunlight-0.4.2/rsunlight/README.md | 79 +----- rsunlight-0.4.2/rsunlight/build/vignette.rds |binary rsunlight-0.4.2/rsunlight/inst/doc/rsunlight_vignette.Rmd | 127 ---------- rsunlight-0.4.2/rsunlight/inst/doc/rsunlight_vignette.html | 122 +-------- rsunlight-0.4.2/rsunlight/inst/ignore/rt_ind_exp.R |only rsunlight-0.4.2/rsunlight/inst/ignore/rt_new_filing.R |only rsunlight-0.4.2/rsunlight/inst/img/unnamed-chunk-10-1.png |binary rsunlight-0.4.2/rsunlight/man/cg_amendments.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_bills.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_committees.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_districts.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_documents.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_floor_updates.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_hearings.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_legislators.Rd | 35 +- rsunlight-0.4.2/rsunlight/man/cg_nominations.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_upcoming_bills.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_votes.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_dates.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_phrases.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_text.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_timeseries.Rd | 14 - rsunlight-0.4.2/rsunlight/man/ie_contr-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_contr_bundled-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_contracts-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_earmarks-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_entities-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_epa-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_faca-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_grants-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_individuals-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_industries-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_lobbying-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_organizations-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_politicians-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_sectors-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/os_billlookup.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_billsearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_legislatorsearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_statemetasearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/rsunlight-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/rsunlight-package.Rd | 15 - rsunlight-0.4.2/rsunlight/man/sessions.Rd | 2 rsunlight-0.4.2/rsunlight/man/type_sum.Rd | 2 rsunlight-0.4.2/rsunlight/tests/testthat/test-cg_bills.R |only rsunlight-0.4.2/rsunlight/tests/testthat/test-cg_legislators.R |only rsunlight-0.4.2/rsunlight/tests/testthat/test-trunc_mat.R |only rsunlight-0.4.2/rsunlight/vignettes/rsunlight_vignette.Rmd | 127 ---------- 90 files changed, 227 insertions(+), 566 deletions(-)
Title: Extreme Value Analysis with Goodness-of-Fit Testing
Description: Goodness-of-fit tests for selection of r in the r-largest order
statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the
peaks-over-threshold approach. Random number generation and density functions
for the GEVr distribution. Profile likelihood for return level estimation
using the GEVr and generalized pareto distributions. P-value adjustments for
sequential, multiple testing error control.
Author: Brian Bader [aut, cre],
Jun Yan [aut]
Maintainer: Brian Bader <brianbader@mail.com>
Diff between eva versions 0.1.1 dated 2015-12-29 and 0.1.2 dated 2015-12-31
DESCRIPTION | 8 +-- MD5 | 88 +++++++++++++++++++------------------- R/gevr.R | 19 ++++---- R/gevrEd.R | 10 ++-- R/gevrFit.R | 3 - R/gevrMultScore.R | 9 ++- R/gevrPbScore.R | 9 ++- R/gevrProfShape.R | 7 +-- R/gevrRl.R | 13 +++-- R/gevrSeqTests.R | 20 ++++---- R/gpd.R | 104 +++++++++++++++++++++++---------------------- R/gpdAd.R | 7 +-- R/gpdCvm.R | 7 +-- R/gpdImAsym.R | 11 ++-- R/gpdImPb.R | 9 ++- R/gpdMultScore.R | 9 ++- R/gpdPbScore.R | 7 +-- R/gpdProfShape.R | 7 +-- R/gpdRl.R | 11 ++-- R/gpdSeqTests.R | 17 +++---- R/lowestoft.R | 2 R/mrlPlot.R | 7 +-- R/pSeqStop.R | 9 ++- inst/doc/introduction.html | 2 man/gevr.Rd | 3 - man/gevrEd.Rd | 10 +--- man/gevrFit.Rd | 3 - man/gevrMultScore.Rd | 10 +--- man/gevrPbScore.Rd | 10 +--- man/gevrProfShape.Rd | 8 +-- man/gevrRl.Rd | 15 ++---- man/gevrSeqTests.Rd | 25 +++------- man/gpd.Rd | 37 +++++++++------- man/gpdAd.Rd | 8 +-- man/gpdCvm.Rd | 8 +-- man/gpdImAsym.Rd | 13 ++--- man/gpdImPb.Rd | 11 +--- man/gpdMultScore.Rd | 8 +-- man/gpdPbScore.Rd | 8 +-- man/gpdProfShape.Rd | 8 +-- man/gpdRl.Rd | 13 ++--- man/gpdSeqTests.Rd | 23 +++------ man/lowestoft.Rd | 2 man/mrlPlot.Rd | 2 man/pSeqStop.Rd | 10 +--- 45 files changed, 309 insertions(+), 321 deletions(-)
Title: Estimation and Comparison of Dynamic Treatment Regimes
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials.
Author: Xinyu Tang [aut, cre],
Maria Melguizo [aut]
Maintainer: Xinyu Tang <xtang@uams.edu>
Diff between DTR versions 1.6 dated 2015-05-06 and 1.7 dated 2015-12-31
DESCRIPTION | 14 ++++----- MD5 | 14 ++++----- NAMESPACE | 4 -- R/plot.CHR.R | 75 ++++++++++++++++-------------------------------- R/plot.DTR.R | 80 ++++++++++++++++++---------------------------------- inst/NEWS.Rd | 6 +++ man/DTR-internal.Rd | 5 --- man/DTR-package.Rd | 4 +- 8 files changed, 78 insertions(+), 124 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.9 dated 2015-12-22 and 0.9.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/beamer_presentation.R | 4 ++-- R/html_resources.R | 2 +- R/pdf_document.R | 6 +++--- R/render.R | 12 +++++++++--- R/tufte_handout.R | 2 +- inst/NEWS | 9 +++++++++ man/beamer_presentation.Rd | 4 ++-- man/pdf_document.Rd | 4 ++-- man/tufte_handout.Rd | 4 ++-- tests/testthat/test-resources.R | 13 +++++++++++++ 12 files changed, 59 insertions(+), 31 deletions(-)
Title: Financial Functions & More
Description: This fills the gaps credit analysts and loan modellers at
Optimum Credit identify in the existing R code body.
It allows for the production of documentation with less coding,
replicates a number of Microsoft Excel functions useful for
modelling loans (without rounding), and other helpful functions
for producing charts and tables. It also has some additional scales for
use, including a GBP scale.
Author: Stephanie Locke [aut, cre]
Maintainer: Stephanie Locke <stephanie.g.locke@gmail.com>
Diff between optiRum versions 0.37.1 dated 2015-11-07 and 0.37.3 dated 2015-12-31
optiRum-0.37.1/optiRum/inst/doc/index.Rmd |only optiRum-0.37.1/optiRum/inst/doc/presentation.Rmd |only optiRum-0.37.1/optiRum/vignettes |only optiRum-0.37.3/optiRum/DESCRIPTION | 10 ++-- optiRum-0.37.3/optiRum/MD5 | 28 +++++------- optiRum-0.37.3/optiRum/NAMESPACE | 9 +++- optiRum-0.37.3/optiRum/NEWS | 10 ++++ optiRum-0.37.3/optiRum/R/optiRum-package.r | 6 +- optiRum-0.37.3/optiRum/R/theme_optimum.R | 35 +++++++++++++--- optiRum-0.37.3/optiRum/README.md | 4 - optiRum-0.37.3/optiRum/build/vignette.rds |binary optiRum-0.37.3/optiRum/inst/doc/index.html | 10 ++-- optiRum-0.37.3/optiRum/inst/doc/presentation.html | 6 +- optiRum-0.37.3/optiRum/man/theme_optimum.Rd | 4 - optiRum-0.37.3/optiRum/tests/testthat/datatabletest.Rnw | 2 optiRum-0.37.3/optiRum/tests/testthat/datatabletest.pdf |binary 16 files changed, 79 insertions(+), 45 deletions(-)
Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3.1 dated 2015-10-11 and 0.3.2 dated 2015-12-31
DESCRIPTION | 19 ++++++++------- MD5 | 24 +++++++++---------- NAMESPACE | 2 - R/scales.R | 45 ++++++++++++++++++++++++++++-------- R/viridis.R | 24 +++++++++++-------- build/vignette.rds |binary inst/doc/intro-to-viridis.Rmd | 2 - inst/doc/intro-to-viridis.html | 50 +++++++++++++++++++++++++---------------- man/scale_viridis.Rd | 14 +++++++++-- man/viridis.Rd | 16 ++++++++----- man/viridis.map.Rd | 2 - man/viridis_pal.Rd | 9 +++++-- vignettes/intro-to-viridis.Rmd | 2 - 13 files changed, 134 insertions(+), 75 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.13.1 dated 2015-12-22 and 0.13.1.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Rvcg-package.R | 4 ++-- inst/NEWS.Rd | 10 +++++++++- man/Rvcg-package.Rd | 4 ++-- src/vcglib/vcg/math/base.h | 12 +++++++----- 6 files changed, 29 insertions(+), 19 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb],
Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.6 dated 2015-10-11 and 0.2.8 dated 2015-12-31
networkD3-0.2.6/networkD3/data/MisLinks.tab |only networkD3-0.2.6/networkD3/data/MisNodes.tab |only networkD3-0.2.6/networkD3/man/energy.Rd |only networkD3-0.2.6/networkD3/man/flare.Rd |only networkD3-0.2.8/networkD3/DESCRIPTION | 10 + networkD3-0.2.8/networkD3/MD5 | 50 ++++---- networkD3-0.2.8/networkD3/NAMESPACE | 2 networkD3-0.2.8/networkD3/NEWS | 71 +++++++----- networkD3-0.2.8/networkD3/R/data-definitions.R | 46 +------ networkD3-0.2.8/networkD3/R/sankeyNetwork.R | 42 +++++-- networkD3-0.2.8/networkD3/README.md | 24 ++-- networkD3-0.2.8/networkD3/data/MisLinks.rda |only networkD3-0.2.8/networkD3/data/MisNodes.rda |only networkD3-0.2.8/networkD3/inst/htmlwidgets/forceNetwork.js | 36 ++---- networkD3-0.2.8/networkD3/inst/htmlwidgets/sankeyNetwork.js | 47 ++++++- networkD3-0.2.8/networkD3/man/JS.Rd | 2 networkD3-0.2.8/networkD3/man/MisLinks.Rd | 7 - networkD3-0.2.8/networkD3/man/MisNodes.Rd | 9 + networkD3-0.2.8/networkD3/man/as.radialNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/chordNetwork.Rd | 21 +-- networkD3-0.2.8/networkD3/man/dendroNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/diagonalNetwork.Rd | 5 networkD3-0.2.8/networkD3/man/forceNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/networkD3-package.Rd | 2 networkD3-0.2.8/networkD3/man/networkD3-shiny.Rd | 6 - networkD3-0.2.8/networkD3/man/radialNetwork.Rd | 5 networkD3-0.2.8/networkD3/man/sankeyNetwork.Rd | 31 +++-- networkD3-0.2.8/networkD3/man/saveNetwork.Rd | 4 networkD3-0.2.8/networkD3/man/simpleNetwork.Rd | 3 29 files changed, 253 insertions(+), 179 deletions(-)
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness. This is the 'lite' version of the more complete 'viridis' package
that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.1 dated 2015-11-13 and 0.1.1 dated 2015-12-31
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/viridis.R | 31 ++++++++++++++++--------------- man/viridis.Rd | 17 ++++++++++------- 4 files changed, 35 insertions(+), 30 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 3.0 dated 2015-10-29 and 3.1 dated 2015-12-31
DESCRIPTION | 8 ++-- MD5 | 48 +++++++++++++------------- NEWS | 5 ++ R/fitsde.R | 10 ++--- R/ftpsde.R | 36 +++++++++---------- R/rsde.R | 36 +++++++++---------- R/snssde.R | 80 ++++++++++++++++++++++---------------------- R/st.int.R | 12 +++--- R/zzz.r | 6 +-- build/vignette.rds |binary inst/doc/FitSDE.Rnw | 7 ++- inst/doc/FitSDE.pdf |binary inst/doc/Introduction.Rnw | 2 - inst/doc/Introduction.pdf |binary inst/doc/SDEs.Rnw | 4 +- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |binary man/Sim.DiffProc-package.Rd | 4 +- man/bridgesde2d.Rd | 2 - man/fitsde.Rd | 5 +- vignettes/Core_FitSDE.tex | 29 ++++++++------- vignettes/FitSDE.Rnw | 7 ++- vignettes/Introduction.Rnw | 2 - vignettes/SDEs.Rnw | 4 +- vignettes/Thumbs.db |binary 25 files changed, 157 insertions(+), 150 deletions(-)
Title: Paralellised Versions of Constraint Based Causal Discovery
Algorithms
Description: Parallelise constraint based causality discovery and causal inference methods. The parallelised algorithms in the package will generate the same results as that of the 'pcalg' package but will be much more efficient.
Author: Thuc Duy Le, Tao Hoang, Shu Hu, and Liang Zhang
Maintainer: Thuc Duy Le <Thuc.Le@unisa.edu.au>
Diff between ParallelPC versions 1.1 dated 2015-10-02 and 1.2 dated 2015-12-31
DESCRIPTION | 10 +- MD5 | 53 ++++++------ NAMESPACE | 64 +++++++-------- inst |only man/IDA_parallel.Rd | 112 +++++++++++++------------- man/IDA_stable.Rd | 82 +++++++++---------- man/cor2.Rd | 74 ++++++++--------- man/fci_parallel.Rd | 196 +++++++++++++++++++++++------------------------ man/fci_stable.Rd | 146 +++++++++++++++++------------------ man/jointIDA_direct.Rd | 76 +++++++++--------- man/jointIDA_parallel.Rd | 112 +++++++++++++------------- man/mccor.Rd | 70 ++++++++-------- man/mcmig.Rd | 70 ++++++++-------- man/mczf.Rd | 70 ++++++++-------- man/mig.Rd | 70 ++++++++-------- man/migsh.Rd | 70 ++++++++-------- man/pcSelect_parallel.Rd | 144 +++++++++++++++++----------------- man/pcSelect_stable.Rd | 108 ++++++++++++------------- man/pc_parallel.Rd | 174 ++++++++++++++++++++--------------------- man/pc_stable.Rd | 122 ++++++++++++++--------------- man/rfci_parallel.Rd | 184 ++++++++++++++++++++++---------------------- man/rfci_stable.Rd | 128 +++++++++++++++--------------- man/skeleton_parallel.Rd | 138 ++++++++++++++++----------------- man/skeleton_stable.Rd | 102 ++++++++++++------------ man/smccor.Rd | 70 ++++++++-------- man/smcmig.Rd | 70 ++++++++-------- man/smczf.Rd | 70 ++++++++-------- man/zf.Rd | 70 ++++++++-------- 28 files changed, 1328 insertions(+), 1327 deletions(-)
Title: Symbolic Computation and More with Multivariate Polynomials
Description: Symbolic computing with multivariate polynomials in R.
Author: David Kahle [aut, cre]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between mpoly versions 0.1.0 dated 2015-05-01 and 1.0.0 dated 2015-12-31
mpoly-0.1.0/mpoly/R/is.linear.R |only mpoly-0.1.0/mpoly/R/is.mpoly.R |only mpoly-0.1.0/mpoly/R/is.mpolyList.R |only mpoly-0.1.0/mpoly/R/is.wholenumber.R |only mpoly-0.1.0/mpoly/man/is.linear.Rd |only mpoly-0.1.0/mpoly/man/is.mpoly.Rd |only mpoly-0.1.0/mpoly/man/is.mpolyList.Rd |only mpoly-1.0.0/mpoly/DESCRIPTION | 14 mpoly-1.0.0/mpoly/MD5 | 129 ++++---- mpoly-1.0.0/mpoly/NAMESPACE | 24 + mpoly-1.0.0/mpoly/NEWS | 55 +++ mpoly-1.0.0/mpoly/R/LCM.R | 5 mpoly-1.0.0/mpoly/R/as.function.mpoly.R | 103 +++++- mpoly-1.0.0/mpoly/R/as.function.mpolyList.R | 18 - mpoly-1.0.0/mpoly/R/as.mpoly.R | 55 +++ mpoly-1.0.0/mpoly/R/bernstein.R |only mpoly-1.0.0/mpoly/R/bezier.R |only mpoly-1.0.0/mpoly/R/burst.R | 8 mpoly-1.0.0/mpoly/R/chebyshev.R |only mpoly-1.0.0/mpoly/R/deriv.mpoly.R | 7 mpoly-1.0.0/mpoly/R/grobner.R | 14 mpoly-1.0.0/mpoly/R/help.R | 10 mpoly-1.0.0/mpoly/R/hermite.R |only mpoly-1.0.0/mpoly/R/jacobi.R |only mpoly-1.0.0/mpoly/R/laguerre.R |only mpoly-1.0.0/mpoly/R/legendre.R |only mpoly-1.0.0/mpoly/R/mp.R | 59 +++ mpoly-1.0.0/mpoly/R/mpoly.R | 9 mpoly-1.0.0/mpoly/R/mpolyList.R | 29 + mpoly-1.0.0/mpoly/R/mpolyListArithmetic.R | 2 mpoly-1.0.0/mpoly/R/partitions.R | 5 mpoly-1.0.0/mpoly/R/permutations.R | 3 mpoly-1.0.0/mpoly/R/plug.R |only mpoly-1.0.0/mpoly/R/predicates.R |only mpoly-1.0.0/mpoly/R/print.mpoly.R | 20 - mpoly-1.0.0/mpoly/R/print.mpolyList.R | 13 mpoly-1.0.0/mpoly/R/reorder.mpoly.R | 5 mpoly-1.0.0/mpoly/R/round.mpoly.R | 13 mpoly-1.0.0/mpoly/R/swap.R |only mpoly-1.0.0/mpoly/R/terms.mpoly.R | 4 mpoly-1.0.0/mpoly/R/tuples.R | 56 ++- mpoly-1.0.0/mpoly/README.md | 372 ++++++++++++++++++++++--- mpoly-1.0.0/mpoly/man/LCM.Rd | 5 mpoly-1.0.0/mpoly/man/as.function.mpoly.Rd | 34 +- mpoly-1.0.0/mpoly/man/as.function.mpolyList.Rd | 26 + mpoly-1.0.0/mpoly/man/as.mpoly.Rd | 22 - mpoly-1.0.0/mpoly/man/bernstein.Rd |only mpoly-1.0.0/mpoly/man/bernsteinApprox.Rd |only mpoly-1.0.0/mpoly/man/bezier.Rd |only mpoly-1.0.0/mpoly/man/bezierFunction.Rd |only mpoly-1.0.0/mpoly/man/burst.Rd | 7 mpoly-1.0.0/mpoly/man/chebyshev.Rd |only mpoly-1.0.0/mpoly/man/deriv.mpoly.Rd | 5 mpoly-1.0.0/mpoly/man/gradient.Rd | 2 mpoly-1.0.0/mpoly/man/grobner.Rd | 16 - mpoly-1.0.0/mpoly/man/hermite.Rd |only mpoly-1.0.0/mpoly/man/insert.Rd | 6 mpoly-1.0.0/mpoly/man/is.wholenumber.Rd | 6 mpoly-1.0.0/mpoly/man/jacobi.Rd |only mpoly-1.0.0/mpoly/man/laguerre.Rd |only mpoly-1.0.0/mpoly/man/legendre.Rd |only mpoly-1.0.0/mpoly/man/mp.Rd | 27 + mpoly-1.0.0/mpoly/man/mpoly.Rd | 22 - mpoly-1.0.0/mpoly/man/mpolyArithmetic.Rd | 6 mpoly-1.0.0/mpoly/man/mpolyEqual.Rd | 6 mpoly-1.0.0/mpoly/man/mpolyList.Rd | 17 - mpoly-1.0.0/mpoly/man/mpolyListArithmetic.Rd | 4 mpoly-1.0.0/mpoly/man/partitions.Rd | 7 mpoly-1.0.0/mpoly/man/permutations.Rd | 5 mpoly-1.0.0/mpoly/man/plug.Rd |only mpoly-1.0.0/mpoly/man/predicates.Rd |only mpoly-1.0.0/mpoly/man/print.mpoly.Rd | 13 mpoly-1.0.0/mpoly/man/print.mpolyList.Rd | 13 mpoly-1.0.0/mpoly/man/reorder.mpoly.Rd | 10 mpoly-1.0.0/mpoly/man/round.mpoly.Rd | 7 mpoly-1.0.0/mpoly/man/swap.Rd |only mpoly-1.0.0/mpoly/man/terms.mpoly.Rd | 3 mpoly-1.0.0/mpoly/man/tuples.Rd | 23 + mpoly-1.0.0/mpoly/man/vars.Rd | 6 mpoly-1.0.0/mpoly/tests/testthat/test-mp.r | 2 80 files changed, 978 insertions(+), 354 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Diff between markophylo versions 1.0.3 dated 2015-11-05 and 1.0.4 dated 2015-12-31
DESCRIPTION | 9 +- MD5 | 18 ++--- NEWS | 7 ++ R/custom-general14.R | 141 +++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/estimaterates.Rmd | 5 + inst/doc/estimaterates.html | 129 ++++++++++++++++++++-------------------- man/markophylo-package.Rd | 4 - tests/testthat/test-main.R | 33 +++++----- vignettes/estimaterates.Rmd | 5 + 10 files changed, 183 insertions(+), 168 deletions(-)
Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time
series, possibly mixed with ARMA, regression, transfer-function components.
Exact methods (MLE, forecasting, simulation) are used.
Author: Justin Q. Veenstra [aut, cre],
A.I. McLeod [aut]
Maintainer: Justin Q. Veenstra <justin.veenstra@gmail.com>
Diff between arfima versions 1.3-3 dated 2015-12-28 and 1.3-4 dated 2015-12-31
DESCRIPTION | 6 MD5 | 10 R/arfima.R | 2429 ++++++++++++++++++++++++++++----------------------------- R/arfimaFit.R | 1 man/SeriesJ.Rd | 92 +- man/arfima.Rd | 2 6 files changed, 1275 insertions(+), 1265 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools inspired by Stata to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter, elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.3.0 dated 2015-06-07 and 0.4.0 dated 2015-12-30
statar-0.3.0/statar/R/count_combinations.R |only statar-0.3.0/statar/R/fuzzy_join.R |only statar-0.3.0/statar/R/graph.R |only statar-0.3.0/statar/R/pastem.R |only statar-0.3.0/statar/R/print_all.R |only statar-0.3.0/statar/R/roll.R |only statar-0.3.0/statar/R/sample_mode.R |only statar-0.3.0/statar/inst/doc/macros.Rmd |only statar-0.3.0/statar/inst/doc/macros.html |only statar-0.3.0/statar/inst/doc/merge-records.Rmd |only statar-0.3.0/statar/inst/doc/merge-records.html |only statar-0.3.0/statar/inst/doc/summary.Rmd |only statar-0.3.0/statar/inst/doc/summary.html |only statar-0.3.0/statar/man/compute_distance.Rd |only statar-0.3.0/statar/man/count_combinations.Rd |only statar-0.3.0/statar/man/fuzzy_join.Rd |only statar-0.3.0/statar/man/pastem.Rd |only statar-0.3.0/statar/man/roll.Rd |only statar-0.3.0/statar/tests/testthat/test_roll.R |only statar-0.3.0/statar/vignettes/macros.Rmd |only statar-0.3.0/statar/vignettes/merge-records.Rmd |only statar-0.3.0/statar/vignettes/summary.Rmd |only statar-0.4.0/statar/DESCRIPTION | 22 - statar-0.4.0/statar/MD5 | 51 +-- statar-0.4.0/statar/NAMESPACE | 22 - statar-0.4.0/statar/R/count.R |only statar-0.4.0/statar/R/stat_binmean.R | 44 +- statar-0.4.0/statar/R/statar.R | 11 statar-0.4.0/statar/R/sum_up.R | 2 statar-0.4.0/statar/README.md | 38 -- statar-0.4.0/statar/build/vignette.rds |binary statar-0.4.0/statar/inst/doc/data-frames.Rmd |only statar-0.4.0/statar/inst/doc/data-frames.html |only statar-0.4.0/statar/inst/doc/graph.Rmd |only statar-0.4.0/statar/inst/doc/graph.html |only statar-0.4.0/statar/inst/doc/panel-data.html | 364 +++++++++++++++--------- statar-0.4.0/statar/inst/doc/vector.html | 255 +++++++++++----- statar-0.4.0/statar/man/count.Rd |only statar-0.4.0/statar/man/stat_binmean.Rd | 16 - statar-0.4.0/statar/vignettes/data-frames.Rmd |only statar-0.4.0/statar/vignettes/graph.Rmd |only statar-0.4.0/statar/vignettes/summary.html |only 42 files changed, 509 insertions(+), 316 deletions(-)
Title: Soundscape Ecology
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>
Diff between soundecology versions 1.3 dated 2015-05-02 and 1.3.1 dated 2015-12-30
DESCRIPTION | 8 +- MD5 | 24 ++++--- NAMESPACE | 2 NEWS | 7 ++ R/acoustic_complexity_index.R | 120 +++++++++++++++++++++++++++++---------- R/multiple_sounds.R | 13 ++-- build/vignette.rds |binary inst/doc/ACIandSeewave.R |only inst/doc/ACIandSeewave.Rmd |only inst/doc/ACIandSeewave.html |only inst/doc/intro.Rmd | 2 inst/doc/intro.html | 2 man/acoustic_complexity_index.Rd | 9 ++ vignettes/ACIandSeewave.Rmd |only vignettes/intro.Rmd | 2 15 files changed, 137 insertions(+), 52 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.4 dated 2015-10-14 and 2.0.5 dated 2015-12-30
DESCRIPTION | 32 +-- MD5 | 140 ++++++++------ NAMESPACE | 16 + NEWS | 16 + R/add_basic_meta.R | 12 - R/add_characters.R | 10 - R/add_trees.R | 2 R/character_classes.R | 22 +- R/classes.R | 27 +- R/deprecated.R |only R/get_basic_metadata.R | 6 R/get_characters.R | 328 ++++++++++++----------------------- R/get_level.R |only R/get_metadata.R | 76 +++----- R/get_taxa.R | 9 R/nexml_methods.R | 2 R/nexml_read.R | 71 +++++-- R/nexml_validate.R | 23 +- R/simmap.R | 4 build/vignette.rds |binary data/simmap_ex.rda |binary inst/examples/merge_data.Rmd |only inst/examples/merge_data.md |only inst/examples/meta_taxa.xml |only inst/examples/ontotrace-result.xml |only inst/examples/taxa.xml |only inst/examples/treebase-record.xml |only man/add_basic_meta.Rd | 16 - man/add_characters.Rd | 2 man/add_meta.Rd | 17 - man/add_namespaces.Rd | 17 - man/add_trees.Rd | 6 man/c-ListOfmeta-method.Rd | 10 - man/c-meta-method.Rd | 7 man/c-nexml-method.Rd | 6 man/flatten_multiphylo.Rd | 4 man/get_characters.Rd | 37 ++- man/get_characters_list.Rd | 4 man/get_citation.Rd | 2 man/get_flat_trees.Rd | 2 man/get_level.Rd |only man/get_license.Rd | 2 man/get_metadata.Rd | 18 + man/get_namespaces.Rd | 4 man/get_rdf.Rd | 4 man/get_taxa.Rd | 2 man/get_taxa_list.Rd | 2 man/get_taxa_meta.Rd | 2 man/get_taxa_meta_list.Rd | 2 man/get_trees.Rd | 2 man/get_trees_list.Rd | 2 man/meta.Rd | 10 - man/nexml_add.Rd | 2 man/nexml_figshare.Rd | 2 man/nexml_get.Rd | 2 man/nexml_publish.Rd | 2 man/nexml_read.Rd | 30 ++- man/nexml_to_simmap.Rd | 6 man/nexml_validate.Rd | 4 man/nexml_write.Rd | 26 +- man/reset_id_counter.Rd | 2 man/simmap_ex.Rd | 4 man/simmap_to_nexml.Rd | 8 man/taxize_nexml.Rd | 6 man/toPhylo.Rd | 4 tests/test-all.R | 10 - tests/testthat/helper-RNeXML.R | 1 tests/testthat/test_characters.R | 39 ---- tests/testthat/test_comp_analysis.R | 10 - tests/testthat/test_get_characters.R | 44 ---- tests/testthat/test_meta.R | 30 +-- tests/testthat/test_nexml_read.R |only tests/testthat/test_rdf.R | 1 tests/testthat/test_simmap.R | 7 tests/testthat/test_taxonomy.R | 8 vignettes/metadata.Rmd | 88 ++++++--- 76 files changed, 655 insertions(+), 657 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>
Diff between nat versions 1.7.0 dated 2015-07-01 and 1.8.1 dated 2015-12-30
DESCRIPTION | 11 MD5 | 149 +++++++------ NAMESPACE | 13 + NEWS | 49 ++++ R/amiramesh-io.R | 12 - R/cmtk.R | 21 + R/cmtkreg.R | 18 - R/coordinates.R | 6 R/dotprops.R | 48 +++- R/hxsurf.R | 10 R/im3d.R | 80 ++++--- R/nat-package.R | 109 ++++++++- R/neuron-io-neuroml.R | 2 R/neuron-io.R | 2 R/neuron-plot.R | 8 R/neuron.R | 100 ++++++++ R/neuronlist.R | 74 ++++-- R/neuronlist_interactive_3d.R | 38 ++- R/neuronlistfh.R | 4 R/ngraph.R | 189 +++++++++++++++-- R/nrrd-io.R | 2 R/pop3d.R | 2 R/summary.R |only R/xform.R | 90 ++++++-- R/xformpoints.R | 9 R/zzz.R | 8 README.md | 12 - man/as.im3d.Rd | 24 +- man/boundingbox.Rd | 6 man/cmtk.bindir.Rd | 9 man/cmtkreg.Rd | 4 man/dotprops.Rd | 2 man/find.neuron.Rd | 16 - man/find.soma.Rd | 9 man/im3d.Rd | 2 man/image.im3d.Rd | 2 man/imscalebar.Rd | 2 man/imslice.Rd | 6 man/ind2coord.Rd | 2 man/mirror.Rd | 47 +++- man/nat-package.Rd | 110 ++++++++- man/ngraph.Rd | 4 man/nlapply.Rd | 27 +- man/npop3d.Rd | 2 man/origin.Rd | 2 man/plot.neuron.Rd | 2 man/plot3d.Rd | 2 man/plot3d.boundingbox.Rd | 2 man/plot3d.hxsurf.Rd | 4 man/plot3d.neuron.Rd | 4 man/projection.Rd | 4 man/prune.Rd | 14 + man/prune_strahler.Rd |only man/prune_vertices.Rd |only man/read.neurons.Rd | 2 man/read.nrrd.Rd | 2 man/scale.neuron.Rd | 2 man/segmentgraph.Rd | 25 +- man/spine.Rd | 5 man/strahler_order.Rd |only man/subset.Rd | 8 man/subset.dotprops.Rd | 27 ++ man/subset.neuron.Rd |only man/subset.neuronlist.Rd | 25 +- man/summary.neuron.Rd |only man/write.amiramesh.Rd | 12 - man/xform.Rd | 2 man/xformpoints.Rd | 2 man/xyzmatrix.Rd | 10 tests/test-all.R | 4 tests/testthat/test-cmtkreg.R | 3 tests/testthat/test-im3d.R | 33 ++ tests/testthat/test-neuron.R | 24 +- tests/testthat/test-neuronlist.R | 16 + tests/testthat/test-ngraph.R | 36 +++ tests/testthat/test-summary.R |only tests/testthat/test-xform.R | 11 tests/testthat/testdata/cmtk/FCWB_mirror_level-01.list |only 78 files changed, 1271 insertions(+), 352 deletions(-)
Title: Extension to ggplot2
Description: The R package \href{http://docs.ggplot2.org/current/}{ggplot2}
is a plotting system based on the grammar of graphics. \href{https://
ggobi.github.io/ggally}{GGally} extends ggplot2 by adding several functions to
reduce the complexity of combining geoms with transformed data. Some of these
functions include a pairwise plot matrix, a scatterplot plot matrix, a parallel
coordinates plot, a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs and ggally_*.
contributor for all functions.),
Jason Crowley [aut] (ggparcoord),
Di Cook [aut, ths] (ggscatmat, gglyph),
Heike Hofmann [ths],
Hadley Wickham [ths],
Francois Briatte [aut] (ggcorr, ggnet, ggnet2),
Moritz Marbach [aut] (ggnet, ggnet2),
Edwin Thoen [aut] (ggsurv),
Amos Elberg [aut] (ggnetworkmap)
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 0.5.0 dated 2014-12-01 and 1.0.0 dated 2015-12-30
GGally-0.5.0/GGally/R/data-cityServiceFirms.r |only GGally-0.5.0/GGally/R/data-flea.r |only GGally-0.5.0/GGally/R/data-happy.r |only GGally-0.5.0/GGally/R/data-nasa.r |only GGally-0.5.0/GGally/R/find-combo.r |only GGally-0.5.0/GGally/R/gg-plots.r |only GGally-0.5.0/GGally/R/ggcorr.r |only GGally-0.5.0/GGally/R/gglyph.r |only GGally-0.5.0/GGally/R/ggnet.r |only GGally-0.5.0/GGally/R/ggpairs.r |only GGally-0.5.0/GGally/R/ggpairs_add.r |only GGally-0.5.0/GGally/R/ggparcoord.r |only GGally-0.5.0/GGally/R/ggscatmat.r |only GGally-0.5.0/GGally/R/ggsurv.r |only GGally-0.5.0/GGally/R/print_ggpairs_old.r |only GGally-0.5.0/GGally/R/utils.r |only GGally-0.5.0/GGally/data/cityServiceFirms.rda |only GGally-0.5.0/GGally/man/addAndOverwriteAes.Rd |only GGally-0.5.0/GGally/man/cityServiceFirms.Rd |only GGally-0.5.0/GGally/man/get.VarTypes.Rd |only GGally-0.5.0/GGally/man/get_plot_type.Rd |only GGally-0.5.0/GGally/man/make_ggpair_text.Rd |only GGally-0.5.0/GGally/man/print.ggpairs.Rd |only GGally-0.5.0/GGally/man/print_ggpairs_old.Rd |only GGally-0.5.0/GGally/man/scagOrder.Rd |only GGally-1.0.0/GGally/DESCRIPTION | 64 +++- GGally-1.0.0/GGally/MD5 | 203 +++++++++----- GGally-1.0.0/GGally/NAMESPACE | 47 ++- GGally-1.0.0/GGally/NEWS | 137 ++------- GGally-1.0.0/GGally/R/data-flea.R |only GGally-1.0.0/GGally/R/data-happy.R |only GGally-1.0.0/GGally/R/data-nasa.R |only GGally-1.0.0/GGally/R/data-twitter_spambots.R |only GGally-1.0.0/GGally/R/find-combo.R |only GGally-1.0.0/GGally/R/gg-plots.R |only GGally-1.0.0/GGally/R/ggcorr.R |only GGally-1.0.0/GGally/R/gglyph.R |only GGally-1.0.0/GGally/R/ggmatrix.R |only GGally-1.0.0/GGally/R/ggmatrix_print.R |only GGally-1.0.0/GGally/R/ggnet.R |only GGally-1.0.0/GGally/R/ggnet2.R |only GGally-1.0.0/GGally/R/ggnetworkmap.R |only GGally-1.0.0/GGally/R/ggpairs.R |only GGally-1.0.0/GGally/R/ggpairs_add.R |only GGally-1.0.0/GGally/R/ggpairs_getput.R |only GGally-1.0.0/GGally/R/ggpairs_internal_plots.R |only GGally-1.0.0/GGally/R/ggparcoord.R |only GGally-1.0.0/GGally/R/ggscatmat.R |only GGally-1.0.0/GGally/R/ggsurv.R |only GGally-1.0.0/GGally/R/utils.R |only GGally-1.0.0/GGally/README.md | 16 - GGally-1.0.0/GGally/build |only GGally-1.0.0/GGally/data/twitter_spambots.rda |only GGally-1.0.0/GGally/inst |only GGally-1.0.0/GGally/man/add_and_overwrite_aes.Rd |only GGally-1.0.0/GGally/man/add_ref_boxes.Rd | 3 GGally-1.0.0/GGally/man/add_ref_lines.Rd | 3 GGally-1.0.0/GGally/man/column_is_character.Rd |only GGally-1.0.0/GGally/man/eval_ggpair.Rd | 3 GGally-1.0.0/GGally/man/find_plot_type.Rd | 3 GGally-1.0.0/GGally/man/first_non_null.Rd |only GGally-1.0.0/GGally/man/flea.Rd | 3 GGally-1.0.0/GGally/man/getPlot.Rd | 20 - GGally-1.0.0/GGally/man/get_theme_element.Rd |only GGally-1.0.0/GGally/man/get_x_axis_labels.Rd | 3 GGally-1.0.0/GGally/man/gg-add.Rd | 10 GGally-1.0.0/GGally/man/ggally_barDiag.Rd | 14 - GGally-1.0.0/GGally/man/ggally_blank.Rd | 6 GGally-1.0.0/GGally/man/ggally_box.Rd | 5 GGally-1.0.0/GGally/man/ggally_cor.Rd | 26 + GGally-1.0.0/GGally/man/ggally_density.Rd | 5 GGally-1.0.0/GGally/man/ggally_densityDiag.Rd | 13 GGally-1.0.0/GGally/man/ggally_denstrip.Rd | 5 GGally-1.0.0/GGally/man/ggally_diagAxis.Rd | 5 GGally-1.0.0/GGally/man/ggally_dot.Rd | 5 GGally-1.0.0/GGally/man/ggally_dotAndBox.Rd | 5 GGally-1.0.0/GGally/man/ggally_facetbar.Rd | 5 GGally-1.0.0/GGally/man/ggally_facetdensity.Rd | 5 GGally-1.0.0/GGally/man/ggally_facetdensitystrip.Rd | 7 GGally-1.0.0/GGally/man/ggally_facethist.Rd | 5 GGally-1.0.0/GGally/man/ggally_na.Rd |only GGally-1.0.0/GGally/man/ggally_points.Rd | 3 GGally-1.0.0/GGally/man/ggally_ratio.Rd | 17 - GGally-1.0.0/GGally/man/ggally_smooth.Rd | 5 GGally-1.0.0/GGally/man/ggally_text.Rd | 5 GGally-1.0.0/GGally/man/ggcorr.Rd | 179 ++++++++++-- GGally-1.0.0/GGally/man/ggfluctuation2.Rd | 11 GGally-1.0.0/GGally/man/ggmatrix.Rd |only GGally-1.0.0/GGally/man/ggnet.Rd | 249 +++++++++++++----- GGally-1.0.0/GGally/man/ggnet2.Rd |only GGally-1.0.0/GGally/man/ggnetworkmap.Rd |only GGally-1.0.0/GGally/man/ggpairs.Rd | 78 +++-- GGally-1.0.0/GGally/man/ggparcoord.Rd | 13 GGally-1.0.0/GGally/man/ggscatmat.Rd | 13 GGally-1.0.0/GGally/man/ggsurv.Rd | 6 GGally-1.0.0/GGally/man/glyphplot.Rd |only GGally-1.0.0/GGally/man/glyphs.Rd | 27 + GGally-1.0.0/GGally/man/happy.Rd | 3 GGally-1.0.0/GGally/man/is_blank_plot.Rd | 6 GGally-1.0.0/GGally/man/is_date.Rd |only GGally-1.0.0/GGally/man/lowertriangle.Rd | 5 GGally-1.0.0/GGally/man/mapping_color_fill.Rd | 3 GGally-1.0.0/GGally/man/nasa.Rd | 3 GGally-1.0.0/GGally/man/plot_types.Rd | 3 GGally-1.0.0/GGally/man/plotting_data_type.Rd |only GGally-1.0.0/GGally/man/print.ggmatrix.Rd |only GGally-1.0.0/GGally/man/putPlot.Rd | 22 + GGally-1.0.0/GGally/man/require_pkgs.Rd | 3 GGally-1.0.0/GGally/man/rescale01.Rd |only GGally-1.0.0/GGally/man/scag_order.Rd |only GGally-1.0.0/GGally/man/scatmat.Rd | 9 GGally-1.0.0/GGally/man/set_to_blank_list_if_blank.Rd |only GGally-1.0.0/GGally/man/singleClassOrder.Rd | 3 GGally-1.0.0/GGally/man/skewness.Rd | 3 GGally-1.0.0/GGally/man/str.ggmatrix.Rd |only GGally-1.0.0/GGally/man/twitter_spambots.Rd |only GGally-1.0.0/GGally/man/uppertriangle.Rd | 5 GGally-1.0.0/GGally/man/vplayout.Rd | 3 GGally-1.0.0/GGally/man/wrap_fn_with_param_arg.Rd |only GGally-1.0.0/GGally/tests |only GGally-1.0.0/GGally/vignettes |only 121 files changed, 833 insertions(+), 470 deletions(-)
Title: Data from Gapminder
Description: An excerpt of the data available at Gapminder.org. For each of 142
countries, the package provides values for life expectancy, GDP per capita,
and population, every five years, from 1952 to 2007.
Author: Jennifer Bryan [aut, cre]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>
Diff between gapminder versions 0.1.0 dated 2015-03-17 and 0.2.0 dated 2015-12-30
DESCRIPTION | 17 ++- MD5 | 36 +++++--- NAMESPACE | 2 NEWS.md |only R/country_colors.R | 21 ++-- R/gapminder.R | 8 + R/gapminder_unfiltered.R |only README.md | 139 ++++++++++++++++++++++++++------ data/continent_colors.rdata |binary data/country_colors.rdata |binary data/gapminder.rdata |binary data/gapminder_unfiltered.rdata |only inst/continent-colors.tsv |only inst/country-colors.tsv |only inst/gapminder-unfiltered.tsv | 21 ++-- inst/gapminder.tsv | 22 ++--- man/country_colors.Rd | 28 +++--- man/gapminder.Rd | 14 ++- man/gapminder_unfiltered.Rd |only tests/testthat/continent_colors.rds |only tests/testthat/country_colors.rds |only tests/testthat/gapminder.rds |only tests/testthat/gapminder_unfiltered.rds |only tests/testthat/test-gapminder.R | 9 ++ 24 files changed, 225 insertions(+), 92 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. multicore parallel processing and distributed
processing on compute clusters. The purpose of this package is to provide a
lightweight interface for using futures in R. Functions 'future()' and 'value()'
exist for creating futures and requesting their values. An infix assignment
operator '%<=%' exists for creating futures whose values are accessible by the
assigned variables (as promises). This package implements the synchronous "lazy"
and "eager" futures, and the asynchronous "multicore" future (not on Windows).
Additional types of futures are provided by other packages enhancing this
package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.9.0 dated 2015-12-12 and 0.10.0 dated 2015-12-30
future-0.10.0/future/DESCRIPTION | 8 - future-0.10.0/future/MD5 | 65 ++++++---- future-0.10.0/future/NAMESPACE | 15 ++ future-0.10.0/future/NEWS | 12 + future-0.10.0/future/R/Future-class.R | 22 --- future-0.10.0/future/R/LazyFuture-class.R | 4 future-0.10.0/future/R/MulticoreFuture.R | 7 - future-0.10.0/future/R/availableCores.R | 34 ++++- future-0.10.0/future/R/futureAssign.R | 7 - future-0.10.0/future/R/futureAssign_OP.R | 2 future-0.10.0/future/R/futureOf.R | 85 ++++++++++---- future-0.10.0/future/R/futures.R |only future-0.10.0/future/R/globals.R | 6 future-0.10.0/future/R/resolve.R |only future-0.10.0/future/R/resolved.R |only future-0.10.0/future/R/values.R |only future-0.10.0/future/R/whichIndex.R |only future-0.10.0/future/demo/mandelbrot.R | 2 future-0.10.0/future/inst/doc/future-issues.html | 30 ++++ future-0.10.0/future/inst/doc/future-issues.md.rsp | 28 ++++ future-0.10.0/future/inst/doc/future.html | 4 future-0.10.0/future/inst/doc/future.md.rsp | 4 future-0.10.0/future/man/availableCores.Rd | 8 + future-0.10.0/future/man/futureOf.Rd | 9 - future-0.10.0/future/man/futures.Rd |only future-0.10.0/future/man/resolve.Rd |only future-0.10.0/future/man/resolved.Rd |only future-0.10.0/future/man/values.Rd |only future-0.10.0/future/tests/futureAssign_OP_with_listenv.R | 24 +++ future-0.10.0/future/tests/futureOf_with_environment.R | 72 +++++++++-- future-0.10.0/future/tests/futureOf_with_listenv.R | 69 +++++++++++ future-0.10.0/future/tests/futures.R |only future-0.10.0/future/tests/globals,tricky.R | 3 future-0.10.0/future/tests/globalsOf,tweaks.R | 3 future-0.10.0/future/tests/plan.R | 2 future-0.10.0/future/tests/resolve.R |only future-0.10.0/future/tests/whichIndex.R |only future-0.10.0/future/vignettes/future-issues.md.rsp | 28 ++++ future-0.10.0/future/vignettes/future.md.rsp | 4 future-0.9.0/future/man/resolved.Future.Rd |only 40 files changed, 428 insertions(+), 129 deletions(-)
Title: Contains an Administrative-Level-1 Map of the World
Description: Contains an administrative-level-1 map of the world.
Administrative-level-1 is the generic term for the largest sub-national
subdivision of a country. This package was created for use with the
choroplethr package.
Author: Ari Lamstein <arilamstein@gmail.com>
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethrAdmin1 versions 1.0.0 dated 2014-12-02 and 1.1.0 dated 2015-12-30
DESCRIPTION | 11 +++++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 ++- NEWS |only R/admin1.R | 4 ++++ README.md |only data/admin1.map.rdata |binary man/admin1.map.Rd | 11 ++++++----- man/admin1.regions.Rd | 3 ++- man/admin1_map.Rd | 4 +++- man/get_admin1_countries.Rd | 3 ++- man/get_admin1_map.Rd | 5 +++-- man/get_admin1_regions.Rd | 3 ++- 13 files changed, 43 insertions(+), 26 deletions(-)
More information about choroplethrAdmin1 at CRAN
Permanent link
Title: Gene Regulatory Network Inference with Bc3net
Description: Implementation of the BC3NET algorithm for gene regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624).
Author: Ricardo de Matos Simoes [aut, cre],
Frank Emmert-Streib [aut]
Maintainer: Ricardo de Matos Simoes <ricardo_dematossimoes@dfci.harvard.edu>
Diff between bc3net versions 1.0.2 dated 2013-04-07 and 1.0.3 dated 2015-12-30
bc3net-1.0.2/bc3net/docs |only bc3net-1.0.3/bc3net/DESCRIPTION | 29 +++++++++++++---------------- bc3net-1.0.3/bc3net/MD5 | 5 ++--- bc3net-1.0.3/bc3net/NAMESPACE | 7 +++++++ 4 files changed, 22 insertions(+), 19 deletions(-)
Title: Functions for Processing and Analyzing Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices, and generates data summaries. Also includes functions to plot, analyze, and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Diff between acc versions 1.2.3 dated 2015-12-30 and 1.2.4 dated 2015-12-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 5 +++++ R/aee.R | 2 ++ R/aeefit.R | 2 ++ R/internal.R | 1 + R/summary.aeefit.R | 2 +- 7 files changed, 21 insertions(+), 11 deletions(-)
Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using
the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram,
Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart,
bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>
Diff between RcmdrPlugin.KMggplot2 versions 0.2-2 dated 2015-12-22 and 0.2-3 dated 2015-12-30
RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/aaa-package.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/data-aaa.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-aaa.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-checkboxes.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-radioboxes.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-textfield.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-textfields.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-toolbox.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/guiparts-variableboxes.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-aaa.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-factorise.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gbox.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gcont.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gdiscbar.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gdist.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-ghist.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gkm.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gline.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gpie.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gqq.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gscat.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/plot-gscatmat.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/theme-natrisk.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/theme-natrisk21.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/theme-natriskbg.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/theme-simple.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/theme-wsj2.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/util-gettextKmg2.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/util-ggsaveKmg2.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/util-nonFactors.R |only RcmdrPlugin.KMggplot2-0.2-2/RcmdrPlugin.KMggplot2/R/zzz.R |only RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/DESCRIPTION | 28 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/MD5 | 291 ++++--- RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/NAMESPACE | 10 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/NEWS | 10 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/NEWS.md | 10 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/R/aaa-package.r |only RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/R/data-aaa.r |only RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/R/geom-stepribbon.r |only RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/R/guiparts-aaa.r |only 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RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gcont-windowContour.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gcont.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdiscbar-windowDiscretebar.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdiscbar.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistBeta.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistBinom.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistCauchy.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistChisq.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistExp.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistF.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistGamma.Rd | 2 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RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-plotWindow.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-registRmlist.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-removeRmlist.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-savePlot.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-setBack.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-setDataframe.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base-setFront.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/plot-plot_base.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/theme-natrisk.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/theme-natrisk21.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/theme-natriskbg.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/theme-simple.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/theme-wsj2.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/util-gettextKmg2.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/util-ggsaveKmg2.Rd | 4 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/util-nonFactors.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/man/util-nonFactorsP.Rd | 2 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2-ja.po | 366 +++++----- RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2-sl.po | 364 +++++---- RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2.pot | 361 +++++---- RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/vignettes/extrafont.Rmd | 8 RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/vignettes/geom-stepribbon.Rmd |only RcmdrPlugin.KMggplot2-0.2-3/RcmdrPlugin.KMggplot2/vignettes/plot-km-requirement.Rmd | 2 181 files changed, 925 insertions(+), 835 deletions(-)
More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link
Title: Create Virtual Species for Species Distribution Modelling
Description: A software package help user to create virtual species for species distribution modelling. It includes
several methods to help user to create virtual species distribution map.
Those maps can be used for Species Distribution Modelling (SDM) study. SDM use
environmental data for sites of occurrence of a species to predict all the sites
where the environmental conditions are suitable for the species to persist, and
may be expected to occur.
Author: Xiaoquan Kong [aut, cre, cph],
Renyan Duan [ths],
Minyi Huang [ths]
Maintainer: Xiaoquan Kong <u1mail2me@gmail.com>
Diff between sdmvspecies versions 0.3.1 dated 2014-09-19 and 0.3.2 dated 2015-12-30
DESCRIPTION | 43 ++++++---- MD5 | 64 +++++++-------- NAMESPACE | 9 -- R/artificial_bell_response.R | 19 +--- R/auto_PCA.R | 4 R/config_stack.R | 12 +- R/niche_synthese.R | 45 +++++----- R/pick_mean.R | 19 ++-- R/pick_median.R | 19 ++-- R/rescale.R | 17 +--- R/sdmvspecies.R | 19 ++-- build/vignette.rds |binary inst/doc/sdmvspecies.R | 80 ++++++++++--------- inst/doc/sdmvspecies.Rnw | 82 +++++++++++--------- inst/doc/sdmvspecies.pdf |binary inst/tests/testthat/test_artificial_bell_response.R | 28 +++--- inst/tests/testthat/test_auto_PCA.R | 22 ++--- inst/tests/testthat/test_config_stack.R | 12 +- inst/tests/testthat/test_niche_synthese.R | 20 ++-- inst/tests/testthat/test_pick_mean.R | 34 ++++---- inst/tests/testthat/test_pick_median.R | 36 ++++---- inst/tests/testthat/test_rescale.R | 18 ++-- man/artificialBellResponse.Rd | 3 man/autoPCA.Rd | 3 man/configStack.Rd | 3 man/nicheSynthese.Rd | 3 man/pickMean.Rd | 3 man/pickMedian.Rd | 3 man/rescale.Rd | 3 man/rescaleLayer.Rd | 3 man/rescaleStack.Rd | 3 man/sdmvspecies.Rd | 8 - vignettes/sdmvspecies.Rnw | 82 +++++++++++--------- 33 files changed, 377 insertions(+), 342 deletions(-)
Title: Formula Based PLS Path Modeling
Description: The main objective is to make easy the PLS Path Modeling with R using the package 'plspm'. It compute automatically the inner matrix and the outer list the 'plspm' function need simply by specify the model using formulas.
Author: ACHIEPO Odilon Yapo M. [aut, cre]
Maintainer: ACHIEPO Odilon Yapo M. <kingodilon@gmail.com>
Diff between plspm.formula versions 1.0 dated 2015-12-19 and 1.0.1 dated 2015-12-30
plspm.formula-1.0.1/plspm.formula/DESCRIPTION | 10 +++++----- plspm.formula-1.0.1/plspm.formula/MD5 | 7 +++---- plspm.formula-1.0.1/plspm.formula/R/omatrix.inner.R | 3 +-- plspm.formula-1.0.1/plspm.formula/man/plspm.formula-package.Rd | 9 ++++----- plspm.formula-1.0/plspm.formula/build |only 5 files changed, 13 insertions(+), 16 deletions(-)
Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. Ongoing developments of the package
focus on offering easy to use tools for creating other spatio-dynamic
models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.1.2 dated 2015-11-06 and 1.1.3 dated 2015-12-30
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS | 4 ++++ R/run_model.R | 2 +- build/vignette.rds |binary inst/doc/isem2013_jml.pdf |binary man/run_model.Rd | 2 +- 8 files changed, 19 insertions(+), 15 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.2.3 dated 2015-11-08 and 0.3.0 dated 2015-12-30
DESCRIPTION | 8 +- MD5 | 32 ++++---- NEWS.md | 25 ++++++ R/delay.R | 4 - R/extendShinyjs.R | 132 +++++++++++++++++++++--------------- R/hidden.R | 2 R/reset.R | 4 - R/useShinyjs.R | 20 ++--- README.md | 22 +++--- inst/doc/overview.Rmd | 18 ++-- inst/doc/overview.html | 23 +++--- inst/examples/colourInput/app.R | 11 +-- inst/srcjs/shinyjs-default-funcs.js | 18 ++-- man/delay.Rd | 4 - man/extendShinyjs.Rd | 37 ++++++---- man/reset.Rd | 4 - vignettes/overview.Rmd | 18 ++-- 17 files changed, 228 insertions(+), 154 deletions(-)
Title: Hidden Markov Models for Life Sequences and Other Multivariate,
Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent)
Markov models and mixture hidden Markov models for social
sequence data and other categorical time series. Also some more restricted
versions of these type of models are available: Markov models, mixture
Markov models, and latent class models. The package supports models for one or
multiple subjects with one or multiple parallel sequences (channels). External
covariates can be added to explain cluster membership in mixture models. The
package provides functions for evaluating and comparing models, as well as
functions for easy plotting of multichannel sequence data and hidden Markov
models. Models are estimated using maximum likelihood via the EM algorithm and/or
direct numerical maximization with analytical gradients.
All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between seqHMM versions 1.0.3 dated 2015-12-23 and 1.0.3-1 dated 2015-12-30
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++---------- NEWS | 8 ++++++ R/mhmm_biofam.R | 6 ++--- R/mhmm_mvad.R | 6 ++--- R/mssplot.R | 6 ++--- R/plot.mhmm.R | 35 ++++++++++++++---------------- inst/doc/seqHMM.pdf | 60 ++++++++++++++++++++++++++-------------------------- man/mhmm_biofam.Rd | 6 ++--- man/mhmm_mvad.Rd | 6 ++--- man/mssplot.Rd | 6 ++--- man/plot.mhmm.Rd | 35 ++++++++++++++---------------- 12 files changed, 104 insertions(+), 100 deletions(-)
Title: Italian Fiscal Code ('Codice Fiscale') Utilities
Description: Provides utility functions to deal with Italian fiscal
code ('codice fiscale').
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between ifctools versions 0.3.1 dated 2015-05-27 and 0.3.2 dated 2015-12-30
DESCRIPTION | 16 ++++++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 3 ++- R/guess_fc.R | 2 +- R/ifctools-package.R | 1 + R/wrong_fc.R | 2 +- README.md | 8 ++++++-- man/guess_fc.Rd | 4 +++- man/ifctools.Rd | 2 +- man/wrong_fc.Rd | 4 +++- 10 files changed, 35 insertions(+), 25 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>
Diff between GSE versions 3.2.2 dated 2015-09-24 and 3.2.3 dated 2015-12-30
ChangeLog | 4 ++ DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++---------- R/GSE-utils.R | 70 ++++++++++++++++++++++++++++++++++++++++++++++-- R/GSE.R | 45 +++++++++++++++++------------- R/TSGS.R | 4 ++ R/generic.R | 3 -- R/huberPairwise.R | 4 +- R/simulation-utils.R | 16 +++++----- man/GSE.Rd | 37 ++++++++----------------- man/HuberPairwise.Rd | 2 - man/TSGS.Rd | 14 ++++----- man/boston.Rd | 2 - man/emve.Rd | 33 ---------------------- man/simulation-tools.Rd | 6 ++-- src/gse.cpp | 41 +++++++++++++--------------- 16 files changed, 175 insertions(+), 144 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 1.2-4 dated 2015-09-10 and 1.2-5 dated 2015-12-30
Description: Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 7
DESCRIPTION | 8
MD5 | 14
R/RcppExports.R | 22 -
R/display.R | 5
build/vignette.rds |binary
inst/doc/gRain-intro.R | 674 +++++++++++++++++++++++------------------------
inst/doc/gRain-intro.pdf |binary
8 files changed, 369 insertions(+), 361 deletions(-)
Title: Functions for Processing and Analyzing Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices, and generates data summaries. Also includes functions to plot, analyze, and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Diff between acc versions 1.1.7 dated 2015-07-17 and 1.2.3 dated 2015-12-30
acc-1.1.7/acc/R/readRaw.R |only acc-1.1.7/acc/R/readRawBatch.R |only acc-1.1.7/acc/man/readRaw.Rd |only acc-1.1.7/acc/man/readRawBatch.Rd |only acc-1.2.3/acc/ChangeLog |only acc-1.2.3/acc/DESCRIPTION | 16 ++++++++------ acc-1.2.3/acc/MD5 | 38 +++++++++++++++++++++++------------ acc-1.2.3/acc/NAMESPACE | 14 ++++++++++-- acc-1.2.3/acc/R/NHANES.R |only acc-1.2.3/acc/R/accSummary.R | 10 +++++++-- acc-1.2.3/acc/R/aee.R |only acc-1.2.3/acc/R/aeefit.R |only acc-1.2.3/acc/R/aggAcc.R | 5 ++-- acc-1.2.3/acc/R/internal.R |only acc-1.2.3/acc/R/readCounts.R |only acc-1.2.3/acc/R/readCountsBatch.R |only acc-1.2.3/acc/R/summary.aeefit.R |only acc-1.2.3/acc/R/weight.R |only acc-1.2.3/acc/data |only acc-1.2.3/acc/man/NHANES.Rd |only acc-1.2.3/acc/man/acc.Rd | 14 ++++++------ acc-1.2.3/acc/man/accBatch.Rd | 6 ++--- acc-1.2.3/acc/man/accSummary.Rd | 20 +++++++++--------- acc-1.2.3/acc/man/aee.Rd |only acc-1.2.3/acc/man/aeefit.Rd |only acc-1.2.3/acc/man/readCounts.Rd |only acc-1.2.3/acc/man/readCountsBatch.Rd |only acc-1.2.3/acc/man/simAcc.Rd | 2 - acc-1.2.3/acc/man/summary.aeefit.Rd |only acc-1.2.3/acc/man/weight.Rd |only 30 files changed, 78 insertions(+), 47 deletions(-)
Title: The Transfer Entropy Package
Description: Estimates the transfer entropy from one time series to another, where each time series consists of continuous random variables. The transfer entropy is an extension of mutual information which takes into account the direction of information flow, under the assumption that the underlying processes can be described by a Markov model. Two estimation methods are provided. The first calculates transfer entropy as the difference of mutual information. Mutual information is estimated using the Kraskov method, which builds on a nearest-neighbor framework (see package references). The second estimation method estimate transfer entropy via the a generalized correlation sum.
Author: Ghazaleh Haratinezhad Torbati [aut, cre],
Glenn Lawyer [aut]
Maintainer: Ghazaleh Haratinezhad Torbati <ghazaleh@mpi-inf.mpg.de>
Diff between TransferEntropy versions 1.0 dated 2015-12-26 and 1.1 dated 2015-12-30
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- build/partial.rdb |binary inst |only src/RcppExports.cpp | 20 ++++++++++++++++++++ src/ann_1.1.2/src/kd_split.cpp | 6 +++--- src/compute_TE.cpp | 22 +++++++++++++++++++--- 7 files changed, 54 insertions(+), 17 deletions(-)
More information about TransferEntropy at CRAN
Permanent link
Title: R-Values for Ranking in High-Dimensional Settings
Description: A collection of functions for computing "r-values" from various
kinds of user input such as MCMC output or a list of effect size estimates
and associated standard errors. Given a large collection of measurement units,
the r-value, r, of a particular unit is a reported percentile that may be
interpreted as the smallest percentile at which the unit should be placed in the
top r-fraction of units.
Author: Nicholas Henderson [cre],
Michael Newton [aut]
Maintainer: Nicholas Henderson <nhenders@stat.wisc.edu>
Diff between rvalues versions 0.3 dated 2015-01-28 and 0.6 dated 2015-12-30
DESCRIPTION | 22 +++++++---- MD5 | 57 +++++++++++++++------------- NAMESPACE | 23 ++++------- R/HyperEstimate.R | 3 + R/NPagrid.R | 99 +++++++++++++++++++++++++++++--------------------- R/NPestBinomial.R | 44 +++++++++++++++------- R/NPestNormal.R | 50 ++++++++++++++++--------- R/NPestPoisson.R | 43 ++++++++++++++------- R/NPestT.R | 72 +++++++++++++++++++++--------------- R/PostPercentile.R | 1 R/ThetaQuantiles.R | 3 - R/Valpha.R | 11 ++--- R/agrid_fns.R | 8 ++-- R/npml.R | 15 ++++++- R/rvalueBoot.R | 2 - R/rvalueGuts.R | 27 ++++++++----- R/rvalues.R | 47 +++++++++++++---------- R/rvaluesMCMC.R | 8 ++-- README.md |only data/NBA1314.rda |only data/datalist | 1 man/NBA1314.Rd |only man/OverlapCurve.Rd | 2 - man/PostPercentile.Rd | 2 - man/Valpha.Rd | 4 +- man/mroot.Rd | 2 - man/rvalueBoot.Rd | 2 - man/rvalues.Rd | 6 +-- man/rvaluesMCMC.Rd | 4 +- src/Vcut.c | 32 +++++++++++++--- src/zeroin.c | 2 - 31 files changed, 357 insertions(+), 235 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.2 dated 2015-12-28 and 0.6.2.1 dated 2015-12-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/nhanes.R | 10 +++++----- inst/doc/Introducing_nhanesA.html | 4 ++-- man/browseNHANES.Rd | 10 +++++----- 5 files changed, 20 insertions(+), 20 deletions(-)
Title: Time Value of Money, Time Series Analysis and Computational
Finance
Description: Package for time value of money calculation, time series analysis and computational finance.
Author: Felix Yanhui Fan <nolanfyh@gmail.com>
Maintainer: Felix Yanhui Fan <nolanfyh@gmail.com>
Diff between FinCal versions 0.6 dated 2014-02-24 and 0.6.2 dated 2015-12-30
FinCal-0.6.2/FinCal/DESCRIPTION | 18 - FinCal-0.6.2/FinCal/MD5 | 253 +++++++++++------------ FinCal-0.6.2/FinCal/NAMESPACE | 145 +++++++------ FinCal-0.6.2/FinCal/NEWS | 239 +++++++++++---------- FinCal-0.6.2/FinCal/R/EIR.R | 80 +++---- FinCal-0.6.2/FinCal/R/EPS.R | 26 +- FinCal-0.6.2/FinCal/R/SFRatio.R | 24 +- FinCal-0.6.2/FinCal/R/Sharpe.ratio.R | 26 +- FinCal-0.6.2/FinCal/R/bdy.R | 26 +- FinCal-0.6.2/FinCal/R/bdy2mmy.R | 24 +- FinCal-0.6.2/FinCal/R/candlestickChart.R | 84 +++---- FinCal-0.6.2/FinCal/R/cash.ratio.R | 26 +- FinCal-0.6.2/FinCal/R/coefficient.variation.R | 22 +- FinCal-0.6.2/FinCal/R/cogs.R | 202 +++++++++--------- FinCal-0.6.2/FinCal/R/current.ratio.R | 24 +- FinCal-0.6.2/FinCal/R/ddb.R | 62 ++--- FinCal-0.6.2/FinCal/R/debt.ratio.R | 26 +- FinCal-0.6.2/FinCal/R/diluted.EPS.R | 62 ++--- FinCal-0.6.2/FinCal/R/discount.rate.R | 64 +---- FinCal-0.6.2/FinCal/R/ear.R | 34 +-- FinCal-0.6.2/FinCal/R/ear.continuous.R | 28 +- FinCal-0.6.2/FinCal/R/ear2bey.R | 22 +- FinCal-0.6.2/FinCal/R/ear2hpr.R | 28 +- FinCal-0.6.2/FinCal/R/financial.leverage.R | 26 +- FinCal-0.6.2/FinCal/R/fv.R | 48 ++-- FinCal-0.6.2/FinCal/R/fv.annuity.R | 42 +-- FinCal-0.6.2/FinCal/R/fv.simple.R | 30 +- FinCal-0.6.2/FinCal/R/fv.uneven.R | 36 +-- FinCal-0.6.2/FinCal/R/geometric.mean.R | 20 - FinCal-0.6.2/FinCal/R/get.ohlc.google.R | 90 ++++---- FinCal-0.6.2/FinCal/R/get.ohlc.yahoo.R | 85 +++---- FinCal-0.6.2/FinCal/R/get.ohlcs.google.R | 100 ++++----- FinCal-0.6.2/FinCal/R/get.ohlcs.yahoo.R | 103 ++++----- FinCal-0.6.2/FinCal/R/gpm.R | 22 +- FinCal-0.6.2/FinCal/R/harmonic.mean.R | 16 - FinCal-0.6.2/FinCal/R/hpr.R | 30 +- FinCal-0.6.2/FinCal/R/hpr2bey.R | 24 +- FinCal-0.6.2/FinCal/R/hpr2ear.R | 28 +- FinCal-0.6.2/FinCal/R/hpr2mmy.R | 26 +- FinCal-0.6.2/FinCal/R/irr.R | 36 +-- FinCal-0.6.2/FinCal/R/iss.R | 32 +- FinCal-0.6.2/FinCal/R/lineChart.R | 71 +++--- FinCal-0.6.2/FinCal/R/lineChartMult.R | 88 ++++---- FinCal-0.6.2/FinCal/R/lt.d2e.R | 26 +- FinCal-0.6.2/FinCal/R/mmy2hpr.R | 28 +- FinCal-0.6.2/FinCal/R/n.period.R | 50 ++-- FinCal-0.6.2/FinCal/R/npm.R | 22 +- FinCal-0.6.2/FinCal/R/npv.R | 32 +- FinCal-0.6.2/FinCal/R/pmt.R | 52 ++-- FinCal-0.6.2/FinCal/R/pv.R | 54 ++-- FinCal-0.6.2/FinCal/R/pv.annuity.R | 40 +-- FinCal-0.6.2/FinCal/R/pv.perpetuity.R | 54 ++-- FinCal-0.6.2/FinCal/R/pv.simple.R | 30 +- FinCal-0.6.2/FinCal/R/pv.uneven.R | 36 +-- FinCal-0.6.2/FinCal/R/quick.ratio.R | 28 +- FinCal-0.6.2/FinCal/R/r.continuous.R | 24 +- FinCal-0.6.2/FinCal/R/r.norminal.R | 30 +- FinCal-0.6.2/FinCal/R/r.perpetuity.R | 24 +- FinCal-0.6.2/FinCal/R/sampling.error.R | 22 +- FinCal-0.6.2/FinCal/R/slde.R | 24 +- FinCal-0.6.2/FinCal/R/total.d2e.R | 26 +- FinCal-0.6.2/FinCal/R/twrr.R | 48 ++-- FinCal-0.6.2/FinCal/R/volumeChart.R | 43 +-- FinCal-0.6.2/FinCal/R/was.R | 50 ++-- FinCal-0.6.2/FinCal/R/wpr.R | 30 +- FinCal-0.6.2/FinCal/README.md |only FinCal-0.6.2/FinCal/man/EIR.Rd | 93 ++++---- FinCal-0.6.2/FinCal/man/EPS.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/SFRatio.Rd | 48 ++-- FinCal-0.6.2/FinCal/man/Sharpe.ratio.Rd | 52 ++-- FinCal-0.6.2/FinCal/man/bdy.Rd | 50 ++-- FinCal-0.6.2/FinCal/man/bdy2mmy.Rd | 44 ++-- FinCal-0.6.2/FinCal/man/candlestickChart.Rd | 67 ++---- FinCal-0.6.2/FinCal/man/cash.ratio.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/coefficient.variation.Rd | 44 ++-- FinCal-0.6.2/FinCal/man/cogs.Rd | 68 ++---- FinCal-0.6.2/FinCal/man/current.ratio.Rd | 50 ++-- FinCal-0.6.2/FinCal/man/ddb.Rd | 58 ++--- FinCal-0.6.2/FinCal/man/debt.ratio.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/diluted.EPS.Rd | 96 ++++---- FinCal-0.6.2/FinCal/man/discount.rate.Rd | 78 +++---- FinCal-0.6.2/FinCal/man/ear.Rd | 60 ++--- FinCal-0.6.2/FinCal/man/ear.continuous.Rd | 49 ++-- FinCal-0.6.2/FinCal/man/ear2bey.Rd | 41 +-- FinCal-0.6.2/FinCal/man/ear2hpr.Rd | 52 ++-- FinCal-0.6.2/FinCal/man/financial.leverage.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/fv.Rd | 79 +++---- FinCal-0.6.2/FinCal/man/fv.annuity.Rd | 59 ++--- FinCal-0.6.2/FinCal/man/fv.simple.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/fv.uneven.Rd | 44 ++-- FinCal-0.6.2/FinCal/man/geometric.mean.Rd | 34 +-- FinCal-0.6.2/FinCal/man/get.ohlc.google.Rd | 57 ++--- FinCal-0.6.2/FinCal/man/get.ohlc.yahoo.Rd | 62 ++--- FinCal-0.6.2/FinCal/man/get.ohlcs.google.Rd | 57 ++--- FinCal-0.6.2/FinCal/man/get.ohlcs.yahoo.Rd | 60 ++--- FinCal-0.6.2/FinCal/man/gpm.Rd | 46 ++-- FinCal-0.6.2/FinCal/man/harmonic.mean.Rd | 34 +-- FinCal-0.6.2/FinCal/man/hpr.Rd | 56 ++--- FinCal-0.6.2/FinCal/man/hpr2bey.Rd | 45 ++-- FinCal-0.6.2/FinCal/man/hpr2ear.Rd | 52 ++-- FinCal-0.6.2/FinCal/man/hpr2mmy.Rd | 48 ++-- FinCal-0.6.2/FinCal/man/irr.Rd | 45 ++-- FinCal-0.6.2/FinCal/man/iss.Rd | 50 ++-- FinCal-0.6.2/FinCal/man/lineChart.Rd | 61 ++--- FinCal-0.6.2/FinCal/man/lineChartMult.Rd | 69 +++--- FinCal-0.6.2/FinCal/man/lt.d2e.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/mmy2hpr.Rd | 52 ++-- FinCal-0.6.2/FinCal/man/n.period.Rd | 75 +++--- FinCal-0.6.2/FinCal/man/npm.Rd | 45 ++-- FinCal-0.6.2/FinCal/man/npv.Rd | 55 ++--- FinCal-0.6.2/FinCal/man/pmt.Rd | 75 +++--- FinCal-0.6.2/FinCal/man/pv.Rd | 83 +++---- FinCal-0.6.2/FinCal/man/pv.annuity.Rd | 59 ++--- FinCal-0.6.2/FinCal/man/pv.perpetuity.Rd | 63 ++--- FinCal-0.6.2/FinCal/man/pv.simple.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/pv.uneven.Rd | 49 ++-- FinCal-0.6.2/FinCal/man/quick.ratio.Rd | 57 ++--- FinCal-0.6.2/FinCal/man/r.continuous.Rd | 45 ++-- FinCal-0.6.2/FinCal/man/r.norminal.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/r.perpetuity.Rd | 44 ++-- FinCal-0.6.2/FinCal/man/sampling.error.Rd | 38 +-- FinCal-0.6.2/FinCal/man/slde.Rd | 51 ++-- FinCal-0.6.2/FinCal/man/total.d2e.Rd | 53 ++-- FinCal-0.6.2/FinCal/man/twrr.Rd | 48 ++-- FinCal-0.6.2/FinCal/man/volumeChart.Rd | 60 ++--- FinCal-0.6.2/FinCal/man/was.Rd | 54 ++-- FinCal-0.6.2/FinCal/man/wpr.Rd | 40 +-- FinCal-0.6/FinCal/R/date.breaks.R |only FinCal-0.6/FinCal/man/date.breaks.Rd |only 129 files changed, 3331 insertions(+), 3318 deletions(-)
Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in a (cross-sectional)
population sample into an estimate of the frequency with which
seroconversions (infections) occur in the sampled population.
Author: Peter Teunis [aut] (Author of the method and original code),
Daniel Lewandowski [com, ctb] (Creator of the R package),
Chantal Quinten [ctb, cre] (Project manager and the package maintainer)
Maintainer: Chantal Quinten <seroincidence@ecdc.europa.eu>
Diff between seroincidence versions 1.0.4 dated 2015-05-22 and 1.0.5 dated 2015-12-29
DESCRIPTION | 10 +++-- MD5 | 60 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 8 ++++ R/campylobacterResponseParams.R | 6 +-- R/campylobacterSerologyData.R | 6 +-- R/estimateSeroincidence.R | 7 +-- R/logRhoCdf.R | 8 ++-- R/logRhoPdf.R | 8 ++-- R/rinvgamma.R | 2 - R/salmonellaSerologyData.R | 6 +-- R/seroincidence.R | 6 +-- R/simulateSalmonellaResponseParams.R | 6 +-- R/simulateSerologyData.R | 2 - inst/doc/cover.html | 8 ++-- inst/doc/installation.R | 8 ++-- inst/doc/installation.pdf |binary inst/doc/methodology.Rmd | 1 inst/doc/methodology.pdf |binary inst/doc/tutorial.pdf |binary man/campylobacterResponseParams.Rd | 4 +- man/campylobacterSerologyData.Rd | 4 +- man/estimateSeroincidence.Rd | 4 +- man/print.seroincidence.Rd | 4 +- man/print.summary.seroincidence.Rd | 4 +- man/salmonellaSerologyData.Rd | 4 +- man/seroincidence.Rd | 2 - man/simulateSalmonellaResponseParams.Rd | 4 +- man/simulateSerologyData.Rd | 4 +- man/summary.seroincidence.Rd | 4 +- vignettes/methodology.Rmd | 1 31 files changed, 105 insertions(+), 88 deletions(-)
Title: Crystallization Toolset
Description: This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis.
Author: Qingan Sun, Xiaojun Li
Maintainer: Qingan Sun <quinsun@gmail.com>
Diff between xtal versions 1.0 dated 2014-11-05 and 1.15 dated 2015-12-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/Design8Vertex.R | 2 +- man/xtal-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Total Operating Characteristic Curve and ROC Curve
Diff between TOC versions 0.0-3 dated 2015-08-05 and 0.0-4 dated 2015-12-29
Description: Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating characteristic to measure diagnostic ability for multiple thresholds. Int. J. Geogr. Inf. Sci. 28 (3), 570-583).
Author: Robert G. Pontius
Maintainer: Alí Santacruz
DESCRIPTION | 9 +++++----
MD5 | 12 ++++++------
NAMESPACE | 2 +-
R/TOCnosp.R | 1 +
R/plotROC.R | 4 ++--
R/plotTOC.R | 4 ++--
man/TOC-package.Rd | 4 ++--
7 files changed, 19 insertions(+), 17 deletions(-)
Title: R Wrapper Around the Telegram Bot API
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (e.g. you send messages, images, files from R to your smartphone).
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between telegram versions 0.1 dated 2015-12-24 and 0.3.0 dated 2015-12-29
DESCRIPTION | 8 MD5 | 16 + NAMESPACE | 2 R/TGBot.R | 507 ++++++++++++++++++++++++++++++++++----------------- R/telegram-package.r | 1 README.md | 92 +++++++-- inst |only man/TGBot.Rd | 74 ++----- man/bot_token.Rd |only 9 files changed, 467 insertions(+), 233 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.44-0 dated 2015-12-23 and 1.44-1 dated 2015-12-29
DESCRIPTION | 10 MD5 | 58 NAMESPACE | 16 NEWS | 59 R/anova.mppm.R | 274 ++ R/anova.ppm.R | 48 R/leverage.R | 7 R/mppm.R | 33 R/tess.R | 7 R/texture.R | 6 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 4 inst/doc/updates.Rnw | 55 inst/doc/updates.pdf |binary man/anova.mppm.Rd | 100 - man/anova.ppm.Rd | 72 man/as.function.tess.Rd |only man/logLik.mppm.Rd | 109 - man/logLik.ppm.Rd | 6 man/plot.leverage.ppm.Rd | 36 man/spatstat-internal.Rd | 2 man/textureplot.Rd | 3 man/tileindex.Rd |only src/linSnncross.h | 6 src/linknnd.c | 6 tests/alltests.R | 4215 +++++++++++++++++++++++---------------------- vignettes/packagesizes.txt | 1 vignettes/updates.Rnw | 55 31 files changed, 2914 insertions(+), 2274 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-3 dated 2015-09-20 and 0.7-4 dated 2015-12-29
RDS-0.7-3/RDS/man/summary.svyglm.Rd |only RDS-0.7-4/RDS/DESCRIPTION | 13 +-- RDS-0.7-4/RDS/MD5 | 42 +++++----- RDS-0.7-4/RDS/NAMESPACE | 6 - RDS-0.7-4/RDS/R/bootstrap-intervals.R | 18 ++++ RDS-0.7-4/RDS/R/control.rds.estimates.R | 12 +++ RDS-0.7-4/RDS/R/data-export.R | 2 RDS-0.7-4/RDS/R/data-import.R | 3 RDS-0.7-4/RDS/R/estimate-plots.R | 113 ---------------------------- RDS-0.7-4/RDS/R/estimate-utils.R | 45 +++++++++++ RDS-0.7-4/RDS/R/gile-bootstrap.R | 8 ++ RDS-0.7-4/RDS/R/llmeC.R | 123 ++++++++++++++++--------------- RDS-0.7-4/RDS/R/me.impute.R | 37 ++++++--- RDS-0.7-4/RDS/R/rds-doc.R | 5 + RDS-0.7-4/RDS/R/rds.data.frame-plots.R | 17 ++-- RDS-0.7-4/RDS/R/rds.estimates.local.R | 1 RDS-0.7-4/RDS/R/summary.odds.R | 23 +++-- RDS-0.7-4/RDS/R/utils.R | 1 RDS-0.7-4/RDS/R/weights.R | 1 RDS-0.7-4/RDS/man/impute.visibility.Rd | 9 +- RDS-0.7-4/RDS/man/plot.rds.data.frame.Rd | 10 +- RDS-0.7-4/RDS/man/summary.svyglm.RDS.Rd |only RDS-0.7-4/RDS/src/llmeC.c | 20 +++-- 23 files changed, 261 insertions(+), 248 deletions(-)
Title: Generating Various Numerical Representation Schemes of Protein
Sequence
Description: Comprehensive toolkit for generating various numerical
representation schemes of protein sequence. The descriptors and similarity
scores included are extensively used in bioinformatics and chemogenomics.
For full functionality, the software 'ncbi-blast+' is needed, see
<http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>,
Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between protr versions 1.0-1 dated 2015-11-27 and 1.1-1 dated 2015-12-29
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 16 ++++++++++++++-- R/desc09CTDD.R | 18 +++++++++++++++--- R/desc13PAAC.R | 3 --- R/desc14APAAC.R | 3 --- R/protr-package.R | 4 ++-- README.md | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 6 +++--- inst/doc/protr.R | 2 +- inst/doc/protr.Rnw | 19 ++++++++----------- inst/doc/protr.pdf |binary man/extractAPAAC.Rd | 3 --- man/extractPAAC.Rd | 3 --- man/protr-package.Rd | 4 ++-- vignettes/protr.Rnw | 19 ++++++++----------- 17 files changed, 79 insertions(+), 73 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix (FIM). This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>
Diff between PopED versions 0.2.0 dated 2015-03-20 and 0.3.0 dated 2015-12-29
PopED-0.2.0/PopED/R/PopED-package.R |only PopED-0.2.0/PopED/man/PopED-internal.Rd |only PopED-0.2.0/PopED/man/PopED-package.Rd |only PopED-0.2.0/PopED/tests/test-all.R |only PopED-0.3.0/PopED/DESCRIPTION | 20 PopED-0.3.0/PopED/MD5 | 459 +++++----- PopED-0.3.0/PopED/NAMESPACE | 110 ++ PopED-0.3.0/PopED/NEWS | 14 PopED-0.3.0/PopED/R/Doptim.R | 90 + PopED-0.3.0/PopED/R/Dtrace.R | 4 PopED-0.3.0/PopED/R/LEDoptim.R | 3 PopED-0.3.0/PopED/R/LinMatrixH.R | 5 PopED-0.3.0/PopED/R/LinMatrixL.R | 2 PopED-0.3.0/PopED/R/LinMatrixLH.R | 2 PopED-0.3.0/PopED/R/LinMatrixL_occ.R | 2 PopED-0.3.0/PopED/R/PopED.R |only PopED-0.3.0/PopED/R/RS_opt.R | 2 PopED-0.3.0/PopED/R/RS_opt_gen.R | 2 PopED-0.3.0/PopED/R/a_line_search.R | 1 PopED-0.3.0/PopED/R/bfgsb_min.R | 4 PopED-0.3.0/PopED/R/blockexp.R | 6 PopED-0.3.0/PopED/R/blockfinal.R | 47 - PopED-0.3.0/PopED/R/blockheader.R | 64 - PopED-0.3.0/PopED/R/blockopt.R | 3 PopED-0.3.0/PopED/R/build_sfg.R | 25 PopED-0.3.0/PopED/R/calc_ofv_and_fim.R | 1 PopED-0.3.0/PopED/R/cell.R | 3 PopED-0.3.0/PopED/R/convert_variables.R | 3 PopED-0.3.0/PopED/R/create.poped.database.R | 60 - PopED-0.3.0/PopED/R/create_design.R | 2 PopED-0.3.0/PopED/R/create_design_space.R | 11 PopED-0.3.0/PopED/R/diag_matlab.R | 2 PopED-0.3.0/PopED/R/downsizing_general_design.R | 4 PopED-0.3.0/PopED/R/ed_laplace_ofv.R | 7 PopED-0.3.0/PopED/R/ed_mftot.R | 4 PopED-0.3.0/PopED/R/evaluate.e.ofv.fim.R | 1 PopED-0.3.0/PopED/R/evaluate.fim.R | 7 PopED-0.3.0/PopED/R/feval.R | 4 PopED-0.3.0/PopED/R/fileparts.R | 3 PopED-0.3.0/PopED/R/find.largest.index.R |only PopED-0.3.0/PopED/R/getTruncatedNormal.R |only PopED-0.3.0/PopED/R/get_all_params.R | 2 PopED-0.3.0/PopED/R/get_cv.R | 2 PopED-0.3.0/PopED/R/get_unfixed_params.R | 80 - PopED-0.3.0/PopED/R/get_vector_str.R | 6 PopED-0.3.0/PopED/R/getfulld.R | 5 PopED-0.3.0/PopED/R/inv.R | 10 PopED-0.3.0/PopED/R/isempty.R | 3 PopED-0.3.0/PopED/R/isfield.R | 3 PopED-0.3.0/PopED/R/log_prior_pdf.R | 3 PopED-0.3.0/PopED/R/mf.R | 2 PopED-0.3.0/PopED/R/mf3.R | 26 PopED-0.3.0/PopED/R/mf5.R | 2 PopED-0.3.0/PopED/R/mf6.R | 2 PopED-0.3.0/PopED/R/mf7.R | 2 PopED-0.3.0/PopED/R/mf8.R | 2 PopED-0.3.0/PopED/R/mfea.R | 2 PopED-0.3.0/PopED/R/mftot.R | 3 PopED-0.3.0/PopED/R/mftot0.R | 3 PopED-0.3.0/PopED/R/mftot1.R | 3 PopED-0.3.0/PopED/R/mftot2.R | 3 PopED-0.3.0/PopED/R/mftot3.R | 3 PopED-0.3.0/PopED/R/mftot4.R | 3 PopED-0.3.0/PopED/R/mftot5.R | 2 PopED-0.3.0/PopED/R/mftot6.R | 3 PopED-0.3.0/PopED/R/mftot7.R | 2 PopED-0.3.0/PopED/R/model_prediction.R | 9 PopED-0.3.0/PopED/R/models.R | 13 PopED-0.3.0/PopED/R/ofv_criterion.R | 1 PopED-0.3.0/PopED/R/ofv_fim.R | 6 PopED-0.3.0/PopED/R/ones.R | 2 PopED-0.3.0/PopED/R/optim_ARS.R |only PopED-0.3.0/PopED/R/optim_LS.R |only PopED-0.3.0/PopED/R/pargen.R | 30 PopED-0.3.0/PopED/R/plot_efficiency_of_windows.R | 4 PopED-0.3.0/PopED/R/plot_model_prediction.R | 7 PopED-0.3.0/PopED/R/poped_optim.R |only PopED-0.3.0/PopED/R/poped_optimize.R | 2 PopED-0.3.0/PopED/R/rand.R | 3 PopED-0.3.0/PopED/R/randn.R | 3 PopED-0.3.0/PopED/R/randperm.R | 3 PopED-0.3.0/PopED/R/size.R | 2 PopED-0.3.0/PopED/R/start_parallel.R |only PopED-0.3.0/PopED/R/test_for_max.R | 3 PopED-0.3.0/PopED/R/test_for_min.R | 3 PopED-0.3.0/PopED/R/test_for_zeros.R | 3 PopED-0.3.0/PopED/R/test_mat_size.R | 3 PopED-0.3.0/PopED/R/tic.R | 2 PopED-0.3.0/PopED/R/toc.R | 7 PopED-0.3.0/PopED/R/zeros.R | 2 PopED-0.3.0/PopED/README.md | 6 PopED-0.3.0/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only PopED-0.3.0/PopED/inst/shinyapp/server.R | 13 PopED-0.3.0/PopED/inst/shinyapp/ui.R | 20 PopED-0.3.0/PopED/man/Doptim.Rd | 119 +- PopED-0.3.0/PopED/man/Dtrace.Rd | 21 PopED-0.3.0/PopED/man/LEDoptim.Rd | 79 + PopED-0.3.0/PopED/man/LinMatrixH.Rd | 50 - PopED-0.3.0/PopED/man/LinMatrixL.Rd | 26 PopED-0.3.0/PopED/man/LinMatrixLH.Rd | 52 - PopED-0.3.0/PopED/man/LinMatrixL_occ.Rd | 50 - PopED-0.3.0/PopED/man/PopED.Rd |only PopED-0.3.0/PopED/man/RS_opt.Rd | 72 - PopED-0.3.0/PopED/man/RS_opt_gen.Rd | 78 + PopED-0.3.0/PopED/man/a_line_search.Rd | 42 PopED-0.3.0/PopED/man/bfgsb_min.Rd | 38 PopED-0.3.0/PopED/man/blockexp.Rd | 26 PopED-0.3.0/PopED/man/blockfinal.Rd | 38 PopED-0.3.0/PopED/man/blockheader.Rd | 59 - PopED-0.3.0/PopED/man/blockopt.Rd | 26 PopED-0.3.0/PopED/man/calc_autofocus.Rd | 43 PopED-0.3.0/PopED/man/calc_ofv_and_fim.Rd | 88 + PopED-0.3.0/PopED/man/calc_ofv_and_grad.Rd | 43 PopED-0.3.0/PopED/man/cell.Rd | 16 PopED-0.3.0/PopED/man/convert_variables.Rd | 13 PopED-0.3.0/PopED/man/create.poped.database.Rd | 92 +- PopED-0.3.0/PopED/man/create_design.Rd | 20 PopED-0.3.0/PopED/man/create_design_space.Rd | 24 PopED-0.3.0/PopED/man/diag_matlab.Rd | 21 PopED-0.3.0/PopED/man/downsizing_general_design.Rd | 32 PopED-0.3.0/PopED/man/ed_laplace_ofv.Rd | 56 - PopED-0.3.0/PopED/man/ed_mftot.Rd | 79 + PopED-0.3.0/PopED/man/evaluate.e.ofv.fim.Rd | 95 +- PopED-0.3.0/PopED/man/evaluate.fim.Rd | 70 - PopED-0.3.0/PopED/man/feps.add.Rd | 30 PopED-0.3.0/PopED/man/feps.add.prop.Rd | 30 PopED-0.3.0/PopED/man/feps.prop.Rd | 45 PopED-0.3.0/PopED/man/feval.Rd | 15 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 28 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 28 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 43 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 28 PopED-0.3.0/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 28 PopED-0.3.0/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 26 PopED-0.3.0/PopED/man/fileparts.Rd | 15 PopED-0.3.0/PopED/man/getTruncatedNormal.Rd | 5 PopED-0.3.0/PopED/man/get_all_params.Rd | 19 PopED-0.3.0/PopED/man/get_rse.Rd | 21 PopED-0.3.0/PopED/man/get_unfixed_params.Rd |only PopED-0.3.0/PopED/man/getfulld.Rd | 5 PopED-0.3.0/PopED/man/gradf_eps.Rd | 48 - PopED-0.3.0/PopED/man/inv.Rd |only PopED-0.3.0/PopED/man/isempty.Rd | 15 PopED-0.3.0/PopED/man/isfield.Rd | 15 PopED-0.3.0/PopED/man/log_prior_pdf.Rd | 38 PopED-0.3.0/PopED/man/mf.Rd | 47 - PopED-0.3.0/PopED/man/mf3.Rd | 49 - PopED-0.3.0/PopED/man/mf5.Rd | 57 - PopED-0.3.0/PopED/man/mf6.Rd | 49 - PopED-0.3.0/PopED/man/mf7.Rd | 47 - PopED-0.3.0/PopED/man/mf8.Rd | 51 - PopED-0.3.0/PopED/man/mfea.Rd | 65 - PopED-0.3.0/PopED/man/mftot.Rd | 46 - PopED-0.3.0/PopED/man/mftot0.Rd | 48 - PopED-0.3.0/PopED/man/mftot1.Rd | 50 - PopED-0.3.0/PopED/man/mftot2.Rd | 29 PopED-0.3.0/PopED/man/mftot3.Rd | 29 PopED-0.3.0/PopED/man/mftot4.Rd | 58 - PopED-0.3.0/PopED/man/mftot5.Rd | 50 - PopED-0.3.0/PopED/man/mftot6.Rd | 48 - PopED-0.3.0/PopED/man/mftot7.Rd | 52 - PopED-0.3.0/PopED/man/model_prediction.Rd | 30 PopED-0.3.0/PopED/man/ofv_criterion.Rd | 56 - PopED-0.3.0/PopED/man/ofv_fim.Rd | 66 - PopED-0.3.0/PopED/man/ones.Rd | 14 PopED-0.3.0/PopED/man/optim_ARS.Rd |only PopED-0.3.0/PopED/man/optim_LS.Rd |only PopED-0.3.0/PopED/man/pargen.Rd | 65 - PopED-0.3.0/PopED/man/plot_efficiency_of_windows.Rd | 37 PopED-0.3.0/PopED/man/plot_model_prediction.Rd | 16 PopED-0.3.0/PopED/man/poped.choose.Rd | 11 PopED-0.3.0/PopED/man/poped_optim.Rd |only PopED-0.3.0/PopED/man/poped_optimize.Rd | 70 - PopED-0.3.0/PopED/man/rand.Rd | 15 PopED-0.3.0/PopED/man/randn.Rd | 15 PopED-0.3.0/PopED/man/randperm.Rd | 15 PopED-0.3.0/PopED/man/size.Rd | 14 PopED-0.3.0/PopED/man/start_parallel.Rd |only PopED-0.3.0/PopED/man/test_for_max.Rd | 9 PopED-0.3.0/PopED/man/test_for_min.Rd | 9 PopED-0.3.0/PopED/man/test_for_zeros.Rd | 9 PopED-0.3.0/PopED/man/test_mat_size.Rd | 3 PopED-0.3.0/PopED/man/tic.Rd | 16 PopED-0.3.0/PopED/man/toc.Rd | 16 PopED-0.3.0/PopED/man/zeros.Rd | 16 PopED-0.3.0/PopED/tests/testthat.R |only PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 328 +++---- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt | 118 +- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 112 +- PopED-0.3.0/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 74 - PopED-0.3.0/PopED/tests/testthat/Rplots.pdf |binary PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_Doptim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_Dtrace.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixH.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixLH.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL_occ.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_RS_opt_gen.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_a_line_search.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_bfgsb_min.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockexp.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal.R | 2 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockheader.R | 21 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_blockopt.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_build_sfg.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_autofocus.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_fim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_grad.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_downsizing_general_design.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_ed_mftot.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_evaluate.e.ofv.fim.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_get_all_params.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_gradf_eps.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_log_prior_pdf.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf3.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf5.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf6.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf7.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mf8.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mfea.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot0.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot1.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot4.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot5.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot6.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot7.R | 3 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_optim_ARS.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_optim_LS.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_pargen.R | 26 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 16 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped_optim.R |only PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/examples_poped_optimize.R | 1 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_basic.R | 15 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_ed.R | 20 PopED-0.3.0/PopED/tests/testthat/examples_fcn_doc/warfarin_optimize.R | 18 PopED-0.3.0/PopED/tests/testthat/helper_functions.R |only PopED-0.3.0/PopED/tests/testthat/helper_options.R |only PopED-0.3.0/PopED/tests/testthat/test_create_databases.R | 10 PopED-0.3.0/PopED/tests/testthat/test_distributions.R | 81 - PopED-0.3.0/PopED/tests/testthat/test_examples.R | 2 PopED-0.3.0/PopED/tests/testthat/test_optimization.R |only 244 files changed, 3133 insertions(+), 2290 deletions(-)
Title: Statistical Inference of Variables Driving Systematic Variation
Description: Significance test for association between variables
and their estimated latent variables.
Latent variables may be estimated by principal component analysis (PCA),
logistic factor analysis (LFA), and other techniques.
Author: Neo Christopher Chung <nchchung@gmail.com>, Wei Hao <whao@princeton.edu>, John D. Storey <jstorey@princeton.edu>
Maintainer: Neo Christopher Chung <nchchung@gmail.com>
Diff between jackstraw versions 1.0 dated 2014-01-31 and 1.1 dated 2015-12-29
DESCRIPTION | 25 +- MD5 | 31 ++- NAMESPACE | 12 + R/generic.R | 52 ++--- R/jackstraw.R | 449 +++++++++++++++++++++++++++++++++++++++----- R/jackstraw_parametric.R |only R/lfacorpcor.R |only R/likelihood.R |only R/permutationPA.R | 89 ++++---- man/dev.R.Rd |only man/devdiff.Rd |only man/devdiff_parallel.Rd |only man/efron_Rsq.Rd |only man/jackstraw.FUN.Rd |only man/jackstraw.LFA.Rd |only man/jackstraw.PCA.Rd |only man/jackstraw.Rd | 127 ++++-------- man/jackstraw.parametric.Rd |only man/lfa.corpcor.Rd |only man/permutationPA.Rd | 37 +-- man/pseudo_Rsq.Rd |only vignettes |only 22 files changed, 582 insertions(+), 240 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Diff between doBy versions 4.5-13 dated 2014-12-11 and 4.5-14 dated 2015-12-29
Description: The facilities can roughly be grouped as:
1) Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 6
DESCRIPTION | 18
MD5 | 48 +-
NAMESPACE | 83 ++++
R/BY-lmBy.R | 6
R/LSmeans.R | 6
R/linest.R | 28 +
R/linestGet.R | 37 +
R/linestMatrix.R | 14
build/vignette.rds |binary
data/beets.txt.gz |binary
data/budworm.txt.gz |binary
data/carcass.txt.gz |binary
data/carcassall.txt.gz |binary
data/crimeRate.txt.gz |binary
data/datalist | 23 -
data/haldCement.txt.gz |binary
data/potatoes.txt.gz |only
inst/doc/LSmeans.R | 822 ++++++++++++++++++++++----------------------
inst/doc/LSmeans.pdf |binary
inst/doc/doBy.R | 912 ++++++++++++++++++++++++-------------------------
inst/doc/doBy.pdf |binary
man/DATA-potatoes.Rd |only
man/LSmeans.Rd | 5
man/doBy-internal.Rd | 2
man/lmBy.Rd | 2
26 files changed, 1079 insertions(+), 933 deletions(-)
Title: Metrics of Difference for Comparing Pairs of Maps
Diff between diffeR versions 0.0-3 dated 2015-07-07 and 0.0-4 dated 2015-12-29
Description: Metrics of difference for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr.
Maintainer: Alí Santacruz
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
NAMESPACE | 2 +-
R/overallComponentsPlot.R | 2 +-
man/diffeR-package.Rd | 4 ++--
5 files changed, 13 insertions(+), 12 deletions(-)
Title: A Data Analysis GUI for R
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows with contributions from others (see documentation).
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between Deducer versions 0.7-7 dated 2014-04-30 and 0.7-9 dated 2015-12-29
Deducer-0.7-7/Deducer/java/deducer |only Deducer-0.7-7/Deducer/java/projects |only Deducer-0.7-7/Deducer/man/summary.lm.Rd |only Deducer-0.7-9/Deducer/DESCRIPTION | 11 Deducer-0.7-9/Deducer/MD5 | 801 +++++++++++++-------------- Deducer-0.7-9/Deducer/NAMESPACE | 101 +++ Deducer-0.7-9/Deducer/NEWS | 6 Deducer-0.7-9/Deducer/R/contingency.tables.R | 4 Deducer-0.7-9/Deducer/R/ggcorplot.R | 64 -- Deducer-0.7-9/Deducer/R/perm.t.test.R | 9 Deducer-0.7-9/Deducer/R/summary.lm.R | 2 Deducer-0.7-9/Deducer/R/zzz.R | 56 - Deducer-0.7-9/Deducer/inst/java/deducer.jar |binary Deducer-0.7-9/Deducer/java/org |only Deducer-0.7-9/Deducer/man/summarylm.Rd |only 15 files changed, 558 insertions(+), 496 deletions(-)
Title: Inferring Disease Networks via Differential Network Inference
Description: Performs differential network analysis to infer disease specific gene networks.
Author: Gokmen Altay
Maintainer: Gokmen Altay <altayscience@gmail.com>
Diff between dc3net versions 1.0 dated 2015-10-01 and 1.0.1 dated 2015-12-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- R/dc3net.R | 16 +++++----------- data/datalist |only data/geneNames.csv.gz |only data/normalData.csv.gz |only data/tumorData.csv.gz |only inst/doc/dc3net-manual.pdf |binary man/dc3net.Rd | 7 +++---- 9 files changed, 20 insertions(+), 23 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.48 dated 2015-10-29 and 1.49 dated 2015-12-29
Changelog | 27 +++++++++++++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 19 +++++++++--------- NAMESPACE | 4 +-- R/Functions.R | 48 ++++++++++++++++++++++++++++++---------------- R/plotDendrogram.R |only man/WGCNA-package.Rd | 4 +-- man/goodGenes.Rd | 7 ++++++ man/goodGenesMS.Rd | 8 +++++++ man/goodSamplesGenes.Rd | 8 +++++++ man/goodSamplesGenesMS.Rd | 8 +++++++ 11 files changed, 108 insertions(+), 33 deletions(-)
Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes the multivariate methods
and data visualization tools to implement profile analysis and cross-validation
techniques described in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins
<cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3-1 dated 2015-10-19 and 0.3-2 dated 2015-12-29
profileR-0.3-1/profileR/inst/doc/jss_profileR.rnw |only profileR-0.3-1/profileR/vignettes/jss_profileR.rnw |only profileR-0.3-2/profileR/DESCRIPTION | 21 +++--- profileR-0.3-2/profileR/MD5 | 67 ++++++++++---------- profileR-0.3-2/profileR/NAMESPACE | 49 +++++++++++--- profileR-0.3-2/profileR/R/anova.critpat.R | 8 ++ profileR-0.3-2/profileR/R/cpa.R | 3 profileR-0.3-2/profileR/R/mpa.R | 1 profileR-0.3-2/profileR/R/pams.R | 29 ++++++++ profileR-0.3-2/profileR/R/paos.R | 1 profileR-0.3-2/profileR/R/pbg.R | 2 profileR-0.3-2/profileR/R/pcv.R | 1 profileR-0.3-2/profileR/R/plot.critpat.R | 1 profileR-0.3-2/profileR/R/plot.prof.R | 13 +++ profileR-0.3-2/profileR/R/pr.R | 34 +++++++++- profileR-0.3-2/profileR/R/print.critpat.R | 6 + profileR-0.3-2/profileR/R/print.prof.R | 3 profileR-0.3-2/profileR/R/print.profg.R | 4 - profileR-0.3-2/profileR/R/profileplot.R | 15 ++-- profileR-0.3-2/profileR/R/summary.profg.R | 3 profileR-0.3-2/profileR/build/vignette.rds |binary profileR-0.3-2/profileR/inst/doc/jss_profileR.Rnw |only profileR-0.3-2/profileR/inst/doc/jss_profileR.pdf |binary profileR-0.3-2/profileR/man/anova.critpat.Rd |only profileR-0.3-2/profileR/man/cpa.Rd | 5 - profileR-0.3-2/profileR/man/mpa.Rd | 3 profileR-0.3-2/profileR/man/pams.Rd | 36 ++++------ profileR-0.3-2/profileR/man/paos.Rd | 4 - profileR-0.3-2/profileR/man/pbg.Rd | 57 +++++------------ profileR-0.3-2/profileR/man/pcv.Rd | 8 +- profileR-0.3-2/profileR/man/plot.critpat.Rd | 2 profileR-0.3-2/profileR/man/plot.prof.Rd |only profileR-0.3-2/profileR/man/pr.Rd | 70 +++++---------------- profileR-0.3-2/profileR/man/print.critpat.Rd |only profileR-0.3-2/profileR/man/profileplot.Rd | 49 +++++--------- profileR-0.3-2/profileR/man/summary.critpat.Rd | 2 profileR-0.3-2/profileR/man/wprifm.Rd | 2 profileR-0.3-2/profileR/vignettes/jss_profileR.Rnw |only 38 files changed, 278 insertions(+), 221 deletions(-)
Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between htmltools versions 0.2.6 dated 2014-09-08 and 0.3 dated 2015-12-29
DESCRIPTION | 13 +- MD5 | 71 +++++++----- NAMESPACE | 11 +- NEWS | 28 +++++ R/html_dependency.R | 76 ++++++++++++- R/tags.R | 177 ++++++++++++++++++++++++++++---- R/template.R |only inst/tests/template-document.html |only inst/tests/test-tags.r | 209 ++++++++++++++++++++++++++++++++++++++ inst/tests/test-template.R |only man/HTML.Rd | 4 man/as.tags.Rd | 3 man/browsable.Rd | 3 man/builder.Rd | 3 man/copyDependencyToDir.Rd | 7 - man/css.Rd |only man/findDependencies.Rd | 3 man/htmlDependencies.Rd | 13 +- man/htmlDependency.Rd | 28 +++-- man/htmlEscape.Rd | 3 man/htmlPreserve.Rd | 4 man/htmlTemplate.Rd |only man/html_print.Rd | 5 man/include.Rd | 7 - man/knitr_methods.Rd | 3 man/makeDependencyRelative.Rd | 7 - man/print.html.Rd | 3 man/renderDependencies.Rd | 5 man/renderDocument.Rd |only man/renderTags.Rd | 5 man/resolveDependencies.Rd | 3 man/save_html.Rd | 7 - man/singleton.Rd | 3 man/singleton_tools.Rd | 3 man/subtractDependencies.Rd | 9 - man/suppressDependencies.Rd |only man/tag.Rd | 29 +++-- man/urlEncodePath.Rd | 3 man/validateCssUnit.Rd | 3 man/withTags.Rd | 5 40 files changed, 630 insertions(+), 126 deletions(-)
Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
Author: Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between GiANT versions 1.1 dated 2015-09-08 and 1.2 dated 2015-12-29
DESCRIPTION | 8 +-- MD5 | 21 ++++---- R/evaluateGeneSetUncertainty.R | 71 ++++++++++++++++++++++++++--- R/significance.R | 56 ++++++++++++++++++++++ build/vignette.rds |binary inst/doc/giant_package_vignette.R | 41 ++++++++++++---- inst/doc/giant_package_vignette.Snw | 48 +++++++++++++++++-- inst/doc/giant_package_vignette.pdf |binary man/GiANT-package.Rd | 3 - man/evaluateGeneSetUncertainty.Rd | 4 + vignettes/giant_package_vignette.Snw | 48 +++++++++++++++++-- vignettes/vignette_randomGeneSetValues.pdf |only 12 files changed, 260 insertions(+), 40 deletions(-)
Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steve Culpepper [aut, cph],
James Balamuta [aut, cre, ctb, com, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between cIRT versions 1.0.0 dated 2015-12-06 and 1.1.0 dated 2015-12-29
DESCRIPTION | 10 MD5 | 54 +-- NAMESPACE | 10 R/RcppExports.R | 612 +++++++++++++++++++------------------- R/cIRT-package.R | 54 +-- R/choice_matrix.R | 32 + R/payout_matrix.R | 26 - R/survey_data.R | 34 +- R/trial_matrix.R | 80 ++-- data/choice_matrix.rda |binary inst/CITATION | 40 +- man/Generate_Choice.Rd | 96 ++--- man/Total_Tabulate.Rd | 50 +-- man/TwoPLChoicemcmc.Rd | 138 ++++---- man/cIRT.Rd | 236 +++++++------- man/cIRT_package.Rd | 70 ++-- man/center_matrix.Rd | 70 ++-- man/choice_matrix.Rd | 56 +-- man/direct_sum.Rd | 72 ++-- man/payout_matrix.Rd | 50 +-- man/probitHLM.Rd | 150 ++++----- man/riwishart.Rd | 60 +-- man/rmvnorm.Rd | 66 ++-- man/rwishart.Rd | 88 ++--- man/survey_data.Rd | 58 +-- man/trial_matrix.Rd | 104 +++--- vignettes/parse_results.R | 254 +++++++-------- vignettes/simulation_CIRT_beta2.R | 192 +++++------ 28 files changed, 1381 insertions(+), 1381 deletions(-)
Title: Invoke 'Repast Simphony' Simulation Models
Description: An R and Repast integration tool for running individual-based (IbM)
simulation models developed using 'Repast Simphony' Agent-Based framework
directly from R code. This package integrates 'Repast Simphony' models within
R environment, making easier the tasks of running and analyzing model output
data for automated parameter calibration and for carrying out uncertainty and
sensitivity analysis using the power of R environment.
Author: Antonio Prestes Garcia [aut, cre],
Alfonso Rodriguez-Paton [aut, ths]
Maintainer: Antonio Prestes Garcia <antonio.pgarcia@alumnos.upm.es>
Diff between rrepast versions 0.2 dated 2015-12-05 and 0.3 dated 2015-12-28
DESCRIPTION | 10 - MD5 | 13 +- NAMESPACE | 8 + R/RRepast.R | 244 ++++++++++++++++++++++++++++++++++++++--- man/AddFactor.Rd |only man/ApplyFactorRange.Rd |only man/BuildParameterSet.Rd |only man/GetFactorsSize.Rd |only man/LatinHypercube.Rd |only man/RunExperiment.Rd |only man/SetSimulationParameters.Rd |only 11 files changed, 254 insertions(+), 21 deletions(-)
Title: 'rgl' in 'htmlwidgets' Framework
Description: Provides an 'htmlwidgets' framework for the 'rgl' package.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rglwidget versions 0.1.1431 dated 2015-12-07 and 0.1.1434 dated 2015-12-28
DESCRIPTION | 14 +++--- MD5 | 28 ++++++------ NAMESPACE | 11 +++- R/playwidget.R | 55 +++++++++++++++++++++++ R/rglwidget.R | 26 +++++++++-- demo/00Index | 1 demo/simpleShinyRgl.R |only inst/htmlwidgets/lib/rglClass/rglClass.src.js | 3 + man/ageControl.Rd | 26 ++++------- man/clipplaneControl.Rd | 12 +---- man/import.Rd |only man/playwidget.Rd | 60 +++++++++++++++++++++----- man/rglwidget.Rd | 12 ++++- man/vertexControl.Rd | 19 +++----- vignettes/internals.Rmd | 4 + vignettes/test.Rmd | 28 ++++++++++++ 16 files changed, 224 insertions(+), 75 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1429 dated 2015-12-07 and 0.95.1435 dated 2015-12-28
DESCRIPTION | 10 - MD5 | 14 - inst/doc/WebGL.html | 425 ++++++++++++++++++++++++++++++++++---------------- inst/doc/rgl.html | 279 ++++++++++++++++++++++++-------- man/ageSetter.Rd | 4 man/propertySetter.Rd | 22 +- man/webGLcontrols.Rd | 10 - man/writeWebGL.Rd | 18 +- 8 files changed, 540 insertions(+), 242 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.1 dated 2015-10-08 and 0.6.2 dated 2015-12-28
nhanesA-0.6.1/nhanesA/INDEX |only nhanesA-0.6.2/nhanesA/DESCRIPTION | 14 - nhanesA-0.6.2/nhanesA/MD5 | 32 +-- nhanesA-0.6.2/nhanesA/NAMESPACE | 5 nhanesA-0.6.2/nhanesA/R/nhanes.R | 146 +++++++++++----- nhanesA-0.6.2/nhanesA/README.md | 11 - nhanesA-0.6.2/nhanesA/build/vignette.rds |binary nhanesA-0.6.2/nhanesA/inst/doc/Introducing_nhanesA.R | 12 + nhanesA-0.6.2/nhanesA/inst/doc/Introducing_nhanesA.Rmd | 20 ++ nhanesA-0.6.2/nhanesA/inst/doc/Introducing_nhanesA.html | 118 ++++++++---- nhanesA-0.6.2/nhanesA/man/browseNHANES.Rd | 8 nhanesA-0.6.2/nhanesA/man/nhanes.Rd | 6 nhanesA-0.6.2/nhanesA/man/nhanesAttr.Rd | 4 nhanesA-0.6.2/nhanesA/man/nhanesDXA.Rd |only nhanesA-0.6.2/nhanesA/man/nhanesTableVars.Rd | 2 nhanesA-0.6.2/nhanesA/man/nhanesTables.Rd | 2 nhanesA-0.6.2/nhanesA/man/nhanesTranslate.Rd | 14 - nhanesA-0.6.2/nhanesA/vignettes/Introducing_nhanesA.Rmd | 20 ++ 18 files changed, 285 insertions(+), 129 deletions(-)
Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity
score analysis for multilevel, or clustered, data.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between multilevelPSA versions 1.2.3 dated 2015-11-05 and 1.2.4 dated 2015-12-28
multilevelPSA-1.2.3/multilevelPSA/R/geom_rug_alt.R |only multilevelPSA-1.2.3/multilevelPSA/README.md |only multilevelPSA-1.2.3/multilevelPSA/man/geom_rug_alt.Rd |only multilevelPSA-1.2.4/multilevelPSA/DESCRIPTION | 14 +++---- multilevelPSA-1.2.4/multilevelPSA/MD5 | 23 +++++------- multilevelPSA-1.2.4/multilevelPSA/NAMESPACE | 19 ++++++++- multilevelPSA-1.2.4/multilevelPSA/NEWS | 5 ++ multilevelPSA-1.2.4/multilevelPSA/R/multilevelPSA-package.R | 7 ++- multilevelPSA-1.2.4/multilevelPSA/R/plot.difftable.R | 6 +-- multilevelPSA-1.2.4/multilevelPSA/R/plot.missing.R | 4 +- multilevelPSA-1.2.4/multilevelPSA/R/plot.mlpsa.circ.R | 22 ++++++----- multilevelPSA-1.2.4/multilevelPSA/R/plot.mlpsa.difference.R | 7 ++- multilevelPSA-1.2.4/multilevelPSA/man/missing.plot.Rd | 6 +-- multilevelPSA-1.2.4/multilevelPSA/man/mlpsa.circ.plot.Rd | 13 +++--- 14 files changed, 73 insertions(+), 53 deletions(-)
Title: Short Term Forecasting via GMDH-Type Neural Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH versions 1.1 dated 2015-07-20 and 1.2 dated 2015-12-28
DESCRIPTION | 13 ++++++------- MD5 | 6 +++--- man/GMDH.Rd | 8 ++++---- man/fcast.Rd | 10 +++++----- 4 files changed, 18 insertions(+), 19 deletions(-)
Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time
series, possibly mixed with ARMA, regression, transfer-function components.
Exact methods (MLE, forecasting, simulation) are used.
Author: Justin Q. Veenstra [aut, cre],
A.I. McLeod [aut]
Maintainer: Justin Q. Veenstra <justin.veenstra@gmail.com>
Diff between arfima versions 1.2-7 dated 2014-11-21 and 1.3-3 dated 2015-12-28
DESCRIPTION | 26 MD5 | 50 - NAMESPACE | 2 R/ARToPacf.R | 54 - R/Boot.ARFIMA.R | 257 +++--- R/Boot.R | 8 R/InvertibleQ.R | 260 +++--- R/arfima.R | 2090 ++++++++++++++++++++++++++++---------------------- R/arfima0.R | 80 + R/arfimaFit.R | 1009 +++++++++++++++--------- R/getssq.R | 67 - R/iARMA.R | 1222 ++++++++++++++--------------- R/integ.R | 27 R/lARFIMA.R | 111 +- R/lARFIMAwTF.R | 150 +-- R/mult.R | 88 +- R/plot.predARFIMA.R | 213 ++--- R/predict.ARFIMA.R | 615 +++++++------- R/sims.R | 258 +++--- R/tacf.R | 1061 ++++++++++++------------- R/utilityfcns.R | 1112 +++++++++++++------------- R/wts.R | 176 ++-- man/arfima-package.Rd | 312 +++---- man/arfima.Rd | 373 ++++---- src/Makevars | 2 src/tfcalc.c | 2 26 files changed, 5221 insertions(+), 4404 deletions(-)
Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently scatter
plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.2.0 dated 2015-11-18 and 0.2.1 dated 2015-12-28
DESCRIPTION | 20 ++++++++--------- MD5 | 13 ++++++----- NAMESPACE | 2 + R/vcmap.R | 57 +++++++++++++++++++++++++++++++-------------------- R/vhist.R | 59 +++++++++++++++++++++++++++++------------------------ R/vscat.R | 27 +++++++++++++++--------- build/vignette.rds |binary tests/testthat |only 8 files changed, 104 insertions(+), 74 deletions(-)
Title: Twitter Collector and Export to 'postGIS'
Description: This is an improved implementation of the package 'StreamR' to
capture tweets and store it into a 'postGIS' data base. The package simplifies
the configuration task to capture tweets and facilitates its store into a
'PostGIS' database.
Author: Pau Aragó
Maintainer: Pau Aragó <parago@uji.es>
Diff between tweet2r versions 0.2 dated 2015-11-01 and 0.3 dated 2015-12-28
ChangeLog |only DESCRIPTION | 10 ++++++---- MD5 | 23 ++++++++++++++++------- NAMESPACE | 9 +++++++++ R/t2gis.R |only R/t2pgis.R | 3 ++- R/t2sqlite.R |only R/t2summary.R |only R/tweet2r.R | 7 ++++++- R/valjson.R |only man/t2gis.Rd |only man/t2pgis.Rd | 12 ++++++------ man/t2sqlite.Rd |only man/t2summary.Rd |only man/tweet2r-package.Rd | 5 ++--- man/tweet2r.Rd | 12 +++++------- man/valjson.Rd |only 17 files changed, 52 insertions(+), 29 deletions(-)
More information about markmyassignment at CRAN
Permanent link
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided.
As of release 1.60, the following Boost libraries are included:
algorithm any bind circular_buffer concept config container
date_time detail dynamic_bitset exception filesystem foreach
functional fusion geometry graph heap integer interprocess
intrusive io iostreams iterator math move mpl multiprcecision
numeric pending phoenix preprocessor random range smart_ptr
spirit tuple type_trains typeof unordered utility uuid.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.58.0-1 dated 2015-05-21 and 1.60.0-1 dated 2015-12-28
ChangeLog | 13 DESCRIPTION | 18 MD5 | 4031 ++++++---- README.md | 14 inst/NEWS.Rd | 40 inst/include/boost/align/align.hpp | 10 inst/include/boost/align/detail/address.hpp | 26 inst/include/boost/align/detail/align.hpp | 46 inst/include/boost/align/detail/align_cxx11.hpp | 20 inst/include/boost/align/detail/is_alignment.hpp | 30 inst/include/boost/aligned_storage.hpp | 127 inst/include/boost/archive/archive_exception.hpp | 25 inst/include/boost/archive/basic_archive.hpp | 4 inst/include/boost/archive/basic_binary_iarchive.hpp | 58 inst/include/boost/archive/basic_binary_iprimitive.hpp | 17 inst/include/boost/archive/basic_binary_oarchive.hpp | 33 inst/include/boost/archive/basic_binary_oprimitive.hpp | 24 inst/include/boost/archive/basic_text_iarchive.hpp | 15 inst/include/boost/archive/basic_text_iprimitive.hpp | 8 inst/include/boost/archive/basic_text_oarchive.hpp | 19 inst/include/boost/archive/basic_text_oprimitive.hpp | 8 inst/include/boost/archive/basic_xml_archive.hpp | 16 inst/include/boost/archive/basic_xml_iarchive.hpp | 43 inst/include/boost/archive/basic_xml_oarchive.hpp | 65 inst/include/boost/archive/binary_iarchive.hpp | 2 inst/include/boost/archive/binary_iarchive_impl.hpp | 8 inst/include/boost/archive/binary_oarchive.hpp | 2 inst/include/boost/archive/binary_oarchive_impl.hpp | 8 inst/include/boost/archive/codecvt_null.hpp | 4 inst/include/boost/archive/detail/abi_prefix.hpp | 4 inst/include/boost/archive/detail/abi_suffix.hpp | 4 inst/include/boost/archive/detail/archive_serializer_map.hpp | 9 inst/include/boost/archive/detail/basic_iarchive.hpp | 40 inst/include/boost/archive/detail/basic_iserializer.hpp | 14 inst/include/boost/archive/detail/basic_oarchive.hpp | 28 inst/include/boost/archive/detail/basic_oserializer.hpp | 14 inst/include/boost/archive/detail/basic_pointer_iserializer.hpp | 14 inst/include/boost/archive/detail/basic_pointer_oserializer.hpp | 14 inst/include/boost/archive/detail/basic_serializer_map.hpp | 8 inst/include/boost/archive/detail/common_iarchive.hpp | 2 inst/include/boost/archive/detail/common_oarchive.hpp | 2 inst/include/boost/archive/detail/decl.hpp | 68 inst/include/boost/archive/detail/helper_collection.hpp | 5 inst/include/boost/archive/detail/interface_iarchive.hpp | 12 inst/include/boost/archive/detail/interface_oarchive.hpp | 21 inst/include/boost/archive/detail/iserializer.hpp | 76 inst/include/boost/archive/impl/archive_serializer_map.ipp | 6 inst/include/boost/archive/impl/basic_binary_iarchive.ipp | 10 inst/include/boost/archive/impl/basic_binary_iprimitive.ipp | 14 inst/include/boost/archive/impl/basic_binary_oarchive.ipp | 6 inst/include/boost/archive/impl/basic_binary_oprimitive.ipp | 14 inst/include/boost/archive/impl/basic_text_iarchive.ipp | 8 inst/include/boost/archive/impl/basic_text_iprimitive.ipp | 13 inst/include/boost/archive/impl/basic_text_oarchive.ipp | 4 inst/include/boost/archive/impl/basic_text_oprimitive.ipp | 11 inst/include/boost/archive/impl/basic_xml_grammar.hpp | 14 inst/include/boost/archive/impl/basic_xml_iarchive.ipp | 24 inst/include/boost/archive/impl/basic_xml_oarchive.ipp | 63 inst/include/boost/archive/impl/text_iarchive_impl.ipp | 18 inst/include/boost/archive/impl/text_oarchive_impl.ipp | 12 inst/include/boost/archive/impl/text_wiarchive_impl.ipp | 10 inst/include/boost/archive/impl/text_woarchive_impl.ipp | 8 inst/include/boost/archive/impl/xml_iarchive_impl.ipp | 70 inst/include/boost/archive/impl/xml_oarchive_impl.ipp | 22 inst/include/boost/archive/impl/xml_wiarchive_impl.ipp | 27 inst/include/boost/archive/impl/xml_woarchive_impl.ipp | 28 inst/include/boost/archive/iterators/base64_from_binary.hpp | 6 inst/include/boost/archive/iterators/binary_from_base64.hpp | 5 inst/include/boost/archive/iterators/insert_linebreaks.hpp | 6 inst/include/boost/archive/iterators/mb_from_wchar.hpp | 19 inst/include/boost/archive/iterators/remove_whitespace.hpp | 6 inst/include/boost/archive/iterators/transform_width.hpp | 8 inst/include/boost/archive/iterators/wchar_from_mb.hpp | 37 inst/include/boost/archive/iterators/xml_escape.hpp | 5 inst/include/boost/archive/iterators/xml_unescape.hpp | 5 inst/include/boost/archive/polymorphic_iarchive.hpp | 18 inst/include/boost/archive/polymorphic_oarchive.hpp | 17 inst/include/boost/archive/text_iarchive.hpp | 29 inst/include/boost/archive/text_oarchive.hpp | 18 inst/include/boost/archive/text_wiarchive.hpp | 20 inst/include/boost/archive/text_woarchive.hpp | 12 inst/include/boost/archive/xml_archive_exception.hpp | 7 inst/include/boost/archive/xml_iarchive.hpp | 26 inst/include/boost/archive/xml_oarchive.hpp | 14 inst/include/boost/archive/xml_wiarchive.hpp | 26 inst/include/boost/archive/xml_woarchive.hpp | 16 inst/include/boost/asio |only inst/include/boost/asio.hpp |only inst/include/boost/assert.hpp | 9 inst/include/boost/atomic/detail/atomic_flag.hpp | 6 inst/include/boost/atomic/detail/atomic_template.hpp | 128 inst/include/boost/atomic/detail/bitwise_cast.hpp |only inst/include/boost/atomic/detail/caps_gcc_ppc.hpp | 2 inst/include/boost/atomic/detail/config.hpp | 36 inst/include/boost/atomic/detail/int_sizes.hpp | 4 inst/include/boost/atomic/detail/operations_fwd.hpp | 3 inst/include/boost/atomic/detail/ops_cas_based.hpp | 40 inst/include/boost/atomic/detail/ops_emulated.hpp | 16 inst/include/boost/atomic/detail/ops_extending_cas_based.hpp | 9 inst/include/boost/atomic/detail/ops_gcc_alpha.hpp | 2 inst/include/boost/atomic/detail/ops_gcc_arm.hpp | 2 inst/include/boost/atomic/detail/ops_gcc_atomic.hpp | 15 inst/include/boost/atomic/detail/ops_gcc_ppc.hpp | 379 inst/include/boost/atomic/detail/ops_gcc_sparc.hpp | 27 inst/include/boost/atomic/detail/ops_gcc_sync.hpp | 33 inst/include/boost/atomic/detail/ops_gcc_x86.hpp | 4 inst/include/boost/atomic/detail/ops_gcc_x86_dcas.hpp | 306 inst/include/boost/atomic/detail/ops_linux_arm.hpp | 7 inst/include/boost/atomic/detail/ops_msvc_arm.hpp | 4 inst/include/boost/atomic/detail/ops_msvc_x86.hpp | 57 inst/include/boost/atomic/detail/ops_windows.hpp | 1 inst/include/boost/atomic/detail/platform.hpp | 8 inst/include/boost/atomic/detail/storage_type.hpp | 138 inst/include/boost/bind.hpp | 19 inst/include/boost/bind/arg.hpp | 6 inst/include/boost/bind/bind.hpp | 485 - inst/include/boost/bind/bind_mf_cc.hpp | 54 inst/include/boost/bind/placeholders.hpp | 65 inst/include/boost/chrono/detail/inlined/mac/chrono.hpp | 54 inst/include/boost/chrono/detail/inlined/mac/process_cpu_clocks.hpp | 2 inst/include/boost/chrono/detail/inlined/posix/process_cpu_clocks.hpp | 2 inst/include/boost/chrono/duration.hpp | 3 inst/include/boost/chrono/io/time_point_units.hpp | 15 inst/include/boost/concept/detail/general.hpp | 11 inst/include/boost/concept_check.hpp | 17 inst/include/boost/config/compiler/clang.hpp | 22 inst/include/boost/config/compiler/gcc.hpp | 20 inst/include/boost/config/compiler/intel.hpp | 79 inst/include/boost/config/compiler/sunpro_cc.hpp | 10 inst/include/boost/config/compiler/visualc.hpp | 50 inst/include/boost/config/compiler/xlcpp.hpp |only inst/include/boost/config/platform/cloudabi.hpp |only inst/include/boost/config/platform/haiku.hpp | 2 inst/include/boost/config/platform/macos.hpp | 2 inst/include/boost/config/platform/win32.hpp | 8 inst/include/boost/config/select_compiler_config.hpp | 10 inst/include/boost/config/select_platform_config.hpp | 4 inst/include/boost/config/stdlib/dinkumware.hpp | 28 inst/include/boost/config/stdlib/libcomo.hpp | 12 inst/include/boost/config/stdlib/libcpp.hpp | 10 inst/include/boost/config/stdlib/libstdcpp3.hpp | 29 inst/include/boost/config/stdlib/modena.hpp | 10 inst/include/boost/config/stdlib/msl.hpp | 19 inst/include/boost/config/stdlib/roguewave.hpp | 9 inst/include/boost/config/stdlib/sgi.hpp | 13 inst/include/boost/config/stdlib/stlport.hpp | 18 inst/include/boost/config/stdlib/vacpp.hpp | 13 inst/include/boost/config/suffix.hpp | 20 inst/include/boost/container/adaptive_pool.hpp | 40 inst/include/boost/container/allocator.hpp | 43 inst/include/boost/container/allocator_traits.hpp | 75 inst/include/boost/container/container_fwd.hpp | 40 inst/include/boost/container/deque.hpp | 119 inst/include/boost/container/detail/adaptive_node_pool.hpp | 1 inst/include/boost/container/detail/alloc_lib.h | 122 inst/include/boost/container/detail/auto_link.hpp | 11 inst/include/boost/container/detail/block_list.hpp |only inst/include/boost/container/detail/block_slist.hpp |only inst/include/boost/container/detail/config_begin.hpp | 1 inst/include/boost/container/detail/copy_move_algo.hpp | 79 inst/include/boost/container/detail/dispatch_uses_allocator.hpp |only inst/include/boost/container/detail/dlmalloc.hpp |only inst/include/boost/container/detail/flat_tree.hpp | 128 inst/include/boost/container/detail/iterator.hpp | 1 inst/include/boost/container/detail/iterators.hpp | 12 inst/include/boost/container/detail/mpl.hpp | 175 inst/include/boost/container/detail/mutex.hpp | 4 inst/include/boost/container/detail/node_alloc_holder.hpp | 108 inst/include/boost/container/detail/pair.hpp | 63 inst/include/boost/container/detail/pool_common_alloc.hpp | 12 inst/include/boost/container/detail/pool_resource.hpp |only inst/include/boost/container/detail/std_fwd.hpp | 28 inst/include/boost/container/detail/tree.hpp | 128 inst/include/boost/container/detail/type_traits.hpp | 3 inst/include/boost/container/detail/variadic_templates_tools.hpp | 2 inst/include/boost/container/detail/workaround.hpp | 21 inst/include/boost/container/flat_map.hpp | 21 inst/include/boost/container/flat_set.hpp | 6 inst/include/boost/container/list.hpp | 115 inst/include/boost/container/map.hpp | 6 inst/include/boost/container/new_allocator.hpp | 4 inst/include/boost/container/node_allocator.hpp | 30 inst/include/boost/container/pmr |only 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inst/include/boost/date_time/time_system_counted.hpp | 2 inst/include/boost/detail/is_incrementable.hpp | 54 inst/include/boost/detail/winapi/GetCurrentProcess.hpp | 15 inst/include/boost/detail/winapi/GetCurrentThread.hpp | 22 inst/include/boost/detail/winapi/GetLastError.hpp | 14 inst/include/boost/detail/winapi/GetProcessTimes.hpp | 51 inst/include/boost/detail/winapi/GetThreadTimes.hpp | 42 inst/include/boost/detail/winapi/apc.hpp |only inst/include/boost/detail/winapi/basic_types.hpp | 249 inst/include/boost/detail/winapi/condition_variable.hpp |only inst/include/boost/detail/winapi/config.hpp | 21 inst/include/boost/detail/winapi/critical_section.hpp |only inst/include/boost/detail/winapi/crypt.hpp | 225 inst/include/boost/detail/winapi/detail |only inst/include/boost/detail/winapi/directory_management.hpp | 89 inst/include/boost/detail/winapi/dll.hpp | 230 inst/include/boost/detail/winapi/error_handling.hpp | 159 inst/include/boost/detail/winapi/event.hpp |only 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inst/include/boost/type_traits/is_stateless.hpp | 31 inst/include/boost/type_traits/is_union.hpp | 38 inst/include/boost/type_traits/is_unsigned.hpp | 142 inst/include/boost/type_traits/is_virtual_base_of.hpp | 41 inst/include/boost/type_traits/is_void.hpp | 26 inst/include/boost/type_traits/is_volatile.hpp | 59 inst/include/boost/type_traits/make_signed.hpp | 90 inst/include/boost/type_traits/make_unsigned.hpp | 89 inst/include/boost/type_traits/promote.hpp | 22 inst/include/boost/type_traits/rank.hpp | 9 inst/include/boost/type_traits/remove_all_extents.hpp | 23 inst/include/boost/type_traits/remove_bounds.hpp | 27 inst/include/boost/type_traits/remove_const.hpp | 62 inst/include/boost/type_traits/remove_cv.hpp | 49 inst/include/boost/type_traits/remove_extent.hpp | 23 inst/include/boost/type_traits/remove_pointer.hpp | 18 inst/include/boost/type_traits/remove_reference.hpp | 15 inst/include/boost/type_traits/remove_volatile.hpp | 57 inst/include/boost/type_traits/type_identity.hpp |only inst/include/boost/type_traits/type_with_alignment.hpp | 284 inst/include/boost/units/scaled_base_unit.hpp | 20 inst/include/boost/utility/declval.hpp | 33 inst/include/boost/utility/string_ref.hpp | 6 inst/include/boost/uuid/detail/config.hpp | 22 inst/include/boost/uuid/detail/uuid_x86.hpp | 48 inst/include/boost/uuid/seed_rng.hpp | 131 inst/include/boost/variant/detail/element_index.hpp | 4 inst/include/boost/variant/detail/has_result_type.hpp | 5 inst/include/boost/variant/recursive_wrapper_fwd.hpp | 18 inst/include/boost/variant/static_visitor.hpp | 17 inst/include/boost/variant/variant.hpp | 5 inst/include/boost/version.hpp | 4 man/BH-package.Rd | 4 1825 files changed, 46743 insertions(+), 37550 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from http://www.r-inla.org. It is recommended the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R"). A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the abn website.
Author: Fraser Ian Lewis [aut], Marta Pittavino [cre, ctb], Reinhard Furrer [ctb]
Maintainer: Marta Pittavino <marta.pittavino@math.uzh.ch>
Diff between abn versions 0.85 dated 2014-12-09 and 0.86 dated 2015-12-28
ChangeLog | 6 ++++++ DESCRIPTION | 14 ++++++++------ MD5 | 19 ++++++++++--------- NAMESPACE | 4 ++++ R/build_score_cache.R | 4 ++-- R/fitabn.R | 6 +++--- R/search_hillclimber.R | 6 +++--- R/tographviz.R | 2 +- build/vignette.rds |binary cleanup | 1 + src/Makevars.win |only 11 files changed, 38 insertions(+), 24 deletions(-)
Title: Unimodal Additive Hazards Model
Description: Nonparametric estimation of a unimodal or U-shape covariate effect under additive hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between uniah versions 0.2 dated 2015-12-16 and 0.3 dated 2015-12-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/uniah.ti.known.R | 4 ++-- man/uniah-package.Rd | 4 ++-- man/uniah.Rd | 4 ++-- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: General Non-Linear Optimization
Description: General Non-linear Optimization Using Augmented Lagrange Multiplier Method.
Author: Alexios Ghalanos and Stefan Theussl
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between Rsolnp versions 1.15 dated 2014-11-24 and 1.16 dated 2015-12-28
ChangeLog | 38 +- DESCRIPTION | 20 - MD5 | 14 NAMESPACE | 3 R/gosolnp.R | 918 ++++++++++++++++++++++++++-------------------------- R/solnp.R | 2 inst/doc/manual.pdf |binary man/gosolnp.Rd | 494 +++++++++++++-------------- 8 files changed, 752 insertions(+), 737 deletions(-)
Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rmgarch versions 1.2-9 dated 2015-07-02 and 1.3-0 dated 2015-12-28
ChangeLog | 413 ++++---- DESCRIPTION | 8 MD5 | 28 NAMESPACE | 70 - R/fdcc-main.R | 2 R/rdcc-main.R | 2 R/rmgarch-functions.R | 330 +++--- build/vignette.rds |binary inst/CITATION | 42 inst/COPYRIGHTS | 20 inst/doc/The_rmgarch_models.Rnw | 332 +++--- inst/doc/The_rmgarch_models.pdf |binary vignettes/The_rmgarch_models.Rnw | 332 +++--- vignettes/The_rmgarch_models.tex | 332 +++--- vignettes/rmgarch1.tex | 1948 +++++++++++++++++++-------------------- 15 files changed, 1933 insertions(+), 1926 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 0.1-2 dated 2015-10-08 and 1.0.0 dated 2015-12-28
DESCRIPTION | 8 ++--- MD5 | 18 +++++++------ R/RcppExports.R | 4 ++ build/partial.rdb |binary inst/News.Rd | 41 ++++++++++++++++++++++++------ inst/include |only man/lamW-package.Rd | 4 +- man/lamW.Rd | 2 - src/RcppExports.cpp | 71 +++++++++++++++++++++++++++++++++++++++++++++++----- src/lambertW.cpp | 1 10 files changed, 121 insertions(+), 28 deletions(-)
Title: Biased Urn Model Distributions
Description: Statistical models of biased sampling in the form of
univariate and multivariate noncentral hypergeometric distributions,
including Wallenius' noncentral hypergeometric distribution and
Fisher's noncentral hypergeometric distribution
(also called extended hypergeometric distribution).
See vignette("UrnTheory") for explanation of these distributions.
Author: Agner Fog
Maintainer: Agner Fog <agner@agner.org>
Diff between BiasedUrn versions 1.06.1 dated 2013-12-29 and 1.07 dated 2015-12-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/UrnTheory.pdf |binary src/fnchyppr.cpp | 8 ++++---- src/wnchyppr.cpp | 2 +- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates
for group means and standard deviations and their differences and
effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between BEST versions 0.3.0 dated 2015-07-01 and 0.4.0 dated 2015-12-28
BEST-0.3.0/BEST/inst/tests/test-BESTmcmc.R |only BEST-0.3.0/BEST/inst/tests/test-BESTmcmc_errors.R |only BEST-0.3.0/BEST/inst/tests/test-BESTmcmc_priors.R |only BEST-0.3.0/BEST/inst/tests/test-BESTpower.R |only BEST-0.3.0/BEST/inst/tests/test-hdi.R |only BEST-0.3.0/BEST/inst/tests/test-summary.R |only BEST-0.4.0/BEST/DESCRIPTION | 8 +-- BEST-0.4.0/BEST/MD5 | 38 ++++++++--------- BEST-0.4.0/BEST/NEWS | 6 ++ BEST-0.4.0/BEST/R/BESTmcmc.R | 18 +++++--- BEST-0.4.0/BEST/build/vignette.rds |binary BEST-0.4.0/BEST/inst/doc/BEST.R | 44 +++++++++++--------- BEST-0.4.0/BEST/inst/doc/BEST.Rnw | 47 +++++++++++++--------- BEST-0.4.0/BEST/inst/doc/BEST.pdf |binary BEST-0.4.0/BEST/inst/tests/testthat |only BEST-0.4.0/BEST/man/BESTmcmc.Rd | 11 +---- BEST-0.4.0/BEST/man/figures/BESTmodel.jpg |binary BEST-0.4.0/BEST/man/postPriorOverlap.Rd | 2 BEST-0.4.0/BEST/vignettes/BEST.Rnw | 47 +++++++++++++--------- BEST-0.4.0/BEST/vignettes/BEST.bib | 7 +-- BEST-0.4.0/BEST/vignettes/BESTmodel.jpg |binary 21 files changed, 129 insertions(+), 99 deletions(-)
Title: Tools for Post-Selection Inference
Description: New tools for post-selection inference, for use
with forward stepwise regression, least angle regression, the
lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor,
Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.1.1 dated 2015-09-30 and 1.1.2 dated 2015-12-27
selectiveInference-1.1.1/selectiveInference/man/estimateLambda.Rd |only selectiveInference-1.1.2/selectiveInference/DESCRIPTION | 20 selectiveInference-1.1.2/selectiveInference/MD5 | 50 selectiveInference-1.1.2/selectiveInference/NAMESPACE | 8 selectiveInference-1.1.2/selectiveInference/R/funs.fixed.R | 26 selectiveInference-1.1.2/selectiveInference/R/funs.fs.R | 171 +-- selectiveInference-1.1.2/selectiveInference/R/funs.groupfs.R | 554 +++++++--- selectiveInference-1.1.2/selectiveInference/R/funs.lar.R | 25 selectiveInference-1.1.2/selectiveInference/R/funs.quadratic.R | 267 ++-- selectiveInference-1.1.2/selectiveInference/man/estimateSigma.Rd | 40 selectiveInference-1.1.2/selectiveInference/man/factorDesign.Rd | 2 selectiveInference-1.1.2/selectiveInference/man/fixedLassoInf.Rd | 68 - selectiveInference-1.1.2/selectiveInference/man/forwardStop.Rd | 34 selectiveInference-1.1.2/selectiveInference/man/fs.Rd | 56 - selectiveInference-1.1.2/selectiveInference/man/fsInf.Rd | 64 - selectiveInference-1.1.2/selectiveInference/man/groupfs.Rd | 20 selectiveInference-1.1.2/selectiveInference/man/groupfsInf.Rd | 34 selectiveInference-1.1.2/selectiveInference/man/lar.Rd | 33 selectiveInference-1.1.2/selectiveInference/man/larInf.Rd | 53 selectiveInference-1.1.2/selectiveInference/man/manyMeans.Rd | 16 selectiveInference-1.1.2/selectiveInference/man/plot.fs.Rd | 25 selectiveInference-1.1.2/selectiveInference/man/plot.lar.Rd | 25 selectiveInference-1.1.2/selectiveInference/man/predict.fs.Rd | 25 selectiveInference-1.1.2/selectiveInference/man/predict.groupfs.Rd |only selectiveInference-1.1.2/selectiveInference/man/predict.lar.Rd | 25 selectiveInference-1.1.2/selectiveInference/man/scaleGroups.Rd | 12 selectiveInference-1.1.2/selectiveInference/man/selectiveInference.Rd | 201 +-- 27 files changed, 1068 insertions(+), 786 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: SA Counterparty Credit Risk under Basel III
Description: Computes the Exposure-At-Default based on standardized approach of
the Basel III Regulatory framework (SA-CCR). It also includes an object-oriented
solution for the generation of the trades.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between SACCR versions 1.0 dated 2015-10-11 and 1.1 dated 2015-12-27
DESCRIPTION | 21 +++++++++++---------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 3 ++- R/CSA.R |only R/CalcAddon.R | 24 +++++++++++++++++++++--- R/CalcRC.R | 20 ++++++++++++++++---- R/ExampleIRD.R | 1 + R/ExampleIRDCommMargined.R |only man/CSA-class.Rd |only man/CalcAddon.Rd | 4 +++- man/CalcRC.Rd | 6 +++++- man/Commodity-class.Rd | 1 + man/CreditIndex-class.Rd | 1 + man/CreditSingle-class.Rd | 1 + man/ExampleIRDCommMargined.Rd |only man/FXSwap-class.Rd | 1 + man/IRDSwap-class.Rd | 1 + man/IRDSwaption-class.Rd | 1 + 18 files changed, 82 insertions(+), 33 deletions(-)
Title: Work with QIIME Output Files in R
Description: Open QIIME output files in R, compute statistics, and
create plots from the data.
Author: Kyle Bittinger <kylebittinger@gmail.com>
Maintainer: Kyle Bittinger <kylebittinger@gmail.com>
Diff between qiimer versions 0.9.2 dated 2014-01-02 and 0.9.4 dated 2015-12-27
DESCRIPTION | 14 ++++----- MD5 | 60 ++++++++++++++++++++--------------------- NAMESPACE | 5 +++ R/biom.R | 2 - R/otu_table.R | 44 +++++++++++++----------------- R/qiimer.R | 3 ++ man/biom_raw_data.Rd | 36 +++++++++++------------- man/biom_taxonomy.Rd | 44 +++++++++++++----------------- man/dist_get.Rd | 13 ++++---- man/dist_groups.Rd | 20 ++++++------- man/dist_subset.Rd | 13 ++++---- man/make_otu_table.Rd | 14 ++++----- man/otu_heatmap.Rd | 53 +++++++++++++++++------------------- man/qiimer.Rd | 4 ++ man/rarefaction_stats.Rd | 15 ++++------ man/read_blast_table.Rd | 10 ++++-- man/read_qiime_distmat.Rd | 10 ++++-- man/read_qiime_mapping_file.Rd | 19 ++++++------ man/read_qiime_otu_mapping.Rd | 13 ++++---- man/read_qiime_otu_table.Rd | 31 +++++++++++---------- man/read_qiime_rarefaction.Rd | 12 ++++---- man/relmbeta.Rd | 43 +++++++++++++---------------- man/relmbeta_alpha.Rd | 19 ++++++------ man/relmbeta_assignments.Rd | 18 ++++++------ man/relmbeta_biom.Rd | 21 ++++++-------- man/relmbeta_counts.Rd | 21 ++++++-------- man/relmbeta_dist.Rd | 19 ++++++------ man/saturated_rainbow.Rd | 47 +++++++++++++++----------------- man/simplify_assignments.Rd | 20 ++++++------- man/split_assignments.Rd | 24 +++++++--------- man/taxonomic_ranks.Rd | 8 +++-- 31 files changed, 335 insertions(+), 340 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a=1, b=2); for (i in seq_along(x)) x[[i]] <- x[[i]]^2; y <- as.list(x)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.5.0 dated 2015-10-30 and 0.6.0 dated 2015-12-27
DESCRIPTION | 11 MD5 | 50 ++- NAMESPACE | 9 NEWS | 9 R/get_variable.R | 36 ++ R/listenv.R | 485 ++++++++++++++++++++++++++++++------ R/parse_env_subset.R | 257 ++++++++++++++----- R/undim.R |only R/utils.R | 2 build/vignette.rds |binary inst/doc/listenv.html | 463 +++++++++++++++++++++++++++------- inst/doc/listenv.md.rsp | 422 +++++++++++++++++++++++-------- man/as.list.listenv.Rd | 2 man/cash-.listenv.Rd | 2 man/cash-set-.listenv.Rd | 2 man/get_variable.Rd | 2 man/length.listenv.Rd | 2 man/listenv.Rd | 2 man/map.Rd | 40 +- man/names.listenv.Rd | 2 man/parse_env_subset.Rd | 48 +-- man/undim.Rd |only tests/get_variable,dimensions.R |only tests/listenv,dimensions.R |only tests/listenv.R | 70 +++++ tests/parse_env_subset,dimensions.R |only tests/parse_env_subset.R | 76 +++++ tests/undim.R |only vignettes/listenv.md.rsp | 422 +++++++++++++++++++++++-------- 29 files changed, 1878 insertions(+), 536 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.6 dated 2015-11-05 and 3.4 dated 2015-12-27
DESCRIPTION | 14 - MD5 | 99 +++++++------- NAMESPACE | 7 NEWS | 125 ++++++++++++++++- R/ANOVAz1.R | 2 R/BarChart.R | 4 R/Help.R | 296 +++++++++++++++++++++--------------------- R/Histogram.R | 15 +- R/Logit.R | 51 +++---- R/Merge.R | 2 R/Read.R | 158 +++++++++++++--------- R/Regression.R | 51 +------ R/ScatterPlot.R | 49 +++++- R/SummaryStats.R | 100 +++++--------- R/VariableLabels.R |only R/bc.data.frame.R | 5 R/bc.zmain.R | 159 +++++++++------------- R/details.R | 118 ++++++++-------- R/dist.zknitr.R | 24 ++- R/hst.zmain.R | 10 - R/logit.z4Pred.R | 2 R/pc.zmain.R | 40 +++-- R/plt.zmain.R | 134 +++++++++++-------- R/reg.z2Relations.R | 46 +++--- R/reg.z3resfitResidual.R | 3 R/reg.z5Plot.R | 5 R/set.R | 24 +-- R/ss.zdata.frame.R | 14 + R/ss.zfactor.R | 58 ++++++-- R/tt.z1group.R | 2 R/tt.z2group.R | 5 R/tt.zformula.R | 4 R/ttest.R | 330 +++-------------------------------------------- R/ttp2zgraph.R | 3 R/vl.R |only R/zzz.R | 209 ++++++++++++++++++++++++----- data/dataEmployee.rda |binary data/dataMach4.rda |binary man/BarChart.Rd | 5 man/Histogram.Rd | 3 man/Nest.Rd | 5 man/Read.Rd | 19 +- man/Recode.Rd | 2 man/Regression.Rd | 6 man/ScatterPlot.Rd | 19 +- man/Transform.Rd | 11 - man/VariableLabels.Rd |only man/Write.Rd | 4 man/dataEmployee.Rd | 6 man/dataMach4.Rd | 40 ++--- man/label.Rd | 4 man/ttest.Rd | 3 52 files changed, 1179 insertions(+), 1116 deletions(-)
Title: Learning Algorithms for Dynamic Treatment Regimes
Description: Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each stage by time-varying subject-specific features and intermediate outcomes observed in previous stages. This package implements three methods: O-learning (Zhao et. al. 2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu et. al. 2014, 2015) to estimate the optimal DTRs.
Author: Ying Liu, Yuanjia Wang, Donglin Zeng
Maintainer: Ying Liu <yl2802@cumc.columbia.edu>
Diff between DTRlearn versions 1.1 dated 2015-10-28 and 1.2 dated 2015-12-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Calculate and Analyze Blau Status for Measuring Social Distance
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to organizations. Relational (network) data may be incorporated for additional analyses.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <cwang3@nd.edu>
Diff between Blaunet versions 1.0.1 dated 2014-04-14 and 2.0.1 dated 2015-12-27
DESCRIPTION | 16 ++--- MD5 | 38 ++++++++---- NAMESPACE | 2 R/calc.dyadic.R | 110 +++++++++++++++++------------------ R/calc.niches.R | 153 ++++++++++++++++++++++++------------------------- R/ecology.summary.R | 97 ++++++++++++++++--------------- R/niche.summary.R | 94 ++++++++++++++++-------------- data/TwoCities.rda |binary data/gss74_87.rda |only data/schlattr.rda |only data/schlnet.rda |only inst |only man/BSANet.Rd | 5 - man/TwoCities.Rd | 6 - man/blaunet-package.Rd | 24 ++++--- man/gss74_87.Rd |only man/schlattr.Rd |only man/schlnet.Rd |only 18 files changed, 293 insertions(+), 252 deletions(-)
Title: A GUI for Missing Data Exploration
Description: Provides numeric and graphical
summaries for the missing values from both categorical
and quantitative variables. A variety of imputation
methods are applied, including the univariate imputations
like fixed or random values, multivariate imputations
like the nearest neighbors and multiple imputations,
and imputations conditioned on a categorical variable.
Author: Xiaoyue Cheng, Dianne Cook, Heike Hofmann
Maintainer: Xiaoyue Cheng <xycheng@unomaha.edu>
Diff between MissingDataGUI versions 0.2-2 dated 2014-09-14 and 0.2-4 dated 2015-12-27
DESCRIPTION | 17 ++-- MD5 | 43 +++++----- NAMESPACE | 20 ++++- NEWS | 12 +++ R/MissingDataGUI-package.r | 9 +- R/MissingDataGUI.r | 4 - R/WatchMissingValues.r | 166 +++++++++++++++++++++--------------------- R/imputation.r | 82 +++++++++----------- R/utils.r | 48 ++++++------ build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.Rnw | 2 inst/doc/introduction.pdf |binary man/MissingDataGUI-package.Rd | 9 +- man/MissingDataGUI.Rd | 20 ++--- man/WatchMissingValues.Rd | 20 ++--- man/brfss.Rd | 10 +- man/compute_missing_pct.Rd | 6 - man/imputation.Rd | 10 +- man/scale_colour_discrete.Rd | 3 man/scale_fill_discrete.Rd | 3 man/tao.Rd | 8 +- vignettes/introduction.Rnw | 2 23 files changed, 262 insertions(+), 232 deletions(-)
More information about MissingDataGUI at CRAN
Permanent link
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.3.1 dated 2015-12-01 and 0.3.2 dated 2015-12-27
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/auth.R | 6 +++--- R/date-ranges.R | 29 ++++++++++++++++++----------- R/ga.R | 8 +++----- R/mcf.R | 8 +++----- R/realtime.R | 3 ++- R/report.R | 12 +++++++++--- build/vignette.rds |binary data/ga.rda |binary inst/NEWS.Rd | 9 +++++++++ man/authorize.Rd | 4 ++-- man/get_ga.Rd | 10 +++++----- man/get_mcf.Rd | 2 +- man/get_profile.Rd | 3 ++- man/get_realtime.Rd | 6 +++--- man/list_profiles.Rd | 3 ++- 17 files changed, 82 insertions(+), 61 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currently it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.48 dated 2015-10-22 and 0.49 dated 2015-12-27
ChangeLog | 15 +++++++++++---- DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 5 ----- R/composeURL.R | 18 +++++++++--------- R/misc.R | 41 ++++++++++++++++++++++++++++++----------- R/pointMeteoGalicia.R | 2 +- man/getPoint.Rd | 23 +++++++++++++++-------- man/getRaster.Rd | 22 +++++++++++++--------- man/vars.Rd | 10 +++++----- 10 files changed, 99 insertions(+), 67 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.3.0 dated 2015-10-23 and 1.7.4 dated 2015-12-26
lcmm-1.7.3.0/lcmm/data/data_Jointlcmm.rda |only lcmm-1.7.3.0/lcmm/man/data_Jointlcmm.Rd |only lcmm-1.7.4/lcmm/DESCRIPTION | 9 lcmm-1.7.4/lcmm/MD5 | 102 +++---- lcmm-1.7.4/lcmm/NAMESPACE | 28 + lcmm-1.7.4/lcmm/NEWS | 11 lcmm-1.7.4/lcmm/R/Contlcmm.R | 193 ++++++++++--- lcmm-1.7.4/lcmm/R/Jointlcmm.R | 436 +++++++++++++++++++++++------- lcmm-1.7.4/lcmm/R/Ordlcmm.R | 189 ++++++++++--- lcmm-1.7.4/lcmm/R/cuminc.R | 4 lcmm-1.7.4/lcmm/R/dynpred.R | 13 lcmm-1.7.4/lcmm/R/epoce.R | 34 +- lcmm-1.7.4/lcmm/R/fitY.Jointlcmm.R | 3 lcmm-1.7.4/lcmm/R/fitY.lcmm.R | 3 lcmm-1.7.4/lcmm/R/fitY.multlcmm.R | 3 lcmm-1.7.4/lcmm/R/gridsearch.R |only lcmm-1.7.4/lcmm/R/hlme.R | 215 +++++++++++--- lcmm-1.7.4/lcmm/R/lcmm.R | 13 lcmm-1.7.4/lcmm/R/multlcmm.R | 219 ++++++++++++--- lcmm-1.7.4/lcmm/R/plot.cuminc.R | 4 lcmm-1.7.4/lcmm/R/plot.dynpred.R | 38 +- lcmm-1.7.4/lcmm/R/plotfit.R | 4 lcmm-1.7.4/lcmm/R/postprob.Jointlcmm.R | 2 lcmm-1.7.4/lcmm/R/postprob.hlme.R | 2 lcmm-1.7.4/lcmm/R/postprob.lcmm.R | 2 lcmm-1.7.4/lcmm/R/postprob.multlcmm.R | 2 lcmm-1.7.4/lcmm/R/standardMethods.R |only lcmm-1.7.4/lcmm/R/summary.Jointlcmm.R | 25 + lcmm-1.7.4/lcmm/R/summary.hlme.R | 25 + lcmm-1.7.4/lcmm/R/summary.lcmm.R | 19 + lcmm-1.7.4/lcmm/R/summary.multlcmm.R | 26 + lcmm-1.7.4/lcmm/data/data_lcmm.rda |only lcmm-1.7.4/lcmm/man/Diffepoce.Rd | 161 +++++------ lcmm-1.7.4/lcmm/man/Jointlcmm.Rd | 20 - lcmm-1.7.4/lcmm/man/VarCov.Rd | 7 lcmm-1.7.4/lcmm/man/VarExpl.Rd | 5 lcmm-1.7.4/lcmm/man/data_hlme.Rd | 2 lcmm-1.7.4/lcmm/man/data_lcmm.Rd |only lcmm-1.7.4/lcmm/man/dynpred.Rd | 126 ++++---- lcmm-1.7.4/lcmm/man/epoce.Rd | 165 +++++------ lcmm-1.7.4/lcmm/man/estimates.Rd | 80 ++--- lcmm-1.7.4/lcmm/man/gridsearch.Rd |only lcmm-1.7.4/lcmm/man/hlme.Rd | 74 +++-- lcmm-1.7.4/lcmm/man/lcmm-package.Rd | 4 lcmm-1.7.4/lcmm/man/lcmm.Rd | 32 -- lcmm-1.7.4/lcmm/man/multlcmm.Rd | 15 - lcmm-1.7.4/lcmm/man/paquid.Rd | 3 lcmm-1.7.4/lcmm/man/plot.dynpred.Rd | 5 lcmm-1.7.4/lcmm/man/plot.lcmm.Rd | 13 lcmm-1.7.4/lcmm/man/plot.pred.accuracy.Rd | 3 lcmm-1.7.4/lcmm/man/plot.predict.Rd | 6 lcmm-1.7.4/lcmm/man/postprob.Rd | 1 lcmm-1.7.4/lcmm/man/predictL.Rd | 3 lcmm-1.7.4/lcmm/man/predictY.Rd | 219 +++++++-------- lcmm-1.7.4/lcmm/man/predictlink.Rd | 5 lcmm-1.7.4/lcmm/man/standardMethods.Rd |only 56 files changed, 1687 insertions(+), 886 deletions(-)
More information about TransferEntropy at CRAN
Permanent link
Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut],
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between spacetime versions 1.1-4 dated 2015-04-24 and 1.1-5 dated 2015-12-26
spacetime-1.1-4/spacetime/data/datalist |only spacetime-1.1-5/spacetime/DESCRIPTION | 15 spacetime-1.1-5/spacetime/MD5 | 77 - spacetime-1.1-5/spacetime/NAMESPACE | 8 spacetime-1.1-5/spacetime/R/ST-methods.R | 6 spacetime-1.1-5/spacetime/R/STFDF-methods.R | 11 spacetime-1.1-5/spacetime/R/STIDF-methods.R | 17 spacetime-1.1-5/spacetime/R/coerce.R | 6 spacetime-1.1-5/spacetime/R/eof.R | 25 spacetime-1.1-5/spacetime/R/raster.R | 31 spacetime-1.1-5/spacetime/R/stplot.R | 8 spacetime-1.1-5/spacetime/R/tgrass.R | 7 spacetime-1.1-5/spacetime/TODO | 4 spacetime-1.1-5/spacetime/build/vignette.rds |binary spacetime-1.1-5/spacetime/data/air.rda |binary spacetime-1.1-5/spacetime/data/fires.rda |binary spacetime-1.1-5/spacetime/inst/doc/jss816.Rnw | 2 spacetime-1.1-5/spacetime/inst/doc/jss816.pdf |binary spacetime-1.1-5/spacetime/inst/doc/stgvis.R | 1 spacetime-1.1-5/spacetime/inst/doc/stgvis.Rmd | 5 spacetime-1.1-5/spacetime/inst/doc/stgvis.html | 995 +++++++++--------- spacetime-1.1-5/spacetime/inst/doc/sto.R | 29 spacetime-1.1-5/spacetime/inst/doc/sto.Rnw | 1 spacetime-1.1-5/spacetime/inst/doc/sto.pdf |binary spacetime-1.1-5/spacetime/inst/doc/stpg.R | 25 spacetime-1.1-5/spacetime/inst/doc/stpg.Rnw | 1 spacetime-1.1-5/spacetime/inst/doc/stpg.pdf |binary spacetime-1.1-5/spacetime/inst/doc/stsubs.pdf |binary spacetime-1.1-5/spacetime/man/air.Rd | 3 spacetime-1.1-5/spacetime/man/na.Rd | 1 spacetime-1.1-5/spacetime/tests/basic.Rout.save | 188 +-- spacetime-1.1-5/spacetime/tests/rw.Rout.save | 9 spacetime-1.1-5/spacetime/tests/stconstruct.Rout.save | 12 spacetime-1.1-5/spacetime/tests/subsetting.R | 15 spacetime-1.1-5/spacetime/tests/subsetting.Rout.save | 381 +++--- spacetime-1.1-5/spacetime/tests/wind.Rout.save | 25 spacetime-1.1-5/spacetime/vignettes/jss816.Rnw | 2 spacetime-1.1-5/spacetime/vignettes/stgvis.Rmd | 5 spacetime-1.1-5/spacetime/vignettes/sto.Rnw | 1 spacetime-1.1-5/spacetime/vignettes/stpg.Rnw | 1 40 files changed, 993 insertions(+), 924 deletions(-)
Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <http://landsat.gsfc.nasa.gov/?p=9513>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal pattern including year(s) of inflection, magnitude of change, pre- and post-inflection rates of growth or recovery. In addition, it contains routines for converting a flat map of disturbance agents to time-series disturbance maps and a graphical routine displaying the fitted trajectory of Landsat imagery.
Author: Mary C. Meyer, Xiyue Liao, Elizabeth Freeman, Gretchen G. Moisen
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeSelectForest versions 1.1 dated 2015-09-06 and 1.2 dated 2015-12-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/shape.R | 4 ++-- man/ShapeSelectForest-package.Rd | 4 ++-- man/plotshape.Rd | 6 ++++-- 6 files changed, 18 insertions(+), 16 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: Basic Tools for the Analysis of Disease Outbreaks
Description: Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between OutbreakTools versions 0.1-13 dated 2015-03-23 and 0.1-14 dated 2015-12-25
DESCRIPTION | 10 ++-- MD5 | 28 +++++------ NAMESPACE | 2 R/annotatedTreeReader.R | 107 +++++++++++++++++++++++++++++++++----------- data/FluH1N1pdm2009.RData |binary data/HorseFlu.RData |binary data/HorseFluRaw.RData |binary data/ToyOutbreak.RData |binary data/ToyOutbreakRaw.RData |binary inst/doc/OutbreakTools.Rnw | 3 - inst/doc/OutbreakTools.pdf |binary man/ToyOutbreak.Rd | 2 man/ToyOutbreakRaw.Rd | 2 man/plotggphy.Rd | 4 - vignettes/OutbreakTools.Rnw | 3 - 15 files changed, 110 insertions(+), 51 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided.
Author: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Diff between Matching versions 4.8-3.4 dated 2013-10-29 and 4.9-2 dated 2015-12-25
ChangeLog | 14 +++++ DESCRIPTION | 8 +-- MD5 | 28 +++++------ NAMESPACE | 4 + R/GenMatching.R | 6 +- R/Matching.R | 33 ++++++++----- data/lalonde.rda |binary inst/CITATION | 8 ++- man/GenMatch.Rd | 127 ++++++++++++++++++++++++++-------------------------- man/Match.Rd | 10 ++-- man/MatchBalance.Rd | 7 +- man/Matchby.Rd | 10 ++-- man/balanceUV.Rd | 7 +- man/ks.boot.Rd | 5 +- man/lalonde.Rd | 3 - 15 files changed, 151 insertions(+), 119 deletions(-)
Title: Functions for Extreme Value Distributions
Description: Extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme
value distributions, and provides fitting functions which
calculate maximum likelihood estimates for univariate and
bivariate maxima models, and for univariate and bivariate
threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between evd versions 2.3-0 dated 2012-08-30 and 2.3-2 dated 2015-12-25
DESCRIPTION | 13 +++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 11 ++++++++++- R/profile.R | 11 ++--------- R/uvfit.R | 4 ++-- build |only inst/CHANGES | 27 ++++++++++++++++++++++----- inst/doc/Multivariate_Extremes.R |only inst/doc/Multivariate_Extremes.Rnw | 10 +++++----- inst/doc/Multivariate_Extremes.pdf |binary vignettes/Multivariate_Extremes.Rnw | 10 +++++----- 11 files changed, 63 insertions(+), 41 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.0.0 dated 2015-12-07 and 2.0.5 dated 2015-12-24
randomForestSRC-2.0.0/randomForestSRC/man/impute.Rd |only randomForestSRC-2.0.5/randomForestSRC/DESCRIPTION | 8 randomForestSRC-2.0.5/randomForestSRC/MD5 | 62 - randomForestSRC-2.0.5/randomForestSRC/NAMESPACE | 1 randomForestSRC-2.0.5/randomForestSRC/R/data.utilities.R | 80 + randomForestSRC-2.0.5/randomForestSRC/R/factor.utilities.R | 8 randomForestSRC-2.0.5/randomForestSRC/R/find.interaction.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/generic.impute.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/generic.predict.rfsrc.R | 130 +-- randomForestSRC-2.0.5/randomForestSRC/R/impute.rfsrc.R | 5 randomForestSRC-2.0.5/randomForestSRC/R/max.subtree.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.competing.risk.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.survival.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/plot.variable.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/predict.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/print.rfsrc.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rf2rfz.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rfsrc.R | 121 +- randomForestSRC-2.0.5/randomForestSRC/R/rfsrc.news.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/rfsrcSyn.R | 16 randomForestSRC-2.0.5/randomForestSRC/R/stat.split.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/utilities.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/var.select.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/vimp.R | 2 randomForestSRC-2.0.5/randomForestSRC/R/zzz.R | 2 randomForestSRC-2.0.5/randomForestSRC/configure.ac | 2 randomForestSRC-2.0.5/randomForestSRC/inst/NEWS | 13 randomForestSRC-2.0.5/randomForestSRC/inst/doc/rsf-Rnews.pdf |binary randomForestSRC-2.0.5/randomForestSRC/man/impute.rfsrc.Rd |only randomForestSRC-2.0.5/randomForestSRC/man/rfsrc.Rd | 40 randomForestSRC-2.0.5/randomForestSRC/src/randomForestSRC.c | 426 ++++------ randomForestSRC-2.0.5/randomForestSRC/src/randomForestSRC.h | 2 33 files changed, 496 insertions(+), 450 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between plotKML versions 0.5-3 dated 2015-07-09 and 0.5-4 dated 2015-12-24
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/AAAA.R | 3 ++- R/layer.Raster.R | 3 ++- R/layer.RasterBrick.R | 3 ++- R/layer.SpatialPixels.R | 3 ++- R/legend.whitening.R | 4 ++-- R/plotKML.GDALobj.R | 3 ++- build/vignette.rds |binary inst/doc/jss1079.pdf |binary man/eberg.Rd | 2 +- man/layer.Raster.Rd | 7 ++++--- man/layer.RasterBrick.Rd | 3 ++- man/layer.SpatialPixels.Rd | 7 ++++--- man/legend.whitening.Rd | 3 ++- 15 files changed, 43 insertions(+), 34 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.4 dated 2015-08-11 and 0.5 dated 2015-12-24
dynRB-0.4/dynRB/R/funclist1.R |only dynRB-0.4/dynRB/R/funclist2.R |only dynRB-0.4/dynRB/R/funclist3.R |only dynRB-0.4/dynRB/man/funclist1.Rd |only dynRB-0.4/dynRB/man/funclist2.Rd |only dynRB-0.4/dynRB/man/funclist3.Rd |only dynRB-0.5/dynRB/DESCRIPTION | 7 ++++--- dynRB-0.5/dynRB/MD5 | 30 ++++++++++++++++-------------- dynRB-0.5/dynRB/NAMESPACE | 3 ++- dynRB-0.5/dynRB/R/dynRB-internal.R |only dynRB-0.5/dynRB/R/dynRB_Pn.R | 29 ++++++++++++----------------- dynRB-0.5/dynRB/R/dynRB_VPa.R | 13 ++++--------- dynRB-0.5/dynRB/R/dynRB_Vn.R | 9 ++------- dynRB-0.5/dynRB/R/overview.R | 8 ++------ dynRB-0.5/dynRB/inst |only dynRB-0.5/dynRB/man/dynRB-package.Rd | 4 ++-- dynRB-0.5/dynRB/man/overview.Rd | 2 +- dynRB-0.5/dynRB/tests |only 18 files changed, 45 insertions(+), 60 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between DataCombine versions 0.2.9 dated 2015-02-11 and 0.2.18 dated 2015-12-24
DESCRIPTION | 13 - MD5 | 64 +++--- NAMESPACE | 11 + NEWS | 42 ++++ R/DropNA.R | 80 ++++---- R/FillIn.R | 8 R/PercChange.R | 95 ++++++++- R/internals.R | 1 R/slide.R | 507 ++++++++++++++++++++++++++--------------------------- R/utils.R | 107 +++++++---- README.md | 14 - man/CountSpell.Rd | 8 man/DropNA.Rd | 3 man/FillDown.Rd | 6 man/FillIn.Rd | 3 man/FindDups.Rd |only man/FindReplace.Rd | 3 man/InsertRow.Rd | 3 man/MoveFront.Rd | 3 man/NaVar.Rd | 3 man/PercChange.Rd | 6 man/SpreadDummy.Rd | 3 man/StartEnd.Rd | 9 man/TimeExpand.Rd | 9 man/TimeFill.Rd | 3 man/VarDrop.Rd | 3 man/change.Rd |only man/dMerge.Rd | 2 man/grepl.sub.Rd | 8 man/rmExcept.Rd | 3 man/shift.Rd | 2 man/shiftMA.Rd | 2 man/slide.Rd | 13 - man/slideMA.Rd | 11 - 34 files changed, 617 insertions(+), 431 deletions(-)
Title: Affinity Propagation Clustering
Description: The 'apcluster' package implements Frey's and Dueck's
Affinity Propagation clustering in R. The algorithms are
largely analogous to the 'Matlab' code published by Frey and
Dueck. The package further provides leveraged affinity
propagation and an algorithm for exemplar-based agglomerative
clustering that can also be used to join clusters obtained
from affinity propagation. Various plotting functions are
available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between apcluster versions 1.4.1 dated 2014-12-09 and 1.4.2 dated 2015-12-24
apcluster-1.4.1/apcluster/data |only apcluster-1.4.2/apcluster/DESCRIPTION | 17 apcluster-1.4.2/apcluster/MD5 | 30 - apcluster-1.4.2/apcluster/NAMESPACE | 9 apcluster-1.4.2/apcluster/NEWS | 10 apcluster-1.4.2/apcluster/R/apcluster-methods.R | 20 apcluster-1.4.2/apcluster/R/apclusterL-methods.R | 19 apcluster-1.4.2/apcluster/R/coerce-methods.R | 2 apcluster-1.4.2/apcluster/R/heatmap-methods.R | 2 apcluster-1.4.2/apcluster/build/vignette.rds |binary apcluster-1.4.2/apcluster/inst/doc/apcluster.R | 471 ++++----------------- apcluster-1.4.2/apcluster/inst/doc/apcluster.Rnw | 173 ++++--- apcluster-1.4.2/apcluster/inst/doc/apcluster.pdf |binary apcluster-1.4.2/apcluster/inst/examples |only apcluster-1.4.2/apcluster/man/ch22Promoters.Rd | 27 - apcluster-1.4.2/apcluster/src/apclusterSparseC.cpp | 2 apcluster-1.4.2/apcluster/vignettes/apcluster.Rnw | 173 ++++--- 17 files changed, 395 insertions(+), 560 deletions(-)
Title: Exact Goodness-of-Fit Test for Multinomial Data with Fixed
Probabilities
Description: Tests whether a set of counts fit a given expected ratio. For
example, a genetic cross might be expected to produce four types in the
relative frequencies of 9:3:3:1. To see whether a set of observed counts
fits this expectation, one can examine all possible outcomes with xmulti() or a
random sample of them with xmonte() and find the probability of an observation
deviating from the expectation by at least as much as the observed. As a
measure of deviation from the expected, one can use the log-likelihood
ratio, the multinomial probability, or the classic chi-square statistic. A
histogram of the test statistic can also be plotted and compared with the
asymptotic curve.
Author: Bill Engels <wrengels@wisc.edu>
Maintainer: Bill Engels <wrengels@wisc.edu>
Diff between XNomial versions 1.0.1 dated 2014-02-08 and 1.0.4 dated 2015-12-24
DESCRIPTION | 16 - MD5 | 23 +- NAMESPACE | 9 R/xmonte.R | 5 R/xmulti.R | 15 + build/vignette.rds |binary inst/doc/XNomial.R | 16 - inst/doc/XNomial.Rmd | 32 +-- inst/doc/XNomial.html | 516 ++++++++++++++++---------------------------------- man/xmonte.Rd | 99 +++------ man/xmulti.Rd | 97 +++------ vignettes/XNomial.Rmd | 32 +-- vignettes/XNomial.md |only 13 files changed, 316 insertions(+), 544 deletions(-)
Title: Fisheries Stock Assessment Simulation Testing with Stock
Synthesis
Description: The ss3sim package develops a framework for fisheries stock
assessment simulation testing with Stock Synthesis 3 (SS3).
Author: Sean Anderson [aut, cre],
Cole Monnahan [aut],
Kelli Johnson [aut],
Kotaro Ono [aut],
Juan Valero [aut],
Curry Cunningham [aut],
Allan Hicks [aut],
Felipe Hurtado-Ferro [aut],
Peter Kuriyama [aut],
Roberto Licandeo [aut],
Carey McGilliard [aut],
Melissa Muradian [ctb],
Merrill Rudd [aut],
Christine Stawitz [aut],
Cody Szuwalski [aut],
Ian Taylor [aut],
Katyana Vert-pre [aut],
Athol Whitten [aut]
Maintainer: Sean Anderson <sean@seananderson.ca>
Diff between ss3sim versions 0.8.2 dated 2014-03-09 and 0.9.0 dated 2015-12-24
ss3sim-0.8.2/ss3sim/R/change_agecomp.r |only ss3sim-0.8.2/ss3sim/R/change_index.r |only ss3sim-0.8.2/ss3sim/R/change_lcomp.r |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.R |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.Rnw |only ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.pdf |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/R0-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/R1-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/lcomp100-cod.txt |only ss3sim-0.8.2/ss3sim/inst/extdata/models/fla-em |only ss3sim-0.8.2/ss3sim/inst/extdata/models/fla-om |only ss3sim-0.8.2/ss3sim/inst/extdata/models/sar-em |only ss3sim-0.8.2/ss3sim/inst/extdata/models/sar-om |only ss3sim-0.8.2/ss3sim/inst/ss3-tests |only ss3sim-0.8.2/ss3sim/inst/tests |only ss3sim-0.8.2/ss3sim/man/figures |only ss3sim-0.8.2/ss3sim/man/is_f.Rd |only ss3sim-0.8.2/ss3sim/vignettes/README.md |only ss3sim-0.8.2/ss3sim/vignettes/file-structure.pdf |only ss3sim-0.8.2/ss3sim/vignettes/github.css |only ss3sim-0.8.2/ss3sim/vignettes/knit |only ss3sim-0.8.2/ss3sim/vignettes/solarized-light.css |only ss3sim-0.8.2/ss3sim/vignettes/ss3sim-vignette.Rnw |only ss3sim-0.9.0/ss3sim/DESCRIPTION | 31 ss3sim-0.9.0/ss3sim/LICENSE | 9 ss3sim-0.9.0/ss3sim/MD5 | 304 +- ss3sim-0.9.0/ss3sim/NAMESPACE | 70 ss3sim-0.9.0/ss3sim/R/add_nulls.R |only ss3sim-0.9.0/ss3sim/R/bias_ss3.r | 38 ss3sim-0.9.0/ss3sim/R/calculate_re.R |only ss3sim-0.9.0/ss3sim/R/case-parsing.r | 98 ss3sim-0.9.0/ss3sim/R/case-write.R |only ss3sim-0.9.0/ss3sim/R/change_data.r |only ss3sim-0.9.0/ss3sim/R/change_e.r | 235 +- ss3sim-0.9.0/ss3sim/R/change_em_binning.r |only ss3sim-0.9.0/ss3sim/R/change_f.r | 45 ss3sim-0.9.0/ss3sim/R/change_fltname.r |only ss3sim-0.9.0/ss3sim/R/change_lcomp_constant.R |only ss3sim-0.9.0/ss3sim/R/change_maturity.R |only ss3sim-0.9.0/ss3sim/R/change_rec_devs.r | 31 ss3sim-0.9.0/ss3sim/R/change_retro.r | 16 ss3sim-0.9.0/ss3sim/R/change_tail_compression.R |only ss3sim-0.9.0/ss3sim/R/change_tv.r | 64 ss3sim-0.9.0/ss3sim/R/change_year.R |only ss3sim-0.9.0/ss3sim/R/clean_data.r |only ss3sim-0.9.0/ss3sim/R/copy_ss3models.r | 57 ss3sim-0.9.0/ss3sim/R/create_argfiles.r | 20 ss3sim-0.9.0/ss3sim/R/expand_scenarios.r | 4 ss3sim-0.9.0/ss3sim/R/extract_expected_data.r | 17 ss3sim-0.9.0/ss3sim/R/fill_across.r |only ss3sim-0.9.0/ss3sim/R/get-results.r | 560 +++- ss3sim-0.9.0/ss3sim/R/get_bin.R |only ss3sim-0.9.0/ss3sim/R/get_bin_info.r |only ss3sim-0.9.0/ss3sim/R/growth_estimation.R |only ss3sim-0.9.0/ss3sim/R/make_dummy_data.r |only ss3sim-0.9.0/ss3sim/R/plot_functions.R |only ss3sim-0.9.0/ss3sim/R/profile_fmsy.r |only ss3sim-0.9.0/ss3sim/R/run_bias_ss3.r | 14 ss3sim-0.9.0/ss3sim/R/run_ss3model.r | 69 ss3sim-0.9.0/ss3sim/R/run_ss3sim.r | 183 + ss3sim-0.9.0/ss3sim/R/sample_agecomp.R |only ss3sim-0.9.0/ss3sim/R/sample_calcomp.R |only ss3sim-0.9.0/ss3sim/R/sample_index.r |only ss3sim-0.9.0/ss3sim/R/sample_lcomp.R |only ss3sim-0.9.0/ss3sim/R/sample_mlacomp.R |only ss3sim-0.9.0/ss3sim/R/sample_wtatage.R |only ss3sim-0.9.0/ss3sim/R/setup_parallel.r | 17 ss3sim-0.9.0/ss3sim/R/ss3sim.r | 28 ss3sim-0.9.0/ss3sim/R/ss3sim_base.r | 484 ++-- ss3sim-0.9.0/ss3sim/R/standardize_bounds.R |only ss3sim-0.9.0/ss3sim/R/verify_input.r | 1 ss3sim-0.9.0/ss3sim/README.md | 87 ss3sim-0.9.0/ss3sim/build/vignette.rds |binary ss3sim-0.9.0/ss3sim/data/scalar_dat.rda |binary ss3sim-0.9.0/ss3sim/data/ts_dat.rda |binary ss3sim-0.9.0/ss3sim/inst/CITATION | 27 ss3sim-0.9.0/ss3sim/inst/doc/introduction.R |only ss3sim-0.9.0/ss3sim/inst/doc/introduction.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/introduction.html |only ss3sim-0.9.0/ss3sim/inst/doc/making-functions.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/making-functions.html |only ss3sim-0.9.0/ss3sim/inst/doc/making-models.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/making-models.html |only ss3sim-0.9.0/ss3sim/inst/doc/modifying-models.Rmd |only ss3sim-0.9.0/ss3sim/inst/doc/modifying-models.html |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/agecomp0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/agecomp2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/data0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/index0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/index2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-cod.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-fla.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp1-sar.txt | 1 ss3sim-0.9.0/ss3sim/inst/extdata/cases/lcomp2-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/F0-cod.txt | 11 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp0-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp1-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/agecomp100-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index0-cod.txt | 4 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index1-cod.txt | 2 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/index100-cod.txt | 2 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/lcomp0-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/lcomp1-cod.txt | 9 ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/retro0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/retro1-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/tail_compression0-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/eg-cases/tail_compression1-cod.txt |only ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/codEM.ctl | 176 - ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/forecast.ss | 92 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-em/starter.ss | 21 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/codOM.ctl | 406 ++- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/codOM.dat | 1163 +++++----- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/forecast.ss | 92 ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/ss3.par | 248 +- ss3sim-0.9.0/ss3sim/inst/extdata/models/cod-om/starter.ss | 21 ss3sim-0.9.0/ss3sim/inst/extdata/output |only ss3sim-0.9.0/ss3sim/man/add_nulls.Rd |only ss3sim-0.9.0/ss3sim/man/bias_ss3.Rd | 50 ss3sim-0.9.0/ss3sim/man/calculate_data_units.Rd |only ss3sim-0.9.0/ss3sim/man/calculate_re.Rd |only ss3sim-0.9.0/ss3sim/man/calculate_runtime.Rd | 22 ss3sim-0.9.0/ss3sim/man/case_comp.Rd |only ss3sim-0.9.0/ss3sim/man/case_deparse.Rd |only ss3sim-0.9.0/ss3sim/man/case_fishing.Rd |only ss3sim-0.9.0/ss3sim/man/case_index.Rd |only ss3sim-0.9.0/ss3sim/man/case_tv.Rd |only ss3sim-0.9.0/ss3sim/man/change_agecomp.Rd | 127 - ss3sim-0.9.0/ss3sim/man/change_data.Rd |only ss3sim-0.9.0/ss3sim/man/change_e.Rd | 196 - ss3sim-0.9.0/ss3sim/man/change_em_binning.Rd |only ss3sim-0.9.0/ss3sim/man/change_f.Rd | 59 ss3sim-0.9.0/ss3sim/man/change_fltname.Rd |only ss3sim-0.9.0/ss3sim/man/change_index.Rd | 87 ss3sim-0.9.0/ss3sim/man/change_lcomp.Rd | 126 - ss3sim-0.9.0/ss3sim/man/change_lcomp_constant.Rd |only ss3sim-0.9.0/ss3sim/man/change_maturity.Rd |only ss3sim-0.9.0/ss3sim/man/change_rec_devs.Rd | 28 ss3sim-0.9.0/ss3sim/man/change_retro.Rd | 45 ss3sim-0.9.0/ss3sim/man/change_tail_compression.Rd |only ss3sim-0.9.0/ss3sim/man/change_tv.Rd | 154 - ss3sim-0.9.0/ss3sim/man/change_year.Rd |only ss3sim-0.9.0/ss3sim/man/check_data.Rd |only ss3sim-0.9.0/ss3sim/man/clean_data.Rd |only ss3sim-0.9.0/ss3sim/man/cleanup_ss3.Rd | 13 ss3sim-0.9.0/ss3sim/man/copy_ss3models.Rd | 51 ss3sim-0.9.0/ss3sim/man/create_argfiles.Rd | 77 ss3sim-0.9.0/ss3sim/man/expand_scenarios.Rd | 14 ss3sim-0.9.0/ss3sim/man/extract_expected_data.Rd | 14 ss3sim-0.9.0/ss3sim/man/facet_form.Rd |only ss3sim-0.9.0/ss3sim/man/fill_across.Rd |only ss3sim-0.9.0/ss3sim/man/get_args.Rd | 8 ss3sim-0.9.0/ss3sim/man/get_bin.Rd |only ss3sim-0.9.0/ss3sim/man/get_bin_info.Rd |only ss3sim-0.9.0/ss3sim/man/get_caseargs.Rd | 133 - ss3sim-0.9.0/ss3sim/man/get_caseval.Rd | 12 ss3sim-0.9.0/ss3sim/man/get_fish600_casefolder.Rd | 7 ss3sim-0.9.0/ss3sim/man/get_model_folder.Rd | 21 ss3sim-0.9.0/ss3sim/man/get_nll_components.Rd |only ss3sim-0.9.0/ss3sim/man/get_recdevs.Rd | 18 ss3sim-0.9.0/ss3sim/man/get_results_all.Rd | 115 ss3sim-0.9.0/ss3sim/man/get_results_derived.Rd |only ss3sim-0.9.0/ss3sim/man/get_results_scalar.Rd | 20 ss3sim-0.9.0/ss3sim/man/get_results_scenario.Rd | 48 ss3sim-0.9.0/ss3sim/man/get_results_timeseries.Rd | 18 ss3sim-0.9.0/ss3sim/man/get_sigmar.Rd | 11 ss3sim-0.9.0/ss3sim/man/id_scenarios.Rd |only ss3sim-0.9.0/ss3sim/man/pastef.Rd | 4 ss3sim-0.9.0/ss3sim/man/plot_scalar_boxplot.Rd |only ss3sim-0.9.0/ss3sim/man/plot_scalar_points.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_boxplot.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_lines.Rd |only ss3sim-0.9.0/ss3sim/man/plot_ts_points.Rd |only ss3sim-0.9.0/ss3sim/man/profile_fmsy.Rd |only ss3sim-0.9.0/ss3sim/man/rename_ss3_files.Rd |only ss3sim-0.9.0/ss3sim/man/run_bias_ss3.Rd | 76 ss3sim-0.9.0/ss3sim/man/run_ss3model.Rd | 101 ss3sim-0.9.0/ss3sim/man/run_ss3sim.Rd | 218 - 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Title: Automated Schema on Read
Description: Provides schema-on-read tools including a single function call (e.g., schemaOnRead('filename')) that reads text ('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF', and 'JPG'), R data ('RDS'), HDF5 ('H5'), NetCDF ('CS'), spreadsheet ('XLS', 'XLSX', 'ODS', and 'DIF'), Weka Attribute-Relation File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata ('DTA') files. It also recursively reads folders (e.g., schemaOnRead('folder')), returning a nested list of the contained elements.
Author: Michael North [aut, cre]
Maintainer: Michael North <north@anl.gov>
Diff between SchemaOnRead versions 1.0.1 dated 2015-11-03 and 1.0.2 dated 2015-12-24
SchemaOnRead-1.0.1/SchemaOnRead/man/schemaOnReadDefaultProcessors.Rd |only SchemaOnRead-1.0.1/SchemaOnRead/man/schemaOnReadSimpleProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/DESCRIPTION | 16 SchemaOnRead-1.0.2/SchemaOnRead/MD5 | 93 - SchemaOnRead-1.0.2/SchemaOnRead/NAMESPACE | 77 - SchemaOnRead-1.0.2/SchemaOnRead/NEWS.md | 17 SchemaOnRead-1.0.2/SchemaOnRead/R/CheckExtensions.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/DefaultProcessors.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessARFFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessBitmapFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessCSVFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDBFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDIFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDefaultFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessDirectory.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessEPIINFOFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessGIFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessHTMLFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessNetCDFandHDF5.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessODSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessPajekFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessRDSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSASFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSPSSFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessStataFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessSystatFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessTIFFFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessTextFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessXLSandXLSXFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/ProcessXMLFile.R |only SchemaOnRead-1.0.2/SchemaOnRead/R/SchemaOnRead.R | 700 ---------- SchemaOnRead-1.0.2/SchemaOnRead/R/SimpleProcessors.R |only SchemaOnRead-1.0.2/SchemaOnRead/README.md | 4 SchemaOnRead-1.0.2/SchemaOnRead/inst/Data.xyz |only SchemaOnRead-1.0.2/SchemaOnRead/inst/doc/vignettes.Rmd | 101 - SchemaOnRead-1.0.2/SchemaOnRead/inst/doc/vignettes.html | 248 --- SchemaOnRead-1.0.2/SchemaOnRead/inst/extdata/dir1/Data2.xls |binary SchemaOnRead-1.0.2/SchemaOnRead/man/checkExtensions.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/man/defaultProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/man/schemaOnRead.Rd | 8 SchemaOnRead-1.0.2/SchemaOnRead/man/simpleProcessors.Rd |only SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat.R | 6 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.01.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.02.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.03.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.04.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.05.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.06.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.07.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.08.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.09.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.10.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.11.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.12.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.13.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.14.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.15.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.16.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.17.R | 11 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.18.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.19.R | 9 SchemaOnRead-1.0.2/SchemaOnRead/tests/testthat/test.20.R | 39 SchemaOnRead-1.0.2/SchemaOnRead/vignettes/vignettes.Rmd | 101 - 63 files changed, 361 insertions(+), 1238 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It is best suited to data from a Freesurfer analysis (cortical
thickness, volumes, local gyrification index, surface area), but also works
with e.g., tractography data from FSL. It contains a graphical user
interface for graph visualization and data exploration.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 0.48.0 dated 2015-12-09 and 0.55.0 dated 2015-12-24
DESCRIPTION | 13 +- MD5 | 161 +++++++++++++++++++------------------ NAMESPACE | 10 +- R/assign_lobes.R | 17 ++- R/boot_global.R | 68 +++++++-------- R/brainGraph_init.R | 44 +++++++++- R/centr_lev.R | 3 R/check_resid.R | 2 R/choose_edges.R | 8 - R/corr_matrix.R | 12 +- R/count_homologous.R | 7 + R/count_interlobar.R | 19 ++-- R/dti_create_mats.R | 9 +- R/edge_asymmetry.R | 39 +++++--- R/get_resid.R | 88 ++++++++++++++------ R/graph_contract_brain.R | 5 - R/graph_efficiency.R | 39 ++++++-- R/individ_contrib.R |only R/part_coeff.R | 22 +++-- R/permute_group.R | 21 ++-- R/plot_boot.R |only R/plot_corr_mat.R | 4 R/plot_perm_diffs.R | 4 R/plot_rich_norm.R |only R/rich_club_coeff.R | 3 R/rich_club_norm.R | 3 R/rich_core.R | 6 + R/robustness.R | 8 - R/set_brainGraph_attributes.R | 5 - R/sim_rand_graph_par.R | 6 - R/small_world.R | 9 -- R/spatial_dist.R | 8 + R/vertex_attr_dt.R | 33 ++----- R/vulnerability.R | 3 R/within_module_degree_z_score.R | 3 man/aop.Rd |only man/assign_lobes.Rd | 9 +- man/boot_global.Rd | 23 ++--- man/brainGraph_init.Rd | 3 man/centr_lev.Rd | 2 man/check.resid.Rd | 4 man/choose.edges.Rd | 2 man/color.edges.Rd | 2 man/color.vertices.Rd | 2 man/corr.matrix.Rd | 2 man/count_homologous.Rd | 2 man/count_interlobar.Rd | 9 -- man/dti_create_mats.Rd | 9 +- man/edge_asymmetry.Rd | 2 man/get.resid.Rd | 31 ++++--- man/graph.contract.brain.Rd | 2 man/graph.efficiency.Rd | 8 + man/graph_attr_dt.Rd | 2 man/graph_neighborhood_multiple.Rd | 2 man/group.graph.diffs.Rd | 2 man/loo.Rd |only man/part.coeff.Rd | 2 man/permute.group.Rd | 11 -- man/permute.vertex.Rd | 2 man/plot_boot.Rd |only man/plot_brainGraph.Rd | 2 man/plot_brainGraph_gui.Rd | 2 man/plot_brainGraph_list.Rd | 2 man/plot_brainGraph_mni.Rd | 2 man/plot_corr_mat.Rd | 2 man/plot_group_means.Rd | 2 man/plot_perm_diffs.Rd | 6 - man/plot_rich_norm.Rd |only man/plot_vertex_measures.Rd | 2 man/rich.club.coeff.Rd | 2 man/rich.club.norm.Rd | 2 man/rich.core.Rd | 2 man/robustness.Rd | 2 man/rotation.Rd | 2 man/set.brainGraph.attributes.Rd | 2 man/sim.rand.graph.clust.Rd | 2 man/sim.rand.graph.par.Rd | 2 man/small.world.Rd | 2 man/spatial.dist.Rd | 2 man/update_brainGraph_gui.Rd | 2 man/vec.transform.Rd | 2 man/vertex_attr_dt.Rd | 2 man/vulnerability.Rd | 2 man/within_module_deg_z_score.Rd | 2 man/write.brainnet.Rd | 2 85 files changed, 505 insertions(+), 362 deletions(-)
Title: R Code for Stock Synthesis
Description: A collection of R functions for use with Stock Synthesis, a
fisheries stock assessment modeling platform written in ADMB by Dr. Richard
D. Methot at the NOAA Northwest Fisheries Science Center. The functions
include tools for summarizing and plotting results, manipulating files,
visualizing model parameterizations, and various other common stock
assessment tasks.
Author: Ian G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison,
Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson,
Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz,
Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet,
Sean C. Anderson, and other contributors.
Maintainer: Ian Taylor <Ian.Taylor@noaa.gov>
Diff between r4ss versions 1.22.1 dated 2014-07-12 and 1.24.0 dated 2015-12-23
DESCRIPTION | 26 MD5 | 276 +++---- NAMESPACE | 225 +++--- NEWS.md |only R/IOTCmove.R | 1 R/NegLogInt_Fn.R | 392 ++++++---- R/PinerPlot.R | 116 ++- R/RebuildPlot.R | 27 R/SSMethod.Cond.TA1.8.R |only R/SSMethod.TA1.8.R |only R/SS_ForeCatch.R |only R/SS_RunJitter.R | 51 - R/SS_changepars.R | 273 +++++-- R/SS_decision_table_stuff.R |only R/SS_doRetro.R | 15 R/SS_fitbiasramp.R | 38 - R/SS_html.R | 28 R/SS_makedatlist.R | 15 R/SS_output.R | 345 ++++++--- R/SS_parlines.R | 16 R/SS_plots.R | 331 +++++---- R/SS_readdat.R | 16 R/SS_readstarter.R | 26 R/SS_varadjust.R |only R/SS_writeforecast.R | 10 R/SS_writestarter.R | 29 R/SSgetoutput.R | 5 R/SSplotBiology.R | 903 ++++++++++++++++++++---- R/SSplotCatch.R | 27 R/SSplotCohorts.R | 8 R/SSplotComparisons.R | 956 +++++++++++++++++--------- R/SSplotComps.R | 1577 ++++++++++++++++++++++++------------------- R/SSplotData.R | 23 R/SSplotDiscard.R | 31 R/SSplotIndices.R | 462 +++++++----- R/SSplotMnwt.R | 8 R/SSplotMovementRates.R | 230 +++--- R/SSplotNumbers.R | 206 ++++- R/SSplotPars.R | 95 +- R/SSplotProfile.R | 11 R/SSplotRecdevs.R | 17 R/SSplotRecdist.R | 8 R/SSplotRetroRecruits.R | 33 R/SSplotSPR.R | 39 - R/SSplotSelex.R | 20 R/SSplotSpawnrecruit.R | 118 ++- R/SSplotSummaryF.R | 8 R/SSplotTags.R | 36 R/SSplotTimeseries.R | 57 + R/SSplotYield.R | 12 R/SSsummarize.R | 176 +--- R/SStableComparisons.R | 30 R/bubble3.R | 61 + R/getADMBHessian.R | 2 R/make_multifig.R | 521 ++++++++++---- R/mcmc.nuisance.R | 12 R/mcmc.out.R | 164 ++-- R/movepars.R | 2 R/r4ss-package.R | 39 - R/r4ss_logo.R | 40 - R/read.admbFit.R | 37 - R/stackpoly.R | 44 - R/update_r4ss_files.R | 233 ------ README.md | 56 + man/DoProjectPlots.Rd | 206 ++--- man/IOTCmove.Rd | 75 +- man/NegLogInt_Fn.Rd | 171 ++-- man/PinerPlot.Rd | 242 +++--- man/SSFishGraph.Rd | 61 - man/SSMethod.Cond.TA1.8.Rd |only man/SSMethod.TA1.8.Rd |only man/SS_ForeCatch.Rd |only man/SS_RunJitter.Rd | 72 + man/SS_changepars.Rd | 156 ++-- man/SS_doRetro.Rd | 137 +-- man/SS_fitbiasramp.Rd | 167 ++-- man/SS_html.Rd | 105 +- man/SS_makedatlist.Rd | 255 +++--- man/SS_output.Rd | 211 ++--- man/SS_parlines.Rd | 123 +-- man/SS_plots.Rd | 552 +++++++-------- man/SS_profile.Rd | 291 ++++--- man/SS_readctl.Rd | 67 - man/SS_readdat.Rd | 71 - man/SS_readforecast.Rd | 61 - man/SS_readstarter.Rd | 53 - man/SS_recdevs.Rd | 113 +-- man/SS_splitdat.Rd | 103 +- man/SS_varadjust.Rd |only man/SS_write_length.fit.Rd | 75 +- man/SS_writectl.Rd | 67 - man/SS_writedat.Rd | 65 - man/SS_writeforecast.Rd | 75 +- man/SS_writestarter.Rd | 77 +- man/SSbootstrap.Rd | 55 - man/SSgetMCMC.Rd | 113 +-- man/SSgetoutput.Rd | 109 +- man/SSmakeMmatrix.Rd | 61 - man/SSplotBiology.Rd | 135 +-- man/SSplotCatch.Rd | 221 +++--- man/SSplotCohorts.Rd | 161 ++-- man/SSplotComparisons.Rd | 424 ++++++----- man/SSplotComps.Rd | 388 +++++----- man/SSplotData.Rd | 149 ++-- man/SSplotDiscard.Rd | 135 +-- man/SSplotIndices.Rd | 226 +++--- man/SSplotMCMC_ExtraSelex.Rd | 73 + man/SSplotMnwt.Rd | 137 +-- man/SSplotMovementMap.Rd | 131 +-- man/SSplotMovementRates.Rd | 143 +-- man/SSplotNumbers.Rd | 168 ++-- man/SSplotPars.Rd | 242 +++--- man/SSplotProfile.Rd | 277 +++---- man/SSplotRecdevs.Rd | 143 +-- man/SSplotRecdist.Rd | 121 +-- man/SSplotRetroRecruits.Rd | 185 ++--- man/SSplotSPR.Rd | 141 +-- man/SSplotSelex.Rd | 231 +++--- man/SSplotSpawnrecruit.Rd | 170 ++-- man/SSplotSummaryF.Rd | 105 +- man/SSplotTags.Rd | 177 ++-- man/SSplotTimeseries.Rd | 167 ++-- man/SSplotYield.Rd | 129 +-- man/SSsummarize.Rd | 110 +- man/SStableComparisons.Rd | 115 +-- man/TSCplot.Rd | 231 +++--- man/addSSsummarize.Rd | 187 ++--- man/bubble3.Rd | 156 ++-- man/getADMBHessian.Rd | 62 - man/make_multifig.Rd | 376 +++++----- man/mcmc.nuisance.Rd | 121 +-- man/mcmc.out.Rd | 157 ++-- man/mountains.Rd | 111 +-- man/movepars.Rd | 61 - man/plotCI.Rd | 87 +- man/r4ss-package.Rd | 85 +- man/r4ss_logo.Rd | 31 man/read.admbFit.Rd | 52 - man/rich.colors.short.Rd | 47 - man/sel.line.Rd | 79 +- man/selfit.Rd | 73 + man/selfit_spline.Rd | 97 +- man/stackpoly.Rd | 111 +-- man/update_r4ss_files.Rd | 84 -- 144 files changed, 11088 insertions(+), 8476 deletions(-)
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1.4 dated 2015-11-08 and 1.1.5 dated 2015-12-23
DESCRIPTION | 8 MD5 | 32 - R/Class_MRIaggr.R | 18 R/Functions_AssociatedClass.R | 61 +- R/Functions_GR.R | 2 R/Functions_Potts.R | 15 R/RcppExports.R | 8 inst/List_of_arguments.R | 859 +++++++++++++++++------------------- inst/NEWS | 20 man/MRIaggr-calcGroupsCoords_cpp.Rd | 5 man/MRIaggr-calcGroupsW.Rd | 4 man/MRIaggr-calcGroupsW_cpp.Rd | 3 src/Functions_W.cpp | 10 src/RcppExports.cpp | 17 src/Utilities_General.h | 26 + src/Utilities_Potential.h | 2 src/Utilities_W.h | 350 ++++++++------ 17 files changed, 770 insertions(+), 670 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.1 dated 2015-10-06 and 0.2.0.2 dated 2015-12-23
DESCRIPTION | 7 ++++--- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 7 +++++-- R/add_brackets.R | 3 ++- R/dwplot.R | 27 +++++++++++++++++++++------ R/relabel_predictors.R | 2 +- README.md | 2 +- man/add_brackets.Rd | 3 ++- man/by_2sd.Rd | 3 ++- man/dwplot.Rd | 8 +++++++- man/relabel_predictors.Rd | 3 ++- man/relabel_y_axis.Rd | 3 ++- man/secret_weapon.Rd | 4 +++- man/small_multiple.Rd | 3 ++- vignettes/dotwhisker-vignette.Rmd | 13 ++++++++++++- vignettes/kl2007_examples.Rmd | 4 ++-- 16 files changed, 83 insertions(+), 39 deletions(-)
Title: Plots (Slightly Extended) Bland-Altman Plots
Description: Bland-Altman Plots using either base graphics or ggplot2,
augmented with confidence intervals, with detailed return values and
a sunflowerplot option for data with ties.
Author: Bernhard Lehnert
Maintainer: Bernhard Lehnert <bernhard.lehnert@uni-greifswald.de>
Diff between BlandAltmanLeh versions 0.2.1 dated 2015-12-15 and 0.3.1 dated 2015-12-23
DESCRIPTION | 10 +-- MD5 | 16 ++--- R/bland.altman.R | 62 ++++++++++++-------- inst/doc/Intro.R | 49 +++++++++++----- inst/doc/Intro.Rmd | 125 +++++++++++++++++++++++++----------------- inst/doc/Intro.html | 96 +++++++++++++++++++------------- man/BlandAltmanLeh-package.Rd | 4 - man/bland.altman.plot.Rd | 36 ++++++------ vignettes/Intro.Rmd | 125 +++++++++++++++++++++++++----------------- 9 files changed, 313 insertions(+), 210 deletions(-)
More information about BlandAltmanLeh at CRAN
Permanent link
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.6-11 dated 2015-09-17 and 0.6-12 dated 2015-12-23
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NEWS | 6 ++++++ data/Burt.RData |only inst/doc/vcd-tutorial.R | 8 ++++---- inst/doc/vcd-tutorial.Rnw | 10 +++++----- man/Burt.Rd |only man/Donner.Rd | 4 ++-- man/vcdExtra-package.Rd | 10 ++++++++-- vignettes/vcd-tutorial.Rnw | 10 +++++----- 10 files changed, 43 insertions(+), 29 deletions(-)
Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between sweidnumbr versions 0.8.2 dated 2015-12-05 and 1.0.0 dated 2015-12-23
sweidnumbr-0.8.2/sweidnumbr/man/format.Rd |only sweidnumbr-0.8.2/sweidnumbr/man/format.pin.Rd |only sweidnumbr-0.8.2/sweidnumbr/man/is.pin.Rd |only sweidnumbr-1.0.0/sweidnumbr/DESCRIPTION | 10 - sweidnumbr-1.0.0/sweidnumbr/MD5 | 74 +++++------ sweidnumbr-1.0.0/sweidnumbr/NAMESPACE | 5 sweidnumbr-1.0.0/sweidnumbr/R/create_s3_methods.R | 13 + sweidnumbr-1.0.0/sweidnumbr/R/firstlib.R | 2 sweidnumbr-1.0.0/sweidnumbr/R/format.pin.R | 36 +---- sweidnumbr-1.0.0/sweidnumbr/R/oin.R | 8 - sweidnumbr-1.0.0/sweidnumbr/R/oin_internal.R | 2 sweidnumbr-1.0.0/sweidnumbr/R/pin.R | 46 ++---- sweidnumbr-1.0.0/sweidnumbr/build/vignette.rds |binary sweidnumbr-1.0.0/sweidnumbr/inst/CITATION | 23 ++- sweidnumbr-1.0.0/sweidnumbr/inst/doc/sweidnumbr.R | 4 sweidnumbr-1.0.0/sweidnumbr/inst/doc/sweidnumbr.Rmd | 16 +- sweidnumbr-1.0.0/sweidnumbr/inst/doc/sweidnumbr.html | 35 ++--- sweidnumbr-1.0.0/sweidnumbr/man/as.oin.Rd | 8 - sweidnumbr-1.0.0/sweidnumbr/man/as.pin.Rd | 26 ++- sweidnumbr-1.0.0/sweidnumbr/man/create_s3_method.Rd |only sweidnumbr-1.0.0/sweidnumbr/man/fake_pins.Rd | 2 sweidnumbr-1.0.0/sweidnumbr/man/format_pin.Rd |only sweidnumbr-1.0.0/sweidnumbr/man/is.oin.Rd | 5 sweidnumbr-1.0.0/sweidnumbr/man/luhn_algo.Rd | 7 - sweidnumbr-1.0.0/sweidnumbr/man/oin_ctrl.Rd | 3 sweidnumbr-1.0.0/sweidnumbr/man/oin_group.Rd | 3 sweidnumbr-1.0.0/sweidnumbr/man/oin_group_element.Rd | 4 sweidnumbr-1.0.0/sweidnumbr/man/pin_age.Rd | 5 sweidnumbr-1.0.0/sweidnumbr/man/pin_birthplace.Rd | 11 - sweidnumbr-1.0.0/sweidnumbr/man/pin_birthplace_internal.Rd | 2 sweidnumbr-1.0.0/sweidnumbr/man/pin_century.Rd | 2 sweidnumbr-1.0.0/sweidnumbr/man/pin_convert.Rd | 2 sweidnumbr-1.0.0/sweidnumbr/man/pin_coordn.Rd | 3 sweidnumbr-1.0.0/sweidnumbr/man/pin_coordn_correct.Rd | 2 sweidnumbr-1.0.0/sweidnumbr/man/pin_ctrl.Rd | 5 sweidnumbr-1.0.0/sweidnumbr/man/pin_sex.Rd | 3 sweidnumbr-1.0.0/sweidnumbr/man/pin_to_date.Rd | 3 sweidnumbr-1.0.0/sweidnumbr/man/sweidnumbr.Rd | 6 sweidnumbr-1.0.0/sweidnumbr/tests/testthat/test-format.pin.R | 11 - sweidnumbr-1.0.0/sweidnumbr/vignettes/sweidnumbr.Rmd | 16 +- sweidnumbr-1.0.0/sweidnumbr/vignettes/sweidnumbr.md |only 41 files changed, 210 insertions(+), 193 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of
variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.0.2 dated 2015-07-23 and 0.1.1.0 dated 2015-12-23
DESCRIPTION | 10 - MD5 | 32 +-- NAMESPACE | 11 - R/Interplot.R | 40 ++-- R/Interplot_default.R | 183 ++++++++++++++++--- R/Interplot_mi.R | 352 +++++++++++++++++++++++++++++++------- R/Interplot_mlm.R | 348 +++++++++++++++++++++++++++++++------ R/Interplot_mlmmi.R | 361 +++++++++++++++++++++++++++++++-------- R/Interplot_plot.R | 31 +-- README.md | 5 man/interplot.Rd | 23 +- man/interplot.default.Rd | 4 man/interplot.lmerMod.Rd | 2 man/interplot.lmmi.Rd | 2 man/interplot.mlmmi.Rd | 2 man/interplot.plot.Rd | 2 vignettes/interplot-vignette.Rmd | 11 + 17 files changed, 1119 insertions(+), 300 deletions(-)
Title: Sparse and Non-Sparse Partial Robust M Regression and
Classification
Description: Robust dimension reduction methods for regression and discriminant analysis are implemented that yield estimates with a partial least squares alike interpretability. Partial robust M regression (PRM) is robust to both vertical outliers and leverage points. Sparse partial robust M regression (SPRM) is a related robust method with sparse coefficient estimate, and therefore with intrinsic variable selection. For bianry classification related discriminant methods are PRM-DA and SPRM-DA.
Author: Sven Serneels, BASF Corp and Irene Hoffmann
Maintainer: Irene Hoffmann <irene.hoffmann@tuwien.ac.at>
Diff between sprm versions 1.2 dated 2015-10-15 and 1.2.1 dated 2015-12-23
sprm-1.2.1/sprm/DESCRIPTION | 12 ++++----- sprm-1.2.1/sprm/MD5 | 44 ++++++++++++++---------------------- sprm-1.2.1/sprm/NAMESPACE | 11 ++++----- sprm-1.2.1/sprm/R/daprpr.R | 5 ++++ sprm-1.2.1/sprm/R/prmda.R | 2 - sprm-1.2.1/sprm/man/plot.prm.Rd | 6 ++-- sprm-1.2.1/sprm/man/plot.sprm.Rd | 6 +++- sprm-1.2.1/sprm/man/predict.prm.Rd | 5 +--- sprm-1.2.1/sprm/man/predict.sprm.Rd | 4 ++- sprm-1.2.1/sprm/man/prmda.Rd | 2 - sprm-1.2.1/sprm/man/prmdaCV.Rd | 3 -- sprm-1.2.1/sprm/man/prms.Rd | 6 ++-- sprm-1.2.1/sprm/man/prmsCV.Rd | 4 +-- sprm-1.2.1/sprm/man/sprm-package.Rd | 9 +++---- sprm-1.2.1/sprm/man/sprmdaCV.Rd | 3 -- sprm-1.2.1/sprm/man/sprms.Rd | 6 +++- sprm-1.2.1/sprm/man/sprmsCV.Rd | 4 ++- sprm-1.2.1/sprm/man/summary.prm.Rd | 4 +-- sprm-1.2.1/sprm/man/summary.sprm.Rd | 4 ++- sprm-1.2/sprm/R/biplot.prm.R |only sprm-1.2/sprm/R/biplot.prmda.R |only sprm-1.2/sprm/R/biplot.sprm.R |only sprm-1.2/sprm/R/biplot.sprmda.R |only sprm-1.2/sprm/man/biplot.prm.Rd |only sprm-1.2/sprm/man/biplot.prmda.Rd |only sprm-1.2/sprm/man/biplot.sprm.Rd |only sprm-1.2/sprm/man/biplot.sprmda.Rd |only 27 files changed, 71 insertions(+), 69 deletions(-)
Title: Topological Analysis of Knotted Proteins, Biopolymers and 3D
Structures
Description: Contains functions for the topological analysis of polymers, with a focus on protein structures.
Author: Federico Comoglio and Maurizio Rinaldi
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>
Diff between Rknots versions 1.3.0 dated 2015-12-22 and 1.3.1 dated 2015-12-23
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/makeExamples.R | 2 +- inst/doc/Rknots_vignette.R | 2 +- inst/doc/Rknots_vignette.Rmd | 2 +- inst/doc/Rknots_vignette.html | 8 ++++---- man/skeinIterator.Rd | 2 -- vignettes/Rknots_vignette.Rmd | 2 +- 8 files changed, 20 insertions(+), 22 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.6 dated 2015-10-08 and 0.4.8 dated 2015-12-23
DESCRIPTION | 12 MD5 | 88 ++-- R/domain.R | 14 R/incPercentile.R | 2 R/linarpr.R | 11 R/linarpt.R | 13 R/linarr.R | 6 R/linpoormed.R | 11 R/linqsr.R | 4 R/linrmir.R | 6 R/linrmpg.R | 11 R/vardchanges.R | 205 ++++----- R/vardchangespoor.R | 247 +++++------ R/vardcros.R | 1014 +++++++++++++++++++++++------------------------- R/vardcrospoor.R | 479 +++++++++++----------- R/vardom.R | 20 R/vardom_othstr.R | 8 R/vardomh.R | 16 R/variance_othstr.R | 58 ++ R/varpoord.R | 29 - inst/CITATION | 4 inst/NEWS | 4 man/domain.Rd | 7 man/incPercentile.Rd | 10 man/linarpr.Rd | 16 man/linarpt.Rd | 12 man/linarr.Rd | 20 man/lingini.Rd | 12 man/lingini2.Rd | 12 man/lingpg.Rd | 14 man/linpoormed.Rd | 12 man/linqsr.Rd | 12 man/linrmir.Rd | 14 man/linrmpg.Rd | 12 man/vardchanges.Rd | 43 +- man/vardchangespoor.Rd | 49 +- man/vardcros.Rd | 20 man/vardcrospoor.Rd | 31 - man/vardom.Rd | 26 - man/vardom_othstr.Rd | 22 - man/vardomh.Rd | 32 - man/vardpoor-package.Rd | 4 man/variance_est.Rd | 10 man/variance_othstr.Rd | 3 man/varpoord.Rd | 48 +- 45 files changed, 1378 insertions(+), 1325 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 0.8 dated 2015-11-30 and 1.0 dated 2015-12-23
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- R/dom_optimal_allocation.R | 53 ++++++++++++++++++++++++++++-------------- R/expvar.R | 14 ----------- R/optsize.R | 47 ++++++++++++++++++++++--------------- man/dom_optimal_allocation.Rd | 18 ++++++++------ man/expsize.Rd | 5 ++- man/expvar.Rd | 10 +++---- man/optsize.Rd | 10 +++++-- man/surveyplanning-package.Rd | 4 +-- 10 files changed, 107 insertions(+), 80 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Hidden Markov Models for Life Sequences and Other Multivariate,
Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent)
Markov models and mixture hidden Markov models for social
sequence data and other categorical time series. Also some more restricted
versions of these type of models are available: Markov models, mixture
Markov models, and latent class models. The package supports models for one or
multiple subjects with one or multiple parallel sequences (channels). External
covariates can be added to explain cluster membership in mixture models. The
package provides functions for evaluating and comparing models, as well as
functions for easy plotting of multichannel sequence data and hidden Markov
models. Models are estimated using maximum likelihood via the EM algorithm and/or
direct numerical maximization with analytical gradients.
All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between seqHMM versions 1.0.2-1 dated 2015-12-19 and 1.0.3 dated 2015-12-23
DESCRIPTION | 10 MD5 | 133 ++-- NEWS |only R/HMMplot.R | 35 - R/RcppExports.R | 36 - R/build_hmm.R | 152 ++-- R/build_lcm.R | 1 R/build_mhmm.R | 179 ++--- R/build_mm.R | 213 +++--- R/build_mmm.R | 335 +++++----- R/colorpalette.R | 20 R/fit_model.R | 11 R/gridplot.R | 315 +++++---- R/help_data.R | 182 ++--- R/mc_to_sc.R | 431 ++++++------- R/mhmm_biofam.R | 330 +++++----- R/mhmm_mvad.R | 180 ++--- R/mssplot.R | 256 +++---- R/plot.hmm.R | 1142 +++++++++++++++++------------------ R/plot.mhmm.R | 199 +++--- R/plot.ssp.R | 86 +- R/separate_mhmm.R | 72 +- R/seqHMM-package.R | 69 +- R/ssp.R | 1386 +++++++++++++++++++++---------------------- R/ssplot.R | 470 +++++++------- R/summary.mhmm.R | 224 +++--- R/trim_hmm.R | 562 ++++++++--------- build/vignette.rds |binary inst/doc/seqHMM.R | 692 ++++++++++----------- inst/doc/seqHMM.pdf |binary man/biofam3c.Rd | 338 +++++----- man/build_hmm.Rd | 319 ++++----- man/build_mhmm.Rd | 444 ++++++------- man/colorpalette.Rd | 62 - man/gridplot.Rd | 280 ++++---- man/mc_to_sc.Rd | 88 +- man/mhmm_biofam.Rd | 330 +++++----- man/mhmm_mvad.Rd | 180 ++--- man/mssplot.Rd | 364 +++++------ man/plot.hmm.Rd | 480 +++++++------- man/plot.mhmm.Rd | 411 ++++++------ man/plot.ssp.Rd | 86 +- man/separate_mhmm.Rd | 68 +- man/seqHMM-deprecated.Rd | 256 +++---- man/ssp.Rd | 476 +++++++------- man/ssplot.Rd | 458 +++++++------- man/summary.mhmm.Rd | 128 +-- man/trim_model.Rd | 86 +- src/EM.cpp | 2 src/EMx.cpp | 2 src/RcppExports.cpp | 130 ++-- src/forwardbackward.cpp | 4 src/forwardbackwardx.cpp | 4 src/logLikHMM.cpp | 4 src/logLikMixHMM.cpp | 4 src/log_EM.cpp | 2 src/log_EMx.cpp | 2 src/log_forwardbackward.cpp | 2 src/log_forwardbackwardx.cpp | 2 src/log_logLikHMM.cpp | 2 src/log_logLikMixHMM.cpp | 2 src/log_objective.cpp | 16 src/log_objectivex.cpp | 258 +++----- src/objective.cpp | 60 - src/objectivex.cpp | 6 src/varcoef.cpp | 3 src/viterbi.cpp | 4 src/viterbix.cpp | 4 68 files changed, 6555 insertions(+), 6533 deletions(-)
Title: Gaussian Process Laboratory
Description: Gaussian Process models with customised covariance kernels.
Author: Yves Deville, David Ginsbourger, Olivier Roustant. Contributors: Nicolas Durrande.
Maintainer: Yves Deville <deville.yves@alpestat.com>
Diff between kergp versions 0.1.0 dated 2015-06-22 and 0.2.0 dated 2015-12-23
kergp-0.1.0/kergp/inst |only kergp-0.1.0/kergp/tests/test-all.R |only kergp-0.2.0/kergp/ChangeLog | 10 kergp-0.2.0/kergp/DESCRIPTION | 12 kergp-0.2.0/kergp/MD5 | 29 - kergp-0.2.0/kergp/NAMESPACE | 15 kergp-0.2.0/kergp/R/gp.R | 58 ++ kergp-0.2.0/kergp/R/logLikFuns.R | 299 ++++++------- kergp-0.2.0/kergp/R/methodGLS.R | 4 kergp-0.2.0/kergp/R/methodMLE.R | 18 kergp-0.2.0/kergp/man/gp.Rd | 739 ++++++++++++++++----------------- kergp-0.2.0/kergp/man/kergp-package.Rd | 432 +++++++++---------- kergp-0.2.0/kergp/tests/testthat |only 13 files changed, 839 insertions(+), 777 deletions(-)
Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of SQL and
SQL/MR functions running in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre],
Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.3.1 dated 2015-11-03 and 0.4.1 dated 2015-12-23
DESCRIPTION | 37 ++++----- MD5 | 87 +++++++++++++--------- NAMESPACE | 16 +++- NEWS | 26 ++++++ R/computeAggregates.R | 2 R/computeBarchart.R | 2 R/computeCorrelations.R | 3 R/computeHeatmap.R | 6 + R/computeHistogram.R | 2 R/computeKmeans.R |only R/computePercentiles.R | 2 R/computeSample.R | 7 + R/computeTfIdf.R | 30 +++++++ R/misc.R | 55 ++++++++++++++ R/plotting.R | 93 ++++++++++++++++-------- R/plottingKmeans.R |only R/toaster.R | 5 + R/utils.R | 115 ++++++++++++++++++++++++++++++ README.md | 3 demo/00Index | 1 demo/baseball-kmeans.R |only man/computeClusterSample.Rd |only man/computeCorrelations.Rd | 1 man/computeKmeans.Rd |only man/computeSilhouette.Rd |only man/createBoxplot.Rd | 17 ++-- man/createBubblechart.Rd | 22 ++++- man/createCentroidPlot.Rd |only man/createClusterPairsPlot.Rd |only man/createClusterPlot.Rd |only man/createHeatmap.Rd | 27 ++++++- man/createHistogram.Rd | 7 + man/createPopPyramid.Rd | 7 + man/createSilhouetteProfile.Rd |only man/createSlopegraph.Rd | 9 +- man/getNullCounts.Rd |only man/makeTempTableName.Rd |only tests/testthat/helper-tests.R | 8 ++ tests/testthat/test-computeAggregates.R | 3 tests/testthat/test-computeBarchart.R | 3 tests/testthat/test-computeCorrelations.R | 7 + tests/testthat/test-computeHeatmap.R | 6 + tests/testthat/test-computeHistogram.R | 7 + tests/testthat/test-computeKmeans.R |only tests/testthat/test-computePercentiles.R | 3 tests/testthat/test-computeSample.R | 3 tests/testthat/test-computeTf.R | 21 +++++ tests/testthat/test-computeTfIdf.R | 17 ++++ tests/testthat/test-createBoxplot.R | 2 tests/testthat/test-createClusterPlots.R |only tests/testthat/test-misc.R |only tests/testthat/test-utils.R | 44 +++++++++++ 52 files changed, 582 insertions(+), 124 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.43-0 dated 2015-10-08 and 1.44-0 dated 2015-12-23
DESCRIPTION | 25 MD5 | 2291 ++++++++++++----------- NAMESPACE | 59 NEWS | 197 ++ R/Gest.R | 2 R/Gmulti.R | 2 R/Hest.R | 42 R/Iest.R | 129 - R/Kcom.R | 2 R/Kmeasure.R | 18 R/Kmulti.R | 2 R/Tstat.R | 8 R/addvar.R | 2 R/allstats.R | 2 R/alltypes.R | 2 R/anova.mppm.R | 11 R/badgey.R | 2 R/beginner.R | 2 R/boundingbox.R | 9 R/bw.optim.R | 2 R/bw.ppl.R | 2 R/by.ppp.R | 2 R/clarkevans.R | 4 R/clickpoly.R | 2 R/clickppp.R | 2 R/close3Dpairs.R | 255 +- R/closepairs.R | 2 R/clusterinfo.R | 35 R/colourtables.R | 2 R/compareFit.R | 2 R/convexify.R |only R/covariates.R | 2 R/daogenton.R | 105 - R/dclftest.R | 138 + R/defaultwin.R | 2 R/deldir.R | 37 R/density.ppp.R | 7 R/detpointprocfamilyfun.R | 7 R/dg.R | 2 R/dgs.R | 2 R/diagnoseppm.R | 6 R/diagram.R | 2 R/distances.psp.R | 4 R/distcdf.R | 40 R/distfunlpp.R | 16 R/dppm.R | 2 R/dummy.R | 12 R/effectfun.R | 15 R/envelope.R | 103 - R/envelope3.R | 12 R/envelopelpp.R | 21 R/eval.fasp.R | 117 - R/eval.fv.R | 127 - R/eval.im.R | 86 R/evalcovar.R | 706 +++---- R/fardist.R | 2 R/fasp.R | 148 - R/fiksel.R | 2 R/formulae.R | 6 R/funxy.R | 2 R/fv.R | 363 ++- R/hardcore.R | 2 R/hybrid.R | 4 R/hybrid.family.R | 4 R/hyperframe.R | 16 R/hypersub.R | 26 R/idw.R | 2 R/infline.R | 6 R/intensity.R | 2 R/interact.R | 8 R/interactions.R | 127 - R/iplot.R | 2 R/iplotlayered.R | 4 R/ippm.R | 17 R/istat.R | 2 R/kppm.R | 119 - R/layered.R | 4 R/linearK.R | 2 R/lineardisc.R | 2 R/linearmrkcon.R | 42 R/linearpcf.R | 2 R/linequad.R | 211 +- R/linfun.R | 2 R/linim.R | 74 R/linnet.R | 6 R/lixellate.R |only R/logistic.R | 9 R/lpp.R | 10 R/lppm.R | 69 R/lurking.R | 577 +++-- R/markcorr.R | 2 R/marks.R | 2 R/measures.R | 29 R/mpl.R | 16 R/mppm.R | 916 ++++----- R/multihard.R | 2 R/nnclean.R | 2 R/nncorr.R | 22 R/nndistlpp.R | 351 ++- R/nnmark.R | 72 R/objsurf.R | 2 R/options.R | 22 R/ord.R | 2 R/ord.family.R | 2 R/ordthresh.R | 2 R/pairpiece.R | 2 R/pairs.im.R | 2 R/pairwise.R | 2 R/plot.anylist.R | 16 R/plot.fv.R | 17 R/plot.owin.R | 7 R/plot.ppp.R | 4 R/plot3d.R | 2 R/poisson.R | 2 R/pp3.R | 2 R/ppmclass.R | 45 R/ppqq.R | 93 R/ppx.R | 101 - R/predictmppm.R | 676 +++---- R/profilepl.R | 6 R/progress.R | 226 +- R/psp.R | 5 R/pspcross.R | 2 R/psstG.R | 2 R/quadratcount.R | 24 R/quadratresample.R | 5 R/quadrattest.R | 14 R/quadscheme.R | 2 R/rPerfect.R | 87 R/random.R | 102 - R/randomNS.R | 2 R/randommk.R | 10 R/randomtess.R | 2 R/reduceformula.R | 60 R/relrisk.ppm.R | 24 R/residppm.R | 2 R/resolve.defaults.R | 2 R/rhohat.R | 2 R/rmh.default.R | 16 R/rmhcontrol.R | 2 R/rmhmodel.R | 55 R/rmhmodel.ppm.R | 10 R/rmhtemper.R | 2 R/satpiece.R | 2 R/saturated.R | 2 R/sigtrace.R | 30 R/slrm.R | 27 R/smooth.ppp.R | 8 R/softcore.R | 2 R/split.ppx.R | 2 R/stienen.R | 2 R/strauss.R | 2 R/strausshard.R | 2 R/studpermutest.R | 7 R/summary.quad.R | 92 R/superimpose.R | 5 R/symbolmap.R | 6 R/terse.R | 14 R/tess.R | 34 R/texture.R | 2 R/treebranches.R | 2 R/triangulate.R | 26 R/triplets.R | 2 R/unique.ppp.R | 6 R/update.ppm.R | 2 R/util.R | 92 R/varblock.R | 14 R/varcount.R |only R/window.R | 35 R/wingeom.R | 7 R/xysegment.R | 2 R/zclustermodel.R |only build/vignette.rds |binary data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/cells.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary demo/spatstat.R | 5 demo/sumfun.R | 2 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 22 inst/doc/updates.Rnw | 3752 ++++----------------------------------- inst/doc/updates.pdf |binary man/AreaInter.Rd | 9 man/BadGey.Rd | 9 man/CDF.Rd | 10 man/Concom.Rd | 9 man/DiggleGatesStibbard.Rd | 15 man/DiggleGratton.Rd | 9 man/Emark.Rd | 11 man/Extract.anylist.Rd | 9 man/Extract.fasp.Rd | 10 man/Extract.fv.Rd | 9 man/Extract.hyperframe.Rd | 9 man/Extract.im.Rd | 9 man/Extract.influence.ppm.Rd | 9 man/Extract.layered.Rd | 9 man/Extract.leverage.ppm.Rd | 9 man/Extract.linnet.Rd | 9 man/Extract.listof.Rd | 9 man/Extract.lpp.Rd | 9 man/Extract.msr.Rd | 9 man/Extract.owin.Rd | 9 man/Extract.ppp.Rd | 9 man/Extract.ppx.Rd | 40 man/Extract.psp.Rd | 9 man/Extract.quad.Rd | 10 man/Extract.solist.Rd | 11 man/Extract.splitppp.Rd | 9 man/Extract.tess.Rd | 10 man/F3est.Rd | 6 man/Fest.Rd | 10 man/Fiksel.Rd | 9 man/Finhom.Rd | 8 man/Frame.Rd | 14 man/G3est.Rd | 6 man/Gcom.Rd | 8 man/Gcross.Rd | 10 man/Gdot.Rd | 10 man/Gest.Rd | 10 man/Geyer.Rd | 10 man/Gfox.Rd | 6 man/Ginhom.Rd | 8 man/Gmulti.Rd | 10 man/Gres.Rd | 8 man/Hardcore.Rd | 10 man/Hest.Rd | 41 man/HierHard.Rd | 12 man/HierStrauss.Rd | 12 man/HierStraussHard.Rd | 12 man/Hybrid.Rd | 10 man/Iest.Rd | 10 man/Jcross.Rd | 10 man/Jdot.Rd | 10 man/Jest.Rd | 10 man/Jinhom.Rd | 8 man/Jmulti.Rd | 10 man/K3est.Rd | 6 man/Kcom.Rd | 8 man/Kcross.Rd | 10 man/Kcross.inhom.Rd | 10 man/Kdot.Rd | 10 man/Kdot.inhom.Rd | 10 man/Kest.Rd | 7 man/Kest.fft.Rd | 23 man/Kinhom.Rd | 10 man/Kmark.Rd | 10 man/Kmeasure.Rd | 10 man/Kmodel.Rd | 10 man/Kmodel.dppm.Rd | 14 man/Kmodel.kppm.Rd | 10 man/Kmodel.ppm.Rd | 6 man/Kmulti.Rd | 10 man/Kmulti.inhom.Rd | 10 man/Kres.Rd | 8 man/Kscaled.Rd | 10 man/Ksector.Rd | 14 man/LambertW.Rd | 10 man/Lcross.Rd | 10 man/Lcross.inhom.Rd | 10 man/Ldot.Rd | 10 man/Ldot.inhom.Rd | 10 man/LennardJones.Rd | 10 man/Lest.Rd | 10 man/Linhom.Rd | 10 man/Math.im.Rd | 14 man/Math.linim.Rd | 14 man/MultiHard.Rd | 12 man/MultiStrauss.Rd | 12 man/MultiStraussHard.Rd | 12 man/Ord.Rd | 10 man/OrdThresh.Rd | 10 man/PPversion.Rd | 11 man/PairPiece.Rd | 10 man/Pairwise.Rd | 10 man/Penttinen.Rd | 10 man/Poisson.Rd | 10 man/Replace.im.Rd | 10 man/SatPiece.Rd | 10 man/Saturated.Rd | 10 man/Smooth.Rd | 10 man/Smooth.fv.Rd | 10 man/Smooth.msr.Rd | 6 man/Smooth.ppp.Rd | 7 man/Smoothfun.ppp.Rd | 12 man/Softcore.Rd | 10 man/Strauss.Rd | 12 man/StraussHard.Rd | 12 man/Triplets.Rd | 10 man/Tstat.Rd | 6 man/Window.Rd | 14 man/WindowOnly.Rd | 12 man/adaptive.density.Rd | 17 man/add.texture.Rd | 9 man/addvar.Rd | 7 man/affine.Rd | 10 man/affine.im.Rd | 10 man/affine.linnet.Rd | 10 man/affine.lpp.Rd | 10 man/affine.owin.Rd | 10 man/affine.ppp.Rd | 10 man/affine.psp.Rd | 10 man/affine.tess.Rd | 10 man/allstats.Rd | 10 man/alltypes.Rd | 10 man/angles.psp.Rd | 10 man/anova.lppm.Rd | 6 man/anova.mppm.Rd | 16 man/anova.ppm.Rd | 10 man/anova.slrm.Rd | 8 man/ants.Rd | 2 man/anylist.Rd | 14 man/append.psp.Rd | 10 man/applynbd.Rd | 10 man/area.owin.Rd | 10 man/areaGain.Rd | 10 man/areaLoss.Rd | 10 man/as.box3.Rd | 10 man/as.boxx.Rd | 14 man/as.data.frame.hyperframe.Rd | 10 man/as.data.frame.im.Rd | 10 man/as.data.frame.owin.Rd | 14 man/as.data.frame.ppp.Rd | 10 man/as.data.frame.psp.Rd | 10 man/as.function.fv.Rd | 10 man/as.function.im.Rd | 14 man/as.fv.Rd | 13 man/as.hyperframe.Rd | 10 man/as.hyperframe.ppx.Rd | 10 man/as.im.Rd | 10 man/as.interact.Rd | 10 man/as.layered.Rd | 14 man/as.linim.Rd | 9 man/as.linnet.linim.Rd | 14 man/as.linnet.psp.Rd | 14 man/as.lpp.Rd | 10 man/as.mask.Rd | 10 man/as.mask.psp.Rd | 10 man/as.matrix.im.Rd | 10 man/as.matrix.owin.Rd | 10 man/as.owin.Rd | 14 man/as.polygonal.Rd | 24 man/as.ppm.Rd | 14 man/as.ppp.Rd | 10 man/as.psp.Rd | 10 man/as.rectangle.Rd | 10 man/as.solist.Rd | 14 man/as.tess.Rd | 10 man/auc.Rd | 14 man/bdist.pixels.Rd | 10 man/bdist.points.Rd | 10 man/bdist.tiles.Rd | 10 man/beachcolours.Rd | 10 man/beginner.Rd | 10 man/begins.Rd | 14 man/berman.test.Rd | 12 man/bind.fv.Rd | 10 man/blur.Rd | 10 man/border.Rd | 10 man/bounding.box.xy.Rd | 10 man/boundingbox.Rd | 10 man/box3.Rd | 10 man/boxx.Rd | 10 man/branchlabelfun.Rd | 14 man/bw.diggle.Rd | 10 man/bw.frac.Rd | 10 man/bw.ppl.Rd | 10 man/bw.relrisk.Rd | 10 man/bw.scott.Rd | 10 man/bw.smoothppp.Rd | 10 man/bw.stoyan.Rd | 10 man/by.im.Rd | 10 man/by.ppp.Rd | 10 man/cauchy.estK.Rd | 6 man/cauchy.estpcf.Rd | 6 man/cbind.hyperframe.Rd | 10 man/cdf.test.Rd | 10 man/cdf.test.mppm.Rd | 16 man/centroid.owin.Rd | 12 man/chicago.Rd | 2 man/chop.tess.Rd | 10 man/chorley.Rd | 2 man/circdensity.Rd | 14 man/circumradius.Rd | 4 man/clarkevans.Rd | 6 man/clarkevans.test.Rd | 6 man/clickbox.Rd | 10 man/clickdist.Rd | 14 man/clickjoin.Rd | 4 man/clickpoly.Rd | 10 man/clickppp.Rd | 10 man/clip.infline.Rd | 10 man/closepairs.Rd | 10 man/closepairs.pp3.Rd | 12 man/closing.Rd | 10 man/clusterfield.Rd | 14 man/clusterfit.Rd | 14 man/clusterkernel.Rd | 14 man/clusterradius.Rd | 14 man/clusterset.Rd | 10 man/coef.mppm.Rd | 16 man/coef.ppm.Rd | 10 man/coef.slrm.Rd | 8 man/collapse.fv.Rd | 10 man/colourmap.Rd | 10 man/colourtools.Rd | 10 man/commonGrid.Rd | 10 man/compareFit.Rd | 8 man/compatible.Rd | 10 man/compatible.fasp.Rd | 10 man/compatible.fv.Rd | 10 man/compatible.im.Rd | 10 man/complement.owin.Rd | 10 man/concatxy.Rd | 10 man/connected.Rd | 10 man/connected.ppp.Rd | 10 man/contour.im.Rd | 14 man/contour.imlist.Rd | 14 man/convexhull.Rd | 10 man/convexhull.xy.Rd | 10 man/convexify.Rd |only man/convolve.im.Rd | 10 man/coords.Rd | 10 man/copyExampleFiles.Rd | 14 man/corners.Rd | 10 man/crossdist.Rd | 6 man/crossdist.default.Rd | 6 man/crossdist.lpp.Rd | 6 man/crossdist.pp3.Rd | 6 man/crossdist.ppp.Rd | 6 man/crossdist.ppx.Rd | 6 man/crossdist.psp.Rd | 10 man/crossing.psp.Rd | 10 man/cut.im.Rd | 10 man/cut.ppp.Rd | 10 man/data.ppm.Rd | 10 man/dclf.progress.Rd | 21 man/dclf.sigtrace.Rd | 38 man/dclf.test.Rd | 46 man/default.dummy.Rd | 10 man/default.expand.Rd | 10 man/default.rmhcontrol.Rd | 10 man/delaunay.Rd | 14 man/delaunayDistance.Rd | 14 man/delaunayNetwork.Rd | 14 man/deletebranch.Rd | 14 man/deltametric.Rd | 10 man/demohyper.Rd | 2 man/demopat.Rd | 2 man/density.lpp.Rd | 2 man/density.ppp.Rd | 22 man/density.psp.Rd | 10 man/density.splitppp.Rd | 10 man/deriv.fv.Rd | 10 man/detpointprocfamilyfun.Rd | 14 man/dfbetas.ppm.Rd | 6 man/dg.envelope.Rd | 24 man/dg.progress.Rd | 46 man/dg.sigtrace.Rd | 45 man/dg.test.Rd | 47 man/diagnose.ppm.Rd | 10 man/diameter.Rd | 10 man/diameter.box3.Rd | 10 man/diameter.boxx.Rd | 10 man/diameter.linnet.Rd | 4 man/diameter.owin.Rd | 10 man/dilated.areas.Rd | 10 man/dilation.Rd | 10 man/dim.detpointprocfamily.Rd | 14 man/dirichlet.Rd | 10 man/dirichletAreas.Rd | 14 man/dirichletVertices.Rd | 14 man/dirichletWeights.Rd | 10 man/disc.Rd | 10 man/discpartarea.Rd | 10 man/discretise.Rd | 10 man/discs.Rd | 14 man/distcdf.Rd | 13 man/distfun.Rd | 10 man/distfun.lpp.Rd | 16 man/distmap.Rd | 10 man/distmap.owin.Rd | 10 man/distmap.ppp.Rd | 10 man/distmap.psp.Rd | 10 man/dkernel.Rd | 4 man/dmixpois.Rd | 12 man/domain.Rd | 14 man/dppBessel.Rd | 10 man/dppCauchy.Rd | 14 man/dppGauss.Rd | 14 man/dppMatern.Rd | 14 man/dppPowerExp.Rd | 14 man/dppapproxkernel.Rd | 14 man/dppapproxpcf.Rd | 14 man/dppeigen.Rd | 14 man/dppkernel.Rd | 14 man/dppm.Rd | 16 man/dppparbounds.Rd | 14 man/dppspecden.Rd | 14 man/dppspecdenrange.Rd | 14 man/dummify.Rd | 4 man/dummy.ppm.Rd | 10 man/duplicated.ppp.Rd | 10 man/edge.Ripley.Rd | 10 man/edge.Trans.Rd | 10 man/edges.Rd | 12 man/edges2triangles.Rd | 10 man/edges2vees.Rd | 10 man/edit.hyperframe.Rd | 14 man/edit.ppp.Rd | 14 man/eem.Rd | 10 man/effectfun.Rd | 10 man/ellipse.Rd | 10 man/emend.Rd | 14 man/emend.ppm.Rd | 10 man/endpoints.psp.Rd | 10 man/envelope.Rd | 58 man/envelope.envelope.Rd | 10 man/envelope.lpp.Rd | 29 man/envelope.pp3.Rd | 28 man/eroded.areas.Rd | 10 man/erosion.Rd | 10 man/eval.fasp.Rd | 10 man/eval.fv.Rd | 10 man/eval.im.Rd | 10 man/eval.linim.Rd | 10 man/ewcdf.Rd | 10 man/exactMPLEstrauss.Rd | 10 man/expand.owin.Rd | 10 man/fardist.Rd | 14 man/fasp.object.Rd | 10 man/fitin.Rd | 10 man/fitted.lppm.Rd | 14 man/fitted.mppm.Rd | 16 man/fitted.ppm.Rd | 10 man/fitted.slrm.Rd | 8 man/fixef.mppm.Rd | 16 man/flipxy.Rd | 10 man/foo.Rd | 14 man/formula.fv.Rd | 10 man/formula.ppm.Rd | 6 man/fourierbasis.Rd | 14 man/fryplot.Rd | 10 man/funxy.Rd | 10 man/fv.Rd | 10 man/fv.object.Rd | 10 man/fvnames.Rd | 10 man/gauss.hermite.Rd | 12 man/gridcentres.Rd | 10 man/gridweights.Rd | 10 man/grow.boxx.Rd |only man/grow.rectangle.Rd | 12 man/harmonic.Rd | 10 man/harmonise.Rd | 12 man/harmonise.fv.Rd | 12 man/harmonise.im.Rd | 10 man/harmonise.owin.Rd | 10 man/heather.Rd | 4 man/hextess.Rd | 10 man/hierpair.family.Rd | 12 man/hist.im.Rd | 10 man/hopskel.Rd | 14 man/humberside.Rd | 2 man/hybrid.family.Rd | 10 man/hyperframe.Rd | 10 man/identify.ppp.Rd | 10 man/identify.psp.Rd | 10 man/idw.Rd | 10 man/im.Rd | 10 man/im.apply.Rd | 10 man/im.object.Rd | 10 man/imcov.Rd | 10 man/improve.kppm.Rd | 10 man/incircle.Rd | 10 man/increment.fv.Rd | 14 man/infline.Rd | 10 man/influence.ppm.Rd | 6 man/inforder.family.Rd | 10 man/inside.boxx.Rd |only man/inside.owin.Rd | 10 man/integral.im.Rd | 14 man/integral.linim.Rd | 14 man/integral.msr.Rd | 14 man/intensity.Rd | 10 man/intensity.dppm.Rd | 14 man/intensity.lpp.Rd | 10 man/intensity.ppm.Rd | 6 man/intensity.ppp.Rd | 10 man/intensity.ppx.Rd | 14 man/intensity.quadratcount.Rd | 10 man/interp.colourmap.Rd | 10 man/interp.im.Rd | 10 man/intersect.owin.Rd | 14 man/intersect.tess.Rd | 10 man/invoke.symbolmap.Rd | 12 man/iplot.Rd | 10 man/ippm.Rd | 10 man/is.convex.Rd | 10 man/is.dppm.Rd | 6 man/is.empty.Rd | 10 man/is.hybrid.Rd | 10 man/is.im.Rd | 10 man/is.lpp.Rd | 10 man/is.marked.Rd | 10 man/is.marked.ppm.Rd | 10 man/is.marked.ppp.Rd | 10 man/is.multitype.Rd | 10 man/is.multitype.ppm.Rd | 10 man/is.multitype.ppp.Rd | 10 man/is.owin.Rd | 10 man/is.ppm.Rd | 10 man/is.ppp.Rd | 10 man/is.rectangle.Rd | 10 man/is.stationary.Rd | 14 man/is.subset.owin.Rd | 10 man/istat.Rd | 10 man/kaplan.meier.Rd | 10 man/kernel.factor.Rd | 4 man/km.rs.Rd | 10 man/kppm.Rd | 15 man/latest.news.Rd | 10 man/layered.Rd | 10 man/layerplotargs.Rd | 10 man/layout.boxes.Rd | 10 man/lengths.psp.Rd | 10 man/letterR.Rd | 2 man/levelset.Rd | 10 man/leverage.ppm.Rd | 6 man/lgcp.estK.Rd | 8 man/lgcp.estpcf.Rd | 8 man/linearK.Rd | 6 man/linearKcross.Rd | 6 man/linearKcross.inhom.Rd | 6 man/linearKdot.Rd | 6 man/linearKdot.inhom.Rd | 6 man/linearKinhom.Rd | 6 man/lineardisc.Rd | 6 man/linearmarkconnect.Rd | 6 man/linearmarkequal.Rd | 6 man/linearpcf.Rd | 6 man/linearpcfcross.Rd | 6 man/linearpcfcross.inhom.Rd | 6 man/linearpcfdot.Rd | 6 man/linearpcfdot.inhom.Rd | 6 man/linearpcfinhom.Rd | 6 man/linfun.Rd | 10 man/linim.Rd | 6 man/linnet.Rd | 4 man/lixellate.Rd |only man/localK.Rd | 10 man/localKinhom.Rd | 10 man/localpcf.Rd | 10 man/logLik.dppm.Rd | 14 man/logLik.kppm.Rd | 14 man/logLik.mppm.Rd | 16 man/logLik.ppm.Rd | 38 man/logLik.slrm.Rd | 8 man/lohboot.Rd | 10 man/lpp.Rd | 4 man/lppm.Rd | 6 man/lurking.Rd | 10 man/lut.Rd | 10 man/markconnect.Rd | 10 man/markcorr.Rd | 10 man/markcrosscorr.Rd | 14 man/marks.Rd | 10 man/marks.psp.Rd | 10 man/marks.tess.Rd | 14 man/markstat.Rd | 10 man/marktable.Rd | 10 man/markvario.Rd | 10 man/matclust.estK.Rd | 6 man/matclust.estpcf.Rd | 6 man/maxnndist.Rd | 8 man/mean.im.Rd | 10 man/mergeLevels.Rd | 14 man/methods.box3.Rd | 10 man/methods.boxx.Rd | 10 man/methods.dppm.Rd | 6 man/methods.fii.Rd | 6 man/methods.funxy.Rd | 10 man/methods.kppm.Rd | 6 man/methods.layered.Rd | 10 man/methods.linfun.Rd | 21 man/methods.linim.Rd | 23 man/methods.linnet.Rd | 15 man/methods.lpp.Rd | 16 man/methods.lppm.Rd | 39 man/methods.objsurf.Rd | 8 man/methods.pp3.Rd | 10 man/methods.ppx.Rd | 10 man/methods.rho2hat.Rd | 6 man/methods.rhohat.Rd | 6 man/methods.slrm.Rd | 6 man/methods.units.Rd | 10 man/methods.zclustermodel.Rd |only man/midpoints.psp.Rd | 10 man/mincontrast.Rd | 6 man/miplot.Rd | 10 man/model.depends.Rd | 10 man/model.frame.ppm.Rd | 14 man/model.images.Rd | 14 man/model.matrix.ppm.Rd | 14 man/model.matrix.slrm.Rd | 10 man/moribund.Rd | 12 man/mppm.Rd | 14 man/msr.Rd | 6 man/multiplicity.ppp.Rd | 10 man/nearest.raster.point.Rd | 10 man/nearestsegment.Rd | 10 man/nestsplit.Rd | 14 man/nnclean.Rd | 2 man/nncorr.Rd | 10 man/nncross.Rd | 10 man/nncross.lpp.Rd | 30 man/nncross.pp3.Rd | 10 man/nndensity.Rd | 10 man/nndist.Rd | 6 man/nndist.lpp.Rd | 15 man/nndist.pp3.Rd | 6 man/nndist.ppx.Rd | 6 man/nndist.psp.Rd | 10 man/nnfun.Rd | 10 man/nnfun.lpp.Rd | 10 man/nnmap.Rd | 10 man/nnmark.Rd | 14 man/nnorient.Rd | 12 man/nnwhich.Rd | 6 man/nnwhich.lpp.Rd | 14 man/nnwhich.pp3.Rd | 6 man/nnwhich.ppx.Rd | 6 man/npfun.Rd | 8 man/npoints.Rd | 10 man/nsegments.Rd | 26 man/objsurf.Rd | 2 man/opening.Rd | 10 man/ord.family.Rd | 10 man/osteo.Rd | 2 man/overlap.owin.Rd | 10 man/owin.Rd | 10 man/owin.object.Rd | 10 man/padimage.Rd | 14 man/pairdist.Rd | 6 man/pairdist.default.Rd | 6 man/pairdist.lpp.Rd | 6 man/pairdist.pp3.Rd | 6 man/pairdist.ppp.Rd | 6 man/pairdist.ppx.Rd | 6 man/pairdist.psp.Rd | 10 man/pairorient.Rd | 12 man/pairs.im.Rd | 10 man/pairsat.family.Rd | 10 man/pairwise.family.Rd | 10 man/panel.contour.Rd | 14 man/parameters.Rd | 14 man/parres.Rd | 10 man/pcf.Rd | 10 man/pcf.fasp.Rd | 10 man/pcf.fv.Rd | 10 man/pcf.ppp.Rd | 10 man/pcf3est.Rd | 6 man/pcfcross.Rd | 10 man/pcfcross.inhom.Rd | 10 man/pcfdot.Rd | 10 man/pcfdot.inhom.Rd | 10 man/pcfinhom.Rd | 10 man/pcfmulti.Rd | 10 man/perimeter.Rd | 10 man/periodify.Rd | 10 man/persp.im.Rd | 14 man/perspPoints.Rd | 14 man/pixelcentres.Rd | 12 man/pixellate.Rd | 10 man/pixellate.owin.Rd | 10 man/pixellate.ppp.Rd | 10 man/pixellate.psp.Rd | 14 man/pixelquad.Rd | 10 man/plot.anylist.Rd | 14 man/plot.bermantest.Rd | 12 man/plot.cdftest.Rd | 10 man/plot.colourmap.Rd | 10 man/plot.dppm.Rd | 10 man/plot.envelope.Rd | 10 man/plot.fasp.Rd | 10 man/plot.fv.Rd | 10 man/plot.hyperframe.Rd | 10 man/plot.im.Rd | 10 man/plot.imlist.Rd | 14 man/plot.influence.ppm.Rd | 6 man/plot.kppm.Rd | 28 man/plot.layered.Rd | 10 man/plot.leverage.ppm.Rd | 6 man/plot.linim.Rd | 6 man/plot.linnet.Rd | 4 man/plot.listof.Rd | 10 man/plot.lpp.Rd | 10 man/plot.lppm.Rd | 6 man/plot.mppm.Rd | 16 man/plot.msr.Rd | 10 man/plot.onearrow.Rd | 14 man/plot.owin.Rd | 10 man/plot.plotppm.Rd | 10 man/plot.pp3.Rd | 14 man/plot.ppm.Rd | 10 man/plot.ppp.Rd | 10 man/plot.psp.Rd | 10 man/plot.quad.Rd | 10 man/plot.quadratcount.Rd | 10 man/plot.quadrattest.Rd | 10 man/plot.scan.test.Rd | 10 man/plot.slrm.Rd | 8 man/plot.solist.Rd | 14 man/plot.splitppp.Rd | 10 man/plot.symbolmap.Rd | 12 man/plot.tess.Rd | 10 man/plot.textstring.Rd | 14 man/plot.texturemap.Rd | 12 man/plot.yardstick.Rd | 14 man/pointsOnLines.Rd | 10 man/pool.Rd | 10 man/pool.anylist.Rd | 14 man/pool.envelope.Rd | 10 man/pool.fasp.Rd | 10 man/pool.fv.Rd | 14 man/pool.quadrattest.Rd | 10 man/pool.rat.Rd | 10 man/pp3.Rd | 10 man/ppm.Rd | 113 - man/ppm.object.Rd | 10 man/ppm.ppp.Rd | 94 man/ppp.Rd | 10 man/ppp.object.Rd | 10 man/ppx.Rd | 10 man/predict.dppm.Rd | 14 man/predict.kppm.Rd | 10 man/predict.lppm.Rd | 4 man/predict.mppm.Rd | 16 man/predict.ppm.Rd | 8 man/predict.slrm.Rd | 8 man/print.im.Rd | 10 man/print.owin.Rd | 10 man/print.ppm.Rd | 10 man/print.ppp.Rd | 10 man/print.psp.Rd | 10 man/print.quad.Rd | 10 man/profilepl.Rd | 10 man/progressreport.Rd | 14 man/project2segment.Rd | 10 man/project2set.Rd | 14 man/pseudoR2.Rd |only man/psp.Rd | 10 man/psp.object.Rd | 10 man/psst.Rd | 8 man/psstA.Rd | 8 man/psstG.Rd | 8 man/qqplot.ppm.Rd | 10 man/quad.object.Rd | 10 man/quad.ppm.Rd | 10 man/quadrat.test.Rd | 10 man/quadrat.test.mppm.Rd | 16 man/quadrat.test.splitppp.Rd | 10 man/quadratcount.Rd | 10 man/quadratresample.Rd | 10 man/quadrats.Rd | 10 man/quadscheme.Rd | 10 man/quadscheme.logi.Rd | 12 man/quantess.Rd | 14 man/quantile.density.Rd | 14 man/quantile.ewcdf.Rd | 10 man/quantile.im.Rd | 10 man/quasirandom.Rd | 12 man/rCauchy.Rd | 6 man/rDGS.Rd | 18 man/rDiggleGratton.Rd | 22 man/rGaussPoisson.Rd | 10 man/rHardcore.Rd | 16 man/rLGCP.Rd | 10 man/rMatClust.Rd | 10 man/rMaternI.Rd | 19 man/rMaternII.Rd | 21 man/rMosaicField.Rd | 10 man/rMosaicSet.Rd | 10 man/rNeymanScott.Rd | 10 man/rPenttinen.Rd |only man/rPoissonCluster.Rd | 10 man/rQuasi.Rd | 12 man/rSSI.Rd | 14 man/rStrauss.Rd | 16 man/rStraussHard.Rd | 21 man/rThomas.Rd | 10 man/rVarGamma.Rd | 6 man/ranef.mppm.Rd | 16 man/range.fv.Rd | 8 man/raster.x.Rd | 12 man/rat.Rd | 10 man/rcell.Rd | 10 man/rcellnumber.Rd | 10 man/rdpp.Rd | 14 man/reach.Rd | 10 man/reach.dppm.Rd | 14 man/reduced.sample.Rd | 10 man/redwood.Rd | 2 man/redwoodfull.Rd | 2 man/reflect.Rd | 10 man/relevel.im.Rd | 14 man/reload.or.compute.Rd | 10 man/relrisk.Rd | 14 man/relrisk.ppm.Rd | 14 man/relrisk.ppp.Rd | 10 man/rescale.Rd | 10 man/rescale.im.Rd | 10 man/rescale.owin.Rd | 10 man/rescale.ppp.Rd | 10 man/rescale.psp.Rd | 10 man/rescue.rectangle.Rd | 10 man/residuals.dppm.Rd | 14 man/residuals.kppm.Rd | 14 man/residuals.mppm.Rd | 16 man/residuals.ppm.Rd | 10 man/residualspaper.Rd | 4 man/rgbim.Rd | 10 man/rho2hat.Rd | 2 man/rhohat.Rd | 26 man/ripras.Rd | 10 man/rjitter.Rd | 10 man/rknn.Rd | 10 man/rlabel.Rd | 10 man/rlinegrid.Rd | 10 man/rmh.Rd | 10 man/rmh.default.Rd | 10 man/rmh.ppm.Rd | 10 man/rmhcontrol.Rd | 10 man/rmhexpand.Rd | 10 man/rmhmodel.Rd | 10 man/rmhmodel.default.Rd | 45 man/rmhmodel.list.Rd | 10 man/rmhmodel.ppm.Rd | 42 man/rmhstart.Rd | 10 man/rmpoint.Rd | 10 man/rmpoispp.Rd | 10 man/rnoise.Rd | 14 man/roc.Rd | 14 man/rose.Rd | 14 man/rotate.Rd | 10 man/rotate.im.Rd | 10 man/rotate.owin.Rd | 10 man/rotate.ppp.Rd | 10 man/rotate.psp.Rd | 10 man/rotmean.Rd | 14 man/round.ppp.Rd | 10 man/rounding.Rd | 10 man/rpoint.Rd | 10 man/rpoisline.Rd | 10 man/rpoislinetess.Rd | 10 man/rpoislpp.Rd | 4 man/rpoispp.Rd | 21 man/rpoispp3.Rd | 10 man/rpoisppOnLines.Rd | 24 man/rpoisppx.Rd | 10 man/rshift.Rd | 10 man/rshift.ppp.Rd | 10 man/rshift.psp.Rd | 10 man/rshift.splitppp.Rd | 10 man/rstrat.Rd | 10 man/rsyst.Rd | 10 man/rtemper.Rd | 14 man/rthin.Rd | 10 man/run.simplepanel.Rd | 10 man/runifdisc.Rd | 10 man/runiflpp.Rd | 4 man/runifpoint.Rd | 10 man/runifpoint3.Rd | 10 man/runifpointOnLines.Rd | 10 man/runifpointx.Rd | 10 man/scalardilate.Rd | 10 man/scaletointerval.Rd | 10 man/scan.test.Rd | 10 man/scanLRTS.Rd | 10 man/scanpp.Rd | 10 man/segregation.test.Rd | 14 man/selfcrossing.psp.Rd | 10 man/selfcut.psp.Rd | 14 man/sessionLibs.Rd | 10 man/setcov.Rd | 10 man/sharpen.Rd | 10 man/shift.Rd | 10 man/shift.im.Rd | 10 man/shift.owin.Rd | 10 man/shift.ppp.Rd | 10 man/shift.psp.Rd | 10 man/sidelengths.owin.Rd | 10 man/simba.Rd | 2 man/simplenet.Rd | 2 man/simplepanel.Rd | 10 man/simplify.owin.Rd | 10 man/simulate.dppm.Rd | 14 man/simulate.kppm.Rd | 10 man/simulate.lppm.Rd | 12 man/simulate.ppm.Rd | 10 man/simulate.slrm.Rd | 10 man/slrm.Rd | 8 man/solapply.Rd | 14 man/solist.Rd | 14 man/solutionset.Rd | 10 man/spatdim.Rd | 14 man/spatialcdf.Rd | 14 man/spatstat-internal.Rd | 59 man/spatstat-package.Rd | 29 man/spatstat.options.Rd | 12 man/split.hyperframe.Rd | 12 man/split.im.Rd | 10 man/split.ppp.Rd | 10 man/split.ppx.Rd | 10 man/spokes.Rd | 10 man/square.Rd | 10 man/stieltjes.Rd | 10 man/stienen.Rd | 14 man/stratrand.Rd | 10 man/studpermu.test.Rd | 14 man/subfits.Rd | 16 man/subset.hyperframe.Rd | 14 man/subset.ppp.Rd | 14 man/suffstat.Rd | 14 man/summary.anylist.Rd | 10 man/summary.im.Rd | 10 man/summary.kppm.Rd | 10 man/summary.listof.Rd | 10 man/summary.owin.Rd | 10 man/summary.ppm.Rd | 10 man/summary.ppp.Rd | 10 man/summary.psp.Rd | 10 man/summary.quad.Rd | 10 man/summary.solist.Rd | 14 man/summary.splitppp.Rd | 10 man/sumouter.Rd | 10 man/superimpose.Rd | 10 man/superimpose.lpp.Rd | 14 man/symbolmap.Rd | 12 man/tess.Rd | 14 man/texturemap.Rd | 12 man/textureplot.Rd | 14 man/thomas.estK.Rd | 11 man/thomas.estpcf.Rd | 8 man/tile.areas.Rd | 14 man/tilenames.Rd | 10 man/tiles.Rd | 13 man/tiles.empty.Rd |only man/timed.Rd | 10 man/transect.im.Rd | 10 man/transmat.Rd | 14 man/treebranchlabels.Rd | 14 man/treeprune.Rd | 14 man/triangulate.owin.Rd | 21 man/trim.rectangle.Rd | 10 man/triplet.family.Rd | 10 man/tweak.colourmap.Rd | 10 man/union.quad.Rd | 10 man/unique.ppp.Rd | 10 man/unitname.Rd | 10 man/unmark.Rd | 10 man/unnormdensity.Rd | 10 man/update.detpointprocfamily.Rd | 14 man/update.kppm.Rd | 14 man/update.ppm.Rd | 10 man/update.rmhcontrol.Rd | 10 man/update.symbolmap.Rd | 12 man/valid.Rd | 14 man/valid.detpointprocfamily.Rd | 14 man/valid.ppm.Rd | 10 man/varblock.Rd | 10 man/varcount.Rd |only man/vargamma.estK.Rd | 6 man/vargamma.estpcf.Rd | 6 man/vcov.kppm.Rd | 6 man/vcov.mppm.Rd | 16 man/vcov.ppm.Rd | 12 man/vcov.slrm.Rd | 6 man/vertices.Rd | 10 man/volume.Rd | 14 man/whist.Rd | 10 man/will.expand.Rd | 10 man/with.fv.Rd | 10 man/with.hyperframe.Rd | 10 man/with.msr.Rd | 14 man/yardstick.Rd | 14 man/zapsmall.im.Rd | 8 man/zclustermodel.Rd |only src/Perfect.cc | 2 src/PerfectPenttinen.h |only src/closefuns.h | 18 src/constants.h | 7 src/fastinterv.c |only src/getcif.c | 4 src/linSnncross.c |only src/linSnncross.h |only src/linequad.c |only src/linknnd.c |only src/linnncross.h | 4 src/linvdist.c |only src/linvdist.h |only src/linvknndist.c |only src/lixel.c |only src/penttinen.c |only tests/alltests.R | 118 + vignettes/packagesizes.txt | 1 vignettes/updates.Rnw | 3752 ++++----------------------------------- 1159 files changed, 11974 insertions(+), 15844 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 1.0.1 dated 2015-11-30 and 1.0.2 dated 2015-12-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 2 ++ R/cov.R | 33 ++++++++++++++++----------------- 4 files changed, 25 insertions(+), 24 deletions(-)
Title: Access for Dryad Web Services
Description: Interface to the Dryad Solr API, their OAI-PMH service, and
fetch datasets.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rdryad versions 0.1.1 dated 2013-01-30 and 0.2.0 dated 2015-12-23
rdryad-0.1.1/rdryad/R/download_dryadmetadata.r |only rdryad-0.1.1/rdryad/R/dryad_getfile.r |only rdryad-0.1.1/rdryad/R/getalldryad_metadata.r |only rdryad-0.1.1/rdryad/R/search_dryad.r |only rdryad-0.1.1/rdryad/R/totimp.r |only rdryad-0.1.1/rdryad/R/totimp_dryad.r |only rdryad-0.1.1/rdryad/man/dr_listidentifiers.Rd |only rdryad-0.1.1/rdryad/man/dr_listmetadataformats.Rd |only rdryad-0.1.1/rdryad/man/dr_listsets.Rd |only rdryad-0.1.1/rdryad/man/dryad_getfile.Rd |only rdryad-0.1.1/rdryad/man/totimp.Rd |only rdryad-0.1.1/rdryad/man/totimp_dryad.Rd |only rdryad-0.2.0/rdryad/DESCRIPTION | 39 ++- rdryad-0.2.0/rdryad/LICENSE |only rdryad-0.2.0/rdryad/MD5 | 69 ++++-- rdryad-0.2.0/rdryad/NAMESPACE | 51 +++-- rdryad-0.2.0/rdryad/NEWS | 26 ++ rdryad-0.2.0/rdryad/R/defunct.R |only rdryad-0.2.0/rdryad/R/download_url.r | 39 +-- rdryad-0.2.0/rdryad/R/dr_get_records.R |only rdryad-0.2.0/rdryad/R/dr_identify.r | 14 - rdryad-0.2.0/rdryad/R/dr_list_records.R |only rdryad-0.2.0/rdryad/R/dr_listidentifiers.r | 54 +---- rdryad-0.2.0/rdryad/R/dr_listmetadataformats.r | 14 - rdryad-0.2.0/rdryad/R/dr_listsets.r | 28 +- rdryad-0.2.0/rdryad/R/dryad_fetch.R |only rdryad-0.2.0/rdryad/R/dryad_solr.r |only rdryad-0.2.0/rdryad/R/rdryad-package.R |only rdryad-0.2.0/rdryad/R/zzz.R |only rdryad-0.2.0/rdryad/README.md | 204 ++++++++++++++++++-- rdryad-0.2.0/rdryad/inst |only rdryad-0.2.0/rdryad/man/d_solr_search.Rd |only rdryad-0.2.0/rdryad/man/download_dryadmetadata.Rd | 30 -- rdryad-0.2.0/rdryad/man/download_url.Rd | 19 - rdryad-0.2.0/rdryad/man/dr_get_records.Rd |only rdryad-0.2.0/rdryad/man/dr_identify.Rd | 11 - rdryad-0.2.0/rdryad/man/dr_list_identifiers.Rd |only rdryad-0.2.0/rdryad/man/dr_list_metadata_formats.Rd |only rdryad-0.2.0/rdryad/man/dr_list_records.Rd |only rdryad-0.2.0/rdryad/man/dr_list_sets.Rd |only rdryad-0.2.0/rdryad/man/dryad_fetch.Rd |only rdryad-0.2.0/rdryad/man/getalldryad_metadata.Rd | 33 --- rdryad-0.2.0/rdryad/man/rdryad-package.Rd |only rdryad-0.2.0/rdryad/man/search_dryad.Rd | 64 ------ rdryad-0.2.0/rdryad/tests |only 45 files changed, 407 insertions(+), 288 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g., http://en.wikipedia.org/
wiki/GitHub#Gist, https://help.github.com/articles/about-gists/). A 'gist'
is simply one or more files with code/text/images/etc. This package allows
the user to create new 'gists', update 'gists' with new files, rename files,
delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists',
open a 'gist' in your default browser, get embed code for a 'gist', list
'gist' 'commits', and get rate limit information when 'authenticated'. Some
requests require authentication and some do not. 'Gists' website: https://
gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.3.4 dated 2015-10-09 and 0.3.6 dated 2015-12-23
DESCRIPTION | 29 +++++++++--------- MD5 | 72 ++++++++++++++++++++++----------------------- NAMESPACE | 2 - R/gist.R | 10 ++---- R/gist_create.R | 2 - R/gist_map.R | 2 - R/gistr-package.R | 8 +++++ R/tabl.R | 3 - R/update.R | 4 +- R/utils.R | 1 R/zzz.R | 14 ++++---- build/vignette.rds |binary man/browse.Rd | 2 - man/commits.Rd | 2 - man/create_gists.Rd | 22 ++++++------- man/delete.Rd | 2 - man/embed.Rd | 2 - man/files.Rd | 2 - man/fork.Rd | 2 - man/forks.Rd | 4 +- man/gist.Rd | 10 +++--- man/gist_auth.Rd | 2 - man/gist_create.Rd | 10 +++--- man/gist_create_git.Rd | 38 +++++++++++------------ man/gist_create_obj.Rd | 2 - man/gist_map.Rd | 4 +- man/gist_save.Rd | 14 ++++---- man/gistr-package.Rd | 2 - man/gists.Rd | 2 - man/pipe.Rd | 2 - man/rate_limit.Rd | 2 - man/run.Rd | 2 - man/star.Rd | 4 +- man/tabl.Rd | 19 +++++------ man/update.Rd | 4 +- tests/testthat/test-fork.R | 2 - tests/testthat/test-gist.R | 14 +++++++- 37 files changed, 163 insertions(+), 155 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.5 dated 2015-11-12 and 4.6 dated 2015-12-23
ftsa-4.5/ftsa/R/DataPostProc.r |only ftsa-4.5/ftsa/R/L1median2.r |only ftsa-4.5/ftsa/R/MISE.r |only ftsa-4.5/ftsa/R/ParseControlStructure.r |only ftsa-4.5/ftsa/R/ParseDevString.r |only ftsa-4.5/ftsa/R/Qn.r |only ftsa-4.5/ftsa/R/ScaleAdv.r |only ftsa-4.5/ftsa/R/aveISFE.r |only ftsa-4.5/ftsa/R/colQn.r |only ftsa-4.5/ftsa/R/hossjercroux.r |only ftsa-4.5/ftsa/R/hyman.filter.r |only ftsa-4.5/ftsa/R/isfe.fts.r |only ftsa-4.5/ftsa/R/loadSgnU.r |only ftsa-4.5/ftsa/R/matrix.rank.r |only ftsa-4.5/ftsa/R/metri.p.r |only ftsa-4.5/ftsa/R/mrobj.r |only ftsa-4.5/ftsa/R/nicerange.r |only ftsa-4.5/ftsa/R/norm.r |only ftsa-4.5/ftsa/R/norme.r |only ftsa-4.5/ftsa/R/pegelsna.r |only ftsa-4.5/ftsa/R/rapca.r |only ftsa-4.5/ftsa/R/repmat.r |only ftsa-4.5/ftsa/R/rstep.r |only ftsa-4.5/ftsa/R/rw.drift.r |only ftsa-4.5/ftsa/R/spl.coef.conv.r |only ftsa-4.5/ftsa/R/struct.forecast.r |only ftsa-4.6/ftsa/ChangeLog | 5 ftsa-4.6/ftsa/DESCRIPTION | 12 ftsa-4.6/ftsa/MD5 | 78 ftsa-4.6/ftsa/R/DataPostProc.R |only ftsa-4.6/ftsa/R/L1median2.R |only ftsa-4.6/ftsa/R/MISE.R |only ftsa-4.6/ftsa/R/ParseControlStructure.R |only ftsa-4.6/ftsa/R/ParseDevString.R |only ftsa-4.6/ftsa/R/Qn.R |only ftsa-4.6/ftsa/R/ScaleAdv.R |only ftsa-4.6/ftsa/R/T_stationary.R | 99 ftsa-4.6/ftsa/R/aveISFE.R |only ftsa-4.6/ftsa/R/colQn.R |only ftsa-4.6/ftsa/R/hossjercroux.R |only ftsa-4.6/ftsa/R/hyman.filter.R |only ftsa-4.6/ftsa/R/isfe.fts.R |only ftsa-4.6/ftsa/R/loadSgnU.R |only ftsa-4.6/ftsa/R/matrix.rank.R |only ftsa-4.6/ftsa/R/metri.p.R |only ftsa-4.6/ftsa/R/mrobj.R |only ftsa-4.6/ftsa/R/nicerange.R |only ftsa-4.6/ftsa/R/norm.R |only ftsa-4.6/ftsa/R/norme.R |only ftsa-4.6/ftsa/R/pegelsna.R |only ftsa-4.6/ftsa/R/rapca.R |only ftsa-4.6/ftsa/R/repmat.R |only ftsa-4.6/ftsa/R/rstep.R |only ftsa-4.6/ftsa/R/rw.drift.R |only ftsa-4.6/ftsa/R/spl.coef.conv.R |only ftsa-4.6/ftsa/R/struct.forecast.R |only ftsa-4.6/ftsa/build/vignette.rds |binary ftsa-4.6/ftsa/inst/doc/ftsa.R | 6 ftsa-4.6/ftsa/inst/doc/ftsa.Rnw | 26 ftsa-4.6/ftsa/inst/doc/ftsa.pdf |binary ftsa-4.6/ftsa/man/T_stationary.Rd | 22 ftsa-4.6/ftsa/man/farforecast.Rd | 9 ftsa-4.6/ftsa/man/ftsa-package.Rd | 2 ftsa-4.6/ftsa/man/pcscorebootstrapdata.Rd | 10 ftsa-4.6/ftsa/vignettes/ftsa.Rnw | 26 ftsa-4.6/ftsa/vignettes/master.bib |10322 +++++++++++++++--------------- 66 files changed, 5322 insertions(+), 5295 deletions(-)
Title: An R Package for Data Reduction by Battery Reduction
Description: Battery reduction is a method used in data reduction. It uses Gram-Schmidt orthogonal rotations to find out a subset of variables best representing the original set of variables.
Author: Chunqiao Luo [aut, cre],
Ralph D'Agostino [aut] (This package is derived from Battery Reduction
Macro at http://www.lexjansen.com/nesug/nesug92/NESUG92090.pdf)
Maintainer: Chunqiao Luo <chunqiaoluo@gmail.com>
Diff between batteryreduction versions 0.1.0 dated 2015-10-12 and 0.1.1 dated 2015-12-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/batteryreduction.R | 2 +- man/batteryreduction.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
More information about batteryreduction at CRAN
Permanent link
More information about weathermetrics at CRAN
Permanent link
Title: R Client for the COLOURlovers API
Description: Provides access to the COLOURlovers <http://www.colourlovers.com/> API, which offers color inspiration and color palettes.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between colourlovers versions 0.1.4 dated 2014-12-20 and 0.2.0 dated 2015-12-22
colourlovers-0.1.4/colourlovers/R/clquery.r |only colourlovers-0.2.0/colourlovers/DESCRIPTION | 15 - colourlovers-0.2.0/colourlovers/MD5 | 24 - colourlovers-0.2.0/colourlovers/NAMESPACE | 11 colourlovers-0.2.0/colourlovers/NEWS | 9 colourlovers-0.2.0/colourlovers/R/clQuery.r |only colourlovers-0.2.0/colourlovers/R/clcolors.r | 6 colourlovers-0.2.0/colourlovers/R/cllovers.r | 4 colourlovers-0.2.0/colourlovers/R/clpalettes.r | 4 colourlovers-0.2.0/colourlovers/R/clpatterns.r | 4 colourlovers-0.2.0/colourlovers/R/clstats.r | 6 colourlovers-0.2.0/colourlovers/README.md | 369 ++++++++++++++++--------- colourlovers-0.2.0/colourlovers/man/swatch.Rd | 6 colourlovers-0.2.0/colourlovers/tests |only 14 files changed, 293 insertions(+), 165 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between plotROC versions 1.3.3 dated 2015-03-16 and 2.0.0 dated 2015-12-22
plotROC-1.3.3/plotROC/R/ggroc.R |only plotROC-1.3.3/plotROC/R/modCss.R |only plotROC-1.3.3/plotROC/R/modJs.R |only plotROC-1.3.3/plotROC/R/plot_journal_roc.R |only plotROC-1.3.3/plotROC/inst/shinyApp/shinyapps |only plotROC-1.3.3/plotROC/man/modCss.Rd |only plotROC-1.3.3/plotROC/man/modJs.Rd |only plotROC-1.3.3/plotROC/man/plotROC-package.Rd |only plotROC-2.0.0/plotROC/DESCRIPTION | 15 plotROC-2.0.0/plotROC/MD5 | 79 plotROC-2.0.0/plotROC/NAMESPACE | 37 plotROC-2.0.0/plotROC/NEWS | 11 plotROC-2.0.0/plotROC/R/calculate_roc.R | 146 + plotROC-2.0.0/plotROC/R/deprecated.R |only plotROC-2.0.0/plotROC/R/geom_roc.R |only plotROC-2.0.0/plotROC/R/geom_rocci.R |only plotROC-2.0.0/plotROC/R/getD3.R | 10 plotROC-2.0.0/plotROC/R/interactive_roc.R | 151 - plotROC-2.0.0/plotROC/R/plotROC-package.R |only plotROC-2.0.0/plotROC/R/style_roc.R |only plotROC-2.0.0/plotROC/README.md |only plotROC-2.0.0/plotROC/build/vignette.rds |binary plotROC-2.0.0/plotROC/inst/clickCis.js |only plotROC-2.0.0/plotROC/inst/d3.v3.min.js | 10 plotROC-2.0.0/plotROC/inst/doc/examples.R | 172 + plotROC-2.0.0/plotROC/inst/doc/examples.Rmd | 239 +- plotROC-2.0.0/plotROC/inst/doc/examples.html | 1806 ++++++++++---------- plotROC-2.0.0/plotROC/inst/hoverPoints.js |only plotROC-2.0.0/plotROC/inst/shinyApp/help.html | 18 plotROC-2.0.0/plotROC/inst/shinyApp/help.md | 2 plotROC-2.0.0/plotROC/inst/shinyApp/server.R | 82 plotROC-2.0.0/plotROC/inst/shinyApp/ui.R | 19 plotROC-2.0.0/plotROC/man/calc_auc.Rd |only plotROC-2.0.0/plotROC/man/calculate_multi_roc.Rd | 12 plotROC-2.0.0/plotROC/man/calculate_roc.Rd | 17 plotROC-2.0.0/plotROC/man/direct_label.Rd |only plotROC-2.0.0/plotROC/man/export_interactive_roc.Rd | 58 plotROC-2.0.0/plotROC/man/geom_roc.Rd |only plotROC-2.0.0/plotROC/man/geom_rocci.Rd |only plotROC-2.0.0/plotROC/man/getD3.Rd |only plotROC-2.0.0/plotROC/man/ggroc.Rd | 22 plotROC-2.0.0/plotROC/man/melt_roc.Rd |only plotROC-2.0.0/plotROC/man/multi_ggroc.Rd | 22 plotROC-2.0.0/plotROC/man/plotROC.Rd |only plotROC-2.0.0/plotROC/man/plot_interactive_roc.Rd | 2 plotROC-2.0.0/plotROC/man/plot_journal_roc.Rd | 24 plotROC-2.0.0/plotROC/man/shiny_plotROC.Rd | 2 plotROC-2.0.0/plotROC/man/stat_roc.Rd |only plotROC-2.0.0/plotROC/man/stat_rocci.Rd |only plotROC-2.0.0/plotROC/man/style_roc.Rd |only plotROC-2.0.0/plotROC/man/verify_d.Rd | 6 plotROC-2.0.0/plotROC/tests/testthat/Rplots.pdf |only plotROC-2.0.0/plotROC/tests/testthat/test-calc.R | 28 plotROC-2.0.0/plotROC/vignettes/examples.Rmd | 239 +- 54 files changed, 1864 insertions(+), 1365 deletions(-)
Title: Datasets for 'Statistics: Unlocking the Power of Data'
Description: Data sets and other utilities for
'Statistics: Unlocking the Power of Data'
by Lock, Lock, Lock, Lock and Lock
(ISBN : 978-0-470-60187-7, http://lock5stat.com/).
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between Lock5withR versions 1.2.0 dated 2015-12-18 and 1.2.2 dated 2015-12-22
Lock5withR-1.2.0/Lock5withR/data/AllCountries.R |only Lock5withR-1.2.0/Lock5withR/data/AtmosphericCO2.R |only Lock5withR-1.2.0/Lock5withR/data/BikeCommute.R |only Lock5withR-1.2.0/Lock5withR/data/BodyTemp50.R |only Lock5withR-1.2.0/Lock5withR/data/CaffeineTaps.R |only Lock5withR-1.2.0/Lock5withR/data/EmployedACS.R |only Lock5withR-1.2.0/Lock5withR/data/Flight179.R |only Lock5withR-1.2.0/Lock5withR/data/GPAGender.R |only Lock5withR-1.2.0/Lock5withR/data/ICUAdmissions.R |only Lock5withR-1.2.0/Lock5withR/data/MiamiHeat.R |only Lock5withR-1.2.0/Lock5withR/data/MindsetMatters.R |only Lock5withR-1.2.0/Lock5withR/data/NFLScores2011.R |only Lock5withR-1.2.0/Lock5withR/data/NutritionStudy.R |only Lock5withR-1.2.0/Lock5withR/data/RestaurantTips.R |only Lock5withR-1.2.0/Lock5withR/data/RetailSales.R |only Lock5withR-1.2.0/Lock5withR/data/SalaryGender.R |only Lock5withR-1.2.0/Lock5withR/data/SampCountries.R |only Lock5withR-1.2.0/Lock5withR/data/SandP500.R |only Lock5withR-1.2.0/Lock5withR/data/SleepStudy.R |only Lock5withR-1.2.0/Lock5withR/data/SpeedDating.R |only Lock5withR-1.2.0/Lock5withR/data/StudentSurvey.R |only Lock5withR-1.2.0/Lock5withR/data/USStates.R |only Lock5withR-1.2.0/Lock5withR/data/WaterTaste.R |only Lock5withR-1.2.0/Lock5withR/data/Wetsuits.R |only Lock5withR-1.2.2/Lock5withR/DESCRIPTION | 16 Lock5withR-1.2.2/Lock5withR/MD5 | 218 +++++------- Lock5withR-1.2.2/Lock5withR/data/ACS.rda |binary Lock5withR-1.2.2/Lock5withR/data/APMultipleChoice.rda |binary Lock5withR-1.2.2/Lock5withR/data/AllCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/April14Temps.rda |binary Lock5withR-1.2.2/Lock5withR/data/AtmosphericCO2.rda |binary Lock5withR-1.2.2/Lock5withR/data/BaseballHits.rda |binary Lock5withR-1.2.2/Lock5withR/data/BaseballTimes.rda |binary Lock5withR-1.2.2/Lock5withR/data/Benford.rda |binary Lock5withR-1.2.2/Lock5withR/data/BikeCommute.rda |binary Lock5withR-1.2.2/Lock5withR/data/BodyFat.rda |binary Lock5withR-1.2.2/Lock5withR/data/BodyTemp50.rda |binary Lock5withR-1.2.2/Lock5withR/data/BootAtlantaCorr.rda |binary Lock5withR-1.2.2/Lock5withR/data/CAOSExam.rda |binary Lock5withR-1.2.2/Lock5withR/data/CaffeineTaps.rda |binary Lock5withR-1.2.2/Lock5withR/data/Cereal.rda |binary Lock5withR-1.2.2/Lock5withR/data/CocaineTreatment.rda |binary Lock5withR-1.2.2/Lock5withR/data/ColaCalcium.rda |binary Lock5withR-1.2.2/Lock5withR/data/CommuteAtlanta.rda |binary Lock5withR-1.2.2/Lock5withR/data/CommuteStLouis.rda |binary Lock5withR-1.2.2/Lock5withR/data/CompassionateRats.rda |binary Lock5withR-1.2.2/Lock5withR/data/CricketChirps.rda |binary Lock5withR-1.2.2/Lock5withR/data/Digits.rda |binary Lock5withR-1.2.2/Lock5withR/data/DogOwner.rda |binary Lock5withR-1.2.2/Lock5withR/data/ElectionMargin.rda |binary Lock5withR-1.2.2/Lock5withR/data/EmployedACS.rda |binary Lock5withR-1.2.2/Lock5withR/data/ExerciseHours.rda |binary Lock5withR-1.2.2/Lock5withR/data/FacebookFriends.rda |binary Lock5withR-1.2.2/Lock5withR/data/FatMice18.rda |binary Lock5withR-1.2.2/Lock5withR/data/FishGills12.rda |binary Lock5withR-1.2.2/Lock5withR/data/FishGills3.rda |binary Lock5withR-1.2.2/Lock5withR/data/Flight179.rda |binary Lock5withR-1.2.2/Lock5withR/data/FloridaLakes.rda |binary Lock5withR-1.2.2/Lock5withR/data/GPAGender.rda |binary Lock5withR-1.2.2/Lock5withR/data/GlobalInternet.rda |binary Lock5withR-1.2.2/Lock5withR/data/HappyPlanetIndex.rda |binary Lock5withR-1.2.2/Lock5withR/data/HockeyPenalties.rda |binary Lock5withR-1.2.2/Lock5withR/data/HollywoodMovies2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSale.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleCA.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleCanton.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleNY.rda |binary Lock5withR-1.2.2/Lock5withR/data/HoneybeeCircuits.rda |binary Lock5withR-1.2.2/Lock5withR/data/HoneybeeWaggle.rda |binary Lock5withR-1.2.2/Lock5withR/data/HotDogs.rda |binary Lock5withR-1.2.2/Lock5withR/data/ICUAdmissions.rda |binary Lock5withR-1.2.2/Lock5withR/data/ImmuneTea.rda |binary Lock5withR-1.2.2/Lock5withR/data/InkjetPrinters.rda |binary Lock5withR-1.2.2/Lock5withR/data/LifeExpectancyVehicles.rda |binary Lock5withR-1.2.2/Lock5withR/data/LightatNight.rda |binary Lock5withR-1.2.2/Lock5withR/data/MalevolentUniformsNFL.rda |binary Lock5withR-1.2.2/Lock5withR/data/MalevolentUniformsNHL.rda |binary Lock5withR-1.2.2/Lock5withR/data/MammalLongevity.rda |binary Lock5withR-1.2.2/Lock5withR/data/ManhattanApartments.rda |binary Lock5withR-1.2.2/Lock5withR/data/MarriageAges.rda |binary Lock5withR-1.2.2/Lock5withR/data/MastersGolf.rda |binary Lock5withR-1.2.2/Lock5withR/data/MentalMuscle.rda |binary Lock5withR-1.2.2/Lock5withR/data/MiamiHeat.rda |binary Lock5withR-1.2.2/Lock5withR/data/MindsetMatters.rda |binary Lock5withR-1.2.2/Lock5withR/data/MinistersRum.rda |binary Lock5withR-1.2.2/Lock5withR/data/MustangPrice.rda |binary Lock5withR-1.2.2/Lock5withR/data/NBAPlayers2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/NBAStandings.rda |binary Lock5withR-1.2.2/Lock5withR/data/NFLScores2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/NutritionStudy.rda |binary Lock5withR-1.2.2/Lock5withR/data/OlympicMarathon.rda |binary Lock5withR-1.2.2/Lock5withR/data/OttawaSenators.rda |binary Lock5withR-1.2.2/Lock5withR/data/PizzaGirl.rda |binary Lock5withR-1.2.2/Lock5withR/data/QuizPulse10.rda |binary Lock5withR-1.2.2/Lock5withR/data/RandomP50N200.rda |binary Lock5withR-1.2.2/Lock5withR/data/RestaurantTips.rda |binary Lock5withR-1.2.2/Lock5withR/data/RetailSales.rda |binary Lock5withR-1.2.2/Lock5withR/data/RockandRoll.rda |binary Lock5withR-1.2.2/Lock5withR/data/SalaryGender.rda |binary Lock5withR-1.2.2/Lock5withR/data/SampCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandP500.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandwichAnts.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandwichAnts2.rda |binary Lock5withR-1.2.2/Lock5withR/data/SkateboardPrices.rda |binary Lock5withR-1.2.2/Lock5withR/data/SleepCaffeine.rda |binary Lock5withR-1.2.2/Lock5withR/data/SleepStudy.rda |binary Lock5withR-1.2.2/Lock5withR/data/Smiles.rda |binary Lock5withR-1.2.2/Lock5withR/data/SpeedDating.rda |binary Lock5withR-1.2.2/Lock5withR/data/StatGrades.rda |binary Lock5withR-1.2.2/Lock5withR/data/StatisticsPhD.rda |binary Lock5withR-1.2.2/Lock5withR/data/StockChanges.rda |binary Lock5withR-1.2.2/Lock5withR/data/StorySpoilers.rda |binary Lock5withR-1.2.2/Lock5withR/data/StressedMice.rda |binary Lock5withR-1.2.2/Lock5withR/data/StudentSurvey.rda |binary Lock5withR-1.2.2/Lock5withR/data/TenCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/TextbookCosts.rda |binary Lock5withR-1.2.2/Lock5withR/data/ToenailArsenic.rda |binary Lock5withR-1.2.2/Lock5withR/data/TrafficFlow.rda |binary Lock5withR-1.2.2/Lock5withR/data/USStates.rda |binary Lock5withR-1.2.2/Lock5withR/data/WaterStriders.rda |binary Lock5withR-1.2.2/Lock5withR/data/WaterTaste.rda |binary Lock5withR-1.2.2/Lock5withR/data/Wetsuits.rda |binary 122 files changed, 106 insertions(+), 128 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove <sabanesd@roche.com>,
Wai Yin Yeung <w.yeung1@lancaster.ac.uk>,
Giuseppe Palermo <giuseppe.palermo@roche.com>,
Thomas Jaki <jaki.thomas@gmail.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between crmPack versions 0.1.5 dated 2015-11-12 and 0.1.6 dated 2015-12-22
crmPack-0.1.5/crmPack/man/StoppingGstarsamplesCIRatio-class.Rd |only crmPack-0.1.5/crmPack/man/StoppingGstarsamplesCIRatio.Rd |only crmPack-0.1.5/crmPack/man/StoppingTDsamplesCIRatio-class.Rd |only crmPack-0.1.5/crmPack/man/StoppingTDsamplesCIRatio.Rd |only crmPack-0.1.6/crmPack/DESCRIPTION | 6 crmPack-0.1.6/crmPack/MD5 | 78 ++-- crmPack-0.1.6/crmPack/NAMESPACE | 10 crmPack-0.1.6/crmPack/R/Data-class.R | 76 +++ crmPack-0.1.6/crmPack/R/Data-methods.R | 4 crmPack-0.1.6/crmPack/R/Design-methods.R | 10 crmPack-0.1.6/crmPack/R/Model-class.R | 193 ++++++++-- crmPack-0.1.6/crmPack/R/Rules-class.R | 121 +----- crmPack-0.1.6/crmPack/R/Rules-methods.R | 35 + crmPack-0.1.6/crmPack/R/Simulations-methods.R | 18 crmPack-0.1.6/crmPack/R/crmPack-package.R | 5 crmPack-0.1.6/crmPack/R/fromQuantiles.R | 11 crmPack-0.1.6/crmPack/R/mcmc.R | 14 crmPack-0.1.6/crmPack/inst/NEWS | 28 + crmPack-0.1.6/crmPack/inst/doc/example.R | 27 - crmPack-0.1.6/crmPack/inst/doc/example.Rnw | 54 +- crmPack-0.1.6/crmPack/inst/doc/example.pdf |binary crmPack-0.1.6/crmPack/man/AllModels-class.Rd | 4 crmPack-0.1.6/crmPack/man/DataMixture-class.Rd |only crmPack-0.1.6/crmPack/man/DataMixture.Rd |only crmPack-0.1.6/crmPack/man/LogisticLogNormalMixture-class.Rd |only crmPack-0.1.6/crmPack/man/LogisticLogNormalMixture.Rd |only crmPack-0.1.6/crmPack/man/MinimalInformative.Rd | 4 crmPack-0.1.6/crmPack/man/Quantiles2LogisticNormal.Rd | 8 crmPack-0.1.6/crmPack/man/Stopping-class.Rd | 3 crmPack-0.1.6/crmPack/man/StoppingHighestDose-class.Rd |only crmPack-0.1.6/crmPack/man/StoppingHighestDose.Rd |only crmPack-0.1.6/crmPack/man/examine.Rd | 2 crmPack-0.1.6/crmPack/man/mcmc.Rd | 6 crmPack-0.1.6/crmPack/man/plot-DualSimulations-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-DualSimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-GeneralSimulations-missing-method.Rd | 98 ----- crmPack-0.1.6/crmPack/man/plot-GeneralSimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-PseudoDualFlexiSimulations-missing-method.Rd | 4 crmPack-0.1.6/crmPack/man/plot-PseudoDualSimulations-missing-method.Rd | 4 crmPack-0.1.6/crmPack/man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 72 +-- crmPack-0.1.6/crmPack/man/plot-PseudoSimulationsSummary-missing-method.Rd | 30 - crmPack-0.1.6/crmPack/man/plot-SimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/show-DualSimulationsSummary-method.Rd | 2 crmPack-0.1.6/crmPack/man/stopTrial.Rd | 101 ++++- crmPack-0.1.6/crmPack/vignettes/example.Rnw | 54 +- 45 files changed, 651 insertions(+), 439 deletions(-)
Title: Time-Course Gene Set Analysis
Description: Implementation of TcGSA, a method for analyzing longitudinal
gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre],
Damien Chimits [aut]
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>
Diff between TcGSA versions 0.9.8 dated 2014-04-28 and 0.10.1 dated 2015-12-22
DESCRIPTION | 34 +- LICENSE | 495 +++++++++++++++++++++---------- MD5 | 82 ++--- NAMESPACE | 86 ++++- R/MYheatmap.2.R | 742 +++++++++++++++++++++++------------------------ R/STSdist.R | 5 R/TcGSA-internal.R | 6 R/TcGSA-package.R | 10 R/TcGSA.LR.R | 74 ++-- R/TcGSA.LR.parallel.R | 248 ++++++++------- R/TcGSA.dataLME.R | 16 - R/TcGSA.formula.R | 129 ++++---- R/clustTrend.R | 62 ++- R/multtest.TcGSA.R | 10 R/plot.TcGSA.R | 639 +++++++++++++++++++++------------------- R/plot1GS.R | 286 ++++++++++++------ R/plotFit.GS.R | 30 + R/plotPat.1GS.R | 47 +- R/plotPat.TcGSA.R | 34 +- R/plotSelect.GS.R | 40 +- R/pval_simu.R | 8 R/rmixchisq.R | 9 R/signifLRT.TcGSA.R | 13 R/summary.TcGSA.R | 13 README | 39 +- inst/CITATION | 30 + man/TcGSA-internal.Rd | 8 man/TcGSA-package.Rd | 33 +- man/TcGSA.LR.Rd | 268 +++++++--------- man/TcGSA.LR.parallel.Rd | 294 ++++++++---------- man/clustTrend.Rd | 373 ++++++++++------------- man/multtest.TcGSA.Rd | 77 ++-- man/plot.TcGSA.Rd | 624 +++++++++++++++++---------------------- man/plot1GS.Rd | 483 ++++++++++++++---------------- man/plotFit.GS.Rd | 141 +++----- man/plotPat.1GS.Rd | 424 +++++++++++--------------- man/plotPat.TcGSA.Rd | 592 ++++++++++++++++--------------------- man/plotSelect.GS.Rd | 437 ++++++++++++--------------- man/pval_simu.Rd | 20 - man/rmixchisq.Rd | 65 ++-- man/signifLRT.TcGSA.Rd | 118 +++---- man/summary.TcGSA.Rd | 36 +- 42 files changed, 3676 insertions(+), 3504 deletions(-)
Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between simsalapar versions 1.0-6 dated 2015-12-14 and 1.0-7 dated 2015-12-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/varlist.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Beta-Diversity of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of
why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between betalink versions 2.1.0 dated 2015-08-15 and 2.2.0 dated 2015-12-22
betalink-2.1.0/betalink/data/clownfishes.rdata |only betalink-2.1.0/betalink/man/clownfishes.Rd |only betalink-2.2.0/betalink/DESCRIPTION | 12 +- betalink-2.2.0/betalink/MD5 | 66 +++++++---- betalink-2.2.0/betalink/NAMESPACE | 20 +++ betalink-2.2.0/betalink/R/betalink.r | 15 ++ betalink-2.2.0/betalink/R/measures.r | 106 +++++++++++++++++-- betalink-2.2.0/betalink/R/network_betadiversity.R | 53 ++++----- betalink-2.2.0/betalink/R/prepare_networks.R | 3 betalink-2.2.0/betalink/README.md | 5 betalink-2.2.0/betalink/man/B01.Rd | 6 - betalink-2.2.0/betalink/man/B02.Rd | 6 - betalink-2.2.0/betalink/man/B03.Rd | 6 - betalink-2.2.0/betalink/man/B04.Rd | 6 - betalink-2.2.0/betalink/man/B05.Rd | 6 - betalink-2.2.0/betalink/man/B06.Rd | 6 - betalink-2.2.0/betalink/man/B07.Rd | 6 - betalink-2.2.0/betalink/man/B08.Rd |only betalink-2.2.0/betalink/man/B09.Rd |only betalink-2.2.0/betalink/man/B10.Rd |only betalink-2.2.0/betalink/man/B11.Rd |only betalink-2.2.0/betalink/man/B12.Rd |only betalink-2.2.0/betalink/man/B13.Rd |only betalink-2.2.0/betalink/man/B14.Rd |only betalink-2.2.0/betalink/man/B15.Rd |only betalink-2.2.0/betalink/man/B16.Rd |only betalink-2.2.0/betalink/man/B17.Rd |only betalink-2.2.0/betalink/man/B18.Rd |only betalink-2.2.0/betalink/man/B19.Rd |only betalink-2.2.0/betalink/man/B20.Rd |only betalink-2.2.0/betalink/man/B21.Rd |only betalink-2.2.0/betalink/man/B22.Rd |only betalink-2.2.0/betalink/man/B23.Rd |only betalink-2.2.0/betalink/man/B24.Rd |only betalink-2.2.0/betalink/man/anemonefish.Rd | 4 betalink-2.2.0/betalink/man/beta_os_prime.Rd | 2 betalink-2.2.0/betalink/man/betalink.Rd | 2 betalink-2.2.0/betalink/man/betapart.Rd | 2 betalink-2.2.0/betalink/man/df_from_A.Rd | 4 betalink-2.2.0/betalink/man/metaweb.Rd | 2 betalink-2.2.0/betalink/man/name_networks.Rd |only betalink-2.2.0/betalink/man/network_betadiversity.Rd | 2 betalink-2.2.0/betalink/man/network_betaplot.Rd | 2 betalink-2.2.0/betalink/man/prepare_networks.Rd | 2 44 files changed, 243 insertions(+), 101 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, DOI: 10.1007/s11104-009-0005-2), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) Root System Markup Language: toward a unified root architecture description language, Plant Physiology, DOI: 10.1104/pp.114.253625). More information can be found in Delory et al (2015) archiDART: an R package for the automated computation of plant root architectural traits, Plant and Soil, DOI: 10.1007/s11104-015-2673-4.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 1.1 dated 2015-06-08 and 1.2 dated 2015-12-22
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++-- man/archidraw.Rd | 10 ++++++---- man/archigrow.Rd | 8 +++++--- man/architect.Rd | 10 ++++++---- man/ch7lie.Rd | 2 +- man/ch7rac.Rd | 2 +- man/ch7tps.Rd | 2 +- man/latdist.Rd | 10 ++++++---- man/trajectory.Rd | 10 ++++++---- 11 files changed, 51 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-09 0.1.0
Title: Advanced Data Analysis of Immune Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor and
Immunoglobulin repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.2.1 dated 2015-11-07 and 2.2.1.7 dated 2015-12-22
tcR-2.2.1.7/tcR/DESCRIPTION | 17 +- tcR-2.2.1.7/tcR/MD5 | 200 ++++++++++++------------ tcR-2.2.1.7/tcR/NAMESPACE | 4 tcR-2.2.1.7/tcR/R/dataproc.R | 67 +++++++- tcR-2.2.1.7/tcR/R/datatools.R | 16 + tcR-2.2.1.7/tcR/R/docdata.R | 21 ++ tcR-2.2.1.7/tcR/R/infoanalysis.R | 10 - tcR-2.2.1.7/tcR/R/io.R | 2 tcR-2.2.1.7/tcR/R/parsing.R | 139 ++++++++++++++-- tcR-2.2.1.7/tcR/R/plots.R | 143 +++++++++++++++-- tcR-2.2.1.7/tcR/R/repoverlap.R | 11 - tcR-2.2.1.7/tcR/R/segments.R | 6 tcR-2.2.1.7/tcR/R/strtools.R | 4 tcR-2.2.1.7/tcR/README.md | 6 tcR-2.2.1.7/tcR/inst/doc/tcrvignette.Rmd | 4 tcR-2.2.1.7/tcR/inst/doc/tcrvignette.html | 57 ++---- tcR-2.2.1.7/tcR/man/AA_TABLE.Rd | 2 tcR-2.2.1.7/tcR/man/apply.symm.Rd | 2 tcR-2.2.1.7/tcR/man/assymetry.Rd | 2 tcR-2.2.1.7/tcR/man/barcodes.to.reads.Rd | 2 tcR-2.2.1.7/tcR/man/beta.prob.Rd | 4 tcR-2.2.1.7/tcR/man/bootstrap.tcr.Rd | 2 tcR-2.2.1.7/tcR/man/check.distribution.Rd | 2 tcR-2.2.1.7/tcR/man/clonal.space.homeostasis.Rd | 2 tcR-2.2.1.7/tcR/man/cloneset.stats.Rd | 6 tcR-2.2.1.7/tcR/man/codon.variants.Rd | 6 tcR-2.2.1.7/tcR/man/column.summary.Rd | 2 tcR-2.2.1.7/tcR/man/contamination.stats.Rd | 10 - tcR-2.2.1.7/tcR/man/convergence.index.Rd | 2 tcR-2.2.1.7/tcR/man/cosine.sharing.Rd | 2 tcR-2.2.1.7/tcR/man/cosine.similarity.Rd | 6 tcR-2.2.1.7/tcR/man/entropy.Rd | 6 tcR-2.2.1.7/tcR/man/entropy.seg.Rd | 6 tcR-2.2.1.7/tcR/man/find.clonotypes.Rd | 2 tcR-2.2.1.7/tcR/man/find.similar.sequences.Rd | 2 tcR-2.2.1.7/tcR/man/fix.alleles.Rd | 2 tcR-2.2.1.7/tcR/man/gc.content.Rd | 2 tcR-2.2.1.7/tcR/man/geneUsage.Rd | 8 tcR-2.2.1.7/tcR/man/generate.kmers.Rd | 2 tcR-2.2.1.7/tcR/man/generate.tcr.Rd | 6 tcR-2.2.1.7/tcR/man/get.all.substrings.Rd | 2 tcR-2.2.1.7/tcR/man/get.deletions.alpha.Rd | 6 tcR-2.2.1.7/tcR/man/get.inframes.Rd | 2 tcR-2.2.1.7/tcR/man/get.kmers.Rd | 2 tcR-2.2.1.7/tcR/man/gibbs.sampler.Rd | 2 tcR-2.2.1.7/tcR/man/group.clonotypes.Rd | 2 tcR-2.2.1.7/tcR/man/has.class.Rd | 2 tcR-2.2.1.7/tcR/man/intersectClonesets.Rd | 12 - tcR-2.2.1.7/tcR/man/inverse.simpson.Rd | 6 tcR-2.2.1.7/tcR/man/kmer.profile.Rd | 4 tcR-2.2.1.7/tcR/man/kmer.table.Rd | 2 tcR-2.2.1.7/tcR/man/loglikelihood.Rd | 2 tcR-2.2.1.7/tcR/man/matrixSubgroups.Rd | 2 tcR-2.2.1.7/tcR/man/matrixdiagcopy.Rd | 2 tcR-2.2.1.7/tcR/man/mutated.neighbours.Rd | 2 tcR-2.2.1.7/tcR/man/mutation.network.Rd | 2 tcR-2.2.1.7/tcR/man/ozScore.Rd | 2 tcR-2.2.1.7/tcR/man/parse.cloneset.Rd | 2 tcR-2.2.1.7/tcR/man/parse.folder.Rd | 21 +- tcR-2.2.1.7/tcR/man/pca.segments.Rd | 2 tcR-2.2.1.7/tcR/man/pca2euclid.Rd | 2 tcR-2.2.1.7/tcR/man/permutDistTest.Rd | 2 tcR-2.2.1.7/tcR/man/permutedf.Rd | 2 tcR-2.2.1.7/tcR/man/rarefaction.Rd | 2 tcR-2.2.1.7/tcR/man/repDiversity.Rd | 6 tcR-2.2.1.7/tcR/man/repLoad.Rd | 4 tcR-2.2.1.7/tcR/man/repOverlap.Rd | 10 - tcR-2.2.1.7/tcR/man/repSave.Rd | 2 tcR-2.2.1.7/tcR/man/resample.Rd |only tcR-2.2.1.7/tcR/man/revcomp.Rd | 2 tcR-2.2.1.7/tcR/man/reverse.string.Rd | 2 tcR-2.2.1.7/tcR/man/sample.clones.Rd | 2 tcR-2.2.1.7/tcR/man/sample2D.Rd | 2 tcR-2.2.1.7/tcR/man/segments.alphabets.Rd | 10 - tcR-2.2.1.7/tcR/man/segments.list.Rd | 2 tcR-2.2.1.7/tcR/man/set.group.vector.Rd | 2 tcR-2.2.1.7/tcR/man/set.pb.Rd | 2 tcR-2.2.1.7/tcR/man/set.people.vector.Rd | 2 tcR-2.2.1.7/tcR/man/set.rank.Rd | 2 tcR-2.2.1.7/tcR/man/shared.repertoire.Rd | 2 tcR-2.2.1.7/tcR/man/spectratyping.Rd | 4 tcR-2.2.1.7/tcR/man/startmitcr.Rd | 10 - tcR-2.2.1.7/tcR/man/tailbound.proportion.Rd | 2 tcR-2.2.1.7/tcR/man/top.cross.Rd | 6 tcR-2.2.1.7/tcR/man/top.fun.Rd | 2 tcR-2.2.1.7/tcR/man/twinsdata.Rd | 4 tcR-2.2.1.7/tcR/man/vis.clonal.dynamics.Rd | 2 tcR-2.2.1.7/tcR/man/vis.clonal.space.Rd | 4 tcR-2.2.1.7/tcR/man/vis.count.len.Rd | 2 tcR-2.2.1.7/tcR/man/vis.gene.usage.Rd | 2 tcR-2.2.1.7/tcR/man/vis.group.boxplot.Rd | 4 tcR-2.2.1.7/tcR/man/vis.heatmap.Rd | 11 + tcR-2.2.1.7/tcR/man/vis.kmer.histogram.Rd | 2 tcR-2.2.1.7/tcR/man/vis.logo.Rd | 4 tcR-2.2.1.7/tcR/man/vis.number.count.Rd | 2 tcR-2.2.1.7/tcR/man/vis.pca.Rd | 2 tcR-2.2.1.7/tcR/man/vis.radarlike.Rd | 2 tcR-2.2.1.7/tcR/man/vis.rarefaction.Rd | 2 tcR-2.2.1.7/tcR/man/vis.shared.clonotypes.Rd |only tcR-2.2.1.7/tcR/man/vis.top.proportions.Rd | 2 tcR-2.2.1.7/tcR/vignettes/tcrvignette.Rmd | 4 tcR-2.2.1/tcR/R/tmp.R |only tcR-2.2.1/tcR/man/get.n.barcodes.Rd |only 103 files changed, 658 insertions(+), 349 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.5-88 dated 2015-03-17 and 0.5-92 dated 2015-12-22
ChangeLog | 2236 +++++++++++++++++------------------------- DESCRIPTION | 19 MD5 | 78 - NAMESPACE | 22 R/EBI.R | 24 R/error.spsarlm.R | 3 R/geary.R | 4 R/impacts.R | 2 R/lag.spsarlm.R | 2 R/lm.morantest.R | 4 R/mcmcsamp.R | 2 R/moran.R | 4 R/moran.exact.R | 4 R/mtlocalmoran.R | 4 R/mtmoran.R | 2 R/nb2mat.R | 27 R/sacsarlm.R | 19 R/sarlm.R | 951 ++++++++++++----- R/summary.spsarlm.R | 6 build/vignette.rds |binary inst/ChangeLog | 2236 +++++++++++++++++------------------------- inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/nb_igraph.html | 27 inst/doc/sids.pdf |binary man/EBImoran.mc.Rd | 6 man/boston.Rd | 13 man/dnearneigh.Rd | 2 man/eire.Rd | 2 man/house.Rd | 2 man/invIrM.Rd | 4 man/knearneigh.Rd | 2 man/lm.morantest.exact.Rd | 4 man/lm.morantest.sad.Rd | 2 man/localmoran.Rd | 10 man/localmoran.exact.Rd | 2 man/localmoran.sad.Rd | 13 man/nb2blocknb.Rd | 2 man/predict.sarlm.Rd | 70 - 40 files changed, 2776 insertions(+), 3034 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Author: Dennis Walvoort [aut, cre, cph],
Dick Brus [aut, cph],
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.3-5 dated 2013-05-02 and 0.3-6 dated 2015-12-22
spcosa-0.3-5/spcosa/inst/doc/spcosa.pdf |only spcosa-0.3-6/spcosa/DESCRIPTION | 22 ++++++++++----------- spcosa-0.3-6/spcosa/MD5 | 30 ++++++++++++++++++++--------- spcosa-0.3-6/spcosa/NAMESPACE | 22 ++++++--------------- spcosa-0.3-6/spcosa/R/methods_plot.R | 3 -- spcosa-0.3-6/spcosa/R/onAttach.R | 2 - spcosa-0.3-6/spcosa/build/spcosa.pdf |binary spcosa-0.3-6/spcosa/demo/sphere1.R | 4 +-- spcosa-0.3-6/spcosa/inst/NEWS.Rd | 8 +++++++ spcosa-0.3-6/spcosa/inst/doc/spcosa.html |only spcosa-0.3-6/spcosa/java |only spcosa-0.3-6/spcosa/tests/unitTesting.html | 22 ++++++++++----------- 12 files changed, 62 insertions(+), 51 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.13.0 dated 2015-12-15 and 0.13.1 dated 2015-12-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Rvcg-package.R | 4 ++-- inst/NEWS.Rd | 8 ++++++++ man/Rvcg-package.Rd | 4 ++-- src/vcglib/vcg/math/base.h | 8 ++++++-- 6 files changed, 27 insertions(+), 15 deletions(-)
Title: ProPublica API Client
Description: Client for accessing data journalism APIs from ProPublica <http://www.propublica.org/>.
Author: Thomas J. Leeper [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between RPublica versions 0.1.2 dated 2014-12-20 and 0.1.3 dated 2015-12-22
DESCRIPTION | 14 +- MD5 | 24 ++-- NAMESPACE | 4 NEWS | 8 - R/nonprofitexplorer.R | 12 +- README.md | 242 ++++++++++------------------------------------- man/committees.Rd | 2 man/filing.Rd | 2 man/forensics.Rd | 2 man/market.Rd | 2 man/nonprofitexplorer.Rd | 2 man/ppQuery.Rd | 2 man/station.Rd | 2 13 files changed, 92 insertions(+), 226 deletions(-)
Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using
the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram,
Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart,
bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>
Diff between RcmdrPlugin.KMggplot2 versions 0.2-1 dated 2015-12-14 and 0.2-2 dated 2015-12-22
DESCRIPTION | 12 - MD5 | 36 ++- NEWS | 206 +++++++++++----------- NEWS.md |only R/guiparts-toolbox.R | 22 +- R/plot-aaa.R | 98 ++++++---- R/plot-factorise.R | 2 R/plot-gbox.R | 60 +----- R/plot-gkm.R | 53 +---- R/plot-gqq.R | 8 R/zzz.R | 9 README.md |only build |only inst/doc |only inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.KMggplot2.mo |binary inst/po/sl/LC_MESSAGES/R-RcmdrPlugin.KMggplot2.mo |binary po/R-RcmdrPlugin.KMggplot2-ja.po | 186 +++++++++---------- po/R-RcmdrPlugin.KMggplot2-sl.po | 186 +++++++++---------- vignettes |only 19 files changed, 443 insertions(+), 435 deletions(-)
More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link
Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Bjorn Andersson, Kenny Branberg and Marie Wiberg
Maintainer: Bjorn Andersson <bjoern.h.andersson@gmail.com>
Diff between kequate versions 1.4.0 dated 2014-06-04 and 1.5.0 dated 2015-12-22
DESCRIPTION | 14 MD5 | 20 NAMESPACE | 4 NEWS | 5 R/kernel.R | 2282 ++++++++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/irtguide.pdf |binary inst/doc/kequate.pdf |binary man/irtose.Rd | 27 man/kequate-package.Rd | 6 man/plot-methods.Rd | 52 - 11 files changed, 1692 insertions(+), 718 deletions(-)
Title: Client Package for the U.S. Federal Register API
Description: Access data from the Federal Register API <https://www.federalregister.gov/developers/api/v1>.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between federalregister versions 0.1.2 dated 2014-08-06 and 0.2.0 dated 2015-12-22
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 9 +++++---- NEWS | 6 ++++++ R/agencies.r | 11 ++++------- R/fr_get.r | 14 ++++++-------- R/fr_search.r | 30 +++++++++++++++--------------- R/pi_current.r | 11 ++++------- R/pi_get.r | 11 ++++------- R/pi_search.r | 15 ++++++--------- README.md | 36 ++++++++++++++---------------------- man/agencies.Rd | 3 ++- man/fr_get.Rd | 3 ++- man/fr_search.Rd | 6 +++++- man/pi_current.Rd | 3 ++- man/pi_get.Rd | 3 ++- man/pi_search.Rd | 3 ++- 17 files changed, 102 insertions(+), 108 deletions(-)
More information about federalregister at CRAN
Permanent link
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.3 dated 2015-11-26 and 0.3.4 dated 2015-12-22
DESCRIPTION | 8 +++--- MD5 | 27 +++++++++++----------- NAMESPACE | 1 NEWS | 6 ++++ R/genomic.R | 25 +++++++++++++++----- R/utils.R | 4 +-- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary man/col2value.rd | 1 man/colorRamp2.rd | 2 - man/smartAlign.rd |only 15 files changed, 48 insertions(+), 26 deletions(-)
Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer.
It provides a context-minimal approach for sensitivity analysis using extreme
bounds to assess the sturdiness of regression coefficients.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sValues versions 0.1.2 dated 2015-10-25 and 0.1.4 dated 2015-12-22
DESCRIPTION | 9 +++-- MD5 | 34 +++++++++---------- NAMESPACE | 4 +- R/internal_functions.R | 10 +++-- R/sValues.R | 2 - build/vignette.rds |binary inst/doc/sValues.Rnw | 3 + inst/doc/sValues.pdf |binary man/coef.sValues.Rd | 16 +++++---- man/economic_growth.Rd | 73 +----------------------------------------- man/plot.sValues.Rd | 5 +- man/print.sValues.Rd | 19 ++++++---- man/sValues-package.Rd | 8 ++-- man/sValues.Rd | 39 +++++++++++----------- man/str.sValues.Rd | 4 +- man/summary.sValues.Rd | 2 - tests/testthat/test-sValues.R | 18 +++++++++- vignettes/sValues.Rnw | 3 + 18 files changed, 106 insertions(+), 143 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help organize Monte Carlo simulations in R. The package
controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.4.1 dated 2015-11-20 and 0.5 dated 2015-12-22
DESCRIPTION | 22 +-- MD5 | 52 +++---- NAMESPACE | 2 R/SimDesign.R | 17 +- R/SimDesign_functions.R | 103 +++++++++----- R/add_missing.R |only R/aggregate_simulations.R | 22 +-- R/analysis.R | 34 +++- R/functions.R | 103 ++++++++------ R/runSimulation.R | 313 +++++++++++++++++++++++++++---------------- R/summary_functions.R | 255 +++++++++++++++++++---------------- R/util.R | 22 ++- man/ECR.Rd | 18 +- man/EDR.Rd | 14 + man/MAE.Rd | 31 ++-- man/RE.Rd | 19 +- man/RMSE.Rd | 40 ++--- man/SimDesign.Rd | 15 -- man/SimDesign_functions.Rd | 16 +- man/add_missing.Rd |only man/aggregate_simulations.Rd | 10 - man/analyse.Rd | 33 ++-- man/bias.Rd | 32 ++-- man/check_error.Rd | 7 man/generate.Rd | 18 +- man/runSimulation.Rd | 222 +++++++++++++++++++----------- man/summarise.Rd | 23 +-- tests/tests/test-SimDesign.R | 88 ++++++++++-- 28 files changed, 954 insertions(+), 577 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.8.1 dated 2015-10-09 and 0.9 dated 2015-12-22
DESCRIPTION | 9 +- MD5 | 104 ++++++++++++++--------------- NAMESPACE | 2 R/beamer_presentation.R | 42 +++++++++-- R/html_document.R | 6 - R/html_document_base.R | 3 R/html_resources.R | 5 - R/md_document.R | 6 - R/output_format.R | 17 +++- R/pandoc.R | 22 +++--- R/params.R | 15 +++- R/pdf_document.R | 15 +++- R/render.R | 104 ++++++++++++++++++----------- R/slidy_presentation.R | 5 - R/tufte_handout.R | 2 R/util.R | 111 ++++++++++++++++++++++++++++++- inst/NEWS | 36 +++++++++- inst/rmd/slidy/Slidy2/scripts/slidy.js | 2 man/beamer_presentation.Rd | 25 +++--- man/default_output_format.Rd | 2 man/draft.Rd | 2 man/find_external_resources.Rd | 18 ++--- man/html_document.Rd | 11 +-- man/html_document_base.Rd | 6 - man/html_fragment.Rd | 12 +-- man/html_vignette.Rd | 6 + man/includes.Rd | 2 man/ioslides_presentation.Rd | 2 man/knit_params_ask.Rd | 2 man/knitr_options.Rd | 6 - man/knitr_options_html.Rd | 2 man/knitr_options_pdf.Rd | 2 man/md_document.Rd | 21 +++-- man/metadata.Rd | 7 - man/output_format.Rd | 7 + man/pandoc_args.Rd | 4 - man/pandoc_available.Rd | 14 +-- man/pandoc_convert.Rd | 7 + man/pandoc_options.Rd | 14 ++- man/pandoc_path_arg.Rd | 8 +- man/pandoc_self_contained_html.Rd | 2 man/pandoc_template.Rd | 2 man/pdf_document.Rd | 21 +++-- man/relative_to.Rd | 2 man/render_delayed.Rd | 3 man/render_supporting_files.Rd | 2 man/rmarkdown_format.Rd | 5 - man/run.Rd | 4 - man/slidy_presentation.Rd | 24 +++--- man/tufte_handout.Rd | 10 +- man/word_document.Rd | 9 +- tests/testthat/resources/file-exists.Rmd |only tests/testthat/resources/quotes.Rmd |only tests/testthat/test-resources.R | 30 ++++++++ 54 files changed, 546 insertions(+), 254 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.38 dated 2015-10-26 and 1.39 dated 2015-12-22
aSPU-1.38/aSPU/R/aSPUpathSingle.r |only aSPU-1.38/aSPU/man/aSPUpathSingle.Rd |only aSPU-1.39/aSPU/DESCRIPTION | 15 +++--- aSPU-1.39/aSPU/MD5 | 65 ++++++++++++++++------------ aSPU-1.39/aSPU/NAMESPACE | 11 +++- aSPU-1.39/aSPU/R/GATES2.R | 2 aSPU-1.39/aSPU/R/GEEaSPU.R | 12 +++-- aSPU-1.39/aSPU/R/GatesSimes.R | 2 aSPU-1.39/aSPU/R/Hyst.R | 2 aSPU-1.39/aSPU/R/MTaSPUs.R |only aSPU-1.39/aSPU/R/RcppExports.R |only aSPU-1.39/aSPU/R/aSPU.R | 13 +---- aSPU-1.39/aSPU/R/aSPUpath.r | 6 +- aSPU-1.39/aSPU/R/aSPUpermC2.R |only aSPU-1.39/aSPU/R/aSPUs.R | 22 +++------ aSPU-1.39/aSPU/R/aSPUsPath.r | 18 +++---- aSPU-1.39/aSPU/R/aSPUsimC2.R |only aSPU-1.39/aSPU/R/aSPUw.R | 2 aSPU-1.39/aSPU/R/estcov.R |only aSPU-1.39/aSPU/R/minP.R |only aSPU-1.39/aSPU/R/simPathAR1SNP.R | 2 aSPU-1.39/aSPU/README.md | 81 ++++++++++++++++++++++++++++++++++- aSPU-1.39/aSPU/man/GATES2.Rd | 9 ++- aSPU-1.39/aSPU/man/GEEaSPU.Rd | 18 ++++--- aSPU-1.39/aSPU/man/GatesSimes.Rd | 7 ++- aSPU-1.39/aSPU/man/Hyst.Rd | 6 +- aSPU-1.39/aSPU/man/MTaSPUs.Rd |only aSPU-1.39/aSPU/man/aSPU.Rd | 10 ++-- aSPU-1.39/aSPU/man/aSPUpath.Rd | 16 +++--- aSPU-1.39/aSPU/man/aSPUs.Rd | 28 +++++------- aSPU-1.39/aSPU/man/aSPUsPath.Rd | 18 +++---- aSPU-1.39/aSPU/man/aSPUw.Rd | 10 ++-- aSPU-1.39/aSPU/man/estcov.Rd |only aSPU-1.39/aSPU/man/getlogitp.Rd | 9 ++- aSPU-1.39/aSPU/man/kegg9.Rd | 14 +++++- aSPU-1.39/aSPU/man/minP.Rd |only aSPU-1.39/aSPU/man/simPathAR1Snp.Rd | 12 +++-- aSPU-1.39/aSPU/src/Makevars |only aSPU-1.39/aSPU/src/Makevars.win |only aSPU-1.39/aSPU/src/RcppExports.cpp |only aSPU-1.39/aSPU/src/aSPU.cpp |only 41 files changed, 265 insertions(+), 145 deletions(-)
Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from
environmental monitoring programs. The package name stands for "water quality"
and reflects the original focus on time series data for physical and
chemical properties of water, as well as the plankton. Intended for programs
that sample approximately monthly at discrete stations, a feature of many
legacy data sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>
Diff between wq versions 0.4.4 dated 2015-07-30 and 0.4.5 dated 2015-12-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 4 ++++ R/eofPlot.R | 2 +- build/vignette.rds |binary inst/doc/wq-package.pdf |binary man/wq-package.Rd | 6 +++--- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.2 dated 2015-10-30 and 0.2.0 dated 2015-12-21
DESCRIPTION | 8 MD5 | 106 +++++---- NAMESPACE | 4 NEWS | 11 R/visClustering.R | 40 +++ R/visConfigure.R | 17 + R/visDocumentation.R | 3 R/visEdges.R | 17 + R/visFit.R |only R/visFocus.R |only R/visGroups.R | 34 +- R/visHierarchicalLayout.R | 19 + R/visInteraction.R | 17 + R/visLayout.R | 22 + R/visLegend.R | 12 - R/visNetwork.R | 31 ++ R/visNetworkEvents.R | 12 - R/visNetworkProxy.R |only R/visNodes.R | 17 + R/visOptions.R | 264 +++++++++++++++++----- R/visPhysics.R | 17 + R/visRedraw.R |only README.md | 21 + inst/doc/Introduction-to-visNetwork.R | 2 inst/doc/Introduction-to-visNetwork.Rmd | 2 inst/doc/Introduction-to-visNetwork.html | 100 ++++---- inst/doc/network/index.html | 22 + inst/examples/all_examples.R | 29 ++ inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 42 +-- inst/htmlwidgets/visNetwork.js | 364 +++++++++++++++++++++++-------- inst/shiny/server.R | 69 ----- inst/shiny/src |only inst/shiny/ui.R | 23 - man/visConfigure.Rd | 3 man/visDocumentation.Rd | 3 man/visEdges.Rd | 3 man/visEvents.Rd | 3 man/visFit.Rd |only man/visFocus.Rd |only man/visGroups.Rd | 10 man/visHierarchicalLayout.Rd | 3 man/visInteraction.Rd | 3 man/visLayout.Rd | 3 man/visLegend.Rd | 3 man/visNetwork-shiny.Rd | 8 man/visNetwork.Rd | 3 man/visNetworkProxy.Rd |only man/visNodes.Rd | 3 man/visOptions.Rd | 84 ++++++- man/visPhysics.Rd | 3 man/visRedraw.Rd |only vignettes/Introduction-to-visNetwork.Rmd | 2 54 files changed, 1037 insertions(+), 429 deletions(-)
Title: A Toolbox for Systemic Risk
Description: A toolbox for systemic risk based on liabilities matrices. Contains
a Gibbs sampler for liabilities matrices where only row and column sums of the
liabilities matrix as well as some other fixed entries are observed. Includes models
for power law distribution on the degree distribution.
Author: Axel Gandy and Luitgard A.M. Veraart
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between systemicrisk versions 0.2 dated 2015-03-19 and 0.3 dated 2015-12-21
DESCRIPTION | 18 MD5 | 77 +- NAMESPACE | 22 R/ExponentialFitnessLinkFun.R |only R/HierarchicalModels.R |only R/RcppExports.R | 201 +++--- R/lib_ErdosRenyExponential_MCMC.R | 194 +++-- R/lib_FindFeasibleMatrix.R | 164 +++-- R/lib_Network_Evaluations.R | 408 ++++++------ build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/HierarchicalModels.R |only inst/doc/HierarchicalModels.Rmd |only inst/doc/HierarchicalModels.html |only inst/doc/Introduction.R | 72 +- inst/doc/Introduction.Rmd | 144 ++-- inst/doc/Introduction.html | 654 ++++++++++---------- man/ERE_step_cycle.Rd | 74 +- man/GibbsSteps_kcycle.Rd | 88 +- man/Model.Indep.p.lambda.Rd |only man/Model.additivelink.exponential.fitness.Rd |only man/Model.fitness.conditionalmeandegree.Rd |only man/Model.fitness.genlambdaparprior.Rd |only man/Model.fitness.meandegree.Rd |only man/Model.lambda.GammaPrior.Rd |only man/Model.lambda.Gammaprior_mult.Rd |only man/Model.lambda.constant.Rd |only man/Model.p.BetaPrior.Rd |only man/Model.p.Betaprior_mult.Rd |only man/Model.p.Fitness.Servedio.Rd |only man/Model.p.constant.Rd |only man/choosethin.Rd |only man/cloneMatrix.Rd | 66 +- man/default.Rd | 3 man/default_cascade.Rd | 2 man/default_clearing.Rd | 104 +-- man/diagnose.Rd |only man/findFeasibleMatrix.Rd |only man/findFeasibleMatrix_targetmean.Rd |only man/genL.Rd |only man/getfeasibleMatr.Rd | 58 - man/sample_ERE.Rd | 83 +- man/sample_HierarchicalModel.Rd |only man/steps_ERE.Rd | 81 +- src/RcppExports.cpp | 68 +- src/lib_FeasibleMatrix.cpp |only src/lib_sample_kcycle.cpp | 92 ++ tests/testthat.R | 1 tests/testthat/test-gibbs_kcycle.R | 50 - tests/testthat/test_FeasibleMatrix.R |only tests/testthat/test_HierarchicalModels.R |only tests/testthat/test_HierarchicalModels_choosethin.R |only vignettes/HierarchicalModels.Rmd |only vignettes/Introduction.Rmd | 144 ++-- 54 files changed, 1518 insertions(+), 1350 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 4.4-0 dated 2015-09-28 and 4.4-1 dated 2015-12-21
DESCRIPTION | 8 - MD5 | 55 +++++----- NEWS | 13 ++ R/Glm.s | 34 +++--- R/Gls.s | 54 +++++----- R/bj.s | 226 ++++++++++++++++++++---------------------- R/contrast.s | 2 R/cph.s | 9 + R/ggplot.Predict.s | 21 ++- R/lrm.s | 79 +++++++------- R/npsurv.s | 39 +++++-- R/ols.s | 20 ++- R/orm.s | 8 + R/plot.nomogram.s | 2 R/residuals.lrm.s | 2 R/rms.s | 24 ++-- R/rms.trans.s | 148 +++++++++++++++------------ R/rmsMisc.s | 11 -- R/survplot.npsurv.s | 187 ++++++++++++++++++++-------------- R/survreg.distributions.s | 12 +- R/val.prob.s | 2 R/validate.ols.s | 2 README.md | 3 man/cph.Rd | 3 man/ggplot.Predict.Rd | 7 - man/npsurv.Rd | 37 ++++-- man/survplot.Rd | 64 +++++++++-- tests/anova-ols-mult-impute.r |only tests/latex.r |only tests/rms.r |only 30 files changed, 619 insertions(+), 453 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC Curves
Description: Accurate calculations and visualization of Precision-Recall and ROC
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.1.1 dated 2015-12-04 and 0.2.0 dated 2015-12-21
DESCRIPTION | 8 +- MD5 | 54 +++++++++--------- R/etc_utils_autoplot.R | 134 +++++++++++++++++++-------------------------- R/etc_utils_fortify.R | 55 +++++++++--------- R/etc_utils_plot.R | 93 ++++++++++++++++--------------- R/g_auc.R | 34 ++++++----- R/main_evalmod.R | 77 ++++++++++++------------- R/mm2_join_data.R | 6 +- R/precrec.R | 90 +++++++++++++++--------------- README.md | 6 -- build/vignette.rds |binary inst/doc/introduction.R | 4 - inst/doc/introduction.Rmd | 9 +-- inst/doc/introduction.html | 26 ++++---- man/B1000.Rd | 12 ++-- man/B500.Rd | 12 ++-- man/IB1000.Rd | 12 ++-- man/IB500.Rd | 12 ++-- man/P10N10.Rd | 2 man/auc.Rd | 36 ++++++------ man/autoplot.Rd | 130 +++++++++++++++++++------------------------ man/evalmod.Rd | 77 ++++++++++++------------- man/fortify.Rd | 57 +++++++++---------- man/join_labels.Rd | 2 man/join_scores.Rd | 4 - man/plot.Rd | 95 +++++++++++++++++-------------- man/precrec.Rd | 36 ++++++------ vignettes/introduction.Rmd | 9 +-- 28 files changed, 532 insertions(+), 560 deletions(-)
Title: Cause-Specific Framework for Competing-Risk Analysis
Description: Numerical integration of cause-specific survival curves to arrive at cause-specific cumulative incidence functions,
with three usage modes: 1) Convenient API for parametric survival regression followed by competing-risk analysis, 2) API for
CFC, accepting user-specified survival functions in R, and 3) Same as 2, but accepting survival functions in C++.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between CFC versions 1.0.0 dated 2015-12-18 and 1.0.1 dated 2015-12-21
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cfc_survreg.R | 2 +- inst/doc/cfc.pdf |binary vignettes/weib.cpp | 6 +++--- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.7 dated 2015-11-12 and 1.1.8 dated 2015-12-21
DESCRIPTION | 11 ++-- MD5 | 101 +++++++++++++++++++++---------------------- NAMESPACE | 8 ++- NEWS | 14 +++++ R/paleofire-package.R | 6 +- R/pfAddData.R | 71 +++++++++++++++++++++++++++--- R/pfGridding.R | 3 - R/pfTransform.R | 34 +++++++------- README.md | 2 build/vignette.rds |binary demo/example-1.R | 4 - inst/COPYING | 31 +++++++------ inst/THANKS | 2 inst/doc/paleofire-paper.pdf |binary man/checkGCDversion.Rd | 4 + man/contiguous.Rd | 4 + man/kdffreq.Rd | 9 ++- man/paleofire-internal.Rd | 3 - man/paleofire-package.Rd | 10 ++-- man/pfAddData.Rd | 15 +++--- man/pfBoxCox.Rd | 5 +- man/pfCircular.Rd | 4 + man/pfComposite.Rd | 4 + man/pfCompositeLF.Rd | 5 +- man/pfDiagnostic.Rd | 7 ++ man/pfDotMap.Rd | 16 +++--- man/pfExtract.Rd | 4 + man/pfGridding.Rd | 14 +++-- man/pfInteractive.Rd | 7 ++ man/pfKruskal.Rd | 4 + man/pfMinMax.Rd | 4 + man/pfPublication.Rd | 2 man/pfResolution.Rd | 4 + man/pfSimpleGrid.Rd | 50 +++++++++++---------- man/pfSiteSel.Rd | 9 ++- man/pfToKml.Rd | 4 + man/pfTransform.Rd | 5 +- man/plot.CHAR.Rd | 7 ++ man/plot.contiguous.Rd | 4 + man/plot.kdffreq.Rd | 12 ++--- man/plot.pfCircular.Rd | 4 + man/plot.pfComposite.Rd | 4 + man/plot.pfCompositeLF.Rd | 5 +- man/plot.pfGridding.Rd | 4 + man/plot.pfKruskal.Rd | 4 + man/plot.pfSiteSel.Rd | 5 +- man/plot.potveg.Rd | 10 ++-- man/potveg.Rd | 7 ++ man/pretreatment.Rd | 12 ++--- man/rbind.pfAddData.Rd |only man/summary.pfSiteSel.Rd | 4 + man/triCube.Rd | 4 + 52 files changed, 365 insertions(+), 201 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment
methods. Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.3 dated 2015-10-22 and 0.8.4 dated 2015-12-21
DESCRIPTION | 21 +-- MD5 | 205 ++++++++++++++++++------------------- NAMESPACE | 4 R/CIDists.R | 31 ++--- R/FSAUtils.R | 118 +++++++++++++++------ R/alkSummaries.R | 1 R/fitPlot.R | 14 +- R/lencat.R | 4 R/residPlot.R | 41 +++---- man/BluegillJL.Rd | 3 man/BrookTroutTH.Rd | 5 man/ChinookArg.Rd | 7 - man/CodNorwegian.Rd | 3 man/CutthroatAL.Rd | 5 man/Ecoli.Rd | 4 man/FSA-internals.Rd | 2 man/FSA.Rd | 2 man/FSAUtils.Rd | 3 man/Mirex.Rd | 10 - man/PSDlit.Rd | 3 man/PikeNY.Rd | 3 man/PikeNYPartial1.Rd | 13 +- man/SMBassLS.Rd | 9 - man/SMBassWB.Rd | 3 man/Schnute.Rd | 3 man/SpotVA1.Rd | 3 man/Subset.Rd | 3 man/Summarize.Rd | 7 - man/WR79.Rd | 3 man/WSlit.Rd | 3 man/WhitefishLC.Rd | 9 - man/addRadCap.Rd | 3 man/addZeroCatch.Rd | 5 man/ageBias.Rd | 11 + man/agePrecision.Rd | 3 man/alkAgeDist.Rd | 3 man/alkIndivAge.Rd | 3 man/alkMeanVar.Rd | 5 man/alkPlot.Rd | 7 - man/bcFuns.Rd | 3 man/binCI.Rd | 3 man/bootCase.Rd | 5 man/capHistConvert.Rd | 9 - man/capHistSum.Rd | 3 man/catchCurve.Rd | 3 man/chapmanRobson.Rd | 3 man/chooseColors.Rd | 3 man/col2rgbt.Rd | 3 man/compIntercepts.Rd | 11 + man/compSlopes.Rd | 11 + man/depletion.Rd | 3 man/dunnTest.Rd | 3 man/expandCounts.Rd | 9 - man/expandLenFreq.Rd | 5 man/extraTests.Rd | 5 man/fact2num.Rd | 3 man/fishR.Rd | 3 man/fitPlot.Rd | 3 man/fsaNews.Rd | 3 man/gConvert.Rd | 3 man/geomean.Rd |only man/growthModels.Rd | 5 man/headtail.Rd | 2 man/hist.formula.Rd | 3 man/hoCoef.Rd | 5 man/hyperCI.Rd | 3 man/knitUtil.Rd | 9 - man/ksTest.Rd | 3 man/lagratio.Rd | 3 man/lencat.Rd | 7 - man/logbtcf.Rd | 3 man/lwCompPreds.Rd | 5 man/mapvalues.Rd | 2 man/metaM.Rd | 7 - man/mrClosed.Rd | 5 man/mrOpen.Rd | 3 man/nlsBoot.Rd | 3 man/oddeven.Rd | 2 man/perc.Rd | 3 man/plotBinResp.Rd | 3 man/poiCI.Rd | 3 man/psdAdd.Rd | 3 man/psdCI.Rd | 3 man/psdCalc.Rd | 3 man/psdPlot.Rd | 3 man/psdVal.Rd | 3 man/rcumsum.Rd | 4 man/removal.Rd | 5 man/residPlot.Rd | 3 man/se.Rd | 3 man/srStarts.Rd | 3 man/stockRecruitment.Rd | 5 man/sumTable.Rd | 3 man/tictactoe.Rd | 5 man/validn.Rd | 3 man/vbStarts.Rd | 5 man/wrAdd.Rd | 5 man/wsVal.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test_FSAUtils.R | 47 ++++++++ tests/testthat/test_Internals.R | 6 - tests/testthat/test_addZeroCatch.R | 2 tests/testthat/test_lencat.R | 4 tests/testthat/test_sumTable.R | 8 - 104 files changed, 536 insertions(+), 354 deletions(-)
Title: U.S. State Cartogram Heatmaps in R; an Alternative to Choropleth
Maps for USA States
Description: Cartogram heatmaps are an alternative to choropleth maps for USA States
and are based on work by the Washington Post graphics department in their report
on "The states most threatened by trade". "State bins" preserve as much of the
geographic placement of the states as possible but has the look and feel of a
traditional heatmap. Functions are provided that allow for use of a binned,
discrete scale, a continuous scale or manually specified colors depending on
what is needed for the underlying data.
Author: Bob Rudis (@hrbrmstr)
Maintainer: Bob Rudis <bob@rudis.net>
Diff between statebins versions 1.0 dated 2014-08-27 and 1.2.2 dated 2015-12-21
DESCRIPTION | 29 ++--- LICENSE | 2 MD5 | 17 +-- NAMESPACE | 40 ++++++- R/statebins-package.R | 12 ++ R/statebins.R | 235 +++++++++++++++++++++++++++++++++++++------- man/statebins-package.Rd | 3 man/statebins.Rd | 26 ++-- man/statebins_continuous.Rd | 25 ++-- man/statebins_manual.Rd |only 10 files changed, 304 insertions(+), 85 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different
problems, the package uses statistical tests and corrections to assess the
differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.4 dated 2015-12-01 and 0.2.5 dated 2015-12-21
DESCRIPTION | 15 +++--- MD5 | 93 ++++++++++++++++++++-------------------- R/loading_functions.R | 4 - R/plotting.R | 4 - R/scmamp.R | 2 README.md |only man/adjustBergmannHommel.Rd | 3 - man/adjustFinner.Rd | 3 - man/adjustHolland.Rd | 3 - man/adjustLi.Rd | 2 man/adjustRom.Rd | 2 man/adjustShaffer.Rd | 2 man/anovaTest.Rd | 3 - man/booleanMatrix.Rd | 3 - man/contrastEstimationMatrix.Rd | 4 - man/customPost.Rd | 2 man/data.blum.2015.Rd | 4 - man/data.gh.2008.Rd | 8 +-- man/data.gh.2010.Rd | 10 ++-- man/drawAlgorithmGraph.Rd | 3 - man/exhaustiveSets.Rd | 3 - man/filterData.Rd | 5 +- man/friedmanAlignedRanksPost.Rd | 2 man/friedmanAlignedRanksTest.Rd | 3 - man/friedmanPost.Rd | 2 man/friedmanTest.Rd | 3 - man/imanDavenportTest.Rd | 2 man/multipleComparisonTest.Rd | 34 ++++++-------- man/nemenyiTest.Rd | 2 man/plotCD.Rd | 3 - man/plotDensities.Rd | 5 +- man/plotPvalues.Rd | 3 - man/plotRanking.Rd | 3 - man/postHocTest.Rd | 35 +++++++-------- man/qqplotGaussian.Rd | 4 - man/quadePost.Rd | 3 - man/quadeTest.Rd | 3 - man/rankMatrix.Rd | 3 - man/readComparisonDir.Rd | 8 +-- man/readComparisonFile.Rd | 3 - man/readExperimentDir.Rd | 10 ++-- man/readExperimentFile.Rd | 2 man/scmamp.Rd | 6 +- man/summarizeData.Rd | 14 ++---- man/tukeyPost.Rd | 2 man/tukeyTest.Rd | 2 man/wilcoxonSignedTest.Rd | 2 man/writeTabular.Rd | 6 +- 48 files changed, 181 insertions(+), 162 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.1-1 dated 2015-11-02 and 1.1-3 dated 2015-12-21
ChangeLog | 1522 +++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 MD5 | 42 - R/ogr_write.R | 10 build/vignette.rds |binary configure | 18 data/GridsDatums.rda |binary inst/ChangeLog | 1522 +++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/etc/obj_with_comments.RData |binary man/GridsDatums.Rd | 10 man/project.Rd | 25 man/spTransform-methods.Rd | 30 man/writeOGR.Rd | 5 src/Makevars.in | 1 src/Makevars.win | 10 src/OGR_write.cpp | 42 - src/ogrsource.cpp | 12 src/projectit.cpp | 2 tests/tripup.R | 65 - tests/tripup.Rout.save | 181 +++- 22 files changed, 3391 insertions(+), 116 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.2 dated 2015-10-26 and 0.3 dated 2015-12-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/NlcOptim.R | 17 ++++++++++------- man/NlcOptim.Rd | 6 +++--- 4 files changed, 19 insertions(+), 16 deletions(-)
Title: MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of bioassay data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine
Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon-
Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>
Diff between morse versions 2.1.0 dated 2015-12-14 and 2.1.1 dated 2015-12-21
DESCRIPTION | 8 ++--- MD5 | 28 ++++++++--------- NEWS | 6 +++ R/morse.R | 2 - R/plot.reproData.R | 2 - R/plot.reproFitTT.R | 2 - R/plot.survData.R | 2 - R/plot.survFitTT.R | 2 - inst/doc/modelling.pdf |binary inst/doc/tutorial.html | 78 ++++++++++++++++++++++++------------------------- man/morse-package.Rd | 2 - man/plot.reproData.Rd | 2 - man/plot.reproFitTT.Rd | 2 - man/plot.survData.Rd | 2 - man/plot.survFitTT.Rd | 2 - 15 files changed, 73 insertions(+), 67 deletions(-)
Title: Create Interactive Charts with the JavaScript 'MetricsGraphics'
Library
Description: Provides an 'htmlwidgets' interface to the
'MetricsGraphics.js' ('D3'-based) charting library which is geared towards
displaying time-series data. Chart types include line charts, scatterplots,
histograms and rudimentary bar charts. Support for laying out multiple charts
into a grid layout is also provided. All charts are interactive and many
have an option for line, label and region annotations.
Author: Bob Rudis [aut, cre],
Ali Almossawi [ctb, cph] (MetricsGraphics library),
Hamilton Ulmer [ctb, cph] (MetricsGraphics library),
Mozilla [cph] (MetricsGraphics library),
jQuery Foundation and contributors [ctb, cph] (jQuery library)
Maintainer: Bob Rudis <bob@rudis.net>
Diff between metricsgraphics versions 0.8.5 dated 2015-06-14 and 0.9.0 dated 2015-12-21
metricsgraphics-0.8.5/metricsgraphics/R/metricsgraphics-package.R |only metricsgraphics-0.8.5/metricsgraphics/R/metricsgraphics.R |only metricsgraphics-0.8.5/metricsgraphics/R/mjs_grid.R |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/addons |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/highlightjs-default.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics-demo-dark.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics-demo.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/railscasts.css |only metricsgraphics-0.8.5/metricsgraphics/inst/htmlwidgets/lib/metricsgraphics.yaml |only metricsgraphics-0.9.0/metricsgraphics/DESCRIPTION | 22 metricsgraphics-0.9.0/metricsgraphics/MD5 | 110 metricsgraphics-0.9.0/metricsgraphics/NAMESPACE | 5 metricsgraphics-0.9.0/metricsgraphics/R/annotate.r |only metricsgraphics-0.9.0/metricsgraphics/R/axis.r |only metricsgraphics-0.9.0/metricsgraphics/R/bar.r |only metricsgraphics-0.9.0/metricsgraphics/R/hist.r |only metricsgraphics-0.9.0/metricsgraphics/R/labs.r |only metricsgraphics-0.9.0/metricsgraphics/R/legend.r |only metricsgraphics-0.9.0/metricsgraphics/R/line.r |only metricsgraphics-0.9.0/metricsgraphics/R/metricsgraphics-package.r |only metricsgraphics-0.9.0/metricsgraphics/R/metricsgraphics.r |only metricsgraphics-0.9.0/metricsgraphics/R/mjs_grid.r |only metricsgraphics-0.9.0/metricsgraphics/R/mouseover.r |only metricsgraphics-0.9.0/metricsgraphics/R/point.r |only metricsgraphics-0.9.0/metricsgraphics/R/region.r |only metricsgraphics-0.9.0/metricsgraphics/R/rules.r |only metricsgraphics-0.9.0/metricsgraphics/build/vignette.rds |binary metricsgraphics-0.9.0/metricsgraphics/inst/doc/introductiontometricsgraphics.R | 51 metricsgraphics-0.9.0/metricsgraphics/inst/doc/introductiontometricsgraphics.html | 352 + metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/d3/LICENSE | 2 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/d3/bower.json | 1 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/d3/d3.js | 545 +- metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/d3/d3.min.js | 10 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/d3/package.js |only metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/jquery/bower.json | 3 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/jquery/dist/jquery.js | 13 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/jquery/dist/jquery.min.js | 8 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/jquery/dist/jquery.min.map | 2 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/jquery/src/core.js | 7 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/bower.json | 1 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics.css | 58 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics.js | 1838 +++++----- metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/metricsgraphics.min.js | 6 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/mg_regions.css |only metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/lib/metrics-graphics/dist/mg_regions.js |only metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/metricsgraphics.js | 32 metricsgraphics-0.9.0/metricsgraphics/inst/htmlwidgets/metricsgraphics.yaml | 14 metricsgraphics-0.9.0/metricsgraphics/man/metricsgraphics-exports.Rd | 4 metricsgraphics-0.9.0/metricsgraphics/man/metricsgraphics.Rd | 4 metricsgraphics-0.9.0/metricsgraphics/man/metricsgraphicsOutput.Rd | 4 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_baseline.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_confidence_band.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_css_rule.Rd |only metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_legend.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_line.Rd | 14 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_marker.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_add_mouseover.Rd | 24 metricsgraphics-0.9.0/metricsgraphics/man/mjs_annotate_region.Rd |only metricsgraphics-0.9.0/metricsgraphics/man/mjs_axis_x.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_axis_y.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_bar.Rd | 7 metricsgraphics-0.9.0/metricsgraphics/man/mjs_grid.Rd | 4 metricsgraphics-0.9.0/metricsgraphics/man/mjs_hist.Rd | 6 metricsgraphics-0.9.0/metricsgraphics/man/mjs_histogram.Rd | 8 metricsgraphics-0.9.0/metricsgraphics/man/mjs_labs.Rd | 5 metricsgraphics-0.9.0/metricsgraphics/man/mjs_line.Rd | 16 metricsgraphics-0.9.0/metricsgraphics/man/mjs_plot.Rd | 18 metricsgraphics-0.9.0/metricsgraphics/man/mjs_point.Rd | 10 metricsgraphics-0.9.0/metricsgraphics/man/renderMetricsgraphics.Rd | 4 metricsgraphics-0.9.0/metricsgraphics/tests/testthat/test.R | 10 70 files changed, 1939 insertions(+), 1315 deletions(-)
More information about metricsgraphics at CRAN
Permanent link
Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.5 dated 2015-10-20 and 0.6 dated 2015-12-21
DESCRIPTION | 8 ++-- MD5 | 38 ++++++++++---------- R/annotation.R | 10 +++-- R/axis.R | 20 +++++++++- R/dygraph.R | 81 ++++++++++++++++++++++++++++--------------- R/event.R | 20 +++++++--- R/options.R | 6 +++ R/range-selector.R | 5 ++ R/series.R | 45 ++++++++++++++++++++++- R/shading.R | 14 ++++--- inst/NEWS | 11 +++++ inst/htmlwidgets/dygraphs.js | 71 ++++++++++++++++++++++--------------- man/dyAnnotation.Rd | 5 +- man/dyAxis.Rd | 10 ++++- man/dyEvent.Rd | 16 +++++--- man/dyOptions.Rd | 31 +++++++++------- man/dySeries.Rd | 5 ++ man/dyShading.Rd | 8 ++-- man/dygraph.Rd | 14 +++++-- tests/testthat/test-event.R | 4 +- 20 files changed, 286 insertions(+), 136 deletions(-)
Title: Comparative Phylogenetic Analyses of Diversification
Description: Contains a number of comparative phylogenetic methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
Speciation and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State Speciation and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
speciation and extinction.
Author: Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE' and
'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by Karen
Magnuson-Ford.
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-7 dated 2014-02-20 and 0.9-8 dated 2015-12-21
DESCRIPTION | 37 ++++++++----------- MD5 | 74 ++++++++++++++++++++------------------ NAMESPACE | 13 ++++++ R/asr-bisse.R | 15 +++++++ R/asr.R | 12 ++++-- R/check.R | 2 - R/mcmc.R | 14 +++---- R/mle-methods.R | 4 +- R/mle.R | 10 ++--- R/model-bd.R | 4 +- R/model-pgls.R | 8 ++-- R/model-quasse-common.R | 2 - R/model-quasse.R | 6 +-- R/plot-alt-util.R | 4 +- R/plot-alt.R | 8 ++-- R/profiles-plot.R | 10 ++--- R/split.R | 8 +++- R/t.R | 8 ++-- R/time-machine.R | 13 +++--- build |only configure | 2 - configure.ac | 2 - inst/CONTRIBUTORS.md |only inst/tests/run-tests.R | 1 inst/tests/test-asr.R | 4 +- inst/tests/test-expm.R | 2 - inst/tests/test-mcmc.R | 2 - inst/tests/test-ode.R | 12 +++--- inst/tests/test-pgls.R | 2 - inst/tests/test-quasse-internal.R | 4 ++ inst/tests/test-quasse-split.R | 2 + inst/tests/test-quasse.R | 2 + inst/tests/test-time-machine.R | 2 - inst/tests/test-unresolved.R | 2 - inst/update-gh-pages.sh |only man/diversitree-package.Rd |only man/make.bisse.td.Rd | 2 - man/make.quasse.Rd | 2 - src/TimeMachine.cpp | 9 ++++ src/TimeMachine.h | 15 ++++--- 40 files changed, 188 insertions(+), 131 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.25 dated 2015-11-19 and 2.26 dated 2015-12-21
BDgraph-2.25/BDgraph/data/CellSignal.RData |only BDgraph-2.25/BDgraph/man/CellSignal.Rd |only BDgraph-2.26/BDgraph/DESCRIPTION | 8 ++++---- BDgraph-2.26/BDgraph/MD5 | 10 ++++------ BDgraph-2.26/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.26/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.26/BDgraph/vignettes/BDgraph.pdf |binary 7 files changed, 8 insertions(+), 10 deletions(-)
More information about surveyoutliers at CRAN
Permanent link
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6.5 dated 2015-11-03 and 1.6.7 dated 2015-12-21
DESCRIPTION | 10 - MD5 | 16 - R/checkPrep.R | 24 +- R/linearRelation.R | 458 ++++++++++++++++++++++++++------------------------ R/timeAverage.R | 7 R/trendLevel.R | 21 ++ R/windRose.R | 2 man/linearRelation.Rd | 198 +++++++++++---------- man/trendLevel.Rd | 9 9 files changed, 405 insertions(+), 340 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results.
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.2.1 dated 2015-11-17 and 0.3.0 dated 2015-12-21
coala-0.2.1/coala/R/tempfile.R |only coala-0.3.0/coala/DESCRIPTION | 34 - coala-0.3.0/coala/MD5 | 115 +++--- coala-0.3.0/coala/NAMESPACE | 10 coala-0.3.0/coala/NEWS.md | 27 + coala-0.3.0/coala/R/RcppExports.R | 53 +- coala-0.3.0/coala/R/feature_ignore_singletons.R |only coala-0.3.0/coala/R/feature_selection.R | 182 ++++++++-- coala-0.3.0/coala/R/import_popgenome.R |only coala-0.3.0/coala/R/segsites.R | 29 + coala-0.3.0/coala/R/simulator_class.R | 4 coala-0.3.0/coala/R/simulator_ms.R | 43 -- coala-0.3.0/coala/R/simulator_msms.R | 2 coala-0.3.0/coala/R/sumstat.R | 16 coala-0.3.0/coala/R/sumstat_four_gamete.R | 6 coala-0.3.0/coala/R/sumstat_jsfs.R | 19 - coala-0.3.0/coala/R/sumstat_nucleotide_div.R | 5 coala-0.3.0/coala/R/sumstat_seg_sites.R | 5 coala-0.3.0/coala/R/sumstat_sfs.R | 7 coala-0.3.0/coala/R/sumstat_tajimas_d.R | 5 coala-0.3.0/coala/R/sumstat_trees.R | 5 coala-0.3.0/coala/R/tools.R |only coala-0.3.0/coala/README.md | 32 + coala-0.3.0/coala/build/vignette.rds |binary coala-0.3.0/coala/inst/doc/coala-abc.html | 4 coala-0.3.0/coala/inst/doc/coala-data-import.R |only coala-0.3.0/coala/inst/doc/coala-data-import.Rmd |only coala-0.3.0/coala/inst/doc/coala-data-import.html |only coala-0.3.0/coala/inst/doc/coala-extend.html | 2 coala-0.3.0/coala/inst/doc/coala-install.Rmd | 6 coala-0.3.0/coala/inst/doc/coala-install.html | 9 coala-0.3.0/coala/inst/doc/coala-intro.html | 10 coala-0.3.0/coala/inst/example_fasta_files |only coala-0.3.0/coala/inst/include/coala.h | 8 coala-0.3.0/coala/man/activate_ms.Rd | 15 coala-0.3.0/coala/man/as.segsites.GENOME.Rd |only coala-0.3.0/coala/man/as.segsites.Rd |only coala-0.3.0/coala/man/calc_jsfs.Rd | 17 coala-0.3.0/coala/man/calc_sumstats_from_data.Rd | 10 coala-0.3.0/coala/man/conv_to_ms_arg.Rd | 22 + coala-0.3.0/coala/man/create_segsites.Rd | 38 +- coala-0.3.0/coala/man/feat_ignore_singletons.Rd |only coala-0.3.0/coala/man/feat_selection.Rd | 55 ++- coala-0.3.0/coala/man/sumstat_four_gamete.Rd | 7 coala-0.3.0/coala/man/sumstat_jsfs.Rd | 11 coala-0.3.0/coala/man/sumstat_nucleotide_div.Rd | 6 coala-0.3.0/coala/man/sumstat_seg_sites.Rd | 6 coala-0.3.0/coala/man/sumstat_sfs.Rd | 6 coala-0.3.0/coala/man/sumstat_tajimas_d.Rd | 6 coala-0.3.0/coala/man/sumstat_trees.Rd | 6 coala-0.3.0/coala/src/RcppExports.cpp | 19 - coala-0.3.0/coala/src/seg_sites.cpp | 35 + coala-0.3.0/coala/src/stat_jsfs.cpp | 82 ++-- coala-0.3.0/coala/src/stat_nucleotide_div.cpp | 7 coala-0.3.0/coala/tests/testthat/test-feature-ign-singletons.R |only coala-0.3.0/coala/tests/testthat/test-feature-mutation.R | 2 coala-0.3.0/coala/tests/testthat/test-feature-selection.R | 47 ++ coala-0.3.0/coala/tests/testthat/test-import-popgenome.R |only coala-0.3.0/coala/tests/testthat/test-simulator-ms.R | 9 coala-0.3.0/coala/tests/testthat/test-simulator-msms.R | 2 coala-0.3.0/coala/tests/testthat/test-sumstat-jsfs.R | 103 +++-- coala-0.3.0/coala/tests/testthat/test-sumstat-pi.R | 24 - coala-0.3.0/coala/tests/testthat/test-sumstat-tajimas-d.R | 24 - coala-0.3.0/coala/tests/testthat/test-tools.R |only coala-0.3.0/coala/vignettes/coala-data-import.Rmd |only coala-0.3.0/coala/vignettes/coala-install.Rmd | 6 66 files changed, 854 insertions(+), 349 deletions(-)
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non-Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Diff between PhySortR versions 1.0.2 dated 2015-12-16 and 1.0.3 dated 2015-12-21
DESCRIPTION | 16 MD5 | 12 NAMESPACE | 12 R/sortTrees.R | 1148 ++++++++++++++++++++++++------------------------- man/PhySortR.Rd | 4 man/convert.eNewick.Rd | 52 +- man/sortTrees.Rd | 228 ++++----- 7 files changed, 738 insertions(+), 734 deletions(-)
Title: Linear Time Series Analysis
Description: Methods of developing linear time series modelling.
Methods are given for loglikelihood computation, forecasting
and simulation.
Author: A.I. McLeod, Hao Yu, Zinovi Krougly
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between ltsa versions 1.4.5 dated 2015-08-22 and 1.4.6 dated 2015-12-21
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 2 ++ NEWS | 3 +++ R/innovationVariance.R |only man/PredictionVariance.Rd | 7 ++++--- man/exactLoglikelihood.Rd | 20 +++++++++++++++----- man/innovationVariance.Rd |only 8 files changed, 35 insertions(+), 17 deletions(-)
Title: Redraw Base Graphics Using 'grid' Graphics
Description: Functions to convert a page of plots drawn with the
graphics package into identical output drawn with the grid package.
The result looks like the original graphics-based plot, but consists
of grid grobs and viewports that can then be manipulated with
grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridGraphics versions 0.1-3 dated 2015-02-09 and 0.1-5 dated 2015-12-21
DESCRIPTION | 9 +++-- MD5 | 20 ++++++------ NAMESPACE | 6 +++ R/axis.R | 54 ++++++++++++++++++--------------- R/graphics.R | 6 +++ R/plotdiff.R | 57 ++++++++++++++++++++++++----------- R/title.R | 2 - inst/NEWS.Rd | 27 ++++++++++++++++ inst/test-scripts/test-hist.POSIXt.R | 4 +- man/grid.echo.Rd | 9 +++-- man/plotdiff.Rd | 6 --- 11 files changed, 132 insertions(+), 68 deletions(-)
Title: Offers Various Swiss Maps as ggplot2 Objects
Description: Offers various swiss maps as ggplot2 objects and gives the
possibility to add layers of data on the maps. Data are publicly available
from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre],
Eric Stephani [aut],
Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>
Diff between ggswissmaps versions 0.0.2 dated 2014-11-07 and 0.0.6 dated 2015-12-21
DESCRIPTION | 23 ++++++++++----- MD5 | 29 +++++++++++++----- NAMESPACE | 12 +------ NEWS | 26 ++++++++++++++++- R/ggswissmaps_data.R | 78 +++++++++++++++++++++++++++++++++++++++++++++++++-- R/ggswissmaps_funs.R |only README.md |only build |only data/datalist |only data/maps.rda |binary data/maps2.rda |only data/shp_df.rda |only inst |only man/ggswissmaps.Rd | 3 + man/maps.Rd | 7 ++-- man/maps2.Rd |only man/shp_df.Rd |only man/theme_white.Rd | 28 +++--------------- man/theme_white_f.Rd |only vignettes |only 20 files changed, 151 insertions(+), 55 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.1-0 dated 2015-12-14 and 0.1-1 dated 2015-12-21
DESCRIPTION | 12 ++++-------- MD5 | 8 ++++---- inst/doc/clsrank.Rnw | 6 +++--- inst/doc/clsrank.pdf |binary vignettes/clsrank.Rnw | 6 +++--- 5 files changed, 14 insertions(+), 18 deletions(-)
Title: Boosting Conditional Logit Model
Description: A set of functions to fit a boosting conditional logit model.
Author: Haolun Shi and Guosheng Yin
Maintainer: Haolun Shi <shl2003@connect.hku.hk>
Diff between clogitboost versions 1.0 dated 2015-11-26 and 1.1 dated 2015-12-21
DESCRIPTION | 17 ++----- MD5 | 20 ++++---- R/clogitboost.R | 2 R/fitclogitboost.R | 102 ++++++++++++++++++++++++--------------------- R/plot.clogitboost.R | 4 - man/clogitboost.Rd | 30 ++++++------- man/marginal.Rd | 10 ++-- man/plot.clogitboost.Rd | 12 ++--- man/predict.clogitboost.Rd | 18 +++---- man/summary.clogitboost.Rd | 12 ++--- man/travel.Rd | 14 +++--- 11 files changed, 121 insertions(+), 120 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.3.0 dated 2015-09-28 and 3.3.1 dated 2015-12-21
DESCRIPTION | 10 ++- MD5 | 90 ++++++++++++++++----------------- NAMESPACE | 2 NEWS | 10 +++ R/choropleth.R | 46 ++++++++-------- README.md | 8 ++ build/vignette.rds |binary inst/doc/a-introduction.html | 2 inst/doc/b-state-choropleth.html | 6 +- inst/doc/c-county-choropleth.html | 8 +- inst/doc/d-country-choropleth.html | 6 +- inst/doc/f-world-bank-data.html | 6 +- inst/doc/h-creating-your-own-maps.html | 2 inst/doc/i-creating-admin1-maps.html | 6 +- man/Admin1Choropleth.Rd | 6 -- man/Choropleth.Rd | 6 -- man/CountryChoropleth.Rd | 6 -- man/CountyChoropleth.Rd | 6 -- man/CountyZoomChoropleth.Rd | 6 -- man/StateChoropleth.Rd | 6 -- man/USAChoropleth.Rd | 10 +-- man/admin1_choropleth.Rd | 24 ++++---- man/choroplethr.Rd | 8 +- man/choroplethr_acs.Rd | 8 +- man/choroplethr_animate.Rd | 2 man/choroplethr_wdi.Rd | 11 ++-- man/continental_us_states.Rd | 2 man/country_choropleth.Rd | 12 ++-- man/county_choropleth.Rd | 32 +++++------ man/county_choropleth_acs.Rd | 14 ++--- man/county_zoom_choropleth.Rd | 6 +- man/df_county_demographics.Rd | 2 man/df_japan_census.Rd | 2 man/df_pop_country.Rd | 2 man/df_pop_county.Rd | 2 man/df_pop_state.Rd | 2 man/df_president.Rd | 2 man/df_president_ts.Rd | 4 - man/df_state_demographics.Rd | 2 man/get_acs_data.Rd | 8 +- man/get_acs_df.Rd | 2 man/get_county_demographics.Rd | 4 - man/get_state_demographics.Rd | 4 - man/state_choropleth.Rd | 26 ++++----- man/state_choropleth_acs.Rd | 10 +-- man/zip_map.Rd | 8 +- 46 files changed, 225 insertions(+), 222 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description:
R interface to a W3C Markup Validation service.
See <http://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.1-4 dated 2015-06-24 and 0.1-5 dated 2015-12-20
DESCRIPTION | 9 +++-- MD5 | 6 +-- NAMESPACE | 16 +++++---- R/w3c.R | 98 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 67 insertions(+), 62 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-21 0.1.1
2015-09-10 0.1.0
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.2-1 dated 2015-11-19 and 0.6.3 dated 2015-12-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 2 +- R/classify.R | 24 ++++++++++++++++-------- R/gui.classify.R | 2 ++ R/load.corpus.R | 7 ++++++- R/load.corpus.and.parse.R | 11 +++++++++-- R/make.table.of.frequencies.R | 13 ++++++++++++- R/stylo.R | 28 ++++++++++++++++++++++++++-- R/stylo.default.settings.R | 3 +++ man/load.corpus.Rd | 5 +++-- man/load.corpus.and.parse.Rd | 5 +++-- 12 files changed, 96 insertions(+), 34 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.6 dated 2015-10-20 and 3.6-1 dated 2015-12-20
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 7 +++++++ R/dendrite.R | 34 +++++++++++++++++++++++++--------- R/ehplot.R | 50 +++++++++++++++++++++++++++++++------------------- R/pyramid.plot.R | 8 ++++++-- R/vectorField.R | 10 +++++++--- data/soils.rda |binary man/barNest.Rd | 22 +++++++++++++++++++++- man/ehplot.Rd | 14 +++++++++++--- man/furc.Rd | 9 ++++++++- man/plot.dendrite.Rd | 14 +++++++++++--- man/pyramid.plot.Rd | 5 +++-- 13 files changed, 146 insertions(+), 59 deletions(-)
Title: Harvest Metadata Using OAI-PMH v2.0
Description:
Harvest metadata using the Open Archives Initiative Protocol for Metadata
Harvesting (OAI-PMH) version 2.0.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between OAIHarvester versions 0.1-7 dated 2014-04-02 and 0.2-0 dated 2015-12-20
DESCRIPTION | 11 +++++----- MD5 | 16 +++++++-------- NAMESPACE | 12 ++++++++--- R/get.R | 55 ++++++++++++++++++++++++++--------------------------- R/pmh.R | 7 +++--- build/vignette.rds |binary inst/doc/oaih.Rnw | 2 - inst/doc/oaih.pdf |binary vignettes/oaih.Rnw | 2 - 9 files changed, 56 insertions(+), 49 deletions(-)
More information about ContaminatedMixt at CRAN
Permanent link
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.4.2 dated 2015-10-24 and 0.4.3 dated 2015-12-20
DESCRIPTION | 9 +- MD5 | 30 ++++---- NAMESPACE | 4 - NEWS | 14 ++- R/qic.R | 22 ++++- R/tcc.R | 163 +++++++++++++++++++++++++++----------------- README.md | 11 ++ build/vignette.rds |binary inst/doc/controlcharts.html | 4 - inst/doc/runcharts.html | 4 - man/paretochart.Rd | 2 man/plot.qic.Rd | 3 man/plot.tcc.Rd | 7 + man/qic.Rd | 11 ++ man/tcc.Rd | 37 +++++---- man/trc.Rd | 2 16 files changed, 199 insertions(+), 124 deletions(-)
Title: Create Interactive Web Graphics via Plotly's JavaScript Graphing
Library
Description: Easily translate ggplot2 graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut, cph],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 2.0.3 dated 2015-11-25 and 2.0.16 dated 2015-12-20
plotly-2.0.16/plotly/DESCRIPTION | 8 plotly-2.0.16/plotly/MD5 | 97 +- plotly-2.0.16/plotly/NEWS | 52 + plotly-2.0.16/plotly/R/build_function.R | 9 plotly-2.0.16/plotly/R/colour_conversion.R | 9 plotly-2.0.16/plotly/R/corresp_one_one.R | 171 ++-- plotly-2.0.16/plotly/R/ggplotly.R | 131 +-- plotly-2.0.16/plotly/R/plotly.R | 16 plotly-2.0.16/plotly/R/plotly_IMAGE.R | 2 plotly-2.0.16/plotly/R/plotly_POST.R | 4 plotly-2.0.16/plotly/R/process.R | 1 plotly-2.0.16/plotly/R/subplots.R | 6 plotly-2.0.16/plotly/R/trace_generation.R | 359 +++++----- plotly-2.0.16/plotly/R/utils.R | 33 plotly-2.0.16/plotly/inst/doc/intro.R | 11 plotly-2.0.16/plotly/inst/doc/intro.Rmd | 18 plotly-2.0.16/plotly/inst/doc/intro.html | 91 +- plotly-2.0.16/plotly/inst/docs.R | 4 plotly-2.0.16/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 76 +- plotly-2.0.16/plotly/inst/htmlwidgets/plotly.js | 4 plotly-2.0.16/plotly/inst/htmlwidgets/plotly.yaml | 2 plotly-2.0.16/plotly/man/plotly_IMAGE.Rd | 2 plotly-2.0.16/plotly/man/subplot.Rd | 2 plotly-2.0.16/plotly/tests/testthat.R | 205 +++-- plotly-2.0.16/plotly/tests/testthat/test-cookbook-axes.R | 2 plotly-2.0.16/plotly/tests/testthat/test-cookbook-lines.R | 37 - plotly-2.0.16/plotly/tests/testthat/test-cookbook-scatterplots.R | 8 plotly-2.0.16/plotly/tests/testthat/test-ggplot-abline.R | 54 + plotly-2.0.16/plotly/tests/testthat/test-ggplot-area.R | 45 + plotly-2.0.16/plotly/tests/testthat/test-ggplot-bar.R | 118 +-- plotly-2.0.16/plotly/tests/testthat/test-ggplot-boxplot.R | 58 + plotly-2.0.16/plotly/tests/testthat/test-ggplot-build2.R | 11 plotly-2.0.16/plotly/tests/testthat/test-ggplot-density.R | 27 plotly-2.0.16/plotly/tests/testthat/test-ggplot-density2d.R | 10 plotly-2.0.16/plotly/tests/testthat/test-ggplot-environment.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-hline.R | 61 - plotly-2.0.16/plotly/tests/testthat/test-ggplot-jitter.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-legend-name.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-legend.R | 26 plotly-2.0.16/plotly/tests/testthat/test-ggplot-polygons.R | 71 - plotly-2.0.16/plotly/tests/testthat/test-ggplot-segment.R | 33 plotly-2.0.16/plotly/tests/testthat/test-ggplot-size.R | 21 plotly-2.0.16/plotly/tests/testthat/test-ggplot-stack.R | 16 plotly-2.0.16/plotly/tests/testthat/test-ggplot-step.R | 14 plotly-2.0.16/plotly/tests/testthat/test-ggplot-ticks.R | 40 - plotly-2.0.16/plotly/tests/testthat/test-ggplot-trace-order.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-vline.R | 48 - plotly-2.0.16/plotly/tests/testthat/test-mean-error-bars.R | 63 - plotly-2.0.16/plotly/tests/testthat/test-plotly-subplot.R | 4 plotly-2.0.16/plotly/tests/testthat/test-unimplemented.R | 31 plotly-2.0.16/plotly/vignettes/intro.Rmd | 18 plotly-2.0.3/plotly/tests/testthat/test-ggplot-names.R |only 52 files changed, 1215 insertions(+), 914 deletions(-)
Title: Local Correlation, Spatial Inequalities, Geographically Weighted
Regression and Other Tools
Description: The main purpose of lctools is to provide researchers and educators with easy-to-learn
user friendly tools for calculating key spatial statistics and to apply simple as well as
advanced methods of spatial analysis in real data. These include: Local Pearson and
Geographically Weighted Pearson Correlation Coefficients, Spatial Inequality Measures
(Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I),
several Geographically Weighted Regression techniques and other Spatial Analysis tools
(other geographically weighted statistics). This package also contains functions for
measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <skalo@hua.gr>
Diff between lctools versions 0.2-3 dated 2015-07-05 and 0.2-4 dated 2015-12-20
lctools-0.2-3/lctools/man/gw_variable.Rd |only lctools-0.2-4/lctools/DESCRIPTION | 23 +- lctools-0.2-4/lctools/MD5 | 69 +++++--- lctools-0.2-4/lctools/NAMESPACE | 6 lctools-0.2-4/lctools/R/gw.glm.R |only lctools-0.2-4/lctools/R/gw.glm.bw.R |only lctools-0.2-4/lctools/R/gw.zi.R |only lctools-0.2-4/lctools/R/gw.zi.bw.R |only lctools-0.2-4/lctools/R/gw.zi.mc.test.R |only lctools-0.2-4/lctools/R/gwr.R |only lctools-0.2-4/lctools/R/gwr.bw.R |only lctools-0.2-4/lctools/R/lat2w.R |only lctools-0.2-4/lctools/R/moransI.w.R | 84 +++++----- lctools-0.2-4/lctools/R/random.test.data.R |only lctools-0.2-4/lctools/R/spg.sim.test.R |only lctools-0.2-4/lctools/R/w.matrix.R | 105 +++++++------ lctools-0.2-4/lctools/build/vignette.rds |binary lctools-0.2-4/lctools/data/GR.Municipalities.RData |binary lctools-0.2-4/lctools/data/VotesGR.RData |binary lctools-0.2-4/lctools/inst/doc/SpatialAutocorrelation.R |only lctools-0.2-4/lctools/inst/doc/SpatialAutocorrelation.Rmd |only lctools-0.2-4/lctools/inst/doc/SpatialAutocorrelation.pdf |only lctools-0.2-4/lctools/inst/doc/SpatialInequalities.R | 3 lctools-0.2-4/lctools/inst/doc/SpatialInequalities.Rmd | 7 lctools-0.2-4/lctools/inst/doc/SpatialInequalities.pdf |binary lctools-0.2-4/lctools/man/FLQ.Rd | 2 lctools-0.2-4/lctools/man/GR.Municipalities.Rd | 4 lctools-0.2-4/lctools/man/VotesGR.Rd | 2 lctools-0.2-4/lctools/man/acc.Rd | 7 lctools-0.2-4/lctools/man/gw-variable.Rd |only lctools-0.2-4/lctools/man/gw.glm.Rd |only lctools-0.2-4/lctools/man/gw.glm.bw.Rd |only lctools-0.2-4/lctools/man/gw.glm.cv.Rd |only lctools-0.2-4/lctools/man/gw.zi.Rd |only lctools-0.2-4/lctools/man/gw.zi.bw.Rd |only lctools-0.2-4/lctools/man/gw.zi.cv.Rd |only lctools-0.2-4/lctools/man/gw.zi.light.Rd |only lctools-0.2-4/lctools/man/gw.zi.mc.test.Rd |only lctools-0.2-4/lctools/man/gwr.Rd |only lctools-0.2-4/lctools/man/gwr.bw.Rd |only lctools-0.2-4/lctools/man/gwr.cv.Rd |only lctools-0.2-4/lctools/man/lat2w.Rd |only lctools-0.2-4/lctools/man/lctools-package.Rd | 14 - lctools-0.2-4/lctools/man/moransI.w.Rd | 20 +- lctools-0.2-4/lctools/man/random.test.data.Rd |only lctools-0.2-4/lctools/man/spGini.Rd | 2 lctools-0.2-4/lctools/man/spg.sim.test.Rd |only lctools-0.2-4/lctools/man/w.matrix.Rd | 31 ++- lctools-0.2-4/lctools/vignettes/SpatialAutocorrelation.Rmd | 13 - lctools-0.2-4/lctools/vignettes/SpatialInequalities.Rmd | 7 50 files changed, 244 insertions(+), 155 deletions(-)
Title: Extra Themes, Scales and Geoms for `ggplot2`
Description: Some extra themes, geoms, and scales for `ggplot2`.
Provides `ggplot2` themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, `Fivethirtyeight`, `The Economist`, `Stata`,
`Excel`, and `The Wall Street Journal`, among others.
Provides `geoms` for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre],
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb, cph] (Code from the ggplot2 package.),
Justin Talbot [ctb] (Code from the labeling package)
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 2.2.1 dated 2015-07-01 and 3.0.0 dated 2015-12-20
ggthemes-2.2.1/ggthemes/build/partial.rdb |only ggthemes-2.2.1/ggthemes/man/scale_tufte.Rd |only ggthemes-3.0.0/ggthemes/DESCRIPTION | 36 ggthemes-3.0.0/ggthemes/MD5 | 219 +-- ggthemes-3.0.0/ggthemes/NAMESPACE | 26 ggthemes-3.0.0/ggthemes/NEWS | 16 ggthemes-3.0.0/ggthemes/R/banking.R | 6 ggthemes-3.0.0/ggthemes/R/base.R |only ggthemes-3.0.0/ggthemes/R/calc.R | 23 ggthemes-3.0.0/ggthemes/R/colorblind.R | 7 ggthemes-3.0.0/ggthemes/R/economist.R | 330 ++--- ggthemes-3.0.0/ggthemes/R/excel.R | 19 ggthemes-3.0.0/ggthemes/R/few.R | 20 ggthemes-3.0.0/ggthemes/R/fivethirtyeight.R | 15 ggthemes-3.0.0/ggthemes/R/gdocs.R | 50 ggthemes-3.0.0/ggthemes/R/geom-rangeframe.R | 139 +- ggthemes-3.0.0/ggthemes/R/geom-tufteboxplot.R | 297 ++-- ggthemes-3.0.0/ggthemes/R/ggthemes-data.R | 642 ---------- ggthemes-3.0.0/ggthemes/R/ggthemes-package.R | 15 ggthemes-3.0.0/ggthemes/R/hc.R | 16 ggthemes-3.0.0/ggthemes/R/igray.R | 8 ggthemes-3.0.0/ggthemes/R/pander.R | 7 ggthemes-3.0.0/ggthemes/R/scale-tufte.R | 115 - ggthemes-3.0.0/ggthemes/R/shapes.R | 14 ggthemes-3.0.0/ggthemes/R/show.R |only ggthemes-3.0.0/ggthemes/R/solarized.R | 76 - ggthemes-3.0.0/ggthemes/R/stat-fivenumber.R | 108 + ggthemes-3.0.0/ggthemes/R/stata.R | 73 - ggthemes-3.0.0/ggthemes/R/tableau.R | 36 ggthemes-3.0.0/ggthemes/R/theme-foundation.R | 93 - ggthemes-3.0.0/ggthemes/R/theme-map.R | 3 ggthemes-3.0.0/ggthemes/R/theme-solid.R | 1 ggthemes-3.0.0/ggthemes/R/tufte.R | 1 ggthemes-3.0.0/ggthemes/R/utils.R | 104 - ggthemes-3.0.0/ggthemes/R/wsj.R | 17 ggthemes-3.0.0/ggthemes/build/vignette.rds |binary ggthemes-3.0.0/ggthemes/data |only ggthemes-3.0.0/ggthemes/inst/doc/ggthemes.R | 182 +- ggthemes-3.0.0/ggthemes/inst/doc/ggthemes.html | 295 ++-- ggthemes-3.0.0/ggthemes/man/bank_slopes.Rd | 6 ggthemes-3.0.0/ggthemes/man/calc_pal.Rd | 6 ggthemes-3.0.0/ggthemes/man/calc_shape_pal.Rd | 3 ggthemes-3.0.0/ggthemes/man/circlefill_shape_pal.Rd | 11 ggthemes-3.0.0/ggthemes/man/cleveland_shape_pal.Rd | 23 ggthemes-3.0.0/ggthemes/man/colorblind.Rd | 9 ggthemes-3.0.0/ggthemes/man/economist_pal.Rd | 6 ggthemes-3.0.0/ggthemes/man/excel_pal.Rd | 8 ggthemes-3.0.0/ggthemes/man/few_pal.Rd | 8 ggthemes-3.0.0/ggthemes/man/fivethirtyeight_pal.Rd | 6 ggthemes-3.0.0/ggthemes/man/gdocs_pal.Rd | 8 ggthemes-3.0.0/ggthemes/man/geom_rangeframe.Rd | 69 - 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Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.5.1 dated 2015-12-04 and 0.6.2 dated 2015-12-20
GERGM-0.5.1/GERGM/man/GERGM.Rd |only GERGM-0.6.2/GERGM/DESCRIPTION | 8 GERGM-0.6.2/GERGM/MD5 | 54 +- GERGM-0.6.2/GERGM/NAMESPACE | 1 GERGM-0.6.2/GERGM/R/Add_Intercept_Term.R |only GERGM-0.6.2/GERGM/R/Convert_Simulated_Networks_To_Observed_Scale.R |only GERGM-0.6.2/GERGM/R/Create_GERGM_Object_From_Formula.R | 2 GERGM-0.6.2/GERGM/R/Estimate_GERGM.R | 227 +++++++--- GERGM-0.6.2/GERGM/R/Estimate_Plot.R | 25 - GERGM-0.6.2/GERGM/R/GERGM_Class.R | 4 GERGM-0.6.2/GERGM/R/GOF.R | 58 +- GERGM-0.6.2/GERGM/R/Helper_Functions.R | 8 GERGM-0.6.2/GERGM/R/Log_Likelihood_and_MPLE_Objective.R | 62 ++ GERGM-0.6.2/GERGM/R/MCMCMLE.R | 133 +++-- GERGM-0.6.2/GERGM/R/Network_Statistic_Calculation_Functions.R | 12 GERGM-0.6.2/GERGM/R/Package_Documentation.R | 2 GERGM-0.6.2/GERGM/R/Parse_Formula_Object.R | 3 GERGM-0.6.2/GERGM/R/Prepare_Covariates.R | 154 ++++-- GERGM-0.6.2/GERGM/R/Simulate_GERGM.R | 7 GERGM-0.6.2/GERGM/R/Thin_Statistic_Samples.R |only GERGM-0.6.2/GERGM/R/Trace_Plot.R | 6 GERGM-0.6.2/GERGM/R/gergm.R | 140 ++++-- GERGM-0.6.2/GERGM/R/simulate_networks.R | 103 +++- GERGM-0.6.2/GERGM/README.md | 12 GERGM-0.6.2/GERGM/man/Estimate_Plot.Rd | 4 GERGM-0.6.2/GERGM/man/GOF.Rd | 6 GERGM-0.6.2/GERGM/man/gergm.Rd |only GERGM-0.6.2/GERGM/man/simulate_networks.Rd | 33 - GERGM-0.6.2/GERGM/tests/testthat/test_experimental_features.R |only GERGM-0.6.2/GERGM/tests/testthat/test_gergm.R | 66 +- GERGM-0.6.2/GERGM/tests/testthat/test_gergm_with_downweighting.R | 22 31 files changed, 790 insertions(+), 362 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between ggmap versions 2.5.2 dated 2015-08-21 and 2.6 dated 2015-12-19
DESCRIPTION | 20 +-- MD5 | 119 +++++++++--------- NAMESPACE | 11 + NEWS | 300 ++++++++++++++++++++++++++++------------------- R/XY2LonLat.R | 29 ++-- R/bb2bbox.R | 19 ++ R/file_drawer.R | 6 R/geocode.R | 39 +++--- R/geom_leg.R |only R/get_googlemap.R | 31 +++- R/get_map.R | 4 R/get_stamenmap.R | 4 R/gglocator.R | 4 R/ggmap.R | 57 +++++--- R/ggplot2.R | 10 - R/help.R | 7 - R/inset.R | 71 ++++++----- R/inset_raster.R | 108 ++++++++++++---- R/mapdist.R | 40 ++++-- R/qmap.R | 14 +- R/qmplot.R | 62 +++++---- R/route.R | 170 +++++++++++++++----------- R/theme_nothing.R | 30 ++-- README.md | 25 ++- man/LonLat2XY.Rd | 7 - man/OSM_scale_lookup.Rd | 5 man/XY2LonLat.Rd | 17 ++ man/bb2bbox.Rd | 23 ++- man/calc_zoom.Rd | 2 man/crime.Rd | 2 man/distQueryCheck.Rd | 2 man/file_drawer.Rd | 8 + man/geocode.Rd | 34 +++-- man/geom_leg.Rd | 190 +++++++++++++++++++++++++---- man/get_cloudmademap.Rd | 2 man/get_googlemap.Rd | 12 + man/get_map.Rd | 2 man/get_navermap.Rd | 3 man/get_openstreetmap.Rd | 3 man/get_stamenmap.Rd | 8 - man/ggimage.Rd | 3 man/gglocator.Rd | 5 man/ggmap.Rd | 54 +++++--- man/ggmapplot.Rd | 2 man/hadley.Rd | 2 man/inset.Rd | 6 man/inset_raster.Rd | 34 +++-- man/legs2route.Rd | 4 man/make_bbox.Rd | 3 man/mapdist.Rd | 39 ++++-- man/mutate_geocode.Rd | 5 man/print.ggmap.Rd | 5 man/qmap.Rd | 4 man/qmplot.Rd | 11 - man/revgeocode.Rd | 4 man/route.Rd | 41 ++---- man/routeQueryCheck.Rd | 2 man/theme_inset.Rd | 23 +-- man/theme_nothing.Rd | 8 - man/wind.Rd | 2 man/zips.Rd | 2 61 files changed, 1122 insertions(+), 637 deletions(-)
Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format (described at
<https://github.com/toml-lang/toml>) suitable for both human editing as well
as the common uses of a machine-readable format. This package uses 'Rcpp' to
connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.0.4 dated 2015-07-16 and 0.0.5 dated 2015-12-19
ChangeLog | 16 DESCRIPTION | 8 MD5 | 16 inst/include/cpptoml.h | 1072 +++++++++++++++++++++++++++++++++++------ src/parse.cpp | 17 tests/float.Rout.save | 3 tests/float.toml | 2 tests/tomlExamples.Rout.save | 3 tests/toml_example-v0.4.0.toml | 2 9 files changed, 958 insertions(+), 181 deletions(-)
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 1.5.5 dated 2015-10-05 and 1.5.7 dated 2015-12-19
DESCRIPTION | 6 - MD5 | 22 ++-- NAMESPACE | 2 R/plot.prodlim.R | 153 +++++++++++++++-------------- R/prodlim-package.R | 5 R/prodlim.R | 268 +++++++++++++++++++++++++++------------------------ R/quantile.prodlim.R | 73 +++++++------ R/redist.R |only R/stopTime.R |only R/summary.Hist.R | 23 +++- man/plot.prodlim.Rd | 24 ++-- man/prodlim.Rd | 114 ++++++++++++--------- man/redist.Rd |only man/stopTime.Rd |only 14 files changed, 379 insertions(+), 311 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples to compute Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.2.2 dated 2015-12-11 and 1.2.3 dated 2015-12-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/pnea.R | 10 ++++++++-- 3 files changed, 14 insertions(+), 8 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.3 dated 2015-11-26 and 0.4 dated 2015-12-19
DESCRIPTION | 17 +++---- MD5 | 47 +++++++++++--------- NAMESPACE | 3 - NEWS | 121 ++++++++++++++++++++++++++++++++-------------------- R/coef.arx.R | 2 R/coef.gets.R | 23 ++++----- R/eviews.R |only R/fitted.arx.R | 3 - R/getsm.R | 108 +++++++++++++++++++++++++--------------------- R/getsv.R | 14 ++++-- R/isat.R | 28 ++++++------ R/isattest.R | 1 R/ols.R | 115 ++++++++++++++++++++++++++++++++++++++++++------- R/plot.gets.R | 34 ++++++++++---- R/print.gets.R | 29 ++++++++---- R/recursive.R |only R/stata.R |only R/vcov.arx.R | 3 - man/biascorr.Rd | 9 +-- man/eviews.Rd |only man/gets-package.Rd | 9 +-- man/getsm.Rd | 2 man/iim.Rd | 6 +- man/isat.Rd | 6 -- man/isattest.Rd | 2 man/ols.Rd | 24 +++++++++- man/recursive.Rd |only 27 files changed, 386 insertions(+), 220 deletions(-)
Title: Dynamic Simulations of Autoregressive Relationships
Description: Dynamic simulations and graphical depictions of autoregressive
relationships.
Author: Christopher Gandrud [aut, cre],
Laron K. Williams [aut],
Guy D. Whitten [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between dynsim versions 1.2 dated 2015-07-24 and 1.2.1 dated 2015-12-19
DESCRIPTION | 16 +++++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 3 +-- NEWS | 4 ++++ R/dynsimGG.R | 9 ++++----- README.md | 3 ++- build/vignette.rds |binary demo/grunfeld-examples.R | 4 ++-- inst/doc/dynsim-overview.R | 4 ++-- inst/doc/dynsim-overview.Rnw | 14 +++++++------- inst/doc/dynsim-overview.pdf |binary man/dynsim.Rd | 5 +++-- man/dynsimGG.Rd | 11 ++++++----- man/grunfeld.Rd | 2 +- vignettes/dynsim-overview.Rnw | 14 +++++++------- 15 files changed, 62 insertions(+), 55 deletions(-)
Title: Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bujar versions 0.1-5 dated 2015-10-27 and 0.2-1 dated 2015-12-19
.Rinstignore |only DESCRIPTION | 17 - MD5 | 31 + NAMESPACE | 12 NEWS | 35 ++ R/bstfit.R |only R/bujar.R | 821 +++++++++++++++++++++++--------------------------- R/gcv_enet.R | 2 R/predval.R |only build |only data |only inst/doc |only man/bujar-internal.Rd | 4 man/bujar.Rd | 53 +-- man/chop.Rd |only man/rchop.Rd |only vignettes |only 17 files changed, 495 insertions(+), 480 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.1-2 dated 2015-08-23 and 1.1-3 dated 2015-12-19
DESCRIPTION | 18 - MD5 | 48 ++-- NAMESPACE | 26 +- R/AAAparameter.R | 6 R/criterion.dist.R | 28 ++ R/dissimilartiy.R | 46 +++ R/hmap.R | 56 +++- R/permute.R | 286 +++++++++++++---------- R/robinson.R |only R/seriate.dist.R | 270 +++++++++++++--------- R/seriate.matrix.R | 8 README.md |only inst/NEWS | 47 ++- inst/doc/seriation.R | 70 ++--- inst/doc/seriation.Rnw | 432 ++++++++++++++++++++---------------- inst/doc/seriation.pdf |binary inst/tests/test-dissimilarity.R |only inst/tests/test-permuation_vector.R | 22 + man/criterion.Rd | 150 +++++++----- man/dissimilarity.Rd | 13 - man/hmap.Rd | 25 +- man/permute.Rd | 32 +- man/reorder_hclust.Rd | 2 man/robinson.Rd |only man/seriate.Rd | 202 +++++++++------- vignettes/seriation.Rnw | 432 ++++++++++++++++++++---------------- vignettes/seriation.bib | 43 +++ 27 files changed, 1341 insertions(+), 921 deletions(-)
Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.20.0 dated 2015-02-19 and 0.21.0 dated 2015-12-19
R.rsp-0.20.0/R.rsp/.Rinstignore |only R.rsp-0.20.0/R.rsp/R/rscript.R |only R.rsp-0.20.0/R.rsp/man/rscript.Rd |only R.rsp-0.20.0/R.rsp/tests/rscript.R |only R.rsp-0.21.0/R.rsp/DESCRIPTION | 16 - R.rsp-0.21.0/R.rsp/MD5 | 78 +++--- R.rsp-0.21.0/R.rsp/NAMESPACE | 16 - R.rsp-0.21.0/R.rsp/NEWS | 36 ++ R.rsp-0.21.0/R.rsp/R/HttpDaemon.R | 14 - R.rsp-0.21.0/R.rsp/R/HttpDaemon.processRsp.R | 15 - R.rsp-0.21.0/R.rsp/R/RspFileProduct.R | 79 ++++++ R.rsp-0.21.0/R.rsp/R/RspRSourceCode.R | 2 R.rsp-0.21.0/R.rsp/R/RspRSourceCodeFactory.R | 7 R.rsp-0.21.0/R.rsp/R/findAsciiDoc.R | 22 + R.rsp-0.21.0/R.rsp/R/findPandoc.R | 27 +- R.rsp-0.21.0/R.rsp/R/parseRVignetteMetadata.R | 7 R.rsp-0.21.0/R.rsp/R/rcode.R |only R.rsp-0.21.0/R.rsp/R/translateRspV1.R | 4 R.rsp-0.21.0/R.rsp/R/xweavetangle.R | 2 R.rsp-0.21.0/R.rsp/R/zzz.CmdArgsFunctions.R | 1 R.rsp-0.21.0/R.rsp/build/vignette.rds |binary R.rsp-0.21.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary R.rsp-0.21.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.tex.rsp | 6 R.rsp-0.21.0/R.rsp/inst/doc/RSP_intro.html | 128 ++++++---- R.rsp-0.21.0/R.rsp/inst/doc/RSP_refcard.pdf |binary R.rsp-0.21.0/R.rsp/inst/doc/RSP_refcard.tex.rsp | 2 R.rsp-0.21.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx | 12 R.rsp-0.21.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |binary R.rsp-0.21.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 4 R.rsp-0.21.0/R.rsp/inst/doc/R_packages-RSP_vignettes.md.rsp | 2 R.rsp-0.21.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf |binary R.rsp-0.21.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary R.rsp-0.21.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.tex.rsp | 1 R.rsp-0.21.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.tex.rsp | 8 R.rsp-0.21.0/R.rsp/man/R.rsp-package.Rd | 2 R.rsp-0.21.0/R.rsp/man/RspDocument.Rd | 2 R.rsp-0.21.0/R.rsp/man/RspString.Rd | 2 R.rsp-0.21.0/R.rsp/man/rcode.Rd |only R.rsp-0.21.0/R.rsp/tests/rcode.R |only R.rsp-0.21.0/R.rsp/tests/rsp_tests.R | 2 R.rsp-0.21.0/R.rsp/vignettes/Dynamic_document_creation_using_RSP.tex.rsp | 6 R.rsp-0.21.0/R.rsp/vignettes/RSP_refcard.tex.rsp | 2 R.rsp-0.21.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx | 12 R.rsp-0.21.0/R.rsp/vignettes/R_packages-RSP_vignettes.md.rsp | 2 44 files changed, 366 insertions(+), 153 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-30 dated 2015-12-10 and 2.5-2 dated 2015-12-19
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/as.matrix.R | 9 +++++---- R/contour.R | 15 ++++++++++++++- R/rasterizePolygons.R | 24 ++++++++++++++++-------- R/setValues.R | 8 ++++---- R/stackApply.R | 20 +++++++++++++++++--- inst/doc/Raster.pdf |binary inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary man/as.matrix.Rd | 2 +- 13 files changed, 80 insertions(+), 39 deletions(-)
Title: Qualitative Comparative Analysis
Description: Starting with version 2.0, the package QCA acts as an aggregator for the various packages dealing with Qualitative Comparative Analysis. For the moment, it is a gateway to the QCAGUI package, but more related packages are expected to be loaded at runtime.
Author: Adrian Dusa [aut, cre, cph],
Alrik Thiem [aut] (from version 1.0-0, up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 1.1-4 dated 2014-12-28 and 2.0 dated 2015-12-19
QCA-1.1-4/QCA/R |only QCA-1.1-4/QCA/data |only QCA-1.1-4/QCA/inst/CITATION |only QCA-1.1-4/QCA/inst/TODO |only QCA-1.1-4/QCA/man/QCA-internal.Rd |only QCA-1.1-4/QCA/man/allExpressions.Rd |only QCA-1.1-4/QCA/man/calibrate.Rd |only QCA-1.1-4/QCA/man/createMatrix.Rd |only QCA-1.1-4/QCA/man/d.biodiversity.Rd |only QCA-1.1-4/QCA/man/d.education.Rd |only QCA-1.1-4/QCA/man/d.graduate.Rd |only QCA-1.1-4/QCA/man/d.health.Rd |only QCA-1.1-4/QCA/man/d.homeless.Rd |only QCA-1.1-4/QCA/man/d.jobsecurity.Rd |only QCA-1.1-4/QCA/man/d.napoleon.Rd |only QCA-1.1-4/QCA/man/d.partybans.Rd |only QCA-1.1-4/QCA/man/d.represent.Rd |only QCA-1.1-4/QCA/man/d.socialsecurity.Rd |only QCA-1.1-4/QCA/man/d.stakeholder.Rd |only QCA-1.1-4/QCA/man/d.transport.Rd |only QCA-1.1-4/QCA/man/d.urban.Rd |only QCA-1.1-4/QCA/man/deMorgan.Rd |only QCA-1.1-4/QCA/man/demoChart.Rd |only QCA-1.1-4/QCA/man/eqmcc.Rd |only QCA-1.1-4/QCA/man/factorize.Rd |only QCA-1.1-4/QCA/man/findSubsets.Rd |only QCA-1.1-4/QCA/man/findSupersets.Rd |only QCA-1.1-4/QCA/man/findTh.Rd |only QCA-1.1-4/QCA/man/getRow.Rd |only QCA-1.1-4/QCA/man/pof.Rd |only QCA-1.1-4/QCA/man/solveChart.Rd |only QCA-1.1-4/QCA/man/superSubset.Rd |only QCA-1.1-4/QCA/man/truthTable.Rd |only QCA-1.1-4/QCA/src |only QCA-2.0/QCA/DESCRIPTION | 27 ++---- QCA-2.0/QCA/MD5 | 92 +---------------------- QCA-2.0/QCA/NAMESPACE | 58 +------------- QCA-2.0/QCA/inst/ChangeLog | 3 QCA-2.0/QCA/man/QCA.package.Rd | 134 ++-------------------------------- 39 files changed, 30 insertions(+), 284 deletions(-)
Title: Selecting Variables in Regression Models
Description: A simple method
to select the best model or best subset of variables using
different types of data (binary, Gaussian or Poisson) and
applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between FWDselect versions 2.0.1 dated 2015-10-11 and 2.1.0 dated 2015-12-19
DESCRIPTION | 19 ++++++++------- MD5 | 36 ++++++++++++++-------------- NAMESPACE | 5 +++- NEWS | 13 +++++++++- R/FWDselect.R | 2 - R/print.qselection.R | 10 ++++++-- R/qselection.R | 17 +++++++++---- R/selection.R | 60 ++++++++++++++++++++++++++++++++++++++++-------- R/test.R | 33 ++++++++++++++++---------- man/FWDselect.Rd | 4 +-- man/diabetes.Rd | 3 +- man/episode.Rd | 3 +- man/plot.qselection.Rd | 2 - man/pollution.Rd | 3 +- man/print.qselection.Rd | 5 ++-- man/print.selection.Rd | 2 - man/qselection.Rd | 20 +++++++++++----- man/selection.Rd | 17 +++++++++---- man/test.Rd | 25 ++++++++++++-------- 19 files changed, 190 insertions(+), 89 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.5.0 dated 2015-07-01 and 0.6.0 dated 2015-12-19
DESCRIPTION | 8 - MD5 | 42 ++++++---- NEWS | 8 + R/plot_grid.R | 16 ++- R/save.R | 167 +++++++++++++++++++++-------------------- R/setup.R | 1 R/switch_axis.R | 48 +++++++++-- R/themes.R | 36 ++++++-- TODO | 2 build/vignette.rds |binary inst/doc/axis_position.html | 80 ++++++++++++------- inst/doc/introduction.html | 126 +++++++++++++++++------------- inst/doc/plot_annotations.R |only inst/doc/plot_annotations.Rmd |only inst/doc/plot_annotations.html |only inst/doc/plot_grid.R | 22 +++-- inst/doc/plot_grid.Rmd | 27 ++++-- inst/doc/plot_grid.html | 111 ++++++++++++++++----------- inst/doc/shared_legends.R |only inst/doc/shared_legends.Rmd |only inst/doc/shared_legends.html |only man/ggsave.Rd | 7 - man/plot_grid.Rd | 11 +- vignettes/plot_annotations.Rmd |only vignettes/plot_grid.Rmd | 27 ++++-- vignettes/shared_legends.Rmd |only 26 files changed, 448 insertions(+), 291 deletions(-)
Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and nonconvex loss functions, for both classical and robust regression and classification problems. HingeBoost is implemented for binary and multi-class classification, with unequal misclassification costs for binary case. The algorithm can fit linear and nonlinear classifiers.
Author: Zhu Wang [aut, cre],
Torsten Hothorn [ctb]
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bst versions 0.3-4 dated 2014-06-23 and 0.3-11 dated 2015-12-19
DESCRIPTION | 21 MD5 | 53 +- NAMESPACE | 17 NEWS | 31 + R/bst.R | 1279 +++++++++++++++++++++++++++++++------------------- R/mada.R | 20 R/mbst.R |only R/mhingebst.R | 34 + R/rmbst.R |only TODO |only build |only inst |only man/bst-internal.Rd | 2 man/bst.Rd | 44 + man/bst.sel.Rd | 4 man/bst_control.Rd | 25 man/cv.bst.Rd | 14 man/cv.mbst.Rd |only man/cv.mhingebst.Rd | 4 man/ex1data.Rd | 4 man/mada.Rd | 5 man/mbst.Rd |only man/nsel.mhingebst.Rd |only man/rbst.Rd |only man/rbstpath.Rd |only man/rmbst.Rd |only vignettes |only 27 files changed, 1028 insertions(+), 529 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette <debeaudette@ucdavis.edu>, Pierre Roudier <roudierp@landcareresearch.co.nz>
Maintainer: Dylan Beaudette <debeaudette@ucdavis.edu>
Diff between aqp versions 1.9.2 dated 2015-12-04 and 1.9.3 dated 2015-12-19
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS | 6 ++++++ R/SoilProfileCollection-methods.R | 36 ++++++++++++++++-------------------- 4 files changed, 31 insertions(+), 29 deletions(-)
Title: Variational Bayes Latent Position Cluster Model for Networks
Description: Fit and simulate latent position and cluster
models for network data, using a fast Variational Bayes approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend <mike.saltertownshend@gmail.com>
Diff between VBLPCM versions 2.4.3 dated 2014-03-07 and 2.4.4 dated 2015-12-18
CHANGELOG | 5 DESCRIPTION | 20 MD5 | 16 NAMESPACE | 14 configure | 1107 ++++---------------------------------------------- configure.ac | 26 - man/VBLPCM-package.Rd | 55 -- man/gof.vblpcm.Rd | 6 man/vblpcmBIC.Rd | 7 9 files changed, 141 insertions(+), 1115 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix
design, along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.0.1 dated 2015-12-17 and 1.0.2 dated 2015-12-18
DESCRIPTION | 16 ++++++++-------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 11 +++++++++-- NEWS | 6 ++++++ R/UpSet.plot.R | 9 +++++++++ R/upset.R | 3 +-- inst/doc/attribute.plots.html | 6 +++--- inst/doc/basic.usage.R | 13 +++++++++++++ inst/doc/basic.usage.Rmd | 17 +++++++++++++++++ inst/doc/basic.usage.html | 21 +++++++++++++++++++-- inst/doc/queries.html | 8 ++++---- man/elements.Rd | 2 +- man/fromExpression.Rd | 2 +- man/fromList.Rd | 2 +- man/histogram.Rd | 2 +- man/intersects.Rd | 2 +- man/scatter_plot.Rd | 2 +- man/upset.Rd | 2 +- 18 files changed, 113 insertions(+), 45 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification arose from verifying high-resolution forecasts, where coarser-resolution models generally are favored even when a human forecaster finds the higher-resolution model to be considerably better. Most newly proposed methods, which largely come from image analysis, computer vision, and similar, are available, with more on the way.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.2-4 dated 2015-06-01 and 0.3 dated 2015-12-18
SpatialVx-0.2-4/SpatialVx/man/convthresh.Rd |only SpatialVx-0.3/SpatialVx/DESCRIPTION | 8 SpatialVx-0.3/SpatialVx/MD5 | 43 +- SpatialVx-0.3/SpatialVx/NAMESPACE | 14 SpatialVx-0.3/SpatialVx/R/FeatureFinder.R |only SpatialVx-0.3/SpatialVx/R/Features.R | 365 +++++--------------- SpatialVx-0.3/SpatialVx/R/Vgrams.R | 180 +++++++-- SpatialVx-0.3/SpatialVx/man/FeatureAxis.Rd | 4 SpatialVx-0.3/SpatialVx/man/FeatureFinder.Rd |only SpatialVx-0.3/SpatialVx/man/FeatureMatchAnalyzer.Rd | 6 SpatialVx-0.3/SpatialVx/man/FeatureProps.Rd | 2 SpatialVx-0.3/SpatialVx/man/FeatureTable.Rd | 2 SpatialVx-0.3/SpatialVx/man/MergeForce.Rd | 8 SpatialVx-0.3/SpatialVx/man/SpatialVx-internal.Rd | 1 SpatialVx-0.3/SpatialVx/man/SpatialVx-package.Rd | 2 SpatialVx-0.3/SpatialVx/man/combiner.Rd | 2 SpatialVx-0.3/SpatialVx/man/compositer.Rd | 6 SpatialVx-0.3/SpatialVx/man/craer.Rd | 10 SpatialVx-0.3/SpatialVx/man/deltamm.Rd | 10 SpatialVx-0.3/SpatialVx/man/disjointer.Rd |only SpatialVx-0.3/SpatialVx/man/expvg.Rd |only SpatialVx-0.3/SpatialVx/man/hiw.Rd | 6 SpatialVx-0.3/SpatialVx/man/interester.Rd | 6 SpatialVx-0.3/SpatialVx/man/saller.Rd | 6 SpatialVx-0.3/SpatialVx/man/spatMLD.Rd | 13 25 files changed, 326 insertions(+), 368 deletions(-)
Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geosphere versions 1.4-3 dated 2015-07-01 and 1.5-1 dated 2015-12-18
ChangeLog | 9 ++++++-- DESCRIPTION | 8 +++---- MD5 | 22 ++++++++++----------- R/antipodal.R | 4 ++- R/centroid.R | 7 +++--- R/gcLon.R | 11 ++++------ R/gcMaxLat.R | 48 +++++++++++++++++++++++++++-------------------- R/onGreatCircle.R | 6 ++--- inst/doc/geosphere.pdf |binary man/gcMaxLat.Rd | 2 - man/geosphere-package.Rd | 2 - man/onGreatCircle.Rd | 5 ++-- 12 files changed, 70 insertions(+), 54 deletions(-)
Title: Direct Labels for Multicolor Plots
Description: An extensible framework
for automatically placing direct labels onto multicolor lattice or
ggplot2 plots.
Label positions are described using Positioning Methods
which can be re-used across several different plots.
There are heuristics for examining "trellis" and "ggplot" objects
and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <tdhock5@gmail.com>
Diff between directlabels versions 2013.6.15 dated 2013-07-22 and 2015.12.16 dated 2015-12-18
DESCRIPTION | 18 - MD5 | 100 ++++---- NAMESPACE | 6 NEWS | 72 +++++ R/compare.R | 44 ++- R/doc.R | 10 R/ggplot2.R | 370 +++++++++++++++++++++-------- R/lattice.R | 40 +-- R/lineplot.R | 11 R/positioning.functions.R | 57 +++- R/utility.function.R | 408 +++++++++++++++++++++------------ data/projectionSeconds.RData |only man/GeomDl.Rd |only man/ahull.grid.Rd | 2 man/angled.boxes.Rd |only man/angled.endpoints.Rd | 2 man/apply.method.Rd | 65 +++-- man/big.boxes.Rd | 2 man/chull.grid.Rd | 2 man/direct.label.Rd | 20 - man/direct.label.ggplot.Rd | 3 man/direct.label.trellis.Rd | 3 man/directlabels-package.Rd | 2 man/dl.combine.Rd | 27 +- man/dl.move.Rd | 26 +- man/dlcompare.Rd | 43 ++- man/dlgrob.Rd | 3 man/draw.polygons.Rd |only man/drawDetails.dlgrob.Rd | 20 + man/extreme.grid.Rd | 2 man/far.from.others.borders.Rd |only man/first.bumpup.Rd | 2 man/first.polygons.Rd |only man/first.qp.Rd | 2 man/geom_dl.Rd | 122 +++++---- man/getLegendVariables.Rd |only man/iris.l1.cluster.Rd | 13 - man/lasso.labels.Rd | 2 man/last.bumpup.Rd | 2 man/last.polygons.Rd |only man/last.qp.Rd | 2 man/lattice.translators.Rd | 2 man/legends2hide.Rd |only man/maxvar.qp.Rd | 2 man/merge_recurse.Rd |only man/normal.l2.cluster.Rd | 15 - man/panel.superpose.dl.Rd | 16 - man/pkgFun.Rd |only man/polygon.method.Rd |only man/positioning.functions.Rd | 13 + man/projectionSeconds.Rd |only man/qp.labels.Rd | 26 -- man/reduce.cex.lr.Rd | 18 - man/smart.grid.Rd | 2 man/top.bumpup.Rd | 2 man/top.qp.Rd | 2 tests/doc/lineplot/projectionSeconds.R |only tests/ggplot.R |only tests/unattached.R |only 59 files changed, 1052 insertions(+), 549 deletions(-)
Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>
Diff between astrochron versions 0.4.3 dated 2015-07-01 and 0.5 dated 2015-12-18
astrochron-0.4.3/astrochron/R/FUNCTION-arcsinT_v4.R |only astrochron-0.4.3/astrochron/R/FUNCTION-bandpass_v13.R |only astrochron-0.4.3/astrochron/R/FUNCTION-cosTaper_v8.R |only astrochron-0.4.3/astrochron/R/FUNCTION-dpssTaper_v2.R |only astrochron-0.4.3/astrochron/R/FUNCTION-eha_v17.R |only astrochron-0.4.3/astrochron/R/FUNCTION-gausTaper_v7.R |only astrochron-0.4.3/astrochron/R/FUNCTION-hannTaper_v2.R |only astrochron-0.4.3/astrochron/R/FUNCTION-hilbert_v14.R |only astrochron-0.4.3/astrochron/R/FUNCTION-linterp_v7.R |only astrochron-0.4.3/astrochron/R/FUNCTION-logT_v4.R |only astrochron-0.4.3/astrochron/R/FUNCTION-lowpass_v10.R |only astrochron-0.4.3/astrochron/R/FUNCTION-lowspec_v16.R |only astrochron-0.4.3/astrochron/R/FUNCTION-mtmAR_v6.R |only astrochron-0.4.3/astrochron/R/FUNCTION-mtmML96_v8.R |only astrochron-0.4.3/astrochron/R/FUNCTION-mtm_v13.R |only astrochron-0.4.3/astrochron/R/FUNCTION-pad.R |only astrochron-0.4.3/astrochron/R/FUNCTION-peak_v5.R |only astrochron-0.4.3/astrochron/R/FUNCTION-periodogram_v12.R |only astrochron-0.4.3/astrochron/R/FUNCTION-prewhiteAR1_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-prewhiteAR_v4.R |only astrochron-0.4.3/astrochron/R/FUNCTION-rankSeries.R |only astrochron-0.4.3/astrochron/R/FUNCTION-readMatrix_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-read_v23.R |only astrochron-0.4.3/astrochron/R/FUNCTION-stepHeat_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-strats_v10.R |only astrochron-0.4.3/astrochron/R/FUNCTION-taner_v5.R |only astrochron-0.4.3/astrochron/R/FUNCTION-testPrecession.R |only astrochron-0.4.3/astrochron/R/FUNCTION-trackFreq_v7.R |only astrochron-0.4.3/astrochron/R/FUNCTION-trim_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-trough.R |only astrochron-0.4.3/astrochron/R/FUNCTION-wtMean_v11.R |only astrochron-0.5/astrochron/DESCRIPTION | 8 - astrochron-0.5/astrochron/MD5 | 120 +++++++-------- astrochron-0.5/astrochron/NAMESPACE | 3 astrochron-0.5/astrochron/R/FUNCTION-arcsinT_v5.R |only astrochron-0.5/astrochron/R/FUNCTION-bandpass_v14.R |only astrochron-0.5/astrochron/R/FUNCTION-cosTaper_v9.R |only astrochron-0.5/astrochron/R/FUNCTION-dpssTaper_v3.R |only astrochron-0.5/astrochron/R/FUNCTION-eha_v18.R |only astrochron-0.5/astrochron/R/FUNCTION-gausTaper_v8.R |only astrochron-0.5/astrochron/R/FUNCTION-getData.R |only astrochron-0.5/astrochron/R/FUNCTION-hannTaper_v3.R |only astrochron-0.5/astrochron/R/FUNCTION-hilbert_v15.R |only astrochron-0.5/astrochron/R/FUNCTION-linterp_v8.R |only astrochron-0.5/astrochron/R/FUNCTION-logT_v5.R |only astrochron-0.5/astrochron/R/FUNCTION-lowpass_v11.R |only astrochron-0.5/astrochron/R/FUNCTION-lowspec_v17.R |only astrochron-0.5/astrochron/R/FUNCTION-mtmAR_v7.R |only astrochron-0.5/astrochron/R/FUNCTION-mtmML96_v10.R |only astrochron-0.5/astrochron/R/FUNCTION-mtm_v15.R |only astrochron-0.5/astrochron/R/FUNCTION-pad_v2.R |only astrochron-0.5/astrochron/R/FUNCTION-peak_v6.R |only astrochron-0.5/astrochron/R/FUNCTION-periodogram_v13.R |only astrochron-0.5/astrochron/R/FUNCTION-prewhiteAR1_v4.R |only astrochron-0.5/astrochron/R/FUNCTION-prewhiteAR_v5.R |only astrochron-0.5/astrochron/R/FUNCTION-rankSeries_v2.R |only astrochron-0.5/astrochron/R/FUNCTION-readMatrix_v6.R |only astrochron-0.5/astrochron/R/FUNCTION-read_v27.R |only astrochron-0.5/astrochron/R/FUNCTION-stepHeat_v4.R |only astrochron-0.5/astrochron/R/FUNCTION-strats_v12.R |only astrochron-0.5/astrochron/R/FUNCTION-taner_v7.R |only astrochron-0.5/astrochron/R/FUNCTION-testPrecession_v2.R |only astrochron-0.5/astrochron/R/FUNCTION-timeOptSim_v5c.R |only astrochron-0.5/astrochron/R/FUNCTION-timeOpt_v5c.R |only astrochron-0.5/astrochron/R/FUNCTION-trackFreq_v8.R |only astrochron-0.5/astrochron/R/FUNCTION-trim_v4.R |only astrochron-0.5/astrochron/R/FUNCTION-trough_v2.R |only astrochron-0.5/astrochron/R/FUNCTION-wtMean_v12.R |only astrochron-0.5/astrochron/data/modelA.rda |binary astrochron-0.5/astrochron/inst/CITATION | 2 astrochron-0.5/astrochron/man/ar1.Rd | 2 astrochron-0.5/astrochron/man/arcsinT.Rd | 4 astrochron-0.5/astrochron/man/asm.Rd | 2 astrochron-0.5/astrochron/man/astrochron-package.Rd | 18 +- astrochron-0.5/astrochron/man/eAsm.Rd | 6 astrochron-0.5/astrochron/man/eAsmTrack.Rd | 8 - astrochron-0.5/astrochron/man/eha.Rd | 8 - astrochron-0.5/astrochron/man/getData.Rd |only astrochron-0.5/astrochron/man/logT.Rd | 4 astrochron-0.5/astrochron/man/lowpass.Rd | 2 astrochron-0.5/astrochron/man/lowspec.Rd | 8 - astrochron-0.5/astrochron/man/mtm.Rd | 10 - astrochron-0.5/astrochron/man/mtmAR.Rd | 2 astrochron-0.5/astrochron/man/mtmML96.Rd | 10 - astrochron-0.5/astrochron/man/rankSeries.Rd | 2 astrochron-0.5/astrochron/man/read.Rd | 5 astrochron-0.5/astrochron/man/readMatrix.Rd | 3 astrochron-0.5/astrochron/man/stepHeat.Rd | 19 +- astrochron-0.5/astrochron/man/strats.Rd | 2 astrochron-0.5/astrochron/man/taner.Rd | 15 - astrochron-0.5/astrochron/man/testPrecession.Rd | 7 astrochron-0.5/astrochron/man/timeOpt.Rd |only astrochron-0.5/astrochron/man/timeOptSim.Rd |only astrochron-0.5/astrochron/man/trackFreq.Rd | 4 astrochron-0.5/astrochron/man/wtMean.Rd | 16 +- 95 files changed, 162 insertions(+), 128 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implements the pathwise calibrated sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear regression, sparse logistic regression, and sparse undirected graphical model estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. Moreover, users can choose different regularizers, including L1, MCP, and SCAD regularizers. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Tong Zhang and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>
Diff between picasso versions 0.4.7 dated 2015-09-15 and 0.5.0 dated 2015-12-18
DESCRIPTION | 14 - MD5 | 50 ++-- NAMESPACE | 2 R/lasso.sc.naive.R | 114 +++++------ R/picasso.R | 5 R/picasso.lasso.R | 498 ++++++++++++++++++++++++------------------------- build |only inst |only man/coef.lasso.Rd | 2 man/coef.logit.Rd | 2 man/eyedata.Rd | 2 man/picasso-package.Rd | 6 man/picasso.Rd | 11 - man/plot.lasso.Rd | 2 man/plot.logit.Rd | 2 man/plot.scio.Rd | 2 man/plot.sim.Rd | 2 man/predict.lasso.Rd | 2 man/predict.logit.Rd | 2 man/print.lasso.Rd | 2 man/print.logit.Rd | 2 man/print.scio.Rd | 2 man/print.sim.Rd | 2 man/scio.generator.Rd | 2 man/scio.plot.Rd | 2 vignettes |only 26 files changed, 370 insertions(+), 360 deletions(-)
Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 2.0.1 dated 2015-11-09 and 2.1 dated 2015-12-18
DESCRIPTION | 13 MD5 | 48 +- NAMESPACE | 2 R/pcadapt.R | 69 ++-- R/plotting.R | 11 build/vignette.rds |binary inst/doc/pcadapt.Rmd | 42 ++ inst/doc/pcadapt.html | 733 ++++++++++++++++++++++++++++++++------------- man/computeStats.Rd | 3 man/corpca.Rd | 13 man/fstCalc.Rd | 5 man/fstGeno.Rd | 3 man/getPopColors.Rd | 5 man/manhattanPlot.Rd | 3 man/neutralDistribution.Rd | 3 man/pcadapt-package.Rd | 4 man/pcadapt.Rd | 15 man/plot.pcadapt.Rd | 7 man/pval.Rd | 3 man/pvalqqPlot.Rd | 3 man/read.genotype.Rd | 2 man/read4pcadapt.Rd | 5 man/scoresPlot.Rd | 7 man/screePlot.Rd | 5 vignettes/pcadapt.Rmd | 42 ++ 25 files changed, 715 insertions(+), 331 deletions(-)
Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide provided,
or the paper under citation.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>
Diff between likeLTD versions 6.0.0 dated 2015-12-16 and 6.0.1 dated 2015-12-18
DESCRIPTION | 8 MD5 | 36 R/maximize.R | 2 R/objectives-peaks.R | 58 inst/doc/likeLTDguide.pdf |binary inst/doc/usage.pdf |binary man/defence.hypothesis.Rd | 2 man/load.allele.database.Rd | 2 man/optimisation.params.Rd | 2 man/pack.admin.input.Rd | 2 man/prosecution.hypothesis.Rd | 2 man/read.csp.profile.Rd | 2 man/read.known.profiles.Rd | 2 man/read.peaks.profile.Rd | 2 man/read.unc.profile.Rd | 2 src/gammaDist.cpp | 2 src/maximizePeaks.cpp | 3305 ++++++++++++++++++------------------------ src/maximizePeaks.h | 50 src/module.cpp | 1 19 files changed, 1537 insertions(+), 1943 deletions(-)
Title: Auxiliary Functions for Phenological Data Analysis
Description: Provides some easy-to-use functions for
spatial analyses of (plant-) phenological data
sets and satellite observations of vegetation.
Author: Lange, Maximilian and Doktor, Daniel
Maintainer: Daniel Doktor <daniel.doktor@ufz.de>
Diff between phenex versions 1.0-7 dated 2014-02-11 and 1.1-9 dated 2015-12-18
phenex-1.0-7/phenex/man/bise.Rd |only phenex-1.1-9/phenex/DESCRIPTION | 14 +- phenex-1.1-9/phenex/INDEX | 3 phenex-1.1-9/phenex/MD5 | 28 ++-- phenex-1.1-9/phenex/NAMESPACE | 10 - phenex-1.1-9/phenex/R/analyzeBits.R | 10 + phenex-1.1-9/phenex/R/dLogistic.R | 2 phenex-1.1-9/phenex/R/modelNDVI.R | 39 ++++-- phenex-1.1-9/phenex/R/ndvi-class.R | 159 +++++++++++++++++++++++--- phenex-1.1-9/phenex/man/NDVI-class.Rd | 35 +++++ phenex-1.1-9/phenex/man/analyzeBits.Rd | 5 phenex-1.1-9/phenex/man/bise1.Rd |only phenex-1.1-9/phenex/man/bise2.Rd |only phenex-1.1-9/phenex/man/integrateTimeserie.Rd |only phenex-1.1-9/phenex/man/modelNDVI.Rd | 17 ++ phenex-1.1-9/phenex/src/analyzeBits.c | 17 ++ phenex-1.1-9/phenex/src/analyzeBits.h | 3 17 files changed, 276 insertions(+), 66 deletions(-)
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 1.2-1 dated 2015-11-26 and 1.2-2 dated 2015-12-18
equateIRT-1.2-1/equateIRT/inst/doc/equateIRT5_JSS.R |only equateIRT-1.2-1/equateIRT/inst/doc/equateIRT5_JSS.Rnw |only equateIRT-1.2-1/equateIRT/inst/doc/equateIRT5_JSS.pdf |only equateIRT-1.2-1/equateIRT/vignettes/equateIRT5_JSS.Rnw |only equateIRT-1.2-1/equateIRT/vignettes/jsslogo.jpg |only equateIRT-1.2-2/equateIRT/DESCRIPTION | 8 equateIRT-1.2-2/equateIRT/MD5 | 36 - equateIRT-1.2-2/equateIRT/R/functions.r | 75 +- equateIRT-1.2-2/equateIRT/build/vignette.rds |binary equateIRT-1.2-2/equateIRT/inst/CITATION |only equateIRT-1.2-2/equateIRT/inst/NEWS | 9 equateIRT-1.2-2/equateIRT/inst/doc/equateIRT.R |only equateIRT-1.2-2/equateIRT/inst/doc/equateIRT.Rnw |only equateIRT-1.2-2/equateIRT/inst/doc/equateIRT.pdf |only equateIRT-1.2-2/equateIRT/man/alldirec.Rd | 16 equateIRT-1.2-2/equateIRT/man/bisectorec.Rd | 3 equateIRT-1.2-2/equateIRT/man/chainec.Rd | 7 equateIRT-1.2-2/equateIRT/man/convert.Rd | 7 equateIRT-1.2-2/equateIRT/man/direc.Rd | 7 equateIRT-1.2-2/equateIRT/man/equateIRT-package.Rd | 13 equateIRT-1.2-2/equateIRT/man/import.ltm.Rd | 3 equateIRT-1.2-2/equateIRT/man/modIRT.Rd | 11 equateIRT-1.2-2/equateIRT/vignettes/equateIRT.Rnw |only equateIRT-1.2-2/equateIRT/vignettes/equateIRT.bib | 478 ++++++++--------- 24 files changed, 360 insertions(+), 313 deletions(-)
Title: Configural Frequencies Analysis Using Log-Linear Modeling
Description: Offers several functions for Configural Frequencies
Analysis (CFA), which is a useful statistical tool for the analysis of
multiway contingency tables. CFA was introduced by G. A. Lienert as
'Konfigurations Frequenz Analyse - KFA'.
Author: Joerg-Henrik Heine, R.W. Alexandrowicz (function stirling_cfa() )
and intensive package testing by Mark Stemmler
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between confreq versions 1.3-1 dated 2015-05-01 and 1.4 dated 2015-12-18
DESCRIPTION | 11 +++--- MD5 | 50 +++++++++++++++-------------- NAMESPACE | 14 +++++++- NEWS | 12 +++++++ R/CFA.R | 76 +++++++++++++++++++++++++++------------------ R/binomial_test_cfa.R | 31 ++++++++---------- R/confreq-package.R | 11 ++++++ R/expected_margin_cfa.R |only R/summary.CFA.R | 10 ++++- man/CFA.Rd | 13 +++++-- man/S2CFA.Rd | 4 +- man/binomial_test_cfa.Rd | 11 ++---- man/chi_local_test_cfa.Rd | 4 +- man/confreq-package.Rd | 6 +-- man/dat2fre.Rd | 8 ++-- man/design_cfg_cfa.Rd | 4 +- man/df_des_cfa.Rd | 11 ++---- man/expected_cfa.Rd | 4 +- man/expected_margin_cfa.Rd |only man/fre2dat.Rd | 4 +- man/ftab.Rd | 2 - man/lr.Rd | 3 + man/pos_cfg_cfa.Rd | 4 +- man/stirling_cfa.Rd | 4 +- man/summary.CFA.Rd | 6 ++- man/summary.S2CFA.Rd | 2 - man/z_tests_cfa.Rd | 4 +- 27 files changed, 184 insertions(+), 125 deletions(-)
Title: Attaches and Installs Packages
Description: A simple function for easier package loading and auto-installation.
Author: Josh Katz [aut, cre]
Maintainer: Josh Katz <josh.katz@nytimes.com>
Diff between needs versions 0.0.1 dated 2015-12-15 and 0.0.2 dated 2015-12-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/extdata/promptUser | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 3.17-0 dated 2015-09-21 and 3.17-1 dated 2015-12-18
DESCRIPTION | 14 - MD5 | 68 ++++---- NAMESPACE | 6 NEWS | 14 + R/Key.s | 21 -- R/Misc.s | 5 R/biVar.s | 2 R/dates.s | 2 R/drawPlot.s |only R/html.s |only R/labcurve.s | 393 ------------------------------------------------- R/latex.s | 142 ----------------- R/mdb.get.s | 5 R/rcorrp.cens.s | 2 R/sas.get.s | 7 R/spower.s | 2 R/stat-plsmo.r | 61 ++++--- R/summary.formula.s | 40 +++- R/summaryM.s | 60 +++++-- R/summaryP.s | 4 R/transace.s | 2 R/transcan.s | 2 R/upFirst.s |only man/Save.Rd | 9 - man/addMarginal.Rd | 4 man/ffCompress.Rd | 4 man/html.Rd | 14 - man/labcurve.Rd | 13 - man/legendfunctions.Rd | 6 man/mdb.get.Rd | 10 - man/sasxport.get.Rd | 4 man/stat_plsmo.Rd | 5 man/summaryM.Rd | 25 ++- man/summaryP.Rd | 8 man/transcan.Rd | 3 man/upFirst.Rd |only tests/html-summaryM.r |only tests/mChoice.r |only 38 files changed, 247 insertions(+), 710 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native binary
(ENVI) format directly into R based on the widely applied 'raster' package;
calculate monthly value composites (e.g. maximum value composites, MVC) from the
bi-monthly input data; and derive long-term monotonous trends from the
Mann-Kendall trend test, optionally featuring pre-whitening to
account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.3.0 dated 2015-11-13 and 0.4.0 dated 2015-12-18
gimms-0.3.0/gimms/R/createHeader.R |only gimms-0.3.0/gimms/man/createHeader.Rd |only gimms-0.4.0/gimms/DESCRIPTION | 14 + gimms-0.4.0/gimms/MD5 | 28 +-- gimms-0.4.0/gimms/NAMESPACE | 4 gimms-0.4.0/gimms/NEWS |only gimms-0.4.0/gimms/R/downloadGimms.R | 150 +++++++------------- gimms-0.4.0/gimms/R/gimms-package.R | 57 ++++--- gimms-0.4.0/gimms/R/gimmsControls.R |only gimms-0.4.0/gimms/R/monthlyComposite.R | 217 +++++++++++++++++------------- gimms-0.4.0/gimms/R/rasterizeGimms.R | 167 ++++++++++++++++------- gimms-0.4.0/gimms/R/significantTau.R | 11 - gimms-0.4.0/gimms/README.md | 18 ++ gimms-0.4.0/gimms/man/downloadGimms.Rd | 10 - gimms-0.4.0/gimms/man/monthlyComposite.Rd | 34 +++- gimms-0.4.0/gimms/man/rasterizeGimms.Rd | 30 ++-- gimms-0.4.0/gimms/man/significantTau.Rd | 5 17 files changed, 422 insertions(+), 323 deletions(-)
Title: An Implementation of the Grammar of Graphics
Description: An implementation of the grammar of graphics in R. It combines the
advantages of both base and lattice graphics: conditioning and shared axes
are handled automatically, and you can still build up a plot step by step
from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map
data to aesthetic attributes. See http://ggplot2.org for more information,
documentation and examples.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ggplot2 versions 1.0.1 dated 2015-03-17 and 2.0.0 dated 2015-12-18
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Title: Cause-Specific Framework for Competing-Risk Analysis
Description: Numerical integration of cause-specific survival curves to arrive at cause-specific cumulative incidence functions,
with three usage modes: 1) Convenient API for parametric survival regression followed by competing-risk analysis, 2) API for
CFC, accepting user-specified survival functions in R, and 3) Same as 2, but accepting survival functions in C++.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between CFC versions 0.7.0 dated 2015-03-12 and 1.0.0 dated 2015-12-18
ChangeLog |only DESCRIPTION | 22 +- MD5 | 33 ++- NAMESPACE | 37 ++- R/RcppExports.R |only R/cfc.R | 435 ++++++++++++++++++++------------------------ R/cfc_legacy.R |only R/cfc_survreg.R |only R/zzz.R | 2 build |only inst |only man/cfc.Rd |only man/cfc.prepdata.Rd |only man/cfc.survreg.Rd |only man/cfc.survreg.survprob.Rd |only man/cfc.tbasis.Rd | 166 ++++++++-------- man/summary.cfc.survreg.Rd |only man/summary.cfc.tbasis.Rd | 78 +++---- src |only vignettes |only 20 files changed, 388 insertions(+), 385 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability
of linear structural equation models as described in Drton, Foygel &
Sullivant (Ann. Statist., 2011) and Foygel, Draisma & Drton (Ann. Statist.,
2012). The routines are based on the graphical representation of
structural equation models by a path diagram/mixed graph.
Author: Rina Foygel Barber <rina@uchicago.edu>, Mathias Drton <md5@uw.edu>, Luca
Weihs <lucaw@uw.edu>.
Maintainer: Mathias Drton <md5@uw.edu>
Diff between SEMID versions 0.1 dated 2013-08-16 and 0.2 dated 2015-12-18
SEMID-0.1/SEMID/INDEX |only SEMID-0.2/SEMID/DESCRIPTION | 21 SEMID-0.2/SEMID/MD5 | 38 SEMID-0.2/SEMID/NAMESPACE | 9 SEMID-0.2/SEMID/R/SEMID.R |only SEMID-0.2/SEMID/R/graphID.R | 1166 ++++++++++++++++++++--------- SEMID-0.2/SEMID/README.md |only SEMID-0.2/SEMID/demo/SEMID.R | 3 SEMID-0.2/SEMID/man/SEMID-package.Rd |only SEMID-0.2/SEMID/man/ancestors.Rd |only SEMID-0.2/SEMID/man/descendants.Rd |only SEMID-0.2/SEMID/man/getMaxFlow.Rd |only SEMID-0.2/SEMID/man/getMixedCompForNode.Rd |only SEMID-0.2/SEMID/man/graphID.Rd | 91 +- SEMID-0.2/SEMID/man/graphID.ancestralID.Rd |only SEMID-0.2/SEMID/man/graphID.decompose.Rd |only SEMID-0.2/SEMID/man/graphID.genericID.Rd |only SEMID-0.2/SEMID/man/graphID.globalID.Rd |only SEMID-0.2/SEMID/man/graphID.htcID.Rd |only SEMID-0.2/SEMID/man/graphID.main.Rd |only SEMID-0.2/SEMID/man/graphID.nonHtcID.Rd |only SEMID-0.2/SEMID/man/htr.Rd |only SEMID-0.2/SEMID/man/parents.Rd |only SEMID-0.2/SEMID/man/siblings.Rd |only SEMID-0.2/SEMID/man/validateMatrices.Rd |only SEMID-0.2/SEMID/tests |only 26 files changed, 940 insertions(+), 388 deletions(-)
Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop
recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between recommenderlab versions 0.1-7 dated 2015-07-24 and 0.1-8 dated 2015-12-18
recommenderlab-0.1-7/recommenderlab/man/helper.Rd |only recommenderlab-0.1-8/recommenderlab/DESCRIPTION | 10 recommenderlab-0.1-8/recommenderlab/MD5 | 69 +- recommenderlab-0.1-8/recommenderlab/NAMESPACE | 4 recommenderlab-0.1-8/recommenderlab/R/AAA.R | 17 recommenderlab-0.1-8/recommenderlab/R/AAAparameter.R |only recommenderlab-0.1-8/recommenderlab/R/RECOM_IBCF.R | 32 - recommenderlab-0.1-8/recommenderlab/R/RECOM_PCA.R | 7 recommenderlab-0.1-8/recommenderlab/R/RECOM_POPULAR.R | 182 ++++--- recommenderlab-0.1-8/recommenderlab/R/RECOM_RANDOM.R | 74 +-- recommenderlab-0.1-8/recommenderlab/R/RECOM_SVD.R | 77 +-- recommenderlab-0.1-8/recommenderlab/R/RECOM_UBCF.R | 7 recommenderlab-0.1-8/recommenderlab/R/binaryRatingMatrix.R | 17 recommenderlab-0.1-8/recommenderlab/R/evaluate.R | 4 recommenderlab-0.1-8/recommenderlab/R/evaluationResults.R | 2 recommenderlab-0.1-8/recommenderlab/R/evaluationScheme.R | 13 recommenderlab-0.1-8/recommenderlab/R/normalize.R | 178 +++---- recommenderlab-0.1-8/recommenderlab/R/plot.R | 2 recommenderlab-0.1-8/recommenderlab/R/realRatingMatrix.R | 235 +++++----- recommenderlab-0.1-8/recommenderlab/R/topNList.R | 125 ++--- recommenderlab-0.1-8/recommenderlab/inst/NEWS | 16 recommenderlab-0.1-8/recommenderlab/inst/doc/recommenderlab.R | 118 ++--- recommenderlab-0.1-8/recommenderlab/inst/doc/recommenderlab.Rnw | 108 +++- recommenderlab-0.1-8/recommenderlab/inst/doc/recommenderlab.pdf |binary recommenderlab-0.1-8/recommenderlab/man/Recommender.Rd | 5 recommenderlab-0.1-8/recommenderlab/man/binaryRatingMatrix-class.Rd | 3 recommenderlab-0.1-8/recommenderlab/man/evaluate.Rd | 26 - recommenderlab-0.1-8/recommenderlab/man/evaluationScheme.Rd | 7 recommenderlab-0.1-8/recommenderlab/man/ratingMatrix-class.Rd | 3 recommenderlab-0.1-8/recommenderlab/man/realRatingMatrix-class.Rd | 3 recommenderlab-0.1-8/recommenderlab/man/topNList-class.Rd | 3 recommenderlab-0.1-8/recommenderlab/tests/RECOM.R |only recommenderlab-0.1-8/recommenderlab/vignettes/item-based2.odg |binary recommenderlab-0.1-8/recommenderlab/vignettes/item-based2.pdf |binary recommenderlab-0.1-8/recommenderlab/vignettes/recommenderlab.Rnw | 108 +++- recommenderlab-0.1-8/recommenderlab/vignettes/user-based.odg |binary recommenderlab-0.1-8/recommenderlab/vignettes/user-based.pdf |binary 37 files changed, 788 insertions(+), 667 deletions(-)
More information about recommenderlab at CRAN
Permanent link
Title: High Frequency Portfolio Analytics by PortfolioEffect
Description: R interface to PortfolioEffect cloud service for backtesting
high frequency trading (HFT) strategies, intraday portfolio analysis
and optimization. Includes auto-calibrating model pipeline for market
microstructure noise, risk factors, price jumps/outliers, tail risk
(high-order moments) and price fractality (long memory). Constructed
portfolios could use client-side market data or access HF intraday price
history for all major US Equities. See https://www.portfolioeffect.com/
for more information on the PortfolioEffect high frequency portfolio
analytics platform.
Author: Aleksey Zemnitskiy [aut, cre],
Andrey Kostin [aut],
Oleg Nechaev [aut],
Craig Otis and others [ctb, cph] (OpenFAST library),
Daniel Lemire, Muraoka Taro and others [ctb, cph] (JavaFastPFOR
library),
Joe Walnes, Jorg Schaible and others [ctb, cph] (XStream library),
Dain Sundstrom [ctb, cph] (Snappy library),
Extreme! Lab, Indiana University [ctb, cph] (XPP3 library),
The Apache Software Foundation [ctb, cph] (Apache Log4j and Commons
Lang libraries),
Google, Inc. [ctb, cph] (GSON library),
Free Software Foundation [ctb, cph] (GNU Trove and GNU Crypto
libraries)
Maintainer: Aleksey Zemnitskiy <aleksey.zemnitskiy@portfolioeffect.com>
Diff between PortfolioEffectHFT versions 1.3 dated 2015-11-10 and 1.4 dated 2015-12-18
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS | 11 +++ R/plot.R | 2 R/portfolio.R | 85 ++++++------------------- R/util.R | 3 inst/doc/PortfolioEffectHFT.pdf |binary inst/java/portfolioeffect-quant-client-1.0.jar |binary man/portfolio_settings.Rd | 2 9 files changed, 50 insertions(+), 77 deletions(-)
More information about PortfolioEffectHFT at CRAN
Permanent link
Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4
classes and methods with a focus on Single Program/Multiple Data ('SPMD')
parallel programming style, which is intended for batch parallel
execution.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] (FreeBSD),
Brian Ripley [ctb] (Windows HPC Pack 2012),
R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.2-5 dated 2014-10-05 and 0.3-0 dated 2015-12-18
pbdMPI-0.2-5/pbdMPI/README |only pbdMPI-0.2-5/pbdMPI/data |only pbdMPI-0.2-5/pbdMPI/man/zz_internal.Rd |only pbdMPI-0.3-0/pbdMPI/ChangeLog | 51 + pbdMPI-0.3-0/pbdMPI/DESCRIPTION | 16 pbdMPI-0.3-0/pbdMPI/INSTALL | 10 pbdMPI-0.3-0/pbdMPI/MD5 | 335 +++++----- pbdMPI-0.3-0/pbdMPI/NAMESPACE | 14 pbdMPI-0.3-0/pbdMPI/R/000_globalVariables.r | 5 pbdMPI-0.3-0/pbdMPI/R/111_control.r |only pbdMPI-0.3-0/pbdMPI/R/111_control_io.r |only pbdMPI-0.3-0/pbdMPI/R/111_control_tp.r |only pbdMPI-0.3-0/pbdMPI/R/222_export_env.r |only pbdMPI-0.3-0/pbdMPI/R/api_apply.r | 11 pbdMPI-0.3-0/pbdMPI/R/api_apply_RC.r | 11 pbdMPI-0.3-0/pbdMPI/R/api_apply_general.r | 17 pbdMPI-0.3-0/pbdMPI/R/api_lapply.r | 16 pbdMPI-0.3-0/pbdMPI/R/api_sapply.r | 17 pbdMPI-0.3-0/pbdMPI/R/api_split.r | 22 pbdMPI-0.3-0/pbdMPI/R/api_task_pull.r | 21 pbdMPI-0.3-0/pbdMPI/R/api_tool.r | 15 pbdMPI-0.3-0/pbdMPI/R/comm_allcommon.r | 6 pbdMPI-0.3-0/pbdMPI/R/comm_allpairs.r | 2 pbdMPI-0.3-0/pbdMPI/R/comm_any_all.r | 4 pbdMPI-0.3-0/pbdMPI/R/comm_as_gbd.r | 5 pbdMPI-0.3-0/pbdMPI/R/comm_balance.r | 9 pbdMPI-0.3-0/pbdMPI/R/comm_base.r | 10 pbdMPI-0.3-0/pbdMPI/R/comm_dist.r | 6 pbdMPI-0.3-0/pbdMPI/R/comm_errors.r | 18 pbdMPI-0.3-0/pbdMPI/R/comm_matcharg.r |only pbdMPI-0.3-0/pbdMPI/R/comm_pairwise.r | 6 pbdMPI-0.3-0/pbdMPI/R/comm_range.r | 6 pbdMPI-0.3-0/pbdMPI/R/comm_read.r | 84 +- pbdMPI-0.3-0/pbdMPI/R/comm_seed.r | 35 - pbdMPI-0.3-0/pbdMPI/R/comm_sort.r | 8 pbdMPI-0.3-0/pbdMPI/R/comm_tool.r | 8 pbdMPI-0.3-0/pbdMPI/R/comm_which.r | 6 pbdMPI-0.3-0/pbdMPI/R/comm_write.r | 8 pbdMPI-0.3-0/pbdMPI/R/spmd_allcheck.r | 2 pbdMPI-0.3-0/pbdMPI/R/spmd_allgatherv.r | 18 pbdMPI-0.3-0/pbdMPI/R/spmd_allgatherv_obj.r | 4 pbdMPI-0.3-0/pbdMPI/R/spmd_allreduce.r | 14 pbdMPI-0.3-0/pbdMPI/R/spmd_allreduce_obj.r | 9 pbdMPI-0.3-0/pbdMPI/R/spmd_alltoall.r |only pbdMPI-0.3-0/pbdMPI/R/spmd_bcast.r | 19 pbdMPI-0.3-0/pbdMPI/R/spmd_bcast_obj.r | 21 pbdMPI-0.3-0/pbdMPI/R/spmd_communicator.r | 77 +- pbdMPI-0.3-0/pbdMPI/R/spmd_communicator_spawn.r | 5 pbdMPI-0.3-0/pbdMPI/R/spmd_gatherv.r | 29 pbdMPI-0.3-0/pbdMPI/R/spmd_gatherv_obj.r | 8 pbdMPI-0.3-0/pbdMPI/R/spmd_info.r | 8 pbdMPI-0.3-0/pbdMPI/R/spmd_irecv.r | 20 pbdMPI-0.3-0/pbdMPI/R/spmd_isend.r | 24 pbdMPI-0.3-0/pbdMPI/R/spmd_recv.r | 16 pbdMPI-0.3-0/pbdMPI/R/spmd_reduce.r | 18 pbdMPI-0.3-0/pbdMPI/R/spmd_reduce_obj.r | 8 pbdMPI-0.3-0/pbdMPI/R/spmd_scatterv.r | 21 pbdMPI-0.3-0/pbdMPI/R/spmd_scatterv_obj.r | 6 pbdMPI-0.3-0/pbdMPI/R/spmd_send.r | 12 pbdMPI-0.3-0/pbdMPI/R/spmd_sendrecv.r | 52 - pbdMPI-0.3-0/pbdMPI/R/spmd_sendrecv_replace.r | 56 - pbdMPI-0.3-0/pbdMPI/R/spmd_tool.r | 25 pbdMPI-0.3-0/pbdMPI/R/spmd_utility.r | 16 pbdMPI-0.3-0/pbdMPI/R/spmd_wait.r | 7 pbdMPI-0.3-0/pbdMPI/R/windows/zzz.r | 9 pbdMPI-0.3-0/pbdMPI/R/zzz.r.in | 16 pbdMPI-0.3-0/pbdMPI/README.md |only pbdMPI-0.3-0/pbdMPI/demo/00Index | 2 pbdMPI-0.3-0/pbdMPI/demo/alltoall.r |only pbdMPI-0.3-0/pbdMPI/demo/bcast_msg.r |only pbdMPI-0.3-0/pbdMPI/demo/pbdLapply.r | 7 pbdMPI-0.3-0/pbdMPI/demo/simple_io.r | 6 pbdMPI-0.3-0/pbdMPI/inst/CITATION | 8 pbdMPI-0.3-0/pbdMPI/inst/doc/pbdMPI-guide.Rnw | 27 pbdMPI-0.3-0/pbdMPI/inst/doc/pbdMPI-guide.pdf |binary pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/named.client.r | 4 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/named.server.r | 4 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/simple.client.r | 4 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/simple.server.r | 4 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/allgather.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/allreduce.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/bcast.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/gather.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/reduce.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/scatter.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/send_recv.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_parallel/01_mclapply_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_parallel/02_parMM_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_parallel/03_boot_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_parallel/04_glm_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_performance/demo_allgather_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_performance/demo_scatter_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/allgather_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/allgatherv_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/allreduce_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/bcast_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/gather_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/reduce_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/scatter_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/scatterv_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/sendrecv_spmd.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_s4/01_simple.r | 5 pbdMPI-0.3-0/pbdMPI/inst/examples/test_s4/02_mean.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/allgather.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/allreduce.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/bcast.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/gather.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/isend_irecv_wait.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/reduce.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/replace.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/scatter.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/send_recv.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/sendrecv.r | 2 pbdMPI-0.3-0/pbdMPI/inst/examples/test_spmd/sendrecv_replace.r | 2 pbdMPI-0.3-0/pbdMPI/inst/tests |only pbdMPI-0.3-0/pbdMPI/man/11_d_control.Rd | 16 pbdMPI-0.3-0/pbdMPI/man/aa_allgather-method.Rd | 6 pbdMPI-0.3-0/pbdMPI/man/aa_allreduce-method.Rd | 4 pbdMPI-0.3-0/pbdMPI/man/aa_bcast-method.Rd | 3 pbdMPI-0.3-0/pbdMPI/man/aa_gather-method.Rd | 7 pbdMPI-0.3-0/pbdMPI/man/aa_reduce-method.Rd | 7 pbdMPI-0.3-0/pbdMPI/man/aa_scatter-method.Rd | 5 pbdMPI-0.3-0/pbdMPI/man/ab_recv-method.Rd | 6 pbdMPI-0.3-0/pbdMPI/man/ab_send-method.Rd | 5 pbdMPI-0.3-0/pbdMPI/man/ac_irecv-method.Rd | 7 pbdMPI-0.3-0/pbdMPI/man/ac_isend-method.Rd | 5 pbdMPI-0.3-0/pbdMPI/man/ad_sendrecv-method.Rd | 16 pbdMPI-0.3-0/pbdMPI/man/ad_sendrecv.replace-method.Rd | 16 pbdMPI-0.3-0/pbdMPI/man/ae_alltoall.Rd |only pbdMPI-0.3-0/pbdMPI/man/cc_arrange.mpi.apts.Rd | 2 pbdMPI-0.3-0/pbdMPI/man/cc_comm.Rd | 78 +- pbdMPI-0.3-0/pbdMPI/man/dd_info.Rd | 8 pbdMPI-0.3-0/pbdMPI/man/dd_is.comm.null.Rd | 2 pbdMPI-0.3-0/pbdMPI/man/dd_prob.Rd | 12 pbdMPI-0.3-0/pbdMPI/man/dd_sourcetag.Rd | 6 pbdMPI-0.3-0/pbdMPI/man/dd_wait.Rd | 9 pbdMPI-0.3-0/pbdMPI/man/vv_get_jid.Rd | 4 pbdMPI-0.3-0/pbdMPI/man/vv_print_cat.Rd | 22 pbdMPI-0.3-0/pbdMPI/man/vv_seed.Rd | 9 pbdMPI-0.3-0/pbdMPI/man/ww_comm_as_gbd.Rd | 6 pbdMPI-0.3-0/pbdMPI/man/ww_comm_balance.Rd | 12 pbdMPI-0.3-0/pbdMPI/man/ww_comm_read.Rd | 46 - pbdMPI-0.3-0/pbdMPI/man/ww_comm_write.Rd | 16 pbdMPI-0.3-0/pbdMPI/man/xx_comm_Rprof.Rd | 10 pbdMPI-0.3-0/pbdMPI/man/xx_comm_allpairs.Rd | 3 pbdMPI-0.3-0/pbdMPI/man/xx_comm_any_all.Rd | 8 pbdMPI-0.3-0/pbdMPI/man/xx_comm_base.Rd | 10 pbdMPI-0.3-0/pbdMPI/man/xx_comm_dist.Rd | 5 pbdMPI-0.3-0/pbdMPI/man/xx_comm_match_arg.Rd |only pbdMPI-0.3-0/pbdMPI/man/xx_comm_pairwise.Rd | 4 pbdMPI-0.3-0/pbdMPI/man/xx_comm_range.Rd | 6 pbdMPI-0.3-0/pbdMPI/man/xx_comm_sort.Rd | 5 pbdMPI-0.3-0/pbdMPI/man/xx_comm_stop_warning.Rd | 24 pbdMPI-0.3-0/pbdMPI/man/xx_comm_timer.Rd | 2 pbdMPI-0.3-0/pbdMPI/man/xx_comm_which.Rd | 7 pbdMPI-0.3-0/pbdMPI/man/yy_api_apply.Rd | 40 - pbdMPI-0.3-0/pbdMPI/man/yy_api_task_pull.Rd | 21 pbdMPI-0.3-0/pbdMPI/man/zz_spmd_control.Rd |only pbdMPI-0.3-0/pbdMPI/man/zz_spmd_internal.Rd | 3 pbdMPI-0.3-0/pbdMPI/src/spmd.c | 8 pbdMPI-0.3-0/pbdMPI/src/spmd.h | 51 + pbdMPI-0.3-0/pbdMPI/src/spmd_alltoall.c |only pbdMPI-0.3-0/pbdMPI/src/spmd_alltoallv.c |only pbdMPI-0.3-0/pbdMPI/src/spmd_bcast.c | 8 pbdMPI-0.3-0/pbdMPI/src/zzz.c |only pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-guide.Rnw | 27 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/01-acknowledgement.tex | 2 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/01-copyright.tex | 2 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/01-introduction.tex | 2 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/02-performance.tex | 2 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/03-faq.tex | 59 + pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/05-analog.tex | 4 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/07-simpleio.tex | 5 pbdMPI-0.3-0/pbdMPI/vignettes/pbdMPI-include/pbdMPI.bib | 16 174 files changed, 1274 insertions(+), 836 deletions(-)
Title: Project MOSAIC (mosaic-web.org) data sets
Description: Data sets from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaicData versions 0.9.1 dated 2014-08-22 and 0.13.0 dated 2015-12-18
mosaicData-0.13.0/mosaicData/DESCRIPTION | 9 + mosaicData-0.13.0/mosaicData/MD5 | 70 ++++++++------- mosaicData-0.13.0/mosaicData/NAMESPACE | 2 mosaicData-0.13.0/mosaicData/R/Dimes.R |only mosaicData-0.13.0/mosaicData/R/SaratogaHouses.R |only mosaicData-0.13.0/mosaicData/R/datasets.R | 86 ++++++++++++------- mosaicData-0.13.0/mosaicData/data/Births78.rda |binary mosaicData-0.13.0/mosaicData/data/Dimes.rda |only mosaicData-0.13.0/mosaicData/data/HeatX.R |only mosaicData-0.13.0/mosaicData/data/Riders.rda |only mosaicData-0.13.0/mosaicData/data/SaratogaHouses.rda |only mosaicData-0.13.0/mosaicData/data/datalist | 4 mosaicData-0.13.0/mosaicData/man/Alcohol.Rd | 3 mosaicData-0.13.0/mosaicData/man/Birthdays.Rd | 5 - mosaicData-0.13.0/mosaicData/man/Births78.Rd | 6 - mosaicData-0.13.0/mosaicData/man/CPS85.Rd | 8 + mosaicData-0.13.0/mosaicData/man/Cards.Rd | 6 - mosaicData-0.13.0/mosaicData/man/CoolingWater.Rd | 8 + mosaicData-0.13.0/mosaicData/man/Countries.Rd | 3 mosaicData-0.13.0/mosaicData/man/Dimes.Rd |only mosaicData-0.13.0/mosaicData/man/Galton.Rd | 4 mosaicData-0.13.0/mosaicData/man/Gestation.Rd | 20 ++-- mosaicData-0.13.0/mosaicData/man/HELPfull.Rd | 34 +++---- mosaicData-0.13.0/mosaicData/man/HELPmiss.Rd | 30 +++--- mosaicData-0.13.0/mosaicData/man/HELPrct.Rd | 46 +++++----- mosaicData-0.13.0/mosaicData/man/HeatX.Rd | 7 - mosaicData-0.13.0/mosaicData/man/KidsFeet.Rd | 4 mosaicData-0.13.0/mosaicData/man/Marriage.Rd | 6 - mosaicData-0.13.0/mosaicData/man/Mites.Rd | 4 mosaicData-0.13.0/mosaicData/man/RailTrail.Rd | 14 +-- mosaicData-0.13.0/mosaicData/man/Riders.Rd |only mosaicData-0.13.0/mosaicData/man/SAT.Rd | 9 + mosaicData-0.13.0/mosaicData/man/SaratogaHouses.Rd |only mosaicData-0.13.0/mosaicData/man/SnowGR.Rd | 4 mosaicData-0.13.0/mosaicData/man/SwimRecords.Rd | 4 mosaicData-0.13.0/mosaicData/man/TenMileRace.Rd | 4 mosaicData-0.13.0/mosaicData/man/Utilities.Rd | 4 mosaicData-0.13.0/mosaicData/man/Utilities2.Rd | 6 - mosaicData-0.13.0/mosaicData/man/Whickham.Rd | 6 - mosaicData-0.9.1/mosaicData/data/HeatX.rda |only mosaicData-0.9.1/mosaicData/data/Heightweight.rda |only mosaicData-0.9.1/mosaicData/man/Heightweight.Rd |only 42 files changed, 252 insertions(+), 164 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 0.12 dated 2015-10-12 and 0.13.0 dated 2015-12-18
DESCRIPTION | 11 MD5 | 451 +++++----- NAMESPACE | 19 R/Tukey.R | 3 R/bargraph.R | 14 R/chisq.R | 26 R/confint.R | 141 ++- R/dfapply.R | 25 R/do.R | 5 R/favstats.R | 23 R/fitSpline.R | 8 R/inspect.R |only R/interval.R | 10 R/makeFun.R | 18 R/mplot.R | 65 - R/nmissing.R |only R/plotFun.R | 2 R/plotModel.R | 14 R/pqrdata.R | 109 +- R/read.file.R | 40 R/resample.R | 4 R/rescale.R | 31 R/tally.R | 109 +- build/vignette.rds |binary inst/doc/GraphicsWithMosaic.html | 46 - inst/doc/LessVolume-MoreCreativity.html | 30 inst/doc/MinimalR.R | 16 inst/doc/MinimalR.Rnw | 16 inst/doc/MinimalR.pdf |binary inst/doc/Resampling.R | 6 inst/doc/Resampling.Rnw | 6 inst/doc/Resampling.pdf |binary inst/doc/mosaic-resources.html | 4 inst/doc/plotModel-vignette.R | 74 - inst/doc/plotModel-vignette.Rmd | 11 inst/doc/plotModel-vignette.html | 90 + man/Broyden.Rd | 2 man/CIAdata.Rd | 8 man/CIsim.Rd | 19 man/Calculus.Rd | 42 man/FunctionsFromData.Rd | 2 man/MAD.Rd | 10 man/MAD_.Rd | 2 man/MSPE.Rd | 2 man/TukeyHSD.lm.Rd | 6 man/adapt_seq.Rd | 11 man/aggregating.Rd | 8 man/aggregatingAux.Rd | 7 man/aggregatingFunction1.Rd | 4 man/aggregatingFunction2.Rd | 2 man/as-xtabs.Rd | 2 man/ashplot.Rd | 12 man/bargraph.Rd | 15 man/binom.test.Rd | 25 man/cdist.Rd | 10 man/chisq.Rd | 21 man/clustering.Rd | 4 man/coef.Rd | 2 man/columns.Rd | 2 man/compareMean.Rd | 12 man/compareProportion.Rd | 4 man/confint.Rd | 59 - man/cross.Rd | 3 man/cull_for_do.Rd | 6 man/defunct-fetch.Rd | 2 man/deg2rad.Rd | 2 man/deltaMethod.Rd | 45 man/derivedFactor.Rd | 30 man/dfapply.Rd | 21 man/diffmean.Rd | 6 man/do.Rd | 26 man/docFile.Rd | 2 man/dotPlot.Rd | 4 man/dpqrdist.Rd | 7 man/ediff.Rd | 8 man/evalFormula.Rd | 2 man/evalSubFormula.Rd | 2 man/expandFun.Rd | 2 man/factorize.Rd | 4 man/fav_stats.Rd | 11 man/findZeros.Rd | 12 man/findZerosMult.Rd | 4 man/fitModel.Rd | 14 man/fitSpline.Rd | 14 man/fitdistr.Rd | 2 man/formularise.Rd | 2 man/fortify.Rd | 16 man/fractions.Rd | 2 man/freqpolygon.Rd | 18 man/getVarFormula.Rd | 8 man/googleMap.Rd | 4 man/gwm.Rd | 34 man/inferArgs.Rd | 4 man/inspect.Rd |only man/integrateODE.Rd | 4 man/interval.Rd | 6 man/is.wholenumber.Rd | 4 man/joinFrames.Rd | 4 man/ladd.Rd | 13 man/latlon2xyz.Rd | 6 man/linear.algebra.Rd | 2 man/logical2factor.Rd | 2 man/logit.Rd | 6 man/mPlotting.Rd | 25 man/mUSMap.Rd | 11 man/mWorldMap.Rd | 6 man/makeColorscheme.Rd | 2 man/makeFun.Rd | 29 man/makeMap.Rd | 2 man/mid.Rd | 2 man/mm.Rd | 18 man/modelVars.Rd | 2 man/mosaic-internal.Rd | 12 man/mosaic-package.Rd | 10 man/mosaic.options.Rd | 6 man/mosaicformula.Rd | 8 man/mplot.Rd | 27 man/msummary.Rd | 11 man/n_missing.Rd |only man/named.Rd | 2 man/nicenames.Rd | 4 man/ntiles.Rd | 2 man/numD.Rd | 10 man/oddsRatio.Rd | 6 man/panel.levelcontourplot.Rd | 2 man/panel.lmbands.Rd | 6 man/panel.plotFun.Rd | 24 man/panel.plotFun1.Rd | 26 man/parseFormula.Rd | 8 man/pdist.Rd | 8 man/perctable.Rd | 9 man/plotCumfreq.Rd | 2 man/plotDist.Rd | 35 man/plotFun.Rd | 32 man/plotModel.Rd | 8 man/plotPoints.Rd | 4 man/pqrdata.Rd | 60 - man/pqrdata2.Rd | 16 man/project-methods.Rd | 28 man/prop.Rd | 26 man/prop.test.Rd | 40 man/qdist.Rd | 10 man/r.squared.Rd | 2 man/rand.Rd | 8 man/read.file.Rd | 42 man/relm.Rd | 2 man/repeater-class.Rd | 4 man/resample.Rd | 12 man/rescale.Rd | 17 man/rflip.Rd | 2 man/rfun.Rd | 4 man/rgeo-internals.Rd | 4 man/rgeo.Rd | 20 man/rkintegrate.Rd | 2 man/rspin.Rd | 4 man/rsquared.Rd | 2 man/rstudio.Rd | 4 man/set.rseed.Rd | 2 man/simplify.Rd | 2 man/sp2df.Rd | 13 man/standardName.Rd | 12 man/statTally.Rd | 19 man/surround.Rd | 2 man/swap.Rd | 8 man/symbolicD.Rd | 4 man/symbolicInt.Rd | 2 man/tally.Rd | 52 - man/theme_map.Rd | 4 man/themes.Rd | 13 man/ttest.Rd | 16 man/update_ci.Rd | 2 man/xchisq.test.Rd | 14 man/xhistogram.Rd | 28 man/xpnorm.Rd | 16 man/xqqmath.Rd | 6 man/zscore.Rd | 8 tests/testthat/test-binomtest.R | 9 tests/testthat/test-pqrdata.R | 25 vignettes/GraphicsWithMosaic_files/figure-html/logistic-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-11-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-11-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-12-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-12-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-13-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-15-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-15-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-3-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-8-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-8-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-9-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-31-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-32-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-37-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-6-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-7-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-8-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-9-1.png |binary vignettes/MinimalR.Rnw | 16 vignettes/Resampling.Rnw | 6 vignettes/plotModel-vignette.Rmd | 11 vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-1.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-10.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-11.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-12.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-13.png |only vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-2.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-3.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-4.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-5.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-6.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-7.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-8.png |binary vignettes/plotModel-vignette_files/figure-html/unnamed-chunk-1-9.png |binary 229 files changed, 1720 insertions(+), 1322 deletions(-)
Title: Graphical Analysis of Variance Using ggplot2
Description: This collection of functions in 'granovaGG'
provides what we call elemental graphics for display of
anova results. The term elemental derives from the fact
that each function is aimed at construction of
graphical displays that afford direct visualizations of
data with respect to the fundamental questions that
drive the particular anova methods. This package
represents a modification of the original granova
package; the key change is to use 'ggplot2', Hadley
Wickham's package based on Grammar of Graphics concepts
(due to Wilkinson). The main function is granovagg.1w()
(a graphic for one way ANOVA); two other functions
(granovagg.ds() and granovagg.contr()) are to construct
graphics for dependent sample analyses and
contrast-based analyses respectively. (The function
granova.2w(), which entails dynamic displays of data, is
not currently part of 'granovaGG'.) The 'granovaGG'
functions are to display data for any number of groups,
regardless of their sizes (however, very large data
sets or numbers of groups can be problematic). For
granovagg.1w() a specialized approach is used to
construct data-based contrast vectors for which anova
data are displayed. The result is that the graphics use
a straight line to facilitate clear interpretations
while being faithful to the standard effect test in
anova. The graphic results are complementary to
standard summary tables; indeed, numerical summary
statistics are provided as side effects of the graphic
constructions. granovagg.ds() and granovagg.contr() provide
graphic displays and numerical outputs for a dependent
sample and contrast-based analyses. The graphics based
on these functions can be especially helpful for
learning how the respective methods work to answer the
basic question(s) that drive the analyses. This means
they can be particularly helpful for students and
non-statistician analysts. But these methods can be of
assistance for work-a-day applications of many kinds,
as they can help to identify outliers, clusters or
patterns, as well as highlight the role of non-linear
transformations of data. In the case of granovagg.1w()
and granovagg.ds() several arguments are provided to
facilitate flexibility in the construction of graphics
that accommodate diverse features of data, according to
their corresponding display requirements. See the help
files for individual functions.
Author: Brian A. Danielak <brian@briandk.com>,
Robert M. Pruzek <RMPruzek@yahoo.com>,
with contributions from:
William E. J. Doane <wil@DrDoane.com>,
James E. Helmreich <James.Helmreich@Marist.edu>,
Jason Bryer <jason@bryer.org>
Maintainer: Brian A. Danielak <brian@briandk.com>
Diff between granovaGG versions 1.3 dated 2015-01-01 and 1.4.0 dated 2015-12-18
DESCRIPTION | 34 +++++++++++++------------- MD5 | 49 +++++++++++++++++++++----------------- NAMESPACE | 5 ++- NEWS | 15 +++++++++++ NEWS.md |only R/granovaGG-package.R | 41 +++++++++++++++++++++++++++++--- R/granovagg.1w.R | 6 +++- R/granovagg.contr.R | 2 + R/granovagg.ds.R | 60 ++++++++++++++++++++++++++++++++--------------- R/theme-defaults.R | 5 +-- data/anorexia.rda |only data/anorexia.sub.rda |binary data/shoes.rda |only demo/granovagg.1w.R | 10 +++---- demo/granovagg.ds.R | 10 +++---- inst/CITATION | 2 - man/anorexia.Rd |only man/anorexia.sub.Rd | 8 +++--- man/arousal.Rd | 2 - man/blood_lead.Rd | 2 - man/granovaGG-package.Rd | 2 - man/granovagg.1w.Rd | 12 ++++----- man/granovagg.contr.Rd | 2 - man/granovagg.ds.Rd | 12 ++++----- man/poison.Rd | 2 - man/rat.Rd | 2 - man/shoes.Rd |only man/tobacco.Rd | 2 - 28 files changed, 183 insertions(+), 102 deletions(-)
Title: Foundations and Applications of Statistics Using R
Description: Data sets and utilities to accompany
"Foundations and Applications of Statistics: an Introduction
using R" (R Pruim, published by AMS, 2011), a text covering
topics from probability and mathematical statistics at an advanced
undergraduate level. R is integrated throughout, and access to all
the R code in the book is provided via the snippet function.
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between fastR versions 0.10 dated 2015-05-23 and 0.10.2 dated 2015-12-18
DESCRIPTION | 19 ++-- MD5 | 156 +++++++++++++++++++------------------- NAMESPACE | 36 ++++++++ R/datasets.R | 18 +++- R/fastR-package.R | 7 + README.md | 14 +-- build/vignette.rds |binary inst/doc/Errata.pdf |binary inst/doc/Updates.R | 106 ++++++++++++------------- inst/doc/Updates.Rnw | 106 ++++++++++++------------- inst/doc/Updates.pdf |binary man/Jordan8687.Rd | 4 man/actgpa.Rd | 4 man/airlineArrival.Rd | 6 - man/airpollution.Rd | 4 man/balldrop.Rd | 4 man/batting.Rd | 4 man/births78.Rd | 4 man/buckthorn.Rd | 4 man/bugs.Rd | 4 man/col.fastR.Rd | 3 man/col.perc.Rd | 4 man/concrete.Rd | 4 man/corn.Rd | 4 man/cuckoo.Rd | 7 + man/deathPenalty.Rd | 4 man/drag.Rd | 4 man/endurance.Rd | 4 man/familySmoking.Rd | 4 man/fastR-package.Rd | 4 man/fumbles.Rd | 4 man/fusion.Rd | 12 +- man/geolm.Rd | 8 + man/givenOrder.Rd | 2 man/golfballs.Rd | 4 man/gpa.Rd | 4 man/heliumFootballs.Rd | 4 man/ice.Rd | 4 man/inflation.Rd | 4 man/kids.Rd | 4 man/littleSurvey.Rd | 4 man/mathnoise.Rd | 6 - man/miaa05.Rd | 4 man/mlb2004.Rd | 4 man/ncaa2010.Rd | 4 man/nfl2007.Rd | 16 ++- man/nlmax.Rd | 4 man/noise.Rd | 8 + man/palettes.Rd | 8 + man/paperplanes.Rd | 4 man/pendulum.Rd | 4 man/petstress.Rd | 4 man/pigs.Rd | 4 man/pitching2005.Rd | 4 man/poison.Rd | 10 +- man/punting.Rd | 6 - man/ratpoison.Rd | 4 man/rgolfballs.Rd | 4 man/rubberband.Rd | 4 man/scent.Rd | 4 man/snippet.Rd | 2 man/soap.Rd | 6 - man/spheres.Rd | 2 man/step.Rd | 4 man/stereogram.Rd | 6 - man/students.Rd | 4 man/tastetest.Rd | 4 man/tdf.Rd | 5 - man/tirewear.Rd | 4 man/traffic.Rd | 6 - man/trebuchet.Rd | 4 man/undocumented.Rd | 10 +- man/utilities.Rd | 4 man/vaov.Rd | 4 man/wilson.ci.Rd | 4 man/workingWomen.Rd | 4 man/xplot.Rd | 4 vignettes/Updates-concordance.tex | 2 vignettes/Updates.Rnw | 106 ++++++++++++------------- 79 files changed, 530 insertions(+), 357 deletions(-)
Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between extRemes versions 2.0-6 dated 2015-08-27 and 2.0-7 dated 2015-12-18
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- R/hwmid.R |only man/extRemes-internal.Rd | 1 + man/hwmid.Rd |only 5 files changed, 9 insertions(+), 6 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.7 dated 2015-11-17 and 1.8 dated 2015-12-18
DESCRIPTION | 10 - MD5 | 36 +++---- NAMESPACE | 7 - NEWS | 16 ++- R/DJL-internal.R | 250 ++++++++++++++++++++++++------------------------- R/aps.reg.R |only R/dm.ddf.R | 5 R/dm.dea.R | 10 + R/dm.sbm.R | 6 + R/dm.sf.R | 5 R/map.soa.ddf.R | 6 + R/map.soa.dea.R | 7 + R/map.soa.sbm.R | 7 + R/map.soa.sf.R | 6 + R/roc.dea.R | 7 + R/roc.sf.R | 6 + R/target.arrival.dea.R | 7 + R/target.arrival.sf.R | 6 + R/target.spec.dea.R | 6 + man/aps.reg.Rd |only 20 files changed, 249 insertions(+), 154 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006). This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012).
Author: Pierre Roudier
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.5-4 dated 2014-09-18 and 0.5-5 dated 2015-12-18
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 20 ++++++++++++++++++-- R/plot.R | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 1 - inst/doc/vignette.R | 1 + inst/doc/vignette.Rnw | 1 + inst/doc/vignette.pdf |binary man/clhs.Rd | 4 ++-- vignettes/vignette.Rnw | 1 + 11 files changed, 44 insertions(+), 26 deletions(-)
Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression
with interval censored data or proportional sub-distribution hazards
regression for interval censored competing risks data. The main functions
allow to estimate survival function, cumulative incidence function, Cox
and Fine & Gray regression coefficients and associated variance-covariance
matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the
'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from
the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
Diff between MIICD versions 2.1 dated 2015-03-31 and 2.2 dated 2015-12-17
MIICD-2.1/MIICD/R/DA.ci.R |only MIICD-2.1/MIICD/R/DA.surv.R |only MIICD-2.1/MIICD/man/DA.ci.Rd |only MIICD-2.1/MIICD/man/DA.surv.Rd |only MIICD-2.1/MIICD/man/MIICD-package.Rd |only MIICD-2.1/MIICD/man/plot.DA_ci.Rd |only MIICD-2.1/MIICD/man/plot.DA_surv.Rd |only MIICD-2.2/MIICD/DESCRIPTION | 23 ++-- MIICD-2.2/MIICD/MD5 | 51 ++++---- MIICD-2.2/MIICD/NAMESPACE | 11 - MIICD-2.2/MIICD/R/ANDA.coxph.R | 35 +++--- MIICD-2.2/MIICD/R/ANDA.crreg.R | 26 ++-- MIICD-2.2/MIICD/R/BBCI.R |only MIICD-2.2/MIICD/R/BBS.R |only MIICD-2.2/MIICD/R/MI.ci.R | 148 ++++++++++++++----------- MIICD-2.2/MIICD/R/MI.ci_1.R |only MIICD-2.2/MIICD/R/MI.surv.R | 183 +++++++++++++++++++------------- MIICD-2.2/MIICD/R/MI.surv_1.R |only MIICD-2.2/MIICD/R/MIICD.coxph.R | 24 +--- MIICD-2.2/MIICD/R/MIICD.crreg.R | 27 ++-- MIICD-2.2/MIICD/R/PMDA.coxph.R | 73 ++++++------ MIICD-2.2/MIICD/R/PMDA.crreg.R | 25 ++-- MIICD-2.2/MIICD/man/ICCRD.Rd | 3 MIICD-2.2/MIICD/man/MI.ci.Rd | 38 +++--- MIICD-2.2/MIICD/man/MI.surv.Rd | 36 +++--- MIICD-2.2/MIICD/man/MIICD.coxph.Rd | 27 ++-- MIICD-2.2/MIICD/man/MIICD.crreg.Rd | 33 +++-- MIICD-2.2/MIICD/man/bcos.Rd | 3 MIICD-2.2/MIICD/man/plot.MIICD_coxph.Rd | 3 MIICD-2.2/MIICD/man/plot.MIICD_crreg.Rd | 3 MIICD-2.2/MIICD/man/plot.MI_ci.Rd | 3 MIICD-2.2/MIICD/man/plot.MI_surv.Rd | 9 - 32 files changed, 426 insertions(+), 358 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design,
along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.0.0 dated 2015-10-19 and 1.0.1 dated 2015-12-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/Matrix.R | 6 ++++-- 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between MPSEM versions 0.2-6 dated 2014-12-02 and 0.3-1 dated 2015-12-17
MPSEM-0.2-6/MPSEM/inst/doc/MPSEM.Rmd |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.Rmd |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.bib |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.html |only MPSEM-0.3-1/MPSEM/DESCRIPTION | 10 +++++----- MPSEM-0.3-1/MPSEM/MD5 | 20 ++++++++++---------- MPSEM-0.3-1/MPSEM/NAMESPACE | 16 ++++++++++++++-- MPSEM-0.3-1/MPSEM/R/PEM.R | 7 +++++++ MPSEM-0.3-1/MPSEM/build/vignette.rds |binary MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.R |only MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.Rnw |only MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.pdf |binary MPSEM-0.3-1/MPSEM/man/PEM.Rd | 20 ++++++++++++++++++-- MPSEM-0.3-1/MPSEM/vignettes/MPSEM.Rnw |only MPSEM-0.3-1/MPSEM/vignettes/PEM_with_MPSEM.bib |only 15 files changed, 54 insertions(+), 19 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.21 dated 2015-12-04 and 2.21-1 dated 2015-12-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS | 3 +++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.pdf |binary 6 files changed, 12 insertions(+), 9 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation
of repeatabilities in measurements and matrices, and general evolutionary
quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme
Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.2-1 dated 2015-11-04 and 0.2-2 dated 2015-12-17
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NAMESPACE | 3 +++ R/DriftTest.R | 4 ++-- R/RSProjection.R |only inst/tests/test.DriftTest.r | 20 ++++++++++++++++++++ inst/tests/test.MonteCarloStat.r | 9 +++++++++ man/RSProjection.Rd |only 8 files changed, 47 insertions(+), 13 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.7 dated 2015-10-20 and 1.0.8 dated 2015-12-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/CCAGFA.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: 'TSdbi' Extension to Connect with 'SDMX'
Description: Methods to
retrieve data in the Statistical Data and Metadata Exchange ('SDMX') format
from several database. (For example,
EuroStat, the European Central Bank, the Organisation for Economic
Co-operation and Development, the Unesco Institute for Statistics,
and the International Labor Organization.)
This is a wrapper for package 'RJSDMX'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSsdmx versions 2015.2-2 dated 2015-04-30 and 2015.12-1 dated 2015-12-16
DESCRIPTION | 6 +- MD5 | 22 ++++----- NEWS | 8 +++ R/TSdbiMethods.R | 9 ++- inst/testWithInternet/0serviceCheck.R | 12 ++++- inst/testWithInternet/0serviceCheck_EuroStat.R | 3 - inst/testWithInternet/0serviceCheck_ILO.R | 11 +++- inst/testWithInternet/0serviceCheck_IMF.R | 3 - inst/testWithInternet/0serviceCheck_INEGI.R | 3 - inst/testWithInternet/0serviceCheck_OECD.R | 60 ++++++++++++++++++++++--- inst/testWithInternet/ilo.R | 15 +++++- inst/testWithInternet/oecd.R | 22 +++++++-- 12 files changed, 136 insertions(+), 38 deletions(-)
Title: Time Series Database Interface
Description: Provides a common interface to time series databases. The
objective is to define a standard interface so users can retrieve time
series data from various sources with a simple, common, set of
commands, and so programs can be written to be portable with respect
to the data source. The SQL implementations also provide a database
table design, so users needing to set up a time series database
have a reasonably complete way to do this easily. The interface
provides for a variety of options with respect to the representation
of time series in R. The interface, and the SQL implementations, also
handle vintages of time series data (sometime called editions or
realtime data). There is also a (not yet well tested) mechanism to
handle multilingual data documentation.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSdbi versions 2015.1-1 dated 2015-04-29 and 2015.7-1 dated 2015-12-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 +++++ R/TSdbi.R | 6 +++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://eml.berkeley.edu//~train/trainsonnier.pdf.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.1.1 dated 2015-07-16 and 1.1.2 dated 2015-12-16
RSGHB-1.1.1/RSGHB/R/vech.R |only RSGHB-1.1.1/RSGHB/R/xpnd.R |only RSGHB-1.1.2/RSGHB/DESCRIPTION | 10 +++++----- RSGHB-1.1.2/RSGHB/MD5 | 12 +++++------- RSGHB-1.1.2/RSGHB/NEWS | 5 ++++- RSGHB-1.1.2/RSGHB/R/writeModel.R | 12 ++++-------- RSGHB-1.1.2/RSGHB/build/vignette.rds |binary RSGHB-1.1.2/RSGHB/inst/doc/RSGHB_HowTo.pdf |binary 8 files changed, 18 insertions(+), 21 deletions(-)
Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.devices versions 2.13.1 dated 2015-09-22 and 2.13.2 dated 2015-12-16
R.devices-2.13.1/R.devices/tests/devIndexOf.R |only R.devices-2.13.2/R.devices/DESCRIPTION | 12 - R.devices-2.13.2/R.devices/MD5 | 45 ++--- R.devices-2.13.2/R.devices/NAMESPACE | 1 R.devices-2.13.2/R.devices/NEWS | 9 + R.devices-2.13.2/R.devices/R/capabilitiesX11.R | 108 ++++++------- R.devices-2.13.2/R.devices/R/devNew.R | 2 R.devices-2.13.2/R.devices/R/devOptions.R | 15 + R.devices-2.13.2/R.devices/R/deviceUtils.R | 47 +++-- R.devices-2.13.2/R.devices/build/vignette.rds |binary R.devices-2.13.2/R.devices/inst/doc/R.devices-overview.pdf |binary R.devices-2.13.2/R.devices/man/R.devices-package.Rd | 2 R.devices-2.13.2/R.devices/tests/DevEvalFileProduct.R | 42 ++++- R.devices-2.13.2/R.devices/tests/DevEvalProduct.R | 30 +++ R.devices-2.13.2/R.devices/tests/capabilitiesX11.R | 24 +- R.devices-2.13.2/R.devices/tests/devAll.R | 3 R.devices-2.13.2/R.devices/tests/devEqualTypes.R |only R.devices-2.13.2/R.devices/tests/devEval.R | 14 - R.devices-2.13.2/R.devices/tests/devIsInteractive.R | 4 R.devices-2.13.2/R.devices/tests/devList.R | 25 ++- R.devices-2.13.2/R.devices/tests/devListIndexOf.R |only R.devices-2.13.2/R.devices/tests/devNew.R |only R.devices-2.13.2/R.devices/tests/devOptions.R | 72 ++++++++ R.devices-2.13.2/R.devices/tests/devSet.R | 19 ++ R.devices-2.13.2/R.devices/tests/favicon.R | 50 ++++-- R.devices-2.13.2/R.devices/tests/toNNN.R |only 26 files changed, 380 insertions(+), 144 deletions(-)
Title: Time Frame Coding Kernel
Description: A kernel of functions for programming
time series methods in a way that is relatively independently of the
representation of time. Also provides plotting, time windowing,
and some
other utility functions which are specifically intended for time series.
See the Guide distributed as a vignette, or ?tframe.Intro for more
details. (User utilities are in package tfplot.)
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between tframe versions 2015.1-1 dated 2015-01-05 and 2015.12-1 dated 2015-12-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 7 ++----- NEWS | 9 +++++++++ R/Rts.R | 2 +- build/vignette.rds |binary 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Time Frame User Utilities
Description: Utilities for simple manipulation and quick
plotting of time series data. These utilities use the tframe package
which provides a programming kernel for time series. Extensions to
tframe provided in tframePlus can also be used. See the Guide vignette
for examples.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between tfplot versions 2015.4-1 dated 2015-04-28 and 2015.12-1 dated 2015-12-16
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- NAMESPACE | 4 ++++ NEWS | 11 +++++++++++ R/tfplot.R | 3 ++- man/tfVisPlot.Rd | 3 ++- 6 files changed, 28 insertions(+), 10 deletions(-)
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Author: Bart Smeets [aut],
Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.1.0 dated 2015-12-15 and 3.1.1 dated 2015-12-16
DESCRIPTION | 6 ++-- MD5 | 22 +++++++++--------- R/utils.R | 4 +++ inst/doc/introduction.html | 55 ++++++++++++++++++++++----------------------- inst/doc/terminology.html | 4 +-- inst/doc/trajectories.html | 16 ++++++------- src/activity.cpp | 4 +-- src/activity.h | 4 +-- src/entity.cpp | 2 - src/entity.h | 12 +++++---- src/simulator.h | 7 ++++- tests/testthat/test-wrap.R | 10 ++++---- 12 files changed, 79 insertions(+), 67 deletions(-)
Title: Dynamic Systems Estimation (Time Series Package)
Description: Tools for multivariate, linear, time-invariant,
time series models. This includes ARMA and state-space representations,
and methods for converting between them. It also includes simulation
methods and several estimation functions. The package has functions
for looking at model roots, stability, and forecasts at different
horizons. The ARMA model representation is general, so that VAR, VARX,
ARIMA, ARMAX, ARIMAX can all be considered to be special cases. Kalman
filter and smoother estimates can be obtained from the state space
model, and state-space model reduction techniques are implemented.
An introduction and User's Guide is available in a vignette.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between dse versions 2014.11-1 dated 2014-11-25 and 2015.12-1 dated 2015-12-16
DESCRIPTION | 15 ++++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 12 ++++-------- NEWS | 6 ++++++ R/dse1.R | 16 +++++++++++----- build/vignette.rds |binary data/eg1.DSE.data.diff.rda |binary data/eg1.DSE.data.rda |binary data/egJofF.1dec93.data.rda |binary inst/CITATION | 4 ++-- inst/doc/Guide.pdf |binary man/balanceMittnik.Rd | 2 +- man/estSSMittnik.Rd | 2 +- 13 files changed, 45 insertions(+), 36 deletions(-)
Title: Count All Common Subsequences
Description: Count all common subsequences between 2 string sequences, with
items separated by the same delimiter. The first string input is a length-
one vector, the second string input can be a vector or list containing
multiple strings. The algorithm differentiates between the more strict
definition of subsequence, where a common subsequence cannot be separated
by any other items, from its looser counterpart, where a common subsequence
can be interrupted by other items. For example, q-w is a common subsequence
of q-w-e-r and q-e-w-r on the looser definition, but not the more strict
definition. calACSLoose Algorithm from Wang, H. All common subsequences
(2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between calACS versions 1.1 dated 2015-12-16 and 1.2 dated 2015-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/calACSstr.R | 10 +++++----- R/calACSstrLoose.r | 11 ++++++----- 4 files changed, 18 insertions(+), 17 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.49 dated 2015-11-19 and 0.51 dated 2015-12-16
DESCRIPTION | 18 + MD5 | 22 +- R/classes.R | 30 +- R/lmp.R |only build/vignette.rds |binary inst/doc/customitem.R |only inst/doc/customitem.Rmd |only inst/doc/customitem.html |only inst/doc/diagnostics.html | 42 ++-- inst/tests/test-dTheta.R | 8 inst/tests/test-lmp-icc.R |only man/rpf.1dim.lmp-class.Rd |only man/rpf.lmp.Rd |only man/rpf.rparam.Rd | 1 src/libifa-rpf.cpp | 476 +++++++++++++++++++++++++++++++++++++++++++++- vignettes/customitem.Rmd |only 16 files changed, 542 insertions(+), 55 deletions(-)
Title: Build Regular Expressions in a Human Readable Way
Description: Build regular expressions piece by piece using human readable code.
This package is designed for interactive use. For package development, use
the rebus.* dependencies.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus versions 0.0-5 dated 2015-02-04 and 0.1-0 dated 2015-12-16
rebus-0.0-5/rebus/R/alternation.R |only rebus-0.0-5/rebus/R/backreferences.R |only rebus-0.0-5/rebus/R/capture.R |only rebus-0.0-5/rebus/R/class-groups.R |only rebus-0.0-5/rebus/R/compound-constants.R |only rebus-0.0-5/rebus/R/concatenation.R |only rebus-0.0-5/rebus/R/constants.R |only rebus-0.0-5/rebus/R/datetime.R |only rebus-0.0-5/rebus/R/escape_special.R |only rebus-0.0-5/rebus/R/grouping-and-repetition.R |only rebus-0.0-5/rebus/R/internal.R |only rebus-0.0-5/rebus/R/lookaround.R |only rebus-0.0-5/rebus/R/misc.R |only rebus-0.0-5/rebus/R/number_range.R |only rebus-0.0-5/rebus/R/regex-methods.R |only rebus-0.0-5/rebus/R/unicode-groups.R |only rebus-0.0-5/rebus/R/unicode.R |only rebus-0.0-5/rebus/R/zzz.R |only rebus-0.0-5/rebus/inst |only rebus-0.0-5/rebus/man/recycle.Rd |only rebus-0.0-5/rebus/man/repeat_in_class.Rd |only rebus-0.0-5/rebus/tests |only rebus-0.1-0/rebus/DESCRIPTION | 20 rebus-0.1-0/rebus/MD5 | 86 -- rebus-0.1-0/rebus/NAMESPACE | 55 + rebus-0.1-0/rebus/R/export-base.R |only rebus-0.1-0/rebus/R/export-datetimes.R |only rebus-0.1-0/rebus/R/export-numbers.R |only rebus-0.1-0/rebus/R/export-unicode.R |only rebus-0.1-0/rebus/R/imports.R |only rebus-0.1-0/rebus/R/regex-package.R | 8 rebus-0.1-0/rebus/README.md | 62 - rebus-0.1-0/rebus/man/Anchors.Rd | 27 rebus-0.1-0/rebus/man/Backreferences.Rd | 47 - rebus-0.1-0/rebus/man/CharacterClasses.Rd | 97 -- rebus-0.1-0/rebus/man/ClassGroups.Rd | 146 --- rebus-0.1-0/rebus/man/Concatenation.Rd | 31 rebus-0.1-0/rebus/man/DateTime.Rd | 189 ---- rebus-0.1-0/rebus/man/IsoClasses.Rd |only rebus-0.1-0/rebus/man/SpecialCharacters.Rd | 55 - rebus-0.1-0/rebus/man/Unicode.Rd | 1081 -------------------------- rebus-0.1-0/rebus/man/WordBoundaries.Rd | 25 rebus-0.1-0/rebus/man/as.regex.Rd | 36 rebus-0.1-0/rebus/man/capture.Rd | 29 rebus-0.1-0/rebus/man/char_class.Rd | 29 rebus-0.1-0/rebus/man/escape_special.Rd | 32 rebus-0.1-0/rebus/man/exactly.Rd | 19 rebus-0.1-0/rebus/man/format.regex.Rd | 24 rebus-0.1-0/rebus/man/get_weekdays.Rd | 50 - rebus-0.1-0/rebus/man/literal.Rd | 20 rebus-0.1-0/rebus/man/lookahead.Rd | 31 rebus-0.1-0/rebus/man/modify_mode.Rd |only rebus-0.1-0/rebus/man/number_range.Rd | 37 rebus-0.1-0/rebus/man/or.Rd | 52 - rebus-0.1-0/rebus/man/rebus.Rd |only rebus-0.1-0/rebus/man/recursive.Rd | 21 rebus-0.1-0/rebus/man/regex.Rd | 113 -- rebus-0.1-0/rebus/man/repeated.Rd | 45 - rebus-0.1-0/rebus/man/roman.Rd |only 59 files changed, 243 insertions(+), 2224 deletions(-)
Title: Probabilistic Latent Feature Analysis
Description: Functions for estimating probabilistic latent feature models with a disjunctive or a conjunctive mapping rule on (aggregated) binary three-way data.
Author: Michel Meulders [aut, cre], Philippe De Bruecker [ctb]
Maintainer: Michel Meulders <michel.meulders@kuleuven.be>
Diff between plfm versions 1.1.2 dated 2014-12-28 and 2.1 dated 2015-12-16
DESCRIPTION | 20 MD5 | 37 NAMESPACE | 16 R/plfm.R | 2633 +++++++++++++++++++++++++++++++++++++++- data/anger2.rda |only data/car.rda |binary data/car2.rda |only data/hostility.rda |only man/LCplfm.Rd |only man/anger2.Rd |only man/bayesplfm.Rd | 4 man/car.Rd | 8 man/car2.Rd |only man/gendatLCplfm.Rd |only man/hostility.Rd |only man/plfm-package.Rd | 33 man/plfm.Rd | 55 man/plot.LCplfm.Rd |only man/plot.plfm.Rd |only man/plot.stepLCplfm.Rd |only man/plot.stepplfm.Rd | 3 man/print.LCplfm.Rd |only man/print.stepLCplfm.Rd |only man/print.summary.stepLCplfm.Rd |only man/stepLCplfm.Rd |only man/stepplfm.Rd | 35 man/summary.stepLCplfm.Rd |only src |only 28 files changed, 2738 insertions(+), 106 deletions(-)
Title: Programming with Big Data -- Interface to ZeroMQ
Description: 'ZeroMQ' is a well-known library for high-performance
asynchronous messaging in scalable, distributed applications. This
package provides high level R wrapper functions to easily utilize
'ZeroMQ'. We mainly focus on interactive client/server programming
frameworks. For convenience, a minimal 'ZeroMQ' library (4.1.0 rc1)
is shipped with 'pbdZMQ', which can be used if no system installation
of 'ZeroMQ' is available. A few wrapper functions compatible with
'rzmq' are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Christian Heckendorf [aut] (file transfer),
George Ostrouchov [aut] (Mac OSX),
Whit Armstrong [ctb] (some functions are modified from the rzmq package
for backwards compatibility),
Brian Ripley [ctb] (C code of shellexec, and Solaris),
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.1-1 dated 2015-09-23 and 0.2-0 dated 2015-12-16
pbdZMQ-0.1-1/pbdZMQ/R/111_control_message.r |only pbdZMQ-0.1-1/pbdZMQ/R/111_control_sendrecv.r |only pbdZMQ-0.1-1/pbdZMQ/R/111_control_socket_option.r |only pbdZMQ-0.1-1/pbdZMQ/R/111_control_socket_type.r |only pbdZMQ-0.1-1/pbdZMQ/README |only pbdZMQ-0.1-1/pbdZMQ/data |only pbdZMQ-0.1-1/pbdZMQ/man/00_pbdZMQ-package.Rd |only pbdZMQ-0.1-1/pbdZMQ/man/11_d_control.Rd |only pbdZMQ-0.1-1/pbdZMQ/man/a0_context.Rd |only pbdZMQ-0.1-1/pbdZMQ/man/zz_zmq_internal.Rd |only pbdZMQ-0.2-0/pbdZMQ/ChangeLog | 51 ++ pbdZMQ-0.2-0/pbdZMQ/DESCRIPTION | 40 +- pbdZMQ-0.2-0/pbdZMQ/INSTALL | 67 +++ pbdZMQ-0.2-0/pbdZMQ/MD5 | 136 ++++--- pbdZMQ-0.2-0/pbdZMQ/NAMESPACE | 53 ++ pbdZMQ-0.2-0/pbdZMQ/R/000_globalVariables.r | 2 pbdZMQ-0.2-0/pbdZMQ/R/111_control.r |only pbdZMQ-0.2-0/pbdZMQ/R/222_export_env.r | 65 +++ pbdZMQ-0.2-0/pbdZMQ/R/222_export_opt.r |only pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_context.r | 55 ++- pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_message.r | 101 ++++- pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_sendrecv.r | 128 ++++++- pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_socket.r | 163 ++++++++ pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_transfer.r |only pbdZMQ-0.2-0/pbdZMQ/R/R_zmq_utility.r | 60 ++- pbdZMQ-0.2-0/pbdZMQ/R/address.r |only pbdZMQ-0.2-0/pbdZMQ/R/czmq.r |only pbdZMQ-0.2-0/pbdZMQ/R/pbdZMQ-package.r |only pbdZMQ-0.2-0/pbdZMQ/R/pyzmq_wrapper.r |only pbdZMQ-0.2-0/pbdZMQ/R/random_port.r |only pbdZMQ-0.2-0/pbdZMQ/R/rzmq_wrapper.r | 115 +++++- pbdZMQ-0.2-0/pbdZMQ/R/shellexec_wcc.r | 80 +++- pbdZMQ-0.2-0/pbdZMQ/R/windows/zzz.r | 4 pbdZMQ-0.2-0/pbdZMQ/R/zzz.r.in | 10 pbdZMQ-0.2-0/pbdZMQ/README.md |only pbdZMQ-0.2-0/pbdZMQ/cleanup | 1 pbdZMQ-0.2-0/pbdZMQ/demo/hwclient.r | 2 pbdZMQ-0.2-0/pbdZMQ/demo/hwserver.r | 2 pbdZMQ-0.2-0/pbdZMQ/demo/msreader.r | 6 pbdZMQ-0.2-0/pbdZMQ/demo/tasksink.r | 2 pbdZMQ-0.2-0/pbdZMQ/demo/taskvent.r | 4 pbdZMQ-0.2-0/pbdZMQ/demo/taskwork.r | 4 pbdZMQ-0.2-0/pbdZMQ/demo/wuclient.r | 6 pbdZMQ-0.2-0/pbdZMQ/demo/wuserver.r | 2 pbdZMQ-0.2-0/pbdZMQ/inst/CITATION | 10 pbdZMQ-0.2-0/pbdZMQ/inst/doc/pbdZMQ-guide.Rnw | 13 pbdZMQ-0.2-0/pbdZMQ/inst/doc/pbdZMQ-guide.pdf |binary pbdZMQ-0.2-0/pbdZMQ/inst/examples |only pbdZMQ-0.2-0/pbdZMQ/man/a0_a_pbdZMQ-package.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/a0_b_control.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/a0_c_options.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/a0_d_context.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/a1_socket.Rd | 182 +++++----- pbdZMQ-0.2-0/pbdZMQ/man/a2_message.Rd | 75 ++-- pbdZMQ-0.2-0/pbdZMQ/man/address.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/b0_sendrecv.Rd | 105 +++-- pbdZMQ-0.2-0/pbdZMQ/man/b1_sendrecvfile.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/pyzmq.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/random_port.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/u0_shellexec.wcc.Rd | 98 ++--- pbdZMQ-0.2-0/pbdZMQ/man/xx_czmq_wrapper.Rd |only pbdZMQ-0.2-0/pbdZMQ/man/xx_rzmq_wrapper.Rd | 82 +++- pbdZMQ-0.2-0/pbdZMQ/man/xx_utility.Rd | 55 +-- pbdZMQ-0.2-0/pbdZMQ/man/zz_zmq_control.Rd | 68 +++ pbdZMQ-0.2-0/pbdZMQ/src/Makevars.in | 4 pbdZMQ-0.2-0/pbdZMQ/src/Makevars.win | 2 pbdZMQ-0.2-0/pbdZMQ/src/R_zmq.h | 1 pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_context.c | 21 - pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_message.c | 20 - pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_sendrecv.c | 8 pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_socket.c | 56 +-- pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_transfer.c |only pbdZMQ-0.2-0/pbdZMQ/src/R_zmq_utility.c | 15 pbdZMQ-0.2-0/pbdZMQ/src/build_zmq.in | 3 pbdZMQ-0.2-0/pbdZMQ/src/install.libs.R | 41 ++ pbdZMQ-0.2-0/pbdZMQ/src/shellexec_wcc.c | 18 pbdZMQ-0.2-0/pbdZMQ/tests |only pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-guide.Rnw | 13 pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-include/01-introduction.tex | 2 pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-include/05-cs.tex |only pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-include/06-solaris.tex |only pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-include/99-faq.tex |only pbdZMQ-0.2-0/pbdZMQ/vignettes/pbdZMQ-include/pbdZMQ.bib | 4 83 files changed, 1496 insertions(+), 559 deletions(-)
Title: Knitr Bootstrap Framework
Description: A framework to create Bootstrap 3 HTML reports from knitr
Rmarkdown.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between knitrBootstrap versions 0.9.0 dated 2013-10-17 and 1.0.0 dated 2015-12-16
knitrBootstrap-0.9.0/knitrBootstrap/inst/examples/test.Rmd |only knitrBootstrap-0.9.0/knitrBootstrap/inst/examples/test.html |only knitrBootstrap-0.9.0/knitrBootstrap/inst/examples/three-D.html |only knitrBootstrap-0.9.0/knitrBootstrap/man/create_header.Rd |only knitrBootstrap-0.9.0/knitrBootstrap/man/primerTree.Rd |only knitrBootstrap-1.0.0/knitrBootstrap/DESCRIPTION | 23 knitrBootstrap-1.0.0/knitrBootstrap/LICENSE |only knitrBootstrap-1.0.0/knitrBootstrap/MD5 | 81 knitrBootstrap-1.0.0/knitrBootstrap/NAMESPACE | 7 knitrBootstrap-1.0.0/knitrBootstrap/R/knit_bootstrap.R | 776 +- knitrBootstrap-1.0.0/knitrBootstrap/README.md | 278 knitrBootstrap-1.0.0/knitrBootstrap/build/vignette.rds |binary knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/cars.R | 12 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/cars.Rmd | 19 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/cars.html | 1388 +++- knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/illusions.R | 6 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/illusions.Rmd | 9 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/illusions.html | 1453 +++- knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/maps.R | 2 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/maps.Rmd | 11 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/maps.html | 1318 +++ knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/math.Rmd | 23 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/math.html | 1220 +++ knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/two-D.R | 5 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/two-D.Rmd | 11 knitrBootstrap-1.0.0/knitrBootstrap/inst/doc/two-D.html | 1849 ++++- knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/all.Rmd | 12 knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/all.html | 3347 +++++----- knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/engines.Rmd | 9 knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/engines.html | 2124 +++--- knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/messages.Rmd | 4 knitrBootstrap-1.0.0/knitrBootstrap/inst/examples/messages.html | 2227 +++--- knitrBootstrap-1.0.0/knitrBootstrap/inst/templates/knitr_bootstrap.css | 59 knitrBootstrap-1.0.0/knitrBootstrap/inst/templates/knitr_bootstrap.js | 282 knitrBootstrap-1.0.0/knitrBootstrap/inst/templates/knitr_bootstrap_includes.html | 18 knitrBootstrap-1.0.0/knitrBootstrap/man/bootstrap_HTML.Rd | 40 knitrBootstrap-1.0.0/knitrBootstrap/man/bootstrap_document.Rd |only knitrBootstrap-1.0.0/knitrBootstrap/man/knit_bootstrap.Rd | 72 knitrBootstrap-1.0.0/knitrBootstrap/man/knit_bootstrap_md.Rd | 56 knitrBootstrap-1.0.0/knitrBootstrap/man/knitrBootstrap.Rd |only knitrBootstrap-1.0.0/knitrBootstrap/man/render_bootstrap.Rd |only knitrBootstrap-1.0.0/knitrBootstrap/vignettes/cars.Rmd | 19 knitrBootstrap-1.0.0/knitrBootstrap/vignettes/illusions.Rmd | 9 knitrBootstrap-1.0.0/knitrBootstrap/vignettes/maps.Rmd | 11 knitrBootstrap-1.0.0/knitrBootstrap/vignettes/math.Rmd | 23 knitrBootstrap-1.0.0/knitrBootstrap/vignettes/two-D.Rmd | 11 46 files changed, 11218 insertions(+), 5596 deletions(-)
More information about knitrBootstrap at CRAN
Permanent link
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Barton & Lord's four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2015).
Author: Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0.2 dated 2015-11-13 and 1.0.3 dated 2015-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/Gibbs_2PNO.Rd | 2 +- man/Gibbs_4PNO.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Calculations for DNA Mixtures
Description: Calculations for DNA mixtures accounting for possibly inbred pedigrees (simulations with conditioning, LR). Calculation of exact p-values.
Author: Guro Dorum and Thore Egeland
Maintainer: Guro Dorum <guro.dorum@nmbu.no>
Diff between euroMix versions 1.1 dated 2015-12-10 and 1.1.1 dated 2015-12-16
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: An easily accessible continuous (and discrete) time dynamic
modelling package for panel and time series data, reliant upon the OpenMx.
package (http://openmx.psyc.virginia.edu/) for computation. Most dynamic
modelling approaches to longitudinal data rely on the assumption that time
intervals between observations are consistent. When this assumption is
adhered to, the data gathering process is necessarily limited to a specific
schedule, and when broken, the resulting parameter estimates may be biased
and reduced in power. Continuous time models are conceptually similar to
vector autoregressive models (thus also the latent change models popularised
in a structural equation modelling context), however by explicitly including
the length of time between observations, continuous time models are freed
from the assumption that measurement intervals are consistent. This allows:
data to be gathered irregularly; the elimination of noise and bias due to
varying measurement intervals; parsimonious structures for complex dynamics.
The application of such a model in this SEM framework allows full-information
maximum-likelihood estimates for both N = 1 and N > 1 cases, multiple measured
indicators per latent process, and the flexibility to incorporate additional
elements, including individual heterogeneity in the latent process and
manifest intercepts, and time dependent and independent exogenous covariates.
Furthermore, due to the SEM implementation we are able to estimate a random
effects model where the impact of time dependent and time independent predictors
can be assessed simultaneously, but without the classic problems of random
effects models assuming no covariance between unit level effects and predictors.
Author: Manuel Voelkle [aut, cph] (Original development of continuous time
model specification within OpenMx, advisor for further development),
Han Oud [aut, cph] (Original development of continuous time model
specification within OpenMx),
Charles Driver [aut, cre, cph] (Further development of continuous time
model specification within OpenMx, package development,
documentation and maintenance)
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 1.1.3 dated 2015-10-12 and 1.1.5 dated 2015-12-16
ctsem-1.1.3/ctsem/vignettes/ctsem_paper_source.zip |only ctsem-1.1.5/ctsem/DESCRIPTION | 57 +- ctsem-1.1.5/ctsem/MD5 | 102 ++-- ctsem-1.1.5/ctsem/NAMESPACE | 2 ctsem-1.1.5/ctsem/R/ctCI.R | 13 ctsem-1.1.5/ctsem/R/ctDataHelp.R | 186 +++---- ctsem-1.1.5/ctsem/R/ctFit.R | 397 ++++++++++++---- ctsem-1.1.5/ctsem/R/ctGenerate.R | 44 - ctsem-1.1.5/ctsem/R/ctIndplot.R | 12 ctsem-1.1.5/ctsem/R/ctIntervalise.R | 490 ++++++++++---------- ctsem-1.1.5/ctsem/R/ctLongtowide.r | 109 ++-- ctsem-1.1.5/ctsem/R/ctMultigroupFit.R | 2 ctsem-1.1.5/ctsem/R/ctPSMfit.R | 12 ctsem-1.1.5/ctsem/R/ctWideToLong.R | 200 ++++---- ctsem-1.1.5/ctsem/R/ctsem.R | 42 - ctsem-1.1.5/ctsem/R/ctsemUtils.R | 146 ++--- ctsem-1.1.5/ctsem/R/plot.ctsemFit.R | 22 ctsem-1.1.5/ctsem/R/summary.ctsemFit.R | 124 +++-- ctsem-1.1.5/ctsem/build/vignette.rds |binary ctsem-1.1.5/ctsem/inst/doc/ctsem.R | 172 +++---- ctsem-1.1.5/ctsem/inst/doc/ctsem.pdf |binary ctsem-1.1.5/ctsem/inst/doc/ctsem.rnw | 134 ++--- ctsem-1.1.5/ctsem/inst/tests/test-intervalise.R | 2 ctsem-1.1.5/ctsem/inst/tests/test-knownFits.R |only ctsem-1.1.5/ctsem/inst/tests/test-objectiveEquiv.R |only ctsem-1.1.5/ctsem/inst/tests/test-reshaping.R |only ctsem-1.1.5/ctsem/man/AnomAuth.Rd | 2 ctsem-1.1.5/ctsem/man/Oscillating.Rd | 4 ctsem-1.1.5/ctsem/man/ctCI.Rd | 13 ctsem-1.1.5/ctsem/man/ctDeintervalise.Rd | 2 ctsem-1.1.5/ctsem/man/ctExample1.Rd | 4 ctsem-1.1.5/ctsem/man/ctExample1TIpred.Rd | 4 ctsem-1.1.5/ctsem/man/ctExample2.Rd | 4 ctsem-1.1.5/ctsem/man/ctExample2level.Rd | 2 ctsem-1.1.5/ctsem/man/ctExample3.Rd | 2 ctsem-1.1.5/ctsem/man/ctExample4.Rd | 2 ctsem-1.1.5/ctsem/man/ctFit.Rd | 108 ++-- ctsem-1.1.5/ctsem/man/ctGenerate.Rd | 31 - ctsem-1.1.5/ctsem/man/ctIndplot.Rd | 4 ctsem-1.1.5/ctsem/man/ctIntervalise.Rd | 58 +- ctsem-1.1.5/ctsem/man/ctLongToWide.Rd | 29 - ctsem-1.1.5/ctsem/man/ctModel.Rd | 84 +-- ctsem-1.1.5/ctsem/man/ctMultigroupFit.Rd | 24 ctsem-1.1.5/ctsem/man/ctPSMfit.Rd | 12 ctsem-1.1.5/ctsem/man/ctWideNames.Rd | 4 ctsem-1.1.5/ctsem/man/ctWideToLong.Rd | 14 ctsem-1.1.5/ctsem/man/ctsem.Rd | 30 - ctsem-1.1.5/ctsem/man/datastructure.Rd | 8 ctsem-1.1.5/ctsem/man/longexample.Rd | 8 ctsem-1.1.5/ctsem/man/plot.ctsemFit.Rd | 22 ctsem-1.1.5/ctsem/man/plot.ctsemMultigroupFit.Rd | 2 ctsem-1.1.5/ctsem/man/summary.ctsemFit.Rd | 17 ctsem-1.1.5/ctsem/man/summary.ctsemMultigroupFit.Rd | 9 ctsem-1.1.5/ctsem/vignettes/ctsem.rnw | 134 ++--- 54 files changed, 1633 insertions(+), 1272 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, etc.
Author: Christian Roever [aut, cre], Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 1.0 dated 2015-12-06 and 1.1 dated 2015-12-16
bayesmeta-1.0/bayesmeta/data/Cochran1954.rda |only bayesmeta-1.0/bayesmeta/data/CrinsEtAl2014.rda |only bayesmeta-1.0/bayesmeta/data/HinksEtAl2010.rda |only bayesmeta-1.0/bayesmeta/data/Peto1980.rda |only bayesmeta-1.0/bayesmeta/data/Rubin1981.rda |only bayesmeta-1.0/bayesmeta/data/SidikJonkman2007.rda |only bayesmeta-1.0/bayesmeta/data/SnedecorCochran.rda |only bayesmeta-1.1/bayesmeta/DESCRIPTION | 19 ++++++--------- bayesmeta-1.1/bayesmeta/MD5 | 27 +++++++++++++--------- bayesmeta-1.1/bayesmeta/build |only bayesmeta-1.1/bayesmeta/data/Cochran1954.R |only bayesmeta-1.1/bayesmeta/data/CrinsEtAl2014.R |only bayesmeta-1.1/bayesmeta/data/HinksEtAl2010.R |only bayesmeta-1.1/bayesmeta/data/Peto1980.R |only bayesmeta-1.1/bayesmeta/data/Rubin1981.R |only bayesmeta-1.1/bayesmeta/data/SidikJonkman2007.R |only bayesmeta-1.1/bayesmeta/data/SnedecorCochran.R |only bayesmeta-1.1/bayesmeta/inst |only bayesmeta-1.1/bayesmeta/man/Rubin1981.Rd | 2 - bayesmeta-1.1/bayesmeta/man/bayesmeta-package.Rd | 4 +-- bayesmeta-1.1/bayesmeta/man/bayesmeta.Rd | 3 +- bayesmeta-1.1/bayesmeta/vignettes |only 22 files changed, 29 insertions(+), 26 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author:
Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 1.14-0 dated 2015-10-15 and 1.15-0 dated 2015-12-16
DESCRIPTION | 40 ++++------ MD5 | 96 ++++++++++++------------ R/IRT.likelihood.TAM.R | 4 + R/calc_posterior.v2.R | 9 +- R/designMatrices.R | 1 R/designMatrices.mfr.R | 13 ++- R/designMatrices.mfr2.R | 9 ++ R/designMatrices.mfr_aux.R | 4 - R/designMatrices_aux.R | 19 ++++ R/designMatrices_aux2.R | 19 ++++ R/tam.latreg.R | 4 - R/tam.mml.2pl.R | 46 +++++++++-- R/tam.mml.3pl.R | 18 +++- R/tam.mml.R | 23 ++++- R/tam.mml.mfr.R | 150 ++++++++++++++++++++++++++++++-------- data/data.cqc01.rda |binary data/data.cqc02.rda |binary data/data.cqc03.rda |binary data/data.cqc04.rda |binary data/data.cqc05.rda |binary data/data.ctest1.rda |binary data/data.ctest2.rda |binary data/data.ex08.rda |binary data/data.ex10.rda |binary data/data.ex11.rda |binary data/data.ex12.rda |binary data/data.ex14.rda |binary data/data.ex15.rda |binary data/data.exJ03.rda |binary data/data.fims.Aus.Jpn.raw.rda |binary data/data.fims.Aus.Jpn.scored.rda |binary data/data.geiser.rda |binary data/data.gpcm.rda |binary data/data.janssen.rda |binary data/data.janssen2.rda |binary data/data.mc.rda |binary data/data.numeracy.rda |binary data/data.sim.facets.rda |binary data/data.sim.mfr.rda |binary data/data.sim.rasch.missing.rda |binary data/data.sim.rasch.pweights.rda |binary data/data.sim.rasch.rda |binary data/data.timssAusTwn.rda |binary data/data.timssAusTwn.scored.rda |binary inst/NEWS | 38 +++++++++ man/IRT.data.tam.Rd | 2 man/TAM-package.Rd | 4 - man/tam.mml.3pl.Rd | 6 + man/tam.mml.Rd | 14 ++- 49 files changed, 382 insertions(+), 137 deletions(-)
Title: Evaluation of the Proportional Hazards Assumption with a
Standardized Score Process
Description: Provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
Author: Cecile Chauvel
Maintainer: Cecile Chauvel <chauvel.cecile@gmail.com>
Diff between PHeval versions 0.5.2 dated 2014-12-16 and 0.5.3 dated 2015-12-16
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 1 + man/plotscore.Rd | 3 +-- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide provided,
or the paper under citation.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>
Diff between likeLTD versions 5.5.0 dated 2015-03-12 and 6.0.0 dated 2015-12-16
DESCRIPTION | 14 MD5 | 102 ++++--- NAMESPACE | 35 ++ R/genetics-peaks.R |only R/genetics.R | 143 +++++++++- R/hypothesis-peaks.R |only R/hypothesis.R | 27 + R/maximize-peaks.R |only R/maximize.R | 48 ++- R/objectives-peaks.R |only R/plotter.R | 2 R/reports-peaks.R |only R/reports.R | 91 ++++-- build |only data/DNA17-db.txt.gz |binary data/Identifiler-db.txt.gz |binary data/SGMplus-db.txt.gz |binary data/lgc-allele-freqs-wbp.txt.gz |only inst/doc/likeLTDguide.pdf |binary inst/doc/usage.R | 404 ++++++++++------------------ inst/doc/usage.Rnw | 465 ++++++++++++++------------------- inst/doc/usage.pdf |binary inst/extdata/laboratory |only inst/unitTests/runit_objective.R | 28 - man/CSP.heights.plot.Rd |only man/DNA17-db.Rd | 5 man/Identifiler-db.Rd | 4 man/SGMplus-db.Rd | 4 man/allele.report.Rd | 16 + man/allele.report.peaks.Rd |only man/create.likelihood.log.Rd | 2 man/create.likelihood.vectors.peaks.Rd |only man/defence.hypothesis.Rd | 34 ++ man/defence.hypothesis.peaks.Rd |only man/evaluate.Rd | 47 +++ man/evaluate.from.interim.Rd | 6 man/evaluate.from.interim.peaks.Rd |only man/evaluate.peaks.Rd |only man/get.likely.genotypes.Rd | 44 +++ man/get.likely.genotypes.peaks.Rd |only man/lgc-allele-freqs-wbp.Rd |only man/load.allele.database.Rd | 21 + man/locus.likes.Rd | 42 ++ man/locus.likes.peaks.Rd |only man/optimisation.params.Rd | 33 ++ man/optimisation.params.peaks.Rd |only man/output.report.Rd | 38 ++ man/output.report.peaks.Rd |only man/pack.admin.input.Rd | 25 + man/pack.admin.input.peaks.Rd |only man/peaks.results.plot.Rd |only man/prosecution.hypothesis.Rd | 34 ++ man/prosecution.hypothesis.peaks.Rd |only man/read.csp.profile.Rd | 15 + man/read.known.profiles.Rd | 35 ++ man/read.peaks.profile.Rd |only man/read.unc.profile.Rd | 15 + man/relistArguments.peaks.Rd |only man/unitTests.likeLTD.Rd | 2 src/gammaDist.cpp |only src/gammaDist.h |only src/maximizePeaks.cpp |only src/maximizePeaks.h |only src/module.cpp | 15 + vignettes/usage.Rnw | 465 ++++++++++++++------------------- 65 files changed, 1353 insertions(+), 908 deletions(-)
Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure
to analyse temporal trend in the framework of the OSPAR convention.
The analysis process run through 4 successive steps : 1) manipulate your data, 2)
select the parameters you want to analyse, 3) build your regulated
time series, 4) perform diagnosis and analysis and 5) read the results.
Statistical analysis call other package function such as Kendall tests
or cusum() function.
Author: David DEVREKER [aut],
Alain LEFEBVRE [aut, cre]
Maintainer: Alain LEFEBVRE <Alain.Lefebvre@ifremer.fr>
Diff between TTAinterfaceTrendAnalysis versions 1.5.1 dated 2014-02-21 and 1.5.2 dated 2015-12-16
DESCRIPTION | 26 - MD5 | 37 +- NAMESPACE | 25 + NEWS | 15 - R/About.R |only R/Envir.r | 4 R/FULLoption.r | 543 +++++++++++++++++++----------------- R/TTAinterface.R | 657 ++++++++++++++++++++++---------------------- R/aide3.r | 2 R/fixdata.R | 514 +++++++++++++++++----------------- R/selectdirectory.R | 505 +++++++++++++++++---------------- R/zzz.R | 15 - build/vignette.rds |binary inst/aide/TTAinterface.gif |only inst/aide/iconTTA.ico |only inst/doc/TTAVignette.Rnw | 4 inst/doc/TTAVignette.pdf |binary inst/doc/UserGuide.pdf |binary man/TTAinterface-package.Rd | 4 vignettes/TTAVignette.Rnw | 4 vignettes/figure5.jpg |binary 21 files changed, 1223 insertions(+), 1132 deletions(-)
More information about TTAinterfaceTrendAnalysis at CRAN
Permanent link
More information about rebus.datetimes at CRAN
Permanent link
Title: Interface to the 'OpenBUGS' MCMC Software
Description: Fully-interactive R interface to the 'OpenBUGS' software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between BRugs versions 0.8-5 dated 2015-07-29 and 0.8-6 dated 2015-12-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ data/ratsdata.RData |binary data/ratsinits.RData |binary src/Makefile.win | 14 +++++++------- tests/examples.R | 10 ++++++---- tests/examples.Rout.save | 12 ++++++------ 8 files changed, 34 insertions(+), 28 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.300.2.2 dated 2015-12-13 and 0.6.400.2.2 dated 2015-12-16
ChangeLog | 227 ++++++++++---------- DESCRIPTION | 8 MD5 | 48 ++-- inst/NEWS.Rd | 12 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 1 inst/include/armadillo_bits/Cube_bones.hpp | 13 - inst/include/armadillo_bits/Cube_meat.hpp | 73 ++++++ inst/include/armadillo_bits/Mat_bones.hpp | 12 + inst/include/armadillo_bits/Mat_meat.hpp | 170 ++++++++++++++ inst/include/armadillo_bits/arma_rng_cxx11.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/auxlib_meat.hpp | 39 ++- inst/include/armadillo_bits/compiler_setup.hpp | 1 inst/include/armadillo_bits/field_bones.hpp | 6 inst/include/armadillo_bits/field_meat.hpp | 109 +++++++-- inst/include/armadillo_bits/fn_misc.hpp | 70 ++++++ inst/include/armadillo_bits/gmm_diag_meat.hpp | 2 inst/include/armadillo_bits/subview_bones.hpp | 10 inst/include/armadillo_bits/subview_cube_bones.hpp | 7 inst/include/armadillo_bits/subview_cube_meat.hpp | 84 +++++++ inst/include/armadillo_bits/subview_field_bones.hpp | 1 inst/include/armadillo_bits/subview_field_meat.hpp | 31 ++ inst/include/armadillo_bits/subview_meat.hpp | 204 ++++++++++++++++- 25 files changed, 936 insertions(+), 202 deletions(-)
Title: Power Analysis for Random Effects in Mixed Models
Description: Simulation functions to assess or explore the power of a dataset to estimates significant random effects (intercept or slope) in a mixed model. The functions are based on the "lme4" package.
Author: Julien Martin [aut, cre]
Maintainer: Julien Martin <julienmartin@abdn.ac.uk>
Diff between pamm versions 0.7 dated 2010-05-26 and 0.9 dated 2015-12-16
DESCRIPTION | 29 ++-- MD5 |only NAMESPACE |only R/EAMM.R | 375 ++++++++++++++++++++++++++++++++++------------------ R/PAMM.R | 303 ++++++++++++++++++++++++------------------ R/SSF.R | 255 +++++++++++++++++++---------------- R/plot.EAMM.R | 213 +++++++++++++++-------------- R/plot.PAMM.R | 329 +++++++++++++++++++++++++++++---------------- R/plot.SSF.R | 30 ++-- inst |only man/EAMM.Rd | 11 + man/PAMM.Rd | 5 man/SSF.Rd | 4 man/pamm-package.Rd | 8 - man/plot.EAMM.Rd | 18 +- man/plot.PAMM.Rd | 97 +++++++------ man/plot.SSF.Rd | 2 17 files changed, 1006 insertions(+), 673 deletions(-)
Title: Count All Common Subsequences
Description: Count all common subsequences between 2 string sequences, with
items separated by the same delimiter. The first string input is a length-
one vector, the second string input can be a vector or list containing
multiple strings. The algorithm differentiates between the more strict
definition of subsequence, where a common subsequence cannot be separated
by any other items, from its looser counterpart, where a common subsequence
can be interrupted by other items. For example, q-w is a common subsequence
of q-w-e-r and q-e-w-r on the looser definition, but not the more strict
definition. calACSLoose Algorithm from Wang, H. All common subsequences
(2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between calACS versions 0.2 dated 2015-11-15 and 1.1 dated 2015-12-16
calACS-0.2/calACS/man/calACS.Rd |only calACS-0.2/calACS/man/calACSstr.Rd |only calACS-1.1/calACS/DESCRIPTION | 17 +++++++----- calACS-1.1/calACS/MD5 | 20 ++++++++++---- calACS-1.1/calACS/NAMESPACE | 6 ++-- calACS-1.1/calACS/R/GeneratePossibleSubsequences.r |only calACS-1.1/calACS/R/calACS.R | 9 +++--- calACS-1.1/calACS/R/calACSLoose.r |only calACS-1.1/calACS/R/calACSstr.R | 25 ++++++++++++------ calACS-1.1/calACS/R/calACSstrLoose.r |only calACS-1.1/calACS/R/is.subvector.r |only calACS-1.1/calACS/man/GeneratePossibleSubsequences.Rd |only calACS-1.1/calACS/man/calACSLoose.Rd |only calACS-1.1/calACS/man/calACSStrict.Rd |only calACS-1.1/calACS/man/calACSstrLoose.Rd |only calACS-1.1/calACS/man/calACSstrStrict.Rd |only calACS-1.1/calACS/man/is.subvector.Rd |only 17 files changed, 51 insertions(+), 26 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.128 dated 2015-09-22 and 2.1.129 dated 2015-12-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/labkey.selectRows.R | 10 ++++++++-- R/schemaObjects.R | 2 +- man/Rlabkey-package.Rd | 4 ++-- man/labkey.selectRows.Rd | 3 ++- 7 files changed, 26 insertions(+), 16 deletions(-)
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Author: Bart Smeets [aut],
Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.0.1 dated 2015-11-17 and 3.1.0 dated 2015-12-15
simmer-3.0.1/simmer/src/entitiy.cpp |only simmer-3.0.1/simmer/src/simulator.cpp |only simmer-3.0.1/simmer/tests/testthat/test-activity.R |only simmer-3.0.1/simmer/tests/testthat/test-branch.R |only simmer-3.0.1/simmer/tests/testthat/test-generator.R |only simmer-3.0.1/simmer/tests/testthat/test-resource.R |only simmer-3.1.0/simmer/DESCRIPTION | 10 simmer-3.1.0/simmer/MD5 | 143 +++--- simmer-3.1.0/simmer/NAMESPACE | 10 simmer-3.1.0/simmer/R/RcppExports.R | 68 ++- simmer-3.1.0/simmer/R/activity.R |only simmer-3.1.0/simmer/R/convenience_funcs.R |only simmer-3.1.0/simmer/R/plot.R | 59 ++ simmer-3.1.0/simmer/R/simulator.R | 218 +++++++--- simmer-3.1.0/simmer/R/trajectory.R | 180 +++++--- simmer-3.1.0/simmer/R/utils.R | 12 simmer-3.1.0/simmer/R/wrap.R | 81 +++ simmer-3.1.0/simmer/TODO | 16 simmer-3.1.0/simmer/build/vignette.rds |binary simmer-3.1.0/simmer/inst/doc/introduction.R | 1 simmer-3.1.0/simmer/inst/doc/introduction.Rmd | 1 simmer-3.1.0/simmer/inst/doc/introduction.html | 60 +- simmer-3.1.0/simmer/inst/doc/terminology.R |only simmer-3.1.0/simmer/inst/doc/terminology.Rmd |only simmer-3.1.0/simmer/inst/doc/terminology.html |only simmer-3.1.0/simmer/inst/doc/trajectories.R |only simmer-3.1.0/simmer/inst/doc/trajectories.Rmd |only simmer-3.1.0/simmer/inst/doc/trajectories.html |only simmer-3.1.0/simmer/man/add_generator.Rd | 11 simmer-3.1.0/simmer/man/add_resource.Rd | 7 simmer-3.1.0/simmer/man/at.Rd |only simmer-3.1.0/simmer/man/branch.Rd | 13 simmer-3.1.0/simmer/man/create_trajectory.Rd | 9 simmer-3.1.0/simmer/man/from.Rd |only simmer-3.1.0/simmer/man/get_capacity.Rd | 7 simmer-3.1.0/simmer/man/get_head.Rd | 5 simmer-3.1.0/simmer/man/get_mon_arrivals.Rd | 7 simmer-3.1.0/simmer/man/get_mon_attributes.Rd |only simmer-3.1.0/simmer/man/get_mon_resources.Rd | 7 simmer-3.1.0/simmer/man/get_n_activities.Rd | 5 simmer-3.1.0/simmer/man/get_n_generated.Rd |only simmer-3.1.0/simmer/man/get_next_activity.Rd | 5 simmer-3.1.0/simmer/man/get_prev_activity.Rd |only simmer-3.1.0/simmer/man/get_queue_count.Rd | 7 simmer-3.1.0/simmer/man/get_queue_size.Rd | 7 simmer-3.1.0/simmer/man/get_server_count.Rd | 7 simmer-3.1.0/simmer/man/get_tail.Rd | 5 simmer-3.1.0/simmer/man/needs_attrs.Rd |only simmer-3.1.0/simmer/man/now.Rd | 5 simmer-3.1.0/simmer/man/onestep.Rd | 5 simmer-3.1.0/simmer/man/peek.Rd | 5 simmer-3.1.0/simmer/man/plot_attributes.Rd |only simmer-3.1.0/simmer/man/print_activity.Rd |only simmer-3.1.0/simmer/man/release.Rd | 7 simmer-3.1.0/simmer/man/reset.Rd | 5 simmer-3.1.0/simmer/man/rollback.Rd |only simmer-3.1.0/simmer/man/run.Rd | 5 simmer-3.1.0/simmer/man/seize.Rd | 9 simmer-3.1.0/simmer/man/set_attribute.Rd |only simmer-3.1.0/simmer/man/show_activity.Rd | 7 simmer-3.1.0/simmer/man/show_trajectory.Rd | 5 simmer-3.1.0/simmer/man/simmer.Rd | 5 simmer-3.1.0/simmer/man/timeout.Rd | 11 simmer-3.1.0/simmer/man/wrap.Rd | 5 simmer-3.1.0/simmer/src/Makevars |only simmer-3.1.0/simmer/src/RcppExports.cpp | 186 +++++++- simmer-3.1.0/simmer/src/activity.cpp | 138 ++++++ simmer-3.1.0/simmer/src/activity.h | 159 ++++--- simmer-3.1.0/simmer/src/entity.cpp |only simmer-3.1.0/simmer/src/entity.h | 210 +++++---- simmer-3.1.0/simmer/src/simmer.h |only simmer-3.1.0/simmer/src/simmer_rcpp.cpp | 153 +++++-- simmer-3.1.0/simmer/src/simulator.h | 145 ++---- simmer-3.1.0/simmer/src/stats.h |only simmer-3.1.0/simmer/tests/testthat/test-chaining.R | 1 simmer-3.1.0/simmer/tests/testthat/test-plot.R | 15 simmer-3.1.0/simmer/tests/testthat/test-simmer-generator.R |only simmer-3.1.0/simmer/tests/testthat/test-simmer-resource.R |only simmer-3.1.0/simmer/tests/testthat/test-simmer.R | 18 simmer-3.1.0/simmer/tests/testthat/test-simulation-1.R | 8 simmer-3.1.0/simmer/tests/testthat/test-simulation-2.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory-branch.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory-rollback.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory-seize-release.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory-setattribute.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory-timeout.R |only simmer-3.1.0/simmer/tests/testthat/test-trajectory.R | 97 +++- simmer-3.1.0/simmer/tests/testthat/test-util-funcs.R |only simmer-3.1.0/simmer/tests/testthat/test-wrap.R | 21 simmer-3.1.0/simmer/vignettes/introduction.Rmd | 1 simmer-3.1.0/simmer/vignettes/terminology.Rmd |only simmer-3.1.0/simmer/vignettes/trajectories.Rmd |only 92 files changed, 1547 insertions(+), 640 deletions(-)
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at (http://www.phidot.org/software/mark/downloads/)
but is not open source.
Author: Jeff Laake <jeff.laake@noaa.gov> with code contributions from Eldar
Rakhimberdiev, Ben Augustine and Daniel Turek, and example data and
analysis from Bret Collier, Jay Rotella, David Pavlacky,Andrew Paul and Luke Eberhart-Phillips.
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between RMark versions 2.1.13 dated 2015-06-04 and 2.1.14 dated 2015-12-15
DESCRIPTION | 10 +- MD5 | 37 ++++---- NAMESPACE | 19 ++++ NEWS | 20 ++++ R/RMark-package.R | 182 +++++++++++++++++++++++++++++++++++++++++++ R/compute.design.data.R | 1 R/compute.real.R | 17 +++- R/covariate.predictions.r | 2 R/get.real.R | 49 ++++++++--- R/mark.R | 4 R/process.data.R | 4 R/var.components.reml.r | 3 inst/DerivedPar.txt | 11 ++ inst/MarkModels.pdf |binary inst/extdata/skagit.txt |only inst/models.txt | 8 + inst/parameters.txt | 49 +++++++++++ man/Burnham.Rd |only man/covariate.predictions.Rd | 2 man/get.real.Rd | 7 + man/skagit.Rd |only 21 files changed, 380 insertions(+), 45 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between missMDA versions 1.8.2 dated 2015-07-01 and 1.9 dated 2015-12-15
missMDA-1.8.2/missMDA/R/MIPCA.R |only missMDA-1.9/missMDA/DESCRIPTION | 14 missMDA-1.9/missMDA/MD5 | 34 +- missMDA-1.9/missMDA/NAMESPACE | 11 missMDA-1.9/missMDA/R/MIMCA.r |only missMDA-1.9/missMDA/R/MIPCA.r |only missMDA-1.9/missMDA/R/Overimpute.r |only missMDA-1.9/missMDA/R/estim_ncpFAMD.R |only missMDA-1.9/missMDA/R/estim_ncpMCA.R | 165 +++++---- missMDA-1.9/missMDA/R/estim_ncpPCA.R | 6 missMDA-1.9/missMDA/R/imputeMFA.R | 519 ++++++++++++++++++------------- missMDA-1.9/missMDA/R/plot.MIPCA.R | 6 missMDA-1.9/missMDA/R/prelim.R |only missMDA-1.9/missMDA/data/TitanicNA.rda |only missMDA-1.9/missMDA/man/MIMCA.Rd |only missMDA-1.9/missMDA/man/MIPCA.Rd | 53 ++- missMDA-1.9/missMDA/man/Overimpute.Rd |only missMDA-1.9/missMDA/man/TitanicNA.Rd |only missMDA-1.9/missMDA/man/estim_ncpFAMD.Rd |only missMDA-1.9/missMDA/man/estim_ncpMCA.Rd | 80 ++-- missMDA-1.9/missMDA/man/imputeMCA.Rd | 2 missMDA-1.9/missMDA/man/imputePCA.Rd | 2 missMDA-1.9/missMDA/man/prelim.Rd |only missMDA-1.9/missMDA/man/vnf.Rd | 2 24 files changed, 531 insertions(+), 363 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-23 dated 2015-11-09 and 3.1-24 dated 2015-12-15
HH-3.1-23/HH/R/formatHex.R |only HH-3.1-23/HH/R/showHex.R |only HH-3.1-23/HH/man/formatHex.Rd |only HH-3.1-23/HH/man/showHex.Rd |only HH-3.1-24/HH/DESCRIPTION | 12 ++--- HH-3.1-24/HH/MD5 | 27 +++++------- HH-3.1-24/HH/NAMESPACE | 13 ++--- HH-3.1-24/HH/NEWS | 17 +++++++ HH-3.1-24/HH/R/normal.and.t.R | 2 HH-3.1-24/HH/R/normal.and.t.shiny2.R |only HH-3.1-24/HH/inst/scripts/hh2/RApx.R | 24 +++++----- HH-3.1-24/HH/inst/scripts/hh2/dsgntwo.R | 7 --- HH-3.1-24/HH/inst/scripts/hh2/iinf.R | 28 ++++++------ HH-3.1-24/HH/inst/scripts/hh2/tway.R | 58 +++++++++++++------------- HH-3.1-24/HH/man/LikertPercentCountColumns.Rd | 1 HH-3.1-24/HH/man/print.TwoTrellisColumns.Rd | 1 HH-3.1-24/HH/man/pyramidLikert.Rd | 2 17 files changed, 98 insertions(+), 94 deletions(-)
Title: Fungible Coefficients and Monte Carlo Functions
Description: Functions for computing fungible coefficients and Monte Carlo data.
Author: Niels G. Waller <nwaller@umn.edu> and Jeff Jones <jeff.jones@kornferry.com>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between fungible versions 1.1 dated 2015-10-02 and 1.2 dated 2015-12-15
DESCRIPTION | 11 - MD5 | 12 - NAMESPACE | 5 R/fungibleL.R | 341 +++++++++++++++++++++++++++++++------------ inst/CITATION | 4 inst/doc/fungible-manual.pdf |binary man/fungibleL.Rd | 7 7 files changed, 276 insertions(+), 104 deletions(-)
Title: Functions For Statistics Classes At Carleton College
Description: Includes commands for bootstrapping and permutation tests, a command for created grouped bar plots, and a demo of the quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara
Maintainer: Laura Chihara <lchihara@carleton.edu>
Diff between CarletonStats versions 1.1 dated 2014-07-03 and 1.2 dated 2015-12-15
CarletonStats-1.1/CarletonStats/man/Carleton-package.Rd |only CarletonStats-1.2/CarletonStats/DESCRIPTION | 8 CarletonStats-1.2/CarletonStats/MD5 | 15 CarletonStats-1.2/CarletonStats/NAMESPACE | 8 CarletonStats-1.2/CarletonStats/R/CarletonStats-internal.R | 255 ++++++------- CarletonStats-1.2/CarletonStats/R/corDemo.R | 27 - CarletonStats-1.2/CarletonStats/R/groupedBar.default.R | 78 ++- CarletonStats-1.2/CarletonStats/R/permTest.default.R | 35 - CarletonStats-1.2/CarletonStats/R/permTest.formula.R | 14 9 files changed, 222 insertions(+), 218 deletions(-)
Title: Create Waffle Chart Visualizations in R
Description: Square pie charts (a.k.a. waffle charts) can be used
to communicate parts of a whole for categorical quantities. To emulate the
percentage view of a pie chart, a 10x10 grid should be used with each square
representing 1% of the total. Modern uses of waffle charts do not
necessarily adhere to this rule and can be created with a grid of any
rectangular shape. Best practices suggest keeping the number of categories
small, just as should be done when creating pie charts. Tools are provided
to create waffle charts as well as stitch them together, and to use glyphs
for isotype pictogram creation.
Author: Bob Rudis <bob@rudis.net>
Maintainer: Bob Rudis <bob@rudis.net>
Diff between waffle versions 0.3.1 dated 2015-03-23 and 0.5.0 dated 2015-12-15
DESCRIPTION | 19 ++++++----- MD5 | 22 +++++++++---- NAMESPACE | 39 +++++++++++++++++++++--- R/fontawesome.R |only R/iron.R | 9 ++--- R/waffle-package.R | 21 +++++++++++-- R/waffle.R | 80 +++++++++++++++++++++++++++++++++++++++++--------- inst |only man/fa_grep.Rd |only man/fa_list.Rd |only man/iron.Rd | 2 - man/waffle-package.Rd |only man/waffle.Rd | 32 +++++++++++++++----- 13 files changed, 174 insertions(+), 50 deletions(-)
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 0.9.4 dated 2015-04-07 and 0.9.6 dated 2015-12-15
DESCRIPTION | 9 ++-- MD5 | 76 ++++++++++++++++++++-------------------- NAMESPACE | 20 ++++++++-- R/TriMatch-package.R | 6 ++- demo/tutoring.R | 1 man/OneToN.Rd | 2 - man/TriMatch-package.Rd | 2 - man/as.data.frame.list.Rd | 14 +++---- man/balance.plot.Rd | 4 +- man/boxdiff.plot.Rd | 2 - man/covariateBalance.Rd | 24 ++++++------ man/distance.euclid.Rd | 4 +- man/distances.plot.Rd | 2 - man/loess3.plot.Rd | 8 ++-- man/maximumTreat.Rd | 2 - man/merge.triangle.matches.Rd | 2 - man/merge.triangle.psa.Rd | 2 - man/multibalance.plot.Rd | 4 +- man/nmes.Rd | 26 ++++++------- man/parallel.plot.Rd | 2 - man/perpPt.Rd | 2 - man/plot.balance.plots.Rd | 2 - man/plot.triangle.matches.Rd | 4 +- man/plot.triangle.psa.Rd | 2 - man/print.balance.plots.Rd | 2 - man/print.triangle.plot.Rd | 6 +-- man/print.trimatch.summary.Rd | 4 +- man/segment1.Rd | 2 - man/segment2.Rd | 2 - man/star.Rd | 2 - man/summary.balance.plots.Rd | 2 - man/summary.triangle.matches.Rd | 4 +- man/summary.triangle.psa.Rd | 2 - man/summary.unmatched.Rd | 2 - man/trimatch.Rd | 14 +++---- man/trimatch.apply2.Rd | 10 ++--- man/trips.Rd | 2 - man/tutoring.Rd | 2 - man/unmatched.Rd | 2 - 39 files changed, 149 insertions(+), 131 deletions(-)
Title: Centre of Mass Assessment and Consolidation of Trees
Description: The centre of mass is a crucial data for arborists in order to
consolidate a tree using steel or dynamic cables. Given field-recorded data
on branchiness of a tree, the package: (i) computes and plots the centre of
mass of the tree itself, (ii) computes branches slenderness coefficient in
order to aid the arborist identify potentially dangerous branches, and
(iii) computes the force acting on a ground plinth and its best position
relating to the tree centre of mass, should the tree need to be stabilized
by a steel cable.
Author: Marco Bascietto <marco.bascietto@entecra.it>
Maintainer: Marco Bascietto <marco.bascietto@entecra.it>
Diff between treecm versions 1.2.1 dated 2014-05-22 and 1.2.2 dated 2015-12-15
DESCRIPTION | 17 +++--- MD5 | 104 ++++++++++++++++++++--------------------- NAMESPACE | 12 ++++ R/CM.R | 4 + R/SC.R | 5 + R/moment.R | 2 R/stabilization.R | 4 - R/treecm.R | 6 +- R/vectors.R | 4 + build/vignette.rds |binary inst/doc/treecm.R | 2 inst/doc/treecm.Rnw | 44 ++++++++++------- inst/doc/treecm.pdf |binary man/Dst.Rd | 4 + man/allometryABDC.Rd | 21 ++++---- man/allometryAsca2011.Rd | 17 +++--- man/allometryCutini2009.Rd | 19 +++---- man/allometryPorte2002.Rd | 17 +++--- man/anchorRange.Rd | 11 ++-- man/branchSR.Rd | 7 +- man/buildMomentObject.Rd | 7 +- man/buildTreeMomentObject.Rd | 7 +- man/calcMoment.Rd | 7 +- man/centreOfMass.Rd | 3 - man/centreOfMassAngle.Rd | 14 ++--- man/centreOfMassModulus.Rd | 11 ++-- man/getCoordinatesAndMoment.Rd | 19 +++---- man/getMoment.Rd | 7 +- man/getPlinthForce.Rd | 11 ++-- man/importFieldData.Rd | 5 + man/logBiomass.Rd | 21 ++++---- man/logPathSelection.Rd | 11 ++-- man/plot.CM.Rd | 3 - man/plot.SR.Rd | 7 +- man/plot.vector.Rd | 3 - man/plotPolarSegment.Rd | 3 - man/powerEquation.Rd | 17 +++--- man/print.CM.Rd | 3 - man/pureQuadraticEquation.Rd | 15 +++-- man/setBranchesCM.Rd | 3 - man/stonePine1FieldData.Rd | 7 +- man/stonePine1TreeData.Rd | 7 +- man/stonePine2FieldData.Rd | 7 +- man/summary.CM.Rd | 3 - man/toCartesianXY.Rd | 9 +-- man/toCartesianXYZ.Rd | 11 ++-- man/toPolar.Rd | 3 - man/treeBiomass.Rd | 15 +++-- man/treeSR.Rd | 9 +-- man/treeTotalBiomass.Rd | 15 +++-- man/treeVectors.Rd | 3 - man/treecm-package.Rd | 9 +-- vignettes/treecm.Rnw | 44 ++++++++++------- 53 files changed, 352 insertions(+), 267 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-3 dated 2015-11-23 and 1.3-0 dated 2015-12-15
DESCRIPTION | 8 +- MD5 | 100 ++++++++++++------------- R/jomo.MCMCchain.R | 6 - R/jomo.R | 6 - R/jomo1.MCMCchain.R | 42 +++++----- R/jomo1.R | 42 +++++----- R/jomo1cat.MCMCchain.R | 55 +++++++------ R/jomo1cat.R | 71 +++++++++-------- R/jomo1con.MCMCchain.R | 22 ++--- R/jomo1con.R | 36 ++++----- R/jomo1mix.MCMCchain.R | 71 +++++++++-------- R/jomo1mix.R | 89 +++++++++++----------- R/jomo1ran.MCMCchain.R | 162 ++++++++++++++++++++--------------------- R/jomo1ran.R | 162 ++++++++++++++++++++--------------------- R/jomo1rancat.MCMCchain.R | 76 ++++++++++--------- R/jomo1rancat.R | 104 +++++++++++++------------- R/jomo1rancathr.MCMCchain.R | 78 ++++++++++--------- R/jomo1rancathr.R | 108 ++++++++++++++------------- R/jomo1rancon.MCMCchain.R | 45 ++++++----- R/jomo1rancon.R | 71 +++++++++-------- R/jomo1ranconhr.MCMCchain.R | 47 ++++++----- R/jomo1ranconhr.R | 75 +++++++++--------- R/jomo1ranmix.MCMCchain.R | 95 ++++++++++++------------ R/jomo1ranmix.R | 125 ++++++++++++++++--------------- R/jomo1ranmixhr.MCMCchain.R | 97 +++++++++++++----------- R/jomo1ranmixhr.R | 129 +++++++++++++++++--------------- man/jomo-package.Rd | 4 - man/jomo.MCMCchain.Rd | 21 ++--- man/jomo.Rd | 18 ++-- man/jomo1.MCMCchain.Rd | 8 +- man/jomo1.Rd | 8 +- man/jomo1cat.MCMCchain.Rd | 29 +++---- man/jomo1cat.Rd | 32 ++++---- man/jomo1con.MCMCchain.Rd | 18 ++-- man/jomo1con.Rd | 22 +++-- man/jomo1mix.MCMCchain.Rd | 33 ++++---- man/jomo1mix.Rd | 36 ++++----- man/jomo1ran.MCMCchain.Rd | 18 ++-- man/jomo1ran.Rd | 18 ++-- man/jomo1rancat.MCMCchain.Rd | 49 ++++++------ man/jomo1rancat.Rd | 54 +++++++------ man/jomo1rancathr.MCMCchain.Rd | 54 +++++++------ man/jomo1rancathr.Rd | 58 +++++++------- man/jomo1rancon.MCMCchain.Rd | 35 ++++---- man/jomo1rancon.Rd | 37 +++++---- man/jomo1ranconhr.MCMCchain.Rd | 42 +++++----- man/jomo1ranconhr.Rd | 48 ++++++------ man/jomo1ranmix.MCMCchain.Rd | 53 +++++++------ man/jomo1ranmix.Rd | 54 +++++++------ man/jomo1ranmixhr.MCMCchain.Rd | 58 +++++++------- man/jomo1ranmixhr.Rd | 59 ++++++++------ 51 files changed, 1452 insertions(+), 1336 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.1.0.0 dated 2015-12-15 and 0.1.1.0 dated 2015-12-15
DESCRIPTION | 10 +- MD5 | 48 +++++++------- NAMESPACE | 44 ++++++------ R/RcppExports.R | 108 +++++++++++++++---------------- man/ACD-class.Rd | 22 +++--- man/HPC-class.Rd | 22 +++--- man/MCD-class.Rd | 22 +++--- man/acd_estimation.Rd | 72 ++++++++++----------- man/aids.Rd | 50 +++++++------- man/bootcurve.Rd | 58 ++++++++-------- man/cash-ACD-method.Rd | 36 +++++----- man/cash-HPC-method.Rd | 36 +++++----- man/cash-MCD-method.Rd | 36 +++++----- man/cattle.Rd | 58 ++++++++-------- man/getJMCM.Rd | 154 ++++++++++++++++++++++----------------------- man/hpc_estimation.Rd | 72 ++++++++++----------- man/jmcm.Rd | 86 ++++++++++++------------- man/jmcmControl.Rd | 44 ++++++------ man/jmcmMod-class.Rd | 54 +++++++-------- man/mcd_estimation.Rd | 72 ++++++++++----------- man/meanplot.Rd | 46 ++++++------- man/modular.Rd | 124 ++++++++++++++++++------------------ man/regressogram.Rd | 54 +++++++-------- man/show-jmcmMod-method.Rd | 34 ++++----- src/mcd.cpp | 84 ++++++++++++------------ 25 files changed, 723 insertions(+), 723 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.12 dated 2015-11-05 and 0.0.14 dated 2015-12-15
DESCRIPTION | 6 - MD5 | 25 +++--- inst/include/Basic_utils.h | 2 inst/include/Error_utils.h | 40 ++++++---- inst/include/Solve.h | 64 +++++++++++++---- inst/include/utils.h | 6 - src/Basic_utils.h | 2 src/Error_utils.h | 40 ++++++---- src/R_init.cc | 3 src/R_init.h | 3 src/Solve.h | 64 +++++++++++++---- src/solve.cc | 169 +++++++++++++++++++++++++-------------------- src/sqrt.cc |only src/utils.h | 6 - 14 files changed, 272 insertions(+), 158 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.3 dated 2015-11-05 and 3.1.4 dated 2015-12-15
DESCRIPTION | 6 MD5 | 90 +++++++------- NAMESPACE | 2 R/Methods-aux.R | 2 R/RC_GLOBALS.R | 17 ++ R/RCauto.R | 25 ---- R/RFfit.R | 4 R/RFgui.R | 1 R/RMmodels.R | 18 +- R/fitgauss.R | 17 +- R/getNset.R | 90 +++++++++++++- R/helmholz.R |only man/Bayesian.Rd | 2 man/GaussianFields.Rd | 81 ++++++++++++- man/RFgetModel.Rd |only man/RFgetModelInfo.Rd | 225 +++++++++++++++++++----------------- man/RFoptions.Rd | 112 +++++++++--------- man/RMplus.Rd | 2 man/RPcirculant.Rd | 2 man/RPcoin.Rd | 3 man/RPhyperplane.Rd | 7 - man/RPnugget.Rd | 2 man/RPsequential.Rd | 42 ++---- man/RPspecific.Rd | 8 - man/RPspectral.Rd | 6 man/RPtbm.Rd | 3 src/AutoRandomFields.cc | 12 + src/AutoRandomFields.h | 20 --- src/KeyInfo.cc | 16 +- src/MLE.cc | 19 +-- src/Operator.h | 1 src/RF.h | 46 +++++-- src/Userinterfaces.h | 24 +-- src/circulant.cc | 32 ++--- src/direct.cc | 298 ++++-------------------------------------------- src/extremes.cc | 2 src/gauss.cc | 54 +++++--- src/gausslikeli.cc | 9 - src/getNset.cc | 8 - src/initNerror.cc | 28 +++- src/operator.cc | 5 src/plusmalS.cc | 2 src/rf_interfaces.cc | 12 + src/sequential.cc | 11 + src/userinterfaces.cc | 165 +++++++++++++------------- src/xport.cc | 7 + src/xport.h | 6 47 files changed, 763 insertions(+), 781 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated from Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between simPH versions 1.3.4 dated 2015-09-21 and 1.3.5 dated 2015-12-15
DESCRIPTION | 9 ++-- MD5 | 60 ++++++++++++++--------------- NAMESPACE | 2 NEWS | 22 +++++++--- R/ggfitStrata.R | 90 +++++++++++++++++++++++--------------------- R/simGG.siminteract.R | 12 ++--- R/simGG.simlinear.R | 12 ++--- R/simGG.simpoly.R | 12 ++--- R/simGG.simspline.R | 10 ++-- R/simGG.simtvc.R | 10 ++-- README.md | 2 man/CarpenterFdaData.Rd | 8 +-- man/GolubEUPData.Rd | 8 +-- man/MinMaxLines.Rd | 3 - man/SurvExpand.Rd | 3 - man/as.data.frame.coxsim.Rd | 2 man/coxsimInteract.Rd | 3 - man/coxsimLinear.Rd | 3 - man/coxsimPoly.Rd | 3 - man/coxsimSpline.Rd | 3 - man/coxsimtvc.Rd | 3 - man/ggfitStrata.Rd | 29 ++++++++------ man/setXl.Rd | 2 man/simGG.Rd | 3 - man/simGG.siminteract.Rd | 15 +++---- man/simGG.simlinear.Rd | 16 ++++--- man/simGG.simpoly.Rd | 15 +++---- man/simGG.simspline.Rd | 13 +++--- man/simGG.simtvc.Rd | 13 +++--- man/simPH.Rd | 2 man/tvc.Rd | 3 - 31 files changed, 215 insertions(+), 176 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.12.2 dated 2015-06-26 and 0.13.0 dated 2015-12-15
DESCRIPTION | 31 MD5 | 125 NAMESPACE | 15 R/Rvcg-package.R | 5 R/normorient.r |only R/vcgClost.r | 5 R/vcgClostKD.r | 10 R/vcgIsosurface.r | 81 R/vcgKDtree.r | 7 R/vcgPlatonic.r |only R/vcgPlyWrite.r | 16 R/vcgSample.r | 2 R/vcgUpdateNormals.r | 4 inst/NEWS.Rd | 25 man/Rvcg-package.Rd | 6 man/dummyhead.Rd | 2 man/humface.Rd | 2 man/meshintegrity.Rd | 2 man/setRays.Rd | 2 man/vcgBary.Rd | 2 man/vcgBorder.Rd | 3 man/vcgClean.Rd | 2 man/vcgClost.Rd | 8 man/vcgClostKD.Rd | 14 man/vcgCurve.Rd | 3 man/vcgGetEdge.Rd | 2 man/vcgImport.Rd | 2 man/vcgIsolated.Rd | 5 man/vcgIsosurface.Rd | 8 man/vcgKDtree.Rd | 10 man/vcgMeshres.Rd | 2 man/vcgNonBorderEdge.Rd | 3 man/vcgPlatonic.Rd |only man/vcgPlyRead.Rd | 2 man/vcgPlyWrite.Rd | 9 man/vcgQEdecim.Rd | 8 man/vcgRaySearch.Rd | 3 man/vcgSample.Rd | 3 man/vcgSmooth.Rd | 4 man/vcgStlWrite.Rd | 2 man/vcgUniformRemesh.Rd | 2 man/vcgUpdateNormals.Rd | 2 man/vcgVFadj.Rd | 2 src/Makevars.in | 8 src/Makevars.win | 7 src/Rclost.cpp | 12 src/Rexport.cpp | 45 src/Rintersect.cpp | 46 src/Rkdtree.cpp | 40 src/Rplatonic.cpp |only src/Rsample.cpp | 4 src/Rsmooth.cpp | 2 src/RvcgIO.h | 113 src/RvcgKD.h | 74 src/checkListNames.cpp |only src/checkListNames.h |only src/vcglib/vcg/complex/algorithms/parametrization/tangent_field_operators.h | 562 +++ src/vcglib/vcg/complex/algorithms/parametrization/uv_utils.h | 8 src/vcglib/vcg/complex/algorithms/update/quality.h | 2 src/vcglib/vcg/math/base.h | 1 src/vcglib/vcg/simplex/face/pos.h | 32 src/vcglib/vcg/simplex/face/topology.h | 4 src/vcglib/vcg/space/index/kdtree/kdtree.h | 42 src/vcglib/wrap/gl/gl_mesh_attributes_feeder.h |only src/vcglib/wrap/gl/trimesh.h | 1709 +++++----- src/vcglib/wrap/igl/miq_parametrization.h | 10 src/vcglib/wrap/io_trimesh/import_stl.h | 5 67 files changed, 2023 insertions(+), 1144 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <stefan.schlager@uniklinik-freiburg.de>
Diff between Morpho versions 2.3.0 dated 2015-06-23 and 2.3.1 dated 2015-12-15
DESCRIPTION | 17 +- MD5 | 285 +++++++++++++++++++++-------------------- NAMESPACE | 14 +- R/CVA.r | 15 +- R/ComputeTransform.r | 13 + R/Morpho-package.R | 6 R/ProcGPA.r | 105 +++++++-------- R/angleTest.r |only R/applyTransform.r | 26 +++ R/asymPermu.r | 6 R/classify.r | 9 + R/cutSpace.r | 1 R/deformGrid2d.r | 2 R/meshDist.r | 33 +++- R/meshDistMatrix.r | 19 +- R/meshPlaneIntersect.r | 14 +- R/permudist.r | 2 R/place.patch.r | 14 +- R/pls2B.r | 16 +- R/points2plane.r | 37 +++++ R/qqmat.r | 2 R/relwarps.r | 146 ++++++++++----------- R/rotonto.r | 31 +++- R/typprob.r | 6 inst/NEWS.Rd | 29 ++++ inst/extdata/landmarks.pts | 4 man/CAC.Rd | 2 man/CVA.Rd | 32 +++- man/CreateL.Rd | 5 man/Morpho-deprecated.Rd | 2 man/Morpho-package.Rd | 6 man/NNshapeReg.Rd | 5 man/PCdist.Rd | 5 man/ProcGPA.Rd | 4 man/RegScore.Rd | 3 man/angle.calc.Rd | 4 man/angleTest.Rd |only man/anonymize.Rd | 5 man/applyTransform.Rd | 5 man/areaSphere.Rd |only man/areaSpherePart.Rd |only man/armaGinv.Rd | 2 man/arrMean3.Rd | 2 man/asymPermute.Rd | 8 - man/barycenter.Rd | 3 man/bindArr.Rd | 6 man/boneData.Rd | 2 man/cExtract.Rd | 2 man/cSize.Rd | 4 man/checkLM.Rd | 4 man/classify.Rd | 2 man/closemeshKD.Rd | 4 man/colors.Rd | 2 man/computeTransform.Rd | 5 man/covDist.Rd | 9 + man/covW.Rd | 2 man/createAtlas.Rd | 4 man/createMissingList.Rd | 2 man/cutMeshPlane.Rd | 2 man/cutSpace.Rd | 2 man/deformGrid2d.Rd | 5 man/deformGrid3d.Rd | 2 man/exVar.Rd | 3 man/find.outliers.Rd | 6 man/fixLMmirror.Rd | 2 man/fixLMtps.Rd | 3 man/getFaces.Rd | 2 man/getMeaningfulPCs.Rd | 2 man/getPCtol.Rd | 4 man/getPLSfromScores.Rd | 2 man/getPLSscores.Rd | 2 man/getTrafo4x4.Rd | 2 man/getTrafoRotaxis.Rd | 2 man/groupPCA.Rd | 5 man/histGroup.Rd | 7 - man/icpmat.Rd | 2 man/invertFaces.Rd | 3 man/kendalldist.Rd | 4 man/line2plane.Rd | 2 man/lineplot.Rd | 4 man/list2array.Rd | 2 man/mcNNindex.Rd | 4 man/mergeMeshes.Rd | 4 man/mesh2grey.Rd | 2 man/mesh2ply.Rd | 3 man/meshDist.Rd | 10 + man/meshPlaneIntersect.Rd | 6 man/meshcube.Rd | 4 man/meshres.Rd | 5 man/mirror.Rd | 2 man/mirror2plane.Rd |only man/name2factor.Rd | 6 man/nose.Rd | 2 man/pcAlign.Rd | 2 man/pcaplot3d.Rd | 3 man/permudist.Rd | 7 - man/permuvec.Rd | 4 man/placePatch.Rd | 3 man/plotAtlas.Rd | 3 man/plotNormals.Rd | 4 man/pls2B.Rd | 5 man/plsCoVar.Rd | 7 - man/ply2mesh.Rd | 3 man/points2plane.Rd | 2 man/predictPLSfromData.Rd | 2 man/predictPLSfromScores.Rd | 2 man/predictShape.lm.Rd | 5 man/proc.weight.Rd | 4 man/procAOVsym.Rd | 4 man/procSym.Rd | 5 man/projRead.Rd | 7 - man/qqmat.Rd | 6 man/quad2trimesh.Rd | 5 man/r2morphoj.Rd | 4 man/ray2mesh.Rd | 2 man/read.csv.folder.Rd | 2 man/read.lmdta.Rd | 2 man/read.mpp.Rd | 2 man/read.pts.Rd | 4 man/readLandmarks.csv.Rd | 2 man/readallTPS.Rd | 2 man/regdist.Rd | 4 man/relWarps.Rd | 22 ++- man/relaxLM.Rd | 7 - man/render.Rd | 8 - man/retroDeform3d.Rd | 2 man/retroDeformMesh.Rd | 2 man/rotaxis3d.Rd | 3 man/rotaxisMat.Rd | 2 man/rotmesh.onto.Rd | 4 man/rotonmat.Rd | 4 man/rotonto.Rd | 10 + man/scalemesh.Rd | 4 man/showPC.Rd | 4 man/slider3d.Rd | 3 man/solutionSpace.Rd | 2 man/symmetrize.Rd | 2 man/tangentPlane.Rd | 3 man/tps3d.Rd | 3 man/typprob.Rd | 5 man/updateNormals.Rd | 3 man/vecx.Rd | 5 man/vertex.Rd | 4 man/warpmovie3d.Rd | 5 man/write.pts.Rd | 4 tests/testthat/test-relWarps.r |only tests/testthat/testdata/rW.rds |only 147 files changed, 849 insertions(+), 480 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedians().
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.50.0 dated 2015-12-13 and 0.50.1 dated 2015-12-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 +++++++ build/vignette.rds |binary inst/doc/matrixStats-methods.html | 4 ++-- man/matrixStats-package.Rd | 2 +- src/validateIndices.c | 8 ++++++-- 7 files changed, 26 insertions(+), 15 deletions(-)
Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
<kimkspeer@gmail.com>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between likert versions 1.3.1 dated 2015-11-03 and 1.3.3 dated 2015-12-15
DESCRIPTION | 12 ++++++------ MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 18 +++++++++++++++--- NEWS | 11 +++++++++++ R/align.R | 30 ++++++++++++++---------------- R/likert-package.R | 12 ++++++++++-- R/plot.histogram.R | 4 ++-- R/plot.likert.bar.r | 2 +- R/plot.likert.r | 11 +++++++++++ R/shinyLikert.R | 1 - build/vignette.rds |binary demo/RecodeFactors.R | 4 ++-- demo/UnusedLevels.R | 12 ++++++++++++ demo/likert.R | 4 ++-- inst/doc/likert-xtable.R | 24 ++++++++++++------------ inst/doc/likert-xtable.Rnw | 24 ++++++++++++------------ inst/doc/likert-xtable.pdf |binary inst/shiny/server.R | 24 ++++++++++++------------ man/plot.likert.Rd | 5 ++++- vignettes/likert-xtable.Rnw | 24 ++++++++++++------------ 20 files changed, 157 insertions(+), 103 deletions(-)
Title: Plots (Slightly Extended) Bland-Altman Plots
Description: Bland-Altman Plots using either base graphics or ggplot2,
augmented with confidence intervals, with detailed return values and
a sunflowerplot option for data with ties.
Author: Bernhard Lehnert
Maintainer: Bernhard Lehnert <bernhard.lehnert@uni-greifswald.de>
Diff between BlandAltmanLeh versions 0.1.0 dated 2014-08-13 and 0.2.1 dated 2015-12-15
BlandAltmanLeh-0.1.0/BlandAltmanLeh/R/BlandAltmanLeh.R |only BlandAltmanLeh-0.2.1/BlandAltmanLeh/DESCRIPTION | 15 +- BlandAltmanLeh-0.2.1/BlandAltmanLeh/MD5 | 25 +-- BlandAltmanLeh-0.2.1/BlandAltmanLeh/NAMESPACE | 8 - BlandAltmanLeh-0.2.1/BlandAltmanLeh/R/bland.altman.R | 19 +- BlandAltmanLeh-0.2.1/BlandAltmanLeh/build/vignette.rds |binary BlandAltmanLeh-0.2.1/BlandAltmanLeh/inst/doc/Intro.R | 21 +- BlandAltmanLeh-0.2.1/BlandAltmanLeh/inst/doc/Intro.Rmd | 72 ++++++---- BlandAltmanLeh-0.2.1/BlandAltmanLeh/inst/doc/Intro.html | 71 +++++---- BlandAltmanLeh-0.2.1/BlandAltmanLeh/man/BlandAltmanLeh-package.Rd | 8 - BlandAltmanLeh-0.2.1/BlandAltmanLeh/man/bland.altman.PEFR.Rd | 16 -- BlandAltmanLeh-0.2.1/BlandAltmanLeh/man/bland.altman.plot.Rd | 39 +++-- BlandAltmanLeh-0.2.1/BlandAltmanLeh/man/bland.altman.stats.Rd | 29 ++-- BlandAltmanLeh-0.2.1/BlandAltmanLeh/vignettes/Intro.Rmd | 72 ++++++---- 14 files changed, 230 insertions(+), 165 deletions(-)
More information about BlandAltmanLeh at CRAN
Permanent link
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: Provides the bayesGARCH function which performs the
Bayesian estimation of the GARCH(1,1) model with Student's t innovations.
Author: David Ardia [aut, cre]
Maintainer: David Ardia <david.ardia@fsa.ulaval.ca>
Diff between bayesGARCH versions 2.0.1 dated 2014-01-07 and 2.0.2 dated 2015-12-15
bayesGARCH-2.0.1/bayesGARCH/build |only bayesGARCH-2.0.1/bayesGARCH/demo |only bayesGARCH-2.0.1/bayesGARCH/inst/doc |only bayesGARCH-2.0.1/bayesGARCH/vignettes |only bayesGARCH-2.0.2/bayesGARCH/DESCRIPTION | 18 +++++++------ bayesGARCH-2.0.2/bayesGARCH/MD5 | 27 +++++++------------- bayesGARCH-2.0.2/bayesGARCH/NAMESPACE | 5 +++ bayesGARCH-2.0.2/bayesGARCH/NEWS | 9 ++++++ bayesGARCH-2.0.2/bayesGARCH/R/sampler.R | 8 +++--- bayesGARCH-2.0.2/bayesGARCH/THANKS | 2 - bayesGARCH-2.0.2/bayesGARCH/inst/CITATION | 22 +--------------- bayesGARCH-2.0.2/bayesGARCH/inst/COPYRIGHTS | 2 - bayesGARCH-2.0.2/bayesGARCH/man/bayesGARCH.Rd | 34 ++++++++++++++------------ bayesGARCH-2.0.2/bayesGARCH/man/dem2gbp.Rd | 2 - bayesGARCH-2.0.2/bayesGARCH/man/formSmpl.Rd | 9 +++--- 15 files changed, 65 insertions(+), 73 deletions(-)
Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between simsalapar versions 1.0-5 dated 2015-01-24 and 1.0-6 dated 2015-12-14
DESCRIPTION | 19 +++---- MD5 | 21 ++++---- NAMESPACE | 4 + R/graphics.R | 135 +++++------------------------------------------------ R/grid-stuff.R | 2 R/subjob.R | 44 ++++++++++++++--- R/tables.R | 103 +--------------------------------------- demo/VaRsuperadd.R | 39 ++++++++------- demo/robcovMCD.R | 79 +++++++++++++++++++++---------- man/device.Rd | 15 +++-- man/mayplot.Rd | 16 ++---- tests/tst-wrongs.R |only 12 files changed, 173 insertions(+), 304 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via x509
certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA
for asymmetric (public key) encryption. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.6 dated 2015-11-18 and 0.8 dated 2015-12-14
openssl-0.6/openssl/src/apple.h |only openssl-0.8/openssl/DESCRIPTION | 28 +- openssl-0.8/openssl/MD5 | 112 +++++---- openssl-0.8/openssl/NAMESPACE | 7 openssl-0.8/openssl/NEWS | 11 openssl-0.8/openssl/R/bignum.R | 14 - openssl-0.8/openssl/R/cert.R | 16 - openssl-0.8/openssl/R/hash.R | 142 ++++++------ openssl-0.8/openssl/R/mykey.R | 29 ++ openssl-0.8/openssl/R/stream.R | 19 + openssl-0.8/openssl/R/write.R | 16 + openssl-0.8/openssl/build/vignette.rds |binary openssl-0.8/openssl/configure | 4 openssl-0.8/openssl/inst/doc/bignum.R |only openssl-0.8/openssl/inst/doc/bignum.Rmd |only openssl-0.8/openssl/inst/doc/bignum.html |only openssl-0.8/openssl/inst/doc/crypto_hashing.html | 8 openssl-0.8/openssl/inst/doc/intro.Rmd |only openssl-0.8/openssl/inst/doc/intro.html |only openssl-0.8/openssl/inst/doc/secure_rng.html | 18 - openssl-0.8/openssl/man/aes_cbc.Rd | 2 openssl-0.8/openssl/man/base64_encode.Rd | 2 openssl-0.8/openssl/man/bignum.Rd | 16 + openssl-0.8/openssl/man/certificates.Rd | 14 - openssl-0.8/openssl/man/encrypt_envelope.Rd | 2 openssl-0.8/openssl/man/hash.Rd | 56 ++-- openssl-0.8/openssl/man/keygen.Rd | 2 openssl-0.8/openssl/man/my_key.Rd | 25 +- openssl-0.8/openssl/man/openssl.Rd | 2 openssl-0.8/openssl/man/rand_bytes.Rd | 2 openssl-0.8/openssl/man/read_key.Rd | 2 openssl-0.8/openssl/man/rsa_encrypt.Rd | 2 openssl-0.8/openssl/man/signatures.Rd | 2 openssl-0.8/openssl/man/write_pem.Rd | 8 openssl-0.8/openssl/src/aes.c | 6 openssl-0.8/openssl/src/base64.c | 6 openssl-0.8/openssl/src/bignum.c | 6 openssl-0.8/openssl/src/cert.c | 25 +- openssl-0.8/openssl/src/envelope.c | 6 openssl-0.8/openssl/src/error.c | 1 openssl-0.8/openssl/src/hash.c | 29 +- openssl-0.8/openssl/src/keygen.c | 3 openssl-0.8/openssl/src/onload.c | 3 openssl-0.8/openssl/src/openssh.c | 3 openssl-0.8/openssl/src/rand.c | 6 openssl-0.8/openssl/src/read.c | 6 openssl-0.8/openssl/src/rsa.c | 6 openssl-0.8/openssl/src/signing.c | 7 openssl-0.8/openssl/src/ssl.c | 26 +- openssl-0.8/openssl/src/stream.c | 52 ++++ openssl-0.8/openssl/src/utils.h | 1 openssl-0.8/openssl/src/write.c | 27 +- openssl-0.8/openssl/tests/testthat/test_cert.R |only openssl-0.8/openssl/tests/testthat/test_hash_output_value.R | 59 ++-- openssl-0.8/openssl/tests/testthat/test_keys_dsa.R | 14 + openssl-0.8/openssl/tests/testthat/test_keys_ecdsa.R | 14 + openssl-0.8/openssl/tests/testthat/test_keys_ecdsa384.R | 14 + openssl-0.8/openssl/tests/testthat/test_keys_ecdsa521.R | 14 + openssl-0.8/openssl/tests/testthat/test_keys_rsa.R | 14 + openssl-0.8/openssl/tests/testthat/test_my_key.R |only openssl-0.8/openssl/tools/version.c |only openssl-0.8/openssl/vignettes/bignum.Rmd |only 62 files changed, 603 insertions(+), 306 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb], Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.5.2 dated 2015-11-19 and 0.6.0 dated 2015-12-14
DESCRIPTION | 17 ++++++++------- MD5 | 46 ++++++++++++++++++++++++++++------------- NAMESPACE | 5 ++++ R/arrows3d.R |only R/corner.R |only R/is_square.R |only R/matlib.R | 15 ++++++++++++- R/mpower.R | 15 +++++++++---- R/power_method.R |only R/proj.R | 2 - R/swp.R | 2 - R/vandermode.R |only R/vec.R |only R/vectors.R | 7 ++++-- R/vectors3d.R |only README.md | 25 ++++++++++++---------- inst/doc/gramreg.html | 40 +++++++++++++++++------------------ man/Proj.Rd | 4 ++- man/arrows3d.Rd |only man/cone3d.Rd |only man/corner.Rd |only man/is_square_matrix.Rd |only man/is_symmetric_matrix.Rd |only man/matlib.Rd | 13 +++++++++++ man/mpower.Rd | 7 ++++++ man/point_on_line.Rd |only man/power_method.Rd |only man/swp.Rd | 2 - man/vandermode.Rd |only man/vec.Rd |only man/vectors.Rd | 10 +++++++- man/vectors3d.Rd |only vignettes/plotEqn1snapshot.png |only 33 files changed, 145 insertions(+), 65 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-5 dated 2015-10-05 and 0.9-6 dated 2015-12-14
DESCRIPTION | 13 ++-- MD5 | 60 ++++++++++----------- NAMESPACE | 10 ++- R/LOF.R | 10 +-- R/RcppExports.R | 8 +- R/dbscan.R | 41 ++++++++++---- R/frNN.R | 37 ++++++++++++- R/kNN.R | 39 +++++++++++-- R/kNNdist.R | 12 ---- R/optics.R | 57 ++++++++++++++------ README.md | 47 +++++++++++----- inst/NEWS | 7 ++ inst/test_data |only inst/tests/test-dbscan.R | 7 ++ inst/tests/test-frNN.R | 50 ++--------------- inst/tests/test-kNN.R | 34 ++++-------- inst/tests/test-lof.R | 5 + inst/tests/test-optics.R | 41 ++++++++++---- man/dbscan.Rd | 34 ++++++------ man/frNN.Rd | 16 +++-- man/kNN.Rd | 34 ++++++++---- man/kNNdist.Rd | 15 +---- man/lof.Rd | 10 ++- man/optics.Rd | 67 ++++++++++++----------- src/R_dbscan.cpp | 73 ++++++++++++++++--------- src/R_frNN.cpp | 16 ++--- src/R_kNN.cpp | 1 src/R_optics.cpp | 133 ++++++++++++++++++++++++++++------------------- src/R_regionQuery.cpp | 4 - src/R_regionQuery.h | 2 src/RcppExports.cpp | 14 ++-- 31 files changed, 538 insertions(+), 359 deletions(-)
Title: Tools for Tensor Analysis and Decomposition
Description: A set of tools for creation, manipulation, and modeling
of tensors with arbitrary number of modes. A tensor in the context of data
analysis is a multidimensional array. rTensor does this by providing a S4
class 'Tensor' that wraps around the base 'array' class. rTensor
provides common tensor operations as methods, including matrix unfolding,
summing/averaging across modes, calculating the Frobenius norm, and taking
the inner product between two tensors. Familiar array operations are
overloaded, such as index subsetting via '[' and element-wise operations.
rTensor also implements various tensor decomposition, including CP, GLRAM,
MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements
transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some
auxiliary functions include the Khatri-Rao product, Kronecker product, and
the Hamadard product for a list of matrices.
Author: James Li and Jacob Bien and Martin Wells
Maintainer: James Li <jamesyili@gmail.com>
Diff between rTensor versions 1.2 dated 2014-11-11 and 1.3 dated 2015-12-14
rTensor-1.2/rTensor/man/hamadard_list.Rd |only rTensor-1.3/rTensor/DESCRIPTION | 23 ++--- rTensor-1.3/rTensor/MD5 | 102 +++++++++++----------- rTensor-1.3/rTensor/NAMESPACE | 12 ++ rTensor-1.3/rTensor/NEWS | 17 ++- rTensor-1.3/rTensor/R/rTensor_Class.R | 41 ++++++++- rTensor-1.3/rTensor/R/rTensor_Decomp.R | 69 ++++++++++----- rTensor-1.3/rTensor/R/rTensor_Misc.R | 116 +++++++++++++++++++++++--- rTensor-1.3/rTensor/data |only rTensor-1.3/rTensor/man/Ops-methods.Rd | 15 +-- rTensor-1.3/rTensor/man/Tensor-class.Rd | 7 - rTensor-1.3/rTensor/man/as.tensor.Rd | 3 rTensor-1.3/rTensor/man/cp.Rd | 13 +- rTensor-1.3/rTensor/man/cs_fold.Rd | 3 rTensor-1.3/rTensor/man/cs_unfold-methods.Rd | 3 rTensor-1.3/rTensor/man/dim-methods.Rd | 3 rTensor-1.3/rTensor/man/extract-methods.Rd | 5 - rTensor-1.3/rTensor/man/faces_tnsr.Rd |only rTensor-1.3/rTensor/man/fnorm-methods.Rd | 3 rTensor-1.3/rTensor/man/fold.Rd | 3 rTensor-1.3/rTensor/man/hadamard_list.Rd |only rTensor-1.3/rTensor/man/head-methods.Rd | 3 rTensor-1.3/rTensor/man/hosvd.Rd | 7 - rTensor-1.3/rTensor/man/initialize-methods.Rd | 3 rTensor-1.3/rTensor/man/innerProd-methods.Rd | 3 rTensor-1.3/rTensor/man/k_fold.Rd | 3 rTensor-1.3/rTensor/man/k_unfold-methods.Rd | 3 rTensor-1.3/rTensor/man/khatri_rao.Rd | 3 rTensor-1.3/rTensor/man/khatri_rao_list.Rd | 5 - rTensor-1.3/rTensor/man/kronecker_list.Rd | 7 - rTensor-1.3/rTensor/man/matvec-methods.Rd | 3 rTensor-1.3/rTensor/man/modeMean-methods.Rd | 3 rTensor-1.3/rTensor/man/modeSum-methods.Rd | 3 rTensor-1.3/rTensor/man/mpca.Rd | 7 - rTensor-1.3/rTensor/man/plot_orl.Rd |only rTensor-1.3/rTensor/man/print-methods.Rd | 3 rTensor-1.3/rTensor/man/pvd.Rd | 7 - rTensor-1.3/rTensor/man/rTensor-package.Rd | 2 rTensor-1.3/rTensor/man/rand_tensor.Rd | 3 rTensor-1.3/rTensor/man/rs_fold.Rd | 3 rTensor-1.3/rTensor/man/rs_unfold-methods.Rd | 3 rTensor-1.3/rTensor/man/show-methods.Rd | 3 rTensor-1.3/rTensor/man/t-methods.Rd | 3 rTensor-1.3/rTensor/man/t_mult.Rd | 3 rTensor-1.3/rTensor/man/t_svd.Rd | 3 rTensor-1.3/rTensor/man/t_svd_reconstruct.Rd | 3 rTensor-1.3/rTensor/man/tail-methods.Rd | 3 rTensor-1.3/rTensor/man/tperm-methods.Rd | 3 rTensor-1.3/rTensor/man/ttl.Rd | 5 - rTensor-1.3/rTensor/man/ttm.Rd | 3 rTensor-1.3/rTensor/man/tucker.Rd | 9 +- rTensor-1.3/rTensor/man/unfold-methods.Rd | 3 rTensor-1.3/rTensor/man/unmatvec.Rd | 3 rTensor-1.3/rTensor/man/vec-methods.Rd | 3 54 files changed, 385 insertions(+), 174 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.5 dated 2015-11-22 and 1.8.0 dated 2015-12-14
DESCRIPTION | 9 +++--- MD5 | 21 ++++++++++----- R/build.dist.struct.R | 30 +++++++++++---------- R/count.pairings.R |only R/rcbalance-internal.R | 65 +++++++++++++++++++++++++---------------------- R/rcbalance.R | 32 ++++++++++++++++------- man/build.dist.struct.Rd | 5 ++- man/count.pairings.Rd |only man/rcbalance.Rd | 9 +++++- tests |only 10 files changed, 105 insertions(+), 66 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data.
Author: Yves Croissant [aut, cre],
Giovanni Millo [aut],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb],
Kevin Tappe [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between plm versions 1.4-0 dated 2013-12-28 and 1.5-12 dated 2015-12-14
plm-1.4-0/plm/R/has.intercept.R |only plm-1.4-0/plm/R/pmerge.R |only plm-1.4-0/plm/R/pvcovHC.R |only plm-1.4-0/plm/R/vcovBK.R |only plm-1.4-0/plm/R/vcovSCC.R |only plm-1.4-0/plm/man/pserie.Rd |only plm-1.5-12/plm/DESCRIPTION | 32 plm-1.5-12/plm/MD5 | 180 +- plm-1.5-12/plm/NAMESPACE | 337 ++-- plm-1.5-12/plm/NEWS | 978 +++++++------ plm-1.5-12/plm/R/attributes.R | 18 plm-1.5-12/plm/R/divers.R | 47 plm-1.5-12/plm/R/ercomp.R | 589 +++---- plm-1.5-12/plm/R/fixef.R | 37 plm-1.5-12/plm/R/pFormula.R | 28 plm-1.5-12/plm/R/pcce.R | 3 plm-1.5-12/plm/R/pcdtest.R | 9 plm-1.5-12/plm/R/pfunctions.R | 1179 ++++++++------- plm-1.5-12/plm/R/pggls.R | 8 plm-1.5-12/plm/R/pgmm.R | 1 plm-1.5-12/plm/R/pht.R | 4 plm-1.5-12/plm/R/piest.R |only plm-1.5-12/plm/R/plm.R | 468 ++---- plm-1.5-12/plm/R/plm.list.R | 2 plm-1.5-12/plm/R/plm.methods.R | 562 +++---- plm-1.5-12/plm/R/pmg.R | 3 plm-1.5-12/plm/R/pserial.R | 1349 ++++++++---------- plm-1.5-12/plm/R/ptest.R | 794 +++++----- plm-1.5-12/plm/R/purtest.R | 1043 ++++++------- plm-1.5-12/plm/R/vcovG.R |only plm-1.5-12/plm/build/vignette.rds |binary plm-1.5-12/plm/data/Cigar.rda |binary plm-1.5-12/plm/data/Crime.rda |binary plm-1.5-12/plm/data/EmplUK.rda |binary plm-1.5-12/plm/data/Gasoline.rda |binary plm-1.5-12/plm/data/Grunfeld.rda |binary plm-1.5-12/plm/data/Hedonic.rda |binary plm-1.5-12/plm/data/LaborSupply.rda |binary plm-1.5-12/plm/data/Males.rda |binary plm-1.5-12/plm/data/Parity.rda |only plm-1.5-12/plm/data/Produc.rda |binary plm-1.5-12/plm/data/RiceFarms.rda |only plm-1.5-12/plm/data/Snmesp.rda |binary plm-1.5-12/plm/data/SumHes.rda |binary plm-1.5-12/plm/data/Wages.rda |binary plm-1.5-12/plm/inst/doc/plm.pdf |binary plm-1.5-12/plm/man/Cigar.Rd | 96 - plm-1.5-12/plm/man/Crime.Rd | 137 - plm-1.5-12/plm/man/Gasoline.Rd | 88 - plm-1.5-12/plm/man/Grunfeld.Rd | 122 + plm-1.5-12/plm/man/Hedonic.Rd | 112 - plm-1.5-12/plm/man/Males.Rd | 5 plm-1.5-12/plm/man/Parity.Rd |only plm-1.5-12/plm/man/Produc.Rd | 103 - plm-1.5-12/plm/man/RiceFarms.Rd |only plm-1.5-12/plm/man/Snmesp.Rd | 94 - plm-1.5-12/plm/man/SumHes.Rd | 86 - plm-1.5-12/plm/man/Wages.Rd | 106 - plm-1.5-12/plm/man/aneweytest.Rd |only plm-1.5-12/plm/man/cipstest.Rd | 6 plm-1.5-12/plm/man/ercomp.Rd | 29 plm-1.5-12/plm/man/fixef.plm.Rd | 129 - plm-1.5-12/plm/man/mtest.Rd | 90 - plm-1.5-12/plm/man/nobs.Rd |only plm-1.5-12/plm/man/pbgtest.Rd | 47 plm-1.5-12/plm/man/pbltest.Rd | 4 plm-1.5-12/plm/man/pbsytest.Rd | 4 plm-1.5-12/plm/man/pcce.Rd | 4 plm-1.5-12/plm/man/pcdtest.Rd | 1 plm-1.5-12/plm/man/pdata.frame.Rd | 172 +- plm-1.5-12/plm/man/pdim.Rd | 140 - plm-1.5-12/plm/man/pggls.Rd | 8 plm-1.5-12/plm/man/pgmm.Rd | 10 plm-1.5-12/plm/man/pht.Rd | 14 plm-1.5-12/plm/man/phtest.Rd | 126 + plm-1.5-12/plm/man/piest.Rd |only plm-1.5-12/plm/man/plm.Rd | 85 - plm-1.5-12/plm/man/plmtest.Rd | 24 plm-1.5-12/plm/man/pmg.Rd | 10 plm-1.5-12/plm/man/pooltest.Rd | 4 plm-1.5-12/plm/man/pseries.Rd |only plm-1.5-12/plm/man/purtest.Rd | 158 +- plm-1.5-12/plm/man/pvar.Rd | 4 plm-1.5-12/plm/man/pvcm.Rd | 4 plm-1.5-12/plm/man/pwartest.Rd | 6 plm-1.5-12/plm/man/pwfdtest.Rd | 15 plm-1.5-12/plm/man/pwtest.Rd | 15 plm-1.5-12/plm/man/r.squared.Rd | 55 plm-1.5-12/plm/man/sargan.Rd | 4 plm-1.5-12/plm/man/vcovBK.Rd | 184 +- plm-1.5-12/plm/man/vcovDC.Rd |only plm-1.5-12/plm/man/vcovG.Rd |only plm-1.5-12/plm/man/vcovHC.Rd | 284 +-- plm-1.5-12/plm/man/vcovNW.Rd |only plm-1.5-12/plm/man/vcovSCC.Rd | 154 +- plm-1.5-12/plm/tests/testErrors.Rout.save | 20 plm-1.5-12/plm/tests/testEvaluation.Rout.save | 24 plm-1.5-12/plm/tests/test_Chow.R |only plm-1.5-12/plm/tests/test_Estimators.R |only plm-1.5-12/plm/tests/test_phtest_Hausman_regression.R |only plm-1.5-12/plm/tests/test_plm_na.action.R |only plm-1.5-12/plm/tests/test_preserve_rownames.R |only plm-1.5-12/plm/tests/test_pwfdtest_pwartest.R |only plm-1.5-12/plm/tests/testpbgtest.R |only 104 files changed, 5440 insertions(+), 5014 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.0.0 dated 2015-12-10 and 2.0.1 dated 2015-12-14
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- build/vignette.rds |binary 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.2 dated 2015-11-10 and 1.3.1 dated 2015-12-14
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++----------- NEWS |only R/bm_stats.r | 4 ++-- R/bm_subsetting.r | 16 ++++++++++++++-- build/vignette.rds |binary data/AGT.rda |binary data/LCT.rda |binary data/TTN.rda |binary inst/doc/gaston.pdf |binary src/hwe_chi.cpp | 1 + src/m4_kinship.cpp | 6 +++--- src/m4_kinship_p.cpp | 8 ++++---- 13 files changed, 39 insertions(+), 25 deletions(-)
Title: Temporal Network Autocorrelation Models (TNAM)
Description: Temporal and cross-sectional network autocorrelation models (TNAM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between tnam versions 1.5.3 dated 2015-09-22 and 1.6 dated 2015-12-14
DESCRIPTION | 15 ++++++--------- MD5 | 4 ++-- R/checkDataTypes.R | 2 +- 3 files changed, 9 insertions(+), 12 deletions(-)
Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses by utilizing threshold
approaches under a marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between SimCorMultRes versions 1.3.1 dated 2015-09-08 and 1.4.0 dated 2015-12-14
DESCRIPTION | 11 +- MD5 | 42 ++++++----- NAMESPACE | 2 R/rbin.R |only R/rmult.bcl.R | 13 +-- R/rmult.clm.R | 88 ++++++++++------------- R/rmult.crm.R | 57 ++++++++------- R/rsmvnorm.R | 3 build/vignette.rds |binary inst/CITATION | 4 - inst/NEWS | 14 +++ inst/doc/SCMRvin.R | 59 +++++++++------ inst/doc/SCMRvin.Rnw | 144 +++++++++++++++++++++++--------------- inst/doc/SCMRvin.pdf |binary man/SimCorMultRes-package.Rd | 28 ++++--- man/rbin.Rd |only man/rmult.bcl.Rd | 66 +++++++---------- man/rmult.clm.Rd | 70 ++++++++---------- man/rmult.crm.Rd | 43 +++++++---- man/rnorta.Rd | 23 +++--- man/rsmvnorm.Rd | 4 - vignettes/SCMRvin-concordance.tex |only vignettes/SCMRvin.Rnw | 144 +++++++++++++++++++++++--------------- vignettes/SCMRvin.tex |only 24 files changed, 462 insertions(+), 353 deletions(-)
Title: Circos 2D Track Plot
Description: A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
Author: Hongen Zhang
Maintainer: Hongen Zhang <hzhang@mail.nih.gov>
Diff between RCircos versions 1.1.2 dated 2013-10-30 and 1.1.3 dated 2015-12-14
DESCRIPTION | 10 MD5 | 79 NAMESPACE | 4 R/RCircos.R | 5591 +++++++++++------------- build/vignette.rds |binary data/RCircos.Gene.Label.Data.RData |binary data/RCircos.Heatmap.Data.RData |binary data/RCircos.Histogram.Data.RData |binary data/RCircos.Line.Data.RData |binary data/RCircos.Link.Data.RData |binary data/RCircos.Mouse.Expr.Data.RData |binary data/RCircos.Rat.Expr.Data.RData |binary data/RCircos.Ribbon.Data.RData |binary data/RCircos.Scatter.Data.RData |binary data/RCircos.Tile.Data.RData |binary data/UCSC.Baylor.3.4.Rat.cytoBandIdeogram.RData |binary data/UCSC.HG19.Human.CytoBandIdeogram.RData |binary data/UCSC.Mouse.GRCm38.CytoBandIdeogram.RData |binary demo/00Index | 23 demo/RCircos.Demo.Human.R | 316 - demo/RCircos.Demo.Mouse.And.Rat.R | 311 - demo/RCircos.Gene.Connector.Demo.R | 173 demo/RCircos.Heatmap.Demo.R | 127 demo/RCircos.Histogram.Demo.R | 125 demo/RCircos.Layout.Demo.R | 167 demo/RCircos.Line.Plot.Demo.R | 132 demo/RCircos.Link.Plot.Demo.R | 141 demo/RCircos.Ribbon.Plot.Demo.R | 104 demo/RCircos.Scatter.Plot.Demo.R | 133 demo/RCircos.Tick.Demo.R |only demo/RCircos.Tile.Plot.Demo.R | 132 inst/CITATION | 4 inst/doc/RCircos-manual.pdf |binary inst/doc/Using_RCircos.R | 34 inst/doc/Using_RCircos.Rnw | 5 inst/doc/Using_RCircos.pdf |binary man/RCircos-package.Rd | 4 man/RCircos.Add.Ideogram.Tick.Rd |only man/RCircos.Get.Heatmap.ColorScales.Rd | 2 man/RCircos.Reset.Plot.Positions.Rd |only man/RCircos.Track.Outline.Rd | 17 vignettes/Using_RCircos.Rnw | 5 42 files changed, 3547 insertions(+), 4092 deletions(-)
Title: MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of bioassay data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine
Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon-
Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>
Diff between morse versions 2.0.0 dated 2015-09-01 and 2.1.0 dated 2015-12-14
morse-2.0.0/morse/README.md |only morse-2.1.0/morse/DESCRIPTION | 19 +- morse-2.1.0/morse/MD5 | 119 +++++++------- morse-2.1.0/morse/NAMESPACE | 8 morse-2.1.0/morse/NEWS | 43 ++++- morse-2.1.0/morse/R/as.survData.R | 6 morse-2.1.0/morse/R/morse-internal.R | 13 - morse-2.1.0/morse/R/morse.R | 37 ++-- morse-2.1.0/morse/R/plot.reproData.R | 60 ++++--- morse-2.1.0/morse/R/plot.reproFitTT.R | 200 +++++++++-------------- morse-2.1.0/morse/R/plot.survData.R | 151 ++++++++--------- morse-2.1.0/morse/R/plot.survFitTT.R | 148 ++++++++--------- morse-2.1.0/morse/R/ppc.R |only morse-2.1.0/morse/R/ppc.reproFitTT.R |only morse-2.1.0/morse/R/ppc.survFitTT.R |only morse-2.1.0/morse/R/print.reproFitTT.R | 3 morse-2.1.0/morse/R/print.survFitTT.R | 3 morse-2.1.0/morse/R/reproData.R | 3 morse-2.1.0/morse/R/reproDataCheck.R | 1 morse-2.1.0/morse/R/reproFitTT.R | 184 ++++++++++----------- morse-2.1.0/morse/R/summary.reproData.R | 1 morse-2.1.0/morse/R/summary.reproFitTT.R | 57 +++--- morse-2.1.0/morse/R/summary.survData.R | 17 -- morse-2.1.0/morse/R/summary.survFitTT.R | 56 +++--- morse-2.1.0/morse/R/survData.R | 13 - morse-2.1.0/morse/R/survDataCheck.R | 16 - morse-2.1.0/morse/R/survFitTT.R | 70 ++------ morse-2.1.0/morse/build/vignette.rds |binary morse-2.1.0/morse/data/cadmium2.rda |binary morse-2.1.0/morse/inst/doc/modelling.Snw | 206 ++++++++++++------------ morse-2.1.0/morse/inst/doc/modelling.pdf |binary morse-2.1.0/morse/inst/doc/tutorial.R | 31 ++- morse-2.1.0/morse/inst/doc/tutorial.Rmd | 109 +++++++++--- morse-2.1.0/morse/inst/doc/tutorial.html | 229 +++++++++++++++------------ morse-2.1.0/morse/man/as.survData.Rd | 5 morse-2.1.0/morse/man/cadmium1.Rd | 2 morse-2.1.0/morse/man/cadmium2.Rd | 13 + morse-2.1.0/morse/man/chlordan.Rd | 2 morse-2.1.0/morse/man/copper.Rd | 2 morse-2.1.0/morse/man/morse-package.Rd | 8 morse-2.1.0/morse/man/plot.reproData.Rd | 9 - morse-2.1.0/morse/man/plot.reproFitTT.Rd | 4 morse-2.1.0/morse/man/plot.survData.Rd | 23 +- morse-2.1.0/morse/man/plot.survFitTT.Rd | 20 +- morse-2.1.0/morse/man/ppc.Rd |only morse-2.1.0/morse/man/ppc.reproFitTT.Rd |only morse-2.1.0/morse/man/ppc.survFitTT.Rd |only morse-2.1.0/morse/man/print.reproFitTT.Rd | 7 morse-2.1.0/morse/man/print.survFitTT.Rd | 7 morse-2.1.0/morse/man/reproData.Rd | 4 morse-2.1.0/morse/man/reproDataCheck.Rd | 4 morse-2.1.0/morse/man/reproFitTT.Rd | 16 - morse-2.1.0/morse/man/summary.reproData.Rd | 5 morse-2.1.0/morse/man/summary.reproFitTT.Rd | 5 morse-2.1.0/morse/man/summary.survData.Rd | 5 morse-2.1.0/morse/man/summary.survFitTT.Rd | 7 morse-2.1.0/morse/man/survData.Rd | 4 morse-2.1.0/morse/man/survDataCheck.Rd | 3 morse-2.1.0/morse/man/survFitTT.Rd | 15 - morse-2.1.0/morse/man/zinc.Rd | 2 morse-2.1.0/morse/tests/testthat/test-surv.R | 15 + morse-2.1.0/morse/vignettes/biblio.bib | 4 morse-2.1.0/morse/vignettes/modelling.Snw | 206 ++++++++++++------------ morse-2.1.0/morse/vignettes/tutorial.Rmd | 109 +++++++++--- 64 files changed, 1242 insertions(+), 1067 deletions(-)
Title: Simulation of Inter-Related Genomic Datasets
Description: Generates three inter-related genomic datasets : methylation, gene expression and protein expression.
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Rama Raghavan <rraghavan@kumc.edu>
Diff between InterSIM versions 1.0 dated 2015-08-13 and 2.0 dated 2015-12-14
DESCRIPTION | 8 - MD5 | 10 +- NAMESPACE | 2 R/InterSIM.R | 156 +++++++++++++++++++------------ man/InterSIM-package.Rd | 11 -- man/InterSIM.Rd | 238 +++++++++--------------------------------------- 6 files changed, 154 insertions(+), 271 deletions(-)
Title: Significance Analysis of Event-Related Potentials Data
Description: The functions provided in the package ERP are designed for the significance analysis of ERP data in a linear model framework. The possible procedures are either the collection of FDR or FWER controlling methods available in the generic function p.adjust, the same collection combined with a factor modeling of the time dependence among tests (see Sheu, Perthame, Lee and Causeur, 2016) and the Guthrie and Buchwald (1991) test.
Author: David Causeur (Agrocampus, Rennes, France) and Ching-Fan Sheu (National Cheng-Kung University, Tainan, Taiwan)
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>
Diff between ERP versions 1.0.1 dated 2014-04-04 and 1.1 dated 2015-12-14
DESCRIPTION | 14 ++++++------ MD5 | 18 ++++++++-------- NAMESPACE | 9 ++++++-- R/erpfatest.R | 59 +++++++++++++++++++++++++++++++++-------------------- man/ERP-package.Rd | 8 +++---- man/erpcz.Rd | 4 +-- man/erpfatest.Rd | 6 ++--- man/erptest.Rd | 2 - man/gbtest.Rd | 2 - man/simerp.Rd | 8 +++---- 10 files changed, 75 insertions(+), 55 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.0-4 dated 2015-06-11 and 3.0-5 dated 2015-12-14
DESCRIPTION | 20 + MD5 | 32 +- NAMESPACE | 11 NEWS | 14 + R/effectsmer.R | 13 - R/plot-methods.R | 611 +---------------------------------------------- R/utilities.R | 22 + data/Arrests.rda |binary data/BEPS.rda |binary data/Cowles.rda |binary data/Hartnagel.rda |binary data/Prestige.rda |binary data/TitanicSurvival.rda |binary data/WVS.rda |binary data/Wells.rda |binary man/effects-package.Rd | 8 man/summary.effect.Rd | 3 17 files changed, 97 insertions(+), 637 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.6.1 dated 2015-11-19 and 1.7.3 dated 2015-12-14
DESCRIPTION | 8 - MD5 | 128 +++++++++++++------------- NAMESPACE | 1 R/AllClasses.R | 59 +++++++---- R/add-variable.R | 90 ++++++++++++------ R/categories.R | 3 R/category.R | 3 R/copy.R | 8 + R/cube-result.R | 4 R/dataset-extract.R | 24 +--- R/dataset.R | 8 - R/dichotomize.R | 13 ++ R/expressions.R | 12 +- R/filters.R | 4 R/log.R | 54 +++++++++- R/misc.R | 32 ------ R/multiple-response.R | 2 R/new-dataset.R | 7 + R/shoji.R | 9 + R/show.R | 12 +- R/subvariables.R | 25 +++-- R/teams.R | 20 ---- R/tuple.R | 8 + R/variable-catalog.R | 11 -- R/variable-order.R | 2 R/variable-summary.R | 17 +++ R/variable-type.R | 2 R/variable-update.R | 37 ------- R/variable.R | 85 +++++------------ inst/doc/variables.R | 35 +++++-- inst/doc/variables.Rmd | 25 ++++- man/CrunchVariable.Rd | 4 man/Subvariables.Rd | 3 man/addVariables.Rd |only man/copyVariable.Rd | 2 man/dataset-update.Rd | 3 man/delete.Rd | 3 man/describe-category.Rd | 3 man/expressions.Rd | 5 - man/self.Rd | 5 - man/show-crunch.Rd | 3 man/toVariable.Rd | 5 - man/tuple-methods.Rd | 3 man/var-categories.Rd | 3 man/variable-to-R.Rd | 9 + tests/testthat/test-active-filter.R | 6 + tests/testthat/test-add-array.R | 2 tests/testthat/test-add-variable-definition.R | 59 +++++++++++ tests/testthat/test-add-variable.R | 26 ++--- tests/testthat/test-cube-nway.R |only tests/testthat/test-cube-with-array.R | 4 tests/testthat/test-cubes.R | 39 +++---- tests/testthat/test-dataset.R | 6 + tests/testthat/test-make-array.R | 41 +++++--- tests/testthat/test-variable-catalog.R | 4 tests/testthat/test-variable-delete.R | 18 +++ tests/testthat/test-variable-order.R | 12 ++ tests/testthat/test-variable-summary.R | 48 +++++++-- tests/testthat/test-variables.R | 21 ---- vignettes/analyze.RData |binary vignettes/array-variables.RData |binary vignettes/derive.RData |binary vignettes/getting-started.RData |binary vignettes/variable-order.RData |binary vignettes/variables.RData |binary vignettes/variables.Rmd | 25 ++++- 66 files changed, 650 insertions(+), 460 deletions(-)
Title: Computational Methods for Immune Cell-Type Subsets
Description: Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
Author: Yael Steuerman [aut, cre],
Irit Gat-Viks [aut]
Maintainer: Yael Steuerman <yaelsteu@mail.tau.ac.il>
Diff between ComICS versions 1.0.0 dated 2015-12-09 and 1.0.1 dated 2015-12-14
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/deconvolution.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Companion to Applied Regression
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 2.1-0 dated 2015-09-03 and 2.1-1 dated 2015-12-14
DESCRIPTION | 20 - MD5 | 134 +++---- NAMESPACE | 9 NEWS | 20 + R/Anova.R | 134 ++++++- R/Ellipse.R | 3 R/influencePlot.R | 3 R/qqPlot.R | 4 R/scatter3d.R | 880 ++++++++++++++++++++++++------------------------ R/spreadLevelPlot.R | 38 -- R/utility-functions.R | 30 + build/vignette.rds |binary data/AMSsurvey.rda |binary data/Adler.rda |binary data/Angell.rda |binary data/Anscombe.rda |binary data/Baumann.rda |binary data/Bfox.rda |binary data/Blackmore.rda |binary data/Burt.rda |binary data/CanPop.rda |binary data/Chile.rda |binary data/Chirot.rda |binary data/Cowles.rda |binary data/Davis.rda |binary data/DavisThin.rda |binary data/Depredations.rda |binary data/Duncan.rda |binary data/Ericksen.rda |binary data/Florida.rda |binary data/Freedman.rda |binary data/Friendly.rda |binary data/Ginzberg.rda |binary data/Greene.rda |binary data/Guyer.rda |binary data/Hartnagel.rda |binary data/Highway1.rda |binary data/KosteckiDillon.rda |binary data/Leinhardt.rda |binary data/LoBD.rda |binary data/Mandel.rda |binary data/Migration.rda |binary data/Moore.rda |binary data/Mroz.rda |binary data/OBrienKaiser.rda |binary data/Ornstein.rda |binary data/Pottery.rda |binary data/Prestige.rda |binary data/Quartet.rda |binary data/Robey.rda |binary data/SLID.rda |binary data/Sahlins.rda |binary data/Salaries.rda |binary data/Soils.rda |binary data/States.rda |binary data/Transact.rda |binary data/UN.rda |binary data/USPop.rda |binary data/Vocab.rda |binary data/WeightLoss.rda |binary data/Womenlf.rda |binary data/Wong.rda |binary data/Wool.rda |binary inst/doc/embedding.pdf |binary man/Anova.Rd | 20 - man/car-package.Rd | 4 man/scatter3d.Rd | 6 man/spreadLevelPlot.Rd | 12 68 files changed, 744 insertions(+), 573 deletions(-)
Title: Client for the Captricity API
Description: Get text from images of text using Captricity Optical Character
Recognition (OCR) API. Captricity allows you to get text from handwritten
forms --- think surveys --- and other structured paper documents. And it can
output data in form a delimited file keeping field information intact. For more
information, read https://shreddr.captricity.com/developer/overview/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between captr versions 0.1.2 dated 2015-10-31 and 0.1.3 dated 2015-12-14
DESCRIPTION | 10 +++++----- MD5 | 46 +++++++++++++++++++++++++--------------------- NEWS | 8 ++++++++ R/batch_price.R | 13 ++++++------- R/captr.R | 10 ++++++++++ R/create_batch.R | 6 +++--- R/get_all.R | 11 +++++------ R/get_instance_set.R | 11 +++++------ R/get_template_id.R | 9 ++++----- R/list_instance_sets.R | 11 +++++------ R/set_batch_template.R | 15 +++++++-------- R/set_token.R | 46 +++++++++++++++++++++++++++++++++------------- R/submit_batch.R | 13 ++++++------- R/test_readiness.R | 11 +++++------ R/track_progress.R | 13 ++++++------- R/upload_image.R | 14 +++++++------- README.md | 42 ++++++++++++++++++++++++------------------ inst/doc/using_captr.R | 2 +- inst/doc/using_captr.Rmd | 2 +- inst/doc/using_captr.html | 6 +++--- man/captr_CHECKAUTH.Rd |only man/set_token.Rd | 22 +++++++++++++--------- tests |only vignettes/using_captr.Rmd | 2 +- 24 files changed, 183 insertions(+), 140 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between btergm versions 1.5.9 dated 2015-09-24 and 1.6 dated 2015-12-14
btergm-1.5.9/btergm/R/gof.R |only btergm-1.5.9/btergm/man/gof.Rd |only btergm-1.5.9/btergm/man/plot.btergmgof.Rd |only btergm-1.6/btergm/DESCRIPTION | 23 +-- btergm-1.6/btergm/MD5 | 27 ++-- btergm-1.6/btergm/NAMESPACE | 64 ++++++++++ btergm-1.6/btergm/R/btergm.R | 11 + btergm-1.6/btergm/R/gofmethods.R |only btergm-1.6/btergm/R/gofplot.R |only btergm-1.6/btergm/R/gofstatistics.R |only btergm-1.6/btergm/R/interpretation.R | 3 btergm-1.6/btergm/R/mtergm.R | 182 +++++++++++++++++++++++++----- btergm-1.6/btergm/man/btergm-class.Rd | 36 ++++- btergm-1.6/btergm/man/btergm.Rd | 4 btergm-1.6/btergm/man/getformula.Rd | 3 btergm-1.6/btergm/man/gofmethods.Rd |only btergm-1.6/btergm/man/gofplot.Rd |only btergm-1.6/btergm/man/gofstatistics.Rd |only btergm-1.6/btergm/man/interpret.Rd | 9 + 19 files changed, 297 insertions(+), 65 deletions(-)
Title: Model-Based Estimation of Confounder-Adjusted Attributable
Fractions
Description: Estimates the attributable fraction in different sampling designs adjusted for measured confounders using logistic regression (cross-sectional and case-control designs), conditional logistic regression (matched case-control design) and Cox proportional hazard regression (cohort design with time-to-event outcome). The variance of the estimator is obtained by combining the delta method with the the sandwich formula.
Author: Elisabeth Dahlqwist and Arvid Sjolander
Maintainer: Elisabeth Dahlqwist <elisabeth.dahlqwist@ki.se>
Diff between AF versions 0.1 dated 2015-08-26 and 0.1.1 dated 2015-12-14
AF-0.1.1/AF/DESCRIPTION | 11 ++++++----- AF-0.1.1/AF/MD5 | 25 +++++++++++++++++-------- AF-0.1.1/AF/NAMESPACE | 21 +++++++++++++++++++-- AF-0.1.1/AF/R/AF20151130.R |only AF-0.1.1/AF/R/data-clslowbwt.R |only AF-0.1.1/AF/R/data-rott2.R |only AF-0.1.1/AF/R/data-singapore.R |only AF-0.1.1/AF/data |only AF-0.1.1/AF/man/AF.cc.Rd | 4 ++-- AF-0.1.1/AF/man/AF.ch.Rd | 8 ++++---- AF-0.1.1/AF/man/AF.cs.Rd | 10 +++++----- AF-0.1.1/AF/man/clslowbwt.Rd |only AF-0.1.1/AF/man/plot.AF.Rd | 4 ++-- AF-0.1.1/AF/man/rott2.Rd |only AF-0.1.1/AF/man/singapore.Rd |only AF-0.1.1/AF/man/summary.AF.Rd | 4 ++-- AF-0.1/AF/R/AF20150824.R |only 17 files changed, 57 insertions(+), 30 deletions(-)
Title: Standard Normal Homogeneity Test
Description: Implementation of robust and non-robust Standard Normal Homogeneity Test (SNHT) for changepoint detection. This test statistic is equal sided, as proposed in "Homogenization of Radiosonde Temperature Time Series Using Innovation Statistics" by Haimberger, L., 2007. However, the statistic contains an estimate of sigma^2 in the denominator instead of sigma, which seems to be a more appropriate value (based on the paper "Homogenization of Swedish temperature data. Part I: Homogeneity test for linear trends." by Alexandersson, H., and A. Moberg, 1997).
Author: Josh Browning [aut, cre],
Carina Schneider [aut]
Maintainer: Josh Browning <jbrownin@mines.edu>
Diff between snht versions 1.0.2 dated 2015-03-29 and 1.0.3 dated 2015-12-14
snht-1.0.2/snht/vignettes/figure |only snht-1.0.3/snht/DESCRIPTION | 21 - snht-1.0.3/snht/MD5 | 71 ++-- snht-1.0.3/snht/NAMESPACE | 23 - snht-1.0.3/snht/R/createCandidateMatrix.R | 80 ++-- snht-1.0.3/snht/R/getPairs.R | 44 +- snht-1.0.3/snht/R/getUniquePairs.R | 50 +-- snht-1.0.3/snht/R/pairwiseSNHT.R | 260 ++++++++-------- snht-1.0.3/snht/R/plotSNHT.R | 106 +++--- snht-1.0.3/snht/R/removeSeasonalPeriod.R | 62 +-- snht-1.0.3/snht/R/robustSNHT.R | 300 +++++++++--------- snht-1.0.3/snht/R/robustSNHTunequal.R | 208 ++++++------ snht-1.0.3/snht/R/snht-package.R |only snht-1.0.3/snht/R/snht.R | 257 ++++++++------- snht-1.0.3/snht/R/unconfoundCandidateMatrix.R | 241 +++++++------- snht-1.0.3/snht/build/vignette.rds |binary snht-1.0.3/snht/inst/doc/pairwiseSNHT.R |only snht-1.0.3/snht/inst/doc/pairwiseSNHT.Rnw |only snht-1.0.3/snht/inst/doc/pairwiseSNHT.pdf |only snht-1.0.3/snht/inst/doc/snht.R | 147 ++++----- snht-1.0.3/snht/inst/doc/snht.Rnw | 370 +++++++++++------------ snht-1.0.3/snht/inst/doc/snht.pdf |binary snht-1.0.3/snht/man/createCandidateMatrix.Rd | 74 ++-- snht-1.0.3/snht/man/getPairs.Rd | 48 +- snht-1.0.3/snht/man/getUniquePairs.Rd | 46 +- snht-1.0.3/snht/man/pairwiseSNHT.Rd | 158 ++++----- snht-1.0.3/snht/man/plotSNHT.Rd | 58 +-- snht-1.0.3/snht/man/removeSeasonalPeriod.Rd | 56 +-- snht-1.0.3/snht/man/robustSNHT.Rd | 160 ++++----- snht-1.0.3/snht/man/robustSNHTunequal.Rd | 142 ++++---- snht-1.0.3/snht/man/snht-package.Rd | 45 -- snht-1.0.3/snht/man/snht.Rd | 207 ++++++------ snht-1.0.3/snht/man/unconfoundCandidateMatrix.Rd | 89 ++--- snht-1.0.3/snht/vignettes/mybib.bib | 9 snht-1.0.3/snht/vignettes/pairwiseSNHT.Rnw |only snht-1.0.3/snht/vignettes/snht.Rnw | 370 +++++++++++------------ 36 files changed, 1870 insertions(+), 1832 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), as predictors in a linear regression, or as
dependent variable in a beta-binomial ANOVA. For simulation and bootstrap
purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>
Diff between RRreg versions 0.5.0 dated 2015-11-12 and 0.6.0 dated 2015-12-14
RRreg-0.5.0/RRreg/R/RRanova.R |only RRreg-0.5.0/RRreg/inst/models |only RRreg-0.6.0/RRreg/DESCRIPTION | 10 - RRreg-0.6.0/RRreg/MD5 | 57 ++++---- RRreg-0.6.0/RRreg/NAMESPACE | 2 RRreg-0.6.0/RRreg/NEWS | 6 RRreg-0.6.0/RRreg/R/RRcor.R | 2 RRreg-0.6.0/RRreg/R/RRlog.R | 18 +- RRreg-0.6.0/RRreg/R/RRreg-package.R | 8 - RRreg-0.6.0/RRreg/R/RRsimu.R | 211 ++++++++++++++++++++------------ RRreg-0.6.0/RRreg/R/RRuni.R | 89 ++++++------- RRreg-0.6.0/RRreg/R/RRuni.models.R | 6 RRreg-0.6.0/RRreg/inst/CITATION | 16 -- RRreg-0.6.0/RRreg/inst/doc/RRreg.Rmd | 14 +- RRreg-0.6.0/RRreg/inst/doc/RRreg.html | 109 +++++++--------- RRreg-0.6.0/RRreg/man/RRcor.Rd | 4 RRreg-0.6.0/RRreg/man/RRgen.Rd | 8 - RRreg-0.6.0/RRreg/man/RRlin.Rd | 6 RRreg-0.6.0/RRreg/man/RRlog.Rd | 2 RRreg-0.6.0/RRreg/man/RRmixed.Rd | 6 RRreg-0.6.0/RRreg/man/RRreg-package.Rd | 6 RRreg-0.6.0/RRreg/man/RRsimu.Rd | 6 RRreg-0.6.0/RRreg/man/RRuni.Rd | 45 +++--- RRreg-0.6.0/RRreg/man/getPW.Rd | 2 RRreg-0.6.0/RRreg/man/minarets.Rd | 4 RRreg-0.6.0/RRreg/man/plot.RRlog.Rd | 5 RRreg-0.6.0/RRreg/man/plot.powerplot.Rd | 2 RRreg-0.6.0/RRreg/man/powerplot.Rd | 2 RRreg-0.6.0/RRreg/man/predict.RRlog.Rd | 2 RRreg-0.6.0/RRreg/vignettes/RRreg.Rmd | 14 +- 30 files changed, 362 insertions(+), 300 deletions(-)
Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data collected in an experimental design for statistical
analysis (e.g., analysis of variance ;ANOVA) by taking the individual data
files and preparing one table that contains several possibilities for dependent
variables. Most suitable when measuring reaction-times and/or accuracy, or any
other variable in an interval or ratio scale. Functions included: file_merge(),
read_data() and prep(). The file_merge() function vertically merges individual
data files (in a long format) in which each line is a single trial within the
experiment to one single dataset. The read_data() function reads a file in a
txt or csv format that contains a single dataset in a long format table and
creates a data frame from it. The prep() function aggregates the single dataset
according to any combination of between and within grouping variables (i.e.,
between-subjects and within-subjects independent variables, respectively), and
returns a data frame with a number of dependent measures for further analysis
for each experimental cell according to the combination of provided grouping
variables. Dependent measures for each experimental cell include among others
means before and after rejecting all values according to a flexible standard
deviation criterion/s, number of rejected values according to the flexible
standard deviation criterion/s, proportions of rejected values according to
the flexible standard deviation criterion/s, number of values before rejection,
means after rejecting values according to procedures described in Van Selst &
Jolicoeur (1994) (suitable when measuring reaction-times), standard deviations,
medians, means according to any percentile (e.g., 0.05, 0.25, 0.75, 0.95) and
harmonic means. The data frame prep() returns can also be exported as a txt file
to be used for statistical analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre],
Roy Luria [aut],
Jim Grange [ctb],
Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>
Diff between prepdat versions 1.0.4 dated 2015-11-22 and 1.0.5 dated 2015-12-14
DESCRIPTION | 55 +++++++++++++--------------- MD5 | 30 +++++++-------- NAMESPACE | 2 - NEWS.md | 23 ++++++----- R/hybrid_recursive_mc.R | 2 - R/modified_recursive_mc.R | 2 - R/non_recursive_mc.R | 2 - R/prep.R | 83 ++++++++++++++++++++++++++++++++++--------- README.md | 2 - man/file_merge.Rd | 2 - man/hybrid_recursive_mc.Rd | 4 +- man/modified_recursive_mc.Rd | 4 +- man/non_recursive_mc.Rd | 4 +- man/prep.Rd | 11 +++-- man/read_data.Rd | 2 - man/stroopdata.Rd | 2 - 16 files changed, 141 insertions(+), 89 deletions(-)
Title: Tools for Communication with Lightning-Viz Server
Description: The purpose of this package is to enable usage of lightningviz server to be accessible from R. The
server itself can be found at http://lightning-viz.org/ and is required to work with this package. Package
by itself cannot and will not create any visualizations.
Author: Ermlab
Maintainer: Kolodziejski Kamil <kolodziejski.kamil@hotmail.com>
Diff between LightningR versions 1.0.1 dated 2015-08-26 and 1.0.2 dated 2015-12-14
DESCRIPTION | 6 +- MD5 | 6 +- R/lightning.R | 136 ++++++++++++++++++++++++++++++++++++++++++++++--------- man/Lightning.Rd | 6 +- 4 files changed, 126 insertions(+), 28 deletions(-)
Title: A Button-Based GUI for Financial and Economic Data Analysis
Description: A GUI designed to support the analysis of financial-economic time
series data.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@mail.shu.edu.tw>
Diff between iClick versions 1.0 dated 2015-12-09 and 1.1 dated 2015-12-14
DESCRIPTION | 13 +++++++------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 6 ++++-- R/iClick_GARCH.R | 5 +++-- R/iClick_VisOneReturns.R | 5 ++--- man/boxPlotX.Rd | 2 +- man/cumulatedPlotX.Rd | 2 +- man/drawdownPlotX.Rd | 2 +- man/drawupPlotX.Rd | 2 +- man/drawups.Rd | 2 +- man/iClick.ARIMA.Rd | 21 +++++++++++---------- man/iClick.GARCH.Rd | 29 ++++++++++++++++------------- man/iClick.VisOneReturns.Rd | 16 ++++++++++------ man/qqnormPlotX.Rd | 2 +- man/seriesPlotX.Rd | 2 +- 15 files changed, 74 insertions(+), 63 deletions(-)
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Description: The gap encodes the distance between clusters and improves
interpretation of cluster heatmaps. The gaps can be of the same
distance based on a height threshold to cut the dendrogram. Another
option is to vary the size of gaps based on the distance between
clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo@vda-lab.be>
Diff between gapmap versions 0.0.3 dated 2015-11-16 and 0.0.4 dated 2015-12-14
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.5 dated 2015-11-27 and 0.5.1 dated 2015-12-14
DESCRIPTION | 8 MD5 | 18 - NEWS | 11 + R/scatterD3.R | 2 README.md | 15 + inst/doc/introduction.R | 3 inst/doc/introduction.Rmd | 7 inst/doc/introduction.html | 49 ++--- inst/htmlwidgets/scatterD3.js | 409 +++++++++++++++++++++++------------------- vignettes/introduction.Rmd | 7 10 files changed, 300 insertions(+), 229 deletions(-)
Title: Random Generation of Contingency Tables
Description: Contains functions for random generation of R x C and 2 x 2 x K contingency tables. In addition to the generation of contingency tables over predetermined intraclass-correlated clusters, it is possible to generate contingency tables without intraclass correlations under product multinomial, multinomial, and Poisson sampling plans. It also consists of a function for generation of random data from a given discrete probability distribution function.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>
Diff between rTableICC versions 1.0.2 dated 2015-03-23 and 1.0.3 dated 2015-12-14
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 5 +++-- R/rTable.2x2xK.default.R | 2 +- R/rTable.RxC.default.R | 2 +- R/rTableICC.2x2xK.default.R | 2 +- R/rTableICC.RxC.default.R | 2 +- man/rTable.2x2xK.Rd | 6 +++--- man/rTable.RxC.Rd | 8 ++++---- man/rTableICC-package.Rd | 12 ++++++------ man/rTableICC.2x2xK.Rd | 8 ++++---- man/rTableICC.RxC.Rd | 8 ++++---- 12 files changed, 44 insertions(+), 43 deletions(-)
Title: Functions for Plotting HPO Terms
Description: Collection of functions for manipulating sets of HPO terms and
plotting them with a various options.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between hpoPlot versions 2.2 dated 2015-08-26 and 2.4 dated 2015-12-14
hpoPlot-2.2/hpoPlot/man/get.grey.borders.Rd |only hpoPlot-2.2/hpoPlot/man/get.hpo.terms.Rd |only hpoPlot-2.2/hpoPlot/man/get.no.borders.Rd |only hpoPlot-2.2/hpoPlot/man/get.standard.sizes.Rd |only hpoPlot-2.2/hpoPlot/man/get.white.nodes.Rd |only hpoPlot-2.4/hpoPlot/DESCRIPTION | 12 hpoPlot-2.4/hpoPlot/MD5 | 123 ++++------ hpoPlot-2.4/hpoPlot/NAMESPACE | 7 hpoPlot-2.4/hpoPlot/R/data.R | 92 +++---- hpoPlot-2.4/hpoPlot/R/graphs.R | 66 +---- hpoPlot-2.4/hpoPlot/R/sets.R | 10 hpoPlot-2.4/hpoPlot/build/vignette.rds |binary hpoPlot-2.4/hpoPlot/data/hpo.terms.RData |binary hpoPlot-2.4/hpoPlot/data/mpo.terms.RData |binary hpoPlot-2.4/hpoPlot/data/mpo.to.hpo.RData |binary hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.R | 2 hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.Rmd | 4 hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.html | 6 hpoPlot-2.4/hpoPlot/man/apply.term.filters.Rd | 4 hpoPlot-2.4/hpoPlot/man/calibrate.sizes.Rd | 2 hpoPlot-2.4/hpoPlot/man/clean.terms.Rd | 2 hpoPlot-2.4/hpoPlot/man/exclude.branch.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.ancestors.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.case.based.colours.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.case.based.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.case.term.matrix.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.code.node.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.descendants.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.frequency.based.colours.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.frequency.based.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.frequency.based.sizes.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.full.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.hpo.graph.Rd | 12 hpoPlot-2.4/hpoPlot/man/get.informative.node.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.mpo.to.hpo.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.node.friendly.long.names.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.ontology.Rd | 6 hpoPlot-2.4/hpoPlot/man/get.pop.frequency.based.colours.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.shortened.names.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.significance.based.sizes.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.simple.node.labels.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.term.adjacency.matrix.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.term.descendancy.matrix.Rd | 9 hpoPlot-2.4/hpoPlot/man/get.term.frequencies.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.term.info.content.Rd | 2 hpoPlot-2.4/hpoPlot/man/get.term.pseudo.adjacency.matrix.Rd | 2 hpoPlot-2.4/hpoPlot/man/hpo.plot.Rd | 16 - hpoPlot-2.4/hpoPlot/man/hpo.terms.Rd | 4 hpoPlot-2.4/hpoPlot/man/hpoPlot-package.Rd | 7 hpoPlot-2.4/hpoPlot/man/intersection.with.branches.Rd | 2 hpoPlot-2.4/hpoPlot/man/mpo.terms.Rd | 4 hpoPlot-2.4/hpoPlot/man/mpo.to.hpo.Rd | 4 hpoPlot-2.4/hpoPlot/man/n.most.frequent.terms.Rd | 6 hpoPlot-2.4/hpoPlot/man/p.values.for.occurrence.of.term.in.group.Rd | 2 hpoPlot-2.4/hpoPlot/man/prune.branch.Rd | 2 hpoPlot-2.4/hpoPlot/man/remove.links.Rd | 2 hpoPlot-2.4/hpoPlot/man/remove.non.pa.terms.Rd | 2 hpoPlot-2.4/hpoPlot/man/remove.terms.with.less.than.n.occurrences.Rd | 6 hpoPlot-2.4/hpoPlot/man/remove.uninformative.for.plot.Rd | 6 hpoPlot-2.4/hpoPlot/man/remove.uninformative.terms.Rd | 2 hpoPlot-2.4/hpoPlot/man/setDimNames.Rd | 2 hpoPlot-2.4/hpoPlot/man/simpleCap.Rd | 2 hpoPlot-2.4/hpoPlot/man/swap.out.alt.ids.Rd | 2 hpoPlot-2.4/hpoPlot/man/term.set.list.from.character.Rd | 2 hpoPlot-2.4/hpoPlot/vignettes/hpoPlot-guide.Rmd | 4 65 files changed, 225 insertions(+), 253 deletions(-)
Title: Modular Leaf Ordering Methods for Dendrogram Nodes
Description: An implementation of functions to optimize ordering of nodes in
a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can
be sorted based on the average distance of subtrees, or based on the smallest
distance value. These sorting methods improve readability and interpretability
of tree structure, especially for tasks such as comparison of different distance
measures or linkage types and identification of tight clusters and outliers. As
a result, it also introduces more meaningful reordering for a coupled heatmap
visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo@vda-lab.be>
Diff between dendsort versions 0.3.2 dated 2014-09-29 and 0.3.3 dated 2015-12-14
DESCRIPTION | 30 ++++++++++++++++-------------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 14 +++++++++++++- R/dendsort-package.R | 3 ++- R/dendsort.R | 14 ++++---------- R/sort_smallest.R | 3 --- build/vignette.rds |binary man/cal_length.Rd | 4 +++- man/cal_node_limit.Rd | 4 +++- man/cal_total_length.Rd | 4 +++- man/dendsort-package.Rd | 11 ++++++----- man/dendsort.Rd | 18 ++++++++++-------- man/sample_tcga.Rd | 3 ++- man/sort_average.Rd | 14 ++++++++------ man/sort_average_r.Rd | 14 ++++++++------ man/sort_smallest.Rd | 12 +++++++----- man/sort_smallest_r.Rd | 10 ++++++---- 17 files changed, 107 insertions(+), 83 deletions(-)
Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Managing financial time series objects.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@rmetrics.org>
Diff between timeSeries versions 3022.101.1 dated 2015-12-11 and 3022.101.2 dated 2015-12-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/methods-is.R | 18 ++++++++---------- 3 files changed, 14 insertions(+), 16 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.2 dated 2015-11-12 and 2.3 dated 2015-12-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++----- data |only man/AD.Rd |only man/ThresholdROC-package.Rd | 7 +++---- man/chemo.Rd |only man/diagnostic.Rd | 2 +- man/thres2.Rd | 12 ++++++------ man/thres3.Rd | 6 +++--- 9 files changed, 26 insertions(+), 23 deletions(-)
Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using
the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram,
Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart,
bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>
Diff between RcmdrPlugin.KMggplot2 versions 0.2-0 dated 2013-01-23 and 0.2-1 dated 2015-12-14
RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/package.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-box.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-contour.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-discretebar.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-dist.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-hist.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-km.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-line.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-pie.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-qq.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-scatter.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/R/plot-scattermat.R |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-box-windowBox.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-box.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-contour-windowContour.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-contour.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-discretebar-windowDiscretebar.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-discretebar.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistBeta.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistBinom.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistCauchy.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistChisq.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistExp.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistF.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistGamma.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistGeom.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistHyper.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistLnorm.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistLogis.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistNbinom.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistNorm.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistPois.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistT.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistUnif.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist-windowDistWeibull.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-dist.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-hist-windowHist.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-hist.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-km-windowKM.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-km.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-line-windowLine.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-line.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-pie-windowPie.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-pie.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-qq-windowQQ.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-qq.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-scatter-windowScatter.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-scatter.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-scattermat-windowScattermat.Rd |only RcmdrPlugin.KMggplot2-0.2-0/RcmdrPlugin.KMggplot2/man/plot-scattermat.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/DESCRIPTION | 41 - RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/MD5 | 253 +++--- RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/NAMESPACE | 69 + RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/NEWS | 15 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/aaa-package.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/data-aaa.R | 12 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/guiparts-aaa.R | 13 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/guiparts-textfields.R | 3 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/guiparts-toolbox.R | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/guiparts-variableboxes.R | 3 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-aaa.R | 139 +++ RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-factorise.R | 141 ++- RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gbox.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gcont.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gdiscbar.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gdist.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-ghist.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gkm.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gline.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gpie.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gqq.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gscat.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/plot-gscatmat.R |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/theme-natrisk.R | 4 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/theme-natrisk21.R | 5 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/theme-natriskbg.R | 5 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/theme-simple.R | 7 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/theme-wsj2.R | 10 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/R/util-ggsaveKmg2.R | 37 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.KMggplot2.mo |binary RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/inst/po/sl |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/data-dataContour.Rd | 11 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/data-dataKm.Rd | 11 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/data-dataLine.Rd | 11 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-checkboxes-front.Rd | 24 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-checkboxes.Rd | 38 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-gparts_base-back.Rd | 13 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-gparts_base.Rd | 29 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-radioboxes-front.Rd | 24 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-radioboxes.Rd | 37 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-textfield-front.Rd | 21 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-textfield.Rd | 34 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-textfields-front.Rd | 19 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-textfields.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-toolbox-front.Rd | 38 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-toolbox.Rd | 61 - RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-variableboxes-front.Rd | 19 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/guiparts-variableboxes.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/package-RcmdrPlugin.KMggplot2.Rd | 19 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-factorize-windowFactorize.Rd | 7 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-factorize.Rd | 106 +- RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gbox-windowBox.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gbox.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gcont-windowContour.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gcont.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdiscbar-windowDiscretebar.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdiscbar.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistBeta.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistBinom.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistCauchy.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistChisq.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistExp.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistF.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistGamma.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistGeom.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistHyper.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistLnorm.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistLogis.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistNbinom.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistNorm.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistPois.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistT.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistUnif.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist-windowDistWeibull.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gdist.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-ghist-windowHist.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-ghist.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gkm-windowKM.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gkm.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gline-windowLine.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gline.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gpie-windowPie.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gpie.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gqq-windowQQ.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gqq.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gscat-windowScatter.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gscat.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gscatmat-windowScattermat.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-gscatmat.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-checkError.Rd | 35 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-checkTheme.Rd | 34 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-checkVariable.Rd | 35 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-commandDoIt.Rd |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getCoord.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getFacet.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getGeom.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getGgplot.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getHelp.Rd | 34 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getMain.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getMessage.Rd | 33 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getOpts.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getParms.Rd | 33 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getPlot.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getScale.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getTheme.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getWindowTitle.Rd | 34 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getXlab.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getYlab.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-getZlab.Rd | 36 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-plotWindow.Rd | 28 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-registRmlist.Rd | 32 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-removeRmlist.Rd | 29 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-savePlot.Rd | 31 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-setBack.Rd | 28 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-setDataframe.Rd | 31 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base-setFront.Rd | 28 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/plot-plot_base.Rd | 140 ++- RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/theme-natrisk.Rd | 16 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/theme-natrisk21.Rd | 16 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/theme-natriskbg.Rd | 16 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/theme-simple.Rd | 12 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/theme-wsj2.Rd | 13 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/util-gettextKmg2.Rd | 11 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/util-ggsaveKmg2.Rd | 43 - RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/util-nonFactors.Rd | 9 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/util-nonFactorsP.Rd | 17 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2-ja.po | 390 +++++----- RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2-sl.po |only RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/po/R-RcmdrPlugin.KMggplot2.pot | 385 ++++----- 179 files changed, 1894 insertions(+), 1438 deletions(-)
More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link
Title: Utilities for Official Spanish Microdata
Description: The MicroDatosEs package provides utilities for reading and processing microdata from Spanish official statistics with R.
Author: Carlos J. Gil Bellosta [aut, cre],
Carlos Neira [ctb],
Diego Paniagua Sánchez [ctb],
José Luis Cañadas Reche [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between MicroDatosEs versions 0.6.3.1 dated 2014-08-11 and 0.7.1 dated 2015-12-14
MicroDatosEs-0.6.3.1/MicroDatosEs/inst/extdata/sampleCenso.txt |only MicroDatosEs-0.7.1/MicroDatosEs/DESCRIPTION | 14 MicroDatosEs-0.7.1/MicroDatosEs/MD5 | 38 + MicroDatosEs-0.7.1/MicroDatosEs/NAMESPACE | 7 MicroDatosEs-0.7.1/MicroDatosEs/R/ees2010.R | 2 MicroDatosEs-0.7.1/MicroDatosEs/R/epa2005.R | 2 MicroDatosEs-0.7.1/MicroDatosEs/R/epf.2011.gastos.R |only MicroDatosEs-0.7.1/MicroDatosEs/R/epf.2011.hogares.R |only MicroDatosEs-0.7.1/MicroDatosEs/R/epf.2011.miembros.R |only MicroDatosEs-0.7.1/MicroDatosEs/R/read.fwf.microdata.R | 4 MicroDatosEs-0.7.1/MicroDatosEs/inst/extdata/sampleCenso2010.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/extdata/sample_gastos_a2011.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/extdata/sample_hogares_a2011.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/extdata/sample_miembros_a2011.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/censo_2010_mdat1.txt | 240 +++++----- MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/censo_2010_mdat2.txt | 22 MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_gastos_mdat1.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_gastos_mdat2.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_gastos_mdat3.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_hogares_mdat1.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_hogares_mdat2.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_hogares_mdat3.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_miembros_mdat1.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_miembros_mdat2.txt |only MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/epf_2011_miembros_mdat3.txt |only MicroDatosEs-0.7.1/MicroDatosEs/man/censo2010.Rd | 4 MicroDatosEs-0.7.1/MicroDatosEs/man/ees2010.Rd | 2 MicroDatosEs-0.7.1/MicroDatosEs/man/epf.2011.gastos.Rd |only MicroDatosEs-0.7.1/MicroDatosEs/man/epf.2011.hogares.Rd |only MicroDatosEs-0.7.1/MicroDatosEs/man/epf.2011.miembros.Rd |only 30 files changed, 190 insertions(+), 145 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.3-0 dated 2015-11-14 and 1.3-1 dated 2015-12-14
DESCRIPTION | 12 MD5 | 48 +-- NAMESPACE | 9 R/AllClasses.R | 565 ++++++++++++++++++------------------- R/AllGenerics.R | 6 R/aggregate.R | 143 +++++---- R/associations.R | 3 R/is.maximal.R | 13 R/is.redundant.R |only R/is.significant.R |only R/itemMatrix.R | 17 - R/parameter.R | 92 +++--- R/transactions.R | 2 inst/CITATION | 28 + inst/NEWS | 8 inst/doc/arules.pdf |binary man/APappearance-class.Rd | 7 man/ASparameter-class.Rd | 3 man/affinity.Rd | 2 man/aggregate.Rd | 93 ++++-- man/apriori.Rd | 6 man/is.maximal.Rd | 19 - man/is.redundant.Rd |only man/is.significant.Rd |only man/random.transactions.Rd | 4 src/warm.c | 2 tests/testthat/test-transactions.R | 3 27 files changed, 630 insertions(+), 455 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with the 'qdap' package
that may be useful outside of the context of discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar amounts, email
addresses, hash tags, numbers, percentages, citations, person tags, phone
numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.5.1 dated 2015-10-11 and 0.6.0 dated 2015-12-13
DESCRIPTION | 24 +++--- MD5 | 144 +++++++++++++++++++-------------------- NAMESPACE | 49 +++++++++++++ NEWS | 10 ++ R/rm_abbreviation.R | 10 ++ R/rm_between.R | 27 ++++--- R/rm_bracket.R | 64 ++++++++++++----- R/rm_caps.R | 10 ++ R/rm_caps_phrase.R | 10 ++ R/rm_citation.R | 45 ++++++++---- R/rm_citation_tex.R | 10 ++ R/rm_city_state.R | 10 ++ R/rm_city_state_zip.R | 10 ++ R/rm_date.R | 16 ++-- R/rm_default.R | 6 + R/rm_dollar.R | 10 ++ R/rm_email.R | 12 ++- R/rm_emoticon.R | 10 ++ R/rm_endmark.R | 14 ++- R/rm_hash.R | 10 ++ R/rm_nchar_words.R | 14 ++- R/rm_non_ascii.R | 12 ++- R/rm_non_words.R | 11 +-- R/rm_number.R | 15 ++-- R/rm_percent.R | 10 ++ R/rm_phone.R | 10 ++ R/rm_postal_code.R | 10 ++ R/rm_repeated_characters.R | 10 ++ R/rm_repeated_phrases.R | 10 ++ R/rm_repeated_words.R | 10 ++ R/rm_tag.R | 12 ++- R/rm_time.R | 33 +++++---- R/rm_title_name.R | 10 ++ R/rm_url.R | 20 ++++- R/rm_white.R | 85 ++++++++++++++++++++--- R/rm_zip.R | 18 +++- README.md | 98 +++++++++++++++++++++++--- data/regex_cheat.rda |binary data/regex_supplement.rda |binary data/regex_usa.rda |binary inst/CITATION | 4 - man/rm_abbreviation.Rd | 76 +++++++++++++++----- man/rm_between.Rd | 90 ++++++++++++++++++------ man/rm_bracket.Rd | 124 +++++++++++++++++++++++++-------- man/rm_caps.Rd | 75 +++++++++++++++----- man/rm_caps_phrase.Rd | 76 +++++++++++++++----- man/rm_citation.Rd | 107 +++++++++++++++++++++-------- man/rm_citation_tex.Rd | 75 +++++++++++++++----- man/rm_city_state.Rd | 76 +++++++++++++++----- man/rm_city_state_zip.Rd | 75 +++++++++++++++----- man/rm_date.Rd | 80 ++++++++++++++++----- man/rm_default.Rd | 72 +++++++++++++++---- man/rm_dollar.Rd | 74 +++++++++++++++----- man/rm_email.Rd | 76 +++++++++++++++----- man/rm_emoticon.Rd | 74 +++++++++++++++----- man/rm_endmark.Rd | 78 ++++++++++++++++----- man/rm_hash.Rd | 74 +++++++++++++++----- man/rm_nchar_words.Rd | 78 ++++++++++++++++----- man/rm_non_ascii.Rd | 76 +++++++++++++++----- man/rm_non_words.Rd | 77 +++++++++++++++------ man/rm_number.Rd | 76 +++++++++++++++----- man/rm_percent.Rd | 74 +++++++++++++++----- man/rm_phone.Rd | 74 +++++++++++++++----- man/rm_postal_code.Rd | 74 +++++++++++++++----- man/rm_repeated_characters.Rd | 76 +++++++++++++++----- man/rm_repeated_phrases.Rd | 76 +++++++++++++++----- man/rm_repeated_words.Rd | 76 +++++++++++++++----- man/rm_tag.Rd | 78 ++++++++++++++++----- man/rm_time.Rd | 154 +++++++++++++++++++++++++++++++----------- man/rm_title_name.Rd | 79 ++++++++++++++++----- man/rm_url.Rd | 87 ++++++++++++++++++----- man/rm_white.Rd | 108 +++++++++++++++++++++++++---- man/rm_zip.Rd | 82 ++++++++++++++++------ 73 files changed, 2671 insertions(+), 869 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedians().
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.15.0 dated 2015-10-27 and 0.50.0 dated 2015-12-13
matrixStats-0.15.0/matrixStats/src/logSumExp_internal.c |only matrixStats-0.15.0/matrixStats/src/logSumExp_internal.h |only matrixStats-0.15.0/matrixStats/tests/reports |only matrixStats-0.50.0/matrixStats/DESCRIPTION | 14 matrixStats-0.50.0/matrixStats/MD5 | 387 ++++++---- matrixStats-0.50.0/matrixStats/NAMESPACE | 1 matrixStats-0.50.0/matrixStats/NEWS | 12 matrixStats-0.50.0/matrixStats/R/anyMissing.R | 18 matrixStats-0.50.0/matrixStats/R/binCounts.R | 9 matrixStats-0.50.0/matrixStats/R/binMeans.R | 12 matrixStats-0.50.0/matrixStats/R/diff2.R | 9 matrixStats-0.50.0/matrixStats/R/logSumExp.R | 8 matrixStats-0.50.0/matrixStats/R/meanOver.R | 19 matrixStats-0.50.0/matrixStats/R/product.R | 6 matrixStats-0.50.0/matrixStats/R/rowAvgsPerColSet.R | 26 matrixStats-0.50.0/matrixStats/R/rowCollapse.R | 26 matrixStats-0.50.0/matrixStats/R/rowCounts.R | 99 ++ matrixStats-0.50.0/matrixStats/R/rowCumsums.R | 36 matrixStats-0.50.0/matrixStats/R/rowDiffs.R | 12 matrixStats-0.50.0/matrixStats/R/rowIQRs.R | 17 matrixStats-0.50.0/matrixStats/R/rowLogSumExps.R | 12 matrixStats-0.50.0/matrixStats/R/rowMads.R | 31 matrixStats-0.50.0/matrixStats/R/rowMedians.S4.R | 16 matrixStats-0.50.0/matrixStats/R/rowOrderStats.R | 24 matrixStats-0.50.0/matrixStats/R/rowProds.R | 18 matrixStats-0.50.0/matrixStats/R/rowQuantiles.R | 18 matrixStats-0.50.0/matrixStats/R/rowRanges.R | 28 matrixStats-0.50.0/matrixStats/R/rowRanks.R | 12 matrixStats-0.50.0/matrixStats/R/rowSds.R | 10 matrixStats-0.50.0/matrixStats/R/rowTabulates.R | 18 matrixStats-0.50.0/matrixStats/R/rowVars.R | 35 matrixStats-0.50.0/matrixStats/R/rowWeightedMeans.R | 23 matrixStats-0.50.0/matrixStats/R/rowWeightedMedians.R | 23 matrixStats-0.50.0/matrixStats/R/signTabulate.R | 8 matrixStats-0.50.0/matrixStats/R/sumOver.R | 18 matrixStats-0.50.0/matrixStats/R/validateIndices.R |only matrixStats-0.50.0/matrixStats/R/varDiff.R | 80 +- matrixStats-0.50.0/matrixStats/R/weightedMad.R | 35 matrixStats-0.50.0/matrixStats/R/weightedMean.R | 8 matrixStats-0.50.0/matrixStats/R/weightedMedian.R | 8 matrixStats-0.50.0/matrixStats/R/weightedVar.R | 43 - matrixStats-0.50.0/matrixStats/R/x_OP_y.R | 12 matrixStats-0.50.0/matrixStats/R/zzz.R | 10 matrixStats-0.50.0/matrixStats/build/vignette.rds |binary matrixStats-0.50.0/matrixStats/inst/benchmarking/anyMissing_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/binCounts_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/binMeans_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowAlls_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowAnyMissings_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowAnys_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowCounts_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowCummins_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowCumprods_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowCumsums_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowDiffs_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowLogSumExps_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowMads_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowMedians_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowMins_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowOrderStats_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowProds_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowQuantiles_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowRanges_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowRanks_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowTabulates_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowVars_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowWeightedMeans_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/colRowWeightedMedians_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/count_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/includes/results.md.rsp | 4 matrixStats-0.50.0/matrixStats/inst/benchmarking/logSumExp_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/madDiff_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/meanOver_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/product_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/sumOver_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/t_tx_OP_y_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/varDiff_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/weightedMean_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/weightedMedian_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/benchmarking/x_OP_y_subset.md.rsp |only matrixStats-0.50.0/matrixStats/inst/doc/matrixStats-methods.html | 6 matrixStats-0.50.0/matrixStats/inst/doc/matrixStats-methods.md.rsp | 2 matrixStats-0.50.0/matrixStats/man/anyMissing.Rd | 8 matrixStats-0.50.0/matrixStats/man/binCounts.Rd | 4 matrixStats-0.50.0/matrixStats/man/binMeans.Rd | 4 matrixStats-0.50.0/matrixStats/man/diff2.Rd | 4 matrixStats-0.50.0/matrixStats/man/logSumExp.Rd | 4 matrixStats-0.50.0/matrixStats/man/matrixStats-package.Rd | 6 matrixStats-0.50.0/matrixStats/man/meanOver.Rd | 4 matrixStats-0.50.0/matrixStats/man/rowAvgsPerColSet.Rd | 5 matrixStats-0.50.0/matrixStats/man/rowCollapse.Rd | 8 matrixStats-0.50.0/matrixStats/man/rowCounts.Rd | 18 matrixStats-0.50.0/matrixStats/man/rowCumsums.Rd | 18 matrixStats-0.50.0/matrixStats/man/rowDiffs.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowIQRs.Rd | 8 matrixStats-0.50.0/matrixStats/man/rowLogSumExps.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowMedians.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowOrderStats.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowProds.Rd | 8 matrixStats-0.50.0/matrixStats/man/rowQuantiles.Rd | 10 matrixStats-0.50.0/matrixStats/man/rowRanges.Rd | 14 matrixStats-0.50.0/matrixStats/man/rowRanks.Rd | 7 matrixStats-0.50.0/matrixStats/man/rowSds.Rd | 12 matrixStats-0.50.0/matrixStats/man/rowTabulates.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowVars.Rd | 10 matrixStats-0.50.0/matrixStats/man/rowWeightedMeans.Rd | 6 matrixStats-0.50.0/matrixStats/man/rowWeightedMedians.Rd | 6 matrixStats-0.50.0/matrixStats/man/signTabulate.Rd | 4 matrixStats-0.50.0/matrixStats/man/sumOver.Rd | 4 matrixStats-0.50.0/matrixStats/man/validateIndices.Rd |only matrixStats-0.50.0/matrixStats/man/varDiff.Rd | 26 matrixStats-0.50.0/matrixStats/man/weightedMad.Rd | 8 matrixStats-0.50.0/matrixStats/man/weightedMean.Rd | 4 matrixStats-0.50.0/matrixStats/man/weightedMedian.Rd | 5 matrixStats-0.50.0/matrixStats/man/weightedVar.Rd | 12 matrixStats-0.50.0/matrixStats/man/xUNDERSCOREOPUNDERSCOREy.Rd | 8 matrixStats-0.50.0/matrixStats/src/anyMissing.c | 89 -- matrixStats-0.50.0/matrixStats/src/anyMissing_TYPE-template.h |only matrixStats-0.50.0/matrixStats/src/colCounts.c | 53 - matrixStats-0.50.0/matrixStats/src/colCounts_TYPE-template.h | 86 +- matrixStats-0.50.0/matrixStats/src/colOrderStats.c | 46 - matrixStats-0.50.0/matrixStats/src/colOrderStats_TYPE-template.h | 57 - matrixStats-0.50.0/matrixStats/src/colRanges.c | 77 + matrixStats-0.50.0/matrixStats/src/colRanges_TYPE-template.h | 145 +-- matrixStats-0.50.0/matrixStats/src/diff2.c | 27 matrixStats-0.50.0/matrixStats/src/diff2_TYPE-template.h | 57 - matrixStats-0.50.0/matrixStats/src/logSumExp.c | 25 matrixStats-0.50.0/matrixStats/src/logSumExp_TYPE-template.h |only matrixStats-0.50.0/matrixStats/src/macros.h |only matrixStats-0.50.0/matrixStats/src/meanOver.c | 39 - matrixStats-0.50.0/matrixStats/src/meanOver_TYPE-template.h | 141 +-- matrixStats-0.50.0/matrixStats/src/productExpSumLog.c | 28 matrixStats-0.50.0/matrixStats/src/productExpSumLog_TYPE-template.h | 22 matrixStats-0.50.0/matrixStats/src/rowCounts.c | 40 - matrixStats-0.50.0/matrixStats/src/rowCounts_TYPE-template.h | 116 +- matrixStats-0.50.0/matrixStats/src/rowCumMinMaxs.c | 75 + matrixStats-0.50.0/matrixStats/src/rowCumMinMaxs_TYPE-template.h | 65 + matrixStats-0.50.0/matrixStats/src/rowCumprods.c | 34 matrixStats-0.50.0/matrixStats/src/rowCumprods_TYPE-template.h | 74 + matrixStats-0.50.0/matrixStats/src/rowCumsums.c | 32 matrixStats-0.50.0/matrixStats/src/rowCumsums_TYPE-template.h | 90 +- matrixStats-0.50.0/matrixStats/src/rowDiffs.c | 42 - matrixStats-0.50.0/matrixStats/src/rowDiffs_TYPE-template.h | 156 +++- matrixStats-0.50.0/matrixStats/src/rowLogSumExp.c | 58 - matrixStats-0.50.0/matrixStats/src/rowLogSumExp_TYPE-template.h |only matrixStats-0.50.0/matrixStats/src/rowMads.c | 44 - matrixStats-0.50.0/matrixStats/src/rowMads_TYPE-template.h | 64 - matrixStats-0.50.0/matrixStats/src/rowMedians.c | 48 - matrixStats-0.50.0/matrixStats/src/rowMedians_TYPE-template.h | 58 - matrixStats-0.50.0/matrixStats/src/rowOrderStats.c | 46 - matrixStats-0.50.0/matrixStats/src/rowOrderStats_TYPE-template.h | 70 + matrixStats-0.50.0/matrixStats/src/rowRanges.c | 75 + matrixStats-0.50.0/matrixStats/src/rowRanges_TYPE-template.h | 147 ++- matrixStats-0.50.0/matrixStats/src/rowRanksWithTies.c | 139 +-- matrixStats-0.50.0/matrixStats/src/rowRanksWithTies_TYPE_TIES-template.h | 102 +- matrixStats-0.50.0/matrixStats/src/rowVars.c | 38 matrixStats-0.50.0/matrixStats/src/rowVars_TYPE-template.h | 46 - matrixStats-0.50.0/matrixStats/src/signTabulate.c | 27 matrixStats-0.50.0/matrixStats/src/signTabulate_TYPE-template.h | 22 matrixStats-0.50.0/matrixStats/src/sumOver.c | 37 matrixStats-0.50.0/matrixStats/src/sumOver_TYPE-template.h | 76 - matrixStats-0.50.0/matrixStats/src/templates-gen-matrix-vector.h |only matrixStats-0.50.0/matrixStats/src/templates-gen-matrix.h |only matrixStats-0.50.0/matrixStats/src/templates-gen-vector.h |only matrixStats-0.50.0/matrixStats/src/templates-types.h | 346 +++++++- matrixStats-0.50.0/matrixStats/src/templates-types_undef.h | 25 matrixStats-0.50.0/matrixStats/src/types.h | 25 matrixStats-0.50.0/matrixStats/src/utils.h | 39 - matrixStats-0.50.0/matrixStats/src/validateIndices.c |only matrixStats-0.50.0/matrixStats/src/validateIndices_TYPE-template.h |only matrixStats-0.50.0/matrixStats/src/weightedMean.c | 25 matrixStats-0.50.0/matrixStats/src/weightedMean_TYPE-template.h | 32 matrixStats-0.50.0/matrixStats/src/weightedMedian.c | 25 matrixStats-0.50.0/matrixStats/src/weightedMedian_TYPE-template.h | 65 + matrixStats-0.50.0/matrixStats/src/x_OP_y.c | 138 ++- matrixStats-0.50.0/matrixStats/src/x_OP_y_TYPE-template.h | 305 ++++--- matrixStats-0.50.0/matrixStats/tests/anyMissing_subset.R |only matrixStats-0.50.0/matrixStats/tests/benchmark.R | 3 matrixStats-0.50.0/matrixStats/tests/binCounts_subset.R |only matrixStats-0.50.0/matrixStats/tests/binMeans,binCounts_subset.R |only matrixStats-0.50.0/matrixStats/tests/count_subset.R |only matrixStats-0.50.0/matrixStats/tests/diff2_subset.R |only matrixStats-0.50.0/matrixStats/tests/logSumExp_subset.R |only matrixStats-0.50.0/matrixStats/tests/meanOver_subset.R |only matrixStats-0.50.0/matrixStats/tests/product.R | 18 matrixStats-0.50.0/matrixStats/tests/product_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowAllAnys.R | 8 matrixStats-0.50.0/matrixStats/tests/rowAllAnys_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowAvgsPerColSet_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowCollapse_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowCounts_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowCumMinMaxs.R | 20 matrixStats-0.50.0/matrixStats/tests/rowCumMinMaxs_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowCumprods.R | 10 matrixStats-0.50.0/matrixStats/tests/rowCumprods_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowCumsums.R | 10 matrixStats-0.50.0/matrixStats/tests/rowCumsums_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowDiffs_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowIQRs.R | 1 matrixStats-0.50.0/matrixStats/tests/rowIQRs_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowLogSumExps_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowMads.R | 12 matrixStats-0.50.0/matrixStats/tests/rowMads_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowMedians.R | 3 matrixStats-0.50.0/matrixStats/tests/rowMedians_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowOrderStats.R | 8 matrixStats-0.50.0/matrixStats/tests/rowOrderStats_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowProds.R | 9 matrixStats-0.50.0/matrixStats/tests/rowProds_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowQuantiles.R | 20 matrixStats-0.50.0/matrixStats/tests/rowQuantiles_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowRanges.R | 4 matrixStats-0.50.0/matrixStats/tests/rowRanges_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowRanks.R | 2 matrixStats-0.50.0/matrixStats/tests/rowRanks_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowSds.R | 12 matrixStats-0.50.0/matrixStats/tests/rowSds_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowTabulates_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowVarDiffs_mad,iqr_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowVarDiffs_var,sd_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowVars.R | 12 matrixStats-0.50.0/matrixStats/tests/rowVars_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowWeightedMeans.R | 11 matrixStats-0.50.0/matrixStats/tests/rowWeightedMeans_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowWeightedMedians_subset.R |only matrixStats-0.50.0/matrixStats/tests/rowWeightedVars_subset.R |only matrixStats-0.50.0/matrixStats/tests/signTabulate_subset.R |only matrixStats-0.50.0/matrixStats/tests/sumOver.R | 2 matrixStats-0.50.0/matrixStats/tests/sumOver_subset.R |only matrixStats-0.50.0/matrixStats/tests/utils |only matrixStats-0.50.0/matrixStats/tests/validateIndices.R |only matrixStats-0.50.0/matrixStats/tests/varDiff_etal_subset.R |only matrixStats-0.50.0/matrixStats/tests/weightedMean_subset.R |only matrixStats-0.50.0/matrixStats/tests/weightedMedian_subset.R |only matrixStats-0.50.0/matrixStats/tests/weightedVar_etal_subset.R |only matrixStats-0.50.0/matrixStats/tests/x_OP_y_subset.R |only matrixStats-0.50.0/matrixStats/vignettes/matrixStats-methods.md.rsp | 2 237 files changed, 3312 insertions(+), 2071 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-4 dated 2015-09-15 and 1.1-0 dated 2015-12-13
arulesViz-1.0-4/arulesViz/R/AAA_helpers.R |only arulesViz-1.0-4/arulesViz/R/abbreviate.R |only arulesViz-1.0-4/arulesViz/inst/n.html |only arulesViz-1.0-4/arulesViz/man/abbreviate.Rd |only arulesViz-1.1-0/arulesViz/DESCRIPTION | 16 arulesViz-1.1-0/arulesViz/MD5 | 49 - arulesViz-1.1-0/arulesViz/NAMESPACE | 31 - arulesViz-1.1-0/arulesViz/R/AAAhelpers.R |only arulesViz-1.1-0/arulesViz/R/AAAparameter.R |only arulesViz-1.1-0/arulesViz/R/doubledecker.R | 4 arulesViz-1.1-0/arulesViz/R/gPlots.R | 411 ++++++++-------- arulesViz-1.1-0/arulesViz/R/graph.R | 66 +- arulesViz-1.1-0/arulesViz/R/groupedmatrix.R | 24 arulesViz-1.1-0/arulesViz/R/iplot.R | 4 arulesViz-1.1-0/arulesViz/R/map.R | 3 arulesViz-1.1-0/arulesViz/R/matrix.R | 550 +++++++++++----------- arulesViz-1.1-0/arulesViz/R/paracoord.R | 440 ++++++++--------- arulesViz-1.1-0/arulesViz/R/plot.R | 2 arulesViz-1.1-0/arulesViz/R/save.R | 2 arulesViz-1.1-0/arulesViz/R/scatterplot.R | 521 ++++++++++---------- arulesViz-1.1-0/arulesViz/README.md |only arulesViz-1.1-0/arulesViz/build/vignette.rds |binary arulesViz-1.1-0/arulesViz/inst/NEWS | 8 arulesViz-1.1-0/arulesViz/inst/doc/arulesViz.R | 21 arulesViz-1.1-0/arulesViz/inst/doc/arulesViz.Rnw | 3 arulesViz-1.1-0/arulesViz/inst/doc/arulesViz.pdf |binary arulesViz-1.1-0/arulesViz/man/plot.Rd | 5 arulesViz-1.1-0/arulesViz/man/save.Rd | 2 arulesViz-1.1-0/arulesViz/vignettes/arulesViz.Rnw | 3 29 files changed, 1107 insertions(+), 1058 deletions(-)
Title: An R Interface to SOLAR
Description: SOLAR is the standard software program to perform linkage and
association mappings of the quantitative trait loci (QTLs) in pedigrees of
arbitrary size and complexity. This package allows the user to exploit the
variance component methods implemented in SOLAR. It automates such routine
operations as formatting pedigree and phenotype data. It also parses the model
output and contains summary and plotting functions for exploration of the
results. In addition, solarius enables parallel computing of the linkage and
association analyses, that makes the calculation of genome-wide scans more
efficient. See <http://solar.txbiomedgenetics.org/> for more information about
SOLAR.
Author: Andrey Ziyatdinov [cre, aut],
Helena Brunel [aut],
Angel Martinez-Perez [aut],
Alfonso Buil [aut],
Alexandre Perera [cph],
Jose Manuel Soria [cph]
Maintainer: Andrey Ziyatdinov <andrey.ziyatdinov@upc.edu>
Diff between solarius versions 0.2.3 dated 2015-05-09 and 0.3.0.2 dated 2015-12-13
solarius-0.2.3/solarius/man/solariusPackage.Rd |only solarius-0.3.0.2/solarius/DESCRIPTION | 42 +- solarius-0.3.0.2/solarius/MD5 | 128 ++++-- solarius-0.3.0.2/solarius/NAMESPACE | 44 ++ solarius-0.3.0.2/solarius/NEWS | 24 + solarius-0.3.0.2/solarius/R/assoc.lib.R | 94 ++++- solarius-0.3.0.2/solarius/R/classSolarAssoc.R | 53 ++ solarius-0.3.0.2/solarius/R/classSolarMultipoint.R | 89 ++++ solarius-0.3.0.2/solarius/R/data.lib.R | 2 solarius-0.3.0.2/solarius/R/datasets.R | 20 - solarius-0.3.0.2/solarius/R/files.lib.R | 126 +++++- solarius-0.3.0.2/solarius/R/modelPar.R |only solarius-0.3.0.2/solarius/R/multipoint.lib.R | 112 ++++++ solarius-0.3.0.2/solarius/R/package.R | 4 solarius-0.3.0.2/solarius/R/plot.lib.R | 20 + solarius-0.3.0.2/solarius/R/solar.lib.R | 4 solarius-0.3.0.2/solarius/R/solarAssoc.R | 184 ++++++++-- solarius-0.3.0.2/solarius/R/solarBayesAvg.R |only solarius-0.3.0.2/solarius/R/solarMultipoint.R | 10 solarius-0.3.0.2/solarius/R/solarMultivar.R |only solarius-0.3.0.2/solarius/R/solarPar.R |only solarius-0.3.0.2/solarius/R/solarPolyAssoc.R |only solarius-0.3.0.2/solarius/R/support.lib.R | 28 + solarius-0.3.0.2/solarius/R/transforms.lib.R | 38 +- solarius-0.3.0.2/solarius/README.md | 7 solarius-0.3.0.2/solarius/TODO | 16 solarius-0.3.0.2/solarius/inst/examples/function-solarBayesAvg.R |only solarius-0.3.0.2/solarius/inst/examples/function-solarMultivar.R |only solarius-0.3.0.2/solarius/inst/examples/solar-multipoint-gait1.R |only solarius-0.3.0.2/solarius/inst/extdata/solarAssoc/plink/dat50.ped | 132 +++---- solarius-0.3.0.2/solarius/inst/extdata/solarAssoc/plink/dat50.raw |only solarius-0.3.0.2/solarius/inst/extdata/solarAssoc/plink/dat50.tfam |only solarius-0.3.0.2/solarius/inst/extdata/solarAssoc/plink/dat50.tped |only solarius-0.3.0.2/solarius/inst/extdata/solarAssoc/snp.geno-list |only solarius-0.3.0.2/solarius/inst/tests/test-annotate.R |only solarius-0.3.0.2/solarius/inst/tests/test-kinship.R | 23 - solarius-0.3.0.2/solarius/inst/tests/test-mgafiles.R |only solarius-0.3.0.2/solarius/inst/tests/test-not-passed.R |only solarius-0.3.0.2/solarius/inst/tests/test-plinkfiles.R |only solarius-0.3.0.2/solarius/inst/tests/test-solarAssoc-parallel.R |only solarius-0.3.0.2/solarius/inst/tests/test-solarAssoc.R | 14 solarius-0.3.0.2/solarius/inst/tests/test-solarPar.R |only solarius-0.3.0.2/solarius/man/annotate.Rd | 16 solarius-0.3.0.2/solarius/man/annotateSNPs.Rd | 14 solarius-0.3.0.2/solarius/man/availableTransforms.Rd | 2 solarius-0.3.0.2/solarius/man/dat30.Rd | 13 solarius-0.3.0.2/solarius/man/dat50.Rd | 17 solarius-0.3.0.2/solarius/man/df2solar.Rd | 2 solarius-0.3.0.2/solarius/man/explainedVarProp.Rd |only solarius-0.3.0.2/solarius/man/getFormulaStr.Rd | 2 solarius-0.3.0.2/solarius/man/loadExamplesPhen.Rd | 2 solarius-0.3.0.2/solarius/man/loadMulticPhen.Rd | 2 solarius-0.3.0.2/solarius/man/matchIdNames.Rd | 2 solarius-0.3.0.2/solarius/man/matchMapNames.Rd | 2 solarius-0.3.0.2/solarius/man/modelPar.Rd |only solarius-0.3.0.2/solarius/man/package.file.Rd | 4 solarius-0.3.0.2/solarius/man/plotKinship2.Rd | 2 solarius-0.3.0.2/solarius/man/plotPed.Rd | 2 solarius-0.3.0.2/solarius/man/plotQQManh.Rd | 2 solarius-0.3.0.2/solarius/man/plotRes.Rd | 2 solarius-0.3.0.2/solarius/man/readPhen.Rd | 2 solarius-0.3.0.2/solarius/man/snp2solar.Rd | 2 solarius-0.3.0.2/solarius/man/solar.Rd | 2 solarius-0.3.0.2/solarius/man/solarAssoc.Rd | 37 +- solarius-0.3.0.2/solarius/man/solarAssocClass.Rd | 2 solarius-0.3.0.2/solarius/man/solarBaeysAvgPolygenicClass.Rd |only solarius-0.3.0.2/solarius/man/solarKinship2.Rd | 2 solarius-0.3.0.2/solarius/man/solarMultipoint.Rd | 8 solarius-0.3.0.2/solarius/man/solarMultipointClass.Rd | 22 + solarius-0.3.0.2/solarius/man/solarMultivarClass.Rd |only solarius-0.3.0.2/solarius/man/solarPar.Rd |only solarius-0.3.0.2/solarius/man/solarPolyAssoc.Rd |only solarius-0.3.0.2/solarius/man/solarPolygenic.Rd | 2 solarius-0.3.0.2/solarius/man/solarPolygenicClass.Rd | 2 solarius-0.3.0.2/solarius/man/solarReadFiles.Rd | 2 solarius-0.3.0.2/solarius/man/tabplot.Rd |only solarius-0.3.0.2/solarius/man/transformData.Rd | 2 solarius-0.3.0.2/solarius/man/transformTrait.Rd | 7 78 files changed, 1057 insertions(+), 335 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.300.2.0 dated 2015-12-03 and 0.6.300.2.2 dated 2015-12-13
ChangeLog | 22 ++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 24 ++++++++--------- build/vignette.rds |binary configure | 22 ++++++++-------- inst/NEWS.Rd | 11 ++++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloConfig.h | 2 - inst/include/RcppArmadilloLapack.h.in | 4 +- inst/include/armadillo_bits/arma_version.hpp | 2 - inst/include/armadillo_bits/auxlib_meat.hpp | 35 ++++++++++++++++++++------ inst/include/armadillo_bits/gmm_diag_meat.hpp | 27 ++++++++++++++++---- 13 files changed, 113 insertions(+), 44 deletions(-)
Title: CITation ANalysis Toolpack
Description: Supports quantitative
research in scientometrics and bibliometrics. Provides
various tools for preprocessing bibliographic
data retrieved, e.g., from Elsevier's SciVerse Scopus,
computing bibliometric impact of individuals,
or modeling many phenomena encountered in the social sciences.
Author: Marek Gagolewski [aut, cre]
Maintainer: Marek Gagolewski <gagolews@ibspan.waw.pl>
Diff between CITAN versions 2014.12-1 dated 2014-12-06 and 2015.12-2 dated 2015-12-13
CITAN-2014.12-1/CITAN/data |only CITAN-2015.12-2/CITAN/CHANGELOG | 3 CITAN-2015.12-2/CITAN/DESCRIPTION | 20 +- CITAN-2015.12-2/CITAN/MD5 | 106 ++++++-------- CITAN-2015.12-2/CITAN/NAMESPACE | 16 +- CITAN-2015.12-2/CITAN/R/CITAN-package.R | 23 ++- CITAN-2015.12-2/CITAN/R/biblio.assess.R | 6 CITAN-2015.12-2/CITAN/R/biblio.clear.R | 27 ++- CITAN-2015.12-2/CITAN/R/biblio.connect.R | 19 +- CITAN-2015.12-2/CITAN/R/biblio.create.R | 13 + CITAN-2015.12-2/CITAN/R/biblio.duplicates.authors.R | 24 ++- CITAN-2015.12-2/CITAN/R/biblio.duplicates.documents.R | 11 + CITAN-2015.12-2/CITAN/R/biblio.getcitations.R | 10 - CITAN-2015.12-2/CITAN/R/biblio.import.R | 20 +- CITAN-2015.12-2/CITAN/R/biblio.info.R | 8 - CITAN-2015.12-2/CITAN/R/biblio.internal.R | 2 CITAN-2015.12-2/CITAN/R/biblio.search.R | 6 CITAN-2015.12-2/CITAN/R/biblio.stats.R | 8 - CITAN-2015.12-2/CITAN/R/biblio.tidy.R | 8 - CITAN-2015.12-2/CITAN/R/execquery.R | 2 CITAN-2015.12-2/CITAN/R/rgtk2.R | 2 CITAN-2015.12-2/CITAN/R/scopus.data.R | 6 CITAN-2015.12-2/CITAN/R/scopus.importsources.R | 6 CITAN-2015.12-2/CITAN/R/scopus.readcsv.R | 4 CITAN-2015.12-2/CITAN/R/string.R | 4 CITAN-2015.12-2/CITAN/R/sysdata.rda |only CITAN-2015.12-2/CITAN/man/CITAN-package.Rd | 14 - CITAN-2015.12-2/CITAN/man/Scopus_ASJC.Rd | 6 CITAN-2015.12-2/CITAN/man/Scopus_ImportSources.Rd | 3 CITAN-2015.12-2/CITAN/man/Scopus_ReadCSV.Rd | 5 CITAN-2015.12-2/CITAN/man/Scopus_SourceList.Rd | 6 CITAN-2015.12-2/CITAN/man/as.character.authorinfo.Rd | 3 CITAN-2015.12-2/CITAN/man/as.character.docinfo.Rd | 3 CITAN-2015.12-2/CITAN/man/dbExecQuery.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsAssess.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsClear.Rd | 4 CITAN-2015.12-2/CITAN/man/lbsConnect.Rd | 10 - CITAN-2015.12-2/CITAN/man/lbsCreate.Rd | 18 +- CITAN-2015.12-2/CITAN/man/lbsDeleteAllAuthorsDocuments.Rd | 15 + CITAN-2015.12-2/CITAN/man/lbsDeleteDocuments.Rd | 6 CITAN-2015.12-2/CITAN/man/lbsDescriptiveStats.Rd | 9 - CITAN-2015.12-2/CITAN/man/lbsDisconnect.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsFindDuplicateAuthors.Rd | 7 CITAN-2015.12-2/CITAN/man/lbsFindDuplicateTitles.Rd | 8 - CITAN-2015.12-2/CITAN/man/lbsGetCitations.Rd | 6 CITAN-2015.12-2/CITAN/man/lbsGetInfoAuthors.Rd | 5 CITAN-2015.12-2/CITAN/man/lbsGetInfoDocuments.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsImportDocuments.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsMergeAuthors.Rd | 7 CITAN-2015.12-2/CITAN/man/lbsSearchAuthors.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsSearchDocuments.Rd | 3 CITAN-2015.12-2/CITAN/man/lbsTidy.Rd | 3 CITAN-2015.12-2/CITAN/man/print.authorinfo.Rd | 3 CITAN-2015.12-2/CITAN/man/print.docinfo.Rd | 3 54 files changed, 319 insertions(+), 200 deletions(-)
Title: Embeddable Cairo Graphics Device Driver
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between cairoDevice versions 2.22 dated 2015-02-24 and 2.23 dated 2015-12-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/zzz.R | 9 +++++---- src/cairoDevice.c | 15 ++++++++++++--- 4 files changed, 24 insertions(+), 14 deletions(-)
Title: Functions for Calculating Daily Solar Radiation and
Evapotranspiration
Description: Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.
Author: Jedrzej S. Bojanowski
Maintainer: Jedrzej S. Bojanowski <jedrzej.bojanowski@gmail.com>
Diff between sirad versions 2.3-0 dated 2015-10-18 and 2.3-1 dated 2015-12-12
sirad-2.3-0/sirad/R/ts.CMSAF.R |only sirad-2.3-0/sirad/man/ts.CMSAF.Rd |only sirad-2.3-1/sirad/DESCRIPTION | 10 +++++----- sirad-2.3-1/sirad/MD5 | 8 +++----- sirad-2.3-1/sirad/NAMESPACE | 3 +-- sirad-2.3-1/sirad/man/sirad-package.Rd | 4 ++-- 6 files changed, 11 insertions(+), 14 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-9 dated 2015-10-31 and 1.8-10 dated 2015-12-12
ChangeLog | 25 + DESCRIPTION | 6 MD5 | 163 ++++---- NAMESPACE | 4 R/bam.r | 268 +++++++++++-- R/efam.r | 2 R/gamlss.r | 264 +++++++++++++ R/mgcv.r | 27 + R/misc.r | 31 + R/smooth.r | 14 R/soap.r | 3 man/Predict.matrix.soap.film.Rd | 2 man/Tweedie.Rd | 2 man/bam.Rd | 4 man/bam.update.Rd | 2 man/choose.k.Rd | 2 man/concurvity.Rd | 2 man/coxph.Rd | 2 man/exclude.too.far.Rd | 2 man/extract.lme.cov.Rd | 2 man/family.mgcv.Rd | 6 man/formXtViX.Rd | 2 man/formula.gam.Rd | 2 man/gam.Rd | 2 man/gam.check.Rd | 2 man/gam.control.Rd | 2 man/gam.fit.Rd | 2 man/gam.fit3.Rd | 2 man/gam.outer.Rd | 2 man/gam.selection.Rd | 2 man/gam.side.Rd | 8 man/gam2objective.Rd | 2 man/gamm.Rd | 2 man/gaulss.Rd | 4 man/get.var.Rd | 2 man/in.out.Rd | 2 man/inSide.Rd | 2 man/interpret.gam.Rd | 2 man/jagam.Rd | 2 man/ls.size.Rd | 2 man/magic.Rd | 2 man/mgcv-FAQ.Rd | 2 man/mgcv-package.Rd | 1 man/mono.con.Rd | 2 man/multinom.Rd |only man/mvn.Rd | 3 man/negbin.Rd | 2 man/new.name.Rd | 2 man/notExp.Rd | 2 man/notExp2.Rd | 2 man/null.space.dimension.Rd | 2 man/ocat.Rd | 3 man/pcls.Rd | 2 man/pdIdnot.Rd | 2 man/pdTens.Rd | 2 man/place.knots.Rd | 2 man/predict.bam.Rd | 6 man/print.gam.Rd | 2 man/qq.gam.Rd | 2 man/rig.Rd | 2 man/s.Rd | 2 man/scat.Rd | 3 man/smooth.construct.Rd | 2 man/smooth.construct.so.smooth.spec.Rd | 2 man/smoothCon.Rd | 2 man/te.Rd | 2 man/ziP.Rd | 3 man/ziplss.Rd | 3 src/coxph.c | 60 +-- src/discrete.c | 202 ++++++---- src/gdi.c | 634 ++++++++++++++++----------------- src/init.c | 5 src/magic.c | 96 ++-- src/mat.c | 295 +++++++-------- src/matrix.c | 42 +- src/mgcv.c | 25 - src/mgcv.h | 15 src/misc.c | 42 +- src/mvn.c | 28 - src/qp.c | 11 src/soap.c | 6 src/sparse-smooth.c | 140 +++---- src/tprs.c | 64 +-- 83 files changed, 1611 insertions(+), 995 deletions(-)
Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library 'libamtrack' (http://libamtrack.dkfz.org). 'libamtrack' provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. 'libamtrack' also includes many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>
Diff between libamtrack versions 0.6.2 dated 2015-06-26 and 0.6.3 dated 2015-12-12
libamtrack-0.6.2/libamtrack/man/AT.CSDA.energy.after.slab.E.MeV.u.Rd |only libamtrack-0.6.2/libamtrack/man/AT.CSDA.range.Bethe.g.cm2.Rd |only libamtrack-0.6.2/libamtrack/man/AT.WEPL.Bethe.Rd |only libamtrack-0.6.3/libamtrack/DESCRIPTION | 10 libamtrack-0.6.3/libamtrack/MD5 | 164 ++++------ libamtrack-0.6.3/libamtrack/NAMESPACE | 8 libamtrack-0.6.3/libamtrack/R/initial.R | 2 libamtrack-0.6.3/libamtrack/R/libamtrack.R | 56 --- libamtrack-0.6.3/libamtrack/configure | 2 libamtrack-0.6.3/libamtrack/configure.ac | 2 libamtrack-0.6.3/libamtrack/man/AT.A.from.particle.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.CSDA.range.g.cm2.Rd |only libamtrack-0.6.3/libamtrack/man/AT.D.RDD.Gy.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.E.from.beta.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Gauss.IDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Gauss.PDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.I.eV.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Landau.IDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Landau.PDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Mass.Stopping.Power.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Mass.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Rutherford.SDCS.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Stopping.Power.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Vavilov.IDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Vavilov.PDF.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.Z.from.particle.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.atomic.weight.from.Z.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.average.A.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.average.Z.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.beam.par.physical.to.technical.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.beam.par.technical.to.physical.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.beta.from.E.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.dose.Gy.from.fluence.cm2.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.dose.weighted.E.MeV.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.effective.Z.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.effective.charge.from.E.MeV.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.electron.density.m3.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.electron.density.m3.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.electron.density.m3.from.material.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.energy.loss.from.lambda.gauss.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.energy.loss.from.lambda.landau.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.energy.loss.from.lambda.vavilov.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.energy.straggling.MeV2.cm2.g.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.fluence.cm2.from.dose.Gy.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.fluence.weighted.E.MeV.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.gamma.from.E.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.get.materials.data.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.kappa.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.lambda.landau.from.energy.loss.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.lambda.max.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.lambda.mean.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.lambda.vavilov.from.energy.loss.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.max.E.transfer.MeV.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.max.E.transfer.MeV.new.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.max.electron.ranges.m.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.mean.energy.loss.keV.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.mean.number.of.tracks.contrib.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.nuclear.spin.from.particle.no.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.particle.no.from.Z.and.A.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.r.RDD.m.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.run.CPPSC.method.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.run.GSM.method.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.run.IGK.method.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.set.user.material.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.set.user.material.from.composition.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.stopping.power.ratio.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.total.D.Gy.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.total.fluence.cm2.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.translate.dose.into.DSB.distribution.Rd | 2 libamtrack-0.6.3/libamtrack/man/AT.xi.keV.Rd | 2 libamtrack-0.6.3/libamtrack/man/libamtrack-package.Rd | 9 libamtrack-0.6.3/libamtrack/src/AT.c | 8 libamtrack-0.6.3/libamtrack/src/AT.h | 8 libamtrack-0.6.3/libamtrack/src/AT_DataRange.c | 45 +- libamtrack-0.6.3/libamtrack/src/AT_DataRange.h | 34 -- libamtrack-0.6.3/libamtrack/src/AT_R_Wrapper.c | 96 ----- libamtrack-0.6.3/libamtrack/src/AT_R_Wrapper.h | 20 - libamtrack-0.6.3/libamtrack/src/AT_StoppingPowerDataBethe.h | 2 libamtrack-0.6.3/libamtrack/src/config.h | 8 85 files changed, 218 insertions(+), 386 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code
inspection using various strategies, e.g. conservative or liberal. The objective
of this package is to make it as simple as possible to identify global objects
for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.5.0 dated 2015-10-14 and 0.6.0 dated 2015-12-12
DESCRIPTION | 12 ++++-- MD5 | 27 +++++++------- NAMESPACE | 31 +++++++++-------- NEWS | 11 +++++- R/Globals-class.R | 2 - R/cleanup.R | 2 - R/findGlobals.R | 83 +++++++++++++++++++++++++++++++++++----------- R/globalsOf.R | 12 ++++-- R/packagesOf.R | 2 - README.md |only man/Globals.Rd | 56 +++++++++++++++---------------- man/cleanup.Globals.Rd | 4 +- man/globalsOf.Rd | 20 ++++++----- man/packagesOf.Globals.Rd | 42 +++++++++++------------ tests/globalsOf.R | 35 ++++++++++++++++++- 15 files changed, 220 insertions(+), 119 deletions(-)
Title: Semiparametric Sample Selection Modelling with Continuous or
Discrete Response
Description: Routine for fitting continuous or discrete response copula sample selection models with semiparametric predictors, including linear and nonlinear effects.
Author: Giampiero Marra, Rosalba Radice, Malgorzata Wojtys and Karol Wyszynski
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParSampleSel versions 1.2 dated 2015-01-21 and 1.3 dated 2015-12-12
SemiParSampleSel-1.2/SemiParSampleSel/R/VuongClarke.bcm.r |only SemiParSampleSel-1.2/SemiParSampleSel/R/est.aver.r |only SemiParSampleSel-1.2/SemiParSampleSel/R/fit.SemiParSampleSel1.r |only SemiParSampleSel-1.2/SemiParSampleSel/R/print.est.aver.r |only SemiParSampleSel-1.2/SemiParSampleSel/R/ss.checks.r |only SemiParSampleSel-1.2/SemiParSampleSel/R/working.comp1.r |only SemiParSampleSel-1.2/SemiParSampleSel/man/VuongClarke.bcm.Rd |only SemiParSampleSel-1.2/SemiParSampleSel/man/est.aver.Rd |only SemiParSampleSel-1.2/SemiParSampleSel/man/fit.SemiParSampleSel1.Rd |only SemiParSampleSel-1.2/SemiParSampleSel/man/print.est.aver.Rd |only SemiParSampleSel-1.2/SemiParSampleSel/man/ss.checks.Rd |only SemiParSampleSel-1.2/SemiParSampleSel/man/working.comp1.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/ChangeLog | 5 SemiParSampleSel-1.3/SemiParSampleSel/DESCRIPTION | 8 SemiParSampleSel-1.3/SemiParSampleSel/MD5 | 88 SemiParSampleSel-1.3/SemiParSampleSel/NAMESPACE | 41 SemiParSampleSel-1.3/SemiParSampleSel/R/S.m.r | 78 SemiParSampleSel-1.3/SemiParSampleSel/R/SemiParSampleSel.r | 535 ++ SemiParSampleSel-1.3/SemiParSampleSel/R/VuongClarke.r |only SemiParSampleSel-1.3/SemiParSampleSel/R/aver.r |only SemiParSampleSel-1.3/SemiParSampleSel/R/bitsgHs.r | 415 ++ SemiParSampleSel-1.3/SemiParSampleSel/R/conv.check.r |only SemiParSampleSel-1.3/SemiParSampleSel/R/copulaBitsD.R |only SemiParSampleSel-1.3/SemiParSampleSel/R/fit.SemiParSampleSel.r | 65 SemiParSampleSel-1.3/SemiParSampleSel/R/ghss.r | 139 SemiParSampleSel-1.3/SemiParSampleSel/R/ghssD.r | 2048 +--------- SemiParSampleSel-1.3/SemiParSampleSel/R/ghssDuniv.r |only SemiParSampleSel-1.3/SemiParSampleSel/R/marginBitsD.R |only SemiParSampleSel-1.3/SemiParSampleSel/R/pen.r | 133 SemiParSampleSel-1.3/SemiParSampleSel/R/plot.SemiParSampleSel.r | 48 SemiParSampleSel-1.3/SemiParSampleSel/R/post.check.R |only SemiParSampleSel-1.3/SemiParSampleSel/R/predict.SemiParSampleSel.r | 30 SemiParSampleSel-1.3/SemiParSampleSel/R/print.SemiParSampleSel.r | 188 SemiParSampleSel-1.3/SemiParSampleSel/R/print.aver.r |only SemiParSampleSel-1.3/SemiParSampleSel/R/print.summary.SemiParSampleSel.r | 243 - SemiParSampleSel-1.3/SemiParSampleSel/R/resp.check.R |only SemiParSampleSel-1.3/SemiParSampleSel/R/st.theta.star.R | 7 SemiParSampleSel-1.3/SemiParSampleSel/R/summary.SemiParSampleSel.r | 919 +++- SemiParSampleSel-1.3/SemiParSampleSel/R/theta.tau.r | 26 SemiParSampleSel-1.3/SemiParSampleSel/R/working.comp.r | 87 SemiParSampleSel-1.3/SemiParSampleSel/inst/CITATION | 10 SemiParSampleSel-1.3/SemiParSampleSel/man/SemiParSampleSel-package.Rd | 15 SemiParSampleSel-1.3/SemiParSampleSel/man/SemiParSampleSel.Rd | 214 - SemiParSampleSel-1.3/SemiParSampleSel/man/SemiParSampleSelObject.Rd | 26 SemiParSampleSel-1.3/SemiParSampleSel/man/VuongClarke.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/aver.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/bitsgHs.Rd | 2 SemiParSampleSel-1.3/SemiParSampleSel/man/conv.check.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/copulaBitsD.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/ghssDuniv.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/marginBitsD.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/plot.SemiParSampleSel.Rd | 19 SemiParSampleSel-1.3/SemiParSampleSel/man/post.check.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/predict.SemiParSampleSel.Rd | 6 SemiParSampleSel-1.3/SemiParSampleSel/man/print.aver.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/resp.check.Rd |only SemiParSampleSel-1.3/SemiParSampleSel/man/st.theta.star.Rd | 2 SemiParSampleSel-1.3/SemiParSampleSel/man/summary.SemiParSampleSel.Rd | 30 SemiParSampleSel-1.3/SemiParSampleSel/man/theta.tau.Rd | 3 SemiParSampleSel-1.3/SemiParSampleSel/man/working.comp.Rd | 6 60 files changed, 2998 insertions(+), 2438 deletions(-)
More information about SemiParSampleSel at CRAN
Permanent link
Title: Diagnostic Tools for Hierarchical (Multilevel) Linear Models
Description: A suite of diagnostic tools for hierarchical
(multilevel) linear models. The tools include
not only leverage and traditional deletion diagnostics (Cook's
distance, covratio, covtrace, and MDFFITS) but also
convenience functions and graphics for residual analysis. Models
can be fit using either lmer in the 'lme4' package or lme in the 'nlme' package,
but only two-level models fit using lme are currently supported.
Author: Adam Loy <loyad01@gmail.com>
Maintainer: Adam Loy <loyad01@gmail.com>
Diff between HLMdiag versions 0.3.0 dated 2015-06-22 and 0.3.1 dated 2015-12-12
DESCRIPTION | 14 ++++++++------ MD5 | 14 +++++++------- NAMESPACE | 17 ++++++++++++----- NEWS | 7 +++++++ R/group_level_residual_functions.R | 4 ++-- R/plot_functions.R | 4 ++-- R/utility_functions.R | 3 ++- man/dotplot_diag.Rd | 4 ++-- 8 files changed, 42 insertions(+), 25 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
randomForestSRC package for survival, regression and classification forests and
ggplot2 package plotting.
Author: John Ehrlinger <john.ehrlinger@gmail.com>
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 1.2.0 dated 2015-11-15 and 1.2.1 dated 2015-12-12
DESCRIPTION | 8 +-- MD5 | 53 ++++++++++----------- NEWS | 7 ++ data/interaction_Boston.rda |binary data/interaction_iris.rda |binary data/interaction_pbc.rda |binary data/partial_Boston.rda |binary data/partial_coplot_Boston.rda |binary data/partial_coplot_Boston2.rda |binary data/partial_coplot_pbc.rda |binary data/partial_coplot_pbc2.rda |binary data/partial_iris.rda |binary data/partial_pbc.rda |binary data/rfsrc_Boston.rda |binary data/rfsrc_iris.rda |binary data/rfsrc_pbc.rda |binary data/rfsrc_pbc_test.rda |binary data/varsel_Boston.rda |binary data/varsel_iris.rda |binary data/varsel_pbc.rda |binary inst/doc/randomForestSRC-Regression.R | 10 +-- inst/doc/randomForestSRC-Regression.Rnw | 8 +-- inst/doc/randomForestSRC-Regression.pdf |binary inst/doc/randomForestSRC-Survival.Rnw | 9 ++- inst/doc/randomForestSRC-Survival.pdf |binary vignettes/randomForestSRC-Regression.Rnw | 4 - vignettes/randomForestSRC-Survival-concordance.tex |only vignettes/randomForestSRC-Survival.Rnw | 9 ++- 28 files changed, 60 insertions(+), 48 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. multicore parallel processing and distributed
processing on compute clusters. The purpose of this package is to provide a
lightweight interface for using futures in R. Functions 'future()' and 'value()'
exist for creating futures and requesting their values. An infix assignment
operator '%<=%' exists for creating futures whose values are accessible by the
assigned variables (as promises). This package implements the synchronous "lazy"
and "eager" futures, and the asynchronous "multicore" future (not on Windows).
Additional types of futures are provided by other packages enhancing this
package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.2 dated 2015-10-14 and 0.9.0 dated 2015-12-12
future-0.8.2/future/inst/doc/issues.html |only future-0.8.2/future/inst/doc/issues.md.rsp |only future-0.8.2/future/vignettes/issues.md.rsp |only future-0.9.0/future/DESCRIPTION | 23 + future-0.9.0/future/MD5 | 96 ++++---- future-0.9.0/future/NAMESPACE | 3 future-0.9.0/future/NEWS | 22 + future-0.9.0/future/R/EagerFuture-class.R | 2 future-0.9.0/future/R/Future-class.R | 6 future-0.9.0/future/R/FutureRegistry.R | 4 future-0.9.0/future/R/LazyFuture-class.R | 2 future-0.9.0/future/R/MulticoreFuture.R | 2 future-0.9.0/future/R/availableCores.R | 4 future-0.9.0/future/R/eager.R | 2 future-0.9.0/future/R/future.R | 2 future-0.9.0/future/R/globals.R | 44 +-- future-0.9.0/future/R/lazy.R | 2 future-0.9.0/future/R/multicore.R | 2 future-0.9.0/future/R/plan.R | 5 future-0.9.0/future/R/tweakExpression.R |only future-0.9.0/future/R/utils.R | 5 future-0.9.0/future/build/vignette.rds |binary future-0.9.0/future/inst/doc/future-issues.html |only future-0.9.0/future/inst/doc/future-issues.md.rsp |only future-0.9.0/future/inst/doc/future.html | 22 + future-0.9.0/future/inst/doc/future.md.rsp | 21 + future-0.9.0/future/man/EagerFuture-class.Rd | 4 future-0.9.0/future/man/Future-class.Rd | 4 future-0.9.0/future/man/LazyFuture-class.Rd | 4 future-0.9.0/future/man/MulticoreFuture-class.Rd | 6 future-0.9.0/future/man/availableCores.Rd | 2 future-0.9.0/future/man/eager.Rd | 4 future-0.9.0/future/man/future.Rd | 6 future-0.9.0/future/man/futureAssign.Rd | 2 future-0.9.0/future/man/futureOf.Rd | 2 future-0.9.0/future/man/grapes-plan-grapes.Rd | 4 future-0.9.0/future/man/lazy.Rd | 4 future-0.9.0/future/man/multicore.Rd | 4 future-0.9.0/future/man/plan.Rd | 8 future-0.9.0/future/man/requestCore.Rd | 6 future-0.9.0/future/man/resolved.Future.Rd | 4 future-0.9.0/future/man/supportsMulticore.Rd | 2 future-0.9.0/future/man/usedCores.Rd | 2 future-0.9.0/future/man/value.Future.Rd | 4 future-0.9.0/future/tests/demo.R | 2 future-0.9.0/future/tests/dotdotdot.R | 2 future-0.9.0/future/tests/futureAssign_OP.R | 175 ++++++++------ future-0.9.0/future/tests/globals,tricky.R | 249 ++++++++++++--------- future-0.9.0/future/tests/globalsOf,tweaks.R | 6 future-0.9.0/future/tests/multicore.R | 2 future-0.9.0/future/tests/rng.R |only future-0.9.0/future/vignettes/future-issues.md.rsp |only future-0.9.0/future/vignettes/future.md.rsp | 21 + 53 files changed, 464 insertions(+), 334 deletions(-)
Title: Estimation in Dual Frame Surveys
Description: Point and interval estimation in dual frame surveys. In contrast
to classic sampling theory, where only one sampling frame is considered,
dual frame methodology assumes that there are two frames available for
sampling and that, overall, they cover the entire target population. Then,
two probability samples (one from each frame) are drawn and information
collected is suitably combined to get estimators of the parameter of
interest.
Author: Antonio Arcos <arcos@ugr.es>, Maria del Mar Rueda <mrueda@ugr.es>,
Maria Giovanna Ranalli <giovanna.ranalli@stat.unipg.it> and David Molina
<dmolinam@ugr.es>
Maintainer: David Molina <dmolinam@ugr.es>
Diff between Frames2 versions 0.1.2 dated 2015-10-19 and 0.2.1 dated 2015-12-12
DESCRIPTION | 11 ++-- MD5 | 107 +++++++++++++++++++++++++++--------------- NAMESPACE | 17 ++++++ R/DatMA.R |only R/DatMB.R |only R/DatPopM.R |only R/JackMLCDF.R |only R/JackMLCDW.R |only R/JackMLCSW.R |only R/JackMLDF.R |only R/JackMLDW.R |only R/JackMLSW.R |only R/MLCDF.R |only R/MLCDW.R |only R/MLCSW.R |only R/MLDF.R |only R/MLDW.R |only R/MLSW.R |only R/internal.R | 13 ++++- data/DatMA.txt.gz |only data/DatMB.txt.gz |only data/DatPopM.txt.gz |only inst/doc/estimation.Rnw | 2 inst/doc/estimation.pdf |binary inst/doc/formatting.data.Rnw | 2 inst/doc/formatting.data.pdf |binary man/BKA.Rd | 24 ++++----- man/CalDF.Rd | 30 +++++------ man/CalSF.Rd | 32 ++++++------ man/Compare.Rd | 12 ++-- man/CovHT.Rd | 5 - man/Dat.Rd | 6 +- man/DatA.Rd | 4 - man/DatB.Rd | 4 - man/DatMA.Rd |only man/DatMB.Rd |only man/DatPopM.Rd |only man/Domains.Rd | 2 man/FB.Rd | 8 +-- man/HT.Rd | 2 man/Hartley.Rd | 6 +- man/JackBKA.Rd | 12 ++-- man/JackCalDF.Rd | 14 ++--- man/JackCalSF.Rd | 20 +++---- man/JackFB.Rd | 8 +-- man/JackHartley.Rd | 8 +-- man/JackMLCDF.Rd |only man/JackMLCDW.Rd |only man/JackMLCSW.Rd |only man/JackMLDF.Rd |only man/JackMLDW.Rd |only man/JackMLSW.Rd |only man/JackPEL.Rd | 8 +-- man/JackPML.Rd | 12 ++-- man/JackSFRR.Rd | 22 ++++---- man/MLCDF.Rd |only man/MLCDW.Rd |only man/MLCSW.Rd |only man/MLDF.Rd |only man/MLDW.Rd |only man/MLSW.Rd |only man/PEL.Rd | 26 +++++----- man/PML.Rd | 10 +-- man/PiklA.Rd | 3 - man/PiklB.Rd | 3 - man/SFRR.Rd | 16 +++--- man/VarHT.Rd | 3 - man/WeightsCalDF.Rd | 26 +++++----- man/WeightsCalSF.Rd | 28 +++++----- vignettes/estimation.Rnw | 2 vignettes/formatting.data.Rnw | 2 71 files changed, 288 insertions(+), 222 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.6 dated 2015-11-30 and 1.7 dated 2015-12-12
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NEWS | 6 ++++++ R/anthrCases.R | 3 ++- R/trimmOutl.R | 8 ++++---- inst/doc/Anthropometry.Rnw | 12 ++++++------ inst/doc/Anthropometry.pdf |binary man/Anthropometry-package.Rd | 4 ++-- man/LloydShapes.Rd | 12 ++++++------ man/USAFSurvey.Rd | 4 ++-- man/anthrCases.Rd | 12 ++++++------ man/projShapes.Rd | 10 +++++----- man/shapes3dShapes.Rd | 12 ++++++------ man/trimmOutl.Rd | 12 ++++++------ man/trimmedLloydShapes.Rd | 12 ++++++------ src/cast.c | 41 +++++++++++------------------------------ vignettes/Anthropometry.Rnw | 12 ++++++------ vignettes/hipam1.pdf |binary vignettes/hipam2.pdf |binary vignettes/trimowa1.pdf |binary vignettes/trimowa2.pdf |binary 21 files changed, 98 insertions(+), 110 deletions(-)
Title: Parametric Bootstrap and Kenward-Roger-Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-3 dated 2015-12-10 and 0.4-4 dated 2015-12-12
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
lme4 package.
The package implements a parametric bootstrap test and a Kenward-Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
DESCRIPTION | 10 +++---
MD5 | 30 +++++++++---------
NAMESPACE | 31 +++++++++++++------
R/KR-Sigma-G2.R | 6 +--
R/KR-init-modcomp.R | 2 -
R/KR-modcomp.R | 2 -
R/KR-vcovAdj.R | 2 -
R/PB-modcomp.R | 2 -
R/PB-refdist.R | 2 -
R/PB-utils.R | 4 +-
R/modelCoercion.R | 4 +-
inst/doc/pbkrtest-introduction.pdf |binary
man/KRmodcomp.Rd | 4 +-
man/PBmodcomp.Rd | 9 ++++-
man/pbkrtest-internal.Rd | 59 +++++++++++++++++--------------------
man/vcovAdj.Rd | 5 +--
16 files changed, 94 insertions(+), 78 deletions(-)
Title: R Functions to Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned
online by Google Trends is provided. Trends (number of hits) over the time as
well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.3.0 dated 2015-11-28 and 1.3.1 dated 2015-12-12
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 26 - NEWS.md | 12 R/countries.R | 26 - R/gtrends.R | 1163 ++++++++++++++++++++++++++++------------------------- R/init.R | 32 - R/sport_trend.R | 64 +- README.md | 107 ++-- man/countries.Rd | 36 - man/gconnect.Rd | 110 ++--- man/gtrends.Rd | 187 ++++---- man/sport_trend.Rd | 84 +-- 13 files changed, 986 insertions(+), 893 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant <bjgrant@umich.edu>
Diff between bio3d versions 2.2-3 dated 2015-09-04 and 2.2-4 dated 2015-12-12
DESCRIPTION | 12 +++++------ MD5 | 26 ++++++++++++------------ R/clean.pdb.R | 16 +++++++-------- R/cmap.pdb.R | 2 - R/dm.xyz.R | 5 +++- R/hmmer.R | 31 ++++++++--------------------- R/read.ncdf.R | 44 ++++++++++++++++++++--------------------- R/read.pdb.R | 5 ++++ R/write.ncdf.R | 54 +++++++++++++++++++++++++-------------------------- data/aa.table.rda |binary data/atom.index.rda |binary man/bio3d.package.Rd | 4 +-- man/read.ncdf.Rd | 2 - man/write.ncdf.Rd | 2 - 14 files changed, 99 insertions(+), 104 deletions(-)
Title: Semiparametric Maximum Likelihood Method for Interactions
Gene-Environment in Case-Mother Control-Mother Designs
Description: Implements the method of general semiparametric maximum likelihood estimation for logistic models in case-mother control-mother designs.
Author: Moliere Nguile-Makao [aut, cre], Alexandre Bureau [aut]
Maintainer: Moliere Nguile-Makao <moliere.nguile@gmail.com>
Diff between SPmlficmcm versions 1.3 dated 2014-12-08 and 1.4 dated 2015-12-11
DESCRIPTION | 19 ++- MD5 | 36 +++--- NAMESPACE | 3 R/Est.Inpar.R | 2 R/Nlsysteq.R | 2 R/SPmlficmcm-internal.R | 250 +++++++++++++++++++++++----------------------- R/Spmlficmcm.R | 10 - R/fct_invCap.R | 2 R/fgp_mf1.R | 1 R/fpol1.R | 2 R/fpolm.R | 2 R/ft_gradientCas1.R | 16 +- R/ft_gradientCasM.R | 38 +++--- R/ft_likhoodCas1.R | 2 R/ft_likhoodCasM.R | 14 +- build |only inst |only man/Est.Inpar.Rd | 22 +--- man/SPmlficmcm-package.Rd | 26 ++-- man/Spmlficmcm.Rd | 4 20 files changed, 228 insertions(+), 223 deletions(-)
Title: Ranking-Based Variable Selection
Description: Implements the Ranking-Based Variable Selection
algorithm for variable selection in high-dimensional data.
Author: Rafal Baranowski, Patrick Breheny, Isaac Turner
Maintainer: Rafal Baranowski <r.baranowski@lse.ac.uk>
Diff between rbvs versions 1.0.1 dated 2015-12-10 and 1.0.2 dated 2015-12-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/sort_r.h | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which statistical data are
visualized. This package offers a flexible, layer-based, way to create thematic
maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.0 dated 2015-05-28 and 1.2 dated 2015-12-11
tmap-1.0/tmap/R/get_alpha_col.R |only tmap-1.0/tmap/R/legend_plot.R |only tmap-1.2/tmap/DESCRIPTION | 34 + tmap-1.2/tmap/MD5 | 205 +++++---- tmap-1.2/tmap/NAMESPACE | 140 ++++++ tmap-1.2/tmap/NEWS | 23 + tmap-1.2/tmap/R/animation_tmap.R | 49 -- tmap-1.2/tmap/R/append_data.R | 6 tmap-1.2/tmap/R/approx_areas.R | 3 tmap-1.2/tmap/R/bb.R |only tmap-1.2/tmap/R/calc_densities.R | 1 tmap-1.2/tmap/R/cat2pal.R | 11 tmap-1.2/tmap/R/end_of_the_world.R |only tmap-1.2/tmap/R/get_asp_ratio.R | 17 tmap-1.2/tmap/R/get_proj4_code.R | 78 ++- tmap-1.2/tmap/R/get_raster_data.R | 3 tmap-1.2/tmap/R/get_sepia_col.R |only tmap-1.2/tmap/R/grid_shp.R | 89 ++++ tmap-1.2/tmap/R/gridplot.R | 3 tmap-1.2/tmap/R/is_projected.R | 2 tmap-1.2/tmap/R/itmap.R |only tmap-1.2/tmap/R/kde2D.R |only tmap-1.2/tmap/R/legend_hist.R | 16 tmap-1.2/tmap/R/legend_prepare.R | 90 +--- tmap-1.2/tmap/R/lines_midpoints.R |only tmap-1.2/tmap/R/map2scale.R | 44 +- tmap-1.2/tmap/R/map_coloring.R |only tmap-1.2/tmap/R/meta_plot.R |only tmap-1.2/tmap/R/num2pal.R | 290 +++++++++---- tmap-1.2/tmap/R/onLoad.R |only tmap-1.2/tmap/R/one_line_per_lines.R |only tmap-1.2/tmap/R/pkg.R | 142 +++++- tmap-1.2/tmap/R/plot_all.R |only tmap-1.2/tmap/R/plot_map.R | 626 ++++++++++++------------------ tmap-1.2/tmap/R/plot_misc_functions.R |only tmap-1.2/tmap/R/pointLabelGrid.R |only tmap-1.2/tmap/R/print_tmap.R | 163 ++++++- tmap-1.2/tmap/R/process_bubbles.R | 169 ++------ tmap-1.2/tmap/R/process_col_vector.R |only tmap-1.2/tmap/R/process_color.R |only tmap-1.2/tmap/R/process_data.R | 2 tmap-1.2/tmap/R/process_fill.R | 166 +++---- tmap-1.2/tmap/R/process_layers.R | 43 +- tmap-1.2/tmap/R/process_lines.R | 150 +++---- tmap-1.2/tmap/R/process_meta.R | 87 +++- tmap-1.2/tmap/R/process_raster.R | 143 ++++-- tmap-1.2/tmap/R/process_shapes.R | 164 +++---- tmap-1.2/tmap/R/process_text.R | 386 +++++++++++++++--- tmap-1.2/tmap/R/process_tm.R | 155 +++++-- tmap-1.2/tmap/R/qtm.R | 64 ++- tmap-1.2/tmap/R/read_GPX.R |only tmap-1.2/tmap/R/read_osm.R |only tmap-1.2/tmap/R/read_shape.R | 3 tmap-1.2/tmap/R/sample_dots.R |only tmap-1.2/tmap/R/save_tmap.R |only tmap-1.2/tmap/R/sbind.R | 5 tmap-1.2/tmap/R/set_projection.R | 70 +-- tmap-1.2/tmap/R/smooth_map.R |only tmap-1.2/tmap/R/smooth_raster_cover.R |only tmap-1.2/tmap/R/split_g.R |only tmap-1.2/tmap/R/split_shps.R | 25 - tmap-1.2/tmap/R/split_tm.R | 6 tmap-1.2/tmap/R/style_catalogue.R |only tmap-1.2/tmap/R/tm_layers.R | 361 ++++++++++++----- tmap-1.2/tmap/R/tm_layout.R | 262 +++++++++++- tmap-1.2/tmap/R/tm_misc_elements.R | 104 +++- tmap-1.2/tmap/R/tm_shape.R | 41 - tmap-1.2/tmap/R/to_raster.R |only tmap-1.2/tmap/build/vignette.rds |binary tmap-1.2/tmap/data/Europe.rda |binary tmap-1.2/tmap/data/NLD_muni.rda |binary tmap-1.2/tmap/data/NLD_prov.rda |binary tmap-1.2/tmap/data/World.rda |binary tmap-1.2/tmap/data/land.rda |binary tmap-1.2/tmap/data/rivers.rda |binary tmap-1.2/tmap/inst/doc/tmap-nutshell.Rmd | 2 tmap-1.2/tmap/inst/doc/tmap-nutshell.html | 6 tmap-1.2/tmap/man/Shapes.Rd | 6 tmap-1.2/tmap/man/animation_tmap.Rd | 49 +- tmap-1.2/tmap/man/append_data.Rd | 2 tmap-1.2/tmap/man/approx_areas.Rd | 2 tmap-1.2/tmap/man/bb.Rd |only tmap-1.2/tmap/man/calc_densities.Rd | 4 tmap-1.2/tmap/man/get_IDs.Rd | 2 tmap-1.2/tmap/man/get_asp_ratio.Rd | 11 tmap-1.2/tmap/man/get_proj4.Rd |only tmap-1.2/tmap/man/itmap.Rd |only tmap-1.2/tmap/man/land.Rd | 2 tmap-1.2/tmap/man/map_coloring.Rd |only tmap-1.2/tmap/man/metro.Rd | 2 tmap-1.2/tmap/man/plus-.tmap.Rd | 2 tmap-1.2/tmap/man/points_to_raster.Rd |only tmap-1.2/tmap/man/poly_to_raster.Rd |only tmap-1.2/tmap/man/polygons.Rd | 98 ++-- tmap-1.2/tmap/man/print.tmap.Rd | 5 tmap-1.2/tmap/man/qtm.Rd | 38 + tmap-1.2/tmap/man/read_GPX.Rd |only tmap-1.2/tmap/man/read_osm.Rd |only tmap-1.2/tmap/man/read_shape.Rd | 8 tmap-1.2/tmap/man/rivers.Rd | 2 tmap-1.2/tmap/man/sample_dots.Rd |only tmap-1.2/tmap/man/save_tmap.Rd |only tmap-1.2/tmap/man/sbind.Rd | 2 tmap-1.2/tmap/man/set_projection.Rd | 46 +- tmap-1.2/tmap/man/smooth_map.Rd |only tmap-1.2/tmap/man/smooth_raster_cover.Rd |only tmap-1.2/tmap/man/split_shapes.Rd | 16 tmap-1.2/tmap/man/style_catalogue.Rd |only tmap-1.2/tmap/man/tm_bubbles.Rd | 87 ++-- tmap-1.2/tmap/man/tm_compass.Rd |only tmap-1.2/tmap/man/tm_credits.Rd | 26 - tmap-1.2/tmap/man/tm_facets.Rd | 24 - tmap-1.2/tmap/man/tm_grid.Rd | 25 - tmap-1.2/tmap/man/tm_iso.Rd |only tmap-1.2/tmap/man/tm_layout.Rd | 293 +++++++++++--- tmap-1.2/tmap/man/tm_lines.Rd | 73 ++- tmap-1.2/tmap/man/tm_raster.Rd | 69 +-- tmap-1.2/tmap/man/tm_scale_bar.Rd | 21 - tmap-1.2/tmap/man/tm_shape.Rd | 53 -- tmap-1.2/tmap/man/tm_text.Rd | 124 +++++ tmap-1.2/tmap/man/tmap-element.Rd | 105 ----- tmap-1.2/tmap/man/tmap-package.Rd | 131 +++++- tmap-1.2/tmap/man/write_shape.Rd | 2 tmap-1.2/tmap/vignettes/tmap-nutshell.Rmd | 235 +++++++---- 124 files changed, 3891 insertions(+), 2123 deletions(-)
Title: Functions to Parse and Create XMCDA Files
Description: Functions which allow to read many XMCDA tags and transform them into R variables which are then usable in MCDA algorithms written in R. It also allows to write certain R variables into XML files respecting the XMCDA standard.
Author: Patrick Meyer and Sebastien Bigaret, with contributions from Krzysztof Ciomek.
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between RXMCDA versions 1.5.3 dated 2014-06-12 and 1.5.5 dated 2015-12-11
DESCRIPTION | 12 +-- MD5 | 12 +-- NAMESPACE | 6 - R/libxmcda.R | 98 ++++++++++++++++++++++----- inst/extdata/XMCDA-2.2.1.xsd |only man/putAlternativesAffectationsWithValues.Rd |only man/putCategoriesValues.Rd | 4 - tests/getParameters.R | 25 ++++++ 8 files changed, 122 insertions(+), 35 deletions(-)
Title: Pretty Heatmaps
Description: Implementation of heatmaps that offers more control
over dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde <rkolde@gmail.com>
Diff between pheatmap versions 1.0.7 dated 2015-07-02 and 1.0.8 dated 2015-12-11
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS | 6 ++++ R/pheatmap.r | 79 +++++++++++++++++++++++++++++++++++++------------------- man/pheatmap.Rd | 33 ++++++++++++++--------- 5 files changed, 86 insertions(+), 46 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 0.1 dated 2015-10-29 and 0.2 dated 2015-12-11
DESCRIPTION | 22 ++++-- MD5 | 77 ++++++++++++------------ NAMESPACE | 17 +++-- R/DNE.R | 5 + R/DNE3d.R | 117 +++++++------------------------------ R/DNE_Legend.R |only R/OPC.R | 2 R/OPC3d.R | 117 ++++++++++++++++++++++++++----------- R/OPCr.R | 7 +- R/RFI.R | 5 + R/RFI3d.R | 5 + R/compute_energy_per_face.R | 6 + R/edge_vertices.R | 4 - R/index_paired_directed_faces.R | 4 - R/read.AVIZO.ply.R | 8 +- R/remove_outliers.R | 4 - build/molaR.pdf |only build/vignette.rds |binary man/DNE.Rd | 14 ++-- man/DNE3d.Rd | 29 ++++----- man/DNE_Legend.Rd |only man/Directional_Bins.Rd | 2 man/Equal_Vertex_Normals.Rd | 2 man/Face_Normals.Rd | 2 man/OPC.Rd | 16 ++--- man/OPC3d.Rd | 36 +++++++---- man/OPCr.Rd | 20 +++--- man/RFI.Rd | 6 - man/RFI3d.Rd | 14 ++-- man/clustered_patches.Rd | 2 man/compute_energy_per_face.Rd | 4 - man/edge_vertices.Rd | 4 - man/face_areas.Rd | 4 - man/index_paired_directed_faces.Rd | 4 - man/patch_details.Rd | 2 man/patches_for_each_direction.Rd | 2 man/patches_per.Rd | 2 man/read.AVIZO.ply.Rd | 12 +-- man/remove_boundary_faces.Rd | 2 man/remove_outliers.Rd | 4 - man/vertex_to_face_list.Rd | 2 41 files changed, 312 insertions(+), 273 deletions(-)
Title: Digital PCR Analysis
Description: Analysis, visualisation and simulation of digital polymerase chain
reaction (dPCR).
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut],
Bart Jacobs [aut],
Piotr Sobczyk [ctb]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between dpcR versions 0.1.4.0 dated 2015-04-09 and 0.2 dated 2015-12-11
dpcR-0.1.4.0/dpcR/R/adpcr-class.R |only dpcR-0.1.4.0/dpcR/R/ddpcr-class.R |only dpcR-0.1.4.0/dpcR/R/qpcrpp.R |only dpcR-0.1.4.0/dpcR/man/plot.qpcrpp.Rd |only dpcR-0.1.4.0/dpcR/man/qpcrpp-class.Rd |only dpcR-0.2/dpcR/CHANGELOG | 100 + dpcR-0.2/dpcR/DESCRIPTION | 45 dpcR-0.2/dpcR/MD5 | 271 +++-- dpcR-0.2/dpcR/NAMESPACE | 150 +- dpcR-0.2/dpcR/R/AUCtest.R | 136 +- dpcR-0.2/dpcR/R/White.R |only dpcR-0.2/dpcR/R/adpcr2panel.R |only dpcR-0.2/dpcR/R/adpcr2ppp.R | 146 +- dpcR-0.2/dpcR/R/binarize.R | 92 - dpcR-0.2/dpcR/R/bind_dpcr.R | 343 +++--- dpcR-0.2/dpcR/R/bioamp.R | 152 +- dpcR-0.2/dpcR/R/calc_breaks.R | 24 dpcR-0.2/dpcR/R/calc_coordinates.R |only dpcR-0.2/dpcR/R/calc_lambda.R | 40 dpcR-0.2/dpcR/R/classes.R |only dpcR-0.2/dpcR/R/compare_dens.R | 120 +- dpcR-0.2/dpcR/R/count_test-class.R | 292 ++--- dpcR-0.2/dpcR/R/create_dpcr.R | 148 +- dpcR-0.2/dpcR/R/dPCRmethyl.R |only dpcR-0.2/dpcR/R/dpcR-package.R | 133 +- dpcR-0.2/dpcR/R/dpcReport_gui.R |only dpcR-0.2/dpcR/R/dpcr_calculator.R | 33 dpcR-0.2/dpcR/R/dpcr_density.R | 256 +---- dpcR-0.2/dpcR/R/dpcr_density_gui.R | 25 dpcR-0.2/dpcR/R/dpcr_density_table.R |only dpcR-0.2/dpcR/R/extract_dpcr.R | 131 +- dpcR-0.2/dpcR/R/fit_adpcr.R | 62 - dpcR-0.2/dpcR/R/fl.R | 2 dpcR-0.2/dpcR/R/get_k_n.R | 24 dpcR-0.2/dpcR/R/limit_cq.R | 335 +++--- dpcR-0.2/dpcR/R/many_peaks.R | 38 dpcR-0.2/dpcR/R/moments.R | 233 +--- dpcR-0.2/dpcR/R/num2int.R | 40 dpcR-0.2/dpcR/R/pds.R | 189 +-- dpcR-0.2/dpcR/R/pds_raw.R | 250 ++-- dpcR-0.2/dpcR/R/plot_distr.R | 92 - dpcR-0.2/dpcR/R/plot_panel.R | 304 ++--- dpcR-0.2/dpcR/R/plot_vf_circ.R | 6 dpcR-0.2/dpcR/R/plot_vic_fam.R | 260 ++--- dpcR-0.2/dpcR/R/print_summary.R | 56 - dpcR-0.2/dpcR/R/qdpcr.R |only dpcR-0.2/dpcR/R/qpcr2pp.R |only dpcR-0.2/dpcR/R/qpcr_analyser.R | 320 +++--- dpcR-0.2/dpcR/R/read_dpcr.R |only dpcR-0.2/dpcR/R/rename_dpcr.R |only dpcR-0.2/dpcR/R/rtadpcr.R | 62 - dpcR-0.2/dpcR/R/safe_efficiency.R | 20 dpcR-0.2/dpcR/R/show_dpcr.R | 85 - dpcR-0.2/dpcR/R/sim_adpcr.R | 199 +-- dpcR-0.2/dpcR/R/sim_ddpcr.R | 182 +-- dpcR-0.2/dpcR/R/sim_ddpcr_bkm.R | 596 +++++------ dpcR-0.2/dpcR/R/simulations.R | 129 +- dpcR-0.2/dpcR/R/six_panels.R |only dpcR-0.2/dpcR/R/summary_dpcr.R | 217 ++-- dpcR-0.2/dpcR/R/test_counts.R | 430 ++++---- dpcR-0.2/dpcR/R/test_counts_gui.R | 22 dpcR-0.2/dpcR/R/test_panel.R | 117 +- dpcR-0.2/dpcR/R/test_peaks.R | 210 ++-- dpcR-0.2/dpcR/R/test_ratio.R | 306 +++--- dpcR-0.2/dpcR/R/valid_amp.R | 10 dpcR-0.2/dpcR/R/y_val_conf.R | 26 dpcR-0.2/dpcR/README.md | 56 - dpcR-0.2/dpcR/build/vignette.rds |binary dpcR-0.2/dpcR/data/White.rda |only dpcR-0.2/dpcR/data/dPCRmethyl.rda |only dpcR-0.2/dpcR/data/datalist | 9 dpcR-0.2/dpcR/data/many_peaks.rda |binary dpcR-0.2/dpcR/data/pds.rda |binary dpcR-0.2/dpcR/data/pds_raw.rda |binary dpcR-0.2/dpcR/data/six_panels.rda |only dpcR-0.2/dpcR/inst/CITATION |only dpcR-0.2/dpcR/inst/doc/overview.R | 291 ++++- dpcR-0.2/dpcR/inst/doc/overview.Rmd | 531 ++++++++-- dpcR-0.2/dpcR/inst/doc/overview.html | 1319 +++++++++++++++++++------- dpcR-0.2/dpcR/inst/dpcReport |only dpcR-0.2/dpcR/inst/dpcr_density_gui/server.R | 146 +- dpcR-0.2/dpcR/inst/dpcr_density_gui/ui.R | 48 dpcR-0.2/dpcR/inst/test_counts_gui/readme.md | 20 dpcR-0.2/dpcR/inst/test_counts_gui/server.R | 90 - dpcR-0.2/dpcR/inst/test_counts_gui/ui.R | 54 - dpcR-0.2/dpcR/man/White.Rd |only dpcR-0.2/dpcR/man/adpcr-class.Rd | 117 +- dpcR-0.2/dpcR/man/adpcr2panel.Rd |only dpcR-0.2/dpcR/man/adpcr2ppp.Rd | 124 +- dpcR-0.2/dpcR/man/binarize.Rd | 71 - dpcR-0.2/dpcR/man/bind_dpcr-methods.Rd | 131 +- dpcR-0.2/dpcR/man/bioamp.Rd | 104 +- dpcR-0.2/dpcR/man/calc_coordinates.Rd |only dpcR-0.2/dpcR/man/compare_dens.Rd | 73 - dpcR-0.2/dpcR/man/count_test-class.Rd | 133 +- dpcR-0.2/dpcR/man/create_dpcr.Rd | 156 +-- dpcR-0.2/dpcR/man/dPCRmethyl.Rd |only dpcR-0.2/dpcR/man/ddpcr-class.Rd | 97 - dpcR-0.2/dpcR/man/dpcR-package.Rd | 120 +- dpcR-0.2/dpcR/man/dpcReport.Rd |only dpcR-0.2/dpcR/man/dpcr-class.Rd |only dpcR-0.2/dpcR/man/dpcr_density.Rd | 209 +--- dpcR-0.2/dpcR/man/dpcr_density_gui.Rd | 46 dpcR-0.2/dpcR/man/dpcr_density_table.Rd |only dpcR-0.2/dpcR/man/extract_dpcr.Rd | 116 +- dpcR-0.2/dpcR/man/limit_cq.Rd | 194 +-- dpcR-0.2/dpcR/man/many_peaks.Rd | 44 dpcR-0.2/dpcR/man/moments-methods.Rd | 131 +- dpcR-0.2/dpcR/man/num2int.Rd | 44 dpcR-0.2/dpcR/man/pds.Rd | 209 +--- dpcR-0.2/dpcR/man/pds_raw.Rd | 271 ++--- dpcR-0.2/dpcR/man/plot.qdpcr.Rd |only dpcR-0.2/dpcR/man/plot_panel.Rd | 231 ++-- dpcR-0.2/dpcR/man/plot_vic_fam.Rd | 146 +- dpcR-0.2/dpcR/man/qdpcr-class.Rd |only dpcR-0.2/dpcR/man/qpcr2pp.Rd | 200 ++- dpcR-0.2/dpcR/man/qpcr_analyser.Rd | 226 ++-- dpcR-0.2/dpcR/man/read_BioMark.Rd |only dpcR-0.2/dpcR/man/read_QX100.Rd |only dpcR-0.2/dpcR/man/read_dpcr.Rd |only dpcR-0.2/dpcR/man/read_raw.Rd |only dpcR-0.2/dpcR/man/rename_dpcr.Rd |only dpcR-0.2/dpcR/man/rtadpcr-class.Rd | 74 - dpcR-0.2/dpcR/man/show-methods.Rd | 80 - dpcR-0.2/dpcR/man/sim_adpcr.Rd | 232 ++-- dpcR-0.2/dpcR/man/sim_ddpcr.Rd | 174 +-- dpcR-0.2/dpcR/man/six_panels.Rd |only dpcR-0.2/dpcR/man/summary-methods.Rd | 183 +-- dpcR-0.2/dpcR/man/test_counts.Rd | 163 +-- dpcR-0.2/dpcR/man/test_counts_gui.Rd | 46 dpcR-0.2/dpcR/man/test_panel.Rd | 167 +-- dpcR-0.2/dpcR/man/test_peaks.Rd | 176 +-- dpcR-0.2/dpcR/man/test_ratio.Rd | 202 ++- dpcR-0.2/dpcR/vignettes/adpcr_comp.RData |only dpcR-0.2/dpcR/vignettes/coverage_poster.RData |only dpcR-0.2/dpcR/vignettes/dpcr.bib |only dpcR-0.2/dpcR/vignettes/overview.Rmd | 531 ++++++++-- dpcR-0.2/dpcR/vignettes/vig.RData |only 138 files changed, 8474 insertions(+), 6770 deletions(-)
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Title: Functions for Calculating Tolerance Intervals
Description: Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits for various distributions. Plotting is also available for tolerance limits of continuous random variables.
Author: Derek S. Young [aut, cre]
Maintainer: Derek S. Young <derek.young@uky.edu>
Diff between tolerance versions 1.1.0 dated 2015-04-15 and 1.1.1 dated 2015-12-11
DESCRIPTION | 13 +-- MD5 | 22 +++-- NAMESPACE | 17 ++++ NEWS | 8 ++ R/bayesnormtolint.R |only R/exttolint.R | 20 +++-- R/negbintolint.R | 173 +++++++++++++++++++++++++++++------------------ R/normss.R |only man/bayesnormtolint.Rd |only man/normss.Rd |only man/poislindll.Rd | 82 +++++++++++----------- man/poislindtolint.Rd | 2 man/tolerance.package.Rd | 82 +++++++++++----------- man/zmll.Rd | 128 +++++++++++++++++----------------- 14 files changed, 314 insertions(+), 233 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.6 dated 2015-09-16 and 0.20.1 dated 2015-12-11
DESCRIPTION | 8 - MD5 | 16 +-- R/export_functions.r | 130 +++++++++++++-------------- R/methods_class_dataObj.r | 18 +++ R/methods_class_dimVar.r | 4 R/methods_class_sdcProblem.r | 4 inst/doc/sdcTable.pdf |binary man/protectLinkedTables.Rd | 2 src/suppMultDimTable.cpp | 203 ++++++++++++++++++++++--------------------- 9 files changed, 205 insertions(+), 180 deletions(-)
Title: Statistical Analysis of Fuzzy Data
Description: The aim of the package is to provide some basic functions
for doing statistics with one dimensional Fuzzy Data (in the
form of polygonal fuzzy numbers). In particular, the package
contains functions for the basic operations on the class of
fuzzy numbers (sum, scalar product, mean, median, Hukuhara difference)
as well as for calculating (Bertoluzza) distance,
sample variance, sample covariance, and the
Dempster-Shafer (levelwise) histogram. Moreover a function to
simulate fuzzy random variables, bootstrap tests for the
equality of means, and a function to do linear regression given
trapezoidal fuzzy data is included. Version 1.0 fixes some bugs
of previous versions.
Author: Wolfgang Trutschnig <wolfgang@trutschnig.net>, Asun Lubiano
<lubiano@uniovi.es>
Maintainer: Asun Lubiano <lubiano@uniovi.es>
Diff between SAFD versions 1.0 dated 2015-07-17 and 1.0-1 dated 2015-12-11
DESCRIPTION | 8 +- MD5 | 84 ++++++++++++++--------------- NAMESPACE | 2 R/DSfrequency.R | 12 ++-- R/DShistogram.R | 6 +- R/Fmedian.R | 14 ++-- R/Mmean.R | 12 ++-- R/Msum.R | 12 ++-- R/bertoluzza.R | 2 R/btest.mean.R | 12 ++-- R/btest2.mean.R | 13 ++-- R/btestk.mean.R | 11 +-- R/checking.R | 23 ++++---- R/hukuhara.R | 12 ++-- R/sc_mult.R | 6 +- R/translator.R | 6 +- data/Trees.rda |binary data/XX.rda |binary data/quality.rda |binary man/Bcov.Rd | 66 ----------------------- man/Bvar.Rd | 22 ------- man/DSfrequency.Rd | 99 ---------------------------------- man/DShistogram.Rd | 146 +-------------------------------------------------- man/Fmedian.Rd | 50 +---------------- man/Mmean.Rd | 31 ---------- man/Msum.Rd | 78 --------------------------- man/SAFD-package.Rd | 4 - man/Trees.Rd | 5 + man/XX.Rd | 2 man/bertoluzza.Rd | 44 +-------------- man/btest.mean.Rd | 60 +-------------------- man/btest2.mean.Rd | 80 +--------------------------- man/btestk.mean.Rd | 148 ---------------------------------------------------- man/checking.Rd | 92 -------------------------------- man/checking2.Rd | 81 ---------------------------- man/decomposer.Rd | 19 ------ man/defuzzify.Rd | 26 --------- man/generator.Rd | 100 ----------------------------------- man/hukuhara.Rd | 45 +-------------- man/lrmodel.Rd | 112 --------------------------------------- man/quality.Rd | 4 - man/sc_mult.Rd | 46 +--------------- man/translator.Rd | 50 +---------------- 43 files changed, 173 insertions(+), 1472 deletions(-)
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.1.0 dated 2015-05-28 and 2.2.0 dated 2015-12-11
R.utils-2.1.0/R.utils/.Rinstignore |only R.utils-2.2.0/R.utils/DESCRIPTION | 8 R.utils-2.2.0/R.utils/MD5 | 66 +-- R.utils-2.2.0/R.utils/NAMESPACE | 25 + R.utils-2.2.0/R.utils/NEWS | 32 + R.utils-2.2.0/R.utils/R/Arguments.R | 56 -- R.utils-2.2.0/R.utils/R/GString-class.R | 1 R.utils-2.2.0/R.utils/R/commandArgs.R | 28 + R.utils-2.2.0/R.utils/R/compressFile.R | 10 R.utils-2.2.0/R.utils/R/compressPDF.R | 286 ++++++------- R.utils-2.2.0/R.utils/R/downloadFile.R | 2 R.utils-2.2.0/R.utils/R/extract.array.R | 5 R.utils-2.2.0/R.utils/R/loadObject.R | 42 + R.utils-2.2.0/R.utils/R/mkdirs.R | 114 ++++- R.utils-2.2.0/R.utils/R/resample.R | 8 R.utils-2.2.0/R.utils/R/resetWarnings.R | 16 R.utils-2.2.0/R.utils/R/saveObject.R | 58 +- R.utils-2.2.0/R.utils/R/seqToHumanReadable.R | 89 ++-- R.utils-2.2.0/R.utils/R/seqToIntervals.R | 1 R.utils-2.2.0/R.utils/R/withTimeout.R | 2 R.utils-2.2.0/R.utils/R/writeDataFrame.R | 22 + R.utils-2.2.0/R.utils/man/commandArgs.Rd | 13 R.utils-2.2.0/R.utils/man/compressFile.Rd | 6 R.utils-2.2.0/R.utils/man/getWritablePathname.Arguments.Rd | 15 R.utils-2.2.0/R.utils/man/loadObject.Rd | 7 R.utils-2.2.0/R.utils/man/mkdirs.Rd | 18 R.utils-2.2.0/R.utils/man/resample.Rd | 2 R.utils-2.2.0/R.utils/man/resetWarnings.Rd | 35 - R.utils-2.2.0/R.utils/man/saveObject.Rd | 4 R.utils-2.2.0/R.utils/man/seqToHumanReadable.Rd | 11 R.utils-2.2.0/R.utils/tests/GString.R | 3 R.utils-2.2.0/R.utils/tests/loadObject.R | 34 + R.utils-2.2.0/R.utils/tests/mkdirs.R | 55 ++ R.utils-2.2.0/R.utils/tests/seqToHumanReadable.R | 43 + R.utils-2.2.0/R.utils/tests/withTimeout.R | 21 35 files changed, 740 insertions(+), 398 deletions(-)
Title: Recurrent Neural Network
Description: Implementation of a Recurrent Neural Network in R.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between rnn versions 0.1.0 dated 2015-11-30 and 0.2.0 dated 2015-12-11
rnn-0.1.0/rnn/inst/doc/RNN.R |only rnn-0.1.0/rnn/inst/doc/RNN.Rmd |only rnn-0.1.0/rnn/inst/doc/RNN.html |only rnn-0.1.0/rnn/vignettes/RNN.Rmd |only rnn-0.2.0/rnn/DESCRIPTION | 6 ++-- rnn-0.2.0/rnn/MD5 | 22 +++++++-------- rnn-0.2.0/rnn/NEWS | 7 ++++ rnn-0.2.0/rnn/R/rnn.R | 46 +++++++++++++++++++++----------- rnn-0.2.0/rnn/README.md | 12 ++++++++ rnn-0.2.0/rnn/build/vignette.rds |binary rnn-0.2.0/rnn/inst/doc/rnn.R |only rnn-0.2.0/rnn/inst/doc/rnn.Rmd |only rnn-0.2.0/rnn/inst/doc/rnn.html |only rnn-0.2.0/rnn/man/rnn.Rd | 27 +++++++++++++++--- rnn-0.2.0/rnn/tests/testthat/test_rnn.R | 26 +++++++++++------- rnn-0.2.0/rnn/vignettes/rnn.Rmd |only 16 files changed, 102 insertions(+), 44 deletions(-)
Title: Repeated Measures Proportional Odds Logistic Regression
Description: Fits linear models to repeated ordinal scores using GEE methodology.
Author: Nick Parsons
Maintainer: Nick Parsons <nick.parsons@warwick.ac.uk>
Diff between repolr versions 3.1 dated 2015-12-08 and 3.2 dated 2015-12-11
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- R/repolr.R | 2 - src/cmat.cpp | 101 +++++++++++++++++++++++++++++--------------------------- src/hgmat.cpp | 30 ++++++++-------- src/icormat.cpp | 2 - src/ordgee.cpp | 32 ++++++++--------- src/potest.cpp | 8 ++-- src/smat.cpp | 2 - src/upalpha.cpp | 40 +++++++++++----------- 10 files changed, 124 insertions(+), 119 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples to compute Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.2.1 dated 2015-12-02 and 1.2.2 dated 2015-12-11
pnea-1.2.1/pnea/man/netfromadj.Rd |only pnea-1.2.2/pnea/DESCRIPTION | 10 ++--- pnea-1.2.2/pnea/MD5 | 20 +++++----- pnea-1.2.2/pnea/NAMESPACE | 2 - pnea-1.2.2/pnea/R/pnea.R | 68 +++++++++++++---------------------- pnea-1.2.2/pnea/man/networkmatrix.Rd |only pnea-1.2.2/pnea/man/plot.pnea.Rd | 2 - pnea-1.2.2/pnea/man/pnea-package.Rd | 2 - pnea-1.2.2/pnea/man/pnea.Rd | 12 +++--- pnea-1.2.2/pnea/man/print.pnea.Rd | 6 +-- pnea-1.2.2/pnea/man/summary.pnea.Rd | 2 - pnea-1.2.2/pnea/man/yeast.Rd | 1 12 files changed, 57 insertions(+), 68 deletions(-)
Title: Time Series Clustering with Dynamic Time Warping
Description: Time series clustering using different techniques related to the
Dynamic Time Warping distance and its corresponding lower bounds. Additionally,
an implementation of k-Shape clustering is available.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 1.2.0 dated 2015-11-15 and 1.3.0 dated 2015-12-11
DESCRIPTION | 16 - MD5 | 59 ++-- NAMESPACE | 68 ++-- R/DBA.R | 282 ++++++++++---------- R/NCCc.R | 74 ++--- R/SBD.R | 2 R/TADPole.R | 608 ++++++++++++++++++++++++++------------------ R/all_cent.R |only R/dtw-lb.R | 324 ++++++++++++++--------- R/dtw2.R | 12 R/dtwclust-classes.R | 63 ++-- R/dtwclust-plot.R | 24 - R/dtwclust.R | 484 +++++++++++++++++++---------------- R/dtwdistfun.R |only R/kcca-list.R | 166 ++++++------ R/lb-improved.R | 492 ++++++++++++++++++------------------ R/lb-keogh.R | 428 +++++++++++++++---------------- R/pkg.R | 32 +- R/reinterpolate.R | 36 +- R/shape-extraction.R | 200 +++++++------- R/utils.R | 419 +----------------------------- R/zscore.R | 71 +++-- README.md | 245 +++++++++-------- man/DBA.Rd | 2 man/TADPole.Rd | 39 ++ man/dtw_lb.Rd | 42 ++- man/dtwclust-class.Rd | 29 +- man/dtwclust-package.Rd | 8 man/dtwclust.Rd | 655 +++++++++++++++++++++++++++--------------------- man/plot-methods.Rd | 25 - man/zscore.Rd | 9 src |only 32 files changed, 2517 insertions(+), 2397 deletions(-)
Title: Access to Clarifai API
Description: Get description of images from Clarifai API. For more information,
see http://clarifai.com. Clarifai uses a large deep learning cloud to come
up with descriptive labels of the things in an image. It also provides how
confident it is about each of the labels.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between clarifai versions 0.1 dated 2015-11-12 and 0.2 dated 2015-12-11
DESCRIPTION | 8 +++---- MD5 | 30 ++++++++++++++++++-------- NEWS |only R/tag_image_urls.R | 3 +- R/tag_images.R | 5 ++-- README.md | 12 ++++++++-- build/vignette.rds |binary inst/doc/poligrams.R |only inst/doc/poligrams.Rmd |only inst/doc/poligrams.html |only inst/doc/using_clarifai.R |only inst/doc/using_clarifai.Rmd | 40 +++++++---------------------------- inst/doc/using_clarifai.html | 22 ------------------- inst/extdata/congress.csv |only inst/extdata/labs_df.7z |only tests/testthat/test-feedback.R |only tests/testthat/test-get-token.R |only tests/testthat/test-tag-image-urls.R | 4 +-- tests/testthat/test-tag-images.R |only vignettes/poligrams.Rmd |only vignettes/using_clarifai.Rmd | 40 +++++++---------------------------- vignettes/using_clarifai.md |only 22 files changed, 59 insertions(+), 105 deletions(-)
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Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Managing financial time series objects.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@rmetrics.org>
Diff between timeSeries versions 3022.101 dated 2015-11-09 and 3022.101.1 dated 2015-12-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/base-sort.R | 3 ++- R/methods-is.R | 15 ++++++++------- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-20 dated 2015-09-08 and 2.4-30 dated 2015-12-10
raster-2.4-20/raster/R/VectorLayer.R |only raster-2.4-30/raster/ChangeLog | 11 + raster-2.4-30/raster/DESCRIPTION | 12 - raster-2.4-30/raster/MD5 | 162 ++++++++++---------- raster-2.4-30/raster/NAMESPACE | 4 raster-2.4-30/raster/R/GDALtransient.R | 2 raster-2.4-30/raster/R/aggregate_sp.R | 4 raster-2.4-30/raster/R/area.R | 2 raster-2.4-30/raster/R/bind.R | 12 - raster-2.4-30/raster/R/canProcessInMemory.R | 2 raster-2.4-30/raster/R/clamp.R | 2 raster-2.4-30/raster/R/click.R | 11 - raster-2.4-30/raster/R/colortable.R | 6 raster-2.4-30/raster/R/connection.R | 12 - raster-2.4-30/raster/R/coverPolygons.R | 4 raster-2.4-30/raster/R/crop.R | 5 raster-2.4-30/raster/R/cropSpatial.R | 4 raster-2.4-30/raster/R/destair.R | 2 raster-2.4-30/raster/R/erase.R | 2 raster-2.4-30/raster/R/extractLines.R | 4 raster-2.4-30/raster/R/extractPoints.R | 2 raster-2.4-30/raster/R/extractPoints_sp.R | 2 raster-2.4-30/raster/R/extractPolygons.R | 4 raster-2.4-30/raster/R/getData.R | 2 raster-2.4-30/raster/R/head.R | 4 raster-2.4-30/raster/R/intersect.R | 1 raster-2.4-30/raster/R/intersect_sp.R | 26 ++- raster-2.4-30/raster/R/kml.R | 2 raster-2.4-30/raster/R/mask.R | 2 raster-2.4-30/raster/R/naValue.R | 2 raster-2.4-30/raster/R/names.R | 4 raster-2.4-30/raster/R/netCDFread.R | 80 +--------- raster-2.4-30/raster/R/netCDFreadCells.R | 39 +--- raster-2.4-30/raster/R/netCDFtoRasterCD.R | 104 ++++--------- raster-2.4-30/raster/R/netCDFtoRasterGMT.R | 38 +--- raster-2.4-30/raster/R/netCDFtoStack.R | 14 - raster-2.4-30/raster/R/netCDFutil.R | 50 ------ raster-2.4-30/raster/R/netCDFwriteCD.R | 183 ++++++----------------- raster-2.4-30/raster/R/plotCT.R | 2 raster-2.4-30/raster/R/print.R | 14 - raster-2.4-30/raster/R/progressBar.R | 4 raster-2.4-30/raster/R/projectRaster.R | 2 raster-2.4-30/raster/R/raster.R | 1 raster-2.4-30/raster/R/rasterFromFile.R | 17 -- raster-2.4-30/raster/R/rasterFromGRASSascii.R |only raster-2.4-30/raster/R/rasterFromXYZ.R | 4 raster-2.4-30/raster/R/rasterOptions.R | 6 raster-2.4-30/raster/R/rasterizePolygons.R | 37 ++-- raster-2.4-30/raster/R/resample.R | 2 raster-2.4-30/raster/R/rotate.R | 5 raster-2.4-30/raster/R/select.R | 4 raster-2.4-30/raster/R/shift.R | 10 - raster-2.4-30/raster/R/shp.R | 4 raster-2.4-30/raster/R/simplifyPols.R | 2 raster-2.4-30/raster/R/stackQuick.R | 2 raster-2.4-30/raster/R/text.R | 4 raster-2.4-30/raster/R/tmpFile.R | 2 raster-2.4-30/raster/R/tmppath.R | 5 raster-2.4-30/raster/R/union_sp.R | 6 raster-2.4-30/raster/R/update.R | 43 ++--- raster-2.4-30/raster/R/writeAllGDAL.R | 2 raster-2.4-30/raster/R/writeRaster.R | 2 raster-2.4-30/raster/R/writeStartStopRaster.R | 2 raster-2.4-30/raster/R/xyValuesBuffer.R | 2 raster-2.4-30/raster/R/zoom.R | 2 raster-2.4-30/raster/R/zzz.R | 2 raster-2.4-30/raster/build/vignette.rds |binary raster-2.4-30/raster/inst/doc/Raster.pdf |binary raster-2.4-30/raster/inst/doc/functions.pdf |binary raster-2.4-30/raster/inst/doc/rasterfile.Rnw | 88 ++++++----- raster-2.4-30/raster/inst/doc/rasterfile.pdf |binary raster-2.4-30/raster/inst/external/countries.csv | 2 raster-2.4-30/raster/man/as.matrix.Rd | 12 + raster-2.4-30/raster/man/brick.Rd | 2 raster-2.4-30/raster/man/geom.Rd | 2 raster-2.4-30/raster/man/intersect.Rd | 4 raster-2.4-30/raster/man/mosaic.Rd | 9 + raster-2.4-30/raster/man/plot.Rd | 7 raster-2.4-30/raster/man/raster.Rd | 2 raster-2.4-30/raster/man/rowSums.Rd | 7 raster-2.4-30/raster/man/writeFormats.Rd | 2 raster-2.4-30/raster/man/writeRaster.Rd | 9 - raster-2.4-30/raster/vignettes/rasterfile.Rnw | 88 ++++++----- 83 files changed, 522 insertions(+), 722 deletions(-)
Title: IBM in-Database Analytics for R
Description: Functionality required to efficiently use R with
IBM DB2(C) for Linux, Unix and Windows as well as IBM dashDB(C).
Many basic and complex R operations are pushed down into the database, which removes
the main memory boundary of R and allows to make full use of parallel processing in
the underlying database.
Author: IBM Corporation
Maintainer: Michael Wurst <inza@de.ibm.com>
Diff between ibmdbR versions 1.42.2 dated 2015-08-06 and 1.47.1 dated 2015-12-10
DESCRIPTION | 9 MD5 | 39 +- NAMESPACE | 24 + R/coldef.R | 57 +++ R/connect.R | 14 R/connection.R | 25 - R/data.frame.R | 44 ++ R/lm.R | 730 +++++++++++++++++++++++++++------------------ R/model.management.R | 36 +- R/plot.idaLm.R |only R/sql.R | 136 +++++++- R/statistics.R | 71 ++-- R/tree.R |only R/update.R | 6 inst/doc/ibmdbR.pdf |binary man/ida.col.def.methods.Rd | 1 man/idaArule.Rd | 2 man/idaDropModel.Rd | 4 man/idaLm.Rd | 90 ++++- man/idaQuery.Rd | 3 man/idaTree.Rd |only man/showtables.Rd | 3 22 files changed, 879 insertions(+), 415 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.12.1 dated 2015-12-05 and 0.13.1 dated 2015-12-10
git2r-0.12.1/git2r/src/libgit2/idxmap.h |only git2r-0.12.1/git2r/src/libgit2/stransport_stream.c |only git2r-0.12.1/git2r/src/libgit2/transaction.h |only git2r-0.13.1/git2r/DESCRIPTION | 6 git2r-0.13.1/git2r/MD5 | 216 ++-- git2r-0.13.1/git2r/NEWS | 19 git2r-0.13.1/git2r/R/libgit2.r | 2 git2r-0.13.1/git2r/configure | 140 +- git2r-0.13.1/git2r/configure.ac | 146 +- git2r-0.13.1/git2r/src/Makevars.in | 63 - git2r-0.13.1/git2r/src/Makevars.win | 60 - git2r-0.13.1/git2r/src/git2r_config.c | 83 - git2r-0.13.1/git2r/src/git2r_remote.c | 2 git2r-0.13.1/git2r/src/libgit2/attr_file.c | 6 git2r-0.13.1/git2r/src/libgit2/attrcache.c | 5 git2r-0.13.1/git2r/src/libgit2/blame.c | 2 git2r-0.13.1/git2r/src/libgit2/blame_git.c | 34 git2r-0.13.1/git2r/src/libgit2/blame_git.h | 2 git2r-0.13.1/git2r/src/libgit2/checkout.c | 59 - git2r-0.13.1/git2r/src/libgit2/commit.c | 35 git2r-0.13.1/git2r/src/libgit2/commit_list.c | 8 git2r-0.13.1/git2r/src/libgit2/commit_list.h | 3 git2r-0.13.1/git2r/src/libgit2/common.h | 9 git2r-0.13.1/git2r/src/libgit2/config.c | 46 git2r-0.13.1/git2r/src/libgit2/config.h | 16 git2r-0.13.1/git2r/src/libgit2/config_file.c | 151 --- git2r-0.13.1/git2r/src/libgit2/config_file.h | 10 git2r-0.13.1/git2r/src/libgit2/curl_stream.c | 1 git2r-0.13.1/git2r/src/libgit2/diff.c | 123 -- git2r-0.13.1/git2r/src/libgit2/diff_driver.c | 13 git2r-0.13.1/git2r/src/libgit2/diff_file.c | 25 git2r-0.13.1/git2r/src/libgit2/diff_patch.c | 4 git2r-0.13.1/git2r/src/libgit2/diff_print.c | 2 git2r-0.13.1/git2r/src/libgit2/diff_tform.c | 6 git2r-0.13.1/git2r/src/libgit2/diff_xdiff.c | 7 git2r-0.13.1/git2r/src/libgit2/diff_xdiff.h | 5 git2r-0.13.1/git2r/src/libgit2/filebuf.c | 84 - git2r-0.13.1/git2r/src/libgit2/fileops.c | 308 ++---- git2r-0.13.1/git2r/src/libgit2/fileops.h | 20 git2r-0.13.1/git2r/src/libgit2/ignore.c | 16 git2r-0.13.1/git2r/src/libgit2/include/git2/common.h | 14 git2r-0.13.1/git2r/src/libgit2/include/git2/config.h | 48 git2r-0.13.1/git2r/src/libgit2/include/git2/cred_helpers.h | 2 git2r-0.13.1/git2r/src/libgit2/include/git2/diff.h | 37 git2r-0.13.1/git2r/src/libgit2/include/git2/errors.h | 1 git2r-0.13.1/git2r/src/libgit2/include/git2/index.h | 39 git2r-0.13.1/git2r/src/libgit2/include/git2/merge.h | 12 git2r-0.13.1/git2r/src/libgit2/include/git2/remote.h | 13 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/config.h | 14 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/odb_backend.h | 4 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/refdb_backend.h | 4 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/stream.h | 13 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/transport.h | 28 git2r-0.13.1/git2r/src/libgit2/include/git2/transport.h | 11 git2r-0.13.1/git2r/src/libgit2/index.c | 428 +------- git2r-0.13.1/git2r/src/libgit2/index.h | 2 git2r-0.13.1/git2r/src/libgit2/iterator.c | 500 ++-------- git2r-0.13.1/git2r/src/libgit2/iterator.h | 48 git2r-0.13.1/git2r/src/libgit2/merge.c | 381 ++----- git2r-0.13.1/git2r/src/libgit2/merge_file.c | 98 - git2r-0.13.1/git2r/src/libgit2/merge_file.h |only git2r-0.13.1/git2r/src/libgit2/notes.c | 2 git2r-0.13.1/git2r/src/libgit2/odb.c | 246 +--- git2r-0.13.1/git2r/src/libgit2/odb_loose.c | 4 git2r-0.13.1/git2r/src/libgit2/odb_mempack.c | 8 git2r-0.13.1/git2r/src/libgit2/odb_pack.c | 82 + git2r-0.13.1/git2r/src/libgit2/oidmap.h | 2 git2r-0.13.1/git2r/src/libgit2/openssl_stream.c | 7 git2r-0.13.1/git2r/src/libgit2/pack-objects.c | 3 git2r-0.13.1/git2r/src/libgit2/path.c | 23 git2r-0.13.1/git2r/src/libgit2/path.h | 8 git2r-0.13.1/git2r/src/libgit2/pathspec.c | 36 git2r-0.13.1/git2r/src/libgit2/pool.c | 241 +++- git2r-0.13.1/git2r/src/libgit2/pool.h | 54 - git2r-0.13.1/git2r/src/libgit2/push.c | 3 git2r-0.13.1/git2r/src/libgit2/push.h | 1 git2r-0.13.1/git2r/src/libgit2/refdb.c | 8 git2r-0.13.1/git2r/src/libgit2/refdb_fs.c | 16 git2r-0.13.1/git2r/src/libgit2/remote.c | 46 git2r-0.13.1/git2r/src/libgit2/repository.c | 55 - git2r-0.13.1/git2r/src/libgit2/revwalk.c | 6 git2r-0.13.1/git2r/src/libgit2/signature.c | 18 git2r-0.13.1/git2r/src/libgit2/sortedcache.c | 5 git2r-0.13.1/git2r/src/libgit2/stash.c | 29 git2r-0.13.1/git2r/src/libgit2/stream.h | 3 git2r-0.13.1/git2r/src/libgit2/submodule.c | 406 +++----- git2r-0.13.1/git2r/src/libgit2/sysdir.c | 19 git2r-0.13.1/git2r/src/libgit2/sysdir.h | 14 git2r-0.13.1/git2r/src/libgit2/tls_stream.c | 13 git2r-0.13.1/git2r/src/libgit2/transaction.c | 44 git2r-0.13.1/git2r/src/libgit2/transports/cred.c | 8 git2r-0.13.1/git2r/src/libgit2/transports/git.c | 11 git2r-0.13.1/git2r/src/libgit2/transports/http.c | 16 git2r-0.13.1/git2r/src/libgit2/transports/smart.c | 95 - git2r-0.13.1/git2r/src/libgit2/transports/smart.h | 1 git2r-0.13.1/git2r/src/libgit2/transports/smart_pkt.c | 11 git2r-0.13.1/git2r/src/libgit2/transports/smart_protocol.c | 2 git2r-0.13.1/git2r/src/libgit2/transports/ssh.c | 4 git2r-0.13.1/git2r/src/libgit2/transports/winhttp.c | 18 git2r-0.13.1/git2r/src/libgit2/unix/posix.h | 15 git2r-0.13.1/git2r/src/libgit2/util.c | 26 git2r-0.13.1/git2r/src/libgit2/win32/findfile.c | 10 git2r-0.13.1/git2r/src/libgit2/win32/findfile.h | 1 git2r-0.13.1/git2r/src/libgit2/win32/path_w32.c | 23 git2r-0.13.1/git2r/src/libgit2/win32/posix_w32.c | 11 git2r-0.13.1/git2r/src/libgit2/win32/w32_util.c | 34 git2r-0.13.1/git2r/src/libgit2/win32/w32_util.h | 16 git2r-0.13.1/git2r/src/libgit2/xdiff/xdiff.h | 8 git2r-0.13.1/git2r/src/libgit2/xdiff/xdiffi.c | 12 git2r-0.13.1/git2r/src/libgit2/xdiff/xhistogram.c | 6 git2r-0.13.1/git2r/src/libgit2/xdiff/xmerge.c | 142 -- 111 files changed, 1774 insertions(+), 3532 deletions(-)
Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions
such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>
Diff between forestmodel versions 0.3.3 dated 2015-11-26 and 0.4.0 dated 2015-12-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/forest_breaks.R | 4 ++++ R/forest_model.R | 42 +++++++++++++++++++++++++----------------- R/panel_forest_plot.R | 9 ++++++++- man/forest_breaks.Rd | 3 ++- 7 files changed, 54 insertions(+), 29 deletions(-)
Title: Ranking-Based Variable Selection
Description: Implements the Ranking-Based Variable Selection
algorithm for variable selection in high-dimensional data.
Author: Rafal Baranowski, Patrick Breheny, Isaac Turner
Maintainer: Rafal Baranowski <r.baranowski@lse.ac.uk>
Diff between rbvs versions 1.0 dated 2015-12-08 and 1.0.1 dated 2015-12-10
DESCRIPTION | 6 - MD5 | 10 - src/Makevars | 1 src/rankings.c | 2 src/rbvs.c | 55 +++++++++- src/sort_r.h | 308 ++++++++++++++++++++++++++++++++++++++++++--------------- 6 files changed, 291 insertions(+), 91 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.6 dated 2015-09-21 and 1.0 dated 2015-12-10
DESCRIPTION | 22 ++++++-- MD5 | 92 +++++++++++++++++------------------ NAMESPACE | 3 - R/kde.R | 4 - R/plot.R | 16 +++--- R/provenance.R | 95 +++++++++++++++++++++++++++++++++---- man/CLR.Rd | 2 man/KDE.Rd | 2 man/KDEs.Rd | 7 +- man/KS.diss.Rd | 2 man/MDS.Rd | 2 man/Namib.Rd | 2 man/PCA.Rd | 2 man/SH.diss.Rd | 2 man/amalgamate.Rd | 2 man/as.acomp.Rd | 4 - man/as.compositional.Rd | 4 - man/as.data.frame.compositional.Rd | 2 man/botev.Rd | 2 man/bray.diss.Rd | 2 man/densities.Rd | 2 man/diss.Rd | 2 man/endmembers.Rd | 2 man/get.f.Rd | 2 man/get.n.Rd | 4 - man/get.p.Rd | 2 man/indscal.Rd | 2 man/minsorting.Rd | 2 man/plot.GPA.Rd | 2 man/plot.INDSCAL.Rd | 2 man/plot.KDE.Rd | 2 man/plot.MDS.Rd | 2 man/plot.PCA.Rd | 2 man/plot.compositional.Rd | 2 man/plot.distributional.Rd | 2 man/plot.minsorting.Rd | 2 man/plot.ternary.Rd | 2 man/procrustes.Rd | 16 +++--- man/provenance.Rd | 2 man/read.compositional.Rd | 2 man/read.densities.Rd | 2 man/read.distributional.Rd | 2 man/restore.Rd | 2 man/subset.compositional.Rd | 2 man/subset.distributional.Rd | 2 man/summaryplot.Rd | 2 man/ternary.Rd | 2 47 files changed, 213 insertions(+), 126 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 1.99.14 dated 2015-07-09 and 2.0.0 dated 2015-12-10
phangorn-1.99.14/phangorn/TODO |only phangorn-2.0.0/phangorn/DESCRIPTION | 24 phangorn-2.0.0/phangorn/MD5 | 131 - phangorn-2.0.0/phangorn/NAMESPACE | 32 phangorn-2.0.0/phangorn/NEWS | 36 phangorn-2.0.0/phangorn/R/Densi.R | 28 phangorn-2.0.0/phangorn/R/SH.R |only phangorn-2.0.0/phangorn/R/bootstrap.R |only phangorn-2.0.0/phangorn/R/clanistic.R | 8 phangorn-2.0.0/phangorn/R/dist.p.R | 2 phangorn-2.0.0/phangorn/R/distSeq.R | 98 + phangorn-2.0.0/phangorn/R/distTree.R | 4 phangorn-2.0.0/phangorn/R/fitch.R | 8 phangorn-2.0.0/phangorn/R/hadamard.R | 8 phangorn-2.0.0/phangorn/R/modelTest.R | 59 phangorn-2.0.0/phangorn/R/networx.R | 261 +- phangorn-2.0.0/phangorn/R/parsimony.R | 20 phangorn-2.0.0/phangorn/R/phyDat.R | 73 phangorn-2.0.0/phangorn/R/phylo.R | 1491 +++++++--------- phangorn-2.0.0/phangorn/R/sankoff.R | 6 phangorn-2.0.0/phangorn/R/simSeq.R | 6 phangorn-2.0.0/phangorn/R/treeManipulation.R | 27 phangorn-2.0.0/phangorn/R/treedist.R | 6 phangorn-2.0.0/phangorn/README.md | 1 phangorn-2.0.0/phangorn/build/vignette.rds |binary phangorn-2.0.0/phangorn/inst/doc/Ancestral.R | 15 phangorn-2.0.0/phangorn/inst/doc/Ancestral.Rnw | 1 phangorn-2.0.0/phangorn/inst/doc/Ancestral.pdf |binary phangorn-2.0.0/phangorn/inst/doc/Networx.R | 9 phangorn-2.0.0/phangorn/inst/doc/Networx.Rmd | 9 phangorn-2.0.0/phangorn/inst/doc/Networx.html | 38 phangorn-2.0.0/phangorn/inst/doc/Trees.R | 155 + phangorn-2.0.0/phangorn/inst/doc/Trees.Rnw | 142 - phangorn-2.0.0/phangorn/inst/doc/Trees.pdf |binary phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.R | 19 phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.Rnw | 7 phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.pdf |binary phangorn-2.0.0/phangorn/inst/extdata/trees |only phangorn-2.0.0/phangorn/man/Ancestors.Rd | 2 phangorn-2.0.0/phangorn/man/addConfidences.Rd |only phangorn-2.0.0/phangorn/man/allTrees.Rd | 60 phangorn-2.0.0/phangorn/man/ancestral.pml.Rd | 2 phangorn-2.0.0/phangorn/man/as.splits.Rd | 10 phangorn-2.0.0/phangorn/man/bootstrap.pml.Rd | 11 phangorn-2.0.0/phangorn/man/consensusNet.Rd | 5 phangorn-2.0.0/phangorn/man/cophenetic.networx.Rd |only phangorn-2.0.0/phangorn/man/delta.score.Rd |only phangorn-2.0.0/phangorn/man/dfactorial.Rd | 56 phangorn-2.0.0/phangorn/man/dist.hamming.Rd | 19 phangorn-2.0.0/phangorn/man/dist.p.Rd | 2 phangorn-2.0.0/phangorn/man/distanceHadamard.Rd | 4 phangorn-2.0.0/phangorn/man/midpoint.Rd | 3 phangorn-2.0.0/phangorn/man/modelTest.Rd | 24 phangorn-2.0.0/phangorn/man/neighborNet.Rd | 2 phangorn-2.0.0/phangorn/man/nni.Rd | 2 phangorn-2.0.0/phangorn/man/phangorn-package.Rd | 83 phangorn-2.0.0/phangorn/man/phyDat.Rd | 13 phangorn-2.0.0/phangorn/man/plot.networx.Rd | 6 phangorn-2.0.0/phangorn/man/pml.Rd | 19 phangorn-2.0.0/phangorn/man/simSeq.Rd | 2 phangorn-2.0.0/phangorn/man/superTree.Rd | 2 phangorn-2.0.0/phangorn/man/treedist.Rd | 1 phangorn-2.0.0/phangorn/tests/testthat/test_distances.R |only phangorn-2.0.0/phangorn/tests/testthat/test_pml.R |only phangorn-2.0.0/phangorn/vignettes/Ancestral.Rnw | 1 phangorn-2.0.0/phangorn/vignettes/Networx.Rmd | 9 phangorn-2.0.0/phangorn/vignettes/Trees.RData |binary phangorn-2.0.0/phangorn/vignettes/Trees.Rnw | 142 - phangorn-2.0.0/phangorn/vignettes/phangorn-specials.Rnw | 7 phangorn-2.0.0/phangorn/vignettes/phangorn.bib | 205 ++ 70 files changed, 1991 insertions(+), 1425 deletions(-)
Title: Parametric Bootstrap and Kenward-Roger-Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-2 dated 2014-11-13 and 0.4-3 dated 2015-12-10
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
lme4 package.
The package implements a parametric bootstrap test and a Kenward-Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
pbkrtest-0.4-2/pbkrtest/R/KR-vcovAdj2-prev.R |only
pbkrtest-0.4-3/pbkrtest/ChangeLog | 10
pbkrtest-0.4-3/pbkrtest/DESCRIPTION | 24
pbkrtest-0.4-3/pbkrtest/MD5 | 49 -
pbkrtest-0.4-3/pbkrtest/NAMESPACE | 74 ++
pbkrtest-0.4-3/pbkrtest/R/KR-Sigma-G.R | 174 ++---
pbkrtest-0.4-3/pbkrtest/R/KR-Sigma-G2.R | 6
pbkrtest-0.4-3/pbkrtest/R/KR-init-modcomp.R | 104 +--
pbkrtest-0.4-3/pbkrtest/R/KR-linearAlgebra.R | 12
pbkrtest-0.4-3/pbkrtest/R/KR-modcomp.R | 8
pbkrtest-0.4-3/pbkrtest/R/KR-utils.R | 23
pbkrtest-0.4-3/pbkrtest/R/KR-vcovAdj.R | 407 ++++++++-----
pbkrtest-0.4-3/pbkrtest/R/PB-modcomp.R | 37 -
pbkrtest-0.4-3/pbkrtest/R/PB-refdist.R | 26
pbkrtest-0.4-3/pbkrtest/R/PB-utils.R | 2
pbkrtest-0.4-3/pbkrtest/R/modelCoercion.R | 5
pbkrtest-0.4-3/pbkrtest/build/vignette.rds |binary
pbkrtest-0.4-3/pbkrtest/data/beets.txt.gz |binary
pbkrtest-0.4-3/pbkrtest/data/budworm.txt.gz |binary
pbkrtest-0.4-3/pbkrtest/inst/doc/pbkrtest-introduction.R | 304 ++++-----
pbkrtest-0.4-3/pbkrtest/inst/doc/pbkrtest-introduction.pdf |binary
pbkrtest-0.4-3/pbkrtest/man/KRmodcomp.Rd | 13
pbkrtest-0.4-3/pbkrtest/man/PBmodcomp.Rd | 62 +
pbkrtest-0.4-3/pbkrtest/man/PBrefdist.Rd | 11
pbkrtest-0.4-3/pbkrtest/man/pbkrtest-internal.Rd | 7
pbkrtest-0.4-3/pbkrtest/man/vcovAdj.Rd | 4
26 files changed, 845 insertions(+), 517 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputed cross-validation. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included; uses Maarloes Maathius's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.8 dated 2015-10-27 and 1.3.1 dated 2015-12-10
DESCRIPTION | 10 MD5 | 54 +++- NAMESPACE | 10 NEWS | 11 R/Utilities.R | 139 +++++++++++- R/icenReg_CV.R |only R/referenceClasses.R | 7 R/user_functions.R | 331 ++++++++++++++++++++++++----- build |only inst |only man/abs_inv.Rd |only man/diag_baseline.Rd | 2 man/getFitEsts.Rd | 32 +- man/ic_par.Rd | 2 man/ic_sp.Rd | 2 man/icenReg_cv.Rd |only man/imputeCens.Rd |only man/predict.icenReg_fit.Rd |only src/icenReg.cpp | 1 src/icenReg_files/basicUtilities.cpp | 81 +++++++ src/icenReg_files/ic_par.cpp | 71 ++++++ src/icenReg_files/ic_par.h | 10 src/icenReg_files/ic_sp_ch.cpp | 90 ++++++- src/icenReg_files/ic_sp_ch.h | 24 +- src/icenReg_files/ic_sp_gradDescent.cpp | 124 +--------- src/icenReg_files/regressionTransforms.cpp |only src/icenReg_files/regressionTransforms.h |only vignettes |only 28 files changed, 774 insertions(+), 227 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.3 dated 2015-10-01 and 2.2-4 dated 2015-12-10
DESCRIPTION | 12 - MD5 | 36 ++-- NAMESPACE | 1 NEWS | 10 + R/Kdhat.R | 24 +- R/Mhat.R | 12 - R/RcppExports.R | 20 +- R/m_hat.R | 46 +++-- build/vignette.rds |binary inst/doc/dbmss.Rnw | 2 inst/doc/dbmss.pdf |binary man/Rcpp.Rd | 46 ++++- man/dbmss-package.Rd | 20 +- src/CountNbd.cpp | 409 ++++++++++++++++++++++++++++++--------------------- src/Makevars | 29 --- src/Makevars.win | 8 src/RcppExports.cpp | 81 +++++----- vignettes/dbmss.Rnw | 2 vignettes/dbmss.bib | 41 +++-- 19 files changed, 472 insertions(+), 327 deletions(-)
Title: Helper Functions for Structural Equation Modelling in OpenMx
Description: Helper functions for making, running, and reporting SEM
and twin models in OpenMx.
If you are just starting, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.0.0 dated 2015-10-27 and 1.1.0 dated 2015-12-10
umx-1.0.0/umx/man/umxStandardizeACE.Rd |only umx-1.0.0/umx/man/umx_APA_CI.Rd |only umx-1.0.0/umx/man/umx_check_multi_core.Rd |only umx-1.0.0/umx/man/umx_get_CI_as_APA_string.Rd |only umx-1.1.0/umx/DESCRIPTION | 9 umx-1.1.0/umx/MD5 | 332 +++---- umx-1.1.0/umx/NAMESPACE | 18 umx-1.1.0/umx/NEWS | 20 umx-1.1.0/umx/R/build_run_modify.r | 727 ++++++++++++--- umx-1.1.0/umx/R/datasets.R |only umx-1.1.0/umx/R/fit_and_reporting.r | 736 ++++++++-------- umx-1.1.0/umx/R/hermine_original_twinHetMulAceCon.R |only umx-1.1.0/umx/R/misc_and_utility.r | 640 ++++++++----- umx-1.1.0/umx/R/umxCF_SexLim.R |only umx-1.1.0/umx/R/xmu.r | 6 umx-1.1.0/umx/data |only umx-1.1.0/umx/inst/CITATION | 2 umx-1.1.0/umx/man/RMSEA.MxModel.Rd | 27 umx-1.1.0/umx/man/RMSEA.Rd | 27 umx-1.1.0/umx/man/RMSEA.summary.mxmodel.Rd | 27 umx-1.1.0/umx/man/confint.MxModel.Rd | 39 umx-1.1.0/umx/man/dl_from_dropbox.Rd | 8 umx-1.1.0/umx/man/extractAIC.MxModel.Rd | 31 umx-1.1.0/umx/man/figures/ACE.png |only umx-1.1.0/umx/man/figures/CP.png |only umx-1.1.0/umx/man/figures/GxE.png |only umx-1.1.0/umx/man/figures/IP.png |only umx-1.1.0/umx/man/figures/umx_help_figures.graffle |binary umx-1.1.0/umx/man/logLik.Rd | 35 umx-1.1.0/umx/man/plot.MxModel.Rd | 36 umx-1.1.0/umx/man/qm.Rd | 14 umx-1.1.0/umx/man/reliability.Rd | 10 umx-1.1.0/umx/man/residuals.MxModel.Rd | 31 umx-1.1.0/umx/man/summaryAPA.Rd |only umx-1.1.0/umx/man/umx-deprecated.Rd | 2 umx-1.1.0/umx/man/umx.Rd | 152 +-- umx-1.1.0/umx/man/umxACE.Rd | 80 + umx-1.1.0/umx/man/umxACESexLim.Rd |only umx-1.1.0/umx/man/umxAdd1.Rd | 14 umx-1.1.0/umx/man/umxCF_SexLim.Rd |only umx-1.1.0/umx/man/umxCI.Rd | 34 umx-1.1.0/umx/man/umxCI_boot.Rd | 33 umx-1.1.0/umx/man/umxCP.Rd | 66 + umx-1.1.0/umx/man/umxCompare.Rd | 57 - umx-1.1.0/umx/man/umxCov2cor.Rd | 8 umx-1.1.0/umx/man/umxCovData.Rd | 28 umx-1.1.0/umx/man/umxDiagnose.Rd | 23 umx-1.1.0/umx/man/umxDrop1.Rd | 18 umx-1.1.0/umx/man/umxEFA.Rd | 6 umx-1.1.0/umx/man/umxEquate.Rd | 35 umx-1.1.0/umx/man/umxEval.Rd | 51 - umx-1.1.0/umx/man/umxExpCov.Rd | 44 umx-1.1.0/umx/man/umxExpMeans.Rd | 32 umx-1.1.0/umx/man/umxFactor.Rd |only umx-1.1.0/umx/man/umxFitIndices.Rd | 32 umx-1.1.0/umx/man/umxFixAll.Rd | 16 umx-1.1.0/umx/man/umxGetParameters.Rd | 20 umx-1.1.0/umx/man/umxGxE.Rd | 39 umx-1.1.0/umx/man/umxGxE_window.Rd | 40 umx-1.1.0/umx/man/umxHetCor.Rd | 29 umx-1.1.0/umx/man/umxIP.Rd | 36 umx-1.1.0/umx/man/umxJiggle.Rd | 35 umx-1.1.0/umx/man/umxLabel.Rd | 25 umx-1.1.0/umx/man/umxLatent.Rd | 40 umx-1.1.0/umx/man/umxMI.Rd | 20 umx-1.1.0/umx/man/umxPadAndPruneForDefVars.Rd | 25 umx-1.1.0/umx/man/umxPath.Rd | 44 umx-1.1.0/umx/man/umxPlotACE.Rd | 28 umx-1.1.0/umx/man/umxPlotCP.Rd | 12 umx-1.1.0/umx/man/umxPlotGxE.Rd | 12 umx-1.1.0/umx/man/umxPlotIP.Rd | 4 umx-1.1.0/umx/man/umxRAM.Rd | 44 umx-1.1.0/umx/man/umxReRun.Rd | 25 umx-1.1.0/umx/man/umxReduce.Rd | 10 umx-1.1.0/umx/man/umxRun.Rd | 25 umx-1.1.0/umx/man/umxSetParameters.Rd | 40 umx-1.1.0/umx/man/umxStandardizeModel.Rd | 31 umx-1.1.0/umx/man/umxSummary.MxModel.Rd | 63 - umx-1.1.0/umx/man/umxSummary.Rd | 4 umx-1.1.0/umx/man/umxSummaryACE.Rd | 15 umx-1.1.0/umx/man/umxSummaryCP.Rd | 20 umx-1.1.0/umx/man/umxSummaryGxE.Rd | 25 umx-1.1.0/umx/man/umxSummaryIP.Rd | 14 umx-1.1.0/umx/man/umxThresholdMatrix.Rd | 60 - umx-1.1.0/umx/man/umxUnexplainedCausalNexus.Rd | 13 umx-1.1.0/umx/man/umxValues.Rd | 35 umx-1.1.0/umx/man/umx_APA_model_CI.Rd |only umx-1.1.0/umx/man/umx_APA_pval.Rd | 43 umx-1.1.0/umx/man/umx_RAM_ordinal_objective.Rd | 7 umx-1.1.0/umx/man/umx_add_variances.Rd | 42 umx-1.1.0/umx/man/umx_aggregate.Rd | 16 umx-1.1.0/umx/man/umx_apply.Rd | 40 umx-1.1.0/umx/man/umx_as_numeric.Rd | 26 umx-1.1.0/umx/man/umx_check.Rd | 46 - umx-1.1.0/umx/man/umx_check_OS.Rd | 45 umx-1.1.0/umx/man/umx_check_model.Rd | 51 - umx-1.1.0/umx/man/umx_check_names.Rd | 23 umx-1.1.0/umx/man/umx_check_parallel.Rd |only umx-1.1.0/umx/man/umx_cont_2_ordinal.Rd | 26 umx-1.1.0/umx/man/umx_cor.Rd | 17 umx-1.1.0/umx/man/umx_cov2raw.Rd | 28 umx-1.1.0/umx/man/umx_cov_diag.Rd | 4 umx-1.1.0/umx/man/umx_default_option.Rd | 44 umx-1.1.0/umx/man/umx_drop_ok.Rd | 25 umx-1.1.0/umx/man/umx_explode.Rd | 17 umx-1.1.0/umx/man/umx_fake_data.Rd | 16 umx-1.1.0/umx/man/umx_find_object.Rd | 14 umx-1.1.0/umx/man/umx_fix_first_loadings.Rd | 19 umx-1.1.0/umx/man/umx_fix_latents.Rd | 20 umx-1.1.0/umx/man/umx_fun_mean_sd.Rd |only umx-1.1.0/umx/man/umx_get_bracket_addresses.Rd | 44 umx-1.1.0/umx/man/umx_get_checkpoint.Rd | 43 umx-1.1.0/umx/man/umx_get_cores.Rd | 39 umx-1.1.0/umx/man/umx_get_optimizer.Rd | 36 umx-1.1.0/umx/man/umx_grep.Rd | 26 umx-1.1.0/umx/man/umx_has_CIs.Rd | 51 - umx-1.1.0/umx/man/umx_has_been_run.Rd | 50 - umx-1.1.0/umx/man/umx_has_means.Rd | 51 - umx-1.1.0/umx/man/umx_has_square_brackets.Rd | 45 umx-1.1.0/umx/man/umx_is_MxMatrix.Rd | 45 umx-1.1.0/umx/man/umx_is_MxModel.Rd | 45 umx-1.1.0/umx/man/umx_is_RAM.Rd | 51 - umx-1.1.0/umx/man/umx_is_cov.Rd | 45 umx-1.1.0/umx/man/umx_is_endogenous.Rd | 45 umx-1.1.0/umx/man/umx_is_exogenous.Rd | 47 - umx-1.1.0/umx/man/umx_is_ordered.Rd | 48 - umx-1.1.0/umx/man/umx_lower2full.Rd | 39 umx-1.1.0/umx/man/umx_make_bin_cont_pair_data.Rd | 26 umx-1.1.0/umx/man/umx_means.Rd | 8 umx-1.1.0/umx/man/umx_merge_CIs.Rd | 26 umx-1.1.0/umx/man/umx_move_file.Rd | 8 umx-1.1.0/umx/man/umx_msg.Rd | 18 umx-1.1.0/umx/man/umx_names.Rd | 14 umx-1.1.0/umx/man/umx_object_as_str.Rd | 38 umx-1.1.0/umx/man/umx_open.Rd | 9 umx-1.1.0/umx/man/umx_paste_names.Rd | 28 umx-1.1.0/umx/man/umx_pb_note.Rd | 14 umx-1.1.0/umx/man/umx_print.Rd | 30 umx-1.1.0/umx/man/umx_read_lower.Rd | 28 umx-1.1.0/umx/man/umx_rename.Rd | 14 umx-1.1.0/umx/man/umx_rename_file.Rd | 8 umx-1.1.0/umx/man/umx_reorder.Rd | 46 - umx-1.1.0/umx/man/umx_residualize.Rd | 70 - umx-1.1.0/umx/man/umx_rot.Rd | 11 umx-1.1.0/umx/man/umx_round.Rd | 28 umx-1.1.0/umx/man/umx_scale.Rd | 29 umx-1.1.0/umx/man/umx_scale_wide_twin_data.Rd | 28 umx-1.1.0/umx/man/umx_set_checkpoint.Rd | 40 umx-1.1.0/umx/man/umx_set_cores.Rd | 40 umx-1.1.0/umx/man/umx_set_optimizer.Rd | 37 umx-1.1.0/umx/man/umx_show.Rd | 18 umx-1.1.0/umx/man/umx_standardize_ACE.Rd |only umx-1.1.0/umx/man/umx_standardize_CP.Rd |only umx-1.1.0/umx/man/umx_standardize_IP.Rd | 41 umx-1.1.0/umx/man/umx_string_to_algebra.Rd | 38 umx-1.1.0/umx/man/umx_swap_a_block.Rd | 28 umx-1.1.0/umx/man/umx_time.Rd | 18 umx-1.1.0/umx/man/umx_trim.Rd | 11 umx-1.1.0/umx/man/us_skinfold_data.Rd |only umx-1.1.0/umx/man/xmuHasSquareBrackets.Rd | 22 umx-1.1.0/umx/man/xmuLabel_MATRIX_Model.Rd | 32 umx-1.1.0/umx/man/xmuLabel_Matrix.Rd | 22 umx-1.1.0/umx/man/xmuLabel_RAM_Model.Rd | 22 umx-1.1.0/umx/man/xmuMI.Rd | 24 umx-1.1.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 22 umx-1.1.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 22 umx-1.1.0/umx/man/xmuMakeThresholdsMatrices.Rd | 4 umx-1.1.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 22 umx-1.1.0/umx/man/xmuMaxLevels.Rd | 24 umx-1.1.0/umx/man/xmuMinLevels.Rd | 24 umx-1.1.0/umx/man/xmuPropagateLabels.Rd | 28 umx-1.1.0/umx/man/xmu_dot_make_paths.Rd | 22 umx-1.1.0/umx/man/xmu_dot_make_residuals.Rd | 22 umx-1.1.0/umx/man/xmu_start_value_list.Rd | 22 umx-1.1.0/umx/tests/testthat/test_DoF.r |only umx-1.1.0/umx/tests/testthat/test_umxLabel.r |only umx-1.1.0/umx/tests/testthat/test_umx_APA_pval.r |only umx-1.1.0/umx/tests/testthat/test_umx_has_means.r | 16 umx-1.1.0/umx/tests/testthat/test_umx_is_RAM.r |only umx-1.1.0/umx/tests/testthat/test_umx_is_cov.r |only umx-1.1.0/umx/tests/testthat/test_umx_rename.r |only 181 files changed, 3452 insertions(+), 3308 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.6 dated 2015-05-15 and 1.0.8 dated 2015-12-10
rscala-1.0.6/rscala/inst/java/rscala_2.10-1.0.6.jar |only rscala-1.0.6/rscala/inst/java/rscala_2.11-1.0.6.jar |only rscala-1.0.6/rscala/java/rscala_2.10-1.0.6-sources.jar |only rscala-1.0.6/rscala/java/rscala_2.11-1.0.6-sources.jar |only rscala-1.0.8/rscala/DESCRIPTION | 8 +++---- rscala-1.0.8/rscala/MD5 | 18 ++++++++--------- rscala-1.0.8/rscala/NEWS | 9 ++++++++ rscala-1.0.8/rscala/R/scalaInterpreter.R | 9 +++++++- rscala-1.0.8/rscala/inst/doc/readme.html | 5 +--- rscala-1.0.8/rscala/inst/java/rscala_2.10-1.0.8.jar |only rscala-1.0.8/rscala/inst/java/rscala_2.11-1.0.8.jar |only rscala-1.0.8/rscala/java/rscala_2.10-1.0.8-sources.jar |only rscala-1.0.8/rscala/java/rscala_2.11-1.0.8-sources.jar |only rscala-1.0.8/rscala/man/strintrpl.Rd | 4 +-- 14 files changed, 34 insertions(+), 19 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.5-00 dated 2015-09-25 and 0.5-10 dated 2015-12-10
phytools-0.5-00/phytools/README.md |only phytools-0.5-10/phytools/DESCRIPTION | 8 phytools-0.5-10/phytools/MD5 | 65 +++--- phytools-0.5-10/phytools/NAMESPACE | 187 +++++++++---------- phytools-0.5-10/phytools/R/add.species.to.genus.R | 20 ++ phytools-0.5-10/phytools/R/anc.ML.R | 12 - phytools-0.5-10/phytools/R/contMap.R | 43 +++- phytools-0.5-10/phytools/R/cophylo.R | 78 +++++++ phytools-0.5-10/phytools/R/densityMap.R | 30 ++- phytools-0.5-10/phytools/R/fastAnc.R | 27 ++ phytools-0.5-10/phytools/R/fitMk.R | 19 + phytools-0.5-10/phytools/R/make.simmap.R | 39 ++- phytools-0.5-10/phytools/R/mrp.supertree.R | 39 ++- phytools-0.5-10/phytools/R/optim.phylo.ls.R | 106 ++-------- phytools-0.5-10/phytools/R/phylo.to.map.R | 140 ++++++++++---- phytools-0.5-10/phytools/R/plotSimmap.R | 32 +-- phytools-0.5-10/phytools/R/plotTree.wBars.R | 11 - phytools-0.5-10/phytools/R/rerootingMethod.R | 2 phytools-0.5-10/phytools/R/utilities.R | 177 +++++++++++++++-- phytools-0.5-10/phytools/man/add.species.to.genus.Rd | 14 - phytools-0.5-10/phytools/man/bind.tip.Rd | 7 phytools-0.5-10/phytools/man/collapse.to.star.Rd | 2 phytools-0.5-10/phytools/man/contMap.Rd | 4 phytools-0.5-10/phytools/man/cophylo.Rd | 2 phytools-0.5-10/phytools/man/densityMap.Rd | 2 phytools-0.5-10/phytools/man/edgeProbs.Rd |only phytools-0.5-10/phytools/man/fastAnc.Rd | 3 phytools-0.5-10/phytools/man/fastMRCA.Rd | 4 phytools-0.5-10/phytools/man/mrp.supertree.Rd | 7 phytools-0.5-10/phytools/man/nodelabels.cophylo.Rd |only phytools-0.5-10/phytools/man/pbtree.Rd | 4 phytools-0.5-10/phytools/man/plotSimmap.Rd | 2 phytools-0.5-10/phytools/man/plotTree.wBars.Rd | 4 phytools-0.5-10/phytools/man/reroot.Rd | 4 phytools-0.5-10/phytools/man/write.simmap.Rd | 10 - 35 files changed, 720 insertions(+), 384 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty. Supported
models include cumulative logit, probit, cauchit, and complementary log-log.
The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Mike Wurm [aut, cre]
Maintainer: Mike Wurm <wurm@wisc.edu>
Diff between ordinalNet versions 1.3 dated 2015-11-30 and 1.4 dated 2015-12-10
DESCRIPTION | 16 ++++---- MD5 | 17 ++++---- NAMESPACE | 2 - R/ordinalNet.R | 4 +- man/coef.ordinalNetFit.Rd | 2 - man/ordinalNet.Rd | 2 - man/predict.ordinalNetFit.Rd | 2 - man/print.ordinalNetFit.Rd | 2 - tests/testdata.rda |only tests/testthat/test-ordinalNet.R | 78 ++++++++++++++++----------------------- 10 files changed, 56 insertions(+), 69 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre],
Hironobu Takahashi [cph],
Hajime Baba [cph],
Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.6.1 dated 2015-06-26 and 0.6.3 dated 2015-12-10
ChangeLog | 9 +++++++++ DESCRIPTION | 13 ++++++++----- MD5 | 18 +++++++++--------- NAMESPACE | 6 +++++- R/zen2han.R | 7 ++++--- R/zzz.R | 4 +--- man/Nippon-package.Rd | 4 ++-- man/zen2han.Rd | 4 ++-- src/kakasi/Makefile.in | 4 ++-- src/kakasi/Makefile.win | 4 ++-- 10 files changed, 44 insertions(+), 29 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>
Diff between marmap versions 0.9.4 dated 2015-12-01 and 0.9.5 dated 2015-12-10
DESCRIPTION | 8 +++--- MD5 | 45 +++++++++++++++++++----------------- NAMESPACE | 4 ++- R/combine.buffers.R | 55 +++++++++++++++++++++++++++++---------------- R/create.buffer.R | 22 +++++++++++++----- R/get.area.R | 4 ++- R/plot.bathy.R | 2 - R/plot.buffer.R |only R/print.buffer.R |only build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/combine.buffers.Rd | 22 +++++++++--------- man/create.buffer.Rd | 16 +++++++------ man/marmap.Rd | 4 +-- man/outline.buffer.Rd | 27 ++++++++++++++-------- man/plot.buffer.Rd |only man/plotArea.Rd | 2 - 25 files changed, 128 insertions(+), 83 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors, and for
the comparison of predictive errors between models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.3 dated 2015-09-18 and 0.1.4 dated 2015-12-10
loo-0.1.3/loo/R/misc.R |only loo-0.1.4/loo/DESCRIPTION | 21 ++-- loo-0.1.4/loo/MD5 | 53 ++++++------ loo-0.1.4/loo/NAMESPACE | 2 loo-0.1.4/loo/R/compare.R | 59 ++++++------- loo-0.1.4/loo/R/extract_log_lik.R | 20 +--- loo-0.1.4/loo/R/gpdfit.R | 5 - loo-0.1.4/loo/R/helpers.R | 86 ++++++++++++++++---- loo-0.1.4/loo/R/loo.R | 54 +++++------- loo-0.1.4/loo/R/loo_package.R | 17 --- loo-0.1.4/loo/R/print.R | 46 ++++++---- loo-0.1.4/loo/R/psislw.R | 52 ++++++------ loo-0.1.4/loo/R/waic.R | 17 +-- loo-0.1.4/loo/R/zzz.R | 3 loo-0.1.4/loo/man/compare.Rd | 47 +++++----- loo-0.1.4/loo/man/extract_log_lik.Rd | 11 -- loo-0.1.4/loo/man/gpdfit.Rd | 6 - loo-0.1.4/loo/man/loo-package.Rd | 19 +--- loo-0.1.4/loo/man/loo.Rd | 48 +++++------ loo-0.1.4/loo/man/nlist.Rd | 6 - loo-0.1.4/loo/man/print.loo.Rd | 43 +++++----- loo-0.1.4/loo/man/psislw.Rd | 28 +++--- loo-0.1.4/loo/man/waic.Rd | 14 +-- loo-0.1.4/loo/tests/testthat/test_compare.R |only loo-0.1.4/loo/tests/testthat/test_extract_log_lik.R |only loo-0.1.4/loo/tests/testthat/test_gpdfit.R | 12 +- loo-0.1.4/loo/tests/testthat/test_helpers.R | 68 ++++++--------- loo-0.1.4/loo/tests/testthat/test_loo_and_waic.R | 36 ++++---- loo-0.1.4/loo/tests/testthat/test_print_plot.R |only loo-0.1.4/loo/tests/testthat/test_psislw.R |only 30 files changed, 397 insertions(+), 376 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut],
Manuel Oviedo de la Fuente [aut, cre],
Pedro Galeano [ctb],
Alicia Nieto [ctb],
Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Diff between fda.usc versions 1.2.1 dated 2014-12-01 and 1.2.2 dated 2015-12-10
DESCRIPTION | 9 MD5 | 154 ++++---- NAMESPACE | 38 + NEWS | 15 R/GCV.S.R | 2 R/Ginv.R |only R/classif.DD.r | 426 +++++++++++++++++++--- R/classif.gkam.R | 2 R/classif.glm.R | 2 R/classif.np.ldata.R |only R/classif.np.r | 290 +++++++-------- R/classif.univariate.R | 7 R/depth.FM.r | 2 R/depth.mode.r | 243 ++++++------ R/depth.multivariate.R | 19 R/dfv.test.R | 2 R/fda.usc.internal.R | 1 R/flm.Ftest.R | 2 R/flm.test.R | 2 R/fregre.PPC.PPLS.R | 610 ++++++++++++++++--------------- R/fregre.basis.cv.R | 44 -- R/fregre.basis.fr.r | 142 ++++--- R/fregre.gkam.r | 3 R/fregre.glm.R | 2 R/fregre.lm.r | 4 R/fregre.np.cv.r | 2 R/kmeans.centers.update.R | 2 R/metric.dist.R | 85 +++- R/plot.fdata.R | 4 R/plot.lfdata.R |only R/predict.classif.R | 744 +++++++++++++++++++-------------------- R/predict.classif.npp.R |only R/predict.fregre.fr.r | 8 R/quantile.outliers.trim.r | 2 R/subset.lfdata.R |only man/DepthFunctional.Rd | 24 - man/DepthFunctionalIntegrate.Rd | 36 - man/Descriptive.Rd | 3 man/GCV.S.Rd | 3 man/Outliers.fdata.Rd | 5 man/PCvM.statistic.Rd | 138 +++---- man/anova.RPm.Rd | 4 man/classif.DD.Rd | 15 man/classif.depth.Rd | 3 man/classif.gkam.Rd | 5 man/create.fdata.basis.Rd | 6 man/dcor.test.rd | 6 man/dev.S.Rd | 9 man/dfv.test.Rd | 218 +++++------ man/fda.usc-package.Rd | 8 man/fdata.Rd | 5 man/fdata.bootstrap.Rd | 4 man/fdata2fd.Rd | 3 man/fdata2pls.Rd | 6 man/flm.Ftest.Rd | 172 ++++----- man/flm.test.Rd | 436 +++++++++++----------- man/fregre.bootstrap.Rd | 5 man/fregre.gkam.Rd | 7 man/fregre.glm.Rd | 3 man/fregre.lm.Rd | 3 man/fregre.np.cv.Rd | 3 man/fregre.pc.Rd | 3 man/fregre.plm.Rd | 3 man/influence.quan.Rd | 4 man/metric.dist.Rd | 2 man/metric.kl.Rd | 3 man/min.basis.Rd | 3 man/min.np.Rd | 3 man/order.fdata.Rd | 2 man/poblenou.Rd | 2 man/predict.fregre.fd.Rd | 5 man/predict.fregre.functional.Rd | 2 man/predict.fregre.scalar.Rd | 8 man/rproc2fdata.Rd | 8 man/rwild.Rd | 3 man/semimetric.NPFDA.Rd | 3 man/subset.fdata.Rd |only man/summary.fregre.fd.Rd | 6 man/tecator.Rd | 5 src/Adot.f90 | 96 ++--- src/PCvM_statistic.f90 | 18 81 files changed, 2345 insertions(+), 1832 deletions(-)
Title: Fantastic Heatmap
Description: R function to plot high quality, elegant heatmap using 'ggplot2' graphics .
Some of the important features of this package are, coloring of row/column side tree with
respect to the number of user defined cuts in the cluster, add annotations to both columns
and rows, option to input annotation palette for tree and column annotations and multiple
parameters to modify aesthetics (style, color, font) of texts in the plot.
Author: Vaishali Tumulu and Sivasish Sindiri
Maintainer: Sivasish Sindiri<sentisci@gmail.com>
Diff between fheatmap versions 1.0.0 dated 2015-05-03 and 1.0.1 dated 2015-12-09
fheatmap-1.0.0/fheatmap/man/figures |only fheatmap-1.0.1/fheatmap/DESCRIPTION | 14 fheatmap-1.0.1/fheatmap/MD5 | 20 fheatmap-1.0.1/fheatmap/NAMESPACE | 21 fheatmap-1.0.1/fheatmap/NEWS |only fheatmap-1.0.1/fheatmap/R/fheatmap.R | 1805 ++++++++++---------- fheatmap-1.0.1/fheatmap/man/annotation_col.Rd | 38 fheatmap-1.0.1/fheatmap/man/annotation_col_color.Rd | 36 fheatmap-1.0.1/fheatmap/man/annotation_row.Rd | 39 fheatmap-1.0.1/fheatmap/man/annotation_row_color.Rd | 38 fheatmap-1.0.1/fheatmap/man/fheatmap-package.Rd | 321 ++- fheatmap-1.0.1/fheatmap/man/fheatmap_data.Rd | 68 12 files changed, 1261 insertions(+), 1139 deletions(-)
Title: Regularized Cox Model
Description: Cox model regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty, and their adaptive forms, such as adaptive lasso and net adjusting for signs of linked coefficients. Moreover, it treats the number of non-zero coefficients as another tuning parameter and simultaneously selects with the regularization parameter \code{lambda}. In addition, it fits a varying coefficient Cox model by kernel smoothing, incorporated with the aforementioned penalties. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
Author: Xiang Li, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li <xl2473@columbia.edu>
Diff between Coxnet versions 0.1-1 dated 2015-03-22 and 0.2 dated 2015-12-09
DESCRIPTION | 10 MD5 | 31 - NAMESPACE | 4 R/Coxnet.R | 65 ++- R/RcppExports.R | 40 ++ R/coxini.R | 131 +++----- R/coxprep.R | 102 +++--- R/coxsplit.R | 27 + R/loCoxnet.R |only R/print.Coxnet.R | 39 +- inst/include/Coxnet_RcppExports.h | 190 +++++++++++ man/Coxnet-package.Rd | 18 - man/Coxnet.Rd | 103 ++++-- man/coxsplit.Rd | 21 - man/print.Coxnet.Rd | 4 src/Coxnet.cpp | 619 +++++++++++++++++++++++++++++++++++++- src/RcppExports.cpp | 447 +++++++++++++++++++++++++++ 17 files changed, 1578 insertions(+), 273 deletions(-)
Title: Advanced Gene Set Enrichment Analysis
Description: Implements an algorithm to conduct advanced
gene set enrichment analysis on the results of genomics experiments.
Author: Cedric Simillion
Maintainer: Cedric Simillion <cedric.simillion@dkf.unibe.ch>
Diff between SetRank versions 1.0.0 dated 2015-12-08 and 1.0.1 dated 2015-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/analysis.R | 3 ++- R/buildSets.R | 4 +++- inst/doc/vignette.pdf |binary man/buildSetCollection.Rd | 1 + 6 files changed, 14 insertions(+), 10 deletions(-)
More information about sensitivity2x2xk at CRAN
Permanent link
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Hadley Wickham [aut],
JJ Allaire [aut, cre],
Kevin Ushey [ctb],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rstudioapi versions 0.3.1 dated 2015-04-06 and 0.4.0 dated 2015-12-09
DESCRIPTION | 14 +++++++++----- MD5 | 30 +++++++++++++++++++----------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 5 +++++ R/document-api.R |only R/document-methods.R |only R/misc.R |only R/stubs.R | 7 ++++++- man/callFun.Rd | 2 +- man/document-mutation.Rd |only man/document_position.Rd |only man/document_range.Rd |only man/getActiveDocumentContext.Rd |only man/getVersion.Rd | 2 +- man/hasFun.Rd | 2 +- man/isAvailable.Rd | 2 +- man/navigateToFile.Rd |only man/sourceMarkers.Rd | 1 - man/versionInfo.Rd | 1 - man/viewer.Rd | 2 +- 20 files changed, 67 insertions(+), 25 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between rmdformats versions 0.1 dated 2015-12-08 and 0.1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/create.doc.R | 2 -- R/html_clean.R | 13 ------------- R/html_docco.R | 13 ------------- R/pilltabs.R | 6 ++++++ inst/doc/introduction.html | 4 ++-- man/create.doc.Rd | 2 -- man/html_clean.Rd | 14 -------------- man/html_docco.Rd | 14 -------------- man/pilltabs.Rd | 7 +++++++ 11 files changed, 29 insertions(+), 74 deletions(-)
Title: Risk Management
Description: Computes risk measures from data, as well as performs risk management procedures.
Author: Marcelo Brutti Righi
Maintainer: Marcelo Brutti Righi <marcelobrutti@hotmail.com>
Diff between riskR versions 1.0 dated 2015-10-19 and 1.1 dated 2015-12-09
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++++--------------- R/risk.R | 20 ++++++++------------ R/risk.decision.R | 12 ++++++------ R/risk.hedge.R | 10 +++++----- R/risk.port.R | 10 +++++----- R/risk.port2.R |only R/risk.req.R | 6 +++--- R/risk.roll.R | 8 ++++---- build/partial.rdb |binary data |only man/returns.Rd |only man/risk.Rd | 26 +++++++++++++------------- man/risk.decision.Rd | 18 +++++++++++------- man/risk.hedge.Rd | 20 ++++++++++++-------- man/risk.port.Rd | 20 ++++++++++++-------- man/risk.port2.Rd |only man/risk.req.Rd | 18 +++++++++++------- man/risk.roll.Rd | 20 ++++++++++++-------- man/riskR-package.Rd | 2 ++ 20 files changed, 128 insertions(+), 106 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-level, high-performance MongoDB client based on libmongoc and
jsonlite. Includes support for aggregation, indexing, map-reduce, streaming,
SSL encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.6 dated 2015-10-31 and 0.7 dated 2015-12-09
DESCRIPTION | 20 MD5 | 152 ++--- NAMESPACE | 2 NEWS | 7 R/object.R | 23 R/stream.R | 26 configure | 2 inst/doc/intro.Rmd | 9 inst/doc/intro.html | 15 man/mongo.Rd | 23 src/Makevars.in | 6 src/Makevars.win | 4 src/bson/bcon.h | 18 src/bson/bson-atomic.h | 2 src/bson/bson-compat.h | 3 src/bson/bson-config.h | 37 + src/bson/bson-json.c | 54 - src/bson/bson-string.c | 4 src/bson/bson-version.h | 15 src/bson/bson.c | 6 src/mongoc/mongoc-async-cmd.c | 3 src/mongoc/mongoc-bulk-operation-private.h | 1 src/mongoc/mongoc-bulk-operation.c | 12 src/mongoc/mongoc-bulk-operation.h | 2 src/mongoc/mongoc-client-pool.c | 8 src/mongoc/mongoc-client-private.h | 29 - src/mongoc/mongoc-client.c | 186 +++++- src/mongoc/mongoc-client.h | 4 src/mongoc/mongoc-cluster-private.h | 21 src/mongoc/mongoc-cluster.c | 175 +++--- src/mongoc/mongoc-collection-private.h | 2 src/mongoc/mongoc-collection.c | 450 +++++++++++---- src/mongoc/mongoc-collection.h | 12 src/mongoc/mongoc-cursor-array-private.h | 1 src/mongoc/mongoc-cursor-array.c | 29 - src/mongoc/mongoc-cursor-cursorid-private.h | 13 src/mongoc/mongoc-cursor-cursorid.c | 233 ++++++-- src/mongoc/mongoc-cursor-private.h | 57 + src/mongoc/mongoc-cursor.c | 657 ++++++++++++++++++----- src/mongoc/mongoc-cursor.h | 35 - src/mongoc/mongoc-database-private.h | 5 src/mongoc/mongoc-database.c | 135 +++- src/mongoc/mongoc-database.h | 5 src/mongoc/mongoc-error.h | 4 src/mongoc/mongoc-find-and-modify-private.h |only src/mongoc/mongoc-find-and-modify.c |only src/mongoc/mongoc-find-and-modify.h |only src/mongoc/mongoc-gridfs-file-private.h | 3 src/mongoc/mongoc-gridfs-file.c | 69 +- src/mongoc/mongoc-gridfs.c | 4 src/mongoc/mongoc-host-list-private.h | 4 src/mongoc/mongoc-host-list.c | 13 src/mongoc/mongoc-host-list.h | 5 src/mongoc/mongoc-log.c | 7 src/mongoc/mongoc-matcher.h | 6 src/mongoc/mongoc-read-concern-private.h |only src/mongoc/mongoc-read-concern.c |only src/mongoc/mongoc-read-concern.h |only src/mongoc/mongoc-read-prefs-private.h | 3 src/mongoc/mongoc-read-prefs.c | 2 src/mongoc/mongoc-rpc-private.h | 5 src/mongoc/mongoc-rpc.c | 39 + src/mongoc/mongoc-server-description-private.h | 8 src/mongoc/mongoc-server-description.c | 78 ++ src/mongoc/mongoc-server-stream-private.h | 6 src/mongoc/mongoc-server-stream.c | 12 src/mongoc/mongoc-thread-private.h | 2 src/mongoc/mongoc-topology-description-private.h | 1 src/mongoc/mongoc-topology-description.c | 104 +++ src/mongoc/mongoc-topology-scanner.c | 3 src/mongoc/mongoc-uri.c | 26 src/mongoc/mongoc-uri.h | 2 src/mongoc/mongoc-util-private.h | 5 src/mongoc/mongoc-util.c | 45 + src/mongoc/mongoc-version.h | 16 src/mongoc/mongoc-write-command-private.h | 2 src/mongoc/mongoc-write-command.c | 133 +++- src/mongoc/mongoc-write-concern.c | 12 tools/winlibs.R | 4 vignettes/intro.Rmd | 9 80 files changed, 2320 insertions(+), 815 deletions(-)
Title: Robust Linear Quantile Regression
Description: It fits a robust linear quantile regression model using a new family of zero-quantile distributions for the error term.
This family of distribution includes skewed versions of the Normal, Student's t, Laplace, Slash and Contaminated Normal distribution.
It provides estimates and full inference. It also provides envelopes plots for assessing the fit and confidences bands when several quantiles are provided simultaneously.
Author: Christian E. Galarza, Luis Benites, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between lqr versions 1.0 dated 2015-11-06 and 1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/EMonly.R | 2 +- R/FUNCTION.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Tools for Harnessing 'MLBAM' 'Gameday' Data and Visualizing
'pitchfx'
Description: With 'pitchRx', one can easily obtain Major League Baseball Advanced
Media's 'Gameday' data (as well as store it in a remote database). The
'Gameday' website hosts a wealth of data in XML format, but perhaps most
interesting is 'pitchfx'. Among other things, 'pitchfx' data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D 'scatterplots'
of the baseball's flight path. 'pitchfx' data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. 'pitchRx' provides an easy
and robust way to generate strike-zone plots using the 'ggplot2' package.
Author: Carson Sievert <cpsievert1@gmail.com>
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between pitchRx versions 1.8.1 dated 2015-10-25 and 1.8.2 dated 2015-12-09
DESCRIPTION | 25 +++++++++++++------------ MD5 | 6 +++--- NEWS | 6 ++++++ R/scrape.R | 1 + 4 files changed, 23 insertions(+), 15 deletions(-)
Title: Combine Data from Positive and Negative Ionization Mode Finding
Common Entities
Description: Find common entities detected in both positive and negative
ionization mode, delete this entity in the less sensible mode and combine both
matrices.
Author: Monica Calderon-Santiago
Maintainer: Monica Calderon-Santiago <b42casam@uco.es>
Diff between MScombine versions 1.0 dated 2015-11-20 and 1.1 dated 2015-12-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/FilterbyRT.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Linear Regression Based on Linear Structure Between Covariates
Description: Linear regression based on a recursive structural equation model
(explicit multiples correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics (Boxplot with confidence intervals, etc) and regression trees.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <corregeous@correg.org>
Diff between CorReg versions 1.0.5 dated 2015-06-09 and 1.1.1 dated 2015-12-09
DESCRIPTION | 27 +++++++++++----------- MD5 | 56 ++++++++++++++++++++++++---------------------- NAMESPACE | 44 ++++++++++++++++++++++++++++++++++-- NEWS | 11 ++++++--- R/A_clere.R | 2 - R/BoxPlot.R |only R/CorReg-package.R | 7 ++++- R/Estep.R | 2 - R/MSE_loc.R | 3 -- R/Terminator.R | 3 +- R/alphabet.R |only R/anthem.R |only R/correg.R | 33 ++++++++++++++++++--------- R/density_estimation.R | 4 ++- R/mixture_generator.R | 4 ++- R/structureFinder.R | 6 +++- man/BicZ.Rd | 4 +-- man/BoxPlot.Rd |only man/Conan.Rd | 4 +-- man/CorReg-package.Rd | 31 +++++++++++++------------ man/MSE_loc.Rd | 14 ++++------- man/Terminator.Rd | 6 +++- man/compare_struct.Rd | 2 - man/correg.Rd | 16 ++++++------- man/density_estimation.Rd | 6 +++- man/matplot_zone.Rd | 4 +-- man/mixture_generator.Rd | 3 +- man/readZ.Rd | 2 - man/recursive_tree.Rd | 8 +++--- man/showdata.Rd | 8 ++++-- man/structureFinder.Rd | 24 +++++++++++-------- 31 files changed, 208 insertions(+), 126 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web APIs for chemical information.
Author: Eduard Szöcs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szöcs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.3.1 dated 2015-09-27 and 0.0.4.0 dated 2015-12-09
webchem-0.0.3.1/webchem/man/cir_query.Rd |only webchem-0.0.3.1/webchem/man/csid_compinfo.Rd |only webchem-0.0.3.1/webchem/man/csid_extcompinfo.Rd |only webchem-0.0.3.1/webchem/man/ppdb_query.Rd |only webchem-0.0.4.0/webchem/DESCRIPTION | 21 webchem-0.0.4.0/webchem/MD5 | 101 +- webchem-0.0.4.0/webchem/NAMESPACE | 24 webchem-0.0.4.0/webchem/NEWS | 54 + webchem-0.0.4.0/webchem/R/alanwood.R | 24 webchem-0.0.4.0/webchem/R/chemid.R |only webchem-0.0.4.0/webchem/R/chemspider.R | 533 ++++++++++++++- webchem-0.0.4.0/webchem/R/cir.R | 24 webchem-0.0.4.0/webchem/R/cts.R | 12 webchem-0.0.4.0/webchem/R/etox.R | 16 webchem-0.0.4.0/webchem/R/physprop.R | 23 webchem-0.0.4.0/webchem/R/ppdb.R | 22 webchem-0.0.4.0/webchem/R/pubchem.R | 91 +- webchem-0.0.4.0/webchem/R/utils.R |only webchem-0.0.4.0/webchem/R/webchem-defunct.R |only webchem-0.0.4.0/webchem/R/webchem-deprecated.R | 44 + webchem-0.0.4.0/webchem/inst |only webchem-0.0.4.0/webchem/man/alanwood.Rd | 6 webchem-0.0.4.0/webchem/man/chemid.Rd |only webchem-0.0.4.0/webchem/man/cid_compinfo.Rd | 2 webchem-0.0.4.0/webchem/man/cir.Rd |only webchem-0.0.4.0/webchem/man/cs_compinfo.Rd |only webchem-0.0.4.0/webchem/man/cs_convert.Rd |only webchem-0.0.4.0/webchem/man/cs_csid_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_extcompinfo.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_csid.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_inchikey.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_inchi_smiles.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_csid.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_inchi.Rd |only webchem-0.0.4.0/webchem/man/cs_inchikey_mol.Rd |only webchem-0.0.4.0/webchem/man/cs_smiles_inchi.Rd |only webchem-0.0.4.0/webchem/man/cts_compinfo.Rd | 7 webchem-0.0.4.0/webchem/man/cts_convert.Rd | 2 webchem-0.0.4.0/webchem/man/etox_basic.Rd | 2 webchem-0.0.4.0/webchem/man/etox_targets.Rd | 2 webchem-0.0.4.0/webchem/man/etox_tests.Rd | 2 webchem-0.0.4.0/webchem/man/extr_num.Rd |only webchem-0.0.4.0/webchem/man/get_cid.Rd | 2 webchem-0.0.4.0/webchem/man/get_csid.Rd | 2 webchem-0.0.4.0/webchem/man/get_etoxid.Rd | 2 webchem-0.0.4.0/webchem/man/is.cas.Rd |only webchem-0.0.4.0/webchem/man/is.inchikey.Rd |only webchem-0.0.4.0/webchem/man/is.inchikey_cs.Rd |only webchem-0.0.4.0/webchem/man/pan.Rd | 2 webchem-0.0.4.0/webchem/man/parse_mol.Rd |only webchem-0.0.4.0/webchem/man/physprop.Rd | 2 webchem-0.0.4.0/webchem/man/ppdb.Rd |only webchem-0.0.4.0/webchem/man/ppdb_buildidx.Rd | 2 webchem-0.0.4.0/webchem/man/ppdb_idx.Rd | 5 webchem-0.0.4.0/webchem/man/webchem-defunct.Rd |only webchem-0.0.4.0/webchem/man/webchem-deprecated.Rd | 26 webchem-0.0.4.0/webchem/tests/testthat/test-alanwood.R | 7 webchem-0.0.4.0/webchem/tests/testthat/test-chemid.R |only webchem-0.0.4.0/webchem/tests/testthat/test-chemspider.R | 259 ++++++- webchem-0.0.4.0/webchem/tests/testthat/test-cir.R | 16 webchem-0.0.4.0/webchem/tests/testthat/test-cts.R | 18 webchem-0.0.4.0/webchem/tests/testthat/test-etox.R | 4 webchem-0.0.4.0/webchem/tests/testthat/test-physprop.R | 3 webchem-0.0.4.0/webchem/tests/testthat/test-ppdb.R | 8 webchem-0.0.4.0/webchem/tests/testthat/test-pubchem.R | 11 webchem-0.0.4.0/webchem/tests/testthat/test-utils.R |only 67 files changed, 1163 insertions(+), 218 deletions(-)
Title: Common Infrastructure for Extensions of Exponential Random Graph
Models
Description: Datasets and definitions of generic functions used in dependencies of the xergm package.
Author: Philip Leifeld [aut, cre]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between xergm.common versions 1.5.4 dated 2015-09-20 and 1.6 dated 2015-12-09
DESCRIPTION | 14 ++++----- MD5 | 10 +++--- R/preprocess.R | 79 +++++++++++++++++++++++++++++++++++++------------------ data/chemnet.rda |binary data/knecht.rda |binary man/chemnet.Rd | 2 - 6 files changed, 67 insertions(+), 38 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-0 dated 2015-10-27 and 1.2-1 dated 2015-12-09
DESCRIPTION | 10 MD5 | 36 +- R/g.analyse.R | 10 R/g.calibrate.R | 20 - R/g.create.sp.mat.R | 17 - R/g.getbout.R | 9 R/g.getmeta.R | 54 ++-- R/g.part1.R | 531 ++++++++++++++++++++------------------- R/g.part2.R | 4 R/g.part3.R | 167 ++++++------ R/g.part4.R | 78 ++--- R/g.report.part2.R | 2 R/g.report.part4.R | 698 ++++++++++++++++++++++++++-------------------------- R/g.shell.GGIR.R | 109 ++++++-- R/g.sib.det.R | 4 inst/NEWS.Rd | 11 man/GGIR-package.Rd | 9 man/g.part3.Rd | 169 ++++++------ man/g.shell.GGIR.Rd | 325 ++++++++++++------------ 19 files changed, 1184 insertions(+), 1079 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between texreg versions 1.35 dated 2015-04-28 and 1.36 dated 2015-12-08
DESCRIPTION | 29 +- MD5 | 26 - NAMESPACE | 9 R/classDefinition.R | 5 R/extract.R | 736 ++++++++++++++++++++++++++++++++++++++++----------- R/internal.R | 154 ++++++++++ R/texreg.R | 141 ++++++--- build/vignette.rds |binary inst/doc/v55i08.R | 46 +-- inst/doc/v55i08.Rnw | 52 ++- inst/doc/v55i08.pdf |binary man/extract.Rd | 86 +++++ man/texreg.Rd | 35 +- vignettes/v55i08.Rnw | 52 ++- 14 files changed, 1048 insertions(+), 323 deletions(-)
Title: Repeated Measures Proportional Odds Logistic Regression
Description: Fits linear models to repeated ordinal scores using GEE methodology.
Author: Nick Parsons
Maintainer: Nick Parsons <nick.parsons@warwick.ac.uk>
Diff between repolr versions 2.0 dated 2013-04-19 and 3.1 dated 2015-12-08
repolr-2.0/repolr/R/grepolr.R |only repolr-2.0/repolr/R/srepolr.R |only repolr-2.0/repolr/R/summary.gee.R |only repolr-2.0/repolr/data/HHSpain.rda |only repolr-2.0/repolr/data/QoL.rda |only repolr-2.0/repolr/data/achilles.rda |only repolr-2.0/repolr/man/grepolr.Rd |only repolr-2.0/repolr/man/srepolr.Rd |only repolr-2.0/repolr/man/summary.gee.Rd |only repolr-3.1/repolr/DESCRIPTION | 20 repolr-3.1/repolr/MD5 | 51 + repolr-3.1/repolr/NAMESPACE | 23 repolr-3.1/repolr/R/QIC.R | 17 repolr-3.1/repolr/R/RcppExports.R |only repolr-3.1/repolr/R/ord.expand.R | 85 ++ repolr-3.1/repolr/R/polycuts.R | 68 ++ repolr-3.1/repolr/R/print.repolr.R |only repolr-3.1/repolr/R/print.summary.repolr.R |only repolr-3.1/repolr/R/repolr.R | 872 +++++------------------------ repolr-3.1/repolr/R/summary.repolr.R |only repolr-3.1/repolr/data/HHSpain.txt.gz |only repolr-3.1/repolr/data/QoL.txt.gz |only repolr-3.1/repolr/data/achilles.txt.gz |only repolr-3.1/repolr/data/begonia.txt.gz |only repolr-3.1/repolr/data/mobility.txt.gz |only repolr-3.1/repolr/man/QIC.Rd | 30 repolr-3.1/repolr/man/begonia.Rd |only repolr-3.1/repolr/man/mobility.Rd |only repolr-3.1/repolr/man/ord.expand.Rd | 13 repolr-3.1/repolr/man/polycuts.Rd | 35 - repolr-3.1/repolr/man/repolr-package.Rd | 108 ++- repolr-3.1/repolr/man/summary.repolr.Rd |only repolr-3.1/repolr/src |only 33 files changed, 468 insertions(+), 854 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of a joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Multivariate joint frailty models for two types of recurrent events and a terminal event.
7) Joint models for longitudinal data and a terminal event.
8) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.8.1 dated 2015-11-21 and 2.8.2 dated 2015-12-08
frailtypack-2.8.1/frailtypack/src/epoce.f90 |only frailtypack-2.8.1/frailtypack/src/epoce_log.f90 |only frailtypack-2.8.1/frailtypack/vignettes/vignette.Rmd |only frailtypack-2.8.2/frailtypack/DESCRIPTION | 10 +++-- frailtypack-2.8.2/frailtypack/MD5 | 23 ++++++------ frailtypack-2.8.2/frailtypack/NEWS | 6 +++ frailtypack-2.8.2/frailtypack/R/longiPenal.R | 3 + frailtypack-2.8.2/frailtypack/R/prediction.R | 5 +- frailtypack-2.8.2/frailtypack/build |only frailtypack-2.8.2/frailtypack/inst/doc |only frailtypack-2.8.2/frailtypack/man/frailtypack-package.Rd | 2 - frailtypack-2.8.2/frailtypack/man/trivPenal.Rd | 2 - frailtypack-2.8.2/frailtypack/src/aaOptim.f90 | 15 +++++-- frailtypack-2.8.2/frailtypack/src/prediction_tri.f90 | 22 +++++------ frailtypack-2.8.2/frailtypack/vignettes/Package_summary.Rmd |only 15 files changed, 52 insertions(+), 36 deletions(-)
Title: Package for Deep Architectures and Restricted Boltzmann Machines
Description: The darch package is built on the basis of the code from G. E.
Hinton and R. R. Salakhutdinov (available under Matlab Code for deep belief
nets). This package is for generating neural networks with many layers (deep
architectures) and train them with the method introduced by the publications
"A fast learning algorithm for deep belief nets" (G. E. Hinton, S. Osindero,
Y. W. Teh; doi: 10.1162/neco.2006.18.7.1527) and "Reducing the
dimensionality of data with neural networks" (G. E. Hinton, R. R.
Salakhutdinov; doi: 10.1126/science.1127647). This method includes a pre
training with the contrastive divergence method published by G.E Hinton
(2002; doi: 10.1162/089976602760128018) and a fine tuning with common known
training algorithms like backpropagation or conjugate gradients.
Additionally, supervised fine-tuning can be enhanced with maxout and
dropout, two recently developed techniques to improve fine-tuning for deep
learning.
Author: Martin Drees [aut, cre],
Johannes Rueckert [ctb],
Geoffrey Hinton [cph],
Ruslan Salakhutdinov [cph],
Carl Edward Rasmussen [cph],
Maintainer: Martin Drees <mdrees@stud.fh-dortmund.de>
Diff between darch versions 0.9.1 dated 2014-03-16 and 0.10.0 dated 2015-12-08
darch-0.10.0/darch/DESCRIPTION | 65 - darch-0.10.0/darch/LICENSE |only darch-0.10.0/darch/MD5 | 394 ++++--- darch-0.10.0/darch/NAMESPACE | 67 + darch-0.10.0/darch/R/backpropagation.R | 181 +-- darch-0.10.0/darch/R/darch.Add.R | 108 +- darch-0.10.0/darch/R/darch.Getter.R | 533 ++++++---- darch-0.10.0/darch/R/darch.Learn.R | 404 ++++--- darch-0.10.0/darch/R/darch.R | 116 +- darch-0.10.0/darch/R/darch.Remove.R | 19 darch-0.10.0/darch/R/darch.Reset.R | 22 darch-0.10.0/darch/R/darch.Setter.R | 180 +++ darch-0.10.0/darch/R/darchUnitFunctions.R | 345 +++--- darch-0.10.0/darch/R/dataset.R |only darch-0.10.0/darch/R/dropout.R |only darch-0.10.0/darch/R/errorFunctions.R | 55 - darch-0.10.0/darch/R/generateRBMs.R | 23 darch-0.10.0/darch/R/generateWeights.R | 18 darch-0.10.0/darch/R/interface.R |only darch-0.10.0/darch/R/loadDArch.R | 21 darch-0.10.0/darch/R/loadRBM.R | 19 darch-0.10.0/darch/R/loadRBMFFWeights.R | 21 darch-0.10.0/darch/R/makeStartEndPoints.R | 19 darch-0.10.0/darch/R/minimize.R | 78 - darch-0.10.0/darch/R/minimizeAutoencoder.R | 42 darch-0.10.0/darch/R/minimizeClassifier.R | 49 darch-0.10.0/darch/R/mnist.R |only darch-0.10.0/darch/R/net.Getter.R | 94 + darch-0.10.0/darch/R/net.R | 66 - darch-0.10.0/darch/R/net.Setter.R | 93 + darch-0.10.0/darch/R/newDArch.R | 26 darch-0.10.0/darch/R/newRBM.R | 17 darch-0.10.0/darch/R/rbm.Getter.R | 31 darch-0.10.0/darch/R/rbm.Learn.R | 146 +- darch-0.10.0/darch/R/rbm.R | 145 +- darch-0.10.0/darch/R/rbm.Reset.R | 17 darch-0.10.0/darch/R/rbm.Setter.R | 45 darch-0.10.0/darch/R/rbmUnitFunctions.R | 61 - darch-0.10.0/darch/R/rbmUpdate.R | 26 darch-0.10.0/darch/R/rpropagation.R | 128 +- darch-0.10.0/darch/R/runDArch.R | 32 darch-0.10.0/darch/R/saveDArch.R | 35 darch-0.10.0/darch/R/saveRBM.R | 23 darch-0.10.0/darch/R/saveRBMFFWeights.R | 21 darch-0.10.0/darch/README |only darch-0.10.0/darch/inst |only darch-0.10.0/darch/man/DArch-class.Rd |only darch-0.10.0/darch/man/DataSet-class.Rd |only darch-0.10.0/darch/man/Net-class.Rd |only darch-0.10.0/darch/man/RBM-class.Rd |only darch-0.10.0/darch/man/addExecOutput-DArch-method.Rd |only darch-0.10.0/darch/man/addExecOutput.Rd |only darch-0.10.0/darch/man/addLayer-DArch-method.Rd |only darch-0.10.0/darch/man/addLayer.Rd |only darch-0.10.0/darch/man/addLayerField-DArch-method.Rd |only darch-0.10.0/darch/man/addLayerField.Rd |only darch-0.10.0/darch/man/applyDropoutMask.Rd |only darch-0.10.0/darch/man/backpropagation.Rd | 52 darch-0.10.0/darch/man/binSigmoidUnit.Rd | 37 darch-0.10.0/darch/man/createDataSet-ANY-ANY-missing-DataSet-method.Rd |only darch-0.10.0/darch/man/createDataSet-ANY-ANY-missing-missing-method.Rd |only darch-0.10.0/darch/man/createDataSet-ANY-missing-formula-missing-method.Rd |only darch-0.10.0/darch/man/createDataSet.Rd |only darch-0.10.0/darch/man/crossEntropyError.Rd | 18 darch-0.10.0/darch/man/darch.DataSet.Rd |only darch-0.10.0/darch/man/darch.Rd |only darch-0.10.0/darch/man/darch.default.Rd |only darch-0.10.0/darch/man/darch.formula.Rd |only darch-0.10.0/darch/man/fineTuneDArch-DArch-method.Rd |only darch-0.10.0/darch/man/fineTuneDArch.Rd |only darch-0.10.0/darch/man/generateDropoutMask.Rd |only darch-0.10.0/darch/man/generateRBMs-methods.Rd | 21 darch-0.10.0/darch/man/generateWeights.Rd | 13 darch-0.10.0/darch/man/getBatchSize-methods.Rd | 4 darch-0.10.0/darch/man/getCancel-DArch-method.Rd |only darch-0.10.0/darch/man/getCancel.Rd |only darch-0.10.0/darch/man/getCancelMessage-DArch-method.Rd |only darch-0.10.0/darch/man/getCancelMessage.Rd |only darch-0.10.0/darch/man/getDropoutHiddenLayers-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutHiddenLayers.Rd |only darch-0.10.0/darch/man/getDropoutInputLayer-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutInputLayer.Rd |only darch-0.10.0/darch/man/getDropoutMask-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutMask.Rd |only darch-0.10.0/darch/man/getDropoutMasks-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutMasks.Rd |only darch-0.10.0/darch/man/getDropoutOneMaskPerEpoch-DArch-method.Rd |only darch-0.10.0/darch/man/getDropoutOneMaskPerEpoch.Rd |only darch-0.10.0/darch/man/getEpochs-Net-method.Rd |only darch-0.10.0/darch/man/getEpochs.Rd |only darch-0.10.0/darch/man/getErrorFunction-methods.Rd | 4 darch-0.10.0/darch/man/getExecOutput-DArch-method.Rd |only darch-0.10.0/darch/man/getExecOutput.Rd |only darch-0.10.0/darch/man/getExecOutputs-DArch-method.Rd |only darch-0.10.0/darch/man/getExecOutputs.Rd |only darch-0.10.0/darch/man/getExecuteFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getExecuteFunction.Rd |only darch-0.10.0/darch/man/getFF-methods.Rd | 4 darch-0.10.0/darch/man/getFinalMomentum-methods.Rd | 4 darch-0.10.0/darch/man/getFineTuneFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getFineTuneFunction.Rd |only darch-0.10.0/darch/man/getGenWeightFunction-methods.Rd | 4 darch-0.10.0/darch/man/getHiddenBiases-methods.Rd | 4 darch-0.10.0/darch/man/getHiddenBiasesInc-methods.Rd | 7 darch-0.10.0/darch/man/getHiddenUnitStates-methods.Rd | 4 darch-0.10.0/darch/man/getInitialMomentum-Net-method.Rd |only darch-0.10.0/darch/man/getInitialMomentum.Rd |only darch-0.10.0/darch/man/getLayer-DArch-method.Rd |only darch-0.10.0/darch/man/getLayer.Rd |only darch-0.10.0/darch/man/getLayerField-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerField.Rd |only darch-0.10.0/darch/man/getLayerFunction-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerFunction.Rd |only darch-0.10.0/darch/man/getLayerWeights-DArch-method.Rd |only darch-0.10.0/darch/man/getLayerWeights.Rd |only darch-0.10.0/darch/man/getLayers-DArch-method.Rd |only darch-0.10.0/darch/man/getLayers.Rd |only darch-0.10.0/darch/man/getLearnRateBiasHidden-methods.Rd | 4 darch-0.10.0/darch/man/getLearnRateBiasVisible-methods.Rd | 4 darch-0.10.0/darch/man/getLearnRateBiases-DArch-method.Rd |only darch-0.10.0/darch/man/getLearnRateBiases.Rd |only darch-0.10.0/darch/man/getLearnRateWeights-methods.Rd | 4 darch-0.10.0/darch/man/getMomentum-methods.Rd | 8 darch-0.10.0/darch/man/getMomentumSwitch-methods.Rd | 4 darch-0.10.0/darch/man/getNormalizeWeights-Net-method.Rd |only darch-0.10.0/darch/man/getNormalizeWeights.Rd |only darch-0.10.0/darch/man/getNumHidden-methods.Rd | 4 darch-0.10.0/darch/man/getNumVisible-methods.Rd | 7 darch-0.10.0/darch/man/getOutput-methods.Rd | 4 darch-0.10.0/darch/man/getPosPhaseData-methods.Rd | 10 darch-0.10.0/darch/man/getRBMList-DArch-method.Rd |only darch-0.10.0/darch/man/getRBMList.Rd |only darch-0.10.0/darch/man/getStats-methods.Rd | 10 darch-0.10.0/darch/man/getVisibleBiases-methods.Rd | 4 darch-0.10.0/darch/man/getVisibleBiasesInc-methods.Rd | 7 darch-0.10.0/darch/man/getVisibleUnitStates-methods.Rd | 4 darch-0.10.0/darch/man/getWeightCost-methods.Rd | 4 darch-0.10.0/darch/man/getWeightInc-methods.Rd | 4 darch-0.10.0/darch/man/getWeights-methods.Rd | 8 darch-0.10.0/darch/man/incrementEpochs-Net-method.Rd |only darch-0.10.0/darch/man/incrementEpochs.Rd |only darch-0.10.0/darch/man/linearUnit.Rd | 33 darch-0.10.0/darch/man/linearUnitDerivative.Rd | 37 darch-0.10.0/darch/man/linearUnitFunc.Rd | 31 darch-0.10.0/darch/man/loadDArch.Rd | 16 darch-0.10.0/darch/man/loadRBM.Rd | 19 darch-0.10.0/darch/man/loadRBMFFWeights.Rd | 18 darch-0.10.0/darch/man/makeStartEndPoints.Rd | 19 darch-0.10.0/darch/man/maxoutUnitDerivative.Rd |only darch-0.10.0/darch/man/minimize.Rd | 91 - darch-0.10.0/darch/man/minimizeAutoencoder.Rd | 44 darch-0.10.0/darch/man/minimizeClassifier.Rd | 52 darch-0.10.0/darch/man/mseError.Rd | 21 darch-0.10.0/darch/man/newDArch.Rd | 27 darch-0.10.0/darch/man/newRBM.Rd | 19 darch-0.10.0/darch/man/preTrainDArch-DArch-method.Rd |only darch-0.10.0/darch/man/preTrainDArch.Rd |only darch-0.10.0/darch/man/predict.DArch.Rd |only darch-0.10.0/darch/man/print.DArch.Rd |only darch-0.10.0/darch/man/provideMNIST.Rd |only darch-0.10.0/darch/man/quadraticError.Rd | 18 darch-0.10.0/darch/man/rbmUpdate.Rd | 12 darch-0.10.0/darch/man/readMNIST.Rd | 23 darch-0.10.0/darch/man/removeLayerField-methods.Rd | 11 darch-0.10.0/darch/man/resetDArch-methods.Rd | 18 darch-0.10.0/darch/man/resetExecOutput-methods.Rd | 9 darch-0.10.0/darch/man/resetRBM-methods.Rd | 7 darch-0.10.0/darch/man/rpropagation.Rd | 134 +- darch-0.10.0/darch/man/runDArch.Rd | 11 darch-0.10.0/darch/man/saveDArch-methods.Rd | 34 darch-0.10.0/darch/man/saveRBM-methods.Rd | 20 darch-0.10.0/darch/man/saveRBMFFWeights-methods.Rd | 19 darch-0.10.0/darch/man/setBatchSize-methods.Rd | 8 darch-0.10.0/darch/man/setCancel-methods.Rd | 10 darch-0.10.0/darch/man/setCancelMessage-methods.Rd | 9 darch-0.10.0/darch/man/setDropoutHiddenLayers-methods.Rd |only darch-0.10.0/darch/man/setDropoutInputLayer-methods.Rd |only darch-0.10.0/darch/man/setDropoutMask-methods.Rd |only darch-0.10.0/darch/man/setDropoutMasks-methods.Rd |only darch-0.10.0/darch/man/setDropoutOneMaskPerEpoch-set-DArch-method.Rd |only darch-0.10.0/darch/man/setDropoutOneMaskPerEpoch-set.Rd |only darch-0.10.0/darch/man/setErrorFunction-methods.Rd | 8 darch-0.10.0/darch/man/setExecuteFunction-methods.Rd | 9 darch-0.10.0/darch/man/setFF-methods.Rd | 10 darch-0.10.0/darch/man/setFinalMomentum-methods.Rd | 8 darch-0.10.0/darch/man/setFineTuneFunction-methods.Rd | 9 darch-0.10.0/darch/man/setGenWeightFunction-methods.Rd | 14 darch-0.10.0/darch/man/setHiddenBiases-methods.Rd | 12 darch-0.10.0/darch/man/setHiddenBiasesInc-methods.Rd | 9 darch-0.10.0/darch/man/setHiddenUnitFunction-methods.Rd | 8 darch-0.10.0/darch/man/setHiddenUnitStates-methods.Rd | 8 darch-0.10.0/darch/man/setInitialMomentum-set-Net-method.Rd |only darch-0.10.0/darch/man/setInitialMomentum-set.Rd |only darch-0.10.0/darch/man/setLayer-methods.Rd | 11 darch-0.10.0/darch/man/setLayerField-methods.Rd | 17 darch-0.10.0/darch/man/setLayerFunction-methods.Rd | 11 darch-0.10.0/darch/man/setLayerWeights-methods.Rd | 11 darch-0.10.0/darch/man/setLayers-methods.Rd | 9 darch-0.10.0/darch/man/setLearnRateBiasHidden-methods.Rd | 13 darch-0.10.0/darch/man/setLearnRateBiasVisible-methods.Rd | 11 darch-0.10.0/darch/man/setLearnRateBiases-methods.Rd | 9 darch-0.10.0/darch/man/setLearnRateWeights-methods.Rd | 8 darch-0.10.0/darch/man/setLogLevel-methods.Rd | 21 darch-0.10.0/darch/man/setMomentumSwitch-methods.Rd | 8 darch-0.10.0/darch/man/setNormalizeWeights-set-Net-method.Rd |only darch-0.10.0/darch/man/setNormalizeWeights-set.Rd |only darch-0.10.0/darch/man/setNumHidden-methods.Rd | 8 darch-0.10.0/darch/man/setNumVisible-methods.Rd | 8 darch-0.10.0/darch/man/setOutput-methods.Rd | 8 darch-0.10.0/darch/man/setPosPhaseData-methods.Rd | 8 darch-0.10.0/darch/man/setRBMList-methods.Rd | 10 darch-0.10.0/darch/man/setStats-methods.Rd | 14 darch-0.10.0/darch/man/setUpdateFunction-methods.Rd | 9 darch-0.10.0/darch/man/setVisibleBiases-methods.Rd | 12 darch-0.10.0/darch/man/setVisibleBiasesInc-methods.Rd | 9 darch-0.10.0/darch/man/setVisibleUnitFunction-methods.Rd | 8 darch-0.10.0/darch/man/setVisibleUnitStates-methods.Rd | 8 darch-0.10.0/darch/man/setWeightCost-methods.Rd | 8 darch-0.10.0/darch/man/setWeightInc-methods.Rd | 8 darch-0.10.0/darch/man/setWeights-methods.Rd | 9 darch-0.10.0/darch/man/sigmUnitFunc.Rd | 32 darch-0.10.0/darch/man/sigmUnitFuncSwitch.Rd | 42 darch-0.10.0/darch/man/sigmoidUnit.Rd | 30 darch-0.10.0/darch/man/sigmoidUnitDerivative.Rd | 37 darch-0.10.0/darch/man/softmaxUnit.Rd | 32 darch-0.10.0/darch/man/softmaxUnitDerivative.Rd | 37 darch-0.10.0/darch/man/tanSigmoidUnit.Rd |only darch-0.10.0/darch/man/tanSigmoidUnitDerivative.Rd |only darch-0.10.0/darch/man/trainRBM-RBM-method.Rd |only darch-0.10.0/darch/man/trainRBM.Rd |only darch-0.10.0/darch/man/validateDataSet-DataSet-method.Rd |only darch-0.10.0/darch/man/validateDataSet.Rd |only darch-0.9.1/darch/R/package-darch.R |only darch-0.9.1/darch/R/readMNIST.R |only darch-0.9.1/darch/README.md |only darch-0.9.1/darch/man/DArch.Rd |only darch-0.9.1/darch/man/Net.Rd |only darch-0.9.1/darch/man/RBM.Rd |only darch-0.9.1/darch/man/addExecOutput-methods.Rd |only darch-0.9.1/darch/man/addLayer-methods.Rd |only darch-0.9.1/darch/man/addLayerField-methods.Rd |only darch-0.9.1/darch/man/darch-package.Rd |only darch-0.9.1/darch/man/fineTuneDArch-methods.Rd |only darch-0.9.1/darch/man/getCancel-methods.Rd |only darch-0.9.1/darch/man/getCancelMessage-methods.Rd |only darch-0.9.1/darch/man/getExecOutput-methods.Rd |only darch-0.9.1/darch/man/getExecOutputs-methods.Rd |only darch-0.9.1/darch/man/getExecuteFunction-methods.Rd |only darch-0.9.1/darch/man/getFineTuneFunction-methods.Rd |only darch-0.9.1/darch/man/getLayer-methods.Rd |only darch-0.9.1/darch/man/getLayerField-methods.Rd |only darch-0.9.1/darch/man/getLayerFunction-methods.Rd |only darch-0.9.1/darch/man/getLayerWeights-methods.Rd |only darch-0.9.1/darch/man/getLayers-methods.Rd |only darch-0.9.1/darch/man/getLearnRateBiases-methods.Rd |only darch-0.9.1/darch/man/getRBMList-methods.Rd |only darch-0.9.1/darch/man/preTrainDArch-methods.Rd |only darch-0.9.1/darch/man/setMomentum-methods.Rd |only darch-0.9.1/darch/man/trainRBM-methods.Rd |only 259 files changed, 3352 insertions(+), 2030 deletions(-)
Title: Pathway Analysis Methods for Genomewide Association Data
Description: Bayesian hierarchical methods for pathway analysis of genomewide association data: Normal/Bayes factors and Sparse Normal/Adaptive lasso. The Frequentist Fisher's product method is included as well.
Author: Marina Evangelou
Maintainer: Marina Evangelou <m.evangelou@ic.ac.uk>
Diff between PAGWAS versions 1.0 dated 2013-11-13 and 2.0 dated 2015-12-08
PAGWAS-1.0/PAGWAS/R/GWAS.analysis.R |only PAGWAS-1.0/PAGWAS/R/PAGWAS-internal.R |only PAGWAS-1.0/PAGWAS/R/TPR.FPR.R |only PAGWAS-1.0/PAGWAS/R/bf.TPR.FPR.R |only PAGWAS-1.0/PAGWAS/R/bf.area.R |only PAGWAS-1.0/PAGWAS/R/create.pathway.matrix.R |only PAGWAS-1.0/PAGWAS/R/internal.function.simulations.R |only PAGWAS-1.0/PAGWAS/R/return.a.SNAL.R |only PAGWAS-1.0/PAGWAS/R/return.bf.NBF.R |only PAGWAS-1.0/PAGWAS/R/return.hyperparameters.NBF.R |only PAGWAS-1.0/PAGWAS/R/return.s2.SNAL.R |only PAGWAS-1.0/PAGWAS/R/roc.convex.R |only PAGWAS-1.0/PAGWAS/data/list.of.parameters.rda |only PAGWAS-1.0/PAGWAS/man/create.pathway.matrix.Rd |only PAGWAS-1.0/PAGWAS/man/list.of.parameters.Rd |only PAGWAS-1.0/PAGWAS/man/return.a.SNAL.Rd |only PAGWAS-1.0/PAGWAS/man/return.bf.NBF.Rd |only PAGWAS-1.0/PAGWAS/man/return.hyperparameters.NBF.Rd |only PAGWAS-1.0/PAGWAS/man/return.s2.SNAL.Rd |only PAGWAS-1.0/PAGWAS/man/roc.convex.Rd |only PAGWAS-2.0/PAGWAS/DESCRIPTION | 16 ++-- PAGWAS-2.0/PAGWAS/MD5 | 75 +++++++------------- PAGWAS-2.0/PAGWAS/NAMESPACE | 6 + PAGWAS-2.0/PAGWAS/R/FM.chi.pvalue.R | 5 - PAGWAS-2.0/PAGWAS/R/NBF.R | 9 +- PAGWAS-2.0/PAGWAS/R/SNAL.R | 8 +- PAGWAS-2.0/PAGWAS/R/SNAL.calculation.R | 75 +++++++++----------- PAGWAS-2.0/PAGWAS/R/create.pathway.df.R |only PAGWAS-2.0/PAGWAS/R/lars.calculation.R | 1 PAGWAS-2.0/PAGWAS/R/logproby.R | 4 - PAGWAS-2.0/PAGWAS/R/matrix.inv.calculation.R | 3 PAGWAS-2.0/PAGWAS/R/matrix.invroot.calculation.R | 3 PAGWAS-2.0/PAGWAS/R/snps.to.genes.R | 8 +- PAGWAS-2.0/PAGWAS/R/snps.to.pathways.R | 35 ++------- PAGWAS-2.0/PAGWAS/data/SNPs.rda |binary PAGWAS-2.0/PAGWAS/data/genes.rda |binary PAGWAS-2.0/PAGWAS/data/genotypes.rda |binary PAGWAS-2.0/PAGWAS/data/pathways.rda |binary PAGWAS-2.0/PAGWAS/man/FM.chi.pvalue.Rd | 16 +--- PAGWAS-2.0/PAGWAS/man/NBF.Rd | 38 +++++----- PAGWAS-2.0/PAGWAS/man/PAGWAS-package.Rd | 18 ++-- PAGWAS-2.0/PAGWAS/man/SNAL.Rd | 30 ++++---- PAGWAS-2.0/PAGWAS/man/SNAL.calculation.Rd |only PAGWAS-2.0/PAGWAS/man/SNPs.Rd | 6 - PAGWAS-2.0/PAGWAS/man/create.pathway.df.Rd |only PAGWAS-2.0/PAGWAS/man/genes.Rd | 11 +- PAGWAS-2.0/PAGWAS/man/genotypes.Rd | 10 -- PAGWAS-2.0/PAGWAS/man/pathways.Rd | 6 - PAGWAS-2.0/PAGWAS/man/snps.to.genes.Rd | 12 +-- PAGWAS-2.0/PAGWAS/man/snps.to.pathways.Rd | 22 ++--- 50 files changed, 190 insertions(+), 227 deletions(-)
Title: Truncated Maximum Likelihood Fit and Robust Accelerated Failure
Time Regression for Gaussian and Log-Weibull Case
Description: R functions for the computation of the truncated maximum
likelihood and the robust accelerated failure time regression
for gaussian and log-Weibull case.
Author: Alfio Marazzi <Alfio.Marazzi@chuv.ch>, Jean-Luc Muralti
Maintainer: A. Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Diff between RobustAFT versions 1.3 dated 2014-11-06 and 1.4-1 dated 2015-12-08
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- NAMESPACE | 13 ++++++++++--- man/RobustAFT-internal.Rd |only 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Tools for Time Series Analysis Based on Symbolic Aggregate
Dicretization
Description: Implements z-normalization, SAX, HOT-SAX, VSM, and SAX-VSM algorithms
facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.0.1 dated 2015-10-19 and 1.0.2 dated 2015-12-08
jmotif-1.0.1/jmotif/tests/testthat/test_SAX.R |only jmotif-1.0.1/jmotif/tests/testthat/test_SAX2.R |only jmotif-1.0.2/jmotif/DESCRIPTION | 21 jmotif-1.0.2/jmotif/MD5 | 81 - jmotif-1.0.2/jmotif/NAMESPACE | 5 jmotif-1.0.2/jmotif/R/RcppExports.R | 205 +- jmotif-1.0.2/jmotif/R/data.R | 5 jmotif-1.0.2/jmotif/R/jmotif.R | 7 jmotif-1.0.2/jmotif/README.md | 131 + jmotif-1.0.2/jmotif/data/ECG0606.rda |only jmotif-1.0.2/jmotif/data/datalist | 1 jmotif-1.0.2/jmotif/man/alphabet_to_cuts.Rd | 4 jmotif-1.0.2/jmotif/man/bags_to_tfidf.Rd | 6 jmotif-1.0.2/jmotif/man/col_means.Rd | 8 jmotif-1.0.2/jmotif/man/cosine_sim.Rd | 8 jmotif-1.0.2/jmotif/man/early_abandoned_dist.Rd |only jmotif-1.0.2/jmotif/man/ecg0606.Rd |only jmotif-1.0.2/jmotif/man/euclidean_dist.Rd |only jmotif-1.0.2/jmotif/man/find_discords_brute_force.Rd |only jmotif-1.0.2/jmotif/man/find_discords_hot_sax.Rd |only jmotif-1.0.2/jmotif/man/idx_to_letter.Rd | 6 jmotif-1.0.2/jmotif/man/is_equal_mindist.Rd |only jmotif-1.0.2/jmotif/man/is_equal_str.Rd | 8 jmotif-1.0.2/jmotif/man/letter_to_idx.Rd | 6 jmotif-1.0.2/jmotif/man/letters_to_idx.Rd | 6 jmotif-1.0.2/jmotif/man/manyseries_to_wordbag.Rd | 16 jmotif-1.0.2/jmotif/man/min_dist.Rd | 4 jmotif-1.0.2/jmotif/man/paa.Rd | 8 jmotif-1.0.2/jmotif/man/sax_by_chunking.Rd | 12 jmotif-1.0.2/jmotif/man/sax_distance_matrix.Rd | 8 jmotif-1.0.2/jmotif/man/sax_via_window.Rd | 17 jmotif-1.0.2/jmotif/man/series_to_chars.Rd | 8 jmotif-1.0.2/jmotif/man/series_to_string.Rd | 8 jmotif-1.0.2/jmotif/man/series_to_wordbag.Rd | 16 jmotif-1.0.2/jmotif/man/subseries.Rd | 12 jmotif-1.0.2/jmotif/man/znorm.Rd | 9 jmotif-1.0.2/jmotif/src/RcppExports.cpp | 83 - jmotif-1.0.2/jmotif/src/jmotif.cpp | 788 ++++++++-- jmotif-1.0.2/jmotif/tests/testthat/test_SAX_simple.R |only jmotif-1.0.2/jmotif/tests/testthat/test_SAX_strategies.R |only jmotif-1.0.2/jmotif/tests/testthat/test_SAX_via_window.R |only jmotif-1.0.2/jmotif/tests/testthat/test_discord_brute_force.R |only jmotif-1.0.2/jmotif/tests/testthat/test_discord_hot_sax.R |only jmotif-1.0.2/jmotif/tests/testthat/test_early_abandoned_dist.R |only jmotif-1.0.2/jmotif/tests/testthat/test_euclidean_dist.R |only jmotif-1.0.2/jmotif/tests/testthat/test_min_dist.R | 24 jmotif-1.0.2/jmotif/tests/testthat/test_min_dist_equal.R |only jmotif-1.0.2/jmotif/tests/testthat/test_subseries.R | 7 jmotif-1.0.2/jmotif/tests/testthat/test_wordbag.R | 24 jmotif-1.0.2/jmotif/tests/testthat/test_znorm.R | 11 50 files changed, 1166 insertions(+), 397 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al (doi: 10.2307/2533043) and the two level random effects model in Beath and Heller (doi: 10.1177/1471082X0800900302). Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-5 dated 2015-11-12 and 1.0-6 dated 2015-12-08
DESCRIPTION | 11 MD5 | 21 - NAMESPACE | 97 +++---- R/bestlca.R | 63 ++-- R/fitAdaptRandom.R | 535 ++++++++++++++++++++-------------------- R/fitAdaptRandom2.R | 3 R/fitFixed.R | 335 ++++++++++++------------- R/randomLCA.R | 346 ++++++++++++------------- inst/NEWS | 12 man/hivtests.Rd | 5 man/randomLCA.Rd | 174 ++++++------- vignettes/randomLCA-example.tex |only 12 files changed, 811 insertions(+), 791 deletions(-)
Title: NCA Calculation and Population PK Model Diagnosis
Description: A flexible tool is presented here that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) simulation-based posterior predictive checks for a population
pharmacokinetic (PK) model using NCA metrics.
Author: Chayan Acharya [aut, cre],
Andrew C. Hooker [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut]
Maintainer: Chayan Acharya <chayan.acharya@farmbio.uu.se>
Diff between ncappc versions 0.2 dated 2015-07-16 and 0.2.1.0 dated 2015-12-08
DESCRIPTION | 11 MD5 | 70 NAMESPACE | 2 R/calc.stat.R | 24 R/dv.plot.R | 24 R/est.nca.R | 258 ++- R/histobs.plot.R | 30 R/histpop.plot.R | 27 R/nca.deviation.plot.R | 18 R/nca.npde.plot.R | 21 R/nca.pde.deviation.outlier.R | 40 R/ncappc.R | 2221 ++++++++++++++++--------------- R/read_nm_table.R |only README.md | 2 build/vignette.rds |binary inst/doc/ncappc-vignette.Rmd | 13 inst/doc/ncappc-vignette.html | 477 +++--- inst/extdata |only inst/misc/ncappcReport-NCA-PPC.Rmd | 61 inst/misc/ncappcReport-NCA-PPC.Rnw | 76 - inst/misc/ncappcReport-NCA.Rmd | 26 inst/misc/ncappcReport-NCA.Rnw | 36 man/est.nca.Rd | 30 man/nca.pde.deviation.outlier.Rd | 4 man/ncappc.Rd | 154 +- man/read_nm_table.Rd |only tests/testthat/ncappcexamples/example1.R | 29 vignettes/Deviation-vgn.png |only vignettes/HistObs-vgn.png |only vignettes/NPDE-vgn.png |only vignettes/Outlier-vgn.png |only vignettes/Sub-CommandLineArguments.Rmd | 235 +-- vignettes/Sub-EstimatedNCAmetrics.Rmd | 4 vignettes/Sub-Output.Rmd | 45 vignettes/conc-vgn.png |only vignettes/forest-vgn.png |only vignettes/histNPDE-vgn.png |only vignettes/ncappc-Schema.png |only vignettes/ncappc-vignette.Rmd | 13 vignettes/ncappc-vignette.md | 295 ++-- vignettes/ncappc-vignette.txt |only vignettes/ncappc_Schema.tif |only vignettes/popMean-vgn.png |only 43 files changed, 2365 insertions(+), 1881 deletions(-)
Title: Gapped-Kmer Support Vector Machine
Description: Imports the 'gkmSVM' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.
Author: Mahmoud Ghandi
Maintainer: Mahmoud Ghandi <mghandi@gmail.com>
Diff between gkmSVM versions 0.55 dated 2015-06-30 and 0.65 dated 2015-12-08
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- NAMESPACE | 4 ++++ R/RcppExports.R | 12 ++++++------ R/gkmsvm_train.R | 19 +++++++++++++++---- R/gkmsvm_trainCV.R |only man/gkmSVM-package.Rd | 20 +++++++++++++------- man/gkmsvm_train.Rd | 3 ++- man/gkmsvm_trainCV.Rd |only src/EstimLogRatio.cpp | 2 +- 10 files changed, 55 insertions(+), 31 deletions(-)
Title: High Frequency Price Estimators by PortfolioEffect
Description: R interface to PortfolioEffect Quant service for estimating
high frequency price variance, quarticity, microstructure noise variance,
and other metrics in both aggregate and rolling window flavors.
Constructed estimators could use client-side market data or access
HF intraday price history for all major US Equities.
See https://www.portfolioeffect.com/ for more information on the
PortfolioEffect high frequency portfolio analytics platform.
Author: Andrey Kostin [aut, cre],
Aleksey Zemnitskiy [aut],
Oleg Nechaev [aut]
Maintainer: Andrey Kostin <andrey.kostin@portfolioeffect.com>
Diff between PortfolioEffectEstim versions 1.0 dated 2015-11-13 and 1.1 dated 2015-12-07
DESCRIPTION | 8 +-- MD5 | 13 +++-- NEWS | 7 +++ build/vignette.rds |binary inst/doc/PortfolioEffectEstim.Rnw | 81 +++++++++++++++++++++++++++++++------ inst/doc/PortfolioEffectEstim.pdf |binary vignettes/PortfolioEffectEstim.Rnw | 81 +++++++++++++++++++++++++++++++------ vignettes/img/Table.pdf |only 8 files changed, 156 insertions(+), 34 deletions(-)
More information about PortfolioEffectEstim at CRAN
Permanent link
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information.
Author: Thibaut Jombart <thibautjombart@gmail.com>, Anne Cori, Joel Hellewell
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between outbreaker versions 1.1-6 dated 2015-09-11 and 1.1-7 dated 2015-12-07
outbreaker-1.1-6/outbreaker/man/Rstat.Rd |only outbreaker-1.1-6/outbreaker/man/fakeOutbreak.Rd |only outbreaker-1.1-6/outbreaker/man/getMu.Rd |only outbreaker-1.1-6/outbreaker/man/mainplots.Rd |only outbreaker-1.1-7/outbreaker/ChangeLog | 14 outbreaker-1.1-7/outbreaker/DESCRIPTION | 15 outbreaker-1.1-7/outbreaker/MD5 | 57 - outbreaker-1.1-7/outbreaker/NAMESPACE | 87 + outbreaker-1.1-7/outbreaker/R/data.R |only outbreaker-1.1-7/outbreaker/R/interface.R | 343 ++++++- outbreaker-1.1-7/outbreaker/R/mutationRates.R | 45 outbreaker-1.1-7/outbreaker/R/package.R |only outbreaker-1.1-7/outbreaker/R/plot.R | 130 ++ outbreaker-1.1-7/outbreaker/R/reproRate.R | 67 + outbreaker-1.1-7/outbreaker/R/selectChains.R | 41 outbreaker-1.1-7/outbreaker/R/simOutbreak.R | 150 ++- outbreaker-1.1-7/outbreaker/R/tTree.R | 139 ++ outbreaker-1.1-7/outbreaker/README.md | 29 outbreaker-1.1-7/outbreaker/configure | 10 outbreaker-1.1-7/outbreaker/configure.ac | 4 outbreaker-1.1-7/outbreaker/man/get.mu.Rd |only outbreaker-1.1-7/outbreaker/man/outbreaker.Rd | 483 ++++------ outbreaker-1.1-7/outbreaker/man/outbreaker.package.Rd |only outbreaker-1.1-7/outbreaker/man/plot.Rd |only outbreaker-1.1-7/outbreaker/man/repro.Rd |only outbreaker-1.1-7/outbreaker/man/selectChains.Rd | 82 - outbreaker-1.1-7/outbreaker/man/simOutbreak.Rd | 200 +--- outbreaker-1.1-7/outbreaker/man/simulated-outbreak-dataset.Rd |only outbreaker-1.1-7/outbreaker/man/tTree.Rd | 147 +-- outbreaker-1.1-7/outbreaker/src/distances.c | 7 outbreaker-1.1-7/outbreaker/src/genclasses.c | 26 outbreaker-1.1-7/outbreaker/src/genclasses.h | 2 outbreaker-1.1-7/outbreaker/src/outbreaker.c | 4 outbreaker-1.1-7/outbreaker/src/structures.c | 21 outbreaker-1.1-7/outbreaker/src/structures.h | 2 35 files changed, 1431 insertions(+), 674 deletions(-)
Title: Conditional Logistic Regression: A Two-Step Estimation Method
Description: Conditional logistic regression with longitudinal follow up and
individual-level random coefficients: A stable and efficient
two-step estimation method.
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie Baillargeon
Maintainer: Thierry Duchesne <thierry.duchesne@mat.ulaval.ca>
Diff between TwoStepCLogit versions 1.2.3 dated 2014-10-24 and 1.2.4 dated 2015-12-07
DESCRIPTION | 16 ++++++------ MD5 | 23 +++++++++-------- NAMESPACE | 9 ++++++ R/Ts.estim.R | 52 ++++++++++++++++++++------------------- R/TwoStepCLogit.R | 8 +++--- R/ddim.R | 13 +++++---- R/internal.R | 8 +++--- inst/NEWS.Rd | 6 ++++ inst/tests |only man/Ts.estim.Rd | 56 ++++++++++++++++++++++--------------------- man/TwoStepCLogit-package.Rd | 17 ++++++------- man/bison.Rd | 31 +++++++++++------------ man/ddim.Rd | 18 ++++++------- 13 files changed, 139 insertions(+), 118 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
or van der Waerden's normal score test can be employed,
if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the omnibus test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
(such as Nemenyi's test, Dunn's test, Conover's test,
van der Waerden's test). Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test
or the Quade-test. The consequent post-hoc pairwise
multiple comparison tests according to Nemenyi, Conover and Quade
are also provided in this package. Finally Durbin's test for
a two-way balanced incomplete block design (BIBD) is also given
in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 3.0 dated 2015-11-24 and 4.0 dated 2015-12-07
DESCRIPTION | 25 +- MD5 | 60 +++--- NAMESPACE | 22 +- R/dunn.test.control.R | 2 R/durbin.test.R |only R/jonckheere.test.R |only R/posthoc.durbin.test.R |only R/posthoc.friedman.conover.R | 38 ---- R/posthoc.friedman.nemenyi.test.R | 2 R/posthoc.kruskal.conover.R | 2 R/posthoc.kruskal.dunn.test.R | 2 R/posthoc.kruskal.nemenyi.test.R | 2 R/posthoc.quade.test.R |only R/posthoc.vanWaerden.test.R | 2 R/print.PMCMR.R |only inst/NEWS.Rd | 50 +++++ inst/doc/PMCMR.R | 155 ++++++++++++++-- inst/doc/PMCMR.Rnw | 321 ++++++++++++++++++++++++++++++++--- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 55 ++++- man/dunn.test.control.Rd | 6 man/durbin.test.Rd |only man/get.pvalues.Rd |only man/jonckheere.test.Rd |only man/posthoc.durbin.test.Rd |only man/posthoc.friedman.conover.test.Rd | 37 ++-- man/posthoc.friedman.nemenyi.test.Rd | 7 man/posthoc.kruskal.conover.Rd | 5 man/posthoc.kruskal.dunn.test.Rd | 18 - man/posthoc.kruskal.nemenyi.test.Rd | 7 man/posthoc.quade.test.Rd |only man/posthoc.vanWaerden.test.Rd | 5 man/print.PMCMR.Rd |only man/summary.PMCMR.Rd |only man/vanWaerden.test.Rd | 5 vignettes/PMCMR.Rnw | 321 ++++++++++++++++++++++++++++++++--- vignettes/PMCMR.bib | 32 +++ 37 files changed, 968 insertions(+), 213 deletions(-)
Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
Author: Thijs Janzen
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between nLTT versions 1.1 dated 2015-04-21 and 1.1.1 dated 2015-12-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 7 +++++-- R/ABC_SMC.R | 27 --------------------------- man/nLTT-internal.Rd | 1 - man/nLTT-package.Rd | 2 ++ 6 files changed, 17 insertions(+), 40 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.5.0 dated 2015-12-03 and 0.5.1 dated 2015-12-07
DESCRIPTION | 12 +- MD5 | 78 +++++++++--------- NEWS | 22 +++++ R/Luminescence-package.R | 8 - R/extract_IrradiationTimes.R | 4 R/get_RLum.R | 12 +- R/plot_RLum.Analysis.R | 130 +++++++++++++++---------------- R/read_BIN2R.R | 4 R/read_SPE2R.R | 4 R/set_RLum.R | 12 +- R/write_R2BIN.R | 4 inst/CITATION | 6 - inst/NEWS.Rd | 34 ++++++-- man/Luminescence-package.Rd | 8 - man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Risoe.BINfileData2RLum.Data.Curve.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_gSGC.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/fit_LMCurve.Rd | 2 man/get_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 2 man/read_Daybreak2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/set_RLum.Rd | 2 man/use_DRAC.Rd | 2 man/write_R2BIN.Rd | 2 40 files changed, 218 insertions(+), 172 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.4 dated 2015-10-14 and 1.1.5 dated 2015-12-07
DESCRIPTION | 12 MD5 | 8 R/GDM_Table_Funcs.R | 858 ++++++++++++++++---------------------------------- man/formatsitepair.Rd | 15 man/predict.gdm.Rd | 2 5 files changed, 295 insertions(+), 600 deletions(-)
Title: Grain-Size Statistics and Description of Sediment
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves.
Author: Regis K. Gallon (MNHN), Jerome Fournier (CNRS|MNHN)
Maintainer: Regis K. Gallon <reg.gallon@gmail.com>
Diff between G2Sd versions 2.1.4 dated 2015-08-11 and 2.1.5 dated 2015-12-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/G2Sd-internal.R | 49 +++++++++++++++++++++++++------------------------ 3 files changed, 31 insertions(+), 30 deletions(-)
Title: Download Logs from the 'RStudio' 'CRAN' Mirror
Description: 'API' to the database of 'CRAN' package downloads from the
'RStudio' 'CRAN mirror'. The database itself is at <http://cranlogs.r-pkg.org>,
see <https://github.com/metacran/cranlogs.app> for the raw 'API'.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cranlogs versions 2.0.0 dated 2015-05-07 and 2.1.0 dated 2015-12-07
DESCRIPTION | 15 ++++++----- MD5 | 14 ++++++---- NAMESPACE | 3 +- R/cranlogs.R | 59 +++++++++++++++++++++++++++++++++------------- inst |only man/cran_downloads.Rd | 16 ++++++++++-- man/cran_top_downloads.Rd | 4 ++- man/cranlogs.Rd | 2 - 8 files changed, 78 insertions(+), 35 deletions(-)
Title: The Chopthin Resampler
Description: Resampling is a standard step in particle filtering and in
sequential Monte Carlo. This package implements the chopthin resampler, which
keeps a bound on the ratio between the largest and the smallest weights after
resampling.
Author: Axel Gandy and F. Din-Houn Lau
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between chopthin versions 0.1 dated 2015-03-26 and 0.2 dated 2015-12-07
DESCRIPTION | 14 +- MD5 | 21 ++- NAMESPACE | 2 R/RcppExports.R | 16 +- inst/NEWS.Rd |only man/chopthin.Rd | 14 +- src/RcppExports.cpp | 8 - src/chopthin.cpp | 19 ++- src/chopthin_internal.h | 163 +++++++++++++++++++++++------ tests/testthat.R | 1 tests/testthat/test-chopthin_exact.R | 71 +++++++++++- tests/testthat/test-chopthin_rcauchy.R |only tests/testthat/test-oneverysmallparticle.R |only 13 files changed, 257 insertions(+), 72 deletions(-)
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 3.6.1 dated 2015-07-02 and 4.0.0 dated 2015-12-07
DESCRIPTION | 11 +- MD5 | 8 - R/WriteXLS.R | 228 ++++++++++++++++++++++++++++---------------------------- R/testPerl.R | 45 +++++------ man/WriteXLS.Rd | 60 +++++++++----- 5 files changed, 184 insertions(+), 168 deletions(-)
Title: Semiparametric Bivariate Regression Models
Description: Routines for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.6 dated 2015-08-24 and 3.6-1 dated 2015-12-07
ChangeLog | 4 DESCRIPTION | 8 MD5 | 50 +- NAMESPACE | 9 R/AT.r | 885 ++++--------------------------------- R/AT2.r |only R/OR.r | 459 ++----------------- R/RR.r | 366 ++------------- R/SemiParBIVProbit.fit.post.r | 15 R/SemiParBIVProbit.r | 32 - R/bprobgHsCont3.r | 10 R/bprobgHsContUniv3.r | 7 R/distrHs.r | 28 - R/distrHsAT.r | 23 R/print.AT2.r |only R/print.SemiParBIVProbit.r | 10 R/print.summary.SemiParBIVProbit.r | 8 R/resp.check.R | 25 - R/summary.SemiParBIVProbit.r | 61 +- man/AT.Rd | 13 man/AT2.Rd |only man/OR.Rd | 18 man/RR.Rd | 16 man/SemiParBIVProbit.Rd | 31 - man/copgHs2.Rd | 2 man/prev.Rd | 10 man/print.AT2.Rd |only man/summary.SemiParBIVProbit.Rd | 10 28 files changed, 459 insertions(+), 1641 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters
heaped data, i.e. data which are rounded (to a possibly different degree
of coarseness). While this is mostly a minor problem in parametric density
estimation the bias can be very large for non-parametric methods such as kernel
density estimation. This package implements a partly Bayesian algorithm treating
the true unknown values as additional parameters and estimates the rounding
parameters to give a corrected kernel density estimate. It supports various
standard bandwidth selection methods. Varying rounding probabilities (depending
on the true value) and asymmetric rounding is estimable as well. Additionally,
bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>
Diff between Kernelheaping versions 1.0 dated 2015-07-31 and 1.2 dated 2015-12-07
DESCRIPTION | 25 ++- MD5 | 30 +-- NAMESPACE | 4 R/Kernelheaping.R | 2 R/functions.R | 310 ++++++++++++++++++++++++++-------------- man/Kernelheaping.Rd | 12 - man/createSim.Kernelheaping.Rd | 2 man/dbivr.Rd | 2 man/dheaping.Rd | 14 + man/plot.Kernelheaping.Rd | 2 man/plot.bivrounding.Rd | 2 man/sim.Kernelheaping.Rd | 4 man/simSummary.Kernelheaping.Rd | 2 man/students.Rd | 4 man/summary.Kernelheaping.Rd | 2 man/tracePlots.Rd | 2 16 files changed, 265 insertions(+), 154 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.9.5 dated 2015-06-15 and 2.10.0 dated 2015-12-07
secr-2.10.0/secr/DESCRIPTION | 11 secr-2.10.0/secr/MD5 | 207 +++--- secr-2.10.0/secr/NAMESPACE | 36 - secr-2.10.0/secr/NEWS | 65 + secr-2.10.0/secr/R/DENSITY.R | 44 + secr-2.10.0/secr/R/Dsurface.R | 9 secr-2.10.0/secr/R/LLsurface.secr.R | 5 secr-2.10.0/secr/R/addSightings.R |only secr-2.10.0/secr/R/autoini.R | 34 - secr-2.10.0/secr/R/closure.R | 7 secr-2.10.0/secr/R/confint.secr.R | 11 secr-2.10.0/secr/R/derivedMS.R | 9 secr-2.10.0/secr/R/discretize.R |only secr-2.10.0/secr/R/esa.R | 25 secr-2.10.0/secr/R/fxi.R | 88 +- secr-2.10.0/secr/R/homerange.R | 53 + secr-2.10.0/secr/R/ip.secr.R | 71 +- secr-2.10.0/secr/R/join.R | 147 +++- secr-2.10.0/secr/R/make.capthist.R | 115 +-- secr-2.10.0/secr/R/make.grid.R | 2 secr-2.10.0/secr/R/make.mask.R | 5 secr-2.10.0/secr/R/make.tri.R | 2 secr-2.10.0/secr/R/mask.check.R | 13 secr-2.10.0/secr/R/methods.R | 406 ++++++++++-- secr-2.10.0/secr/R/model.average.R | 53 - secr-2.10.0/secr/R/par.secr.fit.R | 13 secr-2.10.0/secr/R/plot.capthist.r | 85 +- secr-2.10.0/secr/R/pmixProfileLL.R |only secr-2.10.0/secr/R/predict.secr.R | 31 secr-2.10.0/secr/R/rbind.capthist.R | 35 - secr-2.10.0/secr/R/read.traps.R | 17 secr-2.10.0/secr/R/reduce.R | 1 secr-2.10.0/secr/R/regionN.R | 19 secr-2.10.0/secr/R/score.test.R | 4 secr-2.10.0/secr/R/secr.design.MS.R | 30 secr-2.10.0/secr/R/secr.fit.R | 275 ++++---- secr-2.10.0/secr/R/secr.make.newdata.R | 4 secr-2.10.0/secr/R/secrloglik.R | 298 +++++---- secr-2.10.0/secr/R/sighting.chat.R |only secr-2.10.0/secr/R/sim.capthist.R | 341 +++++++--- secr-2.10.0/secr/R/sim.popn.R | 25 secr-2.10.0/secr/R/sim.secr.R | 12 secr-2.10.0/secr/R/split.capthist.R | 8 secr-2.10.0/secr/R/split.traps.R | 10 secr-2.10.0/secr/R/suggest.buffer.R | 2 secr-2.10.0/secr/R/telemetry.R | 9 secr-2.10.0/secr/R/utility.R | 196 +++++ secr-2.10.0/secr/R/verify.R | 172 +++-- secr-2.10.0/secr/build/vignette.rds |binary secr-2.10.0/secr/data/deermouse.RData |binary secr-2.10.0/secr/data/housemouse.RData |binary secr-2.10.0/secr/data/ovenbird.RData |binary secr-2.10.0/secr/data/ovensong.RData |binary secr-2.10.0/secr/data/possum.RData |binary secr-2.10.0/secr/data/secrdemo.RData |binary secr-2.10.0/secr/data/stoatDNA.RData |binary secr-2.10.0/secr/inst/doc/secr-datainput.Rmd | 7 secr-2.10.0/secr/inst/doc/secr-datainput.pdf |binary secr-2.10.0/secr/inst/doc/secr-manual.pdf |binary secr-2.10.0/secr/inst/doc/secr-overview.R | 21 secr-2.10.0/secr/inst/doc/secr-overview.Rmd | 51 + secr-2.10.0/secr/inst/doc/secr-overview.pdf |binary secr-2.10.0/secr/man/DENSITY.Rd | 12 secr-2.10.0/secr/man/Parallel.Rd | 136 ++-- secr-2.10.0/secr/man/addSightings.Rd |only secr-2.10.0/secr/man/autoini.Rd | 6 secr-2.10.0/secr/man/capthist.Rd | 9 secr-2.10.0/secr/man/details.Rd | 31 secr-2.10.0/secr/man/discretize.Rd |only secr-2.10.0/secr/man/fx.total.Rd | 7 secr-2.10.0/secr/man/ip.secr.Rd | 11 secr-2.10.0/secr/man/join.Rd | 2 secr-2.10.0/secr/man/model.average.Rd | 9 secr-2.10.0/secr/man/plot.capthist.Rd | 6 secr-2.10.0/secr/man/plot.mask.Rd | 6 secr-2.10.0/secr/man/pmixProfileLL.Rd |only secr-2.10.0/secr/man/predict.secr.Rd | 12 secr-2.10.0/secr/man/rbind.traps.Rd | 2 secr-2.10.0/secr/man/read.traps.Rd | 4 secr-2.10.0/secr/man/reduce.capthist.Rd | 7 secr-2.10.0/secr/man/score.test.Rd | 2 secr-2.10.0/secr/man/secr-package.Rd | 5 secr-2.10.0/secr/man/secr.fit.Rd | 26 secr-2.10.0/secr/man/sighting.Rd |only secr-2.10.0/secr/man/sim.capthist.Rd | 57 + secr-2.10.0/secr/man/smooths.Rd | 2 secr-2.10.0/secr/man/sort.Rd | 11 secr-2.10.0/secr/man/speed.Rd | 6 secr-2.10.0/secr/man/traps.Rd | 5 secr-2.10.0/secr/man/usage.Rd | 20 secr-2.10.0/secr/man/vcov.secr.Rd | 2 secr-2.10.0/secr/src/secr.c | 817 ++++++++++++++++--------- secr-2.10.0/secr/src/secr.h | 197 +++--- secr-2.10.0/secr/src/sighting.c |only secr-2.10.0/secr/src/trapping.c | 22 secr-2.10.0/secr/src/utils.c | 10 secr-2.10.0/secr/vignettes/capt.txt |only secr-2.10.0/secr/vignettes/secr-datainput.Rmd | 7 secr-2.10.0/secr/vignettes/secr-datainput.html |only secr-2.10.0/secr/vignettes/secr-overview.Rmd | 51 + secr-2.10.0/secr/vignettes/secr-overview.html |only secr-2.10.0/secr/vignettes/secr-overview_cache |only secr-2.10.0/secr/vignettes/secr-overview_files |only secr-2.10.0/secr/vignettes/trap.txt |only secr-2.9.5/secr/R/joinold.R |only 105 files changed, 3079 insertions(+), 1505 deletions(-)
Title: 'rgl' in 'htmlwidgets' Framework
Description: Provides an 'htmlwidgets' framework for the 'rgl' package.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rglwidget versions 0.1.1402 dated 2015-11-09 and 0.1.1431 dated 2015-12-07
rglwidget-0.1.1402/rglwidget/inst/htmlwidgets/rglcontroller.js |only rglwidget-0.1.1402/rglwidget/inst/htmlwidgets/rglcontroller.yaml |only rglwidget-0.1.1402/rglwidget/inst/htmlwidgets/rglwidget.js |only rglwidget-0.1.1402/rglwidget/inst/htmlwidgets/rglwidget.yaml |only rglwidget-0.1.1402/rglwidget/man/rglcontroller.Rd |only rglwidget-0.1.1431/rglwidget/DESCRIPTION | 10 rglwidget-0.1.1431/rglwidget/MD5 | 52 - rglwidget-0.1.1431/rglwidget/NAMESPACE | 7 rglwidget-0.1.1431/rglwidget/R/Sweave_knitr.R | 3 rglwidget-0.1.1431/rglwidget/R/convertScene.R | 3 rglwidget-0.1.1431/rglwidget/R/playwidget.R |only rglwidget-0.1.1431/rglwidget/R/rglcontroller.R | 130 +--- rglwidget-0.1.1431/rglwidget/R/rglwidget.R | 6 rglwidget-0.1.1431/rglwidget/R/webGLcontrols.R | 39 - rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/lib/rglClass/rgl.css |only rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/lib/rglClass/rglClass.src.js | 293 +++++++--- rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/rglPlayer.js |only rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/rglPlayer.yaml |only rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/rglWebGL.js |only rglwidget-0.1.1431/rglwidget/inst/htmlwidgets/rglWebGL.yaml |only rglwidget-0.1.1431/rglwidget/inst/shinyDemo/server.R | 17 rglwidget-0.1.1431/rglwidget/inst/shinyDemo/ui.R | 4 rglwidget-0.1.1431/rglwidget/inst/todo.txt | 39 + rglwidget-0.1.1431/rglwidget/man/ageControl.Rd | 31 - rglwidget-0.1.1431/rglwidget/man/clipplaneControl.Rd |only rglwidget-0.1.1431/rglwidget/man/playwidget.Rd | 62 +- rglwidget-0.1.1431/rglwidget/man/rglwidget.Rd | 15 rglwidget-0.1.1431/rglwidget/man/sceneChange.Rd | 2 rglwidget-0.1.1431/rglwidget/man/shiny.Rd | 14 rglwidget-0.1.1431/rglwidget/man/vertexControl.Rd | 35 - rglwidget-0.1.1431/rglwidget/man/webGLcontrols.Rd | 27 rglwidget-0.1.1431/rglwidget/vignettes/internals.Rmd | 54 + rglwidget-0.1.1431/rglwidget/vignettes/test.Rmd | 124 ---- 33 files changed, 547 insertions(+), 420 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1367 dated 2015-10-06 and 0.95.1429 dated 2015-12-07
rgl-0.95.1367/rgl/inst/WebGL/CanvasMatrix.src.js |only rgl-0.95.1367/rgl/src/osx |only rgl-0.95.1429/rgl/DESCRIPTION | 12 rgl-0.95.1429/rgl/MD5 | 74 rgl-0.95.1429/rgl/R/Sweave_knitr.R | 104 rgl-0.95.1429/rgl/R/getscene.R | 11 rgl-0.95.1429/rgl/R/webGL.R | 2159 --- rgl-0.95.1429/rgl/R/webGLcontrols.R | 471 rgl-0.95.1429/rgl/R/zzz.R | 12 rgl-0.95.1429/rgl/README | 6 rgl-0.95.1429/rgl/build/vignette.rds |binary rgl-0.95.1429/rgl/configure | 37 rgl-0.95.1429/rgl/configure.ac | 25 rgl-0.95.1429/rgl/configure.win | 1 rgl-0.95.1429/rgl/inst/NEWS | 14 rgl-0.95.1429/rgl/inst/doc/WebGL.Rmd | 145 rgl-0.95.1429/rgl/inst/doc/WebGL.html |11332 +++-------------- rgl-0.95.1429/rgl/inst/doc/rgl.Rmd | 36 rgl-0.95.1429/rgl/inst/doc/rgl.html |14866 ++++------------------- rgl-0.95.1429/rgl/man/attributes.Rd | 2 rgl-0.95.1429/rgl/man/propertySetter.Rd | 6 rgl-0.95.1429/rgl/man/rgl.open.Rd | 3 rgl-0.95.1429/rgl/man/texts.Rd | 3 rgl-0.95.1429/rgl/man/writeWebGL.Rd | 16 rgl-0.95.1429/rgl/src/Makevars.in | 22 rgl-0.95.1429/rgl/src/PlaneSet.cpp | 29 rgl-0.95.1429/rgl/src/PlaneSet.h | 1 rgl-0.95.1429/rgl/src/api.cpp | 8 rgl-0.95.1429/rgl/src/config.h | 6 rgl-0.95.1429/rgl/src/init.cpp | 7 rgl-0.95.1429/rgl/src/rglview.cpp | 7 rgl-0.95.1429/rgl/src/scene.cpp | 9 rgl-0.95.1429/rgl/src/scene.h | 8 rgl-0.95.1429/rgl/src/subscene.cpp | 31 rgl-0.95.1429/rgl/src/subscene.h | 1 rgl-0.95.1429/rgl/vignettes/WebGL.Rmd | 145 rgl-0.95.1429/rgl/vignettes/rgl.Rmd | 36 rgl-0.95.1429/rgl/vignettes/setup.R | 54 38 files changed, 6023 insertions(+), 23676 deletions(-)
Title: R Interface to Bloomberg
Description: An R Interface to Bloomberg is provided via the Blp API.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.1 dated 2015-10-20 and 0.3.2 dated 2015-12-07
ChangeLog | 68 ++++++++++++++++++++++++ DESCRIPTION | 9 +-- MD5 | 57 ++++++++++---------- NAMESPACE | 3 - R/RcppExports.R | 8 ++ R/bdh.R | 2 R/beqs.R | 132 +++++++++++++++++++++++------------------------ R/getBars.R | 21 +++++-- R/getTicks.R | 25 +++----- R/subscribe.R |only configure | 24 ++++++-- inst/NEWS.Rd | 26 ++++++++- man/bdh.Rd | 6 +- man/bdp.Rd | 2 man/bds.Rd | 2 man/beqs.Rd | 17 +++--- man/blpAuthenticate.Rd | 2 man/blpConnect.Rd | 2 man/blpDisconnect.Rd | 4 - man/defaultConnection.Rd | 4 - man/fieldSearch.Rd | 3 - man/getBars.Rd | 21 ++++--- man/getMultipleTicks.Rd | 2 man/getTicks.Rd | 7 ++ man/subscribe.Rd |only src/RcppExports.cpp | 24 +++++++- src/beqs.cpp | 53 ++++++++++++------ src/blpapi_utils.cpp | 10 +++ src/blpapi_utils.h | 2 src/getBars.cpp | 24 +++++--- src/subscribe.cpp |only 31 files changed, 373 insertions(+), 187 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 1.6.1 dated 2015-03-04 and 2.0.0 dated 2015-12-07
randomForestSRC-1.6.1/randomForestSRC/inst/doc/index.html |only randomForestSRC-1.6.1/randomForestSRC/src/bootstrap.c |only randomForestSRC-1.6.1/randomForestSRC/src/bootstrap.h |only randomForestSRC-1.6.1/randomForestSRC/src/classification.c |only randomForestSRC-1.6.1/randomForestSRC/src/classification.h |only randomForestSRC-1.6.1/randomForestSRC/src/dataParser.c |only randomForestSRC-1.6.1/randomForestSRC/src/dataParser.h |only randomForestSRC-1.6.1/randomForestSRC/src/entry.c |only randomForestSRC-1.6.1/randomForestSRC/src/entry.h |only randomForestSRC-1.6.1/randomForestSRC/src/extern.h |only randomForestSRC-1.6.1/randomForestSRC/src/factor.h |only randomForestSRC-1.6.1/randomForestSRC/src/factorOps.c |only randomForestSRC-1.6.1/randomForestSRC/src/factorOps.h |only randomForestSRC-1.6.1/randomForestSRC/src/global.h |only randomForestSRC-1.6.1/randomForestSRC/src/importance.c |only randomForestSRC-1.6.1/randomForestSRC/src/importance.h |only randomForestSRC-1.6.1/randomForestSRC/src/impute.c |only randomForestSRC-1.6.1/randomForestSRC/src/impute.h |only randomForestSRC-1.6.1/randomForestSRC/src/node.h |only randomForestSRC-1.6.1/randomForestSRC/src/nodeOps.c |only randomForestSRC-1.6.1/randomForestSRC/src/nodeOps.h |only randomForestSRC-1.6.1/randomForestSRC/src/nrutil.c |only randomForestSRC-1.6.1/randomForestSRC/src/nrutil.h |only randomForestSRC-1.6.1/randomForestSRC/src/random.c |only randomForestSRC-1.6.1/randomForestSRC/src/random.h |only randomForestSRC-1.6.1/randomForestSRC/src/regression.c |only randomForestSRC-1.6.1/randomForestSRC/src/regression.h |only randomForestSRC-1.6.1/randomForestSRC/src/rfsrc.c |only randomForestSRC-1.6.1/randomForestSRC/src/rfsrc.h |only randomForestSRC-1.6.1/randomForestSRC/src/rfsrcUtil.c |only randomForestSRC-1.6.1/randomForestSRC/src/rfsrcUtil.h |only randomForestSRC-1.6.1/randomForestSRC/src/split.c |only randomForestSRC-1.6.1/randomForestSRC/src/split.h |only randomForestSRC-1.6.1/randomForestSRC/src/splitClas.c |only randomForestSRC-1.6.1/randomForestSRC/src/splitClas.h |only randomForestSRC-1.6.1/randomForestSRC/src/splitRegr.c |only randomForestSRC-1.6.1/randomForestSRC/src/splitRegr.h |only randomForestSRC-1.6.1/randomForestSRC/src/splitSurv.c |only randomForestSRC-1.6.1/randomForestSRC/src/splitSurv.h |only randomForestSRC-1.6.1/randomForestSRC/src/splitUspv.c |only randomForestSRC-1.6.1/randomForestSRC/src/splitUspv.h |only randomForestSRC-1.6.1/randomForestSRC/src/splitUtil.c |only randomForestSRC-1.6.1/randomForestSRC/src/splitUtil.h |only randomForestSRC-1.6.1/randomForestSRC/src/stack.c |only randomForestSRC-1.6.1/randomForestSRC/src/stack.h |only randomForestSRC-1.6.1/randomForestSRC/src/stackOutput.c |only randomForestSRC-1.6.1/randomForestSRC/src/stackOutput.h |only randomForestSRC-1.6.1/randomForestSRC/src/stackPreDefined.c |only randomForestSRC-1.6.1/randomForestSRC/src/stackPreDefined.h |only randomForestSRC-1.6.1/randomForestSRC/src/survival.c |only randomForestSRC-1.6.1/randomForestSRC/src/survival.h |only randomForestSRC-1.6.1/randomForestSRC/src/survivalE.c |only randomForestSRC-1.6.1/randomForestSRC/src/survivalE.h |only randomForestSRC-1.6.1/randomForestSRC/src/termOps.c |only randomForestSRC-1.6.1/randomForestSRC/src/termOps.h |only randomForestSRC-1.6.1/randomForestSRC/src/terminal.h |only randomForestSRC-1.6.1/randomForestSRC/src/trace.c |only randomForestSRC-1.6.1/randomForestSRC/src/trace.h |only randomForestSRC-1.6.1/randomForestSRC/src/tree.c |only randomForestSRC-1.6.1/randomForestSRC/src/tree.h |only randomForestSRC-1.6.1/randomForestSRC/src/treeUtil.c |only randomForestSRC-1.6.1/randomForestSRC/src/treeUtil.h |only randomForestSRC-2.0.0/randomForestSRC/DESCRIPTION | 10 randomForestSRC-2.0.0/randomForestSRC/MD5 | 186 - randomForestSRC-2.0.0/randomForestSRC/NAMESPACE | 9 randomForestSRC-2.0.0/randomForestSRC/R/data.utilities.R | 752 +++-- randomForestSRC-2.0.0/randomForestSRC/R/factor.utilities.R | 142 - randomForestSRC-2.0.0/randomForestSRC/R/find.interaction.R | 155 - randomForestSRC-2.0.0/randomForestSRC/R/generic.impute.rfsrc.R | 12 randomForestSRC-2.0.0/randomForestSRC/R/generic.predict.rfsrc.R | 1382 +++++----- randomForestSRC-2.0.0/randomForestSRC/R/impute.rfsrc.R | 156 - randomForestSRC-2.0.0/randomForestSRC/R/max.subtree.R | 430 +-- randomForestSRC-2.0.0/randomForestSRC/R/plot.competing.risk.R | 14 randomForestSRC-2.0.0/randomForestSRC/R/plot.rfsrc.R | 303 +- randomForestSRC-2.0.0/randomForestSRC/R/plot.survival.R | 290 +- randomForestSRC-2.0.0/randomForestSRC/R/plot.variable.R | 377 +- randomForestSRC-2.0.0/randomForestSRC/R/predict.rfsrc.R | 22 randomForestSRC-2.0.0/randomForestSRC/R/print.rfsrc.R | 185 - randomForestSRC-2.0.0/randomForestSRC/R/rf2rfz.R | 22 randomForestSRC-2.0.0/randomForestSRC/R/rfsrc.R | 733 +++-- randomForestSRC-2.0.0/randomForestSRC/R/rfsrc.news.R | 10 randomForestSRC-2.0.0/randomForestSRC/R/rfsrcSyn.R | 224 - randomForestSRC-2.0.0/randomForestSRC/R/stat.split.R | 32 randomForestSRC-2.0.0/randomForestSRC/R/utilities.R | 658 ++-- randomForestSRC-2.0.0/randomForestSRC/R/var.select.R | 472 +-- randomForestSRC-2.0.0/randomForestSRC/R/vimp.R | 90 randomForestSRC-2.0.0/randomForestSRC/R/zzz.R | 26 randomForestSRC-2.0.0/randomForestSRC/configure.ac | 2 randomForestSRC-2.0.0/randomForestSRC/data/breast.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/follic.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/hd.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/nutrigenomic.rda |only randomForestSRC-2.0.0/randomForestSRC/data/pbc.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/vdv.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/veteran.rda |binary randomForestSRC-2.0.0/randomForestSRC/data/wihs.rda |binary randomForestSRC-2.0.0/randomForestSRC/inst/CITATION | 20 randomForestSRC-2.0.0/randomForestSRC/inst/NEWS | 18 randomForestSRC-2.0.0/randomForestSRC/inst/doc/rsf-Rnews.pdf |binary randomForestSRC-2.0.0/randomForestSRC/man/breast.Rd | 52 randomForestSRC-2.0.0/randomForestSRC/man/find.interaction.Rd | 171 - randomForestSRC-2.0.0/randomForestSRC/man/follic.Rd | 25 randomForestSRC-2.0.0/randomForestSRC/man/hd.Rd | 26 randomForestSRC-2.0.0/randomForestSRC/man/impute.Rd | 178 - randomForestSRC-2.0.0/randomForestSRC/man/max.subtree.Rd | 168 - randomForestSRC-2.0.0/randomForestSRC/man/nutrigenomic.Rd |only randomForestSRC-2.0.0/randomForestSRC/man/pbc.Rd | 28 randomForestSRC-2.0.0/randomForestSRC/man/plot.competing.risk.Rd | 18 randomForestSRC-2.0.0/randomForestSRC/man/plot.rfsrc.Rd | 16 randomForestSRC-2.0.0/randomForestSRC/man/plot.survival.Rd | 74 randomForestSRC-2.0.0/randomForestSRC/man/plot.variable.Rd | 162 - randomForestSRC-2.0.0/randomForestSRC/man/predict.rfsrc.Rd | 292 +- randomForestSRC-2.0.0/randomForestSRC/man/print.rfsrc.Rd | 21 randomForestSRC-2.0.0/randomForestSRC/man/randomForestSRC_package.Rd | 197 - randomForestSRC-2.0.0/randomForestSRC/man/rf2rfz.Rd | 28 randomForestSRC-2.0.0/randomForestSRC/man/rfsrc.Rd | 1176 ++++---- randomForestSRC-2.0.0/randomForestSRC/man/rfsrc.news.Rd | 8 randomForestSRC-2.0.0/randomForestSRC/man/rfsrcSyn.Rd | 75 randomForestSRC-2.0.0/randomForestSRC/man/stat.split.Rd | 96 randomForestSRC-2.0.0/randomForestSRC/man/var.select.Rd | 306 +- randomForestSRC-2.0.0/randomForestSRC/man/veteran.Rd | 18 randomForestSRC-2.0.0/randomForestSRC/man/vimp.Rd | 63 randomForestSRC-2.0.0/randomForestSRC/man/wihs.Rd | 21 randomForestSRC-2.0.0/randomForestSRC/src/randomForestSRC.c |only randomForestSRC-2.0.0/randomForestSRC/src/randomForestSRC.h |only randomForestSRC-2.0.0/randomForestSRC/src/splitCustom.c | 704 ++++- randomForestSRC-2.0.0/randomForestSRC/src/splitCustom.h | 179 - 127 files changed, 6091 insertions(+), 4743 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Scale Bar, North Arrow, and Pretty Margins in R
Description: Automates the process of creating a scale bar and north arrow in
any package that uses base graphics to plot in R. Bounding box tools help find and manipulate
extents. Finally, there is a function to automate the process of setting margins, plotting
the map, scalebar, and north arrow, and resetting graphic parameters upon completion.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between prettymapr versions 0.1.1 dated 2015-10-11 and 0.1.3 dated 2015-12-07
DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- R/prettymap.R | 9 +++++---- man/prettymap.Rd | 10 ++++++---- man/prettymapr-package.Rd | 11 ++++------- 5 files changed, 26 insertions(+), 24 deletions(-)
Title: NeuroAnatomy Toolbox ('nat') Extension for Handling Template
Brains
Description: Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects
and functions for handling template brains.
Author: James Manton and Gregory Jefferis
Maintainer: James Manton <ajd.manton@googlemail.com>
Diff between nat.templatebrains versions 0.6.1 dated 2015-10-08 and 0.6.2 dated 2015-12-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 4 ++++ R/reg_repos.R | 18 +++++++++++++++--- 4 files changed, 27 insertions(+), 11 deletions(-)
More information about nat.templatebrains at CRAN
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Title: Calculate Agreement or Consensus in Ordered Rating Scales
Description: Calculate agreement or consensus in ordered rating scales. The package implements van der Eijk's (2001) measure of agreement A, which can be used to describe agreement, consensus, or polarization among respondents. It also implements measures of consensus (dispersion) by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, and Berry and Mielke. Furthermore, an implementation of Galtungs AJUS-system is provided to classify distributions, as well as a function to identify the position of multiple modes.
Author: Didier Ruedin
Maintainer: Didier Ruedin <didier.ruedin@wolfson.oxon.org>
Diff between agrmt versions 1.39 dated 2014-12-06 and 1.39.3 dated 2015-12-07
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 2 ++ R/BerryMielke.R | 2 +- build/vignette.rds |binary 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Competing Risks Regression Models with Covariate-Adjusted
Censoring Weights
Description: Estimation and regression modeling of subdistribution functions for competing risks data with adjustment for covariate-dependent censoring, as described in He et al. (2015).
Author: Peng He
Maintainer: Peng He <saturnhp@gmail.com>
Diff between wtcrsk versions 1.5 dated 2015-11-28 and 1.6 dated 2015-12-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/wtcrsk-package.Rd | 4 ++-- src/p1.cc | 8 ++++---- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <http://www.openstreetmap.org/>,
Mapquest <http://www.mapquest.com/>, Bing Maps <http://www.bing.com/maps>
and other tiled map sources in a way that works seamlessly with plotting
from the 'sp' package. Use to create high-resolution basemaps and add hillshade
to vector based maps.
Author: Dewey Dunnington [aut, cre],
Timothée Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.1.2 dated 2015-10-20 and 0.1.3 dated 2015-12-06
DESCRIPTION | 15 ++++++++---- MD5 | 16 +++++++----- NAMESPACE | 1 R/osmplot.R | 31 +++++++++++++++++++------ R/osmraster.R |only R/osmtile.R | 16 ++++-------- R/projections.R | 63 ++++++++++++++++++++++++++++++++++++++++----------- man/osm.raster.Rd |only man/rosm-package.Rd | 20 +++++++++------- tests/manual/tests.R | 53 +++++++++++++++++++++++++++++++++++++++++- 10 files changed, 163 insertions(+), 52 deletions(-)
Title: Spatial Nonparametric Covariance Functions
Description: R functions for analyzing spatial (cross-)covariance: the
nonparametric (cross-)covariance, the spline correlogram, the
nonparametric phase coherence function, and related.
Author: Ottar N. Bjornstad <onb1@psu.edu>
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between ncf versions 1.1-5 dated 2013-11-21 and 1.1-6 dated 2015-12-06
ncf-1.1-5/ncf/TODO |only ncf-1.1-6/ncf/CHANGES | 3 ncf-1.1-6/ncf/DESCRIPTION | 12 - ncf-1.1-6/ncf/MD5 | 34 ++-- ncf-1.1-6/ncf/NAMESPACE | 11 + ncf-1.1-6/ncf/R/ncf.r | 223 +++++++++++++++++++++++++------ ncf-1.1-6/ncf/man/Sncf.Rd | 4 ncf-1.1-6/ncf/man/correlog.Rd | 6 ncf-1.1-6/ncf/man/correlog.nc.Rd | 2 ncf-1.1-6/ncf/man/gcdist.Rd | 1 ncf-1.1-6/ncf/man/lisa.Rd | 23 +-- ncf-1.1-6/ncf/man/lisa.nc.Rd | 16 +- ncf-1.1-6/ncf/man/mSynch.Rd | 2 ncf-1.1-6/ncf/man/mantel.correlog.Rd |only ncf-1.1-6/ncf/man/mantel.test.Rd | 2 ncf-1.1-6/ncf/man/partial.mantel.test.Rd | 2 ncf-1.1-6/ncf/man/plot.lisa.Rd | 22 +-- ncf-1.1-6/ncf/man/plot.lisa.nc.Rd |only ncf-1.1-6/ncf/man/spatial.plot.Rd |only ncf-1.1-6/ncf/man/spline.correlog.Rd | 6 20 files changed, 265 insertions(+), 104 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.4.1 dated 2015-09-28 and 1.4-3 dated 2015-12-06
DESCRIPTION | 10 +-- MD5 | 144 ++++++++++++++++++++++----------------------- NAMESPACE | 3 NEWS | 26 +++++++- R/AbdFreqCount.R | 4 - R/AllenH.R | 26 ++++++-- R/ChaoPD.R | 26 ++++++-- R/CommunityProfile.R | 10 +-- R/Coverage.R | 22 +++++- R/DivEst.R | 2 R/DivPart.R | 2 R/DivProfile.R | 6 - R/Diversity.R | 22 +++++- R/Dqz.R | 18 +++++ R/GammaEntropy.R | 6 - R/Hqz.R | 55 ++++++++++++----- R/HqzBeta.R | 15 ++-- R/Hurlbert.R | 31 +++++++-- R/HurlbertD.R | 30 +++++++-- R/MCdiversity.R | 2 R/MCentropy.R | 2 R/MetaCommunity.R | 4 - R/PDFD.R | 2 R/PhyloApply.R | 2 R/PhyloBetaEntropy.R | 4 - R/PhyloDiversity.R | 18 +++++ R/PhyloEntropy.R | 16 ++++- R/PhyloValue.R | 4 - R/Rao.R | 38 +++++++++-- R/Richness.R | 27 +++++++- R/Shannon.R | 83 +++++++++++++++++++------ R/ShannonBeta.R | 14 ++-- R/Simpson.R | 30 +++++++-- R/SimpsonBeta.R | 8 +- R/SpeciesDistribution.R | 6 - R/Tsallis.R | 87 +++++++++++++++++++++------ R/TsallisBeta.R | 18 +++-- R/lnq.R | 6 - build/vignette.rds |binary inst/doc/entropart.R | 114 ++++++++++++++++------------------- inst/doc/entropart.Rnw | 99 +++++++++++++++--------------- inst/doc/entropart.pdf |binary man/AllenH.Rd | 9 ++ man/AlphaDiversity.Rd | 4 - man/AlphaEntropy.Rd | 8 +- man/BetaDiversity.Rd | 4 - man/BetaEntropy.Rd | 8 +- man/ChaoPD.Rd | 14 ++-- man/CommunityProfile.Rd | 12 ++- man/Coverage.Rd | 4 - man/DivEst.Rd | 4 - man/Diversity.Rd | 4 - man/Dqz.Rd | 4 - man/GammaDiversity.Rd | 6 - man/GammaEntropy.Rd | 10 ++- man/Hqz.Rd | 2 man/HqzBeta.Rd | 2 man/Hurlbert.Rd | 2 man/KLq.Rd | 2 man/PDFD.Rd | 2 man/PhyloDiversity.Rd | 3 man/PhyloEntropy.Rd | 3 man/Rao.Rd | 2 man/Richness.Rd | 4 - man/Shannon.Rd | 10 +-- man/Simpson.Rd | 2 man/SimpsonBeta.Rd | 4 - man/SpeciesDistribution.Rd | 8 +- man/Tsallis.Rd | 18 +++-- man/TsallisBeta.Rd | 2 man/entropart-package.Rd | 19 +---- vignettes/entropart.Rnw | 99 +++++++++++++++--------------- vignettes/entropart.bib | 9 ++ 73 files changed, 848 insertions(+), 478 deletions(-)
Title: Performance Analysis and Companion Functions for Binary
Classification Models
Description: Provides companion function for analysing the performance of classification models. Also, provides function to optimise probability cut-off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, 'KS Statistic' etc to aid accuracy improvement in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>
Diff between InformationValue versions 1.1.1 dated 2015-08-27 and 1.2.1 dated 2015-12-06
DESCRIPTION | 15 MD5 | 59 + NAMESPACE | 43 - R/Main.R | 1232 ++++++++++++++++++++++------------------- R/StandAloneFuncs.R | 10 R/playground.R |only README.md | 414 ++++++------- build/vignette.rds |binary inst/doc/InformationValue.R | 134 ++-- inst/doc/InformationValue.Rmd | 424 +++++++------- inst/doc/InformationValue.html | 556 ++++++++++-------- man/AUROC.Rd | 60 - man/ActualsAndScores.Rd | 44 - man/Concordance.Rd | 72 +- man/IV.Rd | 64 +- man/SimData.Rd | 44 - man/WOE.Rd | 64 +- man/WOETable.Rd | 84 +- man/confusionMatrix.Rd | 64 +- man/kappaCohen.Rd | 64 +- man/ks_plot.Rd |only man/ks_stat.Rd |only man/misClassError.Rd | 66 +- man/npv.Rd |only man/optimalCutoff.Rd | 88 +- man/plotROC.Rd | 68 +- man/precision.Rd |only man/sensitivity.Rd | 64 +- man/somersD.Rd | 60 - man/specificity.Rd | 64 +- man/youdensIndex.Rd | 64 +- vignettes/InformationValue.Rmd | 424 +++++++------- vignettes/custom.css | 202 +++--- 33 files changed, 2409 insertions(+), 2138 deletions(-)
More information about InformationValue at CRAN
Permanent link
Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel
(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
'xl[a1] = current.graphics()'. There is an Excel workbook with examples of
calling R from Excel in the 'doc' folder. It tries to keep things as
simple as possible - there are no needs in any additional
installations besides R, only 'VBA' code in the Excel workbook.
Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy
includes source code from 'RDCOMClient' (http://www.omegahat.org/RDCOMClient) by
Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>
Diff between excel.link versions 0.9.1 dated 2015-07-14 and 0.9.3 dated 2015-12-06
DESCRIPTION | 23 +++++++++------- MD5 | 38 +++++++++++++------------- NAMESPACE | 2 - NEWS | 5 +++ R/current.graphics.R | 3 -- build/vignette.rds |binary inst/doc/R_connection_examples.xlsm |binary man/RDCOMClient.Rd | 10 ++----- man/current.graphics.Rd | 28 ++++++++++--------- man/excel.link.Rd | 36 ++++++++++++------------- man/xl.Rd | 47 ++++++++++++++++----------------- man/xl.bind.range.Rd | 46 ++++++++++++++++---------------- man/xl.connect.table.Rd | 48 +++++++++++++++++---------------- man/xl.current.region.Rd | 51 ++++++++++++++++++------------------ man/xl.get.excel.Rd | 9 +++--- man/xl.index2address.Rd | 8 +++-- man/xl.read.file.Rd | 8 +++-- man/xl.sheet.add.Rd | 21 +++++++------- man/xl.workbook.add.Rd | 16 +++++------ man/xl.write.Rd | 12 ++++---- 20 files changed, 214 insertions(+), 197 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between capm versions 0.8.0 dated 2015-05-01 and 0.9.0 dated 2015-12-06
DESCRIPTION | 11 +++--- MD5 | 60 +++++++++++++++++------------------ NAMESPACE | 17 ++++++++- NEWS | 39 +++++++++++++++++++++- R/PlotGlobalSens.R | 4 +- R/PlotLocalSens.R | 5 +- R/PlotModels.R | 1 R/PlotPopPyramid.R | 4 +- R/capm-package.R | 12 ++++--- inst/CITATION | 4 +- man/Calculate2StageSampleSize.Rd | 2 - man/CalculateGlobalSens.Rd | 13 ++++--- man/CalculateLocalSens.Rd | 11 +++--- man/CalculatePopChange.Rd | 9 ++--- man/CalculateSimpleSampleSize.Rd | 2 - man/CalculateStratifiedSampleSize.Rd | 6 +-- man/DesignSurvey.Rd | 5 +- man/GraphicInterface.Rd | 3 + man/MapkmlPSU.Rd | 8 ++-- man/PlotGlobalSens.Rd | 19 +++++------ man/PlotLocalSens.Rd | 16 +++++---- man/PlotModels.Rd | 33 +++++++++---------- man/PlotPopPyramid.Rd | 5 +- man/SamplePPS.Rd | 3 + man/SampleSystematic.Rd | 6 +-- man/SetRanges.Rd | 6 ++- man/SolveIASA.Rd | 21 ++++++------ man/SolveSI.Rd | 13 ++++--- man/SolveTC.Rd | 17 +++++---- man/SummarySurvey.Rd | 7 ++-- man/capm-package.Rd | 8 ++-- 31 files changed, 222 insertions(+), 148 deletions(-)
Title: Discrete and Global Optimization Routines
Description:
The R package 'adagio' will provide methods and algorithms for
discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between adagio versions 0.6.1 dated 2015-07-27 and 0.6.3 dated 2015-12-06
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++++--- NAMESPACE | 9 +++++---- NEWS | 10 +++++++++- R/hamiltonian.R |only R/lsqlincon.R |only man/hamiltonian.Rd |only man/lsqlincon.Rd |only 8 files changed, 28 insertions(+), 15 deletions(-)
Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character
Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with
machine readable zones, e.g. passports. Get the results in a variety of formats
including plain text and XML. To learn more about the Abbyy OCR API, see http://
ocrsdk.com/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between abbyyR versions 0.2.2 dated 2015-11-06 and 0.2.3 dated 2015-12-06
DESCRIPTION | 8 +- MD5 | 87 +++++++++++++++--------------- NAMESPACE | 2 NEWS | 9 +++ R/abbyyR.R | 7 +- R/compareText.R | 3 + R/deleteTask.R | 37 ++++++++---- R/getResults.R | 36 ++++++++---- R/getTaskStatus.R | 11 +-- R/listFinishedTasks.R | 16 +++-- R/listTasks.R | 37 ++++++++---- R/ocrFile.R | 13 +++- R/processBarcodeField.R | 6 +- R/processBusinessCard.R | 7 +- R/processCheckmarkField.R | 8 +- R/processDocument.R | 2 R/processFields.R | 9 +-- R/processImage.R | 15 ++--- R/processMRZ.R | 4 - R/processPhotoId.R | 15 ++--- R/processRemoteImage.R | 8 +- R/processTextField.R | 19 ++++-- R/submitImage.R | 23 ++++--- inst/doc/example.html | 4 - inst/doc/overview.html | 4 - inst/doc/wiscads.html | 4 - inst/extdata/t1.png |only man/deleteTask.Rd | 9 ++- man/getResults.Rd | 6 +- man/getTaskStatus.Rd | 2 man/listTasks.Rd | 13 ++-- man/ocrFile.Rd | 7 +- man/processBarcodeField.Rd | 2 man/processBusinessCard.Rd | 4 - man/processCheckmarkField.Rd | 4 - man/processDocument.Rd | 2 man/processFields.Rd | 6 +- man/processImage.Rd | 2 man/processMRZ.Rd | 2 man/processPhotoId.Rd | 2 man/processTextField.Rd | 2 man/submitImage.Rd | 4 - tests/testthat/test-get-info.R | 2 tests/testthat/test-get-results.R |only tests/testthat/test-list-finished-tasks.R |only tests/testthat/test-list-tasks.R |only tests/testthat/test-submit-image.R |only 47 files changed, 271 insertions(+), 192 deletions(-)
Title: Data Preparation, Estimation and Prediction in Multi-State
Models
Description: The mstate packages contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco, with contributions by
Ronald Geskus
Maintainer: Hein Putter <H.Putter@lumc.nl>
Diff between mstate versions 0.2.7 dated 2014-05-30 and 0.2.8 dated 2015-12-06
mstate-0.2.7/mstate/R/crprep.r |only mstate-0.2.7/mstate/R/expandcovs.R |only mstate-0.2.7/mstate/man/expandcovs.Rd |only mstate-0.2.8/mstate/ChangeLog | 30 ++ mstate-0.2.8/mstate/DESCRIPTION | 17 - mstate-0.2.8/mstate/MD5 | 68 +++--- mstate-0.2.8/mstate/NAMESPACE | 25 +- mstate-0.2.8/mstate/R/ELOS.R | 2 mstate-0.2.8/mstate/R/create.wData.omega.R |only mstate-0.2.8/mstate/R/crprep.R |only mstate-0.2.8/mstate/R/cuminc.R | 210 ++++++------------- mstate-0.2.8/mstate/R/cutLMms.R | 2 mstate-0.2.8/mstate/R/events.R | 2 mstate-0.2.8/mstate/R/expand.covs.R |only mstate-0.2.8/mstate/R/msprep.R | 32 +-- mstate-0.2.8/mstate/R/mssample.R | 15 - mstate-0.2.8/mstate/R/plot.Cuminc.R |only mstate-0.2.8/mstate/R/plot.probtrans.R | 51 ++-- mstate-0.2.8/mstate/R/print.Cuminc.R |only mstate-0.2.8/mstate/R/probtrans.R | 20 + mstate-0.2.8/mstate/R/summary.Cuminc.R |only mstate-0.2.8/mstate/R/xsect.R | 5 mstate-0.2.8/mstate/build/vignette.rds |binary mstate-0.2.8/mstate/data/aidssi2.RData |only mstate-0.2.8/mstate/inst/CITATION | 2 mstate-0.2.8/mstate/inst/doc/Tutorial.R | 1 mstate-0.2.8/mstate/inst/doc/Tutorial.Rnw | 1 mstate-0.2.8/mstate/inst/doc/Tutorial.pdf |binary mstate-0.2.8/mstate/man/ELOS.Rd | 3 mstate-0.2.8/mstate/man/aidssi.Rd | 100 ++++++--- mstate-0.2.8/mstate/man/crprep.Rd | 277 ++++++++++++-------------- mstate-0.2.8/mstate/man/cuminc.Rd | 35 +-- mstate-0.2.8/mstate/man/cutLMms.Rd | 11 - mstate-0.2.8/mstate/man/ebmt1.Rd | 8 mstate-0.2.8/mstate/man/ebmt4.Rd | 15 + mstate-0.2.8/mstate/man/expand.covs.Rd |only mstate-0.2.8/mstate/man/expand.covs.msdata.Rd |only mstate-0.2.8/mstate/man/msfit.Rd | 10 mstate-0.2.8/mstate/man/mstate-package.Rd | 16 - mstate-0.2.8/mstate/man/probtrans.Rd | 10 mstate-0.2.8/mstate/vignettes/Tutorial.Rnw | 1 41 files changed, 504 insertions(+), 465 deletions(-)
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.6 dated 2015-10-01 and 0.7 dated 2015-12-06
jiebaR-0.6/jiebaR/tests/testthat/C_API/R/RcppExports.R |only jiebaR-0.7/jiebaR/DESCRIPTION | 13 jiebaR-0.7/jiebaR/MD5 | 89 +++-- jiebaR-0.7/jiebaR/NAMESPACE | 8 jiebaR-0.7/jiebaR/NEWS | 47 +- jiebaR-0.7/jiebaR/R/RcppExports.R | 24 + jiebaR-0.7/jiebaR/R/gen_idf.R |only jiebaR-0.7/jiebaR/R/get_tuple.R |only jiebaR-0.7/jiebaR/R/simhash.R | 48 +++ jiebaR-0.7/jiebaR/R/tobin.R |only jiebaR-0.7/jiebaR/R/zzz.R | 2 jiebaR-0.7/jiebaR/inst/include/jiebaRAPI.h | 42 +- jiebaR-0.7/jiebaR/inst/include/lib/Simhasher.hpp | 53 +++ jiebaR-0.7/jiebaR/inst/include/segtype.hpp | 63 +++ jiebaR-0.7/jiebaR/inst/other |only jiebaR-0.7/jiebaR/man/DICTPATH.Rd | 4 jiebaR-0.7/jiebaR/man/distance.Rd | 9 jiebaR-0.7/jiebaR/man/edit_dict.Rd | 10 jiebaR-0.7/jiebaR/man/filecoding.Rd | 2 jiebaR-0.7/jiebaR/man/filter_segment.Rd | 2 jiebaR-0.7/jiebaR/man/freq.Rd | 2 jiebaR-0.7/jiebaR/man/get_idf.Rd |only jiebaR-0.7/jiebaR/man/get_tuple.Rd |only jiebaR-0.7/jiebaR/man/jiebaR.Rd | 17 - jiebaR-0.7/jiebaR/man/keywords.Rd | 8 jiebaR-0.7/jiebaR/man/less-than-equals-.keywords.Rd | 2 jiebaR-0.7/jiebaR/man/less-than-equals-.qseg.Rd | 17 - jiebaR-0.7/jiebaR/man/less-than-equals-.segment.Rd | 2 jiebaR-0.7/jiebaR/man/less-than-equals-.simhash.Rd | 2 jiebaR-0.7/jiebaR/man/less-than-equals-.tagger.Rd | 2 jiebaR-0.7/jiebaR/man/print.hmmseg.Rd | 2 jiebaR-0.7/jiebaR/man/segment.Rd | 30 - jiebaR-0.7/jiebaR/man/set_qsegmodel.Rd | 4 jiebaR-0.7/jiebaR/man/show_dictpath.Rd | 4 jiebaR-0.7/jiebaR/man/simhash.Rd | 9 jiebaR-0.7/jiebaR/man/tagging.Rd | 12 jiebaR-0.7/jiebaR/man/tobin.Rd |only jiebaR-0.7/jiebaR/man/worker.Rd | 123 +++---- jiebaR-0.7/jiebaR/src/RcppExports.cpp | 74 ++++ jiebaR-0.7/jiebaR/src/get_idf.cpp |only jiebaR-0.7/jiebaR/src/get_tuple.cpp |only jiebaR-0.7/jiebaR/src/segtype.cpp | 18 + jiebaR-0.7/jiebaR/tests/testthat/CPP_API/DESCRIPTION | 2 jiebaR-0.7/jiebaR/tests/testthat/CPP_API/R/Rcpps.R | 48 +-- jiebaR-0.7/jiebaR/tests/testthat/CPP_API/src/test_api.cpp | 159 +++++++--- jiebaR-0.7/jiebaR/tests/testthat/CPP_API/tests/testthat/test-cpp.R | 57 +++ jiebaR-0.7/jiebaR/tests/testthat/C_API/DESCRIPTION | 6 jiebaR-0.7/jiebaR/tests/testthat/C_API/R/Rcpps.R |only jiebaR-0.7/jiebaR/tests/testthat/C_API/src/test_api.c | 159 +++++++--- jiebaR-0.7/jiebaR/tests/testthat/C_API/tests/testthat/test-c.R | 58 +++ jiebaR-0.7/jiebaR/tests/testthat/test-api.R | 14 51 files changed, 925 insertions(+), 322 deletions(-)
Title: Classical Jacobi Eigensolution Algorithm
Description: Implements the classical Jacobi (1846) algorithm for the
eigenvalues and eigenvectors of a real symmetric matrix, both in
pure R and in C++ using Rcpp. Mainly as a programming example
for teaching purposes.
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between JacobiEigen versions 0.2-1 dated 2015-11-29 and 0.2-2 dated 2015-12-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/JacobiR.R | 6 ++---- inst/doc/JacobiEigen.R | 2 +- inst/doc/JacobiEigen.Rmd | 25 +++++++++++++++---------- inst/doc/JacobiEigen.pdf |binary man/Jacobi.Rd | 3 +-- man/JacobiR.Rd | 4 ++-- vignettes/JacobiEigen.Rmd | 25 +++++++++++++++---------- vignettes/header.tex | 5 +---- 10 files changed, 50 insertions(+), 46 deletions(-)
Title: CRISPR AnalyzeR for Pooled CRISPR Screens
Description: CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <https://en.wikipedia.org/wiki/CRISPR> for more information on
CRISPR.
Author: Jan Winter, Florian Heigwer
Maintainer: Jan Winter <jan.winter@dkfz-heidelberg.de>
Diff between caRpools versions 0.82.5 dated 2015-11-04 and 0.83 dated 2015-12-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get.gene.info.R | 6 +++--- inst/doc/CaRpools.R | 14 ++++++++------ inst/doc/CaRpools.Rmd | 23 +++++++++++++++-------- inst/doc/CaRpools.html | 24 +++++++++++++++--------- man/get.gene.info.Rd | 18 ++++++++++++------ vignettes/CaRpools.Rmd | 23 +++++++++++++++-------- 8 files changed, 79 insertions(+), 51 deletions(-)
Title: A Program for Missing Data
Description: A tool that "multiply imputes" missing data in a single cross-section
(such as a survey), from a time series (like variables collected for
each year in a country), or from a time-series-cross-sectional data
set (such as collected by years for each of several countries).
Amelia II implements our bootstrapping-based algorithm that gives
essentially the same answers as the standard IP or EMis approaches,
is usually considerably faster than existing approaches and can
handle many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but please
let us know if you find to the contrary!). The program also
generalizes existing approaches by allowing for trends in time series
across observations within a cross-sectional unit, as well as priors
that allow experts to incorporate beliefs they have about the values
of missing cells in their data. Amelia II also includes useful
diagnostics of the fit of multiple imputation models. The program
works from the R command line or via a graphical user interface that
does not require users to know R.
Author: James Honaker <jhonaker@iq.harvard.edu>,
Gary King <king@harvard.edu>,
Matthew Blackwell <mblackwell@gov.harvard.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>
Diff between Amelia versions 1.7.3 dated 2014-11-15 and 1.7.4 dated 2015-12-06
Amelia-1.7.3/Amelia/tests/collinear.R |only Amelia-1.7.4/Amelia/DESCRIPTION | 14 +++++------ Amelia-1.7.4/Amelia/MD5 | 38 +++++++++++++++---------------- Amelia-1.7.4/Amelia/NAMESPACE | 11 ++++++++ Amelia-1.7.4/Amelia/NEWS | 8 ++++++ Amelia-1.7.4/Amelia/R/amcheck.r | 20 ++++++++-------- Amelia-1.7.4/Amelia/R/ameliagui.r | 8 ++++-- Amelia-1.7.4/Amelia/R/diag.r | 26 +++++++++++++-------- Amelia-1.7.4/Amelia/R/mo.R | 15 +++++------- Amelia-1.7.4/Amelia/R/prep.r | 19 ++++++++------- Amelia-1.7.4/Amelia/README.md | 2 - Amelia-1.7.4/Amelia/inst/CITATION | 9 ++++--- Amelia-1.7.4/Amelia/inst/doc/amelia.R | 15 ++++++------ Amelia-1.7.4/Amelia/inst/doc/amelia.Rnw | 14 +++++------ Amelia-1.7.4/Amelia/inst/doc/amelia.pdf |binary Amelia-1.7.4/Amelia/man/mi.meld.Rd | 4 +-- Amelia-1.7.4/Amelia/man/moPrep.Rd | 2 - Amelia-1.7.4/Amelia/src/Makevars | 2 - Amelia-1.7.4/Amelia/src/Makevars.win | 2 - Amelia-1.7.4/Amelia/vignettes/amelia.Rnw | 14 +++++------ Amelia-1.7.4/Amelia/vignettes/auto |only 21 files changed, 129 insertions(+), 94 deletions(-)
Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>
Diff between tablaxlsx versions 1.0.1 dated 2015-11-30 and 1.0.3 dated 2015-12-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/escribirTabla.R | 9 ++++++--- data/estilosDGE.rda |binary man/escribirTabla.Rd | 8 +++++--- 5 files changed, 18 insertions(+), 13 deletions(-)
Title: '--omics' Data Analysis Toolbox
Description: A collection of functions to analyse '--omics' datasets such as DNA
methylation and gene expression profiles.
Author: Gianluca Campanella [aut, cre]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between omics versions 0.1-0 dated 2015-12-04 and 0.1-1 dated 2015-12-05
DESCRIPTION | 8 ++--- MD5 | 11 ++++--- R/mlm.R | 53 +++++++++++++++++++++--------------- R/mlmer.R | 86 ++++++++++++++++++++++++++++++----------------------------- inst |only man/mlm.Rd | 17 +++++------ man/mlmer.Rd | 25 +++++++---------- 7 files changed, 106 insertions(+), 94 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 4.2-0 dated 2015-07-10 and 5.0-0 dated 2015-12-05
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Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova, Adrian Raftery; original WinBugs code written by Jennifer Chunn
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesLife versions 2.2-0 dated 2015-03-12 and 3.0-0 dated 2015-12-05
bayesLife-2.2-0/bayesLife/data/include_2008.R |only bayesLife-2.2-0/bayesLife/data/include_2008.txt |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country530.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country736.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/k.c_country530.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/k.c_country736.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/z.c_country530.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc1/z.c_country736.txt.bz2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/mc2 |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/predictions/traj_country530.rda |only bayesLife-2.2-0/bayesLife/inst/ex-data/bayesLife.output/predictions/traj_country736.rda |only bayesLife-3.0-0/bayesLife/ChangeLog | 14 bayesLife-3.0-0/bayesLife/DESCRIPTION | 12 bayesLife-3.0-0/bayesLife/MD5 | 1891 +++------- bayesLife-3.0-0/bayesLife/NAMESPACE | 5 bayesLife-3.0-0/bayesLife/R/plot_functions.R | 22 bayesLife-3.0-0/bayesLife/R/projection_fcns.R | 41 bayesLife-3.0-0/bayesLife/R/run_mcmc.R | 8 bayesLife-3.0-0/bayesLife/R/wpp_data.R | 4 bayesLife-3.0-0/bayesLife/data/include_2015.R |only bayesLife-3.0-0/bayesLife/data/include_2015.txt |only bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/bayesLife.mcmc.meta.rda |binary bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country100.txt.bz2 |binary bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country104.txt.bz2 |binary bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country112.txt.bz2 |binary bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country116.txt.bz2 |binary bayesLife-3.0-0/bayesLife/inst/ex-data/bayesLife.output/mc1/Triangle.c_country12.txt.bz2 |binary 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Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between sweidnumbr versions 0.6.5 dated 2015-09-06 and 0.8.2 dated 2015-12-05
sweidnumbr-0.6.5/sweidnumbr/inst/doc/sweidnumbr.md |only sweidnumbr-0.8.2/sweidnumbr/DESCRIPTION | 12 sweidnumbr-0.8.2/sweidnumbr/MD5 | 31 sweidnumbr-0.8.2/sweidnumbr/NAMESPACE | 2 sweidnumbr-0.8.2/sweidnumbr/R/format.pin.R |only sweidnumbr-0.8.2/sweidnumbr/R/pin.R | 89 +- sweidnumbr-0.8.2/sweidnumbr/R/pin_internal.R | 4 sweidnumbr-0.8.2/sweidnumbr/inst/doc/sweidnumbr.R | 4 sweidnumbr-0.8.2/sweidnumbr/inst/doc/sweidnumbr.Rmd | 39 sweidnumbr-0.8.2/sweidnumbr/inst/doc/sweidnumbr.html | 469 +++++++---- sweidnumbr-0.8.2/sweidnumbr/man/as.pin.Rd | 12 sweidnumbr-0.8.2/sweidnumbr/man/format.Rd |only sweidnumbr-0.8.2/sweidnumbr/man/format.pin.Rd |only sweidnumbr-0.8.2/sweidnumbr/man/luhn_algo.Rd | 4 sweidnumbr-0.8.2/sweidnumbr/man/pin_age.Rd | 3 sweidnumbr-0.8.2/sweidnumbr/tests/testthat/test-as.pin.R | 19 sweidnumbr-0.8.2/sweidnumbr/tests/testthat/test-format.pin.R |only sweidnumbr-0.8.2/sweidnumbr/tests/testthat/test-pin_age.R | 13 sweidnumbr-0.8.2/sweidnumbr/vignettes/sweidnumbr.Rmd | 9 19 files changed, 491 insertions(+), 219 deletions(-)
Title: A Soil Survey Toolkit
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: USDA-NRCS Soil Survey Staff
Maintainer: Dylan Beaudette <dylan.beaudette@ca.usda.gov>
Diff between sharpshootR versions 0.7-2 dated 2015-02-19 and 0.9.1 dated 2015-12-05
DESCRIPTION | 22 +++--- MD5 | 33 ++++++--- NAMESPACE | 24 ++++++- R/aggregateColorPlot.R |only R/diagnosticPropertyPlot.R | 137 +++++++++++++++++++++++++++++++++++++---- R/generateLineHash.R |only R/hillslope.probability.R | 2 R/joinAdjacency.R |only R/multinominal2logical.R |only R/plotSoilRelationChordGraph.R |only R/polygonAdjacency.R | 13 ++- R/sample.by.poly.R | 71 ++++++++++++++++++--- data/CDEC.snow.courses.rda |binary data/amador.rda |binary man/aggregateColorPlot.Rd |only man/diagnosticPropertyPlot.Rd | 11 +-- man/generateLineHash.Rd |only man/joinAdjacency.Rd |only man/multinominal2logical.Rd |only man/plotSoilRelationGraph.Rd | 4 - man/polygonAdjacency.Rd | 12 ++- man/sample.by.poly.Rd | 19 +++-- 22 files changed, 282 insertions(+), 66 deletions(-)
Title: Invoke 'Repast Simphony' Simulation Models
Description: An R and Repast integration tool for running individual-based (IbM)
simulation models developed using 'Repast Simphony' Agent-Based framework
directly from R code. This package integrates 'Repast Simphony' models within
R environment, making easier the tasks of running and analyzing model output
data for automated parameter calibration and for carrying out uncertainty and
sensitivity analysis using the power of R environment.
Author: Antonio Prestes Garcia [aut, cre],
Alfonso Rodriguez-Paton [aut, ths]
Maintainer: Antonio Prestes Garcia <antonio.pgarcia@alumnos.upm.es>
Diff between rrepast versions 0.1 dated 2015-11-07 and 0.2 dated 2015-12-05
DESCRIPTION | 12 ++-- MD5 | 14 ++-- NAMESPACE | 3 + R/RRepast.R | 129 +++++++++++++++++++++++++++++++++++++------ inst/java/rrepast-engine.jar |binary man/Run.Rd | 13 +++- man/getKeyRandom.Rd |only man/jvm.init.Rd | 5 + man/setKeyRandom.Rd |only 9 files changed, 144 insertions(+), 32 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website
where registered users can submit and discuss content. This package uses
Reddit API to extract Reddit data using Reddit API. Note that due to the API
limitations, the number of comments that can extracted is limited to 500 per
thread. The package consists of 4 functions, one for extracting relevant URLs,
one for extracting features out of given URLs, one that does both together and
one that constructs graphs based on the structure of a thread.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 2.0.1 dated 2015-11-21 and 2.0.2 dated 2015-12-05
DESCRIPTION | 9 +++++---- MD5 | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.3.1 dated 2015-11-25 and 1.3.2 dated 2015-12-05
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 102 +- R/foo.R | 1797 ++++++++++++++++++++++++++++++----------- man/linear.model.MLE.Rd | 17 man/spatial.pred.linear.MLE.Rd | 5 6 files changed, 1406 insertions(+), 533 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for multi-
label data sets along with an interactive Shiny application to ease their use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.82 dated 2015-10-18 and 0.3.18 dated 2015-12-05
DESCRIPTION | 19 +- MD5 | 67 ++++---- NAMESPACE | 4 R/filters.R | 2 R/generics.R | 2 R/measures.R | 27 ++- R/mldr.R | 124 ++++++---------- R/operators.R | 4 R/read.arff.R | 152 ++++++++++++++++++-- README.md | 6 build/vignette.rds |binary data/birds.rda |binary data/emotions.rda |binary data/genbase.rda |binary inst/doc/mldr.pdf |binary inst/shiny/rsconnect/shinyapps.io/fdavidcl/mldr.dcf | 4 man/birds.Rd | 2 man/concurrenceReport.Rd | 3 man/emotions.Rd | 2 man/equals-.mldr.Rd | 2 man/genbase.Rd | 2 man/labelInteractions.Rd | 3 man/mldr.Rd | 12 + man/mldrGUI.Rd | 2 man/mldr_evaluate.Rd | 2 man/mldr_from_dataframe.Rd | 9 - man/mldr_transform.Rd | 2 man/plot.mldr.Rd | 3 man/plus-.mldr.Rd | 2 man/print.mldr.Rd | 4 man/read.arff.Rd |only man/remedial.Rd | 3 man/sub-.mldr.Rd | 4 man/summary.mldr.Rd | 4 man/write_arff.Rd | 3 35 files changed, 308 insertions(+), 167 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff <larsko@cs.ubc.ca>
Diff between llama versions 0.9 dated 2015-11-22 and 0.9.1 dated 2015-12-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/helpers.R | 2 +- inst/manual/llama.pdf |binary man/input.Rd | 18 ++++++++---------- tests/testthat/test.classify.R | 11 +++++++++-- tests/testthat/test.classifyPairs.R | 4 ++-- 8 files changed, 35 insertions(+), 26 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.11.0 dated 2015-08-12 and 0.12.1 dated 2015-12-05
git2r-0.11.0/git2r/man/config-methods.Rd |only git2r-0.11.0/git2r/man/cred_ssh_key-methods.Rd |only git2r-0.11.0/git2r/src/libgit2/merge_file.h |only git2r-0.11.0/git2r/src/winhttp/winhttp-x64.def |only git2r-0.11.0/git2r/src/winhttp/winhttp.def |only git2r-0.12.1/git2r/DESCRIPTION | 8 git2r-0.12.1/git2r/MD5 | 588 +++++----- git2r-0.12.1/git2r/NAMESPACE | 12 git2r-0.12.1/git2r/NEWS | 53 git2r-0.12.1/git2r/R/S4_classes.r | 45 git2r-0.12.1/git2r/R/checkout.r | 141 +- git2r-0.12.1/git2r/R/config.r | 132 +- git2r-0.12.1/git2r/R/credential.r | 98 - git2r-0.12.1/git2r/R/diff.r | 2 git2r-0.12.1/git2r/R/fetch.r | 3 git2r-0.12.1/git2r/R/index.r | 93 + git2r-0.12.1/git2r/R/libgit2.r | 17 git2r-0.12.1/git2r/R/pull.r | 11 git2r-0.12.1/git2r/R/push.r | 3 git2r-0.12.1/git2r/R/remote.r | 105 + git2r-0.12.1/git2r/R/repository.r | 61 - git2r-0.12.1/git2r/configure | 208 ++- git2r-0.12.1/git2r/configure.ac |only git2r-0.12.1/git2r/configure.win | 19 git2r-0.12.1/git2r/inst/AUTHORS | 1 git2r-0.12.1/git2r/man/add-methods.Rd | 51 git2r-0.12.1/git2r/man/add_session_info.Rd | 2 git2r-0.12.1/git2r/man/ahead_behind-methods.Rd | 2 git2r-0.12.1/git2r/man/blame-methods.Rd | 2 git2r-0.12.1/git2r/man/blob_create-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_create-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_delete-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_get_upstream-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_remote_name-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_remote_url-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_rename-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_set_upstream-methods.Rd | 2 git2r-0.12.1/git2r/man/branch_target-methods.Rd | 2 git2r-0.12.1/git2r/man/branches-methods.Rd | 2 git2r-0.12.1/git2r/man/bundle_r_package-methods.Rd | 2 git2r-0.12.1/git2r/man/checkout-methods.Rd | 24 git2r-0.12.1/git2r/man/clone-methods.Rd | 7 git2r-0.12.1/git2r/man/coerce-git_repository-method.Rd | 2 git2r-0.12.1/git2r/man/coerce-git_tree-data.frame-method.Rd | 2 git2r-0.12.1/git2r/man/coerce-git_tree-list-method.Rd | 2 git2r-0.12.1/git2r/man/commit-methods.Rd | 2 git2r-0.12.1/git2r/man/commits-methods.Rd | 2 git2r-0.12.1/git2r/man/config.Rd |only git2r-0.12.1/git2r/man/content-methods.Rd | 2 git2r-0.12.1/git2r/man/contributions-methods.Rd | 2 git2r-0.12.1/git2r/man/cred_env-class.Rd | 2 git2r-0.12.1/git2r/man/cred_env-methods.Rd | 15 git2r-0.12.1/git2r/man/cred_ssh_key-class.Rd | 2 git2r-0.12.1/git2r/man/cred_ssh_key.Rd |only git2r-0.12.1/git2r/man/cred_token-class.Rd |only git2r-0.12.1/git2r/man/cred_token.Rd |only git2r-0.12.1/git2r/man/cred_user_pass-class.Rd | 2 git2r-0.12.1/git2r/man/cred_user_pass-methods.Rd | 6 git2r-0.12.1/git2r/man/default_signature-methods.Rd | 2 git2r-0.12.1/git2r/man/descendant_of-methods.Rd | 2 git2r-0.12.1/git2r/man/diff-methods.Rd | 2 git2r-0.12.1/git2r/man/discover_repository-methods.Rd | 37 git2r-0.12.1/git2r/man/fetch-methods.Rd | 5 git2r-0.12.1/git2r/man/fetch_heads-methods.Rd | 2 git2r-0.12.1/git2r/man/get_refspec.Rd | 2 git2r-0.12.1/git2r/man/git2r.Rd | 2 git2r-0.12.1/git2r/man/git_blame-class.Rd | 2 git2r-0.12.1/git2r/man/git_blame_hunk-class.Rd | 2 git2r-0.12.1/git2r/man/git_blob-class.Rd | 2 git2r-0.12.1/git2r/man/git_branch-class.Rd | 2 git2r-0.12.1/git2r/man/git_commit-class.Rd | 2 git2r-0.12.1/git2r/man/git_diff-class.Rd | 2 git2r-0.12.1/git2r/man/git_diff_file-class.Rd | 2 git2r-0.12.1/git2r/man/git_diff_hunk-class.Rd | 2 git2r-0.12.1/git2r/man/git_diff_line-class.Rd | 2 git2r-0.12.1/git2r/man/git_fetch_head.Rd | 2 git2r-0.12.1/git2r/man/git_merge_result.Rd | 2 git2r-0.12.1/git2r/man/git_note-class.Rd | 2 git2r-0.12.1/git2r/man/git_reference-class.Rd | 2 git2r-0.12.1/git2r/man/git_reflog_entry-class.Rd | 2 git2r-0.12.1/git2r/man/git_repository-class.Rd | 2 git2r-0.12.1/git2r/man/git_signature-class.Rd | 2 git2r-0.12.1/git2r/man/git_stash-class.Rd | 2 git2r-0.12.1/git2r/man/git_tag-class.Rd | 2 git2r-0.12.1/git2r/man/git_time-class.Rd | 2 git2r-0.12.1/git2r/man/git_transfer_progress-class.Rd | 2 git2r-0.12.1/git2r/man/git_tree-class.Rd | 2 git2r-0.12.1/git2r/man/hash-methods.Rd | 2 git2r-0.12.1/git2r/man/hashfile-methods.Rd | 2 git2r-0.12.1/git2r/man/head-methods.Rd | 2 git2r-0.12.1/git2r/man/in_repository-methods.Rd | 2 git2r-0.12.1/git2r/man/init-methods.Rd | 2 git2r-0.12.1/git2r/man/is_bare-methods.Rd | 2 git2r-0.12.1/git2r/man/is_binary-methods.Rd | 2 git2r-0.12.1/git2r/man/is_blob.Rd | 2 git2r-0.12.1/git2r/man/is_commit.Rd | 2 git2r-0.12.1/git2r/man/is_detached-methods.Rd | 2 git2r-0.12.1/git2r/man/is_empty-methods.Rd | 2 git2r-0.12.1/git2r/man/is_head-methods.Rd | 2 git2r-0.12.1/git2r/man/is_local-methods.Rd | 2 git2r-0.12.1/git2r/man/is_merge-methods.Rd | 2 git2r-0.12.1/git2r/man/is_shallow-methods.Rd | 2 git2r-0.12.1/git2r/man/length-git_blob-method.Rd | 2 git2r-0.12.1/git2r/man/length-git_diff-method.Rd | 3 git2r-0.12.1/git2r/man/length-git_tree-method.Rd | 2 git2r-0.12.1/git2r/man/libgit2_features.Rd | 2 git2r-0.12.1/git2r/man/libgit2_sha.Rd | 2 git2r-0.12.1/git2r/man/libgit2_version.Rd | 2 git2r-0.12.1/git2r/man/lookup-methods.Rd | 2 git2r-0.12.1/git2r/man/lookup_repository.Rd | 2 git2r-0.12.1/git2r/man/merge-methods.Rd | 2 git2r-0.12.1/git2r/man/merge_base-methods.Rd | 2 git2r-0.12.1/git2r/man/merge_branch.Rd | 2 git2r-0.12.1/git2r/man/merge_named_branch.Rd | 2 git2r-0.12.1/git2r/man/note_create-methods.Rd | 2 git2r-0.12.1/git2r/man/note_default_ref-methods.Rd | 2 git2r-0.12.1/git2r/man/note_remove-methods.Rd | 2 git2r-0.12.1/git2r/man/notes-methods.Rd | 2 git2r-0.12.1/git2r/man/odb_blobs-methods.Rd | 2 git2r-0.12.1/git2r/man/odb_objects-methods.Rd | 2 git2r-0.12.1/git2r/man/parents-methods.Rd | 2 git2r-0.12.1/git2r/man/plot-methods.Rd | 2 git2r-0.12.1/git2r/man/pull-methods.Rd | 11 git2r-0.12.1/git2r/man/punch_card-methods.Rd | 2 git2r-0.12.1/git2r/man/push-methods.Rd | 5 git2r-0.12.1/git2r/man/references-methods.Rd | 3 git2r-0.12.1/git2r/man/reflog-methods.Rd | 2 git2r-0.12.1/git2r/man/remote_add-methods.Rd | 2 git2r-0.12.1/git2r/man/remote_ls-methods.Rd |only git2r-0.12.1/git2r/man/remote_remove-methods.Rd | 2 git2r-0.12.1/git2r/man/remote_rename-methods.Rd | 2 git2r-0.12.1/git2r/man/remote_set_url-methods.Rd |only git2r-0.12.1/git2r/man/remote_url-methods.Rd | 2 git2r-0.12.1/git2r/man/remotes-methods.Rd | 2 git2r-0.12.1/git2r/man/repository-methods.Rd | 2 git2r-0.12.1/git2r/man/reset-methods.Rd | 2 git2r-0.12.1/git2r/man/revparse_single-methods.Rd | 2 git2r-0.12.1/git2r/man/rm_file-methods.Rd | 3 git2r-0.12.1/git2r/man/show-git_blob-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_branch-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_commit-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_diff-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_merge_result-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_note-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_reference-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_reflog_entry-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_repository-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_signature-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_stash-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_tag-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_time-method.Rd | 2 git2r-0.12.1/git2r/man/show-git_tree-method.Rd | 2 git2r-0.12.1/git2r/man/ssl_cert_locations.Rd |only git2r-0.12.1/git2r/man/stash-methods.Rd | 2 git2r-0.12.1/git2r/man/stash_drop-methods.Rd | 2 git2r-0.12.1/git2r/man/stash_list-methods.Rd | 2 git2r-0.12.1/git2r/man/status-methods.Rd | 2 git2r-0.12.1/git2r/man/summary-git_blob-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_commit-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_diff-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_repository-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_stash-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_tag-method.Rd | 2 git2r-0.12.1/git2r/man/summary-git_tree-method.Rd | 2 git2r-0.12.1/git2r/man/tag-methods.Rd | 2 git2r-0.12.1/git2r/man/tags-methods.Rd | 2 git2r-0.12.1/git2r/man/tree-index-methods.Rd | 2 git2r-0.12.1/git2r/man/tree-methods.Rd | 2 git2r-0.12.1/git2r/man/when-methods.Rd | 2 git2r-0.12.1/git2r/man/workdir-methods.Rd | 2 git2r-0.12.1/git2r/src/Makevars.in | 60 - git2r-0.12.1/git2r/src/Makevars.win | 77 - git2r-0.12.1/git2r/src/git2r.c | 6 git2r-0.12.1/git2r/src/git2r_arg.c | 6 git2r-0.12.1/git2r/src/git2r_checkout.c | 60 + git2r-0.12.1/git2r/src/git2r_checkout.h | 1 git2r-0.12.1/git2r/src/git2r_config.c | 83 - git2r-0.12.1/git2r/src/git2r_cred.c | 52 git2r-0.12.1/git2r/src/git2r_error.c | 2 git2r-0.12.1/git2r/src/git2r_error.h | 1 git2r-0.12.1/git2r/src/git2r_libgit2.c | 38 git2r-0.12.1/git2r/src/git2r_libgit2.h | 1 git2r-0.12.1/git2r/src/git2r_remote.c | 111 + git2r-0.12.1/git2r/src/git2r_remote.h | 2 git2r-0.12.1/git2r/src/git2r_repository.c | 18 git2r-0.12.1/git2r/src/git2r_repository.h | 2 git2r-0.12.1/git2r/src/libgit2/attr_file.c | 6 git2r-0.12.1/git2r/src/libgit2/attrcache.c | 5 git2r-0.12.1/git2r/src/libgit2/blame.c | 2 git2r-0.12.1/git2r/src/libgit2/blame_git.c | 34 git2r-0.12.1/git2r/src/libgit2/blame_git.h | 2 git2r-0.12.1/git2r/src/libgit2/checkout.c | 59 - git2r-0.12.1/git2r/src/libgit2/commit.c | 35 git2r-0.12.1/git2r/src/libgit2/commit_list.c | 8 git2r-0.12.1/git2r/src/libgit2/commit_list.h | 3 git2r-0.12.1/git2r/src/libgit2/common.h | 9 git2r-0.12.1/git2r/src/libgit2/config.c | 46 git2r-0.12.1/git2r/src/libgit2/config.h | 16 git2r-0.12.1/git2r/src/libgit2/config_file.c | 151 ++ git2r-0.12.1/git2r/src/libgit2/config_file.h | 10 git2r-0.12.1/git2r/src/libgit2/curl_stream.c | 1 git2r-0.12.1/git2r/src/libgit2/diff.c | 123 +- git2r-0.12.1/git2r/src/libgit2/diff_driver.c | 13 git2r-0.12.1/git2r/src/libgit2/diff_file.c | 25 git2r-0.12.1/git2r/src/libgit2/diff_patch.c | 4 git2r-0.12.1/git2r/src/libgit2/diff_print.c | 2 git2r-0.12.1/git2r/src/libgit2/diff_tform.c | 6 git2r-0.12.1/git2r/src/libgit2/diff_xdiff.c | 7 git2r-0.12.1/git2r/src/libgit2/diff_xdiff.h | 5 git2r-0.12.1/git2r/src/libgit2/filebuf.c | 84 + git2r-0.12.1/git2r/src/libgit2/fileops.c | 308 +++-- git2r-0.12.1/git2r/src/libgit2/fileops.h | 20 git2r-0.12.1/git2r/src/libgit2/idxmap.h |only git2r-0.12.1/git2r/src/libgit2/ignore.c | 16 git2r-0.12.1/git2r/src/libgit2/include/git2/common.h | 14 git2r-0.12.1/git2r/src/libgit2/include/git2/config.h | 48 git2r-0.12.1/git2r/src/libgit2/include/git2/cred_helpers.h | 2 git2r-0.12.1/git2r/src/libgit2/include/git2/diff.h | 37 git2r-0.12.1/git2r/src/libgit2/include/git2/errors.h | 1 git2r-0.12.1/git2r/src/libgit2/include/git2/index.h | 39 git2r-0.12.1/git2r/src/libgit2/include/git2/merge.h | 12 git2r-0.12.1/git2r/src/libgit2/include/git2/remote.h | 13 git2r-0.12.1/git2r/src/libgit2/include/git2/sys/config.h | 14 git2r-0.12.1/git2r/src/libgit2/include/git2/sys/odb_backend.h | 4 git2r-0.12.1/git2r/src/libgit2/include/git2/sys/refdb_backend.h | 4 git2r-0.12.1/git2r/src/libgit2/include/git2/sys/stream.h | 13 git2r-0.12.1/git2r/src/libgit2/include/git2/sys/transport.h | 28 git2r-0.12.1/git2r/src/libgit2/include/git2/transport.h | 11 git2r-0.12.1/git2r/src/libgit2/index.c | 428 +++++-- git2r-0.12.1/git2r/src/libgit2/index.h | 2 git2r-0.12.1/git2r/src/libgit2/iterator.c | 500 ++++++-- git2r-0.12.1/git2r/src/libgit2/iterator.h | 48 git2r-0.12.1/git2r/src/libgit2/merge.c | 381 ++++-- git2r-0.12.1/git2r/src/libgit2/merge_file.c | 98 + git2r-0.12.1/git2r/src/libgit2/notes.c | 2 git2r-0.12.1/git2r/src/libgit2/odb.c | 246 ++-- git2r-0.12.1/git2r/src/libgit2/odb_loose.c | 4 git2r-0.12.1/git2r/src/libgit2/odb_mempack.c | 8 git2r-0.12.1/git2r/src/libgit2/odb_pack.c | 82 - git2r-0.12.1/git2r/src/libgit2/oidmap.h | 2 git2r-0.12.1/git2r/src/libgit2/openssl_stream.c | 7 git2r-0.12.1/git2r/src/libgit2/pack-objects.c | 3 git2r-0.12.1/git2r/src/libgit2/path.c | 23 git2r-0.12.1/git2r/src/libgit2/path.h | 8 git2r-0.12.1/git2r/src/libgit2/pathspec.c | 36 git2r-0.12.1/git2r/src/libgit2/pool.c | 241 ---- git2r-0.12.1/git2r/src/libgit2/pool.h | 54 git2r-0.12.1/git2r/src/libgit2/push.c | 3 git2r-0.12.1/git2r/src/libgit2/push.h | 1 git2r-0.12.1/git2r/src/libgit2/refdb.c | 8 git2r-0.12.1/git2r/src/libgit2/refdb_fs.c | 16 git2r-0.12.1/git2r/src/libgit2/remote.c | 46 git2r-0.12.1/git2r/src/libgit2/repository.c | 55 git2r-0.12.1/git2r/src/libgit2/revwalk.c | 6 git2r-0.12.1/git2r/src/libgit2/signature.c | 18 git2r-0.12.1/git2r/src/libgit2/sortedcache.c | 5 git2r-0.12.1/git2r/src/libgit2/stash.c | 29 git2r-0.12.1/git2r/src/libgit2/stream.h | 3 git2r-0.12.1/git2r/src/libgit2/submodule.c | 406 ++++-- git2r-0.12.1/git2r/src/libgit2/sysdir.c | 19 git2r-0.12.1/git2r/src/libgit2/sysdir.h | 14 git2r-0.12.1/git2r/src/libgit2/tls_stream.c | 13 git2r-0.12.1/git2r/src/libgit2/transaction.c | 44 git2r-0.12.1/git2r/src/libgit2/transaction.h |only git2r-0.12.1/git2r/src/libgit2/transports/cred.c | 8 git2r-0.12.1/git2r/src/libgit2/transports/git.c | 11 git2r-0.12.1/git2r/src/libgit2/transports/http.c | 16 git2r-0.12.1/git2r/src/libgit2/transports/smart.c | 95 + git2r-0.12.1/git2r/src/libgit2/transports/smart.h | 1 git2r-0.12.1/git2r/src/libgit2/transports/smart_pkt.c | 11 git2r-0.12.1/git2r/src/libgit2/transports/smart_protocol.c | 2 git2r-0.12.1/git2r/src/libgit2/transports/ssh.c | 4 git2r-0.12.1/git2r/src/libgit2/transports/winhttp.c | 18 git2r-0.12.1/git2r/src/libgit2/unix/posix.h | 15 git2r-0.12.1/git2r/src/libgit2/util.c | 26 git2r-0.12.1/git2r/src/libgit2/win32/findfile.c | 10 git2r-0.12.1/git2r/src/libgit2/win32/findfile.h | 1 git2r-0.12.1/git2r/src/libgit2/win32/path_w32.c | 23 git2r-0.12.1/git2r/src/libgit2/win32/posix_w32.c | 11 git2r-0.12.1/git2r/src/libgit2/win32/w32_util.c | 34 git2r-0.12.1/git2r/src/libgit2/win32/w32_util.h | 16 git2r-0.12.1/git2r/src/libgit2/xdiff/xdiff.h | 8 git2r-0.12.1/git2r/src/libgit2/xdiff/xdiffi.c | 12 git2r-0.12.1/git2r/src/libgit2/xdiff/xhistogram.c | 6 git2r-0.12.1/git2r/src/libgit2/xdiff/xmerge.c | 142 +- git2r-0.12.1/git2r/src/winhttp/winhttp32.def.in |only git2r-0.12.1/git2r/src/winhttp/winhttp64.def.in |only git2r-0.12.1/git2r/tests/blame.R | 12 git2r-0.12.1/git2r/tests/checkout.R | 28 git2r-0.12.1/git2r/tests/checkout_branch.R | 2 git2r-0.12.1/git2r/tests/config.R | 24 git2r-0.12.1/git2r/tests/diff.R | 25 git2r-0.12.1/git2r/tests/fetch.R | 18 git2r-0.12.1/git2r/tests/index.R | 2 git2r-0.12.1/git2r/tests/note.R | 20 git2r-0.12.1/git2r/tests/pre-process-path.R |only git2r-0.12.1/git2r/tests/reflog.R | 14 git2r-0.12.1/git2r/tests/remotes.R | 31 git2r-0.12.1/git2r/tests/repository.R | 7 git2r-0.12.1/git2r/tests/reset.R | 20 git2r-0.12.1/git2r/tests/signature.R | 2 git2r-0.12.1/git2r/tests/status.R | 31 git2r-0.12.1/git2r/tests/time.R | 5 git2r-0.12.1/git2r/tests/when.R | 2 304 files changed, 4903 insertions(+), 2451 deletions(-)
Title: Estimate Correlations Between Repeatedly Measured Endpoints
(E.g., Reliability) Based on Linear Mixed-Effects Models
Description: In clinical practice and research settings in medicine and the behavioral sciences, it is often of interest to quantify the correlation of a continuous endpoint that was repeatedly measured (e.g., test-retest correlations, ICC, etc.). This package allows for estimating these correlations based on mixed-effects models. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Geert Molenberghs, Dieter Hilgers, & Nicole Heussen
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between CorrMixed versions 0.1-11 dated 2015-05-08 and 0.1-12 dated 2015-12-05
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 31 +++++++++++++++++++++++++++++++ man/Explore.WS.Corr.Rd | 2 +- man/Fract.Poly.Rd | 2 +- man/Heatmap.Rd | 4 ++-- man/Model.Fit.Rd | 2 +- man/Spaghetti.Plot.Rd | 2 +- man/WS.Corr.Mixed.Rd | 4 ++-- man/WS.Corr.Mixed.SAS.Rd | 2 +- man/plot.Explore.WS.Corr.Rd | 2 +- man/plot.WS.Corr.Mixed.Rd | 2 +- 12 files changed, 57 insertions(+), 26 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette <dylan.beaudette@ca.usda.gov>
Diff between soilDB versions 1.5-4 dated 2015-04-23 and 1.6.6 dated 2015-12-04
soilDB-1.5-4/soilDB/R/MUKEYS_by_ll_bbox.R |only soilDB-1.5-4/soilDB/man/MUKEYS_by_ll_bbox.Rd |only soilDB-1.6.6/soilDB/DESCRIPTION | 18 - soilDB-1.6.6/soilDB/MD5 | 60 +-- soilDB-1.6.6/soilDB/NAMESPACE | 23 - soilDB-1.6.6/soilDB/NEWS | 29 + soilDB-1.6.6/soilDB/R/SDA_query.R | 226 +++++++++---- soilDB-1.6.6/soilDB/R/SSURGO_spatial_query.R | 2 soilDB-1.6.6/soilDB/R/fetchHenry.R | 276 +++++++++++++++- soilDB-1.6.6/soilDB/R/fetchKSSL.R | 45 ++ soilDB-1.6.6/soilDB/R/fetchNASIS.R | 8 soilDB-1.6.6/soilDB/R/fetchNASISLabData.R | 2 soilDB-1.6.6/soilDB/R/fetchOSD.R | 2 soilDB-1.6.6/soilDB/R/fetchRaCA.R | 5 soilDB-1.6.6/soilDB/R/fetchSCAN.R | 98 +++++ soilDB-1.6.6/soilDB/R/get_extended_data_from_NASIS_db.R | 17 soilDB-1.6.6/soilDB/R/get_site_data_from_NASIS_db.R | 5 soilDB-1.6.6/soilDB/R/get_vegplot_data_from_NASIS_db.R |only soilDB-1.6.6/soilDB/R/get_vegplot_from_NASIS_db.R |only soilDB-1.6.6/soilDB/R/mapunit_geom_by_ll_bbox.R | 2 soilDB-1.6.6/soilDB/R/utils.R | 23 + soilDB-1.6.6/soilDB/data/andic.subset.rda |binary soilDB-1.6.6/soilDB/data/cisne.rda |binary soilDB-1.6.6/soilDB/data/gSSURGO.chunk.rda |binary soilDB-1.6.6/soilDB/data/gopheridge.rda |binary soilDB-1.6.6/soilDB/data/loafercreek.rda |binary soilDB-1.6.6/soilDB/man/SDA_query.Rd | 66 +-- soilDB-1.6.6/soilDB/man/SDA_query_features.Rd |only soilDB-1.6.6/soilDB/man/SSURGO_spatial_query.Rd | 14 soilDB-1.6.6/soilDB/man/fetchHenry.Rd |only soilDB-1.6.6/soilDB/man/fetchKSSL.Rd | 13 soilDB-1.6.6/soilDB/man/fetchNASIS.Rd | 1 soilDB-1.6.6/soilDB/man/fetchSCAN.Rd | 3 soilDB-1.6.6/soilDB/man/mapunit_geom_by_ll_bbox.Rd | 2 34 files changed, 740 insertions(+), 200 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.2 dated 2015-09-01 and 2.3 dated 2015-12-04
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++----------- R/BayesID.R | 91 +++++++++++++++++++++--------------------- R/BayesSurv.R | 24 +++-------- R/FreqID.R | 45 ++++++++++++++++---- R/internalFunc.R | 62 ++++++++++++++++++++++++++++ R/methods.R | 27 +++++++++--- man/BayesID.Rd | 2 man/FreqID.Rd | 9 ++-- man/SemiCompRisks-package.Rd | 4 - man/simID.Rd | 4 - src/BpeDpCorScr.c | 2 src/BpeDpCorScrSM.c | 4 - src/BpeDpCorScrSM_Updates.c | 3 - src/BpeDpCorScr_Updates.c | 2 src/BpeDpCorSurv.c | 2 src/BpeDpCorSurv_Updates.c | 2 src/BweibDpCorScr.c | 2 src/BweibDpCorScrSM.c | 2 src/BweibDpCorScrSM_Updates.c | 6 +- src/BweibDpCorScr_Updates.c | 4 + src/BweibDpCorSurv.c | 2 src/BweibDpCorSurv_Updates.c | 2 src/Utilities.c | 8 +-- 24 files changed, 234 insertions(+), 129 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.20-23 dated 2015-10-10 and 2.21 dated 2015-12-04
DESCRIPTION | 10 ++++---- MD5 | 54 +++++++++++++++++++++++---------------------- NAMESPACE | 23 +++++++++++++++---- R/MCMC-support.R | 4 +-- R/countreg-support.R |only R/helpers.R | 34 ++++++++++++++++++++-------- R/lsmeans.R | 26 +++++++++++---------- R/lsmip.R | 8 +++--- R/multinom-support.R | 2 - R/nonlin-support.R | 2 - R/ordinal-support.R | 6 ++--- R/pmmeans.R |only R/rbind.R | 11 +-------- R/ref.grid.R | 38 ++++++++++++++++++++++--------- R/summary.R | 8 ++++++ inst/NEWS | 15 ++++++++++++ inst/doc/extending.R | 18 +++++---------- inst/doc/extending.pdf |binary inst/doc/extending.rnw | 33 +++++++++++++++++++++++---- inst/doc/using-lsmeans.pdf |binary man/extending.Rd | 23 ++++++++----------- man/glht.Rd | 4 ++- man/lsmeans.Rd | 26 +++++++++++++++------ man/lsmip.Rd | 9 +++++-- man/models.Rd | 21 ++++++++++++++++- man/summary.Rd | 2 - man/update.Rd | 7 +++++ tests/tests1.Rout.save | 29 ++++++++++-------------- vignettes/extending.rnw | 33 +++++++++++++++++++++++---- 29 files changed, 293 insertions(+), 153 deletions(-)
Title: Hierarchical Inference Testing
Description: Hierarchical inference testing (HIT) for (generalized) linear
models with correlated covariates applicable to high-dimensional settings.
Author: Jonas Klasen [aut, cre]
Maintainer: Jonas Klasen <qtcat@gmx.de>
Diff between hit versions 0.1-0 dated 2015-10-21 and 0.2-0 dated 2015-12-04
DESCRIPTION | 13 +- MD5 | 43 +++---- NAMESPACE | 14 ++ NEWS.md |only R/anova.R | 116 ++++++++++++++++++-- R/hit.R | 266 ++++++++++++++++++++++++++++++---------------- R/hitPackage.R | 4 README.md | 8 - man/as.hierarchy.Rd | 13 +- man/dend2hier.Rd | 6 - man/fast.anova.Rd | 25 ++-- man/fast.glmanova.Rd |only man/fast.lmanova.Rd |only man/heightDendrogram.Rd | 2 man/heightHierarchy.Rd | 2 man/hit-package.Rd | 6 - man/hit.Rd | 83 ++++++++------ man/names.hierarchy.Rd | 2 man/reorder.hierarchy.Rd | 4 man/samp1.lasso.Rd | 31 +++-- man/samp2.sigHierarchy.Rd | 34 +++-- man/samp2.sigNode.Rd | 11 + man/summary.hit.Rd | 2 tests/testthat/test_hit.R | 6 - 24 files changed, 474 insertions(+), 217 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette <debeaudette@ucdavis.edu>, Pierre Roudier <roudierp@landcareresearch.co.nz>
Maintainer: Dylan Beaudette <debeaudette@ucdavis.edu>
Diff between aqp versions 1.8-6 dated 2015-04-23 and 1.9.2 dated 2015-12-04
DESCRIPTION | 20 +- MD5 | 49 ++--- NAMESPACE | 20 ++ NEWS | 15 + R/aggregateColor.R |only R/get.ml.hz.R | 4 R/getSoilDepthClass.R | 4 R/guessGenHzLevels.R |only R/profile_plot.R | 79 +++++++- data/amarillo.rda |binary data/ca630.rda |binary data/munsell.rda |binary data/rruff.sample.rda |binary data/sp1.rda |binary data/sp2.rda |binary data/sp3.rda |binary data/sp4.rda |binary data/sp5.rda |binary man/SPC-plotting.Rd | 4 man/aggregateColor.Rd |only man/groupedProfilePlot.Rd |only man/guessGenHzLevels.Rd |only man/munsell2rgb.Rd | 3 man/plotMultipleSPC.Rd | 6 man/profileApply-methods.Rd | 99 +++++----- man/profile_compare-methods.Rd | 372 ++++++++++++++++++++--------------------- man/sp2.Rd | 4 man/sp3.Rd | 25 +- 28 files changed, 413 insertions(+), 291 deletions(-)
Title: Spatial Position Models
Description: Computes spatial position models: Stewart potentials, Reilly
catchment areas, Huff catchment areas.
Author: Timothée Giraud [cre, aut],
Hadrien Commenges [aut],
Joël Boulier [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between SpatialPosition versions 0.9 dated 2015-05-06 and 1.0 dated 2015-12-04
DESCRIPTION | 28 +++++---- MD5 | 64 ++++++++++++---------- NAMESPACE | 4 + NEWS |only R/contourStewart.R |only R/gridandmat.R | 7 +- R/huff.R | 2 R/package.R | 10 ++- R/reilly.R | 5 + R/stewart.R | 122 +++++++----------------------------------- README.md | 40 ++++++++++++- build/vignette.rds |binary inst/doc/SpatialPosition.R | 6 +- inst/doc/SpatialPosition.Rmd | 2 inst/doc/SpatialPosition.html | 10 +-- inst/doc/StewartExample.R |only inst/doc/StewartExample.Rmd |only inst/doc/StewartExample.html |only man/CreateDistMatrix.Rd | 16 ++--- man/CreateGrid.Rd | 8 +- man/SpatialPosition.Rd | 18 ++++-- man/contourStewart.Rd | 90 ++++++++++++++++++++++-------- man/huff.Rd | 42 +++++++------- man/plotHuff.Rd | 2 man/plotReilly.Rd | 2 man/plotStewart.Rd | 4 - man/rasterHuff.Rd | 4 - man/rasterReilly.Rd | 6 +- man/rasterStewart.Rd | 4 - man/reilly.Rd | 42 +++++++------- man/spatMask.Rd | 2 man/spatPts.Rd | 4 - man/spatUnits.Rd | 2 man/stewart.Rd | 40 ++++++------- vignettes/SpatialPosition.Rmd | 2 vignettes/StewartExample.Rmd |only 36 files changed, 304 insertions(+), 284 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 8.0-0.0 dated 2014-01-20 and 12.0-0.0 dated 2015-12-04
SGPdata-12.0-0.0/SGPdata/DESCRIPTION | 20 ++++----- SGPdata-12.0-0.0/SGPdata/MD5 | 26 ++++++------ SGPdata-12.0-0.0/SGPdata/NAMESPACE | 1 SGPdata-12.0-0.0/SGPdata/R/zzz.R |only SGPdata-12.0-0.0/SGPdata/data/datalist | 1 SGPdata-12.0-0.0/SGPdata/data/sgpData.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgpData_INSTRUCTOR_NUMBER.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgpData_LONG.rda |binary SGPdata-12.0-0.0/SGPdata/data/sgptData_LONG.rda |only SGPdata-12.0-0.0/SGPdata/inst/CITATION | 12 ++--- SGPdata-12.0-0.0/SGPdata/inst/NEWS | 18 +++++++- SGPdata-12.0-0.0/SGPdata/man/SGPdata-package.Rd | 11 ++--- SGPdata-12.0-0.0/SGPdata/man/sgpData.Rd | 20 ++++----- SGPdata-12.0-0.0/SGPdata/man/sgpData_LONG.Rd | 6 +- SGPdata-12.0-0.0/SGPdata/man/sgptData_LONG.Rd |only SGPdata-8.0-0.0/SGPdata/R/dummy.R |only 16 files changed, 68 insertions(+), 47 deletions(-)
Title: Thurstonian Models for Sensory Discrimination
Description: Provides methods for sensory discrimination methods;
duotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-different,
2-AC and degree-of-difference.
This enables the calculation of d-primes, standard errors of
d-primes, sample size and power computations, and
comparisons of different d-primes. Methods for profile likelihood
confidence intervals and plotting are included.
Author: Rune Haubo Bojesen Christensen [aut],
Per Bruun Brockhoff [aut, cre]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between sensR versions 1.4-5 dated 2015-01-21 and 1.4-6 dated 2015-12-04
DESCRIPTION | 23 +++++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 10 ++++++++++ NEWS | 15 ++++++++++++++- R/discrim.R | 3 ++- R/discrimR.R | 2 +- build/vignette.rds |binary inst/doc/methodology.pdf |binary inst/doc/twoACexamples.pdf |binary 9 files changed, 48 insertions(+), 21 deletions(-)
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, Rmpfr interfaces to
the LGPL'ed MPFR (Multiple Precision Floating-Point Reliable) Library
which itself is based on the GMP (GNU Multiple Precision) Library.
Author: Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.5-7 dated 2014-11-27 and 0.6-0 dated 2015-12-04
ChangeLog | 32 ++++ DESCRIPTION | 17 +- MD5 | 98 +++++++------- NAMESPACE | 110 ++++++++------- R/Arith.R | 4 R/Consts.R | 5 R/Math.R | 28 ++-- R/Summary.R | 38 +++++ R/array.R | 50 ++++++- R/as.R | 117 ++++++++++------ R/formatHex.R |only R/hjk.R | 31 ++-- R/mpfr.R | 103 +++++++++++--- R/special-fun.R | 174 +++++++++++------------- TODO | 38 ++--- build/vignette.rds |binary configure | 237 ++++++++++++++++++++-------------- configure.ac | 6 inst/NEWS.Rd |only inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.R | 99 ++++++++++++-- inst/doc/Rmpfr-pkg.Rnw | 112 ++++++++++++++-- inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.Rnw | 5 inst/doc/log1mexp-note.pdf |binary man/Bessel_mpfr.Rd | 10 + man/chooseMpfr.Rd | 6 man/factorialMpfr.Rd | 5 man/formatHex.Rd |only man/formatMpfr.Rd | 51 ++++++- man/mpfr-class.Rd | 66 ++++++++- man/mpfr.Rd | 49 +++++-- man/mpfrMatrix-class.Rd | 13 + man/pbetaI.Rd | 4 man/roundMpfr.Rd | 6 man/str.mpfr.Rd | 28 +++- man/utils.Rd | 72 +++------- src/Rmpfr_utils.h | 38 ++--- src/Syms.h | 6 src/convert.c | 11 - src/init.c | 50 +++---- src/utils.c | 95 ++++++------- tests/arith-ex.R | 13 + tests/bit-repr.R | 3 tests/bit-repr.Rout.save | 74 +++++----- tests/create.R | 17 +- tests/lowlevel.R | 13 + tests/matrix-ex.R | 12 + tests/special-fun-ex.R | 2 tests/tstHexBin.R |only vignettes/Rmpfr-pkg.Rnw | 112 ++++++++++++++-- vignettes/log1mexp-note.Rnw | 5 52 files changed, 1366 insertions(+), 699 deletions(-)
Title: Search and Extract Data from the OECD
Description: Search and extract data from the OECD.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between OECD versions 0.1 dated 2015-09-21 and 0.2.0 dated 2015-12-04
OECD-0.1/OECD/vignettes/figuresplot-1.pdf |only OECD-0.2.0/OECD/DESCRIPTION | 23 ++-- OECD-0.2.0/OECD/MD5 | 23 ++-- OECD-0.2.0/OECD/NAMESPACE | 4 OECD-0.2.0/OECD/R/main.R | 123 +++++++++++------------ OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.R | 63 ++++++----- OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.Rmd | 109 +++++++++++--------- OECD-0.2.0/OECD/inst/doc/oecd_vignette_main.pdf |binary OECD-0.2.0/OECD/man/browse_metadata.Rd | 4 OECD-0.2.0/OECD/man/get_dataset.Rd | 5 OECD-0.2.0/OECD/man/get_datasets.Rd | 10 + OECD-0.2.0/OECD/man/search_dataset.Rd | 5 OECD-0.2.0/OECD/vignettes/oecd_vignette_main.Rmd | 109 +++++++++++--------- 13 files changed, 262 insertions(+), 216 deletions(-)
Title: Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Description: Returns nonparametric aligned rank tests for the interaction in two-way factorial designs, on R data sets with repeated measures in 'wide' format. Five ANOVAs tables are reported. A PARAMETRIC one on the original data, one for a CHECK upon the interaction alignments, and three aligned rank tests: one on the aligned REGULAR, one on the FRIEDMAN, and one on the KOCH ranks. In these rank tests, only the resulting values for the interaction are relevant.
Author: Jos Feys
Maintainer: Jos Feys <jos.feys@faber.kuleuven.be>
Diff between npIntFactRep versions 1.4 dated 2015-11-11 and 1.5 dated 2015-12-04
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut],
Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.6 dated 2015-11-26 and 2.7 dated 2015-12-04
mlr-2.6/mlr/R/generateBenchmarkSummary.R |only mlr-2.6/mlr/R/generateRankMatrixAsBar.R |only mlr-2.6/mlr/R/plotBenchmarkResult.R |only mlr-2.6/mlr/man/generateBenchmarkSummaryData.Rd |only mlr-2.6/mlr/man/generateRankMatrixAsBarData.Rd |only mlr-2.6/mlr/man/plotBenchmarkResult.Rd |only mlr-2.6/mlr/man/plotBenchmarkSummary.Rd |only mlr-2.6/mlr/man/plotRankMatrixAsBar.Rd |only mlr-2.6/mlr/tests/testthat/test_base_plotBenchmarkResult.R |only mlr-2.6/mlr/tests/testthat/test_base_plotBenchmarkSummary.R |only mlr-2.7/mlr/DESCRIPTION | 6 mlr-2.7/mlr/MD5 | 124 +++++----- mlr-2.7/mlr/NAMESPACE | 8 mlr-2.7/mlr/NEWS | 9 mlr-2.7/mlr/R/BenchmarkResultOrderLevels.R | 37 +- mlr-2.7/mlr/R/benchmark.R | 46 ++- mlr-2.7/mlr/R/checkBMRMeasure.R |only mlr-2.7/mlr/R/convertBMRToRankMatrix.R | 61 ++-- mlr-2.7/mlr/R/generateCritDifferences.R | 81 +++--- mlr-2.7/mlr/R/helpers.R | 4 mlr-2.7/mlr/R/plotBMRBoxplots.R |only mlr-2.7/mlr/R/plotBMRRanksAsBarChart.R |only mlr-2.7/mlr/R/plotBMRSummary.R |only mlr-2.7/mlr/inst/doc/mlr.html | 2 mlr-2.7/mlr/man/BenchmarkResult.Rd | 10 mlr-2.7/mlr/man/benchmark.Rd | 28 +- mlr-2.7/mlr/man/convertBMRToRankMatrix.Rd | 24 - mlr-2.7/mlr/man/friedmanPostHocTestBMR.Rd | 10 mlr-2.7/mlr/man/friedmanTestBMR.Rd | 10 mlr-2.7/mlr/man/generateCalibrationData.Rd | 4 mlr-2.7/mlr/man/generateCritDifferencesData.Rd | 14 - mlr-2.7/mlr/man/generateFilterValuesData.Rd | 4 mlr-2.7/mlr/man/generateLearningCurveData.Rd | 4 mlr-2.7/mlr/man/generatePartialPredictionData.Rd | 4 mlr-2.7/mlr/man/generateROCRCurvesData.Rd | 4 mlr-2.7/mlr/man/generateThreshVsPerfData.Rd | 4 mlr-2.7/mlr/man/getBMRAggrPerformances.Rd | 10 mlr-2.7/mlr/man/getBMRFeatSelResults.Rd | 10 mlr-2.7/mlr/man/getBMRFilteredFeatures.Rd | 10 mlr-2.7/mlr/man/getBMRLearnerIds.Rd | 10 mlr-2.7/mlr/man/getBMRLearners.Rd | 10 mlr-2.7/mlr/man/getBMRMeasureIds.Rd | 10 mlr-2.7/mlr/man/getBMRMeasures.Rd | 10 mlr-2.7/mlr/man/getBMRPerformances.Rd | 10 mlr-2.7/mlr/man/getBMRPredictions.Rd | 10 mlr-2.7/mlr/man/getBMRTaskIds.Rd | 10 mlr-2.7/mlr/man/getBMRTuneResults.Rd | 10 mlr-2.7/mlr/man/getFilterValues.Rd | 4 mlr-2.7/mlr/man/plotBMRBoxplots.Rd |only mlr-2.7/mlr/man/plotBMRRanksAsBarChart.Rd |only mlr-2.7/mlr/man/plotBMRSummary.Rd |only mlr-2.7/mlr/man/plotCalibration.Rd | 6 mlr-2.7/mlr/man/plotCritDifferences.Rd | 16 - mlr-2.7/mlr/man/plotFilterValues.Rd | 6 mlr-2.7/mlr/man/plotFilterValuesGGVIS.Rd | 6 mlr-2.7/mlr/man/plotLearningCurve.Rd | 6 mlr-2.7/mlr/man/plotLearningCurveGGVIS.Rd | 6 mlr-2.7/mlr/man/plotPartialPrediction.Rd | 6 mlr-2.7/mlr/man/plotPartialPredictionGGVIS.Rd | 6 mlr-2.7/mlr/man/plotROCCurves.Rd | 6 mlr-2.7/mlr/man/plotROCRCurves.Rd | 6 mlr-2.7/mlr/man/plotROCRCurvesGGVIS.Rd | 6 mlr-2.7/mlr/man/plotThreshVsPerf.Rd | 6 mlr-2.7/mlr/man/plotThreshVsPerfGGVIS.Rd | 6 mlr-2.7/mlr/tests/testthat/Rplots.pdf |binary mlr-2.7/mlr/tests/testthat/helper_helpers.R | 6 mlr-2.7/mlr/tests/testthat/test_base_benchmark.R | 20 + mlr-2.7/mlr/tests/testthat/test_base_convertBMRToRankMatrix.R |only mlr-2.7/mlr/tests/testthat/test_base_plotBMRBoxplots.R |only mlr-2.7/mlr/tests/testthat/test_base_plotBMRSummary.R |only mlr-2.7/mlr/tests/testthat/test_base_plotCritDifferences.R | 24 + mlr-2.7/mlr/tests/testthat/test_base_plotRankMatrixAsBar.R | 47 --- mlr-2.7/mlr/tests/testthat/test_base_plotViperCharts.R | 33 +- 73 files changed, 393 insertions(+), 437 deletions(-)
Title: Estimation and Tests of Hierarchical F-Statistics
Description: Allows the estimation of hierarchical F-statistics from haploid or diploid genetic data
with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956;
<DOI:10.2307/2411227>. Functions are also given to test via randomisations the significance of each F and variance components,
using the likelihood-ratio statistics G.
Author: Jerome Goudet [aut, cre],
Thibaut Jombart [aut]
Maintainer: Jerome Goudet <jerome.goudet@unil.ch>
Diff between hierfstat versions 0.04-14 dated 2014-09-29 and 0.04-22 dated 2015-12-04
hierfstat-0.04-14/hierfstat/R/beta.R |only hierfstat-0.04-14/hierfstat/data/exhier.txt.gz |only hierfstat-0.04-14/hierfstat/data/yangex.txt.gz |only hierfstat-0.04-14/hierfstat/inst/doc/hierfstat.pdf |only hierfstat-0.04-14/hierfstat/man/betai.rd |only hierfstat-0.04-14/hierfstat/man/cfe.dist.rd |only hierfstat-0.04-14/hierfstat/man/da.dist.rd |only hierfstat-0.04-14/hierfstat/man/nei.dist.rd |only hierfstat-0.04-14/hierfstat/man/prepdata.Rd |only hierfstat-0.04-22/hierfstat/CHANGES | 33 + hierfstat-0.04-22/hierfstat/DESCRIPTION | 30 - hierfstat-0.04-22/hierfstat/MD5 | 77 ++- hierfstat-0.04-22/hierfstat/NAMESPACE | 32 + hierfstat-0.04-22/hierfstat/R/betas.R |only hierfstat-0.04-22/hierfstat/R/fstat.from.adegenet.R |only hierfstat-0.04-22/hierfstat/R/genetdist.R |only hierfstat-0.04-22/hierfstat/R/genind2hierfstat.R |only hierfstat-0.04-22/hierfstat/R/gstat.randtest.R |only hierfstat-0.04-22/hierfstat/R/hierana.r | 11 hierfstat-0.04-22/hierfstat/R/indpca.R | 5 hierfstat-0.04-22/hierfstat/R/misc.R | 210 ++-------- hierfstat-0.04-22/hierfstat/R/nwc.R | 21 - hierfstat-0.04-22/hierfstat/R/pairwise.fst.R |only hierfstat-0.04-22/hierfstat/R/readQN.R |only hierfstat-0.04-22/hierfstat/R/sexbiaseddisp.R |only hierfstat-0.04-22/hierfstat/R/simgenot_new.R |only hierfstat-0.04-22/hierfstat/R/w2c.R |only hierfstat-0.04-22/hierfstat/R/writebayescan.R |only hierfstat-0.04-22/hierfstat/R/writeped.R | 30 + hierfstat-0.04-22/hierfstat/build |only hierfstat-0.04-22/hierfstat/data/crocrussula.rda |only hierfstat-0.04-22/hierfstat/data/exhier.txt |only hierfstat-0.04-22/hierfstat/data/gtrunchier.rda |binary hierfstat-0.04-22/hierfstat/data/yangex.txt |only hierfstat-0.04-22/hierfstat/inst/doc/demeeusgoudet_ige_tut_2007.pdf |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.R |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.Rmd |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat.html |only hierfstat-0.04-22/hierfstat/inst/doc/hierfstat_note.pdf |only hierfstat-0.04-22/hierfstat/inst/extdata/qn2_sex.dat |only hierfstat-0.04-22/hierfstat/man/AIc.Rd |only hierfstat-0.04-22/hierfstat/man/basic.stats.rd | 6 hierfstat-0.04-22/hierfstat/man/betas.Rd |only hierfstat-0.04-22/hierfstat/man/crocrussula.Rd |only hierfstat-0.04-22/hierfstat/man/eucl.dist.rd | 2 hierfstat-0.04-22/hierfstat/man/fstat.from.adegenet.Rd |only hierfstat-0.04-22/hierfstat/man/genet.dist.Rd |only hierfstat-0.04-22/hierfstat/man/genind2hierfstat.Rd |only hierfstat-0.04-22/hierfstat/man/gstat.randtest.Rd |only hierfstat-0.04-22/hierfstat/man/hierfstat.Rd | 6 hierfstat-0.04-22/hierfstat/man/pairwise.WCfst.Rd |only hierfstat-0.04-22/hierfstat/man/pairwise.neifst.Rd |only hierfstat-0.04-22/hierfstat/man/pcoa.rd | 2 hierfstat-0.04-22/hierfstat/man/ppfst.rd | 8 hierfstat-0.04-22/hierfstat/man/qn2.read.fstat.Rd |only hierfstat-0.04-22/hierfstat/man/sexbias.test.Rd |only hierfstat-0.04-22/hierfstat/man/sim.genot.rd | 2 hierfstat-0.04-22/hierfstat/man/sim.genot.t.Rd |only hierfstat-0.04-22/hierfstat/man/wc.rd | 2 hierfstat-0.04-22/hierfstat/man/write.bayescan.Rd |only hierfstat-0.04-22/hierfstat/man/write.ped.Rd |only hierfstat-0.04-22/hierfstat/vignettes |only 62 files changed, 245 insertions(+), 232 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-11 dated 2015-10-03 and 0.2-12 dated 2015-12-04
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/03rules.R | 11 ++++++----- R/05read_write.R | 3 ++- R/10timed.R | 2 ++ man/sequencerules-class.Rd | 3 ++- 7 files changed, 26 insertions(+), 17 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Assessment and Evaluation of Formations in United
Description: United is a software tool which can be downloaded at the following
website <http://www.schroepl.net/pbm/software/united/>. In general, it is
a virtual manager game for football teams. This package contains helpful
functions for determining an optimal formation for a virtual match in
United. E.g. knowing that the opponent has a strong defensive it is
advisable to beat him in the midfield. Furthermore, this package contains
functions for computing the optimal usage of hardness in a game.
Author: David Schindler [aut, cre]
Maintainer: David Schindler <dv.schindler@gmail.com>
Diff between unitedR versions 0.1 dated 2015-10-13 and 0.2 dated 2015-12-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/unitedRPackage.R | 2 +- R/unitedSimOne.R | 4 ++-- inst/doc/unitedR.pdf |binary man/unitedR-package.Rd | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.0 dated 2015-03-09 and 0.1.1 dated 2015-12-04
GetoptLong-0.1.0/GetoptLong/R/global.R |only GetoptLong-0.1.1/GetoptLong/DESCRIPTION | 12 GetoptLong-0.1.1/GetoptLong/MD5 | 55 GetoptLong-0.1.1/GetoptLong/NAMESPACE | 24 GetoptLong-0.1.1/GetoptLong/NEWS | 133 GetoptLong-0.1.1/GetoptLong/R/0_global.R |only GetoptLong-0.1.1/GetoptLong/R/GetoptLong.R | 1559 +++++----- GetoptLong-0.1.1/GetoptLong/R/qq.R | 400 +- GetoptLong-0.1.1/GetoptLong/README | 8 GetoptLong-0.1.1/GetoptLong/build/vignette.rds |binary GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.R | 159 - GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.Rnw | 597 +-- GetoptLong-0.1.1/GetoptLong/inst/doc/GetoptLong.pdf |binary GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.R | 316 +- GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.Rnw | 582 +-- GetoptLong-0.1.1/GetoptLong/inst/doc/variable_interpolation.pdf |binary GetoptLong-0.1.1/GetoptLong/inst/tests/test.R | 2 GetoptLong-0.1.1/GetoptLong/inst/tests/test_GetoptLong.R | 518 +-- GetoptLong-0.1.1/GetoptLong/inst/tests/test_qq.R | 222 - GetoptLong-0.1.1/GetoptLong/man/GetOptions.rd | 45 GetoptLong-0.1.1/GetoptLong/man/GetoptLong.options.rd | 60 GetoptLong-0.1.1/GetoptLong/man/GetoptLong.rd | 98 GetoptLong-0.1.1/GetoptLong/man/get_scriptname.rd | 34 GetoptLong-0.1.1/GetoptLong/man/qq.options.rd | 60 GetoptLong-0.1.1/GetoptLong/man/qq.rd | 62 GetoptLong-0.1.1/GetoptLong/man/qqcat.rd | 99 GetoptLong-0.1.1/GetoptLong/man/source.rd |only GetoptLong-0.1.1/GetoptLong/tests/test-all.R | 28 GetoptLong-0.1.1/GetoptLong/vignettes/GetoptLong.Rnw | 597 +-- GetoptLong-0.1.1/GetoptLong/vignettes/variable_interpolation.Rnw | 582 +-- 30 files changed, 3132 insertions(+), 3120 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002), seq-gen (Rambaut and Grassly 1997),
Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for
simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-15 dated 2013-12-14 and 0.1-16 dated 2015-12-04
phyclust-0.1-15/phyclust/vignettes/phyclust-include/jss.bst |only phyclust-0.1-15/phyclust/vignettes/phyclust-include/jss.cls |only phyclust-0.1-16/phyclust/ChangeLog | 28 ++++ phyclust-0.1-16/phyclust/DESCRIPTION | 13 +- phyclust-0.1-16/phyclust/MD5 | 41 +++--- phyclust-0.1-16/phyclust/NAMESPACE | 29 ++++ phyclust-0.1-16/phyclust/R/000_globalVariables.r |only phyclust-0.1-16/phyclust/R/p_ms.r | 42 +++++-- phyclust-0.1-16/phyclust/demo/00Index | 1 phyclust-0.1-16/phyclust/demo/simu_ms_tbs.r |only phyclust-0.1-16/phyclust/inst/doc/phyclust-guide.Rnw | 60 +++++----- phyclust-0.1-16/phyclust/inst/doc/phyclust-guide.pdf |binary phyclust-0.1-16/phyclust/man/ms.Rd | 40 ++++-- phyclust-0.1-16/phyclust/man/seqgen.Rd | 25 ++-- phyclust-0.1-16/phyclust/src/R_phyclust.c | 2 phyclust-0.1-16/phyclust/src/R_phyclust_em_step.c | 9 + phyclust-0.1-16/phyclust/src/msdir/ms.c | 12 +- phyclust-0.1-16/phyclust/src/msdir/ms_main.c | 2 phyclust-0.1-16/phyclust/src/phyclust/phyclust_em_step.c | 46 ++++++- phyclust-0.1-16/phyclust/src/phyclust/phyclust_qmatrix_array.c | 4 phyclust-0.1-16/phyclust/vignettes/build_pdf.sh | 15 ++ phyclust-0.1-16/phyclust/vignettes/phyclust-guide.Rnw | 60 +++++----- phyclust-0.1-16/phyclust/vignettes/phyclust-include/01-introduction.tex | 21 ++- phyclust-0.1-16/phyclust/vignettes/phyclust-include/my_jss.cls |only 24 files changed, 311 insertions(+), 139 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to
data files written using Unidata's
netCDF library (version 4 or earlier), which are binary data files that are portable
across platforms and include metadata information in addition to the data sets.
Using this package, netCDF files (either version 4
or "classic" version 3) can be opened and data sets read in easily.
It is also easy to create new netCDF dimensions, variables, and files,
in either version 3 or 4 format, and manipulate existing netCDF files.
This package replaces the former ncdf package, which only worked with
netcdf version 3 files. For various reasons the names of the functions
have had to be changed from the names in the ncdf package. The old ncdf package is still
available at the URL given below, if you need to have backward compatibility.
It should be possible to have both the ncdf and ncdf4 packages installed
simultaneously without a problem.
However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.14 dated 2015-11-10 and 1.15 dated 2015-12-04
ncdf4-1.14/ncdf4/tools/autom4te.cache |only ncdf4-1.15/ncdf4/DESCRIPTION | 8 ++++---- ncdf4-1.15/ncdf4/MD5 | 15 +++------------ ncdf4-1.15/ncdf4/R/ncdf4.R | 2 +- ncdf4-1.15/ncdf4/src/Makevars.win | 2 +- 5 files changed, 9 insertions(+), 18 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0-2 dated 2015-10-02 and 3.0.1 dated 2015-12-04
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/db.r | 35 +++++++++++++++++++---------------- inst/NEWS.Rd | 8 ++++++++ man/legacy_world.Rd | 2 +- man/map.Rd | 4 ++-- man/match.map.Rd | 2 +- man/world.Rd | 2 +- man/world2.Rd | 2 +- src/world.name | 8 ++++---- 10 files changed, 50 insertions(+), 39 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 0.3 dated 2015-11-05 and 0.4 dated 2015-12-04
imputeTS-0.3/imputeTS/R/vis.differences.R |only imputeTS-0.3/imputeTS/man/vis.differences.Rd |only imputeTS-0.4/imputeTS/DESCRIPTION | 8 ++++---- imputeTS-0.4/imputeTS/MD5 | 18 +++++++++++------- imputeTS-0.4/imputeTS/NAMESPACE | 7 ++++++- imputeTS-0.4/imputeTS/NEWS | 15 ++++++++++++++- imputeTS-0.4/imputeTS/R/na.interpolation.R | 22 +++++++++++++++------- imputeTS-0.4/imputeTS/R/vis.barMissing.R |only imputeTS-0.4/imputeTS/R/vis.imputations.R |only imputeTS-0.4/imputeTS/R/vis.missing.R |only imputeTS-0.4/imputeTS/man/na.interpolation.Rd | 9 ++++++--- imputeTS-0.4/imputeTS/man/vis.barMissing.Rd |only imputeTS-0.4/imputeTS/man/vis.imputations.Rd |only imputeTS-0.4/imputeTS/man/vis.missing.Rd |only 14 files changed, 56 insertions(+), 23 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.4.2 dated 2015-11-17 and 0.5.1 dated 2015-12-04
DESCRIPTION | 13 +++-- MD5 | 42 ++++++++++--------- NAMESPACE | 1 R/Create_GERGM_Object.R | 15 +++++- R/Create_GERGM_Object_From_Formula.R | 4 + R/Estimate_GERGM.R | 4 - R/Estimate_Plot.R | 5 +- R/GERGM_Class.R | 3 - R/GOF.R | 2 R/Helper_Functions.R | 39 ++++++++++++++--- R/MCMCMLE.R | 50 ++++++++-------------- R/Network_Statistic_Calculation_Functions.R | 32 ++++++++++++++ R/Package_Documentation.R | 3 + R/Parse_Formula_Object.R | 13 +++++ R/Parse_Undirected_Structural_Terms.R |only R/Prepare_Covariates.R | 11 ++--- R/Simulate_GERGM.R | 10 ++-- R/Trace_Plot.R | 8 ++- R/gergm.R | 61 +++++++++++++++------------- README.md | 12 +++-- man/GERGM.Rd | 13 +---- tests |only 22 files changed, 209 insertions(+), 132 deletions(-)
Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the
field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre],
Lúcia Anjos [ths],
Gustavo Vasques [ths],
Gerard Heuvelink [ths],
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb],
Frank Harrell Jr [ctb],
Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-5 dated 2015-12-01 and 0.6-6 dated 2015-12-03
DESCRIPTION | 13 +++-- MD5 | 12 ++--- R/AAAA.R | 1 R/pedometrics.R | 4 - R/vgmICP.R | 105 +++++++++++++++++++++++---------------------- man/pedometrics-package.Rd | 4 - man/vgmICP.Rd | 46 +++++++++++-------- 7 files changed, 100 insertions(+), 85 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.6 dated 2015-09-21 and 0.5.0 dated 2015-12-03
Luminescence-0.4.6/Luminescence/R/readBIN2R.R |only Luminescence-0.4.6/Luminescence/R/readSPE2R.R |only Luminescence-0.4.6/Luminescence/R/readXSYG2R.R |only Luminescence-0.4.6/Luminescence/R/writeR2BIN.R |only Luminescence-0.4.6/Luminescence/man/readBIN2R.Rd |only Luminescence-0.4.6/Luminescence/man/readSPE2R.Rd |only Luminescence-0.4.6/Luminescence/man/readXSYG2R.Rd |only Luminescence-0.4.6/Luminescence/man/writeR2BIN.Rd |only Luminescence-0.5.0/Luminescence/DESCRIPTION | 53 Luminescence-0.5.0/Luminescence/MD5 | 351 +- Luminescence-0.5.0/Luminescence/NAMESPACE | 170 Luminescence-0.5.0/Luminescence/NEWS | 648 +++ Luminescence-0.5.0/Luminescence/R/Analyse_SAR.OSLdata.R | 87 Luminescence-0.5.0/Luminescence/R/CW2pHMi.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pLM.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pLMi.R | 2 Luminescence-0.5.0/Luminescence/R/CW2pPMi.R | 2 Luminescence-0.5.0/Luminescence/R/Luminescence-package.R | 41 Luminescence-0.5.0/Luminescence/R/RLum-class.R | 53 Luminescence-0.5.0/Luminescence/R/RLum.Analysis-class.R | 473 +- Luminescence-0.5.0/Luminescence/R/RLum.Data-class.R | 8 Luminescence-0.5.0/Luminescence/R/RLum.Data.Curve-class.R | 273 + Luminescence-0.5.0/Luminescence/R/RLum.Data.Image-class.R | 205 - Luminescence-0.5.0/Luminescence/R/RLum.Data.Spectrum-class.R | 250 - Luminescence-0.5.0/Luminescence/R/RLum.Results-class.R | 598 +-- Luminescence-0.5.0/Luminescence/R/RcppExports.R | 4 Luminescence-0.5.0/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 180 - Luminescence-0.5.0/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 82 Luminescence-0.5.0/Luminescence/R/RisoeBINfileData-class.R | 28 Luminescence-0.5.0/Luminescence/R/Second2Gray.R | 74 Luminescence-0.5.0/Luminescence/R/analyse_IRSAR.RF.R | 363 +- Luminescence-0.5.0/Luminescence/R/analyse_SAR.CWOSL.R | 1750 ++++++---- Luminescence-0.5.0/Luminescence/R/analyse_SAR.TL.R | 35 Luminescence-0.5.0/Luminescence/R/analyse_pIRIRSequence.R | 292 + Luminescence-0.5.0/Luminescence/R/apply_CosmicRayRemoval.R | 2 Luminescence-0.5.0/Luminescence/R/apply_EfficiencyCorrection.R | 2 Luminescence-0.5.0/Luminescence/R/calc_AliquotSize.R | 2 Luminescence-0.5.0/Luminescence/R/calc_CentralDose.R | 304 - Luminescence-0.5.0/Luminescence/R/calc_CommonDose.R | 1 Luminescence-0.5.0/Luminescence/R/calc_CosmicDoseRate.R | 2 Luminescence-0.5.0/Luminescence/R/calc_FadingCorr.R | 2 Luminescence-0.5.0/Luminescence/R/calc_FiniteMixture.R | 1 Luminescence-0.5.0/Luminescence/R/calc_FuchsLang2001.R | 2 Luminescence-0.5.0/Luminescence/R/calc_HomogeneityTest.R | 1 Luminescence-0.5.0/Luminescence/R/calc_IEU.R | 2 Luminescence-0.5.0/Luminescence/R/calc_MaxDose.R | 4 Luminescence-0.5.0/Luminescence/R/calc_MinDose.R | 2 Luminescence-0.5.0/Luminescence/R/calc_OSLLxTxRatio.R | 208 - Luminescence-0.5.0/Luminescence/R/calc_SourceDoseRate.R | 71 Luminescence-0.5.0/Luminescence/R/calc_Statistics.R | 55 Luminescence-0.5.0/Luminescence/R/calc_TLLxTxRatio.R | 4 Luminescence-0.5.0/Luminescence/R/calc_gSGC.R |only Luminescence-0.5.0/Luminescence/R/extract_IrradiationTimes.R | 24 Luminescence-0.5.0/Luminescence/R/fit_CWCurve.R | 2 Luminescence-0.5.0/Luminescence/R/fit_LMCurve.R | 249 - Luminescence-0.5.0/Luminescence/R/get_Layout.R | 1 Luminescence-0.5.0/Luminescence/R/get_Quote.R | 39 Luminescence-0.5.0/Luminescence/R/get_RLum.R | 67 Luminescence-0.5.0/Luminescence/R/get_Risoe.BINfileData.R | 12 Luminescence-0.5.0/Luminescence/R/get_rightAnswer.R |only Luminescence-0.5.0/Luminescence/R/internal_as.latex.table.R |only Luminescence-0.5.0/Luminescence/R/internals_RLum.R |only Luminescence-0.5.0/Luminescence/R/length_RLum.R | 6 Luminescence-0.5.0/Luminescence/R/merge_RLum.Analysis.R | 3 Luminescence-0.5.0/Luminescence/R/merge_RLum.Data.Curve.R | 10 Luminescence-0.5.0/Luminescence/R/merge_RLum.R | 134 Luminescence-0.5.0/Luminescence/R/merge_RLum.Results.R |only Luminescence-0.5.0/Luminescence/R/merge_Risoe.BINfileData.R | 22 Luminescence-0.5.0/Luminescence/R/methods_DRAC.R |only Luminescence-0.5.0/Luminescence/R/methods_RLum.R |only Luminescence-0.5.0/Luminescence/R/names_RLum.R |only Luminescence-0.5.0/Luminescence/R/plot_AbanicoPlot.R | 214 - Luminescence-0.5.0/Luminescence/R/plot_DRTResults.R | 55 Luminescence-0.5.0/Luminescence/R/plot_GrowthCurve.R | 788 +++- Luminescence-0.5.0/Luminescence/R/plot_Histogram.R | 1 Luminescence-0.5.0/Luminescence/R/plot_KDE.R | 1 Luminescence-0.5.0/Luminescence/R/plot_NRt.R |only Luminescence-0.5.0/Luminescence/R/plot_RLum.Analysis.R | 142 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Curve.R | 10 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Image.R | 4 Luminescence-0.5.0/Luminescence/R/plot_RLum.Data.Spectrum.R | 48 Luminescence-0.5.0/Luminescence/R/plot_RLum.R | 72 Luminescence-0.5.0/Luminescence/R/plot_RLum.Results.R | 222 - Luminescence-0.5.0/Luminescence/R/plot_RadialPlot.R | 1 Luminescence-0.5.0/Luminescence/R/plot_Risoe.BINfileData.R | 10 Luminescence-0.5.0/Luminescence/R/plot_ViolinPlot.R |only Luminescence-0.5.0/Luminescence/R/read_BIN2R.R |only Luminescence-0.5.0/Luminescence/R/read_Daybreak2R.R |only Luminescence-0.5.0/Luminescence/R/read_SPE2R.R |only Luminescence-0.5.0/Luminescence/R/read_XSYG2R.R |only Luminescence-0.5.0/Luminescence/R/replicate_RLum.R |only Luminescence-0.5.0/Luminescence/R/set_RLum.R | 112 Luminescence-0.5.0/Luminescence/R/set_Risoe.BINfileData.R | 6 Luminescence-0.5.0/Luminescence/R/structure_RLum.R | 13 Luminescence-0.5.0/Luminescence/R/template_DRAC.R |only Luminescence-0.5.0/Luminescence/R/tune_Data.R |only Luminescence-0.5.0/Luminescence/R/use_DRAC.R |only Luminescence-0.5.0/Luminescence/R/write_R2BIN.R |only Luminescence-0.5.0/Luminescence/R/zzz.R | 7 Luminescence-0.5.0/Luminescence/inst/CITATION | 22 Luminescence-0.5.0/Luminescence/inst/NEWS.Rd | 552 +++ Luminescence-0.5.0/Luminescence/inst/doc/S4classObjects.pdf |binary Luminescence-0.5.0/Luminescence/man/Analyse_SAR.OSLdata.Rd | 28 Luminescence-0.5.0/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd | 3 Luminescence-0.5.0/Luminescence/man/CW2pHMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pLM.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pLMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/CW2pPMi.Rd | 8 Luminescence-0.5.0/Luminescence/man/ExampleData.BINfileData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.CW_OSL_Curve.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.DeValues.Rd | 99 Luminescence-0.5.0/Luminescence/man/ExampleData.FittingLM.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.LxTxData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.LxTxOSLData.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.RLum.Analysis.Rd | 4 Luminescence-0.5.0/Luminescence/man/ExampleData.RLum.Data.Image.Rd | 6 Luminescence-0.5.0/Luminescence/man/ExampleData.XSYG.Rd | 8 Luminescence-0.5.0/Luminescence/man/Luminescence-package.Rd | 21 Luminescence-0.5.0/Luminescence/man/RLum-class.Rd | 30 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Luminescence-0.5.0/Luminescence/man/apply_EfficiencyCorrection.Rd | 7 Luminescence-0.5.0/Luminescence/man/as.Rd |only Luminescence-0.5.0/Luminescence/man/calc_AliquotSize.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_CentralDose.Rd | 24 Luminescence-0.5.0/Luminescence/man/calc_CommonDose.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_CosmicDoseRate.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_FadingCorr.Rd | 5 Luminescence-0.5.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_FuchsLang2001.Rd | 7 Luminescence-0.5.0/Luminescence/man/calc_HomogeneityTest.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_IEU.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_MaxDose.Rd | 6 Luminescence-0.5.0/Luminescence/man/calc_MinDose.Rd | 7 Luminescence-0.5.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 84 Luminescence-0.5.0/Luminescence/man/calc_SourceDoseRate.Rd | 60 Luminescence-0.5.0/Luminescence/man/calc_Statistics.Rd | 11 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Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. Whether or not this is the case is now decided by leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS(). Further documentation and FAQ around this package is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.6 dated 2015-11-02 and 1.6.1 dated 2015-12-03
DESCRIPTION | 12 ++++----- MD5 | 20 ++++++++-------- R/assignQuantityToSP.R | 56 +++++++++++++++++++++++++++++++++------------- R/buildMultiSamplePhylo.R | 6 ++++ R/buildPhylo.R | 40 +++++++++----------------------- R/runExPANdS.R | 11 ++++++--- inst/doc/expands.R | 2 - inst/doc/expands.Rnw | 2 - inst/doc/expands.pdf |binary man/assignQuantityToSP.Rd | 6 ++-- vignettes/expands.Rnw | 2 - 11 files changed, 88 insertions(+), 69 deletions(-)
Title: Dynamic Models in Epidemiology
Description: Mathematical models of infectious diseases in humans and animals.
Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre],
Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between EpiDynamics versions 0.2 dated 2014-08-21 and 0.3.0 dated 2015-12-03
DESCRIPTION | 13 +++---- MD5 | 68 ++++++++++++++++++++------------------ NAMESPACE | 14 ++++++- NEWS | 7 +++ R/EpiDynamics-package.R | 11 +++--- R/SIR.R | 2 - R/SIR2Stages.R |only R/SISPairwiseApprox.R |only man/EpiDynamics-package.Rd | 9 ++--- man/MultiStrainPartialImmunity.Rd | 8 ++-- man/PlotMods.Rd | 16 +++++--- man/SEIR.Rd | 3 + man/SEIR4AgeClasses.Rd | 10 +++-- man/SEIRnStages.Rd | 7 ++- man/SIR.Rd | 6 ++- man/SIR2Stages.Rd |only man/SIR2TypesImports.Rd | 4 +- man/SIRAdditiveNoise.Rd | 4 +- man/SIRBirthDeath.Rd | 6 ++- man/SIRCarrierState.Rd | 8 ++-- man/SIRDemogStoch.Rd | 6 ++- man/SIRInducedMortality.Rd | 8 ++-- man/SIRInducedMortality2.Rd | 7 ++- man/SIRPartialImmunity.Rd | 10 +++-- man/SIRScaledAdditiveNoise.Rd | 8 ++-- man/SIRSinusoidalBirth.Rd | 8 ++-- man/SIRSinusoidalForcing.Rd | 12 +++--- man/SIRTauLeap.Rd | 4 +- man/SIRTermTimeForcing.Rd | 5 +- man/SIRVector.Rd | 10 +++-- man/SIS.Rd | 4 +- man/SIS2RiskGroups.Rd | 4 +- man/SISDemogStoch.Rd | 4 +- man/SISPairwiseApprox.Rd |only man/SISinusoidalTransmBrith.Rd | 4 +- man/SISnRiskGroups.Rd | 10 +++-- man/sir2AgeClasses.Rd | 6 ++- 37 files changed, 190 insertions(+), 116 deletions(-)
Title: Autoregressive Conditional Poisson
Description: Analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios <Siakoulis.Vasilios@atticabank.gr>
Diff between acp versions 2.0 dated 2015-05-22 and 2.1 dated 2015-12-03
DESCRIPTION | 8 +++---- MD5 | 8 +++---- NAMESPACE | 5 +++- R/acp.R | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++--------- man/acp.Rd | 5 ++++ 5 files changed, 71 insertions(+), 18 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.200.2.0 dated 2015-10-31 and 0.6.300.2.0 dated 2015-12-03
ChangeLog | 25 DESCRIPTION | 8 MD5 | 124 +- inst/NEWS.Rd | 17 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloAs.h | 88 ++ inst/include/armadillo_bits/Base_bones.hpp | 6 inst/include/armadillo_bits/Base_meat.hpp | 100 +- inst/include/armadillo_bits/Cube_bones.hpp | 8 inst/include/armadillo_bits/Cube_meat.hpp | 31 inst/include/armadillo_bits/Mat_bones.hpp | 8 inst/include/armadillo_bits/Mat_meat.hpp | 35 inst/include/armadillo_bits/Proxy.hpp | 39 inst/include/armadillo_bits/arma_forward.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/auxlib_bones.hpp | 41 inst/include/armadillo_bits/auxlib_meat.hpp | 828 +++++++++++++++----- inst/include/armadillo_bits/compiler_setup.hpp | 8 inst/include/armadillo_bits/def_lapack.hpp | 99 ++ inst/include/armadillo_bits/def_superlu.hpp | 5 inst/include/armadillo_bits/diagview_meat.hpp | 12 inst/include/armadillo_bits/diskio_bones.hpp | 9 inst/include/armadillo_bits/diskio_meat.hpp | 132 --- inst/include/armadillo_bits/fft_engine.hpp | 2 inst/include/armadillo_bits/field_bones.hpp | 17 inst/include/armadillo_bits/field_meat.hpp | 210 ++++- inst/include/armadillo_bits/fn_cond.hpp | 14 inst/include/armadillo_bits/fn_det.hpp | 152 --- inst/include/armadillo_bits/fn_eig_gen.hpp | 32 inst/include/armadillo_bits/fn_inv.hpp | 195 +++- inst/include/armadillo_bits/fn_solve.hpp | 223 +++-- inst/include/armadillo_bits/fn_spsolve.hpp | 28 inst/include/armadillo_bits/glue_solve_bones.hpp | 68 + inst/include/armadillo_bits/glue_solve_meat.hpp | 184 +++- inst/include/armadillo_bits/glue_times_meat.hpp | 27 inst/include/armadillo_bits/include_superlu.hpp | 15 inst/include/armadillo_bits/memory.hpp | 14 inst/include/armadillo_bits/op_inv_bones.hpp | 4 inst/include/armadillo_bits/op_inv_meat.hpp | 8 inst/include/armadillo_bits/op_symmat_meat.hpp | 4 inst/include/armadillo_bits/op_trimat_meat.hpp | 6 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 11 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 329 ++++++- inst/include/armadillo_bits/strip.hpp | 11 inst/include/armadillo_bits/subview_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_meat.hpp | 29 inst/include/armadillo_bits/subview_each_bones.hpp | 8 inst/include/armadillo_bits/subview_each_meat.hpp | 66 - inst/include/armadillo_bits/subview_elem1_meat.hpp | 2 inst/include/armadillo_bits/subview_elem2_meat.hpp | 2 inst/include/armadillo_bits/subview_field_bones.hpp | 5 inst/include/armadillo_bits/subview_field_meat.hpp | 63 + inst/include/armadillo_bits/subview_meat.hpp | 45 + inst/include/armadillo_bits/traits.hpp | 28 inst/include/armadillo_bits/typedef_elem.hpp | 24 inst/include/armadillo_bits/wall_clock_bones.hpp | 4 inst/include/armadillo_bits/wall_clock_meat.hpp | 8 inst/include/armadillo_bits/wrapper_blas.hpp | 4 inst/include/armadillo_bits/wrapper_lapack.hpp | 197 ++++ inst/include/armadillo_bits/wrapper_superlu.hpp | 46 + inst/unitTests/cpp/cube.cpp |only inst/unitTests/runit.cube.R |only 64 files changed, 2749 insertions(+), 969 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.2.5 dated 2014-05-28 and 0.3.1 dated 2015-12-03
pairwise-0.2.5/pairwise/data/datalist |only pairwise-0.3.1/pairwise/DESCRIPTION | 22 - pairwise-0.3.1/pairwise/MD5 | 115 ++++--- pairwise-0.3.1/pairwise/NAMESPACE | 47 +++ pairwise-0.3.1/pairwise/NEWS | 31 ++ pairwise-0.3.1/pairwise/R/andersentest.pers.R |only pairwise-0.3.1/pairwise/R/grm.R | 28 + pairwise-0.3.1/pairwise/R/i.pvx.matrix.R | 5 pairwise-0.3.1/pairwise/R/i.pvx.super.R | 42 +- pairwise-0.3.1/pairwise/R/logLik.pers.R | 39 +- pairwise-0.3.1/pairwise/R/lrtest.pers.R |only pairwise-0.3.1/pairwise/R/pair.R | 59 +++ pairwise-0.3.1/pairwise/R/pairSE.R | 13 pairwise-0.3.1/pairwise/R/pairwise-package.r | 31 +- pairwise-0.3.1/pairwise/R/pairwise.item.fit.R | 2 pairwise-0.3.1/pairwise/R/pairwise.person.fit.R | 2 pairwise-0.3.1/pairwise/R/pers.R | 15 - pairwise-0.3.1/pairwise/R/plot.grm.R | 28 + pairwise-0.3.1/pairwise/R/plot.pair.R | 4 pairwise-0.3.1/pairwise/R/plot.pairSE.R | 33 +- pairwise-0.3.1/pairwise/R/plot.pers.R | 27 + pairwise-0.3.1/pairwise/R/plot.rfa.R | 5 pairwise-0.3.1/pairwise/R/simra.R |only pairwise-0.3.1/pairwise/R/summary.grm.R | 10 pairwise-0.3.1/pairwise/R/summary.pair.R | 7 pairwise-0.3.1/pairwise/R/summary.pairSE.R | 24 + pairwise-0.3.1/pairwise/R/summary.pairwise.item.fit.R |only pairwise-0.3.1/pairwise/R/summary.pairwise.person.fit.R |only pairwise-0.3.1/pairwise/R/summary.pers.R | 2 pairwise-0.3.1/pairwise/R/summary.rfa.R | 7 pairwise-0.3.1/pairwise/build/vignette.rds |binary pairwise-0.3.1/pairwise/data/bfi_cov.RData |only pairwise-0.3.1/pairwise/man/andersentest.pers.Rd |only pairwise-0.3.1/pairwise/man/bfiN.Rd | 33 +- pairwise-0.3.1/pairwise/man/bfiN_miss.Rd | 9 pairwise-0.3.1/pairwise/man/bfi_cov.Rd |only pairwise-0.3.1/pairwise/man/catprob.Rd | 31 -- pairwise-0.3.1/pairwise/man/esc.Rd | 35 -- pairwise-0.3.1/pairwise/man/ftab.Rd | 28 - pairwise-0.3.1/pairwise/man/gif.Rd | 39 -- pairwise-0.3.1/pairwise/man/grm.Rd | 142 ++------- pairwise-0.3.1/pairwise/man/iff.Rd | 66 +--- pairwise-0.3.1/pairwise/man/logLik.pers.Rd | 18 - pairwise-0.3.1/pairwise/man/lrtest.pers.Rd |only pairwise-0.3.1/pairwise/man/make.incidenz.Rd | 44 -- pairwise-0.3.1/pairwise/man/pair.Rd | 137 ++------- pairwise-0.3.1/pairwise/man/pairSE.Rd | 152 ++-------- pairwise-0.3.1/pairwise/man/pairwise-package.Rd | 192 +++---------- pairwise-0.3.1/pairwise/man/pairwise.item.fit.Rd | 38 -- pairwise-0.3.1/pairwise/man/pairwise.person.fit.Rd | 35 -- pairwise-0.3.1/pairwise/man/pers.Rd | 111 +------ pairwise-0.3.1/pairwise/man/plot.grm.Rd | 46 +-- pairwise-0.3.1/pairwise/man/plot.pair.Rd | 42 +- pairwise-0.3.1/pairwise/man/plot.pairSE.Rd | 46 +-- pairwise-0.3.1/pairwise/man/plot.pers.Rd | 43 +- pairwise-0.3.1/pairwise/man/plot.rfa.Rd | 41 +- pairwise-0.3.1/pairwise/man/ptbis.Rd | 25 - pairwise-0.3.1/pairwise/man/rfa.Rd | 84 +---- pairwise-0.3.1/pairwise/man/simra.Rd |only pairwise-0.3.1/pairwise/man/summary.grm.Rd |only pairwise-0.3.1/pairwise/man/summary.pair.Rd |only pairwise-0.3.1/pairwise/man/summary.pairSE.Rd |only pairwise-0.3.1/pairwise/man/summary.pairwise.item.fit.Rd |only pairwise-0.3.1/pairwise/man/summary.pairwise.person.fit.Rd |only pairwise-0.3.1/pairwise/man/summary.pers.Rd | 20 - pairwise-0.3.1/pairwise/man/summary.rfa.Rd |only pairwise-0.3.1/pairwise/man/tff.Rd | 67 +--- 67 files changed, 922 insertions(+), 1200 deletions(-)
Title: Streamlining Design and Deployment of Complex Workflows
Description: This framework allows you to design and implement complex
pipelines, and deploy them on your institution's computing cluster. This has
been built keeping in mind the needs of bioinformatics workflows. However, it is
easily extendable to any field where a series of steps (shell commands) are to
be executed in a (work)flow.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between flowr versions 0.9.8.2 dated 2015-10-03 and 0.9.9.5 dated 2015-12-03
flowr-0.9.8.2/flowr/inst/scripts/flowr2 |only flowr-0.9.8.2/flowr/man/opts_flow.Rd |only flowr-0.9.8.2/flowr/tests/fastq_mutect_err1.def |only flowr-0.9.9.5/flowr/DESCRIPTION | 20 flowr-0.9.9.5/flowr/MD5 | 193 +- flowr-0.9.9.5/flowr/NAMESPACE | 6 flowr-0.9.9.5/flowr/NEWS.md | 87 + flowr-0.9.9.5/flowr/R/check-args.R | 4 flowr-0.9.9.5/flowr/R/check.R | 24 flowr-0.9.9.5/flowr/R/class-def.R | 10 flowr-0.9.9.5/flowr/R/conf.R | 45 flowr-0.9.9.5/flowr/R/errors.R | 4 flowr-0.9.9.5/flowr/R/fetch.r | 32 flowr-0.9.9.5/flowr/R/kill-flow.R | 2 flowr-0.9.9.5/flowr/R/limit_runs.R | 1 flowr-0.9.9.5/flowr/R/parse-jobids.R | 11 flowr-0.9.9.5/flowr/R/plot.R | 21 flowr-0.9.9.5/flowr/R/render-dependency.R | 9 flowr-0.9.9.5/flowr/R/rerun.R | 414 ++--- flowr-0.9.9.5/flowr/R/run.R | 84 - flowr-0.9.9.5/flowr/R/setup.R | 27 flowr-0.9.9.5/flowr/R/status.R | 39 flowr-0.9.9.5/flowr/R/submit-flow.R | 240 +-- flowr-0.9.9.5/flowr/R/submit-job.R | 6 flowr-0.9.9.5/flowr/R/submit-local.R | 2 flowr-0.9.9.5/flowr/R/to-flow.R | 780 +++++----- flowr-0.9.9.5/flowr/R/to-flowdef.R | 341 +++- flowr-0.9.9.5/flowr/R/to-flowdet.R | 2 flowr-0.9.9.5/flowr/R/to-flowmat.R | 49 flowr-0.9.9.5/flowr/R/verbose.R | 2 flowr-0.9.9.5/flowr/R/zz-db.R | 4 flowr-0.9.9.5/flowr/R/zz-parse-resources.R | 8 flowr-0.9.9.5/flowr/R/zzz.R | 4 flowr-0.9.9.5/flowr/README.md | 57 flowr-0.9.9.5/flowr/inst/CITATION |only flowr-0.9.9.5/flowr/inst/conf/flowr.conf | 14 flowr-0.9.9.5/flowr/inst/conf/local.sh | 3 flowr-0.9.9.5/flowr/inst/conf/lsf.sh | 3 flowr-0.9.9.5/flowr/inst/conf/moab.sh | 3 flowr-0.9.9.5/flowr/inst/conf/sge.sh | 3 flowr-0.9.9.5/flowr/inst/conf/slurm.sh | 3 flowr-0.9.9.5/flowr/inst/conf/torque.sh | 3 flowr-0.9.9.5/flowr/inst/conf/torque_comm.sh | 3 flowr-0.9.9.5/flowr/inst/doc/flowr_install.R | 15 flowr-0.9.9.5/flowr/inst/doc/flowr_install.Rmd | 96 + flowr-0.9.9.5/flowr/inst/doc/flowr_install.html | 103 - flowr-0.9.9.5/flowr/inst/doc/flowr_overview.R | 32 flowr-0.9.9.5/flowr/inst/doc/flowr_overview.Rmd | 148 - flowr-0.9.9.5/flowr/inst/doc/flowr_overview.html | 195 -- flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.R | 143 + flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.Rmd | 350 +++- flowr-0.9.9.5/flowr/inst/doc/flowr_tutorial.html | 408 +++-- flowr-0.9.9.5/flowr/inst/pipelines/README.md |only flowr-0.9.9.5/flowr/inst/pipelines/fastq_bam_bwa.R | 46 flowr-0.9.9.5/flowr/inst/pipelines/sleep_pipe.def | 8 flowr-0.9.9.5/flowr/inst/scripts/flowr | 377 ---- flowr-0.9.9.5/flowr/inst/scripts/flowr.v1 |only flowr-0.9.9.5/flowr/man/check.Rd | 44 flowr-0.9.9.5/flowr/man/check_args.Rd | 2 flowr-0.9.9.5/flowr/man/create_jobs_mat.Rd | 2 flowr-0.9.9.5/flowr/man/error.Rd | 2 flowr-0.9.9.5/flowr/man/fetch.Rd | 38 flowr-0.9.9.5/flowr/man/flow.Rd | 12 flowr-0.9.9.5/flowr/man/flowopts.Rd |only flowr-0.9.9.5/flowr/man/generate_flow_code.Rd | 2 flowr-0.9.9.5/flowr/man/get_unique_id.Rd | 2 flowr-0.9.9.5/flowr/man/get_wds.Rd | 2 flowr-0.9.9.5/flowr/man/job.Rd | 2 flowr-0.9.9.5/flowr/man/kill.Rd | 11 flowr-0.9.9.5/flowr/man/plot_flow.Rd | 10 flowr-0.9.9.5/flowr/man/queue.Rd | 2 flowr-0.9.9.5/flowr/man/replace_slots.Rd | 2 flowr-0.9.9.5/flowr/man/rerun.Rd | 26 flowr-0.9.9.5/flowr/man/run.Rd | 41 flowr-0.9.9.5/flowr/man/setup.Rd | 18 flowr-0.9.9.5/flowr/man/status.Rd | 18 flowr-0.9.9.5/flowr/man/submit_flow.Rd | 12 flowr-0.9.9.5/flowr/man/submit_job.Rd | 2 flowr-0.9.9.5/flowr/man/submit_run.Rd | 2 flowr-0.9.9.5/flowr/man/test_queue.Rd | 4 flowr-0.9.9.5/flowr/man/to_flow.Rd | 76 flowr-0.9.9.5/flowr/man/to_flowdef.Rd | 114 + flowr-0.9.9.5/flowr/man/to_flowdet.Rd | 4 flowr-0.9.9.5/flowr/man/to_flowmat.Rd | 45 flowr-0.9.9.5/flowr/man/verbose.Rd | 59 flowr-0.9.9.5/flowr/man/whisker_render.Rd | 6 flowr-0.9.9.5/flowr/man/write_flow_details.Rd | 2 flowr-0.9.9.5/flowr/tests/testthat.R | 2 flowr-0.9.9.5/flowr/tests/testthat/test-toflow.R | 10 flowr-0.9.9.5/flowr/vignettes/files/googl.js |only flowr-0.9.9.5/flowr/vignettes/files/logo.png |binary flowr-0.9.9.5/flowr/vignettes/files/logo_black.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_blue.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_green.png |only flowr-0.9.9.5/flowr/vignettes/files/logo_red.png |only flowr-0.9.9.5/flowr/vignettes/flowr_install.Rmd | 96 + flowr-0.9.9.5/flowr/vignettes/flowr_install.md |only flowr-0.9.9.5/flowr/vignettes/flowr_overview.Rmd | 148 - flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plot_abcd-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plot_one_one-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_overview_files/figure-html/plotit-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_tutorial.Rmd | 350 +++- flowr-0.9.9.5/flowr/vignettes/flowr_tutorial_files/figure-html/plot_skeleton_def-1.png |binary flowr-0.9.9.5/flowr/vignettes/flowr_tutorial_files/figure-html/plot_tweaked_def-1.png |binary 104 files changed, 3209 insertions(+), 2443 deletions(-)
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast
Clustering Using Adaptive Density Peak Detection). The work is built and
improved upon Rodriguez and Laio[2014]'s idea. ADPclust clusters data by finding
density peaks in a density-distance plot generated from local multivariate
Gaussian density estimation. It includes an automatic centroids selection and
parameter optimization algorithm, which finds the number of clusters and cluster
centroids by comparing average silhouettes on a grid of testing clustering
results; It also includes an user interactive algorithm that allows the user
to manually selects cluster centroids from a two dimensional "density-distance
plot".
Author: Yifan "Ethan" Xu [aut, cre],
Xiao-Feng Wang [aut]
Maintainer: Yifan "Ethan" Xu <ethan.yifanxu@gmail.com>
Diff between ADPclust versions 0.6.3 dated 2015-04-20 and 0.6.5 dated 2015-12-03
ADPclust-0.6.3/ADPclust/vignettes/ADPclust_files |only ADPclust-0.6.5/ADPclust/DESCRIPTION | 29 + ADPclust-0.6.5/ADPclust/MD5 | 60 +-- ADPclust-0.6.5/ADPclust/NAMESPACE | 6 ADPclust-0.6.5/ADPclust/R/ADPclust-package.r | 2 ADPclust-0.6.5/ADPclust/R/ADPclust.R | 67 ++- ADPclust-0.6.5/ADPclust/R/AMISE.R | 8 ADPclust-0.6.5/ADPclust/R/ROT.R | 15 ADPclust-0.6.5/ADPclust/R/findCluster.R | 10 ADPclust-0.6.5/ADPclust/R/findClusterAuto.R | 2 ADPclust-0.6.5/ADPclust/R/findFd.R | 8 ADPclust-0.6.5/ADPclust/R/plot.adpclust.R | 5 ADPclust-0.6.5/ADPclust/README.md |only ADPclust-0.6.5/ADPclust/build/vignette.rds |binary ADPclust-0.6.5/ADPclust/inst/CITATION |only ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.R | 45 +- ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.Rmd | 95 +++-- ADPclust-0.6.5/ADPclust/inst/doc/ADPclust.html | 410 +++++++---------------- ADPclust-0.6.5/ADPclust/man/ADPclust.Rd | 37 +- ADPclust-0.6.5/ADPclust/man/AMISE.Rd | 7 ADPclust-0.6.5/ADPclust/man/ROT.Rd | 7 ADPclust-0.6.5/ADPclust/man/clust10.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust3.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust5.1.Rd | 2 ADPclust-0.6.5/ADPclust/man/clust5.Rd | 2 ADPclust-0.6.5/ADPclust/man/dat_gene.Rd | 2 ADPclust-0.6.5/ADPclust/man/findCluster.Rd | 14 ADPclust-0.6.5/ADPclust/man/findClusterAuto.Rd | 6 ADPclust-0.6.5/ADPclust/man/findFd.Rd | 12 ADPclust-0.6.5/ADPclust/man/plot.adpclust.Rd | 2 ADPclust-0.6.5/ADPclust/man/summary.adpclust.Rd | 2 ADPclust-0.6.5/ADPclust/vignettes/ADPclust.Rmd | 95 +++-- 32 files changed, 467 insertions(+), 487 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.1 dated 2015-09-11 and 0.4.2 dated 2015-12-03
ChangeLog | 59 ++++++++++++++++ DESCRIPTION | 19 ++--- MD5 | 48 +++++++------ NAMESPACE | 123 ++++++++++++++++++----------------- R/RcppExports.R | 27 +++++++ R/bond.R | 4 - R/zzz.R | 22 +++++- README.md | 2 cleanup | 2 configure | 18 ++--- configure.ac | 2 inst/NEWS.Rd | 28 ++++++- inst/include/RQuantLib_RcppExports.h | 38 ++++++++++ inst/unitTests/runit.dates.R | 38 ++++++---- inst/unitTests/runit.options.R | 3 man/BondUtilities.Rd | 3 man/EuropeanOption.Rd | 8 +- man/getQuantLibCapabilities.Rd |only man/getQuantLibVersion.Rd |only src/RcppExports.cpp | 62 +++++++++++++++++ src/asian.cpp | 11 ++- src/barrier_binary.cpp | 31 ++++++++ src/implieds.cpp | 20 +++++ src/utils.cpp | 49 +++++++++++++ src/vanilla.cpp | 33 ++++++++- tests/doRUnit.R | 47 ++++++++----- 26 files changed, 540 insertions(+), 157 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.37-11 dated 2015-08-25 and 1.38-4 dated 2015-12-03
DESCRIPTION | 8 +- MD5 | 46 +++++++-------- R/arithscan.R | 133 --------------------------------------------- R/discan.R | 27 --------- R/read.cross.mm.R | 2 R/refineqtl.R | 7 +- R/scanone.R | 37 +----------- R/scantwo.R | 58 ------------------- R/summary.scanone.R | 111 ++----------------------------------- R/summary.scantwo.R | 69 +---------------------- R/vbscan.R | 27 --------- inst/INSTALL_ME.txt | 12 ++-- inst/README.md | 1 inst/STATUS.txt | 21 +++++++ inst/TODO.txt | 5 + inst/doc/rqtltour.pdf |binary man/max.scanone.Rd | 4 - man/max.scantwo.Rd | 12 +--- man/qtl-internal.Rd | 8 +- man/scanone.Rd | 44 +++++++------- man/summary.scanone.Rd | 18 ++---- man/summary.scanoneperm.Rd | 12 +--- man/summary.scantwo.Rd | 26 ++++---- man/summary.scantwoperm.Rd | 4 - 24 files changed, 145 insertions(+), 547 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.2 dated 2015-10-09 and 1.3 dated 2015-12-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/ChannelAttribution-package.Rd | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2.1 dated 2015-06-04 and 1.2.2 dated 2015-12-03
ChangeLog | 4 - DESCRIPTION | 9 +- MD5 | 22 +++--- NAMESPACE | 4 + R/make_sglasso.R | 5 - R/sglasso.R | 6 - R/sglasso.fit.R | 16 +++- man/sglasso.Rd | 6 + src/sglasso_ccd_path.f90 | 148 +++++++++++++++++++++++---------------------- src/sglasso_ccd_single.f90 | 108 +++++++++++++++++--------------- src/sglasso_ccm_path.f90 | 71 ++++++++++++--------- src/sglasso_ccm_single.f90 | 46 ++++++++----- 12 files changed, 250 insertions(+), 195 deletions(-)
Title: Companion to the Forthcoming Book - R you Ready?
Description: Package contains some data and functions that
are used in my forthcoming "R you ready?" book.
Author: Mark Heckmann [aut, cre]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between ryouready versions 0.3 dated 2013-12-15 and 0.4 dated 2015-12-03
ryouready-0.3/ryouready/data/d.eta.txt |only ryouready-0.3/ryouready/data/d.ngo.txt |only ryouready-0.3/ryouready/data/d.superiority.txt |only ryouready-0.4/ryouready/DESCRIPTION | 24 ++--- ryouready-0.4/ryouready/MD5 | 67 ++++++++------- ryouready-0.4/ryouready/NAMESPACE | 11 ++ ryouready-0.4/ryouready/NEWS | 9 +- ryouready-0.4/ryouready/R/association_measures.r | 3 ryouready-0.4/ryouready/R/collapse_response_set.R | 23 +++-- ryouready-0.4/ryouready/R/qq-plot.R |only ryouready-0.4/ryouready/R/ryouready-package.r | 11 +- ryouready-0.4/ryouready/R/utils.r | 83 ++++++++++++++++++- ryouready-0.4/ryouready/README.md | 6 - ryouready-0.4/ryouready/data/d.eta.txt.gz |only ryouready-0.4/ryouready/data/d.ngo.txt.gz |only ryouready-0.4/ryouready/data/d.superiority.txt.gz |only ryouready-0.4/ryouready/inst |only ryouready-0.4/ryouready/man/collapse_responseset.Rd | 34 +++---- ryouready-0.4/ryouready/man/count_na.Rd |only ryouready-0.4/ryouready/man/d.eta.Rd | 5 - ryouready-0.4/ryouready/man/d.ngo.Rd | 10 +- ryouready-0.4/ryouready/man/d.superiority.Rd | 5 - ryouready-0.4/ryouready/man/eta.Rd | 25 ++--- ryouready-0.4/ryouready/man/foo.Rd | 14 +-- ryouready-0.4/ryouready/man/ggplot.qqnorm.spss.Rd |only ryouready-0.4/ryouready/man/intervals.Rd | 55 +++++------- ryouready-0.4/ryouready/man/nom.lambda.Rd | 24 ++--- ryouready-0.4/ryouready/man/nom.uncertainty.Rd | 27 ++---- ryouready-0.4/ryouready/man/ord.gamma.Rd | 16 ++- ryouready-0.4/ryouready/man/ord.somers.d.Rd | 24 ++--- ryouready-0.4/ryouready/man/ord.tau.Rd | 22 ++--- ryouready-0.4/ryouready/man/plot.qqnorm.spss.Rd |only ryouready-0.4/ryouready/man/print.nom.lambda.Rd | 12 +- ryouready-0.4/ryouready/man/print.nom.uncertainty.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.gamma.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.somersd.Rd | 12 +- ryouready-0.4/ryouready/man/print.ord.tau.Rd | 12 +- ryouready-0.4/ryouready/man/qqnorm_spss.Rd |only ryouready-0.4/ryouready/man/recode2.Rd |only ryouready-0.4/ryouready/man/rowMeans2.Rd | 45 ++++------ ryouready-0.4/ryouready/man/ryouready.Rd | 17 +-- 41 files changed, 366 insertions(+), 254 deletions(-)
Title: One-Way Independent Groups Design
Description: Two or more samples in one-way independent groups design are compared via different tests.
Author: Osman Dag, Anil Dolgun, N. Meric Konar
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between onewaytests versions 1.0 dated 2015-08-24 and 1.1 dated 2015-12-03
DESCRIPTION | 10 +++---- MD5 | 34 +++++++++++++------------- NAMESPACE | 2 - R/ag.test.R | 26 ++++++++++++++++++- R/aov.test.R | 26 ++++++++++++++++--- R/bf.test.R | 69 +++++++++++++++++++++++++---------------------------- R/james.test.R | 26 ++++++++++++++++--- R/kw.test.R | 29 +++++++++++++++++++--- R/mood.test.R | 31 +++++++++++++++++++---- R/welch.test.R | 41 +++++++++++++++++++------------ man/ag.test.Rd | 8 +++--- man/aov.test.Rd | 9 +++--- man/bf.test.Rd | 10 +++---- man/james.test.Rd | 11 +++----- man/kw.test.Rd | 9 +++--- man/mood.test.Rd | 9 +++--- man/onewaytests.Rd | 4 +-- man/welch.test.Rd | 11 +++----- 18 files changed, 233 insertions(+), 132 deletions(-)
Title: Joint Modelling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Description: Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Author: Rudradev Sengupta, Nolen Joy Perualila
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between IntegratedJM versions 1.2 dated 2015-11-12 and 1.3 dated 2015-12-03
DESCRIPTION | 12 ++--- MD5 | 6 +- NEWS | 3 + R/Functions.R | 123 +++++++++++++++++++++++++++++----------------------------- 4 files changed, 75 insertions(+), 69 deletions(-)
Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to
approximate maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct many
simulations, but works best when the data is approximately Poisson distributed.
It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using
the 'coala' package.
Author: Paul Staab [aut, cre],
Lisha Mathew [aut],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between jaatha versions 2.7.0 dated 2014-11-26 and 3.0.0 dated 2015-12-03
jaatha-2.7.0/jaatha/NEWS |only jaatha-2.7.0/jaatha/R/RcppExports.R |only jaatha-2.7.0/jaatha/R/confidence_intervals.R |only jaatha-2.7.0/jaatha/R/demographic_model.R |only jaatha-2.7.0/jaatha/R/estimate_log_likelihood.R |only jaatha-2.7.0/jaatha/R/find_best_par_in_block.R |only jaatha-2.7.0/jaatha/R/helper_functions.R |only jaatha-2.7.0/jaatha/R/initial_search.R |only jaatha-2.7.0/jaatha/R/normalize.R |only jaatha-2.7.0/jaatha/R/package_info.R |only jaatha-2.7.0/jaatha/R/parallelization.R |only jaatha-2.7.0/jaatha/R/read_fasta.R |only jaatha-2.7.0/jaatha/R/refined_search.R |only jaatha-2.7.0/jaatha/R/run_simulations.R |only jaatha-2.7.0/jaatha/R/sim_likelihood.R |only jaatha-2.7.0/jaatha/R/sim_program.R |only jaatha-2.7.0/jaatha/R/sim_program_ms.R |only jaatha-2.7.0/jaatha/R/sim_program_msms.R |only jaatha-2.7.0/jaatha/R/sim_program_seqgen.R |only jaatha-2.7.0/jaatha/R/simulate_within_block.R |only jaatha-2.7.0/jaatha/R/sum_stat_fpc.R |only jaatha-2.7.0/jaatha/R/sum_stat_generate.R |only jaatha-2.7.0/jaatha/R/sum_stat_jsfs.R |only jaatha-2.7.0/jaatha/R/sum_stat_pmc.R |only jaatha-2.7.0/jaatha/inst/example_fasta_files |only jaatha-2.7.0/jaatha/man/Jaatha-class.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.confidenceIntervals.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getCIsFromLogs.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getLikelihoods.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.getStartingPoints.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.initialSearch.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.initialize.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.refinedSearch.Rd |only jaatha-2.7.0/jaatha/man/Jaatha.setSeqgenExecutable.Rd |only jaatha-2.7.0/jaatha/man/addFeature.Rd |only jaatha-2.7.0/jaatha/man/calcJsfs.Rd |only jaatha-2.7.0/jaatha/man/calculateJsfs.Rd |only jaatha-2.7.0/jaatha/man/checkType.Rd |only jaatha-2.7.0/jaatha/man/convertSimResultsToDataFrame.Rd |only jaatha-2.7.0/jaatha/man/denormalize.Rd |only jaatha-2.7.0/jaatha/man/dm.addGrowth.Rd |only jaatha-2.7.0/jaatha/man/dm.addMigration.Rd |only jaatha-2.7.0/jaatha/man/dm.addMutation.Rd |only jaatha-2.7.0/jaatha/man/dm.addMutationRateHeterogenity.Rd |only jaatha-2.7.0/jaatha/man/dm.addOutgroup.Rd |only jaatha-2.7.0/jaatha/man/dm.addParameter.Rd |only jaatha-2.7.0/jaatha/man/dm.addRecombination.Rd |only jaatha-2.7.0/jaatha/man/dm.addSampleSize.Rd |only jaatha-2.7.0/jaatha/man/dm.addSizeChange.Rd |only jaatha-2.7.0/jaatha/man/dm.addSpeciationEvent.Rd |only jaatha-2.7.0/jaatha/man/dm.addSummaryStatistic.Rd |only jaatha-2.7.0/jaatha/man/dm.addSymmetricMigration.Rd |only jaatha-2.7.0/jaatha/man/dm.createDemographicModel.Rd |only jaatha-2.7.0/jaatha/man/dm.createThetaTauModel.Rd |only jaatha-2.7.0/jaatha/man/dm.getGroups.Rd |only jaatha-2.7.0/jaatha/man/dm.getLociLength.Rd |only jaatha-2.7.0/jaatha/man/dm.getLociNumber.Rd |only jaatha-2.7.0/jaatha/man/dm.setLociLength.Rd |only jaatha-2.7.0/jaatha/man/dm.setLociNumber.Rd |only jaatha-2.7.0/jaatha/man/dm.setMutationModel.Rd |only jaatha-2.7.0/jaatha/man/dm.simSumStats.Rd |only jaatha-2.7.0/jaatha/man/estimateLogLikelihood.Rd |only jaatha-2.7.0/jaatha/man/findBestParInBlock.Rd |only jaatha-2.7.0/jaatha/man/fitGlm.Rd |only jaatha-2.7.0/jaatha/man/fitGlmPoiTransformed.Rd |only jaatha-2.7.0/jaatha/man/fitPoiSmoothed.Rd |only jaatha-2.7.0/jaatha/man/normalize.Rd |only jaatha-2.7.0/jaatha/man/runSimulations.Rd |only jaatha-2.7.0/jaatha/man/setCores.Rd |only jaatha-2.7.0/jaatha/man/simulateWithinBlock.Rd |only jaatha-2.7.0/jaatha/src |only jaatha-2.7.0/jaatha/tests/integration |only jaatha-2.7.0/jaatha/tests/testthat/setup-custom-simulation-interface.R |only jaatha-2.7.0/jaatha/tests/testthat/setup-demographic-models.R |only jaatha-2.7.0/jaatha/tests/testthat/test-aaa-setup.R |only jaatha-2.7.0/jaatha/tests/testthat/test-calc-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-confidence-intervals.R |only jaatha-2.7.0/jaatha/tests/testthat/test-demographic-model-class.R |only jaatha-2.7.0/jaatha/tests/testthat/test-estimate-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-initial-search.R |only jaatha-2.7.0/jaatha/tests/testthat/test-jaatha-class.R |only jaatha-2.7.0/jaatha/tests/testthat/test-normalize.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-ms-output.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-seqgen-output.R |only jaatha-2.7.0/jaatha/tests/testthat/test-parse-trees.R |only jaatha-2.7.0/jaatha/tests/testthat/test-read-fasta.R |only jaatha-2.7.0/jaatha/tests/testthat/test-refined-search.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sim-likelihood.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sim-program.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-ms.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-msms.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simprog-seqgen.R |only jaatha-2.7.0/jaatha/tests/testthat/test-simulate-within-block.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-fpc.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-jsfs.R |only jaatha-2.7.0/jaatha/tests/testthat/test-sumstat-pmc.R |only jaatha-2.7.0/jaatha/tests/testthat/test-zzz-temp-files.R |only jaatha-3.0.0/jaatha/DESCRIPTION | 62 - jaatha-3.0.0/jaatha/MD5 | 171 +-- jaatha-3.0.0/jaatha/NAMESPACE | 66 - jaatha-3.0.0/jaatha/NEWS.md |only jaatha-3.0.0/jaatha/R/block.R | 143 +- jaatha-3.0.0/jaatha/R/boot_jaatha.R |only jaatha-3.0.0/jaatha/R/coala_interface.R |only jaatha-3.0.0/jaatha/R/fit_glm.R | 157 -- jaatha-3.0.0/jaatha/R/initialization.R |only jaatha-3.0.0/jaatha/R/jaatha.R | 525 +--------- jaatha-3.0.0/jaatha/R/jaatha_data.R |only jaatha-3.0.0/jaatha/R/jaatha_log.R |only jaatha-3.0.0/jaatha/R/jaatha_model.R |only jaatha-3.0.0/jaatha/R/likelihood.R |only jaatha-3.0.0/jaatha/R/par_ranges.R |only jaatha-3.0.0/jaatha/R/simulation_cache.R |only jaatha-3.0.0/jaatha/R/stat_basic.R |only jaatha-3.0.0/jaatha/R/stat_cube.R |only jaatha-3.0.0/jaatha/R/tools.R |only jaatha-3.0.0/jaatha/README.md | 101 + jaatha-3.0.0/jaatha/build |only jaatha-3.0.0/jaatha/inst/CITATION | 30 jaatha-3.0.0/jaatha/inst/doc |only jaatha-3.0.0/jaatha/man/boot_jaatha.Rd |only jaatha-3.0.0/jaatha/man/coarsen_jsfs.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_data.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.coalmodel.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_model.function.Rd |only jaatha-3.0.0/jaatha/man/create_jaatha_stat.Rd |only jaatha-3.0.0/jaatha/man/estimate_llh.Rd |only jaatha-3.0.0/jaatha/man/jaatha-package.Rd | 20 jaatha-3.0.0/jaatha/man/jaatha.Rd |only jaatha-3.0.0/jaatha/tests/testthat/test-block.R |only jaatha-3.0.0/jaatha/tests/testthat/test-coala-interface.R |only jaatha-3.0.0/jaatha/tests/testthat/test-fit-glm.R | 82 - jaatha-3.0.0/jaatha/tests/testthat/test-initialization.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-data.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-function.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-log.R |only jaatha-3.0.0/jaatha/tests/testthat/test-jaatha-model.R |only jaatha-3.0.0/jaatha/tests/testthat/test-likelihood.R |only jaatha-3.0.0/jaatha/tests/testthat/test-par-ranges.R |only jaatha-3.0.0/jaatha/tests/testthat/test-sim-cache.R |only jaatha-3.0.0/jaatha/tests/testthat/test-stat-cubes.R |only jaatha-3.0.0/jaatha/tests/testthat/test-tools.R |only jaatha-3.0.0/jaatha/tests/testthat/test-zzz-bootstrapping.R |only jaatha-3.0.0/jaatha/vignettes |only 145 files changed, 428 insertions(+), 929 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.2 dated 2015-07-16 and 1.0.3 dated 2015-12-03
DESCRIPTION | 8 MD5 | 31 +-- R/computeDurations.R | 75 ++++--- R/diurnalAdj.R | 19 + R/plotHistAcd.R | 2 data/adjDurData.RData |binary data/durData.RData |binary inst/NEWS.Rd |only man/computeDurations.Rd | 10 - man/data.Rd | 2 man/diurnalAdj.Rd | 3 man/plotDescTrans.Rd | 4 man/plotHazard.Rd | 3 man/plotHistAcd.Rd | 3 man/plotScatterAcd.Rd | 4 man/resiDensityAcd.Rd | 8 src/computeDurations.c | 458 ++++++++++++++++++++++++------------------------ 17 files changed, 341 insertions(+), 289 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.2 dated 2015-10-19 and 1.6.5 dated 2015-12-03
TMB-1.6.2/TMB/inst/include/tmbutils/R_inla.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/array.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/autodiff.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/density.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/kronecker.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/matexp.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/order.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/romberg.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/splines.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/spmat.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils_extra.cpp |only TMB-1.6.2/TMB/inst/include/tmbutils/vector.cpp |only TMB-1.6.5/TMB/DESCRIPTION | 14 - TMB-1.6.5/TMB/MD5 | 122 +++++++------- TMB-1.6.5/TMB/NAMESPACE | 5 TMB-1.6.5/TMB/NEWS | 34 +++ TMB-1.6.5/TMB/R/TMB.R | 102 +++++++---- TMB-1.6.5/TMB/R/header_tool.R |only TMB-1.6.5/TMB/R/mcmc.R |only TMB-1.6.5/TMB/R/sdreport.R | 87 +++++++-- TMB-1.6.5/TMB/inst/COPYRIGHTS | 2 TMB-1.6.5/TMB/inst/examples/mcmc_examples.R |only TMB-1.6.5/TMB/inst/examples/simple.cpp | 5 TMB-1.6.5/TMB/inst/include/Rstream.hpp | 8 TMB-1.6.5/TMB/inst/include/TMB.hpp | 28 ++- TMB-1.6.5/TMB/inst/include/Vectorize.hpp | 114 ------------- TMB-1.6.5/TMB/inst/include/atomic_macro.hpp | 12 - TMB-1.6.5/TMB/inst/include/atomic_math.hpp | 9 - TMB-1.6.5/TMB/inst/include/checkpoint_macro.hpp | 6 TMB-1.6.5/TMB/inst/include/config.hpp | 25 +- TMB-1.6.5/TMB/inst/include/convenience.hpp | 24 ++ TMB-1.6.5/TMB/inst/include/convert.hpp | 33 +-- TMB-1.6.5/TMB/inst/include/cppad/local/ad_fun.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/for_jac_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/forward0sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/local/forward1sweep.hpp | 16 - TMB-1.6.5/TMB/inst/include/cppad/local/forward2sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/local/fun_construct.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/kasper.hpp | 28 +-- TMB-1.6.5/TMB/inst/include/cppad/local/near_equal_ext.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/optimize.hpp | 12 - TMB-1.6.5/TMB/inst/include/cppad/local/print_for.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/rev_hes_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/rev_jac_sweep.hpp | 10 - TMB-1.6.5/TMB/inst/include/cppad/local/reverse.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/local/reverse_sweep.hpp | 20 +- TMB-1.6.5/TMB/inst/include/cppad/memory_leak.hpp | 17 - TMB-1.6.5/TMB/inst/include/cppad/near_equal.hpp | 7 TMB-1.6.5/TMB/inst/include/cppad/speed_test.hpp | 27 +-- TMB-1.6.5/TMB/inst/include/cppad/thread_alloc.hpp | 13 - TMB-1.6.5/TMB/inst/include/cppad/time_test.hpp | 2 TMB-1.6.5/TMB/inst/include/cppad/track_new_del.hpp | 41 ++-- TMB-1.6.5/TMB/inst/include/cppad/vector.hpp | 4 TMB-1.6.5/TMB/inst/include/precompile.hpp |only TMB-1.6.5/TMB/inst/include/start_parallel.hpp | 20 +- TMB-1.6.5/TMB/inst/include/tmb_core.hpp | 108 +++++++----- TMB-1.6.5/TMB/inst/include/tmbutils/R_inla.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/array.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/autodiff.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/density.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/kronecker.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/matexp.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/order.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/romberg.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/splines.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/spmat.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/tmbutils.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/tmbutils_extra.hpp |only TMB-1.6.5/TMB/inst/include/tmbutils/vector.hpp |only TMB-1.6.5/TMB/man/MakeADFun.Rd | 14 - TMB-1.6.5/TMB/man/compile.Rd | 2 TMB-1.6.5/TMB/man/mcmc.Rd |only TMB-1.6.5/TMB/man/mcmc.hmc.Rd |only TMB-1.6.5/TMB/man/mcmc.nuts.Rd |only TMB-1.6.5/TMB/man/mcmc.rwm.Rd |only TMB-1.6.5/TMB/man/precompile.Rd | 41 +++- TMB-1.6.5/TMB/man/sdreport.Rd | 54 +++++- TMB-1.6.5/TMB/man/summary.sdreport.Rd | 3 79 files changed, 638 insertions(+), 509 deletions(-)
Title: Software for the Analysis of Genetic Architecture
Description: Implements an information theory approach to the analysis of line
cross data providing model averaged results of parameter estimates and
unconditional standard errors. Also includes functions to provide a
visualization of models space, custom plots of multi-model inference results, and traditional
line cross analysis plots.
Author: Heath Blackmon and Jeffery P. Demuth
Maintainer: Heath Blackmon <coleoguy@gmail.com>
Diff between SAGA versions 1.0 dated 2015-09-07 and 2.0.0 dated 2015-12-03
SAGA-1.0/SAGA/inst/Cmatrix.mp.csv |only SAGA-1.0/SAGA/inst/doc/model-averaged-analysis.html |only SAGA-1.0/SAGA/vignettes/1.png |only SAGA-1.0/SAGA/vignettes/2.png |only SAGA-1.0/SAGA/vignettes/3.png |only SAGA-1.0/SAGA/vignettes/4.png |only SAGA-1.0/SAGA/vignettes/5.png |only SAGA-1.0/SAGA/vignettes/6.png |only SAGA-2.0.0/SAGA/DESCRIPTION | 15 SAGA-2.0.0/SAGA/MD5 | 43 - SAGA-2.0.0/SAGA/NAMESPACE | 12 SAGA-2.0.0/SAGA/R/AICtoMW.R |only SAGA-2.0.0/SAGA/R/AnalyzeCrossesMM.R | 151 ++++-- SAGA-2.0.0/SAGA/R/DisplayCmatrix.R | 15 SAGA-2.0.0/SAGA/R/cohortID.R |only SAGA-2.0.0/SAGA/R/plot.genarch.R |only SAGA-2.0.0/SAGA/R/plotObserved.R |only SAGA-2.0.0/SAGA/build/vignette.rds |binary SAGA-2.0.0/SAGA/inst/cmatrix.esd.csv |only SAGA-2.0.0/SAGA/inst/cmatrix.xy.csv |only SAGA-2.0.0/SAGA/inst/cmatrix.zw.csv |only SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.R | 72 ++ SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.Rmd | 442 ++++++++++++++---- SAGA-2.0.0/SAGA/inst/doc/model-averaged-analysis.pdf |only SAGA-2.0.0/SAGA/inst/genome.scale.csv |only SAGA-2.0.0/SAGA/man/AICtoMW.Rd |only SAGA-2.0.0/SAGA/man/AnalyzeCrossesMM.Rd | 19 SAGA-2.0.0/SAGA/man/DisplayCmatrix.Rd | 8 SAGA-2.0.0/SAGA/man/SAGA-package.Rd | 6 SAGA-2.0.0/SAGA/man/cohortID.Rd |only SAGA-2.0.0/SAGA/man/plot.genarch.Rd |only SAGA-2.0.0/SAGA/man/plotObserved.Rd |only SAGA-2.0.0/SAGA/vignettes/model-averaged-analysis.Rmd | 442 ++++++++++++++---- 33 files changed, 924 insertions(+), 301 deletions(-)
Title: Random Ferns Classifier
Description: An R implementation of the random ferns classifier by Ozuysal et al., modified for generic and multi-label classification and featuring OOB error approximation and importance measure.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between rFerns versions 1.1.0 dated 2014-11-30 and 2.0.0 dated 2015-12-03
rFerns-1.1.0/rFerns/man/rFerns.predict.Rd |only rFerns-2.0.0/rFerns/DESCRIPTION | 8 - rFerns-2.0.0/rFerns/MD5 | 22 +-- rFerns-2.0.0/rFerns/NAMESPACE | 12 + rFerns-2.0.0/rFerns/R/ferns.R | 206 ++++++++++++++++++++++++++---- rFerns-2.0.0/rFerns/R/tools.R |only rFerns-2.0.0/rFerns/inst/NEWS | 10 + rFerns-2.0.0/rFerns/man/merge.rFerns.Rd |only rFerns-2.0.0/rFerns/man/predict.rFerns.Rd |only rFerns-2.0.0/rFerns/man/rFerns.Rd | 132 +++++++++++-------- rFerns-2.0.0/rFerns/src/fern.h | 155 ++++++++++++++++++++++ rFerns-2.0.0/rFerns/src/ferns.c | 43 ++++-- rFerns-2.0.0/rFerns/src/forest.h | 145 +++++++++------------ rFerns-2.0.0/rFerns/src/tools.h | 25 +++ 14 files changed, 564 insertions(+), 194 deletions(-)
Title: Partial and Semi-Partial (Part) Correlation
Description: Calculates partial and semi-partial
(part) correlations along with p-value.
Author: Seongho Kim
Maintainer: Seongho Kim <biostatistician.kim@gmail.com>
Diff between ppcor versions 1.0 dated 2011-06-15 and 1.1 dated 2015-12-03
ppcor-1.0/ppcor/R/ppcor_v1.R |only ppcor-1.1/ppcor/DESCRIPTION | 14 ++++++++------ ppcor-1.1/ppcor/MD5 |only ppcor-1.1/ppcor/NAMESPACE |only ppcor-1.1/ppcor/R/ppcor_v1.01.R |only ppcor-1.1/ppcor/man/pcor.Rd | 10 ++++------ ppcor-1.1/ppcor/man/pcor.test.Rd | 10 ++++------ ppcor-1.1/ppcor/man/ppcor-package.Rd | 12 +++++------- ppcor-1.1/ppcor/man/spcor.Rd | 10 ++++------ ppcor-1.1/ppcor/man/spcor.test.Rd | 10 ++++------ 10 files changed, 29 insertions(+), 37 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-1 dated 2015-11-20 and 0.1-2 dated 2015-12-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/JRF.Rd | 34 ++++++++++++++++++---------------- man/importance.Rd | 11 ++++++----- 4 files changed, 30 insertions(+), 27 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.1 dated 2015-09-22 and 2.0.2 dated 2015-12-03
DESCRIPTION | 28 ++ MD5 | 70 +++---- NAMESPACE | 4 R/GHCN_FUNCTIONS.R | 361 ++++++++++++++++++++++++++++++++++--- R/SSURGO_FUNCTIONS.R | 43 ++-- R/UTILITY_FUNCTIONS.R | 18 + man/curl_download.Rd | 2 man/download_ghcn_daily_station.Rd | 2 man/download_huc4.Rd | 2 man/download_itrdb.Rd | 4 man/download_ned_tile.Rd | 8 man/download_nhd_subregion.Rd | 2 man/download_ssurgo_inventory.Rd | 2 man/download_ssurgo_study_area.Rd | 4 man/extract_ssurgo_data.Rd | 4 man/get_ghcn_daily.Rd | 152 ++++++++++++++- man/get_ghcn_daily_station.Rd | 142 ++++++++++++++ man/get_ghcn_inventory.Rd | 4 man/get_huc4.Rd | 6 man/get_itrdb.Rd | 16 - man/get_ned.Rd | 4 man/get_ned_tile.Rd | 8 man/get_nhd.Rd | 6 man/get_nhd_subregion.Rd | 4 man/get_ssurgo.Rd | 8 man/get_ssurgo_inventory.Rd | 4 man/get_ssurgo_study_area.Rd | 10 - man/pkg_test.Rd | 2 man/polygon_from_extent.Rd | 4 man/read_crn.Rd | 4 man/read_crn_data.Rd | 4 man/read_crn_metadata.Rd | 4 man/sequential_duplicated.Rd | 2 man/spdf_from_polygon.Rd | 2 man/station_to_data_frame.Rd |only man/substr_right.Rd | 2 man/unwrap_rows.Rd |only 37 files changed, 789 insertions(+), 153 deletions(-)
Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of
JSON like document that support JavaScript typed data (https://github.com/amaurel/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>
Diff between rtson versions 1.0 dated 2015-11-25 and 1.1 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 1 + R/deserializer.R | 19 ++++++++++++++----- R/utils.R | 16 ++++++++++++++++ README.md | 8 ++++++++ man/tson.scalar.Rd |only tests/testthat/test_rtson.R | 21 ++++++++++++++++----- 8 files changed, 65 insertions(+), 19 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which time-scale cladograms of
fossil taxa into dated phylogenies. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.
Author: David W. Bapst
Maintainer: David W. Bapst <dwbapst@gmail.com>
Diff between paleotree versions 2.5 dated 2015-09-21 and 2.6 dated 2015-12-02
paleotree-2.5/paleotree/R/getSampProbDisc.R |only paleotree-2.5/paleotree/R/getSampRateCont.R |only paleotree-2.5/paleotree/R/simFossilTaxa.R |only paleotree-2.5/paleotree/R/simFossilTaxa_SRCond.R |only paleotree-2.5/paleotree/R/simPaleoTrees.R |only paleotree-2.5/paleotree/man/getSampProbDisc.Rd |only paleotree-2.5/paleotree/man/getSampRateCont.Rd |only paleotree-2.5/paleotree/man/simFossilTaxa.Rd |only paleotree-2.5/paleotree/man/simFossilTaxa_SRCond.Rd |only paleotree-2.5/paleotree/man/simPaleoTrees.Rd |only paleotree-2.6/paleotree/CHANGELOG | 15 + paleotree-2.6/paleotree/DESCRIPTION | 31 +- paleotree-2.6/paleotree/MD5 | 215 +++++++--------- paleotree-2.6/paleotree/NAMESPACE | 7 paleotree-2.6/paleotree/R/DiversityCurves.R | 23 + paleotree-2.6/paleotree/R/SamplingConv.R | 4 paleotree-2.6/paleotree/R/binTimeData.R | 12 paleotree-2.6/paleotree/R/branchClasses.R | 6 paleotree-2.6/paleotree/R/cal3TimePaleoPhy.R | 80 +++-- paleotree-2.6/paleotree/R/cladogeneticTraitCont.R | 33 +- paleotree-2.6/paleotree/R/compareTimescaling.R | 12 paleotree-2.6/paleotree/R/constrainParPaleo.R | 4 paleotree-2.6/paleotree/R/dateNodes.R | 8 paleotree-2.6/paleotree/R/depthRainbow.R | 2 paleotree-2.6/paleotree/R/divCurveFossilRecordSim.R | 33 ++ paleotree-2.6/paleotree/R/durationFreq.R | 24 + paleotree-2.6/paleotree/R/freqRat.R | 66 +++- paleotree-2.6/paleotree/R/horizonSampRate.R | 5 paleotree-2.6/paleotree/R/inverseSurv.R | 9 paleotree-2.6/paleotree/R/macroperforateForam.R | 10 paleotree-2.6/paleotree/R/minBranchLength.R | 10 paleotree-2.6/paleotree/R/modelMethods.R | 4 paleotree-2.6/paleotree/R/modifyTerminalBranches.R | 30 +- paleotree-2.6/paleotree/R/multiDiv.R | 43 +-- paleotree-2.6/paleotree/R/paleotree-package.R | 6 paleotree-2.6/paleotree/R/parentChild2taxonTree.R | 6 paleotree-2.6/paleotree/R/perCapitaRates.R | 9 paleotree-2.6/paleotree/R/plotTraitgram.R | 6 paleotree-2.6/paleotree/R/sampleRanges.R | 22 + paleotree-2.6/paleotree/R/seqTimeList.R | 12 paleotree-2.6/paleotree/R/simFossilRecord.R | 23 + paleotree-2.6/paleotree/R/simFossilRecordInternal.R | 5 paleotree-2.6/paleotree/R/simFossilRecordMethods.R | 15 - paleotree-2.6/paleotree/R/taxa2cladogram.R | 32 +- paleotree-2.6/paleotree/R/taxa2phylo.R | 36 +- paleotree-2.6/paleotree/R/taxonSortPBDBocc.R | 17 - paleotree-2.6/paleotree/R/termTaxa.R | 97 ++++--- paleotree-2.6/paleotree/R/timeLadderTree.R | 4 paleotree-2.6/paleotree/R/timePaleoPhy.R | 14 - paleotree-2.6/paleotree/R/timeSliceTree.R | 26 + paleotree-2.6/paleotree/README | 6 paleotree-2.6/paleotree/man/DiversityCurves.Rd | 41 +-- paleotree-2.6/paleotree/man/SamplingConv.Rd | 9 paleotree-2.6/paleotree/man/SongZhangDicrano.Rd | 11 paleotree-2.6/paleotree/man/binTimeData.Rd | 16 - paleotree-2.6/paleotree/man/branchClasses.Rd | 22 - paleotree-2.6/paleotree/man/cal3TimePaleoPhy.Rd | 100 ++++--- paleotree-2.6/paleotree/man/cladogeneticTraitCont.Rd | 27 +- paleotree-2.6/paleotree/man/communityEcology.Rd | 7 paleotree-2.6/paleotree/man/compareTimescaling.Rd | 8 paleotree-2.6/paleotree/man/constrainParPaleo.Rd | 23 - paleotree-2.6/paleotree/man/createMrBayesConstraints.Rd | 6 paleotree-2.6/paleotree/man/dateNodes.Rd | 10 paleotree-2.6/paleotree/man/degradeTree.Rd | 14 - paleotree-2.6/paleotree/man/depthRainbow.Rd | 4 paleotree-2.6/paleotree/man/divCurveFossilRecordSim.Rd | 7 paleotree-2.6/paleotree/man/durationFreq.Rd | 35 +- paleotree-2.6/paleotree/man/equation2function.Rd | 2 paleotree-2.6/paleotree/man/expandTaxonTree.Rd | 4 paleotree-2.6/paleotree/man/footeValues.Rd | 44 +-- paleotree-2.6/paleotree/man/freqRat.Rd | 68 +++-- paleotree-2.6/paleotree/man/graptDisparity.Rd | 16 - paleotree-2.6/paleotree/man/graptPBDB.Rd | 6 paleotree-2.6/paleotree/man/horizonSampRate.Rd | 9 paleotree-2.6/paleotree/man/inverseSurv.Rd | 39 +- paleotree-2.6/paleotree/man/kanto.Rd | 7 paleotree-2.6/paleotree/man/macroperforateForam.Rd | 34 +- paleotree-2.6/paleotree/man/makePBDBtaxonTree.Rd | 15 - paleotree-2.6/paleotree/man/minBranchLength.Rd | 9 paleotree-2.6/paleotree/man/minCharChange.Rd | 29 +- paleotree-2.6/paleotree/man/modelMethods.Rd | 9 paleotree-2.6/paleotree/man/modifyTerminalBranches.Rd | 22 + paleotree-2.6/paleotree/man/multiDiv.Rd | 52 ++- paleotree-2.6/paleotree/man/nearestNeighborDist.Rd | 17 - paleotree-2.6/paleotree/man/occData2timeList.Rd | 10 paleotree-2.6/paleotree/man/optimPaleo.Rd | 5 paleotree-2.6/paleotree/man/paleotree-package.Rd | 12 paleotree-2.6/paleotree/man/parentChild2taxonTree.Rd | 14 - paleotree-2.6/paleotree/man/perCapitaRates.Rd | 31 +- paleotree-2.6/paleotree/man/perfectParsCharTree.Rd | 8 paleotree-2.6/paleotree/man/plotOccData.Rd | 9 paleotree-2.6/paleotree/man/plotTraitgram.Rd | 4 paleotree-2.6/paleotree/man/pqr2Ps.Rd | 4 paleotree-2.6/paleotree/man/probAnc.Rd | 27 +- paleotree-2.6/paleotree/man/resolveTreeChar.Rd | 20 - paleotree-2.6/paleotree/man/retiolitinae.Rd | 11 paleotree-2.6/paleotree/man/reverseList.Rd | 4 paleotree-2.6/paleotree/man/rootSplit.Rd | 4 paleotree-2.6/paleotree/man/sampleRanges.Rd | 26 + paleotree-2.6/paleotree/man/seqTimeList.Rd | 22 - paleotree-2.6/paleotree/man/simFossilRecord.Rd | 77 +++-- paleotree-2.6/paleotree/man/simFossilRecordMethods.Rd | 14 - paleotree-2.6/paleotree/man/taxa2cladogram.Rd | 29 +- paleotree-2.6/paleotree/man/taxa2phylo.Rd | 29 +- paleotree-2.6/paleotree/man/taxonSortPBDBocc.Rd | 32 +- paleotree-2.6/paleotree/man/taxonTable2taxonTree.Rd | 4 paleotree-2.6/paleotree/man/termTaxa.Rd | 63 ++-- paleotree-2.6/paleotree/man/testEdgeMat.Rd | 3 paleotree-2.6/paleotree/man/timeLadderTree.Rd | 10 paleotree-2.6/paleotree/man/timeList2fourDate.Rd | 3 paleotree-2.6/paleotree/man/timePaleoPhy.Rd | 46 +-- paleotree-2.6/paleotree/man/timeSliceTree.Rd | 20 - paleotree-2.6/paleotree/man/unitLengthTree.Rd | 4 paleotree-2.6/paleotree/tests |only 114 files changed, 1367 insertions(+), 922 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.7.0 dated 2015-10-15 and 0.8.0 dated 2015-12-02
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 5 ++++- R/ndtvAnimationWidget.R | 5 ++++- inst/doc/ndtv.pdf |binary inst/htmlwidgets/ndtvAnimationWidget.js | 19 +++++++++++++++---- man/ndtvAnimationWidget.Rd |only man/stergm.sim.1.Rd | 4 +++- 9 files changed, 43 insertions(+), 19 deletions(-)
Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov models.
These include processing of tracking data, fitting HMMs to movement data, visualization of
data and fitted model, decoding of the state process...
Author: Theo Michelot, Roland Langrock, Toby Patterson, Eric Rexstad
Maintainer: Theo Michelot <theo.michelot@insa-rouen.fr>
Diff between moveHMM versions 1.0 dated 2015-10-23 and 1.1 dated 2015-12-02
moveHMM-1.0/moveHMM/inst/doc/moveHMM-guide.pdf.asis |only moveHMM-1.0/moveHMM/vignettes/moveHMM-guide.pdf.asis |only moveHMM-1.1/moveHMM/DESCRIPTION | 19 +- moveHMM-1.1/moveHMM/MD5 | 133 +++++++++---------- moveHMM-1.1/moveHMM/NAMESPACE | 3 moveHMM-1.1/moveHMM/R/CI.R | 24 +++ moveHMM-1.1/moveHMM/R/angleCI.R | 3 moveHMM-1.1/moveHMM/R/exGen.R | 2 moveHMM-1.1/moveHMM/R/fitHMM.R | 46 +++++- moveHMM-1.1/moveHMM/R/logAlpha.R | 4 moveHMM-1.1/moveHMM/R/logBeta.R | 4 moveHMM-1.1/moveHMM/R/moveHMM.R | 11 - moveHMM-1.1/moveHMM/R/parDef.R | 19 +- moveHMM-1.1/moveHMM/R/plotPR.R | 21 ++- moveHMM-1.1/moveHMM/R/plotStates.R | 4 moveHMM-1.1/moveHMM/R/plot_moveData.R | 1 moveHMM-1.1/moveHMM/R/plot_moveHMM.R | 53 ++++--- moveHMM-1.1/moveHMM/R/prepData.R | 1 moveHMM-1.1/moveHMM/R/print_moveHMM.R | 30 ---- moveHMM-1.1/moveHMM/R/pseudoRes.R | 9 - moveHMM-1.1/moveHMM/R/simData.R | 127 ++++++++++++++---- moveHMM-1.1/moveHMM/R/summary_moveData.R | 5 moveHMM-1.1/moveHMM/R/viterbi.R | 4 moveHMM-1.1/moveHMM/README.md |only moveHMM-1.1/moveHMM/build/vignette.rds |binary moveHMM-1.1/moveHMM/data/example.RData |binary moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.R |only moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.Rnw |only moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.pdf |binary moveHMM-1.1/moveHMM/man/AIC.moveHMM.Rd | 3 moveHMM-1.1/moveHMM/man/CI.Rd | 3 moveHMM-1.1/moveHMM/man/allProbs.Rd | 2 moveHMM-1.1/moveHMM/man/angleCI.Rd | 2 moveHMM-1.1/moveHMM/man/dexp_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dgamma_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dlnorm_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dvm_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dweibull_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dwrpcauchy_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/exGen.Rd | 2 moveHMM-1.1/moveHMM/man/example.Rd | 2 moveHMM-1.1/moveHMM/man/fitHMM.Rd | 7 - moveHMM-1.1/moveHMM/man/is.moveData.Rd | 2 moveHMM-1.1/moveHMM/man/is.moveHMM.Rd | 2 moveHMM-1.1/moveHMM/man/logAlpha.Rd | 2 moveHMM-1.1/moveHMM/man/logBeta.Rd | 2 moveHMM-1.1/moveHMM/man/moveData.Rd | 2 moveHMM-1.1/moveHMM/man/moveHMM.Rd | 10 - moveHMM-1.1/moveHMM/man/n2w.Rd | 3 moveHMM-1.1/moveHMM/man/nLogLike.Rd | 3 moveHMM-1.1/moveHMM/man/nLogLike_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/parDef.Rd | 5 moveHMM-1.1/moveHMM/man/plot.moveData.Rd | 3 moveHMM-1.1/moveHMM/man/plot.moveHMM.Rd | 9 + moveHMM-1.1/moveHMM/man/plotPR.Rd | 12 + moveHMM-1.1/moveHMM/man/plotStates.Rd | 3 moveHMM-1.1/moveHMM/man/prepData.Rd | 3 moveHMM-1.1/moveHMM/man/print.moveHMM.Rd | 3 moveHMM-1.1/moveHMM/man/pseudoRes.Rd | 5 moveHMM-1.1/moveHMM/man/simData.Rd | 49 ++++--- moveHMM-1.1/moveHMM/man/stateProbs.Rd | 3 moveHMM-1.1/moveHMM/man/summary.moveData.Rd | 3 moveHMM-1.1/moveHMM/man/trMatrix_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/turnAngle.Rd | 2 moveHMM-1.1/moveHMM/man/viterbi.Rd | 3 moveHMM-1.1/moveHMM/man/w2n.Rd | 4 moveHMM-1.1/moveHMM/tests/testthat/test_fitHMM.R | 1 moveHMM-1.1/moveHMM/tests/testthat/test_parDef.R | 4 moveHMM-1.1/moveHMM/vignettes/models.RData |only moveHMM-1.1/moveHMM/vignettes/moveHMM-guide.Rnw |only moveHMM-1.1/moveHMM/vignettes/step_angle_figure.pdf |only moveHMM-1.1/moveHMM/vignettes/struct.pdf |only 72 files changed, 433 insertions(+), 265 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and timespans: fast and user
friendly parsing of date-time data, extraction and updating of components of
a date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and timespan objects. The 'lubridate' package has
a consistent and memorable syntax that makes working with dates easy and
fun.
Author: Garrett Grolemund [aut],
Vitalie Spinu [aut, cre],
Hadley Wickham [aut],
Jan Lyttle [ctb],
Imanuel Constigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.3.3 dated 2013-12-31 and 1.5.0 dated 2015-12-02
lubridate-1.3.3/lubridate/NEWS |only lubridate-1.3.3/lubridate/inst/tests |only lubridate-1.3.3/lubridate/man/ceiling_date.Rd |only lubridate-1.3.3/lubridate/man/dseconds.Rd |only lubridate-1.3.3/lubridate/man/floor_date.Rd |only lubridate-1.3.3/lubridate/man/is.duration.Rd |only lubridate-1.3.3/lubridate/man/is.interval.Rd |only lubridate-1.3.3/lubridate/man/is.period.Rd |only lubridate-1.3.3/lubridate/man/lubridate.Rd |only lubridate-1.3.3/lubridate/man/lubridate_formats.Rd |only lubridate-1.3.3/lubridate/man/new_difftime.Rd |only lubridate-1.3.3/lubridate/man/new_duration.Rd |only lubridate-1.3.3/lubridate/man/new_interval.Rd |only lubridate-1.3.3/lubridate/man/new_period.Rd |only lubridate-1.3.3/lubridate/man/seconds.Rd |only lubridate-1.3.3/lubridate/man/seconds_to_period.Rd |only lubridate-1.3.3/lubridate/man/sundays.Rd |only lubridate-1.3.3/lubridate/man/wday.Rd |only lubridate-1.3.3/lubridate/man/yday.Rd |only lubridate-1.3.3/lubridate/tests/test-all.R |only lubridate-1.5.0/lubridate/DESCRIPTION | 81 +-- lubridate-1.5.0/lubridate/MD5 | 298 ++++++------- lubridate-1.5.0/lubridate/NAMESPACE | 50 +- lubridate-1.5.0/lubridate/NEWS.md |only lubridate-1.5.0/lubridate/R/POSIXt.r | 16 lubridate-1.5.0/lubridate/R/accessors-day.r | 143 +++--- lubridate-1.5.0/lubridate/R/accessors-dst.r | 6 lubridate-1.5.0/lubridate/R/accessors-hour.r | 11 lubridate-1.5.0/lubridate/R/accessors-minute.r | 9 lubridate-1.5.0/lubridate/R/accessors-month.r | 69 ++- lubridate-1.5.0/lubridate/R/accessors-second.r | 7 lubridate-1.5.0/lubridate/R/accessors-tz.r | 11 lubridate-1.5.0/lubridate/R/accessors-week.r | 30 - lubridate-1.5.0/lubridate/R/accessors-year.r | 21 lubridate-1.5.0/lubridate/R/coercion.r | 293 ++++++++----- lubridate-1.5.0/lubridate/R/constants.r |only lubridate-1.5.0/lubridate/R/decimal-dates.r | 60 +- lubridate-1.5.0/lubridate/R/deprecated.r |only lubridate-1.5.0/lubridate/R/difftimes.r | 117 +++-- lubridate-1.5.0/lubridate/R/durations.r | 389 ++++++++---------- lubridate-1.5.0/lubridate/R/epochs.r | 16 lubridate-1.5.0/lubridate/R/guess.r | 322 ++++++-------- lubridate-1.5.0/lubridate/R/help.r | 13 lubridate-1.5.0/lubridate/R/instants.r | 2 lubridate-1.5.0/lubridate/R/intervals.r | 217 +++++----- lubridate-1.5.0/lubridate/R/ops-%m+%.r | 169 ++++--- lubridate-1.5.0/lubridate/R/ops-addition.r | 22 - lubridate-1.5.0/lubridate/R/ops-division.r | 35 - lubridate-1.5.0/lubridate/R/ops-modulo.r | 27 - lubridate-1.5.0/lubridate/R/parse.r | 176 ++++---- lubridate-1.5.0/lubridate/R/periods.r | 452 +++++++++------------ lubridate-1.5.0/lubridate/R/pretty.r | 62 +- lubridate-1.5.0/lubridate/R/round.r | 208 ++++----- lubridate-1.5.0/lubridate/R/stamp.r | 13 lubridate-1.5.0/lubridate/R/timespans.r | 51 ++ lubridate-1.5.0/lubridate/R/update.r | 216 +++++----- lubridate-1.5.0/lubridate/R/util.r | 2 lubridate-1.5.0/lubridate/README.md |only lubridate-1.5.0/lubridate/build/vignette.rds |binary lubridate-1.5.0/lubridate/inst/doc/lubridate.R | 25 - 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lubridate-1.5.0/lubridate/man/guess_formats.Rd | 34 - lubridate-1.5.0/lubridate/man/here.Rd | 10 lubridate-1.5.0/lubridate/man/hm.Rd | 32 - lubridate-1.5.0/lubridate/man/hms.Rd | 36 - lubridate-1.5.0/lubridate/man/hour.Rd | 15 lubridate-1.5.0/lubridate/man/int_aligns.Rd | 26 - lubridate-1.5.0/lubridate/man/int_diff.Rd | 19 lubridate-1.5.0/lubridate/man/int_end.Rd | 20 lubridate-1.5.0/lubridate/man/int_flip.Rd | 21 lubridate-1.5.0/lubridate/man/int_length.Rd | 17 lubridate-1.5.0/lubridate/man/int_overlaps.Rd | 19 lubridate-1.5.0/lubridate/man/int_shift.Rd | 26 - lubridate-1.5.0/lubridate/man/int_standardize.Rd | 12 lubridate-1.5.0/lubridate/man/int_start.Rd | 20 lubridate-1.5.0/lubridate/man/interval.Rd |only lubridate-1.5.0/lubridate/man/is.Date.Rd | 13 lubridate-1.5.0/lubridate/man/is.POSIXt.Rd | 14 lubridate-1.5.0/lubridate/man/is.difftime.Rd | 16 lubridate-1.5.0/lubridate/man/is.instant.Rd | 17 lubridate-1.5.0/lubridate/man/is.timespan.Rd | 15 lubridate-1.5.0/lubridate/man/lakers.Rd | 22 - 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Title: Robust Geostatistical Analysis of Spatial Data
Description: The georob package provides functions for efficiently fitting
linear models with spatially correlated errors by robust and
Gaussian (Restricted) Maximum Likelihood and for computing robust
and customary point and block external-drift kriging predictions,
along with utility functions for variogram modelling
in ad-hoc geostatistical analyses, model building, model evaluation
by cross-validation and for unbiased back-transformation of kriging
predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.2-1 dated 2015-09-02 and 0.2-2 dated 2015-12-02
ChangeLog | 12 + DESCRIPTION | 10 MD5 | 47 ++-- NAMESPACE | 10 NEWS | 2 R/georob.S3methods.R | 2 R/georob.cv.R | 158 +++++++++----- R/georob.exported.functions.R | 86 ++++++-- R/georob.predict.R | 136 +++++++----- R/georob.private.functions.R | 76 +++++-- R/variogram.R | 447 ++++++++++++++++++++++++++++++++++-------- man/S3methods.georob.Rd | 10 man/compress.Rd | 4 man/control.georob.Rd | 20 - man/cv.georob.Rd | 10 man/fit.variogram.model.Rd | 62 ++--- man/georob.Rd | 123 ++++++----- man/georobModelBuilding.Rd | 2 man/lgnpp.Rd | 6 man/param.defaults.Rd |only man/plot.georob.Rd | 81 +++++-- man/predict.georob.Rd | 6 man/profilelogLik.Rd | 15 - man/sample.variogram.Rd | 72 +++++- man/validate.predictions.Rd | 27 +- 25 files changed, 991 insertions(+), 433 deletions(-)
Title: Batch Effect Removal (in Phenotype Prediction using Gene Data)
Description: Various tools dealing with batch effects, in particular enabling the
removal of discrepancies between training and test sets in prediction scenarios.
The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA,
mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide
an additional function which enables a posteriori ('addon') batch effect removal
in independent batches ('test data'). Here, the (already batch effect adjusted)
training data is not altered. For evaluating the success of batch effect adjustment
several metrics are provided. Moreover, the package implements a plot for the
visualization of batch effects using principal component analysis. The main functions
of the package are ba() and baaddon() which enable batch effect removal and addon
batch effect removal, respectively, with one of the seven methods mentioned above.
Another important function is bametric() which is a wrapper function for all implemented
methods for evaluating the success of batch effect removal.
Author: Roman Hornung, David Causeur
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between bapred versions 0.1 dated 2015-09-04 and 0.2 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/svaba.R | 41 ++++++++++++++++++++++++++++------------- R/svabaaddon.R | 12 ++++++++---- 4 files changed, 42 insertions(+), 23 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.2.0 dated 2015-11-23 and 1.2.1 dated 2015-12-02
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/pnea.R | 10 ++++++++-- man/pnea.Rd | 10 +++------- 4 files changed, 19 insertions(+), 17 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided.
'CCTZ' is a C++ library for translating between absolute and civil times
using the rules of a time zone.
The 'CCTZ' source code, released under the Apache 2.0 License, is included in
this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.0.1 dated 2015-12-01 and 0.0.2 dated 2015-12-02
ChangeLog | 11 +++++++++++ DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ README.md | 6 ++++-- inst/NEWS.Rd |only inst/include/src/cctz_libc.h | 4 ++++ src/cctz_if.cc | 4 +++- src/cctz_libc.cc | 4 ++++ 8 files changed, 37 insertions(+), 13 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-01 dated 2015-09-30 and 1.3-02 dated 2015-12-02
DESCRIPTION | 13 +++++++------ MD5 | 21 ++++++++++++++------- NAMESPACE | 5 ++++- NEWS | 4 ++++ R/SampleSize.R | 8 ++++---- R/power_RSABE_pure.R |only R/power_scABEL.R | 4 ++-- R/power_scABEL_pure.R |only R/power_type1_2TOST.R |only R/sampleN_2TOST.R |only man/power.2TOST.Rd |only man/power.NTIDFDA.Rd | 19 ++++++++++++++++++- man/sampleN.2TOST.Rd |only man/sampleN.NTIDFDA.Rd | 14 +++++++++++++- man/type1error.2TOST.Rd |only 15 files changed, 66 insertions(+), 22 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.3-1 dated 2015-11-16 and 4.3-2 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 12 ++++++++++++ R/metacont.R | 12 ++++-------- R/metaprop.R | 2 +- 5 files changed, 25 insertions(+), 17 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.2.3 dated 2015-10-09 and 1.3.2 dated 2015-12-02
HelpersMG-1.2.3/HelpersMG/R/compassRose2.R |only HelpersMG-1.2.3/HelpersMG/R/map.scale2.R |only HelpersMG-1.2.3/HelpersMG/man/compassRose2.Rd |only HelpersMG-1.2.3/HelpersMG/man/map.scale2.Rd |only HelpersMG-1.3.2/HelpersMG/DESCRIPTION | 10 - HelpersMG-1.3.2/HelpersMG/MD5 | 96 ++++++++--------- HelpersMG-1.3.2/HelpersMG/NAMESPACE | 6 - HelpersMG-1.3.2/HelpersMG/NEWS | 7 + HelpersMG-1.3.2/HelpersMG/R/BinomialConfidence.R | 2 HelpersMG-1.3.2/HelpersMG/R/HelpersMG-package.R | 4 HelpersMG-1.3.2/HelpersMG/R/MHalgoGen.R | 29 ++--- HelpersMG-1.3.2/HelpersMG/R/ind_long_lat.R | 31 ++--- HelpersMG-1.3.2/HelpersMG/R/local.search.R | 2 HelpersMG-1.3.2/HelpersMG/R/newcompassRose.R |only HelpersMG-1.3.2/HelpersMG/R/newmap.scale.R |only HelpersMG-1.3.2/HelpersMG/R/plot.mcmcComposite.R | 7 - HelpersMG-1.3.2/HelpersMG/R/similar.R | 2 HelpersMG-1.3.2/HelpersMG/R/wget.R | 2 HelpersMG-1.3.2/HelpersMG/man/ChangeCoordinate.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/HelpersMG-package.Rd | 38 +++--- HelpersMG-1.3.2/HelpersMG/man/LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/MHalgoGen.Rd | 28 ++-- HelpersMG-1.3.2/HelpersMG/man/ScalePreviousPlot.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/as.mcmc.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/as.parameters.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/asc.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/barplot_errbar.Rd | 22 +-- HelpersMG-1.3.2/HelpersMG/man/chr.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/clean.knitr.Rd | 4 HelpersMG-1.3.2/HelpersMG/man/compare_AIC.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/convert.tz.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/growlnotify.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/ind_long_lat.Rd | 11 + HelpersMG-1.3.2/HelpersMG/man/index.periodic.Rd | 20 +-- HelpersMG-1.3.2/HelpersMG/man/inside.search.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/local.search.Rd | 4 HelpersMG-1.3.2/HelpersMG/man/logLik.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/merge.mcmcComposite.Rd | 28 ++-- HelpersMG-1.3.2/HelpersMG/man/minmax.periodic.Rd | 22 +-- HelpersMG-1.3.2/HelpersMG/man/moon.info.Rd | 14 +- HelpersMG-1.3.2/HelpersMG/man/newcompassRose.Rd |only HelpersMG-1.3.2/HelpersMG/man/newmap.scale.Rd |only HelpersMG-1.3.2/HelpersMG/man/plot.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/plot.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/plot_add.Rd | 8 - HelpersMG-1.3.2/HelpersMG/man/plot_errbar.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/predict.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/read_folder.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/similar.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/summary.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/sun.info.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/tide.info.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/wget.Rd | 4 53 files changed, 304 insertions(+), 299 deletions(-)
Title: wrapper for the Gnu Scientific Library
Description:
An R wrapper for the special functions and quasi random number
generators of the Gnu Scientific Library
(http://www.gnu.org/software/gsl/). See gsl-package.Rd for details of
overall package organization, and Misc.Rd for some functions that are
widely used in the package, and some tips on installation.
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and
multimin by Andrew Clausen
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 1.9-10 dated 2013-12-10 and 1.9-10.1 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- configure | 2 +- configure.ac | 2 +- src/ellint.c | 5 +++++ src/legendre.c | 6 ++++++ 6 files changed, 22 insertions(+), 11 deletions(-)
Title: Zelig Choice Models
Description: Add-on package for Zelig 5. Enables the use of a variety of logit
and probit regressions.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between ZeligChoice versions 0.8-1 dated 2013-09-23 and 0.9-0 dated 2015-12-02
ZeligChoice-0.8-1/ZeligChoice/R/ZeligChoice-package.R |only ZeligChoice-0.8-1/ZeligChoice/R/blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/common-methods.R |only ZeligChoice-0.8-1/ZeligChoice/R/describe.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/summarize.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/summarize.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/build |only ZeligChoice-0.8-1/ZeligChoice/demo/blogit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/ologit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/inst/doc |only ZeligChoice-0.8-1/ZeligChoice/man/ZeligChoice-package.R.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.mlogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/summarize.ologit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/summarize.oprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2mlogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2ologit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2oprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/tests/tests.R |only ZeligChoice-0.8-1/ZeligChoice/vignettes |only ZeligChoice-0.9-0/ZeligChoice/DESCRIPTION | 30 +--- ZeligChoice-0.9-0/ZeligChoice/MD5 | 89 ++++-------- ZeligChoice-0.9-0/ZeligChoice/NAMESPACE | 54 ++----- ZeligChoice-0.9-0/ZeligChoice/R/create-json.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-bbinchoice.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-blogit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-bprobit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-mlogit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-obinchoice.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-ologit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-oprobit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/00Index | 10 - ZeligChoice-0.9-0/ZeligChoice/demo/demo-blogit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-bprobit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-mlogit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-ologit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-oprobit.R |only ZeligChoice-0.9-0/ZeligChoice/inst/JSON |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-bbinchoice-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-blogit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-bprobit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-mlogit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-obinchoice-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-ologit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-oprobit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/construct.v.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/createJSONzeligchoice.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/ev.mlogit.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/pv.mlogit.Rd |only ZeligChoice-0.9-0/ZeligChoice/tests/testthat |only ZeligChoice-0.9-0/ZeligChoice/tests/testthat.R |only 80 files changed, 67 insertions(+), 116 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.4.0 dated 2015-11-26 and 0.4.1 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 20 +++++++++++--------- R/bigsearch.R | 32 +++++++++++++++++--------------- R/searchbyterm.R | 14 +++++++------- R/vert_id.R | 12 +++++++----- R/vertmap.R | 3 ++- build/vignette.rds |binary man/bigsearch.Rd | 2 +- man/vert_id.Rd | 13 +++++++++---- tests/testthat/test-dump.R |only tests/testthat/test-vert_id.R |only tests/testthat/test-vertmap.R | 14 ++++++++++++++ 12 files changed, 71 insertions(+), 45 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Hart Edmund [ctb],
Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.4.2 dated 2015-07-07 and 0.5.0 dated 2015-12-02
DESCRIPTION | 31 +++-- MD5 | 154 +++++++++++++++------------- NAMESPACE | 26 ++++ R/buoy.R | 78 +++++--------- R/ersst.R |only R/gefs.R |only R/ghcnd.R | 39 +++++-- R/homr_definitions.R | 1 R/isd.R | 202 ++++++++++++++++++++++++++----------- R/isd_stations.R |only R/ncdc.r | 2 R/ncdc_plot.r | 38 +++--- R/ncdc_stations.r | 1 R/rnoaa-package.r | 45 +++++--- R/seaice.r | 5 R/swdi.r | 7 - R/zzz.r | 12 ++ README.md | 191 +++++++++++++--------------------- build/vignette.rds |binary inst/isd_stations.rds |only inst/js/LICENSE-turf-buffer |only inst/js/LICENSE-turf-extent |only man/buoy.Rd | 17 ++- man/caching.Rd | 2 man/check_response.Rd | 2 man/check_response_swdi.Rd | 2 man/erddap_clear_cache-defunct.Rd | 2 man/erddap_data-defunct.Rd | 2 man/erddap_datasets-defunct.Rd | 2 man/erddap_grid-defunct.Rd | 2 man/erddap_info-defunct.Rd | 2 man/erddap_search-defunct.Rd | 2 man/erddap_table-defunct.Rd | 2 man/ersst.Rd |only man/fipscodes.Rd | 2 man/gefs.Rd |only man/ghcnd.Rd | 4 man/homr.Rd | 4 man/homr_definitions.Rd | 2 man/is.ncdc_data.Rd | 2 man/isd.Rd | 63 +++++++++-- man/isd_stations.Rd |only man/ncdc.Rd | 16 +- man/ncdc_combine.Rd | 2 man/ncdc_datacats.Rd | 2 man/ncdc_datasets.Rd | 14 +- man/ncdc_datatypes.Rd | 16 +- man/ncdc_leg_data-defunct.Rd | 2 man/ncdc_leg_site_info-defunct.Rd | 2 man/ncdc_leg_sites-defunct.Rd | 2 man/ncdc_leg_variables-defunct.Rd | 2 man/ncdc_locs.Rd | 2 man/ncdc_locs_cats.Rd | 2 man/ncdc_plot.Rd | 2 man/ncdc_stations.Rd | 26 ++-- man/ncdc_theme.Rd | 2 man/noaa-defunct.Rd | 2 man/noaa_combine-defunct.Rd | 2 man/noaa_datacats-defunct.Rd | 2 man/noaa_datasets-defunct.Rd | 2 man/noaa_datatypes-defunct.Rd | 2 man/noaa_locs-defunct.Rd | 2 man/noaa_locs_cats-defunct.Rd | 2 man/noaa_plot-defunct.Rd | 2 man/noaa_seaice-defunct.Rd | 2 man/noaa_stations-defunct.Rd | 2 man/readshpfile.Rd | 2 man/rnoaa-defunct.Rd | 4 man/rnoaa-package.Rd | 31 ++--- man/seaice.Rd | 2 man/seaiceeurls.Rd | 2 man/storm_columns.Rd | 2 man/storm_names.Rd | 2 man/storms.Rd | 2 man/swdi.Rd | 6 - man/theme_ice.Rd | 2 man/tornadoes.Rd | 2 man/type_summ.Rd | 2 tests/testthat/plot_data.Rds |only tests/testthat/test-buoy.R | 51 +++++++-- tests/testthat/test-gefs.R |only tests/testthat/test-isd.R | 12 -- tests/testthat/test-isd_stations.R |only tests/testthat/test-ncdc_plot.r | 13 +- 84 files changed, 687 insertions(+), 506 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 2.0-0 dated 2015-04-24 and 2.0-1 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 6 ++++++ R/mma.r | 37 +++++++++++++++++++++++++------------ man/boot.med.binx.Rd | 14 +++++++++----- man/boot.med.contx.Rd | 9 ++++++--- man/mma-package.Rd | 7 ++++--- man/mma.Rd | 19 ++++++++++++------- 8 files changed, 73 insertions(+), 41 deletions(-)
Title: Curve Fitting and Mixture Toxicity Assessment
Description: Curve Fitting for monotonic(sigmoidal) & non-monotonic(J-shaped)
concentration-response data. Toxicity prediction of chemical mixtures using reference
models such as 'concentration addition' and 'independent action' (Backhaus, T., Faust,
M., Environmental Science and Technology. 2012, 46, 2564-2573. doi:10.1021/es2034125).
Author: Xiangwei Zhu
Maintainer: Xiangwei Zhu <xwzhunc@gmail.com>
Diff between mixtox versions 1.1 dated 2015-10-19 and 1.2 dated 2015-12-02
DESCRIPTION | 17 ++-- MD5 | 58 +++++++------ NAMESPACE | 2 R/CEx.R | 36 +++++++- R/ECx.R | 21 ++++- R/NOEC.R | 3 R/curveFit.R | 209 ++++++++++++++++++++++++++++++++++++++++---------- R/ecaPred.R | 7 + R/eiaPred.R | 5 - R/gcaHill.R | 4 R/gcaPred.R | 7 + R/iaPred.R | 5 - R/nmECx.R |only R/showEq.R | 45 ++++++++-- data/antibiotox.rda |only data/hormesis.rda |only man/CEx.Rd | 43 +++------- man/ECx.Rd | 49 ++++++----- man/NOEC.Rd | 8 - man/antibiotox.Rd |only man/caPred.Rd | 17 +--- man/curveFit.Rd | 199 +++++++++++++++++++++++++++++++++-------------- man/cytotox.Rd | 20 ++-- man/ecaPred.Rd | 19 ++-- man/eiaPred.Rd | 33 ++++++- man/gcaHill.Rd | 25 +++-- man/gcaPred.Rd | 27 ++---- man/hormesis.Rd |only man/iaPred.Rd | 38 ++++----- man/mixtox-package.Rd | 30 ++++--- man/nmECx.Rd |only man/showEq.Rd | 49 +++++++---- man/unidTab.Rd | 2 33 files changed, 662 insertions(+), 316 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical workflow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and reweighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-8 dated 2015-11-18 and 5.0-9 dated 2015-12-01
DESCRIPTION | 8 - MD5 | 8 - R/model-zelig.R | 37 +++++++- R/plots.R | 237 ++++++++++++++++++++++++++++++++++++++++++++++++++------ R/utils.R | 17 ++-- 5 files changed, 261 insertions(+), 46 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.5 dated 2015-10-01 and 1.5.0.1 dated 2015-12-01
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/Rsomoclu.R | 10 +++++----- data/rgbs.txt.gz |binary man/Rsomoclu.train.Rd | 12 +++++++----- src/Makefile.in | 20 +++++++++++++------- src/Rsomoclu.cpp | 42 +++++++++++++++--------------------------- src/denseCpuKernels.cpp | 4 ++-- src/denseGpuKernels.cu | 28 +++++++++++++--------------- src/mapDistanceFunctions.cpp | 19 ++++++++++--------- src/somoclu.h | 21 ++++++++++++--------- src/sparseCpuKernels.cpp | 4 ++-- src/training.cpp | 40 ++++++++++++++++++++++++++++++---------- tests/R_interface_test.R | 6 ++++-- 14 files changed, 130 insertions(+), 110 deletions(-)
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package,
using external configuration files. This attempts to provide a cleaner
alternative to options().
Author: Sahil Seth [aut, cre],
Yihui Xie [ctb] (kable from knitr R/table.R)
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between params versions 0.3.0 dated 2015-09-22 and 0.4 dated 2015-12-01
params-0.3.0/params/man/write_sheet.Rd |only params-0.4/params/DESCRIPTION | 20 +++---- params-0.4/params/MD5 | 35 +++++++----- params-0.4/params/NAMESPACE | 3 - params-0.4/params/NEWS.md | 5 + params-0.4/params/R/check_args.R |only params-0.4/params/R/conf.R | 4 - params-0.4/params/R/kable.R | 47 +++------------- params-0.4/params/R/pkg-opts.R | 4 - params-0.4/params/R/read-sheet.R | 92 ++++++++++++++++++++++++++------- params-0.4/params/R/write-sheet.R | 32 +++++++++-- params-0.4/params/README.md | 4 + params-0.4/params/inst/conf/build.R |only params-0.4/params/inst/extdata |only params-0.4/params/man/check_args.Rd |only params-0.4/params/man/kable.Rd | 52 +----------------- params-0.4/params/man/opts.Rd | 5 - params-0.4/params/man/params.Rd | 15 ++--- params-0.4/params/man/parse_opts.Rd | 2 params-0.4/params/man/read_sheet.Rd | 66 ++++++++++++++++++++--- 20 files changed, 224 insertions(+), 162 deletions(-)
Title: Analyze Paleontological Time-Series
Description: Facilitates analysis of paleontological sequences of trait values from an evolving lineage. Functions are provided to fit, using maximum likelihood, evolutionary models including unbiased random walks, directional evolution, stasis, Ornstein-Uhlenbeck, punctuated change, and evolutionary models in which traits track some measured covariate.
Author: Gene Hunt
Maintainer: Gene Hunt <hunte@si.edu>
Diff between paleoTS versions 0.4-4 dated 2012-06-12 and 0.5-1 dated 2015-12-01
paleoTS-0.4-4/paleoTS/R/IC.R |only paleoTS-0.4-4/paleoTS/R/LRI.R |only paleoTS-0.4-4/paleoTS/R/akaike.wts.R |only paleoTS-0.4-4/paleoTS/R/as.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/as.paleoTSfit.R |only paleoTS-0.4-4/paleoTS/R/cat.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/compareModels.R |only paleoTS-0.4-4/paleoTS/R/fit.sgs.R |only paleoTS-0.4-4/paleoTS/R/fit3models.R |only paleoTS-0.4-4/paleoTS/R/fitGpunc.R |only paleoTS-0.4-4/paleoTS/R/ln.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/logL.GRW.R |only paleoTS-0.4-4/paleoTS/R/logL.Mult.R |only paleoTS-0.4-4/paleoTS/R/logL.Mult.covTrack.R |only paleoTS-0.4-4/paleoTS/R/logL.SameMs.R |only paleoTS-0.4-4/paleoTS/R/logL.SameVs.R |only paleoTS-0.4-4/paleoTS/R/logL.Stasis.R |only paleoTS-0.4-4/paleoTS/R/logL.URW.R |only paleoTS-0.4-4/paleoTS/R/logL.covTrack.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.GRW.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.OU.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.Stasis.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.URW.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.punc.R |only paleoTS-0.4-4/paleoTS/R/logL.joint.punc.omega.R |only paleoTS-0.4-4/paleoTS/R/logL.punc.R |only paleoTS-0.4-4/paleoTS/R/logL.punc.omega.R |only paleoTS-0.4-4/paleoTS/R/logL.sgs.R |only paleoTS-0.4-4/paleoTS/R/logL.sgs.omega.R |only paleoTS-0.4-4/paleoTS/R/lynchD.R |only paleoTS-0.4-4/paleoTS/R/mle.GRW.R |only paleoTS-0.4-4/paleoTS/R/mle.Stasis.R |only paleoTS-0.4-4/paleoTS/R/mle.URW.R |only paleoTS-0.4-4/paleoTS/R/modelCurves.R |only paleoTS-0.4-4/paleoTS/R/opt.GRW.R |only paleoTS-0.4-4/paleoTS/R/opt.GRW.shift.R |only paleoTS-0.4-4/paleoTS/R/opt.RW.Mult.R |only paleoTS-0.4-4/paleoTS/R/opt.RW.SameMs.R |only paleoTS-0.4-4/paleoTS/R/opt.RW.SameVs.R |only paleoTS-0.4-4/paleoTS/R/opt.Stasis.R |only paleoTS-0.4-4/paleoTS/R/opt.URW.R |only paleoTS-0.4-4/paleoTS/R/opt.covTrack.Mult.R |only paleoTS-0.4-4/paleoTS/R/opt.covTrack.R |only paleoTS-0.4-4/paleoTS/R/opt.joint.GRW.R |only paleoTS-0.4-4/paleoTS/R/opt.joint.OU.R |only paleoTS-0.4-4/paleoTS/R/opt.joint.Stasis.R |only paleoTS-0.4-4/paleoTS/R/opt.joint.URW.R |only paleoTS-0.4-4/paleoTS/R/opt.joint.punc.R |only paleoTS-0.4-4/paleoTS/R/opt.punc.R |only paleoTS-0.4-4/paleoTS/R/opt.sgs.R |only paleoTS-0.4-4/paleoTS/R/ou.M.R |only paleoTS-0.4-4/paleoTS/R/ou.V.R |only paleoTS-0.4-4/paleoTS/R/plot.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/pool.var.R |only paleoTS-0.4-4/paleoTS/R/read.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/shift2gg.R |only paleoTS-0.4-4/paleoTS/R/shifts.R |only paleoTS-0.4-4/paleoTS/R/sim.GRW.R |only paleoTS-0.4-4/paleoTS/R/sim.GRW.shift.R |only paleoTS-0.4-4/paleoTS/R/sim.OU.R |only paleoTS-0.4-4/paleoTS/R/sim.Stasis.R |only paleoTS-0.4-4/paleoTS/R/sim.covTrack.R |only paleoTS-0.4-4/paleoTS/R/sim.punc.R |only paleoTS-0.4-4/paleoTS/R/sim.sgs.R |only paleoTS-0.4-4/paleoTS/R/split4punc.R |only paleoTS-0.4-4/paleoTS/R/std.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/sub.paleoTS.R |only paleoTS-0.4-4/paleoTS/R/test.var.het.R |only paleoTS-0.4-4/paleoTS/man/opt.RW.Mult.Rd |only paleoTS-0.4-4/paleoTS/man/paleoTS-internal.Rd |only paleoTS-0.5-1/paleoTS/DESCRIPTION | 20 +-- paleoTS-0.5-1/paleoTS/MD5 | 128 ++++++------------------ paleoTS-0.5-1/paleoTS/NAMESPACE | 18 +-- paleoTS-0.5-1/paleoTS/R/paleoTS_0.5-1.R |only paleoTS-0.5-1/paleoTS/data/dorsal.spines.rda |binary paleoTS-0.5-1/paleoTS/man/ESD.Rd |only paleoTS-0.5-1/paleoTS/man/IC.Rd | 2 paleoTS-0.5-1/paleoTS/man/LRI.Rd | 5 paleoTS-0.5-1/paleoTS/man/as.paleoTS.Rd | 10 + paleoTS-0.5-1/paleoTS/man/bootSimpleComplex.Rd |only paleoTS-0.5-1/paleoTS/man/cat.paleoTS.Rd | 5 paleoTS-0.5-1/paleoTS/man/compareModels.Rd | 4 paleoTS-0.5-1/paleoTS/man/fit.sgs.Rd | 11 +- paleoTS-0.5-1/paleoTS/man/fit3models.Rd | 16 ++- paleoTS-0.5-1/paleoTS/man/fitGpunc.Rd | 39 +++---- paleoTS-0.5-1/paleoTS/man/fitModeShift.Rd |only paleoTS-0.5-1/paleoTS/man/fitMult.Rd |only paleoTS-0.5-1/paleoTS/man/fitSimple.Rd |only paleoTS-0.5-1/paleoTS/man/logL.GRW.Rd | 7 + paleoTS-0.5-1/paleoTS/man/logL.joint.GRW.Rd | 17 ++- paleoTS-0.5-1/paleoTS/man/lynchD.Rd | 8 - paleoTS-0.5-1/paleoTS/man/modelCurves.Rd | 2 paleoTS-0.5-1/paleoTS/man/opt.GRW.Rd | 14 +- paleoTS-0.5-1/paleoTS/man/opt.GRW.shift.Rd | 12 +- paleoTS-0.5-1/paleoTS/man/opt.covTrack.Rd | 26 +++- paleoTS-0.5-1/paleoTS/man/opt.joint.GRW.Rd | 16 +-- paleoTS-0.5-1/paleoTS/man/paleoTS-package.Rd | 5 paleoTS-0.5-1/paleoTS/man/plot.paleoTS.Rd | 9 - paleoTS-0.5-1/paleoTS/man/sim.OU.Rd | 7 - paleoTS-0.5-1/paleoTS/man/sim.covTrack.Rd | 3 paleoTS-0.5-1/paleoTS/man/sim.punc.Rd | 9 + paleoTS-0.5-1/paleoTS/man/sub.paleoTS.Rd | 2 paleoTS-0.5-1/paleoTS/man/test.var.het.Rd | 13 +- 103 files changed, 197 insertions(+), 211 deletions(-)
Title: Multivariate Survival Trees
Description: Constructs trees for multivariate survival data using marginal and frailty models.
Author: Xiaogang Su [aut],
Peter Calhoun [aut, cre],
Juanjuan Fan [aut]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between MST versions 1.1 dated 2015-08-08 and 1.2 dated 2015-12-01
MST-1.1/MST/R/MST-internal.R |only MST-1.2/MST/DESCRIPTION | 18 +++-- MST-1.2/MST/MD5 | 52 ++++++++-------- MST-1.2/MST/NAMESPACE | 1 MST-1.2/MST/R/MST.R | 104 ++++++++++---------------------- MST-1.2/MST/R/MST.plot.R | 8 -- MST-1.2/MST/R/MST.plot.latex.R | 3 MST-1.2/MST/R/bootstrap.grow.prune.R | 47 +++++--------- MST-1.2/MST/R/bootstrap.size.R | 24 +++---- MST-1.2/MST/R/grow.MST.R | 45 +++---------- MST-1.2/MST/R/is.odd.R | 2 MST-1.2/MST/R/obtain.btree.R | 3 MST-1.2/MST/R/ordinalizeFunc.R | 10 --- MST-1.2/MST/R/partition.MST.R | 43 ++++--------- MST-1.2/MST/R/power.set.R | 2 MST-1.2/MST/R/prune.size.testsample.R | 7 -- MST-1.2/MST/R/rmultime.R | 26 ++------ MST-1.2/MST/R/send.down.R | 49 +++++++-------- MST-1.2/MST/R/sortTree.R | 8 +- MST-1.2/MST/R/splitting.stat.MST2.R | 6 - MST-1.2/MST/man/MST-package.Rd | 5 - MST-1.2/MST/man/MST.Rd | 38 +++++------ MST-1.2/MST/man/MST.plot.Rd | 17 ++--- MST-1.2/MST/man/MST.plot.latex.Rd | 17 ++--- MST-1.2/MST/man/bootstrap.grow.prune.Rd | 15 ++-- MST-1.2/MST/man/grow.MST.Rd | 14 ++-- MST-1.2/MST/man/rmultime.Rd | 24 +++---- MST-1.2/MST/man/send.down.Rd |only 28 files changed, 245 insertions(+), 343 deletions(-)
Title: Simple Utility Providing Terminal Access to all R Functions
Description: A small utility which wraps Rscript and provides access to all R
functions from the shell.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between funr versions 0.1.1 dated 2015-09-23 and 0.2.0 dated 2015-12-01
DESCRIPTION | 12 ++++-- LICENSE |only MD5 | 25 +++++++++----- NAMESPACE | 3 + R/parse_params.R | 44 ++++++++++++++++--------- R/render.R | 4 +- R/sys_script.R |only README.md | 85 +++++++++++++++++++++++++++++++++++++++++-------- inst/scripts/README.md |only inst/scripts/devtools |only inst/scripts/funr | 2 - inst/scripts/lit |only inst/testfun.csv |only man/funr.Rd | 3 + man/render_funr.Rd | 2 - man/setup.Rd | 2 - man/sys.script.Rd |only 17 files changed, 133 insertions(+), 49 deletions(-)
Title: Feature Extraction for Discretely-Sampled Functional Data
Description: Discretely-sampled function is first smoothed. Features
of the smoothed function are then extracted. Some of the key
features include mean value, first and second derivatives,
critical points (i.e. local maxima and minima), curvature of
cunction at critical points, wiggliness of the function, noise
in data, and outliers in data.
Author: Ravi Varadhan, Johns Hopkins University, and MKG Subramaniam,
AT&T Reserach Labs.
Maintainer: Ravi Varadhan <rvaradhan@jhmi.edu>
Diff between features versions 2011.8-2 dated 2011-08-17 and 2015.12-1 dated 2015-12-01
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NAMESPACE | 3 +++ NEWS | 6 ++++++ R/features.R | 14 +++++++------- demo/features.R | 1 + 6 files changed, 27 insertions(+), 16 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.0.3 dated 2015-10-15 and 1.0.4 dated 2015-12-01
cycleRtools-1.0.3/cycleRtools/R/format_tcx2.R |only cycleRtools-1.0.3/cycleRtools/R/read_pwx2.R |only cycleRtools-1.0.3/cycleRtools/R/read_tcx2.R |only cycleRtools-1.0.4/cycleRtools/DESCRIPTION | 11 cycleRtools-1.0.4/cycleRtools/MD5 | 120 +++++----- cycleRtools-1.0.4/cycleRtools/NAMESPACE | 7 cycleRtools-1.0.4/cycleRtools/NEWS | 14 + cycleRtools-1.0.4/cycleRtools/R/GC.R |only cycleRtools-1.0.4/cycleRtools/R/Ptmodels_S3.R | 12 - cycleRtools-1.0.4/cycleRtools/R/RcppExports.R | 23 -- cycleRtools-1.0.4/cycleRtools/R/Wbal.R | 9 cycleRtools-1.0.4/cycleRtools/R/convert_time.R | 16 + cycleRtools-1.0.4/cycleRtools/R/data_doc.R | 7 cycleRtools-1.0.4/cycleRtools/R/format_GC.R |only cycleRtools-1.0.4/cycleRtools/R/format_fit.R | 5 cycleRtools-1.0.4/cycleRtools/R/format_pwx.R | 3 cycleRtools-1.0.4/cycleRtools/R/format_srm.R | 3 cycleRtools-1.0.4/cycleRtools/R/format_tcx.R | 5 cycleRtools-1.0.4/cycleRtools/R/misc.R | 32 +- cycleRtools-1.0.4/cycleRtools/R/mmv.R | 22 - cycleRtools-1.0.4/cycleRtools/R/read.R | 21 - cycleRtools-1.0.4/cycleRtools/R/read_pwx.R | 65 ++--- cycleRtools-1.0.4/cycleRtools/R/read_tcx.R | 125 +++++------ cycleRtools-1.0.4/cycleRtools/R/ride_time.R | 1 cycleRtools-1.0.4/cycleRtools/data/cycling_data.rda |binary cycleRtools-1.0.4/cycleRtools/inst/doc/cycling_analysis.R | 17 - cycleRtools-1.0.4/cycleRtools/inst/doc/cycling_analysis.Rmd | 18 - cycleRtools-1.0.4/cycleRtools/inst/doc/cycling_analysis.html | 24 -- cycleRtools-1.0.4/cycleRtools/man/CP_model_inv.Rd | 2 cycleRtools-1.0.4/cycleRtools/man/GC.Rd |only cycleRtools-1.0.4/cycleRtools/man/LT.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/NP.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/Pt_model.Rd | 4 cycleRtools-1.0.4/cycleRtools/man/Pt_prof.Rd | 7 cycleRtools-1.0.4/cycleRtools/man/TSS.Rd | 2 cycleRtools-1.0.4/cycleRtools/man/Wbal.Rd | 14 + cycleRtools-1.0.4/cycleRtools/man/Wbal_plots.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/convert_time.Rd | 4 cycleRtools-1.0.4/cycleRtools/man/cycling_data.Rd | 4 cycleRtools-1.0.4/cycleRtools/man/diff_section.Rd | 7 cycleRtools-1.0.4/cycleRtools/man/download_elev_data.Rd | 6 cycleRtools-1.0.4/cycleRtools/man/elevation_correct.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/interval_data.Rd | 2 cycleRtools-1.0.4/cycleRtools/man/interval_detect.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/mmv.Rd | 9 cycleRtools-1.0.4/cycleRtools/man/mmv2.Rd | 17 - cycleRtools-1.0.4/cycleRtools/man/predict.Ptmodels.Rd | 2 cycleRtools-1.0.4/cycleRtools/man/pwr_TRIMP.Rd | 2 cycleRtools-1.0.4/cycleRtools/man/read.Rd | 46 +--- cycleRtools-1.0.4/cycleRtools/man/reset.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/ride_time.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/rollmean_smth.Rd | 4 cycleRtools-1.0.4/cycleRtools/man/smth_plot.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/summary.cycleRdata.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/uniform.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/zdist_plot.Rd | 5 cycleRtools-1.0.4/cycleRtools/man/zone_index.Rd | 3 cycleRtools-1.0.4/cycleRtools/man/zone_time.Rd | 4 cycleRtools-1.0.4/cycleRtools/src/RcppExports.cpp | 24 +- cycleRtools-1.0.4/cycleRtools/src/Wbal_.cpp | 2 cycleRtools-1.0.4/cycleRtools/src/mmv2_.cpp | 23 -- cycleRtools-1.0.4/cycleRtools/src/rollmean_.cpp | 8 cycleRtools-1.0.4/cycleRtools/src/rollmean_ema_.cpp | 4 cycleRtools-1.0.4/cycleRtools/vignettes/cycling_analysis.Rmd | 18 - 64 files changed, 422 insertions(+), 401 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.3 dated 2015-10-22 and 0.3.1 dated 2015-12-01
RGA-0.3.1/RGA/DESCRIPTION | 15 +- RGA-0.3.1/RGA/MD5 | 136 +++++++++++------------ RGA-0.3.1/RGA/NAMESPACE | 4 RGA-0.3.1/RGA/R/accounts.R | 35 ----- RGA-0.3.1/RGA/R/auth.R | 39 ++++-- RGA-0.3.1/RGA/R/convert.R | 19 +-- RGA-0.3.1/RGA/R/custom-dims.R | 77 +------------ RGA-0.3.1/RGA/R/custom-mets.R | 83 +------------- RGA-0.3.1/RGA/R/custom-sources.R | 39 ------ RGA-0.3.1/RGA/R/date-ranges.R | 4 RGA-0.3.1/RGA/R/experiments.R | 105 +---------------- RGA-0.3.1/RGA/R/filters.R | 90 +-------------- RGA-0.3.1/RGA/R/firstdate.R | 10 - RGA-0.3.1/RGA/R/ga.R | 35 ++--- RGA-0.3.1/RGA/R/get-data.R | 60 +++++----- RGA-0.3.1/RGA/R/goals.R | 79 +------------ RGA-0.3.1/RGA/R/mcf.R | 21 --- RGA-0.3.1/RGA/R/metadata.R | 19 +-- RGA-0.3.1/RGA/R/mgmt.R | 34 ++--- RGA-0.3.1/RGA/R/profiles.R | 92 +-------------- RGA-0.3.1/RGA/R/query.R | 2 RGA-0.3.1/RGA/R/realtime.R | 14 +- RGA-0.3.1/RGA/R/report.R | 47 +++++-- RGA-0.3.1/RGA/R/request.R | 99 ++++++++-------- RGA-0.3.1/RGA/R/segments.R | 33 ----- RGA-0.3.1/RGA/R/unsampled.R | 88 +------------- RGA-0.3.1/RGA/R/uploads.R | 64 +--------- RGA-0.3.1/RGA/R/url.R | 2 RGA-0.3.1/RGA/R/utils.R | 54 ++++++--- RGA-0.3.1/RGA/R/webproperties.R | 84 +------------- RGA-0.3.1/RGA/R/zzz.R | 5 RGA-0.3.1/RGA/inst/NEWS.Rd | 18 +++ RGA-0.3.1/RGA/inst/doc/authorize.Rmd | 34 +---- RGA-0.3.1/RGA/inst/doc/authorize.html | 43 +------ RGA-0.3.1/RGA/man/RGA-package.Rd | 3 RGA-0.3.1/RGA/man/authorize.Rd | 31 +++-- RGA-0.3.1/RGA/man/firstdate.Rd | 16 +- RGA-0.3.1/RGA/man/ga.Rd | 2 RGA-0.3.1/RGA/man/get_custom_dimension.Rd | 51 +++----- RGA-0.3.1/RGA/man/get_custom_metric.Rd | 51 +++----- RGA-0.3.1/RGA/man/get_experiment.Rd | 109 ++++++++---------- RGA-0.3.1/RGA/man/get_filter.Rd | 77 +++++++------ RGA-0.3.1/RGA/man/get_ga.Rd | 31 ++--- RGA-0.3.1/RGA/man/get_goal.Rd | 70 +++++++---- RGA-0.3.1/RGA/man/get_mcf.Rd | 24 +--- RGA-0.3.1/RGA/man/get_profile.Rd | 61 ++++------ RGA-0.3.1/RGA/man/get_realtime.Rd | 19 +-- RGA-0.3.1/RGA/man/get_unsampled_report.Rd | 55 ++++----- RGA-0.3.1/RGA/man/get_upload.Rd | 51 ++++---- RGA-0.3.1/RGA/man/get_webproperty.Rd | 54 +++------ RGA-0.3.1/RGA/man/list_accounts.Rd | 48 +++----- RGA-0.3.1/RGA/man/list_custom_data_sources.Rd |only RGA-0.3.1/RGA/man/list_custom_dimensions.Rd | 48 +++----- RGA-0.3.1/RGA/man/list_custom_metrics.Rd | 48 +++----- RGA-0.3.1/RGA/man/list_dimsmets.Rd | 3 RGA-0.3.1/RGA/man/list_experiments.Rd | 88 ++++++++------ RGA-0.3.1/RGA/man/list_filters.Rd | 85 ++++++++++---- RGA-0.3.1/RGA/man/list_goals.Rd | 79 ++++++++----- RGA-0.3.1/RGA/man/list_profiles.Rd | 64 +++++----- RGA-0.3.1/RGA/man/list_segments.Rd | 53 ++++---- RGA-0.3.1/RGA/man/list_unsampled_reports.Rd | 57 +++++---- RGA-0.3.1/RGA/man/list_uploads.Rd | 51 ++++---- RGA-0.3.1/RGA/man/list_webproperties.Rd | 53 ++++---- RGA-0.3.1/RGA/man/shiny_dimsmets.Rd | 2 RGA-0.3.1/RGA/tests/testthat/test-auth.R | 7 - RGA-0.3.1/RGA/tests/testthat/test-convert-case.R |only RGA-0.3.1/RGA/tests/testthat/test-convert-mcf.R | 42 +++---- RGA-0.3.1/RGA/tests/testthat/test-query.R | 6 - RGA-0.3.1/RGA/vignettes/authorize.Rmd | 34 +---- RGA-0.3/RGA/R/env.R |only RGA-0.3/RGA/man/list_custom_sources.Rd |only 71 files changed, 1215 insertions(+), 1841 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>
Diff between marmap versions 0.9.3 dated 2015-10-06 and 0.9.4 dated 2015-12-01
DESCRIPTION | 12 ++++++------ MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 3 ++- R/as.SpatialGridDataFrame.R | 3 --- R/as.bathy.R | 3 --- R/as.raster.R | 3 --- R/readGEBCO.bathy.R | 8 ++++---- build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary inst/doc/marmap-ImportExport.pdf |binary man/marmap.Rd | 4 ++-- man/readGEBCO.bathy.Rd | 4 ++-- 20 files changed, 35 insertions(+), 43 deletions(-)
Title: Atomic Force Microscope Image Analysis
Description: Provides Atomic Force Microscope images analysis such as Power
Spectrum Density, roughness against lengthscale, variogram and variance,
fractal dimension and scale. The AFM images can be exported to STL format for 3D
printing.
Author: Mathieu Beauvais [aut, cre],
Irma Liascukiene [aut],
Jessem Landoulsi [aut]
Maintainer: Mathieu Beauvais <beauvais.escp@gmail.com>
Diff between AFM versions 1.0.0 dated 2015-10-29 and 1.1.0 dated 2015-12-01
CHANGES |only DESCRIPTION | 13 MD5 | 55 NAMESPACE | 4 R/AFM3DPrinter.R | 23 R/AFMFractalDimensionAnalyser.R | 97 + R/AFMImage.R | 18 R/AFMImageAnalyser.R | 90 - R/AFMPSDAnalyser.R | 282 +++- R/AFMReportMaker.R | 631 +++++----- R/AFMVariogramAnalyser.R | 215 ++- man/AFMFractalDimensionAnalyser-getFractalDimensions.Rd | 6 man/AFMImage-sampleAFMImage.Rd | 4 man/AFMImageAnalyser-class-initialize.Rd | 6 man/AFMImageAnalyser-class.Rd | 4 man/AFMImageFractalDimensionsAnalysis-class.Rd | 2 man/AFMImagePSDAnalysis-class.Rd | 44 man/AFMImageVariogramAnalyser-calculateDirectionalVariograms.Rd | 11 man/AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram.Rd | 11 man/AFMImageVariogramAnalysis-class.Rd | 22 man/AFMImageVariogramAnalysis-evaluateVariogramModels-method.Rd | 12 man/AFMImageVariogramAnalysis-updateProgress-method.Rd |only man/AFMVariogramAnalyser-getSpplotFromAFMImage.Rd |only man/PSD1DAgainstFrequency-methods.Rd | 6 man/PSD2DAgainstFrequency-methods.Rd | 6 man/RoughnessByLengthScale-methods.Rd | 12 man/analyse.Rd | 9 man/checkIsotropy.Rd | 7 man/generateAFMImageReport.Rd | 6 man/performAllPSDCalculation.Rd |only man/printVariogramModelEvaluations.Rd |only 31 files changed, 1075 insertions(+), 521 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.3 dated 2015-10-01 and 0.2.4 dated 2015-12-01
scmamp-0.2.3/scmamp/README.md |only scmamp-0.2.4/scmamp/DESCRIPTION | 10 - scmamp-0.2.4/scmamp/MD5 | 35 ++--- scmamp-0.2.4/scmamp/R/latex.R | 68 +++++++--- scmamp-0.2.4/scmamp/R/scmamp.R | 4 scmamp-0.2.4/scmamp/R/sysdata.rda |binary scmamp-0.2.4/scmamp/build/vignette.rds |binary scmamp-0.2.4/scmamp/data/data_blum_2015.RData |binary scmamp-0.2.4/scmamp/data/data_gh_2008.RData |binary scmamp-0.2.4/scmamp/data/data_gh_2010.RData |binary scmamp-0.2.4/scmamp/inst/CITATION | 24 +-- scmamp-0.2.4/scmamp/inst/doc/Data_loading_and_manipulation.R | 12 - scmamp-0.2.4/scmamp/inst/doc/Data_loading_and_manipulation.Rmd | 2 scmamp-0.2.4/scmamp/inst/doc/Data_loading_and_manipulation.html | 35 +---- scmamp-0.2.4/scmamp/inst/doc/Statistical_assessment_of_the_differences.R | 2 scmamp-0.2.4/scmamp/inst/doc/Statistical_assessment_of_the_differences.Rmd | 2 scmamp-0.2.4/scmamp/inst/doc/Statistical_assessment_of_the_differences.html | 48 +++---- scmamp-0.2.4/scmamp/man/writeTabular.Rd | 20 ++ scmamp-0.2.4/scmamp/vignettes/Data_loading_and_manipulation.Rmd | 2 19 files changed, 156 insertions(+), 108 deletions(-)
Title: International Assessment Data Manager
Description:
Provides tools for importing, merging, and analysing data from
international assessment studies (TIMSS, PIRLS, PISA. ICILS, and PIAAC).
Author: Daniel Caro <daniel.caro@education.ox.ac.uk>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <daniel.caro@education.ox.ac.uk>
Diff between intsvy versions 1.7 dated 2015-07-28 and 1.8 dated 2015-12-01
DESCRIPTION | 14 MD5 | 249 +++--- NAMESPACE | 159 ++-- R/adj.input.R | 22 R/adj.measlev.R | 12 R/intsvy.ben.pv.R |only R/intsvy.config.R |only R/intsvy.log.R |only R/intsvy.log.pv.R |only R/intsvy.mean.R |only R/intsvy.mean.pv.R |only R/intsvy.per.pv.R |only R/intsvy.reg.R |only R/intsvy.reg.pv.R |only R/intsvy.rho.R |only R/intsvy.rho.pv.R |only R/intsvy.select.merge.R |only R/intsvy.table.R |only R/intsvy.var.label.R |only R/is.vlabeled.R | 24 R/piaac.ben.pv.R | 69 - R/piaac.mean.R | 36 R/piaac.mean.pv.R | 19 R/piaac.reg.R | 50 - R/piaac.reg.pv.R | 75 - R/piaac.table.R | 23 R/pirls.ben.pv.R | 51 - R/pirls.log.R | 78 -- R/pirls.log.pv.R | 89 -- R/pirls.mean.R | 36 R/pirls.mean.pv.R | 59 - R/pirls.per.pv.R | 64 - R/pirls.reg.R | 58 - R/pirls.reg.pv.R | 74 - R/pirls.rho.R | 37 R/pirls.rho.pv.R | 80 -- R/pirls.select.merge.R | 239 ------ R/pirls.table.R | 47 - R/pirls.var.label.R | 48 - R/pisa.ben.pv.R | 70 - R/pisa.log.R | 75 - R/pisa.log.pv.R | 94 -- R/pisa.mean.R | 43 - R/pisa.mean.pv.R | 87 -- R/pisa.per.pv.R | 60 - R/pisa.reg.R | 58 - R/pisa.reg.pv.R | 79 -- R/pisa.rho.R | 37 R/pisa.table.R | 64 - R/pisa.var.label.R | 94 +- R/plot.intsvy.mean.R | 72 - R/plot.intsvy.reg.R | 2 R/plot.intsvy.table.R | 110 +- R/surv_conf.R |only R/sysdata.rda |binary R/timss.ben.pv.R | 50 - R/timss.log.R | 78 -- R/timss.log.pv.R | 91 -- R/timss.mean.R | 34 R/timss.mean.pv.R | 60 - R/timss.per.pv.R | 66 - R/timss.reg.R | 60 - R/timss.reg.pv.R | 74 - R/timss.rho.R | 37 R/timss.rho.pv.R | 80 -- R/timss.table.R | 47 - R/timssg4.select.merge.R | 247 ------ R/timssg4.var.label.R | 47 - R/timssg8.select.merge.R | 193 ----- R/timssg8.var.label.R | 44 - README.md | 34 data |only man/adj.input.Rd | 72 - man/adj.measlev.Rd | 76 +- man/confs.Rd |only man/intsvy-package.Rd | 8 man/intsvy.ben.pv.Rd |only man/intsvy.config.Rd |only man/intsvy.log.Rd |only man/intsvy.log.pv.Rd |only man/intsvy.mean.Rd |only man/intsvy.mean.pv.Rd |only man/intsvy.per.pv.Rd |only man/intsvy.reg.Rd |only man/intsvy.reg.pv.Rd |only man/intsvy.rho.Rd |only man/intsvy.rho.pv.Rd |only man/intsvy.select.merge.Rd |only man/intsvy.table.Rd |only man/intsvy.var.label.Rd |only man/is.vlabeled.Rd | 72 - man/piaac.ben.pv.Rd | 109 +- man/piaac.mean.Rd | 94 +- man/piaac.mean.pv.Rd | 96 +- man/piaac.reg.Rd | 100 +- man/piaac.reg.pv.Rd | 106 +- man/piaac.table.Rd | 94 +- man/pirls.ben.pv.Rd | 106 +- man/pirls.log.Rd | 30 man/pirls.log.pv.Rd | 21 man/pirls.mean.Rd | 97 +- man/pirls.mean.pv.Rd | 101 +- man/pirls.per.pv.Rd | 13 man/pirls.reg.Rd | 5 man/pirls.reg.pv.Rd | 5 man/pirls.rho.Rd | 95 +- man/pirls.rho.pv.Rd | 99 +- man/pirls.select.merge.Rd | 24 man/pirls.table.Rd | 95 +- man/pirls.var.label.Rd | 74 - man/pisa.ben.pv.Rd | 96 +- man/pisa.log.Rd | 32 man/pisa.log.pv.Rd | 24 man/pisa.mean.Rd | 107 +- man/pisa.mean.pv.Rd | 113 +- man/pisa.per.pv.Rd | 21 man/pisa.reg.Rd | 9 man/pisa.reg.pv.Rd | 5 man/pisa.rho.Rd | 23 man/pisa.select.merge.Rd | 118 +-- man/pisa.table.Rd | 96 +- man/pisa.var.label.Rd | 96 +- man/plot.intsvy.mean.Rd | 134 +-- man/plot.intsvy.reg.Rd | 8 man/plot.intsvy.table.Rd | 114 +-- man/timss.ben.pv.Rd | 112 +- man/timss.log.Rd | 32 man/timss.log.pv.Rd | 21 man/timss.mean.Rd | 103 +- man/timss.mean.pv.Rd | 103 +- man/timss.per.pv.Rd | 15 man/timss.reg.Rd | 5 man/timss.reg.pv.Rd | 5 man/timss.rho.Rd | 95 +- man/timss.rho.pv.Rd | 99 +- man/timss.table.Rd | 115 +-- man/timssg4.var.label.Rd | 70 - man/timssg8.var.label.Rd | 72 - vignettes/piaac.html | 652 ++++++++--------- vignettes/piaacProficiencyLevels.Rmd | 80 +- vignettes/piaacProficiencyLevels.html | 1288 +++++++++++++++++----------------- 141 files changed, 3362 insertions(+), 5992 deletions(-)
Title: R for Amplicon-Sequencing-Based Microbial-Ecology
Description: Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.
Author: Wen Chen, Joshua Simpson, C. Andre Levesque
Maintainer: Wen Chen <Wen.Chen@agr.gc.ca>
Diff between RAM versions 1.2.1 dated 2015-05-23 and 1.2.1.2 dated 2015-12-01
ChangeLog | 16 + DESCRIPTION | 20 + MD5 | 36 +-- NAMESPACE | 53 ++--- NEWS | 53 +++++ R/group.Taxa.R | 458 +++++++++++++++++++++++--------------------- R/internal_functions.R | 31 -- R/ordination_functions.R | 18 - R/process_data.R | 2 R/seq_var.R | 48 +++- R/summary.R | 174 ++++++++-------- R/taxonomy_functions.R | 126 ++++++------ R/utility_function.R | 4 build/RAM.pdf |binary inst/CITATION | 7 man/group.Taxa.bar.Rd | 23 +- man/group.Taxa.box.Rd | 5 man/group.abundance.meta.Rd | 2 man/seq_var.Rd | 8 19 files changed, 607 insertions(+), 477 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 2.0.2 dated 2015-07-18 and 2.1.0 dated 2015-12-01
poppr-2.0.2/poppr/R/global_memory.R |only poppr-2.0.2/poppr/man/bitwise.IA.Rd |only poppr-2.0.2/poppr/man/snpclone-class.Rd |only poppr-2.0.2/poppr/vignettes/simulated_dist_fig.pdf |only poppr-2.0.2/poppr/vignettes/simulated_param_fig.pdf |only poppr-2.1.0/poppr/DESCRIPTION | 18 poppr-2.1.0/poppr/MD5 | 276 +-- poppr-2.1.0/poppr/NAMESPACE | 23 poppr-2.1.0/poppr/NEWS | 557 +++++-- poppr-2.1.0/poppr/R/Index_calculations.r | 21 poppr-2.1.0/poppr/R/aaaMLGclass.R | 50 poppr-2.1.0/poppr/R/aaaMLGmethods.R | 253 +++ poppr-2.1.0/poppr/R/amova.r | 172 +- poppr-2.1.0/poppr/R/bitwise.r | 286 +-- poppr-2.1.0/poppr/R/bootstraping.R | 82 - poppr-2.1.0/poppr/R/bruvo.r | 80 - poppr-2.1.0/poppr/R/classes.r | 96 - poppr-2.1.0/poppr/R/data_subset.r | 45 poppr-2.1.0/poppr/R/deprecated.R | 4 poppr-2.1.0/poppr/R/distances.r | 22 poppr-2.1.0/poppr/R/file_handling.r | 24 poppr-2.1.0/poppr/R/filter_stats.R | 89 - poppr-2.1.0/poppr/R/global_memory.r |only poppr-2.1.0/poppr/R/imsn.R | 4 poppr-2.1.0/poppr/R/internal.r | 552 +++++-- poppr-2.1.0/poppr/R/internal_methods.R | 4 poppr-2.1.0/poppr/R/messages.r | 4 poppr-2.1.0/poppr/R/methods.r | 166 +- poppr-2.1.0/poppr/R/mlg.r | 10 poppr-2.1.0/poppr/R/poppr.R | 20 poppr-2.1.0/poppr/R/print_methods.r | 27 poppr-2.1.0/poppr/R/round_robin.R |only poppr-2.1.0/poppr/R/sample_schemes.r | 4 poppr-2.1.0/poppr/R/sandbox.r | 69 poppr-2.1.0/poppr/R/visualizations.r | 283 ++- poppr-2.1.0/poppr/R/zzz.r | 17 poppr-2.1.0/poppr/README.md | 62 poppr-2.1.0/poppr/build/vignette.rds |binary poppr-2.1.0/poppr/data/Aeut.rda |binary poppr-2.1.0/poppr/data/Pinf.rda |binary poppr-2.1.0/poppr/data/Pram.rda |binary poppr-2.1.0/poppr/data/monpop.rda |binary poppr-2.1.0/poppr/data/partial_clone.rda |binary poppr-2.1.0/poppr/inst/CITATION | 3 poppr-2.1.0/poppr/inst/doc/algo.R | 2 poppr-2.1.0/poppr/inst/doc/algo.Rnw | 57 poppr-2.1.0/poppr/inst/doc/algo.pdf |binary poppr-2.1.0/poppr/inst/doc/how_to_migrate.pdf |binary poppr-2.1.0/poppr/inst/doc/mlg.html | 36 poppr-2.1.0/poppr/inst/doc/poppr_manual.R | 4 poppr-2.1.0/poppr/inst/doc/poppr_manual.Rnw | 19 poppr-2.1.0/poppr/inst/doc/poppr_manual.pdf |binary poppr-2.1.0/poppr/man/Aeut.Rd | 8 poppr-2.1.0/poppr/man/MLG-accessors.Rd |only poppr-2.1.0/poppr/man/MLG-class.Rd | 45 poppr-2.1.0/poppr/man/MLG-method.Rd | 11 poppr-2.1.0/poppr/man/Pinf.Rd | 22 poppr-2.1.0/poppr/man/Pram.Rd | 53 poppr-2.1.0/poppr/man/aboot.Rd | 121 - poppr-2.1.0/poppr/man/bitwise.dist.Rd | 18 poppr-2.1.0/poppr/man/bitwise.ia.Rd |only poppr-2.1.0/poppr/man/bootgen-class.Rd | 4 poppr-2.1.0/poppr/man/bootgen-methods.Rd | 6 poppr-2.1.0/poppr/man/bruvo.boot.Rd | 51 poppr-2.1.0/poppr/man/bruvo.dist.Rd | 92 - poppr-2.1.0/poppr/man/bruvo.msn.Rd | 142 - poppr-2.1.0/poppr/man/bruvomat-class.Rd | 4 poppr-2.1.0/poppr/man/bruvomat-methods.Rd | 4 poppr-2.1.0/poppr/man/clonecorrect.Rd | 34 poppr-2.1.0/poppr/man/coercion-methods.Rd | 6 poppr-2.1.0/poppr/man/cutoff_predictor.Rd | 31 poppr-2.1.0/poppr/man/deprecated.Rd | 8 poppr-2.1.0/poppr/man/diss.dist.Rd | 19 poppr-2.1.0/poppr/man/diversity_boot.Rd | 38 poppr-2.1.0/poppr/man/diversity_ci.Rd | 82 - poppr-2.1.0/poppr/man/diversity_stats.Rd | 18 poppr-2.1.0/poppr/man/filter_stats.Rd | 33 poppr-2.1.0/poppr/man/fix_replen.Rd | 23 poppr-2.1.0/poppr/man/genclone-class.Rd | 66 poppr-2.1.0/poppr/man/genclone-method.Rd | 6 poppr-2.1.0/poppr/man/genetic_distance.Rd | 54 poppr-2.1.0/poppr/man/genind2genalex.Rd | 42 poppr-2.1.0/poppr/man/genotype_curve.Rd | 40 poppr-2.1.0/poppr/man/getfile.Rd | 12 poppr-2.1.0/poppr/man/greycurve.Rd | 8 poppr-2.1.0/poppr/man/ia.Rd | 180 +- poppr-2.1.0/poppr/man/imsn.Rd | 16 poppr-2.1.0/poppr/man/info_table.Rd | 47 poppr-2.1.0/poppr/man/informloci.Rd | 36 poppr-2.1.0/poppr/man/is.clone.Rd | 4 poppr-2.1.0/poppr/man/levels-methods.Rd | 10 poppr-2.1.0/poppr/man/locus_table.Rd | 51 poppr-2.1.0/poppr/man/missingno.Rd | 55 poppr-2.1.0/poppr/man/mlg.Rd | 67 poppr-2.1.0/poppr/man/mlg.filter.Rd | 68 poppr-2.1.0/poppr/man/mll-method.Rd | 7 poppr-2.1.0/poppr/man/mll.custom.Rd | 4 poppr-2.1.0/poppr/man/mll.reset-method.Rd | 8 poppr-2.1.0/poppr/man/monpop.Rd | 19 poppr-2.1.0/poppr/man/old2new_genclone.Rd | 2 poppr-2.1.0/poppr/man/partial_clone.Rd | 8 poppr-2.1.0/poppr/man/pgen.Rd |only poppr-2.1.0/poppr/man/plot_filter_stats.Rd | 25 poppr-2.1.0/poppr/man/plot_poppr_msn.Rd | 179 +- poppr-2.1.0/poppr/man/poppr-package.Rd | 90 - poppr-2.1.0/poppr/man/poppr.Rd | 227 +- poppr-2.1.0/poppr/man/poppr.all.Rd | 2 poppr-2.1.0/poppr/man/poppr.amova.Rd | 175 +- poppr-2.1.0/poppr/man/poppr.msn.Rd | 126 - poppr-2.1.0/poppr/man/poppr_has_parallel.Rd | 4 poppr-2.1.0/poppr/man/popsub.Rd | 2 poppr-2.1.0/poppr/man/private_alleles.Rd | 25 poppr-2.1.0/poppr/man/psex.Rd |only poppr-2.1.0/poppr/man/read.genalex.Rd | 95 - poppr-2.1.0/poppr/man/recode_polyploids.Rd | 36 poppr-2.1.0/poppr/man/rraf.Rd |only poppr-2.1.0/poppr/man/rrmlg.Rd |only poppr-2.1.0/poppr/man/samp.ia.Rd | 18 poppr-2.1.0/poppr/man/shufflepop.Rd | 24 poppr-2.1.0/poppr/man/snpclone-coercion-methods.Rd | 6 poppr-2.1.0/poppr/man/snpclone-method.Rd | 2 poppr-2.1.0/poppr/man/test_replen.Rd | 18 poppr-2.1.0/poppr/man/unique-methods.Rd | 7 poppr-2.1.0/poppr/man/win.ia.Rd | 28 poppr-2.1.0/poppr/src/bitwise_distance.c | 1145 ++++++++++++--- poppr-2.1.0/poppr/src/mlg_clustering.c | 85 - poppr-2.1.0/poppr/src/mlg_counter.c |only poppr-2.1.0/poppr/src/msn.c | 27 poppr-2.1.0/poppr/src/permut_shuffler.c | 4 poppr-2.1.0/poppr/src/poppr_distance.c | 179 -- poppr-2.1.0/poppr/tests/testthat/test-MLG-class.R |only poppr-2.1.0/poppr/tests/testthat/test-amova.R | 38 poppr-2.1.0/poppr/tests/testthat/test-bitwise.R | 50 poppr-2.1.0/poppr/tests/testthat/test-import.R | 50 poppr-2.1.0/poppr/tests/testthat/test-informloci.R | 8 poppr-2.1.0/poppr/tests/testthat/test-mlg.R | 37 poppr-2.1.0/poppr/tests/testthat/test-msn.R | 74 poppr-2.1.0/poppr/tests/testthat/test-plots.R | 48 poppr-2.1.0/poppr/tests/testthat/test-polyploids.R | 2 poppr-2.1.0/poppr/tests/testthat/test-round-robin.R |only poppr-2.1.0/poppr/tests/testthat/test-trees.R | 22 poppr-2.1.0/poppr/tests/testthat/test-values.R | 72 poppr-2.1.0/poppr/vignettes/algo-concordance.tex | 2 poppr-2.1.0/poppr/vignettes/algo.Rnw | 57 poppr-2.1.0/poppr/vignettes/poppr_manual-concordance.tex | 4 poppr-2.1.0/poppr/vignettes/poppr_manual.Rnw | 19 poppr-2.1.0/poppr/vignettes/the_bibliography.bib | 44 147 files changed, 5210 insertions(+), 2970 deletions(-)
Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the
field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre],
Lúcia Anjos [ths],
Gustavo Vasques [ths],
Gerard Heuvelink [ths],
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb],
Frank Harrell Jr [ctb],
Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-4 dated 2015-11-28 and 0.6-5 dated 2015-12-01
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/pedometrics.R | 4 ++-- R/vgmLags.R | 15 ++------------- man/pedometrics-package.Rd | 4 ++-- 5 files changed, 16 insertions(+), 27 deletions(-)
Title: Visualization and Analysis Tools for Neural Networks
Description: Visualization and analysis tools to aid in the interpretation of
neural network models. Functions are available for plotting,
quantifying variable importance, conducting a sensitivity analysis, and
obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between NeuralNetTools versions 1.3.1 dated 2015-04-27 and 1.4.0 dated 2015-12-01
DESCRIPTION | 11 MD5 | 42 - NAMESPACE | 21 R/NeuralNetTools_gar.R | 398 ++----------- R/NeuralNetTools_lek.R | 329 +++++------ R/NeuralNetTools_neuraldat.R | 5 R/NeuralNetTools_old.R | 437 +++----------- R/NeuralNetTools_plot.R | 1277 +++++-------------------------------------- R/NeuralNetTools_utils.R | 473 ++++++++++++++- README.md | 6 data/neuraldat.RData |binary man/bias_lines.Rd |only man/bias_points.Rd |only man/garson.Rd | 41 - man/get_ys.Rd |only man/layer_lines.Rd |only man/layer_points.Rd |only man/lekgrps.Rd |only man/lekprofile.Rd | 76 +- man/neuraldat.Rd | 4 man/neuralskips.Rd | 6 man/neuralweights.Rd | 13 man/olden.Rd | 54 - man/plotnet.Rd | 100 ++- man/pred_sens.Rd | 14 25 files changed, 1189 insertions(+), 2118 deletions(-)
More information about NeuralNetTools at CRAN
Permanent link
Title: Mixture and Flexible Discriminant Analysis
Description: Mixture and flexible discriminant analysis, multivariate
adaptive regression splines (MARS), BRUTO, ...
Author: S original by Trevor Hastie & Robert Tibshirani. Original R port by Friedrich Leisch, Kurt Hornik and Brian D. Ripley.
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between mda versions 0.4-7 dated 2015-05-25 and 0.4-8 dated 2015-12-01
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NAMESPACE | 5 +++++ data/glass.rda |binary src/mspline.f | 4 +++- src/rat/README |only src/rat/sspl00.r |only src/sspl00.f90 |only 8 files changed, 19 insertions(+), 9 deletions(-)
Title: Latent Structure Learning
Description: Conduct structural equation modeling via penalized likelihood.
Author: Po-Hsien Huang [aut, cre]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>
Diff between lsl versions 0.5.0 dated 2015-07-29 and 0.5.1 dated 2015-12-01
DESCRIPTION | 12 +++--- MD5 | 12 +++--- NAMESPACE | 3 + R/lsl.R | 2 - R/lslSEM.R | 65 +++++++++++++++++++++++++++++++- man/lsl.Rd | 10 ++--- man/lslSEM-class.Rd | 104 ++++++++++++++++++++++++++++++++++++++++------------ 7 files changed, 163 insertions(+), 45 deletions(-)
Title: GPU Computing in R
Description: A general framework for utilizing R to harness the power of NVIDIA GPU's. The "gmatrix" and "gvector" classes allow for easy management of the separate device and host memory spaces. Numerous numerical operations are implemented for these objects on the GPU. These operations include matrix multiplication, addition, subtraction, the kronecker product, the outer product, comparison operators, logical operators, trigonometric functions, indexing, sorting, random number generation and many more.
Author: Nathan Morris
Maintainer: Nathan Morris <njm18@case.edu>
Diff between gmatrix versions 0.2 dated 2014-08-26 and 0.3 dated 2015-12-01
gmatrix-0.2/gmatrix/man/rowLogSums.Rd |only gmatrix-0.2/gmatrix/src/Makefile |only gmatrix-0.3/gmatrix/DESCRIPTION | 18 - gmatrix-0.3/gmatrix/LICENSE |only gmatrix-0.3/gmatrix/MD5 | 66 +++-- gmatrix-0.3/gmatrix/NAMESPACE | 15 - gmatrix-0.3/gmatrix/R/00general.R | 26 +- gmatrix-0.3/gmatrix/R/01gmatrix.R | 48 ++- gmatrix-0.3/gmatrix/R/02gvector.R | 89 +++---- gmatrix-0.3/gmatrix/R/03dist.R | 2 gmatrix-0.3/gmatrix/R/04operations.R | 23 + gmatrix-0.3/gmatrix/R/05test.R | 67 ++++- gmatrix-0.3/gmatrix/R/06solve.R |only gmatrix-0.3/gmatrix/R/07MCMC.R |only gmatrix-0.3/gmatrix/README.md | 45 ++- gmatrix-0.3/gmatrix/cleanup |only gmatrix-0.3/gmatrix/configure |only gmatrix-0.3/gmatrix/configure.ac |only gmatrix-0.3/gmatrix/man/chol.Rd |only gmatrix-0.3/gmatrix/man/g.rep.Rd | 2 gmatrix-0.3/gmatrix/man/gBasicHMC.Rd |only gmatrix-0.3/gmatrix/man/gRowLogSums.Rd |only gmatrix-0.3/gmatrix/man/gmatrix-class.Rd | 3 gmatrix-0.3/gmatrix/man/gmm.Rd | 5 gmatrix-0.3/gmatrix/man/gqr-class.Rd |only gmatrix-0.3/gmatrix/man/gset.seed.Rd |only gmatrix-0.3/gmatrix/man/gsvd-class.Rd |only gmatrix-0.3/gmatrix/man/indexing-methods.Rd | 30 +- gmatrix-0.3/gmatrix/man/lpgr-class.Rd |only gmatrix-0.3/gmatrix/man/rsample.Rd | 2 gmatrix-0.3/gmatrix/man/setTuningPameters.Rd | 7 gmatrix-0.3/gmatrix/src/Makefile.in |only gmatrix-0.3/gmatrix/src/conversions.cu | 15 - gmatrix-0.3/gmatrix/src/dist.cu | 203 ++++++++-------- gmatrix-0.3/gmatrix/src/fact.cu |only gmatrix-0.3/gmatrix/src/general.cu | 24 + gmatrix-0.3/gmatrix/src/gmatrix.h | 82 +++--- gmatrix-0.3/gmatrix/src/manipulation.cu | 108 ++++---- gmatrix-0.3/gmatrix/src/matrix.cu | 335 +++++++++++++++------------ gmatrix-0.3/gmatrix/src/ops.cu | 168 +++++++------ gmatrix-0.3/gmatrix/tools |only 41 files changed, 843 insertions(+), 540 deletions(-)
Title: Empirical Bayesian Lasso and Elastic Net Methods for Generalized
Linear Models
Description: Provides Empirical Bayesian Lasso and Elastic Net algorithms for variable selection and effect estimation. Key features include sparse variable selection and effect estimation via generalized linear regression models, high dimensionality with p>>n, and significant test for nonzero effects. This package outperforms other popular methods such as Lasso and Elastic Net methods in terms of Power of Detection, False Discovery Rate, and Power of Detection Grouping Effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBglmnet versions 3.6 dated 2014-12-14 and 4.0 dated 2015-12-01
EBglmnet-3.6/EBglmnet/data |only EBglmnet-3.6/EBglmnet/man/BASIS.Rd |only EBglmnet-3.6/EBglmnet/man/BASISbinomial.Rd |only EBglmnet-3.6/EBglmnet/man/EBelasticNet.Binomial.Rd |only EBglmnet-3.6/EBglmnet/man/EBelasticNet.BinomialCV.Rd |only EBglmnet-3.6/EBglmnet/man/EBelasticNet.Gaussian.Rd |only EBglmnet-3.6/EBglmnet/man/EBelasticNet.GaussianCV.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNE.BinomialCV.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNE.GaussianCV.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNEG.Binomial.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNEG.BinomialCV.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNEG.Gaussian.Rd |only EBglmnet-3.6/EBglmnet/man/EBlassoNEG.GaussianCV.Rd |only EBglmnet-3.6/EBglmnet/man/y.Rd |only EBglmnet-3.6/EBglmnet/man/yBinomial.Rd |only EBglmnet-4.0/EBglmnet/DESCRIPTION | 14 ++- EBglmnet-4.0/EBglmnet/MD5 | 71 ++++++++---------- EBglmnet-4.0/EBglmnet/NAMESPACE | 3 EBglmnet-4.0/EBglmnet/R/EBelasticNet.Binomial.R | 27 +++--- EBglmnet-4.0/EBglmnet/R/EBelasticNet.BinomialCV.R | 44 ++++++----- EBglmnet-4.0/EBglmnet/R/EBelasticNet.Gaussian.R | 28 +++---- EBglmnet-4.0/EBglmnet/R/EBelasticNet.GaussianCV.R | 43 ++++++---- EBglmnet-4.0/EBglmnet/R/EBglmnet.R |only EBglmnet-4.0/EBglmnet/R/EBlassoNE.BinomialCV.R | 44 ++++++----- EBglmnet-4.0/EBglmnet/R/EBlassoNE.GaussianCV.R | 53 +++++++------ EBglmnet-4.0/EBglmnet/R/EBlassoNEG.Binomial.R | 33 ++++---- EBglmnet-4.0/EBglmnet/R/EBlassoNEG.BinomialCV.R | 56 +++++++------- EBglmnet-4.0/EBglmnet/R/EBlassoNEG.Gaussian.R | 30 +++---- EBglmnet-4.0/EBglmnet/R/EBlassoNEG.GaussianCV.R | 59 ++++++++------ EBglmnet-4.0/EBglmnet/R/cv.EBglmnet.R |only EBglmnet-4.0/EBglmnet/build |only EBglmnet-4.0/EBglmnet/inst |only EBglmnet-4.0/EBglmnet/man/EBglmnet-internal.Rd |only EBglmnet-4.0/EBglmnet/man/EBglmnet-package.Rd | 56 ++++++++------ EBglmnet-4.0/EBglmnet/man/EBglmnet.Rd |only EBglmnet-4.0/EBglmnet/man/cv.EBglmnet.Rd |only EBglmnet-4.0/EBglmnet/src/ElasticNetBinaryNEmainEff.c | 11 +- EBglmnet-4.0/EBglmnet/src/ElasticNetBinaryNeFull.c | 11 +- EBglmnet-4.0/EBglmnet/src/elasticNetLinearNeFull2.c | 6 - EBglmnet-4.0/EBglmnet/src/elasticNetLinearNeMainEff.c | 6 - EBglmnet-4.0/EBglmnet/src/fEBBinaryNegFull.c | 20 ++--- EBglmnet-4.0/EBglmnet/src/fEBBinaryNegMainEff.c | 2 EBglmnet-4.0/EBglmnet/src/fEBLinearFullFloat.c | 26 +++--- EBglmnet-4.0/EBglmnet/src/fEBLinearMainEff.c | 4 - EBglmnet-4.0/EBglmnet/vignettes |only 45 files changed, 351 insertions(+), 296 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as verifying species names, and getting taxonomic 'hierarchies'.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.6 dated 2015-10-01 and 0.7.0 dated 2015-11-30
taxize-0.6.6/taxize/man/phylomatic_format.Rd |only taxize-0.6.6/taxize/man/phylomatic_tree-deprecated.Rd |only taxize-0.6.6/taxize/man/taxize-deprecated.Rd |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_format.R |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_tree.R |only taxize-0.7.0/taxize/DESCRIPTION | 15 taxize-0.7.0/taxize/MD5 | 471 +++++----- taxize-0.7.0/taxize/NAMESPACE | 14 taxize-0.7.0/taxize/R/children.R | 4 taxize-0.7.0/taxize/R/classification.R | 6 taxize-0.7.0/taxize/R/comm2sci.R | 4 taxize-0.7.0/taxize/R/downstream.R | 30 taxize-0.7.0/taxize/R/eubon.R |only taxize-0.7.0/taxize/R/fungorum.R |only taxize-0.7.0/taxize/R/gbif_downstream.R |only taxize-0.7.0/taxize/R/get_ids.R | 5 taxize-0.7.0/taxize/R/get_nbnid.R | 1 taxize-0.7.0/taxize/R/gisd_isinvasive.R | 1 taxize-0.7.0/taxize/R/gni_search.R | 4 taxize-0.7.0/taxize/R/gnr_resolve.R | 22 taxize-0.7.0/taxize/R/ion.R |only taxize-0.7.0/taxize/R/itis.R | 10 taxize-0.7.0/taxize/R/iucn_getname.R | 23 taxize-0.7.0/taxize/R/iucn_id.R | 15 taxize-0.7.0/taxize/R/iucn_summary.R | 7 taxize-0.7.0/taxize/R/nbn_classification.R | 1 taxize-0.7.0/taxize/R/nbn_search.R | 1 taxize-0.7.0/taxize/R/nbn_synonyms.R | 1 taxize-0.7.0/taxize/R/phylomatic_format.R | 45 taxize-0.7.0/taxize/R/phylomatic_tree.R | 185 --- taxize-0.7.0/taxize/R/ping.R | 11 taxize-0.7.0/taxize/R/resolve.R | 3 taxize-0.7.0/taxize/R/sci2comm.R | 5 taxize-0.7.0/taxize/R/synonyms.R | 4 taxize-0.7.0/taxize/R/tax_agg.R | 8 taxize-0.7.0/taxize/R/tax_rank.R | 4 taxize-0.7.0/taxize/R/taxize-package.R | 41 taxize-0.7.0/taxize/R/taxize_capwords.r | 35 taxize-0.7.0/taxize/R/taxize_cite.R | 4 taxize-0.7.0/taxize/R/tp_dist.R | 1 taxize-0.7.0/taxize/R/tp_refs.R | 1 taxize-0.7.0/taxize/R/tp_search.R | 1 taxize-0.7.0/taxize/R/tp_summary.R | 1 taxize-0.7.0/taxize/R/tp_synonyms.R | 1 taxize-0.7.0/taxize/R/ubio_synonyms.R | 2 taxize-0.7.0/taxize/R/upstream.R | 3 taxize-0.7.0/taxize/R/vascan_search.r | 1 taxize-0.7.0/taxize/R/zzz.R | 25 taxize-0.7.0/taxize/README.md | 73 - taxize-0.7.0/taxize/build/vignette.rds |binary taxize-0.7.0/taxize/inst/doc/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/inst/doc/taxize_infotable.html | 2 taxize-0.7.0/taxize/inst/doc/taxize_vignette.Rmd | 14 taxize-0.7.0/taxize/inst/doc/taxize_vignette.html | 14 taxize-0.7.0/taxize/inst/ignore/wikispecies.R |only taxize-0.7.0/taxize/inst/vign/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/inst/vign/taxize_infotable.md | 2 taxize-0.7.0/taxize/inst/vign/taxize_vignette.md | 14 taxize-0.7.0/taxize/man/apg.Rd | 2 taxize-0.7.0/taxize/man/apg_families.Rd | 2 taxize-0.7.0/taxize/man/apg_lookup.Rd | 2 taxize-0.7.0/taxize/man/apg_orders.Rd | 2 taxize-0.7.0/taxize/man/bold_search.Rd | 2 taxize-0.7.0/taxize/man/children.Rd | 7 taxize-0.7.0/taxize/man/class2tree.Rd | 2 taxize-0.7.0/taxize/man/classification.Rd | 8 taxize-0.7.0/taxize/man/col_children.Rd | 2 taxize-0.7.0/taxize/man/col_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/col_downstream.Rd | 2 taxize-0.7.0/taxize/man/col_search.Rd | 2 taxize-0.7.0/taxize/man/comm2sci.Rd | 6 taxize-0.7.0/taxize/man/downstream.Rd | 15 taxize-0.7.0/taxize/man/eol_dataobjects.Rd | 2 taxize-0.7.0/taxize/man/eol_hierarchy-defunct.Rd | 2 taxize-0.7.0/taxize/man/eol_invasive-defunct.Rd | 4 taxize-0.7.0/taxize/man/eol_pages.Rd | 2 taxize-0.7.0/taxize/man/eol_search.Rd | 2 taxize-0.7.0/taxize/man/eubon.Rd |only taxize-0.7.0/taxize/man/fungorum.Rd |only taxize-0.7.0/taxize/man/gbif_downstream.Rd |only taxize-0.7.0/taxize/man/gbif_name_usage.Rd | 7 taxize-0.7.0/taxize/man/gbif_parse.Rd | 2 taxize-0.7.0/taxize/man/genbank2uid.Rd | 2 taxize-0.7.0/taxize/man/get_boldid.Rd | 2 taxize-0.7.0/taxize/man/get_colid.Rd | 2 taxize-0.7.0/taxize/man/get_eolid.Rd | 2 taxize-0.7.0/taxize/man/get_gbifid.Rd | 2 taxize-0.7.0/taxize/man/get_genes-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_genes_avail-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_ids.Rd | 7 taxize-0.7.0/taxize/man/get_nbnid.Rd | 2 taxize-0.7.0/taxize/man/get_seqs-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_tpsid.Rd | 2 taxize-0.7.0/taxize/man/get_tsn.Rd | 2 taxize-0.7.0/taxize/man/get_ubioid-defunct.Rd | 2 taxize-0.7.0/taxize/man/get_uid.Rd | 2 taxize-0.7.0/taxize/man/getacceptednamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getanymatchcount.Rd | 2 taxize-0.7.0/taxize/man/getcommentdetailfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcommonnamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcoremetadatafromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcoveragefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcredibilityratingfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcredibilityratings.Rd | 2 taxize-0.7.0/taxize/man/getcurrencyfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getdatedatafromtsn.Rd | 2 taxize-0.7.0/taxize/man/getdescription.Rd | 4 taxize-0.7.0/taxize/man/getexpertsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getfullhierarchyfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getfullrecordfromlsid.Rd | 2 taxize-0.7.0/taxize/man/getfullrecordfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getgeographicdivisionsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getgeographicvalues.Rd | 2 taxize-0.7.0/taxize/man/getglobalspeciescompletenessfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gethierarchydownfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gethierarchyupfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getitisterms.Rd | 2 taxize-0.7.0/taxize/man/getitistermsfromcommonname.Rd | 2 taxize-0.7.0/taxize/man/getitistermsfromscientificname.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionoriginvalues.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionvalues.Rd | 2 taxize-0.7.0/taxize/man/getkey.Rd | 2 taxize-0.7.0/taxize/man/getkingdomnamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getkingdomnames.Rd | 2 taxize-0.7.0/taxize/man/getlastchangedate.Rd | 2 taxize-0.7.0/taxize/man/getlsidfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getothersourcesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getparenttsnfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getpublicationsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getranknames.Rd | 2 taxize-0.7.0/taxize/man/getrecordfromlsid.Rd | 4 taxize-0.7.0/taxize/man/getreviewyearfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getscientificnamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getsynonymnamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonauthorshipfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonomicranknamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonomicusagefromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.7.0/taxize/man/gettsnfromlsid.Rd | 2 taxize-0.7.0/taxize/man/getunacceptabilityreasonfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getvernacularlanguages.Rd | 2 taxize-0.7.0/taxize/man/gisd_invasive-defunct.Rd | 2 taxize-0.7.0/taxize/man/gni_details.Rd | 2 taxize-0.7.0/taxize/man/gni_parse.Rd | 2 taxize-0.7.0/taxize/man/gni_search.Rd | 2 taxize-0.7.0/taxize/man/gnr_datasources.Rd | 2 taxize-0.7.0/taxize/man/gnr_resolve.Rd | 17 taxize-0.7.0/taxize/man/ion.Rd |only taxize-0.7.0/taxize/man/iplant_resolve.Rd | 2 taxize-0.7.0/taxize/man/ipni_search.Rd | 2 taxize-0.7.0/taxize/man/itis-api.Rd | 2 taxize-0.7.0/taxize/man/itis_acceptname.Rd | 2 taxize-0.7.0/taxize/man/itis_downstream.Rd | 2 taxize-0.7.0/taxize/man/itis_getrecord.Rd | 2 taxize-0.7.0/taxize/man/itis_hierarchy.Rd | 2 taxize-0.7.0/taxize/man/itis_kingdomnames.Rd | 2 taxize-0.7.0/taxize/man/itis_lsid.Rd | 2 taxize-0.7.0/taxize/man/itis_name-deprecated.Rd | 2 taxize-0.7.0/taxize/man/itis_native.Rd | 2 taxize-0.7.0/taxize/man/itis_refs.Rd | 2 taxize-0.7.0/taxize/man/itis_searchcommon.Rd | 2 taxize-0.7.0/taxize/man/itis_taxrank.Rd | 2 taxize-0.7.0/taxize/man/itis_terms.Rd | 2 taxize-0.7.0/taxize/man/iucn_getname.Rd | 20 taxize-0.7.0/taxize/man/iucn_id.Rd | 13 taxize-0.7.0/taxize/man/iucn_status.Rd | 2 taxize-0.7.0/taxize/man/iucn_summary.Rd | 11 taxize-0.7.0/taxize/man/names_list.Rd | 2 taxize-0.7.0/taxize/man/nbn_classification.Rd | 2 taxize-0.7.0/taxize/man/nbn_search.Rd | 2 taxize-0.7.0/taxize/man/nbn_synonyms.Rd | 2 taxize-0.7.0/taxize/man/ncbi_children.Rd | 2 taxize-0.7.0/taxize/man/ncbi_get_taxon_summary.Rd | 2 taxize-0.7.0/taxize/man/ncbi_getbyid-defunct.Rd | 2 taxize-0.7.0/taxize/man/ncbi_getbyname-defunct.Rd | 6 taxize-0.7.0/taxize/man/ncbi_search-defunct.Rd | 6 taxize-0.7.0/taxize/man/phylomatic_format-defunct.Rd |only taxize-0.7.0/taxize/man/phylomatic_tree-defunct.Rd |only taxize-0.7.0/taxize/man/ping.Rd | 5 taxize-0.7.0/taxize/man/plantGenusNames.Rd | 2 taxize-0.7.0/taxize/man/plantNames.Rd | 2 taxize-0.7.0/taxize/man/plantminer.Rd | 2 taxize-0.7.0/taxize/man/rank_ref.Rd | 2 taxize-0.7.0/taxize/man/rankagg.Rd | 2 taxize-0.7.0/taxize/man/resolve.Rd | 7 taxize-0.7.0/taxize/man/sci2comm.Rd | 8 taxize-0.7.0/taxize/man/scrapenames.Rd | 2 taxize-0.7.0/taxize/man/searchbycommonname.Rd | 8 taxize-0.7.0/taxize/man/searchbycommonnamebeginswith.Rd | 2 taxize-0.7.0/taxize/man/searchbycommonnameendswith.Rd | 2 taxize-0.7.0/taxize/man/searchbyscientificname.Rd | 2 taxize-0.7.0/taxize/man/searchforanymatch.Rd | 2 taxize-0.7.0/taxize/man/searchforanymatchpaged.Rd | 2 taxize-0.7.0/taxize/man/status_codes.Rd | 2 taxize-0.7.0/taxize/man/synonyms.Rd | 6 taxize-0.7.0/taxize/man/tax_agg.Rd | 7 taxize-0.7.0/taxize/man/tax_name.Rd | 2 taxize-0.7.0/taxize/man/tax_rank.Rd | 6 taxize-0.7.0/taxize/man/taxize-defunct.Rd | 6 taxize-0.7.0/taxize/man/taxize-package.Rd | 18 taxize-0.7.0/taxize/man/taxize_capwords.Rd | 2 taxize-0.7.0/taxize/man/taxize_cite.Rd | 2 taxize-0.7.0/taxize/man/taxize_ldfast.Rd | 2 taxize-0.7.0/taxize/man/theplantlist.Rd | 9 taxize-0.7.0/taxize/man/tnrs.Rd | 2 taxize-0.7.0/taxize/man/tnrs_sources.Rd | 2 taxize-0.7.0/taxize/man/tp_acceptednames-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_accnames.Rd | 2 taxize-0.7.0/taxize/man/tp_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/tp_dist.Rd | 2 taxize-0.7.0/taxize/man/tp_namedistributions-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_namereferences-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_refs.Rd | 2 taxize-0.7.0/taxize/man/tp_search.Rd | 2 taxize-0.7.0/taxize/man/tp_summary.Rd | 2 taxize-0.7.0/taxize/man/tp_synonyms.Rd | 2 taxize-0.7.0/taxize/man/tpl_families.Rd | 2 taxize-0.7.0/taxize/man/tpl_get.Rd | 2 taxize-0.7.0/taxize/man/tpl_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_classification_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_id-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_ping-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_synonyms-defunct.Rd | 2 taxize-0.7.0/taxize/man/upstream.Rd | 7 taxize-0.7.0/taxize/man/vascan_search.Rd | 2 taxize-0.7.0/taxize/tests/testthat/Rplots.pdf |binary taxize-0.7.0/taxize/tests/testthat/test-apgscraping.R | 32 taxize-0.7.0/taxize/tests/testthat/test-classification.R | 7 taxize-0.7.0/taxize/tests/testthat/test-col_children.R | 41 taxize-0.7.0/taxize/tests/testthat/test-col_downstream.R | 21 taxize-0.7.0/taxize/tests/testthat/test-downstream.R |only taxize-0.7.0/taxize/tests/testthat/test-eubon.R |only taxize-0.7.0/taxize/tests/testthat/test-fungorum.R |only taxize-0.7.0/taxize/tests/testthat/test-gbif_downstream.R |only taxize-0.7.0/taxize/tests/testthat/test-ion.R |only taxize-0.7.0/taxize/tests/testthat/test-ipni_search.R | 10 taxize-0.7.0/taxize/tests/testthat/test-itis_downstream.R | 4 taxize-0.7.0/taxize/tests/testthat/test-iucn_getname.R | 6 taxize-0.7.0/taxize/tests/testthat/test-iucn_id.R | 3 taxize-0.7.0/taxize/tests/testthat/test-iucn_summary.R | 2 taxize-0.7.0/taxize/tests/testthat/test-ping.R | 7 taxize-0.7.0/taxize/tests/testthat/test-tax_name.R | 8 taxize-0.7.0/taxize/vignettes/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/vignettes/taxize_vignette.Rmd | 14 247 files changed, 894 insertions(+), 900 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty.
Supported models include cumulative logit, probit, cauchit, and complementary log-log.
The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Mike Wurm [aut, cre]
Maintainer: Mike Wurm <wurm@wisc.edu>
Diff between ordinalNet versions 1.2 dated 2015-11-25 and 1.3 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/testthat.R | 4 ++-- tests/testthat/test-ordinalNet.R | 30 +++++++++++++++++++++--------- 4 files changed, 30 insertions(+), 18 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.3 dated 2015-11-15 and 0.4.4 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/miive.R | 20 +++++++++++--------- 3 files changed, 16 insertions(+), 14 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre],
Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>
Diff between alineR versions 1.1.1 dated 2015-08-06 and 1.1.2 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/features.plot.R | 32 ++++++++++++++++---------------- man/features.plot.Rd | 8 +++++++- src/Word.cpp | 3 ++- src/Word.h | 3 +-- 7 files changed, 36 insertions(+), 30 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 1.0.0 dated 2015-10-01 and 1.0.1 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 2 ++ R/krige_tools.R | 3 +++ man/krige.ok.Rd | 7 ++++--- man/krige.sk.Rd | 13 +++++++------ man/krige.uk.Rd | 4 +++- 7 files changed, 29 insertions(+), 20 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.6.0 dated 2015-10-11 and 1.6.1 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/getConstraint.R | 38 +++++++++++--------------------------- R/getIndex.R | 51 +++++++++++---------------------------------------- R/internal.R | 2 +- 5 files changed, 30 insertions(+), 75 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Package implements projection based methods for preprocessing,
exploring and analysis of multivariate data used in chemometrics.
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.6.0 dated 2015-01-19 and 0.7.0 dated 2015-11-30
DESCRIPTION | 17 - MD5 | 500 ++++++++++++++++----------------- NAMESPACE | 212 +++++++++++++ NEWS | 22 + R/classmodel.R | 8 R/classres.R | 102 ++++-- R/crossval.R | 36 ++ R/defaults.R | 69 ++++ R/ipls.R |only R/ldecomp.R | 93 +++--- R/mdaplots.R | 455 +++++++++++++++++++++++------- R/pca.R | 271 +++++++++++++---- R/pcares.R | 125 +++++++- R/pls.R | 494 ++++++++++++++++++++++++++++---- R/plsda.R | 260 ++++++++++++++--- R/plsdares.R | 151 ++++++++- R/plsres.R | 169 +++++++++-- R/prep.R | 40 ++ R/randtest.R | 126 ++++++-- R/regcoeffs.R | 13 R/regres.R | 19 - R/simca.R | 198 +++++++++---- R/simcam.R | 154 ++++++++-- R/simcamres.R | 166 ++++++++-- R/simcares.R | 117 ++++++- README.md | 13 man/as.matrix.classres.Rd | 2 man/as.matrix.ldecomp.Rd | 2 man/as.matrix.plsdares.Rd | 2 man/as.matrix.plsres.Rd | 2 man/as.matrix.regcoeffs.Rd | 2 man/as.matrix.regres.Rd | 2 man/bars.Rd | 6 man/classify.plsda.Rd | 2 man/classres.Rd | 57 +-- man/crossval.Rd | 2 man/crossval.str.Rd |only man/erfinv.Rd | 2 man/errorbars.Rd | 2 man/getCalibrationData.Rd | 2 man/getCalibrationData.pca.Rd | 2 man/getCalibrationData.simcam.Rd | 2 man/getClassificationPerformance.Rd | 2 man/getMainTitle.Rd | 2 man/getRegcoeffs.Rd |only man/getRegcoeffs.pls.Rd |only man/getSelectedComponents.Rd | 2 man/getSelectedComponents.classres.Rd | 2 man/getSelectivityRatio.Rd | 2 man/getSelectivityRatio.pls.Rd | 2 man/getVIPScores.Rd | 2 man/getVIPScores.pls.Rd | 2 man/ipls.Rd |only man/ipls.backward.Rd |only man/ipls.forward.Rd |only man/ldecomp.Rd | 8 man/ldecomp.getDistances.Rd | 9 man/ldecomp.getResLimits.Rd | 8 man/ldecomp.getVariances.Rd | 6 man/mdaplot.Rd | 156 ++++++---- man/mdaplot.areColors.Rd | 2 man/mdaplot.formatValues.Rd | 2 man/mdaplot.getAxesLim.Rd | 2 man/mdaplot.getColors.Rd | 2 man/mdaplot.plotAxes.Rd | 2 man/mdaplot.showColorbar.Rd | 2 man/mdaplot.showGrid.Rd | 2 man/mdaplot.showLabels.Rd | 2 man/mdaplot.showLegend.Rd | 8 man/mdaplot.showLines.Rd | 2 man/mdaplot.showRegressionLine.Rd | 2 man/mdaplotg.Rd | 131 +++++--- man/mdatools.Rd | 2 man/pca.Rd | 132 ++++---- man/pca.cal.Rd | 2 man/pca.crossval.Rd | 2 man/pca.mvreplace.Rd | 66 ++-- man/pca.nipals.Rd | 7 man/pca.svd.Rd | 2 man/pcares.Rd | 87 ++--- man/pinv.Rd | 2 man/plot.classres.Rd | 2 man/plot.ipls.Rd |only man/plot.pca.Rd | 2 man/plot.pcares.Rd | 4 man/plot.pls.Rd | 2 man/plot.plsda.Rd | 6 man/plot.plsdares.Rd | 7 man/plot.plsres.Rd | 2 man/plot.randtest.Rd | 2 man/plot.regcoeffs.Rd | 4 man/plot.regres.Rd | 2 man/plot.simca.Rd | 2 man/plot.simcam.Rd | 2 man/plot.simcamres.Rd | 2 man/plotCooman.Rd | 2 man/plotCooman.simcam.Rd | 2 man/plotCooman.simcamres.Rd | 2 man/plotCorr.Rd | 2 man/plotCorr.randtest.Rd | 2 man/plotCumVariance.Rd | 2 man/plotCumVariance.ldecomp.Rd | 2 man/plotCumVariance.pca.Rd | 2 man/plotDiscriminationPower.Rd | 2 man/plotDiscriminationPower.simcam.Rd | 2 man/plotHist.Rd | 2 man/plotHist.randtest.Rd | 2 man/plotLoadings.Rd | 2 man/plotLoadings.pca.Rd | 2 man/plotMisclassified.Rd | 2 man/plotMisclassified.classmodel.Rd | 2 man/plotMisclassified.classres.Rd | 2 man/plotModelDistance.Rd | 2 man/plotModelDistance.simcam.Rd | 2 man/plotModellingPower.Rd | 2 man/plotModellingPower.simca.Rd | 2 man/plotModellingPower.simcam.Rd | 2 man/plotPerformance.Rd | 2 man/plotPerformance.classmodel.Rd | 2 man/plotPerformance.classres.Rd | 2 man/plotPredictions.Rd | 2 man/plotPredictions.classmodel.Rd | 2 man/plotPredictions.classres.Rd | 2 man/plotPredictions.pls.Rd | 2 man/plotPredictions.plsres.Rd | 2 man/plotPredictions.regres.Rd | 2 man/plotRMSE.Rd | 2 man/plotRMSE.ipls.Rd |only man/plotRMSE.pls.Rd | 2 man/plotRMSE.plsres.Rd | 2 man/plotRMSE.regres.Rd | 2 man/plotRegcoeffs.Rd | 2 man/plotRegcoeffs.pls.Rd | 6 man/plotResiduals.Rd | 2 man/plotResiduals.ldecomp.Rd | 7 man/plotResiduals.pca.Rd | 7 man/plotResiduals.simcam.Rd | 2 man/plotResiduals.simcamres.Rd | 8 man/plotResiduals.simcares.Rd | 8 man/plotScores.Rd | 2 man/plotScores.ldecomp.Rd | 2 man/plotScores.pca.Rd | 2 man/plotSelection.Rd |only man/plotSelection.ipls.Rd |only man/plotSelectivityRatio.Rd | 2 man/plotSelectivityRatio.pls.Rd | 2 man/plotSensitivity.Rd | 2 man/plotSensitivity.classmodel.Rd | 2 man/plotSensitivity.classres.Rd | 2 man/plotSpecificity.Rd | 2 man/plotSpecificity.classmodel.Rd | 2 man/plotSpecificity.classres.Rd | 2 man/plotVIPScores.Rd | 2 man/plotVIPScores.pls.Rd | 2 man/plotVariance.Rd | 2 man/plotVariance.ldecomp.Rd | 2 man/plotVariance.pca.Rd | 2 man/plotVariance.pls.Rd | 2 man/plotXCumVariance.Rd | 2 man/plotXCumVariance.pls.Rd | 2 man/plotXCumVariance.plsres.Rd | 2 man/plotXLoadings.Rd | 2 man/plotXLoadings.pls.Rd | 2 man/plotXResiduals.Rd | 2 man/plotXResiduals.pls.Rd | 7 man/plotXResiduals.plsres.Rd | 4 man/plotXScores.Rd | 2 man/plotXScores.pls.Rd | 2 man/plotXScores.plsres.Rd | 2 man/plotXVariance.Rd | 2 man/plotXVariance.pls.Rd | 2 man/plotXVariance.plsres.Rd | 2 man/plotXYLoadings.Rd | 2 man/plotXYLoadings.pls.Rd | 2 man/plotXYScores.Rd | 2 man/plotXYScores.pls.Rd | 2 man/plotXYScores.plsres.Rd | 2 man/plotYCumVariance.Rd | 2 man/plotYCumVariance.pls.Rd | 2 man/plotYCumVariance.plsres.Rd | 2 man/plotYResiduals.Rd | 2 man/plotYResiduals.pls.Rd | 2 man/plotYResiduals.regres.Rd | 2 man/plotYVariance.Rd | 2 man/plotYVariance.pls.Rd | 2 man/plotYVariance.plsres.Rd | 2 man/pls.Rd | 204 +++++++------ man/pls.cal.Rd | 7 man/pls.calculateSelectivityRatio.Rd | 2 man/pls.calculateVIPScores.Rd | 2 man/pls.crossval.Rd | 2 man/pls.simpls.Rd | 2 man/plsda.Rd | 143 +++++---- man/plsda.crossval.Rd | 6 man/plsda.getReferenceValues.Rd | 2 man/plsdares.Rd | 124 +++----- man/plsres.Rd | 133 ++++---- man/predict.pca.Rd | 2 man/predict.pls.Rd | 2 man/predict.plsda.Rd | 2 man/predict.simca.Rd | 2 man/predict.simcam.Rd | 2 man/prep.autoscale.Rd | 2 man/prep.msc.Rd | 2 man/prep.norm.Rd |only man/prep.savgol.Rd | 2 man/prep.snv.Rd | 2 man/print.classres.Rd | 2 man/print.ipls.Rd |only man/print.ldecomp.Rd | 2 man/print.pca.Rd | 2 man/print.pcares.Rd | 2 man/print.pls.Rd | 2 man/print.plsda.Rd | 2 man/print.plsdares.Rd | 2 man/print.plsres.Rd | 2 man/print.randtest.Rd | 2 man/print.regcoeffs.Rd | 2 man/print.regres.Rd | 2 man/print.simca.Rd | 2 man/print.simcam.Rd | 2 man/print.simcamres.Rd | 2 man/print.simcares.Rd | 2 man/randtest.Rd | 104 +++--- man/regcoeffs.Rd | 2 man/regcoeffs.getStat.Rd | 2 man/regres.Rd | 2 man/regres.bias.Rd | 2 man/regres.r2.Rd | 2 man/regres.rmse.Rd | 2 man/regres.slope.Rd | 2 man/selectCompNum.Rd | 2 man/selectCompNum.pca.Rd | 2 man/selectCompNum.pls.Rd | 5 man/showPredictions.Rd | 2 man/showPredictions.classres.Rd | 2 man/simca.Rd | 160 +++++----- man/simca.classify.Rd | 4 man/simca.crossval.Rd | 2 man/simcam.Rd | 112 +++---- man/simcam.getPerformanceStatistics.Rd | 2 man/simcamres.Rd | 94 ++---- man/simcares.Rd | 93 ++---- man/summary.classres.Rd | 2 man/summary.ipls.Rd |only man/summary.ldecomp.Rd | 2 man/summary.pca.Rd | 2 man/summary.pcares.Rd | 2 man/summary.pls.Rd | 2 man/summary.plsda.Rd | 2 man/summary.plsdares.Rd | 2 man/summary.plsres.Rd | 2 man/summary.randtest.Rd | 2 man/summary.regres.Rd | 2 man/summary.simca.Rd | 2 man/summary.simcam.Rd | 2 man/summary.simcamres.Rd | 2 man/summary.simcares.Rd | 2 258 files changed, 4211 insertions(+), 1921 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath
expressions, used to enter mathematical formulas and symbols to be rendered as
text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.3.3 dated 2015-08-12 and 0.4.0 dated 2015-11-30
latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.R |only latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.Rmd |only latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.html |only latex2exp-0.3.3/latex2exp/tests/testthat/Rplots.pdf |only latex2exp-0.3.3/latex2exp/vignettes/latex2exp.Rmd |only latex2exp-0.4.0/latex2exp/DESCRIPTION | 15 +++-- latex2exp-0.4.0/latex2exp/MD5 | 30 +++++------ latex2exp-0.4.0/latex2exp/NAMESPACE | 1 latex2exp-0.4.0/latex2exp/R/latex2exp.R | 42 ++++++++++------ latex2exp-0.4.0/latex2exp/build/vignette.rds |binary latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.R |only latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.Rmd |only latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.html |only latex2exp-0.4.0/latex2exp/man/TeX.Rd |only latex2exp-0.4.0/latex2exp/man/latex2exp.Rd | 13 +--- latex2exp-0.4.0/latex2exp/man/latex2exp_examples.Rd | 6 +- latex2exp-0.4.0/latex2exp/man/latex2exp_supported.Rd | 2 latex2exp-0.4.0/latex2exp/man/plot.expression.Rd | 2 latex2exp-0.4.0/latex2exp/man/print.latextoken.Rd | 6 +- latex2exp-0.4.0/latex2exp/man/toString.latextoken.Rd | 8 +-- latex2exp-0.4.0/latex2exp/vignettes/using-latex2exp.Rmd |only 21 files changed, 68 insertions(+), 57 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between broom versions 0.3.7 dated 2015-05-06 and 0.4.0 dated 2015-11-30
DESCRIPTION | 24 ++- MD5 | 148 +++++++++++++-------- NAMESPACE | 49 +++++++ R/anova_tidiers.R | 35 ++++- R/arima_tidiers.R | 2 R/auc_tidiers.R |only R/augment.R | 13 + R/biglm_tidiers.R | 10 + R/bingroup_tidiers.R |only R/boot_tidiers.R |only R/broom.R | 5 R/btergm_tidiers.R |only R/data.frame_tidiers.R | 2 R/ergm_tidiers.R |only R/felm_tidiers.R | 18 +- R/fitdistr_tidiers.R |only R/gamlss_tidiers.R |only R/geeglm_tidiers.R |only R/glmnet_tidiers.R | 18 +- R/globals.R | 4 R/htest_tidiers.R | 14 ++ R/list_tidiers.R | 19 ++ R/lm_tidiers.R | 28 ++-- R/lme4_tidiers.R | 194 +++++++++++++++++++++++----- R/loess_tidiers.R | 2 R/map_tidiers.R | 2 R/mcmc_tidiers.R |only R/mle2_tidiers.R |only R/multcomp_tidiers.R | 2 R/multinom_tidiers.R | 15 +- R/nlme_tidiers.R | 4 R/nls_tidiers.R | 21 ++- R/plm_tidiers.R | 2 R/psych_tidiers.R |only R/rcorr_tidiers.R |only R/ridgelm_tidiers.R | 13 + R/rowwise_df_tidiers.R | 75 +++++++++-- R/rq_tidiers.R |only R/smooth.spline_tidiers.R | 4 R/stats_tidiers.R | 4 R/summary_tidiers.R | 12 + R/survival_tidiers.R | 30 ++-- R/svd_tidiers.R |only R/utilities.R | 38 ++--- R/xyz_tidiers.R |only README.md | 283 ++++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/bootstrapping.Rmd | 2 inst/doc/bootstrapping.html | 46 +++--- inst/doc/broom_and_dplyr.html | 158 ++++++++++++----------- inst/doc/kmeans.html | 8 - inst/extdata |only man/auc_tidiers.Rd |only man/augment.Rd | 10 - man/biglm_tidiers.Rd | 5 man/binDesign_tidiers.Rd |only man/binWidth_tidiers.Rd |only man/boot_tidiers.Rd |only man/btergm_tidiers.Rd |only man/cch_tidiers.Rd | 4 man/confint.geeglm.Rd |only man/confint_tidy.Rd | 4 man/coxph_tidiers.Rd | 2 man/ergm_tidiers.Rd |only man/fitdistr_tidiers.Rd |only man/gamlss_tidiers.Rd |only man/geeglm_tidiers.Rd |only man/kappa_tidiers.Rd |only man/list_tidiers.Rd | 8 - man/lm_tidiers.Rd | 14 +- man/lme4_tidiers.Rd | 39 +++-- man/loess_tidiers.Rd | 2 man/mcmc_tidiers.Rd |only man/mle2_tidiers.Rd |only man/nls_tidiers.Rd | 6 man/plm_tidiers.Rd | 2 man/process_ergm.Rd |only man/process_geeglm.Rd |only man/process_rq.Rd |only man/rcorr_tidiers.Rd |only man/ridgelm_tidiers.Rd | 5 man/rowwise_df_tidiers.Rd | 43 ++++-- man/rq_tidiers.Rd |only man/summary_tidiers.Rd | 4 man/survreg_tidiers.Rd | 4 man/svd_tidiers.Rd |only man/xyz_tidiers.Rd |only tests/testthat/test-dplyr.R | 2 tests/testthat/test-lme4.R | 24 +++ tests/testthat/test-nlme.R | 61 ++++----- tests/testthat/test-rowwise.R |only tests/testthat/test-tidy.R | 12 + vignettes/bootstrapping.Rmd | 2 93 files changed, 1065 insertions(+), 492 deletions(-)
Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.0.1 dated 2015-11-12 and 1.1.0 dated 2015-11-30
BEDMatrix-1.0.1/BEDMatrix/cleanup |only BEDMatrix-1.0.1/BEDMatrix/configure |only BEDMatrix-1.0.1/BEDMatrix/configure.ac |only BEDMatrix-1.0.1/BEDMatrix/src/Makevars.in |only BEDMatrix-1.0.1/BEDMatrix/tools |only BEDMatrix-1.1.0/BEDMatrix/DESCRIPTION | 11 +++++------ BEDMatrix-1.1.0/BEDMatrix/MD5 | 18 +++++------------- BEDMatrix-1.1.0/BEDMatrix/README.md | 10 ---------- BEDMatrix-1.1.0/BEDMatrix/src/BEDMatrix.cpp | 21 ++++++++++++++------- BEDMatrix-1.1.0/BEDMatrix/src/Makevars |only BEDMatrix-1.1.0/BEDMatrix/src/Makevars.win |only 11 files changed, 24 insertions(+), 36 deletions(-)
Title: A Toolbox for Writing Pretty Papers and Reports
Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based
reports and to prettify the output of various estimated models.
Author: Benjamin Hofner, with contributions by many others (see inst/CONTRIBUTIONS)
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between papeR versions 0.6-1 dated 2015-06-09 and 1.0-0 dated 2015-11-30
papeR-0.6-1/papeR/R/latex_table.R |only papeR-0.6-1/papeR/tests/regtest-prettify.R |only papeR-1.0-0/papeR/ChangeLog | 492 +++++++++++++++++++++++++++- papeR-1.0-0/papeR/DESCRIPTION | 21 - papeR-1.0-0/papeR/MD5 | 58 ++- papeR-1.0-0/papeR/NAMESPACE | 48 +- papeR-1.0-0/papeR/R/helpers.R | 41 +- papeR-1.0-0/papeR/R/labels.R | 199 +++-------- papeR-1.0-0/papeR/R/plot.R | 20 - papeR-1.0-0/papeR/R/prettify.R | 127 ++++--- papeR-1.0-0/papeR/R/summarize.R |only papeR-1.0-0/papeR/R/toLatex.R | 25 - papeR-1.0-0/papeR/README.md |only papeR-1.0-0/papeR/build |only papeR-1.0-0/papeR/inst/CITATION | 6 papeR-1.0-0/papeR/inst/NEWS.Rd | 37 +- papeR-1.0-0/papeR/inst/SPSS |only papeR-1.0-0/papeR/inst/doc |only papeR-1.0-0/papeR/man/get_options.Rd | 6 papeR-1.0-0/papeR/man/labels.data.frame.Rd | 104 ++--- papeR-1.0-0/papeR/man/latex_table_cont.Rd | 159 +-------- papeR-1.0-0/papeR/man/latex_table_fac.Rd | 134 +------ papeR-1.0-0/papeR/man/papeR-package.Rd | 18 - papeR-1.0-0/papeR/man/summarize.Rd |only papeR-1.0-0/papeR/man/summarize_factor.Rd |only papeR-1.0-0/papeR/man/summarize_numeric.Rd |only papeR-1.0-0/papeR/man/toLatex.Rd | 8 papeR-1.0-0/papeR/man/xtable_summary.Rd |only papeR-1.0-0/papeR/tests/regtest-plot.R |only papeR-1.0-0/papeR/tests/regtest-summarize.R |only papeR-1.0-0/papeR/tests/testthat |only papeR-1.0-0/papeR/tests/testthat.R |only papeR-1.0-0/papeR/vignettes |only 33 files changed, 910 insertions(+), 593 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.3 dated 2015-09-09 and 1.1.0 dated 2015-11-30
warbleR-1.0.3/warbleR/vignettes/Phae.ad.csv |only warbleR-1.1.0/warbleR/DESCRIPTION | 10 warbleR-1.1.0/warbleR/MD5 | 92 +- warbleR-1.1.0/warbleR/NAMESPACE | 8 warbleR-1.1.0/warbleR/R/autodetec.R | 99 +- warbleR-1.1.0/warbleR/R/checkwavs.R | 5 warbleR-1.1.0/warbleR/R/coor.graph.R |only warbleR-1.1.0/warbleR/R/coor.sing-data.R |only warbleR-1.1.0/warbleR/R/coor.test.R |only warbleR-1.1.0/warbleR/R/dfts.R |only warbleR-1.1.0/warbleR/R/imp.raven.R |only warbleR-1.1.0/warbleR/R/imp.syrinx.R |only warbleR-1.1.0/warbleR/R/lspec.R | 17 warbleR-1.1.0/warbleR/R/manualoc.R | 10 warbleR-1.1.0/warbleR/R/mp32wav.R | 26 warbleR-1.1.0/warbleR/R/querxc.R | 36 warbleR-1.1.0/warbleR/R/selection.files-data.R |only warbleR-1.1.0/warbleR/R/sig2noise.R | 26 warbleR-1.1.0/warbleR/R/sim.coor.sing-data.R |only warbleR-1.1.0/warbleR/R/snrspecs.R | 19 warbleR-1.1.0/warbleR/R/specan.R | 21 warbleR-1.1.0/warbleR/R/specreator.R | 26 warbleR-1.1.0/warbleR/R/trackfreqs.R | 31 warbleR-1.1.0/warbleR/R/warbleR-package.R | 27 warbleR-1.1.0/warbleR/R/xcmaps.R | 124 ++- warbleR-1.1.0/warbleR/R/xcorr.R |only warbleR-1.1.0/warbleR/R/xcorr.graph.R |only warbleR-1.1.0/warbleR/R/zzz.R |only warbleR-1.1.0/warbleR/data/coor.sing.rda |only warbleR-1.1.0/warbleR/data/selection.files.rda |only warbleR-1.1.0/warbleR/data/sim.coor.sing.rda |only warbleR-1.1.0/warbleR/inst/CITATION | 5 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.R | 22 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.Rmd | 35 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.html | 628 ++++++++-------- warbleR-1.1.0/warbleR/man/autodetec.Rd | 31 warbleR-1.1.0/warbleR/man/checkwavs.Rd | 5 warbleR-1.1.0/warbleR/man/coor.graph.Rd |only warbleR-1.1.0/warbleR/man/coor.sing.Rd |only warbleR-1.1.0/warbleR/man/coor.test.Rd |only warbleR-1.1.0/warbleR/man/dfts.Rd |only warbleR-1.1.0/warbleR/man/imp.raven.Rd |only warbleR-1.1.0/warbleR/man/imp.syrinx.Rd |only warbleR-1.1.0/warbleR/man/lspec.Rd | 6 warbleR-1.1.0/warbleR/man/mp32wav.Rd | 13 warbleR-1.1.0/warbleR/man/querxc.Rd | 18 warbleR-1.1.0/warbleR/man/selection.files.Rd |only warbleR-1.1.0/warbleR/man/sig2noise.Rd | 14 warbleR-1.1.0/warbleR/man/sim.coor.sing.Rd |only warbleR-1.1.0/warbleR/man/snrspecs.Rd | 10 warbleR-1.1.0/warbleR/man/specan.Rd | 6 warbleR-1.1.0/warbleR/man/specreator.Rd | 10 warbleR-1.1.0/warbleR/man/trackfreqs.Rd | 18 warbleR-1.1.0/warbleR/man/warbleR.Rd | 30 warbleR-1.1.0/warbleR/man/xcmaps.Rd | 14 warbleR-1.1.0/warbleR/man/xcorr.Rd |only warbleR-1.1.0/warbleR/man/xcorr.graph.Rd |only warbleR-1.1.0/warbleR/vignettes/Phae.snr.csv |only warbleR-1.1.0/warbleR/vignettes/acoustic_parameters.csv | 60 - warbleR-1.1.0/warbleR/vignettes/warbleR_workflow.Rmd | 35 60 files changed, 898 insertions(+), 639 deletions(-)
Title: Tools for Estimating Causal Dose Response Functions
Description: Functions and data to estimate causal dose response functions given continuous, ordinal, or binary treatments.
Author: Douglas Galagate [cre],
Joseph Schafer [aut]
Maintainer: Douglas Galagate <galagated@gmail.com>
Diff between causaldrf versions 0.2 dated 2015-10-17 and 0.3 dated 2015-11-30
DESCRIPTION | 16 +++++--- MD5 | 92 ++++++++++++++++++++++++++++++------------------- R/add_spl_est.R | 22 ++++++++++- R/aipwee_est.R | 40 +++++++++++++++++++-- R/bart_est.R | 37 ++++++++++++++++++- R/gam_est.R | 38 +++++++++++++++++--- R/hi_est.R | 72 +++++++++++++++++++++++++++++++++++--- R/hi_sim_data.R | 2 - R/iptw_est.R | 39 +++++++++++++++++++- R/ismw_est.R | 11 +++-- R/iw_est.R | 87 +++++++++++++++++++++++++++++++++++++++++++--- R/nw_est.R | 45 +++++++++++++++++++++-- R/overlap_fun.R | 38 ++++++++++++++------ R/prop_spline_est.R | 48 ++++++++++++++++--------- R/reg_est.R | 16 ++++++-- R/scalar_wts.R | 30 +++++++++++++++ R/sim_data.R | 2 - R/t_mod.R | 52 +++++++++++++++++++++++++++ R/wtrg_est.R | 8 +++- build |only inst |only man/add_spl_est.Rd | 10 ++++- man/aipwee_est.Rd | 33 +++++++++++++++++ man/bart_est.Rd | 34 +++++++++++++++++- man/gam_est.Rd | 22 +++++++++-- man/hi_est.Rd | 53 ++++++++++++++++++++++++++-- man/hi_sim_data.Rd | 2 - man/iptw_est.Rd | 19 +++++++++- man/ismw_est.Rd | 9 ++-- man/iw_est.Rd | 22 +++++++++-- man/nw_est.Rd | 14 +++++-- man/overlap_fun.Rd | 17 ++++----- man/prop_spline_est.Rd | 42 ++++++++++++++-------- man/reg_est.Rd | 10 ++++- man/scalar_wts.Rd | 2 + man/sim_data.Rd | 2 - man/t_mod.Rd | 2 + man/wtrg_est.Rd | 8 +++- vignettes |only 39 files changed, 827 insertions(+), 169 deletions(-)
Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness
correlations (HFCs) based on microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre],
Mareike Esser [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>
Diff between inbreedR versions 0.2.0 dated 2015-10-06 and 0.3.0 dated 2015-11-30
inbreedR-0.2.0/inbreedR/R/resample_g2.R |only inbreedR-0.2.0/inbreedR/man/resample_g2.Rd |only inbreedR-0.2.0/inbreedR/tests/testthat/test-resample-g2.R |only inbreedR-0.3.0/inbreedR/DESCRIPTION | 16 inbreedR-0.3.0/inbreedR/MD5 | 84 - inbreedR-0.3.0/inbreedR/NAMESPACE | 32 inbreedR-0.3.0/inbreedR/R/HHC.R | 144 +- inbreedR-0.3.0/inbreedR/R/check_data.R | 158 +- inbreedR-0.3.0/inbreedR/R/convert_raw.R | 118 +- inbreedR-0.3.0/inbreedR/R/g2_microsats.R | 337 ++--- inbreedR-0.3.0/inbreedR/R/g2_snps.R | 460 +++---- inbreedR-0.3.0/inbreedR/R/inbreedR.R | 128 +- inbreedR-0.3.0/inbreedR/R/mouse_msats.R | 30 inbreedR-0.3.0/inbreedR/R/mouse_snps.R | 32 inbreedR-0.3.0/inbreedR/R/plot.inbreed.R | 415 +++---- inbreedR-0.3.0/inbreedR/R/print.inbreed.R | 238 ++-- inbreedR-0.3.0/inbreedR/R/r2_Wf.R | 292 ++--- inbreedR-0.3.0/inbreedR/R/r2_hf.R | 454 +++---- inbreedR-0.3.0/inbreedR/R/sMLH.R | 151 +- inbreedR-0.3.0/inbreedR/R/simulate_g2.R |only inbreedR-0.3.0/inbreedR/R/simulate_r2_hf.R |only inbreedR-0.3.0/inbreedR/README.md | 86 - inbreedR-0.3.0/inbreedR/build/vignette.rds |binary inbreedR-0.3.0/inbreedR/inst/CITATION |only inbreedR-0.3.0/inbreedR/man/HHC.Rd | 83 - inbreedR-0.3.0/inbreedR/man/MLH.Rd |only inbreedR-0.3.0/inbreedR/man/bodyweight.Rd | 30 inbreedR-0.3.0/inbreedR/man/check_data.Rd | 88 - inbreedR-0.3.0/inbreedR/man/convert_raw.Rd | 67 - inbreedR-0.3.0/inbreedR/man/g2_microsats.Rd | 120 +- inbreedR-0.3.0/inbreedR/man/g2_snps.Rd | 135 +- inbreedR-0.3.0/inbreedR/man/inbreedR.Rd | 130 +- inbreedR-0.3.0/inbreedR/man/mouse_msats.Rd | 36 inbreedR-0.3.0/inbreedR/man/mouse_snps.Rd | 36 inbreedR-0.3.0/inbreedR/man/plot.inbreed.Rd | 60 - inbreedR-0.3.0/inbreedR/man/print.inbreed.Rd | 46 inbreedR-0.3.0/inbreedR/man/r2_Wf.Rd | 128 +- inbreedR-0.3.0/inbreedR/man/r2_hf.Rd | 127 +- inbreedR-0.3.0/inbreedR/man/sMLH.Rd | 69 - inbreedR-0.3.0/inbreedR/man/simulate_g2.Rd |only inbreedR-0.3.0/inbreedR/man/simulate_r2_hf.Rd |only inbreedR-0.3.0/inbreedR/tests/testthat/test-HHC.R | 2 inbreedR-0.3.0/inbreedR/tests/testthat/test-MLH.R |only inbreedR-0.3.0/inbreedR/tests/testthat/test-r2_Wf.R | 8 inbreedR-0.3.0/inbreedR/tests/testthat/test-r2_hf.R | 86 - inbreedR-0.3.0/inbreedR/tests/testthat/test-simulate_g2.R |only inbreedR-0.3.0/inbreedR/tests/testthat/test-simulate_r2_hf.R |only inbreedR-0.3.0/inbreedR/vignettes/bibliography.bib | 11 inbreedR-0.3.0/inbreedR/vignettes/inbreedR_step_by_step.Rmd | 635 +++++------ 49 files changed, 2615 insertions(+), 2457 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Description: This is the R Interface to the C API of IBM ILOG CPLEX. It necessarily depends on IBM ILOG CPLEX (>= 12.1).
Author: C. Jonathan Fritzemeier [cre, ctb], Gabriel Gelius-Dietrich [aut]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between cplexAPI versions 1.2.11 dated 2014-07-28 and 1.3.1 dated 2015-11-30
DESCRIPTION | 19 - LICENSE |only MD5 | 424 +++++++++++++++++----------------- README.md |only build/vignette.rds |binary inst/doc/cplexAPI.pdf |binary man/addChannelCPLEX.Rd | 5 man/addColsCPLEX.Rd | 5 man/addFpDestCPLEX.Rd | 5 man/addIndConstrCPLEX.Rd | 5 man/addMIPstartsCPLEX.Rd | 5 man/addQConstrCPLEX.Rd | 5 man/addRowsCPLEX.Rd | 5 man/baroptCPLEX.Rd | 5 man/baseWriteCPLEX.Rd | 5 man/basicPresolveCPLEX.Rd | 5 man/boundSaCPLEX.Rd | 5 man/cLpWriteCPLEX.Rd | 5 man/checkAddColsCPLEX.Rd | 5 man/checkAddRowsCPLEX.Rd | 5 man/checkChgCoefListCPLEX.Rd | 5 man/checkCopyColTypeCPLEX.Rd | 5 man/checkCopyLpCPLEX.Rd | 5 man/checkCopyLpwNamesCPLEX.Rd | 5 man/checkCopyQPsepCPLEX.Rd | 5 man/checkCopyQuadCPLEX.Rd | 5 man/checkValsCPLEX.Rd | 5 man/chgBndsCPLEX.Rd | 5 man/chgCoefCPLEX.Rd | 5 man/chgCoefListCPLEX.Rd | 5 man/chgColNameCPLEX.Rd | 5 man/chgColTypeCPLEX.Rd | 5 man/chgColsBndsCPLEX.Rd | 5 man/chgMIPstartsCPLEX.Rd | 5 man/chgNameCPLEX.Rd | 5 man/chgObjCPLEX.Rd | 5 man/chgProbNameCPLEX.Rd | 5 man/chgProbTypeCPLEX.Rd | 5 man/chgQPcoefCPLEX.Rd | 5 man/chgRhsCPLEX.Rd | 5 man/chgRngValCPLEX.Rd | 5 man/chgRowNameCPLEX.Rd | 5 man/chgSenseCPLEX.Rd | 5 man/chgTerminateCPLEX.Rd | 5 man/cleanupCoefCPLEX.Rd | 5 man/cloneProbCPLEX.Rd | 5 man/closeEnvCPLEX.Rd | 5 man/closeFileCPLEX.Rd | 5 man/closeProbCPLEX.Rd | 5 man/completelpCPLEX.Rd | 5 man/copyBaseCPLEX.Rd | 5 man/copyColTypeCPLEX.Rd | 5 man/copyLpCPLEX.Rd | 5 man/copyLpwNamesCPLEX.Rd | 5 man/copyObjNameCPLEX.Rd | 5 man/copyOrderCPLEX.Rd | 5 man/copyPartBaseCPLEX.Rd | 5 man/copyQPsepCPLEX.Rd | 5 man/copyQuadCPLEX.Rd | 5 man/copyStartCPLEX.Rd | 5 man/cplexAPI-package.Rd | 5 man/cplexConstants.Rd | 5 man/cplexError-class.Rd | 5 man/cplexPtr-class.Rd | 5 man/delChannelCPLEX.Rd | 5 man/delColsCPLEX.Rd | 5 man/delFpDestCPLEX.Rd | 5 man/delIndConstrsCPLEX.Rd | 5 man/delMIPstartsCPLEX.Rd | 5 man/delNamesCPLEX.Rd | 5 man/delProbCPLEX.Rd | 5 man/delQConstrsCPLEX.Rd | 5 man/delRowsCPLEX.Rd | 5 man/delSetColsCPLEX.Rd | 5 man/delSetRowsCPLEX.Rd | 5 man/delTerminateCPLEX.Rd | 5 man/disconnectChannelCPLEX.Rd | 5 man/dualWriteCPLEX.Rd | 5 man/dualoptCPLEX.Rd | 5 man/feasOptCPLEX.Rd | 5 man/fileputCPLEX.Rd | 5 man/flushChannelCPLEX.Rd | 5 man/flushStdChannelsCPLEX.Rd | 5 man/freePresolveCPLEX.Rd | 5 man/getBaseCPLEX.Rd | 5 man/getBestObjValCPLEX.Rd | 5 man/getChannelsCPLEX.Rd | 5 man/getChgParmCPLEX.Rd | 5 man/getCoefCPLEX.Rd | 5 man/getColIndexCPLEX.Rd | 5 man/getColInfeasCPLEX.Rd | 5 man/getColNameCPLEX.Rd | 5 man/getColTypeCPLEX.Rd | 5 man/getColsCPLEX.Rd | 5 man/getConflictCPLEX.Rd | 5 man/getConflictExtCPLEX.Rd | 5 man/getCutoffCPLEX.Rd | 5 man/getDblParmCPLEX.Rd | 5 man/getDblQualCPLEX.Rd | 5 man/getDbsCntCPLEX.Rd | 5 man/getDjCPLEX.Rd | 5 man/getErrorStrCPLEX.Rd | 5 man/getGradCPLEX.Rd | 5 man/getIndConstrCPLEX.Rd | 5 man/getInfoDblParmCPLEX.Rd | 5 man/getInfoIntParmCPLEX.Rd | 5 man/getInfoLongParmCPLEX.Rd | 5 man/getInfoStrParmCPLEX.Rd | 5 man/getIntParmCPLEX.Rd | 5 man/getIntQualCPLEX.Rd | 5 man/getItCntCPLEX.Rd | 5 man/getLogFileCPLEX.Rd | 5 man/getLongParmCPLEX.Rd | 5 man/getLowBndsIdsCPLEX.Rd | 5 man/getLowerBndsCPLEX.Rd | 5 man/getMIPrelGapCPLEX.Rd | 5 man/getMIPstartIndexCPLEX.Rd | 5 man/getMIPstartNameCPLEX.Rd | 5 man/getMIPstartsCPLEX.Rd | 5 man/getMethodCPLEX.Rd | 5 man/getNumColsCPLEX.Rd | 5 man/getNumMIPstartsCPLEX.Rd | 5 man/getNumNnzCPLEX.Rd | 5 man/getNumQPnzCPLEX.Rd | 5 man/getNumQuadCPLEX.Rd | 5 man/getNumRowsCPLEX.Rd | 5 man/getObjCPLEX.Rd | 5 man/getObjDirCPLEX.Rd | 5 man/getObjNameCPLEX.Rd | 5 man/getObjOffsetCPLEX.Rd | 5 man/getObjValCPLEX.Rd | 5 man/getOrderCPLEX.Rd | 5 man/getParmNameCPLEX.Rd | 5 man/getParmNumCPLEX.Rd | 5 man/getParmTypeCPLEX.Rd | 5 man/getParmValCPLEX.Rd | 5 man/getPhase1CntCPLEX.Rd | 5 man/getPiCPLEX.Rd | 5 man/getPreStatCPLEX.Rd | 5 man/getProbNameCPLEX.Rd | 5 man/getProbTypeCPLEX.Rd | 5 man/getProbVarCPLEX.Rd | 5 man/getQConstrCPLEX.Rd | 5 man/getQPcoefCPLEX.Rd | 5 man/getQuadCPLEX.Rd | 5 man/getRedLpCPLEX.Rd | 5 man/getRhsCPLEX.Rd | 5 man/getRngValCPLEX.Rd | 5 man/getRowIndexCPLEX.Rd | 5 man/getRowInfeasCPLEX.Rd | 5 man/getRowNameCPLEX.Rd | 5 man/getRowsCPLEX.Rd | 5 man/getSenseCPLEX.Rd | 5 man/getSiftItCntCPLEX.Rd | 5 man/getSiftPase1CntCPLEX.Rd | 5 man/getSlackCPLEX.Rd | 5 man/getStatCPLEX.Rd | 5 man/getStatStrCPLEX.Rd | 5 man/getStrParmCPLEX.Rd | 5 man/getSubMethodCPLEX.Rd | 5 man/getSubStatCPLEX.Rd | 5 man/getTimeCPLEX.Rd | 5 man/getUppBndsIdsCPLEX.Rd | 5 man/getUpperBndsCPLEX.Rd | 5 man/getVersionCPLEX.Rd | 5 man/hybbaroptCPLEX.Rd | 5 man/hybnetoptCPLEX.Rd | 5 man/initProbCPLEX.Rd | 5 man/lpoptCPLEX.Rd | 5 man/mipoptCPLEX.Rd | 5 man/newColsCPLEX.Rd | 5 man/newRowsCPLEX.Rd | 5 man/objSaCPLEX.Rd | 5 man/openEnvCPLEX.Rd | 5 man/openFileCPLEX.Rd | 5 man/openProbCPLEX.Rd | 5 man/ordWriteCPLEX.Rd | 5 man/preslvWriteCPLEX.Rd | 5 man/presolveCPLEX.Rd | 5 man/primoptCPLEX.Rd | 5 man/printTerminateCPLEX.Rd | 5 man/qpoptCPLEX.Rd | 5 man/readCopyBaseCPLEX.Rd | 5 man/readCopyMIPstartsCPLEX.Rd | 5 man/readCopyOrderCPLEX.Rd | 5 man/readCopyParmCPLEX.Rd | 5 man/readCopyProbCPLEX.Rd | 5 man/readCopySolCPLEX.Rd | 5 man/refineConflictCPLEX.Rd | 5 man/refineConflictExtCPLEX.Rd | 5 man/refineMIPstartConflictCPLEX.Rd | 5 man/refineMIPstartConflictExtCPLEX.Rd | 5 man/return_codeCPLEX.Rd | 5 man/rhsSaCPLEX.Rd | 5 man/setDblParmCPLEX.Rd | 5 man/setDefaultParmCPLEX.Rd | 5 man/setIntParmCPLEX.Rd | 5 man/setLogFileCPLEX.Rd | 5 man/setLongParmCPLEX.Rd | 5 man/setObjDirCPLEX.Rd | 5 man/setStrParmCPLEX.Rd | 5 man/setTerminateCPLEX.Rd | 5 man/siftoptCPLEX.Rd | 5 man/solWriteCPLEX.Rd | 5 man/solnInfoCPLEX.Rd | 5 man/solutionCPLEX.Rd | 5 man/status_codeCPLEX.Rd | 5 man/tightenBndsCPLEX.Rd | 5 man/tuneParmCPLEX.Rd | 5 man/unscaleProbCPLEX.Rd | 5 man/writeMIPstartsCPLEX.Rd | 5 man/writeParmCPLEX.Rd | 5 man/writeProbCPLEX.Rd | 5 src/Makevars.win | 2 214 files changed, 845 insertions(+), 635 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.5 dated 2015-08-27 and 1.6 dated 2015-11-30
DESCRIPTION | 8 +- MD5 | 104 ++++++++++++++------------- NAMESPACE | 2 NEWS | 14 +++ R/anthrCases.R | 51 +++++-------- R/computSizesHipamAnthropom.R |only R/computSizesTrimowa.R |only R/matPercs.R | 2 R/plotPrototypes.R | 8 +- R/plotTrimmOutl.R | 8 +- R/trimmOutl.R | 57 ++++++--------- inst/doc/Anthropometry.R | 55 ++++++-------- inst/doc/Anthropometry.Rnw | 147 +++++++++++++++++++-------------------- inst/doc/Anthropometry.pdf |binary man/Anthropometry-package.Rd | 6 + man/HartiganShapes.Rd | 113 +++-------------------------- man/LloydShapes.Rd | 98 ++------------------------ man/TDDclust.Rd | 12 +-- man/USAFSurvey.Rd | 4 + man/anthrCases.Rd | 37 ++++----- man/archetypesBoundary.Rd | 23 +++--- man/archetypoids.Rd | 89 +++-------------------- man/array3Dlandm.Rd | 2 man/cdfDissWomenPrototypes.Rd | 50 ++++++------- man/checkBranchLocalIMO.Rd | 3 man/checkBranchLocalMO.Rd | 3 man/computSizesHipamAnthropom.Rd |only man/computSizesTrimowa.Rd |only man/descrDissTrunks.Rd | 17 ++-- man/figures8landm.Rd | 6 - man/getDistMatrix.Rd | 6 - man/hipamAnthropom.Rd | 36 +++------ man/matPercs.Rd | 28 +++---- man/nearestToArchetypes.Rd | 21 ++--- man/optraShapes.Rd | 2 man/overlapBiclustersByRows.Rd | 2 man/percentilsArchetypoid.Rd | 23 +++--- man/plotPrototypes.Rd | 98 +++----------------------- man/plotTreeHipamAnthropom.Rd | 22 +---- man/plotTrimmOutl.Rd | 82 +++------------------ man/preprocessing.Rd | 3 man/projShapes.Rd | 31 +++----- man/qtranShapes.Rd | 2 man/screeArchetypal.Rd | 47 ++++++------ man/shapes3dShapes.Rd | 22 ++--- man/skeletonsArchetypal.Rd | 32 -------- man/stepArchetypesRawData.Rd | 24 +++--- man/stepArchetypoids.Rd | 19 ++--- man/trimmOutl.Rd | 34 ++++----- man/trimmedLloydShapes.Rd | 20 ++--- man/trimmedoid.Rd | 8 -- man/trimowa.Rd | 32 ++++++-- man/xyplotPCArchetypes.Rd | 20 +++-- vignettes/AA.pdf |binary vignettes/Anthropometry.Rnw | 147 +++++++++++++++++++-------------------- 55 files changed, 656 insertions(+), 1024 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 0.6 dated 2015-11-25 and 0.8 dated 2015-11-30
DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/dom_optimal_allocation.R | 55 ++++++++++++++++++++++-------------------- R/s2.R | 4 ++- man/dom_optimal_allocation.Rd | 5 --- man/surveyplanning-package.Rd | 4 +-- 6 files changed, 44 insertions(+), 42 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Genome-Wide Association Analysis of a Biomarker Accounting for
Limit of Detection
Description: Genome-wide association (GWAS) analyses
of a biomarker that account for the limit of detection.
Author: Ahmad Vaez, Ilja M. Nolte, Peter J. van der Most
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between lodGWAS versions 1.0-6 dated 2015-10-26 and 1.0-7 dated 2015-11-30
lodGWAS-1.0-6/lodGWAS/R/packaging_v10-6.r |only lodGWAS-1.0-6/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_6.txt |only lodGWAS-1.0-7/lodGWAS/DESCRIPTION | 8 ++++---- lodGWAS-1.0-7/lodGWAS/MD5 | 12 ++++++------ lodGWAS-1.0-7/lodGWAS/R/packaging_v10-7.r |only lodGWAS-1.0-7/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_7.txt |only lodGWAS-1.0-7/lodGWAS/man/lodGWAS-package.Rd | 4 ++-- lodGWAS-1.0-7/lodGWAS/man/lod_GWAS.Rd | 12 ++++++------ lodGWAS-1.0-7/lodGWAS/man/lod_QC.Rd | 2 +- 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>
Diff between fitdistrplus versions 1.0-5 dated 2015-09-21 and 1.0-6 dated 2015-11-30
DESCRIPTION | 14 +++++++------- MD5 | 11 ++++++----- R/util-startarg.R | 12 ++++++------ inst/NEWS | 7 +++++++ inst/doc/paper2JSS.pdf |binary man/fitdist.Rd | 22 +++++++++++++++++++++- tests/test-startingvalues.R |only 7 files changed, 47 insertions(+), 19 deletions(-)
Title: R Interface to 'EPP-Lab', a Java Program for Exploratory
Projection Pursuit
Description: An R Interface to 'EPP-lab' v1.0. 'EPP-lab' is a Java program for
projection pursuit using genetic algorithms written by Alain Berro and S. Larabi
Marie-Sainte and is included in the package. The 'EPP-lab' sources are available
under https://github.com/fischuu/EPP-lab.git.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between REPPlab versions 0.9.2 dated 2015-10-02 and 0.9.3 dated 2015-11-30
DESCRIPTION | 18 ++++++++++------- MD5 | 44 +++++++++++++++++++++---------------------- NAMESPACE | 2 - R/EPPlabAgg.R | 2 - R/REPPlab-package.R | 19 ++++++++++-------- inst/ChangeLog | 7 ++++++ man/EPPlab.Rd | 6 +++-- man/EPPlabAgg.Rd | 28 ++++++++++++++------------- man/EPPlabOutlier.Rd | 8 ++++--- man/REPPlab-package.Rd | 11 ++++++---- man/ReliabilityData.Rd | 14 +++++++------ man/WhitenSVD.Rd | 5 +++- man/coef.epplab.Rd | 4 ++- man/fitted.epplab.Rd | 4 ++- man/pairs.epplab.Rd | 4 ++- man/plot.epplab.Rd | 4 ++- man/plot.epplabOutlier.Rd | 8 ++++--- man/predict.epplab.Rd | 4 ++- man/print.epplab.Rd | 4 ++- man/print.epplabOutlier.Rd | 8 ++++--- man/screeplot.epplab.Rd | 4 ++- man/summary.epplab.Rd | 4 ++- man/summary.epplabOutlier.Rd | 8 ++++--- 23 files changed, 135 insertions(+), 85 deletions(-)
Title: R Dependency Injection
Description: R dependency injection framework. Dependency injection allows
a program design to follow the dependency inversion principle. The user
delegates to external code (the injector) the responsibility of providing its
dependencies. This separates the responsibilities of use and construction.
Author: Lev Kuznetsov
Maintainer: Lev Kuznetsov <levk@jimmy.harvard.edu>
Diff between injectoR versions 0.2.3 dated 2015-11-23 and 0.2.4 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/injector.R | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Modern Functions for Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'),
using a GUI - graphical user interface.
QCA is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a boolean algorithm that results in a minimal
causal combination which explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Thomas Richter [ctb, cph] (raphael.boolean.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [ctb] (package QCA versions from 1.0-0 to 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCAGUI versions 1.9-6 dated 2013-03-19 and 2.0 dated 2015-11-30
QCAGUI-1.9-6/QCAGUI/NEWS |only QCAGUI-1.9-6/QCAGUI/R/Rexcel-specific.R |only QCAGUI-1.9-6/QCAGUI/R/analyze-menu.R |only QCAGUI-1.9-6/QCAGUI/R/commander.R |only QCAGUI-1.9-6/QCAGUI/R/data-menu.R |only QCAGUI-1.9-6/QCAGUI/R/file-menu.R |only QCAGUI-1.9-6/QCAGUI/R/globals.R |only QCAGUI-1.9-6/QCAGUI/R/graphs-menu.R |only QCAGUI-1.9-6/QCAGUI/R/ismdi.R |only QCAGUI-1.9-6/QCAGUI/R/sciviews-specific.R |only QCAGUI-1.9-6/QCAGUI/R/startup.R |only QCAGUI-1.9-6/QCAGUI/R/statistics-summaries-menu.R |only QCAGUI-1.9-6/QCAGUI/R/statistics-tables-menu.R |only QCAGUI-1.9-6/QCAGUI/R/utilities.R |only QCAGUI-1.9-6/QCAGUI/inst/doc |only QCAGUI-1.9-6/QCAGUI/inst/etc |only QCAGUI-1.9-6/QCAGUI/man/CFA.Rd |only QCAGUI-1.9-6/QCAGUI/man/Commander-es.Rd |only QCAGUI-1.9-6/QCAGUI/man/Commander.Rd |only QCAGUI-1.9-6/QCAGUI/man/Compute.Rd |only QCAGUI-1.9-6/QCAGUI/man/Hist.Rd |only QCAGUI-1.9-6/QCAGUI/man/Plugins.Rd |only QCAGUI-1.9-6/QCAGUI/man/QCAGUI-package.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr-internal.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr.Utilities.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr.sciviews-specific.Rd |only QCAGUI-1.9-6/QCAGUI/man/RcmdrPager.Rd |only QCAGUI-1.9-6/QCAGUI/man/RecodeDialog.Rd |only QCAGUI-1.9-6/QCAGUI/man/generalizedLinearModel.Rd |only QCAGUI-1.9-6/QCAGUI/man/hierarchicalCluster.Rd |only QCAGUI-1.9-6/QCAGUI/man/linearModel.Rd |only QCAGUI-1.9-6/QCAGUI/man/mergeRows.Rd |only QCAGUI-1.9-6/QCAGUI/man/numSummary.Rd |only QCAGUI-1.9-6/QCAGUI/man/partial.cor.Rd |only QCAGUI-1.9-6/QCAGUI/man/plotMeans.Rd |only QCAGUI-1.9-6/QCAGUI/man/reliability.Rd |only QCAGUI-1.9-6/QCAGUI/man/totPercents.Rd |only QCAGUI-1.9-6/QCAGUI/src/Makevars.win |only QCAGUI-1.9-6/QCAGUI/src/ismdi.c |only QCAGUI-2.0/QCAGUI/DESCRIPTION | 72 ++++--- QCAGUI-2.0/QCAGUI/MD5 | 201 ++++++++++++++------- QCAGUI-2.0/QCAGUI/NAMESPACE | 140 ++++++++------ QCAGUI-2.0/QCAGUI/R/allExpressions.R |only QCAGUI-2.0/QCAGUI/R/base3rows.R |only QCAGUI-2.0/QCAGUI/R/calibrate.R |only QCAGUI-2.0/QCAGUI/R/createChart.R |only QCAGUI-2.0/QCAGUI/R/createMatrix.R |only QCAGUI-2.0/QCAGUI/R/createString.R |only QCAGUI-2.0/QCAGUI/R/deMorgan.R |only QCAGUI-2.0/QCAGUI/R/demoChart.R |only QCAGUI-2.0/QCAGUI/R/eqmcc.R |only QCAGUI-2.0/QCAGUI/R/eqmccLoop.R |only QCAGUI-2.0/QCAGUI/R/export.R |only QCAGUI-2.0/QCAGUI/R/factorize.R |only QCAGUI-2.0/QCAGUI/R/findSubsets.R |only QCAGUI-2.0/QCAGUI/R/findSupersets.R |only QCAGUI-2.0/QCAGUI/R/findTh.R |only QCAGUI-2.0/QCAGUI/R/fuzzyand.R |only QCAGUI-2.0/QCAGUI/R/fuzzyor.R |only QCAGUI-2.0/QCAGUI/R/getRow.R |only QCAGUI-2.0/QCAGUI/R/getSolution.R |only QCAGUI-2.0/QCAGUI/R/intersection.R |only QCAGUI-2.0/QCAGUI/R/is.print.R |only QCAGUI-2.0/QCAGUI/R/onAttach.R |only QCAGUI-2.0/QCAGUI/R/pof.R |only QCAGUI-2.0/QCAGUI/R/possibleNumeric.R |only QCAGUI-2.0/QCAGUI/R/prettyString.R |only QCAGUI-2.0/QCAGUI/R/prettyTable.R |only QCAGUI-2.0/QCAGUI/R/recode.R |only QCAGUI-2.0/QCAGUI/R/rowDominance.R |only QCAGUI-2.0/QCAGUI/R/runGUI.R |only QCAGUI-2.0/QCAGUI/R/solveChart.R |only QCAGUI-2.0/QCAGUI/R/sortMatrix.R |only QCAGUI-2.0/QCAGUI/R/sortVector.R |only QCAGUI-2.0/QCAGUI/R/string.R |only QCAGUI-2.0/QCAGUI/R/superSubset.R |only QCAGUI-2.0/QCAGUI/R/superSubsetOld.R |only QCAGUI-2.0/QCAGUI/R/truthTable.R |only QCAGUI-2.0/QCAGUI/R/verifyQCA.R |only QCAGUI-2.0/QCAGUI/R/writePrimeimp.R |only QCAGUI-2.0/QCAGUI/R/writeSolution.R |only QCAGUI-2.0/QCAGUI/data |only QCAGUI-2.0/QCAGUI/inst/CITATION | 75 ++++++- QCAGUI-2.0/QCAGUI/inst/ChangeLog |only QCAGUI-2.0/QCAGUI/inst/TODO |only QCAGUI-2.0/QCAGUI/inst/gui |only QCAGUI-2.0/QCAGUI/man/QCAGUI-internal.Rd |only QCAGUI-2.0/QCAGUI/man/QCAGUI.package.Rd |only QCAGUI-2.0/QCAGUI/man/allExpressions.Rd |only QCAGUI-2.0/QCAGUI/man/calibrate.Rd |only QCAGUI-2.0/QCAGUI/man/createMatrix.Rd |only QCAGUI-2.0/QCAGUI/man/d.biodiversity.Rd |only QCAGUI-2.0/QCAGUI/man/d.education.Rd |only QCAGUI-2.0/QCAGUI/man/d.graduate.Rd |only QCAGUI-2.0/QCAGUI/man/d.health.Rd |only QCAGUI-2.0/QCAGUI/man/d.homeless.Rd |only QCAGUI-2.0/QCAGUI/man/d.jobsecurity.Rd |only QCAGUI-2.0/QCAGUI/man/d.napoleon.Rd |only QCAGUI-2.0/QCAGUI/man/d.partybans.Rd |only QCAGUI-2.0/QCAGUI/man/d.represent.Rd |only QCAGUI-2.0/QCAGUI/man/d.socialsecurity.Rd |only QCAGUI-2.0/QCAGUI/man/d.stakeholder.Rd |only QCAGUI-2.0/QCAGUI/man/d.transport.Rd |only QCAGUI-2.0/QCAGUI/man/d.urban.Rd |only QCAGUI-2.0/QCAGUI/man/deMorgan.Rd |only QCAGUI-2.0/QCAGUI/man/demoChart.Rd |only QCAGUI-2.0/QCAGUI/man/eqmcc.Rd |only QCAGUI-2.0/QCAGUI/man/export.Rd |only QCAGUI-2.0/QCAGUI/man/factorize.Rd |only QCAGUI-2.0/QCAGUI/man/findSubsets.Rd |only QCAGUI-2.0/QCAGUI/man/findSupersets.Rd |only QCAGUI-2.0/QCAGUI/man/findTh.Rd |only QCAGUI-2.0/QCAGUI/man/getRow.Rd |only QCAGUI-2.0/QCAGUI/man/intersection.Rd |only QCAGUI-2.0/QCAGUI/man/pof.Rd |only QCAGUI-2.0/QCAGUI/man/recode.Rd |only QCAGUI-2.0/QCAGUI/man/runGUI.Rd |only QCAGUI-2.0/QCAGUI/man/solveChart.Rd |only QCAGUI-2.0/QCAGUI/man/superSubset.Rd |only QCAGUI-2.0/QCAGUI/man/truthTable.Rd |only QCAGUI-2.0/QCAGUI/src/allSol.c |only QCAGUI-2.0/QCAGUI/src/findSubsets.c |only QCAGUI-2.0/QCAGUI/src/m2.c |only QCAGUI-2.0/QCAGUI/src/removeRedundants.c |only QCAGUI-2.0/QCAGUI/src/solveChart.c |only QCAGUI-2.0/QCAGUI/src/superSubset.c |only QCAGUI-2.0/QCAGUI/src/truthTable.c |only 127 files changed, 332 insertions(+), 156 deletions(-)
Title: Discretization-Based Direct Random Sample Generation
Description: Two discretization-based Monte Carlo algorithms, namely the Fu-Wang algorithm and the Wang-Lee algorithm, are provided for random sample generation from a high dimensional distribution of complex structure. The normalizing constant of the target distribution needs not to be known.
Author: Chel Hee Lee [aut, cre],
Liqun Wang [aut]
Maintainer: Chel Hee Lee <gnustats@gmail.com>
Diff between dsample versions 0.91.1.5 dated 2015-07-02 and 0.91.2.2 dated 2015-11-30
dsample-0.91.1.5/dsample/man/summary.dsample.Rd |only dsample-0.91.2.2/dsample/ChangeLog | 8 + dsample-0.91.2.2/dsample/DESCRIPTION | 10 - dsample-0.91.2.2/dsample/MD5 | 16 +- dsample-0.91.2.2/dsample/NAMESPACE | 1 dsample-0.91.2.2/dsample/R/dsample.R | 162 ++++++++++++------------ dsample-0.91.2.2/dsample/demo |only dsample-0.91.2.2/dsample/man/dsample.Rd | 25 +-- dsample-0.91.2.2/dsample/man/plot.Rd |only dsample-0.91.2.2/dsample/man/summary_dsample.Rd |only 10 files changed, 115 insertions(+), 107 deletions(-)
Title: A Toolbox for Writing 'swirl' Courses
Description: A set of tools for writing and sharing interactive courses
to be used with swirl.
Author: Sean Kross [aut, cre],
Nick Carchedi [aut],
Chih-Cheng Liang [ctb],
Wush Wu [ctb]
Maintainer: Sean Kross <sean@seankross.com>
Diff between swirlify versions 0.4 dated 2015-11-25 and 0.4.1 dated 2015-11-29
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.2.1 dated 2015-09-15 and 0.2.3 dated 2015-11-29
DESCRIPTION | 9 +-- MD5 | 48 ++++++++--------- NAMESPACE | 2 NEWS | 9 +++ R/rhandsontable.R | 39 +++++++------- inst/doc/intro_rhandsontable.Rmd | 2 inst/doc/intro_rhandsontable.html | 100 ++++++++++++++++++------------------ inst/htmlwidgets/rhandsontable.js | 18 +++++- inst/htmlwidgets/rhandsontable.yaml | 2 man/hot_cell.Rd | 2 man/hot_col.Rd | 6 +- man/hot_cols.Rd | 2 man/hot_context_menu.Rd | 2 man/hot_heatmap.Rd | 4 - man/hot_rows.Rd | 2 man/hot_table.Rd | 6 +- man/hot_to_r.Rd | 2 man/hot_validate_character.Rd | 2 man/hot_validate_numeric.Rd | 4 - man/rHandsontableOutput.Rd | 4 - man/renderRHandsontable.Rd | 8 +- man/rhandsontable-exports.Rd | 2 man/rhandsontable-package.Rd | 2 man/rhandsontable.Rd | 2 vignettes/intro_rhandsontable.Rmd | 2 25 files changed, 156 insertions(+), 125 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi <sinhrks@gmail.com> and Yuan Tang
<terrytangyuan@gmail.com>
Maintainer: Masaaki Horikoshi <sinhrks@gmail.com>
Diff between ggfortify versions 0.0.4 dated 2015-10-04 and 0.1.0 dated 2015-11-29
DESCRIPTION | 27 ++- MD5 | 256 ++++++++++++++++++++---------------- NAMESPACE | 13 + R/base_fortify_list.R | 39 ++++- R/base_fortify_ts.R | 7 R/fortify_MSwM.R | 3 R/fortify_base.R | 6 R/fortify_changepoint.R | 4 R/fortify_cluster.R | 10 - R/fortify_forecast.R | 6 R/fortify_glmnet.R |only R/fortify_stats.R | 22 +-- R/fortify_stats_density.R | 1 R/fortify_stats_lm.R | 34 ++-- R/fortify_surv.R | 15 +- R/geom.R | 75 +++++++--- R/ggfortify.R | 2 R/plotlib.R | 145 ++++++++++++++++++-- R/tslib.R | 10 - R/util.R | 25 +++ build/vignette.rds |binary inst/doc/basics.R | 53 +++++++ inst/doc/basics.Rmd | 119 +++++++++++++++- inst/doc/basics.html | 145 +++++++++++++++++--- inst/doc/intro_Chinese.R |only inst/doc/intro_Chinese.Rmd |only inst/doc/intro_Chinese.html |only inst/doc/plot_dist.R |only inst/doc/plot_dist.Rmd |only inst/doc/plot_dist.html |only inst/doc/plot_lm.R |only inst/doc/plot_lm.Rmd |only inst/doc/plot_lm.html |only inst/doc/plot_pca.R |only inst/doc/plot_pca.Rmd |only inst/doc/plot_pca.html |only inst/doc/plot_surv.R |only inst/doc/plot_surv.Rmd |only inst/doc/plot_surv.html |only inst/doc/plot_ts.R |only inst/doc/plot_ts.Rmd |only inst/doc/plot_ts.html |only man/apply_facets.Rd | 2 man/autoplot.MSM.lm.Rd | 2 man/autoplot.aareg.Rd | 2 man/autoplot.acf.Rd | 2 man/autoplot.breakpoints.Rd | 2 man/autoplot.cpt.Rd | 2 man/autoplot.cv.glmnet.Rd |only man/autoplot.density.Rd | 2 man/autoplot.forecast.Rd | 2 man/autoplot.ggmultiplot.Rd |only man/autoplot.ggplot.Rd |only man/autoplot.glmnet.Rd |only man/autoplot.kmeans.Rd | 2 man/autoplot.list.Rd | 13 + man/autoplot.lm.Rd | 2 man/autoplot.matrix.Rd | 2 man/autoplot.pca_common.Rd | 2 man/autoplot.spec.Rd | 2 man/autoplot.stepfun.Rd | 2 man/autoplot.survfit.Rd | 4 man/autoplot.ts.Rd | 2 man/autoplot.tsmodel.Rd | 2 man/autoplot.varprd.Rd | 2 man/cbind_wraps.Rd | 2 man/check_names.Rd | 2 man/confint.acf.Rd | 2 man/deprecate.warning.Rd | 2 man/fitted.ar.Rd | 2 man/fortify.MSM.lm.Rd | 2 man/fortify.aareg.Rd | 2 man/fortify.acf.Rd | 2 man/fortify.cpt.Rd | 2 man/fortify.cv.glmnet.Rd |only man/fortify.density.Rd | 2 man/fortify.dist.Rd | 2 man/fortify.ets.Rd | 2 man/fortify.factanal.Rd | 2 man/fortify.forecast.Rd | 2 man/fortify.glmnet.Rd |only man/fortify.kmeans.Rd | 2 man/fortify.lfda.Rd | 4 man/fortify.list.Rd | 2 man/fortify.matrix.Rd | 2 man/fortify.prcomp.Rd | 2 man/fortify.spec.Rd | 2 man/fortify.stepfun.Rd | 2 man/fortify.survfit.Rd | 2 man/fortify.table.Rd | 2 man/fortify.ts.Rd | 2 man/fortify.tsmodel.Rd | 2 man/fortify.varprd.Rd | 2 man/fortify_base.Rd | 2 man/geom_confint.Rd | 2 man/geom_factory.Rd | 2 man/get.dtindex.Rd | 2 man/get.dtindex.continuous.Rd | 2 man/get.layout.Rd | 2 man/get_geom_function.Rd | 2 man/ggcpgram.Rd | 2 man/ggdistribution.Rd | 2 man/ggfortify.Rd | 2 man/ggfreqplot.Rd | 2 man/gglagplot.Rd | 2 man/ggmultiplot-class.Rd | 31 ++++ man/ggtsdiag.Rd | 2 man/infer.Rd | 2 man/is.univariate.Rd | 2 man/is_derived_from.Rd |only man/plot_confint.Rd | 2 man/plot_label.Rd | 15 +- man/plus-ggmultiplot-ANY-method.Rd | 2 man/post_autoplot.Rd | 2 man/post_fortify.Rd | 2 man/print-ggmultiplot-method.Rd | 2 man/rbind_ts.Rd | 2 man/residuals.ar.Rd | 2 man/show-ggmultiplot-method.Rd | 2 man/support_autoplot.Rd |only man/unscale.Rd | 2 tests/test-all.R | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-MSwM.R |only tests/testthat/test-base-infer.R | 24 ++- tests/testthat/test-base.R | 32 ++++ tests/testthat/test-base_ts.R | 4 tests/testthat/test-changepoint.R | 8 - tests/testthat/test-cluster.R | 12 + tests/testthat/test-forecast.R | 27 ++- tests/testthat/test-glmnet.R |only tests/testthat/test-plotlib.R | 240 +++++++++++++++++++++++++++++---- tests/testthat/test-stats-density.R |only tests/testthat/test-stats-lm.R | 2 tests/testthat/test-stats.R | 109 ++++++--------- tests/testthat/test-surv.R | 43 +++++- tests/testthat/test-ts.R | 47 ++++++ tests/testthat/test-tslib.R | 23 +++ tests/testthat/test-util.R | 2 tests/testthat/test-vars.R | 11 + tests/testthat/test_lint.R |only vignettes/basics.Rmd | 119 +++++++++++++++- vignettes/intro_Chinese.Rmd |only vignettes/plot_dist.Rmd |only vignettes/plot_lm.Rmd |only vignettes/plot_pca.Rmd |only vignettes/plot_surv.Rmd |only vignettes/plot_ts.Rmd |only 148 files changed, 1450 insertions(+), 471 deletions(-)
Title: Estimation of the Number of Fatalities from Carcass Searches
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt, Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner, Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between carcass versions 1.4 dated 2015-04-20 and 1.5 dated 2015-11-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/estimateN.r | 17 ++++++++++------- man/search.efficiency.Rd | 4 ++-- 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Interface to Unidata netCDF Data Files
Description: This is deprecated and will be removed
from CRAN in early 2016: use 'RNetCDF' or 'ncdf4' instead.
The original description follows: it refers to 'netCDF' version 3 files.
This package provides a high-level R interface to
Unidata's 'netCDF' data files, which are portable across
platforms and include metadata information in addition to the
data sets. Using this package 'netCDF' files can be opened and
data sets read in easily. It is also easy to create new 'netCDF'
dimensions, variables, and files, or manipulate existing 'netCDF'
files. This interface provides considerably more functionality
than the old 'netCDF' package for R, and is not compatible with
the old 'netCDF' package for R. Release 1.2 (2005-01-24) adds
better support for character variables, and miscellaneous bug
fixes. Release 1.3 (2005-03-27) is for miscellaneous bug
fixes, and improves the documentation. Release 1.4
(2005-06-27) improves the efficiency, and adds small bug fixes.
Release 1.5 (2006-02-27) adds support for byte variables, plus
small bug fixes. Release 1.6 (2006-06-19) adds various bug
fixes, plus support for making dimensions WITHOUT dimvars
(coordinate variables), although I think this is a bad idea in
general. ALSO, the default behavior for 'put.var.ncdf()' with
unlimited variables and NO specified start and count parameters
has changed! Before, the default was to append to the end of
the existing variable. Now, the default is to assume a start
of 1 along each dimension, and a count of the current length of
each dimension. This really can be ambiguous when using an
unlimited dimension. I always specify both start and count when
writing to a variable with an unlimited dimension, and suggest
you do as well. I may require this in a future release, as it
seems to cause people problems.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between ncdf versions 1.6.8 dated 2014-08-25 and 1.6.9 dated 2015-11-29
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 6 +++--- NAMESPACE | 2 ++ R/ncdf.R | 7 ++++++- 4 files changed, 26 insertions(+), 16 deletions(-)
Title: Efficient and Accurate P-Value Computation for Position Weight
Matrices
Description: In putative Transcription Factor Binding Sites (TFBSs)
identification from sequence/alignments,
we are interested in the significance of certain match score.
TFMPvalue provides the accurate calculation of P-value with
score threshold for Position Weight Matrices,
or the score with given P-value.
This package is an interface to code originally made available by
Helene Touzet and Jean-Stephane Varre, 2007,
Algorithms Mol Biol:2, 15.
Author: Ge Tan <ge.tan09@imperial.ac.uk>
Maintainer: Ge Tan <ge.tan09@imperial.ac.uk>
Diff between TFMPvalue versions 0.0.5 dated 2014-05-10 and 0.0.6 dated 2015-11-29
TFMPvalue-0.0.5/TFMPvalue/inst/unitTests |only TFMPvalue-0.0.5/TFMPvalue/tests/runTests.R |only TFMPvalue-0.0.6/TFMPvalue/DESCRIPTION | 26 +++++++++++++------ TFMPvalue-0.0.6/TFMPvalue/MD5 | 14 +++++----- TFMPvalue-0.0.6/TFMPvalue/inst/TFMPvalueBuild |only TFMPvalue-0.0.6/TFMPvalue/man/TFMPvalue-lazyScore.Rd | 6 ++-- TFMPvalue-0.0.6/TFMPvalue/man/TFMPvalue-package.Rd | 8 ++++- TFMPvalue-0.0.6/TFMPvalue/tests/testthat |only 8 files changed, 35 insertions(+), 19 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo, ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.30 dated 2015-08-26 and 1.31 dated 2015-11-29
DESCRIPTION | 11 MD5 | 22 - NEWS | 6 R/EZR.R | 376 ++++++++++++++++++++++++++-- inst/CHANGES | 6 inst/doc/EZR.htm | 8 inst/doc/EZR.pdf |binary inst/etc/menus.txt | 3 inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary man/EZR.Rd | 10 man/EZR.dialogs.Rd | 3 po/R-RcmdrPlugin.EZR.po | 28 +- 12 files changed, 430 insertions(+), 43 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 3.3 dated 2015-05-29 and 3.4 dated 2015-11-29
DESCRIPTION | 11 - MD5 | 81 ++++++------ NAMESPACE | 23 ++- R/CDF.birth.death.R | 11 - R/DNA.R | 34 +++++ R/as.phylo.R | 33 ++--- R/balance.R | 6 R/checkValidPhylo.R |only R/clustal.R | 33 ++++- R/collapse.singles.R | 101 +++++++++------ R/drop.tip.R | 11 - R/ladderize.R | 5 R/makeLabel.R | 44 ++++++ R/nodelabels.R | 28 ++-- R/parafit.R | 1 R/phydataplot.R | 89 +++++++++++-- R/plot.phylo.R | 106 +++++++++------- R/reorder.phylo.R | 8 - R/root.R | 287 ++++++++++++++++----------------------------- R/rtt.R | 78 ++++++------ build/vignette.rds |binary data/hivtree.newick.rda |binary data/landplants.newick.rda |binary data/opsin.newick.rda |binary inst/doc/MoranI.pdf |binary man/DNAbin2indel.Rd |only man/LTT.Rd | 3 man/alex.Rd | 2 man/alview.Rd |only man/ape-internal.Rd | 1 man/as.phylo.Rd | 10 - man/checkValidPhylo.Rd |only man/clustal.Rd | 20 ++- man/collapse.singles.Rd | 36 ++++- man/image.DNAbin.Rd | 2 man/label2table.Rd |only man/makeLabel.Rd | 2 man/makeNodeLabel.Rd | 2 man/mixedFontLabel.Rd | 2 man/phydataplot.Rd | 70 ++++++++++ man/plot.phylo.Rd | 11 + man/rlineage.Rd | 1 src/ape.c | 6 src/dist_dna.c | 145 ++++++++++++++-------- 44 files changed, 802 insertions(+), 501 deletions(-)
Title: Maximum Likelihood Estimation for Generalized Linear Mixed
Models
Description: Maximum likelihood estimation for generalized linear mixed models via Monte Carlo EM.
Author: Felipe Acosta Archila
Maintainer: Felipe Acosta Archila <acosta@umn.edu>
Diff between mcemGLM versions 1.0 dated 2015-08-14 and 1.1 dated 2015-11-29
DESCRIPTION | 8 MD5 | 97 ++++-- NAMESPACE | 5 R/RcppExports.R | 64 ++++ R/anova.mcemGLMM.R | 40 +- R/coef.mcemGLMM.R |only R/covMat.mcemGLMM.R |only R/mcemGLMM.R | 33 +- R/mcemGLMMext.R | 20 - R/mcemMLEGamma_n.R |only R/mcemMLEGamma_t_fixed_df.R |only R/mcemMLENegBinom_n.R | 58 ++-- R/mcemMLENegBinom_t_fixed_df.R | 58 ++-- R/mcemMLEPoisson_n.R | 58 ++-- R/mcemMLEPoisson_t_fixed_df.R | 58 ++-- R/mcemMLE_n.R | 56 ++- R/mcemMLE_t_fixed_df.R | 58 ++-- R/predict.mcemGLMM.R | 102 +++++-- R/ranef.mcemGLMM.R |only R/residuals.mcemGLMM.R | 15 - R/summary.mcemGLMM.R | 16 - R/toMaxDiagGamma_n.R |only R/toMaxDiagGamma_t.R |only build/vignette.rds |binary data/epilepsy.rdata |only data/salamander.rdata |only inst/doc/mcemGLM-vignette.R | 218 +++------------ inst/doc/mcemGLM-vignette.Rnw | 505 +++++++++++++++++------------------ inst/doc/mcemGLM-vignette.pdf |binary man/anova.mcemGLMM.Rd | 11 man/coef.mcemGLMM.Rd |only man/covMat.mcemGLMM.Rd |only man/epilepsy.Rd |only man/mcemGLMM.Rd | 31 +- man/mcemGLMMext.Rd | 6 man/predict.mcemGLMM.Rd | 3 man/ranef.mcemGLMM.Rd |only man/salamander.Rd |only man/summary.mcemGLMM.Rd | 6 src/MCMCloglikelihoodGamma_n.cpp |only src/MCMCloglikelihoodGamma_t.cpp |only src/RcppExports.cpp | 320 ++++++++++++++++++++++ src/iMatrixDiagGamma_n.cpp |only src/iMatrixDiagGamma_t.cpp |only src/loglikelihoodGammaGradient_n.cpp |only src/loglikelihoodGammaGradient_t.cpp |only src/loglikelihoodGammaHessian_n.cpp |only src/loglikelihoodGammaHessian_t.cpp |only src/loglikelihoodGamma_n.cpp |only src/loglikelihoodGamma_t.cpp |only src/margloglikelihoodLogit_n.cpp |only src/margloglikelihoodLogit_t.cpp |only src/mcemGLM.h | 65 ++++ src/qFunctionDiagGamma_n.cpp |only src/qFunctionDiagGamma_t.cpp |only src/uSampler.cpp | 5 src/uSamplerGamma_n.cpp |only src/uSamplerGamma_t.cpp |only src/uSamplerNegBinom_n.cpp | 5 src/uSamplerNegBinom_t.cpp | 5 src/uSamplerPoisson_n.cpp | 5 src/uSamplerPoisson_t.cpp | 5 src/uSampler_n.cpp | 5 vignettes/mcemGLM-vignette.Rnw | 505 +++++++++++++++++------------------ vignettes/references.bib |only 65 files changed, 1497 insertions(+), 949 deletions(-)
Title: Classical Jacobi Eigensolution Algorithm
Description: Implements the classical Jacobi (1846) algorithm for the
eigenvalues and eigenvectors of a real symmetric matrix, both in
pure R and in C++ using Rcpp. Mainly as a programming example
for teaching purposes.
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between JacobiEigen versions 0.1 dated 2015-08-09 and 0.2-1 dated 2015-11-29
JacobiEigen-0.1/JacobiEigen/man/JacobiCpp.Rd |only JacobiEigen-0.1/JacobiEigen/vignettes/JacobiEigen.html |only JacobiEigen-0.2-1/JacobiEigen/DESCRIPTION | 16 +-- JacobiEigen-0.2-1/JacobiEigen/MD5 | 26 ++--- JacobiEigen-0.2-1/JacobiEigen/NAMESPACE | 4 JacobiEigen-0.2-1/JacobiEigen/R/JacobiR.R | 49 ++++++++- JacobiEigen-0.2-1/JacobiEigen/R/RcppExports.R | 19 --- JacobiEigen-0.2-1/JacobiEigen/build/vignette.rds |binary JacobiEigen-0.2-1/JacobiEigen/inst/doc/JacobiEigen.R | 26 +++-- JacobiEigen-0.2-1/JacobiEigen/inst/doc/JacobiEigen.Rmd | 80 ++++++++++------ JacobiEigen-0.2-1/JacobiEigen/inst/doc/JacobiEigen.pdf |binary JacobiEigen-0.2-1/JacobiEigen/man/Jacobi.Rd |only JacobiEigen-0.2-1/JacobiEigen/man/JacobiR.Rd | 17 ++- JacobiEigen-0.2-1/JacobiEigen/src/JacobiCpp.cpp | 33 ------ JacobiEigen-0.2-1/JacobiEigen/vignettes/JacobiEigen.Rmd | 80 ++++++++++------ JacobiEigen-0.2-1/JacobiEigen/vignettes/header.tex |only 16 files changed, 202 insertions(+), 148 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.8 dated 2015-11-02 and 1.8.9 dated 2015-11-29
forestFloor-1.8.8/forestFloor/man/ggPlotForestFloor.Rd |only forestFloor-1.8.8/forestFloor/man/ggplotGrob.Rd |only forestFloor-1.8.8/forestFloor/tests/ggplotUsage.R |only forestFloor-1.8.9/forestFloor/DESCRIPTION | 11 - forestFloor-1.8.9/forestFloor/MD5 | 31 +-- forestFloor-1.8.9/forestFloor/NAMESPACE | 26 +- forestFloor-1.8.9/forestFloor/R/fcol.R | 17 + forestFloor-1.8.9/forestFloor/R/forestFloor_randomForest_multiClass.R | 3 forestFloor-1.8.9/forestFloor/R/forestFloor_randomForest_regression.R | 3 forestFloor-1.8.9/forestFloor/R/forestFloor_source.R | 11 - forestFloor-1.8.9/forestFloor/R/ggPlotForestFloor.R | 98 +++++----- forestFloor-1.8.9/forestFloor/R/plot.forestFloor_regression.R | 4 forestFloor-1.8.9/forestFloor/R/show3d.R | 51 ++++- forestFloor-1.8.9/forestFloor/man/fcol.Rd | 8 forestFloor-1.8.9/forestFloor/man/forestFloor.Rd | 10 - forestFloor-1.8.9/forestFloor/man/show3d.Rd | 4 forestFloor-1.8.9/forestFloor/src/testcpp_rec6.cpp | 8 forestFloor-1.8.9/forestFloor/tests/testMultiClass.cpp.R | 1 18 files changed, 173 insertions(+), 113 deletions(-)
Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the
field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre],
Lúcia Anjos [ths],
Gustavo Vasques [ths],
Gerard Heuvelink [ths],
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb],
Frank Harrell Jr [ctb],
Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-3 dated 2015-07-29 and 0.6-4 dated 2015-11-28
DESCRIPTION | 38 +++++-------- MD5 | 90 +++++++++++++++++--------------- NAMESPACE | 9 ++- R/AAAA.R | 12 +++- R/adjR2.R | 2 R/buildMS.R | 4 - R/cdfPlot.R | 2 R/cdfStats.R | 4 - R/cdfTable.R | 8 +- R/checkGMU.R |only R/coordenadas.R | 2 R/cramer.R | 2 R/gcpDiff.R | 4 - R/gcpVector.R | 17 ------ R/optimRandomForest.R |only R/pedometrics.R | 32 ++++++----- R/plotESDA.R | 4 - R/plotHD.R | 4 - R/plotMS.R | 4 - R/statsMS.R | 4 - R/stepVIF.R | 2 R/trend.R | 4 - R/vgmICP.R |only R/vgmLags.R | 124 +++++++++++++++++++++++++++++++-------------- R/vgmSCV.R |only man/adjR2.Rd | 6 +- man/bbox2sp.Rd | 2 man/buildMS.Rd | 50 +++++++++--------- man/cdfPlot.Rd | 6 +- man/cdfStats.Rd | 8 +- man/cdfTable.Rd | 12 ++-- man/checkGMU.Rd |only man/cont2cat.Rd | 9 +-- man/coordenadas.Rd | 8 +- man/cramer.Rd | 10 ++- man/gcpDiff.Rd | 10 ++- man/gcpVector.Rd | 4 + man/numint.Rd | 2 man/optimRandomForest.Rd |only man/pedometrics-package.Rd | 38 +++++++------ man/plotESDA.Rd | 31 +++++------ man/plotHD.Rd | 45 ++++++++-------- man/plotMS.Rd | 117 +++++++++++++++++++++--------------------- man/rowMinCpp.Rd | 2 man/statsMS.Rd | 77 ++++++++++++++------------- man/stepVIF.Rd | 67 ++++++++++++------------ man/trend.Rd | 2 man/vgmICP.Rd |only man/vgmLags.Rd | 60 +++++++++++---------- man/vgmSCV.Rd |only 50 files changed, 510 insertions(+), 428 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.2.9 dated 2015-10-14 and 0.3.0 dated 2015-11-28
ctmm-0.2.9/ctmm/man/summary.akde.Rd |only ctmm-0.3.0/ctmm/DESCRIPTION | 10 ctmm-0.3.0/ctmm/MD5 | 72 +- ctmm-0.3.0/ctmm/NAMESPACE | 14 ctmm-0.3.0/ctmm/NEWS | 19 ctmm-0.3.0/ctmm/R/generic.R | 28 - ctmm-0.3.0/ctmm/R/kde.R | 67 +- ctmm-0.3.0/ctmm/R/krige.R | 215 ++++---- ctmm-0.3.0/ctmm/R/likelihood.R | 825 +++++++++++++++++++++++--------- ctmm-0.3.0/ctmm/R/periodogram.R | 17 ctmm-0.3.0/ctmm/R/telemetry.R | 267 ++++++---- ctmm-0.3.0/ctmm/R/variogram.R | 30 - ctmm-0.3.0/ctmm/TODO | 31 - ctmm-0.3.0/ctmm/inst/doc/akde.R | 15 ctmm-0.3.0/ctmm/inst/doc/akde.Rmd | 21 ctmm-0.3.0/ctmm/inst/doc/akde.html | 35 - ctmm-0.3.0/ctmm/inst/doc/variogram.R | 52 +- ctmm-0.3.0/ctmm/inst/doc/variogram.Rmd | 78 +-- ctmm-0.3.0/ctmm/inst/doc/variogram.html | 107 ++-- ctmm-0.3.0/ctmm/man/akde.Rd | 22 ctmm-0.3.0/ctmm/man/akde.bandwidth.Rd | 6 ctmm-0.3.0/ctmm/man/as.telemetry.Rd | 15 ctmm-0.3.0/ctmm/man/ctmm-package.Rd | 11 ctmm-0.3.0/ctmm/man/ctmm.fit.Rd | 47 + ctmm-0.3.0/ctmm/man/ctmm.loglike.Rd | 3 ctmm-0.3.0/ctmm/man/export.Rd | 28 - ctmm-0.3.0/ctmm/man/homerange.Rd |only ctmm-0.3.0/ctmm/man/mean.variogram.Rd | 8 ctmm-0.3.0/ctmm/man/occurrence.Rd |only ctmm-0.3.0/ctmm/man/periodogram.Rd | 7 ctmm-0.3.0/ctmm/man/plot.telemetry.Rd | 29 - ctmm-0.3.0/ctmm/man/plot.variogram.Rd | 8 ctmm-0.3.0/ctmm/man/simulate.ctmm.Rd | 6 ctmm-0.3.0/ctmm/man/summary.UD.Rd |only ctmm-0.3.0/ctmm/man/summary.ctmm.Rd | 21 ctmm-0.3.0/ctmm/man/variogram.Rd | 18 ctmm-0.3.0/ctmm/man/variogram.fit.Rd | 4 ctmm-0.3.0/ctmm/vignettes/akde.Rmd | 21 ctmm-0.3.0/ctmm/vignettes/variogram.Rmd | 78 +-- 39 files changed, 1418 insertions(+), 817 deletions(-)
More information about rPowerSampleSize at CRAN
Permanent link
Title: Radiomic Image Processing Toolbox
Description: Functions to extract first and second order statistics from
images.
Author: Joel Carlson
Maintainer: Joel Carlson <jnkcarlson@gmail.com>
Diff between radiomics versions 0.1.0 dated 2015-11-22 and 0.1.1 dated 2015-11-28
radiomics-0.1.0/radiomics/man/glcm-class.Rd |only radiomics-0.1.0/radiomics/man/glrlm-class.Rd |only radiomics-0.1.0/radiomics/man/glszm-class.Rd |only radiomics-0.1.0/radiomics/man/mglszm-class.Rd |only radiomics-0.1.1/radiomics/DESCRIPTION | 8 +- radiomics-0.1.1/radiomics/MD5 | 37 +++++----- radiomics-0.1.1/radiomics/NAMESPACE | 8 +- radiomics-0.1.1/radiomics/R/GLCM.R | 53 ++++++--------- radiomics-0.1.1/radiomics/R/GLRLM.R | 29 +++++--- radiomics-0.1.1/radiomics/R/GLSZM.R | 25 ++++--- radiomics-0.1.1/radiomics/R/ImageQuantize.R | 25 ++++--- radiomics-0.1.1/radiomics/R/MGLSZM.R | 21 ++++-- radiomics-0.1.1/radiomics/R/startupMessage.R |only radiomics-0.1.1/radiomics/README.md | 31 +++++---- radiomics-0.1.1/radiomics/build/vignette.rds |binary radiomics-0.1.1/radiomics/inst/doc/TextureAnalysis.R | 17 ++-- radiomics-0.1.1/radiomics/inst/doc/TextureAnalysis.Rmd | 49 +++++++++----- radiomics-0.1.1/radiomics/inst/doc/TextureAnalysis.html | 55 +++++++++------- radiomics-0.1.1/radiomics/man/discretizeImage.Rd | 4 - radiomics-0.1.1/radiomics/man/glcm.Rd |only radiomics-0.1.1/radiomics/man/glrlm.Rd |only radiomics-0.1.1/radiomics/man/glszm.Rd |only radiomics-0.1.1/radiomics/man/mglszm.Rd |only radiomics-0.1.1/radiomics/vignettes/TextureAnalysis.Rmd | 49 +++++++++----- 24 files changed, 243 insertions(+), 168 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-2 dated 2015-07-08 and 1.2-3 dated 2015-11-28
DESCRIPTION | 8 - MD5 | 141 ++++++++++---------- NAMESPACE | 5 R/Auxiliaries.R | 39 +++-- R/Csparse.R | 8 - R/Math.R | 2 R/Matrix.R | 4 R/abIndex.R | 6 R/bind2.R | 16 +- R/dgCMatrix.R | 8 - R/dgeMatrix.R | 4 R/diagMatrix.R | 4 R/dsCMatrix.R | 4 R/dspMatrix.R | 13 - R/dtrMatrix.R | 2 R/kronecker.R | 4 R/ldenseMatrix.R | 14 -- R/ndenseMatrix.R | 14 -- R/sparseMatrix.R | 111 ++++++++++----- R/sparseVector.R | 5 TODO | 8 - build/vignette.rds |binary inst/NEWS.Rd | 31 ++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix.h | 28 +++- inst/include/Matrix_stubs.c | 18 +- inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary inst/po/ko/LC_MESSAGES/R-Matrix.mo |binary inst/test-tools-Matrix.R | 8 - man/Matrix-class.Rd | 2 man/MatrixClass.Rd |only man/SparseM-conv.Rd | 9 - man/abIndex-class.Rd | 3 man/dgCMatrix-class.Rd | 2 man/dgeMatrix-class.Rd | 2 man/diagonalMatrix-class.Rd | 2 man/dsCMatrix-class.Rd | 2 man/externalFormats.Rd | 4 man/formatSparseM.Rd | 10 + man/graph2T.Rd | 4 man/ldenseMatrix-class.Rd | 2 man/lgeMatrix-class.Rd | 2 man/ndenseMatrix-class.Rd | 2 man/ngeMatrix-class.Rd | 2 man/printSpMatrix.Rd | 26 ++- man/sparseMatrix.Rd | 3 man/sparseVector-class.Rd | 3 po/Matrix.pot | 4 po/R-Matrix.pot | 4 po/R-ko.po | 61 +++++--- po/ko.po | 224 +++++++++++++++++--------------- po/update-me.sh | 7 - src/Csparse.c | 37 +++-- src/Mutils.c | 4 src/Mutils.h | 41 ++++- src/Tsparse.c | 2 src/chm_common.c | 10 - src/chm_common.h | 2 src/cs_utils.c | 4 src/dgCMatrix.c | 4 src/dgeMatrix.c | 3 src/t_Csparse_subassign.c | 4 tests/Class+Meth.R | 11 + tests/Simple.R | 6 tests/bind.R | 12 + tests/bind.Rout.save | 34 ++-- tests/indexing.Rout.save | 64 ++++----- 72 files changed, 643 insertions(+), 480 deletions(-)
Title: Imprecise Inferential Framework for Poisson Sampling Model
Description: A collection of tools for conducting an imprecise inference is provided. Imprecise prior is used for this inference, and imprecise probability theory introduced by Peter Walley (1991) is its underlying theoretical foundation. The package is developed based on the PhD thesis work of Lee (2014). Poisson and zero-truncated Poisson sampling models are mainly studied with two types of prior distributions.
Author: Chel Hee Lee [aut, cre, cph], Mikelis Bickis [aut, ths, cph]
Maintainer: Chel Hee Lee <chl948@mail.usask.ca>
Diff between imPois versions 0.0.6.4 dated 2015-11-21 and 0.0.7.5 dated 2015-11-28
imPois-0.0.6.4/imPois/R/visualize.R |only imPois-0.0.6.4/imPois/TODO |only imPois-0.0.6.4/imPois/inst |only imPois-0.0.6.4/imPois/man/BL.dist.Rd |only imPois-0.0.6.4/imPois/man/cgf.Rd |only imPois-0.0.6.4/imPois/man/evfn.Rd |only imPois-0.0.6.4/imPois/man/ipeglim.Rd |only imPois-0.0.6.4/imPois/man/iprior.Rd |only imPois-0.0.6.4/imPois/man/kcpm.Rd |only imPois-0.0.6.4/imPois/man/summary.impinf.Rd |only imPois-0.0.6.4/imPois/man/update.impinf.Rd |only imPois-0.0.7.5/imPois/ChangeLog | 5 imPois-0.0.7.5/imPois/DESCRIPTION | 14 - imPois-0.0.7.5/imPois/MD5 | 46 ++- imPois-0.0.7.5/imPois/NAMESPACE | 14 + imPois-0.0.7.5/imPois/R/graphics.R |only imPois-0.0.7.5/imPois/R/imPois.R | 120 +++++----- imPois-0.0.7.5/imPois/R/optim.R |only imPois-0.0.7.5/imPois/R/tools.R |only imPois-0.0.7.5/imPois/R/ztrunc.R |only imPois-0.0.7.5/imPois/demo/00Index | 4 imPois-0.0.7.5/imPois/demo/convh.R |only imPois-0.0.7.5/imPois/demo/focus.R |only imPois-0.0.7.5/imPois/demo/levels.R | 64 ++--- imPois-0.0.7.5/imPois/demo/optim.R |only imPois-0.0.7.5/imPois/demo/trans.R | 24 +- imPois-0.0.7.5/imPois/demo/ztrunc.R |only imPois-0.0.7.5/imPois/man/characterize_imprecise_prior.Rd |only imPois-0.0.7.5/imPois/man/expected_value_of_imprecise_distribution.Rd |only imPois-0.0.7.5/imPois/man/hyperpara_optim.Rd |only imPois-0.0.7.5/imPois/man/imPois.Rd |only imPois-0.0.7.5/imPois/man/imprecise_distribution.Rd |only imPois-0.0.7.5/imPois/man/imprecise_learning_from_observation.Rd |only imPois-0.0.7.5/imPois/man/kernel_of_imprecise_prob_measure.Rd |only imPois-0.0.7.5/imPois/man/normalize_imprecise_prob_measure.Rd |only imPois-0.0.7.5/imPois/man/plot_imprecise_object.Rd |only imPois-0.0.7.5/imPois/man/print_imprecise_objects.Rd |only imPois-0.0.7.5/imPois/man/summary_imprecise_object.Rd |only 38 files changed, 160 insertions(+), 131 deletions(-)
Title: Competing Risks Regression Models with Covariate-Adjusted
Censoring Weights
Description: Estimation and regression modeling of subdistribution functions for competing risks data with adjustment for covariate-dependent censoring, as described in He et al. (2015).
Author: Peng He
Maintainer: Peng He <saturnhp@gmail.com>
Diff between wtcrsk versions 1.4 dated 2015-09-22 and 1.5 dated 2015-11-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/wrap.R | 8 ++++++-- man/wtcrsk-package.Rd | 4 ++-- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.2 dated 2015-11-03 and 0.1.3 dated 2015-11-28
RStoolbox-0.1.2/RStoolbox/inst/external/training.rds |only RStoolbox-0.1.3/RStoolbox/DESCRIPTION | 15 RStoolbox-0.1.3/RStoolbox/MD5 | 122 ++-- RStoolbox-0.1.3/RStoolbox/NAMESPACE | 3 RStoolbox-0.1.3/RStoolbox/NEWS | 13 RStoolbox-0.1.3/RStoolbox/R/classifyQA.R | 2 RStoolbox-0.1.3/RStoolbox/R/encodeQA.R | 2 RStoolbox-0.1.3/RStoolbox/R/histMatch.R | 8 RStoolbox-0.1.3/RStoolbox/R/internalFunctions.R | 4 RStoolbox-0.1.3/RStoolbox/R/mlc.R | 13 RStoolbox-0.1.3/RStoolbox/R/panSharpen.R | 4 RStoolbox-0.1.3/RStoolbox/R/readMeta.R | 2 RStoolbox-0.1.3/RStoolbox/R/saveRSTBX.R | 45 + RStoolbox-0.1.3/RStoolbox/R/stackMeta.R | 2 RStoolbox-0.1.3/RStoolbox/R/superClass.R | 246 ++++++---- RStoolbox-0.1.3/RStoolbox/R/unsuperClass.R | 5 RStoolbox-0.1.3/RStoolbox/README.md | 2 RStoolbox-0.1.3/RStoolbox/inst/external/trainingPoints.rds |only RStoolbox-0.1.3/RStoolbox/inst/external/trainingPolygons.rds |only RStoolbox-0.1.3/RStoolbox/man/ImageMetaData.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/RStoolbox.Rd | 4 RStoolbox-0.1.3/RStoolbox/man/classifyQA.Rd | 8 RStoolbox-0.1.3/RStoolbox/man/cloudMask.Rd | 15 RStoolbox-0.1.3/RStoolbox/man/cloudShadowMask.Rd | 15 RStoolbox-0.1.3/RStoolbox/man/coregisterImages.Rd | 18 RStoolbox-0.1.3/RStoolbox/man/decodeQA.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/encodeQA.Rd | 4 RStoolbox-0.1.3/RStoolbox/man/estimateHaze.Rd | 12 RStoolbox-0.1.3/RStoolbox/man/fCover.Rd | 32 - RStoolbox-0.1.3/RStoolbox/man/fortify.raster.Rd | 3 RStoolbox-0.1.3/RStoolbox/man/getMeta.Rd | 7 RStoolbox-0.1.3/RStoolbox/man/ggR.Rd | 22 RStoolbox-0.1.3/RStoolbox/man/ggRGB.Rd | 13 RStoolbox-0.1.3/RStoolbox/man/histMatch.Rd | 8 RStoolbox-0.1.3/RStoolbox/man/lsat.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/normImage.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/panSharpen.Rd | 15 RStoolbox-0.1.3/RStoolbox/man/pifMatch.Rd | 12 RStoolbox-0.1.3/RStoolbox/man/predict.superClass.Rd |only RStoolbox-0.1.3/RStoolbox/man/radCor.Rd | 16 RStoolbox-0.1.3/RStoolbox/man/rasterCVA.Rd | 10 RStoolbox-0.1.3/RStoolbox/man/rasterEntropy.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/rasterPCA.Rd | 5 RStoolbox-0.1.3/RStoolbox/man/readEE.Rd | 7 RStoolbox-0.1.3/RStoolbox/man/readMeta.Rd | 3 RStoolbox-0.1.3/RStoolbox/man/readSLI.Rd | 4 RStoolbox-0.1.3/RStoolbox/man/rescaleImage.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/rlogo.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/rsOpts.Rd | 3 RStoolbox-0.1.3/RStoolbox/man/sam.Rd | 8 RStoolbox-0.1.3/RStoolbox/man/saveRSTBX.Rd | 14 RStoolbox-0.1.3/RStoolbox/man/spectralIndices.Rd | 8 RStoolbox-0.1.3/RStoolbox/man/srtm.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/stackMeta.Rd | 6 RStoolbox-0.1.3/RStoolbox/man/superClass.Rd | 24 RStoolbox-0.1.3/RStoolbox/man/tasseledCap.Rd | 2 RStoolbox-0.1.3/RStoolbox/man/topCor.Rd | 9 RStoolbox-0.1.3/RStoolbox/man/unsuperClass.Rd | 10 RStoolbox-0.1.3/RStoolbox/man/writeSLI.Rd | 4 RStoolbox-0.1.3/RStoolbox/src/gainOffsetRescale.cpp | 2 RStoolbox-0.1.3/RStoolbox/src/predictKmeans.cpp | 2 RStoolbox-0.1.3/RStoolbox/tests/testthat/test-ggplot.R | 6 RStoolbox-0.1.3/RStoolbox/tests/testthat/test-histMatch.R |only RStoolbox-0.1.3/RStoolbox/tests/testthat/test-panSharpen.R |only RStoolbox-0.1.3/RStoolbox/tests/testthat/test-saveReadRSTBX.R |only RStoolbox-0.1.3/RStoolbox/tests/testthat/test-superClass.R |only 66 files changed, 484 insertions(+), 351 deletions(-)
Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of 'RJSONIO', but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with a web API. The implementation is
based on the mapping described in the vignette (Ooms, 2014). In addition to
converting JSON data from/to R objects, 'jsonlite' contains functions to
stream, validate, and prettify JSON data. The unit tests included with the
package verify that all edge cases are encoded and decoded consistently for
use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between jsonlite versions 0.9.18 dated 2015-11-25 and 0.9.19 dated 2015-11-28
jsonlite-0.9.18/jsonlite/R/onLoad.R |only jsonlite-0.9.19/jsonlite/DESCRIPTION | 6 +++--- jsonlite-0.9.19/jsonlite/MD5 | 15 +++++++-------- jsonlite-0.9.19/jsonlite/NAMESPACE | 1 - jsonlite-0.9.19/jsonlite/NEWS | 4 ++++ jsonlite-0.9.19/jsonlite/R/fromJSON.R | 4 ++-- jsonlite-0.9.19/jsonlite/R/toJSON.R | 10 ---------- jsonlite-0.9.19/jsonlite/inst/doc/json-mapping.pdf |binary jsonlite-0.9.19/jsonlite/man/fromJSON.Rd | 1 - 9 files changed, 16 insertions(+), 25 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.4 dated 2015-11-23 and 0.5 dated 2015-11-27
DESCRIPTION | 10 +- MD5 | 20 ++-- NEWS | 10 ++ R/scatterD3.R | 7 + README.md | 8 + inst/doc/introduction.R | 6 + inst/doc/introduction.Rmd | 12 ++ inst/doc/introduction.html | 49 ++++++---- inst/htmlwidgets/scatterD3.js | 195 +++++++++++++++++++++++++++++++++--------- man/scatterD3.Rd | 11 +- vignettes/introduction.Rmd | 12 ++ 11 files changed, 263 insertions(+), 77 deletions(-)
Title: Practical Numerical Math Functions
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 1.8.6 dated 2015-07-14 and 1.8.8 dated 2015-11-27
pracma-1.8.6/pracma/man/invperm.Rd |only pracma-1.8.8/pracma/DESCRIPTION | 13 +++++++----- pracma-1.8.8/pracma/MD5 | 25 +++++++++++------------ pracma-1.8.8/pracma/NEWS | 11 ++++++++++ pracma-1.8.8/pracma/R/findpeaks.R | 32 +++++++++++++++++++++++------- pracma-1.8.8/pracma/R/interp1.R | 2 - pracma-1.8.8/pracma/R/legendre.R | 14 ++++++++----- pracma-1.8.8/pracma/R/perms.R | 9 -------- pracma-1.8.8/pracma/data/brown72.rda |binary pracma-1.8.8/pracma/data/nile.rda |binary pracma-1.8.8/pracma/data/titanium.rda |binary pracma-1.8.8/pracma/man/interp1.Rd | 6 ++--- pracma-1.8.8/pracma/man/pracma-package.Rd | 2 - pracma-1.8.8/pracma/man/rkf54.Rd | 3 -- 14 files changed, 71 insertions(+), 46 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.3 dated 2015-10-13 and 0.3.4 dated 2015-11-27
DESCRIPTION | 8 - MD5 | 94 ++++++------- NAMESPACE | 12 + R/checkConstraint.R | 11 + R/convertDVH.R | 156 +++++++++++++++++----- R/dvhDistance.R | 2 R/getEUD.R | 6 R/getMeanDVH.R |only R/getMetric.R | 65 ++++++--- R/parseCadplan.R | 3 R/parseEclipse.R | 3 R/parseHiArt.R | 15 -- R/parseMasterplan.R | 3 R/parseMonaco.R | 15 -- R/parsePinnacleDVH.R | 15 -- R/parseRayStation.R | 17 -- R/print.R | 12 + R/readDVH.R | 29 ++++ R/showConstraint.R | 8 - R/showDVH.R | 302 ++++++++++++++++++++++++++++++++------------ R/smoothDVH.R | 169 +++++++++++++++++++----- R/unitConversion.R | 20 +- inst/ChangeLog | 25 +++ inst/DVHshiny/ABOUT.md | 2 inst/DVHshiny/helper.R | 5 inst/DVHshiny/server.R | 72 ++++++++-- inst/DVHshiny/ui.R | 39 +++-- inst/doc/DVHmetrics.R | 18 ++ inst/doc/DVHmetrics.Rnw | 39 ++++- inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 2 inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 man/checkConstraint.Rd | 4 man/convertDVH.Rd | 13 + man/getDMEAN.Rd | 4 man/getMeanDVH.Rd |only man/getMetric.Rd | 18 +- man/getNTCP.Rd | 2 man/getTCP.Rd | 2 man/readDVH.Rd | 4 man/saveDVH.Rd | 2 man/saveMetric.Rd | 2 man/showConstraint.Rd | 2 man/showDVH.Rd | 28 ++-- vignettes/DVHmetrics.Rnw | 39 ++++- vignettes/DVHshiny.Rnw | 2 vignettes/appShowConstr.jpg |binary vignettes/lit.bib | 12 - 49 files changed, 917 insertions(+), 388 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 3.8.1 dated 2015-05-17 and 3.9 dated 2015-11-27
bnlearn-3.8.1/bnlearn/R/frontend-mvber.R |only bnlearn-3.8.1/bnlearn/R/mvber.R |only bnlearn-3.8.1/bnlearn/man/bn.var.Rd |only bnlearn-3.8.1/bnlearn/src/all.monte.carlo.c |only bnlearn-3.8.1/bnlearn/src/discrete.mutual.information.c |only bnlearn-3.8.1/bnlearn/src/gaussian.mutual.information.c |only bnlearn-3.8.1/bnlearn/src/mvber.c |only bnlearn-3.8.1/bnlearn/src/pearson.x2.c |only bnlearn-3.9/bnlearn/Changelog | 27 bnlearn-3.9/bnlearn/DESCRIPTION | 8 bnlearn-3.9/bnlearn/MD5 | 249 ++++---- bnlearn-3.9/bnlearn/NAMESPACE | 15 bnlearn-3.9/bnlearn/R/custom.fit.R | 15 bnlearn-3.9/bnlearn/R/cv.R | 34 - bnlearn-3.9/bnlearn/R/fast-iamb.R | 45 - bnlearn-3.9/bnlearn/R/fitted.assignment.R | 9 bnlearn-3.9/bnlearn/R/frontend-bn.R | 32 - bnlearn-3.9/bnlearn/R/frontend-bootstrap.R | 46 + bnlearn-3.9/bnlearn/R/frontend-lattice.R | 10 bnlearn-3.9/bnlearn/R/frontend-learning.R | 2 bnlearn-3.9/bnlearn/R/frontend-plot.R | 65 ++ bnlearn-3.9/bnlearn/R/frontend-predict.R | 4 bnlearn-3.9/bnlearn/R/frontend-print.R | 44 - bnlearn-3.9/bnlearn/R/frontend-score.R | 4 bnlearn-3.9/bnlearn/R/frontend-strength.R | 5 bnlearn-3.9/bnlearn/R/globals.R | 25 bnlearn-3.9/bnlearn/R/incremental-association.R | 41 - bnlearn-3.9/bnlearn/R/inter-iamb.R | 43 - bnlearn-3.9/bnlearn/R/lattice.R | 198 ++++-- bnlearn-3.9/bnlearn/R/learning-algorithms.R | 4 bnlearn-3.9/bnlearn/R/loss.R | 41 - bnlearn-3.9/bnlearn/R/nparams.R | 29 - bnlearn-3.9/bnlearn/R/scores.R | 5 bnlearn-3.9/bnlearn/R/test.R | 23 bnlearn-3.9/bnlearn/R/utils-misc.R | 32 + bnlearn-3.9/bnlearn/R/utils-sanitization.R | 62 +- bnlearn-3.9/bnlearn/inst/CITATION | 19 bnlearn-3.9/bnlearn/man/alarm.Rd | 116 +--- bnlearn-3.9/bnlearn/man/arc.strength.Rd | 144 ++--- bnlearn-3.9/bnlearn/man/arcops.Rd | 82 +- bnlearn-3.9/bnlearn/man/asia.Rd | 46 - bnlearn-3.9/bnlearn/man/bn.class.Rd | 123 +--- bnlearn-3.9/bnlearn/man/bn.cv.Rd | 168 ++++- bnlearn-3.9/bnlearn/man/bn.fit.Rd | 57 + bnlearn-3.9/bnlearn/man/bn.fit.class.Rd | 85 +- bnlearn-3.9/bnlearn/man/bn.fit.methods.Rd | 96 +-- bnlearn-3.9/bnlearn/man/bn.fit.plots.Rd | 41 - bnlearn-3.9/bnlearn/man/bn.kcv.class.Rd | 13 bnlearn-3.9/bnlearn/man/bn.strength-class.Rd | 24 bnlearn-3.9/bnlearn/man/bnboot.Rd | 53 - bnlearn-3.9/bnlearn/man/bnlearn-package.Rd | 292 +++++----- bnlearn-3.9/bnlearn/man/choose.direction.Rd | 46 - bnlearn-3.9/bnlearn/man/ci.test.Rd | 57 - bnlearn-3.9/bnlearn/man/clgaussian-test.Rd | 10 bnlearn-3.9/bnlearn/man/compare.Rd | 33 - bnlearn-3.9/bnlearn/man/configs.Rd | 6 bnlearn-3.9/bnlearn/man/constraint.Rd | 94 +-- bnlearn-3.9/bnlearn/man/coronary.Rd | 41 - bnlearn-3.9/bnlearn/man/cpdag.Rd | 82 +- bnlearn-3.9/bnlearn/man/cpquery.Rd | 107 +-- bnlearn-3.9/bnlearn/man/deal.Rd | 10 bnlearn-3.9/bnlearn/man/dsep.Rd | 2 bnlearn-3.9/bnlearn/man/foreign.Rd | 36 - bnlearn-3.9/bnlearn/man/gRain.Rd | 6 bnlearn-3.9/bnlearn/man/gaussian-test.Rd | 8 bnlearn-3.9/bnlearn/man/graph.Rd | 20 bnlearn-3.9/bnlearn/man/graphgen.Rd | 106 +-- bnlearn-3.9/bnlearn/man/graphviz.plot.Rd | 80 +- bnlearn-3.9/bnlearn/man/hailfinder.Rd | 212 +++++-- bnlearn-3.9/bnlearn/man/hc.Rd | 70 +- bnlearn-3.9/bnlearn/man/hybrid.Rd | 110 +-- bnlearn-3.9/bnlearn/man/insurance.Rd | 90 ++- bnlearn-3.9/bnlearn/man/learn.Rd | 64 +- bnlearn-3.9/bnlearn/man/learning-test.Rd | 28 bnlearn-3.9/bnlearn/man/lizards.Rd | 36 - bnlearn-3.9/bnlearn/man/marks.Rd | 15 bnlearn-3.9/bnlearn/man/mb.Rd | 41 - bnlearn-3.9/bnlearn/man/mmpc.Rd | 72 +- bnlearn-3.9/bnlearn/man/modelstring.Rd | 25 bnlearn-3.9/bnlearn/man/naive.bayes.Rd | 77 +- bnlearn-3.9/bnlearn/man/ordering.Rd | 46 - bnlearn-3.9/bnlearn/man/parallel.Rd | 10 bnlearn-3.9/bnlearn/man/plot.bn.Rd | 17 bnlearn-3.9/bnlearn/man/plot.bn.strength.Rd | 6 bnlearn-3.9/bnlearn/man/preprocessing.Rd | 24 bnlearn-3.9/bnlearn/man/rbn.Rd | 28 bnlearn-3.9/bnlearn/man/relevant.Rd | 32 - bnlearn-3.9/bnlearn/man/score.Rd | 104 +-- bnlearn-3.9/bnlearn/man/strength.plot.Rd | 84 +- bnlearn-3.9/bnlearn/man/test.counter.Rd | 6 bnlearn-3.9/bnlearn/src/allocations.c | 74 -- bnlearn-3.9/bnlearn/src/allsubs.test.c | 458 +++------------- bnlearn-3.9/bnlearn/src/bind.c | 4 bnlearn-3.9/bnlearn/src/cache.structure.c | 4 bnlearn-3.9/bnlearn/src/cg.mutual.information.c | 18 bnlearn-3.9/bnlearn/src/configurations.c | 1 bnlearn-3.9/bnlearn/src/contincency.tables.c |only bnlearn-3.9/bnlearn/src/covariance.c | 22 bnlearn-3.9/bnlearn/src/cpdist.c | 18 bnlearn-3.9/bnlearn/src/ctest.c | 427 ++++---------- bnlearn-3.9/bnlearn/src/data.frame.c | 32 + bnlearn-3.9/bnlearn/src/dedup.c | 26 bnlearn-3.9/bnlearn/src/df.adjust.c | 4 bnlearn-3.9/bnlearn/src/discrete.monte.carlo.c | 282 +++------ bnlearn-3.9/bnlearn/src/discrete.tests.c |only bnlearn-3.9/bnlearn/src/enums.c |only bnlearn-3.9/bnlearn/src/fitted.c | 10 bnlearn-3.9/bnlearn/src/gaussian.monte.carlo.c | 189 +++--- bnlearn-3.9/bnlearn/src/gaussian.tests.c |only bnlearn-3.9/bnlearn/src/globals.c | 2 bnlearn-3.9/bnlearn/src/graph.priors.c | 37 + bnlearn-3.9/bnlearn/src/hc.cache.lookup.c | 6 bnlearn-3.9/bnlearn/src/htest.c | 17 bnlearn-3.9/bnlearn/src/include/allocations.h | 10 bnlearn-3.9/bnlearn/src/include/covariance.h | 7 bnlearn-3.9/bnlearn/src/include/dataframe.h | 2 bnlearn-3.9/bnlearn/src/include/rcore.h | 3 bnlearn-3.9/bnlearn/src/include/sampling.h | 4 bnlearn-3.9/bnlearn/src/include/tests.h | 124 ++-- bnlearn-3.9/bnlearn/src/jonckheere.c | 45 - bnlearn-3.9/bnlearn/src/likelihood.weighting.c | 19 bnlearn-3.9/bnlearn/src/linear.algebra.c | 76 -- bnlearn-3.9/bnlearn/src/linear.correlation.c | 43 - bnlearn-3.9/bnlearn/src/map.lw.c | 10 bnlearn-3.9/bnlearn/src/mi.matrix.c | 40 - bnlearn-3.9/bnlearn/src/nparams.c | 157 ++--- bnlearn-3.9/bnlearn/src/rcont2.c | 226 +++---- bnlearn-3.9/bnlearn/src/roundrobin.test.c |only bnlearn-3.9/bnlearn/src/shrinkage.c | 134 +--- bnlearn-3.9/bnlearn/src/strings.c | 22 bnlearn-3.9/bnlearn/src/utest.c | 319 +++-------- bnlearn-3.9/bnlearn/src/which.max.c | 22 132 files changed, 3434 insertions(+), 3877 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.7 dated 2015-09-25 and 1.8 dated 2015-11-27
DESCRIPTION | 14 - MD5 | 126 +++++---- NAMESPACE | 27 + NEWS.md | 76 +++++ R/Repository.R | 64 +++- R/Tags.R | 69 ++--- R/addTagsRepo.R | 104 ++++--- R/ahistory.R | 60 +++- R/archive.R |only R/archivist-package.R | 49 +++ R/archivistOptions.R | 84 +++++- R/aread.R | 21 - R/asearch.R | 18 - R/cache.R | 5 R/cloneGithubRepo.R |only R/copyToRepo.R | 164 ++++++++--- R/createEmptyRepo.R | 310 +++++++++++++++++++--- R/deleteRepo.R | 76 +++-- R/extractMiniature.R | 27 - R/getTags.R | 121 ++++++-- R/githubFunctions.R |only R/loadFromRepo.R | 110 +++++-- R/magrittr.R | 57 ++-- R/md5hash.R | 29 +- R/rmFromRepo.R | 400 +++++++++++++++++------------ R/saveToRepo.R | 235 ++++++++++++----- R/searchInRepo.R | 95 +++--- R/setRepo.R | 192 ++++++++----- R/shinySearchInLocalRepo.R | 16 - R/showRepo.R | 78 +++-- R/splitTags.R |only R/summaryRepo.R | 53 +-- R/zipRepo.R | 92 +++--- R/zzz.R | 33 ++ man/Repository.Rd | 73 ++++- man/Tags.Rd | 81 +++-- man/addTagsRepo.Rd | 101 +++++-- man/ahistory.Rd | 71 ++--- man/archive.Rd |only man/archivist-github-integration.Rd |only man/archivist-package.Rd | 29 +- man/archivistOptions.Rd | 90 +++++- man/aread.Rd | 36 +- man/asearch.Rd | 31 +- man/cache.Rd | 20 + man/cloneGithubRepo.Rd |only man/copyToRepo.Rd | 132 +++++++-- man/createEmptyRepo.Rd | 155 +++++++++-- man/deleteRepo.Rd | 73 +++-- man/getTags.Rd | 136 +++++++-- man/loadFromRepo.Rd | 90 ++++-- man/magrittr.Rd | 67 +++- man/md5hash.Rd | 43 +-- man/pipe.Rd |only man/rmFromRepo.Rd | 227 +++++++++------- man/saveToRepo.Rd | 125 +++++---- man/searchInRepo.Rd | 101 ++++--- man/setRepo.Rd | 178 +++++++----- man/shinySearchInRepo.Rd | 26 + man/showRepo.Rd | 83 +++--- man/splitTags.Rd |only man/summaryRepo.Rd | 61 ++-- man/zipRepo.Rd | 74 ++--- tests/testthat.R | 2 tests/testthat/test_aoptions.R | 1 tests/testthat/test_base_functionalities.R | 6 tests/testthat/test_jss_artilce.R | 4 tests/testthat/test_showLocal.R |only tests/testthat/test_splitTags.R |only tests/testthat/test_zip.R |only 70 files changed, 3362 insertions(+), 1559 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.6-0 dated 2015-10-15 and 0.9.0-1 dated 2015-11-27
DESCRIPTION | 9 MD5 | 127 ++++++----- NAMESPACE | 13 + NEWS | 37 +++ R/RcppExports.R | 12 - R/collocations.R | 424 ++++++++++++++++++++-------------------- R/converters.R | 7 R/corpus.R | 257 ++++++++++++++++-------- R/dataDocs.R | 3 R/dfm-classes.R | 7 R/dfm-main.R | 38 +-- R/dfm-methods.R | 109 +++++++--- R/dictionaries.R | 26 +- R/encoding.R | 4 R/kwic.R | 69 ++++-- R/ngrams.R | 213 +++++--------------- R/plots.R | 70 ++++-- R/readability.R | 14 + R/stopwords.R | 179 ++++++++-------- R/textfile.R | 12 + R/textmodel-wordfish.R | 31 ++ R/toLower.R | 5 R/tokenize.R | 108 +++------- R/wordstem.R | 24 +- README.md | 154 +------------- build/vignette.rds |binary demo/quanteda.R | 150 ++++++++++++-- inst/doc/LitVignette.R |only inst/doc/LitVignette.Rmd |only inst/doc/LitVignette.html |only inst/doc/development-plans.R | 3 inst/doc/development-plans.Rmd | 25 +- inst/doc/development-plans.html | 24 +- inst/doc/quickstart.html | 84 +++---- man/applyDictionary.Rd | 16 - man/cbind.dfm.Rd |only man/changeunits.Rd | 20 + man/collocations.Rd | 20 + man/convert.Rd | 4 man/corpus.Rd | 17 + man/dfm.Rd | 20 - man/docfreq.Rd | 2 man/docnames.Rd | 4 man/docvars.Rd | 8 man/head.dfm.Rd | 2 man/ie2010Corpus.Rd | 9 man/kwic.Rd | 20 + man/metacorpus.Rd | 9 man/metadoc.Rd | 17 + man/ngrams.Rd | 72 +++--- man/ntoken.Rd | 6 man/plot.dfm.Rd | 50 +++- man/plot.kwic.Rd |only man/readability.Rd | 2 man/sample.Rd | 2 man/segment.Rd | 14 - man/selectFeatures.Rd | 1 man/summary.corpus.Rd | 2 man/textmodel_wordfish.Rd | 5 man/texts.Rd | 29 +- man/tokenize.Rd | 25 +- man/trim.Rd | 43 ++-- src/RcppExports.cpp | 35 +++ src/ngrams.cpp |only src/wordfish.cpp | 73 +++++- tests/testthat/testDfm.R | 18 + vignettes/LitVignette.Rmd |only vignettes/development-plans.Rmd | 25 +- 68 files changed, 1604 insertions(+), 1204 deletions(-)
Title: Generating Various Numerical Representation Schemes of Protein
Sequence
Description: Comprehensive toolkit for generating various numerical
representation schemes of protein sequence. The descriptors and similarity
scores included are extensively used in bioinformatics and chemogenomics.
For full functionality, the software 'ncbi-blast+' is needed, see
<http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>,
Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between protr versions 0.5-1 dated 2014-12-23 and 1.0-1 dated 2015-11-27
protr-0.5-1/protr/NEWS |only protr-0.5-1/protr/README |only protr-1.0-1/protr/DESCRIPTION | 18 protr-1.0-1/protr/LICENSE | 2 protr-1.0-1/protr/MD5 | 250 - protr-1.0-1/protr/NAMESPACE | 11 protr-1.0-1/protr/NEWS.md |only protr-1.0-1/protr/R/desc01AAC.R | 40 protr-1.0-1/protr/R/desc02DC.R | 114 protr-1.0-1/protr/R/desc03TC.R | 1822 ++++++------- protr-1.0-1/protr/R/desc04MoreauBroto.R | 116 protr-1.0-1/protr/R/desc05Moran.R | 148 - protr-1.0-1/protr/R/desc06Geary.R | 150 - protr-1.0-1/protr/R/desc07CTDC.R | 88 protr-1.0-1/protr/R/desc07CTDCClass.R | 45 protr-1.0-1/protr/R/desc08CTDT.R | 80 protr-1.0-1/protr/R/desc08CTDTClass.R | 77 protr-1.0-1/protr/R/desc09CTDD.R | 72 protr-1.0-1/protr/R/desc09CTDDClass.R | 53 protr-1.0-1/protr/R/desc10CTriad.R | 3578 +++++++++++++-------------- protr-1.0-1/protr/R/desc10CTriadClass.R | 51 protr-1.0-1/protr/R/desc11SOCN.R | 68 protr-1.0-1/protr/R/desc12QSO.R | 84 protr-1.0-1/protr/R/desc13PAAC.R | 190 - protr-1.0-1/protr/R/desc14APAAC.R | 186 - protr-1.0-1/protr/R/desc15PSSM.R | 295 +- protr-1.0-1/protr/R/desc15PSSMAcc.R | 93 protr-1.0-1/protr/R/desc15PSSMFeature.R | 45 protr-1.0-1/protr/R/misc01readFASTA.R | 156 - protr-1.0-1/protr/R/misc02readPDB.R | 71 protr-1.0-1/protr/R/misc03protcheck.R | 28 protr-1.0-1/protr/R/misc04protseg.R | 47 protr-1.0-1/protr/R/misc05getUniProt.R | 41 protr-1.0-1/protr/R/misc06acc.R | 75 protr-1.0-1/protr/R/par01parSeqSim.R | 86 protr-1.0-1/protr/R/par02parGOSim.R | 106 protr-1.0-1/protr/R/pcm01extractScales.R | 23 protr-1.0-1/protr/R/pcm01extractScalesGap.R | 33 protr-1.0-1/protr/R/pcm02extractDescScales.R | 61 protr-1.0-1/protr/R/pcm03extractProtFP.R | 13 protr-1.0-1/protr/R/pcm04extractFAScales.R | 65 protr-1.0-1/protr/R/pcm05extractMDSScales.R | 59 protr-1.0-1/protr/R/pcm06extractBLOSUM.R | 37 protr-1.0-1/protr/R/protr-datalist.R | 350 +- protr-1.0-1/protr/R/protr-package.R | 18 protr-1.0-1/protr/README.md |only protr-1.0-1/protr/build/vignette.rds |binary protr-1.0-1/protr/inst/CITATION | 29 protr-1.0-1/protr/inst/doc/protr.R | 28 protr-1.0-1/protr/inst/doc/protr.Rnw | 58 protr-1.0-1/protr/inst/doc/protr.pdf |binary protr-1.0-1/protr/man/AA2DACOR.Rd | 3 protr-1.0-1/protr/man/AA3DMoRSE.Rd | 3 protr-1.0-1/protr/man/AAACF.Rd | 3 protr-1.0-1/protr/man/AABLOSUM100.Rd | 3 protr-1.0-1/protr/man/AABLOSUM45.Rd | 3 protr-1.0-1/protr/man/AABLOSUM50.Rd | 3 protr-1.0-1/protr/man/AABLOSUM62.Rd | 3 protr-1.0-1/protr/man/AABLOSUM80.Rd | 3 protr-1.0-1/protr/man/AABurden.Rd | 3 protr-1.0-1/protr/man/AACPSA.Rd | 3 protr-1.0-1/protr/man/AAConn.Rd | 3 protr-1.0-1/protr/man/AAConst.Rd | 3 protr-1.0-1/protr/man/AADescAll.Rd | 3 protr-1.0-1/protr/man/AAEdgeAdj.Rd | 3 protr-1.0-1/protr/man/AAEigIdx.Rd | 3 protr-1.0-1/protr/man/AAFGC.Rd | 3 protr-1.0-1/protr/man/AAGETAWAY.Rd | 3 protr-1.0-1/protr/man/AAGeom.Rd | 3 protr-1.0-1/protr/man/AAInfo.Rd | 3 protr-1.0-1/protr/man/AAMOE2D.Rd | 3 protr-1.0-1/protr/man/AAMOE3D.Rd | 3 protr-1.0-1/protr/man/AAMetaInfo.Rd | 3 protr-1.0-1/protr/man/AAMolProp.Rd | 3 protr-1.0-1/protr/man/AAPAM120.Rd | 3 protr-1.0-1/protr/man/AAPAM250.Rd | 3 protr-1.0-1/protr/man/AAPAM30.Rd | 3 protr-1.0-1/protr/man/AAPAM40.Rd | 3 protr-1.0-1/protr/man/AAPAM70.Rd | 3 protr-1.0-1/protr/man/AARDF.Rd | 3 protr-1.0-1/protr/man/AARandic.Rd | 3 protr-1.0-1/protr/man/AATopo.Rd | 3 protr-1.0-1/protr/man/AATopoChg.Rd | 3 protr-1.0-1/protr/man/AAWHIM.Rd | 3 protr-1.0-1/protr/man/AAWalk.Rd | 3 protr-1.0-1/protr/man/AAindex.Rd | 3 protr-1.0-1/protr/man/OptAA3d.Rd | 2 protr-1.0-1/protr/man/acc.Rd | 4 protr-1.0-1/protr/man/extractAAC.Rd | 4 protr-1.0-1/protr/man/extractAPAAC.Rd | 44 protr-1.0-1/protr/man/extractBLOSUM.Rd | 4 protr-1.0-1/protr/man/extractCTDC.Rd | 4 protr-1.0-1/protr/man/extractCTDCClass.Rd | 4 protr-1.0-1/protr/man/extractCTDD.Rd | 4 protr-1.0-1/protr/man/extractCTDDClass.Rd | 4 protr-1.0-1/protr/man/extractCTDT.Rd | 4 protr-1.0-1/protr/man/extractCTDTClass.Rd | 4 protr-1.0-1/protr/man/extractCTriad.Rd | 4 protr-1.0-1/protr/man/extractCTriadClass.Rd | 4 protr-1.0-1/protr/man/extractDC.Rd | 4 protr-1.0-1/protr/man/extractDescScales.Rd | 10 protr-1.0-1/protr/man/extractFAScales.Rd | 10 protr-1.0-1/protr/man/extractGeary.Rd | 54 protr-1.0-1/protr/man/extractMDSScales.Rd | 8 protr-1.0-1/protr/man/extractMoran.Rd | 54 protr-1.0-1/protr/man/extractMoreauBroto.Rd | 54 protr-1.0-1/protr/man/extractPAAC.Rd | 48 protr-1.0-1/protr/man/extractPSSM.Rd | 4 protr-1.0-1/protr/man/extractPSSMAcc.Rd | 4 protr-1.0-1/protr/man/extractPSSMFeature.Rd | 4 protr-1.0-1/protr/man/extractProtFP.Rd | 10 protr-1.0-1/protr/man/extractProtFPGap.Rd | 9 protr-1.0-1/protr/man/extractQSO.Rd | 4 protr-1.0-1/protr/man/extractSOCN.Rd | 4 protr-1.0-1/protr/man/extractScales.Rd | 10 protr-1.0-1/protr/man/extractScalesGap.Rd | 10 protr-1.0-1/protr/man/extractTC.Rd | 4 protr-1.0-1/protr/man/getUniProt.Rd | 7 protr-1.0-1/protr/man/parGOSim.Rd | 6 protr-1.0-1/protr/man/parSeqSim.Rd | 4 protr-1.0-1/protr/man/protcheck.Rd | 8 protr-1.0-1/protr/man/protr-package.Rd | 17 protr-1.0-1/protr/man/protseg.Rd | 16 protr-1.0-1/protr/man/readFASTA.Rd | 20 protr-1.0-1/protr/man/readPDB.Rd | 14 protr-1.0-1/protr/man/twoGOSim.Rd | 6 protr-1.0-1/protr/man/twoSeqSim.Rd | 4 protr-1.0-1/protr/vignettes/protr.Rnw | 58 128 files changed, 4867 insertions(+), 4853 deletions(-)
Title: Coclustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The blockcluster package provides a bridge between the C++
core library and the R statistical computing environment. This package
allows to co-cluster binary, contingency, continuous and categorical
data-sets. It also provides utility functions to visualize the results.
This package may be useful for various applications in fields of Data
mining,Information retrieval, Biology, computer vision and many more. More
information about the project and comprehensive tutorial can be found on
the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Vincent Kubicki [ctb],
Gerard Goavert [ctb],
Vincent Brault [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 3.0.2 dated 2015-01-23 and 4.0.2 dated 2015-11-27
blockcluster-3.0.2/blockcluster/R/Rcoclust.R |only blockcluster-3.0.2/blockcluster/R/Strategy.R |only blockcluster-3.0.2/blockcluster/R/plot.R |only blockcluster-3.0.2/blockcluster/R/summary.R |only blockcluster-3.0.2/blockcluster/inst/doc/blockcluster_tutorial_V3.0.Rnw |only blockcluster-3.0.2/blockcluster/inst/doc/blockcluster_tutorial_V3.0.pdf |only blockcluster-3.0.2/blockcluster/man/cocluststrategy.Rd |only blockcluster-3.0.2/blockcluster/man/strategy-class.Rd |only blockcluster-3.0.2/blockcluster/src/Makevars.win |only blockcluster-3.0.2/blockcluster/vignettes/blockcluster_tutorial_V3.0.Rnw |only blockcluster-4.0.2/blockcluster/DESCRIPTION | 48 blockcluster-4.0.2/blockcluster/MD5 | 176 +- blockcluster-4.0.2/blockcluster/NAMESPACE | 20 blockcluster-4.0.2/blockcluster/R/RCocluster.R |only blockcluster-4.0.2/blockcluster/R/cocluster.R | 335 ++-- blockcluster-4.0.2/blockcluster/R/coclusterBinary.R |only blockcluster-4.0.2/blockcluster/R/coclusterCategorical.R |only blockcluster-4.0.2/blockcluster/R/coclusterContingency.R |only blockcluster-4.0.2/blockcluster/R/coclusterContinuous.R |only blockcluster-4.0.2/blockcluster/R/coclusterStrategy.R |only blockcluster-4.0.2/blockcluster/R/optionclasses.R | 745 +++++++++- blockcluster-4.0.2/blockcluster/build/vignette.rds |binary blockcluster-4.0.2/blockcluster/cleanup |only blockcluster-4.0.2/blockcluster/data/binarydata.rda |binary blockcluster-4.0.2/blockcluster/data/categoricaldata.rda |binary blockcluster-4.0.2/blockcluster/data/contingencydatalist.rda |binary blockcluster-4.0.2/blockcluster/data/contingencydataunknown.rda |binary blockcluster-4.0.2/blockcluster/data/gaussiandata.rda |binary blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.R |only blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.Rnw |only blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.pdf |only blockcluster-4.0.2/blockcluster/man/BinaryOptions-class.Rd | 20 blockcluster-4.0.2/blockcluster/man/CategoricalOptions-class.Rd | 18 blockcluster-4.0.2/blockcluster/man/CommonOptions-class.Rd | 44 blockcluster-4.0.2/blockcluster/man/ContingencyOptions-class.Rd | 20 blockcluster-4.0.2/blockcluster/man/ContinuousOptions-class.Rd | 18 blockcluster-4.0.2/blockcluster/man/XEMStrategy.Rd | 35 blockcluster-4.0.2/blockcluster/man/blockcluster.Rd | 53 blockcluster-4.0.2/blockcluster/man/cocluster.Rd | 104 - blockcluster-4.0.2/blockcluster/man/coclusterBinary.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterCategorical.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterContingency.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterContinuous.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterStrategy.Rd |only blockcluster-4.0.2/blockcluster/man/getter-methods.Rd | 33 blockcluster-4.0.2/blockcluster/man/plot-methods.Rd | 36 blockcluster-4.0.2/blockcluster/man/summary-methods.Rd | 31 blockcluster-4.0.2/blockcluster/src/BinaryDataExchange.cpp | 223 +- blockcluster-4.0.2/blockcluster/src/BinaryDataExchange.h | 6 blockcluster-4.0.2/blockcluster/src/CategoricalDataExchange.cpp | 150 -- blockcluster-4.0.2/blockcluster/src/CategoricalDataExchange.h | 4 blockcluster-4.0.2/blockcluster/src/ContingencyDataExchange.cpp | 77 - blockcluster-4.0.2/blockcluster/src/ContingencyDataExchange.h | 12 blockcluster-4.0.2/blockcluster/src/ContinuousDataExchange.cpp | 75 - blockcluster-4.0.2/blockcluster/src/ContinuousDataExchange.h | 4 blockcluster-4.0.2/blockcluster/src/IDataExchange.cpp | 36 blockcluster-4.0.2/blockcluster/src/IDataExchange.h | 17 blockcluster-4.0.2/blockcluster/src/Makevars | 16 blockcluster-4.0.2/blockcluster/src/Rcoclustmain.cpp | 46 blockcluster-4.0.2/blockcluster/src/coclust/makefile | 12 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/CEMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/CEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/EMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/EMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/IAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/SEMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/SEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/CoClustFacade/CoCluster.cpp | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/CoClustFacade/CoCluster.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/CEMInit.h | 4 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/FuzzyCEMInit.h | 16 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/IInit.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/RandomInit.h | 4 blockcluster-4.0.2/blockcluster/src/coclust/src/InputParameters/InputParameters.cpp | 16 blockcluster-4.0.2/blockcluster/src/coclust/src/InputParameters/InputParameters.h | 28 blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModel.cpp | 514 +++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModel.h | 108 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.cpp | 469 ++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.h | 144 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/CategoricalLBModel.cpp | 577 +++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/CategoricalLBModel.h | 54 blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel.cpp | 412 ++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel.h | 101 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.cpp | 245 +-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.h | 100 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModel.cpp | 327 ++-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModel.h | 113 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.cpp | 289 +-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.h | 104 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ICoClustModel.cpp | 637 ++++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ICoClustModel.h | 403 ++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/IStrategy.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyAlgo.cpp | 133 - blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyforSEMAlgo.cpp | 30 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyforSEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/enumerations/enumerations.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/typedefs/typedef.h | 31 blockcluster-4.0.2/blockcluster/src/conversion.h | 30 blockcluster-4.0.2/blockcluster/src/test/test.cpp | 2 blockcluster-4.0.2/blockcluster/vignettes/biblio.bib | 13 blockcluster-4.0.2/blockcluster/vignettes/blockcluster_tutorial.Rnw |only 102 files changed, 3882 insertions(+), 3512 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.2.0 dated 2015-07-15 and 1.2.1 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 10 ++++++++-- R/wrappers.R | 20 +++++++++++++++++--- build/vignette.rds |binary data/exrates.RData |binary inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary man/svsample.Rd | 18 +++++++++++------- src/progutils.cpp | 4 ++-- src/progutils.h | 16 +++++++++++----- src/sampler.cpp | 24 +++++++++++++++--------- src/sampler.h | 2 +- 13 files changed, 81 insertions(+), 45 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. In both cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.8.1 dated 2015-11-19 and 2.8.2 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/expose_stan_functions.R | 10 +++++++--- R/rstan.R | 12 +++++++----- R/stanc.R | 4 +--- R/stanmodel-class.R | 25 +++++++++++++++++-------- inst/NEWS | 14 ++++++++++++++ inst/doc/rstan_vignette.R | 2 +- inst/doc/rstan_vignette.Rnw | 2 +- inst/doc/rstan_vignette.pdf |binary man/rstan.Rd | 4 ++-- man/stan.Rd | 3 --- man/stan_model.Rd | 6 ++++-- vignettes/rstan_vignette.Rnw | 2 +- 14 files changed, 72 insertions(+), 46 deletions(-)
Title: A Wrapper for the Pinnacle Sports API
Description: An R interface to the Pinnaclesports.com API.
Author: Marco Blume, Nicholas Jhirad, Amine Gassem
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between pinnacle.API versions 1.89 dated 2015-09-18 and 1.90 dated 2015-11-27
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 1 + NEWS | 7 +++++++ R/pinnRawXMLResponse.R |only R/showOddsDF.R | 10 +++++++--- man/pinnRawXMLResponse.Rd |only 7 files changed, 24 insertions(+), 10 deletions(-)
Title: Calculate Indices and Theoretical Properties of Protein
Sequences
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio <daniel.osorio@correo.uis.edu.co>
Diff between Peptides versions 1.1.0 dated 2015-06-03 and 1.1.1 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 5 ++++- NEWS | 4 ++++ R/aacomp.R | 2 +- R/aindex.R | 2 +- R/boman.R | 2 +- R/charge.R | 2 +- R/hmoment.R | 2 +- R/hydrophobicity.R | 2 +- R/instaindex.R | 2 +- R/kidera.R | 2 +- R/lengthpep.R | 2 +- R/membpos.R | 2 +- R/mw.R | 24 ++++++++++++++++-------- R/pI.R | 2 +- man/Peptides-package.Rd | 4 ++-- man/mw.Rd | 6 +++--- 18 files changed, 61 insertions(+), 46 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.4.0 dated 2015-08-26 and 1.4.6 dated 2015-11-27
DESCRIPTION | 16 ++--- MD5 | 43 ++++++++----- NAMESPACE | 12 ++- R/colourScale.R | 6 + R/geonames.R | 28 ++++++++- R/gridlinesWrap.R |only R/legendBreaks.R | 152 +++++++++++++------------------------------------ R/legendTable.R | 2 R/map.new.R | 10 +++ R/moll.R |only R/omerc.R | 17 ----- R/openmap.R | 18 ++--- R/openmapAttribution.R | 4 - R/utils.R | 39 +++++++++--- R/wrapPoly.R |only inst/doc/mapLayers.pdf |binary inst/doc/mapmisc.pdf |binary man/colourScale.Rd | 3 man/geocode.Rd |only man/gridlinesWrap.Rd |only man/legendBreaks.Rd | 4 + man/omerc.Rd | 29 ++++++++- man/scaleBar.Rd | 7 -- man/wrapPoly.Rd |only tests/omerc.R | 1 tests/worldMap.R |only 26 files changed, 203 insertions(+), 188 deletions(-)
Title: Ensemble Partial Least Squares Regression
Description: Ensemble partial least squares regression, a unified
framework for feature selection, outlier detection, and ensemble learning.
Author: Nan Xiao <road2stat@gmail.com>, Dong-Sheng Cao <oriental-cds@163.com>,
Qing-Song Xu <dasongxu@gmail.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between enpls versions 1.0 dated 2014-10-03 and 1.1 dated 2015-11-27
enpls-1.0/enpls/vignettes/fig/plot-cv-enpls.pdf |only enpls-1.1/enpls/DESCRIPTION | 13 ++-- enpls-1.1/enpls/MD5 | 67 ++++++++++++------------ enpls-1.1/enpls/NAMESPACE | 11 +++ enpls-1.1/enpls/NEWS |only enpls-1.1/enpls/R/cv.enpls.R | 4 - enpls-1.1/enpls/R/enpls-package.R | 19 +++--- enpls-1.1/enpls/R/enpls.en.R | 8 +- enpls-1.1/enpls/R/enpls.fs.R | 8 +- enpls-1.1/enpls/R/enpls.od.R | 8 +- enpls-1.1/enpls/R/plot.R | 15 ++--- enpls-1.1/enpls/R/predict.R | 5 - enpls-1.1/enpls/R/print.R | 20 ++----- enpls-1.1/enpls/README.md |only enpls-1.1/enpls/build/vignette.rds |binary enpls-1.1/enpls/inst/doc/enpls.R | 23 +++----- enpls-1.1/enpls/inst/doc/enpls.Rnw | 29 +++------- enpls-1.1/enpls/inst/doc/enpls.pdf |binary enpls-1.1/enpls/man/alkanes.Rd | 11 ++- enpls-1.1/enpls/man/cv.enpls.Rd | 17 ++---- enpls-1.1/enpls/man/enpls-package.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.en.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.en.core.Rd | 3 - enpls-1.1/enpls/man/enpls.fs.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.fs.core.Rd | 3 - enpls-1.1/enpls/man/enpls.od.Rd | 23 ++++---- enpls-1.1/enpls/man/enpls.od.core.Rd | 5 + enpls-1.1/enpls/man/plot.cv.enpls.Rd | 8 +- enpls-1.1/enpls/man/plot.enpls.fs.Rd | 8 +- enpls-1.1/enpls/man/plot.enpls.od.Rd | 10 +-- enpls-1.1/enpls/man/predict.enpls.en.Rd | 14 ++--- enpls-1.1/enpls/man/print.cv.enpls.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.en.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.fs.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.od.Rd | 8 +- enpls-1.1/enpls/vignettes/enpls.Rnw | 29 +++------- 36 files changed, 216 insertions(+), 240 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient
and robust C library for convex problems. Conic and equality
constraints can be specified in addition to integer and
boolean variable constraints for mixed-integer problems. This
R interface is inspired by the python interface and has
similar calling conventions.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.1-1 dated 2015-11-25 and 0.2 dated 2015-11-27
ECOSolveR-0.1-1/ECOSolveR/inst/misc/ECOS.Rmd |only ECOSolveR-0.1-1/ECOSolveR/inst/misc/ECOSolver.Rmd |only ECOSolveR-0.1-1/ECOSolveR/src/configure |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.orig |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.unix |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.win |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/ecos.mk.orig |only ECOSolveR-0.2/ECOSolveR/DESCRIPTION | 20 ++++--- ECOSolveR-0.2/ECOSolveR/MD5 | 35 +++++-------- ECOSolveR-0.2/ECOSolveR/README.md | 14 ++++- ECOSolveR-0.2/ECOSolveR/inst/doc/examples.html | 4 - ECOSolveR-0.2/ECOSolveR/src/Makevars.in | 4 + ECOSolveR-0.2/ECOSolveR/src/Makevars.win | 6 +- ECOSolveR-0.2/ECOSolveR/src/ecos/Makefile | 22 +++----- ECOSolveR-0.2/ECOSolveR/src/ecos/README.md | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/__.SYMDEF |binary ECOSolveR-0.2/ECOSolveR/src/ecos/ecos-unix.mk | 30 ++++------- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos-win.mk | 18 +++--- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos.mk | 30 ++++------- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos_bb/ecos_bb_preproc.c | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/external/amd/Makefile | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/external/ldl/Makefile | 2 22 files changed, 94 insertions(+), 97 deletions(-)
Title: Feature Selection and Classification with the Embedded
Validation Procedures for Biomedical Data Analysis
Description: Contains functions for the data analysis with the emphasis on biological data, including several algorithms for feature ranking, feature selection, classification
algorithms with the embedded validation procedures.
The functions can deal with numerical as well as with nominal features. Includes also the functions for calculation
of feature AUC (Area Under the ROC Curve) and HUM (hypervolume under manifold) values and construction 2D- and 3D- ROC curves.
Biocomb provides the calculation of Area Above the RCC (AAC) values and construction of Relative Cost Curves
(RCC) to estimate the classifier performance under unequal misclassification costs problem.
Biocomb has the special function to deal with missing values, including different imputing schemes.
Author: Natalia Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn
Maintainer: Natalia Novoselova <novos65@mail.ru>
Diff between Biocomb versions 0.1 dated 2015-10-28 and 0.2 dated 2015-11-27
DESCRIPTION | 16 - MD5 | 52 +++-- NAMESPACE | 2 R/CalculateHUM_ROC.R | 4 R/CalculateHUM_seq.R | 2 R/ROC_Plot.R | 7 R/RcppExports.R | 24 ++ R/class_cross.R | 38 +++- R/input_miss.R | 4 R/select.feature.info.R | 375 +++++------------------------------------- man/Biocomb-package.Rd | 2 man/CalculateHUM_Ex.Rd | 4 man/chi2.algorithm.Rd | 6 man/classifier.loop.Rd | 2 man/compute.aucs.Rd | 2 man/data_test.Rd | 2 man/input_miss.Rd | 2 man/leukemia72.Rd | 3 man/leukemia72_2.Rd | 3 man/select.cfs.Rd |only man/select.fast.filter.Rd | 2 man/select.forward.wrapper.Rd | 2 man/select.inf.gain.Rd | 2 man/select.inf.symm.Rd | 2 man/select.process.Rd | 6 man/select.relief.Rd |only src/CHI2.cpp |only src/CorrF.cpp |only src/RcppExports.cpp | 87 +++++++++ 29 files changed, 252 insertions(+), 399 deletions(-)
Title: Planing, Monitoring and Evaluating Oncological Phase 2 Studies
Description: Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with this package a good starting point is to take a closer look at the functions getSolutions() and getSolutionsSub1().
Author: Marius Wirths
Maintainer: Marius Wirths <wirths@imbi.uni-heidelberg.de>
Diff between OneArmPhaseTwoStudy versions 0.1.3 dated 2015-07-01 and 0.1.4 dated 2015-11-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/result.h | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++++ src/resultsub1.h | 36 ++++++++++++++++++++++++++++++++++++ 4 files changed, 95 insertions(+), 7 deletions(-)
More information about OneArmPhaseTwoStudy at CRAN
Permanent link
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 1.2 dated 2014-11-14 and 1.2-1 dated 2015-11-26
DESCRIPTION | 15 ++++++++------- MD5 | 15 +++++++++++---- NAMESPACE | 3 ++- build |only inst/NEWS | 11 ++--------- inst/doc |only man/equateIRT-package.Rd | 4 ++-- vignettes |only 8 files changed, 25 insertions(+), 23 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 1.0.11 dated 2015-02-10 and 1.0.13 dated 2015-11-26
treeclim-1.0.11/treeclim/R/zzz.R |only treeclim-1.0.13/treeclim/DESCRIPTION | 11 treeclim-1.0.13/treeclim/MD5 | 100 - treeclim-1.0.13/treeclim/NAMESPACE | 4 treeclim-1.0.13/treeclim/R/RcppExports.R | 54 treeclim-1.0.13/treeclim/R/dcc.R | 686 ++++----- treeclim-1.0.13/treeclim/R/exclude_from.R | 94 - treeclim-1.0.13/treeclim/R/generics.R | 702 +++++----- treeclim-1.0.13/treeclim/R/gershunov.R | 352 ++--- treeclim-1.0.13/treeclim/R/ptest.R | 4 treeclim-1.0.13/treeclim/R/seascorr.R | 569 ++++---- treeclim-1.0.13/treeclim/R/tc_mfunc.R | 2 treeclim-1.0.13/treeclim/inst/CITATION | 6 treeclim-1.0.13/treeclim/inst/Changelog | 163 +- treeclim-1.0.13/treeclim/man/abbrev_name.Rd | 3 treeclim-1.0.13/treeclim/man/as_tcclimate.Rd | 3 treeclim-1.0.13/treeclim/man/check_months.Rd | 3 treeclim-1.0.13/treeclim/man/correct_continuous.Rd | 3 treeclim-1.0.13/treeclim/man/dcc.Rd | 27 treeclim-1.0.13/treeclim/man/eval_selection.Rd | 3 treeclim-1.0.13/treeclim/man/exclude_from.Rd | 3 treeclim-1.0.13/treeclim/man/format_month.Rd | 3 treeclim-1.0.13/treeclim/man/g_test.Rd | 5 treeclim-1.0.13/treeclim/man/init_boot_data.Rd | 3 treeclim-1.0.13/treeclim/man/is_continuous.Rd | 3 treeclim-1.0.13/treeclim/man/make_pmat.Rd | 3 treeclim-1.0.13/treeclim/man/make_range_list.Rd | 3 treeclim-1.0.13/treeclim/man/muc_clim.Rd | 3 treeclim-1.0.13/treeclim/man/muc_fake.Rd | 3 treeclim-1.0.13/treeclim/man/muc_spruce.Rd | 3 treeclim-1.0.13/treeclim/man/norw015.Rd | 3 treeclim-1.0.13/treeclim/man/norway_prec.Rd | 3 treeclim-1.0.13/treeclim/man/norway_temp.Rd | 3 treeclim-1.0.13/treeclim/man/ptest.Rd | 5 treeclim-1.0.13/treeclim/man/rt_prec.Rd | 3 treeclim-1.0.13/treeclim/man/rt_spruce.Rd | 5 treeclim-1.0.13/treeclim/man/rt_temp.Rd | 3 treeclim-1.0.13/treeclim/man/seascorr.Rd | 139 - treeclim-1.0.13/treeclim/man/skills.Rd | 21 treeclim-1.0.13/treeclim/man/spai020.Rd | 3 treeclim-1.0.13/treeclim/man/spain_prec.Rd | 3 treeclim-1.0.13/treeclim/man/spain_temp.Rd | 3 treeclim-1.0.13/treeclim/man/tc_correlation.Rd | 3 treeclim-1.0.13/treeclim/man/tc_design.Rd | 3 treeclim-1.0.13/treeclim/man/tc_mfunc.Rd | 3 treeclim-1.0.13/treeclim/man/tc_response.Rd | 3 treeclim-1.0.13/treeclim/man/treeclim-modifiers.Rd | 3 treeclim-1.0.13/treeclim/man/truncate_input.Rd | 3 treeclim-1.0.13/treeclim/src/Makevars | 1 treeclim-1.0.13/treeclim/src/Makevars.win | 2 treeclim-1.0.13/treeclim/src/RcppExports.cpp | 129 - treeclim-1.0.13/treeclim/tests/testthat/test_moving_windows.R |only 52 files changed, 1595 insertions(+), 1570 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.4 dated 2015-07-22 and 1.5 dated 2015-11-26
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/SdmxClient.R | 39 +++++++++++++++++++++++++++++++++------ R/TSConverter.R | 29 ++++++++++++++++++++++------- inst/java/SDMX.jar |binary man/RJSDMX-package.Rd | 7 ++++--- man/addProvider.Rd | 10 ++++------ man/getTimeSeriesRevisions.Rd | 20 ++++++++++++-------- man/getTimeSeriesTable.Rd |only man/sdmxHelp.Rd | 6 +++--- man/sdmxdf.Rd | 10 +++++----- 12 files changed, 98 insertions(+), 51 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.4.2 dated 2015-08-24 and 0.4.3 dated 2015-11-26
markovchain-0.4.2/markovchain/inst/doc/BayesianInference.R |only markovchain-0.4.2/markovchain/inst/doc/BayesianInference.Rmd |only markovchain-0.4.2/markovchain/inst/doc/BayesianInference.pdf |only markovchain-0.4.2/markovchain/inst/doc/CTMC.R |only markovchain-0.4.2/markovchain/inst/doc/CTMC.Rmd |only markovchain-0.4.2/markovchain/inst/doc/CTMC.pdf |only markovchain-0.4.2/markovchain/tests/testthat/Rplots.pdf |only markovchain-0.4.2/markovchain/vignettes/BayesianInference.Rmd |only markovchain-0.4.2/markovchain/vignettes/CTMC.Rmd |only markovchain-0.4.2/markovchain/vignettes/jss.dtx |only markovchain-0.4.2/markovchain/vignettes/jsslogo.jpg |only markovchain-0.4.3/markovchain/ChangeLog | 4 markovchain-0.4.3/markovchain/DESCRIPTION | 8 markovchain-0.4.3/markovchain/MD5 | 51 - markovchain-0.4.3/markovchain/NEWS | 8 markovchain-0.4.3/markovchain/R/0_classesAndMethods.R | 45 + markovchain-0.4.3/markovchain/R/1_supplementaryPlot.R | 2 markovchain-0.4.3/markovchain/build/vignette.rds |binary markovchain-0.4.3/markovchain/data/blanden.rda |binary markovchain-0.4.3/markovchain/data/craigsendi.rda |binary markovchain-0.4.3/markovchain/data/holson.rda |binary markovchain-0.4.3/markovchain/data/preproglucacon.rda |binary markovchain-0.4.3/markovchain/data/rain.rda |binary markovchain-0.4.3/markovchain/inst/CITATION | 4 markovchain-0.4.3/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 175 +++++- markovchain-0.4.3/markovchain/inst/doc/an_introduction_to_markovchain_package.Rnw | 278 +++++++++- markovchain-0.4.3/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary markovchain-0.4.3/markovchain/inst/doc/markovchainCrashIntro.pdf |binary markovchain-0.4.3/markovchain/man/markovchain-class.Rd | 2 markovchain-0.4.3/markovchain/man/markovchain-package.Rd | 4 markovchain-0.4.3/markovchain/tests/testthat/testPlot.R | 3 markovchain-0.4.3/markovchain/vignettes/an_introduction_to_markovchain_package.Rnw | 278 +++++++++- 32 files changed, 774 insertions(+), 88 deletions(-)
Title: Feature-Based Landscape Analysis of Continuous and Constraint
Optimization Problems
Description: Contains tools and features, which can be used for an exploratory
landscape analysis of continuous optimization problems. Those are able to
quantify rather complex properties, such as the global structure,
separability, etc., of continuous optimization problems.
Author: Pascal Kerschke [aut, cre],
Jan Dagefoerde [aut]
Maintainer: Pascal Kerschke <kerschke@uni-muenster.de>
Diff between flacco versions 1.0 dated 2015-10-28 and 1.1 dated 2015-11-26
flacco-1.0/flacco/R/createInitialDesign.R |only flacco-1.0/flacco/man/createInitialDesign.Rd |only flacco-1.0/flacco/tests/testthat/test-base-createInitialDesign.R |only flacco-1.1/flacco/DESCRIPTION | 7 flacco-1.1/flacco/MD5 | 77 +-- flacco-1.1/flacco/NAMESPACE | 4 flacco-1.1/flacco/NEWS |only flacco-1.1/flacco/R/calculateFeatures.R | 12 flacco-1.1/flacco/R/cm_findNearestPrototype.R | 9 flacco-1.1/flacco/R/createFeatureObject.R | 236 +++++----- flacco-1.1/flacco/R/createInitialSample.R |only flacco-1.1/flacco/R/feature_ela_local_search.R | 2 flacco-1.1/flacco/R/feature_gcm_barriertree.R | 3 flacco-1.1/flacco/R/feature_ic_infocontent.R | 4 flacco-1.1/flacco/R/plotBarrierTree2D.R | 8 flacco-1.1/flacco/R/plotBarrierTree3D.R | 2 flacco-1.1/flacco/R/plotCellMapping.R | 6 flacco-1.1/flacco/R/plotFeatureImportance.R | 4 flacco-1.1/flacco/R/plotInformationContent.R | 10 flacco-1.1/flacco/man/FeatureObject.Rd | 24 - flacco-1.1/flacco/man/computeGridCenters.Rd | 3 flacco-1.1/flacco/man/convertInitDesignToGrid.Rd | 3 flacco-1.1/flacco/man/createInitialSample.Rd |only flacco-1.1/flacco/man/featureList.Rd | 2 flacco-1.1/flacco/man/features.Rd | 19 flacco-1.1/flacco/man/findLinearNeighbours.Rd | 11 flacco-1.1/flacco/man/findNearestPrototype.Rd | 16 flacco-1.1/flacco/man/listAvailableFeatureSets.Rd | 2 flacco-1.1/flacco/man/measureTime.Rd | 2 flacco-1.1/flacco/man/plotBarrierTree2D.Rd | 4 flacco-1.1/flacco/man/plotBarrierTree3D.Rd | 4 flacco-1.1/flacco/man/plotCellMapping.Rd | 2 flacco-1.1/flacco/man/plotFeatureImportance.Rd | 10 flacco-1.1/flacco/man/plotInformationContent.Rd | 12 flacco-1.1/flacco/tests/test-features.R | 14 flacco-1.1/flacco/tests/test-general.R | 5 flacco-1.1/flacco/tests/testthat/Rplots.pdf |binary flacco-1.1/flacco/tests/testthat/test-base-createFeatureObject.R | 20 flacco-1.1/flacco/tests/testthat/test-base-createInitialSample.R |only flacco-1.1/flacco/tests/testthat/test-base-printFeatureObject.R | 33 + flacco-1.1/flacco/tests/testthat/test-calculateFeatures.R | 3 flacco-1.1/flacco/tests/testthat/test-gcm-BarrierTrees.R | 4 flacco-1.1/flacco/tests/testthat/test-plot-plotBarrierTree3D.R | 2 43 files changed, 336 insertions(+), 243 deletions(-)
Title: Tools for Collecting Social Media Data and Generating Networks
for Analysis
Description: A suite of tools for collecting and constructing networks from social media data. Provides easy-to-use functions for collecting data across popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating different types of networks for analysis.
Author: Timothy Graham & Robert Ackland
Maintainer: Timothy Graham <timothy.graham3@uq.net.au>
Diff between SocialMediaLab versions 0.18.0 dated 2015-11-15 and 0.19.0 dated 2015-11-26
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 5 ++++- R/CollectDataFacebook.R | 29 ++++++++++++++--------------- R/CollectDataInstagram.R | 6 ++++-- R/CreateActorNetwork.list.R | 7 +++++++ R/CreateEgoNetwork.R |only man/CollectDataInstagram.Rd | 2 +- man/CreateEgoNetwork.Rd |only 9 files changed, 42 insertions(+), 29 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.3.4 dated 2015-09-16 and 0.4.0 dated 2015-11-26
rvertnet-0.3.4/rvertnet/inst/ignore |only rvertnet-0.4.0/rvertnet/DESCRIPTION | 9 rvertnet-0.4.0/rvertnet/MD5 | 51 ++--- rvertnet-0.4.0/rvertnet/NAMESPACE | 16 + rvertnet-0.4.0/rvertnet/R/bigsearch.R | 6 rvertnet-0.4.0/rvertnet/R/rvertnet-package.R | 6 rvertnet-0.4.0/rvertnet/R/searchbyterm.R | 14 + rvertnet-0.4.0/rvertnet/R/vertdump.R |only rvertnet-0.4.0/rvertnet/R/vertmap.R | 62 +++--- rvertnet-0.4.0/rvertnet/R/zzz.R | 15 + rvertnet-0.4.0/rvertnet/README.md | 126 ++++++------- rvertnet-0.4.0/rvertnet/man/bigsearch.Rd | 12 - rvertnet-0.4.0/rvertnet/man/dump.Rd |only rvertnet-0.4.0/rvertnet/man/rvertnet-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/rvertnet-package.Rd | 11 - rvertnet-0.4.0/rvertnet/man/searchbyterm.Rd | 2 rvertnet-0.4.0/rvertnet/man/spatialsearch.Rd | 4 rvertnet-0.4.0/rvertnet/man/vert_id.Rd | 4 rvertnet-0.4.0/rvertnet/man/vertavailablemaps-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/vertlocations-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/vertmap.Rd | 19 + rvertnet-0.4.0/rvertnet/man/vertoccurrence-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/vertoccurrencecount-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/vertproviders-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/man/vertsearch.Rd | 4 rvertnet-0.4.0/rvertnet/man/vertsummary.Rd | 4 rvertnet-0.4.0/rvertnet/man/verttaxa-defunct.Rd | 2 rvertnet-0.4.0/rvertnet/tests/testthat/test-searchbyterm.R | 19 + 28 files changed, 242 insertions(+), 156 deletions(-)
Title: A Simple Data Science Challenge System
Description: A simple data science challenge system using R Markdown and Dropbox <https://www.dropbox.com/>.
It requires no network configuration, does not depend on external platforms
like e.g. Kaggle <https://www.kaggle.com/> and can be easily installed on a personal computer.
Author: Adrien Todeschini [aut, cre],
Robin Genuer [ctb]
Maintainer: Adrien Todeschini <adrien.todeschini@gmail.com>
Diff between rchallenge versions 1.1 dated 2015-05-17 and 1.1.1 dated 2015-11-26
rchallenge-1.1.1/rchallenge/DESCRIPTION | 17 - rchallenge-1.1.1/rchallenge/MD5 | 90 ++------ rchallenge-1.1.1/rchallenge/NAMESPACE | 16 + rchallenge-1.1.1/rchallenge/R/data.r | 2 rchallenge-1.1.1/rchallenge/R/plots.r | 6 rchallenge-1.1.1/rchallenge/R/rchallenge.r |only rchallenge-1.1.1/rchallenge/R/update.r | 9 rchallenge-1.1.1/rchallenge/README.md | 138 ++++++------- rchallenge-1.1.1/rchallenge/inst/template/challenge_en.rmd | 28 +- rchallenge-1.1.1/rchallenge/inst/template/challenge_fr.rmd | 35 ++- rchallenge-1.1.1/rchallenge/man/compute_metrics.Rd | 7 rchallenge-1.1.1/rchallenge/man/countdown.Rd | 2 rchallenge-1.1.1/rchallenge/man/data_partition.Rd | 6 rchallenge-1.1.1/rchallenge/man/data_split.Rd | 2 rchallenge-1.1.1/rchallenge/man/german.Rd | 18 - rchallenge-1.1.1/rchallenge/man/get_best.Rd | 2 rchallenge-1.1.1/rchallenge/man/get_data.Rd | 2 rchallenge-1.1.1/rchallenge/man/glyphicon.Rd | 2 rchallenge-1.1.1/rchallenge/man/html_img.Rd | 2 rchallenge-1.1.1/rchallenge/man/last_update.Rd | 2 rchallenge-1.1.1/rchallenge/man/new_challenge.Rd | 2 rchallenge-1.1.1/rchallenge/man/new_team.Rd | 2 rchallenge-1.1.1/rchallenge/man/plot_activity.Rd | 6 rchallenge-1.1.1/rchallenge/man/plot_history.Rd | 6 rchallenge-1.1.1/rchallenge/man/print_leaderboard.Rd | 2 rchallenge-1.1.1/rchallenge/man/print_readerr.Rd | 2 rchallenge-1.1.1/rchallenge/man/publish.Rd | 8 rchallenge-1.1.1/rchallenge/man/rchallenge-package.Rd |only rchallenge-1.1.1/rchallenge/man/store_new_submissions.Rd | 6 rchallenge-1.1.1/rchallenge/man/str_rank.Rd | 2 rchallenge-1.1.1/rchallenge/man/update_rank_diff.Rd | 2 rchallenge-1.1/rchallenge/inst/staticdocs |only rchallenge-1.1/rchallenge/inst/web |only 33 files changed, 215 insertions(+), 209 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs via simulations
- Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use both point estimate (PE) and mse from stage 1
also for the power monitoring steps.
- The third function power.2stage.fC() calculates power and sample-size
distribution of 2-stage BE studies with a futility criterion
for the PE or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
This function has a sibling power.2stage.pAF(), which performs exactly as
described in A.Fuglsang 2014
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.4-2 dated 2015-07-17 and 0.4-3 dated 2015-11-26
DESCRIPTION | 10 +-- MD5 | 36 ++++++------ NAMESPACE | 1 NEWS | 20 +++++- R/power.R | 126 +++++++++++++++++++++++++++++-------------- R/power_2stage.R | 32 ++++++++-- R/power_2stage_GS.R | 2 R/power_2stage_KM.R | 10 +-- R/power_2stage_SSR.R | 2 R/power_2stage_fC.R | 75 +++++++++++++++++-------- R/power_2stage_parallel.R | 2 R/power_2stage_parallel_AF.R | 2 R/print_pwrtsd_s3.R | 13 +++- man/power.2stage.GS.Rd | 11 +-- man/power.2stage.KM.Rd | 8 -- man/power.2stage.Rd | 19 ++---- man/power.2stage.fC.Rd | 30 ++++++---- man/power.2stage.p.Rd | 10 +-- man/power.2stage.ssr.Rd | 9 --- 19 files changed, 260 insertions(+), 158 deletions(-)
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 2.9 dated 2015-09-06 and 2.9.1 dated 2015-11-26
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NEWS | 5 +++++ R/nleqslv.R | 16 +++++++++++----- man/nleqslv.Rd | 8 ++++---- tests/control-try.R |only tests/control-try.Rout.save |only 7 files changed, 30 insertions(+), 17 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut],
Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.5 dated 2015-11-20 and 2.6 dated 2015-11-26
DESCRIPTION | 6 - MD5 | 78 +++++++++++--------- NAMESPACE | 6 + NEWS | 12 +++ R/RLearner_classif_LiblineaRL1L2SVC.R | 2 R/RLearner_classif_LiblineaRL1LogReg.R | 4 - R/RLearner_classif_LiblineaRL2L1SVC.R | 2 R/RLearner_classif_LiblineaRL2LogReg.R | 4 - R/RLearner_classif_LiblineaRL2SVC.R | 2 R/RLearner_classif_LiblineaRMultiClassSVC.R | 2 R/RLearner_classif_ranger.R | 8 +- R/RLearner_classif_rknn.R | 2 R/RLearner_cluster_Cobweb.R |only R/RLearner_cluster_kmeans.R | 7 + R/RLearner_regr_LiblineaRL2L1SVR.R | 2 R/RLearner_regr_LiblineaRL2L2SVR.R | 2 R/RLearner_regr_glmboost.R |only R/RLearner_regr_glmnet.R | 5 - R/RLearner_regr_lm.R | 6 - R/RLearner_regr_ranger.R | 4 - R/RLearner_regr_rknn.R | 4 - R/RLearner_surv_ranger.R | 4 - R/ResampleDesc.R | 2 R/Task_operators.R | 31 ++++++-- R/getResampleExtract.R | 10 +- R/plotLearnerPrediction.R | 4 - inst/doc/mlr.html | 4 - man/getTaskClassLevels.Rd | 3 man/getTaskFormula.Rd | 3 man/getTaskTargetNames.Rd | 3 man/getTaskTargets.Rd | 7 + tests/testthat/helper_objects.R | 74 ------------------- tests/testthat/test_base_TuneWrapper.R | 2 tests/testthat/test_base_measures.R | 93 ++++++++++++++++++++++--- tests/testthat/test_base_multilabel.R | 13 +++ tests/testthat/test_base_plotViperCharts.R | 33 ++++---- tests/testthat/test_base_relativeOverfitting.R | 2 tests/testthat/test_cluster_Cobweb.R |only tests/testthat/test_cluster_kmeans.R | 14 +++ tests/testthat/test_regr_glmboost.R |only tests/testthat/test_regr_glmnet.R | 12 +++ tests/testthat/test_regr_lm.R | 2 42 files changed, 280 insertions(+), 194 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Felix Pretis, James Reade, Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.2 dated 2014-12-22 and 0.3 dated 2015-11-26
gets-0.2/gets/R/skewness.test.R |only gets-0.2/gets/man/skewness.test.Rd |only gets-0.3/gets/DESCRIPTION | 10 +- gets-0.3/gets/MD5 | 63 +++++++----- gets-0.3/gets/NAMESPACE | 6 + gets-0.3/gets/NEWS | 34 ++++++ gets-0.3/gets/R/arx.R | 57 ++++++++--- gets-0.3/gets/R/biascorr.R |only gets-0.3/gets/R/getsm.R | 73 +++++++++++--- gets-0.3/gets/R/getsv.R | 5 - gets-0.3/gets/R/iim.R |only gets-0.3/gets/R/isat.R | 172 +++++++++++++++++++++++----------- gets-0.3/gets/R/isattest.R |only gets-0.3/gets/R/isatvar.R | 178 ++++++++++++++++++++++++++++++++++-- gets-0.3/gets/R/logLik.arx.R |only gets-0.3/gets/R/plot.arx.R | 149 +++++++++++++++--------------- gets-0.3/gets/R/plot.gets.R | 45 ++++++--- gets-0.3/gets/R/print.arx.R | 55 +++++++++-- gets-0.3/gets/R/print.gets.R | 3 gets-0.3/gets/R/sim.R |only gets-0.3/gets/R/tim.R |only gets-0.3/gets/man/arx.Rd | 14 +- gets-0.3/gets/man/biascorr.Rd |only gets-0.3/gets/man/coef.arx.Rd | 18 ++- gets-0.3/gets/man/coef.gets.Rd | 8 - gets-0.3/gets/man/diagnostics.Rd | 1 gets-0.3/gets/man/dropvar.Rd | 5 - gets-0.3/gets/man/eqwma.Rd | 1 gets-0.3/gets/man/gets-package.Rd | 4 gets-0.3/gets/man/getsm.Rd | 1 gets-0.3/gets/man/hpdata.Rd | 2 gets-0.3/gets/man/iim.Rd |only gets-0.3/gets/man/info.criterion.Rd | 5 - gets-0.3/gets/man/isat.Rd | 38 +++++-- gets-0.3/gets/man/isattest.Rd |only gets-0.3/gets/man/isatvar.Rd | 63 +++++++----- gets-0.3/gets/man/jb.test.Rd | 5 - gets-0.3/gets/man/ols.Rd | 9 + 38 files changed, 739 insertions(+), 285 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.2 dated 2015-10-21 and 0.3.3 dated 2015-11-26
DESCRIPTION | 10 - MD5 | 119 +++++++++++----------- NAMESPACE | 4 NEWS | 9 + R/genomic.R | 58 +++++++++- R/plot.R | 101 ++++++++++++++++++ R/utils.R | 95 ++++++++++++++++- inst/doc/circlize.R | 6 - inst/doc/circlize.Rnw | 11 +- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary man/chordDiagramFromDataFrame.rd | 27 ++-- man/chordDiagramFromMatrix.rd | 31 +++-- man/circlize-package.rd | 5 man/circlize.rd | 5 man/circos.axis.rd | 7 - man/circos.clear.rd | 5 man/circos.dendrogram.rd | 2 man/circos.genomicDensity.rd | 2 man/circos.genomicInitialize.rd | 2 man/circos.genomicLines.rd | 4 man/circos.genomicPoints.rd | 4 man/circos.genomicPosTransformLines.rd | 2 man/circos.genomicRainfall.rd | 2 man/circos.genomicText.rd | 2 man/circos.genomicTrack.rd | 5 man/circos.genomicTrackPlotRegion.rd | 9 + man/circos.initialize.rd | 2 man/circos.initializeWithIdeogram.rd | 8 - man/circos.lines.rd | 4 man/circos.link.rd | 12 +- man/circos.par.rd | 21 ++- man/circos.points.rd | 5 man/circos.rect.rd | 5 man/circos.segments.rd | 5 man/circos.track.rd | 5 man/circos.trackHist.rd | 4 man/circos.trackLines.rd | 7 + man/circos.trackPlotRegion.rd | 15 +- man/circos.trackPoints.rd | 5 man/circos.trackText.rd | 5 man/circos.update.rd | 5 man/circos.updatePlotRegion.rd | 5 man/circos.xaxis.rd |only man/circos.yaxis.rd |only man/col2value.rd |only man/genomicDensity.rd | 6 - man/getI.rd | 5 man/highlight.sector.rd | 2 man/posTransform.default.rd | 2 man/posTransform.text.rd | 2 man/rainfallTransform.rd | 7 - man/rand_color.rd | 5 man/read.chromInfo.rd | 9 + man/read.cytoband.rd | 4 man/show.index.rd | 5 vignettes/circlize.Rnw | 11 +- vignettes/src/intro-11-axis.R | 14 ++ 62 files changed, 543 insertions(+), 169 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the LZ77
algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but
offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.3 dated 2015-10-06 and 0.4 dated 2015-11-26
DESCRIPTION | 10 MD5 | 86 - build/vignette.rds |binary inst/doc/benchmarks.R |only inst/doc/benchmarks.Rmd |only inst/doc/benchmarks.html |only src/dec/bit_reader.c | 21 src/dec/bit_reader.h | 257 ++-- src/dec/decode.c | 2294 ++++++++++++++++++++++++++--------------- src/dec/decode.h | 26 src/dec/dictionary.h | 2 src/dec/huffman.c | 41 src/dec/huffman.h | 24 src/dec/port.h | 91 + src/dec/prefix.h | 4 src/dec/state.c | 106 + src/dec/state.h | 96 + src/dec/streams.c | 6 src/dec/streams.h | 2 src/dec/types.h | 27 src/enc/backward_references.cc | 120 +- src/enc/backward_references.h | 2 src/enc/block_splitter.cc | 71 - src/enc/brotli_bit_stream.cc | 72 - src/enc/cluster.h | 25 src/enc/command.h | 53 src/enc/context.h | 5 src/enc/encode.cc | 24 src/enc/encode.h | 11 src/enc/encode_parallel.cc | 39 src/enc/entropy_encode.cc | 53 src/enc/hash.h | 164 +- src/enc/histogram.cc | 2 src/enc/histogram.h | 4 src/enc/literal_cost.cc | 30 src/enc/metablock.cc | 24 src/enc/port.h | 7 src/enc/prefix.h | 7 src/enc/ringbuffer.h | 20 src/enc/streams.cc | 11 src/enc/streams.h | 3 src/enc/transform.h | 5 src/enc/types.h | 16 src/enc/utf8_util.cc | 10 src/enc/write_bits.h | 7 vignettes/benchmarks.Rmd |only 46 files changed, 2359 insertions(+), 1519 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS) for convex
problems. Conic and equality constraints can be specified in addition
to mixed integer problems.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.1 dated 2015-11-25 and 0.1-1 dated 2015-11-25
ECOSolveR |only 1 file changed
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 1.8-10 dated 2015-07-14 and 1.8-11 dated 2015-11-25
DESCRIPTION | 14 +- MD5 | 52 ++++----- NAMESPACE | 197 +++++++++++++++++------------------ NEWS | 22 +++ R/TraMineR-seqdist.R | 12 +- R/plot.stslist.meant.R | 92 +++++++++------- R/seqdist.R | 22 +++ R/seqmeant.R | 34 ++++-- R/seqplot.R | 42 +++---- R/stslist.meant-methods.R | 2 build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/CITATION | 15 ++ inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 8 - man/TraMineRInternal.Rd | 2 man/dissrep.Rd | 2 man/ex1.Rd | 2 man/ex2.Rd | 2 man/plot.stslist.meant.Rd | 7 + man/seqdist.Rd | 16 +- man/seqmeant.Rd | 12 +- man/seqplot.Rd | 2 man/seqrecode.Rd | 4 man/seqtreedisplay.Rd | 4 27 files changed, 326 insertions(+), 239 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 0.2 dated 2015-11-03 and 0.6 dated 2015-11-25
DESCRIPTION | 10 ++-- MD5 | 18 ++++--- NAMESPACE | 1 R/dom_optimal_allocation.R |only R/expsize.R | 2 R/expvar.R | 100 +++++++++++++++++++++++++++--------------- R/optsize.R | 2 README | 2 man/dom_optimal_allocation.Rd |only man/expvar.Rd | 25 ++++++++-- man/surveyplanning-package.Rd | 6 +- 11 files changed, 108 insertions(+), 58 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Sparse Group Partial Least Square Methods
Description: The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.
Author: Benoit Liquet and Pierre Lafaye de Micheaux
Maintainer: Benoit Liquet <b.liquet@uq.edu.au>
Diff between sgPLS versions 1.3 dated 2015-08-27 and 1.4 dated 2015-11-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plotcim.R | 5 +++-- man/perf.Rd | 2 +- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.3 dated 2015-11-20 and 1.3.1 dated 2015-11-25
DESCRIPTION | 8 ++-- MD5 | 4 +- NAMESPACE | 100 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 57 insertions(+), 55 deletions(-)
Title: An API Client for Wikimedia Traffic Data
Description: Pageview data from the 'Wikimedia' sites, such as 'Wikipedia' (https://www.wikipedia.org/), from entire projects to per-article
levels of granularity, through the new RESTful API and data source (https://wikimedia.org/api/rest_v1/?doc).
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between pageviews versions 0.1.0 dated 2015-11-19 and 0.1.1 dated 2015-11-25
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS |only R/query.R | 23 ++++++++++++++++++----- README.md | 8 ++++++-- inst/doc/Accessing_Wikimedia_pageviews.html | 4 ++-- 6 files changed, 35 insertions(+), 17 deletions(-)
Title: Connect MonetDB to R
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Thomas Lumley [ctb]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>
Diff between MonetDB.R versions 0.9.7 dated 2015-03-29 and 1.0.0 dated 2015-11-25
DESCRIPTION | 19 - MD5 | 23 +- NAMESPACE | 7 NEWS | 28 ++ R/control.R | 56 +---- R/dbapply.R |only R/dbi.R | 533 ++++++++++++++++++++++++++++++++++-------------- R/dplyr.R | 28 +- R/mapi.R | 24 +- man/MonetDB.R.Rd | 7 man/MonetDBLite.Rd |only man/dbApply.Rd |only man/monetdb.read.csv.Rd | 12 - man/src_monetdb.Rd | 6 14 files changed, 509 insertions(+), 234 deletions(-)
Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of 'RJSONIO', but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with a web API. The implementation is
based on the mapping described in the vignette (Ooms, 2014). In addition to
converting JSON data from/to R objects, 'jsonlite' contains functions to
stream, validate, and prettify JSON data. The unit tests included with the
package verify that all edge cases are encoded and decoded consistently for
use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between jsonlite versions 0.9.17 dated 2015-09-06 and 0.9.18 dated 2015-11-25
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NEWS | 6 +++++ R/asJSON.int64.R | 8 +++---- R/fromJSON.R | 4 ++- R/onLoad.R | 12 +++-------- R/stream.R | 49 +++++++++++++++++++++------------------------- R/toJSON.R | 10 ++------- inst/doc/json-mapping.pdf |binary man/stream_in.Rd | 46 +++++++++++++++++++------------------------ 10 files changed, 76 insertions(+), 83 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.5 dated 2015-11-12 and 0.0.6 dated 2015-11-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ configure | 11 +++++++++++ 4 files changed, 21 insertions(+), 6 deletions(-)
Title: Bayesian Analysis of a Vector Autoregressive Model with
Stochastic Volatility and Time-Varying Parameters
Description: R/C++ implementation of the model proposed by Primiceri ("Time Varying Structural Vector Autoregressions and Monetary Policy", Review of Economic Studies, 2005), with functionality for computing posterior predictive distributions and impulse responses.
Author: Fabian Krueger
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>
Diff between bvarsv versions 1.0 dated 2014-08-28 and 1.1 dated 2015-11-25
DESCRIPTION | 10 - MD5 | 25 ++- NAMESPACE | 4 R/RcppExports.R | 134 ++++++++++---------- R/bvarsv.R | 293 +++++++++++++++++++++++++++++++++++++-------- README.md |only data/usmacro.RData |binary data/usmacro.update.RData |only man/bvar.sv.tvp.Rd | 19 +- man/bvarsv-package.Rd | 10 - man/helpers.Rd | 15 ++ man/impulse.responses.Rd |only man/sim.var1.sv.tvp.Rd | 102 +++++++-------- man/usmacro.Rd | 27 +++- src/RcppExports.cpp | 298 ++++++++++++++++++---------------------------- 15 files changed, 550 insertions(+), 387 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects.
Author: Meinhard Ploner
Maintainer: Meinhard Ploner <meinhard.ploner@prosiebensat1digital.de>
Diff between RMixpanel versions 0.1-1 dated 2015-11-24 and 0.1-2 dated 2015-11-25
RMixpanel-0.1-1/RMixpanel/R/mixpanelGetEventsForUsers.R |only RMixpanel-0.1-1/RMixpanel/man/mixpanelGetEventsForUsers.Rd |only RMixpanel-0.1-2/RMixpanel/DESCRIPTION | 12 +- RMixpanel-0.1-2/RMixpanel/MD5 | 40 +++---- RMixpanel-0.1-2/RMixpanel/NAMESPACE | 2 RMixpanel-0.1-2/RMixpanel/R/mixpanelGetEventsForProfiles.R |only RMixpanel-0.1-2/RMixpanel/README.md | 10 + RMixpanel-0.1-2/RMixpanel/build/partial.rdb |binary RMixpanel-0.1-2/RMixpanel/man/RMixpanel-package.Rd | 12 -- RMixpanel-0.1-2/RMixpanel/man/createDateSequence.Rd | 8 - RMixpanel-0.1-2/RMixpanel/man/eventsJson2RMatrix.Rd | 14 -- RMixpanel-0.1-2/RMixpanel/man/merge.matrix.Rd | 25 +--- RMixpanel-0.1-2/RMixpanel/man/mixpanelCreateAccount.Rd | 2 RMixpanel-0.1-2/RMixpanel/man/mixpanelGetAddiction.Rd | 34 ++---- RMixpanel-0.1-2/RMixpanel/man/mixpanelGetData.Rd | 2 RMixpanel-0.1-2/RMixpanel/man/mixpanelGetEvents.Rd | 8 - RMixpanel-0.1-2/RMixpanel/man/mixpanelGetEventsForProfiles.Rd |only RMixpanel-0.1-2/RMixpanel/man/mixpanelGetEventsFromFiles.Rd | 56 ++-------- RMixpanel-0.1-2/RMixpanel/man/mixpanelGetProfiles.Rd | 2 RMixpanel-0.1-2/RMixpanel/man/mixpanelGetProfilesCount.Rd | 2 RMixpanel-0.1-2/RMixpanel/man/mixpanelGetRetention.Rd | 34 ++---- RMixpanel-0.1-2/RMixpanel/man/mixpanelGetSegmentation.Rd | 18 +-- RMixpanel-0.1-2/RMixpanel/man/profilesJson2RMatrix.Rd | 2 23 files changed, 116 insertions(+), 167 deletions(-)
Title: Accurate Timing Functions
Description: Provides infrastructure to accurately measure and compare
the execution time of R expressions.
Author: Olaf Mersmann [aut, cre],
Claudia Beleites [ctb],
Rainer Hurling [ctb],
Ari Friedman [ctb]
Maintainer: Olaf Mersmann <olafm@p-value.net>
Diff between microbenchmark versions 1.4-2 dated 2014-09-28 and 1.4-2.1 dated 2015-11-25
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 9 insertions(+), 7 deletions(-)
More information about microbenchmark at CRAN
Permanent link
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.9 dated 2015-10-07 and 0.9.0 dated 2015-11-25
DESCRIPTION | 9 - MD5 | 225 +++++++++++++++++------------------ NAMESPACE | 40 +++++- R/count_facet.r | 2 R/elevation.r | 2 R/enumeration.R | 10 - R/gbif_citation.R |only R/gbifmap.r | 24 ++- R/name_usage.r | 3 R/oai-pmh.R |only R/occ_download.R | 3 R/occ_download_cancel.R | 2 R/occ_download_get.r | 2 R/occ_download_import.R | 4 R/occ_download_list.R | 21 +-- R/occ_download_meta.R | 9 - R/occ_issues.r | 21 ++- R/occ_metadata.r | 24 ++- R/occ_search.r | 98 +++++++++------ R/parsenames.R | 4 R/read_wkt.R | 2 R/rgb_country_codes.r | 4 R/rgbif-package.r | 18 ++ R/tbl_df_utils.R | 4 R/zzz.r | 23 +++ README.md | 1 inst/doc/issues_vignette.Rmd | 237 +++++++++++++++++-------------------- inst/doc/issues_vignette.html | 237 +++++++++++++++++-------------------- inst/doc/rgbif_vignette.html | 121 +++++++++--------- inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 237 +++++++++++++++++-------------------- inst/vign/rgbif_vignette.md | 119 +++++++++--------- man/blanktheme.Rd | 2 man/check_wkt.Rd | 2 man/commas_to_periods.Rd | 2 man/count_facet.Rd | 2 man/create_gist.Rd | 2 man/dataset_metrics.Rd | 2 man/dataset_search.Rd | 4 man/dataset_suggest.Rd | 2 man/datasetparser.Rd | 2 man/datasets.Rd | 2 man/density_spplist.Rd | 2 man/densitylist.Rd | 2 man/downloads.Rd | 2 man/elevation.Rd | 2 man/enumeration.Rd | 2 man/gbif_bbox2wkt.Rd | 2 man/gbif_capwords.Rd | 2 man/gbif_citation.Rd |only man/gbif_issues.Rd | 2 man/gbif_names.Rd | 2 man/gbif_oai.Rd |only man/gbif_photos.Rd | 2 man/gbifdata.Rd | 2 man/gbifmap.Rd | 11 + man/gbifmap_dens.Rd | 2 man/gbifmap_list.Rd | 2 man/gbifparser.Rd | 2 man/gbifparser_verbatim.Rd | 2 man/get_credentials.Rd | 2 man/gist.Rd | 2 man/installations.Rd | 6 man/isocodes.Rd | 2 man/name_backbone.Rd | 2 man/name_lookup.Rd | 8 - man/name_suggest.Rd | 2 man/name_usage.Rd | 2 man/namelkupparser.Rd | 2 man/networks.Rd | 6 man/nodes.Rd | 6 man/occ_count.Rd | 2 man/occ_download.Rd | 2 man/occ_download_cancel.Rd | 2 man/occ_download_get.Rd | 2 man/occ_download_import.Rd | 6 man/occ_download_list.Rd | 2 man/occ_download_meta.Rd | 2 man/occ_fields.Rd | 2 man/occ_get.Rd | 2 man/occ_issues.Rd | 5 man/occ_issues_lookup.Rd | 2 man/occ_metadata.Rd | 13 +- man/occ_search.Rd | 16 +- man/occurrencecount.Rd | 2 man/occurrencedensity.Rd | 2 man/occurrenceget.Rd | 2 man/occurrencelist.Rd | 2 man/occurrencelist_all.Rd | 2 man/occurrencelist_many.Rd | 2 man/organizations.Rd | 2 man/parsenames.Rd | 2 man/parseresults.Rd | 2 man/pipe.Rd | 2 man/providers.Rd | 2 man/read_wkt.Rd | 2 man/resources.Rd | 2 man/rgb_country_codes.Rd | 2 man/rgbif-defunct.Rd | 2 man/rgbif-package.Rd | 2 man/stylegeojson.Rd | 2 man/suggestfields.Rd | 2 man/taxoncount.Rd | 2 man/taxonget.Rd | 2 man/taxonsearch.Rd | 2 man/taxrank.Rd | 2 man/togeojson.Rd | 2 man/type_sum.Rd | 2 man/typestatus.Rd | 2 tests/testthat/test-enumeration.r | 4 tests/testthat/test-name_usage.r | 4 tests/testthat/test-oai.R |only tests/testthat/test-occ_metadata.r | 15 +- tests/testthat/test-occ_search.r | 6 vignettes/issues_vignette.Rmd | 237 +++++++++++++++++-------------------- vignettes/rgbif_vignette.Rmd | 119 +++++++++--------- 116 files changed, 1095 insertions(+), 1007 deletions(-)
Title: Finding the Optimal Cluster Number Using Progeny Clustering
Description: Implementing the Progeny Clustering algorithm, the progenyClust package assesses the clustering stability and identifies the optimal clustering number for a given data matrix. It uses kmeans clustering as default, but can be customized to work with other clustering algorithms and different parameter settings. The package includes one main function progenyClust(), plot and summary methods for progenyClust object, and two example datasets (test and cell) for testing.
Author: C.W. Hu
Maintainer: C.W. Hu <wendyhu001@gmail.com>
Diff between progenyClust versions 1.0 dated 2015-11-09 and 1.1 dated 2015-11-25
progenyClust-1.0/progenyClust/data/example.rda |only progenyClust-1.0/progenyClust/man/example.Rd |only progenyClust-1.1/progenyClust/DESCRIPTION | 10 +++++----- progenyClust-1.1/progenyClust/MD5 | 12 +++++++----- progenyClust-1.1/progenyClust/data/cell.rda |only progenyClust-1.1/progenyClust/data/test.rda |only progenyClust-1.1/progenyClust/man/cell.Rd |only progenyClust-1.1/progenyClust/man/progenyClust-package.Rd | 6 +++--- progenyClust-1.1/progenyClust/man/progenyClust.Rd | 4 ++-- progenyClust-1.1/progenyClust/man/test.Rd |only 10 files changed, 17 insertions(+), 15 deletions(-)
Title: Create Interactive Web Graphics via Plotly's JavaScript Graphing
Library
Description: Easily translate ggplot2 graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut, cph],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 2.0.2 dated 2015-11-17 and 2.0.3 dated 2015-11-25
plotly-2.0.2/plotly/vignettes/intro.html |only plotly-2.0.3/plotly/DESCRIPTION | 7 ++++--- plotly-2.0.3/plotly/MD5 | 21 ++++++++++++--------- plotly-2.0.3/plotly/NEWS | 4 ++++ plotly-2.0.3/plotly/R/plotly.R | 2 +- plotly-2.0.3/plotly/R/print.R | 5 +++-- plotly-2.0.3/plotly/README.md | 8 +++++++- plotly-2.0.3/plotly/build |only plotly-2.0.3/plotly/inst/doc |only plotly-2.0.3/plotly/man/knit_print.plotly.Rd | 4 +++- plotly-2.0.3/plotly/man/plot_ly.Rd | 2 +- plotly-2.0.3/plotly/vignettes/intro.Rmd | 11 ++++++++--- 12 files changed, 43 insertions(+), 21 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty.
Supported models include cumulative logit, probit, cauchit, and complementary log-log.
The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Mike Wurm [aut, cre]
Maintainer: Mike Wurm <wurm@wisc.edu>
Diff between ordinalNet versions 1.1 dated 2015-11-22 and 1.2 dated 2015-11-25
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/ordinalNet.R | 2 +- man/predict.ordinalNetFit.Rd | 1 - 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Betting Odds Conversion
Description: Conversion between the most common odds types for sports betting. Hong Kong odds, US odds, Decimal odds, Indonesian odds, Malaysian odds, and raw Probability are covered in this package.
Author: Marco Blume
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between odds.converter versions 1.2 dated 2015-09-25 and 1.3 dated 2015-11-25
DESCRIPTION | 8 +++---- MD5 | 10 ++++---- NEWS | 9 ++++++++ R/odds.fv.R | 64 ++++++++++++++++++++++++++++++++++++++++----------------- README.md | 53 ++++++++++++++++++++++++++++++++++++++++++++++- man/odds.fv.Rd | 14 ++++++------ 6 files changed, 122 insertions(+), 36 deletions(-)
More information about odds.converter at CRAN
Permanent link
Title: Distributed Data Structures in R
Description: Provides distributed data structures and simplifies
distributed computing in R.
Author: Edward Ma, Indrajit Roy, Michael Lawrence
Maintainer: Edward Ma <ema@hpe.com>
Diff between ddR versions 0.1.1 dated 2015-11-12 and 0.1.2 dated 2015-11-25
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/pdriver.R | 2 +- build/vignette.rds |binary inst/doc/README.Rmd | 2 +- inst/doc/user_guide.Rmd | 2 +- vignettes/README.Rmd | 2 +- vignettes/user_guide.Rmd | 2 +- 9 files changed, 20 insertions(+), 16 deletions(-)
Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab. Thus they
are available to the user as a script file or as an aide for the user to
learn R or to copy-and-paste directly into R itself.
Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (Author of original print.summary.nnet),
Jose Magana [ctb] (Contributed the ggpairs plots.)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 4.0.0 dated 2015-11-05 and 4.0.5 dated 2015-11-24
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/appendLibLog.R | 6 +++--- R/data.R | 19 ++++++++++++++++--- R/evaluate.R | 10 +++++----- R/executePairsPlotSelect2.R | 9 +++++++-- R/explore.R | 4 ++-- R/log.R | 4 ++-- R/rattle.R | 4 ++-- R/textminer.R | 4 ++-- inst/doc/rattle.pdf |binary 11 files changed, 53 insertions(+), 35 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions, where showing the progress is
useful for the user (e.g. bootstrap).
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.1-2 dated 2015-11-22 and 1.1-3 dated 2015-11-24
DESCRIPTION | 9 - MD5 | 42 ++--- NAMESPACE | 14 - R/closepb.R | 10 - R/pbapply.R | 198 +++++++++++++------------- R/pblapply.R | 38 ++--- R/pboptions.R | 32 ++-- R/pbreplicate.R | 8 - R/pbsapply.R | 22 +- R/unix/dopb.R | 24 +-- R/unix/getpb.R | 24 +-- R/unix/setpb.R | 24 +-- R/unix/startpb.R | 26 +-- R/windows/dopb.R | 24 +-- R/windows/getpb.R | 26 +-- R/windows/setpb.R | 26 +-- R/windows/startpb.R | 30 ++-- R/zzz.R | 26 +-- inst/ChangeLog | 108 +++++++------- man/pbapply.Rd | 388 ++++++++++++++++++++++++++-------------------------- man/pboptions.Rd | 274 ++++++++++++++++++------------------ tests/tests.R | 82 +++++----- 22 files changed, 732 insertions(+), 723 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.4.0 dated 2015-10-22 and 0.4.1 dated 2015-11-24
DESCRIPTION | 6 MD5 | 52 +++---- NEWS.md | 10 + R/RcppExports.R | 28 ++-- R/dprhkdecop.R | 2 R/eval_tt.R | 27 ---- R/generics.R | 2 R/helpers.R | 243 ++++++++++++++++++------------------- R/kdecop.R | 13 + R/plot.kdecopula.R | 2 README.md | 8 - inst/README-unnamed-chunk-12-1.png |binary inst/README-unnamed-chunk-6-1.png |binary inst/include/evaluators.h | 6 inst/include/hfunc.h | 29 +++- inst/include/integrate.h | 8 - inst/include/interp.h | 40 ++++-- inst/include/kernels.h | 12 + inst/include/renorm.h | 9 + man/kdecop.Rd | 6 src/RcppExports.cpp | 196 +++++++++++++++++------------ src/evaluators.cpp | 132 ++++++++++++-------- src/hfunc.cpp | 30 +++- src/integrate.cpp | 11 + src/interp.cpp | 56 +++++--- src/kernels.cpp | 77 ++++++++--- src/renorm.cpp | 81 ++++++------ 27 files changed, 639 insertions(+), 447 deletions(-)
Title: A Simple XML Tree Parser and Generator
Description: Provides a simple XML tree parser/generator. It includes functions
to read XML files into R objects, get information out of and into nodes, and
write R objects back to XML code. It's not as powerful as the 'XML' package
and doesn't aim to be, but for simple XML handling it could be useful. It was
originally developed for the R GUI and IDE RKWard (https://rkward.kde.org), to
make plugin development easier.
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between XiMpLe versions 0.03-21 dated 2013-12-21 and 0.03-23 dated 2015-11-24
XiMpLe-0.03-21/XiMpLe/R/XiMpLe-internal.roxy.all.R |only XiMpLe-0.03-21/XiMpLe/R/XiMpLe.doc-class.R |only XiMpLe-0.03-21/XiMpLe/R/XiMpLe.node-class.R |only XiMpLe-0.03-21/XiMpLe/R/node.R |only XiMpLe-0.03-21/XiMpLe/R/pasteXML-methods.R |only XiMpLe-0.03-21/XiMpLe/R/show-methods.R |only XiMpLe-0.03-21/XiMpLe/inst/tests |only XiMpLe-0.03-21/XiMpLe/inst/vignettes |only XiMpLe-0.03-21/XiMpLe/tests/test_XiMpLe_package.R |only XiMpLe-0.03-23/XiMpLe/ChangeLog | 19 XiMpLe-0.03-23/XiMpLe/DESCRIPTION | 39 XiMpLe-0.03-23/XiMpLe/MD5 | 80 +- XiMpLe-0.03-23/XiMpLe/NAMESPACE | 53 - XiMpLe-0.03-23/XiMpLe/R/00_class_01_XiMpLe.node.R |only XiMpLe-0.03-23/XiMpLe/R/00_class_02_XiMpLe.doc.R |only XiMpLe-0.03-23/XiMpLe/R/01_method_01_pasteXML.R |only XiMpLe-0.03-23/XiMpLe/R/01_method_02_node.R |only XiMpLe-0.03-23/XiMpLe/R/01_method_03_show.R |only XiMpLe-0.03-23/XiMpLe/R/XMLNode.R | 70 - XiMpLe-0.03-23/XiMpLe/R/XMLTree.R | 64 - XiMpLe-0.03-23/XiMpLe/R/XiMpLe-internal.R | 836 ++++++++++----------- XiMpLe-0.03-23/XiMpLe/R/XiMpLe-package.R | 14 XiMpLe-0.03-23/XiMpLe/R/parseXMLTree.R | 108 +- XiMpLe-0.03-23/XiMpLe/R/pasteXMLTag.R | 182 ++-- XiMpLe-0.03-23/XiMpLe/R/zzz_is_get_utils.R | 649 ++++++++-------- XiMpLe-0.03-23/XiMpLe/inst/CITATION | 22 XiMpLe-0.03-23/XiMpLe/inst/NEWS.Rd | 42 + XiMpLe-0.03-23/XiMpLe/inst/doc |only XiMpLe-0.03-23/XiMpLe/man/XMLGetters-methods.Rd | 227 +++-- XiMpLe-0.03-23/XiMpLe/man/XMLNode.Rd | 46 - XiMpLe-0.03-23/XiMpLe/man/XMLTree.Rd | 50 - XiMpLe-0.03-23/XiMpLe/man/XiMpLe-package.Rd | 37 XiMpLe-0.03-23/XiMpLe/man/node.Rd | 86 +- XiMpLe-0.03-23/XiMpLe/man/parseXMLTree.Rd | 50 - XiMpLe-0.03-23/XiMpLe/man/pasteXML-methods.Rd | 63 - XiMpLe-0.03-23/XiMpLe/man/pasteXMLTag.Rd | 95 +- XiMpLe-0.03-23/XiMpLe/man/show-methods.Rd | 23 XiMpLe-0.03-23/XiMpLe/tests/testthat |only XiMpLe-0.03-23/XiMpLe/tests/testthat.R |only XiMpLe-0.03-23/XiMpLe/vignettes |only 40 files changed, 1542 insertions(+), 1313 deletions(-)
Title: Concurrent Generation of Ordinal and Normal Data with Given
Correlation Matrix and Marginal Distributions
Description: Implementation of a procedure for generating samples from a mixed distribution of ordinal and normal random variables with pre-specified correlation matrix and marginal distributions.
Author: Anup Amatya and Hakan Demirtas
Maintainer: Anup Amatya<aamatya@nmsu.edu>
Diff between OrdNor versions 1.0 dated 2013-12-02 and 2.0 dated 2015-11-24
DESCRIPTION | 15 ++++++++------- MD5 | 7 ++++--- NAMESPACE | 2 ++ inst |only man/genOrdNor.Rd | 3 +++ 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Variance Component Analysis
Description: ANOVA-type estimation (prediction) of random effects in linear mixed models is implemented, following
Searle et al. 1991 (ANOVA for unbalanced data). For better performance the SWEEP-Operator is now implemented
for generating the ANOVA Type-1 error sum of squares. The primary objective of this package is to perform
Variance Component Analyses (VCA). This is a special type of analysis frequently used in verifying the
precision performance of diagnostics.
The Satterthwaite approximation of the total degrees of freedom and for individual variance components is
implemented. These are used in the Chi-Squared tests against a claimed value, and in the respective confidence intervals.
Satterthwaite's approximation of denominator degrees of freedom in t-/F-tests of fixed effects are also
available.
There are several functions for extracting, random effects, fixed effects, variance-covariance
matrices of random and fixed effects. Residuals (marginal, conditional) can be extracted as raw, standardized
and studentized residuals.
Additionally, plotting methods for residuals and random effects and a variability chart are available. The latter
is useful for visualizing the variability in sub-classes emerging from the experimental design.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.2 dated 2015-07-20 and 1.2.1 dated 2015-11-24
DESCRIPTION | 8 MD5 | 41 +-- R/plot.R | 27 +- R/vca.R | 211 +++++++++++------- data/HugeData.RData |only data/chol2invData.RData |only inst/ChangeLog.txt | 347 ++++++++++++++++++++++++++++++ inst/UnitTests/VCA_UnitTest_Protocol.html |only inst/UnitTests/runit.anovaMM.R | 14 + inst/UnitTests/runit.anovaVCA.R | 14 + inst/UnitTests/runit.misc.R | 24 +- man/Csweep.Rd | 9 man/HugeData.Rd |only man/Solve.Rd | 9 man/VCA-Package.Rd | 6 man/VCAinference.Rd | 2 man/anovaDF.Rd | 2 man/anovaMM.Rd | 24 +- man/anovaVCA.Rd | 51 ++-- man/chol2invData.Rd |only man/getSSQsweep.Rd | 11 man/getVCvar.Rd | 2 man/vcov.VCA.Rd | 7 man/vcovFixed.Rd | 7 24 files changed, 647 insertions(+), 169 deletions(-)
Title: Sparse Discriminant Analysis
Description: Performs sparse linear discriminant analysis for gaussians and mixture of gaussians models.
Author: Line Clemmensen <lhc@imm.dtu.dk>, contributions by Max Kuhn
Maintainer: Max Kuhn <max.kuhn@pfizer.com>
Diff between sparseLDA versions 0.1-6 dated 2012-06-19 and 0.1-7 dated 2015-11-24
DESCRIPTION | 20 +- MD5 | 8 NAMESPACE | 7 R/smda.R | 581 +++++++++++++++++++++++++++++------------------------------- man/smda.Rd | 8 5 files changed, 311 insertions(+), 313 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.0 dated 2015-05-18 and 1.1 dated 2015-11-24
smoof-1.0/smoof/R/sof.bochachevsky.R |only smoof-1.0/smoof/man/makeBochachevskyFunction.Rd |only smoof-1.1/smoof/DESCRIPTION | 17 smoof-1.1/smoof/MD5 | 426 +++++----- smoof-1.1/smoof/NAMESPACE | 45 + smoof-1.1/smoof/NEWS |only smoof-1.1/smoof/R/RcppExports.R |only smoof-1.1/smoof/R/filterFunctionByTags.R | 36 smoof-1.1/smoof/R/getBoxConstraints.R |only smoof-1.1/smoof/R/getGlobalOptimum.R | 4 smoof-1.1/smoof/R/getTags.R | 5 smoof-1.1/smoof/R/hasTags.R |only smoof-1.1/smoof/R/makeFunctionByName.R |only smoof-1.1/smoof/R/makeMultiObjectiveFunction.R | 7 smoof-1.1/smoof/R/makeObjectiveFunction.R | 9 smoof-1.1/smoof/R/makeSingleObjectiveFunction.R | 7 smoof-1.1/smoof/R/makeUFFunction.R | 3 smoof-1.1/smoof/R/mof.dtlz1.R |only smoof-1.1/smoof/R/mof.dtlz2.R |only smoof-1.1/smoof/R/mof.dtlz3.R |only smoof-1.1/smoof/R/mof.dtlz4.R |only smoof-1.1/smoof/R/mof.dtlz5.R |only smoof-1.1/smoof/R/mof.dtlz6.R |only smoof-1.1/smoof/R/mof.dtlz7.R |only smoof-1.1/smoof/R/mof.zdt1.R | 2 smoof-1.1/smoof/R/mof.zdt2.R | 2 smoof-1.1/smoof/R/mof.zdt3.R | 2 smoof-1.1/smoof/R/mof.zdt4.R | 2 smoof-1.1/smoof/R/mof.zdt6.R | 2 smoof-1.1/smoof/R/shouldBeMinimized.R |only smoof-1.1/smoof/R/sof.ackley.R | 4 smoof-1.1/smoof/R/sof.adjiman.R | 4 smoof-1.1/smoof/R/sof.alpine01.R | 4 smoof-1.1/smoof/R/sof.alpine02.R | 3 smoof-1.1/smoof/R/sof.aluffi-pentini.R |only smoof-1.1/smoof/R/sof.bartels.conn.R | 2 smoof-1.1/smoof/R/sof.beale.R | 2 smoof-1.1/smoof/R/sof.bent.cigar.R |only smoof-1.1/smoof/R/sof.bird.R | 2 smoof-1.1/smoof/R/sof.bohachevsky.n1.R |only smoof-1.1/smoof/R/sof.booth.R | 2 smoof-1.1/smoof/R/sof.branin.R | 2 smoof-1.1/smoof/R/sof.brent.R | 2 smoof-1.1/smoof/R/sof.brown.R | 2 smoof-1.1/smoof/R/sof.bukin.n2.R | 2 smoof-1.1/smoof/R/sof.bukin.n4.R | 2 smoof-1.1/smoof/R/sof.bukin.n6.R | 2 smoof-1.1/smoof/R/sof.carrom.table.R | 2 smoof-1.1/smoof/R/sof.chichinadze.R | 2 smoof-1.1/smoof/R/sof.chung.reynolds.R | 2 smoof-1.1/smoof/R/sof.complex.R |only smoof-1.1/smoof/R/sof.cosine.mixture.R | 3 smoof-1.1/smoof/R/sof.cross.in.tray.R | 2 smoof-1.1/smoof/R/sof.cube.R | 2 smoof-1.1/smoof/R/sof.deckkers.aarts.R | 2 smoof-1.1/smoof/R/sof.deflected.corrugated.spring.R |only smoof-1.1/smoof/R/sof.dixon.price.R | 2 smoof-1.1/smoof/R/sof.double.sum.R | 2 smoof-1.1/smoof/R/sof.drop.wave.R | 2 smoof-1.1/smoof/R/sof.easom.R | 2 smoof-1.1/smoof/R/sof.eggcrate.R | 2 smoof-1.1/smoof/R/sof.eggholder.R | 5 smoof-1.1/smoof/R/sof.el.attar.vidyasagar.dutta.R | 2 smoof-1.1/smoof/R/sof.engvall.R |only smoof-1.1/smoof/R/sof.exponential.R | 4 smoof-1.1/smoof/R/sof.freudenstein.roth.R | 2 smoof-1.1/smoof/R/sof.giunta.R | 6 smoof-1.1/smoof/R/sof.goldstein.price.R | 2 smoof-1.1/smoof/R/sof.griewank.R | 2 smoof-1.1/smoof/R/sof.hansen.R | 2 smoof-1.1/smoof/R/sof.himmelblau.R | 2 smoof-1.1/smoof/R/sof.holder.table.n1.R | 2 smoof-1.1/smoof/R/sof.holder.table.n2.R | 2 smoof-1.1/smoof/R/sof.hosaki.R | 2 smoof-1.1/smoof/R/sof.hyper.ellipsoid.R | 4 smoof-1.1/smoof/R/sof.jennrichsampson.R |only smoof-1.1/smoof/R/sof.judge.R |only smoof-1.1/smoof/R/sof.keane.R | 3 smoof-1.1/smoof/R/sof.kearfott.R |only smoof-1.1/smoof/R/sof.leon.R | 2 smoof-1.1/smoof/R/sof.matyas.R | 4 smoof-1.1/smoof/R/sof.mccormick.R | 2 smoof-1.1/smoof/R/sof.michalewicz.R | 20 smoof-1.1/smoof/R/sof.periodic.R | 2 smoof-1.1/smoof/R/sof.powell.sum.R | 2 smoof-1.1/smoof/R/sof.price.n1.R | 2 smoof-1.1/smoof/R/sof.price.n2.R | 2 smoof-1.1/smoof/R/sof.price.n4.R | 2 smoof-1.1/smoof/R/sof.rastrigin.R | 4 smoof-1.1/smoof/R/sof.rosenbrock.R | 10 smoof-1.1/smoof/R/sof.schaffer.function.2.R | 2 smoof-1.1/smoof/R/sof.schaffer.function.4.R | 2 smoof-1.1/smoof/R/sof.schwefel.R | 4 smoof-1.1/smoof/R/sof.shubert.R | 2 smoof-1.1/smoof/R/sof.six.hump.camel.back.function.R | 2 smoof-1.1/smoof/R/sof.sphere.R | 2 smoof-1.1/smoof/R/sof.styblinski.tang.R | 2 smoof-1.1/smoof/R/sof.sum.of.different.powers.R | 4 smoof-1.1/smoof/R/sof.three.hump.camel.R | 2 smoof-1.1/smoof/R/sof.trecanni.R | 2 smoof-1.1/smoof/R/sof.zettl.R | 2 smoof-1.1/smoof/R/zzz.R | 4 smoof-1.1/smoof/man/addCountingWrapper.Rd | 2 smoof-1.1/smoof/man/addLoggingWrapper.Rd | 3 smoof-1.1/smoof/man/autoplot.smoof_function.Rd | 2 smoof-1.1/smoof/man/computeExpectedRunningTime.Rd | 2 smoof-1.1/smoof/man/doesCountEvaluations.Rd | 2 smoof-1.1/smoof/man/filterFunctionsByTags.Rd | 15 smoof-1.1/smoof/man/getAvailableTags.Rd | 2 smoof-1.1/smoof/man/getDescription.Rd | 2 smoof-1.1/smoof/man/getGlobalOptimum.Rd | 3 smoof-1.1/smoof/man/getLoggedValues.Rd | 2 smoof-1.1/smoof/man/getLowerBoxConstraints.Rd |only smoof-1.1/smoof/man/getName.Rd | 2 smoof-1.1/smoof/man/getNumberOfEvaluations.Rd | 2 smoof-1.1/smoof/man/getNumberOfObjectives.Rd | 2 smoof-1.1/smoof/man/getNumberOfParameters.Rd | 2 smoof-1.1/smoof/man/getParamSet.Rd | 2 smoof-1.1/smoof/man/getTags.Rd | 2 smoof-1.1/smoof/man/getUpperBoxConstraints.Rd |only smoof-1.1/smoof/man/getWrappedFunction.Rd | 2 smoof-1.1/smoof/man/hasBoxConstraints.Rd | 2 smoof-1.1/smoof/man/hasConstraints.Rd | 2 smoof-1.1/smoof/man/hasGlobalOptimum.Rd | 2 smoof-1.1/smoof/man/hasOtherConstraints.Rd | 2 smoof-1.1/smoof/man/hasTags.Rd |only smoof-1.1/smoof/man/isMultiobjective.Rd | 2 smoof-1.1/smoof/man/isNoisy.Rd | 2 smoof-1.1/smoof/man/isSingleobjective.Rd | 2 smoof-1.1/smoof/man/isSmoofFunction.Rd | 2 smoof-1.1/smoof/man/isVectorized.Rd | 2 smoof-1.1/smoof/man/isWrappedSmoofFunction.Rd | 2 smoof-1.1/smoof/man/makeAckleyFunction.Rd | 2 smoof-1.1/smoof/man/makeAdjimanFunction.Rd | 2 smoof-1.1/smoof/man/makeAlpine01Function.Rd | 2 smoof-1.1/smoof/man/makeAlpine02Function.Rd | 2 smoof-1.1/smoof/man/makeAluffiPentiniFunction.Rd |only smoof-1.1/smoof/man/makeBBOBFunction.Rd | 2 smoof-1.1/smoof/man/makeBartelsConnFunction.Rd | 2 smoof-1.1/smoof/man/makeBealeFunction.Rd | 2 smoof-1.1/smoof/man/makeBentCigarFunction.Rd |only smoof-1.1/smoof/man/makeBirdFunction.Rd | 2 smoof-1.1/smoof/man/makeBohachevskyN1Function.Rd |only smoof-1.1/smoof/man/makeBoothFunction.Rd | 2 smoof-1.1/smoof/man/makeBraninFunction.Rd | 2 smoof-1.1/smoof/man/makeBrentFunction.Rd | 2 smoof-1.1/smoof/man/makeBrownFunction.Rd | 2 smoof-1.1/smoof/man/makeBukinN2Function.Rd | 2 smoof-1.1/smoof/man/makeBukinN4Function.Rd | 2 smoof-1.1/smoof/man/makeBukinN6Function.Rd | 2 smoof-1.1/smoof/man/makeCarromTableFunction.Rd | 2 smoof-1.1/smoof/man/makeChichinadzeFunction.Rd | 2 smoof-1.1/smoof/man/makeChungReynoldsFunction.Rd | 2 smoof-1.1/smoof/man/makeComplexFunction.Rd |only smoof-1.1/smoof/man/makeCosineMixtureFunction.Rd | 2 smoof-1.1/smoof/man/makeCrossInTrayFunction.Rd | 2 smoof-1.1/smoof/man/makeCubeFunction.Rd | 2 smoof-1.1/smoof/man/makeDTLZ1Function.Rd |only smoof-1.1/smoof/man/makeDTLZ2Function.Rd |only smoof-1.1/smoof/man/makeDTLZ3Function.Rd |only smoof-1.1/smoof/man/makeDTLZ4Function.Rd |only smoof-1.1/smoof/man/makeDTLZ5Function.Rd |only smoof-1.1/smoof/man/makeDTLZ6Function.Rd |only smoof-1.1/smoof/man/makeDTLZ7Function.Rd |only smoof-1.1/smoof/man/makeDeckkersAartsFunction.Rd | 2 smoof-1.1/smoof/man/makeDeflectedCorrugatedSpringFunction.Rd |only smoof-1.1/smoof/man/makeDixonPriceFunction.Rd | 2 smoof-1.1/smoof/man/makeDoubleSumFunction.Rd | 2 smoof-1.1/smoof/man/makeEasomFunction.Rd | 2 smoof-1.1/smoof/man/makeEggCrateFunction.Rd | 2 smoof-1.1/smoof/man/makeEggholderFunction.Rd | 2 smoof-1.1/smoof/man/makeElAttarVidyasagarDuttaFunction.Rd | 2 smoof-1.1/smoof/man/makeEngvallFunction.Rd |only smoof-1.1/smoof/man/makeExponentialFunction.Rd | 2 smoof-1.1/smoof/man/makeFreudensteinRothFunction.Rd | 2 smoof-1.1/smoof/man/makeFunctionByName.Rd |only smoof-1.1/smoof/man/makeGeneralizedDropWaveFunction.Rd | 2 smoof-1.1/smoof/man/makeGiuntaFunction.Rd | 2 smoof-1.1/smoof/man/makeGoldsteinPriceFunction.Rd | 2 smoof-1.1/smoof/man/makeGriewankFunction.Rd | 2 smoof-1.1/smoof/man/makeHansenFunction.Rd | 2 smoof-1.1/smoof/man/makeHimmelblauFunction.Rd | 2 smoof-1.1/smoof/man/makeHolderTableN1Function.Rd | 2 smoof-1.1/smoof/man/makeHolderTableN2Function.Rd | 2 smoof-1.1/smoof/man/makeHosakiFunction.Rd | 2 smoof-1.1/smoof/man/makeHyperEllipsoidFunction.Rd | 2 smoof-1.1/smoof/man/makeJennrichSampsonFunction.Rd |only smoof-1.1/smoof/man/makeJudgeFunction.Rd |only smoof-1.1/smoof/man/makeKeaneFunction.Rd | 2 smoof-1.1/smoof/man/makeKearfottFunction.Rd |only smoof-1.1/smoof/man/makeLeonFunction.Rd | 2 smoof-1.1/smoof/man/makeMPM2Function.Rd | 3 smoof-1.1/smoof/man/makeMatyasFunction.Rd | 4 smoof-1.1/smoof/man/makeMcCormickFunction.Rd | 2 smoof-1.1/smoof/man/makeMichalewiczFunction.Rd | 2 smoof-1.1/smoof/man/makeMultiObjectiveFunction.Rd | 10 smoof-1.1/smoof/man/makePeriodicFunction.Rd | 2 smoof-1.1/smoof/man/makePowellSumFunction.Rd | 2 smoof-1.1/smoof/man/makePriceN1Function.Rd | 2 smoof-1.1/smoof/man/makePriceN2Function.Rd | 2 smoof-1.1/smoof/man/makePriceN4Function.Rd | 2 smoof-1.1/smoof/man/makeRastriginFunction.Rd | 2 smoof-1.1/smoof/man/makeRosenbrockFunction.Rd | 2 smoof-1.1/smoof/man/makeSchafferN2Function.Rd | 2 smoof-1.1/smoof/man/makeSchafferN4Function.Rd | 2 smoof-1.1/smoof/man/makeSchwefelFunction.Rd | 2 smoof-1.1/smoof/man/makeShubertFunction.Rd | 2 smoof-1.1/smoof/man/makeSingleObjectiveFunction.Rd | 11 smoof-1.1/smoof/man/makeSixHumpCamelFunction.Rd | 2 smoof-1.1/smoof/man/makeSphereFunction.Rd | 2 smoof-1.1/smoof/man/makeStyblinkskiTangFunction.Rd | 2 smoof-1.1/smoof/man/makeSumOfDifferentSquaresFunction.Rd | 2 smoof-1.1/smoof/man/makeThreeHumpCamelFunction.Rd | 2 smoof-1.1/smoof/man/makeTrecanniFunction.Rd | 2 smoof-1.1/smoof/man/makeUFFunction.Rd | 6 smoof-1.1/smoof/man/makeZDT1Function.Rd | 2 smoof-1.1/smoof/man/makeZDT2Function.Rd | 2 smoof-1.1/smoof/man/makeZDT3Function.Rd | 2 smoof-1.1/smoof/man/makeZDT4Function.Rd | 2 smoof-1.1/smoof/man/makeZDT6Function.Rd | 2 smoof-1.1/smoof/man/makeZettlFunction.Rd | 2 smoof-1.1/smoof/man/plot.smoof_function.Rd | 2 smoof-1.1/smoof/man/plot1DNumeric.Rd | 2 smoof-1.1/smoof/man/plot2DNumeric.Rd | 2 smoof-1.1/smoof/man/plot3D.Rd | 2 smoof-1.1/smoof/man/resetEvaluationCounter.Rd | 2 smoof-1.1/smoof/man/shouldBeMinimized.Rd |only smoof-1.1/smoof/man/smoof-package.Rd | 2 smoof-1.1/smoof/man/violatesConstraints.Rd | 2 smoof-1.1/smoof/man/visualizeParetoOptimalFront.Rd | 2 smoof-1.1/smoof/src/RcppExports.cpp |only smoof-1.1/smoof/src/dtlz.cpp |only smoof-1.1/smoof/tests/testthat/Rplots.pdf |binary smoof-1.1/smoof/tests/testthat/helper_zzz.R | 2 smoof-1.1/smoof/tests/testthat/test_filterFunctionByTags.R |only smoof-1.1/smoof/tests/testthat/test_helpers.R |only smoof-1.1/smoof/tests/testthat/test_makeFunctionByName.R |only smoof-1.1/smoof/tests/testthat/test_makeSingleObjectiveFunction.R | 2 smoof-1.1/smoof/tests/testthat/test_soofuns.R | 7 239 files changed, 599 insertions(+), 416 deletions(-)
Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling
algorithm and related algorithms. The algorithm implementations aim for
computational efficiency using matrix algebra and covariance data. The
package is designed toward Monte Carlo simulations and includes functions
to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>
Diff between matrixpls versions 0.5.0 dated 2014-11-29 and 0.6.0 dated 2015-11-24
matrixpls-0.5.0/matrixpls/R/matrixpls.plsc.R |only matrixpls-0.5.0/matrixpls/demo |only matrixpls-0.5.0/matrixpls/man/AVE.Rd |only matrixpls-0.5.0/matrixpls/man/CR.Rd |only matrixpls-0.5.0/matrixpls/man/GoF.Rd |only matrixpls-0.5.0/matrixpls/man/R2.Rd |only matrixpls-0.5.0/matrixpls/man/convCheck.absolute.Rd |only matrixpls-0.5.0/matrixpls/man/convCheck.relative.Rd |only matrixpls-0.5.0/matrixpls/man/convCheck.square.Rd |only matrixpls-0.5.0/matrixpls/man/inner.GSCA.Rd |only matrixpls-0.5.0/matrixpls/man/inner.Horst.Rd |only matrixpls-0.5.0/matrixpls/man/inner.centroid.Rd |only matrixpls-0.5.0/matrixpls/man/inner.factor.Rd |only matrixpls-0.5.0/matrixpls/man/inner.identity.Rd |only matrixpls-0.5.0/matrixpls/man/inner.path.Rd |only matrixpls-0.5.0/matrixpls/man/loadings.Rd |only matrixpls-0.5.0/matrixpls/man/optim.GCCA.Rd |only matrixpls-0.5.0/matrixpls/man/optim.GSCA.Rd |only matrixpls-0.5.0/matrixpls/man/optim.maximizeInnerR2.Rd |only matrixpls-0.5.0/matrixpls/man/optim.maximizePrediction.Rd |only matrixpls-0.5.0/matrixpls/man/outer.GSCA.Rd |only matrixpls-0.5.0/matrixpls/man/outer.RGCCA.Rd |only matrixpls-0.5.0/matrixpls/man/outer.factor.Rd |only matrixpls-0.5.0/matrixpls/man/outer.fixedWeights.Rd |only matrixpls-0.5.0/matrixpls/man/outer.modeA.Rd |only matrixpls-0.5.0/matrixpls/man/outer.modeB.Rd |only matrixpls-0.5.0/matrixpls/man/params.plsc.Rd |only matrixpls-0.5.0/matrixpls/man/params.plsregression.Rd |only matrixpls-0.5.0/matrixpls/man/params.regression.Rd |only matrixpls-0.5.0/matrixpls/man/params.tsls.Rd |only matrixpls-0.5.0/matrixpls/man/signChange.construct.Rd |only matrixpls-0.5.0/matrixpls/man/signChange.individual.Rd |only matrixpls-0.5.0/matrixpls/man/weight.fixed.Rd |only matrixpls-0.5.0/matrixpls/man/weight.optim.Rd |only matrixpls-0.5.0/matrixpls/man/weight.pls.Rd |only matrixpls-0.6.0/matrixpls/DESCRIPTION | 28 matrixpls-0.6.0/matrixpls/MD5 | 102 matrixpls-0.6.0/matrixpls/NAMESPACE | 121 matrixpls-0.6.0/matrixpls/R/matrixpls.R | 1793 ---------- matrixpls-0.6.0/matrixpls/R/matrixpls.boot.R | 90 matrixpls-0.6.0/matrixpls/R/matrixpls.convergenceCheck.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.estimators.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.inner.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.optim.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.outer.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.params.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.plspm.R | 184 - matrixpls-0.6.0/matrixpls/R/matrixpls.postestimation.R | 508 ++ matrixpls-0.6.0/matrixpls/R/matrixpls.reliability.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.sempls.R | 14 matrixpls-0.6.0/matrixpls/R/matrixpls.signAmbiquityCorrection.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.signChangeCorrection.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.sim.R | 104 matrixpls-0.6.0/matrixpls/R/matrixpls.util.R |only matrixpls-0.6.0/matrixpls/R/matrixpls.weights.R |only matrixpls-0.6.0/matrixpls/man/GSCA.Rd |only matrixpls-0.6.0/matrixpls/man/ave.Rd |only matrixpls-0.6.0/matrixpls/man/convergenceCheck.Rd |only matrixpls-0.6.0/matrixpls/man/cr.Rd |only matrixpls-0.6.0/matrixpls/man/effects.matrixpls.Rd | 13 matrixpls-0.6.0/matrixpls/man/fitSummary.Rd | 15 matrixpls-0.6.0/matrixpls/man/fitted.matrixpls.Rd |only matrixpls-0.6.0/matrixpls/man/gof.Rd |only matrixpls-0.6.0/matrixpls/man/htmt.Rd |only matrixpls-0.6.0/matrixpls/man/innerEstimators.Rd |only matrixpls-0.6.0/matrixpls/man/loadings.matrixpls.Rd |only matrixpls-0.6.0/matrixpls/man/matrixpls-common.Rd |only matrixpls-0.6.0/matrixpls/man/matrixpls-package.Rd | 185 - matrixpls-0.6.0/matrixpls/man/matrixpls.Rd | 66 matrixpls-0.6.0/matrixpls/man/matrixpls.boot.Rd | 15 matrixpls-0.6.0/matrixpls/man/matrixpls.plspm.Rd | 95 matrixpls-0.6.0/matrixpls/man/matrixpls.sempls.Rd | 100 matrixpls-0.6.0/matrixpls/man/matrixpls.sim.Rd | 137 matrixpls-0.6.0/matrixpls/man/optimCriterion.Rd |only matrixpls-0.6.0/matrixpls/man/outerEstimators.Rd |only matrixpls-0.6.0/matrixpls/man/parameterEstimators.Rd |only matrixpls-0.6.0/matrixpls/man/params.separate.Rd |only matrixpls-0.6.0/matrixpls/man/predict.matrixpls.Rd | 11 matrixpls-0.6.0/matrixpls/man/r2.Rd |only matrixpls-0.6.0/matrixpls/man/reliability.weightLoadingProduct.Rd |only matrixpls-0.6.0/matrixpls/man/residuals.matrixpls.Rd | 35 matrixpls-0.6.0/matrixpls/man/signAmbiquityCorrection.Rd |only matrixpls-0.6.0/matrixpls/man/signChangeCorrection.Rd |only matrixpls-0.6.0/matrixpls/man/weightAlgorithms.Rd |only 84 files changed, 1159 insertions(+), 2457 deletions(-)
Title: Tools for Pre-Processing Emission-Excitation-Matrix (EEM)
Description: Provides various tools to calculate EEM metrics and preprocess EEM for PARAFAC analysis.
Author: Philippe Massicotte [aut, cre]
Maintainer: Philippe Massicotte <pm@bios.au.dk>
Diff between eemR versions 0.1.0 dated 2015-11-19 and 0.1.1 dated 2015-11-24
DESCRIPTION |only MD5 |only NAMESPACE |only R |only README.md |only data |only inst/extdata/aqualog |only inst/extdata/cary/eem/sample2.csv |only inst/extdata/cary/eem/sample3.csv | 1533 +++++++++++++++++++++++++++++++++++++- inst/extdata/shimadzu |only man |only src |only 12 files changed, 1532 insertions(+), 1 deletion(-)
Title: Gene Enrichment Analysis from ACSN Maps or Gmt Files
Description: Compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported maps.
The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections.
Visualization of data can be done either by barplots or heatmaps.
Author: Paul Deveau [aut, cre],
Eric Bonnet [aut]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between ACSNMineR versions 0.10.15 dated 2015-10-27 and 0.15.11 dated 2015-11-24
DESCRIPTION | 8 MD5 | 6 R/ACSN_Enrichment.R | 431 +++++++++++++++++++++++++------------------- inst/doc/ACSN-vignette.html | 49 ----- 4 files changed, 267 insertions(+), 227 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data (Nemenyi's test, Dunn's test, Conover's test,
van der Waerden's test). Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison tests according
to Nemenyi and Conover are also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 2.0 dated 2015-11-13 and 3.0 dated 2015-11-24
DESCRIPTION | 15 +-- MD5 | 42 +++++---- NAMESPACE | 14 ++- R/dunn.test.control.R | 21 ++++ R/posthoc.friedman.conover.R |only R/posthoc.friedman.nemenyi.test.R | 22 ++++ R/posthoc.kruskal.conover.R |only R/posthoc.kruskal.dunn.test.R | 26 ++++- R/posthoc.kruskal.nemenyi.test.R | 20 ++++ R/posthoc.vanWaerden.test.R |only R/vanWaerden.test.R |only inst/NEWS.Rd | 29 ++++++ inst/doc/PMCMR.R | 81 ++++++++++++++--- inst/doc/PMCMR.Rnw | 158 +++++++++++++++++++++++++++++------ inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 19 +++- man/dunn.test.control.Rd | 2 man/posthoc.friedman.conover.test.Rd |only man/posthoc.friedman.nemenyi.test.Rd | 3 man/posthoc.kruskal.conover.Rd |only man/posthoc.kruskal.dunn.test.Rd | 4 man/posthoc.kruskal.nemenyi.test.Rd | 2 man/posthoc.vanWaerden.test.Rd |only man/vanWaerden.test.Rd |only vignettes/PMCMR.Rnw | 158 +++++++++++++++++++++++++++++------ vignettes/PMCMR.bib | 17 +++ 26 files changed, 522 insertions(+), 111 deletions(-)
Title: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Description: The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker
Maintainer: Katharine M. Mullen <mullenkate@gmail.com>
Diff between minpack.lm versions 1.1-9 dated 2015-09-04 and 1.2-0 dated 2015-11-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 29 ++++++++++++++++------------- R/nlsLM.R | 13 +++++-------- man/nlsLM.Rd | 10 +++------- 5 files changed, 31 insertions(+), 35 deletions(-)
Title: A Genetic Algorithm for Fixed-Size Subset Selection
Description: Function kofnGA uses a genetic algorithm to choose a subset of a
fixed size k from the integers 1:n, such that a user-supplied objective function
is minimized at that subset. The selection step is done by tournament selection
based on ranks, and elitism may be used to retain a portion of the best solutions
from one generation to the next.
Author: Mark A. Wolters
Maintainer: Mark A. Wolters <mark@mwolters.com>
Diff between kofnGA versions 1.1 dated 2015-02-04 and 1.2 dated 2015-11-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/kofnGA.R | 18 ++++++++++++++---- inst/CITATION | 31 ++++++++++++++++--------------- man/kofnGA-package.Rd | 9 ++++----- man/kofnGA.Rd | 14 ++++++++++---- 7 files changed, 57 insertions(+), 38 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.2.0.3 dated 2015-09-22 and 3.6.0.8 dated 2015-11-24
h2o-3.2.0.3/h2o/R/ast.R |only h2o-3.2.0.3/h2o/R/exec.R |only h2o-3.2.0.3/h2o/R/ops.R |only h2o-3.2.0.3/h2o/R/shim.R |only h2o-3.2.0.3/h2o/demo/h2o.anomaly.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.deeplearning.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.gbm.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.glm.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.kmeans.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.naiveBayes.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.prcomp.remote.R |only h2o-3.2.0.3/h2o/demo/h2o.randomForest.remote.R |only h2o-3.2.0.3/h2o/man/ASTNode-class.Rd |only h2o-3.2.0.3/h2o/man/H2OFrame-Extract.Rd |only h2o-3.2.0.3/h2o/man/H2OFrame-class.Rd |only h2o-3.2.0.3/h2o/man/H2OObject-class.Rd |only h2o-3.2.0.3/h2o/man/H2ORawData-class.Rd |only h2o-3.2.0.3/h2o/man/H2OS4groupGeneric.Rd |only h2o-3.2.0.3/h2o/man/H2OW2V-class.Rd |only h2o-3.2.0.3/h2o/man/Node-class.Rd |only h2o-3.2.0.3/h2o/man/apply-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/as.character-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/as.data.frame.H2OFrame.Rd |only h2o-3.2.0.3/h2o/man/as.environment-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/as.factor-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/as.numeric-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/h2o.colnames.Rd |only h2o-3.2.0.3/h2o/man/h2o.cummax.Rd |only h2o-3.2.0.3/h2o/man/h2o.cummin.Rd |only h2o-3.2.0.3/h2o/man/h2o.cumprod.Rd |only h2o-3.2.0.3/h2o/man/h2o.cumsum.Rd |only h2o-3.2.0.3/h2o/man/h2o.dim.Rd |only h2o-3.2.0.3/h2o/man/h2o.length.Rd |only h2o-3.2.0.3/h2o/man/h2o.nlevels.Rd |only h2o-3.2.0.3/h2o/man/h2o.nrow.Rd |only h2o-3.2.0.3/h2o/man/h2o.setLevel.Rd |only h2o-3.2.0.3/h2o/man/h2o.shim.Rd |only h2o-3.2.0.3/h2o/man/h2o.subset.Rd |only h2o-3.2.0.3/h2o/man/h2o.transform.Rd |only h2o-3.2.0.3/h2o/man/h2o.which.Rd |only h2o-3.2.0.3/h2o/man/is.factor-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/is.numeric-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/na.omit-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/range-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/sapply-H2OFrame-method.Rd |only h2o-3.2.0.3/h2o/man/str.H2OFrame.Rd |only h2o-3.2.0.3/h2o/tests |only h2o-3.6.0.8/h2o/DESCRIPTION | 10 h2o-3.6.0.8/h2o/MD5 | 351 - h2o-3.6.0.8/h2o/NAMESPACE | 166 h2o-3.6.0.8/h2o/R/astfun.R | 516 -- h2o-3.6.0.8/h2o/R/classes.R | 322 - h2o-3.6.0.8/h2o/R/communication.R | 138 h2o-3.6.0.8/h2o/R/connection.R | 172 h2o-3.6.0.8/h2o/R/constants.R | 150 h2o-3.6.0.8/h2o/R/datasets.R |only h2o-3.6.0.8/h2o/R/deeplearning.R | 100 h2o-3.6.0.8/h2o/R/export.R | 52 h2o-3.6.0.8/h2o/R/frame.R | 2902 ++++++---------- h2o-3.6.0.8/h2o/R/gbm.R | 80 h2o-3.6.0.8/h2o/R/glm.R | 94 h2o-3.6.0.8/h2o/R/glrm.R | 134 h2o-3.6.0.8/h2o/R/grid.R | 31 h2o-3.6.0.8/h2o/R/import.R | 108 h2o-3.6.0.8/h2o/R/kmeans.R | 30 h2o-3.6.0.8/h2o/R/kvstore.R | 185 - h2o-3.6.0.8/h2o/R/logging.R | 49 h2o-3.6.0.8/h2o/R/models.R | 415 +- h2o-3.6.0.8/h2o/R/naivebayes.R | 17 h2o-3.6.0.8/h2o/R/parse.R | 116 h2o-3.6.0.8/h2o/R/pca.R | 57 h2o-3.6.0.8/h2o/R/randomforest.R | 65 h2o-3.6.0.8/h2o/R/svd.R | 30 h2o-3.6.0.8/h2o/R/word2vec.R | 20 h2o-3.6.0.8/h2o/demo/00Index | 9 h2o-3.6.0.8/h2o/demo/h2o.anomaly.R | 6 h2o-3.6.0.8/h2o/demo/h2o.deeplearning.R | 4 h2o-3.6.0.8/h2o/demo/h2o.gbm.R | 6 h2o-3.6.0.8/h2o/demo/h2o.glm.R | 4 h2o-3.6.0.8/h2o/demo/h2o.glrm.R |only h2o-3.6.0.8/h2o/demo/h2o.kmeans.R | 4 h2o-3.6.0.8/h2o/demo/h2o.naiveBayes.R | 6 h2o-3.6.0.8/h2o/demo/h2o.prcomp.R | 4 h2o-3.6.0.8/h2o/demo/h2o.randomForest.R | 6 h2o-3.6.0.8/h2o/inst/branch.txt | 2 h2o-3.6.0.8/h2o/inst/buildnum.txt | 2 h2o-3.6.0.8/h2o/inst/extdata/walking.csv |only h2o-3.6.0.8/h2o/man/Frame-Extract.Rd |only h2o-3.6.0.8/h2o/man/Frame.Rd |only h2o-3.6.0.8/h2o/man/H2OClusteringModel-class.Rd | 10 h2o-3.6.0.8/h2o/man/H2OGrid-class.Rd | 2 h2o-3.6.0.8/h2o/man/H2OModel-class.Rd | 7 h2o-3.6.0.8/h2o/man/H2OModelFuture-class.Rd | 2 h2o-3.6.0.8/h2o/man/apply.Rd |only h2o-3.6.0.8/h2o/man/as.character.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.data.frame.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.factor.Rd |only h2o-3.6.0.8/h2o/man/as.h2o.Rd | 9 h2o-3.6.0.8/h2o/man/as.matrix.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.numeric.Rd |only h2o-3.6.0.8/h2o/man/as.vector.Rd |only h2o-3.6.0.8/h2o/man/australia.Rd |only h2o-3.6.0.8/h2o/man/colnames.Rd |only h2o-3.6.0.8/h2o/man/dim.Frame.Rd |only h2o-3.6.0.8/h2o/man/dimnames.Frame.Rd |only h2o-3.6.0.8/h2o/man/h2o-package.Rd | 12 h2o-3.6.0.8/h2o/man/h2o.anomaly.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.anyFactor.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.assign.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.cbind.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.clearLog.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.clusterInfo.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.clusterIsUp.Rd | 2 h2o-3.6.0.8/h2o/man/h2o.clusterStatus.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.confusionMatrix.Rd | 2 h2o-3.6.0.8/h2o/man/h2o.createFrame.Rd | 23 h2o-3.6.0.8/h2o/man/h2o.cut.Rd | 14 h2o-3.6.0.8/h2o/man/h2o.day.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.dayOfWeek.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.dct.Rd | 12 h2o-3.6.0.8/h2o/man/h2o.ddply.Rd | 22 h2o-3.6.0.8/h2o/man/h2o.deepfeatures.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.deeplearning.Rd | 78 h2o-3.6.0.8/h2o/man/h2o.downloadAllLogs.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.downloadCSV.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.download_pojo.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.exportFile.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.exportHDFS.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.find_row_by_threshold.Rd |only h2o-3.6.0.8/h2o/man/h2o.find_threshold_by_max_metric.Rd |only h2o-3.6.0.8/h2o/man/h2o.gbm.Rd | 63 h2o-3.6.0.8/h2o/man/h2o.getFrame.Rd | 14 h2o-3.6.0.8/h2o/man/h2o.getFutureModel.Rd |only h2o-3.6.0.8/h2o/man/h2o.getGrid.Rd | 12 h2o-3.6.0.8/h2o/man/h2o.getId.Rd |only h2o-3.6.0.8/h2o/man/h2o.getModel.Rd | 14 h2o-3.6.0.8/h2o/man/h2o.getTimezone.Rd | 9 h2o-3.6.0.8/h2o/man/h2o.getTypes.Rd |only h2o-3.6.0.8/h2o/man/h2o.getVersion.Rd |only h2o-3.6.0.8/h2o/man/h2o.glm.Rd | 54 h2o-3.6.0.8/h2o/man/h2o.glrm.Rd | 43 h2o-3.6.0.8/h2o/man/h2o.grid.Rd | 9 h2o-3.6.0.8/h2o/man/h2o.group_by.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.gsub.Rd | 3 h2o-3.6.0.8/h2o/man/h2o.head.Rd | 27 h2o-3.6.0.8/h2o/man/h2o.hist.Rd | 2 h2o-3.6.0.8/h2o/man/h2o.hour.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.ifelse.Rd | 12 h2o-3.6.0.8/h2o/man/h2o.importFile.Rd | 48 h2o-3.6.0.8/h2o/man/h2o.impute.Rd | 14 h2o-3.6.0.8/h2o/man/h2o.init.Rd | 25 h2o-3.6.0.8/h2o/man/h2o.insertMissingValues.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.interaction.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.killMinus3.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.kmeans.Rd | 14 h2o-3.6.0.8/h2o/man/h2o.levels.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.listTimezones.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.loadModel.Rd | 16 h2o-3.6.0.8/h2o/man/h2o.logAndEcho.Rd | 7 h2o-3.6.0.8/h2o/man/h2o.ls.Rd | 11 h2o-3.6.0.8/h2o/man/h2o.match.Rd | 16 h2o-3.6.0.8/h2o/man/h2o.mean.Rd | 17 h2o-3.6.0.8/h2o/man/h2o.median.Rd | 13 h2o-3.6.0.8/h2o/man/h2o.merge.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.mktime.Rd |only h2o-3.6.0.8/h2o/man/h2o.month.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.naiveBayes.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.nchar.Rd |only h2o-3.6.0.8/h2o/man/h2o.networkTest.Rd | 5 h2o-3.6.0.8/h2o/man/h2o.openLog.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.parseRaw.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.parseSetup.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.performance.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.prcomp.Rd | 21 h2o-3.6.0.8/h2o/man/h2o.quantile.Rd | 19 h2o-3.6.0.8/h2o/man/h2o.r2.Rd | 2 h2o-3.6.0.8/h2o/man/h2o.randomForest.Rd | 47 h2o-3.6.0.8/h2o/man/h2o.rbind.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.removeAll.Rd | 15 h2o-3.6.0.8/h2o/man/h2o.removeVecs.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.rep_len.Rd | 2 h2o-3.6.0.8/h2o/man/h2o.rm.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.runif.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.saveModel.Rd | 6 h2o-3.6.0.8/h2o/man/h2o.scale.Rd | 9 h2o-3.6.0.8/h2o/man/h2o.sd.Rd | 11 h2o-3.6.0.8/h2o/man/h2o.setTimezone.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.shutdown.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.splitFrame.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.startGLMJob.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.startLogging.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.stopLogging.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.sub.Rd | 3 h2o-3.6.0.8/h2o/man/h2o.summary.Rd | 13 h2o-3.6.0.8/h2o/man/h2o.svd.Rd | 8 h2o-3.6.0.8/h2o/man/h2o.table.Rd | 13 h2o-3.6.0.8/h2o/man/h2o.tabulate.Rd | 7 h2o-3.6.0.8/h2o/man/h2o.tolower.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.toupper.Rd | 4 h2o-3.6.0.8/h2o/man/h2o.var.Rd | 13 h2o-3.6.0.8/h2o/man/h2o.week.Rd | 10 h2o-3.6.0.8/h2o/man/h2o.year.Rd | 10 h2o-3.6.0.8/h2o/man/housevotes.Rd |only h2o-3.6.0.8/h2o/man/iris.Rd |only h2o-3.6.0.8/h2o/man/is.factor.Rd |only h2o-3.6.0.8/h2o/man/is.numeric.Rd |only h2o-3.6.0.8/h2o/man/na.omit.Rd |only h2o-3.6.0.8/h2o/man/names.Frame.Rd |only h2o-3.6.0.8/h2o/man/plot.H2OModel.Rd |only h2o-3.6.0.8/h2o/man/plot.H2OTabulate.Rd |only h2o-3.6.0.8/h2o/man/predict.H2OModel.Rd | 7 h2o-3.6.0.8/h2o/man/print.Frame.Rd |only h2o-3.6.0.8/h2o/man/prostate.Rd |only h2o-3.6.0.8/h2o/man/range.Frame.Rd |only h2o-3.6.0.8/h2o/man/str.Frame.Rd |only h2o-3.6.0.8/h2o/man/summary-H2OGrid-method.Rd | 2 h2o-3.6.0.8/h2o/man/walking.Rd |only h2o-3.6.0.8/h2o/man/zzz.Rd | 8 218 files changed, 3301 insertions(+), 4212 deletions(-)
Title: Automatic Generation of Exams in R
Description: Automatic generation of exams based on exercises in Sweave (R/LaTeX) or R/Markdown format,
including multiple-choice questions and arithmetic problems. Exams can be produced in various formats,
including PDF, HTML, Moodle XML, QTI 1.2 (for OLAT/OpenOLAT), QTI 2.1, ARSnova, and TCExam.
In addition to fully customizable PDF exams, a standardized PDF format is provided that can be
printed, scanned, and automatically evaluated.
Author: Achim Zeileis [aut, cre],
Bettina Gruen [aut],
Friedrich Leisch [aut],
Nikolaus Umlauf [aut],
Dominik Ernst [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between exams versions 2.0-2 dated 2015-01-14 and 2.1-0 dated 2015-11-24
DESCRIPTION | 23 + MD5 | 165 ++++++++----- NAMESPACE | 39 ++- NEWS | 58 ++++ R/exams.R | 2 R/exams2arsnova.R |only R/exams2html.R | 16 + R/exams2moodle.R | 27 +- R/exams2nops.R |only R/exams2pdf.R | 14 - R/exams2qti12.R | 13 - R/exams2qti21.R | 16 - R/exams2tcexam.R |only R/exams_skeleton.R | 466 ++++++++++++++++++++++++++++++++++---- R/formatters.R | 71 +++++ R/nops_eval.R |only R/nops_scan.R |only R/pandoc.R |only R/read_exercise.R | 41 ++- R/read_metainfo.R | 160 +++++++++---- R/tex2image.R | 67 +++-- R/to_choice.R |only R/transformers.R | 28 +- R/xexams.R | 63 ++++- build/vignette.rds |binary inst/doc/exams.Rnw | 2 inst/doc/exams.pdf |binary inst/doc/exams2.R | 8 inst/doc/exams2.Rnw | 23 - inst/doc/exams2.pdf |binary inst/exercises/anova.Rmd |only inst/exercises/anova.Rnw | 97 +++---- inst/exercises/boxhist.Rmd |only inst/exercises/boxplots.Rmd |only inst/exercises/boxplots.Rnw | 11 inst/exercises/cholesky.Rmd |only inst/exercises/cholesky.Rnw | 73 ----- inst/exercises/confint2.Rmd |only inst/exercises/confint2.Rnw | 5 inst/exercises/countrycodes.Rmd |only inst/exercises/countrycodes.Rnw |only inst/exercises/currency8.Rmd |only inst/exercises/dist.Rmd |only inst/exercises/dist2.Rmd |only inst/exercises/dist2.Rnw | 2 inst/exercises/dist3.Rmd |only inst/exercises/dist3.Rnw |only inst/exercises/fourfold.Rmd |only inst/exercises/function.Rmd |only inst/exercises/lagrange.Rmd |only inst/exercises/lagrange.Rnw | 22 - inst/exercises/regression.Rmd |only inst/exercises/regression.Rnw | 27 +- inst/exercises/relfreq.Rmd |only inst/exercises/relfreq.Rnw | 26 -- inst/exercises/scatterplot.Rmd |only inst/exercises/scatterplot.Rnw | 38 +-- inst/exercises/swisscapital.Rmd |only inst/exercises/swisscapital.Rnw |only inst/exercises/switzerland.Rmd |only inst/exercises/switzerland.Rnw |only inst/exercises/tstat.Rmd |only inst/exercises/tstat.Rnw | 34 +- inst/exercises/tstat2.Rmd |only inst/exercises/tstat2.Rnw | 62 ++--- inst/exercises/tstat_verbatim.Rnw |only inst/exercises/ttest.Rmd |only inst/exercises/ttest.Rnw | 40 +-- inst/nops |only inst/tex/exam.tex | 2 inst/tex/html-plain.tex | 2 inst/tex/plain.tex | 2 inst/tex/plain8.tex | 2 inst/tex/plain9.tex | 2 inst/tex/solution.tex | 2 inst/xml/plain.html | 3 inst/xml/plain8.html | 1 inst/xml/plain9.html | 1 man/exams.Rd | 14 - man/exams2arsnova.Rd |only man/exams2html.Rd | 44 +-- man/exams2lops.Rd | 8 man/exams2moodle.Rd | 27 +- man/exams2nops.Rd |only man/exams2pdf.Rd | 12 man/exams2qti12.Rd | 16 - man/exams2tcexam.Rd |only man/exams_skeleton.Rd | 33 +- man/fmt.Rd |only man/matrix_to_schoice.Rd |only man/mchoice2string.Rd | 6 man/nops_eval.Rd |only man/nops_scan.Rd |only man/num_to_schoice.Rd |only man/read_exercise.Rd | 42 ++- man/tex2image.Rd | 25 +- man/xexams.Rd | 29 +- man/xweave.Rd |only vignettes/exams.Rnw | 2 vignettes/exams2.Rnw | 23 - 100 files changed, 1390 insertions(+), 647 deletions(-)
Title: R Bindings for Yummly API
Description:
Yummly.com is one of the world's largest and most powerful recipe search sites and this package aims to provide R bindings for publicly available Yummly.com Recipe API (https://developer.yummly.com/).
Author: Roman Tsegelskyi
Maintainer: Roman Tsegelskyi <roman.tsegelskyi@gmail.com>
Diff between yummlyr versions 0.1.0 dated 2015-11-13 and 0.1.1 dated 2015-11-24
yummlyr-0.1.0/yummlyr/NEWS.md |only yummlyr-0.1.1/yummlyr/DESCRIPTION | 7 +++---- yummlyr-0.1.1/yummlyr/MD5 | 5 ++--- yummlyr-0.1.1/yummlyr/tests/testthat/test-search.R | 16 ++++++++-------- 4 files changed, 13 insertions(+), 15 deletions(-)
Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis. The 'poppr'
R package allows import of GenAlEx formatted CSV data. This package serves as a
small 'poppr' add on for those who have trouble or simply do not want to export
their data into CSV format.
Author: Zhian N. Kamvar [cre, aut]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between popprxl versions 0.1 dated 2015-07-19 and 0.1.1 dated 2015-11-24
popprxl-0.1.1/popprxl/DESCRIPTION | 18 ++++++++---- popprxl-0.1.1/popprxl/MD5 | 16 ++++++---- popprxl-0.1.1/popprxl/NAMESPACE | 2 - popprxl-0.1.1/popprxl/NEWS |only popprxl-0.1.1/popprxl/R/read_genalexcel.R | 17 ++++++++--- popprxl-0.1.1/popprxl/README.md | 5 +++ popprxl-0.1.1/popprxl/inst/files/geo_ex.xls |only popprxl-0.1.1/popprxl/inst/files/nancycats_extra_rows.xlsx |only popprxl-0.1.1/popprxl/man/read.genalexcel.Rd | 16 ++++++++-- popprxl-0.1.1/popprxl/tests/testthat/test-import.R | 14 ++++++++- popprxl-0.1/popprxl/inst/files/nancycats_extra_columns.xlsx |only 11 files changed, 66 insertions(+), 22 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between netassoc versions 0.6.0 dated 2015-09-09 and 0.6.2 dated 2015-11-24
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 5 +++-- R/make_netassoc_network.R | 29 ++++++++++++----------------- R/pairwise_association.R |only R/partial_correlation.R | 3 +-- R/plot.R | 4 ++-- man/make_netassoc_network.Rd | 34 +++++++++++++++++++++++----------- man/netassoc-package.Rd | 4 ++-- man/pairwise_association.Rd |only man/plot_netassoc_network.Rd | 4 ++-- 11 files changed, 60 insertions(+), 51 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.11.4 dated 2015-10-22 and 3.11.5 dated 2015-11-24
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ R/anova.manyany.R | 33 ++++++++------------------------- R/manyany.R | 45 +++++++++++++++++++++++++++++---------------- R/manyglm.R | 27 +++++++++++++++++---------- R/predict.manyglm.R | 3 ++- R/predict.traitglm.R | 6 +++++- R/residuals.manyglm.R | 9 +++++---- README.md | 5 +++-- man/anova.manyglm.Rd | 4 ++-- man/manyany.Rd | 9 ++++++++- 12 files changed, 97 insertions(+), 78 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic
data on species' distributions and environmental variables as well as species'
description and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>
Diff between letsR versions 2.3 dated 2015-09-17 and 2.4 dated 2015-11-24
DESCRIPTION | 15 +++--- MD5 | 84 +++++++++++++++++------------------ NAMESPACE | 3 - R/getcode.R | 5 +- R/letsR-package.R | 4 - man/IUCN.Rd | 4 - man/PAM.Rd | 4 - man/Phyllomedusa.Rd | 6 +- man/PresenceAbsence.Rd | 32 ++++++------- man/lets.addpoly.Rd | 7 +- man/lets.addvar.Rd | 9 ++- man/lets.classvar.Rd | 19 ++++--- man/lets.correl.Rd | 15 +++--- man/lets.distmat.Rd | 11 ++-- man/lets.field.Rd | 23 +++++---- man/lets.gridirizer.Rd | 3 - man/lets.iucn.Rd | 7 +- man/lets.iucn.ha.Rd | 7 +- man/lets.iucn.his.Rd | 5 +- man/lets.iucncont.Rd | 7 +- man/lets.maplizer.Rd | 17 +++---- man/lets.midpoint.Rd | 11 ++-- man/lets.overlap.Rd | 21 ++++---- man/lets.pamcrop.Rd | 5 +- man/lets.presab.Rd | 56 ++++++++++++----------- man/lets.presab.birds.Rd | 63 +++++++++++++------------- man/lets.presab.grid.Rd | 30 ++++++------ man/lets.presab.points.Rd | 16 +++--- man/lets.rangesize.Rd | 24 +++++----- man/lets.shFilter.Rd | 24 +++++----- man/lets.subsetPAM.Rd | 7 +- man/lets.summarizer.Rd | 15 +++--- man/lets.transf.Rd | 5 +- man/letsR-package.Rd | 44 +++++++++--------- man/plot.PresenceAbsence.Rd | 3 - man/print.PresenceAbsence.Rd | 2 man/print.summary.PresenceAbsence.Rd | 2 man/summary.PresenceAbsence.Rd | 2 man/temp.Rd | 10 ++-- tests/testthat/test-TimLucas.r | 2 tests/testthat/test-lets_iucn.R | 4 - tests/testthat/test-lets_iucn_ha.R | 6 +- tests/testthat/test-lets_iucn_his.R | 6 +- 43 files changed, 337 insertions(+), 308 deletions(-)
Title: Data Pre-Processing and Visualization Functions for
Classification
Description: Data preprocessing techniques for classification. Functions for normalization, handling of missing values,discretization, outlier detection, feature selection, and data visualization are included.
Author: Edgar Acuna and the CASTLE research group at The University of Puerto Rico-Mayaguez
Maintainer: Edgar Acuna <edgar.acuna@upr.edu>
Diff between dprep versions 3.0 dated 2015-11-19 and 3.0.2 dated 2015-11-24
dprep-3.0.2/dprep/DESCRIPTION | 8 ++++---- dprep-3.0.2/dprep/MD5 | 19 +++++++++---------- dprep-3.0.2/dprep/R/discretevar.R | 3 ++- dprep-3.0.2/dprep/R/midpoints1.R | 3 ++- dprep-3.0.2/dprep/man/arboleje1.Rd | 2 +- dprep-3.0.2/dprep/man/cvnaiveBayesd.Rd | 4 ++-- dprep-3.0.2/dprep/man/disc.mentr.Rd | 4 +++- dprep-3.0.2/dprep/man/dprep-package.Rd | 19 +++++++++++++++++-- dprep-3.0.2/dprep/man/mo3.Rd | 3 ++- dprep-3.0.2/dprep/src/Discrete.cpp | 3 ++- dprep-3.0/dprep/build |only 11 files changed, 44 insertions(+), 24 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between cmvnorm versions 1.0-1 dated 2015-02-09 and 1.0-3 dated 2015-11-24
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++------- NAMESPACE | 14 +++++++++++++- R/cmvnorm.R | 31 +++++++++++++++++++++++++++++++ R/onloader.R |only build/vignette.rds |binary inst/doc/complicator.Rnw | 25 ++++++++++++++----------- inst/doc/complicator.pdf |binary man/var.Rd |only vignettes/complicator.Rnw | 25 ++++++++++++++----------- 10 files changed, 84 insertions(+), 33 deletions(-)
Title: Central Limit Theorem Experiments (Theoretical and Simulation)
Description: Central limit theorem experiments presented by data frames or plots. Functions include generating theoretical sample space, corresponding probability, and simulated results as well.
Author: Simiao Ye, Jingning Mei
Maintainer: Simiao Ye <simiao.ye@gmail.com>
Diff between clttools versions 1.1 dated 2015-08-25 and 1.2 dated 2015-11-24
DESCRIPTION | 8 ++--- MD5 | 4 +- R/clttools.R | 94 ++++++++++++----------------------------------------------- 3 files changed, 26 insertions(+), 80 deletions(-)
Title: Bayesian Model Averaging Library
Description: Bayesian model averaging for linear models with a wide choice of (customizable) priors. Built-in priors include coefficient priors (fixed, flexible and hyper-g priors), 5 kinds of model priors, moreover model sampling by enumeration or various MCMC approaches. Post-processing functions allow for inferring posterior inclusion and model probabilities, various moments, coefficient and predictive densities. Plotting functions available for posterior model size, MCMC convergence, predictive and coefficient densities, best models representation, BMA comparison.
Author: Martin Feldkircher and Stefan Zeugner
Maintainer: Stefan Zeugner <bms@zeugner.eu>
Diff between BMS versions 0.3.3 dated 2013-11-22 and 0.3.4 dated 2015-11-24
DESCRIPTION | 15 ++++----- MD5 | 43 +++++++++++++------------- NAMESPACE | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++-- NEWS |only R/BMS-internal.R | 42 ++++++++++++++++++++++++++ R/bms.R | 40 +++++++++++++++++------- R/c.bma.R | 2 + R/estimates.bma.R | 4 +- R/info.bma.R | 4 +- R/z[.bma.R | 6 +-- R/z[.topmod.R | 4 +- R/zzz.R | 33 ++++++++++++++++++-- inst/CITATION | 32 +++++++++++++------ inst/doc/bms.Rnw | 2 - man/BMS-package.Rd | 6 +-- man/bma-class.Rd | 5 ++- man/bms.Rd | 20 +++++++++--- man/coef.bma.Rd | 5 +-- man/summary.bma.Rd | 3 - man/topmod-class.Rd | 3 + man/z[.bma.Rd | 15 ++++----- man/zlm-class.Rd | 8 ++++ vignettes/bms.Rnw | 2 - 23 files changed, 293 insertions(+), 85 deletions(-)
Title: Easy to Use Tools for Common Forms of Random Assignment
Description: Generates random assignments for common experimental
designs: simple, complete, blocked, and clustered.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <ac3242@columbia.edu>
Diff between randomizr versions 0.2.2 dated 2015-03-20 and 0.3.0 dated 2015-11-23
randomizr-0.2.2/randomizr/R/randomizr.r |only randomizr-0.2.2/randomizr/README.md |only randomizr-0.3.0/randomizr/DESCRIPTION | 11 randomizr-0.3.0/randomizr/MD5 | 46 + randomizr-0.3.0/randomizr/NAMESPACE | 13 randomizr-0.3.0/randomizr/R/block_and_cluster_ra.R |only randomizr-0.3.0/randomizr/R/block_ra.R |only randomizr-0.3.0/randomizr/R/cluster_ra.R |only randomizr-0.3.0/randomizr/R/complete_ra.R |only randomizr-0.3.0/randomizr/R/declare_ra.R |only randomizr-0.3.0/randomizr/R/ra_probabilities.R |only randomizr-0.3.0/randomizr/R/simple_ra.R |only randomizr-0.3.0/randomizr/build/vignette.rds |binary randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.R | 92 +-- randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.Rmd | 140 +++-- randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.html | 279 ++++++---- randomizr-0.3.0/randomizr/man/block_and_cluster_ra.Rd |only randomizr-0.3.0/randomizr/man/block_and_cluster_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/block_ra.Rd | 29 - randomizr-0.3.0/randomizr/man/block_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/cluster_ra.Rd | 31 - randomizr-0.3.0/randomizr/man/cluster_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/complete_ra.Rd | 32 - randomizr-0.3.0/randomizr/man/complete_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/conduct_ra.Rd |only randomizr-0.3.0/randomizr/man/declare_ra.Rd |only randomizr-0.3.0/randomizr/man/obtain_condition_probabilities.Rd |only randomizr-0.3.0/randomizr/man/randomizr.Rd | 2 randomizr-0.3.0/randomizr/man/simple_ra.Rd | 25 randomizr-0.3.0/randomizr/man/simple_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/tests |only randomizr-0.3.0/randomizr/vignettes/randomizr_vignette.Rmd | 140 +++-- 32 files changed, 516 insertions(+), 324 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-5 dated 2015-11-20 and 0.1-6 dated 2015-11-23
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/DESP-package.Rd | 4 ++-- src/scsSRL_B.c | 13 +++++++++---- src/scsSolveSOCP.c | 2 +- 6 files changed, 26 insertions(+), 16 deletions(-)
Title: D3 Javascript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.3 dated 2015-10-26 and 0.4 dated 2015-11-23
DESCRIPTION | 10 +- MD5 | 19 ++--- NEWS | 9 ++ R/scatterD3.R | 14 +++ inst/doc/introduction.Rmd | 8 +- inst/doc/introduction.html | 46 ++++++------ inst/htmlwidgets/scatterD3.js | 153 +++++++++++++++++++++++++++--------------- man/clean_var_levels.Rd |only man/scatterD3-shiny.Rd | 2 man/scatterD3.Rd | 1 vignettes/introduction.Rmd | 8 +- 11 files changed, 168 insertions(+), 102 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-2 dated 2015-11-18 and 1.2-3 dated 2015-11-23
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++++--------------------- R/jomo1cat.MCMCchain.R | 2 + R/jomo1cat.R | 2 + R/jomo1con.MCMCchain.R | 2 + R/jomo1con.R | 2 + R/jomo1mix.MCMCchain.R | 3 + R/jomo1mix.R | 3 + R/jomo1rancat.MCMCchain.R | 8 ++++ R/jomo1rancat.R | 8 ++++ R/jomo1rancathr.MCMCchain.R | 8 ++++ R/jomo1rancathr.R | 8 ++++ R/jomo1rancon.MCMCchain.R | 8 ++++ R/jomo1rancon.R | 8 ++++ R/jomo1ranconhr.MCMCchain.R | 8 ++++ R/jomo1ranconhr.R | 8 ++++ R/jomo1ranmix.MCMCchain.R | 9 ++++ R/jomo1ranmix.R | 9 ++++ R/jomo1ranmixhr.MCMCchain.R | 9 ++++ R/jomo1ranmixhr.R | 9 ++++ man/jomo1cat.MCMCchain.Rd | 2 - man/jomo1cat.Rd | 2 - man/jomo1mix.MCMCchain.Rd | 2 - man/jomo1mix.Rd | 2 - man/jomo1ran.MCMCchain.Rd | 2 - man/jomo1ran.Rd | 2 - man/jomo1rancat.MCMCchain.Rd | 4 +- man/jomo1rancat.Rd | 4 +- man/jomo1rancathr.MCMCchain.Rd | 4 +- man/jomo1rancathr.Rd | 4 +- man/jomo1rancon.MCMCchain.Rd | 2 - man/jomo1rancon.Rd | 2 - man/jomo1ranconhr.MCMCchain.Rd | 2 - man/jomo1ranconhr.Rd | 2 - man/jomo1ranmix.MCMCchain.Rd | 4 +- man/jomo1ranmix.Rd | 4 +- man/jomo1ranmixhr.MCMCchain.Rd | 4 +- man/jomo1ranmixhr.Rd | 4 +- 38 files changed, 181 insertions(+), 67 deletions(-)
Title: Flexible Parametric Models for Censored and Truncated Data
Description: Estimation of flexible parametric models for survival data.
Author: Paolo Frumento <paolo.frumento@ki.se>
Maintainer: Paolo Frumento <paolo.frumento@ki.se>
Diff between flexPM versions 1.0 dated 2015-06-08 and 2.0 dated 2015-11-23
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 34 ++ R/flexPM.R | 621 ++++++++++++++++++++++++------------------------- man/flexPM-internal.Rd | 19 - man/flexPM.Rd | 109 ++++---- man/predict.flexPM.Rd | 7 7 files changed, 420 insertions(+), 392 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-58 dated 2015-10-22 and 6.0-62 dated 2015-11-23
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++----------------------- NAMESPACE | 2 + R/adaptive.R | 47 ++++++++++++++++++++++++++++-------------- R/avNNet.R | 8 ++++++- R/ggplot.R | 8 +++---- R/learning_curve.R |only R/misc.R | 2 - R/plot.varImp.train.R | 34 ++++++++++++++++++++++++++++++ R/print.train.R | 1 R/train.default.R | 9 +++++++- inst/NEWS.Rd | 17 +++++++++++++++ inst/models/models.RData |binary man/avNNet.Rd | 5 +++- man/confusionMatrix.Rd | 2 - man/extractPrediction.Rd | 2 - man/ga_functions.Rd | 2 - man/gafs.default.Rd | 6 +++-- man/learning_curve.Rd |only man/models.Rd | 37 +++++++++++++++++++++++++++++++++ man/plot.rfe.Rd | 9 ++++---- man/plot.train.Rd | 9 +++++--- man/plot.varImp.train.Rd | 11 +++++++-- man/preProcess.Rd | 2 - man/safs.default.Rd | 4 ++- man/sensitivity.Rd | 2 - man/train.Rd | 2 - man/trainControl.Rd | 4 ++- 28 files changed, 213 insertions(+), 74 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects mergers under different competitive regimes.
Author: Charles Taragin and Michael Sandfort
Maintainer: Charles Taragin <charles.taragin@usdoj.gov>
Diff between antitrust versions 0.95 dated 2015-11-19 and 0.95.1 dated 2015-11-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/manual.Rnw | 2 +- inst/doc/manual.pdf |binary vignettes/manual.Rnw | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: The Residual-Based Predictiveness Curve
Description: The RBP curve is a visual tool to assess the
performance of prediction models.
Author: Giuseppe Casalicchio, Bernd Bischl
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between RBPcurve versions 1.0-20 dated 2015-01-09 and 1.0-33 dated 2015-11-23
RBPcurve-1.0-20/RBPcurve/README.md |only RBPcurve-1.0-33/RBPcurve/DESCRIPTION | 17 ++--- RBPcurve-1.0-33/RBPcurve/MD5 | 31 ++++------ RBPcurve-1.0-33/RBPcurve/NAMESPACE | 11 +++ RBPcurve-1.0-33/RBPcurve/R/addGoodCalib.R | 2 RBPcurve-1.0-33/RBPcurve/R/addPrevalence.R | 5 - RBPcurve-1.0-33/RBPcurve/R/addRates.R | 20 ++++-- RBPcurve-1.0-33/RBPcurve/R/addWellCalib.R | 80 +++++++++++++++++--------- RBPcurve-1.0-33/RBPcurve/R/plotRBPCurve.R | 29 ++++++--- RBPcurve-1.0-33/RBPcurve/R/zzz.R | 2 RBPcurve-1.0-33/RBPcurve/man/addGoodCalib.Rd | 6 - RBPcurve-1.0-33/RBPcurve/man/addPEV.Rd | 2 RBPcurve-1.0-33/RBPcurve/man/addPrevalence.Rd | 9 ++ RBPcurve-1.0-33/RBPcurve/man/addRates.Rd | 23 +++++-- RBPcurve-1.0-33/RBPcurve/man/addWellCalib.Rd | 23 ++++--- RBPcurve-1.0-33/RBPcurve/man/makeRBPObj.Rd | 6 - RBPcurve-1.0-33/RBPcurve/man/plotRBPCurve.Rd | 21 ++++-- 17 files changed, 188 insertions(+), 99 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-16 0.7.3
2015-07-04 0.6.1
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett@lshtm.ac.uk>
Diff between smcfcs versions 1.1.0 dated 2015-08-21 and 1.1.1 dated 2015-11-23
DESCRIPTION | 7 ++++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/smcfcs.r | 15 +++++++++++---- README.md | 6 ++++++ man/ex_compet.Rd | 2 +- man/ex_coxquad.Rd | 2 +- man/ex_lininter.Rd | 2 +- man/ex_linquad.Rd | 2 +- man/ex_logisticquad.Rd | 2 +- man/smcfcs.Rd | 4 ++-- vignettes/smcfcs-vignette.Rmd | 2 +- 12 files changed, 41 insertions(+), 27 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.2 dated 2015-10-12 and 1.3 dated 2015-11-23
sjmisc-1.2/sjmisc/man/to_sjPlot.Rd |only sjmisc-1.3/sjmisc/DESCRIPTION | 29 - sjmisc-1.3/sjmisc/MD5 | 210 +++---- sjmisc-1.3/sjmisc/NAMESPACE | 231 ++++---- sjmisc-1.3/sjmisc/NEWS | 18 sjmisc-1.3/sjmisc/R/add_labels.R | 62 +- sjmisc-1.3/sjmisc/R/as_labelled.R | 3 sjmisc-1.3/sjmisc/R/copy_labels.R | 4 sjmisc-1.3/sjmisc/R/cronb.R | 2 sjmisc-1.3/sjmisc/R/dicho.R | 25 sjmisc-1.3/sjmisc/R/fill_labels.R | 11 sjmisc-1.3/sjmisc/R/get_label.R | 233 ++++---- sjmisc-1.3/sjmisc/R/get_labels.R | 517 +++++++++--------- sjmisc-1.3/sjmisc/R/get_values.R | 2 sjmisc-1.3/sjmisc/R/group_var.R | 52 - sjmisc-1.3/sjmisc/R/helpfunctions.R | 263 ++++----- sjmisc-1.3/sjmisc/R/is_even.R | 3 sjmisc-1.3/sjmisc/R/is_odd.R | 3 sjmisc-1.3/sjmisc/R/labelled.R | 6 sjmisc-1.3/sjmisc/R/mic.R | 12 sjmisc-1.3/sjmisc/R/rec.R | 38 + sjmisc-1.3/sjmisc/R/ref_lvl.R |only sjmisc-1.3/sjmisc/R/reliab_test.R | 11 sjmisc-1.3/sjmisc/R/remove_all_labels.R |only sjmisc-1.3/sjmisc/R/remove_labels.R | 126 +++- sjmisc-1.3/sjmisc/R/replace_na.R | 136 +++- sjmisc-1.3/sjmisc/R/se.R | 182 +++--- sjmisc-1.3/sjmisc/R/set_label.R | 346 ++++++------ sjmisc-1.3/sjmisc/R/set_labels.R | 805 +++++++++++++++-------------- sjmisc-1.3/sjmisc/R/set_na.R | 46 + sjmisc-1.3/sjmisc/R/split_var.R |only sjmisc-1.3/sjmisc/R/to_factor.R | 271 +++++---- sjmisc-1.3/sjmisc/R/to_label.R | 2 sjmisc-1.3/sjmisc/R/to_value.R | 8 sjmisc-1.3/sjmisc/R/trim.R | 3 sjmisc-1.3/sjmisc/R/unlabel.R | 123 ++-- sjmisc-1.3/sjmisc/R/word_wrap.R | 123 ++-- sjmisc-1.3/sjmisc/R/zap_labels.R | 6 sjmisc-1.3/sjmisc/README.md | 19 sjmisc-1.3/sjmisc/man/add_labels.Rd | 38 - sjmisc-1.3/sjmisc/man/as_labelled.Rd | 7 sjmisc-1.3/sjmisc/man/chisq_gof.Rd | 3 sjmisc-1.3/sjmisc/man/cod.Rd | 3 sjmisc-1.3/sjmisc/man/converge_ok.Rd | 105 +-- sjmisc-1.3/sjmisc/man/copy_labels.Rd | 5 sjmisc-1.3/sjmisc/man/cramer.Rd | 7 sjmisc-1.3/sjmisc/man/cronb.Rd | 4 sjmisc-1.3/sjmisc/man/cv.Rd | 3 sjmisc-1.3/sjmisc/man/dicho.Rd | 11 sjmisc-1.3/sjmisc/man/efc.Rd | 3 sjmisc-1.3/sjmisc/man/eta_sq.Rd | 3 sjmisc-1.3/sjmisc/man/fill_labels.Rd | 5 sjmisc-1.3/sjmisc/man/frq.Rd | 3 sjmisc-1.3/sjmisc/man/get_label.Rd | 154 ++--- sjmisc-1.3/sjmisc/man/get_labels.Rd | 322 +++++------ sjmisc-1.3/sjmisc/man/get_na.Rd | 3 sjmisc-1.3/sjmisc/man/get_na_flags.Rd | 3 sjmisc-1.3/sjmisc/man/get_values.Rd | 4 sjmisc-1.3/sjmisc/man/group_labels.Rd | 10 sjmisc-1.3/sjmisc/man/group_str.Rd | 5 sjmisc-1.3/sjmisc/man/group_var.Rd | 25 sjmisc-1.3/sjmisc/man/hoslem_gof.Rd | 3 sjmisc-1.3/sjmisc/man/icc.Rd | 3 sjmisc-1.3/sjmisc/man/is_crossed.Rd | 3 sjmisc-1.3/sjmisc/man/is_empty.Rd | 3 sjmisc-1.3/sjmisc/man/is_even.Rd | 6 sjmisc-1.3/sjmisc/man/is_labelled.Rd | 2 sjmisc-1.3/sjmisc/man/is_nested.Rd | 3 sjmisc-1.3/sjmisc/man/is_num_fac.Rd | 3 sjmisc-1.3/sjmisc/man/is_odd.Rd | 6 sjmisc-1.3/sjmisc/man/labelled.Rd | 11 sjmisc-1.3/sjmisc/man/levene_test.Rd | 3 sjmisc-1.3/sjmisc/man/mean_n.Rd | 5 sjmisc-1.3/sjmisc/man/mic.Rd | 17 sjmisc-1.3/sjmisc/man/mwu.Rd | 3 sjmisc-1.3/sjmisc/man/phi.Rd | 7 sjmisc-1.3/sjmisc/man/pseudo_r2.Rd | 3 sjmisc-1.3/sjmisc/man/read_sas.Rd | 2 sjmisc-1.3/sjmisc/man/read_spss.Rd | 3 sjmisc-1.3/sjmisc/man/read_stata.Rd | 2 sjmisc-1.3/sjmisc/man/rec.Rd | 17 sjmisc-1.3/sjmisc/man/recode_to.Rd | 3 sjmisc-1.3/sjmisc/man/ref_lvl.Rd |only sjmisc-1.3/sjmisc/man/reliab_test.Rd | 7 sjmisc-1.3/sjmisc/man/remove_all_labels.Rd |only sjmisc-1.3/sjmisc/man/remove_labels.Rd | 44 + sjmisc-1.3/sjmisc/man/replace_na.Rd | 11 sjmisc-1.3/sjmisc/man/rmse.Rd | 3 sjmisc-1.3/sjmisc/man/se.Rd | 6 sjmisc-1.3/sjmisc/man/set_label.Rd | 220 ++++--- sjmisc-1.3/sjmisc/man/set_labels.Rd | 280 +++++----- sjmisc-1.3/sjmisc/man/set_na.Rd | 28 - sjmisc-1.3/sjmisc/man/sjmisc-package.Rd | 4 sjmisc-1.3/sjmisc/man/split_var.Rd |only sjmisc-1.3/sjmisc/man/std_beta.Rd | 3 sjmisc-1.3/sjmisc/man/str_pos.Rd | 5 sjmisc-1.3/sjmisc/man/table_values.Rd | 3 sjmisc-1.3/sjmisc/man/to_factor.Rd | 191 +++--- sjmisc-1.3/sjmisc/man/to_label.Rd | 3 sjmisc-1.3/sjmisc/man/to_na.Rd | 3 sjmisc-1.3/sjmisc/man/to_value.Rd | 7 sjmisc-1.3/sjmisc/man/trim.Rd | 8 sjmisc-1.3/sjmisc/man/unlabel.Rd |only sjmisc-1.3/sjmisc/man/weight.Rd | 7 sjmisc-1.3/sjmisc/man/weight2.Rd | 3 sjmisc-1.3/sjmisc/man/word_wrap.Rd | 6 sjmisc-1.3/sjmisc/man/write_spss.Rd | 4 sjmisc-1.3/sjmisc/man/write_stata.Rd | 4 sjmisc-1.3/sjmisc/man/zap_labels.Rd | 7 sjmisc-1.3/sjmisc/man/zap_unlabelled.Rd | 7 110 files changed, 3029 insertions(+), 2600 deletions(-)
Title: Nonparametric Simulation of RNA-Seq Data
Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.
Author: Samuel Benidt
Maintainer: Samuel Benidt <sgbenidt@gmail.com>
Diff between SimSeq versions 1.3.0 dated 2015-03-07 and 1.4.0 dated 2015-11-23
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 4 +++- NEWS | 3 +++ R/SimData.R | 2 +- inst/CITATION | 4 +++- man/CalcPvalWilcox.Rd | 2 +- man/SimData.Rd | 10 +++++----- man/SimSeq-package.Rd | 6 +++--- man/SortData.Rd | 2 +- man/kidney.Rd | 6 +++--- 11 files changed, 38 insertions(+), 31 deletions(-)
Title: Quantile Universal Threshold
Description: Selection of a threshold parameter for GLM-lasso to obtain a sparse model
with a good compromise between high true positive rate and low false discovery rate.
Author: Jairo Diaz, Sylvain Sardy, Caroline Giacobino, Nick Hengartner.
Maintainer: Jairo Diaz <jairo.diaz@unige.ch>
Diff between qut versions 1.0 dated 2015-09-20 and 1.0.1 dated 2015-11-23
DESCRIPTION | 6 - MD5 | 15 ++-- NAMESPACE | 5 - R/coef.qut.R |only R/lambdaqut.R | 30 ++++---- R/qut.R | 198 +++++++++++++++++++++++++++++++---------------------- man/lambdaqut.Rd | 6 + man/predict.qut.Rd | 8 +- man/qut.Rd | 15 ++-- 9 files changed, 168 insertions(+), 115 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.1.1 dated 2015-09-30 and 1.2.0 dated 2015-11-23
pnea-1.1.1/pnea/build |only pnea-1.2.0/pnea/DESCRIPTION | 10 - pnea-1.2.0/pnea/MD5 | 22 +-- pnea-1.2.0/pnea/NAMESPACE | 1 pnea-1.2.0/pnea/R/pnea.R | 260 +++++++++++++++++++++++------------- pnea-1.2.0/pnea/data/yeast.RData |binary pnea-1.2.0/pnea/man/netfromadj.Rd |only pnea-1.2.0/pnea/man/plot.pnea.Rd | 11 - pnea-1.2.0/pnea/man/pnea-package.Rd | 4 pnea-1.2.0/pnea/man/pnea.Rd | 92 ++++++------ pnea-1.2.0/pnea/man/print.pnea.Rd | 6 pnea-1.2.0/pnea/man/summary.pnea.Rd | 11 - pnea-1.2.0/pnea/man/yeast.Rd | 6 13 files changed, 249 insertions(+), 174 deletions(-)
Title: An R Pandoc Writer
Description: Contains some functions catching all messages, stdout and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in pandoc's markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex pandoc documents to e.g. HTML, PDF, docx or odt. This
latter reporting feature is supported in brew syntax or with a custom
reference class with a smarty caching backend.
Author: Gergely Daróczi <daroczig@rapporter.net>, Roman Tsegelskyi
<roman.tsegelskyi@gmail.com>
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between pander versions 0.5.2 dated 2015-05-18 and 0.6.0 dated 2015-11-23
pander-0.5.2/pander/man/pander.option.Rd |only pander-0.5.2/pander/man/pander.return.Rd |only pander-0.6.0/pander/DESCRIPTION | 19 pander-0.6.0/pander/MD5 | 286 +- pander-0.6.0/pander/NAMESPACE | 62 pander-0.6.0/pander/NEWS | 73 pander-0.6.0/pander/R/R5.R | 42 pander-0.6.0/pander/R/S3.R | 1466 +++++++++++---- pander-0.6.0/pander/R/brew.R | 182 + pander-0.6.0/pander/R/convert.R | 76 pander-0.6.0/pander/R/ess-functions.R | 11 pander-0.6.0/pander/R/evals.R | 784 +++++--- pander-0.6.0/pander/R/graph.R | 93 pander-0.6.0/pander/R/helpers.R | 232 +- pander-0.6.0/pander/R/options.R | 74 pander-0.6.0/pander/R/pandoc.R | 714 ++++--- pander-0.6.0/pander/README.md | 230 +- pander-0.6.0/pander/build |only pander-0.6.0/pander/inst/README.brew | 152 + pander-0.6.0/pander/inst/doc |only pander-0.6.0/pander/inst/tests/test-S3.R | 956 ++++++++- pander-0.6.0/pander/inst/tests/test-brew.R | 49 pander-0.6.0/pander/inst/tests/test-convert.R |only pander-0.6.0/pander/inst/tests/test-evals.R | 336 ++- pander-0.6.0/pander/inst/tests/test-helpers.R | 87 pander-0.6.0/pander/inst/tests/test-missing.R | 16 pander-0.6.0/pander/man/Pandoc-class.Rd | 2 pander-0.6.0/pander/man/Pandoc.brew.Rd | 2 pander-0.6.0/pander/man/Pandoc.convert.Rd | 4 pander-0.6.0/pander/man/add.blank.lines.Rd | 2 pander-0.6.0/pander/man/add.lattice.grid.Rd | 2 pander-0.6.0/pander/man/add.lattice.xsubticks.Rd | 2 pander-0.6.0/pander/man/add.minor.ticks.Rd | 2 pander-0.6.0/pander/man/add.significance.stars.Rd | 2 pander-0.6.0/pander/man/brew.Rd | 2 pander-0.6.0/pander/man/cache.off.Rd | 2 pander-0.6.0/pander/man/check_caption.Rd | 2 pander-0.6.0/pander/man/check_digits.Rd |only pander-0.6.0/pander/man/coef_mat.Rd |only pander-0.6.0/pander/man/emphasize.rows.Rd | 20 pander-0.6.0/pander/man/eval.msgs.Rd | 4 pander-0.6.0/pander/man/evals.Rd | 74 pander-0.6.0/pander/man/evalsOptions.Rd | 11 pander-0.6.0/pander/man/get.alignment.Rd | 2 pander-0.6.0/pander/man/get.caption.Rd | 2 pander-0.6.0/pander/man/get.emphasize.Rd | 2 pander-0.6.0/pander/man/get.storage.Rd | 2 pander-0.6.0/pander/man/has.rownames.Rd | 2 pander-0.6.0/pander/man/multitable.Rd |only pander-0.6.0/pander/man/openFileInOS.Rd | 2 pander-0.6.0/pander/man/p.Rd | 31 pander-0.6.0/pander/man/pander.Arima.Rd |only pander-0.6.0/pander/man/pander.CrossTable.Rd | 9 pander-0.6.0/pander/man/pander.Date.Rd | 2 pander-0.6.0/pander/man/pander.NULL.Rd | 2 pander-0.6.0/pander/man/pander.POSIXct.Rd | 2 pander-0.6.0/pander/man/pander.POSIXlt.Rd | 2 pander-0.6.0/pander/man/pander.Rd | 3 pander-0.6.0/pander/man/pander.anova.Rd | 7 pander-0.6.0/pander/man/pander.aov.Rd | 2 pander-0.6.0/pander/man/pander.aovlist.Rd | 2 pander-0.6.0/pander/man/pander.call.Rd | 2 pander-0.6.0/pander/man/pander.cast_df.Rd | 2 pander-0.6.0/pander/man/pander.character.Rd | 2 pander-0.6.0/pander/man/pander.clogit.Rd | 2 pander-0.6.0/pander/man/pander.coxph.Rd | 2 pander-0.6.0/pander/man/pander.cph.Rd |only pander-0.6.0/pander/man/pander.data.frame.Rd | 2 pander-0.6.0/pander/man/pander.default.Rd | 2 pander-0.6.0/pander/man/pander.density.Rd | 2 pander-0.6.0/pander/man/pander.describe.Rd | 10 pander-0.6.0/pander/man/pander.evals.Rd | 2 pander-0.6.0/pander/man/pander.factor.Rd | 2 pander-0.6.0/pander/man/pander.formula.Rd | 2 pander-0.6.0/pander/man/pander.ftable.Rd | 2 pander-0.6.0/pander/man/pander.function.Rd | 2 pander-0.6.0/pander/man/pander.glm.Rd | 2 pander-0.6.0/pander/man/pander.glm.rms.Rd |only pander-0.6.0/pander/man/pander.gtable.Rd |only pander-0.6.0/pander/man/pander.htest.Rd | 2 pander-0.6.0/pander/man/pander.image.Rd | 2 pander-0.6.0/pander/man/pander.irts.Rd |only pander-0.6.0/pander/man/pander.list.Rd | 2 pander-0.6.0/pander/man/pander.lm.Rd | 6 pander-0.6.0/pander/man/pander.lme.Rd | 6 pander-0.6.0/pander/man/pander.logical.Rd | 2 pander-0.6.0/pander/man/pander.lrm.Rd |only pander-0.6.0/pander/man/pander.manova.Rd |only pander-0.6.0/pander/man/pander.matrix.Rd | 2 pander-0.6.0/pander/man/pander.microbenchmark.Rd | 4 pander-0.6.0/pander/man/pander.mtable.Rd | 2 pander-0.6.0/pander/man/pander.name.Rd |only pander-0.6.0/pander/man/pander.nls.Rd |only pander-0.6.0/pander/man/pander.numeric.Rd | 2 pander-0.6.0/pander/man/pander.ols.Rd |only pander-0.6.0/pander/man/pander.orm.Rd |only pander-0.6.0/pander/man/pander.polr.Rd |only pander-0.6.0/pander/man/pander.prcomp.Rd | 2 pander-0.6.0/pander/man/pander.randomForest.Rd |only pander-0.6.0/pander/man/pander.rapport.Rd | 2 pander-0.6.0/pander/man/pander.rlm.Rd | 2 pander-0.6.0/pander/man/pander.sessionInfo.Rd | 2 pander-0.6.0/pander/man/pander.smooth.spline.Rd | 2 pander-0.6.0/pander/man/pander.stat.table.Rd | 2 pander-0.6.0/pander/man/pander.summary.aov.Rd | 2 pander-0.6.0/pander/man/pander.summary.aovlist.Rd | 2 pander-0.6.0/pander/man/pander.summary.glm.Rd | 2 pander-0.6.0/pander/man/pander.summary.lm.Rd | 2 pander-0.6.0/pander/man/pander.summary.lme.Rd |only pander-0.6.0/pander/man/pander.summary.manova.Rd |only pander-0.6.0/pander/man/pander.summary.nls.Rd |only pander-0.6.0/pander/man/pander.summary.polr.Rd |only pander-0.6.0/pander/man/pander.summary.prcomp.Rd | 2 pander-0.6.0/pander/man/pander.summary.rms.Rd |only pander-0.6.0/pander/man/pander.summary.survreg.Rd |only pander-0.6.0/pander/man/pander.summary.table.Rd |only pander-0.6.0/pander/man/pander.survdiff.Rd | 2 pander-0.6.0/pander/man/pander.survfit.Rd | 4 pander-0.6.0/pander/man/pander.survreg.Rd |only pander-0.6.0/pander/man/pander.table.Rd | 2 pander-0.6.0/pander/man/pander.tabular.Rd | 20 pander-0.6.0/pander/man/pander.ts.Rd | 2 pander-0.6.0/pander/man/pander.vector.Rd | 2 pander-0.6.0/pander/man/pander.zoo.Rd | 2 pander-0.6.0/pander/man/panderOptions.Rd | 11 pander-0.6.0/pander/man/pander_return.Rd | 2 pander-0.6.0/pander/man/pandoc.date.return.Rd | 2 pander-0.6.0/pander/man/pandoc.emphasis.return.Rd | 2 pander-0.6.0/pander/man/pandoc.footnote.return.Rd | 2 pander-0.6.0/pander/man/pandoc.formula.return.Rd | 4 pander-0.6.0/pander/man/pandoc.header.return.Rd | 2 pander-0.6.0/pander/man/pandoc.horizontal.rule.return.Rd | 2 pander-0.6.0/pander/man/pandoc.image.return.Rd | 2 pander-0.6.0/pander/man/pandoc.indent.Rd | 2 pander-0.6.0/pander/man/pandoc.link.return.Rd | 2 pander-0.6.0/pander/man/pandoc.list.return.Rd | 2 pander-0.6.0/pander/man/pandoc.p.return.Rd | 2 pander-0.6.0/pander/man/pandoc.strikeout.return.Rd | 2 pander-0.6.0/pander/man/pandoc.strong.return.Rd | 2 pander-0.6.0/pander/man/pandoc.table.return.Rd | 47 pander-0.6.0/pander/man/pandoc.title.return.Rd | 2 pander-0.6.0/pander/man/pandoc.verbatim.return.Rd | 2 pander-0.6.0/pander/man/redraw.recordedplot.Rd | 2 pander-0.6.0/pander/man/redrawPlot.Rd | 8 pander-0.6.0/pander/man/remove.extra.newlines.Rd | 2 pander-0.6.0/pander/man/repChar.Rd | 2 pander-0.6.0/pander/man/set.alignment.Rd | 2 pander-0.6.0/pander/man/set.caption.Rd | 2 pander-0.6.0/pander/man/splitLine.Rd | 8 pander-0.6.0/pander/man/trim.spaces.Rd | 2 pander-0.6.0/pander/man/wrap.Rd | 6 pander-0.6.0/pander/vignettes |only 152 files changed, 4458 insertions(+), 1939 deletions(-)
Title: Kaplan-Meier Estimator with Constraints for Right Censored Data
-- a Recursive Computational Algorithm
Description: Linearly constrained Kaplan-Meier estimator for right censored data. This version does empirical likelihood ratio test with right censored data with linear type constraint and hypothesis testing for coefficients in accelerated failure time model.
Author: Yifan Yang [aut,cre], Mai Zhou [aut]
Maintainer: Yifan Yang <yifan.yang@uky.edu>
Diff between kmc versions 0.1-2 dated 2013-12-25 and 0.2-2 dated 2015-11-23
DESCRIPTION | 20 +++--- MD5 | 25 ++++---- NAMESPACE | 7 +- R/RcppExport.R | 30 +++++++++ R/kmc.R | 106 ++++++++++++++++++++++++++++++---- inst |only man/kmc.bjtest.Rd |only man/kmc.solve.Rd | 25 +++----- man/plotkmc.Rd | 27 +++----- man/print.kmcS3.Rd | 25 ++------ src/Makevars.win | 6 - src/RcppExport.cpp | 17 +++++ src/common.h |only src/common_kmc.h |only src/kmc.cpp | 161 ++++++++++++++++++++++++++++++++++++++++++----------- src/surv2.c |only 16 files changed, 335 insertions(+), 114 deletions(-)
More information about ForecastCombinations at CRAN
Permanent link
Title: Probabilities for Pedigrees Given DNA Data
Description:
An interface to the core Familias functions (www.familias.name),
which are programmed in C++.
Author: Petter Mostad, Thore Egeland, Ivar Simonsson
Maintainer: Petter Mostad <mostad@chalmers.se>
Diff between Familias versions 2.2 dated 2015-03-09 and 2.3 dated 2015-11-23
DESCRIPTION | 12 +- MD5 | 24 ++-- NAMESPACE | 2 R/ConvertPed.R | 4 R/FamiliasLocus.R | 204 +++++++++++++++++++++++++++++++++--------- R/FamiliasPedigree.R | 16 +-- R/FamiliasPosterior.R | 40 ++++---- R/FamiliasPrior.R | 26 ++--- R/plot.FamiliasPedigree.R | 2 data/NorwegianFrequencies.rda |binary man/Familias-package.Rd | 6 - man/FamiliasLocus.Rd | 65 +++++++------ man/FamiliasPosterior.Rd | 30 +++--- 13 files changed, 280 insertions(+), 151 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.0 dated 2015-11-12 and 1.5 dated 2015-11-23
DESCRIPTION | 6 ++-- MD5 | 56 ++++++++++++++++++++++----------------------- R/spml.reg.R | 17 ++++++++----- man/Arotation.Rd | 6 ++-- man/Directional-package.Rd | 2 - man/f.rbing.Rd | 5 +--- man/fb.saddle.Rd | 2 - man/kent.datacontour.Rd | 4 +-- man/kent.mle.Rd | 6 ++-- man/meandir.test.Rd | 4 +-- man/mix.vmf.Rd | 10 ++++---- man/mixvmf.contour.Rd | 14 +++++------ man/rayleigh.Rd | 4 +-- man/rbingham.Rd | 4 +-- man/rfb.Rd | 22 ++++++++--------- man/rmixvmf.Rd | 10 ++++---- man/rot.matrix.Rd | 6 ++-- man/rotation.Rd | 10 ++++---- man/rvmf.Rd | 4 +-- man/spher.reg.Rd | 28 +++++++++++----------- man/spherconc.tet.Rd | 4 +-- man/spml.reg.Rd | 10 ++++++-- man/vm.kde.Rd | 10 ++++---- man/vmf.da.Rd | 4 +-- man/vmf.kde.Rd | 8 +++--- man/vmf.kerncontour.Rd | 6 ++-- man/vmfkde.tune.Rd | 3 -- man/vmfkde.tune_2.Rd | 3 -- man/vmkde.tune_2.Rd | 2 - 29 files changed, 139 insertions(+), 131 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where
blocks can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each
set of nested blocks optimized within the levels of any existing higher-level
blocks. Block sizes are equal if the number of blocks exactly divides the number
of plots, otherwise they differ by at most one plot. The design output is a
data table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.8 dated 2015-10-11 and 1.9 dated 2015-11-23
blocksdesign-1.8/blocksdesign/R/pairwise_effics.r |only blocksdesign-1.8/blocksdesign/man/efficiencies.Rd |only blocksdesign-1.9/blocksdesign/DESCRIPTION | 23 blocksdesign-1.9/blocksdesign/MD5 | 18 blocksdesign-1.9/blocksdesign/NAMESPACE | 3 blocksdesign-1.9/blocksdesign/R/blocks.r | 458 ++++++-------- blocksdesign-1.9/blocksdesign/R/blocksdesign-package.r | 52 - blocksdesign-1.9/blocksdesign/R/upper_bounds.r | 109 +-- blocksdesign-1.9/blocksdesign/man/blocks.Rd | 79 +- blocksdesign-1.9/blocksdesign/man/blocksdesign-package.Rd | 62 - blocksdesign-1.9/blocksdesign/man/upper_bounds.Rd | 22 11 files changed, 393 insertions(+), 433 deletions(-)
Title: Aggregate Numeric, Date and Categorical Variables by an ID
Description: Convenience functions for aggregating data frame. Currently mean, sum and variance are supported. For Date variables, recency and duration are supported. There is also support for dummy variables in predictive contexts.
Author: Matthias Bogaert, Michel Ballings, Dirk Van den Poel
Maintainer: Matthias Bogaert <matthias.bogaert@ugent.be>
Diff between AggregateR versions 0.0.1 dated 2015-10-01 and 0.0.2 dated 2015-11-23
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- R/Aggregate.R | 53 +++++++++++++++++++++++++++++++++++++++++------------ inst/NEWS | 4 ++++ man/Aggregate.Rd | 14 ++++++++++---- 6 files changed, 68 insertions(+), 29 deletions(-)
Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for Cox's partial likelihood.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between isoph versions 0.3 dated 2015-11-17 and 0.4 dated 2015-11-22
DESCRIPTION | 10 ++++---- MD5 | 15 ++++++------ R/isoph.R | 19 +++++++++------ R/isoph.td.R | 57 +++++++++++------------------------------------ R/isoph.ti.R | 61 +++++++++++++-------------------------------------- R/picm.R |only R/print.isoph.R | 4 +-- man/isoph-package.Rd | 6 ++--- man/isoph.Rd | 49 +++++++++++++++++++--------------------- 9 files changed, 82 insertions(+), 139 deletions(-)
Title: A Comprehensive, General Purpose Population Genetics Analysis
Package
Description: Allows the calculation of both genetic diversity partition
statistics, genetic differentiation statistics, and locus informativeness
for ancestry assignment.
It also provides users with various option to calculate
bootstrapped 95\% confidence intervals both across loci,
for pairwise population comparisons, and to plot these results interactively.
Parallel computing capabilities and pairwise results without
bootstrapping are provided.
Weir and Cockerham's 1984 F-statistics are also calculated.
Various plotting features are also provided, as well as Chi-square tests of
genetic heterogeneity are also provided.
Functionality for the calculation of various diversity parameters is
possible for RAD-seq derived SNP data sets containing thousands of marker loci.
A shiny application for the development of microsatellite multiplexes is
also available.
Author: Kevin Keenan <kkeenan02@qub.ac.uk>
Maintainer: Kevin Keenan <kkeenan02@qub.ac.uk>
Diff between diveRsity versions 1.9.73 dated 2014-12-22 and 1.9.89 dated 2015-11-22
DESCRIPTION | 41 MD5 | 88 - NAMESPACE | 68 R/RcppExports.R | 114 - R/arSample.R |only R/basicStats.R |only R/diffCalc.R | 2503 ++++++++++++++-------------- R/diffPlot.R | 741 ++++---- R/divBasic.R | 1244 +++++++------- R/divMigrate.R | 1126 ++++++------ R/divMigrateOnline.R | 455 ++--- R/divMigrateOnline_test.R |only R/divRatio.R | 1269 +++++++------- R/fastDivPart.R | 3725 +++++++++++++++++++++---------------------- R/fstOnly.R | 773 -------- R/gpSampler.R | 24 R/haploDiv.R | 12 R/inCalc.R | 552 +++--- R/plotter.R | 811 ++++----- R/polyIn.R | 349 ++-- R/rarefactor.R |only R/regroup.R |only R/snp2gen.R | 203 -- R/writeBoot.R | 1839 ++++++++++----------- build/vignette.rds |binary data/pop_stats.rda |binary inst/microPlexer/server.R | 768 ++++---- man/allCount.Rd |only man/arSample.Rd |only man/basicStats.Rd |only man/bigDivPart.Rd | 158 - man/bsHetCalc.Rd |only man/chiCalc.Rd | 12 man/diffCalc.Rd | 202 +- man/divBasic.Rd | 6 man/divMigrateOnline.Rd | 4 man/divMigrateOnline_test.Rd |only man/divPart.Rd | 14 man/divRatio.Rd | 12 man/expHet.Rd |only man/fastDivPart.Rd | 14 man/haploDiv.Rd | 4 man/hweTab.Rd |only man/inCalc.Rd | 14 man/obsHet.Rd |only man/polyIn.Rd | 52 man/rarefactor.Rd |only man/regroup.Rd |only man/snp2gen.Rd | 62 src/RcppExports.cpp | 235 +- src/allCount.cpp |only src/bsHetCalc.cpp |only src/expHet.cpp |only src/hweTab.cpp |only src/obsHet.cpp |only 55 files changed, 8414 insertions(+), 9080 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-07 1.0
Title: Resource Selection (Probability) Functions for Use-Availability
Data
Description: Resource Selection (Probability) Functions for
use-availability wildlife data as described in
Lele and Keim (2006, Ecology 87, 3021--3028),
and Lele (2009, J. Wildlife Management 73, 122--127).
Author: Subhash R. Lele, Jonah L. Keim, Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between ResourceSelection versions 0.2-4 dated 2014-05-20 and 0.2-5 dated 2015-11-22
DESCRIPTION | 14 - MD5 | 68 ++++---- NAMESPACE | 53 +++--- R/CAIC.R | 6 R/CAIC.default.R | 60 +++---- R/confint.rsf.R | 76 ++++----- R/fitted.rsf.R | 20 +- R/hoslem.test.R | 42 ++--- R/kdepairs.R | 6 R/kdepairs.default.R | 93 +++++------ R/kdepairs.rsf.R | 12 - R/logLik.rsf.R | 18 +- R/makeUsedAvail.R | 4 R/makeUsedAvail.default.R | 30 +-- R/makeUsedAvail.formula.R | 34 ++-- R/model.frame.rsf.R | 12 - R/model.matrix.rsf.R | 18 +- R/plot.rsf.R | 62 +++---- R/predict.rsf.R | 94 ++++++----- R/print.rsf.R | 66 ++++---- R/print.summary.rsf.R | 108 ++++++------- R/rsf.R | 130 ++++++++-------- R/rsf.fit.R | 288 ++++++++++++++++++------------------ R/rspf.R | 128 ++++++++-------- R/summary.rsf.R | 100 ++++++------ R/vcov.rsf.R | 58 +++---- inst/ChangeLog | 129 +++++++++------- man/CAIC.Rd | 160 ++++++++++---------- man/ResourceSelection-package.Rd | 72 ++++----- man/goats.Rd | 112 +++++++------- man/hoslem.test.Rd | 114 +++++++------- man/kdepairs.Rd | 102 ++++++------- man/makeUsedAvail.Rd | 100 ++++++------ man/rsf.Rd | 306 +++++++++++++++++++-------------------- man/simulateUsedAvail.Rd | 92 +++++------ 35 files changed, 1409 insertions(+), 1378 deletions(-)
More information about ResourceSelection at CRAN
Permanent link
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.4 dated 2015-11-15 and 1.7.5 dated 2015-11-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rcbalance.R | 8 ++++---- man/rcbalance-package.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data collected in an experimental design for statistical
analysis (e.g., analysis of variance ;ANOVA) by taking the individual data
files and preparing one table that contains several possibilities for
dependent variables. Most suitable when measuring reaction-times and/or
accuracy, or any other variable in an interval or ratio scale. Functions
included: file_merge(), read_data() and prep(). The file_merge() function
vertically merges individual data files (in a long format) in which each line
is a single trial within the experiment to one single dataset. The
read_data() function reads a file in a txt or csv format that contains a
single dataset in a long format table and creates a data frame from it. The
prep() function aggregates the single dataset according to any combination of
between and within grouping variables (i.e., between-subjects and
within-subjects independent variables, respectively), and returns a data
frame with a number of dependent measures for further analysis for each
experimental cell according to the combination of provided grouping
variables. Dependent measures for each experimental cell include among
others means before and after rejecting all values according to a flexible
standard deviation criterion/s, number of rejected values according to the
flexible standard deviation criterion/s, proportions of rejected values
according to the flexible standard deviation criterion/s, number of values
before rejection, means after rejecting values according to procedures
described in Van Selst & Jolicoeur (1994) (suitable when measuring
reaction-times), standard deviations, medians, means according to any
percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The data frame
prep() returns can also be exported as a txt file to be used for statistical
analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre],
Roy Luria [aut],
Jim Grange [ctb],
Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>
Diff between prepdat versions 1.0.3 dated 2015-10-22 and 1.0.4 dated 2015-11-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/file_merge.R | 14 ++++++++++---- README.md | 2 +- 5 files changed, 24 insertions(+), 12 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions, where showing the progress is
useful for the user (e.g. bootstrap).
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.1-1 dated 2014-05-16 and 1.1-2 dated 2015-11-22
DESCRIPTION | 11 - MD5 | 39 ++--- NAMESPACE | 14 - R/closepb.R | 10 - R/pbapply.R | 189 +++++++++++++------------- R/pblapply.R | 37 ++--- R/pboptions.R | 32 ++-- R/pbreplicate.R | 9 - R/pbsapply.R | 32 +--- R/unix/dopb.R | 24 +-- R/unix/getpb.R | 24 +-- R/unix/setpb.R | 24 +-- R/unix/startpb.R | 26 +-- R/windows/dopb.R | 24 +-- R/windows/getpb.R | 26 +-- R/windows/setpb.R | 26 +-- R/windows/startpb.R | 30 ++-- inst/ChangeLog | 82 ++++++----- man/pbapply.Rd | 375 ++++++++++++++++++++++++++-------------------------- man/pboptions.Rd | 272 ++++++++++++++++++------------------- tests |only 21 files changed, 670 insertions(+), 636 deletions(-)
Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between mpath versions 0.1-19 dated 2015-07-23 and 0.1-20 dated 2015-11-22
DESCRIPTION | 6 +++--- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 6 ++++++ build/vignette.rds |binary inst/doc/german.pdf |binary inst/doc/static_german.pdf |binary man/be_zeroinfl.Rd | 4 ++-- man/breadReg.Rd | 5 +++-- man/cv.zipath.Rd | 4 ++-- man/estfunReg.Rd | 3 +-- man/hessianReg.Rd | 2 +- man/meatReg.Rd | 2 +- man/methods.Rd | 5 ++--- man/p_zipath.Rd | 4 ++-- man/predict.zipath.Rd | 4 ++-- man/rzi.Rd | 4 ++-- man/sandwichReg.Rd | 2 +- man/se.Rd | 2 +- man/tuning_zipath.Rd | 4 ++-- man/zipath.Rd | 6 +++--- src/midloop.f | 2 +- vignettes/mpath.bib | 2 ++ 22 files changed, 58 insertions(+), 51 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors, nested multiple imputation, and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 1.4-0 dated 2015-11-04 and 1.5-0 dated 2015-11-22
DESCRIPTION | 9 MD5 | 52 +-- NAMESPACE | 2 R/save.data.R | 3 data/data.allison.gssexp.rda |binary data/data.allison.hip.rda |binary data/data.allison.usnews.rda |binary data/data.enders.depression.rda |binary data/data.enders.eatingattitudes.rda |binary data/data.enders.employee.rda |binary data/data.graham.ex3.rda |binary data/data.graham.ex6.rda |binary data/data.graham.ex8a.rda |binary data/data.graham.ex8b.rda |binary data/data.graham.ex8c.rda |binary data/data.internet.rda |binary data/data.largescale.rda |binary data/data.ma01.rda |binary data/data.ma02.rda |binary data/data.ma03.rda |binary data/data.ma04.rda |binary data/data.ma05.rda |binary data/data.ma06.rda |binary data/data.smallscale.rda |binary inst/NEWS | 478 +++++++++++++++++------------------ man/miceadds-package.Rd | 2 man/write.pspp.Rd | 2 27 files changed, 276 insertions(+), 272 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-1 dated 2014-05-16 and 0.3-2 dated 2015-11-22
mefa4-0.3-1/mefa4/build |only mefa4-0.3-1/mefa4/inst/doc |only mefa4-0.3-1/mefa4/vignettes |only mefa4-0.3-2/mefa4/DESCRIPTION | 10 mefa4-0.3-2/mefa4/MD5 | 45 +- mefa4-0.3-2/mefa4/NAMESPACE | 38 + mefa4-0.3-2/mefa4/R/mefa4classes.R | 398 ++++++++++---------- mefa4-0.3-2/mefa4/R/mefa4extras.R | 644 ++++++++++++++++----------------- mefa4-0.3-2/mefa4/R/mefa4methods.R | 408 ++++++++++---------- mefa4-0.3-2/mefa4/R/mefa4utilities.R | 208 +++++----- mefa4-0.3-2/mefa4/R/r2rmd.R |only mefa4-0.3-2/mefa4/inst/CITATION | 38 - mefa4-0.3-2/mefa4/inst/ChangeLog | 179 ++++----- mefa4-0.3-2/mefa4/inst/extras |only mefa4-0.3-2/mefa4/inst/r2rmd_example.R |only mefa4-0.3-2/mefa4/man/Mefa.Rd | 306 +++++++-------- mefa4-0.3-2/mefa4/man/Melt.Rd | 92 ++-- mefa4-0.3-2/mefa4/man/Xtab.Rd | 168 ++++---- mefa4-0.3-2/mefa4/man/abmibirds.Rd | 314 ++++++++-------- mefa4-0.3-2/mefa4/man/groupSums.Rd | 206 +++++----- mefa4-0.3-2/mefa4/man/mbind.Rd | 170 ++++---- mefa4-0.3-2/mefa4/man/mefa4-package.Rd | 120 +++--- mefa4-0.3-2/mefa4/man/nameAlnum.Rd | 122 +++--- mefa4-0.3-2/mefa4/man/nonDuplicated.Rd | 104 ++--- mefa4-0.3-2/mefa4/man/r2rmd.Rd |only mefa4-0.3-2/mefa4/man/samp.Rd | 192 ++++----- 26 files changed, 1888 insertions(+), 1874 deletions(-)
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa versions 3.2-5 dated 2013-12-03 and 3.2-6 dated 2015-11-22
DESCRIPTION | 11 MD5 | 68 +- NAMESPACE | 178 +++---- R/image.dist.R | 60 +- R/label.R | 28 - R/mefadocs.R | 32 - R/qvector.R | 22 R/samp.R | 4 R/samp.default.R | 19 R/segm.R | 4 R/segm.default.R | 20 R/stack.dist.R | 4 R/taxa.R | 4 R/taxa.default.R | 18 R/xtab.R | 4 R/xtab.default.R | 10 build/vignette.rds |binary demo/00Index | 2 inst/CITATION | 38 - inst/ChangeLog | 802 ++++++++++++++++---------------- inst/SampleReport | 80 +-- inst/doc/mefa.R | 732 ++++++++++++++--------------- inst/doc/mefa.Rnw | 1304 ++++++++++++++++++++++++++--------------------------- inst/doc/mefa.pdf |binary man/aoplot.Rd | 92 +-- man/dolina.Rd | 6 man/image.dist.Rd | 84 +-- man/mat2list.Rd | 138 ++--- man/mefadocs.Rd | 50 +- man/mefalogo.Rd | 84 +-- man/mefaweb.Rd | 58 +- man/qvector.Rd | 86 +-- man/stack.dist.Rd | 136 ++--- vignettes/mefa.Rnw | 1304 ++++++++++++++++++++++++++--------------------------- vignettes/mefa.bib | 452 +++++++++--------- 35 files changed, 2976 insertions(+), 2958 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff <larsko@cs.ubc.ca>
Diff between llama versions 0.8.1 dated 2015-02-03 and 0.9 dated 2015-11-22
DESCRIPTION | 14 +- LICENSE | 2 MD5 | 87 +++++++++--------- NAMESPACE | 13 ++ NEWS | 10 ++ R/bsFolds.R | 14 +- R/classify.R | 160 +++++++++++++++++++++------------ R/classifyPairs.R | 165 ++++++++++++++++++++++------------- R/cluster.R | 35 +++---- R/cvFolds.R | 18 ++- R/helpers.R | 14 ++ R/input.R | 4 R/misc.R | 8 - R/misclassificationPenalties.R | 4 R/parscores.R | 4 R/plot.R | 26 ++--- R/regression.R | 31 +++--- R/regressionPairs.R | 37 ++++--- R/successes.R | 4 R/trainTest.R | 10 +- R/tune.R |only R/zzz.R | 2 inst/manual/llama.pdf |binary man/bsFolds.Rd | 12 +- man/classify.Rd | 15 +-- man/classifyPairs.Rd | 8 + man/cluster.Rd | 2 man/cvFolds.Rd | 6 - man/helpers.Rd | 26 +++++ man/llama-package.Rd | 18 +-- man/regression.Rd | 2 man/regressionPairs.Rd | 2 man/trainTest.Rd | 2 man/tune.Rd |only tests/testthat/helper_mockLearners.R | 26 ++++- tests/testthat/helper_testData.R | 11 ++ tests/testthat/test.bsFolds.R | 17 ++- tests/testthat/test.classify.R | 79 ++++++++++++++-- tests/testthat/test.classifyPairs.R | 53 +++++++++-- tests/testthat/test.cluster.R | 12 +- tests/testthat/test.cvFolds.R | 28 +++++ tests/testthat/test.input.R | 10 ++ tests/testthat/test.regression.R | 11 ++ tests/testthat/test.satsolvers.R | 15 +++ tests/testthat/test.trainTest.R | 11 ++ tests/testthat/test.tune.R |only 46 files changed, 709 insertions(+), 319 deletions(-)
Title: Collapsed Gibbs Sampling Methods for Topic Models
Description: Implements latent Dirichlet allocation (LDA)
and related models. This includes (but is not limited
to) sLDA, corrLDA, and the mixed-membership stochastic
blockmodel. Inference for all of these models is
implemented via a fast collapsed Gibbs sampler written
in C. Utility functions for reading/writing data
typically used in topic models, as well as tools for
examining posterior distributions are also included.
Author: Jonathan Chang
Maintainer: Jonathan Chang <slycoder@gmail.com>
Diff between lda versions 1.3.2 dated 2012-10-14 and 1.4.2 dated 2015-11-22
lda-1.3.2/lda/DESCRIPTION.orig |only lda-1.3.2/lda/DESCRIPTION.rej |only lda-1.4.2/lda/DESCRIPTION | 30 lda-1.4.2/lda/MD5 | 79 - lda-1.4.2/lda/NAMESPACE | 1 lda-1.4.2/lda/R/lda-internal.R | 52 - lda-1.4.2/lda/R/lda.cvb0.R |only lda-1.4.2/lda/R/rtm.em.R | 58 - lda-1.4.2/lda/R/slda.em.R | 40 lda-1.4.2/lda/R/slda.predict.R | 2 lda-1.4.2/lda/data/cora.cites.rda |binary lda-1.4.2/lda/data/cora.documents.rda |binary lda-1.4.2/lda/data/cora.titles.rda |binary lda-1.4.2/lda/data/cora.vocab.rda |binary lda-1.4.2/lda/data/datalist |only lda-1.4.2/lda/data/newsgroup.label.map.rda |only lda-1.4.2/lda/data/newsgroup.test.documents.rda |only lda-1.4.2/lda/data/newsgroup.test.labels.rda |only lda-1.4.2/lda/data/newsgroup.train.documents.rda |only lda-1.4.2/lda/data/newsgroup.train.labels.rda |only lda-1.4.2/lda/data/newsgroup.vocab.rda |only lda-1.4.2/lda/data/poliblog.documents.rda |binary lda-1.4.2/lda/data/poliblog.ratings.rda |binary lda-1.4.2/lda/data/poliblog.vocab.rda |binary lda-1.4.2/lda/data/sampson.rda |binary lda-1.4.2/lda/demo/00Index | 1 lda-1.4.2/lda/demo/lda.R | 6 lda-1.4.2/lda/demo/mmsb.R | 26 lda-1.4.2/lda/demo/nubbi.R | 4 lda-1.4.2/lda/demo/slda.R | 2 lda-1.4.2/lda/demo/sldamc.R |only lda-1.4.2/lda/man/filter.words.Rd | 2 lda-1.4.2/lda/man/lda-package.Rd | 2 lda-1.4.2/lda/man/lda.collapsed.gibbs.sampler.Rd | 33 lda-1.4.2/lda/man/lexicalize.Rd | 2 lda-1.4.2/lda/man/links.as.edgelist.Rd | 2 lda-1.4.2/lda/man/newsgroups.Rd |only lda-1.4.2/lda/man/nubbi.collapsed.gibbs.sampler.Rd | 17 lda-1.4.2/lda/man/predictive.distribution.Rd | 2 lda-1.4.2/lda/man/predictive.link.probability.Rd | 2 lda-1.4.2/lda/man/read.documents.Rd | 2 lda-1.4.2/lda/man/rtm.collapsed.gibbs.sampler.Rd | 23 lda-1.4.2/lda/man/slda.predict.Rd | 2 lda-1.4.2/lda/man/top.topic.words.Rd | 2 lda-1.4.2/lda/man/word.counts.Rd | 2 lda-1.4.2/lda/src/cvb0.c |only lda-1.4.2/lda/src/gibbs.c | 1034 +++++++++++---------- 47 files changed, 773 insertions(+), 655 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-2 dated 2015-04-14 and 1.7-3 dated 2015-11-22
ChangeLog | 95 ++++++++++++++++++ DESCRIPTION | 20 +-- MD5 | 258 ++++++++++++++++++++++++------------------------- NAMESPACE | 10 + R/cca.R | 21 +++ R/dudi.R | 4 R/dudi.fca.R | 1 R/ktab.R | 4 R/mbpcaiv.R | 22 +++- R/mbpls.R | 18 +++ R/multiblock.R | 10 + R/pta.R | 17 +-- R/randtest-internal.R | 3 R/randtest.discrimin.R | 2 R/randtest.rlq.R | 4 R/scalewt.R | 22 +++- R/utilities.R | 2 data/abouheif.eg.rda |binary data/acacia.rda |binary data/aminoacyl.rda |binary data/apis108.rda |binary data/aravo.rda |binary data/ardeche.rda |binary data/arrival.rda |binary data/atlas.rda |binary data/atya.rda |binary data/avijons.rda |binary data/avimedi.rda |binary data/aviurba.rda |binary data/bacteria.rda |binary data/banque.rda |binary data/baran95.rda |binary data/bf88.rda |binary data/bordeaux.rda |binary data/bsetal97.rda |binary data/buech.rda |binary data/butterfly.rda |binary data/capitales.rda |binary data/carni19.rda |binary data/carni70.rda |binary data/carniherbi49.rda |binary data/casitas.rda |binary data/chatcat.rda |binary data/chats.rda |binary data/chazeb.rda |binary data/chevaine.rda |binary data/chickenk.rda |binary data/clementines.rda |binary data/cnc2003.rda |binary data/coleo.rda |binary data/corvus.rda |binary data/deug.rda |binary data/doubs.rda |binary data/dunedata.rda |binary data/ecg.rda |binary data/ecomor.rda |binary data/elec88.rda |binary data/escopage.rda |binary data/euro123.rda |binary data/fission.rda |binary data/friday87.rda |binary data/fruits.rda |binary data/ggtortoises.rda |binary data/granulo.rda |binary data/hdpg.rda |binary data/housetasks.rda |binary data/humDNAm.rda |binary data/ichtyo.rda |binary data/irishdata.rda |binary data/julliot.rda |binary data/jv73.rda |binary data/kcponds.rda |binary data/lascaux.rda |binary data/lizards.rda |binary data/macaca.rda |binary data/macon.rda |binary data/macroloire.rda |binary data/mafragh.rda |binary data/maples.rda |binary data/mariages.rda |binary data/meau.rda |binary data/meaudret.rda |binary data/microsatt.rda |binary data/mjrochet.rda |binary data/mollusc.rda |binary data/monde84.rda |binary data/morphosport.rda |binary data/newick.eg.rda |binary data/njplot.rda |binary data/olympic.rda |binary data/oribatid.rda |binary data/ours.rda |binary data/palm.rda |binary data/pap.rda |binary data/pcw.rda |binary data/perthi02.rda |binary data/piosphere.rda |binary data/presid2002.rda |binary data/procella.rda |binary data/rankrock.rda |binary data/rhizobium.rda |binary data/rhone.rda |binary data/rpjdl.rda |binary data/santacatalina.rda |binary data/sarcelles.rda |binary data/seconde.rda |binary data/skulls.rda |binary data/steppe.rda |binary data/syndicats.rda |binary data/t3012.rda |binary data/tarentaise.rda |binary data/taxo.eg.rda |binary data/tintoodiel.rda |binary data/tithonia.rda |binary data/tortues.rda |binary data/toxicity.rda |binary data/trichometeo.rda |binary data/ungulates.rda |binary data/vegtf.rda |binary data/veuvage.rda |binary data/westafrica.rda |binary data/woangers.rda |binary data/worksurv.rda |binary data/yanomama.rda |binary data/zealand.rda |binary man/add.scatter.Rd | 4 man/cca.Rd | 7 + man/scalewt.Rd | 2 src/fourthcorner.c | 6 - src/tests.c | 14 +- 130 files changed, 359 insertions(+), 187 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: James Keirstead <james.keirstead@gmail.com>
Maintainer: James Keirstead <james.keirstead@gmail.com>
Diff between scholar versions 0.1.3 dated 2015-09-28 and 0.1.4 dated 2015-11-21
DESCRIPTION | 14 +-- MD5 | 21 ++--- NAMESPACE | 20 ++++- NEWS | 13 +++ R/compare.r | 68 +++++++++-------- R/predict.r | 164 ++++++++++++++++++++--------------------- R/publications.r | 192 +++++++++++++++++++++++++----------------------- R/scholar-package.r | 83 +++++++++++--------- R/scholar.r | 53 +++++++------ R/zzz.r |only inst/CITATION | 4 - man/get_publications.Rd | 2 12 files changed, 348 insertions(+), 286 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-08-02 2.0
2007-03-06 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-25 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-02 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-08-30 0.3
2011-08-23 0.2
2011-08-08 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-19 0.14.6
2014-06-28 0.14.5
2014-06-20 0.14.4
2012-12-27 0.14.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-15 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-17 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-16 0.1-11
2013-06-29 0.1-6
2013-04-12 0.1-5
2013-03-05 0.1-4
2013-02-18 0.1-3
2013-02-15 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-18 1.4.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-01 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-09 1.0
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-63 dated 2015-10-09 and 0.1-64 dated 2015-11-21
DESCRIPTION | 8 +-- MD5 | 46 ++++++++++---------- R/FixedBinBinIT.r | 24 +++------- R/FixedBinContIT.r | 8 +-- R/FixedContBinIT.r | 2 R/FixedContContIT.r | 7 +-- R/ICABinBin.R | 70 ++++++++++++------------------- R/MixedContContIT.R | 15 +----- R/SummaryITContCont.R | 12 ++--- R/SurvSurv.R | 37 +++++++++++----- R/TrialLevelMA.R | 3 - R/plot.SurvSurv.R | 2 R/summary.SurvSurv.R | 32 ++++++++------ R/summaryBinContCombnIT.R | 14 ++---- man/FixedBinBinIT.Rd | 4 - man/FixedBinContIT.Rd | 6 +- man/FixedContBinIT.Rd | 6 +- man/FixedContContIT.Rd | 6 +- man/ICABinBin.Rd | 4 - man/MixedContContIT.Rd | 4 - man/SurvSurv.Rd | 16 +++---- man/TrialLevelMA.Rd | 1 man/plot.InformationTheoretic.Rd | 6 -- man/plot.InformationTheoreticSurvSurv.Rd | 2 24 files changed, 163 insertions(+), 172 deletions(-)
Title: SubScore Computing Functions in Classical Test Theory
Description: Functions that compute sub-scores for a test using different methods in classical test theory (CTT).
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <dais@indiana.edu>
Diff between subscore versions 1.1 dated 2015-08-19 and 1.2 dated 2015-11-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/CTTsub.R | 12 ++++++------ R/CTTsub.RegOnSub.r | 8 ++++---- R/CTTsub.RegOnTot.R | 10 +++++----- R/CTTsub.RegOnTotSub.R | 10 +++++----- R/data.prep.R | 2 +- 7 files changed, 31 insertions(+), 31 deletions(-)
Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as
CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy
<jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between spcadjust versions 0.9 dated 2015-06-26 and 1.0 dated 2015-11-21
spcadjust-0.9/spcadjust/inst/doc/Methods.pdf |only spcadjust-0.9/spcadjust/inst/doc/papers.bib |only spcadjust-0.9/spcadjust/inst/doc/spcadjust-intro.R |only spcadjust-0.9/spcadjust/inst/doc/spcadjust-intro.Rnw |only spcadjust-0.9/spcadjust/inst/doc/spcadjust-intro.pdf |only spcadjust-0.9/spcadjust/man/ARLCUSUM-class.Rd |only spcadjust-0.9/spcadjust/man/ARLShew-class.Rd |only spcadjust-0.9/spcadjust/man/Pofdata-methods.Rd |only spcadjust-0.9/spcadjust/man/SPCARL-class.Rd |only spcadjust-0.9/spcadjust/man/SPCCUSUMNonpar-class.Rd |only spcadjust-0.9/spcadjust/man/SPCCUSUMNonparCenterScale-class.Rd |only spcadjust-0.9/spcadjust/man/SPCCUSUMNormal-class.Rd |only spcadjust-0.9/spcadjust/man/SPCCUSUMlm-class.Rd |only spcadjust-0.9/spcadjust/man/SPCCUSUMlogreg-class.Rd |only spcadjust-0.9/spcadjust/man/SPCShewNonparCenterScale-class.Rd |only spcadjust-0.9/spcadjust/man/SPCShewNormalCenterScale-class.Rd |only spcadjust-0.9/spcadjust/man/SPCcalARL-class.Rd |only spcadjust-0.9/spcadjust/man/SPCcalhitprob-class.Rd |only spcadjust-0.9/spcadjust/man/SPChitprob-class.Rd |only spcadjust-0.9/spcadjust/man/SPCoutput-methods.Rd |only spcadjust-0.9/spcadjust/man/SPCproperty-class.Rd |only spcadjust-0.9/spcadjust/man/SPCq-methods.Rd |only spcadjust-0.9/spcadjust/man/calARLCUSUM-class.Rd |only spcadjust-0.9/spcadjust/man/calARLShew-class.Rd |only spcadjust-0.9/spcadjust/man/calhitprobCUSUM-class.Rd |only spcadjust-0.9/spcadjust/man/calhitprobShew-class.Rd |only spcadjust-0.9/spcadjust/man/getcdfupdates-methods.Rd |only spcadjust-0.9/spcadjust/man/hitprobCUSUM-class.Rd |only spcadjust-0.9/spcadjust/man/hitprobShew-class.Rd |only spcadjust-0.9/spcadjust/man/qtrafo-methods.Rd |only spcadjust-0.9/spcadjust/man/resample-methods.Rd |only spcadjust-0.9/spcadjust/man/runchart-methods.Rd |only spcadjust-0.9/spcadjust/man/updates-methods.Rd |only spcadjust-0.9/spcadjust/man/xiofP-methods.Rd |only spcadjust-0.9/spcadjust/man/xiofdata-methods.Rd |only spcadjust-0.9/spcadjust/vignettes/Methods.pdf |only spcadjust-0.9/spcadjust/vignettes/papers.bib |only spcadjust-0.9/spcadjust/vignettes/spcadjust-intro.Rnw |only spcadjust-0.9/spcadjust/vignettes/spcadjustClasses.pdf |only spcadjust-1.0/spcadjust/DESCRIPTION | 23 spcadjust-1.0/spcadjust/MD5 | 129 +- spcadjust-1.0/spcadjust/NAMESPACE | 40 spcadjust-1.0/spcadjust/R/CUSUM.R |only spcadjust-1.0/spcadjust/R/CUSUMlib.R | 93 + spcadjust-1.0/spcadjust/R/EWMA.R |only spcadjust-1.0/spcadjust/R/EWMAlib.R |only spcadjust-1.0/spcadjust/R/lm.R |only spcadjust-1.0/spcadjust/R/logreg.R |only spcadjust-1.0/spcadjust/R/main.R | 530 +++----- spcadjust-1.0/spcadjust/R/model.R |only spcadjust-1.0/spcadjust/R/shewhart.R |only spcadjust-1.0/spcadjust/build/vignette.rds |binary spcadjust-1.0/spcadjust/inst/NEWS.Rd |only spcadjust-1.0/spcadjust/inst/doc/CUSUM_LinearRegression.R | 100 - spcadjust-1.0/spcadjust/inst/doc/CUSUM_LinearRegression.Rmd | 10 spcadjust-1.0/spcadjust/inst/doc/CUSUM_LinearRegression.html | 600 ++++----- spcadjust-1.0/spcadjust/inst/doc/CUSUM_LogisticRegression.R | 109 - spcadjust-1.0/spcadjust/inst/doc/CUSUM_LogisticRegression.Rmd | 19 spcadjust-1.0/spcadjust/inst/doc/CUSUM_LogisticRegression.html | 630 +++++----- spcadjust-1.0/spcadjust/inst/doc/CUSUM_NormalNormal.R | 90 - spcadjust-1.0/spcadjust/inst/doc/CUSUM_NormalNormal.Rmd | 7 spcadjust-1.0/spcadjust/inst/doc/CUSUM_NormalNormal.html | 601 ++++----- spcadjust-1.0/spcadjust/inst/doc/EWMA_NormalNormal.R |only spcadjust-1.0/spcadjust/inst/doc/EWMA_NormalNormal.Rmd |only spcadjust-1.0/spcadjust/inst/doc/EWMA_NormalNormal.html |only spcadjust-1.0/spcadjust/inst/doc/Extensions.R |only spcadjust-1.0/spcadjust/inst/doc/Extensions.Rmd |only spcadjust-1.0/spcadjust/inst/doc/Extensions.html |only spcadjust-1.0/spcadjust/inst/doc/Shewhart_NormalNormal.R | 105 - spcadjust-1.0/spcadjust/inst/doc/Shewhart_NormalNormal.Rmd | 5 spcadjust-1.0/spcadjust/inst/doc/Shewhart_NormalNormal.html | 583 ++++----- spcadjust-1.0/spcadjust/man/SPC2sidedconfint.Rd | 69 - spcadjust-1.0/spcadjust/man/SPCCUSUM-class.Rd | 52 spcadjust-1.0/spcadjust/man/SPCDataModel-class.Rd |only spcadjust-1.0/spcadjust/man/SPCEWMA-class.Rd |only spcadjust-1.0/spcadjust/man/SPCModelNonpar.Rd |only spcadjust-1.0/spcadjust/man/SPCModelNonparCenterScale.Rd |only spcadjust-1.0/spcadjust/man/SPCModelNormal.Rd |only spcadjust-1.0/spcadjust/man/SPCModellm.Rd |only spcadjust-1.0/spcadjust/man/SPCModellogregLikRatio.Rd |only spcadjust-1.0/spcadjust/man/SPCModellogregOE.Rd |only spcadjust-1.0/spcadjust/man/SPCShew-class.Rd | 102 + spcadjust-1.0/spcadjust/man/SPCchart-class.Rd | 27 spcadjust-1.0/spcadjust/man/SPCproperty.Rd | 89 - spcadjust-1.0/spcadjust/man/SPCpropertyres-class.Rd |only spcadjust-1.0/spcadjust/man/getcdfupdates.Rd |only spcadjust-1.0/spcadjust/man/getq.Rd |only spcadjust-1.0/spcadjust/man/runchart.Rd |only spcadjust-1.0/spcadjust/man/updates.Rd |only spcadjust-1.0/spcadjust/man/xiofdata.Rd |only spcadjust-1.0/spcadjust/tests |only spcadjust-1.0/spcadjust/vignettes/CUSUM_LinearRegression.Rmd | 10 spcadjust-1.0/spcadjust/vignettes/CUSUM_LogisticRegression.Rmd | 19 spcadjust-1.0/spcadjust/vignettes/CUSUM_NormalNormal.Rmd | 7 spcadjust-1.0/spcadjust/vignettes/EWMA_NormalNormal.Rmd |only spcadjust-1.0/spcadjust/vignettes/Extensions.Rmd |only spcadjust-1.0/spcadjust/vignettes/Shewhart_NormalNormal.Rmd | 5 97 files changed, 2047 insertions(+), 2007 deletions(-)
Title: An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting
any single variable in a multiclass dataset. It is an enhanced jitter strip
chart, where the width of the jitter is controlled by the density
distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre],
Sina Hadi Sohi [aut],
Nicolas Rapin [aut],
Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Diff between sinaplot versions 0.1.2 dated 2015-10-03 and 0.1.3 dated 2015-11-21
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NEWS | 6 ++++++ R/sinaplot.R | 14 +++++++------- README.md |only inst/CITATION |only inst/doc/SinaPlot.html | 24 ++++++++++++------------ 7 files changed, 35 insertions(+), 27 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website
where registered users can submit and discuss content. This package uses
Reddit API to extract Reddit data using Reddit API. Note that due to the API
limitations, the number of comments that can extracted is limited to 500 per
thread. The package consists of 4 functions, one for extracting relevant URLs,
one for extracting features out of given URLs, one that does both together and
one that constructs graphs based on the structure of a thread.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 2.0.0 dated 2015-10-25 and 2.0.1 dated 2015-11-21
DESCRIPTION | 17 - MD5 | 14 NAMESPACE | 12 R/RedditExtractoR.R | 739 ++++++++++++++++++++++++------------------------- man/construct_graph.Rd | 61 ++-- man/get_reddit.Rd | 83 ++--- man/reddit_content.Rd | 59 +-- man/reddit_urls.Rd | 73 ++-- 8 files changed, 538 insertions(+), 520 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: GPU Functions for R Objects
Description: Provides GPU enabled functions for R objects in a simple and
approachable manner. New gpu* and vcl* classes have been provided to
wrap typical R objects (e.g. vector, matrix), in both host and device
spaces, to mirror typical R syntax without the need to know OpenCL.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr. <cdetermanjr@gmail.com>
Diff between gpuR versions 1.0.0 dated 2015-11-20 and 1.0.1 dated 2015-11-21
DESCRIPTION | 6 MD5 | 77 +++++---- NAMESPACE | 1 R/RcppExports.R | 80 +++++----- R/test_utils.R | 16 ++ README.md | 4 configure | 218 ++++++++++++++++------------ configure.ac | 51 ++++-- configure.win | 8 - inst/include/gpuR/cl_helpers.hpp | 22 +- man/has_cpu_skip.Rd |only src/Makevars.win | 1 src/RcppExports.cpp | 166 ++++++++++----------- src/gpuMatrix_iaxpy.cpp | 38 +++- src/gpuMatrix_igemm.cpp | 36 +++- src/gpuVector_iaxpy.cpp | 40 +++-- tests/testthat/test_cpu_gpuMatrix_algebra.R | 28 +++ tests/testthat/test_cpu_gpuMatrix_classes.R | 6 tests/testthat/test_cpu_gpuMatrix_cov.R | 2 tests/testthat/test_cpu_gpuMatrix_dist.R | 5 tests/testthat/test_cpu_gpuMatrix_eigen.R | 2 tests/testthat/test_cpu_gpuMatrix_math.R | 6 tests/testthat/test_cpu_gpuMatrix_row_col.R | 8 + tests/testthat/test_cpu_gpuMatrix_utils.R | 4 tests/testthat/test_cpu_gpuVector_algebra.R | 12 + tests/testthat/test_cpu_gpuVector_classes.R | 3 tests/testthat/test_cpu_gpuVector_math.R | 2 tests/testthat/test_cpu_gpuVector_utils.R | 7 tests/testthat/test_cpu_vclMatrix_algebra.R | 14 + tests/testthat/test_cpu_vclMatrix_classes.R | 10 - tests/testthat/test_cpu_vclMatrix_cov.R | 2 tests/testthat/test_cpu_vclMatrix_dist.R | 5 tests/testthat/test_cpu_vclMatrix_eigen.R | 4 tests/testthat/test_cpu_vclMatrix_row_col.R | 10 + tests/testthat/test_cpu_vclMatrtix_math.R | 6 tests/testthat/test_cpu_vclMatrtix_utils.R | 4 tests/testthat/test_cpu_vclVector_algebra.R | 12 + tests/testthat/test_cpu_vclVector_classes.R | 3 tests/testthat/test_cpu_vclVector_math.R | 4 tests/testthat/test_cpu_vclVector_utils.R | 17 +- 40 files changed, 608 insertions(+), 332 deletions(-)
Title: Calculate Textures from Grey-Level Co-Occurrence Matrices
(GLCMs)
Description: Enables calculation of image textures derived from grey-level
co-occurrence matrices (GLCMs). Supports processing images that cannot
fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff <azvoleff@conservation.org>
Diff between glcm versions 1.2 dated 2015-01-03 and 1.4 dated 2015-11-21
DESCRIPTION | 16 ++++--- MD5 | 30 ++++++------- NAMESPACE | 3 - NEWS | 6 ++ R/glcm.R | 36 +++++++++++----- man/L5TSR_1986.Rd | 4 - man/calc_texture.Rd | 12 ++--- man/expected_textures_3x3_1x1.Rd | 14 +++--- man/expected_textures_5x3_n1xn2.Rd | 14 +++--- man/expected_textures_5x7_2x3.Rd | 14 +++--- man/glcm-package.Rd | 6 +- man/glcm.Rd | 80 ++++++++++++++++++------------------- man/test_raster.Rd | 2 src/RcppExports.cpp | 26 +++++------- src/calc_texture.cpp | 8 +++ tests/testthat/test-glcm.R | 3 - 16 files changed, 147 insertions(+), 127 deletions(-)
Title: Tools for Working with Hansen et al. Global Forest Change
Dataset
Description: The gfcanalysis package supports analyses using the Global
Forest Change dataset released by Hansen et al. gfcanalysis was
written for the Tropical Ecology Assessment and Monitoring (TEAM) Network
(http://www.teamnetwork.org). For additional details on the Global Forest
Change dataset, see: Hansen, M. et al. 2013. "High-Resolution Global Maps
of 21st-Century Forest Cover Change." Science 342 (15 November): 850-53.
The forest change data and more information on the product is available at
http://earthenginepartners.appspot.com.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff <azvoleff@conservation.org>
Diff between gfcanalysis versions 1.2 dated 2014-09-17 and 1.4 dated 2015-11-21
DESCRIPTION | 27 +++++++++++----------- MD5 | 52 ++++++++++++++++++++++---------------------- NAMESPACE | 17 ++++++++++++-- NEWS | 9 +++++++ R/animate_annual.R | 34 ++++++++++++++++++++++------ R/annual_stack.R | 7 +++-- R/download_tiles.R | 24 +++++++++++--------- R/extract_gfc.R | 19 +++++++++------- R/gfc_stats.R | 42 +++++++++++++++++++++++++++-------- R/threshold_gfc.R | 7 +++++ README.md | 4 +-- inst/examples/analyze_GFC.R | 27 +++++----------------- man/animate_annual.Rd | 34 ++++++++++++++++------------ man/annual_stack.Rd | 19 +++++++++------- man/calc_gfc_tiles.Rd | 9 ++++--- man/calc_pixel_areas.Rd | 5 ++-- man/download_tiles.Rd | 24 +++++++++++--------- man/extract_gfc.Rd | 36 ++++++++++++++++-------------- man/gen_grid.Rd | 11 +++++---- man/gfc_stats.Rd | 46 +++++++++++++++++++++----------------- man/gfc_tiles.Rd | 7 +++-- man/plot_gfc.Rd | 13 +++++------ man/scale_by_pixel_area.Rd | 19 ++++++++-------- man/scale_toar.Rd | 13 +++++------ man/test_poly.Rd | 7 +++-- man/threshold_gfc.Rd | 34 ++++++++++++++++------------ man/utm_zone.Rd | 13 +++++------ 27 files changed, 327 insertions(+), 232 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of a joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Multivariate joint frailty models for two types of recurrent events and a terminal event.
7) Joint models for longitudinal data and a terminal event.
8) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.7.6.1 dated 2015-09-01 and 2.8.1 dated 2015-11-21
DESCRIPTION | 41 MD5 | 169 NAMESPACE | 128 NEWS | 17 R/Diffepoce.R | 66 R/additivePenal.R | 92 R/epoce.R | 699 ++- R/factor.names.R | 45 R/frailtyPenal.R | 245 + R/longiPenal.R |only R/multivPenal.R | 351 + R/plot.Diffepoce.R | 2 R/plot.epoce.R | 12 R/plot.frailtyPenal.R | 6 R/plot.jointPenal.R | 6 R/plot.longiPenal.R |only R/plot.multivPenal.R | 10 R/plot.nestedPenal.additivePenal.R | 140 R/plot.predLongi.R |only R/plot.trivPenal.R |only R/prediction.R | 1591 +++++--- R/print.Diffepoce.R | 4 R/print.epoce.R | 38 R/print.jointPenal.R | 6 R/print.longiPenal.R |only R/print.predLongi.R |only R/print.trivPenal.R |only R/summary.jointPenal.R | 4 R/summary.longiPenal.R |only R/summary.trivPenal.R |only R/trivPenal.R |only R/waldtest.R | 18 data/colorectal.rda |only data/colorectalLongi.rda |only man/Diffepoce.Rd | 55 man/additivePenal.Rd | 27 man/colorectal.Rd |only man/colorectalLongi.Rd |only man/dataAdditive.Rd | 2 man/dataNested.Rd | 4 man/epoce.Rd | 96 man/frailtyPenal.Rd | 87 man/frailtypack-package.Rd | 52 man/longiPenal.Rd |only man/multivPenal.Rd | 29 man/num.id.Rd | 2 man/plot.Diffepoce.Rd | 15 man/plot.epoce.Rd | 12 man/plot.multivPenal.Rd | 12 man/plot.predFrailty.Rd | 6 man/plot.predJoint.Rd | 4 man/plot.predLongi.Rd |only man/plotAdditive.Rd | 6 man/plotFrailtyPenal.Rd | 8 man/plotJointPenal.Rd | 26 man/plotLongiPenal.Rd |only man/plotNestedPenal.Rd | 8 man/plotTrivPenal.Rd |only man/prediction.Rd | 694 ++- man/print.multivPenal.Rd | 2 man/print.prediction.Rd | 69 man/printAdditive.Rd | 2 man/printFrailtyPenal.Rd | 2 man/printJointPenal.Rd | 2 man/printLongiPenal.Rd |only man/printNestedPenal.Rd | 2 man/printTrivPenal.Rd |only man/readmission.Rd | 2 man/summary.multivPenal.Rd | 2 man/summaryAdditive.Rd | 2 man/summaryFrailtyPenal.Rd | 4 man/summaryJointPenal.Rd | 6 man/summaryLongiPenal.Rd |only man/summaryNestedPenal.Rd | 6 man/summaryTrivPenal.Rd |only man/terminal.Rd | 2 man/timedep.Rd | 4 man/trivPenal.Rd |only src/Adonnees.f90 | 76 src/Aparameters.f90 | 164 src/Makevars | 7 src/aaOptim.f90 | 100 src/aaUseFunction.f90 | 596 ++- src/afuncpasres.f90 | 395 ++ src/ahrmsym.f90 |only src/aresidusMartingale.f90 | 526 ++ src/atestWald.f90 | 4 src/distance.f90 | 6616 +++++++++++++++++++------------------ src/epoce_long.f90 |only src/frailtypack.f90 | 1 src/funcpaGsplines.f90 | 1 src/funcpaMultivWeib.f90 | 1 src/funcpajlongisplines.f90 |only src/funcpajlongiweib.f90 |only src/joint.f90 | 19 src/joint_longi.f90 |only src/multiveJoint.f90 | 17 src/prediction_biv.f90 |only src/prediction_tri.f90 |only vignettes |only 100 files changed, 8370 insertions(+), 5095 deletions(-)
Title: Platform for EDGAR Filing Management
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR quarterly master index, daily master index, filings from SEC.org site and do sentiment analysis of 10-K statements.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.3 dated 2015-10-28 and 1.0.4 dated 2015-11-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/download_filings.R | 12 ++++++------ R/download_master_index.R | 2 +- R/get_wordfrquency.R | 4 ++-- R/negative_words_histogram.R | 8 ++++---- R/positive_words_histogram.R | 8 ++++---- man/DownloadMasterIndex.Rd | 2 +- man/Downloadfilings.Rd | 16 ++++++++-------- man/NegWorsdHist.Rd | 12 ++++++------ man/PosWorsdHist.Rd | 12 ++++++------ 11 files changed, 52 insertions(+), 52 deletions(-)
Title: Create American Psychological Association (APA) Style Tables
Description: A common task faced by researchers is the creation of APA style (i.e., American Psychological Association style) tables from statistical output. In R a large number of function calls are often needed to obtain all of the desired information for a single APA style table. As well, the process of manually creating APA style tables in a word processor is prone to transcription errors. This package creates Word files (.doc files) containing APA style tables for several types of analyses. Using this package minimizes transcription errors and reduces the number commands needed by the user.
Author: David Stanley [aut, cre]
Maintainer: David Stanley <dstanley@uoguelph.ca>
Diff between apaTables versions 1.0.3 dated 2015-08-27 and 1.0.4 dated 2015-11-21
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- R/apaANOVATable1way.R | 8 +++--- R/apaANOVATable2way.R | 4 +-- R/apaCorrelationTable.R | 2 - R/apaDvalueTable.R | 6 ++-- R/apaRegressionTable.R | 59 +++++++++++++++++++++++++++++++++--------------- R/apaTables.R | 10 ++++++-- man/apa.reg.table.Rd | 31 +++++++++++++++++-------- man/apaTables.Rd | 4 +-- 10 files changed, 96 insertions(+), 54 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.73 dated 2015-07-15 and 1.0.77 dated 2015-11-20
DESCRIPTION | 6 MD5 | 32 - NAMESPACE | 388 ++++++++-------- NEWS | 7 R/ClassCogarch.R | 2 R/PseudoLogLikCOGARCH.R |only R/llag.R | 528 ++++++++++++++++++++++ R/mllag.R |only R/qmle.R | 1088 +++++++++++++++++++++++----------------------- R/simulate.R | 488 ++++++++++---------- R/spectralcov.R |only man/cce.Rd | 66 ++ man/llag.Rd | 120 ++++- man/mllag.Rd |only man/mpv.Rd | 234 ++++----- man/noisy.sampling.Rd | 320 ++++++------- man/qmle.Rd | 154 +++++- man/spectralcov.Rd |only src/PseudoLoglikCOGARCH.c |only src/cce_functions.c | 188 +++++++ 20 files changed, 2301 insertions(+), 1320 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8.5 dated 2015-11-06 and 0.8.6 dated 2015-11-20
vegdata-0.8.5/vegdata/R/vw.site.r |only vegdata-0.8.5/vegdata/R/vw.veg.r |only vegdata-0.8.6/vegdata/DESCRIPTION | 6 vegdata-0.8.6/vegdata/MD5 | 36 ++-- vegdata-0.8.6/vegdata/NAMESPACE | 4 vegdata-0.8.6/vegdata/R/child.r | 2 vegdata-0.8.6/vegdata/R/reflist.r | 7 vegdata-0.8.6/vegdata/R/tax.r | 11 - vegdata-0.8.6/vegdata/R/tax_add.r | 43 ++--- vegdata-0.8.6/vegdata/R/taxval.r | 16 + vegdata-0.8.6/vegdata/R/tv.compRefl.r | 71 ++++---- vegdata-0.8.6/vegdata/R/tv.home.r | 2 vegdata-0.8.6/vegdata/R/vegetweb.r | 108 +++++++++++-- vegdata-0.8.6/vegdata/inst/ChangeLog | 3 vegdata-0.8.6/vegdata/inst/doc/vegdata.pdf |binary vegdata-0.8.6/vegdata/inst/tvdata/Data/elbaue/TvAdmin.dbf |binary vegdata-0.8.6/vegdata/inst/tvdata/Data/elbaue/metadata.txt | 12 - vegdata-0.8.6/vegdata/man/vegetweb.Rd | 13 + vegdata-0.8.6/vegdata/tests/testthat/obs.rds |binary vegdata-0.8.6/vegdata/tests/testthat/test.R | 19 +- 20 files changed, 232 insertions(+), 121 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.2.3 dated 2015-09-17 and 1.3 dated 2015-11-20
DESCRIPTION | 9 MD5 | 80 NAMESPACE | 98 R/foo.R |13264 +++++++++++++++++++------------------ man/Laplace.sampling.Rd | 141 man/Laplace.sampling.lr.Rd | 109 man/adjust.sigma2.Rd | 98 man/autocor.plot.Rd | 51 man/binary.probit.Bayes.Rd | 179 man/binomial.logistic.Bayes.Rd | 263 man/binomial.logistic.MCML.Rd | 264 man/coef.PrevMap.Rd | 49 man/continuous.sample.Rd | 118 man/contour.pred.PrevMap.Rd | 51 man/control.mcmc.Bayes.Rd | 133 man/control.mcmc.MCML.Rd | 73 man/control.prior.Rd | 97 man/control.profile.Rd | 73 man/create.ID.coords.Rd | 64 man/data_sim.Rd | 47 man/dens.plot.Rd | 61 man/discrete.sample.Rd | 142 man/linear.model.Bayes.Rd | 207 man/linear.model.MLE.Rd | 215 man/loaloa.Rd | 67 man/loglik.ci.Rd | 53 man/loglik.linear.model.Rd | 83 man/matern.kernel.Rd | 67 man/plot.pred.PrevMap.Rd | 51 man/plot.profile.PrevMap.Rd | 59 man/plot.shape.matern.Rd | 59 man/poisson.log.MCML.Rd |only man/shape.matern.Rd | 91 man/spatial.pred.binomial.Bayes.Rd | 101 man/spatial.pred.binomial.MCML.Rd | 109 man/spatial.pred.linear.Bayes.Rd | 101 man/spatial.pred.linear.MLE.Rd | 105 man/spatial.pred.poisson.MCML.Rd |only man/summary.Bayes.PrevMap.Rd | 93 man/summary.PrevMap.Rd | 87 man/trace.plot.MCML.Rd | 47 man/trace.plot.Rd | 55 42 files changed, 8796 insertions(+), 8318 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut],
Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.4 dated 2015-06-12 and 2.5 dated 2015-11-20
mlr-2.4/mlr/R/CostSensWeightedPairsLearner.R |only mlr-2.4/mlr/R/RLearner_classif_LiblineaRBinary.R |only mlr-2.4/mlr/R/RLearner_classif_LiblineaRLogReg.R |only mlr-2.4/mlr/R/RLearner_classif_LiblineaRMultiClass.R |only mlr-2.4/mlr/R/checkTaskCreation.R |only mlr-2.4/mlr/R/fixupData.R |only mlr-2.4/mlr/tests/testthat/test_classif_LiblineaRBinary.R |only mlr-2.4/mlr/tests/testthat/test_classif_LiblineaRLogReg.R |only mlr-2.4/mlr/tests/testthat/test_classif_LiblineaRMultiClass.R |only mlr-2.4/mlr/tests/testthat/test_learners_all.R |only mlr-2.5/mlr/DESCRIPTION | 41 mlr-2.5/mlr/MD5 | 1073 +++++----- mlr-2.5/mlr/NAMESPACE | 184 + mlr-2.5/mlr/NEWS | 111 + mlr-2.5/mlr/R/Aggregation.R | 11 mlr-2.5/mlr/R/BaggingWrapper.R | 20 mlr-2.5/mlr/R/BaseEnsemble.R | 7 mlr-2.5/mlr/R/BaseWrapper.R | 21 mlr-2.5/mlr/R/BenchmarkResultOrderLevels.R |only mlr-2.5/mlr/R/BenchmarkResult_operators.R | 94 mlr-2.5/mlr/R/ChainModel.R | 12 mlr-2.5/mlr/R/ClassifTask.R | 47 mlr-2.5/mlr/R/ClusterTask.R | 24 mlr-2.5/mlr/R/CostSensClassifWrapper.R | 15 mlr-2.5/mlr/R/CostSensRegrWrapper.R | 17 mlr-2.5/mlr/R/CostSensTask.R | 55 mlr-2.5/mlr/R/CostSensWeightedPairsWrapper.R |only mlr-2.5/mlr/R/FeatSelControl.R | 3 mlr-2.5/mlr/R/FeatSelWrapper.R | 2 mlr-2.5/mlr/R/Filter.R | 43 mlr-2.5/mlr/R/HomogeneousEnsemble.R | 28 mlr-2.5/mlr/R/ImputeMethods.R | 2 mlr-2.5/mlr/R/ImputeWrapper.R | 7 mlr-2.5/mlr/R/Learner.R | 94 mlr-2.5/mlr/R/Learner_properties.R | 39 mlr-2.5/mlr/R/Measure.R | 42 mlr-2.5/mlr/R/Measure_custom_resampled.R | 63 mlr-2.5/mlr/R/Measure_make_cost.R | 15 mlr-2.5/mlr/R/ModelMultiplexer.R | 14 mlr-2.5/mlr/R/ModelMultiplexerParamSet.R | 2 mlr-2.5/mlr/R/MulticlassWrapper.R | 24 mlr-2.5/mlr/R/MultilabelBinaryRelevanceWrapper.R |only mlr-2.5/mlr/R/MultilabelTask.R |only mlr-2.5/mlr/R/OptControl.R | 3 mlr-2.5/mlr/R/OptResult.R | 8 mlr-2.5/mlr/R/OverBaggingWrapper.R | 9 mlr-2.5/mlr/R/Prediction.R | 30 mlr-2.5/mlr/R/Prediction_operators.R | 115 - mlr-2.5/mlr/R/PreprocWrapper.R | 2 mlr-2.5/mlr/R/PreprocWrapperCaret.R | 19 mlr-2.5/mlr/R/RLearner.R | 55 mlr-2.5/mlr/R/RLearner_classif_IBk.R | 3 mlr-2.5/mlr/R/RLearner_classif_J48.R | 8 mlr-2.5/mlr/R/RLearner_classif_JRip.R | 5 mlr-2.5/mlr/R/RLearner_classif_LiblineaRL1L2SVC.R |only mlr-2.5/mlr/R/RLearner_classif_LiblineaRL1LogReg.R |only mlr-2.5/mlr/R/RLearner_classif_LiblineaRL2L1SVC.R |only mlr-2.5/mlr/R/RLearner_classif_LiblineaRL2LogReg.R |only mlr-2.5/mlr/R/RLearner_classif_LiblineaRL2SVC.R |only mlr-2.5/mlr/R/RLearner_classif_LiblineaRMultiClassSVC.R |only mlr-2.5/mlr/R/RLearner_classif_OneR.R | 3 mlr-2.5/mlr/R/RLearner_classif_PART.R | 4 mlr-2.5/mlr/R/RLearner_classif_ada.R | 1 mlr-2.5/mlr/R/RLearner_classif_avNNet.R |only mlr-2.5/mlr/R/RLearner_classif_bartMachine.R | 12 mlr-2.5/mlr/R/RLearner_classif_bdk.R | 5 mlr-2.5/mlr/R/RLearner_classif_binomial.R | 3 mlr-2.5/mlr/R/RLearner_classif_blackboost.R | 4 mlr-2.5/mlr/R/RLearner_classif_boosting.R | 2 mlr-2.5/mlr/R/RLearner_classif_bst.R | 2 mlr-2.5/mlr/R/RLearner_classif_cforest.R | 22 mlr-2.5/mlr/R/RLearner_classif_clusterSVM.R |only mlr-2.5/mlr/R/RLearner_classif_ctree.R | 4 mlr-2.5/mlr/R/RLearner_classif_dbnDNN.R |only mlr-2.5/mlr/R/RLearner_classif_dcSVM.R |only mlr-2.5/mlr/R/RLearner_classif_extraTrees.R | 4 mlr-2.5/mlr/R/RLearner_classif_fnn.R | 4 mlr-2.5/mlr/R/RLearner_classif_gaterSVM.R |only mlr-2.5/mlr/R/RLearner_classif_gbm.R | 19 mlr-2.5/mlr/R/RLearner_classif_geoDA.R | 4 mlr-2.5/mlr/R/RLearner_classif_glmboost.R | 14 mlr-2.5/mlr/R/RLearner_classif_glmnet.R | 11 mlr-2.5/mlr/R/RLearner_classif_hdrda.R | 3 mlr-2.5/mlr/R/RLearner_classif_kknn.R | 5 mlr-2.5/mlr/R/RLearner_classif_knn.R | 1 mlr-2.5/mlr/R/RLearner_classif_ksvm.R | 22 mlr-2.5/mlr/R/RLearner_classif_lda.R | 5 mlr-2.5/mlr/R/RLearner_classif_linDA.R | 1 mlr-2.5/mlr/R/RLearner_classif_lqa.R | 14 mlr-2.5/mlr/R/RLearner_classif_lssvm.R | 10 mlr-2.5/mlr/R/RLearner_classif_mda.R | 3 mlr-2.5/mlr/R/RLearner_classif_mlp.R |only mlr-2.5/mlr/R/RLearner_classif_multinom.R | 9 mlr-2.5/mlr/R/RLearner_classif_neuralnet.R |only mlr-2.5/mlr/R/RLearner_classif_nnTrain.R |only mlr-2.5/mlr/R/RLearner_classif_nnet.R | 13 mlr-2.5/mlr/R/RLearner_classif_nodeHarvest.R | 2 mlr-2.5/mlr/R/RLearner_classif_qda.R | 2 mlr-2.5/mlr/R/RLearner_classif_quaDA.R | 1 mlr-2.5/mlr/R/RLearner_classif_rFerns.R | 6 mlr-2.5/mlr/R/RLearner_classif_randomForest.R | 10 mlr-2.5/mlr/R/RLearner_classif_randomForestSRC.R | 15 mlr-2.5/mlr/R/RLearner_classif_ranger.R |only mlr-2.5/mlr/R/RLearner_classif_rda.R | 13 mlr-2.5/mlr/R/RLearner_classif_rknn.R |only mlr-2.5/mlr/R/RLearner_classif_rotationForest.R |only mlr-2.5/mlr/R/RLearner_classif_rpart.R | 2 mlr-2.5/mlr/R/RLearner_classif_saeDNN.R |only mlr-2.5/mlr/R/RLearner_classif_sda.R | 2 mlr-2.5/mlr/R/RLearner_classif_sparseLDA.R | 2 mlr-2.5/mlr/R/RLearner_classif_svm.R | 20 mlr-2.5/mlr/R/RLearner_classif_xgboost.R |only mlr-2.5/mlr/R/RLearner_classif_xyf.R | 2 mlr-2.5/mlr/R/RLearner_cluster_EM.R | 6 mlr-2.5/mlr/R/RLearner_cluster_FarthestFirst.R | 5 mlr-2.5/mlr/R/RLearner_cluster_SimpleKMeans.R | 5 mlr-2.5/mlr/R/RLearner_cluster_XMeans.R | 8 mlr-2.5/mlr/R/RLearner_cluster_cmeans.R | 6 mlr-2.5/mlr/R/RLearner_cluster_kmeans.R | 2 mlr-2.5/mlr/R/RLearner_multilabel_rFerns.R |only mlr-2.5/mlr/R/RLearner_regr_IBk.R | 3 mlr-2.5/mlr/R/RLearner_regr_LiblineaRL2L1SVR.R |only mlr-2.5/mlr/R/RLearner_regr_LiblineaRL2L2SVR.R |only mlr-2.5/mlr/R/RLearner_regr_avNNet.R |only mlr-2.5/mlr/R/RLearner_regr_bartMachine.R | 8 mlr-2.5/mlr/R/RLearner_regr_bcart.R | 8 mlr-2.5/mlr/R/RLearner_regr_bdk.R | 5 mlr-2.5/mlr/R/RLearner_regr_bgp.R | 8 mlr-2.5/mlr/R/RLearner_regr_bgpllm.R | 8 mlr-2.5/mlr/R/RLearner_regr_blackBoost.R | 4 mlr-2.5/mlr/R/RLearner_regr_blm.R | 8 mlr-2.5/mlr/R/RLearner_regr_brnn.R | 2 mlr-2.5/mlr/R/RLearner_regr_bst.R | 8 mlr-2.5/mlr/R/RLearner_regr_btgp.R | 12 mlr-2.5/mlr/R/RLearner_regr_btgpllm.R | 10 mlr-2.5/mlr/R/RLearner_regr_btlm.R | 8 mlr-2.5/mlr/R/RLearner_regr_cforest.R | 4 mlr-2.5/mlr/R/RLearner_regr_crs.R | 13 mlr-2.5/mlr/R/RLearner_regr_ctree.R | 4 mlr-2.5/mlr/R/RLearner_regr_cubist.R | 2 mlr-2.5/mlr/R/RLearner_regr_earth.R | 13 mlr-2.5/mlr/R/RLearner_regr_extraTrees.R | 5 mlr-2.5/mlr/R/RLearner_regr_fnn.R | 4 mlr-2.5/mlr/R/RLearner_regr_frbs.R | 44 mlr-2.5/mlr/R/RLearner_regr_gbm.R | 7 mlr-2.5/mlr/R/RLearner_regr_glmnet.R | 3 mlr-2.5/mlr/R/RLearner_regr_kknn.R | 5 mlr-2.5/mlr/R/RLearner_regr_km.R | 6 mlr-2.5/mlr/R/RLearner_regr_ksvm.R | 20 mlr-2.5/mlr/R/RLearner_regr_laGP.R | 3 mlr-2.5/mlr/R/RLearner_regr_lm.R | 11 mlr-2.5/mlr/R/RLearner_regr_mars.R | 1 mlr-2.5/mlr/R/RLearner_regr_mob.R | 4 mlr-2.5/mlr/R/RLearner_regr_nnet.R | 13 mlr-2.5/mlr/R/RLearner_regr_nodeHarvest.R | 2 mlr-2.5/mlr/R/RLearner_regr_pcr.R | 9 mlr-2.5/mlr/R/RLearner_regr_penalized_lasso.R | 3 mlr-2.5/mlr/R/RLearner_regr_penalized_ridge.R | 3 mlr-2.5/mlr/R/RLearner_regr_plsr.R | 5 mlr-2.5/mlr/R/RLearner_regr_randomForest.R | 10 mlr-2.5/mlr/R/RLearner_regr_randomForestSRC.R | 15 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mlr-2.5/mlr/R/tuneMultiCritGrid.R | 2 mlr-2.5/mlr/R/tuneParams.R | 11 mlr-2.5/mlr/R/tuneParamsMultiCrit.R | 4 mlr-2.5/mlr/R/tuneRandom.R | 4 mlr-2.5/mlr/R/tuneThreshold.R | 31 mlr-2.5/mlr/R/zzz.R | 30 mlr-2.5/mlr/build/vignette.rds |binary mlr-2.5/mlr/data/agri.task.RData |binary mlr-2.5/mlr/data/bc.task.RData |binary mlr-2.5/mlr/data/bh.task.RData |binary mlr-2.5/mlr/data/costiris.task.RData |binary mlr-2.5/mlr/data/iris.task.RData |binary mlr-2.5/mlr/data/lung.task.RData |binary mlr-2.5/mlr/data/mtcars.task.RData |binary mlr-2.5/mlr/data/pid.task.RData |binary mlr-2.5/mlr/data/sonar.task.RData |binary mlr-2.5/mlr/data/wpbc.task.RData |binary mlr-2.5/mlr/data/yeast.task.RData |only mlr-2.5/mlr/inst/doc/mlr.R | 2 mlr-2.5/mlr/inst/doc/mlr.Rmd | 57 mlr-2.5/mlr/inst/doc/mlr.html | 39 mlr-2.5/mlr/inst/makeData.R | 9 mlr-2.5/mlr/man/Aggregation.Rd | 2 mlr-2.5/mlr/man/BenchmarkResult.Rd | 58 mlr-2.5/mlr/man/FailureModel.Rd | 2 mlr-2.5/mlr/man/FeatSelControl.Rd | 8 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mlr-2.5/mlr/man/getBMRFilteredFeatures.Rd | 39 mlr-2.5/mlr/man/getBMRLearnerIds.Rd | 37 mlr-2.5/mlr/man/getBMRLearners.Rd |only mlr-2.5/mlr/man/getBMRMeasureIds.Rd |only mlr-2.5/mlr/man/getBMRMeasures.Rd |only mlr-2.5/mlr/man/getBMRPerformances.Rd | 33 mlr-2.5/mlr/man/getBMRPredictions.Rd | 35 mlr-2.5/mlr/man/getBMRTaskIds.Rd | 35 mlr-2.5/mlr/man/getBMRTuneResults.Rd | 37 mlr-2.5/mlr/man/getCaretParamSet.Rd |only mlr-2.5/mlr/man/getClassWeightParam.Rd |only mlr-2.5/mlr/man/getConfMatrix.Rd | 2 mlr-2.5/mlr/man/getDefaultMeasure.Rd |only mlr-2.5/mlr/man/getFailureModelMsg.Rd | 2 mlr-2.5/mlr/man/getFeatSelResult.Rd | 14 mlr-2.5/mlr/man/getFilterValues.Rd | 37 mlr-2.5/mlr/man/getFilteredFeatures.Rd | 14 mlr-2.5/mlr/man/getHomogeneousEnsembleModels.Rd | 17 mlr-2.5/mlr/man/getHyperPars.Rd | 16 mlr-2.5/mlr/man/getLearnerModel.Rd | 12 mlr-2.5/mlr/man/getMlrOptions.Rd | 4 mlr-2.5/mlr/man/getMultilabelBinaryPerformances.Rd |only mlr-2.5/mlr/man/getNestedTuneResultsOptPathDf.Rd | 28 mlr-2.5/mlr/man/getNestedTuneResultsX.Rd | 28 mlr-2.5/mlr/man/getParamSet.Rd | 14 mlr-2.5/mlr/man/getPredictionProbabilities.Rd |only mlr-2.5/mlr/man/getPredictionResponse.Rd |only mlr-2.5/mlr/man/getProbabilities.Rd | 40 mlr-2.5/mlr/man/getRRPredictions.Rd | 18 mlr-2.5/mlr/man/getStackedBaseLearnerPredictions.Rd | 4 mlr-2.5/mlr/man/getTaskClassLevels.Rd |only mlr-2.5/mlr/man/getTaskCosts.Rd | 19 mlr-2.5/mlr/man/getTaskData.Rd | 19 mlr-2.5/mlr/man/getTaskDescription.Rd | 18 mlr-2.5/mlr/man/getTaskFeatureNames.Rd | 18 mlr-2.5/mlr/man/getTaskFormula.Rd | 33 mlr-2.5/mlr/man/getTaskId.Rd | 23 mlr-2.5/mlr/man/getTaskNFeats.Rd | 25 mlr-2.5/mlr/man/getTaskSize.Rd | 25 mlr-2.5/mlr/man/getTaskTargetNames.Rd | 25 mlr-2.5/mlr/man/getTaskTargets.Rd | 27 mlr-2.5/mlr/man/getTaskType.Rd | 26 mlr-2.5/mlr/man/getTuneResult.Rd | 26 mlr-2.5/mlr/man/hasProperties.Rd |only mlr-2.5/mlr/man/imputations.Rd | 12 mlr-2.5/mlr/man/impute.Rd | 11 mlr-2.5/mlr/man/iris.task.Rd | 2 mlr-2.5/mlr/man/isFailureModel.Rd | 2 mlr-2.5/mlr/man/joinClassLevels.Rd | 2 mlr-2.5/mlr/man/learnerArgsToControl.Rd | 2 mlr-2.5/mlr/man/learners.Rd | 4 mlr-2.5/mlr/man/listFilterMethods.Rd | 2 mlr-2.5/mlr/man/listLearners.Rd | 26 mlr-2.5/mlr/man/listMeasures.Rd | 2 mlr-2.5/mlr/man/lung.task.Rd | 2 mlr-2.5/mlr/man/makeAggregation.Rd | 11 mlr-2.5/mlr/man/makeBaggingWrapper.Rd | 36 mlr-2.5/mlr/man/makeCostMeasure.Rd | 48 mlr-2.5/mlr/man/makeCostSensClassifWrapper.Rd | 48 mlr-2.5/mlr/man/makeCostSensRegrWrapper.Rd | 48 mlr-2.5/mlr/man/makeCostSensWeightedPairsWrapper.Rd | 20 mlr-2.5/mlr/man/makeCustomResampledMeasure.Rd | 68 mlr-2.5/mlr/man/makeDownsampleWrapper.Rd | 34 mlr-2.5/mlr/man/makeFeatSelWrapper.Rd | 51 mlr-2.5/mlr/man/makeFilter.Rd | 2 mlr-2.5/mlr/man/makeFilterWrapper.Rd | 46 mlr-2.5/mlr/man/makeFixedHoldoutInstance.Rd | 2 mlr-2.5/mlr/man/makeImputeMethod.Rd | 9 mlr-2.5/mlr/man/makeImputeWrapper.Rd | 41 mlr-2.5/mlr/man/makeLearner.Rd | 15 mlr-2.5/mlr/man/makeMeasure.Rd | 51 mlr-2.5/mlr/man/makeModelMultiplexer.Rd | 25 mlr-2.5/mlr/man/makeModelMultiplexerParamSet.Rd | 31 mlr-2.5/mlr/man/makeMulticlassWrapper.Rd | 34 mlr-2.5/mlr/man/makeMultilabelBinaryRelevanceWrapper.Rd |only mlr-2.5/mlr/man/makeOverBaggingWrapper.Rd | 44 mlr-2.5/mlr/man/makePreprocWrapper.Rd | 34 mlr-2.5/mlr/man/makePreprocWrapperCaret.Rd | 36 mlr-2.5/mlr/man/makeResampleDesc.Rd | 32 mlr-2.5/mlr/man/makeResampleInstance.Rd | 16 mlr-2.5/mlr/man/makeSMOTEWrapper.Rd | 34 mlr-2.5/mlr/man/makeStackedLearner.Rd | 79 mlr-2.5/mlr/man/makeTuneWrapper.Rd | 77 mlr-2.5/mlr/man/makeUndersampleWrapper.Rd | 40 mlr-2.5/mlr/man/makeWeightedClassesWrapper.Rd | 54 mlr-2.5/mlr/man/makeWrappedModel.Rd | 8 mlr-2.5/mlr/man/measures.Rd | 18 mlr-2.5/mlr/man/mergeBenchmarkResultLearner.Rd |only mlr-2.5/mlr/man/mergeBenchmarkResultTask.Rd |only mlr-2.5/mlr/man/mergeSmallFactorLevels.Rd | 14 mlr-2.5/mlr/man/mtcars.task.Rd | 2 mlr-2.5/mlr/man/normalizeFeatures.Rd | 14 mlr-2.5/mlr/man/oversample.Rd | 7 mlr-2.5/mlr/man/performance.Rd | 43 mlr-2.5/mlr/man/pid.task.Rd | 2 mlr-2.5/mlr/man/plotBenchmarkResult.Rd |only mlr-2.5/mlr/man/plotBenchmarkSummary.Rd |only mlr-2.5/mlr/man/plotCalibration.Rd |only mlr-2.5/mlr/man/plotCritDifferences.Rd |only mlr-2.5/mlr/man/plotFilterValues.Rd | 34 mlr-2.5/mlr/man/plotFilterValuesGGVIS.Rd | 53 mlr-2.5/mlr/man/plotLearnerPrediction.Rd | 7 mlr-2.5/mlr/man/plotLearningCurve.Rd | 30 mlr-2.5/mlr/man/plotLearningCurveGGVIS.Rd | 30 mlr-2.5/mlr/man/plotPartialPrediction.Rd |only mlr-2.5/mlr/man/plotPartialPredictionGGVIS.Rd |only mlr-2.5/mlr/man/plotROCCurves.Rd |only mlr-2.5/mlr/man/plotROCRCurves.Rd | 43 mlr-2.5/mlr/man/plotROCRCurvesGGVIS.Rd | 43 mlr-2.5/mlr/man/plotRankMatrixAsBar.Rd |only mlr-2.5/mlr/man/plotThreshVsPerf.Rd | 36 mlr-2.5/mlr/man/plotThreshVsPerfGGVIS.Rd | 34 mlr-2.5/mlr/man/plotTuneMultiCritResult.Rd | 10 mlr-2.5/mlr/man/plotTuneMultiCritResultGGVIS.Rd | 16 mlr-2.5/mlr/man/plotViperCharts.Rd | 23 mlr-2.5/mlr/man/predict.WrappedModel.Rd | 26 mlr-2.5/mlr/man/predictLearner.Rd | 2 mlr-2.5/mlr/man/reimpute.Rd | 9 mlr-2.5/mlr/man/removeConstantFeatures.Rd | 12 mlr-2.5/mlr/man/removeHyperPars.Rd | 12 mlr-2.5/mlr/man/resample.Rd | 17 mlr-2.5/mlr/man/selectFeatures.Rd | 19 mlr-2.5/mlr/man/setAggregation.Rd | 5 mlr-2.5/mlr/man/setHyperPars.Rd | 12 mlr-2.5/mlr/man/setHyperPars2.Rd | 2 mlr-2.5/mlr/man/setId.Rd | 14 mlr-2.5/mlr/man/setPredictThreshold.Rd | 27 mlr-2.5/mlr/man/setPredictType.Rd | 27 mlr-2.5/mlr/man/setThreshold.Rd | 13 mlr-2.5/mlr/man/smote.Rd | 9 mlr-2.5/mlr/man/sonar.task.Rd | 2 mlr-2.5/mlr/man/subsetTask.Rd | 20 mlr-2.5/mlr/man/summarizeColumns.Rd | 12 mlr-2.5/mlr/man/summarizeLevels.Rd | 2 mlr-2.5/mlr/man/train.Rd | 7 mlr-2.5/mlr/man/trainLearner.Rd | 4 mlr-2.5/mlr/man/tuneParams.Rd | 35 mlr-2.5/mlr/man/tuneParamsMultiCrit.Rd | 16 mlr-2.5/mlr/man/tuneThreshold.Rd | 38 mlr-2.5/mlr/man/wpbc.task.Rd | 2 mlr-2.5/mlr/man/yeast.task.Rd |only mlr-2.5/mlr/tests/testthat/Rplots.pdf |binary mlr-2.5/mlr/tests/testthat/helper_helpers.R | 12 mlr-2.5/mlr/tests/testthat/helper_mock_learners.R | 72 mlr-2.5/mlr/tests/testthat/helper_objects.R | 118 + mlr-2.5/mlr/tests/testthat/test_base_BMRhypothesisTests.R |only mlr-2.5/mlr/tests/testthat/test_base_BaggingWrapper.R | 10 mlr-2.5/mlr/tests/testthat/test_base_FailureModel.R | 4 mlr-2.5/mlr/tests/testthat/test_base_Learner.R | 4 mlr-2.5/mlr/tests/testthat/test_base_MulticlassWrapper.R | 4 mlr-2.5/mlr/tests/testthat/test_base_PreprocWrapperCaret.R | 6 mlr-2.5/mlr/tests/testthat/test_base_SupervisedTask.R | 30 mlr-2.5/mlr/tests/testthat/test_base_TaskDesc.R | 72 mlr-2.5/mlr/tests/testthat/test_base_UnsupervisedTask.R | 7 mlr-2.5/mlr/tests/testthat/test_base_benchmark.R | 78 mlr-2.5/mlr/tests/testthat/test_base_benchmark_merger.R |only mlr-2.5/mlr/tests/testthat/test_base_blocking.R | 2 mlr-2.5/mlr/tests/testthat/test_base_checkData.R | 6 mlr-2.5/mlr/tests/testthat/test_base_checkTaskLearner.R | 1 mlr-2.5/mlr/tests/testthat/test_base_clustering.R | 5 mlr-2.5/mlr/tests/testthat/test_base_convertMLBenchObjToTask.R |only mlr-2.5/mlr/tests/testthat/test_base_costs.R | 4 mlr-2.5/mlr/tests/testthat/test_base_downsample.R | 9 mlr-2.5/mlr/tests/testthat/test_base_generateCalibration.R |only mlr-2.5/mlr/tests/testthat/test_base_generateLearningCurve.R | 26 mlr-2.5/mlr/tests/testthat/test_base_generatePartialPrediction.R |only mlr-2.5/mlr/tests/testthat/test_base_generateThreshVsPerf.R | 83 mlr-2.5/mlr/tests/testthat/test_base_getCaretParamSet.R |only mlr-2.5/mlr/tests/testthat/test_base_getHyperPars.R | 6 mlr-2.5/mlr/tests/testthat/test_base_getParamSet.R | 2 mlr-2.5/mlr/tests/testthat/test_base_getTaskData.R | 29 mlr-2.5/mlr/tests/testthat/test_base_hyperpars.R | 18 mlr-2.5/mlr/tests/testthat/test_base_imbal_overbagging.R | 2 mlr-2.5/mlr/tests/testthat/test_base_imbal_smote.R | 12 mlr-2.5/mlr/tests/testthat/test_base_imbal_weightedclasses.R | 81 mlr-2.5/mlr/tests/testthat/test_base_impute.R | 6 mlr-2.5/mlr/tests/testthat/test_base_measures.R | 325 +++ mlr-2.5/mlr/tests/testthat/test_base_multilabel.R |only mlr-2.5/mlr/tests/testthat/test_base_normalizeFeatures.R | 2 mlr-2.5/mlr/tests/testthat/test_base_orderBMRLevels.R |only mlr-2.5/mlr/tests/testthat/test_base_orderedfactors.R | 4 mlr-2.5/mlr/tests/testthat/test_base_performance.R | 37 mlr-2.5/mlr/tests/testthat/test_base_plotBenchmarkResult.R |only mlr-2.5/mlr/tests/testthat/test_base_plotBenchmarkSummary.R |only mlr-2.5/mlr/tests/testthat/test_base_plotCritDifferences.R |only mlr-2.5/mlr/tests/testthat/test_base_plotLearnerPrediction.R | 5 mlr-2.5/mlr/tests/testthat/test_base_plotRankMatrixAsBar.R |only mlr-2.5/mlr/tests/testthat/test_base_predict.R | 32 mlr-2.5/mlr/tests/testthat/test_base_prediction_operators.R |only mlr-2.5/mlr/tests/testthat/test_base_relativeOverfitting.R |only mlr-2.5/mlr/tests/testthat/test_base_resample.R | 9 mlr-2.5/mlr/tests/testthat/test_base_resample_dps.R |only mlr-2.5/mlr/tests/testthat/test_base_resample_stratify.R | 2 mlr-2.5/mlr/tests/testthat/test_base_selectFeatures.R | 2 mlr-2.5/mlr/tests/testthat/test_base_setPredictType.R | 4 mlr-2.5/mlr/tests/testthat/test_base_tuning.R | 47 mlr-2.5/mlr/tests/testthat/test_classif_LibLineaRMultiClassSVC.R |only mlr-2.5/mlr/tests/testthat/test_classif_LiblineaRL1L2SVC.R |only mlr-2.5/mlr/tests/testthat/test_classif_LiblineaRL1LogReg.R |only mlr-2.5/mlr/tests/testthat/test_classif_LiblineaRL2L1SVC.R |only mlr-2.5/mlr/tests/testthat/test_classif_LiblineaRL2LogReg.R |only mlr-2.5/mlr/tests/testthat/test_classif_LiblineaRL2SVC.R |only mlr-2.5/mlr/tests/testthat/test_classif_avNNet.R |only mlr-2.5/mlr/tests/testthat/test_classif_clusterSVM.R |only mlr-2.5/mlr/tests/testthat/test_classif_dbnDNN.R |only mlr-2.5/mlr/tests/testthat/test_classif_dcSVM.R |only mlr-2.5/mlr/tests/testthat/test_classif_gaterSVM.R |only mlr-2.5/mlr/tests/testthat/test_classif_gbm.R | 2 mlr-2.5/mlr/tests/testthat/test_classif_mlp.R |only mlr-2.5/mlr/tests/testthat/test_classif_multinom.R | 4 mlr-2.5/mlr/tests/testthat/test_classif_neuralnet.R |only mlr-2.5/mlr/tests/testthat/test_classif_nnTrain.R |only mlr-2.5/mlr/tests/testthat/test_classif_nnet.R | 28 mlr-2.5/mlr/tests/testthat/test_classif_ranger.R |only mlr-2.5/mlr/tests/testthat/test_classif_rknn.R |only mlr-2.5/mlr/tests/testthat/test_classif_rotationForest.R |only mlr-2.5/mlr/tests/testthat/test_classif_saeDNN.R |only mlr-2.5/mlr/tests/testthat/test_classif_svm.R | 9 mlr-2.5/mlr/tests/testthat/test_classif_xgboost.R |only mlr-2.5/mlr/tests/testthat/test_featsel_FilterWrapper.R | 1 mlr-2.5/mlr/tests/testthat/test_featsel_filterFeatures.R | 25 mlr-2.5/mlr/tests/testthat/test_learners_all_classif.R |only mlr-2.5/mlr/tests/testthat/test_learners_all_clusters.R |only mlr-2.5/mlr/tests/testthat/test_learners_all_general.R |only mlr-2.5/mlr/tests/testthat/test_learners_all_regr.R |only mlr-2.5/mlr/tests/testthat/test_learners_classiflabelswitch.R | 7 mlr-2.5/mlr/tests/testthat/test_parallel_all.R | 16 mlr-2.5/mlr/tests/testthat/test_regr_IBk.R |only mlr-2.5/mlr/tests/testthat/test_regr_LiblineaRL2L1SVR.R |only mlr-2.5/mlr/tests/testthat/test_regr_LiblineaRL2L2SVR.R |only mlr-2.5/mlr/tests/testthat/test_regr_avNNet.R |only mlr-2.5/mlr/tests/testthat/test_regr_bartMachine.R |only mlr-2.5/mlr/tests/testthat/test_regr_bcart.R |only mlr-2.5/mlr/tests/testthat/test_regr_bdk.R |only mlr-2.5/mlr/tests/testthat/test_regr_bgp.R |only mlr-2.5/mlr/tests/testthat/test_regr_bgpllm.R |only mlr-2.5/mlr/tests/testthat/test_regr_blackboost.R |only mlr-2.5/mlr/tests/testthat/test_regr_blm.R |only mlr-2.5/mlr/tests/testthat/test_regr_brnn.R |only mlr-2.5/mlr/tests/testthat/test_regr_bst.R |only mlr-2.5/mlr/tests/testthat/test_regr_btgp.R |only mlr-2.5/mlr/tests/testthat/test_regr_btgpllm.R |only mlr-2.5/mlr/tests/testthat/test_regr_btlm.R |only mlr-2.5/mlr/tests/testthat/test_regr_cforest.R |only mlr-2.5/mlr/tests/testthat/test_regr_crs.R |only mlr-2.5/mlr/tests/testthat/test_regr_ctree.R |only mlr-2.5/mlr/tests/testthat/test_regr_cubist.R |only mlr-2.5/mlr/tests/testthat/test_regr_earth.R |only mlr-2.5/mlr/tests/testthat/test_regr_elmNN.R |only mlr-2.5/mlr/tests/testthat/test_regr_extraTrees.R |only mlr-2.5/mlr/tests/testthat/test_regr_fnn.R |only mlr-2.5/mlr/tests/testthat/test_regr_frbs.R |only mlr-2.5/mlr/tests/testthat/test_regr_gbm.R |only mlr-2.5/mlr/tests/testthat/test_regr_glmnet.R |only mlr-2.5/mlr/tests/testthat/test_regr_kknn.R |only mlr-2.5/mlr/tests/testthat/test_regr_km.R |only mlr-2.5/mlr/tests/testthat/test_regr_ksvm.R |only mlr-2.5/mlr/tests/testthat/test_regr_laGP.R |only mlr-2.5/mlr/tests/testthat/test_regr_lm.R |only mlr-2.5/mlr/tests/testthat/test_regr_mob.R |only mlr-2.5/mlr/tests/testthat/test_regr_nnet.R |only mlr-2.5/mlr/tests/testthat/test_regr_nodeHarvest.R |only mlr-2.5/mlr/tests/testthat/test_regr_penalized_lasso.R |only mlr-2.5/mlr/tests/testthat/test_regr_penalized_ridge.R |only mlr-2.5/mlr/tests/testthat/test_regr_plsr.R |only mlr-2.5/mlr/tests/testthat/test_regr_randomForest.R |only mlr-2.5/mlr/tests/testthat/test_regr_randomForestSRC.R |only mlr-2.5/mlr/tests/testthat/test_regr_randomForest_se.R |only mlr-2.5/mlr/tests/testthat/test_regr_ranger.R |only mlr-2.5/mlr/tests/testthat/test_regr_rknn.R |only mlr-2.5/mlr/tests/testthat/test_regr_rpart.R |only mlr-2.5/mlr/tests/testthat/test_regr_rsm.R |only mlr-2.5/mlr/tests/testthat/test_regr_slim.R |only mlr-2.5/mlr/tests/testthat/test_regr_svm.R |only mlr-2.5/mlr/tests/testthat/test_regr_xgboost.R |only mlr-2.5/mlr/tests/testthat/test_regr_xyf.R |only mlr-2.5/mlr/tests/testthat/test_stack.R | 64 mlr-2.5/mlr/tests/testthat/test_surv_glmboost.R | 2 mlr-2.5/mlr/tests/testthat/test_surv_randomForestSRC.R | 2 mlr-2.5/mlr/tests/testthat/test_surv_ranger.R |only mlr-2.5/mlr/tests/testthat/test_surv_rpart.R |only mlr-2.5/mlr/tests/testthat/test_tune_ModelMultiplexer.R | 10 mlr-2.5/mlr/tests/testthat/test_tune_tuneCMAES.R | 21 mlr-2.5/mlr/tests/testthat/test_tune_tuneGenSA.R |only mlr-2.5/mlr/tests/testthat/test_tune_tuneGrid.R | 13 mlr-2.5/mlr/tests/testthat/test_tune_tuneIrace.R | 116 - mlr-2.5/mlr/tests/testthat/test_tune_tuneMBO.R | 35 mlr-2.5/mlr/tests/testthat/test_tune_tuneParamsMultiCrit.R | 48 mlr-2.5/mlr/tests/testthat/test_tune_tuneRandom.R | 15 mlr-2.5/mlr/tests/testthat/test_tune_tuneThreshold.R | 2 mlr-2.5/mlr/vignettes/mlr.Rmd | 57 629 files changed, 6860 insertions(+), 3810 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9.3 dated 2015-08-25 and 0.9.4 dated 2015-11-20
curl-0.9.3/curl/src/winhttp32.def |only curl-0.9.3/curl/src/winhttp64.def |only curl-0.9.3/curl/tools/options.R |only curl-0.9.4/curl/DESCRIPTION | 6 +++--- curl-0.9.4/curl/MD5 | 18 +++++++++--------- curl-0.9.4/curl/NEWS | 5 +++++ curl-0.9.4/curl/R/options.R |only curl-0.9.4/curl/R/utilities.R | 18 ------------------ curl-0.9.4/curl/man/curl_options.Rd | 22 ++++++++++++++-------- curl-0.9.4/curl/src/Makevars.in | 5 ----- curl-0.9.4/curl/src/Makevars.win | 20 ++++++++------------ curl-0.9.4/curl/src/winhttp32.def.in |only curl-0.9.4/curl/src/winhttp64.def.in |only 13 files changed, 39 insertions(+), 55 deletions(-)
Title: Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Description: Implements a wide variety of one and two-parameter Bayesian CRM
designs. The program can run interactively, allowing the user to enter outcomes
after each cohort has been recruited, or via simulation to assess operating
characteristics.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between bcrm versions 0.4.5 dated 2015-09-23 and 0.4.6 dated 2015-11-20
bcrm-0.4.5/bcrm/R/bcrm_0.4.5.R |only bcrm-0.4.6/bcrm/DESCRIPTION | 18 +++++++++++------- bcrm-0.4.6/bcrm/MD5 | 14 +++++++------- bcrm-0.4.6/bcrm/NAMESPACE | 4 ++-- bcrm-0.4.6/bcrm/NEWS | 7 +++++++ bcrm-0.4.6/bcrm/R/bcrm_0.4.6.R |only bcrm-0.4.6/bcrm/man/bcrm-package.Rd | 4 ++-- bcrm-0.4.6/bcrm/man/bcrm.Rd | 6 +++++- bcrm-0.4.6/bcrm/man/print.bcrm.Rd | 6 +++++- 9 files changed, 39 insertions(+), 20 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.2.1 dated 2015-11-15 and 0.3.0 dated 2015-11-20
rnrfa-0.2.1/rnrfa/R/NRFA_TSdata.R |only rnrfa-0.2.1/rnrfa/R/NRFA_TSmetadata.R |only rnrfa-0.2.1/rnrfa/man/NRFA_TSdata.Rd |only rnrfa-0.2.1/rnrfa/man/NRFA_TSmetadata.Rd |only rnrfa-0.3.0/rnrfa/DESCRIPTION | 6 +++--- rnrfa-0.3.0/rnrfa/MD5 | 16 ++++++++++------ rnrfa-0.3.0/rnrfa/NAMESPACE | 6 ++++-- rnrfa-0.3.0/rnrfa/R/CMR.R |only rnrfa-0.3.0/rnrfa/R/CMRmeta.R |only rnrfa-0.3.0/rnrfa/R/GDF.R |only rnrfa-0.3.0/rnrfa/R/GDFmeta.R |only rnrfa-0.3.0/rnrfa/man/CMR.Rd |only rnrfa-0.3.0/rnrfa/man/CMRmeta.Rd |only rnrfa-0.3.0/rnrfa/man/GDF.Rd |only rnrfa-0.3.0/rnrfa/man/GDFmeta.Rd |only 15 files changed, 17 insertions(+), 11 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-4 dated 2015-10-23 and 0.1-5 dated 2015-11-20
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 28 +++++----- NAMESPACE | 2 R/DESP_SRL_B.R | 38 ++++++++----- R/sqR_Lasso.R | 131 +++++++++++++---------------------------------- man/DESP-internal.Rd | 2 man/DESP-package.Rd | 4 - man/DESP_SRL_B.Rd | 9 ++- man/scsSOCP.Rd | 94 +++++++++++++++++++++++++++++++++ man/sqR_Lasso.Rd | 14 +++-- src/Makevars | 4 - src/scsSRL_B.c |only src/scsSolveSOCP.c | 24 ++++++-- src/scsSqR_Lasso.c |only src/scsSqR_Lasso_solve.c |only src/scsSqR_Lasso_solve.h |only 17 files changed, 224 insertions(+), 139 deletions(-)
Title: Model-Based Clustering and Classification with the Multivariate
t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the expectation conditional-maximization algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Jaymeson R. Wickins, Nicholas M. Boers, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews <jeff.andrews@ubc.ca>
Diff between teigen versions 2.0.81 dated 2015-05-27 and 2.1.0 dated 2015-11-20
teigen-2.0.81/teigen/R/deltaup.R |only teigen-2.0.81/teigen/R/estimateTime.R |only teigen-2.0.81/teigen/R/modelgen.R |only teigen-2.0.81/teigen/R/plot.teigen.R |only teigen-2.0.81/teigen/R/print.teigen.R |only teigen-2.0.81/teigen/R/summary.teigen.R |only teigen-2.0.81/teigen/R/tBICcalc.R |only teigen-2.0.81/teigen/R/tICLcalc.R |only teigen-2.0.81/teigen/R/taginit.R |only teigen-2.0.81/teigen/R/tagupdate.R |only teigen-2.0.81/teigen/R/tcontrandz.R |only teigen-2.0.81/teigen/R/tdginit.R |only teigen-2.0.81/teigen/R/tdgupdate.R |only teigen-2.0.81/teigen/R/tdiscrandz.R |only teigen-2.0.81/teigen/R/teigen.R |only teigen-2.0.81/teigen/R/teigen.parallel.R |only teigen-2.0.81/teigen/R/tfminup.R |only teigen-2.0.81/teigen/R/tft.R |only teigen-2.0.81/teigen/R/tgivenz.R |only teigen-2.0.81/teigen/R/tkmeansz.R |only teigen-2.0.81/teigen/R/tlambdaginit.R |only teigen-2.0.81/teigen/R/tlambdagupdate.R |only teigen-2.0.81/teigen/R/tmuginit.R |only teigen-2.0.81/teigen/R/tmugupdate.R |only teigen-2.0.81/teigen/R/tngupdate.R |only teigen-2.0.81/teigen/R/tpigupdate.R |only teigen-2.0.81/teigen/R/tsginit.R |only teigen-2.0.81/teigen/R/tsginitc.R |only teigen-2.0.81/teigen/R/tsgupdate.R |only teigen-2.0.81/teigen/R/tsigmainvup.R |only teigen-2.0.81/teigen/R/tsigmaup.R |only teigen-2.0.81/teigen/R/tuniformz.R |only teigen-2.0.81/teigen/R/tvginit.R |only teigen-2.0.81/teigen/R/twinit.R |only teigen-2.0.81/teigen/R/twupdate.R |only teigen-2.0.81/teigen/R/tzupdate.R |only teigen-2.0.81/teigen/R/yxf7.R |only teigen-2.0.81/teigen/R/yxf8.R |only teigen-2.0.81/teigen/man/teigen.parallel.Rd |only teigen-2.1.0/teigen/ChangeLog | 14 +++++ teigen-2.1.0/teigen/DESCRIPTION | 16 +++--- teigen-2.1.0/teigen/MD5 | 62 ++++++------------------- teigen-2.1.0/teigen/NAMESPACE | 8 ++- teigen-2.1.0/teigen/R/teigen.r |only teigen-2.1.0/teigen/data |only teigen-2.1.0/teigen/man/ckd.Rd |only teigen-2.1.0/teigen/man/plot.teigen.Rd | 59 +++++++++++++++++++---- teigen-2.1.0/teigen/man/print.teigen.Rd | 4 - teigen-2.1.0/teigen/man/summary.teigen.Rd | 13 ++++- teigen-2.1.0/teigen/man/teigen-package.Rd | 10 ++-- teigen-2.1.0/teigen/man/teigen.Rd | 69 ++++++++++++++++++---------- teigen-2.1.0/teigen/src |only 52 files changed, 154 insertions(+), 101 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.3.6 dated 2015-09-17 and 1.3.7 dated 2015-11-20
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/glmmLasso_noRE.R | 77 +++++++++++++++++++++++++++++---------------- R/glmm_final.smooth_noRE.R | 26 ++++----------- man/glmmLasso.rd | 4 +- 5 files changed, 68 insertions(+), 55 deletions(-)
Title: A Package for Bayesian Meta-Analysis and Meta-Regression
Description: Provides a collection of functions for conducting meta-analyses under Bayesian context in R. The package includes functions for computing various effect size or outcome measures (e.g. odds ratios, mean difference and incidence rate ratio) for different types of data based on MCMC simulations. Users are allowed to fit fixed- and random-effects models with different priors to the data. Meta-regression can be carried out if effects of additional covariates are observed. Furthermore, the package provides functions for creating posterior distribution plots and forest plot to display main model output. Traceplots and some other diagnostic plots are also available for assessing model fit and performance.
Author: Tao Ding, Gianluca Baio
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between bmeta versions 0.1 dated 2015-10-29 and 0.1.1 dated 2015-11-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bmeta.R | 44 ++++++++++++++++++++++++++------------------ man/bmeta-package.Rd | 4 ++-- 4 files changed, 35 insertions(+), 27 deletions(-)
Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between snplist versions 0.14 dated 2015-09-21 and 0.15 dated 2015-11-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 8 ++++++-- R/getBioMartData.R | 2 +- inst/doc/snplist.Rnw | 2 +- inst/doc/snplist.pdf |binary man/getBioMartData.Rd | 17 ++++++++++++++--- man/snplist-package.Rd | 4 ++-- vignettes/snplist.Rnw | 2 +- 9 files changed, 37 insertions(+), 22 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help organize Monte Carlo simulations in R. The
tools provided control the structure and back-end of the Monte Carlo simulations
by utilizing a generate-analyse-summarise strategy. The functions control common
simulation issues such as re-simulating non-convergent results, support parallel
back-end computations, save and restore temporary files, aggregate results
across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.3 dated 2015-10-05 and 0.4.1 dated 2015-11-20
SimDesign-0.3/SimDesign/man/main.Rd |only SimDesign-0.4.1/SimDesign/DESCRIPTION | 23 +- SimDesign-0.4.1/SimDesign/MD5 | 51 ++--- SimDesign-0.4.1/SimDesign/NAMESPACE | 6 SimDesign-0.4.1/SimDesign/R/SimDesign.R | 3 SimDesign-0.4.1/SimDesign/R/SimDesign_functions.R | 48 +++- SimDesign-0.4.1/SimDesign/R/aggregate_simulations.R | 31 ++- SimDesign-0.4.1/SimDesign/R/analysis.R | 49 +++- SimDesign-0.4.1/SimDesign/R/functions.R | 116 ++++++----- SimDesign-0.4.1/SimDesign/R/runSimulation.R | 168 ++++++++++------- SimDesign-0.4.1/SimDesign/R/summary_functions.R | 160 +++++++++++----- SimDesign-0.4.1/SimDesign/R/util.R | 5 SimDesign-0.4.1/SimDesign/man/ECR.Rd | 9 SimDesign-0.4.1/SimDesign/man/EDR.Rd | 13 - SimDesign-0.4.1/SimDesign/man/MAE.Rd | 29 ++ SimDesign-0.4.1/SimDesign/man/RE.Rd | 10 - SimDesign-0.4.1/SimDesign/man/RMSE.Rd | 33 ++- SimDesign-0.4.1/SimDesign/man/SimDesign.Rd | 2 SimDesign-0.4.1/SimDesign/man/SimDesign_functions.Rd | 16 + SimDesign-0.4.1/SimDesign/man/aggregate_simulations.Rd | 12 - SimDesign-0.4.1/SimDesign/man/analyse.Rd | 21 +- SimDesign-0.4.1/SimDesign/man/bias.Rd | 30 ++- SimDesign-0.4.1/SimDesign/man/check_error.Rd | 6 SimDesign-0.4.1/SimDesign/man/generate.Rd | 13 - SimDesign-0.4.1/SimDesign/man/runSimulation.Rd | 163 +++++++++------- SimDesign-0.4.1/SimDesign/man/summarise.Rd | 17 + SimDesign-0.4.1/SimDesign/tests/tests/test-SimDesign.R | 58 +++++ 27 files changed, 696 insertions(+), 396 deletions(-)
Title: Efficient Score Statistics for Genome-Wide SNP Set Analysis
Description: An implementation of the use of efficient score statistics
in genome-wide SNP set analysis with complex traits. Three standard score statistics
(Cox, binomial, and Gaussian) are provided, but the package is easily extensible to
include others. Code implementing the inferential procedure is primarily written in C++ and
utilizes parallelization of the analysis to reduce runtime. A supporting function offers
simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between RSNPset versions 0.4 dated 2015-02-11 and 0.5 dated 2015-11-20
RSNPset-0.4/RSNPset/inst/doc/rsnpset.R |only RSNPset-0.4/RSNPset/inst/doc/rsnpset.Rnw |only RSNPset-0.4/RSNPset/inst/doc/rsnpset.pdf |only RSNPset-0.4/RSNPset/vignettes/rsnpset.Rnw |only RSNPset-0.5/RSNPset/DESCRIPTION | 18 +++++++++--------- RSNPset-0.5/RSNPset/MD5 | 22 +++++++++++----------- RSNPset-0.5/RSNPset/NAMESPACE | 1 + RSNPset-0.5/RSNPset/NEWS | 5 +++++ RSNPset-0.5/RSNPset/R/rsnpset.R | 2 +- RSNPset-0.5/RSNPset/build/vignette.rds |binary RSNPset-0.5/RSNPset/inst/doc/RSNPset.R |only RSNPset-0.5/RSNPset/inst/doc/RSNPset.Rnw |only RSNPset-0.5/RSNPset/inst/doc/RSNPset.pdf |only RSNPset-0.5/RSNPset/man/RSNPset-package.Rd | 6 +++--- RSNPset-0.5/RSNPset/man/rsnpset.Rd | 6 ++++-- RSNPset-0.5/RSNPset/vignettes/RSNPset.Rnw |only 16 files changed, 34 insertions(+), 26 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.6.2 dated 2015-10-11 and 0.6.3 dated 2015-11-20
PRIMsrc-0.6.2/PRIMsrc/inst/doc/Abstract.JCB2016.pdf |only PRIMsrc-0.6.2/PRIMsrc/inst/doc/PRIMsrc_0.6.2.pdf |only PRIMsrc-0.6.3/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.3/PRIMsrc/MD5 | 51 PRIMsrc-0.6.3/PRIMsrc/NAMESPACE | 28 PRIMsrc-0.6.3/PRIMsrc/R/PRIMsrc.internal.r | 344 +- PRIMsrc-0.6.3/PRIMsrc/R/PRIMsrc.r | 3094 ++++++++++---------- PRIMsrc-0.6.3/PRIMsrc/inst/CITATION | 232 - PRIMsrc-0.6.3/PRIMsrc/inst/NEWS | 298 + PRIMsrc-0.6.3/PRIMsrc/inst/doc/PRIMsrc_0.6.3.pdf |only PRIMsrc-0.6.3/PRIMsrc/man/PrimSRC-package.Rd | 34 PRIMsrc-0.6.3/PRIMsrc/man/PrimSRC.news.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/Real.1-data.Rd | 13 PRIMsrc-0.6.3/PRIMsrc/man/Real.2-data.Rd | 25 PRIMsrc-0.6.3/PRIMsrc/man/Synthetic.1-data.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/Synthetic.1b-data.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/Synthetic.2-data.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/Synthetic.3-data.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/Synthetic.4-data.Rd | 8 PRIMsrc-0.6.3/PRIMsrc/man/plot.Rd | 80 PRIMsrc-0.6.3/PRIMsrc/man/plot_boxkm.Rd | 42 PRIMsrc-0.6.3/PRIMsrc/man/plot_boxtrace.Rd | 38 PRIMsrc-0.6.3/PRIMsrc/man/plot_boxtraj.Rd | 62 PRIMsrc-0.6.3/PRIMsrc/man/plot_profile.Rd | 48 PRIMsrc-0.6.3/PRIMsrc/man/predict.Rd | 83 PRIMsrc-0.6.3/PRIMsrc/man/print.Rd | 54 PRIMsrc-0.6.3/PRIMsrc/man/sbh.Rd | 184 - PRIMsrc-0.6.3/PRIMsrc/man/summary.Rd | 54 28 files changed, 2509 insertions(+), 2311 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4.1 dated 2015-10-16 and 1.4.2 dated 2015-11-20
DESCRIPTION | 6 MD5 | 20 - R/gwas.R | 1 R/gwas2.R | 1 R/wgr.R | 4 build/vignette.rds |binary inst/CITATION | 1 inst/doc/vignette.Rmd | 428 +++++++++++-------------- inst/doc/vignette.html | 838 +++++++++++++++++++------------------------------ man/NAM-package.Rd | 2 vignettes/vignette.Rmd | 428 +++++++++++-------------- 11 files changed, 738 insertions(+), 991 deletions(-)
Title: Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Description: Tools for detecting and summarize influential cases that
can affect exploratory and confirmatory factor analysis models as well as
structural equation models more generally.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between faoutlier versions 0.5 dated 2015-04-27 and 0.6.1 dated 2015-11-20
faoutlier-0.5/faoutlier/inst/doc |only faoutlier-0.6.1/faoutlier/DESCRIPTION | 11 ++--- faoutlier-0.6.1/faoutlier/MD5 | 40 +++++++++--------- faoutlier-0.6.1/faoutlier/NAMESPACE | 6 ++ faoutlier-0.6.1/faoutlier/R/GOF.R | 37 ++++++++++++---- faoutlier-0.6.1/faoutlier/R/LD.R | 32 +++++++------- faoutlier-0.6.1/faoutlier/R/faoutlier.R | 34 ++++++++------- faoutlier-0.6.1/faoutlier/R/gCD.R | 44 ++++++++++++++++---- faoutlier-0.6.1/faoutlier/inst/CITATION |only faoutlier-0.6.1/faoutlier/man/GOF.Rd | 21 +++++++-- faoutlier-0.6.1/faoutlier/man/LD.Rd | 10 ++-- faoutlier-0.6.1/faoutlier/man/faoutlier.Rd | 2 faoutlier-0.6.1/faoutlier/man/forward.search.Rd | 7 +-- faoutlier-0.6.1/faoutlier/man/gCD.Rd | 18 +++++++- faoutlier-0.6.1/faoutlier/man/holzinger.Rd | 2 faoutlier-0.6.1/faoutlier/man/holzinger.outlier.Rd | 2 faoutlier-0.6.1/faoutlier/man/obs.resid.Rd | 5 +- faoutlier-0.6.1/faoutlier/man/robustMD.Rd | 3 - faoutlier-0.6.1/faoutlier/man/setCluster.Rd | 3 - faoutlier-0.6.1/faoutlier/tests/testthat/test-GOF.R | 2 faoutlier-0.6.1/faoutlier/tests/testthat/test-LD.R | 34 +++++++-------- faoutlier-0.6.1/faoutlier/tests/testthat/test-gCD.R | 6 ++ 22 files changed, 206 insertions(+), 113 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.2 dated 2015-11-10 and 0.6.2-1 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/make.table.of.frequencies.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.48 dated 2015-08-11 and 0.49 dated 2015-11-19
DESCRIPTION | 9 +- MD5 | 170 +++++++++++++++++++++---------------------- NAMESPACE | 2 R/diagnose.R | 22 ++++- R/util.R | 17 ++-- build/vignette.rds |binary configure | 2 inst/doc/diagnostics.html | 44 +++++------ inst/include/libifa-rpf.h | 3 inst/tests/test-sumscore.R | 6 + man/ChenThissen1997.Rd | 6 + man/EAPscores.Rd | 2 man/LSAT6.Rd | 2 man/LSAT7.Rd | 2 man/SitemFit.Rd | 7 + man/SitemFit1.Rd | 2 man/as.IFAgroup.Rd | 2 man/bestToOmit.Rd | 2 man/compressDataFrame.Rd | 2 man/crosstabTest.Rd | 2 man/expandDataFrame.Rd | 2 man/fromFactorLoading.Rd | 2 man/fromFactorThreshold.Rd | 2 man/itemOutcomeBySumScore.Rd | 2 man/kct.Rd | 2 man/logit.Rd | 2 man/multinomialFit.Rd | 2 man/observedSumScore.Rd | 2 man/omitItems.Rd | 2 man/omitMostMissing.Rd | 2 man/orderCompletely.Rd | 2 man/ordinal.gamma.Rd | 2 man/ptw2011.gof.test.Rd | 2 man/read.flexmirt.Rd | 2 man/rpf.1dim-class.Rd | 2 man/rpf.1dim.drm-class.Rd | 2 man/rpf.1dim.fit.Rd | 2 man/rpf.1dim.graded-class.Rd | 2 man/rpf.1dim.grm-class.Rd | 2 man/rpf.1dim.moment.Rd | 2 man/rpf.1dim.residual.Rd | 2 man/rpf.1dim.stdresidual.Rd | 2 man/rpf.base-class.Rd | 2 man/rpf.dLL.Rd | 2 man/rpf.dTheta.Rd | 2 man/rpf.drm.Rd | 2 man/rpf.grm.Rd | 2 man/rpf.id_of.Rd | 2 man/rpf.info.Rd | 2 man/rpf.introduction.Rd | 2 man/rpf.logprob.Rd | 2 man/rpf.mcm.Rd | 2 man/rpf.mdim-class.Rd | 2 man/rpf.mdim.drm-class.Rd | 2 man/rpf.mdim.graded-class.Rd | 2 man/rpf.mdim.grm-class.Rd | 2 man/rpf.mdim.mcm-class.Rd | 2 man/rpf.mdim.nrm-class.Rd | 2 man/rpf.mean.info.Rd | 2 man/rpf.mean.info1.Rd | 2 man/rpf.modify.Rd | 2 man/rpf.nrm.Rd | 2 man/rpf.numParam.Rd | 2 man/rpf.numSpec.Rd | 2 man/rpf.ogive.Rd | 5 - man/rpf.paramInfo.Rd | 2 man/rpf.prob.Rd | 2 man/rpf.rescale.Rd | 2 man/rpf.rparam.Rd | 2 man/rpf.sample.Rd | 2 man/science.Rd | 2 man/stripData.Rd | 2 man/sumScoreEAP.Rd | 6 - man/sumScoreEAPTest.Rd | 8 +- man/tabulateRows.Rd | 2 man/toFactorLoading.Rd | 2 man/toFactorThreshold.Rd | 2 man/write.flexmirt.Rd | 2 src/Makevars | 6 - src/ba81quad.cpp | 35 +++----- src/ba81quad.h | 8 +- src/diagnose.cpp | 32 ++++---- src/eap.cpp | 3 src/glue.cpp | 68 +++++++++-------- src/libifa-rpf.cpp | 3 src/m2.cpp | 3 86 files changed, 313 insertions(+), 278 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.6 dated 2015-10-04 and 0.6.1 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/TestClass.R | 16 ++++++++-------- R/generate.mirt_object.R | 2 +- R/selection_criteria.R | 14 ++++++-------- 5 files changed, 24 insertions(+), 26 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.13 dated 2015-09-09 and 1.14 dated 2015-11-19
DESCRIPTION | 9 MD5 | 241 ++++++++++----------- NAMESPACE | 4 NEWS | 39 +++ R/00-classes.R | 289 +++++-------------------- R/02-item_methods.R | 65 ++--- R/03-estimation.R | 408 ++++++++++++------------------------ R/DIF.R | 24 +- R/DTF.R | 48 +--- R/Discrete-methods.R | 68 +++--- R/EMstep.group.R | 23 -- R/EMstep.utils.R | 18 - R/LoadPars.R | 4 R/M2.R | 48 ++-- R/MHRM.group.R | 6 R/Mixed-methods.R | 95 ++++---- R/MultipleGroup-methods.R | 44 +-- R/PLCI.mirt.R | 74 +++--- R/PrepData.R | 8 R/SE.methods.R | 36 --- R/SingleGroup-methods.R | 320 +++++++++++++++------------- R/boot.mirt.R | 26 -- R/calcLogLik.R | 58 ++--- R/empirical_rxx.R |only R/expected.test.R | 6 R/extract.group.R | 6 R/extract.item.R | 11 R/extract.mirt.R |only R/fixef.R | 4 R/fscores.R | 41 ++- R/fscores.internal.R | 130 +++++------ R/imputeMissing.R | 16 - R/itemGAM.R | 8 R/itemfit.R | 42 +-- R/iteminfo.R | 13 - R/itemplot.R | 16 - R/itemplot.internal.R | 77 +++--- R/key2binary.R | 16 + R/marginal_rxx.R | 9 R/mdirt.R | 13 - R/mirt-package.R | 2 R/mirt.R | 19 + R/mirt.model.R | 12 - R/mod2values.R | 12 - R/model.elements.R | 30 ++ R/multipleGroup.R | 4 R/personfit.R | 22 - R/randef.R | 35 +-- R/shinyItemplot.R | 8 R/simdata.R | 2 R/testinfo.R | 7 R/utils.R | 94 +++----- R/wald.R | 16 - README.md | 4 man/Bock1997.Rd | 5 man/DIF.Rd | 2 man/DTF.Rd | 2 man/DiscreteClass-class.Rd | 55 +--- man/LSAT6.Rd | 3 man/LSAT7.Rd | 3 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/MixedClass-class.Rd | 57 +---- man/MultipleGroupClass-class.Rd | 56 +--- man/PLCI.mirt.Rd | 3 man/SAT12.Rd | 3 man/Science.Rd | 3 man/SingleGroupClass-class.Rd | 52 +--- man/anova-method.Rd | 3 man/averageMI.Rd | 3 man/bfactor.Rd | 4 man/boot.mirt.Rd | 3 man/coef-method.Rd | 3 man/createItem.Rd | 3 man/deAyala.Rd | 3 man/empirical_rxx.Rd |only man/expand.table.Rd | 4 man/expected.item.Rd | 3 man/expected.test.Rd | 3 man/extract.group.Rd | 5 man/extract.item.Rd | 5 man/extract.mirt.Rd |only man/fixef.Rd | 2 man/fscores.Rd | 39 ++- man/imputeMissing.Rd | 6 man/itemGAM.Rd | 9 man/itemfit.Rd | 6 man/iteminfo.Rd | 10 man/itemplot.Rd | 5 man/key2binary.Rd | 18 + man/marginal_rxx.Rd | 10 man/mdirt.Rd | 11 man/mirt-package.Rd | 2 man/mirt.Rd | 24 +- man/mirt.model.Rd | 12 - man/mirtCluster.Rd | 3 man/mixedmirt.Rd | 5 man/mod2values.Rd | 2 man/multipleGroup.Rd | 6 man/personfit.Rd | 4 man/plot-method.Rd | 9 man/print-method.Rd | 5 man/probtrace.Rd | 3 man/randef.Rd | 2 man/residuals-method.Rd | 5 man/show-method.Rd | 5 man/simdata.Rd | 8 man/summary-method.Rd | 3 man/testinfo.Rd | 5 man/wald.Rd | 2 src/dpars.cpp | 211 +++++++++++------- tests/extratests/test-02-wideData.R | 4 tests/tests/test-00-basics.R |only tests/tests/test-01-mirtOne.R | 31 +- tests/tests/test-02-mirtTwo.R | 34 +-- tests/tests/test-03-bfactor.R | 22 - tests/tests/test-04-multipleGroup.R | 21 - tests/tests/test-05-confmirtOne.R | 8 tests/tests/test-06-confmirtTwo.R | 20 + tests/tests/test-07-mixedmirt.R | 20 - tests/tests/test-08-createItem.R | 3 tests/tests/test-10-extras.R | 20 - tests/tests/test-11-discrete.R | 19 + 124 files changed, 1681 insertions(+), 1875 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.2.2 dated 2015-09-08 and 2.2.3 dated 2015-11-19
emil-2.2.2/emil/man/has_na.Rd |only emil-2.2.2/emil/src/has_na.cpp |only emil-2.2.3/emil/DESCRIPTION | 17 +++--- emil-2.2.3/emil/MD5 | 33 +++++++------ emil-2.2.3/emil/NAMESPACE | 7 +- emil-2.2.3/emil/NEWS.md | 10 +++- emil-2.2.3/emil/R/RcppExports.R | 16 ------ emil-2.2.3/emil/R/RcppWrappers.r | 28 ----------- emil-2.2.3/emil/R/e1071.r |only emil-2.2.3/emil/R/modeling_procedure.r | 55 +++++++++++++++------- emil-2.2.3/emil/R/preprocessing.r | 2 emil-2.2.3/emil/R/resampling.r | 11 ++-- emil-2.2.3/emil/man/fit_naive_bayes.Rd |only emil-2.2.3/emil/man/fit_svm.Rd |only emil-2.2.3/emil/man/image.resample.Rd | 2 emil-2.2.3/emil/man/learning_curve.Rd | 2 emil-2.2.3/emil/man/predict_naive_bayes.Rd |only emil-2.2.3/emil/man/predict_svm.Rd |only emil-2.2.3/emil/man/subtree.Rd | 2 emil-2.2.3/emil/src/RcppExports.cpp | 44 ----------------- emil-2.2.3/emil/tests/testthat/test-cppfunction.r | 17 ------ 21 files changed, 88 insertions(+), 158 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.4.2 dated 2015-08-04 and 1.6.1 dated 2015-11-19
DESCRIPTION | 8 MD5 | 287 +++++----- NAMESPACE | 29 - R/AllClasses.R | 85 ++ R/AllGenerics.R | 12 R/R-to-variable.R | 32 - R/add-variable.R | 49 + R/api.R | 63 +- R/append-dataset.R | 42 - R/as-data-frame.R | 2 R/auth.R | 9 R/batches.R | 7 R/categorical-array.R | 26 R/categories.R | 66 +- R/combine.R |only R/context-manager.R |only R/copy.R |only R/crest.R | 10 R/crunch.R | 1 R/cube-query.R | 50 - R/cube-result.R | 54 + R/dataset-extract.R | 96 ++- R/dataset.R | 53 + R/edit-lock.R |only R/expressions.R | 2 R/filters.R |only R/find.R | 10 R/get-datasets.R | 4 R/github.R |only R/hide-variables.R | 37 + R/json.R | 5 R/log.R | 58 +- R/misc.R | 58 +- R/multiple-response.R | 6 R/new-dataset.R | 14 R/share.R | 16 R/show.R | 7 R/subvariables.R | 90 ++- R/teams.R | 7 R/tuple.R | 13 R/univariate.R | 76 +- R/user.R | 4 R/variable-definition.R |only R/variable-summary.R | 43 - R/variable-to-R.R | 38 + R/variable-update.R | 105 ++- R/variable.R | 7 R/versions.R | 2 R/zcl.R | 1 inst/doc/analyze.R | 21 inst/doc/analyze.Rmd | 42 + inst/doc/analyze.html | 69 +- inst/doc/array-variables.R | 23 inst/doc/array-variables.Rmd | 23 inst/doc/array-variables.html | 256 +++----- inst/doc/datasets.R | 9 inst/doc/datasets.Rmd | 9 inst/doc/datasets.html | 11 inst/doc/derive.html | 4 inst/doc/getting-started.html | 12 inst/doc/variable-order.html | 6 inst/doc/variables.R | 13 inst/doc/variables.Rmd | 31 - inst/doc/variables.html | 40 + man/Categories.Rd | 32 - man/ContextManager.Rd |only man/Subvariables.Rd | 5 man/VariableDefinition.Rd |only man/VariableOrder-extract.Rd | 16 man/appendDataset.Rd | 9 man/as.environment-CrunchDataset-method.Rd |only man/c-categories.Rd |only man/catalog-extract.Rd | 40 - man/checkForNewVersion.Rd |only man/consent.Rd |only man/copyVariable.Rd |only man/crunch-uni.Rd | 18 man/crunchAPI.Rd | 14 man/dataset-extract.Rd | 38 - man/dataset-update.Rd | 6 man/delete.Rd | 9 man/deleteSubvariables.Rd |only man/deleteVariables.Rd |only man/describe-catalog.Rd | 5 man/describe.Rd | 8 man/exclusion.Rd |only man/handleAPIresponse.Rd |only man/lock.Rd |only man/logMessage.Rd |only man/makeArray.Rd | 5 man/startLog.Rd |only man/subvars-extract.Rd | 25 man/table.Rd | 2 man/temp.options.Rd |only man/toVariable.Rd | 3 man/tojson-crunch.Rd | 3 man/tuple-methods.Rd | 2 man/variable-extract.Rd | 12 man/variable-to-R.Rd | 12 man/variable-update.Rd | 6 man/with-context-manager.Rd |only tests/testthat/api/datasets/dataset1/variables.json | 8 tests/testthat/api/datasets/dataset1/variables/birthyr.json | 3 tests/testthat/api/datasets/dataset1/variables/catarray.json | 5 tests/testthat/api/datasets/dataset1/variables/gender.json | 3 tests/testthat/api/datasets/dataset1/variables/mymrset.json | 3 tests/testthat/api/datasets/dataset1/variables/starttime.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar1.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar2.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar3.json | 3 tests/testthat/api/datasets/dataset1/variables/textVar.json | 3 tests/testthat/dataset-fixtures |only tests/testthat/github-versions.json |only tests/testthat/helper.R | 126 +++- tests/testthat/test-active-filter.R |only tests/testthat/test-add-array.R | 4 tests/testthat/test-add-variable-definition.R |only tests/testthat/test-add-variable.R | 43 + tests/testthat/test-api.R | 18 tests/testthat/test-append-arrays.R | 105 +++ tests/testthat/test-appending.R | 34 - tests/testthat/test-as-data-frame.R | 35 - tests/testthat/test-auth.R | 12 tests/testthat/test-categories.R | 148 ++++- tests/testthat/test-combine.R |only tests/testthat/test-context-manager.R |only tests/testthat/test-copy-variable.R |only tests/testthat/test-cube-errors.R | 7 tests/testthat/test-cube-with-array.R | 56 + tests/testthat/test-cube-with-expression.R |only tests/testthat/test-cubes.R | 57 + tests/testthat/test-dataset.R | 21 tests/testthat/test-deep-copy-variable.R |only tests/testthat/test-edit-lock.R |only tests/testthat/test-exclusion-filter.R |only tests/testthat/test-expression.R | 23 tests/testthat/test-filters.R |only tests/testthat/test-github.R |only tests/testthat/test-helper.R |only tests/testthat/test-logging.R |only tests/testthat/test-make-array.R | 35 - tests/testthat/test-misc.R | 23 tests/testthat/test-new-dataset.R | 42 + tests/testthat/test-share.R | 43 - tests/testthat/test-teams.R | 6 tests/testthat/test-update-array.R | 10 tests/testthat/test-update-with-missing.R |only tests/testthat/test-update.R | 75 -- tests/testthat/test-variable-catalog.R | 4 tests/testthat/test-variable-delete.R |only tests/testthat/test-variable-summary.R | 54 - tests/testthat/test-variables.R | 31 - tests/testthat/test-versioning.R | 62 +- tests/testthat/test-weighting.R | 54 + vignettes/analyze.RData |binary vignettes/analyze.Rmd | 42 + vignettes/array-variables.RData |binary vignettes/array-variables.Rmd | 23 vignettes/datasets.Rmd | 9 vignettes/derive.RData |binary vignettes/getting-started.RData |binary vignettes/variable-order.RData |binary vignettes/variables.RData |binary vignettes/variables.Rmd | 31 - 164 files changed, 2459 insertions(+), 1234 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.6 dated 2015-10-19 and 1.0.7 dated 2015-11-19
CHNOSZ-1.0.6/CHNOSZ/demo/CO2Ac.R |only CHNOSZ-1.0.6/CHNOSZ/demo/diagram.R |only CHNOSZ-1.0.6/CHNOSZ/demo/nonideal.R |only CHNOSZ-1.0.6/CHNOSZ/demo/phosphate.R |only CHNOSZ-1.0.6/CHNOSZ/tests/testthat/test-mosaic.R.old |only CHNOSZ-1.0.7/CHNOSZ/DESCRIPTION | 8 CHNOSZ-1.0.7/CHNOSZ/MD5 | 114 CHNOSZ-1.0.7/CHNOSZ/NAMESPACE | 3 CHNOSZ-1.0.7/CHNOSZ/R/EOSregress.R | 8 CHNOSZ-1.0.7/CHNOSZ/R/diagram.R | 12 CHNOSZ-1.0.7/CHNOSZ/R/equilibrate.R | 82 CHNOSZ-1.0.7/CHNOSZ/R/examples.R | 6 CHNOSZ-1.0.7/CHNOSZ/R/mosaic.R | 11 CHNOSZ-1.0.7/CHNOSZ/R/nonideal.R |only CHNOSZ-1.0.7/CHNOSZ/R/protein.info.R | 34 CHNOSZ-1.0.7/CHNOSZ/R/species.R | 6 CHNOSZ-1.0.7/CHNOSZ/R/swap.basis.R | 24 CHNOSZ-1.0.7/CHNOSZ/R/util.affinity.R | 5 CHNOSZ-1.0.7/CHNOSZ/R/util.expression.R | 8 CHNOSZ-1.0.7/CHNOSZ/R/util.misc.R | 63 CHNOSZ-1.0.7/CHNOSZ/R/util.plot.R | 42 CHNOSZ-1.0.7/CHNOSZ/R/util.program.R | 11 CHNOSZ-1.0.7/CHNOSZ/R/water.R | 2 CHNOSZ-1.0.7/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.7/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.7/CHNOSZ/demo/00Index | 5 CHNOSZ-1.0.7/CHNOSZ/demo/buffer.R | 4 CHNOSZ-1.0.7/CHNOSZ/demo/copper.R |only CHNOSZ-1.0.7/CHNOSZ/demo/nucleobase.R | 27 CHNOSZ-1.0.7/CHNOSZ/demo/solubility.R | 4 CHNOSZ-1.0.7/CHNOSZ/demo/wjd.R | 6 CHNOSZ-1.0.7/CHNOSZ/demo/yeastgfp.R | 2 CHNOSZ-1.0.7/CHNOSZ/inst/NEWS | 45 CHNOSZ-1.0.7/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.R | 411 - CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.Rnw | 1010 ++- CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/hotspring.R | 86 CHNOSZ-1.0.7/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.7/CHNOSZ/man/CHNOSZ-package.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/man/buffer.Rd | 30 CHNOSZ-1.0.7/CHNOSZ/man/data.Rd | 39 CHNOSZ-1.0.7/CHNOSZ/man/diagram.Rd | 5 CHNOSZ-1.0.7/CHNOSZ/man/equilibrate.Rd | 11 CHNOSZ-1.0.7/CHNOSZ/man/examples.Rd | 13 CHNOSZ-1.0.7/CHNOSZ/man/nonideal.Rd |only CHNOSZ-1.0.7/CHNOSZ/man/protein.info.Rd | 3 CHNOSZ-1.0.7/CHNOSZ/man/species.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/man/swap.basis.Rd | 17 CHNOSZ-1.0.7/CHNOSZ/man/util.misc.Rd | 7 CHNOSZ-1.0.7/CHNOSZ/man/util.plot.Rd | 25 CHNOSZ-1.0.7/CHNOSZ/man/util.water.Rd | 12 CHNOSZ-1.0.7/CHNOSZ/man/water.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-affinity.R | 5 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-diagram.R | 6 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-equilibrate.R | 65 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-makeup.R | 2 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-util.affinity.R | 2 CHNOSZ-1.0.7/CHNOSZ/vignettes/equilibrium.Rnw | 1010 ++- CHNOSZ-1.0.7/CHNOSZ/vignettes/equilibrium.lyx | 4912 +++++++++++----- CHNOSZ-1.0.7/CHNOSZ/vignettes/vig.bib | 215 62 files changed, 6017 insertions(+), 2411 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.24 dated 2015-11-18 and 2.25 dated 2015-11-19
DESCRIPTION | 8 +- MD5 | 26 +++---- src/Ig.cpp | 10 +- src/copula.cpp | 26 +++---- src/gcgm_bd.cpp | 142 +++++++++++++++++++++-------------------- src/gcgm_bd_multi_update.cpp | 146 +++++++++++++++++++++---------------------- src/gcgm_rj.cpp | 139 +++++++++++++++++++++------------------- src/ggm_bd.cpp | 140 ++++++++++++++++++++--------------------- src/ggm_bd_multi_update.cpp | 138 ++++++++++++++++++++-------------------- src/ggm_rj.cpp | 128 +++++++++++++++++++------------------ src/matrix.cpp | 35 ++++------ src/matrix.h | 2 src/rgwish.cpp | 32 ++++----- src/scaleFree.cpp | 2 14 files changed, 489 insertions(+), 485 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.3-1 dated 2015-09-25 and 2.3-2 dated 2015-11-19
DESCRIPTION | 8 +-- MD5 | 56 +++++++++++++-------------- R/adonis.R | 7 ++- R/capscale.R | 4 + R/howHead.R | 4 - R/lines.procrustes.R | 13 ++++-- R/mso.R | 9 +++- R/ordiArgAbsorber.R | 2 R/ordicluster.R | 11 ++--- R/ordiellipse.R | 2 R/points.procrustes.R | 22 +++++++--- R/rrarefy.R | 16 ++++++- R/vegdist.R | 4 - inst/NEWS.Rd | 49 +++++++++++++++++++++++ inst/doc/FAQ-vegan.pdf |binary inst/doc/NEWS.html | 61 +++++++++++++++++++++++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary man/clamtest.Rd | 2 man/mso.Rd | 13 +++--- man/procrustes.Rd | 12 +++-- man/rarefy.Rd | 23 ++++++----- man/vegan-internal.Rd | 2 vignettes/FAQ-vegan.pdf |binary vignettes/NEWS.html | 61 +++++++++++++++++++++++++++++ vignettes/decision-vegan.tex | 20 ++++----- vignettes/diversity-vegan.tex | 86 +++++++++++++++++++++--------------------- vignettes/intro-vegan.tex | 45 ++++++++++----------- 29 files changed, 375 insertions(+), 157 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.2 dated 2015-09-09 and 1.7.3 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TimeIntervalDataFrame.R | 2 +- man/timetools-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Biclustering via Sparse Singular Value Decomposition
Incorporating Stability Selection
Description: The main function s4vd() performs a biclustering via sparse
singular value decomposition with a nested stability selection.
The results is an biclust object and thus all methods of the
biclust package can be applied.
Author: Martin Sill, Sebastian Kaiser
Maintainer: Martin Sill <m.sill@dkfz.de>
Diff between s4vd versions 1.0 dated 2011-07-23 and 1.1-1 dated 2015-11-19
s4vd-1.0/s4vd/.project |only s4vd-1.0/s4vd/data/datalist |only s4vd-1.0/s4vd/data/lung.RData |only s4vd-1.0/s4vd/man/lung.Rd |only s4vd-1.1-1/s4vd/DESCRIPTION | 21 +- s4vd-1.1-1/s4vd/MD5 |only s4vd-1.1-1/s4vd/NAMESPACE | 10 + s4vd-1.1-1/s4vd/R/heatmap.r | 312 +++++++++++++++++++------------------ s4vd-1.1-1/s4vd/R/s4vd.R | 2 s4vd-1.1-1/s4vd/R/spca.R |only s4vd-1.1-1/s4vd/R/ssvd.R | 241 ++++++++++++++-------------- s4vd-1.1-1/s4vd/R/ssvdBC.R | 48 +++-- s4vd-1.1-1/s4vd/data/lung200.RData |binary s4vd-1.1-1/s4vd/man/BCheatmap.Rd | 10 - s4vd-1.1-1/s4vd/man/BCs4vd.Rd | 26 --- s4vd-1.1-1/s4vd/man/BCssvd.Rd | 10 - s4vd-1.1-1/s4vd/man/jaccard.Rd | 2 s4vd-1.1-1/s4vd/man/stabpath.Rd | 11 - 18 files changed, 361 insertions(+), 332 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.5.1 dated 2015-11-10 and 0.5.2 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++++------------- R/QR.R | 6 +++++- R/eig.R | 13 +++++++++++++ R/gaussian-elimination.R | 8 +++++--- R/len.R | 2 +- R/swp.R |only R/vectors.R | 22 ++++++++++++++-------- README.md | 7 ++++++- build/vignette.rds |binary inst/doc/gramreg.R |only inst/doc/gramreg.Rmd |only inst/doc/gramreg.html |only man/Ginv.Rd | 8 +++++--- man/QR.Rd | 6 +++++- man/SVD.Rd | 11 +++++++++++ man/len.Rd | 2 +- man/swp.Rd |only man/vectors.Rd | 19 +++++++++++++------ vignettes/gramreg.Rmd |only 20 files changed, 103 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-04 1.0.3
2015-03-05 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-20 1.0.3
2014-08-20 1.0.2
2014-05-25 1.0.1
2014-05-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-20 1.1
2014-11-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-22 1.1.2
2013-09-26 1.1.1
2012-09-28 1.0.3
2012-03-29 1.0.2
2011-11-21 1.0.1
2011-10-27 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 0.7-4
2014-08-15 0.7-3
2014-01-25 0.7-2
2012-07-03 0.7-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-05 1.2.2
2015-04-20 1.2.1
2015-04-13 1.2
2014-10-06 1.1.1
2014-10-01 1.1
2014-05-29 1.0.1
2014-01-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-04 2.0.0.3
2014-12-22 2.0.0.2
2014-11-01 2.0.0.1
2014-03-06 2.0.0.0
2013-12-03 1.0.4.5
2012-10-24 1.0.4.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-17 0.4
2014-06-04 0.3
2014-02-07 0.2
2013-05-27 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-27 0.3.3
2012-02-06 0.3.1.1
2011-11-25 0.3
2011-09-23 0.2
Title: Variable Selection for Model-Based Clustering
Description: A function which implements variable selection methodology for model-based clustering which allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting MCLUST models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean, Adrian E. Raftery, and Luca Scrucca
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between clustvarsel versions 2.1 dated 2014-10-15 and 2.2 dated 2015-11-19
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 9 +++++++-- R/clustvarsel.R | 29 +++++++++++++++++++++-------- R/clvarselhlbkw.R | 4 ++++ R/clvarselhlfwd.R | 23 +++++++++-------------- inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/clustvarsel.Rd | 46 ++++++++++++++++++++++++++-------------------- 9 files changed, 87 insertions(+), 61 deletions(-)
Title: Generalized Linear Models Extended
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses,
including parametric links and heteroskedastic latent variables.
Author: Achim Zeileis [aut, cre],
Roger Koenker [aut],
Philipp Doebler [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glmx versions 0.1-0 dated 2013-12-10 and 0.1-1 dated 2015-11-19
DESCRIPTION | 10 ++++----- MD5 | 22 ++++++++++---------- NAMESPACE | 3 +- NEWS | 7 ++++++ R/glmx.R | 46 +++++++++++++++++++++++++++++++++++++++++-- R/pregibon.R | 12 +++-------- data/AbortionAmbivalence.rda |binary data/BeetleMortality.rda |binary data/MexicanLabor.rda |binary data/WECO.rda |binary man/AbortionAmbivalence.Rd | 2 - man/glmx.Rd | 1 12 files changed, 75 insertions(+), 28 deletions(-)
Title: Spatial Exposure-Hazard Model for Exposure and Impact Assessment
on Exposed Individuals
Description: A model coupling polygon and point processes for assessing
risk due to contaminant sources and their impact on exposed individuals.
Author: Marc Bourotte [ctb],
Melen Leclerc [aut],
Jean-Francois Rey [aut, cre],
Samuel Soubeyrand [ctb],
Emily Walker [aut]
Maintainer: Jean-Francois Rey <jean-francois.rey@paca.inra.fr>
Diff between SEHmodel versions 0.0.9 dated 2015-10-02 and 0.0.10 dated 2015-11-19
SEHmodel-0.0.10/SEHmodel/DESCRIPTION | 9 +++-- SEHmodel-0.0.10/SEHmodel/MD5 | 16 +++++----- SEHmodel-0.0.10/SEHmodel/NAMESPACE | 3 + SEHmodel-0.0.10/SEHmodel/R/Class-Individuals.R | 4 +- SEHmodel-0.0.10/SEHmodel/R/Individuals-Methods.R | 15 +++++---- SEHmodel-0.0.10/SEHmodel/R/ecoToxic.R | 15 ++++++--- SEHmodel-0.0.10/SEHmodel/R/toxicIntensity.R | 3 + SEHmodel-0.0.10/SEHmodel/man/Individuals-class.Rd | 2 - SEHmodel-0.0.10/SEHmodel/man/Individuals-get-methods.Rd |only SEHmodel-0.0.9/SEHmodel/man/sub-Individuals-numeric-numeric-logical-method.Rd |only 10 files changed, 39 insertions(+), 28 deletions(-)
Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional
code contributions from Edzer Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between lgcp versions 1.3-11 dated 2015-09-10 and 1.3-13 dated 2015-11-19
DESCRIPTION | 13 +++++++------ MD5 | 13 +++++++------ R/lgcpMethods.R | 3 ++- README.md |only data/wpopdata.rda |binary data/wtowncoords.rda |binary data/wtowns.rda |binary inst/doc/lgcp.pdf |binary 8 files changed, 16 insertions(+), 13 deletions(-)
Title: A Simple Approach to Scale Gene Expression Data Derived from
Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene
expression generated across different experiments, and on
different platforms; that does not require global
renormalization, and is not restricted to comparison of
identical probes. YuGene works on a range of microarray dataset
distributions, such as between manufacturers. The resulting
output allows direct comparisons of gene expression between
experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>
Diff between YuGene versions 1.1.4 dated 2015-07-30 and 1.1.5 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 5 +++++ R/pca.YuGene.R | 11 +++++------ man/pca.YuGene.Rd | 5 ++--- man/pca.default.Rd | 5 ++--- 6 files changed, 24 insertions(+), 22 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. In both cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.8.0 dated 2015-09-19 and 2.8.1 dated 2015-11-19
DESCRIPTION | 13 ++- MD5 | 60 ++++++++--------- NAMESPACE | 11 ++- R/AllClass.R | 1 R/cxxdso-class.R | 2 R/expose_stan_functions.R | 57 ++++++++++++---- R/extract_sparse_parts.R | 12 +-- R/misc.R | 13 ++- R/pairs.R | 4 - R/plugin.R | 2 R/rstan.R | 8 +- R/rstan_package_skeleton.R |only R/stan_plot.R | 71 ++++++++++---------- R/stan_plot_helpers.R | 83 +++++++++++++---------- R/stanc.R | 48 ++++++++----- R/stanfit-class.R | 26 ++++--- R/stanmodel-class.R | 129 ++++++++++++++++++++++++------------- inst/doc/rstan_vignette.R | 2 inst/doc/rstan_vignette.Rnw | 2 inst/doc/rstan_vignette.pdf |binary man/rstan-internal.Rd | 2 man/rstan.package.skeleton.Rd |only man/sflist2stanfit.Rd | 17 ++-- man/stan_plot.Rd | 9 +- man/stan_plot_diagnostics.Rd | 62 +++++++++++++++-- man/stanc.Rd | 55 ++++++++++----- man/stanfit-method-plot.Rd | 59 +++++----------- man/stanmodel-class.Rd | 3 man/stanmodel-method-optimizing.Rd | 18 ++++- src/sparse_extractors.cpp | 2 src/stanc.cpp | 24 ++++++ vignettes/rstan_vignette.Rnw | 2 32 files changed, 499 insertions(+), 298 deletions(-)
Title: Data and Functions from the Book R Graphics, Second Edition
Description: Data and Functions from the book R Graphics, Second Edition. There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between RGraphics versions 2.0-12 dated 2014-09-12 and 2.0-13 dated 2015-11-19
DESCRIPTION | 11 - MD5 | 18 +- NAMESPACE | 23 +++ R/figures.R | 382 ++++++++++++++++++++++++++++---------------------------- R/globals.R | 11 + data/ocean.rda |binary data/ozTemp.rda |binary data/wind.rda |binary data/xmm.rda |binary man/ozTemp.Rd | 3 10 files changed, 239 insertions(+), 209 deletions(-)
Title: Use Python from Within R
Description: Interact with Python from within R.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-2 dated 2015-11-14 and 0.1-3 dated 2015-11-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- README.md | 22 ++++++++++++---------- inst/testing/NA_NaN_Inf.R | 1 + inst/testing/PyExec.R | 3 ++- inst/testing/PyOptions.R | 3 +++ inst/testing/all.R | 9 +++++---- src/PythonFunctions.c | 2 +- src/PythonFunctions.h | 4 ++++ src/Python_Explicit_Linking.c | 2 +- src/Python_Explicit_Linking.h | 15 ++++++++------- 11 files changed, 50 insertions(+), 37 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, unit conversions.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 0.6-3 dated 2015-07-10 and 1.0 dated 2015-11-19
DESCRIPTION | 14 +++-- MD5 | 45 ++++++++++++++---- R/LeafEnergyBalance.R | 11 +++- R/Tresponsefunctions.R | 12 ++-- R/fitBB.R | 55 +++++++++++++--------- R/fitaci.R | 118 ++++++++++++++++++++++++++++++++++++------------- R/fitacis.R | 42 +++++++++++++++-- R/photosyn.R | 22 ++++++--- inst |only man/Photosyn.Rd | 17 +++++-- man/fitBB.Rd | 8 ++- man/fitaci.Rd | 32 ++++++++++--- 12 files changed, 278 insertions(+), 98 deletions(-)
Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')
to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and
q variables are measured on the same samples or individuals n. These data may come from high throughput
technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other
large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with
the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting
the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent
Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration
of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found
on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 5.1.2 dated 2015-08-29 and 5.2.0 dated 2015-11-19
mixOmics-5.1.2/mixOmics/R/network.rcc.R |only mixOmics-5.1.2/mixOmics/R/network.spls.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.splsda1fact.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.splsda2fact.R |only mixOmics-5.1.2/mixOmics/R/plot3dIndiv.R |only mixOmics-5.1.2/mixOmics/R/plot3dVar.R |only mixOmics-5.1.2/mixOmics/man/pheatmap.multilevel.Rd |only mixOmics-5.1.2/mixOmics/man/plot3dIndiv.Rd |only mixOmics-5.1.2/mixOmics/man/plot3dVar.Rd |only mixOmics-5.1.2/mixOmics/man/tau.estimate.Rd |only mixOmics-5.2.0/mixOmics/DESCRIPTION | 10 mixOmics-5.2.0/mixOmics/MD5 | 131 - mixOmics-5.2.0/mixOmics/NAMESPACE | 42 mixOmics-5.2.0/mixOmics/NEWS | 30 mixOmics-5.2.0/mixOmics/R/Mfold.R | 2 mixOmics-5.2.0/mixOmics/R/bin.color.R | 5 mixOmics-5.2.0/mixOmics/R/cim.R | 865 ++---- mixOmics-5.2.0/mixOmics/R/helpers.R | 6 mixOmics-5.2.0/mixOmics/R/image.tune.rcc.R | 77 mixOmics-5.2.0/mixOmics/R/imageMap.R |only mixOmics-5.2.0/mixOmics/R/imgCor.R | 290 +- mixOmics-5.2.0/mixOmics/R/ipca.R | 310 +- mixOmics-5.2.0/mixOmics/R/loo.R | 2 mixOmics-5.2.0/mixOmics/R/nearZeroVar.R | 2 mixOmics-5.2.0/mixOmics/R/network.R | 1543 +++++++----- mixOmics-5.2.0/mixOmics/R/nipals.R | 76 mixOmics-5.2.0/mixOmics/R/pca.R | 271 +- mixOmics-5.2.0/mixOmics/R/plot.pca.R | 53 mixOmics-5.2.0/mixOmics/R/plotArrow.R |only mixOmics-5.2.0/mixOmics/R/plotContrib.R | 451 +-- mixOmics-5.2.0/mixOmics/R/plotIndiv.R | 1082 ++++++-- mixOmics-5.2.0/mixOmics/R/plotVar.R | 585 +++- mixOmics-5.2.0/mixOmics/R/rcc.R | 219 + mixOmics-5.2.0/mixOmics/R/scatterutil.R | 602 ++-- mixOmics-5.2.0/mixOmics/R/selectVar.R | 181 - mixOmics-5.2.0/mixOmics/R/sipca.R | 14 mixOmics-5.2.0/mixOmics/R/spca.R | 6 mixOmics-5.2.0/mixOmics/R/spls.R | 4 mixOmics-5.2.0/mixOmics/R/srgcca.R | 8 mixOmics-5.2.0/mixOmics/R/wrappers.R | 12 mixOmics-5.2.0/mixOmics/R/zzz.R |only mixOmics-5.2.0/mixOmics/data/breast.tumors.rda |binary mixOmics-5.2.0/mixOmics/data/linnerud.rda |binary mixOmics-5.2.0/mixOmics/data/liver.toxicity.rda |binary mixOmics-5.2.0/mixOmics/data/multidrug.rda |binary mixOmics-5.2.0/mixOmics/data/nutrimouse.rda |binary mixOmics-5.2.0/mixOmics/data/prostate.rda |binary mixOmics-5.2.0/mixOmics/data/srbct.rda |binary mixOmics-5.2.0/mixOmics/data/vac18.rda |binary mixOmics-5.2.0/mixOmics/data/vac18.simulated.rda |binary mixOmics-5.2.0/mixOmics/data/yeast.rda |binary mixOmics-5.2.0/mixOmics/man/cim.Rd | 250 - mixOmics-5.2.0/mixOmics/man/imgCor.Rd | 65 mixOmics-5.2.0/mixOmics/man/internal-functions.Rd | 2 mixOmics-5.2.0/mixOmics/man/ipca.Rd | 22 mixOmics-5.2.0/mixOmics/man/multilevel.Rd | 1 mixOmics-5.2.0/mixOmics/man/network.Rd | 243 - mixOmics-5.2.0/mixOmics/man/pca.Rd | 29 mixOmics-5.2.0/mixOmics/man/plotArrow.Rd |only mixOmics-5.2.0/mixOmics/man/plotContrib.Rd | 88 mixOmics-5.2.0/mixOmics/man/plotIndiv.Rd | 275 +- mixOmics-5.2.0/mixOmics/man/plotVar.Rd | 265 -- mixOmics-5.2.0/mixOmics/man/plsda.Rd | 2 mixOmics-5.2.0/mixOmics/man/rcc.Rd | 36 mixOmics-5.2.0/mixOmics/man/s.match.Rd | 1 mixOmics-5.2.0/mixOmics/man/selectVar.Rd | 36 mixOmics-5.2.0/mixOmics/man/sipca.Rd | 12 mixOmics-5.2.0/mixOmics/man/spca.Rd | 11 mixOmics-5.2.0/mixOmics/man/spls.Rd | 1 mixOmics-5.2.0/mixOmics/man/splsda.Rd | 3 mixOmics-5.2.0/mixOmics/man/tune.pca.Rd | 4 mixOmics-5.2.0/mixOmics/man/withinVariation.Rd | 1 mixOmics-5.2.0/mixOmics/man/wrappers.Rd | 45 74 files changed, 4889 insertions(+), 3382 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.6 dated 2015-11-13 and 0.0.7 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/Information-vignette.Rmd | 22 +++++++++++----------- inst/doc/Information-vignette.html | 28 ++++++++++++++-------------- vignettes/Information-vignette.Rmd | 22 +++++++++++----------- 5 files changed, 44 insertions(+), 44 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer).
Author: Steven P. Millard <EnvStats@ProbStatInfo.com>
Maintainer: Steven P. Millard <EnvStats@ProbStatInfo.com>
Diff between EnvStats versions 2.0.1 dated 2015-05-25 and 2.0.2 dated 2015-11-19
EnvStats-2.0.1/EnvStats/man/EnvStats-internal.Rd |only EnvStats-2.0.2/EnvStats/DESCRIPTION | 8 EnvStats-2.0.2/EnvStats/MD5 | 209 ++-- EnvStats-2.0.2/EnvStats/NAMESPACE | 21 EnvStats-2.0.2/EnvStats/NEWS | 21 EnvStats-2.0.2/EnvStats/R/rosnerTest.R | 23 EnvStats-2.0.2/EnvStats/R/stripChart.default.R | 60 - EnvStats-2.0.2/EnvStats/data/Air.df.rda |binary EnvStats-2.0.2/EnvStats/data/Benthic.df.rda |binary EnvStats-2.0.2/EnvStats/data/Distribution.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.02d.Ex.2.ug.per.L.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.02d.Ex.4.mg.per.kg.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.02d.Ex.6.mg.per.kg.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.02d.Ex.9.mg.per.L.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.10.1.nickel.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.11.1.arsenic.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.12.1.ccl4.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.12.4.naphthalene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.13.1.iron.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.14.1.manganese.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.14.3.alkalinity.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.14.4.arsenic.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.14.8.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.15.1.manganese.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.16.1.sulfate.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.16.2.benzene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.16.4.copper.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.16.5.PCE.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.1.loglead.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.2.toluene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.3.chrysene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.3.log.chrysene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.4.copper.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.5.chloride.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.6.sulfate.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.17.7.sodium.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.18.1.arsenic.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.18.2.chrysene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.18.3.TCE.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.18.4.xylene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.19.1.sulfate.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.19.2.chloride.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.19.5.mercury.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.20.1.nickel.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.21.1.aldicarb.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.21.2.benzene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.21.5.beryllium.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.21.6.nitrate.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.21.7.TCE.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.22.1.VC.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.22.2.Specific.Conductance.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.6.3.sulfate.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Ex.7.1.arsenic.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Table.9.1.TCE.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Table.9.3.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.09.Table.9.4.nickel.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.aldicarb1.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.aldicarb2.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.benzene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.cadmium.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.chlordane1.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.chlordane2.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.89b.edb.df.rda |binary 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EnvStats-2.0.2/EnvStats/data/EPA.92c.nickel1.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.92c.nickel2.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.92c.toluene.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.92c.zinc.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.92d.chromium.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.92d.chromium.vec.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.94b.lead.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.94b.tccb.df.rda |binary EnvStats-2.0.2/EnvStats/data/EPA.97.cadmium.111.df.rda |binary EnvStats-2.0.2/EnvStats/data/Environmental.df.rda |binary EnvStats-2.0.2/EnvStats/data/Gibbons.et.al.09.Alkilinity.vec.rda |binary EnvStats-2.0.2/EnvStats/data/Gibbons.et.al.09.Vinyl.Chloride.vec.rda |binary EnvStats-2.0.2/EnvStats/data/Graham.et.al.75.etu.df.rda |binary EnvStats-2.0.2/EnvStats/data/Helsel.Cohn.88.app.b.df.rda |binary EnvStats-2.0.2/EnvStats/data/Helsel.Cohn.88.silver.df.rda |binary EnvStats-2.0.2/EnvStats/data/Lin.Evans.80.df.rda |binary EnvStats-2.0.2/EnvStats/data/Millard.Deverel.88.df.rda |binary EnvStats-2.0.2/EnvStats/data/Modified.TcCB.df.rda |binary EnvStats-2.0.2/EnvStats/data/NIOSH.89.air.lead.vec.rda |binary EnvStats-2.0.2/EnvStats/data/Olympic.NH4.df.rda |binary EnvStats-2.0.2/EnvStats/data/Ozone.NE.df.rda |binary EnvStats-2.0.2/EnvStats/data/Refinery.CO.df.rda |binary EnvStats-2.0.2/EnvStats/data/Skagit.NH3_N.df.rda |binary EnvStats-2.0.2/EnvStats/data/Total.P.df.rda |binary EnvStats-2.0.2/EnvStats/inst/doc/EnvStats-manual.pdf |binary EnvStats-2.0.2/EnvStats/man/EnvStats-package.Rd | 4 EnvStats-2.0.2/EnvStats/man/rosnerTest.Rd | 458 +++++++++- 106 files changed, 646 insertions(+), 158 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.2 dated 2015-10-28 and 1.3 dated 2015-11-19
bWGR-1.2/bWGR/R/mgr.R |only bWGR-1.2/bWGR/man/mgr.Rd |only bWGR-1.3/bWGR/DESCRIPTION | 8 ++++---- bWGR-1.3/bWGR/MD5 | 8 +++----- bWGR-1.3/bWGR/R/wgr.R | 6 +++--- bWGR-1.3/bWGR/man/bWGR.Rd | 4 ++-- 6 files changed, 12 insertions(+), 14 deletions(-)
Title: Learning Discrete Bayesian Network Classifiers from Data
Description: Implements state-of-the art algorithms for learning discrete Bayesian network classifiers from data, as well as functions for using these classifiers for prediction, assessing their predictive performance, and inspecting their properties.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut],
Wickham Hadley [ctb] (some code extracted from memoise package)
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
Diff between bnclassify versions 0.3.1 dated 2015-10-29 and 0.3.2 dated 2015-11-19
bnclassify-0.3.1/bnclassify/R/wrap-crossval.R |only bnclassify-0.3.1/bnclassify/inst/doc/bnclassify.R |only bnclassify-0.3.1/bnclassify/inst/doc/bnclassify.Rmd |only bnclassify-0.3.1/bnclassify/inst/doc/bnclassify.pdf |only bnclassify-0.3.1/bnclassify/man/as_grain.Rd |only bnclassify-0.3.1/bnclassify/man/as_graphNEL.Rd |only bnclassify-0.3.1/bnclassify/man/bnc_bn_object.Rd |only bnclassify-0.3.1/bnclassify/man/bnc_dag_object.Rd |only bnclassify-0.3.1/bnclassify/man/wrapper.Rd |only bnclassify-0.3.1/bnclassify/vignettes/bnclassify.Rmd |only bnclassify-0.3.1/bnclassify/vignettes/bnclassify_cache |only bnclassify-0.3.2/bnclassify/DESCRIPTION | 25 bnclassify-0.3.2/bnclassify/MD5 | 164 ++-- bnclassify-0.3.2/bnclassify/NAMESPACE | 11 bnclassify-0.3.2/bnclassify/R/0bnclassify-doc.R | 331 +++++++--- bnclassify-0.3.2/bnclassify/R/anb-bn-operate.R |only bnclassify-0.3.2/bnclassify/R/anb-bn.R | 14 bnclassify-0.3.2/bnclassify/R/anb-cpts.R | 25 bnclassify-0.3.2/bnclassify/R/anb-dag.R | 14 bnclassify-0.3.2/bnclassify/R/basic-misc.R | 6 bnclassify-0.3.2/bnclassify/R/bnc-dag-operate.R | 57 + bnclassify-0.3.2/bnclassify/R/cv.R |only bnclassify-0.3.2/bnclassify/R/data-statistics.R | 14 bnclassify-0.3.2/bnclassify/R/infer.R | 6 bnclassify-0.3.2/bnclassify/R/learn-hc-operators.R | 5 bnclassify-0.3.2/bnclassify/R/learn-hc.R | 20 bnclassify-0.3.2/bnclassify/R/learn-params-awnb.R | 7 bnclassify-0.3.2/bnclassify/R/learn-params-manb.R |only bnclassify-0.3.2/bnclassify/R/learn-params.R | 89 ++ bnclassify-0.3.2/bnclassify/R/learn-struct.R | 62 + bnclassify-0.3.2/bnclassify/R/memoise.R |only bnclassify-0.3.2/bnclassify/R/optim-multi-override.R | 67 -- bnclassify-0.3.2/bnclassify/R/optim-multi.R | 2 bnclassify-0.3.2/bnclassify/R/predict.R | 28 bnclassify-0.3.2/bnclassify/R/release.R | 6 bnclassify-0.3.2/bnclassify/R/update.R | 45 - bnclassify-0.3.2/bnclassify/R/wrap-gRain.R | 3 bnclassify-0.3.2/bnclassify/R/wrap-mlr.R | 53 - bnclassify-0.3.2/bnclassify/README.md | 60 + bnclassify-0.3.2/bnclassify/build/vignette.rds |binary bnclassify-0.3.2/bnclassify/inst/doc/bnclassify.bib |only bnclassify-0.3.2/bnclassify/inst/doc/fan.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/introduction.R |only bnclassify-0.3.2/bnclassify/inst/doc/introduction.Rmd |only bnclassify-0.3.2/bnclassify/inst/doc/introduction.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/nb.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/runtimes.R |only bnclassify-0.3.2/bnclassify/inst/doc/runtimes.Rmd |only bnclassify-0.3.2/bnclassify/inst/doc/runtimes.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/sn.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/tan.pdf |only bnclassify-0.3.2/bnclassify/inst/doc/technical.Rnw |only bnclassify-0.3.2/bnclassify/inst/doc/technical.pdf |only bnclassify-0.3.2/bnclassify/man/accuracy.Rd | 8 bnclassify-0.3.2/bnclassify/man/as_mlr.Rd | 28 bnclassify-0.3.2/bnclassify/man/bnc.Rd | 23 bnclassify-0.3.2/bnclassify/man/bnc_bn.Rd |only bnclassify-0.3.2/bnclassify/man/bnc_dag.Rd |only bnclassify-0.3.2/bnclassify/man/bnclassify.Rd | 77 +- bnclassify-0.3.2/bnclassify/man/car.Rd | 3 bnclassify-0.3.2/bnclassify/man/cmi.Rd | 11 bnclassify-0.3.2/bnclassify/man/compute_ll.Rd | 3 bnclassify-0.3.2/bnclassify/man/cv.Rd | 39 - 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bnclassify-0.3.2/bnclassify/tests/testthat/test-predict.R | 77 -- bnclassify-0.3.2/bnclassify/tests/testthat/test-update.R | 68 -- bnclassify-0.3.2/bnclassify/vignettes/.install_extras |only bnclassify-0.3.2/bnclassify/vignettes/bnclassify.bib |only bnclassify-0.3.2/bnclassify/vignettes/fan.pdf |only bnclassify-0.3.2/bnclassify/vignettes/introduction.Rmd |only bnclassify-0.3.2/bnclassify/vignettes/nb.pdf |only bnclassify-0.3.2/bnclassify/vignettes/runtimes.Rmd |only bnclassify-0.3.2/bnclassify/vignettes/sn.pdf |only bnclassify-0.3.2/bnclassify/vignettes/tan.pdf |only bnclassify-0.3.2/bnclassify/vignettes/technical.Rnw |only 107 files changed, 1105 insertions(+), 753 deletions(-)
Title: Linearized Bregman Algorithms for Generalized Linear Models
Description: Efficient procedures for fitting the regularization path
for linear, binomial, multinomial, Ising and Potts models with lasso,
group lasso or column lasso(only for multinomial) penalty.
The package uses Linearized Bregman Algorithm to solve the
regularization path through iterations. Bregman Inverse Scale Space Differential
Inclusion solver is also provided for linear model with lasso penalty.
Author: Feng Ruan, Jiechao Xiong and Yuan Yao
Maintainer: Jiechao Xiong <xiongjiechao@pku.edu.cn>
Diff between Libra versions 1.3-2 dated 2015-11-09 and 1.4 dated 2015-11-18
DESCRIPTION | 18 ++- MD5 | 44 +++++---- NAMESPACE | 2 R/cv.iss.R | 2 R/cv.lb.R | 41 ++++---- R/ising.R |only R/iss.R | 31 +----- R/lb.R | 239 ++++++++++++++++++++++++++++---------------------- R/plot.lb.R | 31 +++--- R/potts.R |only R/predict.lb.R | 34 +++---- man/cv.iss.Rd | 11 +- man/cv.lb.Rd | 42 +++++--- man/ising.Rd |only man/iss.Rd | 39 ++------ man/lb.Rd | 96 ++++++++++---------- man/plot.lb.Rd | 11 +- man/potts.Rd |only man/predict.lb.Rd | 10 +- src/LBLasso.c | 166 +++++++++++++++++++++++----------- src/LBheader.c | 157 +++++++++++++++++++++++--------- src/LBheader.h | 9 + src/LBlogistic.c | 163 ++++++++++++++++++++++------------ src/LBmultilogistic.c | 210 +++++++++++++++++++++++++++++++++---------- src/ising.c |only src/potts.c |only 26 files changed, 838 insertions(+), 518 deletions(-)
Title: R Interface to the EcoData Retriever
Description: Provides an R interface to the EcoData Retriever
(http://ecodataretriever.org/) via the EcoData Retriever's
command line interface. The EcoData Retriever automates the
tasks of finding, downloading, and cleaning ecological datasets,
and then stores them in a local database.
Author: Daniel McGlinn [aut, cre],
Ethan White [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Diff between ecoretriever versions 0.2 dated 2015-11-13 and 0.2.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ecoretriever.R | 15 ++++++++++----- 3 files changed, 16 insertions(+), 11 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.23 dated 2015-09-30 and 2.24 dated 2015-11-18
BDgraph-2.23/BDgraph/R/log_Ig.R |only BDgraph-2.23/BDgraph/R/phat.R |only BDgraph-2.23/BDgraph/R/prob.R |only BDgraph-2.23/BDgraph/man/log_Ig.Rd |only BDgraph-2.23/BDgraph/man/phat.Rd |only BDgraph-2.23/BDgraph/man/prob.Rd |only BDgraph-2.24/BDgraph/DESCRIPTION | 10 BDgraph-2.24/BDgraph/MD5 | 96 ++--- BDgraph-2.24/BDgraph/NAMESPACE | 8 BDgraph-2.24/BDgraph/NEWS | 4 BDgraph-2.24/BDgraph/R/bdgraph.R | 334 ++++++++++-------- BDgraph-2.24/BDgraph/R/bdgraph.sim.R | 10 BDgraph-2.24/BDgraph/R/compare.R | 43 +- BDgraph-2.24/BDgraph/R/gnorm.R |only BDgraph-2.24/BDgraph/R/pgraph.R |only BDgraph-2.24/BDgraph/R/plinks.R |only BDgraph-2.24/BDgraph/R/plotcoda.R | 26 - BDgraph-2.24/BDgraph/R/plotroc.R | 96 ++++- BDgraph-2.24/BDgraph/R/rgwish.R | 6 BDgraph-2.24/BDgraph/R/select.R | 41 +- BDgraph-2.24/BDgraph/R/traceplot.R | 44 +- BDgraph-2.24/BDgraph/build/vignette.rds |binary BDgraph-2.24/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.24/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.24/BDgraph/man/BDgraph-package.Rd | 4 BDgraph-2.24/BDgraph/man/bdgraph.Rd | 63 ++- BDgraph-2.24/BDgraph/man/bdgraph.npn.Rd | 18 - BDgraph-2.24/BDgraph/man/bdgraph.sim.Rd | 10 BDgraph-2.24/BDgraph/man/compare.Rd | 37 +- BDgraph-2.24/BDgraph/man/gnorm.Rd |only BDgraph-2.24/BDgraph/man/pgraph.Rd |only BDgraph-2.24/BDgraph/man/plinks.Rd |only BDgraph-2.24/BDgraph/man/plot.bdgraph.Rd | 12 BDgraph-2.24/BDgraph/man/plot.sim.Rd | 2 BDgraph-2.24/BDgraph/man/plotcoda.Rd | 12 BDgraph-2.24/BDgraph/man/plotroc.Rd | 40 +- BDgraph-2.24/BDgraph/man/print.bdgraph.Rd | 12 BDgraph-2.24/BDgraph/man/rgwish.Rd | 14 BDgraph-2.24/BDgraph/man/select.Rd | 16 BDgraph-2.24/BDgraph/man/summary.bdgraph.Rd | 18 - BDgraph-2.24/BDgraph/man/surveyData.Rd | 2 BDgraph-2.24/BDgraph/man/traceplot.Rd | 18 - BDgraph-2.24/BDgraph/src/Ig.cpp | 4 BDgraph-2.24/BDgraph/src/copula.cpp | 100 ++--- BDgraph-2.24/BDgraph/src/copula.h | 12 BDgraph-2.24/BDgraph/src/gcgm_bd.cpp | 383 +++++++++++++-------- BDgraph-2.24/BDgraph/src/gcgm_bd_multi_update.cpp |only BDgraph-2.24/BDgraph/src/gcgm_rj.cpp | 301 +++++++++------- BDgraph-2.24/BDgraph/src/ggm_bd.cpp | 390 +++++++++++++--------- BDgraph-2.24/BDgraph/src/ggm_bd_multi_update.cpp |only BDgraph-2.24/BDgraph/src/ggm_rj.cpp | 309 +++++++++-------- BDgraph-2.24/BDgraph/src/matrix.cpp | 162 +++++++-- BDgraph-2.24/BDgraph/src/matrix.h | 21 - BDgraph-2.24/BDgraph/src/rgwish.cpp | 142 +++----- BDgraph-2.24/BDgraph/src/rgwish.h | 4 BDgraph-2.24/BDgraph/vignettes/BDgraph.pdf |binary 56 files changed, 1661 insertions(+), 1163 deletions(-)
Title: Software for Analysis of Weighted, Two-Mode, and Longitudinal
Networks
Description: R package for analyzing weighted, two-mode, and longitudinal networks.
Author: Tore Opsahl
Maintainer: Tore Opsahl <tore@opsahl.co.uk>
Diff between tnet versions 3.0.11 dated 2012-11-20 and 3.0.14 dated 2015-11-18
tnet-3.0.11/tnet/LICENSE |only tnet-3.0.14/tnet/ChangeLog | 4 + tnet-3.0.14/tnet/DESCRIPTION | 18 ++-- tnet-3.0.14/tnet/MD5 | 25 +++--- tnet-3.0.14/tnet/R/clustering_w.R | 4 - tnet-3.0.14/tnet/R/growth_l.R | 2 tnet-3.0.14/tnet/R/rg_reshuffling_w.R | 110 ++++++++++++++-------------- tnet-3.0.14/tnet/R/rg_tm.R | 2 tnet-3.0.14/tnet/R/rg_w.R | 2 tnet-3.0.14/tnet/R/tnet_ucinet.R | 2 tnet-3.0.14/tnet/data/tnet.RData |binary tnet-3.0.14/tnet/man/growth_l.Rd | 3 tnet-3.0.14/tnet/man/tnet-package.Rd | 4 - tnet-3.0.14/tnet/man/weighted_richclub_w.Rd | 3 14 files changed, 93 insertions(+), 86 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES block
cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key)
encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary
sized data. Other utilities include key generators, hash functions (md5, sha1, sha256,
etc), base64 encoder, a secure random number generator, and 'bignum' math methods for
manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.5 dated 2015-11-15 and 0.6 dated 2015-11-18
openssl-0.5/openssl/R/encrypt.R |only openssl-0.5/openssl/man/base64.Rd |only openssl-0.5/openssl/man/certs.Rd |only openssl-0.5/openssl/man/encrypt.Rd |only openssl-0.5/openssl/src/encrypt.c |only openssl-0.6/openssl/DESCRIPTION | 6 openssl-0.6/openssl/MD5 | 52 +-- openssl-0.6/openssl/NAMESPACE | 1 openssl-0.6/openssl/NEWS | 6 openssl-0.6/openssl/R/base64.R | 5 openssl-0.6/openssl/R/bignum.R | 22 + openssl-0.6/openssl/R/cert.R | 12 openssl-0.6/openssl/R/hash.R | 5 openssl-0.6/openssl/R/openssl.R | 2 openssl-0.6/openssl/R/read.R | 4 openssl-0.6/openssl/R/rsa.R |only openssl-0.6/openssl/configure | 2 openssl-0.6/openssl/inst/doc/crypto_hashing.html | 325 ++++++----------------- openssl-0.6/openssl/inst/doc/secure_rng.html | 308 +++++---------------- openssl-0.6/openssl/man/base64_encode.Rd |only openssl-0.6/openssl/man/certificates.Rd |only openssl-0.6/openssl/man/hash.Rd | 2 openssl-0.6/openssl/man/openssl.Rd | 2 openssl-0.6/openssl/man/read_key.Rd | 3 openssl-0.6/openssl/man/rsa_encrypt.Rd |only openssl-0.6/openssl/src/aes.c | 26 - openssl-0.6/openssl/src/base64.c | 2 openssl-0.6/openssl/src/bignum.c | 16 + openssl-0.6/openssl/src/envelope.c | 4 openssl-0.6/openssl/src/rand.c | 2 openssl-0.6/openssl/src/rsa.c |only openssl-0.6/openssl/src/ssl.c | 63 +++- 32 files changed, 337 insertions(+), 533 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.13 dated 2015-09-16 and 1.14 dated 2015-11-18
DESCRIPTION | 10 ++++---- MD5 | 30 ++++++++++++------------ NAMESPACE | 1 NEWS | 24 +++++++++++++++++++ R/Deprecated.R | 11 -------- R/as.matrix-functions.R | 3 +- R/averageMassSpectra-functions.R | 2 - R/constructor-functions.R | 9 ++++--- R/determineWarpingFunctions-functions.R | 2 - build/vignette.rds |binary inst/doc/MALDIquant-intro.pdf |binary man/MALDIquant-defunct.Rd | 1 man/createMassPeaks-functions.Rd | 2 - man/estimateBaseline-methods.Rd | 3 +- tests/testthat/test_as.matrix-functions.R | 10 ++++---- tests/testthat/test_intensityMatrix-functions.R | 2 - 16 files changed, 63 insertions(+), 47 deletions(-)
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data
manipulation and the creation of new data, structured from basic forest
inventory data. The purpose of this package is provide functions to support
these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.3 dated 2015-11-03 and 0.4 dated 2015-11-18
DESCRIPTION | 20 ++++++++++++-------- MD5 | 42 ++++++++++++++++++++++++++++++++++++++---- NAMESPACE | 27 +++++++++++++++++++++++++++ NEWS | 8 ++++++-- R/R21a.R |only R/R29a.R |only R/atualizaCampoBase.R | 8 ++++++++ R/avaliaAjuste.R |only R/bias.R |only R/calculaA.R |only R/calculaPerc.R |only R/ce.R |only R/fator_bias.R |only R/isfinitedataframe.R |only R/mae.R |only R/mse.R |only R/mspr.R |only R/residuoPerc.R |only R/rmse.R |only R/rrmse.R |only R/syx.R |only R/syxPerc.R |only man/R21a.Rd |only man/R29a.Rd |only man/avaliaAjuste.Rd |only man/bias.Rd |only man/calculaA.Rd |only man/calculaPerc.Rd |only man/ce.Rd |only man/fator_bias.Rd |only man/isfinitedataframe.Rd |only man/mae.Rd |only man/mse.Rd |only man/mspr.Rd |only man/residuoPerc.Rd |only man/rmse.Rd |only man/rrmse.Rd |only man/syx.Rd |only man/syxPerc.Rd |only 39 files changed, 91 insertions(+), 14 deletions(-)
Title: Fits a Catenary to Given Points
Description: Gives methods to create a catenary object and then plot it and get
properties of it. Can construct from parameters or endpoints. Also can get
catenary fitted to data.
Author: Jonathan Tuke [aut, cre],
Matthew Roughan [aut]
Maintainer: Jonathan Tuke <simon.tuke@adelaide.edu.au>
Diff between catenary versions 1.1 dated 2013-02-17 and 1.1.1 dated 2015-11-18
catenary-1.1.1/catenary/DESCRIPTION | 32 +++--- catenary-1.1.1/catenary/MD5 | 58 +++++------ catenary-1.1.1/catenary/NAMESPACE | 23 +++- catenary-1.1.1/catenary/NEWS | 5 catenary-1.1.1/catenary/R/catenary.R | 88 +++++++++-------- catenary-1.1.1/catenary/R/fittedCatenary.R | 44 +++++--- catenary-1.1.1/catenary/R/getFunctionEnvelopeCat.R | 2 catenary-1.1.1/catenary/R/getFunctionEnvelopePara.R | 2 catenary-1.1.1/catenary/R/package.R | 9 + catenary-1.1.1/catenary/inst/shiny/dataCat |only catenary-1.1.1/catenary/man/L.Rd |only catenary-1.1.1/catenary/man/Summary.Rd | 27 ++--- catenary-1.1.1/catenary/man/catenary-class.Rd | 23 +++- catenary-1.1.1/catenary/man/catenary.Rd | 39 +++---- catenary-1.1.1/catenary/man/ctesiphon.Rd | 16 +-- catenary-1.1.1/catenary/man/f.Rd | 21 ++-- catenary-1.1.1/catenary/man/fitCat.Rd | 20 ++- catenary-1.1.1/catenary/man/fitCatEndPts.Rd | 20 ++- catenary-1.1.1/catenary/man/fitMaxCat.Rd | 18 +-- catenary-1.1.1/catenary/man/fitNaturalCat.Rd | 18 +-- catenary-1.1.1/catenary/man/fittedCatenary-class.Rd | 26 +++-- catenary-1.1.1/catenary/man/fittedCatenary.Rd | 19 +-- catenary-1.1.1/catenary/man/getCatLength.Rd | 21 ++-- catenary-1.1.1/catenary/man/getFunctionEnvelopeCat.Rd | 18 +-- catenary-1.1.1/catenary/man/getFunctionEnvelopePara.Rd | 16 +-- catenary-1.1.1/catenary/man/getPoints.Rd | 6 - catenary-1.1.1/catenary/man/minmax.Rd | 9 + catenary-1.1.1/catenary/man/minmaxLength.Rd | 16 +-- catenary-1.1.1/catenary/man/plot.Rd | 31 ++++- catenary-1.1.1/catenary/man/vertex.Rd | 9 + catenary-1.1/catenary/man/accessor-methods.Rd |only 31 files changed, 370 insertions(+), 266 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows
various cartographic representations: proportional symbols, chroropleth,
typology, flows, discontinuities... It also proposes some additional useful
features: cartographic palettes, layout (scale, north arrow, title...), labels,
legends, access to cartographic API...
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between cartography versions 1.0 dated 2015-10-06 and 1.1 dated 2015-11-18
DESCRIPTION | 15 ++- MD5 | 117 ++++++++++++----------- NAMESPACE | 3 NEWS |only R/choroLayer.R | 2 R/gradLinkTypoLayer.R |only R/layoutLayer.R | 17 +-- R/legends.R | 214 +++++++++++++++++++++++++++++++------------ R/palettes.R | 1 README.md | 2 build/vignette.rds |binary inst/doc/cartography.Rmd | 2 inst/doc/cartography.html | 33 +++--- man/carto.pal.Rd | 18 +-- man/cartography.Rd | 16 +-- man/cartography.colors.Rd | 2 man/choroLayer.Rd | 28 ++--- man/coasts.spdf.Rd | 2 man/countries.spdf.Rd | 2 man/discLayer.Rd | 26 ++--- man/discretization.Rd | 8 - man/display.carto.all.Rd | 2 man/display.carto.pal.Rd | 2 man/dotDensityLayer.Rd | 22 ++-- man/frame.spdf.Rd | 2 man/getBorders.Rd | 10 +- man/getGridData.Rd | 16 +-- man/getGridLayer.Rd | 12 +- man/getLinkLayer.Rd | 18 +-- man/getTiles.Rd | 20 ++-- man/gradLinkLayer.Rd | 14 +- man/gradLinkTypoLayer.Rd |only man/graticule.spdf.Rd | 2 man/labelLayer.Rd | 14 +- man/layoutLayer.Rd | 15 +-- man/legendBarsSymbols.Rd | 12 +- man/legendChoro.Rd | 10 +- man/legendCirclesSymbols.Rd | 14 +- man/legendGradLines.Rd | 12 +- man/legendPropLines.Rd | 8 - man/legendPropTriangles.Rd | 12 +- man/legendSquaresSymbols.Rd | 15 +-- man/legendTypo.Rd | 12 +- man/nuts0.df.Rd | 12 +- man/nuts0.spdf.Rd | 2 man/nuts1.df.Rd | 12 +- man/nuts1.spdf.Rd | 2 man/nuts2.df.Rd | 12 +- man/nuts2.spdf.Rd | 2 man/nuts3.df.Rd | 8 - man/nuts3.spdf.Rd | 2 man/propLinkLayer.Rd | 16 +-- man/propSymbolsChoroLayer.Rd | 56 +++++------ man/propSymbolsLayer.Rd | 62 ++++++------ man/propSymbolsTypoLayer.Rd | 26 ++--- man/propTrianglesLayer.Rd | 28 ++--- man/tilesLayer.Rd | 10 +- man/twincities.Rd | 10 +- man/typoLayer.Rd | 20 ++-- man/world.spdf.Rd | 2 vignettes/cartography.Rmd | 2 61 files changed, 575 insertions(+), 461 deletions(-)
Title: Generate APA Tables for MS Word
Description: Most psychological journals require that tables in a manuscript comply to APA (American Association of Psychology) standards. Creating APA tables manually is often time consuming and prone to transcription errors. This package generates tables for MS Word ('.docx' extension) in APA format automatically with just a few lines of code.
Author: Jort de Vreeze [aut, cre]
Maintainer: Jort de Vreeze <j.devreeze@iwm-tuebingen.de>
Diff between apaStyle versions 0.1 dated 2015-10-23 and 0.2 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS |only R/apaTable.R | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical workflow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and reweighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-7 dated 2015-11-10 and 5.0-8 dated 2015-11-18
Zelig-5.0-7/Zelig/tests/test-all.R |only Zelig-5.0-8/Zelig/DESCRIPTION | 14 +-- Zelig-5.0-8/Zelig/MD5 | 54 +++++++----- Zelig-5.0-8/Zelig/NAMESPACE | 6 - Zelig-5.0-8/Zelig/R/model-lognorm.R | 2 Zelig-5.0-8/Zelig/R/model-ls.R | 2 Zelig-5.0-8/Zelig/R/model-relogit.R | 3 Zelig-5.0-8/Zelig/R/model-zelig.R | 101 +++++++++++++++++------- Zelig-5.0-8/Zelig/R/plots.R | 14 +-- Zelig-5.0-8/Zelig/R/utils.R | 6 - Zelig-5.0-8/Zelig/man/cluster.formula.Rd | 12 +- Zelig-5.0-8/Zelig/man/coef-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/fitted-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/plot-Zelig-ANY-method.Rd |only Zelig-5.0-8/Zelig/man/predict-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/reduce.Rd | 14 +-- Zelig-5.0-8/Zelig/man/relogit.Rd | 4 Zelig-5.0-8/Zelig/man/setfactor.Rd | 10 +- Zelig-5.0-8/Zelig/man/setval.Rd | 10 +- Zelig-5.0-8/Zelig/man/stat.Rd | 10 +- Zelig-5.0-8/Zelig/man/statlevel.Rd | 10 +- Zelig-5.0-8/Zelig/man/statmat.Rd | 8 - Zelig-5.0-8/Zelig/man/summary-Zelig-method.Rd |only Zelig-5.0-8/Zelig/man/table.levels.Rd | 22 +++-- Zelig-5.0-8/Zelig/man/vcov-Zelig-method.Rd |only Zelig-5.0-8/Zelig/tests/testthat.R |only Zelig-5.0-8/Zelig/tests/testthat/test-logit.R | 79 ------------------ Zelig-5.0-8/Zelig/tests/testthat/test-lognom.R | 40 --------- Zelig-5.0-8/Zelig/tests/testthat/test-ls.R | 87 -------------------- Zelig-5.0-8/Zelig/tests/testthat/test-negbin.R | 16 --- Zelig-5.0-8/Zelig/tests/testthat/test-poisson.R | 16 --- Zelig-5.0-8/Zelig/tests/testthat/test-probit.R | 18 ---- 32 files changed, 202 insertions(+), 356 deletions(-)
Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently
scatter plots, histograms, parallel coordinate plots and choropleth maps are
supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.1.1 dated 2015-06-07 and 0.2.0 dated 2015-11-18
DESCRIPTION | 8 +- MD5 | 30 ++++----- NAMESPACE | 3 R/misc.R | 2 R/vcmap.R | 1 R/vhist.R | 2 R/vlaunch.R | 42 +++++++++--- R/vpcp.R | 1 R/vscat.R | 10 ++- build/vignette.rds |binary exec/vdmr_cmap.js | 99 ++++++++++++++++++++++++++++- exec/vdmr_hist.js | 134 +++++++++++++++++++++++++++++++++------- exec/vdmr_main.js | 120 +++++++++++++++++++++++++++--------- exec/vdmr_pcp.js | 175 +++++++++++++++++++++++++++++++++++++++++++++-------- exec/vdmr_scat.js | 167 ++++++++++++++++++++++++++++++++++++++++++++------ man/vlaunch.Rd | 4 - 16 files changed, 665 insertions(+), 133 deletions(-)
Title: A Predictive Model for Trait Based Community Assembly of Plant
Species
Description: Implements a predictive model of community assembly called 'Traitspace' (Laughlin et al. 2012, Ecology Letters). Traitspace is a hierarchical Bayesian model that translates the theory of trait-based environmental filtering into a statistical model that incorporates intraspecific trait variation to predict the relative abundances and the distributions of species.
The package includes functions to plot the predicted and the observed values. It also includes functions to compare the predicted values against the observed values using a variety of different distance measures and to implement permutation tests to test their statistical significance.
Author: Chaitanya Joshi, Xin Li, Daniel Laughlin
Maintainer: Chaitanya Joshi <cjoshi@waikato.ac.nz>
Diff between Traitspace versions 1.0 dated 2015-07-07 and 1.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Traitspace.R | 2 +- R/TraitspaceMod.R | 2 +- R/step_2D.R | 8 ++++---- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB), pre-formatted for general analysis and genome-wide association analysis using the NAM package.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Reka Howard, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between SoyNAM versions 1.1 dated 2015-10-15 and 1.2 dated 2015-11-18
SoyNAM-1.1/SoyNAM/R/BLUPs.R |only SoyNAM-1.1/SoyNAM/man/BLUP1.Rd |only SoyNAM-1.1/SoyNAM/man/BLUP2.Rd |only SoyNAM-1.2/SoyNAM/DESCRIPTION | 10 +++++----- SoyNAM-1.2/SoyNAM/MD5 | 17 ++++++++--------- SoyNAM-1.2/SoyNAM/R/BLUP.R |only SoyNAM-1.2/SoyNAM/data/datalist | 4 ++-- SoyNAM-1.2/SoyNAM/data/soybase.RData |binary SoyNAM-1.2/SoyNAM/data/soynam.RData |binary SoyNAM-1.2/SoyNAM/man/BLUP.Rd |only SoyNAM-1.2/SoyNAM/man/SoyNAM-package.Rd | 6 +++--- SoyNAM-1.2/SoyNAM/man/soynam.Rd | 23 ++++++----------------- 12 files changed, 24 insertions(+), 36 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis <martha.ellis@gmail.com>
Diff between rSPACE versions 1.1.1 dated 2015-04-08 and 1.2.0 dated 2015-11-18
DESCRIPTION | 11 ++++---- MD5 | 14 +++++----- NAMESPACE | 6 +++- R/Create_Landscapes.r | 47 +++++++++++++++++++++++++++++------ R/Encounter_history.R | 1 R/Test_Samples.r | 8 ++++- R/Test_file.r | 14 +++++----- inst/external/ExampleSampleFrame.tif |binary 8 files changed, 73 insertions(+), 28 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.8-1 dated 2015-10-31 and 0.9-0 dated 2015-11-18
DESCRIPTION | 8 +++--- MD5 | 8 +++--- inst/NEWS.Rd | 8 ++++++ inst/include/Spectra/GenEigsSolver.h | 46 ++++++++++++++++++++--------------- inst/include/Spectra/SymEigsSolver.h | 41 +++++++++++++++++++------------ 5 files changed, 68 insertions(+), 43 deletions(-)
Title: A Report Templating System
Description: Facilitating the creation of reproducible statistical
report templates. Once created, rapport templates can be exported to
various external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as the
converter backend.
Author: Aleksandar Blagotić <alex@rapporter.net> and Gergely Daróczi
<daroczig@rapporter.net>
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between rapport versions 0.51 dated 2013-05-08 and 1.0 dated 2015-11-18
rapport-0.51/rapport/R/graphs.R |only rapport-0.51/rapport/R/misc.R |only rapport-0.51/rapport/R/stat_helpers.R |only rapport-0.51/rapport/R/stats_univar.R |only rapport-0.51/rapport/R/tables.R |only rapport-0.51/rapport/R/utils.R |only rapport-0.51/rapport/inst/templates/anova.tpl |only rapport-0.51/rapport/inst/templates/correlations.tpl |only rapport-0.51/rapport/inst/templates/crosstable.tpl |only rapport-0.51/rapport/inst/templates/deprecated/anova.tpl |only rapport-0.51/rapport/inst/templates/deprecated/correlations.tpl |only rapport-0.51/rapport/inst/templates/deprecated/crosstable.tpl |only rapport-0.51/rapport/inst/templates/deprecated/descriptives.tpl |only rapport-0.51/rapport/inst/templates/deprecated/example.tpl |only rapport-0.51/rapport/inst/templates/deprecated/generate-beta.tpl |only rapport-0.51/rapport/inst/templates/deprecated/i18n/hu/correlations.tpl |only rapport-0.51/rapport/inst/templates/deprecated/nortest.tpl |only rapport-0.51/rapport/inst/templates/deprecated/outlier-test.tpl |only rapport-0.51/rapport/inst/templates/deprecated/t-test.tpl |only rapport-0.51/rapport/inst/templates/descriptives.tpl |only rapport-0.51/rapport/inst/templates/example.tpl |only rapport-0.51/rapport/inst/templates/generate-beta.tpl |only rapport-0.51/rapport/inst/templates/i18n/hu/correlations.tpl |only rapport-0.51/rapport/inst/templates/nortest.tpl |only rapport-0.51/rapport/inst/templates/outlier-test.tpl |only rapport-0.51/rapport/inst/templates/t-test.tpl |only rapport-0.51/rapport/inst/tests/test-inputs-deprecated.R |only rapport-0.51/rapport/inst/tests/test-rp_helpers.R |only rapport-0.51/rapport/inst/tests/test-stat_helpers.R |only rapport-0.51/rapport/man/adj.rle.Rd |only rapport-0.51/rapport/man/alike.integer.Rd |only rapport-0.51/rapport/man/as.character.rp.inputs.Rd |only rapport-0.51/rapport/man/as.character.rp.meta.Rd |only rapport-0.51/rapport/man/capitalise.Rd |only rapport-0.51/rapport/man/catn.Rd |only rapport-0.51/rapport/man/fml.Rd |only rapport-0.51/rapport/man/htest.Rd |only rapport-0.51/rapport/man/htest.short.Rd |only rapport-0.51/rapport/man/is.boolean.Rd |only rapport-0.51/rapport/man/is.empty.Rd |only rapport-0.51/rapport/man/is.heading.Rd |only rapport-0.51/rapport/man/is.number.Rd |only rapport-0.51/rapport/man/is.rp.heading.Rd |only rapport-0.51/rapport/man/is.string.Rd |only rapport-0.51/rapport/man/is.tabular.Rd |only rapport-0.51/rapport/man/is.variable.Rd |only rapport-0.51/rapport/man/kurtosis.Rd |only rapport-0.51/rapport/man/lambda.test.Rd |only rapport-0.51/rapport/man/messagef.Rd |only rapport-0.51/rapport/man/pct.Rd |only rapport-0.51/rapport/man/print.rp.info.Rd |only rapport-0.51/rapport/man/print.rp.inputs.Rd |only rapport-0.51/rapport/man/print.rp.meta.Rd |only rapport-0.51/rapport/man/purge.comments.Rd |only rapport-0.51/rapport/man/rp.barplot.Rd |only rapport-0.51/rapport/man/rp.boxplot.Rd |only rapport-0.51/rapport/man/rp.densityplot.Rd |only rapport-0.51/rapport/man/rp.desc.Rd |only rapport-0.51/rapport/man/rp.dotplot.Rd |only rapport-0.51/rapport/man/rp.freq.Rd |only rapport-0.51/rapport/man/rp.graph.check.Rd |only rapport-0.51/rapport/man/rp.hist.Rd |only rapport-0.51/rapport/man/rp.iqr.Rd |only rapport-0.51/rapport/man/rp.kurtosis.Rd |only rapport-0.51/rapport/man/rp.label-set.Rd |only rapport-0.51/rapport/man/rp.label.Rd |only rapport-0.51/rapport/man/rp.lineplot.Rd |only rapport-0.51/rapport/man/rp.max.Rd |only rapport-0.51/rapport/man/rp.mean.Rd |only rapport-0.51/rapport/man/rp.median.Rd |only rapport-0.51/rapport/man/rp.min.Rd |only rapport-0.51/rapport/man/rp.missing.Rd |only rapport-0.51/rapport/man/rp.name.Rd |only rapport-0.51/rapport/man/rp.outlier.Rd |only rapport-0.51/rapport/man/rp.percent.Rd |only rapport-0.51/rapport/man/rp.qqplot.Rd |only rapport-0.51/rapport/man/rp.range.Rd |only rapport-0.51/rapport/man/rp.scatterplot.Rd |only rapport-0.51/rapport/man/rp.sd.Rd |only 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rapport-0.51/rapport/man/tpl.paths.reset.Rd |only rapport-0.51/rapport/man/tpl.renew.Rd |only rapport-0.51/rapport/man/tpl.rerun.Rd |only rapport-0.51/rapport/man/trim.space.Rd |only rapport-0.51/rapport/man/vgsub.Rd |only rapport-0.51/rapport/man/warningf.Rd |only rapport-1.0/rapport/DESCRIPTION | 32 rapport-1.0/rapport/MD5 | 255 ++---- rapport-1.0/rapport/NAMESPACE | 139 +-- rapport-1.0/rapport/NEWS | 65 + rapport-1.0/rapport/R/deprecated.R | 58 - rapport-1.0/rapport/R/export.R | 89 +- rapport-1.0/rapport/R/init.R | 18 rapport-1.0/rapport/R/inputs.R | 42 rapport-1.0/rapport/R/print.methods.R | 32 rapport-1.0/rapport/R/rapport.R | 93 ++ rapport-1.0/rapport/R/rp_helpers.R | 302 +------ rapport-1.0/rapport/R/template.R | 425 ++++++---- rapport-1.0/rapport/R/tpl-check.R | 15 rapport-1.0/rapport/data/ius2008.rda |binary rapport-1.0/rapport/demo/rapport.R | 109 +- rapport-1.0/rapport/inst/includes/stylesheets/custom.css | 4 rapport-1.0/rapport/inst/templates/ANOVA.rapport |only rapport-1.0/rapport/inst/templates/AnalyzeWizard.rapport |only rapport-1.0/rapport/inst/templates/BartlettsTest.rapport |only rapport-1.0/rapport/inst/templates/BrownForsythTest.rapport |only rapport-1.0/rapport/inst/templates/Correlation.rapport |only rapport-1.0/rapport/inst/templates/Crosstable.rapport |only rapport-1.0/rapport/inst/templates/Descriptives.rapport |only rapport-1.0/rapport/inst/templates/Example.rapport |only rapport-1.0/rapport/inst/templates/FTest.rapport |only rapport-1.0/rapport/inst/templates/FactorAnalysis.rapport |only rapport-1.0/rapport/inst/templates/GLM.rapport |only rapport-1.0/rapport/inst/templates/GenerateBeta.rapport |only rapport-1.0/rapport/inst/templates/HierarchicalClusterAnalysis.rapport |only rapport-1.0/rapport/inst/templates/HomogeneityCrosstable.rapport |only rapport-1.0/rapport/inst/templates/KMeansCluster.rapport |only rapport-1.0/rapport/inst/templates/KolmogorovSmirnovTest.rapport |only rapport-1.0/rapport/inst/templates/KruskalWallisTest.rapport |only rapport-1.0/rapport/inst/templates/LinearRegression.rapport |only rapport-1.0/rapport/inst/templates/MDS.rapport |only rapport-1.0/rapport/inst/templates/Minimal.rapport |only rapport-1.0/rapport/inst/templates/NormalityTest.rapport |only rapport-1.0/rapport/inst/templates/OutlierTest.rapport |only rapport-1.0/rapport/inst/templates/PCA.rapport |only rapport-1.0/rapport/inst/templates/TTestOneSample.rapport |only rapport-1.0/rapport/inst/templates/TTestTwoSample.rapport |only rapport-1.0/rapport/inst/templates/WilcoxonTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/ANOVA.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Correlation.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Crosstable.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Descriptives.rapport |only rapport-1.0/rapport/inst/templates/deprecated/Example.rapport |only rapport-1.0/rapport/inst/templates/deprecated/GenerateBeta.rapport |only rapport-1.0/rapport/inst/templates/deprecated/NormalityTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/OutlierTest.rapport |only rapport-1.0/rapport/inst/templates/deprecated/i18n/hu/correlations.rapport |only rapport-1.0/rapport/inst/templates/graphs |only rapport-1.0/rapport/inst/templates/i18n/hu/correlations.rapport |only rapport-1.0/rapport/inst/tests/test-deprecated.R |only rapport-1.0/rapport/inst/tests/test-internals.R |only rapport-1.0/rapport/inst/tests/test-rapport.R | 20 rapport-1.0/rapport/man/as.character.rapport.inputs.Rd |only rapport-1.0/rapport/man/as.character.rapport.meta.Rd |only rapport-1.0/rapport/man/as.yaml.bool.Rd | 10 rapport-1.0/rapport/man/check.input.value.Rd | 19 rapport-1.0/rapport/man/check.input.value.class.Rd | 15 rapport-1.0/rapport/man/check.report.chunks.Rd | 11 rapport-1.0/rapport/man/check.tpl.Rd |only rapport-1.0/rapport/man/extract.meta.Rd | 40 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rapport-1.0/rapport/man/rapport.docx.Rd | 15 rapport-1.0/rapport/man/rapport.example.Rd |only rapport-1.0/rapport/man/rapport.export.Rd |only rapport-1.0/rapport/man/rapport.header.Rd |only rapport-1.0/rapport/man/rapport.html.Rd | 15 rapport-1.0/rapport/man/rapport.info.Rd |only rapport-1.0/rapport/man/rapport.inputs.Rd |only rapport-1.0/rapport/man/rapport.ls.Rd |only rapport-1.0/rapport/man/rapport.meta.Rd |only rapport-1.0/rapport/man/rapport.odt.Rd | 15 rapport-1.0/rapport/man/rapport.path.Rd |only rapport-1.0/rapport/man/rapport.path.add.Rd |only rapport-1.0/rapport/man/rapport.path.remove.Rd |only rapport-1.0/rapport/man/rapport.path.reset.Rd |only rapport-1.0/rapport/man/rapport.pdf.Rd | 15 rapport-1.0/rapport/man/rapport.read.Rd |only rapport-1.0/rapport/man/rapport.renew.Rd |only rapport-1.0/rapport/man/rapport.rerun.Rd |only rapport-1.0/rapport/man/rapport.tangle.Rd |only 210 files changed, 1200 insertions(+), 1312 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.50.0 dated 2015-10-15 and 0.60.0 dated 2015-11-18
PSCBS-0.50.0/PSCBS/R/PairedPSCBS.BOOT,DEFUNCT.R |only PSCBS-0.60.0/PSCBS/DESCRIPTION | 12 PSCBS-0.60.0/PSCBS/MD5 | 33 PSCBS-0.60.0/PSCBS/NAMESPACE | 3 PSCBS-0.60.0/PSCBS/NEWS | 3481 +++++------ PSCBS-0.60.0/PSCBS/R/999.DEPRECATED.R |only PSCBS-0.60.0/PSCBS/R/PairedPSCBS.BOOT.R | 17 PSCBS-0.60.0/PSCBS/R/PairedPSCBS.BOOT.sets.R | 17 PSCBS-0.60.0/PSCBS/R/PairedPSCBS.PLOT,many.R | 17 PSCBS-0.60.0/PSCBS/R/randomSeed.R |only PSCBS-0.60.0/PSCBS/R/segmentByCBS.R | 192 PSCBS-0.60.0/PSCBS/R/segmentByPairedPSCBS.R | 78 PSCBS-0.60.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.60.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.60.0/PSCBS/man/randomSeed.Rd |only PSCBS-0.60.0/PSCBS/tests/randomSeed.R |only PSCBS-0.60.0/PSCBS/tests/segmentByCBS,futures.R |only PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,calls.R | 2 PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,futures.R |only PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS,noNormalBAFs.R | 2 PSCBS-0.60.0/PSCBS/tests/segmentByPairedPSCBS.R | 2 21 files changed, 1921 insertions(+), 1935 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Description: Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can in
general be programmed on. A useful OptPath object (archive) to log function
evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Karin Schork [aut]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between ParamHelpers versions 1.5 dated 2015-02-03 and 1.6 dated 2015-11-18
DESCRIPTION | 33 ++- MD5 | 245 ++++++++++++++------------- NAMESPACE | 15 + NEWS | 17 + R/LearnerParam.R | 16 + R/OptPath.R | 4 R/OptPathDF.R | 2 R/OptPathDF_getter.R | 15 - R/OptPathDF_setter.R | 5 R/OptPath_getter.R | 2 R/OptPath_plotEAF.R |only R/OptPath_plotYTraces.R |only R/OptPath_plotter.R |only R/OptPath_setter.R | 4 R/ParamSet.R | 30 +-- R/aParam.R | 22 ++ R/convertParamSetToIrace.R | 30 +-- R/convertTypesToCInts.R | 4 R/dfRowsToList.R | 8 R/dropParams.R | 2 R/filterParams.R | 51 ++++- R/generateDesign.R | 14 + R/generateGridDesign.R | 31 +-- R/generateRandomDesign.R | 8 R/getDefaults.R | 3 R/getParamIds.R | 4 R/getParamLengths.R | 4 R/getParamNr.R | 4 R/getParamTypeCounts.R | 1 R/getParamTypes.R | 15 - R/hasForbidden.R | 2 R/hasRequires.R | 4 R/hasTrafo.R | 4 R/hasType.R | 24 +- R/isFeasible.R | 24 +- R/isForbidden.R | 2 R/isMissingValue.R | 4 R/isRequiresOk.R |only R/isType.R | 14 + R/isVector.R | 2 R/makeLearnerParamFuns.R | 56 +++--- R/makeParamFuns.R | 98 ++++++++-- R/paramValueToString.R | 4 R/removeMissingValues.R | 2 R/renderOptPathPlot.R |only R/renderOptPathPlot_helpers.R |only R/renderOptPathPlot_workers.R |only R/sample.R | 6 R/utils.R | 10 - R/zzz.R | 3 man/LearnerParam.Rd | 28 +-- man/OptPath.Rd | 24 +- man/Param.Rd | 47 +++-- man/addOptPathEl.Rd | 23 +- man/as.data.frame.OptPathDF.Rd | 2 man/convertParamSetToIrace.Rd | 8 man/dfRowsToList.Rd | 9 man/discreteNameToValue.Rd | 2 man/discreteValueToName.Rd | 2 man/dropParams.Rd | 6 man/extractParamSetFromSooFunction.Rd | 2 man/filterParams.Rd | 34 ++- man/generateDesign.Rd | 9 man/generateGridDesign.Rd | 7 man/generateRandomDesign.Rd | 7 man/getDefaults.Rd | 2 man/getLower.Rd | 2 man/getOptPathBestIndex.Rd | 21 +- man/getOptPathCol.Rd | 25 +- man/getOptPathCols.Rd | 23 +- man/getOptPathDOB.Rd | 25 +- man/getOptPathEOL.Rd | 25 +- man/getOptPathEl.Rd | 25 +- man/getOptPathErrorMessages.Rd | 23 +- man/getOptPathExecTimes.Rd | 23 +- man/getOptPathLength.Rd | 23 +- man/getOptPathParetoFront.Rd | 23 +- man/getOptPathX.Rd | 23 +- man/getOptPathY.Rd | 23 +- man/getParamIds.Rd | 2 man/getParamLengths.Rd | 2 man/getParamNr.Rd | 2 man/getParamTypeCounts.Rd | 2 man/getParamTypes.Rd | 6 man/hasFiniteBoxConstraints.Rd | 2 man/hasForbidden.Rd | 2 man/hasRequires.Rd | 2 man/hasTrafo.Rd | 2 man/hasType.Rd | 5 man/isEmpty.Rd | 2 man/isFeasible.Rd | 4 man/isForbidden.Rd | 2 man/isRequiresOk.Rd |only man/isType.Rd | 5 man/makeParamSet.Rd | 4 man/paramValueToString.Rd | 2 man/plotEAF.Rd |only man/plotOptPath.Rd |only man/plotYTraces.Rd |only man/removeMissingValues.Rd | 2 man/renderOptPathPlot.Rd |only man/renderYTraces.Rd |only man/repairPoint.Rd | 2 man/sampleValue.Rd | 6 man/sampleValues.Rd | 6 man/setOptPathElDOB.Rd | 23 +- man/setOptPathElEOL.Rd | 23 +- man/setValueCNames.Rd | 2 man/trafoOptPath.Rd | 2 man/trafoValue.Rd | 2 src/c_dfRowsToList.c | 11 - tests/testthat/helper_zzz.R |only tests/testthat/test_LearnerParam.R | 40 ++-- tests/testthat/test_OptPath.R | 31 +-- tests/testthat/test_Param.R | 29 +++ tests/testthat/test_ParamSet.R | 28 ++- tests/testthat/test_convertDiscrete.R | 18 - tests/testthat/test_convertParamSetToIrace.R | 21 +- tests/testthat/test_dfRowToList.R | 20 +- tests/testthat/test_dropParams.R | 12 - tests/testthat/test_filterParams.R | 91 +++++++--- tests/testthat/test_generateDesign.R | 15 + tests/testthat/test_generateGridDesign.R | 14 + tests/testthat/test_getDefaults.R | 5 tests/testthat/test_getParamTypeCounts.R | 4 tests/testthat/test_getParamTypes.R | 28 +-- tests/testthat/test_hasIsType.R | 27 +- tests/testthat/test_paramValueToString.R | 9 tests/testthat/test_plotEAF.R |only tests/testthat/test_plotYTrace.R |only tests/testthat/test_renderOptPathPlot.R |only tests/testthat/test_sample.R | 1 132 files changed, 1168 insertions(+), 694 deletions(-)
Title: Naive Discriminative Learning
Description: Naive discriminative learning implements learning and
classification models based on the Rescorla-Wagner equations and their
equilibrium equations.
Author: Antti Arppe [aut],
Peter Hendrix [aut],
Petar Milin [aut],
R. Harald Baayen [aut],
Tino Sering [aut, cre],
Cyrus Shaoul [aut]
Maintainer: Tino Sering <konstantin.sering@uni-tuebingen.de>
Diff between ndl versions 0.2.16 dated 2014-02-27 and 0.2.17 dated 2015-11-18
DESCRIPTION | 29 +++++++++++------- MD5 | 34 ++++++++++----------- NAMESPACE | 34 +++++++++++++++++++++ NEWS | 9 +++++ R/anova.ndlClassify.R | 29 ++++++++---------- R/estimateWeights.R | 67 ++++++++++++++++++++++++------------------- R/modelStatistics.R | 6 +-- R/ndlClassify.R | 9 +++-- R/ndlCuesOutcomes.R | 3 - R/predict.ndlClassify.R | 2 - R/summary.ndlClassify.R | 6 ++- R/summary.ndlCrossvalidate.R | 2 - README.md | 24 +++++++-------- man/learnLegacy.Rd | 7 ++-- man/lexample.Rd | 2 + man/ndl.package.Rd | 4 +- man/serbianUniCyr.Rd | 2 + src/learn.module.cpp | 28 ++++++++++++++--- 18 files changed, 188 insertions(+), 109 deletions(-)
Title: Normalize NanoString miRNA and mRNA Data
Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
Author: Daryl M. Waggott
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between NanoStringNorm versions 1.1.19 dated 2015-03-20 and 1.1.21 dated 2015-11-18
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 16 +++++++++++++++- R/Plot.NanoStringNorm.R | 4 ++-- R/read.xls.RCC.R | 8 +++----- build/vignette.rds |binary inst/doc/NanoStringNorm_Introduction.Rnw | 2 +- inst/doc/NanoStringNorm_Introduction.pdf |binary man/Plot.NanoStringNorm.Rd | 2 +- vignettes/NanoStringNorm_Introduction.Rnw | 2 +- 10 files changed, 39 insertions(+), 27 deletions(-)
More information about NanoStringNorm at CRAN
Permanent link
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.5 dated 2015-01-06 and 1.6 dated 2015-11-18
msm-1.5/msm/TODO |only msm-1.5/msm/inst/NEWS.mine |only msm-1.5/msm/inst/NEWS.r57 |only msm-1.5/msm/inst/NEWS.r64 |only msm-1.6/msm/ChangeLog | 83 ++++ msm-1.6/msm/DESCRIPTION | 23 - msm-1.6/msm/MD5 | 71 ++-- msm-1.6/msm/NAMESPACE | 19 - msm-1.6/msm/R/hmm-dists.R | 10 msm-1.6/msm/R/hmm.R | 175 +++++++--- msm-1.6/msm/R/msm.R | 135 +++++-- msm-1.6/msm/R/optim.R | 19 - msm-1.6/msm/R/outputs.R | 12 msm-1.6/msm/R/phase.R | 3 msm-1.6/msm/R/simul.R | 7 msm-1.6/msm/build/vignette.rds |binary msm-1.6/msm/inst/NEWS | 52 ++- msm-1.6/msm/inst/doc/msm-manual.R | 78 ++-- msm-1.6/msm/inst/doc/msm-manual.pdf |binary msm-1.6/msm/man/MatrixExp.Rd | 12 msm-1.6/msm/man/draic.msm.Rd | 20 - msm-1.6/msm/man/hmmMV.Rd |only msm-1.6/msm/man/hmodel.object.Rd | 1 msm-1.6/msm/man/msm.Rd | 81 ++-- msm-1.6/msm/man/pearson.msm.Rd | 2 msm-1.6/msm/man/simmulti.msm.Rd | 7 msm-1.6/msm/man/sojourn.msm.Rd | 7 msm-1.6/msm/man/totlos.msm.Rd | 2 msm-1.6/msm/src/doc/msm-manual.Rnw | 42 +- msm-1.6/msm/src/hmm.h | 1 msm-1.6/msm/src/hmmderiv.c | 1 msm-1.6/msm/src/lik.c | 376 ++++++++++++++++------ msm-1.6/msm/src/msm.h | 2 msm-1.6/msm/src/pijt.c | 19 - msm-1.6/msm/tests/testthat/test_datasumm.r | 1 msm-1.6/msm/tests/testthat/test_models.r | 85 ++-- msm-1.6/msm/tests/testthat/test_models_hmm.r | 48 +- msm-1.6/msm/tests/testthat/test_models_hmmmulti.r |only msm-1.6/msm/tests/testthat/test_models_misc.r | 40 +- msm-1.6/msm/vignettes |only 40 files changed, 980 insertions(+), 454 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.7.5 dated 2015-11-16 and 0.7.7 dated 2015-11-18
DESCRIPTION | 14 MD5 | 64 +- NAMESPACE | 32 - NEWS | 178 +++---- R/Qm.R | 34 - R/af.R | 986 ++++++++++++++++++++-------------------- R/bglmnet.R | 624 ++++++++++++------------- R/glmfence.R | 252 +++++----- R/lmfence.R | 300 ++++++------ R/mplot-package.R | 792 ++++++++++++++++---------------- R/mplot.R | 560 +++++++++++----------- R/qrange.R | 118 ++-- R/sigMM.R | 50 +- R/vis.R | 1250 +++++++++++++++++++++++++-------------------------- README.md | 146 ++--- inst/CITATION | 42 - man/af.Rd | 244 ++++----- man/artificialeg.Rd | 84 +-- man/bglmnet.Rd | 102 ++-- man/bodyfat.Rd | 102 ++-- man/diabetes.Rd | 88 +-- man/fev.Rd | 100 ++-- man/mplot-package.Rd | 22 man/mplot.Rd | 73 +- man/plot.af.Rd | 150 +++--- man/plot.bglmnet.Rd | 179 +++---- man/plot.vis.Rd | 269 +++++----- man/print.af.Rd | 48 - man/print.vis.Rd | 48 - man/summary.af.Rd | 48 - man/txt.fn.Rd | 42 - man/vis.Rd | 160 +++--- man/wallabies.Rd | 116 ++-- 33 files changed, 3683 insertions(+), 3634 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-1 dated 2015-10-03 and 1.2-2 dated 2015-11-18
DESCRIPTION | 8 +++--- MD5 | 54 +++++++++++++++++++++++--------------------- R/jomo.MCMCchain.R |only R/jomo.R |only R/jomo1.MCMCchain.R | 2 - R/jomo1.R | 2 - R/jomo1cat.MCMCchain.R | 21 ++++++----------- R/jomo1cat.R | 19 +++++---------- R/jomo1con.MCMCchain.R | 4 +-- R/jomo1con.R | 4 +-- R/jomo1mix.MCMCchain.R | 23 +++++++----------- R/jomo1mix.R | 23 +++++++----------- R/jomo1ran.MCMCchain.R | 2 - R/jomo1ran.R | 2 - R/jomo1rancat.MCMCchain.R | 25 ++++++++------------ R/jomo1rancat.R | 25 ++++++++------------ R/jomo1rancathr.MCMCchain.R | 25 ++++++++------------ R/jomo1rancathr.R | 25 ++++++++------------ R/jomo1rancon.MCMCchain.R | 8 +++--- R/jomo1rancon.R | 8 +++--- R/jomo1ranconhr.MCMCchain.R | 8 +++--- R/jomo1ranconhr.R | 8 +++--- R/jomo1ranmix.MCMCchain.R | 27 ++++++++-------------- R/jomo1ranmix.R | 27 ++++++++-------------- R/jomo1ranmixhr.MCMCchain.R | 27 ++++++++-------------- R/jomo1ranmixhr.R | 27 ++++++++-------------- man/jomo-package.Rd | 1 man/jomo.MCMCchain.Rd |only man/jomo.Rd |only man/jomo1ran.MCMCchain.Rd | 2 - 30 files changed, 175 insertions(+), 232 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between hypervolume versions 1.4 dated 2015-09-24 and 1.4.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/hypervolume.R | 6 +++--- R/hypervolume_inclusion_test.R | 4 ++-- R/hypervolume_plot.R | 5 ++++- R/hypervolume_set.R | 14 +++++++------- man/hypervolume_inclusion_test.Rd | 8 ++++++-- man/hypervolume_set.Rd | 12 ++++++++++-- 8 files changed, 43 insertions(+), 28 deletions(-)
Title: Joint Generalized Estimating Equation Solver
Description: Fits two different joint generalized estimating equation models to multivariate longitudinal data.
Author: Gul Inan
Maintainer: Gul Inan <inanx002@umn.edu>
Diff between JGEE versions 1.0 dated 2015-08-18 and 1.1 dated 2015-11-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/JGEE-package.Rd | 2 +- man/JGee2.Rd | 40 ++++++++++++++++++++++++++++++++-------- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, identify cutpoints, and quickly combine shapefiles and
dataframes for plotting. Includes four alternative themes for ggplot2. Also
includes three example datasets of administrative education records for
learning how to process records with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between eeptools versions 0.9.0 dated 2015-09-23 and 0.9.1 dated 2015-11-18
DESCRIPTION | 15 +++---- MD5 | 84 ++++++++++++++++++++--------------------- NAMESPACE | 4 - NEWS.md | 10 ++++ R/autoplot.lm.R | 14 +++--- R/eeptools.R | 2 R/mapfunctions.R | 22 +++++----- R/max_mis.R | 11 +++-- R/theme_dpi.R | 4 - inst/doc/intro.html | 13 +++--- man/age_calc.Rd | 14 +++--- man/autoplot.lm.Rd | 7 +-- man/cleanTex.Rd | 8 +-- man/crosstabplot.Rd | 12 ++--- man/crosstabs.Rd | 8 +-- man/cutoff.Rd | 13 +++--- man/decomma.Rd | 9 ++-- man/defac.Rd | 7 +-- man/eeptools.Rd | 10 ++-- man/gelmansim.Rd | 12 ++--- man/ggmapmerge.Rd | 8 +-- man/lag_data.Rd | 9 ++-- man/leading_zero.Rd | 14 +++--- man/makenum.Rd | 15 +++---- man/mapmerge.Rd | 10 ++-- man/max_mis.Rd | 11 ++--- man/midsch.Rd | 14 +++--- man/moves_calc.Rd | 35 ++++++++--------- man/nth_max.Rd | 6 ++ man/profpoly.Rd | 4 - man/profpoly.data.Rd | 4 - man/remove_char.Rd | 12 ++--- man/retained_calc.Rd | 16 +++---- man/statamode.Rd | 24 +++++------ man/stuatt.Rd | 10 ++-- man/stulevel.Rd | 10 ++-- man/theme_dpi.Rd | 6 +- man/theme_dpi_map.Rd | 10 ++-- man/theme_dpi_map2.Rd | 12 ++--- man/theme_dpi_mapPNG.Rd | 12 ++--- man/thresh.Rd | 12 ++--- tests/testthat/test-maptools.R | 2 tests/testthat/test-utils.R | 6 +- 43 files changed, 282 insertions(+), 259 deletions(-)
Title: Optimisation with Continuous Convex Piecewise (Linear and
Quadratic) Functions
Description: Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.
Author: Robin Girard
Maintainer: Robin Girard <robin.girard@mines-paristech.fr>
Diff between ConConPiWiFun versions 0.4.4 dated 2014-10-02 and 0.4.6 dated 2015-11-18
ConConPiWiFun-0.4.4/ConConPiWiFun/R/test |only ConConPiWiFun-0.4.6/ConConPiWiFun/DESCRIPTION | 6 ConConPiWiFun-0.4.6/ConConPiWiFun/MD5 | 30 - ConConPiWiFun-0.4.6/ConConPiWiFun/NAMESPACE | 1 ConConPiWiFun-0.4.6/ConConPiWiFun/R/OptimStorage.R |only ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/convex_function_manip.hpp | 9 ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cplfunction.hpp | 6 ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cplfunctionvec.hpp | 151 +++++++++- ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cpqfunction.hpp | 21 + ConConPiWiFun-0.4.6/ConConPiWiFun/inst/include/cpqfunctionvec.hpp | 124 ++++++++ ConConPiWiFun-0.4.6/ConConPiWiFun/man/OptimPriceStorage.Rd |only ConConPiWiFun-0.4.6/ConConPiWiFun/man/cplfunctionvec.Rd | 9 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Makevars | 5 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Makevars.win | 7 ConConPiWiFun-0.4.6/ConConPiWiFun/src/Modules.cc | 15 15 files changed, 331 insertions(+), 53 deletions(-)
Title: Efficient Constrained Based Modelling in R
Description: This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybil versions 1.3.0 dated 2015-06-17 and 1.3.2 dated 2015-11-17
DESCRIPTION | 14 +- MD5 | 37 +++--- NAMESPACE | 4 R/deadEndMetabolite.R | 2 R/fluxDistributionClass.R | 2 R/generateWT.R | 92 +++++++++------ R/optObj_cplexAPIClass.R | 8 - R/optObj_glpkAPIClass.R | 24 +-- R/optObj_lpSolveAPIClass.R | 4 R/rmReact.R | 2 R/sysBiolAlg_fbaEasyConstraintClass.R |only R/sysBiolAlg_mtfEasyConstraintClass.R |only README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 24 +++ inst/doc/sybil.R | 181 ++++++++++++++++++++---------- inst/doc/sybil.Rnw | 75 ++++++++++++ inst/doc/sybil.pdf |binary man/readTSVmod.Rd | 2 man/sysBiolAlg_fbaEasyConstraint-class.Rd |only vignettes/sybil.Rnw | 75 ++++++++++++ 21 files changed, 407 insertions(+), 141 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.6.0 dated 2015-07-24 and 1.6.1 dated 2015-11-17
ChangeLog | 3 DESCRIPTION | 18 - MD5 | 41 +-- R/AllGenerics.R | 4 R/emomLM.R | 13 - R/margskewnorm.R |only R/modelSelection.R | 92 ++++++-- R/pmomLM.R | 12 - R/pmomPM.R | 2 R/rmom.R | 11 - R/zellnerLM.R | 12 - build/vignette.rds |binary data/hald.rda |binary inst/doc/mombf.pdf |binary man/msfit-class.Rd | 3 man/postProb.Rd | 6 man/rnlp.Rd | 4 src/cstat.cpp | 130 ++++++------ src/cstat.h | 4 src/do_mombf.h | 3 src/modelSel.cpp | 559 +++++++++++++++++++++++++++++++++++++---------------- src/modelSel.h | 26 +- 22 files changed, 636 insertions(+), 307 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results.
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre, cph],
Dirk Metzler [ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.2.0 dated 2015-11-11 and 0.2.1 dated 2015-11-17
coala-0.2.0/coala/man/coala.Rd |only coala-0.2.1/coala/DESCRIPTION | 20 +-- coala-0.2.1/coala/MD5 | 62 +++++---- coala-0.2.1/coala/NAMESPACE | 8 + coala-0.2.1/coala/NEWS.md | 11 + coala-0.2.1/coala/R/RcppExports.R | 74 ++++++++--- coala-0.2.1/coala/R/coala.R | 11 - coala-0.2.1/coala/R/feature_mutation.R | 2 coala-0.2.1/coala/R/feature_recombination.R | 3 coala-0.2.1/coala/R/feature_sample.R | 2 coala-0.2.1/coala/R/segsites.R | 13 + coala-0.2.1/coala/R/simulator_ms.R | 4 coala-0.2.1/coala/R/simulator_msms.R | 4 coala-0.2.1/coala/R/simulator_scrm.R | 4 coala-0.2.1/coala/R/simulator_seqgen.R | 8 - coala-0.2.1/coala/R/sumstat.R | 98 +++++++++++++-- coala-0.2.1/coala/README.md |only coala-0.2.1/coala/inst/doc/coala-abc.html | 2 coala-0.2.1/coala/inst/doc/coala-extend.html | 2 coala-0.2.1/coala/inst/doc/coala-install.Rmd | 2 coala-0.2.1/coala/inst/doc/coala-install.html | 4 coala-0.2.1/coala/inst/doc/coala-intro.html | 18 +- coala-0.2.1/coala/inst/include/coala.h | 4 coala-0.2.1/coala/man/activate_seqgen.Rd | 2 coala-0.2.1/coala/man/calc_sumstats_from_data.Rd |only coala-0.2.1/coala/man/coala-package.Rd |only coala-0.2.1/coala/man/create_locus_trio.Rd |only coala-0.2.1/coala/man/create_segsites.Rd |only coala-0.2.1/coala/src/RcppExports.cpp | 40 +++--- coala-0.2.1/coala/src/parse_seqgen_output.cpp | 2 coala-0.2.1/coala/src/seg_sites.cpp | 63 +++++++-- coala-0.2.1/coala/tests/testthat/test-simulator-seqgen.R | 6 coala-0.2.1/coala/tests/testthat/test-sumstat-class.R | 72 ++++++++--- coala-0.2.1/coala/tests/testthat/test-travis-setup.R | 5 coala-0.2.1/coala/vignettes/coala-install.Rmd | 2 35 files changed, 384 insertions(+), 164 deletions(-)
Title: Benford Analysis for Data Validation and Forensic Analytics
Description: The Benford Analysis package provides tools that make it easier to
validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between benford.analysis versions 0.1.2.1 dated 2015-10-07 and 0.1.3 dated 2015-11-17
DESCRIPTION | 7 ++-- MD5 | 66 +++++++++++++++++++------------------- NAMESPACE | 2 - R/functions-new.R | 14 ++------ R/get.functions.R | 2 - R/internal.functions-new-code-2.R | 16 ++++----- README.md | 2 - man/MAD.Rd | 2 - man/benford.Rd | 17 +++++---- man/benford.analysis.Rd | 13 ++++--- man/census.2000_2010.Rd | 2 - man/census.2009.Rd | 4 +- man/chisq.Rd | 2 - man/corporate.payment.Rd | 2 - man/dfactor.Rd | 4 +- man/duplicatesTable.Rd | 2 - man/extract.digits.Rd | 12 +++--- man/getBfd.Rd | 4 +- man/getData.Rd | 4 +- man/getDigits.Rd | 6 +-- man/getDuplicates.Rd | 2 - man/getSuspects.Rd | 2 - man/lakes.perimeter.Rd | 2 - man/mantissa.Rd | 4 +- man/marc.Rd | 4 +- man/p.these.digits.Rd | 2 - man/p.this.digit.at.n.Rd | 2 - man/plot.Benford.Rd | 2 - man/print.Benford.Rd | 2 - man/sino.forest.Rd | 2 - man/suspectsTable.Rd | 6 +-- man/taxable.incomes.1978.Rd | 2 - tests/testthat/test-benford.R | 25 +++++++++++++- tests/testthat/test-extract.R | 5 ++ 34 files changed, 135 insertions(+), 110 deletions(-)
More information about benford.analysis at CRAN
Permanent link
Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R
that records plots in a LaTeX-friendly format. The device transforms
plotting commands issued by R functions into LaTeX code blocks. When
included in a LaTeX document, these blocks are interpreted with the
help of 'TikZ'---a graphics package for TeX and friends written by Till
Tantau. Using the 'tikzDevice', the text of R plots can contain LaTeX
commands such as mathematical formula. The device also allows arbitrary
LaTeX code to be inserted into the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb, cre],
Yihui Xie [ctb]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tikzDevice versions 0.8.1 dated 2015-01-07 and 0.9 dated 2015-11-17
tikzDevice-0.8.1/tikzDevice/inst/NEWS.Rd |only tikzDevice-0.8.1/tikzDevice/tests/testthat/Rplots.tex |only tikzDevice-0.8.1/tikzDevice/tests/testthat/Rplots_colors.tex |only tikzDevice-0.8.1/tikzDevice/vignettes/figs |only tikzDevice-0.9/tikzDevice/DESCRIPTION | 24 +-- tikzDevice-0.9/tikzDevice/MD5 | 72 +++------- tikzDevice-0.9/tikzDevice/NAMESPACE | 14 + tikzDevice-0.9/tikzDevice/R/cacheMetrics.R | 11 + tikzDevice-0.9/tikzDevice/R/latexStrWidth.R | 43 +++-- tikzDevice-0.9/tikzDevice/R/tikz.R | 8 - tikzDevice-0.9/tikzDevice/R/tikzDevice-package.R | 6 tikzDevice-0.9/tikzDevice/R/tikzInternal.R | 26 --- tikzDevice-0.9/tikzDevice/R/zzz.R | 2 tikzDevice-0.9/tikzDevice/build/vignette.rds |binary tikzDevice-0.9/tikzDevice/inst/doc/tikzDevice.R | 2 tikzDevice-0.9/tikzDevice/inst/doc/tikzDevice.pdf |binary tikzDevice-0.9/tikzDevice/man/anyMultibyteUTF8Characters.Rd | 4 tikzDevice-0.9/tikzDevice/man/getLatexStrWidth.Rd | 26 ++- tikzDevice-0.9/tikzDevice/man/gridToDevice.Rd | 4 tikzDevice-0.9/tikzDevice/man/sanitizeTexString.Rd | 4 tikzDevice-0.9/tikzDevice/man/setTikzDefaults.Rd | 6 tikzDevice-0.9/tikzDevice/man/tikz.Rd | 13 + tikzDevice-0.9/tikzDevice/man/tikzAnnotate.Rd | 17 +- tikzDevice-0.9/tikzDevice/man/tikzCompilerInfo.Rd | 4 tikzDevice-0.9/tikzDevice/man/tikzDevice-package.Rd | 2 tikzDevice-0.9/tikzDevice/src/tikzDevice.c | 18 +- tikzDevice-0.9/tikzDevice/src/tikzDevice.h | 3 tikzDevice-0.9/tikzDevice/tests/testthat/helper_reporters.R | 29 +--- tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/base_raster.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/grid_raster.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/standard_graphs/raster_reflection.pdf |binary tikzDevice-0.9/tikzDevice/tests/testthat/test_graphics.R | 1 tikzDevice-0.9/tikzDevice/tests/testthat/test_metrics_dict.R | 51 ++++--- 33 files changed, 223 insertions(+), 167 deletions(-)
Title: Sparse Learning Algorithms Using a LASSO-Type Penalty for
Coefficient Estimation and Model Prediction
Description: Coefficient estimation and model prediction based on the LASSO sparse
learning algorithm and its improved versions such as Bolasso, bootstrap ranking
LASSO, two-stage hybrid LASSO and others. These LASSO estimation procedures are
applied in the fields of variable selection, graphical modeling and ensemble
learning. The bagging LASSO model uses a Monte Carlo cross-entropy algorithm to
determine the best base-level models and improve predictive performance.
Author: Pi Guo, Yuantao Hao
Maintainer: Pi Guo <guopi.01@163.com>
Diff between SparseLearner versions 1.0.1 dated 2015-10-13 and 1.0-2 dated 2015-11-17
DESCRIPTION | 20 +++++++++++--------- MD5 | 12 ++++++++++-- NAMESPACE | 10 +++++++++- R/Bagging.lasso.R |only R/Plot.importance.R |only R/Predict.bagging.R |only R/Print.bagging.R |only man/Bagging.lasso.Rd |only man/Plot.importance.Rd |only man/Predict.bagging.Rd |only man/Print.bagging.Rd |only 11 files changed, 30 insertions(+), 12 deletions(-)
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Author: Bart Smeets [aut],
Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.0.0 dated 2015-11-15 and 3.0.1 dated 2015-11-17
DESCRIPTION | 11 +++---- MD5 | 45 ++++++++++++++--------------- R/simulator.R | 60 +++++++++++++++++++++------------------ R/wrap.R | 12 ++++++- inst/doc/introduction.html | 42 +++++++++++++-------------- man/add_generator.Rd | 2 - man/add_resource.Rd | 2 - man/get_capacity.Rd | 2 - man/get_mon_arrivals.Rd | 2 - man/get_mon_resources.Rd | 2 - man/get_queue_count.Rd | 2 - man/get_queue_size.Rd | 2 - man/get_server_count.Rd | 2 - man/now.Rd | 2 - man/peek.Rd | 2 - man/reset.Rd | 2 - man/run.Rd | 2 - man/simmer.Rd | 2 - src/simmer_rcpp.cpp | 2 - src/simulator.h | 2 - tests/testthat/test-activity.R | 3 + tests/testthat/test-simmer.R | 10 ++++++ tests/testthat/test-trajectory.R | 18 +++++++++++ tests/testthat/test-wrap.R |only 24 files changed, 137 insertions(+), 94 deletions(-)
Title: Binning and Plotting of Linearly Referenced Data
Description: Short for 'linear binning', the linbin package provides functions
for manipulating, binning, and plotting linearly referenced data. Although
developed for data collected on river networks, it can be used with any interval
or point data referenced to a 1-dimensional coordinate system. Flexible bin
generation and batch processing makes it easy to compute and visualize variables
at multiple scales, useful for identifying patterns within and between variables
and investigating the influence of scale of observation on data interpretation.
Author: Ethan Z. Welty [aut, cre],
Christian E. Torgersen [ctb] (author support and guidance),
Samuel J. Brenkman [ctb] (elwha and quinault datasets),
Jeffrey J. Duda [ctb] (elwha dataset),
Jonathan B. Armstrong [ctb] (fishmotion dataset)
Maintainer: Ethan Z. Welty <ethan.welty+linbin@gmail.com>
Diff between linbin versions 0.1.0 dated 2015-02-17 and 0.1.1 dated 2015-11-17
DESCRIPTION | 25 +++++---- MD5 | 90 ++++++++++++++++---------------- NAMESPACE | 3 - R/datasets.R | 40 +++++++------- R/event_creation.R | 4 - R/event_metrics.R | 2 R/plot_events.R | 6 +- R/sample_events.R | 2 README.md | 4 + build/vignette.rds |binary inst/CITATION | 16 ++++- inst/doc/examples.R | 14 ++--- inst/doc/examples.Rmd | 8 +- inst/doc/examples.html | 86 ++++++++++++++++++------------- inst/doc/introduction.R | 28 +++++----- inst/doc/introduction.html | 110 +++++++++++++++++++++++----------------- man/as_events.Rd | 4 - man/build_function_call.Rd | 2 man/crop_events.Rd | 2 man/cut_events.Rd | 2 man/elwha.Rd | 16 ++--- man/event_coverage.Rd | 2 man/event_gaps.Rd | 4 - man/event_overlaps.Rd | 2 man/event_range.Rd | 2 man/events.Rd | 4 - man/fill_event_gaps.Rd | 2 man/find_intersecting_events.Rd | 4 - man/fishmotion.Rd | 4 - man/if_else.Rd | 2 man/is_events.Rd | 2 man/is_not_integer.Rd | 2 man/netmap.Rd | 2 man/overlapping_events.Rd | 4 - man/plot_events.Rd | 10 +-- man/plot_events_single.Rd | 14 ++--- man/quinault.Rd | 26 ++++----- man/read_events.Rd | 4 - man/rgrep_exact.Rd | 2 man/sample_events.Rd | 4 - man/sampling_functions.Rd | 2 man/seq_events.Rd | 2 man/simple.Rd | 2 man/sorted_events.Rd | 2 man/transform_events.Rd | 2 vignettes/examples.Rmd | 8 +- 46 files changed, 314 insertions(+), 264 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.4.1 dated 2015-11-16 and 0.4.2 dated 2015-11-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gergm.R | 8 ++++++-- man/GERGM.Rd | 7 ++++++- src/Makevars | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.6 dated 2015-11-07 and 1.7 dated 2015-11-17
DESCRIPTION | 9 - MD5 | 34 ++--- NEWS | 22 +++ R/DJL-internal.R | 250 ++++++++++++++++++++--------------------- data/dataset.airplane.2017.rda |binary data/dataset.engine.2015.rda |binary data/dataset.hev.2013.rda |binary man/dataset.airplane.2017.Rd | 4 man/dataset.hev.2013.Rd | 2 man/map.soa.ddf.Rd | 6 man/map.soa.dea.Rd | 6 man/map.soa.sbm.Rd | 6 man/map.soa.sf.Rd | 20 +-- man/roc.dea.Rd | 12 - man/roc.sf.Rd | 18 +- man/target.arrival.dea.Rd | 4 man/target.arrival.sf.Rd | 6 man/target.spec.dea.Rd | 10 - 18 files changed, 209 insertions(+), 200 deletions(-)
Title: Grammatical Evolution for R
Description: A native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian <farzad.noorian@gmail.com>
Diff between gramEvol versions 2.0-2 dated 2015-02-11 and 2.1-2 dated 2015-11-16
gramEvol-2.0-2/gramEvol/ChangeLog |only gramEvol-2.1-2/gramEvol/DESCRIPTION | 14 ++-- gramEvol-2.1-2/gramEvol/MD5 | 34 +++++---- gramEvol-2.1-2/gramEvol/NAMESPACE | 3 gramEvol-2.1-2/gramEvol/NEWS |only gramEvol-2.1-2/gramEvol/R/GERule.R | 5 + gramEvol-2.1-2/gramEvol/R/GERule_Concat.R | 6 + gramEvol-2.1-2/gramEvol/R/SymbolicRuleToListRule.R | 21 +++++- gramEvol-2.1-2/gramEvol/README.md | 37 ++++------ gramEvol-2.1-2/gramEvol/build/vignette.rds |binary gramEvol-2.1-2/gramEvol/inst/CITATION |only gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.R | 72 ++++++++++----------- gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.Rnw | 10 -- gramEvol-2.1-2/gramEvol/inst/doc/ge-intro.pdf |binary gramEvol-2.1-2/gramEvol/man/CreateGrammar.Rd | 16 ++++ gramEvol-2.1-2/gramEvol/man/GeneticAlg.int.Rd | 4 - gramEvol-2.1-2/gramEvol/man/c.GERule.Rd |only gramEvol-2.1-2/gramEvol/tests/grammar_newstyle.R | 5 + gramEvol-2.1-2/gramEvol/vignettes/ge-intro.Rnw | 10 -- gramEvol-2.1-2/gramEvol/vignettes/vig_refs.bib | 12 --- 20 files changed, 137 insertions(+), 112 deletions(-)
Title: Noncentral Dunnett's Test Distribution
Description: Computes the noncentral Dunnett's test distribution (pdf, cdf and quantile) and generates random numbers.
Author: Siomara Cristina Broch, Daniel Furtado Ferreira
Maintainer: Daniel Furtado Ferreira <danielff@dex.ufla.br>
Diff between nCDunnett versions 1.0.0 dated 2013-02-01 and 1.1.0 dated 2015-11-16
nCDunnett-1.0.0/nCDunnett/Rplots.pdf |only nCDunnett-1.1.0/nCDunnett/DESCRIPTION | 14 +++++----- nCDunnett-1.1.0/nCDunnett/MD5 | 17 +++++------- nCDunnett-1.1.0/nCDunnett/NAMESPACE | 1 nCDunnett-1.1.0/nCDunnett/R/dNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/nonCentralDunnett.R | 33 ++++++++++++++---------- nCDunnett-1.1.0/nCDunnett/R/pNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/qNCDun.R | 2 - nCDunnett-1.1.0/nCDunnett/R/rNCDun.R | 4 +- nCDunnett-1.1.0/nCDunnett/man/nCDunnett.Rd | 26 +++++++++--------- 10 files changed, 54 insertions(+), 47 deletions(-)
Title: Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Description: A method for obtain nonparametric estimates of regression models
with or without factor-by-curve interactions using local polynomial
kernel smoothers. Additionally, a parametric model (allometric model)
can be estimated.
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between npregfast versions 1.0 dated 2015-11-09 and 1.0.1 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS |only R/allotest.R | 13 +++++++++---- R/frfast.R | 8 +++++++- R/globaltest.R | 9 +++++++-- R/localtest.R | 7 ++++++- R/predict.frfast.R | 7 ++++++- man/allotest.Rd | 2 +- src/program2.f90 | 11 ++++++----- 10 files changed, 55 insertions(+), 27 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.3-0 dated 2015-07-02 and 4.3-1 dated 2015-11-16
DESCRIPTION | 8 +- MD5 | 34 ++++----- NEWS | 30 ++++++++ R/chkchar.R | 9 +- R/chkclass.R | 5 - R/chklength.R | 5 - R/chklevel.R | 5 - R/chklogical.R | 5 - R/chkmiss.R | 5 - R/chknull.R | 5 - R/chknumeric.R | 6 + R/forest.meta.R | 66 +++++++++++------ R/format.p.R | 7 + R/format.tau.R | 6 - R/paulemandel.R | 11 +- R/setchar.R | 5 - R/settings.meta.R | 201 +++++++++++++++++++++++++++++++++++++----------------- man/forest.Rd | 45 ++++++++---- 18 files changed, 313 insertions(+), 145 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based
on the Clinical Scenario Evaluation (CSE) approach. The package supports a
broad class of data models (including clinical trials with continuous, binary,
survival-type and count-type endpoints as well as multivariate outcomes that are
based on combinations of different endpoints), analysis strategies and commonly
used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0.1 dated 2015-07-26 and 1.0.2 dated 2015-11-16
Mediana-1.0.1/Mediana/R/Mediana.R |only Mediana-1.0.2/Mediana/DESCRIPTION | 18 + Mediana-1.0.2/Mediana/MD5 | 160 ++++++++++++++- Mediana-1.0.2/Mediana/NAMESPACE | 2 Mediana-1.0.2/Mediana/R/AnalysisModel.Interim.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdj.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.Statistic.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.Test.R |only Mediana-1.0.2/Mediana/R/AnalysisModel.default.R |only Mediana-1.0.2/Mediana/R/BinomDist.R |only Mediana-1.0.2/Mediana/R/BonferroniAdj.R |only Mediana-1.0.2/Mediana/R/BonferroniAdj.global.R |only Mediana-1.0.2/Mediana/R/BroadClaimPower.R |only Mediana-1.0.2/Mediana/R/CSE.R |only Mediana-1.0.2/Mediana/R/CSE.default.R |only Mediana-1.0.2/Mediana/R/ChainAdj.R |only Mediana-1.0.2/Mediana/R/ConjunctivePower.R |only Mediana-1.0.2/Mediana/R/CreateAnalysisStructure.R |only Mediana-1.0.2/Mediana/R/CreateDataScenarioEvent.R |only Mediana-1.0.2/Mediana/R/CreateDataScenarioSampleSize.R |only Mediana-1.0.2/Mediana/R/CreateDataSlice.R |only Mediana-1.0.2/Mediana/R/CreateDataStack.R |only Mediana-1.0.2/Mediana/R/CreateDataStructure.R |only Mediana-1.0.2/Mediana/R/CreateEvaluationStructure.R |only Mediana-1.0.2/Mediana/R/CreateReportStructure.R |only Mediana-1.0.2/Mediana/R/CreateSummaryTable.R |only Mediana-1.0.2/Mediana/R/CreateTableDesign.R |only Mediana-1.0.2/Mediana/R/CreateTableOutcome.R |only Mediana-1.0.2/Mediana/R/CreateTableSampleSize.R |only Mediana-1.0.2/Mediana/R/CreateTableStatistic.R |only Mediana-1.0.2/Mediana/R/CreateTableStructure.R |only Mediana-1.0.2/Mediana/R/CreateTableTest.R |only Mediana-1.0.2/Mediana/R/Criterion.R |only Mediana-1.0.2/Mediana/R/CustomLabel.R |only Mediana-1.0.2/Mediana/R/DataModel.Design.R |only Mediana-1.0.2/Mediana/R/DataModel.Event.R |only Mediana-1.0.2/Mediana/R/DataModel.OutcomeDist.R |only Mediana-1.0.2/Mediana/R/DataModel.R |only Mediana-1.0.2/Mediana/R/DataModel.SampleSize.R |only Mediana-1.0.2/Mediana/R/DataModel.default.R |only Mediana-1.0.2/Mediana/R/Design.R |only Mediana-1.0.2/Mediana/R/DiffMeanStat.R |only Mediana-1.0.2/Mediana/R/DiffPropStat.R |only Mediana-1.0.2/Mediana/R/DisjunctivePower.R |only Mediana-1.0.2/Mediana/R/EffectSizeContStat.R |only Mediana-1.0.2/Mediana/R/EffectSizeEventStat.R |only Mediana-1.0.2/Mediana/R/EffectSizePropStat.R |only Mediana-1.0.2/Mediana/R/EnhancedClaimPower.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.Criterion.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.R |only Mediana-1.0.2/Mediana/R/EvaluationModel.default.R |only Mediana-1.0.2/Mediana/R/Event.R |only Mediana-1.0.2/Mediana/R/EventCountStat.R |only Mediana-1.0.2/Mediana/R/ExpectedRejPower.R |only Mediana-1.0.2/Mediana/R/ExpoDist.R |only Mediana-1.0.2/Mediana/R/FisherTest.R |only Mediana-1.0.2/Mediana/R/GLMNegBinomTest.R |only Mediana-1.0.2/Mediana/R/GLMPoissonTest.R |only Mediana-1.0.2/Mediana/R/GeneratePatients.R |only Mediana-1.0.2/Mediana/R/GenerateReport.R |only Mediana-1.0.2/Mediana/R/GenerateReport.default.R |only Mediana-1.0.2/Mediana/R/HazardRatioStat.R |only Mediana-1.0.2/Mediana/R/HochbergAdj.R |only Mediana-1.0.2/Mediana/R/HochbergAdj.global.R |only Mediana-1.0.2/Mediana/R/HolmAdj.R |only Mediana-1.0.2/Mediana/R/HolmAdj.global.R |only Mediana-1.0.2/Mediana/R/HommelAdj.R |only Mediana-1.0.2/Mediana/R/HommelAdj.global.R |only Mediana-1.0.2/Mediana/R/InfluencePower.R |only Mediana-1.0.2/Mediana/R/InteractionPower.R |only Mediana-1.0.2/Mediana/R/Interim.R |only Mediana-1.0.2/Mediana/R/LogrankTest.R |only Mediana-1.0.2/Mediana/R/MVBinomDist.R |only Mediana-1.0.2/Mediana/R/MVExpoDist.R |only Mediana-1.0.2/Mediana/R/MVExpoPFSOSDist.R |only Mediana-1.0.2/Mediana/R/MVMixedDist.R |only Mediana-1.0.2/Mediana/R/MVNormalDist.R |only Mediana-1.0.2/Mediana/R/MarginalPower.R |only Mediana-1.0.2/Mediana/R/MaxStat.R |only Mediana-1.0.2/Mediana/R/MeanStat.R |only Mediana-1.0.2/Mediana/R/MeanSumm.R |only Mediana-1.0.2/Mediana/R/MedianStat.R |only Mediana-1.0.2/Mediana/R/MedianSumm.R |only Mediana-1.0.2/Mediana/R/MinStat.R |only Mediana-1.0.2/Mediana/R/MultAdj.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdj.MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/MultAdj.R |only Mediana-1.0.2/Mediana/R/MultAdj.default.R |only Mediana-1.0.2/Mediana/R/MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.MultAdjProc.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.R |only Mediana-1.0.2/Mediana/R/MultAdjStrategy.default.R |only Mediana-1.0.2/Mediana/R/MultipleSequenceGatekeepingAdj.R |only Mediana-1.0.2/Mediana/R/NegBinomDist.R |only Mediana-1.0.2/Mediana/R/NormalDist.R |only Mediana-1.0.2/Mediana/R/NormalParamAdj.R |only Mediana-1.0.2/Mediana/R/NormalParamDist.R |only Mediana-1.0.2/Mediana/R/OutcomeDist.R |only Mediana-1.0.2/Mediana/R/ParallelGatekeepingAdj.R |only Mediana-1.0.2/Mediana/R/PatientCountStat.R |only Mediana-1.0.2/Mediana/R/PerformAnalysis.R |only Mediana-1.0.2/Mediana/R/PoissonDist.R |only Mediana-1.0.2/Mediana/R/PresentationModel.CustomLabel.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Project.R |only Mediana-1.0.2/Mediana/R/PresentationModel.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Section.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Subsection.R |only Mediana-1.0.2/Mediana/R/PresentationModel.Table.R |only Mediana-1.0.2/Mediana/R/PresentationModel.default.R |only Mediana-1.0.2/Mediana/R/Project.R |only Mediana-1.0.2/Mediana/R/PropTest.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizeContStat.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizeEventStat.R |only Mediana-1.0.2/Mediana/R/RatioEffectSizePropStat.R |only Mediana-1.0.2/Mediana/R/RestrictedClaimPower.R |only Mediana-1.0.2/Mediana/R/Sample.R |only Mediana-1.0.2/Mediana/R/SampleSize.R |only Mediana-1.0.2/Mediana/R/SdStat.R |only Mediana-1.0.2/Mediana/R/Section.R |only Mediana-1.0.2/Mediana/R/SimParameters.R |only Mediana-1.0.2/Mediana/R/Statistic.R |only Mediana-1.0.2/Mediana/R/Subsection.R |only Mediana-1.0.2/Mediana/R/TTest.R |only Mediana-1.0.2/Mediana/R/TTestNI.R |only Mediana-1.0.2/Mediana/R/Table.R |only Mediana-1.0.2/Mediana/R/Test.R |only Mediana-1.0.2/Mediana/R/UniformDist.R |only Mediana-1.0.2/Mediana/R/WeightedPower.R |only Mediana-1.0.2/Mediana/R/WilcoxTest.R |only Mediana-1.0.2/Mediana/R/appendList.R |only Mediana-1.0.2/Mediana/R/argmin.R |only Mediana-1.0.2/Mediana/R/capwords.R |only Mediana-1.0.2/Mediana/R/errorfrac.R |only Mediana-1.0.2/Mediana/R/families.R |only Mediana-1.0.2/Mediana/R/is.AnalysisModel.R |only Mediana-1.0.2/Mediana/R/is.DataModel.R |only Mediana-1.0.2/Mediana/R/is.EvaluationModel.R |only Mediana-1.0.2/Mediana/R/is.PresentationModel.R |only Mediana-1.0.2/Mediana/R/mergeOutcomeParameter.R |only Mediana-1.0.2/Mediana/R/parameters.R |only Mediana-1.0.2/Mediana/R/samples.R |only Mediana-1.0.2/Mediana/R/seq_vector.R |only Mediana-1.0.2/Mediana/R/statistics.R |only Mediana-1.0.2/Mediana/R/summary.CSE.R |only Mediana-1.0.2/Mediana/R/tests.R |only Mediana-1.0.2/Mediana/R/z+.AnalysisModel.R |only Mediana-1.0.2/Mediana/R/z+.DataModel.R |only Mediana-1.0.2/Mediana/R/z+.EvaluationModel.R |only Mediana-1.0.2/Mediana/R/z+.PresentationModel.R |only Mediana-1.0.2/Mediana/README.md |only Mediana-1.0.2/Mediana/man/DataModel.Rd | 2 Mediana-1.0.2/Mediana/man/Mediana-package.Rd | 8 Mediana-1.0.2/Mediana/man/OutcomeDist.Rd | 14 + 156 files changed, 184 insertions(+), 20 deletions(-)
Title: Determining and Evaluating High-Risk Zones
Description: Functions for determining and evaluating high-risk zones and
simulating and thinning point process data, as described in 'Determining
high risk zones using point process methodology - Realization by building
an R package' (Seibold, 2012) and 'Determining high-risk zones for
unexploded World War II bombs by using point process methodology' (Mahling
et al., 2013).
Author: Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia Mahling
<monia.mahling@stat.uni-muenchen.de>, Sebastian Linne
<Sebastian.Linne@campus.lmu.de>
Maintainer: Heidi Seibold <Heidi.Seibold@uzh.ch>
Diff between highriskzone versions 1.2 dated 2015-07-22 and 1.3 dated 2015-11-16
DESCRIPTION | 16 +++++++--------- MD5 | 10 +++++----- R/detnsintens_restr.R | 4 ++-- R/simulationbase.R | 2 +- data/craterA.RData |binary data/craterB.RData |binary 6 files changed, 15 insertions(+), 17 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.3.2 dated 2015-08-11 and 0.4.1 dated 2015-11-16
GERGM-0.3.2/GERGM/man/GERGM-package.Rd |only GERGM-0.3.2/GERGM/man/gergm.Rd |only GERGM-0.4.1/GERGM/DESCRIPTION | 23 GERGM-0.4.1/GERGM/MD5 | 58 GERGM-0.4.1/GERGM/NAMESPACE | 10 GERGM-0.4.1/GERGM/R/Create_GERGM_Object_From_Formula.R | 18 GERGM-0.4.1/GERGM/R/Estimate_GERGM.R | 48 GERGM-0.4.1/GERGM/R/Estimate_Plot.R | 23 GERGM-0.4.1/GERGM/R/GERGM_Class.R | 9 GERGM-0.4.1/GERGM/R/GOF.R | 36 GERGM-0.4.1/GERGM/R/Helper_Functions.R | 6 GERGM-0.4.1/GERGM/R/Log_Likelihood_and_MPLE_Objective.R | 38 GERGM-0.4.1/GERGM/R/MCMCMLE.R | 81 GERGM-0.4.1/GERGM/R/Network_Statistic_Calculation_Functions.R | 66 GERGM-0.4.1/GERGM/R/Package_Documentation.R | 15 GERGM-0.4.1/GERGM/R/Parse_Formula_Object.R | 6 GERGM-0.4.1/GERGM/R/Prepare_Covariates.R | 107 GERGM-0.4.1/GERGM/R/RcppExports.R | 4 GERGM-0.4.1/GERGM/R/Simulate_GERGM.R | 17 GERGM-0.4.1/GERGM/R/Trace_Plot.R | 3 GERGM-0.4.1/GERGM/R/Transform_Correlations.R |only GERGM-0.4.1/GERGM/R/gergm.R | 289 ++ GERGM-0.4.1/GERGM/R/plot_network.R |only GERGM-0.4.1/GERGM/R/simulate_networks.R |only GERGM-0.4.1/GERGM/README.md | 21 GERGM-0.4.1/GERGM/man/Estimate_Plot.Rd | 5 GERGM-0.4.1/GERGM/man/GERGM.Rd |only GERGM-0.4.1/GERGM/man/GOF.Rd | 5 GERGM-0.4.1/GERGM/man/Trace_Plot.Rd | 5 GERGM-0.4.1/GERGM/man/plot_network.Rd |only GERGM-0.4.1/GERGM/man/simulate_networks.Rd |only GERGM-0.4.1/GERGM/src/Makevars |only GERGM-0.4.1/GERGM/src/Makevars.win |only GERGM-0.4.1/GERGM/src/Metropolis_Hastings_Sampler.cpp | 1076 +++++----- GERGM-0.4.1/GERGM/src/RcppExports.cpp | 8 35 files changed, 1273 insertions(+), 704 deletions(-)
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Description: The gap encodes the distance between clusters and improves
interpretation of cluster heatmaps. The gaps can be of the same
distance based on a height threshold to cut the dendrogram. Another
option is to vary the size of gaps based on the distance between
clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo.sakai@esat.kuleuven.be>
Diff between gapmap versions 0.0.2 dated 2014-09-29 and 0.0.3 dated 2015-11-16
DESCRIPTION | 14 +++++---- MD5 | 62 ++++++++++++++++++++--------------------- NAMESPACE | 24 +++++++++++++-- R/gap_dendrogram.R | 18 +++++------ R/gap_heatmap.R | 8 ++--- R/gap_label.R | 12 +++---- R/gapmap-package.R | 9 +++-- R/gapmap.R | 36 +++++++++++------------ build/vignette.rds |binary man/as.gapdata.Rd | 7 ++-- man/assign_branch_positions.Rd | 3 + man/assign_positions.Rd | 3 + man/calculate_gap.Rd | 5 +-- man/count_gap.Rd | 3 + man/extract_list.Rd | 3 + man/format_number.Rd | 3 + man/gap_data.Rd | 3 + man/gap_dendrogram.Rd | 3 + man/gap_heatmap.Rd | 3 + man/gap_label.Rd | 3 + man/gapmap-package.Rd | 3 + man/gapmap.Rd | 4 +- man/get_most_left_leaf.Rd | 3 + man/get_most_right_leaf.Rd | 3 + man/get_segment_df.Rd | 3 + man/is.gapdata.Rd | 3 + man/map.Rd | 3 + man/map.exp.Rd | 3 + man/sample_tcga.Rd | 7 ++-- man/set_most_right_leaf.Rd | 3 + man/sum_distance.Rd | 5 +-- vignettes/tcga_example.Rmd | 6 +-- 32 files changed, 155 insertions(+), 113 deletions(-)
Title: Dynamic Slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye <yechao1009@gmail.com>
Diff between dslice versions 1.1.4 dated 2014-11-25 and 1.1.5 dated 2015-11-16
DESCRIPTION | 11 +- MD5 | 62 +++++++------- NAMESPACE | 5 - R/RcppExports.R | 39 ++++----- R/ds_gsa.R | 216 +++++++++++++++++++++++++-------------------------- R/ds_test.R | 140 ++++++++++++++++----------------- R/export_res.R | 154 ++++++++++++++++++------------------ R/load_cls.R | 16 +-- R/load_gct.R | 40 ++++----- R/load_gmt.R | 28 +++--- R/rank_by_s2n.R | 26 +++--- R/relabel.R | 48 +++++------ R/slice_show.R | 53 ++++++------ build |only data/gsa_exp.RData |binary data/gsa_label.RData |binary data/gsa_set.RData |binary inst/CITATION |only inst/doc/dslice.Rnw | 4 inst/doc/dslice.pdf |binary man/ds_eqp_k.Rd | 4 man/ds_gsa.Rd | 2 man/ds_k.Rd | 4 man/ds_test.Rd | 4 src/RcppExports.cpp | 175 +++++++++++++++++++++-------------------- src/ds_1.cpp | 2 src/ds_eqp_1.cpp | 6 - src/ds_eqp_k.cpp | 2 src/ds_k.cpp | 2 src/dslice_eqp_k.cpp | 4 src/dslice_k.cpp | 8 - vignettes/dslice.Rnw | 4 vignettes/dslice.bib | 7 - 33 files changed, 538 insertions(+), 528 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-1 dated 2015-10-26 and 1.1-2 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/MonteCarloDistributions.R | 2 +- R/Transformations.R | 7 ++----- R/helpers.R | 5 +++++ inst/NEWS.Rd | 16 ++++++++++++++++ inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary man/MarginalHomogeneityTests.Rd | 3 ++- tests/Examples/coin-Ex.Rout.save | 11 ++++++----- tests/bugfixes.R | 3 +++ tests/bugfixes.Rout.save | 9 +++++++-- 14 files changed, 59 insertions(+), 31 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.97.1 dated 2015-08-05 and 0.98.0 dated 2015-11-16
camtrapR-0.97.1/camtrapR/R/cameraOperation.r |only camtrapR-0.98.0/camtrapR/DESCRIPTION | 47 - camtrapR-0.98.0/camtrapR/MD5 | 100 ++- camtrapR-0.98.0/camtrapR/NAMESPACE | 6 camtrapR-0.98.0/camtrapR/NEWS | 48 + camtrapR-0.98.0/camtrapR/R/appendSpeciesNames.R | 71 +- camtrapR-0.98.0/camtrapR/R/cameraOperation.R |only camtrapR-0.98.0/camtrapR/R/checkSpeciesFolders.R | 123 +++ camtrapR-0.98.0/camtrapR/R/createSpeciesFolders.R | 8 camtrapR-0.98.0/camtrapR/R/createStationFolders.R |only camtrapR-0.98.0/camtrapR/R/detectionHistory.R | 122 ++- camtrapR-0.98.0/camtrapR/R/detectionMaps.R | 38 + camtrapR-0.98.0/camtrapR/R/exifTagNames.R | 8 camtrapR-0.98.0/camtrapR/R/getSpeciesImages.R | 112 ++- camtrapR-0.98.0/camtrapR/R/imageRename.R | 72 +- camtrapR-0.98.0/camtrapR/R/recordDatabase.R | 309 +++++++--- camtrapR-0.98.0/camtrapR/R/recordDatabaseIndividual.R |only camtrapR-0.98.0/camtrapR/R/spatialDetectionHistory.R |only camtrapR-0.98.0/camtrapR/data/recordDatabaseIndividualSample.rda |only camtrapR-0.98.0/camtrapR/inst/pictures/sample_images_tagged |only camtrapR-0.98.0/camtrapR/man/activityDensity.Rd | 10 camtrapR-0.98.0/camtrapR/man/activityHistogram.Rd | 4 camtrapR-0.98.0/camtrapR/man/activityOverlap.Rd | 22 camtrapR-0.98.0/camtrapR/man/activityRadial.Rd | 18 camtrapR-0.98.0/camtrapR/man/appendSpeciesNames.Rd | 26 camtrapR-0.98.0/camtrapR/man/cameraOperation.Rd | 56 - camtrapR-0.98.0/camtrapR/man/camtrapR-package.Rd | 70 +- camtrapR-0.98.0/camtrapR/man/camtraps.Rd | 6 camtrapR-0.98.0/camtrapR/man/checkSpeciesFolders.Rd | 53 + camtrapR-0.98.0/camtrapR/man/createSpeciesFolders.Rd | 22 camtrapR-0.98.0/camtrapR/man/createStationFolders.Rd |only camtrapR-0.98.0/camtrapR/man/detectionHistory.Rd | 107 +-- camtrapR-0.98.0/camtrapR/man/detectionMaps.Rd | 57 + camtrapR-0.98.0/camtrapR/man/exifTagNames.Rd | 6 camtrapR-0.98.0/camtrapR/man/exiftoolPath.Rd | 6 camtrapR-0.98.0/camtrapR/man/getSpeciesImages.Rd | 18 camtrapR-0.98.0/camtrapR/man/imageRename.Rd | 42 - camtrapR-0.98.0/camtrapR/man/recordDatabase.Rd | 92 +- camtrapR-0.98.0/camtrapR/man/recordDatabaseIndividual.Rd |only camtrapR-0.98.0/camtrapR/man/recordDatabaseIndividualsSample.Rd |only camtrapR-0.98.0/camtrapR/man/spatialDetectionHistory.Rd |only camtrapR-0.98.0/camtrapR/man/surveyReport.Rd | 64 +- camtrapR-0.98.0/camtrapR/man/timeShiftImages.Rd | 34 - camtrapR-0.98.0/camtrapR/man/timeShiftTable.Rd | 2 44 files changed, 1165 insertions(+), 614 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-31 1.4.5
2014-02-01 1.4.3
2013-12-31 1.4.2
2013-10-20 1.4.0
2013-08-04 1.3.0
2013-07-23 1.2.2
Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example datasets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>
Diff between PracTools versions 0.2 dated 2015-05-31 and 0.3 dated 2015-11-16
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 4 ++++ R/NRFUopt.R | 8 ++++---- data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/hospital.RData |binary data/labor.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary man/BW2stagePPS.Rd | 4 ++-- man/BW3stagePPS.Rd | 2 +- man/NRFUopt.Rd | 4 ++-- 16 files changed, 33 insertions(+), 29 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.
2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.7.1 dated 2015-09-09 and 0.7.5 dated 2015-11-16
DESCRIPTION | 17 MD5 | 64 +- NAMESPACE | 32 - NEWS | 163 +++--- R/Qm.R | 34 - R/af.R | 978 ++++++++++++++++++++-------------------- R/bglmnet.R | 616 ++++++++++++------------- R/glmfence.R | 252 +++++----- R/lmfence.R | 300 ++++++------ R/mplot-package.R | 695 ++++++++++++++++------------ R/mplot.R | 556 +++++++++++----------- R/qrange.R | 118 ++-- R/sigMM.R | 50 +- R/vis.R | 1236 +++++++++++++++++++++++++-------------------------- README.md | 140 +++-- data/fev.rda |only data/wallabies.rda |only inst/CITATION | 42 - man/af.Rd | 244 +++++----- man/artificialeg.Rd | 84 +-- man/bglmnet.Rd | 102 ++-- man/bodyfat.Rd | 102 ++-- man/diabetes.Rd | 85 +-- man/fev.Rd |only man/mplot-package.Rd | 22 man/mplot.Rd | 72 +- man/plot.af.Rd | 143 +++-- man/plot.bglmnet.Rd | 171 +++---- man/plot.vis.Rd | 261 +++++----- man/print.af.Rd | 48 - man/print.vis.Rd | 48 - man/summary.af.Rd | 48 - man/txt.fn.Rd | 42 - man/vis.Rd | 160 +++--- man/wallabies.Rd |only 35 files changed, 3532 insertions(+), 3393 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-0 dated 2015-09-15 and 1.1-1 dated 2015-11-16
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/gen.R | 17 ++++++++++++----- man/rmix.Rd | 3 ++- man/rmmix.Rd | 3 ++- 6 files changed, 28 insertions(+), 15 deletions(-)
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.4-3 dated 2015-01-27 and 1.5-0 dated 2015-11-16
DESCRIPTION | 10 MD5 | 39 +-- NAMESPACE | 8 R/attrib.R | 1 R/devsvg.R | 5 R/filters.R | 7 R/griddev.R | 4 R/gridsvg.R | 7 R/svg.R | 541 ++++++++++++++++++++++++++------------------- R/zzz.R |only build/vignette.rds |binary inst/NEWS.Rd | 27 ++ inst/doc/animation.R | 4 inst/doc/animation.Rnw | 4 inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary inst/svg |only man/grid.export.Rd | 12 man/gridsvg.Rd | 4 vignettes/animation.Rnw | 4 21 files changed, 421 insertions(+), 256 deletions(-)
Title: Debugging 'grid' Graphics
Description: Functions for drawing scene trees representing
scenes that have been drawn using grid graphics.
Author: Paul Murrell and Velvet Ly.
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between gridDebug versions 0.4-0 dated 2012-03-31 and 0.5-0 dated 2015-11-16
DESCRIPTION | 16 +++++----- MD5 | 14 ++++----- NAMESPACE | 6 +-- R/svg.R | 32 --------------------- R/tree.R | 77 ++++++++++++++++++++++++++++----------------------- inst/doc/changes.txt | 25 ++++++++++++++++ man/gridTree.Rd | 18 +++++++++++ tests/test.R | 1 8 files changed, 104 insertions(+), 85 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.2 dated 2015-11-13 and 0.3.3 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ src/betaprior.f90 | 5 +---- src/mcsp2.f90 | 12 +++++++++--- 5 files changed, 21 insertions(+), 15 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 1.1 dated 2015-03-10 and 1.3 dated 2015-11-16
forestplot-1.1/forestplot/vignettes/forestplot_files |only forestplot-1.3/forestplot/DESCRIPTION | 24 forestplot-1.3/forestplot/MD5 | 100 +-- forestplot-1.3/forestplot/NAMESPACE | 4 forestplot-1.3/forestplot/NEWS | 14 forestplot-1.3/forestplot/R/forestplot.R | 94 ++- forestplot-1.3/forestplot/R/forestplot_helpers.R | 146 ++++- forestplot-1.3/forestplot/R/private.R | 185 +++++- forestplot-1.3/forestplot/build/vignette.rds |binary forestplot-1.3/forestplot/inst/doc/forestplot.R | 108 +++ forestplot-1.3/forestplot/inst/doc/forestplot.Rmd | 144 ++++ forestplot-1.3/forestplot/inst/doc/forestplot.html | 250 ++++++-- forestplot-1.3/forestplot/man/HRQoL.Rd | 10 forestplot-1.3/forestplot/man/forestplot-package.Rd | 40 - forestplot-1.3/forestplot/man/forestplot.Rd | 378 ++++++------- forestplot-1.3/forestplot/man/fpColors.Rd | 62 -- forestplot-1.3/forestplot/man/fpDrawCI.Rd | 110 ++- forestplot-1.3/forestplot/man/fpLegend.Rd | 71 -- forestplot-1.3/forestplot/man/fpTxtGp.Rd | 42 - forestplot-1.3/forestplot/man/getTicks.Rd | 27 forestplot-1.3/forestplot/man/heightDetails.xaxis.Rd | 9 forestplot-1.3/forestplot/man/prFpConvertMultidimArray.Rd | 4 forestplot-1.3/forestplot/man/prFpDrawLegend.Rd | 76 +- forestplot-1.3/forestplot/man/prFpDrawLine.Rd | 58 + forestplot-1.3/forestplot/man/prFpDrawLines.Rd | 19 forestplot-1.3/forestplot/man/prFpFetchRowLabel.Rd | 36 - forestplot-1.3/forestplot/man/prFpFindWidestGrob.Rd | 11 forestplot-1.3/forestplot/man/prFpGetConfintFnList.Rd | 32 - forestplot-1.3/forestplot/man/prFpGetGraphTicksAndClips.Rd | 76 +- forestplot-1.3/forestplot/man/prFpGetLabels.Rd | 64 -- forestplot-1.3/forestplot/man/prFpGetLayoutVP.Rd | 30 - forestplot-1.3/forestplot/man/prFpGetLegendBoxPosition.Rd | 32 - forestplot-1.3/forestplot/man/prFpGetLegendGrobs.Rd | 20 forestplot-1.3/forestplot/man/prFpGetLines.Rd | 20 forestplot-1.3/forestplot/man/prFpPrepareLegendMarker.Rd | 8 forestplot-1.3/forestplot/man/prFpPrintLabels.Rd | 15 forestplot-1.3/forestplot/man/prFpPrintXaxis.Rd | 15 forestplot-1.3/forestplot/man/prFpValidateLabelList.Rd | 8 forestplot-1.3/forestplot/man/prFpXrange.Rd | 61 -- forestplot-1.3/forestplot/man/prGetTextGrobCex.Rd | 4 forestplot-1.3/forestplot/man/prGparMerge.Rd | 9 forestplot-1.3/forestplot/man/prGridPlotTitle.Rd | 12 forestplot-1.3/forestplot/man/prListRep.Rd | 11 forestplot-1.3/forestplot/man/prPopulateList.Rd |only forestplot-1.3/forestplot/man/prPushMarginViewport.Rd | 16 forestplot-1.3/forestplot/vignettes/forestplot.Rmd | 144 ++++ 46 files changed, 1647 insertions(+), 952 deletions(-)
Title: Elastic Functional Data Analysis
Description: Functions to support functional data analysis using the square root velocity framework.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.4.2 dated 2014-01-29 and 1.5.1 dated 2015-11-16
fdasrvf-1.4.2/fdasrvf/src/DynamicProgrammingQ2.c |only fdasrvf-1.4.2/fdasrvf/src/dp_grid.c |only fdasrvf-1.4.2/fdasrvf/src/dp_grid.h |only fdasrvf-1.4.2/fdasrvf/src/dp_nbhd.h |only fdasrvf-1.5.1/fdasrvf/DESCRIPTION | 26 fdasrvf-1.5.1/fdasrvf/MD5 | 233 ++++- fdasrvf-1.5.1/fdasrvf/NAMESPACE | 24 fdasrvf-1.5.1/fdasrvf/NEWS | 13 fdasrvf-1.5.1/fdasrvf/R/SqrtMean.R | 110 +- fdasrvf-1.5.1/fdasrvf/R/align_fPCA.R | 513 ++++++------ fdasrvf-1.5.1/fdasrvf/R/elastic.distance.R | 36 fdasrvf-1.5.1/fdasrvf/R/elastic_logistic.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_mlogistic.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_prediction.R |only fdasrvf-1.5.1/fdasrvf/R/elastic_regression.R |only fdasrvf-1.5.1/fdasrvf/R/f_to_srvf.R | 20 fdasrvf-1.5.1/fdasrvf/R/fdasrvf-package.r | 75 - fdasrvf-1.5.1/fdasrvf/R/gauss_model.R | 162 +-- fdasrvf-1.5.1/fdasrvf/R/gradient.R | 58 - fdasrvf-1.5.1/fdasrvf/R/horizFPCA.R | 118 +- fdasrvf-1.5.1/fdasrvf/R/optimum.reparam.R | 95 +- fdasrvf-1.5.1/fdasrvf/R/outlier.detection.R | 42 fdasrvf-1.5.1/fdasrvf/R/regression_functions.R |only fdasrvf-1.5.1/fdasrvf/R/rgam.R | 68 - fdasrvf-1.5.1/fdasrvf/R/smooth.data.R | 30 fdasrvf-1.5.1/fdasrvf/R/srsf_to_f.R |only fdasrvf-1.5.1/fdasrvf/R/time_warping.R | 462 +++++----- fdasrvf-1.5.1/fdasrvf/R/utility_functions.R | 971 +++++++++++++++-------- fdasrvf-1.5.1/fdasrvf/R/vertFPCA.R | 146 +-- fdasrvf-1.5.1/fdasrvf/R/warp_f_gamma.R |only fdasrvf-1.5.1/fdasrvf/R/warp_q_gamma.R |only fdasrvf-1.5.1/fdasrvf/README.md | 51 - fdasrvf-1.5.1/fdasrvf/man/SqrtMean.Rd | 30 fdasrvf-1.5.1/fdasrvf/man/align_fPCA.Rd | 58 - fdasrvf-1.5.1/fdasrvf/man/elastic.distance.Rd | 26 fdasrvf-1.5.1/fdasrvf/man/elastic.logistic.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.mlogistic.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.prediction.Rd |only fdasrvf-1.5.1/fdasrvf/man/elastic.regression.Rd |only fdasrvf-1.5.1/fdasrvf/man/f_to_srvf.Rd | 19 fdasrvf-1.5.1/fdasrvf/man/fdasrvf.Rd | 35 fdasrvf-1.5.1/fdasrvf/man/gauss_model.Rd | 28 fdasrvf-1.5.1/fdasrvf/man/gradient.Rd | 9 fdasrvf-1.5.1/fdasrvf/man/horizFPCA.Rd | 30 fdasrvf-1.5.1/fdasrvf/man/optimum.reparam.Rd | 43 - fdasrvf-1.5.1/fdasrvf/man/outlier.detection.Rd | 31 fdasrvf-1.5.1/fdasrvf/man/rgam.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/simu_data.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/simu_warp.Rd | 21 fdasrvf-1.5.1/fdasrvf/man/smooth.data.Rd | 23 fdasrvf-1.5.1/fdasrvf/man/srsf_to_f.Rd |only fdasrvf-1.5.1/fdasrvf/man/time_warping.Rd | 71 - fdasrvf-1.5.1/fdasrvf/man/toy_data.Rd | 13 fdasrvf-1.5.1/fdasrvf/man/toy_warp.Rd | 13 fdasrvf-1.5.1/fdasrvf/man/vertFPCA.Rd | 41 fdasrvf-1.5.1/fdasrvf/man/warp_f_gamma.Rd |only fdasrvf-1.5.1/fdasrvf/man/warp_q_gamma.Rd |only fdasrvf-1.5.1/fdasrvf/src/Makevars |only fdasrvf-1.5.1/fdasrvf/src/Makevars.win |only fdasrvf-1.5.1/fdasrvf/src/fdasrsf |only fdasrvf-1.5.1/fdasrvf/src/gropt |only fdasrvf-1.5.1/fdasrvf/src/wrapper.cpp |only 62 files changed, 2227 insertions(+), 1559 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.0 dated 2015-11-06 and 0.1.1 dated 2015-11-16
DESCRIPTION | 20 - MD5 | 129 ++++---- NAMESPACE | 13 R/data_prep.R | 56 ++- R/eyetrackingR.R | 22 + R/helpers.R | 220 ++++++++++---- R/time_cluster_data.R | 355 +++++++++++------------ R/time_sequence_data.R | 84 +++-- R/time_spline_data.R | 28 - R/time_window_data.R | 26 + README.md | 16 - data/word_recognition.rda |binary inst/doc/divergence_vignette.R | 26 + inst/doc/divergence_vignette.Rmd | 60 +++ inst/doc/divergence_vignette.html | 96 +++--- inst/doc/growth_curve_analysis_vignette.html | 4 inst/doc/onset_contingent_analysis_vignette.html | 4 inst/doc/preparing_your_data_vignette.R | 2 inst/doc/preparing_your_data_vignette.Rmd | 2 inst/doc/preparing_your_data_vignette.html | 35 +- inst/doc/window_analysis_vignette.Rmd | 2 inst/doc/window_analysis_vignette.html | 19 - man/add_aoi.Rd | 10 man/analyze_boot_splines.Rd | 15 man/analyze_time_bins.Rd | 20 - man/analyze_time_clusters.Rd | 29 + man/clean_by_trackloss.Rd | 17 - man/describe_data.Rd | 7 man/eyetrackingR.Rd | 2 man/filter_.Rd | 18 - man/get_time_clusters.Rd |only man/group_by_.Rd | 18 - man/left_join.Rd | 18 - man/make_boot_splines_data.Rd | 32 +- man/make_eyetrackingr_data.Rd | 27 - man/make_onset_data.Rd | 9 man/make_switch_data.Rd | 19 - man/make_time_cluster_data.Rd | 30 + man/make_time_sequence_data.Rd | 32 +- man/make_time_window_data.Rd | 21 - man/mutate_.Rd | 18 - man/plot.bin_analysis.Rd | 2 man/plot.boot_splines_analysis.Rd | 2 man/plot.boot_splines_data.Rd | 2 man/plot.cluster_analysis.Rd | 2 man/plot.eyetrackingR_data_summary.Rd | 4 man/plot.onset_data.Rd | 2 man/plot.switch_data.Rd | 2 man/plot.time_cluster_data.Rd | 2 man/plot.time_sequence_data.Rd | 12 man/plot.time_window_data.Rd | 9 man/print.cluster_analysis.Rd | 2 man/simulate_eyetrackingr_data.Rd |only man/subset.Rd | 18 - man/subset_by_window.Rd | 35 +- man/summary.bin_analysis.Rd | 2 man/summary.boot_splines_analysis.Rd | 2 man/summary.cluster_analysis.Rd | 2 man/summary.time_cluster_data.Rd | 2 man/trackloss_analysis.Rd | 5 man/ungroup.Rd | 18 - man/word_recognition.Rd | 24 - tests/testthat/test_arbitrary_dv.R |only tests/testthat/test_cluster_analysis.R | 71 +--- vignettes/divergence_vignette.Rmd | 60 +++ vignettes/preparing_your_data_vignette.Rmd | 2 vignettes/window_analysis_vignette.Rmd | 2 67 files changed, 1082 insertions(+), 763 deletions(-)
Title: Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre],
David Welch [aut],
David Hunter [ctb]
Maintainer: Chris Groendyke <cgroendyke@gmail.com>
Diff between epinet versions 2.1.5 dated 2015-11-13 and 2.1.6 dated 2015-11-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/epi2newick.Rd | 2 +- man/write.epinet.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-51 dated 2015-10-17 and 0.9-52 dated 2015-11-15
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 +++---
MD5 | 14 +++++------
NEWS | 5 +++-
R/MVA.biplot.R | 34 ++++++++++++---------------
R/MVA.cor.R | 53 ++++++++++++++++++++++++-------------------
R/zzz.R | 2 -
man/MVA.biplot.Rd | 4 +--
man/RVAideMemoire-package.Rd | 4 +--
8 files changed, 66 insertions(+), 58 deletions(-)
Title: Package Allowing R to Call Python
Description: Run Python code, make function calls, assign and retrieve variables, etc. from R.
Author: Carlos J. Gil Bellosta
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between rPython versions 0.0-5 dated 2014-08-03 and 0.0-6 dated 2015-11-15
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/python.assign.R | 47 +++++++++++++++++++++++------------------------ R/python.method.call.R | 2 +- man/python.assign.Rd | 5 +++-- 5 files changed, 37 insertions(+), 37 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.6 dated 2015-05-03 and 0.0.7 dated 2015-11-15
ChangeLog | 18 ++ DESCRIPTION | 8 - MD5 | 11 - README.md | 2 inst/include/annoylib.h | 347 +++++++++++++++++++++------------------------- inst/include/kissrandom.h |only src/annoy.cpp | 135 ++++++++++++----- 7 files changed, 281 insertions(+), 240 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.1 dated 2015-09-10 and 0.12.2 dated 2015-11-15
ChangeLog | 95 ++++ DESCRIPTION | 8 MD5 | 73 +-- build/Rcpp.pdf |binary inst/NEWS.Rd | 119 +++-- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 22 - inst/include/Rcpp/Dimension.h | 2 inst/include/Rcpp/Nullable.h | 9 inst/include/Rcpp/String.h | 566 +++++++++++++------------- inst/include/Rcpp/api/meat/is.h | 5 inst/include/Rcpp/complex.h | 25 - inst/include/Rcpp/config.h | 4 inst/include/Rcpp/sugar/functions/cummax.h |only inst/include/Rcpp/sugar/functions/cummin.h |only inst/include/Rcpp/sugar/functions/cumprod.h |only inst/include/Rcpp/sugar/functions/functions.h | 5 inst/include/Rcpp/vector/Matrix.h | 51 ++ inst/include/Rcpp/vector/MatrixColumn.h | 8 inst/include/Rcpp/vector/Subsetter.h | 28 + inst/unitTests/cpp/Matrix.cpp | 16 inst/unitTests/cpp/Subset.cpp | 7 inst/unitTests/cpp/misc.cpp | 22 + inst/unitTests/cpp/sugar.cpp | 46 ++ inst/unitTests/runit.Matrix.R | 27 + inst/unitTests/runit.misc.R | 17 inst/unitTests/runit.subset.R | 4 inst/unitTests/runit.sugar.R | 62 ++ src/attributes.cpp | 8 src/barrier.cpp | 4 vignettes/Rcpp.bib | 22 - 39 files changed, 844 insertions(+), 411 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.2 dated 2015-11-04 and 0.4.3 dated 2015-11-15
DESCRIPTION | 10 +++-- MD5 | 14 ++++---- R/MIIVsem-data.R | 2 - R/miivs.R | 44 ++++++++++++++++++++------ man/MIIVsem.Rd | 6 +-- man/bollen1989a.Rd | 10 ++--- man/miive.Rd | 89 +++++++++++++++++++++++++++-------------------------- man/miivs.Rd | 31 +++++++++--------- 8 files changed, 118 insertions(+), 88 deletions(-)
Title: Hierarchical Latent Space Network Model (HLSM)
Description: Hierarchical latent space network model for fitting ensemble of networks.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari <asam.cmu@gmail.com>
Diff between HLSM versions 0.4 dated 2014-08-23 and 0.5 dated 2015-11-15
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 8 ++++++++ R/HLSM_run.R | 16 +++++++++++----- R/HLSM_run_fixedEF.R | 19 ++++++++++++------- R/covFunction.R | 7 +++++-- demo/HLSM.school.advice.R | 4 ++++ man/plots.Rd | 23 +++++++++++++++++++++++ src/HLSM.cpp | 14 ++++++-------- 9 files changed, 84 insertions(+), 37 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES block
cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key)
encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary
sized data. Other utilities include key generators, hash functions (md5, sha1, sha256,
etc), base64 encoder, a secure random number generator, and 'bignum' math methods for
manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.4 dated 2015-05-11 and 0.5 dated 2015-11-15
openssl-0.4/openssl/R/onload.R |only openssl-0.4/openssl/R/rand_bytes.R |only openssl-0.4/openssl/src/Makevars |only openssl-0.4/openssl/src/digest.c |only openssl-0.4/openssl/src/rand_bytes.c |only openssl-0.5/openssl/DESCRIPTION | 31 - openssl-0.5/openssl/MD5 | 141 ++++- openssl-0.5/openssl/NAMESPACE | 94 +++ openssl-0.5/openssl/NEWS | 4 openssl-0.5/openssl/R/aes.R |only openssl-0.5/openssl/R/base64.R | 8 openssl-0.5/openssl/R/bignum.R |only openssl-0.5/openssl/R/cert.R |only openssl-0.5/openssl/R/encrypt.R |only openssl-0.5/openssl/R/envelope.R |only openssl-0.5/openssl/R/hash.R | 86 ++- openssl-0.5/openssl/R/keygen.R |only openssl-0.5/openssl/R/list.R |only openssl-0.5/openssl/R/mykey.R |only openssl-0.5/openssl/R/openssh.R |only openssl-0.5/openssl/R/openssl.R | 20 openssl-0.5/openssl/R/rand.R |only openssl-0.5/openssl/R/read.R |only openssl-0.5/openssl/R/signing.R |only openssl-0.5/openssl/R/ssh2.R |only openssl-0.5/openssl/R/stream.R | 4 openssl-0.5/openssl/R/write.R |only openssl-0.5/openssl/build/vignette.rds |binary openssl-0.5/openssl/configure | 94 +++ openssl-0.5/openssl/inst/cacert.pem |only openssl-0.5/openssl/inst/doc/crypto_hashing.html | 326 ++++++++---- openssl-0.5/openssl/inst/doc/secure_rng.html | 308 ++++++++--- openssl-0.5/openssl/man/aes_cbc.Rd |only openssl-0.5/openssl/man/base64.Rd | 8 openssl-0.5/openssl/man/bignum.Rd |only openssl-0.5/openssl/man/certs.Rd |only openssl-0.5/openssl/man/encrypt.Rd |only openssl-0.5/openssl/man/encrypt_envelope.Rd |only openssl-0.5/openssl/man/hash.Rd | 26 openssl-0.5/openssl/man/keygen.Rd |only openssl-0.5/openssl/man/my_key.Rd |only openssl-0.5/openssl/man/openssl.Rd | 18 openssl-0.5/openssl/man/rand_bytes.Rd | 2 openssl-0.5/openssl/man/read_key.Rd |only openssl-0.5/openssl/man/signatures.Rd |only openssl-0.5/openssl/man/write_pem.Rd |only openssl-0.5/openssl/src/Makevars.in |only openssl-0.5/openssl/src/Makevars.win | 4 openssl-0.5/openssl/src/aes.c |only openssl-0.5/openssl/src/base64.c | 11 openssl-0.5/openssl/src/bignum.c |only openssl-0.5/openssl/src/cert.c |only openssl-0.5/openssl/src/encrypt.c |only openssl-0.5/openssl/src/envelope.c |only openssl-0.5/openssl/src/error.c |only openssl-0.5/openssl/src/hash.c |only openssl-0.5/openssl/src/keygen.c |only openssl-0.5/openssl/src/onload.c | 21 openssl-0.5/openssl/src/openssh.c |only openssl-0.5/openssl/src/rand.c |only openssl-0.5/openssl/src/read.c |only openssl-0.5/openssl/src/signing.c |only openssl-0.5/openssl/src/ssl.c |only openssl-0.5/openssl/src/stream.c | 1 openssl-0.5/openssl/src/utils.h |only openssl-0.5/openssl/src/write.c |only openssl-0.5/openssl/tests/keys |only openssl-0.5/openssl/tests/testthat/test_bignum.R |only openssl-0.5/openssl/tests/testthat/test_encrypt.R |only openssl-0.5/openssl/tests/testthat/test_hash.R |only openssl-0.5/openssl/tests/testthat/test_hash_output_value.R | 12 openssl-0.5/openssl/tests/testthat/test_keys_dsa.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa384.R |only openssl-0.5/openssl/tests/testthat/test_keys_ecdsa521.R |only openssl-0.5/openssl/tests/testthat/test_keys_rsa.R |only openssl-0.5/openssl/tools/winlibs.R | 6 77 files changed, 920 insertions(+), 305 deletions(-)
Title: Non-Parametric Survival Analysis
Description: Contains functions for non-parametric survival analysis of
exact and interval-censored observations.
Author: Yong Wang
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Diff between npsurv versions 0.3-3 dated 2015-11-12 and 0.3-4 dated 2015-11-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Uhaz.R | 34 +++++++++++++++++++++++++--------- man/gastric.Rd | 19 ++++++++++++++----- 4 files changed, 46 insertions(+), 21 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Spatial Microsimulation
Description: Produce small area population estimates by fitting census data to
survey data.
Author: Dimitris Kavroudakis <dimitris123@gmail.com>
Maintainer: Dimitris Kavroudakis <dimitris123@gmail.com>
Diff between sms versions 2.3 dated 2014-07-08 and 2.3.1 dated 2015-11-15
sms-2.3.1/sms/DESCRIPTION | 11 +-- sms-2.3.1/sms/MD5 | 56 +++++++-------- sms-2.3.1/sms/NAMESPACE | 12 ++- sms-2.3.1/sms/NEWS | 4 + sms-2.3.1/sms/R/sms.R | 72 +++++++++++++++----- sms-2.3.1/sms/inst/CITATION |only sms-2.3.1/sms/man/addDataAssociation.Rd | 7 + sms-2.3.1/sms/man/calculate_error.Rd | 9 +- sms-2.3.1/sms/man/census.Rd | 9 +- sms-2.3.1/sms/man/checkIfNamesInDataColumns.Rd | 7 + sms-2.3.1/sms/man/check_lexicon.Rd | 7 + sms-2.3.1/sms/man/createLexicon.Rd | 3 sms-2.3.1/sms/man/find_best_selection.Rd | 9 +- sms-2.3.1/sms/man/find_best_selection_SA.Rd | 11 +-- sms-2.3.1/sms/man/getInfo-microsimulation-method.Rd | 3 sms-2.3.1/sms/man/getInfo.Rd | 3 sms-2.3.1/sms/man/getTAEs-microsimulation-method.Rd | 5 - sms-2.3.1/sms/man/getTAEs.Rd | 3 sms-2.3.1/sms/man/microsimulation-class.Rd | 9 +- sms-2.3.1/sms/man/mysetSeed.Rd |only sms-2.3.1/sms/man/plotTries.Rd | 5 - sms-2.3.1/sms/man/random_panel_selection.Rd | 5 - sms-2.3.1/sms/man/run_parallel_HC.Rd | 12 ++- sms-2.3.1/sms/man/run_parallel_SA.Rd | 11 +-- sms-2.3.1/sms/man/run_serial.Rd | 5 - sms-2.3.1/sms/man/selection_for_area.Rd | 9 +- sms-2.3.1/sms/man/sms-package.Rd | 14 ++- sms-2.3.1/sms/man/survey.Rd | 13 +-- sms-2.3/sms/inst/doc |only 29 files changed, 196 insertions(+), 118 deletions(-)
Title: Change-Point Estimation using Shape-Restricted Splines
Description: In a scatterplot where the response variable is Gaussian, Poisson or binomial, we consider the case in which the mean function is smooth with a change-point, which is a mode, an inflection point or a jump point. The main routine estimates the mean curve and the change-point as well using shape-restricted B-splines. An optional subroutine delivering a bootstrapping confidence interval for the change-point is incorporated in the main routine.
Author: Xiyue Liao and Mary C Meyer
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeChange versions 1.0 dated 2015-10-07 and 1.1 dated 2015-11-15
DESCRIPTION | 8 MD5 | 14 R/ShapeChange.R | 1481 ++++++++++++++++++++++++++------------------- man/ShapeChange-package.Rd | 4 man/changept.Rd | 65 + man/ip.Rd | 3 man/jp.Rd | 18 man/tp.Rd | 7 8 files changed, 931 insertions(+), 669 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.2.0 dated 2015-07-02 and 0.2.1 dated 2015-11-15
rnrfa-0.2.0/rnrfa/R/NRFA_TS.R |only rnrfa-0.2.0/rnrfa/man/NRFA_TS.Rd |only rnrfa-0.2.1/rnrfa/DESCRIPTION | 7 ++- rnrfa-0.2.1/rnrfa/MD5 | 34 +++++++++--------- rnrfa-0.2.1/rnrfa/NAMESPACE | 3 + rnrfa-0.2.1/rnrfa/R/FindTS.R | 31 ++++++++++------- rnrfa-0.2.1/rnrfa/R/NRFA_Catalogue.R | 18 +++++---- rnrfa-0.2.1/rnrfa/R/NRFA_TSdata.R |only rnrfa-0.2.1/rnrfa/R/NRFA_TSmetadata.R |only rnrfa-0.2.1/rnrfa/R/OSG2LatLon.R | 48 ++++++++++++-------------- rnrfa-0.2.1/rnrfa/R/OSGParse.R | 56 ++++++++++++++----------------- rnrfa-0.2.1/rnrfa/R/ToJSONarray.R | 22 +++++------- rnrfa-0.2.1/rnrfa/R/zzz.R | 4 +- rnrfa-0.2.1/rnrfa/man/FindInfo.Rd | 2 - rnrfa-0.2.1/rnrfa/man/FindTS.Rd | 2 - rnrfa-0.2.1/rnrfa/man/NRFA_Catalogue.Rd | 7 ++- rnrfa-0.2.1/rnrfa/man/NRFA_TSdata.Rd |only rnrfa-0.2.1/rnrfa/man/NRFA_TSmetadata.Rd |only rnrfa-0.2.1/rnrfa/man/OSG2LatLon.Rd | 2 - rnrfa-0.2.1/rnrfa/man/OSGParse.Rd | 3 + rnrfa-0.2.1/rnrfa/man/ToJSONarray.Rd | 3 + 21 files changed, 127 insertions(+), 115 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.3 dated 2015-11-05 and 1.7.4 dated 2015-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/build.dist.struct.R | 13 +++++++------ R/rcbalance.R | 2 +- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Analysis of Large-Scale Pharmacogenomic Data
Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Diff between PharmacoGx versions 1.0.6 dated 2015-07-24 and 1.1.2 dated 2015-11-15
PharmacoGx-1.0.6/PharmacoGx/R/geneIdMap.R |only PharmacoGx-1.0.6/PharmacoGx/R/probeGeneMapping.R |only PharmacoGx-1.0.6/PharmacoGx/R/summarizeGeneExpression.R |only PharmacoGx-1.0.6/PharmacoGx/R/summarizeSensitivityPhenotype.R |only PharmacoGx-1.0.6/PharmacoGx/data/CGPsmall.rda |only PharmacoGx-1.0.6/PharmacoGx/man/CGPsmall.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/cnvInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/dnaInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/downloadSignatures.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/drugPertubrationSig.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/geneNames.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/probeGeneMapping.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/rnaInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/sensitivityData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/sensitivityData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpData-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpData.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpInfo-set.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/snpInfo.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/summarizeGeneExpression.Rd |only PharmacoGx-1.0.6/PharmacoGx/man/summarizeSensitivityPhenotype.Rd |only PharmacoGx-1.1.2/PharmacoGx/DESCRIPTION | 12 PharmacoGx-1.1.2/PharmacoGx/MD5 | 158 -- PharmacoGx-1.1.2/PharmacoGx/NAMESPACE | 54 PharmacoGx-1.1.2/PharmacoGx/R/GWC.R | 49 PharmacoGx-1.1.2/PharmacoGx/R/LogLogisticRegression.R | 40 PharmacoGx-1.1.2/PharmacoGx/R/PharmacoSetClass.R | 779 ++++------ PharmacoGx-1.1.2/PharmacoGx/R/callingWaterfall.R | 8 PharmacoGx-1.1.2/PharmacoGx/R/computeAUC.R | 42 PharmacoGx-1.1.2/PharmacoGx/R/computeDrugSensitivity.R | 188 +- PharmacoGx-1.1.2/PharmacoGx/R/computeIC50.R | 28 PharmacoGx-1.1.2/PharmacoGx/R/connectivityScore.R | 11 PharmacoGx-1.1.2/PharmacoGx/R/corWeighted.R | 20 PharmacoGx-1.1.2/PharmacoGx/R/datasets.R | 12 PharmacoGx-1.1.2/PharmacoGx/R/distancePointLine.R | 6 PharmacoGx-1.1.2/PharmacoGx/R/distancePointSegment.R | 6 PharmacoGx-1.1.2/PharmacoGx/R/downloadPSet.R | 89 - PharmacoGx-1.1.2/PharmacoGx/R/downloadSignatures.R | 87 - PharmacoGx-1.1.2/PharmacoGx/R/drugDoseResponseCurve.R | 195 +- PharmacoGx-1.1.2/PharmacoGx/R/drugPerturbationSig.R | 107 - PharmacoGx-1.1.2/PharmacoGx/R/drugSensitivitySig.R | 222 +- PharmacoGx-1.1.2/PharmacoGx/R/geneDrugSensitivity.R | 90 - PharmacoGx-1.1.2/PharmacoGx/R/getRawSensitivityMatrix.R |only PharmacoGx-1.1.2/PharmacoGx/R/intersectList.R | 5 PharmacoGx-1.1.2/PharmacoGx/R/intersectPSets.R | 269 +-- PharmacoGx-1.1.2/PharmacoGx/R/rankGeneDrugPerturbation.R | 22 PharmacoGx-1.1.2/PharmacoGx/R/rankGeneDrugSensitivity.R | 22 PharmacoGx-1.1.2/PharmacoGx/R/signatureClass.R | 9 PharmacoGx-1.1.2/PharmacoGx/R/stripWhiteSpace.R | 10 PharmacoGx-1.1.2/PharmacoGx/R/summarizeMolecularProfiles.R |only PharmacoGx-1.1.2/PharmacoGx/R/summarizeSensitivityProfiles.R |only PharmacoGx-1.1.2/PharmacoGx/R/unionList.R | 13 PharmacoGx-1.1.2/PharmacoGx/build/vignette.rds |binary PharmacoGx-1.1.2/PharmacoGx/data/CCLEsmall.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/CMAPsmall.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/GDSCsmall.rda |only PharmacoGx-1.1.2/PharmacoGx/data/HDAC_genes.rda |binary PharmacoGx-1.1.2/PharmacoGx/data/datalist |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.R |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.Rnw |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/CreatingPharmacoSet.pdf |only PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.R | 183 +- PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.Rnw | 241 ++- PharmacoGx-1.1.2/PharmacoGx/inst/doc/PharmacoGx.pdf |binary PharmacoGx-1.1.2/PharmacoGx/man/GDSCsmall.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/LogLogisticRegression.Rd | 8 PharmacoGx-1.1.2/PharmacoGx/man/PharmacoSet-class.Rd | 127 - PharmacoGx-1.1.2/PharmacoGx/man/PharmacoSet.Rd | 22 PharmacoGx-1.1.2/PharmacoGx/man/availablePSets.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/checkPSetStructure.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/computeAUC.Rd | 7 PharmacoGx-1.1.2/PharmacoGx/man/computeIC50.Rd | 11 PharmacoGx-1.1.2/PharmacoGx/man/connectivityScore.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/downloadPSet.Rd | 8 PharmacoGx-1.1.2/PharmacoGx/man/downloadPertSig.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/drugDoseResponseCurve.Rd | 7 PharmacoGx-1.1.2/PharmacoGx/man/drugPerturbationSig.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/drugSensitivitySig.Rd | 59 PharmacoGx-1.1.2/PharmacoGx/man/featureInfo-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/featureInfo.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/featureNames.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/intersectPSet.Rd | 54 PharmacoGx-1.1.2/PharmacoGx/man/molecularProfiles-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/molecularProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/phenoInfo-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/phenoInfo.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/sensitivityInfo-set.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityInfo.Rd | 4 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityMeasures.Rd | 6 PharmacoGx-1.1.2/PharmacoGx/man/sensitivityProfiles-set.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/sensitivityProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/subsetTo.Rd | 13 PharmacoGx-1.1.2/PharmacoGx/man/summarizeMolecularProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/man/summarizeSensitivityProfiles.Rd |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet-concordance.tex |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet.Rnw |only PharmacoGx-1.1.2/PharmacoGx/vignettes/CreatingPharmacoSet.tex |only PharmacoGx-1.1.2/PharmacoGx/vignettes/PharmacoGx.Rnw | 241 ++- PharmacoGx-1.1.2/PharmacoGx/vignettes/pharmacogx.bib |only 110 files changed, 1876 insertions(+), 1676 deletions(-)
Title: Bayesian Semi and Nonparametric Growth Curve Models that
Additionally Include Multiple Membership Random Effects
Description: Employs a non-parametric formulation for by-subject random effect
parameters to borrow strength over a constrained number of repeated
measurement waves in a fashion that permits multiple effects per subject.
One class of models employs a Dirichlet process (DP) prior for the subject
random effects and includes an additional set of random effects that
utilize a different grouping factor and are mapped back to clients through
a multiple membership weight matrix; e.g. treatment(s) exposure or dosage.
A second class of models employs a dependent DP (DDP) prior for the subject
random effects that directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growcurves versions 0.2.3.9 dated 2014-02-23 and 0.2.4.0 dated 2015-11-15
growcurves-0.2.3.9/growcurves/tests/run-all.R |only growcurves-0.2.4.0/growcurves/DESCRIPTION | 26 growcurves-0.2.4.0/growcurves/MD5 | 154 +-- growcurves-0.2.4.0/growcurves/NAMESPACE | 16 growcurves-0.2.4.0/growcurves/NEWS | 12 growcurves-0.2.4.0/growcurves/R/XZcov.R | 8 growcurves-0.2.4.0/growcurves/R/ddpMCMCplots.R | 28 growcurves-0.2.4.0/growcurves/R/ddpeffectsplot.R | 82 +- growcurves-0.2.4.0/growcurves/R/ddpgrow.R | 9 growcurves-0.2.4.0/growcurves/R/dpgrow.R | 197 +++- growcurves-0.2.4.0/growcurves/R/dpgrowmm.R | 9 growcurves-0.2.4.0/growcurves/R/dpgrowmult.R | 9 growcurves-0.2.4.0/growcurves/R/getmf.R | 7 growcurves-0.2.4.0/growcurves/R/growplot.R | 184 ++-- growcurves-0.2.4.0/growcurves/R/growthCurve.R | 8 growcurves-0.2.4.0/growcurves/R/help.R | 7 growcurves-0.2.4.0/growcurves/R/mcmcPlots.R | 2 growcurves-0.2.4.0/growcurves/man/XZcov.Rd | 82 -- growcurves-0.2.4.0/growcurves/man/datbrghtmodterms.Rd | 190 +--- growcurves-0.2.4.0/growcurves/man/datbrghtterms.Rd | 152 +-- growcurves-0.2.4.0/growcurves/man/dateduc.Rd | 65 - growcurves-0.2.4.0/growcurves/man/datsim.Rd | 70 - growcurves-0.2.4.0/growcurves/man/datsimcov.Rd | 81 -- growcurves-0.2.4.0/growcurves/man/datsimmult.Rd | 134 +-- growcurves-0.2.4.0/growcurves/man/ddpEffectsplot.Rd | 142 +-- growcurves-0.2.4.0/growcurves/man/ddpMCMCplots.Rd | 166 +--- growcurves-0.2.4.0/growcurves/man/ddpPost.Rd | 66 - growcurves-0.2.4.0/growcurves/man/ddp_quantiles.Rd | 102 -- growcurves-0.2.4.0/growcurves/man/ddpgrow.Rd | 324 +++----- growcurves-0.2.4.0/growcurves/man/dpPost.Rd | 33 growcurves-0.2.4.0/growcurves/man/dpgrow.Rd | 331 +++----- growcurves-0.2.4.0/growcurves/man/dpgrowmm.Rd | 395 +++------- growcurves-0.2.4.0/growcurves/man/dpgrowmult.Rd | 391 +++------ growcurves-0.2.4.0/growcurves/man/effectsplot.Rd | 120 +-- growcurves-0.2.4.0/growcurves/man/getmf.Rd | 37 growcurves-0.2.4.0/growcurves/man/growcurves-package.Rd | 296 +++---- growcurves-0.2.4.0/growcurves/man/growplot.Rd | 115 +- growcurves-0.2.4.0/growcurves/man/growthCurve.Rd | 172 +--- growcurves-0.2.4.0/growcurves/man/lgmPost.Rd | 25 growcurves-0.2.4.0/growcurves/man/mcmcPlots.Rd | 152 +-- growcurves-0.2.4.0/growcurves/man/mmCmvplusDpPost.Rd | 73 - growcurves-0.2.4.0/growcurves/man/mmCplusDpPost.Rd | 58 - growcurves-0.2.4.0/growcurves/man/mmIgroupDpPost.Rd | 50 - growcurves-0.2.4.0/growcurves/man/mmIplusDpPost.Rd | 44 - growcurves-0.2.4.0/growcurves/man/mmmultPost.Rd | 99 -- growcurves-0.2.4.0/growcurves/man/plot.ddpgrow.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrow.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrowmm.Rd | 32 growcurves-0.2.4.0/growcurves/man/plot.dpgrowmult.Rd | 32 growcurves-0.2.4.0/growcurves/man/relabel.Rd | 23 growcurves-0.2.4.0/growcurves/man/samples.Rd | 13 growcurves-0.2.4.0/growcurves/man/samples.ddpgrow.Rd | 10 growcurves-0.2.4.0/growcurves/man/samples.dpgrow.Rd | 10 growcurves-0.2.4.0/growcurves/man/samples.dpgrowmult.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary.ddpgrow.Rd | 6 growcurves-0.2.4.0/growcurves/man/summary.dpgrow.Rd | 6 growcurves-0.2.4.0/growcurves/man/summary.dpgrowmm.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary.dpgrowmult.Rd | 10 growcurves-0.2.4.0/growcurves/man/summary_quantiles.Rd | 70 - growcurves-0.2.4.0/growcurves/man/trtplot.Rd | 65 - growcurves-0.2.4.0/growcurves/src/DPre.cpp | 2 growcurves-0.2.4.0/growcurves/src/ddp.cpp | 5 growcurves-0.2.4.0/growcurves/src/lgm.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmC.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCchol.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCmiar.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCmvplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmCplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmI.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIgroup.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIgroupDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmIplusDP.cpp | 2 growcurves-0.2.4.0/growcurves/src/mmmult.cpp | 2 growcurves-0.2.4.0/growcurves/tests/test-all.R |only growcurves-0.2.4.0/growcurves/tests/testthat/test-XZcov.R | 2 growcurves-0.2.4.0/growcurves/tests/testthat/test-ddpgrow.R | 2 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmm-mv.R | 4 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmm.R | 6 growcurves-0.2.4.0/growcurves/tests/testthat/test-dpgrowmult.R | 2 79 files changed, 2041 insertions(+), 3088 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
randomForestSRC package for survival, regression and classification forests and
ggplot2 package plotting.
Author: John Ehrlinger <john.ehrlinger@gmail.com>
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 1.1.4 dated 2015-03-29 and 1.2.0 dated 2015-11-15
DESCRIPTION | 17 MD5 | 233 ++++++----- NAMESPACE | 15 NEWS | 10 R/calc_roc.R | 36 + R/combine.gg_partial.R | 66 +-- R/gg_error.R | 19 R/gg_interaction.R | 36 - R/gg_minimal_depth.R | 26 - R/gg_minimal_vimp.R | 24 - R/gg_partial.R | 29 - R/gg_partial_coplot.R | 13 R/gg_rfsrc.R | 13 R/gg_roc.R | 4 R/gg_variable.R | 12 R/gg_vimp.R | 41 + R/help.R | 2 R/interaction_data.R | 18 R/kaplan.R | 8 R/logit_loess.R |only R/nelson.R | 6 R/partial.rfsrc.R | 8 R/partial_coplot_data.R | 12 R/partial_data.R | 16 R/partial_surface_data.R | 22 - R/plot.gg_error.R | 12 R/plot.gg_interaction.R | 16 R/plot.gg_minimal_depth.R | 62 ++ R/plot.gg_minimal_vimp.R | 44 +- R/plot.gg_partial.R | 38 - R/plot.gg_partial_list.R | 24 - R/plot.gg_rfsrc.R | 14 R/plot.gg_roc.R | 4 R/plot.gg_survival.R | 2 R/plot.gg_variable.R | 212 ++++++---- R/plot.gg_vimp.R | 22 - R/quantile_pts.R | 1 R/rfsrc_cache_datasets.R | 234 ++++++----- R/rfsrc_data.R | 18 R/varsel_data.R | 18 README.md | 5 build/vignette.rds |binary data/interaction_Boston.rda |binary data/interaction_iris.rda |binary data/interaction_pbc.rda |binary data/partial_Boston.rda |binary data/partial_coplot_Boston.rda |binary data/partial_coplot_Boston2.rda |binary data/partial_coplot_pbc.rda |binary data/partial_coplot_pbc2.rda |binary data/partial_iris.rda |binary data/partial_pbc.rda |binary data/rfsrc_Boston.rda |binary data/rfsrc_iris.rda |binary data/rfsrc_pbc.rda |binary data/rfsrc_pbc_test.rda |binary data/varsel_Boston.rda |binary data/varsel_iris.rda |binary data/varsel_pbc.rda |binary inst/doc/randomForestSRC-Regression.R | 71 ++- inst/doc/randomForestSRC-Regression.Rnw | 65 +-- inst/doc/randomForestSRC-Regression.pdf |binary inst/doc/randomForestSRC-Survival.R | 280 ++++++------- inst/doc/randomForestSRC-Survival.Rnw | 393 +++++++++---------- inst/doc/randomForestSRC-Survival.pdf |binary man/calc_auc.Rd | 10 man/calc_roc.rfsrc.Rd | 11 man/combine.gg_partial.Rd | 46 +- man/ggRandomForests-package.Rd | 58 +- man/gg_error.Rd | 19 man/gg_interaction.Rd | 49 +- man/gg_minimal_depth.Rd | 35 - man/gg_minimal_vimp.Rd | 33 - man/gg_partial.Rd | 62 +- man/gg_partial_coplot.rfsrc.Rd | 24 - man/gg_rfsrc.rfsrc.Rd | 17 man/gg_roc.rfsrc.Rd | 10 man/gg_survival.Rd | 21 - man/gg_variable.rfsrc.Rd | 32 - man/gg_vimp.rfsrc.Rd | 19 man/interaction_data.Rd | 114 +++-- man/kaplan.Rd | 12 man/logit_loess.Rd |only man/nelson.Rd | 16 man/partial.rfsrc.Rd | 32 - man/partial_coplot_data.Rd | 52 +- man/partial_data.Rd | 102 ++-- man/partial_surface_data.Rd | 99 ++-- man/plot.gg_error.Rd | 19 man/plot.gg_interaction.Rd | 21 - man/plot.gg_minimal_depth.Rd | 16 man/plot.gg_minimal_vimp.Rd | 30 - man/plot.gg_partial.Rd | 41 - man/plot.gg_partial_list.Rd | 31 - man/plot.gg_rfsrc.Rd | 16 man/plot.gg_roc.Rd | 9 man/plot.gg_survival.Rd | 19 man/plot.gg_variable.Rd | 27 - man/plot.gg_vimp.Rd | 25 - man/print.gg_minimal_depth.Rd | 7 man/quantile_pts.Rd | 13 man/rfsrc_cache_datasets.Rd | 43 +- man/rfsrc_data.Rd | 95 ++-- man/shift.Rd | 8 man/surface_matrix.Rd | 12 man/varsel_data.Rd | 100 ++-- tests |only vignettes/ggRandomForests.bib | 121 ++--- vignettes/randomForestSRC-Regression-concordance.tex |only vignettes/randomForestSRC-Regression.Rnw | 65 +-- vignettes/randomForestSRC-Survival.Rnw | 393 +++++++++---------- 111 files changed, 2301 insertions(+), 1904 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Time Series Clustering with Dynamic Time Warping
Description: Time series clustering using different techniques related to the
Dynamic Time Warping distance and its corresponding lower bounds. Additionally,
an implementation of k-Shape clustering is available.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 1.1.0 dated 2015-09-12 and 1.2.0 dated 2015-11-15
DESCRIPTION | 14 - MD5 | 66 ++--- NAMESPACE | 63 ++--- R/SBD.R | 76 +++++- R/TADPole.R | 67 +++-- R/dtw-lb.R | 2 R/dtwclust-classes.R | 4 R/dtwclust-plot.R | 15 - R/dtwclust.R | 233 ++++++++++++------- R/kcca-list.R | 4 R/lb-improved.R | 4 R/lb-keogh.R | 2 R/pkg.R | 2 R/shape-extraction.R | 4 R/uciCT.R | 44 +-- R/utils.R | 571 ++++++++++++++++++++++++++---------------------- R/zscore.R | 1 README.md | 106 +++++++- inst/REFERENCES.bib | 274 +++++++++++------------ man/DBA.Rd | 124 +++++----- man/NCCc.Rd | 2 man/SBD.Rd | 114 +++++---- man/TADPole.Rd | 2 man/dtw_lb.Rd | 7 man/dtwclust-class.Rd | 3 man/dtwclust-package.Rd | 2 man/dtwclust.Rd | 114 +++++---- man/lb_improved.Rd | 148 ++++++------ man/lb_keogh.Rd | 154 ++++++------ man/plot-methods.Rd | 100 ++++---- man/reinterpolate.Rd | 2 man/shape_extraction.Rd | 6 man/uciCT.Rd | 2 man/zscore.Rd | 2 34 files changed, 1325 insertions(+), 1009 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong <ykong@cuhk.edu.hk>
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.3.2 dated 2015-09-29 and 1.3.3 dated 2015-11-14
DESCRIPTION | 12 ++++++------ MD5 | 50 +++++++++++++++++++++++++------------------------- R/fixed.R | 4 ++-- R/fixed0.R | 6 +++--- R/fixed01.R | 8 ++++---- R/fixed1.R | 6 +++--- R/joint.1z.R | 4 ++-- R/joint.1z0.R | 6 +++--- R/joint.1z01.R | 8 ++++---- R/joint.1z1.R | 6 +++--- R/joint.2z.R | 11 +++++++---- R/joint.2z0.R | 30 +++++++++++++++--------------- R/joint.2z01.R | 33 +++++++++++++++++---------------- R/joint.2z1.R | 30 +++++++++++++++--------------- R/sep.1z.R | 8 ++++---- R/sep.1z0.R | 6 +++--- R/sep.1z01.R | 8 ++++---- R/sep.1z1.R | 6 +++--- R/sep.2z.R | 8 ++++---- R/sep.2z0.R | 30 +++++++++++++++--------------- R/sep.2z01.R | 32 ++++++++++++++++---------------- R/sep.2z1.R | 30 +++++++++++++++--------------- R/zoib.R | 1 - man/zoib-package.Rd | 4 ++-- man/zoib.Rd | 2 +- tests/test2.R | 28 +++++++++++++++++++++++++++- 26 files changed, 203 insertions(+), 174 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous data and utility functions
for manipulating data and your R environment.
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.1 dated 2015-07-31 and 0.1.2 dated 2015-11-14
DESCRIPTION | 9 ++-- MD5 | 82 +++++++++++++++++++++++--------------------- NAMESPACE | 4 +- R/Tcols.R | 3 - R/counts2fpkm.R |only R/datename.R | 7 +-- R/deseqresult2tbl.R | 5 +- R/dfsigfig.R | 5 +- R/lsa.R | 5 +- R/lsp.R | 5 +- R/nin.R | 5 +- R/nn.R | 5 +- R/o.R | 5 +- R/peek.R |only R/propmiss.R | 5 +- R/read.cb.R | 5 +- R/registration.R | 5 +- R/rownames_to_symprobe.R | 5 +- R/saveit.R | 4 +- R/sicb.R | 5 +- R/unfactor.R | 5 +- R/unrowname.R | 4 +- README.md | 16 +++++--- man/Tcols.Rd | 7 +-- man/Tmisc.Rd | 2 - man/counts2fpkm.Rd |only man/datename.Rd | 3 + man/deseqresult2tbl.Rd | 3 + man/dfsigfig.Rd | 3 + man/grapes-nin-grapes.Rd | 3 + man/lsa.Rd | 7 ++- man/lsp.Rd | 3 + man/nn.Rd | 3 + man/o.Rd | 3 + man/peek.Rd |only man/propmiss.Rd | 3 + man/quartet.Rd | 6 +-- man/read.cb.Rd | 3 + man/registration.Rd | 7 ++- man/rownames_to_symprobe.Rd | 3 + man/saveit.Rd | 3 + man/sicb.Rd | 3 + man/unfactor.Rd | 3 + man/unrowname.Rd | 3 + 44 files changed, 138 insertions(+), 127 deletions(-)
Title: Import Stata Data Files
Description: Function to read and write the Stata file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph],
Magnus Thor Torfason [ctb]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.8 dated 2015-10-07 and 0.8.1 dated 2015-11-14
DESCRIPTION | 12 +++-- MD5 | 22 +++++----- R/read.R | 65 ++++++++++++++------------------ R/save.R | 6 +- R/tools.R | 6 ++ README.md | 11 +++-- inst/include/readstata.h | 18 ++++++++ inst/include/swap_endian.h | 2 man/read.dta13.Rd | 39 +++++++++---------- man/save.dta13.Rd | 4 - src/rcpp_pre13_savestata.cpp | 4 - src/read_dta.cpp | 87 ++++++++++++++++++++++++++----------------- 12 files changed, 162 insertions(+), 114 deletions(-)
Title: Use Python from Within R
Description: Interact with Python from within R.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-1 dated 2015-09-19 and 0.1-2 dated 2015-11-14
ChangeLog |only DESCRIPTION | 6 ++--- MD5 | 25 ++++++++++++----------- R/PyImport.R | 4 +-- R/PySet.R | 10 ++++----- R/PySource.R | 54 ++++++++++++++++++++++++++++++++++++-------------- R/PythonInR.R | 1 R/zzz.R | 2 + README.md | 33 ++++++++++++++++++++++++++++++ man/BEGIN.Python.Rd | 10 ++++++++- man/pyConnect.Rd | 3 ++ man/pyImport.Rd | 4 +-- man/pySet.Rd | 14 ++++++++++++ src/PythonFunctions.c | 9 +++----- 14 files changed, 130 insertions(+), 45 deletions(-)
Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between kyotil versions 2015.5-20 dated 2015-05-20 and 2015.11-13 dated 2015-11-14
kyotil-2015.11-13/kyotil/DESCRIPTION | 13 +- kyotil-2015.11-13/kyotil/MD5 | 52 +++++---- kyotil-2015.11-13/kyotil/NAMESPACE | 30 ++++- kyotil-2015.11-13/kyotil/R/age_calc.R | 3 kyotil-2015.11-13/kyotil/R/base.R | 15 ++ kyotil-2015.11-13/kyotil/R/matrix2.R | 60 ++++++----- kyotil-2015.11-13/kyotil/R/misc.R | 49 +++++++-- kyotil-2015.11-13/kyotil/R/plotting.R | 70 ++++--------- kyotil-2015.11-13/kyotil/R/print.R | 32 ++--- kyotil-2015.11-13/kyotil/R/random.R | 10 + kyotil-2015.11-13/kyotil/R/regression.model.functions.R | 33 +++++- kyotil-2015.11-13/kyotil/R/stat.R | 6 - kyotil-2015.11-13/kyotil/R/tests.R | 2 kyotil-2015.11-13/kyotil/build/vignette.rds |binary kyotil-2015.11-13/kyotil/inst/unitTests/runit.matrix2.R | 4 kyotil-2015.11-13/kyotil/man/base.Rd | 8 + kyotil-2015.11-13/kyotil/man/get.sim.res.Rd |only kyotil-2015.11-13/kyotil/man/math.Rd | 5 kyotil-2015.11-13/kyotil/man/matrix2.Rd | 6 - kyotil-2015.11-13/kyotil/man/misc.Rd | 6 - kyotil-2015.11-13/kyotil/man/plotting.Rd | 19 +-- kyotil-2015.11-13/kyotil/man/random.Rd | 9 + kyotil-2015.11-13/kyotil/man/regression.model.functions.Rd | 7 - kyotil-2015.11-13/kyotil/man/stat.Rd | 7 - kyotil-2015.11-13/kyotil/man/tests.Rd | 6 - kyotil-2015.11-13/kyotil/src/Call_matrix.c | 24 ++++ kyotil-2015.11-13/kyotil/src/wilcoxpp_test.c |only kyotil-2015.11-13/kyotil/vignettes/kyotil-vignette.tex |only kyotil-2015.5-20/kyotil/vignettes/kyotil-vignette.bib |only 29 files changed, 312 insertions(+), 164 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.2.0 dated 2015-11-13 and 1.2.1 dated 2015-11-14
biogas-1.2.0/biogas/inst/doc/predBg.R |only biogas-1.2.0/biogas/inst/doc/predBg.Rnw |only biogas-1.2.0/biogas/inst/doc/predBg.pdf |only biogas-1.2.0/biogas/vignettes/predBg.Rnw |only biogas-1.2.1/biogas/ChangeLog | 21 +++++++ biogas-1.2.1/biogas/DESCRIPTION | 8 +- biogas-1.2.1/biogas/MD5 | 42 +++++++------- biogas-1.2.1/biogas/R/calcCOD.R | 6 +- biogas-1.2.1/biogas/build/vignette.rds |binary biogas-1.2.1/biogas/inst/doc/biogas_quick_start.Rnw | 12 ++-- biogas-1.2.1/biogas/inst/doc/biogas_quick_start.pdf |binary biogas-1.2.1/biogas/inst/doc/predBg_function.R |only biogas-1.2.1/biogas/inst/doc/predBg_function.Rnw |only biogas-1.2.1/biogas/inst/doc/predBg_function.pdf |only biogas-1.2.1/biogas/man/biogas-package.Rd | 32 ++++++----- biogas-1.2.1/biogas/man/calcCOD.Rd | 11 +++ biogas-1.2.1/biogas/man/cumBg.Rd | 43 +++++++++------ biogas-1.2.1/biogas/man/interp.Rd | 6 +- biogas-1.2.1/biogas/man/mass2vol.Rd | 12 ++-- biogas-1.2.1/biogas/man/molMass.Rd | 11 +++ biogas-1.2.1/biogas/man/predBg.Rd | 9 +-- biogas-1.2.1/biogas/man/stdVol.Rd | 19 ++++-- biogas-1.2.1/biogas/man/summBg.Rd | 54 +++++++++++-------- biogas-1.2.1/biogas/man/vol2mass.Rd | 24 +++++--- biogas-1.2.1/biogas/vignettes/biogas_quick_start.Rnw | 12 ++-- biogas-1.2.1/biogas/vignettes/predBg_function.Rnw |only 26 files changed, 201 insertions(+), 121 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.2-1 dated 2015-09-21 and 1.3-0 dated 2015-11-14
arules-1.2-1/arules/inst/tests |only arules-1.2-1/arules/vignettes/arules-classes.eps |only arules-1.3-0/arules/DESCRIPTION | 10 - arules-1.3-0/arules/MD5 | 144 +++++++++++------------ arules-1.3-0/arules/NAMESPACE | 5 arules-1.3-0/arules/R/AAADefs.R | 2 arules-1.3-0/arules/R/AllClasses.R | 2 arules-1.3-0/arules/R/AllGenerics.R | 10 - arules-1.3-0/arules/R/Matrix.R | 2 arules-1.3-0/arules/R/abbreviate.R | 69 ++++------- arules-1.3-0/arules/R/addComplement.R | 2 arules-1.3-0/arules/R/aggregate.R | 39 +++--- arules-1.3-0/arules/R/appearance.R | 2 arules-1.3-0/arules/R/apriori.R | 7 - arules-1.3-0/arules/R/associations.R | 13 -- arules-1.3-0/arules/R/control.R | 2 arules-1.3-0/arules/R/coverage.R | 2 arules-1.3-0/arules/R/crossTable.R | 2 arules-1.3-0/arules/R/discretize.R | 2 arules-1.3-0/arules/R/dissimilarity.R | 2 arules-1.3-0/arules/R/eclat.R | 7 - arules-1.3-0/arules/R/image.R | 2 arules-1.3-0/arules/R/inspect.R | 2 arules-1.3-0/arules/R/interestMeasures.R | 2 arules-1.3-0/arules/R/is.closed.R | 2 arules-1.3-0/arules/R/is.maximal.R | 2 arules-1.3-0/arules/R/is.superset.R | 2 arules-1.3-0/arules/R/itemCoding.R | 2 arules-1.3-0/arules/R/itemFrequency.R | 2 arules-1.3-0/arules/R/itemMatrix.R | 32 ++++- arules-1.3-0/arules/R/itemsets.R | 10 + arules-1.3-0/arules/R/parameter.R | 2 arules-1.3-0/arules/R/pmml.R | 2 arules-1.3-0/arules/R/predict.R | 2 arules-1.3-0/arules/R/random.transactions.R | 2 arules-1.3-0/arules/R/read_write.R | 85 ++++++------- arules-1.3-0/arules/R/ruleInduction.R | 69 +++++++---- arules-1.3-0/arules/R/rules.R | 9 + arules-1.3-0/arules/R/sample.R | 2 arules-1.3-0/arules/R/sets.R | 2 arules-1.3-0/arules/R/setsItemwise.R | 2 arules-1.3-0/arules/R/subset.R | 2 arules-1.3-0/arules/R/support.R | 2 arules-1.3-0/arules/R/supportingTransactions.R | 2 arules-1.3-0/arules/R/tidLists.R | 21 +++ arules-1.3-0/arules/R/transactions.R | 9 + arules-1.3-0/arules/R/warm.R | 2 arules-1.3-0/arules/README.md |only arules-1.3-0/arules/inst/NEWS | 14 ++ arules-1.3-0/arules/inst/doc/arules.pdf |binary arules-1.3-0/arules/man/abbreviate.Rd | 27 +++- arules-1.3-0/arules/man/aggregate.Rd | 73 +++++++---- arules-1.3-0/arules/man/interestMeasure.Rd | 26 ++-- arules-1.3-0/arules/man/read.transactions.Rd | 38 +++--- arules-1.3-0/arules/man/ruleInduction.Rd | 17 +- arules-1.3-0/arules/man/tidLists-class.Rd | 1 arules-1.3-0/arules/man/transactions-class.Rd | 26 +++- arules-1.3-0/arules/man/write.Rd | 16 -- arules-1.3-0/arules/src/ptree.c | 14 +- arules-1.3-0/arules/src/rapriori.c | 32 ++--- arules-1.3-0/arules/src/reclat.c | 6 arules-1.3-0/arules/src/warm.c | 1 arules-1.3-0/arules/tests/testthat |only arules-1.3-0/arules/tests/testthat.R | 4 64 files changed, 534 insertions(+), 358 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.5 dated 2015-10-02 and 2.1.6 dated 2015-11-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/ReadGrib.R | 23 ++++++++++++++++++++--- man/PlotWindProfile.Rd | 2 +- man/ReadGrib.Rd | 9 +++++++-- 6 files changed, 40 insertions(+), 15 deletions(-)
Title: Penalized Regression-Based Clustering Method
Description: Clustering is unsupervised and exploratory in nature. Yet, it can be performed through penalized regression with grouping pursuit. In this package, we provide two algorithms for fitting the penalized regression-based clustering (PRclust). One algorithm is based on quadratic penalty and difference convex method. Another algorithm is based on difference convex and ADMM, called DC-ADD, which is more efficient. Generalized cross validation was provided to select the tuning parameters. Rand index, adjusted Rand index and Jaccard index were provided to estimate the agreement between estimated cluster memberships and the truth.
Author: Chong Wu, Wei Pan
Maintainer: Chong Wu <wuxx0845@umn.edu>
Diff between prclust versions 1.0 dated 2015-11-06 and 1.1 dated 2015-11-13
prclust-1.0/prclust/README.md |only prclust-1.1/prclust/DESCRIPTION | 10 +++++----- prclust-1.1/prclust/MD5 | 9 ++++----- prclust-1.1/prclust/R/GCVOrignial.R | 2 +- prclust-1.1/prclust/man/PRclust.Rd | 6 ------ prclust-1.1/prclust/man/prclust-package.Rd | 4 ++-- 6 files changed, 12 insertions(+), 19 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 1.3 dated 2015-11-07 and 2.0 dated 2015-11-13
DESCRIPTION | 8 +-- MD5 | 29 ++++++----- NAMESPACE | 8 ++- R/dunn.test.control.R |only R/posthoc.kruskal.dunn.test.R |only R/posthoc.kruskal.nemenyi.test.R | 2 inst/CITATION |only inst/NEWS.Rd | 15 +++++ inst/doc/PMCMR.R | 54 +++++++++++++++++---- inst/doc/PMCMR.Rnw | 89 +++++++++++++++++++++++++++++++---- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 24 ++++++--- man/dunn.test.control.Rd |only man/posthoc.friedman.nemenyi.test.Rd | 4 + man/posthoc.kruskal.dunn.test.Rd |only man/posthoc.kruskal.nemenyi.test.Rd | 2 vignettes/PMCMR.Rnw | 89 +++++++++++++++++++++++++++++++---- vignettes/PMCMR.bib | 35 +++++++++++++ 18 files changed, 303 insertions(+), 56 deletions(-)
Title: Bayesian Non-Parametric Dependent Models for Time-Indexed
Functional Data
Description: Estimates a collection of time-indexed functions under
either of Gaussian process (GP) or intrinsic Gaussian Markov
random field (iGMRF) prior formulations where a Dirichlet process
mixture allows sub-groupings of the functions to share the same
covariance or precision parameters. The GP and iGMRF formulations
both support any number of additive covariance or precision terms,
respectively, expressing either or both of multiple trend and
seasonality.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growfunctions versions 0.11 dated 2014-12-09 and 0.12 dated 2015-11-13
DESCRIPTION | 19 +- MD5 | 72 +++++----- NAMESPACE | 5 NEWS | 10 + R/gp_car_fit_compare_facet.R | 129 ++++++++++------- R/gp_informative_compare_plot.R | 8 - R/gpdpgrow.R | 8 - R/help.R | 219 +++++++++++++++++------------- man/MSPE.Rd | 91 ++++++------ man/cluster_plot.Rd | 43 +++-- man/cps.Rd | 19 +- man/fit_compare.Rd | 142 +++++++++++-------- man/gen_informative_sample.Rd | 55 +++---- man/gmrfdpPost.Rd | 31 ++-- man/gmrfdpgrow.Rd | 63 ++++---- man/gpBFixPost.Rd | 9 - man/gpFixPost.Rd | 9 - man/gpPost.Rd | 9 - man/gpdpPost.Rd | 11 - man/gpdpbPost.Rd | 11 - man/gpdpgrow.Rd | 107 +++++++------- man/growfunctions-package.Rd | 259 ++++++++++++++++++++---------------- man/informative_plot.Rd | 85 +++++------ man/plot_cluster.Rd | 11 - man/predict_functions.Rd | 3 man/predict_functions.gmrfdpgrow.Rd | 29 ++-- man/predict_functions.gpdpgrow.Rd | 27 +-- man/predict_plot.Rd | 55 +++---- man/samples.Rd | 3 man/samples.gmrfdpgrow.Rd | 3 src/dpmix.cpp | 4 src/gp.cpp | 2 src/gpbfix.cpp | 2 src/gpdpbmix.cpp | 6 src/gpdpmix.cpp | 6 src/gpdpmix_moves.cpp | 14 - src/gpfix.cpp | 2 37 files changed, 863 insertions(+), 718 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native binary
(ENVI) format directly into R based on the widely applied 'raster' package;
calculate monthly value composites (e.g. maximum value composites, MVC) from the
bi-monthly input data; and derive long-term monotonous trends from the
Mann-Kendall trend test, optionally featuring pre-whitening to
account for lag-1 autocorrelation.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.2.0 dated 2015-10-26 and 0.3.0 dated 2015-11-13
DESCRIPTION | 25 +- MD5 | 36 +-- NAMESPACE | 5 R/downloadGimms.R | 91 ++++++- R/gimms-package.R | 54 ++-- R/monthlyComposite.R | 180 +++++++-------- R/rasterizeGimms.R | 2 R/rearrangeFiles.R | 171 +++++++------- R/significantTau.R |only R/updateInventory.R | 19 + README.md | 562 +----------------------------------------------- man/createHeader.Rd | 3 man/downloadGimms.Rd | 36 ++- man/gimms-package.Rd | 2 man/monthlyComposite.Rd | 7 man/monthlyIndices.Rd | 5 man/rasterizeGimms.Rd | 5 man/rearrangeFiles.Rd | 10 man/significantTau.Rd |only man/updateInventory.Rd | 12 - 20 files changed, 404 insertions(+), 821 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.1 dated 2015-10-04 and 0.3.2 dated 2015-11-13
DESCRIPTION | 18 +- MD5 | 71 +++++----- NAMESPACE | 2 NEWS | 6 R/bf.R | 10 - R/bfse.R | 1 R/calcbf.R | 18 +- R/comparebinlinks.R | 6 R/geobayes-package.R | 6 R/geoesteb.R | 25 +-- R/mcsp2.R | 24 ++- demo/rhizoctonia5.R | 22 +-- demo/yield3.R | 6 demo/yield4.R | 6 man/bf1skel.Rd | 9 - man/bf2new.Rd | 9 - man/bf2optim.Rd | 3 man/bfse.Rd | 4 man/comparebinlinks.Rd | 3 man/ebsglmm.Rd | 11 - man/ebstrga.Rd | 3 man/geoBayes.Rd | 9 - man/linkfcn.Rd | 7 man/mcmcmake.Rd | 3 man/mcsglmm.Rd | 3 man/mcstrga.Rd | 3 man/mkpredgrid2d.Rd | 3 man/plotbf2.Rd | 3 man/rhizoctonia.Rd | 3 man/stackdata.Rd | 3 src/Makevars | 11 - src/betaprior.f90 |only src/bfsp.f90 | 29 ---- src/calcb2.f90 | 114 ++++------------ src/llik.f90 | 45 ------ src/mcsp2.f90 | 346 ++++++++++++++++++++++++------------------------- src/pdfw.f90 | 6 37 files changed, 393 insertions(+), 458 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 0.6 dated 2015-04-14 and 0.7 dated 2015-11-13
DESCRIPTION | 17 +- MD5 | 55 ++++---- NAMESPACE | 20 ++ R/custom.R | 7 - R/deriv.R | 26 ++- R/flexsurvreg.R | 119 ++++++++++------- R/spline.R | 255 ++++++++++++++++++++++++++------------ R/utils.R | 12 + build/vignette.rds |binary inst/NEWS | 39 +++++ inst/doc/flexsurv-examples.R | 12 - inst/doc/flexsurv-examples.pdf |binary inst/doc/flexsurv.R | 58 ++++---- inst/doc/flexsurv.pdf |binary man/Survspline.Rd | 13 + man/WeibullPH.Rd |only man/flexsurvreg.Rd | 9 + man/flexsurvspline.Rd | 33 +++- man/msfit.flexsurvreg.Rd | 6 man/summary.flexsurvreg.Rd | 14 +- tests/test_base.R | 5 tests/testthat/test_deriv.R | 8 - tests/testthat/test_flexsurvreg.R | 13 + tests/testthat/test_mstate.R | 6 tests/testthat/test_outputs.R | 36 +++++ tests/testthat/test_spline.R | 56 +++++--- tests/testthat/test_utils.R | 41 +++++- vignettes/flexsurv-examples.Rnw | 19 +- vignettes/flexsurv.Rnw | 64 +++++---- 29 files changed, 636 insertions(+), 307 deletions(-)
Title: Easy Analysis and Visualization of Factorial Experiments
Description: Facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. "repeated measures"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.
Author: Michael A. Lawrence <mike.lwrnc@gmail.com>
Maintainer: Michael A. Lawrence <mike.lwrnc@gmail.com>
Diff between ez versions 4.2-2 dated 2013-09-13 and 4.3 dated 2015-11-13
CHANGES | 3 ++ DESCRIPTION | 12 ++++----- MD5 | 18 +++++++------- NAMESPACE | 26 +++++++++++++-------- R/ezCor.R | 65 +++++++++++++++++++++++++++--------------------------- R/ezDesign.R | 17 ++------------ R/ezPlot.R | 4 +-- R/ezPredict.R | 2 - man/ez-package.Rd | 4 +-- man/ezPlot.Rd | 10 -------- 10 files changed, 76 insertions(+), 85 deletions(-)
Title: Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre],
David Welch [aut],
David Hunter [ctb]
Maintainer: Chris Groendyke <cgroendyke@gmail.com>
Diff between epinet versions 2.0.9 dated 2014-12-16 and 2.1.5 dated 2015-11-13
epinet-2.0.9/epinet/R/BuildDyadicCovMatrix.R |only epinet-2.0.9/epinet/R/BuildDyadicLinearERGM.R |only epinet-2.0.9/epinet/man/BuildDyadicCovMatrix.Rd |only epinet-2.0.9/epinet/man/BuildDyadicLinearERGM.Rd |only epinet-2.0.9/epinet/man/NetworkEpiBayesSEIR.Rd |only epinet-2.1.5/epinet/DESCRIPTION | 12 - epinet-2.1.5/epinet/MD5 | 45 ++- epinet-2.1.5/epinet/NAMESPACE | 9 epinet-2.1.5/epinet/R/BuildX.R |only epinet-2.1.5/epinet/R/Epinet.R |only epinet-2.1.5/epinet/R/NetworkEpiBayesSEIR.R | 64 ++--- epinet-2.1.5/epinet/R/PlotEpiTree.R | 230 ++++++++++++++------ epinet-2.1.5/epinet/R/SEIR.simulator.R | 22 - epinet-2.1.5/epinet/R/SimulateDyadicLinearERGM.R |only epinet-2.1.5/epinet/R/ess.R | 2 epinet-2.1.5/epinet/data/Hagelloch.rda |binary epinet-2.1.5/epinet/man/BuildX.Rd |only epinet-2.1.5/epinet/man/Epinet.Rd |only epinet-2.1.5/epinet/man/Hagelloch.Rd | 2 epinet-2.1.5/epinet/man/MCMCcontrol.Rd |only epinet-2.1.5/epinet/man/PlotEpiTree.Rd | 49 ++-- epinet-2.1.5/epinet/man/Priorcontrol.Rd |only epinet-2.1.5/epinet/man/SEIR.simulator.Rd | 18 - epinet-2.1.5/epinet/man/SimulateDyadicLinearERGM.Rd |only epinet-2.1.5/epinet/man/epi2newick.Rd |only epinet-2.1.5/epinet/man/epinet-internal.Rd | 3 epinet-2.1.5/epinet/man/ess.Rd | 6 epinet-2.1.5/epinet/man/print.epinet.Rd |only epinet-2.1.5/epinet/man/summary.epinet.Rd |only epinet-2.1.5/epinet/man/write.epinet.Rd |only epinet-2.1.5/epinet/src/NetworkEpiMCMCSEIR.c | 47 +--- epinet-2.1.5/epinet/src/NetworkEpiMCMCSEIR.h | 4 32 files changed, 308 insertions(+), 205 deletions(-)
Title: R Interface to the EcoData Retriever
Description: Provides an R interface to the EcoData Retriever
(http://ecodataretriever.org/) via the EcoData Retriever's
command line interface. The EcoData Retriever automates the
tasks of finding, downloading, and cleaning ecological datasets,
and then stores them in a local database.
Author: Daniel McGlinn [aut, cre],
Ethan White [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Diff between ecoretriever versions 0.1 dated 2014-09-28 and 0.2 dated 2015-11-13
DESCRIPTION | 13 ++++---- MD5 | 19 ++++++------ NAMESPACE | 4 +- R/ecoretriever.R | 79 ++++++++++++++++++++++++++++++++++++---------------- README.md | 4 +- man/datasets.Rd | 9 +++-- man/download.Rd | 7 +++- man/ecoretriever.Rd | 3 + man/fetch.Rd | 3 + man/get_updates.Rd |only man/install.Rd | 7 ++-- 11 files changed, 97 insertions(+), 51 deletions(-)
Title: Diversity-Dependent Diversification
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 2.7 dated 2015-03-20 and 3.0 dated 2015-11-13
DDD-2.7/DDD/R/L2phylo.R |only DDD-2.7/DDD/R/bd_simplex.R |only DDD-2.7/DDD/R/brts2phylo.R |only DDD-2.7/DDD/R/conv.R |only DDD-2.7/DDD/R/dd_KI_simplex.R |only DDD-2.7/DDD/R/dd_SR_simplex.R |only DDD-2.7/DDD/R/dd_simplex.R |only DDD-2.7/DDD/R/flavec.R |only DDD-3.0/DDD/DESCRIPTION | 11 DDD-3.0/DDD/MD5 | 77 ++- DDD-3.0/DDD/NAMESPACE | 7 DDD-3.0/DDD/R/bd_ML.R | 171 ++++---- DDD-3.0/DDD/R/bd_loglik.R | 652 +++++++++++++++++---------------- DDD-3.0/DDD/R/bd_loglik_choosepar.R | 6 DDD-3.0/DDD/R/dd_KI_ML.R | 9 DDD-3.0/DDD/R/dd_KI_loglik.R | 22 - DDD-3.0/DDD/R/dd_KI_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_KI_sim.R |only DDD-3.0/DDD/R/dd_LR.R |only DDD-3.0/DDD/R/dd_ML.R | 12 DDD-3.0/DDD/R/dd_MS_ML.R |only DDD-3.0/DDD/R/dd_MS_loglik.R |only DDD-3.0/DDD/R/dd_MS_loglik_choosepar.R |only DDD-3.0/DDD/R/dd_MS_sim.R |only DDD-3.0/DDD/R/dd_SR_ML.R | 13 DDD-3.0/DDD/R/dd_SR_loglik.R | 29 - DDD-3.0/DDD/R/dd_SR_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_loglik.R | 18 DDD-3.0/DDD/R/dd_loglik_M.R |only DDD-3.0/DDD/R/dd_loglik_choosepar.R | 4 DDD-3.0/DDD/R/dd_logliknorm_rhs3.R |only DDD-3.0/DDD/R/dd_sim.R | 60 +-- DDD-3.0/DDD/R/dd_utils.R |only DDD-3.0/DDD/R/lamu_dd_td.R |only DDD-3.0/DDD/R/td_loglik_rhs.R | 91 +--- DDD-3.0/DDD/R/td_loglik_rhs_sim.R |only DDD-3.0/DDD/R/td_sim.R |only DDD-3.0/DDD/man/DDD-internal.Rd | 18 DDD-3.0/DDD/man/DDD-package.Rd | 20 - DDD-3.0/DDD/man/bd_ML.Rd | 10 DDD-3.0/DDD/man/bd_loglik.Rd | 8 DDD-3.0/DDD/man/dd_KI_ML.Rd | 7 DDD-3.0/DDD/man/dd_KI_loglik.Rd | 5 DDD-3.0/DDD/man/dd_KI_sim.Rd |only DDD-3.0/DDD/man/dd_LR.Rd |only DDD-3.0/DDD/man/dd_ML.Rd | 10 DDD-3.0/DDD/man/dd_MS_ML.Rd |only DDD-3.0/DDD/man/dd_MS_loglik.Rd |only DDD-3.0/DDD/man/dd_MS_sim.Rd |only DDD-3.0/DDD/man/dd_SR_ML.Rd | 15 DDD-3.0/DDD/man/dd_SR_loglik.Rd | 5 DDD-3.0/DDD/man/dd_loglik.Rd | 5 52 files changed, 685 insertions(+), 608 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full
Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.5.0 dated 2015-09-13 and 0.6.0 dated 2015-11-13
brms-0.5.0/brms/R/deprecated.R |only brms-0.5.0/brms/man/brmdata.Rd |only brms-0.5.0/brms/man/brmpars.Rd |only brms-0.5.0/brms/man/cor.brms.Rd |only brms-0.5.0/brms/tests/testthat/tests.deprecated.R |only brms-0.6.0/brms/DESCRIPTION | 21 brms-0.6.0/brms/MD5 | 135 - brms-0.6.0/brms/NAMESPACE | 35 brms-0.6.0/brms/R/brm.R | 393 ++-- brms-0.6.0/brms/R/brmsfit-helpers.R | 392 +++- brms-0.6.0/brms/R/brmsfit-methods.R | 695 ++++--- brms-0.6.0/brms/R/correlations.R | 196 +- brms-0.6.0/brms/R/data.R | 332 ++- brms-0.6.0/brms/R/distributions.R | 136 + brms-0.6.0/brms/R/families.R |only brms-0.6.0/brms/R/fitted.R |only brms-0.6.0/brms/R/generics.R | 110 - brms-0.6.0/brms/R/loglik.R | 488 +++-- brms-0.6.0/brms/R/misc.R | 123 + brms-0.6.0/brms/R/predict.R | 388 +++- brms-0.6.0/brms/R/priors.R |only brms-0.6.0/brms/R/rename.R | 28 brms-0.6.0/brms/R/stan.R | 1576 ++++++++++++----- brms-0.6.0/brms/R/validate.R | 606 +----- brms-0.6.0/brms/R/zzz-example.R |only brms-0.6.0/brms/README.md | 32 brms-0.6.0/brms/inst/NEWS.Rd |only brms-0.6.0/brms/inst/doc/brms.ltx | 156 - brms-0.6.0/brms/inst/doc/brms.pdf |binary brms-0.6.0/brms/man/LOO.Rd | 31 brms-0.6.0/brms/man/VarCorr.Rd | 19 brms-0.6.0/brms/man/WAIC.Rd | 13 brms-0.6.0/brms/man/brm.Rd | 415 ++-- brms-0.6.0/brms/man/brms-package.Rd | 2 brms-0.6.0/brms/man/brmsfamily.Rd |only brms-0.6.0/brms/man/brmsfit-class.Rd | 56 brms-0.6.0/brms/man/cor_ar.Rd | 34 brms-0.6.0/brms/man/cor_arma.Rd | 50 brms-0.6.0/brms/man/cor_arr.Rd |only brms-0.6.0/brms/man/cor_brms.Rd |only brms-0.6.0/brms/man/cor_ma.Rd | 27 brms-0.6.0/brms/man/epilepsy.Rd | 33 brms-0.6.0/brms/man/fitted.brmsfit.Rd | 31 brms-0.6.0/brms/man/fixef.Rd | 5 brms-0.6.0/brms/man/get_prior.Rd | 102 - brms-0.6.0/brms/man/hypothesis.Rd | 11 brms-0.6.0/brms/man/inhaler.Rd | 25 brms-0.6.0/brms/man/kidney.Rd | 25 brms-0.6.0/brms/man/launch_shiny.Rd | 9 brms-0.6.0/brms/man/logLik.brmsfit.Rd | 4 brms-0.6.0/brms/man/macf.Rd | 13 brms-0.6.0/brms/man/make_stancode.Rd |only brms-0.6.0/brms/man/make_standata.Rd |only brms-0.6.0/brms/man/ngrps.Rd | 2 brms-0.6.0/brms/man/parnames.Rd | 2 brms-0.6.0/brms/man/plot.brmsfit.Rd | 23 brms-0.6.0/brms/man/posterior_samples.Rd | 19 brms-0.6.0/brms/man/predict.brmsfit.Rd | 47 brms-0.6.0/brms/man/print.brmsfit.Rd | 9 brms-0.6.0/brms/man/prior_samples.Rd | 16 brms-0.6.0/brms/man/ranef.Rd | 7 brms-0.6.0/brms/man/residuals.brmsfit.Rd | 25 brms-0.6.0/brms/man/set_prior.Rd | 197 +- brms-0.6.0/brms/man/stancode.Rd | 3 brms-0.6.0/brms/man/standata.Rd | 3 brms-0.6.0/brms/man/stanplot.Rd |only brms-0.6.0/brms/man/summary.brmsfit.Rd | 7 brms-0.6.0/brms/man/update.brmsfit.Rd |only brms-0.6.0/brms/man/vcov.brmsfit.Rd | 4 brms-0.6.0/brms/tests/testthat/tests.brm.R | 110 + brms-0.6.0/brms/tests/testthat/tests.brmsfit-helpers.R | 40 brms-0.6.0/brms/tests/testthat/tests.data.R | 313 ++- brms-0.6.0/brms/tests/testthat/tests.priors.R |only brms-0.6.0/brms/tests/testthat/tests.stan.R | 260 ++ brms-0.6.0/brms/tests/testthat/tests.validate.R | 137 - brms-0.6.0/brms/vignettes/brms.ltx | 156 - brms-0.6.0/brms/vignettes/citations.bib | 250 +- brms-0.6.0/brms/vignettes/flowchart.pdf |only 78 files changed, 5486 insertions(+), 2891 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.1.0 dated 2015-07-29 and 1.2.0 dated 2015-11-13
ChangeLog | 122 ++++++++++++++ DESCRIPTION | 10 - MD5 | 74 ++++---- NAMESPACE | 3 NEWS | 41 ++++ R/checkArgClassValue.R | 8 R/constants.R |only R/cumBg.R | 11 - R/mass2vol.R | 11 - R/molMass.R | 31 +-- R/predBg.R | 105 +++++++++--- R/readFormula.R | 18 +- R/summBg.R | 10 - R/vol2mass.R | 5 R/vol2mol.R |only build/vignette.rds |binary data/comp.rda |binary data/comp2.rda |binary data/mass.rda |binary data/massw.rda |binary data/oldcomp.rda |binary data/setup.rda |binary data/setup2.rda |binary data/vol.rda |binary data/vol2.rda |binary inst/doc/biogas_quick_start.R | 56 +++--- inst/doc/biogas_quick_start.Rnw | 109 +++--------- inst/doc/biogas_quick_start.pdf |binary inst/doc/predBg.R |only inst/doc/predBg.Rnw |only inst/doc/predBg.pdf |only man/biogas-package.Rd | 2 man/cumBg.Rd | 2 man/mass2vol.Rd | 264 +++++++++++++++---------------- man/predBg.Rd | 59 +++++- man/stdVol.Rd | 10 - man/vol2mol.Rd |only tests/testthat/test.mass.csv |only tests/testthat/test_HighLevelFunctions.R | 40 +++- tests/testthat/test_LowLevelFunctions.R | 11 - vignettes/biogas_quick_start.Rnw | 109 +++--------- vignettes/predBg.Rnw |only 42 files changed, 666 insertions(+), 445 deletions(-)
Title: Inference, Aggregation and Visualization for Top-K Ranked Lists
Description: For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Author: Michael G. Schimek, Eva Budinska, Jie Ding, Karl G. Kugler, Vendula Svendova, Shili Lin
Maintainer: Michael G. Schimek <michael.schimek@medunigraz.at>
Diff between TopKLists versions 1.0.3 dated 2014-11-11 and 1.0.6 dated 2015-11-13
TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-Results.png |only TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-SummaryTable.png |only TopKLists-1.0.3/TopKLists/vignettes/TopKListsGUI-2-Venn.png |only TopKLists-1.0.6/TopKLists/DESCRIPTION | 17 TopKLists-1.0.6/TopKLists/MD5 | 35 TopKLists-1.0.6/TopKLists/NAMESPACE | 4 TopKLists-1.0.6/TopKLists/NEWS | 21 TopKLists-1.0.6/TopKLists/R/TopKCEMC.R | 54 TopKLists-1.0.6/TopKLists/R/TopKGraphics.R | 28 TopKLists-1.0.6/TopKLists/R/TopKInference.R | 690 +++++----- TopKLists-1.0.6/TopKLists/build/vignette.rds |binary TopKLists-1.0.6/TopKLists/data/TopKSpaceSampleInput.rda |binary TopKLists-1.0.6/TopKLists/data/breast.rda |binary TopKLists-1.0.6/TopKLists/inst/CITATION |only TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.R | 20 TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.Rnw | 268 +-- TopKLists-1.0.6/TopKLists/inst/doc/TopKLists.pdf |binary TopKLists-1.0.6/TopKLists/man/TopKLists-package.Rd | 4 TopKLists-1.0.6/TopKLists/vignettes/TopKLists.Rnw | 268 +-- TopKLists-1.0.6/TopKLists/vignettes/aggmap.png |only TopKLists-1.0.6/TopKLists/vignettes/summarytable.png |only TopKLists-1.0.6/TopKLists/vignettes/venndiagram.png |only 22 files changed, 726 insertions(+), 683 deletions(-)
Title: Companion Package to the Book 'R: Einführung durch angewandte
Statistik'
Description: Provides functions used in the 'R: Einführung durch angewandte Statistik' (second edition).
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between REdaS versions 0.9.2 dated 2015-01-04 and 0.9.3 dated 2015-11-13
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- NAMESPACE | 3 +++ build/partial.rdb |binary inst/CITATION | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
More information about PortfolioEffectEstim at CRAN
Permanent link
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.0.9.2 dated 2015-07-26 and 1.1.0 dated 2015-11-13
DESCRIPTION | 11 MD5 | 19 - NAMESPACE | 10 NEWS |only R/borrowed.R | 243 --------------------- R/lm.R | 119 +--------- R/mixlm.R | 11 R/statistics.R | 602 ++++++++++++----------------------------------------- R/utilities.R | 31 -- man/Anova.Rd | 32 -- man/simple.glht.Rd | 3 11 files changed, 200 insertions(+), 881 deletions(-)
Title: Standard and Nonstandard Statistical Models and Methods for Test
Equating
Description: Contains functions to perform various models and
methods for test equating. It currently implements the traditional
mean, linear and equipercentile equating methods, as well as the
mean-mean, mean-sigma, Haebara and Stocking-Lord IRT linking methods.
It also supports newest methods such that local equating, kernel
equating (using Gaussian, logistic and uniform kernels) with presmoothing,
and IRT parameter linking methods based on asymmetric item characteristic
functions. Functions to obtain both standard error of equating (SEE)
and standard error of equating difference between two equating
functions (SEED) are also implemented for the kernel method of
equating.
Author: Jorge Gonzalez Burgos [cre, aut],
Daniel Acu<c3><b1>a Leon [ctb]
Maintainer: Jorge Gonzalez Burgos <jgonzale@mat.puc.cl>
Diff between SNSequate versions 1.1-1 dated 2014-08-09 and 1.2.1 dated 2015-11-13
DESCRIPTION | 24 MD5 | 17 NAMESPACE | 21 R/PREp.R | 45 - R/fitmeasures.R |only R/helperfuncs.R |only R/ker.eq.R | 1971 +++++++++++++++++++++++++++++---------------------- R/loglin.smooth.R | 371 +++++---- man/fitmeasures.Rd |only man/ker.eq.Rd | 32 man/loglin.smooth.Rd | 52 + 11 files changed, 1506 insertions(+), 1027 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation.
Author: Andrew T. Karl (Adsurgo LLC), Jennifer Broatch (Arizona State University)
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.1-1 dated 2015-07-19 and 1.1-2 dated 2015-11-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 9 +++++++++ R/NB_cre.R | 14 ++++++++++++-- R/NB_mov.r | 2 +- R/PB_cre.R | 4 ++-- R/binary_cre.R | 2 +- R/mvglmmRank.R | 1 - R/normal_cre.R | 13 +++++++++++-- R/poisson_cre.R | 4 ++-- man/mvglmmRank-package.Rd | 4 ++-- 11 files changed, 54 insertions(+), 27 deletions(-)
Title: Mapping Markers to the Nearest Genomic Feature
Description: Allows the user to generate a list of features (gene, pseudo, RNA,
CDS, and/or UTR) directly from NCBI database for any species with a current
build available. Option to save downloaded and formatted files is available,
and the user can prioritize the feature list based on type and assembly builds
present in the current build used. The user can then use the list of features
generated or provide a list to map a set of markers (designed for SNP markers
with a single base pair position available) to the closest feature based on
the map build. This function does require map positions of the markers to be
provided and the positions should be based on the build being queried through
NCBI.
Author: Lauren L. Hulsman Hanna and David G. Riley
Maintainer: Lauren Hanna <Lauren.Hanna@ndsu.edu>
Diff between Map2NCBI versions 1.0 dated 2013-09-24 and 1.1 dated 2015-11-13
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/GetGeneList.R | 22 ++++++++++++++-------- R/MapMarkers.R | 20 ++++++++++---------- man/GetGeneList.Rd | 10 +++++----- man/Map2NCBI-package.Rd | 8 ++++---- man/MapMarkers.Rd | 2 +- 8 files changed, 56 insertions(+), 49 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.5 dated 2015-10-14 and 0.0.6 dated 2015-11-13
DESCRIPTION | 10 +++---- MD5 | 14 +++++----- NAMESPACE | 23 ++++++++++++++--- R/CheckInputs.R | 49 +++++++++++++++++++++++++------------ R/MultiPlot.R | 2 - R/SinglePlot.R | 2 - R/create_infotables.R | 6 ++-- inst/doc/Information-vignette.html | 4 +-- 8 files changed, 72 insertions(+), 38 deletions(-)
More information about listWithDefaults at CRAN
Permanent link
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Lord & Barton's four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2015).
Author: Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0.1 dated 2015-10-13 and 1.0.2 dated 2015-11-13
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- NAMESPACE | 2 +- src/fourpno_101315.cpp | 12 ++++++------ 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Engle-Granger Cointegration Models
Description: An easy-to-use implementation of the Engle-Granger
two-step procedure for identifying pairs of cointegrated series. It is geared towards
the analysis of pairs of securities. Summary and plot functions are provided,
and the package is able to fetch closing prices of securities from Yahoo.
A variety of unit root tests are supported, and an improved unit root test is included.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg <matthewcleggphd@gmail.com>
Diff between egcm versions 1.0.6 dated 2015-02-06 and 1.0.8 dated 2015-11-13
CHANGELOG | 1 + DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 6 +++++- R/egcm.R | 17 +++++++++-------- 5 files changed, 26 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-21 0.9-3
2011-05-24 0.9-2
2011-05-20 0.9-1
2011-05-19 0.9-0
2009-08-01 0.8-5
2008-11-02 0.8-4
2008-09-16 0.8-3
2007-12-24 0.8-2
2007-06-16 0.8-1
Title: Modelling Space Time AutoRegressive Moving Average (STARMA)
Processes
Description: Statistical functions to identify, estimate and diagnose a Space-Time AutoRegressive Moving Average (STARMA) model.
Author: Felix Cheysson
Maintainer: Felix Cheysson <felix@cheysson.fr>
Diff between starma versions 1.1 dated 2015-10-05 and 1.2 dated 2015-11-12
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- man/stacf.Rd | 2 +- man/starma-package.Rd | 6 +++--- man/stcor.test.Rd | 2 +- src/starma.cpp | 2 +- 6 files changed, 18 insertions(+), 17 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Provides statistical methods for the analysis of data areal data, with a focus on cluster detection.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 0.1.6 dated 2015-10-06 and 0.2.2 dated 2015-11-12
DESCRIPTION | 13 ++-- MD5 | 35 ++++++++--- NAMESPACE | 8 ++ R/flex.test.R |only R/flex.zones.R |only R/scan.stat.R | 18 +++-- R/scan.test.R | 125 +++++++++++++++++++++------------------- R/uls.test.R | 45 ++++---------- man/flex.test.Rd |only man/flex.zones.Rd |only man/scan.stat.Rd | 12 +-- man/scan.test.Rd | 5 - man/uls.test.Rd | 9 +- tests/flex_nycases.txt |only tests/flex_nycoords.txt |only tests/flex_nyw.mt0 |only tests/flex_nyw.txt |only tests/flex_out.ed$ |only tests/flex_out.fl$ |only tests/flex_out.la$ |only tests/flex_out.no$ |only tests/flex_out.txt |only tests/flex_out.txt.clt |only tests/flexscanformat.R |only tests/satscanformat.R |only tests/testthat/test-flex.test.R |only tests/testthat/test-scan.test.R | 3 27 files changed, 148 insertions(+), 125 deletions(-)
Title: Bayesian Variable Selection with Hierarchical Priors
Description:
Bayesian variable selection for linear regression models using hierarchical
priors. There is a prior that combines information across responses and one
that combines information across covariates, as well as a standard spike and
slab prior for comparison. An MCMC samples from the marginal posterior
distribution for the 0-1 variables indicating if each covariate belongs to the
model for each response.
Author: Laurel Stell and Chiara Sabatti
Maintainer: Laurel Stell <lstell@stanford.edu>
Diff between ptycho versions 1.1-2 dated 2015-09-12 and 1.1-4 dated 2015-11-12
ptycho-1.1-2/ptycho/man/data.Rd |only ptycho-1.1-2/ptycho/man/mcmcLoop.Rd |only ptycho-1.1-4/ptycho/DESCRIPTION | 9 +- ptycho-1.1-4/ptycho/MD5 | 17 ++--- ptycho-1.1-4/ptycho/NAMESPACE | 4 - ptycho-1.1-4/ptycho/R/batch.R | 65 ++++++++++--------- ptycho-1.1-4/ptycho/R/gendata.R | 39 ++++++++++- ptycho-1.1-4/ptycho/R/mh.R | 48 +++++++++----- ptycho-1.1-4/ptycho/man/Data.Rd |only ptycho-1.1-4/ptycho/man/createData.Rd | 17 +++-- ptycho-1.1-4/ptycho/man/ptycho.Rd | 112 ++++++++++++++++++++++------------ 11 files changed, 202 insertions(+), 109 deletions(-)
Title: Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
Description: Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.cache versions 0.10.0 dated 2014-06-11 and 0.12.0 dated 2015-11-12
DESCRIPTION | 20 ++++++++--------- MD5 | 49 +++++++++++++++++++++++++++----------------- NAMESPACE | 1 NEWS | 23 ++++++++++++++++++++ R/999.package.R | 20 ++++++----------- R/addMemoization.R | 24 +++++++++++++++++---- R/clearCache.R | 6 ++--- R/getChecksum.R | 2 - R/loadCache.R | 10 +------- R/memoizedCall.R | 24 +++++++++++++-------- R/private.assertDigest.R | 4 +-- R/readCacheHeader.R | 8 ++----- R/saveCache.R | 10 +------- R/zzz.R | 2 + README.md |only man/R.cache-package.Rd | 10 +------- man/addMemoization.Rd | 6 ++++- man/loadCache.Rd | 10 +------- man/memoizedCall.Rd | 9 +++++--- man/saveCache.Rd | 8 ------- tests/Object.getChecksum.R |only tests/addMemoization.R |only tests/clearCache.R |only tests/evalWithMemoization.R |only tests/getCachePath.R |only tests/getCacheRootPath.R |only tests/loadCache.R |only tests/memoizedCall.R |only tests/readCacheHeader.R |only tests/setCachePath.R |only tests/setCacheRootPath.R |only tests/textPrompt.R |only 32 files changed, 137 insertions(+), 109 deletions(-)
Title: Utilities to Fit Paired Comparison Models for Preferences
Description: Generates design matrix for analysing real paired comparisons and derived paired comparison data (Likert type items/ratings or rankings) using a loglinear approach. Fits loglinear Bradley-Terry model (LLBT) exploiting an eliminate feature. Computes pattern models for paired comparisons, rankings, and ratings. Some treatment of missing values (MCAR and MNAR). Fits latent class (mixture) models for paired comparison, rating and ranking patterns using a non-parametric ML approach.
Author: Reinhold Hatzinger [aut],
Marco Johannes Maier [cre]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between prefmod versions 0.8-32 dated 2014-05-20 and 0.8-33 dated 2015-11-12
.Rinstignore |only DESCRIPTION | 17 ++-- MD5 | 42 +++++----- NAMESPACE | 55 +++++++------- R/plotworth.R | 188 +++++++++++++++++++++++++----------------------- build/partial.rdb |binary data/baseball.RData |binary data/carconf.RData |binary data/cemspc.RData |binary data/dat4.RData |binary data/euro55.2.des.RData |binary data/immig.RData |binary data/issp2000.RData |binary data/music.RData |binary data/salad.RData |binary data/tennis.RData |binary data/trdel.RData |binary data/xmpl.RData |binary inst/CITATION | 2 man/issp2000.Rd | 24 +++--- man/music.Rd | 3 man/plot.wmat.Rd | 6 + man/prefmod-package.Rd | 2 23 files changed, 184 insertions(+), 155 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0.1 dated 2015-09-22 and 1.0.2 dated 2015-11-12
DESCRIPTION | 8 MD5 | 36 ++-- NAMESPACE | 7 R/find.ladder.R | 392 ++++++++++++++++++++++++++++++++++++++-------- R/jm.conv.R | 2 R/ladder.corrector.R |only R/ladder.info.attach.R | 36 +++- R/overview.R | 2 R/overview2.R | 8 R/pullup.R | 3 R/score.easy.R | 29 +-- R/storing.inds.R | 44 ++++- man/Fragman-package.Rd | 8 man/find.ladder.Rd | 6 man/ladder.corrector.Rd |only man/ladder.info.attach.Rd | 10 - man/overview.Rd | 4 man/overview2.Rd | 6 man/score.easy.Rd | 8 man/storing.inds.Rd | 6 20 files changed, 486 insertions(+), 129 deletions(-)
Title: Extended Rasch Modeling
Description: The eRm package fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Löf-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices. An eRm platform is provided at R-forge (see URL).
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Thomas Rusch [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between eRm versions 0.15-5 dated 2015-01-10 and 0.15-6 dated 2015-11-12
DESCRIPTION | 13 ++++---- MD5 | 62 ++++++++++++++++++++-------------------- NAMESPACE | 2 - NEWS | 8 +++++ R/plotGOF.LR.R | 36 ++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/llraDat1.rda |binary data/llraDat2.rda |binary data/llradat3.rda |binary data/lltmdat1.rda |binary data/lltmdat2.rda |binary data/lpcmdat.rda |binary data/lrsmdat.rda |binary data/pcmdat.rda |binary data/pcmdat2.rda |binary data/raschdat1.rda |binary data/raschdat1_RM_fitted.RData |binary data/raschdat1_RM_lrres2.RData |binary data/raschdat1_RM_plotDIF.RData |binary data/raschdat2.rda |binary data/raschdat3.rda |binary data/raschdat4.rda |binary data/rsmdat.rda |binary data/xmpl.RData |binary data/xmplbig.RData |binary inst/CITATION | 8 ++--- inst/NEWS.Rd | 6 +++ inst/NEWS.pdf |binary inst/doc/eRm.pdf |binary man/LRtest.Rd | 26 ++++++++++++++-- man/NPtest.Rd | 2 - 32 files changed, 100 insertions(+), 63 deletions(-)
Title: Dirichlet Regression in R
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between DirichletReg versions 0.6-2 dated 2015-02-09 and 0.6-3 dated 2015-11-12
DirichletReg-0.6-2/DirichletReg/R/lines.DirichletRegData.R |only DirichletReg-0.6-3/DirichletReg/DESCRIPTION | 8 - DirichletReg-0.6-3/DirichletReg/MD5 | 67 ++++---- DirichletReg-0.6-3/DirichletReg/NAMESPACE | 2 DirichletReg-0.6-3/DirichletReg/NEWS | 2 DirichletReg-0.6-3/DirichletReg/R/DR_LL_alt.R | 44 ++--- DirichletReg-0.6-3/DirichletReg/R/DR_LL_common.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/DR_data.R | 38 ++-- DirichletReg-0.6-3/DirichletReg/R/DirichReg.R | 78 +++++----- DirichletReg-0.6-3/DirichletReg/R/DirichReg_fit.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/Dirichlet.R | 36 ++-- DirichletReg-0.6-3/DirichletReg/R/confint.DirichletRegModel.R | 2 DirichletReg-0.6-3/DirichletReg/R/drop1.DirichletRegModel.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/get_starting_values.R | 12 - DirichletReg-0.6-3/DirichletReg/R/make.VT.R | 16 +- DirichletReg-0.6-3/DirichletReg/R/plot.DirichletRegData.R | 20 +- DirichletReg-0.6-3/DirichletReg/R/plot.DirichletRegModel.R | 8 - DirichletReg-0.6-3/DirichletReg/R/plot_DRdata_3d.R | 22 +- DirichletReg-0.6-3/DirichletReg/R/plot_DRdata_4d.R | 22 +- DirichletReg-0.6-3/DirichletReg/R/predict.DirichletRegModel.R | 10 - DirichletReg-0.6-3/DirichletReg/R/residuals.DirichletRegModel.R | 8 - DirichletReg-0.6-3/DirichletReg/R/summary.DirichletRegModel.R | 12 - DirichletReg-0.6-3/DirichletReg/R/sysdata.rda |binary DirichletReg-0.6-3/DirichletReg/R/toTernaryQuaternary.R | 10 - DirichletReg-0.6-3/DirichletReg/R/zzz.R | 12 - DirichletReg-0.6-3/DirichletReg/build/partial.rdb |binary DirichletReg-0.6-3/DirichletReg/build/vignette.rds |binary DirichletReg-0.6-3/DirichletReg/data/ArcticLake.RData |binary DirichletReg-0.6-3/DirichletReg/data/BloodSamples.RData |binary DirichletReg-0.6-3/DirichletReg/data/GlacialTills.RData |binary DirichletReg-0.6-3/DirichletReg/data/ReadingSkills.RData |binary DirichletReg-0.6-3/DirichletReg/data/Rocks.RData |binary DirichletReg-0.6-3/DirichletReg/inst/NEWS.Rd | 1 DirichletReg-0.6-3/DirichletReg/inst/NEWS.pdf |binary DirichletReg-0.6-3/DirichletReg/inst/doc/DirichletReg-vig.pdf |binary 35 files changed, 258 insertions(+), 256 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
Liang et al hyper-g priors (JASA 2008) or mixtures of
g-priors in GLMS of Li and Clyde 2015. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models, and may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.6 dated 2015-10-27 and 1.0.8 dated 2015-11-12
CHANGELOG | 11 +++++ DESCRIPTION | 8 +-- MD5 | 39 ++++++++++------- R/bas.R | 4 - R/bas.gglm.R | 84 ++++++++++++++++++++++++++++++++++---- R/betapriors.R | 42 +++++++++++++++++++ R/cch.R |only R/hypergeometric1F1.R | 3 - man/hyper-g-n.Rd |only man/hyper2d.Rd |only man/hypergeometric1F1.Rd | 8 +-- man/intrinsic.Rd |only man/jeffreys.Rd |only man/tcchpriors.Rd |only src/ZS.approx.null.np.c | 19 ++++---- src/bayesreg.c | 66 ++++++++++++++++++++---------- src/betapriorfamily.c | 102 ++++++++++++++++++++++++++++++++++++++++++----- src/betapriorfamily.h | 6 ++ src/cch.c |only src/family.c | 4 - src/hg.approx.null.np.c | 20 +++++---- src/hyperg.c | 2 src/hypergeometric1F1.c | 5 +- src/sampleworep.c | 27 ++++++++---- 24 files changed, 350 insertions(+), 100 deletions(-)
Title: Tools for Mapping Multiple Complex Traits
Description: Provides tools for joint analysis of multiple traits in a backcross (BC) or recombinant inbred lines (RIL) population. It can be used to select an optimal subset of traits for multiple-trait mapping, analyze multiple traits via the SURE model, which can associate different QTL with different traits, and perform multiple-trait composite multiple-interval mapping.
Author: Riyan Cheng <riyan.cheng@anu.edu.au>
Maintainer: Riyan Cheng <riyan.cheng@anu.edu.au>
Diff between qtlmt versions 0.1-3 dated 2013-03-12 and 0.1-4 dated 2015-11-12
ChangeLog | 9 +++++-- DESCRIPTION | 18 ++++---------- MD5 | 24 +++++++++---------- NAMESPACE | 3 ++ R/mstep.R | 40 +++++++++++++++++++-------------- R/mtcmim.R | 40 +++++++++++++++------------------ R/sure.R | 65 ++++++++++++++++++++++++++++++++---------------------- data/etrait.RData |binary man/mtcmim.Rd | 16 ++++++------- man/mtcmimStep.Rd | 18 +++++++------- man/sureEps.Rd | 8 +++--- man/sureEst.Rd | 15 ++++++------ man/sureStep.Rd | 18 +++++++------- 13 files changed, 148 insertions(+), 126 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package provides the Mann-Kendall Trend Test,
seasonal Mann-Kendall Test,
correlated seasonal Mann-Kendall Test,
partial Mann-Kendall Trend test,
(Seasonal) Sen's slope, partial correlation trend test and
change-point test after Pettitt.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 0.0.1 dated 2015-03-24 and 0.0.2 dated 2015-11-12
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 10 +++++++++- inst/NEWS.Rd |only inst/doc/trend.pdf |binary man/trend-package.Rd | 10 +++++++--- 6 files changed, 25 insertions(+), 12 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.6.1 dated 2015-09-07 and 0.6.2 dated 2015-11-12
DESCRIPTION | 10 ++--- MD5 | 58 ++++++++++++++--------------- R/compareGroups.R | 7 ++- R/getCEP.R | 89 +++++++++++++++++++++++++++++++++++++--------- R/getHitProb.R | 9 +++- R/groupShape.R | 24 ++++++------ R/groupSpread.R | 41 ++++++++++++++------- R/hoyt.R | 6 +-- R/maxwell.R | 2 - R/mvnEll.R | 8 ++-- R/rayleigh.R | 2 - R/simRingCount.R | 2 - build/vignette.rds |binary data/DF300BLK.rda |binary data/DF300BLKhl.rda |binary data/DFcciHV.rda |binary data/DFcm.rda |binary data/DFinch.rda |binary data/DFlistCm.rda |binary data/DFsavage.rda |binary data/DFscar17.rda |binary data/DFtalon.rda |binary data/targets.rda |binary inst/ChangeLog | 9 ++++ inst/doc/shotGroups.Rnw | 5 +- inst/doc/shotGroups.pdf |binary man/getCEP.Rd | 3 + man/shotGroups-package.Rd | 6 +-- vignettes/lit.bib | 48 ++++++++++++++---------- vignettes/shotGroups.Rnw | 5 +- 30 files changed, 216 insertions(+), 118 deletions(-)
Title: Tabular Reporting Functions
Description: Provides tabular reporting functionalities to work with 'ReporteRs'
package: 'as.FlexTable' methods are available for 'ftable' and 'xtable' objects,
function 'FlexPivot' is producing a pivot table and 'freqtable' a percentage table,
a 'knitr' print method and a 'shiny' render function are provided for 'FlexTable' objects.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between rtable versions 0.1.0 dated 2015-03-24 and 0.1.5 dated 2015-11-12
DESCRIPTION | 19 ++-- MD5 | 26 +++-- NAMESPACE | 11 ++ NEWS |only R/FlexPivot.R | 194 +++++++++++++++++++++++--------------------- R/FlexTable_coef.R |only R/FlexTable_quality.R |only R/freqtable.R | 2 R/get_color_dataset.R |only man/FlexPivot.Rd | 11 +- man/FlexTable_coef.Rd |only man/FlexTable_quality.Rd |only man/as.FlexTable.ftable.Rd | 2 man/as.FlexTable.xtable.Rd | 2 man/freqtable.Rd | 2 man/knit_print.FlexTable.Rd | 2 man/renderFlexTable.Rd | 2 17 files changed, 152 insertions(+), 121 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), as predictors in a linear regression, or as
dependent variable in a beta-binomial ANOVA. For simulation and bootstrap
purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>
Diff between RRreg versions 0.4.1 dated 2015-07-28 and 0.5.0 dated 2015-11-12
RRreg-0.4.1/RRreg/R/RRlog.CDM.R |only RRreg-0.4.1/RRreg/R/RRlog.FR.R |only RRreg-0.4.1/RRreg/R/RRlog.Kuk.R |only RRreg-0.4.1/RRreg/R/RRlog.Mangat.R |only RRreg-0.4.1/RRreg/R/RRlog.SLD.R |only RRreg-0.4.1/RRreg/R/RRlog.UQTknown.R |only RRreg-0.4.1/RRreg/R/RRlog.UQTunknown.R |only RRreg-0.4.1/RRreg/R/RRlog.Warner.R |only RRreg-0.5.0/RRreg/DESCRIPTION | 19 +- RRreg-0.5.0/RRreg/MD5 | 66 +++---- RRreg-0.5.0/RRreg/NAMESPACE | 3 RRreg-0.5.0/RRreg/NEWS | 10 + RRreg-0.5.0/RRreg/R/RRanova.R |only RRreg-0.5.0/RRreg/R/RRcheck.R | 114 +++++++----- RRreg-0.5.0/RRreg/R/RRgen.R | 86 +++++---- RRreg-0.5.0/RRreg/R/RRlin.R | 6 RRreg-0.5.0/RRreg/R/RRlin.getPW.R | 45 +++- RRreg-0.5.0/RRreg/R/RRlog.R | 200 +++++++++++----------- RRreg-0.5.0/RRreg/R/RRlog_fit.R |only RRreg-0.5.0/RRreg/R/RRmixed.R |only RRreg-0.5.0/RRreg/R/RRreg-package.R | 32 ++- RRreg-0.5.0/RRreg/R/RRsimu.R | 20 +- RRreg-0.5.0/RRreg/R/RRuni.R | 143 ++++++++++----- RRreg-0.5.0/RRreg/R/RRuni.models.R | 21 +- RRreg-0.5.0/RRreg/R/RRuni_ll.R |only RRreg-0.5.0/RRreg/R/helper_functions.R | 25 ++ RRreg-0.5.0/RRreg/R/powerplot.R | 7 RRreg-0.5.0/RRreg/data |only RRreg-0.5.0/RRreg/inst/doc/RRreg.R | 9 RRreg-0.5.0/RRreg/inst/doc/RRreg.Rmd | 107 ++++++++--- RRreg-0.5.0/RRreg/inst/doc/RRreg.html | 262 +++++++++++++++++------------ RRreg-0.5.0/RRreg/inst/models |only RRreg-0.5.0/RRreg/man/RRgen.Rd | 8 RRreg-0.5.0/RRreg/man/RRlog.Rd | 16 + RRreg-0.5.0/RRreg/man/RRmixed.Rd |only RRreg-0.5.0/RRreg/man/RRreg-package.Rd | 10 - RRreg-0.5.0/RRreg/man/RRsimu.Rd | 4 RRreg-0.5.0/RRreg/man/RRuni.Rd | 47 ++--- RRreg-0.5.0/RRreg/man/getPW.Rd |only RRreg-0.5.0/RRreg/man/minarets.Rd |only RRreg-0.5.0/RRreg/vignettes/RRreg.Rmd | 107 ++++++++--- RRreg-0.5.0/RRreg/vignettes/markdown10.css | 6 42 files changed, 867 insertions(+), 506 deletions(-)
Title: Fast Network Modularity and Roles Computation by Simulated
Annealing (Rgraph C Library Wrapper for R)
Description: It provides functions to compute the modularity and modularity-related roles in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 2005, doi:10.1038/nature03288).
Author: Guilhem Doulcier [aut, cre] (R bindings, current implementation of the
simulated annealing algorithm),
Roger Guimera [ctb] (Author of the original rgraph library),
Daniel B. Stouffer [aut, ths]
Maintainer: Guilhem Doulcier <guilhem.doulcier@ens.fr>
Diff between rnetcarto versions 0.2.3 dated 2015-11-11 and 0.2.4 dated 2015-11-12
DESCRIPTION | 8 ++--- MD5 | 6 ++-- inst/doc/getting-started.html | 55 +++++++++++++++++++--------------------- src/rgraph/src/fillpartitions.c | 41 ++++++++++------------------- 4 files changed, 49 insertions(+), 61 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al (doi: 10.2307/2533043) and the two level random effects model in Beath and Heller (doi: 10.1177/1471082X0800900302). Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-3 dated 2015-09-30 and 1.0-5 dated 2015-11-12
randomLCA-1.0-3/randomLCA/vignettes/randomLCA-example.tex |only randomLCA-1.0-5/randomLCA/DESCRIPTION | 16 randomLCA-1.0-5/randomLCA/MD5 | 25 randomLCA-1.0-5/randomLCA/NAMESPACE | 94 +- randomLCA-1.0-5/randomLCA/R/fitAdaptRandom.R | 555 ++++++-------- randomLCA-1.0-5/randomLCA/R/outcomeProbs.R | 4 randomLCA-1.0-5/randomLCA/R/randomLCA.R | 342 ++++---- randomLCA-1.0-5/randomLCA/R/refit.randomLCA.R | 90 +- randomLCA-1.0-5/randomLCA/build/vignette.rds |binary randomLCA-1.0-5/randomLCA/inst/NEWS | 14 randomLCA-1.0-5/randomLCA/man/plot.Rd | 72 - randomLCA-1.0-5/randomLCA/man/refit.Rd | 8 randomLCA-1.0-5/randomLCA/man/simulate.Rd | 27 randomLCA-1.0-5/randomLCA/man/uterinecarcinoma.Rd | 6 14 files changed, 644 insertions(+), 609 deletions(-)
Title: Permutations and Mallows Distributions
Description: Includes functions to work with the Mallows and Generalized Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances. It is also possible to generate random permutations at a given distance, or with a given number of inversions, or cycles, or fixed points or even with a given length on LIS (longest increasing subsequence).
Author: Ekhine Irurozki <ekhine.irurozqui@ehu.eus>, Borja Calvo <borja.calvo@ehu.eus>, Jose A. Lozano <ja.lozano@ehu.eus>
Maintainer: Ekhine Irurozki <ekhine.irurozqui@ehu.eus>
Diff between PerMallows versions 1.8 dated 2015-01-27 and 1.10 dated 2015-11-12
PerMallows-1.10/PerMallows/DESCRIPTION | 15 PerMallows-1.10/PerMallows/MD5 | 92 PerMallows-1.10/PerMallows/NAMESPACE | 1 PerMallows-1.10/PerMallows/R/PerMallows.R | 441 +--- PerMallows-1.10/PerMallows/man/compose.Rd | 2 PerMallows-1.10/PerMallows/man/count.perms.Rd |only PerMallows-1.10/PerMallows/man/cycle2str.Rd | 4 PerMallows-1.10/PerMallows/man/cycles2perm.Rd |only PerMallows-1.10/PerMallows/man/data.apa.Rd | 2 PerMallows-1.10/PerMallows/man/data.order.Rd | 2 PerMallows-1.10/PerMallows/man/decomp2perm.Rd |only PerMallows-1.10/PerMallows/man/dgmm.Rd | 6 PerMallows-1.10/PerMallows/man/distance.Rd | 2 PerMallows-1.10/PerMallows/man/dmm.Rd | 6 PerMallows-1.10/PerMallows/man/expectation.gmm.Rd | 2 PerMallows-1.10/PerMallows/man/expectation.mm.Rd | 2 PerMallows-1.10/PerMallows/man/freq.matrix.Rd | 2 PerMallows-1.10/PerMallows/man/generate.aux.files.Rd | 2 PerMallows-1.10/PerMallows/man/identity.permutation.Rd | 2 PerMallows-1.10/PerMallows/man/insert.Rd |only PerMallows-1.10/PerMallows/man/inverse.perm.Rd |only PerMallows-1.10/PerMallows/man/inversion.Rd |only PerMallows-1.10/PerMallows/man/is.permutation.Rd | 4 PerMallows-1.10/PerMallows/man/lgmm.Rd | 16 PerMallows-1.10/PerMallows/man/lgmm.theta.Rd | 16 PerMallows-1.10/PerMallows/man/lmm.Rd | 18 PerMallows-1.10/PerMallows/man/lmm.theta.Rd | 18 PerMallows-1.10/PerMallows/man/marginal.Rd | 2 PerMallows-1.10/PerMallows/man/maxi.dist.Rd | 2 PerMallows-1.10/PerMallows/man/order.ratings.Rd | 2 PerMallows-1.10/PerMallows/man/perm.sample.med.Rd | 2 PerMallows-1.10/PerMallows/man/perm.sample.small.Rd | 2 PerMallows-1.10/PerMallows/man/perm2cycles.Rd |only PerMallows-1.10/PerMallows/man/perm2decomp.Rd |only PerMallows-1.10/PerMallows/man/permutations.of.Rd | 2 PerMallows-1.10/PerMallows/man/rdist.Rd |only PerMallows-1.10/PerMallows/man/read.perms.Rd |only PerMallows-1.10/PerMallows/man/rgmm.Rd | 5 PerMallows-1.10/PerMallows/man/rmm.Rd | 8 PerMallows-1.10/PerMallows/man/runif.permutation.Rd | 2 PerMallows-1.10/PerMallows/man/swap.Rd | 2 PerMallows-1.10/PerMallows/src/Cayley.cpp | 71 PerMallows-1.10/PerMallows/src/Cayley.h | 6 PerMallows-1.10/PerMallows/vignettes/PerMallows.tex | 1066 +++++----- PerMallows-1.8/PerMallows/man/count.derangements.Rd |only PerMallows-1.8/PerMallows/man/count.perms.cycles.Rd |only PerMallows-1.8/PerMallows/man/count.perms.distance.Rd |only PerMallows-1.8/PerMallows/man/count.perms.fixed.points.Rd |only PerMallows-1.8/PerMallows/man/count.perms.unfixed.points.gtet.Rd |only PerMallows-1.8/PerMallows/man/cycles2permutation.Rd |only PerMallows-1.8/PerMallows/man/decomposition2permutation.Rd |only PerMallows-1.8/PerMallows/man/insert.at.Rd |only PerMallows-1.8/PerMallows/man/inverse.permutation.Rd |only PerMallows-1.8/PerMallows/man/inversion.at.Rd |only PerMallows-1.8/PerMallows/man/permutation2cycles.Rd |only PerMallows-1.8/PerMallows/man/permutation2decomposition.Rd |only PerMallows-1.8/PerMallows/man/r.derangement.Rd |only PerMallows-1.8/PerMallows/man/r.dist.d.Rd |only PerMallows-1.8/PerMallows/man/r.perms.cycles.Rd |only PerMallows-1.8/PerMallows/man/read.permutation.file.Rd |only 60 files changed, 936 insertions(+), 891 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.6 dated 2015-04-22 and 1.1.7 dated 2015-11-12
DESCRIPTION | 8 +-- MD5 | 92 +++++++++++++++++++++---------------------- NAMESPACE | 20 +++++++-- NEWS | 12 +++++ R/pfCompositeLF.R | 2 R/pfGridding.R | 44 ++++++++++++-------- R/pfTransform.R | 36 ++++++++++++++-- build/vignette.rds |binary inst/CITATION | 2 inst/doc/paleofire-paper.pdf |binary man/checkGCDversion.Rd | 3 - man/contiguous.Rd | 3 - man/kdffreq.Rd | 3 - man/paleofire-internal.Rd | 3 - man/paleofire-package.Rd | 3 - man/pfAddData.Rd | 3 - man/pfBoxCox.Rd | 3 - man/pfCircular.Rd | 3 - man/pfComposite.Rd | 3 - man/pfCompositeLF.Rd | 11 ++--- man/pfDiagnostic.Rd | 9 ++-- man/pfDotMap.Rd | 13 +++--- man/pfExtract.Rd | 3 - man/pfGridding.Rd | 3 - man/pfInteractive.Rd | 3 - man/pfKruskal.Rd | 3 - man/pfMinMax.Rd | 3 - man/pfPublication.Rd | 3 - man/pfResolution.Rd | 3 - man/pfSimpleGrid.Rd | 3 - man/pfSiteSel.Rd | 3 - man/pfToKml.Rd | 3 - man/pfTransform.Rd | 9 ++-- man/plot.CHAR.Rd | 3 - man/plot.contiguous.Rd | 3 - man/plot.kdffreq.Rd | 7 +-- man/plot.pfCircular.Rd | 3 - man/plot.pfComposite.Rd | 7 +-- man/plot.pfCompositeLF.Rd | 3 - man/plot.pfGridding.Rd | 3 - man/plot.pfKruskal.Rd | 3 - man/plot.pfSiteSel.Rd | 3 - man/plot.potveg.Rd | 3 - man/potveg.Rd | 3 - man/pretreatment.Rd | 9 ++-- man/summary.pfSiteSel.Rd | 3 - man/triCube.Rd | 3 - 47 files changed, 233 insertions(+), 138 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids, which can be used
for multivariate quadrature. This grids can be based on different quadrature
rules like Newton-Cotes formulas (trapezoidal-, Simpson's- rule, ...) or Gauss
quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the construction of the
multidimensional grid the product-rule or the combination- technique can be
applied.
Author: Constantin Weiser (HHU of Duesseldorf / Germany)
Maintainer: Constantin Weiser <weiserc@hhu.de>
Diff between mvQuad versions 1.0-3 dated 2015-11-03 and 1.0-4 dated 2015-11-12
DESCRIPTION | 22 +++++++++++----------- MD5 | 6 +++--- R/mvQuad.R | 23 ++++++++++++++--------- inst/NEWS | 7 ++++++- 4 files changed, 34 insertions(+), 24 deletions(-)
Title: Morse-Smale Approximation, Regression and Visualization
Description: Discrete Morse-Smale complex approximation based on kNN graph. The Morse-Smale complex provides a decomposition of the domain. This package provides methods to compute a hierarchical sequence of Morse-Smale complicies and tools that exploit this domain decomposition for regression and visualization of scalar functions.
Author: Samuel Gerber <sgerber@uoregon.edu>,
Kristi Potter <kpotter@sci.utah.edu>,
Oliver Ruebel <ruebel1@llnl.gov>
Maintainer: Samuel Gerber <sgerber@uoregon.edu>
Diff between msr versions 0.4.1 dated 2012-07-11 and 0.4.4 dated 2015-11-12
msr-0.4.1/msr/src/kd_dump.cpp |only msr-0.4.4/msr/ChangeLog | 6 msr-0.4.4/msr/DESCRIPTION | 29 msr-0.4.4/msr/MD5 | 61 - msr-0.4.4/msr/NAMESPACE | 16 msr-0.4.4/msr/data/camera_estimation.rda |binary msr-0.4.4/msr/data/diagonal.rda |binary msr-0.4.4/msr/data/fourpeaks.rda |binary msr-0.4.4/msr/data/uci_crime_subset.rda |binary msr-0.4.4/msr/man/msr-package.Rd | 9 msr-0.4.4/msr/src/ANN.cpp | 2 msr-0.4.4/msr/src/ANN/ANN.h | 6 msr-0.4.4/msr/src/DenseMatrix.h | 11 msr-0.4.4/msr/src/DenseVector.h | 12 msr-0.4.4/msr/src/EuclideanMetric.h | 16 msr-0.4.4/msr/src/GaussianKernel.h | 45 - msr-0.4.4/msr/src/Geometry.h | 31 msr-0.4.4/msr/src/Kernel.h | 14 msr-0.4.4/msr/src/KernelDensity.h | 14 msr-0.4.4/msr/src/LapackDefs.h |only msr-0.4.4/msr/src/Linalg.h | 984 +++++++++++++++-------------- msr-0.4.4/msr/src/LinalgIO.h | 5 msr-0.4.4/msr/src/Matrix.h | 3 msr-0.4.4/msr/src/Metric.h | 10 msr-0.4.4/msr/src/NNMSComplex.h | 99 +- msr-0.4.4/msr/src/NNMSComplex2old.h | 35 - msr-0.4.4/msr/src/SquaredEuclideanMetric.h |only msr-0.4.4/msr/src/Vector.h | 2 msr-0.4.4/msr/src/bd_tree.cpp | 2 msr-0.4.4/msr/src/bd_tree.h | 2 msr-0.4.4/msr/src/kd_tree.cpp | 7 msr-0.4.4/msr/src/kd_tree.h | 6 msr-0.4.4/msr/src/msr.cc | 9 33 files changed, 803 insertions(+), 633 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset and routines
to analyse this data. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-5 dated 2015-09-14 and 1.1-1 dated 2015-11-12
ChangeLog | 12 ++ DESCRIPTION | 21 ++-- MD5 | 39 +++++---- NAMESPACE | 10 ++ R/codes.R | 169 +++++++++++++++++++++++++++++++++++---- R/corpus.R | 49 +++++++++-- R/db_api.R | 30 ++++-- R/globals.R | 11 +- R/issue_attention.R |only R/manifesto.R | 53 ++---------- R/manifestoR-package.r | 11 +- R/nicheness.R |only R/pipe_helpers.R |only R/scaling_rile.R | 25 ++++- build/vignette.rds |binary man/ManifestoCorpus.Rd | 4 man/ManifestoSource.Rd | 6 + man/aggregate_pers.Rd |only man/categories.Rd |only man/count_codes.Rd | 6 + man/iff.Rd |only man/issue_attention_diversity.Rd |only man/mp_nicheness.Rd |only man/prefix.Rd |only vignettes/manifestoRworkflow.Rmd | 14 ++- 25 files changed, 342 insertions(+), 118 deletions(-)
Title: Joint Modelling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Description: Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Author: Rudradev Sengupta, Nolen Joy Perualila
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between IntegratedJM versions 1.1 dated 2015-09-24 and 1.2 dated 2015-11-12
DESCRIPTION | 16 ++++---- MD5 | 9 ++-- NAMESPACE | 4 +- NEWS | 4 +- R/Functions.R | 112 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-- man/volcano.Rd |only 6 files changed, 128 insertions(+), 17 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for displaying and analyzing functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.4 dated 2015-08-05 and 4.5 dated 2015-11-12
ftsa-4.4/ftsa/R/ftsmPI.r |only ftsa-4.5/ftsa/ChangeLog | 9 ftsa-4.5/ftsa/DESCRIPTION | 12 - ftsa-4.5/ftsa/MD5 | 76 +++---- ftsa-4.5/ftsa/NAMESPACE | 152 +++++++-------- ftsa-4.5/ftsa/R/T_stationary.R | 280 +++++++++++++--------------- ftsa-4.5/ftsa/R/dynamic_FLR.R |only ftsa-4.5/ftsa/R/farforecast.R | 119 +++++------ ftsa-4.5/ftsa/R/ftsmPI.R |only ftsa-4.5/ftsa/R/pcscorebootstrapdata.R | 122 ++++++------ ftsa-4.5/ftsa/build/vignette.rds |binary ftsa-4.5/ftsa/man/MFDM.Rd | 38 ++- ftsa-4.5/ftsa/man/T_stationary.Rd | 32 +-- ftsa-4.5/ftsa/man/centre.Rd | 58 ++--- ftsa-4.5/ftsa/man/diff.fts.Rd | 4 ftsa-4.5/ftsa/man/dynamic_FLR.Rd |only ftsa-4.5/ftsa/man/dynupdate.Rd | 6 ftsa-4.5/ftsa/man/error.Rd | 2 ftsa-4.5/ftsa/man/extract.Rd | 6 ftsa-4.5/ftsa/man/farforecast.Rd | 24 +- ftsa-4.5/ftsa/man/fbootstrap.Rd | 90 ++++----- ftsa-4.5/ftsa/man/forecast.ftsm.Rd | 12 + ftsa-4.5/ftsa/man/forecastfplsr.Rd | 66 +++--- ftsa-4.5/ftsa/man/fplsr.Rd | 20 +- ftsa-4.5/ftsa/man/ftsa-package.Rd | 6 ftsa-4.5/ftsa/man/ftsm.Rd | 4 ftsa-4.5/ftsa/man/ftsmiterativeforecasts.Rd | 4 ftsa-4.5/ftsa/man/ftsmweightselect.Rd | 2 ftsa-4.5/ftsa/man/isfe.fts.Rd | 2 ftsa-4.5/ftsa/man/mean.fts.Rd | 6 ftsa-4.5/ftsa/man/median.fts.Rd | 6 ftsa-4.5/ftsa/man/pcscorebootstrapdata.Rd | 127 ++++++------ ftsa-4.5/ftsa/man/plot.fmres.Rd | 2 ftsa-4.5/ftsa/man/plot.ftsf.Rd | 2 ftsa-4.5/ftsa/man/plot.ftsm.Rd | 2 ftsa-4.5/ftsa/man/plotfplsr.Rd | 82 ++++---- ftsa-4.5/ftsa/man/pm_10_GR.Rd | 4 ftsa-4.5/ftsa/man/residuals.fm.Rd | 60 +++--- ftsa-4.5/ftsa/man/sd.fts.Rd | 4 ftsa-4.5/ftsa/man/summary.fm.Rd | 2 ftsa-4.5/ftsa/man/var.fts.Rd | 4 41 files changed, 739 insertions(+), 708 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2.1 dated 2015-10-07 and 2.2.2 dated 2015-11-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/evenn.R | 2 ++ man/eVenn-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Distributed Data Structures in R
Description: Provides distributed data structures and simplifies
distributed computing in R.
Author: Edward Ma, Indrajit Roy, Michael Lawrence
Maintainer: Edward Ma <ema@hpe.com>
Diff between ddR versions 0.1 dated 2015-10-24 and 0.1.1 dated 2015-11-12
ddR-0.1.1/ddR/DESCRIPTION | 9 +++++---- ddR-0.1.1/ddR/MD5 | 21 +++++++++++++-------- ddR-0.1.1/ddR/NEWS.md |only ddR-0.1.1/ddR/README.md | 5 +++++ ddR-0.1.1/ddR/build |only ddR-0.1.1/ddR/inst |only ddR-0.1.1/ddR/man/package.Rd | 16 ++++++++-------- ddR-0.1.1/ddR/vignettes/README.Rmd | 5 +++-- ddR-0.1.1/ddR/vignettes/user_guide.Rmd | 9 +++++---- ddR-0.1/ddR/vignettes/user_guide.html |only ddR-0.1/ddR/vignettes/user_guide.md |only ddR-0.1/ddR/vignettes/user_guide.pdf |only 12 files changed, 39 insertions(+), 26 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.1 dated 2015-10-07 and 0.1-1 dated 2015-11-12
DESCRIPTION | 10 +-- MD5 | 37 +++++------ NAMESPACE | 4 - NEWS |only R/00class.R | 8 +- R/blav_fit.R | 6 + R/blav_fit_measures.R | 26 ++++--- R/blav_object_methods.R | 56 ++++++++++++---- R/blav_test.R | 15 +++- R/blav_utils.R | 43 ++++++++++++ R/blavaan.R | 138 ++++++++++++++++++++++++++++------------- R/dpriors.R | 4 - R/lav_export_jags.R | 118 ++++++++++++++++++++++++----------- R/set_inits.R | 6 + R/set_priors.R | 159 ++++++++++++++++++++++++++++-------------------- man/bcfa.Rd | 9 ++ man/bgrowth.Rd | 8 +- man/blavaan.Rd | 9 ++ man/bsem.Rd | 9 ++ man/dpriors.Rd | 6 - 20 files changed, 449 insertions(+), 222 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.1 dated 2015-07-12 and 2.2 dated 2015-11-12
DESCRIPTION | 8 MD5 | 14 - R/ThresholdROC-2states.R | 163 ++++++++++--------- R/ThresholdROC-3states.R | 365 +++++++++++++++++++++----------------------- R/diagnostic.R | 52 +++--- man/ThresholdROC-package.Rd | 8 man/diagnostic.Rd | 6 man/lines-thres3.Rd | 2 8 files changed, 316 insertions(+), 302 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng <riyan.cheng@anu.edu.au>
Maintainer: Riyan Cheng <riyan.cheng@anu.edu.au>
Diff between QTLRel versions 0.2-14 dated 2013-12-11 and 0.2-15 dated 2015-11-12
ChangeLog | 16 ---- DESCRIPTION | 18 ++-- MD5 | 45 ++++++------ NAMESPACE | 12 ++- R/aic.R | 10 ++ R/estVC.R | 34 +++------ R/hapSim.R | 196 ------------------------------------------------------ R/ibsFn.R | 3 R/idcoef.R | 4 - R/imFn.R | 1 R/pedRecode.R |only R/qtl2rel.R | 2 R/rel2qtl.R | 1 R/scan.R | 10 +- data/miscEx.RData |binary man/genoImpute.Rd | 2 man/genoProb.Rd | 6 - man/genoSim.Rd | 4 - man/hapSim.Rd | 4 - man/mAIC.Rd | 2 man/nullSim.Rd | 2 man/plots.Rd | 2 man/rem.Rd | 2 src/rgdat.c | 50 +++++++++---- 24 files changed, 119 insertions(+), 307 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.4 dated 2015-10-28 and 0.0.5 dated 2015-11-12
DESCRIPTION | 8 +-- MD5 | 20 +++++---- NAMESPACE | 1 NEWS | 5 ++ R/RcppExports.R | 8 +++ R/raster.R | 27 +++++++++++++ inst/include/gdtools_RcppExports.h | 38 ++++++++++++++++++ man/raster_write.Rd |only src/RcppExports.cpp | 76 +++++++++++++++++++++++++++++++++++++ src/raster_to_base64.cpp | 59 ++++++++++++++++++++++++++++ tests |only 11 files changed, 229 insertions(+), 13 deletions(-)
Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.0.0 dated 2015-11-06 and 1.0.1 dated 2015-11-12
DESCRIPTION | 6 MD5 | 11 NEWS.md |only README.md | 20 + configure | 504 +++++++++++++---------------------------- configure.ac | 20 + tools/m4/ax_boost_iostreams.m4 | 8 7 files changed, 215 insertions(+), 354 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudion [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 0.3.0 dated 2015-09-22 and 0.3.1 dated 2015-11-11
DESCRIPTION | 7 +++--- MD5 | 50 +++++++++++++++++++++---------------------- NAMESPACE | 2 - R/encoding.R | 2 - R/form.R | 8 +++--- R/session.R | 2 - R/table.R | 2 - inst/doc/selectorgadget.html | 4 +-- man/encoding.Rd | 4 +-- man/google_form.Rd | 2 - man/html.Rd | 2 - man/html_form.Rd | 2 - man/html_nodes.Rd | 4 +-- man/html_session.Rd | 2 - man/html_table.Rd | 4 +-- man/html_tag.Rd | 2 - man/html_text.Rd | 2 - man/jump_to.Rd | 2 - man/minimal_html.Rd | 2 - man/pipe.Rd | 2 - man/pluck.Rd | 2 - man/session_history.Rd | 2 - man/set_values.Rd | 2 - man/submit_form.Rd | 2 - man/xml.Rd | 2 - tests/testthat/test-forms.R | 11 +++++++++ 26 files changed, 70 insertions(+), 58 deletions(-)
Title: (Robust) Canonical Correlation Analysis via Projection Pursuit
Description: Canonical correlation analysis and maximum correlation via
projection pursuit, as well as fast implementations of correlation
estimators, with a focus on robust and nonparametric methods.
Author: Andreas Alfons [aut, cre],
David Simcha [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between ccaPP versions 0.3.0 dated 2013-11-01 and 0.3.1 dated 2015-11-11
DESCRIPTION | 18 +-- MD5 | 45 ++++---- NAMESPACE | 6 - NEWS | 18 ++- R/cca.R | 38 ++---- R/cor.R | 11 - R/fastMAD.R | 5 R/fastMedian.R | 3 R/maxCor.R | 32 +---- R/permTest.R | 20 +-- R/print.R | 10 - build |only data |only man/ccaGrid.Rd | 282 ++++++++++++++++++++++----------------------------- man/ccaPP-package.Rd | 45 +------- man/ccaProj.Rd | 180 ++++++++++++++------------------ man/corFunctions.Rd | 116 +++++++++----------- man/diabetes.Rd |only man/fastMAD.Rd | 30 ++--- man/fastMedian.Rd | 17 +-- man/maxCorGrid.Rd | 236 ++++++++++++++++++------------------------ man/maxCorProj.Rd | 139 +++++++++++-------------- man/permTest.Rd | 118 +++++++++------------ src/Makevars.win | 6 - src/cca.cpp | 2 25 files changed, 602 insertions(+), 775 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-11 0.1-2
2013-09-09 0.1-1
2012-12-26 0.0.1
Title: Wrap Around Time Series Graphics
Description: Wrap-around Time Series (WATS) plots for interrupted time series
designs with seasonal patterns.
Author: Will Beasley [aut, cre], Joe Rodgers [aut], Matthew Schuelke [ctb],
Ronnie Coleman [ctb], Mark Joseph Lachowicz [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between Wats versions 0.10.1 dated 2015-08-26 and 0.10.3 dated 2015-11-11
DESCRIPTION | 13 +- MD5 | 60 ++++----- NAMESPACE | 2 NEWS | 10 + R/AnnotateData.R | 1 R/CartesianPeriodic.R | 19 +-- R/CartesianRolling.R | 3 R/PolarPeriodic.R | 5 R/PolarizeCartesian.R | 1 README.md | 6 inst/doc/MbrFigures.html | 60 ++++----- inst/doc/OkFertilityWithIntercensalEstimates.html | 63 ++++------ man/AnnotateData.Rd | 2 man/AugmentCycleData.Rd | 5 man/CartesianPeriodic.Rd | 2 man/CartesianRolling.Rd | 12 - man/CountyMonthBirthRate.Rd | 46 +++---- man/PolarPeriodic.Rd | 40 +++--- man/PolarizeCartesian.Rd | 20 +-- man/Wats-package.Rd | 36 ++--- vignettes/figure_mbr_rmd/Figure2IndividualBasic-1.png |binary vignettes/figure_mbr_rmd/Figure2Stylized-1.png |binary vignettes/figure_mbr_rmd/Figure4Basic-1.png |binary vignettes/figure_mbr_rmd/Figure4Stylized-1.png |binary vignettes/figure_mbr_rmd/Figure6-1.png |binary vignettes/figure_mbr_rmd/Figure7-1.png |binary vignettes/figure_mbr_rmd/Figure7AllCounties-1.png |binary vignettes/figure_mbr_rmd/Figure8-1.png |binary vignettes/figure_okc_fertility_intercensal_rmd/CartesianPeriodic-1.png |binary vignettes/figure_okc_fertility_intercensal_rmd/CartesianRolling-1.png |binary vignettes/figure_okc_fertility_intercensal_rmd/PolarPeriodic-1.png |binary 31 files changed, 199 insertions(+), 207 deletions(-)
Title: n-Gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix <lmiratrix@stat.harvard.edu>
Diff between textreg versions 0.1.2 dated 2015-02-06 and 0.1.3 dated 2015-11-11
textreg-0.1.2/textreg/inst/testthat |only textreg-0.1.2/textreg/src/RcppExports.cpp |only textreg-0.1.2/textreg/vignettes/bathtub_vignette-concordance.tex |only textreg-0.1.2/textreg/vignettes/figure |only textreg-0.1.3/textreg/DESCRIPTION | 12 textreg-0.1.3/textreg/MD5 | 134 - textreg-0.1.3/textreg/NAMESPACE | 8 textreg-0.1.3/textreg/R/cross_validation_code.R | 330 ++-- textreg-0.1.3/textreg/R/make_word_lists.R | 226 ++- textreg-0.1.3/textreg/R/stempp.R | 2 textreg-0.1.3/textreg/R/text_searching.R | 3 textreg-0.1.3/textreg/R/textreg.R | 651 ++++---- textreg-0.1.3/textreg/R/vizualize_phrases.R | 2 textreg-0.1.3/textreg/build/vignette.rds |binary textreg-0.1.3/textreg/data/bathtub.RData |binary textreg-0.1.3/textreg/data/dirtyBathtub.RData |binary textreg-0.1.3/textreg/data/testCorpora.RData |binary textreg-0.1.3/textreg/inst/doc/bathtub_vignette.Rnw | 732 ++++------ textreg-0.1.3/textreg/man/bathtub.Rd | 3 textreg-0.1.3/textreg/man/build.corpus.Rd | 3 textreg-0.1.3/textreg/man/calc.loss.Rd | 3 textreg-0.1.3/textreg/man/clean.text.Rd | 3 textreg-0.1.3/textreg/man/cluster.phrases.Rd | 3 textreg-0.1.3/textreg/man/convert.tm.to.character.Rd | 3 textreg-0.1.3/textreg/man/cpp_build.corpus.Rd | 3 textreg-0.1.3/textreg/man/cpp_textreg.Rd | 3 textreg-0.1.3/textreg/man/dirtyBathtub.Rd | 3 textreg-0.1.3/textreg/man/find.CV.C.Rd | 7 textreg-0.1.3/textreg/man/find.threshold.C.Rd | 11 textreg-0.1.3/textreg/man/grab.fragments.Rd | 3 textreg-0.1.3/textreg/man/is.fragment.sample.Rd | 3 textreg-0.1.3/textreg/man/is.textreg.corpus.Rd | 3 textreg-0.1.3/textreg/man/is.textreg.result.Rd | 3 textreg-0.1.3/textreg/man/list.table.chart.Rd | 14 textreg-0.1.3/textreg/man/make.CV.chart.Rd | 16 textreg-0.1.3/textreg/man/make.appearance.matrix.Rd | 3 textreg-0.1.3/textreg/man/make.count.table.Rd | 3 textreg-0.1.3/textreg/man/make.list.table.Rd | 6 textreg-0.1.3/textreg/man/make.path.matrix.Rd | 3 textreg-0.1.3/textreg/man/make.phrase.correlation.chart.Rd | 3 textreg-0.1.3/textreg/man/make.phrase.matrix.Rd | 3 textreg-0.1.3/textreg/man/make.similarity.matrix.Rd | 3 textreg-0.1.3/textreg/man/make_search_phrases.Rd | 3 textreg-0.1.3/textreg/man/path.matrix.chart.Rd | 3 textreg-0.1.3/textreg/man/phrase.count.Rd | 3 textreg-0.1.3/textreg/man/phrase.matrix.Rd | 3 textreg-0.1.3/textreg/man/plot.textreg.result.Rd | 3 textreg-0.1.3/textreg/man/predict.textreg.result.Rd | 3 textreg-0.1.3/textreg/man/print.fragment.sample.Rd | 3 textreg-0.1.3/textreg/man/print.textreg.corpus.Rd | 3 textreg-0.1.3/textreg/man/print.textreg.result.Rd | 3 textreg-0.1.3/textreg/man/reformat.textreg.model.Rd | 3 textreg-0.1.3/textreg/man/sample.fragments.Rd | 3 textreg-0.1.3/textreg/man/save.corpus.to.files.Rd | 3 textreg-0.1.3/textreg/man/stem.corpus.Rd | 3 textreg-0.1.3/textreg/man/testCorpora.Rd | 3 textreg-0.1.3/textreg/man/textreg-package.Rd | 3 textreg-0.1.3/textreg/man/textreg.Rd | 12 textreg-0.1.3/textreg/man/tm_gregexpr.Rd | 3 textreg-0.1.3/textreg/src/textreg.cpp | 20 60 files changed, 1244 insertions(+), 1047 deletions(-)
Title: Qt-Based Painting Infrastructure
Description: Low-level interface to functionality in Qt for efficiently drawing
dynamic graphics and handling basic user input.
Author: Michael Lawrence, Deepayan Sarkar
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between qtpaint versions 0.9.0 dated 2012-03-03 and 0.9.1 dated 2015-11-11
qtpaint-0.9.0/qtpaint/.gitignore |only qtpaint-0.9.0/qtpaint/NOTES |only qtpaint-0.9.0/qtpaint/inst/profiling/.Rhistory |only qtpaint-0.9.0/qtpaint/kdebindings |only qtpaint-0.9.0/qtpaint/vignettes/.gitignore |only qtpaint-0.9.1/qtpaint/DESCRIPTION | 17 ++--- qtpaint-0.9.1/qtpaint/MD5 | 45 +++++++------- qtpaint-0.9.1/qtpaint/NAMESPACE | 4 + qtpaint-0.9.1/qtpaint/R/layer.R | 45 +++++++++++++- qtpaint-0.9.1/qtpaint/build |only qtpaint-0.9.1/qtpaint/demo/canvas.R | 76 ++++++++++++------------- qtpaint-0.9.1/qtpaint/inst/NOTES |only qtpaint-0.9.1/qtpaint/inst/doc/intro.R |only qtpaint-0.9.1/qtpaint/inst/doc/intro.pdf |binary qtpaint-0.9.1/qtpaint/man/qlayer.Rd | 27 ++++++-- qtpaint-0.9.1/qtpaint/src/CMakeLists.txt | 47 ++++++++++----- qtpaint-0.9.1/qtpaint/src/Makefile | 26 -------- qtpaint-0.9.1/qtpaint/src/Makefile.common |only qtpaint-0.9.1/qtpaint/src/Makefile.win | 32 +--------- qtpaint-0.9.1/qtpaint/src/OpenGLPainter.cpp | 22 ++++++- qtpaint-0.9.1/qtpaint/src/PainterWrappers.cpp | 4 - qtpaint-0.9.1/qtpaint/src/PlotView.cpp | 4 - qtpaint-0.9.1/qtpaint/src/PlotView.hpp | 2 qtpaint-0.9.1/qtpaint/src/TestWidget.cpp | 14 ++-- qtpaint-0.9.1/qtpaint/src/kdebindings |only 25 files changed, 206 insertions(+), 159 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
This package allows to specify such models, transparently calls a suitable
simulator, parses the results and calculates additional summary statistics.
It supports the simulators 'ms', 'msms' and 'scrm' and can simulate
finite-sites mutation models by combining the simulators with the program
'seq-gen'.
Author: Paul Staab [aut, cre, cph],
Dirk Metzler [ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.1.1 dated 2015-07-17 and 0.2.0 dated 2015-11-11
coala-0.1.1/coala/NEWS |only coala-0.1.1/coala/R/sumstat_nsl.R |only coala-0.1.1/coala/R/sumstat_omegaprime.R |only coala-0.1.1/coala/inst/doc/abc.R |only coala-0.1.1/coala/inst/doc/abc.Rmd |only coala-0.1.1/coala/inst/doc/abc.html |only coala-0.1.1/coala/inst/doc/installation.Rmd |only coala-0.1.1/coala/inst/doc/installation.html |only coala-0.1.1/coala/inst/doc/introduction.R |only coala-0.1.1/coala/inst/doc/introduction.Rmd |only coala-0.1.1/coala/inst/doc/introduction.html |only coala-0.1.1/coala/man/sumstat_nSL.Rd |only coala-0.1.1/coala/man/sumstat_omegaprime.Rd |only coala-0.1.1/coala/src/seg_sites.h |only coala-0.1.1/coala/src/stat_omegaprime.cpp |only coala-0.1.1/coala/tests/testthat/test-sumstat-nSL.R |only coala-0.1.1/coala/tests/testthat/test-sumstat-omegaprime.R |only coala-0.1.1/coala/vignettes/abc.Rmd |only coala-0.1.1/coala/vignettes/installation.Rmd |only coala-0.1.1/coala/vignettes/introduction.Rmd |only coala-0.2.0/coala/DESCRIPTION | 28 coala-0.2.0/coala/MD5 | 250 +++--- coala-0.2.0/coala/NAMESPACE | 13 coala-0.2.0/coala/NEWS.md |only coala-0.2.0/coala/R/RcppExports.R | 46 - coala-0.2.0/coala/R/feature.R | 8 coala-0.2.0/coala/R/feature_growth.R | 7 coala-0.2.0/coala/R/feature_mutation.R | 36 coala-0.2.0/coala/R/feature_outgroup.R | 7 coala-0.2.0/coala/R/feature_sample.R | 39 - coala-0.2.0/coala/R/feature_size_change.R | 25 coala-0.2.0/coala/R/feature_unphased.R | 39 - coala-0.2.0/coala/R/locus.R | 2 coala-0.2.0/coala/R/model.R | 35 coala-0.2.0/coala/R/model_build.R | 3 coala-0.2.0/coala/R/model_getters.R | 35 coala-0.2.0/coala/R/model_simulate.R | 17 coala-0.2.0/coala/R/par_zero_inflation.R | 23 coala-0.2.0/coala/R/parameter.R | 3 coala-0.2.0/coala/R/search_executable.R | 14 coala-0.2.0/coala/R/segsites.R |only coala-0.2.0/coala/R/simulator_class.R | 13 coala-0.2.0/coala/R/simulator_scrm.R | 4 coala-0.2.0/coala/R/simulator_seqgen.R | 91 +- coala-0.2.0/coala/R/sumstat.R | 37 - coala-0.2.0/coala/R/sumstat_dna.R | 19 coala-0.2.0/coala/R/sumstat_file.R | 4 coala-0.2.0/coala/R/sumstat_four_gamete.R | 12 coala-0.2.0/coala/R/sumstat_ihh.R | 156 ++-- coala-0.2.0/coala/R/sumstat_jsfs.R | 33 coala-0.2.0/coala/R/sumstat_mcmf.R |only coala-0.2.0/coala/R/sumstat_nucleotide_div.R | 9 coala-0.2.0/coala/R/sumstat_omega.R |only coala-0.2.0/coala/R/sumstat_seg_sites.R | 23 coala-0.2.0/coala/R/sumstat_sfs.R | 15 coala-0.2.0/coala/R/sumstat_tajimas_d.R | 9 coala-0.2.0/coala/R/sumstat_trees.R | 4 coala-0.2.0/coala/build/vignette.rds |binary coala-0.2.0/coala/inst/doc/coala-abc.R |only coala-0.2.0/coala/inst/doc/coala-abc.Rmd |only coala-0.2.0/coala/inst/doc/coala-abc.html |only coala-0.2.0/coala/inst/doc/coala-extend.R |only coala-0.2.0/coala/inst/doc/coala-extend.Rmd |only coala-0.2.0/coala/inst/doc/coala-extend.html |only coala-0.2.0/coala/inst/doc/coala-install.Rmd |only coala-0.2.0/coala/inst/doc/coala-install.html |only coala-0.2.0/coala/inst/doc/coala-intro.R |only coala-0.2.0/coala/inst/doc/coala-intro.Rmd |only coala-0.2.0/coala/inst/doc/coala-intro.html |only coala-0.2.0/coala/inst/include |only coala-0.2.0/coala/man/activate_ms.Rd | 2 coala-0.2.0/coala/man/activate_msms.Rd | 2 coala-0.2.0/coala/man/activate_seqgen.Rd | 2 coala-0.2.0/coala/man/calc_jsfs.Rd | 6 coala-0.2.0/coala/man/check_model.Rd | 2 coala-0.2.0/coala/man/coal_model.Rd | 13 coala-0.2.0/coala/man/coala.Rd | 2 coala-0.2.0/coala/man/conv_to_ms_arg.Rd | 2 coala-0.2.0/coala/man/feat_growth.Rd | 9 coala-0.2.0/coala/man/feat_migration.Rd | 2 coala-0.2.0/coala/man/feat_mutation.Rd | 8 coala-0.2.0/coala/man/feat_outgroup.Rd | 2 coala-0.2.0/coala/man/feat_pop_merge.Rd | 2 coala-0.2.0/coala/man/feat_recombination.Rd | 2 coala-0.2.0/coala/man/feat_sample.Rd | 9 coala-0.2.0/coala/man/feat_selection.Rd | 3 coala-0.2.0/coala/man/feat_size_change.Rd | 10 coala-0.2.0/coala/man/feat_unphased.Rd | 9 coala-0.2.0/coala/man/get_features.Rd | 15 coala-0.2.0/coala/man/list_simulators.Rd | 2 coala-0.2.0/coala/man/locus_single.Rd | 4 coala-0.2.0/coala/man/locus_trio.Rd | 2 coala-0.2.0/coala/man/par_expr.Rd | 18 coala-0.2.0/coala/man/par_variation.Rd | 2 coala-0.2.0/coala/man/par_zero_inflation.Rd | 11 coala-0.2.0/coala/man/plus-.coalmodel.Rd | 2 coala-0.2.0/coala/man/scale_model.Rd | 2 coala-0.2.0/coala/man/search_executable.Rd | 2 coala-0.2.0/coala/man/simulate.coalmodel.Rd | 10 coala-0.2.0/coala/man/sumstat_class.Rd |only coala-0.2.0/coala/man/sumstat_dna.Rd | 8 coala-0.2.0/coala/man/sumstat_file.Rd | 2 coala-0.2.0/coala/man/sumstat_four_gamete.Rd | 9 coala-0.2.0/coala/man/sumstat_ihh.Rd | 70 + coala-0.2.0/coala/man/sumstat_jsfs.Rd | 13 coala-0.2.0/coala/man/sumstat_mcmf.Rd |only coala-0.2.0/coala/man/sumstat_nucleotide_div.Rd | 9 coala-0.2.0/coala/man/sumstat_omega.Rd |only coala-0.2.0/coala/man/sumstat_seg_sites.Rd | 8 coala-0.2.0/coala/man/sumstat_sfs.Rd | 8 coala-0.2.0/coala/man/sumstat_tajimas_d.Rd | 9 coala-0.2.0/coala/man/sumstat_trees.Rd | 2 coala-0.2.0/coala/src/RcppExports.cpp | 130 ++- coala-0.2.0/coala/src/parse_ms_output.cpp | 21 coala-0.2.0/coala/src/parse_seqgen_output.cpp | 259 ++----- coala-0.2.0/coala/src/seg_sites.cpp |only coala-0.2.0/coala/src/stat_fpc.cpp | 21 coala-0.2.0/coala/src/stat_jsfs.cpp | 25 coala-0.2.0/coala/src/stat_mcmf.cpp |only coala-0.2.0/coala/src/stat_nucleotide_div.cpp | 5 coala-0.2.0/coala/src/unphase_segsites.cpp | 52 - coala-0.2.0/coala/tests/testthat/test-feature-mutation.R | 32 coala-0.2.0/coala/tests/testthat/test-feature-outgroup.R | 2 coala-0.2.0/coala/tests/testthat/test-feature-samples.R | 8 coala-0.2.0/coala/tests/testthat/test-feature-size-change.R | 23 coala-0.2.0/coala/tests/testthat/test-feature-unphased.R | 81 +- coala-0.2.0/coala/tests/testthat/test-locus.R | 7 coala-0.2.0/coala/tests/testthat/test-model-class.R | 50 - coala-0.2.0/coala/tests/testthat/test-model-simulation.R | 17 coala-0.2.0/coala/tests/testthat/test-parameter-zero-inflation.R | 23 coala-0.2.0/coala/tests/testthat/test-search-executables.R |only coala-0.2.0/coala/tests/testthat/test-segsites-class.R |only coala-0.2.0/coala/tests/testthat/test-simulator-class.R | 2 coala-0.2.0/coala/tests/testthat/test-simulator-ms.R | 47 - coala-0.2.0/coala/tests/testthat/test-simulator-msms.R | 54 + coala-0.2.0/coala/tests/testthat/test-simulator-scrm.R | 17 coala-0.2.0/coala/tests/testthat/test-simulator-seqgen.R | 367 ++++------ coala-0.2.0/coala/tests/testthat/test-sumstat-class.R | 44 - coala-0.2.0/coala/tests/testthat/test-sumstat-dna.R | 53 - coala-0.2.0/coala/tests/testthat/test-sumstat-fpc.R | 62 - coala-0.2.0/coala/tests/testthat/test-sumstat-iHH.R | 156 +++- coala-0.2.0/coala/tests/testthat/test-sumstat-jsfs.R | 194 +++-- coala-0.2.0/coala/tests/testthat/test-sumstat-mcmf.R |only coala-0.2.0/coala/tests/testthat/test-sumstat-omega.R |only coala-0.2.0/coala/tests/testthat/test-sumstat-segsites.R | 28 coala-0.2.0/coala/tests/testthat/test-sumstat-sfs.R | 47 - coala-0.2.0/coala/tests/testthat/test-travis-setup.R |only coala-0.2.0/coala/vignettes/coala-abc.Rmd |only coala-0.2.0/coala/vignettes/coala-extend.Rmd |only coala-0.2.0/coala/vignettes/coala-install.Rmd |only coala-0.2.0/coala/vignettes/coala-intro.Rmd |only 151 files changed, 1872 insertions(+), 1309 deletions(-)
Title: R Client for the MTurk Requester API
Description: Provides programmatic access to the Amazon Mechanical Turk (MTurk) Requester API.
Author: Thomas J. Leeper [aut, cre],
Solomon Messing [ctb],
Sean Murphy [ctb],
Jonathan Chang [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between MTurkR versions 0.6.5.1 dated 2015-05-23 and 0.6.17 dated 2015-11-11
MTurkR-0.6.17/MTurkR/DESCRIPTION | 10 - MTurkR-0.6.17/MTurkR/MD5 | 102 +++++------ MTurkR-0.6.17/MTurkR/NAMESPACE | 14 + MTurkR-0.6.17/MTurkR/NEWS | 27 ++ MTurkR-0.6.17/MTurkR/R/ApproveAllAssignments.R | 2 MTurkR-0.6.17/MTurkR/R/ApproveAssignment.R | 4 MTurkR-0.6.17/MTurkR/R/BlockWorker.R | 2 MTurkR-0.6.17/MTurkR/R/BulkCreate.R | 8 MTurkR-0.6.17/MTurkR/R/ContactWorker.R | 16 - MTurkR-0.6.17/MTurkR/R/CreateHIT.R | 17 - MTurkR-0.6.17/MTurkR/R/CreateQualificationType.R | 10 - MTurkR-0.6.17/MTurkR/R/DisableHIT.R | 5 MTurkR-0.6.17/MTurkR/R/ExtendHIT.R | 4 MTurkR-0.6.17/MTurkR/R/GenerateAnswerKey.R | 2 MTurkR-0.6.17/MTurkR/R/GenerateExternalQuestion.R | 2 MTurkR-0.6.17/MTurkR/R/GenerateHITLayoutParameter.R | 2 MTurkR-0.6.17/MTurkR/R/GenerateHTMLQuestion.R | 2 MTurkR-0.6.17/MTurkR/R/GenerateQualificationRequirement.R | 10 - MTurkR-0.6.17/MTurkR/R/GenerateReviewPolicy.R | 4 MTurkR-0.6.17/MTurkR/R/GetAssignment.R | 5 MTurkR-0.6.17/MTurkR/R/GetFileUpload.R | 4 MTurkR-0.6.17/MTurkR/R/GetHIT.R | 9 MTurkR-0.6.17/MTurkR/R/GetHITsForQualificationType.R | 3 MTurkR-0.6.17/MTurkR/R/GetReviewResultsForHIT.R | 24 +- MTurkR-0.6.17/MTurkR/R/GetReviewableHITs.R | 2 MTurkR-0.6.17/MTurkR/R/GrantBonus.R | 6 MTurkR-0.6.17/MTurkR/R/HITStatus.R | 40 ++-- MTurkR-0.6.17/MTurkR/R/RegisterHITType.R | 12 - MTurkR-0.6.17/MTurkR/R/RejectAssignment.R | 4 MTurkR-0.6.17/MTurkR/R/RejectQualification.R | 2 MTurkR-0.6.17/MTurkR/R/RevokeQualification.R | 2 MTurkR-0.6.17/MTurkR/R/SearchHITs.R | 9 MTurkR-0.6.17/MTurkR/R/SearchQualificationTypes.R | 2 MTurkR-0.6.17/MTurkR/R/SufficientFunds.R | 9 MTurkR-0.6.17/MTurkR/R/UnblockWorker.R | 2 MTurkR-0.6.17/MTurkR/R/UpdateQualificationType.R | 6 MTurkR-0.6.17/MTurkR/R/makeGETparameters.R | 2 MTurkR-0.6.17/MTurkR/R/request.R | 30 +-- MTurkR-0.6.17/MTurkR/R/wizard.R | 25 +- MTurkR-0.6.17/MTurkR/R/wizardsimple.R | 4 MTurkR-0.6.17/MTurkR/README.md | 32 ++- MTurkR-0.6.17/MTurkR/inst/templates/categorization1.xml |only MTurkR-0.6.17/MTurkR/inst/templates/htmlquestion1.xml | 3 MTurkR-0.6.17/MTurkR/inst/templates/htmlquestion2.xml | 3 MTurkR-0.6.17/MTurkR/inst/templates/htmlquestion3.xml |only MTurkR-0.6.17/MTurkR/inst/templates/sentiment1.xml |only MTurkR-0.6.17/MTurkR/inst/templates/surveylink.xml | 20 +- MTurkR-0.6.17/MTurkR/man/AccountBalance.Rd | 10 - MTurkR-0.6.17/MTurkR/man/BulkCreate.Rd | 6 MTurkR-0.6.17/MTurkR/man/GenerateHTMLQuestion.Rd | 5 MTurkR-0.6.17/MTurkR/man/GenerateQualificationRequirement.Rd | 11 - MTurkR-0.6.17/MTurkR/man/GenerateReviewPolicy.Rd | 43 +++- MTurkR-0.6.17/MTurkR/man/MTurkR-package.Rd | 12 - MTurkR-0.6.5.1/MTurkR/R/authenticate.R |only 54 files changed, 346 insertions(+), 244 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.7.2 dated 2015-10-25 and 0.7.3 dated 2015-11-11
DESCRIPTION | 9 - MD5 | 52 ++++---- NAMESPACE | 2 NEWS | 8 + inst/doc/smd.R | 6 inst/doc/smd.Rmd | 6 inst/doc/smd.html | 272 ++++++++++++++++++++++---------------------- man/CreateCatTable.Rd | 4 man/CreateContTable.Rd | 4 man/CreateTableOne.Rd | 4 man/ExtractSmd.Rd | 4 man/ShowRegTable.Rd | 4 man/print.CatTable.Rd | 4 man/print.ContTable.Rd | 4 man/print.TableOne.Rd | 4 man/print.svyCatTable.Rd | 4 man/print.svyContTable.Rd | 4 man/summary.CatTable.Rd | 4 man/summary.ContTable.Rd | 4 man/summary.TableOne.Rd | 4 man/summary.svyCatTable.Rd | 4 man/summary.svyContTable.Rd | 4 man/svyCreateCatTable.Rd | 4 man/svyCreateContTable.Rd | 4 man/svyCreateTableOne.Rd | 4 man/tableone-package.Rd | 4 vignettes/smd.Rmd | 6 27 files changed, 242 insertions(+), 195 deletions(-)
Title: Sparklines and Graphical Tables for TeX and HTML
Description: Create sparklines and graphical tables for documents and websites.
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between sparkTable versions 1.0.0 dated 2015-04-20 and 1.1.0 dated 2015-11-11
DESCRIPTION | 12 +++--- MD5 | 12 +++--- NAMESPACE | 5 ++ R/auxFunctions.r | 95 +++++++++++++++++++++++++++++++++++------------------ R/checkerplot.R | 13 ++++--- R/methods.r | 15 ++++---- man/checkerplot.Rd | 4 +- 7 files changed, 98 insertions(+), 58 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-4 dated 2015-08-25 and 1.3-0 dated 2015-11-11
DESCRIPTION | 11 - MD5 | 30 ++- NAMESPACE | 33 +--- NEWS | 9 + R/sn-funct.R | 396 ++++++++++++++++++++++++++++++++++++++++++++-------- data/ais.rda |binary data/barolo.rda |binary data/frontier.rda |binary data/wines.rda |binary inst/CITATION | 4 inst/doc |only man/dmsn.Rd | 22 +- man/dp2cp.Rd | 62 ++++---- man/dst.Rd | 6 man/profile.selm.Rd |only man/sn-package.Rd | 20 ++ man/wines.Rd | 10 - 17 files changed, 461 insertions(+), 142 deletions(-)
Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.2-2 dated 2015-10-19 and 2.2-3 dated 2015-11-11
DESCRIPTION | 8 MD5 | 12 NEWS | 771 +-- inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 136 po/R-sl.po | 9577 ++++++++++++++++++-------------------- 7 files changed, 5237 insertions(+), 5267 deletions(-)
Title: Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Description: Returns nonparametric aligned rank tests for the interaction in two-way factorial designs, on R data sets with repeated measures in 'wide' format. Five ANOVAs tables are reported. A PARAMETRIC one on the original data, one for a CHECK upon the interaction alignments, and three aligned rank tests: one on the aligned REGULAR, one on the FRIEDMAN, and one on the KOCH ranks. In these rank tests, only the resulting values for the interaction are relevant.
Author: Jos Feys
Maintainer: Jos Feys <jos.feys@faber.kuleuven.be>
Diff between npIntFactRep versions 1.3 dated 2015-09-28 and 1.4 dated 2015-11-11
DESCRIPTION | 10 - MD5 | 6 - R/npIntFactRep.R | 310 ++++++++++++++++++++++++++-------------------------- man/npIntFactRep.Rd | 37 ++---- 4 files changed, 179 insertions(+), 184 deletions(-)
Title: A Few GPU Enabled Functions
Description: Provides R interfaces to a handful of common
functions implemented using the Nvidia CUDA toolkit. Some of the
functions require at least GPU Compute Capability 1.3.
Thanks to Craig Stark at UC Irvine for donating time on his lab's Mac.
Author: Josh Buckner [aut, cre],
Mark Seligman [aut],
Justin Wilson [ctb]
Maintainer: Josh Buckner <nullsatz@gmail.com>
Diff between gputools versions 0.28 dated 2013-05-09 and 1.0 dated 2015-11-11
gputools-0.28/gputools/src/Makefile |only gputools-0.28/gputools/src/config.mk |only gputools-1.0/gputools/DESCRIPTION | 29 ++-- gputools-1.0/gputools/INSTALL | 34 ++--- gputools-1.0/gputools/MD5 | 34 +++-- gputools-1.0/gputools/NAMESPACE | 13 ++ gputools-1.0/gputools/NEWS | 3 gputools-1.0/gputools/R/gpuMatMult.R | 2 gputools-1.0/gputools/cleanup | 1 gputools-1.0/gputools/configure |only gputools-1.0/gputools/configure.ac |only gputools-1.0/gputools/man/gpuLsfit.Rd | 6 gputools-1.0/gputools/src/Makefile.in |only gputools-1.0/gputools/src/cuseful.cu | 22 --- gputools-1.0/gputools/src/cuseful.h | 5 gputools-1.0/gputools/src/matmult.cu | 197 ++++++++++++-------------------- gputools-1.0/gputools/src/matmult.h | 1 gputools-1.0/gputools/src/rinterface.cu | 1 gputools-1.0/gputools/tools |only 19 files changed, 155 insertions(+), 193 deletions(-)
Title: Fit the GamBin Model to Species Abundance Distributions
Description: Fits the gambin distribution to species-abundance distributions from
ecological data. 'gambin' is short for 'gamma-binomial'. The main function is
fitGambin, which estimates the 'alpha' parameter of the gambin distribution using
maximum likelihood. Functions are also provided to generate the gambin distribution
and for calculating likelihood statistics.
Author: Michael Krabbe Borregaard, Thomas Matthews & Karl Ugland
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between gambin versions 1.1 dated 2014-05-17 and 1.3 dated 2015-11-11
DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/dgambin.R | 28 ++++++++++------------------ inst/CITATION | 14 +++++++------- man/dgambin.Rd | 4 ++-- man/fitGambin.Rd | 4 ++-- man/gambin-package.Rd | 6 +++--- 8 files changed, 42 insertions(+), 49 deletions(-)
Title: Augments the Use of 'Asreml' in Fitting Mixed Models
Description: Assists in automating the testing of terms in mixed models when 'asreml' is used
to fit the models. The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the
fitting of a sequence of models is kept in a data frame. Procedures are available for choosing
models that conform to the hierarchy or marginality principle and for displaying predictions
for significant terms in tables and graphs. The package 'asreml' provides a computationally
efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It can be
purchased from 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R', who will supply a zip file for
local installation/updating.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between asremlPlus versions 2.0-2 dated 2015-10-29 and 2.0-3 dated 2015-11-11
asremlPlus-2.0-2/asremlPlus/R/reml.v19.r |only asremlPlus-2.0-3/asremlPlus/DESCRIPTION | 8 +++---- asremlPlus-2.0-3/asremlPlus/MD5 | 14 ++++++------- asremlPlus-2.0-3/asremlPlus/R/reml.v20.r |only asremlPlus-2.0-3/asremlPlus/build/partial.rdb |binary asremlPlus-2.0-3/asremlPlus/inst/NEWS.Rd | 5 ++++ asremlPlus-2.0-3/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-2.0-3/asremlPlus/man/pred.present.asreml.Rd | 2 - asremlPlus-2.0-3/asremlPlus/man/predictionplot.asreml.Rd | 2 - 9 files changed, 18 insertions(+), 13 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical workflow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did use in their own research and might not themselves support.
These include bootstrapping, jackknifing, and reweighting of data, and in
particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 4.2-1 dated 2013-09-21 and 5.0-7 dated 2015-11-10
Zelig-4.2-1/Zelig/CHANGES |only Zelig-4.2-1/Zelig/COPYING |only Zelig-4.2-1/Zelig/NEWS |only Zelig-4.2-1/Zelig/R/GetObject.R |only Zelig-4.2-1/Zelig/R/GetSlot.R |only Zelig-4.2-1/Zelig/R/GetSlot.zelig.R |only Zelig-4.2-1/Zelig/R/MCMChook.R |only Zelig-4.2-1/Zelig/R/MLutils.R |only Zelig-4.2-1/Zelig/R/Zelig-package.R |only Zelig-4.2-1/Zelig/R/as.dataframe.setx.R |only Zelig-4.2-1/Zelig/R/as.matrix.pooled.setx.R |only Zelig-4.2-1/Zelig/R/as.matrix.setx.R |only Zelig-4.2-1/Zelig/R/as.parameters.R |only Zelig-4.2-1/Zelig/R/as.qi.R |only Zelig-4.2-1/Zelig/R/as.summarized.R |only Zelig-4.2-1/Zelig/R/as.summarized.list.R |only Zelig-4.2-1/Zelig/R/attach.env.R |only Zelig-4.2-1/Zelig/R/bootfn.default.R |only Zelig-4.2-1/Zelig/R/bootstrap.R |only Zelig-4.2-1/Zelig/R/bootstrap.gamma.R |only Zelig-4.2-1/Zelig/R/bootstrap.negbinom.R |only Zelig-4.2-1/Zelig/R/bootstrap.normal.R |only Zelig-4.2-1/Zelig/R/callToString.R |only Zelig-4.2-1/Zelig/R/cluster.formula.R |only Zelig-4.2-1/Zelig/R/cmvglm.R |only Zelig-4.2-1/Zelig/R/common-methods.R |only Zelig-4.2-1/Zelig/R/describe.R |only Zelig-4.2-1/Zelig/R/describe.default.R |only Zelig-4.2-1/Zelig/R/describe.zelig.R |only Zelig-4.2-1/Zelig/R/description.R |only Zelig-4.2-1/Zelig/R/exp.R |only Zelig-4.2-1/Zelig/R/factor.bayes.R |only Zelig-4.2-1/Zelig/R/gamma.R |only Zelig-4.2-1/Zelig/R/gamma.gee.R |only Zelig-4.2-1/Zelig/R/gamma.survey.R |only Zelig-4.2-1/Zelig/R/get.package.R |only Zelig-4.2-1/Zelig/R/getPredictorTerms.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.formula.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.list.R |only Zelig-4.2-1/Zelig/R/help.zelig.R |only Zelig-4.2-1/Zelig/R/ignore.R |only Zelig-4.2-1/Zelig/R/is.formula.R |only Zelig-4.2-1/Zelig/R/list.depth.R |only Zelig-4.2-1/Zelig/R/logit.R |only Zelig-4.2-1/Zelig/R/logit.bayes.R |only Zelig-4.2-1/Zelig/R/logit.gee.R |only Zelig-4.2-1/Zelig/R/logit.survey.R |only Zelig-4.2-1/Zelig/R/lognorm.R |only Zelig-4.2-1/Zelig/R/ls.R |only Zelig-4.2-1/Zelig/R/make.parameters.R |only Zelig-4.2-1/Zelig/R/makeModelMatrix.R |only Zelig-4.2-1/Zelig/R/mi.R |only Zelig-4.2-1/Zelig/R/mlogit.bayes.R |only Zelig-4.2-1/Zelig/R/model.frame.multiple.R |only Zelig-4.2-1/Zelig/R/model.matrix.multiple.R |only Zelig-4.2-1/Zelig/R/model.matrix.parseFormula.R |only Zelig-4.2-1/Zelig/R/model.warnings.R |only Zelig-4.2-1/Zelig/R/multi.dataset.R |only Zelig-4.2-1/Zelig/R/multipleUtil.R |only Zelig-4.2-1/Zelig/R/names.relogit.R |only Zelig-4.2-1/Zelig/R/negbinom.R |only Zelig-4.2-1/Zelig/R/normal.R |only Zelig-4.2-1/Zelig/R/normal.bayes.R |only Zelig-4.2-1/Zelig/R/normal.gee.R |only Zelig-4.2-1/Zelig/R/normal.survey.R |only Zelig-4.2-1/Zelig/R/oprobit.bayes.R |only Zelig-4.2-1/Zelig/R/param.R |only Zelig-4.2-1/Zelig/R/parameters.R |only Zelig-4.2-1/Zelig/R/parse.formula.R |only Zelig-4.2-1/Zelig/R/parseFormula.R |only Zelig-4.2-1/Zelig/R/poisson.R |only Zelig-4.2-1/Zelig/R/poisson.bayes.R |only Zelig-4.2-1/Zelig/R/poisson.gee.R |only Zelig-4.2-1/Zelig/R/poisson.survey.R |only Zelig-4.2-1/Zelig/R/print.R |only Zelig-4.2-1/Zelig/R/probit.R |only Zelig-4.2-1/Zelig/R/probit.bayes.R |only Zelig-4.2-1/Zelig/R/probit.gee.R |only Zelig-4.2-1/Zelig/R/probit.survey.R |only Zelig-4.2-1/Zelig/R/qi.R |only Zelig-4.2-1/Zelig/R/qi.summarized.R |only Zelig-4.2-1/Zelig/R/relogit.R |only Zelig-4.2-1/Zelig/R/repl.R |only Zelig-4.2-1/Zelig/R/robust.glm.hook.R |only Zelig-4.2-1/Zelig/R/robust.hook.R |only Zelig-4.2-1/Zelig/R/setx.R |only Zelig-4.2-1/Zelig/R/sim.MI.R |only Zelig-4.2-1/Zelig/R/sim.R |only Zelig-4.2-1/Zelig/R/sim.default.R |only Zelig-4.2-1/Zelig/R/simulation.matrix.R |only Zelig-4.2-1/Zelig/R/simulations.plot.R |only Zelig-4.2-1/Zelig/R/summarize.R |only Zelig-4.2-1/Zelig/R/summary.R |only Zelig-4.2-1/Zelig/R/t.setx.R |only Zelig-4.2-1/Zelig/R/terms.R |only Zelig-4.2-1/Zelig/R/termsFromFormula.R |only Zelig-4.2-1/Zelig/R/tobit.R |only Zelig-4.2-1/Zelig/R/twosls.R |only Zelig-4.2-1/Zelig/R/user.prompt.R |only Zelig-4.2-1/Zelig/R/vcov.R |only Zelig-4.2-1/Zelig/R/z.R |only Zelig-4.2-1/Zelig/R/zelig.R |only Zelig-4.2-1/Zelig/R/zelig.skeleton.R |only Zelig-4.2-1/Zelig/R/zelig2.R |only Zelig-4.2-1/Zelig/R/zeligBuildWeights.R |only Zelig-4.2-1/Zelig/R/zzz.R |only Zelig-4.2-1/Zelig/README |only Zelig-4.2-1/Zelig/build |only Zelig-4.2-1/Zelig/data/PErisk.txt.bz2 |only Zelig-4.2-1/Zelig/data/approval.tab.bz2 |only Zelig-4.2-1/Zelig/data/bivariate.tab.bz2 |only Zelig-4.2-1/Zelig/data/coalition.tab.xz |only Zelig-4.2-1/Zelig/data/coalition2.txt.xz |only Zelig-4.2-1/Zelig/data/free1.tab.bz2 |only Zelig-4.2-1/Zelig/data/free2.tab.bz2 |only Zelig-4.2-1/Zelig/data/homerun.txt.xz |only Zelig-4.2-1/Zelig/data/immi1.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi2.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi3.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi4.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi5.tab.bz2 |only Zelig-4.2-1/Zelig/data/immigration.tab.bz2 |only Zelig-4.2-1/Zelig/data/macro.tab.xz |only Zelig-4.2-1/Zelig/data/mexico.tab.bz2 |only Zelig-4.2-1/Zelig/data/mid.tab.bz2 |only Zelig-4.2-1/Zelig/data/newpainters.txt.bz2 |only Zelig-4.2-1/Zelig/data/sanction.tab.bz2 |only Zelig-4.2-1/Zelig/data/swiss.txt.bz2 |only Zelig-4.2-1/Zelig/data/turnout.tab.bz2 |only Zelig-4.2-1/Zelig/data/voteincome.txt.bz2 |only Zelig-4.2-1/Zelig/demo/Zelig.HelloWorld.R |only Zelig-4.2-1/Zelig/demo/exp.R |only Zelig-4.2-1/Zelig/demo/factor.bayes.R |only Zelig-4.2-1/Zelig/demo/gamma.R |only Zelig-4.2-1/Zelig/demo/gamma.gee.R |only Zelig-4.2-1/Zelig/demo/gamma.survey.R |only Zelig-4.2-1/Zelig/demo/logit.R |only Zelig-4.2-1/Zelig/demo/logit.bayes.R |only Zelig-4.2-1/Zelig/demo/logit.gee.R |only Zelig-4.2-1/Zelig/demo/logit.survey.R |only Zelig-4.2-1/Zelig/demo/lognorm.R |only Zelig-4.2-1/Zelig/demo/ls.R |only Zelig-4.2-1/Zelig/demo/mi.R |only Zelig-4.2-1/Zelig/demo/mlogit.bayes.R |only Zelig-4.2-1/Zelig/demo/negbinom.R |only Zelig-4.2-1/Zelig/demo/normal.R |only Zelig-4.2-1/Zelig/demo/normal.bayes.R 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Zelig-5.0-7/Zelig/data/mid.tab.gz |only Zelig-5.0-7/Zelig/data/newpainters.txt.gz |only Zelig-5.0-7/Zelig/data/sanction.tab.gz |only Zelig-5.0-7/Zelig/data/sna.ex.RData |binary Zelig-5.0-7/Zelig/data/swiss.txt.gz |only Zelig-5.0-7/Zelig/data/turnout.tab.gz |only Zelig-5.0-7/Zelig/data/voteincome.txt.gz |only Zelig-5.0-7/Zelig/demo/00Index | 72 Zelig-5.0-7/Zelig/demo/demo-amelia.R |only Zelig-5.0-7/Zelig/demo/demo-data-table.R |only Zelig-5.0-7/Zelig/demo/demo-dplyr.R |only Zelig-5.0-7/Zelig/demo/demo-exp.R |only Zelig-5.0-7/Zelig/demo/demo-factor-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-feedback.R |only Zelig-5.0-7/Zelig/demo/demo-gamma-gee.R |only Zelig-5.0-7/Zelig/demo/demo-gamma.R |only Zelig-5.0-7/Zelig/demo/demo-json.R |only Zelig-5.0-7/Zelig/demo/demo-logit-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-logit-gee.R |only Zelig-5.0-7/Zelig/demo/demo-logit.R |only Zelig-5.0-7/Zelig/demo/demo-lognorm.R |only Zelig-5.0-7/Zelig/demo/demo-ls.R |only Zelig-5.0-7/Zelig/demo/demo-mlogit-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-negbinom.R |only Zelig-5.0-7/Zelig/demo/demo-normal-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-normal-gee.R |only Zelig-5.0-7/Zelig/demo/demo-normal.R |only Zelig-5.0-7/Zelig/demo/demo-oprobit-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-poisson-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-poisson-gee.R |only Zelig-5.0-7/Zelig/demo/demo-poisson.R |only Zelig-5.0-7/Zelig/demo/demo-probit-bayes.R |only Zelig-5.0-7/Zelig/demo/demo-probit-gee.R |only Zelig-5.0-7/Zelig/demo/demo-probit.R |only Zelig-5.0-7/Zelig/demo/demo-quantile.R |only Zelig-5.0-7/Zelig/demo/demo-range.R |only Zelig-5.0-7/Zelig/demo/demo-relogit.R |only Zelig-5.0-7/Zelig/demo/demo-roc.R |only Zelig-5.0-7/Zelig/demo/demo-scope.R |only Zelig-5.0-7/Zelig/demo/demo-setx-2.R |only Zelig-5.0-7/Zelig/demo/demo-setx.R |only Zelig-5.0-7/Zelig/demo/demo-show.R |only Zelig-5.0-7/Zelig/demo/demo-signif-stars.R |only Zelig-5.0-7/Zelig/demo/demo-strata.R |only Zelig-5.0-7/Zelig/demo/demo-tobit.R |only Zelig-5.0-7/Zelig/demo/demo-tobitbayes.R |only Zelig-5.0-7/Zelig/demo/demo-weibull.R |only Zelig-5.0-7/Zelig/demo/demo-wrappers.R |only Zelig-5.0-7/Zelig/demo/demo-zip.R |only Zelig-5.0-7/Zelig/inst/CITATION |only Zelig-5.0-7/Zelig/inst/JSON |only Zelig-5.0-7/Zelig/man/Median.Rd | 14 Zelig-5.0-7/Zelig/man/Mode.Rd | 14 Zelig-5.0-7/Zelig/man/Zelig-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-binchoice-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-binchoice-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-exp-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-factor-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-gamma-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-gamma-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-glm-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-logit-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-logit-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-logit-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-lognorm-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-ls-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-mlogit-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-negbin-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-normal-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-normal-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-normal-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-oprobit-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-poisson-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-poisson-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-poisson-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-probit-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-probit-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-probit-gee-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-quantile-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-relogit-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-tobit-bayes-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-tobit-class.Rd |only Zelig-5.0-7/Zelig/man/Zelig-weibull-class.Rd |only Zelig-5.0-7/Zelig/man/avg.Rd |only Zelig-5.0-7/Zelig/man/ci.plot.Rd |only Zelig-5.0-7/Zelig/man/cluster.formula.Rd | 16 Zelig-5.0-7/Zelig/man/createJSON.Rd |only Zelig-5.0-7/Zelig/man/mid.Rd | 3 Zelig-5.0-7/Zelig/man/qi.plot.Rd |only Zelig-5.0-7/Zelig/man/reduce.Rd |only Zelig-5.0-7/Zelig/man/relogit.Rd | 27 Zelig-5.0-7/Zelig/man/rocplot.Rd | 99 Zelig-5.0-7/Zelig/man/setfactor.Rd |only Zelig-5.0-7/Zelig/man/setval.Rd |only Zelig-5.0-7/Zelig/man/setx.Rd | 71 Zelig-5.0-7/Zelig/man/sim.Rd | 189 - Zelig-5.0-7/Zelig/man/simulations.plot.Rd | 48 Zelig-5.0-7/Zelig/man/stat.Rd |only Zelig-5.0-7/Zelig/man/statlevel.Rd |only Zelig-5.0-7/Zelig/man/statmat.Rd |only Zelig-5.0-7/Zelig/man/table.levels.Rd | 25 Zelig-5.0-7/Zelig/man/zelig.Rd | 104 Zelig-5.0-7/Zelig/man/zeligPlyrMutate.Rd |only Zelig-5.0-7/Zelig/tests/test-all.R |only Zelig-5.0-7/Zelig/tests/testthat |only 523 files changed, 1177 insertions(+), 1772 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen, Chuan Hong, Haitao Chu
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.0-1 dated 2015-10-12 and 1.0-2 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++++++++--------- NAMESPACE | 5 ++++- R/galaxy.R | 7 +++---- R/mmeta.R | 43 +++++++++++++++++++++++++------------------ R/mpbt.R | 7 +++++-- R/summary.galaxy.R |only R/summary.mmeta.R |only R/summary.mpbt.R |only data |only man/ca125.Rd |only man/galaxy.Rd | 18 +++++------------- man/mmeta.Rd | 27 +++++++++++++-------------- man/mpbt.Rd | 16 +++------------- man/nat2.Rd |only man/prostate.Rd |only man/summary.galaxy.rd |only man/summary.mmeta.rd |only man/summary.mpbt.rd |only man/xmeta-package.Rd | 4 ++-- 20 files changed, 85 insertions(+), 80 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.20 dated 2015-11-05 and 0.5.21 dated 2015-11-10
DESCRIPTION | 8 - MD5 | 22 +-- R/vtreat.R | 33 ++--- README.md | 2 build/vignette.rds |binary inst/doc/vtreat.html | 272 ++++++++++++++++++++++---------------------- inst/doc/vtreatOverfit.R | 5 inst/doc/vtreatOverfit.Rmd | 7 - inst/doc/vtreatOverfit.html | 162 +++++++++++--------------- man/designTreatmentsC.Rd | 7 - man/designTreatmentsN.Rd | 7 - man/vtreat-package.Rd | 4 12 files changed, 253 insertions(+), 276 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.1 dated 2015-09-28 and 0.6.2 dated 2015-11-10
DESCRIPTION | 10 ++- MD5 | 61 ++++++++++++-------- NAMESPACE | 2 NEWS | 20 ++++++ R/classify.R | 12 +++- R/crossv.R |only R/delete.markup.R | 111 +++++++++++++++++++++++++------------- R/delete.stop.words.R | 37 ++++++++---- R/gui.classify.R | 7 +- R/gui.oppose.R | 1 R/gui.stylo.R | 4 - R/make.frequency.list.R | 2 R/make.frequency.list.optimized.R |only R/make.ngrams.R | 25 +++++++- R/make.samples.R | 1 R/make.table.of.frequencies.R | 40 ++++++++----- R/oppose.R | 38 ++++++++----- R/parse.corpus.R |only R/perform.nsc.R | 10 +-- R/perform.svm.R | 5 - R/rolling.classify.r | 4 - R/rolling.delta.R | 7 +- R/stylo.R | 86 +++++++++++++++++------------ R/stylo.default.settings.R | 16 +++-- R/txt.to.features.R | 38 +++++++++++-- R/txt.to.words.R | 38 ++++++++++++- R/txt.to.words.ext.R | 44 +++++++++++++-- data |only man/galbraith.Rd |only man/lee.Rd |only man/make.frequency.list.Rd | 2 man/novels.Rd |only man/parse.corpus.Rd |only man/perform.nsc.Rd | 10 +++ 34 files changed, 444 insertions(+), 187 deletions(-)
Title: Transmission Ratio Distortion
Description: Transmission Ratio Distortion (TRD) is a genetic phenomenon where the two alleles from either parent are not transmitted to the offspring at the expected 1:1 ratio under Mendelian inheritance, leading to spurious signals in genetic association studies. Functions in this package are developed to account for this phenomenon using loglinear model and Transmission Disequilibrium Test (TDT). Some population information can also be calculated.
Author: Lam Opal Huang
Maintainer: Lam Opal Huang <opal.huang@mail.mcgill.ca>
Diff between TRD versions 1.0 dated 2015-01-21 and 1.1 dated 2015-11-10
TRD-1.0/TRD/R/findr.R |only TRD-1.0/TRD/man/findr.Rd |only TRD-1.0/TRD/man/tdt.cnt.Rd |only TRD-1.1/TRD/DESCRIPTION | 12 +- TRD-1.1/TRD/MD5 | 46 ++++---- TRD-1.1/TRD/NAMESPACE | 7 - TRD-1.1/TRD/R/find.maf.R | 214 +++++++++++++++++++++++++++----------- TRD-1.1/TRD/R/find.t.R |only TRD-1.1/TRD/R/gcount.R | 134 ++++++++++++++++++++--- TRD-1.1/TRD/R/ll.R | 43 ++++++- TRD-1.1/TRD/R/ll.domi.R |only TRD-1.1/TRD/R/ll.gdi.R |only TRD-1.1/TRD/R/ll.grri.R |only TRD-1.1/TRD/R/out.stats.R | 229 +++++++++++++++++++++++++++++------------ TRD-1.1/TRD/R/prev.R | 48 +++++--- TRD-1.1/TRD/R/rtrios.R | 90 +++++++++++----- TRD-1.1/TRD/R/strata.cnt.R | 92 ++++++++++------ TRD-1.1/TRD/R/tdt.R | 67 ++++++++--- TRD-1.1/TRD/R/tdt.cnt.R | 49 ++++++-- TRD-1.1/TRD/man/TRD-package.Rd | 28 +++-- TRD-1.1/TRD/man/find.maf.Rd | 50 ++------ TRD-1.1/TRD/man/find.t.Rd |only TRD-1.1/TRD/man/gcount.Rd | 46 ++------ TRD-1.1/TRD/man/ll.Rd | 53 ++++----- TRD-1.1/TRD/man/prev.Rd | 43 +------ TRD-1.1/TRD/man/rtrios.Rd | 53 +++------ TRD-1.1/TRD/man/strata.cnt.Rd | 53 +++------ TRD-1.1/TRD/man/tdt.Rd | 47 ++------ 28 files changed, 857 insertions(+), 547 deletions(-)
Title: In-Source Documentation for R
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 5.0.0 dated 2015-10-28 and 5.0.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/object-from-call.R | 4 ++-- R/parse-preref.R | 8 ++++++-- R/roclet-rd.R | 2 +- R/roxygenize.R | 2 +- R/tag-registry.R | 2 +- build/vignette.rds |binary inst/doc/collate.html | 4 ++-- inst/doc/formatting.html | 4 ++-- inst/doc/namespace.html | 4 ++-- inst/doc/rd.html | 4 ++-- inst/doc/rdkeywords.html | 4 ++-- inst/doc/roxygen2.html | 4 ++-- tests/testthat/test-namespace.R | 12 ++++++++++++ tests/testthat/test-package-doc.R | 2 -- 16 files changed, 54 insertions(+), 40 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for
quickly placing data summaries and formatted regression results into .Rnw or
.Rmd files. Functions for generating commonly used graphics, such as receiver
operating curves or Bland-Altman plots, are also provided by 'qwraps2'.
'qwraps2' is a updated version of a package 'qwraps'. The original version
'qwraps' was never submitted to CRAN but can be found at
https://github.com/dewittpe/qwraps. The implementation and limited scope of the
functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally
different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.1.1 dated 2015-04-20 and 0.1.2 dated 2015-11-10
DESCRIPTION | 17 +++++++---- MD5 | 42 +++++++++++++++------------ NAMESPACE | 19 +++++++++++- R/confusion_matrix.R |only R/extract.R | 2 - R/mean_sd.R | 2 - R/median_iqr.R |only R/n_perc.R | 63 ++++++++++++++++++++++++++++++++++++++++- R/qable.R |only R/qkmplot.R | 73 ++++++++++++++++++++++++++++++++++++++++++++++-- R/qroc.R | 2 - README.md | 10 +++++- man/confusion_matrix.Rd |only man/extract.Rd | 2 - man/frmt.Rd | 2 - man/frmtp.Rd | 2 - man/mean_sd.Rd | 2 - man/median_iqr.Rd |only man/n_perc.Rd | 21 +++++++++++++ man/qable.Rd |only man/qacf.Rd | 2 - man/qblandaltman.Rd | 2 - man/qkmplot.Rd | 16 +++++++++- man/qroc.Rd | 2 - man/qwraps2.Rd | 2 - 25 files changed, 237 insertions(+), 46 deletions(-)
Title: Taxonomic Monographs Tools
Description: Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology charts and distributional and diversity maps are also available.
Author: Marcelo Reginato
Maintainer: Marcelo Reginato <reginatobio@yahoo.com.br>
Diff between monographaR versions 1.0 dated 2015-09-07 and 1.01 dated 2015-11-10
monographaR-1.0/monographaR/R/monographaR-package.r |only monographaR-1.01/monographaR/DESCRIPTION | 12 monographaR-1.01/monographaR/MD5 | 48 +- monographaR-1.01/monographaR/NAMESPACE | 16 monographaR-1.01/monographaR/R/buildMonograph.R |only monographaR-1.01/monographaR/R/collectorList.R | 9 monographaR-1.01/monographaR/R/collectorList2.R |only monographaR-1.01/monographaR/R/examinedSpecimens.R | 4 monographaR-1.01/monographaR/R/examinedSpecimens2.R |only monographaR-1.01/monographaR/R/mapBatch.R | 177 ++++++--- monographaR-1.01/monographaR/R/mapDiversity.R | 7 monographaR-1.01/monographaR/R/mapTable.R | 4 monographaR-1.01/monographaR/R/monographaR-internal.R | 251 ++++++------- monographaR-1.01/monographaR/R/phenoHist.R | 4 monographaR-1.01/monographaR/R/tableToDescription.R | 5 monographaR-1.01/monographaR/R/tableToDescription2.R |only monographaR-1.01/monographaR/data/monographaR_examples.rda |binary monographaR-1.01/monographaR/inst/CITATION | 4 monographaR-1.01/monographaR/inst/doc/tutorial.R | 73 ++- monographaR-1.01/monographaR/inst/doc/tutorial.Rmd | 127 ++++-- monographaR-1.01/monographaR/inst/doc/tutorial.html | 136 ++++--- monographaR-1.01/monographaR/man/buildMonograph.Rd |only monographaR-1.01/monographaR/man/collectorList.Rd | 116 +++--- monographaR-1.01/monographaR/man/mapBatch.Rd | 103 +++-- monographaR-1.01/monographaR/man/monographaR-package.Rd | 14 monographaR-1.01/monographaR/man/monographaR_examples.Rd | 3 monographaR-1.01/monographaR/man/phenoHist.Rd | 222 +++++------ monographaR-1.01/monographaR/vignettes/tutorial.Rmd | 127 ++++-- 28 files changed, 878 insertions(+), 584 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>
Diff between MicSim versions 1.0.9 dated 2015-07-24 and 1.0.10 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/micSim.r | 22 +++++++++++++++++----- inst/NEWS.Rd | 13 ++++++++++--- man/MicSim-package.Rd | 8 ++++---- 5 files changed, 39 insertions(+), 20 deletions(-)
Title: Convert GBM Object Trees to SAS Code
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
Author: John R. Dixon
Maintainer: John R. Dixon <gbm2sas@gmail.com>
Diff between gbm2sas versions 2.0 dated 2015-11-08 and 2.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/gbm2sas.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp <bbnkmp@gmail.com>
Diff between DoseFinding versions 0.9-12 dated 2014-09-28 and 0.9-13 dated 2015-11-10
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NAMESPACE | 9 ++++++++- R/MCTtest.R | 8 +++++--- R/bFitMod.R | 33 ++++++++++++++++++--------------- R/qmvtDF.R |only man/DoseFinding-package.Rd | 10 ++-------- src/Makevars | 2 +- 9 files changed, 55 insertions(+), 40 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Efficient statistical testing and scalable visualization of intersections among multiple sets.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 0.99.1 dated 2015-11-09 and 0.99.2 dated 2015-11-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/set_html.html | 4 ++-- src/dmvhyper.c | 3 +-- src/dmvhyperLog.c | 9 +-------- 5 files changed, 11 insertions(+), 19 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Software Tools for the Statistical Analysis of Network Data
Description: An integrated set of tools for the representation, visualization, analysis, and simulation of network data. For an introduction, type help(package='statnet').
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut],
Martina Morris [aut, cre]
Maintainer: Martina Morris <morrism@u.washington.edu>
Diff between statnet versions 2015.6.2 dated 2015-07-18 and 2015.11.0 dated 2015-11-10
DESCRIPTION | 20 +-- MD5 | 4 man/statnet-package.Rd | 302 +++++++++++++++++++------------------------------ 3 files changed, 134 insertions(+), 192 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and
symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.2.2 dated 2015-09-24 and 0.2.3 dated 2015-11-10
DESCRIPTION | 18 MD5 | 87 NAMESPACE | 3 R/GuanTestGrid.R | 12 R/GuanTestGrid_help.R | 46 R/GuanTestUnif.R | 36 R/GuanTestUnif_help.R | 46 R/LuTest.R | 8 R/LuTest_help.R | 21 R/MaityTest.R | 10 R/MaityTest_help.R | 40 R/coords_aniso.R | 2 R/htestIso_class.R |only build/vignette.rds |binary inst/doc/spTest-vig.R | 8 inst/doc/spTest-vig.pdf |binary inst/doc/spTest-vig.rnw | 8 man/GuanTestGrid.Rd | 8 man/GuanTestUnif.Rd | 34 man/LuTest.Rd | 4 man/MaityTest.Rd | 8 man/WRFG.Rd | 8 man/coords.aniso.Rd | 12 man/htestIso-class.Rd |only man/print.htestIso.Rd |only man/spTest.Rd | 6 vignettes/figures/fig-dirsemi1-eps-converted-to.pdf |binary vignettes/figures/fig-dsvar2-eps-converted-to.pdf |binary vignettes/figures/fig-elev-eps-converted-to.pdf |binary vignettes/figures/fig-elev.eps | 735 vignettes/figures/fig-grid-eps-converted-to.pdf |binary vignettes/figures/fig-grid.eps | 686 vignettes/figures/fig-heatmap1-eps-converted-to.pdf |binary vignettes/figures/fig-heatmap1.eps | 146 vignettes/figures/fig-iso2-eps-converted-to.pdf |binary vignettes/figures/fig-iso2.eps | 125 vignettes/figures/fig-narccap-eps-converted-to.pdf |binary vignettes/figures/fig-narccap.eps |16095 +++++++++----------- vignettes/figures/fig-narccap2-eps-converted-to.pdf |binary vignettes/figures/fig-narccap2.eps | 5414 +++--- vignettes/figures/fig-precipdv-eps-converted-to.pdf |binary vignettes/figures/fig-rain-eps-converted-to.pdf |binary vignettes/figures/fig-rain.eps | 785 vignettes/figures/fig-rain1-eps-converted-to.pdf |binary vignettes/figures/fig-rain2-eps-converted-to.pdf |binary vignettes/spTest-vig.rnw | 8 46 files changed, 11525 insertions(+), 12894 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.5 dated 2015-07-07 and 1.3.6 dated 2015-11-10
Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_ceemdan.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_eemd.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_emd.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_emd_num_imfs.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_extrema.R |only Rlibeemd-1.3.6/Rlibeemd/DESCRIPTION | 9 +- Rlibeemd-1.3.6/Rlibeemd/MD5 | 30 +++---- Rlibeemd-1.3.6/Rlibeemd/R/ceemdan.R | 31 +++++-- Rlibeemd-1.3.6/Rlibeemd/R/ecg.R | 32 +++---- Rlibeemd-1.3.6/Rlibeemd/R/eemd.R | 26 ++++-- Rlibeemd-1.3.6/Rlibeemd/R/emd.R | 15 ++- Rlibeemd-1.3.6/Rlibeemd/R/emd_num_imfs.R | 2 Rlibeemd-1.3.6/Rlibeemd/configure.ac | 54 ++++++------- Rlibeemd-1.3.6/Rlibeemd/man/nIMFs.Rd | 2 Rlibeemd-1.3.6/Rlibeemd/src/eemdR.cpp | 3 Rlibeemd-1.3.6/Rlibeemd/tests/test-all.R | 4 Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-ceemdan.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-eemd.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-emd.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-emd_num_imfs.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-extrema.R |only 21 files changed, 122 insertions(+), 86 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to http://www.sealifebase.org data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.3 dated 2015-09-09 and 2.1.0 dated 2015-11-10
rfishbase-2.0.3/rfishbase/inst/doc/tutorial.R |only rfishbase-2.1.0/rfishbase/DESCRIPTION | 17 - rfishbase-2.1.0/rfishbase/MD5 | 134 ++++++------ rfishbase-2.1.0/rfishbase/NAMESPACE | 16 + rfishbase-2.1.0/rfishbase/NEWS | 6 rfishbase-2.1.0/rfishbase/R/00-endpoint.R | 20 + rfishbase-2.1.0/rfishbase/R/check_and_parse.R | 2 rfishbase-2.1.0/rfishbase/R/common_names.R | 17 - rfishbase-2.1.0/rfishbase/R/distribution.R | 14 - rfishbase-2.1.0/rfishbase/R/docs.R | 1 rfishbase-2.1.0/rfishbase/R/fishbase.R | 6 rfishbase-2.1.0/rfishbase/R/heartbeat.R | 6 rfishbase-2.1.0/rfishbase/R/list_fields.R | 4 rfishbase-2.1.0/rfishbase/R/species.R | 7 rfishbase-2.1.0/rfishbase/R/species_list.R | 9 rfishbase-2.1.0/rfishbase/R/species_names.R | 4 rfishbase-2.1.0/rfishbase/R/synonyms.R | 9 rfishbase-2.1.0/rfishbase/R/trophic_ecology.R | 1 rfishbase-2.1.0/rfishbase/build/vignette.rds |binary rfishbase-2.1.0/rfishbase/data/datalist |only rfishbase-2.1.0/rfishbase/data/sealifebase.rda |binary rfishbase-2.1.0/rfishbase/inst/doc/tutorial.Rmd | 128 ----------- rfishbase-2.1.0/rfishbase/inst/doc/tutorial.html | 133 ----------- rfishbase-2.1.0/rfishbase/man/common_names.Rd | 4 rfishbase-2.1.0/rfishbase/man/common_to_sci.Rd | 6 rfishbase-2.1.0/rfishbase/man/diet.Rd | 2 rfishbase-2.1.0/rfishbase/man/distribution.Rd | 2 rfishbase-2.1.0/rfishbase/man/docs.Rd | 6 rfishbase-2.1.0/rfishbase/man/ecology.Rd | 2 rfishbase-2.1.0/rfishbase/man/ecosystem.Rd | 2 rfishbase-2.1.0/rfishbase/man/faoareas.Rd | 2 rfishbase-2.1.0/rfishbase/man/fecundity.Rd | 2 rfishbase-2.1.0/rfishbase/man/fishbase.Rd | 2 rfishbase-2.1.0/rfishbase/man/fooditems.Rd | 2 rfishbase-2.1.0/rfishbase/man/heartbeat.Rd | 2 rfishbase-2.1.0/rfishbase/man/introductions.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_freq.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_length.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_weight.Rd | 12 - rfishbase-2.1.0/rfishbase/man/list_fields.Rd | 2 rfishbase-2.1.0/rfishbase/man/load_taxa.Rd | 4 rfishbase-2.1.0/rfishbase/man/maturity.Rd | 2 rfishbase-2.1.0/rfishbase/man/morphology.Rd | 2 rfishbase-2.1.0/rfishbase/man/morphometrics.Rd | 2 rfishbase-2.1.0/rfishbase/man/occurrence.Rd | 2 rfishbase-2.1.0/rfishbase/man/oxygen.Rd | 2 rfishbase-2.1.0/rfishbase/man/ping.Rd | 2 rfishbase-2.1.0/rfishbase/man/popchar.Rd | 4 rfishbase-2.1.0/rfishbase/man/popgrowth.Rd | 2 rfishbase-2.1.0/rfishbase/man/popqb.Rd | 2 rfishbase-2.1.0/rfishbase/man/predators.Rd | 2 rfishbase-2.1.0/rfishbase/man/ration.Rd | 2 rfishbase-2.1.0/rfishbase/man/reproduction.Rd | 2 rfishbase-2.1.0/rfishbase/man/rfishbase-package.Rd | 9 rfishbase-2.1.0/rfishbase/man/sci_to_common.Rd | 6 rfishbase-2.1.0/rfishbase/man/sealifebase.Rd | 2 rfishbase-2.1.0/rfishbase/man/spawning.Rd | 2 rfishbase-2.1.0/rfishbase/man/species.Rd | 8 rfishbase-2.1.0/rfishbase/man/species_fields.Rd | 2 rfishbase-2.1.0/rfishbase/man/species_list.Rd | 10 rfishbase-2.1.0/rfishbase/man/species_names.Rd | 2 rfishbase-2.1.0/rfishbase/man/speed.Rd | 2 rfishbase-2.1.0/rfishbase/man/stocks.Rd | 2 rfishbase-2.1.0/rfishbase/man/swimming.Rd | 2 rfishbase-2.1.0/rfishbase/man/synonyms.Rd | 8 rfishbase-2.1.0/rfishbase/man/validate_names.Rd | 2 rfishbase-2.1.0/rfishbase/tests/testthat/helper_rfishbase.R | 12 - rfishbase-2.1.0/rfishbase/tests/testthat/test_ecology.R | 4 rfishbase-2.1.0/rfishbase/tests/testthat/test_synonyms.R | 8 69 files changed, 242 insertions(+), 457 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data.
Ensembles of classification, regression, survival and probability prediction trees are
supported. Data from genome-wide association studies can be analyzed efficiently. In addition to
data frames, datasets of class 'gwaa.data' (R package GenABEL) can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.2.7 dated 2015-07-29 and 0.3.0 dated 2015-11-10
DESCRIPTION | 20 +--- MD5 | 36 ++++--- NEWS |only R/predict.R | 71 +++++++++++---- R/ranger.R | 15 ++- man/ranger.Rd | 8 + src/Forest.cpp | 206 ++++++++++++++++++++++++++++++++++----------- src/Forest.h | 11 +- src/Makevars | 1 src/Makevars.win | 2 src/Tree.cpp | 31 +++--- src/Tree.h | 9 - src/TreeClassification.cpp | 2 src/TreeProbability.cpp | 2 src/TreeRegression.cpp | 2 src/rangerCpp.cpp | 4 src/utility.h | 15 +++ src/version.h | 2 tests |only 19 files changed, 310 insertions(+), 127 deletions(-)
Title: High Frequency Portfolio Analytics by PortfolioEffect
Description: R interface to PortfolioEffect Quant service for backtesting
high frequency trading (HFT) strategies, intraday portfolio analysis
and optimization. Includes auto-calibrating model pipeline for market
microstructure noise, risk factors, price jumps/outliers, tail risk
(high-order moments) and price fractality (long memory). Constructed
portfolios could use client-side market data or access HF intraday price
history for all major US Equities. See https://www.portfolioeffect.com/
for more information on the PortfolioEffect high frequency portfolio
analytics platform.
Author: Aleksey Zemnitskiy [aut, cre],
Andrey Kostin [aut],
Oleg Nechaev [aut],
Craig Otis and others [ctb, cph] (OpenFAST library),
Daniel Lemire, Muraoka Taro and others [ctb, cph] (JavaFastPFOR
library),
Joe Walnes, Jorg Schaible and others [ctb, cph] (XStream library),
Dain Sundstrom [ctb, cph] (Snappy library),
Extreme! Lab, Indiana University [ctb, cph] (XPP3 library),
The Apache Software Foundation [ctb, cph] (Apache Log4j and Commons
Lang libraries),
Google, Inc. [ctb, cph] (GSON library),
Free Software Foundation [ctb, cph] (GNU Trove and GNU Crypto
libraries)
Maintainer: Aleksey Zemnitskiy <aleksey.zemnitskiy@portfolioeffect.com>
Diff between PortfolioEffectHFT versions 1.2 dated 2015-09-29 and 1.3 dated 2015-11-10
DESCRIPTION | 6 MD5 | 316 ++++++++++----------- NAMESPACE | 1 NEWS |only R/message.R | 2 R/optimization.R | 10 R/plot.R | 69 ++-- R/portfolio.R | 58 +-- R/util.R | 2 build/vignette.rds |binary demo/alpha_decay_demo.R | 18 - demo/efficient_frontier_demo.R | 10 demo/holding_period_risks_demo.R | 32 +- demo/lf_hf_strategy_demo.R | 12 demo/portfolio_metrics_demo.R | 24 - demo/portfolio_optimization_demo.R | 12 demo/txnCosts_demo.R | 24 - inst/doc/PortfolioEffectHFT.Rnw | 130 +++++--- inst/doc/PortfolioEffectHFT.pdf |binary inst/java/portfolioeffect-quant-client-1.0.jar |binary man/aapl.data.Rd | 7 man/optimization_constraint_CVaR.Rd | 5 man/optimization_constraint_VaR.Rd | 5 man/optimization_constraint_allWeights.Rd | 1 man/optimization_constraint_beta.Rd | 1 man/optimization_constraint_expectedReturn.Rd | 1 man/optimization_constraint_modifiedSharpeRatio.Rd | 5 man/optimization_constraint_portfolioValue.Rd | 1 man/optimization_constraint_return.Rd | 1 man/optimization_constraint_sharpeRatio.Rd | 1 man/optimization_constraint_starrRatio.Rd | 3 man/optimization_constraint_sumOfAbsWeights.Rd | 1 man/optimization_constraint_variance.Rd | 1 man/optimization_constraint_weight.Rd | 1 man/optimization_forecast.Rd | 5 man/optimization_goal.Rd | 3 man/optimization_info.Rd | 1 man/optimization_run.Rd | 1 man/optimizer-class.Rd | 1 man/portfolio-class.Rd | 1 man/portfolioPlot-class.Rd | 1 man/portfolio_CVaR.Rd | 7 man/portfolio_VaR.Rd | 7 man/portfolio_addPosition.Rd | 1 man/portfolio_alpha.Rd | 1 man/portfolio_availableSymbols.Rd |only man/portfolio_beta.Rd | 1 man/portfolio_calmarRatio.Rd | 1 man/portfolio_create.Rd | 1 man/portfolio_cumulant.Rd | 1 man/portfolio_downCaptureRatio.Rd | 1 man/portfolio_downNumberRatio.Rd | 1 man/portfolio_downPercentageRatio.Rd | 1 man/portfolio_downsideVariance.Rd | 1 man/portfolio_endBatch.Rd | 13 man/portfolio_expectedDownsideReturn.Rd | 1 man/portfolio_expectedReturn.Rd | 1 man/portfolio_expectedUpsideReturn.Rd | 1 man/portfolio_fractalDimension.Rd | 1 man/portfolio_gainLossVarianceRatio.Rd | 1 man/portfolio_gainVariance.Rd | 1 man/portfolio_getSettings.Rd | 3 man/portfolio_hurstExponent.Rd | 1 man/portfolio_informationRatio.Rd | 1 man/portfolio_jensensAlpha.Rd | 1 man/portfolio_kurtosis.Rd | 1 man/portfolio_lossVariance.Rd | 1 man/portfolio_maxDrawdown.Rd | 1 man/portfolio_modifiedSharpeRatio.Rd | 7 man/portfolio_moment.Rd | 1 man/portfolio_omegaRatio.Rd | 1 man/portfolio_pdf.Rd | 1 man/portfolio_profit.Rd | 1 man/portfolio_rachevRatio.Rd | 7 man/portfolio_removePosition.Rd | 1 man/portfolio_return.Rd | 1 man/portfolio_settings.Rd | 6 man/portfolio_sharpeRatio.Rd | 1 man/portfolio_skewness.Rd | 1 man/portfolio_sortinoRatio.Rd | 1 man/portfolio_starrRatio.Rd | 5 man/portfolio_startBatch.Rd | 13 man/portfolio_symbols.Rd | 1 man/portfolio_treynorRatio.Rd | 1 man/portfolio_txnCosts.Rd | 1 man/portfolio_upCaptureRatio.Rd | 1 man/portfolio_upNumberRatio.Rd | 1 man/portfolio_upPercentageRatio.Rd | 1 man/portfolio_upsideDownsideVarianceRatio.Rd | 1 man/portfolio_upsideVariance.Rd | 1 man/portfolio_value.Rd | 1 man/portfolio_variance.Rd | 1 man/position_CVaR.Rd | 7 man/position_VaR.Rd | 7 man/position_alpha.Rd | 1 man/position_beta.Rd | 1 man/position_calmarRatio.Rd | 1 man/position_correlation.Rd | 1 man/position_correlationMatrix.Rd | 1 man/position_covariance.Rd | 1 man/position_covarianceMatrix.Rd | 1 man/position_cumulant.Rd | 1 man/position_downCaptureRatio.Rd | 1 man/position_downNumberRatio.Rd | 1 man/position_downPercentageRatio.Rd | 1 man/position_downsideVariance.Rd | 1 man/position_expectedDownsideReturn.Rd | 1 man/position_expectedReturn.Rd | 1 man/position_expectedUpsideReturn.Rd | 1 man/position_fractalDimension.Rd | 1 man/position_gainLossVarianceRatio.Rd | 1 man/position_gainVariance.Rd | 1 man/position_hurstExponent.Rd | 1 man/position_informationRatio.Rd | 1 man/position_jensensAlpha.Rd | 1 man/position_kurtosis.Rd | 1 man/position_lossVariance.Rd | 1 man/position_maxDrawdown.Rd | 1 man/position_modifiedSharpeRatio.Rd | 7 man/position_moment.Rd | 1 man/position_omegaRatio.Rd | 1 man/position_pdf.Rd | 1 man/position_price.Rd | 1 man/position_profit.Rd | 1 man/position_quantity.Rd | 1 man/position_rachevRatio.Rd | 7 man/position_return.Rd | 1 man/position_returnAutocovariance.Rd | 1 man/position_returnJumpSize.Rd | 1 man/position_setQuantity.Rd | 1 man/position_sharpeRatio.Rd | 1 man/position_skewness.Rd | 1 man/position_sortinoRatio.Rd | 5 man/position_starrRatio.Rd | 7 man/position_treynorRatio.Rd | 1 man/position_txnCosts.Rd | 1 man/position_upCaptureRatio.Rd | 1 man/position_upNumberRatio.Rd | 1 man/position_upPercentageRatio.Rd | 1 man/position_upsideDownsideVarianceRatio.Rd | 1 man/position_upsideVariance.Rd | 1 man/position_value.Rd | 1 man/position_variance.Rd | 1 man/position_weight.Rd | 1 man/util_POSIXTimeToDate.Rd | 1 man/util_cleanCredentials.Rd | 1 man/util_colorScheme.Rd | 3 man/util_dateToPOSIXTime.Rd | 1 man/util_fillScheme.Rd | 1 man/util_getComputeTime.Rd | 1 man/util_ggplot.Rd | 1 man/util_line2d.Rd | 11 man/util_multiplot.Rd | 1 man/util_plot2d.Rd | 5 man/util_plot2df.Rd | 9 man/util_plotDensity.Rd | 1 man/util_plotTheme.Rd | 3 man/util_setCredentials.Rd | 1 man/util_summary.Rd | 1 vignettes/PortfolioEffectHFT.Rnw | 130 +++++--- 160 files changed, 692 insertions(+), 447 deletions(-)
More information about PortfolioEffectHFT at CRAN
Permanent link
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between paco versions 0.2.2 dated 2015-10-09 and 0.2.3 dated 2015-11-10
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/PACo.r | 8 +++++--- man/PACo.Rd | 9 ++++++--- man/add_pcoord.Rd | 2 +- man/coordpcoa.Rd | 2 +- man/gl_links.Rd | 2 +- man/gophertree.Rd | 2 +- man/licetree.Rd | 2 +- man/paco_links.Rd | 2 +- man/prepare_paco_data.Rd | 2 +- man/residuals.paco.Rd | 2 +- 13 files changed, 39 insertions(+), 33 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.5.1 dated 2015-09-21 and 0.6 dated 2015-11-10
nlsem-0.5.1/nlsem/R/fscores.R |only nlsem-0.5.1/nlsem/man/get_factor_scores.Rd |only nlsem-0.6/nlsem/ChangeLog | 11 + nlsem-0.6/nlsem/DESCRIPTION | 8 nlsem-0.6/nlsem/MD5 | 26 +- nlsem-0.6/nlsem/NAMESPACE | 1 nlsem-0.6/nlsem/R/em.R | 4 nlsem-0.6/nlsem/R/qml.R | 6 nlsem-0.6/nlsem/R/s3generics.R | 286 +++++++++++++---------------- nlsem-0.6/nlsem/R/semm.R | 58 +++++ nlsem-0.6/nlsem/data/australia.txt.gz |only nlsem-0.6/nlsem/man/australia.Rd |only nlsem-0.6/nlsem/man/em.Rd | 8 nlsem-0.6/nlsem/man/jordan.Rd | 47 +++- nlsem-0.6/nlsem/man/nlsem-package.Rd | 9 nlsem-0.6/nlsem/man/qml.Rd | 3 16 files changed, 272 insertions(+), 195 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.4.1 dated 2015-11-05 and 0.5.1 dated 2015-11-10
matlib-0.4.1/matlib/man/proj.Rd |only matlib-0.5.1/matlib/DESCRIPTION | 9 matlib-0.5.1/matlib/MD5 | 69 +-- matlib-0.5.1/matlib/NAMESPACE | 14 matlib-0.5.1/matlib/R/QR.R | 6 matlib-0.5.1/matlib/R/R.R |only matlib-0.5.1/matlib/R/eig.R | 4 matlib-0.5.1/matlib/R/gaussian-elimination.R | 4 matlib-0.5.1/matlib/R/gsorth.R | 3 matlib-0.5.1/matlib/R/len.R |only matlib-0.5.1/matlib/R/matlib.R | 58 -- matlib-0.5.1/matlib/R/plotEqn.R | 144 ++++-- matlib-0.5.1/matlib/R/proj.R |only matlib-0.5.1/matlib/R/rowops.R | 2 matlib-0.5.1/matlib/R/showEqn.R | 17 matlib-0.5.1/matlib/R/vectors.R |only matlib-0.5.1/matlib/README.md | 25 - matlib-0.5.1/matlib/build/vignette.rds |binary matlib-0.5.1/matlib/inst/doc/eigen-ex1.html | 466 +++++++++++++++----- matlib-0.5.1/matlib/inst/doc/eigen-ex2.R | 9 matlib-0.5.1/matlib/inst/doc/eigen-ex2.Rmd | 12 matlib-0.5.1/matlib/inst/doc/eigen-ex2.html | 467 ++++++++++++++++----- matlib-0.5.1/matlib/inst/doc/linear-equations.R |only matlib-0.5.1/matlib/inst/doc/linear-equations.Rmd |only matlib-0.5.1/matlib/inst/doc/linear-equations.html |only matlib-0.5.1/matlib/man/Ginv.Rd | 3 matlib-0.5.1/matlib/man/Proj.Rd |only matlib-0.5.1/matlib/man/QR.Rd | 6 matlib-0.5.1/matlib/man/R.Rd | 21 matlib-0.5.1/matlib/man/SVD.Rd | 4 matlib-0.5.1/matlib/man/cholesky.Rd | 3 matlib-0.5.1/matlib/man/echelon.Rd | 3 matlib-0.5.1/matlib/man/gsorth.Rd | 3 matlib-0.5.1/matlib/man/len.Rd |only matlib-0.5.1/matlib/man/matlib.Rd |only matlib-0.5.1/matlib/man/plotEqn.Rd | 20 matlib-0.5.1/matlib/man/plotEqn3d.Rd |only matlib-0.5.1/matlib/man/rowswap.Rd | 4 matlib-0.5.1/matlib/man/showEqn.Rd | 10 matlib-0.5.1/matlib/man/vectors.Rd |only matlib-0.5.1/matlib/vignettes/CanvasMatrix.js |only matlib-0.5.1/matlib/vignettes/eigen-ex2.Rmd | 12 matlib-0.5.1/matlib/vignettes/linear-equations.Rmd |only 43 files changed, 1020 insertions(+), 378 deletions(-)
Title: Stable Isotope Mixing Model
Description: Estimates diet contributions from isotopic sources using JAGS.
Includes estimation of concentration dependence and measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson <troutinthemilk@gmail.com>
Diff between IsotopeR versions 0.5 dated 2015-11-07 and 0.5.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + NEWS | 4 +++- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-3 dated 2015-06-24 and 1.0-4 dated 2015-11-10
adegraphics-1.0-3/adegraphics/R/s.hist.R |only adegraphics-1.0-4/adegraphics/DESCRIPTION | 21 +- adegraphics-1.0-4/adegraphics/MD5 | 41 ++-- adegraphics-1.0-4/adegraphics/NAMESPACE | 136 ++++++++-------- adegraphics-1.0-4/adegraphics/R/ADEg.S2.R | 32 +++ adegraphics-1.0-4/adegraphics/R/ADEgS.R | 5 adegraphics-1.0-4/adegraphics/R/S2.distri.R | 2 adegraphics-1.0-4/adegraphics/R/ade4-plot.R | 2 adegraphics-1.0-4/adegraphics/R/ade4-scatter.R | 25 ++ adegraphics-1.0-4/adegraphics/R/adeGsenv.R | 2 adegraphics-1.0-4/adegraphics/R/panelfunctions.R | 65 ++++++- adegraphics-1.0-4/adegraphics/build/vignette.rds |binary adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.Rnw | 10 - adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.pdf |binary adegraphics-1.0-4/adegraphics/man/adeg.panel.hist.Rd |only adegraphics-1.0-4/adegraphics/man/adeg.panel.join.Rd |only adegraphics-1.0-4/adegraphics/man/adeg.panel.label.Rd | 2 adegraphics-1.0-4/adegraphics/man/adeg.panel.nb.Rd | 23 +- adegraphics-1.0-4/adegraphics/man/adeg.panel.values.Rd | 2 adegraphics-1.0-4/adegraphics/man/changelatticetheme.Rd | 6 adegraphics-1.0-4/adegraphics/tests/panelSpatial.R | 3 adegraphics-1.0-4/adegraphics/tests/parameter.R | 9 + adegraphics-1.0-4/adegraphics/vignettes/adegraphics.Rnw | 10 - 23 files changed, 255 insertions(+), 141 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-44 dated 2015-08-30 and 7.3-45 dated 2015-11-10
DESCRIPTION | 10 ++++---- INDEX |only LICENCE.note |only MD5 | 6 ++-- R/fitdistr.R | 2 - inst/NEWS | 3 +- man/Animals.Rd |only man/Boston.Rd |only man/Cars93.Rd |only man/GAGurine.Rd |only man/Skye.Rd |only man/Traffic.Rd |only man/VA.Rd |only man/abbey.Rd |only man/addterm.Rd |only man/area.Rd |only man/bandwidth.nrd.Rd |only man/beav2.Rd |only man/birthwt.Rd |only man/caith.Rd |only man/contr.sdif.Rd |only man/cov.trob.Rd |only man/crabs.Rd |only man/deaths.Rd |only man/epil.Rd |only man/fgl.Rd |only man/gamma.dispersion.Rd |only man/gehan.Rd |only man/hills.Rd |only man/leuk.Rd |only man/mcycle.Rd |only man/menarche.Rd |only man/newcomb.Rd |only man/npr1.Rd |only man/petrol.Rd |only man/plot.lda.Rd |only man/plot.profile.Rd | 59 ++++++++++++++++++++++++++++++++++++++++++++++++ man/predict.lda.Rd |only man/predict.qda.Rd |only man/quine.Rd |only man/rational.Rd |only man/rotifer.Rd |only man/shoes.Rd |only man/snails.Rd |only man/steam.Rd |only man/stepAIC.Rd |only man/studres.Rd |only man/summary.rlm.Rd |only man/waders.Rd |only 49 files changed, 70 insertions(+), 10 deletions(-)
More information about TruncatedNormal at CRAN
Permanent link
Title: Six Sigma Tools for Quality Control and Improvement
Description: Functions and utilities to perform
Statistical Analyses in the Six Sigma way.
Through the DMAIC cycle (Define, Measure, Analyze, Improve, Control),
you can manage several Quality Management studies:
Gage R&R, Capability Analysis, Control Charts, Loss Function Analysis,
etc. Data frames used in the books "Six Sigma with R" (Springer, 2012)
and "Quality Control with R" (Springer, 2015)
are also included in the package.
Author: Emilio L. Cano, Javier M. Moguerza, Mariano Prieto and Andrés Redchuk
Maintainer: Emilio L. Cano <emilio.lopez@urjc.es>
Diff between SixSigma versions 0.8-1 dated 2014-03-07 and 0.9-0 dated 2015-11-10
DESCRIPTION | 21 MD5 | 102 +- NAMESPACE | 53 - NEWS | 145 ++-- R/SixSigma-package.R | 179 ++-- R/auxf.R | 74 -- R/data.R | 1305 ++++++++++++++++++++---------------- R/qcr.profiles.R |only R/ss.ca.R | 1167 ++++++++++++++++---------------- R/ss.rr.R | 578 ++++++++------- build/vignette.rds |binary data/ss.data.bills.RData |only data/ss.data.density.RData |only data/ss.data.thickness.RData |only data/ss.data.thickness2.RData |only data/ss.data.wbx.RData |only data/ss.data.wby.RData |only inst/CITATION | 48 - inst/doc/HelicopterInstructions.R | 19 inst/doc/HelicopterInstructions.pdf |binary inst/doc/ShewhartConstants.R |only inst/doc/ShewhartConstants.Rnw |only inst/doc/ShewhartConstants.pdf |only man/SixSigma.Rd | 174 ++-- man/climProfiles.Rd |only man/outProfiles.Rd |only man/plotControlProfiles.Rd |only man/plotProfiles.Rd |only man/smoothProfiles.Rd |only man/ss.ca.yield.Rd | 94 +- man/ss.ca.z.Rd | 117 +-- man/ss.cc.Rd | 140 +-- man/ss.cc.constants.Rd | 82 +- man/ss.ceDiag.Rd | 142 +-- man/ss.ci.Rd | 156 ++-- man/ss.data.batteries.Rd | 87 +- man/ss.data.bills.Rd |only man/ss.data.bolts.Rd | 81 +- man/ss.data.ca.Rd | 80 +- man/ss.data.density.Rd |only man/ss.data.doe1.Rd | 88 +- man/ss.data.doe2.Rd | 88 +- man/ss.data.pastries.Rd | 84 +- man/ss.data.pb1.Rd | 84 +- man/ss.data.pb2.Rd | 88 +- man/ss.data.pb3.Rd | 90 +- man/ss.data.pb4.Rd | 73 +- man/ss.data.pc.Rd | 84 +- man/ss.data.pc.big.Rd | 81 +- man/ss.data.pc.r.Rd | 80 +- man/ss.data.rr.Rd | 84 +- man/ss.data.strings.Rd | 82 +- man/ss.data.thickness.Rd |only man/ss.data.thickness2.Rd |only man/ss.data.wbx.Rd |only man/ss.data.wby.Rd |only man/ss.heli.Rd | 80 +- man/ss.lf.Rd | 99 +- man/ss.lfa.Rd | 144 +-- man/ss.pMap.Rd | 216 ++--- man/ss.rr.Rd | 178 ++-- man/ss.study.ca.Rd | 115 +-- vignettes/ShewhartConstants.Rnw |only 63 files changed, 3459 insertions(+), 3223 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.1 dated 2015-10-02 and 1.2 dated 2015-11-10
gaston-1.1/gaston/src/export-crossprod.cpp |only gaston-1.1/gaston/src/export-inverse.cpp |only gaston-1.1/gaston/src/m4_kinship2.cpp |only gaston-1.2/gaston/DESCRIPTION | 6 ++-- gaston-1.2/gaston/MD5 | 36 ++++++++++++-------------- gaston-1.2/gaston/R/bm_grm.r | 13 ++------- gaston-1.2/gaston/R/lmm_simu.r | 2 - gaston-1.2/gaston/inst/doc/gaston.R | 26 +++++++++--------- gaston-1.2/gaston/inst/doc/gaston.Rnw | 18 ++++++++++--- gaston-1.2/gaston/inst/doc/gaston.pdf |binary gaston-1.2/gaston/man/gaston-package.Rd | 6 ++-- gaston-1.2/gaston/man/lik.contour.Rd | 2 - gaston-1.2/gaston/src/ai-reml-1k-covar.h | 2 - gaston-1.2/gaston/src/ai-reml-1k.h | 2 - gaston-1.2/gaston/src/ai-reml-nk-covar.h | 2 - gaston-1.2/gaston/src/ai-reml-nk.h | 2 - gaston-1.2/gaston/src/loubar.h | 2 - gaston-1.2/gaston/src/m4_kinship.cpp | 40 +++++++++++++++-------------- gaston-1.2/gaston/src/m4_kinship_p.cpp | 35 +++++++++++++------------ gaston-1.2/gaston/src/m4_kinship_type.h |only gaston-1.2/gaston/vignettes/gaston.Rnw | 18 ++++++++++--- 21 files changed, 115 insertions(+), 97 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-1 dated 2015-05-19 and 0.0-3 dated 2015-11-10
qrmtools-0.0-1/qrmtools/R/device.R |only qrmtools-0.0-1/qrmtools/R/worst_VaR.R |only qrmtools-0.0-1/qrmtools/demo |only qrmtools-0.0-1/qrmtools/man/device.Rd |only qrmtools-0.0-1/qrmtools/man/worst_VaR.Rd |only qrmtools-0.0-1/qrmtools/src/worst_VaR.c |only qrmtools-0.0-1/qrmtools/src/worst_VaR.h |only qrmtools-0.0-3/qrmtools/DESCRIPTION | 11 ++++--- qrmtools-0.0-3/qrmtools/MD5 | 38 +++++++++++++++++---------- qrmtools-0.0-3/qrmtools/NAMESPACE | 20 +++++++++----- qrmtools-0.0-3/qrmtools/R/GPD.R | 18 ++++++++++++ qrmtools-0.0-3/qrmtools/R/VaR_bounds.R |only qrmtools-0.0-3/qrmtools/R/risk_measures.R |only qrmtools-0.0-3/qrmtools/TODO | 5 +-- qrmtools-0.0-3/qrmtools/build |only qrmtools-0.0-3/qrmtools/inst |only qrmtools-0.0-3/qrmtools/man/VaR_bounds.Rd |only qrmtools-0.0-3/qrmtools/man/risk_measures.Rd |only qrmtools-0.0-3/qrmtools/src/VaR_bounds.c |only qrmtools-0.0-3/qrmtools/src/VaR_bounds.h |only qrmtools-0.0-3/qrmtools/src/init.c | 9 +++--- qrmtools-0.0-3/qrmtools/vignettes |only 22 files changed, 68 insertions(+), 33 deletions(-)
Title: Construction and Analysis of Matrix Population Models
Description: Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Author: Chris Stubben, Brook Milligan, Patrick Nantel
Maintainer: Chris Stubben <stubben@lanl.gov>
Diff between popbio versions 2.4 dated 2012-03-20 and 2.4.2 dated 2015-11-10
popbio-2.4.2/popbio/DESCRIPTION | 21 +++++------ popbio-2.4.2/popbio/MD5 | 52 +++++++++++++++-------------- popbio-2.4.2/popbio/NAMESPACE | 14 ++++++- popbio-2.4.2/popbio/R/QPmat.R | 19 ++++++---- popbio-2.4.2/popbio/R/logi.hist.plot.R | 2 - popbio-2.4.2/popbio/R/secder.R |only popbio-2.4.2/popbio/R/stoch.sens.R |only popbio-2.4.2/popbio/data/grizzly.rda |binary popbio-2.4.2/popbio/data/hudsonia.rda |binary popbio-2.4.2/popbio/data/hudvrs.rda |binary popbio-2.4.2/popbio/data/nematode.rda |binary popbio-2.4.2/popbio/data/teasel.rda |binary popbio-2.4.2/popbio/data/tortoise.rda |binary popbio-2.4.2/popbio/data/whale.rda |binary popbio-2.4.2/popbio/data/woodpecker.rda |binary popbio-2.4.2/popbio/inst/ChangeLog | 13 ++++++- popbio-2.4.2/popbio/man/02Caswell.Rd | 41 +++++++++++----------- popbio-2.4.2/popbio/man/LTRE.Rd | 6 ++- popbio-2.4.2/popbio/man/QPmat.Rd | 14 ++++--- popbio-2.4.2/popbio/man/betaval.Rd | 9 +---- popbio-2.4.2/popbio/man/eigen.analysis.Rd | 12 ++---- popbio-2.4.2/popbio/man/hudcorrs.Rd | 5 +- popbio-2.4.2/popbio/man/hudmxdef.Rd | 4 +- popbio-2.4.2/popbio/man/pfister.plot.Rd | 15 +++++--- popbio-2.4.2/popbio/man/secder.Rd |only popbio-2.4.2/popbio/man/stoch.quasi.ext.Rd | 6 +-- popbio-2.4.2/popbio/man/stoch.sens.Rd |only popbio-2.4.2/popbio/man/vitalsim.Rd | 18 +++++----- popbio-2.4/popbio/R/colorguide.R |only popbio-2.4/popbio/man/colorguide.Rd |only 30 files changed, 138 insertions(+), 113 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters). It specifies basic functions that allow many visual field tests to be constructed. As of February 2015 it is fully implemented on the Octopus 600 and Octopus 900 and partially on the Heidelberg Edge Perimeter and the Kowa AP 7000. It also has a cousin: the R package visualFields, which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin, David Lawson, Matthias Muller
Maintainer: Andrew Turpin <aturpin@unimelb.edu.au>
Diff between OPI versions 2.1 dated 2014-12-21 and 2.3 dated 2015-11-10
ChangeLog | 10 + DESCRIPTION | 12 - MD5 | 30 ++-- NAMESPACE | 6 R/kowaAP7000Client.r | 294 +++++++++++++++++++++++++++++---------------- R/octopus900Client.r | 198 ++++++++++++++++-------------- R/opi.r | 8 + man/chooseOpi.Rd | 6 man/opiClose.Rd | 2 man/opiInitialize.Rd | 30 +++- man/opiKineticStimulus.Rd | 21 ++- man/opiPresent.Rd | 31 +++- man/opiQueryDevice.Rd | 15 ++ man/opiSetBackground.Rd | 18 +- man/opiStaticStimulus.Rd | 17 ++ man/opiTemporalStimulus.Rd | 5 16 files changed, 459 insertions(+), 244 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to
data files written using Unidata's
netCDF library (version 4 or earlier), which are binary data files that are portable
across platforms and include metadata information in addition to the data sets.
Using this package, netCDF files (either version 4
or "classic" version 3) can be opened and data sets read in easily.
It is also easy to create new netCDF dimensions, variables, and files,
in either version 3 or 4 format, and manipulate existing netCDF files.
This package replaces the former ncdf package, which only worked with
netcdf version 3 files. For various reasons the names of the functions
have had to be changed from the names in the ncdf package. The old ncdf package is still
available at the URL given below, if you need to have backward compatibility.
It should be possible to have both the ncdf and ncdf4 packages installed
simultaneously without a problem.
However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.13 dated 2014-09-16 and 1.14 dated 2015-11-10
ncdf4-1.13/ncdf4/tools/configure.in |only ncdf4-1.14/ncdf4/DESCRIPTION | 16 ncdf4-1.14/ncdf4/MD5 | 24 ncdf4-1.14/ncdf4/R/ncdf4.R | 2 ncdf4-1.14/ncdf4/R/ncdf4_priv_var.R | 5 ncdf4-1.14/ncdf4/configure | 1044 ++++++++++++++++++++++++- ncdf4-1.14/ncdf4/tools/autom4te.cache/output.0 | 1020 ++++++++++++++++++++++++ ncdf4-1.14/ncdf4/tools/autom4te.cache/output.1 | 1020 ++++++++++++++++++++++++ ncdf4-1.14/ncdf4/tools/autom4te.cache/output.2 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/output.3 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/requests | 93 ++ ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.0 | 16 ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.1 | 48 + ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.2 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.3 |only ncdf4-1.14/ncdf4/tools/configure.ac |only 16 files changed, 3253 insertions(+), 35 deletions(-)
Title: Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Description: Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Author: Mathias Borritz Milfeldt [aut, cre]
Maintainer: Mathias Borritz Milfeldt <mathias@milfeldt.dk>
Diff between epandist versions 1.0.1 dated 2015-10-01 and 1.0.2 dated 2015-11-10
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/cepan.R | 22 ++++++++++++++-------- R/depan.R | 11 +++++++++-- R/evepan.R | 17 ++++++++++++++++- R/pepan.R | 13 ++++++++++++- R/qepan.R | 11 +++++++++-- R/repan.R | 3 ++- inst/doc/Vignette_epandist.Rmd | 2 +- inst/doc/Vignette_epandist.html | 13 ++++++------- man/cepan.Rd | 7 ++++++- man/depan.Rd | 11 +++++++++-- man/evepan.Rd | 17 ++++++++++++++++- man/pepan.Rd | 13 ++++++++++++- man/qepan.Rd | 9 ++++++++- man/repan.Rd | 3 ++- vignettes/Vignette_epandist.Rmd | 2 +- 18 files changed, 144 insertions(+), 52 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-
control association tests of highly polymorphic genetic data [e.g., human
leukocyte antigen (HLA) data]. Performs association tests at multiple levels of
polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to
a common class to account for sparse cells in tables as described by Hollenbach
JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association
studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.1.1 dated 2015-10-29 and 1.2.1 dated 2015-11-10
DESCRIPTION | 20 +- MD5 | 87 +++++----- NEWS |only R/BIGDAWG.R | 99 ++++++----- R/HWE.R | 156 +++++++++--------- R/check_functions.R | 374 ++++++++++++++++++++++---------------------- R/general_functions.R | 327 +++++++++++++++++++------------------- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 312 ++++++++++++++++++------------------ inst/doc/BIGDAWG.html | 382 ++++++++++++++++++++++----------------------- man/A.Rd | 64 +++---- man/AA.df.check.Rd | 36 ++-- man/AAtable.builder.Rd | 40 ++-- man/AlignObj.Create.Rd | 44 ++--- man/AlignObj.Update.Rd | 44 ++--- man/AlignmentFilter.Rd | 44 ++--- man/BIGDAWG.Rd | 108 ++++++------ man/CheckAlleles.Rd | 48 ++--- man/CheckHLA.Rd | 36 ++-- man/CheckLoci.Rd | 40 ++-- man/EVSremoval.Rd | 40 ++-- man/ExonPtnAlign.Create.Rd | 40 ++-- man/ExonPtnList.Rd | 30 +-- man/GetField.Rd | 40 ++-- man/GetFiles.Rd | 36 ++-- man/H.Rd | 40 ++-- man/HLA_data.Rd | 30 +-- man/HWEChiSq.Rd | 40 ++-- man/L.Rd | 56 +++--- man/PgrpExtract.Rd | 40 ++-- man/PgrpFormat.Rd | 40 ++-- man/PreCheck.Rd | 48 ++--- man/RunChiSq.Rd | 36 ++-- man/TableMaker.Rd | 36 ++-- man/UpdateRelease.Rd | 44 ++--- man/cci.Rd | 100 +++++------ man/cci.pval.Rd | 36 ++-- man/cci.pval.list.Rd | 36 ++-- man/getCS.Mat.Rd | 48 ++--- man/getObsFreq.Rd | 40 ++-- man/make2x2.Rd | 48 ++--- man/makeComb.Rd | 36 ++-- man/rmABstrings.Rd | 36 ++-- vignettes/BIGDAWG.Rmd | 312 ++++++++++++++++++------------------ 45 files changed, 1792 insertions(+), 1757 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.0.6 dated 2015-09-11 and 2.1.0 dated 2015-11-10
BAMMtools-2.0.6/BAMMtools/R/BAMMtools-internal.R |only BAMMtools-2.0.6/BAMMtools/R/as.phylo.branchprior.R |only BAMMtools-2.0.6/BAMMtools/R/bayesFactorBranches.R |only BAMMtools-2.0.6/BAMMtools/R/print.branchprior.R |only BAMMtools-2.0.6/BAMMtools/R/summary.branchprior.R |only BAMMtools-2.0.6/BAMMtools/data/prior.primates.rda |only BAMMtools-2.0.6/BAMMtools/data/prior.whales.rda |only BAMMtools-2.0.6/BAMMtools/man/bayesFactorBranches.Rd |only BAMMtools-2.0.6/BAMMtools/man/summary.branchprior.Rd |only BAMMtools-2.1.0/BAMMtools/DESCRIPTION | 12 BAMMtools-2.1.0/BAMMtools/MD5 | 134 +++---- BAMMtools-2.1.0/BAMMtools/NAMESPACE | 85 ++++ BAMMtools-2.1.0/BAMMtools/R/BAMMlikelihood.R |only BAMMtools-2.1.0/BAMMtools/R/addBAMMlegend.R | 208 +++++++++-- BAMMtools-2.1.0/BAMMtools/R/assignColorBreaks.R | 2 BAMMtools-2.1.0/BAMMtools/R/computeBayesFactors.R | 67 +-- BAMMtools-2.1.0/BAMMtools/R/credibleShiftSet.R | 24 - BAMMtools-2.1.0/BAMMtools/R/distinctShiftConfigurations.R | 36 - BAMMtools-2.1.0/BAMMtools/R/generateControlFile.R |only BAMMtools-2.1.0/BAMMtools/R/getBestShiftConfiguration.R | 8 BAMMtools-2.1.0/BAMMtools/R/getBranchShiftPriors.R | 32 - BAMMtools-2.1.0/BAMMtools/R/getCladeRates.R | 16 BAMMtools-2.1.0/BAMMtools/R/getEventData.R | 4 BAMMtools-2.1.0/BAMMtools/R/getJenksBreaks.R | 5 BAMMtools-2.1.0/BAMMtools/R/marginalOddsRatioBranches.R |only BAMMtools-2.1.0/BAMMtools/R/plot.bammdata.R | 32 + BAMMtools-2.1.0/BAMMtools/R/plotPrior.R |only BAMMtools-2.1.0/BAMMtools/R/ratesHistogram.R |only BAMMtools-2.1.0/BAMMtools/R/setBAMMpriors.R | 19 - BAMMtools-2.1.0/BAMMtools/data/events.fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/events.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/events.whales.rda |binary BAMMtools-2.1.0/BAMMtools/data/fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/mass.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/mcmc.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/mcmc.whales.rda |binary BAMMtools-2.1.0/BAMMtools/data/primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/traits.fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/whales.rda |binary BAMMtools-2.1.0/BAMMtools/inst/CITATION | 2 BAMMtools-2.1.0/BAMMtools/man/BAMMlikelihood.Rd |only BAMMtools-2.1.0/BAMMtools/man/BAMMtools-data.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/BAMMtools-internal.Rd | 14 BAMMtools-2.1.0/BAMMtools/man/BAMMtools-package.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/ShiftProbsTree.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/addBAMMlegend.Rd | 78 +++- BAMMtools-2.1.0/BAMMtools/man/addBAMMshifts.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/assignColorBreaks.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/cohorts.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/computeBayesFactors.Rd | 19 - BAMMtools-2.1.0/BAMMtools/man/credibleShiftSet.Rd | 30 - BAMMtools-2.1.0/BAMMtools/man/distinctShiftConfigurations.Rd | 38 +- BAMMtools-2.1.0/BAMMtools/man/dtRates.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/generateControlFile.Rd |only BAMMtools-2.1.0/BAMMtools/man/getBestShiftConfiguration.Rd | 23 - BAMMtools-2.1.0/BAMMtools/man/getBranchShiftPriors.Rd | 52 -- BAMMtools-2.1.0/BAMMtools/man/getCladeRates.Rd | 12 BAMMtools-2.1.0/BAMMtools/man/getCohortMatrix.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/getEventData.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/getJenksBreaks.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getMeanBranchLengthTree.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getShiftNodesFromIndex.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getTipRates.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/marginalOddsRatioBranches.Rd |only BAMMtools-2.1.0/BAMMtools/man/maximumShiftCredibility.Rd | 5 BAMMtools-2.1.0/BAMMtools/man/plot.bammdata.Rd | 15 BAMMtools-2.1.0/BAMMtools/man/plot.bammshifts.Rd | 17 BAMMtools-2.1.0/BAMMtools/man/plot.credibleshiftset.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/plotPrior.Rd |only BAMMtools-2.1.0/BAMMtools/man/ratesHistogram.Rd |only BAMMtools-2.1.0/BAMMtools/man/setBAMMpriors.Rd | 19 - BAMMtools-2.1.0/BAMMtools/man/speciesByRatesMatrix.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/subsetEventData.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/subtreeBAMM.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/summary.credibleshiftset.Rd | 11 BAMMtools-2.1.0/BAMMtools/man/testTimeVariableBranches.Rd | 3 BAMMtools-2.1.0/BAMMtools/man/traitDependentBAMM.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/transparentColor.Rd |only 78 files changed, 642 insertions(+), 443 deletions(-)
Title: The Short-Term and Long-Term Hazard Ratio Model for Survival
Data
Description: Inference procedures accommodate a flexible range of hazard ratio patterns with a two-sample semi-parametric model. This model contains the proportional hazards model and the proportional odds model as sub-models, and accommodates non-proportional hazards situations to the extreme of having crossing hazards and crossing survivor functions. Overall, this package has four major functions: 1) the parameter estimation, namely short-term and long-term hazard ratio parameters; 2) 95 percent and 90 percent point-wise confidence intervals and simultaneous confidence bands for the hazard ratio function; 3) p-value of the adaptive weighted log-rank test; 4) p-values of two lack-of-fit tests for the model. See the included "read_me_first.pdf" for brief instructions. In this version (1.1), there is no need to sort the data before applying this package.
Author: Junlong Sun and Song Yang
Maintainer: Junlong Sun <junlong.sun@gmail.com>
Diff between YPmodel versions 1.2 dated 2015-09-22 and 1.3 dated 2015-11-09
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 6 +++--- R/plot.YPmodel.IntervalBands.R | 6 +++--- R/plot.YPmodel.R | 1 + R/plot.YPmodel.lackfittest.R | 5 ++++- R/plot.YPmodel.martint.R | 5 ++--- R/plot.YPmodel.survf.R | 6 +++--- R/summary.YPmodel.R | 4 ++-- R/summary.YPmodel.estimate.R | 6 +++--- man/YPmodel-internal.Rd | 1 + 11 files changed, 37 insertions(+), 33 deletions(-)
Title: Boost Mutex Functionality in R
Description: Boost mutex functionality in R.
Author: Michael J. Kane <kaneplusplus@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between synchronicity versions 1.1.4 dated 2014-03-27 and 1.1.9 dated 2015-11-09
synchronicity-1.1.4/synchronicity/README |only synchronicity-1.1.4/synchronicity/src/Makevars |only synchronicity-1.1.4/synchronicity/src/uuid_create.cpp |only synchronicity-1.1.9/synchronicity/DESCRIPTION | 19 - synchronicity-1.1.9/synchronicity/MD5 | 36 +-- synchronicity-1.1.9/synchronicity/NAMESPACE | 46 ++-- synchronicity-1.1.9/synchronicity/R/RcppExports.R |only synchronicity-1.1.9/synchronicity/R/mutexes.R | 113 ++++++++-- synchronicity-1.1.9/synchronicity/R/uuid.R | 5 synchronicity-1.1.9/synchronicity/R/zzz.R | 2 synchronicity-1.1.9/synchronicity/README.md |only synchronicity-1.1.9/synchronicity/cleanup | 3 synchronicity-1.1.9/synchronicity/inst/synchronicity/util.h | 17 - synchronicity-1.1.9/synchronicity/man/attach.mutex-methods.Rd |only synchronicity-1.1.9/synchronicity/man/boost.mutex.descriptor-class.Rd | 43 +-- synchronicity-1.1.9/synchronicity/man/describe.Rd | 9 synchronicity-1.1.9/synchronicity/man/description-methods.Rd |only synchronicity-1.1.9/synchronicity/man/descriptor-class.Rd |only synchronicity-1.1.9/synchronicity/man/read-methods.Rd |only synchronicity-1.1.9/synchronicity/man/synchronicity-package.Rd | 5 synchronicity-1.1.9/synchronicity/src/RcppExports.cpp |only synchronicity-1.1.9/synchronicity/src/SharedCounter.cpp | 4 synchronicity-1.1.9/synchronicity/src/synchronicity.cpp | 79 +++--- synchronicity-1.1.9/synchronicity/src/util.cpp | 18 - 24 files changed, 236 insertions(+), 163 deletions(-)
Title: Range Ancestral State Estimation for Phylogeography and
Comparative Analyses
Description: The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015). Historical Biogeography Using Species Geographical Ranges. Systematic biology, 64(6), 1059-1073. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.
Author: Ignacio Quintero [aut, cre],
Forrest W. Crawford [aut],
Petr Keil [aut]
Maintainer: Ignacio Quintero <ignacio.quintero@yale.edu>
Diff between rase versions 0.2-2 dated 2015-08-13 and 0.2-21 dated 2015-11-09
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NAMESPACE | 2 +- R/rase_source.r | 10 ++++++++-- README.md | 12 +++++------- inst |only 6 files changed, 24 insertions(+), 19 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package 'CDVine' are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler, Thomas Nagler, Tobias Erhardt
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 1.6 dated 2015-07-22 and 1.6-1 dated 2015-11-09
VineCopula-1.6-1/VineCopula/DESCRIPTION | 12 +-- VineCopula-1.6-1/VineCopula/MD5 | 12 +-- VineCopula-1.6-1/VineCopula/inst/ChangeLog | 38 ++++++---- VineCopula-1.6-1/VineCopula/man/C2RVine.Rd | 30 ++----- VineCopula-1.6-1/VineCopula/man/D2RVine.Rd | 28 ++----- VineCopula-1.6-1/VineCopula/man/pobs.Rd | 3 VineCopula-1.6-1/VineCopula/tests/Examples/VineCopula-Ex_i386.Rout |only VineCopula-1.6/VineCopula/tests/Examples/VineCopula-Ex.Rout.save |only 8 files changed, 58 insertions(+), 65 deletions(-)
Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Managing financial time series objects.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@rmetrics.org>
Diff between timeSeries versions 3012.99 dated 2015-01-23 and 3022.101 dated 2015-11-09
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 20 ++--- NAMESPACE | 2 R/base-rank.R | 106 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/timeSeriesPlot.R | 146 ++++++++++++++++++++------------------ inst/doc/timeSeriesPlot.Rnw | 3 inst/doc/timeSeriesPlot.pdf |binary man/base-rank.Rd | 161 +++++++++++++++++++++---------------------- vignettes/timeSeriesPlot.Rnw | 3 11 files changed, 236 insertions(+), 218 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Author: Karl W Broman [aut, cre],
Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib, http://d3js.org),
Justin Palmer [ctb, cph] (d3.tip library in htmlwidgets/lib, https://github.com/caged/d3-tip),
Cynthia Brewer [cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org),
Mark Harrower [cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org),
The Pennsylvania State University [cph] (ColorBrewer library in htmlwidgets/lib,
http://colorbrewer2.org),
jQuery Foundation [cph] (jQuery library in htmlwidgets/lib, http://jquery.com),
jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see
https://github.com/jquery/jquery/blob/master/AUTHORS.txt),
jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see http://jqueryui.com/about)
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtlcharts versions 0.5-23 dated 2015-11-08 and 0.5-25 dated 2015-11-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/NEWS.md | 5 +++++ inst/ReadMe.md | 14 ++++++++++---- tests/Rmdtest.R | 10 +++++++--- tests/htmltest.R | 44 ++++++++++++++++++++++++-------------------- 7 files changed, 56 insertions(+), 37 deletions(-)
Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 2.0 dated 2015-11-04 and 2.0.1 dated 2015-11-09
DESCRIPTION | 8 +- MD5 | 22 ++--- R/pcadapt.R | 43 ++++++----- R/plotting.R | 8 +- R/utilities.R | 6 + inst/doc/pcadapt.R | 3 inst/doc/pcadapt.Rmd | 180 ++++++++++++++++++++++++++++++++++--------------- inst/doc/pcadapt.html | 126 +++++++++++++++++++++------------- man/pcadapt-package.Rd | 6 - man/pcadapt.Rd | 7 + man/read4pcadapt.Rd | 6 + vignettes/pcadapt.Rmd | 180 ++++++++++++++++++++++++++++++++++--------------- 12 files changed, 396 insertions(+), 199 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm. Each variable has its own imputation
model. Built-in imputation models are provided for continuous data
(predictive mean matching, normal), binary data (logistic regression),
unordered categorical data (polytomous logistic regression) and ordered
categorical data (proportional odds). MICE can also impute continuous
two-level data (normal model, pan, second-level variables). Passive
imputation can be used to maintain consistency between variables. Various
diagnostic plots are available to inspect the quality of the imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Alexander Robitzsch [ctb],
Gerko Vink [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 2.22 dated 2014-06-11 and 2.25 dated 2015-11-09
DESCRIPTION | 18 +- MD5 | 297 ++++++++++++++++++++-------------------- NAMESPACE | 42 +++++ R/as.r | 76 ++++++---- R/auxiliary.r | 2 R/boys.r | 3 R/bwplot.r | 5 R/densityplot.r | 9 - R/imports.R |only R/mice.impute.2l.norm.r | 2 R/mice.impute.2l.pan.r | 7 R/mice.impute.polyreg.r | 18 +- R/mice.impute.rf.r | 7 R/mice.r | 21 +- R/nelsonaalen.r | 1 R/plot.r | 7 R/pool.compare.r | 7 R/pool.r | 260 +++++++++++++++++------------------ R/print.r | 6 R/selfreport.r | 2 R/stripplot.r | 9 - R/summary.r | 6 R/windspeed.r | 4 R/with.r | 1 R/xyplot.r | 5 data/boys.rda |binary data/fdd.pred.rda |binary data/fdd.rda |binary data/fdgs.rda |binary data/leiden85.rda |binary data/mammalsleep.rda |binary data/nhanes.rda |binary data/nhanes2.rda |binary data/pattern1.rda |binary data/pattern2.rda |binary data/pattern3.rda |binary data/pattern4.rda |binary data/popmis.rda |binary data/pops.pred.rda |binary data/pops.rda |binary data/potthoffroy.rda |binary data/selfreport.rda |binary data/tbc.rda |binary data/tbc.target.rda |binary data/walking.rda |binary data/windspeed.rda |binary inst/NEWS | 8 + inst/doc/JSScode.R | 2 inst/doc/fimd1.r | 2 inst/doc/fimd2.r | 3 inst/doc/fimd3.r | 2 inst/doc/fimd4.r | 3 inst/doc/fimd5.r | 2 inst/doc/fimd6.r | 1 inst/doc/fimd7.r | 5 inst/doc/fimd8.r | 3 inst/doc/fimd9.r | 2 man/appendbreak.Rd | 3 man/as.mids.Rd | 38 +++-- man/as.mira.Rd | 3 man/boys.Rd | 6 man/bwplot.mids.Rd | 11 - man/cbind.mids.Rd | 3 man/cc-methods.Rd | 3 man/cci-methods.Rd | 3 man/ccn-methods.Rd | 3 man/complete.Rd | 3 man/densityplot.mids.Rd | 25 +-- man/extractBS.Rd | 3 man/fdd.Rd | 3 man/fdgs.Rd | 3 man/fico.Rd | 3 man/flux.Rd | 3 man/fluxplot.Rd | 3 man/getfit.Rd | 3 man/glm.mids.Rd | 3 man/ibind.Rd | 3 man/ic-methods.Rd | 3 man/ici-methods.Rd | 3 man/icn-methods.Rd | 3 man/ifdo.Rd | 3 man/is.mids.Rd | 3 man/is.mipo.Rd | 3 man/is.mira.Rd | 3 man/leiden85.Rd | 3 man/lm.mids.Rd | 3 man/long2mids.Rd | 3 man/mammalsleep.Rd | 3 man/md.pairs.Rd | 3 man/md.pattern.Rd | 3 man/mdc.Rd | 3 man/mice.Rd | 13 - man/mice.impute.2l.norm.Rd | 3 man/mice.impute.2l.pan.Rd | 3 man/mice.impute.2lonly.mean.Rd | 3 man/mice.impute.2lonly.norm.Rd | 3 man/mice.impute.2lonly.pmm.Rd | 3 man/mice.impute.cart.Rd | 3 man/mice.impute.fastpmm.Rd | 3 man/mice.impute.lda.Rd | 3 man/mice.impute.logreg.Rd | 3 man/mice.impute.logreg.boot.Rd | 3 man/mice.impute.mean.Rd | 3 man/mice.impute.norm.Rd | 3 man/mice.impute.norm.boot.Rd | 3 man/mice.impute.norm.nob.Rd | 3 man/mice.impute.norm.predict.Rd | 3 man/mice.impute.passive.Rd | 3 man/mice.impute.pmm.Rd | 3 man/mice.impute.polr.Rd | 3 man/mice.impute.polyreg.Rd | 3 man/mice.impute.quadratic.Rd | 3 man/mice.impute.rf.Rd | 3 man/mice.impute.ri.Rd | 3 man/mice.impute.sample.Rd | 3 man/mice.mids.Rd | 3 man/mice.theme.Rd | 3 man/mids-class.Rd | 3 man/mids2mplus.Rd | 3 man/mids2spss.Rd | 3 man/mipo-class.Rd | 3 man/mira-class.Rd | 3 man/nelsonaalen.Rd | 3 man/nhanes.Rd | 3 man/nhanes2.Rd | 3 man/norm.draw.Rd | 3 man/pattern.Rd | 3 man/plot.mids.Rd | 3 man/pool.Rd | 3 man/pool.compare.Rd | 5 man/pool.r.squared.Rd | 3 man/pool.scalar.Rd | 3 man/popmis.Rd | 3 man/pops.Rd | 3 man/potthoffroy.Rd | 3 man/print.Rd | 3 man/quickpred.Rd | 3 man/rbind.mids.Rd | 3 man/selfreport.Rd | 5 man/squeeze.Rd | 3 man/stripplot.mids.Rd | 23 +-- man/summary.Rd | 3 man/supports.transparent.Rd | 3 man/tbc.Rd | 3 man/version.Rd | 3 man/walking.Rd | 3 man/windspeed.Rd | 7 man/with.mids.Rd | 3 man/xyplot.mids.Rd | 11 - src/RcppExports.cpp | 18 -- 150 files changed, 716 insertions(+), 540 deletions(-)
Title: Linearized Bregman Algorithms for Generalized Linear Models
Description: Efficient procedures for fitting the regularization path for linear, binomial, multinomial models with lasso, group lasso or block lasso penalty. The package uses Linearized Bregman Algorithm to solve the regularization path through iterations. Bregman Inverse Scale Space Differential Inclusion solver is also provided for linear model with lasso penalty.
Author: Feng Ruan, Jiechao Xiong and Yuan Yao
Maintainer: Jiechao Xiong <xiongjiechao@pku.edu.cn>
Diff between Libra versions 1.3 dated 2015-11-07 and 1.3-2 dated 2015-11-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/LBlogistic.c | 22 ++++++++++++---------- 3 files changed, 18 insertions(+), 16 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.3.5 dated 2015-08-17 and 1.3.10 dated 2015-11-09
DESCRIPTION | 14 +- MD5 | 41 ++++---- NAMESPACE | 2 R/0gm.R | 87 ++++++++++++----- R/conditionalGmrf.R | 2 R/excProb.R | 16 ++- R/glgm.R | 28 ++--- R/lgcp.R | 14 ++ R/lgm.R | 22 ---- R/lgm.Raster.R | 165 +++++++++++++++++++++++++------- R/loglikGmrf.R | 246 +++++++++++++++++++++++++++++-------------------- R/maternGmrfPrec.R | 4 R/profLlgm.R | 41 +++----- R/spdfToBrick.R | 63 +++++++++--- man/profLlgm.Rd | 4 man/stackRasterList.Rd | 2 man/swissRain.Rd | 2 tests/glgm.R | 48 +++++---- tests/lgcp.R | 38 +++++++ tests/lgmRaster.R | 126 ++++++++++++++++++++++++- tests/loaFitted.png |only tests/profLlgm.R | 3 22 files changed, 671 insertions(+), 297 deletions(-)
Title: Rmetrics - Pricing and Evaluating Basic Options
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Pricing and Evaluating Basic Options.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@rmetrics.org>
Diff between fOptions versions 3010.83 dated 2013-06-23 and 3022.85 dated 2015-11-09
fOptions-3010.83/fOptions/src/085A-LowDiscrepancy.f |only fOptions-3022.85/fOptions/ChangeLog | 5 fOptions-3022.85/fOptions/DESCRIPTION | 32 fOptions-3022.85/fOptions/MD5 | 33 fOptions-3022.85/fOptions/NAMESPACE | 122 - fOptions-3022.85/fOptions/R/BasicAmericanOptions.R | 12 fOptions-3022.85/fOptions/R/BinomialTreeOptions.R | 922 ++++------ fOptions-3022.85/fOptions/R/HestonNandiGarchFit.R | 12 fOptions-3022.85/fOptions/R/HestonNandiOptions.R | 12 fOptions-3022.85/fOptions/R/LowDiscrepancy.R | 27 fOptions-3022.85/fOptions/R/MonteCarloOptions.R | 12 fOptions-3022.85/fOptions/R/PlainVanillaOptions.R | 12 fOptions-3022.85/fOptions/R/fOptionsEnv.R | 23 fOptions-3022.85/fOptions/R/zzz.R | 76 fOptions-3022.85/fOptions/inst/unitTests/runit.MonteCarloOptions.R | 248 +- fOptions-3022.85/fOptions/man/00fOptions-package.Rd |only fOptions-3022.85/fOptions/man/MonteCarloOptions.Rd | 586 +++--- fOptions-3022.85/fOptions/man/PlainVanillaOptions.Rd | 9 fOptions-3022.85/fOptions/src/LowDiscrepancy.f |only 19 files changed, 1000 insertions(+), 1143 deletions(-)
Title: Diversity Measures for Complex Systems
Description: Computes the most common diversity measures used in social and natural sciences, and includes new measures from interdisciplinary research.
Author: Miguel R. Guevara <miguel.guevara@upla.cl>, Dominik Hartmann
<d.hartmann@uni-hohenheim.de>, Marcelo Mendoza
<marcelo.mendoza@usm.cl>
Maintainer: Miguel R. Guevara <miguel.guevara@upla.cl>
Diff between diverse versions 0.1.0 dated 2015-10-20 and 0.1.1 dated 2015-11-09
diverse-0.1.0/diverse/man/dim_balance.Rd |only diverse-0.1.0/diverse/man/dim_disparity.Rd |only diverse-0.1.0/diverse/man/dim_variety.Rd |only diverse-0.1.0/diverse/man/diver_bio.Rd |only diverse-0.1.0/diverse/man/u_distances.Rd |only diverse-0.1.0/diverse/man/u_ubiquity.Rd |only diverse-0.1.1/diverse/DESCRIPTION | 13 diverse-0.1.1/diverse/MD5 | 37 + diverse-0.1.1/diverse/NAMESPACE | 13 diverse-0.1.1/diverse/R/data.R | 43 +- diverse-0.1.1/diverse/R/diversity.R | 528 ++++++++++++++++------------ diverse-0.1.1/diverse/R/pkgname.R | 8 diverse-0.1.1/diverse/R/utils.R | 8 diverse-0.1.1/diverse/data/scidat.RData |only diverse-0.1.1/diverse/man/balance.Rd |only diverse-0.1.1/diverse/man/dis_categories.Rd |only diverse-0.1.1/diverse/man/dis_entities.Rd |only diverse-0.1.1/diverse/man/disparity.Rd |only diverse-0.1.1/diverse/man/diverse.Rd | 8 diverse-0.1.1/diverse/man/diversity.Rd | 23 - diverse-0.1.1/diverse/man/geese.Rd | 9 diverse-0.1.1/diverse/man/pantheon.Rd | 10 diverse-0.1.1/diverse/man/read_data.Rd | 10 diverse-0.1.1/diverse/man/scidat.Rd |only diverse-0.1.1/diverse/man/ubiquity.Rd |only diverse-0.1.1/diverse/man/values.Rd |only diverse-0.1.1/diverse/man/variety.Rd |only 27 files changed, 416 insertions(+), 294 deletions(-)
Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Claire Ramus, Christophe Bruley, Yohann Couté, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between cp4p versions 0.3.2 dated 2015-10-08 and 0.3.3 dated 2015-11-09
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/tutorial-cp4p.pdf |binary man/calibration.plot.Rd | 8 ++------ man/cp4p-package.Rd | 6 +++--- 5 files changed, 14 insertions(+), 18 deletions(-)
Title: Model-Free Covariate Selection
Description: Model-free selection of covariates under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-ordinate hypothesis testing is used in situations where all covariates are continuous while kernel-based smoothing appropriate for mixed data is used otherwise.
Author: Jenny Häggström, Emma Persson,
Maintainer: Jenny Häggström <jenny.haggstrom@umu.se>
Diff between CovSel versions 1.1 dated 2014-06-26 and 1.2.1 dated 2015-11-09
DESCRIPTION | 18 ++++++++---------- MD5 | 23 +++++++++++++---------- NAMESPACE | 3 ++- R/cov.sel.np.R | 6 +++--- data/datf.rda |binary data/datfc.rda |binary data/lalonde.rda |only inst |only man/cov.sel.Rd | 4 +++- man/cov.sel.np.Rd | 4 +++- man/datf.Rd | 39 ++++++++++++++++++++++----------------- man/datfc.Rd | 46 ++++++++++++++++++++++++---------------------- man/lalonde.Rd |only man/summary.cov.sel.Rd | 2 +- 14 files changed, 79 insertions(+), 66 deletions(-)
Title: Methods for Changepoint Detection
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(), cpt.meanvar() functions should be your first point of call.
Author: Rebecca Killick [aut, cre],
Kaylea Haynes [aut],
Idris Eckley [ths, aut],
Paul Fearnhead [ctb, ths],
Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between changepoint versions 2.1.1 dated 2015-09-30 and 2.2 dated 2015-11-09
changepoint-2.1.1/changepoint/man/seg.size-methods.Rd |only changepoint-2.1.1/changepoint/man/seg.size.Rd |only changepoint-2.2/changepoint/DESCRIPTION | 18 changepoint-2.2/changepoint/MD5 | 201 ++-- changepoint-2.2/changepoint/NEWS | 21 changepoint-2.2/changepoint/R/BinSeg_one_func_minseglen.R | 1 changepoint-2.2/changepoint/R/CROPS.R | 25 changepoint-2.2/changepoint/R/SegNeigh_one_func_minseglen.R | 1 changepoint-2.2/changepoint/R/class_input.R | 5 changepoint-2.2/changepoint/R/cpt.R | 51 - changepoint-2.2/changepoint/R/cpt.class.R | 322 ++++++ changepoint-2.2/changepoint/R/data_input.R | 2 changepoint-2.2/changepoint/R/decision.R | 30 changepoint-2.2/changepoint/R/exp.R | 227 ---- changepoint-2.2/changepoint/R/gamma.R | 220 ---- changepoint-2.2/changepoint/R/multiple.nonparametric.R | 167 --- changepoint-2.2/changepoint/R/multiple.norm.R | 564 ------------ changepoint-2.2/changepoint/R/penalty_decision.R | 29 changepoint-2.2/changepoint/R/poisson.R | 220 ---- changepoint-2.2/changepoint/R/range_of_penalties.R | 42 changepoint-2.2/changepoint/R/single.nonparametric.R | 64 - changepoint-2.2/changepoint/R/single.norm.R | 148 --- changepoint-2.2/changepoint/R/zzz.R | 3 changepoint-2.2/changepoint/man/changepoint-package.Rd | 9 changepoint-2.2/changepoint/man/coef-methods.Rd | 1 changepoint-2.2/changepoint/man/cpt-class.Rd | 25 changepoint-2.2/changepoint/man/cpt.mean.Rd | 31 changepoint-2.2/changepoint/man/cpt.meanvar.Rd | 22 changepoint-2.2/changepoint/man/cpt.range-class.Rd | 21 changepoint-2.2/changepoint/man/cpt.reg-class.Rd | 4 changepoint-2.2/changepoint/man/cpt.var.Rd | 13 changepoint-2.2/changepoint/man/cpts--methods.Rd | 1 changepoint-2.2/changepoint/man/cpts-.Rd | 1 changepoint-2.2/changepoint/man/cpts-methods.Rd | 1 changepoint-2.2/changepoint/man/cpts.Rd | 1 changepoint-2.2/changepoint/man/cpts.full--methods.Rd | 1 changepoint-2.2/changepoint/man/cpts.full-.Rd | 1 changepoint-2.2/changepoint/man/cpts.full-methods.Rd | 1 changepoint-2.2/changepoint/man/cpts.full.Rd | 1 changepoint-2.2/changepoint/man/cpts.ts-methods.Rd | 1 changepoint-2.2/changepoint/man/cpts.ts.Rd | 1 changepoint-2.2/changepoint/man/cpttype--methods.Rd | 1 changepoint-2.2/changepoint/man/cpttype-.Rd | 3 changepoint-2.2/changepoint/man/cpttype-methods.Rd | 1 changepoint-2.2/changepoint/man/cpttype.Rd | 1 changepoint-2.2/changepoint/man/data.set--methods.Rd | 1 changepoint-2.2/changepoint/man/data.set-.Rd | 1 changepoint-2.2/changepoint/man/data.set-methods.Rd | 1 changepoint-2.2/changepoint/man/data.set.Rd | 1 changepoint-2.2/changepoint/man/data.set.ts-methods.Rd | 1 changepoint-2.2/changepoint/man/data.set.ts.Rd | 1 changepoint-2.2/changepoint/man/distribution--methods.Rd | 1 changepoint-2.2/changepoint/man/distribution-.Rd | 1 changepoint-2.2/changepoint/man/distribution-methods.Rd | 1 changepoint-2.2/changepoint/man/distribution.Rd | 1 changepoint-2.2/changepoint/man/likelihood-methods.Rd | 1 changepoint-2.2/changepoint/man/likelihood.Rd | 5 changepoint-2.2/changepoint/man/logLik-methods.Rd | 6 changepoint-2.2/changepoint/man/method--methods.Rd | 1 changepoint-2.2/changepoint/man/method-.Rd | 1 changepoint-2.2/changepoint/man/method-methods.Rd | 1 changepoint-2.2/changepoint/man/method.Rd | 1 changepoint-2.2/changepoint/man/minseglen--methods.Rd | 9 changepoint-2.2/changepoint/man/minseglen-.Rd | 1 changepoint-2.2/changepoint/man/minseglen-methods.Rd | 9 changepoint-2.2/changepoint/man/minseglen.Rd | 1 changepoint-2.2/changepoint/man/ncpts-methods.Rd | 1 changepoint-2.2/changepoint/man/ncpts.Rd | 2 changepoint-2.2/changepoint/man/ncpts.max--methods.Rd | 1 changepoint-2.2/changepoint/man/ncpts.max-.Rd | 1 changepoint-2.2/changepoint/man/ncpts.max-methods.Rd | 1 changepoint-2.2/changepoint/man/ncpts.max.Rd | 1 changepoint-2.2/changepoint/man/nseg-methods.Rd | 1 changepoint-2.2/changepoint/man/param-methods.Rd | 9 changepoint-2.2/changepoint/man/param.Rd | 1 changepoint-2.2/changepoint/man/param.est--methods.Rd | 1 changepoint-2.2/changepoint/man/param.est-.Rd | 1 changepoint-2.2/changepoint/man/param.est-methods.Rd | 1 changepoint-2.2/changepoint/man/param.est.Rd | 1 changepoint-2.2/changepoint/man/pen.type--methods.Rd | 1 changepoint-2.2/changepoint/man/pen.type-.Rd | 1 changepoint-2.2/changepoint/man/pen.type-methods.Rd | 1 changepoint-2.2/changepoint/man/pen.type.Rd | 1 changepoint-2.2/changepoint/man/pen.value--methods.Rd | 1 changepoint-2.2/changepoint/man/pen.value-.Rd | 3 changepoint-2.2/changepoint/man/pen.value-methods.Rd | 1 changepoint-2.2/changepoint/man/pen.value.Rd | 1 changepoint-2.2/changepoint/man/pen.value.full--methods.Rd | 1 changepoint-2.2/changepoint/man/pen.value.full-.Rd | 1 changepoint-2.2/changepoint/man/pen.value.full-methods.Rd | 1 changepoint-2.2/changepoint/man/pen.value.full.Rd | 1 changepoint-2.2/changepoint/man/plot-methods.Rd | 5 changepoint-2.2/changepoint/man/seg.len-methods.Rd |only changepoint-2.2/changepoint/man/seg.len.Rd |only changepoint-2.2/changepoint/man/show-methods.Rd | 1 changepoint-2.2/changepoint/man/summary-methods.Rd | 1 changepoint-2.2/changepoint/man/test.stat--methods.Rd | 1 changepoint-2.2/changepoint/man/test.stat-.Rd | 1 changepoint-2.2/changepoint/man/test.stat-methods.Rd | 1 changepoint-2.2/changepoint/man/test.stat.Rd | 1 changepoint-2.2/changepoint/src/PELT_one_func_minseglen.c | 17 changepoint-2.2/changepoint/tests/testthat/test-cptmean.R | 14 changepoint-2.2/changepoint/tests/testthat/test-cptvar.R | 29 changepoint-2.2/changepoint/tests/testthat/test-examples.R |only 104 files changed, 840 insertions(+), 1816 deletions(-)
Title: 'ade4' Tcl/Tk Graphical User Interface
Description: A Tcl/Tk GUI for some basic functions in the 'ade4' package.
Author: Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, Stéphane Dray <stephane.dray@univ-lyon1.fr>, Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4TkGUI versions 0.2-6 dated 2012-11-13 and 0.2-9 dated 2015-11-09
DESCRIPTION | 28 MD5 | 72 - NAMESPACE | 18 R/ade4TkGUI.R | 470 +++++------ R/choose.R | 337 ++----- R/dialog.MCTests.R | 9 R/dialog.between.R | 13 R/dialog.cca.R | 9 R/dialog.coinertia.R | 9 R/dialog.discrimin.R | 9 R/dialog.dpcoa.R | 9 R/dialog.dudi.acm.R | 9 R/dialog.dudi.coa.R | 9 R/dialog.dudi.dec.R | 9 R/dialog.dudi.display.R | 745 +++++++---------- R/dialog.dudi.fca.R | 9 R/dialog.dudi.fpca.R | 9 R/dialog.dudi.mix.R | 9 R/dialog.dudi.nsc.R | 9 R/dialog.dudi.pca.R | 12 R/dialog.dudi.pco.R | 9 R/dialog.pcaiv.R | 11 R/dialog.pcaivortho.R | 9 R/dialog.s.arrow.R | 307 ++----- R/dialog.s.chull.R | 343 ++------ R/dialog.s.class.R | 323 +++++++ R/dialog.s.corcircle.R | 184 +--- R/dialog.s.label.R | 324 ++----- R/dialog.s.match.R | 311 ++----- R/dialog.s.value.R | 413 +++------ R/dialog.within.R | 11 R/ordiClust.R | 1584 ++++++++++++++++++------------------- R/s.explore.R | 1944 +++++++++++++++++++++++----------------------- man/ade4TkGUI-internal.Rd | 9 man/ade4TkGUI.Rd | 41 man/explore.Rd | 4 man/ordiClust.Rd | 4 37 files changed, 3534 insertions(+), 4100 deletions(-)
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RSEIS versions 3.4-5 dated 2015-04-28 and 3.5-2 dated 2015-11-09
DESCRIPTION | 8 +- MD5 | 28 ++++----- NAMESPACE | 14 ++++ R/GLUE.GET.seis.R | 6 - R/JSEGY.seis.R | 78 ++++++++++++++----------- R/PLOT.SEISN.R | 62 +++++++++++--------- R/read1segy.R | 34 ++++++++-- R/rseis2segy.R | 164 ++++++++++++++++++++++++++++++++++++++++------------- R/sigconvGR.R | 4 - R/swig.R | 4 - R/write1segy.R | 13 +++- man/PLOT.SEISN.Rd | 3 man/grotseis.Rd | 2 man/sigconvGR.Rd | 16 +---- man/uwpfile2ypx.Rd | 17 +++++ 15 files changed, 302 insertions(+), 151 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.7-2 dated 2015-05-04 and 0.7-8 dated 2015-11-09
DESCRIPTION | 8 +++--- MD5 | 48 +++++++++++++++++++-------------------- NAMESPACE | 34 ++++++++++++++------------- R/MCMCfit.R | 56 ++++++++++++++++++++++++++++------------------ R/ModelMats.R | 9 ++++--- R/S.b.R | 5 ++-- R/dropAttr.R | 12 ++++++--- R/dynInfo.R | 4 +-- R/fixNames.R | 4 ++- R/globals.R | 2 - R/initSurvival.R | 11 +++++++-- R/jointModelBayes.R | 9 ++++--- R/log.posterior.b.R | 3 -- R/predict.JMbayes.R | 4 +-- R/print.summary.JMbayes.R | 11 ++++----- R/summary.JMbayes.R | 5 +--- R/survfitJM.JMbayes.R | 4 +-- data/aids.id.rda |binary data/aids.rda |binary data/pbc2.id.rda |binary data/pbc2.rda |binary data/prothro.rda |binary data/prothros.rda |binary inst/NEWS | 18 ++++++++++++++ man/JMbayes.Rd | 4 +-- 25 files changed, 151 insertions(+), 100 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JM versions 1.4-0 dated 2015-06-23 and 1.4-2 dated 2015-11-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 30 +++++++++++++++++++----------- R/jointModel.R | 3 +-- R/plot.jointModel.R | 3 +-- R/predict.jointModel.R | 1 + R/survfitJM.jointModel.R | 4 ++-- inst/NEWS | 8 ++++++++ man/JM.Rd | 4 ++-- 9 files changed, 46 insertions(+), 31 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are
implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.5.1 dated 2015-10-30 and 0.5.2 dated 2015-11-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/gvc.R | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Generating Multi-State Survival Data
Description: Generation of survival data with one (binary)
time-dependent covariate. Generation of survival data arising
from a progressive illness-death model.
Author: Artur Araujo, Luis Meira-Machado
<lmachado@math.uminho.pt> and Susana Faria
<sfaria@math.uminho.pt>
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between genSurv versions 1.0.2 dated 2014-05-07 and 1.0.3 dated 2015-11-09
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + inst/CITATION | 4 ++-- inst/NEWS.Rd | 8 +++++++- man/as.CMM.Rd | 2 +- man/as.TDCM.Rd | 2 +- man/as.THMM.Rd | 2 +- man/genCMM.Rd | 2 +- man/genCPHM.Rd | 2 +- man/genSurv-package.Rd | 10 +++++----- man/genTDCM.Rd | 2 +- man/genTHMM.Rd | 2 +- 13 files changed, 41 insertions(+), 34 deletions(-)
Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the
illness-death model and or the three-state progressive model.
Author: Artur Araujo, Javier Roca-Pardinas <roca@uvigo.es>
and Luis Meira-Machado <lmachado@math.uminho.pt>
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between TPmsm versions 1.2.0 dated 2014-12-09 and 1.2.1 dated 2015-11-09
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 4 ++-- inst/NEWS.Rd | 6 ++++++ man/TPmsm-package.Rd | 4 ++-- 5 files changed, 19 insertions(+), 13 deletions(-)
Title: Smooth Hazard Ratio Curves Taking a Reference Value
Description: Provides flexible hazard ratio curves allowing non-linear
relationships between continuous predictors and survival. To
better understand the effects that each continuous covariate
has on the outcome, results are ex pressed in terms of hazard
ratio curves, taking a specific covariate value as reference.
Confidence bands for these curves are also derived.
Author: Artur Araujo and Luis Meira-Machado
<lmachado@math.uminho.pt>
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between smoothHR versions 1.0.1 dated 2014-04-08 and 1.0.2 dated 2015-11-09
DESCRIPTION | 14 - MD5 | 26 +-- NAMESPACE | 4 R/dfmacox.R | 386 ++++++++++++++++++++++++------------------------ R/smoothHR.R | 184 +++++++++++----------- inst/CITATION | 76 ++++----- inst/NEWS.Rd | 6 man/dfmacox.Rd | 162 ++++++++++---------- man/plot.HR.Rd | 154 +++++++++---------- man/predict.HR.Rd | 130 ++++++++-------- man/print.HR.Rd | 106 ++++++------- man/smoothHR-package.Rd | 66 ++++---- man/smoothHR.Rd | 146 +++++++++--------- man/whas500.Rd | 64 +++---- 14 files changed, 766 insertions(+), 758 deletions(-)
Title: Analysis of Queueing Networks and Models
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models
and Single and Multiclass Product-Form Queueing Networks.
It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K,
Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,
Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks
and Single Channel Multiple Class Mixed Networks.
Also it provides a B-Erlang, C-Erlang and Engset calculators.
This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla <pedro.canadilla@gmail.com>
Diff between queueing versions 0.2.5 dated 2015-05-15 and 0.2.6 dated 2015-11-09
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 7 +++++++ 4 files changed, 17 insertions(+), 7 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-40 dated 2015-07-21 and 0.9-41 dated 2015-11-09
mkin-0.9-40/mkin/vignettes/compiled_models.html |only mkin-0.9-41/mkin/DESCRIPTION | 10 +- mkin-0.9-41/mkin/MD5 | 54 ++++++++------ mkin-0.9-41/mkin/NAMESPACE | 3 mkin-0.9-41/mkin/NEWS.md | 92 ++++++++++++++---------- mkin-0.9-41/mkin/R/mkinds.R |only mkin-0.9-41/mkin/R/mkinfit.R | 15 ++- mkin-0.9-41/mkin/R/mkinmod.R | 16 ++++ mkin-0.9-41/mkin/R/mkinsub.R | 6 - mkin-0.9-41/mkin/R/plot.mkinfit.R | 10 ++ mkin-0.9-41/mkin/README.md | 11 ++ mkin-0.9-41/mkin/build/vignette.rds |binary mkin-0.9-41/mkin/inst/doc/FOCUS_D.html | 4 - mkin-0.9-41/mkin/inst/doc/FOCUS_L.html | 4 - mkin-0.9-41/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-41/mkin/inst/doc/compiled_models.R |only mkin-0.9-41/mkin/inst/doc/compiled_models.Rmd |only mkin-0.9-41/mkin/inst/doc/compiled_models.html |only mkin-0.9-41/mkin/inst/doc/mkin.pdf |binary mkin-0.9-41/mkin/inst/examples |only mkin-0.9-41/mkin/man/mkin_long_to_wide.Rd | 2 mkin-0.9-41/mkin/man/mkin_wide_to_long.Rd | 2 mkin-0.9-41/mkin/man/mkinds.Rd |only mkin-0.9-41/mkin/man/mkinfit.Rd | 2 mkin-0.9-41/mkin/man/mkinmod.Rd | 4 - mkin-0.9-41/mkin/man/mkinplot.Rd | 3 mkin-0.9-41/mkin/man/mkinsub.Rd | 13 +++ mkin-0.9-41/mkin/man/plot.mkinfit.Rd | 3 mkin-0.9-41/mkin/man/plot.mmkin.Rd | 2 mkin-0.9-41/mkin/man/print.mkinds.Rd |only mkin-0.9-41/mkin/man/print.mkinmod.Rd |only mkin-0.9-41/mkin/man/summary.mkinfit.Rd | 2 mkin-0.9-41/mkin/vignettes/compiled_models.Rmd |only 33 files changed, 165 insertions(+), 93 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.3-2 dated 2015-10-29 and 1.3-4 dated 2015-11-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 11 +++++++++++ R/maxNR.R | 5 ----- R/maxNRCompute.R | 39 ++++++++++++++++++++++++++++++--------- R/maxOptim.R | 3 ++- R/summary.maxLik.R | 2 +- man/maxBFGS.Rd | 4 +++- 8 files changed, 58 insertions(+), 28 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-21 dated 2015-08-23 and 3.1-23 dated 2015-11-09
HH-3.1-21/HH/inst/shiny/NormalAndTplot |only HH-3.1-23/HH/DESCRIPTION | 8 HH-3.1-23/HH/MD5 | 81 ++--- HH-3.1-23/HH/NAMESPACE | 5 HH-3.1-23/HH/NEWS | 69 ++++ HH-3.1-23/HH/R/ancovaplot.R | 4 HH-3.1-23/HH/R/formatHex.R | 82 +++-- HH-3.1-23/HH/R/lm.case.R | 366 ++++++++++++++------------ HH-3.1-23/HH/R/lmplot.R | 18 - HH-3.1-23/HH/R/normal.and.t.R | 14 HH-3.1-23/HH/R/regrDiagn.R | 1 HH-3.1-23/HH/R/residual.plots.lattice.R | 30 +- HH-3.1-23/HH/inst/scripts/hh2/PrcnApx.R | 42 +- HH-3.1-23/HH/inst/scripts/hh2/ShinyApx.R | 8 HH-3.1-23/HH/inst/scripts/hh2/conc.R | 39 +- HH-3.1-23/HH/inst/scripts/hh2/dsgn.R | 84 +++-- HH-3.1-23/HH/inst/scripts/hh2/dsgntwo.R | 118 ++++---- HH-3.1-23/HH/inst/scripts/hh2/dstr.R | 145 ++++++---- HH-3.1-23/HH/inst/scripts/hh2/grap.R | 138 +++++---- HH-3.1-23/HH/inst/scripts/hh2/hotdog-ancova.r | 9 HH-3.1-23/HH/inst/scripts/hh2/iinf.R | 66 ++-- HH-3.1-23/HH/inst/scripts/hh2/logi.R | 65 ++-- HH-3.1-23/HH/inst/scripts/hh2/mcomp.R | 66 +--- HH-3.1-23/HH/inst/scripts/hh2/mthp.R | 6 HH-3.1-23/HH/inst/scripts/hh2/npar.R | 8 HH-3.1-23/HH/inst/scripts/hh2/oway.R | 30 +- HH-3.1-23/HH/inst/scripts/hh2/rega.R | 80 +++-- HH-3.1-23/HH/inst/scripts/hh2/regb.R | 24 - HH-3.1-23/HH/inst/scripts/hh2/regbb.R | 57 ++-- HH-3.1-23/HH/inst/scripts/hh2/regc.R | 48 +-- HH-3.1-23/HH/inst/scripts/hh2/tser.R | 74 ++--- HH-3.1-23/HH/inst/scripts/hh2/tway.R | 92 +++--- HH-3.1-23/HH/inst/scripts/hh2/twtb.R | 70 ++-- HH-3.1-23/HH/inst/scripts/hh2/typg.R | 23 + HH-3.1-23/HH/man/NormalAndTplot.Rd | 16 + HH-3.1-23/HH/man/ancovaplot.Rd | 5 HH-3.1-23/HH/man/formatHex.Rd | 18 - HH-3.1-23/HH/man/lm.case.Rd | 98 +++--- HH-3.1-23/HH/man/lmplot.Rd | 19 + HH-3.1-23/HH/man/print.latticeresids.Rd | 47 ++- HH-3.1-23/HH/man/residual.plots.lattice.Rd | 12 41 files changed, 1246 insertions(+), 939 deletions(-)
Title: Topographic and Geologic Mapping
Description: Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between GEOmap versions 2.3-5 dated 2015-04-29 and 2.3-8 dated 2015-11-09
DESCRIPTION | 10 +++--- MD5 | 16 ++++++---- NAMESPACE | 11 +++++++ R/GETXprofile.R | 8 ++--- R/distaz.R | 2 + R/getETOPO.R |only R/subsetTOPO.R | 79 ++++++++++++++++++++++------------------------------- demo/GMAP.R | 45 ++++++++++++++++++++++++------ man/GETXprofile.Rd | 3 +- man/getETOPO.Rd |only 10 files changed, 102 insertions(+), 72 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between diseasemapping versions 1.2.3 dated 2015-07-07 and 1.2.7 dated 2015-11-09
diseasemapping-1.2.3/diseasemapping/R/mergeBugsData.R |only diseasemapping-1.2.3/diseasemapping/man/mergeBugsData.Rd |only diseasemapping-1.2.7/diseasemapping/DESCRIPTION | 14 - diseasemapping-1.2.7/diseasemapping/MD5 | 18 - diseasemapping-1.2.7/diseasemapping/NAMESPACE | 1 diseasemapping-1.2.7/diseasemapping/R/bym.R | 128 ++++-------- diseasemapping-1.2.7/diseasemapping/data/casedata.RData |binary diseasemapping-1.2.7/diseasemapping/data/kentucky.RData |binary diseasemapping-1.2.7/diseasemapping/data/popdata.RData |binary diseasemapping-1.2.7/diseasemapping/data/referencepop.RData |binary diseasemapping-1.2.7/diseasemapping/tests/bym.R | 54 ++++- 11 files changed, 112 insertions(+), 103 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Complex Survey Structural Equation Modeling (SEM)
Description: Fit structural equation models (SEM) including factor analysis,
multivariate regression models with latent variables and many other latent
variable models while correcting estimates, standard errors, and
chi-square-derived fit measures for a complex sampling design.
Incorporate clustering, stratification, sampling weights, and
finite population corrections into a SEM analysis.
Wrapper around packages lavaan and survey.
Author: Daniel Oberski
Maintainer: Daniel Oberski <daniel.oberski@gmail.com>
Diff between lavaan.survey versions 1.1 dated 2014-02-21 and 1.1.3 dated 2015-11-09
DESCRIPTION | 15 ++++---- MD5 | 22 +++++++----- NAMESPACE | 15 ++++++-- R/lavaan.survey.R | 89 ++++++++++++++++++++++++-------------------------- data/cardinale.rda |binary data/ess.dk.rda |binary data/ess4.gb.rda |binary data/liss.rda |binary data/pisa.be.2003.rda |binary tests |only 10 files changed, 76 insertions(+), 65 deletions(-)
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1.3 dated 2015-11-02 and 1.1.4 dated 2015-11-08
DESCRIPTION | 14 MD5 | 26 - NAMESPACE | 2 R/Class_MRIaggr.R | 2 R/Functions_AssociatedClass.R | 2 R/Functions_GR.R | 2 R/RcppExports.R | 118 +++---- inst/List_of_arguments.R | 630 +++++++++++++++++++++-------------------- man/MRIaggr-calcGroupsW_cpp.Rd | 37 +- man/sfMM-calcPottsParameter.Rd | 148 +++++---- man/sfMM-rhoLvfree.Rd | 10 src/Functions_Potts.cpp | 36 +- src/Functions_W.cpp | 12 src/RcppExports.cpp | 13 14 files changed, 554 insertions(+), 498 deletions(-)
Title: Convert GBM Object Trees to SAS Code
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
Author: John R. Dixon
Maintainer: John R. Dixon <gbm2sas@gmail.com>
Diff between gbm2sas versions 1.0 dated 2015-04-18 and 2.0 dated 2015-11-08
gbm2sas-1.0/gbm2sas/R/gbm2sas.r |only gbm2sas-2.0/gbm2sas/DESCRIPTION | 8 ++++---- gbm2sas-2.0/gbm2sas/MD5 | 8 ++++---- gbm2sas-2.0/gbm2sas/NAMESPACE | 1 + gbm2sas-2.0/gbm2sas/R/gbm2sas.R |only gbm2sas-2.0/gbm2sas/man/gbm2sas.Rd | 11 ++++++++--- 6 files changed, 17 insertions(+), 11 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank ordering statistics method is presented to search for
differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
This method may be useful for high-throughput biological data (microarray, sequencing, ...).
Probabilities are associated with genes/probes in the dataset and there is no problem of
multiple tests when using this method. For aCGH data, segmentation results are obtained by
merging the significant probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.4 dated 2015-07-29 and 1.4.1 dated 2015-11-08
DESCRIPTION | 10 +++++----- MD5 | 46 ++++++++++++++++++++++++++++------------------ NAMESPACE | 10 +++++++--- R/fcrosC.R |only R/fcrosChrMerge.R |only R/fcrosChrSegmentC.R |only R/fcrosChrSummary.R | 30 ++++++++++++++---------------- R/fcrosMod.R | 4 ++-- R/rmat.R |only R/rmatCalc.R |only data/cghInfo.rda |binary man/cghData.Rd | 2 +- man/cghInfo.Rd | 2 +- man/fcros-package.Rd | 16 ++++++++-------- man/fcros.Rd | 2 +- man/fcros2.Rd | 2 +- man/fcrosC.Rd |only man/fcrosChrMerge.Rd |only man/fcrosChrPlot.Rd | 8 ++++---- man/fcrosChrPlot2.Rd | 8 ++++---- man/fcrosChrSegment.Rd | 8 ++++---- man/fcrosChrSegmentC.Rd |only man/fcrosChrSummary.Rd | 12 ++++++------ man/fcrosFCmat.Rd | 2 +- man/fcrosHistoPlot.Rd | 2 +- man/fcrosMod.Rd | 2 +- man/fcrosTopN.Rd | 2 +- man/rmatCalc.Rd |only src |only 29 files changed, 90 insertions(+), 78 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de> and Matthias Schmid <matthias.schmid@imbie.uni-bonn.de>
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.1.1 dated 2015-10-21 and 1.1.2 dated 2015-11-08
DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- NAMESPACE | 13 +++++-------- man/discSurv-package.Rd | 4 ++-- man/fprUno.Rd | 2 +- man/fprUnoShort.Rd | 2 +- man/tprUno.Rd | 2 +- man/tprUnoShort.Rd | 2 +- 8 files changed, 26 insertions(+), 28 deletions(-)
Title: Age-Specific Survival Analysis from Incomplete
Capture-Recapture/Recovery Data
Description: Estimates survival and mortality with covariates from capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots.
Author: Fernando Colchero, Owen Jones, Maren Rebke
Maintainer: Fernando Colchero <colchero@imada.sdu.dk>
Diff between BaSTA versions 1.9.3 dated 2014-03-01 and 1.9.4 dated 2015-11-08
BaSTA-1.9.3/BaSTA/build |only BaSTA-1.9.3/BaSTA/inst/doc/BaSTAoverview.R |only BaSTA-1.9.3/BaSTA/inst/doc/BaSTAoverview.Rnw |only BaSTA-1.9.3/BaSTA/vignettes |only BaSTA-1.9.4/BaSTA/DESCRIPTION | 18 BaSTA-1.9.4/BaSTA/MD5 | 44 BaSTA-1.9.4/BaSTA/NAMESPACE | 18 BaSTA-1.9.4/BaSTA/R/MakeCovMat.R | 40 BaSTA-1.9.4/BaSTA/R/basta.R | 3065 ++++++++++++++------------- BaSTA-1.9.4/BaSTA/R/basta.default.R | 56 BaSTA-1.9.4/BaSTA/R/multibasta.R |only BaSTA-1.9.4/BaSTA/R/plot.basta.R | 333 +- BaSTA-1.9.4/BaSTA/R/summary.basta.R | 4 BaSTA-1.9.4/BaSTA/data/sim1.RData |binary BaSTA-1.9.4/BaSTA/data/sim1Out.RData |binary BaSTA-1.9.4/BaSTA/man/BaSTA-package.Rd | 6 BaSTA-1.9.4/BaSTA/man/CensusToCaptHist.Rd | 10 BaSTA-1.9.4/BaSTA/man/MakeCovMat.Rd | 2 BaSTA-1.9.4/BaSTA/man/basta.Rd | 78 BaSTA-1.9.4/BaSTA/man/multibasta.Rd |only BaSTA-1.9.4/BaSTA/man/sim1.Rd | 2 BaSTA-1.9.4/BaSTA/man/summary.basta.Rd | 43 22 files changed, 1967 insertions(+), 1752 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.2.0 dated 2015-09-06 and 0.2.3 dated 2015-11-08
DESCRIPTION | 18 +-- MD5 | 63 ++++++----- NAMESPACE | 2 NEWS.md | 20 +++ R/colourInput.R | 8 - R/extendShinyjs.R | 3 R/useShinyjs.R | 53 +++++++-- R/utils.R | 42 ++++--- README.md | 191 +++++++++++++++++++++++++----------- inst/doc/overview.Rmd | 91 +++++++++++++---- inst/doc/overview.html | 139 +++++++++++++++++--------- inst/srcjs/inject.js |only inst/srcjs/shinyjs-default-funcs.js | 19 +++ man/classFuncs.Rd | 2 man/colourInput.Rd | 2 man/delay.Rd | 2 man/disabled.Rd | 2 man/extendShinyjs.Rd | 2 man/hidden.Rd | 2 man/inlineCSS.Rd | 2 man/js.Rd | 5 man/messageFuncs.Rd | 2 man/onevent.Rd | 2 man/reset.Rd | 2 man/runExample.Rd | 2 man/runjs.Rd | 2 man/shinyjs.Rd | 2 man/stateFuncs.Rd | 2 man/text.Rd | 2 man/updateColourInput.Rd | 2 man/useShinyjs.Rd | 20 ++- man/visibilityFuncs.Rd | 2 vignettes/overview.Rmd | 91 +++++++++++++---- 33 files changed, 556 insertions(+), 243 deletions(-)
More information about kernDeepStackNet at CRAN
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Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 0.1 dated 2014-03-07 and 0.2 dated 2015-11-08
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + R/gSeg.r | 10 ++++++++-- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3 and K4 to characterize
distributions with left and right, symmetric or asymmetric fat tails in market
finance, neuroscience and other disciplines. Two algorithms to estimate with
a high accuracy distribution parameters, quantiles, value-at-risk and expected
shortfall. Also, power hyperbolas and power hyperbolic functions. Some functions
introduced in v1.2-0 were suppressed.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.4-1 dated 2015-10-25 and 1.5-0 dated 2015-11-08
DESCRIPTION | 14 +++--- MD5 | 20 ++++----- NAMESPACE | 6 ++ NEWS | 15 +++++-- R/a_FatTailsR-package.R | 1 R/e_conversion.R | 42 +++++++++++++------- R/j_moments.R | 4 - R/l_estimation.R | 15 +++---- R/n_estimation2.R | 98 ++++++++++++++++++++++++++++++++++++------------ man/checkquantiles.Rd | 11 ++--- man/dimdim.Rd | 23 +++++++---- 11 files changed, 168 insertions(+), 81 deletions(-)
Title: PCA, Transpose and Multicore Functionality for 'big.matrix'
Objects
Description: Adds wrappers to add functionality for big.matrix objects (see the bigmemory project).
This allows fast scalable principle components analysis (PCA), or singular value decomposition (SVD).
There are also functions for transposing, using multicore 'apply' functionality, data importing
and for compact display of big.matrix objects. Most functions also work for standard matrices if
RAM is sufficient.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <nick.cooper@cimr.cam.ac.uk>
Diff between bigpca versions 1.0 dated 2014-03-04 and 1.0.3 dated 2015-11-08
DESCRIPTION | 24 +- MD5 | 50 ++--- NAMESPACE | 8 R/bigpca.R | 387 ++++++++++++++++++++++++++++++---------- man/PC.correct.Rd | 126 ++++++------- man/big.PCA.Rd | 183 +++++++++--------- man/big.algebra.install.help.Rd | 49 ++--- man/big.select.Rd | 89 +++------ man/big.t.Rd | 90 ++++----- man/bigpca-internal.Rd | 3 man/bigpca-package.Rd | 8 man/bmcapply.Rd | 148 ++++++--------- man/estimate.eig.vpcs.Rd | 110 ++++------- man/generate.test.matrix.Rd | 86 +++----- man/get.big.matrix.Rd | 29 +- man/import.big.data.Rd | 200 ++++++++------------ man/pca.scree.plot.Rd | 95 ++++----- man/prv.big.matrix.Rd | 59 ++---- man/quick.elbow.Rd | 47 +--- man/quick.pheno.assocs.Rd | 82 +++----- man/select.least.assoc.Rd | 69 +++---- man/subcor.select.Rd | 85 +++----- man/subpc.select.Rd | 91 +++------ man/svn.bigalgebra.install.Rd | 43 ++-- man/thin.Rd | 139 ++++++-------- man/uniform.select.Rd | 77 +++---- 26 files changed, 1168 insertions(+), 1209 deletions(-)
Title: Fit ARTFIMA Model
Description: Fit and simulate ARTFIMA. Theoretical autocovariance function and spectral density function for stationary ARTFIMA.
Author: A. I. McLeod, Farzad Sabzikar, Mark M. Meerschaert
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between artfima versions 1.0 dated 2015-08-27 and 1.1 dated 2015-11-08
DESCRIPTION | 8 +++---- MD5 | 9 ++++---- NEWS |only R/artfima.R | 60 ++++++++++++++++++++++++++++++++++-------------------- build/partial.rdb |binary man/artfima.Rd | 13 ++++++++++- 6 files changed, 59 insertions(+), 31 deletions(-)
Title: Financial Functions & More
Description: This fills the gaps credit analysts and loan modellers at
Optimum Credit identify in the existing R code body.
It allows for the production of documentation with less coding,
replicates a number of Microsoft Excel functions useful for
modelling loans (without rounding), and other helpful functions
for producing charts and tables. It also has some additional scales for
use, including a GBP scale.
Author: Stephanie Locke [aut, cre]
Maintainer: Stephanie Locke <stephanie.g.locke@gmail.com>
Diff between optiRum versions 0.35 dated 2014-12-08 and 0.37.1 dated 2015-11-07
optiRum-0.35/optiRum/tests/testthat/test-formatters.R |only optiRum-0.37.1/optiRum/DESCRIPTION | 21 optiRum-0.37.1/optiRum/MD5 | 162 ++-- optiRum-0.37.1/optiRum/NAMESPACE | 74 +- optiRum-0.37.1/optiRum/NEWS | 116 +-- optiRum-0.37.1/optiRum/R/APR.R | 66 - optiRum-0.37.1/optiRum/R/CJ.dt.R | 58 - optiRum-0.37.1/optiRum/R/PMT.R | 56 - optiRum-0.37.1/optiRum/R/PV.R | 68 +- optiRum-0.37.1/optiRum/R/RATE.R | 98 +- optiRum-0.37.1/optiRum/R/calcNetIncome.R |only optiRum-0.37.1/optiRum/R/convertToXML.R | 98 +- optiRum-0.37.1/optiRum/R/generatePDF.R | 104 +-- optiRum-0.37.1/optiRum/R/giniChart.R | 72 +- optiRum-0.37.1/optiRum/R/giniCoef.R | 52 - optiRum-0.37.1/optiRum/R/logit.odd.R | 36 - optiRum-0.37.1/optiRum/R/logit.prob.R | 36 - optiRum-0.37.1/optiRum/R/multiplot.R | 104 +-- optiRum-0.37.1/optiRum/R/odd.logit.R | 36 - optiRum-0.37.1/optiRum/R/odd.prob.R | 36 - optiRum-0.37.1/optiRum/R/optiRum-package.r | 24 optiRum-0.37.1/optiRum/R/pounds.R | 76 +- optiRum-0.37.1/optiRum/R/prob.logit.R | 36 - optiRum-0.37.1/optiRum/R/prob.odd.R | 36 - optiRum-0.37.1/optiRum/R/sanitise.R | 74 +- optiRum-0.37.1/optiRum/R/scaledScore.R | 40 - optiRum-0.37.1/optiRum/R/taxYear.R |only optiRum-0.37.1/optiRum/R/theme_optimum.R | 48 - optiRum-0.37.1/optiRum/R/thousands.R | 42 - optiRum-0.37.1/optiRum/R/wordwrap.R | 36 - optiRum-0.37.1/optiRum/README.md | 79 +- optiRum-0.37.1/optiRum/build |only optiRum-0.37.1/optiRum/inst |only optiRum-0.37.1/optiRum/man/APR.Rd | 90 +- optiRum-0.37.1/optiRum/man/CJ.dt.Rd | 68 +- optiRum-0.37.1/optiRum/man/PMT.Rd | 81 +- optiRum-0.37.1/optiRum/man/PV.Rd | 85 +- optiRum-0.37.1/optiRum/man/RATE.Rd | 83 +- optiRum-0.37.1/optiRum/man/calcNetIncome.Rd |only optiRum-0.37.1/optiRum/man/convertToXML.Rd | 74 +- optiRum-0.37.1/optiRum/man/generatePDF.Rd | 130 +-- optiRum-0.37.1/optiRum/man/giniChart.Rd | 68 +- optiRum-0.37.1/optiRum/man/giniCoef.Rd | 72 +- optiRum-0.37.1/optiRum/man/logit.odd.Rd | 65 - optiRum-0.37.1/optiRum/man/logit.prob.Rd | 67 + optiRum-0.37.1/optiRum/man/multiplot.Rd | 63 - optiRum-0.37.1/optiRum/man/odd.logit.Rd | 67 + optiRum-0.37.1/optiRum/man/odd.prob.Rd | 67 + optiRum-0.37.1/optiRum/man/optiRum.Rd | 27 optiRum-0.37.1/optiRum/man/pounds_format.Rd | 75 +- optiRum-0.37.1/optiRum/man/prob.logit.Rd | 67 + optiRum-0.37.1/optiRum/man/prob.odd.Rd | 67 + optiRum-0.37.1/optiRum/man/sanitise.Rd | 56 - optiRum-0.37.1/optiRum/man/scaledScore.Rd | 69 +- optiRum-0.37.1/optiRum/man/taxYear.Rd |only optiRum-0.37.1/optiRum/man/theme_optimum.Rd | 54 - optiRum-0.37.1/optiRum/man/thousands_format.Rd | 57 - optiRum-0.37.1/optiRum/man/wordwrap.Rd | 58 - optiRum-0.37.1/optiRum/tests/test-all.R | 4 optiRum-0.37.1/optiRum/tests/testthat/basic.Rnw | 18 optiRum-0.37.1/optiRum/tests/testthat/datatabletest.Rnw | 42 - optiRum-0.37.1/optiRum/tests/testthat/test-APR.R | 54 - optiRum-0.37.1/optiRum/tests/testthat/test-CJ.dt.R | 28 optiRum-0.37.1/optiRum/tests/testthat/test-PMT.R | 36 - optiRum-0.37.1/optiRum/tests/testthat/test-PV.R | 56 - optiRum-0.37.1/optiRum/tests/testthat/test-RATE.R | 56 - optiRum-0.37.1/optiRum/tests/testthat/test-calcNetIncome.R |only optiRum-0.37.1/optiRum/tests/testthat/test-convertToXML.R | 58 - optiRum-0.37.1/optiRum/tests/testthat/test-generatePDF.R | 437 ++++++------- optiRum-0.37.1/optiRum/tests/testthat/test-giniChart.R | 66 - optiRum-0.37.1/optiRum/tests/testthat/test-giniCoef.R | 68 +- optiRum-0.37.1/optiRum/tests/testthat/test-logit.odd.R | 20 optiRum-0.37.1/optiRum/tests/testthat/test-logit.prob.R | 14 optiRum-0.37.1/optiRum/tests/testthat/test-odd.logit.R | 18 optiRum-0.37.1/optiRum/tests/testthat/test-odd.prob.R | 12 optiRum-0.37.1/optiRum/tests/testthat/test-pounds.R |only optiRum-0.37.1/optiRum/tests/testthat/test-prob.logit.R | 12 optiRum-0.37.1/optiRum/tests/testthat/test-prob.odd.R | 16 optiRum-0.37.1/optiRum/tests/testthat/test-sanitise.R | 16 optiRum-0.37.1/optiRum/tests/testthat/test-scaledScore.R | 56 - optiRum-0.37.1/optiRum/tests/testthat/test-taxYear.R |only optiRum-0.37.1/optiRum/tests/testthat/test-theme_optimum.R | 14 optiRum-0.37.1/optiRum/tests/testthat/test-thousands.R |only optiRum-0.37.1/optiRum/tests/testthat/test-wordwrap.R |only optiRum-0.37.1/optiRum/vignettes |only 85 files changed, 2291 insertions(+), 2204 deletions(-)
Title: Stable Isotope Mixing Model
Description: Estimates diet contributions from isotopic sources using JAGS.
Includes estimation of concentration dependence and measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson <troutinthemilk@gmail.com>
Diff between IsotopeR versions 0.4.7 dated 2013-10-01 and 0.5 dated 2015-11-07
IsotopeR-0.4.7/IsotopeR/R/Data_Example/DisfcrimSD.csv |only IsotopeR-0.4.7/IsotopeR/R/Data_Example/SourceCD4source.csv |only IsotopeR-0.4.7/IsotopeR/R/Data_Example/Sources2source.csv |only IsotopeR-0.4.7/IsotopeR/R/Data_Example/Sources4source.csv |only IsotopeR-0.4.7/IsotopeR/R/Plot_jags.r |only IsotopeR-0.5/IsotopeR/DESCRIPTION | 16 IsotopeR-0.5/IsotopeR/MD5 | 65 IsotopeR-0.5/IsotopeR/NAMESPACE | 6 IsotopeR-0.5/IsotopeR/NEWS | 12 IsotopeR-0.5/IsotopeR/R/Data_Example/Data_Example.zip |only IsotopeR-0.5/IsotopeR/R/Data_Example/DiscrimSD.csv |only IsotopeR-0.5/IsotopeR/R/Data_Example/Mixtures.csv | 10 IsotopeR-0.5/IsotopeR/R/Data_Example/Sources.csv | 50 IsotopeR-0.5/IsotopeR/R/IsotopeRModelsGroups.R | 1289 +--------- IsotopeR-0.5/IsotopeR/R/IsotopeRModelsNoGroups.R | 1555 ------------- IsotopeR-0.5/IsotopeR/R/IsotopeRgui.R | 251 +- IsotopeR-0.5/IsotopeR/R/Plot_jags.R |only IsotopeR-0.5/IsotopeR/build/vignette.rds |binary IsotopeR-0.5/IsotopeR/man/Bi.plots.Rd | 8 IsotopeR-0.5/IsotopeR/man/IsoWrapper.Rd | 13 IsotopeR-0.5/IsotopeR/man/IsotopeR-package.Rd | 5 IsotopeR-0.5/IsotopeR/man/IsotopeR.Rd | 6 IsotopeR-0.5/IsotopeR/man/RGL.plots.Rd |only IsotopeR-0.5/IsotopeR/man/Tri.plots.Rd | 10 IsotopeR-0.5/IsotopeR/man/curves.plot.Rd | 8 IsotopeR-0.5/IsotopeR/man/load.prev.func.Rd | 3 IsotopeR-0.5/IsotopeR/vignettes/Fig1.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig10.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig11.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig12.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig13.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig14.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig15.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig16.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig17.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig18.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig19.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig2.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig20.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig21.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig22.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig3.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig4.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig5.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig6.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig7.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig8.png |only IsotopeR-0.5/IsotopeR/vignettes/Fig9.png |only IsotopeR-0.5/IsotopeR/vignettes/IsotopeR.Rnw | 488 +--- 49 files changed, 727 insertions(+), 3068 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate an play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.1.3 dated 2015-09-25 and 0.2.3 dated 2015-11-07
ProTrackR-0.1.3/ProTrackR/man/as.raw-method.Rd |only ProTrackR-0.1.3/ProTrackR/man/plot-methods.Rd |only ProTrackR-0.2.3/ProTrackR/DESCRIPTION | 26 ProTrackR-0.2.3/ProTrackR/MD5 | 67 ProTrackR-0.2.3/ProTrackR/NAMESPACE | 16 ProTrackR-0.2.3/ProTrackR/NEWS | 55 ProTrackR-0.2.3/ProTrackR/R/01supporting_functions.r | 52 ProTrackR-0.2.3/ProTrackR/R/02PTCell.r | 6 ProTrackR-0.2.3/ProTrackR/R/03PTTrack.r | 4 ProTrackR-0.2.3/ProTrackR/R/04PTPattern.r | 4 ProTrackR-0.2.3/ProTrackR/R/05PTSample.r | 120 + ProTrackR-0.2.3/ProTrackR/R/06PTModule.r | 76 - ProTrackR-0.2.3/ProTrackR/R/09playing_routines.r | 1421 ++++++++++++++++++- ProTrackR-0.2.3/ProTrackR/R/ProTrackR.r | 144 + ProTrackR-0.2.3/ProTrackR/data/mod.intro.rda |binary ProTrackR-0.2.3/ProTrackR/man/PTModule-class.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/ProTrackR.Rd | 142 + ProTrackR-0.2.3/ProTrackR/man/appendPattern.Rd | 11 ProTrackR-0.2.3/ProTrackR/man/as.raw.Rd |only ProTrackR-0.2.3/ProTrackR/man/clearSamples.Rd |only ProTrackR-0.2.3/ProTrackR/man/clearSong.Rd |only ProTrackR-0.2.3/ProTrackR/man/deletePattern.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/effect.Rd | 2 ProTrackR-0.2.3/ProTrackR/man/modToWave.Rd |only ProTrackR-0.2.3/ProTrackR/man/moduleSize.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/name.Rd | 4 ProTrackR-0.2.3/ProTrackR/man/patternLength.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/patternOrder.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/patternOrderLength.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/playMod.Rd |only ProTrackR-0.2.3/ProTrackR/man/playSample.Rd | 5 ProTrackR-0.2.3/ProTrackR/man/playWave.Rd |only ProTrackR-0.2.3/ProTrackR/man/playingtable.Rd |only ProTrackR-0.2.3/ProTrackR/man/plot.Rd |only ProTrackR-0.2.3/ProTrackR/man/read.module.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/resample.Rd |only ProTrackR-0.2.3/ProTrackR/man/sampleRate.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/trackerFlag.Rd | 10 ProTrackR-0.2.3/ProTrackR/man/waveform.Rd | 30 ProTrackR-0.2.3/ProTrackR/man/write.module.Rd | 10 40 files changed, 2046 insertions(+), 239 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.5-19 dated 2015-10-03 and 0.5-20 dated 2015-11-07
DESCRIPTION | 6 MD5 | 60 ++++---- R/ctr_estfun.R | 23 ++- R/ctr_pml_plrt_nested.R | 4 R/lav_bootstrap.R | 8 - R/lav_bootstrap_lrt.R | 4 R/lav_constraints.R | 37 +++++ R/lav_fit_measures.R | 74 ++++++---- R/lav_func_deriv.R | 31 +++- R/lav_model_information.R | 8 - R/lav_model_vcov.R | 30 ++-- R/lav_modification.R | 6 R/lav_object_inspect.R | 145 ++++++++++++++----- R/lav_object_methods.R | 55 +++---- R/lav_options.R | 37 +++-- R/lav_partable_unrestricted.R | 1 R/lav_print.R | 65 ++++++++ R/lav_start.R | 14 - R/lav_test_LRT.R | 14 - R/lav_test_diff.R | 36 ++-- R/lav_test_satorra_bentler.R | 2 R/lavaan.R | 307 ++++++++++++------------------------------ man/InformativeTesting.Rd | 6 man/cfa.Rd | 13 + man/estfun.Rd | 6 man/growth.Rd | 13 + man/lavInspect.Rd | 92 +++++++++--- man/lav_func.Rd | 11 - man/lavaan-class.Rd | 28 +++ man/lavaan.Rd | 13 + man/sem.Rd | 13 + 31 files changed, 699 insertions(+), 463 deletions(-)
Title: Linearized Bregman Algorithms for Generalized Linear Models
Description: Efficient procedures for fitting the regularization path for linear, binomial, multinomial models with lasso, group lasso or block lasso penalty. The package uses Linearized Bregman Algorithm to solve the regularization path through iterations. Bregman Inverse Scale Space Differential Inclusion solver is also provided for linear model with lasso penalty.
Author: Feng Ruan, Jiechao Xiong and Yuan Yao
Maintainer: Jiechao Xiong <xiongjiechao@pku.edu.cn>
Diff between Libra versions 1.2 dated 2015-10-20 and 1.3 dated 2015-11-07
Libra-1.2/Libra/R/LB.R |only Libra-1.2/Libra/R/plot.LB.R |only Libra-1.2/Libra/man/LB.Rd |only Libra-1.2/Libra/man/plot.LB.Rd |only Libra-1.3/Libra/DESCRIPTION | 12 ++++----- Libra-1.3/Libra/MD5 | 32 ++++++++++++++++--------- Libra-1.3/Libra/NAMESPACE | 12 +++++---- Libra-1.3/Libra/R/cv.iss.R |only Libra-1.3/Libra/R/cv.lb.R |only Libra-1.3/Libra/R/iss.R |only Libra-1.3/Libra/R/lb.R |only Libra-1.3/Libra/R/plot.lb.R |only Libra-1.3/Libra/R/predict.lb.R |only Libra-1.3/Libra/man/cv.iss.Rd |only Libra-1.3/Libra/man/cv.lb.Rd |only Libra-1.3/Libra/man/iss.Rd |only Libra-1.3/Libra/man/lb.Rd |only Libra-1.3/Libra/man/plot.lb.Rd |only Libra-1.3/Libra/man/predict.lb.Rd |only Libra-1.3/Libra/src/LBLasso.c | 18 ++++---------- Libra-1.3/Libra/src/LBheader.c | 25 ++++++++++++-------- Libra-1.3/Libra/src/LBheader.h | 6 ++-- Libra-1.3/Libra/src/LBlogistic.c | 18 ++++---------- Libra-1.3/Libra/src/LBmultilogistic.c | 42 +++++++++++++--------------------- Libra-1.3/Libra/src/Makevars | 7 ++++- 25 files changed, 86 insertions(+), 86 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 1.2 dated 2015-08-22 and 1.3 dated 2015-11-07
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 - inst/NEWS.Rd | 8 ++++++++ inst/doc/PMCMR.R | 22 ++++++++++++++-------- inst/doc/PMCMR.Rnw | 15 ++++++++++----- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 4 ++-- man/posthoc.friedman.nemenyi.test.Rd | 2 +- vignettes/PMCMR.Rnw | 15 ++++++++++----- 10 files changed, 58 insertions(+), 35 deletions(-)
Title: Post-Hoc Interaction Analysis
Description: Analysis of terms in linear, generalized and mixed linear models,
on the basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
Author: Helios De Rosario-Martinez [aut, cre],
John Fox [ctb],
R Core Team [ctb]
Maintainer: Helios De Rosario-Martinez <helios.derosario@gmail.com>
Diff between phia versions 0.2-0 dated 2015-02-16 and 0.2-1 dated 2015-11-07
ChangeLog | 17 +++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 9 +++++++-- R/interactionMeans.R | 13 ++++++++----- R/testFactors.R | 19 ++++++++++++++----- build/vignette.rds |binary inst/doc/phia.R |only inst/doc/phia.Rnw | 24 +++++++++++++++++++----- inst/doc/phia.pdf |binary man/contrastCoefficients.Rd | 2 +- man/interactionMeans.Rd | 10 +++++----- man/phia-package.Rd | 4 ++-- man/testFactors.Rd | 4 ++-- man/testInteractions.Rd | 2 +- vignettes/bibliography.bib | 40 +++++++++------------------------------- vignettes/phia.Rnw | 24 +++++++++++++++++++----- 17 files changed, 126 insertions(+), 85 deletions(-)
Title: Convert Text into Speech
Description: Convert text into speech (voice file in 'wav' format) with API offered by ITRI TTS (Text-To-Speech service, Industrial Technology Research Institute, Taiwan. http://tts.itri.org.tw/). One main function is given, tts_ITRI(). English and Chinese (both traditional and simplified) are supported, and user can specify the speaker accent, speed and volume. Using this package requires internet connection.
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between Rtts versions 0.3.2 dated 2015-09-01 and 0.3.3 dated 2015-11-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 11 +++++++++++ R/tts_ITRI.R | 2 +- R/tts_google.R | 20 +++++--------------- man/tts_google.Rd | 9 ++------- 6 files changed, 29 insertions(+), 33 deletions(-)
Title: Implementation of the Panel Data Approach Method for Program
Evaluation
Description: Implements the Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an intervention by comparing the evolution of the outcome for a unit affected by an intervention or treatment to the evolution of the unit had it not been affected by the intervention.
Author: Ainhoa Vega-Bayo
Maintainer: Ainhoa Vega-Bayo <ainhoa.vega@gmail.com>
Diff between pampe versions 1.1.1 dated 2015-05-11 and 1.1.2 dated 2015-11-07
pampe-1.1.1/pampe/R/pampeData.R |only pampe-1.1.1/pampe/man/pampeData.Rd |only pampe-1.1.2/pampe/DESCRIPTION | 8 +- pampe-1.1.2/pampe/MD5 | 13 +-- pampe-1.1.2/pampe/NAMESPACE | 5 + pampe-1.1.2/pampe/R/pampe.R | 120 +++++++----------------------- pampe-1.1.2/pampe/R/print.summary.pampe.R |only pampe-1.1.2/pampe/R/summary.pampe.R | 55 +++---------- pampe-1.1.2/pampe/man/pampe.Rd | 9 +- 9 files changed, 60 insertions(+), 150 deletions(-)
Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the
estimation of multinomial logit models with random coefficients.
Specifically, it allows estimating models with continuous heterogeneity
such as the mixed multinomial logit and the generalized multinomial logit.
It also allows estimating models with discrete heterogeneity such as the
latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre],
Ricardo Daziano [aut],
Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between gmnl versions 1.1 dated 2015-05-31 and 1.1-1 dated 2015-11-07
DESCRIPTION | 20 ++++--- MD5 | 38 +++++++------- NAMESPACE | 8 +- R/glogitform.R | 39 ++++++++------ R/gmnl.R | 124 +++++++++++++++++++++++----------------------- R/gmnl.draws.R | 96 ++++++++++++++++++----------------- R/gmnl.logliks.R | 4 + R/gmnl.methods.R | 132 ++++++++++++++++++++++++++----------------------- inst/NEWS.Rd | 9 +++ man/AIC.gmnl.Rd | 7 +- man/bread.gmnl.Rd | 4 - man/cov.gmnl.Rd | 10 +-- man/effect.gmnl.Rd | 10 +-- man/estfun.gmnl.Rd | 4 - man/gFormula.Rd | 2 man/getSummary.gmnl.Rd | 10 +-- man/gmnl.Rd | 18 +++--- man/plot.gmnl.Rd | 10 +-- man/vcov.gmnl.Rd | 2 man/wtp.gmnl.Rd | 7 +- 20 files changed, 298 insertions(+), 256 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.3.0 dated 2015-09-06 and 0.3.1 dated 2015-11-07
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- NEWS.md | 7 ++++ R/ggMarginal.R | 73 ++++++++++++++++++++++++++++++++++--------------- README.md | 14 +++------ inst/doc/overview.Rmd | 5 ++- inst/doc/overview.html | 34 ++++++++++++---------- vignettes/overview.Rmd | 5 ++- 8 files changed, 99 insertions(+), 59 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include productivity evaluation using distance measures, benchmarking,
risk analysis, technology adoption model, inverse optimization, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.5 dated 2015-10-01 and 1.6 dated 2015-11-07
DESCRIPTION | 8 - MD5 | 47 ++++--- NAMESPACE | 1 NEWS |only R/DJL-internal.R | 250 ++++++++++++++++++++--------------------- R/dm.sf.R | 4 R/roc.dea.R | 7 - R/roc.sf.R | 27 ++-- R/target.arrival.dea.R | 21 +-- R/target.arrival.sf.R |only data/dataset.airplane.2017.rda |only man/dataset.airplane.2017.Rd |only man/dataset.engine.2015.Rd | 2 man/dataset.hev.2013.Rd | 2 man/dm.ddf.Rd | 2 man/dm.dea.Rd | 2 man/dm.sbm.Rd | 5 man/dm.sf.Rd | 4 man/map.soa.ddf.Rd | 6 man/map.soa.dea.Rd | 6 man/map.soa.sbm.Rd | 8 - man/map.soa.sf.Rd | 6 man/roc.dea.Rd | 22 --- man/roc.sf.Rd | 2 man/target.arrival.dea.Rd | 33 ++--- man/target.arrival.sf.Rd |only man/target.spec.dea.Rd | 4 27 files changed, 231 insertions(+), 238 deletions(-)
Title: Computes Copula using Ranks and Subsampling
Description: Essentially a discussion tool about estimation of copula using ranks and subsampling.
Author: Jerome Collet
Maintainer: Jerome Collet <jeromepcollet@gmail.com>
Diff between subrank versions 0.9.1 dated 2014-12-12 and 0.9.4 dated 2015-11-06
DESCRIPTION | 12 ++-- MD5 | 26 ++++----- NAMESPACE | 2 R/corc0.R | 20 ++++--- R/predonfly.R | 10 ++- R/simany.R | 73 +++++++++++++++------------ man/corc0.Rd | 2 man/predonfly.Rd | 10 ++- man/simany.Rd | 16 ++--- man/subrank-package.Rd | 4 - src/copc.c | 132 ++++++++++++++++++++++++++++++++++++++----------- src/copc.h | 6 +- src/lienR.c | 7 +- src/lienR.h | 6 ++ 14 files changed, 219 insertions(+), 107 deletions(-)
Title: Simulation of Evolutionary and Epidemiological Dynamics
Description: Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.
Author: Colin Worby
Maintainer: Colin Worby <cworby@hsph.harvard.edu>
Diff between seedy versions 1.2 dated 2015-04-22 and 1.3 dated 2015-11-06
DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 5 R/deepseqmat.r |only R/sharedvariants.r |only R/simfixoutbreak.r | 257 +++++++++++++++++++++++--------------------------- R/simulateoutbreak.R | 145 ++++++++++++---------------- man/deepseqmat.Rd |only man/seedy-package.Rd | 4 man/sharedvariants.Rd |only man/simfixoutbreak.Rd | 9 + 11 files changed, 213 insertions(+), 231 deletions(-)
Title: Distributed 'randomForest' for Big Data using 'ddR' API
Description: Distributed training and prediction of random forest models based upon 'randomForest' package using 'ddR' (Distributed Data Structures) API in the 'ddR' package.
Author: Vishrut Gupta, Arash Fard, Winston Li, Matthew Saltz
Maintainer: Vishrut Gupta <vishrut.gupta@hpe.com>
Diff between randomForest.ddR versions 0.1.0 dated 2015-10-28 and 0.1.1 dated 2015-11-06
randomForest.ddR-0.1.0/randomForest.ddR/man/drandomForest-package.Rd |only randomForest.ddR-0.1.1/randomForest.ddR/DESCRIPTION | 10 +++---- randomForest.ddR-0.1.1/randomForest.ddR/MD5 | 14 +++++----- randomForest.ddR-0.1.1/randomForest.ddR/NAMESPACE | 1 randomForest.ddR-0.1.1/randomForest.ddR/README.md | 2 - randomForest.ddR-0.1.1/randomForest.ddR/man/drandomForest.Rd | 6 ++-- randomForest.ddR-0.1.1/randomForest.ddR/man/predict.drandomForest.Rd | 2 - randomForest.ddR-0.1.1/randomForest.ddR/man/randomForest.ddR-package.Rd |only randomForest.ddR-0.1.1/randomForest.ddR/tests/testthat/test-drandomForest.R | 4 +- 9 files changed, 20 insertions(+), 19 deletions(-)
More information about randomForest.ddR at CRAN
Permanent link
Title: Pictographic Representation of Treatment Effects
Description: Visualizes treatment effects using person icons, similar to Cates (NNT) charts.
Author: Joel Kuiper [aut, cre], Iain Marshall [aut]
Maintainer: Joel Kuiper <jkuiper@doctorevidence.com>
Diff between personograph versions 0.1.1 dated 2015-09-21 and 0.1.3 dated 2015-11-06
DESCRIPTION | 10 +-- MD5 | 20 +++--- NAMESPACE | 3 - R/personograph.R | 130 +++++++++++++++++++++++++++++++------------- R/test.R | 12 ++++ README.md | 13 ++-- man/calc.ier.Rd | 2 man/personograph-package.Rd | 11 +-- man/personograph.Rd | 21 +++++-- man/uplift.Rd | 4 - man/w.approx.cer.Rd | 15 +++-- 11 files changed, 165 insertions(+), 76 deletions(-)
Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, with contributions from Bertrand Pages
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between codep versions 0.4-1 dated 2014-07-30 and 0.5-1 dated 2015-11-06
codep-0.4-1/codep/src/permut.c |only codep-0.4-1/codep/src/permut.h |only codep-0.5-1/codep/DESCRIPTION | 10 - codep-0.5-1/codep/MD5 | 13 - codep-0.5-1/codep/NAMESPACE | 20 ++ codep-0.5-1/codep/R/mca.R | 187 +++++++++++++++----------- codep-0.5-1/codep/man/mca-class.Rd | 2 codep-0.5-1/codep/man/product-distribution.Rd |only codep-0.5-1/codep/src/codep.c |only codep-0.5-1/codep/src/codep.h |only 10 files changed, 144 insertions(+), 88 deletions(-)
Title: Graphical User Interface (GUI) for Interactive R Analysis
Sessions
Description: Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RPMG versions 2.1-7 dated 2015-04-26 and 2.2-1 dated 2015-11-06
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NAMESPACE | 7 +++++++ R/RESCALE.R | 18 +++++++++++++----- R/itoxyz.R | 31 +++++++++++++++++++------------ R/jpng.R | 2 +- man/RESCALE.Rd | 8 +++++--- man/itoxyz.Rd | 33 ++++++++++++++++++++------------- man/jpng.Rd | 2 +- man/xyztoi.Rd |only 10 files changed, 79 insertions(+), 47 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.9-1 dated 2015-06-12 and 1.10-0 dated 2015-11-06
Description: Implementation of statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g., discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models,
or continuous-space point process data such as the
occurrence of infectious diseases. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of communicable diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently, the package contains implementations of many typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Höhle and Paul (2008). A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Furthermore, inference methods for the retrospective infectious
disease models in Held et al (2005), Held et al (2006),
Paul et al (2008), Paul and Held (2011), Held and Paul (2012),
and Meyer and Held (2014) are provided.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ('twinSIR', discrete
space) and Meyer et al (2012) ('twinstim', continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: Using the 'boda' algorithm requires the 'INLA'
package, which should be installed automatically through the
specified Additional_repositories, if uninstalled dependencies
are also requested. As this might not work under OS X it
might be necessary to manually install the 'INLA' package as
specified at
Author: Michael Höhle [aut, ths], Sebastian Meyer [aut, cre],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <Sebastian.Meyer@ifspm.uzh.ch>
DESCRIPTION | 23 -
MD5 | 225 ++++++++--------
NAMESPACE | 51 +++
R/AllClass.R | 2
R/AllGeneric.R | 25 +
R/addSeason2formula.R | 2
R/algo_bayes.R | 12
R/algo_glrnb.R | 52 +--
R/algo_outbreakP.R | 68 ++--
R/bodaDelay.R | 425 +++++++++++++++----------------
R/calibration.R |only
R/calibration_null.R |only
R/checkDerivatives.R | 2
R/epidata.R | 49 ++-
R/epidataCS.R | 2
R/epidataCS_aggregate.R | 8
R/epidataCS_animate.R | 2
R/epidataCS_methods.R | 2
R/epidataCS_plot.R | 8
R/epidata_animate.R | 2
R/epidata_plot.R | 2
R/glm_epidataCS.R | 2
R/gpc.poly-methods.R | 2
R/graphs.R | 2
R/hhh4.R | 237 ++++++++++-------
R/hhh4_W.R | 2
R/hhh4_W_np.R | 2
R/hhh4_W_powerlaw.R | 2
R/hhh4_calibration.R |only
R/hhh4_methods.R | 105 +++++--
R/hhh4_oneStepAhead.R | 62 +++-
R/hhh4_plot.R | 245 +++++++++++++++--
R/hhh4_simulate.R | 111 ++++++--
R/hhh4_simulate_plot.R |only
R/hhh4_simulate_scores.R |only
R/intersectPolyCircle.R | 2
R/knox.R | 2
R/modifyListcall.R | 2
R/options.R | 2
R/permutationTest.R | 2
R/pit.R | 70 +++--
R/plapply.R | 2
R/qlomax.R | 2
R/scores.R | 176 ++++++++----
R/spatial_tools.R | 11
R/stK.R | 2
R/sts.R | 6
R/stsNC.R | 7
R/sts_animate.R | 24 +
R/sts_coerce.R | 6
R/sts_creation.R | 2
R/stsplot_space.R | 2
R/stsplot_spacetime.R | 2
R/stsplot_time.R | 119 ++++----
R/twinSIR.R | 2
R/twinSIR_helper.R | 2
R/twinSIR_methods.R | 2
R/twinSIR_profile.R | 2
R/twinSIR_simulation.R | 2
R/twinstim.R | 2
R/twinstim_epitest.R | 2
R/twinstim_helper.R | 2
R/twinstim_iafplot.R | 2
R/twinstim_intensity.R | 2
R/twinstim_methods.R | 36 +-
R/twinstim_siaf.R | 2
R/twinstim_siaf_powerlaw.R | 2
R/twinstim_siaf_powerlawL.R | 2
R/twinstim_siaf_step.R | 2
R/twinstim_simulation.R | 2
R/twinstim_step.R | 2
R/twinstim_tiaf.R | 2
R/twinstim_tiaf_exponential.R | 2
R/twinstim_tiaf_step.R | 2
R/untie.R | 2
R/wrap_univariate.R | 20 -
build/partial.rdb |binary
build/vignette.rds |binary
inst/CITATION | 14 +
inst/NEWS.Rd | 266 +++++++++++++++----
inst/THANKS | 1
inst/doc/glrnb.pdf |binary
inst/doc/hhh4.R | 10
inst/doc/hhh4.Rnw | 4
inst/doc/hhh4.pdf |binary
inst/doc/surveillance.pdf |binary
man/abattoir.Rd | 7
man/addFormattedXAxis.Rd |only
man/algo.outbreakP.Rd | 20 -
man/bodaDelay.Rd | 8
man/calibration.Rd |only
man/categoricalCUSUM.Rd | 4
man/epidata.Rd | 55 ++--
man/farringtonFlexible.Rd | 4
man/fluBYBW.Rd | 2
man/hhh4.Rd | 19 -
man/hhh4_calibration.Rd |only
man/hhh4_methods.Rd | 15 -
man/hhh4_plot.Rd | 100 +++++--
man/hhh4_simulate.Rd | 29 +-
man/hhh4_simulate_plot.Rd |only
man/hhh4_validation.Rd | 96 +++++--
man/layout.labels.Rd | 15 -
man/linelist2sts.Rd | 2
man/momo.Rd | 2
man/pit.Rd | 15 -
man/salmNewportTruncated.Rd | 6
man/sts-class.Rd | 1
man/sts_animate.Rd | 16 +
man/stsplot_time.Rd | 91 ++----
man/surveillance.options.Rd | 8
man/twinstim_methods.Rd | 15 -
man/twinstim_simulation.Rd | 5
man/wrap.algo.Rd | 15 -
src/surveillance.c | 238 ++++++++---------
tests/testthat/test-calibration.R |only
tests/testthat/test-hhh4+derivatives.R | 5
tests/testthat/test-hhh4_NegBinGrouped.R |only
vignettes/hhh4.Rnw | 4
119 files changed, 2121 insertions(+), 1242 deletions(-)
Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. Ongoing developments of the package
focus on offering easy to use tools for creating other spatio-dynamic
models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.1.1 dated 2015-08-19 and 1.1.2 dated 2015-11-06
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 3 ++- NEWS | 5 ++++- R/plot_maps.R | 28 +++++++++++++++++----------- inst/doc/isem2013_jml.pdf |binary 6 files changed, 33 insertions(+), 23 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the OSRM API. OSRM is a routing
service based on OpenStreetMap data. See <http://project-osrm.org/> for more
information. A public API exists but one can run its own instance. This package
allows to compute distance (travel time and kilometric distance) between points
and travel time matrices.
Author: Timothée Giraud [cre, aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between osrm versions 1.0 dated 2015-09-30 and 1.1 dated 2015-11-06
DESCRIPTION | 17 +++++++++++------ MD5 | 32 +++++++++++++++++--------------- NAMESPACE | 2 +- NEWS |only R/osrmTable.R | 4 +++- R/osrmTableErrors.R | 2 ++ R/osrmTableOD.R | 2 ++ R/osrmViaroute.R | 2 ++ R/osrmViarouteGeom.R | 40 ++++++++++++++++++++++++++++++++++++++-- README.md | 8 +++++++- inst |only man/com.Rd | 2 +- man/osrm.Rd | 10 +++++----- man/osrmTable.Rd | 16 +++++++++------- man/osrmTableErrors.Rd | 4 +++- man/osrmTableOD.Rd | 18 ++++++++++-------- man/osrmViaroute.Rd | 8 +++++--- man/osrmViarouteGeom.Rd | 29 +++++++++++++++++++++++++---- 18 files changed, 141 insertions(+), 55 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8.1 dated 2015-09-11 and 0.8.5 dated 2015-11-06
vegdata-0.8.1/vegdata/man/tv.metainfo.Rd |only vegdata-0.8.5/vegdata/DESCRIPTION | 12 vegdata-0.8.5/vegdata/MD5 | 69 vegdata-0.8.5/vegdata/NAMESPACE | 11 vegdata-0.8.5/vegdata/R/internal.r | 17 vegdata-0.8.5/vegdata/R/isc.r |only vegdata-0.8.5/vegdata/R/reflist.r | 6 vegdata-0.8.5/vegdata/R/syntab.r | 6 vegdata-0.8.5/vegdata/R/tax_add.r | 59 vegdata-0.8.5/vegdata/R/taxval.r | 32 vegdata-0.8.5/vegdata/R/tv.coverperc.r | 5 vegdata-0.8.5/vegdata/R/tv.home.r | 6 vegdata-0.8.5/vegdata/R/tv.metainfo.r | 4 vegdata-0.8.5/vegdata/R/tv.obs.r | 14 vegdata-0.8.5/vegdata/R/tv.site.r | 24 vegdata-0.8.5/vegdata/R/tv.traits.r | 49 vegdata-0.8.5/vegdata/R/tv.veg.r | 2 vegdata-0.8.5/vegdata/R/tv.write.r | 49 vegdata-0.8.5/vegdata/R/vw.site.r |only vegdata-0.8.5/vegdata/R/vw.veg.r |only vegdata-0.8.5/vegdata/inst/CITATION | 6 vegdata-0.8.5/vegdata/inst/ChangeLog | 4 vegdata-0.8.5/vegdata/inst/doc/vegdata.R | 30 vegdata-0.8.5/vegdata/inst/doc/vegdata.Rnw | 990 +++++------ vegdata-0.8.5/vegdata/inst/doc/vegdata.pdf |binary vegdata-0.8.5/vegdata/inst/tvdata/Data/elbaue/tvabund.dbf |binary vegdata-0.8.5/vegdata/inst/tvdata/Data/elbaue/tvhabita.dbf |binary vegdata-0.8.5/vegdata/inst/tvdata/Data/elbaue/tvwin.set |binary vegdata-0.8.5/vegdata/inst/tvdata/Data/taxatest/tvabund.dbf |binary vegdata-0.8.5/vegdata/inst/tvdata/Data/taxatest/tvhabita.dbf |binary vegdata-0.8.5/vegdata/man/isc.Rd |only vegdata-0.8.5/vegdata/man/tv.metadata.Rd |only vegdata-0.8.5/vegdata/man/tv.site.Rd | 4 vegdata-0.8.5/vegdata/man/tv.traits.Rd | 7 vegdata-0.8.5/vegdata/man/tv.write.Rd | 4 vegdata-0.8.5/vegdata/man/vegdata-internal.Rd | 3 vegdata-0.8.5/vegdata/man/vegetweb.Rd |only vegdata-0.8.5/vegdata/tests/testthat/test.R | 93 - vegdata-0.8.5/vegdata/vignettes/vegdata.Rnw | 990 +++++------ 39 files changed, 1261 insertions(+), 1235 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between eHOF versions 1.5.9 dated 2015-07-08 and 1.6 dated 2015-11-06
DESCRIPTION | 8 ++++---- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 5 +---- R/Para.deriv.r | 8 ++++---- R/Para.niche.r | 2 +- R/Para.opt.r | 13 ++++++------- R/Para.r | 8 ++++---- R/plot.HOF.r | 4 +++- inst/ChangeLog | 10 +++++++--- inst/doc/eHOF.R | 10 +++++----- inst/doc/eHOF.Rnw | 10 +++++----- inst/doc/eHOF.pdf |binary man/HOF-internal.Rd | 5 ++--- man/HOF.Rd | 5 ++--- man/Para-deriv.Rd |only man/Para.Rd | 9 ++++----- vignettes/eHOF.Rnw | 10 +++++----- 17 files changed, 69 insertions(+), 69 deletions(-)
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between textreuse versions 0.1.1 dated 2015-11-04 and 0.1.2 dated 2015-11-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ R/TextReuseTextDocument.R | 10 ++++++++++ R/lsh.R | 3 ++- src/shingle_ngrams.cpp | 4 +++- tests/testthat/test-TextReuseCorpus.R | 7 +++---- tests/testthat/test-wordcount.R | 3 --- 8 files changed, 35 insertions(+), 20 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) and all of its variants in generalized linear models and the Cox proportional hazards model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana <diego@stat.columbia.edu>
Diff between SIS versions 0.7-5 dated 2015-03-16 and 0.7-6 dated 2015-11-06
SIS-0.7-5/SIS/data/leukemia.RData |only SIS-0.7-6/SIS/DESCRIPTION | 8 ++++---- SIS-0.7-6/SIS/MD5 | 29 ++++++++++++++--------------- SIS-0.7-6/SIS/NAMESPACE | 1 + SIS-0.7-6/SIS/R/SIS.R | 2 +- SIS-0.7-6/SIS/R/setsize.R | 2 +- SIS-0.7-6/SIS/data/datalist | 3 +-- SIS-0.7-6/SIS/data/leukemia.test.RData |binary SIS-0.7-6/SIS/data/leukemia.train.RData |binary SIS-0.7-6/SIS/data/prostate.test.RData |binary SIS-0.7-6/SIS/data/prostate.train.RData |binary SIS-0.7-6/SIS/man/SIS.Rd | 6 +++--- SIS-0.7-6/SIS/man/leukemia.test.Rd | 2 +- SIS-0.7-6/SIS/man/leukemia.train.Rd | 2 +- SIS-0.7-6/SIS/man/prostate.test.Rd | 2 +- SIS-0.7-6/SIS/man/prostate.train.Rd | 2 +- 16 files changed, 29 insertions(+), 30 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.30 dated 2015-10-14 and 0.4.31 dated 2015-11-06
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS | 3 +++ R/checkFuncs.r | 6 +++--- README.md |only build/RUnit.pdf |binary inst/doc/RUnit.pdf |binary 7 files changed, 16 insertions(+), 12 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery <raftery@uw.edu>, Jennifer Hoeting,
Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.4 dated 2015-06-22 and 3.18.6 dated 2015-11-06
ChangeLog | 6 ++++++ DESCRIPTION | 19 ++++++++++--------- MD5 | 6 +++--- NAMESPACE | 8 +++++++- 4 files changed, 26 insertions(+), 13 deletions(-)
Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character
Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with
machine readable zones, e.g. passports. Get the results in a variety of formats
including plain text and XML. To learn more about the Abbyy OCR API, see http://
ocrsdk.com/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between abbyyR versions 0.2.1 dated 2015-11-04 and 0.2.2 dated 2015-11-06
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS | 8 ++++++++ R/abbyyR.R | 10 +++++----- R/getTaskStatus.R | 2 +- R/processPhotoId.R | 5 +++-- R/setapp.R | 41 ++++++++++++++++++++++++++++++++++------- inst/doc/example.Rmd | 4 ---- inst/doc/example.html | 5 ++--- inst/doc/overview.html | 4 ++-- inst/doc/wiscads.html | 4 ++-- man/abbyyR-package.Rd | 6 +++--- man/processPhotoId.Rd | 2 +- man/setapp.Rd | 10 ++++++++-- vignettes/example.Rmd | 4 ---- 15 files changed, 86 insertions(+), 53 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Diff between markophylo versions 1.0.2 dated 2015-08-31 and 1.0.3 dated 2015-11-05
DESCRIPTION | 22 +++-- MD5 | 24 +++-- NAMESPACE | 6 - NEWS | 12 ++ R/custom-general14.R | 85 ++++++++++++++------ inst/CITATION |only inst/doc/estimaterates.R | 30 +++++-- inst/doc/estimaterates.Rmd | 59 +++++++++++--- inst/doc/estimaterates.html | 179 +++++++++++++++++++++++++------------------- man/estimaterates.Rd | 4 man/markophylo-package.Rd | 6 - man/patterns.Rd |only man/plottree.Rd | 4 vignettes/estimaterates.Rmd | 59 +++++++++++--- 14 files changed, 327 insertions(+), 163 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.18 dated 2015-10-07 and 0.5.20 dated 2015-11-05
vtreat-0.5.18/vtreat/man/getNewVarNames.Rd |only vtreat-0.5.18/vtreat/tests/testthat/testRareCases.R |only vtreat-0.5.20/vtreat/DESCRIPTION | 8 vtreat-0.5.20/vtreat/MD5 | 22 - vtreat-0.5.20/vtreat/NAMESPACE | 2 vtreat-0.5.20/vtreat/R/vtreat.R | 269 +++++++++++++------- vtreat-0.5.20/vtreat/README.md | 2 vtreat-0.5.20/vtreat/man/designTreatmentsC.Rd | 6 vtreat-0.5.20/vtreat/man/designTreatmentsN.Rd | 6 vtreat-0.5.20/vtreat/man/designTreatmentsZ.Rd |only vtreat-0.5.20/vtreat/man/prepare.Rd | 4 vtreat-0.5.20/vtreat/man/vtreat-package.Rd | 4 vtreat-0.5.20/vtreat/tests/testthat/testNoY.R |only vtreat-0.5.20/vtreat/vignettes/vtreatOverfit.Rmd | 7 14 files changed, 216 insertions(+), 114 deletions(-)
Title: Survival Prediction by Joint Analysis of Microarray Gene
Expression Data
Description: Microarray gene expression data can be analyzed individually or jointly using merging methods or meta-analysis to predict patients' survival and risk assessment.
Author: Haleh Yasrebi
Maintainer: Haleh Yasrebi<hyasrebi@yahoo.com>
Diff between survJamda versions 1.1.3 dated 2015-05-02 and 1.1.4 dated 2015-11-05
DESCRIPTION | 8 ++-- MD5 | 76 ++++++++++++++++++++------------------ NAMESPACE | 9 ++++ R/calPerformance.auc.plot.R | 6 ++- R/calPerformance.merge.indep.R | 5 +- R/calPerformance.meta.R | 2 - R/calPerformance.single.indep.R | 3 + R/comb.surv.censor.R | 6 +-- R/compute.combat.R | 4 +- R/cross.val.combat.R | 4 +- R/cross.val.surv.R | 5 +- R/det.batchID.R | 2 - R/det.set.ind.R | 15 +------ R/eval.subset.R | 4 +- R/featureselection.R | 1 R/main.merge.indep.valid.R | 8 ++-- R/main.process.R | 13 +++--- R/plot.roc.curves.R |only R/plot.time.dep.R |only R/plotROC.R | 20 ++-------- R/pred.time.indep.valid.R | 8 ++-- R/prepcombat.R | 10 ++--- R/prepzscore1.R | 7 +-- R/prepzscore2.R | 1 R/splitMerged.auc.plot.R | 7 +-- R/splitMerged.indep.R | 14 +++---- R/splitZscore2.auc.plot.R | 4 +- R/splitZscore2.merge.indep.R | 5 +- inst/doc/survJamda.pdf |binary man/calPerformance.auc.plot.Rd | 9 +++- man/calPerformance.merge.indep.Rd | 6 +-- man/main.process.Rd | 10 +++-- man/plot.roc.curves.Rd |only man/plot.time.dep.Rd |only man/plotROC.Rd | 11 +++-- man/pred.time.indep.valid.Rd | 6 ++- man/splitMerged.auc.plot.Rd | 4 +- man/splitMerged.indep.Rd | 10 ++--- man/splitZscore2.auc.plot.Rd | 5 ++ man/splitZscore2.merge.indep.Rd | 5 ++ man/survJamda-package.Rd | 11 +++-- 41 files changed, 172 insertions(+), 152 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.0-23 dated 2015-08-16 and 1.0-25 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 4 ++-- inst/NEWS | 10 ++++++++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.11 dated 2015-08-26 and 0.0.12 dated 2015-11-05
DESCRIPTION | 11 - MD5 | 31 ++-- NAMESPACE | 7 - R/UTA.R | 16 ++ R/UTADIS.R | 18 ++ R/UTASTAR.R | 15 ++ R/additiveValueFunctionElicitation.R | 2 R/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R | 23 +++ R/plotAlternativesValuesPreorder.R |only R/weightedSum.R | 70 +++++------ man/UTA.Rd | 42 ++---- man/UTASTAR.Rd | 10 - man/applyPiecewiseLinearValueFunctionsOnPerformanceTable.Rd | 10 - man/assignAlternativesToCategoriesByThresholds.Rd | 3 man/plotAlternativesValuesPreorder.Rd |only tests/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R | 2 tests/assignAlternativesToCategoriesByThresholds.R | 2 tests/plotAlternativesValuesPreorder.R |only 18 files changed, 156 insertions(+), 106 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 0.1 dated 2015-07-22 and 0.3 dated 2015-11-05
imputeTS-0.1/imputeTS/R/int.precheck.R |only imputeTS-0.1/imputeTS/man/precheck.Rd |only imputeTS-0.3/imputeTS/DESCRIPTION | 12 ++++--- imputeTS-0.3/imputeTS/MD5 | 42 +++++++++++++++++--------- imputeTS-0.3/imputeTS/NAMESPACE | 11 ++++++ imputeTS-0.3/imputeTS/NEWS | 17 ++++++++++ imputeTS-0.3/imputeTS/R/data.heating.R |only imputeTS-0.3/imputeTS/R/data.nh4.R |only imputeTS-0.3/imputeTS/R/imputeTS-package.R |only imputeTS-0.3/imputeTS/R/int.algoInterface.R |only imputeTS-0.3/imputeTS/R/int.preCheck.R |only imputeTS-0.3/imputeTS/R/na.replace.R | 2 - imputeTS-0.3/imputeTS/R/na.seadec.R |only imputeTS-0.3/imputeTS/R/na.seasplit.R |only imputeTS-0.3/imputeTS/R/vis.differences.R |only imputeTS-0.3/imputeTS/data |only imputeTS-0.3/imputeTS/inst/TODO | 18 +++++++++-- imputeTS-0.3/imputeTS/man/heating.Rd |only imputeTS-0.3/imputeTS/man/imputeTS-package.Rd |only imputeTS-0.3/imputeTS/man/na.interpolation.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.locf.Rd | 11 +++--- imputeTS-0.3/imputeTS/man/na.mean.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.random.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.remove.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.replace.Rd | 9 +++-- imputeTS-0.3/imputeTS/man/na.seadec.Rd |only imputeTS-0.3/imputeTS/man/na.seasplit.Rd |only imputeTS-0.3/imputeTS/man/nh4.Rd |only imputeTS-0.3/imputeTS/man/vis.differences.Rd |only 29 files changed, 111 insertions(+), 47 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2.2 dated 2015-10-21 and 2.3 dated 2015-11-05
pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.R |only pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.Rd |only pcnetmeta-2.3/pcnetmeta/DESCRIPTION | 12 ++++---- pcnetmeta-2.3/pcnetmeta/MD5 | 32 +++++++++++------------ pcnetmeta-2.3/pcnetmeta/NAMESPACE | 4 +- pcnetmeta-2.3/pcnetmeta/R/absolute.plot.R | 9 +++++- pcnetmeta-2.3/pcnetmeta/R/contrast.plot.R | 10 +++++-- pcnetmeta-2.3/pcnetmeta/R/nma.ab.bin.R |only pcnetmeta-2.3/pcnetmeta/R/nma.ab.cont.R | 25 ++++++++++++----- pcnetmeta-2.3/pcnetmeta/R/nma.ab.followup.R | 9 +++++- pcnetmeta-2.3/pcnetmeta/R/nma.ab.py.R | 8 +++++ pcnetmeta-2.3/pcnetmeta/man/absolute.plot.Rd | 10 +++++-- pcnetmeta-2.3/pcnetmeta/man/contrast.plot.Rd | 12 +++++--- pcnetmeta-2.3/pcnetmeta/man/nma.ab.bin.Rd |only pcnetmeta-2.3/pcnetmeta/man/nma.ab.cont.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/nma.ab.followup.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/nma.ab.py.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/pcnetmeta-package.Rd | 2 - pcnetmeta-2.3/pcnetmeta/man/rank.prob.Rd | 4 +- 19 files changed, 92 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-02 0.5
2014-09-07 0.4
2014-08-26 0.3
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 0.94-3 dated 2015-08-26 and 0.94-4 dated 2015-11-05
DESCRIPTION | 10 - MD5 | 15 +- NAMESPACE | 1 R/RSAGA-core.R | 9 - R/RSAGA-modules.R | 257 +++++++++++++++++++++++++++++++++++++++--- R/RSAGA-package.R | 2 inst/doc/RSAGA-landslides.pdf |binary man/RSAGA-package.Rd | 2 man/rsaga.pisr2.Rd |only 9 files changed, 262 insertions(+), 34 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.4 dated 2015-08-22 and 3.3.6 dated 2015-11-05
DESCRIPTION | 14 - MD5 | 67 ++++----- NAMESPACE | 5 NEWS | 47 ++++++ R/ANOVA.R | 190 ++++++++++++++++++++++---- R/ANOVAz1.R | 265 ++++++++++++++++++++++--------------- R/ANOVAz2.R | 331 +++++++++++++++++++++++++++++------------------ R/Logit.R | 35 ++++ R/Read.R | 82 ++++++++--- R/Regression.R | 50 ++----- R/ScatterPlot.R | 4 R/anova.zknitr.R |only R/details.R | 9 - R/logit.z4Pred.R | 2 R/plt.zmain.R | 17 -- R/print.outall.r | 2 R/reg.z1anvBasic.R | 7 R/reg.z1bckBasic.R | 10 - R/reg.z1modelBasic.R | 2 R/reg.z2Relations.R | 21 +- R/reg.z3resfitResidual.R | 2 R/reg.z4Pred.R | 2 R/reg.z5Plot.R | 51 +++---- R/reg.zknitr.R | 14 - R/ttest.R | 4 R/ttp2zgraph.R | 3 R/zzz.R | 67 ++++++--- man/ANOVA.Rd | 51 ++++++- man/BoxPlot.Rd | 2 man/Density.Rd | 2 man/Histogram.Rd | 2 man/Logit.Rd | 2 man/Read.Rd | 7 man/Regression.Rd | 18 -- man/ScatterPlot.Rd | 15 -- 35 files changed, 904 insertions(+), 498 deletions(-)
Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet'
software.
Author: Emily Beylerian [cre, aut],
Kirk Li [ctb],
Samuel Jenness [ctb],
Martina Morris [ctb]
Maintainer: Emily Beylerian <ebey@uw.edu>
Diff between statnetWeb versions 0.3.6 dated 2015-08-21 and 0.4.0 dated 2015-11-05
DESCRIPTION | 15 +-- MD5 | 24 ++--- NAMESPACE | 4 R/run_sw.R | 1 R/statnetWeb-package.R | 2 README.md | 45 +-------- inst/shiny/global.R | 40 ++++++-- inst/shiny/server.R | 213 ++++++++++++++++++++++++++++++++++++++++------- inst/shiny/ui.R | 43 +++++++-- inst/shiny/www/alert.js | 9 + inst/shiny/www/style.css | 10 +- man/run_sw.Rd | 4 man/statnetWeb.Rd | 2 13 files changed, 299 insertions(+), 113 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.4.11 dated 2015-08-18 and 1.4.12 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 2 +- R/CDCabove.R | 4 +++- R/CDCbelow.R | 5 +++-- R/Effectsize.R | 25 +++++++++++++++++++++++++ R/RobustCDCabove.R | 7 ++++++- R/RobustCDCbelow.R | 5 ++++- R/meanES.R |only man/meanES.Rd |only 10 files changed, 55 insertions(+), 17 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.2 dated 2015-10-27 and 1.7.3 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/build.dist.struct.R | 11 +++++++---- R/rcbalance.R | 4 +++- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab. Thus they
are available to the user as a script file or as an aide for the user to
learn R or to copy-and-paste directly into R itself.
Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (Author of original print.summary.nnet),
Jose Magana [ctb] (Contributed the ggpairs plots.)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 3.5.0 dated 2015-07-14 and 4.0.0 dated 2015-11-05
rattle-3.5.0/rattle/R/pam.R |only rattle-3.5.0/rattle/inst/etc/rattle.ui.140722 |only rattle-3.5.0/rattle/inst/etc/rattle.ui.150207 |only rattle-4.0.0/rattle/DESCRIPTION | 35 rattle-4.0.0/rattle/MD5 | 69 - rattle-4.0.0/rattle/NAMESPACE | 5 rattle-4.0.0/rattle/R/acquireAuditData.R | 12 rattle-4.0.0/rattle/R/appendLibLog.R |only rattle-4.0.0/rattle/R/binning.R | 12 rattle-4.0.0/rattle/R/data.R | 91 + rattle-4.0.0/rattle/R/evaluate.R | 56 - rattle-4.0.0/rattle/R/executeBoxPlot2.R |only rattle-4.0.0/rattle/R/executeHistPlot2.R | 99 +- rattle-4.0.0/rattle/R/executePairsPlotSelect2.R |only rattle-4.0.0/rattle/R/explore.R | 300 +----- rattle-4.0.0/rattle/R/fancyRpartPlot.R | 41 rattle-4.0.0/rattle/R/hclust.R | 28 rattle-4.0.0/rattle/R/help.R | 8 rattle-4.0.0/rattle/R/kmeans.R | 21 rattle-4.0.0/rattle/R/log.R | 24 rattle-4.0.0/rattle/R/rattle.R | 36 rattle-4.0.0/rattle/R/rattleInfo.R | 20 rattle-4.0.0/rattle/R/riskchart.R | 6 rattle-4.0.0/rattle/R/rpart.R | 9 rattle-4.0.0/rattle/build/vignette.rds |binary rattle-4.0.0/rattle/data/locationsAUS.RData |binary rattle-4.0.0/rattle/data/weather.RData |binary rattle-4.0.0/rattle/data/weatherAUS.RData |binary rattle-4.0.0/rattle/inst/NEWS | 88 + rattle-4.0.0/rattle/inst/doc/rattle.R | 8 rattle-4.0.0/rattle/inst/doc/rattle.Rnw | 23 rattle-4.0.0/rattle/inst/doc/rattle.pdf |binary rattle-4.0.0/rattle/inst/etc/ConnectRlogo.png |only rattle-4.0.0/rattle/inst/etc/rattle.ui | 1187 +++++++++++------------- rattle-4.0.0/rattle/inst/etc/tooltips.xml | 3 rattle-4.0.0/rattle/man/fancyRpartPlot.Rd | 11 rattle-4.0.0/rattle/man/internal.Rd | 1 rattle-4.0.0/rattle/man/riskchart.Rd | 10 rattle-4.0.0/rattle/vignettes/rattle.Rnw | 23 39 files changed, 1133 insertions(+), 1093 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.10 dated 2015-07-10 and 0.0.12 dated 2015-11-05
DESCRIPTION | 8 - MD5 | 18 +-- inst/include/Error_utils.h | 40 ++++---- inst/include/Solve.h | 2 inst/include/utils.h | 3 src/Error_utils.h | 40 ++++---- src/RFutils.cc | 2 src/Solve.h | 2 src/solve.cc | 223 ++++++++++++++++++++++++++++----------------- src/utils.h | 3 10 files changed, 204 insertions(+), 137 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.1 dated 2015-07-25 and 3.1.3 dated 2015-11-05
DESCRIPTION | 6 MD5 | 48 +++--- NAMESPACE | 8 - R/Methods-aux.R | 6 R/RFgui.R | 231 +++++++++++++------------------- R/convert.R | 7 R/fitgauss.R | 310 +++++++++++++++++++++---------------------- R/internal_use.R | 1 R/rf-plots.R | 40 +---- man/RFgridDataFrame-class.Rd | 2 man/RFgui.Rd | 7 src/MLE.cc | 7 src/Primitive.cc | 2 src/RF.h | 9 - src/direct.cc | 9 - src/error.h | 11 - src/gausslikeli.cc | 117 +++++++++++++--- src/getNset.cc | 5 src/hyperplan.cc | 10 - src/initNerror.cc | 12 - src/nugget.cc | 9 - src/plusmalS.cc | 12 + src/sequential.cc | 10 - src/trend.cc | 2 src/variogramAndCo.cc | 7 25 files changed, 452 insertions(+), 436 deletions(-)
Title: Permutation Significance for Random Forests
Description: Estimate False Discovery Rates (FDRs) for importance metrics from random forest runs.
Author: Ankur Chakravarthy
Maintainer: Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>
Diff between pRF versions 1.0 dated 2015-03-03 and 1.1 dated 2015-11-05
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/AC_pRF.R | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.6 dated 2015-11-03 and 0.4.6-1 dated 2015-11-05
DESCRIPTION | 8 +- MD5 | 69 +++++++++++---------- NAMESPACE | 2 R/bundle.R | 19 ++++-- R/utils.R | 18 +++++ inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 man/appDependencies.Rd | 9 +- man/bundle.Rd | 9 ++ man/clean.Rd | 2 man/disable.Rd | 2 man/init.Rd | 2 man/install.Rd | 2 man/install_github.Rd | 10 +-- man/install_local.Rd | 2 man/migrate.Rd | 2 man/packify.Rd | 2 man/packrat-external.Rd | 2 man/packrat-mode.Rd | 2 man/packrat-options.Rd | 2 man/packrat.Rd | 3 man/repos_create.Rd | 2 man/repos_upload.Rd | 2 man/repository-management.Rd | 4 - man/restore.Rd | 2 man/search_path.Rd | 2 man/snapshot.Rd | 10 +-- man/snapshotImpl.Rd | 10 +-- man/status.Rd | 2 man/unbundle.Rd | 2 man/unused_packages.Rd | 2 tests/testthat/helper-bundle.R |only tests/testthat/test-bundle.R | 98 ++++++++----------------------- tests/testthat/test-downloader.R | 4 + tests/testthat/test-hash.R | 8 ++ tests/testthat/test-local-repositories.R | 5 - 36 files changed, 158 insertions(+), 166 deletions(-)
Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity
score analysis for multilevel, or clustered, data.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between multilevelPSA versions 1.2.2 dated 2014-11-25 and 1.2.3 dated 2015-11-05
DESCRIPTION | 13 ++-- MD5 | 92 ++++++++++++++++----------------- NAMESPACE | 18 ++++++ NEWS | 6 ++ R/mlpsa.logistic.R | 2 R/multilevelPSA-package.R | 3 + R/plot.mlpsa.circ.R | 65 +++++++++++------------ R/plot.mlpsa.distribution.R | 15 +++-- R/xtable.mlpsa.r | 6 +- README.md | 10 ++- man/align.plots.Rd | 3 - man/as.data.frame.covariate.balance.Rd | 3 - man/covariate.balance.Rd | 3 - man/covariateBalance.Rd | 25 ++++---- man/cv.trans.psa.Rd | 13 ++-- man/difftable.plot.Rd | 3 - man/geom_rug_alt.Rd | 3 - man/getPropensityScores.Rd | 3 - man/getStrata.Rd | 3 - man/is.mlpsa.Rd | 3 - man/loess.plot.Rd | 11 ++- man/lsos.Rd | 7 +- man/missing.plot.Rd | 3 - man/mlpsa.Rd | 11 ++- man/mlpsa.circ.plot.Rd | 13 ++-- man/mlpsa.ctree.Rd | 5 + man/mlpsa.difference.plot.Rd | 9 +-- man/mlpsa.distribution.plot.Rd | 7 +- man/mlpsa.logistic.Rd | 3 - man/multilevelPSA-package.Rd | 7 +- man/pisa.colnames.Rd | 3 - man/pisa.countries.Rd | 3 - man/pisa.psa.cols.Rd | 3 - man/pisana.Rd | 7 +- man/plot.covariate.balance.Rd | 3 - man/plot.mlpsa.Rd | 11 ++- man/plot.psrange.Rd | 3 - man/print.covariate.balance.Rd | 3 - man/print.mlpsa.Rd | 3 - man/print.psrange.Rd | 3 - man/print.xmlpsa.Rd | 3 - man/psrange.Rd | 7 +- man/summary.mlpsa.Rd | 3 - man/summary.psrange.Rd | 3 - man/tree.plot.Rd | 5 + man/xtable.mlpsa.Rd | 9 ++- man/zeroGrob.Rd | 3 - 47 files changed, 259 insertions(+), 184 deletions(-)
Title: Linear Parametric Models Applied to Hydrological Series
Description: Apply Univariate Long Memory Models,
Multivariate Short Memory Models To Hydrological Dataset.
Author: Corrado Tallerini [aut, cre],
Salvatore Grimaldi [aut]
Maintainer: Corrado Tallerini <corrado.tallerini@vodafone.it>
Diff between LPM versions 2.5 dated 2015-07-08 and 2.6 dated 2015-11-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++---- NAMESPACE | 2 +- R/IDFcurve.R |only build/partial.rdb |binary data/Hourly.rainfall.series.rda |only man/Hourly.rainfall.series.Rd |only man/IDFcurve.Rd |only man/restrict.Rd | 7 +++++++ 9 files changed, 21 insertions(+), 10 deletions(-)
Title: Multiresolution Kriging Based on Markov Random Fields
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. An extension of this
version over previous ones ( < 5.4 ) is the support for different
geometries besides a rectangular domain.
One benefit of the LatticeKrig model/approach
is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 5.4 dated 2015-10-22 and 5.4-1 dated 2015-11-05
DESCRIPTION | 8 +- MD5 | 44 ++++++------ R/LKrig.precision.R | 7 +- R/LKrigNormalizeBasis.R | 3 R/Radial.basis.R | 2 R/Tensor.basis.R | 2 man/LKrig.Rd | 2 man/LKrig.basis.Rd | 15 ++++ man/LatticeKrig.Rd | 11 +-- man/gridList-class.Rd | 119 +++++++++++++++++------------------ tests/LKrig.FindNorm.test.Rout.save | 6 - tests/LKrig.basis.test.R | 4 - tests/LKrig.basis.test.Rout.save | 6 - tests/LKrig.lnPLike.test.R | 4 - tests/LKrig.lnPlike.test.Rout.save | 6 - tests/LKrig.nullspace.test.Rout.save | 6 - tests/LKrig.precision.test.R | 18 ++--- tests/LKrig.precision.test.Rout.save | 6 - tests/LKrig.se.test.Rout.save | 6 - tests/LKrig.test.3D.Rout.save | 6 - tests/LKrig.test.R | 6 - tests/LKrig.test.Rout.save | 6 - tests/LKrig.test.inverse.R | 6 - 23 files changed, 158 insertions(+), 141 deletions(-)
Title: Read and Preprocess Fluorescence Excitation-Emission Matrix
(EEM) Data
Description: Read raw EEM data and prepares them for further analysis.
Author: Vipavee Trivittayasil
Maintainer: Vipavee Trivittayasil <vipavee.tri@gmail.com>
Diff between EEM versions 1.0.1 dated 2015-08-05 and 1.0.4 dated 2015-11-05
EEM-1.0.1/EEM/README.md |only EEM-1.0.4/EEM/DESCRIPTION | 12 +-- EEM-1.0.4/EEM/MD5 | 31 ++++----- EEM-1.0.4/EEM/R/EEM.R | 2 EEM-1.0.4/EEM/R/drawEEM.R | 116 +++++++++++++++++++++-------------- EEM-1.0.4/EEM/R/findLocalMax.R | 6 + EEM-1.0.4/EEM/R/plotScore.R | 22 +++--- EEM-1.0.4/EEM/R/plotScorem.R | 8 +- EEM-1.0.4/EEM/inst/doc/vignette.R | 10 +-- EEM-1.0.4/EEM/inst/doc/vignette.Rmd | 12 +-- EEM-1.0.4/EEM/inst/doc/vignette.html | 19 +++-- EEM-1.0.4/EEM/man/EEM.Rd | 2 EEM-1.0.4/EEM/man/drawEEM.Rd | 47 +++++++------- EEM-1.0.4/EEM/man/findLocalMax.Rd | 2 EEM-1.0.4/EEM/man/plotScore.Rd | 10 +-- EEM-1.0.4/EEM/man/plotScorem.Rd | 4 - EEM-1.0.4/EEM/vignettes/vignette.Rmd | 12 +-- 17 files changed, 171 insertions(+), 144 deletions(-)
Title: Double Generalized Linear Models
Description: Model fitting and evaluation tools for double generalized linear models (DGLMs).
This class of models uses one generalized linear model (GLM) to fit the specified response and
a second GLM to fit the deviance of the first model.
Author: Peter K Dunn <pdunn2@usc.edu.au> and Gordon K Smyth
Maintainer: Robert Corty <robert_corty@med.unc.edu>
Diff between dglm versions 1.8.1 dated 2014-11-07 and 1.8.2 dated 2015-11-05
dglm-1.8.1/dglm/R/dglmall.R |only dglm-1.8.2/dglm/DESCRIPTION | 16 +++++++++------- dglm-1.8.2/dglm/MD5 | 15 +++++++++++---- dglm-1.8.2/dglm/NAMESPACE | 5 +++++ dglm-1.8.2/dglm/R/anova.dglm.R |only dglm-1.8.2/dglm/R/dglm.R |only dglm-1.8.2/dglm/R/dglm.constant.R |only dglm-1.8.2/dglm/R/dglm.control.R |only dglm-1.8.2/dglm/R/print.summary.dglm.R |only dglm-1.8.2/dglm/R/summary.dglm.R |only dglm-1.8.2/dglm/man/dglm.Rd | 2 +- dglm-1.8.2/dglm/tests |only 12 files changed, 26 insertions(+), 12 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.8.2 dated 2015-09-28 and 0.8.3 dated 2015-11-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/LoadAPSIMouts.R | 21 ++++++++++++++------- R/MetFunctions.R | 49 ++++++++++++++++++++++++++++++++++--------------- README.md | 7 +++++++ man/checkMet.Rd | 4 ++++ man/loadApsim.Rd | 12 +++++++----- man/prepareMet.Rd | 22 ++++++++++++++++------ 8 files changed, 93 insertions(+), 44 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.1 dated 2015-09-17 and 0.4.2 dated 2015-11-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/miivboot.R | 7 +++++++ R/miivs.R | 19 +++++++++++++------ 4 files changed, 26 insertions(+), 12 deletions(-)
Title: CRISPR AnalyzeR for Pooled CRISPR Screens
Description: CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <https://en.wikipedia.org/wiki/CRISPR> for more information on
CRISPR.
Author: Jan Winter, Florian Heigwer
Maintainer: Jan Winter <jan.winter@dkfz-heidelberg.de>
Diff between caRpools versions 0.82.3 dated 2015-08-14 and 0.82.5 dated 2015-11-04
DESCRIPTION | 8 MD5 | 31 - NAMESPACE | 17 R/carpools.read.count.vs.R | 1173 ++++++++++++++++------------------------- R/carpools.read.count.vs_OLD.R |only R/data.extract.R | 9 R/get.gene.info.R | 5 R/load.file.R | 227 +++++++ R/stat.mageck.R | 66 +- build/vignette.rds |binary data/caRpools.RData |binary inst/doc/CaRpools.R | 38 + inst/doc/CaRpools.Rmd | 116 +++- inst/doc/CaRpools.html | 113 +++ man/carpools.read.count.vs.Rd | 9 man/data.extract.Rd | 9 vignettes/CaRpools.Rmd | 116 +++- 17 files changed, 1130 insertions(+), 807 deletions(-)
Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character
Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with
machine readable zones, e.g. passports. Get the results in a variety of formats
including plain text and XML. To learn more about the Abbyy OCR API, see http://
ocrsdk.com/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between abbyyR versions 0.2 dated 2015-09-12 and 0.2.1 dated 2015-11-04
abbyyR-0.2.1/abbyyR/DESCRIPTION | 17 ++- abbyyR-0.2.1/abbyyR/LICENSE |only abbyyR-0.2.1/abbyyR/MD5 | 109 +++++++++++--------- abbyyR-0.2.1/abbyyR/NAMESPACE | 2 abbyyR-0.2.1/abbyyR/NEWS |only abbyyR-0.2.1/abbyyR/R/abbyyR.R | 71 ++++++++++++- abbyyR-0.2.1/abbyyR/R/compareText.R | 5 abbyyR-0.2.1/abbyyR/R/deleteTask.R | 9 - abbyyR-0.2.1/abbyyR/R/getAppInfo.R | 9 - abbyyR-0.2.1/abbyyR/R/getResults.R | 2 abbyyR-0.2.1/abbyyR/R/getTaskStatus.R | 10 - abbyyR-0.2.1/abbyyR/R/listFinishedTasks.R | 6 - abbyyR-0.2.1/abbyyR/R/listTasks.R | 11 -- abbyyR-0.2.1/abbyyR/R/processBarcodeField.R | 13 +- abbyyR-0.2.1/abbyyR/R/processBusinessCard.R | 13 -- abbyyR-0.2.1/abbyyR/R/processCheckmarkField.R | 13 +- abbyyR-0.2.1/abbyyR/R/processDocument.R | 9 - abbyyR-0.2.1/abbyyR/R/processFields.R | 7 - abbyyR-0.2.1/abbyyR/R/processImage.R | 16 +- abbyyR-0.2.1/abbyyR/R/processMRZ.R | 13 -- abbyyR-0.2.1/abbyyR/R/processPhotoId.R | 15 +- abbyyR-0.2.1/abbyyR/R/processRemoteImage.R | 7 - abbyyR-0.2.1/abbyyR/R/processTextField.R | 14 +- abbyyR-0.2.1/abbyyR/R/submitImage.R | 10 - abbyyR-0.2.1/abbyyR/README.md |only abbyyR-0.2.1/abbyyR/build |only abbyyR-0.2.1/abbyyR/inst/doc |only abbyyR-0.2.1/abbyyR/man/abbyyR-package.Rd | 12 +- abbyyR-0.2.1/abbyyR/man/abbyy_GET.Rd |only abbyyR-0.2.1/abbyyR/man/abbyy_POST.Rd |only abbyyR-0.2.1/abbyyR/man/abbyy_check.Rd |only abbyyR-0.2.1/abbyyR/man/compareText.Rd | 8 - abbyyR-0.2.1/abbyyR/man/deleteTask.Rd | 2 abbyyR-0.2.1/abbyyR/man/getAppInfo.Rd | 2 abbyyR-0.2.1/abbyyR/man/getResults.Rd | 2 abbyyR-0.2.1/abbyyR/man/getTaskStatus.Rd | 2 abbyyR-0.2.1/abbyyR/man/listFinishedTasks.Rd | 6 - abbyyR-0.2.1/abbyyR/man/listTasks.Rd | 6 - abbyyR-0.2.1/abbyyR/man/ocrFile.Rd | 4 abbyyR-0.2.1/abbyyR/man/processBarcodeField.Rd | 2 abbyyR-0.2.1/abbyyR/man/processBusinessCard.Rd | 2 abbyyR-0.2.1/abbyyR/man/processCheckmarkField.Rd | 2 abbyyR-0.2.1/abbyyR/man/processDocument.Rd | 4 abbyyR-0.2.1/abbyyR/man/processFields.Rd | 2 abbyyR-0.2.1/abbyyR/man/processImage.Rd | 4 abbyyR-0.2.1/abbyyR/man/processMRZ.Rd | 2 abbyyR-0.2.1/abbyyR/man/processPhotoId.Rd | 2 abbyyR-0.2.1/abbyyR/man/processRemoteImage.Rd | 2 abbyyR-0.2.1/abbyyR/man/processTextField.Rd | 2 abbyyR-0.2.1/abbyyR/man/setapp.Rd | 2 abbyyR-0.2.1/abbyyR/man/submitImage.Rd | 2 abbyyR-0.2.1/abbyyR/tests |only abbyyR-0.2.1/abbyyR/vignettes/example.Rmd |only abbyyR-0.2.1/abbyyR/vignettes/overview.Rmd |only abbyyR-0.2.1/abbyyR/vignettes/wiscads.Rmd |only abbyyR-0.2/abbyyR/inst/extdata/t1.TIF |only abbyyR-0.2/abbyyR/vignettes/Overview_of_abbyyR.html |only abbyyR-0.2/abbyyR/vignettes/abbyyR_example.html |only abbyyR-0.2/abbyyR/vignettes/wiscads.html |only 59 files changed, 255 insertions(+), 198 deletions(-)
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between textreuse versions 0.1.0 dated 2015-10-30 and 0.1.1 dated 2015-11-04
DESCRIPTION | 10 MD5 | 32 +- NEWS | 4 README.md | 18 - inst/doc/textreuse-alignment.html | 6 inst/doc/textreuse-introduction.R | 12 - inst/doc/textreuse-introduction.Rmd | 27 ++ inst/doc/textreuse-introduction.html | 47 +--- inst/doc/textreuse-minhash.R | 20 + inst/doc/textreuse-minhash.Rmd | 33 +-- inst/doc/textreuse-minhash.html | 379 ++--------------------------------- inst/doc/textreuse-pairwise.R | 7 inst/doc/textreuse-pairwise.Rmd | 7 inst/doc/textreuse-pairwise.html | 89 -------- vignettes/textreuse-introduction.Rmd | 11 - vignettes/textreuse-minhash.Rmd | 9 vignettes/textreuse-pairwise.Rmd | 7 17 files changed, 165 insertions(+), 553 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables. The package also contains many plotting
features (to help the user interpret the results) and a graphical
user interface based on shiny (which is also available on-line at
http://shiny.nathalievilla.org/sombrero).
Author: Laura Bendhaiba [aut],
Julien Boelaert [aut],
Madalina Olteanu [aut],
Nathalie Villa-Vialaneix [aut, cre]
Maintainer: Nathalie Villa-Vialaneix <nathalie.villa@toulouse.inra.fr>
Diff between SOMbrero versions 1.0 dated 2015-03-27 and 1.1 dated 2015-11-04
DESCRIPTION | 15 ++-- MD5 | 22 +++--- NAMESPACE | 8 ++ NEWS | 10 ++ R/init.R | 2 R/quality.R | 9 +- R/som.R | 121 +++++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/doc-korrespSOM.html | 147 ++++++++++++++++++++++--------------------- inst/shiny/ui.R | 2 man/SOMbrero-package.Rd | 11 ++- man/trainSOM.Rd | 9 ++ 12 files changed, 223 insertions(+), 133 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), latent regression models,
DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 1.8-9 dated 2015-06-28 and 1.9-0 dated 2015-11-04
DESCRIPTION | 16 +++--- MD5 | 58 +++++++++++------------ NAMESPACE | 77 +++++++++++++++++++++++-------- R/data.prep.R | 11 ---- R/f1d.irt.R | 4 - R/greenyang.reliability.R | 10 ++-- R/lsdm.R | 5 -- R/mirt.wrapper.posterior.R | 2 R/np.dich.R | 16 +----- R/plot.mcmc.sirt.R | 2 R/qmc.nodes.R | 5 -- R/rasch.jml.R | 19 ------- R/rasch.mml2.R | 2 R/rasch.pairwise.R | 15 ++++-- R/rasch.pairwise.itemcluster.R | 11 +++- inst/NEWS | 40 ++++++++++++---- man/data.read.Rd | 2 man/dif.logistic.regression.Rd | 92 ++++++++++++++++++++++++++++++++++++++ man/f1d.irt.Rd | 2 man/likelihood.adjustment.Rd | 2 man/pbivnorm2.Rd | 4 + man/pcm.fit.Rd | 14 ++--- man/polychoric2.Rd | 3 - man/qmc.nodes.Rd | 5 +- man/rasch.pairwise.Rd | 34 ++++++++++++-- man/rasch.pairwise.itemcluster.Rd | 6 ++ man/rasch.pml.Rd | 3 - man/sia.sirt.Rd | 4 - man/sirt-package.Rd | 63 ++++++++++++-------------- man/tetrachoric2.Rd | 3 - 30 files changed, 346 insertions(+), 184 deletions(-)
Title: Regression Models with Breakpoints/Changepoints Estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 0.5-1.2 dated 2015-09-08 and 0.5-1.4 dated 2015-11-04
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS | 19 ++++++++++++++++++- R/intercept.r | 1 + R/plot.segmented.R | 23 ++++++++++++++++++----- R/points.segmented.r | 4 +++- R/print.summary.segmented.R | 6 +++--- R/seg.Ar.fit.r | 1 + R/segmented.Arima.r | 6 ++++-- R/segmented.default.r | 2 +- R/segmented.glm.R | 2 +- R/segmented.lm.R | 2 +- R/slope.R | 4 ++-- man/intercept.Rd | 2 +- man/plot.segmented.Rd | 4 +++- man/points.segmented.Rd | 6 +++++- man/segmented-package.Rd | 4 ++-- man/segmented.Rd | 10 +++++++++- 18 files changed, 94 insertions(+), 44 deletions(-)
Title: Detecting Correlated Genomic Regions
Description: Performs correlation matrix segmentation and applies a test
procedure to detect highly correlated regions in gene expression.
Author: Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, Francois
Radvanyi, Stephane Robin, Jennifer Wong
Maintainer: Eleni Ioanna Delatola <eldelatola@yahoo.gr>
Diff between SegCorr versions 1.0 dated 2015-02-09 and 1.1 dated 2015-11-04
DESCRIPTION | 17 ++++++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 7 +++++-- R/SegCorr.R | 9 ++++++--- R/segmentation.R | 12 ++++++++---- man/CNV_correction.Rd | 6 +++--- man/SegCorr-package.Rd | 5 ++--- man/SegCorr.Rd | 15 ++++++++++----- man/segmentation.Rd | 11 +++++++---- man/segmented_signal.Rd | 2 +- 10 files changed, 61 insertions(+), 41 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-14 dated 2015-10-26 and 0.3-15 dated 2015-11-04
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ configure | 18 +++++++++--------- inst/ChangeLog | 8 ++++++++ inst/SVN_VERSION | 2 +- src/rgeos_buffer.c | 43 +++++++++++++++++++++++++++++++++---------- 7 files changed, 69 insertions(+), 30 deletions(-)
Title: Robust Ordinal Regression UTADIS
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek <k.ciomek@gmail.com>
Diff between rorutadis versions 0.3.0 dated 2015-10-22 and 0.3.1 dated 2015-11-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/model.R | 6 +++--- man/rorutadis-package.Rd | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.2 dated 2015-06-07 and 1.6.3 dated 2015-11-04
pgirmess-1.6.2/pgirmess/R/rwhatpoly.r |only pgirmess-1.6.2/pgirmess/man/rwhatpoly.rd |only pgirmess-1.6.3/pgirmess/DESCRIPTION | 8 +- pgirmess-1.6.3/pgirmess/MD5 | 16 +--- pgirmess-1.6.3/pgirmess/NAMESPACE | 8 +- pgirmess-1.6.3/pgirmess/data/preybiom.rda |binary pgirmess-1.6.3/pgirmess/data/siegelp179.rda |binary pgirmess-1.6.3/pgirmess/man/rwhatbufCat.rd | 86 +++++++++++----------- pgirmess-1.6.3/pgirmess/man/rwhatbufCat2.rd | 96 ++++++++++++------------ pgirmess-1.6.3/pgirmess/man/rwhatbufNum.rd | 108 ++++++++++++++-------------- 10 files changed, 162 insertions(+), 160 deletions(-)
Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 1.0 dated 2015-09-05 and 2.0 dated 2015-11-04
pcadapt-1.0/pcadapt/man/fdrCalc.Rd |only pcadapt-1.0/pcadapt/man/fdrControl.Rd |only pcadapt-1.0/pcadapt/man/fdrList.Rd |only pcadapt-1.0/pcadapt/man/kurtosis.Rd |only pcadapt-1.0/pcadapt/man/outlier.Rd |only pcadapt-1.0/pcadapt/man/plot.outlier.Rd |only pcadapt-1.0/pcadapt/man/sdevEstimation.Rd |only pcadapt-1.0/pcadapt/man/sdevList.Rd |only pcadapt-1.0/pcadapt/vignettes/pcadapt.html |only pcadapt-2.0/pcadapt/DESCRIPTION | 13 pcadapt-2.0/pcadapt/MD5 | 47 +- pcadapt-2.0/pcadapt/NAMESPACE | 19 - pcadapt-2.0/pcadapt/R/fst.R |only pcadapt-2.0/pcadapt/R/pcadapt.R | 531 +++++++++-------------------- pcadapt-2.0/pcadapt/R/plotting.R | 229 ++++++------ pcadapt-2.0/pcadapt/R/utilities.R | 70 ++- pcadapt-2.0/pcadapt/build |only pcadapt-2.0/pcadapt/inst/doc |only pcadapt-2.0/pcadapt/inst/extdata/pool3pops |only pcadapt-2.0/pcadapt/man/computeStats.Rd |only pcadapt-2.0/pcadapt/man/corpca.Rd | 18 pcadapt-2.0/pcadapt/man/fstCalc.Rd |only pcadapt-2.0/pcadapt/man/fstGeno.Rd |only pcadapt-2.0/pcadapt/man/manhattanPlot.Rd | 9 pcadapt-2.0/pcadapt/man/pcadapt-package.Rd | 20 - pcadapt-2.0/pcadapt/man/pcadapt.Rd | 79 ++-- pcadapt-2.0/pcadapt/man/plot.pcadapt.Rd | 20 - pcadapt-2.0/pcadapt/man/pval.Rd | 15 pcadapt-2.0/pcadapt/man/read.genotype.Rd | 11 pcadapt-2.0/pcadapt/man/read4pcadapt.Rd | 23 - pcadapt-2.0/pcadapt/man/scoresPlot.Rd | 6 pcadapt-2.0/pcadapt/vignettes/pcadapt.Rmd |only 32 files changed, 482 insertions(+), 628 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors, nested multiple imputation, and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 1.3-0 dated 2015-07-10 and 1.4-0 dated 2015-11-04
DESCRIPTION | 12 +-- MD5 | 100 ++++++++++++++++----------------- R/Rhat.mice.R | 5 - R/cppfunction.R | 3 R/draw.pv.ctt.R | 3 R/latent.regression.em.R | 3 R/mi.anova.R | 3 R/mice.impute.2l.contextual.norm.R | 3 R/mice.impute.2l.contextual.pmm.R | 3 R/mice.impute.2l.groupmean.R | 3 R/mice.impute.2l.groupmean.elim.R | 3 R/mice.impute.2l.latentgroupmean.R | 9 +- R/mice.impute.2l.plausible.values.R | 3 R/mice.impute.2l.pls.R | 3 R/mice.impute.2l.pls2.R | 3 R/mice.impute.2l.pls2_aux.R | 3 R/mice.impute.grouped.R | 3 R/mice.impute.norm3.R | 3 R/mice.impute.pmm3.R | 3 R/mice.impute.pmm4.R | 3 R/mice.impute.pmm5.R | 3 R/mice.impute.pmm6.R | 3 R/mice.impute.tricube.pmm.R | 3 R/mice.impute.tricube.pmm2.R | 3 R/mice.impute.weighted.norm.R | 3 R/mice.impute.weighted.pmm.R | 3 R/micombine.F.R | 3 R/micombine.chisquare.R | 3 R/micombine.cor.R | 10 +-- R/pca.covridge.R | 3 R/plausible.value.draw.R | 3 R/plausible.value.imputation.R | 3 R/save.data.R | 5 + R/sumpreserving.rounding.R | 7 -- R/tw.imputation.R | 3 R/tw.mcmc.imputation.R | 3 R/write.mice.imputation.R | 3 R/write.pspp.R | 3 inst/NEWS | 16 +++++ man/Reval.Rd | 2 man/lm.cluster.Rd | 14 ++-- man/load.Rdata.Rd | 2 man/load.data.Rd | 5 - man/mice.impute.2l.plausible.values.Rd | 26 ++++++-- man/mice.impute.2l.pls.Rd | 2 man/mice.impute.pmm3.Rd | 6 + man/miceadds-package.Rd | 9 +- man/micombine.cor.Rd | 42 +++++++++++++ man/pca.covridge.Rd | 2 man/save.data.Rd | 19 +++--- man/with.miceadds.Rd | 6 - 51 files changed, 216 insertions(+), 176 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 0.6 dated 2015-09-29 and 0.7 dated 2015-11-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/generics.R | 8 ++++---- R/mams.R | 49 ++++++++++++++++++++++++++++++------------------- inst/NEWS | 6 ++++++ 5 files changed, 47 insertions(+), 30 deletions(-)
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.1-1 dated 2015-09-14 and 0.2-0 dated 2015-11-04
DESCRIPTION | 10 ++-- MD5 | 23 +++++------ R/immer_reshape_wideformat.R | 31 +++++++++++++- R/lpcm_data_prep.R | 2 data/data.immer07.rda |only inst/NEWS | 18 +++++++- man/data.immer.Rd | 12 +++++ man/immer-package.Rd | 5 -- man/immer_HRM.Rd | 2 man/immer_cml.Rd | 83 +++++++++++++++++++++++++++++++++++++++- man/immer_opcat.Rd | 2 man/immer_reshape_wideformat.Rd | 19 ++++++++- man/simulate_HRM.Rd | 2 13 files changed, 177 insertions(+), 32 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation
of repeatabilities in measurements and matrices, and general evolutionary
quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme
Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-9 dated 2015-09-11 and 0.2-1 dated 2015-11-04
DESCRIPTION | 18 ++- MD5 | 112 ++++++++++++----------- NAMESPACE | 6 + R/DriftTest.R | 2 R/LinearParsimony.R |only R/MonteCarloStat.R | 4 R/Rarefaction.R | 166 ++++++++++++++++++++++++----------- inst/tests/test.DriftTest.r | 6 - inst/tests/test.PCScoreCorrelation.r | 2 inst/tests/test.Rarefaction.r | 10 +- man/AlphaRep.Rd | 2 man/AncestralStates.Rd | 3 man/BootstrapR2.Rd | 4 man/BootstrapRep.Rd | 4 man/BootstrapStat.Rd | 4 man/CalcICV.Rd | 4 man/CalcR2.Rd | 4 man/CalcR2CvCorrected.Rd | 8 - man/CalcRepeatability.Rd | 2 man/CalculateMatrix.Rd | 2 man/ComparisonMap.Rd | 2 man/DriftTest.Rd | 7 - man/ExtendMatrix.Rd | 2 man/KrzCor.Rd | 5 - man/KrzProjection.Rd | 2 man/LModularity.Rd | 2 man/LinearParsimony.Rd |only man/MantelCor.Rd | 6 - man/MatrixCompare.Rd | 3 man/MatrixDistance.Rd | 2 man/MeanMatrixStatistics.Rd | 2 man/MonteCarloR2.Rd | 2 man/MonteCarloRep.Rd | 4 man/MonteCarloStat.Rd | 2 man/MultiMahalanobis.Rd | 4 man/MultivDriftTest.Rd | 16 +-- man/Normalize.Rd | 2 man/OverlapDist.Rd | 6 - man/PCAsimilarity.Rd | 2 man/PCScoreCorrelation.Rd | 6 - man/PhyloCompare.Rd | 2 man/PhyloW.Rd | 2 man/PlotRarefaction.Rd |only man/PlotTreeDriftTest.Rd | 2 man/PrintMatrix.Rd | 2 man/RandCorr.Rd | 2 man/RandomMatrix.Rd | 2 man/RandomSkewers.Rd | 5 - man/Rarefaction.Rd | 42 +------- man/RarefactionStat.Rd |only man/RemoveSize.Rd | 2 man/RiemannDist.Rd | 2 man/SRD.Rd | 2 man/SingleComparisonMap.Rd | 2 man/TestModularity.Rd | 2 man/TreeDriftTest.Rd | 2 man/dentus.Rd | 12 +- man/dentus.tree.Rd | 2 man/evolqg.Rd | 2 59 files changed, 295 insertions(+), 232 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.5.6 dated 2015-09-24 and 3.6.0 dated 2015-11-04
DESCRIPTION | 8 +- MD5 | 20 +++--- NAMESPACE | 2 NEWS | 9 ++ R/Deriv.R | 134 ++++++++++++++++++++++++++--------------- R/Simplify.R | 4 - inst/CITATION | 2 man/Deriv-package.Rd | 4 - man/Deriv.Rd | 26 +++++-- tests/testthat/test_Deriv.R | 16 ++++ tests/testthat/test_Simplify.R | 6 - 11 files changed, 154 insertions(+), 77 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.5-0 dated 2015-08-29 and 4.6-0 dated 2015-11-04
DESCRIPTION | 13 ++++++------- MD5 | 10 +++++----- R/din.R | 18 +++++++++++++++++- inst/NEWS | 12 ++++++++++++ man/CDM-package.Rd | 13 ++++++------- man/din.Rd | 7 +++++-- 6 files changed, 51 insertions(+), 22 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 1.6-0 dated 2015-10-15 and 1.7-0 dated 2015-11-04
DESCRIPTION | 10 ++++---- MD5 | 11 +++++---- R/BIFIE.univar.R | 2 - R/BIFIE.univar.test.R | 48 ++++++++++++++++++++++++------------------- R/BIFIE_create_pseudogroup.R |only inst/NEWS | 14 ++++++++++++ man/BIFIEsurvey-package.Rd | 6 +++-- 7 files changed, 57 insertions(+), 34 deletions(-)
Title: Automated Schema on Read
Description: Provides schema-on-read tools including a single function call (e.g., schemaOnRead("filename")) that reads text ('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF', and 'JPG'), R data ('RDS'), HDF5, NetCDF, spreadsheet ('XLS', 'XLSX', 'ODS', and 'DIF'), Weka Attribute-Relation File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata ('DTA') files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.
Author: Michael North [aut, cre]
Maintainer: Michael North <north@anl.gov>
Diff between SchemaOnRead versions 1.0.0 dated 2015-10-24 and 1.0.1 dated 2015-11-03
DESCRIPTION | 17 MD5 | 20 - NAMESPACE | 6 NEWS.md |only R/SchemaOnRead.R | 813 ++++++++++++++++++++++++----------------------- README.md |only tests/testthat/test.08.R | 1 tests/testthat/test.12.R | 1 tests/testthat/test.13.R | 1 tests/testthat/test.14.R | 1 tests/testthat/test.15.R | 1 tests/testthat/test.19.R | 1 12 files changed, 439 insertions(+), 423 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such
as calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.1 dated 2015-09-08 and 0.1.2 dated 2015-11-03
DESCRIPTION | 17 ++--- MD5 | 78 +++++++++++++------------ NAMESPACE | 2 NEWS | 9 ++ R/RStoolbox.R | 6 + R/RcppExports.R | 8 +- R/coregisterImages.R | 10 +-- R/ggR.R | 29 ++++++--- R/ggRGB.R | 2 R/internalFunctions.R | 25 +++++++- R/mlc.R |only R/panSharpen.R | 14 ++-- R/radCor.R | 14 +++- R/rasterCVA.R | 12 +-- R/readMeta.R | 4 - R/readSLI.R | 38 +++++------- R/sam.R | 2 R/spectralIndices.R | 104 ++++++++++++++++++++-------------- R/superClass.R | 47 +++++++++++---- R/tasseledCap.R | 9 +- man/coregisterImages.Rd | 10 +-- man/ggR.Rd | 10 +++ man/panSharpen.Rd | 13 +--- man/radCor.Rd | 4 - man/rasterCVA.Rd | 10 --- man/rlogo.Rd | 1 man/spectralIndices.Rd | 28 +++++---- man/srtm.Rd | 1 man/superClass.Rd | 14 ++-- man/tasseledCap.Rd | 9 +- src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 39 ++++++++---- src/classQA.cpp | 4 - src/gainOffsetRescale.cpp | 4 - src/predictMlc.cpp |only src/spectralIndices.cpp | 39 ++++++++---- tests/testthat.R | 1 tests/testthat/test-entropy.R | 4 - tests/testthat/test-ggplot.R | 2 tests/testthat/test-multicore.R | 2 tests/testthat/test-spectralIndices.R | 7 +- 42 files changed, 390 insertions(+), 242 deletions(-)
Title: An Algorithm to Infer Relatedness
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Diff between Relatedness versions 1.1 dated 2015-09-16 and 1.2 dated 2015-11-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/RelCoef.R | 2 +- src/BoucleEMacc.c | 1 - 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between
samples is based on a modified kriging method that
accepts a genetic distance matrix and generates a map of
probability of lineage presence. This package also offers
tools to generate a map of potential contact zones
between groups with user-defined thresholds in the tree
to account for old and recent divergence. Additionally,
it has functions for IDW interpolation using genetic data
and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>
Diff between phylin versions 1.0 dated 2014-07-25 and 1.1.1 dated 2015-11-03
DESCRIPTION | 31 ++++++++++++----------- MD5 | 23 ++++++++++++----- NAMESPACE | 10 ++++++- R/gen.variogram.R | 56 ++++++++++++++++++++---------------------- R/gen.variogram.multi.R |only R/gen.variogram.single.R |only R/krig.R | 5 +++ R/plot.gv_WITHMULTI.R |only build |only inst |only man/gen.variogram.Rd | 62 ++++++++++++++++++++++++++++++----------------- man/phylin-package.Rd | 4 +-- man/plot.gv.Rd | 6 +++- vignettes |only 14 files changed, 119 insertions(+), 78 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6.4 dated 2015-10-23 and 1.6.5 dated 2015-11-03
DESCRIPTION | 7 +- MD5 | 132 ++++++++++++++++++++++----------------------- NAMESPACE | 2 R/TaylorDiagram.R | 58 ++++++++++--------- R/TheilSen.R | 2 R/corPlot.R | 2 R/getMeta.R | 2 R/import.R | 21 +------ R/importAURN.R | 6 +- R/importKCL.R | 6 +- R/polarCluster.R | 4 - R/scatterPlot.R | 65 ++++++++++++---------- R/utilities.R | 6 +- README.md | 2 man/GoogleMapsPlot.Rd | 13 ++-- man/TaylorDiagram.Rd | 9 ++- man/TheilSen.Rd | 10 ++- man/airbaseFindCode.Rd | 3 - man/airbaseInfo.Rd | 2 man/airbaseSplice.Rd | 2 man/airbaseStats.Rd | 2 man/aqStats.Rd | 5 + man/calcFno2.Rd | 4 + man/calcPercentile.Rd | 5 + man/calendarPlot.Rd | 5 + man/conditionalEval.Rd | 5 + man/conditionalQuantile.Rd | 7 ++ man/corPlot.Rd | 5 + man/cutData.Rd | 7 +- man/drawOpenKey.Rd | 6 +- man/import.Rd | 23 +------ man/importADMS.Rd | 6 +- man/importAURN.Rd | 12 ++-- man/importAURNCsv.Rd | 6 +- man/importAirbase.Rd | 2 man/importKCL.Rd | 14 +++- man/importMeta.Rd | 4 - man/importSAQN.Rd | 6 +- man/importTraj.Rd | 8 +- man/kernelExceed.Rd | 6 +- man/linearRelation.Rd | 6 +- man/modStats.Rd | 5 + man/mydata.Rd | 6 +- man/openColours.Rd | 5 + man/openair.Rd | 5 + man/percentileRose.Rd | 5 + man/polarAnnulus.Rd | 6 +- man/polarCluster.Rd | 8 +- man/polarFreq.Rd | 7 +- man/polarPlot.Rd | 6 +- man/quickText.Rd | 6 +- man/rollingMean.Rd | 5 + man/scatterPlot.Rd | 40 +++++++------ man/selectByDate.Rd | 4 + man/selectRunning.Rd | 4 + man/smoothTrend.Rd | 4 + man/splitByDate.Rd | 5 + man/summaryPlot.Rd | 6 +- man/timeAverage.Rd | 23 ++++--- man/timePlot.Rd | 5 + man/timeProp.Rd | 4 + man/timeVariation.Rd | 9 ++- man/trajCluster.Rd | 2 man/trajLevel.Rd | 3 - man/trajPlot.Rd | 4 + man/trendLevel.Rd | 8 ++ man/windRose.Rd | 5 + 67 files changed, 409 insertions(+), 279 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids,
which can be used for multivariate quadrature. This grids can be based on
different quadrature rules like Newton-Cotes formulas (trapezoidal-, Simpson's-
rule, ...) or Gauss quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the
construction of the multidimensional grid the product-rule or the combination-
technique can be applied.
Author: Constantin Weiser (HHU of Duesseldorf / Germany)
Maintainer: Constantin Weiser <weiserc@hhu.de>
Diff between mvQuad versions 1.0-2 dated 2015-11-01 and 1.0-3 dated 2015-11-03
mvQuad-1.0-2/mvQuad/vignettes/library.bib |only mvQuad-1.0-3/mvQuad/DESCRIPTION | 8 +- mvQuad-1.0-3/mvQuad/MD5 | 15 ++-- mvQuad-1.0-3/mvQuad/R/mvQuad.R | 7 +- mvQuad-1.0-3/mvQuad/inst/CITATION |only mvQuad-1.0-3/mvQuad/inst/NEWS |only mvQuad-1.0-3/mvQuad/inst/doc/mvQuad_intro.Rmd | 84 ++++++++++++++++++++++++- mvQuad-1.0-3/mvQuad/inst/doc/mvQuad_intro.html | 6 - mvQuad-1.0-3/mvQuad/man/mvQuad-package.Rd | 4 - mvQuad-1.0-3/mvQuad/vignettes/mvQuad_intro.Rmd | 84 ++++++++++++++++++++++++- 10 files changed, 185 insertions(+), 23 deletions(-)
Title: Generalized Hermite Distribution
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and MarÃa Oliveira
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between hermite versions 1.1.0 dated 2015-04-27 and 1.1.1 dated 2015-11-03
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- NAMESPACE | 5 +++++ data/hot100.rda |only man/hot100.Rd |only 5 files changed, 13 insertions(+), 6 deletions(-)
Title: The Bayesian Causal Effect Estimation Algorithm
Description: Implementation of the Bayesian Causal Effect Estimation algorithm,
a data-driven method for the estimation of the causal effect of an exposure
on a continuous outcome. For more details, see Talbot et al. (2015) DOI:10.1515/jci-2014-0035.
Author: Denis Talbot, Geneviève Lefebvre, Juli Atherton.
Maintainer: Denis Talbot <denis.talbot@fmed.ulaval.ca>
Diff between BCEE versions 1.0 dated 2015-06-24 and 1.1 dated 2015-11-03
ChangeLog |only DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 4 +++- R/ABCEE.R | 4 ++-- R/NBCEE.R | 15 ++++++++------- man/ABCEE.Rd | 10 +++++++--- man/BCEE-package.Rd | 6 +++--- man/NBCEE.Rd | 10 ++++++---- 9 files changed, 43 insertions(+), 33 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 1.2 dated 2014-03-18 and 1.3 dated 2015-11-03
RSDA-1.2/RSDA/inst |only RSDA-1.3/RSDA/DESCRIPTION | 17 +-- RSDA-1.3/RSDA/MD5 | 85 +++++++++++------- RSDA-1.3/RSDA/NAMESPACE | 11 +- RSDA-1.3/RSDA/R/SDS.to.RSDA.R |only RSDA-1.3/RSDA/R/centers.interval.R |only RSDA-1.3/RSDA/R/classic.to.sym.R | 103 +++++++++++----------- RSDA-1.3/RSDA/R/dist.vect.R |only RSDA-1.3/RSDA/R/dist.vect.matrix.R |only RSDA-1.3/RSDA/R/neighbors.vertex.R |only RSDA-1.3/RSDA/R/norm.vect.R |only RSDA-1.3/RSDA/R/process.continuum.variable.R | 2 RSDA-1.3/RSDA/R/process.histogram.variable.R | 62 ++++++------- RSDA-1.3/RSDA/R/process.interval.variable.R | 8 - RSDA-1.3/RSDA/R/process.set.variable.R | 46 +++++----- RSDA-1.3/RSDA/R/sym.interval.pc.R |only RSDA-1.3/RSDA/R/sym.interval.pc.limits.R |only RSDA-1.3/RSDA/R/variance.princ.curve.R |only RSDA-1.3/RSDA/R/vertex.interval.R |only RSDA-1.3/RSDA/data/Cardiological.rda |binary RSDA-1.3/RSDA/data/StudentsGrades.rda |binary RSDA-1.3/RSDA/data/USCrime.rda |binary RSDA-1.3/RSDA/data/VeterinaryData.rda |binary RSDA-1.3/RSDA/data/abalone.rda |binary RSDA-1.3/RSDA/data/ex1_db2so.rda |binary RSDA-1.3/RSDA/data/ex_cfa1.rda |binary RSDA-1.3/RSDA/data/ex_cfa2.rda |binary RSDA-1.3/RSDA/data/example1.rda |binary RSDA-1.3/RSDA/data/example2.rda |binary RSDA-1.3/RSDA/data/example3.rda |binary RSDA-1.3/RSDA/data/example4.rda |binary RSDA-1.3/RSDA/data/example5.rda |binary RSDA-1.3/RSDA/data/example6.rda |binary RSDA-1.3/RSDA/data/example7.rda |binary RSDA-1.3/RSDA/data/facedata.rda |only RSDA-1.3/RSDA/data/int_prost_test.rda |binary RSDA-1.3/RSDA/data/int_prost_train.rda |binary RSDA-1.3/RSDA/data/lynne1.rda |binary RSDA-1.3/RSDA/data/lynne2.rda |binary RSDA-1.3/RSDA/data/oils.rda |binary RSDA-1.3/RSDA/data/uscrime_int.rda |binary RSDA-1.3/RSDA/man/RSDA-package.Rd | 8 - RSDA-1.3/RSDA/man/SDS.to.RSDA.Rd |only RSDA-1.3/RSDA/man/SODAS.to.RSDA.Rd | 6 - RSDA-1.3/RSDA/man/centers.interval.Rd |only RSDA-1.3/RSDA/man/dist.vect.Rd |only RSDA-1.3/RSDA/man/dist.vect.matrix.Rd |only RSDA-1.3/RSDA/man/facedata.Rd |only RSDA-1.3/RSDA/man/neighbors.vertex.Rd |only RSDA-1.3/RSDA/man/norm.vect.Rd |only RSDA-1.3/RSDA/man/sym.interval.pc.Rd |only RSDA-1.3/RSDA/man/sym.interval.pc.limits.Rd |only RSDA-1.3/RSDA/man/sym.interval.pca.Rd | 122 +++++++++++++-------------- RSDA-1.3/RSDA/man/variance.princ.curve.Rd |only RSDA-1.3/RSDA/man/vertex.interval.Rd |only 55 files changed, 248 insertions(+), 222 deletions(-)
Title: Randomized Response Techniques for Complex Surveys
Description: Point and interval estimation of linear parameters with data
obtained from complex surveys (including stratified and clustered samples)
when randomization techniques are used. The randomized response technique
was developed to obtain estimates that are more valid when studying
sensitive topics. Estimators and variances for 14 randomized response
methods for qualitative variables and 7 randomized response methods for
quantitative variables are also implemented. In addition, some data sets
from surveys with these randomization methods are included in the package.
Author: Beatriz Cobo RodrÃguez, MarÃa del Mar Rueda GarcÃa, Antonio Arcos
Cebrián
Maintainer: Beatriz Cobo RodrÃguez <beacr@ugr.es>
Diff between RRTCS versions 0.0.2 dated 2015-07-02 and 0.0.3 dated 2015-11-03
DESCRIPTION | 8 +++-- MD5 | 63 +++++++++++++++++++++++++---------------- R/DianaPerri1.R | 14 ++++----- R/DianaPerri2.R | 16 +++++----- R/Estimator.R | 14 ++++----- R/ForcedResponse.R | 9 +++++ R/ForcedResponseData.R | 2 - R/ForcedResponseDataSt.R |only R/Horvitz.R | 12 +++++++ R/HorvitzData.R | 2 - R/HorvitzDataRealSurvey.R |only R/HorvitzDataStCl.R | 2 - R/JackknifeVariance.R | 6 +-- R/Qualitative.R | 39 ++++++++++++++----------- R/Quantitative.R | 6 +-- R/RRTCS-internal.R | 2 - R/ResamplingVariance.R | 20 +++++++------ R/Saha.R | 12 +++---- build |only data/EichhornHayreData.rda |binary data/ForcedResponseDataSt.rda |only data/HorvitzDataRealSurvey.rda |only inst |only man/DianaPerri1.Rd | 2 - man/DianaPerri2.Rd | 2 - man/ForcedResponse.Rd | 10 ++++++ man/ForcedResponseData.Rd | 2 - man/ForcedResponseDataSt.Rd |only man/Horvitz.Rd | 14 +++++++++ man/HorvitzData.Rd | 2 - man/HorvitzDataRealSurvey.Rd |only man/HorvitzDataStCl.Rd | 2 - man/ResamplingVariance.Rd | 6 +++ vignettes |only 34 files changed, 173 insertions(+), 94 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-5 dated 2015-10-29 and 2.7-6 dated 2015-11-03
DESCRIPTION | 8 - MD5 | 16 +- R/proj.canon.v4.r | 4 R/proj.r | 64 +++++---- R/projs.canon.v4.r | 330 ++++++++++++++++++++++++++---------------------- build/partial.rdb |binary inst/NEWS.Rd | 6 inst/doc/dae-manual.pdf |binary man/summary.pcanon.Rd | 3 9 files changed, 240 insertions(+), 191 deletions(-)
Title: Sample Selection Models
Description: Two-step estimation
and maximum likelihood estimation
of Heckman-type sample selection models:
standard sample selection models (Tobit-2)
and endogenous switching regression models (Tobit-5).
Author: Arne Henningsen <arne.henningsen@gmail.com>,
Ott Toomet <otoomet@ut.ee>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between sampleSelection versions 1.0-2 dated 2014-06-24 and 1.0-4 dated 2015-11-03
DESCRIPTION | 19 MD5 | 74 NAMESPACE | 29 NEWS | 16 R/CB.R |only R/checkIMRCollinearity.R |only R/coef.selection.R | 2 R/detectModelType.R |only R/heckit5fit.R | 7 R/heckitTfit.R |only R/invMillsRatio.R | 2 R/lambda.R |only R/model.frame.selection.R | 56 R/model.matrix.selection.R | 36 R/predict.selection.R | 93 R/selection.R | 94 R/selectionVariableName.R |only R/summary.probit.R | 2 R/summary.selection.R | 35 R/tobit2Bfit.R | 1 R/tobitTfit.R |only R/tobitType.R |only R/vcov.selection.R | 2 build/vignette.rds |binary demo |only inst/doc/selection.R | 7 inst/doc/selection.Rnw | 5 man/Mroz87.Rd | 130 man/RandHIE.Rd | 281 man/heckit2fit.Rd | 7 man/model.matrix.selection.Rd | 13 man/sampleSelection-internal.Rd | 3 man/selection.Rd | 28 tests/Mroz87SelectionTest.Rout.save | 22 tests/binarySelectionOutcome.R | 5 tests/binarySelectionOutcome.Rout.save | 95 tests/fail.Rout.save | 46 tests/invMillsRatioTest.Rout.save | 58 tests/probit.Rout.save | 10 tests/selection.R | 130 tests/selection.Rout.save |22117 ++++++++++++++++++++++++++++++++- vignettes/selection.Rnw | 5 42 files changed, 22309 insertions(+), 1121 deletions(-)
More information about sampleSelection at CRAN
Permanent link
Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing. Latest version can be found at github/DeveauP/QuantumClone .
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 0.9.15 dated 2015-09-15 and 0.15.11 dated 2015-11-03
QuantumClone-0.15.11/QuantumClone/DESCRIPTION | 11 + QuantumClone-0.15.11/QuantumClone/MD5 | 65 ++++++---- QuantumClone-0.15.11/QuantumClone/NAMESPACE | 35 ++++- QuantumClone-0.15.11/QuantumClone/R/EM.R | 25 ++- QuantumClone-0.15.11/QuantumClone/R/QuantumClone.R |only QuantumClone-0.15.11/QuantumClone/R/data.R |only QuantumClone-0.15.11/QuantumClone/R/plots.R |only QuantumClone-0.15.11/QuantumClone/README.md |only QuantumClone-0.15.11/QuantumClone/build |only QuantumClone-0.15.11/QuantumClone/data |only QuantumClone-0.15.11/QuantumClone/inst |only QuantumClone-0.15.11/QuantumClone/man/CellularitiesFromFreq.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Cluster_plot_from_cell.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/From_freq_to_cell.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Input_Example.Rd |only QuantumClone-0.15.11/QuantumClone/man/One_D_plot.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/One_step_clustering.Rd | 21 +-- QuantumClone-0.15.11/QuantumClone/man/Patient_schrodinger_cellularities.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/Probability.to.belong.to.clone.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/QC_output.Rd |only QuantumClone-0.15.11/QuantumClone/man/QuantumClone.Rd | 13 -- QuantumClone-0.15.11/QuantumClone/man/ThreeD_plot.Rd | 7 - QuantumClone-0.15.11/QuantumClone/man/Tree.Rd |only QuantumClone-0.15.11/QuantumClone/man/Tree_generation.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/add_leaf_list.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/evolution_plot.Rd |only QuantumClone-0.15.11/QuantumClone/man/find_x_position.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/is_included.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/longueur.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/manual_plot_trees.Rd | 9 + QuantumClone-0.15.11/QuantumClone/man/multiplot_trees.Rd | 7 - QuantumClone-0.15.11/QuantumClone/man/plot_QC_out.Rd |only QuantumClone-0.15.11/QuantumClone/man/plot_cell_from_Return_out.Rd | 2 QuantumClone-0.15.11/QuantumClone/man/plot_with_margins_densities.Rd | 12 - QuantumClone-0.15.11/QuantumClone/man/strcount.Rd | 2 QuantumClone-0.15.11/QuantumClone/vignettes |only QuantumClone-0.9.15/QuantumClone/R/QuantumClone_v3.R |only 37 files changed, 138 insertions(+), 93 deletions(-)
Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and
generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre],
Pedro G. Lind [aut],
David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>
Diff between Langevin versions 1.0.3 dated 2015-08-26 and 1.1.1 dated 2015-11-03
Langevin-1.0.3/Langevin/R/RcppExports.R |only Langevin-1.1.1/Langevin/ChangeLog | 26 ++ Langevin-1.1.1/Langevin/DESCRIPTION | 19 - Langevin-1.1.1/Langevin/MD5 | 49 ++-- Langevin-1.1.1/Langevin/NAMESPACE | 9 Langevin-1.1.1/Langevin/R/Langevin-package.r | 6 Langevin-1.1.1/Langevin/R/Langevin1D.r |only Langevin-1.1.1/Langevin/R/Langevin2D.r |only Langevin-1.1.1/Langevin/R/plot.Langevin.r |only Langevin-1.1.1/Langevin/R/print.Langevin.r |only Langevin-1.1.1/Langevin/R/summary.Langevin.r |only Langevin-1.1.1/Langevin/R/timeseries1D.r |only Langevin-1.1.1/Langevin/R/timeseries2D.r | 6 Langevin-1.1.1/Langevin/build/vignette.rds |binary Langevin-1.1.1/Langevin/inst/CITATION |only Langevin-1.1.1/Langevin/inst/doc/Langevin.Rnw | 274 +++++++++++++----------- Langevin-1.1.1/Langevin/inst/doc/Langevin.pdf |binary Langevin-1.1.1/Langevin/man/Langevin-package.Rd | 6 Langevin-1.1.1/Langevin/man/Langevin1D.Rd | 10 Langevin-1.1.1/Langevin/man/Langevin2D.Rd | 11 Langevin-1.1.1/Langevin/man/plot.Langevin.Rd |only Langevin-1.1.1/Langevin/man/print.Langevin.Rd |only Langevin-1.1.1/Langevin/man/summary.Langevin.Rd |only Langevin-1.1.1/Langevin/man/timeseries1D.Rd | 8 Langevin-1.1.1/Langevin/man/timeseries2D.Rd | 6 Langevin-1.1.1/Langevin/src/Langevin1D.cpp | 81 ------- Langevin-1.1.1/Langevin/src/Langevin2D.cpp | 84 +------ Langevin-1.1.1/Langevin/src/RcppExports.cpp | 14 - Langevin-1.1.1/Langevin/src/timeseries1D.cpp | 45 --- Langevin-1.1.1/Langevin/src/timeseries2D.cpp | 28 +- Langevin-1.1.1/Langevin/vignettes/Langevin.Rnw | 274 +++++++++++++----------- 31 files changed, 448 insertions(+), 508 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.2.1 dated 2015-07-24 and 1.2.2 dated 2015-11-03
EpiModel-1.2.1/EpiModel/man/netsim_parallel.Rd |only EpiModel-1.2.2/EpiModel/DESCRIPTION | 20 EpiModel-1.2.2/EpiModel/MD5 | 221 +++++------ EpiModel-1.2.2/EpiModel/NAMESPACE | 9 EpiModel-1.2.2/EpiModel/NEWS | 38 + EpiModel-1.2.2/EpiModel/R/EpiModel-package.r | 5 EpiModel-1.2.2/EpiModel/R/as.data.frame.R | 29 + EpiModel-1.2.2/EpiModel/R/control.R | 4 EpiModel-1.2.2/EpiModel/R/dendo.R |only EpiModel-1.2.2/EpiModel/R/get.R | 14 EpiModel-1.2.2/EpiModel/R/init.R | 4 EpiModel-1.2.2/EpiModel/R/netdx.R | 2 EpiModel-1.2.2/EpiModel/R/netsim.R | 27 - EpiModel-1.2.2/EpiModel/R/plot.R | 42 +- EpiModel-1.2.2/EpiModel/R/print.r | 15 EpiModel-1.2.2/EpiModel/R/saveout.R | 1 EpiModel-1.2.2/EpiModel/R/shiny.R | 31 - EpiModel-1.2.2/EpiModel/build/vignette.rds |binary EpiModel-1.2.2/EpiModel/inst/doc/Intro.html | 16 EpiModel-1.2.2/EpiModel/inst/shiny/epiicm/server.R | 2 EpiModel-1.2.2/EpiModel/inst/shiny/epinet |only EpiModel-1.2.2/EpiModel/man/EpiModel-package.Rd | 6 EpiModel-1.2.2/EpiModel/man/as.data.frame.dcm.Rd | 3 EpiModel-1.2.2/EpiModel/man/as.data.frame.icm.Rd | 22 - EpiModel-1.2.2/EpiModel/man/as.network.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/as.phylo.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/bipvals.Rd | 3 EpiModel-1.2.2/EpiModel/man/births.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/births.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/brewer_ramp.Rd | 5 EpiModel-1.2.2/EpiModel/man/calc_eql.Rd | 5 EpiModel-1.2.2/EpiModel/man/check_bip_degdist.Rd | 3 EpiModel-1.2.2/EpiModel/man/color_tea.Rd | 2 EpiModel-1.2.2/EpiModel/man/comp_plot.Rd | 3 EpiModel-1.2.2/EpiModel/man/control.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/control.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/control.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/copy_toall_attr.Rd | 4 EpiModel-1.2.2/EpiModel/man/crosscheck.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/crosscheck.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/crosscheck.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/dcm.Rd | 5 EpiModel-1.2.2/EpiModel/man/dcm.mods.Rd | 4 EpiModel-1.2.2/EpiModel/man/deaths.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/deaths.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/deleteAttr.Rd | 2 EpiModel-1.2.2/EpiModel/man/discord_edgelist.Rd | 2 EpiModel-1.2.2/EpiModel/man/dissolution_coefs.Rd | 6 EpiModel-1.2.2/EpiModel/man/edgelist_censor.Rd | 7 EpiModel-1.2.2/EpiModel/man/edgelist_meanage.Rd | 5 EpiModel-1.2.2/EpiModel/man/edges_correct.Rd | 2 EpiModel-1.2.2/EpiModel/man/epiweb.Rd | 30 - EpiModel-1.2.2/EpiModel/man/get_attr_prop.Rd | 4 EpiModel-1.2.2/EpiModel/man/get_formula_terms.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_network.Rd | 5 EpiModel-1.2.2/EpiModel/man/get_nwparam.Rd | 4 EpiModel-1.2.2/EpiModel/man/get_nwstats.Rd | 5 EpiModel-1.2.2/EpiModel/man/get_prev.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_prev.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/get_sims.Rd | 13 EpiModel-1.2.2/EpiModel/man/get_transmat.Rd | 11 EpiModel-1.2.2/EpiModel/man/icm.Rd | 5 EpiModel-1.2.2/EpiModel/man/idmode.Rd | 5 EpiModel-1.2.2/EpiModel/man/infection.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/infection.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/init.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/init.icm.Rd | 4 EpiModel-1.2.2/EpiModel/man/init.net.Rd | 4 EpiModel-1.2.2/EpiModel/man/init_pids.Rd | 3 EpiModel-1.2.2/EpiModel/man/init_status.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/init_status.net.Rd | 4 EpiModel-1.2.2/EpiModel/man/initialize.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/initialize.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/mcat.Rd | 2 EpiModel-1.2.2/EpiModel/man/merge.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/merge.netsim.Rd | 3 EpiModel-1.2.2/EpiModel/man/modeids.Rd | 3 EpiModel-1.2.2/EpiModel/man/modules.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/modules.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/netdx.Rd | 5 EpiModel-1.2.2/EpiModel/man/netest.Rd | 3 EpiModel-1.2.2/EpiModel/man/netsim.Rd | 5 EpiModel-1.2.2/EpiModel/man/param.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/param.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/param.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/plot.dcm.Rd | 5 EpiModel-1.2.2/EpiModel/man/plot.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/plot.netdx.Rd | 3 EpiModel-1.2.2/EpiModel/man/plot.netsim.Rd | 25 + EpiModel-1.2.2/EpiModel/man/plot.transmat.Rd |only EpiModel-1.2.2/EpiModel/man/recovery.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/recovery.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/resim_nets.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/saveout.net.Rd | 2 EpiModel-1.2.2/EpiModel/man/sim_nets.Rd | 2 EpiModel-1.2.2/EpiModel/man/split_bip.Rd | 2 EpiModel-1.2.2/EpiModel/man/ssample.Rd | 4 EpiModel-1.2.2/EpiModel/man/summary.dcm.Rd | 3 EpiModel-1.2.2/EpiModel/man/summary.icm.Rd | 3 EpiModel-1.2.2/EpiModel/man/summary.netest.Rd | 2 EpiModel-1.2.2/EpiModel/man/summary.netsim.Rd | 3 EpiModel-1.2.2/EpiModel/man/test_icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/test_net.Rd | 2 EpiModel-1.2.2/EpiModel/man/transco.Rd | 3 EpiModel-1.2.2/EpiModel/man/update_nwattr.Rd | 4 EpiModel-1.2.2/EpiModel/man/verbose.dcm.Rd | 2 EpiModel-1.2.2/EpiModel/man/verbose.icm.Rd | 2 EpiModel-1.2.2/EpiModel/man/verbose.net.Rd | 2 EpiModel-1.2.2/EpiModel/tests/testthat/test-netdx.R | 18 EpiModel-1.2.2/EpiModel/tests/testthat/test-print.R | 16 EpiModel-1.2.2/EpiModel/tests/testthat/test-transmat-dendo.R |only EpiModel-1.2.2/EpiModel/tests/testthat/test-utils.R | 2 114 files changed, 505 insertions(+), 353 deletions(-)
Title: Sorted L1 Penalized Estimation (SLOPE)
Description: Efficient procedures for Sorted L1 Penalized Estimation (SLOPE).
The sorted L1 norm is useful for statistical estimation and testing,
particularly for variable selection in the linear model.
Author: Malgorzata Bogdan, Ewout van den Berg, Chiara Sabatti, Weijie Su,
Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson <epatters@stanford.edu>
Diff between SLOPE versions 0.1.1 dated 2015-04-27 and 0.1.3 dated 2015-11-03
DESCRIPTION | 13 - MD5 | 30 +-- NAMESPACE | 6 R/SLOPE.R | 6 R/SLOPE_solver.R | 5 R/util.R | 17 ++ build/vignette.rds |binary inst/doc/intro.html | 96 +++++++---- man/SLOPE.Rd | 4 man/SLOPE_solver.Rd | 4 man/SLOPE_solver_matlab.Rd | 8 man/lambda.Rd | 2 man/prox_sorted_L1.Rd | 4 tests/testthat.R | 9 + tests/testthat/MatlabServer.m | 353 +++++++++++++++++++++++------------------- tests/testthat/test_slope.R | 1 16 files changed, 325 insertions(+), 233 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.2.3 dated 2015-09-25 and 0.2.4 dated 2015-11-03
DESCRIPTION | 8 MD5 | 68 +++--- NAMESPACE | 8 NEWS | 10 R/distr.R |only R/fitbs.R | 2 R/fitgamma.R | 2 R/fitgeom.R | 2 R/fitgs.R | 2 R/fitlnorm.R | 2 R/fitls.R | 2 R/fitmand.R | 2 R/fitmzsm.R | 2 R/fitnbinom.R | 2 R/fitpareto.R | 2 R/fitpoilog.R | 2 R/fitpower.R | 2 R/fitrbs.R | 2 R/fitvolkov.R | 8 R/fitweibull.R | 2 R/fitzipf.R | 2 R/octav.R | 20 + R/sads-classes.R | 13 + R/sads-methods.R | 466 +++++++++++++++++++++++----------------------- inst/doc/sads_intro.Rnw | 2 inst/doc/sads_intro.pdf |binary man/distr.Rd |only man/dvolkov.Rd | 5 man/fitrad-class.Rd | 3 man/fitsad-class.Rd | 3 man/octavpred.Rd | 6 man/qqsad.Rd | 13 - man/radpred.Rd | 15 - man/sads-package.Rd | 4 man/stats.Rd |only man/summary.sads-class.Rd |only vignettes/sads_intro.Rnw | 2 37 files changed, 366 insertions(+), 318 deletions(-)
Title: P-Values for Classification
Description: Computes nonparametric p-values for the potential class
memberships of new observations as well as cross-validated
p-values for the training data. The p-values are based on
permutation tests applied to an estimated Bayesian likelihood
ratio, using a plug-in statistic for the Gaussian model, 'k
nearest neighbors', 'weighted nearest neighbors' or
'penalized logistic regression'.
Additionally, it provides graphical displays and quantitative
analyses of the p-values.
Author: Niki Zumbrunnen <niki.zumbrunnen@gmail.com>,
Lutz Duembgen <lutz.duembgen@stat.unibe.ch>.
Maintainer: Niki Zumbrunnen <niki.zumbrunnen@gmail.com>
Diff between pvclass versions 1.2 dated 2014-11-24 and 1.3 dated 2015-11-03
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 3 +++ R/cvpvs.gaussian.R | 11 ++++++++--- R/cvpvs.knn.R | 9 +++++++-- R/cvpvs.logreg.R | 10 ++++++++-- R/cvpvs.wnn.R | 10 ++++++++-- R/pvs.gaussian.R | 30 ++++++++++++++++-------------- R/pvs.knn.R | 39 ++++++++++++++++++++++----------------- R/pvs.logreg.R | 34 +++++++++++++++++++++++++++------- R/pvs.wnn.R | 29 ++++++++++++++++------------- R/sigmaSym.R | 23 ++++++++++++----------- 12 files changed, 143 insertions(+), 87 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.5 dated 2015-10-22 and 0.4.6 dated 2015-11-03
DESCRIPTION | 11 +++-- MD5 | 70 +++++++++++++++++++++++++++++++------ R/dependencies.R | 8 ++-- R/options.R | 59 +++++++++++++++++++++++-------- R/recursive-package-dependencies.R | 10 ++++- R/restore.R | 53 ++++++++++++++++++++-------- R/utils.R | 18 +++++++++ inst/resources/init-rprofile.R | 2 - inst/resources/init.R | 2 - man/appDependencies.Rd | 6 +-- man/packrat-options.Rd | 6 +++ tests |only 12 files changed, 192 insertions(+), 53 deletions(-)
Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
<kimkspeer@gmail.com>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between likert versions 1.3.0 dated 2015-10-23 and 1.3.1 dated 2015-11-03
DESCRIPTION | 9 ++--- MD5 | 72 +++++++++++++++++++++--------------------- NAMESPACE | 2 - NEWS | 7 +++- R/xtable.likert.r | 6 ++- build/vignette.rds |binary inst/doc/likert-xtable.pdf |binary man/MathAnxiety.Rd | 6 +-- man/MathAnxietyGender.Rd | 8 ++-- man/abs_formatter.Rd | 2 - man/align.plots.Rd | 2 - man/gap.Rd | 2 - man/label_wrap_mod.Rd | 2 - man/likert-package.Rd | 2 - man/likert.Rd | 6 +-- man/likert.bar.plot.Rd | 6 +-- man/likert.density.plot.Rd | 2 - man/likert.heat.plot.Rd | 2 - man/likert.histogram.plot.Rd | 2 - man/likert.matrix.plot.Rd | 2 - man/mass.Rd | 6 +-- man/pisaitems.Rd | 2 - man/plot.likert.Rd | 4 +- man/plot.likert.gap.Rd | 4 +- man/print.likert.Rd | 2 - man/print.likert.bar.plot.Rd | 6 +-- man/print.likert.gap.Rd | 2 - man/print.likert.heat.plot.Rd | 2 - man/print.xlikert.Rd | 2 - man/recode.Rd | 4 +- man/reverse.levels.Rd | 2 - man/sasr.Rd | 6 +-- man/shinyLikert.Rd | 2 - man/summary.likert.Rd | 6 +-- man/summary.likert.gap.Rd | 4 +- man/xtable.likert.Rd | 18 ++++++---- man/zeroGrob.Rd | 2 - 37 files changed, 114 insertions(+), 100 deletions(-)
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.2 dated 2015-10-22 and 0.3 dated 2015-11-03
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++++---- NAMESPACE | 5 +++++ NEWS | 3 +++ R/classificaClasseDAP.R |only R/criaDadosPareados.R | 20 ++++++++++++++++++++ R/defineClasses2.R |only R/ifrm.R |only R/whichmedian.R |only man/classificaClasseDAP.Rd |only man/defineClasses2.Rd |only man/ifrm.Rd |only man/whichmedian.Rd |only 13 files changed, 45 insertions(+), 9 deletions(-)
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2S versions 1.0.3 dated 2015-08-12 and 1.0.4 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++++----------- NEWS | 5 +++++ R/PredictionsBarplot.R |only R/PredictionsDistributionBoxplot.R |only R/PredictionsDistributionPie.R |only README | 6 ++++++ inst/doc/MM2S.R | 15 +++++++++++++-- inst/doc/MM2S.Rnw | 28 ++++++++++++++++++++++++---- inst/doc/MM2S.pdf |binary inst/doc/MM2S_Vignette_FrozenCapture.pdf |binary man/MM2S.human.Rd | 4 ++-- man/MM2S.mouse.Rd | 8 ++++---- man/PCARender.Rd | 12 ++++++------ man/PredictionsBarplot.Rd |only man/PredictionsDistributionBoxplot.Rd |only man/PredictionsDistributionPie.Rd |only vignettes/MM2S.Rnw | 28 ++++++++++++++++++++++++---- 18 files changed, 105 insertions(+), 37 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 2.1 dated 2015-11-01 and 2.1.1 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/MSE_source.R | 2 +- inst/doc/DLMtool.Rnw | 9 +++++++-- inst/doc/DLMtool.pdf |binary man/DLMtool-package.Rd | 4 ++-- vignettes/DLMtool.Rnw | 9 +++++++-- 7 files changed, 27 insertions(+), 17 deletions(-)
Title: Epidemiological Data Display Package
Description: Package for data exploration and result presentation.
Full 'epicalc' package with data management functions is available
at the author's repository.
Author: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Maintainer: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Diff between epiDisplay versions 3.2.0.6 dated 2015-07-01 and 3.2.2.0 dated 2015-11-02
DESCRIPTION | 8 - MD5 | 13 +- NAMESPACE | 37 +++--- R/epiDisplay.R | 260 +++++++++++++++++++++++++++++++++---------------- man/matchTab.rd | 4 man/print.matchTab.rd |only man/print.statStack.rd |only man/statStack.rd |only man/tableStack.rd | 22 +++- 9 files changed, 228 insertions(+), 116 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.0-7 dated 2015-09-06 and 1.1-1 dated 2015-11-02
ChangeLog | 1370 ------------------------------------ DESCRIPTION | 8 MD5 | 31 R/make_EPSG.R | 9 configure | 18 inst/ChangeLog | 1370 ------------------------------------ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/etc/obj_with_comments.RData |only inst/etc/obj_without_comments.RData |only inst/etc/test_dfs.RData |only man/readOGR.Rd | 2 man/showWKT.Rd | 2 man/writeOGR.Rd | 21 src/OGR_write.cpp | 226 ++++- src/ogrdrivers.cpp | 10 src/ogrsource.cpp | 2 tests/tripup.R |only tests/tripup.Rout.save |only 19 files changed, 242 insertions(+), 2829 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.8.14 dated 2015-10-30 and 1.8.15 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/servers.R | 2 ++ inst/shiny/server.R | 5 ----- inst/shiny/ui.R | 2 ++ 6 files changed, 15 insertions(+), 14 deletions(-)
Title: Implementation of Unobserved Components Model (UCM)
Description: Unobserved Components Models (introduced in Harvey, A. (1989),
Forecasting, structural time series models and the Kalman filter, Cambridge
New York: Cambridge University Press) decomposes a time series into
components such as trend, seasonal, cycle, and the regression effects due
to predictor series which captures the salient features of the series to
predict its behavior.
Author: Kaushik Roy Chowdhury
Maintainer: Kaushik Roy Chowdhury <kaushikrch@gmail.com>
Diff between rucm versions 0.4 dated 2014-09-07 and 0.5 dated 2015-11-02
rucm-0.4/rucm/vignettes/figure |only rucm-0.5/rucm/DESCRIPTION | 12 - rucm-0.5/rucm/MD5 | 32 +-- rucm-0.5/rucm/NAMESPACE | 9 - rucm-0.5/rucm/NEWS | 6 rucm-0.5/rucm/R/predict.ucm.R | 5 rucm-0.5/rucm/R/print.ucm.R | 1 rucm-0.5/rucm/R/ucm.R | 256 ++++++++++++++++------------- rucm-0.5/rucm/README.md |only rucm-0.5/rucm/build/vignette.rds |binary rucm-0.5/rucm/inst/doc/rucm_vignettes.R | 1 rucm-0.5/rucm/inst/doc/rucm_vignettes.Rmd | 7 rucm-0.5/rucm/inst/doc/rucm_vignettes.html | 21 -- rucm-0.5/rucm/man/predict.ucm.Rd | 8 rucm-0.5/rucm/man/print.ucm.Rd | 3 rucm-0.5/rucm/man/rucm-package.Rd | 17 + rucm-0.5/rucm/man/ucm.Rd | 3 rucm-0.5/rucm/vignettes/rucm_vignettes.Rmd | 7 18 files changed, 218 insertions(+), 170 deletions(-)
Title: Multivariate Probit Models
Description: Tools for estimating multivariate probit models,
calculating conditional and unconditional expectations,
and calculating marginal effects on conditional and unconditional
expectations.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between mvProbit versions 0.1-4 dated 2015-09-03 and 0.1-8 dated 2015-11-02
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/logLik.mvProbit.R | 2 R/summary.mvProbit.R | 2 man/mvProbit.Rd | 4 - tests/mvProbitEst.R | 34 +++++++------- tests/mvProbitEst.Rout.save | 104 ++++++++++++++++++++++---------------------- 7 files changed, 83 insertions(+), 83 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.7 dated 2015-10-15 and 1.8 dated 2015-11-02
geigen-1.7/geigen/tests/tgeigen1.Rout |only geigen-1.7/geigen/tests/tgeigen2.Rout |only geigen-1.7/geigen/tests/tgqz1.Rout |only geigen-1.7/geigen/tests/tgqz2.Rout |only geigen-1.7/geigen/tests/tgqz3.Rout |only geigen-1.7/geigen/tests/tgqz4.Rout |only geigen-1.7/geigen/tests/tgqz5.Rout |only geigen-1.7/geigen/tests/tgqz6.Rout |only geigen-1.7/geigen/tests/tgsvd5.R |only geigen-1.7/geigen/tests/tgsvd5.Rout.save |only geigen-1.7/geigen/tests/tgsvd6.R |only geigen-1.7/geigen/tests/tgsvd6.Rout.save |only geigen-1.7/geigen/tests/tgsvd7.R |only geigen-1.7/geigen/tests/tgsvd7.Rout.save |only geigen-1.7/geigen/tests/tgsvd8.R |only geigen-1.7/geigen/tests/tgsvd8.Rout.save |only geigen-1.8/geigen/DESCRIPTION | 8 +- geigen-1.8/geigen/MD5 | 52 +++++++------------ geigen-1.8/geigen/NAMESPACE | 4 - geigen-1.8/geigen/NEWS | 4 + geigen-1.8/geigen/R/gsvd.R | 67 +++++++++++++++++-------- geigen-1.8/geigen/inst/COPYRIGHTS | 1 geigen-1.8/geigen/man/geigen-package.Rd | 4 - geigen-1.8/geigen/man/geigen.Rd | 2 geigen-1.8/geigen/man/gqz.Rd | 2 geigen-1.8/geigen/man/gsvd.Rd | 41 +++++++++++---- geigen-1.8/geigen/src/xzggsvd.f |only geigen-1.8/geigen/src/zggsvdall.f |only geigen-1.8/geigen/tests/testgsvd.R | 11 +++- geigen-1.8/geigen/tests/tgqz2.Rout.save | 8 +- geigen-1.8/geigen/tests/tgsvd2.R | 12 +++- geigen-1.8/geigen/tests/tgsvd2.Rout.save | 40 ++++++++++---- geigen-1.8/geigen/tests/tgsvd3.R | 29 ++++++++-- geigen-1.8/geigen/tests/tgsvd3.Rout.save | 60 ++++++++++++++-------- geigen-1.8/geigen/tests/tgsvd4.R | 54 ++++++++++++++++++-- geigen-1.8/geigen/tests/tgsvd4.Rout.save | 83 +++++++++++++++++++++++-------- 36 files changed, 332 insertions(+), 150 deletions(-)
Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl <dahl@stat.byu.edu>
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between xtable versions 1.7-4 dated 2014-09-12 and 1.8-0 dated 2015-11-02
xtable-1.7-4/xtable/inst/doc/xtableGallery.snw |only xtable-1.7-4/xtable/vignettes/xtableGallery.snw |only xtable-1.8-0/xtable/DESCRIPTION | 15 xtable-1.8-0/xtable/MD5 | 41 xtable-1.8-0/xtable/NAMESPACE | 14 xtable-1.8-0/xtable/NEWS | 35 xtable-1.8-0/xtable/R/autoformat.R |only xtable-1.8-0/xtable/R/toLatex.R | 2 xtable-1.8-0/xtable/R/xtable.R | 93 + xtable-1.8-0/xtable/build/vignette.rds |binary xtable-1.8-0/xtable/data/tli.txt.gz |binary xtable-1.8-0/xtable/inst/doc/margintable.R | 13 xtable-1.8-0/xtable/inst/doc/margintable.Rnw | 13 xtable-1.8-0/xtable/inst/doc/margintable.pdf |binary xtable-1.8-0/xtable/inst/doc/xtableGallery.R | 744 ++++----------- xtable-1.8-0/xtable/inst/doc/xtableGallery.Rnw |only xtable-1.8-0/xtable/inst/doc/xtableGallery.pdf |binary xtable-1.8-0/xtable/man/autoformat.Rd |only xtable-1.8-0/xtable/man/print.xtable.Rd | 89 - xtable-1.8-0/xtable/man/table.attributes.Rd | 7 xtable-1.8-0/xtable/man/tli.Rd | 3 xtable-1.8-0/xtable/man/xtable.Rd | 56 - xtable-1.8-0/xtable/tests/test.xalign.xdigits.xdisplay.R |only xtable-1.8-0/xtable/vignettes/margintable.Rnw | 13 xtable-1.8-0/xtable/vignettes/xtableGallery.Rnw |only 25 files changed, 432 insertions(+), 706 deletions(-)
Title: Interface to Colombos Compendia using the Exposed REST API
Description: Provides programmatic access to Colombos, a web based
interface for exploring and analyzing comprehensive organism-specific
cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego <paolo.sonego@fmach.it>
Maintainer: Paolo Sonego <paolo.sonego@fmach.it>
Diff between Rcolombos versions 1.5.3 dated 2015-09-07 and 2.0.2 dated 2015-11-02
DESCRIPTION | 8 +- MD5 | 38 ++++++------ NAMESPACE | 2 R/Rcolombos.R | 34 ++++++----- R/utilities.R | 111 ++++++++++++++++++++++++++++-------- R/zzz.R | 6 - README.md |only man/Rcolombos.Rd |only man/advanced_search.Rd | 2 man/advanced_search_by_both.Rd | 2 man/advanced_search_by_contrasts.Rd | 2 man/advanced_search_by_genes.Rd | 2 man/getCompendium.Rd | 12 ++- man/get_contrast_annotations.Rd |only man/listAnnotationTypes.Rd | 2 man/listContrasts.Rd | 2 man/listEntities.Rd | 2 man/listGenes.Rd | 2 man/listOrganisms.Rd | 4 - man/parseCompendium.Rd | 12 ++- man/quick_search.Rd | 2 man/switchVersion.Rd |only 22 files changed, 165 insertions(+), 80 deletions(-)
Title: Unsampled Data in R for Google Analytics Premium Accounts
Description: It fires a query to the API to get the unsampled data in R for Google Analytics Premium Accounts. It retrieves data from the Google drive document and stores it into the local drive. The path to the excel file is returned by this package. The user can read data from the excel file into R using read.csv() function.
Author: Jalpa Joshi Dave
Maintainer: Jalpa Joshi Dave <jalpa@tatvic.com>
Diff between RGoogleAnalyticsPremium versions 0.1 dated 2015-10-29 and 0.1.1 dated 2015-11-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- demo/data_extraction_final.R | 8 +++----- 3 files changed, 8 insertions(+), 10 deletions(-)
More information about RGoogleAnalyticsPremium at CRAN
Permanent link
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1.2 dated 2015-05-12 and 1.1.3 dated 2015-11-02
MRIaggr-1.1.2/MRIaggr/R/Associated_functions.R |only MRIaggr-1.1.2/MRIaggr/R/GR_functions.R |only MRIaggr-1.1.2/MRIaggr/R/Generic_functions.R |only MRIaggr-1.1.2/MRIaggr/inst/calcCriteriaGR.Rd |only MRIaggr-1.1.2/MRIaggr/inst/calcSigmaGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/Carto3D2MRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/EDK.Rd |only MRIaggr-1.1.2/MRIaggr/man/GRalgo.Rd |only MRIaggr-1.1.2/MRIaggr/man/MRIaggr-package.Rd |only MRIaggr-1.1.2/MRIaggr/man/MRIaggr.Pat1_red.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocTable.Rd |only MRIaggr-1.1.2/MRIaggr/man/array2df.Rd |only MRIaggr-1.1.2/MRIaggr/man/boxplotMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcAUPRC.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcBrainMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcContro_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcControlateral.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcDistMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcDistTissues.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcFilter.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsCoords.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsCoords_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsW.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsW_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcHemi_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcROCthreshold.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcRadius_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcRegionaContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcSmoothMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTableHypoReperf.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTableLesion.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcThresholdMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTissueType.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcW.Rd |only MRIaggr-1.1.2/MRIaggr/man/constCarto3D.Rd |only MRIaggr-1.1.2/MRIaggr/man/constCompressMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/constLatex.Rd |only MRIaggr-1.1.2/MRIaggr/man/constMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/constReduceMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/df2array.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage2D_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage2Dmed_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage3D_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage3Dmed_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/heatmapMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/initCol.Rd |only MRIaggr-1.1.2/MRIaggr/man/initConstLatex.Rd |only MRIaggr-1.1.2/MRIaggr/man/initDisplayWindow.Rd |only MRIaggr-1.1.2/MRIaggr/man/initFilter.Rd |only MRIaggr-1.1.2/MRIaggr/man/initGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/initIndex.Rd |only MRIaggr-1.1.2/MRIaggr/man/initMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/initNeighborhood.Rd |only MRIaggr-1.1.2/MRIaggr/man/initNum.Rd |only MRIaggr-1.1.2/MRIaggr/man/initParameter.Rd |only MRIaggr-1.1.2/MRIaggr/man/initWindow.Rd |only MRIaggr-1.1.2/MRIaggr/man/legendMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/multiplot.Rd |only MRIaggr-1.1.2/MRIaggr/man/outline.Rd |only MRIaggr-1.1.2/MRIaggr/man/outlineMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotDistClass.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotLesion3D.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotOutline.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotTableLesion.Rd |only MRIaggr-1.1.2/MRIaggr/man/pointsHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/readMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectCoords.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectDefault_value.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectHemispheres.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectHistory.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectIdentifier.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectMidplane.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectN.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectParameter.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectTable.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectVoxelDim.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectVoxelSize.Rd |only MRIaggr-1.1.2/MRIaggr/man/summary.MRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/supprContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/supprDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/writeMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/writeMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/src/Associated_functions.cpp |only MRIaggr-1.1.3/MRIaggr/DESCRIPTION | 23 MRIaggr-1.1.3/MRIaggr/MD5 | 278 MRIaggr-1.1.3/MRIaggr/NAMESPACE | 32 MRIaggr-1.1.3/MRIaggr/R/Class_Carto3D.R | 477 MRIaggr-1.1.3/MRIaggr/R/Class_MRIaggr.R | 9119 +++++----- MRIaggr-1.1.3/MRIaggr/R/Functions_AssociatedClass.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_GR.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Miscellaneous.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Options.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Potts.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Valid.R |only MRIaggr-1.1.3/MRIaggr/R/Generic_Functions.R |only MRIaggr-1.1.3/MRIaggr/R/RcppExports.R | 48 MRIaggr-1.1.3/MRIaggr/data/MRIaggr.Pat1_red.RData |binary MRIaggr-1.1.3/MRIaggr/demo/Analysis.R | 108 MRIaggr-1.1.3/MRIaggr/demo/ExtractNifti.R | 95 MRIaggr-1.1.3/MRIaggr/demo/preProcessing.R | 282 MRIaggr-1.1.3/MRIaggr/inst/Data_Tests |only MRIaggr-1.1.3/MRIaggr/inst/Functions_Segmentation.R |only MRIaggr-1.1.3/MRIaggr/inst/Functions_UserSegmentation.R |only MRIaggr-1.1.3/MRIaggr/inst/List_of_arguments.R | 3049 +-- MRIaggr-1.1.3/MRIaggr/inst/NEWS | 28 MRIaggr-1.1.3/MRIaggr/inst/TODO | 9 MRIaggr-1.1.3/MRIaggr/inst/hist |only 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insertions(+), 6664 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-4 dated 2015-07-03 and 0.7-5 dated 2015-11-02
metaplus-0.7-4/metaplus/R/outlier.probs.metaplus.R |only metaplus-0.7-4/metaplus/R/outlier.probs.profilemix.metaplus.R |only metaplus-0.7-4/metaplus/R/plot.outlier.probs.R |only metaplus-0.7-4/metaplus/R/test.outliers.metaplus.R |only metaplus-0.7-4/metaplus/R/test.outliers.profilemix.metaplus.R |only metaplus-0.7-4/metaplus/R/test.outliers.profilet.metaplus.R |only metaplus-0.7-4/metaplus/man/outlier.probs.Rd |only metaplus-0.7-4/metaplus/man/plot.outlier.probs.Rd |only metaplus-0.7-4/metaplus/man/test.outliers.Rd |only metaplus-0.7-5/metaplus/DESCRIPTION | 17 metaplus-0.7-5/metaplus/MD5 | 73 metaplus-0.7-5/metaplus/NAMESPACE | 16 metaplus-0.7-5/metaplus/R/metaplus.R | 33 metaplus-0.7-5/metaplus/R/mymle.R | 1451 ++++------ metaplus-0.7-5/metaplus/R/outlierProbs.metaplus.R |only metaplus-0.7-5/metaplus/R/outlierProbs.profilemix.metaplus.R |only metaplus-0.7-5/metaplus/R/plot.outlierProbs.R |only metaplus-0.7-5/metaplus/R/print.metaplus.R |only metaplus-0.7-5/metaplus/R/profilemix.metaplus.R | 178 - metaplus-0.7-5/metaplus/R/profilenorm.metaplus.R | 7 metaplus-0.7-5/metaplus/R/profilet.metaplus.R | 62 metaplus-0.7-5/metaplus/R/profilet.profile.R | 2 metaplus-0.7-5/metaplus/R/testOutliers.metaplus.R |only metaplus-0.7-5/metaplus/R/testOutliers.profilemix.metaplus.R |only metaplus-0.7-5/metaplus/R/testOutliers.profilet.metaplus.R |only metaplus-0.7-5/metaplus/inst/NEWS | 20 metaplus-0.7-5/metaplus/inst/doc/beath-examples.R | 193 - metaplus-0.7-5/metaplus/man/cdp.Rd | 59 metaplus-0.7-5/metaplus/man/exercise.Rd | 83 metaplus-0.7-5/metaplus/man/logLik.Rd | 34 metaplus-0.7-5/metaplus/man/mag.Rd | 5 metaplus-0.7-5/metaplus/man/marinho.Rd | 69 metaplus-0.7-5/metaplus/man/metaplus-package.Rd | 99 metaplus-0.7-5/metaplus/man/metaplus.Rd | 9 metaplus-0.7-5/metaplus/man/outlierProbs.Rd |only metaplus-0.7-5/metaplus/man/plot.metaplus.Rd | 106 metaplus-0.7-5/metaplus/man/plot.outlierProbs.Rd |only metaplus-0.7-5/metaplus/man/summary.Rd | 4 metaplus-0.7-5/metaplus/man/testOutliers.Rd |only metaplus-0.7-5/metaplus/vignettes/metaplus-examples-003.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-004.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-005.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-013.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-014.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-016.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples-018.pdf |binary metaplus-0.7-5/metaplus/vignettes/metaplus-examples.tex | 108 47 files changed, 1270 insertions(+), 1358 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.6 dated 2015-09-13 and 1.8.8 dated 2015-11-02
forestFloor-1.8.6/forestFloor/R/forestFloor_multiClass.R |only forestFloor-1.8.8/forestFloor/DESCRIPTION | 10 forestFloor-1.8.8/forestFloor/MD5 | 80 - forestFloor-1.8.8/forestFloor/NAMESPACE | 130 +- forestFloor-1.8.8/forestFloor/R/RcppExports.R | 22 forestFloor-1.8.8/forestFloor/R/append.overwrite.alists.R | 18 forestFloor-1.8.8/forestFloor/R/as.numeric.factor.R | 12 forestFloor-1.8.8/forestFloor/R/box.outliers.R | 58 - forestFloor-1.8.8/forestFloor/R/convolute_ff.R | 72 - forestFloor-1.8.8/forestFloor/R/convolute_ff2.R | 198 +-- forestFloor-1.8.8/forestFloor/R/fcol.R | 466 ++++---- forestFloor-1.8.8/forestFloor/R/forestFloor_randomForest_multiClass.R |only forestFloor-1.8.8/forestFloor/R/forestFloor_randomForest_regression.R |only forestFloor-1.8.8/forestFloor/R/forestFloor_source.R | 224 ---- forestFloor-1.8.8/forestFloor/R/ggPlotForestFloor.R | 98 - forestFloor-1.8.8/forestFloor/R/plot.forestFloor_multiClass.R | 184 +-- forestFloor-1.8.8/forestFloor/R/plot.forestFloor_regression.R | 244 ++-- forestFloor-1.8.8/forestFloor/R/plot_simplex3.R | 260 ++-- forestFloor-1.8.8/forestFloor/R/print.forestFloor_regression.R | 14 forestFloor-1.8.8/forestFloor/R/show3d.R | 342 +++--- forestFloor-1.8.8/forestFloor/R/vec.plot.R | 76 - forestFloor-1.8.8/forestFloor/man/append.overwrite.alists.Rd | 90 - forestFloor-1.8.8/forestFloor/man/as.numeric.factor.Rd | 84 - forestFloor-1.8.8/forestFloor/man/box.outliers.Rd | 120 +- forestFloor-1.8.8/forestFloor/man/convolute_ff.Rd | 160 +-- forestFloor-1.8.8/forestFloor/man/convolute_ff2.Rd | 180 +-- forestFloor-1.8.8/forestFloor/man/convolute_grid.Rd | 352 +++--- forestFloor-1.8.8/forestFloor/man/fcol.Rd | 266 ++--- forestFloor-1.8.8/forestFloor/man/forestFloor-package.Rd | 74 - forestFloor-1.8.8/forestFloor/man/forestFloor.Rd | 509 ++++----- forestFloor-1.8.8/forestFloor/man/ggPlotForestFloor.Rd | 136 +- forestFloor-1.8.8/forestFloor/man/ggplotGrob.Rd | 30 forestFloor-1.8.8/forestFloor/man/plot.forestFloor.Rd | 524 +++++----- forestFloor-1.8.8/forestFloor/man/plot_simplex3.Rd | 270 ++--- forestFloor-1.8.8/forestFloor/man/print.forestFloor.Rd | 112 +- forestFloor-1.8.8/forestFloor/man/recTree.Rd | 250 ++-- forestFloor-1.8.8/forestFloor/man/show3d.Rd | 412 +++---- forestFloor-1.8.8/forestFloor/man/vec.plot.Rd | 192 +-- forestFloor-1.8.8/forestFloor/tests/ggplotUsage.R | 38 forestFloor-1.8.8/forestFloor/tests/rfPermute_supported.R |only forestFloor-1.8.8/forestFloor/tests/stdUsage.R | 106 +- forestFloor-1.8.8/forestFloor/tests/testBinaryClass.R | 102 - forestFloor-1.8.8/forestFloor/tests/testMultiClass.cpp.R | 172 +-- 43 files changed, 3296 insertions(+), 3391 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: ExPANdS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in EXPANDS version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. This version of expands decides whether or not this is the case leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS. Further documentation and FAQ around ExPANdS is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.5 dated 2014-09-28 and 1.6 dated 2015-11-02
expands-1.5/expands/java/ExPANdS.java |only expands-1.6/expands/DESCRIPTION | 16 expands-1.6/expands/MD5 | 56 - expands-1.6/expands/NAMESPACE | 5 expands-1.6/expands/R/assignMutations.R | 255 ++++- expands-1.6/expands/R/assignQuantityToSP.R | 66 - expands-1.6/expands/R/buildMultiSamplePhylo.R | 64 + expands-1.6/expands/R/buildPhylo.R | 224 +++-- expands-1.6/expands/R/cellfrequency_pdf.R | 59 - expands-1.6/expands/R/clusterCellFrequencies.R | 474 +++++------ expands-1.6/expands/R/computeCellFrequencyDistributions.R | 96 +- expands-1.6/expands/R/plotSPs.R | 125 +- expands-1.6/expands/R/runExPANdS.R | 421 +++++---- expands-1.6/expands/inst/doc/expands.R | 43 expands-1.6/expands/inst/doc/expands.Rnw | 50 - expands-1.6/expands/inst/doc/expands.pdf |binary expands-1.6/expands/inst/java/expands.jar |binary expands-1.6/expands/java/expands.jar |only expands-1.6/expands/man/assignMutations.Rd | 33 expands-1.6/expands/man/assignQuantityToSP.Rd | 30 expands-1.6/expands/man/buildMultiSamplePhylo.Rd | 26 expands-1.6/expands/man/buildPhylo.Rd | 22 expands-1.6/expands/man/cellfrequency_pdf.Rd | 48 - expands-1.6/expands/man/clusterCellFrequencies.Rd | 8 expands-1.6/expands/man/computeCellFrequencyDistributions.Rd | 9 expands-1.6/expands/man/plotSPs.Rd | 9 expands-1.6/expands/man/roi.Rd | 2 expands-1.6/expands/man/runExPANdS.Rd | 42 expands-1.6/expands/man/snv.Rd | 4 expands-1.6/expands/vignettes/expands.Rnw | 48 - 30 files changed, 1288 insertions(+), 947 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.3 dated 2015-10-01 and 0.0.4 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++++++++--------------- NAMESPACE | 7 +++++++ NEWS | 10 ++++++++++ R/AIC.epifit.R | 6 +++--- R/calcAge.R |only R/convertNA.R |only R/countNA.R |only R/epifit-package.R | 10 ++++++++-- R/epifit.R | 4 ++++ R/extractVariable.R |only R/modules.R | 8 ++++---- R/print.epifit.R | 4 ++-- R/pullOneValue.R |only R/pytable.R | 7 +++---- R/removeVariable.R |only man/AIC.epifit.Rd | 10 +++++----- man/calcAge.Rd |only man/convertNA.Rd |only man/countNA.Rd |only man/epifit-package.Rd | 10 ++++++++-- man/epifit.Rd | 4 ++++ man/extractVariable.Rd |only man/print.epifit.Rd | 2 +- man/pullOneValue.Rd |only man/pytable.Rd | 9 +++------ man/removeVariable.Rd |only src/select.h | 4 +--- 28 files changed, 94 insertions(+), 51 deletions(-)
Title: Plot Categorical Data Using Quasirandom Noise and Density
Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Author: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
Diff between vipor versions 0.3.1 dated 2015-10-31 and 0.3.2 dated 2015-11-01
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/doc/methodComparison.Rnw | 8 ++++---- inst/doc/methodComparison.pdf |binary inst/doc/usageExamples.Rnw | 8 ++++---- inst/doc/usageExamples.pdf |binary vignettes/methodComparison.Rnw | 8 ++++---- vignettes/usageExamples.Rnw | 8 ++++---- 9 files changed, 28 insertions(+), 28 deletions(-)
Title: Twitter Collector and Export to 'postGIS'
Description: This is an improved implementation of the package 'StreamR' to
capture tweets and store it into a 'postGIS' data base. The package simplifies
the configuration task to capture tweets and facilitates its store into a
'PostGIS' database.
Author: Pau Aragó
Maintainer: Pau Aragó <parago@uji.es>
Diff between tweet2r versions 0.1 dated 2015-10-23 and 0.2 dated 2015-11-01
DESCRIPTION | 12 ++++++++---- MD5 | 12 ++++++------ NAMESPACE | 6 +++++- R/t2pgis.R | 2 ++ R/tweet2r.R | 2 ++ man/tweet2r-package.Rd | 1 + man/tweet2r.Rd | 14 +++++++++++--- 7 files changed, 35 insertions(+), 14 deletions(-)
Title: Statistical Process Control -- Collection of Some Useful
Functions
Description: Evaluation of control charts by means of
the zero-state, steady-state ARL (Average Run Length) and RL quantiles.
Setting up control charts for given in-control ARL. The control charts
under consideration are one- and two-sided EWMA, CUSUM, and
Shiryaev-Roberts schemes for monitoring the mean of normally
distributed independent data. ARL calculation
of the same set of schemes under drift are added.
Other charts and parameters are in preparation.
Further SPC areas will be covered as well
(sampling plans, capability indices ...).
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>
Diff between spc versions 0.5.1 dated 2015-05-18 and 0.5.2 dated 2015-11-01
DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 6 R/mewma.ad.R |only R/mewma.arl.R | 9 R/mewma.arl.f.R |only R/mewma.psi.R |only R/xewma.arl.R | 16 R/xewma.crit.R | 12 R/xtcusum.arl.R |only man/mewma.arl.Rd | 19 man/mewma.psi.Rd |only man/xDcusum.arl.Rd | 4 man/xtcusum.arl.Rd |only man/xtewma.ad.Rd | 2 man/xtewma.arl.Rd | 4 src/allspc.c | 1630 ++++++++++++++++++++++++++++++++++++++++++++++++++--- src/mewma_ad.c |only src/mewma_arl_f.c |only src/mewma_psi.c |only src/sewma_sf.c | 2 src/xtcusum_arl.c |only 22 files changed, 1615 insertions(+), 129 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.0.0.2 dated 2015-06-06 and 1.1.0.0 dated 2015-11-01
SpatPCA-1.0.0.2/SpatPCA/man/SpatPCAinternal6.Rd |only SpatPCA-1.0.0.2/SpatPCA/man/SpatPCAinternal7.Rd |only SpatPCA-1.0.0.2/SpatPCA/man/SpatPCAinternal8.Rd |only SpatPCA-1.0.0.2/SpatPCA/man/cv.covfn.Rd |only SpatPCA-1.0.0.2/SpatPCA/man/cv.spatpca.Rd |only SpatPCA-1.0.0.2/SpatPCA/man/plot.spatpca.Rd |only SpatPCA-1.1.0.0/SpatPCA/DESCRIPTION | 15 SpatPCA-1.1.0.0/SpatPCA/MD5 | 37 - SpatPCA-1.1.0.0/SpatPCA/NAMESPACE | 13 SpatPCA-1.1.0.0/SpatPCA/R/RcppExports.R | 16 SpatPCA-1.1.0.0/SpatPCA/R/SpatPCA.R | 550 +++-------------- SpatPCA-1.1.0.0/SpatPCA/man/SpatPCA-package.Rd | 4 SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal1.Rd | 4 SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal2.Rd | 5 SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal3.Rd | 4 SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal4.Rd | 4 SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal5.Rd | 4 SpatPCA-1.1.0.0/SpatPCA/man/covfn.Rd |only SpatPCA-1.1.0.0/SpatPCA/man/spatpca.Rd | 87 +- SpatPCA-1.1.0.0/SpatPCA/src/Makevars | 1 SpatPCA-1.1.0.0/SpatPCA/src/Makevars.win | 4 SpatPCA-1.1.0.0/SpatPCA/src/RcppExports.cpp | 70 -- SpatPCA-1.1.0.0/SpatPCA/src/rcpp_SpatPCA.cpp | 775 ++++++++++++++++-------- 23 files changed, 806 insertions(+), 787 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@univ-montp2.fr>
Diff between spaMM versions 1.5.1 dated 2015-02-22 and 1.6.2 dated 2015-11-01
spaMM-1.5.1/spaMM/src/Bessel.h |only spaMM-1.5.1/spaMM/src/BesselK_R.h |only spaMM-1.5.1/spaMM/src/chol.cpp |only spaMM-1.5.1/spaMM/src/chol.h |only spaMM-1.6.2/spaMM/DESCRIPTION | 23 spaMM-1.6.2/spaMM/MD5 | 183 - spaMM-1.6.2/spaMM/NAMESPACE | 14 spaMM-1.6.2/spaMM/R/Beta.R | 2 spaMM-1.6.2/spaMM/R/HLCor.R | 138 spaMM-1.6.2/spaMM/R/HLFactorList.R | 15 spaMM-1.6.2/spaMM/R/HLfit.R | 1994 ++--------- spaMM-1.6.2/spaMM/R/HLfit_Internals.R |only spaMM-1.6.2/spaMM/R/HLframes.R | 75 spaMM-1.6.2/spaMM/R/LR.R | 8 spaMM-1.6.2/spaMM/R/LevenbergMstep.R | 46 spaMM-1.6.2/spaMM/R/MakeCovEst.R | 158 spaMM-1.6.2/spaMM/R/SEMbetalambda.R |only spaMM-1.6.2/spaMM/R/auglinmodfit.R | 328 + spaMM-1.6.2/spaMM/R/calc.p_v.R | 16 spaMM-1.6.2/spaMM/R/confint.R | 85 spaMM-1.6.2/spaMM/R/corMatern.R | 8 spaMM-1.6.2/spaMM/R/corrHLfit.R | 404 -- spaMM-1.6.2/spaMM/R/corrMM.LRT.R | 14 spaMM-1.6.2/spaMM/R/correlationFns.R | 123 spaMM-1.6.2/spaMM/R/extractors.R | 90 spaMM-1.6.2/spaMM/R/is.diagonal.R | 7 spaMM-1.6.2/spaMM/R/iterateSmooth.R |only spaMM-1.6.2/spaMM/R/locoptim.R | 15 spaMM-1.6.2/spaMM/R/locoptimthroughsmooth.R | 162 spaMM-1.6.2/spaMM/R/mapMM.R | 97 spaMM-1.6.2/spaMM/R/migraineLike.R | 16 spaMM-1.6.2/spaMM/R/plot.HLfit.R | 6 spaMM-1.6.2/spaMM/R/predict.R | 400 +- spaMM-1.6.2/spaMM/R/predictor.R | 6 spaMM-1.6.2/spaMM/R/preprocess.R | 224 - spaMM-1.6.2/spaMM/R/profile.R | 9 spaMM-1.6.2/spaMM/R/separator.R | 254 - spaMM-1.6.2/spaMM/R/simulate.HL.R | 55 spaMM-1.6.2/spaMM/R/spaMM.data.R | 5 spaMM-1.6.2/spaMM/R/summary.HL.R | 105 spaMM-1.6.2/spaMM/R/update.HL.R | 3 spaMM-1.6.2/spaMM/R/utils.R | 14 spaMM-1.6.2/spaMM/data/Loaloa.RData |binary spaMM-1.6.2/spaMM/data/arabidopsis.RData |binary spaMM-1.6.2/spaMM/data/blackcap.RData |binary spaMM-1.6.2/spaMM/data/landMask.RData |binary spaMM-1.6.2/spaMM/data/oceanmask.RData |only spaMM-1.6.2/spaMM/data/salamander.RData |binary spaMM-1.6.2/spaMM/data/scotlip.RData |binary spaMM-1.6.2/spaMM/data/seaMask.RData |binary spaMM-1.6.2/spaMM/data/seeds.RData |binary spaMM-1.6.2/spaMM/data/wafers.RData |binary spaMM-1.6.2/spaMM/data/welding.RData |binary spaMM-1.6.2/spaMM/data/worldcountries.RData |only spaMM-1.6.2/spaMM/inst/NEWS.Rd | 39 spaMM-1.6.2/spaMM/man/GHK_oneside.Rd |only spaMM-1.6.2/spaMM/man/HLCor.Rd | 33 spaMM-1.6.2/spaMM/man/HLfit.Rd | 22 spaMM-1.6.2/spaMM/man/Loaloa.Rd | 6 spaMM-1.6.2/spaMM/man/Matern.corr.Rd | 9 spaMM-1.6.2/spaMM/man/arabidopsis.Rd | 8 spaMM-1.6.2/spaMM/man/autoregressive.Rd |only spaMM-1.6.2/spaMM/man/confint.Rd | 2 spaMM-1.6.2/spaMM/man/corMatern.Rd | 5 spaMM-1.6.2/spaMM/man/corrHLfit.Rd | 14 spaMM-1.6.2/spaMM/man/designL.from.Corr.Rd | 14 spaMM-1.6.2/spaMM/man/extractors.Rd | 14 spaMM-1.6.2/spaMM/man/make.scaled.dist.Rd | 10 spaMM-1.6.2/spaMM/man/mapMM.Rd | 14 spaMM-1.6.2/spaMM/man/options.Rd | 7 spaMM-1.6.2/spaMM/man/plot.HL.Rd | 8 spaMM-1.6.2/spaMM/man/predict.Rd | 77 spaMM-1.6.2/spaMM/man/raster.Rd |only spaMM-1.6.2/spaMM/man/seaMask.Rd | 23 spaMM-1.6.2/spaMM/man/seeds.Rd | 1 spaMM-1.6.2/spaMM/man/spaMM-internal.Rd | 49 spaMM-1.6.2/spaMM/man/spaMM.Rd | 29 spaMM-1.6.2/spaMM/man/spaMM.filled.contour.Rd | 3 spaMM-1.6.2/spaMM/man/update.Rd | 3 spaMM-1.6.2/spaMM/src/RcppExports.cpp | 264 - spaMM-1.6.2/spaMM/src/corMatern.cpp | 57 spaMM-1.6.2/spaMM/src/ghk.cpp |only spaMM-1.6.2/spaMM/src/gsl_bessel.cpp | 27 spaMM-1.6.2/spaMM/src/gsl_bessel.h | 26 spaMM-1.6.2/spaMM/src/spaMM_linear.cpp | 2 spaMM-1.6.2/spaMM/tests/testthat/test-CAR.R |only spaMM-1.6.2/spaMM/tests/testthat/test-HLCor.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-HLfit.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-Nugget.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-confint.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-corMatern.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-filled.mapMM.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-fixedLRT.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-inverse.Gamma.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-predVar.R |only spaMM-1.6.2/spaMM/tests/testthat/test-random-slope.R | 3 spaMM-1.6.2/spaMM/tests/testthat/test-salamander.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-sp-nsp.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-spaMM.R | 2 spaMM-1.6.2/spaMM/tests/testthat/test-spaMM.filled.contour.R | 2 100 files changed, 2709 insertions(+), 3186 deletions(-)
Title: Portfolio Risk Analysis
Description: Risk Attribution of a portfolio with Volatility Risk Analysis.
Author: Sourish Das [aut, cre],
Tamal Kanti Panja [aut]
Maintainer: Sourish Das <sourish.das@gmail.com>
Diff between PortRisk versions 1.0 dated 2014-06-07 and 1.1.0 dated 2015-11-01
DESCRIPTION | 20 +++- MD5 | 16 ++- NAMESPACE | 3 R/cctr.Bayes.R |only R/mctr.Bayes.R |only R/portvol.Bayes.R |only R/risk.attrib.Copula.R |only man/PortRisk-package.Rd | 11 +- man/portvol.Bayes.Rd |only man/portvol.Rd | 194 +++++++++++++++++++++++----------------------- man/risk.attrib.Copula.Rd |only man/risk.attribution.Rd | 168 +++++++++++++++++++-------------------- 12 files changed, 213 insertions(+), 199 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms quickly using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable
matching for two-sided markets, such as the stable marriage
problem and the college-admissions problem. Implements Irving's
Algorithm for the stable roommate problem. Implements the top
trading cycle algorithm for the indivisible goods trading problem.
Author: Jan Tilly, Nick Janetos
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.2 dated 2015-10-28 and 1.2.1 dated 2015-11-01
DESCRIPTION | 18 ++-- MD5 | 26 +++---- NEWS.md | 6 + R/galeshapley.R | 132 ++++++++++++++++++------------------ R/matchingR.R | 13 +-- README.md | 10 +- build/vignette.rds |binary inst/doc/matchingR-intro.Rmd | 6 - inst/doc/matchingR-intro.html | 57 +++++++++------ inst/doc/matchingR-performance.Rmd | 4 - inst/doc/matchingR-performance.html | 108 +++++++++++++++-------------- man/matchingR-package.Rd | 3 vignettes/matchingR-intro.Rmd | 6 - vignettes/matchingR-performance.Rmd | 4 - 14 files changed, 209 insertions(+), 184 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 2.0 dated 2015-08-26 and 2.1 dated 2015-11-01
DLMtool-2.0/DLMtool/inst/Canary_Rockfish.csv |only DLMtool-2.0/DLMtool/inst/Simulation_2.csv |only DLMtool-2.1/DLMtool/DESCRIPTION | 8 DLMtool-2.1/DLMtool/MD5 | 67 - DLMtool-2.1/DLMtool/NAMESPACE | 20 DLMtool-2.1/DLMtool/R/DLM_output.R | 279 ++++-- DLMtool-2.1/DLMtool/R/MSE_source.R | 778 ++++++++++++------ DLMtool-2.1/DLMtool/R/Source.r | 212 ++++ DLMtool-2.1/DLMtool/data/DLMdat.RData |binary DLMtool-2.1/DLMtool/inst/Atlantic_mackerel.csv | 6 DLMtool-2.1/DLMtool/inst/China_rockfish.csv | 6 DLMtool-2.1/DLMtool/inst/Cobia.csv | 6 DLMtool-2.1/DLMtool/inst/Example_datafile.csv | 6 DLMtool-2.1/DLMtool/inst/Gulf_blue_tilefish.csv | 6 DLMtool-2.1/DLMtool/inst/Red_snapper.csv | 6 DLMtool-2.1/DLMtool/inst/Simulation_1.csv | 6 DLMtool-2.1/DLMtool/inst/doc/DLMtool.R | 84 - DLMtool-2.1/DLMtool/inst/doc/DLMtool.Rnw | 175 ++-- DLMtool-2.1/DLMtool/inst/doc/DLMtool.pdf |binary DLMtool-2.1/DLMtool/inst/ourReefFish.csv | 6 DLMtool-2.1/DLMtool/man/CSRA.Rd |only DLMtool-2.1/DLMtool/man/CSRAfunc.Rd |only DLMtool-2.1/DLMtool/man/CheckConverg.Rd |only DLMtool-2.1/DLMtool/man/DLM_data-class.Rd | 6 DLMtool-2.1/DLMtool/man/DLM_fease-class.Rd |only DLMtool-2.1/DLMtool/man/DLM_general-class.Rd |only DLMtool-2.1/DLMtool/man/DLMtool-package.Rd | 4 DLMtool-2.1/DLMtool/man/EDCAC.Rd |only DLMtool-2.1/DLMtool/man/Fease.Rd |only DLMtool-2.1/DLMtool/man/Fleet-class.Rd | 6 DLMtool-2.1/DLMtool/man/Fratio_CC.Rd | 5 DLMtool-2.1/DLMtool/man/OM-class.Rd | 13 DLMtool-2.1/DLMtool/man/Observation-class.Rd | 3 DLMtool-2.1/DLMtool/man/Stock-class.Rd | 4 DLMtool-2.1/DLMtool/man/Tplot2.Rd |only DLMtool-2.1/DLMtool/man/getAFC.Rd |only DLMtool-2.1/DLMtool/man/initialize-methods.Rd | 10 DLMtool-2.1/DLMtool/man/runMSE.Rd | 5 DLMtool-2.1/DLMtool/vignettes/DLMtool-concordance.tex | 16 DLMtool-2.1/DLMtool/vignettes/DLMtool.Rnw | 175 ++-- 40 files changed, 1295 insertions(+), 623 deletions(-)
Title: Import Multiple File Types
Description: Functions to import multiple files of multiple data file types ('.xlsx', '.xls', '.csv', '.txt')
from a given directory into R data frames.
Author: Srivenkatesh Gandhi<srivenkateshg@sase.ssn.edu.in>,
Kreshnaa Raam S Bethusamy <kreshnaaraamsb@sase.ssn.edu.in>
Maintainer: Srivenkatesh Gandhi <srivenkateshg@sase.ssn.edu.in>
Diff between DataLoader versions 1.2 dated 2015-10-15 and 1.3 dated 2015-11-01
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NAMESPACE | 1 + R/DataLoader.R | 40 ++++++++++++++++++++++++++++++++++++++++ man/importCsv2.Rd |only 5 files changed, 48 insertions(+), 6 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.8-0 dated 2015-10-31 and 0.8-1 dated 2015-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS.Rd | 8 ++++++++ src/svds.cpp | 4 +++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Import/Export Routines for MALDIquant
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from MALDIquant objects.
Author: Sebastian Gibb [aut, cre],
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.9 dated 2014-08-11 and 0.10 dated 2015-10-31
MALDIquantForeign-0.10/MALDIquantForeign/DESCRIPTION | 27 - MALDIquantForeign-0.10/MALDIquantForeign/MD5 | 174 ++++----- MALDIquantForeign-0.10/MALDIquantForeign/NAMESPACE | 16 MALDIquantForeign-0.10/MALDIquantForeign/NEWS | 41 ++ MALDIquantForeign-0.10/MALDIquantForeign/R/AllGenerics.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/MALDIquantForeign-parallel.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/analyze-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/base64encode-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/compression-functions.R | 39 -- MALDIquantForeign-0.10/MALDIquantForeign/R/createMassObject-functions.R | 38 +- MALDIquantForeign-0.10/MALDIquantForeign/R/download-function.R | 20 - MALDIquantForeign-0.10/MALDIquantForeign/R/export-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/export-methods.R | 111 +++++ MALDIquantForeign-0.10/MALDIquantForeign/R/exportImzMl-methods.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/exportMsd-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/exportMzMl-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/exportTab-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/fileFormats.R | 26 - MALDIquantForeign-0.10/MALDIquantForeign/R/filename-functions.R | 34 - MALDIquantForeign-0.10/MALDIquantForeign/R/filename-methods.R | 5 MALDIquantForeign-0.10/MALDIquantForeign/R/ibd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/import-functions.R | 77 +++- MALDIquantForeign-0.10/MALDIquantForeign/R/importAnalyze-functions.R | 16 MALDIquantForeign-0.10/MALDIquantForeign/R/importAuto-functions.R | 14 MALDIquantForeign-0.10/MALDIquantForeign/R/importBrukerFlex-functions.R | 9 MALDIquantForeign-0.10/MALDIquantForeign/R/importCdf-functions.R | 9 MALDIquantForeign-0.10/MALDIquantForeign/R/importCiphergenXml-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/importImzMl-functions.R | 121 +++--- MALDIquantForeign-0.10/MALDIquantForeign/R/importMsd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/importMzMl-functions.R | 18 MALDIquantForeign-0.10/MALDIquantForeign/R/importMzXml-functions.R | 18 MALDIquantForeign-0.10/MALDIquantForeign/R/importTab-functions.R | 25 - MALDIquantForeign-0.10/MALDIquantForeign/R/imzMl-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/list.files-functions.R | 7 MALDIquantForeign-0.10/MALDIquantForeign/R/msd-functions.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/msg-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/mzMl-functions.R | 189 +++++++++- MALDIquantForeign-0.10/MALDIquantForeign/R/package.R | 7 MALDIquantForeign-0.10/MALDIquantForeign/R/parseCiphergenXml.R | 5 MALDIquantForeign-0.10/MALDIquantForeign/R/parseMsd.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/parseMzMl.R | 38 -- MALDIquantForeign-0.10/MALDIquantForeign/R/sanitize-functions.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/testChecksum-functions.R | 14 MALDIquantForeign-0.10/MALDIquantForeign/R/uuid-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/build/vignette.rds |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/doc/MALDIquantForeign-intro.pdf |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/compressed/csv1.csv.gz |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny1.msd |only MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_continuous.ibd |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_continuous.imzML | 4 MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_processed.ibd |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_processed.imzML | 4 MALDIquantForeign-0.10/MALDIquantForeign/man/MALDIquantForeign-package.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/MALDIquantForeign-parallel.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/base64-encode.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/export-methods.Rd | 12 MALDIquantForeign-0.10/MALDIquantForeign/man/exportImzMl-methods.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/exportMsd-methods.Rd | 13 MALDIquantForeign-0.10/MALDIquantForeign/man/exportMzMl-methods.Rd | 25 - MALDIquantForeign-0.10/MALDIquantForeign/man/exportTab-methods.Rd | 11 MALDIquantForeign-0.10/MALDIquantForeign/man/import-functions.Rd | 13 MALDIquantForeign-0.10/MALDIquantForeign/man/importAnalyze-functions.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/importBrukerFlex-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importCdf-functions.Rd | 7 MALDIquantForeign-0.10/MALDIquantForeign/man/importCiphergenXml-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importImzMl-functions.Rd | 17 MALDIquantForeign-0.10/MALDIquantForeign/man/importMsd-functions.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/importMzMl-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importMzXml-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importTab-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/supportedFileFormats-functions.Rd | 6 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_compression-functions.R | 10 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_createMassObject-functions.R | 27 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_download-functions.R | 36 + MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportImzMl-methods.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportMsd-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportMzMl-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportTab-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_fileFormats.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_filename-functions.R | 20 + MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_ibd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importBrukerFlex-functions.R | 11 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importCdf-functions.R | 12 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importCiphergenXml-functions.R | 10 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importImzMl-functions.R | 44 +- MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMsd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMzMl-functions.R | 28 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMzXml-functions.R | 28 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importTab-functions.R | 26 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_list.files-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_msg-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_sanitize-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_testChecksum-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_uuid-functions.R |only MALDIquantForeign-0.9/MALDIquantForeign/man/cleanFilename.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/composeFilename-methods.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/createMassObject.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/fileExtension.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/mzMlHandlers.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/parseCiphergenXml.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/parseMzMl.Rd |only 101 files changed, 995 insertions(+), 561 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
Title: Client for the Captricity API
Description: Get text from images of text using Captricity Optical Character
Recognition (OCR) API. Captricity allows you to get text from handwritten
forms --- think surveys --- and other structured paper documents. And it can
output data in form a delimited file keeping field information intact. For more
information, read https://shreddr.captricity.com/developer/overview/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between captr versions 0.1 dated 2015-10-04 and 0.1.2 dated 2015-10-31
DESCRIPTION | 22 +++++++++++++--------- LICENSE |only MD5 | 40 ++++++++++++++++++++++++---------------- NAMESPACE | 2 +- NEWS |only R/set_batch_template.R | 2 +- README.md |only build |only inst/doc |only man/batch_price.Rd | 2 +- man/captr-package.Rd | 6 +++--- man/create_batch.Rd | 2 +- man/get_all.Rd | 2 +- man/get_instance_set.Rd | 2 +- man/get_template_id.Rd | 4 ++-- man/list_instance_sets.Rd | 4 ++-- man/set_batch_template.Rd | 6 +++--- man/set_token.Rd | 4 ++-- man/submit_batch.Rd | 2 +- man/test_readiness.Rd | 2 +- man/track_progress.Rd | 2 +- man/upload_image.Rd | 2 +- vignettes |only 23 files changed, 59 insertions(+), 47 deletions(-)
Title: Ternary Search Tree for Auto-Completion and Spell Checking
Description: A ternary search tree is a type of prefix tree with up to three children and the ability for incremental string search. The package uses this ability for word auto-completion and spell checking. Includes a dataset with the 10001 most frequent English words.
Author: Ricardo Merino [aut, cre],
Samantha Fernandez [ctb]
Maintainer: Ricardo Merino <ricardo.merino.raldua@gmail.com>
Diff between TSTr versions 1.1 dated 2015-10-07 and 1.2 dated 2015-10-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/TSTr.pdf |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.100.0.0 dated 2015-10-04 and 0.6.200.2.0 dated 2015-10-31
RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/arpack_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/arpack_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/atlas_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/atlas_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/blas_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/blas_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_norm_sparse.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/lapack_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/lapack_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/superlu_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/superlu_wrapper.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/ChangeLog | 23 RcppArmadillo-0.6.200.2.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/MD5 | 889 +-- RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/NEWS.Rd | 21 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo | 34 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/BaseCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/BaseCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Base_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Base_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 28 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Gen_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Gen_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Glue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Glue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 28 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/OpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/OpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Op_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Op_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Proxy.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/ProxyCube.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeMat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeMat_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_bones.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 36 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpProxy.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_bones.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/access.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_boost.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_cmath.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng_cxx11.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng_cxx98.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_static_check.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 79 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 2402 ++++------ RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup_post.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/cond_rel_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/cond_rel_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 27 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp.cmake |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/constants.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/constants_compat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 80 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_arpack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_atlas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_blas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_hdf5.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_lapack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_superlu.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagmat_proxy.hpp | 120 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagview_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagview_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diskio_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/distr_param.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eglue_core_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eglue_core_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fft_engine.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/field_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 24 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_all.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_any.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_chol.hpp | 35 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_clamp.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cond.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cor.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cov.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cross.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cumprod.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cumsum.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_det.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diagmat.hpp | 42 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diagvec.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diff.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_dot.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_gen.hpp | 298 - RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_pair.hpp | 221 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_sym.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eigs_gen.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eigs_sym.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eps.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_expmat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eye.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft2.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_find.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_find_unique.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_flip.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_hist.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_histc.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_strans.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_trans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_interp1.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_join.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_kron.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_log_det.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_lu.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_max.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_mean.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_median.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_min.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_misc.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_n_unique.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_nonzeros.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_norm.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_normalise.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_numel.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_ones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_pinv.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_princomp.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_prod.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_qr.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_qz.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randg.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randi.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randn.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randu.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_rank.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_repmat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_reshape.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_resize.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_schur.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_shuffle.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_size.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_solve.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sort.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sort_index.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_speye.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_spones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandn.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandu.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_spsolve.hpp | 19 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_stddev.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_strans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sum.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_svd.hpp | 20 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_svds.hpp | 35 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_syl_lyap.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_symmat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_toeplitz.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp | 102 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trig.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trimat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trunc_exp.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trunc_log.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_unique.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_var.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_vectorise.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_zeros.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cor_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cor_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cov_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cov_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cross_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cross_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_hist_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_hist_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_histc_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_histc_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_join_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_join_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_kron_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_kron_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_relational_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_relational_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp | 79 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_toeplitz_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_toeplitz_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_meat.hpp | 27 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_misc_bones.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_misc_meat.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_misc.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_atlas.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_hdf5.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_superlu.hpp | 20 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/injector_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/injector_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm_mixed.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_herk.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_syrk.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_all_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_all_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_any_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_any_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_chol_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_chol_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cor_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cor_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cov_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cov_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumprod_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumprod_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumsum_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumsum_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cx_scalar_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cx_scalar_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagmat_bones.hpp | 19 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagmat_meat.hpp | 134 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagvec_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagvec_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diff_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diff_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dotext_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dotext_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_expmat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_expmat_meat.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_fft_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_fft_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_unique_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_unique_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_flip_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_flip_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_hist_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_hist_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_max_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_max_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_median_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_median_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_min_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_min_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_misc_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_misc_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_normalise_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_normalise_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_princomp_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_princomp_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_prod_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_prod_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_relational_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_relational_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_repmat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_repmat_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_reshape_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_reshape_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_resize_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_resize_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_shuffle_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_shuffle_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_index_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_index_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_stddev_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_stddev_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_toeplitz_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_toeplitz_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_unique_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_unique_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_var_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_var_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_vectorise_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_vectorise_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_div.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_minus.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_plus.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_relational.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_schur.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_times.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_minus.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_ostream.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_plus.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_relational.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_schur.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/podarray_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/podarray_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/promote_type.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/restrictors.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_vec_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_vec_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 59 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/span.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_bones.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_meat.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_mean_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_mean_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_bones.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp | 107 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_var_bones.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_var_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/strip.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_elem.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_elem_check.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_mat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_mat_fixed.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap_cube.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap_spmat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/upgrade_val.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wall_clock_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wall_clock_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_arpack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_atlas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_blas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_lapack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_superlu.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xtrans_mat_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xtrans_mat_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_meat.hpp | 5 459 files changed, 4144 insertions(+), 3685 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.5 dated 2015-07-27 and 0.6 dated 2015-10-31
mongolite-0.5/mongolite/src/Makevars |only mongolite-0.5/mongolite/src/bson/bson-version.c |only mongolite-0.6/mongolite/DESCRIPTION | 6 mongolite-0.6/mongolite/MD5 | 260 mongolite-0.6/mongolite/NAMESPACE | 1 mongolite-0.6/mongolite/NEWS | 6 mongolite-0.6/mongolite/R/iter.R | 2 mongolite-0.6/mongolite/R/mongo.R | 12 mongolite-0.6/mongolite/R/object.R | 12 mongolite-0.6/mongolite/build/vignette.rds |binary mongolite-0.6/mongolite/configure | 115 mongolite-0.6/mongolite/inst/CITATION | 2 mongolite-0.6/mongolite/inst/doc/intro.html | 4 mongolite-0.6/mongolite/src/Makevars.in |only mongolite-0.6/mongolite/src/Makevars.win | 4 mongolite-0.6/mongolite/src/bson/bcon.c | 6 mongolite-0.6/mongolite/src/bson/bson-compat.h | 10 mongolite-0.6/mongolite/src/bson/bson-config.h | 2 mongolite-0.6/mongolite/src/bson/bson-endian.h | 1 mongolite-0.6/mongolite/src/bson/bson-iter.c | 113 mongolite-0.6/mongolite/src/bson/bson-json.c | 30 mongolite-0.6/mongolite/src/bson/bson-macros.h | 81 mongolite-0.6/mongolite/src/bson/bson-memory.c | 20 mongolite-0.6/mongolite/src/bson/bson-memory.h | 1 mongolite-0.6/mongolite/src/bson/bson-oid.c | 36 mongolite-0.6/mongolite/src/bson/bson-reader.c | 36 mongolite-0.6/mongolite/src/bson/bson-stdint.h | 2 mongolite-0.6/mongolite/src/bson/bson-string.c | 16 mongolite-0.6/mongolite/src/bson/bson-thread-private.h | 2 mongolite-0.6/mongolite/src/bson/bson-types.h | 4 mongolite-0.6/mongolite/src/bson/bson-utf8.c | 12 mongolite-0.6/mongolite/src/bson/bson-value.c | 4 mongolite-0.6/mongolite/src/bson/bson-version-functions.c |only mongolite-0.6/mongolite/src/bson/bson-version-functions.h |only mongolite-0.6/mongolite/src/bson/bson-version.h | 33 mongolite-0.6/mongolite/src/bson/bson-writer.c | 12 mongolite-0.6/mongolite/src/bson/bson.c | 235 mongolite-0.6/mongolite/src/bson/bson.h | 1 mongolite-0.6/mongolite/src/client.c | 4 mongolite-0.6/mongolite/src/collection.c | 10 mongolite-0.6/mongolite/src/cursor.c | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-array-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-array.c | 42 mongolite-0.6/mongolite/src/mongoc/mongoc-async-cmd-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-async-cmd.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-async-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-async.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-buffer-private.h | 7 mongolite-0.6/mongolite/src/mongoc/mongoc-buffer.c | 86 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation-private.h | 32 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation.c | 140 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation.h | 7 mongolite-0.6/mongolite/src/mongoc/mongoc-client-pool.c | 100 mongolite-0.6/mongolite/src/mongoc/mongoc-client-pool.h | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-client-private.h | 74 mongolite-0.6/mongolite/src/mongoc/mongoc-client.c | 594 - mongolite-0.6/mongolite/src/mongoc/mongoc-client.h | 18 mongolite-0.6/mongolite/src/mongoc/mongoc-cluster-private.h | 188 mongolite-0.6/mongolite/src/mongoc/mongoc-cluster.c | 3074 +++------- mongolite-0.6/mongolite/src/mongoc/mongoc-collection.c | 352 - mongolite-0.6/mongolite/src/mongoc/mongoc-config.h | 13 mongolite-0.6/mongolite/src/mongoc/mongoc-counters-private.h | 1 mongolite-0.6/mongolite/src/mongoc/mongoc-counters.c | 12 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-array.c | 16 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-cursorid-private.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-cursorid.c | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-private.h | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-transform.c | 8 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor.c | 386 - mongolite-0.6/mongolite/src/mongoc/mongoc-database.c | 47 mongolite-0.6/mongolite/src/mongoc/mongoc-error.h | 6 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-list.c | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-page-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-page.c | 64 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-private.h | 1 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file.c | 237 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file.h | 68 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs.c | 17 mongolite-0.6/mongolite/src/mongoc/mongoc-host-list.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-host-list.h | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-index.c | 41 mongolite-0.6/mongolite/src/mongoc/mongoc-index.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-init.c | 10 mongolite-0.6/mongolite/src/mongoc/mongoc-iovec.h | 10 mongolite-0.6/mongolite/src/mongoc/mongoc-list.c | 12 mongolite-0.6/mongolite/src/mongoc/mongoc-log-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-log.c | 163 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher-op-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher-op.c | 45 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher.c | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-memcmp-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-memcmp.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-opcode-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-opcode.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-queue.c | 18 mongolite-0.6/mongolite/src/mongoc/mongoc-read-prefs-private.h | 21 mongolite-0.6/mongolite/src/mongoc/mongoc-read-prefs.c | 359 - mongolite-0.6/mongolite/src/mongoc/mongoc-rpc-private.h | 30 mongolite-0.6/mongolite/src/mongoc/mongoc-rpc.c | 229 mongolite-0.6/mongolite/src/mongoc/mongoc-sasl-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-sasl.c | 32 mongolite-0.6/mongolite/src/mongoc/mongoc-scram.c | 19 mongolite-0.6/mongolite/src/mongoc/mongoc-server-description-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-description.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-description.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-stream-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-stream.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-set-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-set.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-socket-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-socket.c | 378 - mongolite-0.6/mongolite/src/mongoc/mongoc-socket.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-ssl.c | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-buffered.c | 44 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-file.c | 24 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-gridfs.c | 14 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-private.h | 11 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-socket.c | 74 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-tls.c | 162 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-tls.h | 3 mongolite-0.6/mongolite/src/mongoc/mongoc-stream.c | 253 mongolite-0.6/mongolite/src/mongoc/mongoc-stream.h | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-thread-private.h | 41 mongolite-0.6/mongolite/src/mongoc/mongoc-topology-description-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-description.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-scanner-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-scanner.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-trace.h | 105 mongolite-0.6/mongolite/src/mongoc/mongoc-uri-private.h | 58 mongolite-0.6/mongolite/src/mongoc/mongoc-uri.c | 655 +- mongolite-0.6/mongolite/src/mongoc/mongoc-uri.h | 6 mongolite-0.6/mongolite/src/mongoc/mongoc-util-private.h | 24 mongolite-0.6/mongolite/src/mongoc/mongoc-util.c | 21 mongolite-0.6/mongolite/src/mongoc/mongoc-version-functions.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-version-functions.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-version.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-write-command-private.h | 49 mongolite-0.6/mongolite/src/mongoc/mongoc-write-command.c | 969 +-- mongolite-0.6/mongolite/src/mongoc/mongoc-write-concern.c | 57 mongolite-0.6/mongolite/src/mongoc/mongoc-write-concern.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc.h | 1 mongolite-0.6/mongolite/src/mongoc/utlist.h |only mongolite-0.6/mongolite/src/tests/has_sasl_client_done.c | 3 mongolite-0.6/mongolite/src/win32/ipv6.c | 7 mongolite-0.6/mongolite/tools/winlibs.R | 2 147 files changed, 5825 insertions(+), 4932 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' package.
It also implements the two-stage SEM approach to conduct meta-analytic
structural equation modeling on correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 0.9.4 dated 2015-06-08 and 0.9.6 dated 2015-10-31
DESCRIPTION | 12 - MD5 | 94 ++++---- NAMESPACE | 10 NEWS | 27 ++ R/asyCov.R | 26 ++ R/hidden.R | 90 +------- R/meta2semPlot.R | 2 R/plot.meta.R | 6 R/summary.R | 64 ++++- R/tssem.R | 526 +++++++++++++++++++++++++------------------------ R/zzz.R | 6 data/Aloe14.rda |binary data/BCG.rda |binary data/Becker09.rda |binary data/Becker83.rda |binary data/Becker92.rda |binary data/Becker94.rda |binary data/Berkey98.rda |binary data/Bornmann07.rda |binary data/Cheung00.rda |binary data/Cheung09.rda |binary data/Cooper03.rda |binary data/Digman97.rda |binary data/HedgesOlkin85.rda |binary data/Hox02.rda |binary data/Hunter83.rda |binary data/Jaramillo05.rda |binary data/Mak09.rda |binary data/Norton13.rda |only data/Roorda11.rda |only data/issp05.rda |binary data/issp89.rda |binary data/wvs94a.rda |binary data/wvs94b.rda |binary inst/doc/metaSEM.pdf |binary man/Becker92.Rd | 2 man/Cheung00.Rd | 4 man/Hunter83.Rd | 4 man/Norton13.Rd |only man/Roorda11.Rd |only man/anova.Rd | 8 man/asyCov.Rd | 10 man/issp05.Rd | 1 man/metaSEM-package.Rd | 21 + man/plot.meta.Rd | 2 man/readData.Rd | 3 man/rerun.Rd | 9 man/tssem1.Rd | 40 ++- man/wls.Rd | 6 man/wvs94b.Rd | 4 50 files changed, 537 insertions(+), 440 deletions(-)
Title: Exact Test from the Combinations of Mutually Exclusive
Alterations (CoMEt) Algorithm
Description: An algorithm for identifying combinations of mutually exclusive alterations in cancer genomes. CoMEt represents the mutations in a set M of k genes with a 2^k dimensional contingency table, and then computes the tail probability of observing T(M) exclusive alterations using an exact statistical test.
Author: Max Leiserson [aut, cre],
Hsin-Ta Wu [aut],
Fabio Vandin [ctb],
Vivian Hsiao [ctb],
Benjamin Raphael [ctb]
Maintainer: Max Leiserson <mdml@cs.brown.edu>
Diff between cometExactTest versions 0.1.2 dated 2015-06-24 and 0.1.3 dated 2015-10-31
DESCRIPTION | 9 +-- MD5 | 10 ++- NAMESPACE | 6 +- R/cometexacttest.R | 146 +++++++++++++++++++++++++++++++++++++++++++++++++++-- man/comet.Rd | 20 ++++++- man/figures |only 6 files changed, 176 insertions(+), 15 deletions(-)
More information about cometExactTest at CRAN
Permanent link
Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.1.0 dated 2015-07-30 and 1.1.2 dated 2015-10-31
dendextend-1.1.0/dendextend/inst/doc/dendextend-tutorial.pdf |only dendextend-1.1.2/dendextend/ChangeLog | 71 ++ dendextend-1.1.2/dendextend/DESCRIPTION | 12 dendextend-1.1.2/dendextend/MD5 | 53 - dendextend-1.1.2/dendextend/NAMESPACE | 2 dendextend-1.1.2/dendextend/NEWS | 17 dendextend-1.1.2/dendextend/R/ggdend.R | 16 dendextend-1.1.2/dendextend/R/labels.R | 129 +--- dendextend-1.1.2/dendextend/R/prune.R | 5 dendextend-1.1.2/dendextend/R/rect.dendrogram.R | 28 - dendextend-1.1.2/dendextend/R/zzz.R | 2 dendextend-1.1.2/dendextend/README.md | 2 dendextend-1.1.2/dendextend/build/vignette.rds |binary dendextend-1.1.2/dendextend/inst/CITATION | 4 dendextend-1.1.2/dendextend/inst/doc/Cluster_Analysis.R | 44 - dendextend-1.1.2/dendextend/inst/doc/Cluster_Analysis.html | 175 +++--- dendextend-1.1.2/dendextend/inst/doc/FAQ.R | 18 dendextend-1.1.2/dendextend/inst/doc/FAQ.html | 78 +- dendextend-1.1.2/dendextend/inst/doc/Quick_Introduction.R | 2 dendextend-1.1.2/dendextend/inst/doc/Quick_Introduction.html | 51 + dendextend-1.1.2/dendextend/inst/doc/introduction.R | 94 +-- dendextend-1.1.2/dendextend/inst/doc/introduction.html | 304 +++++------ dendextend-1.1.2/dendextend/inst/tests/test-ggdend.R | 29 + dendextend-1.1.2/dendextend/inst/tests/test-labels-assign.R | 47 - dendextend-1.1.2/dendextend/man/ggdend.Rd | 8 dendextend-1.1.2/dendextend/man/identify.dendrogram.Rd | 6 dendextend-1.1.2/dendextend/man/labels-assign.Rd | 24 dendextend-1.1.2/dendextend/man/rect.dendrogram.Rd | 7 28 files changed, 709 insertions(+), 519 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete
non-equally spaced observations on a finite time interval based on expansions
of the convolution kernel, the unknown function and the observed signal over
Laguerre functions basis. It implements the methodology proposed in the paper
"Laplace deconvolution on the basis of time domain data and its application to
Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y.
Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University
of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.2 dated 2015-10-29 and 1.0.3 dated 2015-10-31
DESCRIPTION | 18 +++++++++++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 7 +------ R/LagLaplaceDeconvolution.R | 5 +++++ data/EX_DCEMRI_t0.rda |binary data/EX_DCEMRI_t1.rda |binary man/BuildLaguerreSystem.Rd | 14 +++++++------- man/EX_DCEMRI_t0.rda-EX_DCEMRI_t1.rda.Rd | 2 +- man/LagLaplDeconv.Rd | 4 ++-- man/LaguerreLaplaceConvolution.Rd | 12 ++++++------ man/LaplaceConvolution.Rd | 10 +++++----- man/MakeLaguerreMatrix.Rd | 6 +++--- 12 files changed, 54 insertions(+), 46 deletions(-)
Title: Regression Estimation Based on the Compound Covariate Method
Under the Cox Proportional Hazard Model
Description: Calculate regression coefficients and their standard deviations under the Cox proportional hazard model with a large number of covariates. A shrinkage type estimation based on the compound covariate method (Emura, Chen & Chen, 2012 PLoS ONE) and a univariate gene selection method under dependent censoring (Emura & Chen, 2014 Statistical Methods in Medical Research) are implemented. Algorithms for simulating gene expressions in these references are also given.
Author: Takeshi Emura & Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 1.4 dated 2014-04-13 and 2.0 dated 2015-10-31
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++++------ NAMESPACE | 4 +++- R/X.pathway.R |only R/X.tag.R |only man/X.pathway.Rd |only man/X.tag.Rd |only man/cindex.CV.Rd | 35 ++++++++++++++++++++--------------- man/compound.Cox-package.Rd | 19 ++++++++++--------- man/dependCox.reg.CV.Rd | 4 ++-- man/dependCox.reg.Rd | 9 ++++++--- 11 files changed, 59 insertions(+), 44 deletions(-)
Title: Simple Network of Workstations
Description: Support for simple parallel computing in R.
Author: Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between snow versions 0.3-13 dated 2013-09-27 and 0.4-1 dated 2015-10-31
snow-0.3-13/snow/R/pvm.R |only snow-0.4-1/snow/DESCRIPTION | 12 +-- snow-0.4-1/snow/MD5 | 21 +++--- snow-0.4-1/snow/NAMESPACE | 29 +++++++++ snow-0.4-1/snow/R/mpi.R | 44 ++++++------- snow-0.4-1/snow/R/nws.R | 28 ++++---- snow-0.4-1/snow/R/snow.R | 107 ++++++++++++++++++---------------- snow-0.4-1/snow/README | 40 +++++------- snow-0.4-1/snow/inst/RMPISNOW | 2 snow-0.4-1/snow/man/snow-internal.Rd | 26 ++++---- snow-0.4-1/snow/man/snow-rand.Rd | 1 snow-0.4-1/snow/man/snow-startstop.Rd | 20 +++--- 12 files changed, 185 insertions(+), 145 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.7-0 dated 2014-11-02 and 0.8-0 dated 2015-10-31
rARPACK-0.7-0/rARPACK/AUTHORS |only rARPACK-0.7-0/rARPACK/COPYRIGHTS |only rARPACK-0.7-0/rARPACK/NEWS |only rARPACK-0.7-0/rARPACK/R/25_eigs_function.R |only rARPACK-0.7-0/rARPACK/inst/LICENSE |only rARPACK-0.7-0/rARPACK/src/ARPACK |only rARPACK-0.7-0/rARPACK/src/ARPACK.h |only rARPACK-0.7-0/rARPACK/src/Eigs.cpp |only rARPACK-0.7-0/rARPACK/src/Eigs.h |only rARPACK-0.7-0/rARPACK/src/EigsGen.cpp |only rARPACK-0.7-0/rARPACK/src/EigsGen.h |only rARPACK-0.7-0/rARPACK/src/EigsSym.cpp |only rARPACK-0.7-0/rARPACK/src/EigsSym.h |only rARPACK-0.7-0/rARPACK/src/MatOp.h |only rARPACK-0.7-0/rARPACK/src/MatOp_dgeMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_dsyMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_function.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_function.h |only rARPACK-0.7-0/rARPACK/src/MatOp_matrix.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_matrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_sparseMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.h |only rARPACK-0.7-0/rARPACK/src/MatTypes.h |only rARPACK-0.7-0/rARPACK/src/SVDsGen.cpp |only rARPACK-0.7-0/rARPACK/src/SVDsGen.h |only rARPACK-0.7-0/rARPACK/src/SVDsSym.cpp |only rARPACK-0.7-0/rARPACK/src/SVDsSym.h |only rARPACK-0.7-0/rARPACK/src/eigs_funs.cpp |only rARPACK-0.7-0/rARPACK/src/message.cpp |only rARPACK-0.7-0/rARPACK/src/rARPACK-win.def |only rARPACK-0.7-0/rARPACK/src/svds_funs.cpp |only rARPACK-0.7-0/rARPACK/src/wrapper.f |only rARPACK-0.8-0/rARPACK/DESCRIPTION | 22 +- rARPACK-0.8-0/rARPACK/LICENSE | 2 rARPACK-0.8-0/rARPACK/MD5 | 194 +++++++------------------ rARPACK-0.8-0/rARPACK/NAMESPACE | 6 rARPACK-0.8-0/rARPACK/R/00_eigs.R | 112 ++++++++++---- rARPACK-0.8-0/rARPACK/R/10_eigs_real_gen.R | 104 ++++++------- rARPACK-0.8-0/rARPACK/R/20_eigs_real_sym.R | 62 ++++--- rARPACK-0.8-0/rARPACK/R/30_svds.R | 22 +- rARPACK-0.8-0/rARPACK/R/40_svds_real_gen.R | 32 ++-- rARPACK-0.8-0/rARPACK/R/50_svds_real_sym.R | 28 ++- rARPACK-0.8-0/rARPACK/inst/AUTHORS | 22 ++ rARPACK-0.8-0/rARPACK/inst/COPYRIGHTS | 5 rARPACK-0.8-0/rARPACK/inst/NEWS.Rd |only rARPACK-0.8-0/rARPACK/inst/include |only rARPACK-0.8-0/rARPACK/man/eigs.Rd | 30 ++- rARPACK-0.8-0/rARPACK/man/svds.Rd | 7 rARPACK-0.8-0/rARPACK/src/Makevars | 13 - rARPACK-0.8-0/rARPACK/src/Makevars.win | 13 - rARPACK-0.8-0/rARPACK/src/c_interface.c |only rARPACK-0.8-0/rARPACK/src/c_interface.h |only rARPACK-0.8-0/rARPACK/src/eigs_gen.cpp |only rARPACK-0.8-0/rARPACK/src/eigs_sym.cpp |only rARPACK-0.8-0/rARPACK/src/matops.cpp |only rARPACK-0.8-0/rARPACK/src/matops.h |only rARPACK-0.8-0/rARPACK/src/svds.cpp |only 58 files changed, 341 insertions(+), 333 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-8 dated 2015-10-24 and 1.8-9 dated 2015-10-31
ChangeLog | 6 ++++++ DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- man/gamm.Rd | 18 +++++++++++++++++- man/mgcv-parallel.Rd | 10 +++++++++- man/smooth.construct.gp.smooth.spec.Rd | 6 +++--- src/discrete.c | 33 +++++++++------------------------ src/gdi.c | 2 +- src/mat.c | 2 +- 9 files changed, 57 insertions(+), 42 deletions(-)
More information about AlgebraicHaploPackage at CRAN
Permanent link
Title: GUI Tools to Process, Analyze and Plot Fisheries Data
Description: The tools you need to process, analyze, combine, integrate and
plot your fishery data: the georeferenced dataset from the Vessel Monitoring
System (VMS), from the Automatic Information System (AIS) or other tracking
devices, as well as the catches or landings dataset from the Logbook or Vessel
Register. Package 'vmsbase' is equipped by Viewer Tools to visually inspect data
at different steps of the analyses and to produce effective outputs for reports
and scientific publications. Viewers are conceived to show the VMS pings, to
visualize single or multiple tracks for fishing vessels, or to represent the VMS
data on Google Viewer, so that the user can produce easy to interpret and more
realistic visualization of both fishing effort and effort behaviour. Package
'vmsbase' represents the implementation of several R routines which have been
developed by the "Tor Vergata" University of Rome Team involved in the Italian
National Program for the Data Collection Framework for Fisheries Data between
2009-2012.
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea <support@vmsbase.org>
Diff between vmsbase versions 2.0 dated 2015-03-10 and 2.1 dated 2015-10-30
DESCRIPTION | 25 ++- MD5 | 120 +++++++++--------- NAMESPACE | 13 +- R/fun_vms_db_clean.R | 141 ++++++++++++--------- R/gui_main.R | 4 R/gui_vms_db_cut.R | 297 ++++++++++++++++++++++++++-------------------- R/gui_vms_db_dep.R | 12 - R/gui_vms_db_intr.R | 82 ++++-------- R/gui_vms_save_bat.R | 38 +++-- R/latsex2dec.R | 14 -- R/lonsex2dec.R | 14 -- R/saveRawVms.R | 40 +++--- README.md | 23 ++- man/Assign_Area.Rd | 2 man/CountMap.Rd | 2 man/Join2shp.Rd | 2 man/bathymetry.Rd | 2 man/gui_dcf_ind.Rd | 2 man/gui_join_lb_vms.Rd | 2 man/gui_lb_db_create.Rd | 4 man/gui_lb_db_edit.Rd | 4 man/gui_lb_db_stat.Rd | 2 man/gui_lb_editraw.Rd | 6 man/gui_lb_met_cla.Rd | 2 man/gui_lb_met_dis.Rd | 4 man/gui_lb_met_edi.Rd | 4 man/gui_main.Rd | 2 man/gui_mark_fis_poi.Rd | 2 man/gui_out_grid.Rd | 4 man/gui_vms_db_are.Rd | 2 man/gui_vms_db_clean.Rd | 11 - man/gui_vms_db_create.Rd | 4 man/gui_vms_db_cut.Rd | 11 - man/gui_vms_db_dep.Rd | 13 -- man/gui_vms_db_intr.Rd | 11 - man/gui_vms_db_sel.Rd | 11 - man/gui_vms_db_stat.Rd | 11 - man/gui_vms_editraw.Rd | 6 man/gui_vms_met_pred.Rd | 11 - man/gui_vms_save_bat.Rd | 11 - man/gui_vms_view_intrp.Rd | 11 - man/gui_vms_view_ping.Rd | 11 - man/gui_vms_view_track.Rd | 11 - man/gui_vms_viz_adv.Rd | 11 - man/gui_vmsdb_mixsou.Rd | 2 man/harbCoo.Rd | 2 man/kno2kmh.Rd | 2 man/latsex2dec.Rd | 2 man/log_Cla.Rd | 2 man/log_DB.Rd | 2 man/log_File.Rd | 2 man/lonsex2dec.Rd | 2 man/plotNet.Rd | 2 man/polymap.Rd | 2 man/que_vms_DB.Rd | 2 man/rad2deg.Rd | 2 man/saveRawLogBook.Rd | 2 man/saveRawVms.Rd | 2 man/vms_DB.Rd | 2 man/vms_File.Rd | 2 man/vmsbase.Rd | 6 61 files changed, 559 insertions(+), 494 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.1 dated 2015-09-18 and 0.1.2 dated 2015-10-30
DESCRIPTION | 10 MD5 | 97 NAMESPACE | 3 NEWS | 12 R/utils.R | 10 R/visClustering.R | 2 R/visConfigure.R | 3 R/visDocumentation.R | 15 R/visEdges.R | 9 R/visGroups.R | 3 R/visHierarchicalLayout.R | 3 R/visInteraction.R | 3 R/visLayout.R | 5 R/visLegend.R |only R/visNetwork.R | 63 R/visNetworkEvents.R | 3 R/visNodes.R | 8 R/visOptions.R | 77 R/visPhysics.R | 5 README.md | 2 inst/doc/Introduction-to-visNetwork.R | 34 inst/doc/Introduction-to-visNetwork.Rmd | 63 inst/doc/Introduction-to-visNetwork.html | 141 - inst/doc/css/prettify.css | 172 - inst/doc/network/index.html | 3112 +++++++++++++++---------------- inst/doc/network/layout.html | 312 +-- inst/doc/network/manipulation.html | 406 ++-- inst/doc/network/nodes.html | 1429 +++++++------- inst/doc/network/physics.html | 446 ++-- inst/examples |only inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 88 inst/htmlwidgets/visNetwork.js | 396 +++ inst/htmlwidgets/visNetwork.yaml | 2 inst/shiny/server.R | 17 man/visClusteringOutliers.Rd | 2 man/visConfigure.Rd | 3 man/visDocumentation.Rd | 4 man/visEdges.Rd | 9 man/visEvents.Rd | 3 man/visGroups.Rd | 3 man/visHierarchicalLayout.Rd | 3 man/visInteraction.Rd | 3 man/visLayout.Rd | 5 man/visLegend.Rd |only man/visNetwork.Rd | 30 man/visNodes.Rd | 8 man/visOptions.Rd | 37 man/visPhysics.Rd | 5 vignettes/Introduction-to-visNetwork.Rmd | 63 51 files changed, 3893 insertions(+), 3240 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.0.0 dated 2015-09-11 and 1.8.14 dated 2015-10-30
treescape-1.0.0/treescape/man/penEdgeTree.Rd |only treescape-1.0.0/treescape/man/penEdgeTreematch.Rd |only treescape-1.0.0/treescape/man/rcpp_hello_world.Rd |only treescape-1.0.0/treescape/src/rcpp_hello_world.cpp |only treescape-1.8.14/treescape/DESCRIPTION | 11 treescape-1.8.14/treescape/MD5 | 63 treescape-1.8.14/treescape/NAMESPACE | 5 treescape-1.8.14/treescape/R/RcppExports.R | 18 treescape-1.8.14/treescape/R/findGroves.R | 39 treescape-1.8.14/treescape/R/medTree.R | 98 treescape-1.8.14/treescape/R/metrics.R | 133 - treescape-1.8.14/treescape/R/plotGroves.R | 3 treescape-1.8.14/treescape/R/servers.R | 15 treescape-1.8.14/treescape/R/treescape.R | 68 treescape-1.8.14/treescape/README.md | 92 treescape-1.8.14/treescape/inst/shiny/server.R | 1217 +++++++--- treescape-1.8.14/treescape/inst/shiny/ui.R | 679 +++-- treescape-1.8.14/treescape/inst/shiny/www/bootstrap.simplex.css |only treescape-1.8.14/treescape/inst/shiny/www/html/help.html | 180 + treescape-1.8.14/treescape/inst/shiny/www/styles.css |only treescape-1.8.14/treescape/man/findGroves.Rd | 15 treescape-1.8.14/treescape/man/linearMrca.Rd | 10 treescape-1.8.14/treescape/man/medTree.Rd | 31 treescape-1.8.14/treescape/man/multiDist.Rd | 11 treescape-1.8.14/treescape/man/plotGroves.Rd | 4 treescape-1.8.14/treescape/man/treeDist.Rd | 16 treescape-1.8.14/treescape/man/treeVec.Rd | 12 treescape-1.8.14/treescape/man/treescape.Rd | 24 treescape-1.8.14/treescape/man/treescapeServer.Rd | 4 treescape-1.8.14/treescape/src/RcppExports.cpp | 10 treescape-1.8.14/treescape/tests/testthat/testbasics.R | 27 treescape-1.8.14/treescape/vignettes/figs/findgroves-with-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/figs/treescape3d.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeDensiTree.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeTree.png |only treescape-1.8.14/treescape/vignettes/figs/woodmice-tip-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/treescape.Rmd | 48 treescape-1.8.14/treescape/vignettes/treescape.md | 94 38 files changed, 2031 insertions(+), 896 deletions(-)
Title: Datasets for Agresti and Finlay's "Statistical Methods for the
Social Sciences"
Description: Datasets used in "Statistical Methods for the Social Sciences"
(SMSS) by Alan Agresti and Barbara Finlay.
Author: Jeffrey B. Arnold [aut, cre],
Alan Agresti [cph],
Barbara Finlay [cph]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between smss versions 1.0-1 dated 2013-08-22 and 1.0-2 dated 2015-10-30
DESCRIPTION | 15 +----- MD5 | 80 +++++++++++++++++------------------ NEWS | 7 ++- R/crime2005.R | 4 + build/partial.rdb |binary data/UNdata.rda |binary data/anorexia.rda |binary data/birth.rates.rda |binary data/crime2005.rda |binary data/fertility.gdp.rda |binary data/fl.crime.rda |binary data/house.selling.price.2.rda |binary data/house.selling.price.rda |binary data/inc.ed.race.13p1.rda |binary data/income.credit.rda |binary data/mental.impairment.rda |binary data/oecd.data.rda |binary data/statewide.crime.2.rda |binary data/student.survey.rda |binary data/us.pop.size.rda |binary data/zagat.rda |binary inst/extdata/fl-crime.csv | 10 ++-- inst/scripts/download_agresti_csv.sh | 3 - inst/scripts/save_data.R | 2 man/UNdata.Rd | 12 ++--- man/anorexia.Rd | 12 ++--- man/birth.rates.Rd | 8 +-- man/crime2005.Rd | 10 +++- man/fertility.gdp.Rd | 7 +-- man/fl.crime.Rd | 10 ++-- man/house.selling.price.2.Rd | 10 ++-- man/house.selling.price.Rd | 10 ++-- man/inc.ed.race.13p1.Rd | 10 ++-- man/income.credit.Rd | 15 ++---- man/mental.impairment.Rd | 11 ++-- man/oecd.data.Rd | 13 ++--- man/smss-package.Rd | 21 ++++----- man/statewide.crime.2.Rd | 10 +--- man/student.survey.Rd | 9 +-- man/us.pop.size.Rd | 8 ++- man/zagat.Rd | 9 ++- 41 files changed, 154 insertions(+), 152 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that can be indexed similarly to lists, e.g. 'x <- listenv(); x[[2]] <- "b"; names(x)[2] <- "B"; print(x$B)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.4.0 dated 2015-08-08 and 0.5.0 dated 2015-10-30
listenv-0.4.0/listenv/.Rinstignore |only listenv-0.5.0/listenv/DESCRIPTION | 8 listenv-0.5.0/listenv/MD5 | 26 +-- listenv-0.5.0/listenv/NAMESPACE | 6 listenv-0.5.0/listenv/NEWS | 12 + listenv-0.5.0/listenv/R/get_variable.R | 4 listenv-0.5.0/listenv/R/listenv.R | 225 +++++++++++++++++++++------ listenv-0.5.0/listenv/R/utils.R | 30 --- listenv-0.5.0/listenv/build |only listenv-0.5.0/listenv/inst |only listenv-0.5.0/listenv/man/as.list.listenv.Rd | 8 listenv-0.5.0/listenv/man/listenv.Rd | 18 +- listenv-0.5.0/listenv/man/map.Rd | 42 ++--- listenv-0.5.0/listenv/tests/get_variable.R | 16 + listenv-0.5.0/listenv/tests/listenv.R | 171 ++++++++++++++++++++ listenv-0.5.0/listenv/vignettes |only 16 files changed, 439 insertions(+), 127 deletions(-)
Title: Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between kedd versions 1.0.2 dated 2015-01-28 and 1.0.3 dated 2015-10-30
DESCRIPTION | 11 +++++---- MD5 | 53 ++++++++++++++++++++++++------------------------ NAMESPACE | 4 +++ NEWS | 2 + build/vignette.rds |binary inst/doc/Thumbs.db |only inst/doc/intro.Rnw | 2 - inst/doc/intro.pdf |binary inst/doc/kedd.Rnw | 8 +++---- inst/doc/kedd.pdf |binary man/dkde.Rd | 2 - man/h.bcv.Rd | 2 - man/h.ucv.Rd | 2 - man/kedd-package.Rd | 6 ++--- man/kernel.conv.Rd | 2 - man/kernel.fun.Rd | 2 - man/plot.dkde.Rd | 4 +-- man/plot.h.amise.Rd | 2 - man/plot.h.bcv.Rd | 2 - man/plot.h.ccv.Rd | 2 - man/plot.h.mcv.Rd | 2 - man/plot.h.mlcv.Rd | 2 - man/plot.h.tcv.Rd | 2 - man/plot.h.ucv.Rd | 2 - man/plot.kernel.conv.Rd | 2 - man/plot.kernel.fun.Rd | 2 - vignettes/intro.Rnw | 2 - vignettes/kedd.Rnw | 8 +++---- 28 files changed, 68 insertions(+), 60 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are
implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.5.0 dated 2015-10-05 and 0.5.1 dated 2015-10-30
DESCRIPTION | 10 ++++--- MD5 | 42 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 8 ++++++ R/downstream.R | 10 +++---- R/gvc.R | 6 ++++ R/nrca.R | 23 ++++++++++++++++++ R/upstream.R | 10 +++---- README.md | 5 +++ inst/doc/gvc.R | 5 ++- inst/doc/gvc.Rmd | 9 +++---- inst/doc/gvc.html | 69 ++++++++++++++++++++---------------------------------- man/dfddva.Rd | 4 +-- man/dfdfva.Rd | 2 - man/downstream.Rd | 14 +++++----- man/e2r.Rd | 4 +-- man/ffddva.Rd | 2 - man/gvc.Rd | 4 +-- man/i2e.Rd | 4 +-- man/nrca.Rd | 25 ++++++++++++++++++- man/upstream.Rd | 14 +++++----- vignettes/gvc.Rmd | 9 +++---- 22 files changed, 167 insertions(+), 114 deletions(-)
Title: Dynamic Nomograms for Linear, Generalized Linear and
Proportional Hazard Models
Description: Demonstrate the results of an lm(), glm() or coxph() model object as a dynamic nomogram that can be displayed in an 'RStudio' panel or web browser.
Author: Amirhossein Jalali, Alberto Alvarez-Iglesias, Davood Roshan Sangachin, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>
Diff between DynNom versions 1.0.1 dated 2015-03-09 and 2.0 dated 2015-10-30
DynNom-1.0.1/DynNom/man/DynNom-package.Rd |only DynNom-2.0/DynNom/DESCRIPTION | 21 - DynNom-2.0/DynNom/MD5 | 15 - DynNom-2.0/DynNom/NAMESPACE | 9 DynNom-2.0/DynNom/R/DynNom.R | 393 +++++------------------------- DynNom-2.0/DynNom/R/DynNom_coxph.R |only DynNom-2.0/DynNom/R/DynNom_glm.R |only DynNom-2.0/DynNom/R/DynNom_lm.R |only DynNom-2.0/DynNom/man/DynNom.Rd | 65 +++- DynNom-2.0/DynNom/man/DynNom.coxph.Rd |only DynNom-2.0/DynNom/man/DynNom.glm.Rd |only DynNom-2.0/DynNom/man/DynNom.lm.Rd |only 12 files changed, 139 insertions(+), 364 deletions(-)
Title: CShapes Dataset and Utilities
Description: Package for CShapes, a GIS dataset of country boundaries (1946-2015). Includes functions for data extraction and the computation of distance matrices and -lists.
Author: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>, Kristian Skrede Gleditsch <ksg@essex.ac.uk>
Maintainer: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>
Diff between cshapes versions 0.4-2 dated 2013-05-07 and 0.5-1 dated 2015-10-30
cshapes-0.4-2/cshapes/inst/shp/cshapes.qpj |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbn |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbx |only cshapes-0.4-2/cshapes/inst/shp/cshapes.shp.xml |only cshapes-0.5-1/cshapes/ChangeLog | 5 + cshapes-0.5-1/cshapes/DESCRIPTION | 17 ++-- cshapes-0.5-1/cshapes/MD5 | 22 ++--- cshapes-0.5-1/cshapes/R/cshp.R | 2 cshapes-0.5-1/cshapes/R/distlist.R | 2 cshapes-0.5-1/cshapes/R/distmatrix.R | 2 cshapes-0.5-1/cshapes/inst/shp/cshapes.dbf |binary cshapes-0.5-1/cshapes/inst/shp/cshapes.shp |binary cshapes-0.5-1/cshapes/inst/shp/cshapes_shapefile_documentation.txt | 37 +++++++--- cshapes-0.5-1/cshapes/man/cshapes-package.Rd | 4 - 14 files changed, 53 insertions(+), 38 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as defined by Kalbfleisch and Prentice. The underlying survival functions of the event of interest in each group can be estimated using either the (weighted) Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition probabilities in Markov multi-state models. Right-censored and left-truncated data is supported. Moreover, the difference in restricted mean survival can be estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.2 dated 2015-07-05 and 1.3 dated 2015-10-30
AHR-1.2/AHR/TODO |only AHR-1.3/AHR/DESCRIPTION | 8 ++++---- AHR-1.3/AHR/MD5 | 11 +++++------ AHR-1.3/AHR/R/AHR-package.R | 2 +- AHR-1.3/AHR/R/ahr.R | 34 ++++++++++++++++++++-------------- AHR-1.3/AHR/R/util.R | 2 +- AHR-1.3/AHR/src/prodlim.cpp | 1 - 7 files changed, 31 insertions(+), 27 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.47 dated 2015-06-15 and 1.48 dated 2015-10-29
Changelog | 65 +++++++++ DESCRIPTION | 12 - MD5 | 46 +++--- NAMESPACE | 20 ++ R/Functions.R | 272 +++++++++++++++++++++++---------------- R/blockwiseModulesC.R | 92 +++++++++++-- R/consensusTOM.R | 5 R/empiricalBayesLM.R | 18 ++ R/internalConstants.R | 2 R/labelPoints.R | 8 - R/useNThreads.R | 2 man/WGCNA-package.Rd | 4 man/bicovWeights.Rd | 13 + man/blockSize.Rd | 2 man/blockwiseConsensusModules.Rd | 2 man/consensusKME.Rd | 3 man/consensusProjectiveKMeans.Rd | 5 man/labelPoints.Rd | 8 - man/mergeCloseModules.Rd | 2 man/moduleEigengenes.Rd | 2 man/multiSetMEs.Rd | 6 man/projectiveKMeans.Rd | 5 src/corFunctions-unified.c | 8 - src/networkFunctions.c | 2 24 files changed, 429 insertions(+), 175 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-2 dated 2015-10-01 and 0.1-3 dated 2015-10-29
DESCRIPTION | 24 +++++---- MD5 | 112 ++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++ R/ants-data.R |only R/dispersion.R |only R/download.prism.R | 22 +++++--- R/gaussian.kernel.R |only R/insert.values.R |only R/land.metrics.R | 79 +++++++++++++++++++------------ R/pu-data.R |only R/sample.line.R | 16 ++++-- R/sample.poly.R |only R/shannons.R |only R/similarity.R |only R/tri.R |only data |only inst/NEWS | 15 +++++- man/ants.Rd |only man/bearing.distance.Rd | 12 +++- man/breeding.density.Rd | 30 +++++++----- man/concordance.Rd | 32 ++++++++---- man/conf.interval.Rd | 20 ++++---- man/correlogram.Rd | 23 +++++---- man/csi.Rd | 23 +++++---- man/dispersion.Rd |only man/download.daymet.Rd | 39 ++++++++++----- man/download.hansen.Rd | 20 +++++--- man/download.prism.Rd | 24 ++++++--- man/gaussian.kernel.Rd |only man/group.pdf.Rd | 15 ++++-- man/hexagons.Rd | 16 ++++-- man/idw.smoothing.Rd | 30 +++++++----- man/insert.values.Rd |only man/kl.divergence.Rd | 13 +++-- man/land.metrics.Rd | 67 ++++++++++++++++---------- man/local.min.max.Rd | 20 +++++--- man/loess.boot.Rd | 51 ++++++++++++-------- man/loess.ci.Rd | 26 ++++++---- man/logistic.regression.Rd | 61 ++++++++++++++---------- man/moments.Rd | 40 ++++++++-------- man/nni.Rd | 14 ++++- man/o.ring.Rd | 19 +++++-- man/optimal.k.Rd | 14 ++++- man/outliers.Rd | 24 ++++++--- man/parea.sample.Rd | 21 +++++--- man/plot.loess.boot.Rd | 16 ++++-- man/point.in.poly.Rd | 25 ++++++---- man/pp.subsample.Rd | 48 ++++++++++++------- man/print.loess.boot.Rd | 2 man/pseudo.absence.Rd | 52 ++++++++++++-------- man/pu.Rd |only man/raster.entropy.Rd | 16 ++++-- man/raster.vol.Rd | 21 +++++--- man/sample.line.Rd | 39 ++++++++------- man/sample.poly.Rd |only man/separability.Rd | 61 ++++++++++++++---------- man/shannons.Rd |only man/similarity.Rd |only man/sp.na.omit.Rd | 20 ++++---- man/stratified.random.Rd | 19 +++++-- man/summary.loess.boot.Rd | 2 man/tpi.Rd | 18 ++++--- man/trend.line.Rd | 6 ++ man/tri.Rd |only man/wt.centroid.Rd | 26 ++++++---- man/zonal.stats.Rd | 43 ++++++++++------- 66 files changed, 848 insertions(+), 497 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 2.9 dated 2014-09-10 and 3.0 dated 2015-10-29
DESCRIPTION | 14 +++--- LICENCE | 2 MD5 | 62 +++++++++++++------------- NAMESPACE | 17 ++++++- NEWS | 3 + R/STS.R | 8 +-- R/zzz.r | 2 build/vignette.rds |binary demo/Sim.DiffProc.R | 38 ++++++++++++++++ inst/doc/FitSDE.Rnw | 2 inst/doc/FitSDE.pdf |binary inst/doc/Introduction.R | 6 +- inst/doc/Introduction.Rnw | 20 ++++---- inst/doc/Introduction.pdf |binary inst/doc/SDEs.R | 81 +++++++++++++++++++++++++--------- inst/doc/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |only man/Sim.DiffProc-package.Rd | 21 +++------ man/bridgesde1d.Rd | 1 man/bridgesde2d.Rd | 1 man/bridgesde3d.Rd | 1 man/fitsde.Rd | 2 man/plot2d.Rd | 2 man/snssde1d.Rd | 2 man/snssde2d.Rd | 2 man/snssde3d.Rd | 2 src/Sim.DiffProc.c | 24 ++-------- vignettes/Core_FitSDE.tex | 22 ++++----- vignettes/FitSDE.Rnw | 2 vignettes/Introduction.Rnw | 20 ++++---- vignettes/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- vignettes/Thumbs.db |only 33 files changed, 365 insertions(+), 196 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as Ghostscript is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-3 dated 2015-09-20 and 0.4-4 dated 2015-10-29
DESCRIPTION | 21 +++++++++++---------- MD5 | 14 +++++++------- inst/NEWS.Rd | 8 +++++++- man/showtext.auto.Rd | 2 +- man/showtext.begin.Rd | 10 +++++----- man/showtext.end.Rd | 2 +- man/showtext.opts.Rd | 10 +++++----- src/devfuns.c | 35 +++++++++++++++++++---------------- 8 files changed, 56 insertions(+), 46 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.16 dated 2015-04-08 and 1.17 dated 2015-10-29
DESCRIPTION | 8 +- MD5 | 28 ++++--- NAMESPACE | 9 +- R/ancRECON.R | 196 ++++++++++++++++++++++++++++++-------------------- R/corDISC.R | 77 +++++++++++-------- R/corHMM.R | 43 ++++++---- R/corPAINT.R | 67 +++++++++-------- R/lewisMkv.R |only R/rayDISC.R | 82 +++++++++++--------- R/readNexusMorph.R |only man/ancRECON.Rd | 7 - man/corDISC.Rd | 8 +- man/corHMM.Rd | 12 ++- man/corPAINT.Rd | 2 man/lewisMkv.Rd |only man/rayDISC.Rd | 4 - man/readNexusMorph.Rd |only 17 files changed, 319 insertions(+), 224 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.1 dated 2015-06-13 and 1.1.1 dated 2015-10-29
DESCRIPTION | 8 MD5 | 22 - NAMESPACE | 5 R/A_ExonPtnAlign_functions.R | 2 R/BIGDAWG.R | 934 +++++++++++++++++++++---------------------- R/update_wrapper.R | 7 build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 6 inst/doc/BIGDAWG.html | 14 man/BIGDAWG.Rd | 6 man/UpdateRelease.Rd | 4 vignettes/BIGDAWG.Rmd | 6 12 files changed, 510 insertions(+), 504 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-20 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-29 2.1.1
2015-07-28 2.1
2015-05-14 2.0
2015-03-21 1.3
2015-01-10 1.1
2014-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-22 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-13 1.1.1
2014-05-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-28 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-17 0.1.3
2014-12-04 0.1.1
2014-11-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-12 1.7-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-12 1.1.3
2014-01-24 1.1.2
2013-04-06 1.1.1
2013-03-05 1.1
2013-02-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-07 1.1.3
2013-09-12 1.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-20 1.01
2012-10-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-01 1.0.12
2015-06-19 1.0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-02 1.1
2013-11-26 1.0
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-2 dated 2015-06-24 and 2.7-5 dated 2015-10-29
dae-2.7-2/dae/R/proj.canon.v3.r |only dae-2.7-2/dae/R/projs.canon.v3.r |only dae-2.7-5/dae/DESCRIPTION | 11 +++-- dae-2.7-5/dae/MD5 | 38 ++++++++++--------- dae-2.7-5/dae/NAMESPACE | 9 ++++ dae-2.7-5/dae/R/Interaction.ABC.Plot.r | 12 ++++-- dae-2.7-5/dae/R/NoReps.r | 59 +++++++++++++++++++++++++++--- dae-2.7-5/dae/R/mat.functions.r | 2 - dae-2.7-5/dae/R/proj.canon.v4.r |only dae-2.7-5/dae/R/projs.canon.v4.r |only dae-2.7-5/dae/build |only dae-2.7-5/dae/inst/NEWS.Rd | 22 +++++++++++ dae-2.7-5/dae/inst/doc/dae-manual.pdf |binary dae-2.7-5/dae/man/dae-package.Rd | 23 ++++------- dae-2.7-5/dae/man/detect.diff.Rd |only dae-2.7-5/dae/man/efficiency.criteria.Rd | 17 +++++--- dae-2.7-5/dae/man/interaction.ABC.plot.Rd | 23 ++++++++--- dae-2.7-5/dae/man/no.reps.Rd | 10 ++--- dae-2.7-5/dae/man/power.exp.Rd | 2 - dae-2.7-5/dae/man/projs.canon.Rd | 27 +++++++++---- dae-2.7-5/dae/man/projs.structure.Rd | 47 ++++++++++++++++------- dae-2.7-5/dae/man/summary.p2canon.Rd | 26 +++++++------ dae-2.7-5/dae/man/summary.pcanon.Rd | 20 +++++----- 23 files changed, 239 insertions(+), 109 deletions(-)
Title: Learning Bayesian Network Classifiers from Data
Description: Implementation of different algorithms for learning discrete Bayesian network classifiers from data, including wrapper algorithms and those based on Chow-Liu's algorithm.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut]
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
Diff between bnclassify versions 0.3.0 dated 2015-07-30 and 0.3.1 dated 2015-10-29
DESCRIPTION | 9 +++--- MD5 | 42 ++++++++++++++++++----------- NAMESPACE | 1 R/0bnclassify-doc.R | 45 ++++++++++++++++++++++++------- R/bnc-dag-operate.R | 10 +++++- R/learn-params-awnb.R | 2 - R/learn-params.R | 2 - README.md | 2 - build/vignette.rds |binary man/bnc.Rd | 4 +- man/cv.Rd | 4 +- man/learn_params.Rd | 53 +++++++++++++++++++++++++------------ man/plot.bnc_dag.Rd | 4 ++ man/wrapper.Rd | 4 +- tests/testthat/test-learn-params.R | 11 +++++++ tests/testthat/test-wrap-grain.R | 6 ++-- vignettes/bnclassify.Rmd | 27 +++++++++++------- vignettes/bnclassify_cache |only 18 files changed, 154 insertions(+), 72 deletions(-)
Title: Augments the Use of 'Asreml' in Fitting Mixed Models
Description: Assists in automating the testing of terms in mixed models when 'asreml' is used
to fit the models. The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the
fitting of a sequence of models is kept in a data frame. Procedures are available for choosing
models that conform to the hierarchy or marginality principle and for displaying predictions
for significant terms in tables and graphs. The package 'asreml' provides a computationally
efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It can be
purchased from 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R', who will supply a zip file for
local installation/updating.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between asremlPlus versions 2.0-0 dated 2015-06-24 and 2.0-2 dated 2015-10-29
DESCRIPTION | 10 ++--- MD5 | 26 +++++++------- NAMESPACE | 8 +++- R/reml.v19.r | 76 +++++++++++++++++++++++++++++++++++++---- R/variogram.faces.v2.r | 6 ++- build |only inst/NEWS.Rd | 14 +++++++ inst/doc/asremlPlus-manual.pdf |binary man/addrm.terms.asrtests.Rd | 10 ++++- man/asremlPlus-package.Rd | 22 +++++------ man/newrcov.asrtests.Rd |only man/pred.present.asreml.Rd | 9 ++-- man/predictionplot.asreml.Rd | 11 +++-- man/testrcov.asrtests.Rd | 13 +++---- man/variofaces.Rd | 11 ++++- 15 files changed, 160 insertions(+), 56 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 0.65-1 dated 2015-05-27 and 1.0-0 dated 2015-10-29
vegan3d-0.65-1/vegan3d/README.md |only vegan3d-1.0-0/vegan3d/DESCRIPTION | 10 - vegan3d-1.0-0/vegan3d/MD5 | 38 ++-- vegan3d-1.0-0/vegan3d/NAMESPACE | 15 + vegan3d-1.0-0/vegan3d/R/ordiplot3d.R | 11 + vegan3d-1.0-0/vegan3d/R/ordirgl.R | 33 +++- vegan3d-1.0-0/vegan3d/R/orditree3d.R |only vegan3d-1.0-0/vegan3d/R/orglellipse.R |only vegan3d-1.0-0/vegan3d/R/orglpoints.R | 18 +- vegan3d-1.0-0/vegan3d/R/orglsegments.R | 20 ++ vegan3d-1.0-0/vegan3d/R/orglspantree.R |only vegan3d-1.0-0/vegan3d/R/orglspider.R | 16 +- vegan3d-1.0-0/vegan3d/R/orgltext.R | 12 + vegan3d-1.0-0/vegan3d/R/rgl.isomap.R | 16 +- vegan3d-1.0-0/vegan3d/R/rgl.renyiaccum.R | 5 vegan3d-1.0-0/vegan3d/R/scores.ordiplot3d.R |only vegan3d-1.0-0/vegan3d/build |only vegan3d-1.0-0/vegan3d/inst |only vegan3d-1.0-0/vegan3d/man/ordiplot3d.Rd | 123 ++++++++------- vegan3d-1.0-0/vegan3d/man/ordirgl.Rd | 208 +++++++++++++++++---------- vegan3d-1.0-0/vegan3d/man/orditree3d.Rd |only vegan3d-1.0-0/vegan3d/man/rgl.isomap.Rd | 32 ++-- vegan3d-1.0-0/vegan3d/man/rgl.renyiaccum.Rd | 6 vegan3d-1.0-0/vegan3d/man/vegan3d-package.Rd |only 24 files changed, 360 insertions(+), 203 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete non-equally spaced observations on a finite time interval based on expansions of the convolution kernel, the unknown function and the observed signal over Laguerre functions basis. It implements the methodology proposed in the paper "Laplace deconvolution on the basis of time domain data and its application to Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y. Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.1 dated 2015-10-29 and 1.0.2 dated 2015-10-29
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/LagLaplaceDeconvolution.R | 62 +++++++++++++++++--------------------------- man/LagLaplDeconv.Rd | 36 ++++++++++++------------- 4 files changed, 48 insertions(+), 64 deletions(-)
Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine)
and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate
as well as vine copula selection are provided. Models can be estimated
either sequentially or by joint maximum likelihood estimation.
Sampling algorithms and plotting methods are also included.
Data is assumed to lie in the unit hypercube (so-called copula
data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt
<tobias.erhardt@tum.de>
Diff between CDVine versions 1.3 dated 2015-07-30 and 1.4 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/zzz.R | 5 +++++ man/CDVine-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015).
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology).
Author: Thomas Yee [aut, cre, cph],
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 0.9-7 dated 2015-03-17 and 1.0-0 dated 2015-10-29
DESCRIPTION | 20 +++++++++------ MD5 | 68 ++++++++++++++++++++++++++------------------------- NAMESPACE | 6 ++++ NEWS | 18 +++++++++++++ R/family.fishing.R | 51 ++++---------------------------------- data/bb.de.rda |binary data/bd.us.rda |only data/belcap.rda |binary data/crashf.au.rda |binary data/crime.us.rda |binary data/datalist | 1 data/exam1.rda |binary data/fibre15.rda |binary data/fibre1dot5.rda |binary data/gala.rda |binary data/hued.rda |binary data/huie.rda |binary data/huse.rda |binary data/oly12.rda |binary data/prison.us.rda |binary data/profs.nz.rda |binary data/rainfall.rda |binary data/rugby.rda |binary data/rugby.ties.rda |binary data/students.tw.rda |binary data/trapO.rda |binary data/tube10.rda |binary data/ugss.rda |binary data/vtinpat.rda |binary data/wffc.indiv.rda |binary data/wffc.nc.rda |binary data/wffc.rda |binary data/wffc.teams.rda |binary data/xs.nz.rda |binary inst/CITATION | 39 +++++++++++++++++++++++++++++ man/bd.us.Rd |only 36 files changed, 118 insertions(+), 85 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 0.9-8 dated 2015-05-11 and 1.0-0 dated 2015-10-29
ChangeLog |only DESCRIPTION | 20 - LICENCE.note |only MD5 | 263 +++++++------- NAMESPACE | 68 +++ NEWS | 63 +++ R/Links.R | 14 R/build.terms.vlm.q | 36 + R/calibrate.q | 15 R/coef.vlm.q | 9 R/confint.vlm.R |only R/family.aunivariate.R | 20 - R/family.basics.R | 30 + R/family.binomial.R | 147 +++++-- R/family.bivariate.R | 66 ++- R/family.categorical.R | 37 + R/family.censored.R | 268 ++++++++++++++ R/family.circular.R | 4 R/family.exp.R | 2 R/family.extremes.R | 14 R/family.genetic.R | 20 - R/family.glmgam.R | 70 ++- R/family.loglin.R | 4 R/family.mixture.R | 8 R/family.nonlinear.R | 4 R/family.normal.R | 758 ++++++++++++++++++++++++++-------------- R/family.others.R | 12 R/family.positive.R | 31 - R/family.qreg.R | 144 ++++--- R/family.rcim.R | 25 + R/family.robust.R | 2 R/family.rrr.R | 317 ++++++++--------- R/family.survival.R | 4 R/family.ts.R | 130 ++++--- R/family.univariate.R | 199 ++++++---- R/family.zeroinf.R | 31 + R/formula.vlm.q | 99 +++++ R/links.q | 797 +++++++++++++++++++++++-------------------- R/model.matrix.vglm.q | 38 +- R/qtplot.q | 20 - R/summary.vglm.q | 39 +- R/vglm.R | 6 R/vglm.fit.q | 2 R/vlm.wfit.q | 2 build/vignette.rds |binary data/Huggins89.t1.rda |binary data/Huggins89table1.rda |binary data/alclevels.rda |binary data/alcoff.rda |binary data/auuc.rda |binary data/backPain.rda |binary data/beggs.rda |binary data/car.all.rda |binary data/cfibrosis.rda |binary data/corbet.rda |binary data/crashbc.rda |binary data/crashf.rda |binary data/crashi.rda |binary data/crashmc.rda |binary data/crashp.rda |binary data/crashtr.rda |binary data/deermice.rda |binary data/ducklings.rda |binary data/finney44.rda |binary data/flourbeetle.rda |binary data/hspider.rda |binary data/lakeO.rda |binary data/leukemia.rda |binary data/marital.nz.rda |binary data/melbmaxtemp.rda |binary data/pneumo.rda |binary data/prinia.rda |binary data/ruge.rda |binary data/toxop.rda |binary data/venice.rda |binary data/venice90.rda |binary data/wine.rda |binary inst/CITATION | 61 ++- inst/doc/categoricalVGAM.pdf |binary inst/doc/crVGAM.R | 4 inst/doc/crVGAM.Rnw | 46 +- inst/doc/crVGAM.pdf |binary man/AA.Aa.aa.Rd | 1 man/AR1.Rd | 11 man/CommonVGAMffArguments.Rd | 29 + man/Links.Rd | 127 +++++- man/SURff.Rd | 2 man/VGAM-package.Rd | 9 man/acat.Rd | 4 man/alaplace3.Rd | 7 man/betabinomUC.Rd | 20 + man/binomialff.Rd | 10 man/binormal.Rd | 10 man/brat.Rd | 4 man/bratUC.Rd | 4 man/cauchit.Rd | 2 man/cens.poisson.Rd | 32 + man/cloglog.Rd | 5 man/confintvglm.Rd |only man/cratio.Rd | 4 man/cumulative.Rd | 6 man/explink.Rd | 2 man/fisherz.Rd | 2 man/foldsqrt.Rd | 2 man/formulavlm.Rd |only man/gengamma.Rd | 10 man/golf.Rd | 22 - man/has.intercept.Rd |only man/identitylink.Rd | 2 man/logc.Rd | 2 man/loge.Rd | 2 man/logit.Rd | 18 man/lognormal.Rd | 6 man/multilogit.Rd | 2 man/multinomial.Rd | 4 man/nbcanlink.Rd | 19 - man/nbolf.Rd | 16 man/negbinomial.Rd | 16 man/notdocumentedyet.Rd | 34 + man/polf.Rd | 17 man/posnormal.Rd | 69 ++- man/probit.Rd | 2 man/propodds.Rd | 2 man/rayleigh.Rd | 3 man/rhobit.Rd | 7 man/sratio.Rd | 6 man/summaryvglm.Rd |only man/tobit.Rd | 100 ++--- man/triangle.Rd | 9 man/undocumented-methods.Rd | 12 man/vcovvlm.Rd |only man/vglm.Rd | 17 man/weibull.mean.Rd |only man/weibullR.Rd | 1 man/wine.Rd | 6 vignettes/crVGAM.Rnw | 46 +- vignettes/crVGAM.bib | 20 + 137 files changed, 3133 insertions(+), 1579 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with SparseM/Matrix are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 1.2-1 dated 2015-09-30 and 1.3-0 dated 2015-10-29
ChangeLog | 36 ++++++++++ DESCRIPTION | 8 +- MD5 | 80 +++++++++++------------ R/definitions.R | 2 R/math.R | 103 +++++++++++++++--------------- inst/NEWS | 21 +++++- man/allequal.Rd | 7 -- man/nearestdist.Rd | 10 +- man/operations.Rd | 4 + man/rdist.Rd | 13 +++ tests/constructors.Rout.save | 4 - tests/covmat.Rout.save | 4 - tests/crossprod.Rout.save | 4 - tests/demo_article-jss-example1.Rout.save | 4 - tests/demo_article-jss-example2.Rout.save | 4 - tests/demo_article-jss.Rout.save | 4 - tests/demo_cholesky.Rout.save | 4 - tests/demo_jss15-BYM.Rout.save | 4 - tests/demo_jss15-Leroux.Rout.save | 4 - tests/demo_spam.Rout.save | 4 - tests/demo_timing.Rout.save | 4 - tests/diff.Rout.save | 4 - tests/dim.Rout.save | 4 - tests/displays.Rout.save | 4 - tests/dist.Rout.save | 4 - tests/foreign.Rout.save | 2 tests/helper.Rout.save | 4 - tests/jss_areal_counts.Rout.save | 4 - tests/kronecker.Rout.save | 4 - tests/math.R | 18 ++++- tests/math.Rout.save | 22 +++++- tests/mle.Rout.save | 4 - tests/norm.Rout.save | 4 - tests/ops.Rout.save | 5 - tests/overall.Rout.save | 4 - tests/permutation.Rout.save | 4 - tests/rowcolstats.Rout.save | 4 - tests/solve.Rout.save | 4 - tests/spamlist.Rout.save | 4 - tests/subsetting.Rout.save | 4 - tests/xybind.Rout.save | 4 - 41 files changed, 266 insertions(+), 173 deletions(-)
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Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between onlinePCA versions 1.2 dated 2015-08-12 and 1.3 dated 2015-10-29
DESCRIPTION | 12 ++++---- MD5 | 52 +++++++++++++++++++----------------- NAMESPACE | 12 ++++---- NEWS | 16 ++++++++++- R/batchpca.R | 23 +++++++++++----- R/bsoipca.R |only R/incRpca.R | 2 - R/incRpca.block.R |only R/incRpca.rc.R | 2 - R/perturbationRpca.R | 2 - R/secularRpca.R | 35 +++++++++++++++++------- man/batchpca.Rd | 63 +++++++++++++++++++------------------------- man/bsoipca.Rd |only man/ccipca.Rd | 33 +++++++++++------------ man/coef2fd.Rd | 24 ++++------------ man/create.basis.Rd | 41 +++++++++------------------- man/fd2coef.Rd | 26 ++++-------------- man/ghapca.Rd | 19 ++++--------- man/impute.Rd | 2 - man/incRpca.Rd | 47 ++++++++++++++------------------ man/incRpca.block.Rd |only man/incRpca.rc.Rd | 67 +++++++++++++++++++++-------------------------- man/onlinePCA-package.Rd | 10 ++----- man/perturbationRpca.Rd | 50 ++++++++++++++--------------------- man/secularRpca.Rd | 31 +++++++-------------- man/sgapca.Rd | 19 ++++--------- man/snlpca.Rd | 36 ++++++++----------------- man/updateCovariance.Rd | 10 +++---- man/updateMean.Rd | 13 ++++----- 29 files changed, 293 insertions(+), 354 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.3-0 dated 2015-10-24 and 1.3-2 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/25-addControlList.R | 19 +++++++++++++------ R/maxBFGS.R | 2 +- R/maxBFGSR.R | 2 +- R/maxCG.R | 2 +- R/maxNM.R | 2 +- R/maxNR.R | 2 +- R/maxOptim.R | 2 +- R/maxSANN.R | 2 +- man/maxNR.Rd | 2 +- 12 files changed, 41 insertions(+), 29 deletions(-)
Title: Purge Training Data from Models
Description: Enables the removal of training data from fitted R models while
retaining predict functionality. The purged models are more portable as their
memory footprints do not scale with the training sample size.
Author: Marc Maier [cre],
Chaoqun Jia [ctb],
MassMutual Advanced Analytics [aut] (http://datascience.massmutual.com)
Maintainer: Marc Maier <mmaier@massmutual.com>
Diff between purge versions 0.1.0 dated 2015-09-02 and 0.2.0 dated 2015-10-28
DESCRIPTION | 22 +++--- MD5 | 12 +-- NAMESPACE | 7 -- R/purge.R | 29 +++++++- man/purge.Rd | 13 +++ tests/purged.filesizes.R | 15 ++++ tests/testthat/test.purge.R | 148 +++++++++++++++++++++++++++++++------------- 7 files changed, 181 insertions(+), 65 deletions(-)
Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.2.0 dated 2015-09-05 and 1.3.0 dated 2015-10-28
DESCRIPTION | 10 +- MD5 | 44 ++++----- NAMESPACE | 5 - NEWS | 17 +++ R/WiSEBoot.R | 53 ++++++++++- R/WiSEHypothesisTest.R | 52 +++++++++-- R/smoothTimeSeries.R | 7 + inst/doc/WiSEBoot_Examples_Vignette.R | 11 +- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- inst/doc/WiSEBoot_Examples_Vignette.pdf |binary man/SimulatedSNR0.5Series.Rd | 2 man/SimulatedSNR1.0Series.Rd | 2 man/SimulatedSNR1.5Series.Rd | 2 man/SimulatedSNR2.0Series.Rd | 2 man/SimulatedSmoothSeries.Rd | 2 man/WiSEBoot-package.Rd | 16 +-- man/WiSEBoot.Rd | 38 +++++--- man/WiSEConfidenceRegion.Rd | 17 ++- man/WiSEHypothesisTest.Rd | 31 ++++-- man/padMatrix.Rd | 2 man/padVector.Rd | 2 man/smoothTimeSeries.Rd | 2 vignettes/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- 23 files changed, 416 insertions(+), 177 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.2-1 dated 2015-09-09 and 1.2-2 dated 2015-10-28
DESCRIPTION | 16 +-- MD5 | 124 ++++++++++++------------- R/AAA.R | 2 R/DSC_DBSTREAM.R | 2 R/DSC_DStream.R | 2 R/DSD_Memory.R | 4 R/evaluate.R | 23 +++- inst/NEWS | 9 + inst/doc/stream.R | 203 +++++++++++++++--------------------------- inst/doc/stream.Rnw | 90 +++++++----------- inst/doc/stream.pdf |binary inst/doc/stream_extension.pdf |binary man/DSC.Rd | 5 + man/DSC_DBSCAN.Rd | 4 man/DSC_DBSTREAM.Rd | 25 ++--- man/DSC_DStream.Rd | 4 man/DSC_Hierarchical.Rd | 5 + man/DSC_Kmeans.Rd | 4 man/DSC_Macro.Rd | 5 + man/DSC_Micro.Rd | 5 + man/DSC_Reachability.Rd | 4 man/DSC_Sample.Rd | 13 +- man/DSC_Static.Rd | 4 man/DSC_TwoStage.Rd | 4 man/DSC_Window.Rd | 5 + man/DSClassify.Rd | 5 + man/DSD.Rd | 4 man/DSD_BarsAndGaussians.Rd | 5 + man/DSD_Benchmark.Rd | 5 + man/DSD_Cubes.Rd | 5 + man/DSD_Gaussians.Rd | 6 + man/DSD_MG.Rd | 4 man/DSD_Memory.Rd | 4 man/DSD_ReadCSV.Rd | 4 man/DSD_ReadDB.Rd | 4 man/DSD_ScaleStream.Rd | 4 man/DSD_Target.Rd | 5 + man/DSD_UniformNoise.Rd | 5 + man/DSD_mlbenchData.Rd | 5 + man/DSD_mlbenchGenerator.Rd | 5 + man/DSFP.Rd | 5 + man/DSO.Rd | 5 + man/DSO_Sampling.Rd | 4 man/DSO_Window.Rd | 4 man/DST.Rd | 5 + man/MGC.Rd | 6 + man/animation.Rd | 3 man/evaluate.Rd | 31 +++++- man/get_assignment.Rd | 5 + man/get_centers.Rd | 5 + man/get_copy.Rd | 5 + man/get_points.Rd | 5 + man/get_weights.Rd | 5 + man/microToMacro.Rd | 5 + man/nclusters.Rd | 5 + man/plot.Rd | 5 + man/prune_clusters.Rd | 5 + man/recluster.Rd | 5 + man/reset_stream.Rd | 5 + man/save.Rd | 7 + man/update.Rd | 5 + man/write_stream.Rd | 5 + vignettes/stream.Rnw | 90 +++++++----------- 63 files changed, 511 insertions(+), 346 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier <annie.bouvier@jouy.inra.fr>
Diff between sivipm versions 1.0-0 dated 2015-04-14 and 1.1-2 dated 2015-10-28
DESCRIPTION | 13 + MD5 | 59 ++++---- NAMESPACE | 9 - NEWS | 36 +++++ R/allmono.R |only R/class-sivip.R |only R/fastregpls2.R |only R/polynome.R | 165 +++++++++++------------ R/regpls2.R | 310 +++++++++++++++++++++++++++------------------ R/sivipm.R | 236 ++++++++++++++++++++++------------ R/vect2poly.R | 6 inst/doc/Vignette.pdf |binary man/cornell1.Rd | 2 man/crpolyX.Rd | 4 man/crpolyXT.Rd | 4 man/poly-class.Rd | 8 + man/polyX-class.Rd | 8 + man/sivip-class.Rd |only man/sivipboot.Rd | 18 ++ man/sivipm-package.Rd | 6 man/sivipm.Rd | 87 ++++++------ man/vect2polyX.Rd | 2 man/vect2polyXT.Rd | 2 src |only tests/exX18Y14.R | 3 tests/exX18Y14.Rout.save | 65 +++++---- tests/exX18Y2.R | 4 tests/exX18Y2.Rout.save | 115 ++++++++-------- tests/exXY180.R | 6 tests/exXY180.Rout.save | 42 +++--- tests/excornell0.R | 20 ++ tests/excornell0.Rout.save | 211 ++++++++++++++++++++---------- tests/excornell1.Rout.save | 31 ++-- 33 files changed, 896 insertions(+), 576 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 0.6 dated 2015-08-23 and 0.7 dated 2015-10-28
DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++------------------ NAMESPACE | 9 ++++++ NEWS | 24 ++++++++-------- R/RcppExports.R | 46 +++++++++++++++---------------- R/base-pref-macros.R | 38 +++++++++++++++----------- R/base-pref.r | 28 +++++++++++++------ R/complex-pref.r | 45 ++++++++++++++----------------- R/general-pref.r |only R/pred-succ.r | 26 ++++++++--------- R/pref-classes.r | 35 +++++++++++++++--------- R/pref-eval.r | 68 +++++++++++++++++++++++++++++------------------ R/rPref.r | 18 +++++++----- R/show-pref.r | 56 ++++++++++++++++++++------------------ R/visualize.r | 22 +++++++-------- inst/test/test-pref.r | 21 ++++++++++++++ inst/test/test-psel.R | 13 ++++++++ inst/test/test-strings.R | 3 +- man/base_pref.Rd | 28 ++++++++++++------- man/base_pref_macros.Rd | 38 +++++++++++++++----------- man/complex_pref.Rd | 32 ++++++++-------------- man/general_pref.Rd |only man/get_btg.Rd | 6 ++-- man/get_hasse_diag.Rd | 4 +- man/plot_front.Rd | 6 ++-- man/pred_succ.Rd | 23 ++++++++------- man/psel.Rd | 41 ++++++++++++++++------------ man/rPref.Rd | 17 ++++++----- man/show.pref.Rd | 29 +++++++++----------- man/show.query.Rd | 5 ++- 30 files changed, 428 insertions(+), 317 deletions(-)
Title: Ridge Regression and Other Kernels for Genomic Selection
Description: Software for genomic prediction with the RR-BLUP mixed model. One application is to estimate marker effects by ridge regression; alternatively, BLUPs can be calculated based on an additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman <endelman@wisc.edu>
Diff between rrBLUP versions 4.3 dated 2014-03-06 and 4.4 dated 2015-10-28
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- NAMESPACE | 3 ++ NEWS | 5 ++++ R/A.mat.R | 7 ++---- R/GWAS.R | 17 ++++++++------- R/kin.blup.R | 59 +++++++++++++++++++++++++++++++++++-------------------- R/kinship.BLUP.R | 5 +--- man/GWAS.Rd | 6 +++-- man/kin.blup.Rd | 8 +++++-- 10 files changed, 83 insertions(+), 53 deletions(-)
Title: In-Source Documentation for R
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 4.1.1 dated 2015-04-15 and 5.0.0 dated 2015-10-28
roxygen2-4.1.1/roxygen2/R/parse-registry.R |only roxygen2-4.1.1/roxygen2/man/roxygen.Rd |only roxygen2-4.1.1/roxygen2/src/parser.cpp |only roxygen2-4.1.1/roxygen2/src/roxygen.h |only roxygen2-4.1.1/roxygen2/tests/testthat/test-complete.R |only roxygen2-4.1.1/roxygen2/tests/testthat/test-cpp-parser.R |only roxygen2-5.0.0/roxygen2/DESCRIPTION | 35 roxygen2-5.0.0/roxygen2/MD5 | 211 +- roxygen2-5.0.0/roxygen2/NAMESPACE | 22 roxygen2-5.0.0/roxygen2/R/RcppExports.R | 12 roxygen2-5.0.0/roxygen2/R/alias.R | 2 roxygen2-5.0.0/roxygen2/R/default-data-format.R |only roxygen2-5.0.0/roxygen2/R/family.R | 30 roxygen2-5.0.0/roxygen2/R/minidesc.R | 6 roxygen2-5.0.0/roxygen2/R/object-defaults.R | 29 roxygen2-5.0.0/roxygen2/R/object-from-call.R | 32 roxygen2-5.0.0/roxygen2/R/object.R | 8 roxygen2-5.0.0/roxygen2/R/order-params.R | 1 roxygen2-5.0.0/roxygen2/R/parse-preref.R | 233 +- roxygen2-5.0.0/roxygen2/R/parse.R | 37 roxygen2-5.0.0/roxygen2/R/rc.R | 4 roxygen2-5.0.0/roxygen2/R/rd-file-api.R | 9 roxygen2-5.0.0/roxygen2/R/rd-parse.R | 8 roxygen2-5.0.0/roxygen2/R/rd-tag-api.R | 64 roxygen2-5.0.0/roxygen2/R/roclet-collate.R | 25 roxygen2-5.0.0/roxygen2/R/roclet-namespace.R | 58 roxygen2-5.0.0/roxygen2/R/roclet-rd.R | 311 +-- roxygen2-5.0.0/roxygen2/R/roclet-vignette.R | 1 roxygen2-5.0.0/roxygen2/R/roxygen-tag.R |only roxygen2-5.0.0/roxygen2/R/roxygen.R | 11 roxygen2-5.0.0/roxygen2/R/roxygenize.R | 21 roxygen2-5.0.0/roxygen2/R/safety.R | 16 roxygen2-5.0.0/roxygen2/R/source.R | 4 roxygen2-5.0.0/roxygen2/R/tag-registry.R |only roxygen2-5.0.0/roxygen2/R/template.R | 12 roxygen2-5.0.0/roxygen2/R/usage.R | 5 roxygen2-5.0.0/roxygen2/R/utils.R | 14 roxygen2-5.0.0/roxygen2/README.md | 14 roxygen2-5.0.0/roxygen2/build/vignette.rds |binary roxygen2-5.0.0/roxygen2/inst/doc/collate.R | 10 roxygen2-5.0.0/roxygen2/inst/doc/collate.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/collate.html | 251 --- roxygen2-5.0.0/roxygen2/inst/doc/formatting.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/formatting.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/formatting.html | 345 +--- roxygen2-5.0.0/roxygen2/inst/doc/namespace.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/namespace.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/namespace.html | 261 --- roxygen2-5.0.0/roxygen2/inst/doc/rd.R | 29 roxygen2-5.0.0/roxygen2/inst/doc/rd.Rmd | 67 roxygen2-5.0.0/roxygen2/inst/doc/rd.html | 880 +++-------- roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.html | 428 +---- roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.html | 221 -- roxygen2-5.0.0/roxygen2/man/default_data_format.Rd |only roxygen2-5.0.0/roxygen2/man/is_s3_generic.Rd | 2 roxygen2-5.0.0/roxygen2/man/load_options.Rd |only roxygen2-5.0.0/roxygen2/man/namespace_roclet.Rd | 5 roxygen2-5.0.0/roxygen2/man/new_roclet.Rd | 2 roxygen2-5.0.0/roxygen2/man/object.Rd | 4 roxygen2-5.0.0/roxygen2/man/rd_roclet.Rd | 11 roxygen2-5.0.0/roxygen2/man/register-parser.Rd | 18 roxygen2-5.0.0/roxygen2/man/roc_proc_text.Rd | 2 roxygen2-5.0.0/roxygen2/man/roxygen2-package.Rd |only roxygen2-5.0.0/roxygen2/man/roxygenize.Rd | 2 roxygen2-5.0.0/roxygen2/man/source_package.Rd | 2 roxygen2-5.0.0/roxygen2/man/update_collate.Rd | 2 roxygen2-5.0.0/roxygen2/man/vignette_roclet.Rd | 6 roxygen2-5.0.0/roxygen2/src/RcppExports.cpp | 29 roxygen2-5.0.0/roxygen2/src/isComplete.cpp | 70 roxygen2-5.0.0/roxygen2/src/parser2.cpp |only roxygen2-5.0.0/roxygen2/src/wrapString.cpp | 41 roxygen2-5.0.0/roxygen2/tests/testthat/collate/belt.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/helper-pkg.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-alias.R | 22 roxygen2-5.0.0/roxygen2/tests/testthat/test-collate.R | 22 roxygen2-5.0.0/roxygen2/tests/testthat/test-data.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-describein.R | 3 roxygen2-5.0.0/roxygen2/tests/testthat/test-doctype.R | 12 roxygen2-5.0.0/roxygen2/tests/testthat/test-examples.R | 19 roxygen2-5.0.0/roxygen2/tests/testthat/test-family.R | 36 roxygen2-5.0.0/roxygen2/tests/testthat/test-field.R | 2 roxygen2-5.0.0/roxygen2/tests/testthat/test-format.R | 76 roxygen2-5.0.0/roxygen2/tests/testthat/test-inline.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-introduction.R | 51 roxygen2-5.0.0/roxygen2/tests/testthat/test-keyword.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/test-merge.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-namespace.R | 51 roxygen2-5.0.0/roxygen2/tests/testthat/test-object.R | 4 roxygen2-5.0.0/roxygen2/tests/testthat/test-package-doc.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-param.R | 30 roxygen2-5.0.0/roxygen2/tests/testthat/test-preref.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-raw.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-rc.R | 12 roxygen2-5.0.0/roxygen2/tests/testthat/test-rd.R | 11 roxygen2-5.0.0/roxygen2/tests/testthat/test-rdComplete.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-reexport.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-slot.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/test-srcref-comment.R | 6 roxygen2-5.0.0/roxygen2/tests/testthat/test-template.R | 15 roxygen2-5.0.0/roxygen2/tests/testthat/test-tokenize-block.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-topic-name.R | 17 roxygen2-5.0.0/roxygen2/tests/testthat/test-usage.R | 60 roxygen2-5.0.0/roxygen2/tests/testthat/testCollateOverwrite |only roxygen2-5.0.0/roxygen2/tests/testthat/testEagerData |only roxygen2-5.0.0/roxygen2/tests/testthat/testLazyData |only roxygen2-5.0.0/roxygen2/vignettes/collate.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/formatting.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/namespace.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/rd.Rmd | 67 roxygen2-5.0.0/roxygen2/vignettes/rd.md | 46 roxygen2-5.0.0/roxygen2/vignettes/rdkeywords.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/roxygen2.Rmd | 24 116 files changed, 2060 insertions(+), 2712 deletions(-)
Title: Rank-Hazard Plots
Description: Rank-hazard plots (Karvanen and Harrell, Statistics in Medicine 2009) visualize the relative importance of covariates in a proportional hazards model. The key idea is to rank the covariate values and plot the relative hazard as a function of ranks scaled to interval [0,1]. The relative hazard is plotted in respect to the reference hazard, which can bee.g. the hazard related to the median of the covariate.
Author: Juha Karvanen, Nanni Koski
Maintainer: Nanni Koski <nanni.t.koski@student.jyu.fi>
Diff between rankhazard versions 1.0 dated 2014-04-02 and 1.0-2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/rankhazardplot.Rd | 3 ++- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-8 dated 2015-10-22 and 0.1-9 dated 2015-10-28
DESCRIPTION | 11 ++-- MD5 | 21 ++++---- NAMESPACE | 2 R/RcppExports.R | 12 ---- R/allPerm.R | 18 +++--- R/initMC.r | 20 +++---- R/nextPerm.R | 19 +++---- R/zzz.R |only man/initMC.Rd | 87 ++++++++++++++++----------------- man/nextPerm.Rd | 74 ++++++++++++++-------------- src/RcppExports.cpp | 33 ------------ src/multicool.cpp | 134 +++++++++++++++++++++++----------------------------- 12 files changed, 186 insertions(+), 245 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms efficiently using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable
matching for two-sided markets, such as the stable marriage
problem and the college-admissions problem. Implements Irving's
Algorithm for the stable roommate problem. Implements the top
trading cycle algorithm for the indivisible goods trading problem.
Author: Jan Tilly, Nick Janetos
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.1.1 dated 2015-09-21 and 1.2 dated 2015-10-28
matchingR-1.1.1/matchingR/man/checkPreferenceOrder.Rd |only matchingR-1.1.1/matchingR/man/checkPreferenceOrderOnesided.Rd |only matchingR-1.1.1/matchingR/man/checkStability.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityRoommate.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityTopTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/galeShapleyMatching.Rd |only matchingR-1.1.1/matchingR/man/many2one.Rd |only matchingR-1.1.1/matchingR/man/one2many.Rd |only matchingR-1.1.1/matchingR/man/one2one.Rd |only matchingR-1.1.1/matchingR/man/onesided.Rd |only matchingR-1.1.1/matchingR/man/pkg.env.Rd |only matchingR-1.1.1/matchingR/man/set.column.major.Rd |only matchingR-1.1.1/matchingR/man/set.row.major.Rd |only matchingR-1.1.1/matchingR/man/stableRoommateMatching.Rd |only matchingR-1.1.1/matchingR/man/topTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/validateInputs.Rd |only matchingR-1.1.1/matchingR/man/validateInputsOneSided.Rd |only matchingR-1.2/matchingR/DESCRIPTION | 22 matchingR-1.2/matchingR/MD5 | 107 - matchingR-1.2/matchingR/NEWS.md | 9 matchingR-1.2/matchingR/R/RcppExports.R | 211 +- matchingR-1.2/matchingR/R/deprecated.R |only matchingR-1.2/matchingR/R/galeshapley.R | 740 ++++++---- matchingR-1.2/matchingR/R/matchingR.R | 137 - matchingR-1.2/matchingR/R/roommate.R | 260 ++- matchingR-1.2/matchingR/R/toptradingcycle.R | 117 + matchingR-1.2/matchingR/R/utils.R | 17 matchingR-1.2/matchingR/README.md | 60 matchingR-1.2/matchingR/inst/doc/matchingR-intro.R | 54 matchingR-1.2/matchingR/inst/doc/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/inst/doc/matchingR-intro.html | 115 + matchingR-1.2/matchingR/inst/doc/matchingR-performance.R | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.Rmd | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.html | 84 - matchingR-1.2/matchingR/inst/include/matchingR.h | 17 matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc_check_stability.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkPreferences.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkStability.Rd |only matchingR-1.2/matchingR/man/galeShapley.collegeAdmissions.Rd |only matchingR-1.2/matchingR/man/galeShapley.marriageMarket.Rd |only matchingR-1.2/matchingR/man/galeShapley.validate.Rd |only matchingR-1.2/matchingR/man/matchingR-deprecated.Rd |only matchingR-1.2/matchingR/man/matchingR-package.Rd | 74 - matchingR-1.2/matchingR/man/rankIndex.Rd | 4 matchingR-1.2/matchingR/man/roommate.Rd |only matchingR-1.2/matchingR/man/roommate.checkPreferences.Rd |only matchingR-1.2/matchingR/man/roommate.checkStability.Rd |only matchingR-1.2/matchingR/man/roommate.validate.Rd |only matchingR-1.2/matchingR/man/sortIndex.Rd | 4 matchingR-1.2/matchingR/man/sortIndexOneSided.Rd | 13 matchingR-1.2/matchingR/man/toptrading.Rd | 62 matchingR-1.2/matchingR/man/toptrading.checkStability.Rd |only matchingR-1.2/matchingR/src/RcppExports.cpp | 48 matchingR-1.2/matchingR/src/galeshapley.cpp | 163 +- matchingR-1.2/matchingR/src/galeshapley.h | 21 matchingR-1.2/matchingR/src/roommate.cpp | 118 + matchingR-1.2/matchingR/src/roommate.h | 23 matchingR-1.2/matchingR/src/toptradingcycle.cpp | 141 + matchingR-1.2/matchingR/src/toptradingcycle.h | 21 matchingR-1.2/matchingR/src/utils.cpp | 47 matchingR-1.2/matchingR/src/utils.h | 17 matchingR-1.2/matchingR/tests/testthat/test_galeshapley.R | 161 +- matchingR-1.2/matchingR/tests/testthat/test_roommate.R | 64 matchingR-1.2/matchingR/tests/testthat/test_toptradingcycle.R | 17 matchingR-1.2/matchingR/vignettes/bibliography.bib | 2 matchingR-1.2/matchingR/vignettes/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/vignettes/matchingR-performance.Rmd | 28 72 files changed, 2131 insertions(+), 1093 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.3 dated 2015-10-22 and 0.0.4 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS |only R/raster.R | 1 - configure | 11 +++++++++++ man/raster_str.Rd | 1 - 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Learning Algorithms for Dynamic Treatment Regimes
Description: Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each stage by time-varying subject-specific features and intermediate outcomes observed in previous stages. This package implements three methods: O-learning (Zhao et. al. 2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu et. al. 2014, 2015) to estimate the optimal DTRs.
Author: Ying Liu, Yuanjia Wang, Donglin Zeng
Maintainer: Ying Liu <yl2802@cumc.columbia.edu>
Diff between DTRlearn versions 1.0 dated 2015-10-23 and 1.1 dated 2015-10-28
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++------------ man/DTRlearn-package.Rd | 22 ++++++++++------- man/Olearning.Rd | 27 ++++++++++----------- man/Olearning_Single.Rd | 43 ++++++++++++++++++++++----------- man/Plearning.Rd | 31 +++++++++++------------- man/Qlearning.Rd | 12 ++++----- man/Qlearning_Single.Rd | 16 +++++------- man/make_2classification.Rd | 16 ++++++------ man/make_classification.Rd | 30 +++++++++++++---------- man/plot.linearcl.Rd | 17 ++++++------- man/plot.qlearn.Rd | 27 ++++++--------------- man/predict.linearcl.Rd | 9 ++----- man/predict.qlearn.Rd | 10 +++---- man/predict.rbfcl.Rd | 8 +++--- man/wsvm.Rd | 56 +++++++++++++++++++++++--------------------- 16 files changed, 186 insertions(+), 180 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.5 dated 2015-10-25 and 1.7 dated 2015-10-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/C_CIT_V12.R | 14 ++++++++++++-- man/cit-package.Rd | 4 ++-- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Multivariate Chebyshev Interpolation
Description: Contains methods for creating multivariate Chebyshev
approximation of functions on a hypercube. Some methods for
non-Chebyshev grids are also provided.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo, Norway
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 1.3-1367 dated 2014-09-01 and 1.3-1789 dated 2015-10-28
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- NAMESPACE | 1 + R/chebpol.R | 2 ++ build/vignette.rds |binary inst/doc/chebpol.pdf |binary 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.1 dated 2015-10-21 and 1.2 dated 2015-10-28
DESCRIPTION | 10 +-- MD5 | 23 ++++--- R/RcppExports.R | 4 + R/mgr.R |only R/mkr.R | 156 ++++++++++++++++++++++++---------------------------- R/wgr.R | 116 +++++++++++++++++++++++++++++--------- R/wgr2.R |only inst/CITATION | 2 man/bWGR.Rd | 4 - man/mgr.Rd |only man/mkr.Rd | 25 +++----- man/wgr.Rd | 12 ++-- man/wgr2.Rd |only src/KMUP2.cpp |only src/RcppExports.cpp | 19 ++++++ 15 files changed, 225 insertions(+), 146 deletions(-)
Title: Advanced Analysis of B Cell Receptor Repertoire Data
Description: Methods for advanced analysis of B cell receptor repertoire data, like gene usage, mutations, clones and diversity and their visualisation.
Author: Julia Bischof
Maintainer: Julia Bischof <Julia.Bischof@uksh.de>
Diff between bcRep versions 1.1 dated 2015-10-12 and 1.2.2 dated 2015-10-28
DESCRIPTION | 14 +- MD5 | 79 +++++++++---- NAMESPACE | 6 - R/clones.CDR3Length.R | 4 R/clones.R | 10 + R/clones.filterFunctionality.R |only R/clones.filterJunctionFrame.R |only R/clones.filterSize.R |only R/clones.giniIndex.R |only R/clones.shared.R | 10 + R/clones.shared.summary.R | 2 R/combineIMGT.R |only R/compare.aaDistribution.R |only R/compare.geneUsage.R |only R/compare.trueDiversity.R |only R/geneUsage.R | 34 +++-- R/plotAADistribution.R | 61 ++++++---- R/plotClonesCDR3Length.R | 6 - R/plotClonesCopyNumber.R | 9 + R/plotCompareAADistribution.R |only R/plotCompareGeneUsage.R |only R/plotCompareTrueDiversity.R |only R/plotGeneComb.R | 13 +- R/plotGeneUsage.R | 73 +++++++++--- R/plotTrueDiversity.R | 20 ++- R/sequences.functionality.R | 2 R/sequences.geneComb.R | 43 ++++++- R/sequences.junctionFrame.R | 2 build |only data/aaseqtab2.rda |only inst |only man/aaDistribution.Rd | 7 - man/aaseqtab.Rd | 2 man/aaseqtab2.Rd |only man/bcRep-package.Rd | 198 +++++++++++++++++++--------------- man/clones.Rd | 218 +++++++++++++++++++------------------- man/clones.filterFunctionality.Rd |only man/clones.filterJunctionFrame.Rd |only man/clones.filterSize.Rd |only man/clones.giniIndex.Rd |only man/clones.shared.Rd | 202 +++++++++++++++++------------------ man/combineIMGT.Rd |only man/compare.aaDistribution.Rd |only man/compare.geneUsage.Rd |only man/compare.trueDiversity.Rd |only man/geneUsage.Rd | 10 - man/mutationtab.Rd | 3 man/plotClonesCopyNumber.Rd | 7 - man/sequences.geneComb.Rd | 7 - man/trueDiversity.Rd | 2 vignettes |only 51 files changed, 607 insertions(+), 437 deletions(-)
Title: Diversification Rate Estimation and Fast Simulation of
Reconstructed Phylogenetic Trees under Tree-Wide
Time-Heterogeneous Birth-Death Processes Including
Mass-Extinction Events
Description: Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna and Michael R. May
Maintainer: Sebastian Hoehna <Sebastian.Hoehna@gmail.com>
Diff between TESS versions 2.0.0 dated 2015-06-18 and 2.1.0 dated 2015-10-28
TESS-2.0.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.pdf |only TESS-2.1.0/TESS/DESCRIPTION | 10 TESS-2.1.0/TESS/MD5 | 85 ++++-- TESS-2.1.0/TESS/NAMESPACE | 4 TESS-2.1.0/TESS/R/tess.analysis.R | 124 ---------- TESS-2.1.0/TESS/R/tess.plot.output.R | 4 TESS-2.1.0/TESS/R/tess.process.output.R | 2 TESS-2.1.0/TESS/R/tess.sim.age.R | 4 TESS-2.1.0/TESS/R/tess.sim.taxa.R | 29 +- TESS-2.1.0/TESS/R/tess.sim.taxa.age.R | 15 - TESS-2.1.0/TESS/build |only TESS-2.1.0/TESS/inst/doc |only TESS-2.1.0/TESS/man/TESS-package.Rd | 17 + TESS-2.1.0/TESS/man/cettiidae.Rd | 13 - TESS-2.1.0/TESS/man/conifers.Rd | 13 - TESS-2.1.0/TESS/man/mammalia.Rd | 13 - TESS-2.1.0/TESS/man/tess.PosteriorPrediction.Rd | 8 TESS-2.1.0/TESS/man/tess.analysis.Rd | 68 +++-- TESS-2.1.0/TESS/man/tess.likelihood.Rd | 33 ++ TESS-2.1.0/TESS/man/tess.likelihood.rateshift.Rd | 30 +- TESS-2.1.0/TESS/man/tess.mcmc.Rd | 17 + TESS-2.1.0/TESS/man/tess.nTaxa.expected.Rd | 8 TESS-2.1.0/TESS/man/tess.pathSampling.Rd | 15 - TESS-2.1.0/TESS/man/tess.plot.multichain.diagnostics.Rd | 26 +- TESS-2.1.0/TESS/man/tess.plot.output.Rd | 14 - TESS-2.1.0/TESS/man/tess.plot.singlechain.diagnostics.Rd | 14 - TESS-2.1.0/TESS/man/tess.process.output.Rd | 18 - TESS-2.1.0/TESS/man/tess.sim.age.Rd | 2 TESS-2.1.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.Rnw |only TESS-2.1.0/TESS/vignettes/ext_figures |only TESS-2.1.0/TESS/vignettes/literature.bib |only TESS-2.1.0/TESS/vignettes/results |only 32 files changed, 313 insertions(+), 273 deletions(-)
Title: Integrates R and Essentia
Description: Contains three functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.essentia' takes an Essentia script and captures the output csv data into R, where you can save the output to a dataframe or stream it directly into additional analysis. 'capture.essentia' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>
Diff between RESS versions 1.2 dated 2015-07-30 and 1.3 dated 2015-10-28
RESS-1.2/RESS/R/essquery.R |only RESS-1.2/RESS/R/readudb.R |only RESS-1.2/RESS/man/read.udb.Rd |only RESS-1.3/RESS/DESCRIPTION | 10 +++++----- RESS-1.3/RESS/MD5 | 16 +++++++++------- RESS-1.3/RESS/NAMESPACE | 1 + RESS-1.3/RESS/R/captureessentia.R |only RESS-1.3/RESS/R/essQuery.R |only RESS-1.3/RESS/R/readessentia.R |only RESS-1.3/RESS/man/RESS-package.Rd | 24 +++++++++++++++--------- RESS-1.3/RESS/man/capture.essentia.Rd |only RESS-1.3/RESS/man/essQuery.Rd | 8 ++++---- RESS-1.3/RESS/man/read.essentia.Rd |only 13 files changed, 34 insertions(+), 25 deletions(-)
More information about randomForest.ddR at CRAN
Permanent link
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://bit.ly/1Nwo4CB.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.qpcr versions 1.2 dated 2015-05-23 and 1.2.2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/HPDsummary.R | 2 +- R/getNormalizedData.R | 11 ++++++++--- R/mcmc.qpcr.R | 13 +++++++++---- R/mcmc.qpcr.lognormal.R | 13 +++++++++---- man/MCMC.qpcr-package.Rd | 6 +++--- man/getNormalizedData.Rd | 5 ++++- 9 files changed, 54 insertions(+), 30 deletions(-)
Title: Citations for 'Knitr' Markdown Files
Description: Provides the ability to create dynamic citations
in which the bibliographic information is pulled from the web rather
than having to be entered into a local database such as 'bibtex' ahead of
time. The package is primarily aimed at authoring in the R 'markdown'
format, and can provide outputs for web-based authoring such as linked
text for inline citations. Cite using a 'DOI', URL, or
'bibtex' file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between knitcitations versions 1.0.6 dated 2015-05-25 and 1.0.7 dated 2015-10-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ NEWS | 6 +++--- R/bibliography.R | 2 +- R/cleanbib.R | 3 ++- R/knitcitations.R | 1 + build/vignette.rds |binary inst/doc/tutorial.pdf |binary man/bibliography.Rd | 2 +- man/cleanbib.Rd | 10 +--------- tests/testthat/test_bib_metadata.R | 1 + tests/testthat/test_cite.R | 14 +++++++++++++- 13 files changed, 47 insertions(+), 38 deletions(-)
Title: Multiple Ordinal Tobit (MOT) Model
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between lmmot versions 0.1.2 dated 2014-12-16 and 0.1.3 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 +++- R/lmmot.R | 7 +++---- R/motFisher.R | 5 +++-- R/motGradient.R | 5 +++-- R/motHessian.R | 5 +++-- R/motLogLik.R | 6 ++++-- man/lmmot.Rd | 5 +++-- man/motFisher.Rd | 7 ++++--- man/motGradient.Rd | 7 ++++--- man/motHessian.Rd | 7 ++++--- man/motLogLik.Rd | 7 ++++--- man/print.lmmot.Rd | 3 ++- man/summary.lmmot.Rd | 3 ++- 15 files changed, 61 insertions(+), 48 deletions(-)
Title: Platform for EDGAR Filing Management
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR quarterly master index, daily master index, filings from SEC.org site and do sentiment analysis of 10-K statements.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.2 dated 2015-09-24 and 1.0.3 dated 2015-10-28
edgar-1.0.2/edgar/R/downlaod_master_index.R |only edgar-1.0.3/edgar/DESCRIPTION | 10 - edgar-1.0.3/edgar/MD5 | 24 +- edgar-1.0.3/edgar/R/download_filings.R | 2 edgar-1.0.3/edgar/R/download_master_index.R |only edgar-1.0.3/edgar/R/get_wordfrquency.R | 5 edgar-1.0.3/edgar/R/polarity_histogram.R | 87 +++++----- edgar-1.0.3/edgar/R/runEDGAR_shiny.R | 9 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/edgar_shiny_functions.R | 14 + edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/server.R | 10 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/ui.R | 2 edgar-1.0.3/edgar/man/RunEdgarShiny.Rd | 5 edgar-1.0.3/edgar/man/negwords.Rd | 8 edgar-1.0.3/edgar/man/poswords.Rd | 8 14 files changed, 99 insertions(+), 85 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy ``And'' Gate (DINA) cognitive diagnostic model parameters using the Gibbs sampler described by Culpepper (2015) DOI: 10.3102/1076998615595403.
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between dina versions 1.0 dated 2015-10-27 and 1.0.1 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/DINA_Gibbs.Rd | 18 +++++++++--------- man/DINAsim.Rd | 8 ++++---- man/dina-package.Rd | 2 +- src/DINAcpp101315.cpp | 12 ++++++------ 6 files changed, 28 insertions(+), 28 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included; uses Maarloes Maathius's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.7 dated 2015-07-20 and 1.2.8 dated 2015-10-27
icenReg-1.2.7/icenReg/src/icenReg_files/pavaAlgorithm.cpp |only icenReg-1.2.8/icenReg/DESCRIPTION | 17 icenReg-1.2.8/icenReg/MD5 | 45 icenReg-1.2.8/icenReg/NAMESPACE | 10 icenReg-1.2.8/icenReg/NEWS | 11 icenReg-1.2.8/icenReg/R/Utilities.R | 126 - icenReg-1.2.8/icenReg/R/optCliq.R |only icenReg-1.2.8/icenReg/R/referenceClasses.R |only icenReg-1.2.8/icenReg/R/user_functions.R | 85 - icenReg-1.2.8/icenReg/man/ICNPMLE.Rd |only icenReg-1.2.8/icenReg/man/diag_baseline.Rd | 7 icenReg-1.2.8/icenReg/man/diag_covar.Rd | 4 icenReg-1.2.8/icenReg/man/essIncData.Rd | 18 icenReg-1.2.8/icenReg/man/ic_par.Rd | 6 icenReg-1.2.8/icenReg/man/ic_sp.Rd | 29 icenReg-1.2.8/icenReg/man/optCliq.Rd |only icenReg-1.2.8/icenReg/man/simBVCen.Rd |only icenReg-1.2.8/icenReg/man/simIC_weib.Rd | 4 icenReg-1.2.8/icenReg/src/icenReg.cpp | 4 icenReg-1.2.8/icenReg/src/icenReg_files/basicUtilities.cpp | 269 +++ icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.h |only icenReg-1.2.8/icenReg/src/icenReg_files/experimentalCode.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.cpp | 174 ++ icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.h | 52 icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.cpp | 702 +++------- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.h | 145 +- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_gradDescent.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/myPAVAalgorithm.cpp |only 29 files changed, 1008 insertions(+), 700 deletions(-)
Title: CLUster Evaluation (CLUE)
Description: CLUE is an R package for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms.
Author: Pengyi Yang & Raja Jothi
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between ClueR versions 1.0 dated 2015-02-04 and 1.1 dated 2015-10-27
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NAMESPACE | 7 ++- R/runClue.R | 12 +++-- README.md | 113 ++++++++++++++++++++++++++++++++++++++++++++++++- man/ClueR-package.Rd | 8 ++- man/clustEnrichment.Rd | 2 man/clustOptimal.Rd | 2 man/enrichmentTest.Rd | 2 man/fuzzPlot.Rd | 2 man/runClue.Rd | 6 +- man/temporalSimu.Rd | 2 12 files changed, 152 insertions(+), 34 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
Liang et al hyper-g priors (JASA 2008) or mixtures of
g-priors in GLMS of Li and Clyde 2015. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models, and may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.5 dated 2015-09-10 and 1.0.6 dated 2015-10-27
BAS-1.0.5/BAS/R/coefpriors.R |only BAS-1.0.6/BAS/CHANGELOG | 11 + BAS-1.0.6/BAS/DESCRIPTION | 8 - BAS-1.0.6/BAS/INDEX |only BAS-1.0.6/BAS/MD5 | 70 ++++++---- BAS-1.0.6/BAS/NAMESPACE | 5 BAS-1.0.6/BAS/R/bas.R | 17 +- BAS-1.0.6/BAS/R/bas.gglm.R | 64 ++++----- BAS-1.0.6/BAS/R/betapriors.R |only BAS-1.0.6/BAS/R/coefficients.R | 4 BAS-1.0.6/BAS/R/predict.bma.R | 58 ++++++-- BAS-1.0.6/BAS/R/summary.bma.R | 5 BAS-1.0.6/BAS/man/EB.Rd |only BAS-1.0.6/BAS/man/TG-priors.Rd |only BAS-1.0.6/BAS/man/bas.Rd | 12 - BAS-1.0.6/BAS/man/bas.glm.Rd | 73 +++++++---- BAS-1.0.6/BAS/man/beta.prime.Rd |only BAS-1.0.6/BAS/man/cchpriors.Rd |only BAS-1.0.6/BAS/man/coefpriors.Rd | 2 BAS-1.0.6/BAS/man/hyper-g.Rd |only BAS-1.0.6/BAS/man/predict.basglm.Rd |only BAS-1.0.6/BAS/man/predict.bma.Rd | 28 ++-- BAS-1.0.6/BAS/man/robust.Rd |only BAS-1.0.6/BAS/man/summary.bma.Rd | 16 +- BAS-1.0.6/BAS/src/amcmc.c | 4 BAS-1.0.6/BAS/src/bas-glm.h | 4 BAS-1.0.6/BAS/src/bayesreg.c | 6 BAS-1.0.6/BAS/src/betapriorfamily.c |only BAS-1.0.6/BAS/src/betapriorfamily.h |only BAS-1.0.6/BAS/src/deterministic.c | 4 BAS-1.0.6/BAS/src/glm_deterministic.c | 21 +-- BAS-1.0.6/BAS/src/glm_lpy.c | 224 ++++++++++++++++++---------------- BAS-1.0.6/BAS/src/glm_mcmc.c | 71 ++-------- BAS-1.0.6/BAS/src/glm_mcmcbas.c | 30 ++-- BAS-1.0.6/BAS/src/glm_sampleworep.c | 44 ++++-- BAS-1.0.6/BAS/src/hypergeometric1F1.c | 69 ++++++---- BAS-1.0.6/BAS/src/mcmc.c | 4 BAS-1.0.6/BAS/src/mcmc_new.c | 4 BAS-1.0.6/BAS/src/mcmcbas.c | 4 BAS-1.0.6/BAS/src/posisearch.c | 4 BAS-1.0.6/BAS/src/sampleworep.c | 8 - BAS-1.0.6/BAS/src/sampleworep_new.c | 8 - 42 files changed, 490 insertions(+), 392 deletions(-)
Title: Helper Functions for Structural Equation Modelling in OpenMx
Description: Helper functions for making, running, and reporting SEM
and twin models in OpenMx.
If you are just starting, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 0.50 dated 2015-08-27 and 1.0.0 dated 2015-10-27
umx-0.50/umx/man/coef.MxModel.Rd |only umx-1.0.0/umx/DESCRIPTION | 13 umx-1.0.0/umx/INSTALL | 16 umx-1.0.0/umx/MD5 | 257 +++--- umx-1.0.0/umx/NAMESPACE | 28 umx-1.0.0/umx/NEWS | 15 umx-1.0.0/umx/R/build_run_modify.r | 956 +++++++++++++++++++---- umx-1.0.0/umx/R/deprecated.r | 44 - umx-1.0.0/umx/R/fit_and_reporting.r | 778 +++++++++++++++++- umx-1.0.0/umx/R/misc_and_utility.r | 223 ++++- umx-1.0.0/umx/R/xmu.r | 58 - umx-1.0.0/umx/README.md | 15 umx-1.0.0/umx/man/RMSEA.MxModel.Rd | 3 umx-1.0.0/umx/man/RMSEA.Rd | 1 umx-1.0.0/umx/man/RMSEA.summary.mxmodel.Rd | 3 umx-1.0.0/umx/man/confint.MxModel.Rd | 1 umx-1.0.0/umx/man/extractAIC.MxModel.Rd | 1 umx-1.0.0/umx/man/logLik.Rd | 1 umx-1.0.0/umx/man/plot.MxModel.Rd | 14 umx-1.0.0/umx/man/qm.Rd | 9 umx-1.0.0/umx/man/residuals.MxModel.Rd | 1 umx-1.0.0/umx/man/umx-deprecated.Rd | 30 umx-1.0.0/umx/man/umx.Rd | 58 - umx-1.0.0/umx/man/umxACE.Rd | 6 umx-1.0.0/umx/man/umxAdd1.Rd | 3 umx-1.0.0/umx/man/umxCI.Rd | 1 umx-1.0.0/umx/man/umxCI_boot.Rd | 1 umx-1.0.0/umx/man/umxCP.Rd |only umx-1.0.0/umx/man/umxCompare.Rd | 1 umx-1.0.0/umx/man/umxCovData.Rd | 13 umx-1.0.0/umx/man/umxDiagnose.Rd | 12 umx-1.0.0/umx/man/umxDrop1.Rd | 3 umx-1.0.0/umx/man/umxEFA.Rd | 3 umx-1.0.0/umx/man/umxEquate.Rd | 3 umx-1.0.0/umx/man/umxEval.Rd | 14 umx-1.0.0/umx/man/umxExpCov.Rd | 1 umx-1.0.0/umx/man/umxExpMeans.Rd | 1 umx-1.0.0/umx/man/umxFitIndices.Rd | 1 umx-1.0.0/umx/man/umxFixAll.Rd | 3 umx-1.0.0/umx/man/umxGetParameters.Rd | 3 umx-1.0.0/umx/man/umxGxE.Rd |only umx-1.0.0/umx/man/umxHetCor.Rd | 3 umx-1.0.0/umx/man/umxIP.Rd |only umx-1.0.0/umx/man/umxJiggle.Rd | 14 umx-1.0.0/umx/man/umxLabel.Rd | 4 umx-1.0.0/umx/man/umxLatent.Rd | 4 umx-1.0.0/umx/man/umxMI.Rd | 3 umx-1.0.0/umx/man/umxPadAndPruneForDefVars.Rd | 4 umx-1.0.0/umx/man/umxPath.Rd | 91 +- umx-1.0.0/umx/man/umxPlotACE.Rd | 1 umx-1.0.0/umx/man/umxPlotCP.Rd |only umx-1.0.0/umx/man/umxPlotGxE.Rd |only umx-1.0.0/umx/man/umxPlotIP.Rd |only umx-1.0.0/umx/man/umxRAM.Rd | 30 umx-1.0.0/umx/man/umxReRun.Rd | 4 umx-1.0.0/umx/man/umxReduce.Rd | 5 umx-1.0.0/umx/man/umxRun.Rd | 4 umx-1.0.0/umx/man/umxSetParameters.Rd | 3 umx-1.0.0/umx/man/umxStandardizeACE.Rd | 3 umx-1.0.0/umx/man/umxStandardizeModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.MxModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.Rd | 14 umx-1.0.0/umx/man/umxSummaryCP.Rd |only umx-1.0.0/umx/man/umxSummaryGxE.Rd |only umx-1.0.0/umx/man/umxSummaryIP.Rd |only umx-1.0.0/umx/man/umxThresholdMatrix.Rd | 4 umx-1.0.0/umx/man/umxUnexplainedCausalNexus.Rd | 3 umx-1.0.0/umx/man/umxValues.Rd | 4 umx-1.0.0/umx/man/umx_APA_CI.Rd | 9 umx-1.0.0/umx/man/umx_APA_pval.Rd | 25 umx-1.0.0/umx/man/umx_RAM_ordinal_objective.Rd | 4 umx-1.0.0/umx/man/umx_add_variances.Rd | 16 umx-1.0.0/umx/man/umx_aggregate.Rd | 9 umx-1.0.0/umx/man/umx_apply.Rd | 14 umx-1.0.0/umx/man/umx_as_numeric.Rd | 3 umx-1.0.0/umx/man/umx_check.Rd | 14 umx-1.0.0/umx/man/umx_check_OS.Rd | 32 umx-1.0.0/umx/man/umx_check_model.Rd | 14 umx-1.0.0/umx/man/umx_check_multi_core.Rd | 14 umx-1.0.0/umx/man/umx_cont_2_ordinal.Rd | 3 umx-1.0.0/umx/man/umx_cov2raw.Rd | 3 umx-1.0.0/umx/man/umx_cov_diag.Rd | 4 umx-1.0.0/umx/man/umx_default_option.Rd | 15 umx-1.0.0/umx/man/umx_drop_ok.Rd | 1 umx-1.0.0/umx/man/umx_explode.Rd | 39 umx-1.0.0/umx/man/umx_find_object.Rd | 9 umx-1.0.0/umx/man/umx_fix_first_loadings.Rd | 4 umx-1.0.0/umx/man/umx_fix_latents.Rd | 4 umx-1.0.0/umx/man/umx_get_CI_as_APA_string.Rd | 14 umx-1.0.0/umx/man/umx_get_bracket_addresses.Rd | 14 umx-1.0.0/umx/man/umx_get_checkpoint.Rd | 18 umx-1.0.0/umx/man/umx_get_cores.Rd | 14 umx-1.0.0/umx/man/umx_get_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_grep.Rd | 7 umx-1.0.0/umx/man/umx_has_CIs.Rd | 14 umx-1.0.0/umx/man/umx_has_been_run.Rd | 14 umx-1.0.0/umx/man/umx_has_means.Rd | 14 umx-1.0.0/umx/man/umx_has_square_brackets.Rd | 14 umx-1.0.0/umx/man/umx_is_MxMatrix.Rd | 14 umx-1.0.0/umx/man/umx_is_MxModel.Rd | 14 umx-1.0.0/umx/man/umx_is_RAM.Rd | 14 umx-1.0.0/umx/man/umx_is_cov.Rd | 14 umx-1.0.0/umx/man/umx_is_endogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_exogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_ordered.Rd | 14 umx-1.0.0/umx/man/umx_lower2full.Rd | 26 umx-1.0.0/umx/man/umx_make_bin_cont_pair_data.Rd | 3 umx-1.0.0/umx/man/umx_merge_CIs.Rd | 3 umx-1.0.0/umx/man/umx_msg.Rd | 40 umx-1.0.0/umx/man/umx_names.Rd | 40 umx-1.0.0/umx/man/umx_object_as_str.Rd | 11 umx-1.0.0/umx/man/umx_paste_names.Rd | 38 umx-1.0.0/umx/man/umx_pb_note.Rd | 7 umx-1.0.0/umx/man/umx_print.Rd | 49 - umx-1.0.0/umx/man/umx_read_lower.Rd | 3 umx-1.0.0/umx/man/umx_rename.Rd | 44 - umx-1.0.0/umx/man/umx_reorder.Rd | 12 umx-1.0.0/umx/man/umx_residualize.Rd | 3 umx-1.0.0/umx/man/umx_rot.Rd | 44 - umx-1.0.0/umx/man/umx_round.Rd | 3 umx-1.0.0/umx/man/umx_scale.Rd | 3 umx-1.0.0/umx/man/umx_scale_wide_twin_data.Rd | 3 umx-1.0.0/umx/man/umx_set_checkpoint.Rd | 14 umx-1.0.0/umx/man/umx_set_cores.Rd | 15 umx-1.0.0/umx/man/umx_set_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_show.Rd | 13 umx-1.0.0/umx/man/umx_standardize_IP.Rd |only umx-1.0.0/umx/man/umx_string_to_algebra.Rd | 15 umx-1.0.0/umx/man/umx_swap_a_block.Rd | 3 umx-1.0.0/umx/man/umx_time.Rd | 9 umx-1.0.0/umx/man/umx_trim.Rd | 39 umx-1.0.0/umx/man/xmuLabel_Matrix.Rd | 4 umx-1.0.0/umx/man/xmu_dot_make_paths.Rd | 2 umx-1.0.0/umx/man/xmu_dot_make_residuals.Rd | 13 umx-1.0.0/umx/tests/testthat |only umx-1.0.0/umx/tests/testthat.R |only 136 files changed, 2508 insertions(+), 1230 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future. Web applications are provided
(via 'shiny') for the implemented methods to help in designing and deploying the
computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 0.25.3 dated 2015-08-01 and 0.25.4 dated 2015-10-27
distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/STCoxMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.R |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/SVDMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite3Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.R |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.rds |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full-new.Rout |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full.Rout |only distcomp-0.25.3/distcomp/inst/webApps/setupSlaveApp |only distcomp-0.25.3/distcomp/man/coxMaster.Rd |only distcomp-0.25.3/distcomp/man/coxSlave.Rd |only distcomp-0.25.3/distcomp/man/makeSlave.Rd |only distcomp-0.25.3/distcomp/man/setupSlave.Rd |only distcomp-0.25.3/distcomp/man/svdMaster.Rd |only distcomp-0.25.3/distcomp/man/svdSlave.Rd |only distcomp-0.25.4/distcomp/DESCRIPTION | 6 distcomp-0.25.4/distcomp/MD5 | 97 distcomp-0.25.4/distcomp/NAMESPACE | 8 distcomp-0.25.4/distcomp/R/coxstuff.R | 16 distcomp-0.25.4/distcomp/R/distcomp.R | 72 distcomp-0.25.4/distcomp/R/svdstuff.R | 25 distcomp-0.25.4/distcomp/README.md | 15 distcomp-0.25.4/distcomp/inst/doc/examples.html | 60 distcomp-0.25.4/distcomp/inst/doc/examples.pdf |binary distcomp-0.25.4/distcomp/inst/doc_src/examples.Rmd | 10 distcomp-0.25.4/distcomp/inst/doc_src/examples.md | 64 distcomp-0.25.4/distcomp/inst/ex/README.Rmd | 70 distcomp-0.25.4/distcomp/inst/ex/README.html | 82 distcomp-0.25.4/distcomp/inst/ex/README.md | 70 distcomp-0.25.4/distcomp/inst/ex/Rprofile |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.R |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxTest.rds |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.R |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDTestDefn.rds |only distcomp-0.25.4/distcomp/inst/ex/svd-example.R | 3 distcomp-0.25.4/distcomp/inst/ex/svd-example.Rout | 5051 +++++++++- distcomp-0.25.4/distcomp/inst/ex/uis-example.R | 2 distcomp-0.25.4/distcomp/inst/ex/uis-example.Rout | 38 distcomp-0.25.4/distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R | 4 distcomp-0.25.4/distcomp/inst/webApps/setupWorkerApp |only distcomp-0.25.4/distcomp/man/CoxMaster.Rd |only distcomp-0.25.4/distcomp/man/CoxWorker.Rd |only distcomp-0.25.4/distcomp/man/SVDMaster.Rd |only distcomp-0.25.4/distcomp/man/SVDWorker.Rd |only distcomp-0.25.4/distcomp/man/availableComputations.Rd | 8 distcomp-0.25.4/distcomp/man/distcomp-internal.Rd | 12 distcomp-0.25.4/distcomp/man/makeWorker.Rd |only distcomp-0.25.4/distcomp/man/runDistcompApp.Rd | 8 distcomp-0.25.4/distcomp/man/saveNewComputation.Rd | 2 distcomp-0.25.4/distcomp/man/setupWorker.Rd |only distcomp-0.25.4/distcomp/man/writeCode.Rd | 2 65 files changed, 5380 insertions(+), 345 deletions(-)
Title: Continuous Time Autoregressive Models
Description: Functions to Fit Continuous Time Autoregressive Models with the Kalman Filter.
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port by Zhu Wang with contribution from John Nash, Netlib and NAG authors
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between cts versions 1.0-19 dated 2014-02-26 and 1.0-20 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- build/vignette.rds |binary inst/doc/kf.pdf |binary 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Including L_2 boosting with componentwise linear least squares, componentwise smoothing splines, P-splines, regression trees and boosted MARS. Other high-dimensional tools include elastic net and MARS.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bujar versions 0.1-4 dated 2014-06-24 and 0.1-5 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 7 +++++++ NEWS | 5 +++++ 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.6.0 dated 2015-02-24 and 1.6.1 dated 2015-10-27
aroma.cn-1.6.0/aroma.cn/R/makeSmoothSplinePredict.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/DESCRIPTION | 21 +- aroma.cn-1.6.1/aroma.cn/MD5 | 16 - aroma.cn-1.6.1/aroma.cn/NAMESPACE | 14 + aroma.cn-1.6.1/aroma.cn/NEWS | 11 + aroma.cn-1.6.1/aroma.cn/R/021.dynamic_imports.R | 100 +++++----- aroma.cn-1.6.1/aroma.cn/R/999.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/R/CartesianSnpData.R | 4 aroma.cn-1.6.1/aroma.cn/R/PeaksAndValleys.EXTS.R | 12 - aroma.cn-1.6.1/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 6 10 files changed, 96 insertions(+), 88 deletions(-)
Title: Utility Functions for Web Applications
Description: Utility functions for developing web applications. Includes parsers
for application/x-www-form-urlencoded as well as multipart/form-data
and examples of using the parser with either httpuv or rhttpd.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between webutils versions 0.3 dated 2015-01-24 and 0.4 dated 2015-10-27
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/demo_httpuv.R | 2 ++ man/demo_httpuv.Rd | 3 ++- man/demo_rhttpd.Rd | 3 ++- man/parse_http.Rd | 3 ++- man/parse_multipart.Rd | 3 ++- man/parse_query.Rd | 3 ++- 9 files changed, 31 insertions(+), 19 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: Functions for estimating split-duration regression models and various associated generic function methods.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel Hill [aut],
Nils Metternich [aut],
Shahryar Minhas [aut],
Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.13.1 dated 2015-07-09 and 0.14.0 dated 2015-10-27
spduration-0.13.1/spduration/R/attemptDate.R |only spduration-0.13.1/spduration/R/forecast.default.R |only spduration-0.13.1/spduration/R/forecast.spdur.R |only spduration-0.13.1/spduration/R/model.coups.R |only spduration-0.13.1/spduration/R/plot_hazard.r |only spduration-0.13.1/spduration/man/attemptDate.Rd |only spduration-0.13.1/spduration/man/loglog_hazard.Rd |only spduration-0.13.1/spduration/man/weibull_hazard.Rd |only spduration-0.14.0/spduration/DESCRIPTION | 11 spduration-0.14.0/spduration/MD5 | 93 +++--- spduration-0.14.0/spduration/NAMESPACE | 4 spduration-0.14.0/spduration/R/RcppExports.R | 8 spduration-0.14.0/spduration/R/add_duration.R | 89 ------ spduration-0.14.0/spduration/R/attempt_date.R |only spduration-0.14.0/spduration/R/data-docs.R |only spduration-0.14.0/spduration/R/forecast.R | 193 +++++++++++++ spduration-0.14.0/spduration/R/panel_lag.R | 25 - spduration-0.14.0/spduration/R/plot.spdur.R | 264 +++++++++++++------ spduration-0.14.0/spduration/R/predict.spdur.R | 28 -- spduration-0.14.0/spduration/R/spdur.R | 7 spduration-0.14.0/spduration/R/spduration-package.R | 38 -- spduration-0.14.0/spduration/R/sploglog.R | 4 spduration-0.14.0/spduration/R/spweibull.R | 4 spduration-0.14.0/spduration/R/summary.spdur.R | 9 spduration-0.14.0/spduration/README.md | 41 -- spduration-0.14.0/spduration/data/bscoup.rda |only spduration-0.14.0/spduration/man/add_duration.Rd | 3 spduration-0.14.0/spduration/man/attempt_date.Rd |only spduration-0.14.0/spduration/man/bscoup.Rd |only spduration-0.14.0/spduration/man/coups.Rd | 2 spduration-0.14.0/spduration/man/forecast.Rd | 2 spduration-0.14.0/spduration/man/forecast.default.Rd | 2 spduration-0.14.0/spduration/man/forecast.spdur.Rd | 2 spduration-0.14.0/spduration/man/hazard.Rd | 7 spduration-0.14.0/spduration/man/loglog.Rd | 1 spduration-0.14.0/spduration/man/loglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/model.coups.Rd | 2 spduration-0.14.0/spduration/man/plot.spdur.Rd | 21 - spduration-0.14.0/spduration/man/plot_hazard.Rd |only spduration-0.14.0/spduration/man/plot_hazard1.Rd | 16 - spduration-0.14.0/spduration/man/plot_hazard2.Rd | 20 - spduration-0.14.0/spduration/man/spdur.Rd | 2 spduration-0.14.0/spduration/man/sploglog.Rd | 1 spduration-0.14.0/spduration/man/sploglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweib_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweibull.Rd | 1 spduration-0.14.0/spduration/man/weib_lnl.Rd | 1 spduration-0.14.0/spduration/man/weibull.Rd | 1 spduration-0.14.0/spduration/src/loglog_lnl.cpp | 3 spduration-0.14.0/spduration/src/sploglog_lnl.cpp | 2 spduration-0.14.0/spduration/src/spweib_lnl.cpp | 2 spduration-0.14.0/spduration/src/weib_lnl.cpp | 2 spduration-0.14.0/spduration/tests |only 53 files changed, 540 insertions(+), 374 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.6 dated 2015-09-05 and 0.10.7 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- configure | 17 +++++++++-------- 3 files changed, 17 insertions(+), 16 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.4-0 dated 2015-05-04 and 3.5-0 dated 2015-10-27
ncvreg-3.4-0/ncvreg/inst/tests/test.R |only ncvreg-3.5-0/ncvreg/DESCRIPTION | 8 +- ncvreg-3.5-0/ncvreg/MD5 | 43 +++++------ ncvreg-3.5-0/ncvreg/NAMESPACE | 10 +- ncvreg-3.5-0/ncvreg/NEWS | 19 ++++ ncvreg-3.5-0/ncvreg/R/auc.R |only ncvreg-3.5-0/ncvreg/R/convexMin.R | 23 ++--- ncvreg-3.5-0/ncvreg/R/cv.ncvreg.R | 34 ++++---- ncvreg-3.5-0/ncvreg/R/cv.ncvsurv.R | 116 ++++++++++++++++++------------ ncvreg-3.5-0/ncvreg/R/loss.R | 4 - ncvreg-3.5-0/ncvreg/R/ncvreg.R | 31 ++++---- ncvreg-3.5-0/ncvreg/R/ncvsurv.R | 22 ++--- ncvreg-3.5-0/ncvreg/R/plot.cv.ncvreg.R | 2 ncvreg-3.5-0/ncvreg/R/setupLambda.R | 6 - ncvreg-3.5-0/ncvreg/R/setupLambdaCox.R | 10 +- ncvreg-3.5-0/ncvreg/inst/tests/auc.R |only ncvreg-3.5-0/ncvreg/inst/tests/ncvreg.R |only ncvreg-3.5-0/ncvreg/inst/tests/parallel.R | 34 ++++++++ ncvreg-3.5-0/ncvreg/inst/tests/surv.R | 13 +++ ncvreg-3.5-0/ncvreg/man/auc.Rd |only ncvreg-3.5-0/ncvreg/man/cv.ncvreg.Rd | 14 +++ ncvreg-3.5-0/ncvreg/man/cv.ncvsurv.Rd | 43 ++++++++--- ncvreg-3.5-0/ncvreg/man/ncvreg-package.Rd | 4 - ncvreg-3.5-0/ncvreg/man/ncvreg.Rd | 2 ncvreg-3.5-0/ncvreg/src/cox-dh.c | 41 +++++++--- 25 files changed, 310 insertions(+), 169 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-5 dated 2015-10-20 and 0.1-6 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/gimme.R | 18 ++++++++++-------- 3 files changed, 17 insertions(+), 15 deletions(-)
Title: Create a Simple Web API for your R Functions
Description: A set of convenience functions to build simple APIs.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between jug versions 0.1.0 dated 2015-10-27 and 0.1.1 dated 2015-10-27
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/middleware_core.R | 6 +++--- R/middleware_error.R | 1 + R/response.R | 4 ++++ build/vignette.rds |binary inst/doc/jug.Rmd | 4 ++-- inst/doc/jug.html | 2 +- man/Error.Rd | 2 +- man/Middleware.Rd | 2 +- man/MiddlewareHandler.Rd | 2 +- man/RawTestRequest.Rd | 2 +- man/Request.Rd | 2 +- man/Response.Rd | 2 +- vignettes/jug.Rmd | 4 ++-- 15 files changed, 36 insertions(+), 31 deletions(-)
Title: Graph Edge Computations for Spatial Point Patterns
Description: Graphs (or networks) and graph component
calculations for spatial locations in *D.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatgraphs versions 2.62 dated 2012-09-26 and 3.0 dated 2015-10-27
spatgraphs-2.62/spatgraphs/R/First.R |only spatgraphs-2.62/spatgraphs/R/adjacency.R |only spatgraphs-2.62/spatgraphs/R/class.R |only spatgraphs-2.62/spatgraphs/R/clip.R |only spatgraphs-2.62/spatgraphs/R/clustering.R |only spatgraphs-2.62/spatgraphs/R/edgelengths.R |only spatgraphs-2.62/spatgraphs/R/mstoperations.R |only spatgraphs-2.62/spatgraphs/R/others.R |only spatgraphs-2.62/spatgraphs/R/plot.R |only spatgraphs-2.62/spatgraphs/R/runif3d.R |only spatgraphs-2.62/spatgraphs/R/spectral.R |only spatgraphs-2.62/spatgraphs/R/summary.R |only spatgraphs-2.62/spatgraphs/R/weights.R |only spatgraphs-2.62/spatgraphs/ToAdd.TXT0 |only spatgraphs-2.62/spatgraphs/change.log |only spatgraphs-2.62/spatgraphs/man/spatgraphs-clip.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-cut.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-legacy.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-mailer.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-other.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-package.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-plot.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-print.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-runif3d.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2dxf.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2igraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sgc.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shake.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shortestPath.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatcluster.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatgraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spectral.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-weight.Rd |only spatgraphs-2.62/spatgraphs/src/Point.cpp |only spatgraphs-2.62/spatgraphs/src/Point.h |only spatgraphs-2.62/spatgraphs/src/Rextras.cpp |only spatgraphs-2.62/spatgraphs/src/Rextras.h |only spatgraphs-2.62/spatgraphs/src/clustering.cpp |only spatgraphs-2.62/spatgraphs/src/cutprune.cpp |only spatgraphs-2.62/spatgraphs/src/dists.cpp |only spatgraphs-2.62/spatgraphs/src/dists.h |only spatgraphs-2.62/spatgraphs/src/rgraph.cpp |only spatgraphs-3.0/spatgraphs/DESCRIPTION | 22 spatgraphs-3.0/spatgraphs/MD5 | 119 - spatgraphs-3.0/spatgraphs/NAMESPACE | 57 spatgraphs-3.0/spatgraphs/NEWS |only spatgraphs-3.0/spatgraphs/R/RcppExports.R |only spatgraphs-3.0/spatgraphs/R/adjacency_matrix.R |only spatgraphs-3.0/spatgraphs/R/class_sg.R |only spatgraphs-3.0/spatgraphs/R/class_sgc.R |only spatgraphs-3.0/spatgraphs/R/constants.R |only spatgraphs-3.0/spatgraphs/R/cut_sg.R |only spatgraphs-3.0/spatgraphs/R/edgeLengths.R |only spatgraphs-3.0/spatgraphs/R/parse_input_coordinates.R |only spatgraphs-3.0/spatgraphs/R/plot_sg.R |only spatgraphs-3.0/spatgraphs/R/plot_sgc.R |only spatgraphs-3.0/spatgraphs/R/prune_sg.R |only spatgraphs-3.0/spatgraphs/R/set_weights.R |only spatgraphs-3.0/spatgraphs/R/sg2dxf.R | 100 - spatgraphs-3.0/spatgraphs/R/sg2igraph.R | 96 - spatgraphs-3.0/spatgraphs/R/shortestPath.R | 157 +- spatgraphs-3.0/spatgraphs/R/spatcluster.R |only spatgraphs-3.0/spatgraphs/R/spatgraph.R | 245 --- spatgraphs-3.0/spatgraphs/R/spectral_sg.R |only spatgraphs-3.0/spatgraphs/R/verify_parameters.R |only spatgraphs-3.0/spatgraphs/man/SG_GRAPH_PARAMETERS.Rd |only spatgraphs-3.0/spatgraphs/man/adj2sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/cut.sg.Rd |only spatgraphs-3.0/spatgraphs/man/edgeLengths.Rd |only spatgraphs-3.0/spatgraphs/man/is_sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgspectral.Rd |only spatgraphs-3.0/spatgraphs/man/plot3.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/prune.sg.Rd |only spatgraphs-3.0/spatgraphs/man/sg2adj.Rd |only spatgraphs-3.0/spatgraphs/man/sg2dxf.Rd |only spatgraphs-3.0/spatgraphs/man/sg2igraph.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sparse.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sym.Rd |only spatgraphs-3.0/spatgraphs/man/sg2wadj.Rd |only spatgraphs-3.0/spatgraphs/man/sg_parse_coordinates.Rd |only spatgraphs-3.0/spatgraphs/man/sg_verify_parameters.Rd |only spatgraphs-3.0/spatgraphs/man/shortestPath.Rd |only spatgraphs-3.0/spatgraphs/man/sparse2sg.Rd |only spatgraphs-3.0/spatgraphs/man/spatcluster.Rd |only spatgraphs-3.0/spatgraphs/man/spatgraph.Rd |only spatgraphs-3.0/spatgraphs/man/spectral.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/t.sg.Rd |only spatgraphs-3.0/spatgraphs/man/t.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/weight.sg.Rd |only spatgraphs-3.0/spatgraphs/src/Graph.cpp | 1096 ++++---------- spatgraphs-3.0/spatgraphs/src/Graph.h | 97 - spatgraphs-3.0/spatgraphs/src/Pp.cpp | 298 --- spatgraphs-3.0/spatgraphs/src/Pp.h | 107 - spatgraphs-3.0/spatgraphs/src/RcppExports.cpp |only spatgraphs-3.0/spatgraphs/src/cut.cpp |only spatgraphs-3.0/spatgraphs/src/prune.cpp |only spatgraphs-3.0/spatgraphs/src/spatcluster.cpp |only spatgraphs-3.0/spatgraphs/src/spatgraph.cpp |only 110 files changed, 842 insertions(+), 1552 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.21 dated 2015-03-30 and 1.4.22 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 10 ++++++++++ R/elda.R | 4 ++-- inst/NEWS | 5 +++++ 5 files changed, 26 insertions(+), 10 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names, default values and
(if so desired) ranges or sets of allowed option values that will be
automatically checked. Settings can then be retrieved, altered and reset
to defaults with ease. For R programmers and package developers it offers
cloning and merging functionality which allows for conveniently defining
global and local options, possibly in a multilevel options hierarchy. See
the package vignette for some examples concerning functions, S4 classes,
and reference classes. There are convenience functions to reset par()
and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.2 dated 2015-06-01 and 0.2.4 dated 2015-10-27
DESCRIPTION | 26 ++++++------ MD5 | 23 +++++----- NAMESPACE | 2 NEWS | 4 + R/options.R | 91 +++++++++++++++++++++++++++++++++++++++++-- inst/doc/settings.R | 14 ++++++ inst/doc/settings.Rmd | 31 ++++++++++++++ inst/doc/settings.html | 32 ++++++++++++++- man/clone_and_merge.Rd | 15 +++++++ man/inlist.Rd |only man/options_manager.Rd | 16 +++++++ tests/testthat/testOptions.R | 20 +++++++++ vignettes/settings.Rmd | 31 ++++++++++++++ 13 files changed, 276 insertions(+), 29 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.1-5 dated 2015-05-11 and 1.2-0 dated 2015-10-27
DESCRIPTION | 10 +- MD5 | 30 ++++-- NAMESPACE | 9 + R/g.analyse.R | 1 R/g.create.sp.mat.R |only R/g.getbout.R |only R/g.loadlog.R |only R/g.part3.R |only R/g.part4.R |only R/g.plot5.R |only R/g.report.part2.R | 6 - R/g.report.part4.R |only R/g.shell.GGIR.R | 95 ++++++++++++++++++-- R/g.sib.det.R |only R/g.sib.plot.R |only R/g.sib.sum.R |only data/datalist | 6 - inst/NEWS.Rd | 192 +++++++++++++++++++++-------------------- man/GGIR-package.Rd | 238 ++++++++++++++++++++++++++-------------------------- man/g.part3.Rd |only man/g.part4.Rd |only man/g.shell.GGIR.Rd | 124 ++++++++++++++++++++++----- 22 files changed, 450 insertions(+), 261 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.7 dated 2015-09-21 and 2.1.7-1 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- NEWS | 9 ++++- R/advanced.procD.lm.r | 36 +++++++++++----------- R/bilat.symmetry.r | 23 ++++---------- R/geomorph.support.code.r | 75 ++++++++++++++++++++++++++++++---------------- R/gpagen.r | 2 - R/morphol.disparity.r | 7 ++-- R/plotAllometry.r | 50 ++++++++++++++---------------- R/procD.lm.r | 2 - R/procD.pgls.r | 22 +++++++++---- R/readland.nts.r | 6 ++- R/trajectory.analysis.r | 5 +-- R/two.b.pls.r | 17 +++++----- R/warpRefMesh.r | 15 ++++----- README.md |only man/gpagen.Rd | 2 - man/plotAllometry.Rd | 8 ++-- man/procD.pgls.Rd | 4 +- man/two.b.pls.Rd | 11 ++++-- src/geomorph.c | 7 +++- 21 files changed, 195 insertions(+), 153 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.1 dated 2015-09-01 and 1.7.2 dated 2015-10-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/build.dist.struct.R | 3 +-- R/rcbalance-internal.R | 6 ++---- R/rcbalance.R | 6 ++++-- man/dist2net.Rd | 6 +++++- 6 files changed, 21 insertions(+), 18 deletions(-)
Title: Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information
Description: Convert the Odds Ratio to the Relative Risk in Cohort Studies with Partial Data Information.
Author: Zhu Wang
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between orsk versions 1.0-1 dated 2013-10-10 and 1.0-2 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 ++- build/vignette.rds |binary 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between mclust versions 5.0.2 dated 2015-07-08 and 5.1 dated 2015-10-27
DESCRIPTION | 10 MD5 | 68 ++--- R/bootstrap.R | 4 R/densityMclust.R | 48 ++- R/mclust.R | 34 ++ R/mclustaddson.R | 82 +++--- R/mclustda.R | 148 +++++------ R/mclustdr.R | 12 R/util.R | 5 build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/NEWS | 6 inst/doc/mclust.Rmd | 1 inst/doc/mclust.html | 410 ++++++++++++++++---------------- man/Mclust.Rd | 2 man/MclustDA.Rd | 4 man/bic.Rd | 2 man/clustCombi.Rd | 2 man/diabetes.Rd | 2 man/emControl.Rd | 15 - man/estep.Rd | 2 man/mclustModel.Rd | 4 man/mvn.Rd | 2 man/mvnX.Rd | 2 man/plot.densityMclust.Rd | 36 +- man/summary.mclustBIC.Rd | 4 src/mclustaddson.f | 240 ++++++++++++++++-- vignettes/mclust.Rmd | 1 35 files changed, 698 insertions(+), 448 deletions(-)
Title: Methods that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.14.2 dated 2015-06-24 and 0.15.0 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 64 +++++++++++++++++++---------------- NAMESPACE | 4 ++ NEWS | 22 ++++++++++-- R/rowMads.R | 8 ++-- R/weightedMad.R | 13 ++++--- R/weightedMean.R | 12 +++++- R/weightedMedian.R | 8 +++- R/weightedVar.R | 45 ++++++++++++++++-------- build/vignette.rds |binary inst/doc/matrixStats-methods.html | 4 +- man/matrixStats-package.Rd | 2 - man/weightedMad.Rd | 2 - man/weightedMean.Rd | 2 - man/weightedMedian.Rd | 3 - man/weightedVar.Rd | 11 +++++- src/allocMatrix2.c | 2 - src/binMeans-BINBY-template.h | 3 + src/diff2_TYPE-template.h | 2 - src/logSumExp_internal.c | 36 ++++++++++++------- src/meanOver_TYPE-template.h | 22 +++++++++--- src/productExpSumLog_TYPE-template.h | 7 +++ src/rowDiffs_TYPE-template.h | 2 - src/sumOver_TYPE-template.h | 10 ++++- src/weightedMean_TYPE-template.h | 13 ++++++- src/weightedMedian_TYPE-template.h | 8 ---- tests/reports |only tests/rowWeightedVars.R | 7 ++- tests/weightedMedian.R | 13 +++++++ tests/weightedVar.R |only tests/weightedVar_etal.R | 3 - 31 files changed, 228 insertions(+), 108 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 2.0 dated 2015-09-16 and 2.1 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 15 ++++++++++++++- R/hdnom.calibrate.R | 2 +- R/hdnom.models.R | 47 ++++++++++++++++++++++++++++++++++++++++++----- README.md | 2 +- TODO | 2 +- inst/doc/hdnom.Rmd | 4 ++-- inst/doc/hdnom.html | 12 ++++++------ man/hdcox.mcp.Rd | 10 +++++----- man/hdnom.calibrate.Rd | 2 +- vignettes/hdnom.Rmd | 4 ++-- 12 files changed, 91 insertions(+), 41 deletions(-)
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between calmate versions 0.12.0 dated 2015-02-23 and 0.12.1 dated 2015-10-27
DESCRIPTION | 14 ++++---- MD5 | 10 +++--- NAMESPACE | 3 + NEWS | 6 +++ tests/calmateByTotalAndFracB.R | 68 ++++++++++++++++++++--------------------- tests/thetaAB2TotalAndFracB.R | 28 ++++++++-------- 6 files changed, 68 insertions(+), 61 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between ACNE versions 0.8.0 dated 2015-02-23 and 0.8.1 dated 2015-10-27
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 6 ++++++ NEWS | 4 ++++ man/ACNE-package.Rd | 2 +- 5 files changed, 25 insertions(+), 14 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.1 dated 2015-10-12 and 0.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/NlcOptim.R | 6 +++++- man/NlcOptim.Rd | 8 +++++++- 4 files changed, 19 insertions(+), 9 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.37 dated 2015-08-03 and 1.38 dated 2015-10-26
DESCRIPTION | 10 +-- MD5 | 22 ++++--- NAMESPACE | 6 +- R/GEEaSPU.R |only R/aSPUs.R | 21 ++++--- R/aSPUsPath.r | 4 + R/aSPUsim1.R | 6 +- R/aSPUsim2.R | 7 ++ R/util.R | 157 +++++++++++++++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary man/GEEaSPU.Rd |only man/aSPUs.Rd | 20 ++++-- man/aSPUsPath.Rd | 4 + 13 files changed, 223 insertions(+), 34 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-13 dated 2015-09-28 and 0.3-14 dated 2015-10-26
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/ChangeLog | 14 ++++++++++++++ inst/SVN_VERSION | 2 +- man/topo-bin-gIntersection.Rd | 26 ++++++++++++++++++++++++++ src/rgeos_topology_binary.c | 8 ++++---- 7 files changed, 69 insertions(+), 15 deletions(-)
Title: D3 Javascript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.1.1 dated 2015-06-30 and 0.3 dated 2015-10-26
scatterD3-0.1.1/scatterD3/inst/htmlwidgets/lib/d3-3.5.5.min.js |only scatterD3-0.3/scatterD3/DESCRIPTION | 14 scatterD3-0.3/scatterD3/MD5 | 33 scatterD3-0.3/scatterD3/NAMESPACE | 2 scatterD3-0.3/scatterD3/NEWS | 21 scatterD3-0.3/scatterD3/R/scatterD3.R | 85 scatterD3-0.3/scatterD3/README.md | 54 scatterD3-0.3/scatterD3/build/vignette.rds |binary scatterD3-0.3/scatterD3/inst/doc/introduction.R | 6 scatterD3-0.3/scatterD3/inst/doc/introduction.Rmd | 84 scatterD3-0.3/scatterD3/inst/doc/introduction.html | 118 scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/d3-3.5.6.min.js |only scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/d3-legend.min.js |only scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/scatterD3.css | 5 scatterD3-0.3/scatterD3/inst/htmlwidgets/scatterD3.js | 1268 ++++++---- scatterD3-0.3/scatterD3/inst/htmlwidgets/scatterD3.yaml | 6 scatterD3-0.3/scatterD3/man/scatterD3-shiny.Rd | 4 scatterD3-0.3/scatterD3/man/scatterD3.Rd | 40 scatterD3-0.3/scatterD3/vignettes/introduction.Rmd | 84 19 files changed, 1093 insertions(+), 731 deletions(-)
Title: Data Integration Feature for Force.com and Salesforce.com
Description: Insert, update,
retrieve, delete and bulk operate datasets with a SaaS based CRM
Salesforce.com and a PaaS based application platform Force.com from R.
Author: Takekatsu Hiramura [aut, cre],
Steven Mortimer [ctb],
Alexis Iglauer [ctb]
Maintainer: Takekatsu Hiramura <thira@plavox.info>
Diff between RForcecom versions 0.7 dated 2013-10-23 and 0.8 dated 2015-10-26
RForcecom-0.7/RForcecom/man/RForcecom-package.Rd |only RForcecom-0.8/RForcecom/DESCRIPTION | 48 ++- RForcecom-0.8/RForcecom/MD5 | 64 +++-- RForcecom-0.8/RForcecom/NAMESPACE | 58 +++- RForcecom-0.8/RForcecom/R/RForcecom.R |only RForcecom-0.8/RForcecom/R/rforcecom.abortBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.api.R | 19 + RForcecom-0.8/RForcecom/R/rforcecom.bulkQuery.R |only RForcecom-0.8/RForcecom/R/rforcecom.checkBatchStatus.R |only RForcecom-0.8/RForcecom/R/rforcecom.closeBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.create.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.createBulkBatch.R |only RForcecom-0.8/RForcecom/R/rforcecom.createBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.debug.R | 1 RForcecom-0.8/RForcecom/R/rforcecom.delete.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getBatchDetails.R |only RForcecom-0.8/RForcecom/R/rforcecom.getBulkQueryResult.R |only RForcecom-0.8/RForcecom/R/rforcecom.getObjectDescription.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getObjectList.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getServerTimestamp.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.insertBulkAttachments.R |only RForcecom-0.8/RForcecom/R/rforcecom.login.R | 127 ++++++---- RForcecom-0.8/RForcecom/R/rforcecom.logout.R |only RForcecom-0.8/RForcecom/R/rforcecom.query.R | 20 - RForcecom-0.8/RForcecom/R/rforcecom.queryMore.R | 14 - RForcecom-0.8/RForcecom/R/rforcecom.retrieve.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.search.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.submitBulkQuery.R |only RForcecom-0.8/RForcecom/R/rforcecom.update.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.upsert.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.write.csv.R |only RForcecom-0.8/RForcecom/man/RForcecom.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.abortBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.api.Rd | 2 RForcecom-0.8/RForcecom/man/rforcecom.bulkQuery.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.checkBatchStatus.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.closeBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.createBulkBatch.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.createBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.getBatchDetails.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.getBulkQueryResult.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.insertBulkAttachments.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.login.Rd | 70 +---- RForcecom-0.8/RForcecom/man/rforcecom.logout.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.query.Rd | 8 RForcecom-0.8/RForcecom/man/rforcecom.submitBulkQuery.Rd |only 46 files changed, 290 insertions(+), 204 deletions(-)
Title: Talk to the NCBI EUtils
Description: An interface to NCBI databases such as PubMed, GenBank, or GEO
powered by the Entrez Programming Utilities (EUtils). The nine EUtils
provide programmatic access to the NCBI Entrez query and database
system for searching and retrieving biological data.
Author: Gerhard Schöfl <gerhard.schofl@gmail.com>
Maintainer: Gerhard Schöfl <gerhard.schofl@gmail.com>
Diff between reutils versions 0.2.1 dated 2015-08-29 and 0.2.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 ++++++- R/elink.R | 33 ++++++++++++++++++++------------- R/reutils-package.R | 1 + R/utils.R | 1 + man/elink.Rd | 2 +- 7 files changed, 39 insertions(+), 25 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.4-1786 dated 2015-10-21 and 2.4-1788 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/bccorr.R | 26 ++++++++++++++++++-------- R/cgsolve.R | 4 ++-- exec/lfescript | 10 ++++++++-- inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary src/lfe.c | 4 ++-- src/lfe.h | 4 ++-- 10 files changed, 45 insertions(+), 29 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert <marius.hofert@uwaterloo.ca>,
Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>, and
Jun Yan <jun.yan@uconn.edu>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 0.999-13 dated 2015-03-05 and 0.999-14 dated 2015-10-26
copula-0.999-13/copula/R/device.R |only copula-0.999-13/copula/demo/AC-Liouville-demo.R |only copula-0.999-13/copula/demo/GIG-demo.R |only copula-0.999-13/copula/demo/QARClayton.R |only copula-0.999-13/copula/demo/copula_garch.R |only copula-0.999-13/copula/demo/dnac-demo.R |only copula-0.999-13/copula/demo/gof_radial.R |only copula-0.999-13/copula/demo/logL-vis.R |only copula-0.999-13/copula/demo/qrng.R |only copula-0.999-13/copula/demo/tail_compatibility.R |only copula-0.999-13/copula/man/device.Rd |only copula-0.999-14/copula/DESCRIPTION | 32 ++-- copula-0.999-14/copula/MD5 | 120 +++++++++------- copula-0.999-14/copula/NAMESPACE | 111 ++++++++------ copula-0.999-14/copula/R/aux-acopula.R | 5 copula-0.999-14/copula/R/cop_objects.R | 1 copula-0.999-14/copula/R/empcop.R | 2 copula-0.999-14/copula/R/estimation.R | 8 - copula-0.999-14/copula/R/gofTests.R | 2 copula-0.999-14/copula/R/gofTrafos.R | 7 copula-0.999-14/copula/R/graphics.R | 10 - copula-0.999-14/copula/R/nacopula.R | 2 copula-0.999-14/copula/R/normalCopula.R | 5 copula-0.999-14/copula/R/tCopula.R | 3 copula-0.999-14/copula/TODO | 25 +++ copula-0.999-14/copula/build/partial.rdb |only copula-0.999-14/copula/build/vignette.rds |binary copula-0.999-14/copula/demo/00Index | 10 - copula-0.999-14/copula/demo/estimation_via_HAC.R |only copula-0.999-14/copula/demo/gofCopula.R | 17 +- copula-0.999-14/copula/demo/gof_graph.R | 6 copula-0.999-14/copula/demo/retstable.R | 14 + copula-0.999-14/copula/inst/NEWS.Rd | 31 +++- copula-0.999-14/copula/inst/Rsource/GIG.R | 116 ++++++++------- copula-0.999-14/copula/inst/Rsource/dnac.R | 9 - copula-0.999-14/copula/inst/Rsource/utils.R | 2 copula-0.999-14/copula/inst/doc/AC_Liouville.Rmd |only copula-0.999-14/copula/inst/doc/AC_Liouville.html |only copula-0.999-14/copula/inst/doc/AR_Clayton.Rmd |only copula-0.999-14/copula/inst/doc/AR_Clayton.html |only copula-0.999-14/copula/inst/doc/Frank-Rmpfr.pdf |binary copula-0.999-14/copula/inst/doc/GIG.Rmd |only copula-0.999-14/copula/inst/doc/GIG.html |only copula-0.999-14/copula/inst/doc/NALC.Rmd |only copula-0.999-14/copula/inst/doc/NALC.html |only copula-0.999-14/copula/inst/doc/copula_GARCH.Rmd |only copula-0.999-14/copula/inst/doc/copula_GARCH.html |only copula-0.999-14/copula/inst/doc/dNAC.Rmd |only copula-0.999-14/copula/inst/doc/dNAC.html |only copula-0.999-14/copula/inst/doc/logL_visualization.Rmd |only copula-0.999-14/copula/inst/doc/logL_visualization.html |only copula-0.999-14/copula/inst/doc/nacopula-pkg.pdf |binary copula-0.999-14/copula/inst/doc/qrng.Rmd |only copula-0.999-14/copula/inst/doc/qrng.html |only copula-0.999-14/copula/inst/doc/rhoAMH-dilog.Rnw | 3 copula-0.999-14/copula/inst/doc/rhoAMH-dilog.pdf |binary copula-0.999-14/copula/inst/doc/tail_compatibility.Rmd |only copula-0.999-14/copula/inst/doc/tail_compatibility.html |only copula-0.999-14/copula/inst/doc/wild_animals.Rmd |only copula-0.999-14/copula/inst/doc/wild_animals.html |only copula-0.999-14/copula/man/An.Rd | 4 copula-0.999-14/copula/man/Mvdc.Rd | 2 copula-0.999-14/copula/man/coeffG.Rd |only copula-0.999-14/copula/man/contour-methods.Rd | 10 - copula-0.999-14/copula/man/copula-package.Rd | 14 - copula-0.999-14/copula/man/ellipCopula.Rd | 39 +++++ copula-0.999-14/copula/man/fitMvdc.Rd | 7 copula-0.999-14/copula/man/gofCopula.Rd | 19 +- copula-0.999-14/copula/man/pobs.Rd | 5 copula-0.999-14/copula/man/qqplot2.Rd | 10 - copula-0.999-14/copula/tests/estim-ex.R | 21 ++ copula-0.999-14/copula/tests/fitting-ex.R | 1 copula-0.999-14/copula/vignettes/AC_Liouville.Rmd |only copula-0.999-14/copula/vignettes/AR_Clayton.Rmd |only copula-0.999-14/copula/vignettes/GIG.Rmd |only copula-0.999-14/copula/vignettes/NALC.Rmd |only copula-0.999-14/copula/vignettes/copula_GARCH.Rmd |only copula-0.999-14/copula/vignettes/dNAC.Rmd |only copula-0.999-14/copula/vignettes/logL_visualization.Rmd |only copula-0.999-14/copula/vignettes/qrng.Rmd |only copula-0.999-14/copula/vignettes/rhoAMH-dilog.Rnw | 3 copula-0.999-14/copula/vignettes/tail_compatibility.Rmd |only copula-0.999-14/copula/vignettes/wild_animals.Rmd |only 83 files changed, 411 insertions(+), 265 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1.1 dated 2015-08-21 and 1.1.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot.spv.R | 2 +- man/plot.spv.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Gene Network Inference from Time-Series Transcriptomic Data
Description: The Time-Delay Correlation algorithm (TDCor) reconstructs the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developed to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset which was used in this study is included in the package to illustrate how to use it.
Author: Julien Lavenus
Maintainer: Mikael Lucas <mikael.lucas@ird.fr>
Diff between TDCor versions 0.1-1 dated 2015-04-18 and 0.1-2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 4 ++++ R/TDCOR.R | 4 ++-- data/LR_dataset.rda |binary data/TF.rda |binary data/l_genes.rda |binary data/l_names.rda |binary data/l_prior.rda |binary data/times.rda |binary man/TDCOR.Rd | 11 +++++++---- man/TDCor-package.Rd | 4 ++-- 12 files changed, 30 insertions(+), 23 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams
(q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler).
An implementation of soundex is provided as well. Distances can be computed
between character vectors while taking proper care of encoding or between
integer vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.3 dated 2015-08-21 and 0.9.4 dated 2015-10-26
DESCRIPTION | 6 +- MD5 | 12 ++-- NEWS | 4 + src/Rstringdist.c | 9 ++- src/jaro.c | 116 ++++++++++++++++++---------------------- src/stringdist.c | 4 + tests/testthat/testStringdist.R | 7 ++ 7 files changed, 86 insertions(+), 72 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.1 dated 2015-10-08 and 1.1.2 dated 2015-10-26
DESCRIPTION | 8 +-- MD5 | 10 +-- R/Add_to_data_object.R | 125 ++++++++++++++++++++++++++----------------------- R/Prepare_data.R | 2 man/add_sitestat.Rd | 6 +- man/nodiv-package.Rd | 4 - 6 files changed, 83 insertions(+), 72 deletions(-)
Title: Genome-Wide Association Analysis of a Biomarker Accounting for
Limit of Detection
Description: Genome-wide association (GWAS) analyses
of a biomarker that account for the limit of detection.
Author: Ahmad Vaez, Ilja M. Nolte, Peter J. van der Most
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between lodGWAS versions 1.0-3 dated 2015-02-20 and 1.0-6 dated 2015-10-26
lodGWAS-1.0-3/lodGWAS/R/packaging_v10-0.r |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_geno.dose |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_geno.map |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_pheno.txt |only lodGWAS-1.0-6/lodGWAS/DESCRIPTION | 10 +++---- lodGWAS-1.0-6/lodGWAS/MD5 | 17 ++++++------ lodGWAS-1.0-6/lodGWAS/NAMESPACE | 2 + lodGWAS-1.0-6/lodGWAS/R/packaging_v10-6.r |only lodGWAS-1.0-6/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_6.txt |only lodGWAS-1.0-6/lodGWAS/inst/extdata |only lodGWAS-1.0-6/lodGWAS/man/lodGWAS-package.Rd | 4 +- lodGWAS-1.0-6/lodGWAS/man/lod_GWAS.Rd | 15 +++++++--- 12 files changed, 29 insertions(+), 19 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description:
We provide a set of functions to retrieve information about GIMMS NDVI3g
files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native
binary (ENVI) format directly into R based on the widely applied 'raster'
package; and calculate monthly value composites (e.g. maximum value
composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.1.1 dated 2015-10-09 and 0.2.0 dated 2015-10-26
gimms-0.1.1/gimms/R/createHdr.R |only gimms-0.1.1/gimms/man/createHdr.Rd |only gimms-0.2.0/gimms/DESCRIPTION | 8 gimms-0.2.0/gimms/MD5 | 32 +-- gimms-0.2.0/gimms/NAMESPACE | 2 gimms-0.2.0/gimms/R/createHeader.R |only gimms-0.2.0/gimms/R/downloadGimms.R | 30 ++- gimms-0.2.0/gimms/R/monthlyComposite.R | 14 + gimms-0.2.0/gimms/R/monthlyIndices.R | 121 +++++++++---- gimms-0.2.0/gimms/R/rasterizeGimms.R | 43 ++-- gimms-0.2.0/gimms/R/rearrangeFiles.R | 161 ++++++++++-------- gimms-0.2.0/gimms/R/updateInventory.R | 106 ++++++------ gimms-0.2.0/gimms/README.md | 261 +++++++++++++++++++++++++----- gimms-0.2.0/gimms/man/createHeader.Rd |only gimms-0.2.0/gimms/man/downloadGimms.Rd | 17 + gimms-0.2.0/gimms/man/monthlyComposite.Rd | 14 + gimms-0.2.0/gimms/man/monthlyIndices.Rd | 11 + gimms-0.2.0/gimms/man/rasterizeGimms.Rd | 30 +-- gimms-0.2.0/gimms/man/rearrangeFiles.Rd | 8 19 files changed, 568 insertions(+), 290 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong <tarn.duong@gmail.com> & Matt Wand <Matt.Wand@uts.edu.au>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.12 dated 2015-09-08 and 1.2.13 dated 2015-10-26
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- R/dfltCounts.R |only R/drvkde.R |only R/featureSignif.R | 13 +++++-------- R/plot.fs.R | 36 ++++++++++++++++-------------------- inst/doc/feature.pdf |binary man/feature-package.Rd | 2 +- man/featureSignifGUI.Rd | 4 ++-- man/plot.fs.Rd | 3 ++- 10 files changed, 40 insertions(+), 44 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-0 dated 2015-08-16 and 1.1-1 dated 2015-10-26
DESCRIPTION | 9 - MD5 | 56 +++--- NAMESPACE | 3 R/ContingencyTests.R | 5 R/ContrastTest.R | 7 R/CorrelationTests.R | 20 +- R/MTP.R | 3 R/MaximallySelectedStatisticsTests.R | 5 R/helpers.R | 53 ++---- build/vignette.rds |binary inst/NEWS.Rd | 18 +- inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.R | 133 +++++++-------- inst/doc/coin.Rnw | 291 +++++++++++++++++---------------- inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary man/IndependenceTest.Rd | 6 man/PermutationDistribution-methods.Rd | 11 + man/SymmetryTest.Rd | 4 man/ocarcinoma.Rd | 4 man/pvalue-methods.Rd | 4 tests/Examples/coin-Ex.Rout.save | 10 - tests/regtest_contingency.R | 25 +- tests/regtest_contingency.Rout.save | 29 +-- tests/regtest_distribution.R | 4 tests/regtest_distribution.Rout.save | 8 vignettes/coin.Rnw | 291 +++++++++++++++++---------------- vignettes/coin.Rout.save | 115 +++++-------- 29 files changed, 553 insertions(+), 561 deletions(-)
Title: API for UK Gas Market Information
Description: Allows users to access live UK gas market information via National Grid's API.
Author: Timothy Wong [aut, cre]
Maintainer: Timothy Wong <timothy.wong@hotmail.co.uk>
Diff between ukgasapi versions 0.10 dated 2015-10-18 and 0.13 dated 2015-10-25
DESCRIPTION | 12 +++++------ MD5 | 6 ++--- R/dataItemExplorer.R | 52 +++++++++++++++++++++++------------------------- man/dataItemExplorer.Rd | 19 ++++++----------- 4 files changed, 41 insertions(+), 48 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.7.1 dated 2015-08-12 and 0.7.2 dated 2015-10-25
DESCRIPTION | 8 - MD5 | 14 +- NEWS | 9 + R/modules-smd.R | 8 + R/tableone-package.R | 2 build/vignette.rds |binary inst/doc/smd.html | 254 ++++++++++++++++++++++++------------------------ man/tableone-package.Rd | 2 8 files changed, 155 insertions(+), 142 deletions(-)
Title: Optimization of Sample Configurations using Spatial Simulated
Annealing
Description: Methods to optimize sample configurations using spatial simulated
annealing. Multiple objective functions are implemented for various
purposes, such as variogram estimation, trend estimation, and spatial
interpolation. A general purpose spatial simulated annealing function
enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre],
Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths],
Gerard B M Heuvelink [ths],
Edzer Pebesma [ctb],
Jon Skoien [ctb],
Joshua French [ctb],
Pierre Roudier [ctb],
Dick Brus [ctb],
Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between spsann versions 1.0.1 dated 2015-07-31 and 1.0-2 dated 2015-10-25
DESCRIPTION | 8 ++++---- MD5 | 45 ++++++++++++++++++++++++--------------------- NAMESPACE | 2 ++ R/AAA.R | 8 +++++--- R/SPSANNtools.R | 28 +++++++++++++++++++--------- R/check-spsann-arguments.R | 1 + R/optimACDC.R | 22 +++++++++++++++++----- R/optimCLHS.R |only R/optimCORR.R | 16 ++++++++++++++-- R/optimDIST.R | 4 ++-- R/optimPPL.R | 21 +++++++++++---------- R/optimSPAN.R | 25 +++++++++++++++++++++---- R/plotting-options.R | 8 +++++++- R/prepare-clhs-covars.R |only R/spsann.R | 4 ++-- man/optimACDC.Rd | 28 ++++++++++++++-------------- man/optimCLHS.Rd |only man/optimCORR.Rd | 22 +++++++++++----------- man/optimDIST.Rd | 22 +++++++++++----------- man/optimMKV.Rd | 18 +++++++++--------- man/optimMSSD.Rd | 18 +++++++++--------- man/optimPPL.Rd | 18 +++++++++--------- man/optimSPAN.Rd | 24 ++++++++++++------------ man/optimUSER.Rd | 18 +++++++++--------- man/spsann-package.Rd | 4 ++-- 25 files changed, 215 insertions(+), 149 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert <cpsievert1@gmail.com>
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between pitchRx versions 1.8 dated 2015-10-13 and 1.8.1 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 22 ++++++++++++++-------- R/animateFX.R | 1 - R/scrape.R | 1 - 5 files changed, 23 insertions(+), 19 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3 and K4 to characterize
distributions with left and right, symmetric or asymmetric fat tails in market
finance, neuroscience and other disciplines. Two algorithms to estimate with
a high accuracy distribution parameters, quantiles, value-at-risk and expected
shortfall. Also, power hyperbolas and power hyperbolic functions. This is a
major update that breaks compatibility with previous versions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.2-3 dated 2015-07-08 and 1.4-1 dated 2015-10-25
FatTailsR-1.2-3/FatTailsR/R/b_trigohp.R |only FatTailsR-1.2-3/FatTailsR/R/c_logishp.R |only FatTailsR-1.2-3/FatTailsR/R/d_conversion.R |only FatTailsR-1.2-3/FatTailsR/R/e_kiener1.R |only FatTailsR-1.2-3/FatTailsR/R/f_kiener2.R |only FatTailsR-1.2-3/FatTailsR/R/g_kiener3.R |only FatTailsR-1.2-3/FatTailsR/R/h_kiener4.R |only FatTailsR-1.2-3/FatTailsR/R/i_moments.R |only FatTailsR-1.2-3/FatTailsR/R/j_tailskiener.R |only FatTailsR-1.2-3/FatTailsR/R/k_estimation.R |only FatTailsR-1.2-3/FatTailsR/R/l_regression.R |only FatTailsR-1.2-3/FatTailsR/R/m_regression2.R |only FatTailsR-1.2-3/FatTailsR/R/n_regression3.R |only FatTailsR-1.2-3/FatTailsR/R/z_data.R |only FatTailsR-1.2-3/FatTailsR/man/ckiener.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkappa6.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkienerX.Rd |only FatTailsR-1.2-3/FatTailsR/man/fitkienerLX.Rd |only FatTailsR-1.4-1/FatTailsR/DESCRIPTION | 29 +-- FatTailsR-1.4-1/FatTailsR/MD5 | 103 ++++++------ FatTailsR-1.4-1/FatTailsR/NAMESPACE | 87 +++++++++- FatTailsR-1.4-1/FatTailsR/NEWS | 69 ++++++-- FatTailsR-1.4-1/FatTailsR/R/a_FatTailsR-package.R | 150 ++++++++++------- FatTailsR-1.4-1/FatTailsR/R/b_data.R |only FatTailsR-1.4-1/FatTailsR/R/c_trigohp.R |only FatTailsR-1.4-1/FatTailsR/R/d_logishp.R |only FatTailsR-1.4-1/FatTailsR/R/e_conversion.R |only FatTailsR-1.4-1/FatTailsR/R/f_kiener1.R |only FatTailsR-1.4-1/FatTailsR/R/g_kiener2.R |only FatTailsR-1.4-1/FatTailsR/R/h_kiener3.R |only FatTailsR-1.4-1/FatTailsR/R/i_kiener4.R |only FatTailsR-1.4-1/FatTailsR/R/j_moments.R |only FatTailsR-1.4-1/FatTailsR/R/k_tailskiener.R |only FatTailsR-1.4-1/FatTailsR/R/l_estimation.R |only FatTailsR-1.4-1/FatTailsR/R/m_laplaceroll.R |only FatTailsR-1.4-1/FatTailsR/R/n_estimation2.R |only FatTailsR-1.4-1/FatTailsR/R/o_regression.R |only FatTailsR-1.4-1/FatTailsR/data/datalist |only FatTailsR-1.4-1/FatTailsR/data/dfData.rda |binary FatTailsR-1.4-1/FatTailsR/data/tData.rda |binary FatTailsR-1.4-1/FatTailsR/data/xData.rda |binary FatTailsR-1.4-1/FatTailsR/data/zData.rda |binary FatTailsR-1.4-1/FatTailsR/man/FatTailsR.Rd | 145 +++++++++-------- FatTailsR-1.4-1/FatTailsR/man/aw2k.Rd | 119 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/checkquantiles.Rd | 46 ++++- FatTailsR-1.4-1/FatTailsR/man/ckiener1234.Rd |only FatTailsR-1.4-1/FatTailsR/man/dfData.Rd | 56 ------ FatTailsR-1.4-1/FatTailsR/man/dimdim.Rd |only FatTailsR-1.4-1/FatTailsR/man/elevenprobs.Rd | 51 ++---- FatTailsR-1.4-1/FatTailsR/man/estimkiener11.Rd | 118 ++++++------- FatTailsR-1.4-1/FatTailsR/man/exfit0.Rd |only FatTailsR-1.4-1/FatTailsR/man/exphp.Rd | 13 - FatTailsR-1.4-1/FatTailsR/man/extractData.Rd |only FatTailsR-1.4-1/FatTailsR/man/fitkienerX.Rd |only FatTailsR-1.4-1/FatTailsR/man/getDSdata.Rd | 44 ++--- FatTailsR-1.4-1/FatTailsR/man/getnamesk.Rd |only FatTailsR-1.4-1/FatTailsR/man/kashp.Rd | 8 FatTailsR-1.4-1/FatTailsR/man/kiener1.Rd | 96 +++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener2.Rd | 103 ++++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener3.Rd | 120 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kiener4.Rd | 113 ++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kmoments.Rd | 186 +++++++++++----------- FatTailsR-1.4-1/FatTailsR/man/laplacegaussnorm.Rd | 17 +- FatTailsR-1.4-1/FatTailsR/man/loghp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logishp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logit.Rd | 44 +++-- FatTailsR-1.4-1/FatTailsR/man/pk2pk.Rd | 80 ++++----- FatTailsR-1.4-1/FatTailsR/man/pprobs0.Rd |only FatTailsR-1.4-1/FatTailsR/man/regkienerLX.Rd | 139 +++++++++------- FatTailsR-1.4-1/FatTailsR/man/roundcoefk.Rd |only FatTailsR-1.4-1/FatTailsR/man/tData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/xData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/zData.Rd | 6 73 files changed, 1251 insertions(+), 711 deletions(-)
Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sValues versions 0.1.1 dated 2015-09-13 and 0.1.2 dated 2015-10-25
sValues-0.1.1/sValues/README.md |only sValues-0.1.2/sValues/DESCRIPTION | 9 +-- sValues-0.1.2/sValues/MD5 | 21 ++++--- sValues-0.1.2/sValues/NAMESPACE | 2 sValues-0.1.2/sValues/R/internal_functions.R | 12 +--- sValues-0.1.2/sValues/R/sValues.R | 74 +++++++++++++++------------ sValues-0.1.2/sValues/inst/doc/sValues.R | 3 - sValues-0.1.2/sValues/inst/doc/sValues.Rnw | 3 - sValues-0.1.2/sValues/inst/doc/sValues.pdf |binary sValues-0.1.2/sValues/man/sValues.Rd | 36 ++++++++----- sValues-0.1.2/sValues/tests |only sValues-0.1.2/sValues/vignettes/sValues.Rnw | 3 - 12 files changed, 86 insertions(+), 77 deletions(-)
Title: Mixed Tempered Stable Distribution
Description: We provide detailed functions for univariate Mixed Tempered Stable distribution.
Author: Lorenzo Mercuri, Edit Rroji
Maintainer: Lorenzo Mercuri <lorenzo.mercuri@unimi.it>
Diff between MixedTS versions 1.0.3 dated 2015-07-17 and 1.0.4 dated 2015-10-25
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/MixedTS.R | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.14 dated 2015-10-11 and 0.99.15 dated 2015-10-25
DescTools-0.99.14/DescTools/R/test.DescTools.r |only DescTools-0.99.15/DescTools/DESCRIPTION | 8 DescTools-0.99.15/DescTools/MD5 | 47 +- DescTools-0.99.15/DescTools/NAMESPACE | 4 DescTools-0.99.15/DescTools/NEWS | 17 + DescTools-0.99.15/DescTools/R/DescTools.r | 282 ++++++++++------- DescTools-0.99.15/DescTools/inst/doc/Combinatorics.pdf |binary DescTools-0.99.15/DescTools/inst/doc/TablesInR.pdf |binary DescTools-0.99.15/DescTools/man/Abind.Rd | 11 DescTools-0.99.15/DescTools/man/BarnardTest.Rd |only DescTools-0.99.15/DescTools/man/BubbleLegend.Rd | 36 +- DescTools-0.99.15/DescTools/man/DateFunctions.Rd | 15 DescTools-0.99.15/DescTools/man/DescTools-package.Rd | 2 DescTools-0.99.15/DescTools/man/FindColor.Rd | 23 - DescTools-0.99.15/DescTools/man/Keywords.Rd | 6 DescTools-0.99.15/DescTools/man/PlotFun.Rd | 36 +- DescTools-0.99.15/DescTools/man/PlotMosaic.Rd | 14 DescTools-0.99.15/DescTools/man/Stamp.Rd | 4 DescTools-0.99.15/DescTools/man/StrPos.Rd | 9 DescTools-0.99.15/DescTools/man/SysInfo.Rd | 14 DescTools-0.99.15/DescTools/man/VarCI.Rd | 15 DescTools-0.99.15/DescTools/src/Barnard.c |only DescTools-0.99.15/DescTools/src/aux_fct.cpp | 25 - DescTools-0.99.15/DescTools/src/between.c | 91 +++-- DescTools-0.99.15/DescTools/src/between.h | 16 DescTools-0.99.15/DescTools/tests/misc.R | 26 - 26 files changed, 410 insertions(+), 291 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.3.0 dated 2015-06-16 and 3.3.1 dated 2015-10-25
BUGS | 2 DESCRIPTION | 12 - MD5 | 43 +++--- NAMESPACE | 7 - R/InitMHP.DynMLE.blockdiag.R | 203 +++++++++++++++++--------------- R/combine.networks.R | 108 +++++++++++++++-- R/ergm.godfather.R | 2 R/stergm.EGMME.SA.R | 4 R/stergm.getMCMCsample.R | 4 R/zzz.R | 10 + inst/NEWS.Rd | 74 ++++++++--- inst/doc/STERGM.pdf |binary man/ergm-terms.Rd | 4 man/stergm.Rd | 8 - man/tergm-package.Rd | 5 src/MHproposals_DynMLE.c | 2 src/MHproposals_DynMLE_block.c | 132 ++++++++++++++++++++ src/MHproposals_DynMoME.c | 2 tests/combine.networks.R | 34 +++++ tests/dynamic_MLE.R | 36 +++-- tests/dynamic_MLE_2.R | 38 ++++- tests/dynamic_MLE_blockdiag.R | 27 ++-- tests/dynamic_MLE_blockdiag.bipartite.R |only 23 files changed, 556 insertions(+), 201 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 4 functions, one for extracting relevant URLs, one for extracting features out of given URLs, one that does both together and one that constructs graphs based on the structure of a thread.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 1.1.1 dated 2015-07-04 and 2.0.0 dated 2015-10-25
DESCRIPTION | 12 +-- MD5 | 13 ++- NAMESPACE | 1 R/RedditExtractoR.R | 170 +++++++++++++++++++++++++++++++++++++++++-------- man/construct_graph.Rd |only man/get_reddit.Rd | 5 - man/reddit_content.Rd | 3 man/reddit_urls.Rd | 6 - 8 files changed, 167 insertions(+), 43 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The "M" in the name "geeM" is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel <lmcda4@lsuhsc.edu>
Diff between geeM versions 0.7.4 dated 2015-05-25 and 0.8.0 dated 2015-10-25
DESCRIPTION | 9 MD5 | 14 - NAMESPACE | 5 R/geem.R | 717 ++++++++++++++++++++++++++++++-------------------------- R/print.R | 142 ++++++----- R/updatealpha.R | 301 ++++++++++++----------- R/utility.R | 54 +++- man/geem.Rd | 332 +++++++++++++------------ 8 files changed, 861 insertions(+), 713 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010). Please see an eprint at http://arxiv.org/pdf/1507.06055.pdf for more details.
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.1 dated 2015-07-27 and 1.1.2 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.4 dated 2015-03-10 and 1.5 dated 2015-10-25
cit-1.4/cit/R/C_CIT_V5.R |only cit-1.4/cit/man/cit.Rd |only cit-1.4/cit/man/plotcit.Rd |only cit-1.4/cit/src/cit_v7.cpp |only cit-1.5/cit/DESCRIPTION | 12 ++++++------ cit-1.5/cit/MD5 | 24 +++++++++++++++++------- cit-1.5/cit/NAMESPACE | 4 +++- cit-1.5/cit/R/C_CIT_V12.R |only cit-1.5/cit/man/cit-package.Rd | 10 +++++----- cit-1.5/cit/man/cit.bp.Rd |only cit-1.5/cit/man/cit.cp.Rd |only cit-1.5/cit/man/fdr.cit.Rd |only cit-1.5/cit/man/fdr.od.Rd |only cit-1.5/cit/man/iuq.Rd |only cit-1.5/cit/man/linreg.Rd |only cit-1.5/cit/src/citconlog2_perm_v5.cpp |only cit-1.5/cit/src/citconlog2_v3.cpp |only cit-1.5/cit/src/citconlog2cvr_v3.cpp |only cit-1.5/cit/src/citconlog3_perm_v5.cpp |only cit-1.5/cit/src/citconlog3cvr_perm_v6.cpp |only cit-1.5/cit/src/logisticfunc.cpp |only cit-1.5/cit/src/logisticfunc.h |only 22 files changed, 31 insertions(+), 19 deletions(-)
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Diff between bayou versions 1.0.1 dated 2014-07-31 and 1.1.0 dated 2015-10-25
DESCRIPTION | 15 - MD5 | 112 +++++----- NAMESPACE | 6 R/bayou-likelihood.R | 19 - R/bayou-mcmc-utilities.R | 60 ++++- R/bayou-mcmc.R | 14 - R/bayou-package.R | 5 R/bayou-plotting.R | 364 +++++++++++++++------------------- R/bayou-prior.R | 47 ++-- R/bayou-simulation.r | 5 R/bayou-steppingstone.R | 60 +++-- R/conversion-utilities.R | 7 R/probability.R | 12 - man/Lposterior.Rd | 34 +-- man/OU.lik.Rd | 41 +-- man/OU.repar.Rd | 14 - man/OUphenogram.Rd | 40 +-- man/OUwie2bayou.Rd | 14 - man/QG.alpha.Rd | 13 - man/QG.sig2.Rd | 13 - man/bayou-package.Rd | 11 - man/bayou.lik.Rd | 29 +- man/bayou.mcmc.Rd | 102 +++------ man/bayou2OUwie.Rd | 22 -- man/cdpois.Rd | 25 +- man/combine.chains.Rd | 15 - man/dataSim.Rd | 33 +-- man/dhalfcauchy.Rd | 28 +- man/dloc.Rd | 32 +- man/dsb.Rd | 63 ++--- man/gelman.R.Rd | 27 +- man/identifyBranches.Rd | 37 +-- man/load.bayou.Rd | 32 +- man/make.powerposteriorFn.Rd | 29 +- man/make.prior.Rd | 128 +++++------ man/make.refFn.Rd | 46 +--- man/makeTransparent.Rd | 13 - man/overparameterize.startingPoint.Rd |only man/parmap.W.Rd | 28 +- man/pars2simmap.Rd | 28 +- man/phenogram.density.Rd | 47 +--- man/plot.bayouMCMC.Rd | 13 - man/plot.ssMCMC.Rd | 19 - man/plotBayoupars.Rd | 12 - man/plotRegimes.Rd |only man/plotSimmap.mcmc.Rd | 113 ++-------- man/print.bayouFit.Rd | 11 - man/print.priorFn.Rd | 11 - man/print.refFn.Rd | 11 - man/print.ssMCMC.Rd | 10 man/priorSim.Rd | 22 -- man/pull.pars.Rd | 28 +- man/regime.plot.Rd | 27 +- man/set.burnin.Rd | 14 - man/simmap.W.Rd | 34 +-- man/steppingstone.Rd | 98 ++------- man/summary.bayouMCMC.Rd | 17 - src/RcppExports.cpp | 50 +--- 58 files changed, 978 insertions(+), 1182 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.13.2 dated 2015-05-27 and 2.14.0 dated 2015-10-25
DESCRIPTION | 14 MD5 | 40 +- NAMESPACE | 29 + NEWS | 18 - R/999.AromaAffymetrix.R | 6 R/999.DEPRECATED.R | 50 -- R/AffyGenePDInfo.writeCdf.R | 2 R/AffymetrixCdfFile.COUNTS.R | 1 R/AffymetrixCelSet.R | 34 - R/AvgPlm.R | 2 R/DChipGenomeInformation.R | 3 R/DChipSnpInformation.R | 3 R/SnpChipEffectSet.extractAlleleSet.R | 9 R/UnitModel.fitCnProbes.R | 8 inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R | 178 +++++----- inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R | 1 man/ArrayExplorer.Rd | 2 man/DChipGenomeInformation.Rd | 3 man/DChipSnpInformation.Rd | 3 man/Non-documented_objects.Rd | 7 man/nbrOfGroupsPerUnit.AffymetrixCdfFile.Rd | 4 21 files changed, 188 insertions(+), 229 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.2-4 dated 2014-12-31 and 1.3-0 dated 2015-10-24
maxLik-1.2-4/maxLik/man/returnMessage.Rd |only maxLik-1.2-4/maxLik/tests/fitExpDist.R |only maxLik-1.2-4/maxLik/tests/fitExpDist.Rout.save |only maxLik-1.2-4/maxLik/tests/fitNormalDist.R |only maxLik-1.2-4/maxLik/tests/fitNormalDist.Rout.save |only maxLik-1.3-0/maxLik/DESCRIPTION | 20 maxLik-1.3-0/maxLik/MD5 | 116 maxLik-1.3-0/maxLik/NAMESPACE | 12 maxLik-1.3-0/maxLik/NEWS | 17 maxLik-1.3-0/maxLik/R/05-classes.R |only maxLik-1.3-0/maxLik/R/10-MaxControl_class.R |only maxLik-1.3-0/maxLik/R/20-maxControl.R |only maxLik-1.3-0/maxLik/R/25-addControlList.R |only maxLik-1.3-0/maxLik/R/30-addControlDddot.R |only maxLik-1.3-0/maxLik/R/condiNumber.R | 7 maxLik-1.3-0/maxLik/R/logLikAttr.R | 16 maxLik-1.3-0/maxLik/R/maxBFGS.R | 17 maxLik-1.3-0/maxLik/R/maxBFGSR.R | 113 maxLik-1.3-0/maxLik/R/maxBFGSRCompute.R | 88 maxLik-1.3-0/maxLik/R/maxBHHH.R | 4 maxLik-1.3-0/maxLik/R/maxCG.R | 28 maxLik-1.3-0/maxLik/R/maxNM.R | 25 maxLik-1.3-0/maxLik/R/maxNR.R | 95 maxLik-1.3-0/maxLik/R/maxNRCompute.R | 211 + maxLik-1.3-0/maxLik/R/maxOptim.R | 164 - maxLik-1.3-0/maxLik/R/maxSANN.R | 32 maxLik-1.3-0/maxLik/R/openParam.R |only maxLik-1.3-0/maxLik/R/showMaxControl.R |only maxLik-1.3-0/maxLik/R/stdEr.maxLik.R | 4 maxLik-1.3-0/maxLik/R/summary.maxLik.R | 2 maxLik-1.3-0/maxLik/R/sumt.R | 10 maxLik-1.3-0/maxLik/man/activePar.Rd | 13 maxLik-1.3-0/maxLik/man/bread.maxLik.Rd | 21 maxLik-1.3-0/maxLik/man/compareDerivatives.Rd | 49 maxLik-1.3-0/maxLik/man/condiNumber.Rd | 59 maxLik-1.3-0/maxLik/man/estfun.maxLik.Rd | 23 maxLik-1.3-0/maxLik/man/fnSubset.Rd | 83 maxLik-1.3-0/maxLik/man/hessian.Rd | 16 maxLik-1.3-0/maxLik/man/logLik.maxLik.Rd | 4 maxLik-1.3-0/maxLik/man/maxBFGS.Rd | 165 - maxLik-1.3-0/maxLik/man/maxControl.Rd |only maxLik-1.3-0/maxLik/man/maxLik-internal.Rd | 1 maxLik-1.3-0/maxLik/man/maxLik-methods.Rd | 50 maxLik-1.3-0/maxLik/man/maxLik-package.Rd |only maxLik-1.3-0/maxLik/man/maxLik.Rd | 69 maxLik-1.3-0/maxLik/man/maxNR.Rd | 295 +- maxLik-1.3-0/maxLik/man/maximType.Rd | 10 maxLik-1.3-0/maxLik/man/nIter.Rd | 11 maxLik-1.3-0/maxLik/man/nObs.Rd | 15 maxLik-1.3-0/maxLik/man/nParam.Rd | 8 maxLik-1.3-0/maxLik/man/numericGradient.Rd | 33 maxLik-1.3-0/maxLik/man/returnCode.Rd | 42 maxLik-1.3-0/maxLik/man/summary.maxLik.Rd | 51 maxLik-1.3-0/maxLik/man/summary.maxim.Rd | 33 maxLik-1.3-0/maxLik/man/sumt.Rd | 86 maxLik-1.3-0/maxLik/man/vcov.maxLik.Rd | 36 maxLik-1.3-0/maxLik/tests/BFGSR.R | 26 maxLik-1.3-0/maxLik/tests/BFGSR.Rout.save | 68 maxLik-1.3-0/maxLik/tests/constraints.R | 184 + maxLik-1.3-0/maxLik/tests/constraints.Rout.save | 1223 +--------- maxLik-1.3-0/maxLik/tests/examples.R | 35 maxLik-1.3-0/maxLik/tests/examples.Rout.save | 860 +++++-- maxLik-1.3-0/maxLik/tests/finalHessian.Rout.save | 14 maxLik-1.3-0/maxLik/tests/fitNormalDist_privateTest.Rout.save |only maxLik-1.3-0/maxLik/tests/methods.R | 14 maxLik-1.3-0/maxLik/tests/methods.Rout.save | 92 maxLik-1.3-0/maxLik/tests/parameters_privateTest.Rout.save |only 67 files changed, 2417 insertions(+), 2253 deletions(-)
Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(),
aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within
(i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating
multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and
computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM
only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums
of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Frederik Aust [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.14-2 dated 2015-08-17 and 0.15-2 dated 2015-10-24
afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-basic.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-bugs.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-structural.R |only afex-0.15-2/afex/DESCRIPTION | 40 afex-0.15-2/afex/MD5 | 77 afex-0.15-2/afex/NAMESPACE | 1 afex-0.15-2/afex/NEWS | 956 +++---- afex-0.15-2/afex/R/afex-package.R | 6 afex-0.15-2/afex/R/allFit.R | 176 - afex-0.15-2/afex/R/aov_car.R | 778 ++--- afex-0.15-2/afex/R/compare.2.vectors.R | 186 - afex-0.15-2/afex/R/deprecated.R | 58 afex-0.15-2/afex/R/ems.R | 214 - afex-0.15-2/afex/R/helpers.R | 96 afex-0.15-2/afex/R/ks2013.3-data.R | 56 afex-0.15-2/afex/R/md_12.1-data.R | 90 afex-0.15-2/afex/R/md_15.1-data.R | 122 afex-0.15-2/afex/R/md_16.1-data.R | 68 afex-0.15-2/afex/R/md_16.4-data.R | 68 afex-0.15-2/afex/R/methods.afex_aov.R | 286 +- afex-0.15-2/afex/R/mixed.R | 1328 +++++----- afex-0.15-2/afex/R/nice.R | 286 +- afex-0.15-2/afex/R/obk.long-data.R | 92 afex-0.15-2/afex/R/round_ps.R | 56 afex-0.15-2/afex/R/set_contrasts.R | 90 afex-0.15-2/afex/R/sk2011.1-data.R | 90 afex-0.15-2/afex/R/sk2011.2-data.R | 64 afex-0.15-2/afex/inst/doc/anova_posthoc.R | 2 afex-0.15-2/afex/inst/doc/anova_posthoc.Rmd | 2 afex-0.15-2/afex/inst/doc/anova_posthoc.html | 154 - afex-0.15-2/afex/man/afex-package.Rd | 6 afex-0.15-2/afex/man/afex_aov-methods.Rd | 11 afex-0.15-2/afex/man/mixed.Rd | 6 afex-0.15-2/afex/man/nice.Rd | 11 afex-0.15-2/afex/tests/testthat.R | 8 afex-0.15-2/afex/tests/testthat/test-afex_aov.R | 106 afex-0.15-2/afex/tests/testthat/test-aov_car-basic.R |only afex-0.15-2/afex/tests/testthat/test-aov_car-bugs.R |only afex-0.15-2/afex/tests/testthat/test-aov_car-structural.R |only afex-0.15-2/afex/tests/testthat/test-mixed-bugs.R |only afex-0.15-2/afex/tests/testthat/test-mixed-mw.R | 92 afex-0.15-2/afex/tests/testthat/test-mixed-structure.R | 324 +- afex-0.15-2/afex/vignettes/anova_posthoc.Rmd | 2 43 files changed, 3029 insertions(+), 2979 deletions(-)
Title: R Interface to FOAAS
Description: R access to the FOAAS (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rfoaas versions 0.1.6 dated 2015-05-31 and 0.1.8 dated 2015-10-24
ChangeLog | 35 ++++++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 14 +++---- NAMESPACE | 3 + R/foaas.R | 15 +++++++ README.md | 2 - man/rfoaas-package.Rd | 27 ++++++++++++- tests/runTestsAgainstFOAAS.R | 83 ++++++++++++++++++++++++------------------- 8 files changed, 135 insertions(+), 52 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.4.0 dated 2015-06-16 and 3.5.1 dated 2015-10-24
ergm-3.4.0/ergm/R/edgelist.R |only ergm-3.4.0/ergm/R/ergm.sample.eta2theta.R |only ergm-3.4.0/ergm/man/vector.namesmatch.Rd |only ergm-3.4.0/ergm/tests/samplike_condoutdeg.R |only ergm-3.5.1/ergm/DESCRIPTION | 21 ergm-3.5.1/ergm/MD5 | 109 ++-- ergm-3.5.1/ergm/NAMESPACE | 38 + ergm-3.5.1/ergm/R/InitErgmTerm.R | 26 ergm-3.5.1/ergm/R/InitMHP.blockdiag.R | 105 +++ ergm-3.5.1/ergm/R/approx.hotelling.diff.test.R | 48 + ergm-3.5.1/ergm/R/build_term_index.R | 617 +++++++++++------------ ergm-3.5.1/ergm/R/ergm.CD.fixed.R | 12 ergm-3.5.1/ergm/R/ergm.MCMCse.R | 141 +---- ergm-3.5.1/ergm/R/ergm.MCMCse.lognormal.R | 113 +--- ergm-3.5.1/ergm/R/ergm.MCMLE.R | 19 ergm-3.5.1/ergm/R/ergm.R | 266 +++++---- ergm-3.5.1/ergm/R/ergm.bridge.R | 5 ergm-3.5.1/ergm/R/ergm.estimate.R | 2 ergm-3.5.1/ergm/R/ergm.llik.R | 5 ergm-3.5.1/ergm/R/ergm.llik.obs.R | 44 - ergm-3.5.1/ergm/R/ergm.model.utils.R | 23 ergm-3.5.1/ergm/R/ergm.san.R | 5 ergm-3.5.1/ergm/R/ergm.utility.R | 2 ergm-3.5.1/ergm/R/formula.utils.R | 82 --- ergm-3.5.1/ergm/R/is.curved.R |only ergm-3.5.1/ergm/R/is.inCH.R | 23 ergm-3.5.1/ergm/R/logLik.ergm.R | 4 ergm-3.5.1/ergm/R/mcmc.diagnostics.ergm.R | 12 ergm-3.5.1/ergm/R/parallel.utils.R | 26 ergm-3.5.1/ergm/inst/NEWS.Rd | 128 +++- ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.html | 35 - ergm-3.5.1/ergm/inst/doc/ergm.pdf |binary ergm-3.5.1/ergm/man/Getting.Started.Rd | 13 ergm-3.5.1/ergm/man/as.edgelist.Rd | 50 - ergm-3.5.1/ergm/man/control.ergm.Rd | 21 ergm-3.5.1/ergm/man/ergm-constraints.Rd | 12 ergm-3.5.1/ergm/man/ergm-package.Rd | 13 ergm-3.5.1/ergm/man/ergm-parallel.Rd | 2 ergm-3.5.1/ergm/man/ergm-terms.Rd | 54 +- ergm-3.5.1/ergm/man/ergm.Rd | 13 ergm-3.5.1/ergm/man/ergm.init.methods.Rd | 12 ergm-3.5.1/ergm/man/ergm.mple.Rd | 2 ergm-3.5.1/ergm/man/ergm_formula_utils.Rd | 38 - ergm-3.5.1/ergm/man/is.curved.Rd |only ergm-3.5.1/ergm/man/mcmc.diagnostics.ergm.Rd | 9 ergm-3.5.1/ergm/man/standardize.network.Rd | 3 ergm-3.5.1/ergm/man/vcov.ergm.Rd | 4 ergm-3.5.1/ergm/src/MHproposals_block.c | 100 +++ ergm-3.5.1/ergm/src/changestats.c | 12 ergm-3.5.1/ergm/src/changestats.h | 2 ergm-3.5.1/ergm/tests/constrain_blockdiag.R | 36 + ergm-3.5.1/ergm/tests/constrain_degrees.R | 3 ergm-3.5.1/ergm/tests/constrain_observed.R | 4 ergm-3.5.1/ergm/tests/constraint_conflict.R | 10 ergm-3.5.1/ergm/tests/estflo.R | 4 ergm-3.5.1/ergm/tests/miss_tests.R | 1 ergm-3.5.1/ergm/tests/off/samplike_condoutdeg.R |only ergm-3.5.1/ergm/tests/target_offset.R | 20 ergm-3.5.1/ergm/tests/termTests.flexible.R | 14 59 files changed, 1289 insertions(+), 1074 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between statnet.common versions 3.2.3 dated 2015-08-05 and 3.3.0 dated 2015-10-24
DESCRIPTION | 14 ++++++++------ MD5 | 11 +++++++---- NAMESPACE | 2 +- NEWS | 9 +++++++-- R/formula.utilities.R |only R/misc.utilities.R | 21 +++++++++++++++++++++ man/formula.utilities.Rd |only man/vector.namesmatch.Rd |only 8 files changed, 44 insertions(+), 13 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Random Effects and/or Sample Selection Models for Panel Count
Data
Description: A high performance package implementing random effects and/or sample selection models for panel count data.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between PanelCount versions 1.0.1 dated 2015-08-31 and 1.0.9 dated 2015-10-24
DESCRIPTION | 14 ++++++------ MD5 | 34 ++++++++++++++--------------- NAMESPACE | 1 R/CRE.R | 44 ++++++++++++++++++++++++++++++------- R/CRE_SS.R | 63 +++++++++++++++++++++++++++++++++++++++++++----------- R/PLN_RE.R | 28 ++++++++++++++++++------ R/PanelCount.R | 4 ++- R/PoissonRE.R | 24 ++++++++++++++++---- R/ProbitRE.R | 26 +++++++++++++++++----- R/data.R | 4 +-- data/rt.RData |binary man/CRE.Rd | 25 ++++++++++++++++++--- man/CRE_SS.Rd | 31 +++++++++++++++++++++----- man/PLN_RE.Rd | 24 +++++++++++++++++--- man/PanelCount.Rd | 5 ++++ man/PoissonRE.Rd | 14 +++++++++--- man/ProbitRE.Rd | 15 ++++++++++-- man/rt.Rd | 4 +-- 18 files changed, 274 insertions(+), 86 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.4.1 dated 2015-10-17 and 0.4.2 dated 2015-10-24
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++--------- NEWS | 5 ++++ R/qic.R | 6 +++-- R/tcc.R | 12 ++++++----- inst/doc/controlcharts.R | 8 +++---- inst/doc/controlcharts.Rmd | 16 +++++++------- inst/doc/controlcharts.html | 48 ++++++++++++++++++++++---------------------- inst/doc/runcharts.html | 18 ++++++++-------- man/plot.tcc.Rd | 4 +-- vignettes/controlcharts.Rmd | 16 +++++++------- 11 files changed, 85 insertions(+), 76 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-7 dated 2015-07-23 and 1.8-8 dated 2015-10-24
ChangeLog | 55 +++ DESCRIPTION | 6 MD5 | 67 ++-- NAMESPACE | 4 R/bam.r | 268 ++++++++++++++---- R/efam.r | 89 +++--- R/fast-REML.r | 21 - R/gam.fit3.r | 38 +- R/gam.fit4.r | 151 +++++++--- R/gamlss.r | 13 R/mgcv.r | 74 +++-- R/plots.r | 19 - R/smooth.r | 291 ++++++++++++++++++-- R/soap.r | 17 - man/bam.Rd | 13 man/mgcv-package.Rd | 2 man/mgcv-parallel.Rd | 5 man/negbin.Rd | 2 man/plot.gam.Rd | 10 man/predict.bam.Rd | 12 man/predict.gam.Rd | 12 man/single.index.Rd | 2 man/smooth.construct.Rd | 4 man/smooth.construct.gp.smooth.spec.Rd |only man/smooth.construct.sos.smooth.spec.Rd | 3 man/smooth.terms.Rd | 21 - man/smoothCon.Rd | 8 man/t2.Rd | 9 man/uniquecombs.Rd | 22 + man/ziP.Rd | 46 ++- po/R-mgcv.pot | 67 +++- src/gdi.c | 464 ++++++++++++++++++++------------ src/init.c | 4 src/mat.c | 18 - src/mgcv.h | 12 35 files changed, 1343 insertions(+), 506 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.2.1 dated 2015-09-09 and 0.2.4 dated 2015-10-24
DESCRIPTION | 8 MD5 | 34 - NAMESPACE | 2 NEWS | 12 R/node.R | 10 R/node_actives.R | 3 R/node_methods.R | 23 - R/node_methods_traversal.R | 6 data/acme.rda |binary inst/doc/applications.R | 70 --- inst/doc/applications.Rmd | 84 ---- inst/doc/applications.html | 161 +------- inst/doc/data.tree.html | 35 - inst/extdata/flare.json | 758 +++++++++++++++++++------------------- man/NODE_RESERVED_NAMES_CONST.Rd | 2 man/Node.Rd | 1 tests/testthat/test-treeMethods.R | 31 + vignettes/applications.Rmd | 84 ---- 18 files changed, 528 insertions(+), 796 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: A high performance package estimating Cox Model when an even has more than one causes. It also supports random and fixed effects, tied events, and time-varying variables.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between CoxPlus versions 1.1.0 dated 2015-09-06 and 1.1.1 dated 2015-10-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fastCox.R | 2 ++ man/CoxPlus.Rd | 5 +++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Interactive Visualization of Topic Models
Description: Tools to create an interactive web-based visualization of a
topic model that has been fit to a corpus of text data using
Latent Dirichlet Allocation (LDA). Given the estimated parameters of
the topic model, it computes various summary statistics as input to
an interactive visualization built with D3.js that is accessed via
a browser. The goal is to help users interpret the topics in their
LDA topic model.
Author: Carson Sievert [aut, cre],
Kenny Shirley [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between LDAvis versions 0.2 dated 2015-01-23 and 0.3.2 dated 2015-10-24
LDAvis-0.2/LDAvis/inst/examples |only LDAvis-0.3.2/LDAvis/DESCRIPTION | 10 +- LDAvis-0.3.2/LDAvis/MD5 | 47 +++++----- LDAvis-0.3.2/LDAvis/NAMESPACE | 4 LDAvis-0.3.2/LDAvis/NEWS | 20 ++++ LDAvis-0.3.2/LDAvis/R/createJSON.R | 65 +++++++++----- LDAvis-0.3.2/LDAvis/R/imports.R |only LDAvis-0.3.2/LDAvis/R/runShiny.R | 2 LDAvis-0.3.2/LDAvis/R/serVis.R | 6 - LDAvis-0.3.2/LDAvis/R/shiny.R |only LDAvis-0.3.2/LDAvis/README.md | 25 ++++- LDAvis-0.3.2/LDAvis/build/vignette.rds |binary LDAvis-0.3.2/LDAvis/inst/doc/details.Rnw | 9 +- LDAvis-0.3.2/LDAvis/inst/doc/details.pdf |binary LDAvis-0.3.2/LDAvis/inst/htmljs/index.html | 7 - LDAvis-0.3.2/LDAvis/inst/htmljs/lda.css | 77 +---------------- LDAvis-0.3.2/LDAvis/inst/htmljs/ldavis.js | 46 ++++------ LDAvis-0.3.2/LDAvis/inst/shiny |only LDAvis-0.3.2/LDAvis/man/TwentyNewsgroups.Rd | 3 LDAvis-0.3.2/LDAvis/man/createJSON.Rd | 126 +++++++++++++--------------- LDAvis-0.3.2/LDAvis/man/jsPCA.Rd | 13 +- LDAvis-0.3.2/LDAvis/man/renderVis.Rd |only LDAvis-0.3.2/LDAvis/man/runShiny.Rd | 25 ++--- LDAvis-0.3.2/LDAvis/man/serVis.Rd | 44 ++++----- LDAvis-0.3.2/LDAvis/man/visOutput.Rd |only LDAvis-0.3.2/LDAvis/vignettes/details.Rnw | 9 +- 26 files changed, 259 insertions(+), 279 deletions(-)
Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms for design and
analysis of probability surveys. The functions are tailored for Generalized
Random Tessellation Stratified survey designs.
Author: Tom Kincaid [aut, cre],
Tony Olsen [aut],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Tom Kincaid <Kincaid.Tom@epa.gov>
Diff between spsurvey versions 3.0 dated 2015-05-22 and 3.1 dated 2015-10-23
spsurvey-3.0/spsurvey/src/insideGridCell.c |only spsurvey-3.0/spsurvey/src/pickSamplePoints.c |only spsurvey-3.0/spsurvey/vignettes/FL_lakes.tab |only spsurvey-3.0/spsurvey/vignettes/IN_streams.tab |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.dbf |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.shp |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.shx |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.dbf |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.prj |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.shp |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.shx |only spsurvey-3.0/spsurvey/vignettes/NLA_2007.tab |only spsurvey-3.0/spsurvey/vignettes/SC_estuaries.tab |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.dbf |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.prj |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.shp |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.shx |only spsurvey-3.0/spsurvey/vignettes/decon_data.tab |only spsurvey-3.0/spsurvey/vignettes/lLuck_Ash_streams.prj |only spsurvey-3.1/spsurvey/DESCRIPTION | 11 spsurvey-3.1/spsurvey/MD5 | 173 ++++------ spsurvey-3.1/spsurvey/NAMESPACE | 19 - spsurvey-3.1/spsurvey/R/AAA.R | 2 spsurvey-3.1/spsurvey/R/SpatialDesign-methods.R | 3 spsurvey-3.1/spsurvey/R/change.analysis.R | 13 spsurvey-3.1/spsurvey/R/change.est.R | 13 spsurvey-3.1/spsurvey/R/changevar.mean.R | 11 spsurvey-3.1/spsurvey/R/changevar.prop.R | 11 spsurvey-3.1/spsurvey/R/changevar.size.R | 11 spsurvey-3.1/spsurvey/build/vignette.rds |binary spsurvey-3.1/spsurvey/data/FL_lakes.rda |binary spsurvey-3.1/spsurvey/data/IN_streams.rda |binary spsurvey-3.1/spsurvey/data/Luck_Ash_streams.rda |binary spsurvey-3.1/spsurvey/data/NE_lakes.rda |binary spsurvey-3.1/spsurvey/data/NLA_2007.rda |binary spsurvey-3.1/spsurvey/data/SC_estuaries.rda |binary spsurvey-3.1/spsurvey/data/UT_ecoregions.rda |binary spsurvey-3.1/spsurvey/data/decon_data.rda |binary spsurvey-3.1/spsurvey/inst/CITATION | 4 spsurvey-3.1/spsurvey/inst/NEWS.Rd | 17 + spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Area_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Area_Design.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Area_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.R | 4 spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.Rnw | 14 spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CHANGES.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Finite_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Finite_Design.Rnw | 20 - spsurvey-3.1/spsurvey/inst/doc/Finite_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Linear_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Linear_Design.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Linear_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/README.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/UserGuide.pdf |binary spsurvey-3.1/spsurvey/man/change.analysis.Rd | 13 spsurvey-3.1/spsurvey/man/change.est.Rd | 13 spsurvey-3.1/spsurvey/man/spsurvey-internal.Rd | 5 spsurvey-3.1/spsurvey/src/dbfFileParser.c | 100 ++---- spsurvey-3.1/spsurvey/src/grts.c | 28 - spsurvey-3.1/spsurvey/src/grtsarea.c | 7 spsurvey-3.1/spsurvey/src/grtslin.c | 28 - spsurvey-3.1/spsurvey/src/grtspts.c | 5 spsurvey-3.1/spsurvey/src/insideAreaGridCell.c | 28 - spsurvey-3.1/spsurvey/src/insideLinearGridCell.c | 28 - spsurvey-3.1/spsurvey/src/irsarea.c | 29 - spsurvey-3.1/spsurvey/src/irslin.c | 32 - spsurvey-3.1/spsurvey/src/pickAreaSamplePoints.c | 28 - spsurvey-3.1/spsurvey/src/pickGridCells.c | 11 spsurvey-3.1/spsurvey/src/pickLinearSamplePoints.c | 28 - spsurvey-3.1/spsurvey/src/ranho.c | 5 spsurvey-3.1/spsurvey/src/shapeParser.c | 289 +++++++----------- spsurvey-3.1/spsurvey/src/spsurvey.h | 6 spsurvey-3.1/spsurvey/vignettes/Area_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Area_Design.Rnw | 16 spsurvey-3.1/spsurvey/vignettes/CDF_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/CDF_Deconvolution.Rnw | 14 spsurvey-3.1/spsurvey/vignettes/Finite_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Finite_Design.Rnw | 20 - spsurvey-3.1/spsurvey/vignettes/Linear_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Linear_Design.Rnw | 16 spsurvey-3.1/spsurvey/vignettes/Risk_Analysis.Rnw | 16 97 files changed, 743 insertions(+), 677 deletions(-)
Title: An Information About Deputies and Votings in Polish Diet
Description: Set of functions that access information about deputies and votings in Polish diet from webpage http://www.sejm.gov.pl/.
The package was developed as a result of an internship in MI2 Group - http://mi2.mini.pw.edu.pl/, Faculty of Mathematics and Information Science, Warsaw University of Technology.
Author: Piotr Smuda [aut, cre],
Przemyslaw Biecek [aut],
Tomasz Mikolajczyk [ctb]
Maintainer: Piotr Smuda <piotrsmuda@gmail.com>
Diff between sejmRP versions 1.1 dated 2015-09-27 and 1.2 dated 2015-10-23
DESCRIPTION | 11 - MD5 | 67 +++++----- NAMESPACE | 3 R/create_database.R | 6 R/deputies_get_data.R | 2 R/get_deputies_table.R | 28 ++-- R/get_filtered_votes.R | 86 ++++++------- R/get_statements_table.R | 33 ++--- R/get_votes_table.R | 34 ++--- R/get_votings_table.R | 30 ++-- R/safe_html.R |only R/statements_create_table.R | 14 +- R/statements_get_statement.R | 9 - R/statements_get_statements_data.R | 2 R/statements_get_statements_table.R |only R/statements_update_table.R | 33 ++++- R/votes_get_clubs_links.R | 2 R/votes_update_table.R | 12 + R/votings_get_date.R | 2 R/votings_get_votings_links.R | 2 R/votings_update_table.R | 10 + man/create_database.Rd | 3 man/get_deputies_table.Rd | 2 man/get_filtered_votes.Rd | 4 man/get_statements_table.Rd | 4 man/get_votes_table.Rd | 6 man/get_votings_table.Rd | 2 man/safe_html.Rd |only man/statements_get_statement.Rd | 4 man/statements_get_statements_table.Rd |only man/statements_update_table.Rd | 5 man/votes_update_table.Rd | 5 man/votings_update_table.Rd | 5 tests/testthat/test_get_statements_table.R | 2 tests/testthat/test_statements_get_statements_data.R | 2 tests/testthat/test_statements_get_statements_table.R |only vignettes/INSTRUCTION.Rmd | 111 +++++++++--------- 37 files changed, 306 insertions(+), 235 deletions(-)
Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
<kimkspeer@gmail.com>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between likert versions 1.2 dated 2014-10-17 and 1.3.0 dated 2015-10-23
DESCRIPTION | 14 ++--- MD5 | 105 +++++++++++++++++++------------------- NAMESPACE | 23 ++++++-- NEWS | 13 ++++ R/likert-package.R | 27 +++++++-- R/likert.R | 37 ++++++++++--- R/plot.histogram.R | 4 + R/plot.likert.bar.r | 115 ++++++++++++++++++++++++++++-------------- R/plot.likert.gap.R | 2 R/plot.likert.heat.r | 2 R/plot.likert.matrix.r | 2 R/shinyLikert.R | 1 R/summary.likert.r | 7 ++ build/vignette.rds |binary data/datalist | 1 data/sasr.rda |only demo/00Index | 1 demo/GroupedFactors.R |only demo/RecodeFactors.R | 2 demo/likert.R | 9 +-- inst/doc/likert-xtable.R | 11 +--- inst/doc/likert-xtable.Rnw | 5 - inst/doc/likert-xtable.pdf |binary inst/shiny/server.R | 2 man/MathAnxiety.Rd | 3 - man/MathAnxietyGender.Rd | 3 - man/abs_formatter.Rd | 3 - man/align.plots.Rd | 3 - man/gap.Rd | 3 - man/label_wrap_mod.Rd | 3 - man/likert-package.Rd | 3 - man/likert.Rd | 9 ++- man/likert.bar.plot.Rd | 20 ++++--- man/likert.density.plot.Rd | 3 - man/likert.heat.plot.Rd | 3 - man/likert.histogram.plot.Rd | 3 - man/likert.matrix.plot.Rd | 3 - man/mass.Rd | 3 - man/pisaitems.Rd | 3 - man/plot.likert.Rd | 3 - man/plot.likert.gap.Rd | 3 - man/print.likert.Rd | 3 - man/print.likert.bar.plot.Rd | 3 - man/print.likert.gap.Rd | 3 - man/print.likert.heat.plot.Rd | 3 - man/print.xlikert.Rd | 3 - man/recode.Rd | 3 - man/reverse.levels.Rd | 3 - man/sasr.Rd |only man/shinyLikert.Rd | 3 - man/summary.likert.Rd | 3 - man/summary.likert.gap.Rd | 3 - man/xtable.likert.Rd | 3 - man/zeroGrob.Rd | 3 - vignettes/likert-xtable.Rnw | 5 - 55 files changed, 322 insertions(+), 176 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-3 dated 2015-06-16 and 0.1-4 dated 2015-10-23
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- man/DESP-package.Rd | 4 ++-- man/DESP_MST.Rd | 2 +- man/DESP_PML.Rd | 2 +- man/DESP_RML.Rd | 2 +- man/DESP_RV.Rd | 2 +- man/DESP_SPT.Rd | 2 +- src/Makevars | 2 ++ src/scs/scs.mk | 8 +++++++- 11 files changed, 36 insertions(+), 23 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: An implementation of the jDE variant of the Differential Evolution
stochastic algorithm for global optimization of nonlinear programming problems.
Author: Eduardo L. T. Conceicao and Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.0-3 dated 2015-07-19 and 1.0-4 dated 2015-10-23
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/JDEoptim.Rd | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Forecast Verification Routines for the SPECS FP7 Project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.4-0 dated 2015-09-11 and 0.4-1 dated 2015-10-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Detrend.R | 5 +++-- R/ReliabilityDiagram.R | 23 ++++++++++++++++++++--- man/ClimEns.Rd | 2 +- man/GetDensity.Rd | 2 +- man/PlotDressedEns.Rd | 6 +++--- man/ReliabilityDiagram.Rd | 7 ++++--- 9 files changed, 45 insertions(+), 26 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and, for binomial data, the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 2.0.1 dated 2015-06-19 and 2.0.2 dated 2015-10-23
DESCRIPTION | 10 ++-- MD5 | 36 +++++++-------- NAMESPACE | 3 + R/CV.G.Poisson.R | 2 R/CV.Poisson.R | 13 ++++- R/Performance.G.Poisson.R | 2 R/Performance.Poisson.R | 2 man/Analyze.Binomial.Rd | 36 +++++++-------- man/AnalyzeSetUp.Binomial.Rd | 28 ++++++------ man/CV.Binomial.Rd | 12 ++--- man/CV.G.Binomial.Rd | 10 ++-- man/CV.G.Poisson.Rd | 46 ++++++++++---------- man/CV.Poisson.Rd | 61 +++++++++++++------------- man/Performance.G.Binomial.Rd | 10 ++-- man/Performance.G.Poisson.Rd | 84 ++++++++++++++++++------------------ man/Performance.Poisson.Rd | 96 ++++++++++++++++++++++++++---------------- man/SampleSize.Binomial.Rd | 14 +++--- man/SampleSize.Poisson.Rd | 83 ++++++++++++++++++++---------------- man/Sequential-package.Rd | 22 +++++---- 19 files changed, 311 insertions(+), 259 deletions(-)
Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
Description: An implementation of multiscale bootstrap resampling for
assessing the uncertainty in hierarchical cluster analysis.
It provides AU (approximately unbiased) p-value as well as
BP (bootstrap probability) value for each cluster in a dendrogram.
Author: Ryota Suzuki <suzuki@ef-prime.com>, Hidetoshi Shimodaira
<shimo@sigmath.es.osaka-u.ac.jp>
Maintainer: Ryota Suzuki <suzuki@ef-prime.com>
Diff between pvclust versions 1.3-2 dated 2014-12-22 and 2.0-0 dated 2015-10-23
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 6 R/pvclust-internal.R | 347 ++++++++++++++++++++++++++------ R/pvclust.R | 538 +++++++++++++++++++++++---------------------------- man/pvclust.Rd | 79 +++++-- 6 files changed, 591 insertions(+), 397 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.2 dated 2015-07-26 and 1.6.3 dated 2015-10-23
checkmate-1.6.2/checkmate/NEWS |only checkmate-1.6.3/checkmate/DESCRIPTION | 6 checkmate-1.6.3/checkmate/MD5 | 180 +++++----- checkmate-1.6.3/checkmate/NAMESPACE | 3 checkmate-1.6.3/checkmate/R/AssertCollection.r |only checkmate-1.6.3/checkmate/R/asInteger.r | 14 checkmate-1.6.3/checkmate/R/checkAccess.r | 4 checkmate-1.6.3/checkmate/R/checkArray.r | 4 checkmate-1.6.3/checkmate/R/checkAtomic.r | 4 checkmate-1.6.3/checkmate/R/checkAtomicVector.r | 4 checkmate-1.6.3/checkmate/R/checkCharacter.r | 13 checkmate-1.6.3/checkmate/R/checkChoice.r | 4 checkmate-1.6.3/checkmate/R/checkClass.r | 4 checkmate-1.6.3/checkmate/R/checkComplex.r | 4 checkmate-1.6.3/checkmate/R/checkCount.r | 4 checkmate-1.6.3/checkmate/R/checkDataFrame.r | 13 checkmate-1.6.3/checkmate/R/checkDirectory.r | 4 checkmate-1.6.3/checkmate/R/checkEnvironment.r | 4 checkmate-1.6.3/checkmate/R/checkFactor.r | 11 checkmate-1.6.3/checkmate/R/checkFile.r | 5 checkmate-1.6.3/checkmate/R/checkFlag.r | 4 checkmate-1.6.3/checkmate/R/checkFunction.r | 4 checkmate-1.6.3/checkmate/R/checkInt.r | 4 checkmate-1.6.3/checkmate/R/checkInteger.r | 4 checkmate-1.6.3/checkmate/R/checkIntegerish.r | 4 checkmate-1.6.3/checkmate/R/checkList.r | 4 checkmate-1.6.3/checkmate/R/checkLogical.r | 4 checkmate-1.6.3/checkmate/R/checkMatrix.r | 4 checkmate-1.6.3/checkmate/R/checkNamed.r | 4 checkmate-1.6.3/checkmate/R/checkNames.r | 4 checkmate-1.6.3/checkmate/R/checkNull.r | 4 checkmate-1.6.3/checkmate/R/checkNumber.r | 4 checkmate-1.6.3/checkmate/R/checkNumeric.r | 4 checkmate-1.6.3/checkmate/R/checkPathForOutput.r | 4 checkmate-1.6.3/checkmate/R/checkPercentage.r | 4 checkmate-1.6.3/checkmate/R/checkScalar.r | 4 checkmate-1.6.3/checkmate/R/checkScalarNA.r | 4 checkmate-1.6.3/checkmate/R/checkSetEqual.r | 14 checkmate-1.6.3/checkmate/R/checkString.r | 4 checkmate-1.6.3/checkmate/R/checkSubset.r | 4 checkmate-1.6.3/checkmate/R/checkVector.r | 4 checkmate-1.6.3/checkmate/R/helper.r | 16 checkmate-1.6.3/checkmate/build/vignette.rds |binary checkmate-1.6.3/checkmate/inst/NEWS.md |only checkmate-1.6.3/checkmate/inst/README.md |only checkmate-1.6.3/checkmate/inst/doc/checkmate.R | 26 - checkmate-1.6.3/checkmate/inst/doc/checkmate.Rmd | 52 -- checkmate-1.6.3/checkmate/inst/doc/checkmate.html | 39 -- checkmate-1.6.3/checkmate/man/AssertCollection.Rd |only checkmate-1.6.3/checkmate/man/asInteger.Rd | 9 checkmate-1.6.3/checkmate/man/checkAccess.Rd | 5 checkmate-1.6.3/checkmate/man/checkArray.Rd | 5 checkmate-1.6.3/checkmate/man/checkAtomic.Rd | 5 checkmate-1.6.3/checkmate/man/checkAtomicVector.Rd | 5 checkmate-1.6.3/checkmate/man/checkCharacter.Rd | 5 checkmate-1.6.3/checkmate/man/checkChoice.Rd | 5 checkmate-1.6.3/checkmate/man/checkClass.Rd | 5 checkmate-1.6.3/checkmate/man/checkComplex.Rd | 5 checkmate-1.6.3/checkmate/man/checkCount.Rd | 5 checkmate-1.6.3/checkmate/man/checkDataFrame.Rd | 6 checkmate-1.6.3/checkmate/man/checkDirectory.Rd | 5 checkmate-1.6.3/checkmate/man/checkEnvironment.Rd | 5 checkmate-1.6.3/checkmate/man/checkFactor.Rd | 5 checkmate-1.6.3/checkmate/man/checkFile.Rd | 5 checkmate-1.6.3/checkmate/man/checkFlag.Rd | 5 checkmate-1.6.3/checkmate/man/checkFunction.Rd | 6 checkmate-1.6.3/checkmate/man/checkInt.Rd | 5 checkmate-1.6.3/checkmate/man/checkInteger.Rd | 5 checkmate-1.6.3/checkmate/man/checkIntegerish.Rd | 5 checkmate-1.6.3/checkmate/man/checkList.Rd | 5 checkmate-1.6.3/checkmate/man/checkLogical.Rd | 5 checkmate-1.6.3/checkmate/man/checkMatrix.Rd | 5 checkmate-1.6.3/checkmate/man/checkNamed.Rd | 5 checkmate-1.6.3/checkmate/man/checkNames.Rd | 5 checkmate-1.6.3/checkmate/man/checkNull.Rd | 5 checkmate-1.6.3/checkmate/man/checkNumber.Rd | 5 checkmate-1.6.3/checkmate/man/checkNumeric.Rd | 5 checkmate-1.6.3/checkmate/man/checkPathForOutput.Rd | 5 checkmate-1.6.3/checkmate/man/checkPercentage.Rd | 5 checkmate-1.6.3/checkmate/man/checkScalar.Rd | 5 checkmate-1.6.3/checkmate/man/checkScalarNA.Rd | 5 checkmate-1.6.3/checkmate/man/checkSetEqual.Rd | 9 checkmate-1.6.3/checkmate/man/checkString.Rd | 5 checkmate-1.6.3/checkmate/man/checkSubset.Rd | 5 checkmate-1.6.3/checkmate/man/checkVector.Rd | 5 checkmate-1.6.3/checkmate/src/all_missing.h | 1 checkmate-1.6.3/checkmate/src/any_missing.c | 25 - checkmate-1.6.3/checkmate/src/any_missing.h | 1 checkmate-1.6.3/checkmate/src/qassert.c | 10 checkmate-1.6.3/checkmate/tests/testthat/test_AssertCollection.r |only checkmate-1.6.3/checkmate/tests/testthat/test_checkSetEqual.r | 3 checkmate-1.6.3/checkmate/tests/testthat/test_qtest.r | 20 + checkmate-1.6.3/checkmate/tests/testthat/test_qtestr.r | 3 checkmate-1.6.3/checkmate/vignettes/checkmate.Rmd | 57 ++- 94 files changed, 463 insertions(+), 359 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.2 dated 2015-02-27 and 1.7.3.0 dated 2015-10-23
DESCRIPTION | 8 MD5 | 135 +-- NAMESPACE | 7 NEWS | 18 R/Contlcmm.R | 1470 ++++++++++++++++++++------------------ R/Jointlcmm.R | 289 ++++++- R/Ordlcmm.R | 1109 +++++++++++++++-------------- R/VarCov.Jointlcmm.R | 2 R/VarCov.lcmm.R | 2 R/VarCov.multlcmm.R | 2 R/VarCovRE.hlme.R | 280 +++---- R/VarExpl.Jointlcmm.R | 2 R/VarExpl.lcmm.R | 2 R/VarExpl.multlcmm.R | 7 R/WaldMult.R | 302 ++++--- R/cuminc.R | 22 R/dynpred.R | 44 - R/epoce.R | 7 R/estimates.Jointlcmm.R | 2 R/estimates.lcmm.R | 2 R/estimates.multlcmm.R | 2 R/hlme.R | 1255 +++++++++++++++++---------------- R/lcmm.R | 19 R/multlcmm.R | 1743 ++++++++++++++++++++++++---------------------- R/plot.R | 8 R/plot.predictlink.R | 4 R/plotbaselinerisk.R | 2 R/plotlinkfunction.R | 2 R/plotlinkfunctionmult.R | 43 - R/plotpostprob.R | 2 R/plotresid.R | 2 R/plotsurvival.R | 2 R/postprob.Jointlcmm.R | 2 R/predictL.Jointlcmm.R | 30 R/predictL.lcmm.R | 20 R/predictL.multlcmm.R | 20 R/predictY.Jointlcmm.R | 51 + R/predictY.hlme.R | 18 R/predictY.lcmm.R | 53 + R/predictY.multlcmm.R | 99 +- R/predictlink.Jointlcmm.R | 30 R/predictlink.lcmm.R | 30 R/predictlink.multlcmm.R | 35 R/print.Jointlcmm.R | 13 R/print.hlme.R | 15 R/print.lcmm.R | 17 R/print.multlcmm.R | 16 R/summary.Jointlcmm.R | 751 ++++++++++--------- R/summary.hlme.R | 400 ++++++---- R/summary.lcmm.R | 526 ++++++++----- R/summary.multlcmm.R | 724 ++++++++++--------- R/summarytable.R | 4 inst |only man/Jointlcmm.Rd | 21 man/hlme.Rd | 20 man/lcmm-package.Rd | 4 man/lcmm.Rd | 25 man/multlcmm.Rd | 27 src/AOptim.f90 | 95 ++ src/Jointhet.f90 | 161 ++-- src/Makevars | 1 src/cvpl.f90 | 147 ++- src/hetmixCont.f90 | 190 +++-- src/hetmixContMult.f90 | 308 ++++---- src/hetmixOrd.f90 | 215 ++++- src/hetmixlin.f90 | 106 ++ src/postprob2.f90 | 2 src/predictCont.f90 | 15 src/predictMult.f90 | 13 69 files changed, 6380 insertions(+), 4620 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6 dated 2015-07-23 and 1.6.4 dated 2015-10-23
DESCRIPTION | 12 +++++------ MD5 | 52 ++++++++++++++++++++++++------------------------ R/GoogleMapsPlot.R | 26 ++++++++++++------------ R/RcppExports.R |only R/TheilSen.R | 16 ++++++++++++-- R/aqStats.R | 12 +++++------ R/calendarPlot.R | 4 ++- R/checkPrep.R | 32 ++++++++++++++++------------- R/conditionalQuantile.R | 10 +++++---- R/cutData.R | 4 +-- R/importAURN.R | 8 +++++-- R/openColours.R | 4 +-- R/polarAnnulus.R | 3 +- R/scatterPlot.R | 2 - R/summaryPlot.R | 2 - R/timeAverage.R | 19 ++++++++++------- R/timeProp.R | 2 - R/timeVariation.R | 2 - R/utilities.R | 6 +++-- man/TheilSen.Rd | 6 +++-- man/calendarPlot.Rd | 4 ++- man/openColours.Rd | 4 +-- man/polarAnnulus.Rd | 3 +- man/summaryPlot.Rd | 2 - man/timeAverage.Rd | 17 ++++++++------- man/timeVariation.Rd | 2 - src/Cquantile.cpp | 6 +++-- src/RcppExports.cpp |only 28 files changed, 151 insertions(+), 109 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.2 dated 2015-10-03 and 2.3 dated 2015-10-23
DESCRIPTION | 8 +-- MD5 | 10 +-- NAMESPACE | 3 - R/F.window.R | 121 ++++++++++++++++++++++++++--------------------- man/F.window.Rd | 23 ++------ man/joint.Cox-package.Rd | 4 - 6 files changed, 88 insertions(+), 81 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.4 dated 2015-08-31 and 0.3 dated 2015-10-22
RGA-0.2.4/RGA/inst/doc/common-queries.R |only RGA-0.2.4/RGA/inst/doc/common-queries.Rmd |only RGA-0.2.4/RGA/inst/doc/common-queries.html |only RGA-0.2.4/RGA/vignettes/common-queries.Rmd |only RGA-0.3/RGA/DESCRIPTION | 25 +-- RGA-0.3/RGA/MD5 | 163 +++++++++++++------------ RGA-0.3/RGA/NAMESPACE | 18 -- RGA-0.3/RGA/R/accounts.R | 4 RGA-0.3/RGA/R/auth.R | 85 +++++++------ RGA-0.3/RGA/R/convert.R | 108 ++++++---------- RGA-0.3/RGA/R/custom-dims.R | 8 - RGA-0.3/RGA/R/custom-mets.R | 8 - RGA-0.3/RGA/R/custom-sources.R | 4 RGA-0.3/RGA/R/date-ranges.R |only RGA-0.3/RGA/R/env.R |only RGA-0.3/RGA/R/experiments.R | 8 - RGA-0.3/RGA/R/filters.R | 8 - RGA-0.3/RGA/R/ga.R | 23 ++- RGA-0.3/RGA/R/get-data.R | 64 +++++---- RGA-0.3/RGA/R/goals.R | 8 - RGA-0.3/RGA/R/mcf.R | 21 +-- RGA-0.3/RGA/R/metadata.R | 45 +++--- RGA-0.3/RGA/R/mgmt.R | 36 +++-- RGA-0.3/RGA/R/profiles.R | 14 +- RGA-0.3/RGA/R/query.R | 33 ++--- RGA-0.3/RGA/R/realtime.R | 18 -- RGA-0.3/RGA/R/report.R | 74 +++-------- RGA-0.3/RGA/R/request.R | 120 ++++++++---------- RGA-0.3/RGA/R/segments.R | 2 RGA-0.3/RGA/R/unsampled.R | 8 - RGA-0.3/RGA/R/uploads.R |only RGA-0.3/RGA/R/url.R | 29 ++-- RGA-0.3/RGA/R/utils.R | 52 ++----- RGA-0.3/RGA/R/webproperties.R | 14 +- RGA-0.3/RGA/R/zzz.R | 3 RGA-0.3/RGA/README.md | 8 - RGA-0.3/RGA/build/vignette.rds |binary RGA-0.3/RGA/data/ga.rda |binary RGA-0.3/RGA/inst/NEWS.Rd | 17 ++ RGA-0.3/RGA/inst/doc/authorize.Rmd | 18 +- RGA-0.3/RGA/inst/doc/authorize.html | 102 +++++++++------ RGA-0.3/RGA/inst/doc/management-api.html | 52 +++++-- RGA-0.3/RGA/inst/doc/metadata-api.html | 56 +++++--- RGA-0.3/RGA/inst/doc/reporting-api.Rmd | 19 +- RGA-0.3/RGA/inst/doc/reporting-api.html | 73 ++++++----- RGA-0.3/RGA/inst/shiny-examples |only RGA-0.3/RGA/man/authorize.Rd | 6 RGA-0.3/RGA/man/get_custom_dimension.Rd | 5 RGA-0.3/RGA/man/get_custom_metric.Rd | 5 RGA-0.3/RGA/man/get_experiment.Rd | 5 RGA-0.3/RGA/man/get_filter.Rd | 5 RGA-0.3/RGA/man/get_ga.Rd | 16 +- RGA-0.3/RGA/man/get_goal.Rd | 5 RGA-0.3/RGA/man/get_mcf.Rd | 14 +- RGA-0.3/RGA/man/get_profile.Rd | 9 + RGA-0.3/RGA/man/get_realtime.Rd | 4 RGA-0.3/RGA/man/get_unsampled_report.Rd | 5 RGA-0.3/RGA/man/get_upload.Rd |only RGA-0.3/RGA/man/get_webproperty.Rd | 9 + RGA-0.3/RGA/man/list_accounts.Rd | 7 - RGA-0.3/RGA/man/list_custom_dimensions.Rd | 5 RGA-0.3/RGA/man/list_custom_metrics.Rd | 5 RGA-0.3/RGA/man/list_custom_sources.Rd | 5 RGA-0.3/RGA/man/list_dimsmets.Rd | 5 RGA-0.3/RGA/man/list_experiments.Rd | 5 RGA-0.3/RGA/man/list_filters.Rd | 5 RGA-0.3/RGA/man/list_goals.Rd | 5 RGA-0.3/RGA/man/list_profiles.Rd | 7 - RGA-0.3/RGA/man/list_segments.Rd | 5 RGA-0.3/RGA/man/list_unsampled_reports.Rd | 5 RGA-0.3/RGA/man/list_uploads.Rd |only RGA-0.3/RGA/man/list_webproperties.Rd | 9 - RGA-0.3/RGA/man/shiny_dimsmets.Rd |only RGA-0.3/RGA/tests/testthat/test-auth.R | 12 - RGA-0.3/RGA/tests/testthat/test-convert-ga.R | 15 +- RGA-0.3/RGA/tests/testthat/test-convert-mcf.R | 92 +++++++------- RGA-0.3/RGA/tests/testthat/test-convert-mgmt.R | 19 +- RGA-0.3/RGA/tests/testthat/test-metadata.R | 4 RGA-0.3/RGA/tests/testthat/test-url.R | 4 RGA-0.3/RGA/vignettes/authorize.Rmd | 18 +- RGA-0.3/RGA/vignettes/reporting-api.Rmd | 19 +- 81 files changed, 899 insertions(+), 788 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.9.5 dated 2015-10-07 and 1.10.0 dated 2015-10-22
CHANGELOG | 12 ++ DESCRIPTION | 8 - MD5 | 68 ++++++------ NAMESPACE | 7 - R/binning.R | 278 +++++++++++++---------------------------------------- R/kcde.R | 8 - R/kcopula.R | 6 - R/kda.R | 53 +++++----- R/kdde.R | 219 ++++++++++++++++++++++++++++++++++------- R/kde-test.R | 2 R/kde.R | 32 +++--- R/kfe.R | 147 ---------------------------- R/normal.R | 55 ++++------ R/prelim.R | 17 +-- R/selector.R | 86 ++++++++-------- inst/doc/kde.pdf |binary man/Hlscv.Rd | 24 ++-- man/Hns.Rd | 7 - man/Hpi.Rd | 4 man/Hscv.Rd | 4 man/binning.Rd | 18 ++- man/contour.Rd | 2 man/ise.mixt.Rd | 2 man/kcde.Rd | 5 man/kcopula.Rd | 4 man/kda.Rd | 21 ++-- man/kdde.Rd | 13 +- man/kde.Rd | 14 +- man/kroc.Rd | 4 man/ks-internal.Rd | 10 - man/ks-package.Rd | 7 - man/plot.kda.Rd | 6 - man/plot.kdde.Rd | 10 - man/plot.kde.Rd | 6 - man/plotmixt.Rd | 6 - 35 files changed, 538 insertions(+), 627 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.1 dated 2015-10-10 and 0.8.3 dated 2015-10-22
DESCRIPTION | 10 +-- MD5 | 136 ++++++++++++++++++++++++------------------------ R/BluegillJL.R | 19 +++--- R/BrookTroutTH.R | 8 +- R/ChinookArg.R | 12 ++-- R/CodNorwegian.R | 13 ++-- R/CutthroatAL.R | 35 ++++++------ R/Ecoli.R | 12 +++- R/Mirex.R | 18 ++++-- R/PikeNY.R | 21 +++---- R/PikeNYPartial1.R | 27 ++++----- R/SMBassLS.R | 10 +-- R/SMBassWB.R | 47 ++++++++-------- R/SpotVA1.R | 8 +- R/WR79.R | 12 ++-- R/WhitefishLC.R | 33 ++++++----- R/ageComparisons.R | 16 ++--- R/alkIndivAge.R | 2 R/bcFuns.R | 5 - R/capHistConvert.R | 2 R/catchCurve.R | 2 R/chapmanRobson.R | 2 R/depletion.R | 2 R/growthModels.R | 22 +++---- R/metaM.R | 12 ++-- R/mrClosed.R | 2 R/mrOpen.R | 2 R/psdAdd.R | 6 +- R/psdCI.R | 2 R/psdCalc.R | 6 +- R/psdPlot.R | 6 +- R/psdVal.R | 6 +- R/removal.R | 2 R/srStarts.R | 2 R/stockRecruitment.R | 2 man/BluegillJL.Rd | 19 +++--- man/BrookTroutTH.Rd | 8 +- man/ChinookArg.Rd | 13 ++-- man/CodNorwegian.Rd | 13 ++-- man/CutthroatAL.Rd | 36 +++++++----- man/Ecoli.Rd | 13 +++- man/Mirex.Rd | 19 ++++-- man/PikeNY.Rd | 21 +++---- man/PikeNYPartial1.Rd | 27 ++++----- man/SMBassLS.Rd | 10 +-- man/SMBassWB.Rd | 45 ++++++++------- man/SpotVA1.Rd | 8 +- man/WR79.Rd | 12 ++-- man/WhitefishLC.Rd | 33 ++++++----- man/ageBias.Rd | 6 +- man/agePrecision.Rd | 10 +-- man/alkIndivAge.Rd | 2 man/bcFuns.Rd | 7 +- man/capHistConvert.Rd | 2 man/catchCurve.Rd | 2 man/chapmanRobson.Rd | 2 man/depletion.Rd | 2 man/growthModels.Rd | 22 +++---- man/metaM.Rd | 12 ++-- man/mrClosed.Rd | 2 man/mrOpen.Rd | 2 man/psdAdd.Rd | 6 +- man/psdCI.Rd | 2 man/psdCalc.Rd | 6 +- man/psdPlot.Rd | 6 +- man/psdVal.Rd | 6 +- man/removal.Rd | 2 man/srStarts.Rd | 2 man/stockRecruitment.Rd | 2 69 files changed, 475 insertions(+), 427 deletions(-)
Title: Estimation of Distribution Algorithms Based on Copulas
Description: Provides a platform where EDAs (estimation of
distribution algorithms) based on copulas can be implemented and
studied. The package offers complete implementations of various
EDAs based on copulas and vines, a group of well-known
optimization problems, and utility functions to study the
performance of the algorithms. Newly developed EDAs can be easily
integrated into the package by extending an S4 class with generic
functions for their main components.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>
Diff between copulaedas versions 1.4.1 dated 2014-06-21 and 1.4.2 dated 2015-10-22
copulaedas-1.4.1/copulaedas/src |only copulaedas-1.4.2/copulaedas/DESCRIPTION | 30 ++++--- copulaedas-1.4.2/copulaedas/MD5 | 69 ++++++++-------- copulaedas-1.4.2/copulaedas/NAMESPACE | 10 +- copulaedas-1.4.2/copulaedas/NEWS | 20 +++- copulaedas-1.4.2/copulaedas/R/CEDA.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/EDA.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/VEDA.R | 34 +++----- copulaedas-1.4.2/copulaedas/R/edaCriticalPopSize.R | 28 +++--- copulaedas-1.4.2/copulaedas/R/edaIndepRuns.R | 46 +++++------ copulaedas-1.4.2/copulaedas/R/edaOptimize.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaReplace.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaReport.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaRun.R | 34 ++++---- copulaedas-1.4.2/copulaedas/R/edaSeed.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/edaSelect.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaTerminate.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/margins.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/problems.R | 24 ++--- copulaedas-1.4.2/copulaedas/inst/CITATION | 35 ++++---- copulaedas-1.4.2/copulaedas/man/CEDA-class.Rd | 42 +++++----- copulaedas-1.4.2/copulaedas/man/EDA-class.Rd | 20 ++-- copulaedas-1.4.2/copulaedas/man/EDAResult-class.Rd | 18 ++-- copulaedas-1.4.2/copulaedas/man/EDAResults-class.Rd | 14 +-- copulaedas-1.4.2/copulaedas/man/VEDA-class.Rd | 74 +++++++++--------- copulaedas-1.4.2/copulaedas/man/edaCriticalPopSize.Rd | 24 ++--- copulaedas-1.4.2/copulaedas/man/edaIndepRuns.Rd | 6 - copulaedas-1.4.2/copulaedas/man/edaOptimize.Rd | 16 +-- copulaedas-1.4.2/copulaedas/man/edaReplace.Rd | 14 +-- copulaedas-1.4.2/copulaedas/man/edaReport.Rd | 22 ++--- copulaedas-1.4.2/copulaedas/man/edaRun.Rd | 34 ++++---- copulaedas-1.4.2/copulaedas/man/edaSeed.Rd | 20 ++-- copulaedas-1.4.2/copulaedas/man/edaSelect.Rd | 21 ++--- copulaedas-1.4.2/copulaedas/man/edaTerminate.Rd | 32 +++---- copulaedas-1.4.2/copulaedas/man/margins.Rd | 60 +++++++------- copulaedas-1.4.2/copulaedas/man/problems.Rd | 27 +++--- 36 files changed, 502 insertions(+), 494 deletions(-)
Title: Weighted Scores Method for Regression Models with Dependent Data
Description: Has functions to implement the weighted scores method and CL1 information criteria as an intermediate step for variable/correlation selection for longitudinal categorical and count data in Nikoloulopoulos, Joe and Chaganty (2011, Biostatistics, 12: 653-665) and Nikoloulopoulos (2015a,2015b).
Author: A. K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk> and H. Joe <harry.joe@ubc.ca>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Diff between weightedScores versions 0.9.1 dated 2014-11-06 and 0.9.5.1 dated 2015-10-22
DESCRIPTION | 12 - INDEX | 21 +-- MD5 | 58 ++++++-- NAMESPACE | 23 ++- R/CLIC-ord.R |only R/exchmvn.R |only R/mvn.deriv.R |only R/mvnapp.R |only R/ord.reg.univar.R |only R/wtsc-ord.R |only data/arthritis.rda |only man/CLIC.Rd |only man/arthritis.Rd |only man/bcl.Rd | 145 ++++++++++----------- man/cl1.Rd | 273 +++++++++++++++++++++++----------------- man/exchmvn.Rd |only man/godambe.Rd | 354 +++++++++++++++++++++++++++++++--------------------- man/iee.Rd | 169 ++++++++++++------------ man/iee.ord.Rd |only man/marglik.Rd | 104 +++++++-------- man/margmodel.Rd | 149 ++++++++++++--------- man/mvn.deriv.Rd |only man/mvnapp.Rd |only man/scoreCov.Rd | 68 +++++---- man/solvewtsc.Rd | 322 ++++++++++++++++++++++++++++------------------- man/weightMat.Rd | 289 +++++++++++++++++++++++++----------------- man/wtsc.Rd | 149 +++++++++++---------- man/wtsc.wrapper.Rd | 214 ++++++++++++++++--------------- src |only 29 files changed, 1349 insertions(+), 1001 deletions(-)
More information about weightedScores at CRAN
Permanent link
Title: Simple TCGA Data Access for Integrated Statistical Analysis in R
Description: Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
Author: Ying-Wooi Wan, Genevera I. Allen, Matthew L. Anderson, Zhandong Liu
Maintainer: Ying-Wooi Wan <yingwoow@bcm.edu>
Diff between TCGA2STAT versions 1.0 dated 2015-07-17 and 1.2 dated 2015-10-22
TCGA2STAT-1.0/TCGA2STAT/man/GeneMerge.Rd |only TCGA2STAT-1.2/TCGA2STAT/DESCRIPTION | 12 TCGA2STAT-1.2/TCGA2STAT/MD5 | 39 +- TCGA2STAT-1.2/TCGA2STAT/NAMESPACE | 2 TCGA2STAT-1.2/TCGA2STAT/R/TCGA2STAT.R | 394 +++++++++++++---------- TCGA2STAT-1.2/TCGA2STAT/build |only TCGA2STAT-1.2/TCGA2STAT/inst |only TCGA2STAT-1.2/TCGA2STAT/man/OMICSBind.Rd |only TCGA2STAT-1.2/TCGA2STAT/man/SampleSplit.Rd | 4 TCGA2STAT-1.2/TCGA2STAT/man/TCGA2STAT-package.Rd | 23 - TCGA2STAT-1.2/TCGA2STAT/man/TumorNormalMatch.Rd | 9 TCGA2STAT-1.2/TCGA2STAT/man/geneinfo.Rd | 4 TCGA2STAT-1.2/TCGA2STAT/man/getTCGA.Rd | 44 +- TCGA2STAT-1.2/TCGA2STAT/vignettes |only 14 files changed, 303 insertions(+), 228 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Among available
features there are: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.5-5 dated 2015-06-29 and 1.0-1 dated 2015-10-22
DESCRIPTION | 18 - INSTALL | 18 + LICENSE | 58 +++ MD5 | 53 +-- NEWS | 13 R/compare.R | 210 -------------- R/encoding_detection.R | 12 R/join.R | 8 R/sort.R |only R/trans_casemap.R | 4 R/trans_normalization.R | 20 - configure | 20 - man/stri_duplicated.Rd | 2 man/stri_order.Rd | 2 man/stri_unique.Rd | 2 src/Makevars.win | 6 src/install.libs.R.in | 65 ++++ src/stri_compare.cpp | 568 +++++++++------------------------------ src/stri_container_listutf8.cpp | 2 src/stri_cpp.txt | 1 src/stri_encoding_detection.cpp | 86 +++++ src/stri_exports.h |only src/stri_join.cpp | 292 ++++++++++---------- src/stri_sort.cpp |only src/stri_stringi.cpp | 58 ++- src/stri_stringi.h | 277 +------------------ src/stri_sub.cpp | 18 - src/stri_trans_casemap.cpp | 48 ++- src/stri_trans_normalization.cpp | 173 ++++++++++- 29 files changed, 875 insertions(+), 1159 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood
Maintainer: Ben Sherwood <bsherwo2@jhu.edu>
Diff between rqPen versions 1.1 dated 2015-03-15 and 1.2 dated 2015-10-22
DESCRIPTION | 12 - MD5 | 47 ++-- NAMESPACE | 27 ++ NEWS | 9 R/rqPen.R | 460 ++++++++++++++++++++++++++++++++++++++++- man/beta_plots.Rd | 6 man/coef.cv.rq.group.pen.Rd |only man/coef.cv.rq.pen.Rd |only man/cv.rq.group.pen.Rd |only man/cv.rq.pen.Rd | 8 man/cv_plots.Rd | 4 man/getRho.Rd |only man/groupMultLambda.Rd |only man/groupQICD.Rd |only man/group_derivs.Rd |only man/kernel_estimates.Rd |only man/kernel_weights.Rd |only man/mcp.Rd | 4 man/mcp_deriv.Rd | 4 man/model_eval.Rd | 2 man/nonzero.Rd |only man/nonzero.cv.rq.group.pen.Rd |only man/plot.cv.rq.group.pen.Rd |only man/predict.cv.rq.pen.Rd | 2 man/predict.rq.pen.Rd | 4 man/rq.group.fit.Rd |only man/rq.group.lin.prog.Rd |only man/rq.lasso.fit.Rd | 4 man/rq.lasso.fit.mult.Rd |only man/rq.nc.fit.Rd | 9 man/scad.Rd | 4 man/scad_deriv.Rd | 4 32 files changed, 553 insertions(+), 57 deletions(-)
Title: Multiresolution Kriging Based on Markov Random Fields
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. An extension of this
version over previous ones ( < 5.4 ) is the support for different
geometries besides a rectangular domain.
One benefit of the LatticeKrig model/approach
is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 3.4 dated 2014-08-28 and 5.4 dated 2015-10-22
LatticeKrig-3.4/LatticeKrig/R/LKrig.MRF.precision.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.cyl.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.a.wght.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.alpha.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.centers.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.grid.info.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.normalize.basis.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.setup.R |only LatticeKrig-3.4/LatticeKrig/man/LKinfo.Rd |only LatticeKrig-3.4/LatticeKrig/tests/LKrig.test.NonStationary.R |only LatticeKrig-5.4/LatticeKrig/DESCRIPTION | 23 LatticeKrig-5.4/LatticeKrig/MD5 | 172 ++- LatticeKrig-5.4/LatticeKrig/NAMESPACE | 61 + LatticeKrig-5.4/LatticeKrig/R/BACK |only LatticeKrig-5.4/LatticeKrig/R/GridList.R |only LatticeKrig-5.4/LatticeKrig/R/LKDist.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistComponents.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistGrid.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistGridComponents.R |only LatticeKrig-5.4/LatticeKrig/R/LKGridCheck.R |only LatticeKrig-5.4/LatticeKrig/R/LKGridFindNmax.R |only LatticeKrig-5.4/LatticeKrig/R/LKRectangleFastNormalization.R |only LatticeKrig-5.4/LatticeKrig/R/LKinfoCheck.R |only LatticeKrig-5.4/LatticeKrig/R/LKinfoUpdate.R | 42 LatticeKrig-5.4/LatticeKrig/R/LKrig.MLE.R | 32 LatticeKrig-5.4/LatticeKrig/R/LKrig.R | 362 +++---- LatticeKrig-5.4/LatticeKrig/R/LKrig.basis.R | 119 +- LatticeKrig-5.4/LatticeKrig/R/LKrig.coef.R | 30 LatticeKrig-5.4/LatticeKrig/R/LKrig.cov.R | 87 - LatticeKrig-5.4/LatticeKrig/R/LKrig.cov.plot.R | 6 LatticeKrig-5.4/LatticeKrig/R/LKrig.lnPlike.R | 141 +- LatticeKrig-5.4/LatticeKrig/R/LKrig.make.par.grid.R | 6 LatticeKrig-5.4/LatticeKrig/R/LKrig.misc.R | 56 + LatticeKrig-5.4/LatticeKrig/R/LKrig.precision.R | 67 - LatticeKrig-5.4/LatticeKrig/R/LKrig.quadraticform.R |only LatticeKrig-5.4/LatticeKrig/R/LKrig.sim.R | 54 - LatticeKrig-5.4/LatticeKrig/R/LKrig.sim.conditional.R | 96 + LatticeKrig-5.4/LatticeKrig/R/LKrig.spind2spam.R | 20 LatticeKrig-5.4/LatticeKrig/R/LKrig.traceA.R | 14 LatticeKrig-5.4/LatticeKrig/R/LKrigCovWieghtedObs.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigDefaultFixedFunction.R | 75 + LatticeKrig-5.4/LatticeKrig/R/LKrigDistance.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigFindLambda.R | 132 +- LatticeKrig-5.4/LatticeKrig/R/LKrigLatticeCenters.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigMakewU.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigMakewX.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigNormalizeBasis.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSAR.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetup.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupAlpha.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupAwght.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupLattice.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigUnrollGrid.R | 21 LatticeKrig-5.4/LatticeKrig/R/LatticeKrig.R | 69 - LatticeKrig-5.4/LatticeKrig/R/LatticeKrigEasyDefaults.R |only LatticeKrig-5.4/LatticeKrig/R/ModelBox.R |only LatticeKrig-5.4/LatticeKrig/R/ModelCylinder.R |only LatticeKrig-5.4/LatticeKrig/R/ModelInterval.R |only LatticeKrig-5.4/LatticeKrig/R/ModelRectangle.R |only LatticeKrig-5.4/LatticeKrig/R/ModelRing.R |only LatticeKrig-5.4/LatticeKrig/R/Radial.basis.R | 94 - LatticeKrig-5.4/LatticeKrig/R/Tensor.basis.R |only LatticeKrig-5.4/LatticeKrig/R/WendlandFunction.R |only LatticeKrig-5.4/LatticeKrig/R/convertIndexPeriodic.R |only LatticeKrig-5.4/LatticeKrig/R/createLKrigObject.R |only LatticeKrig-5.4/LatticeKrig/R/directionCosines.R |only LatticeKrig-5.4/LatticeKrig/R/predict.LKrig.R | 75 - LatticeKrig-5.4/LatticeKrig/R/predictLKrigFixedFunction.R | 19 LatticeKrig-5.4/LatticeKrig/R/predictSE.LKrig.R | 130 +- LatticeKrig-5.4/LatticeKrig/R/predictSurface.LKrig.R | 102 +- LatticeKrig-5.4/LatticeKrig/R/print.LKinfo.R | 87 + LatticeKrig-5.4/LatticeKrig/R/print.LKrig.R | 49 LatticeKrig-5.4/LatticeKrig/R/print.LatticeKrig.R |only LatticeKrig-5.4/LatticeKrig/R/setDefaultsLKinfo.R |only LatticeKrig-5.4/LatticeKrig/R/triWeight.R |only LatticeKrig-5.4/LatticeKrig/man/LKDistance.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKRing.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKgeometry.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKinfoCheck.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrig.MLE.Rd | 76 + LatticeKrig-5.4/LatticeKrig/man/LKrig.Rd | 491 +++++----- LatticeKrig-5.4/LatticeKrig/man/LKrig.basis.Rd | 138 +- LatticeKrig-5.4/LatticeKrig/man/LKrig.fixed.Rd | 3 LatticeKrig-5.4/LatticeKrig/man/LKrig.internal.Rd | 76 - LatticeKrig-5.4/LatticeKrig/man/LKrig.misc.Rd | 60 + LatticeKrig-5.4/LatticeKrig/man/LKrig.sim.Rd | 21 LatticeKrig-5.4/LatticeKrig/man/LKrigDistance-methods.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigLatticeCenters.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigNormalizeBasisFast.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSAR.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetup.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupAlpha.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupAwght.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupLattice.Rd |only LatticeKrig-5.4/LatticeKrig/man/LatticeKrig.Rd | 180 ++- LatticeKrig-5.4/LatticeKrig/man/Radial.Basis.Rd | 84 + LatticeKrig-5.4/LatticeKrig/man/gridList-class.Rd |only LatticeKrig-5.4/LatticeKrig/man/setDefaultsLKinfo.Rd |only LatticeKrig-5.4/LatticeKrig/src/LKdist.f |only LatticeKrig-5.4/LatticeKrig/src/LKdistgrid.f |only LatticeKrig-5.4/LatticeKrig/src/dfind1d.f |only LatticeKrig-5.4/LatticeKrig/src/findNorm.f | 3 LatticeKrig-5.4/LatticeKrig/tests/LKrig.FindNorm.test.R | 91 + LatticeKrig-5.4/LatticeKrig/tests/LKrig.FindNorm.test.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.LKCylinder.test.R |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.basis.test.R | 159 ++- LatticeKrig-5.4/LatticeKrig/tests/LKrig.basis.test.Rout.save | 39 LatticeKrig-5.4/LatticeKrig/tests/LKrig.lnPlike.test.Rout.save | 16 LatticeKrig-5.4/LatticeKrig/tests/LKrig.nullspace.test.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.precision.test.R | 226 +--- LatticeKrig-5.4/LatticeKrig/tests/LKrig.precision.test.Rout.save | 39 LatticeKrig-5.4/LatticeKrig/tests/LKrig.se.test.R | 110 +- LatticeKrig-5.4/LatticeKrig/tests/LKrig.se.test.Rout.save | 95 - LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.3D.R |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.3D.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.R | 59 - LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.Rout.save | 25 LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.inverse.R |only 118 files changed, 2470 insertions(+), 1762 deletions(-)
Title: Data to Support Fish Stock Assessment (FSA) Package
Description: The datasets to support the Fish Stock Assessment (FSA) package.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSAdata versions 0.3.0 dated 2015-10-06 and 0.3.2 dated 2015-10-22
DESCRIPTION | 11 MD5 | 566 ++++++++++++++++++++++++---------------------- NAMESPACE | 2 R/AHerringChile.R | 2 R/AfricanRivers.R | 9 R/AlewifeLH.R | 14 - R/AnchovetaChile.R | 2 R/BGHRfish.R |only R/BGHRsample.R |only R/BSkateGB.R | 19 - R/BassFL.R | 4 R/BlackDrum2001.R |only R/BloaterLH.R | 17 - R/BlueCatfish.R | 8 R/BlueCrab.R | 2 R/BluefishAge.R | 14 - R/BluegillLM.R | 11 R/BluntnoseIL1.R | 14 - R/BrookTroutNC.R | 19 - R/BrookTroutNEWP.R | 2 R/BrookTroutNEWP1.R | 2 R/BrookTroutOnt.R | 21 - R/BrownTroutVC1.R | 21 - R/BullTroutRML1.R | 19 - R/BullTroutRML2.R | 6 R/BullTroutTC.R | 4 R/CCatfishNB.R |only R/Cabezon.R | 8 R/Casselman1990.R | 13 - R/ChinookKR.R | 17 - R/CiscoTL.R | 25 +- R/CrappieARMS.R | 8 R/CreekChub.R |only R/CreelMN.R | 7 R/Croaker1.R | 12 R/Croaker2.R | 2 R/CutthroatALf.R | 17 - R/DarterOnt.R | 4 R/Deckeretal1999.R | 2 R/EuroPerchTJ.R | 2 R/FHCatfish.R | 8 R/FHCatfishATL.R | 2 R/FSAdata.R | 39 +-- R/FWDrumLE2.R | 4 R/Ghats.R | 9 R/GreensCreekMine.R | 2 R/Hake.R | 11 R/HalibutPAC.R | 17 - R/Herman.R | 6 R/HerringBWE.R | 17 - R/HerringISS.R | 19 - R/HumpbackWFCR.R | 21 - R/InchLake1.R | 14 - R/InchLake2.R | 17 - R/JobfishSIO.R | 2 R/Jonubi2.R | 12 R/KingCrabAK.R | 17 - R/LMBassBL.R | 8 R/LMBassLCB.R | 8 R/LakeTroutALTER.R | 14 - R/LakeTroutEggs.R | 9 R/LakeTroutGIS.R | 15 - R/LakeTroutMI.R | 19 - R/Lizardfish.R | 15 - R/LobsterHI.R | 2 R/Menhaden1.R | 2 R/Morwong1.R | 12 R/Morwong2.R | 12 R/Morwong3.R | 12 R/Morwong4a.R | 10 R/MulletBS.R | 12 R/MuskieSLR.R | 12 R/MuskieWI06MR.R | 23 - R/PSalmonAK.R | 19 - R/Pallid.R | 10 R/Pathfinder.R | 2 R/PikeHL.R | 21 - R/PikeNYPartial2.R | 21 - R/PikeWindermere.R | 21 - R/PygmyWFBC.R | 39 +-- R/RBSmeltErie.R | 4 R/RBSmeltLM.R | 8 R/RBTroutKenai.R | 2 R/RBTroutUNSP.R | 17 - R/RWhitefishAI.R | 2 R/RWhitefishIR.R | 2 R/RedDrum.R | 8 R/Riffleshell.R | 23 - R/RockBassL02.R | 12 R/RuffeSLRH92.R | 30 +- R/RuffeTL89.R | 4 R/SLampreyGL.R | 51 ++-- R/SalmonidsMCCA.R | 2 R/SardineLK.R | 2 R/SardinesPacific.R | 58 ++-- R/SculpinALTER.R | 18 - R/ShadCR.R |only R/ShrimpGuam.R | 2 R/SiscowetMI2004.R |only R/Snapper.R | 51 ++-- R/SnapperHG1.R | 10 R/SnapperHG2.R | 10 R/SockeyeKL.R | 57 ++-- R/SockeyeSR.R | 63 ++--- R/SpotVA2.R | 12 R/SpottedSucker1.R | 2 R/StripedBass1.R | 15 - R/StripedBass2.R | 5 R/StripedBass3.R | 11 R/StripedBass4.R | 12 R/StripedBass5.R | 12 R/StripedBass6.R | 12 R/SturgeonBL.R | 63 ++--- R/SturgeonGB.R |only R/SunfishIN.R | 29 +- R/SunfishLP.R | 55 ++-- R/TPrawnsEG.R | 21 - R/TroutperchLM2.R | 8 R/TroutperchLM3.R | 14 - R/VendaceLP.R | 15 - R/VendaceLP2.R | 13 - R/WShrimpGA.R | 17 - R/WalleyeConsumption.R | 2 R/WalleyeEL.R | 17 - R/WalleyeErie.R | 6 R/WalleyeErie2.R | 21 - R/WalleyeKS.R | 2 R/WalleyeMN06a.R | 9 R/WalleyeMN06b.R | 25 +- R/WalleyePL.R | 23 - R/WalleyePS.R | 16 - R/WalleyeWad.R |only R/WalleyeWyrlng.R |only R/WhiteGrunt1.R | 2 R/WhiteGrunt2.R | 8 R/WhitefishLS.R | 9 R/WhitefishMB.R | 14 - R/WhitefishTB.R | 17 - R/YERockfish.R | 6 R/YPerchCB1.R | 2 R/YPerchCB2.R | 15 - R/YPerchGB.R | 2 R/YPerchGL.R | 15 - R/YPerchRL.R | 2 R/YPerchSB.R | 13 - R/YPerchSB1.R | 6 R/YPerchTL.R | 20 - R/YTFlounder.R | 14 - data/BGHRfish.rdata |only data/BGHRsample.rdata |only data/BlackDrum2001.rdata |only data/CCatfishNB.rdata |only data/CreekChub.rdata |only data/ShadCR.rdata |only data/SiscowetMI2004.rdata |only data/SturgeonGB.rdata |only data/WalleyeWad.rdata |only data/WalleyeWyrlng.rdata |only man/AHerringChile.Rd | 2 man/AfricanRivers.Rd | 9 man/AlewifeLH.Rd | 12 man/BGHRfish.Rd |only man/BGHRsample.Rd |only man/BSkateGB.Rd | 15 - man/BassFL.Rd | 2 man/BlackDrum2001.Rd |only man/BloaterLH.Rd | 15 - man/BlueCatfish.Rd | 6 man/BluefishAge.Rd | 12 man/BluegillLM.Rd | 11 man/BluntnoseIL1.Rd | 12 man/BrookTroutNC.Rd | 15 - man/BrookTroutOnt.Rd | 19 - man/BrownTroutVC1.Rd | 17 - man/BullTroutRML1.Rd | 17 - man/BullTroutRML2.Rd | 4 man/BullTroutTC.Rd | 2 man/CCatfishNB.Rd |only man/Cabezon.Rd | 6 man/Casselman1990.Rd | 13 - man/ChinookKR.Rd | 15 - man/CiscoTL.Rd | 23 - man/CrappieARMS.Rd | 7 man/CreekChub.Rd |only man/CreelMN.Rd | 9 man/Croaker1.Rd | 12 man/Croaker2.Rd | 2 man/CutthroatALf.Rd | 17 - man/DarterOnt.Rd | 4 man/Deckeretal1999.Rd | 2 man/EuroPerchTJ.Rd | 2 man/FHCatfish.Rd | 8 man/FHCatfishATL.Rd | 2 man/FSAdata.Rd | 35 +- man/FWDrumLE2.Rd | 4 man/Ghats.Rd | 11 man/GreensCreekMine.Rd | 2 man/Hake.Rd | 9 man/HalibutPAC.Rd | 17 - man/Herman.Rd | 6 man/HerringBWE.Rd | 15 - man/HerringISS.Rd | 17 - man/HumpbackWFCR.Rd | 19 - man/InchLake1.Rd | 14 - man/InchLake2.Rd | 17 - man/JobfishSIO.Rd | 2 man/Jonubi2.Rd | 12 man/KingCrabAK.Rd | 15 - man/LMBassBL.Rd | 8 man/LMBassLCB.Rd | 8 man/LakeTroutALTER.Rd | 14 - man/LakeTroutEggs.Rd | 11 man/LakeTroutGIS.Rd | 13 - man/LakeTroutMI.Rd | 15 - man/Lizardfish.Rd | 13 - man/LobsterHI.Rd | 2 man/Menhaden1.Rd | 2 man/Morwong1.Rd | 12 man/Morwong2.Rd | 12 man/Morwong3.Rd | 12 man/Morwong4a.Rd | 10 man/MulletBS.Rd | 12 man/MuskieSLR.Rd | 12 man/MuskieWI06MR.Rd | 21 - man/PSalmonAK.Rd | 17 - man/Pallid.Rd | 10 man/Pathfinder.Rd | 2 man/PikeHL.Rd | 19 - man/PikeNYPartial2.Rd | 19 - man/PikeWindermere.Rd | 21 - man/PygmyWFBC.Rd | 39 +-- man/RBSmeltErie.Rd | 4 man/RBSmeltLM.Rd | 8 man/RBTroutKenai.Rd | 2 man/RBTroutUNSP.Rd | 15 - man/RWhitefishAI.Rd | 2 man/RWhitefishIR.Rd | 2 man/RedDrum.Rd | 8 man/Riffleshell.Rd | 21 - man/RockBassLO2.Rd | 12 man/RuffeSLRH92.Rd | 30 +- man/RuffeTL89.Rd | 4 man/SLampreyGL.Rd | 21 - man/SalmonidsMCCA.Rd | 2 man/SardineLK.Rd | 2 man/SardinesPacific.Rd | 18 - man/SculpinALTER.Rd | 18 - man/ShadCR.Rd |only man/ShrimpGuam.Rd | 2 man/SiscowetMI2004.Rd |only man/Snapper.Rd | 17 - man/SnapperHG1.Rd | 11 man/SnapperHG2.Rd | 10 man/SockeyeKL.Rd | 21 - man/SockeyeSR.Rd | 24 - man/SpotVA2.Rd | 12 man/SpottedSucker1.Rd | 2 man/StripedBass1.Rd | 15 - man/StripedBass2.Rd | 5 man/StripedBass3.Rd | 9 man/StripedBass4.Rd | 12 man/StripedBass5.Rd | 12 man/StripedBass6.Rd | 12 man/SturgeonBL.Rd | 33 +- man/SturgeonGB.Rd |only man/SunfishIN.Rd | 25 +- man/SunfishLP.Rd | 18 - man/TPrawnsEG.Rd | 19 - man/TroutperchLM2.Rd | 8 man/TroutperchLM3.Rd | 15 - man/VendaceLP.Rd | 11 man/VendaceLP2.Rd | 11 man/WShrimpGA.Rd | 13 - man/WalleyeConsumption.Rd | 2 man/WalleyeEL.Rd | 15 - man/WalleyeErie.Rd | 2 man/WalleyeErie2.Rd | 21 - man/WalleyeKS.Rd | 2 man/WalleyeMN06a.Rd | 8 man/WalleyeMN06b.Rd | 23 - man/WalleyePL.Rd | 21 - man/WalleyePS.Rd | 16 - man/WalleyeWad.Rd |only man/WalleyeWyrlng.Rd |only man/WhiteGrunt1.Rd | 2 man/WhiteGrunt2.Rd | 8 man/WhitefishLS.Rd | 11 man/WhitefishMB.Rd | 14 - man/WhitefishTB.Rd | 17 - man/YERockfish.Rd | 6 man/YPerchCB1.Rd | 2 man/YPerchCB2.Rd | 13 - man/YPerchGB.Rd | 2 man/YPerchGL.Rd | 15 - man/YPerchRL.Rd | 2 man/YPerchSB.Rd | 13 - man/YPerchSB1.Rd | 6 man/YPerchTL.Rd | 20 - man/YTFlounder.Rd | 14 - 299 files changed, 2130 insertions(+), 1861 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.8 dated 2015-10-03 and 1.9 dated 2015-10-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/coneproj.R | 11 ++++++++--- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Simulating Data to Study Performance of Clustering Algorithms
Description: The utility of this package is in simulating mixtures of Gaussian
distributions with different levels of overlap between mixture
components. Pairwise overlap, defined as a sum of two
misclassification probabilities, measures the degree of
interaction between components and can be readily employed to
control the clustering complexity of datasets simulated from
mixtures. These datasets can then be used for systematic
performance investigation of clustering and finite mixture
modeling algorithms. Among other capabilities of 'MixSim', there
are computing the exact overlap for Gaussian mixtures,
simulating Gaussian and non-Gaussian data, simulating outliers
and noise variables, calculating various measures of agreement
between two partitionings, and constructing parallel
distribution plots for the graphical display of finite mixture
models.
Author: Volodymyr Melnykov [aut],
Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Robert Davies [ctb] (quadratic form probabilities),
Stephen Moshier [ctb] (eigenvalue calculations),
Rouben Rostamian [ctb] (memory allocation)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between MixSim versions 1.1-1 dated 2015-05-24 and 1.1-2 dated 2015-10-22
MixSim-1.1-1/MixSim/NEWS |only MixSim-1.1-2/MixSim/ChangeLog | 6 ++++++ MixSim-1.1-2/MixSim/DESCRIPTION | 34 +++++++++++++++++++++++----------- MixSim-1.1-2/MixSim/MD5 | 11 +++++------ MixSim-1.1-2/MixSim/NAMESPACE | 4 ++++ MixSim-1.1-2/MixSim/cleanup | 3 ++- MixSim-1.1-2/MixSim/src/libAdjRand.c | 26 +++++++++++++++++++++++++- 7 files changed, 65 insertions(+), 19 deletions(-)
Title: Simulating Data for PLS Mode B Structural Models
Description: A set of functions have been implemented to generate random data to perform Monte Carlo simulations on structural models with formative constructs and interaction and nonlinear effects (Two-Step PLS Mode B structural models). The setup of the true model considers a simple structure with three formative exogenous constructs related to one formative endogenous construct. The routines take into account the interaction and nonlinear effects of the exogenous constructs on the endogenous construct.
Author: Alba Martinez-Ruiz <amartine@ucsc.cl> and Claudia Martinez-Araneda <cmartinez@ucsc.cl>
Maintainer: Alba Martinez-Ruiz <amartine@ucsc.cl>
Diff between dgmb versions 1.1 dated 2014-06-25 and 1.2 dated 2015-10-22
DESCRIPTION | 16 ++++++++-------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 4 +++- R/dgmbGui.R | 18 +++++++++--------- inst/docs/dgmb-manual.pdf |binary man/ErrEnLV.Rd | 2 +- man/ExoLVsCor.Rd | 5 ++--- man/ExoMVs.Rd | 3 +-- man/IntPar.Rd | 2 +- man/NIEffects.Rd | 3 +-- man/ToProcess.Rd | 2 +- man/ViewHelp.Rd | 2 +- man/dgmb-package.Rd | 17 +++++++++-------- man/dgmbGui.Rd | 29 +++-------------------------- man/figures |only 15 files changed, 57 insertions(+), 76 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between rjags versions 3-15 dated 2015-04-15 and 4-4 dated 2015-10-22
rjags-3-15/rjags/README |only rjags-4-4/rjags/DESCRIPTION | 17 - rjags-4-4/rjags/INSTALL |only rjags-4-4/rjags/MD5 | 36 +-- rjags-4-4/rjags/NAMESPACE | 9 rjags-4-4/rjags/R/jags.R | 36 ++- rjags-4-4/rjags/R/jags.object.R | 3 rjags-4-4/rjags/R/mcarray.R | 43 +++- rjags-4-4/rjags/R/unix/zzz.R.in | 3 rjags-4-4/rjags/R/windows/zzz.R | 3 rjags-4-4/rjags/configure | 353 ++++++++++++++++++++++++----------- rjags-4-4/rjags/configure.ac | 189 ++++++++++++------ rjags-4-4/rjags/man/adapt.Rd | 8 rjags-4-4/rjags/man/coda.samples.Rd | 19 + rjags-4-4/rjags/man/jags.model.Rd | 7 rjags-4-4/rjags/src/Makevars.in | 4 rjags-4-4/rjags/src/Makevars.win | 2 rjags-4-4/rjags/src/jags.cc | 32 +-- rjags-4-4/rjags/src/jags.cc.orig |only rjags-4-4/rjags/src/parallel.cc | 4 rjags-4-4/rjags/src/parallel.cc.orig |only 21 files changed, 524 insertions(+), 244 deletions(-)
Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data collected in an experimental design for statistical
analysis (e.g., analysis of variance ;ANOVA) by taking the individual data
files and preparing one table that contains several possibilities for
dependent variables. Most suitable when measuring reaction-times and/or
accuracy, or any other variable in an interval or ratio scale. Functions
included: file_merge(), read_data() and prep(). The file_merge() function
vertically merges individual data files (in a long format) in which each line
is a single trial within the experiment to one single dataset. The
read_data() function reads a file in a txt or csv format that contains a
single dataset in a long format table and creates a data frame from it. The
prep() function aggregates the single dataset according to any combination of
between and within grouping variables (i.e., between-subjects and
within-subjects independent variables, respectively), and returns a data
frame with a number of dependent measures for further analysis for each
experimental cell according to the combination of provided grouping
variables. Dependent measures for each experimental cell include among
others means before and after rejecting all values according to a flexible
standard deviation criterion/s, number of rejected values according to the
flexible standard deviation criterion/s, proportions of rejected values
according to the flexible standard deviation criterion/s, number of values
before rejection, means after rejecting values according to procedures
described in Van Selst & Jolicoeur (1994) (suitable when measuring
reaction-times), standard deviations, medians, means according to any
percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The data frame
prep() returns can also be exported as a txt file to be used for statistical
analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre],
Roy Luria [aut],
Jim Grange [ctb],
Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>
Diff between prepdat versions 1.0.2 dated 2015-09-01 and 1.0.3 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 5 +++++ NEWS.md | 33 +++++++++++++++++++++++++++++++++ R/prep.R | 16 +++++++--------- README.md | 26 +++++++++++++++++++++++--- 6 files changed, 76 insertions(+), 20 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.47 dated 2015-10-08 and 0.48 dated 2015-10-22
ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++++++----- DESCRIPTION | 8 ++--- MD5 | 6 ++-- man/vars.Rd | 3 ++ 4 files changed, 85 insertions(+), 13 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.3.0 dated 2015-10-06 and 0.4.0 dated 2015-10-22
DESCRIPTION | 6 - MD5 | 19 +-- NEWS.md | 9 + R/eval_tt.R |only R/generics.R | 65 +++++++----- R/helpers.R | 254 +++++++++++++++++++++++++++++++++++++++++++++++--- R/kdecop.R | 125 +++++++++++++++--------- R/kdecopula-package.R | 5 README.md | 5 man/kdecop.Rd | 76 +++++++++----- man/kdecopula.Rd | 5 11 files changed, 439 insertions(+), 130 deletions(-)
Title: Optimal Transport in Various Forms
Description: Solve optimal transport problems in statistics. Compute Wasserstein metrics (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p metrics), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, point patterns, and mass vectors.
Author: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de> with substantial contributions of code by Bjoern Baehre and Carsten Gottschlich
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.6-3 dated 2014-10-16 and 0.7-0 dated 2015-10-22
DESCRIPTION | 13 - MD5 | 20 - NAMESPACE | 7 NEWS | 35 +++ R/fundament.R | 481 ++++++++++++++++++++++++++++++++++++---------- R/lilhelpers.R | 10 man/transport-internal.Rd | 2 man/transport.Rd | 21 +- man/trcontrol.Rd | 2 src/revsimplex.c | 129 +++++++++++- src/shortsimplex.c | 11 - 11 files changed, 585 insertions(+), 146 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.4 dated 2015-10-12 and 0.4.1 dated 2015-10-22
DESCRIPTION | 11 - MD5 | 6 R/get_isd_station_data.R | 3 README.md | 496 ++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 506 insertions(+), 10 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.3 dated 2015-06-04 and 1.5.4 dated 2015-10-22
DESCRIPTION | 9 ++- MD5 | 86 +++++++++++++++++------------------ NAMESPACE | 41 ++++++++++++---- R/envelope.R | 18 ++++--- R/estfun.ssym.R | 2 R/extra.parameter.R | 53 ++++++++++++++++----- R/itpE.R | 23 ++++++--- R/itpE2.R | 20 ++++---- R/itpE3.R | 19 +++++-- R/itpEC.R | 21 +++++--- R/itpEC2.R | 25 ++++++---- R/ncs.R | 2 R/plot.ssym.R | 4 - R/psp.R | 2 R/ssym.l.R | 119 ++++++++++++++++++++++++++++++++++++++----------- R/ssym.l2.R | 119 +++++++++++++++++++++++++++++++++++++++---------- R/ssym.nl.R | 72 +++++++++++++++++++++-------- R/summary.ssym.R | 10 ++-- man/AIC.ssym.Rd | 2 man/BIC.ssym.Rd | 2 man/Ovocytes.Rd | 4 - man/coef.ssym.Rd | 2 man/envelope.Rd | 10 +++- man/extra.parameter.Rd | 5 +- man/fitted.ssym.Rd | 2 man/influence.ssym.Rd | 3 - man/itpE.Rd | 2 man/itpE2.Rd | 2 man/itpE3.Rd | 2 man/itpEC.Rd | 4 - man/itpEC2.Rd | 2 man/logLik.ssym.Rd | 2 man/ncs.Rd | 2 man/np.graph.Rd | 2 man/plot.ssym.Rd | 2 man/psp.Rd | 2 man/residuals.ssym.Rd | 2 man/rvgs.Rd | 6 +- man/ssym-package.Rd | 8 +-- man/ssym.l.Rd | 12 ++-- man/ssym.l2.Rd | 8 ++- man/ssym.nl.Rd | 9 ++- man/summary.ssym.Rd | 4 - man/vcov.ssym.Rd | 2 44 files changed, 510 insertions(+), 238 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.9 dated 2015-09-16 and 5.0 dated 2015-10-22
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/seqminer.R | 8 ++++++-- inst/CITATION | 6 ++++-- 5 files changed, 26 insertions(+), 12 deletions(-)
Title: Robust Ordinal Regression UTADIS
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek <k.ciomek@gmail.com>
Diff between rorutadis versions 0.1.3 dated 2014-07-29 and 0.3.0 dated 2015-10-22
rorutadis-0.1.3/rorutadis/man/removeConstraintsByRestrictions.Rd |only rorutadis-0.3.0/rorutadis/DESCRIPTION | 11 rorutadis-0.3.0/rorutadis/MD5 | 88 rorutadis-0.3.0/rorutadis/NAMESPACE | 9 rorutadis-0.3.0/rorutadis/R/drawing.R | 270 +- rorutadis-0.3.0/rorutadis/R/explanations.R | 217 - rorutadis-0.3.0/rorutadis/R/inconsistencies.R |only rorutadis-0.3.0/rorutadis/R/main.R | 439 +-- rorutadis-0.3.0/rorutadis/R/model.R | 1247 +++------- rorutadis-0.3.0/rorutadis/R/postFactumAnalysis.R | 100 rorutadis-0.3.0/rorutadis/R/problem.R | 9 rorutadis-0.3.0/rorutadis/R/sampling.R |only rorutadis-0.3.0/rorutadis/R/solution.R | 283 +- rorutadis-0.3.0/rorutadis/man/addAssignmentPairwiseAtLeastComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentPairwiseAtMostComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentsLB.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentsUB.Rd | 3 rorutadis-0.3.0/rorutadis/man/addMaximalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/addMinimalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/buildProblem.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateAssignments.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateExtremeClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateStochasticResults.Rd |only rorutadis-0.3.0/rorutadis/man/checkConsistency.Rd | 7 rorutadis-0.3.0/rorutadis/man/compareAssignments.Rd | 9 rorutadis-0.3.0/rorutadis/man/deteriorateAssignment.Rd | 3 rorutadis-0.3.0/rorutadis/man/drawUtilityPlots.Rd | 28 rorutadis-0.3.0/rorutadis/man/explainAssignment.Rd | 10 rorutadis-0.3.0/rorutadis/man/findInconsistencies.Rd |only rorutadis-0.3.0/rorutadis/man/findRepresentativeFunction.Rd | 30 rorutadis-0.3.0/rorutadis/man/findSimpleFunction.Rd |only rorutadis-0.3.0/rorutadis/man/getAssignments.Rd | 19 rorutadis-0.3.0/rorutadis/man/getCharacteristicPoints.Rd | 19 rorutadis-0.3.0/rorutadis/man/getMarginalUtilities.Rd | 19 rorutadis-0.3.0/rorutadis/man/getPreferentialCore.Rd | 3 rorutadis-0.3.0/rorutadis/man/getRestrictions.Rd | 5 rorutadis-0.3.0/rorutadis/man/getThresholds.Rd | 21 rorutadis-0.3.0/rorutadis/man/improveAssignment.Rd | 3 rorutadis-0.3.0/rorutadis/man/investigateUtility.Rd | 5 rorutadis-0.3.0/rorutadis/man/mergeAssignments.Rd | 3 rorutadis-0.3.0/rorutadis/man/plotComprehensiveValue.Rd |only rorutadis-0.3.0/rorutadis/man/plotVF.Rd |only rorutadis-0.3.0/rorutadis/man/removeAssignmentPairwiseAtLeastComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentPairwiseAtMostComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentsLB.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentsUB.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeMaximalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeMinimalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/rorutadis-package.Rd | 4 49 files changed, 1291 insertions(+), 1615 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between readr versions 0.2.1 dated 2015-10-21 and 0.2.2 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- inst/doc/column-types.html | 4 ++-- inst/doc/locales.html | 4 ++-- src/QiParsers.h | 2 -- src/TokenizerDelim.cpp | 9 ++++++++- src/TokenizerDelim.h | 2 +- src/parse.cpp | 2 +- src/read.cpp | 6 +++--- 9 files changed, 28 insertions(+), 23 deletions(-)
Title: Inverse-Regression Estimation of Radioactive Doses
Description: Radioactive doses estimation using individual chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm K. (2015). A new inverse regression model applied to radiation biodosimetry. Proceedings of the Royal Society A, 471.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between radir versions 1.0 dated 2015-01-08 and 1.0.1 dated 2015-10-22
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 13 ++++++++++--- inst/CITATION | 20 ++++++++++++++++++++ man/radir-package.Rd | 19 ------------------- 5 files changed, 40 insertions(+), 32 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.4 dated 2015-06-15 and 0.4.5 dated 2015-10-22
DESCRIPTION | 8 - MD5 | 56 +++++----- NAMESPACE | 3 R/aaa-globals.R | 2 R/augment-rprofile.R | 3 R/clean-search-path.R | 2 R/cranlike-repositories.R | 18 ++- R/dependencies.R | 218 +++++++++++++++++++++++++++-------------- R/downloader.R | 174 +++++++++++++++++++++++++------- R/external.R | 21 +-- R/hooks.R | 2 R/install.R | 23 +++- R/options.R | 12 +- R/packrat-mode.R | 20 +++ R/packrat.R | 45 -------- R/paths.R | 13 +- R/pkg.R | 3 R/restore.R | 15 +- R/snapshot.R | 83 ++++++++------- R/status.R | 2 R/utils.R | 73 ++++++++++++- README.md | 2 inst/resources/init-rprofile.R | 2 inst/resources/init.R | 61 ++++++++--- man/appDependencies.Rd | 8 + man/packrat-external.Rd | 6 - man/packrat-options.Rd | 2 man/repository-management.Rd | 3 man/snapshotImpl.Rd | 7 + 29 files changed, 589 insertions(+), 298 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.10.4 dated 2015-05-12 and 3.11.4 dated 2015-10-22
mvabund-3.10.4/mvabund/configure |only mvabund-3.10.4/mvabund/configure.ac |only mvabund-3.10.4/mvabund/src/Makevars.in |only mvabund-3.10.4/mvabund/src/RtoAnovaCpp.cpp |only mvabund-3.10.4/mvabund/src/RtoGlm.cpp |only mvabund-3.10.4/mvabund/src/RtoGlmAnova.cpp |only mvabund-3.10.4/mvabund/src/RtoGlmSmry.cpp |only mvabund-3.10.4/mvabund/src/RtoSmryCpp.cpp |only mvabund-3.11.4/mvabund/DESCRIPTION | 14 mvabund-3.11.4/mvabund/MD5 | 76 +-- mvabund-3.11.4/mvabund/NAMESPACE | 199 ++++--- mvabund-3.11.4/mvabund/R/RcppExports.R |only mvabund-3.11.4/mvabund/R/RcppVersion.R | 28 - mvabund-3.11.4/mvabund/R/anova.manyany.R | 166 ++++-- mvabund-3.11.4/mvabund/R/anova.manyglm.R | 37 - mvabund-3.11.4/mvabund/R/anova.manylm.R | 55 +- mvabund-3.11.4/mvabund/R/anova.traitglm.R | 8 mvabund-3.11.4/mvabund/R/cv.glm1path.R | 41 - mvabund-3.11.4/mvabund/R/default.plot.mvformula.R | 47 + mvabund-3.11.4/mvabund/R/is.wholenumber.R | 8 mvabund-3.11.4/mvabund/R/manyany.R | 4 mvabund-3.11.4/mvabund/R/manyglm.R | 107 ++-- mvabund-3.11.4/mvabund/R/print.anova.manyglm.R | 10 mvabund-3.11.4/mvabund/R/print.summary.manyglm.R | 10 mvabund-3.11.4/mvabund/R/summary.manyglm.R | 550 +++++++++++----------- mvabund-3.11.4/mvabund/R/summary.manylm.R | 468 +++++++++--------- mvabund-3.11.4/mvabund/R/traitglm.R | 91 ++- mvabund-3.11.4/mvabund/R/transAxis.SW.R | 240 ++++----- mvabund-3.11.4/mvabund/README.md |only mvabund-3.11.4/mvabund/cleanup | 17 mvabund-3.11.4/mvabund/data/Tasmania.RData |binary mvabund-3.11.4/mvabund/data/antTraits.RData |binary mvabund-3.11.4/mvabund/data/solberg.RData |binary mvabund-3.11.4/mvabund/data/spider.RData |binary mvabund-3.11.4/mvabund/data/tikus.RData |binary mvabund-3.11.4/mvabund/man/anova.manyany.Rd | 4 mvabund-3.11.4/mvabund/man/traitglm.Rd | 16 mvabund-3.11.4/mvabund/src/Makevars |only mvabund-3.11.4/mvabund/src/Makevars.win | 5 mvabund-3.11.4/mvabund/src/RcppExports.cpp |only mvabund-3.11.4/mvabund/src/Rinterface.cpp |only mvabund-3.11.4/mvabund/src/glm.cpp | 22 mvabund-3.11.4/mvabund/src/io.cpp | 2 mvabund-3.11.4/mvabund/src/mvabund_types.h |only mvabund-3.11.4/mvabund/src/resampTest.h | 36 + mvabund-3.11.4/mvabund/src/simutility.cpp | 4 46 files changed, 1255 insertions(+), 1010 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-7 dated 2015-08-17 and 0.1-8 dated 2015-10-22
DESCRIPTION | 8 ++--- MD5 | 4 +- R/initMC.r | 94 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 53 insertions(+), 53 deletions(-)
Title: Estimation of ICA Mixture Models
Description: The icamix package provides R functions as well as a C++ library which facilitate the estimation of ICA mixture models. We have developed and implemented the NSMM-ICA algorithm that currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture models. We will continue to build in algorithms that interweave the EM step with other types of ICA techniques.
Author: Xiaotian Zhu, David R. Hunter
Maintainer: Xiaotian Zhu <xiaotian.zhu@abbvie.com>
Diff between icamix versions 1.0.2 dated 2015-04-20 and 1.0.4 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ man/EMFASTICAALG.Rd | 7 ++----- man/ESTIMATEDMEMBER.Rd | 3 +-- man/plot.EMFASTICAALG.Rd | 3 +-- man/plot.summary.EMFASTICAALG.Rd | 3 +-- man/print.EMFASTICAALG.Rd | 3 +-- man/print.summary.EMFASTICAALG.Rd | 3 +-- man/summary.EMFASTICAALG.Rd | 3 +-- 10 files changed, 22 insertions(+), 29 deletions(-)
Title: Hot Deck Imputation Methods for Missing Data
Description: Hot deck imputation methods to resolve missing data.
Author: Dieter William Joenssen [aut, cre, cph]
Maintainer: Dieter William Joenssen <Dieter.Joenssen@googlemail.com>
Diff between HotDeckImputation versions 1.0.0 dated 2014-09-28 and 1.1.0 dated 2015-10-22
DESCRIPTION | 20 MD5 | 33 - NAMESPACE | 4 NEWS | 18 R/HotDeckImputation.R | 781 +++++++++++++++++++++++++-------------- R/SeqentialHotDeck.R | 42 +- R/zzz.R | 22 - man/HotDeckImputation-package.Rd | 6 man/impute.CPS_SEQ_HD.Rd | 4 man/impute.NN_HD.Rd | 36 + man/impute.SEQ_HD.Rd | 2 man/impute.mean.Rd | 2 man/match.d_r_odd.Rd | 5 man/match.d_r_vam.Rd | 5 src/Distmatrix.c | 61 ++- src/VAM.c | 2 src/seq_HD.c | 66 +++ src/test_functions.c |only 18 files changed, 771 insertions(+), 338 deletions(-)
More information about HotDeckImputation at CRAN
Permanent link
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.1 dated 2015-10-14 and 0.2 dated 2015-10-22
DESCRIPTION | 17 ++++++++++------- MD5 | 25 +++++++++++++++++-------- NAMESPACE | 4 +++- NEWS |only R/check.integer.R |only R/converteCampoParaCharacter.R | 8 ++++---- R/getAnoMedicao.R | 30 ++++++++++++++++++++---------- R/listToDataFrame.R |only R/verificaTipoColuna.R | 4 ++-- man/check.integer.Rd |only man/converteCampoParaCharacter.Rd | 8 ++++---- man/getAnoMedicao.Rd | 20 ++++++++++++-------- man/listToDataFrame.Rd |only man/verificaTipoColuna.Rd | 4 ++-- tests |only 15 files changed, 74 insertions(+), 46 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-57 dated 2015-10-11 and 6.0-58 dated 2015-10-22
DESCRIPTION | 8 - MD5 | 36 +++---- R/extractProb.R | 9 - R/ggplot.R | 153 ++++++++++++++++++-------------- R/pcaNNet.R | 16 ++- R/preProcess.R | 90 +++++++++++++++---- R/train.default.R | 17 +++ R/workflows.R | 11 +- inst/NEWS.Rd | 13 ++ man/confusionMatrix.Rd | 2 man/extractPrediction.Rd | 2 man/models.Rd | 221 ++++++++++++++++++++++++++++++++++++++++++++++- man/pcaNNet.Rd | 2 man/plot.rfe.Rd | 2 man/plot.train.Rd | 4 man/preProcess.Rd | 23 +++- man/sensitivity.Rd | 2 man/train.Rd | 2 man/trainControl.Rd | 4 19 files changed, 476 insertions(+), 141 deletions(-)
Title: Table, Apply, and Split Functionality for Matrix and
'big.matrix' Objects
Description: Extend the bigmemory package with 'table', 'tapply', and 'split' support for 'big.matrix' objects. The functions may also be used with native R matrices for improving speed and memory-efficiency.
Author: Michael J. Kane <kaneplusplus@gmail.com> and John W. Emerson <jayemerson@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigtabulate versions 1.1.2 dated 2013-11-05 and 1.1.4 dated 2015-10-22
bigtabulate-1.1.2/bigtabulate/inst |only bigtabulate-1.1.4/bigtabulate/DESCRIPTION | 24 +++++++-------- bigtabulate-1.1.4/bigtabulate/MD5 | 14 ++++---- bigtabulate-1.1.4/bigtabulate/NAMESPACE | 1 bigtabulate-1.1.4/bigtabulate/R/bigtabulate.R | 8 ++--- bigtabulate-1.1.4/bigtabulate/R/zzz.R | 2 - bigtabulate-1.1.4/bigtabulate/configure | 3 + bigtabulate-1.1.4/bigtabulate/man/bigtabulate-package.Rd | 6 +-- bigtabulate-1.1.4/bigtabulate/src/Makevars |only 9 files changed, 30 insertions(+), 28 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2.1 dated 2015-06-05 and 2.2.2 dated 2015-10-21
pcnetmeta-2.2.1/pcnetmeta/R/model.binary.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.binary.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.cont.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.cont.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.followup.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.followup.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.py.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.py.hom.ind.R |only pcnetmeta-2.2.2/pcnetmeta/DESCRIPTION | 8 +- pcnetmeta-2.2.2/pcnetmeta/MD5 | 42 ++++------ pcnetmeta-2.2.2/pcnetmeta/NAMESPACE | 6 + pcnetmeta-2.2.2/pcnetmeta/R/absolute.plot.R | 56 ++++++-------- pcnetmeta-2.2.2/pcnetmeta/R/contrast.plot.R | 40 ++++++---- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.R | 74 +++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.cont.R | 76 ++++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.followup.R | 70 ++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.py.R | 70 ++++------------- pcnetmeta-2.2.2/pcnetmeta/R/rank.prob.R | 19 +++- pcnetmeta-2.2.2/pcnetmeta/man/absolute.plot.Rd | 16 +++- pcnetmeta-2.2.2/pcnetmeta/man/contrast.plot.Rd | 12 +-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.Rd | 24 +++--- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.cont.Rd | 23 +++-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.followup.Rd | 27 ++++-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.py.Rd | 27 ++++-- pcnetmeta-2.2.2/pcnetmeta/man/pcnetmeta-package.Rd | 2 pcnetmeta-2.2.2/pcnetmeta/man/rank.prob.Rd | 11 ++ 26 files changed, 259 insertions(+), 344 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.1.0 dated 2015-05-27 and 1.1.1 dated 2015-10-21
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 4 ++++ man/dataLongCompRisks.Rd | 27 +++++++++++++++++++++++++++ man/discSurv-package.Rd | 18 +++++++++++++----- 5 files changed, 53 insertions(+), 14 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-10 dated 2015-07-10 and 0.9-11 dated 2015-10-21
DESCRIPTION | 9 +-- MD5 | 43 ++++++++++----- NAMESPACE | 7 ++ R/GMRF.R | 23 ++++++++ R/calibratemcmc.R | 15 +++++ R/log_posteriors_and_derivatives_polygonal.R | 3 + R/nonspatial_log_likelihood_and_derivatives.R | 16 +++++ R/outputSummary.R |only R/plottingfunctions.R | 27 +++++++++- R/postprocessing.R | 13 +++- R/spatgrid.R | 70 ++++++++++++++++++++++++++ R/spatsurv.R | 4 - R/spatsurvMisc.R | 5 + R/survsim.R | 2 R/survspat.R | 11 ++-- README.md | 2 data |only man/Summarise.Rd |only man/fs.Rd |only man/fstimes.Rd |only man/getOptCellwidth.Rd |only man/getbb.Rd |only man/print.textSummary.Rd |only man/showGrid.Rd |only man/spatsurv-package.Rd | 2 man/spplot1.Rd | 4 + man/textSummary.Rd |only 27 files changed, 217 insertions(+), 39 deletions(-)
Title: Bias, Precision, and Power for Multi-Level Random Regressions
Description: Calculates bias, precision, and power for multi-level random regressions. Random regressions are types of hierarchical models in which data are structured in groups and (regression) coefficients can vary by groups. Tools to estimate model performance are designed mostly for scenarios where (regression) coefficients vary at just one level. 'MultiRR' provides simulation and analytical tools (based on 'lme4') to study model performance for random regressions that vary at more than one level (multi-level random regressions), allowing researchers to determine optimal sampling designs.
Author: Yimen G. Araya-Ajoy
Maintainer: Yimen G. Araya-Ajoy <yimencr@gmail.com>
Diff between MultiRR versions 1.0 dated 2015-05-13 and 1.1 dated 2015-10-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 6 +++++- man/Anal.MultiRR.Rd | 2 +- man/Bias.Rd | 2 +- man/Imprecision.Rd | 2 +- man/MultiRR-package.Rd | 2 +- man/Plot.Sim.Rd | 2 +- man/Power.Rd | 2 +- man/Sim.MultiRR.Rd | 2 +- man/Summary.Rd | 2 +- 11 files changed, 27 insertions(+), 23 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.3-1709 dated 2015-05-26 and 2.4-1786 dated 2015-10-21
DESCRIPTION | 10 - MD5 | 75 +++++---- NAMESPACE | 13 + R/bccorr.R | 189 +++++++++++++++++++----- R/cgsolve.R | 14 + R/compfactor.R | 4 R/efactory.R | 8 - R/felm.R | 333 +++++++++++++++++++++++++++++++++----------- R/generics.R | 16 +- R/is.estimable.R | 9 - R/kaczmarz.R | 9 - R/startup.R | 7 R/trace.R | 27 ++- R/utils.R | 23 ++- exec/lfescript | 94 ++++++++---- inst/NEWS.Rd | 26 +++ inst/doc/CHANGELOG | 3 inst/doc/identification.pdf |binary inst/doc/lfeguide.txt | 1 inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/bccorr.Rd | 4 man/condfstat.Rd | 4 man/demeanlist.Rd | 8 + man/felm.Rd | 23 ++- man/fevcov.Rd | 8 + man/lfe-package.Rd | 10 - src/Makevars.in | 6 src/demean.c | 11 - src/lfe.c | 12 + src/lfe.h | 4 src/ppf.c |only tests/bctest.Rout.save | 22 +- tests/intact.R |only tests/intact.Rout.save |only tests/interact.Rout.save | 6 tests/verify.R | 5 tests/verify.Rout.save | 11 + tests/weights.R | 1 tests/weights.Rout.save | 28 ++- 40 files changed, 747 insertions(+), 277 deletions(-)
Title: Enhanced Analytics for Marketers Navigating the Ocean of Web
Data
Description: Provides a web analytics toolbox for marketers using services such as Google Analytics, Facebook Insights, etc.
Author: Felix MIKAELIAN <felix.mikaelian@essec.edu>
Maintainer: Felix MIKAELIAN <felix.mikaelian@essec.edu>
Diff between marketeR versions 0.1.0 dated 2015-09-10 and 0.1.1 dated 2015-10-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/AutoReport.R | 6 +++--- R/WeekSummary.R | 2 +- inst/AutoReport/AutoReport.Rmd | 8 ++++---- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Interface to the Agave API
Description: Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see <http://www.iplantcollaborative.org/> for more information about iPlant, and <http://www.iplantcollaborative.org/ci/iplant-science-apis> for its APIs. Currently, 'rPlant' functions interact with the iPlant Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant Collaborative. See <http://agaveapi.co/> for more information on the Agave API and <http://user.iplantcollaborative.org/> to register with iPlant.
Author: Barb Banbury <darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Kurt Michels <kamichels@math.arizona.edu>
Diff between rPlant versions 2.11 dated 2015-09-28 and 2.12 dated 2015-10-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Muscle.R | 6 ++---- 3 files changed, 7 insertions(+), 9 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between readr versions 0.2.0 dated 2015-10-19 and 0.2.1 dated 2015-10-21
DESCRIPTION | 12 ++++-------- MD5 | 16 ++++++++-------- R/encoding.R | 2 +- inst/doc/column-types.html | 4 ++-- inst/doc/locales.html | 4 ++-- man/encoding.Rd | 2 +- src/Collector.cpp | 2 +- src/Iconv.cpp | 16 +++++++++++++++- src/localtime.c | 6 ++++++ 9 files changed, 40 insertions(+), 24 deletions(-)
Title: Nonparametric Combination of Hypothesis Tests
Description: An implementation of nonparametric combination of hypothesis tests.
This package performs nonparametric combination (Pesarin and Salmaso 2010),
a permutation-based procedure for jointly testing multiple hypotheses. The
tests are conducted under the global "sharp" null hypothesis of no effects,
and the component tests are combined on the metric of their p-values. A
key feature of nonparametric combination is that it accounts for the
dependence among tests under the null hypothesis. In addition to the
"NPC" function, which performs nonparametric combination itself, the
package also contains a number of helper functions, many of which calculate
a test statistic given an input of data.
Author: Devin Caughey [aut, cre]
Maintainer: Devin Caughey <devin.caughey@gmail.com>
Diff between NPC versions 1.0.0 dated 2015-04-18 and 1.0.2 dated 2015-10-21
DESCRIPTION | 10 +++---- MD5 | 19 +++++++------ NEWS.md |only R/HarmonicWtdMean.R | 2 - R/KS.R | 7 +++- R/NPC.R | 7 +++- R/NormalCF.R | 2 - R/StudentsT.R | 3 +- man/FWE.Rd | 49 +++++++++++++++++++--------------- man/HoggAdapt.Rd | 24 ++++++++-------- man/t2p.Rd | 74 ++++++++++++++++++---------------------------------- 11 files changed, 96 insertions(+), 101 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using capture-recapture data consisting of a single conventional mark or multiple non-invasive marks.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 1.3.0 dated 2015-07-28 and 1.3.1 dated 2015-10-21
DESCRIPTION | 8 MD5 | 40 NAMESPACE | 54 NEWS | 123 + R/CJS.R | 2830 ++++++++++++++++++++++---------------------- R/Closed.R | 2166 ++++++++++++++++----------------- R/multimark_functions.R | 1634 ++++++++++++------------- inst/CITATION | 86 - man/bobcat.Rd | 50 man/getprobsCJS.Rd | 92 - man/getprobsClosed.Rd | 84 - man/markCJS.Rd | 252 +-- man/markClosed.Rd | 188 +- man/multimarkCJS.Rd | 320 ++-- man/multimarkClosed.Rd | 258 ++-- man/multimarksetup-class.Rd | 108 - man/multimodelCJS.Rd | 200 +-- man/multimodelClosed.Rd | 172 +- man/processdata.Rd | 116 - man/simdataCJS.Rd | 126 - man/simdataClosed.Rd | 122 - 21 files changed, 4505 insertions(+), 4524 deletions(-)
Title: Wrapper Functions for FSL (FMRIB Software Library) from
Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL
(http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used
neuroimaging software, using system commands. The goal is to be able to
interface with FSL completely in R, where you pass R objects of class "nifti",
implemented by package 'oro.nifti', and the function executes an FSL command
and returns an R object of class "nifti" if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 1.4.4 dated 2015-05-21 and 1.5.0 dated 2015-10-21
fslr-1.4.4/fslr/NEWS |only fslr-1.5.0/fslr/DESCRIPTION | 16 ++++++------ fslr-1.5.0/fslr/MD5 | 27 ++++++++++++-------- fslr-1.5.0/fslr/NAMESPACE | 8 ++++++ fslr-1.5.0/fslr/R/dropEmptyImageDimensions.R | 10 ++++++- fslr-1.5.0/fslr/R/fslfill2.R | 2 - fslr-1.5.0/fslr/R/fslhd.R | 35 +++++++++++++++++++++++---- fslr-1.5.0/fslr/R/ortho2.R | 5 ++- fslr-1.5.0/fslr/R/ortho_diff.R |only fslr-1.5.0/fslr/R/readNIfTI2.R |only fslr-1.5.0/fslr/R/rescale_img.R | 4 ++- fslr-1.5.0/fslr/R/writenii.R |only fslr-1.5.0/fslr/README.md | 4 ++- fslr-1.5.0/fslr/build/vignette.rds |binary fslr-1.5.0/fslr/man/cog.Rd | 4 ++- fslr-1.5.0/fslr/man/ortho_diff.Rd |only fslr-1.5.0/fslr/man/readNIfTI2.Rd |only fslr-1.5.0/fslr/man/writeNIfTI2.Rd |only 18 files changed, 85 insertions(+), 30 deletions(-)
Title: Two-Locus Family-Based Association Test with Polytomic Outcome
Description: Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models
defined by some design matrix.
Author: Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca> and Jordie Croteau
<jordie.croteau@crulrg.ulaval.ca>
Maintainer: Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca>
Diff between fat2Lpoly versions 1.1.1 dated 2014-10-17 and 1.2.2 dated 2015-10-21
DESCRIPTION | 16 MD5 | 90 NAMESPACE | 6 R/alleles2sums.R | 88 R/calcule.poids.Chen.R | 70 R/calcule.poids.alphafixe.r | 70 R/converti.terme.R | 16 R/cov.score.interfunction.R | 90 R/cov.score.poly.R | 158 R/design.1locus.R | 56 R/design.dichotomique.R | 66 R/design.endo2disease.R | 82 R/design.full.R | 66 R/design.polytomous.R | 416 R/fat2Lpoly.R | 116 R/fat2Lpoly.withinR.R | 555 R/get.scores.pvalues.R | 144 R/ibd.terms.R | 316 R/ibd.terms.w.r | 300 R/produits.paires.R | 16 R/read.merlin.files.R | 394 R/score.poly.R | 50 R/score.poly.w.r | 62 R/scores.covs.R | 552 data/fat2Lpoly.allSNPs.rda |binary data/ped.x.all.rda |binary inst/extdata/loc1.dat | 12 inst/extdata/loc1.freq | 12 inst/extdata/loc1.ibd |32642 ++++++++++++++++++++++---------------------- inst/extdata/loc1.ped | 1280 - inst/extdata/loc2.dat | 12 inst/extdata/loc2.freq | 18 inst/extdata/loc2.ibd |32642 ++++++++++++++++++++++---------------------- inst/extdata/loc2.ped | 1280 - man/design.1locus.Rd | 102 man/design.dichotomous.Rd | 82 man/design.endo2disease.Rd | 100 man/design.full.Rd | 106 man/fat2Lpoly-internal.Rd | 52 man/fat2Lpoly-package.Rd | 108 man/fat2Lpoly.Rd | 392 man/fat2Lpoly.allSNPs.Rd | 50 man/fat2Lpoly.withinR.Rd | 174 man/get.scores.pvalues.Rd | 108 man/ped.x.all.Rd | 80 man/read.merlin.files.Rd | 182 46 files changed, 36619 insertions(+), 36610 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.1 dated 2015-08-18 and 0.3.2 dated 2015-10-21
DESCRIPTION | 12 +++++------ MD5 | 24 +++++++++++----------- NAMESPACE | 1 NEWS | 7 ++++++ R/chordDiagram.R | 5 ++++ R/genomic.R | 4 ++- build/vignette.rds |binary inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary 13 files changed, 34 insertions(+), 19 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques (Bagging and Bootstrapping) and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.0 dated 2015-09-25 and 1.1 dated 2015-10-21
DESCRIPTION | 12 ++++++------ MD5 | 6 ++++-- R/mkr.R |only man/bWGR.Rd | 6 +++--- man/mkr.Rd |only 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Utilities for 'big.matrix' Objects from Package 'bigmemory'
Description: Extend the 'bigmemory' package with various analytics.
Functions 'bigkmeans' and 'binit' may also be used with native R objects.
For 'tapply'-like functions, the bigtabulate package may also be helpful.
For linear algebra support, see 'bigalgebra'. For mutex (locking) support
for advanced shared-memory usage, see 'synchronicity'.
Author: John W. Emerson <jayemerson@gmail.com> and Michael J. Kane <kaneplusplus@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between biganalytics versions 1.1.1 dated 2013-04-01 and 1.1.12 dated 2015-10-21
DESCRIPTION | 32 ++--- MD5 | 22 ++- NAMESPACE | 13 +- R/biglm.big.matrix.R | 2 R/kmeans.R | 28 ++-- R/zzz.R | 2 configure.win |only inst |only man/biganalytics-package.Rd | 10 - man/bigkmeans.Rd | 21 +-- man/summary.stat.Rd | 10 - src/kmeans.cpp | 264 ++++++++++++++++++++++++++++++++++++++------ src/summary_stat.cpp | 11 - 13 files changed, 298 insertions(+), 117 deletions(-)
Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics
interface to visualize backtest results of different financial
instruments, such as equities, futures, and credit default swaps.
The package does not run backtests on the given data set but
displays a graphical explanation of the backtest results. Users can
look at backtest graphics for different instruments, investment
strategies, and portfolios. Summary statistics of different
portfolio holdings are shown in the left panel, and interactive
plots of profit and loss (P\&L), net market value (NMV) and
gross market value (GMV) are displayed in the right panel.
Author: as.person(c(
"David Kane <dave.kane@gmail.com> [aut]",
"Ziqi Lu <ziqi.lu@williams.edu> [aut]",
"Fan Zhang <fan.zhang@williams.edu> [aut]",
"Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]"
))
Maintainer: Miller Zijie Zhu <zijie.miller.zhu@gmail.com>
Diff between backtestGraphics versions 0.1.5 dated 2015-08-13 and 0.1.6 dated 2015-10-21
backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_cumpnl_plot.R |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_cumpnl_plot.RData |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_interactive_plot.R |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_interactive_plot.RData |only backtestGraphics-0.1.6/backtestGraphics/DESCRIPTION | 8 backtestGraphics-0.1.6/backtestGraphics/MD5 | 22 backtestGraphics-0.1.6/backtestGraphics/R/backtestGraphics.R | 986 +++++----- backtestGraphics-0.1.6/backtestGraphics/R/cleanup_column.R | 373 +-- backtestGraphics-0.1.6/backtestGraphics/README.md | 40 backtestGraphics-0.1.6/backtestGraphics/build/vignette.rds |binary backtestGraphics-0.1.6/backtestGraphics/data/datalist | 6 backtestGraphics-0.1.6/backtestGraphics/inst/doc/backtestGraphics.R | 76 backtestGraphics-0.1.6/backtestGraphics/inst/doc/backtestGraphics.pdf |binary backtestGraphics-0.1.6/backtestGraphics/tests/testthat/test_calc_pnl.R | 20 14 files changed, 767 insertions(+), 764 deletions(-)
More information about backtestGraphics at CRAN
Permanent link
Title: Backward Pipe Operator
Description: Provides a backward-pipe operator for 'magrittr' (%<%) or
'pipeR' (%<<%) that allows for a performing operations from right-to-left.
This is useful in instances where there is right-to-left ordering commonly
observed with nested structures such as trees/directories and markup
languages such as HTML and XML.
Author: Christopher Brown [cre, aut],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between backpipe versions 0.1.2 dated 2015-09-03 and 0.1.5 dated 2015-10-21
backpipe-0.1.2/backpipe/inst/www |only backpipe-0.1.5/backpipe/DESCRIPTION | 13 ++-- backpipe-0.1.5/backpipe/LICENSE |only backpipe-0.1.5/backpipe/MD5 | 15 ++-- backpipe-0.1.5/backpipe/NEWS |only backpipe-0.1.5/backpipe/README.md | 79 ++++++++++++++++++++++++- backpipe-0.1.5/backpipe/inst/doc/backpipe.Rmd | 53 ++++++++-------- backpipe-0.1.5/backpipe/inst/doc/backpipe.html | 36 ++++++----- backpipe-0.1.5/backpipe/vignettes/backpipe.Rmd | 53 ++++++++-------- 9 files changed, 164 insertions(+), 85 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 2.13.1 dated 2015-05-26 and 2.14.0 dated 2015-10-21
aroma.core-2.13.1/aroma.core/R/whatDataType.R |only aroma.core-2.14.0/aroma.core/DESCRIPTION | 14 - aroma.core-2.14.0/aroma.core/MD5 | 48 +++-- aroma.core-2.14.0/aroma.core/NAMESPACE | 26 ++- aroma.core-2.14.0/aroma.core/NEWS | 14 + aroma.core-2.14.0/aroma.core/R/999.DEPRECATED.R | 85 ++++++++-- aroma.core-2.14.0/aroma.core/R/AromaMicroarrayDataSet.ATTRS.R | 2 aroma.core-2.14.0/aroma.core/R/AromaTabularBinarySet.ATTRS.R | 2 aroma.core-2.14.0/aroma.core/R/ChromosomeExplorer.LAYERS.R | 51 +----- aroma.core-2.14.0/aroma.core/R/ChromosomeExplorer.R | 50 ----- aroma.core-2.14.0/aroma.core/R/CopyNumberSegmentationModel.R | 5 aroma.core-2.14.0/aroma.core/R/Explorer.R | 34 ---- aroma.core-2.14.0/aroma.core/R/GladModel.R | 5 aroma.core-2.14.0/aroma.core/R/SampleAnnotationFile.R | 3 aroma.core-2.14.0/aroma.core/R/fitWHRCModel.matrix.R | 2 aroma.core-2.14.0/aroma.core/man/ChromosomeExplorer.Rd | 2 aroma.core-2.14.0/aroma.core/man/Non-documented_objects.Rd | 17 +- aroma.core-2.14.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2 aroma.core-2.14.0/aroma.core/man/RawSequenceReads.Rd | 2 aroma.core-2.14.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 2 aroma.core-2.14.0/aroma.core/man/SegmentedCopyNumbers.Rd | 2 aroma.core-2.14.0/aroma.core/man/mergeBoxplotStats.list.Rd | 2 aroma.core-2.14.0/aroma.core/tests/binScatter.R |only aroma.core-2.14.0/aroma.core/tests/colBinnedSmoothing.R |only aroma.core-2.14.0/aroma.core/tests/colKernelSmoothing.R |only aroma.core-2.14.0/aroma.core/tests/fitGenotypeCone.R |only aroma.core-2.14.0/aroma.core/tests/fitMultiDimensionalCone.R |only aroma.core-2.14.0/aroma.core/tests/matrixBlockPolish.R |only aroma.core-2.14.0/aroma.core/tests/mergeBoxplotStats.R |only 29 files changed, 189 insertions(+), 181 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <http://www.openstreetmap.org/>,
Mapquest <http://www.mapquest.com/>, Bing Maps <http://www.bing.com/maps>
and other tiled map sources in a way that works seamlessly with plotting
from the 'sp' package. Use to create high-resolution basemaps and add hillshade
to vector based maps.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.1.1 dated 2015-10-19 and 0.1.2 dated 2015-10-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/osmtile.R | 2 +- R/projections.R | 3 +++ tests/manual/tests.R | 4 ++-- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 0.5 dated 2015-10-19 and 0.5.1 dated 2015-10-20
CHANGELOG | 10 ++++++++++ DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- NAMESPACE | 3 +++ R/ClasGenMetDef.R | 13 ++++--------- man/MAINT.Data-package.Rd | 4 ++-- 6 files changed, 29 insertions(+), 22 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-4 dated 2015-10-16 and 0.1-5 dated 2015-10-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/gimme-data.R | 10 +++++----- R/gimme.R | 2 +- man/ts1.Rd | 2 +- man/ts2.Rd | 2 +- man/ts3.Rd | 2 +- man/ts4.Rd | 2 +- man/ts5.Rd | 2 +- 10 files changed, 25 insertions(+), 24 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.6 dated 2015-06-11 and 1.0.7 dated 2015-10-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ NEWS | 4 ++++ inst/CITATION | 16 ++++++++++++++++ 5 files changed, 30 insertions(+), 8 deletions(-)
Title: Quantile-Based Spectral Analysis of Time Series
Description: Methods to determine, smooth and plot quantile periodograms for
univariate and multivariate time series.
Author: Tobias Kley [aut, cre],
Stefan Birr [ctb] (Contributions to lag window estimation)
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between quantspec versions 1.1-0 dated 2015-09-27 and 1.2-0 dated 2015-10-20
DESCRIPTION | 12 MD5 | 116 +- NAMESPACE | 4 NEWS | 13 R/Class-ClippedCov.R | 13 R/Class-ClippedFT.R | 61 - R/Class-FreqRep.R | 177 ++- R/Class-LagEstimator.R | 2 R/Class-LagOperator.R | 125 ++ R/Class-QRegEstimator.R | 45 - R/Class-QSpecQuantity.R | 35 R/Class-QuantilePG.R | 53 - R/Class-QuantileSD.R | 293 +++++- R/Class-SmoothedPG.R | 1529 ++++++++++++++++++++++++---------- R/RcppExports.R | 27 R/aux-functions.R | 50 + R/generics.R | 11 R/quantspec-package.R | 24 inst/doc/quantspec.pdf |binary inst/examples/QuantileSD.R | 18 inst/extdata/ref-results.rdata |binary man/ClippedCov-class.Rd | 3 man/ClippedCov-constructor.Rd | 4 man/ClippedFT-class.Rd | 9 man/ClippedFT-constructor.Rd | 13 man/FreqRep-class.Rd | 28 man/LagEstimator-class.Rd | 4 man/LagOperator-class.Rd | 3 man/QRegEstimator-constructor.Rd | 2 man/QSpecQuantity-class.Rd | 13 man/QuantilePG-constructor.Rd | 2 man/QuantileSD-class.Rd | 22 man/SmoothedPG-class.Rd | 9 man/SmoothedPG-constructor.Rd | 4 man/figures/csd-mv.pdf |only man/figures/csd-mv.png |only man/figures/main-mv.pdf |only man/figures/main-mv.png |only man/figures/main2-mv.pdf |only man/figures/main2-mv.png |only man/generics-accessors.Rd | 6 man/getCoherency-QuantileSD.Rd |only man/getCoherency-SmoothedPG.Rd |only man/getCoherencySdNaive-SmoothedPG.Rd |only man/getMeanPG-QuantileSD.Rd | 8 man/getPointwiseCIs-SmoothedPG.Rd | 54 - man/getSdBoot-SmoothedPG.Rd | 2 man/getSdNaive-SmoothedPG.Rd | 19 man/getStdError-QuantileSD.Rd | 8 man/getValues-FreqRep.Rd | 6 man/getValues-QuantilePG.Rd | 10 man/getValues-QuantileSD.Rd | 12 man/getValues-SmoothedPG.Rd | 15 man/getY-FreqRep.Rd | 5 man/lenTS.Rd |only man/plot-FreqRep.Rd | 6 man/plot-LagOperator.Rd | 31 man/plot-QuantilePG.Rd | 3 man/plot-QuantileSD.Rd | 3 man/plot-SmoothedPG.Rd | 3 man/quantspec-package.Rd | 24 man/timeSeriesValidator.Rd | 2 src/RcppExports.cpp | 13 src/computeCoherency.cpp |only tests/testthat/test-multivariate.R |only 65 files changed, 2217 insertions(+), 737 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 0.34-2 dated 2015-05-06 and 0.36-2 dated 2015-10-20
DESCRIPTION | 12 +- MD5 | 41 ++++----- NAMESPACE | 59 +++++++------ NEWS | 28 ++++++ R/EuropeanCallBE.R | 9 - R/LSopt.R | 208 ++++++++++++++++++++++++---------------------- R/TAopt.R | 5 - R/pm.R |only R/randomp.R | 14 +-- build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/unitTests/report.txt | 20 ++-- man/LS.info.Rd |only man/TA.info.Rd | 10 +- man/callMerton.Rd | 2 man/pm.Rd |only 23 files changed, 233 insertions(+), 175 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.5 dated 2015-10-12 and 1.6 dated 2015-10-20
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NAMESPACE | 1 R/barnard.test.R |only R/barnardw.test.R | 74 --------------------------------------------------- man/Barnard.Rd | 2 - man/barnard.test.Rd |only man/barnardw.test.Rd | 63 ++----------------------------------------- src/Barnard.c | 36 +++++++++++++++++++++--- 9 files changed, 50 insertions(+), 148 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.8.0 dated 2015-08-07 and 2.9.0 dated 2015-10-20
DESCRIPTION | 21 ++++---- MD5 | 16 +++--- NAMESPACE | 10 +--- NEWS | 8 +++ R/999.DEPRECATED.R | 52 ---------------------- R/GenericDataFileSet.PARALLEL.R | 80 +++++++++++++++++++++++++++++++--- man/Deprecated_and_defunct_objects.Rd | 17 ------- man/dsApply.GenericDataFileSet.Rd | 6 +- tests/GenericDataFileSet,dsApply.R | 57 ++++++++++++++++++++---- 9 files changed, 159 insertions(+), 108 deletions(-)
Title: R Interface to Bloomberg
Description: An R Interface to Bloomberg is provided via the Blp API.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.0 dated 2015-08-14 and 0.3.1 dated 2015-10-20
ChangeLog | 78 ++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 19 +++++----- MD5 | 81 ++++++++++++++++++++++++++++++++------------ NAMESPACE | 1 R/RcppExports.R | 4 ++ R/bdh.R | 8 ++++ R/bdp.R | 3 + R/bds.R | 2 - R/beqs.R |only R/getTicks.R | 7 ++- README.md | 15 ++++---- build/vignette.rds |binary cleanup | 3 + configure | 23 +++++++----- inst/NEWS.Rd | 18 +++++++++ inst/doc/rblpapi-intro.R | 3 + inst/doc/rblpapi-intro.Rmd | 9 ++++ inst/doc/rblpapi-intro.html | 5 ++ inst/include |only man/bdh.Rd | 8 ++++ man/bdp.Rd | 3 + man/beqs.Rd |only src/Makevars.win | 16 +++----- src/RcppExports.cpp | 17 +++++++++ src/beqs.cpp |only src/blpapi_utils.cpp | 1 vignettes/rblpapi-intro.Rmd | 9 ++++ 27 files changed, 273 insertions(+), 60 deletions(-)
Title: Pretty Descriptive Stats
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon <drjimlemon@gmail.com>,
Philippe Grosjean <phgrosjean@sciviews.org>
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between prettyR versions 2.1-1 dated 2015-04-29 and 2.2 dated 2015-10-20
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS | 4 ++++ man/rep_n_stack.Rd | 3 ++- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.5-12 dated 2015-05-16 and 3.6 dated 2015-10-20
DESCRIPTION | 9 +++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 14 ++++++++++++++ NEWS | 9 +++++++++ R/addtable2plot.R | 1 + R/pyramid.plot.R | 2 +- R/sizetree.R | 5 ++++- R/starPie.R | 10 +++++++++- R/twoord.plot.R | 9 ++++++--- data/soils.rda |binary man/addtable2plot.Rd | 5 +++-- man/color2D.matplot.Rd | 5 +++-- man/feather.plot.Rd | 5 +++-- man/pyramid.plot.Rd | 14 ++++++++++++++ man/sizetree.Rd | 5 ++++- man/starPie.Rd | 15 ++++++++++++++- 16 files changed, 105 insertions(+), 33 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman <Rob.Hyndman@monash.edu>.
Contributors include George Athanasopoulos, Christoph Bergmeir,
Carlos Cinelli, Yousaf Khan, Zach Mayer, Slava Razbash,
Drew Schmidt, David Shaub, Yuan Tang, Earo Wang, Zhenyu Zhou.
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 6.1 dated 2015-05-12 and 6.2 dated 2015-10-20
forecast-6.1/forecast/inst/tests |only forecast-6.1/forecast/tests/test-all.R |only forecast-6.2/forecast/ChangeLog | 16 + forecast-6.2/forecast/DESCRIPTION | 14 - forecast-6.2/forecast/MD5 | 121 +++++---- forecast-6.2/forecast/NAMESPACE | 26 + forecast-6.2/forecast/R/HoltWintersNew.R | 11 forecast-6.2/forecast/R/acf.R | 22 - forecast-6.2/forecast/R/arima.R | 23 + forecast-6.2/forecast/R/attach.R | 5 forecast-6.2/forecast/R/bootstrap.R | 83 ------ forecast-6.2/forecast/R/calendar.R | 35 +- forecast-6.2/forecast/R/checkAdmissibility.R | 2 forecast-6.2/forecast/R/clean.R | 106 ++++--- forecast-6.2/forecast/R/errors.R | 11 forecast-6.2/forecast/R/ets.R | 28 +- forecast-6.2/forecast/R/etsforecast.R | 18 - forecast-6.2/forecast/R/fitTBATS.R | 227 ++++------------- forecast-6.2/forecast/R/forecast.R | 4 forecast-6.2/forecast/R/forecast.varest.R | 4 forecast-6.2/forecast/R/forecast2.R | 5 forecast-6.2/forecast/R/forecastTBATS.R | 7 forecast-6.2/forecast/R/getResponse.R | 12 forecast-6.2/forecast/R/graph.R | 11 forecast-6.2/forecast/R/lm.R | 7 forecast-6.2/forecast/R/newarima2.R | 38 +- forecast-6.2/forecast/R/nnetar.R | 7 forecast-6.2/forecast/R/tbats.R | 35 +- forecast-6.2/forecast/README.md | 5 forecast-6.2/forecast/man/bizdays.Rd | 12 forecast-6.2/forecast/man/ets.Rd | 2 forecast-6.2/forecast/man/fitted.Arima.Rd | 2 forecast-6.2/forecast/man/forecast.Arima.Rd | 2 forecast-6.2/forecast/man/forecast.HoltWinters.Rd | 2 forecast-6.2/forecast/man/forecast.Rd | 2 forecast-6.2/forecast/man/forecast.StructTS.Rd | 2 forecast-6.2/forecast/man/forecast.bats.Rd | 2 forecast-6.2/forecast/man/forecast.ets.Rd | 2 forecast-6.2/forecast/man/forecast.lm.Rd | 2 forecast-6.2/forecast/man/forecast.stl.Rd | 2 forecast-6.2/forecast/man/meanf.Rd | 2 forecast-6.2/forecast/man/naive.Rd | 2 forecast-6.2/forecast/man/rw.f.Rd | 2 forecast-6.2/forecast/man/ses.Rd | 4 forecast-6.2/forecast/man/spline.f.Rd | 2 forecast-6.2/forecast/man/theta.Rd | 2 forecast-6.2/forecast/man/ts.display.Rd | 6 forecast-6.2/forecast/src/etsTargetFunction.cpp | 10 forecast-6.2/forecast/src/etsTargetFunction.h | 6 forecast-6.2/forecast/src/etsTargetFunctionWrapper.cpp | 2 forecast-6.2/forecast/src/etscalc.c | 15 - forecast-6.2/forecast/tests/testthat |only forecast-6.2/forecast/tests/testthat.R |only 53 files changed, 458 insertions(+), 510 deletions(-)
Title: Sequential Event Interval Analysis
Description: Functions for analysis of rate changes in sequential events.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between eventInterval versions 1.2 dated 2015-01-20 and 1.3 dated 2015-10-20
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 6 +++--- NEWS | 8 ++++++++ R/EIdist.R | 6 ++++++ 5 files changed, 27 insertions(+), 13 deletions(-)
Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.4.5 dated 2015-06-11 and 0.5 dated 2015-10-20
dygraphs-0.4.5/dygraphs/NEWS |only dygraphs-0.5/dygraphs/DESCRIPTION | 8 dygraphs-0.5/dygraphs/MD5 | 35 - dygraphs-0.5/dygraphs/NAMESPACE | 2 dygraphs-0.5/dygraphs/R/axis.R | 4 dygraphs-0.5/dygraphs/R/dygraph.R | 19 dygraphs-0.5/dygraphs/R/legend.R | 9 dygraphs-0.5/dygraphs/R/options.R | 33 - dygraphs-0.5/dygraphs/R/utils.R | 13 dygraphs-0.5/dygraphs/inst/NEWS |only dygraphs-0.5/dygraphs/inst/examples/examples.html | 277 ---------- dygraphs-0.5/dygraphs/inst/htmlwidgets/dygraphs.js | 229 ++++---- dygraphs-0.5/dygraphs/inst/htmlwidgets/dygraphs.yaml | 2 dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph-combined-dev.js |only dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph-combined.js | 8 dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph.css | 4 dygraphs-0.5/dygraphs/man/dyLegend.Rd | 11 dygraphs-0.5/dygraphs/man/dyOptions.Rd | 25 dygraphs-0.5/dygraphs/man/dyRangeSelector.Rd | 6 dygraphs-0.5/dygraphs/man/dygraph.Rd | 7 20 files changed, 258 insertions(+), 434 deletions(-)
Title: Completing Ranks
Description: Functions for completing and recalculating rankings.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between crank versions 1.0-7 dated 2015-01-20 and 1.1 dated 2015-10-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + NEWS | 4 ++++ 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson <jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.4.6 dated 2013-11-18 and 4.5.8 dated 2015-10-20
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Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden <kieran.alden@gmail.com>
Diff between spartan versions 2.2.1 dated 2015-04-13 and 2.3 dated 2015-10-19
DESCRIPTION | 10 +-- MD5 | 26 +++++--- NAMESPACE | 4 + R/lhc_calculatePRCCForMultipleTimepoints.R |only R/lhc_countSignificantParametersOverTime.R |only R/lhc_generatePRCoEffs.R | 2 R/lhc_generateTimepointFiles.R |only R/lhc_graphPRCCForMultipleTimepoints.R |only R/oat_csv_result_file_analysis.R | 23 +++++-- R/oat_graph_Leish_ATestsMultipleTimepoints.R |only R/plotATestsFromTimepointFiles.R |only R/plotPRCCSFromTimepointFiles.R |only R/ploteFASTSiFromTimepointFiles.R |only R/prepare_parameter_value_list.R | 2 R/subset_results_by_param_value_set.R | 1 man/Technique2-oat_generate_analysis.Rd | 31 +++++++++- man/Technique3-lhc_perform_analysis.Rd | 67 +++++++++++++++++++++- man/Technique4-efast_generate_analysis_results.Rd | 10 +++ 18 files changed, 149 insertions(+), 27 deletions(-)
Title: Pacific Decadal Oscillation Index
Description: Monthly Pacific Decadal Oscillation (PDO) index
values from January 1900 to present.
Author: Joe Thorley [aut, cre],
Nathan Mantua [aut, dtc],
Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rpdo versions 0.0.1 dated 2015-08-21 and 0.1.0 dated 2015-10-19
DESCRIPTION | 14 ++++++-------- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/data.R | 2 +- README.md | 54 ++++++++++++++++++++++++++++++++---------------------- data/pdo.rda |binary man/pdo.Rd | 2 +- 7 files changed, 51 insertions(+), 39 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: ORPHANED
Diff between readr versions 0.1.1 dated 2015-05-29 and 0.2.0 dated 2015-10-19
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Title: Determine Optimal Clustering Algorithm and Number of Clusters
Description: Cluster analysis using statistical and biological
validation measures for both continuous and count data.
Author: Michael Sekula <michael.sekula@louisville.edu>,
Somnath Datta <somnath.datta@louisville.edu>,
and Susmita Datta <susmita.datta@louisville.edu>
Maintainer: Michael Sekula <michael.sekula@louisville.edu>
Diff between optCluster versions 1.0.0 dated 2015-06-09 and 1.0.1 dated 2015-10-19
DESCRIPTION | 14 ++-- MD5 | 16 ++--- NAMESPACE | 5 + R/optCluster-Functions.R | 13 +++- man/optCluster-class.Rd | 127 ++++++++++++++++++++++---------------------- man/optCluster.Rd | 133 +++++++++++++++++++++++------------------------ man/optHeatmap.Rd | 47 +++++++--------- man/repRankAggreg.Rd | 67 ++++++++++++----------- man/valPlot.Rd | 55 +++++++++---------- 9 files changed, 245 insertions(+), 232 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the 'pan' package, and
several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.2-3 dated 2015-07-09 and 0.2-4 dated 2015-10-19
DESCRIPTION | 8 - MD5 | 30 ++--- NEWS | 65 +++++++----- R/clusterMeans.R | 17 ++- R/panImpute.R | 12 +- R/print.mitml.summary.R | 52 ++++++--- R/print.mitml.testEstimates.R | 18 +-- R/summary.mitml.R | 76 ++++++-------- R/testConstraints.R | 103 +++++++++++++------ R/testEstimates.R | 221 ++++++++++++++++++++++++++---------------- R/testModels.R | 1 R/zzz.R | 49 +++++++++ man/panImpute.Rd | 13 -- man/summary.mitml.Rd | 24 +++- man/testConstraints.Rd | 38 ++++--- man/testEstimates.Rd | 13 ++ 16 files changed, 469 insertions(+), 271 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.5 dated 2015-05-19 and 1.0.6 dated 2015-10-19
CHNOSZ-1.0.5/CHNOSZ/demo/cordierite.R |only CHNOSZ-1.0.5/CHNOSZ/demo/orp.R |only CHNOSZ-1.0.5/CHNOSZ/inst/tests |only CHNOSZ-1.0.5/CHNOSZ/tests/test-all.R |only CHNOSZ-1.0.6/CHNOSZ/DESCRIPTION | 13 +- CHNOSZ-1.0.6/CHNOSZ/MD5 | 130 ++++++++++++++------------- CHNOSZ-1.0.6/CHNOSZ/NAMESPACE | 12 ++ CHNOSZ-1.0.6/CHNOSZ/R/IAPWS95.R | 51 ---------- CHNOSZ-1.0.6/CHNOSZ/R/affinity.R | 6 - CHNOSZ-1.0.6/CHNOSZ/R/diagram.R | 5 - CHNOSZ-1.0.6/CHNOSZ/R/equilibrate.R | 8 - CHNOSZ-1.0.6/CHNOSZ/R/examples.R | 12 +- CHNOSZ-1.0.6/CHNOSZ/R/iprotein.R | 7 + CHNOSZ-1.0.6/CHNOSZ/R/mosaic.R | 6 - CHNOSZ-1.0.6/CHNOSZ/R/objective.R | 2 CHNOSZ-1.0.6/CHNOSZ/R/swap.basis.R | 10 +- CHNOSZ-1.0.6/CHNOSZ/R/util.fasta.R | 8 - CHNOSZ-1.0.6/CHNOSZ/R/util.list.R | 50 ++++++---- CHNOSZ-1.0.6/CHNOSZ/R/util.program.R | 19 ++- CHNOSZ-1.0.6/CHNOSZ/R/util.water.R |only CHNOSZ-1.0.6/CHNOSZ/R/water.R | 90 ------------------ CHNOSZ-1.0.6/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.6/CHNOSZ/data/OBIGT.csv | 4 CHNOSZ-1.0.6/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.6/CHNOSZ/demo/00Index | 4 CHNOSZ-1.0.6/CHNOSZ/demo/ORP.R |only CHNOSZ-1.0.6/CHNOSZ/demo/density.R |only CHNOSZ-1.0.6/CHNOSZ/inst/NEWS | 45 +++++++++ CHNOSZ-1.0.6/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.6/CHNOSZ/man/CHNOSZ-package.Rd | 3 CHNOSZ-1.0.6/CHNOSZ/man/IAPWS95.Rd | 12 -- CHNOSZ-1.0.6/CHNOSZ/man/data.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/examples.Rd | 12 +- CHNOSZ-1.0.6/CHNOSZ/man/swap.basis.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/util.fasta.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/util.program.Rd | 18 ++- CHNOSZ-1.0.6/CHNOSZ/man/util.water.Rd |only CHNOSZ-1.0.6/CHNOSZ/man/water.Rd | 35 +------ CHNOSZ-1.0.6/CHNOSZ/tests/testthat |only CHNOSZ-1.0.6/CHNOSZ/tests/testthat.R |only 43 files changed, 249 insertions(+), 323 deletions(-)
Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre],
Dominik Ernst [ctb],
Madison Giacofci [ctb],
Sophie Lambert-Lacroix [ctb],
Guillemette Marot [ctb],
Franck Picard [ctb],
Nicoleta Serban [ctb],
Huijing Jiang [ctb],
Gareth James [ctb],
Catherine Sugar [ctb],
Hans-Georg Mueller [ctb],
Jie Peng [ctb],
Chiou Jeng-Min [ctb],
Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>
Diff between funcy versions 0.8 dated 2015-10-13 and 0.8.3 dated 2015-10-19
funcy-0.8.3/funcy/DESCRIPTION | 12 - funcy-0.8.3/funcy/MD5 | 129 +++++--------- funcy-0.8.3/funcy/NEWS.md |only funcy-0.8.3/funcy/R/distclust.R | 2 funcy-0.8.3/funcy/R/funPrinComp.R | 2 funcy-0.8.3/funcy/R/functions.R | 2 funcy-0.8.3/funcy/R/plot.R | 7 funcy-0.8.3/funcy/man/funcit.Rd | 4 funcy-0.8.3/funcy/man/funcyOutList.Rd | 2 funcy-0.8.3/funcy/man/plotFuncy.Rd | 4 funcy-0.8.3/funcy/src/Makevars | 23 +- funcy-0.8.3/funcy/src/base/ansi_colors.h | 2 funcy-0.8.3/funcy/src/base/base.h | 11 + funcy-0.8.3/funcy/src/base/cc.h | 4 funcy-0.8.3/funcy/src/base/ccmem.h | 5 funcy-0.8.3/funcy/src/base/common.c | 39 ++-- funcy-0.8.3/funcy/src/base/common.h | 61 +++--- funcy-0.8.3/funcy/src/base/debug.h | 47 +---- funcy-0.8.3/funcy/src/base/deprecated.h | 4 funcy-0.8.3/funcy/src/base/otrav.cc | 32 +-- funcy-0.8.3/funcy/src/base/otrav.h | 91 +++------- funcy-0.8.3/funcy/src/base/otrav_impl.h | 245 +++++++++++++-------------- funcy-0.8.3/funcy/src/base/test.h | 8 funcy-0.8.3/funcy/src/col/arraylist.h | 176 +++++++++---------- funcy-0.8.3/funcy/src/col/col.cc | 12 - funcy-0.8.3/funcy/src/col/col_string.h | 44 ++-- funcy-0.8.3/funcy/src/col/fastalloc.h | 2 funcy-0.8.3/funcy/src/col/heap.h | 24 +- funcy-0.8.3/funcy/src/col/intmap.h | 18 - funcy-0.8.3/funcy/src/col/rangeset.h | 10 - funcy-0.8.3/funcy/src/data/crossvalidation.h | 80 ++++---- funcy-0.8.3/funcy/src/data/dataset.cc | 110 ++++++------ funcy-0.8.3/funcy/src/data/dataset.h | 46 ++--- funcy-0.8.3/funcy/src/file/textfile.cc | 35 ++- funcy-0.8.3/funcy/src/file/textfile.h | 12 - funcy-0.8.3/funcy/src/fscm.cc | 218 ++++++++++++------------ funcy-0.8.3/funcy/src/fx/datanode.c | 10 - funcy-0.8.3/funcy/src/fx/fx.c | 122 ++++++++----- funcy-0.8.3/funcy/src/fx/stopwatch.c | 12 - funcy-0.8.3/funcy/src/la/la.h | 22 +- funcy-0.8.3/funcy/src/la/matrix.h | 124 +++++++------ funcy-0.8.3/funcy/src/la/uselapack.cc | 42 ++-- funcy-0.8.3/funcy/src/la/uselapack.h | 70 +++---- funcy-0.8.3/funcy/src/libmain.cc | 6 funcy-0.8.3/funcy/src/math/discrete.cc | 22 +- funcy-0.8.3/funcy/src/math/discrete.h | 16 - funcy-0.8.3/funcy/src/math/kernel.h | 14 - funcy-0.8.3/funcy/src/math/math_lib.h | 46 ++--- funcy-0.8.3/funcy/src/par/grain.h | 6 funcy-0.8.3/funcy/src/par/thread.h | 6 funcy-0.8/funcy/src/sparse |only funcy-0.8/funcy/src/thor |only funcy-0.8/funcy/src/tree |only 53 files changed, 1031 insertions(+), 1010 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-24 0.1.83
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-28 0.4.4
2014-10-06 0.4.2
2014-10-01 0.4.1
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.1 dated 2015-10-15 and 1.6.2 dated 2015-10-19
TMB-1.6.1/TMB/inst/include/Eigen |only TMB-1.6.2/TMB/DESCRIPTION | 34 + TMB-1.6.2/TMB/MD5 | 419 +---------------- TMB-1.6.2/TMB/R/TMB.R | 14 TMB-1.6.2/TMB/R/benchmark.R | 3 TMB-1.6.2/TMB/R/config.R | 3 TMB-1.6.2/TMB/R/examples.R | 9 TMB-1.6.2/TMB/R/gdbsource.R | 3 TMB-1.6.2/TMB/R/sdreport.R | 3 TMB-1.6.2/TMB/R/tmbprofile.R | 3 TMB-1.6.2/TMB/R/validation.R | 6 TMB-1.6.2/TMB/R/zzz.R | 7 TMB-1.6.2/TMB/inst/COPYRIGHTS |only TMB-1.6.2/TMB/inst/include/Rstream.hpp | 6 TMB-1.6.2/TMB/inst/include/TMB.hpp | 3 TMB-1.6.2/TMB/inst/include/Vectorize.hpp | 3 TMB-1.6.2/TMB/inst/include/atomic_macro.hpp | 3 TMB-1.6.2/TMB/inst/include/atomic_math.hpp | 13 TMB-1.6.2/TMB/inst/include/checkpoint_macro.hpp | 3 TMB-1.6.2/TMB/inst/include/config.hpp | 3 TMB-1.6.2/TMB/inst/include/convenience.hpp | 3 TMB-1.6.2/TMB/inst/include/convert.hpp | 3 TMB-1.6.2/TMB/inst/include/distributions_R.hpp | 5 TMB-1.6.2/TMB/inst/include/dnorm.hpp | 3 TMB-1.6.2/TMB/inst/include/expm.hpp | 7 TMB-1.6.2/TMB/inst/include/lgamma.hpp | 3 TMB-1.6.2/TMB/inst/include/start_parallel.hpp | 3 TMB-1.6.2/TMB/inst/include/tmb_core.hpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/R_inla.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/array.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/autodiff.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/density.cpp | 5 TMB-1.6.2/TMB/inst/include/tmbutils/kronecker.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/matexp.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/order.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/romberg.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/splines.cpp | 15 TMB-1.6.2/TMB/inst/include/tmbutils/spmat.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils_extra.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/vector.cpp | 3 TMB-1.6.2/TMB/man/compile.Rd | 3 TMB-1.6.2/TMB/man/oneStepPredict.Rd | 3 TMB-1.6.2/TMB/man/precompile.Rd | 2 TMB-1.6.2/TMB/man/runExample.Rd | 4 TMB-1.6.2/TMB/man/template.Rd | 6 TMB-1.6.2/TMB/src/external_metis.c | 3 TMB-1.6.2/TMB/src/local_stubs.c | 3 TMB-1.6.2/TMB/src/solve_subset.c | 13 TMB-1.6.2/TMB/src/utils.c | 3 50 files changed, 245 insertions(+), 416 deletions(-)
Title: Fitting Separable Nonlinear Models in Spectroscopy and
Microscopy
Description: A problem-solving environment (PSE) for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments; has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg <j.snellenburg@vu.nl>
Diff between TIMP versions 1.12.1 dated 2014-12-11 and 1.13.0 dated 2015-10-19
DESCRIPTION | 21 ++++++++----------- MD5 | 40 ++++++++++++++++++++----------------- NAMESPACE | 46 +++++++++++++++++++++++++++---------------- R/compCoh.R | 4 ++- R/displayEst.R | 38 +++++++++++++++++++---------------- R/initModelClassTest.R |only R/matlinlogplot.R | 28 +++++++++++++------------- R/plotFLIM.R | 1 R/set_plotter_kin.R | 1 R/set_plotter_spec.R | 1 data/denS4.rda |binary data/denS5.rda |binary data/donorAcceptorTagged.rda |binary data/donorTagged.rda |binary data/mea_IRF.rda |binary data/target.rda |binary man/TIMP-package.Rd | 7 ++---- man/readData.Rd | 5 ++-- man/spec-class.Rd | 2 - man/target.Rd | 2 - tests/_paramEst.txt |only tests/_selectedtraces.ps |only tests/_summary.ps |only 23 files changed, 109 insertions(+), 87 deletions(-)
Title: Constrained Single Index Model Estimation
Description: Estimation of function and index vector in single index model with and without shape constraints including different smoothness conditions.
Author: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>,
Rohit Kumar Patra <rkp2117@columbia.edu>
Maintainer: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>
Diff between simest versions 0.1 dated 2015-09-20 and 0.2 dated 2015-10-19
DESCRIPTION | 13 ++-- MD5 | 33 ++++++------ NAMESPACE | 3 - R/CvxLipReg.r | 4 + R/CvxLseReg.r | 22 ++++---- R/CvxPenReg.r | 137 ++++++++------------------------------------------ R/SimEst.r | 43 +++++++++------ R/SolvePenta.r | 8 +- R/merge.r | 3 - README | 5 + inst/CITATION | 5 + man/cvx.lip.reg.Rd | 2 man/cvx.lse.reg.Rd | 7 ++ man/cvx.pen.reg.Rd | 2 man/sim.est.Rd | 13 ++-- man/smooth.pen.reg.Rd | 2 src/Mfun.c | 6 +- src/pred.c |only 18 files changed, 120 insertions(+), 188 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.0.8 dated 2015-07-24 and 3.0.11 dated 2015-10-19
ChangeLog | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- R/K1.R | 39 ++++++++++++++++++++++++++++++++++++++- R/K2.R | 39 ++++++++++++++++++++++++++++++++++++++- R/pCa.R | 2 +- R/pTA.R | 2 +- R/pmix.R | 2 +- R/ppH.R | 2 +- man/K1.Rd | 8 ++++++-- man/K2.Rd | 8 ++++++-- man/Om.Rd | 2 +- man/buffer.Rd | 2 +- man/buffesm.Rd | 2 +- man/carb.Rd | 4 +++- man/oa.Rd | 4 +++- man/pCa.Rd | 6 ++++-- man/pHinsi.Rd | 4 +++- man/pTA.Rd | 4 +++- man/pgas.Rd | 4 +++- man/pmix.Rd | 4 +++- man/ppH.Rd | 4 +++- man/psi.Rd | 4 +++- 23 files changed, 162 insertions(+), 49 deletions(-)
More information about RcmdrPlugin.Export at CRAN
Permanent link
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on the 'htmlwidgets'
package, it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced
but can easily be added in the constructors. Complex properties (e.g.
'JavaScript' object) can be passed as named list. See examples at <http://
dataknowledge.github.io/rAmCharts/>. and <http://www.amcharts.com/> for
more information about the library. The package includes the free version of
'AmCharts' Library. Its only limitation is that a small link to the web site
will be displayed in your charts. If you enjoy this library, do not hesitate
to refer to this page <http://www.amcharts.com/online-store/> to purchase a
licence, and thus support its creators and get a period of Priority Support.
See also <http://www.amcharts.com/about/> for more information about
'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
DataKnowledge [ctb] (See official web site at http://www.datak.fr)
Maintainer: Jeffery Petit <jeff@datak.fr>
Diff between rAmCharts versions 1.1.1 dated 2015-09-16 and 1.1.2 dated 2015-10-19
rAmCharts-1.1.1/rAmCharts/R/AmChart_getSet.R |only rAmCharts-1.1.1/rAmCharts/R/AmChart_plot.R |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amAngularGauge.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amAngularGauge.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amFunnelChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amFunnelChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amGanttChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amGanttChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amPieChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amPieChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amRadarChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amRadarChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amSerialChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amSerialChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amStockChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amStockChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amXYChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amXYChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/lib/amcharts |only rAmCharts-1.1.1/rAmCharts/man/addArrow.Rd |only rAmCharts-1.1.1/rAmCharts/man/addAxe.Rd |only rAmCharts-1.1.1/rAmCharts/man/addGraph.Rd |only rAmCharts-1.1.1/rAmCharts/man/addGuide.Rd |only rAmCharts-1.1.1/rAmCharts/man/addLabel.Rd |only rAmCharts-1.1.1/rAmCharts/man/addSegment.Rd |only rAmCharts-1.1.1/rAmCharts/man/addSubData.Rd |only rAmCharts-1.1.1/rAmCharts/man/addTitle.Rd |only rAmCharts-1.1.1/rAmCharts/man/addTrendLine.Rd |only rAmCharts-1.1.1/rAmCharts/man/addValueAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setAllLabels.Rd |only rAmCharts-1.1.1/rAmCharts/man/setArrows.Rd |only rAmCharts-1.1.1/rAmCharts/man/setAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setBalloon.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCategoryAxis.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCategoryField.Rd |only rAmCharts-1.1.1/rAmCharts/man/setChartCursor.Rd |only rAmCharts-1.1.1/rAmCharts/man/setChartScrollbar.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCreditsPosition.Rd |only rAmCharts-1.1.1/rAmCharts/man/setDataProvider.Rd |only rAmCharts-1.1.1/rAmCharts/man/setExport.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGraph.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGraphs.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGuides.Rd |only rAmCharts-1.1.1/rAmCharts/man/setLegend.Rd |only rAmCharts-1.1.1/rAmCharts/man/setSubChartProperties.Rd |only rAmCharts-1.1.1/rAmCharts/man/setTitles.Rd |only rAmCharts-1.1.1/rAmCharts/man/setTrendLines.Rd |only rAmCharts-1.1.1/rAmCharts/man/setType.Rd |only rAmCharts-1.1.1/rAmCharts/man/setValueAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setValueAxis.Rd |only rAmCharts-1.1.2/rAmCharts/DESCRIPTION | 52 rAmCharts-1.1.2/rAmCharts/MD5 | 697 ++++----- rAmCharts-1.1.2/rAmCharts/NAMESPACE | 19 rAmCharts-1.1.2/rAmCharts/R/AmBalloon.R | 16 rAmCharts-1.1.2/rAmCharts/R/AmChart.R | 284 ++-- rAmCharts-1.1.2/rAmCharts/R/AmChart_constructors.R | 14 rAmCharts-1.1.2/rAmCharts/R/AmChart_setters.R |only rAmCharts-1.1.2/rAmCharts/R/AmChart_shinyUtils.R | 55 rAmCharts-1.1.2/rAmCharts/R/AmCharts_plot.R |only rAmCharts-1.1.2/rAmCharts/R/AmGraph.R | 53 rAmCharts-1.1.2/rAmCharts/R/AmLegend.R | 22 rAmCharts-1.1.2/rAmCharts/R/AmObject.R | 45 rAmCharts-1.1.2/rAmCharts/R/AmStockChart.R | 706 +--------- rAmCharts-1.1.2/rAmCharts/R/AmStockChart_setters.R |only rAmCharts-1.1.2/rAmCharts/R/AxisBase.R | 48 rAmCharts-1.1.2/rAmCharts/R/AxisBase_setters.R |only rAmCharts-1.1.2/rAmCharts/R/CategoryAxis.R | 49 rAmCharts-1.1.2/rAmCharts/R/ChartCursor.R | 106 - rAmCharts-1.1.2/rAmCharts/R/ChartCursor_setters.R |only rAmCharts-1.1.2/rAmCharts/R/ChartScrollbar.R | 124 - rAmCharts-1.1.2/rAmCharts/R/ChartScrollbar_setters.R |only rAmCharts-1.1.2/rAmCharts/R/DataSet.R | 112 - rAmCharts-1.1.2/rAmCharts/R/DataSetSelector.R |only rAmCharts-1.1.2/rAmCharts/R/DataSet_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeArrow.R | 64 rAmCharts-1.1.2/rAmCharts/R/GaugeArrow_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeAxis.R | 68 rAmCharts-1.1.2/rAmCharts/R/GaugeAxis_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeBand.R | 21 rAmCharts-1.1.2/rAmCharts/R/Guide.R | 100 - rAmCharts-1.1.2/rAmCharts/R/Guide_setters.R |only rAmCharts-1.1.2/rAmCharts/R/Label.R | 21 rAmCharts-1.1.2/rAmCharts/R/PeriodSelector.R | 17 rAmCharts-1.1.2/rAmCharts/R/StockEvent.R | 53 rAmCharts-1.1.2/rAmCharts/R/StockEvent_setters.R |only rAmCharts-1.1.2/rAmCharts/R/StockPanel.R | 288 +--- rAmCharts-1.1.2/rAmCharts/R/StockPanel_setters.R |only rAmCharts-1.1.2/rAmCharts/R/Title.R | 22 rAmCharts-1.1.2/rAmCharts/R/TrendLine.R | 186 -- rAmCharts-1.1.2/rAmCharts/R/TrendLine_setters.R |only rAmCharts-1.1.2/rAmCharts/R/ValueAxis.R | 56 rAmCharts-1.1.2/rAmCharts/R/amBoxplot.R |only rAmCharts-1.1.2/rAmCharts/R/amHist.R | 95 - rAmCharts-1.1.2/rAmCharts/R/basicClassUnions.R |only rAmCharts-1.1.2/rAmCharts/R/classUnion.R |only rAmCharts-1.1.2/rAmCharts/R/data.R |only rAmCharts-1.1.2/rAmCharts/R/sharedGenerics.R | 14 rAmCharts-1.1.2/rAmCharts/R/shinyExamples.R | 2 rAmCharts-1.1.2/rAmCharts/data |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/amDrillChart.js | 8 rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/amDrillChart.yaml | 28 rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/amcharts.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/amstock.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/funnel.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/gantt.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/gauge.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/images |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/lang |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/patterns |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/pie.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/plugins |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/radar.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/serial.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/themes |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/xy.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/ramcharts_base.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/ramcharts_base.yaml |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/style.css | 86 - rAmCharts-1.1.2/rAmCharts/inst/shiny/server.R | 6 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/drilldown/drilldown_server.R | 67 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/drilldown/drilldown_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/funnel/funnel_server.R | 110 + rAmCharts-1.1.2/rAmCharts/inst/shiny/src/funnel/funnel_ui.R | 22 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/gauge/gauge_server.R | 58 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/gauge/gauge_ui.R | 12 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/pie/pie_server.R | 160 +- rAmCharts-1.1.2/rAmCharts/inst/shiny/src/pie/pie_ui.R | 52 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/radar/radar_server.R | 94 - rAmCharts-1.1.2/rAmCharts/inst/shiny/src/radar/radar_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/serial/serial_server.R | 608 ++++++-- rAmCharts-1.1.2/rAmCharts/inst/shiny/src/serial/serial_ui.R | 49 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/stock |only rAmCharts-1.1.2/rAmCharts/inst/shiny/src/xy/xy_server.R | 50 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/xy/xy_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/ui.R | 13 rAmCharts-1.1.2/rAmCharts/man/AmBalloon-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/AmChart-class.Rd | 132 - rAmCharts-1.1.2/rAmCharts/man/AmGraph-class.Rd | 21 rAmCharts-1.1.2/rAmCharts/man/AmLegend-class.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/AmObject-class.Rd | 6 rAmCharts-1.1.2/rAmCharts/man/AmStockChart-class.Rd | 153 -- rAmCharts-1.1.2/rAmCharts/man/AxisBase-class.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/CategoryAxis-class.Rd | 14 rAmCharts-1.1.2/rAmCharts/man/ChartCursor-class.Rd | 16 rAmCharts-1.1.2/rAmCharts/man/ChartScrollbar-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/DataSet-class.Rd | 19 rAmCharts-1.1.2/rAmCharts/man/DataSetSelector-class.Rd |only rAmCharts-1.1.2/rAmCharts/man/GaugeArrow-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/GaugeAxis-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/GaugeBand-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/Guide-class.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/Label-class.Rd | 21 rAmCharts-1.1.2/rAmCharts/man/PeriodSelector-class.Rd | 6 rAmCharts-1.1.2/rAmCharts/man/StockEvent-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/StockPanel-class.Rd | 138 + rAmCharts-1.1.2/rAmCharts/man/Title-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/TrendLine-class.Rd | 34 rAmCharts-1.1.2/rAmCharts/man/ValueAxis-class.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/amBoxplot.Rd |only rAmCharts-1.1.2/rAmCharts/man/amChartsOutput.Rd | 7 rAmCharts-1.1.2/rAmCharts/man/amHist.Rd | 37 rAmCharts-1.1.2/rAmCharts/man/controlShinyPlot.Rd |only rAmCharts-1.1.2/rAmCharts/man/data_gdp.Rd |only rAmCharts-1.1.2/rAmCharts/man/data_stock1.Rd |only rAmCharts-1.1.2/rAmCharts/man/initialize-AmChart.Rd | 566 +++++++- rAmCharts-1.1.2/rAmCharts/man/initialize-AmGraph.Rd | 12 rAmCharts-1.1.2/rAmCharts/man/initialize-AmStockChart.Rd | 202 +- rAmCharts-1.1.2/rAmCharts/man/initialize-AxisBase.Rd | 27 rAmCharts-1.1.2/rAmCharts/man/initialize-ChartCursor.Rd | 28 rAmCharts-1.1.2/rAmCharts/man/initialize-ChartScrollbar.Rd | 59 rAmCharts-1.1.2/rAmCharts/man/initialize-DataSet.Rd | 20 rAmCharts-1.1.2/rAmCharts/man/initialize-DataSetSelector.Rd |only rAmCharts-1.1.2/rAmCharts/man/initialize-GaugeArrow.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/initialize-GaugeAxis.Rd | 28 rAmCharts-1.1.2/rAmCharts/man/initialize-Guide.Rd | 23 rAmCharts-1.1.2/rAmCharts/man/initialize-PeriodSelector.Rd | 4 rAmCharts-1.1.2/rAmCharts/man/initialize-StockEvent.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/initialize-StockPanel.Rd | 55 rAmCharts-1.1.2/rAmCharts/man/initialize-TrendLine.Rd | 41 rAmCharts-1.1.2/rAmCharts/man/listProperties-AmChart-method.Rd | 2 rAmCharts-1.1.2/rAmCharts/man/listProperties-AmObject.Rd | 11 rAmCharts-1.1.2/rAmCharts/man/plot.AmChart.Rd | 14 rAmCharts-1.1.2/rAmCharts/man/print-AmObject-method.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/renderAmCharts.Rd | 7 rAmCharts-1.1.2/rAmCharts/man/runShinyExamples.Rd | 2 rAmCharts-1.1.2/rAmCharts/man/shared-generics.Rd | 20 rAmCharts-1.1.2/rAmCharts/man/show-AmChart-method.Rd |only rAmCharts-1.1.2/rAmCharts/man/show-AmObject-method.Rd | 11 rAmCharts-1.1.2/rAmCharts/man/show-AmStockChart-method.Rd |only rAmCharts-1.1.2/rAmCharts/tests |only 190 files changed, 3544 insertions(+), 3249 deletions(-)
Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes the multivariate methods and data visualization tools
to implement profile analysis and cross-validation techniques described
in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins <cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3 dated 2015-08-26 and 0.3-1 dated 2015-10-19
DESCRIPTION | 12 ++++++------ MD5 | 44 +++++++++++++++++++++++++++++--------------- NAMESPACE | 4 ++-- NEWS | 9 ++++++++- R/anova.critpat.R | 3 ++- R/print.critpat.R | 4 ++-- README.md |only build |only data/spouse.rda |only inst |only man/EEGS.Rd | 4 ++-- man/IPMMc.Rd | 6 +++--- man/PS.Rd | 2 +- man/leisure.Rd | 5 ++--- man/mod_data.Rd | 2 +- man/nutrient.Rd | 3 +-- man/pams.Rd | 2 +- man/pbg.Rd | 3 +-- man/pr.Rd | 2 +- man/profiler-package.Rd | 2 +- man/spouse.Rd |only vignettes |only 22 files changed, 63 insertions(+), 44 deletions(-)
Title: Predictive Toxicity Assessment of Chemical Mixtures
Description: Toxicity prediction of chemical mixtures using reference models such as
'concentration addition' and 'independent action' (Backhaus, T., Faust, M., Environmental
Science and Technology. 2012, 46, 2564-2573. doi:10.1021/es2034125).
Author: Xiangwei Zhu
Maintainer: Xiangwei Zhu <xwzhunc@gmail.com>
Diff between mixtox versions 1.0 dated 2015-06-03 and 1.1 dated 2015-10-19
DESCRIPTION | 15 ++++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 5 +++++ R/curveFit.R | 10 ++++++---- R/ecaPred.R | 2 ++ R/eiaPred.R | 2 ++ man/CEx.Rd | 2 +- man/ECx.Rd | 2 +- man/NOEC.Rd | 2 +- man/caPred.Rd | 2 +- man/curveFit.Rd | 2 +- man/cytotox.Rd | 2 +- man/ecaPred.Rd | 2 +- man/eiaPred.Rd | 2 +- man/gcaPred.Rd | 2 +- man/iaPred.Rd | 2 +- man/mixtox-package.Rd | 4 ++-- 17 files changed, 51 insertions(+), 39 deletions(-)
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: "Pierre-Andre Cornillon" <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 1.4.5 dated 2013-09-02 and 2.0-0 dated 2015-10-19
ibr-1.4.5/ibr/R/npregression.R |only ibr-1.4.5/ibr/R/predict.npregression.R |only ibr-1.4.5/ibr/R/print.npregression.R |only ibr-1.4.5/ibr/R/print.summary.npregression.R |only ibr-1.4.5/ibr/R/summary.npregression.R |only ibr-1.4.5/ibr/man/npregression.Rd |only ibr-1.4.5/ibr/man/predict.npregression.Rd |only ibr-1.4.5/ibr/man/print.summary.npregression.Rd |only ibr-1.4.5/ibr/man/summary.npregression.Rd |only ibr-2.0-0/ibr/DESCRIPTION | 16 ibr-2.0-0/ibr/MD5 | 109 ++++-- ibr-2.0-0/ibr/NAMESPACE | 18 - ibr-2.0-0/ibr/R/betaS1lr.R |only ibr-2.0-0/ibr/R/fittedS1lr.R |only ibr-2.0-0/ibr/R/forward.R | 26 + ibr-2.0-0/ibr/R/ibr.R | 258 +-------------- ibr-2.0-0/ibr/R/ibr.fit.R |only ibr-2.0-0/ibr/R/iterchoiceS1cv.R | 2 ibr-2.0-0/ibr/R/iterchoiceS1lrcv.R |only ibr-2.0-0/ibr/R/iterchoiceS1lrcve.R |only ibr-2.0-0/ibr/R/lambdachoicelr.R |only ibr-2.0-0/ibr/R/lrsmoother.R |only ibr-2.0-0/ibr/R/npregress.R |only ibr-2.0-0/ibr/R/predict.ibr.R | 41 +- ibr-2.0-0/ibr/R/predict.npregress.R |only ibr-2.0-0/ibr/R/print.ibr.R | 3 ibr-2.0-0/ibr/R/print.npregress.R |only ibr-2.0-0/ibr/R/print.summary.ibr.R | 14 ibr-2.0-0/ibr/R/print.summary.npregress.R |only ibr-2.0-0/ibr/R/summary.ibr.R | 63 ++- ibr-2.0-0/ibr/R/summary.npregress.R |only ibr-2.0-0/ibr/data/ozone.rda |binary ibr-2.0-0/ibr/man/betaA.Rd | 4 ibr-2.0-0/ibr/man/betaS1lr.Rd |only ibr-2.0-0/ibr/man/cvobs.Rd | 4 ibr-2.0-0/ibr/man/fittedA.Rd | 4 ibr-2.0-0/ibr/man/fittedS1.Rd | 4 ibr-2.0-0/ibr/man/fittedS1lr.Rd |only ibr-2.0-0/ibr/man/forward.Rd | 37 +- ibr-2.0-0/ibr/man/ibr.Rd | 125 +++++-- ibr-2.0-0/ibr/man/ibr.fit.Rd |only ibr-2.0-0/ibr/man/iterchoiceA.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceAcv.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceAcve.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceAe.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceS1.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceS1cv.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceS1cve.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceS1e.Rd | 4 ibr-2.0-0/ibr/man/iterchoiceS1lrcv.Rd |only ibr-2.0-0/ibr/man/iterchoiceS1lrcve.Rd |only ibr-2.0-0/ibr/man/lambdachoicelr.Rd |only ibr-2.0-0/ibr/man/lrsmoother.Rd |only ibr-2.0-0/ibr/man/npregress.Rd |only ibr-2.0-0/ibr/man/plot.forwardibr.Rd | 4 ibr-2.0-0/ibr/man/plot.ibr.Rd | 4 ibr-2.0-0/ibr/man/predict.ibr.Rd | 4 ibr-2.0-0/ibr/man/predict.npregress.Rd |only ibr-2.0-0/ibr/man/print.summary.ibr.Rd | 4 ibr-2.0-0/ibr/man/print.summary.npregress.Rd |only ibr-2.0-0/ibr/man/summary.npregress.Rd |only ibr-2.0-0/ibr/man/sumvalpr.Rd | 4 ibr-2.0-0/ibr/src/dssplines.c | 408 ++++++++++++------------ ibr-2.0-0/ibr/src/regression.c | 12 ibr-2.0-0/ibr/tests |only 65 files changed, 577 insertions(+), 623 deletions(-)
Title: Estimation in Dual Frame Surveys
Description: Point and interval estimation in dual frame surveys. In contrast
to classic sampling theory, where only one sampling frame is considered,
dual frame methodology assumes that there are two frames available for
sampling and that, overall, they cover the entire target population. Then,
two probability samples (one from each frame) are drawn and information
collected is suitably combined to get estimators of the parameter of
interest.
Author: Antonio Arcos <arcos@ugr.es>, Maria del Mar Rueda <mrueda@ugr.es>,
Maria Giovanna Ranalli <giovanna.ranalli@stat.unipg.it> and David Molina
<dmolinam@ugr.es>
Maintainer: David Molina <dmolinam@ugr.es>
Diff between Frames2 versions 0.1.1 dated 2015-04-20 and 0.1.2 dated 2015-10-19
DESCRIPTION | 10 ++-- MD5 | 91 +++++++++++++++++++++--------------------- NAMESPACE | 2 R/BKA.R | 2 R/Dat.R | 9 ++-- R/JackCalDF.R | 6 +- R/JackCalSF.R | 6 +- R/JackHartley.R | 2 R/JackPEL.R | 8 +-- R/PEL.R | 12 ++--- build/vignette.rds |binary data/Dat.txt.gz |binary inst/CITATION |only inst/doc/estimation.Rnw | 2 inst/doc/estimation.pdf |binary inst/doc/formatting.data.Rnw | 2 inst/doc/formatting.data.pdf |binary man/BKA.Rd | 3 - man/CalDF.Rd | 3 - man/CalSF.Rd | 3 - man/Compare.Rd | 3 - man/CovHT.Rd | 3 - man/Dat.Rd | 9 +++- man/DatA.Rd | 3 - man/DatB.Rd | 3 - man/Domains.Rd | 3 - man/FB.Rd | 3 - man/HT.Rd | 3 - man/Hartley.Rd | 3 - man/JackBKA.Rd | 3 - man/JackCalDF.Rd | 3 - man/JackCalSF.Rd | 3 - man/JackFB.Rd | 3 - man/JackHartley.Rd | 3 - man/JackPEL.Rd | 3 - man/JackPML.Rd | 3 - man/JackSFRR.Rd | 3 - man/PEL.Rd | 5 +- man/PML.Rd | 3 - man/PiklA.Rd | 3 - man/PiklB.Rd | 3 - man/SFRR.Rd | 3 - man/VarHT.Rd | 3 - man/WeightsCalDF.Rd | 3 - man/WeightsCalSF.Rd | 3 - vignettes/estimation.Rnw | 2 vignettes/formatting.data.Rnw | 2 47 files changed, 142 insertions(+), 106 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-4 dated 2013-12-14 and 0.2-5 dated 2015-10-19
EMCluster-0.2-4/EMCluster/data/myiris.rda |only EMCluster-0.2-4/EMCluster/vignettes/EMCluster-include/jss.bst |only EMCluster-0.2-4/EMCluster/vignettes/EMCluster-include/jss.cls |only EMCluster-0.2-5/EMCluster/COPYING | 711 +++++----- EMCluster-0.2-5/EMCluster/ChangeLog | 28 EMCluster-0.2-5/EMCluster/DESCRIPTION | 21 EMCluster-0.2-5/EMCluster/INSTALL | 2 EMCluster-0.2-5/EMCluster/MD5 | 133 + EMCluster-0.2-5/EMCluster/NAMESPACE | 19 EMCluster-0.2-5/EMCluster/R/000_globalVariables.r |only EMCluster-0.2-5/EMCluster/R/fcn_Jaccard.r |only EMCluster-0.2-5/EMCluster/R/fcn_dlmvnorm.r | 11 EMCluster-0.2-5/EMCluster/R/fcn_emcluster.r | 2 EMCluster-0.2-5/EMCluster/R/fcn_emgroup.r | 2 EMCluster-0.2-5/EMCluster/R/fcn_init_EM.r | 1 EMCluster-0.2-5/EMCluster/R/fcn_init_other_shortem.r | 2 EMCluster-0.2-5/EMCluster/R/fcn_init_svd.r | 2 EMCluster-0.2-5/EMCluster/R/fcn_m_step.r | 2 EMCluster-0.2-5/EMCluster/R/lmt_information.r |only EMCluster-0.2-5/EMCluster/R/lmt_libControurPlotNew.r |only EMCluster-0.2-5/EMCluster/R/lmt_main.r |only EMCluster-0.2-5/EMCluster/R/lmt_project_to_2d.r |only EMCluster-0.2-5/EMCluster/R/lmt_q.map.new.r |only EMCluster-0.2-5/EMCluster/R/logit_PI_I_information.r |only EMCluster-0.2-5/EMCluster/R/partial_logL.r |only EMCluster-0.2-5/EMCluster/R/partial_q.r |only EMCluster-0.2-5/EMCluster/R/post_I_information.r |only EMCluster-0.2-5/EMCluster/R/recolor.r |only EMCluster-0.2-5/EMCluster/README |only EMCluster-0.2-5/EMCluster/data/color.ppcontour.r |only EMCluster-0.2-5/EMCluster/demo/00Index | 3 EMCluster-0.2-5/EMCluster/demo/lmt.r |only EMCluster-0.2-5/EMCluster/demo/logit.r |only EMCluster-0.2-5/EMCluster/demo/myiris.r | 2 EMCluster-0.2-5/EMCluster/demo/ppcontour.r |only EMCluster-0.2-5/EMCluster/inst/CITATION | 20 EMCluster-0.2-5/EMCluster/inst/doc/EMCluster-guide.Rnw | 17 EMCluster-0.2-5/EMCluster/inst/doc/EMCluster-guide.pdf |binary EMCluster-0.2-5/EMCluster/inst/workflow |only EMCluster-0.2-5/EMCluster/man/00_EMCluster-package.Rd | 3 EMCluster-0.2-5/EMCluster/man/11_d.EMControl.Rd | 5 EMCluster-0.2-5/EMCluster/man/12_d.dataset.Rd | 3 EMCluster-0.2-5/EMCluster/man/21_init.EM.Rd | 5 EMCluster-0.2-5/EMCluster/man/22_emcluster.Rd | 5 EMCluster-0.2-5/EMCluster/man/23_emgroup.Rd | 5 EMCluster-0.2-5/EMCluster/man/30_assign.class.Rd | 5 EMCluster-0.2-5/EMCluster/man/31_em.ic.Rd | 5 EMCluster-0.2-5/EMCluster/man/32_em.step.Rd | 5 EMCluster-0.2-5/EMCluster/man/40_lmt.Rd |only EMCluster-0.2-5/EMCluster/man/91_mvn.Rd | 12 EMCluster-0.2-5/EMCluster/man/92_convert.Rd | 5 EMCluster-0.2-5/EMCluster/man/99_plotem.Rd | 5 EMCluster-0.2-5/EMCluster/man/99_plotmd.Rd | 5 EMCluster-0.2-5/EMCluster/man/a0_project.on.2d.Rd |only EMCluster-0.2-5/EMCluster/man/a1_plotppcontour.Rd |only EMCluster-0.2-5/EMCluster/man/xx_Jaccard.Rd |only EMCluster-0.2-5/EMCluster/man/xx_RRand.Rd | 5 EMCluster-0.2-5/EMCluster/man/xx_recolor.Rd |only EMCluster-0.2-5/EMCluster/man/yy_print.summary.Rd | 5 EMCluster-0.2-5/EMCluster/man/zx_all.post_I_information.Rd |only EMCluster-0.2-5/EMCluster/man/zy_all.lmt.Rd |only EMCluster-0.2-5/EMCluster/man/zz_all.internal.Rd | 3 EMCluster-0.2-5/EMCluster/src/RRand.c | 32 EMCluster-0.2-5/EMCluster/vignettes/EMCluster-guide.Rnw | 17 EMCluster-0.2-5/EMCluster/vignettes/EMCluster-include/01-acknowledgement.tex | 23 EMCluster-0.2-5/EMCluster/vignettes/EMCluster-include/01-introduction.tex | 13 EMCluster-0.2-5/EMCluster/vignettes/EMCluster-include/EMCluster.bib | 6 EMCluster-0.2-5/EMCluster/vignettes/EMCluster-include/my_jss.cls |only EMCluster-0.2-5/EMCluster/vignettes/build_pdf.sh | 11 69 files changed, 668 insertions(+), 493 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design,
along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 0.0.5 dated 2015-07-28 and 1.0.0 dated 2015-10-19
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++++--------- NAMESPACE | 2 ++ NEWS | 11 +++++++++++ R/Helper.funcs.R | 15 ++++++++++++--- R/MainBar.R | 20 +++++++++----------- R/fromExpression.R |only R/fromList.R |only R/upset.R | 8 ++++---- README.md | 10 ++++++++++ man/fromExpression.Rd |only man/fromList.Rd |only man/upset.Rd | 15 +++++++++------ vignettes/basic.usage.Rmd | 17 +++++++++++++++++ 14 files changed, 90 insertions(+), 36 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.7 dated 2015-08-13 and 1.3.8 dated 2015-10-19
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Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.2-1 dated 2015-09-17 and 2.2-2 dated 2015-10-19
DESCRIPTION | 8 MD5 | 38 NEWS | 748 +-- R/commander.R | 2732 +++++------ R/data-menu.R | 28 R/distributions-sample.R | 4 R/startup.R | 32 R/statistics-models-menu.R | 12 R/utilities.R | 6204 ++++++++++++------------- inst/etc/R-logo-old.gif |only inst/etc/R-logo-old.ico |only inst/etc/R-logo.gif |binary inst/etc/R-logo.ico |binary inst/po/gl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 136 man/Rcmdr.Utilities.Rd | 1248 ++--- po/R-Rcmdr.pot | 88 po/R-fr.po | 6 po/R-gl.po | 9160 +++++++++++++++++++------------------- po/R-zh.po | 161 21 files changed, 10402 insertions(+), 10203 deletions(-)
Title: Moment-Based Estimation for Hierarchical Models
Description:
Implements methods from the paper "Fast Moment-Based Estimation
for Hierarchical Models," by Perry (2015).
Author: Patrick O. Perry
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between mbest versions 0.3 dated 2015-04-20 and 0.4 dated 2015-10-19
mbest-0.3/mbest/README.md |only mbest-0.4/mbest/DESCRIPTION | 8 ++++---- mbest-0.4/mbest/MD5 | 5 ++--- mbest-0.4/mbest/NAMESPACE | 18 ++++++++++++++---- 4 files changed, 20 insertions(+), 11 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 0.4 dated 2015-05-03 and 0.5 dated 2015-10-19
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 7 ++----- R/ClasGenMetDef.R | 4 ++-- man/MAINT.Data-package.Rd | 4 ++-- 5 files changed, 15 insertions(+), 18 deletions(-)
Title: High Dimensional Discriminant Analysis
Description: Performs linear discriminant analysis in high dimensional
problems based on reliable covariance estimators for problems
with (many) more variables than observations. Includes routines
for classifier training, prediction, cross-validation and
variable selection.
Author: Antonio Pedro Duarte Silva <psilva@porto.ucp.pt>
Maintainer: Antonio Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between HiDimDA versions 0.2-3 dated 2015-03-27 and 0.2-4 dated 2015-10-19
CHANGELOG | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ man/HiDimDA-package.Rd | 4 ++-- 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Clinical Significance Functions
Description: Functions for calculating clinical significance.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between clinsig versions 1.0-5 dated 2015-01-20 and 1.1 dated 2015-10-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 4 ++++ NEWS | 4 ++++ 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization and EM clustering. Furthermore, there are specialized
distance measures, plotting functions and some helper functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.2 dated 2015-10-16 and 1.0.3 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + R/svs.r | 31 +++++++++++++++++-------------- inst/extdata/Ctxt_Dut.txt | 2 +- inst/extdata/Ctxt_Eng.txt | 2 +- inst/extdata/Ctxt_Fra.txt | 2 +- man/InvT_Eng.txt.Rd | 2 +- man/InvT_Fra.txt.Rd | 2 +- man/SndT_Eng.txt.Rd | 2 +- man/SndT_Fra.txt.Rd | 2 +- man/svs-package.Rd | 2 +- 12 files changed, 42 insertions(+), 38 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions
from Il-Youp Kwak
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between xoi versions 0.61-1 dated 2013-01-14 and 0.66-9 dated 2015-10-18
xoi-0.61-1/xoi/README.txt |only xoi-0.61-1/xoi/inst/README.txt |only xoi-0.61-1/xoi/man/xoi-internal.Rd |only xoi-0.66-9/xoi/DESCRIPTION | 24 xoi-0.66-9/xoi/MD5 | 149 ++-- xoi-0.66-9/xoi/NAMESPACE | 45 - xoi-0.66-9/xoi/R/bssbsb-data.R |only xoi-0.66-9/xoi/R/chiasma.R | 154 ++-- xoi-0.66-9/xoi/R/coi_um.R |only xoi-0.66-9/xoi/R/coincidence.R | 171 ++-- xoi-0.66-9/xoi/R/fitGamma.R | 389 ++++++---- xoi-0.66-9/xoi/R/fitStahl.R | 462 +++++++------ xoi-0.66-9/xoi/R/gammaDensities.R | 1099 +++++++++++++++++++++++-------- xoi-0.66-9/xoi/R/kfunc.R | 140 +-- xoi-0.66-9/xoi/R/kwak_coincidence.R | 132 +-- xoi-0.66-9/xoi/R/kwak_get_n_xo.R | 25 xoi-0.66-9/xoi/R/kwak_identify_xo.R | 45 - xoi-0.66-9/xoi/R/kwak_intensity.R | 124 +-- xoi-0.66-9/xoi/R/recrate.R | 281 ++++--- xoi-0.66-9/xoi/R/simStahl.R | 219 ++++-- xoi-0.66-9/xoi/R/util.R | 437 +++++++----- xoi-0.66-9/xoi/R/xoiversion.R | 26 xoi-0.66-9/xoi/data/bssbsb.RData |binary xoi-0.66-9/xoi/inst/README.md |only xoi-0.66-9/xoi/inst/STATUS.txt | 38 - xoi-0.66-9/xoi/man/bssbsb.Rd | 60 - xoi-0.66-9/xoi/man/chiasma.Rd | 98 +- xoi-0.66-9/xoi/man/coincidence.Rd | 57 - xoi-0.66-9/xoi/man/convertxoloc.Rd | 45 - xoi-0.66-9/xoi/man/countxo.Rd | 46 - xoi-0.66-9/xoi/man/distance.given.two.Rd | 134 +-- xoi-0.66-9/xoi/man/est.coi.Rd | 88 +- xoi-0.66-9/xoi/man/est.coi.um.Rd |only xoi-0.66-9/xoi/man/est.recrate.Rd | 71 +- xoi-0.66-9/xoi/man/find.breaks.Rd | 78 +- xoi-0.66-9/xoi/man/first.given.two.Rd | 133 +-- xoi-0.66-9/xoi/man/firstden.Rd | 107 +-- xoi-0.66-9/xoi/man/fitGamma.Rd | 176 ++-- xoi-0.66-9/xoi/man/fitStahl.Rd | 116 +-- xoi-0.66-9/xoi/man/gammacoi.Rd | 93 +- xoi-0.66-9/xoi/man/intensity.Rd | 57 - xoi-0.66-9/xoi/man/ioden.Rd | 98 +- xoi-0.66-9/xoi/man/joint.given.two.Rd | 122 +-- xoi-0.66-9/xoi/man/kfunc.Rd |only xoi-0.66-9/xoi/man/location.given.one.Rd | 125 +-- xoi-0.66-9/xoi/man/recrate2scanone.Rd |only xoi-0.66-9/xoi/man/simStahl.Rd | 88 +- xoi-0.66-9/xoi/man/stahlLoglik.Rd | 94 +- xoi-0.66-9/xoi/man/stahlcoi.Rd | 104 +- xoi-0.66-9/xoi/man/xoiversion.Rd | 32 xoi-0.66-9/xoi/man/xoprob.Rd | 110 +-- xoi-0.66-9/xoi/src/GammaDensities.c | 298 ++++---- xoi-0.66-9/xoi/src/GammaIntegral.c | 88 +- xoi-0.66-9/xoi/src/GammaLoglik.c | 50 - xoi-0.66-9/xoi/src/GammaS.c | 331 ++++----- xoi-0.66-9/xoi/src/GammaS.h | 102 +- xoi-0.66-9/xoi/src/GammaUtil.c | 122 +-- xoi-0.66-9/xoi/src/chiasma.c | 348 ++++----- xoi-0.66-9/xoi/src/chiasma.h | 15 xoi-0.66-9/xoi/src/coi_um.c |only xoi-0.66-9/xoi/src/coi_um.h |only xoi-0.66-9/xoi/src/coincidence.c | 300 ++++---- xoi-0.66-9/xoi/src/coincidence.h | 22 xoi-0.66-9/xoi/src/fitStahl.c | 333 ++++----- xoi-0.66-9/xoi/src/fitStahl.h | 25 xoi-0.66-9/xoi/src/kfunc.c | 146 ++-- xoi-0.66-9/xoi/src/kfunc.h | 24 xoi-0.66-9/xoi/src/kwak.h | 46 - xoi-0.66-9/xoi/src/kwak_coincidence.c | 266 +++---- xoi-0.66-9/xoi/src/kwak_get_n_xo.c | 68 - xoi-0.66-9/xoi/src/kwak_identify.c | 96 +- xoi-0.66-9/xoi/src/kwak_intensity.c | 121 +-- xoi-0.66-9/xoi/src/recrate.c | 150 ++-- xoi-0.66-9/xoi/src/recrate.h | 14 xoi-0.66-9/xoi/src/simStahl.c | 329 ++++++--- xoi-0.66-9/xoi/src/simStahl.h |only xoi-0.66-9/xoi/src/stahl_util.c | 72 +- xoi-0.66-9/xoi/src/stahl_util.h | 18 xoi-0.66-9/xoi/src/zeroin.c | 184 ++--- xoi-0.66-9/xoi/src/zeroin.h | 30 xoi-0.66-9/xoi/tests |only 81 files changed, 5380 insertions(+), 4310 deletions(-)
Title: Weighted Likelihood Estimation
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it>, SLATEC Common Mathematical Library <www.netlib.org/slatec>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between wle versions 0.9-9 dated 2013-12-11 and 0.9-91 dated 2015-10-18
wle-0.9-9/wle/R/mle.cv.robust.bootstrap.R |only wle-0.9-9/wle/R/wle.normal.high.R |only wle-0.9-9/wle/R/wle.normal.high.chisq.R |only wle-0.9-9/wle/R/wle.normal.high.r.R |only wle-0.9-9/wle/man/wle.lm.control.Rd |only wle-0.9-9/wle/src/wleaicls.f |only wle-0.9-91/wle/DESCRIPTION | 14 +-- wle-0.9-91/wle/MD5 | 100 ++++++++++++------------- wle-0.9-91/wle/NAMESPACE | 115 ++++++++++++++++++++++++++++ wle-0.9-91/wle/R/densitynormalmulti.R |only wle-0.9-91/wle/R/wle.control.R | 119 +++++++++++++++++++++++++++++- wle-0.9-91/wle/R/wle.weights2.R |only wle-0.9-91/wle/README | 4 - wle-0.9-91/wle/data/artificial.rda |binary wle-0.9-91/wle/data/cavendish.rda |binary wle-0.9-91/wle/data/hald.rda |binary wle-0.9-91/wle/data/rocky.rda |binary wle-0.9-91/wle/data/selection.rda |binary wle-0.9-91/wle/man/wle.aic.ar.Rd | 16 ++-- wle-0.9-91/wle/man/wle.fracdiff.Rd | 46 ++++++----- wle-0.9-91/wle/man/wle.glm.Rd | 2 wle-0.9-91/wle/man/wle.glm.weights.Rd | 8 +- wle-0.9-91/wle/man/wle.weights.Rd | 4 - wle-0.9-91/wle/src/dbetawrapper.c | 2 wle-0.9-91/wle/src/densitynormalmulti.f |only wle-0.9-91/wle/src/dqagie.f | 6 + wle-0.9-91/wle/src/dqagpe.f | 3 wle-0.9-91/wle/src/genprm.f | 4 - wle-0.9-91/wle/src/initds.f | 4 + wle-0.9-91/wle/src/mleaic.f | 5 - wle-0.9-91/wle/src/mlecp.f | 26 ------ wle-0.9-91/wle/src/mlecv.f | 2 wle-0.9-91/wle/src/mlestepwise.f | 3 wle-0.9-91/wle/src/weights.f | 2 wle-0.9-91/wle/src/weights2.f |only wle-0.9-91/wle/src/wleaic.f | 2 wle-0.9-91/wle/src/wlecp.f | 22 ----- wle-0.9-91/wle/src/wlecv.f | 2 wle-0.9-91/wle/src/wlecvone.f | 6 - wle-0.9-91/wle/src/wlecvonem.f | 5 - wle-0.9-91/wle/src/wlecvonemc.f | 5 - wle-0.9-91/wle/src/wlegamma.f | 12 +-- wle-0.9-91/wle/src/wleinvga.f | 2 wle-0.9-91/wle/src/wlenmix.f | 2 wle-0.9-91/wle/src/wlenorm.f | 8 +- wle-0.9-91/wle/src/wlenormalhigh.f | 8 +- wle-0.9-91/wle/src/wlenormalmulti.f | 8 +- wle-0.9-91/wle/src/wleonestepfix.f | 43 +--------- wle-0.9-91/wle/src/wleregfix.f | 6 - wle-0.9-91/wle/src/wlestepwise.f | 1 wle-0.9-91/wle/src/wwlecv.f | 2 wle-0.9-91/wle/src/xercnt.f | 6 + wle-0.9-91/wle/src/xerhlt.f | 1 wle-0.9-91/wle/src/xermsg.f | 2 wle-0.9-91/wle/src/xerprn.f | 4 - wle-0.9-91/wle/src/xersve.f | 14 +-- 56 files changed, 416 insertions(+), 230 deletions(-)
Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to libsodium: a modern, easy-to-use software library for
encryption, decryption, signatures, password hashing and more. Sodium uses
curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein,
which has become very popular after it was discovered that the NSA had
backdoored Dual EC DRBG.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between sodium versions 0.1 dated 2015-10-11 and 0.2 dated 2015-10-18
DESCRIPTION | 8 +++++--- MD5 | 12 +++++++++++- NEWS |only build |only inst |only vignettes |only 6 files changed, 16 insertions(+), 4 deletions(-)
Title: Functions for Calculating Daily Solar Radiation and
Evapotranspiration
Description: Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.
Author: Jedrzej S. Bojanowski
Maintainer: Jedrzej S. Bojanowski <jedrzej.bojanowski@gmail.com>
Diff between sirad versions 2.0-7 dated 2013-01-23 and 2.3-0 dated 2015-10-18
sirad-2.0-7/sirad/data/CFC.rda |only sirad-2.0-7/sirad/data/CSTmap.rda |only sirad-2.0-7/sirad/man/CFC.Rd |only sirad-2.0-7/sirad/man/CSTmap.Rd |only sirad-2.3-0/sirad/DESCRIPTION | 23 ++---- sirad-2.3-0/sirad/MD5 | 105 +++++++++++++++---------------- sirad-2.3-0/sirad/NAMESPACE | 5 + sirad-2.3-0/sirad/R/ap.R | 20 +++-- sirad-2.3-0/sirad/R/apcal.R | 32 ++++----- sirad-2.3-0/sirad/R/bc.R | 10 +- sirad-2.3-0/sirad/R/bcauto.R | 35 +++++----- sirad-2.3-0/sirad/R/bccal.R | 14 ++-- sirad-2.3-0/sirad/R/corrEarthSunDist.R | 4 - sirad-2.3-0/sirad/R/cst.R | 38 +++++------ sirad-2.3-0/sirad/R/cstRead.r | 7 -- sirad-2.3-0/sirad/R/dayLength.R | 12 +-- sirad-2.3-0/sirad/R/dayOfYear.R | 8 +- sirad-2.3-0/sirad/R/daylightTimeFactor.R | 8 +- sirad-2.3-0/sirad/R/degrees.R | 8 +- sirad-2.3-0/sirad/R/deltaVP.r | 4 - sirad-2.3-0/sirad/R/es.r | 4 - sirad-2.3-0/sirad/R/et0.r | 18 ++--- sirad-2.3-0/sirad/R/exd.R | 14 ++-- sirad-2.3-0/sirad/R/exh.R | 16 ++-- sirad-2.3-0/sirad/R/extrat.R | 18 ++--- sirad-2.3-0/sirad/R/ha.R | 20 +++-- sirad-2.3-0/sirad/R/hacal.R | 18 ++--- sirad-2.3-0/sirad/R/hauto.r | 23 +++--- sirad-2.3-0/sirad/R/hourAngle.R | 4 - sirad-2.3-0/sirad/R/mh.R | 22 +++--- sirad-2.3-0/sirad/R/modeval.r | 38 +++++------ sirad-2.3-0/sirad/R/opticalAirMass.R | 8 +- sirad-2.3-0/sirad/R/psychC.r | 4 - sirad-2.3-0/sirad/R/radians.R | 8 +- sirad-2.3-0/sirad/R/rnl.r | 4 - sirad-2.3-0/sirad/R/rns.r | 4 - sirad-2.3-0/sirad/R/solarDecl.R | 4 - sirad-2.3-0/sirad/R/solarZenithAngle.R | 4 - sirad-2.3-0/sirad/R/su.R | 22 ++++-- sirad-2.3-0/sirad/R/sucal.R | 26 +++---- sirad-2.3-0/sirad/R/sunElevationAngle.R | 8 +- sirad-2.3-0/sirad/R/sysdata.rda |only sirad-2.3-0/sirad/R/timeOfSunrise.R | 4 - sirad-2.3-0/sirad/R/timeOfSunset.R | 4 - sirad-2.3-0/sirad/R/ts.CMSAF.R | 64 ++++++++++++------ sirad-2.3-0/sirad/R/wind2.r | 8 +- sirad-2.3-0/sirad/man/ap.Rd | 24 ++++--- sirad-2.3-0/sirad/man/bcauto.Rd | 11 ++- sirad-2.3-0/sirad/man/bccal.Rd | 7 +- sirad-2.3-0/sirad/man/et0.Rd | 11 +-- sirad-2.3-0/sirad/man/ha.Rd | 16 +++- sirad-2.3-0/sirad/man/hauto.Rd | 6 + sirad-2.3-0/sirad/man/modeval.Rd | 8 +- sirad-2.3-0/sirad/man/sirad-package.Rd | 10 +- sirad-2.3-0/sirad/man/su.Rd | 19 +++-- sirad-2.3-0/sirad/man/ts.CMSAF.Rd | 6 - 56 files changed, 443 insertions(+), 375 deletions(-)
Title: Fits the FastRCS Robust Multivariable Linear Regression Model
Description: The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the multivariable linear regression model and outliers detection.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>
Diff between FastRCS versions 0.0.6 dated 2015-01-09 and 0.0.7 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 3 +++ R/FastRCS.R | 8 ++++++-- man/FRCSnumStarts.Rd | 2 +- man/FastRCS-package.Rd | 1 + man/FastRCS.Rd | 8 +++++--- man/plot.FastRCS.Rd | 2 +- man/quanf.Rd | 2 +- src/FastRCS.cpp | 10 +++++----- 10 files changed, 37 insertions(+), 27 deletions(-)
Title: Average and Conditional Effects
Description: Use structural equation modeling to estimate average and conditional effects of a treatment variable
on an outcome variable, taking into account multiple continuous and categorical covariates.
Author: Axel Mayer [aut, cre],
Lisa Dietzfelbinger [ctb]
Maintainer: Axel Mayer <amayer2010@gmail.com>
Diff between EffectLiteR versions 0.3-3 dated 2015-04-30 and 0.4-1 dated 2015-10-18
DESCRIPTION | 12 - MD5 | 13 - NAMESPACE | 13 + R/effectliter.R | 417 ++++++++++++++++++++++++++++++++++++++----------- inst/elrshiny/server.R | 271 ++++++++++++++++++++++++------- inst/elrshiny/ui.R | 46 ++++- man/effectLite.Rd | 4 man/elrReadData.Rd |only 8 files changed, 606 insertions(+), 170 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.8 dated 2015-09-05 and 0.9 dated 2015-10-18
V8-0.8/V8/man/new_context.Rd |only V8-0.9/V8/DESCRIPTION | 6 +-- V8-0.9/V8/MD5 | 17 +++++----- V8-0.9/V8/NAMESPACE | 1 V8-0.9/V8/NEWS | 9 +++++ V8-0.9/V8/R/V8.R | 72 ++++++++++++++++++++++++++++--------------- V8-0.9/V8/configure | 8 ++-- V8-0.9/V8/man/V8.Rd |only V8-0.9/V8/src/Makevars.win | 10 ++--- V8-0.9/V8/src/tests |only V8-0.9/V8/tools/winlibs.R | 25 +++++++------- 11 files changed, 89 insertions(+), 59 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.2-0 dated 2015-09-08 and 1.2-1 dated 2015-10-18
sp-1.2-0/sp/tests/mp.R |only sp-1.2-0/sp/tests/over.R |only sp-1.2-1/sp/ChangeLog | 91 ++++++ sp-1.2-1/sp/DESCRIPTION | 10 sp-1.2-1/sp/MD5 | 64 ++-- sp-1.2-1/sp/R/CRS-methods.R | 8 sp-1.2-1/sp/R/SpatialLines-methods.R | 16 - sp-1.2-1/sp/R/SpatialLinesDataFrame-methods.R | 4 sp-1.2-1/sp/R/SpatialMultiPoints-methods.R | 9 sp-1.2-1/sp/R/SpatialMultiPointsDataFrame-methods.R | 2 sp-1.2-1/sp/R/merge.R | 65 ++-- sp-1.2-1/sp/R/over.R | 4 sp-1.2-1/sp/R/spsample.R | 4 sp-1.2-1/sp/demo/depend.R | 45 --- sp-1.2-1/sp/demo/mp.R | 2 sp-1.2-1/sp/inst/ChangeLog | 91 ++++++ sp-1.2-1/sp/inst/NEWS.Rd | 19 + sp-1.2-1/sp/inst/doc/csdacm.pdf |binary sp-1.2-1/sp/inst/doc/intro_sp.R | 52 +-- sp-1.2-1/sp/inst/doc/intro_sp.Rnw | 276 ++++++++++---------- sp-1.2-1/sp/inst/doc/intro_sp.pdf |binary sp-1.2-1/sp/inst/doc/over.R | 54 +++ sp-1.2-1/sp/inst/doc/over.Rnw | 67 ++++ sp-1.2-1/sp/inst/doc/over.pdf |binary sp-1.2-1/sp/inst/include/sp.h | 2 sp-1.2-1/sp/man/CRS-class.Rd | 7 sp-1.2-1/sp/man/SpatialLines-class.Rd | 2 sp-1.2-1/sp/man/SpatialLinesDataFrame-class.Rd | 1 sp-1.2-1/sp/man/aggregate.Rd | 5 sp-1.2-1/sp/src/sp.h | 2 sp-1.2-1/sp/tests/agg.R |only sp-1.2-1/sp/tests/agg.Rout.save |only sp-1.2-1/sp/tests/pass1.Rout.save | 33 +- sp-1.2-1/sp/vignettes/intro_sp.Rnw | 276 ++++++++++---------- sp-1.2-1/sp/vignettes/over.Rnw | 67 ++++ 35 files changed, 837 insertions(+), 441 deletions(-)
Title: Basic Wireless Communications Simulation
Description: A communications simulation package supporting common wireless modulation
formats including BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. The package includes AWGN
noise generation, and raised cosine and square root raised cosine pulse shaping. It also
includes convenience functions for plotting constellation diagrams, density plots, stem
plots and eye diagrams. Together these functions enable the evaluation of bit error and
symbol error rates, evaluation of pulse shaping and inter-symbol interference and support
visualization of the respective signals and noise in a variety of formats.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.4.2 dated 2015-10-15 and 1.4.3 dated 2015-10-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/rwirelesscom.cpp | 26 +++++++++++++++++--------- 3 files changed, 22 insertions(+), 14 deletions(-)
Title: Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Description: Provides an interface to the National Topographic System (NTS), which is
the way in which a number of freely available Canadian datasets
are organized. CanVec and CanVec+ datasets, which include all data used
to create Canadian topographic maps, are two such datasets that are useful
in creating vector-based maps for locations across Canada. This packages searches
CanVec data by location, plots it using pretty defaults, and exports it to
human-readable shapefiles for use in another GIS.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rcanvec versions 0.1.2 dated 2015-10-06 and 0.1.3 dated 2015-10-18
rcanvec-0.1.2/rcanvec/R/bboxtools.R |only rcanvec-0.1.2/rcanvec/R/geocode.R |only rcanvec-0.1.2/rcanvec/man/makebbox.Rd |only rcanvec-0.1.2/rcanvec/man/searchbbox.Rd |only rcanvec-0.1.2/rcanvec/man/zoom.Rd |only rcanvec-0.1.3/rcanvec/DESCRIPTION | 14 +- rcanvec-0.1.3/rcanvec/MD5 | 31 ++---- rcanvec-0.1.3/rcanvec/NAMESPACE | 3 rcanvec-0.1.3/rcanvec/R/canvec.R | 115 ++++++++++++++++++------ rcanvec-0.1.3/rcanvec/R/canvec.qplot.R | 65 +++++++++++-- rcanvec-0.1.3/rcanvec/R/nts.R | 4 rcanvec-0.1.3/rcanvec/data/canvec_layers.rda |binary rcanvec-0.1.3/rcanvec/man/canvec.export.Rd | 25 +++-- rcanvec-0.1.3/rcanvec/man/canvec.plot.Rd | 4 rcanvec-0.1.3/rcanvec/man/canvec.qplot.Rd | 36 +++++-- rcanvec-0.1.3/rcanvec/man/nts.Rd | 2 rcanvec-0.1.3/rcanvec/man/ntsstring.Rd | 2 rcanvec-0.1.3/rcanvec/man/rcanvec-package.Rd | 34 ++----- rcanvec-0.1.3/rcanvec/tests/testthat/test_nts.R | 6 - 19 files changed, 232 insertions(+), 109 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.51 dated 2015-09-16 and 0.2.82 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 33 ++++++++++++++++++++------------- NAMESPACE | 4 ++++ R/concurrence.R |only R/measures.R | 13 +++++++++++-- R/mldr.R | 5 ++--- R/read.arff.R | 4 ++-- data/birds.rda |binary data/emotions.rda |binary data/genbase.rda |binary demo/00Index | 1 + demo/decouple.R | 2 +- demo/rebuild_datasets.R |only inst/CITATION |only inst/doc/mldr.pdf |binary inst/shiny/rsconnect |only inst/shiny/server.R | 41 ++++++++++++++++++++++++++++++++--------- inst/shiny/ui.R | 15 ++++++++++----- man/concurrenceReport.Rd |only man/labelInteractions.Rd |only man/remedial.Rd |only 21 files changed, 88 insertions(+), 40 deletions(-)
Title: Hydrologic Indices for Daily Time Series Data
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond <n.bond@griffith.edu.au>
Diff between hydrostats versions 0.2.3 dated 2014-12-21 and 0.2.4 dated 2015-10-18
hydrostats-0.2.3/hydrostats/data/Acheron.txt |only hydrostats-0.2.3/hydrostats/data/Cooper.txt |only hydrostats-0.2.4/hydrostats/DESCRIPTION | 13 - hydrostats-0.2.4/hydrostats/MD5 | 30 +-- hydrostats-0.2.4/hydrostats/NAMESPACE | 3 hydrostats-0.2.4/hydrostats/NEWS | 11 + hydrostats-0.2.4/hydrostats/R/baseflows.R | 172 +++++++++--------- hydrostats-0.2.4/hydrostats/R/flood.length.max.R | 2 hydrostats-0.2.4/hydrostats/R/high.spell.lengths.R | 3 hydrostats-0.2.4/hydrostats/R/high.spells.R | 4 hydrostats-0.2.4/hydrostats/README.md | 2 hydrostats-0.2.4/hydrostats/data/Acheron.txt.gz |only hydrostats-0.2.4/hydrostats/data/Cooper.txt.gz |only hydrostats-0.2.4/hydrostats/man/baseflows.Rd | 7 hydrostats-0.2.4/hydrostats/man/daily.cv.Rd | 2 hydrostats-0.2.4/hydrostats/man/flood.length.max.Rd | 12 - hydrostats-0.2.4/hydrostats/man/high.spell.lengths.Rd | 2 hydrostats-0.2.4/hydrostats/man/hydrostats-package.Rd | 4 18 files changed, 152 insertions(+), 115 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-26 dated 2015-08-26 and 1.1-0 dated 2015-10-18
gstat-1.0-26/gstat/LICENCE |only gstat-1.0-26/gstat/configure |only gstat-1.0-26/gstat/configure.in |only gstat-1.0-26/gstat/configure.win |only gstat-1.0-26/gstat/src/chfactor.c |only gstat-1.0-26/gstat/src/config.hin |only gstat-1.0-26/gstat/src/config.w32 |only gstat-1.0-26/gstat/src/copy.c |only gstat-1.0-26/gstat/src/err.c |only gstat-1.0-26/gstat/src/err.h |only gstat-1.0-26/gstat/src/ext_dbase.h |only gstat-1.0-26/gstat/src/hsehldr.c |only gstat-1.0-26/gstat/src/init.c |only gstat-1.0-26/gstat/src/ivecop.c |only gstat-1.0-26/gstat/src/lex.l |only gstat-1.0-26/gstat/src/lufactor.c |only gstat-1.0-26/gstat/src/machine.c |only gstat-1.0-26/gstat/src/machine.hin |only gstat-1.0-26/gstat/src/machine.w32 |only gstat-1.0-26/gstat/src/matop.c |only gstat-1.0-26/gstat/src/matrix.h |only gstat-1.0-26/gstat/src/matrix2.h |only gstat-1.0-26/gstat/src/meminfo.c |only gstat-1.0-26/gstat/src/meminfo.h |only gstat-1.0-26/gstat/src/memory.c |only gstat-1.0-26/gstat/src/meschach |only gstat-1.0-26/gstat/src/norm.c |only gstat-1.0-26/gstat/src/polygon.c |only gstat-1.0-26/gstat/src/polygon.h |only gstat-1.0-26/gstat/src/pxop.c |only gstat-1.0-26/gstat/src/qrfactor.c |only gstat-1.0-26/gstat/src/solve.c |only gstat-1.0-26/gstat/src/sparse.c |only gstat-1.0-26/gstat/src/sparse.h |only gstat-1.0-26/gstat/src/sparse2.h |only gstat-1.0-26/gstat/src/sprow.c |only gstat-1.0-26/gstat/src/submat.c |only gstat-1.0-26/gstat/src/vecop.c |only gstat-1.0-26/gstat/src/version.c |only gstat-1.0-26/gstat/src/zmatrix.h |only gstat-1.0-26/gstat/src/zmatrix2.h |only gstat-1.1-0/gstat/DESCRIPTION | 10 gstat-1.1-0/gstat/MD5 | 193 - gstat-1.1-0/gstat/R/gstat.cv.R | 8 gstat-1.1-0/gstat/R/krige0.R | 41 gstat-1.1-0/gstat/R/load.variogram.model.R | 18 gstat-1.1-0/gstat/R/predict.gstat.R | 19 gstat-1.1-0/gstat/R/stVariogramModels.R | 33 gstat-1.1-0/gstat/R/vgm.R | 2 gstat-1.1-0/gstat/R/zzz.R | 1 gstat-1.1-0/gstat/build/vignette.rds |binary gstat-1.1-0/gstat/cleanup | 3 gstat-1.1-0/gstat/data/coalash.rda |binary gstat-1.1-0/gstat/data/fulmar.rda |binary gstat-1.1-0/gstat/data/jura.rda |binary gstat-1.1-0/gstat/data/meuse.all.rda |binary gstat-1.1-0/gstat/data/meuse.alt.rda |binary gstat-1.1-0/gstat/data/ncp.grid.rda |binary gstat-1.1-0/gstat/data/oxford.rda |binary gstat-1.1-0/gstat/data/pcb.rda |binary gstat-1.1-0/gstat/data/sic2004.rda |binary gstat-1.1-0/gstat/data/sic97.rda |binary gstat-1.1-0/gstat/data/tull.rda |binary gstat-1.1-0/gstat/data/vv.rda |binary gstat-1.1-0/gstat/data/walker.rda |binary gstat-1.1-0/gstat/data/wind.rda |binary gstat-1.1-0/gstat/inst/ChangeLog | 276 + gstat-1.1-0/gstat/inst/NEWS.Rd |only gstat-1.1-0/gstat/inst/doc/gstat.pdf |binary gstat-1.1-0/gstat/inst/doc/prs.pdf |binary gstat-1.1-0/gstat/inst/doc/spatio-temporal-kriging.pdf |binary gstat-1.1-0/gstat/inst/doc/st.R | 6 gstat-1.1-0/gstat/inst/doc/st.Rnw | 6 gstat-1.1-0/gstat/inst/doc/st.pdf |binary gstat-1.1-0/gstat/man/fit.StVariogram.Rd | 11 gstat-1.1-0/gstat/man/krigeST.Rd | 12 gstat-1.1-0/gstat/man/predict.gstat.Rd | 4 gstat-1.1-0/gstat/man/sic2004.Rd | 4 gstat-1.1-0/gstat/man/sic97.Rd | 6 gstat-1.1-0/gstat/man/vgmST.Rd | 3 gstat-1.1-0/gstat/man/walker.Rd | 5 gstat-1.1-0/gstat/src/Makevars |only gstat-1.1-0/gstat/src/chol.c |only gstat-1.1-0/gstat/src/config.h |only gstat-1.1-0/gstat/src/data.c | 1353 -------- gstat-1.1-0/gstat/src/data.h | 5 gstat-1.1-0/gstat/src/defs.h | 59 gstat-1.1-0/gstat/src/fit.c | 198 - gstat-1.1-0/gstat/src/gcdist.c | 12 gstat-1.1-0/gstat/src/getest.c | 55 gstat-1.1-0/gstat/src/gls.c | 279 - gstat-1.1-0/gstat/src/glvars.c | 152 gstat-1.1-0/gstat/src/glvars.h | 14 gstat-1.1-0/gstat/src/lex.c | 247 - gstat-1.1-0/gstat/src/lm.c | 73 gstat-1.1-0/gstat/src/mapio.c | 2847 ----------------- gstat-1.1-0/gstat/src/msim.c | 414 -- gstat-1.1-0/gstat/src/mtrx.c |only gstat-1.1-0/gstat/src/mtrx.h |only gstat-1.1-0/gstat/src/nsearch.c | 2 gstat-1.1-0/gstat/src/parse.c | 107 gstat-1.1-0/gstat/src/predict.c | 539 --- gstat-1.1-0/gstat/src/random.c | 75 gstat-1.1-0/gstat/src/reml.c | 46 gstat-1.1-0/gstat/src/s.c | 94 gstat-1.1-0/gstat/src/select.c | 49 gstat-1.1-0/gstat/src/sem.c | 216 - gstat-1.1-0/gstat/src/sem.h | 2 gstat-1.1-0/gstat/src/sim.c | 17 gstat-1.1-0/gstat/src/stat.c | 51 gstat-1.1-0/gstat/src/userio.c | 107 gstat-1.1-0/gstat/src/utils.c | 136 gstat-1.1-0/gstat/src/vario.c | 73 gstat-1.1-0/gstat/src/vario.h | 2 gstat-1.1-0/gstat/src/vario_fn.c | 6 gstat-1.1-0/gstat/tests/fit.Rout.save | 18 gstat-1.1-0/gstat/tests/merge.Rout.save | 44 gstat-1.1-0/gstat/tests/unproj.Rout.save | 68 gstat-1.1-0/gstat/tests/windst.Rout.save | 16 gstat-1.1-0/gstat/vignettes/st.Rnw | 6 120 files changed, 817 insertions(+), 7226 deletions(-)
Title: A Multi-Platform GUI for Drawing Customizable Graphs in R
Diff between GrapheR versions 1.9-84 dated 2014-07-27 and 1.9-85 dated 2015-10-18
Description: A multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé
GrapheR-1.9-84/GrapheR/man/Env.Rd |only
GrapheR-1.9-84/GrapheR/man/active.erreur.Rd |only
GrapheR-1.9-85/GrapheR/DESCRIPTION | 12 -
GrapheR-1.9-85/GrapheR/MD5 | 16 +-
GrapheR-1.9-85/GrapheR/NAMESPACE | 11 +
GrapheR-1.9-85/GrapheR/NEWS | 29 ----
GrapheR-1.9-85/GrapheR/R/Sources.R | 179 +++++++-------------------
GrapheR-1.9-85/GrapheR/R/zzzz.R | 2
GrapheR-1.9-85/GrapheR/build/vignette.rds |binary
GrapheR-1.9-85/GrapheR/man/GrapheR-package.Rd | 8 -
10 files changed, 86 insertions(+), 171 deletions(-)
Title: Comparing Correlations
Description: Statistical tests for the comparison between two
correlations based on either independent or dependent groups.
Dependent correlations can either be overlapping or
nonoverlapping. A web interface is available at
http://comparingcorrelations.org. A plugin for the R GUI and
IDE RKWard is included. Please install RKWard from
https://rkward.kde.org to use this feature. The respective R
package 'rkward' cannot be installed directly from a
repository, as it is a part of RKWard.
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen <mail@birkdiedenhofen.de>
Diff between cocor versions 1.1-1 dated 2015-04-10 and 1.1-2 dated 2015-10-18
ChangeLog | 6 ++++ DESCRIPTION | 27 ++++++++++++--------- MD5 | 35 ++++++++++++++-------------- NAMESPACE | 3 +- R/0helper.r | 4 +-- R/cocor-package.R | 8 +++--- R/cocor.dep.groups.nonoverlap.r | 8 +++--- inst/CITATION | 7 +++-- inst/doc |only inst/rkward/rkwarddev.cocor.plugin.script.R | 4 +-- inst/tests/test.r | 5 ++++ man/as.htest.Rd | 3 +- man/cocor-package.Rd | 12 +++++---- man/cocor.Rd | 3 +- man/cocor.dep.groups.nonoverlap.Rd | 11 ++++---- man/cocor.dep.groups.overlap.Rd | 3 +- man/cocor.indep.groups.Rd | 3 +- man/get.cocor.input.Rd | 3 +- man/get.cocor.results.Rd | 3 +- 19 files changed, 88 insertions(+), 60 deletions(-)
Title: Robust Linear Regression with Compositional Data as Covariates
Description: Provides functionality to perform robust regression
on compositional data. To get information on the distribution of the
estimates, various bootstrapping methods are implemented for the
compositional as well as for standard robust regression models, to provide
a direct comparison between them.
Author: David Kepplinger <david.kepplinger@gmail.com>
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between complmrob versions 0.5.8 dated 2014-12-09 and 0.6.1 dated 2015-10-18
ChangeLog | 5 ++++ DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++--------------- NAMESPACE | 21 +++++++++++++++++- R/complmrob.R | 4 +++ R/plot-methods.R | 46 ++++++++++++++++++++++++++++------------ man/bootStat-methods.Rd | 17 +++++++------- man/bootcoefs.Rd | 3 +- man/complmrob.Rd | 3 +- man/confint.Rd | 3 +- man/format.perc.Rd | 3 +- man/isomLR.Rd | 5 ++-- man/plot.bootcoefs.Rd | 3 +- man/plot.complmrob.Rd | 3 +- man/predictdf.complmrob.part.Rd | 13 ++++++----- man/print-methods.Rd | 7 +++--- man/print.summary.complmrob.Rd | 3 +- man/summary-methods.Rd | 7 +++--- 18 files changed, 124 insertions(+), 64 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.0.1 dated 2015-08-28 and 3.0.3 dated 2015-10-18
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NAMESPACE | 2 - R/CMplot.r | 65 ++++++++++++++++++++++++++++++++++++++++++-------- man/CMplot-package.Rd | 9 ++++-- 5 files changed, 70 insertions(+), 22 deletions(-)
Title: Prepare Species Distributions for the Use in Phylogenetic
Analyses
Description: Preparation of species occurrences and distribution data for the use in phylogenetic analyses. SpeciesgeocodeR is built for data cleaning, data exploration and data analysis and especially suited for biogeographical and ecological questions on large datasets. The package includes the easy creation of summary-tables and -graphs and geographical maps, the automatic cleaning of geographic occurrence data, the calculating of coexistence matrices and species ranges (EOO) as well as mapping diversity in geographic areas.
Author: Alexander Zizka [aut, cre]
Maintainer: Alexander Zizka <alexander.zizka@bioenv.gu.se>
Diff between speciesgeocodeR versions 1.0-3 dated 2015-07-14 and 1.0-4 dated 2015-10-17
speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.Rmd |only speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.html |only speciesgeocodeR-1.0-4/speciesgeocodeR/DESCRIPTION | 15 - speciesgeocodeR-1.0-4/speciesgeocodeR/MD5 | 70 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/NAMESPACE | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/R/GeoClean.R | 35 ++- speciesgeocodeR-1.0-4/speciesgeocodeR/R/ReadPoints.R | 80 +++++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCod.R | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCodH.R | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpeciesGeoCoder.R | 38 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/Spgc2BioGeoBEARS.R |only speciesgeocodeR-1.0-4/speciesgeocodeR/R/WriteOut.R | 62 +++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/speciesgeocodeR-internal.R | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.pdf |binary speciesgeocodeR-1.0-4/speciesgeocodeR/man/CoExClass.Rd | 62 ++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GeoClean.Rd | 43 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GetElevation.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapGrid.Rd | 74 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapRichness.Rd | 112 +++++----- speciesgeocodeR-1.0-4/speciesgeocodeR/man/PlotHull.Rd | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/man/ReadPoints.Rd | 18 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/RichnessGrid.Rd | 3 speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCod.Rd | 21 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCodH.Rd | 23 -- speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpeciesGeoCoder.Rd | 23 +- speciesgeocodeR-1.0-4/speciesgeocodeR/man/Spgc2Biogeobears.Rd |only speciesgeocodeR-1.0-4/speciesgeocodeR/man/WriteOut.Rd | 11 speciesgeocodeR-1.0-4/speciesgeocodeR/man/WwfLoad.Rd | 71 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/countryref.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_in.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_test.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_biomes.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_poly.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/plot.spgeoOUT.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/speciesgeocodeR-package.Rd | 99 ++++---- speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoIN.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoOUT.Rd | 6 38 files changed, 504 insertions(+), 420 deletions(-)
More information about speciesgeocodeR at CRAN
Permanent link
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-50 dated 2015-08-08 and 0.9-51 dated 2015-10-17
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 -
MD5 | 22 ++--
NEWS | 7 +
R/MVA.biplot.R | 56 +++++++++--
R/MVA.load.R | 2
R/MVA.scores.R | 2
R/byf.hist.R | 16 +--
R/plotresid.R | 215 +++++++++++++++++++++++--------------------
R/zzz.R | 2
man/RVAideMemoire-package.Rd | 4
man/byf.hist.Rd | 8 +
man/plotresid.Rd | 8 -
12 files changed, 212 insertions(+), 138 deletions(-)
Title: Discrete Weibull Distributions (Type 1 and 3)
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.
Author: Alessandro Barbiero
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteWeibull versions 1.0.1 dated 2015-07-08 and 1.1 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 28 ++++++------- R/Edweibull.R | 75 ++++++++++++++++++++++-------------- man/DiscreteWeibull-package.Rd | 9 ++-- man/Edweibull.Rd | 19 ++++++--- man/Edweibull3.Rd | 40 +++++++++---------- man/ddweibull.Rd | 22 +++++----- man/ddweibull3.Rd | 84 ++++++++++++++++++++--------------------- man/estdweibull.Rd | 23 +++++------ man/estdweibull3.Rd | 72 +++++++++++++++++------------------ man/loglikedw.Rd | 10 ++-- man/loglikedw3.Rd | 12 ++--- man/lossdw.Rd | 8 +-- man/lossdw3.Rd | 12 ++--- man/varFisher.Rd | 7 +-- 15 files changed, 228 insertions(+), 201 deletions(-)
More information about DiscreteWeibull at CRAN
Permanent link
Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.6 dated 2015-07-21 and 0.8 dated 2015-10-17
DESCRIPTION | 14 +++++++------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/model.R | 17 +++++++---------- R/plot.R | 4 +++- inst/itemModelExplorer/server.R | 16 +++++++++++++++- inst/itemModelExplorer/ui.R | 3 ++- inst/modelBuilder/www/sort.css | 2 ++ man/SitemPlot.Rd | 3 ++- man/addExploratoryFactors.Rd | 3 ++- man/iccPlot.Rd | 3 ++- man/itemModelExplorer.Rd | 3 ++- man/itemResponseMap.Rd | 7 ++++++- man/modelBuilder.Rd | 3 ++- man/plotInformation.Rd | 3 ++- man/replicateModelBy.Rd | 3 ++- man/uniquenessPrior.Rd | 3 ++- man/univariatePrior.Rd | 3 ++- 18 files changed, 78 insertions(+), 48 deletions(-)
Title: Creates a Model Matrix via Feature Hashing with a Formula
Interface
Description: Feature hashing, also called as the hashing trick, is a method to transform
features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix.
Without looking up the indices in an associative array,
it applies a hash function to the features and uses their hash values as indices directly.
The method of feature hashing in this package was proposed in Weinberger et al. (2009).
The hashing algorithm is the murmurhash3 from the digest package.
Please see the README in https://github.com/wush978/FeatureHashing for more information.
Author: Wush Wu [aut, cre],
Michael Benesty [aut, ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between FeatureHashing versions 0.9.1 dated 2015-09-22 and 0.9.1.1 dated 2015-10-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/FeatureHashing.html | 4 ++-- src/hash_function.h | 1 + src/hash_internal.cpp | 3 ++- tests/test-progress_bar.R | 4 ++-- 6 files changed, 15 insertions(+), 13 deletions(-)
More information about FeatureHashing at CRAN
Permanent link
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.0 dated 2015-07-24 and 2.0.1 dated 2015-10-17
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 1 R/cjoint.R | 889 +++++++++++++++++++++++++++++++++++++------------------ man/plot.amce.Rd | 6 5 files changed, 625 insertions(+), 287 deletions(-)
Title: Search and Download Papers from the bioRxiv Preprint Server
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
Diff between biorxivr versions 0.1.1 dated 2015-05-28 and 0.1.2 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 32 ++++++------ NAMESPACE | 6 +- R/bx_download.R | 1 R/bx_extract.R | 1 R/bx_search.R | 1 inst/doc/vignette.R | 3 + inst/doc/vignette.Rmd | 4 + inst/doc/vignette.html | 94 ++++++++++++++++++------------------ man/bx_download.Rd | 2 man/bx_extract.Rd | 2 man/bx_extract_single.Rd | 2 man/bx_search.Rd | 2 man/plot.biorxiv_paper.Rd | 2 man/print.summary.biorxiv_search.Rd | 2 man/summary.biorxiv_search.Rd | 2 vignettes/vignette.Rmd | 4 + 17 files changed, 95 insertions(+), 73 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.3.2 dated 2015-09-03 and 0.4.1 dated 2015-10-17
DESCRIPTION | 11 +-- MD5 | 19 +++-- NAMESPACE | 7 +- NEWS | 12 +++ R/qic.R | 196 +++++++++++++++++++++++++++++++++++++++++--------------- R/tcc.R |only R/trc.R | 54 ++++++++++----- README.md | 3 man/plot.tcc.Rd |only man/qic.Rd | 26 ++++--- man/tcc.Rd |only man/trc.Rd | 7 +- 12 files changed, 240 insertions(+), 95 deletions(-)
Title: Diagnostics Plots for Bicluster Data
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between BcDiag versions 1.0.9 dated 2015-10-10 and 1.0.10 dated 2015-10-17
DESCRIPTION | 12 +-- MD5 | 6 - R/profileBic.R | 209 ++++++++++++++++++++++++++++++++++++++++++++++-------- man/profileBic.Rd | 5 + 4 files changed, 192 insertions(+), 40 deletions(-)
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization and EM clustering. Furthermore, there are specialized
distance measures, plotting functions and some helper functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.1 dated 2015-10-15 and 1.0.2 dated 2015-10-16
svs-1.0.1/svs/inst/extdata/Ctxt_Dut.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Eng.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Fra.csv |only svs-1.0.1/svs/inst/extdata/InvT_Eng.csv |only svs-1.0.1/svs/inst/extdata/InvT_Fra.csv |only svs-1.0.1/svs/inst/extdata/SndT_Eng.csv |only svs-1.0.1/svs/inst/extdata/SndT_Fra.csv |only svs-1.0.1/svs/man/Ctxt_Dut.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Eng.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Fra.csv.Rd |only svs-1.0.1/svs/man/InvT_Eng.csv.Rd |only svs-1.0.1/svs/man/InvT_Fra.csv.Rd |only svs-1.0.1/svs/man/SndT_Eng.csv.Rd |only svs-1.0.1/svs/man/SndT_Fra.csv.Rd |only svs-1.0.2/svs/DESCRIPTION | 8 +-- svs-1.0.2/svs/MD5 | 48 ++++++++++---------- svs-1.0.2/svs/R/svs.r | 74 +++++++++++++++++++------------- svs-1.0.2/svs/inst/extdata/Ctxt_Dut.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Eng.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Fra.txt |only svs-1.0.2/svs/inst/extdata/InvT_Eng.txt |only svs-1.0.2/svs/inst/extdata/InvT_Fra.txt |only svs-1.0.2/svs/inst/extdata/SndT_Eng.txt |only svs-1.0.2/svs/inst/extdata/SndT_Fra.txt |only svs-1.0.2/svs/man/Ctxt_Dut.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Eng.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Fra.txt.Rd |only svs-1.0.2/svs/man/InvT_Eng.txt.Rd |only svs-1.0.2/svs/man/InvT_Fra.txt.Rd |only svs-1.0.2/svs/man/SndT_Eng.txt.Rd |only svs-1.0.2/svs/man/SndT_Fra.txt.Rd |only svs-1.0.2/svs/man/fast_E_M.Rd | 3 - svs-1.0.2/svs/man/fast_dca.Rd | 3 - svs-1.0.2/svs/man/fast_lsa.Rd | 3 - svs-1.0.2/svs/man/fast_mca.Rd | 3 - svs-1.0.2/svs/man/fast_nmf.Rd | 3 - svs-1.0.2/svs/man/fast_psa.Rd | 3 - svs-1.0.2/svs/man/fast_sca.Rd | 3 - svs-1.0.2/svs/man/svs-package.Rd | 18 ++++--- 39 files changed, 97 insertions(+), 72 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.0.1 dated 2015-09-22 and 2.1.0 dated 2015-10-16
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS | 9 +++++++++ R/xform.R | 34 ++++++++++++++++++++++++++++------ man/xform.Rd | 26 ++++++++++++++++++++------ src/DeformationField.cpp | 2 +- src/main.cpp | 35 +++++++++++++++++++++++++++++++++++ src/reg-lib/_reg_aladin.h | 22 +++++++++++----------- tests/testthat/test-10-xform.R | 7 +++++++ tests/testthat/test-20-niftyreg.R | 4 ++-- tests/testthat/test-25-transform.R | 3 +++ 12 files changed, 134 insertions(+), 42 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.1 dated 2015-10-14 and 1.5.2 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/idendro.R | 9 +++++---- man/hca5000.Rd | 8 ++++---- man/idendr0-package.Rd | 4 ++-- man/idendro.Rd | 8 ++++---- 7 files changed, 31 insertions(+), 24 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-3 dated 2015-10-05 and 0.1-4 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/gimme.R | 12 ++++++------ man/gimmeSEM.Rd | 2 +- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.1 dated 2015-10-12 and 6.1.1 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 7 ++++--- NEWS | 4 ++++ R/FormatNests.R | 2 +- R/STSRE_TSD.R | 8 ++++---- R/TRN_MHmcmc_p.R | 4 ++-- R/embryogrowth-package.R | 4 ++-- R/hist.NestsResult.R | 4 ++-- R/info.nests.R | 18 +++++++++--------- R/likelihoodR.R | 10 +++++----- R/nest.R | 2 +- R/plot.NestsResult.R | 10 +++++----- R/plotR.R | 8 ++++---- R/plotR_hist.R | 2 +- R/searchR.R | 10 +++++----- R/tsd_MHmcmc_p.R | 2 +- R/weightmaxentropy.R | 2 +- man/STSRE_TSD.Rd | 8 ++++---- man/embryogrowth-package.Rd | 4 ++-- man/nest.Rd | 2 +- 21 files changed, 82 insertions(+), 77 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between coda versions 0.17-1 dated 2015-03-03 and 0.18-1 dated 2015-10-16
CHANGELOG | 15 ++++++++++ DESCRIPTION | 16 ++++++----- MD5 | 20 +++++++------- NAMESPACE | 17 ++++++++--- R/codamenu.R | 16 ----------- R/mcextractor.R | 8 ++++- R/mcmclist.R | 80 +++++++++++++++++++++++++++++++++++--------------------- R/util.R | 3 -- data/line.rda |binary inst/AUTHORS | 15 +++++++++- man/cumuplot.Rd | 4 -- 11 files changed, 118 insertions(+), 76 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between survsim versions 1.1.3 dated 2015-03-26 and 1.1.4 dated 2015-10-16
survsim-1.1.3/survsim/R/survsim-internal.R |only survsim-1.1.3/survsim/README.md |only survsim-1.1.4/survsim/DESCRIPTION | 11 +-- survsim-1.1.4/survsim/MD5 | 16 ++--- survsim-1.1.4/survsim/NAMESPACE | 8 +- survsim-1.1.4/survsim/R/crisk.ncens.sim.R | 85 +++++++++++++++++---------- survsim-1.1.4/survsim/man/crisk.sim.Rd | 4 - survsim-1.1.4/survsim/man/mult.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/rec.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/simple.surv.sim.Rd | 4 - 10 files changed, 79 insertions(+), 53 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.3 dated 2015-09-12 and 1.2.4 dated 2015-10-16
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/likelihood.R | 5 +++-- R/mnlogit.R | 2 ++ 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The HistData package provides a collection of small data sets
that are interesting and important in the history of statistics and data visualization.
The goal of the package is to make these available, both for instructional use
and for historical research. Some of these present interesting challenges for graphics
or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.7-5 dated 2014-04-26 and 0.7-6 dated 2015-10-16
DESCRIPTION | 16 ++++---- MD5 | 92 +++++++++++++++++++++++----------------------- NEWS | 4 ++ data/Arbuthnot.RData |binary data/Armada.RData |only data/Bowley.RData |binary data/Cavendish.RData |binary data/ChestSizes.RData |binary data/CushnyPeebles.RData |binary data/CushnyPeeblesN.RData |binary data/Dactyl.RData |binary data/DrinksWages.RData |binary data/Fingerprints.RData |binary data/Galton.RData |binary data/GaltonFamilies.RData |binary data/Guerry.RData |binary data/Jevons.RData |binary data/Langren.all.RData |binary data/Langren1644.RData |binary data/Macdonell.RData |binary data/MacdonellDF.RData |binary data/Michelson.RData |binary data/MichelsonSets.RData |binary data/Minard.cities.RData |binary data/Minard.temp.RData |binary data/Minard.troops.RData |binary data/Nightingale.RData |binary data/OldMaps.RData |binary data/PearsonLee.RData |binary data/PolioTrials.RData |binary data/Prostitutes.RData |binary data/Pyx.RData |binary data/Quarrels.RData |binary data/Snow.deaths.RData |binary data/Snow.polygons.RData |binary data/Snow.pumps.RData |binary data/Snow.streets.RData |binary data/Wheat.RData |binary data/Wheat.monarchs.RData |binary data/Yeast.RData |binary data/YeastD.mat.RData |binary data/ZeaMays.RData |binary man/Armada.Rd |only man/Cavendish.Rd | 2 - man/HistData-package.Rd | 9 ++-- man/Michelson.Rd | 2 - man/PolioTrials.Rd | 2 - man/Snow.Rd | 7 ++- 48 files changed, 71 insertions(+), 63 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.0 dated 2015-10-11 and 1.1 dated 2015-10-16
DESCRIPTION | 8 +-- MD5 | 26 +++++----- NAMESPACE | 2 R/graduallyvariedflow_v2.r | 7 ++ R/route_wave_v4.r | 1 inst/doc/quickstart.R | 2 inst/doc/quickstart.Rmd | 6 +- inst/doc/quickstart.html | 91 ++++++-------------------------------- inst/doc/technical-vignette.Rmd | 6 ++ inst/doc/technical-vignette.html | 6 ++ man/compute_profile.Rd | 4 + src/rivmech_characteristic_v7.cpp | 21 ++++++-- vignettes/quickstart.Rmd | 6 +- vignettes/technical-vignette.Rmd | 6 ++ 14 files changed, 83 insertions(+), 109 deletions(-)
Title: CAlibrating Penalities Using Slope HEuristics
Description: Calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.
Author: Sylvain Arlot, Vincent Brault, Jean-Patrick Baudry, Cathy Maugis and Bertrand Michel
Maintainer: Vincent Brault <vincent.brault@agroparistech.fr>
Diff between capushe versions 1.0 dated 2012-02-17 and 1.1 dated 2015-10-16
capushe-1.0/capushe/main.R |only capushe-1.0/capushe/testsDev |only capushe-1.1/capushe/DESCRIPTION | 20 ++--- capushe-1.1/capushe/MD5 | 29 +++---- capushe-1.1/capushe/NAMESPACE | 43 ++++++----- capushe-1.1/capushe/R/DDSE.R | 6 - capushe-1.1/capushe/R/Djump.R | 109 ++++++++++++++++++++++++----- capushe-1.1/capushe/R/capushe.R | 99 ++++++++++++++++++++++---- capushe-1.1/capushe/R/prog.R | 4 - capushe-1.1/capushe/man/BICAICcapushe.Rd | 2 capushe-1.1/capushe/man/DDSE.Rd | 2 capushe-1.1/capushe/man/Djump.Rd | 32 +++++++- capushe-1.1/capushe/man/capushe-package.Rd | 4 - capushe-1.1/capushe/man/capushe.Rd | 15 +++ capushe-1.1/capushe/man/validation.Rd | 2 15 files changed, 276 insertions(+), 91 deletions(-)
Title: R Wrapper for the Bit.ly, Ow.ly and Goo.gl API
Description: Allows users accessing 'Bit.ly API' http://dev.bitly.com/ and retrieve many useful statistics. Additionally provides an experimental support of 'Ow.ly' http://ow.ly/api-docs and 'Goo.gl' http://goo.gl.
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>
Diff between RBitly versions 0.6.1 dated 2015-07-04 and 0.7.3 dated 2015-10-16
DESCRIPTION | 20 - MD5 | 92 ++++---- NAMESPACE | 9 NEWS | 20 + R/ApiKey.R | 113 ++++++++-- R/Domains.R | 4 R/Links.R | 210 +++++++++++++++++-- R/LinksMetrics.R | 67 ++++-- R/UserInfo.R | 22 -- R/UserMetrics.R | 24 +- README.md | 97 ++++----- build/vignette.rds |binary inst/doc/Tutorial.R | 53 +++- inst/doc/Tutorial.Rmd | 64 +++-- inst/doc/Tutorial.html | 134 ++++++++---- man/bitly_pro_domain.Rd | 2 man/link_Metrics_Clicks.Rd | 4 man/link_Metrics_Countries.Rd | 2 man/link_Metrics_Encoders.Rd | 2 man/link_Metrics_EncodersByCount.Rd | 2 man/link_Metrics_EncodersCount.Rd | 2 man/link_Metrics_Owly.Rd |only man/link_Metrics_Referrers.Rd | 2 man/link_Metrics_ReferrersByDomain.Rd | 2 man/link_Metrics_ReferringDomains.Rd | 2 man/links_Expand.Rd | 2 man/links_ExpandGoogl.Rd |only man/links_ExpandOwly.Rd |only man/links_Info.Rd | 2 man/links_InfoOwly.Rd |only man/links_Lookup.Rd | 2 man/links_Shorten.Rd | 9 man/links_ShortenGoogl.Rd |only man/links_ShortenOwly.Rd |only man/rbitlyApi.Rd | 24 +- man/rbitlyApi_up.Rd | 2 man/user_Info.Rd | 2 man/user_LinkHistory.Rd | 2 man/user_Metrics_Clicks.Rd | 2 man/user_Metrics_Countries.Rd | 2 man/user_Metrics_PopularLinks.Rd | 2 man/user_Metrics_Referrers.Rd | 2 man/user_Metrics_ReferringDomains.Rd | 2 man/user_Metrics_ShortenCounts.Rd | 2 man/user_TrackingDomains.Rd | 2 tests/testthat/test-Domains.R | 2 tests/testthat/test-Links.R | 39 +++ tests/testthat/test-UserInfo_LinkMetrics.R | 7 tests/testthat/test-UserMetrics.R | 4 vignettes/Tutorial.Rmd | 312 +++++++++++++++-------------- 50 files changed, 918 insertions(+), 454 deletions(-)
Title: Preprocessing of Aligned Sequences from HTS Analyses
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil@mssm.edu>
Diff between Pasha versions 0.99.16 dated 2015-08-01 and 0.99.18 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pipelineChipSeq.R | 30 ++++++++++++++---------------- inst/doc/Pasha.pdf |binary src/MultireadCSEMBcTree.h | 2 +- tests/test_Pasha.Rout.save | 25 ++++++++++++++++--------- 6 files changed, 40 insertions(+), 35 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4 dated 2015-09-02 and 1.4.1 dated 2015-10-16
DESCRIPTION | 14 ++++--- MD5 | 42 +++++++++++++-------- R/Fst.R | 24 +++++++++--- R/GenDist.R |only R/MCreml.R | 59 +++++++++++++++++++++++++++++- R/RcppExports.R | 4 ++ R/gibbs.R | 26 +++++++++++++ R/gwas.R | 49 ++++++++++++++++--------- R/gwas2.R | 57 ++++++++++++++--------------- R/manhattan.R | 4 +- R/reml.R | 100 ++++++++++++++++++++++++++-------------------------- R/wgr.R |only build |only inst/doc |only man/Internals.Rd | 28 +++++++++++++- man/NAM-package.Rd | 6 +-- man/gibbs.Rd | 1 man/reference.Rd | 66 +++++++++++++++++----------------- man/reml.Rd | 9 ++++ man/snpQC.Rd | 2 - man/tpod.Rd | 41 ++++++++++----------- man/wgr.Rd |only src/KMUP.cpp |only src/RcppExports.cpp | 18 +++++++++ vignettes |only 25 files changed, 360 insertions(+), 190 deletions(-)
Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB), pre-formatted for general analysis and genome-wide association analysis using the NAM package.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between SoyNAM versions 1.0 dated 2015-07-29 and 1.1 dated 2015-10-15
SoyNAM-1.0/SoyNAM/R/BLUP.R |only SoyNAM-1.0/SoyNAM/man/BLUP.Rd |only SoyNAM-1.0/SoyNAM/man/ENV.Rd |only SoyNAM-1.1/SoyNAM/DESCRIPTION | 10 +++++----- SoyNAM-1.1/SoyNAM/MD5 | 17 +++++++++-------- SoyNAM-1.1/SoyNAM/R/BLUPs.R |only SoyNAM-1.1/SoyNAM/data/datalist | 1 + SoyNAM-1.1/SoyNAM/data/soybase.RData |only SoyNAM-1.1/SoyNAM/data/soynam.RData |binary SoyNAM-1.1/SoyNAM/man/BLUP1.Rd |only SoyNAM-1.1/SoyNAM/man/BLUP2.Rd |only SoyNAM-1.1/SoyNAM/man/SoyNAM-package.Rd | 8 ++++---- SoyNAM-1.1/SoyNAM/man/soynam.Rd | 20 ++++++++++++++++---- 13 files changed, 35 insertions(+), 21 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function
fitting with an emphasis on splines, spatial data and spatial
statistics. The major methods include cubic, and thin plate splines,
Kriging and compact covariances for large data sets. The splines and
Kriging methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross validation
and also by restricted maximum likelihood. For Kriging there is
an easy to function that also estimates the correlation scale (range).
A major feature is that
any covariance function implemented in R and following a simple fields
format can be used for spatial prediction. There are also many useful
functions for plotting and
working with spatial data as images. This package also contains an
implementation of sparse matrix methods for large spatial data sets and
currently requires the sparse matrix (spam) package.
Use help(fields) to get started and for an
overview. The fields source code is deliberately commented and
provides useful explanations of numerical details in addition to the
manual pages. The commented source code can be viewed by expanding the
source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between fields versions 8.2-1 dated 2015-02-28 and 8.3-5 dated 2015-10-15
fields-8.2-1/fields/R/ozone.R |only fields-8.2-1/fields/R/vgram.R |only fields-8.2-1/fields/man/predict.surface.Rd |only fields-8.3-5/fields/DESCRIPTION | 14 fields-8.3-5/fields/MD5 | 196 ++++--- fields-8.3-5/fields/NAMESPACE | 16 fields-8.3-5/fields/R/ChicagoO3.R |only fields-8.3-5/fields/R/ExponentialUpper.R |only fields-8.3-5/fields/R/Krig.family.R | 10 fields-8.3-5/fields/R/MLESpatialProcess.R | 356 +++++++++----- fields-8.3-5/fields/R/as.image.R | 17 fields-8.3-5/fields/R/compactToMat.R |only fields-8.3-5/fields/R/cubic.cov.R | 9 fields-8.3-5/fields/R/exp.cov.R | 123 +++- fields-8.3-5/fields/R/exp.simple.cov.R | 7 fields-8.3-5/fields/R/image.family.R | 7 fields-8.3-5/fields/R/mKrig.MLE.R | 235 +++++---- fields-8.3-5/fields/R/mKrig.MLE.joint.R |only fields-8.3-5/fields/R/mKrig.R |only fields-8.3-5/fields/R/mKrig.family.R | 180 ------- fields-8.3-5/fields/R/predict.Krig.R | 24 fields-8.3-5/fields/R/predictSurface.Krig.R |only fields-8.3-5/fields/R/predictSurface.family.R | 5 fields-8.3-5/fields/R/quilt.plot.R | 15 fields-8.3-5/fields/R/rad.cov.R | 5 fields-8.3-5/fields/R/rdist.R | 40 - fields-8.3-5/fields/R/rdist.earth.R | 4 fields-8.3-5/fields/R/rdist.earth.vec.R |only fields-8.3-5/fields/R/rdist.vec.R |only fields-8.3-5/fields/R/spatialProcess.R | 8 fields-8.3-5/fields/R/stationary.cov.R | 205 ++++---- fields-8.3-5/fields/R/stationary.taper.cov.R | 4 fields-8.3-5/fields/R/supportsArg.R |only fields-8.3-5/fields/R/unrollZGrid.R |only fields-8.3-5/fields/R/vgram.family.R |only fields-8.3-5/fields/R/vgram.matrix.R | 36 - fields-8.3-5/fields/R/wendland.family.R | 12 fields-8.3-5/fields/README |only fields-8.3-5/fields/data/COmonthlyMet.rda |binary fields-8.3-5/fields/man/CO.Rd | 14 fields-8.3-5/fields/man/CovarianceUpper.Rd |only fields-8.3-5/fields/man/Krig.Amatrix.Rd | 6 fields-8.3-5/fields/man/Krig.Rd | 12 fields-8.3-5/fields/man/Krig.engine.default.Rd | 4 fields-8.3-5/fields/man/MLESpatialProcess.Rd | 204 +++++--- fields-8.3-5/fields/man/Tps.Rd | 61 +- fields-8.3-5/fields/man/as.image.Rd | 6 fields-8.3-5/fields/man/compactToMat.Rd |only fields-8.3-5/fields/man/exp.cov.Rd | 44 + fields-8.3-5/fields/man/fields-internal.Rd | 10 fields-8.3-5/fields/man/gcv.Krig.Rd | 2 fields-8.3-5/fields/man/grid.list.Rd | 20 fields-8.3-5/fields/man/image.plot.Rd | 18 fields-8.3-5/fields/man/mKrig.MLE.Rd | 222 ++++++-- fields-8.3-5/fields/man/mKrig.Rd | 193 ++++--- fields-8.3-5/fields/man/ozone.Rd | 13 fields-8.3-5/fields/man/plot.Krig.Rd | 4 fields-8.3-5/fields/man/predict.Krig.Rd | 4 fields-8.3-5/fields/man/predictSE.Krig.Rd | 2 fields-8.3-5/fields/man/predictSurface.Rd | 51 +- fields-8.3-5/fields/man/print.Krig.Rd | 2 fields-8.3-5/fields/man/quilt.plot.Rd | 5 fields-8.3-5/fields/man/rdist.Rd | 35 + fields-8.3-5/fields/man/rdist.earth.Rd | 24 fields-8.3-5/fields/man/spatialProcess.Rd | 7 fields-8.3-5/fields/man/summary.Krig.Rd | 2 fields-8.3-5/fields/man/supportsArg.Rd |only fields-8.3-5/fields/man/surface.Krig.Rd | 2 fields-8.3-5/fields/man/transformx.Rd | 2 fields-8.3-5/fields/man/vgram.Rd | 95 +++ fields-8.3-5/fields/src/ExponentialUpperC.c |only fields-8.3-5/fields/src/addToDiagC.c |only fields-8.3-5/fields/src/compactToMatC.c |only fields-8.3-5/fields/src/expfnC.c |only fields-8.3-5/fields/src/multebC.c |only fields-8.3-5/fields/src/rdist.f |only fields-8.3-5/fields/src/rdistC.c |only fields-8.3-5/fields/tests/Krig.Z.test.R | 4 fields-8.3-5/fields/tests/Krig.Z.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.W.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.grid.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.test.R | 8 fields-8.3-5/fields/tests/Krig.se.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.test.R | 26 - fields-8.3-5/fields/tests/Krig.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.test.W.Rout.save | 14 fields-8.3-5/fields/tests/KrigGCVREML.test.R | 25 fields-8.3-5/fields/tests/KrigGCVREML.test.Rout.save | 21 fields-8.3-5/fields/tests/Likelihood.test.Rout.save | 14 fields-8.3-5/fields/tests/REMLest.test.Rout.save | 14 fields-8.3-5/fields/tests/Tps.test.R | 6 fields-8.3-5/fields/tests/Tps.test.Rout.save | 14 fields-8.3-5/fields/tests/Wend.test.Rout.save | 14 fields-8.3-5/fields/tests/cov.test.Rout.save | 14 fields-8.3-5/fields/tests/derivative.test.Rout.save | 14 fields-8.3-5/fields/tests/diag.multiply.test.Rout.save | 14 fields-8.3-5/fields/tests/diagonal2.test.Rout.save | 14 fields-8.3-5/fields/tests/evlpoly.test.Rout.save | 14 fields-8.3-5/fields/tests/fastTpsPredict.test.Rout.save |only fields-8.3-5/fields/tests/mKrig.MLE.test.R |only fields-8.3-5/fields/tests/mKrig.MLE.test.Rout.save |only fields-8.3-5/fields/tests/mKrig.Z.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.parameters.test.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.se.test.R | 18 fields-8.3-5/fields/tests/mKrig.se.test.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.test.R | 157 ++++-- fields-8.3-5/fields/tests/mKrig.test.Rout.save | 33 + fields-8.3-5/fields/tests/misc.test.Rout.save | 14 fields-8.3-5/fields/tests/spam.test.Rout.save | 14 fields-8.3-5/fields/tests/sreg.test.Rout.save | 14 fields-8.3-5/fields/tests/test.cov.R |only fields-8.3-5/fields/tests/test.cov.Rout.save |only fields-8.3-5/fields/tests/vgram.test.R | 15 fields-8.3-5/fields/tests/vgram.test.Rout.save | 14 114 files changed, 2059 insertions(+), 1154 deletions(-)
Title: Sparse and Non-Sparse Partial Robust M Regression and
Classification
Description: Robust dimension reduction methods for regression and discriminant analysis are implemented that yield estimates with a partial least squares alike interpretability. Partial robust M regression (PRM) is robust to both vertical outliers and leverage points. Sparse partial robust M regression (SPRM) is a related robust method with sparse coefficient estimate, and therefore with intrinsic variable selection. For bianry classification related discriminant methods are PRM-DA and SPRM-DA.
Author: Sven Serneels, BASF Corp and Irene Hoffmann
Maintainer: Irene Hoffmann <irene.hoffmann@tuwien.ac.at>
Diff between sprm versions 1.1 dated 2014-12-10 and 1.2 dated 2015-10-15
DESCRIPTION | 16 ++-- MD5 | 89 +++++++++++++++++--------- NAMESPACE | 36 ++++++++++ R/balancedfolds.R |only R/biplot.prm.R | 10 +- R/biplot.prmda.R |only R/biplot.sprm.R | 6 - R/biplot.sprmda.R |only R/biweight.R |only R/daprpr.R | 4 - R/dbshdy.R | 2 R/int_weight.R |only R/intervals.prm.R | 2 R/intervals.sprm.R | 2 R/ldafitfun.R |only R/nipls.R | 5 - R/plot.prm.R | 25 ++++++- R/plot.sprm.R | 19 +++++ R/predict.prm.R | 4 - R/predict.prmda.R |only R/predict.sprm.R | 3 R/predict.sprmda.R |only R/print.prmda.R |only R/print.sprmda.R |only R/prmda.R |only R/prmdaCV.R |only R/prms.R | 89 ++++++++++---------------- R/prmsCV.R | 34 ++++++---- R/snipls.R | 22 +++--- R/sprmda.R |only R/sprmdaCV.R |only R/sprms.R | 167 +++++++++++++++++++++++--------------------------- R/sprmsCV.R | 13 ++- R/summary.prmda.R |only R/summary.sprmda.R |only R/weig.R |only man/biplot.prm.Rd | 9 +- man/biplot.prmda.Rd |only man/biplot.sprm.Rd | 11 ++- man/biplot.sprmda.Rd |only man/plot.prm.Rd | 8 +- man/plot.sprm.Rd | 6 - man/predict.prm.Rd | 10 -- man/predict.prmda.Rd |only man/predict.sprm.Rd | 2 man/predict.sprmda.Rd |only man/prmda.Rd |only man/prmdaCV.Rd |only man/prms.Rd | 5 - man/prmsCV.Rd | 6 - man/sprm-package.Rd | 12 ++- man/sprmda.Rd |only man/sprmdaCV.Rd |only man/sprms.Rd | 5 - man/sprmsCV.Rd | 14 ++-- man/summary.prm.Rd | 2 man/summary.prmda.Rd |only man/summary.sprm.Rd | 2 man/summary.sprmda.Rd |only 59 files changed, 369 insertions(+), 271 deletions(-)
Title: Choi and Hall Style Data Sharpening
Description: Functions for use in perturbing data prior to use of nonparametric smoothers
and clustering.
Author: Douglas Woolford and John Braun
Maintainer: John Braun <braun@stats.uwo.ca>
Diff between CHsharp versions 0.3 dated 2012-11-05 and 0.4 dated 2015-10-15
DESCRIPTION | 23 ++++++++++++----------- MD5 | 20 +++++++++++++++++--- NAMESPACE | 9 ++++----- R/MISE.R |only R/SecondDerivativePenalty.R |only R/lambda.R |only R/numericalDerivative.R |only R/penlocreg.R |only R/pllr.R |only R/sharpen.R |only data/d.rda |binary man/MISE.Rd |only man/SecondDerivativePenalty.Rd |only man/lambda.Rd |only man/numericalDerivative.Rd |only man/penlocreg.Rd |only man/pllr.Rd |only man/sharpen.Rd |only 18 files changed, 33 insertions(+), 19 deletions(-)
More information about easyVerification at CRAN
Permanent link
Title: World Population Prospects 2015
Description: Provides data from the United Nation's World Population Prospects 2015.
Author: Population Division, Department of Economic and Social Affairs, United Nations.
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wpp2015 versions 1.0-0 dated 2015-08-08 and 1.0-1 dated 2015-10-15
ChangeLog | 4 DESCRIPTION | 8 MD5 | 8 data/UNlocations.txt | 550 ++++++++++++++++++++++++------------------------- man/wpp2015-package.Rd | 4 5 files changed, 289 insertions(+), 285 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 1.0.1 dated 2015-10-12 and 1.0.2 dated 2015-10-15
DESCRIPTION | 10 +++--- MD5 | 10 ++++-- NEWS | 7 ++++ tests/testthat/case_win32_test_iris.R |only tests/testthat/case_win32b_test_orange.R |only tests/testthat/test_iris.R | 46 +++++++------------------------ tests/testthat/test_orange.R | 39 +++++--------------------- 7 files changed, 36 insertions(+), 76 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.13-0 dated 2015-08-29 and 1.14-0 dated 2015-10-15
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- R/designMatrices_aux2.R | 6 ++++-- R/stud_prior.R | 2 +- R/tam.pv.R | 7 ++++--- inst/NEWS | 24 ++++++++++++++++++++++++ man/TAM-package.Rd | 3 +-- man/tam.pv.Rd | 2 +- 8 files changed, 47 insertions(+), 22 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 1.4 dated 2014-11-27 and 2.0 dated 2015-10-15
DESCRIPTION | 22 MD5 | 96 NAMESPACE | 32 R/RcppExports.R |only R/rags2ridges.R | 6392 +++++++++++++++++++++------------------ R/rags2ridgesFused.R |only R/rags2ridgesMisc.R |only README.md |only inst/CITATION | 74 inst/NEWS.Rd |only man/GGMblockNullPenalty.Rd | 34 man/GGMblockTest.Rd | 41 man/GGMmutualInfo.Rd |only man/GGMnetworkStats.Rd | 16 man/GGMnetworkStats.fused.Rd |only man/GGMpathStats.Rd | 54 man/GGMpathStats.fused.Rd |only man/KLdiv.Rd | 20 man/KLdiv.fused.Rd |only man/NLL.Rd |only man/Ugraph.Rd | 41 man/adjacentMat.Rd | 9 man/armaRidgeP.Rd |only man/conditionNumberPlot.Rd | 36 man/covML.Rd | 10 man/covMLknown.Rd |only man/createS.Rd |only man/default.penalty.Rd |only man/default.target.Rd | 20 man/default.target.fused.Rd |only man/edgeHeat.Rd | 14 man/evaluateS.Rd | 12 man/evaluateSfit.Rd | 24 man/fullMontyS.Rd | 20 man/fused.test.Rd |only man/getKEGGPathway.Rd |only man/is.Xlist.Rd |only man/isSymmetricPD.Rd |only man/kegg.target.Rd |only man/loss.Rd | 26 man/optPenalty.LOOCV.Rd | 31 man/optPenalty.LOOCVauto.Rd | 18 man/optPenalty.aLOOCV.Rd | 41 man/optPenalty.fused.Rd |only man/pcor.Rd | 8 man/plot.ptest.Rd |only man/pooledS.Rd |only man/print.optPenaltyFusedGrid.Rd |only man/print.ptest.Rd |only man/rags2ridges-package.Rd | 94 man/ridgeP.Rd |only man/ridgeP.fused.Rd |only man/ridgePathS.Rd | 35 man/ridgeS.Rd | 43 man/rmvnormal.Rd |only man/sparsify.Rd | 20 man/sparsify.fused.Rd |only src |only tests |only 59 files changed, 4006 insertions(+), 3277 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.4-2 dated 2015-09-09 and 0.8.6-0 dated 2015-10-15
DESCRIPTION | 11 MD5 | 63 - NAMESPACE | 5 NEWS | 30 R/corpus.R | 21 R/dfm-classes.R | 137 ++ R/dfm-main.R | 123 +- R/dfm-methods.R | 32 R/dictionaries.R | 51 + R/kwic.R | 244 ++++- R/ngrams.R | 131 -- R/settings.R | 2 R/stopwords.R | 242 ++++- R/textfile.R | 15 R/toLower.R | 2 R/tokenize.R | 80 - R/tokenize_outtakes.R |only R/wordstem.R | 24 inst/doc/development-plans.html | 842 ++++++++++-------- inst/doc/quickstart.Rmd | 1 inst/doc/quickstart.html | 1833 ++++++++++++++++++++++------------------ man/corpus.Rd | 8 man/dfm.Rd | 59 - man/dictionary.Rd | 2 man/head.dfm.Rd |only man/kwic.Rd | 49 - man/ngrams.Rd | 9 man/print.dfm.Rd | 19 man/print.tokenizedTexts.Rd |only man/selectFeatures.Rd | 34 man/textfile.Rd | 2 man/tokenize.Rd | 9 man/weight.Rd | 17 vignettes/quickstart.Rmd | 1 34 files changed, 2508 insertions(+), 1590 deletions(-)
Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.4 dated 2015-08-04 and 0.9.4-2 dated 2015-10-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/introduction.Rnw | 4 ++-- man/hamlet-package.Rd | 4 ++-- vignettes/introduction.Rnw | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.0.2 dated 2015-10-14 and 1.0.3 dated 2015-10-15
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++----------- NAMESPACE | 3 +- NEWS | 4 +++ R/Wbal.R | 8 ------- R/convert_time.R | 48 ++++++++++++++++++++++++++++------------------ R/download_elev_data.R | 7 ------ R/elevation_correct.R | 3 +- man/Wbal.Rd | 8 ------- man/convert_time.Rd | 20 +++++++++---------- man/download_elev_data.Rd | 7 ------ man/elevation_correct.Rd | 2 + 12 files changed, 66 insertions(+), 72 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.5-0 dated 2015-10-08 and 1.6-0 dated 2015-10-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/BIFIE.data.jack.R | 19 +++++++++---------- R/BIFIE.univar.R | 2 +- R/BIFIE.univar.test.R | 28 +++++++++++++++++++++++++++- R/BIFIE_table_multiple_groupings.R | 2 +- inst/NEWS | 14 ++++++++++++++ man/BIFIE.univar.test.Rd | 32 +++++++++++++++++++++++++++++++- man/BIFIEsurvey-package.Rd | 7 ++++++- 9 files changed, 101 insertions(+), 27 deletions(-)
Title: Basic Wireless Communications Simulation
Description: A communications simulation package supporting common wireless modulation
formats including BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. The package includes AWGN
noise generation, and raised cosine and square root raised cosine pulse shaping. It also
includes convenience functions for plotting constellation diagrams, density plots, stem
plots and eye diagrams. Together these functions enable the evaluation of bit error and
symbol error rates, evaluation of pulse shaping and inter-symbol interference and support
visualization of the respective signals and noise in a variety of formats.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.3 dated 2015-09-11 and 1.4.2 dated 2015-10-15
DESCRIPTION | 26 +++-- MD5 | 50 ++++++----- NAMESPACE | 15 +++ R/RcppExports.R |only R/rwirelesscom.R | 216 +++++++++++++++++++++++++++++++++++++++---------- man/eyediagram.Rd |only man/f16pskdemod.Rd | 16 +-- man/f16pskmod.Rd | 25 +++-- man/f16qamdemod.Rd | 16 +-- man/f16qammod.Rd | 25 +++-- man/f64qamdemod.Rd | 16 +-- man/f64qammod.Rd | 25 +++-- man/f8pskdemod.Rd | 16 +-- man/f8pskmod.Rd | 25 +++-- man/fNo.Rd | 16 +-- man/fbpskdemod.Rd | 16 +-- man/fbpskmod.Rd | 25 +++-- man/fqpskdemod.Rd | 16 +-- man/fqpskmod.Rd | 19 +--- man/iqdensityplot.Rd | 18 ++-- man/iqscatterplot.Rd | 16 +-- man/rcosine.Rd |only man/rwirelesscom.Rd | 17 ++- man/sinc.Rd |only man/sqrtrcosine.Rd |only man/stemplot.Rd |only src |only tests/testthat.R | 2 tests/testthat/test1.R | 104 ++++++++++++++++++++--- 29 files changed, 491 insertions(+), 229 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.45.1 dated 2015-09-17 and 0.50.0 dated 2015-10-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 9 +++++++++ R/segmentByPairedPSCBS.R | 15 +++++---------- inst/doc/CBS.pdf |binary inst/doc/PairedPSCBS.pdf |binary man/segmentByPairedPSCBS.Rd | 8 ++------ 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Description: The introduction of the broom package has made converting model objects into data
frames as simple as a single function. While the broom package focuses on providing tidy
data frames that can be used in advanced analysis, it deliberately stops short of providing
functionality for reporting models in publication-ready tables. pixiedust provides this
functionality with a programming interface intended to be similar to ggplot2's system of
layers with fine tuned control over each cell of the table. Options for output include
printing to the console and to the common markdown formats (markdown, HTML, and LaTeX).
With a little pixiedust (and happy thoughts) tables can really fly.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <nutter@battelle.org>
Diff between pixiedust versions 0.1.1 dated 2015-08-03 and 0.5.0 dated 2015-10-15
pixiedust-0.1.1/pixiedust/R/add_sprinkles.R |only pixiedust-0.1.1/pixiedust/R/sprinkles.R |only pixiedust-0.1.1/pixiedust/man/add_sprinkles.Rd |only pixiedust-0.1.1/pixiedust/man/sprinkles.Rd |only pixiedust-0.5.0/pixiedust/DESCRIPTION | 13 pixiedust-0.5.0/pixiedust/LICENSE | 6 pixiedust-0.5.0/pixiedust/MD5 | 107 pixiedust-0.5.0/pixiedust/NAMESPACE | 69 pixiedust-0.5.0/pixiedust/NEWS | 252 pixiedust-0.5.0/pixiedust/R/as.data.frame.dust.R |only pixiedust-0.5.0/pixiedust/R/chain.R | 28 pixiedust-0.5.0/pixiedust/R/dust.R | 414 - pixiedust-0.5.0/pixiedust/R/glance_foot.R |only pixiedust-0.5.0/pixiedust/R/medley.R |only pixiedust-0.5.0/pixiedust/R/perform_function.R | 62 pixiedust-0.5.0/pixiedust/R/pixiedust-pkg.R |only pixiedust-0.5.0/pixiedust/R/print.dust.R | 70 pixiedust-0.5.0/pixiedust/R/print_dust_console.R | 153 pixiedust-0.5.0/pixiedust/R/print_dust_html.R | 322 - pixiedust-0.5.0/pixiedust/R/print_dust_latex.R |only pixiedust-0.5.0/pixiedust/R/print_dust_markdown.R | 190 pixiedust-0.5.0/pixiedust/R/pvalString.R | 84 pixiedust-0.5.0/pixiedust/R/redust.R |only pixiedust-0.5.0/pixiedust/R/sprinkle.R |only pixiedust-0.5.0/pixiedust/R/sprinkle_colnames.R | 175 pixiedust-0.5.0/pixiedust/R/sprinkle_print_method.R |only pixiedust-0.5.0/pixiedust/R/sprinkle_table.R |only pixiedust-0.5.0/pixiedust/R/tidy_levels_labels.R |only pixiedust-0.5.0/pixiedust/R/zzz.R | 16 pixiedust-0.5.0/pixiedust/README.md | 432 - pixiedust-0.5.0/pixiedust/build/vignette.rds |binary pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.R |only pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.Rmd |only pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.html |only pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.R | 114 pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.Rmd | 556 +- pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.html | 2736 ++-------- pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.R | 10 pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.Rmd | 108 pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.html | 525 - pixiedust-0.5.0/pixiedust/inst/sprinkles.csv | 57 pixiedust-0.5.0/pixiedust/man/as.data.frame.dust.Rd |only pixiedust-0.5.0/pixiedust/man/chain.Rd | 36 pixiedust-0.5.0/pixiedust/man/dust.Rd | 214 pixiedust-0.5.0/pixiedust/man/glance_foot.Rd |only pixiedust-0.5.0/pixiedust/man/medley.Rd |only pixiedust-0.5.0/pixiedust/man/pixiedust.Rd |only pixiedust-0.5.0/pixiedust/man/print.dust.Rd | 52 pixiedust-0.5.0/pixiedust/man/pvalString.Rd | 100 pixiedust-0.5.0/pixiedust/man/sprinkle.Rd |only pixiedust-0.5.0/pixiedust/man/sprinkle_colnames.Rd | 89 pixiedust-0.5.0/pixiedust/man/tidy_levels_labels.Rd |only pixiedust-0.5.0/pixiedust/tests/testthat.R | 6 pixiedust-0.5.0/pixiedust/tests/testthat/test-as.data.frame.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-dust.R | 124 pixiedust-0.5.0/pixiedust/tests/testthat/test-glance_foot.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-medley.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-perform_function.R | 48 pixiedust-0.5.0/pixiedust/tests/testthat/test-print.dust.R | 212 pixiedust-0.5.0/pixiedust/tests/testthat/test-print_dust_methods.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-pvalString.R | 26 pixiedust-0.5.0/pixiedust/tests/testthat/test-redust.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-roundSafe.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkle_colnames.R | 56 pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkle_table.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkles.R | 944 +-- pixiedust-0.5.0/pixiedust/tests/testthat/test-tidy_label_level.R |only pixiedust-0.5.0/pixiedust/vignettes/advancedMagic.Rmd |only pixiedust-0.5.0/pixiedust/vignettes/pixiedust.Rmd | 556 +- pixiedust-0.5.0/pixiedust/vignettes/pixiedust_in_latex.Rmd |only pixiedust-0.5.0/pixiedust/vignettes/sprinkles.Rmd | 108 71 files changed, 4256 insertions(+), 4814 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.6.1 dated 2015-04-30 and 0.7.0 dated 2015-10-15
ChangeLog | 11 ++ DESCRIPTION | 17 +-- MD5 | 59 +++++++----- NAMESPACE | 14 ++ R/export.movie.R | 54 ++++++++--- R/layout_centering.R | 10 +- R/ndtvAnimationWidget.R |only R/render.d3_animation.R | 125 ++++++++++++++++---------- R/specialEffects.R |only R/tea_utils.R | 4 R/timecube.R |only R/transmissionTimeline.R |only build/vignette.rds |binary inst/doc/ndtv.R | 80 +++++++++++----- inst/doc/ndtv.Rnw | 44 +++++++-- inst/doc/ndtv.pdf |binary inst/htmlwidgets |only inst/javascript/ndtv-d3/src/css/styles.css | 1 inst/javascript/ndtv-d3/src/js/ndtv-d3.js | 16 +-- inst/javascript/ndtv-d3/src/lib/d3.slider.css | 1 man/effectFun.Rd |only man/install.ffmpeg.Rd | 4 man/ndtv-package.Rd | 2 man/render.animation.Rd | 11 +- man/render.d3movie.Rd | 16 ++- man/timePrism.Rd |only man/timeline.Rd | 4 man/toy_epi_sim.Rd | 2 man/transmissionTimeline.Rd |only tests/d3_animation_tests.R | 6 + tests/effects_tests.R |only tests/networkAnimationTest.R | 2 tests/timeline_test.R | 7 + tests/transmissionTimelineTests.R |only vignettes/ndtv.Rnw | 44 +++++++-- 35 files changed, 369 insertions(+), 165 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.6 dated 2015-07-16 and 1.7 dated 2015-10-15
geigen-1.6/geigen/inst/CITATION |only geigen-1.7/geigen/DESCRIPTION | 20 ++++++++++++-------- geigen-1.7/geigen/MD5 | 13 ++++++------- geigen-1.7/geigen/NEWS | 6 ++++++ geigen-1.7/geigen/R/gsvd.R | 2 ++ geigen-1.7/geigen/man/geigen-package.Rd | 2 +- geigen-1.7/geigen/man/geigen.Rd | 2 +- geigen-1.7/geigen/man/gsvd.Rd | 8 ++++---- 8 files changed, 32 insertions(+), 21 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.1 dated 2015-10-05 and 0.8.2 dated 2015-10-14
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS | 11 ++- R/MulticoreFuture.R | 2 R/futureAssign.R | 2 R/globals.R | 62 ++++++++++++++--- demo/mandelbrot.R | 4 - man/eager.Rd | 136 +++++++++++++++++++-------------------- man/multicore.Rd | 166 ++++++++++++++++++++++++------------------------ tests/demo.R |only tests/dotdotdot.R | 6 + tests/futureAssign_OP.R | 6 - tests/globals,tricky.R |only 13 files changed, 240 insertions(+), 185 deletions(-)
Title: Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between ClusterStability versions 1.0.1 dated 2015-09-15 and 1.0.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/ClusterStability.R | 4 ++-- man/ClusterStability-package.Rd | 4 ++-- man/ClusterStability.Rd | 4 ++-- man/ClusterStability_exact.Rd | 4 ++-- 7 files changed, 24 insertions(+), 18 deletions(-)
More information about ClusterStability at CRAN
Permanent link
Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging
algorithm using classification trees as individual classifiers. Once these classifiers have been
trained, they can be used to predict on new data. Also, cross validation estimation of the error can
be done. Since version 2.0 the function margins() is available to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument
of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu
et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as
a function of the number of iterations. In addition, the ensembles can be pruned using the option
'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of
each class for observations can be obtained. Version 3.1 modifies the relative importance measure
to take into account the gain of the Gini index given by a variable in each tree and the weights of
these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo
and Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, three new plots are also
available importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on
unlabeled data.
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from Li Guo
Maintainer: Esteban Alfaro <Esteban.Alfaro@uclm.es>
Diff between adabag versions 4.0 dated 2014-12-21 and 4.1 dated 2015-10-14
DESCRIPTION | 23 ++++++++++---------- MD5 | 38 ++++++++++++++++----------------- NAMESPACE | 4 +++ R/adaboost.M1.R | 28 ++++++++++++++++++------ R/bagging.R | 29 +++++++++++++++++++++---- R/errorevol.R | 8 ++++--- R/predict.bagging.R | 41 +++++++++++++++++++++--------------- R/predict.boosting.R | 30 ++++++++++++++++++++------ R/select.R | 8 +++---- man/MarginOrderedPruning.Bagging.rd | 3 +- man/adabag-internal.Rd | 2 - man/adabag-package.Rd | 39 ++++++++++++++++++++-------------- man/bagging.Rd | 5 ++-- man/boosting.Rd | 5 ++-- man/errorevol.rd | 2 - man/margins.Rd | 2 - man/plot.errorevol.rd | 2 - man/plot.margins.rd | 2 - man/predict.bagging.Rd | 4 +-- man/predict.boosting.Rd | 4 +-- 20 files changed, 176 insertions(+), 103 deletions(-)
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.3 dated 2015-06-26 and 2.4 dated 2015-10-14
DESCRIPTION | 12 ++- MD5 | 31 +++++---- NAMESPACE | 9 ++ NEWS | 7 ++ R/itreemap.R | 9 +- R/pkg.R | 4 - R/tmAggregate.R | 32 +++++++-- R/tmColorsLegend.R | 6 - R/tmGenerateRect.R | 6 - R/treemap.R | 160 ++++++++++++++++++++++++++++++++++++------------- R/value2col.R | 71 +++++++++++++-------- build |only inst |only man/itreemap.Rd | 5 + man/treemap-package.Rd | 4 - man/treemap.Rd | 41 +++++++++--- vignettes |only 17 files changed, 277 insertions(+), 120 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.1.1 dated 2015-06-16 and 0.1.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 4 +--- NEWS | 6 ++++++ R/metadata.R | 4 +++- man/cache_treebase.Rd | 2 +- man/clean_data.Rd | 2 +- man/download_metadata.Rd | 2 +- man/drop_nonascii.Rd | 2 +- man/drop_nontrees.Rd | 2 +- man/dryad_metadata.Rd | 2 +- man/get_nex.Rd | 2 +- man/get_study.Rd | 2 +- man/get_study_id.Rd | 2 +- man/have_branchlength.Rd | 2 +- man/metadata.Rd | 3 ++- man/metadata_from_oai.Rd | 2 +- man/oai_metadata.Rd | 2 +- man/phylo_metadata.Rd | 2 +- man/search_treebase.Rd | 2 +- man/show_metadata.Rd | 2 +- man/treebase.Rd | 2 +- tests/testthat/test_basic.R | 4 ++-- 23 files changed, 56 insertions(+), 49 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.5 dated 2014-12-09 and 0.6 dated 2015-10-14
GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerPIC.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedPIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/DESCRIPTION | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/MD5 | 34 +++++----- GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetOptimizer.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetter.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetterCombined.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/HET.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/MTK.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/SubsetterMTK.R | 2 GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetOptimizer.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetter.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetterCombined.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/GeneticSubsetter.Rd | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/man/MTK.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/MtkCalc.Rd | 6 - GeneticSubsetter-0.6/GeneticSubsetter/man/PIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/PicCalc.Rd | 12 +-- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterMTK.Rd | 8 -- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterPIC.Rd | 5 - GeneticSubsetter-0.6/GeneticSubsetter/man/genotypes.Rd | 2 27 files changed, 40 insertions(+), 49 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Statistical Comparisons with Distance-Function Based Permutation
Tests
Description: Provides tools for making statistical comparisons with distance-function based permutation tests developed by P. W. Mielke, Jr. and colleagues at Colorado State University (Mielke, P. W. & Berry, K. J. Permutation Methods: A Distance Function Approach (Springer, New York, 2001)) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U. S. Geological Survey.
Author: Marian Talbert, Jon Richards, Paul Mielke, and Brian Cade
Maintainer: Marian Talbert <mtalbert@usgs.gov>
Diff between Blossom versions 1.2 dated 2015-10-14 and 1.3 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/InternalFcts.f90 | 11 ++++++----- 3 files changed, 13 insertions(+), 12 deletions(-)
Title: Easier cluster computing (based on snow).
Description: Usability wrapper around snow for easier development of
parallel R programs. This package offers e.g. extended error
checks, and additional functions. All functions work in
sequential mode, too, if no cluster is present or wished.
Package is also designed as connector to the cluster management
tool sfCluster, but can also used without it.
Author: Jochen Knaus
Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>
Diff between snowfall versions 1.84-6 dated 2013-12-18 and 1.84-6.1 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/init.R | 10 +++++----- R/sysdata.rda |binary data/test.rda |binary 5 files changed, 13 insertions(+), 13 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.1.2 dated 2014-03-12 and 1.2.0 dated 2015-10-14
reportr-1.1.2/reportr/R/infix.R |only reportr-1.1.2/reportr/R/substitute.R |only reportr-1.1.2/reportr/man/infix.Rd |only reportr-1.1.2/reportr/man/substitute.Rd |only reportr-1.2.0/reportr/DESCRIPTION | 15 +- reportr-1.2.0/reportr/MD5 | 17 +- reportr-1.2.0/reportr/NAMESPACE | 13 + reportr-1.2.0/reportr/R/00_constants.R | 13 + reportr-1.2.0/reportr/R/reportr.R | 227 ++++++++++++++++++++++++++------ reportr-1.2.0/reportr/README.md |only reportr-1.2.0/reportr/man/reportr.Rd | 164 +++++++++++++++++------ reportr-1.2.0/reportr/tests |only 12 files changed, 348 insertions(+), 101 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.4.1 dated 2015-10-06 and 0.5.0 dated 2015-10-14
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS | 8 ++ R/Globals-class.R | 2 R/cleanup.R | 30 ++++++---- R/globalsOf.R | 20 +++++- R/utils.R | 20 ++++++ man/cleanup.Globals.Rd | 41 ++++++------- man/globalsOf.Rd | 144 ++++++++++++++++++++++++------------------------- tests/globalsOf.R | 69 +++++++++++++++++++++++ tests/utils.R | 57 +++++++++++++++++++ 11 files changed, 295 insertions(+), 122 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.3 dated 2015-10-06 and 1.1.4 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/GDM_Table_Funcs.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.3.1 dated 2015-09-30 and 0.3.2 dated 2015-10-14
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- R/examples/main.R | 17 +++++++----- R/main.R | 71 ++++++++++++++++++++++++++++++++-------------------- man/Defficiency.Rd | 6 ++-- man/Dsensitivity.Rd | 16 ++++++++--- man/FedorovWynn.Rd | 5 ++- man/design.Rd | 3 +- man/numDerivLogf.Rd | 16 +++++------ man/param.Rd | 17 +++++++----- man/plot.desigh.Rd | 10 +++++-- 11 files changed, 113 insertions(+), 74 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) in Item Response models.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 1.0.0 dated 2015-04-28 and 1.1.0 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/DIFtree.R | 52 +++++++++++++++++++++++++++++++++++++++++----------- R/plot.DIFtree.R | 8 +++----- man/DIFtree.Rd | 3 ++- 5 files changed, 54 insertions(+), 25 deletions(-)
Title: Tools for Structural Reliability Analysis
Description: A variety of tools useful for performing structural
reliability analysis, such as with structure function and
system signatures. Plans to expand more widely.
Author: Louis Aslett <aslett@stats.ox.ac.uk>
Maintainer: Louis Aslett <aslett@stats.ox.ac.uk>
Diff between ReliabilityTheory versions 0.1.4 dated 2014-06-12 and 0.1.5 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS | 5 +++++ R/MinimalVertexPairCutSets.R | 2 +- README.md |only man/ReliabilityTheory-package.Rd | 4 ++-- 7 files changed, 20 insertions(+), 13 deletions(-)
More information about ReliabilityTheory at CRAN
Permanent link
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test.
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between AdaptGauss versions 1.0 dated 2015-10-09 and 1.1.0 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 +- R/AdaptGauss.R | 6 +++--- R/Chi2testMixtures.R | 3 +++ R/KStestMixtures.R |only man/AdaptGauss-package.Rd | 4 ++-- man/AdaptGauss.Rd | 19 ++++++++++--------- man/BayesDecisionBoundaries.Rd | 2 +- man/BayesForMixes.Rd | 1 + man/CDFMixtures.Rd | 2 +- man/Chi2testMixtures.Rd | 9 +++++++-- man/EMGauss.Rd | 1 + man/KStestMixtures.Rd |only man/paretoDensityEstimationForGMM.Rd | 6 +++--- man/paretoRadiusForGMM.Rd | 4 ++-- man/qqplotGMM.Rd | 2 +- 17 files changed, 57 insertions(+), 44 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 0.10.0 dated 2015-05-22 and 0.11.0 dated 2015-10-14
DESCRIPTION | 13 ++-- MD5 | 103 ++++++++++++++++++------------------ NAMESPACE | 8 ++ R/auto-test.r | 27 +++++---- R/compare.r | 41 ++++++++------ R/expect-that.r | 17 +++-- R/expectation.r | 7 +- R/expectations-equality.R | 4 - R/expectations-matches.R | 48 ++++++++++++---- R/expectations-silent.R |only R/expectations.r | 67 ++++++++++++++++++++++- R/mock.r | 5 + R/praise.R |only R/reporter-stop.r | 2 R/reporter-summary.r | 24 +++----- R/reporter-tap.r | 2 R/reporter.r | 2 R/test-example.R | 2 R/test-files.r | 21 +++++-- R/test-package.r | 28 +++++---- R/test-results.r | 2 R/test-that.r | 15 ++--- R/utils.r | 38 ++++++++++++- R/watcher.r | 9 +-- README.md | 23 ++------ man/StopReporter-class.Rd | 2 man/compare.Rd | 2 man/equivalence.Rd | 10 ++- man/expect-compare.Rd | 15 ++++- man/expect_equal_to_reference.Rd | 8 +- man/expect_is.Rd | 6 +- man/expect_named.Rd | 6 +- man/expect_null.Rd | 6 +- man/expect_silent.Rd |only man/expect_true.Rd | 8 +- man/expectation.Rd | 6 +- man/find_test_scripts.Rd | 4 + man/matching-expectations.Rd | 21 ++++--- man/not.Rd | 4 + man/skip.Rd | 12 ++++ man/takes_less_than.Rd | 7 +- man/test_examples.Rd | 2 man/test_package.Rd | 21 +++---- man/test_that.Rd | 10 +-- man/with_mock.Rd | 3 + tests/testthat/test-bare.r | 4 + tests/testthat/test-compare.r | 26 +++++++++ tests/testthat/test-expectations.r | 13 ++++ tests/testthat/test-mock.r | 2 tests/testthat/test-reporter-list.r | 10 ++- tests/testthat/test-reporter-tap.r |only tests/testthat/test-silence.R | 2 tests/testthat/test-test_dir.r | 16 +++-- tests/testthat/test-watcher.r | 8 ++ tests/testthat/test_dir/test-skip.r |only 55 files changed, 500 insertions(+), 242 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.29 dated 2015-08-11 and 0.4.30 dated 2015-10-14
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS | 3 +++ R/junitProtocol.r |only build/RUnit.pdf |binary inst/doc/RUnit.pdf |binary inst/unitTests/runitJUnitProtocol.r |only man/textProtocol.Rd | 22 ++++++++++++++++++---- 9 files changed, 35 insertions(+), 14 deletions(-)
Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added.
Author: Bryan Stanfill <bstanfill2003@gmail.com>, Heike Hofmann
<hofmann@iastate.edu>, Ulrike Genschel <ulrike@iastate.edu>
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.3 dated 2014-12-16 and 1.4 dated 2015-10-14
DESCRIPTION | 12 LICENSE | 2 MD5 | 164 +-- NAMESPACE | 234 ++-- NEWS | 270 ++--- R/RcppExports.R | 362 +++--- R/bayes.R | 534 ++++----- R/distributions.R | 1131 +++++++++++---------- R/estimators.R | 592 +++++------ R/grid-search.R | 200 +-- R/help.R | 20 R/kappa.R | 233 ++-- R/parameterizations.R | 1002 +++++++++--------- R/plot.R | 1060 ++++++++++--------- R/preliminary.R | 1423 +++++++++++++------------- R/primatives.R | 670 ++++++------ R/regions.R | 1076 ++++++++++---------- R/robust.R | 188 +-- build/vignette.rds |binary data/datalist | 4 inst/CITATION | 32 inst/REFERENCES.bib | 367 +++--- inst/doc/rotations-intro.R | 156 +- inst/doc/rotations-intro.Rnw | 732 ++++++------- inst/doc/rotations-intro.pdf |binary inst/include/rotations.h | 18 inst/include/rotations_RcppExports.h | 1713 ++++++++++++++++---------------- man/Angular-distributions.Rd | 40 man/Arithmetic.Rd | 155 +- man/Cayley.Rd | 164 +-- man/Fisher.Rd | 154 +- man/Haar.Rd | 142 +- man/MCMCSO3.Rd | 166 +-- man/Maxwell.Rd |only man/Mises.Rd | 142 +- man/Q4-class.Rd | 20 man/Q4.Rd | 212 +-- man/SO3-class.Rd | 22 man/SO3.Rd | 218 ++-- man/UARS.Rd | 172 +-- man/bayes.mean.Rd | 188 +-- man/bayesCR.Rd | 186 +-- man/cayley.kappa.Rd | 84 - man/center.Rd | 88 - man/chang.Rd | 122 +- man/discord.Rd | 104 - man/drill.Rd | 114 +- man/fisher.kappa.Rd | 85 - man/fisheretal.Rd | 134 +- man/genR.Rd | 92 - man/gradient.search.Rd | 98 - man/log.SO3.Rd | 86 - man/maxwell.kappa.Rd |only man/mean.SO3.Rd | 166 +-- man/median.SO3.Rd | 152 +- man/mis.angle.Rd | 108 +- man/mis.axis.Rd | 116 +- man/nickel.Rd | 120 +- man/plot.SO3.Rd | 182 +-- man/pointsXYZ.Rd | 68 - man/prentice.Rd | 118 +- man/project.SO3.Rd | 88 - man/region.Rd | 140 +- man/rot.dist.Rd | 132 +- man/rotations.Rd | 30 man/rotdist.sum.Rd | 130 +- man/skew.exp.Rd | 68 - man/vmises.kappa.Rd | 85 - man/weighted.mean.SO3.Rd | 168 +-- man/zhang.Rd | 122 +- src/CppBayesFunctions.cpp | 106 + src/Makevars.win | 12 src/RcppExports.cpp | 649 ++++-------- src/basics.cpp | 1 tests/test-all.R | 2 tests/testthat/test_arithmetic.R | 78 - tests/testthat/test_basics.R | 90 - tests/testthat/test_conversions.R | 40 tests/testthat/test_discord.R | 28 tests/testthat/test_estimators.R | 60 - tests/testthat/test_metrics.R | 24 vignettes/RJournal_edited.sty | 670 ++++++------ vignettes/rotations-intro.Rnw | 732 ++++++------- vignettes/stanfill-hofmann-genschel.bib | 754 +++++++------- 84 files changed, 10304 insertions(+), 10118 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in NeXML format. The
package should add new functionality to R such as the possibility to
manipulate NeXML objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.3 dated 2015-05-26 and 2.0.4 dated 2015-10-14
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ NEWS | 5 +++++ R/add_basic_meta.R | 2 ++ R/classes.R | 3 ++- R/get_characters.R | 11 ++++++----- R/simmap.R | 4 ++++ build/vignette.rds |binary tests/testthat/test_publish.R | 7 ++++++- tests/testthat/test_rdf.R | 2 ++ 11 files changed, 44 insertions(+), 20 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.4 dated 2015-10-01 and 0.0.5 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Aggregate.R | 2 +- R/create_infotables.R | 1 + inst/doc/Information-vignette.html | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.0 dated 2015-10-07 and 1.5.1 dated 2015-10-14
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 11 +++++++++-- R/idendro.R | 40 ++++++++++++++++++++++++++++++---------- README.md | 4 ++-- demo/idendroWithGgobi.R | 1 - man/idendr0-package.Rd | 7 ++++--- man/idendro.Rd | 3 +-- 8 files changed, 59 insertions(+), 32 deletions(-)
Title: Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
Description: We consider studies in which information from error-prone
diagnostic tests or self-reports are gathered sequentially to determine the
occurrence of a silent event. Using a likelihood-based approach
incorporating the proportional hazards assumption, we provide functions to
estimate the survival distribution and covariate effects. We also provide
functions for power and sample size calculations for this setting.
Author: Xiangdong Gu and Raji Balasubramanian
Maintainer: Xiangdong Gu <ustcgxd@gmail.com>
Diff between icensmis versions 1.2.1 dated 2014-06-27 and 1.3.0 dated 2015-10-14
DESCRIPTION | 15 MD5 | 30 + NAMESPACE | 11 R/HighDimCR.R | 20 - R/RcppExports.R | 16 R/datasim.R | 27 + R/icpower.R | 221 +++++-------- README.md |only man/datasim.Rd | 11 man/icmis.Rd | 3 man/icpower.Rd | 10 man/icpower.val.Rd | 3 man/icpowerpf.Rd | 3 src/HighDimCR.cpp | 24 - src/RcppExports.cpp | 878 +++++++++++++++++++++++----------------------------- src/powerfuncs.cpp |only tests |only 17 files changed, 594 insertions(+), 678 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.2 dated 2015-05-11 and 1.3 dated 2015-10-14
DESCRIPTION | 9 ++-- MD5 | 74 +++++++++++++++++----------------- NAMESPACE | 6 ++ R/Calc_Hepatic_Clearance.r | 2 R/Calc_ratioblood2plasma.R | 2 R/Calc_volume_of_distribution.R | 59 ++++++++++++++++++++------- R/Export_PBTK_Jarnac.R | 26 +++++------ R/Export_PBTK_SBML.R | 24 +++++------ R/Get_lumped_tissues.R | 32 +++++++++----- R/Parameterize_PBTK.r | 44 ++++++-------------- R/Predict_partitioning_Schmitt.R | 17 +++---- R/add_chemtable.R | 6 +- R/calc_analytic_css.R | 14 +++--- R/calc_css.R | 47 +++++++++++++-------- R/get_Wetmore_Css.R | 17 +++++-- R/get_Wetmore_Oral_Equiv.R | 5 +- R/get_chem_id.R | 1 R/get_cheminfo.R | 1 R/in.list.R |only R/ionization_functions.R | 17 +++++-- R/solve_3comp.R | 7 +-- R/solve_pbtk.R | 5 +- data/Tables.RData |binary man/Parameterize_PBTK.Rd | 12 ++--- man/Wetmore.data.Rd | 2 man/Wetmore_Css.Rd | 2 man/Wetmore_Oral_Equiv.Rd | 9 ++++ man/calc_analytic_css.Rd | 2 man/calc_css.Rd | 10 ++-- man/calc_ionization.Rd |only man/chem.lists.Rd |only man/chem_physical_and_invitro_data.Rd | 3 + man/get_cheminfo.Rd | 29 +++++++++++++ man/get_wetmore_cheminfo.Rd | 7 +++ man/in_list.Rd |only man/parameterize_3comp.Rd | 8 +-- man/solve_3comp_pbpk.Rd | 2 man/solve_pbtk.Rd | 2 tests/cheminfo_test.Rout.save | 22 +++++----- tests/other_tests.Rout.save | 64 ++++++++++++++--------------- 40 files changed, 352 insertions(+), 237 deletions(-)
Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doParallel versions 1.0.8 dated 2014-02-28 and 1.0.10 dated 2015-10-14
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 4 +++- R/doParallel.R | 9 ++++++--- build/vignette.rds |binary inst/doc/gettingstartedParallel.pdf |binary 7 files changed, 31 insertions(+), 18 deletions(-)
Title: Foreach Parallel Adaptor for the 'snow' Package
Description: Provides a parallel backend for the %dopar% function using
Luke Tierney's snow package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Stephen Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doSNOW versions 1.0.12 dated 2014-03-13 and 1.0.14 dated 2015-10-14
DESCRIPTION | 22 ++++++---- MD5 | 8 +-- NAMESPACE | 1 R/doSNOW.R | 102 +++++++++++++++++++++++++++++++++++++++++++++----- man/registerDoSNOW.Rd | 1 5 files changed, 113 insertions(+), 21 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.2.8 dated 2015-08-26 and 0.2.9 dated 2015-10-14
DESCRIPTION | 12 - MD5 | 68 +++++---- NAMESPACE | 1 NEWS | 20 ++ R/generic.R | 72 ++++++++++ R/kde.R | 331 +++++++++++++++++++++++++++++++++++------------- R/krige.R | 151 +++++++++++++++++++++ R/likelihood.R | 95 +++++++++---- R/periodogram.R | 186 ++++++++++++++++++++++++-- R/telemetry.R | 116 ++++++++++++---- R/variogram.R | 124 ++++++++++++----- TODO | 27 ++- build/vignette.rds |binary data/gazelle.rda |only inst/doc/akde.html | 14 +- inst/doc/variogram.R | 50 +++++-- inst/doc/variogram.Rmd | 63 ++++++--- inst/doc/variogram.html | 83 +++++++----- man/akde.Rd | 20 +- man/akde.bandwidth.Rd | 7 - man/as.telemetry.Rd | 3 man/buffalo.Rd | 4 man/ctmm-package.Rd | 4 man/ctmm.fit.Rd | 7 - man/ctmm.loglike.Rd | 2 man/export.Rd | 6 man/gazelle.Rd |only man/mean.variogram.Rd | 6 man/periodogram.Rd | 25 ++- man/plot.variogram.Rd | 4 man/simulate.ctmm.Rd | 2 man/summary.akde.Rd | 8 - man/summary.ctmm.Rd | 2 man/variogram.Rd | 14 +- man/variogram.fit.Rd | 6 vignettes/variogram.Rmd | 63 ++++++--- 36 files changed, 1196 insertions(+), 400 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-23 0.7-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-15 0.5-4
2014-05-19 0.5-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-25 0.94
2014-03-07 0.93
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-24 1.54
2012-04-24 1.53
2012-04-19 1.52
2011-11-23 1.50
2011-09-24 1.49
2011-09-02 1.48
2011-08-12 1.47
2011-08-10 1.46
2011-07-23 1.45
2011-06-01 1.44
2011-05-16 1.43
2011-03-31 1.42
2011-02-28 1.41
2011-02-18 1.31.1
2010-12-12 1.31
2010-11-08 1.3
2010-09-22 1.2
2010-08-17 1.01
2010-06-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-28 1.3
2014-01-11 1.2
2013-12-08 1.1
2013-10-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-14 1.1
2013-06-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-19 1.1
2015-02-03 1.0
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Lord & Barton's four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2015).
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0 dated 2015-10-12 and 1.0.1 dated 2015-10-13
fourPNO-1.0.1/fourPNO/DESCRIPTION | 6 +++--- fourPNO-1.0.1/fourPNO/MD5 | 18 +++++++++--------- fourPNO-1.0.1/fourPNO/R/RcppExports.R | 18 +++++++++--------- fourPNO-1.0.1/fourPNO/man/Gibbs_2PNO.Rd | 6 +++--- fourPNO-1.0.1/fourPNO/man/Gibbs_4PNO.Rd | 8 ++++---- fourPNO-1.0.1/fourPNO/man/Y_4pno_simulate.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/man/min2LL_4pno.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/man/update_WKappaZ_NA.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/src/RcppExports.cpp | 24 ++++++++++++------------ fourPNO-1.0.1/fourPNO/src/fourpno_101315.cpp |only fourPNO-1.0/fourPNO/src/fourpno_012915.cpp |only 11 files changed, 46 insertions(+), 46 deletions(-)
Title: Learning Causal Cyclic Graphs from Unknown Shift Interventions
Description: Code for 'backShift', an algorithm to estimate the connectivity
matrix of a directed (possibly cyclic) graph with hidden variables. The
underlying system is required to be linear and we assume that observations
under different shift interventions are available. For more details,
see <http://arxiv.org/abs/1506.02494>.
Author: Christina Heinze <heinze@stat.math.ethz.ch>
Maintainer: Christina Heinze <heinze@stat.math.ethz.ch>
Diff between backShift versions 0.1.2 dated 2015-08-19 and 0.1.3 dated 2015-10-13
DESCRIPTION | 10 +- MD5 | 16 ++-- R/checkDiagonalization.R | 14 ++- R/computeVarEnv.R | 3 R/plotGraph.R | 146 ++++++++++++++++++++--------------------- R/simulate.R | 2 inst/doc/exampleBackShift.html | 2 man/plotDiagonalization.Rd | 4 - tests |only 9 files changed, 103 insertions(+), 94 deletions(-)
Title: Analysis of Means
Description: Analysis of means (ANOM) as used in technometrical computing. The package takes results from multiple comparisons with the grand mean (obtained with 'multcomp', 'SimComp', 'nparcomp', or 'MCPAN') or corresponding simultaneous confidence intervals as input and produces ANOM decision charts that illustrate which group means deviate significantly from the grand mean.
Author: Philip Pallmann
Maintainer: Philip Pallmann <p.pallmann@lancaster.ac.uk>
Diff between ANOM versions 0.4 dated 2015-08-14 and 0.4.2 dated 2015-10-13
ANOM-0.4.2/ANOM/DESCRIPTION | 10 +++++----- ANOM-0.4.2/ANOM/MD5 | 11 +++++------ ANOM-0.4.2/ANOM/R/ANOM.R | 2 ++ ANOM-0.4.2/ANOM/R/ANOMgen.R | 1 + ANOM-0.4.2/ANOM/inst/NEWS | 12 ++++++++++++ ANOM-0.4.2/ANOM/inst/doc/ANOM.pdf |binary ANOM-0.4/ANOM/inst/CITATION |only 7 files changed, 25 insertions(+), 11 deletions(-)
Title: Sparse Learning Algorithms Using a LASSO-Type Penalty for
Coefficient Estimation and Model Prediction
Description: Coefficient estimation and model prediction based on
the LASSO sparse learning algorithm and its improved versions
such as Bolasso, bootstrap ranking LASSO, two-stage hybrid LASSO
and others. These estimation procedures are applied in the fields
of variable selection, graphical modeling and forecasting.
Author: Pi Guo, Yuantao Hao
Maintainer: Pi Guo <guopi.01@163.com>
Diff between SparseLearner versions 1.0 dated 2015-10-10 and 1.0.1 dated 2015-10-13
SparseLearner-1.0.1/SparseLearner/DESCRIPTION | 17 ++-- SparseLearner-1.0.1/SparseLearner/MD5 | 20 ++--- SparseLearner-1.0.1/SparseLearner/NAMESPACE | 2 SparseLearner-1.0.1/SparseLearner/R/BRLasso.R | 18 ++--- SparseLearner-1.0.1/SparseLearner/R/Bolasso.R | 16 ++-- SparseLearner-1.0.1/SparseLearner/R/Sparse.graph.R |only SparseLearner-1.0.1/SparseLearner/R/TSLasso.R | 20 +++-- SparseLearner-1.0.1/SparseLearner/man/BRLasso.Rd | 57 ++++++++++++---- SparseLearner-1.0.1/SparseLearner/man/Bolasso.Rd | 45 ++++++++---- SparseLearner-1.0.1/SparseLearner/man/Sparse.graph.Rd |only SparseLearner-1.0.1/SparseLearner/man/TSLasso.Rd | 64 ++++++++++++------ SparseLearner-1.0/SparseLearner/R/SGraph.R |only SparseLearner-1.0/SparseLearner/man/SGraph.Rd |only 13 files changed, 172 insertions(+), 87 deletions(-)
Title: Inference and Analysis for Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic diffusion processes for both scalar and bivariate diffusion systems. For scalar diffusions, a module is provided for solving first passage time problems for both time-homogeneous and time-inhomogeneous GQDs.
Author: Etienne A.D. Pienaar [aut, cre],
Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>
Diff between DiffusionRgqd versions 0.1.0 dated 2015-10-12 and 0.1.1 dated 2015-10-13
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 5 data/SDEsim1.txt | 800 +++++++++++++++++++++---------------------- man/DiffusionRgqd-package.Rd | 10 man/GQD.aic.Rd | 2 man/GQD.dic.Rd | 21 - man/GQD.estimates.Rd | 10 man/GQD.mcmc.Rd | 10 man/GQD.mle.Rd | 8 man/SDEsim1.Rd | 6 11 files changed, 441 insertions(+), 457 deletions(-)
Title: Functions and Methods for Correspondence Regression
Description: A collection of tools for correspondence regression, i.e. the
correspondence analysis of the crosstabulation of a categorical variable Y
in function of another one X, where X can in turn be made up of the
combination of various categorical variables. Consequently, correspondence
regression can be used to analyze the effects for a polytomous or
multinomial outcome variable.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between corregp versions 0.1.3 dated 2015-09-07 and 0.1.4 dated 2015-10-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/corregp.r | 1 - inst/CITATION | 4 ++-- man/plot3d.corregp.Rd | 1 - 5 files changed, 10 insertions(+), 12 deletions(-)
Title: Methods to Analyse Ring Re-Encounter Data
Description: R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to http://www.tandfonline.com/doi/full/10.1080/03078698.2014.933053.
Author: Fraenzi Korner-Nievergelt, Rob Robinson
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@vogelwarte.ch>
Diff between birdring versions 1.2 dated 2014-09-24 and 1.3 dated 2015-10-13
DESCRIPTION | 14 +++++++------- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 7 +++++++ R/bootci.dc.r | 9 +-------- R/critical.check.ringing.event.r |only R/dayofyear.R | 1 - R/dc.r | 8 +------- R/decimal.coord.r | 2 +- R/loxodrom.dir.r | 6 +++--- R/loxodrom.dist.r | 2 +- R/mercatorlat.R | 2 +- R/overlap.r | 36 ++++++++++++++++++++++++++++-------- R/read.euring2000.r | 2 +- R/read.euring2000plus.r | 2 +- man/birdring-package.Rd | 3 ++- man/critical.check.ringing.event.Rd |only man/loxodrom.dir.Rd | 8 ++++---- man/orthodrom.dist.Rd | 8 ++++---- man/overlap.Rd | 28 +++++++++++++++++++++++++--- man/read.euring2000plus.rd | 4 ++-- 20 files changed, 108 insertions(+), 70 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.1 dated 2015-08-05 and 0.3.3 dated 2015-10-13
DESCRIPTION | 15 +-- MD5 | 63 ++++++------ R/convertDVH.R | 228 +++++++++++++++++++++++++++++----------------- R/dvhDistance.R | 3 R/getDMEAN.R | 74 ++++++++------ R/getMetric.R | 37 +++---- R/parseCadplan.R | 64 +++++++++--- R/parseEclipse.R | 55 ++++++++--- R/parseHiArt.R | 4 R/parseMasterplan.R | 9 - R/parseMonaco.R | 7 - R/parsePinnacleDVH.R | 28 +++-- R/parseRayStation.R |only R/readDVH.R | 7 - R/showDVH.R | 15 --- R/smoothDVH.R | 69 ++++++++++--- R/unix/parseDVH.R | 6 + R/windows/parseDVH.R | 6 + inst/ChangeLog | 20 +++- inst/DVHshiny/ABOUT.md | 4 inst/DVHshiny/server.R | 3 inst/DVHshiny/ui.R | 3 inst/doc/DVHmetrics.Rnw | 4 inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 2 inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 man/convertDVH.Rd | 6 - man/getDMEAN.Rd | 13 +- man/readDVH.Rd | 8 + man/showDVH.Rd | 2 vignettes/DVHmetrics.Rnw | 4 vignettes/DVHshiny.Rnw | 2 33 files changed, 485 insertions(+), 280 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-24 1.0.1
2015-09-22 1.0.0
Title: Stochastic Mortality Modelling
Description: Implementation of the family of generalised age-period-cohort
stochastic mortality models. This family of models encompasses many models
proposed in the actuarial and demographic literature including the Lee-Carter model
and the Cairns-Blake-Dowd model. It includes functions for fitting mortality models,
analysing their goodness-of-fit and performing mortality projections and
simulations.
Author: Andres Villegas <andresmauriciovillegas@gmail.com>,
Pietro Millossovich <Pietro.Millossovich.1@city.ac.uk>,
Vladimir Kaishev <Vladimir.Kaishev.1@city.ac.uk>
Maintainer: Andres Villegas <andresmauriciovillegas@gmail.com>
Diff between StMoMo versions 0.2.0 dated 2015-06-10 and 0.3.0 dated 2015-10-13
DESCRIPTION | 6 MD5 | 37 NAMESPACE | 29 R/docStMoMo.R | 5 R/fitStMoMo.R | 8 R/forecastfitStMoMo.R | 53 + R/simulatebootStMoMo.R | 9 R/simulatefitStMoMo.R | 13 README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/StMoMoVignette.R | 5 inst/doc/StMoMoVignette.Rnw | 88 +- inst/doc/StMoMoVignette.pdf |binary man/fit.StMoMo.Rd | 8 man/forecast.fitStMoMo.Rd | 40 + man/simulate.bootStMoMo.Rd | 15 man/simulate.fitStMoMo.Rd | 15 vignettes/StMoMoVignette.Rnw | 88 +- vignettes/elsarticle.cls | 1618 +++++++++++++++++++++---------------------- 20 files changed, 1108 insertions(+), 931 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert <sievert@iastate.edu>
Maintainer: Carson Sievert <sievert@iastate.edu>
Diff between pitchRx versions 1.7 dated 2015-04-04 and 1.8 dated 2015-10-13
DESCRIPTION | 7 +- MD5 | 46 ++++++++--------- NAMESPACE | 11 +++- NEWS | 6 ++ R/animateFX.R | 38 +++++++------- R/help.R | 5 + R/scrape.R | 132 +++++++++++++++++++++++++------------------------ data/gids.rda |binary man/animateFX.Rd | 42 ++++++--------- man/export.Rd | 27 +++------- man/fields.Rd | 9 +-- man/getSnapshots.Rd | 13 +--- man/gids.Rd | 5 - man/interactiveFX.Rd | 21 +++---- man/makeUrls.Rd | 19 ++----- man/nonMLBgids.Rd | 5 - man/pitchRx.Rd | 2 man/pitches.Rd | 5 - man/players.Rd | 11 +--- man/scrape.Rd | 72 ++++++++------------------ man/scrapeFX.Rd | 10 +-- man/strikeFX.Rd | 67 ++++++++---------------- man/update_db.Rd | 16 ++--- man/urlsToDataFrame.Rd | 15 +---- 24 files changed, 259 insertions(+), 325 deletions(-)
Title: Compute the Top Decile Lift and Plot the Lift Curve
Description: Compute the top decile lift and plot the lift curve. Cumulative lift curves are also supported.
Author: Steven Hoornaert, Michel Ballings, Dirk Van den Poel
Maintainer: Steven Hoornaert <Steven.Hoornaert@UGent.be>
Diff between lift versions 0.0.1 dated 2015-10-01 and 0.0.2 dated 2015-10-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plotLift.R | 2 +- inst/NEWS | 5 ++++- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Provides Iterator Construct for R
Description: Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection
of data.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between iterators versions 1.0.7 dated 2014-04-11 and 1.0.8 dated 2015-10-13
DESCRIPTION | 21 +++++++++++++-------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/iterators.pdf |binary inst/doc/writing.pdf |binary 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Provides Foreach Looping Construct for R
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation
of a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between foreach versions 1.4.2 dated 2014-04-11 and 1.4.3 dated 2015-10-13
DESCRIPTION | 21 +++++++++++++-------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/foreach.pdf |binary inst/doc/nested.pdf |binary 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Foreach Parallel Adaptor for 'parallel'
Description: Provides a parallel backend for the %dopar% function using
the multicore functionality of the parallel package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doMC versions 1.3.3 dated 2014-02-28 and 1.3.4 dated 2015-10-13
DESCRIPTION | 23 ++++++++++++++--------- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/gettingstartedMC.pdf |binary 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Create Graph Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Andrei Kashcha [aut, cph] (vivagraphjs library in htmlwidgets/lib,
https://github.com/anvaka/VivaGraphJS),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.8 dated 2015-10-08 and 0.8.1 dated 2015-10-13
DiagrammeR-0.8.1/DiagrammeR/DESCRIPTION | 10 +-- DiagrammeR-0.8.1/DiagrammeR/MD5 | 31 +++------ DiagrammeR-0.8.1/DiagrammeR/NAMESPACE | 6 - DiagrammeR-0.8.1/DiagrammeR/R/combine_graphs.R | 3 DiagrammeR-0.8.1/DiagrammeR/R/grViz.R | 32 ---------- DiagrammeR-0.8.1/DiagrammeR/R/render_graph.R | 14 ---- DiagrammeR-0.8.1/DiagrammeR/R/visnetwork.R | 5 + DiagrammeR-0.8.1/DiagrammeR/README.md | 2 DiagrammeR-0.8.1/DiagrammeR/man/combine_graphs.Rd | 3 DiagrammeR-0.8.1/DiagrammeR/man/grViz.Rd | 32 ---------- DiagrammeR-0.8.1/DiagrammeR/man/render_graph.Rd | 5 - DiagrammeR-0.8/DiagrammeR/R/graphviz_export.R |only DiagrammeR-0.8/DiagrammeR/R/roll_palette.R |only DiagrammeR-0.8/DiagrammeR/R/scale_edges.R |only DiagrammeR-0.8/DiagrammeR/R/scale_nodes.R |only DiagrammeR-0.8/DiagrammeR/man/exportSVG.Rd |only DiagrammeR-0.8/DiagrammeR/man/roll_palette.Rd |only DiagrammeR-0.8/DiagrammeR/man/scale_edges.Rd |only DiagrammeR-0.8/DiagrammeR/man/scale_nodes.Rd |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-export_SVG.R |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-roll_palette.R |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-scale_nodes_edges.R |only 22 files changed, 33 insertions(+), 110 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.3 dated 2015-08-11 and 0.9.4 dated 2015-10-12
DESCRIPTION | 16 +-- MD5 | 47 ++++---- NAMESPACE | 2 R/CommonFG.R | 28 +++++ R/H5File.R | 99 +++++++++++++++--- R/H5Group.R | 6 - R/H5Location-Attribute.R | 14 +- R/RcppExports.R | 12 +- inst/NEWS.Rd | 13 ++ inst/test-f32.h5 |only inst/test-f32.py |only man/CommonFG.Rd | 8 + man/H5File.Rd | 96 +++++++++++++++--- src/Attribute.cpp | 56 +++++++++- src/Attribute.h | 4 src/Dataset.cpp | 9 - src/Group.cpp | 29 +---- src/Group.h | 3 src/Helpers.cpp | 192 +++++++++++++++++++----------------- src/RcppExports.cpp | 31 +++++ tests/testthat/test-Attribute.R | 44 ++++++++ tests/testthat/test-DataSet-IO-NA.R |only tests/testthat/test-DataSet.R | 17 +++ tests/testthat/test-H5File.R | 16 +++ tests/testthat/test-H5Group.R | 69 ++++++++++++ tests/testthat/test-vlen.R | 47 ++++++++ 26 files changed, 660 insertions(+), 198 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.6.0 dated 2015-08-03 and 1.0.6.1 dated 2015-10-12
DESCRIPTION | 10 +- MD5 | 53 ++++++------ NEWS | 10 ++ R/coord-tern.R | 39 ++------- R/data.R | 8 + R/geom-confidence.R | 59 +++++++------- R/gg-internal.R | 1 R/ggtern-build.R | 1 R/onLoad.R | 4 R/scales.R | 26 ++++-- R/stat-interpolate-tern.R | 10 ++ R/tern-render.R | 59 ++++++++------ R/theme-defaults.R | 180 +++++++++++++++++++++++++------------------- R/theme-elements.R | 5 - R/theme-noarrows.R | 4 R/utilities.R | 37 ++++++++- README.md | 3 build/partial.rdb |binary data/Feldspar.RData |binary man/coord_tern.Rd | 5 - man/data_Feldspar.Rd | 11 +- man/getBreaks.Rd |only man/scale_TLR_continuous.Rd | 26 +++--- man/theme_custom.Rd | 9 +- man/theme_elements.Rd | 1 man/theme_gray.Rd | 1 man/theme_rgbw.Rd | 4 man/themeshowhidearrows.Rd | 4 28 files changed, 335 insertions(+), 235 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.2 dated 2015-08-28 and 1.3 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GEE.var.mbn.R | 2 +- man/GEE.var.mbn.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate. The analysis of paired
receiver operating curves is supported as well, so that a comparison of two predictors is possible.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.3.0 dated 2015-10-08 and 0.3.1 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fbroc.methods.R | 6 ++++-- man/plot.fbroc.roc.Rd | 2 ++ 4 files changed, 14 insertions(+), 10 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen, Chuan Hong, Haitao Chu
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.0 dated 2015-10-02 and 1.0-1 dated 2015-10-12
DESCRIPTION | 16 ++++++++-------- MD5 | 8 +++++--- NAMESPACE | 2 +- R/galaxy.R |only man/galaxy.Rd |only man/xmeta-package.Rd | 3 ++- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.7 dated 2015-09-09 and 0.7-1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ inst/gemtc.randomeffects.txt | 2 +- 4 files changed, 15 insertions(+), 8 deletions(-)
More information about batteryreduction at CRAN
Permanent link
Title: Bayesian Network Feature Finder
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan <zlan6@gatech.edu>
Diff between BANFF versions 0.3 dated 2015-02-16 and 1.0 dated 2015-10-12
BANFF-0.3/BANFF/R/All_functions.R |only BANFF-0.3/BANFF/R/main.R |only BANFF-1.0/BANFF/DESCRIPTION | 9 +-- BANFF-1.0/BANFF/MD5 | 43 ++++++++++++++- BANFF-1.0/BANFF/NAMESPACE | 74 ++++++++++++++------------- BANFF-1.0/BANFF/R/DPM.HODC.R |only BANFF-1.0/BANFF/R/DPdensitycluster.R |only BANFF-1.0/BANFF/R/EM.HODC.R |only BANFF-1.0/BANFF/R/Generating_Zi.R |only BANFF-1.0/BANFF/R/Gibbsfortheta.R |only BANFF-1.0/BANFF/R/Grid.Adjmatrix.Transfer.R |only BANFF-1.0/BANFF/R/HODCMclust.R |only BANFF-1.0/BANFF/R/HyperPara.Select.R |only BANFF-1.0/BANFF/R/Initial_mu_var.R |only BANFF-1.0/BANFF/R/Innerfunc.R |only BANFF-1.0/BANFF/R/Inte_Distance.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity_Par.R |only BANFF-1.0/BANFF/R/Iteration3_Mclust.R |only BANFF-1.0/BANFF/R/Kmeans.R |only BANFF-1.0/BANFF/R/LikelihoodHistory.R |only BANFF-1.0/BANFF/R/Mixture.R |only BANFF-1.0/BANFF/R/Model.R |only BANFF-1.0/BANFF/R/Networks.Fast.R |only BANFF-1.0/BANFF/R/Networks.STD.R |only BANFF-1.0/BANFF/R/Parameter_Define.R |only BANFF-1.0/BANFF/R/Pi_rho_gen.R |only BANFF-1.0/BANFF/R/Pi_rho_selecting.R |only BANFF-1.0/BANFF/R/Plot.Subnetwork.R |only BANFF-1.0/BANFF/R/Step1_1_Update_gi_zi.R |only BANFF-1.0/BANFF/R/Step1_2_Check.R |only BANFF-1.0/BANFF/R/Step_2_Update_mu_var.R |only BANFF-1.0/BANFF/R/Step_3_switch_the_label.R |only BANFF-1.0/BANFF/R/Subnetwork.Select.R |only BANFF-1.0/BANFF/R/SummaryAccuracy.R |only BANFF-1.0/BANFF/R/TPR.R |only BANFF-1.0/BANFF/R/Transfer.R |only BANFF-1.0/BANFF/R/biGaussian.R |only BANFF-1.0/BANFF/R/plot.Networks.Fast.R |only BANFF-1.0/BANFF/R/plot.Networks.STD.R |only BANFF-1.0/BANFF/R/summary.Networks.Fast.R |only BANFF-1.0/BANFF/R/summary.Networks.STD.R |only 42 files changed, 83 insertions(+), 43 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.4 dated 2015-10-09 and 1.5 dated 2015-10-12
DESCRIPTION | 9 ++++---- MD5 | 6 ++--- R/barnardw.test.R | 57 ++++++++++++++++++++++++++++++--------------------- man/barnardw.test.Rd | 26 +++++++++++------------ 4 files changed, 55 insertions(+), 43 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 1.0.0 dated 2015-05-15 and 1.0.1 dated 2015-10-12
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 14 +++++++++++++- NEWS | 9 ++++++++- R/VSURF.R | 16 ++++++++-------- R/VSURF_interp.R | 18 +++++++----------- R/VSURF_pred.R | 2 +- R/VSURF_thres.R | 27 ++++++++++++--------------- R/plot.VSURF.R | 1 + man/VSURF.Rd | 6 +++--- man/VSURF_interp.Rd | 4 ++-- man/VSURF_thres.Rd | 5 +++-- tests |only 13 files changed, 78 insertions(+), 59 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.3 dated 2015-08-26 and 1.8.4 dated 2015-10-12
DESCRIPTION | 8 MD5 | 58 NAMESPACE | 1 NEWS | 1290 +++++++------- R/helpfunctions.R | 1555 ++++++++--------- R/sjPlotAnova.R | 2 R/sjPlotFrequencies.R | 14 R/sjPlotGLME.R | 4231 +++++++++++++++++++++++------------------------ R/sjPlotInteractions.R | 2967 ++++++++++++++++---------------- R/sjPlotLinreg.R | 9 R/sjPlotLinregMultiple.R | 6 R/sjPlotPCA.R | 2 R/sjTabCorr.R | 1020 +++++------ R/sjTabDataFrame.R | 3 R/sjTabFrequencies.R | 2 R/sjTabItemAnalysis.R | 13 R/sjTabLinReg.R | 3062 +++++++++++++++++----------------- R/sjTabOdds.R | 2720 +++++++++++++++--------------- R/sjTabPCA.R | 1188 ++++++------- R/sjTabSPSS.R | 792 ++++---- R/sjTabStackFrq.R | 1038 +++++------ README.md | 36 man/sjPlot-package.Rd | 102 - man/sjp.glmer.Rd | 7 man/sjp.int.Rd | 783 ++++---- man/sjp.lm.Rd | 496 ++--- man/sjp.lmer.Rd | 7 man/sjt.glmer.Rd | 17 man/sjt.lmer.Rd | 17 man/view_df.Rd | 26 30 files changed, 10817 insertions(+), 10655 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/or who are new to R), supporting following common tasks:
1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc.
2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values.
3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.1 dated 2015-08-26 and 1.2 dated 2015-10-12
DESCRIPTION | 11 - MD5 | 34 +-- NAMESPACE | 1 NEWS | 12 + R/as_labelled.R | 2 R/converge_ok.R |only R/reliab_test.R | 8 R/set_na.R | 461 ++++++++++++++++++++++++-------------------------- R/to_na.R | 136 +++++++------- R/weight.R | 8 README.md | 136 +++++--------- man/as_labelled.Rd | 2 man/converge_ok.Rd |only man/mean_n.Rd | 144 +++++++-------- man/sjmisc-package.Rd | 4 man/std_beta.Rd | 128 ++++++------- man/to_na.Rd | 2 man/weight.Rd | 10 - man/weight2.Rd | 4 19 files changed, 549 insertions(+), 554 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-2 dated 2015-08-23 and 0.1-3 dated 2015-10-12
ChangeLog | 1066 ---------------------------------------------------------- DESCRIPTION | 8 MD5 | 6 R/vect_link.R | 91 ++-- 4 files changed, 52 insertions(+), 1119 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 0.11 dated 2015-09-10 and 0.12 dated 2015-10-12
DESCRIPTION | 8 MD5 | 146 ++- NAMESPACE | 31 R/Clustering.R | 3 R/aggregatingAux.R | 10 R/aggregatingMeta.R | 21 R/cdist.R | 70 + R/do.R | 370 ++++++---- R/dotPlot.R | 5 R/dpqrdist.R | 32 R/favstats.R | 5 R/frequencyPolygon.R | 2 R/groupwiseModels.R |only R/integrateODE.R | 1 R/makeFun.R | 6 R/maps2.R | 9 R/mm.R | 148 ---- R/mosaic-package.R | 2 R/mplot.R | 44 - R/plotModel.R | 195 +++-- R/resample.R | 57 - R/statTally.R | 4 R/xpnorm.R | 38 - build/vignette.rds |binary inst/doc/GraphicsWithMosaic.html | 38 - inst/doc/LessVolume-MoreCreativity.Rmd | 6 inst/doc/LessVolume-MoreCreativity.html | 14 inst/doc/MinimalR.pdf |binary inst/doc/Resampling.R | 2 inst/doc/Resampling.Rnw | 2 inst/doc/Resampling.pdf |binary inst/doc/mosaic-resources.html | 4 inst/doc/plotModel-vignette.R |only inst/doc/plotModel-vignette.Rmd |only inst/doc/plotModel-vignette.html |only man/MSPE.Rd |only man/aggregating.Rd | 3 man/cdist.Rd | 23 man/cull_for_do.Rd |only man/do.Rd | 5 man/dotPlot.Rd | 2 man/freqpolygon.Rd | 2 man/gwm.Rd |only man/makeFun.Rd | 4 man/mm.Rd | 51 - man/mosaic-internal.Rd | 7 man/mplot.Rd | 12 man/nicenames.Rd | 4 man/plotModel.Rd | 9 man/pqrdata2.Rd | 15 man/qdist.Rd | 16 man/resample.Rd | 2 tests/testthat/test-aggregating.R | 11 tests/testthat/test-do.R |only tests/testthat/test-groupwiseModels.R | 34 vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-8-2.png |binary vignettes/LessVolume-MoreCreativity.Rmd | 6 vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-50-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-51-1.png |binary vignettes/Resampling.Rnw | 2 vignettes/plotModel-vignette.Rmd |only vignettes/plotModel-vignette_files |only 68 files changed, 785 insertions(+), 696 deletions(-)
Title: Preference Rating for Visual Stimuli Based on Elo Ratings
Description: Allows calculating global scores for characteristics of visual stimuli. Stimuli are presented as sequence of pairwise comparisons ('contests'), during each of which a rater expresses preference for one stimulus over the other. The algorithm for calculating global scores is based on Elo rating, which updates individual scores after each single pairwise contest. Elo rating is widely used to rank chess players according to their performance. Its core feature is that dyadic contests with expected outcomes lead to smaller changes of participants' scores than outcomes that were unexpected. As such, Elo rating is an efficient tool to rate individual stimuli when a large number of such stimuli are paired against each other in the context of experiments where the goal is to rank stimuli according to some characteristic of interest.
Author: Christof Neumann
Maintainer: Christof Neumann <christofneumann1@gmail.com>
Diff between EloChoice versions 0.28 dated 2015-10-11 and 0.29 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/NEWS.Rd | 6 ++++++ inst/doc/tutorial.Rnw | 2 +- inst/doc/tutorial.pdf |binary man/EloChoice-package.Rd | 4 ++-- src/eloint.cpp | 41 +++++++++++++++++------------------------ vignettes/tutorial.Rnw | 2 +- 8 files changed, 38 insertions(+), 39 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.0 dated 2015-04-15 and 6.1 dated 2015-10-12
embryogrowth-6.0/embryogrowth/R/fonctionfit.R |only embryogrowth-6.1/embryogrowth/DESCRIPTION | 12 embryogrowth-6.1/embryogrowth/MD5 | 202 - embryogrowth-6.1/embryogrowth/NAMESPACE | 9 embryogrowth-6.1/embryogrowth/NEWS | 32 embryogrowth-6.1/embryogrowth/R/ChangeSSM.R | 8 embryogrowth-6.1/embryogrowth/R/Exponential.R | 2 embryogrowth-6.1/embryogrowth/R/FormatNests.R | 40 embryogrowth-6.1/embryogrowth/R/GRTRN_MHmcmc.R | 32 embryogrowth-6.1/embryogrowth/R/GenerateTest.R | 3 embryogrowth-6.1/embryogrowth/R/Gompertz.R | 2 embryogrowth-6.1/embryogrowth/R/Linear.R | 2 embryogrowth-6.1/embryogrowth/R/MovingIncubation.R | 337 -- embryogrowth-6.1/embryogrowth/R/SSM.R | 6 embryogrowth-6.1/embryogrowth/R/STRN_MHmcmc.R | 19 embryogrowth-6.1/embryogrowth/R/STRN_fit.R | 2 embryogrowth-6.1/embryogrowth/R/TRN_MHmcmc_p.R | 22 embryogrowth-6.1/embryogrowth/R/TSP.list.R |only embryogrowth-6.1/embryogrowth/R/embryogrowth-package.R | 12 embryogrowth-6.1/embryogrowth/R/fonctionMCMC.R | 6 embryogrowth-6.1/embryogrowth/R/gradientRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hessianRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hist.Nests.R | 6 embryogrowth-6.1/embryogrowth/R/hist.NestsResult.R | 7 embryogrowth-6.1/embryogrowth/R/info.nests.R | 952 +++++-- embryogrowth-6.1/embryogrowth/R/likelihoodR.R | 10 embryogrowth-6.1/embryogrowth/R/modelTSD.R | 5 embryogrowth-6.1/embryogrowth/R/plot.NestsResult.R | 1275 +--------- embryogrowth-6.1/embryogrowth/R/plot.tsd.R | 4 embryogrowth-6.1/embryogrowth/R/plotR.R | 14 embryogrowth-6.1/embryogrowth/R/plotR_hist.R | 36 embryogrowth-6.1/embryogrowth/R/plot_transition.R | 4 embryogrowth-6.1/embryogrowth/R/resultNest_4p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_4p_weight.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_6p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_newp.R | 8 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p.R | 4 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p_weight.R | 9 embryogrowth-6.1/embryogrowth/R/result_mcmc_6p.R | 2 embryogrowth-6.1/embryogrowth/R/result_mcmc_newp.R | 21 embryogrowth-6.1/embryogrowth/R/searchR.R | 138 - embryogrowth-6.1/embryogrowth/R/summary.Nests.R | 4 embryogrowth-6.1/embryogrowth/R/tempConst.R | 2 embryogrowth-6.1/embryogrowth/R/tsd.R | 47 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc.R | 12 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc_p.R | 11 embryogrowth-6.1/embryogrowth/R/weightmaxentropy.R | 10 embryogrowth-6.1/embryogrowth/data/STSRE_TSD.rda |binary embryogrowth-6.1/embryogrowth/data/TSP.list.rda |only embryogrowth-6.1/embryogrowth/data/resultNest_4p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_6p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_newp.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p_weight.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_6p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_newp.rda |binary embryogrowth-6.1/embryogrowth/man/ChangeSSM.Rd | 10 embryogrowth-6.1/embryogrowth/man/FormatNests.Rd | 2 embryogrowth-6.1/embryogrowth/man/GRTRN_MHmcmc.Rd | 32 embryogrowth-6.1/embryogrowth/man/GenerateAnchor.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateConstInc.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateTest.Rd | 2 embryogrowth-6.1/embryogrowth/man/MovingIncubation.Rd | 43 embryogrowth-6.1/embryogrowth/man/STRN.Rd | 2 embryogrowth-6.1/embryogrowth/man/STRN_MHmcmc.Rd | 9 embryogrowth-6.1/embryogrowth/man/STSRE_NestingArea.Rd | 2 embryogrowth-6.1/embryogrowth/man/STSRE_TSD.Rd | 8 embryogrowth-6.1/embryogrowth/man/TRN_MHmcmc_p.Rd | 8 embryogrowth-6.1/embryogrowth/man/TSP.list.Rd |only embryogrowth-6.1/embryogrowth/man/TestParallel.Rd | 2 embryogrowth-6.1/embryogrowth/man/dydt.Gompertz.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.exponential.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.linear.Rd | 4 embryogrowth-6.1/embryogrowth/man/embryogrowth-package.Rd | 14 embryogrowth-6.1/embryogrowth/man/hist.Nests.Rd | 2 embryogrowth-6.1/embryogrowth/man/hist.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/info.nests.Rd | 86 embryogrowth-6.1/embryogrowth/man/likelihoodR.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/nest.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot.NestsResult.Rd | 105 embryogrowth-6.1/embryogrowth/man/plot.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/plotR.Rd | 6 embryogrowth-6.1/embryogrowth/man/plotR_hist.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot_transition.Rd | 4 embryogrowth-6.1/embryogrowth/man/predict.tsd.Rd | 6 embryogrowth-6.1/embryogrowth/man/resultNest_4p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_4p_transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/resultNest_4p_weight.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_newp.Rd | 10 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p.Rd | 6 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p_weight.Rd | 11 embryogrowth-6.1/embryogrowth/man/result_mcmc_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/result_mcmc_newp.Rd | 23 embryogrowth-6.1/embryogrowth/man/searchR.Rd | 47 embryogrowth-6.1/embryogrowth/man/summary.Nests.Rd | 6 embryogrowth-6.1/embryogrowth/man/switch.transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/tempConst.Rd | 4 embryogrowth-6.1/embryogrowth/man/tsd.Rd | 16 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc.Rd | 6 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc_p.Rd | 6 embryogrowth-6.1/embryogrowth/man/weightmaxentropy.Rd | 4 104 files changed, 1694 insertions(+), 2177 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.2 dated 2015-10-03 and 1.0.3 dated 2015-10-12
DESCRIPTION | 10 +++++----- INSTALL | 2 +- MD5 | 12 ++++++------ inst/doc/compendiumdb.pdf |binary man/compendiumdb-package.Rd | 4 ++-- man/downloadGEOdata.Rd | 2 +- man/loadDatabaseSchema.Rd | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses and geolocating them to country, city, timezone and other geographic ranges. For individual connectors, see the package index.
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 0.4.1 dated 2015-07-25 and 0.5.0 dated 2015-10-12
rgeolocate-0.4.1/rgeolocate/R/freegeoip.R |only rgeolocate-0.4.1/rgeolocate/man/freegeoip.Rd |only rgeolocate-0.4.1/rgeolocate/tests/testthat/test_freegeoip.R |only rgeolocate-0.5.0/rgeolocate/DESCRIPTION | 12 rgeolocate-0.5.0/rgeolocate/MD5 | 49 - rgeolocate-0.5.0/rgeolocate/NAMESPACE | 1 rgeolocate-0.5.0/rgeolocate/NEWS | 13 rgeolocate-0.5.0/rgeolocate/R/maxmind.R | 17 rgeolocate-0.5.0/rgeolocate/R/telize.R | 2 rgeolocate-0.5.0/rgeolocate/README.md | 5 rgeolocate-0.5.0/rgeolocate/build/vignette.rds |binary rgeolocate-0.5.0/rgeolocate/configure | 29 - rgeolocate-0.5.0/rgeolocate/configure.ac | 14 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.html | 276 ++-------- rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Anonymous-IP-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Precision-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/man/maxmind.Rd | 15 rgeolocate-0.5.0/rgeolocate/man/telize.Rd | 2 rgeolocate-0.5.0/rgeolocate/src/Makevars.win | 2 rgeolocate-0.5.0/rgeolocate/src/config.h.in | 6 rgeolocate-0.5.0/rgeolocate/src/maxmind.cpp | 71 ++ rgeolocate-0.5.0/rgeolocate/src/maxmind.h | 4 rgeolocate-0.5.0/rgeolocate/src/maxminddb_config.h | 25 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_ip_api.R | 13 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_maxmind.R | 35 + rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.md |only 29 files changed, 239 insertions(+), 356 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network
representation that offers unmatched efficiency, modularity,
and extensibility. FCNN4R provides standard teaching
(backpropagation, Rprop, simulated annealing) and pruning algorithms
(minimum magnitude, Optimal Brain Surgeon), but it is first
and foremost an efficient computational engine. Users can easily
implement their algorithms by taking advantage of fast gradient
computing routines, as well as network reconstruction functionality
(removing weights and redundant neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.4.1 dated 2015-08-26 and 0.5.0 dated 2015-10-12
DESCRIPTION | 29 ++++------ MD5 | 39 +++++++------ NAMESPACE | 3 + R/mlp_gteach.R |only R/mlp_net.R | 97 +++++++++++++++++++++------------- R/mlp_plot.R | 41 ++++++++------ R/mlp_teach.R | 6 +- man/FCNN4R-package.Rd | 50 ++++++++++------- man/mlp_export_C.Rd | 10 +-- man/mlp_net-combining-two-networks.Rd | 6 +- man/mlp_net-export-import.Rd | 8 +- man/mlp_net.Rd | 6 +- man/mlp_teach_bp.Rd | 2 man/mlp_teach_grprop.Rd |only man/mlp_teach_rprop.Rd | 4 - man/mlp_teach_sa.Rd |only src/fcnn/export.cpp | 6 +- src/fcnn/level1.h | 42 ++++++++------ src/fcnn/level3.cpp | 3 - src/fcnn/struct.cpp | 48 ++++++++++++---- src/fcnn/utils.cpp | 12 ++++ src/fcnn/utils.h | 4 + 22 files changed, 253 insertions(+), 163 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: An easily accessible continuous (and discrete) time dynamic
modelling package for panel and time series data, reliant upon the OpenMx.
package (http://openmx.psyc.virginia.edu/) for computation. Most
dynamic modelling approaches to longitudinal data rely on the assumption
that time intervals between observations are consistent. When this
assumption is adhered to, the data gathering process is necessarily limited
to a specific schedule, and when broken, the resulting parameter estimates
may be biased and reduced in power. Continuous time models are
conceptually similar to vector autoregressive models (thus also the latent
change models popularised in a structural equation modelling context),
however by explicitly including the length of time between observations,
continuous time models are freed from the assumption that measurement
intervals are consistent. This allows: data to be gathered irregularly;
the elimination of noise and bias due to varying measurement intervals;
parsimonious structures for complex dynamics.
The application of such a model in this SEM framework allows full-information
maximum-likelihood estimates for both N = 1 and N > 1 cases, multiple
measured indicators per latent process, and the flexibility to incorporate
additional elements, including individual heterogeneity in the latent
process and manifest intercepts, and time dependent and independent
exogenous covariates. Furthermore, due to the SEM implementation we are
able to estimate a random effects model where the impact of time dependent
and time independent predictors can be assessed simultaneously, but without
the classic problems of random effects models assuming no covariance
between unit level effects and predictors.
Author: Manuel Voelkle [aut, cph] (Original development of continuous time
model specification within OpenMx, advisor for further development),
Han Oud [aut, cph] (Original development of continuous time model
specification within OpenMx),
Charles Driver [aut, cre, cph] (Further development of continuous time
model specification within OpenMx, package development,
documentation and maintenance)
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 1.1.1 dated 2015-08-10 and 1.1.3 dated 2015-10-12
DESCRIPTION | 12 MD5 | 63 - NAMESPACE | 4 R/ctCI.R |only R/ctDeintervalise.R | 12 R/ctFit.R | 807 ++++++++++++------ R/ctGenerate.R | 30 R/ctLabel.R | 1 R/ctModel.R | 4 R/ctMultigroupFit.R | 31 R/ctPSMfit.R |only R/ctsem.R | 5 R/plot.ctsemFit.R | 247 ++++- R/summary.ctsemFit.R | 424 ++++++--- build/vignette.rds |binary data/ctExample1.rda |binary data/ctExample1TIpred.rda |binary inst/doc/ctsem.R | 296 ++++-- inst/doc/ctsem.pdf |binary inst/doc/ctsem.rnw | 640 +++++++++----- man/ctCI.Rd |only man/ctFit.Rd | 75 + man/ctGenerate.Rd | 22 man/ctModel.Rd | 3 man/ctMultigroupFit.Rd | 14 man/ctPSMfit.Rd |only man/ctsem.Rd | 5 man/plot.ctsemFit.Rd | 17 man/plot.ctsemMultigroupFit.Rd |only man/summary.ctsemFit.Rd | 16 man/summary.ctsemMultigroupFit.Rd |only vignettes/ctsem.rnw | 640 +++++++++----- vignettes/ctsem_paper_source.zip |only vignettes/pathdiagramtwoprocessbasic.pdf |binary vignettes/pathdiagramtwoprocessfull2.pdf |binary vignettes/references.bib | 1343 +++++++++++++++++-------------- 36 files changed, 2996 insertions(+), 1715 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.3 dated 2015-06-23 and 0.4 dated 2015-10-12
DESCRIPTION | 14 MD5 | 32 NAMESPACE | 13 R/get_isd_station_data.R | 2211 ++++++++++++++++++++++++++++++++++++++++++-- R/get_isd_stations.R | 79 + R/map_isd_stations.R |only R/select_isd_station.R | 45 README.md | 246 +++- inst/000000-00000-2015.gz |only inst/999999-63897-2013.gz |only inst/999999-63897-2014.gz |only inst/999999-63897-2015.gz |only inst/stations.rda |binary inst/stations_map.png |only man/get_isd_station_data.Rd | 104 +- man/get_isd_stations.Rd | 37 man/map_isd_stations.Rd |only man/select_isd_station.Rd | 11 tests |only 19 files changed, 2569 insertions(+), 223 deletions(-)
Title: Integration of One-Dimensional Functions with Double Exponential
Formulas
Description: Numerical quadrature of functions of one variable over a finite or infinite interval
with double exponential formulas.
Author: Hiroyuki Okamura
Maintainer: Hiroyuki Okamura <okamu@rel.hiroshima-u.ac.jp>
Diff between deformula versions 0.1.0 dated 2015-10-09 and 0.1.1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/deformula-package.Rd | 4 ++-- src/R_deformula.cpp | 4 ++-- src/deformula.cpp | 3 ++- src/include/deformula.hpp | 7 +++++-- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely
used simulator of agricultural systems. This package includes
functions to create, edit and run APSIM simulations from R. It
also includes functions to visualize the results of an APSIM simulation
and perform sensitivity/uncertainty analysis of APSIM either via functions
in the sensitivity package or by novel emulator-based functions.
For more on APSIM including download instructions go to
\url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between apsimr versions 1.1 dated 2015-07-29 and 1.2 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 9 +++++++++ R/runAPSIM.R | 6 +++--- R/visualize.R | 9 +++++++-- build/vignette.rds |binary inst/doc/apsimr-basics.pdf |binary man/apsimr-package.Rd | 6 +++--- 8 files changed, 34 insertions(+), 20 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 0.9.2 dated 2015-04-01 and 1.0 dated 2015-10-11
DESCRIPTION | 14 ++--- MD5 | 45 +++++++++------- NAMESPACE | 15 ++++- R/graduallyvariedflow_v2.r | 94 +++++++++++++++++++---------------- R/rivr-methods.r |only R/route_wave_v4.r | 36 +++++++++---- R/zzz.r |only build/vignette.rds |binary inst/doc/quickstart.R | 4 + inst/doc/quickstart.Rmd | 24 ++++++++ inst/doc/quickstart.html | 102 +++++++++++++++++++++++++++++++++----- inst/doc/technical-vignette.R |only inst/doc/technical-vignette.Rmd |only inst/doc/technical-vignette.html |only man/channel_geom.Rd | 2 man/compute_profile.Rd | 2 man/conveyance.Rd | 2 man/critical_depth.Rd | 2 man/froude.Rd | 2 man/normal_depth.Rd | 2 man/rivr-package.Rd | 9 --- man/route_wave.Rd | 2 man/waterolympics.Rd | 2 src/rivmech_characteristic_v7.cpp | 20 ++++++- vignettes/channeldiagram.png |only vignettes/quickstart.Rmd | 24 ++++++++ vignettes/technical-vignette.Rmd |only 27 files changed, 292 insertions(+), 111 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.6.1 dated 2015-10-11 and 0.6.2 dated 2015-10-11
PRIMsrc-0.6.1/PRIMsrc/inst/doc/PRIMsrc_0.6.1.pdf |only PRIMsrc-0.6.2/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.2/PRIMsrc/MD5 | 8 PRIMsrc-0.6.2/PRIMsrc/R/PRIMsrc.r | 22 - PRIMsrc-0.6.2/PRIMsrc/inst/NEWS | 268 +++++++++++------------ PRIMsrc-0.6.2/PRIMsrc/inst/doc/PRIMsrc_0.6.2.pdf |only 6 files changed, 153 insertions(+), 153 deletions(-)
Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks
using R. Bayesian networks are directed acyclic graphs representing joint
probability distributions, where each node represents a random variable and
each edge represents conditionality. The full joint distribution is
therefore factorized as a product of conditional densities, where each node
is assumed to be independent of its non-descendents given information on its
parent nodes. Since exact, closed-form algorithms are computationally
burdensome for inference within hybrid networks that contain a combination
of continuous and discrete nodes, particle-based approximation techniques
like Markov Chain Monte Carlo are popular. We provide a user-friendly
interface to constructing these networks and running inference using the 'rjags' package.
Econometric analyses (maximum expected utility under competing policies,
value of information) involving decision and utility nodes are also
supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between HydeNet versions 0.9.0 dated 2015-07-02 and 0.10.0 dated 2015-10-11
DESCRIPTION | 16 MD5 | 120 ++- NEWS | 27 R/HydeNetwork.R | 181 ++-- R/HydePosterior.R | 9 R/HydeUtilities.R | 53 + R/PolicyMatrix.R | 21 R/bindPosterior.R | 43 - R/compileDecisionModel.R | 157 +++- R/compileJagsModel.R | 84 -- R/cpt.R | 155 +--- R/inputCPT.R | 46 - R/modelToNode.R | 15 R/plot.HydeNetwork.R | 16 R/rToJags.R | 2 R/setNode.R | 150 ++-- R/setNodeModels.R | 51 - R/writeJagsModel.R | 8 README.md | 7 build/vignette.rds |binary data/jagsFunctions.RData |binary inst/doc/DecisionNetworks.R | 11 inst/doc/DecisionNetworks.Rmd | 30 inst/doc/DecisionNetworks.html | 981 +++++++++++--------------- inst/doc/GettingStartedWithHydeNet.R | 12 inst/doc/GettingStartedWithHydeNet.Rmd | 29 inst/doc/GettingStartedWithHydeNet.html | 723 ++++++------------- inst/doc/HydeNetPlots.R | 76 +- inst/doc/HydeNetPlots.Rmd | 42 - inst/doc/HydeNetPlots.html | 501 ++++--------- inst/doc/WorkingWithHydeNetObjects.R | 8 inst/doc/WorkingWithHydeNetObjects.Rmd | 32 inst/doc/WorkingWithHydeNetObjects.html | 1187 ++++++++++++-------------------- inst/img |only man/HydeNetwork.Rd | 6 man/HydePosterior.Rd | 14 man/compileDecisionModel.Rd | 11 man/setNode.Rd | 18 man/setNodeModels.Rd | 2 tests |only vignettes/DecisionNetworks.Rmd | 30 vignettes/GettingStartedWithHydeNet.Rmd | 29 vignettes/HydeNetPlots.Rmd | 42 - vignettes/WorkingWithHydeNetObjects.Rmd | 32 vignettes/vignette_images |only 45 files changed, 2198 insertions(+), 2779 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de> and Alexander Ristig <alexander.ristig@univie.ac.at>
Maintainer: Alexander Ristig <alexander.ristig@univie.ac.at>
Diff between HAC versions 1.0-3 dated 2015-05-12 and 1.0-4 dated 2015-10-11
DESCRIPTION | 14 - MD5 | 24 +-- NAMESPACE | 5 R/estimate.r | 2 build/vignette.rds |binary inst/ChangeLog | 12 - inst/doc/HAC.R | 333 +++++++++++++++++++++++------------------------ inst/doc/HAC.Rnw | 86 +++++------- inst/doc/HAC.pdf |binary man/estimate.copula.Rd | 4 vignettes/HAC-speed2.pdf |binary vignettes/HAC.Rnw | 86 +++++------- vignettes/ref.bib | 34 ++++ 13 files changed, 307 insertions(+), 293 deletions(-)
Title: Selecting Variables in Regression Models
Description: A simple method
to select the best model or best subset of variables using
different types of data (binary, Gaussian or Poisson) and
applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between FWDselect versions 2.0 dated 2015-05-17 and 2.0.1 dated 2015-10-11
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 12 +++++++++++- NEWS | 16 +++++++++++++--- R/FWDselect.R | 2 +- R/plot.qselection.R | 2 ++ R/qselection.R | 8 +++++++- R/selection.R | 31 ++++++++++++++++++++++--------- R/test.R | 40 ++++++++++++++++++++++++++++++---------- man/FWDselect.Rd | 2 +- man/qselection.Rd | 8 +++++++- man/selection.Rd | 8 +++++++- man/test.Rd | 14 +++++++++++--- 13 files changed, 129 insertions(+), 48 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.13 dated 2015-08-24 and 0.99.14 dated 2015-10-11
DESCRIPTION | 8 MD5 | 73 - NAMESPACE | 13 NEWS | 37 R/DescTools.r | 2879 +++------------------------------------- R/FastDesc.R | 389 +++++ R/SpecialPlots.r |only R/Tables.r |only data/d.whisky.rda |only demo/plots.R | 16 inst/doc/DescToolsCompanion.pdf |binary inst/doc/TablesInR.pdf |binary man/Assocs.Rd | 4 man/Canvas.Rd | 9 man/ColToRgb.Rd | 10 man/CramerV.Rd | 10 man/Desc.table.Rd | 26 man/DescTools-package.Rd | 5 man/GCD.Rd | 2 man/Gini.Rd | 3 man/HotellingsT.Rd | 2 man/PDFManual.Rd | 6 man/PercTable.Rd | 18 man/Permn.Rd | 18 man/PlotBubble.Rd | 24 man/PlotDesc.Rd | 10 man/PlotFdist.Rd | 3 man/PlotHorizBar.Rd | 2 man/PlotMiss.Rd |only man/PlotQQ.Rd | 18 man/PlotRCol.Rd | 6 man/RgbToCol.Rd | 11 man/SmoothSpline.Rd |only man/Stamp.Rd | 18 man/TOne.Rd | 9 man/d.whisky.Rd |only man/identify.formula.Rd | 12 man/like.Rd | 3 man/lines.loess.Rd | 18 src/aux_fct.cpp | 7 tests |only 41 files changed, 907 insertions(+), 2762 deletions(-)
Title: Robust Selection of Cluster Number K
Description: Facilitates optimal clustering of a data set. Provides a framework to run a wide range of clustering algorithms to determine the optimal number (k) of clusters in the data. Then analyzes the cluster assignments from each clustering algorithm to identify samples that repeatedly classify to the same group. We call these 'core clusters', providing a basis for later class discovery.
Author: Albert Chen [aut, cre], Timothy E Sweeney [aut], Olivier Gevaert [ths]
Maintainer: Albert Chen <acc2015@stanford.edu>
Diff between COMMUNAL versions 1.0 dated 2015-02-11 and 1.1.0 dated 2015-10-11
COMMUNAL-1.0/COMMUNAL/vignettes/COMMUNAL-001.pdf |only COMMUNAL-1.1.0/COMMUNAL/DESCRIPTION | 14 COMMUNAL-1.1.0/COMMUNAL/MD5 | 51 COMMUNAL-1.1.0/COMMUNAL/NAMESPACE | 8 COMMUNAL-1.1.0/COMMUNAL/R/communal.R | 738 ++++++++----- COMMUNAL-1.1.0/COMMUNAL/R/extract_core.R | 9 COMMUNAL-1.1.0/COMMUNAL/R/plot_range_3d.R | 418 +++++-- COMMUNAL-1.1.0/COMMUNAL/R/test_range.R | 106 + COMMUNAL-1.1.0/COMMUNAL/build/vignette.rds |binary COMMUNAL-1.1.0/COMMUNAL/data/BRCA.100.RData |binary COMMUNAL-1.1.0/COMMUNAL/data/BRCA.results.RData |binary COMMUNAL-1.1.0/COMMUNAL/inst/CITATION |only COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.R | 227 +-- COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.Rnw | 302 ++--- COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.pdf |binary COMMUNAL-1.1.0/COMMUNAL/man/BRCA.results.Rd | 7 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL-class.Rd | 2 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL-package.Rd | 31 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL.Rd | 212 ++- COMMUNAL-1.1.0/COMMUNAL/man/clusterKeys.Rd | 13 COMMUNAL-1.1.0/COMMUNAL/man/clusterRange.Rd | 118 +- COMMUNAL-1.1.0/COMMUNAL/man/examineCounts.Rd | 6 COMMUNAL-1.1.0/COMMUNAL/man/measureMonotonic.Rd |only COMMUNAL-1.1.0/COMMUNAL/man/plotRange3D.Rd | 51 COMMUNAL-1.1.0/COMMUNAL/man/returnCore.Rd | 6 COMMUNAL-1.1.0/COMMUNAL/man/testAlgsMinSize.Rd |only COMMUNAL-1.1.0/COMMUNAL/vignettes/COMMUNAL-concordance.tex |only COMMUNAL-1.1.0/COMMUNAL/vignettes/COMMUNAL.Rnw | 302 ++--- COMMUNAL-1.1.0/COMMUNAL/vignettes/framed.sty |only COMMUNAL-1.1.0/COMMUNAL/vignettes/snapshot.png |only 30 files changed, 1511 insertions(+), 1110 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each set of
nested blocks optimized within the levels of any existing higher-level blocks.
Block sizes are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.7 dated 2015-08-21 and 1.8 dated 2015-10-11
DESCRIPTION | 8 MD5 | 8 R/blocks.r | 503 +++++++++++++++++++++++++------------------------------ R/upper_bounds.r | 25 +- man/blocks.Rd | 33 +-- 5 files changed, 267 insertions(+), 310 deletions(-)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and
fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between sets versions 1.0-15 dated 2015-07-08 and 1.0-16 dated 2015-10-11
sets-1.0-15/sets/inst/doc/sets.bib |only sets-1.0-16/sets/DESCRIPTION | 6 +++--- sets-1.0-16/sets/MD5 | 18 +++++++++--------- sets-1.0-16/sets/NAMESPACE | 10 ++++++++++ sets-1.0-16/sets/build/vignette.rds |binary sets-1.0-16/sets/data/fuzzy_docs.rda |binary sets-1.0-16/sets/inst/NEWS.Rd | 13 ++++++++++--- sets-1.0-16/sets/inst/doc/sets.Rnw | 2 +- sets-1.0-16/sets/inst/doc/sets.pdf |binary sets-1.0-16/sets/man/sets-internal.Rd |only sets-1.0-16/sets/vignettes/sets.Rnw | 2 +- 11 files changed, 34 insertions(+), 17 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-5 dated 2015-04-30 and 0.6-6 dated 2015-10-11
DESCRIPTION | 8 ++-- MD5 | 36 ++++++++++----------- R/algebra.R | 2 - R/charfun.R | 4 +- R/domain.R | 2 - R/dual.R | 2 - R/getters.R | 2 - R/graph.R | 14 ++++---- R/relation.R | 8 ++-- R/utilities.R | 2 - build/vignette.rds |binary data/Cetacea.rda |binary data/Felines.rda |binary data/SVM_Benchmarking_Classification.rda |binary data/SVM_Benchmarking_Classification_Consensus.rda |binary data/SVM_Benchmarking_Regression.rda |binary data/SVM_Benchmarking_Regression_Consensus.rda |binary inst/NEWS.Rd | 27 +++++++++++++++ inst/doc/relations.pdf |binary 19 files changed, 66 insertions(+), 41 deletions(-)
Title: Matplotlib Default Color Map
Description: Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/>
is a popular plotting library for 'python'. These color maps are designed in
such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3 dated 2015-10-11 and 0.3.1 dated 2015-10-11
DESCRIPTION | 22 ++++++++++++---------- MD5 | 6 +++--- README.md | 3 +++ inst/doc/intro-to-viridis.html | 6 +++--- 4 files changed, 21 insertions(+), 16 deletions(-)
Title: Quantification of Pinned Microbial Cultures
Description: The goal of this package is to allow users to robustly
and quickly grid and quantify sizes of pinned colonies in plate images.
gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately.
It includes several image pre-processing techniques, such
as autorotation of plates, noise removal, contrast adjustment and image
resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>
Diff between gitter versions 1.1 dated 2015-10-09 and 1.1.1 dated 2015-10-11
gitter-1.1.1/gitter/CHANGES | 6 ++++++ gitter-1.1.1/gitter/DESCRIPTION | 15 +++++++-------- gitter-1.1.1/gitter/MD5 | 18 +++++++++--------- gitter-1.1.1/gitter/R/Help.R |only gitter-1.1.1/gitter/R/Main.R |only gitter-1.1.1/gitter/R/Peaks.R |only gitter-1.1.1/gitter/build/BUILD.R | 2 +- gitter-1.1.1/gitter/man/gitter.Rd | 2 +- gitter-1.1.1/gitter/man/gitter.batch.Rd | 2 +- gitter-1.1.1/gitter/man/gitter.demo.Rd | 2 +- gitter-1.1/gitter/R/help.r |only gitter-1.1/gitter/R/main.r |only gitter-1.1/gitter/R/peaks.r |only 13 files changed, 26 insertions(+), 21 deletions(-)
Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. It provides
syntactic sugar for the S4 class system and two alternative new
implementations. One is an experimental version built around S4
and the other one makes it more convenient to work with lists as objects.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between aoos versions 0.3.0 dated 2015-08-06 and 0.4.0 dated 2015-10-11
aoos-0.3.0/aoos/R/Accessor.R |only aoos-0.3.0/aoos/R/Binary.R |only aoos-0.3.0/aoos/R/Infix.R |only aoos-0.3.0/aoos/R/Private.R |only aoos-0.3.0/aoos/R/Show.R |only aoos-0.3.0/aoos/R/aoos.R |only aoos-0.3.0/aoos/R/defineClass.R |only aoos-0.3.0/aoos/R/defineRefClass.R |only aoos-0.3.0/aoos/R/helper.R |only aoos-0.3.0/aoos/R/packageStartupMessage.R |only aoos-0.3.0/aoos/R/public-interfaces.R |only aoos-0.3.0/aoos/R/retList.R |only aoos-0.3.0/aoos/tests/testthat/test-Accessor.R |only aoos-0.3.0/aoos/tests/testthat/test-Binary.R |only aoos-0.3.0/aoos/tests/testthat/test-Class.R |only aoos-0.3.0/aoos/tests/testthat/test-Infix.R |only aoos-0.3.0/aoos/tests/testthat/test-basics.R |only aoos-0.3.0/aoos/tests/testthat/test-inheritance.R |only aoos-0.3.0/aoos/tests/testthat/test-publicInterface.R |only aoos-0.3.0/aoos/tests/testthat/test-retList.R |only aoos-0.3.0/aoos/tests/testthat/test-self.R |only aoos-0.3.0/aoos/tests/testthat/test-summary.R |only aoos-0.4.0/aoos/DESCRIPTION | 25 +- aoos-0.4.0/aoos/MD5 | 106 ++++++----- aoos-0.4.0/aoos/NAMESPACE | 16 + aoos-0.4.0/aoos/NEWS | 63 +++++- aoos-0.4.0/aoos/R/DC-Binary.R |only aoos-0.4.0/aoos/R/DC-Show.R |only aoos-0.4.0/aoos/R/DC-aoos.R |only aoos-0.4.0/aoos/R/DC-defineClass.R |only aoos-0.4.0/aoos/R/DC-public-interfaces.R |only aoos-0.4.0/aoos/R/NAMESPACE.R | 7 aoos-0.4.0/aoos/R/RL-Infix.R |only aoos-0.4.0/aoos/R/RL-envHelper.R |only aoos-0.4.0/aoos/R/RL-retList.R |only aoos-0.4.0/aoos/R/S4-expressions.R |only aoos-0.4.0/aoos/R/S4-generics-test.R |only aoos-0.4.0/aoos/R/S4-generics.R |only aoos-0.4.0/aoos/R/S4-roxygen-parser.R |only aoos-0.4.0/aoos/R/S4-types.R |only aoos-0.4.0/aoos/R/S4RC-Accessor.R |only aoos-0.4.0/aoos/R/S4RC-Private.R |only aoos-0.4.0/aoos/R/S4RC-defineRefClass.R |only aoos-0.4.0/aoos/build/vignette.rds |binary aoos-0.4.0/aoos/inst/doc/Introduction.R | 3 aoos-0.4.0/aoos/inst/doc/Introduction.Rmd | 51 ++++- aoos-0.4.0/aoos/inst/doc/Introduction.html | 6 aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.R |only aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.Rmd |only aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.html |only aoos-0.4.0/aoos/inst/doc/aoosClasses.html | 4 aoos-0.4.0/aoos/inst/doc/performance.html | 26 +- aoos-0.4.0/aoos/inst/doc/referenceClasses.html | 4 aoos-0.4.0/aoos/inst/doc/retListClasses.html | 8 aoos-0.4.0/aoos/man/Accessor.Rd | 2 aoos-0.4.0/aoos/man/Binary.Rd | 2 aoos-0.4.0/aoos/man/Infix.Rd | 2 aoos-0.4.0/aoos/man/Private.Rd | 2 aoos-0.4.0/aoos/man/S4generics.Rd |only aoos-0.4.0/aoos/man/Show.Rd | 2 aoos-0.4.0/aoos/man/aoos.Rd | 6 aoos-0.4.0/aoos/man/defineClass.Rd | 2 aoos-0.4.0/aoos/man/defineRefClass.Rd | 2 aoos-0.4.0/aoos/man/envHelper.Rd | 2 aoos-0.4.0/aoos/man/genericTest.Rd |only aoos-0.4.0/aoos/man/grapes-type-grapes.Rd |only aoos-0.4.0/aoos/man/parser.Rd |only aoos-0.4.0/aoos/man/publicInterface.Rd | 2 aoos-0.4.0/aoos/man/retList.Rd | 24 +- aoos-0.4.0/aoos/tests/testthat/test-00-S4RC-defineRefClass.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-Binary.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-basics.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-inheritance.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-publicInterface.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-self.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-summary.R |only aoos-0.4.0/aoos/tests/testthat/test-RL-Infix.R |only aoos-0.4.0/aoos/tests/testthat/test-RL-retList.R |only aoos-0.4.0/aoos/tests/testthat/test-S4-generics.R |only aoos-0.4.0/aoos/tests/testthat/test-S4-types.R |only aoos-0.4.0/aoos/tests/testthat/test-S4RC-Accessor.R |only aoos-0.4.0/aoos/vignettes/Introduction.Rmd | 51 ++++- aoos-0.4.0/aoos/vignettes/S4SyntacticSugar.Rmd |only 83 files changed, 301 insertions(+), 117 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with
the 'qdap' package that may be useful outside of the context of
discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar
amounts, email addresses, hash tags, numbers, percentages,
citations, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.5.0 dated 2015-08-16 and 0.5.1 dated 2015-10-11
DESCRIPTION | 18 +- MD5 | 16 +- NEWS | 10 + README.md | 246 ++++++++++++++++++++-------------------- data/regex_cheat.rda |binary data/regex_supplement.rda |binary data/regex_usa.rda |binary inst/CITATION | 4 tests/testthat/test-rm_number.R | 10 - 9 files changed, 162 insertions(+), 142 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for
the sample selection bias from observed outcomes in matching
markets. This includes one-sided matching of agents into
groups as well as two-sided matching of students to schools.
The package also contains R code for three matching algorithms:
the deferred-acceptance (or Gale-Shapley) algorithm for
stable marriage and college admissions problems, the
top-trading-cycles algorithm for house allocation and a
partitioning linear programme for the roommates problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 0.1-6 dated 2015-10-06 and 0.1-7 dated 2015-10-11
matchingMarkets-0.1-6/matchingMarkets/NEWS |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/1_Introduction.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/2_Example.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/3_StructuralModel.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixA.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixC.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixD.Rnw |only matchingMarkets-0.1-7/matchingMarkets/DESCRIPTION | 31 ++-- matchingMarkets-0.1-7/matchingMarkets/MD5 | 34 ++--- matchingMarkets-0.1-7/matchingMarkets/NEWS.md |only matchingMarkets-0.1-7/matchingMarkets/README.md |only matchingMarkets-0.1-7/matchingMarkets/inst/doc/matching.Rnw | 43 +----- matchingMarkets-0.1-7/matchingMarkets/inst/doc/matching.pdf |binary matchingMarkets-0.1-7/matchingMarkets/man/matchingMarkets-package.Rd | 3 matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/1_Introduction.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/2_Example.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/3_StructuralModel.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/4_MonteCarloResults.Rnw | 35 ++--- matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/5_Application.Rnw | 6 matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/6_Conclusion.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixA.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixB.Rnw | 66 +++++----- matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixC.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixD.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/matching.Rnw | 43 +----- matchingMarkets-0.1-7/matchingMarkets/vignettes/matching.bib | 39 +++++ 26 files changed, 158 insertions(+), 142 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb],
Tengfei Yin [ctb],
Nan Xiao [aut, cre]
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between liftr versions 0.2 dated 2015-07-31 and 0.3 dated 2015-10-11
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NEWS.md | 11 +++++++++++ R/drender.R | 10 +++++++--- R/lift.R | 18 +++++++++++------- build/vignette.rds |binary inst/Dockerfile.Rmd | 4 +++- inst/cranpkg.Rmd |only inst/doc/liftr-intro.Rmd | 6 +++--- inst/doc/liftr-intro.html | 12 ++++++------ man/drender.Rd | 8 +++++--- man/lift.Rd | 4 ++-- vignettes/liftr-intro.Rmd | 6 +++--- 13 files changed, 67 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-03 1.0.3
Title: Matplotlib Default Color Map
Description: Port of the new Matplotlib default color map ('viridis') to R.
This color map is designed in such a way that it will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. It is also designed to be perceived by
readers with the most common form of color blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.2.5 dated 2015-09-14 and 0.3 dated 2015-10-11
DESCRIPTION | 14 - MD5 | 31 +- NAMESPACE | 4 R/scales.R | 192 +++++++++-------- R/viridis.R | 71 +++++- README.md | 35 +-- build/vignette.rds |binary data/viridis.map.rda |binary inst/doc/intro-to-viridis.R | 145 +++++++++---- inst/doc/intro-to-viridis.Rmd | 276 +++++++++++++++++++------ inst/doc/intro-to-viridis.html | 213 ++++++++++++------- man/scale_viridis.Rd | 25 +- man/viridis.Rd | 29 ++ man/viridis.map.Rd | 3 man/viridis_pal.Rd | 6 vignettes/intro-to-viridis.Rmd | 276 +++++++++++++++++++------ vignettes/us.tmax_nohads_ll_20150219_float.tif |only 17 files changed, 933 insertions(+), 387 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.5.1 dated 2015-09-11 and 1.6.0 dated 2015-10-11
DESCRIPTION | 8 +-- MD5 | 20 +++---- R/allShortestPaths.R | 2 R/cypherToList.R | 2 R/internal.R | 12 ++-- R/shortestPath.R | 2 man/allShortestPaths.Rd | 2 man/shortestPath.Rd | 2 tests/testthat/test-cypherToList.R | 39 +++++++++++++++ tests/testthat/test-nodes.R | 96 +++++++++++++++++++++++++++++++++---- tests/testthat/test-paths.R | 26 ++++++++-- 11 files changed, 176 insertions(+), 35 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.6.0 dated 2015-09-16 and 0.6.1 dated 2015-10-11
PRIMsrc-0.6.0/PRIMsrc/data/Synthetic.5.rda |only PRIMsrc-0.6.0/PRIMsrc/inst/doc/PRIMsrc_0.6.0.pdf |only PRIMsrc-0.6.0/PRIMsrc/man/Synthetic.5-data.Rd |only PRIMsrc-0.6.1/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.1/PRIMsrc/MD5 | 52 PRIMsrc-0.6.1/PRIMsrc/R/PRIMsrc.internal.r | 1 PRIMsrc-0.6.1/PRIMsrc/R/PRIMsrc.r | 3036 ++++++++++---------- PRIMsrc-0.6.1/PRIMsrc/data/Synthetic.1b.rda |only PRIMsrc-0.6.1/PRIMsrc/data/Synthetic.4.rda |binary PRIMsrc-0.6.1/PRIMsrc/data/datalist | 2 PRIMsrc-0.6.1/PRIMsrc/inst/NEWS | 18 PRIMsrc-0.6.1/PRIMsrc/inst/doc/Abstract.JCB2016.pdf |binary PRIMsrc-0.6.1/PRIMsrc/inst/doc/PRIMsrc_0.6.1.pdf |only PRIMsrc-0.6.1/PRIMsrc/man/PrimSRC-package.Rd | 44 PRIMsrc-0.6.1/PRIMsrc/man/Real.1-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Real.2-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.1-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.1b-data.Rd |only PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.2-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.3-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.4-data.Rd | 16 PRIMsrc-0.6.1/PRIMsrc/man/plot.Rd | 69 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxkm.Rd | 3 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxtrace.Rd | 7 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxtraj.Rd | 7 PRIMsrc-0.6.1/PRIMsrc/man/plot_profile.Rd | 5 PRIMsrc-0.6.1/PRIMsrc/man/predict.Rd | 35 PRIMsrc-0.6.1/PRIMsrc/man/print.Rd | 34 PRIMsrc-0.6.1/PRIMsrc/man/sbh.Rd | 39 PRIMsrc-0.6.1/PRIMsrc/man/summary.Rd | 31 30 files changed, 1765 insertions(+), 1652 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb],
Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.4 dated 2015-10-02 and 0.2.6 dated 2015-10-11
DESCRIPTION | 14 ++-- MD5 | 28 +++++---- NAMESPACE | 3 + NEWS | 12 ++++ R/chordNetwork.R |only R/diagonalNetwork.R | 4 - R/sankeyNetwork.R | 25 ++++++-- README.md | 2 inst/examples/examples.R | 42 ++++++++++++-- inst/htmlwidgets/chordNetwork.js |only inst/htmlwidgets/chordNetwork.yaml |only inst/htmlwidgets/lib/sankey.js | 107 +++++++++++++++++++++++++++++++------ inst/htmlwidgets/sankeyNetwork.js | 90 +++++++++++++++++++++++++++---- man/chordNetwork.Rd |only man/diagonalNetwork.Rd | 4 - man/networkD3-shiny.Rd | 10 ++- man/sankeyNetwork.Rd | 22 +++++-- 17 files changed, 294 insertions(+), 69 deletions(-)
Title: Fast Truncated SVD, PCA and Symmetric Eigendecomposition for
Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principal component analysis of large sparse or dense matrices.
Author: Jim Baglama and Lothar Reichel
Maintainer: Bryan W. Lewis <blewis@illposed.net>
Diff between irlba versions 1.0.3 dated 2014-01-25 and 2.0.0 dated 2015-10-11
irlba-1.0.3/irlba/NEWS |only irlba-1.0.3/irlba/inst/doc/irlba.R |only irlba-2.0.0/irlba/DESCRIPTION | 19 - irlba-2.0.0/irlba/MD5 | 23 - irlba-2.0.0/irlba/NAMESPACE | 8 irlba-2.0.0/irlba/R/eigen.R |only irlba-2.0.0/irlba/R/irlba.R | 626 ++++++++++++++++++--------------- irlba-2.0.0/irlba/R/utility.R |only irlba-2.0.0/irlba/README.md |only irlba-2.0.0/irlba/build |only irlba-2.0.0/irlba/inst/doc/irlba.Rnw | 194 ++++++---- irlba-2.0.0/irlba/inst/doc/irlba.pdf |binary irlba-2.0.0/irlba/man/irlba.Rd | 191 +++++++--- irlba-2.0.0/irlba/man/partial_eigen.Rd |only irlba-2.0.0/irlba/tests/test.R | 86 ++-- irlba-2.0.0/irlba/vignettes/irlba.Rnw | 194 ++++++---- 16 files changed, 850 insertions(+), 491 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-52 dated 2015-07-17 and 6.0-57 dated 2015-10-11
DESCRIPTION | 23 - MD5 | 73 +-- NAMESPACE | 5 R/aaa.R | 417 ++++++++++-------- R/adaptive.R | 14 R/confusionMatrix.R | 4 R/createDataPartition.R | 1 R/createFolds.R | 3 R/createResample.R | 4 R/ggplot.R | 99 ++++ R/lift.R | 1 R/misc.R | 101 +--- R/modelLookup.R | 40 + R/preProcess.R | 817 ++++++++++++++++++++++++------------ R/print.train.R | 75 ++- R/reg_sims.R | 15 R/rfe.R | 42 - R/train.default.R | 44 + R/trainControl.R | 4 R/updates.R | 4 R/varImp.R | 129 +---- R/workflows.R | 7 build/vignette.rds |binary inst/NEWS.Rd | 28 + inst/doc/caret.pdf |binary inst/models/models.RData |binary man/confusionMatrix.Rd | 2 man/extractPrediction.Rd | 2 man/plot.rfe.Rd | 2 man/plot.train.Rd | 2 man/postResample.Rd | 9 man/preProcess.Rd | 19 man/sensitivity.Rd | 2 man/train.Rd | 7 man/trainControl.Rd | 11 man/twoClassSim.Rd | 24 - tests/testthat/preProcess_methods.R |only vignettes/caret.Rnw | 2 38 files changed, 1248 insertions(+), 784 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb],
Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.3.1 dated 2015-10-07 and 1.3.2 dated 2015-10-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ README.md | 2 +- src/parsing.cpp | 3 ++- tests/testthat/test_parsing.R | 6 ++++++ 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Model Checking and Variable Selection in Nonparametric
Regression
Description: Provides tests of significance for covariates (or groups of covariates) in a fully nonparametric regression model and a variable (or group) selection procedure based on False Discovery Rate. In addition, it provides a function for local polynomial regression for any number of dimensions, using a bandwidth specified by the user or automatically chosen by cross validation or an adaptive procedure.
Author: Adriano Zanin Zambom
Maintainer: Adriano Zanin Zambom <adriano.zambom@gmail.com>
Diff between NonpModelCheck versions 1.0 dated 2012-09-22 and 2.0 dated 2015-10-10
DESCRIPTION | 20 MD5 | 29 - NAMESPACE | 5 R/group.npvarselec.R | 935 +++++++++++++++++++++----------------------- R/localpoly.reg.R | 481 +++++++++++----------- R/npmodelcheck.R | 485 +++++++++++----------- R/npvarselec.R | 595 +++++++++++++--------------- R/plot3d.localpoly.reg.R | 131 +++--- man/group.npvarselec.Rd | 27 - man/localpoly.reg.Rd | 48 +- man/npmodelcheck.Rd | 37 - man/npvarselec.Rd | 25 - man/plot3d.localpoly.reg.Rd | 25 - src/Makevars | 2 src/Makevars.win |only src/local_poly_estimator.c | 54 -- 16 files changed, 1435 insertions(+), 1464 deletions(-)
More information about NonpModelCheck at CRAN
Permanent link
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scatterpoints by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.8.1 dated 2015-06-03 and 1.9.0 dated 2015-10-10
berryFunctions-1.8.1/berryFunctions/ChangeLog |only berryFunctions-1.9.0/berryFunctions/DESCRIPTION | 11 berryFunctions-1.9.0/berryFunctions/MD5 | 64 - berryFunctions-1.9.0/berryFunctions/NAMESPACE | 5 berryFunctions-1.9.0/berryFunctions/NEWS |only berryFunctions-1.9.0/berryFunctions/R/approx2.R |only berryFunctions-1.9.0/berryFunctions/R/ciBand.R |only berryFunctions-1.9.0/berryFunctions/R/climateGraph.r | 5 berryFunctions-1.9.0/berryFunctions/R/combineFiles.r | 9 berryFunctions-1.9.0/berryFunctions/R/createDoc.r | 6 berryFunctions-1.9.0/berryFunctions/R/exp4p.r | 20 berryFunctions-1.9.0/berryFunctions/R/linLogHist.R | 3 berryFunctions-1.9.0/berryFunctions/R/linLogTrans.R | 353 +++---- berryFunctions-1.9.0/berryFunctions/R/linReg.R | 24 berryFunctions-1.9.0/berryFunctions/R/logSpaced.R | 2 berryFunctions-1.9.0/berryFunctions/R/mReg.r | 473 +++++----- berryFunctions-1.9.0/berryFunctions/R/movAv.R | 35 berryFunctions-1.9.0/berryFunctions/R/pastec.R | 14 berryFunctions-1.9.0/berryFunctions/R/pointZoom.R | 21 berryFunctions-1.9.0/berryFunctions/R/sortDF.R |only berryFunctions-1.9.0/berryFunctions/R/timer.R |only berryFunctions-1.9.0/berryFunctions/inst/extdata/solitaire.txt | 2 berryFunctions-1.9.0/berryFunctions/man/approx2.Rd |only berryFunctions-1.9.0/berryFunctions/man/berryFunctions-package.Rd | 31 berryFunctions-1.9.0/berryFunctions/man/ci.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/ciBand.Rd |only berryFunctions-1.9.0/berryFunctions/man/combineFiles.Rd | 3 berryFunctions-1.9.0/berryFunctions/man/expReg.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/linLogHist.Rd | 6 berryFunctions-1.9.0/berryFunctions/man/linLogTrans.Rd | 5 berryFunctions-1.9.0/berryFunctions/man/linReg.Rd | 99 +- berryFunctions-1.9.0/berryFunctions/man/logSpaced.Rd | 4 berryFunctions-1.9.0/berryFunctions/man/mReg.Rd | 405 ++++---- berryFunctions-1.9.0/berryFunctions/man/movAv.Rd | 10 berryFunctions-1.9.0/berryFunctions/man/pointZoom.Rd | 11 berryFunctions-1.9.0/berryFunctions/man/quantileBands.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/sortDF.Rd |only berryFunctions-1.9.0/berryFunctions/man/timer.Rd |only 38 files changed, 875 insertions(+), 752 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Diagnostics Plots for Bicluster Data
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between BcDiag versions 1.0.8 dated 2015-01-22 and 1.0.9 dated 2015-10-10
DESCRIPTION | 16 +++++++-------- MD5 | 8 +++---- NAMESPACE | 4 +++ R/profileBic.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++---- man/profileBic.Rd | 4 ++- 5 files changed, 72 insertions(+), 17 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2015. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods)
NCA identifies necessary (but not sufficient) conditions in datasets. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or input) is necessary but not sufficient for a (desired) level of y (e.g. good performance or output).
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 1.0 dated 2015-07-02 and 1.1 dated 2015-10-10
NCA-1.0/NCA/R/p_bottleneck_fdh.R |only NCA-1.1/NCA/DESCRIPTION | 11 ++--- NCA-1.1/NCA/MD5 | 63 ++++++++++++++++-------------- NCA-1.1/NCA/NAMESPACE | 4 - NCA-1.1/NCA/R/nca.R | 72 ++++++++++++++++++++++++----------- NCA-1.1/NCA/R/nca_ce_fdh.R | 31 ++++++++------- NCA-1.1/NCA/R/nca_ce_vrs.R | 42 +++++++++++--------- NCA-1.1/NCA/R/nca_cols.R | 7 +-- NCA-1.1/NCA/R/nca_cr_fdh.R | 32 +++++++++------ NCA-1.1/NCA/R/nca_cr_vrs.R | 34 +++++++++------- NCA-1.1/NCA/R/nca_lh.R | 2 NCA-1.1/NCA/R/nca_ols.R | 2 NCA-1.1/NCA/R/nca_qr.R | 9 ++-- NCA-1.1/NCA/R/nca_sfa.R | 26 ++++++++++-- NCA-1.1/NCA/R/onAttach.R | 2 NCA-1.1/NCA/R/p_above.R | 4 + NCA-1.1/NCA/R/p_bottleneck_ce.R |only NCA-1.1/NCA/R/p_ceiling.R | 49 ++++++++++++++++++----- NCA-1.1/NCA/R/p_display_bottleneck.R | 10 ++-- NCA-1.1/NCA/R/p_display_graphs.R | 32 ++++++++------- NCA-1.1/NCA/R/p_display_tables.R | 6 +- NCA-1.1/NCA/R/p_fast_peers.R |only NCA-1.1/NCA/R/p_ineffs.R | 40 ++++++++++--------- NCA-1.1/NCA/R/p_optimal_peers.R | 6 +- NCA-1.1/NCA/R/p_utils.R | 9 ++-- NCA-1.1/NCA/man/NCA-package.Rd | 2 NCA-1.1/NCA/man/nca.Rd | 21 +++++++--- NCA-1.1/NCA/man/nca.example.Rd | 20 ++++----- NCA-1.1/NCA/man/nca_ce_fdh.Rd | 4 + NCA-1.1/NCA/man/nca_ce_vrs.Rd | 9 +++- NCA-1.1/NCA/man/nca_cr_fdh.Rd | 3 - NCA-1.1/NCA/man/nca_cr_vrs.Rd | 3 - NCA-1.1/NCA/man/nca_qr.Rd | 8 ++- NCA-1.1/NCA/tests |only 34 files changed, 351 insertions(+), 212 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.20-2 dated 2015-09-02 and 2.20-23 dated 2015-10-10
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++------------- NAMESPACE | 4 ++- R/helpers.R | 19 ++++++++++++-- R/lsmip.R | 2 - R/plot.lsm.R | 5 +++ R/ref.grid.R | 30 +++++++++++++++------- R/summary.R | 23 ++--------------- inst/NEWS | 11 ++++++++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 58 ++++++++++++++++++++++++-------------------- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 8 ++++-- man/models.Rd | 4 ++- man/ref.grid.Rd | 2 - man/summary.Rd | 5 ++- man/update.Rd | 14 ++++++++-- vignettes/using-lsmeans.rnw | 8 ++++-- 18 files changed, 144 insertions(+), 91 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 2.0.1.5 dated 2015-10-04 and 2.0.1.7 dated 2015-10-10
DESCRIPTION | 13 ++++++++----- MD5 | 6 +++--- R/gdal_chooseInstallation.R | 12 ++++++++++-- R/gdal_setInstallation.R | 8 +++++--- 4 files changed, 26 insertions(+), 13 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.0 dated 2015-10-08 and 0.8.1 dated 2015-10-10
DESCRIPTION | 10 ++-- MD5 | 39 +++++++++-------- NAMESPACE | 5 ++ R/FSA-internals.R | 16 +++---- R/FSAUtils.R | 37 +++++++++++++++- R/comparisonsDVR.R |only man/col2rgbt.Rd |only man/compIntercepts.Rd |only man/compSlopes.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test_AgeLengthKey.R | 57 ++++++++++++------------- tests/testthat/test_CatchCurve_ChapmanRobson.R | 5 -- tests/testthat/test_FSAUtils.R | 15 ++++++ tests/testthat/test_PSD.R | 47 ++++++++++++-------- tests/testthat/test_StockRecruit.R | 6 -- tests/testthat/test_VonBertalanffy.R | 4 - tests/testthat/test_WSWR.R | 4 - tests/testthat/test_capHistConvert.R | 9 --- tests/testthat/test_comparisonsDVR.R |only tests/testthat/test_depletion.R | 4 - tests/testthat/test_mrClosed.R | 4 - tests/testthat/test_mrOpen.R | 4 - tests/testthat/test_removal.R | 4 - 23 files changed, 148 insertions(+), 122 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.5.24 dated 2015-07-07 and 1.5.29 dated 2015-10-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/wsrf-guide.html | 6 +++--- src/dataset.cpp | 2 +- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero <favero@cbs.dtu.dk>
Diff between sequenza versions 2.1.1 dated 2015-01-27 and 2.1.2 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 46 +++++++++++++++++++++++++++++++++++++++++++++- NEWS | 4 ++++ R/next.R | 12 +++++++++++- build/vignette.rds |binary data/CP.example.RData |binary data/example.seqz.rda |binary inst/doc/sequenza.pdf |binary 9 files changed, 72 insertions(+), 14 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.8 dated 2015-08-30 and 0.8.1 dated 2015-10-09
rmarkdown-0.8.1/rmarkdown/DESCRIPTION | 8 - rmarkdown-0.8.1/rmarkdown/MD5 | 32 +++-- rmarkdown-0.8.1/rmarkdown/R/html_dependencies.R | 55 ++-------- rmarkdown-0.8.1/rmarkdown/R/html_resources.R | 24 ++-- rmarkdown-0.8.1/rmarkdown/R/output_format.R | 12 +- rmarkdown-0.8.1/rmarkdown/R/render.R | 3 rmarkdown-0.8.1/rmarkdown/R/word_document.R | 12 +- rmarkdown-0.8.1/rmarkdown/inst/NEWS |only rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/default.html | 2 rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/js/slide-deck.js | 2 rmarkdown-0.8.1/rmarkdown/man/knitr_options.Rd | 8 + rmarkdown-0.8.1/rmarkdown/man/word_document.Rd | 10 + rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/csvs |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/directory-refs.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/empty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/nonempty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/resource-files.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/test-resources.R | 45 ++++++++ rmarkdown-0.8/rmarkdown/NEWS |only 19 files changed, 132 insertions(+), 81 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between paco versions 0.2.1 dated 2015-07-18 and 0.2.2 dated 2015-10-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/PACo.r | 8 +++++--- R/add_pcoord.r | 16 ++++++++-------- R/paco_links.r | 1 + man/PACo.Rd | 4 +++- man/add_pcoord.Rd | 4 +++- 7 files changed, 29 insertions(+), 22 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-62 dated 2015-08-24 and 0.1-63 dated 2015-10-09
Surrogate-0.1-62/Surrogate/R/SummaryTrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/plot.TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/man/TrialLevelContCont.Rd |only Surrogate-0.1-62/Surrogate/man/plot.TrialLevelContCont.Rd |only Surrogate-0.1-63/Surrogate/DESCRIPTION | 8 Surrogate-0.1-63/Surrogate/MD5 | 80 +++-- Surrogate-0.1-63/Surrogate/NAMESPACE | 27 + Surrogate-0.1-63/Surrogate/NEWS | 6 Surrogate-0.1-63/Surrogate/R/FixedBinBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedBinContIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContContIT.r | 27 - Surrogate-0.1-63/Surrogate/R/ICABinBin.R | 142 ++++------ Surrogate-0.1-63/Surrogate/R/MarginalProbs.R | 2 Surrogate-0.1-63/Surrogate/R/Pred.TrialT.ContCont.R |only Surrogate-0.1-63/Surrogate/R/Prentice.R |only Surrogate-0.1-63/Surrogate/R/SummaryITContCont.R | 4 Surrogate-0.1-63/Surrogate/R/SummaryTrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/TwoStageSurvSurv.R | 14 Surrogate-0.1-63/Surrogate/R/UnifixedContCont.R | 4 Surrogate-0.1-63/Surrogate/R/UnimixedContCont.R | 7 Surrogate-0.1-63/Surrogate/R/plot.BinContCombnIT.R |only Surrogate-0.1-63/Surrogate/R/plot.InfoTheoretic.R | 1 Surrogate-0.1-63/Surrogate/R/plot.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/summary.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/summary.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/summary.TwoStageSurvSurv.R | 6 Surrogate-0.1-63/Surrogate/R/summaryBinContCombnIT.R |only Surrogate-0.1-63/Surrogate/data/Schizo.rda |binary Surrogate-0.1-63/Surrogate/man/FixedBinBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedBinContIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContContIT.Rd | 13 Surrogate-0.1-63/Surrogate/man/ICABinBin.Rd | 32 +- Surrogate-0.1-63/Surrogate/man/MixedContContIT.Rd | 5 Surrogate-0.1-63/Surrogate/man/Plot.PredTrialTContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Pred.TrialT.ContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Prentice.Rd |only Surrogate-0.1-63/Surrogate/man/Schizo.Rd | 7 Surrogate-0.1-63/Surrogate/man/SurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/TwoStageSurvSurv.Rd | 6 Surrogate-0.1-63/Surrogate/man/UnifixedContCont.Rd | 5 Surrogate-0.1-63/Surrogate/man/UnimixedContCont.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticBinCombn.Rd |only Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticSurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/plot.MetaAnalytic.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TwoStageSurvSurv.Rd | 12 Surrogate-0.1-63/Surrogate/man/summary.gen.Rd | 20 + 58 files changed, 261 insertions(+), 173 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.2.0 dated 2015-07-01 and 0.3.0 dated 2015-10-09
rerddap-0.2.0/rerddap/R/cache.R |only rerddap-0.2.0/rerddap/tests/testthat/test-griddap.R |only rerddap-0.3.0/rerddap/DESCRIPTION | 6 rerddap-0.3.0/rerddap/MD5 | 62 ++++--- rerddap-0.3.0/rerddap/NAMESPACE | 20 ++ rerddap-0.3.0/rerddap/NEWS | 20 ++ rerddap-0.3.0/rerddap/R/cache_delete.R |only rerddap-0.3.0/rerddap/R/cache_details.R |only rerddap-0.3.0/rerddap/R/cache_list.R |only rerddap-0.3.0/rerddap/R/convert_time.R | 2 rerddap-0.3.0/rerddap/R/convert_units.R | 2 rerddap-0.3.0/rerddap/R/fipscounty.R | 2 rerddap-0.3.0/rerddap/R/grid.R | 19 +- rerddap-0.3.0/rerddap/R/info.R | 3 rerddap-0.3.0/rerddap/R/keywords.R | 2 rerddap-0.3.0/rerddap/R/ncdf_helpers.R | 20 ++ rerddap-0.3.0/rerddap/R/rerddap-package.r | 6 rerddap-0.3.0/rerddap/R/search_adv.R | 1 rerddap-0.3.0/rerddap/R/table.R | 8 - rerddap-0.3.0/rerddap/README.md | 2 rerddap-0.3.0/rerddap/build/vignette.rds |binary rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.Rmd | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.html | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.Rmd | 15 + rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.md | 148 +++++++++---------- rerddap-0.3.0/rerddap/man/cache_delete.Rd |only rerddap-0.3.0/rerddap/man/cache_details.Rd |only rerddap-0.3.0/rerddap/man/cache_list.Rd | 29 +-- rerddap-0.3.0/rerddap/man/convert_time.Rd | 2 rerddap-0.3.0/rerddap/man/convert_units.Rd | 2 rerddap-0.3.0/rerddap/man/fipscounty.Rd | 2 rerddap-0.3.0/rerddap/man/griddap.Rd | 10 + rerddap-0.3.0/rerddap/man/key_words.Rd | 2 rerddap-0.3.0/rerddap/man/tabledap.Rd | 5 rerddap-0.3.0/rerddap/tests/testthat/test-griddap.r |only rerddap-0.3.0/rerddap/vignettes/rerddap_vignette.Rmd | 148 +++++++++---------- 36 files changed, 456 insertions(+), 378 deletions(-)
Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.7 dated 2015-08-03 and 2.9 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/pedgene.R | 25 ++++++++++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ tests/test.pedgene.expanded.R | 5 +++++ tests/test.pedgene.expanded.Rout.save | 25 +++++++++++++++++-------- 7 files changed, 53 insertions(+), 27 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g.,
http://en.wikipedia.org/wiki/GitHub#Gist,
https://help.github.com/articles/about-gists/). A 'gist' is simply one or
more files with code/text/images/etc. This package allows the user to
create new 'gists', update 'gists' with new files, rename files, delete files,
get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in
your default browser, get embed code for a 'gist', list 'gist' 'commits', and
get rate limit information when 'authenticated'. Some requests require
authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.3.0 dated 2015-07-03 and 0.3.4 dated 2015-10-09
gistr-0.3.0/gistr/tests/localtests/figure |only gistr-0.3.0/gistr/tests/testthat/figure |only gistr-0.3.4/gistr/DESCRIPTION | 8 - gistr-0.3.4/gistr/MD5 | 34 ++---- gistr-0.3.4/gistr/NAMESPACE | 2 gistr-0.3.4/gistr/R/gist_create.R | 19 ++- gistr-0.3.4/gistr/R/gist_create_git.R |only gistr-0.3.4/gistr/R/gist_create_obj.R | 2 gistr-0.3.4/gistr/R/gistr-package.R | 45 ++++++-- gistr-0.3.4/gistr/R/tabl.R | 90 ++++++++++++---- gistr-0.3.4/gistr/README.md | 2 gistr-0.3.4/gistr/build/vignette.rds |binary gistr-0.3.4/gistr/inst/ignore/gist_create_git.R | 21 +++ gistr-0.3.4/gistr/man/create_gists.Rd |only gistr-0.3.4/gistr/man/gist_create.Rd | 2 gistr-0.3.4/gistr/man/gist_create_git.Rd |only gistr-0.3.4/gistr/man/gist_create_obj.Rd | 2 gistr-0.3.4/gistr/man/tabl.Rd | 33 +++++ gistr-0.3.4/gistr/tests/testthat/test-gist_create_git.R |only 19 files changed, 198 insertions(+), 62 deletions(-)
Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>
Diff between fishmethods versions 1.8-0 dated 2015-05-28 and 1.9-0 dated 2015-10-09
DESCRIPTION | 10 - MD5 | 20 ++- NAMESPACE | 14 ++ R/agesurv.R | 25 ++++ R/astrocalc4r.R |only R/bhnoneq.R | 271 +++++++++++++++++++++++++++++------------------------ R/cpuekapp.R |only data/kappenman.rda |only man/agesurv.Rd | 12 +- man/astrocalc4r.Rd |only man/bheq2.Rd | 2 man/bhnoneq.Rd | 27 ++--- man/cpuekapp.Rd |only man/kappenman.Rd |only 14 files changed, 231 insertions(+), 150 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.3 dated 2015-07-09 and 1.31.4 dated 2015-10-09
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++--------- R/CA.R | 9 +++--- R/FAMD.R | 3 +- R/HCPC.R | 4 +-- R/MCA.R | 7 +++-- R/MFA.R | 5 ++- R/PCA.R | 4 +-- R/plot.HCPC.R | 2 - R/plotellipses.r | 9 ++++-- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary 12 files changed, 40 insertions(+), 33 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare and David Loris
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-09
ChannelAttribution-1.1/ChannelAttribution/man/Dy.Rd |only ChannelAttribution-1.1/ChannelAttribution/vignettes |only ChannelAttribution-1.2/ChannelAttribution/DESCRIPTION | 10 ChannelAttribution-1.2/ChannelAttribution/MD5 | 21 ChannelAttribution-1.2/ChannelAttribution/R/ChannelAttribution.R | 21 ChannelAttribution-1.2/ChannelAttribution/data/PathData.rda |binary ChannelAttribution-1.2/ChannelAttribution/man/ChannelAttribution-package.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/man/Data.Rd |only ChannelAttribution-1.2/ChannelAttribution/man/heuristic_models.Rd | 16 ChannelAttribution-1.2/ChannelAttribution/man/markov_model.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.cpp | 1026 ++++++---- ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.h | 8 12 files changed, 741 insertions(+), 427 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (including memory profiling) in a visually appealing way.
It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.2.5 dated 2015-07-20 and 0.3.1 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 12 - R/aprof.R | 416 +++++++++++++++++++++++++++---------------------- man/aprof.Rd | 50 +++-- man/plot.Rd | 10 - man/print.Rd | 2 man/readLineDensity.Rd | 4 7 files changed, 283 insertions(+), 223 deletions(-)
Title: An R Package for Quantification of Pinned Microbial Culture
Description: The goal of this package is to allow users to robustly
and quickly grid and quantify sizes of pinned colonies in plate images.
gitter works by first finding the grid of colonies from a preprocessed image
and then locating the bounds of each colony separately.
It includes several image pre-processing techniques, such
as autorotation of plates, noise removal, contrast adjustment and image
resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>
Diff between gitter versions 1.0.4 dated 2014-01-23 and 1.1 dated 2015-10-09
gitter-1.0.4/gitter/R/Help.R |only gitter-1.0.4/gitter/R/Main.R |only gitter-1.0.4/gitter/R/Peaks.R |only gitter-1.0.4/gitter/man/gitter-package.Rd |only gitter-1.1/gitter/DESCRIPTION | 20 ++-- gitter-1.1/gitter/MD5 | 29 +++--- gitter-1.1/gitter/NAMESPACE | 27 +++++- gitter-1.1/gitter/R/help.r |only gitter-1.1/gitter/R/io.r |only gitter-1.1/gitter/R/main.r |only gitter-1.1/gitter/R/peaks.r |only gitter-1.1/gitter/R/plot.r |only gitter-1.1/gitter/build/BUILD.R | 21 +++- gitter-1.1/gitter/man/gitter.Rd | 131 +++++++++--------------------- gitter-1.1/gitter/man/gitter.batch.Rd | 68 ++++----------- gitter-1.1/gitter/man/gitter.demo.Rd | 45 +--------- gitter-1.1/gitter/man/gitter.read.Rd | 46 ++-------- gitter-1.1/gitter/man/plate.warnings.Rd | 43 ++------- gitter-1.1/gitter/man/plot.gitter.Rd | 106 ++++++++---------------- gitter-1.1/gitter/man/summary.gitter.Rd | 47 ++-------- 20 files changed, 205 insertions(+), 378 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description:
We provide a set of functions to retrieve information about GIMMS NDVI3g
files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native
binary (ENVI) format directly into R based on the widely applied 'raster'
package; and calculate monthly value composites (e.g. maximum value
composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.1 dated 2015-10-08 and 0.1.1 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/createHdr.R | 2 ++ man/createHdr.Rd | 2 ++ 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Utility Sparse Matrix Functions for Quantitative Language
Comparison
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>
Diff between qlcMatrix versions 0.9.4 dated 2015-04-27 and 0.9.5 dated 2015-10-09
DESCRIPTION | 9 +- MD5 | 28 ++++---- NAMESPACE | 5 + NEWS.md |only R/array.R |only R/assoc.R | 4 - R/base.R | 84 +++++++++++++----------- R/split.R | 7 +- R/utils.R | 42 ++++++++---- build/vignette.rds |binary inst/doc/transformingDataSparse.html | 19 ++++- man/array.Rd |only man/bibles.Rd | 6 - man/qlcMatrix-package.Rd | 6 - man/rowMax.Rd | 2 man/unfold.Rd | 118 ++++++++++++++++++++--------------- man/unfoldBlockMatrix.Rd |only 17 files changed, 196 insertions(+), 134 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative
discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences,
turns of talk, syllables and other assorted analysis tasks. The
package provides parsing tools for preparing transcript data.
Many functions enable the user to aggregate data by any number
of grouping variables, providing analysis and seamless
integration with other R packages that undertake higher level
analysis and visualization of text. This affords the user a
more efficient and targeted analysis. 'qdap' is designed for
transcript analysis, however, many functions are applicable to
other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.2 dated 2015-07-05 and 2.2.4 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 44 ++--- NAMESPACE | 1 NEWS | 30 +++ R/add_s.R |only R/as.tdm.R | 2 R/automated_readability_index.R | 2 R/common.R | 3 R/formality.R | 3 R/lexical_classification.R | 28 ++- R/name2sex.R | 64 ++++++-- R/pos.R | 22 +- R/question_type.R | 4 R/word_cor.R | 15 + README.md | 3 inst/CITATION | 6 inst/Rmd_vignette/qdap_vignette.Rmd | 265 +++++++++++++++++----------------- inst/doc/cleaning_and_debugging.pdf |binary inst/doc/tm_package_compatibility.pdf |binary man/add_s.Rd |only man/as.tdm.Rd | 2 man/lexical_classification.Rd | 4 man/pos.Rd | 7 man/word_cor.Rd | 16 +- 24 files changed, 313 insertions(+), 220 deletions(-)
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite,
and topographic map servers are directly supported, including CloudMade,
Mapnik, Bing, stamen, and MapQuest. Maps can be plotted using either base
graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Author: Ian Fellows, using the JMapViewer library by Jan Peter Stotz
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.3.1 dated 2013-04-14 and 0.3.2 dated 2015-10-09
OpenStreetMap-0.3.1/OpenStreetMap/javasrc |only OpenStreetMap-0.3.1/OpenStreetMap/man/raster.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/DESCRIPTION | 24 - OpenStreetMap-0.3.2/OpenStreetMap/MD5 | 123 +++++----- OpenStreetMap-0.3.2/OpenStreetMap/NAMESPACE | 13 - OpenStreetMap-0.3.2/OpenStreetMap/R/OpenStreetMap-package.R | 4 OpenStreetMap-0.3.2/OpenStreetMap/R/autoplot.R | 23 - OpenStreetMap-0.3.2/OpenStreetMap/R/osm.R | 20 - OpenStreetMap-0.3.2/OpenStreetMap/R/zzz.R | 13 - OpenStreetMap-0.3.2/OpenStreetMap/inst/java/RTileController.jar |binary OpenStreetMap-0.3.2/OpenStreetMap/java |only OpenStreetMap-0.3.2/OpenStreetMap/man/LA_places.Rd | 5 OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.OpenStreetMap.Rd | 15 - OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.osmtile.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/getMapInfo.Rd | 7 OpenStreetMap-0.3.2/OpenStreetMap/man/launchMapHelper.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/longlat.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/openmap.Rd | 42 +-- OpenStreetMap-0.3.2/OpenStreetMap/man/openproj.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/osm.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/osmtile.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.OpenStreetMap.Rd | 19 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.osmtile.Rd | 18 - OpenStreetMap-0.3.2/OpenStreetMap/man/print.OpenStreetMap.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/projectMercator.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/raster-OpenStreetMap-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/raster-osmtile-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/setCloudMadeKey.Rd | 9 OpenStreetMap-0.3.2/OpenStreetMap/man/states.Rd | 5 29 files changed, 224 insertions(+), 206 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.2 dated 2015-06-29 and 1.2.3 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS | 7 +++++++ R/HelpersMG-package.R | 4 ++-- R/LD50.R | 4 ++-- R/MHalgoGen.R | 20 +++++++++----------- R/sun.info.R | 18 ++++++++---------- R/wget.R |only man/HelpersMG-package.Rd | 4 ++-- man/sun.info.Rd | 14 +++++++------- man/wget.Rd |only 12 files changed, 53 insertions(+), 47 deletions(-)
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-09
DESCRIPTION | 6 MD5 | 61 ++--- NAMESPACE | 22 - R/GUI.R | 11 R/RcppExports.R | 272 ++++++++++++------------ R/arrMat.R | 10 R/basisFunctions.R | 42 +-- R/boldContrast.R | 148 ++++++------- R/fd.R | 34 +-- R/fiach.R | 18 + R/gaussKernel.R | 20 - R/highBasis.R | 18 - R/highPass.R | 34 +-- R/kaiserWin.R | 48 ++-- R/kmeansMask.R | 14 - R/lowBasis.R | 22 - R/matArr.R | 6 R/naSpline.R | 82 +++---- R/quantMask.r | 18 - R/rawPeriodogram.R | 64 ++--- R/sinc.R | 30 +- R/spmHrf.R | 18 - R/spmOrth.R | 24 +- R/t2Grey.R | 12 - R/t2sGrey.R | 26 +- R/viewR.R | 531 +++++++++++------------------------------------- inst/extdata/mni.nii.gz |only man/GUI.Rd | 42 +-- man/rawPeriodogram.Rd | 108 ++++----- man/rp.Rd | 68 +++--- man/sinc.Rd | 86 +++---- man/viewR.Rd | 5 32 files changed, 827 insertions(+), 1073 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.0 dated 2015-09-23 and 0.6.1 dated 2015-10-08
DESCRIPTION | 8 - INDEX | 1 MD5 | 27 ++--- NAMESPACE | 6 + R/nhanes.R | 204 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/Introducing_nhanesA.R | 9 - inst/doc/Introducing_nhanesA.Rmd | 22 ++-- inst/doc/Introducing_nhanesA.html | 47 ++++---- man/browseNHANES.Rd |only man/nhanes.Rd | 4 man/nhanesAttr.Rd | 2 man/nhanesTables.Rd | 10 + man/nhanesTranslate.Rd | 1 vignettes/Introducing_nhanesA.Rmd | 22 ++-- 15 files changed, 218 insertions(+), 145 deletions(-)
Title: Create Graph Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Andrei Kashcha [aut, cph] (vivagraphjs library in htmlwidgets/lib,
https://github.com/anvaka/VivaGraphJS),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.7 dated 2015-06-11 and 0.8 dated 2015-10-08
DiagrammeR-0.7/DiagrammeR/R/edge_relationship.R |only DiagrammeR-0.7/DiagrammeR/build |only DiagrammeR-0.7/DiagrammeR/inst/doc |only DiagrammeR-0.7/DiagrammeR/man/edge_relationship.Rd |only DiagrammeR-0.7/DiagrammeR/vignettes |only DiagrammeR-0.8/DiagrammeR/DESCRIPTION | 61 DiagrammeR-0.8/DiagrammeR/LICENSE | 2 DiagrammeR-0.8/DiagrammeR/MD5 | 250 + DiagrammeR-0.8/DiagrammeR/NAMESPACE | 24 DiagrammeR-0.8/DiagrammeR/R/DiagrammeR.R | 46 DiagrammeR-0.8/DiagrammeR/R/add_edges.R | 217 + DiagrammeR-0.8/DiagrammeR/R/add_node.R | 295 +- DiagrammeR-0.8/DiagrammeR/R/add_to_series.R | 45 DiagrammeR-0.8/DiagrammeR/R/combine_edges.R | 15 DiagrammeR-0.8/DiagrammeR/R/combine_graphs.R |only DiagrammeR-0.8/DiagrammeR/R/combine_nodes.R | 11 DiagrammeR-0.8/DiagrammeR/R/country_graph.R |only DiagrammeR-0.8/DiagrammeR/R/create_edges.R | 13 DiagrammeR-0.8/DiagrammeR/R/create_graph.R | 863 +++--- DiagrammeR-0.8/DiagrammeR/R/create_nodes.R | 26 DiagrammeR-0.8/DiagrammeR/R/create_random_graph.R |only DiagrammeR-0.8/DiagrammeR/R/create_series.R | 24 DiagrammeR-0.8/DiagrammeR/R/create_subgraph.R | 19 DiagrammeR-0.8/DiagrammeR/R/delete_edge.R | 17 DiagrammeR-0.8/DiagrammeR/R/delete_node.R | 10 DiagrammeR-0.8/DiagrammeR/R/display_graph_object.R | 9 DiagrammeR-0.8/DiagrammeR/R/edge_count.R | 80 DiagrammeR-0.8/DiagrammeR/R/edge_info.R | 52 DiagrammeR-0.8/DiagrammeR/R/edge_present.R | 15 DiagrammeR-0.8/DiagrammeR/R/edge_rel.R |only DiagrammeR-0.8/DiagrammeR/R/get_edges.R | 18 DiagrammeR-0.8/DiagrammeR/R/get_nodes.R | 11 DiagrammeR-0.8/DiagrammeR/R/get_predecessors.R | 5 DiagrammeR-0.8/DiagrammeR/R/get_successors.R | 7 DiagrammeR-0.8/DiagrammeR/R/grViz.R | 69 DiagrammeR-0.8/DiagrammeR/R/graph_count.R | 25 DiagrammeR-0.8/DiagrammeR/R/graphviz_export.R | 39 DiagrammeR-0.8/DiagrammeR/R/import_graph.R |only DiagrammeR-0.8/DiagrammeR/R/is_graph_directed.R | 3 DiagrammeR-0.8/DiagrammeR/R/is_graph_empty.R | 4 DiagrammeR-0.8/DiagrammeR/R/mermaid.R | 4 DiagrammeR-0.8/DiagrammeR/R/node_count.R | 81 DiagrammeR-0.8/DiagrammeR/R/node_info.R | 20 DiagrammeR-0.8/DiagrammeR/R/node_present.R | 8 DiagrammeR-0.8/DiagrammeR/R/node_type.R | 18 DiagrammeR-0.8/DiagrammeR/R/remove_from_series.R | 31 DiagrammeR-0.8/DiagrammeR/R/render_graph.R | 251 - DiagrammeR-0.8/DiagrammeR/R/render_graph_from_series.R | 42 DiagrammeR-0.8/DiagrammeR/R/roll_palette.R | 41 DiagrammeR-0.8/DiagrammeR/R/scale_edges.R | 27 DiagrammeR-0.8/DiagrammeR/R/scale_nodes.R | 26 DiagrammeR-0.8/DiagrammeR/R/select_graph_from_series.R |only DiagrammeR-0.8/DiagrammeR/R/series_info.R | 6 DiagrammeR-0.8/DiagrammeR/R/spectools.R | 3 DiagrammeR-0.8/DiagrammeR/R/subset_series.R | 36 DiagrammeR-0.8/DiagrammeR/R/trigger_script.R | 6 DiagrammeR-0.8/DiagrammeR/R/visnetwork.R |only DiagrammeR-0.8/DiagrammeR/R/vivagraph.R |only DiagrammeR-0.8/DiagrammeR/R/x11_hex.R | 3 DiagrammeR-0.8/DiagrammeR/README.md | 36 DiagrammeR-0.8/DiagrammeR/inst/examples |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/VivaGraphJS |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.css | 284 +- DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 23 DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/viz/viz.js | 1337 ---------- DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/vivagraph.js |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/vivagraph.yaml |only DiagrammeR-0.8/DiagrammeR/man/DiagrammeR.Rd | 13 DiagrammeR-0.8/DiagrammeR/man/DiagrammeROutput.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/add_edges.Rd | 40 DiagrammeR-0.8/DiagrammeR/man/add_node.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/add_to_series.Rd | 27 DiagrammeR-0.8/DiagrammeR/man/combine_edges.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/combine_graphs.Rd |only DiagrammeR-0.8/DiagrammeR/man/combine_nodes.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/country_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/create_edges.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/create_graph.Rd | 71 DiagrammeR-0.8/DiagrammeR/man/create_nodes.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/create_random_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/create_series.Rd | 23 DiagrammeR-0.8/DiagrammeR/man/create_subgraph.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/delete_edge.Rd | 7 DiagrammeR-0.8/DiagrammeR/man/display_graph_object.Rd | 9 DiagrammeR-0.8/DiagrammeR/man/edge_count.Rd | 18 DiagrammeR-0.8/DiagrammeR/man/edge_info.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/edge_present.Rd | 9 DiagrammeR-0.8/DiagrammeR/man/edge_rel.Rd |only DiagrammeR-0.8/DiagrammeR/man/exportSVG.Rd | 11 DiagrammeR-0.8/DiagrammeR/man/get_edges.Rd | 14 DiagrammeR-0.8/DiagrammeR/man/get_nodes.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/get_predecessors.Rd | 5 DiagrammeR-0.8/DiagrammeR/man/get_successors.Rd | 5 DiagrammeR-0.8/DiagrammeR/man/grViz.Rd | 17 DiagrammeR-0.8/DiagrammeR/man/grVizOutput.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/graph_count.Rd | 25 DiagrammeR-0.8/DiagrammeR/man/import_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/is_graph_directed.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/is_graph_empty.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/mermaid.Rd | 4 DiagrammeR-0.8/DiagrammeR/man/node_count.Rd | 11 DiagrammeR-0.8/DiagrammeR/man/node_info.Rd | 20 DiagrammeR-0.8/DiagrammeR/man/node_present.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/node_type.Rd | 18 DiagrammeR-0.8/DiagrammeR/man/remove_from_series.Rd | 31 DiagrammeR-0.8/DiagrammeR/man/renderDiagrammeR.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/renderGrViz.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/render_graph.Rd | 41 DiagrammeR-0.8/DiagrammeR/man/render_graph_from_series.Rd | 36 DiagrammeR-0.8/DiagrammeR/man/replace_in_spec.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/roll_palette.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/scale_edges.Rd | 24 DiagrammeR-0.8/DiagrammeR/man/scale_nodes.Rd | 23 DiagrammeR-0.8/DiagrammeR/man/select_graph_from_series.Rd |only DiagrammeR-0.8/DiagrammeR/man/series_info.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/subset_series.Rd | 38 DiagrammeR-0.8/DiagrammeR/man/trigger_script.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/visnetwork.Rd |only DiagrammeR-0.8/DiagrammeR/man/vivagraph.Rd |only DiagrammeR-0.8/DiagrammeR/man/x11_hex.Rd | 3 DiagrammeR-0.8/DiagrammeR/tests |only 121 files changed, 2277 insertions(+), 2984 deletions(-)
More information about SurvRegCensCov at CRAN
Permanent link
Title: Path Manipulation Utilities
Description: Utilities for paths, files and directories.
Author: Richard Cotton [aut, cre], Janko Thyson [ctb]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between pathological versions 0.0-6 dated 2015-05-10 and 0.0-7 dated 2015-10-08
pathological-0.0-6/pathological/inst |only pathological-0.0-6/pathological/tests/run-all.R |only pathological-0.0-7/pathological/DESCRIPTION | 12 pathological-0.0-7/pathological/MD5 | 35 +- pathological-0.0-7/pathological/NAMESPACE | 99 +++--- pathological-0.0-7/pathological/NEWS | 7 pathological-0.0-7/pathological/R/paths.R | 247 +++++++++++++--- pathological-0.0-7/pathological/README.md | 3 pathological-0.0-7/pathological/man/choose_files.Rd |only pathological-0.0-7/pathological/man/r_profile.Rd | 23 + pathological-0.0-7/pathological/man/standardize_path.Rd | 7 pathological-0.0-7/pathological/tests/testthat |only pathological-0.0-7/pathological/tests/testthat.R |only 13 files changed, 310 insertions(+), 123 deletions(-)
Title: NeuroAnatomy Toolbox (nat) Extension for Handling Template
Brains
Description: Extends package nat (NeuroAnatomy Toolbox) by providing objects
and functions for handling template brains.
Author: James Manton and Gregory Jefferis
Maintainer: James Manton <ajd.manton@googlemail.com>
Diff between nat.templatebrains versions 0.6 dated 2015-07-01 and 0.6.1 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 4 ++++ R/reg_repos.R | 4 ++-- R/transformation.R | 2 +- README.md | 2 ++ man/add_reg_folders.Rd | 2 +- 7 files changed, 20 insertions(+), 14 deletions(-)
More information about nat.templatebrains at CRAN
Permanent link
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate. The analysis of paired
receiver operating curves is supported as well, so that a comparison of two predictors is possible.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.2.1 dated 2015-06-07 and 0.3.0 dated 2015-10-08
fbroc-0.2.1/fbroc/man/conf.roc.Rd |only fbroc-0.2.1/fbroc/man/perf.roc.Rd |only fbroc-0.3.0/fbroc/DESCRIPTION | 13 + fbroc-0.3.0/fbroc/MD5 | 61 +++++---- fbroc-0.3.0/fbroc/NAMESPACE | 21 ++- fbroc-0.3.0/fbroc/R/RcppExports.R | 44 +++++- fbroc-0.3.0/fbroc/R/fbroc.R | 72 ++++++++-- fbroc-0.3.0/fbroc/R/fbroc.helper.functions.R |only fbroc-0.3.0/fbroc/R/fbroc.methods.R | 115 +++++++++++------ fbroc-0.3.0/fbroc/R/fbroc.paired.R |only fbroc-0.3.0/fbroc/R/fbroc.paired.methods.R |only fbroc-0.3.0/fbroc/R/fbroc.perf.R | 19 +- fbroc-0.3.0/fbroc/R/fbroc.roc.R | 76 +++++++---- fbroc-0.3.0/fbroc/R/perf.paired.roc.R |only fbroc-0.3.0/fbroc/README.md | 6 fbroc-0.3.0/fbroc/man/boot.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/boot.roc.Rd | 1 fbroc-0.3.0/fbroc/man/conf.Rd |only fbroc-0.3.0/fbroc/man/conf.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/conf.fbroc.roc.Rd |only fbroc-0.3.0/fbroc/man/extract.roc.Rd |only fbroc-0.3.0/fbroc/man/fbroc.Rd | 42 ++++-- fbroc-0.3.0/fbroc/man/perf.Rd |only fbroc-0.3.0/fbroc/man/perf.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/perf.fbroc.roc.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.conf.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.conf.paired.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.perf.Rd | 12 - fbroc-0.3.0/fbroc/man/plot.fbroc.perf.paired.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.roc.Rd | 12 + fbroc-0.3.0/fbroc/man/print.fbroc.perf.Rd | 2 fbroc-0.3.0/fbroc/man/print.fbroc.perf.paired.Rd |only fbroc-0.3.0/fbroc/src/RcppExports.cpp | 147 ++++++++++++++++++++-- fbroc-0.3.0/fbroc/src/interface.common.cpp | 16 ++ fbroc-0.3.0/fbroc/src/interface.common.h | 5 fbroc-0.3.0/fbroc/src/interface.paired.cpp | 151 +++++++++++++++++++++++ fbroc-0.3.0/fbroc/src/interface.single.cpp | 49 ++++--- fbroc-0.3.0/fbroc/src/performance.h | 3 fbroc-0.3.0/fbroc/src/roc.cpp | 133 +++++++++++++------- fbroc-0.3.0/fbroc/src/roc.h | 2 41 files changed, 766 insertions(+), 236 deletions(-)
Title: Fast, Low Memory-Footprint Digests of R Objects
Description: Provides an R interface to Bob Jenkin's streaming,
non-cryptographic 'SpookyHash' hash algorithm for use in digest-based
comparisons of R objects. 'fastdigest' plugs directly into R's internal
serialization machinery, allowing digests of all R objects the serialize()
function supports, including reference-style objects via custom hooks. Speed is
high and scales linearly by object size; memory usage is constant and
negligible.
Author: Gabriel Becker, Bob Jenkins (SpookyHash algorithm and C++ implementation)
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between fastdigest versions 0.6-2 dated 2015-10-07 and 0.6-3 dated 2015-10-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 ++++- src/SpookyV2.cpp | 3 ++- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.3.0 dated 2015-09-24 and 1.3.1 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/dunn.test.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.4-0 dated 2015-09-08 and 1.5-0 dated 2015-10-08
DESCRIPTION | 11 +++++------ MD5 | 7 ++++--- inst/CITATION |only inst/NEWS | 12 +++++++++--- man/BIFIEsurvey-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.4 dated 2015-09-10 and 0.4.6 dated 2015-10-08
DESCRIPTION | 12 MD5 | 100 ++-- NAMESPACE | 1 R/incPercentile.R | 37 - R/linarpr.R | 43 -- R/linarpt.R | 40 - R/linarr.R | 65 +-- R/lingini.R | 41 - R/lingini2.R | 40 - R/lingpg.R | 50 +- R/linpoormed.R | 41 - R/linqsr.R | 39 - R/linrmir.R | 47 +- R/linrmpg.R | 45 -- R/residual_est.R | 2 R/var_srs.R | 10 R/vardchanges.R | 58 -- R/vardchangespoor.R | 84 +-- R/vardcros.R | 1030 +++++++++++++++++++++++------------------------- R/vardcrospoor.R | 80 +-- R/vardom.R | 89 +--- R/vardom_othstr.R | 94 +--- R/vardomh.R | 97 +--- R/variance_est.R | 52 -- R/variance_othstr.R | 80 +-- R/varpoord.R | 101 ++-- inst/CITATION | 4 inst/NEWS | 10 man/domain.Rd | 10 man/incPercentile.Rd | 12 man/linarpr.Rd | 20 man/linarpt.Rd | 14 man/linarr.Rd | 32 - man/lingini.Rd | 14 man/lingini2.Rd | 14 man/lingpg.Rd | 19 man/linpoormed.Rd | 16 man/linqsr.Rd | 14 man/linrmir.Rd | 24 - man/linrmpg.Rd | 26 - man/vardchanges.Rd | 21 man/vardchangespoor.Rd | 32 - man/vardcros.Rd | 20 man/vardcrospoor.Rd | 34 - man/vardom.Rd | 42 - man/vardom_othstr.Rd | 49 -- man/vardomh.Rd | 47 -- man/vardpoor-package.Rd | 6 man/variance_est.Rd | 61 -- man/variance_othstr.Rd | 19 man/varpoord.Rd | 58 +- 51 files changed, 1351 insertions(+), 1645 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm, dppm similar to glm. Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm. The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-2 dated 2015-06-29 and 1.43-0 dated 2015-10-08
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spatstat-1.43-0/spatstat/man/as.owin.Rd | 9 spatstat-1.43-0/spatstat/man/as.ppm.Rd | 15 spatstat-1.43-0/spatstat/man/austates.Rd |only spatstat-1.43-0/spatstat/man/bdspots.Rd | 3 spatstat-1.43-0/spatstat/man/branchlabelfun.Rd | 4 spatstat-1.43-0/spatstat/man/bw.ppl.Rd | 6 spatstat-1.43-0/spatstat/man/cdf.test.mppm.Rd | 36 spatstat-1.43-0/spatstat/man/coef.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/collapse.fv.Rd | 22 spatstat-1.43-0/spatstat/man/colourtools.Rd | 82 + spatstat-1.43-0/spatstat/man/contour.im.Rd | 26 spatstat-1.43-0/spatstat/man/dclf.progress.Rd | 40 spatstat-1.43-0/spatstat/man/dclf.sigtrace.Rd |only spatstat-1.43-0/spatstat/man/dclf.test.Rd | 53 - spatstat-1.43-0/spatstat/man/default.expand.Rd | 6 spatstat-1.43-0/spatstat/man/default.rmhcontrol.Rd | 8 spatstat-1.43-0/spatstat/man/density.lpp.Rd | 33 spatstat-1.43-0/spatstat/man/detpointprocfamilyfun.Rd |only spatstat-1.43-0/spatstat/man/dg.envelope.Rd |only spatstat-1.43-0/spatstat/man/dg.progress.Rd |only spatstat-1.43-0/spatstat/man/dg.sigtrace.Rd |only spatstat-1.43-0/spatstat/man/dg.test.Rd |only spatstat-1.43-0/spatstat/man/diagnose.ppm.Rd | 3 spatstat-1.43-0/spatstat/man/dim.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/distfun.lpp.Rd | 2 spatstat-1.43-0/spatstat/man/dkernel.Rd |only spatstat-1.43-0/spatstat/man/domain.Rd | 5 spatstat-1.43-0/spatstat/man/dppBessel.Rd |only spatstat-1.43-0/spatstat/man/dppCauchy.Rd |only spatstat-1.43-0/spatstat/man/dppGauss.Rd |only spatstat-1.43-0/spatstat/man/dppMatern.Rd |only spatstat-1.43-0/spatstat/man/dppPowerExp.Rd |only spatstat-1.43-0/spatstat/man/dppapproxkernel.Rd |only spatstat-1.43-0/spatstat/man/dppapproxpcf.Rd |only spatstat-1.43-0/spatstat/man/dppeigen.Rd |only spatstat-1.43-0/spatstat/man/dppkernel.Rd |only spatstat-1.43-0/spatstat/man/dppm.Rd |only spatstat-1.43-0/spatstat/man/dppparbounds.Rd |only spatstat-1.43-0/spatstat/man/dppspecden.Rd |only spatstat-1.43-0/spatstat/man/dppspecdenrange.Rd |only spatstat-1.43-0/spatstat/man/emend.Rd |only spatstat-1.43-0/spatstat/man/emend.ppm.Rd |only spatstat-1.43-0/spatstat/man/envelope.Rd | 35 spatstat-1.43-0/spatstat/man/envelope.lpp.Rd | 15 spatstat-1.43-0/spatstat/man/envelope.pp3.Rd | 13 spatstat-1.43-0/spatstat/man/fitted.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/fixef.mppm.Rd |only spatstat-1.43-0/spatstat/man/fourierbasis.Rd |only spatstat-1.43-0/spatstat/man/gordon.Rd | 5 spatstat-1.43-0/spatstat/man/hierpair.family.Rd | 8 spatstat-1.43-0/spatstat/man/intensity.dppm.Rd |only spatstat-1.43-0/spatstat/man/intensity.lpp.Rd | 2 spatstat-1.43-0/spatstat/man/intensity.ppx.Rd |only spatstat-1.43-0/spatstat/man/is.stationary.Rd | 23 spatstat-1.43-0/spatstat/man/kernel.factor.Rd |only spatstat-1.43-0/spatstat/man/kppm.Rd | 5 spatstat-1.43-0/spatstat/man/lgcp.estK.Rd | 13 spatstat-1.43-0/spatstat/man/linearKcross.Rd | 4 spatstat-1.43-0/spatstat/man/linearKcross.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/linearKdot.Rd | 6 spatstat-1.43-0/spatstat/man/linearKdot.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/linearmarkconnect.Rd | 4 spatstat-1.43-0/spatstat/man/linearmarkequal.Rd | 2 spatstat-1.43-0/spatstat/man/linearpcfcross.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfcross.inhom.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfdot.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfdot.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/logLik.dppm.Rd |only spatstat-1.43-0/spatstat/man/logLik.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/logLik.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/lpp.Rd | 7 spatstat-1.43-0/spatstat/man/markcorr.Rd | 13 spatstat-1.43-0/spatstat/man/markcrosscorr.Rd |only spatstat-1.43-0/spatstat/man/mergeLevels.Rd | 12 spatstat-1.43-0/spatstat/man/methods.dppm.Rd |only spatstat-1.43-0/spatstat/man/methods.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/methods.linfun.Rd | 6 spatstat-1.43-0/spatstat/man/methods.lppm.Rd | 18 spatstat-1.43-0/spatstat/man/model.frame.ppm.Rd | 16 spatstat-1.43-0/spatstat/man/model.images.Rd | 18 spatstat-1.43-0/spatstat/man/model.matrix.ppm.Rd | 19 spatstat-1.43-0/spatstat/man/mppm.Rd | 68 + spatstat-1.43-0/spatstat/man/nnfun.lpp.Rd | 7 spatstat-1.43-0/spatstat/man/objsurf.Rd | 11 spatstat-1.43-0/spatstat/man/parameters.Rd | 5 spatstat-1.43-0/spatstat/man/plot.bermantest.Rd | 6 spatstat-1.43-0/spatstat/man/plot.dppm.Rd |only spatstat-1.43-0/spatstat/man/plot.influence.ppm.Rd | 2 spatstat-1.43-0/spatstat/man/plot.linim.Rd | 6 spatstat-1.43-0/spatstat/man/plot.mppm.Rd | 61 - spatstat-1.43-0/spatstat/man/plot.ppp.Rd | 5 spatstat-1.43-0/spatstat/man/plot.slrm.Rd | 4 spatstat-1.43-0/spatstat/man/pool.envelope.Rd | 1 spatstat-1.43-0/spatstat/man/ppm.Rd | 2 spatstat-1.43-0/spatstat/man/ppm.ppp.Rd | 18 spatstat-1.43-0/spatstat/man/predict.dppm.Rd |only spatstat-1.43-0/spatstat/man/predict.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/predict.lppm.Rd | 2 spatstat-1.43-0/spatstat/man/predict.mppm.Rd | 24 spatstat-1.43-0/spatstat/man/predict.slrm.Rd | 2 spatstat-1.43-0/spatstat/man/progressreport.Rd | 41 spatstat-1.43-0/spatstat/man/quadrat.test.mppm.Rd | 25 spatstat-1.43-0/spatstat/man/quantile.density.Rd |only spatstat-1.43-0/spatstat/man/rCauchy.Rd | 4 spatstat-1.43-0/spatstat/man/rLGCP.Rd | 5 spatstat-1.43-0/spatstat/man/rMatClust.Rd | 4 spatstat-1.43-0/spatstat/man/rVarGamma.Rd | 4 spatstat-1.43-0/spatstat/man/ranef.mppm.Rd |only spatstat-1.43-0/spatstat/man/rdpp.Rd |only spatstat-1.43-0/spatstat/man/reach.dppm.Rd |only spatstat-1.43-0/spatstat/man/relrisk.ppm.Rd | 1 spatstat-1.43-0/spatstat/man/residuals.dppm.Rd |only spatstat-1.43-0/spatstat/man/residuals.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/residuals.mppm.Rd | 27 spatstat-1.43-0/spatstat/man/rgbim.Rd | 12 spatstat-1.43-0/spatstat/man/rmh.ppm.Rd | 2 spatstat-1.43-0/spatstat/man/rmpoispp.Rd | 7 spatstat-1.43-0/spatstat/man/rpoispp.Rd | 15 spatstat-1.43-0/spatstat/man/rtemper.Rd |only spatstat-1.43-0/spatstat/man/rthin.Rd | 6 spatstat-1.43-0/spatstat/man/simulate.dppm.Rd |only spatstat-1.43-0/spatstat/man/simulate.ppm.Rd | 7 spatstat-1.43-0/spatstat/man/slrm.Rd | 2 spatstat-1.43-0/spatstat/man/spatdim.Rd |only spatstat-1.43-0/spatstat/man/spatstat-internal.Rd | 91 +- spatstat-1.43-0/spatstat/man/spatstat-package.Rd | 70 + spatstat-1.43-0/spatstat/man/spatstat.options.Rd | 27 spatstat-1.43-0/spatstat/man/split.ppp.Rd | 3 spatstat-1.43-0/spatstat/man/studpermu.test.Rd | 6 spatstat-1.43-0/spatstat/man/subfits.Rd | 21 spatstat-1.43-0/spatstat/man/subset.ppp.Rd | 29 spatstat-1.43-0/spatstat/man/suffstat.Rd | 9 spatstat-1.43-0/spatstat/man/superimpose.Rd | 6 spatstat-1.43-0/spatstat/man/unitname.Rd | 6 spatstat-1.43-0/spatstat/man/update.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/valid.Rd |only spatstat-1.43-0/spatstat/man/valid.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/valid.ppm.Rd | 10 spatstat-1.43-0/spatstat/man/vcov.mppm.Rd | 29 spatstat-1.43-0/spatstat/man/waterstriders.Rd | 2 spatstat-1.43-0/spatstat/src/methas.c | 18 spatstat-1.43-0/spatstat/src/methas.h | 2 spatstat-1.43-0/spatstat/src/mhloop.h | 74 + spatstat-1.43-0/spatstat/src/mhv4.h | 4 spatstat-1.43-0/spatstat/src/mhv5.h |only spatstat-1.43-0/spatstat/src/rthin.c |only spatstat-1.43-0/spatstat/tests/alltests.R | 121 +- spatstat-1.43-0/spatstat/vignettes/datasets.Rnw | 20 spatstat-1.43-0/spatstat/vignettes/packagesizes.txt | 3 spatstat-1.43-0/spatstat/vignettes/replicated.Rnw | 151 +++ spatstat-1.43-0/spatstat/vignettes/updates.Rnw | 359 +++++++- 341 files changed, 6319 insertions(+), 2301 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 1.0.0 dated 2015-08-14 and 1.1.0 dated 2015-10-08
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 17 +++++++++++++++-- R/diagnostics.R | 4 ++-- R/extractors.R | 4 ++-- R/out.R | 4 ++-- R/parse_spc.R | 3 +++ R/plot.R | 4 ++-- R/read_series.R | 3 +++ R/seas.R | 5 ++--- R/series.R | 11 +++++++++-- R/static.R | 4 ++-- README.md | 27 ++++++++++++--------------- inst/doc/seas.pdf |binary man/final.Rd | 4 ++-- man/out.Rd | 4 ++-- man/plot.seas.Rd | 4 ++-- man/qs.Rd | 4 ++-- man/seas.Rd | 5 ++--- man/series.Rd | 11 +++++++++-- man/static.Rd | 4 ++-- vignettes/README.tex | 24 ++++++++++++------------ 22 files changed, 113 insertions(+), 85 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.0 dated 2015-06-14 and 1.1.1 dated 2015-10-08
nodiv-1.1.0/nodiv/tests/testthat/test_initial.R |only nodiv-1.1.1/nodiv/DESCRIPTION | 6 nodiv-1.1.1/nodiv/MD5 | 16 + nodiv-1.1.1/nodiv/NAMESPACE | 7 nodiv-1.1.1/nodiv/R/Add_to_data_object.R | 102 ++++++++---- nodiv-1.1.1/nodiv/R/Methods_for_data_objects.R | 60 ++++++- nodiv-1.1.1/nodiv/R/Node_based_analysis.R | 13 - nodiv-1.1.1/nodiv/R/Prepare_data.R | 132 ++++++++++++---- nodiv-1.1.1/nodiv/man/gridData.Rd |only nodiv-1.1.1/nodiv/tests/testthat/test_access.R |only nodiv-1.1.1/nodiv/tests/testthat/test_basic_functions.R |only 11 files changed, 258 insertions(+), 78 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.45 dated 2015-05-21 and 0.47 dated 2015-10-08
meteoForecast-0.45/meteoForecast/data |only meteoForecast-0.47/meteoForecast/DESCRIPTION | 10 - meteoForecast-0.47/meteoForecast/MD5 | 23 +-- meteoForecast-0.47/meteoForecast/NAMESPACE | 50 ++++++-- meteoForecast-0.47/meteoForecast/R/composeURL.R | 89 ++++++++++----- meteoForecast-0.47/meteoForecast/R/grepVar.R | 25 ++-- meteoForecast-0.47/meteoForecast/R/pointNCDC.R | 12 +- meteoForecast-0.47/meteoForecast/R/rasterMeteoGalicia.R | 2 meteoForecast-0.47/meteoForecast/man/getPoint.Rd | 10 - meteoForecast-0.47/meteoForecast/man/getRaster.Rd | 2 meteoForecast-0.47/meteoForecast/man/vars.Rd | 94 ++-------------- 11 files changed, 152 insertions(+), 165 deletions(-)
Title: Lightweight Logging for R Scripts
Description: Provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.
Author: Ben Bond-Lamberty [aut, cre]
Maintainer: Ben Bond-Lamberty <bondlamberty@pnnl.gov>
Diff between luzlogr versions 0.1.0 dated 2015-10-05 and 0.1.1 dated 2015-10-08
luzlogr-0.1.0/luzlogr/vignettes/Introduction.Rmd |only luzlogr-0.1.1/luzlogr/DESCRIPTION | 9 +++++---- luzlogr-0.1.1/luzlogr/MD5 | 14 +++++++++----- luzlogr-0.1.1/luzlogr/NEWS | 6 ++++++ luzlogr-0.1.1/luzlogr/README.md | 10 +++++----- luzlogr-0.1.1/luzlogr/build |only luzlogr-0.1.1/luzlogr/inst |only luzlogr-0.1.1/luzlogr/tests/testthat/test_logging.R | 12 ++++++++++++ luzlogr-0.1.1/luzlogr/vignettes/intro-luzlogr.Rmd |only 9 files changed, 37 insertions(+), 14 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 0.1-1 dated 2015-05-20 and 0.1-2 dated 2015-10-08
lamW-0.1-1/lamW/inst/NEWS.Rd |only lamW-0.1-2/lamW/DESCRIPTION | 8 ++++---- lamW-0.1-2/lamW/MD5 | 14 +++++++------- lamW-0.1-2/lamW/build/partial.rdb |binary lamW-0.1-2/lamW/inst/News.Rd |only lamW-0.1-2/lamW/man/lamW-package.Rd | 9 +++------ lamW-0.1-2/lamW/man/lamW.Rd | 4 ++-- lamW-0.1-2/lamW/src/lambertW.cpp | 8 ++++++-- lamW-0.1-2/lamW/tests/testthat/test-lamW.R | 10 +++++----- 9 files changed, 27 insertions(+), 26 deletions(-)
Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between cp4p versions 0.3.1 dated 2015-08-17 and 0.3.2 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 2 +- R/calibration_plot.R | 25 ++++++++++--------------- inst |only man/LFQRatio2.Rd | 4 ++-- man/LFQRatio25.Rd | 4 ++-- man/adjust.p.Rd | 2 +- man/calibration.plot.Rd | 2 +- man/cp4p-package.Rd | 2 +- man/estim.pi0.Rd | 2 +- 11 files changed, 33 insertions(+), 37 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma DB et al. - 2013).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.1 dated 2015-10-01 and 1.1.2 dated 2015-10-08
clere-1.1.1/clere/vignettes/RJpaper-vignette.ltx |only clere-1.1.1/clere/vignettes/biblio.bib |only clere-1.1.1/clere/vignettes/images |only clere-1.1.2/clere/DESCRIPTION | 10 +++---- clere-1.1.2/clere/MD5 | 31 +++++++++++------------ clere-1.1.2/clere/R/fitPacs.R | 6 ++++ clere-1.1.2/clere/build/vignette.rds |binary clere-1.1.2/clere/data/algoComp.RData |binary clere-1.1.2/clere/data/numExpRealData.RData |binary clere-1.1.2/clere/data/numExpSimData.RData |binary clere-1.1.2/clere/inst/doc/RJpaper-vignette.pdf |binary clere-1.1.2/clere/inst/doc/Vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf.asis |only clere-1.1.2/clere/man/clere-package.Rd | 4 +- clere-1.1.2/clere/man/fitPacs.Rd | 21 ++++++++------- clere-1.1.2/clere/man/numExpRealData.Rd | 2 - clere-1.1.2/clere/src/Model.cpp | 5 +-- clere-1.1.2/clere/src/pacs.cpp | 29 ++++++++++++--------- clere-1.1.2/clere/vignettes/Vignette.pdf.asis |only 19 files changed, 60 insertions(+), 48 deletions(-)
Title: Calibration Functions for Analytical Chemistry
Description: Simple functions for plotting linear
calibration functions and estimating standard errors for measurements
according to the Handbook of Chemometrics and Qualimetrics: Part A
by Massart et al. There are also functions estimating the limit
of detection (LOD) and limit of quantification (LOQ).
The functions work on model objects from - optionally weighted - linear
regression (lm) or robust linear regression ('rlm' from the 'MASS' package).
Author: Johannes Ranke [aut, cre, cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between chemCal versions 0.1-34 dated 2014-04-25 and 0.1-37 dated 2015-10-08
DESCRIPTION | 24 +++++++++++++----------- MD5 | 35 +++++++++++++++++++++++++++++------ NAMESPACE | 8 ++++++++ build/vignette.rds |binary data/din32645.rda |binary inst/doc/chemCal.pdf |binary inst/staticdocs |only inst/web |only man/din32645.Rd | 4 ++-- 9 files changed, 52 insertions(+), 19 deletions(-)
Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-2 dated 2015-10-06 and 0.0-3 dated 2015-10-08
DESCRIPTION | 8 +- MD5 | 14 ++-- NEWS | 1 R/assert-identical-to-true-false-na.R | 19 +++-- R/assert-is-true-false-na.R | 107 +++++++++++++++++++++++++++++---- R/is-true-false-na.R | 44 +++++++------ man/Truth.Rd | 34 +++++----- tests/testthat/test-is-true-false-na.R | 92 ++++++++++++++++++++++++++++ 8 files changed, 251 insertions(+), 68 deletions(-)
More information about assertive.base at CRAN
Permanent link
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.3-0 dated 2015-07-15 and 0.3-1 dated 2015-10-08
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Title: Ternary Search Tree for Auto-Completion and Spell Checking
Description: A ternary search tree is a type of prefix tree with up to three children and the ability for incremental string search. The package uses this ability for word auto-completion and spell checking. Includes a dataset with the 10001 most frequent English words.
Author: Ricardo Merino [aut, cre],
Samantha Fernandez [ctb]
Maintainer: Ricardo Merino <ricardo.merino.raldua@gmail.com>
Diff between TSTr versions 1.0 dated 2015-09-06 and 1.1 dated 2015-10-07
TSTr-1.0/TSTr/R/updateTree.R |only TSTr-1.0/TSTr/R/updateTree.default.R |only TSTr-1.0/TSTr/R/updateTree.tstTree.R |only TSTr-1.0/TSTr/inst/doc/index.html |only TSTr-1.0/TSTr/man/updateTree.Rd |only TSTr-1.1/TSTr/DESCRIPTION | 14 +- TSTr-1.1/TSTr/MD5 | 73 ++++++++--- TSTr-1.1/TSTr/NAMESPACE | 24 +++ TSTr-1.1/TSTr/R/Add.R | 2 TSTr-1.1/TSTr/R/Addlist.R |only TSTr-1.1/TSTr/R/PNcheck.R |only TSTr-1.1/TSTr/R/PNcheck.default.R |only TSTr-1.1/TSTr/R/PNcheck.tstTree.R |only TSTr-1.1/TSTr/R/SDcheck.R |only TSTr-1.1/TSTr/R/SDcheck.default.R |only TSTr-1.1/TSTr/R/SDcheck.dist1_DT.R |only TSTr-1.1/TSTr/R/SDcheck.dist2_DT.R |only TSTr-1.1/TSTr/R/SDcheck.dist3_DT.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_1.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_2.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_3.R |only TSTr-1.1/TSTr/R/SDkeeper.R |only TSTr-1.1/TSTr/R/SDkeeper.default.R |only TSTr-1.1/TSTr/R/addToTree.R |only TSTr-1.1/TSTr/R/addToTree.default.R |only TSTr-1.1/TSTr/R/addToTree.tstTree.R |only TSTr-1.1/TSTr/R/crearDT.R |only TSTr-1.1/TSTr/R/crearFullDT.R |only TSTr-1.1/TSTr/R/crearFullTree.R |only TSTr-1.1/TSTr/R/delList.R |only TSTr-1.1/TSTr/R/delete.R |only TSTr-1.1/TSTr/R/deletion1.R |only TSTr-1.1/TSTr/R/deletion2.R |only TSTr-1.1/TSTr/R/deletion3.R |only TSTr-1.1/TSTr/R/insertion.R |only TSTr-1.1/TSTr/R/matricear.R |only TSTr-1.1/TSTr/R/newTree.R | 1 TSTr-1.1/TSTr/R/replace.R |only TSTr-1.1/TSTr/R/searchTreeSD.R |only TSTr-1.1/TSTr/R/searchWordSD.R |only TSTr-1.1/TSTr/R/spellSD.R |only TSTr-1.1/TSTr/R/spellTree_1.R |only TSTr-1.1/TSTr/R/spellTree_2.R |only TSTr-1.1/TSTr/R/spellTree_3.R |only TSTr-1.1/TSTr/R/suggestions.R |only TSTr-1.1/TSTr/R/transpose.R |only TSTr-1.1/TSTr/R/variations.R |only TSTr-1.1/TSTr/build/TSTr.pdf |only TSTr-1.1/TSTr/build/vignette.rds |binary TSTr-1.1/TSTr/inst/doc/TSTr.R | 19 ++- TSTr-1.1/TSTr/inst/doc/TSTr.Rmd | 113 +++++++++++++++--- TSTr-1.1/TSTr/inst/doc/TSTr.html | 213 ++++++++++++++++++++++++++-------- TSTr-1.1/TSTr/man/PNcheck.Rd |only TSTr-1.1/TSTr/man/SDcheck.Rd |only TSTr-1.1/TSTr/man/SDkeeper.Rd |only TSTr-1.1/TSTr/man/TSTr-package.Rd | 20 +-- TSTr-1.1/TSTr/man/addToTree.Rd |only TSTr-1.1/TSTr/man/newTree.Rd | 2 TSTr-1.1/TSTr/vignettes/TSTr.Rmd | 113 +++++++++++++++--- TSTr-1.1/TSTr/vignettes/Thumbs.db |binary TSTr-1.1/TSTr/vignettes/banner.jpg |only TSTr-1.1/TSTr/vignettes/bannera.html |only 62 files changed, 482 insertions(+), 112 deletions(-)
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System. These tools address common challenges
associated with continuous time series data for environmental decision
making.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between SWMPr versions 2.1.0 dated 2015-08-10 and 2.1.4 dated 2015-10-07
DESCRIPTION | 8 +- MD5 | 24 +++---- NAMESPACE | 2 R/swmpr_analyze.R | 166 +++++++++++++++++++++++++++++++------------------ R/swmpr_misc.R | 4 - R/swmpr_organize.R | 20 +++-- R/swmpr_retrieval.R | 6 - man/aggremetab.Rd | 10 ++ man/comb.Rd | 2 man/na.approx.swmpr.Rd | 1 man/plot_metab.Rd | 3 man/setstep.Rd | 8 +- man/smoother.Rd | 12 +-- 13 files changed, 161 insertions(+), 105 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.8.0 dated 2015-09-21 and 0.8.1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/networkDynamic.pdf |binary tests/utils_tests.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2 dated 2015-10-05 and 1.2.1 dated 2015-10-07
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- R/symscorestat.R | 2 +- inst/Makefile |only inst/testperm.f90 | 4 +++- src/signtestperm.f90 | 12 +++++++++--- 6 files changed, 21 insertions(+), 12 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.9.4 dated 2015-03-06 and 1.9.5 dated 2015-10-07
CHANGELOG | 9 ++++- DESCRIPTION | 10 +++--- MD5 | 66 +++++++++++++++++++++---------------------- NAMESPACE | 10 +++++- R/kcde.R | 29 +++++++++---------- R/kcopula.R | 12 ++++++- R/kda.R | 73 +++++++++++++++++++++--------------------------- R/kdde.R | 20 ++----------- R/kde.R | 44 +++++++++++++--------------- R/normal.R | 2 - build/vignette.rds |binary inst/doc/kde.pdf |binary man/Hlscv.Rd | 3 - man/Hns.Rd | 3 - man/Hpi.Rd | 21 ++++++------- man/Hscv.Rd | 5 +-- man/binning.Rd | 1 man/contour.Rd | 3 + man/ise.mixt.Rd | 1 man/kcde.Rd | 16 +++++----- man/kcopula.Rd | 4 +- man/kda.Rd | 8 ++--- man/kdde.Rd | 3 - man/kde.Rd | 14 ++++----- man/kfe.Rd | 7 +--- man/kroc.Rd | 9 +++-- man/ks-package.Rd | 8 ++--- man/mixt.Rd | 2 - man/plot.kcde.Rd | 10 +++--- man/plot.kda.Rd | 17 +++++------ man/plot.kdde.Rd | 9 ++--- man/plot.kde.Rd | 31 ++++++++++---------- man/plot.kde.loctest.Rd | 6 +-- man/pre.transform.Rd | 4 -- 34 files changed, 222 insertions(+), 238 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.4-0 dated 2015-10-01 and 0.4-1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ICP.R | 3 ++- R/hiddenICP.R | 4 ++-- R/print.InvariantCausalPrediction.R | 8 ++++---- R/print.hiddenInvariantCausalPrediction.R | 6 +++--- 6 files changed, 20 insertions(+), 19 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Dose-Response Data Evaluation
Description: A somewhat outdated package of basic and easy-to-use functions for
fitting dose-response curves to continuous dose-response data, calculating some
(eco)toxicological parameters and plotting the results. Please consider using
the more powerful and actively developed 'drc' package. Functions that are
fitted are the cumulative density function of the lognormal distribution
(probit fit), of the logistic distribution (logit fit), of the weibull
distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
derived from the latter, which is used to describe data showing stimulation at
low doses (hormesis). In addition, functions checking, plotting and retrieving
dose-response data retrieved from a database accessed via RODBC are included.
As an alternative to the original fitting methods, the algorithms from the drc
package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between drfit versions 0.6.3 dated 2014-07-28 and 0.6.4 dated 2015-10-07
DESCRIPTION | 40 +++++++++++++++++++++------------------- MD5 | 14 +++++++------- NAMESPACE | 10 +++------- R/checkexperiment.R | 14 +++++++++----- R/checksubstance.R | 10 +++++++--- R/drdata.R | 16 ++++++++++------ data/XY.rda |binary inst/doc/drfit-Rnews.pdf |binary 8 files changed, 57 insertions(+), 47 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.16 dated 2015-09-13 and 0.5.18 dated 2015-10-07
DESCRIPTION | 8 MD5 | 37 +-- NAMESPACE | 1 R/vtreat.R | 232 ++++++++++++++--------- README.md | 27 +- build/vignette.rds |binary inst/doc/vtreat.R | 16 + inst/doc/vtreat.Rmd | 66 ++++-- inst/doc/vtreat.html | 393 +++++++++++++++++++++++----------------- inst/doc/vtreatOverfit.R | 4 inst/doc/vtreatOverfit.Rmd | 20 +- inst/doc/vtreatOverfit.html | 123 ++++++------ man/designTreatmentsC.Rd | 22 +- man/designTreatmentsN.Rd | 14 - man/prepare.Rd | 6 man/vtreat-package.Rd | 4 tests/testthat/testRareCases.R |only tests/testthat/testWeirdTypes.R | 30 +-- vignettes/vtreat.Rmd | 50 ++--- vignettes/vtreatOverfit.Rmd | 20 +- 20 files changed, 609 insertions(+), 464 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Description: Implementation of the vine graphical model for building
high-dimensional probability distributions as a factorization of
bivariate copulas and marginal density functions. This package
provides S4 classes for vines (C-vines and D-vines) and methods
for inference, goodness-of-fit tests, density/distribution
function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut],
Joris Meys [ctb]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>
Diff between vines versions 1.1.3 dated 2015-03-25 and 1.1.4 dated 2015-10-07
vines-1.1.3/vines/tests/hfunctions.R |only vines-1.1.4/vines/DESCRIPTION | 33 ++++++++------ vines-1.1.4/vines/MD5 | 57 +++++++++++++------------ vines-1.1.4/vines/NAMESPACE | 5 -- vines-1.1.4/vines/NEWS | 8 +++ vines-1.1.4/vines/R/Vine.R | 24 +++++----- vines-1.1.4/vines/R/dimnames.R | 24 +++++----- vines-1.1.4/vines/R/dvine.R | 24 +++++----- vines-1.1.4/vines/R/h.R | 67 ++++++++++++++---------------- vines-1.1.4/vines/R/hinverse.R | 54 +++++++++++------------- vines-1.1.4/vines/R/pvine.R | 24 +++++----- vines-1.1.4/vines/R/rvine.R | 24 +++++----- vines-1.1.4/vines/R/show.R | 24 +++++----- vines-1.1.4/vines/R/vineFit.R | 24 +++++----- vines-1.1.4/vines/R/vineFitML.R | 24 +++++----- vines-1.1.4/vines/R/vineGoF.R | 24 +++++----- vines-1.1.4/vines/R/vineIter.R | 24 +++++----- vines-1.1.4/vines/R/vineOrder.R | 24 +++++----- vines-1.1.4/vines/R/vinePIT.R | 24 +++++----- vines-1.1.4/vines/R/vineParameters.R | 24 +++++----- vines-1.1.4/vines/inst/CITATION | 2 vines-1.1.4/vines/man/h-methods.Rd | 31 ++++++++----- vines-1.1.4/vines/man/hinverse-methods.Rd | 25 ++++++----- vines-1.1.4/vines/src/h.c | 61 +++++++++++++-------------- vines-1.1.4/vines/src/h.h | 47 ++++++++++----------- vines-1.1.4/vines/src/hinverse.c | 49 ++++++++++----------- vines-1.1.4/vines/src/hinverse.h | 41 ++++++++---------- vines-1.1.4/vines/src/register.c | 55 ++++++++++++------------ vines-1.1.4/vines/tests/testthat |only vines-1.1.4/vines/tests/testthat.R |only 30 files changed, 431 insertions(+), 416 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb],
Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.2.1 dated 2015-08-31 and 1.3.1 dated 2015-10-07
urltools-1.2.1/urltools/man/suffix_refresh.Rd |only urltools-1.2.1/urltools/man/url_parameters.Rd |only urltools-1.3.1/urltools/DESCRIPTION | 8 - urltools-1.3.1/urltools/MD5 | 45 +++--- urltools-1.3.1/urltools/NAMESPACE | 4 urltools-1.3.1/urltools/NEWS | 24 +++ urltools-1.3.1/urltools/R/RcppExports.R | 109 +++++++++++---- urltools-1.3.1/urltools/R/suffix.R | 48 ------ urltools-1.3.1/urltools/R/urltools.R | 8 - urltools-1.3.1/urltools/README.md | 2 urltools-1.3.1/urltools/inst/doc/urltools.R | 32 +++- urltools-1.3.1/urltools/inst/doc/urltools.Rmd | 56 +++++-- urltools-1.3.1/urltools/inst/doc/urltools.html | 54 +++++-- urltools-1.3.1/urltools/man/param_get.Rd |only urltools-1.3.1/urltools/man/param_remove.Rd |only urltools-1.3.1/urltools/man/param_set.Rd |only urltools-1.3.1/urltools/man/suffix_dataset.Rd | 1 urltools-1.3.1/urltools/man/suffix_extract.Rd | 3 urltools-1.3.1/urltools/src/RcppExports.cpp | 49 +++++- urltools-1.3.1/urltools/src/param.cpp |only urltools-1.3.1/urltools/src/parameter.cpp |only urltools-1.3.1/urltools/src/parameter.h |only urltools-1.3.1/urltools/src/parsing.cpp | 76 +++++----- urltools-1.3.1/urltools/src/parsing.h | 42 ++--- urltools-1.3.1/urltools/src/urltools.cpp | 42 ----- urltools-1.3.1/urltools/tests/testthat/test_parameters.R |only urltools-1.3.1/urltools/tests/testthat/test_parsing.R | 31 ++-- urltools-1.3.1/urltools/vignettes/urltools.Rmd | 56 +++++-- 28 files changed, 411 insertions(+), 279 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.8 dated 2015-07-24 and 0.8.9 dated 2015-10-07
DESCRIPTION | 6 MD5 | 72 ++-- R/dataset_metrics.r | 20 - R/downloads.R | 40 +- R/elevation.r | 67 ++-- R/name_lookup.r | 4 R/name_usage.r | 59 +-- R/occ_count.r | 2 R/occ_download.R | 14 R/occ_download_import.R | 1 R/occ_search.r | 10 R/rgbif-package.r | 1 R/zzz.r | 26 - README.md | 99 +++-- build/vignette.rds |binary inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 153 ++++----- inst/doc/issues_vignette.html | 153 ++++----- inst/doc/rgbif_vignette.html | 563 +++++++++++++++++----------------- inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 153 ++++----- inst/vign/rgbif_vignette.Rmd | 2 inst/vign/rgbif_vignette.md | 561 +++++++++++++++++---------------- man/dataset_metrics.Rd | 4 man/downloads.Rd | 12 man/name_usage.Rd | 4 man/occ_count.Rd | 2 man/occ_download.Rd | 11 tests/testthat/test-dataset_metrics.r | 11 tests/testthat/test-dataset_suggest.r | 4 tests/testthat/test-elevation.R | 22 + tests/testthat/test-gbifmap.r | 3 tests/testthat/test-name_lookup.r | 7 tests/testthat/test-name_usage.r | 168 +++++++++- tests/testthat/test-occ_search.r | 82 +++- vignettes/issues_vignette.Rmd | 153 ++++----- vignettes/rgbif_vignette.Rmd | 561 +++++++++++++++++---------------- 37 files changed, 1686 insertions(+), 1364 deletions(-)
Title: Visualisation of Sequential Probability Distributions Using Fan
Charts
Description: Visualise sequential distributions using a range of plotting
styles. Sequential distribution data can be input as either simulations or
values corresponding to percentiles over time. Plots are added to
existing graphic devices using the fan function. Users can choose from four
different styles, including fan chart type plots, where a set of coloured
polygon, with shadings corresponding to the percentile values are layered
to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel" <g.j.abel@gmail.com>
Diff between fanplot versions 3.4.0 dated 2015-01-28 and 3.4.1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ R/fan.R | 3 ++- R/fan0.R | 10 ++++------ inst/CITATION |only man/fan.Rd | 9 +++++++-- man/fanplot-pacakge.Rd |only 8 files changed, 29 insertions(+), 18 deletions(-)
Title: Benford Analysis for Data Validation and Forensic Analytics
Description: The Benford Analysis package provides tools that make it easier to
validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between benford.analysis versions 0.1.1 dated 2014-05-01 and 0.1.2.1 dated 2015-10-07
DESCRIPTION | 10 +- MD5 | 68 +++++++------- NAMESPACE | 51 ++++++----- R/data.documentation.R | 174 +++++++++++++++++++------------------- R/functions-new.R | 10 +- R/get.functions.R | 18 +-- R/internal.functions-new-code-2.R | 12 -- README.md |only man/MAD.Rd | 9 + man/benford.Rd | 143 ++++++++++++++----------------- man/benford.analysis.Rd | 45 +++------ man/census.2000_2010.Rd | 9 - man/census.2009.Rd | 6 - man/chisq.Rd | 12 +- man/corporate.payment.Rd | 10 +- man/dfactor.Rd | 9 + man/duplicatesTable.Rd | 8 - man/extract.digits.Rd | 53 ++++------- man/getBfd.Rd | 10 +- man/getData.Rd | 13 +- man/getDigits.Rd | 15 +-- man/getDuplicates.Rd | 10 +- man/getSuspects.Rd | 20 +--- man/lakes.perimeter.Rd | 10 +- man/mantissa.Rd | 10 +- man/marc.Rd | 12 +- man/p.these.digits.Rd | 4 man/p.this.digit.at.n.Rd | 10 +- man/plot.Benford.Rd | 20 +--- man/print.Benford.Rd | 10 +- man/sino.forest.Rd | 9 - man/suspectsTable.Rd | 18 +-- man/taxable.incomes.1978.Rd | 9 - tests/testthat/test-benford.R | 33 ++++++- tests/testthat/test-extract.R | 108 ++++++++++++----------- tests/testthat/test-get.R |only 36 files changed, 488 insertions(+), 480 deletions(-)
More information about benford.analysis at CRAN
Permanent link
Title: Matrix Exponential
Description: Computation of the matrix exponential, logarithm, and related quantities.
Author: Vincent Goulet, Christophe Dutang, Martin Maechler,
David Firth, Marina Shapira, Michael Stadelmann,
expm-developers@lists.R-forge.R-project.org
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between expm versions 0.99-1.1 dated 2014-02-12 and 0.999-0 dated 2015-10-07
ChangeLog | 17 + DESCRIPTION | 16 - MD5 | 84 ++++---- NAMESPACE | 10 R/balance.R | 2 R/expm.R | 29 +- R/expm2.R | 287 ++++++++++++++-------------- R/expmCond-all.R | 24 -- R/expm_vec.R | 2 R/logm.Higham08.R | 28 ++ R/logm.R | 2 R/sqrtm.R | 2 build/vignette.rds |binary demo/balanceTst.R | 8 demo/exact-fn.R | 4 demo/expm.R | 2 inst/doc/expm.R | 1 inst/doc/expm.pdf |binary inst/po/en@quot |only inst/po/fr/LC_MESSAGES/expm.mo |only inst/test-tools.R | 2 man/balance.Rd | 5 man/expAtv.Rd | 2 man/expm.Rd | 26 +- man/expmCond.Rd | 4 man/expmFrechet.Rd | 2 man/logm.Rd | 11 - po/R-expm.pot |only po/expm.pot | 78 ++++++- po/fr.po | 88 +++++++- src/R_dgebal.c | 19 + src/expm.h | 5 src/init.c | 3 src/matexp_MH09.c |only src/matpow.c | 13 - src/matrexp.f | 12 - src/matrexpO.f | 420 +++++++++++++++++++++-------------------- src/mexp-common.f | 23 +- tests/bal-ex.R | 15 + tests/ex.R | 68 +++--- tests/ex2.R | 21 +- tests/exact-ex.R | 83 +++++--- tests/expm-Cond.R | 16 - tests/log+sqrt.R | 23 +- tests/matpow-ex.R |only 45 files changed, 870 insertions(+), 587 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2 dated 2015-03-10 and 2.2.1 dated 2015-10-07
DESCRIPTION | 12 - MD5 | 18 - NAMESPACE | 6 R/autoevenn.R | 22 -- R/evenn.R | 502 +++++++++++++++++++++++++++++++-------------------- R/man.evenn.R | 56 +++-- man/autoevenn.Rd | 5 man/eVenn-package.Rd | 7 man/evenn.Rd | 14 - man/man.evenn.Rd | 2 10 files changed, 385 insertions(+), 259 deletions(-)
Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth <russell-lenth@uiowa.edu>
Diff between rsm versions 2.7-3 dated 2015-09-03 and 2.7-4 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/rsm.R | 7 +++++-- inst/NEWS | 4 ++++ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary 7 files changed, 19 insertions(+), 12 deletions(-)
Title: Import Stata Data Files
Description: Function to read and write the Stata file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.7.1 dated 2015-08-07 and 0.8 dated 2015-10-07
readstata13-0.7.1/readstata13/src/statadefines.h |only readstata13-0.7.1/readstata13/src/swap_endian.h |only readstata13-0.8/readstata13/DESCRIPTION | 10 readstata13-0.8/readstata13/MD5 | 45 readstata13-0.8/readstata13/NAMESPACE | 1 readstata13-0.8/readstata13/NEWS | 8 readstata13-0.8/readstata13/R/RcppExports.R | 17 readstata13-0.8/readstata13/R/dbcal.R | 1 readstata13-0.8/readstata13/R/read.R | 246 +++-- readstata13-0.8/readstata13/R/readstata13.R | 8 readstata13-0.8/readstata13/R/save.R | 205 +++- readstata13-0.8/readstata13/R/tools.R | 2 readstata13-0.8/readstata13/README.md | 26 readstata13-0.8/readstata13/inst/include |only readstata13-0.8/readstata13/man/read.dta13.Rd | 110 +- readstata13-0.8/readstata13/man/readstata13.Rd | 4 readstata13-0.8/readstata13/man/save.dta13.Rd | 49 - readstata13-0.8/readstata13/man/stata_pre13_save.Rd |only readstata13-0.8/readstata13/src/Makevars |only readstata13-0.8/readstata13/src/Makevars.win |only readstata13-0.8/readstata13/src/RcppExports.cpp | 28 readstata13-0.8/readstata13/src/rcpp_pre13_savestata.cpp |only readstata13-0.8/readstata13/src/rcpp_readstata.cpp | 718 --------------- readstata13-0.8/readstata13/src/rcpp_savestata.cpp | 160 ++- readstata13-0.8/readstata13/src/read_dta.cpp |only readstata13-0.8/readstata13/src/read_pre13_dta.cpp |only 26 files changed, 639 insertions(+), 999 deletions(-)
Title: Paternity Exclusion in Autopolyploid Species
Description: Functions to perform paternity exclusion via allele
matching, in autopolyploid species having ploidy 4, 6, or 8. The
marker data data used can be genotypic (copy numbers known) or
'phenotypic' (copy numbers not known).
Author: Alexander Zwart
Maintainer: Alexander Zwart <Alec.Zwart@csiro.au>
Diff between PolyPatEx versions 0.9 dated 2014-07-02 and 0.9.1 dated 2015-10-07
DESCRIPTION | 12 +++--- LICENSE | 4 +- MD5 | 54 +++++++++++++-------------- NAMESPACE | 5 ++ R/PolyPatEx-package.R | 76 +++++++++++++++++++-------------------- R/convertToPhenot.R | 8 ++-- R/genotPPE.R | 5 +- R/inputData.R | 3 + R/multilocusTypes.R | 9 ++-- R/phenotPPE.R | 5 +- R/potentialFatherIDs.R | 3 + build/vignette.rds |binary inst/doc/PolyPatEx-vignette.Rnw | 20 +++++----- inst/doc/PolyPatEx-vignette.pdf |binary man/FR_Genotype.Rd | 3 + man/GF_Phenotype.Rd | 3 + man/PolyPatEx-package.Rd | 3 + man/convertToPhenot.Rd | 3 + man/fixCSV.Rd | 3 + man/foreignAlleles.Rd | 3 + man/genotPPE.Rd | 3 + man/inputData.Rd | 3 + man/multilocusTypes.Rd | 3 + man/phenotPPE.Rd | 3 + man/potentialFatherCounts.Rd | 3 + man/potentialFatherIDs.Rd | 3 + man/preprocessData.Rd | 3 + vignettes/PolyPatEx-vignette.Rnw | 20 +++++----- 28 files changed, 144 insertions(+), 119 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.2.6 dated 2015-07-17 and 2.3.1 dated 2015-10-07
DESCRIPTION | 10 MD5 | 415 ++++++++-------- NAMESPACE | 1 R/MxAlgebra.R | 5 R/MxCompute.R | 8 R/MxDataWLS.R | 2 R/MxExpectation.R | 15 R/MxExpectationGREML.R | 18 R/MxExpectationLISREL.R | 207 +++---- R/MxExpectationNormal.R | 169 +++--- R/MxExpectationRAM.R | 73 +- R/MxExpectationStateSpace.R | 4 R/MxFactorScores.R | 91 +++ R/MxFitFunctionGREML.R | 9 R/MxFitFunctionWLS.R | 87 ++- R/MxMatrix.R | 8 R/MxModelFunctions.R | 13 R/MxRestore.R | 36 + R/MxRun.R | 406 ++++++++------- R/MxRunHelperFunctions.R | 1 R/MxSummary.R | 19 R/MxVersion.R | 2 R/sysdata.rda |binary data/LongitudinalOverdispersedCounts.rda |only data/datalist | 1 inst/CITATION | 2 inst/models/enormous/lib/stderrlib.R | 5 inst/models/nightly/FactorScores.R | 46 + inst/models/nightly/GREML_monophenotype_1GRM.R |only inst/models/nightly/GREML_monophenotype_1GRM_GradDesc.R |only inst/models/passing/ContinuousOnlyWLSTest.R | 2 inst/models/passing/GeneralizedEstimatingEquations.R |only inst/models/passing/IntroSEM-BivariateStd.R | 7 inst/models/passing/IntroSEM-ThreeFactorScale2Test.R | 3 inst/models/passing/MatrixCreation.R | 19 inst/models/passing/MatrixErrorDetection.R | 7 inst/models/passing/MultilevelUniRandomSlopeInt.R | 25 inst/models/passing/MultipleGroupWLS.R |only inst/models/passing/RemoveEntriesTest.R | 19 inst/models/passing/SimpleConfidenceIntervals.R | 5 inst/models/passing/SimpleMLAlgebraCIs.R | 5 inst/models/passing/StateSpaceInputs.R | 47 + inst/models/passing/UnivariateRandomInterceptWide.R | 49 + inst/models/passing/rfitfunc.R | 9 man/BaseCompute-class.Rd | 3 man/LongitudinalOverdispersedCounts.Rd |only man/MxAlgebraFormula-class.Rd | 3 man/MxBaseExpectation-class.Rd | 3 man/MxBaseFitFunction-class.Rd | 3 man/MxBaseNamed-class.Rd | 3 man/MxBaseObjectiveMetaData-class.Rd | 3 man/MxCharOrList-class.Rd | 3 man/MxCharOrNumber-class.Rd | 3 man/MxCompute-class.Rd | 3 man/MxDataFrameOrMatrix-class.Rd | 3 man/MxDataStatic-class.Rd | 3 man/MxDirectedGraph-class.Rd | 3 man/MxExpectationXclass.Rd | 3 man/MxFitFunction-class.Rd | 3 man/MxFlatModel-class.Rd | 3 man/MxInterval-class.Rd | 3 man/MxLISRELModel-class.Rd | 3 man/MxListOrNull-class.Rd | 3 man/MxOptionalChar-class.Rd | 3 man/MxOptionalCharOrNumber-class.Rd | 3 man/MxOptionalLogical-class.Rd | 3 man/MxOptionalMatrix-class.Rd | 3 man/MxOptionalNumeric-class.Rd | 3 man/MxRAMGraph-class.Rd | 3 man/MxRAMMetaData-class.Rd | 3 man/MxRAMModel-class.Rd | 3 man/OpenMx.Rd | 3 man/expm.Rd | 3 man/genericFitDependencies-MxBaseFitFunction-method.Rd | 3 man/imxAddDependency.Rd | 3 man/imxCheckMatrices.Rd | 3 man/imxCheckVariables.Rd | 3 man/imxConDecMatrixSlots.Rd | 3 man/imxConstraintRelations.Rd | 3 man/imxConvertIdentifier.Rd | 3 man/imxConvertLabel.Rd | 3 man/imxConvertSubstitution.Rd | 3 man/imxCreateMatrix.Rd | 3 man/imxDataTypes.Rd | 3 man/imxDefaultGetSlotDisplayNames.Rd | 3 man/imxDeparse.Rd | 3 man/imxDependentModels.Rd | 3 man/imxDetermineDefaultOptimizer.Rd | 3 man/imxDiff.Rd | 3 man/imxDmvnorm.Rd | 3 man/imxEvalByName.Rd | 3 man/imxExtractMethod.Rd | 3 man/imxExtractNames.Rd | 3 man/imxExtractReferences.Rd | 3 man/imxExtractSlot.Rd | 3 man/imxFlattenModel.Rd | 3 man/imxFreezeModel.Rd | 3 man/imxGenSwift.Rd | 3 man/imxGenerateLabels.Rd | 3 man/imxGenerateNamespace.Rd | 3 man/imxGenericModelBuilder.Rd | 3 man/imxGetSlotDisplayNames.Rd | 3 man/imxHasNPSOL.Rd | 3 man/imxHasOpenMP.Rd | 3 man/imxIdentifier.Rd | 3 man/imxIndependentModels.Rd | 3 man/imxInitModel.Rd | 3 man/imxIsDefinitionVariable.Rd | 3 man/imxIsPath.Rd | 3 man/imxLocateFunction.Rd | 3 man/imxLocateIndex.Rd | 3 man/imxLocateLabel.Rd | 3 man/imxLog.Rd | 3 man/imxLookupSymbolTable.Rd | 3 man/imxModelBuilder.Rd | 3 man/imxModelTypes.Rd | 3 man/imxMpiWrap.Rd | 3 man/imxOriginalMx.Rd | 3 man/imxPPML.Rd | 3 man/imxPPML.Test.Battery.Rd | 3 man/imxPPML.Test.Test.Rd | 3 man/imxPreprocessModel.Rd | 3 man/imxReplaceMethod.Rd | 3 man/imxReplaceModels.Rd | 3 man/imxReplaceSlot.Rd | 3 man/imxReservedNames.Rd | 3 man/imxReverseIdentifier.Rd | 3 man/imxSameType.Rd | 3 man/imxSeparatorChar.Rd | 3 man/imxSfClient.Rd | 3 man/imxSimpleRAMPredicate.Rd | 3 man/imxSparseInvert.Rd | 3 man/imxSquareMatrix.Rd | 3 man/imxSymmetricMatrix.Rd | 3 man/imxTypeName.Rd | 3 man/imxUntitledName.Rd | 3 man/imxUntitledNumber.Rd | 3 man/imxUntitledNumberReset.Rd | 3 man/imxUpdateModelValues.Rd | 3 man/imxVariableTypes.Rd | 3 man/imxVerifyMatrix.Rd | 3 man/imxVerifyModel.Rd | 3 man/imxVerifyName.Rd | 3 man/imxVerifyReference.Rd | 3 man/logm.Rd | 3 man/mxAlgebraFromString.Rd | 3 man/mxAvailableOptimizers.Rd | 3 man/mxComputeConfidenceInterval.Rd | 3 man/mxComputeDefault.Rd | 3 man/mxComputeEM.Rd | 3 man/mxComputeGradientDescent.Rd | 11 man/mxComputeHessianQuality.Rd | 3 man/mxComputeIterate.Rd | 3 man/mxComputeNewtonRaphson.Rd | 3 man/mxComputeNothing.Rd | 3 man/mxComputeNumericDeriv.Rd | 3 man/mxComputeOnce.Rd | 3 man/mxComputeReportDeriv.Rd | 3 man/mxComputeSequence.Rd | 3 man/mxComputeStandardError.Rd | 3 man/mxDataDynamic.Rd | 3 man/mxExpectationBA81.Rd | 3 man/mxFactorScores.Rd | 14 man/mxFitFunctionMultigroup.Rd | 10 man/mxGenerateData.Rd | 5 man/mxGetExpected.Rd | 15 man/mxMI.Rd | 3 man/mxMakeNames.Rd | 3 man/mxMatrix.Rd | 17 man/mxOption.Rd | 3 man/mxRestore.Rd | 10 man/mxSetDefaultOptions.Rd | 3 man/mxSimplify2Array.Rd | 3 man/mxTryHard.Rd | 6 man/omxCheckCloseEnough.Rd | 3 man/omxCheckError.Rd | 3 man/omxCheckNamespace.Rd | 3 man/omxCheckWarning.Rd | 3 man/omxConstrainMLThresholds.Rd | 3 man/omxDetectCores.Rd | 3 man/omxGetNPSOL.Rd | 3 man/omxGetRAMDepth.Rd | 3 man/omxManifestModelByParameterJacobian.Rd |only man/omxNameAnonymousParameters.Rd | 3 man/omxNormalQuantiles.Rd | 3 man/omxParallelCI.Rd | 3 man/omxQuotes.Rd | 3 man/omxRAMtoML.Rd | 3 man/omxSaturatedModel.Rd | 2 man/summary-MxModel.Rd | 13 src/Compute.cpp | 11 src/Compute.h | 2 src/ComputeGD.cpp | 31 + src/glue.cpp | 2 src/nloptcpp.cpp | 2 src/omxAlgebra.cpp | 5 src/omxData.cpp | 43 - src/omxData.h | 11 src/omxDefines.h | 1 src/omxFIMLSingleIteration.cpp | 19 src/omxGREMLExpectation.cpp | 7 src/omxGREMLfitfunction.cpp | 125 ++-- src/omxHessianCalculation.cpp | 9 src/omxImportFrontendState.cpp | 4 src/omxMatrix.cpp | 8 src/omxMatrix.h | 11 src/omxRowFitFunction.cpp | 3 src/omxSadmvnWrapper.cpp | 2 src/omxState.cpp | 52 +- src/omxState.h | 7 src/omxStateSpaceExpectation.cpp | 14 src/omxWLSFitFunction.cpp | 19 212 files changed, 1681 insertions(+), 1062 deletions(-)
Title: Solving Least Squares Problems under Equality/Inequality
Constraints
Description: It contains functions that solve least squares linear
regression problems under linear equality/inequality
constraints. It is developed based on the 'Fortran' program of
Lawson and Hanson (1974, 1995), which is public domain and
available at http://www.netlib.org/lawson-hanson.
Author: Yong Wang [aut, cre],
Charles L. Lawson [aut],
Richard J. Hanson [aut]
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Diff between lsei versions 1.1-0 dated 2015-09-27 and 1.1-1 dated 2015-10-07
Changes | 7 +++++ DESCRIPTION | 11 ++++---- MD5 | 14 +++++----- NAMESPACE | 2 - R/lsei.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++--------- man/hfti.Rd | 12 ++++----- man/lsei.Rd | 78 ++++++++++++++++++++++++++++++++++++++++++++++-------------- man/nnls.Rd | 75 +++++++++++++++++++++++++++++++++++++++++++++------------ 8 files changed, 211 insertions(+), 65 deletions(-)
Title: Empirical Bayesian Elastic Net
Description: Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet'
package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBEN versions 4.1 dated 2015-06-26 and 4.6 dated 2015-10-07
DESCRIPTION | 8 MD5 | 26 NAMESPACE | 3 R/EBelasticNet.Binomial.R | 2 R/EBelasticNet.BinomialCV.R | 44 + R/EBelasticNet.Gaussian.R | 22 R/EBelasticNet.GaussianCV.R | 13 man/EBEN-package.Rd | 5 man/EBelasticNet.Binomial.Rd | 8 man/EBelasticNet.BinomialCV.Rd | 11 src/ElasticNetBinaryNEmainEff.c | 605 ++++++++++++++++--- src/ElasticNetBinaryNeFull.c | 1211 ++++++++++++++++++++++++++++++++++------ src/elasticNetLinearNeFull2.c | 140 +++- src/elasticNetLinearNeMainEff.c | 330 +++++++--- 14 files changed, 1924 insertions(+), 504 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks,
including the methods 'backShift' (from package 'backShift'),
'bivariateANM' (bivariate additive noise model),
'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'),
'hiddenICP' (invariant causal prediction with hidden variables),
'ICP' (invariant causal prediction) (from package 'InvariantCausalPrediction'),
'GES' (greedy equivalence search),
'GIES' (greedy interventional equivalence search),
'LINGAM', 'PC' (PC Algorithm),
'RFCI' (really fast causal inference)
(all from package 'pcalg') and regression.
Author: Christina Heinze <heinze@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze <heinze@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.1.1 dated 2015-06-23 and 0.1.4 dated 2015-10-07
DESCRIPTION | 10 ++++----- MD5 | 10 ++++----- NAMESPACE | 3 ++ R/runHiddenICP.R | 14 +++++++------ R/runICP.R | 19 +++++++++--------- tests/testthat/test_getParents_defaults_all_methods.R | 3 -- 6 files changed, 32 insertions(+), 27 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Breiman and Cutler's Random Forests for Classification and
Regression
Description: Classification and regression based on a forest of trees
using random inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by
Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between randomForest versions 4.6-10 dated 2014-07-17 and 4.6-12 dated 2015-10-07
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 9 +++++++++ R/MDSplot.R | 4 ++-- R/combine.R | 33 ++++++++++++++++++--------------- R/margin.R | 4 ++-- R/randomForest.default.R | 4 +++- inst/NEWS | 13 +++++++++++++ man/randomForest.Rd | 2 +- man/rfImpute.Rd | 2 +- src/regrf.c | 6 +++--- src/rf.c | 14 +++++++------- src/rfutils.c | 2 +- 13 files changed, 79 insertions(+), 52 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Provides statistical methods for the analysis of data aggregated spatially over regions (areal data).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 0.1.5 dated 2015-10-01 and 0.1.6 dated 2015-10-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/scan.test.R | 2 +- man/scan.test.Rd | 2 +- tests/testthat/test-scan.test.R | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.5 dated 2015-09-25 and 1.6 dated 2015-10-06
DESCRIPTION | 8 +++---- MD5 | 30 +++++++++++++------------- R/Biplot.R | 26 ++++++++++++++-------- R/CA.R | 20 ++++++++--------- R/GSVD.R | 21 ++++++++++++++---- R/IM.R | 2 - R/MFA.R | 12 +++++----- R/NormData.R | 2 - R/PCA.R | 13 ++++++----- R/Plot.CA.R | 56 ++++++++++++++++++++++++------------------------- R/Plot.MFA.R | 10 ++++---- R/Plot.PCA.R | 6 ++--- man/CA.Rd | 4 +-- man/DataQuali.Rd | 2 - man/MFA.Rd | 4 +-- man/MVar.pt-package.Rd | 4 +-- 16 files changed, 121 insertions(+), 99 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.0 dated 2015-08-30 and 0.2.0.1 dated 2015-10-06
DESCRIPTION | 8 - MD5 | 10 +- inst/doc/dotwhisker-vignette.html | 180 ++++++++++++++++---------------------- inst/doc/dwplot-vignette.R |only inst/doc/kl2007_examples.html | 90 +++++++------------ inst/doc/vignette.bib |only inst/doc/vignette_dwplot.bib |only vignettes/vignette_dwplot.bib |only 8 files changed, 123 insertions(+), 165 deletions(-)
Title: Statistical Procedures for Agricultural Research
Description: Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>
Diff between agricolae versions 1.2-2 dated 2015-08-13 and 1.2-3 dated 2015-10-06
DESCRIPTION | 12 - MD5 | 110 +++++----- NAMESPACE | 3 NEWS | 10 R/BIB.test.R | 10 R/DAU.test.R | 6 R/HSD.test.R | 5 R/LSD.test.R | 7 R/PBIB.test.r | 480 +++++++++++++++++++++++------------------------ R/REGW.test.R |only R/SNK.test.R | 4 R/design.ab.R | 8 R/design.alpha.R | 11 - R/design.bib.R | 8 R/design.crd.R | 7 R/design.cyclic.R | 8 R/design.dau.R | 13 - R/design.graeco.R | 16 - R/design.lattice.R | 14 - R/design.lsd.R | 10 R/design.rcbd.R | 13 - R/design.split.R | 14 - R/design.strip.R | 10 R/design.youden.r | 11 - R/diffograph.R |only R/duncan.test.r | 4 R/durbin.test.R | 4 R/friedman.R | 5 R/kruskal.R | 10 R/median.test.r | 3 R/order.group.R | 9 R/scheffe.test.R | 4 R/waerden.test.R | 5 R/waller.test.R | 2 build/vignette.rds |binary inst/doc/tutorial.R | 274 ++++++++++++++------------ inst/doc/tutorial.Rnw | 81 +++++-- inst/doc/tutorial.pdf |binary man/HSD.test.Rd | 9 man/REGW.test.Rd |only man/SNK.test.Rd | 9 man/agricolae-package.Rd | 7 man/design.ab.Rd | 3 man/design.alpha.Rd | 3 man/design.bib.Rd | 4 man/design.crd.Rd | 3 man/design.cyclic.Rd | 4 man/design.dau.Rd | 4 man/design.graeco.Rd | 3 man/design.lattice.Rd | 3 man/design.lsd.Rd | 3 man/design.rcbd.Rd | 3 man/design.split.Rd | 3 man/design.strip.Rd | 3 man/design.youden.rd | 4 man/diffograph.Rd |only man/duncan.test.Rd | 9 vignettes/tutorial.Rnw | 81 +++++-- 58 files changed, 765 insertions(+), 584 deletions(-)
Title: Structural Estimators and Algorithms for the Analysis of Stable
Matchings
Description: Implements structural estimators to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.co.uk>
Diff between matchingMarkets versions 0.1-5 dated 2015-07-08 and 0.1-6 dated 2015-10-06
DESCRIPTION | 12 +++++---- MD5 | 54 +++++++++++++++++++++++++++++------------ NEWS |only R/khb.R | 12 ++++----- R/mfx.R | 3 ++ R/stabit.R | 30 ++++++++++++++++++---- build |only data/baac00.RData |binary data/klein15a.RData |binary data/klein15b.RData |binary inst |only man/baac00.Rd | 22 ++++++++-------- man/khb.Rd | 2 - man/klein15a.Rd | 2 - man/klein15b.Rd | 29 +++++++++++----------- man/matchingMarkets-package.Rd | 2 - man/mfx.Rd | 4 +++ man/stabit.Rd | 6 +++- src/stabitCpp.cpp | 20 +++++++++++---- tests |only vignettes |only 21 files changed, 131 insertions(+), 67 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data. Methods might be relevant to other categorical data situations on non-migration data, where for example, marginal totals are known and only auxiliary bilateral data is available.
Author: Guy J. Abel
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 1.7 dated 2015-06-18 and 1.7.1 dated 2015-10-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- demo/cfplot_nat.R | 4 ++-- demo/cfplot_reg.R | 2 +- man/migest-package.Rd | 10 +++++++--- man/rc9.Rd | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness correlations (HFCs) from
microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre],
Mareike Esser [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>
Diff between inbreedR versions 0.1.0 dated 2015-09-05 and 0.2.0 dated 2015-10-06
DESCRIPTION | 9 +- MD5 | 32 ++++---- R/g2_microsats.R | 2 R/plot.inbreed.R | 85 ++++++++++++++++++++++- R/print.inbreed.R | 12 ++- R/r2_Wf.R | 78 +++++++++++++++++---- R/r2_hf.R | 130 ++++++++++++++++++++++++------------ README.md | 8 +- inst/doc/inbreedR_step_by_step.R | 7 + inst/doc/inbreedR_step_by_step.Rmd | 13 +++ inst/doc/inbreedR_step_by_step.html | 44 ++++++------ man/plot.inbreed.Rd | 6 + man/r2_Wf.Rd | 20 ++++- man/r2_hf.Rd | 30 +++++--- tests/testthat/test-r2_Wf.R | 11 +++ tests/testthat/test-r2_hf.R | 28 +++++-- vignettes/inbreedR_step_by_step.Rmd | 13 +++ 17 files changed, 394 insertions(+), 134 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.3.0 dated 2015-07-28 and 0.3.1 dated 2015-10-06
ChangeLog | 9 DESCRIPTION | 8 MD5 | 28 +- R/nri_methods.R | 31 ++ R/rastermeta.R | 2 R/spectral_resampling_response.R | 37 ++ inst/doc/References.pdf |binary inst/doc/hsdar-intro.pdf |binary man/Clman-methods.Rd | 2 man/derivative_speclib.Rd | 2 man/normalized.ratio.index-methods.Rd | 3 man/subset_speclib.Rd | 2 src/apply_response.f90 | 2 src/dataSpec_P5B_PROSAIL.f90 | 422 +++++++++++++++++----------------- src/dataSpec_P5B_PROSPECT.f90 | 2 15 files changed, 303 insertions(+), 247 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.2 dated 2015-09-12 and 1.1.3 dated 2015-10-06
DESCRIPTION | 8 +- MD5 | 6 - R/GDM_Table_Funcs.R | 165 ++++++++++++++++++++++++++++++++++----------------- man/gdm.transform.Rd | 4 - 4 files changed, 118 insertions(+), 65 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1337 dated 2015-09-19 and 0.95.1367 dated 2015-10-06
rgl-0.95.1337/rgl/R/interpSetter.R |only rgl-0.95.1337/rgl/inst/doc/WebGL.R |only rgl-0.95.1337/rgl/inst/doc/rgl.R |only rgl-0.95.1337/rgl/po |only rgl-0.95.1337/rgl/vignettes/WebGL.md |only rgl-0.95.1337/rgl/vignettes/plotsnapshot.png |only rgl-0.95.1337/rgl/vignettes/rgl.md |only rgl-0.95.1337/rgl/vignettes/test.Rmd |only rgl-0.95.1337/rgl/vignettes/unnamed_chunk_1snapshot.png |only rgl-0.95.1337/rgl/vignettes/unnamed_chunk_2snapshot.png |only rgl-0.95.1367/rgl/DESCRIPTION | 11 rgl-0.95.1367/rgl/MD5 | 45 rgl-0.95.1367/rgl/NAMESPACE | 4 rgl-0.95.1367/rgl/R/bgplot3d.R | 89 rgl-0.95.1367/rgl/R/scene.R | 4 rgl-0.95.1367/rgl/R/webGL.R | 150 rgl-0.95.1367/rgl/build/vignette.rds |binary rgl-0.95.1367/rgl/configure | 9 rgl-0.95.1367/rgl/configure.ac | 8 rgl-0.95.1367/rgl/configure.win | 1 rgl-0.95.1367/rgl/inst/NEWS | 9 rgl-0.95.1367/rgl/inst/doc/WebGL.html | 1412 ++-- rgl-0.95.1367/rgl/inst/doc/rgl.Rmd | 4 rgl-0.95.1367/rgl/inst/doc/rgl.html | 4664 +++++++--------- rgl-0.95.1367/rgl/man/show2d.Rd |only rgl-0.95.1367/rgl/src/build/autoconf/config.guess | 384 - rgl-0.95.1367/rgl/src/build/autoconf/config.sub | 148 rgl-0.95.1367/rgl/src/glgui.cpp | 4 rgl-0.95.1367/rgl/vignettes/rgl.Rmd | 4 29 files changed, 3423 insertions(+), 3527 deletions(-)
Title: Seamless Interface to Octave -- And Matlab
Description: Direct interface to Octave. The primary goal is to facilitate the
port of Matlab/Octave scripts to R. The package enables to call any Octave
functions from R and as well as browsing their documentation, passing
variables between R and Octave, using R core RNGs in Octave, which ensures
that stochastic computations are also reproducible.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>
Diff between RcppOctave versions 0.14.5 dated 2014-09-20 and 0.18.1 dated 2015-10-06
RcppOctave-0.14.5/RcppOctave/configure.win |only RcppOctave-0.14.5/RcppOctave/man/dot-DollarNames-commaOctave-method.Rd |only RcppOctave-0.14.5/RcppOctave/man/show-commaOctave-method.Rd |only RcppOctave-0.14.5/RcppOctave/src/Makevars.win.in |only RcppOctave-0.18.1/RcppOctave/DESCRIPTION | 14 RcppOctave-0.18.1/RcppOctave/MD5 | 144 +- RcppOctave-0.18.1/RcppOctave/NAMESPACE | 39 RcppOctave-0.18.1/RcppOctave/NEWS | 18 RcppOctave-0.18.1/RcppOctave/R/Octave-class.R | 39 RcppOctave-0.18.1/RcppOctave/R/OctaveFunction-class.R | 4 RcppOctave-0.18.1/RcppOctave/R/base-functions.R | 42 RcppOctave-0.18.1/RcppOctave/R/config-vars.R.in | 28 RcppOctave-0.18.1/RcppOctave/R/config.R | 69 - RcppOctave-0.18.1/RcppOctave/R/eval.R | 1 RcppOctave-0.18.1/RcppOctave/R/interface.R | 5 RcppOctave-0.18.1/RcppOctave/R/package.R | 125 ++ RcppOctave-0.18.1/RcppOctave/R/random.R | 42 RcppOctave-0.18.1/RcppOctave/R/utils.R | 16 RcppOctave-0.18.1/RcppOctave/README | 4 RcppOctave-0.18.1/RcppOctave/build/RcppOctave.pdf |binary RcppOctave-0.18.1/RcppOctave/build/vignette.rds |binary RcppOctave-0.18.1/RcppOctave/cleanup | 9 RcppOctave-0.18.1/RcppOctave/configure | 484 ++++++---- RcppOctave-0.18.1/RcppOctave/configure.ac | 207 ++-- RcppOctave-0.18.1/RcppOctave/exec/configure-win |only RcppOctave-0.18.1/RcppOctave/exec/m4.R |only RcppOctave-0.18.1/RcppOctave/exec/m4.win | 113 ++ RcppOctave-0.18.1/RcppOctave/exec/octave.m4 |only RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.R | 2 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.Rnw | 44 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.pdf |binary RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave.R | 30 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave.pdf |binary RcppOctave-0.18.1/RcppOctave/inst/unitTests/runit.stats.R | 7 RcppOctave-0.18.1/RcppOctave/man/Octave-class.Rd | 36 RcppOctave-0.18.1/RcppOctave/man/Octave.config.Rd | 66 - RcppOctave-0.18.1/RcppOctave/man/Octave.home.Rd | 38 RcppOctave-0.18.1/RcppOctave/man/OctaveFunction-class.Rd | 26 RcppOctave-0.18.1/RcppOctave/man/OctaveInterface.Rd | 83 - RcppOctave-0.18.1/RcppOctave/man/RcppOctave-package.Rd | 57 - RcppOctave-0.18.1/RcppOctave/man/autocomplete.Rd |only RcppOctave-0.18.1/RcppOctave/man/check.equal.Rd | 7 RcppOctave-0.18.1/RcppOctave/man/dot-CallOctave.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/dot-isPlatformCompatible.Rd |only RcppOctave-0.18.1/RcppOctave/man/mfiles.Rd | 14 RcppOctave-0.18.1/RcppOctave/man/o_addpath.Rd | 24 RcppOctave-0.18.1/RcppOctave/man/o_assign.Rd | 43 RcppOctave-0.18.1/RcppOctave/man/o_clear.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/o_config_info.Rd | 20 RcppOctave-0.18.1/RcppOctave/man/o_eval.Rd | 11 RcppOctave-0.18.1/RcppOctave/man/o_exist.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/o_help.Rd | 35 RcppOctave-0.18.1/RcppOctave/man/o_identity.Rd | 10 RcppOctave-0.18.1/RcppOctave/man/o_load.Rd | 5 RcppOctave-0.18.1/RcppOctave/man/o_ls.Rd | 26 RcppOctave-0.18.1/RcppOctave/man/o_rexp.Rd | 22 RcppOctave-0.18.1/RcppOctave/man/o_rgamma.Rd | 29 RcppOctave-0.18.1/RcppOctave/man/o_rnorm.Rd | 22 RcppOctave-0.18.1/RcppOctave/man/o_rpois.Rd |only RcppOctave-0.18.1/RcppOctave/man/o_runif.Rd | 20 RcppOctave-0.18.1/RcppOctave/man/o_source.Rd | 14 RcppOctave-0.18.1/RcppOctave/man/o_version.Rd | 6 RcppOctave-0.18.1/RcppOctave/man/o_who.Rd | 16 RcppOctave-0.18.1/RcppOctave/man/o_whos.Rd | 11 RcppOctave-0.18.1/RcppOctave/man/octave-ll.Rd | 24 RcppOctave-0.18.1/RcppOctave/man/octave_config.Rd | 27 RcppOctave-0.18.1/RcppOctave/man/sourceExamples.Rd | 7 RcppOctave-0.18.1/RcppOctave/man/system.mfile.Rd | 15 RcppOctave-0.18.1/RcppOctave/src/Makevars.in | 31 RcppOctave-0.18.1/RcppOctave/src/Makevars.win |only RcppOctave-0.18.1/RcppOctave/src/compatibility.h |only RcppOctave-0.18.1/RcppOctave/src/conversion.cpp | 32 RcppOctave-0.18.1/RcppOctave/src/modules/Makefile.in | 34 RcppOctave-0.18.1/RcppOctave/src/modules/PKG_ADD | 1 RcppOctave-0.18.1/RcppOctave/src/modules/Rrng.cc | 21 RcppOctave-0.18.1/RcppOctave/src/rcpp_octave.cpp | 27 RcppOctave-0.18.1/RcppOctave/src/rcpp_octave.h | 26 RcppOctave-0.18.1/RcppOctave/tests/doRUnit.R | 3 RcppOctave-0.18.1/RcppOctave/vignettes/RcppOctave-unitTests.Rnw | 44 79 files changed, 1502 insertions(+), 944 deletions(-)
Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MFAg versions 1.2 dated 2015-09-16 and 1.3 dated 2015-10-06
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/GSVD.R | 25 +++++++++++++++++++------ R/IM.R | 23 ++++++++++++++--------- R/MFA.R | 12 ++++++------ R/NormData.R | 2 +- R/Plot.MFA.R | 8 ++++---- man/DataQuali.Rd | 2 +- man/GSVD.Rd | 8 ++++---- man/MFA.Rd | 8 ++++---- man/MFAg-package.Rd | 4 ++-- man/NormData.Rd | 2 +- man/Plot.MFA.Rd | 5 +++-- 13 files changed, 75 insertions(+), 56 deletions(-)
Title: Combinatorial Efficient Global Optimization
Description: Model building, surrogate model
based optimization and Efficient Global Optimization in combinatorial
or mixed search spaces.
Author: Martin Zaefferer <mzaefferer@gmail.com>
Maintainer: Martin Zaefferer <mzaefferer@gmail.com>
Diff between CEGO versions 1.0.1108 dated 2015-01-06 and 2.0.0 dated 2015-10-06
CEGO-1.0.1108/CEGO/R/optimizer.R |only CEGO-1.0.1108/CEGO/man/combinatorialKrigingLikelihood.Rd |only CEGO-1.0.1108/CEGO/man/initializeDesign.Rd |only CEGO-1.0.1108/CEGO/man/longestIncreasingSubsequence.Rd |only CEGO-1.0.1108/CEGO/man/predict.CKriging.Rd |only CEGO-1.0.1108/CEGO/man/predict.CLM.Rd |only CEGO-1.0.1108/CEGO/man/predict.CRBFN.Rd |only CEGO-2.0.0/CEGO/DESCRIPTION | 10 CEGO-2.0.0/CEGO/MD5 | 170 ++-- CEGO-2.0.0/CEGO/NAMESPACE | 20 CEGO-2.0.0/CEGO/NEWS | 33 CEGO-2.0.0/CEGO/R/DoE.R |only CEGO-2.0.0/CEGO/R/binaryBenchmarkFunctions.R | 2 CEGO-2.0.0/CEGO/R/cegoPackage.R | 11 CEGO-2.0.0/CEGO/R/distanceBasedLandscapeGenerators.R | 53 - CEGO-2.0.0/CEGO/R/distanceCalculation.R | 67 + CEGO-2.0.0/CEGO/R/misc.R | 46 - CEGO-2.0.0/CEGO/R/modelKriging.R | 369 ++++++---- CEGO-2.0.0/CEGO/R/modelLm.R | 49 - CEGO-2.0.0/CEGO/R/modelRBFN.R | 83 +- CEGO-2.0.0/CEGO/R/optim2opt.R |only CEGO-2.0.0/CEGO/R/optimCEGO.R |only CEGO-2.0.0/CEGO/R/optimEA.R |only CEGO-2.0.0/CEGO/R/optimInterface.R | 61 - CEGO-2.0.0/CEGO/R/optimRS.R |only CEGO-2.0.0/CEGO/R/permutationBenchmarkFunctions.R | 26 CEGO-2.0.0/CEGO/R/permutationDistances.r | 169 ++-- CEGO-2.0.0/CEGO/R/permutationOperators.R | 135 +++ CEGO-2.0.0/CEGO/man/CEGO-package.Rd | 12 CEGO-2.0.0/CEGO/man/benchmarkGeneratorFSP.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorNKL.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorQAP.Rd | 6 CEGO-2.0.0/CEGO/man/benchmarkGeneratorTSP.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorWT.Rd | 2 CEGO-2.0.0/CEGO/man/buildModel.Rd | 16 CEGO-2.0.0/CEGO/man/combinatorialKriging.Rd | 90 -- CEGO-2.0.0/CEGO/man/combinatorialLM.Rd | 50 - CEGO-2.0.0/CEGO/man/combinatorialRBFN.Rd | 61 - CEGO-2.0.0/CEGO/man/designRandom.Rd |only CEGO-2.0.0/CEGO/man/distanceMatrix.Rd | 3 CEGO-2.0.0/CEGO/man/distanceMatrixUpdate.Rd |only CEGO-2.0.0/CEGO/man/distanceMatrixWrapper.Rd |only CEGO-2.0.0/CEGO/man/distancePermutationAdjacency.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationChebyshev.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationCos.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationEuclidean.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationHamming.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationInsert.Rd | 14 CEGO-2.0.0/CEGO/man/distancePermutationInterchange.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLCSeq.Rd | 20 CEGO-2.0.0/CEGO/man/distancePermutationLCStr.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLee.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLevenshtein.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLex.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationManhattan.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationPosition.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationPosition2.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationR.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationSwap.Rd | 2 CEGO-2.0.0/CEGO/man/distanceVector.Rd | 3 CEGO-2.0.0/CEGO/man/fcorrCubic.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrGauss.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrLinear.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrSphere.Rd | 4 CEGO-2.0.0/CEGO/man/infillExpectedImprovement.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussian.Rd | 9 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussianBuild.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussianEval.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorMUL.Rd | 24 CEGO-2.0.0/CEGO/man/landscapeGeneratorUNI.Rd | 16 CEGO-2.0.0/CEGO/man/lexicographicPermutationOrderNumber.Rd | 2 CEGO-2.0.0/CEGO/man/modelKriging.Rd |only CEGO-2.0.0/CEGO/man/modelKrigingLikelihood.Rd |only CEGO-2.0.0/CEGO/man/modelLinear.Rd |only CEGO-2.0.0/CEGO/man/modelRBFN.Rd |only CEGO-2.0.0/CEGO/man/mutationBinary.Rd | 2 CEGO-2.0.0/CEGO/man/mutationBinaryFast.Rd | 2 CEGO-2.0.0/CEGO/man/mutationPermutationInterchange.Rd | 9 CEGO-2.0.0/CEGO/man/mutationPermutationReversal.Rd |only CEGO-2.0.0/CEGO/man/mutationPermutationSwap.Rd | 9 CEGO-2.0.0/CEGO/man/optim2Opt.Rd | 21 CEGO-2.0.0/CEGO/man/optimCEGO.Rd | 56 - CEGO-2.0.0/CEGO/man/optimEA.Rd | 35 CEGO-2.0.0/CEGO/man/optimInterface.Rd | 28 CEGO-2.0.0/CEGO/man/optimRS.Rd | 23 CEGO-2.0.0/CEGO/man/optimizeModel.Rd |only CEGO-2.0.0/CEGO/man/predict.modelKriging.Rd |only CEGO-2.0.0/CEGO/man/predict.modelLinear.Rd |only CEGO-2.0.0/CEGO/man/predict.modelRBFN.Rd |only CEGO-2.0.0/CEGO/man/recombinationBinaryUniformCrossoverFast.Rd | 2 CEGO-2.0.0/CEGO/man/recombinationPermutationCycleCrossover.Rd | 2 CEGO-2.0.0/CEGO/man/removeDuplicates.Rd | 2 CEGO-2.0.0/CEGO/man/removeDuplicatesOffspring.Rd | 6 CEGO-2.0.0/CEGO/man/solutionFunctionGeneratorBinary.Rd | 2 CEGO-2.0.0/CEGO/man/solutionFunctionGeneratorPermutation.Rd | 2 CEGO-2.0.0/CEGO/man/step2Opt.Rd | 4 CEGO-2.0.0/CEGO/man/tournamentSelection.Rd | 4 CEGO-2.0.0/CEGO/src/permutationDistance.c | 341 ++++++--- 98 files changed, 1259 insertions(+), 981 deletions(-)
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Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-10 dated 2015-06-16 and 0.11-22 dated 2015-10-06
DESCRIPTION | 19 ++++--- MD5 | 25 +++++----- NAMESPACE | 27 ++++++----- R/codeGeno.r | 110 ++++++++++++++++++++------------------------- R/kinship.r | 4 - R/plot.pedigree.r | 30 ++++++------ R/read.write.vcf.r | 15 +++--- man/add.individuals.Rd | 32 +++++++++++-- man/codeGeno.Rd | 2 man/create.gpData.Rd | 18 ++++--- man/discard.individuals.Rd |only man/discard.markers.Rd | 29 +++++------ man/kinship.Rd | 4 - man/write.vcf.Rd | 11 ++++ 14 files changed, 182 insertions(+), 144 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>
Diff between marmap versions 0.9.2 dated 2015-01-28 and 0.9.3 dated 2015-10-06
marmap-0.9.2/marmap/data/datalist |only marmap-0.9.3/marmap/DESCRIPTION | 10 ++--- marmap-0.9.3/marmap/MD5 | 37 ++++++++++--------- marmap-0.9.3/marmap/NAMESPACE | 18 ++++++--- marmap-0.9.3/marmap/R/griddify.R |only marmap-0.9.3/marmap/R/plot.bathy.R | 4 +- marmap-0.9.3/marmap/build/vignette.rds |binary marmap-0.9.3/marmap/data/aleutians.rda |binary marmap-0.9.3/marmap/data/celt.rda |binary marmap-0.9.3/marmap/data/florida.rda |binary marmap-0.9.3/marmap/data/hawaii.rda |binary marmap-0.9.3/marmap/data/hawaii.sites.rda |binary marmap-0.9.3/marmap/data/irregular.rda |only marmap-0.9.3/marmap/data/metallo.rda |binary marmap-0.9.3/marmap/data/nw.atlantic.coast.rda |binary marmap-0.9.3/marmap/data/nw.atlantic.rda |binary marmap-0.9.3/marmap/inst/doc/marmap-DataAnalysis.pdf |binary marmap-0.9.3/marmap/inst/doc/marmap-ImportExport.pdf |binary marmap-0.9.3/marmap/inst/doc/marmap.pdf |binary marmap-0.9.3/marmap/man/griddify.Rd |only marmap-0.9.3/marmap/man/irregular.Rd |only marmap-0.9.3/marmap/man/marmap.Rd | 4 +- 22 files changed, 41 insertions(+), 32 deletions(-)
Title: Flow Selection and Analysis
Description: Selections on flow matrices, statistics on selected flows, map and graph visualisations.
Author: Timothée Giraud [cre, aut],
Laurent Beauguitte [aut],
Marianne Guérois [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between flows versions 1.0 dated 2015-07-17 and 1.1 dated 2015-10-06
DESCRIPTION | 8 +- MD5 | 27 ++++---- NEWS |only R/flows.R | 151 +++++-------------------------------------------- build/vignette.rds |binary inst/doc/flows.R | 4 - inst/doc/flows.Rmd | 6 - inst/doc/flows.html | 16 ++--- man/compmat.Rd | 3 man/domflows.Rd | 9 -- man/flows.Rd | 3 man/plotDomFlows.Rd | 3 man/plotMapDomFlows.Rd | 3 man/statmat.Rd | 8 +- vignettes/flows.Rmd | 6 - 15 files changed, 64 insertions(+), 183 deletions(-)
Title: Enhanced Least Absolute Shrinkage and Selection Operator
Regression Model
Description: Performs some enhanced variable selection algorithms
based on the least absolute shrinkage and selection operator for regression model.
Author: Pi Guo
Maintainer: Pi Guo <guopi.01@163.com>
Diff between elasso versions 1.0 dated 2015-09-17 and 1.1 dated 2015-10-06
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/BRLasso.R | 18 +++++++++++------- man/BRLasso.Rd | 17 +++++++++++------ 4 files changed, 31 insertions(+), 21 deletions(-)
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Title: An Interface for MIXMOD
Description: A collection of functions designed to run supervised and
unsupervised classification with MIXture MODelling.
Author: Remi Lebret [aut, cre],
Serge Iovleff [aut],
Florent Langrognet [aut],
Benjamin Auder [ctb],
C. Biernacki [ctb],
G. Celeux [ctb],
G. Govaert [ctb]
Maintainer: Remi Lebret <remi@lebret.ch>
Diff between Rmixmod versions 2.0.2 dated 2014-03-21 and 2.0.3 dated 2015-10-06
DESCRIPTION | 46 +++++++++++++++++----------------- MD5 | 40 +++++++++++++++-------------- NAMESPACE | 15 +++++++++++ R/CompositeModel.R | 3 +- R/CompositeParameter.R | 7 +++-- R/GaussianModel.R | 3 +- R/GaussianParameter.R | 8 ++--- R/MixmodCluster.R | 2 + R/MixmodLearn.R | 2 + R/MixmodPredict.R | 2 + R/MixmodResults.R | 6 ++++ R/MultinomialModel.R | 3 +- R/Rmixmod.R | 7 ++--- R/Strategy.R | 4 ++ R/global.R | 1 R/zzz.R | 2 - README |only inst/CITATION |only man/Rmixmod-package.Rd | 4 +- src/mixmod/Kernel/Model/ModelType.cpp | 5 --- src/mixmod/Matrix/GeneralMatrix.cpp | 5 --- tests/test.R | 2 - 22 files changed, 99 insertions(+), 68 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the LZ77
algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but
offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.2 dated 2015-10-03 and 0.3 dated 2015-10-06
DESCRIPTION | 18 ++++++++---------- MD5 | 5 +++-- src/Makevars | 5 +++-- src/config.h |only 4 files changed, 14 insertions(+), 14 deletions(-)
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Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-1 dated 2015-07-14 and 0.0-2 dated 2015-10-06
assertive.base-0.0-1/assertive.base/man/DIM.Rd |only assertive.base-0.0-1/assertive.base/man/n_elements.Rd |only assertive.base-0.0-2/assertive.base/DESCRIPTION | 49 ++ assertive.base-0.0-2/assertive.base/MD5 | 66 ++- assertive.base-0.0-2/assertive.base/NAMESPACE | 110 ++--- assertive.base-0.0-2/assertive.base/NEWS | 4 assertive.base-0.0-2/assertive.base/R/are-identical.R |only assertive.base-0.0-2/assertive.base/R/assert-are-identical.R |only assertive.base-0.0-2/assertive.base/R/assert-identical-to-true-false-na.R | 52 +- assertive.base-0.0-2/assertive.base/R/assert-is-true-false-na.R | 132 ++++-- assertive.base-0.0-2/assertive.base/R/cause.R | 29 - assertive.base-0.0-2/assertive.base/R/coercion.R | 2 assertive.base-0.0-2/assertive.base/R/conditions.R |only assertive.base-0.0-2/assertive.base/R/engine.R | 19 assertive.base-0.0-2/assertive.base/R/internal.R | 4 assertive.base-0.0-2/assertive.base/R/is-identical-to-true-false-na.R | 23 - assertive.base-0.0-2/assertive.base/R/is-true-false-na.R | 20 assertive.base-0.0-2/assertive.base/R/utils.R | 81 ---- assertive.base-0.0-2/assertive.base/README.md | 121 ++++-- assertive.base-0.0-2/assertive.base/inst |only assertive.base-0.0-2/assertive.base/man/Truth.Rd | 64 ++- assertive.base-0.0-2/assertive.base/man/are_identical.Rd |only assertive.base-0.0-2/assertive.base/man/assert_engine.Rd | 5 assertive.base-0.0-2/assertive.base/man/assertionError.Rd |only assertive.base-0.0-2/assertive.base/man/call_and_name.Rd | 4 assertive.base-0.0-2/assertive.base/man/is2.Rd | 2 assertive.base-0.0-2/assertive.base/man/merge.list.Rd | 9 assertive.base-0.0-2/assertive.base/po/R-assertive.base.pot | 201 ++++------ assertive.base-0.0-2/assertive.base/po/R-de.po |only assertive.base-0.0-2/assertive.base/po/R-el.po |only assertive.base-0.0-2/assertive.base/po/R-fr.po |only assertive.base-0.0-2/assertive.base/po/R-hu.po |only assertive.base-0.0-2/assertive.base/po/R-ko.po |only assertive.base-0.0-2/assertive.base/po/R-nl.po |only assertive.base-0.0-2/assertive.base/po/R-ru.po |only assertive.base-0.0-2/assertive.base/po/R-sv.po |only assertive.base-0.0-2/assertive.base/po/R-tr.po |only assertive.base-0.0-2/assertive.base/po/R-uk.po |only assertive.base-0.0-2/assertive.base/tests/testthat/test-are-identical.R |only 39 files changed, 619 insertions(+), 378 deletions(-)
More information about assertive.base at CRAN
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Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.4-7 dated 2015-07-14 and 0.5-0 dated 2015-10-06
DESCRIPTION | 41 +++-- MD5 | 47 ++++-- NAMESPACE | 15 +- R/Class-SDMXComponents.R | 2 R/Class-SDMXDataStructure.R | 2 R/Class-SDMXRESTRequestBuilder.R |only R/Class-SDMXRequestBuilder.R |only R/Class-SDMXServiceProvider.R |only R/Class-SDMXStructureType.R | 1 R/SDMXDataStructure-methods.R | 13 + R/SDMXDataStructures-methods.R | 49 +++++++ R/SDMXRESTRequestBuilder-methods.R |only R/SDMXRequestBuilder-methods.R |only R/SDMXServiceProvider-methods.R |only R/profile.R |only R/readSDMX.R | 238 ++++++++++++++++++++-------------- README.md | 166 +++++++++++++++++++++-- build |only inst/doc |only man/SDMXRESTRequestBuilder-class.Rd |only man/SDMXRequestBuilder-class.Rd |only man/SDMXServiceProvider-class.Rd |only man/addSDMXServiceProvider.Rd |only man/findSDMXServiceProvider.Rd |only man/getSDMXServiceProviders.Rd |only man/readSDMX.Rd | 24 +++ man/rsdmx-package.Rd | 4 man/setSDMXServiceProviders.Rd |only tests/testthat/test_DataStructures.R | 25 +++ tests/testthat/test_Main_Helpers.R |only tests/testthat/test_RequestBuilder.R |only tests/testthat/test_ServiceProvider.R |only vignettes/quickstart.Rmd | 42 ++++-- 33 files changed, 511 insertions(+), 158 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut], Martin Maechler [aut],
Ben Bolker [aut, cre], Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb], Bin Dai [ctb],
Gabor Grothendieck [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-9 dated 2015-08-20 and 1.1-10 dated 2015-10-06
lme4-1.1-10/lme4/DESCRIPTION | 6 +- lme4-1.1-10/lme4/MD5 | 36 ++++++------ lme4-1.1-10/lme4/NAMESPACE | 25 ++++++-- lme4-1.1-10/lme4/R/AllClass.R | 6 +- lme4-1.1-10/lme4/R/bootMer.R | 14 ++++ lme4-1.1-10/lme4/R/lmer.R | 85 +++++++++++++++-------------- lme4-1.1-10/lme4/R/predict.R | 28 ++++++--- lme4-1.1-10/lme4/R/profile.R | 8 +- lme4-1.1-10/lme4/R/utilities.R | 53 +++++++++--------- lme4-1.1-10/lme4/README.md | 9 +-- lme4-1.1-10/lme4/inst/CITATION | 48 ++++++++-------- lme4-1.1-10/lme4/inst/NEWS.Rd | 57 +++++++++++++++---- lme4-1.1-10/lme4/inst/tests/test-lmer.R | 18 ++++++ lme4-1.1-10/lme4/inst/tests/test-methods.R | 25 ++++++-- lme4-1.1-10/lme4/man/bootMer.Rd | 7 ++ lme4-1.1-10/lme4/man/devcomp.Rd | 4 - lme4-1.1-10/lme4/man/golden-class.Rd | 23 ++++++- lme4-1.1-10/lme4/man/lmerControl.Rd | 50 ++++++++--------- lme4-1.1-10/lme4/man/utilities.Rd |only lme4-1.1-9/lme4/man/golden.Rd |only 20 files changed, 317 insertions(+), 185 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.2.0 dated 2015-09-25 and 0.3.0 dated 2015-10-06
DESCRIPTION | 6 - MD5 | 33 ++++--- NAMESPACE | 4 NEWS.md | 19 ++++ R/generics.R | 161 +++++++++++++++++++++++++++++-------- R/helpers.R | 2 R/kdecop.R | 9 ++ R/plot.kdecopula.R | 33 ++++--- README.md | 128 +++++++++++++++++++---------- inst/README-unnamed-chunk-10-1.png |only inst/README-unnamed-chunk-12-1.png |only inst/README-unnamed-chunk-3-1.png |binary inst/README-unnamed-chunk-6-1.png |binary inst/README-unnamed-chunk-7-1.png |binary inst/README-unnamed-chunk-8-1.png |binary inst/README-unnamed-chunk-9-1.png |binary man/logLik.kdecopula.Rd |only src/interp.cpp | 3 src/renorm.cpp | 6 - 19 files changed, 292 insertions(+), 112 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.4.0 dated 2015-09-18 and 0.4.1 dated 2015-10-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 28 ++++++++++++++-------------- NEWS | 5 +++++ R/globalsOf.R | 7 ++++++- tests/globalsOf.R | 42 ++++++++++++++++++++++++++++-------------- 6 files changed, 61 insertions(+), 37 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the system
clipboards of Windows, OS X, and Linux.
Author: Matthew Lincoln [aut, cre],
Louis Maddox [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.1.1 dated 2015-09-03 and 0.2.0 dated 2015-10-06
DESCRIPTION | 7 ++--- MD5 | 25 ++++++++++-------- NAMESPACE | 1 NEWS.md | 23 ++++++++++++++++- R/clipboard.R | 70 +++++++++++++++++++++++++++++++++++++++------------- R/flat_str.R | 37 +++++++++++++++++++++++++-- R/linux_clipboard.R | 27 ++++++++++++-------- R/osx_clipboard.R | 32 ++++++++++++++--------- R/win_clipboard.R | 24 ++++++++++++----- README.md | 32 +++++++++++++++++++---- man/clear_clip.Rd |only man/read_clip.Rd | 7 +++++ man/write_clip.Rd | 44 +++++++++++++++++++++++++------- tests |only 14 files changed, 248 insertions(+), 81 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++++-- NAMESPACE | 2 +- R/symscorestat.R |only inst |only man/symscorestat.Rd |only src/signtestperm.f90 |only 7 files changed, 11 insertions(+), 7 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.7.0 dated 2015-10-01 and 0.7.1 dated 2015-10-05
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Allele Imputation and Haplotype Reconstruction from Pedigree
Databases
Description: Simulation of alphanumeric alleles, imputation of genetic missing data and reconstruction of non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many different factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used either simulated datasets or loaded databases (in .ped file biallelic format). Haplotype reconstruction can be performed even with missing data because of alleHap, firstly imputes the genotypes. All this considering that each member (due to meiosis) should unequivocally have two alleles, one inherited from each parent.
Author: Nathan Medina-Rodriguez and Angelo Santana
Maintainer: Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>
Diff between alleHap versions 0.7.2 dated 2014-08-10 and 0.9.2 dated 2015-10-05
alleHap-0.7.2/alleHap/R/buildFunctions.R |only alleHap-0.7.2/alleHap/R/buildHaps.R |only alleHap-0.7.2/alleHap/R/simFams.R |only alleHap-0.7.2/alleHap/R/simFunctions.R |only alleHap-0.7.2/alleHap/man/buildHaps.Rd |only alleHap-0.7.2/alleHap/man/simFams.Rd |only alleHap-0.9.2/alleHap/DESCRIPTION | 26 ++++------ alleHap-0.9.2/alleHap/MD5 | 33 +++++++++---- alleHap-0.9.2/alleHap/NAMESPACE | 13 +++-- alleHap-0.9.2/alleHap/R/alleImputer.R |only alleHap-0.9.2/alleHap/R/alleLoader.R |only alleHap-0.9.2/alleHap/R/alleSimulator.R |only alleHap-0.9.2/alleHap/R/hapPhaser.R |only alleHap-0.9.2/alleHap/build |only alleHap-0.9.2/alleHap/inst |only alleHap-0.9.2/alleHap/man/alleHap-package.Rd | 65 ++++++++++++++++++--------- alleHap-0.9.2/alleHap/man/alleImputer.Rd |only alleHap-0.9.2/alleHap/man/alleLoader.Rd |only alleHap-0.9.2/alleHap/man/alleSimulator.Rd |only alleHap-0.9.2/alleHap/man/hapPhaser.Rd |only alleHap-0.9.2/alleHap/vignettes |only 21 files changed, 88 insertions(+), 49 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>
Diff between mev versions 1.2 dated 2015-08-24 and 1.3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 2 NEWS | 21 ++ R/RcppExports.R | 93 ++++++++-- R/rmev_wrapper.R | 263 +++++++++++++++++++++++----- man/rmev.Rd | 22 +- man/rmevspec.Rd | 2 src/RcppExports.cpp | 78 +++++++- src/ev_sampling.cpp | 472 +++++++++++++++++++++++++++++++++++----------------- 10 files changed, 736 insertions(+), 243 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-2 dated 2015-09-11 and 0.1-3 dated 2015-10-05
gimme-0.1-2/gimme/man/gimme.Rd |only gimme-0.1-3/gimme/DESCRIPTION | 20 - gimme-0.1-3/gimme/MD5 | 34 + gimme-0.1-3/gimme/NAMESPACE | 25 + gimme-0.1-3/gimme/R/aggSEM.R | 41 +- gimme-0.1-3/gimme/R/deconvolve_funcs.R |only gimme-0.1-3/gimme/R/gimme-pkg.R | 21 - gimme-0.1-3/gimme/R/gimme.R | 529 +++++++++++++++--------------- gimme-0.1-3/gimme/R/gimmeInteractive.R |only gimme-0.1-3/gimme/R/indSEM.R | 40 +- gimme-0.1-3/gimme/R/spm_funcs.R |only gimme-0.1-3/gimme/man/aggSEM.Rd | 28 - gimme-0.1-3/gimme/man/gimme-package.Rd | 14 gimme-0.1-3/gimme/man/gimmeInteractive.Rd |only gimme-0.1-3/gimme/man/gimmeSEM.Rd |only gimme-0.1-3/gimme/man/indSEM.Rd | 33 - gimme-0.1-3/gimme/man/ts1.Rd | 3 gimme-0.1-3/gimme/man/ts2.Rd | 3 gimme-0.1-3/gimme/man/ts3.Rd | 3 gimme-0.1-3/gimme/man/ts4.Rd | 3 gimme-0.1-3/gimme/man/ts5.Rd | 3 21 files changed, 435 insertions(+), 365 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.0 dated 2015-09-07 and 0.8.1 dated 2015-10-05
future-0.8.0/future/R/tweakExpression.R |only future-0.8.0/future/tests/MulticoreFutureRegistry.R |only future-0.8.1/future/DESCRIPTION | 8 future-0.8.1/future/MD5 | 43 ++-- future-0.8.1/future/NEWS | 14 + future-0.8.1/future/R/FutureRegistry.R |only future-0.8.1/future/R/MulticoreFuture.R | 48 ---- future-0.8.1/future/R/availableCores.R | 2 future-0.8.1/future/R/eager.R | 13 + future-0.8.1/future/R/globals.R |only future-0.8.1/future/R/lazy.R | 32 --- future-0.8.1/future/R/multicore.R | 14 + future-0.8.1/future/build/vignette.rds |binary future-0.8.1/future/inst/doc/future.html | 10 future-0.8.1/future/inst/doc/future.md.rsp | 10 future-0.8.1/future/inst/doc/issues.html |only future-0.8.1/future/inst/doc/issues.md.rsp |only future-0.8.1/future/man/eager.Rd | 130 ++++++------ future-0.8.1/future/man/lazy.Rd | 212 ++++++++++---------- future-0.8.1/future/man/multicore.Rd | 161 +++++++-------- future-0.8.1/future/man/plan.Rd | 190 ++++++++--------- future-0.8.1/future/tests/FutureRegistry.R |only future-0.8.1/future/tests/dotdotdot.R |only future-0.8.1/future/tests/eager.R | 15 - future-0.8.1/future/tests/multicore.R | 29 +- future-0.8.1/future/vignettes/future.md.rsp | 10 future-0.8.1/future/vignettes/issues.md.rsp |only 27 files changed, 475 insertions(+), 466 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfmta versions 1.3-2 dated 2015-04-29 and 1.3-3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 12 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 7 files changed, 63 insertions(+), 89 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-4 dated 2015-09-11 and 2.1-5 dated 2015-10-05
DESCRIPTION | 8 MD5 | 14 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 src/plateau.cpp | 4 8 files changed, 66 insertions(+), 92 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements t-tests (independent and dependent samples), ANOVA (including between-within subject designs) and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut],
Felix Schoenbrodt [ctr]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.3-2 dated 2015-07-23 and 0.4-0 dated 2015-10-05
WRS2-0.3-2/WRS2/R/tsplit.R |only WRS2-0.3-2/WRS2/man/tsplit.Rd |only WRS2-0.4-0/WRS2/DESCRIPTION | 29 +++++------ WRS2-0.4-0/WRS2/MD5 | 92 +++++++++++++++++++++++------------- WRS2-0.4-0/WRS2/NAMESPACE | 12 ++++ WRS2-0.4-0/WRS2/R/ancboot.R | 8 ++- WRS2-0.4-0/WRS2/R/ancova.R | 22 +++++++- WRS2-0.4-0/WRS2/R/bwtrim.R |only WRS2-0.4-0/WRS2/R/mest.R |only WRS2-0.4-0/WRS2/R/msmedse.R | 2 WRS2-0.4-0/WRS2/R/pairdepb.R | 3 - WRS2-0.4-0/WRS2/R/pb2gen.R | 2 WRS2-0.4-0/WRS2/R/pbad2way.R | 34 +++++++------ WRS2-0.4-0/WRS2/R/print.mcp2.R |only WRS2-0.4-0/WRS2/R/print.pb2.R |only WRS2-0.4-0/WRS2/R/print.rmanovab.R | 2 WRS2-0.4-0/WRS2/R/print.yuen.R | 3 - WRS2-0.4-0/WRS2/R/rmmcp.R | 2 WRS2-0.4-0/WRS2/R/rungen.R |only WRS2-0.4-0/WRS2/R/runhat.R |only WRS2-0.4-0/WRS2/R/runmbo.R |only WRS2-0.4-0/WRS2/R/runmean.R |only WRS2-0.4-0/WRS2/R/sppba.R | 66 ++++++++++++------------- WRS2-0.4-0/WRS2/R/sppbb.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/sppbi.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/t2way.R | 9 ++- WRS2-0.4-0/WRS2/R/trimse.R | 2 WRS2-0.4-0/WRS2/R/tsub.R | 2 WRS2-0.4-0/WRS2/R/winmean.R |only WRS2-0.4-0/WRS2/R/winse.R |only WRS2-0.4-0/WRS2/R/yuen.R | 3 - WRS2-0.4-0/WRS2/R/yuenbt.R | 7 +- WRS2-0.4-0/WRS2/R/yuend.R | 43 +++++++++------- WRS2-0.4-0/WRS2/build |only WRS2-0.4-0/WRS2/data/Pygmalion.rda |only WRS2-0.4-0/WRS2/data/chile.rda |only WRS2-0.4-0/WRS2/data/electric.rda |only WRS2-0.4-0/WRS2/data/eurosoccer.rda |only WRS2-0.4-0/WRS2/data/goggles.rda |binary WRS2-0.4-0/WRS2/data/hangover.rda |only WRS2-0.4-0/WRS2/data/swimming.rda |only WRS2-0.4-0/WRS2/inst/NEWS.Rd | 12 ++++ WRS2-0.4-0/WRS2/inst/doc |only WRS2-0.4-0/WRS2/man/Pygmalion.Rd |only WRS2-0.4-0/WRS2/man/WineTasting.Rd | 2 WRS2-0.4-0/WRS2/man/ancova.Rd | 16 +----- WRS2-0.4-0/WRS2/man/bwtrim.Rd |only WRS2-0.4-0/WRS2/man/chile.Rd |only WRS2-0.4-0/WRS2/man/electric.Rd |only WRS2-0.4-0/WRS2/man/eurosoccer.Rd |only WRS2-0.4-0/WRS2/man/goggles.Rd | 8 ++- WRS2-0.4-0/WRS2/man/hangover.Rd |only WRS2-0.4-0/WRS2/man/rmanova.Rd | 2 WRS2-0.4-0/WRS2/man/rmanovab.Rd | 2 WRS2-0.4-0/WRS2/man/runmean.Rd |only WRS2-0.4-0/WRS2/man/swimming.Rd |only WRS2-0.4-0/WRS2/man/t3way.Rd | 2 WRS2-0.4-0/WRS2/man/trimse.Rd |only WRS2-0.4-0/WRS2/man/yuen.Rd | 21 +++----- WRS2-0.4-0/WRS2/man/yuend.Rd |only WRS2-0.4-0/WRS2/vignettes |only 61 files changed, 310 insertions(+), 202 deletions(-)
Title: Simulating Phylogenetic Trees
Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>
Diff between TreeSim versions 2.1 dated 2014-09-18 and 2.2 dated 2015-10-05
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- R/LTT.plot.gen.R | 35 ++++++++++++++++++++++------------- R/collapse.singles.R |only man/LTT.plot.Rd | 13 +++++++++++++ man/LTT.plot.gen.Rd | 40 +++++++++++++++++++++------------------- man/TreeSim-package.Rd | 8 ++++---- 8 files changed, 77 insertions(+), 50 deletions(-)
Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE).
Includes routines that: (1) generate gradient and Jacobian matrices (full and banded),
(2) find roots of non-linear equations by the Newton-Raphson method,
(3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running,
(4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ODEs
by numerical differencing (using the method-of-lines approach).
Includes fortran code.
Author: Karline Soetaert [aut, cre],
yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between rootSolve versions 1.6.5.1 dated 2014-11-06 and 1.6.6 dated 2015-10-05
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 6 ++++-- R/stode.R | 5 ++++- R/stodes.R | 3 +++ build/vignette.rds |binary 6 files changed, 24 insertions(+), 15 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.5 dated 2015-07-17 and 0.1.6 dated 2015-10-05
RcppRedis-0.1.5/RcppRedis/R/RcppExports.R |only RcppRedis-0.1.5/RcppRedis/src/RcppExports.cpp |only RcppRedis-0.1.6/RcppRedis/ChangeLog | 27 +++ RcppRedis-0.1.6/RcppRedis/DESCRIPTION | 8 - RcppRedis-0.1.6/RcppRedis/MD5 | 15 - RcppRedis-0.1.6/RcppRedis/README.md | 4 RcppRedis-0.1.6/RcppRedis/inst/NEWS.Rd | 23 ++ RcppRedis-0.1.6/RcppRedis/inst/tests/runit.basicRtests.R | 7 RcppRedis-0.1.6/RcppRedis/inst/tests/runit.listTests.R |only RcppRedis-0.1.6/RcppRedis/src/Redis.cpp | 117 +++++++++++++-- 10 files changed, 174 insertions(+), 27 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.2.0 dated 2015-03-31 and 0.5.0 dated 2015-10-05
gvc-0.2.0/gvc/R/block_matrix.R |only gvc-0.2.0/gvc/R/minus_block_matrix.R |only gvc-0.2.0/gvc/man/block_matrix.Rd |only gvc-0.2.0/gvc/man/minus_block_matrix.Rd |only gvc-0.2.0/gvc/tests/testthat/test_block_matrix.R |only gvc-0.2.0/gvc/tests/testthat/test_minus_block_matrix.R |only gvc-0.5.0/gvc/DESCRIPTION | 18 +-- gvc-0.5.0/gvc/MD5 | 47 +++++--- gvc-0.5.0/gvc/NAMESPACE | 9 + gvc-0.5.0/gvc/NEWS | 32 +++++ gvc-0.5.0/gvc/R/dfddva.R |only gvc-0.5.0/gvc/R/dfdfva.R |only gvc-0.5.0/gvc/R/downstream.R |only gvc-0.5.0/gvc/R/e2r.R | 18 +++ gvc-0.5.0/gvc/R/ffddva.R |only gvc-0.5.0/gvc/R/gvc.R |only gvc-0.5.0/gvc/R/i2e.R | 19 +++ gvc-0.5.0/gvc/R/nrca.R | 36 +----- gvc-0.5.0/gvc/R/upstream.R |only gvc-0.5.0/gvc/README.md | 96 ++++++++++++++--- gvc-0.5.0/gvc/build |only gvc-0.5.0/gvc/inst |only gvc-0.5.0/gvc/man/dfddva.Rd |only gvc-0.5.0/gvc/man/dfdfva.Rd |only gvc-0.5.0/gvc/man/downstream.Rd |only gvc-0.5.0/gvc/man/e2r.Rd | 19 +++ gvc-0.5.0/gvc/man/ffddva.Rd |only gvc-0.5.0/gvc/man/gvc.Rd |only gvc-0.5.0/gvc/man/i2e.Rd | 19 +++ gvc-0.5.0/gvc/man/nrca.Rd | 8 - gvc-0.5.0/gvc/man/upstream.Rd |only gvc-0.5.0/gvc/tests/testthat/test_e2r.R |only gvc-0.5.0/gvc/tests/testthat/test_i2e.R |only gvc-0.5.0/gvc/tests/testthat/test_nrca.R |only gvc-0.5.0/gvc/vignettes |only 35 files changed, 240 insertions(+), 81 deletions(-)
Title: Risk Regression Models for Survival Analysis with Competing
Risks
Description: Risk regression models for survival analysis with and without
competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 1.1.1 dated 2014-12-10 and 1.1.7 dated 2015-10-05
riskRegression-1.1.1/riskRegression/src/matrix.h |only riskRegression-1.1.7/riskRegression/DESCRIPTION | 17 riskRegression-1.1.7/riskRegression/MD5 | 71 +-- riskRegression-1.1.7/riskRegression/NAMESPACE | 23 + riskRegression-1.1.7/riskRegression/R/CSC.R | 180 ++++++---- riskRegression-1.1.7/riskRegression/R/FGR.R | 8 riskRegression-1.1.7/riskRegression/R/coef.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/plot.CauseSpecificCox.R | 34 + riskRegression-1.1.7/riskRegression/R/plot.predictedRisk.R | 2 riskRegression-1.1.7/riskRegression/R/plot.riskRegression.R | 9 riskRegression-1.1.7/riskRegression/R/plotEffects.R | 9 riskRegression-1.1.7/riskRegression/R/predict.CauseSpecificCox.R | 2 riskRegression-1.1.7/riskRegression/R/predict.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/predict.riskRegression.R | 5 riskRegression-1.1.7/riskRegression/R/print.CauseSpecificCox.R | 12 riskRegression-1.1.7/riskRegression/R/print.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/print.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/print.subjectWeights.R | 2 riskRegression-1.1.7/riskRegression/R/print.timevarCoefList.R | 2 riskRegression-1.1.7/riskRegression/R/riskRegression-package.R | 4 riskRegression-1.1.7/riskRegression/R/riskRegression.R | 11 riskRegression-1.1.7/riskRegression/R/subjectWeights.R | 14 riskRegression-1.1.7/riskRegression/R/summary.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/summary.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/man/CSC.Rd | 78 ++-- riskRegression-1.1.7/riskRegression/man/FGR.Rd | 44 +- riskRegression-1.1.7/riskRegression/man/Melanoma.Rd | 21 - riskRegression-1.1.7/riskRegression/man/plot.riskRegression.Rd | 52 +- riskRegression-1.1.7/riskRegression/man/plotEffects.Rd | 58 +-- riskRegression-1.1.7/riskRegression/man/predict.riskRegression.Rd | 21 - riskRegression-1.1.7/riskRegression/man/riskRegression.Rd | 100 ++--- riskRegression-1.1.7/riskRegression/man/subjectWeights.Rd | 61 +-- riskRegression-1.1.7/riskRegression/src/matrix.c | 2 riskRegression-1.1.7/riskRegression/src/riskregression.h | 50 ++ riskRegression-1.1.7/riskRegression/tests/test-FGR.R | 21 + riskRegression-1.1.7/riskRegression/tests/testthat/CauseSpecificCoxRegression.R | 7 riskRegression-1.1.7/riskRegression/tests/testthat/brier.R | 4 37 files changed, 547 insertions(+), 389 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 1.5.1 dated 2014-12-10 and 1.5.5 dated 2015-10-05
prodlim-1.5.1/prodlim/R/contrastMethods.R |only prodlim-1.5.1/prodlim/R/modelMatrix.R |only prodlim-1.5.1/prodlim/R/readFormula.R |only prodlim-1.5.5/prodlim/DESCRIPTION | 11 prodlim-1.5.5/prodlim/MD5 | 132 ++++----- prodlim-1.5.5/prodlim/NAMESPACE | 34 ++ prodlim-1.5.5/prodlim/R/EventHistory.frame.R | 3 prodlim-1.5.5/prodlim/R/Hist.R | 4 prodlim-1.5.5/prodlim/R/List2Matrix.R |only prodlim-1.5.5/prodlim/R/atRisk.R | 113 ++++---- prodlim-1.5.5/prodlim/R/backGround.R | 63 ++-- prodlim-1.5.5/prodlim/R/checkCauses.R |only prodlim-1.5.5/prodlim/R/dimColor.R | 4 prodlim-1.5.5/prodlim/R/followup.R |only prodlim-1.5.5/prodlim/R/getStates.R | 6 prodlim-1.5.5/prodlim/R/jackknife.R | 4 prodlim-1.5.5/prodlim/R/lifeTab.competing.risks.R | 275 ++++++++++---------- prodlim-1.5.5/prodlim/R/lifeTab.survival.R | 4 prodlim-1.5.5/prodlim/R/plot.Hist.R | 3 prodlim-1.5.5/prodlim/R/plot.prodlim.R | 161 ++++++++--- prodlim-1.5.5/prodlim/R/predict.prodlim.R | 77 ++--- prodlim-1.5.5/prodlim/R/print.Hist.R | 3 prodlim-1.5.5/prodlim/R/print.IntIndex.R | 3 prodlim-1.5.5/prodlim/R/print.neighborhood.R | 3 prodlim-1.5.5/prodlim/R/print.prodlim.R | 3 prodlim-1.5.5/prodlim/R/print.quantile.prodlim.R | 31 +- prodlim-1.5.5/prodlim/R/print.summary.prodlim.R | 39 +- prodlim-1.5.5/prodlim/R/prodlim-package.R |only prodlim-1.5.5/prodlim/R/prodlim.R | 90 +++--- prodlim-1.5.5/prodlim/R/prodlimIcensSurv.R | 158 +++++------ prodlim-1.5.5/prodlim/R/quantile.prodlim.R | 50 ++- prodlim-1.5.5/prodlim/R/strip.terms.R | 4 prodlim-1.5.5/prodlim/R/summary.Hist.R | 3 prodlim-1.5.5/prodlim/R/summary.prodlim.R | 154 ++++++----- prodlim-1.5.5/prodlim/man/EventHistory.frame.Rd | 71 ++--- prodlim-1.5.5/prodlim/man/Hist.Rd | 159 +++++------ prodlim-1.5.5/prodlim/man/List2Matrix.Rd |only prodlim-1.5.5/prodlim/man/PercentAxis.Rd | 13 prodlim-1.5.5/prodlim/man/SimCompRisk.Rd | 14 - prodlim-1.5.5/prodlim/man/SimSurv.Rd | 17 - prodlim-1.5.5/prodlim/man/SmartControl.Rd | 47 +-- prodlim-1.5.5/prodlim/man/atRisk.Rd | 61 +--- prodlim-1.5.5/prodlim/man/backGround.Rd | 31 +- prodlim-1.5.5/prodlim/man/confInt.Rd | 47 +-- prodlim-1.5.5/prodlim/man/crModel.Rd | 13 prodlim-1.5.5/prodlim/man/dimColor.Rd | 17 - prodlim-1.5.5/prodlim/man/getEvent.Rd | 22 - prodlim-1.5.5/prodlim/man/getStates.Rd | 7 prodlim-1.5.5/prodlim/man/jackknife.Rd | 35 +- prodlim-1.5.5/prodlim/man/leaveOneOut.Rd | 16 - prodlim-1.5.5/prodlim/man/markTime.Rd | 24 - prodlim-1.5.5/prodlim/man/meanNeighbors.Rd | 11 prodlim-1.5.5/prodlim/man/model.design.Rd | 91 ++---- prodlim-1.5.5/prodlim/man/neighborhood.Rd | 49 +-- prodlim-1.5.5/prodlim/man/parseSpecialNames.Rd | 21 - prodlim-1.5.5/prodlim/man/plot.Hist.Rd | 85 ++---- prodlim-1.5.5/prodlim/man/plot.prodlim.Rd | 275 ++++++++++---------- prodlim-1.5.5/prodlim/man/plotCompetingRiskModel.Rd | 12 prodlim-1.5.5/prodlim/man/plotIllnessDeathModel.Rd | 18 - prodlim-1.5.5/prodlim/man/predict.prodlim.Rd | 94 +++--- prodlim-1.5.5/prodlim/man/predictSurvIndividual.Rd | 14 - prodlim-1.5.5/prodlim/man/print.prodlim.Rd | 15 - prodlim-1.5.5/prodlim/man/prodlim.Rd | 266 ++++++++----------- prodlim-1.5.5/prodlim/man/quantile.prodlim.Rd | 32 +- prodlim-1.5.5/prodlim/man/row.match.Rd | 21 - prodlim-1.5.5/prodlim/man/sindex.Rd | 42 +-- prodlim-1.5.5/prodlim/man/strip.terms.Rd | 35 +- prodlim-1.5.5/prodlim/man/summary.Hist.Rd | 21 - prodlim-1.5.5/prodlim/man/summary.prodlim.Rd | 90 +++--- prodlim-1.5.5/prodlim/man/survModel.Rd | 12 prodlim-1.5.5/prodlim/tests/testthat/prodlim.R | 29 +- 71 files changed, 1708 insertions(+), 1554 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2.4.4 dated 2014-12-05 and 2.4.7 dated 2015-10-05
pec-2.4.4/pec/data/GBSG2.RData |only pec-2.4.7/pec/DESCRIPTION | 15 pec-2.4.7/pec/MD5 | 152 +++-- pec-2.4.7/pec/NAMESPACE | 63 ++ pec-2.4.7/pec/R/R2.R | 2 pec-2.4.7/pec/R/calPlot.R | 625 +++++++++++++++-------- pec-2.4.7/pec/R/cindex.R | 92 +-- pec-2.4.7/pec/R/crps.R | 2 pec-2.4.7/pec/R/ibs.R | 2 pec-2.4.7/pec/R/ipcw.R | 16 pec-2.4.7/pec/R/marginal.prodlim.R | 6 pec-2.4.7/pec/R/pec-package.R | 5 pec-2.4.7/pec/R/pec.R | 78 +- pec-2.4.7/pec/R/plot.Cindex.R | 2 pec-2.4.7/pec/R/plot.calibrationPlot.R |only pec-2.4.7/pec/R/plot.confScoreSurv.R | 2 pec-2.4.7/pec/R/plot.pec.R | 94 ++- pec-2.4.7/pec/R/plot.riskReclassification.R |only pec-2.4.7/pec/R/plotPredictEventProb.R | 2 pec-2.4.7/pec/R/plotPredictSurvProb.R | 2 pec-2.4.7/pec/R/predictEventProb.R | 32 - pec-2.4.7/pec/R/predictEventProb.coxboost.R | 8 pec-2.4.7/pec/R/predictEventProb.pseudoForest.R | 4 pec-2.4.7/pec/R/predictEventProb.selectFGR.R | 6 pec-2.4.7/pec/R/predictLifeYearsLost.R | 19 pec-2.4.7/pec/R/predictRestrictedMeanTime.R |only pec-2.4.7/pec/R/predictSurvProb.FastBw.R | 35 - pec-2.4.7/pec/R/predictSurvProb.R | 60 +- pec-2.4.7/pec/R/predictSurvProb.cforest.R | 6 pec-2.4.7/pec/R/predictSurvProb.ctree.R | 4 pec-2.4.7/pec/R/predictSurvProb.penfitS3.R | 2 pec-2.4.7/pec/R/predictSurvProb.pseudoForest.R | 4 pec-2.4.7/pec/R/print.Cindex.R | 2 pec-2.4.7/pec/R/print.ConfScoreSurv.R | 2 pec-2.4.7/pec/R/print.IPCW.R | 2 pec-2.4.7/pec/R/print.R2.R | 2 pec-2.4.7/pec/R/print.calibrationPlot.R |only pec-2.4.7/pec/R/print.crps.R | 2 pec-2.4.7/pec/R/print.method.R | 2 pec-2.4.7/pec/R/print.multiSplitTest.R | 2 pec-2.4.7/pec/R/print.pec.R | 19 pec-2.4.7/pec/R/print.reclassification.R |only pec-2.4.7/pec/R/print.splitMethod.R | 2 pec-2.4.7/pec/R/print.vandeWielTest.R | 2 pec-2.4.7/pec/R/pseudoPecMethods.R | 41 - pec-2.4.7/pec/R/reclass.R |only pec-2.4.7/pec/R/resolveSplitMethod.R | 2 pec-2.4.7/pec/R/selectCox.R | 7 pec-2.4.7/pec/R/simCost.R | 4 pec-2.4.7/pec/R/summary.Cindex.R | 2 pec-2.4.7/pec/R/summary.confScoreSurv.R | 2 pec-2.4.7/pec/R/summary.pec.R | 2 pec-2.4.7/pec/R/wallyPlot.R |only pec-2.4.7/pec/data/GBSG2.csv.gz |only pec-2.4.7/pec/man/GBSG2.Rd | 21 pec-2.4.7/pec/man/Pbc3.Rd | 35 - pec-2.4.7/pec/man/R2.Rd | 58 +- pec-2.4.7/pec/man/Special.Rd | 48 - pec-2.4.7/pec/man/calPlot.Rd | 248 +++++---- pec-2.4.7/pec/man/cindex.Rd | 395 ++++++-------- pec-2.4.7/pec/man/cost.Rd | 19 pec-2.4.7/pec/man/coxboost.Rd | 42 - pec-2.4.7/pec/man/crps.Rd | 49 - pec-2.4.7/pec/man/ipcw.Rd | 100 +-- pec-2.4.7/pec/man/pec.Rd | 635 ++++++++++-------------- pec-2.4.7/pec/man/pecCforest.Rd | 17 pec-2.4.7/pec/man/pecCtree.Rd | 4 pec-2.4.7/pec/man/pecRpart.Rd | 11 pec-2.4.7/pec/man/plot.calibrationPlot.Rd |only pec-2.4.7/pec/man/plot.pec.Rd | 118 ++-- pec-2.4.7/pec/man/plotPredictEventProb.Rd | 85 +-- pec-2.4.7/pec/man/plotPredictSurvProb.Rd | 84 +-- pec-2.4.7/pec/man/predictEventProb.Rd | 43 - pec-2.4.7/pec/man/predictLifeYearsLost.Rd | 49 - pec-2.4.7/pec/man/predictRestrictedMeanTime.Rd |only pec-2.4.7/pec/man/predictSurvProb.Rd | 103 ++- pec-2.4.7/pec/man/print.pec.Rd | 24 pec-2.4.7/pec/man/reclass.Rd |only pec-2.4.7/pec/man/resolvesplitMethod.Rd | 39 - pec-2.4.7/pec/man/selectCox.Rd | 31 - pec-2.4.7/pec/man/selectFGR.Rd | 35 - pec-2.4.7/pec/man/simCost.Rd | 7 pec-2.4.7/pec/man/wallyPlot.Rd |only pec-2.4.7/pec/src/auc.c |only 84 files changed, 1949 insertions(+), 1788 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.3.0 dated 2015-06-15 and 0.4.0 dated 2015-10-05
diagonals-0.3.0/diagonals/R/diag.R |only diagonals-0.3.0/diagonals/man/diag-set.Rd |only diagonals-0.4.0/diagonals/DESCRIPTION | 6 diagonals-0.4.0/diagonals/MD5 | 20 - diagonals-0.4.0/diagonals/NEWS | 6 diagonals-0.4.0/diagonals/R/fatdiag.R | 139 ++++++---- diagonals-0.4.0/diagonals/R/matricise.R |only diagonals-0.4.0/diagonals/README.md | 1 diagonals-0.4.0/diagonals/build/vignette.rds |binary diagonals-0.4.0/diagonals/inst/doc/fatdiag.html | 323 +++++++++++++++++------- diagonals-0.4.0/diagonals/man/fatdiag.Rd | 12 diagonals-0.4.0/diagonals/man/matricise.Rd |only diagonals-0.4.0/diagonals/tests |only 13 files changed, 357 insertions(+), 150 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-4 dated 2015-09-17 and 0.9-5 dated 2015-10-05
DESCRIPTION | 14 ++++----- MD5 | 41 ++++++++++++++-------------- NAMESPACE | 1 R/optics.R | 66 +++++++++++++++++++++++----------------------- README.md |only inst/NEWS | 8 ++++- inst/tests/test-lof.R | 11 +++++-- inst/tests/test-optics.R | 26 +++++++++++++++--- man/dbscan.Rd | 2 + man/lof.Rd | 1 man/optics.Rd | 17 +++++++++-- src/ANN.cpp | 6 ++-- src/R_kNN.cpp | 7 ++-- src/R_optics.cpp | 44 ++++++++++++++++++------------ src/R_regionQuery.cpp | 2 - src/kd_dump.cpp | 2 - src/kd_fix_rad_search.cpp | 10 +++--- src/kd_pr_search.cpp | 12 ++++---- src/kd_search.cpp | 12 ++++---- src/kd_util.cpp | 10 +++--- src/pr_queue.h | 10 +++--- src/pr_queue_k.h | 2 - 22 files changed, 177 insertions(+), 127 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.3 dated 2015-09-09 and 1.0.4 dated 2015-10-05
DESCRIPTION | 10 - MD5 | 37 +++---- NAMESPACE | 1 R/adjust_functions.R | 21 ++-- R/cate.R | 225 +++++++++++++++++++++++++++++++------------- R/factor_functions.R | 1 R/other_methods.R | 81 +++++++++------ R/simulate_functions.R | 5 build/vignette.rds |binary inst/doc/cate-vignette.R | 21 ++-- inst/doc/cate-vignette.Rnw | 43 +++++--- inst/doc/cate-vignette.pdf |binary man/adjust.latent.Rd | 8 - man/cate.Rd | 54 +++++++--- man/est.confounder.num.Rd | 15 +- man/gen.sim.data.Rd | 4 man/gender.sm.Rd | 1 man/parse.cate.formula.Rd |only man/wrapper.Rd | 32 +++--- vignettes/cate-vignette.Rnw | 43 +++++--- 20 files changed, 397 insertions(+), 205 deletions(-)
Title: Graphing Nonlinear Relations Among Latent Variables from
Structural Equation Mixture Models
Description: Contains a graphical user interface to generate the
diagnostic plots proposed by Bauer (2005) and Pek & Chalmers (2015) to investigate
nonlinear bivariate relationships in latent regression models using
structural equation mixture models (SEMMs).
Author: Bethany Kok [ctb],
Jolynn Pek [ctb],
Sonya Sterba [ctb],
Dan Bauer [ctb],
Phil Chalmers [cre, ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between plotSEMM versions 2.0 dated 2014-07-07 and 2.1 dated 2015-10-04
DESCRIPTION | 24 ++-- MD5 | 67 +++++++++-- NAMESPACE | 6 - R/plotSEMM-package.R | 35 +----- R/plotSEMM_GUI.R | 252 ++++++++++++++++++++++++-------------------- R/plotSEMM_ci.R | 58 +++++----- R/plotSEMM_contour.R | 5 R/plotSEMM_probability.R | 100 ++++++++--------- R/plotSEMM_setup.R | 118 ++++++++++---------- R/plotSEMM_setup2.R | 5 R/read.plotSEMM_wACOV.R | 2 inst |only man/plotSEMM.Rd | 28 +--- man/plotSEMM_GUI.Rd | 30 +++-- man/plotSEMM_contour.Rd | 8 + man/plotSEMM_probability.Rd | 11 + man/plotSEMM_setup.Rd | 5 17 files changed, 410 insertions(+), 344 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.5 dated 2015-05-09 and 0.6 dated 2015-10-04
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 7 +++++++ NEWS | 5 +++++ R/ShinyGUIClass.R | 7 ++++--- R/mirtCAT-package.R | 1 + R/mirtCAT.R | 11 +++++++---- R/server.R | 2 +- R/zzz-methods.R | 18 +++++++++++++----- README.md | 5 +++++ build/vignette.rds |binary man/mirtCAT.Rd | 21 +++++++++++++++------ tests/GUI-tests/GUI-tests.R | 14 ++++++++++++-- 13 files changed, 87 insertions(+), 38 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.0 dated 2015-10-03 and 0.3.1 dated 2015-10-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 ++++- src/Makevars | 13 +++++++------ 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 0.3.1 dated 2014-01-30 and 2.0.1.5 dated 2015-10-04
DESCRIPTION | 13 - MD5 | 94 +++++--- NAMESPACE | 17 + R/align_rasters.R |only R/gdal_contour.R |only R/gdal_grid.R |only R/gdal_rasterize.R | 13 - R/gdal_setInstallation.R | 34 ++- R/gdal_translate.R | 42 ++- R/gdaladdo.R | 15 - R/gdalbuildvrt.R | 16 - R/gdaldem.R | 7 R/gdalinfo.R | 70 ++++-- R/gdallocationinfo.R |only R/gdalmanage.R |only R/gdalsrsinfo.R | 6 R/gdaltindex.R |only R/gdaltransform.R |only R/gdalwarp.R | 53 +++- R/get_subdatasets.R | 3 R/mosaic_rasters.R | 73 ++++++ R/nearblack.R |only R/ogr2ogr.R | 145 +++++++++---- R/ogrinfo.R | 22 +- R/ogrlineref.R |only R/ogrtindex.R |only man/align_rasters.Rd |only man/batch_gdal_translate.Rd | 48 +--- man/gdal_chooseInstallation.Rd | 22 -- man/gdal_cmd_builder.Rd | 63 ++--- man/gdal_contour.Rd |only man/gdal_grid.Rd |only man/gdal_rasterize.Rd | 209 ++++++------------- man/gdal_setInstallation.Rd | 73 ++---- man/gdal_translate.Rd | 252 ++++++++--------------- man/gdaladdo.Rd | 69 ++---- man/gdalbuildvrt.Rd | 204 +++++------------- man/gdaldem.Rd | 183 +++++----------- man/gdalinfo.Rd | 192 +++++------------ man/gdallocationinfo.Rd |only man/gdalmanage.Rd |only man/gdalsrsinfo.Rd | 72 ++---- man/gdaltindex.Rd |only man/gdaltransform.Rd |only man/gdalwarp.Rd | 327 +++++++++++------------------- man/get_subdatasets.Rd | 38 +-- man/mosaic_rasters.Rd | 39 +-- man/nearblack.Rd |only man/ogr2ogr.Rd | 412 ++++++++++++++------------------------ man/ogrinfo.Rd | 155 +++++--------- man/ogrlineref.Rd |only man/ogrtindex.Rd |only man/qm.Rd | 7 man/remove_file_extension.Rd | 7 man/tahoe_highrez_training.Rd | 2 man/tahoe_lidar_bareearth.tif.Rd | 5 man/tahoe_lidar_highesthit.tif.Rd | 5 man/test_modis.hdf.Rd | 2 58 files changed, 1301 insertions(+), 1708 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.600.2.0 dated 2015-09-19 and 0.6.100.0.0 dated 2015-10-04
ChangeLog | 16 DESCRIPTION | 8 MD5 | 144 +- inst/NEWS.Rd | 22 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 6 inst/include/armadillo_bits/Col_bones.hpp | 2 inst/include/armadillo_bits/Cube_bones.hpp | 33 inst/include/armadillo_bits/Cube_meat.hpp | 216 ++-- inst/include/armadillo_bits/Glue_bones.hpp | 15 inst/include/armadillo_bits/Mat_bones.hpp | 27 inst/include/armadillo_bits/Mat_meat.hpp | 205 +--- inst/include/armadillo_bits/Op_bones.hpp | 20 inst/include/armadillo_bits/Row_bones.hpp | 2 inst/include/armadillo_bits/SpMat_bones.hpp | 201 +-- inst/include/armadillo_bits/arma_forward.hpp |only inst/include/armadillo_bits/arma_ostream_meat.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 8 inst/include/armadillo_bits/arrayops_bones.hpp | 31 inst/include/armadillo_bits/arrayops_meat.hpp | 198 --- inst/include/armadillo_bits/atlas_bones.hpp | 10 inst/include/armadillo_bits/atlas_wrapper.hpp | 58 + inst/include/armadillo_bits/auxlib_bones.hpp | 20 inst/include/armadillo_bits/auxlib_meat.hpp | 110 +- inst/include/armadillo_bits/blas_bones.hpp | 28 inst/include/armadillo_bits/blas_wrapper.hpp | 68 + inst/include/armadillo_bits/compiler_setup.hpp | 4 inst/include/armadillo_bits/field_bones.hpp | 12 inst/include/armadillo_bits/field_meat.hpp | 1 inst/include/armadillo_bits/fn_conv.hpp | 15 inst/include/armadillo_bits/fn_cumprod.hpp | 6 inst/include/armadillo_bits/fn_cumsum.hpp | 6 inst/include/armadillo_bits/fn_diff.hpp | 6 inst/include/armadillo_bits/fn_hist.hpp | 62 - inst/include/armadillo_bits/fn_histc.hpp | 30 inst/include/armadillo_bits/fn_join.hpp | 111 +- inst/include/armadillo_bits/fn_norm.hpp | 861 ++--------------- inst/include/armadillo_bits/fn_reshape.hpp | 2 inst/include/armadillo_bits/fn_schur.hpp |only inst/include/armadillo_bits/fn_shuffle.hpp | 56 - inst/include/armadillo_bits/fn_sort.hpp | 54 - inst/include/armadillo_bits/glue_conv_bones.hpp | 6 inst/include/armadillo_bits/glue_conv_meat.hpp | 69 - inst/include/armadillo_bits/glue_hist_bones.hpp | 20 inst/include/armadillo_bits/glue_hist_meat.hpp | 291 ++--- inst/include/armadillo_bits/glue_histc_bones.hpp | 17 inst/include/armadillo_bits/glue_histc_meat.hpp | 193 +-- inst/include/armadillo_bits/glue_join_bones.hpp | 28 inst/include/armadillo_bits/glue_join_meat.hpp | 147 +- inst/include/armadillo_bits/mtGlue_bones.hpp | 21 inst/include/armadillo_bits/mtOp_bones.hpp | 41 inst/include/armadillo_bits/mul_gemm.hpp | 6 inst/include/armadillo_bits/mul_gemv.hpp | 6 inst/include/armadillo_bits/mul_herk.hpp | 4 inst/include/armadillo_bits/mul_syrk.hpp | 4 inst/include/armadillo_bits/op_cumprod_bones.hpp | 4 inst/include/armadillo_bits/op_cumprod_meat.hpp | 21 inst/include/armadillo_bits/op_cumsum_bones.hpp | 4 inst/include/armadillo_bits/op_cumsum_meat.hpp | 21 inst/include/armadillo_bits/op_diff_bones.hpp | 4 inst/include/armadillo_bits/op_diff_meat.hpp | 25 inst/include/armadillo_bits/op_dot_meat.hpp | 4 inst/include/armadillo_bits/op_hist_bones.hpp | 7 inst/include/armadillo_bits/op_hist_meat.hpp | 60 - inst/include/armadillo_bits/op_norm_bones.hpp |only inst/include/armadillo_bits/op_norm_meat.hpp |only inst/include/armadillo_bits/op_prod_bones.hpp | 9 inst/include/armadillo_bits/op_prod_meat.hpp | 73 - inst/include/armadillo_bits/op_shuffle_bones.hpp | 15 inst/include/armadillo_bits/op_shuffle_meat.hpp | 52 - inst/include/armadillo_bits/op_sort_bones.hpp | 12 inst/include/armadillo_bits/op_sort_meat.hpp | 44 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 176 ++- inst/include/armadillo_bits/subview_meat.hpp | 14 75 files changed, 1870 insertions(+), 2206 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xzhu20@crimson.ua.edu>
Diff between ManlyMix versions 0.1.1 dated 2015-10-02 and 0.1.2 dated 2015-10-04
DESCRIPTION | 25 +++++++++++++++++-------- MD5 | 8 ++++---- NEWS | 4 ++++ man/ManlyMix-package.Rd | 48 ++++++++++++++++++++++++++++++------------------ src/crosen.c | 32 ++++++++++++++++++++++++++++---- 5 files changed, 83 insertions(+), 34 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.5-18 dated 2015-04-04 and 0.5-19 dated 2015-10-03
DESCRIPTION | 13 - MD5 | 97 +++++------ NAMESPACE | 56 ++++-- R/00class.R | 14 + R/00generic.R | 9 + R/ctr_estfun.R | 16 + R/ctr_pml_plrt.R | 148 ++++++++-------- R/ctr_pml_plrt2.R |only R/ctr_pml_plrt_nested.R | 12 - R/lav_fit.R | 60 ------ R/lav_fit_measures.R | 16 + R/lav_matrix.R | 4 R/lav_model.R | 12 + R/lav_model_compute.R | 15 + R/lav_model_estimate.R | 16 + R/lav_model_gradient.R | 19 +- R/lav_model_implied.R |only R/lav_model_information.R | 14 + R/lav_model_objective.R | 5 R/lav_model_vcov.R | 83 ++++++++- R/lav_modification.R | 322 ++++++++++++------------------------ R/lav_object_generate.R | 92 ++++++++++ R/lav_object_inspect.R | 243 ++++++++++++++++++++++++--- R/lav_object_methods.R | 246 ++++++++++++++++++++------- R/lav_object_post_check.R |only R/lav_partable.R | 45 +++-- R/lav_partable_complete.R | 101 ++++++----- R/lav_partable_constraints.R | 212 ++++++------------------ R/lav_partable_vnames.R | 66 ++++--- R/lav_predict.R | 113 ++++++++++-- R/lav_print.R | 361 +++++++++++++++++++++++++++++++++++++++++ R/lav_representation_lisrel.R | 183 ++++++++++++++++++-- R/lav_residuals.R | 14 + R/lav_standardize.R | 12 - R/lav_start.R | 7 R/lav_syntax.R | 122 +++++++------ R/lav_test.R | 19 ++ R/lav_test_LRT.R | 18 +- R/lav_test_diff.R | 198 ++++++++++++++-------- R/lav_test_score.R | 316 ++++++++++++++++++++++++++--------- R/lavaan.R | 110 +++++++----- man/fitMeasures.Rd | 2 man/lavInspect.Rd | 11 + man/lavMatrixRepresentation.Rd | 8 man/lavPredict.Rd | 17 + man/lavTestScore.Rd |only man/lav_model.Rd |only man/lav_partable.Rd | 22 ++ man/lavaan-class.Rd | 6 man/modificationIndices.Rd | 8 man/parameterEstimates.Rd | 41 +++- man/standardizedSolution.Rd | 9 - 52 files changed, 2396 insertions(+), 1137 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.2.150402 dated 2015-04-02 and 0.3.0 dated 2015-10-03
geoBayes-0.2.150402/geoBayes/src/skelpnts.f90 |only geoBayes-0.3.0/geoBayes/DESCRIPTION | 18 - geoBayes-0.3.0/geoBayes/MD5 | 68 ++-- geoBayes-0.3.0/geoBayes/NAMESPACE | 19 + geoBayes-0.3.0/geoBayes/NEWS | 5 geoBayes-0.3.0/geoBayes/R/bf.R | 75 ++-- geoBayes-0.3.0/geoBayes/R/calcbf.R | 3 geoBayes-0.3.0/geoBayes/R/comparebinlinks.R | 2 geoBayes-0.3.0/geoBayes/R/geoesteb.R | 17 - geoBayes-0.3.0/geoBayes/R/linkfcn.R | 44 ++ geoBayes-0.3.0/geoBayes/R/mcsp2.R | 16 geoBayes-0.3.0/geoBayes/man/bf1skel.Rd | 8 geoBayes-0.3.0/geoBayes/man/bf2new.Rd | 3 geoBayes-0.3.0/geoBayes/man/bf2optim.Rd | 3 geoBayes-0.3.0/geoBayes/man/bfse.Rd | 3 geoBayes-0.3.0/geoBayes/man/comparebinlinks.Rd | 3 geoBayes-0.3.0/geoBayes/man/ebsglmm.Rd | 16 geoBayes-0.3.0/geoBayes/man/ebstrga.Rd | 3 geoBayes-0.3.0/geoBayes/man/geoBayes.Rd | 3 geoBayes-0.3.0/geoBayes/man/linkfcn.Rd | 17 - geoBayes-0.3.0/geoBayes/man/mcmcmake.Rd | 3 geoBayes-0.3.0/geoBayes/man/mcsglmm.Rd | 13 geoBayes-0.3.0/geoBayes/man/mcstrga.Rd | 3 geoBayes-0.3.0/geoBayes/man/mkpredgrid2d.Rd | 3 geoBayes-0.3.0/geoBayes/man/plotbf2.Rd | 3 geoBayes-0.3.0/geoBayes/man/rhizoctonia.Rd | 3 geoBayes-0.3.0/geoBayes/man/stackdata.Rd | 3 geoBayes-0.3.0/geoBayes/src/Makevars | 7 geoBayes-0.3.0/geoBayes/src/auxfcns.c | 12 geoBayes-0.3.0/geoBayes/src/bfsp.f90 | 107 ++++-- geoBayes-0.3.0/geoBayes/src/calcb2.f90 | 416 ++++++++++++++----------- geoBayes-0.3.0/geoBayes/src/linkfcn.f90 | 33 + geoBayes-0.3.0/geoBayes/src/llik.f90 | 92 +++++ geoBayes-0.3.0/geoBayes/src/mcsp2.f90 | 150 ++++++++- geoBayes-0.3.0/geoBayes/src/pdfw.f90 |only geoBayes-0.3.0/geoBayes/src/pdfy.f90 | 104 ++++++ 36 files changed, 925 insertions(+), 353 deletions(-)
Title: An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting
any single variable in a multiclass dataset. It is an enhanced jitter strip
chart, where the width of the jitter is controlled by the density
distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre],
Sina Hadi Sohi [aut],
Nicolas Rapin [aut],
Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Diff between sinaplot versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-03
sinaplot-0.1.1/sinaplot/inst/temp.Rmd |only sinaplot-0.1.2/sinaplot/DESCRIPTION | 15 ++++++++------- sinaplot-0.1.2/sinaplot/MD5 | 14 +++++++++----- sinaplot-0.1.2/sinaplot/NEWS |only sinaplot-0.1.2/sinaplot/R/sinaplot.R | 8 ++------ sinaplot-0.1.2/sinaplot/build |only sinaplot-0.1.2/sinaplot/inst/doc |only sinaplot-0.1.2/sinaplot/man/sinaplot.Rd | 8 ++++---- sinaplot-0.1.2/sinaplot/vignettes/SinaPlot.Rmd | 11 +++++++---- 9 files changed, 30 insertions(+), 26 deletions(-)
Title: Nonparametric Methods for Cognitive Diagnosis
Description: An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre],
Chia-Yi Chiu [aut],
Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng <yi.isabel.zheng@asu.edu>
Diff between NPCD versions 1.0-8 dated 2015-05-02 and 1.0-9 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 5 ++++- R/AlphaMLE.R | 2 +- R/AlphaNP.R | 2 +- R/CDL.R | 4 ++-- R/CDP.R |only R/ItemFit.R |only R/JMLE.R | 2 +- R/ParMLE.R | 4 ++-- man/AlphaMLE.Rd | 3 ++- man/AlphaNP.Rd | 3 +++ man/CDL.Rd | 2 +- man/CDP.Rd |only man/ItemFit.Rd |only man/JMLE.Rd | 3 ++- man/NPCD.Rd | 4 ++-- man/ParMLE.Rd | 4 ++-- 18 files changed, 44 insertions(+), 32 deletions(-)
Title: Generalized Linear Autoregressive Moving Average Models
Description: Functions are provided for estimation, testing, diagnostic checking and forecasting of generalized linear autoregressive moving average (GLARMA) models for discrete valued time series with regression variables. These are a class of observation driven non-linear non-Gaussian state space models. The state vector consists of a linear regression component plus an observation driven component consisting of an autoregressive-moving average (ARMA) filter of past predictive residuals. Currently three distributions (Poisson, negative binomial and binomial) can be used for the response series. Three options (Pearson, score-type and unscaled) for the residuals in the observation driven component are available. Estimation is via maximum likelihood (conditional on initializing values for the ARMA process) optimized using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald tests for the observation driven component allow testing for serial dependence in generalized linear model settings. Graphical diagnostics including model fits, autocorrelation functions and probability integral transform residuals are included in the package. Several standard data sets are included in the package.
Author: William T.M. Dunsmuir <w.dunsmuir@unsw.edu.au>, Cenanning Li
<cli113@aucklanduni.ac.nz>, and David J. Scott
<d.scott@auckland.ac.nz>
Maintainer: "William T.M. Dunsmuir" <w.dunsmuir@unsw.edu.au>
Diff between glarma versions 1.3-0 dated 2014-09-25 and 1.4-0 dated 2015-10-03
ChangeLog | 9 ++++++++- DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- build/vignette.rds |binary inst/CITATION | 36 +++++++++++++++++++----------------- inst/doc/glarma.pdf |binary inst/unitTests/Makefile | 44 ++++++++++++++++++++++---------------------- man/glarma.Rd | 20 ++++++++++++++------ 9 files changed, 83 insertions(+), 60 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.7 dated 2015-09-02 and 1.8 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/coneproj.R | 2 +- man/qprog.Rd | 1 + src/coneproj.cpp | 7 +++++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.1 dated 2015-06-15 and 1.0.2 dated 2015-10-03
DESCRIPTION | 11 INSTALL | 9 MD5 | 22 NAMESPACE | 33 - R/checkUpdates.R |only R/createESET.R | 236 ++++---- inst/doc/compendiumdb.pdf |binary inst/extdata/compendiumSchema.sql | 4 inst/scripts/Perl/loadAllforGSEeset.pl | 915 ++++++++++++++++----------------- inst/scripts/README | 2 man/checkUpdates.Rd |only man/compendiumdb-package.Rd | 4 man/createESET.Rd | 2 13 files changed, 631 insertions(+), 607 deletions(-)
Title: Tools for Sotkanet Open Data Portal
Description: Tools to download data from the Sotkanet open data portal.
Author: Leo Lahti, Einari Happonen, Juuso Parkkinen, Joona Lehtomaki
Maintainer: Leo Lahti <louhos@googlegroups.com>
Diff between sotkanet versions 0.9.14 dated 2015-06-24 and 0.9.21 dated 2015-10-03
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 1 R/base_url.R | 2 R/csv.R | 10 -- inst/doc/tutorial.R | 107 +++++++++++----------- inst/doc/tutorial.Rmd | 11 +- inst/doc/tutorial.html | 217 +++++++++++++++++++++++++++++++++++++++++++++- man/sotkanet.csv_query.Rd | 9 - vignettes/tutorial.Rmd | 11 +- 10 files changed, 300 insertions(+), 94 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.1 dated 2015-09-25 and 2.2 dated 2015-10-03
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 3 + R/F.window.R | 45 ++++++++++++++++++++++++++--- man/F.window.Rd | 70 ++++++++++++++++++++++++++++------------------ man/joint.Cox-package.Rd | 4 +- man/jointCox.indep.reg.Rd | 2 - man/jointCox.reg.Rd | 2 - 8 files changed, 101 insertions(+), 47 deletions(-)
Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L Davis. Some documentation and examples ported from Allen Day's
getopt package. Some documentation from the optparse Python module by the
Python Software Foundation. Contributions from Steve Lianoglou, Jim
Nikelski, Kirill Müller, Peter Humburg, and Rich FitzJohn.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between optparse versions 1.3.0 dated 2014-12-11 and 1.3.2 dated 2015-10-03
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NAMESPACE | 3 ++- NEWS | 5 ++++- R/optparse.R | 24 +++++++++++++++--------- build/vignette.rds |binary inst/COPYRIGHTS | 4 +++- inst/doc/optparse.pdf |binary man/OptionParser-class.Rd | 2 +- man/OptionParser.Rd | 2 +- man/OptionParserOption-class.Rd | 2 +- man/add_make_option.Rd | 4 +++- man/optparse-package.Rd | 2 +- man/parse_args.Rd | 2 +- man/print_help.Rd | 2 +- tests/testthat/test-optparse.R | 36 +++++++++++++++++++++++++++++++----- 16 files changed, 85 insertions(+), 45 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-0 dated 2015-06-26 and 1.2-1 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/jomo1.MCMCchain.R | 4 +++- R/jomo1.R | 4 +++- R/jomo1cat.MCMCchain.R | 15 +++++++++------ R/jomo1cat.R | 16 ++++++++++------ R/jomo1mix.MCMCchain.R | 15 +++++++++------ R/jomo1mix.R | 15 +++++++++------ R/jomo1ran.MCMCchain.R | 4 +++- R/jomo1ran.R | 4 +++- R/jomo1rancat.MCMCchain.R | 15 +++++++++------ R/jomo1rancat.R | 15 +++++++++------ R/jomo1rancathr.MCMCchain.R | 15 +++++++++------ R/jomo1rancathr.R | 15 +++++++++------ R/jomo1rancon.MCMCchain.R | 1 - R/jomo1rancon.R | 1 - R/jomo1ranconhr.MCMCchain.R | 1 - R/jomo1ranconhr.R | 1 - R/jomo1ranmix.MCMCchain.R | 15 +++++++++------ R/jomo1ranmix.R | 16 ++++++++++------ R/jomo1ranmixhr.MCMCchain.R | 16 ++++++++++------ R/jomo1ranmixhr.R | 16 ++++++++++------ 22 files changed, 149 insertions(+), 105 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.2 dated 2015-09-25 and 1.3 dated 2015-10-03
DESCRIPTION | 8 MD5 | 14 R/supportRegion.R | 46 ++ build/vignette.rds |binary inst/doc/hisse-vignette.Rmd | 18 - inst/doc/hisse-vignette.html | 693 +++++++++++++------------------------------ man/supportRegion.Rd | 3 vignettes/hisse-vignette.Rmd | 18 - 8 files changed, 288 insertions(+), 512 deletions(-)
Title: Streamlining Design and Deployment of Complex Workflows
Description:
This framework allows you to design and implement complex pipelines, and
deploy them on your institution's computing cluster. This has been built
keeping in mind the needs of bioinformatics workflows. However, it is
easily extendable to any field where a series of steps (shell commands)
are to be executed in a (work)flow.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between flowr versions 0.9.7.10 dated 2015-08-22 and 0.9.8.2 dated 2015-10-03
flowr-0.9.7.10/flowr/inst/doc/build-pipes.R |only flowr-0.9.7.10/flowr/inst/doc/build-pipes.Rmd |only flowr-0.9.7.10/flowr/inst/doc/build-pipes.html |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.R |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.Rmd |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.html |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.R |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.Rmd |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.html |only flowr-0.9.7.10/flowr/inst/doc/quick-start.R |only flowr-0.9.7.10/flowr/inst/doc/quick-start.Rmd |only flowr-0.9.7.10/flowr/inst/doc/quick-start.html |only flowr-0.9.7.10/flowr/man/as.flowdef.Rd |only flowr-0.9.7.10/flowr/man/as.flowmat.Rd |only flowr-0.9.7.10/flowr/man/calc_boxdim.Rd |only flowr-0.9.7.10/flowr/man/cmds_to_flow.Rd |only flowr-0.9.7.10/flowr/man/detect_dep_type.Rd |only flowr-0.9.7.10/flowr/man/flow-class.Rd |only flowr-0.9.7.10/flowr/man/get_resources.Rd |only flowr-0.9.7.10/flowr/man/get_resources_lsf.Rd |only flowr-0.9.7.10/flowr/man/parse_jobids.Rd |only flowr-0.9.7.10/flowr/man/parse_lsf_out.Rd |only flowr-0.9.7.10/flowr/man/queue-class.Rd |only flowr-0.9.7.10/flowr/man/read_fobj.Rd |only flowr-0.9.7.10/flowr/man/render_dependency.Rd |only flowr-0.9.7.10/flowr/man/render_queue_cmd.Rd |only flowr-0.9.7.10/flowr/man/split_multi_dep.Rd |only flowr-0.9.7.10/flowr/man/subset_fdef.Rd |only flowr-0.9.7.10/flowr/man/subset_fmat.Rd |only flowr-0.9.7.10/flowr/man/update_flow_det.Rd |only flowr-0.9.7.10/flowr/tests/testthat/test-rerun.R |only flowr-0.9.7.10/flowr/tests/testthat/test_plots.R |only flowr-0.9.7.10/flowr/vignettes/build-pipes.Rmd |only flowr-0.9.7.10/flowr/vignettes/example_sleep.Rmd |only flowr-0.9.7.10/flowr/vignettes/hpcc-support.Rmd |only flowr-0.9.7.10/flowr/vignettes/imgs |only flowr-0.9.7.10/flowr/vignettes/quick-start.Rmd |only flowr-0.9.8.2/flowr/DESCRIPTION | 25 - 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flowr-0.9.8.2/flowr/man/job.Rd | 4 flowr-0.9.8.2/flowr/man/kill.Rd | 35 + flowr-0.9.8.2/flowr/man/opts_flow.Rd | 23 flowr-0.9.8.2/flowr/man/plot_flow.Rd | 16 flowr-0.9.8.2/flowr/man/queue.Rd | 17 flowr-0.9.8.2/flowr/man/rerun.Rd | 47 +- flowr-0.9.8.2/flowr/man/run.Rd | 46 + flowr-0.9.8.2/flowr/man/setup.Rd | 21 flowr-0.9.8.2/flowr/man/status.Rd | 40 + flowr-0.9.8.2/flowr/man/submit_flow.Rd | 10 flowr-0.9.8.2/flowr/man/submit_job.Rd | 4 flowr-0.9.8.2/flowr/man/submit_run.Rd |only flowr-0.9.8.2/flowr/man/test_queue.Rd | 5 flowr-0.9.8.2/flowr/man/to_flow.Rd | 72 ++- flowr-0.9.8.2/flowr/man/to_flowdef.Rd | 103 ++++ flowr-0.9.8.2/flowr/man/to_flowdet.Rd | 11 flowr-0.9.8.2/flowr/man/to_flowmat.Rd | 49 +- flowr-0.9.8.2/flowr/man/verbose.Rd |only flowr-0.9.8.2/flowr/man/whisker_render.Rd | 5 flowr-0.9.8.2/flowr/tests/README.md |only flowr-0.9.8.2/flowr/tests/fastq_mutect_err1.def |only flowr-0.9.8.2/flowr/tests/testthat.R | 11 flowr-0.9.8.2/flowr/tests/testthat/test-plots.R |only flowr-0.9.8.2/flowr/tests/testthat/test-toflow.R |only flowr-0.9.8.2/flowr/vignettes/files |only flowr-0.9.8.2/flowr/vignettes/flowr_install.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_overview.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_overview_files |only flowr-0.9.8.2/flowr/vignettes/flowr_tutorial.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_tutorial_files |only 124 files changed, 3123 insertions(+), 1448 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-10 dated 2015-09-16 and 0.2-11 dated 2015-10-03
CHANGELOG | 12 + DESCRIPTION | 8 - MD5 | 43 +++--- NAMESPACE | 5 R/02sequences.R | 50 ++++++- R/03rules.R | 159 +++++++++++++++++++----- R/20support.R | 278 +++++++++++++++++++++++++++---------------- man/cspade.Rd | 9 + man/itemFrequency-methods.Rd | 2 man/ruleInduction-methods.Rd | 34 +++-- man/sequences-class.Rd | 4 man/support-methods.Rd | 9 + man/times-methods.Rd | 2 src/ptree.c |only tests/arules.Rout.save | 8 - tests/idlists.R | 13 +- tests/idlists.Rout.save | 20 ++- tests/makebin.Rout.save | 12 - tests/native.Rout.save | 12 - tests/ptree.R |only tests/ptree.Rout.save |only tests/similarity.Rout.save | 12 - tests/zaki.R | 17 ++ tests/zaki.Rout.save | 36 ++++- 24 files changed, 519 insertions(+), 226 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.0 dated 2015-10-01 and 1.1 dated 2015-10-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ inst/doc/gaston.pdf |binary src/diago.h | 2 +- src/diago_full.h | 2 +- src/diago_full_nocovar.h | 2 +- src/diago_nocovar.h | 2 +- 7 files changed, 13 insertions(+), 13 deletions(-)
Title: Paralellised Versions of Constraint Based Causal Discovery
Algorithms
Description: Parallelise constraint based causality discovery and causal inference methods. The parallelised algorithms in the package will generate the same results as that of the pcalg package but will be much more efficient.
Author: Thuc Duy Le, Tao Hoang, Shu Hu, and Liang Zhang
Maintainer: Thuc Duy Le <Thuc.Le@unisa.edu.au>
Diff between ParallelPC versions 1.0 dated 2015-10-01 and 1.1 dated 2015-10-02
DESCRIPTION | 6 ++-- MD5 | 4 +-- R/ParallelPC.R | 71 ++++++++++++++++++++++++++++++++++++++++++++------------- 3 files changed, 60 insertions(+), 21 deletions(-)
Title: Spherical K-Function
Description: Spherical K-function for point-pattern analysis on the sphere.
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li<liao@umail.iu.edu>
Diff between SphericalK versions 1.1 dated 2015-02-12 and 1.2 dated 2015-10-02
SphericalK-1.1/SphericalK/man/SphericalK-package.Rd |only SphericalK-1.2/SphericalK/DESCRIPTION | 8 - SphericalK-1.2/SphericalK/MD5 | 9 -- SphericalK-1.2/SphericalK/NAMESPACE | 1 SphericalK-1.2/SphericalK/R/SphericalK.R | 88 +++++++++----------- SphericalK-1.2/SphericalK/man/sphere_grid.Rd | 8 - 6 files changed, 55 insertions(+), 59 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.4 dated 2015-06-03 and 2.1.5 dated 2015-10-02
DESCRIPTION | 15 ++++++++------- MD5 | 17 +++++++++-------- NAMESPACE | 5 ++++- NEWS | 3 +++ R/GetArchiveGrib.R | 25 +++++++++---------------- R/GetDODS.R | 14 ++++---------- R/GetRealTimeGrib.R | 6 ++---- R/Models.R | 13 +++++-------- R/RNomadsTools.R | 25 ++++++++++++++++++++++++- man/LinkExtractor.Rd |only 10 files changed, 68 insertions(+), 55 deletions(-)
Title: Multidimensional Numerical Integration
Description: It is a wrapper around the Cuba-1.6 library by Thomas Hahn available from the URL http://www.feynarts.de/cuba/. Implement four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre.
Author: The Cuba library has been written by Thomas Hahn (http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was written by Annie Bouvier and Kiên Kiêu
Maintainer: Annie Bouvier <Annie.Bouvier@jouy.inra.fr>
Diff between R2Cuba versions 1.0-11 dated 2013-04-15 and 1.1-0 dated 2015-10-02
R2Cuba-1.0-11/R2Cuba/ChangeLog |only R2Cuba-1.0-11/R2Cuba/tests/essaiArgu.R |only R2Cuba-1.0-11/R2Cuba/tests/essaiArgu.Rout.save |only R2Cuba-1.0-11/R2Cuba/tests/kk.R |only R2Cuba-1.0-11/R2Cuba/tests/kk.Rout.save |only R2Cuba-1.0-11/R2Cuba/tests/vegas.Rout.save.sv |only R2Cuba-1.1-0/R2Cuba/DESCRIPTION | 20 ++--- R2Cuba-1.1-0/R2Cuba/MD5 | 94 ++++++++++++------------ R2Cuba-1.1-0/R2Cuba/NAMESPACE | 5 - R2Cuba-1.1-0/R2Cuba/NEWS |only R2Cuba-1.1-0/R2Cuba/R/commoncuba.R | 33 ++++++++ R2Cuba-1.1-0/R2Cuba/R/cuhre.R | 38 ++++++++- R2Cuba-1.1-0/R2Cuba/R/divonne.R | 28 +++++++ R2Cuba-1.1-0/R2Cuba/R/suave.R | 26 ++++++ R2Cuba-1.1-0/R2Cuba/R/vegas.R | 28 +++++++ R2Cuba-1.1-0/R2Cuba/build |only R2Cuba-1.1-0/R2Cuba/demo/00Index | 2 R2Cuba-1.1-0/R2Cuba/man/R2Cuba-package.Rd | 24 +----- R2Cuba-1.1-0/R2Cuba/man/cuhre.Rd | 6 - R2Cuba-1.1-0/R2Cuba/man/divonne.Rd | 2 R2Cuba-1.1-0/R2Cuba/man/suave.Rd | 4 - R2Cuba-1.1-0/R2Cuba/man/vegas.Rd | 2 R2Cuba-1.1-0/R2Cuba/src/common_stddecl.h | 60 +++++++-------- R2Cuba-1.1-0/R2Cuba/src/cuhre_Cuhre.c | 96 ++++++++----------------- R2Cuba-1.1-0/R2Cuba/src/cuhre_DoSample.c | 59 ++++++++++++++- R2Cuba-1.1-0/R2Cuba/src/cuhre_Integrate.c | 87 ++++++++++++---------- R2Cuba-1.1-0/R2Cuba/src/cuhre_Rule.c | 23 ++++- R2Cuba-1.1-0/R2Cuba/src/cuhre_Rule.h | 20 ++--- R2Cuba-1.1-0/R2Cuba/src/cuhre_common.c | 2 R2Cuba-1.1-0/R2Cuba/src/cuhre_decl.h | 5 - R2Cuba-1.1-0/R2Cuba/src/cuhre_util.h | 8 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Divonne.c | 10 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Explore.c | 3 R2Cuba-1.1-0/R2Cuba/src/divonne_FindMinimum.c | 1 R2Cuba-1.1-0/R2Cuba/src/divonne_Integrate.c | 3 R2Cuba-1.1-0/R2Cuba/src/divonne_Rule.h | 9 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Sample.c | 2 R2Cuba-1.1-0/R2Cuba/src/divonne_Split.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Fluct.h | 1 R2Cuba-1.1-0/R2Cuba/src/suave_Integrate.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Sample.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Suave.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_util.h | 3 R2Cuba-1.1-0/R2Cuba/src/vegas_Grid.c | 3 R2Cuba-1.1-0/R2Cuba/src/vegas_Vegas.c | 3 R2Cuba-1.1-0/R2Cuba/tests/Gtilde2.R |only R2Cuba-1.1-0/R2Cuba/tests/Gtilde2.Rout.save |only R2Cuba-1.1-0/R2Cuba/tests/MWE.R |only R2Cuba-1.1-0/R2Cuba/tests/MWE.Rout.save |only R2Cuba-1.1-0/R2Cuba/tests/cuhre.R | 8 -- R2Cuba-1.1-0/R2Cuba/tests/cuhre.Rout.save | 17 +--- R2Cuba-1.1-0/R2Cuba/tests/divonne.Rout.save | 7 - R2Cuba-1.1-0/R2Cuba/tests/peak.Rout.save | 7 - R2Cuba-1.1-0/R2Cuba/tests/suave.Rout.save | 7 - 54 files changed, 464 insertions(+), 304 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.1 dated 2015-08-25 and 0.2.4 dated 2015-10-02
networkD3-0.2.1/networkD3/man/JSONtoDF.Rd |only networkD3-0.2.4/networkD3/DESCRIPTION | 16 +- networkD3-0.2.4/networkD3/MD5 | 45 ++--- networkD3-0.2.4/networkD3/NAMESPACE | 4 networkD3-0.2.4/networkD3/NEWS | 33 ++++ networkD3-0.2.4/networkD3/R/dendroNetwork.R | 7 networkD3-0.2.4/networkD3/R/diagonalNetwork.R | 25 +-- networkD3-0.2.4/networkD3/R/forceNetwork.R | 19 +- networkD3-0.2.4/networkD3/R/radialNetwork.R | 25 +-- networkD3-0.2.4/networkD3/R/sankeyNetwork.R | 35 ++-- networkD3-0.2.4/networkD3/R/utils.R | 78 ++++----- networkD3-0.2.4/networkD3/README.md | 19 +- networkD3-0.2.4/networkD3/inst/examples/examples.R | 18 +- networkD3-0.2.4/networkD3/inst/examples/shiny/server.R | 20 +- networkD3-0.2.4/networkD3/inst/examples/shiny/ui.R | 2 networkD3-0.2.4/networkD3/inst/htmlwidgets/dendroNetwork.js | 2 networkD3-0.2.4/networkD3/inst/htmlwidgets/diagonalNetwork.js | 69 +++++++- networkD3-0.2.4/networkD3/inst/htmlwidgets/lib/sankey.js | 48 ++++-- networkD3-0.2.4/networkD3/inst/htmlwidgets/radialNetwork.js | 80 +++++++++- networkD3-0.2.4/networkD3/inst/htmlwidgets/sankeyNetwork.js | 14 + networkD3-0.2.4/networkD3/man/diagonalNetwork.Rd | 18 +- networkD3-0.2.4/networkD3/man/forceNetwork.Rd | 17 -- networkD3-0.2.4/networkD3/man/radialNetwork.Rd | 18 +- networkD3-0.2.4/networkD3/man/sankeyNetwork.Rd | 23 +- 24 files changed, 403 insertions(+), 232 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0-1 dated 2015-09-28 and 3.0.0-2 dated 2015-10-02
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- src/Makefile | 34 ++++++++++++++++------------------ src/Makefile.win | 20 +++++++++++++++----- src/legacy_convert.awk |only src/world.name | 2 +- 6 files changed, 41 insertions(+), 32 deletions(-)
More information about imputeMissings at CRAN
Permanent link
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and `iDigBio`. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.3.2 dated 2015-09-12 and 0.4.0 dated 2015-10-02
DESCRIPTION | 17 +- MD5 | 44 ++--- NAMESPACE | 7 R/as.vertnet.R |only R/inat.R | 148 +++++++---------- R/methods.r | 53 ++++-- R/occ.r | 108 +++++++++---- R/occ2df.R | 20 ++ R/plugins.r | 55 +++--- R/tbldf.R | 6 R/wkt_bbox.R | 20 ++ R/wkt_vis.r | 88 +++++++--- R/zzz.r | 9 + README.md | 126 ++++----------- inst/doc/spocc_vignette.Rmd | 343 +++++++++++++++++++---------------------- inst/doc/spocc_vignette.html | 346 +++++++++++++++++++----------------------- man/as.vertnet.Rd |only man/occ.Rd | 131 ++++++++++++++- man/spocc_objects.Rd | 9 + man/wkt_vis.Rd | 14 + tests/testthat/test-occ.R | 149 +++++++++++++++--- tests/testthat/test-occ2df.R |only tests/testthat/test-options.R | 5 tests/testthat/test-wkt_vis.R |only vignettes/spocc_vignette.Rmd | 343 +++++++++++++++++++---------------------- 25 files changed, 1156 insertions(+), 885 deletions(-)
Title: R Interface to EPP-Lab, a Java Program for Exploratory
Projection Pursuit
Description: An R Interface to EPP-lab v1.0. EPP-lab is a Java program for projection pursuit using genetic algorithms written by Alain Berro and S. Larabi Marie-Sainte and is included in the package.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between REPPlab versions 0.9.1 dated 2015-02-05 and 0.9.2 dated 2015-10-02
DESCRIPTION | 13 +- MD5 | 69 +++++++------- NAMESPACE | 39 ++++---- R/EPPlabAgg.R |only R/REPPlab-package.R |only R/REPPlab.R | 131 +++++++++++++++++++++++++++ R/coef.epplab.R | 22 ++++ R/fitted.epplab.R | 31 ++++++ R/outlier.R | 56 +++++++++++ R/pairs.epplab.R | 23 ++++ R/plot.epplab.R | 49 ++++++++++ R/plot.epplabOutlier.R | 43 ++++++++- R/predict.epplab.R | 39 ++++++++ R/print.epplab.R | 22 ++++ R/print.epplabOutlier.R | 33 ++++++ R/screeplot.epplab.R | 35 +++++++ R/summary.epplab.R | 23 ++++ R/summary.epplabOutlier.R | 39 +++++++- R/whitenSVD.R | 96 ++++++++++++++------ inst/ChangeLog | 7 + man/EPPlab.Rd | 204 ++++++++++++++++++++++++------------------- man/EPPlabAgg.Rd |only man/EPPlabOutlier.Rd | 101 +++++++++------------ man/REPPlab-package.Rd | 67 ++++++-------- man/ReliabilityData.Rd | 47 ++++----- man/WhitenSVD.Rd | 117 ++++++++++++------------ man/coef.epplab.Rd | 37 +++---- man/fitted.epplab.Rd | 43 ++++----- man/pairs.epplab.Rd | 41 ++++---- man/plot.epplab.Rd | 70 ++++++++------ man/plot.epplabOutlier.Rd | 57 ++++++------ man/predict.epplab.Rd | 49 +++++----- man/print.epplab.Rd | 37 +++---- man/print.epplabOutlier.Rd | 39 ++++---- man/screeplot.epplab.Rd | 57 ++++++------ man/summary.epplab.Rd | 40 ++++---- man/summary.epplabOutlier.Rd | 42 ++++---- 37 files changed, 1221 insertions(+), 597 deletions(-)
Title: Fungible Coefficients and Monte Carlo Functions
Description: Functions for computing fungible coefficients and Monte Carlo data.
Author: Niels G. Waller <nwaller@umn.edu> and Jeff Jones <jeff.jones@kornferry.com>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between fungible versions 1.0 dated 2015-08-18 and 1.1 dated 2015-10-02
DESCRIPTION | 8 MD5 | 24 +- R/corSmooth.R | 22 +- R/fungible.R | 16 - R/fungibleR.R | 105 +++++++++--- R/seBeta.R | 136 ++++++++------- R/seBetaCor.R | 366 ++++++++++++++++++++++--------------------- inst/CITATION | 4 inst/doc/fungible-manual.pdf |binary man/corSmooth.Rd | 6 man/fungibleR.Rd | 5 man/seBeta.Rd | 101 ++++++----- man/seBetaCor.Rd | 95 +++++------ 13 files changed, 485 insertions(+), 403 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats used in and outside of R.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 0.1.0 dated 2015-08-06 and 0.1.4 dated 2015-10-02
fulltext-0.1.0/fulltext/tests/test-all.R |only fulltext-0.1.4/fulltext/DESCRIPTION | 19 - fulltext-0.1.4/fulltext/MD5 | 60 ++- fulltext-0.1.4/fulltext/NAMESPACE | 11 fulltext-0.1.4/fulltext/R/europe_pmc_utils.R |only fulltext-0.1.4/fulltext/R/extract_tools.R |only fulltext-0.1.4/fulltext/R/ft_extract.R | 15 fulltext-0.1.4/fulltext/R/ft_get.R | 75 ++-- fulltext-0.1.4/fulltext/R/ft_get_si.R |only fulltext-0.1.4/fulltext/R/ft_links.R |only fulltext-0.1.4/fulltext/R/fulltext-package.R | 4 fulltext-0.1.4/fulltext/R/pdfx.R | 16 fulltext-0.1.4/fulltext/R/plugins_get.R | 266 +++------------ fulltext-0.1.4/fulltext/R/plugins_get_old.R |only fulltext-0.1.4/fulltext/R/plugins_links.R |only fulltext-0.1.4/fulltext/R/plugins_search.R | 46 +- fulltext-0.1.4/fulltext/R/zzz.R | 21 + fulltext-0.1.4/fulltext/README.md | 131 +++++-- fulltext-0.1.4/fulltext/build/vignette.rds |binary fulltext-0.1.4/fulltext/inst/doc/fulltext_vignette.Rmd | 88 +++- fulltext-0.1.4/fulltext/inst/doc/fulltext_vignette.html | 92 +++-- fulltext-0.1.4/fulltext/inst/vign/formats.md | 4 fulltext-0.1.4/fulltext/inst/vign/fulltext_vignette.md | 88 +++- fulltext-0.1.4/fulltext/man/eupmc.Rd |only fulltext-0.1.4/fulltext/man/extract_tools.Rd |only fulltext-0.1.4/fulltext/man/ft_extract.Rd | 7 fulltext-0.1.4/fulltext/man/ft_get.Rd | 3 fulltext-0.1.4/fulltext/man/ft_get_si.Rd |only fulltext-0.1.4/fulltext/man/ft_links.Rd |only fulltext-0.1.4/fulltext/man/fulltext-package.Rd | 1 fulltext-0.1.4/fulltext/man/pdfx.Rd | 3 fulltext-0.1.4/fulltext/tests/longtests |only fulltext-0.1.4/fulltext/tests/testthat/test-ft_extract.R | 18 - fulltext-0.1.4/fulltext/tests/testthat/test-ft_get.R | 44 ++ fulltext-0.1.4/fulltext/tests/testthat/test-ft_get_si.r |only fulltext-0.1.4/fulltext/tests/testthat/test-ft_search.R | 30 + fulltext-0.1.4/fulltext/vignettes/fulltext_vignette.Rmd | 88 +++- 37 files changed, 651 insertions(+), 479 deletions(-)
Title: SNPs Enrichment Analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil <mickael.canouil@cnrs.fr>
Diff between snpEnrichment versions 1.6.3 dated 2015-02-09 and 1.7.0 dated 2015-10-01
snpEnrichment-1.6.3/snpEnrichment/README.md |only snpEnrichment-1.7.0/snpEnrichment/ChangeLog | 18 ++++++++++ snpEnrichment-1.7.0/snpEnrichment/DESCRIPTION | 14 +++---- snpEnrichment-1.7.0/snpEnrichment/MD5 | 16 ++++---- snpEnrichment-1.7.0/snpEnrichment/NAMESPACE | 10 ++++- snpEnrichment-1.7.0/snpEnrichment/R/Global.R | 2 - snpEnrichment-1.7.0/snpEnrichment/R/enrichment.R | 15 +++++++- snpEnrichment-1.7.0/snpEnrichment/data/toyEnrichment.RData |binary snpEnrichment-1.7.0/snpEnrichment/man/snpEnrichment-package.Rd | 4 +- snpEnrichment-1.7.0/snpEnrichment/tests |only 10 files changed, 56 insertions(+), 23 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.1 dated 2015-09-23 and 0.2.3 dated 2015-10-01
DESCRIPTION | 10 +- MD5 | 33 ++++----- NAMESPACE | 1 R/plotting.R | 159 ++++++++++++++++++++++++++++++++++++++++++++-- R/post_hoc.R | 16 ++-- R/scmamp.R | 106 ++++++++++++++++++++++++++---- R/sysdata.rda |binary build/vignette.rds |binary data/data_blum_2015.RData |binary data/data_gh_2008.RData |binary data/data_gh_2010.RData |binary man/adjustFinner.Rd | 4 - man/adjustHolland.Rd | 4 - man/adjustLi.Rd | 4 - man/adjustRom.Rd | 4 - man/drawAlgorithmGraph.Rd | 2 man/plotCD.Rd | 2 man/plotRanking.Rd |only 18 files changed, 289 insertions(+), 56 deletions(-)
Title: Distance Weighted Discrimination (DWD) and Kernel Methods
Description: A novel implementation that solves the DWD and the kernel DWD which can be hundred times faster than the existing implementation of DWD based on the second-order-cone programming (SOCP). The package also handles some other general loss functions including large-margin unified machines (LUM).
Author: Boxiang Wang <boxiang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between kerndwd versions 1.1.1 dated 2015-09-06 and 1.1.2 dated 2015-10-01
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/cv.kerndwd.R | 10 +++++++--- R/kerndwd.R | 3 ++- R/predict.kerndwd.R | 8 ++++++-- R/utilities.R | 4 ++-- man/cv.kerndwd.Rd | 2 +- man/dots.Rd | 8 ++++---- man/kerndwd.Rd | 4 ++-- 9 files changed, 37 insertions(+), 28 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Testing
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace and GraceR tests to perform graph-guided hypothesis test on the association between the response and the predictor.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.1 dated 2015-08-18 and 0.1.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/grace.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Cleaning Geometries from Spatial Objects
Description:
Provides a set of utility tools to inspect spatial objects, facilitate
handling and reporting of topology errors and geometry validity issues.
Finally, it provides a geometry cleaner that will fix all geometry problems,
and eliminate (at least reduce) the likelihood of having issues when doing
spatial data processing.
Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between cleangeo versions 0.1-0 dated 2015-09-27 and 0.1-1 dated 2015-10-01
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++++------- R/cleangeo.R | 4 ++-- R/clgeo_Clean.R | 39 ++++++++++++++++++++------------------- README.md | 5 +++-- build |only inst/doc |only man/cleangeo.Rd | 4 ++-- tests/testthat/test_Clean.R | 9 ++++++++- vignettes/quickstart.Rmd | 12 +++++------- 10 files changed, 57 insertions(+), 45 deletions(-)
Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa.
Author: Amy Willis and John Bunge
Maintainer: Amy Willis <adw96@cornell.edu>
Diff between breakaway versions 1.0 dated 2014-08-04 and 2.0 dated 2015-10-01
breakaway-1.0/breakaway/R/betta_basic.R |only breakaway-1.0/breakaway/man/betta_basic.Rd |only breakaway-2.0/breakaway/DESCRIPTION | 12 +-- breakaway-2.0/breakaway/MD5 | 19 +++-- breakaway-2.0/breakaway/NAMESPACE | 9 ++ breakaway-2.0/breakaway/R/betta.R |only breakaway-2.0/breakaway/R/breakaway_nof1.R | 78 ++++++++++++++--------- breakaway-2.0/breakaway/R/hawaii.R |only breakaway-2.0/breakaway/man/betta.Rd |only breakaway-2.0/breakaway/man/betta_pic.Rd |only breakaway-2.0/breakaway/man/breakaway-package.Rd | 17 ++--- breakaway-2.0/breakaway/man/breakaway.Rd | 11 +-- breakaway-2.0/breakaway/man/breakaway_nof1.Rd | 11 +-- breakaway-2.0/breakaway/man/hawaii.Rd |only 14 files changed, 94 insertions(+), 63 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.2 dated 2015-08-07 and 0.6.6 dated 2015-10-01
taxize-0.6.2/taxize/man/get_ubioid.Rd |only taxize-0.6.2/taxize/man/ubio_classification.Rd |only taxize-0.6.2/taxize/man/ubio_classification_search.Rd |only taxize-0.6.2/taxize/man/ubio_id.Rd |only taxize-0.6.2/taxize/man/ubio_search.Rd |only taxize-0.6.2/taxize/man/ubio_synonyms.Rd |only taxize-0.6.2/taxize/tests/testthat/test-ubio_classification.R |only taxize-0.6.6/taxize/DESCRIPTION | 10 taxize-0.6.6/taxize/MD5 | 225 +++++----- taxize-0.6.6/taxize/NAMESPACE | 4 taxize-0.6.6/taxize/R/children.R | 23 - taxize-0.6.6/taxize/R/classification.R | 4 taxize-0.6.6/taxize/R/comm2sci.R | 7 taxize-0.6.6/taxize/R/eol_dataobjects.R | 22 taxize-0.6.6/taxize/R/gbif_parse.R | 2 taxize-0.6.6/taxize/R/get_eolid.R | 16 taxize-0.6.6/taxize/R/get_gbifid.R | 24 - taxize-0.6.6/taxize/R/get_ids.R | 18 taxize-0.6.6/taxize/R/get_nbnid.R | 51 -- taxize-0.6.6/taxize/R/get_tsn.R | 2 taxize-0.6.6/taxize/R/get_ubioid.R | 125 +---- taxize-0.6.6/taxize/R/get_uid.R | 20 taxize-0.6.6/taxize/R/gni_parse.R | 30 - taxize-0.6.6/taxize/R/gnr_resolve.R | 157 +++--- taxize-0.6.6/taxize/R/iplant_resolve.R | 3 taxize-0.6.6/taxize/R/ipni_search.R | 34 - taxize-0.6.6/taxize/R/itis.R | 89 ++- taxize-0.6.6/taxize/R/itis_downstream.R | 62 +- taxize-0.6.6/taxize/R/itis_getrecord.R | 26 - taxize-0.6.6/taxize/R/itis_hierarchy.R | 19 taxize-0.6.6/taxize/R/itis_kingdomnames.R | 18 taxize-0.6.6/taxize/R/itis_lsid.R | 16 taxize-0.6.6/taxize/R/itis_native.R | 22 taxize-0.6.6/taxize/R/itis_refs.R | 7 taxize-0.6.6/taxize/R/itis_taxrank.R | 12 taxize-0.6.6/taxize/R/iucn_getname.R | 3 taxize-0.6.6/taxize/R/iucn_id.R |only taxize-0.6.6/taxize/R/iucn_summary.R | 3 taxize-0.6.6/taxize/R/names_list.r | 3 taxize-0.6.6/taxize/R/nbn_classification.R | 7 taxize-0.6.6/taxize/R/nbn_search.R | 13 taxize-0.6.6/taxize/R/nbn_synonyms.R | 3 taxize-0.6.6/taxize/R/ncbi_children.R | 10 taxize-0.6.6/taxize/R/ncbi_get_taxon_summary.R | 13 taxize-0.6.6/taxize/R/phylomatic_format.R | 2 taxize-0.6.6/taxize/R/ping.R | 19 taxize-0.6.6/taxize/R/plantminer.R | 56 +- taxize-0.6.6/taxize/R/scrapenames.r | 2 taxize-0.6.6/taxize/R/synonyms.R | 31 - taxize-0.6.6/taxize/R/tax_name.R | 34 - taxize-0.6.6/taxize/R/tax_rank.R | 10 taxize-0.6.6/taxize/R/taxize-package.R | 16 taxize-0.6.6/taxize/R/taxize_cite.R | 17 taxize-0.6.6/taxize/R/tnrs.R | 8 taxize-0.6.6/taxize/R/tnrs_sources.r | 4 taxize-0.6.6/taxize/R/tp_refs.R | 3 taxize-0.6.6/taxize/R/ubio_classification.R | 75 --- taxize-0.6.6/taxize/R/ubio_classification_search.R | 35 - taxize-0.6.6/taxize/R/ubio_id.R | 91 ---- taxize-0.6.6/taxize/R/ubio_search.R | 67 -- taxize-0.6.6/taxize/R/ubio_synonyms.R | 59 -- taxize-0.6.6/taxize/R/upstream.R | 6 taxize-0.6.6/taxize/R/vascan_search.r | 49 +- taxize-0.6.6/taxize/R/zzz.R | 3 taxize-0.6.6/taxize/README.md | 63 -- taxize-0.6.6/taxize/build/vignette.rds |binary taxize-0.6.6/taxize/data/rank_ref.RData |binary taxize-0.6.6/taxize/inst/doc/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/doc/taxize_infotable.html | 126 +---- taxize-0.6.6/taxize/inst/doc/taxize_vignette.Rmd | 80 --- taxize-0.6.6/taxize/inst/doc/taxize_vignette.html | 79 --- taxize-0.6.6/taxize/inst/vign/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/vign/taxize_infotable.md | 40 - taxize-0.6.6/taxize/inst/vign/taxize_vignette.Rmd | 7 taxize-0.6.6/taxize/inst/vign/taxize_vignette.md | 80 --- taxize-0.6.6/taxize/man/eol_dataobjects.Rd | 10 taxize-0.6.6/taxize/man/get_eolid.Rd | 2 taxize-0.6.6/taxize/man/get_ids.Rd | 12 taxize-0.6.6/taxize/man/get_ubioid-defunct.Rd |only taxize-0.6.6/taxize/man/get_uid.Rd | 14 taxize-0.6.6/taxize/man/getitistermsfromcommonname.Rd | 4 taxize-0.6.6/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.6.6/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.6.6/taxize/man/gnr_resolve.Rd | 41 + taxize-0.6.6/taxize/man/ipni_search.Rd | 4 taxize-0.6.6/taxize/man/itis_getrecord.Rd | 7 taxize-0.6.6/taxize/man/itis_hierarchy.Rd | 7 taxize-0.6.6/taxize/man/itis_kingdomnames.Rd | 7 taxize-0.6.6/taxize/man/itis_lsid.Rd | 4 taxize-0.6.6/taxize/man/itis_native.Rd | 3 taxize-0.6.6/taxize/man/itis_refs.Rd | 5 taxize-0.6.6/taxize/man/itis_taxrank.Rd | 2 taxize-0.6.6/taxize/man/iucn_id.Rd |only taxize-0.6.6/taxize/man/ncbi_children.Rd | 7 taxize-0.6.6/taxize/man/ncbi_get_taxon_summary.Rd | 4 taxize-0.6.6/taxize/man/ping.Rd | 4 taxize-0.6.6/taxize/man/plantminer.Rd | 24 - taxize-0.6.6/taxize/man/searchforanymatchpaged.Rd | 4 taxize-0.6.6/taxize/man/synonyms.Rd | 16 taxize-0.6.6/taxize/man/tax_rank.Rd | 4 taxize-0.6.6/taxize/man/taxize-defunct.Rd | 7 taxize-0.6.6/taxize/man/taxize-package.Rd | 6 taxize-0.6.6/taxize/man/taxize_cite.Rd | 1 taxize-0.6.6/taxize/man/tnrs.Rd | 6 taxize-0.6.6/taxize/man/ubio_classification-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_classification_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_id-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_ping-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_synonyms-defunct.Rd |only taxize-0.6.6/taxize/man/vascan_search.Rd | 12 taxize-0.6.6/taxize/tests/testthat/Rplots.pdf |only taxize-0.6.6/taxize/tests/testthat/test-eol_dataobjects.R | 2 taxize-0.6.6/taxize/tests/testthat/test-gbif_parse.R | 11 taxize-0.6.6/taxize/tests/testthat/test-gnr_resolve.R | 36 - taxize-0.6.6/taxize/tests/testthat/test-ipni_search.R |only taxize-0.6.6/taxize/tests/testthat/test-itis_lsid.R | 2 taxize-0.6.6/taxize/tests/testthat/test-iucn_id.R |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_tree.R | 1 taxize-0.6.6/taxize/tests/testthat/test-ping.R | 6 taxize-0.6.6/taxize/tests/testthat/test-plantminer.R | 18 taxize-0.6.6/taxize/vignettes/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/vignettes/taxize_vignette.Rmd | 80 --- 123 files changed, 1026 insertions(+), 1636 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling and modelling.
Functions include models for species population density, download utilities for
climate and global deforestation spatial products, spatial smoothing,
multivariate separability, point process model for creating pseudo-absences
and sub-sampling, polygon and point-distance landscape metrics, auto-logistic
model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-1 dated 2015-02-24 and 0.1-2 dated 2015-10-01
DESCRIPTION | 24 ++++--- MD5 | 146 +++++++++++++++++++++++++-------------------- NAMESPACE | 14 ++++ R/bearing.distance.R |only R/breeding.density.R | 35 +++++----- R/concordance.R |only R/conf.interval.R |only R/correlogram.R | 18 ++--- R/csi.R | 7 +- R/download.daymet.R | 5 - R/download.hansen.R | 5 - R/download.prism.R | 7 +- R/group.pdf.R | 10 +-- R/hexagons.R | 7 +- R/idw.smoothing.R | 4 - R/kl.divergence.R | 4 - R/land.metrics.R | 20 +++--- R/local.min.max.R | 25 +++---- R/loess.boot.R |only R/loess.ci.R |only R/logistic.regression.R | 20 +++--- R/moments.R | 52 ++++++++-------- R/nni.R | 2 R/o.ring.R | 27 ++++---- R/optimal.k.R | 9 +- R/outliers.R | 11 +-- R/parea.sample.R | 7 +- R/plot.loess.boot.R |only R/point.in.poly.R | 4 - R/pp.subsample.R | 13 ++-- R/print.loess.boot.R |only R/pseudo.absence.R | 27 ++++---- R/raster.entropy.R | 6 - R/raster.vol.R |only R/sample.line.R |only R/separability.R | 36 +++++------ R/sp.na.omit.R | 3 R/stratified.random.R | 3 R/summary.loess.boot.R |only R/tpi.R |only R/trend.line.R | 24 +++---- R/wt.centroids.R | 5 - R/zonal.stats.R | 12 +-- inst/CITATION | 4 - inst/NEWS | 10 +++ man/bearing.distance.Rd |only man/breeding.density.Rd | 2 man/concordance.Rd |only man/conf.interval.Rd |only man/correlogram.Rd | 2 man/csi.Rd | 2 man/download.daymet.Rd | 2 man/download.hansen.Rd | 2 man/download.prism.Rd | 2 man/group.pdf.Rd | 84 ++++++++++++------------- man/hexagons.Rd | 76 +++++++++++------------ man/idw.smoothing.Rd | 2 man/kl.divergence.Rd | 74 +++++++++++----------- man/land.metrics.Rd | 11 +-- man/local.min.max.Rd | 2 man/loess.boot.Rd |only man/loess.ci.Rd |only man/logistic.regression.Rd | 10 +-- man/moments.Rd | 2 man/nni.Rd | 2 man/o.ring.Rd | 14 ++-- man/optimal.k.Rd | 2 man/outliers.Rd | 2 man/parea.sample.Rd | 2 man/plot.loess.boot.Rd |only man/point.in.poly.Rd | 104 ++++++++++++++++---------------- man/pp.subsample.Rd | 2 man/print.loess.boot.Rd |only man/pseudo.absence.Rd | 2 man/raster.entropy.Rd | 102 +++++++++++++++---------------- man/raster.vol.Rd |only man/sample.line.Rd |only man/separability.Rd | 2 man/sp.na.omit.Rd | 90 +++++++++++++-------------- man/stratified.random.Rd | 2 man/summary.loess.boot.Rd |only man/tpi.Rd |only man/trend.line.Rd | 2 man/wt.centroid.Rd | 86 +++++++++++++------------- man/zonal.stats.Rd | 132 ++++++++++++++++++++-------------------- 85 files changed, 743 insertions(+), 682 deletions(-)
Title: Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Description: Sparse modeling provides a mean selecting a small number of non-zero effects from a large possible number of candidate effects. This package includes a suite of methods for sparse modeling: estimation via EM or MCMC, approximate confidence intervals with nominal coverage, and diagnostic and summary plots. Beyond regression analyses, applications include subgroup analysis, particularly for conjoint experiments, and panel data. Future versions will include extensions to limited dependent variables, models with truncated outcomes, and propensity score and instrumental variable analysis.
Author: Marc Ratkovic and Dustin Tingley
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Diff between sparsereg versions 1.0 dated 2015-07-21 and 1.1 dated 2015-10-01
sparsereg-1.0/sparsereg/R/type2tobit.R |only sparsereg-1.0/sparsereg/man/type2tobit.Rd |only sparsereg-1.0/sparsereg/man/volcanoplot.Rd |only sparsereg-1.1/sparsereg/ChangeLog |only sparsereg-1.1/sparsereg/DESCRIPTION | 12 - sparsereg-1.1/sparsereg/MD5 | 29 +- sparsereg-1.1/sparsereg/NAMESPACE | 7 sparsereg-1.1/sparsereg/R/subgroup.R | 248 +++++++++++++++++++---- sparsereg-1.1/sparsereg/R/updateREs.R | 16 + sparsereg-1.1/sparsereg/R/utility.R | 2 sparsereg-1.1/sparsereg/man/difference.Rd | 2 sparsereg-1.1/sparsereg/man/plot.sparsereg.Rd | 6 sparsereg-1.1/sparsereg/man/print.sparsereg.Rd | 5 sparsereg-1.1/sparsereg/man/sparsereg-package.Rd | 2 sparsereg-1.1/sparsereg/man/sparsereg.Rd | 52 ++-- sparsereg-1.1/sparsereg/man/summary.sparsereg.Rd | 4 sparsereg-1.1/sparsereg/man/violinplot.Rd |only sparsereg-1.1/sparsereg/src/subgroup.cpp | 15 - 18 files changed, 288 insertions(+), 112 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
In addition, various risk estimation methods are included.
Note that the package 'sdcMicroGUI' includes a graphical user interface for various methods
in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 4.5.0 dated 2015-05-04 and 4.6.0 dated 2015-10-01
sdcMicro-4.5.0/sdcMicro/R/localSupp2.R |only sdcMicro-4.5.0/sdcMicro/R/localSupp2Wrapper.R |only sdcMicro-4.5.0/sdcMicro/R/plot.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/print.indivRisk.R |only sdcMicro-4.5.0/sdcMicro/R/print.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/summary.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.pram.r |only sdcMicro-4.5.0/sdcMicro/R/swappNum.R |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-html.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-latex.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-text.brew |only sdcMicro-4.5.0/sdcMicro/man/extractManipData-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/groupVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2Wrapper.Rd |only sdcMicro-4.5.0/sdcMicro/man/removeDirectID-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/renameVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/sdcMicro-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum.Rd |only sdcMicro-4.5.0/sdcMicro/man/varToFactor-methods.Rd |only sdcMicro-4.6.0/sdcMicro/DESCRIPTION | 47 sdcMicro-4.6.0/sdcMicro/MD5 | 238 - sdcMicro-4.6.0/sdcMicro/NAMESPACE | 236 - sdcMicro-4.6.0/sdcMicro/R/0classes.r | 304 + sdcMicro-4.6.0/sdcMicro/R/GUIfunctions.R | 319 + sdcMicro-4.6.0/sdcMicro/R/LLmodGlobalRisk.R | 371 - sdcMicro-4.6.0/sdcMicro/R/LocalRecProg.R | 261 - sdcMicro-4.6.0/sdcMicro/R/RcppExports.R |only sdcMicro-4.6.0/sdcMicro/R/addNoise.r | 245 - sdcMicro-4.6.0/sdcMicro/R/aux_functions.r | 523 +- sdcMicro-4.6.0/sdcMicro/R/dRisk.R | 114 sdcMicro-4.6.0/sdcMicro/R/dRiskRMD.R | 237 - sdcMicro-4.6.0/sdcMicro/R/dUtility.R | 161 sdcMicro-4.6.0/sdcMicro/R/dataGen.r | 125 sdcMicro-4.6.0/sdcMicro/R/dataSets.R |only sdcMicro-4.6.0/sdcMicro/R/freqCalc.r | 968 ++--- sdcMicro-4.6.0/sdcMicro/R/globalRecode.R | 120 sdcMicro-4.6.0/sdcMicro/R/indivRisk.R | 246 - sdcMicro-4.6.0/sdcMicro/R/localSupp.R | 144 sdcMicro-4.6.0/sdcMicro/R/localSuppression.R | 814 +++- sdcMicro-4.6.0/sdcMicro/R/maG.R | 478 +- sdcMicro-4.6.0/sdcMicro/R/mafast.R | 234 - sdcMicro-4.6.0/sdcMicro/R/mdav.R | 53 sdcMicro-4.6.0/sdcMicro/R/measure_risk.R | 723 ++- sdcMicro-4.6.0/sdcMicro/R/methods.r | 224 - sdcMicro-4.6.0/sdcMicro/R/microaggregation.R | 1883 +++++----- sdcMicro-4.6.0/sdcMicro/R/modRisk.R |only sdcMicro-4.6.0/sdcMicro/R/plotFunctions.R |only sdcMicro-4.6.0/sdcMicro/R/plotMicro.R | 271 - sdcMicro-4.6.0/sdcMicro/R/pram.R | 749 ++- sdcMicro-4.6.0/sdcMicro/R/printFunctions.R | 467 +- sdcMicro-4.6.0/sdcMicro/R/rankSwap.R | 194 - sdcMicro-4.6.0/sdcMicro/R/report.R | 811 +--- sdcMicro-4.6.0/sdcMicro/R/sdcMicro-package.R |only sdcMicro-4.6.0/sdcMicro/R/show_sdcMicroObj.R | 57 sdcMicro-4.6.0/sdcMicro/R/shuffle.R | 721 +-- sdcMicro-4.6.0/sdcMicro/R/suda2.R | 220 - sdcMicro-4.6.0/sdcMicro/R/timeEstimation.R | 82 sdcMicro-4.6.0/sdcMicro/R/topBotCoding.R | 171 sdcMicro-4.6.0/sdcMicro/R/valTable.R | 246 - sdcMicro-4.6.0/sdcMicro/R/zzz.R | 20 sdcMicro-4.6.0/sdcMicro/build/vignette.rds |binary sdcMicro-4.6.0/sdcMicro/data/CASCrefmicrodata.rda |binary sdcMicro-4.6.0/sdcMicro/data/EIA.rda |binary sdcMicro-4.6.0/sdcMicro/data/Tarragona.rda |binary sdcMicro-4.6.0/sdcMicro/data/casc1.rda |binary sdcMicro-4.6.0/sdcMicro/data/francdat.rda |binary sdcMicro-4.6.0/sdcMicro/data/free1.rda |binary sdcMicro-4.6.0/sdcMicro/data/microData.rda |binary sdcMicro-4.6.0/sdcMicro/data/testdata.RData |binary sdcMicro-4.6.0/sdcMicro/data/testdata2.RData |binary sdcMicro-4.6.0/sdcMicro/inst/CITATION |only sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.R | 208 - sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.pdf |binary sdcMicro-4.6.0/sdcMicro/inst/templates/report-template.rmd |only sdcMicro-4.6.0/sdcMicro/inst/templates/report.css | 34 sdcMicro-4.6.0/sdcMicro/man/CASCrefmicrodata.Rd | 82 sdcMicro-4.6.0/sdcMicro/man/EIA.Rd | 203 - sdcMicro-4.6.0/sdcMicro/man/LLmodGlobalRisk.Rd | 127 sdcMicro-4.6.0/sdcMicro/man/LocalRecProg.Rd | 193 - sdcMicro-4.6.0/sdcMicro/man/Tarragona.Rd | 81 sdcMicro-4.6.0/sdcMicro/man/addNoise.Rd | 236 - sdcMicro-4.6.0/sdcMicro/man/calcRisks.Rd | 42 sdcMicro-4.6.0/sdcMicro/man/casc1.Rd | 38 sdcMicro-4.6.0/sdcMicro/man/dRisk.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/dRiskRMD.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/dUtility.Rd | 165 sdcMicro-4.6.0/sdcMicro/man/dataGen.Rd | 132 sdcMicro-4.6.0/sdcMicro/man/extractManipData.Rd |only sdcMicro-4.6.0/sdcMicro/man/francdat.Rd | 67 sdcMicro-4.6.0/sdcMicro/man/free1.Rd | 55 sdcMicro-4.6.0/sdcMicro/man/freqCalc.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/generateStrata.Rd | 65 sdcMicro-4.6.0/sdcMicro/man/globalRecode.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/groupVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/indivRisk.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/localSupp.Rd | 153 sdcMicro-4.6.0/sdcMicro/man/localSuppression.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/mafast.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/measure_risk.Rd | 254 - sdcMicro-4.6.0/sdcMicro/man/microData.Rd | 40 sdcMicro-4.6.0/sdcMicro/man/microaggrGower.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/microaggregation.Rd | 353 - sdcMicro-4.6.0/sdcMicro/man/modRisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/plot.localSuppression.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/plot.sdcMicroObj.Rd |only sdcMicro-4.6.0/sdcMicro/man/plotMicro.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/pram.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/print.freqCalc.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.indivRisk.Rd | 68 sdcMicro-4.6.0/sdcMicro/man/print.localSuppression.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.micro.Rd | 58 sdcMicro-4.6.0/sdcMicro/man/print.modrisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.pram.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.sdcMicroObj.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/print.suda2.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/rankSwap.Rd | 220 - sdcMicro-4.6.0/sdcMicro/man/removeDirectID.Rd |only sdcMicro-4.6.0/sdcMicro/man/renameVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/report.Rd | 66 sdcMicro-4.6.0/sdcMicro/man/sdcMicro-package.Rd | 517 +- sdcMicro-4.6.0/sdcMicro/man/sdcMicroObj-class.Rd | 211 - sdcMicro-4.6.0/sdcMicro/man/shuffle.Rd | 248 - sdcMicro-4.6.0/sdcMicro/man/suda2.Rd | 191 - sdcMicro-4.6.0/sdcMicro/man/summary.freqCalc.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/summary.micro.Rd | 110 sdcMicro-4.6.0/sdcMicro/man/summary.pram.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/testdata.Rd | 119 sdcMicro-4.6.0/sdcMicro/man/topBotCoding.Rd | 111 sdcMicro-4.6.0/sdcMicro/man/valTable.Rd | 130 sdcMicro-4.6.0/sdcMicro/man/varToFactor.Rd |only sdcMicro-4.6.0/sdcMicro/src/RcppExports.cpp |only sdcMicro-4.6.0/sdcMicro/src/calcSuppInds.cpp |only sdcMicro-4.6.0/sdcMicro/tests/globalRecoding_test.R | 18 sdcMicro-4.6.0/sdcMicro/tests/microaggregation_test.R | 28 sdcMicro-4.6.0/sdcMicro/tests/reporting_test.R | 41 sdcMicro-4.6.0/sdcMicro/tests/testhat.R |only sdcMicro-4.6.0/sdcMicro/tests/testthat |only 142 files changed, 11288 insertions(+), 8425 deletions(-)
Title: Stratified Analysis with Nonparametric Covariable Adjustment
Description: There are several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between sanon versions 1.4 dated 2014-09-04 and 1.5 dated 2015-10-01
DESCRIPTION | 12 +-- MD5 | 49 +++++++------- NAMESPACE | 32 ++++++++- R/sanon.r | 29 +++++++- data/cpain.rda |binary data/heartburn.rda |binary data/resp.rda |binary data/sebor.rda |binary data/skin.rda |binary inst |only man/catecovar.Rd | 18 ++--- man/coef.sanon.Rd | 20 ++--- man/confint.sanon.Rd | 39 +++-------- man/contrast.Rd | 55 ++++++--------- man/covar.Rd | 10 +- man/cpain.Rd | 30 +++----- man/grp.Rd | 13 +-- man/heartburn.Rd | 44 +++++------- man/resp.Rd | 53 +++++---------- man/sanon-package.Rd | 17 ++-- man/sanon.Rd | 176 ++++++++++++++++++--------------------------------- man/sebor.Rd | 47 +++++-------- man/skin.Rd | 43 ++++-------- man/strt.Rd | 11 +-- man/summary.sanon.Rd | 27 +++---- man/vcov.sanon.Rd | 17 ++-- 26 files changed, 331 insertions(+), 411 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 1.5.2 dated 2015-02-04 and 1.5.3 dated 2015-10-01
DESCRIPTION | 13 +- MD5 | 26 ++-- NAMESPACE | 4 NEWS | 6 + R/branches.R | 3 R/lib.R | 45 ++++++- R/node.labs.R | 2 R/prp.R | 6 - inst/doc/prp.pdf |binary inst/slowtests/make.bat | 2 inst/slowtests/test.prp.R | 168 +++++++++++++++++----------- inst/slowtests/test.prp.Rout.save | 223 ++++++++++++++++++++++---------------- inst/slowtests/user-manual-figs.R | 20 +++ inst/slowtests/webpage-figs.R | 4 14 files changed, 334 insertions(+), 188 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 1.0-9102 dated 2014-12-11 and 3.3.1 dated 2015-10-01
DESCRIPTION | 24 - MD5 | 242 +++++++------- NAMESPACE | 2 R/phreeqc.R | 2 data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 19 - man/ex1.Rd | 33 + man/ex10.Rd | 45 +- man/ex11.Rd | 43 +- man/ex12.Rd | 59 +-- man/ex13.Rd | 42 +- man/ex14.Rd | 52 +-- man/ex15.Rd | 47 +- man/ex15.dat.Rd | 16 man/ex16.Rd | 53 +-- man/ex17.Rd | 52 +-- man/ex18.Rd | 72 ++-- man/ex19.Rd | 38 +- man/ex2.Rd | 29 - man/ex20.Rd | 57 +-- man/ex21.Rd | 52 +-- man/ex22.Rd | 46 +- man/ex3.Rd | 51 +-- man/ex4.Rd | 54 +-- man/ex5.Rd | 41 +- man/ex6.Rd | 36 +- man/ex7.Rd | 61 +-- man/ex8.Rd | 38 +- man/ex9.Rd | 62 +-- man/iso.dat.Rd | 18 - man/llnl.dat.Rd | 17 - man/minteq.dat.Rd | 14 man/minteq.v4.dat.Rd | 14 man/phrAccumulateLine.Rd | 12 man/phrClearAccumulatedLines.Rd | 11 man/phrGetAccumulatedLines.Rd | 6 man/phrGetComponentList.Rd | 5 man/phrGetDumpFileName.Rd | 17 - man/phrGetDumpFileOn.Rd | 12 man/phrGetDumpStrings.Rd | 16 man/phrGetDumpStringsOn.Rd | 12 man/phrGetErrorFileName.Rd | 18 - man/phrGetErrorFileOn.Rd | 12 man/phrGetErrorStrings.Rd | 28 - man/phrGetErrorStringsOn.Rd | 12 man/phrGetLogFileName.Rd | 15 man/phrGetLogFileOn.Rd | 12 man/phrGetLogStrings.Rd | 12 man/phrGetLogStringsOn.Rd | 12 man/phrGetOutputFileName.Rd | 15 man/phrGetOutputFileOn.Rd | 12 man/phrGetOutputStrings.Rd | 12 man/phrGetOutputStringsOn.Rd | 12 man/phrGetSelectedOutput.Rd | 30 - man/phrGetSelectedOutputFileName.Rd | 15 man/phrGetWarningStrings.Rd | 14 man/phrLoadDatabase.Rd | 7 man/phrLoadDatabaseString.Rd | 9 man/phrRunAccumulated.Rd | 27 - man/phrRunFile.Rd | 6 man/phrRunString.Rd | 18 - man/phrSetDumpFileName.Rd | 19 - man/phrSetDumpFileOn.Rd | 20 - man/phrSetDumpStringsOn.Rd | 22 - man/phrSetErrorFileName.Rd | 17 - man/phrSetErrorFileOn.Rd | 23 - man/phrSetErrorStringsOn.Rd | 25 - man/phrSetLogFileName.Rd | 21 - man/phrSetLogFileOn.Rd | 24 - man/phrSetLogStringsOn.Rd | 22 - man/phrSetOutputFileName.Rd | 20 - man/phrSetOutputFileOn.Rd | 22 - man/phrSetOutputStringsOn.Rd | 22 - man/phrSetSelectedOutputFileName.Rd | 20 - man/phrSetSelectedOutputFileOn.Rd | 22 - man/phreeqc-package.Rd | 26 - man/phreeqc.dat.Rd | 17 - man/pitzer.dat.Rd | 17 - man/sit.dat.Rd | 17 - man/wateq4f.dat.Rd | 15 src/IPhreeqc.cpp | 118 +++++-- src/IPhreeqc.h | 30 + src/IPhreeqcLib.cpp | 16 src/IPhreeqchpp.h | 9 src/phreeqcpp/ChartHandler.cpp | 2 src/phreeqcpp/ChartObject.cpp | 20 - src/phreeqcpp/GasPhase.cpp | 18 - src/phreeqcpp/NameDouble.cpp | 1 src/phreeqcpp/PBasic.cpp | 326 ++++++++++++++++++- src/phreeqcpp/PBasic.h | 4 src/phreeqcpp/PPassemblage.cpp | 1 src/phreeqcpp/Phreeqc.cpp | 6 src/phreeqcpp/Phreeqc.h | 43 ++ src/phreeqcpp/Solution.cpp | 61 +++ src/phreeqcpp/Solution.h | 2 src/phreeqcpp/StorageBinList.cpp | 29 + src/phreeqcpp/SurfaceCharge.cpp | 44 ++ src/phreeqcpp/SurfaceCharge.h | 2 src/phreeqcpp/basicsubs.cpp | 444 +++++++++++++++++++++++++- src/phreeqcpp/cvdense.cpp | 5 src/phreeqcpp/cvode.cpp | 9 src/phreeqcpp/dumper.cpp | 4 src/phreeqcpp/dw.cpp | 3 src/phreeqcpp/gases.cpp | 23 + src/phreeqcpp/integrate.cpp | 9 src/phreeqcpp/inverse.cpp | 19 - src/phreeqcpp/isotopes.cpp | 22 + src/phreeqcpp/kinetics.cpp | 4 src/phreeqcpp/mainsubs.cpp | 53 +++ src/phreeqcpp/model.cpp | 170 ++++++++-- src/phreeqcpp/pitzer.cpp | 604 +++++++++++++++++++++++++++++------- src/phreeqcpp/pitzer_structures.cpp | 15 src/phreeqcpp/prep.cpp | 39 +- src/phreeqcpp/print.cpp | 41 ++ src/phreeqcpp/read.cpp | 15 src/phreeqcpp/sit.cpp | 387 +++++++++++++++++++++-- src/phreeqcpp/step.cpp | 4 src/phreeqcpp/structures.cpp | 48 +- src/phreeqcpp/tally.cpp | 8 src/phreeqcpp/tidy.cpp | 67 +++ src/phreeqcpp/utilities.cpp | 5 122 files changed, 3494 insertions(+), 1447 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J. Owens [ctb], Christophe Dutang [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.1.9 dated 2015-07-10 and 1.1.10 dated 2015-10-01
ChangeLog | 4 DESCRIPTION | 10 MD5 | 34 NEWS | 10 R/3_demographicFunctions.R | 4 R/5_actuarialFunctions.R | 904 ++++++++------ R/8_mdtFunctions.R | 8 README.md | 3 build/vignette.rds |binary data/demoGermany.rda |only inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary inst/doc/introToLifecontingencies.Rmd | 2 inst/doc/introToLifecontingencies.pdf |binary man/demoGermany.Rd |only man/demoIta.Rd | 2 man/lifecontingencies-package.Rd | 4 vignettes/introToLifecontingencies.Rmd | 2 vignettes/introToLifecontingencies_files |only 18 files changed, 585 insertions(+), 402 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.5 dated 2015-04-29 and 0.6 dated 2015-10-01
DESCRIPTION | 10 - MD5 | 102 +++++++++------ NAMESPACE | 5 NEWS | 10 + R/RcppExports.R | 24 ++- R/filter.R | 41 +++++- R/jiebar.R | 48 +++++-- R/print.R | 11 + R/quick.R | 2 R/segment.R | 21 ++- R/tagger.R | 17 +- R/words_freq.R |only R/zzz.R | 3 README.md | 3 build/vignette.rds |binary inst/include/jiebaRAPI.h |only inst/include/lib/DictTrie.hpp | 7 - inst/include/lib/HMMSegment.hpp | 2 inst/include/segtype.hpp | 253 ++++++++++++++++++++------------------ man/DICTPATH.Rd | 2 man/distance.Rd | 2 man/edit_dict.Rd | 2 man/filecoding.Rd | 2 man/filter_segment.Rd | 6 man/freq.Rd |only man/jiebaR.Rd | 2 man/keywords.Rd | 2 man/less-than-equals-.keywords.Rd | 2 man/less-than-equals-.qseg.Rd | 2 man/less-than-equals-.segment.Rd | 2 man/less-than-equals-.simhash.Rd | 2 man/less-than-equals-.tagger.Rd | 2 man/print.hmmseg.Rd | 5 man/segment.Rd | 2 man/set_qsegmodel.Rd | 2 man/show_dictpath.Rd | 2 man/simhash.Rd | 2 man/tagging.Rd | 2 man/worker.Rd | 8 - src/RcppExports.cpp | 146 ++++++++++++--------- src/detect.cpp | 3 src/init.c |only src/segtype.cpp | 99 ++++++++++---- src/word_freq.cpp |only tests/testthat/CPP_API |only tests/testthat/C_API |only tests/testthat/test-api.R |only tests/testthat/test-cut.R | 39 +++++ 48 files changed, 571 insertions(+), 326 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.6.0 dated 2015-03-31 and 0.7.0 dated 2015-10-01
DESCRIPTION | 17 +- MD5 | 58 ++++--- NAMESPACE | 37 ++++ R/confounders.R | 96 +++++++++++- R/confounders.emm.R | 119 +++++++++++++-- R/confounders.limit.R | 27 +++ R/confounders.poly.R | 114 +++++++++++++-- R/mbias.R |only R/misclassification.R | 79 +++++++++- R/multidimBias.R | 62 ++++++++ R/plot.mbias.R |only R/print.mbias.R |only R/probsens.R | 311 +++++++++++++++++++++++++++++++++++------ R/probsens.conf.R | 245 ++++++++++++++++++++++++++++---- R/probsens.irr.R |only R/probsens.irr.conf.R |only R/probsens.sel.R | 101 +++++++++++-- R/selection.R | 40 +++++ README.md | 105 +++++++++++++ man/confounders.Rd | 128 +++++++++------- man/confounders.emm.Rd | 161 +++++++++++---------- man/confounders.limit.Rd | 54 ++++--- man/confounders.poly.Rd | 170 +++++++++++----------- man/mbias.Rd |only man/misclassification.Rd | 121 ++++++++------- man/multidimBias.Rd | 128 +++++++++------- man/plot.mbias.Rd |only man/print.mbias.Rd |only man/probsens.Rd | 145 ++++++++++--------- man/probsens.conf.Rd | 114 ++++++++------- man/probsens.irr.Rd |only man/probsens.irr.conf.Rd |only man/probsens.sel.Rd | 88 ++++++----- man/selection.Rd | 74 +++++---- tests/testthat/test-probsens.R | 154 ++++++++++++++++++++ 35 files changed, 2064 insertions(+), 684 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.2 dated 2015-09-01 and 0.0.3 dated 2015-10-01
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 1 NEWS | 7 ++ R/epifit-package.R | 7 +- R/epifit.R | 75 ++++++++++++++------- R/modules.R | 172 +++++++++++++++++++++++++++++++------------------- R/pytable.R |only man/epifit-package.Rd | 7 +- man/epifit.Rd | 42 +++++++++--- man/pytable.Rd |only 11 files changed, 223 insertions(+), 114 deletions(-)
Title: Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Description: Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Author: Mathias Borritz Milfeldt [aut, cre]
Maintainer: Mathias Borritz Milfeldt <mathias@milfeldt.dk>
Diff between epandist versions 1.0.0 dated 2015-09-27 and 1.0.1 dated 2015-10-01
DESCRIPTION | 6 ++-- MD5 | 34 +++++++++++++------------- R/cepan.R | 2 - R/depan.R | 2 - R/evepan.R | 4 +-- R/pepan.R | 2 - R/qepan.R | 2 - R/repan.R | 2 - inst/doc/Vignette_epandist.R | 15 ++++++++++- inst/doc/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- inst/doc/Vignette_epandist.html | 51 +++++++++++++++++++++++++++++++--------- man/cepan.Rd | 2 - man/depan.Rd | 2 - man/evepan.Rd | 4 +-- man/pepan.Rd | 2 - man/qepan.Rd | 2 - man/repan.Rd | 2 - vignettes/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- 18 files changed, 168 insertions(+), 54 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.2 dated 2015-09-17 and 2.2.3 dated 2015-10-01
DESCRIPTION | 8 MD5 | 18 - NEWS | 9 inst/CITATION | 37 +- inst/doc/dbmss.R | 2 inst/doc/dbmss.Rnw | 18 - inst/doc/dbmss.pdf |binary man/dbmss-package.Rd | 4 vignettes/dbmss.Rnw | 18 - vignettes/dbmss.bib | 816 +++++++++++++++++++++++++-------------------------- 10 files changed, 474 insertions(+), 456 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: The R package clere implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma DB et al. - 2013).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1 dated 2014-02-21 and 1.1.1 dated 2015-10-01
clere-1.1.1/clere/DESCRIPTION | 22 ++-- clere-1.1.1/clere/MD5 | 46 ++++++---- clere-1.1.1/clere/NAMESPACE | 5 + clere-1.1.1/clere/R/Clere.R | 91 ------------------- clere-1.1.1/clere/R/fitClere.R |only clere-1.1.1/clere/R/fitPacs.R |only clere-1.1.1/clere/build |only clere-1.1.1/clere/data |only clere-1.1.1/clere/inst |only clere-1.1.1/clere/man/Clere-class.Rd | 138 ++++++++++++++---------------- clere-1.1.1/clere/man/Pacs-class.Rd |only clere-1.1.1/clere/man/algoComp.Rd |only clere-1.1.1/clere/man/clere-package.Rd | 35 +++---- clere-1.1.1/clere/man/clusters-methods.Rd | 18 +-- clere-1.1.1/clere/man/fitClere.Rd |only clere-1.1.1/clere/man/fitPacs.Rd |only clere-1.1.1/clere/man/is.clere.Rd | 16 +-- clere-1.1.1/clere/man/numExpRealData.Rd |only clere-1.1.1/clere/man/numExpSimData.Rd |only clere-1.1.1/clere/man/plot-methods.Rd | 16 +-- clere-1.1.1/clere/man/predict-methods.Rd | 18 +-- clere-1.1.1/clere/man/summary-methods.Rd | 16 +-- clere-1.1.1/clere/src/Model.cpp | 26 +++-- clere-1.1.1/clere/src/clere.cpp | 8 - clere-1.1.1/clere/src/pacs.cpp |only clere-1.1.1/clere/vignettes |only clere-1.1/clere/R/fit.clere.R |only clere-1.1/clere/man/fit.clere.Rd |only clere-1.1/clere/man/ggPlot-methods.Rd |only 29 files changed, 190 insertions(+), 265 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) may be used to select the best combination of variables and shapes. This package depends on the R package coneproj.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between cgam versions 1.2 dated 2014-09-10 and 1.3 dated 2015-10-01
DESCRIPTION | 13 +-- MD5 | 10 +- NAMESPACE | 5 + R/cgam.R | 193 +++++++++++++++++++++++++++++++++++++++++++------------ man/cgam.Rd | 4 - man/plotpersp.Rd | 26 +++++-- 6 files changed, 189 insertions(+), 62 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 0.5.8 dated 2014-07-02 and 1.0.0 dated 2015-10-01
SpatialTools-0.5.8/SpatialTools/R/old_code.R |only SpatialTools-0.5.8/SpatialTools/man/mspe.uk.Rd |only SpatialTools-0.5.8/SpatialTools/man/pweights.uk.Rd |only SpatialTools-1.0.0/SpatialTools/DESCRIPTION | 10 - SpatialTools-1.0.0/SpatialTools/MD5 | 25 +- SpatialTools-1.0.0/SpatialTools/NAMESPACE | 10 - SpatialTools-1.0.0/SpatialTools/NEWS | 2 SpatialTools-1.0.0/SpatialTools/R/arg_check.R | 110 ----------- SpatialTools-1.0.0/SpatialTools/R/contour_tools.R | 4 SpatialTools-1.0.0/SpatialTools/R/cov.R | 4 SpatialTools-1.0.0/SpatialTools/R/generate_norm.R | 2 SpatialTools-1.0.0/SpatialTools/R/krige_tools.R | 194 +-------------------- SpatialTools-1.0.0/SpatialTools/man/krige.ok.Rd | 11 - SpatialTools-1.0.0/SpatialTools/man/krige.sk.Rd | 10 - SpatialTools-1.0.0/SpatialTools/man/krige.uk.Rd | 10 - 15 files changed, 61 insertions(+), 331 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.4.1 dated 2014-09-07 and 1.5 dated 2015-10-01
Rsomoclu-1.4.1/Rsomoclu/src/somocluWrap.h |only Rsomoclu-1.4.1/Rsomoclu/src/trainOneEpoch.cpp |only Rsomoclu-1.5/Rsomoclu/DESCRIPTION | 12 - Rsomoclu-1.5/Rsomoclu/MD5 | 32 +- Rsomoclu-1.5/Rsomoclu/R/Rsomoclu.R | 19 + Rsomoclu-1.5/Rsomoclu/configure |only Rsomoclu-1.5/Rsomoclu/data/rgbs.txt.gz |binary Rsomoclu-1.5/Rsomoclu/man/Rsomoclu.train.Rd | 46 ++-- Rsomoclu-1.5/Rsomoclu/src/Makefile.in |only Rsomoclu-1.5/Rsomoclu/src/Makefile.root.in |only Rsomoclu-1.5/Rsomoclu/src/Rsomoclu.cpp | 238 +++++++-------------- Rsomoclu-1.5/Rsomoclu/src/config.h.in |only Rsomoclu-1.5/Rsomoclu/src/configure |only Rsomoclu-1.5/Rsomoclu/src/denseCpuKernels.cpp | 88 ++++--- Rsomoclu-1.5/Rsomoclu/src/denseGpuKernels.cu |only Rsomoclu-1.5/Rsomoclu/src/install-sh |only Rsomoclu-1.5/Rsomoclu/src/mapDistanceFunctions.cpp | 62 +++-- Rsomoclu-1.5/Rsomoclu/src/somoclu.h | 152 +++++++------ Rsomoclu-1.5/Rsomoclu/src/sparseCpuKernels.cpp | 101 ++++---- Rsomoclu-1.5/Rsomoclu/src/training.cpp |only Rsomoclu-1.5/Rsomoclu/src/uMatrix.cpp | 35 +-- Rsomoclu-1.5/Rsomoclu/tests/R_interface_test.R | 8 22 files changed, 398 insertions(+), 395 deletions(-)
Title: Rcmdr Evidence Based Medicine Plug-in Package
Description: Rcmdr plug-in GUI extension for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...).
Author: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Maintainer: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Diff between RcmdrPlugin.EBM versions 1.0-8 dated 2014-09-08 and 1.0-10 dated 2015-10-01
DESCRIPTION | 12 - MD5 | 8 - NAMESPACE | 2 R/CrossTab.R | 429 ++++++++++++++++++++++++++++++----------------------------- inst/CHANGES | 4 5 files changed, 240 insertions(+), 215 deletions(-)
More information about RcmdrPlugin.EBM at CRAN
Permanent link
Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.4 dated 2015-08-04 and 0.4.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 4 ++-- R/manage_expansion_sim.R | 12 +----------- R/range_raster.R | 3 +-- build/vignette.rds |binary data/cabrera.rda |binary data/landscape_change.rda |binary data/mc_df.rda |binary data/occ.landscape.rda |binary data/occ.landscape2.rda |binary data/param1.rda |binary data/rg_exp.rda |binary data/rland.rda |binary inst/doc/MetaLandSim.pdf |binary inst/logo/logo.gif |binary inst/logo/logo2.gif |binary man/MetaLandSim-package.Rd | 4 ++-- 18 files changed, 27 insertions(+), 38 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.3 dated 2015-09-16 and 0.0.4 dated 2015-10-01
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- R/CheckInputs.R | 2 + R/Information.R | 39 ++++++++++++++++++++++++------------- R/create_infotables.R | 7 +++++- R/plot_infotables.R | 21 ++++++++++++++----- build/vignette.rds |binary inst/doc/Information-vignette.Rmd | 2 - inst/doc/Information-vignette.html | 4 +-- man/Information.Rd | 37 +++++++++++++++++++++++------------ man/create_infotables.Rd | 4 +-- man/plot_infotables.Rd | 21 ++++++++++++++----- vignettes/Information-vignette.Rmd | 2 - 13 files changed, 111 insertions(+), 60 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-4 dated 2015-09-17 and 0.4-0 dated 2015-10-01
DESCRIPTION | 8 +-- MD5 | 25 ++++++----- NAMESPACE | 3 - R/ICP.R | 64 +++++++++++++++++------------- R/getpval.R | 13 ++++-- R/getpvalClassif.R | 29 +++++++------ R/hiddenICP.R | 34 +++++++++++++-- R/plot.InvariantCausalPrediction.R | 2 R/print.InvariantCausalPrediction.R | 31 +++++++------- R/print.hiddenInvariantCausalPrediction.R |only R/pvalfunc.R | 19 +++++++- R/summary.InvariantCausalPrediction.R | 25 +---------- man/ICP.Rd | 61 +++++++++++++++------------- man/hiddenICP.Rd | 45 +++++++++++---------- 14 files changed, 206 insertions(+), 153 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.0 dated 2015-09-30 and 0.1.1 dated 2015-10-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include productivity evaluation using distance measures, benchmarking,
risk analysis, technology adoption model, inverse optimization, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.0 dated 2015-09-27 and 1.5 dated 2015-10-01
DESCRIPTION | 8 - MD5 | 40 ++++---- NAMESPACE | 1 R/DJL-internal.R | 251 ++++++++++++++++++++++++++--------------------------- R/dm.ddf.R | 7 - R/dm.sf.R | 7 - R/map.soa.ddf.R | 43 +++++---- R/map.soa.dea.R | 43 +++++---- R/map.soa.sbm.R | 41 +++++--- R/map.soa.sf.R | 43 +++++---- R/roc.dea.R | 7 - R/roc.sf.R |only man/dm.ddf.Rd | 11 +- man/dm.dea.Rd | 7 - man/dm.sbm.Rd | 8 - man/dm.sf.Rd | 9 - man/map.soa.ddf.Rd | 10 +- man/map.soa.dea.Rd | 11 +- man/map.soa.sbm.Rd | 10 +- man/map.soa.sf.Rd | 39 +++++--- man/roc.dea.Rd | 1 man/roc.sf.Rd |only 22 files changed, 338 insertions(+), 259 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with SparseM/Matrix are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 1.0-1 dated 2014-09-09 and 1.2-1 dated 2015-09-30
ChangeLog | 48 ++++++ DESCRIPTION | 14 + MD5 | 151 ++++++++++--------- NAMESPACE | 57 +++++-- R/constructors.R | 2 R/definitions.R | 34 ++-- R/dim.R | 8 - R/dist.R | 2 R/foreign.R | 28 +-- R/helper.R | 2 R/kronecker.R | 4 R/math.R | 58 +++---- R/permutation.R | 6 R/plotting.R | 2 R/profile.R | 2 R/rowcolstats.R | 8 - R/s4coerce.R | 3 R/spam_solve.R | 34 ++-- R/spamlist.R | 2 R/subset.R | 41 +++-- R/tailhead.R | 2 R/tcrossprod.R | 6 R/toepliz.R | 4 R/xybind.R | 2 build |only demo/00Index | 8 - demo/article-jss-example1.R | 210 --------------------------- demo/article-jss-example2.R | 231 ------------------------------ demo/jss10-example1.R |only demo/jss10-example2.R |only demo/jss15-BYM.R |only demo/jss15-Leroux.R |only inst/CITATION | 17 ++ inst/NEWS | 43 +++++ inst/doc |only man/coerce.Rd | 10 + man/coercion.Rd | 1 man/diag.Rd | 14 - man/foreign.Rd | 24 +-- man/math.Rd | 5 man/operations.Rd | 12 - man/pad.Rd | 2 man/spam-deprecated.Rd |only tests/constructors.R | 7 tests/constructors.Rout.save | 13 + tests/covmat.Rout.save | 10 - tests/crossprod.Rout.save | 10 - tests/demo_article-jss-example1.Rout.save | 10 - tests/demo_article-jss-example2.Rout.save | 10 - tests/demo_article-jss.Rout.save | 10 - tests/demo_cholesky.Rout.save | 10 - tests/demo_jss15-BYM.R |only tests/demo_jss15-BYM.Rout.save |only tests/demo_jss15-Leroux.R |only tests/demo_jss15-Leroux.Rout.save |only tests/demo_spam.Rout.save | 10 - tests/demo_timing.Rout.save | 10 - tests/diff.Rout.save | 10 - tests/dim.R | 5 tests/dim.Rout.save | 73 +-------- tests/displays.Rout.save | 10 - tests/dist.Rout.save | 10 - tests/foreign.Rout.save | 8 - tests/helper.Rout.save | 10 - tests/jss_areal_counts.R | 6 tests/jss_areal_counts.Rout.save | 16 +- tests/kronecker.Rout.save | 10 - tests/math.R | 2 tests/math.Rout.save | 16 +- tests/mle.Rout.save | 10 - tests/norm.Rout.save | 10 - tests/ops.R | 2 tests/ops.Rout.save | 107 ------------- tests/overall.Rout.save | 10 - tests/permutation.Rout.save | 10 - tests/rowcolstats.Rout.save | 10 - tests/solve.R | 6 tests/solve.Rout.save | 16 -- tests/spamlist.Rout.save | 10 - tests/subsetting.Rout.save | 10 - tests/xybind.Rout.save | 10 - vignettes |only 82 files changed, 597 insertions(+), 987 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Description: Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ<matthias.templ@gmail.com>
Diff between simPop versions 0.2.13 dated 2015-09-21 and 0.2.15 dated 2015-09-30
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- NEWS | 8 +++++ R/simContinuous.R | 62 +++++++++++++++++++++++++++++------------- R/utils.R | 72 ++++++++++++++++++++++++++++--------------------- man/set_get-methods.Rd | 3 -- man/simContinuous.Rd | 4 ++ 7 files changed, 107 insertions(+), 62 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.2-09 dated 2015-08-26 and 1.3-01 dated 2015-09-30
DESCRIPTION | 11 +++++++---- MD5 | 28 ++++++++++++++++------------ NAMESPACE | 2 ++ NEWS | 15 ++++++++++++++- R/SampleSize_HVNTID.R |only R/power_HVNTID.R |only R/power_RSABE.R | 24 +++++++++++++----------- R/power_RSABE_NTID.R | 23 ++++++++++++++--------- R/power_TOST_sim.R | 12 ++++++++++++ R/power_scABEL.R | 21 ++++++++++++--------- inst/doc/Implementation_scaledABE_sims.pdf |binary man/power.HVNTID.Rd |only man/power.NTIDFDA.Rd | 26 ++++++++++++++------------ man/power.RSABE.Rd | 14 ++++++++++---- man/power.scABEL.Rd | 20 ++++++++++++-------- man/sampleN.HVNTID.Rd |only man/sampleN.NTIDFDA.Rd | 19 ++++++++++--------- 17 files changed, 136 insertions(+), 79 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.2 dated 2015-05-26 and 0.2.1 dated 2015-09-30
DESCRIPTION | 6 LICENSE | 4 MD5 | 30 +-- NAMESPACE | 10 - R/core.R | 248 ++++++++++++++-------------- R/helpers.R | 96 +++++----- inst/extdata/sql1.sql | 12 - man/infuse.Rd | 64 +++---- man/print.infuse.Rd | 34 +-- man/print_requested_params.Rd | 30 +-- man/read_template.Rd | 30 +-- man/trim.Rd | 30 +-- man/variables_requested.Rd | 44 ++-- tests/testthat.R | 8 tests/testthat/test_core_functionality.R | 244 ++++++++++++++------------- tests/testthat/test_helpers_functionality.R | 46 ++--- 16 files changed, 474 insertions(+), 462 deletions(-)
Title: File Abstraction Interface Layer (FAIL)
Description: More comfortable interface to work with R data or source files
in a key-value fashion.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between fail versions 1.2 dated 2013-09-19 and 1.3 dated 2015-09-30
fail-1.2/fail/inst |only fail-1.3/fail/DESCRIPTION | 17 +-- fail-1.3/fail/MD5 | 48 ++++---- fail-1.3/fail/NAMESPACE | 8 + fail-1.3/fail/NEWS | 17 +-- fail-1.3/fail/R/backends.R | 20 ++- fail-1.3/fail/R/cache.R | 14 +- fail-1.3/fail/R/constructor.R | 40 ++++--- fail-1.3/fail/R/fail.R | 25 ++-- fail-1.3/fail/R/helper.R | 76 +++---------- fail-1.3/fail/R/methods.R | 32 ++--- fail-1.3/fail/R/sail.R | 33 +++-- fail-1.3/fail/R/worker.R | 26 ++-- fail-1.3/fail/R/zzz.R | 9 + fail-1.3/fail/man/fail.Rd | 228 +++++++++++++++++++---------------------- fail-1.3/fail/man/sail.Rd | 53 +++++---- fail-1.3/fail/tests/test_all.R | 3 fail-1.3/fail/tests/testthat |only 18 files changed, 322 insertions(+), 327 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.3.0 dated 2015-09-12 and 0.3.1 dated 2015-09-30
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NAMESPACE | 1 R/base.R | 33 ++++++++++++------ R/docopulae.R | 1 R/examples/main.R | 2 - R/main.R | 96 ++++++++++++++++++++++++++++++------------------------ README.md | 2 - man/buildf.Rd | 11 ++---- man/expr2f.Rd | 3 - man/param.Rd | 2 - 11 files changed, 100 insertions(+), 79 deletions(-)
Title: Changepoint Analysis
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(), cpt.meanvar() functions should be your first point of call.
Author: Rebecca Killick [aut, cre],
Kaylea Haynes [aut],
Idris Eckley [aut],
Paul Fearnhead [ctb],
Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between changepoint versions 2.0.1 dated 2015-07-27 and 2.1.1 dated 2015-09-30
DESCRIPTION | 12 - MD5 | 18 +- NEWS | 9 + R/penalty_decision.R | 12 - R/range_of_penalties.R | 2 R/zzz.R | 2 man/changepoint-package.Rd | 6 src/BinSeg_one_func_minseglen.c | 66 +++++++- src/PELT_one_func_minseglen.c | 306 ++++++++++++++++++---------------------- src/cost_general_functions.c | 168 +++++++-------------- 10 files changed, 294 insertions(+), 307 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables. The main target is to uncover complicated patterns in multivariate data wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.22 dated 2015-08-31 and 2.23 dated 2015-09-30
BDgraph-2.22/BDgraph/R/I.g.R |only BDgraph-2.22/BDgraph/man/I.g.Rd |only BDgraph-2.22/BDgraph/man/plot.simulate.Rd |only BDgraph-2.22/BDgraph/man/print.simulate.Rd |only BDgraph-2.22/BDgraph/src/BDgraph.cpp |only BDgraph-2.23/BDgraph/DESCRIPTION | 10 BDgraph-2.23/BDgraph/MD5 | 89 ++-- BDgraph-2.23/BDgraph/NAMESPACE | 24 - BDgraph-2.23/BDgraph/NEWS | 9 BDgraph-2.23/BDgraph/R/bdgraph.R | 531 +++++++++++++++------------ BDgraph-2.23/BDgraph/R/bdgraph.sim.R | 30 - BDgraph-2.23/BDgraph/R/compare.R | 140 ++++--- BDgraph-2.23/BDgraph/R/log_Ig.R |only BDgraph-2.23/BDgraph/R/phat.R | 35 - BDgraph-2.23/BDgraph/R/plotcoda.R | 46 +- BDgraph-2.23/BDgraph/R/plotroc.R | 80 +--- BDgraph-2.23/BDgraph/R/prob.R | 44 +- BDgraph-2.23/BDgraph/R/rgwish.R | 32 - BDgraph-2.23/BDgraph/R/rwish.R | 17 BDgraph-2.23/BDgraph/R/select.R | 71 +-- BDgraph-2.23/BDgraph/R/traceplot.R | 37 - BDgraph-2.23/BDgraph/man/BDgraph-internal.Rd | 1 BDgraph-2.23/BDgraph/man/BDgraph-package.Rd | 18 BDgraph-2.23/BDgraph/man/CellSignal.Rd | 6 BDgraph-2.23/BDgraph/man/bdgraph.Rd | 50 +- BDgraph-2.23/BDgraph/man/bdgraph.npn.Rd | 4 BDgraph-2.23/BDgraph/man/bdgraph.sim.Rd | 70 +-- BDgraph-2.23/BDgraph/man/compare.Rd | 34 - BDgraph-2.23/BDgraph/man/geneExpression.Rd | 4 BDgraph-2.23/BDgraph/man/log_Ig.Rd |only BDgraph-2.23/BDgraph/man/phat.Rd | 22 - BDgraph-2.23/BDgraph/man/plot.bdgraph.Rd | 32 + BDgraph-2.23/BDgraph/man/plot.sim.Rd |only BDgraph-2.23/BDgraph/man/plotcoda.Rd | 27 - BDgraph-2.23/BDgraph/man/plotroc.Rd | 18 BDgraph-2.23/BDgraph/man/print.bdgraph.Rd | 17 BDgraph-2.23/BDgraph/man/print.sim.Rd |only BDgraph-2.23/BDgraph/man/prob.Rd | 30 - BDgraph-2.23/BDgraph/man/rgwish.Rd | 14 BDgraph-2.23/BDgraph/man/rwish.Rd | 11 BDgraph-2.23/BDgraph/man/select.Rd | 33 - BDgraph-2.23/BDgraph/man/summary.bdgraph.Rd | 26 - BDgraph-2.23/BDgraph/man/surveyData.Rd | 8 BDgraph-2.23/BDgraph/man/traceplot.Rd | 18 BDgraph-2.23/BDgraph/src/Ig.cpp |only BDgraph-2.23/BDgraph/src/copula.cpp |only BDgraph-2.23/BDgraph/src/copula.h |only BDgraph-2.23/BDgraph/src/gcgm_bd.cpp |only BDgraph-2.23/BDgraph/src/gcgm_rj.cpp |only BDgraph-2.23/BDgraph/src/ggm_bd.cpp |only BDgraph-2.23/BDgraph/src/ggm_rj.cpp |only BDgraph-2.23/BDgraph/src/matrix.cpp |only BDgraph-2.23/BDgraph/src/matrix.h |only BDgraph-2.23/BDgraph/src/rgwish.cpp |only BDgraph-2.23/BDgraph/src/rgwish.h |only BDgraph-2.23/BDgraph/src/scaleFree.cpp |only 56 files changed, 878 insertions(+), 760 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 1.3.1 dated 2015-07-08 and 1.4.0 dated 2015-09-30
DESCRIPTION | 8 - MD5 | 11 +- NAMESPACE | 3 R/BAT.R | 265 ++++++++++++++++++++++++++++++++++++++++++++++++----- man/alpha.accum.Rd | 2 man/gdm.Rd |only man/iaor.Rd |only man/sar.Rd |only 8 files changed, 257 insertions(+), 32 deletions(-)
Title: Tools for Selective Inference
Description: New tools for inference after selection, for use
with forward stepwise regression, least angle regression, the
lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor,
Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.1.0 dated 2015-09-20 and 1.1.1 dated 2015-09-30
DESCRIPTION | 12 ++++---- MD5 | 50 ++++++++++++++++++++----------------- NAMESPACE | 11 +++++--- R/funs.common.R | 1 R/funs.fixed.R | 10 +++++++ R/funs.fs.R | 23 ++++++++--------- R/funs.groupfs.R |only R/funs.inf.R | 8 ++++- R/funs.lar.R | 31 +++++++++++++--------- R/funs.quadratic.R |only man/estimateLambda.Rd | 2 - man/estimateSigma.Rd | 2 - man/factorDesign.Rd |only man/fixedLassoInf.Rd | 7 ++--- man/forwardStop.Rd | 2 - man/fs.Rd | 29 +++++++++++---------- man/fsInf.Rd | 9 +++--- man/groupfs.Rd |only man/groupfsInf.Rd |only man/lar.Rd | 5 ++- man/larInf.Rd | 7 ++--- man/manyMeans.Rd | 4 +- man/plot.fs.Rd | 2 - man/plot.lar.Rd | 2 - man/predict.fs.Rd | 2 - man/predict.lar.Rd | 2 - man/scaleGroups.Rd |only man/selectiveInference-internal.Rd | 2 - man/selectiveInference.Rd | 23 ++++++++++++++--- 29 files changed, 150 insertions(+), 96 deletions(-)
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Title: Parametric Network Enrichment Analysis
Description: Collection of functions for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.1.0 dated 2015-09-09 and 1.1.1 dated 2015-09-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pnea.R | 16 ++++++++++------ build/partial.rdb |binary man/pnea.Rd | 12 ++++++++---- man/summary.pnea.Rd | 4 +--- 6 files changed, 28 insertions(+), 22 deletions(-)
Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a
wide range of frailty distributions using a consistent and
asymptotically-normal estimator. Currently supports: gamma, power variance
function, log-normal, and inverse Gaussian frailty models.
Author: John V. Monaco [aut, cre],
Malka Gorfine [aut],
Li Hsu [aut]
Maintainer: John V. Monaco <vincent@vmonaco.com>
Diff between frailtySurv versions 1.2.1 dated 2015-09-28 and 1.2.2 dated 2015-09-30
DESCRIPTION | 8 +++--- MD5 | 8 +++--- README.md | 29 +++++++++++++++--------- src/distributions.cpp | 60 +++++++++++++++++++++++++------------------------- src/estimators.cpp | 28 +++++++++++------------ 5 files changed, 70 insertions(+), 63 deletions(-)
Title: Multiple Change-Point Detection for Nonstationary Time Series
Description: Implements detection for the number and locations of
the change-points in a time series using the Wild Binary Segmentation and
the Locally Stationary Wavelet model.
Author: Karolos Korkas and Piotr Fryzlewicz
Maintainer: Karolos Korkas <kkorkas@yahoo.co.uk>
Diff between wbsts versions 0.1 dated 2015-08-23 and 0.3 dated 2015-09-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/post.processing.Rd | 24 ++++++++++++------------ man/tau.fun.Rd | 2 +- man/uh.wbs.Rd | 2 +- src/innerProd.c | 7 ++++++- 6 files changed, 28 insertions(+), 23 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al (doi: 10.2307/2533043) and the two level random effects model in Beath and Heller (doi: 10.1177/1471082X0800900302). Exampels are given for their use in diagnostic testing.
Author: Ken Beath <ken.beath@mq.edu.au>
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-2 dated 2015-01-09 and 1.0-3 dated 2015-09-30
randomLCA-1.0-2/randomLCA/R/calc.cond.prob.R |only randomLCA-1.0-2/randomLCA/R/calc.cond2.prob.R |only randomLCA-1.0-2/randomLCA/R/calc.marg.prob.R |only randomLCA-1.0-2/randomLCA/R/class.probs.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/fit.adapt.random.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/fit.adapt.random2.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/fit.fixed.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/misc.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/norm.gauss.hermite.R |only randomLCA-1.0-2/randomLCA/R/outcome.probs.randomLCA.R |only randomLCA-1.0-2/randomLCA/R/post.class.probs.randomLCA.R |only randomLCA-1.0-2/randomLCA/man/calc.cond.prob.Rd |only randomLCA-1.0-2/randomLCA/man/calc.cond2.prob.Rd |only randomLCA-1.0-2/randomLCA/man/calc.marg.prob.Rd |only randomLCA-1.0-2/randomLCA/man/class.probs.Rd |only randomLCA-1.0-2/randomLCA/man/outcome.probs.Rd |only randomLCA-1.0-2/randomLCA/man/post.class.probs.Rd |only randomLCA-1.0-2/randomLCA/man/summary.Rd |only randomLCA-1.0-3/randomLCA/DESCRIPTION | 10 randomLCA-1.0-3/randomLCA/MD5 | 84 +- randomLCA-1.0-3/randomLCA/NAMESPACE | 21 randomLCA-1.0-3/randomLCA/R/bestlca.R | 63 - randomLCA-1.0-3/randomLCA/R/calcCond2Prob.R |only randomLCA-1.0-3/randomLCA/R/calcCondProb.R |only randomLCA-1.0-3/randomLCA/R/calcMargProb.R |only randomLCA-1.0-3/randomLCA/R/classProbs.R |only randomLCA-1.0-3/randomLCA/R/fitAdaptRandom.R |only randomLCA-1.0-3/randomLCA/R/fitAdaptRandom2.R |only randomLCA-1.0-3/randomLCA/R/fitFixed.R |only randomLCA-1.0-3/randomLCA/R/misc.R |only randomLCA-1.0-3/randomLCA/R/normGaussHermite.R |only randomLCA-1.0-3/randomLCA/R/outcomeProbs.R |only randomLCA-1.0-3/randomLCA/R/plot.randomLCA.R | 219 ++++-- randomLCA-1.0-3/randomLCA/R/postClassProbs.R |only randomLCA-1.0-3/randomLCA/R/randomLCA.R | 338 ++++----- randomLCA-1.0-3/randomLCA/R/refit.randomLCA.R | 134 +-- randomLCA-1.0-3/randomLCA/R/summary.randomLCA.R | 22 randomLCA-1.0-3/randomLCA/build/vignette.rds |binary randomLCA-1.0-3/randomLCA/data/pap.RData |only randomLCA-1.0-3/randomLCA/inst/NEWS | 18 randomLCA-1.0-3/randomLCA/inst/doc/randomLCA-example.Rnw | 401 ++++++++++- randomLCA-1.0-3/randomLCA/inst/doc/randomLCA-example.pdf |binary randomLCA-1.0-3/randomLCA/man/AIC.Rd | 3 randomLCA-1.0-3/randomLCA/man/AIC3.Rd |only randomLCA-1.0-3/randomLCA/man/calcCond2Prob.Rd |only randomLCA-1.0-3/randomLCA/man/calcCondProb.Rd |only randomLCA-1.0-3/randomLCA/man/calcMargProb.Rd |only randomLCA-1.0-3/randomLCA/man/classProbs.Rd |only randomLCA-1.0-3/randomLCA/man/dentistry.Rd | 7 randomLCA-1.0-3/randomLCA/man/fitted.Rd | 36 randomLCA-1.0-3/randomLCA/man/genderrole.Rd | 119 +-- randomLCA-1.0-3/randomLCA/man/hivtests.Rd | 12 randomLCA-1.0-3/randomLCA/man/myocardial.Rd | 3 randomLCA-1.0-3/randomLCA/man/outcomeProbs.Rd |only randomLCA-1.0-3/randomLCA/man/pap.Rd |only randomLCA-1.0-3/randomLCA/man/plot.Rd | 3 randomLCA-1.0-3/randomLCA/man/postClassProbs.Rd |only randomLCA-1.0-3/randomLCA/man/print.randomLCA.Rd |only randomLCA-1.0-3/randomLCA/man/randomLCA.Rd | 175 ++-- randomLCA-1.0-3/randomLCA/man/summary.randomLCA.Rd |only randomLCA-1.0-3/randomLCA/man/symptoms.Rd | 3 randomLCA-1.0-3/randomLCA/man/uterinecarcinoma.Rd | 8 randomLCA-1.0-3/randomLCA/vignettes/randomLCA-exampleTex.tex | 14 63 files changed, 1096 insertions(+), 597 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong <ykong@cuhk.edu.hk>
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.3.1 dated 2015-08-15 and 1.3.2 dated 2015-09-29
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/joint.1z.R | 25 +++++++++++-------------- R/joint.1z0.R | 15 ++++++--------- R/joint.1z01.R | 23 +++++++++-------------- R/joint.1z1.R | 17 +++++++---------- R/joint.2z.R | 39 +++++++++++++++++++++------------------ R/joint.2z0.R | 40 ++++++++++++++++++++-------------------- R/joint.2z01.R | 45 ++++++++++++++++++++++----------------------- R/joint.2z1.R | 42 +++++++++++++++++++++--------------------- R/sep.2z.R | 28 ++++++++++++++++------------ R/sep.2z0.R | 25 ++++++++++++++----------- R/sep.2z01.R | 25 ++++++++++++++----------- R/sep.2z1.R | 27 +++++++++++++++------------ man/zoib-package.Rd | 4 ++-- man/zoib.Rd | 4 ++-- 16 files changed, 199 insertions(+), 198 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 1.0.1 dated 2015-09-24 and 1.0.2 dated 2015-09-29
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- R/ALL.r | 76 +++++++++++++++++++++++++++++++++++++----------- man/BBconsensus.Rd | 8 +++-- man/BBconsensus2.Rd | 2 - man/ConsRank-package.Rd | 4 +- man/FASTcons.Rd | 5 ++- man/QuickCons.Rd | 5 ++- 8 files changed, 86 insertions(+), 36 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between rfUtilities versions 1.0-1 dated 2015-02-24 and 1.0-2 dated 2015-09-29
DESCRIPTION | 10 +- MD5 | 30 +++---- R/rf.imp.freq.R |only R/rf.modelSel.R | 187 ++++++++++++++++++++++---------------------- R/rf.partial.ci.R | 2 R/rf.partial.prob.R | 22 ++--- R/rf.significance.R | 40 ++++----- inst/NEWS | 6 + man/multi.collinear.Rd | 4 man/rf.class.sensitivity.Rd | 2 man/rf.classBalance.Rd | 2 man/rf.crossValidation.Rd | 2 man/rf.imp.freq.Rd |only man/rf.modelSel.Rd | 21 +++- man/rf.partial.ci.Rd | 2 man/rf.partial.prob.Rd | 2 man/rf.significance.Rd | 2 17 files changed, 175 insertions(+), 159 deletions(-)
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Title: Protracted Birth-Death Model of Diversification
Description: Conducts maximum likelihood analysis and simulation of the protracted speciation model.
Author: Rampal S. Etienne
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between PBD versions 1.0 dated 2014-05-26 and 1.1 dated 2015-09-29
PBD-1.0/PBD/R/brts2phylo.R |only PBD-1.1/PBD/DESCRIPTION | 15 +-- PBD-1.1/PBD/MD5 | 16 +-- PBD-1.1/PBD/NAMESPACE | 7 + PBD-1.1/PBD/R/pbd_ML.R | 1 PBD-1.1/PBD/R/pbd_sim.R | 186 ++++++++++------------------------------ PBD-1.1/PBD/R/pbd_utils.R |only PBD-1.1/PBD/man/PBD-internal.Rd | 8 + PBD-1.1/PBD/man/PBD-package.Rd | 10 +- PBD-1.1/PBD/man/pbd_sim.Rd | 22 +++- 10 files changed, 101 insertions(+), 164 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.4.3 dated 2015-07-28 and 0.5 dated 2015-09-29
DESCRIPTION | 17 +-- MD5 | 39 ++++--- NAMESPACE | 51 ++++++++-- R/SES.R | 248 ++++++++++++++++++++++++++++++------------------- R/censIndLR.R | 43 ++++---- R/gSquare.R | 17 +-- R/testIndBeta.R |only R/testIndFisher.R | 121 +++++++++++++---------- R/testIndLogistic.R | 157 +++++++++++++++++++------------ R/testIndNB.R |only R/testIndPois.R |only R/testIndRQ.R |only R/testIndReg.R |only man/MXM-package.Rd | 12 +- man/MXMCondIndTests.Rd |only man/SES.Rd | 17 ++- man/censIndLR.Rd | 13 +- man/cv.ses.Rd | 2 man/gSquare.Rd | 23 ++-- man/testIndBeta.Rd |only man/testIndFisher.Rd | 20 ++- man/testIndLogistic.Rd | 47 +++++---- man/testIndNB.Rd |only man/testIndPois.Rd |only man/testIndRQ.Rd |only man/testIndReg.Rd |only 26 files changed, 504 insertions(+), 323 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 0.5 dated 2015-06-24 and 0.6 dated 2015-09-29
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 5 +++++ R/generics.R | 25 ++++++++++++++----------- R/mams.sim.R | 4 +++- R/new.bounds.R | 37 ++++++++++++++++++++++++++++--------- R/step_down_mams.R | 2 +- inst/NEWS | 9 +++++++++ man/generic.Rd | 24 +++++++++++++----------- man/mams.Rd | 12 +++++------- man/mams.sim.Rd | 25 +++++++++++++------------ man/new.bounds.Rd | 18 +++++++++--------- man/step_down_mams.Rd | 27 +++++++++++++-------------- man/update_mams.Rd | 38 ++++++++++++++++++-------------------- 14 files changed, 148 insertions(+), 112 deletions(-)
Title: Calculation of Low Flow Statistics for Daily Stream Flow Data
Description: The "Manual on Low-flow Estimation and Prediction", published by the World Meteorological Organisation (WMO), gives a comprehensive summary on how to analyse stream flow data focusing on low-flows. This packages provides functions to compute the described statistics and produces plots similar to the ones in the manual.
Author: Daniel Koffler, Tobias Gauster and Gregor Laaha
Maintainer: Tobias Gauster <t.gauster@boku.ac.at>
Diff between lfstat versions 0.6.1 dated 2014-08-12 and 0.8.0 dated 2015-09-29
DESCRIPTION | 25 MD5 | 76 +- NAMESPACE | 130 +++- NEWS.md |only R/1NAs.R | 66 -- R/2processes.R | 305 +++++----- R/3lfindices.R | 1289 +++++++++++++++++++++++----------------------- R/5extreme.R | 733 +++++++++++++++++++++----- R/6streamdef.R | 306 ++++------ R/7multistation.R | 103 +-- R/hyear.R | 136 ++++ R/lfobj.R | 223 ++++--- R/methods.R | 88 +-- R/misc.R |only R/options.R | 34 - R/pooling.R |only R/readsheets.R | 163 ++--- README.md |only data/ngaruroro.rda |binary data/ray.rda |only man/BFI.Rd | 111 +-- man/as.xts.lfobj.Rd |only man/baseflow.Rd |only man/cdf_ev.Rd |only man/check_distribution.Rd |only man/createlfobj.Rd | 168 +++-- man/evfit.Rd |only man/evquantile.Rd |only man/find_droughts.Rd |only man/gringorten.Rd |only man/hyear_start.Rd |only man/ma.Rd |only man/ngaruroro.Rd | 39 - man/plot.deficit.Rd |only man/pool_ic.Rd |only man/rfa.Rd | 107 +-- man/rpline.Rd |only man/streamdef.Rd | 186 +++--- man/summary.deficit.Rd |only man/trace_value.Rd |only man/tyears.Rd | 181 +++--- man/tyearsS.Rd |only man/vary_threshold.Rd |only man/water_year.Rd |only tests |only 45 files changed, 2559 insertions(+), 1910 deletions(-)
Title: Kernel Factory: An Ensemble of Kernel Machines
Description: Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
Author: Michel Ballings, Dirk Van den Poel
Maintainer: Michel Ballings <Michel.Ballings@GMail.com>
Diff between kernelFactory versions 0.2.2 dated 2015-05-26 and 0.3.0 dated 2015-09-29
DESCRIPTION | 10 +++--- MD5 | 12 ++++---- NAMESPACE | 1 R/kernelFactory.R | 2 - R/predict.kernelFactory.R | 62 ++++++++++++++++++++++++++++++------------- inst/NEWS | 6 +++- man/predict.kernelFactory.Rd | 5 ++- 7 files changed, 66 insertions(+), 32 deletions(-)
Title: Examples of Neural Networks
Description: Implementations of several basic neural network concepts in R, as based on posts on \url{http://qua.st/}.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between learNN versions 0.1.0 dated 2015-09-08 and 0.2.0 dated 2015-09-29
DESCRIPTION | 6 - MD5 | 33 ++--- NAMESPACE | 19 +-- NEWS | 18 +-- R/learNN.R | 10 - R/learn_bp.R | 205 +++++++++++++++++------------------ R/learn_do.R | 179 +++++++++++++++++++++++------- R/learn_gd.R | 237 ++++++++++++++++++++--------------------- README.md | 144 ++++++++++++------------ man/learn_bp.Rd | 75 ++++++------ man/learn_bp11.Rd | 68 ++++++----- man/learn_do.Rd |only man/learn_do15.Rd | 96 ++++++++-------- man/learn_gd.Rd | 96 ++++++++-------- man/learn_gd13.Rd | 72 ++++++------ man/learnn.Rd | 22 +-- tests/testthat.R | 8 - tests/testthat/test_learn_bp.R | 44 +++---- 18 files changed, 725 insertions(+), 607 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb],
R Core Team [ctb, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd9 versions 1.2.2 dated 2015-09-08 and 1.3 dated 2015-09-29
icd9-1.2.2/icd9/configure.ac |only icd9-1.2.2/icd9/tools |only icd9-1.3/icd9/DESCRIPTION | 22 icd9-1.3/icd9/MD5 | 124 icd9-1.3/icd9/NAMESPACE | 2 icd9-1.3/icd9/R/RcppExports.R | 111 icd9-1.3/icd9/R/benchmark.R | 102 icd9-1.3/icd9/R/comorbid.R | 41 icd9-1.3/icd9/R/convert.R | 13 icd9-1.3/icd9/R/explain.R | 6 icd9-1.3/icd9/R/score.R | 35 icd9-1.3/icd9/R/util.R | 68 icd9-1.3/icd9/R/zzz.R | 38 icd9-1.3/icd9/README.md | 33 icd9-1.3/icd9/cleanup | 2 icd9-1.3/icd9/configure | 3425 +++++++++++++++----------- icd9-1.3/icd9/inst/doc/introduction.R | 9 icd9-1.3/icd9/inst/doc/introduction.Rmd | 24 icd9-1.3/icd9/inst/doc/introduction.html | 34 icd9-1.3/icd9/inst/include/icd9_RcppExports.h | 455 ++- icd9-1.3/icd9/man/convert.Rd | 9 icd9-1.3/icd9/man/factor_.Rd |only icd9-1.3/icd9/man/fastIntToString.Rd |only icd9-1.3/icd9/man/icd9ChaptersToMap.Rd | 5 icd9-1.3/icd9/man/icd9Charlson.Rd | 26 icd9-1.3/icd9/man/icd9Comorbid.Rd | 19 icd9-1.3/icd9/man/icd9DropLeadingZeroes.Rd | 5 icd9-1.3/icd9/man/icd9GetMajor.Rd | 7 icd9-1.3/icd9/man/icd9LongToWide.Rd | 5 icd9-1.3/icd9/man/icd9RandomShort.Rd |only icd9-1.3/icd9/man/icd9RandomShortE.Rd |only icd9-1.3/icd9/man/icd9RandomShortN.Rd |only icd9-1.3/icd9/man/icd9RandomShortV.Rd |only icd9-1.3/icd9/man/icd9ShortToDecimal.Rd | 4 icd9-1.3/icd9/man/icd9WideToLong.Rd | 5 icd9-1.3/icd9/src/Makevars.in | 11 icd9-1.3/icd9/src/RcppExports.cpp | 670 ++++- icd9-1.3/icd9/src/comorbid.cpp | 150 - icd9-1.3/icd9/src/comorbidCommon.cpp | 205 - icd9-1.3/icd9/src/comorbidSetup.cpp | 32 icd9-1.3/icd9/src/config.h.in | 15 icd9-1.3/icd9/src/config.h.win | 40 icd9-1.3/icd9/src/convert.cpp | 250 + icd9-1.3/icd9/src/convert.h | 21 icd9-1.3/icd9/src/cutil.c | 12 icd9-1.3/icd9/src/cutil.h | 12 icd9-1.3/icd9/src/is.cpp | 1 icd9-1.3/icd9/src/local.h | 69 icd9-1.3/icd9/src/longToWide.cpp | 38 icd9-1.3/icd9/src/manip.cpp | 70 icd9-1.3/icd9/src/manip.h | 3 icd9-1.3/icd9/src/ranges.cpp | 92 icd9-1.3/icd9/src/ranges.h | 2 icd9-1.3/icd9/src/util.cpp | 256 + icd9-1.3/icd9/src/util.h | 20 icd9-1.3/icd9/tests/testthat/test-billable.R | 1 icd9-1.3/icd9/tests/testthat/test-convert.R | 7 icd9-1.3/icd9/tests/testthat/test-openmp.R |only icd9-1.3/icd9/tests/testthat/test-score.R | 68 icd9-1.3/icd9/vignettes/introduction.Rmd | 24 60 files changed, 4490 insertions(+), 2208 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters 18: 844-852.
Author: Rampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart Haegenan
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 1.0.1 dated 2015-06-03 and 1.0.2 dated 2015-09-29
DESCRIPTION | 15 +++++----- MD5 | 48 +++++++++++++++++------------------ NAMESPACE | 6 +++- R/DAISIE_tutorial.R | 7 ++--- data/Galapagos_datalist.RData |binary data/Galapagos_datalist_2types.RData |binary data/Galapagos_datatable.RData |binary data/islands_10reps_RAW.RData |binary data/islands_1type_1000reps.RData |binary data/islands_2types_1000reps.RData |binary man/DAISIE-package.Rd | 8 ++--- man/DAISIE_ExpEIN.Rd | 3 -- man/DAISIE_ML.Rd | 3 -- man/DAISIE_dataprep.Rd | 3 -- man/DAISIE_format_sim.Rd | 3 -- man/DAISIE_loglik_all.Rd | 5 +-- man/DAISIE_plot_sims.Rd | 3 -- man/DAISIE_sim.Rd | 5 +-- man/DAISIE_tutorial.Rd | 8 +---- man/Galapagos_datalist.Rd | 3 -- man/Galapagos_datalist_2types.Rd | 3 -- man/Galapagos_datatable.Rd | 3 -- man/islands_10reps_RAW.Rd | 3 -- man/islands_1type_1000reps.Rd | 3 -- man/islands_2types_1000reps.Rd | 3 -- 25 files changed, 62 insertions(+), 73 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.0-3 dated 2015-08-14 and 1.0-4 dated 2015-09-29
partykit-1.0-3/partykit/inst/tmp |only partykit-1.0-4/partykit/DESCRIPTION | 8 +-- partykit-1.0-4/partykit/MD5 | 41 +++++++-------- partykit-1.0-4/partykit/NAMESPACE | 1 partykit-1.0-4/partykit/R/glmtree.R | 1 partykit-1.0-4/partykit/R/lmtree.R | 1 partykit-1.0-4/partykit/R/modelparty.R | 4 + partykit-1.0-4/partykit/R/party.R | 4 + partykit-1.0-4/partykit/R/plot.R | 64 +++++++++++++++--------- partykit-1.0-4/partykit/R/simpleparty.R | 12 +++- partykit-1.0-4/partykit/data/HuntingSpiders.rda |binary partykit-1.0-4/partykit/data/WeatherPlay.rda |binary partykit-1.0-4/partykit/inst/NEWS.Rd | 18 ++++++ partykit-1.0-4/partykit/inst/doc/constparty.pdf |binary partykit-1.0-4/partykit/inst/doc/ctree.pdf |binary partykit-1.0-4/partykit/inst/doc/mob.Rnw | 12 ++-- partykit-1.0-4/partykit/inst/doc/mob.pdf |binary partykit-1.0-4/partykit/inst/doc/partykit.pdf |binary partykit-1.0-4/partykit/man/panelfunctions.Rd | 6 +- partykit-1.0-4/partykit/man/party-methods.Rd | 1 partykit-1.0-4/partykit/vignettes/mob.Rnw | 12 ++-- partykit-1.0-4/partykit/vignettes/party.bib | 42 +++++++++------ 22 files changed, 143 insertions(+), 84 deletions(-)
Title: Tools for Reading and Handling Spatial Objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 0.8-36 dated 2015-04-24 and 0.8-37 dated 2015-09-29
ChangeLog | 34 +++++++++++ DESCRIPTION | 15 ++-- MD5 | 39 ++++++------ NAMESPACE | 9 +- R/colslegs.R | 45 +++++++++++--- R/nowrapRecenter.R | 124 ++++++++++++++++++++++++++++++++++++++--- R/sp_spat1.R | 28 +++++++++ R/spmaps.R | 30 ++++++++- build/vignette.rds |binary inst/ChangeLog | 34 +++++++++++ inst/doc/combine_maptools.R | 2 inst/doc/combine_maptools.Rnw | 4 - inst/doc/combine_maptools.pdf |binary man/as.ppp.Rd | 12 +++ man/gzAzimuth.Rd | 2 man/leglabs.Rd | 14 +++- man/map2SpatialPolygons.Rd | 11 +++ man/nowrapRecenter.Rd | 10 +-- man/nowrapSpatialLines.Rd |only man/sp2Mondrian.Rd | 2 vignettes/combine_maptools.Rnw | 4 - 21 files changed, 354 insertions(+), 65 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut],
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-26 dated 2014-12-09 and 0.6-28 dated 2015-09-28
ChangeLog | 440 +++++++++++++++++++++-------------------------------- DESCRIPTION | 18 +- MD5 | 18 +- NAMESPACE | 3 R/gwe.R | 6 build/vignette.rds |binary inst/ChangeLog | 440 +++++++++++++++++++++-------------------------------- inst/doc/GWR.pdf |binary man/georgia.Rd | 2 man/gw.cov.Rd | 12 + 10 files changed, 386 insertions(+), 553 deletions(-)
Title: Convolution-Based Nonstationary Spatial Modeling
Description: Fits convolution-based nonstationary
Gaussian process models to point-referenced spatial data. The nonstationary
covariance function allows the user to specify the underlying correlation
structure and which spatial dependence parameters should be allowed to
vary over space: the anisotropy, nugget variance, and process variance.
The parameters are estimated via maximum likelihood, using a local
likelihood approach. Also provided are functions to fit stationary spatial
models for comparison, calculate the kriging predictor and standard errors,
and create various plots to visualize nonstationarity.
Author: Mark D. Risser [aut, cre]
Maintainer: Mark D. Risser <markdrisser@gmail.com>
Diff between convoSPAT versions 0.1 dated 2015-07-21 and 1.0 dated 2015-09-28
convoSPAT-0.1/convoSPAT/data/USprecip.RData |only convoSPAT-0.1/convoSPAT/man/Aniso_pred.Rd |only convoSPAT-0.1/convoSPAT/man/NSconvo_pred.Rd |only convoSPAT-0.1/convoSPAT/man/USprecip.Rd |only convoSPAT-0.1/convoSPAT/man/plot_correlation.Rd |only convoSPAT-0.1/convoSPAT/man/plot_ellipses.Rd |only convoSPAT-0.1/convoSPAT/man/plot_mc.Rd |only convoSPAT-0.1/convoSPAT/man/plot_preds.Rd |only convoSPAT-0.1/convoSPAT/man/summary_NS.Rd |only convoSPAT-0.1/convoSPAT/vignettes/MDR_package.pdf |only convoSPAT-1.0/convoSPAT/DESCRIPTION | 8 convoSPAT-1.0/convoSPAT/MD5 | 35 convoSPAT-1.0/convoSPAT/NAMESPACE | 15 convoSPAT-1.0/convoSPAT/R/DataDocumentation.R | 30 convoSPAT-1.0/convoSPAT/R/convoSPAT_fitpred.R | 381 +++---- convoSPAT-1.0/convoSPAT/R/convoSPAT_summplot.R | 585 +++++------- convoSPAT-1.0/convoSPAT/data/USmcgrids.RData |only convoSPAT-1.0/convoSPAT/data/USprecip97.RData |only convoSPAT-1.0/convoSPAT/data/USpredictionlocs.RData |only convoSPAT-1.0/convoSPAT/man/NSconvo_fit.Rd | 2 convoSPAT-1.0/convoSPAT/man/US.mc.grids.Rd |only convoSPAT-1.0/convoSPAT/man/US.prediction.locs.Rd |only convoSPAT-1.0/convoSPAT/man/USprecip97.Rd |only convoSPAT-1.0/convoSPAT/man/plot.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/plot.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/man/predict.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/predict.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/man/summary.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/summary.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/vignettes/RisserCalder_LLEpaper.pdf |only 30 files changed, 505 insertions(+), 551 deletions(-)
Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre],
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between classInt versions 0.1-22 dated 2015-01-06 and 0.1-23 dated 2015-09-28
ChangeLog | 34 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NAMESPACE | 3 ++- data/jenks71.rda |binary inst/ChangeLog | 34 ++++++++++++++++++++++++++++++++++ 6 files changed, 83 insertions(+), 14 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.2.0 dated 2015-08-26 and 3.3.0 dated 2015-09-28
DESCRIPTION | 12 ++-- MD5 | 38 +++++++------- NAMESPACE | 6 ++ R/choropleth.R | 88 +++++++++++++++++++++++++++++++-- R/country.R | 1 R/county.R | 52 +++++++++++++------ R/state.R | 37 ++++++++++--- inst/doc/f-world-bank-data.html | 4 - inst/doc/h-creating-your-own-maps.html | 2 inst/tests/test-county.R | 7 ++ inst/tests/test-state.R | 8 +++ man/Admin1Choropleth.Rd | 2 man/Choropleth.Rd | 2 man/CountryChoropleth.Rd | 2 man/CountyChoropleth.Rd | 2 man/CountyZoomChoropleth.Rd | 2 man/StateChoropleth.Rd | 2 man/USAChoropleth.Rd | 2 man/county_choropleth.Rd | 37 +++++++++---- man/state_choropleth.Rd | 27 +++++++--- 20 files changed, 251 insertions(+), 82 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso', a method to model heterogeneity in paired comparison data. Subject-specific covariates are allowed to have an influence on the attractivity/strength of the objects. An L1 penalty on the pairwise differences between the object-specific parameters allows for both clustering of objects with regard to covariates and elimination of irrelevant covariates.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1-1 dated 2015-09-07 and 0.1-2 dated 2015-09-28
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/cppfunctions.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Spatial and Space-Time Point Pattern Analysis
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre],
Barry Rowlingson [aut],
Peter Diggle [aut],
Giovanni Petris [ctb],
Stephen Eglen [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between splancs versions 2.01-37 dated 2015-03-18 and 2.01-38 dated 2015-09-28
ChangeLog | 299 +++++++++++++++++++++------------------------------------ DESCRIPTION | 11 +- MD5 | 8 - NAMESPACE | 8 - inst/ChangeLog | 299 +++++++++++++++++++++------------------------------------ 5 files changed, 239 insertions(+), 386 deletions(-)
Title: Interface Between GRASS 6+ Geographical Information System and R
Description: Interpreted interface between GRASS 6+ geographical
information system and R, based on starting R from within the GRASS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 7, for which
spgrass7 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgrass6 versions 0.8-6 dated 2014-10-14 and 0.8-8 dated 2015-09-28
ChangeLog | 1161 +++------------------------------------------- DESCRIPTION | 20 MD5 | 34 - NAMESPACE | 11 R/AAA.R | 7 R/bin_link.R | 111 ++-- R/initGRASS.R | 8 R/options.R | 10 R/spgrass6.R | 31 + R/vect_link.R | 87 +-- R/xml1.R | 12 inst/ChangeLog | 1161 +++------------------------------------------- inst/doc/spgrass6_0.3.pdf |binary man/gmeta6.Rd | 20 man/initGRASS.Rd | 6 man/readRAST6.Rd | 42 + man/readVECT6.Rd | 30 - man/spgrass6.Rd | 20 18 files changed, 458 insertions(+), 2313 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: James Keirstead <j.keirstead@imperial.ac.uk>
Maintainer: James Keirstead <j.keirstead@imperial.ac.uk>
Diff between scholar versions 0.1.2 dated 2014-08-22 and 0.1.3 dated 2015-09-28
DESCRIPTION | 17 ++-- LICENSE | 4 - MD5 | 29 +++---- NAMESPACE | 1 NEWS | 16 ++++ R/compare.r | 158 ++++++++++++++++++++-------------------- R/predict.r | 18 ++++ R/publications.r | 66 +++++++++++++--- R/scholar.r | 12 +-- README.md | 104 +++++++++++++------------- inst/CITATION | 20 ++--- man/compare_scholars.Rd | 5 + man/get_article_cite_history.Rd |only man/get_citation_history.Rd | 10 +- man/get_publications.Rd | 10 ++ man/predict_h_index.Rd | 8 ++ 16 files changed, 289 insertions(+), 189 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.3.3 dated 2015-09-08 and 1.4.1 dated 2015-09-28
DESCRIPTION | 10 MD5 | 50 +- NAMESPACE | 6 NEWS | 17 R/AllenH.R | 52 +- R/ChaoPD.R | 55 +- R/CheckentropartArguments.R | 14 R/Hqz.R | 8 R/PhyloApply.R | 16 R/Preprocess.Tree.R | 39 + R/Rao.R | 8 R/Richness.R | 49 + R/Shannon.R | 8 R/Simpson.R | 8 R/Tsallis.R | 26 - inst/CITATION | 33 - inst/doc/entropart.Rnw | 10 inst/doc/entropart.pdf |binary man/AllenH.Rd | 6 man/ChaoPD.Rd | 4 man/PPtree.Rd | 5 man/SpeciesDistribution.Rd | 7 man/Tsallis.Rd | 2 man/entropart-package.Rd | 4 vignettes/entropart.Rnw | 10 vignettes/entropart.bib | 1082 +++++++++++++++++++++----------------------- 26 files changed, 795 insertions(+), 734 deletions(-)
Title: Interface to the Agave API
Description: Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see <http://www.iplantcollaborative.org/> for more information about iPlant, and <http://www.iplantcollaborative.org/ci/iplant-science-apis> for its APIs. Currently, 'rPlant' functions interact with the iPlant Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant Collaborative. See <http://agaveapi.co/> for more information on the Agave API and <http://user.iplantcollaborative.org/> to register with iPlant.
Author: Barb Banbury <darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Kurt Michels <kamichels@math.arizona.edu>
Diff between rPlant versions 2.7 dated 2013-05-21 and 2.11 dated 2015-09-28
rPlant-2.11/rPlant/DESCRIPTION | 35 rPlant-2.11/rPlant/MD5 | 82 rPlant-2.11/rPlant/NAMESPACE | 7 rPlant-2.11/rPlant/R/ClustalW.R |only rPlant-2.11/rPlant/R/FaST_LMM.R |only rPlant-2.11/rPlant/R/Fasttree.R |only rPlant-2.11/rPlant/R/Mafft.R |only rPlant-2.11/rPlant/R/Muscle.R |only rPlant-2.11/rPlant/R/PLINK.R |only rPlant-2.11/rPlant/R/PLINKConversion.R |only rPlant-2.11/rPlant/R/RAxML.R |only rPlant-2.11/rPlant/R/TNRS.R | 12 rPlant-2.11/rPlant/R/find.input.R |only rPlant-2.11/rPlant/R/help.R |only rPlant-2.11/rPlant/R/rPlant.R | 3187 ++++++++++++++--- rPlant-2.11/rPlant/data/DNA.fasta.rda |only rPlant-2.11/rPlant/data/PROTEIN.fasta.rda |only rPlant-2.11/rPlant/data/fasta_aa.aln.rda |only rPlant-2.11/rPlant/data/fasta_dna.aln.rda |only rPlant-2.11/rPlant/data/geno_test.tfam.rda |only rPlant-2.11/rPlant/data/geno_test.tped.rda |only rPlant-2.11/rPlant/data/phylip_interleaved_aa.aln.rda |only rPlant-2.11/rPlant/data/phylip_interleaved_dna.aln.rda |only rPlant-2.11/rPlant/data/simulation1.map.rda |only rPlant-2.11/rPlant/data/simulation1.ped.rda |only rPlant-2.11/rPlant/inst/extdata/DNA.fasta |only rPlant-2.11/rPlant/inst/extdata/PROTEIN.fasta |only rPlant-2.11/rPlant/inst/extdata/geno_test.tfam |only rPlant-2.11/rPlant/inst/extdata/geno_test.tped |only rPlant-2.11/rPlant/inst/tests |only rPlant-2.11/rPlant/man/ClustalW.Rd |only rPlant-2.11/rPlant/man/FaST_LMM.Rd |only rPlant-2.11/rPlant/man/Fasttree.Rd |only rPlant-2.11/rPlant/man/GetAppList.Rd | 26 rPlant-2.11/rPlant/man/ListDir.Rd | 67 rPlant-2.11/rPlant/man/Mafft.Rd |only rPlant-2.11/rPlant/man/Muscle.Rd |only rPlant-2.11/rPlant/man/PLINK.Rd |only rPlant-2.11/rPlant/man/PLINKConversion.Rd |only rPlant-2.11/rPlant/man/RAxML.Rd |only rPlant-2.11/rPlant/man/SubmitJob.Rd | 121 rPlant-2.11/rPlant/man/TNRS.Rd | 23 rPlant-2.11/rPlant/man/UploadFile.Rd | 99 rPlant-2.11/rPlant/man/Validate.Rd |only rPlant-2.11/rPlant/man/rPlant-data.Rd |only rPlant-2.11/rPlant/man/rPlant-internal.Rd |only rPlant-2.11/rPlant/man/rplant-package.Rd | 24 rPlant-2.11/rPlant/vignettes |only rPlant-2.7/rPlant/R/GetCitations.R |only rPlant-2.7/rPlant/R/RunClustal.R |only rPlant-2.7/rPlant/R/RunMafft.R |only rPlant-2.7/rPlant/R/RunMuscle.R |only rPlant-2.7/rPlant/R/RunParsdna.R |only rPlant-2.7/rPlant/R/RunParsprotein.R |only rPlant-2.7/rPlant/R/RunQuicktree.R |only rPlant-2.7/rPlant/R/RunRAxMLdna.R |only rPlant-2.7/rPlant/R/RunRAxMLprotein.R |only rPlant-2.7/rPlant/data/ex.lp.fasta.rda |only rPlant-2.7/rPlant/inst/extdata/ex.lp.fasta |only rPlant-2.7/rPlant/inst/extdata/short.landplants.phy |only rPlant-2.7/rPlant/man/GetCitations.Rd |only rPlant-2.7/rPlant/man/GetToken.Rd |only rPlant-2.7/rPlant/man/RunClustal.Rd |only rPlant-2.7/rPlant/man/RunMafft.Rd |only rPlant-2.7/rPlant/man/RunMuscle.Rd |only rPlant-2.7/rPlant/man/RunParsdna.Rd |only rPlant-2.7/rPlant/man/RunParsprotein.Rd |only rPlant-2.7/rPlant/man/RunQuicktree.Rd |only rPlant-2.7/rPlant/man/RunRAxMLdna.Rd |only rPlant-2.7/rPlant/man/RunRAxMLprotein.Rd |only rPlant-2.7/rPlant/man/landplants.Rd |only 71 files changed, 3042 insertions(+), 641 deletions(-)
Title: An API Client for the Internet Archive
Description: Search the Internet Archive, retrieve metadata, and download
files.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between internetarchive versions 0.1.2 dated 2015-03-24 and 0.1.4 dated 2015-09-28
DESCRIPTION | 11 ++++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- NEWS | 4 ++++ R/ia_browse.R | 2 +- README.md | 14 ++++++++++---- build/vignette.rds |binary man/ia_browse.Rd | 2 +- man/ia_download.Rd | 2 +- man/ia_files.Rd | 2 +- man/ia_get_items.Rd | 2 +- man/ia_item_id.Rd | 2 +- man/ia_keyword_search.Rd | 2 +- man/ia_list_fields.Rd | 2 +- man/ia_metadata.Rd | 2 +- man/ia_search.Rd | 2 +- man/internetarchive.Rd | 2 +- vignettes/internet-archive.Rmd | 2 +- 18 files changed, 50 insertions(+), 39 deletions(-)
More information about internetarchive at CRAN
Permanent link
Title: Convert Between Spatial Objects and Well-Known Binary Geometry
Description: Utility functions to convert between the 'Spatial' classes
specified by the package 'sp', and the well-known binary '(WKB)'
representation for geometry specified by the Open Geospatial Consortium.
Supports 'Spatial' objects of class 'SpatialPoints',
'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame',
'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry
types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and
'MultiPolygon'. Includes extensions to enable creation of maps with
'TIBCO Spotfire'.
Author: TIBCO Software Inc.
Maintainer: Ian Cook <icook@tibco.com>
Diff between wkb versions 0.1-0 dated 2015-02-28 and 0.2-0 dated 2015-09-28
DESCRIPTION | 29 - LICENSE | 6 MD5 | 34 +- NAMESPACE | 29 - R/SpatialLinesToWKBLineString.R | 439 +++++++++++++++------------- R/SpatialPointsToWKBPoint.R | 501 +++++++++++++++++--------------- R/SpatialPolygonsToWKBPolygon.R | 255 ++++++++-------- R/hex2raw.R |only R/readWKB.R | 608 ++++++++++++++++++++-------------------- R/writeEnvelope.R | 134 ++++---- R/writeWKB.R | 282 +++++++++--------- man/hex2raw.Rd |only man/readWKB.Rd | 268 ++++++++--------- man/writeEnvelope.Rd | 96 +++--- man/writeWKB.Rd | 240 ++++++++------- tests |only 16 files changed, 1506 insertions(+), 1415 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-12 dated 2015-09-01 and 0.3-13 dated 2015-09-28
ChangeLog | 67 +++++++++++ DESCRIPTION | 8 - MD5 | 54 ++++----- R/over.R | 4 R/rgeos_predicate_binary.R | 130 +++++++++++++++++++--- R/rgeos_topology_binary.R | 55 +++++++-- configure | 18 +-- inst/ChangeLog | 67 +++++++++++ inst/SVN_VERSION | 2 inst/tests/testxml/general/TestFunctionLLPrec.xml | 3 inst/tests/testxml/validate/TestRelateLL.xml | 3 inst/tests/testxml/validate/TestRelatePA.xml | 3 inst/tests/testxml/validate/TestRelatePL.xml | 3 inst/tests/testxml/validate/TestRelatePP.xml | 3 man/labelpt.Rd | 3 man/misc-over.Rd | 2 man/pred-binary-gContains.Rd | 14 +- man/pred-binary-gCrosses.Rd | 9 + man/pred-binary-gEquals.Rd | 9 + man/pred-binary-gIntersects.Rd | 9 + man/pred-binary-gRelate.Rd | 6 - man/pred-binary-gTouches.Rd | 6 - man/topo-bin-gDifference.Rd | 6 - man/topo-bin-gIntersection.Rd | 30 ++++- man/topo-bin-gSymdifference.Rd | 7 + man/topo-bin-gUnion.Rd | 7 + src/rgeos_geos2R.c | 21 ++- src/rgeos_topology_binary.c | 12 ++ 28 files changed, 462 insertions(+), 99 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 1.9-7 dated 2015-05-22 and 1.9-8 dated 2015-09-28
DESCRIPTION | 16 MD5 | 179 +++-- NAMESPACE | 6 NEWS | 71 ++ R/AIC.rma.r | 27 R/BIC.rma.r | 21 R/addpoly.default.r | 4 R/anova.rma.r | 18 R/baujat.rma.mh.r | 16 R/baujat.rma.peto.r | 6 R/baujat.rma.uni.r | 7 R/blup.rma.uni.r | 4 R/coef.permutest.rma.uni.r | 2 R/coef.summary.rma.r | 4 R/confint.rma.mv.r | 406 ++++++++++++- R/confint.rma.uni.r | 249 +++++-- R/cooks.distance.rma.uni.r | 7 R/cumul.rma.mh.r | 18 R/cumul.rma.peto.r | 6 R/cumul.rma.uni.r | 7 R/dfbetas.rma.uni.r | 7 R/escalc.default.r | 30 R/fitstats.rma.r | 32 - R/forest.cumul.rma.r | 4 R/forest.default.r | 4 R/forest.rma.r | 4 R/fsn.r | 4 R/funnel.rma.r | 2 R/influence.rma.uni.r | 7 R/labbe.rma.r | 7 R/leave1out.rma.mh.r | 16 R/leave1out.rma.peto.r | 6 R/leave1out.rma.uni.r | 7 R/llplot.r | 4 R/misc.func.hidden.r | 171 ++++- R/permutest.rma.uni.r | 10 R/predict.rma.r | 4 R/print.anova.rma.r | 16 R/print.confint.rma.r | 6 R/print.infl.rma.uni.r | 3 R/print.permutest.rma.uni.r | 10 R/print.rma.glmm.r | 14 R/print.rma.mv.r | 30 R/print.rma.uni.r | 14 R/print.robust.rma.r |only R/profile.rma.mv.r | 115 +++ R/profile.rma.uni.r | 12 R/radial.rma.r | 2 R/ranktest.rma.r | 2 R/regtest.rma.r | 4 R/rma.glmm.r | 245 ++++--- R/rma.mh.r | 33 - R/rma.mv.r | 208 +++++- R/rma.peto.r | 20 R/rma.uni.r | 148 ++-- R/robust.r |only R/robust.rma.mv.r |only R/robust.rma.uni.r |only R/rstudent.rma.mh.r | 16 R/rstudent.rma.peto.r | 6 R/rstudent.rma.uni.r | 7 R/to.long.r | 49 - R/to.table.r | 49 - R/update.rma.r | 2 R/zzz.R | 2 README.md |only data/dat.konstantopoulos2011.rda |binary inst/CITATION | 4 inst/doc/metafor_diagram.pdf |binary man/anova.rma.Rd | 2 man/confint.rma.Rd | 79 ++ man/dat.fine1993.Rd | 7 man/dat.konstantopoulos2011.Rd | 7 man/dat.nielweise2007.Rd | 3 man/dat.nielweise2008.Rd | 3 man/escalc.Rd | 4 man/fitstats.Rd | 24 man/forest.rma.Rd | 2 man/hc.Rd | 2 man/influence.rma.mv.Rd | 4 man/influence.rma.uni.Rd | 4 man/permutest.Rd | 6 man/predict.rma.Rd | 2 man/print.confint.rma.Rd | 2 man/print.rma.uni.Rd | 2 man/print.robust.rma.Rd |only man/profile.rma.Rd | 15 man/rma.glmm.Rd | 14 man/rma.mv.Rd | 12 man/rma.uni.Rd | 2 man/robust.Rd |only man/weights.rma.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test_analysis_example_konstantopoulos2011.r | 10 tests/testthat/test_rma_handling_nas.r |only 95 files changed, 1827 insertions(+), 791 deletions(-)
Title: Cardiovascular Safety Exposure-Response Modeling in Early-Phase
Clinical Studies
Description: Includes 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
Author: Daniela J Conrado [aut, cre], William S Denney [aut], Gregory J Hather [aut], Danny Chen [ctb]
Maintainer: Daniela J Conrado <danielac@metrumrg.com>
Diff between cardioModel versions 1.1 dated 2015-09-25 and 1.2 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/21_cardioModel.R | 48 ++++++++++++++++++++++++++---------------------- 3 files changed, 32 insertions(+), 28 deletions(-)
Title: Computed ABC Analysis
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many"). Package is based on Ultsch. A ., Lotsch J.: Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data, PLoS One, 2015.
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between ABCanalysis versions 1.0.2 dated 2015-06-15 and 1.1.0 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 4 ++++ R/ABCRemoveSmallYields.R |only R/ABCanalysis.R | 1 - R/ABCanalysisPlot.R | 20 ++++++++++++++++++-- R/ABCcleanData.R | 29 ++++------------------------- R/ABCcurve.R | 8 +++----- R/ABCplot.R | 20 ++++++++++++-------- R/calculatedABCanalysis.R |only man/ABCRemoveSmallYields.Rd |only man/ABCanalysisPlot.Rd | 18 +++++++++++++++++- man/ABCcleanData.Rd | 9 ++------- man/ABCcurve.Rd | 7 ++----- man/ABCplot.Rd | 7 ++----- man/calculatedABCanalysis.Rd |only 16 files changed, 83 insertions(+), 74 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 4.3-1 dated 2015-04-30 and 4.4-0 dated 2015-09-28
DESCRIPTION | 14 - MD5 | 74 +++-- NAMESPACE | 24 + NEWS | 22 + R/Glm.s | 18 - R/Gls.s | 4 R/Predict.s | 19 + R/Rq.s | 4 R/bj.s | 5 R/calibrate.cph.s | 229 ++++++++--------- R/contrast.s | 16 - R/cph.s | 170 +++++++------ R/ggplot.Predict.s | 29 +- R/lrm.s | 12 R/ols.s | 8 R/orm.s | 7 R/plot.Predict.s | 29 +- R/predab.resample.s | 72 ++--- R/predictrms.s | 40 +-- R/print.psm.s | 1 R/psm.s | 4 R/rms.s | 314 ++++++++++++++---------- R/rms.trans.s | 117 ++++----- R/rmsMisc.s | 497 +++++++++++++++++++++------------------ R/summary.rms.s | 2 R/validate.Rq.s | 9 demo/all.R | 79 +++--- man/Predict.Rd | 14 - man/calibrate.Rd | 30 +- man/cph.Rd | 6 man/ggplot.Predict.Rd | 4 man/rmsMisc.Rd | 32 ++ man/survplot.Rd | 30 +- tests/Glm.s | 3 tests/Predict.s | 2 tests/contrast.r |only tests/cph4.r |only tests/ggplot.Predict.Rd.timing.r |only tests/offset.r |only tests/rcs.r |only tests/strat.model.matrix.r |only 41 files changed, 1084 insertions(+), 856 deletions(-)
Title: Permutation Distribution Clustering
Description: Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
Author: Andreas M. Brandmaier
Maintainer: Andreas M. Brandmaier <brandmaier@mpib-berlin.mpg.de>
Diff between pdc versions 1.0.2 dated 2014-11-21 and 1.0.3 dated 2015-09-28
DESCRIPTION | 9 +++++---- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 4 ++++ inst/CITATION | 34 +++++++++++++++++++--------------- man/codebook.Rd | 7 +++++-- man/complex.shapes.Rd | 6 ++++-- man/distance.Rd | 3 +-- man/entropy.heuristic.Rd | 9 +++++---- man/loo1nn.Rd | 8 +++++--- man/mds.plot.Rd | 10 ++++------ man/pdc-package.Rd | 10 +++++----- man/pdc.dist.Rd | 7 +++++-- man/pdclust.Rd | 10 +++++----- man/rasterPlot.Rd | 9 ++++----- man/star.shapes.Rd | 6 ++++-- man/trace.image.Rd | 7 +++++-- 17 files changed, 119 insertions(+), 76 deletions(-)
Title: Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Description: Nonparametric aligned rank tests for interaction in two-way factorial designs, on data set with repeated measures in 'wide' format. There is a choice between 0) CHECK for alignment 1) Aligned REGULAR 2) FRIEDMAN 3) KOCH ranks.
Author: Jos Feys
Maintainer: Jos Feys <jos.feys@faber.kuleuven.be>
Diff between npIntFactRep versions 1.2 dated 2015-02-19 and 1.3 dated 2015-09-28
DESCRIPTION | 14 ++-- MD5 | 8 +- NAMESPACE | 3 R/npIntFactRep.R | 178 ++++++++++++++++++++++++++++++++++------------------ man/npIntFactRep.Rd | 51 +++++++++----- 5 files changed, 163 insertions(+), 91 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.0 dated 2015-08-18 and 0.6.1 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/txt.to.words.ext.R | 5 ++++- man/make.frequency.list.Rd | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Non-Parametric Estimation of the Off-Pulse Interval of a Pulsar
Description: Provides functions to non-parametrically estimate the off-pulse interval of a source
function originating from a pulsar. The technique is based on a sequential application of P-values
obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov,
Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.
Author: Willem Daniel Schutte
Maintainer: Willem Daniel Schutte <wd.schutte@nwu.ac.za>
Diff between SOPIE versions 1.4 dated 2015-06-05 and 1.5 dated 2015-09-28
SOPIE-1.4/SOPIE/R/adgoftestpval.R |only SOPIE-1.4/SOPIE/R/adgofteststat.R |only SOPIE-1.4/SOPIE/R/ppvonmises.R |only SOPIE-1.4/SOPIE/R/r.test.R |only SOPIE-1.5/SOPIE/DESCRIPTION | 11 SOPIE-1.5/SOPIE/MD5 | 48 +-- SOPIE-1.5/SOPIE/NAMESPACE | 6 SOPIE-1.5/SOPIE/NEWS |only SOPIE-1.5/SOPIE/R/CVM_pvall.R | 55 ++-- SOPIE-1.5/SOPIE/R/SOPIE.R | 129 ++------- SOPIE-1.5/SOPIE/R/a.estimate.R | 465 +++++++++++++--------------------- SOPIE-1.5/SOPIE/R/b.estimate.R | 464 +++++++++++++-------------------- SOPIE-1.5/SOPIE/R/circ.kernel.R | 47 +-- SOPIE-1.5/SOPIE/R/findh.R | 179 +++++-------- SOPIE-1.5/SOPIE/R/von_mises_density.R | 8 SOPIE-1.5/SOPIE/R/von_mises_sim.R | 34 +- SOPIE-1.5/SOPIE/data/J1709.rda |binary SOPIE-1.5/SOPIE/data/crab.rda |binary SOPIE-1.5/SOPIE/data/simdata.rda |binary SOPIE-1.5/SOPIE/inst |only SOPIE-1.5/SOPIE/man/SOPIE-package.Rd | 8 SOPIE-1.5/SOPIE/man/SOPIE.Rd | 2 SOPIE-1.5/SOPIE/man/a.estimate.Rd | 12 SOPIE-1.5/SOPIE/man/b.estimate.Rd | 16 - SOPIE-1.5/SOPIE/man/circ.kernel.Rd | 16 - SOPIE-1.5/SOPIE/man/crab.Rd | 4 SOPIE-1.5/SOPIE/man/findh.Rd | 14 - SOPIE-1.5/SOPIE/man/von_mises_sim.Rd | 4 28 files changed, 659 insertions(+), 863 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between Rssa versions 0.13 dated 2015-03-03 and 0.13-1 dated 2015-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 9 +++++++++ inst/CITATION | 40 ++++++++++++++++++++++++++++++++-------- 4 files changed, 47 insertions(+), 14 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0 dated 2015-09-27 and 3.0.0-1 dated 2015-09-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/Makefile | 1 + src/world.name | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Ancona "Politecnica delle Marche")
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.2 dated 2015-07-22 and 1.3 dated 2015-09-28
DESCRIPTION | 10 +++++----- MD5 | 26 ++++++++++++++------------ NAMESPACE | 1 + R/cquad.R |only R/cquad_basic.R | 7 ++++--- R/cquad_equ.R | 7 ++++--- R/cquad_ext.R | 5 +++-- R/cquad_pseudo.R | 9 +++++---- R/summary.cquad.R | 4 ++-- man/cquad-package.Rd | 11 ++++------- man/cquad.Rd |only man/cquad_basic.Rd | 4 +++- man/cquad_equ.Rd | 4 +++- man/cquad_ext.Rd | 4 +++- man/cquad_pseudo.Rd | 4 +++- 15 files changed, 54 insertions(+), 42 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.8.1 dated 2015-07-13 and 0.8.2 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/LoadAPSIMouts.R | 2 +- R/MetFunctions.R | 18 +++++++++++++++--- README.md | 17 +++++++++++++++++ data/met.rda |binary man/checkCont.Rd | 2 +- man/metFile-class.Rd | 2 ++ 8 files changed, 47 insertions(+), 16 deletions(-)
Title: Two-Stage Threshold Estimation
Description: Implements a variety of non-parametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
Author: Shawn Mankad, George Michailidis, Moulinath Banerjee
Maintainer: Shawn Mankad <smankad@cornell.edu>
Diff between twostageTE versions 1.2 dated 2014-08-12 and 1.3 dated 2015-09-27
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 5 +++++ R/estimateSigmaSq.R | 10 ++++++---- inst |only man/twostageTE-package.Rd | 6 ++++-- 6 files changed, 26 insertions(+), 16 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance, Spearman distance, Footrule distance, Hamming distance,
, Weighted-tau distance and Weighted Kendall distance.
Phi-component model and mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 1.1.1 dated 2015-09-16 and 1.1.2 dated 2015-09-27
DESCRIPTION | 12 ++++---- MD5 | 38 +++++++++++++------------- R/class.R | 56 ++++++++++++++++++++++++++++++++++++--- R/rankdist.R | 32 ++++++++++++---------- man/DistanceBlock.Rd | 10 ++---- man/GenerateExample.Rd | 2 - man/GenerateExampleTopQ.Rd | 2 - man/ModelSummary.Rd | 5 --- man/MomentsEst.Rd | 8 ++--- man/OrderingToRanking.Rd | 1 man/RankControl-class.Rd | 7 +++- man/RankControlCayley-class.Rd | 18 ++++++++++++ man/RankControlFootrule-class.Rd | 18 ++++++++++++ man/RankControlHamming-class.Rd | 18 ++++++++++++ man/RankControlSpearman-class.Rd | 18 ++++++++++++ man/RankControlWtau-class.Rd | 20 +++++++++++-- man/RankDistanceModel.Rd | 7 +++- man/RanktoHash.Rd | 2 - man/apa_obj.Rd | 3 ++ man/apa_partial_obj.Rd | 3 ++ 20 files changed, 213 insertions(+), 67 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu and Simon Firestone
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-62 dated 2015-01-08 and 0.9-69 dated 2015-09-27
DESCRIPTION | 15 MD5 | 42 - NAMESPACE | 12 R/epi.2by2.r | 1822 +++++++++++++++++++++++++++++++----------------- R/epi.about.R | 4 R/epi.descriptives.R | 77 +- R/epi.directadj.r | 48 - R/epi.interaction.r | 214 ++++- R/epi.occc.R | 54 - man/epi.2by2.Rd | 605 ++++++++------- man/epi.about.Rd | 6 man/epi.asc.Rd | 4 man/epi.betabuster.Rd | 2 man/epi.clustersize.Rd | 32 man/epi.conf.Rd | 6 man/epi.descriptives.Rd | 18 man/epi.directadj.Rd | 63 - man/epi.interaction.Rd | 35 man/epi.occc.Rd | 39 - man/epi.simplesize.Rd | 11 man/epi.studysize.Rd | 16 man/epi.tests.Rd | 2 22 files changed, 2001 insertions(+), 1126 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 2.3-11 dated 2015-08-03 and 3.0.0 dated 2015-09-27
DESCRIPTION | 12 MD5 | 55 NAMESPACE | 2 R/db.r | 60 R/iso.r |only R/legacy.r |only R/map.r | 10 R/misc.r | 2 R/polygon.r | 4 R/zzz.R | 17 README.md |only data/iso3166.rda |only data/legacy_world2MapEnv.rda |only data/legacy_worldMapEnv.rda |only data/world2MapEnv.rda |binary data/worldMapEnv.rda |binary inst |only man/iso.expand.Rd |only man/iso3166.Rd |only man/legacy_world.Rd |only man/map.Rd | 2 man/world.Rd | 22 man/world.legacy.Rd |only man/world2.Rd | 22 src/Makefile | 17 src/convert.awk | 26 src/legacy_world.gon |only src/legacy_world.gonstats |only src/legacy_world.line |only src/legacy_world.linestats |only src/legacy_world.name |only src/world.gon | 8009 --- src/world.gonstats | 2 src/world.line |113841 ++++++++++++++++++++++++++++++++----------- src/world.linestats | 2 src/world.name | 3945 - 36 files changed, 89182 insertions(+), 36868 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.2 dated 2015-06-25 and 4.4.3 dated 2015-09-27
DESCRIPTION | 6 +- MD5 | 66 +++++++++++++++--------------- NAMESPACE | 9 ++++ NEWS | 12 ++++- R/as.char.R | 9 ++++ R/call.dots.R | 2 R/dot.R | 2 R/dotlib.R | 4 - R/printcall.R | 2 inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 inst/slowtests/test.big.bat | 2 inst/slowtests/test.cv.bat | 2 inst/slowtests/test.earthc.bat | 10 ++-- inst/slowtests/test.earthc.mak | 2 inst/slowtests/test.earthmain.clang.bat | 10 ++-- inst/slowtests/test.earthmain.gcc.bat | 10 ++-- inst/slowtests/test.earthmain.gcc64.bat | 10 ++-- inst/slowtests/test.earthmain.vc.bat | 10 ++-- inst/slowtests/test.full.Rout.save | 13 +++-- inst/slowtests/test.full.bat | 2 inst/slowtests/test.glm.bat | 2 inst/slowtests/test.incorrect.bat | 2 inst/slowtests/test.mods.bat | 2 inst/slowtests/test.plotd.bat | 2 inst/slowtests/test.pmethod.cv.bat | 2 inst/slowtests/test.varmod.R | 2 inst/slowtests/test.varmod.Rout.save | 2 inst/slowtests/test.varmod.bat | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.varmod.mgcv.bat | 2 inst/slowtests/test.weights.Rout.save | 2 inst/slowtests/test.weights.bat | 2 34 files changed, 118 insertions(+), 91 deletions(-)
Title: Easily Source Publicly Available Data on Derivatives
Description: Post-GFC derivatives reforms have lifted the veil off
over-the-counter (OTC) derivative markets. Swap Execution Facilities (SEFs)
and Swap Data Repositories (SDRs) now publish data on swaps that are traded
on or reported to those facilities (respectively). This package provides you
the ability to get this data from supported sources.
Author: Imanuel Costigan [aut, cre]
Maintainer: Imanuel Costigan <i.costigan@me.com>
Diff between dataonderivatives versions 0.2.0 dated 2015-09-10 and 0.2.1 dated 2015-09-27
DESCRIPTION | 8 MD5 | 32 +- NAMESPACE | 14 - R/bsdr.R | 294 ++++++++++++------------- R/bsef.R | 282 ++++++++++++------------ R/cme.R | 520 ++++++++++++++++++++++----------------------- R/ddr.R | 312 +++++++++++++-------------- README.md | 244 ++++++++++----------- man/get_bsdr_data.Rd | 106 ++++----- man/get_bsef_data.Rd | 98 ++++---- man/get_cme_data.Rd | 98 ++++---- man/get_ddr_data.Rd | 92 +++---- tests/testthat.R | 8 tests/testthat/test-bsdr.R | 26 +- tests/testthat/test-cme.R | 47 ++-- tests/testthat/test-ddr.R | 47 ++-- tests/testthat/test_bsef.R | 15 - 17 files changed, 1124 insertions(+), 1119 deletions(-)
More information about dataonderivatives at CRAN
Permanent link
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
Author: Eduard Szoecs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szoecs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.3 dated 2015-09-25 and 0.0.3.1 dated 2015-09-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- tests/testthat.R | 12 ++++++++++-- tests/testthat/test-cts.R | 12 ++++++------ 4 files changed, 22 insertions(+), 14 deletions(-)
Title: Quantile-Based Spectral Analysis of Time Series
Description: Methods to determine, smooth and plot quantile (i. e., Laplace or
copula) periodograms for univariate time series.
Author: Tobias Kley [aut, cre],
Stefan Birr [ctb] (Contributions to lag window estimation)
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between quantspec versions 1.0-3 dated 2015-03-26 and 1.1-0 dated 2015-09-27
quantspec-1.0-3/quantspec/cleanup |only quantspec-1.1-0/quantspec/DESCRIPTION | 32 - quantspec-1.1-0/quantspec/MD5 | 267 +++++----- quantspec-1.1-0/quantspec/NAMESPACE | 23 quantspec-1.1-0/quantspec/NEWS | 13 quantspec-1.1-0/quantspec/R/Class-ClippedCov.R |only quantspec-1.1-0/quantspec/R/Class-ClippedFT.R | 1 quantspec-1.1-0/quantspec/R/Class-IntegrQuantileSD.R | 2 quantspec-1.1-0/quantspec/R/Class-KernelWeight.R | 2 quantspec-1.1-0/quantspec/R/Class-LagEstimator.R |only quantspec-1.1-0/quantspec/R/Class-LagKernelWeight.R |only quantspec-1.1-0/quantspec/R/Class-LagOperator.R |only quantspec-1.1-0/quantspec/R/Class-MovingBlocks.R | 8 quantspec-1.1-0/quantspec/R/Class-QRegEstimator.R | 8 quantspec-1.1-0/quantspec/R/Class-QSpecQuantity.R | 4 quantspec-1.1-0/quantspec/R/Class-QuantilePG.R | 8 quantspec-1.1-0/quantspec/R/Class-QuantileSD.R | 9 quantspec-1.1-0/quantspec/R/Class-SmoothedPG.R | 34 - quantspec-1.1-0/quantspec/R/Class-Weight.R | 7 quantspec-1.1-0/quantspec/R/RcppExports.R | 7 quantspec-1.1-0/quantspec/R/aux-functions.R | 2 quantspec-1.1-0/quantspec/R/generics.R | 18 quantspec-1.1-0/quantspec/R/kernels.R | 28 + quantspec-1.1-0/quantspec/R/models.R | 24 quantspec-1.1-0/quantspec/R/quantspec-package.R | 24 quantspec-1.1-0/quantspec/build/vignette.rds |binary quantspec-1.1-0/quantspec/demo/sp500.R | 14 quantspec-1.1-0/quantspec/inst/doc/quantspec.Rnw | 4 quantspec-1.1-0/quantspec/inst/doc/quantspec.pdf |binary quantspec-1.1-0/quantspec/inst/examples/QuantilePG.R | 4 quantspec-1.1-0/quantspec/inst/examples/SmoothedPG-Kernel.R | 2 quantspec-1.1-0/quantspec/inst/examples/SmoothedPG-SpecDistr.R | 2 quantspec-1.1-0/quantspec/man/BootPos-class.Rd | 2 quantspec-1.1-0/quantspec/man/ClippedCov-class.Rd |only quantspec-1.1-0/quantspec/man/ClippedCov-constructor.Rd |only quantspec-1.1-0/quantspec/man/ClippedFT-class.Rd | 2 quantspec-1.1-0/quantspec/man/ClippedFT-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/FreqRep-class.Rd | 2 quantspec-1.1-0/quantspec/man/IntegrQuantileSD-class.Rd | 4 quantspec-1.1-0/quantspec/man/IntegrQuantileSD-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/KernelWeight-class.Rd | 2 quantspec-1.1-0/quantspec/man/KernelWeight-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/LagEstimator-class.Rd |only quantspec-1.1-0/quantspec/man/LagEstimator-constructor.Rd |only quantspec-1.1-0/quantspec/man/LagKernelWeight-class.Rd |only quantspec-1.1-0/quantspec/man/LagKernelWeight-constructor.Rd |only quantspec-1.1-0/quantspec/man/LagOperator-class.Rd |only quantspec-1.1-0/quantspec/man/MovingBlocks-class.Rd | 8 quantspec-1.1-0/quantspec/man/MovingBlocks-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/QRegEstimator-class.Rd | 9 quantspec-1.1-0/quantspec/man/QRegEstimator-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/QSpecQuantity-class.Rd | 2 quantspec-1.1-0/quantspec/man/QuantilePG-class.Rd | 18 quantspec-1.1-0/quantspec/man/QuantilePG-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/QuantileSD-class.Rd | 6 quantspec-1.1-0/quantspec/man/QuantileSD-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/SmoothedPG-class.Rd | 4 quantspec-1.1-0/quantspec/man/SmoothedPG-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/SpecDistrWeight-class.Rd | 2 quantspec-1.1-0/quantspec/man/SpecDistrWeight-constructor.Rd | 2 quantspec-1.1-0/quantspec/man/Weight-class.Rd | 9 quantspec-1.1-0/quantspec/man/closest.pos.Rd | 2 quantspec-1.1-0/quantspec/man/data-sp500.Rd | 2 quantspec-1.1-0/quantspec/man/data-wheatprices.Rd | 2 quantspec-1.1-0/quantspec/man/figures/csd.pdf |binary quantspec-1.1-0/quantspec/man/figures/csd.png |binary quantspec-1.1-0/quantspec/man/figures/main.pdf |binary quantspec-1.1-0/quantspec/man/figures/main.png |binary quantspec-1.1-0/quantspec/man/figures/main2.pdf |only quantspec-1.1-0/quantspec/man/figures/main2.png |only quantspec-1.1-0/quantspec/man/frequenciesValidator.Rd | 2 quantspec-1.1-0/quantspec/man/generics-accessors.Rd | 8 quantspec-1.1-0/quantspec/man/generics-associations.Rd | 2 quantspec-1.1-0/quantspec/man/generics-functions.Rd | 2 quantspec-1.1-0/quantspec/man/getB-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getB-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getBootPos-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getBootPos-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getBw-KernelWeight.Rd | 2 quantspec-1.1-0/quantspec/man/getBw-LagKernelWeight.Rd |only quantspec-1.1-0/quantspec/man/getDescr-Weight.Rd | 2 quantspec-1.1-0/quantspec/man/getFreqRep-QuantilePG.Rd | 2 quantspec-1.1-0/quantspec/man/getFrequencies-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getFrequencies-QSpecQuantity.Rd | 2 quantspec-1.1-0/quantspec/man/getIsRankBased-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getIsRankBased-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getLagOperator-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getLevels-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getLevels-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getLevels-QSpecQuantity.Rd | 2 quantspec-1.1-0/quantspec/man/getMaxLag-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getMeanPG-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getN-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getParallel-QRegEstimator.Rd | 2 quantspec-1.1-0/quantspec/man/getPointwiseCIs-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getPointwiseCIs-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/getPositions-MovingBlocks.Rd | 2 quantspec-1.1-0/quantspec/man/getQuantilePG-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getQuantilePG-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/getQuantileSD-IntegrQuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getR-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getSdBoot-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getSdBoot-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/getSdNaive-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getSdNaive-SmoothedPG.Rd | 12 quantspec-1.1-0/quantspec/man/getStdError-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getTs-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getType-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-IntegrQuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-KernelWeight.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getValues-LagKernelWeight.Rd |only quantspec-1.1-0/quantspec/man/getValues-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/getValues-QuantilePG.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/getValues-SpecDistrWeight.Rd | 2 quantspec-1.1-0/quantspec/man/getW-KernelWeight.Rd | 2 quantspec-1.1-0/quantspec/man/getW-LagKernelWeight.Rd |only quantspec-1.1-0/quantspec/man/getWeight-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/getWeight-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/getWnj-KernelWeight.Rd | 2 quantspec-1.1-0/quantspec/man/getY-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/increasePrecision-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/is.wholenumber.Rd | 2 quantspec-1.1-0/quantspec/man/kernels.Rd | 10 quantspec-1.1-0/quantspec/man/plot-FreqRep.Rd | 2 quantspec-1.1-0/quantspec/man/plot-IntegrQuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/plot-KernelWeight.Rd | 2 quantspec-1.1-0/quantspec/man/plot-LagEstimator.Rd |only quantspec-1.1-0/quantspec/man/plot-LagKernelWeight.Rd |only quantspec-1.1-0/quantspec/man/plot-LagOperator.Rd |only quantspec-1.1-0/quantspec/man/plot-QuantilePG.Rd | 2 quantspec-1.1-0/quantspec/man/plot-QuantileSD.Rd | 2 quantspec-1.1-0/quantspec/man/plot-SmoothedPG.Rd | 2 quantspec-1.1-0/quantspec/man/plot-SpecDistrWeight.Rd | 2 quantspec-1.1-0/quantspec/man/quantspec-defunct.Rd | 2 quantspec-1.1-0/quantspec/man/quantspec-package.Rd | 26 quantspec-1.1-0/quantspec/man/timeSeriesValidator.Rd | 2 quantspec-1.1-0/quantspec/man/ts-models-AR1.Rd | 2 quantspec-1.1-0/quantspec/man/ts-models-AR2.Rd | 2 quantspec-1.1-0/quantspec/man/ts-models-ARCH1.Rd | 2 quantspec-1.1-0/quantspec/man/ts-models-QAR1.Rd | 2 quantspec-1.1-0/quantspec/man/ts-models.Rd | 8 quantspec-1.1-0/quantspec/src/RcppExports.cpp | 16 quantspec-1.1-0/quantspec/src/computeSdNaive.cpp | 7 quantspec-1.1-0/quantspec/tests/test-all.R |only quantspec-1.1-0/quantspec/tests/testthat/test-ClippedCov.R |only quantspec-1.1-0/quantspec/tests/testthat/test-LagEstimator.R |only quantspec-1.1-0/quantspec/vignettes/quantspec-refs.bib | 9 quantspec-1.1-0/quantspec/vignettes/quantspec.Rnw | 4 152 files changed, 522 insertions(+), 323 deletions(-)
Title: Plot Principal Component Histograms Around a Scatter Plot
Description: Plot principal component histograms around a bivariate
scatter plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotpc versions 1.0.3 dated 2014-12-17 and 1.0.4 dated 2015-09-27
plotpc-1.0.3/plotpc/tests/tests |only plotpc-1.0.4/plotpc/DESCRIPTION | 8 ++++---- plotpc-1.0.4/plotpc/MD5 | 22 +++++++++++----------- plotpc-1.0.4/plotpc/NAMESPACE | 2 ++ plotpc-1.0.4/plotpc/NEWS | 6 +++++- plotpc-1.0.4/plotpc/R/plotld.R | 4 +++- plotpc-1.0.4/plotpc/R/plotpc.R | 10 +++++----- plotpc-1.0.4/plotpc/tests/slowtests |only plotpc-1.0.4/plotpc/tests/test.plotpc.R | 2 +- plotpc-1.0.4/plotpc/tests/test.plotpc.Rout.save | 2 +- 10 files changed, 32 insertions(+), 24 deletions(-)
Title: Tools for Exploring Multivariate Data via ICS/ICA
Description: Implementation of Tyler et al.'s and Oja et al.'s method of two different scatter
matrices to obtain an invariant coordinate system or independent
components, depending on the underlying assumptions.
Author: Klaus Nordhausen, Hannu Oja, David E. Tyler
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between ICS versions 1.2-4 dated 2013-10-11 and 1.2-5 dated 2015-09-27
ICS-1.2-4/ICS/inst/vignettes |only ICS-1.2-5/ICS/DESCRIPTION | 13 +++++++------ ICS-1.2-5/ICS/MD5 | 29 ++++++++++++++++------------- ICS-1.2-5/ICS/NAMESPACE | 4 ++-- ICS-1.2-5/ICS/R/covOrigin.R | 2 +- ICS-1.2-5/ICS/R/ics-class.R | 2 +- ICS-1.2-5/ICS/R/ics.R | 8 ++++---- ICS-1.2-5/ICS/R/internals.R | 4 ++-- ICS-1.2-5/ICS/R/mat.sqrt.R | 2 +- ICS-1.2-5/ICS/R/mvnorm.kur.test.R | 2 +- ICS-1.2-5/ICS/R/mvnorm.skew.test.R | 4 ++-- ICS-1.2-5/ICS/build |only ICS-1.2-5/ICS/inst/CHANGES | 9 ++++++++- ICS-1.2-5/ICS/inst/doc |only ICS-1.2-5/ICS/man/ICS-package.Rd | 4 ++-- ICS-1.2-5/ICS/vignettes |only 16 files changed, 47 insertions(+), 36 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.4 dated 2015-01-06 and 3.5 dated 2015-09-27
DESCRIPTION | 8 +- MD5 | 68 +++++++++--------- NAMESPACE | 13 ++- NEWS | 45 +++++++++++ R/GDI.R |only R/nextItem.R | 70 ++++++++++++++---- R/randomCAT.R | 114 +++++++++++++++++------------- R/semTheta.R | 86 ++++++++++++++-------- R/simulateRespondents.R | 2 R/startItems.R | 1 R/testList.R | 72 ++++++++++++------- R/thetaEst.R | 170 ++++++++++++++++++++++++++++----------------- man/EPV.Rd | 2 man/GDI.Rd |only man/Ii.Rd | 2 man/Ji.Rd | 2 man/KL.Rd | 2 man/MEI.Rd | 2 man/MWI.Rd | 2 man/OIi.Rd | 2 man/Pi.Rd | 2 man/breakBank.Rd | 2 man/eapEst.Rd | 2 man/eapSem.Rd | 2 man/genDichoMatrix.Rd | 5 - man/genPattern.Rd | 2 man/genPolyMatrix.Rd | 2 man/integrate.catR.Rd | 2 man/nextItem.Rd | 46 +++++++++--- man/randomCAT.Rd | 21 +++-- man/semTheta.Rd | 21 ++++- man/simulateRespondents.Rd | 12 ++- man/startItems.Rd | 20 +++-- man/test.cbList.Rd | 2 man/testList.Rd | 8 -- man/thetaEst.Rd | 37 ++++++--- 36 files changed, 543 insertions(+), 306 deletions(-)
Title: Discontinuous Regression and Image Processing
Description: This is a collection of functions for discontinuous regression
analysis and image processing.
Author: Yicheng Kang <kangx276@umn.edu>
Maintainer: Yicheng Kang <kangx276@umn.edu>
Diff between DRIP versions 1.0 dated 2015-09-22 and 1.1 dated 2015-09-26
DRIP-1.0/DRIP/src/modify1.f |only DRIP-1.0/DRIP/src/modify2.f |only DRIP-1.1/DRIP/DESCRIPTION | 8 +-- DRIP-1.1/DRIP/MD5 | 56 ++++++++++++------------- DRIP-1.1/DRIP/man/kid.Rd | 2 DRIP-1.1/DRIP/man/modify1.Rd | 2 DRIP-1.1/DRIP/man/modify2.Rd | 2 DRIP-1.1/DRIP/src/cluster_deblur.f90 | 6 +- DRIP-1.1/DRIP/src/cluster_denoise.f90 | 6 +- DRIP-1.1/DRIP/src/d_KQ.f90 | 6 +- DRIP-1.1/DRIP/src/deblur_3stage.f90 | 8 +-- DRIP-1.1/DRIP/src/deblur_3stage_bandwidth.f90 | 10 ++-- DRIP-1.1/DRIP/src/denoise_3stage.f90 | 8 +-- DRIP-1.1/DRIP/src/denoise_3stage_bandwidth.f90 | 9 +--- DRIP-1.1/DRIP/src/extend.f90 | 2 DRIP-1.1/DRIP/src/extend1.f90 | 2 DRIP-1.1/DRIP/src/jp_llk_cv.f90 | 4 - DRIP-1.1/DRIP/src/jp_llk_fit.f90 | 4 - DRIP-1.1/DRIP/src/lc2k_diff.f90 | 4 - DRIP-1.1/DRIP/src/lck_diff.f90 | 4 - DRIP-1.1/DRIP/src/ll2k_diff.f90 | 4 - DRIP-1.1/DRIP/src/llk_diff.f90 | 4 - DRIP-1.1/DRIP/src/modify1.f90 |only DRIP-1.1/DRIP/src/modify2.f90 |only DRIP-1.1/DRIP/src/roofDetect_deblur.f90 | 8 +-- DRIP-1.1/DRIP/src/roofDetect_denoise.f90 | 8 +-- DRIP-1.1/DRIP/src/roofDiff_deblur.f90 | 4 - DRIP-1.1/DRIP/src/roofDiff_denoise.f90 | 4 - DRIP-1.1/DRIP/src/roofEdgeParSel_deblur.f90 | 8 +-- DRIP-1.1/DRIP/src/roofEdgeParSel_denoise.f90 | 10 ++-- DRIP-1.1/DRIP/src/surfest.f90 | 4 - 31 files changed, 100 insertions(+), 97 deletions(-)
More information about weightTAPSPACK at CRAN
Permanent link
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output
Description: Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.5-8 dated 2015-07-30 and 1.5-9 dated 2015-09-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 +++++ src/cairogd.h | 21 +++++++++++++-------- 4 files changed, 24 insertions(+), 14 deletions(-)
Title: Event-Related Potential (ERP) Data Exploration Made Easy
Description: A set of user-friendly functions to aid in organizing, plotting
and analyzing event-related potential (ERP) data. Provides an easy-to-learn
method to explore ERP data. Should be useful to those without a background
in computer programming, and to those who are new to ERPs (or new to the
more advanced ERP software available). Emphasis has been placed on highly
automated processes using functions with as few arguments as possible.
Expects processed (cleaned) data.
Author: Travis Moore [aut, cre]
Maintainer: Travis Moore <travis.m.moore@vanderbilt.edu>
Diff between erp.easy versions 0.6.2 dated 2015-09-24 and 0.6.3 dated 2015-09-25
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with Oleson et al's modified p-value technique.
Author: Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob McMurray
Maintainer: Michael Seedorff <michael-seedorff@uiowa.edu>
Diff between bdots versions 0.1.1 dated 2015-09-21 and 0.1.2 dated 2015-09-25
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 4 +++- inst/doc/bdots.R | 40 +++++++++++++++++++++++----------------- inst/doc/bdots.Rnw | 13 ++++++++++--- inst/doc/bdots.pdf |binary vignettes/bdots.Rnw | 13 ++++++++++--- 7 files changed, 58 insertions(+), 36 deletions(-)
Title: Bias-Corrected Bayesian Classification with Selected Features
Description: Fully Bayesian Classification with a subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.
Author: Longhai Li <longhai@math.usask.ca>
Maintainer: Longhai Li <longhai@math.usask.ca>
Diff between BCBCSF versions 1.0-0 dated 2013-01-18 and 1.0-1 dated 2015-09-25
DESCRIPTION | 23 ++++++----------------- MD5 | 8 ++++---- NAMESPACE | 6 +++++- R/comp_pred.r | 47 ++++++++++++++++++++++++++--------------------- R/tr-pr.r | 13 +++++++------ 5 files changed, 48 insertions(+), 49 deletions(-)
Title: Detecting Differentially Expressed Genes in Time Course RNA-Seq
Data
Description: Uses a negative binomial mixed-effects (NBME) model to detect nonparallel differential expression(NPDE) genes and parallel differential expression(PDE) genes in the time course RNA-seq data.
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao <fangaohz@gmail.com>
Diff between timeSeq versions 1.0.0 dated 2015-04-19 and 1.0.1 dated 2015-09-25
timeSeq-1.0.0/timeSeq/man/timeSeq_1.0-package.Rd |only timeSeq-1.0.1/timeSeq/DESCRIPTION | 17 ++-- timeSeq-1.0.1/timeSeq/MD5 | 36 ++++++--- timeSeq-1.0.1/timeSeq/NAMESPACE | 2 timeSeq-1.0.1/timeSeq/build |only timeSeq-1.0.1/timeSeq/data/Idgf2.RData |only timeSeq-1.0.1/timeSeq/inst |only timeSeq-1.0.1/timeSeq/man/Idgf2.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.Rd | 6 - timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.geneset.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.Rd | 62 ++++++++--------- timeSeq-1.0.1/timeSeq/man/timeSeq.geneset.Rd | 42 +++++------ timeSeq-1.0.1/timeSeq/man/timeSeq.genesetscreeplot.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.heatmap.Rd | 10 +- timeSeq-1.0.1/timeSeq/man/timeSeq.permutate.Rd | 38 +++++----- timeSeq-1.0.1/timeSeq/man/timeSeq.plot.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.screeplot.Rd | 4 - timeSeq-1.0.1/timeSeq/man/timeSeq.sort.Rd | 20 ++--- timeSeq-1.0.1/timeSeq/man/timeSeq_1.0.1-package.Rd |only timeSeq-1.0.1/timeSeq/vignettes |only 20 files changed, 135 insertions(+), 120 deletions(-)
Title: Betting Odds Conversion
Description: Conversion between the most common odds types for sports betting. Hong Kong odds, US odds, Decimal odds, Indonesian odds, Malaysian odds, and raw Probability are covered in this package.
Author: Marco Blume
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between odds.converter versions 1.1 dated 2015-06-04 and 1.2 dated 2015-09-25
odds.converter-1.1/odds.converter/R/odds.converter-internal.R |only odds.converter-1.2/odds.converter/DESCRIPTION | 8 +++--- odds.converter-1.2/odds.converter/MD5 | 12 ++++++++-- odds.converter-1.2/odds.converter/NEWS |only odds.converter-1.2/odds.converter/R/odds.2all.R |only odds.converter-1.2/odds.converter/README.md |only odds.converter-1.2/odds.converter/man/odds.dec2all.Rd |only odds.converter-1.2/odds.converter/man/odds.hk2all.Rd |only odds.converter-1.2/odds.converter/man/odds.indo2all.Rd |only odds.converter-1.2/odds.converter/man/odds.malay2all.Rd |only odds.converter-1.2/odds.converter/man/odds.prob2all.Rd |only odds.converter-1.2/odds.converter/man/odds.us2all.Rd |only 12 files changed, 14 insertions(+), 6 deletions(-)
More information about odds.converter at CRAN
Permanent link
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.4 dated 2015-09-09 and 1.5 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Plot.CA.R | 36 ++++++++++++++++++++---------------- R/Plot.PCA.R | 36 +++++++++++++++++++++--------------- man/MVar.pt-package.Rd | 4 ++-- man/Plot.CA.Rd | 6 +++--- man/Plot.PCA.Rd | 4 +++- 7 files changed, 59 insertions(+), 47 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.1.0 dated 2015-09-10 and 0.2.0 dated 2015-09-25
kdecopula-0.1.0/kdecopula/man/kdecopula-package.Rd |only kdecopula-0.2.0/kdecopula/DESCRIPTION | 20 kdecopula-0.2.0/kdecopula/MD5 | 26 kdecopula-0.2.0/kdecopula/NAMESPACE | 7 kdecopula-0.2.0/kdecopula/NEWS.md |only kdecopula-0.2.0/kdecopula/R/dprhkdecop.R |only kdecopula-0.2.0/kdecopula/R/generics.R |only kdecopula-0.2.0/kdecopula/R/kdecop.R | 448 ++---------- kdecopula-0.2.0/kdecopula/R/kdecopula-package.R |only kdecopula-0.2.0/kdecopula/R/plot.kdecopula.R |only kdecopula-0.2.0/kdecopula/README.md |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-3-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-6-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-7-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-8-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-9-1.png |only kdecopula-0.2.0/kdecopula/man/dkdecop.Rd |only kdecopula-0.2.0/kdecopula/man/kdecop.Rd | 163 ++-- kdecopula-0.2.0/kdecopula/man/kdecopula.Rd |only kdecopula-0.2.0/kdecopula/man/plot.kdecopula.Rd | 76 -- kdecopula-0.2.0/kdecopula/man/wdbc.Rd | 96 +- 21 files changed, 316 insertions(+), 520 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
Author: Eduard Szoecs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szoecs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.2 dated 2015-08-14 and 0.0.3 dated 2015-09-25
webchem-0.0.2/webchem/R/allanwood.R |only webchem-0.0.2/webchem/man/allanwood.Rd |only webchem-0.0.2/webchem/tests/testthat/test-allanwood.R |only webchem-0.0.3/webchem/DESCRIPTION | 21 ++++--- webchem-0.0.3/webchem/MD5 | 51 +++++++++++------ webchem-0.0.3/webchem/NAMESPACE | 10 +++ webchem-0.0.3/webchem/NEWS | 25 +++++++- webchem-0.0.3/webchem/R/alanwood.R |only webchem-0.0.3/webchem/R/cir.R | 9 ++- webchem-0.0.3/webchem/R/cts.R | 6 +- webchem-0.0.3/webchem/R/etox.R |only webchem-0.0.3/webchem/R/physprop.R |only webchem-0.0.3/webchem/R/ppdb.R |only webchem-0.0.3/webchem/R/webchem-deprecated.R |only webchem-0.0.3/webchem/data |only webchem-0.0.3/webchem/man/alanwood.Rd |only webchem-0.0.3/webchem/man/cir_query.Rd | 3 + webchem-0.0.3/webchem/man/cts_compinfo.Rd | 2 webchem-0.0.3/webchem/man/cts_convert.Rd | 4 - webchem-0.0.3/webchem/man/etox_basic.Rd |only webchem-0.0.3/webchem/man/etox_targets.Rd |only webchem-0.0.3/webchem/man/etox_tests.Rd |only webchem-0.0.3/webchem/man/get_etoxid.Rd |only webchem-0.0.3/webchem/man/pan.Rd | 2 webchem-0.0.3/webchem/man/physprop.Rd |only webchem-0.0.3/webchem/man/ppdb_buildidx.Rd |only webchem-0.0.3/webchem/man/ppdb_idx.Rd |only webchem-0.0.3/webchem/man/ppdb_query.Rd |only webchem-0.0.3/webchem/man/webchem-deprecated.Rd |only webchem-0.0.3/webchem/tests/testthat/test-alanwood.R |only webchem-0.0.3/webchem/tests/testthat/test-chemspider.R | 20 ++++++ webchem-0.0.3/webchem/tests/testthat/test-cir.R | 14 ++++ webchem-0.0.3/webchem/tests/testthat/test-cts.R | 31 +++++++++- webchem-0.0.3/webchem/tests/testthat/test-etox.R |only webchem-0.0.3/webchem/tests/testthat/test-pan.R | 18 ++++-- webchem-0.0.3/webchem/tests/testthat/test-physprop.R |only webchem-0.0.3/webchem/tests/testthat/test-ppdb.R |only webchem-0.0.3/webchem/tests/testthat/test-pubchem.R | 18 +++++- 38 files changed, 186 insertions(+), 48 deletions(-)
Title: Cardiovascular Safety Exposure-Response Modeling in Early-Phase
Clinical Studies
Description: Includes 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
Author: Daniela J Conrado [aut, cre], William S Denney [aut], Gregory J Hather [aut], Danny Chen [ctb]
Maintainer: Daniela J Conrado <danielac@metrumrg.com>
Diff between cardioModel versions 1.0 dated 2015-09-24 and 1.1 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/21_cardioModel.R | 45 ++++++++++++++++++++++++++------------------- R/data.R | 2 +- data/sim_QTcf.RData |binary man/sim_QTcf.Rd | 2 +- 6 files changed, 37 insertions(+), 30 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.3-0 dated 2015-05-26 and 2.3-1 dated 2015-09-25
DESCRIPTION | 10 +-- MD5 | 135 +++++++++++++++++++++--------------------- NAMESPACE | 4 - R/adonis.R | 6 - R/alias.cca.R | 4 - R/anosim.R | 3 R/anova.cca.R | 16 +++- R/anova.ccabyterm.R | 70 ++++++++++++++------- R/anova.ccalist.R | 30 +++++---- R/anova.ccanull.R | 21 ++++-- R/biplot.rda.R | 7 +- R/centroids.cca.R | 2 R/factorfit.R | 3 R/mantel.R | 3 R/mantel.partial.R | 3 R/metaMDS.R | 21 ++++-- R/metaMDSdist.R | 1 R/monoMDS.R | 2 R/mrpp.R | 3 R/mso.R | 4 - R/oecosimu.R | 11 ++- R/ordiR2step.R | 5 + R/ordiareatest.R | 3 R/permustats.R | 37 ++++++++--- R/permutest.betadisper.R | 10 +-- R/permutest.cca.R | 4 - R/plot.cca.R | 10 +-- R/plot.prc.R | 9 +- R/points.cca.R | 9 +- R/predict.cca.R | 11 ++- R/predict.rda.R | 11 ++- R/print.cca.R | 2 R/print.permutest.cca.R | 3 R/protest.R | 3 R/rarecurve.R | 10 +++ R/scalingUtils.R |only R/scores.cca.R | 22 +++--- R/scores.rda.R | 6 + R/simper.R | 3 R/summary.cca.R | 14 ++-- R/summary.prc.R | 7 -- R/text.cca.R | 9 +- R/tolerance.cca.R | 9 +- R/vectorfit.R | 3 data/BCI.env.rda |only inst/NEWS.Rd | 79 ++++++++++++++++++++++++ inst/doc/FAQ-vegan.pdf |binary inst/doc/NEWS.html | 92 ++++++++++++++++++++++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary man/BCI.Rd | 42 +++++++++---- man/adipart.Rd | 6 + man/anova.cca.Rd | 5 + man/biplot.rda.Rd | 22 +++++- man/cca.Rd | 4 - man/diversity.Rd | 107 ++++----------------------------- man/monoMDS.Rd | 2 man/permustats.Rd | 12 +-- man/plot.cca.Rd | 75 +++++++++++++++-------- man/prc.Rd | 23 +++++-- man/predict.cca.Rd | 16 +++- man/rarefy.Rd |only man/specaccum.Rd | 77 ++++++++++------------- man/tolerance.Rd | 8 +- vignettes/FAQ-vegan.pdf |binary vignettes/NEWS.html | 92 ++++++++++++++++++++++++++++ vignettes/decision-vegan.tex | 20 +++--- vignettes/diversity-vegan.tex | 78 ++++++++++++------------ vignettes/intro-vegan.tex | 50 +++++++-------- 70 files changed, 876 insertions(+), 493 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.6 dated 2015-08-15 and 1.7 dated 2015-09-25
archivist-1.6/archivist/R/saveSetToRepo.R |only archivist-1.6/archivist/man/saveSetToRepo.Rd |only archivist-1.7/archivist/DESCRIPTION | 11 +- archivist-1.7/archivist/MD5 | 104 ++++++++++----------- archivist-1.7/archivist/NAMESPACE | 19 ++- archivist-1.7/archivist/NEWS.md |only archivist-1.7/archivist/R/Tags.R | 20 ++-- archivist-1.7/archivist/R/ahistory.R | 32 +++--- archivist-1.7/archivist/R/archivist-package.R | 26 ++--- archivist-1.7/archivist/R/archivistOptions.R | 2 archivist-1.7/archivist/R/aread.R | 30 ++++-- archivist-1.7/archivist/R/asearch.R | 39 +++++-- archivist-1.7/archivist/R/cache.R | 2 archivist-1.7/archivist/R/copyToRepo.R | 6 - archivist-1.7/archivist/R/createEmptyRepo.R | 14 +- archivist-1.7/archivist/R/deleteRepo.R | 11 +- archivist-1.7/archivist/R/getTags.R | 2 archivist-1.7/archivist/R/loadFromRepo.R | 10 +- archivist-1.7/archivist/R/magrittr.R | 4 archivist-1.7/archivist/R/rmFromRepo.R | 2 archivist-1.7/archivist/R/saveToRepo.R | 2 archivist-1.7/archivist/R/searchInRepo.R | 2 archivist-1.7/archivist/R/setRepo.R | 36 ++++--- archivist-1.7/archivist/R/shinySearchInLocalRepo.R | 38 ++++--- archivist-1.7/archivist/R/showRepo.R | 10 -- archivist-1.7/archivist/R/summaryRepo.R | 6 - archivist-1.7/archivist/R/zipRepo.R | 2 archivist-1.7/archivist/R/zzz.R | 2 archivist-1.7/archivist/inst |only archivist-1.7/archivist/man/Repository.Rd | 5 - archivist-1.7/archivist/man/Tags.Rd | 25 ++--- archivist-1.7/archivist/man/addTagsRepo.Rd | 5 - archivist-1.7/archivist/man/ahistory.Rd | 24 ++-- archivist-1.7/archivist/man/archivist-package.Rd | 5 - archivist-1.7/archivist/man/archivistOptions.Rd | 7 - archivist-1.7/archivist/man/aread.Rd | 18 ++- archivist-1.7/archivist/man/asearch.Rd | 15 +-- archivist-1.7/archivist/man/cache.Rd | 7 - archivist-1.7/archivist/man/copyToRepo.Rd | 9 - archivist-1.7/archivist/man/createEmptyRepo.Rd | 9 - archivist-1.7/archivist/man/deleteRepo.Rd | 13 +- archivist-1.7/archivist/man/getTags.Rd | 12 +- archivist-1.7/archivist/man/loadFromRepo.Rd | 7 - archivist-1.7/archivist/man/magrittr.Rd | 7 - archivist-1.7/archivist/man/md5hash.Rd | 5 - archivist-1.7/archivist/man/rmFromRepo.Rd | 6 - archivist-1.7/archivist/man/saveToRepo.Rd | 6 - archivist-1.7/archivist/man/searchInRepo.Rd | 7 - archivist-1.7/archivist/man/setRepo.Rd | 8 - archivist-1.7/archivist/man/shinySearchInRepo.Rd | 14 ++ archivist-1.7/archivist/man/showRepo.Rd | 15 --- archivist-1.7/archivist/man/summaryRepo.Rd | 11 +- archivist-1.7/archivist/man/zipRepo.Rd | 12 +- archivist-1.7/archivist/tests |only 54 files changed, 366 insertions(+), 318 deletions(-)
Title: The Skillings-Mack Test Statistic for Block Designs with Missing
Observations
Description: A generalization of the statistic used in Friedman's ANOVA method and in Durbin's rank test. This nonparametric statistical test is useful for the data obtained from block designs with missing observations occurring randomly. A resulting p-value is based on the chi-squared distribution and Monte Carlo method.
Author: Patchanok Srisuradetchai
Maintainer: Patchanok Srisuradetchai <s.patchanok@gmail.com>
Diff between Skillings.Mack versions 1.0-2 dated 2013-09-17 and 1.10 dated 2015-09-25
Skillings.Mack-1.0-2/Skillings.Mack/R/SkiMack.R |only Skillings.Mack-1.0-2/Skillings.Mack/man/SkiMack.Rd |only Skillings.Mack-1.10/Skillings.Mack/DESCRIPTION | 23 ++++++++++----------- Skillings.Mack-1.10/Skillings.Mack/MD5 | 8 +++---- Skillings.Mack-1.10/Skillings.Mack/NAMESPACE | 5 +++- Skillings.Mack-1.10/Skillings.Mack/R/Ski.Mack.R |only Skillings.Mack-1.10/Skillings.Mack/man/Ski.Mack.Rd |only 7 files changed, 20 insertions(+), 16 deletions(-)
More information about Skillings.Mack at CRAN
Permanent link
Title: Tools for the 'qdap' Package
Description: A collection of tools associated with the 'qdap' package
that may be useful outside of the context of text analysis.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Kirill Muller [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapTools versions 1.1.0 dated 2014-12-21 and 1.3.1 dated 2015-09-25
DESCRIPTION | 24 ++++++------- MD5 | 69 ++++++++++++++++++++++------------------ NAMESPACE | 7 +++- NEWS | 25 +++++++++++++- R/list2df.R | 24 ++++++++----- R/loc_split.R | 43 +++++++++++++++++------- R/mtabulate.R | 50 +++++++++++++++++++++++----- R/read_docx.R | 14 ++++++-- R/repo2github.R | 4 +- R/run_split.R |only R/shift.R |only R/split_vector.R | 3 + R/start_end.R |only R/url_dl.R | 2 - README.md | 24 ++++++++----- inst/CITATION | 10 ++--- man/Deprecated.Rd | 3 + man/hash.Rd | 3 + man/id.Rd | 3 + man/list2df.Rd | 3 + man/loc_split.Rd | 8 ++-- man/lookup.Rd | 3 + man/lookup_e.Rd | 3 + man/mtabulate.Rd | 15 +++++--- man/pad.Rd | 3 + man/print.v_outer.Rd | 3 + man/read_docx.Rd | 15 ++++++-- man/repo2github.Rd | 3 + man/run_split.Rd |only man/shift.Rd |only man/split_vector.Rd | 6 ++- man/start_end.Rd |only man/text2color.Rd | 3 + man/timeconv.Rd | 3 + man/url_dl.Rd | 3 + man/v_outer.Rd | 3 + tests/testthat/test-mtabulate.R | 5 +- tests/testthat/test-run_split.R |only tests/testthat/test-shift.R |only tests/testthat/test-start_end.R |only 40 files changed, 262 insertions(+), 125 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.8-1 dated 2015-06-24 and 0.8-2 dated 2015-09-25
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- NAMESPACE | 12 ++++++--- NEWS | 35 ++++++++++++++++++++++++++++ R/amova.R | 16 ++++--------- R/conversion.R | 8 +++--- R/haplotype.R | 56 ++++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/ReadingFiles.pdf |binary man/haploNet.Rd | 11 ++++++--- man/haplotype.loci.Rd | 4 ++- man/mst.Rd | 7 +++++ man/tajima.test.Rd | 4 +++ src/pegas.c | 16 ++++++++----- 14 files changed, 143 insertions(+), 60 deletions(-)
Title: A System for Embedded Scientific Computing and Reproducible
Research with R
Description: The OpenCPU system exposes an HTTP API for embedded scientific
computing with R. This provides scalable foundations for integrating R
based analysis and visualization modules into pipelines, web applications
or big data infrastructures. The OpenCPU server can run either as a
single-user development server within the interactive R session, or as a
high performance multi-user cloud server that builds on Linux, Nginx and
rApache. The current R package forms the core of the system. When loaded
in R, it automatically initiates the single-user server and displays the
web address in the console. Visit the OpenCPU website for detailed
information and documentation on the API.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between opencpu versions 1.4.6 dated 2015-01-31 and 1.5.1 dated 2015-09-25
DESCRIPTION | 9 +++---- MD5 | 50 ++++++++++++++++++++++---------------------- NEWS | 6 +++++ R/cmd_exists.R | 2 - R/emptyplot.R | 2 - R/eval_fork.R | 2 - R/eval_psock.R | 2 - R/extract.R | 14 ++++++------ R/fixplot.R | 4 +-- R/gettmpdir.R | 2 - R/github_install.R | 3 +- R/httpget_github.R | 2 - R/httpget_object.R | 6 ++--- R/httpget_webhook.R | 2 - R/httpuv_fork.R | 2 - R/listallusers.R | 2 - R/main.R | 2 - R/parse_arg.R | 2 - R/rapachehandler.R | 5 ++++ R/request.R | 5 ++-- R/res.R | 2 - R/rookhandler.R | 7 +++++- R/userlibpath.R | 24 ++++++++++++++++++--- build/vignette.rds |binary inst/doc/opencpu-paper.pdf |binary inst/doc/opencpu-server.pdf |binary 26 files changed, 96 insertions(+), 61 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.3.3 dated 2015-08-22 and 1.4.0 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ NEWS | 5 +++++ R/get_download.R | 10 +++++++--- R/plot-methods.R |only README.md | 7 ++++--- inst/img/Thumbs.db |only 8 files changed, 32 insertions(+), 15 deletions(-)
Title: Tools for Nanoparticle Simulation and Calculation of PDF and
Total Scattering Structure Function
Description: This software package implements functions to simulate spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal structures and to calculate the associated pair-distribution function and X-ray/neutron total-scattering signals. It also provides a target function that can be used for simultaneous fitting of small- and wide-angle total scattering data in real and reciprocal spaces. The target function can be generated either as a sum of weighted residuals for individual datasets or as a vector of residuals suitable for optimization using multi-criteria algorithms (e.g. Pareto methods).
Author: Anton Gagin, Katharine Mullen, Igor Levin
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between nanop versions 2.0-5 dated 2015-04-07 and 2.0-6 dated 2015-09-25
DESCRIPTION | 8 +-- MD5 | 8 +-- NAMESPACE | 3 + inst/CITATION | 54 ++++++++++----------- man/plotPart.Rd | 144 ++++++++++++++++++++++++++++---------------------------- 5 files changed, 110 insertions(+), 107 deletions(-)
Title: Multi-way Standard Error Clustering
Description: Exports two functions implementing
multi-way clustering using the method suggested by Cameron, Gelbach, &
Miller (2011) and cluster (or block)
bootstrapping for estimating variance-covariance matrices. Normal one and
two-way clustering matches the results of other common statistical
packages. Missing values are handled transparently and rudimentary
parallelization support is provided.
Author: Nathaniel Graham and Mahmood Arai and Björn Hagströmer
Maintainer: Nathaniel Graham <npgraham1@gmail.com>
Diff between multiwayvcov versions 1.2.1 dated 2014-10-20 and 1.2.2 dated 2015-09-25
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 13 ++++++++++++- R/cluster_boot.r | 23 ++++++++++++++++++++++- R/cluster_vcov.r | 31 ++++++++++++++++++++++++++++--- man/cluster.boot.Rd | 11 ++++++++++- man/cluster.vcov.Rd | 17 +++++++++++++++-- man/petersen.Rd | 3 ++- 8 files changed, 101 insertions(+), 21 deletions(-)
Title: Estimation of Multinormal Mixture Distribution
Description: Fit multivariate mixture of normal distribution using
covariance structure.
Author: Charles-Edouard Giguere
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.ca>
Diff between mmeln versions 1.1 dated 2013-02-11 and 1.2 dated 2015-09-25
ChangeLog | 3 + DESCRIPTION | 16 +++-- MD5 | 22 +++---- NAMESPACE | 4 + R/cs.R | 147 ++++++++++++++++++++++++++++++--------------------- R/ind.R | 20 +++--- R/mmeln.R | 10 +-- R/mutil.R | 10 +-- man/estim.mmeln.Rd | 6 +- man/mmeln-package.Rd | 7 +- man/mmeln.Rd | 9 ++- man/post.Rd | 7 +- 12 files changed, 152 insertions(+), 109 deletions(-)
Title: Multi-Analysis Distance Sampling
Description: Performs distance sampling analyses on a number of species
accounting for unidentified sightings, model uncertainty and covariate
uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between mads versions 0.1.2 dated 2015-02-27 and 0.1.3 dated 2015-09-25
mads-0.1.2/mads/inst/testData/input_checks/ddf_dat_CD.csv |only mads-0.1.3/mads/DESCRIPTION | 10 mads-0.1.3/mads/MD5 | 91 ++-- mads-0.1.3/mads/NAMESPACE | 1 mads-0.1.3/mads/NEWS | 12 mads-0.1.3/mads/R/calculate.dht.R | 11 mads-0.1.3/mads/R/check.bootstrap.options.r | 2 mads-0.1.3/mads/R/check.covar.uncertainty.R | 4 mads-0.1.3/mads/R/execute.multi.analysis.R | 274 +++++++------- mads-0.1.3/mads/R/fit.ddf.models.R | 1 mads-0.1.3/mads/R/process.bootstrap.results.R | 2 mads-0.1.3/mads/R/resample.covariates.R | 4 mads-0.1.3/mads/R/rtpois.R | 3 mads-0.1.3/mads/R/summary.ma.species.R | 2 mads-0.1.3/mads/R/summary.ma.unid.R | 1 mads-0.1.3/mads/inst/tests/test_DataInputChecks.R | 133 +++++- mads-0.1.3/mads/inst/tests/test_singleObserver.R | 187 ++++----- mads-0.1.3/mads/man/accumulate.results.Rd | 3 mads-0.1.3/mads/man/calculate.dht.Rd | 14 mads-0.1.3/mads/man/check.convergence.Rd | 3 mads-0.1.3/mads/man/check.covar.uncertainty.Rd | 3 mads-0.1.3/mads/man/check.ddf.models.Rd | 3 mads-0.1.3/mads/man/check.species.code.definitions.Rd | 3 mads-0.1.3/mads/man/check.species.presence.Rd | 3 mads-0.1.3/mads/man/create.obs.table.Rd | 3 mads-0.1.3/mads/man/create.param.arrays.Rd | 3 mads-0.1.3/mads/man/create.result.arrays.Rd | 3 mads-0.1.3/mads/man/execute.multi.analysis.Rd | 15 mads-0.1.3/mads/man/fit.ddf.models.Rd | 3 mads-0.1.3/mads/man/format.dht.results.Rd | 3 mads-0.1.3/mads/man/get.datasets.Rd | 3 mads-0.1.3/mads/man/mae.warning.Rd | 3 mads-0.1.3/mads/man/model.description.Rd | 3 mads-0.1.3/mads/man/process.bootstrap.results.Rd | 3 mads-0.1.3/mads/man/process.warnings.Rd | 3 mads-0.1.3/mads/man/prorate.unidentified.Rd | 3 mads-0.1.3/mads/man/renumber.duplicates.Rd | 3 mads-0.1.3/mads/man/resample.covariates.Rd | 3 mads-0.1.3/mads/man/resample.data.Rd | 3 mads-0.1.3/mads/man/rtpois.Rd | 3 mads-0.1.3/mads/man/store.param.ests.Rd | 3 mads-0.1.3/mads/man/summary.ma.Rd | 3 mads-0.1.3/mads/man/summary.ma.allspecies.Rd | 3 mads-0.1.3/mads/man/summary.ma.allunid.Rd | 3 mads-0.1.3/mads/man/summary.ma.analysis.Rd | 3 mads-0.1.3/mads/man/summary.ma.species.Rd | 3 mads-0.1.3/mads/man/summary.ma.unid.Rd | 3 47 files changed, 497 insertions(+), 354 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.1 dated 2015-06-16 and 1.2 dated 2015-09-25
DESCRIPTION | 15 ++++++++------- MD5 | 28 +++++++++++++++++++++------- NAMESPACE | 8 ++++++-- R/marginRecon.R | 7 ++----- R/plotHisse.R | 4 ++++ R/simulateHisse.R |only R/singleModels.R |only README.md |only build |only inst |only man/plotHisse.Rd | 21 +++++++++++---------- man/simToPhylo.Rd |only man/simulateHisse.Rd |only man/transMat.Rd | 2 +- tests/testthat/test_likelihood.R | 4 ++-- tests/testthat/test_simulator.R |only vignettes |only 17 files changed, 55 insertions(+), 34 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.0 dated 2015-06-18 and 2.1 dated 2015-09-25
DESCRIPTION | 13 +++++++------ MD5 | 14 ++++++++------ NAMESPACE | 2 ++ R/F.window.R |only man/F.window.Rd |only man/dataOvarian.Rd | 10 +++++----- man/joint.Cox-package.Rd | 9 +++++---- man/jointCox.indep.reg.Rd | 4 ++-- man/jointCox.reg.Rd | 4 ++-- 9 files changed, 31 insertions(+), 25 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. It repeatedly
generates instances of a user defined population within a given survey
region, generates realisations of a survey design (currently these must
be pre-generated using Distance software) and simulates the detection
process. The data are then analysed so that the results can be compared for
accuracy and precision across all replications. This will allow users to
select survey designs which will give them the best accuracy and precision
given their expectations about population distribution. Any uncertainty in
population distribution or population parameters can be included by running
the different survey designs for a number of different population
descriptions. An example simulation can be found in the help file
for make.simulation.
Author: Laura Marshall <lhm@st-and.ac.uk>
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between DSsim versions 1.0.3 dated 2015-02-27 and 1.0.4 dated 2015-09-25
DESCRIPTION | 60 ++-- MD5 | 194 +++++++------- NAMESPACE | 69 +++-- NEWS | 18 + R/Class.Constructors.R | 73 +++-- R/DDF.Analysis.R | 66 ++--- R/DDF.Data.R | 29 +- R/Density.R | 105 +++----- R/Detectability.R | 42 +-- R/LT.Design.R | 52 +-- R/LT.EqAngle.ZZ.Design.R | 4 R/LT.EqSpace.ZZ.Design.R | 4 R/LT.Random.Design.R | 4 R/LT.Survey.R | 41 --- R/LT.Survey.Results.R | 169 +++++++++--- R/LT.Systematic.Design.R | 3 R/LT.User.Specified.Design.R | 3 R/Line.Transect.R | 38 +- R/Obs.Table.R | 3 R/PT.Design.R | 19 - R/Population.Description.R | 87 ++---- R/Population.R | 53 ++-- R/Region.R | 70 ++--- R/Region.Table.R | 3 R/Sample.Table.R | 3 R/Simulation.R | 431 +++++++++++++++++---------------- R/Simulation.Summary.R | 10 R/Single.Obs.DDF.Data.R | 23 - R/Single.Obs.LT.Survey.R | 34 -- R/Survey.Design.R | 38 -- R/Survey.R | 51 +-- R/add.dist.error.R | 1 R/add.summary.results.R | 1 R/calc.area.R | 13 R/calc.poss.detect.dists.R | 9 R/check.intersection.R | 1 R/check.shapefile.R | 4 R/coords.from.shapefile.R | 3 R/generate.pop.D.R | 20 - R/generate.pop.N.R | 2 R/generic.functions.R | 22 - R/get.ave.density.R | 8 R/get.bound.box.R | 17 - R/get.sampler.info.R | 2 R/get.surface.constant.R | 3 R/get.surface.gam.R | 2 R/hn.detect.R | 2 R/hr.detect.R | 1 R/is.gap.R | 12 R/modify.strata.for.analysis.R |only R/simulate.detections.R | 4 R/single.simulation.loop.R | 8 R/uf.detect.R |only man/DDF.Analysis-class.Rd | 41 +-- man/DDF.Data-class.Rd | 10 man/Density-class.Rd | 99 +------ man/Detectability-class.Rd | 37 +- man/LT.Design-class.Rd | 14 - man/LT.Survey-class.Rd | 14 - man/LT.Survey.Results-class.Rd | 83 +----- man/Line.Transect-class.Rd | 63 ---- man/Obs.Table-class.Rd | 8 man/PT.Design-class.Rd |only man/Population-class.Rd | 45 +-- man/Population.Description-class.Rd | 43 +-- man/Region-class.Rd | 113 ++------ man/Region.Table-class.Rd | 8 man/Sample.Table-class.Rd | 8 man/Simulation-class.Rd | 83 ++---- man/Simulation.Summary-class.Rd | 10 man/Single.Obs.DDF.Data-class.Rd | 47 --- man/Single.Obs.LT.Survey-class.Rd | 3 man/Survey-class.Rd | 15 - man/Survey.Design-class.Rd | 37 +- man/add.hotspot-methods.Rd | 8 man/create.bins.Rd | 3 man/create.region.table-methods.Rd | 9 man/create.sample.table-methods.Rd | 11 man/create.survey.results-methods.Rd | 13 man/description.summary.Rd | 9 man/generate.population-methods.Rd | 19 - man/generate.transects-methods.Rd | 19 - man/get.N-methods.Rd | 3 man/get.area-methods.Rd | 5 man/get.distance.data-methods.Rd | 9 man/make.ddf.analysis.list.Rd | 14 - man/make.density.Rd | 8 man/make.design.Rd | 6 man/make.detectability.Rd | 3 man/make.population.description.Rd | 3 man/make.region.Rd | 3 man/make.simulation.Rd | 3 man/plot.DDF.Data-methods.Rd |only man/plot.Density-methods.Rd |only man/plot.LT.Survey.Results-methods.Rd |only man/plot.Line.Transect-methods.Rd |only man/plot.Population-methods.Rd |only man/plot.Region-methods.Rd |only man/rename.duplicates.Rd | 3 man/run-methods.Rd | 12 man/run.analysis-methods.Rd | 13 man/show.Simulation-methods.Rd |only man/show.Simulation.Summary-methods.Rd |only man/summary.Simulation-methods.Rd |only 104 files changed, 1351 insertions(+), 1540 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.9 dated 2015-08-22 and 0.9.1 dated 2015-09-25
DESCRIPTION | 10 +++--- MD5 | 15 +++++---- R/auxilaryfunctions.R | 79 +++++++++++++++++++++++++++++++---------------- R/boral.jags.R | 83 ++++++++++++++++++++++++++++++-------------------- inst/NEWS.Rd | 82 ++++++++++++++++++++++++------------------------- man/boral-package.Rd | 2 - man/boral.Rd | 6 +-- tests |only 8 files changed, 161 insertions(+), 116 deletions(-)
Title: Extensions of Exponential Random Graph Models
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), Temporal Network Autocorrelation Models (TNAM), and Relational Event Models (REM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between xergm versions 1.5 dated 2015-06-14 and 1.5.3 dated 2015-09-25
xergm-1.5.3/xergm/DESCRIPTION | 32 +++++++------ xergm-1.5.3/xergm/MD5 | 41 +---------------- xergm-1.5.3/xergm/NAMESPACE | 78 +-------------------------------- xergm-1.5.3/xergm/R/xergm.R |only xergm-1.5.3/xergm/man/xergm-package.Rd | 17 ++----- xergm-1.5/xergm/R/RcppExports.R |only xergm-1.5/xergm/R/btergm.R |only xergm-1.5/xergm/R/gof.R |only xergm-1.5/xergm/R/interpretation.R |only xergm-1.5/xergm/R/preprocess.R |only xergm-1.5/xergm/R/tnam.R |only xergm-1.5/xergm/data |only xergm-1.5/xergm/inst/extdata |only xergm-1.5/xergm/man/adjust.Rd |only xergm-1.5/xergm/man/btergm-class.Rd |only xergm-1.5/xergm/man/btergm.Rd |only xergm-1.5/xergm/man/chemnet.Rd |only xergm-1.5/xergm/man/getformula.Rd |only xergm-1.5/xergm/man/gof.Rd |only xergm-1.5/xergm/man/handleMissings.Rd |only xergm-1.5/xergm/man/interpret.Rd |only xergm-1.5/xergm/man/knecht.Rd |only xergm-1.5/xergm/man/plot.btergmgof.Rd |only xergm-1.5/xergm/man/preprocess.Rd |only xergm-1.5/xergm/man/simulate.btergm.Rd |only xergm-1.5/xergm/man/timecov.Rd |only xergm-1.5/xergm/man/tnam-terms.Rd |only xergm-1.5/xergm/man/tnam.Rd |only xergm-1.5/xergm/src |only 29 files changed, 31 insertions(+), 137 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.4-60 dated 2015-07-10 and 0.5-00 dated 2015-09-25
phytools-0.4-60/phytools/R/findMRCA.R |only phytools-0.4-60/phytools/R/getExtant.R |only phytools-0.5-00/phytools/DESCRIPTION | 8 phytools-0.5-00/phytools/MD5 | 179 +++++------ phytools-0.5-00/phytools/NAMESPACE | 37 +- phytools-0.5-00/phytools/R/add.everywhere.R | 7 phytools-0.5-00/phytools/R/add.random.R | 3 phytools-0.5-00/phytools/R/add.species.to.genus.R | 1 phytools-0.5-00/phytools/R/anc.Bayes.R | 4 phytools-0.5-00/phytools/R/anc.ML.R | 49 ++- phytools-0.5-00/phytools/R/anc.trend.R | 3 phytools-0.5-00/phytools/R/ancThresh.R | 2 phytools-0.5-00/phytools/R/backbonePhylo.R | 6 phytools-0.5-00/phytools/R/bmPlot.R | 4 phytools-0.5-00/phytools/R/brownie.lite.R | 2 phytools-0.5-00/phytools/R/brownieREML.R | 43 ++ phytools-0.5-00/phytools/R/collapseTree.R | 15 phytools-0.5-00/phytools/R/contMap.R | 6 phytools-0.5-00/phytools/R/cophylo.R |only phytools-0.5-00/phytools/R/densityMap.R | 14 phytools-0.5-00/phytools/R/drop.tip.simmap.R | 4 phytools-0.5-00/phytools/R/estDiversity.R | 1 phytools-0.5-00/phytools/R/evol.rate.mcmc.R | 8 phytools-0.5-00/phytools/R/evol.vcv.R | 5 phytools-0.5-00/phytools/R/evolvcv.lite.R | 1 phytools-0.5-00/phytools/R/export.as.xml.R | 4 phytools-0.5-00/phytools/R/fancyTree.R | 6 phytools-0.5-00/phytools/R/fastAnc.R | 55 +++ phytools-0.5-00/phytools/R/fastBM.R | 4 phytools-0.5-00/phytools/R/fitBayes.R | 4 phytools-0.5-00/phytools/R/fitDiversityModel.R | 2 phytools-0.5-00/phytools/R/fitMk.R |only phytools-0.5-00/phytools/R/fitPagel.R | 23 - phytools-0.5-00/phytools/R/locate.fossil.R | 3 phytools-0.5-00/phytools/R/locate.yeti.R | 1 phytools-0.5-00/phytools/R/ltt.R | 16 phytools-0.5-00/phytools/R/ltt95.R | 3 phytools-0.5-00/phytools/R/make.era.map.R | 15 phytools-0.5-00/phytools/R/make.simmap.R | 179 +++-------- phytools-0.5-00/phytools/R/map.overlap.R | 19 - phytools-0.5-00/phytools/R/map.to.singleton.R | 3 phytools-0.5-00/phytools/R/mrp.supertree.R | 4 phytools-0.5-00/phytools/R/multiRF.R | 4 phytools-0.5-00/phytools/R/paintSubTree.R | 8 phytools-0.5-00/phytools/R/pgls.Ives.R | 4 phytools-0.5-00/phytools/R/phenogram.R | 8 phytools-0.5-00/phytools/R/phyl.RMA.R | 3 phytools-0.5-00/phytools/R/phyl.cca.R | 3 phytools-0.5-00/phytools/R/phyl.pairedttest.R | 4 phytools-0.5-00/phytools/R/phyl.pca.R | 4 phytools-0.5-00/phytools/R/phyl.resid.R | 4 phytools-0.5-00/phytools/R/phylANOVA.R | 4 phytools-0.5-00/phytools/R/phylo.to.map.R | 12 phytools-0.5-00/phytools/R/phylomorphospace.R | 25 + phytools-0.5-00/phytools/R/phylomorphospace3d.R | 2 phytools-0.5-00/phytools/R/phylosig.R | 2 phytools-0.5-00/phytools/R/plotBranchbyTrait.R | 1 phytools-0.5-00/phytools/R/plotSimmap.R | 63 +++ phytools-0.5-00/phytools/R/plotTree.wBars.R | 1 phytools-0.5-00/phytools/R/ratebystate.R | 1 phytools-0.5-00/phytools/R/rateshift.R | 185 +++++++---- phytools-0.5-00/phytools/R/read.simmap.R | 8 phytools-0.5-00/phytools/R/rerootingMethod.R | 31 - phytools-0.5-00/phytools/R/roundPhylogram.R | 6 phytools-0.5-00/phytools/R/sim.corrs.R | 4 phytools-0.5-00/phytools/R/sim.history.R | 18 - phytools-0.5-00/phytools/R/sim.rates.R | 26 - phytools-0.5-00/phytools/R/splitplotTree.R | 24 + phytools-0.5-00/phytools/R/strahlerNumber.R | 6 phytools-0.5-00/phytools/R/threshBayes.R | 2 phytools-0.5-00/phytools/R/treeSlice.R | 73 +++- phytools-0.5-00/phytools/R/utilities.R | 358 +++++++++++++--------- phytools-0.5-00/phytools/R/write.simmap.R | 127 +++---- phytools-0.5-00/phytools/R/writeAncestors.R | 6 phytools-0.5-00/phytools/R/writeNexus.R | 4 phytools-0.5-00/phytools/README.md |only phytools-0.5-00/phytools/data/anoletree.rda |binary phytools-0.5-00/phytools/man/anoletree.Rd | 2 phytools-0.5-00/phytools/man/brownieREML.Rd | 3 phytools-0.5-00/phytools/man/cladelabels.Rd | 4 phytools-0.5-00/phytools/man/collapseTree.Rd | 2 phytools-0.5-00/phytools/man/cophylo.Rd |only phytools-0.5-00/phytools/man/densityMap.Rd | 2 phytools-0.5-00/phytools/man/fitMk.Rd |only phytools-0.5-00/phytools/man/markChanges.Rd |only phytools-0.5-00/phytools/man/minRotate.Rd | 9 phytools-0.5-00/phytools/man/plotSimmap.Rd | 3 phytools-0.5-00/phytools/man/rateshift.Rd | 7 phytools-0.5-00/phytools/man/reorderSimmap.Rd | 4 phytools-0.5-00/phytools/man/rerootingMethod.Rd | 4 phytools-0.5-00/phytools/man/sim.rates.Rd | 4 phytools-0.5-00/phytools/man/splitEdgeColor.Rd |only phytools-0.5-00/phytools/man/splitplotTree.Rd | 6 phytools-0.5-00/phytools/man/treeSlice.Rd | 4 phytools-0.5-00/phytools/man/write.simmap.Rd | 3 95 files changed, 1124 insertions(+), 707 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.2.2 dated 2015-07-11 and 0.2.3 dated 2015-09-25
DESCRIPTION | 13 +++++++------ MD5 | 34 +++++++++++++++++----------------- NEWS | 8 +++++++- R/dmzsm.R | 4 ++-- R/dvolkov.R | 2 +- R/fitgeom.R | 11 ++++++----- R/fitnbinom.R | 8 ++++---- R/fitpoilog.R | 32 ++++++++++++++++---------------- R/fitsad.R | 12 +++++------- R/sads-methods.R | 6 +++--- README.md | 6 +++--- build/vignette.rds |binary inst/doc/sads_intro.R | 2 +- inst/doc/sads_intro.Rnw | 6 +++--- inst/doc/sads_intro.pdf |binary man/fitsad.Rd | 11 +++++++---- man/sads-package.Rd | 4 ++-- vignettes/sads_intro.Rnw | 6 +++--- 18 files changed, 87 insertions(+), 78 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.1.1.1 dated 2015-08-20 and 1.2.1.1 dated 2015-09-25
pomp-1.1.1.1/pomp/inst/examples/dacca2.R |only pomp-1.1.1.1/pomp/inst/examples/ebola.R |only pomp-1.2.1.1/pomp/DESCRIPTION | 10 +++++----- pomp-1.2.1.1/pomp/MD5 | 22 ++++++++++------------ pomp-1.2.1.1/pomp/R/mif.R | 23 ++++++++++++++--------- pomp-1.2.1.1/pomp/R/pfilter-methods.R | 8 ++++---- pomp-1.2.1.1/pomp/R/pmcmc-methods.R | 20 ++++++++++++++++++++ pomp-1.2.1.1/pomp/build/partial.rdb |binary pomp-1.2.1.1/pomp/inst/NEWS | 17 +++++++++++++++++ pomp-1.2.1.1/pomp/inst/NEWS.Rd | 17 +++++++++++++++++ pomp-1.2.1.1/pomp/man/plugins.Rd | 19 ++++++++++++++++--- pomp-1.2.1.1/pomp/man/pmcmc.Rd | 18 +++++++++++------- pomp-1.2.1.1/pomp/man/sannbox.Rd | 10 ++++++++-- 13 files changed, 122 insertions(+), 42 deletions(-)
Title: Tools for Linear Dimension Reduction
Description: Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace.
Author: Eero Liski [aut], Klaus Nordhausen [aut, cre], Hannu Oja [aut], Anne Ruiz-Gazen [aut]
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between LDRTools versions 0.1 dated 2014-08-08 and 0.2 dated 2015-09-24
LDRTools-0.1/LDRTools/R/SubspaceInternals.R |only LDRTools-0.1/LDRTools/man/subspace-package.Rd |only LDRTools-0.2/LDRTools/DESCRIPTION | 25 +++++++++++-------------- LDRTools-0.2/LDRTools/MD5 | 14 +++++++------- LDRTools-0.2/LDRTools/R/B2P.R | 1 + LDRTools-0.2/LDRTools/R/LDRToolsInternals.R |only LDRTools-0.2/LDRTools/inst/ChangeLog.txt | 10 +++++++++- LDRTools-0.2/LDRTools/man/AOP.Rd | 3 ++- LDRTools-0.2/LDRTools/man/LDRTools-package.Rd |only LDRTools-0.2/LDRTools/man/Pdist.Rd | 3 ++- 10 files changed, 32 insertions(+), 24 deletions(-)
Title: Ecological Regression using Aggregate and Individual Data
Description: Estimating individual-level covariate-outcome associations
using aggregate data ("ecological inference") or a combination of
aggregate and individual-level data ("hierarchical related regression").
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between ecoreg versions 0.2 dated 2010-08-25 and 0.2.1 dated 2015-09-24
DESCRIPTION | 18 +++++++++--------- MD5 |only NAMESPACE | 6 ++++++ R/eco.R | 14 ++++++++------ R/gh.R | 2 +- R/simul.R | 2 +- build |only inst/NEWS | 6 ++++++ inst/doc/ecoreg-guide.pdf |binary man/eco.Rd | 26 +++++++++++++++++++------- man/sim.eco.Rd | 12 ++++++++---- vignettes |only 12 files changed, 58 insertions(+), 28 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.2.4 dated 2015-04-28 and 1.3.0 dated 2015-09-24
DESCRIPTION | 8 - MD5 | 8 - NAMESPACE | 4 R/dunn.test.R | 221 +++++++++++++++++++++++++++++++++---------------------- man/dunn.test.Rd | 17 ++-- 5 files changed, 157 insertions(+), 101 deletions(-)
Title: Dose-Response Modeling with Smoothing Splines
Description: Provides tools for assessing the shape of a dose-response
curve by testing linearity and non-linearity at user-defined cut-offs. It
also provides two methods of estimating a threshold dose, or the dose at
which the dose-response function transitions to significantly increasing:
bi-linear (based on pkg 'segmented') and smoothed with splines (based on
pkg 'mgcv').
Author: Greg Hixon [aut],
Chad Thompson [aut],
Anne Bichteler [aut, cre],
Liz Abraham [ctb]
Maintainer: Anne Bichteler <abichteler@toxstrategies.com>
Diff between drsmooth versions 1.0 dated 2013-12-05 and 1.9.0 dated 2015-09-24
drsmooth-1.0/drsmooth/R/dunnetts1.r |only drsmooth-1.0/drsmooth/R/dunnetts2.r |only drsmooth-1.0/drsmooth/R/dunns1.r |only drsmooth-1.0/drsmooth/R/dunns2.r |only drsmooth-1.0/drsmooth/R/firstDeriv.r |only drsmooth-1.0/drsmooth/R/smooth.r |only drsmooth-1.0/drsmooth/man/dunnetts1.Rd |only drsmooth-1.0/drsmooth/man/dunnetts2.Rd |only drsmooth-1.0/drsmooth/man/dunns1.Rd |only drsmooth-1.0/drsmooth/man/dunns2.Rd |only drsmooth-1.9.0/drsmooth/DESCRIPTION | 45 +++--- drsmooth-1.9.0/drsmooth/MD5 | 131 +++++++++-------- drsmooth-1.9.0/drsmooth/NAMESPACE | 31 ---- drsmooth-1.9.0/drsmooth/NEWS |only drsmooth-1.9.0/drsmooth/R/DIdata.R |only drsmooth-1.9.0/drsmooth/R/bartlett.r | 3 drsmooth-1.9.0/drsmooth/R/chisquare.r | 9 - drsmooth-1.9.0/drsmooth/R/dichot_smooth.R |only drsmooth-1.9.0/drsmooth/R/dosefactor.r | 1 drsmooth-1.9.0/drsmooth/R/drsmooth-package.R | 29 ++- drsmooth-1.9.0/drsmooth/R/drsmooth.R |only drsmooth-1.9.0/drsmooth/R/drsmooth.print.r | 1 drsmooth-1.9.0/drsmooth/R/dunnetts.R |only drsmooth-1.9.0/drsmooth/R/dunnetts.format.r | 1 drsmooth-1.9.0/drsmooth/R/dunnettst3.r | 19 +- drsmooth-1.9.0/drsmooth/R/dunns.R |only drsmooth-1.9.0/drsmooth/R/dunns.format.r | 1 drsmooth-1.9.0/drsmooth/R/expand.R |only drsmooth-1.9.0/drsmooth/R/firstDeriv.R |only drsmooth-1.9.0/drsmooth/R/fishers.exact.R |only drsmooth-1.9.0/drsmooth/R/jonckheere.r | 9 - drsmooth-1.9.0/drsmooth/R/lbcd.r | 4 drsmooth-1.9.0/drsmooth/R/nlaad.r | 8 - drsmooth-1.9.0/drsmooth/R/nlbcd.r | 10 - drsmooth-1.9.0/drsmooth/R/noel.r | 132 +++++++++++++----- drsmooth-1.9.0/drsmooth/R/outlier.r | 5 drsmooth-1.9.0/drsmooth/R/prelimstats.r | 24 ++- drsmooth-1.9.0/drsmooth/R/segment.plot.r | 5 drsmooth-1.9.0/drsmooth/R/segment.print.r | 1 drsmooth-1.9.0/drsmooth/R/segment.r | 14 + drsmooth-1.9.0/drsmooth/R/shapiro.r | 5 drsmooth-1.9.0/drsmooth/R/smooth.R |only drsmooth-1.9.0/drsmooth/R/spline.plot.r | 92 +++++++++--- drsmooth-1.9.0/drsmooth/data/DIdata.rda |only drsmooth-1.9.0/drsmooth/inst/CITATION |only drsmooth-1.9.0/drsmooth/inst/tests/test-nlaad.r | 20 +- drsmooth-1.9.0/drsmooth/inst/tests/test-noel.r | 81 +++++------ drsmooth-1.9.0/drsmooth/inst/tests/test-prelimstats.r | 86 +++++------ drsmooth-1.9.0/drsmooth/inst/tests/test-spline.r | 16 +- drsmooth-1.9.0/drsmooth/man/DIdata.Rd |only drsmooth-1.9.0/drsmooth/man/DRdata.Rd | 9 - drsmooth-1.9.0/drsmooth/man/bartlett.Rd | 8 - drsmooth-1.9.0/drsmooth/man/chisquare.Rd | 8 - drsmooth-1.9.0/drsmooth/man/dichot_smooth.Rd |only drsmooth-1.9.0/drsmooth/man/dosefactor.Rd | 10 - drsmooth-1.9.0/drsmooth/man/drsmooth-package.Rd |only drsmooth-1.9.0/drsmooth/man/drsmooth.Rd | 125 ++++++++++++----- drsmooth-1.9.0/drsmooth/man/drsmooth.print.Rd | 8 - drsmooth-1.9.0/drsmooth/man/dunnetts.Rd |only drsmooth-1.9.0/drsmooth/man/dunnetts.format.Rd | 14 - drsmooth-1.9.0/drsmooth/man/dunnettst3.Rd | 21 +- drsmooth-1.9.0/drsmooth/man/dunns.Rd |only drsmooth-1.9.0/drsmooth/man/dunns.format.Rd | 10 - drsmooth-1.9.0/drsmooth/man/expand.Rd |only drsmooth-1.9.0/drsmooth/man/firstDeriv.Rd | 10 - drsmooth-1.9.0/drsmooth/man/fishers.exact.Rd |only drsmooth-1.9.0/drsmooth/man/jonckheere.Rd | 8 - drsmooth-1.9.0/drsmooth/man/lbcd.Rd | 32 ++-- drsmooth-1.9.0/drsmooth/man/nlaad.Rd | 31 ++-- drsmooth-1.9.0/drsmooth/man/nlbcd.Rd | 42 ++--- drsmooth-1.9.0/drsmooth/man/noel.Rd | 99 ++++++++----- drsmooth-1.9.0/drsmooth/man/outlier.Rd | 8 - drsmooth-1.9.0/drsmooth/man/pkg_prep.Rd | 9 - drsmooth-1.9.0/drsmooth/man/prelimstats.Rd | 77 +++++----- drsmooth-1.9.0/drsmooth/man/segment.Rd | 45 ++---- drsmooth-1.9.0/drsmooth/man/segment.plot.Rd | 15 +- drsmooth-1.9.0/drsmooth/man/segment.print.Rd | 8 - drsmooth-1.9.0/drsmooth/man/shapiro.Rd | 8 - drsmooth-1.9.0/drsmooth/man/smooth.Rd | 61 +------- drsmooth-1.9.0/drsmooth/man/spline.plot.Rd | 42 +++-- drsmooth-1.9.0/drsmooth/tests/test-all.R | 1 81 files changed, 845 insertions(+), 647 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.5.4 dated 2015-06-09 and 3.5.6 dated 2015-09-24
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 5 NEWS | 16 ++- R/Deriv.R | 10 + R/Simplify.R | 214 +++++++++++++++++++++++++---------------- man/Deriv-package.Rd | 4 man/Simplify.Rd | 16 +++ tests/testthat/test_Deriv.R | 10 + tests/testthat/test_Simplify.R | 11 ++ 10 files changed, 211 insertions(+), 101 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.0.0 dated 2015-09-22 and 1.0.1 dated 2015-09-24
DESCRIPTION | 8 +++++--- MD5 | 20 ++++++++++---------- R/CP_model_inv.R | 2 +- R/Wbal.R | 2 +- R/read.R | 25 +++++++++++++++++-------- R/read_fit.R | 6 +++--- R/rollmean_smth.R | 3 ++- man/CP_model_inv.Rd | 2 +- man/Wbal.Rd | 2 +- man/read.Rd | 31 ++++++++++++++++++++----------- man/rollmean_smth.Rd | 2 ++ 11 files changed, 63 insertions(+), 40 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 1.0.0 dated 2015-09-08 and 1.0.1 dated 2015-09-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/USAranks.rda |binary man/ConsRank-package.Rd | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Reading ASD Binary Files in R
Description: A simple driver that reads spectroscopy data created using ASD
instruments such as the FieldSpec in R. The spectra can be extracted
from the ASD file as raw (DN), white reference, radiance, or reflectance.
Additionally, the metadata information contained in the ASD file header can
also be accessed.
Author: Pierre Roudier [aut, cre]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between asdreader versions 0.1-0 dated 2015-09-24 and 0.1-1 dated 2015-09-24
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/asdreader.r | 8 +++++--- R/get-metadata.r | 52 ++++++++++++++++++++++++++-------------------------- R/get-spectrum.r | 12 ++++++------ README.md | 5 ++++- man/asdreader.Rd | 13 ++++++------- man/get_metadata.Rd | 2 +- 8 files changed, 59 insertions(+), 55 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.2.1 dated 2015-09-17 and 0.2.2 dated 2015-09-24
DESCRIPTION | 8 MD5 | 66 - NAMESPACE | 2 R/Data_Description.R | 2 R/GuanTestGrid.R | 30 R/GuanTestUnif.R | 44 R/LuTest.R | 16 R/MaityTest.R | 36 R/coords_aniso.R | 10 inst/doc/spTest-vig.R | 11 inst/doc/spTest-vig.pdf |binary inst/doc/spTest-vig.rnw | 70 - man/GuanTestGrid.Rd | 34 man/GuanTestUnif.Rd | 42 man/LuTest.Rd | 16 man/MaityTest.Rd | 36 man/WRFG.Rd | 2 man/coords.aniso.Rd | 10 vignettes/figures/fig-dirsemi1-eps-converted-to.pdf |binary vignettes/figures/fig-dsvar2-eps-converted-to.pdf |binary vignettes/figures/fig-elev-eps-converted-to.pdf |binary vignettes/figures/fig-grid-eps-converted-to.pdf |binary vignettes/figures/fig-heatmap1-eps-converted-to.pdf |binary vignettes/figures/fig-heatmap1.eps | 1035 ++++++++++---------- vignettes/figures/fig-iso2-eps-converted-to.pdf |binary vignettes/figures/fig-iso2.eps | 8 vignettes/figures/fig-narccap-eps-converted-to.pdf |binary vignettes/figures/fig-narccap2-eps-converted-to.pdf |binary vignettes/figures/fig-precipdv-eps-converted-to.pdf |binary vignettes/figures/fig-rain-eps-converted-to.pdf |binary vignettes/figures/fig-rain1-eps-converted-to.pdf |binary vignettes/figures/fig-rain2-eps-converted-to.pdf |binary vignettes/spTest-vig.rnw | 70 - vignettes/spTestReferences.bib | 2 34 files changed, 779 insertions(+), 771 deletions(-)
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.
Author: Thomas Lumley [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 2.3-3 dated 2015-03-26 and 2.3-4 dated 2015-09-24
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 11 +++++++++++ R/vcovHAC.R | 3 +++ R/vcovHC.R | 5 ++++- build/vignette.rds |binary data/Investment.rda |binary data/PublicSchools.rda |binary inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary 10 files changed, 32 insertions(+), 15 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.5). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel and Romain Francois;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.5.0 dated 2015-07-14 and 0.3.2.5.1 dated 2015-09-24
ChangeLog | 24 +++++ DESCRIPTION | 10 +- MD5 | 32 +++---- NAMESPACE | 3 R/RcppEigen.package.skeleton.R | 10 +- R/RcppExports.R |only R/fastLm.R | 6 - README.md | 4 build/vignette.rds |binary inst/NEWS.Rd | 8 + inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/src/SparseCore/CompressedStorage.h | 6 - inst/unitTests/runit.fastLm.R | 14 +-- man/fastLm.Rd | 10 -- src/RcppEigen.cpp | 43 +++------ src/RcppExports.cpp |only src/fastLm.cpp | 80 +++++++++--------- src/fastLm.h | 4 18 files changed, 140 insertions(+), 114 deletions(-)
Title: Tree Boosting for Multivariate Outcomes
Description: Fits a multivariate model of decision trees for multiple,
continuous outcome variables. A model for each outcome variable is fit separately, selecting
predictors that explain that explain covariance in multiple outcomes.
Package is built on top of 'gbm'.
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Diff between mvtboost versions 0.2.1 dated 2015-07-18 and 0.3 dated 2015-09-24
mvtboost-0.2.1/mvtboost/man/cluster.covex.Rd |only mvtboost-0.2.1/mvtboost/man/heat.covex.Rd |only mvtboost-0.2.1/mvtboost/man/uncomp.mvtb.Rd |only mvtboost-0.3/mvtboost/DESCRIPTION | 8 mvtboost-0.3/mvtboost/MD5 | 77 +++-- mvtboost-0.3/mvtboost/NAMESPACE | 8 mvtboost-0.3/mvtboost/R/mvtb_nonlin_test.R | 23 - mvtboost-0.3/mvtboost/R/mvtb_plots.R | 119 +++++--- mvtboost-0.3/mvtboost/R/mvtb_summary.R | 111 +++++-- mvtboost-0.3/mvtboost/R/mvtboost.R | 196 +++++++++----- mvtboost-0.3/mvtboost/README.md | 13 mvtboost-0.3/mvtboost/build/partial.rdb |binary mvtboost-0.3/mvtboost/build/vignette.rds |binary mvtboost-0.3/mvtboost/data |only mvtboost-0.3/mvtboost/inst/doc/mvtboost_vignette.R | 6 mvtboost-0.3/mvtboost/inst/doc/mvtboost_vignette.Rmd | 31 +- mvtboost-0.3/mvtboost/inst/doc/mvtboost_vignette.html | 64 ++-- mvtboost-0.3/mvtboost/inst/doc/mvtboost_wellbeing.R |only mvtboost-0.3/mvtboost/inst/doc/mvtboost_wellbeing.Rmd |only mvtboost-0.3/mvtboost/inst/doc/mvtboost_wellbeing.html |only mvtboost-0.3/mvtboost/man/addalpha.Rd |only mvtboost-0.3/mvtboost/man/colorRampPaletteAlpha.Rd |only mvtboost-0.3/mvtboost/man/gbm.ri.Rd | 6 mvtboost-0.3/mvtboost/man/mvtb.Rd | 112 +++++--- mvtboost-0.3/mvtboost/man/mvtb.cluster.Rd |only mvtboost-0.3/mvtboost/man/mvtb.heat.Rd |only mvtboost-0.3/mvtboost/man/mvtb.nonlin.Rd | 8 mvtboost-0.3/mvtboost/man/mvtb.perspec.Rd | 20 - mvtboost-0.3/mvtboost/man/mvtb.ri.Rd | 14 - mvtboost-0.3/mvtboost/man/mvtb.uncomp.Rd |only mvtboost-0.3/mvtboost/man/mvtboost-package.Rd | 18 - mvtboost-0.3/mvtboost/man/plot.mvtb.Rd | 9 mvtboost-0.3/mvtboost/man/predict.mvtb.Rd | 10 mvtboost-0.3/mvtboost/man/summary.mvtb.Rd | 9 mvtboost-0.3/mvtboost/man/wellbeing.Rd |only mvtboost-0.3/mvtboost/tests/testthat/Rplots.pdf |binary mvtboost-0.3/mvtboost/tests/testthat/test_covex.R |only mvtboost-0.3/mvtboost/tests/testthat/test_cv.R | 8 mvtboost-0.3/mvtboost/tests/testthat/test_intx.R | 6 mvtboost-0.3/mvtboost/tests/testthat/test_mvloss_shrink.R | 22 - mvtboost-0.3/mvtboost/tests/testthat/test_params.R | 40 ++ mvtboost-0.3/mvtboost/tests/testthat/test_plot.R | 7 mvtboost-0.3/mvtboost/tests/testthat/test_predict.R | 10 mvtboost-0.3/mvtboost/tests/testthat/test_summary.R | 27 + mvtboost-0.3/mvtboost/vignettes/mvtboost_vignette.Rmd | 31 +- mvtboost-0.3/mvtboost/vignettes/mvtboost_wellbeing.Rmd |only mvtboost-0.3/mvtboost/vignettes/wb_cv5.Rdata |only mvtboost-0.3/mvtboost/vignettes/wb_nonlin.Rdata |only 48 files changed, 658 insertions(+), 355 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak, and Paul D. McNicholas.
Maintainer: Cristina Tortora <ctortora@math.mcmaster.ca>
Diff between MixGHD versions 1.7 dated 2015-06-25 and 1.8 dated 2015-09-24
MixGHD-1.7/MixGHD/R/Selection.R |only MixGHD-1.7/MixGHD/man/Selection.Rd |only MixGHD-1.8/MixGHD/DESCRIPTION | 12 MixGHD-1.8/MixGHD/MD5 | 38 MixGHD-1.8/MixGHD/NAMESPACE | 3 MixGHD-1.8/MixGHD/R/DA.R | 12 MixGHD-1.8/MixGHD/R/GHD.R | 2124 ++++++++++++++++++++---------------- MixGHD-1.8/MixGHD/R/MCGHD.R | 79 + MixGHD-1.8/MixGHD/R/MGHD.R | 77 + MixGHD-1.8/MixGHD/R/MGHFA.R | 4 MixGHD-1.8/MixGHD/R/MSGHD.R | 81 + MixGHD-1.8/MixGHD/R/cMSGHD.R | 84 + MixGHD-1.8/MixGHD/R/usedSelection.R | 20 MixGHD-1.8/MixGHD/man/ARI.Rd | 6 MixGHD-1.8/MixGHD/man/DA.Rd | 23 MixGHD-1.8/MixGHD/man/MCGHD.Rd | 12 MixGHD-1.8/MixGHD/man/MGHD.Rd | 12 MixGHD-1.8/MixGHD/man/MGHFA.Rd | 4 MixGHD-1.8/MixGHD/man/MSGHD.Rd | 12 MixGHD-1.8/MixGHD/man/banknote.Rd | 2 MixGHD-1.8/MixGHD/man/cMSGHD.Rd | 14 21 files changed, 1628 insertions(+), 991 deletions(-)
Title: Spatio-Temporal Analysis and Mapping of Meteorological
Observations
Description: Spatio-temporal geostatistical mapping of meteorological data. Global spatio-temporal models calculated using publicly available data are stored in package.
Author: Milan Kilibarda, Aleksandar Sekulic, Tomislav Hengl, Edzer Pebesma, Benedikt Graeler
Maintainer: Milan Kilibarda <kili@grf.bg.ac.rs>
Diff between meteo versions 0.1-4 dated 2015-06-23 and 0.1-5 dated 2015-09-24
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/pred.strk.R | 13 +++++++------ R/tgeom2STFDF.R | 2 +- 5 files changed, 22 insertions(+), 16 deletions(-)
Title: Joint Analysis of Genotype and Group-Specific Variability Using
a Novel Score Test Approach to Map Expression Quantitative
Trait Loci (eQTL)
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya <c.acharya@duke.edu>
Diff between JAGUAR versions 2.0 dated 2015-03-02 and 3.0.0 dated 2015-09-24
JAGUAR-2.0/JAGUAR/data/example.data.rda |only JAGUAR-2.0/JAGUAR/man/ProcessJaguarResults.Rd |only JAGUAR-2.0/JAGUAR/man/RowMin.Rd |only JAGUAR-2.0/JAGUAR/man/RowSums.Rd |only JAGUAR-2.0/JAGUAR/man/SliceGeneData.Rd |only JAGUAR-2.0/JAGUAR/man/calcThreshold.Rd |only JAGUAR-2.0/JAGUAR/man/example.data.Rd |only JAGUAR-2.0/JAGUAR/man/gamma_test.Rd |only JAGUAR-2.0/JAGUAR/man/getMinP.Rd |only JAGUAR-2.0/JAGUAR/man/jag_param.Rd |only JAGUAR-2.0/JAGUAR/man/jaguar.Rd |only JAGUAR-2.0/JAGUAR/man/jaguarSIM.Rd |only JAGUAR-2.0/JAGUAR/man/lin.Rd |only JAGUAR-2.0/JAGUAR/man/plotqtl.Rd |only JAGUAR-2.0/JAGUAR/man/scoreTest.Rd |only JAGUAR-2.0/JAGUAR/man/snpOUT.Rd |only JAGUAR-3.0.0/JAGUAR/DESCRIPTION | 15 JAGUAR-3.0.0/JAGUAR/MD5 | 48 - JAGUAR-3.0.0/JAGUAR/NAMESPACE | 7 JAGUAR-3.0.0/JAGUAR/R/JAGUAR.R | 629 +++++++++++++++----------- JAGUAR-3.0.0/JAGUAR/R/RcppExports.R | 32 - JAGUAR-3.0.0/JAGUAR/README.md | 3 JAGUAR-3.0.0/JAGUAR/data/jaguar_example.rda |only JAGUAR-3.0.0/JAGUAR/man/GENEapply.Rd | 3 JAGUAR-3.0.0/JAGUAR/man/JAGUAR-package.Rd | 22 JAGUAR-3.0.0/JAGUAR/man/cis_eqtl.Rd |only JAGUAR-3.0.0/JAGUAR/man/jagSIM.Rd |only JAGUAR-3.0.0/JAGUAR/man/jag_fun.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_cis.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_example.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_gwa.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_plotqtl.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_process.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_sim.Rd |only JAGUAR-3.0.0/JAGUAR/man/jaguar_slice.Rd |only JAGUAR-3.0.0/JAGUAR/man/rowsumscpp.Rd |only JAGUAR-3.0.0/JAGUAR/man/vcSIM.Rd |only JAGUAR-3.0.0/JAGUAR/src/Makevars.win |only JAGUAR-3.0.0/JAGUAR/src/RcppExports.cpp | 228 +++------ JAGUAR-3.0.0/JAGUAR/src/jaguar.cpp | 473 ++++++++++++------- 40 files changed, 834 insertions(+), 626 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between hypervolume versions 1.3.0 dated 2015-06-03 and 1.4 dated 2015-09-24
hypervolume-1.3.0/hypervolume/data/finch.txt.gz |only hypervolume-1.3.0/hypervolume/man/finch.Rd |only hypervolume-1.4/hypervolume/DESCRIPTION | 8 hypervolume-1.4/hypervolume/MD5 | 26 +- hypervolume-1.4/hypervolume/NAMESPACE | 5 hypervolume-1.4/hypervolume/R/hypervolume_plot.R | 8 hypervolume-1.4/hypervolume/R/hypervolume_prune.R | 11 - hypervolume-1.4/hypervolume/data/morphSnodgrassHeller.txt.gz |only hypervolume-1.4/hypervolume/demo/00Index | 4 hypervolume-1.4/hypervolume/demo/finch.R | 38 ++-- hypervolume-1.4/hypervolume/demo/holes_finch.R | 101 ++++++----- hypervolume-1.4/hypervolume/man/hypervolume_holes.Rd | 2 hypervolume-1.4/hypervolume/man/hypervolume_prune.Rd | 7 hypervolume-1.4/hypervolume/man/morphSnodgrassHeller.Rd |only hypervolume-1.4/hypervolume/man/plot.Hypervolume.Rd | 11 - hypervolume-1.4/hypervolume/src/RcppExports.cpp | 82 +++----- 16 files changed, 166 insertions(+), 137 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>
Diff between GSE versions 3.2.1 dated 2015-07-15 and 3.2.2 dated 2015-09-24
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/GSE.R | 12 +++++++++--- R/emve.R | 17 ++++++++++++++--- man/emve.Rd | 7 ++++--- man/geochem.Rd | 2 ++ 7 files changed, 44 insertions(+), 19 deletions(-)
Title: Platform for EDGAR Filling Management
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR quarterly master index, daily master index, filings from SEC.org site and do sentiment analysis of 10-K statements.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.1 dated 2015-08-27 and 1.0.2 dated 2015-09-24
edgar-1.0.1/edgar/R/download_fillings.R |only edgar-1.0.1/edgar/R/download_master.R |only edgar-1.0.1/edgar/man/DownloadFillings.Rd |only edgar-1.0.1/edgar/man/DownloadMaster.Rd |only edgar-1.0.2/edgar/DESCRIPTION | 14 edgar-1.0.2/edgar/MD5 | 46 - edgar-1.0.2/edgar/NAMESPACE | 5 edgar-1.0.2/edgar/R/downlaod_master_index.R |only edgar-1.0.2/edgar/R/download_filings.R |only edgar-1.0.2/edgar/R/get_wordfrquency.R | 17 edgar-1.0.2/edgar/R/negative_wordcloud.R | 22 edgar-1.0.2/edgar/R/negative_words_histogram.R |only edgar-1.0.2/edgar/R/polarity_histogram.R |only edgar-1.0.2/edgar/R/positive_wordcloud.R | 16 edgar-1.0.2/edgar/R/positive_words_histogram.R |only edgar-1.0.2/edgar/R/runEDGAR_shiny.R | 17 edgar-1.0.2/edgar/inst/shiny-edgar/edgarapp/edgar_shiny_functions.R | 266 ++++----- edgar-1.0.2/edgar/inst/shiny-edgar/edgarapp/server.R | 268 +++++----- edgar-1.0.2/edgar/inst/shiny-edgar/edgarapp/ui.R | 92 ++- edgar-1.0.2/edgar/inst/shiny-edgar/edgarapp/www/edgarimg.jpg |binary edgar-1.0.2/edgar/man/DownloadMasterIndex.Rd |only edgar-1.0.2/edgar/man/Downloadfilings.Rd |only edgar-1.0.2/edgar/man/GetWordfrquency.Rd | 54 +- edgar-1.0.2/edgar/man/NegWorsdHist.Rd |only edgar-1.0.2/edgar/man/NegativeWordcloud.Rd | 90 +-- edgar-1.0.2/edgar/man/PolarityHist.Rd |only edgar-1.0.2/edgar/man/PosWorsdHist.Rd |only edgar-1.0.2/edgar/man/PositiveWordcloud.Rd | 90 +-- edgar-1.0.2/edgar/man/RunEdgarShiny.Rd | 52 - edgar-1.0.2/edgar/man/negwords.Rd | 4 edgar-1.0.2/edgar/man/poswords.Rd | 4 31 files changed, 566 insertions(+), 491 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between btergm versions 1.5.2 dated 2015-08-05 and 1.5.9 dated 2015-09-24
btergm-1.5.2/btergm/R/preprocess.R |only btergm-1.5.2/btergm/man/adjust.Rd |only btergm-1.5.2/btergm/man/handleMissings.Rd |only btergm-1.5.2/btergm/man/preprocess.Rd |only btergm-1.5.9/btergm/DESCRIPTION | 13 btergm-1.5.9/btergm/MD5 | 17 btergm-1.5.9/btergm/NAMESPACE | 3 btergm-1.5.9/btergm/R/btergm.R | 543 ------------------------------ btergm-1.5.9/btergm/R/gof.R | 80 +++- btergm-1.5.9/btergm/R/mtergm.R |only btergm-1.5.9/btergm/R/tergmprepare.R |only btergm-1.5.9/btergm/R/timecov.R |only btergm-1.5.9/btergm/man/plot.btergmgof.Rd | 7 13 files changed, 77 insertions(+), 586 deletions(-)
Title: Parameter Space Exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Also implements the PLUE method.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom <andrechalom@gmail.com>
Diff between pse versions 0.4.2 dated 2015-07-07 and 0.4.3 dated 2015-09-24
DESCRIPTION | 10 ++++++---- MD5 | 26 +++++++++++++------------- NEWS | 5 +++++ README.md | 10 ++++++++-- build/vignette.rds |binary inst/doc/multiple.pdf |binary inst/doc/pse_tutorial.R | 6 +++--- inst/doc/pse_tutorial.Rnw | 15 +++++++++++---- inst/doc/pse_tutorial.pdf |binary man/LHS.Rd | 9 +++++++-- man/LHScorcorr.Rd | 17 ++++++++++------- man/PLUE.Rd | 6 +++++- man/sbma.Rd | 3 ++- vignettes/pse_tutorial.Rnw | 15 +++++++++++---- 14 files changed, 81 insertions(+), 41 deletions(-)
Title: Intermittent Time Series Forecasting
Description: Functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>
Diff between tsintermittent versions 1.7 dated 2015-09-17 and 1.8 dated 2015-09-24
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/crost.R | 3 +++ R/crost.decomp.R | 7 +++++++ R/crost.ma.R | 4 ++++ R/data.frc.R | 44 ++++++++++++++++++++++++++++++++++++++++---- R/idclass.R | 2 +- R/imapa.R | 10 ++++++++-- R/sexsm.R | 4 ++++ R/tsb.R | 4 ++++ man/data.frc.Rd | 10 +++++++--- 12 files changed, 99 insertions(+), 25 deletions(-)
More information about tsintermittent at CRAN
Permanent link
Title: Public Subject Attention via Wikipedia Page Access Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied. For the omnipresent Wikipedia those access statistics
are made available via 'http://stats.grok.se' a server
providing the information as file dumps as well as as web API.
This package provides an easy to use, consistent and traffic
minimizing approach to make those data accessible within R.
Author: Peter Meissner [aut, cre], R Core team [ctb] ('wp_date()'
derived from base package's 'as.Date()')
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 1.1.6 dated 2015-07-21 and 1.1.7 dated 2015-09-23
wikipediatrend-1.1.6/wikipediatrend/README.md |only wikipediatrend-1.1.7/wikipediatrend/DESCRIPTION | 8 wikipediatrend-1.1.7/wikipediatrend/MD5 | 20 wikipediatrend-1.1.7/wikipediatrend/NEWS | 252 +- wikipediatrend-1.1.7/wikipediatrend/R/html.R |only wikipediatrend-1.1.7/wikipediatrend/R/wp_download_data.R | 56 wikipediatrend-1.1.7/wikipediatrend/R/wp_linked_pages.R | 92 wikipediatrend-1.1.7/wikipediatrend/build/vignette.rds |binary wikipediatrend-1.1.7/wikipediatrend/man/html.Rd |only wikipediatrend-1.1.7/wikipediatrend/man/html2.Rd |only wikipediatrend-1.1.7/wikipediatrend/man/wp_cache.Rd | 32 wikipediatrend-1.1.7/wikipediatrend/tests/testthat/test.csv | 62 wikipediatrend-1.1.7/wikipediatrend/vignettes/using-wikipediatrend.Rmd | 1044 +++++----- 13 files changed, 787 insertions(+), 779 deletions(-)
More information about wikipediatrend at CRAN
Permanent link
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2 dated 2015-09-06 and 0.2.1 dated 2015-09-23
scmamp-0.2.1/scmamp/DESCRIPTION | 8 +- scmamp-0.2.1/scmamp/MD5 | 15 ++-- scmamp-0.2.1/scmamp/NAMESPACE | 1 scmamp-0.2.1/scmamp/R/data_manipulation.R | 103 ++++++++++++++++++++++++++++++ scmamp-0.2.1/scmamp/R/latex.R | 5 + scmamp-0.2.1/scmamp/R/plotting.R | 6 + scmamp-0.2.1/scmamp/R/scmamp.R | 7 +- scmamp-0.2.1/scmamp/man/booleanMatrix.Rd |only scmamp-0.2/scmamp/vignettes/images |only 9 files changed, 131 insertions(+), 14 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.5-3 dated 2015-07-23 and 2.5-4 dated 2015-09-23
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NAMESPACE | 3 ++- R/diversityvariables.R |only inst/etc/BiodiversityGUI.R | 32 +++++++++++++++++++++++++++----- inst/etc/BiodiversityR-menus.txt | 5 ++++- inst/etc/Rcmdr-menus.txt | 19 ++++++++++++------- man/diversityresult.Rd | 6 +++++- 8 files changed, 63 insertions(+), 27 deletions(-)
Title: Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Description: Implements a wide variety of one and two-parameter Bayesian CRM designs. The program can run interactively, allowing the user to enter outcomes after each cohort has been recruited, or via simulation to assess operating characteristics.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between bcrm versions 0.4.4 dated 2014-04-08 and 0.4.5 dated 2015-09-23
bcrm-0.4.4/bcrm/R/bcrm_0.4.4.R |only bcrm-0.4.5/bcrm/DESCRIPTION | 16 ++++++++-------- bcrm-0.4.5/bcrm/MD5 | 32 ++++++++++++++++---------------- bcrm-0.4.5/bcrm/NAMESPACE | 10 +++++++++- bcrm-0.4.5/bcrm/NEWS | 9 +++++++++ bcrm-0.4.5/bcrm/R/bcrm_0.4.5.R |only bcrm-0.4.5/bcrm/inst/CITATION | 4 ++-- bcrm-0.4.5/bcrm/man/bcrm-package.Rd | 8 ++++---- bcrm-0.4.5/bcrm/man/bcrm.Rd | 13 ++++++++----- bcrm-0.4.5/bcrm/man/find.x.Rd | 2 +- bcrm-0.4.5/bcrm/man/getprior.Rd | 4 ++-- bcrm-0.4.5/bcrm/man/plot.bcrm.Rd | 2 +- bcrm-0.4.5/bcrm/man/plot.bcrm.sim.Rd | 2 +- bcrm-0.4.5/bcrm/man/plot.threep3.Rd | 2 +- bcrm-0.4.5/bcrm/man/posterior.Rd | 2 +- bcrm-0.4.5/bcrm/man/print.bcrm.Rd | 2 +- bcrm-0.4.5/bcrm/man/print.threep3.Rd | 6 ++++-- bcrm-0.4.5/bcrm/man/threep3.Rd | 22 +++++++++++++++++----- 18 files changed, 85 insertions(+), 51 deletions(-)
Title: R Functions for Elementary Statistics
Description: A collection of data sets and functions that are useful in the
teaching of statistics at an elementary level to students who may have
little or no previous experience with the command line. The functions for
elementary inferential procedures follow a uniform interface for user
input. Some of the functions are instructional applets that can only be
run on the R Studio integrated development environment with package
'manipulate' installed. Other instructional applets are Shiny apps
that may be run locally. In teaching the package is used alongside of
package 'mosaic', 'mosaicData' and 'abd', which are therefore listed as
dependencies.
Author: Rebekah Robinson <rrobinson20@humana.com> and Homer
White <hwhite0@georgetowncollege.edu>
Maintainer: Homer White <hwhite0@georgetowncollege.edu>
Diff between tigerstats versions 0.2-6 dated 2015-05-23 and 0.2.7 dated 2015-09-23
DESCRIPTION | 13 MD5 | 372 +++++++++++++-------------- NAMESPACE | 65 ++++ R/BinomNorm.R | 9 R/BinomSkew.R | 4 R/CIMean.R | 6 R/CIProp.R | 6 R/ChisqSimSlow.R | 2 R/DtrellHist.R | 6 R/DtrellScat.R | 6 R/EmpRule.R | 6 R/EmpRuleGC.R | 6 R/FakeSchool.R | 2 R/FindRegLine.R | 4 R/MeanSampler.R | 4 R/Points2Watch.R | 4 R/PropSampler.R | 4 R/RandomExp.R | 2 R/RegEstimate.R | 6 R/SampDist2Means.R | 6 R/SampDist2Props.R | 4 R/SampDistMean.R | 6 R/ShallowReg.R | 4 R/SimpleRandom.R | 4 R/SimpleRandom2.R | 4 R/Skewer.R | 6 R/SlowGoodness.R | 2 R/Type12Errors.R | 4 R/Variability.R | 6 R/VaryCorrelation.R | 4 R/barchartGC.R | 2 R/binomtestGC.R | 2 R/chisqtestGC.R | 2 R/colPerc.R | 2 R/data.R | 3 R/expCounts.R | 2 R/helpGC.R | 10 R/lmGC.R | 2 R/pbinomGC.R | 2 R/pchisqGC.R | 2 R/pnormGC.R | 2 R/polyfitGC.R | 2 R/ptGC.R | 2 R/qnormGC.R | 2 R/rowPerc.R | 2 R/tExplore.R | 4 R/tSampler.R | 4 R/tigerstats-package.R | 58 ++++ R/ttestGC.R | 2 build/vignette.rds |binary inst/CIMean/server.R | 589 +++++++++++++++++++++++-------------------- inst/CIMean/setup.R |only inst/CIMean/ui.R | 200 ++++++++------ inst/FindRegLine/DESCRIPTION |only inst/FindRegLine/infoFiles |only inst/FindRegLine/rsconnect |only inst/FindRegLine/scores |only inst/FindRegLine/server.R | 330 +++++++++++++++++++----- inst/FindRegLine/ui.R | 134 +++++---- inst/doc/R_Descriptive.html | 12 inst/doc/barchartGC.html | 18 - inst/doc/binomtestGC.html | 2 inst/doc/bwplot.html | 8 inst/doc/chisqtestGC.html | 8 inst/doc/densityplot.html | 14 - inst/doc/favstats.R | 4 inst/doc/favstats.html | 4 inst/doc/histogram.html | 10 inst/doc/lmGC.html | 12 inst/doc/pbinomGC.html | 14 - inst/doc/pnormGC.html | 10 inst/doc/polyfitGC.html | 10 inst/doc/proptestGC.html | 4 inst/doc/qnorm.html | 6 inst/doc/qnormGC.html | 10 inst/doc/ttestGC.html | 4 inst/doc/xyplot.html | 6 man/BinomNorm.Rd | 3 man/BinomSkew.Rd | 3 man/CIMean.Rd | 3 man/CIProp.Rd | 3 man/ChisqSimSlow.Rd | 3 man/DtrellHist.Rd | 3 man/DtrellScat.Rd | 3 man/EmpRule.Rd | 3 man/EmpRuleGC.Rd | 3 man/FakeSchool.Rd | 3 man/FindRegLine.Rd | 3 man/MeanSampler.Rd | 3 man/Ovarian.Rd | 3 man/ParseFormula.Rd | 3 man/Points2Watch.Rd | 3 man/PropSampler.Rd | 3 man/RandomExp.Rd | 3 man/RectShade.Rd | 3 man/RegEstimate.Rd | 3 man/SampDist2Means.Rd | 3 man/SampDist2Props.Rd | 3 man/SampDistMean.Rd | 3 man/ShallowReg.Rd | 3 man/SimpleRandom.Rd | 3 man/SimpleRandom2.Rd | 3 man/Skewer.Rd | 3 man/SlowGoodness.Rd | 3 man/SmallExp.Rd | 3 man/Type12Errors.Rd | 3 man/UnderShade.Rd | 3 man/Variability.Rd | 3 man/VaryCorrelation.Rd | 3 man/alcohol.Rd | 3 man/attitudes.Rd | 3 man/barchartGC.Rd | 3 man/beans.Rd | 3 man/binomtestGC.Rd | 3 man/cabrera.Rd | 3 man/chisqtestGC.Rd | 3 man/chugtime.Rd | 3 man/colPerc.Rd | 3 man/deathpen.Rd | 4 man/expCounts.Rd | 3 man/fuel.Rd | 3 man/galton.Rd | 3 man/gcfeeling.Rd | 3 man/gcstudents.Rd | 3 man/gss02.Rd | 3 man/gss08.Rd | 3 man/gss2012.Rd | 3 man/hair_and_act.Rd | 3 man/handheight.Rd | 3 man/hanford1.Rd | 3 man/hanford2.Rd | 3 man/helpGC.Rd | 3 man/henderson.Rd | 3 man/hofbatting.Rd | 3 man/hofpitching.Rd | 3 man/imagpop.Rd | 3 man/iqsiblings.Rd | 3 man/knifeorgunblock.Rd | 3 man/labels.Rd | 3 man/ledgejump.Rd | 3 man/lmGC.Rd | 3 man/m111survey.Rd | 3 man/m111surveyfa12.Rd | 3 man/m111surveyfa13.Rd | 3 man/music.Rd | 3 man/napkins.Rd | 3 man/nonresponse.Rd | 3 man/nosmokeday.Rd | 3 man/oldfaithful.Rd | 3 man/pbinomGC.Rd | 3 man/pchisqGC.Rd | 3 man/pennstate1.Rd | 3 man/plot.GClm.Rd | 3 man/plot.polyGC.Rd | 3 man/pnormGC.Rd | 3 man/polyfitGC.Rd | 3 man/popsamp.Rd | 3 man/predict.GClm.Rd | 3 man/predict.polyGC.Rd | 3 man/print.GCbinomtest.Rd | 3 man/print.GCchisqtest.Rd | 3 man/print.GClm.Rd | 3 man/print.GCttest.Rd | 3 man/print.gcp1test.Rd | 3 man/print.gcp2test.Rd | 3 man/print.polyGC.Rd | 3 man/proptestGC.Rd | 3 man/ptGC.Rd | 3 man/pushups.Rd | 3 man/qnormGC.Rd | 3 man/rowPerc.Rd | 3 man/saltmarsh.Rd | 3 man/sat.Rd | 3 man/sealsO2.Rd | 3 man/simpleFind.Rd | 3 man/simpleKeyRev.Rd | 3 man/stumps.Rd | 3 man/tExplore.Rd | 3 man/tSampler.Rd | 3 man/temperature.Rd | 3 man/theme.rpres.Rd | 3 man/themerpres.Rd | 3 man/tigerstats-package.Rd | 3 man/tips.Rd | 3 man/tornado.Rd | 3 man/ttestGC.Rd | 3 man/ucdavis1.Rd | 3 man/verlander.Rd | 3 man/youthrisk03.Rd | 3 189 files changed, 1483 insertions(+), 947 deletions(-)
Title: Stochastic Gradient Descent for Scalable Estimation
Description: A fast and flexible set of tools for large scale estimation. It
features many stochastic gradient methods, built-in models, visualization
tools, automated hyperparameter tuning, model checking, interval estimation,
and convergence diagnostics.
Author: Dustin Tran [aut, cre],
Panos Toulis [aut],
Tian Lian [ctb],
Ye Kuang [ctb],
Edoardo Airoldi [ctb]
Maintainer: Dustin Tran <dtran@g.harvard.edu>
Diff between sgd versions 0.1 dated 2015-05-08 and 1.0 dated 2015-09-23
sgd-0.1/sgd/src/sgd.h |only sgd-0.1/sgd/src/sgd_basedef.h |only sgd-0.1/sgd/src/sgd_data.h |only sgd-0.1/sgd/src/sgd_experiment.h |only sgd-0.1/sgd/src/sgd_family.h |only sgd-0.1/sgd/src/sgd_learningrate.h |only sgd-0.1/sgd/src/sgd_transfer.h |only sgd-1.0/sgd/DESCRIPTION | 26 sgd-1.0/sgd/MD5 | 77 +- sgd-1.0/sgd/NAMESPACE | 12 sgd-1.0/sgd/R/RcppExports.R | 4 sgd-1.0/sgd/R/plot.sgd.R |only sgd-1.0/sgd/R/predict.sgd.R |only sgd-1.0/sgd/R/print.sgd.R |only sgd-1.0/sgd/R/sgd.R | 881 +++++++++++++----------- sgd-1.0/sgd/README.md | 47 - sgd-1.0/sgd/build |only sgd-1.0/sgd/demo/00Index | 9 sgd-1.0/sgd/demo/bench-corr-linear-regression.R |only sgd-1.0/sgd/demo/bench-linear-regression.R |only sgd-1.0/sgd/demo/cox-regression.R |only sgd-1.0/sgd/demo/glm-logistic-regression.R |only sgd-1.0/sgd/demo/glm-poisson-regression.R |only sgd-1.0/sgd/demo/linear-regression.R | 5 sgd-1.0/sgd/demo/m-estimation.R |only sgd-1.0/sgd/demo/normal-method-of-moments.R |only sgd-1.0/sgd/inst |only sgd-1.0/sgd/man/plot.sgd.Rd |only sgd-1.0/sgd/man/predict.sgd.Rd |only sgd-1.0/sgd/man/print.sgd.Rd |only sgd-1.0/sgd/man/sgd.Rd | 221 +++--- sgd-1.0/sgd/src/RcppExports.cpp | 25 sgd-1.0/sgd/src/basedef.h |only sgd-1.0/sgd/src/data |only sgd-1.0/sgd/src/learn-rate |only sgd-1.0/sgd/src/model |only sgd-1.0/sgd/src/post-process |only sgd-1.0/sgd/src/sgd |only sgd-1.0/sgd/src/sgd.cpp | 567 ++++++--------- sgd-1.0/sgd/src/validity-check |only sgd-1.0/sgd/tests |only sgd-1.0/sgd/vignettes |only 42 files changed, 977 insertions(+), 897 deletions(-)
Title: Programming with Big Data -- Interface to ZeroMQ
Description: Providing high level R wrapper functions to utilize
ZeroMQ C API functions in detail manners. pbdZMQ mainly focuses on
client/servers programming framework in an interaction style. A
minimum ZeroMQ library 4.1.0 rc1 is built and linked within pbdZMQ
if no external ZerMQ library is not provided. A few compatible wrapper
functions to rzmq are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Whit Armstrong [ctb] (some functions are modified from the rzmq for
backward compatibility),
Brian Ripley [ctb] (C code of shellexec),
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.1-0 dated 2015-09-11 and 0.1-1 dated 2015-09-23
ChangeLog | 15 + DESCRIPTION | 8 MD5 | 39 +- R/get_conf.r | 138 +++++---- configure | 344 +++++++++++++++++++++--- configure.ac | 113 ++++--- inst/doc/pbdZMQ-guide.Rnw | 6 inst/doc/pbdZMQ-guide.pdf |binary src/Makevars.in | 20 - src/build_zmq_mingw.inc | 5 src/pkg.m4 |only src/zmqsrc.win32/src_Makefile | 16 - src/zmqsrc.win64/src_Makefile | 16 - vignettes/pbdZMQ-guide.Rnw | 6 vignettes/pbdZMQ-include/01-acknowledgement.tex | 20 + vignettes/pbdZMQ-include/01-copyright.tex | 2 vignettes/pbdZMQ-include/01-introduction.tex | 56 +-- vignettes/pbdZMQ-include/02-installation.tex | 91 ++++-- vignettes/pbdZMQ-include/03-example.tex | 9 vignettes/pbdZMQ-include/04-backward.tex | 16 - vignettes/pbdZMQ-include/pbdZMQ.bib | 6 21 files changed, 666 insertions(+), 260 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.5 dated 2015-09-01 and 0.6.0 dated 2015-09-23
DESCRIPTION | 14 ++- INDEX | 9 -- MD5 | 20 +++-- NAMESPACE | 5 - R/nhanes.R | 174 +++++++++++++++++++++++++++++++++++-------------- README.md |only build |only inst |only man/nhanesTableVars.Rd | 14 ++- man/nhanesTables.Rd | 14 ++- man/nhanesTranslate.Rd | 22 ++++-- vignettes |only 12 files changed, 185 insertions(+), 87 deletions(-)
Title: Linear Quantile Mixed Models
Description: This is a collection of functions to fit quantile regression models for independent and hierarchical data.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between lqmm versions 1.5.1 dated 2014-12-16 and 1.5.2 dated 2015-09-23
lqmm-1.5.1/lqmm/inst/ChangeLog |only lqmm-1.5.2/lqmm/DESCRIPTION | 12 lqmm-1.5.2/lqmm/MD5 | 34 - lqmm-1.5.2/lqmm/NAMESPACE | 11 lqmm-1.5.2/lqmm/NEWS |only lqmm-1.5.2/lqmm/R/auxiliary.R |only lqmm-1.5.2/lqmm/R/lqm.R |only lqmm-1.5.2/lqmm/R/lqmm.R | 1175 +---------------------------------- lqmm-1.5.2/lqmm/build/vignette.rds |binary lqmm-1.5.2/lqmm/inst/doc/lqmm.pdf |binary lqmm-1.5.2/lqmm/man/dal.Rd | 7 lqmm-1.5.2/lqmm/man/lqm.Rd | 4 lqmm-1.5.2/lqmm/man/lqm.counts.Rd | 2 lqmm-1.5.2/lqmm/man/lqm.fit.gs.Rd | 2 lqmm-1.5.2/lqmm/man/lqmControl.Rd | 25 lqmm-1.5.2/lqmm/man/lqmm-internal.Rd | 4 lqmm-1.5.2/lqmm/man/lqmm-package.Rd | 4 lqmm-1.5.2/lqmm/man/predict.lqmm.Rd | 48 + lqmm-1.5.2/lqmm/man/print.lqm.Rd | 2 lqmm-1.5.2/lqmm/man/summary.lqm.Rd | 11 20 files changed, 183 insertions(+), 1158 deletions(-)
Title: A Copy Number and Expression-Based Classifier for Breast Tumours
Description: Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda <Oscar.Rueda@cruk.cam.ac.uk>
Diff between iC10 versions 1.1.2 dated 2014-12-08 and 1.1.3 dated 2015-09-23
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 2 +- NEWS | 2 ++ R/iC10.R | 4 ++-- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo <danlu.guo@adelaide.edu.au>, Seth Westra <swestra@civeng.adelaide.edu.au>
Maintainer: Danlu Guo <danlu.guo@adelaide.edu.au>
Diff between Evapotranspiration versions 1.6 dated 2015-06-23 and 1.7 dated 2015-09-23
DESCRIPTION | 10 MD5 | 20 NAMESPACE | 6 NEWS | 21 R/Evapotranspiration.R | 938 ++++++++++++++++++++++-------------- R/Reading.R | 1265 ++++++++++++++++++++++++++++++++----------------- man/ET.Abtew.Rd |only man/ET.Hamon.Rd |only man/ET.Linacre.Rd |only man/ET.MortonCRAE.Rd | 2 man/ET.MortonCRWE.Rd | 2 man/ET.Penpan.Rd | 11 man/ET.Romanenko.Rd |only 13 files changed, 1469 insertions(+), 806 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, identify cutpoints, and quickly combine shapefiles and
dataframes for plotting. Includes four alternative themes for ggplot2. Also
includes three example datasets of administrative education records for
learning how to process records with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between eeptools versions 0.3.1 dated 2014-02-23 and 0.9.0 dated 2015-09-23
eeptools-0.3.1/eeptools/NEWS |only eeptools-0.3.1/eeptools/R/dropbox_source.R |only eeptools-0.3.1/eeptools/R/plotForWord.R |only eeptools-0.3.1/eeptools/R/theme_dpi_map.R |only eeptools-0.3.1/eeptools/R/theme_dpi_map2.R |only eeptools-0.3.1/eeptools/R/theme_dpi_mapPNG.R |only eeptools-0.3.1/eeptools/man/destring.Rd |only eeptools-0.3.1/eeptools/man/dropbox_source.Rd |only eeptools-0.3.1/eeptools/man/eeptools-package.Rd |only eeptools-0.3.1/eeptools/man/mapmerge2.Rd |only eeptools-0.3.1/eeptools/man/plotForWord.Rd |only eeptools-0.3.1/eeptools/tests/testthat/test-decomma.r |only eeptools-0.9.0/eeptools/DESCRIPTION | 34 - eeptools-0.9.0/eeptools/MD5 | 128 +++--- eeptools-0.9.0/eeptools/NAMESPACE | 54 ++ eeptools-0.9.0/eeptools/NEWS.md |only eeptools-0.9.0/eeptools/R/age_calc.R | 59 ++ eeptools-0.9.0/eeptools/R/autoplot.lm.R | 56 +- eeptools-0.9.0/eeptools/R/cleanTex.R | 7 eeptools-0.9.0/eeptools/R/cutoff.R | 49 ++ eeptools-0.9.0/eeptools/R/decomma.R | 16 eeptools-0.9.0/eeptools/R/defac.R | 17 eeptools-0.9.0/eeptools/R/destring.R | 30 + eeptools-0.9.0/eeptools/R/eeptools-package.r |only eeptools-0.9.0/eeptools/R/eeptools.R | 17 eeptools-0.9.0/eeptools/R/lags.R | 28 + eeptools-0.9.0/eeptools/R/leading_zero.R |only eeptools-0.9.0/eeptools/R/mapfunctions.R | 35 - eeptools-0.9.0/eeptools/R/max_mis.R | 53 ++ eeptools-0.9.0/eeptools/R/modsims.R | 16 eeptools-0.9.0/eeptools/R/moves_calc.R | 63 +++ eeptools-0.9.0/eeptools/R/proficiency_tools.R |only eeptools-0.9.0/eeptools/R/remove_char.R | 18 eeptools-0.9.0/eeptools/R/retained_calc.R |only eeptools-0.9.0/eeptools/R/statamode.R | 90 +++- eeptools-0.9.0/eeptools/R/theme_dpi.R | 198 +++++++++ eeptools-0.9.0/eeptools/R/thresh.R | 46 +- eeptools-0.9.0/eeptools/R/zzz.R |only eeptools-0.9.0/eeptools/README.md | 289 +++++++++++++- eeptools-0.9.0/eeptools/build |only eeptools-0.9.0/eeptools/inst |only eeptools-0.9.0/eeptools/man/age_calc.Rd | 61 +- eeptools-0.9.0/eeptools/man/autoplot.lm.Rd | 63 +-- eeptools-0.9.0/eeptools/man/cleanTex.Rd | 26 - eeptools-0.9.0/eeptools/man/crosstabplot.Rd |only eeptools-0.9.0/eeptools/man/crosstabs.Rd |only eeptools-0.9.0/eeptools/man/cutoff.Rd | 67 +-- eeptools-0.9.0/eeptools/man/decomma.Rd | 32 - eeptools-0.9.0/eeptools/man/defac.Rd | 39 - eeptools-0.9.0/eeptools/man/eeptools.Rd |only eeptools-0.9.0/eeptools/man/gelmansim.Rd | 33 - eeptools-0.9.0/eeptools/man/ggmapmerge.Rd | 16 eeptools-0.9.0/eeptools/man/lag_data.Rd | 18 eeptools-0.9.0/eeptools/man/leading_zero.Rd |only eeptools-0.9.0/eeptools/man/makenum.Rd |only eeptools-0.9.0/eeptools/man/mapmerge.Rd | 17 eeptools-0.9.0/eeptools/man/max_mis.Rd | 49 -- eeptools-0.9.0/eeptools/man/midsch.Rd | 66 +-- eeptools-0.9.0/eeptools/man/moves_calc.Rd | 98 ++-- eeptools-0.9.0/eeptools/man/nth_max.Rd |only eeptools-0.9.0/eeptools/man/profpoly.Rd |only eeptools-0.9.0/eeptools/man/profpoly.data.Rd |only eeptools-0.9.0/eeptools/man/remove_char.Rd | 42 -- eeptools-0.9.0/eeptools/man/retained_calc.Rd |only eeptools-0.9.0/eeptools/man/statamode.Rd | 62 +-- eeptools-0.9.0/eeptools/man/stuatt.Rd | 59 +- eeptools-0.9.0/eeptools/man/stulevel.Rd | 101 ++-- eeptools-0.9.0/eeptools/man/theme_dpi.Rd | 44 -- eeptools-0.9.0/eeptools/man/theme_dpi_map.Rd | 63 +-- eeptools-0.9.0/eeptools/man/theme_dpi_map2.Rd | 66 +-- eeptools-0.9.0/eeptools/man/theme_dpi_mapPNG.Rd | 67 +-- eeptools-0.9.0/eeptools/man/thresh.Rd | 64 +-- eeptools-0.9.0/eeptools/tests/test-all.R | 7 eeptools-0.9.0/eeptools/tests/testthat/test-calculators.R |only eeptools-0.9.0/eeptools/tests/testthat/test-edutils.R |only eeptools-0.9.0/eeptools/tests/testthat/test-gelmansim.R | 31 + eeptools-0.9.0/eeptools/tests/testthat/test-lintr.R |only eeptools-0.9.0/eeptools/tests/testthat/test-maptools.R |only eeptools-0.9.0/eeptools/tests/testthat/test-plots.R |only eeptools-0.9.0/eeptools/tests/testthat/test-statamode.r | 131 +++++- eeptools-0.9.0/eeptools/tests/testthat/test-utils.R |only eeptools-0.9.0/eeptools/vignettes |only 82 files changed, 1754 insertions(+), 871 deletions(-)
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data.
The methods available closely follow those in chapter 6 of Applied Spatial
Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smacpod versions 1.3.0 dated 2015-09-13 and 1.4.1 dated 2015-09-22
smacpod-1.3.0/smacpod/R/kdest.R |only smacpod-1.4.1/smacpod/DESCRIPTION | 11 - smacpod-1.4.1/smacpod/MD5 | 30 ++- smacpod-1.4.1/smacpod/NAMESPACE | 2 smacpod-1.4.1/smacpod/R/Kdest.R |only smacpod-1.4.1/smacpod/R/kdplus.test.R | 2 smacpod-1.4.1/smacpod/R/nn.R | 2 smacpod-1.4.1/smacpod/R/noc.R |only smacpod-1.4.1/smacpod/R/plot.scan.R | 16 - smacpod-1.4.1/smacpod/R/spscan.test.R | 275 ++++++++++++++++++++----------- smacpod-1.4.1/smacpod/man/kdest.Rd | 2 smacpod-1.4.1/smacpod/man/nn.Rd | 2 smacpod-1.4.1/smacpod/man/noc.Rd |only smacpod-1.4.1/smacpod/man/plot.scan.Rd | 8 smacpod-1.4.1/smacpod/man/spscan.test.Rd | 29 ++- smacpod-1.4.1/smacpod/tests |only 16 files changed, 237 insertions(+), 142 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudion [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 0.2.0 dated 2015-01-01 and 0.3.0 dated 2015-09-22
rvest-0.2.0/rvest/R/scrape-package.r |only rvest-0.2.0/rvest/R/structure.R |only rvest-0.2.0/rvest/R/xml-methods.R |only rvest-0.2.0/rvest/man/scrape.Rd |only rvest-0.2.0/rvest/man/xml_structure.Rd |only rvest-0.3.0/rvest/DESCRIPTION | 30 ++--- rvest-0.3.0/rvest/MD5 | 93 ++++++++--------- rvest-0.3.0/rvest/NAMESPACE | 36 ++---- rvest-0.3.0/rvest/R/deprecated.R |only rvest-0.3.0/rvest/R/encoding.R | 2 rvest-0.3.0/rvest/R/form.R | 56 +++++----- rvest-0.3.0/rvest/R/html.R | 77 ++------------ rvest-0.3.0/rvest/R/minimal-html.R | 2 rvest-0.3.0/rvest/R/parse.R | 79 ++++++++------ rvest-0.3.0/rvest/R/selectors.R | 104 +++---------------- rvest-0.3.0/rvest/R/session.R | 17 +-- rvest-0.3.0/rvest/R/table.R | 25 ++-- rvest-0.3.0/rvest/R/utils.R | 28 ----- rvest-0.3.0/rvest/R/xml.R | 32 ----- rvest-0.3.0/rvest/README.md | 16 ++ rvest-0.3.0/rvest/build/vignette.rds |binary rvest-0.3.0/rvest/demo/tripadvisor.R | 2 rvest-0.3.0/rvest/demo/zillow.R | 2 rvest-0.3.0/rvest/inst/doc/selectorgadget.R | 12 +- rvest-0.3.0/rvest/inst/doc/selectorgadget.Rmd | 9 + rvest-0.3.0/rvest/inst/doc/selectorgadget.html | 120 ++++++++-------------- rvest-0.3.0/rvest/man/encoding.Rd | 4 rvest-0.3.0/rvest/man/google_form.Rd | 2 rvest-0.3.0/rvest/man/html.Rd | 26 +++- rvest-0.3.0/rvest/man/html_form.Rd | 8 - rvest-0.3.0/rvest/man/html_nodes.Rd | 11 +- rvest-0.3.0/rvest/man/html_session.Rd | 4 rvest-0.3.0/rvest/man/html_table.Rd | 8 - rvest-0.3.0/rvest/man/html_tag.Rd |only rvest-0.3.0/rvest/man/html_text.Rd | 30 +---- rvest-0.3.0/rvest/man/jump_to.Rd | 2 rvest-0.3.0/rvest/man/minimal_html.Rd | 2 rvest-0.3.0/rvest/man/pipe.Rd | 4 rvest-0.3.0/rvest/man/pluck.Rd | 2 rvest-0.3.0/rvest/man/session_history.Rd | 2 rvest-0.3.0/rvest/man/set_values.Rd | 4 rvest-0.3.0/rvest/man/submit_form.Rd | 2 rvest-0.3.0/rvest/man/xml.Rd | 35 ------ rvest-0.3.0/rvest/tests/testthat/test-forms.R | 4 rvest-0.3.0/rvest/tests/testthat/test-selectors.R | 2 rvest-0.3.0/rvest/vignettes/selectorgadget-1.png |binary rvest-0.3.0/rvest/vignettes/selectorgadget-2.png |binary rvest-0.3.0/rvest/vignettes/selectorgadget-3.png |binary rvest-0.3.0/rvest/vignettes/selectorgadget-4.png |binary rvest-0.3.0/rvest/vignettes/selectorgadget-5.png |binary rvest-0.3.0/rvest/vignettes/selectorgadget.Rmd | 9 + 51 files changed, 356 insertions(+), 547 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.0.0 dated 2015-09-15 and 2.0.1 dated 2015-09-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ src/reg-lib/_reg_aladin.h | 4 ++-- src/reg-lib/_reg_base.cpp | 2 +- src/reg-lib/cpu/_reg_blockMatching.cpp | 5 +++++ src/reg-lib/cpu/_reg_lncc.cpp | 12 ++++++++++++ src/reg-lib/cpu/_reg_resampling.cpp | 4 ++-- 8 files changed, 39 insertions(+), 16 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.2.0 dated 2015-02-25 and 3.3.0 dated 2015-09-22
DESCRIPTION | 12 MD5 | 29 +- NAMESPACE | 8 NEWS | 14 + R/Matlab.R | 67 ++-- R/readMat.R | 76 ++--- R/writeMat.R | 40 +- inst/externals/MatlabServer.m | 353 ++++++++++++++------------ inst/mat-files/SparseMatrix,empty.mat |only man/1._The_MATLAB_server_running_in_MATLAB.Rd | 353 ++++++++++++++------------ man/R.matlab-package.Rd | 2 man/evaluate.Matlab.Rd | 15 - man/open.Matlab.Rd | 3 man/readMat.Rd | 9 tests/readMat.R | 40 ++ tests/writeMat.R | 16 - 16 files changed, 585 insertions(+), 452 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.127 dated 2015-02-17 and 2.1.128 dated 2015-09-22
DESCRIPTION | 10 ++++------ MD5 | 26 +++++++++++++------------- NAMESPACE | 2 ++ NEWS | 3 +++ R/labkey.getFolders.R | 2 +- R/labkey.importRows.R | 3 ++- R/labkey.insertRows.R | 3 ++- R/labkey.selectRows.R | 2 +- R/schemaObjects.R | 6 +++--- build/vignette.rds |binary man/Rlabkey-package.Rd | 5 ++--- man/labkey.getQueries.Rd | 1 - man/labkey.getSchemas.Rd | 1 - man/makeFilter.Rd | 1 - 14 files changed, 33 insertions(+), 32 deletions(-)
Title: Entrez in R
Description: Provides an R interface to the NCBI's EUtils API
allowing users to search databases like GenBank and PubMed, process the
results of those searches and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb],
Han Guangchun [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 0.4.2 dated 2015-06-26 and 1.0.0 dated 2015-09-22
DESCRIPTION | 31 - MD5 | 86 +-- NAMESPACE | 24 NEWS | 20 R/base.r | 122 +++- R/entrez_citmatch.r | 4 R/entrez_fetch.r | 49 + R/entrez_global_query.r | 3 R/entrez_info.r | 82 +-- R/entrez_link.r | 233 +++++++- R/entrez_post.r | 41 - R/entrez_search.r | 100 ++- R/entrez_summary.r | 221 +++----- R/help.r | 4 R/parse_pubmed_xml.r | 61 +- build/vignette.rds |binary inst/doc/rentrez_tutorial.R | 249 ++++++--- inst/doc/rentrez_tutorial.Rmd | 689 ++++++++++++++++++++----- inst/doc/rentrez_tutorial.html | 1101 ++++++++++++++++++++++++----------------- man/entrez_citmatch.Rd | 6 man/entrez_db_links.Rd | 16 man/entrez_db_searchable.Rd | 11 man/entrez_db_summary.Rd | 2 man/entrez_dbs.Rd | 4 man/entrez_fetch.Rd | 34 + man/entrez_global_query.Rd | 4 man/entrez_info.Rd | 10 man/entrez_link.Rd | 61 +- man/entrez_post.Rd | 29 - man/entrez_search.Rd | 45 + man/entrez_summary.Rd | 59 +- man/extract_from_esummary.Rd |only man/linkout_urls.Rd |only man/parse_pubmed_xml.Rd | 13 man/rentrez.Rd | 4 tests/test-all.R | 10 tests/testthat/test_fetch.r | 49 - tests/testthat/test_info.r | 47 + tests/testthat/test_link.r | 74 ++ tests/testthat/test_parse.r | 35 - tests/testthat/test_post.r |only tests/testthat/test_query.r | 8 tests/testthat/test_search.r | 33 - tests/testthat/test_summary.r |only tests/testthat/test_webenv.r | 16 vignettes/rentrez_tutorial.Rmd | 689 ++++++++++++++++++++----- 46 files changed, 3042 insertions(+), 1337 deletions(-)
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files.
This attempts to provide a cleaner alternative to options().
Author: Sahil Seth [aut, cre],
Yihui Xie [ctb] (kable from knitr R/table.R)
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between params versions 0.2.5 dated 2015-08-22 and 0.3.0 dated 2015-09-22
DESCRIPTION | 9 ++--- MD5 | 26 ++++++++-------- NEWS.md | 10 ++++++ R/conf.R | 69 +++++++++++++++++++++++++++++++++--------- R/opts.R | 18 +++++++---- R/pkg-opts.R | 63 ++++++++++++++++++++++++++------------ R/read-sheet.R | 2 - R/zzz.R | 4 +- README.md | 81 +++++++++++++++++++++++++------------------------- inst/conf/params.conf | 1 man/opts.Rd | 2 - man/params.Rd | 56 ++++++++++++++++++++++++---------- man/parse_opts.Rd | 8 +++- tests |only 14 files changed, 227 insertions(+), 122 deletions(-)
Title: Nonparametric and Stochastic Efficiency and Productivity
Analysis
Description: Provides a variety of tools for nonparametric and parametric efficiency measurement.
Author: Oleg Badunenko [aut, cre],
Yaryna Kolomiytseva [aut],
Pavlo Mozharovskyi [aut]
Maintainer: Oleg Badunenko <obadunen@uni-koeln.de>
Diff between npsf versions 0.1.4 dated 2015-09-20 and 0.1.6 dated 2015-09-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/npsf-package.Rd | 4 ++-- src/libglpk/minisat/minisat.c | 35 ++++++++++++++++++++++++++++------- src/nonradial.c | 2 +- 5 files changed, 39 insertions(+), 18 deletions(-)
More information about MaxentVariableSelection at CRAN
Permanent link
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.
Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between ICSNP versions 1.0-9 dated 2012-03-29 and 1.1-0 dated 2015-09-22
DESCRIPTION | 15 +++++++-------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + R/duembgen.shape.R | 2 +- R/duembgen.shape.wt.R | 4 ++-- R/frobenius.norm.R | 2 +- R/internals.R | 4 ++++ R/mat.sqrt.R | 7 ++++++- R/symm.huber.R | 2 +- R/symm.huber.wt.R | 2 +- data/pulmonary.rda |binary inst/ChangeLog | 5 +++++ man/ICSNP-package.Rd | 10 ++++++---- man/LASERI.Rd | 2 +- man/tyler.shape.Rd | 2 +- 15 files changed, 51 insertions(+), 35 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.2.0.1 dated 2015-09-14 and 3.2.0.3 dated 2015-09-22
DESCRIPTION | 6 +-- MD5 | 14 ++++----- R/deeplearning.R | 9 +++-- R/models.R | 81 +++++++++++++++++++++++++++++++++++++++++++++++------ R/parse.R | 6 +++ inst/buildnum.txt | 2 - man/h2o-package.Rd | 4 +- man/h2o.anomaly.Rd | 8 +++-- 8 files changed, 103 insertions(+), 27 deletions(-)
Title: Tests of Fit for some Probability Distributions
Description: Tests of fit for Gamma, inverse Gaussian, normal, multivariate normal and generalized Pareto distributions. Parameter estimators for the Gamma, inverse Gaussian and generalized Pareto distributions.
Author: Elizabeth Gonzalez-Estrada, Jose A. Villasenor-Alva
Maintainer: Elizabeth Gonzalez-Estrada <egonzalez@colpos.mx>
Diff between goft versions 1.1 dated 2015-03-24 and 1.2 dated 2015-09-22
DESCRIPTION | 12 +-- MD5 | 31 +++++--- NAMESPACE | 6 - R/gamma.fit.R |only R/gamma.test.R | 1 R/gpd.fit.R |only R/gpd.test-internal.R | 182 +++++++++++++++++++++++++------------------------- R/gpd.test.R | 54 +++++++------- R/ig.fit.R |only R/ig.test-internal.R |only R/ig.test.R |only inst/history.txt | 5 + man/gamma.fit.Rd |only man/gamma.test.Rd | 11 +-- man/goats.Rd | 2 man/gpd.fit.Rd |only man/gpd.test.Rd | 24 +++--- man/ig.fit.Rd |only man/ig.test.Rd |only man/mvShapiro.Test.Rd | 16 ++-- man/normal.Rd | 12 +-- 21 files changed, 183 insertions(+), 173 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package allows for retrieval of five datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; and the International Tree Ring Data Bank. Additional data sources are in the works, including global DEM resources (ETOPO1, ETOPO5, ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.0 dated 2015-07-08 and 2.0.1 dated 2015-09-22
DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 37 +++++++++++++++++++------------------ R/GHCN_FUNCTIONS.R | 4 ++++ R/ITRDB_FUNCTIONS.R | 10 ++++++++-- R/NED_FUNCTIONS.R | 5 ++++- R/NHD_FUNCTIONS.R | 5 +++++ R/SSURGO_FUNCTIONS.R | 8 +++++++- R/UTILITY_FUNCTIONS.R | 8 ++++++++ inst/FedDataTester.R | 2 +- man/FedData-package.Rd | 4 ++-- 11 files changed, 75 insertions(+), 41 deletions(-)
Title: Creates a Model Matrix via Feature Hashing with a Formula
Interface
Description: Feature hashing, also called as the hashing trick, is a method to transform
features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix.
Without looking up the indices in an associative array,
it applies a hash function to the features and uses their hash values as indices directly.
The method of feature hashing in this package was proposed in Weinberger et al. (2009).
The hashing algorithm is the murmurhash3 from the digest package.
Please see the README in https://github.com/wush978/FeatureHashing for more information.
Author: Wush Wu [aut, cre],
Michael Benesty [aut, ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between FeatureHashing versions 0.9 dated 2015-03-29 and 0.9.1 dated 2015-09-22
Changelog | 10 DESCRIPTION | 13 MD5 | 61 ++- NAMESPACE | 10 R/RcppExports.R | 9 R/hashed.model.matrix.R | 48 ++- R/zzz.R | 12 README.md | 22 + build |only inst/doc |only man/CSCMatrix-class.Rd | 2 man/hash.mapping.Rd | 2 man/hash.size.Rd | 2 man/hashed.model.matrix.Rd | 20 - man/intToRaw.Rd | 2 man/ipinyou.Rd | 2 man/simulate.split.Rd | 2 man/test.tag.Rd | 2 src/RcppExports.cpp | 18 - src/bswap_32.cpp |only src/bswap_32.h |only src/hash_function.h |only src/hash_internal.cpp | 38 ++ src/hashed_model_matrix.cpp | 604 +-------------------------------------- src/hashed_model_matrix.h |only src/vector_converter.h |only tests/test-as-dgCMatrix.R | 8 tests/test-existence_collision.R |only tests/test-hash.mapping.R | 4 tests/test-hashing.R | 14 tests/test-memcheck.R | 2 tests/test-progress_bar.R |only vignettes |only 33 files changed, 245 insertions(+), 662 deletions(-)
More information about FeatureHashing at CRAN
Permanent link
Title: Udunits-2 Bindings for R
Description: Provides simple bindings to version 2 of Unidata's udunits library.
Author: James Hiebert <hiebert@uvic.ca>
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between udunits2 versions 0.8 dated 2015-08-06 and 0.8.1 dated 2015-09-22
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- configure | 27 +++++++++++---------------- configure.ac | 27 +++++++++++---------------- src/Makevars.win |only 5 files changed, 30 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-14 0.2.0
2013-11-13 0.1.5
Title: Local Principal Curve Methods
Description: Fitting multivariate data patterns with local principal curves; including simple tools for data compression (projection), bandwidth selection, and measuring goodness-of-fit.
Author: Jochen Einbeck and Ludger Evers
Maintainer: Jochen Einbeck <jochen.einbeck@durham.ac.uk>
Diff between LPCM versions 0.44-8 dated 2013-11-16 and 0.45-0 dated 2015-09-22
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/followx.R | 2 +- R/kernels.and.distances.R | 3 ++- R/plot.lpc.R | 4 ++-- data/calspeedflow.rda |binary data/gaia.rda |binary data/gvessel.rda |binary man/coverage.Rd | 3 ++- man/followx.Rd | 2 +- man/lpc.control.Rd | 9 ++++++--- 11 files changed, 29 insertions(+), 24 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0 dated 2015-09-18 and 1.0.1 dated 2015-09-22
Fragman-1.0.1/Fragman/DESCRIPTION | 6 +++--- Fragman-1.0.1/Fragman/MD5 | 22 +++++++++++----------- Fragman-1.0.1/Fragman/R/overview.R | 2 +- Fragman-1.0.1/Fragman/R/overview2.R | 2 +- Fragman-1.0.1/Fragman/R/score.easy.R | 2 +- Fragman-1.0.1/Fragman/inst/CITATION | 12 ++++++------ Fragman-1.0.1/Fragman/man/Fragman-package.Rd |only Fragman-1.0.1/Fragman/man/ladder.info.attach.Rd | 2 +- Fragman-1.0.1/Fragman/man/lapply_pb.Rd | 2 +- Fragman-1.0.1/Fragman/man/overview2.Rd | 2 +- Fragman-1.0.1/Fragman/man/score.easy.Rd | 2 +- Fragman-1.0.1/Fragman/man/storing.inds.Rd | 2 +- Fragman-1.0/Fragman/man/Fragma-package.Rd |only 13 files changed, 28 insertions(+), 28 deletions(-)
Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary
differential equations ('ODE') and differential algebraic equations ('DAE').
The functions provide an interface to the FORTRAN functions
'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Jeff Cash <j.cash@imperial.ac.uk>,
Francesca Mazzia <mazzia@dm.uniba.it>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between bvpSolve versions 1.2.4 dated 2013-08-15 and 1.3.2 dated 2015-09-22
DESCRIPTION | 24 MD5 | 59 - NAMESPACE | 10 R/bvpsolver.R | 2106 +++++++++++++++++++++------------------- R/forcings.R | 10 build |only inst/CITATION |only inst/doc/bvpSolve.R | 30 inst/doc/bvpSolve.Rnw | 22 inst/doc/bvpSolve.pdf |binary inst/doc/bvpTests.R | 2 inst/doc/bvpTests.Rnw | 10 inst/doc/bvpTests.pdf |binary inst/doc/examples/Mathieu.R | 1 inst/doc/examples/Measel.R | 75 - inst/doc/examples/swirl.R | 22 inst/doc/opuscula_math_3424.pdf |only man/bvpSolve.Rd | 5 man/bvpcol.Rd | 14 man/bvptwp.Rd | 15 man/diagnostics.Rd | 2 src/bvpSolve.h | 30 src/call_acdc.c | 194 ++- src/call_colmodsys.c | 219 +++- src/call_colnew.c | 381 +++++-- src/call_twpbvp.c | 200 +++ src/coldaeR.f | 34 src/colmodR.f | 1 src/twpbvpa.f | 41 src/twpbvpc.f | 14 vignettes/bvpSolve.Rnw | 22 vignettes/bvpTests.Rnw | 10 32 files changed, 2186 insertions(+), 1367 deletions(-)
Title: The Short-Term and Long-Term Hazard Ratio Model for Survival
Data
Description: Various inference procedures for a two-sample semi-parametric model that can accommodate a flexible range of hazard ratio patterns. This model contains the proportional hazards model and the proportional odds model as sub-models, and accommodates non-proportional hazards situations to the extreme of having crossing hazards and crossing survivor functions. Overall, this package has four major functions: 1) the parameter estimation, namely short-term and long-term hazard ratio parameters; 2) 95 percent and 90 percent point-wise confidence intervals and simultaneous confidence bands for the hazard ratio function; 3) p-value of the adaptive weighted log-rank test; 4) p-values of two lack-of-fit tests for the model. See the included "read_me_first.pdf" for brief instructions. In this version (1.1), there is no need to sort the data before applying this package.
Author: Junlong Sun and Song Yang
Maintainer: Junlong Sun <junlong.sun@gmail.com>
Diff between YPmodel versions 1.1 dated 2014-02-17 and 1.2 dated 2015-09-22
DESCRIPTION | 14 - MD5 | 102 ++++----- NAMESPACE | 28 ++ R/YPmodel.IntervalBands.R | 146 ++++++------- R/YPmodel.R | 10 R/YPmodel.adlgrk.R | 66 +++--- R/YPmodel.default.R | 48 ++-- R/YPmodel.estimate.R | 312 ++++++++++++++--------------- R/YPmodel.inputData.R | 78 +++---- R/YPmodel.lackfittest.R | 138 ++++++------- R/YPmodel.setParameter.R | 68 +++--- R/YPmodel.setRandom.R | 44 ++-- R/fun.Rjudge.R | 72 +++--- R/fun.YPmodelOriginal.R | 246 +++++++++++------------ R/fun.adlgrk.R | 200 +++++++++---------- R/fun.classCheck.R | 20 - R/fun.cumsum.R | 70 +++--- R/fun.errorMessage.R | 38 +-- R/fun.flipud.R | 82 +++---- R/fun.generateParameters.R | 336 +++++++++++++++---------------- R/fun.hazardRationEstimation.R | 348 ++++++++++++++++----------------- R/fun.hcvxitr1.R | 106 +++++----- R/fun.internalParameters.R | 112 +++++----- R/fun.martint.R | 298 ++++++++++++++-------------- R/fun.newBest.R | 342 ++++++++++++++++---------------- R/fun.ntitr0.R | 68 +++--- R/fun.oldp2.R | 140 ++++++------- R/fun.survf.R | 400 +++++++++++++++++++------------------- R/fun.variance.R | 130 ++++++------ R/fun.zeroORone.R | 48 ++-- R/plot.YPmodel.IntervalBands.R | 146 ++++++------- R/plot.YPmodel.R | 34 +-- R/plot.YPmodel.estimate.R |only R/plot.YPmodel.lackfittest.R |only R/plot.YPmodel.martint.R | 62 ++--- R/plot.YPmodel.survf.R | 68 +++--- R/plot.YPmodel.survivor.R | 204 +++++++++---------- R/print.YPmodel.R | 44 ++-- R/summary.YPmodel.IntervalBands.R | 78 +++---- R/summary.YPmodel.R | 44 ++-- R/summary.YPmodel.adlgrk.R | 24 +- R/summary.YPmodel.estimate.R | 92 ++++---- R/summary.YPmodel.lackfittest.R | 48 ++-- R/summary.YPmodel.overall.R | 54 ++--- data/gastric.rda |binary inst/doc/read_me_first.pdf |binary man/YPmodel-internal.Rd | 1 man/YPmodel-package.Rd | 14 - man/YPmodel.IntervalBands.Rd | 12 - man/YPmodel.Rd | 17 - man/YPmodel.adlgrk.Rd | 8 man/YPmodel.estimate.Rd | 9 man/YPmodel.lackfittest.Rd | 9 53 files changed, 2557 insertions(+), 2521 deletions(-)
Title: Competing Risks Regression Models with Covariate-Adjusted
Censoring Weights
Description: Estimation and regression modeling of subdistribution functions for competing risks data with adjustment for covariate-dependent censoring, as described in He et al. (2013).
Author: Peng He
Maintainer: Peng He <saturnhp@gmail.com>
Diff between wtcrsk versions 1.3 dated 2014-05-05 and 1.4 dated 2015-09-22
DESCRIPTION | 12 ++-- MD5 | 8 +-- NAMESPACE | 6 ++ R/wrap.R | 121 ++++++++++++++++---------------------------------- man/wtcrsk-package.Rd | 10 ++-- 5 files changed, 60 insertions(+), 97 deletions(-)
Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a data.frame, constructing formulas from text and building design and response matrices.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between useful versions 1.1.8 dated 2014-01-20 and 1.1.9 dated 2015-09-22
useful-1.1.8/useful/NEWS |only useful-1.1.8/useful/README |only useful-1.1.9/useful/DESCRIPTION | 16 +- useful-1.1.9/useful/LICENSE | 2 useful-1.1.9/useful/MD5 | 137 ++++++++++++-------- useful-1.1.9/useful/NAMESPACE | 53 ++++++- useful-1.1.9/useful/R/ColumnReorder.r |only useful-1.1.9/useful/R/buildFormula.r | 1 useful-1.1.9/useful/R/buildMatrix.r | 3 useful-1.1.9/useful/R/checkCase.r |only useful-1.1.9/useful/R/classCheck.r |only useful-1.1.9/useful/R/coordinates.r |only useful-1.1.9/useful/R/corner.r | 76 +++++++---- useful-1.1.9/useful/R/hartigan.r | 1 useful-1.1.9/useful/R/impute.r |only useful-1.1.9/useful/R/indices.r |only useful-1.1.9/useful/R/kmeansPlotting.r | 7 - useful-1.1.9/useful/R/reclass.r |only useful-1.1.9/useful/R/regex.r | 1 useful-1.1.9/useful/R/subMultiple.r |only useful-1.1.9/useful/R/subspecials.r | 9 - useful-1.1.9/useful/R/tsPlot.r | 24 ++- useful-1.1.9/useful/R/useful-package.r | 2 useful-1.1.9/useful/README.md |only useful-1.1.9/useful/man/ComputeHartigan.Rd | 14 +- useful-1.1.9/useful/man/FitKMeans.Rd | 41 ++--- useful-1.1.9/useful/man/ForceDataFrame.Rd | 8 - useful-1.1.9/useful/man/MapToInterval.Rd | 11 + useful-1.1.9/useful/man/PlotHartigan.Rd | 34 ++-- useful-1.1.9/useful/man/WhichCorner.Rd |only useful-1.1.9/useful/man/binary.flip.Rd | 4 useful-1.1.9/useful/man/bottomleft.Rd | 18 +- useful-1.1.9/useful/man/bottomright.Rd | 18 +- useful-1.1.9/useful/man/build.formula.Rd | 10 - useful-1.1.9/useful/man/build.x.Rd | 17 +- useful-1.1.9/useful/man/build.y.Rd | 9 - useful-1.1.9/useful/man/cart2pol.Rd |only useful-1.1.9/useful/man/classdf.Rd |only useful-1.1.9/useful/man/colsToFront.Rd |only useful-1.1.9/useful/man/compare.list.Rd | 10 - useful-1.1.9/useful/man/constant.Rd |only useful-1.1.9/useful/man/corner.Rd | 40 +++-- useful-1.1.9/useful/man/find.case.Rd |only useful-1.1.9/useful/man/fortify.acf.Rd | 9 - useful-1.1.9/useful/man/fortify.kmeans.Rd | 20 +- useful-1.1.9/useful/man/fortify.ts.Rd | 13 - useful-1.1.9/useful/man/indexToPosition.Rd |only useful-1.1.9/useful/man/interval.check.Rd | 19 +- useful-1.1.9/useful/man/left.Rd | 16 +- useful-1.1.9/useful/man/lower.case.Rd |only useful-1.1.9/useful/man/mixed.case.Rd |only useful-1.1.9/useful/man/moveToFront.Rd |only useful-1.1.9/useful/man/multiple.Rd | 15 +- useful-1.1.9/useful/man/multiple.comma.Rd | 10 - useful-1.1.9/useful/man/multiple.dollar.Rd | 10 - useful-1.1.9/useful/man/multiple.identity.Rd | 10 - useful-1.1.9/useful/man/multiple_format.Rd | 9 - useful-1.1.9/useful/man/numeric.case.Rd |only useful-1.1.9/useful/man/plot.Rd |only useful-1.1.9/useful/man/plot.acf.Rd | 12 + useful-1.1.9/useful/man/plot.kmeans.Rd | 25 +-- useful-1.1.9/useful/man/plotTimesSeries.Rd | 34 +--- useful-1.1.9/useful/man/pol2cart.Rd |only useful-1.1.9/useful/man/positionToIndex.Rd |only useful-1.1.9/useful/man/reclass.Rd |only useful-1.1.9/useful/man/right.Rd | 16 +- useful-1.1.9/useful/man/shift.column.Rd | 20 +- useful-1.1.9/useful/man/simple.impute.Rd |only useful-1.1.9/useful/man/simple.impute.data.frame.Rd |only useful-1.1.9/useful/man/simple.impute.default.Rd |only useful-1.1.9/useful/man/simple.impute.tbl_df.Rd |only useful-1.1.9/useful/man/subMultiple.Rd |only useful-1.1.9/useful/man/subOut.Rd | 20 +- useful-1.1.9/useful/man/subSpecials.Rd | 26 +-- useful-1.1.9/useful/man/topleft.Rd | 18 +- useful-1.1.9/useful/man/topright.Rd | 18 +- useful-1.1.9/useful/man/ts.plotter.Rd | 14 +- useful-1.1.9/useful/man/upper.case.Rd |only useful-1.1.9/useful/man/useful.Rd | 2 useful-1.1.9/useful/man/vplayout.Rd | 9 - useful-1.1.9/useful/tests |only 81 files changed, 498 insertions(+), 413 deletions(-)
Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.devices versions 2.13.0 dated 2015-02-22 and 2.13.1 dated 2015-09-22
R.devices-2.13.0/R.devices/.Rinstignore |only R.devices-2.13.1/R.devices/DESCRIPTION | 14 - R.devices-2.13.1/R.devices/MD5 | 50 ++--- R.devices-2.13.1/R.devices/NAMESPACE | 5 R.devices-2.13.1/R.devices/NEWS | 8 R.devices-2.13.1/R.devices/R/capabilitiesX11.R |only R.devices-2.13.1/R.devices/R/devOptions.R | 21 +- R.devices-2.13.1/R.devices/R/toNNN.R | 2 R.devices-2.13.1/R.devices/build/vignette.rds |binary R.devices-2.13.1/R.devices/inst/doc/R.devices-overview.pdf |binary R.devices-2.13.1/R.devices/man/R.devices-package.Rd | 4 R.devices-2.13.1/R.devices/man/capabilitiesX11.Rd |only R.devices-2.13.1/R.devices/tests/DevEvalFileProduct.R | 4 R.devices-2.13.1/R.devices/tests/DevEvalProduct.R | 4 R.devices-2.13.1/R.devices/tests/capabilitiesX11.R |only R.devices-2.13.1/R.devices/tests/dataURI.R | 4 R.devices-2.13.1/R.devices/tests/devAll.R | 4 R.devices-2.13.1/R.devices/tests/devDump.R | 4 R.devices-2.13.1/R.devices/tests/devEval,error.R | 128 ++++++------- R.devices-2.13.1/R.devices/tests/devEval.R | 39 +++ R.devices-2.13.1/R.devices/tests/devIndexOf.R | 4 R.devices-2.13.1/R.devices/tests/devIsInteractive.R | 3 R.devices-2.13.1/R.devices/tests/devIsOpen.R | 3 R.devices-2.13.1/R.devices/tests/devList.R | 4 R.devices-2.13.1/R.devices/tests/devOptions.R | 21 ++ R.devices-2.13.1/R.devices/tests/devSet.R | 5 R.devices-2.13.1/R.devices/tests/devTypeName.R | 4 R.devices-2.13.1/R.devices/tests/favicon.R |only R.devices-2.13.1/R.devices/tests/withPar.R | 3 29 files changed, 234 insertions(+), 104 deletions(-)
Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using
structural equations, with emphasis on problems in causal inference.
Specify interventions and simulate from intervened data generating
distributions. Define and evaluate treatment-specific means, the average
treatment effects and coefficients from working marginal structural models.
User interface designed to facilitate the conduct of transparent and
reproducible simulation studies, and allows concise expression of complex
functional dependencies for a large number of time-varying nodes. See the
package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between simcausal versions 0.3.0 dated 2015-08-24 and 0.4.0 dated 2015-09-21
DESCRIPTION | 9 -- MD5 | 51 ++++++------ NAMESPACE | 2 NEWS | 15 +++ R/network.R | 8 + R/parserfunctions_R6.r | 11 ++ R/simcausal-package.r | 1 R/simcausal.r | 18 +++- R/simulation.r | 25 ++++-- R/targetparam.r | 25 +----- README.md | 161 ++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/simcausal_vignette.R | 6 - inst/doc/simcausal_vignette.Rnw | 58 +++++++------- inst/doc/simcausal_vignette.pdf |binary man/NetIndClass.Rd | 4 man/eval.target.Rd | 3 man/plotDAG.Rd | 3 man/set.DAG.Rd | 3 man/sim.Rd | 3 man/simfull.Rd | 3 man/simobs.Rd | 3 tests/RUnit/runittests.R | 8 + tests/bug_networks |only vignettes/R-Pckgs.bib | 5 - vignettes/SimCausal_2014.bib | 9 +- vignettes/simcausal_vignette.Rnw | 58 +++++++------- 27 files changed, 294 insertions(+), 198 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.5 dated 2015-09-16 and 0.6 dated 2015-09-21
provenance-0.5/provenance/man/clr.Rd |only provenance-0.6/provenance/DESCRIPTION | 6 provenance-0.6/provenance/MD5 | 38 +- provenance-0.6/provenance/NAMESPACE | 9 provenance-0.6/provenance/R/documentation.R | 25 + provenance-0.6/provenance/R/minsorting.R | 9 provenance-0.6/provenance/R/plot.R | 38 +- provenance-0.6/provenance/R/provenance.R | 152 +++++++++-- provenance-0.6/provenance/data/Namib.rda |binary provenance-0.6/provenance/data/densities.rda |binary provenance-0.6/provenance/inst/densities.csv | 2 provenance-0.6/provenance/man/CLR.Rd |only provenance-0.6/provenance/man/MDS.Rd | 6 provenance-0.6/provenance/man/as.acomp.Rd |only provenance-0.6/provenance/man/as.compositional.Rd |only provenance-0.6/provenance/man/as.data.frame.compositional.Rd |only provenance-0.6/provenance/man/minsorting.Rd | 9 provenance-0.6/provenance/man/plot.INDSCAL.Rd | 2 provenance-0.6/provenance/man/plot.minsorting.Rd | 13 provenance-0.6/provenance/man/provenance.Rd |only provenance-0.6/provenance/man/subset.compositional.Rd | 2 provenance-0.6/provenance/man/subset.distributional.Rd | 2 provenance-0.6/provenance/man/ternary.Rd | 2 23 files changed, 240 insertions(+), 75 deletions(-)
Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between snplist versions 0.13 dated 2014-12-10 and 0.14 dated 2015-09-21
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NEWS |only R/makeGeneSet.R | 4 ++-- R/setSNPTable.R | 4 ++-- build/vignette.rds |binary inst/doc/snplist.R | 9 ++++----- inst/doc/snplist.Rnw | 11 +++++------ inst/doc/snplist.pdf |binary man/snplist-package.Rd | 6 +++--- vignettes/snplist.Rnw | 11 +++++------ 11 files changed, 36 insertions(+), 38 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.50 dated 2014-09-05 and 0.58 dated 2015-09-21
REBayes-0.50/REBayes/R/TLVmix.R |only REBayes-0.50/REBayes/R/rqss2.R |only REBayes-0.50/REBayes/demo/GLVmix1.R |only REBayes-0.50/REBayes/man/TLVmix.Rd |only REBayes-0.50/REBayes/man/rqss2.Rd |only REBayes-0.58/REBayes/DESCRIPTION | 29 +- REBayes-0.58/REBayes/MD5 | 104 +++++---- REBayes-0.58/REBayes/NAMESPACE | 39 +++ REBayes-0.58/REBayes/R/Bmix.R | 61 +++-- REBayes-0.58/REBayes/R/Cosslett.R |only REBayes-0.58/REBayes/R/GLmix.R | 78 +++++- REBayes-0.58/REBayes/R/GVmix.R | 93 ++++---- REBayes-0.58/REBayes/R/Gammamix.R |only REBayes-0.58/REBayes/R/Gompertzmix.R | 72 ++++-- REBayes-0.58/REBayes/R/KWDual.R | 121 +++++++++- REBayes-0.58/REBayes/R/Pmix.R | 56 +++- REBayes-0.58/REBayes/R/TLmix.R | 64 ++++- REBayes-0.58/REBayes/R/Tncpmix.R |only REBayes-0.58/REBayes/R/WGLVmix.R | 130 ++++++----- REBayes-0.58/REBayes/R/WGVmix.R | 29 ++ REBayes-0.58/REBayes/R/WTLVmix.R | 145 +++++++----- REBayes-0.58/REBayes/R/Weibullmix.R | 72 ++++-- REBayes-0.58/REBayes/R/bball.R |only REBayes-0.58/REBayes/R/flies.R |only REBayes-0.58/REBayes/R/medde.R | 345 ++++++++++++++++++------------ REBayes-0.58/REBayes/R/misc.R | 49 ++++ REBayes-0.58/REBayes/R/predict.R | 20 + REBayes-0.58/REBayes/R/tacks.R |only REBayes-0.58/REBayes/R/tannenbaum.R |only REBayes-0.58/REBayes/data/bball.rda |binary REBayes-0.58/REBayes/demo/00Index | 6 REBayes-0.58/REBayes/demo/Bmix1.R | 3 REBayes-0.58/REBayes/demo/Cosslett1.R |only REBayes-0.58/REBayes/demo/Cosslett2.R |only REBayes-0.58/REBayes/demo/GLmix1.R | 2 REBayes-0.58/REBayes/demo/GLmix2.R |only REBayes-0.58/REBayes/demo/GVmix1.R | 8 REBayes-0.58/REBayes/demo/WGLVmix1.R |only REBayes-0.58/REBayes/demo/WTLVmix1.R |only REBayes-0.58/REBayes/inst/ChangeLog | 29 ++ REBayes-0.58/REBayes/man/Bmix.Rd | 62 +++-- REBayes-0.58/REBayes/man/Cosslett.Rd |only REBayes-0.58/REBayes/man/GLmix.Rd | 111 +++++---- REBayes-0.58/REBayes/man/GVmix.Rd | 67 +++-- REBayes-0.58/REBayes/man/Gammamix.Rd |only REBayes-0.58/REBayes/man/Gompertzmix.Rd | 84 ++++--- REBayes-0.58/REBayes/man/KWDual.Rd | 108 +++++---- REBayes-0.58/REBayes/man/L1norm.Rd | 41 ++- REBayes-0.58/REBayes/man/Pmix.Rd | 65 ++--- REBayes-0.58/REBayes/man/TLmix.Rd | 82 ++++--- REBayes-0.58/REBayes/man/Tncpmix.Rd |only REBayes-0.58/REBayes/man/WGLVmix.Rd | 74 +++--- REBayes-0.58/REBayes/man/WGVmix.Rd | 63 +++-- REBayes-0.58/REBayes/man/WTLVmix.Rd | 74 +++--- REBayes-0.58/REBayes/man/Weibullmix.Rd | 85 +++---- REBayes-0.58/REBayes/man/bball.Rd | 62 ++--- REBayes-0.58/REBayes/man/flies.Rd | 32 +- REBayes-0.58/REBayes/man/medde.Rd | 165 +++++++------- REBayes-0.58/REBayes/man/plot.medde.Rd |only REBayes-0.58/REBayes/man/predict.GLmix.Rd |only REBayes-0.58/REBayes/man/qmedde.Rd |only REBayes-0.58/REBayes/man/rmedde.Rd |only REBayes-0.58/REBayes/man/tacks.Rd | 71 +++--- REBayes-0.58/REBayes/man/tannenbaum.Rd | 25 +- REBayes-0.58/REBayes/man/traprule.Rd | 31 +- 65 files changed, 1780 insertions(+), 1077 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.7.1 dated 2014-12-07 and 0.8.0 dated 2015-09-21
ChangeLog | 7 + DESCRIPTION | 16 +- MD5 | 29 ++-- NAMESPACE | 25 +++ R/access.R | 4 R/age.at.R |only R/utilities.R | 231 ++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/networkDynamic.pdf |binary man/Newcomb.Rd | 4 man/age.at.Rd |only man/as.data.frame.networkDynamic.Rd | 2 man/networkDynamic.Rd | 21 ++- tests/age.at_tests.R |only tests/converter_tests.R | 56 ++++++-- tests/query_tests.R | 17 ++ tests/utils_tests.R | 2 17 files changed, 287 insertions(+), 127 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.5 dated 2015-08-10 and 0.4.6 dated 2015-09-21
DESCRIPTION | 8 MD5 | 138 +++++++------- NAMESPACE | 1 NEWS | 280 ------------------------------ R/Luminescence-package.R | 2 R/RLum.Data.Image-class.R | 4 R/analyse_SAR.CWOSL.R | 2 inst/NEWS.Rd | 289 ------------------------------- man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/Luminescence-package.Rd | 2 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Risoe.BINfileData2RLum.Data.Curve.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 4 man/analyse_SAR.TL.Rd | 2 man/analyse_pIRIRSequence.Rd | 2 man/apply_CosmicRayRemoval.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_IEU.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxRatio.Rd | 2 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_LMCurve.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 2 man/get_Risoe.BINfileData.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_RadialPlot.Rd | 2 man/plot_Risoe.BINfileData.Rd | 2 man/readBIN2R.Rd | 2 man/readSPE2R.Rd | 2 man/readXSYG2R.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/structure_RLum.Rd | 2 man/writeR2BIN.Rd | 2 70 files changed, 153 insertions(+), 697 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 3.16-0 dated 2015-04-30 and 3.17-0 dated 2015-09-21
Hmisc-3.16-0/Hmisc/R/stata.get.s |only Hmisc-3.16-0/Hmisc/inst/NEWS |only Hmisc-3.17-0/Hmisc/DESCRIPTION | 16 Hmisc-3.17-0/Hmisc/MD5 | 57 +- Hmisc-3.17-0/Hmisc/NAMESPACE | 16 Hmisc-3.17-0/Hmisc/NEWS | 20 Hmisc-3.17-0/Hmisc/R/Misc.s | 21 Hmisc-3.17-0/Hmisc/R/ffCompress.r |only Hmisc-3.17-0/Hmisc/R/label.s | 12 Hmisc-3.17-0/Hmisc/R/latex.s | 44 + Hmisc-3.17-0/Hmisc/R/minor.tick.s | 51 -- Hmisc-3.17-0/Hmisc/R/misc.get.s |only Hmisc-3.17-0/Hmisc/R/plsmo.s | 86 ++- Hmisc-3.17-0/Hmisc/R/sas.get.s | 579 -------------------------- Hmisc-3.17-0/Hmisc/R/summaryM.s | 166 +++---- Hmisc-3.17-0/Hmisc/R/summaryS.s | 6 Hmisc-3.17-0/Hmisc/R/tabulr.s | 8 Hmisc-3.17-0/Hmisc/R/transcan.s | 312 ++++++-------- Hmisc-3.17-0/Hmisc/R/upData.s |only Hmisc-3.17-0/Hmisc/README.md | 4 Hmisc-3.17-0/Hmisc/man/Hmisc-internal.Rd | 1 Hmisc-3.17-0/Hmisc/man/ffCompress.Rd |only Hmisc-3.17-0/Hmisc/man/getRs.Rd | 12 Hmisc-3.17-0/Hmisc/man/html.Rd | 10 Hmisc-3.17-0/Hmisc/man/knitrSet.Rd | 3 Hmisc-3.17-0/Hmisc/man/label.Rd | 9 Hmisc-3.17-0/Hmisc/man/minor.tick.Rd | 13 Hmisc-3.17-0/Hmisc/man/plsmo.Rd | 35 + Hmisc-3.17-0/Hmisc/man/string.bounding.box.Rd | 17 Hmisc-3.17-0/Hmisc/man/upData.Rd | 17 Hmisc-3.17-0/Hmisc/tests/aregImpute4.r |only Hmisc-3.17-0/Hmisc/tests/cut2.r |only Hmisc-3.17-0/Hmisc/tests/latex-html.Rmd |only Hmisc-3.17-0/Hmisc/tests/latex.summaryM.Rnw | 7 34 files changed, 528 insertions(+), 994 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Description: Algorithms to create prognostic biomarkers using biological networks.
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider <Syed.Haider@oicr.on.ca>
Diff between SIMMS versions 1.0.1 dated 2015-02-22 and 1.0.2 dated 2015-09-21
DESCRIPTION | 9 +- MD5 | 29 ++++---- NAMESPACE | 32 +++++++++ NEWS | 7 ++ R/create.classifier.multivariate.R | 3 R/fit.coxmodel.R | 4 - R/fit.interaction.model.R | 26 ++++++- R/prepare.training.validation.datasets.R | 33 ++++++++- build/vignette.rds |binary inst/doc/Using-SIMMS.R | 25 +++++++ inst/doc/Using-SIMMS.Rmd | 45 ++++++++++--- inst/doc/Using-SIMMS.html | 106 +++++++++++++++++++++++++++---- inst/programdata/networkdb/HiC.gm06690 |only man/SIMMS.Rd | 2 vignettes/Using-SIMMS.Rmd | 45 ++++++++++--- 15 files changed, 306 insertions(+), 60 deletions(-)
Title: Fitting Linear and Generalized Linear Models to Large Data Sets
Description: Fitting linear models and generalized linear models to large data sets by updating algorithms.
Author: Marco Enea [aut, cre], Ronen Meiri [ctb] (on behalf of DMWay Analytics LTD), Tomer Kalimi [ctb] (on behalf of DMWay Analytics LTD)
Maintainer: Marco Enea <emarco76@libero.it>
Diff between speedglm versions 0.3 dated 2015-05-25 and 0.3-1 dated 2015-09-21
DESCRIPTION | 16 ++++++--- MD5 | 20 ++++++------ NAMESPACE | 14 +++++++- NEWS | 11 ++++++ R/speedglm.r | 21 ++++++++----- R/speedlm.r | 77 +++++++++++++++++++++++++++++++----------------- R/summary.speedglm.r | 33 +++++++++++++++++++- R/summary.speedlm.r | 22 +++++++++++++ man/speedglm-package.rd | 6 +-- man/speedlm.Rd | 10 +++--- man/summary.speedglm.Rd | 7 +++- 11 files changed, 176 insertions(+), 61 deletions(-)
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MCMCglmm versions 2.21 dated 2014-06-09 and 2.22 dated 2015-09-21
MCMCglmm-2.21/MCMCglmm/R/test.R |only MCMCglmm-2.21/MCMCglmm/R/test2.R |only MCMCglmm-2.21/MCMCglmm/man/leg.Rd |only MCMCglmm-2.22/MCMCglmm/.Rinstignore | 4 MCMCglmm-2.22/MCMCglmm/DESCRIPTION | 12 MCMCglmm-2.22/MCMCglmm/MD5 | 426 MCMCglmm-2.22/MCMCglmm/NAMESPACE | 19 MCMCglmm-2.22/MCMCglmm/R/Ddivergence.R | 8 MCMCglmm-2.22/MCMCglmm/R/Dtensor.R | 62 MCMCglmm-2.22/MCMCglmm/R/KPPM.R | 4 MCMCglmm-2.22/MCMCglmm/R/MCMCglmm.R | 662 MCMCglmm-2.22/MCMCglmm/R/buildV.R |only MCMCglmm-2.22/MCMCglmm/R/buildZ.R | 169 MCMCglmm-2.22/MCMCglmm/R/close.bracket.R |only MCMCglmm-2.22/MCMCglmm/R/find.components.R | 5 MCMCglmm-2.22/MCMCglmm/R/gelman.prior.R | 2 MCMCglmm-2.22/MCMCglmm/R/mterms.R | 28 MCMCglmm-2.22/MCMCglmm/R/path.R |only MCMCglmm-2.22/MCMCglmm/R/plotsubspace.R | 32 MCMCglmm-2.22/MCMCglmm/R/posterior.ante.R |only MCMCglmm-2.22/MCMCglmm/R/posterior.cor.R | 2 MCMCglmm-2.22/MCMCglmm/R/posterior.inverse.R |only MCMCglmm-2.22/MCMCglmm/R/predict.MCMCglmm.R | 391 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|binary MCMCglmm-2.22/MCMCglmm/vignettes/Lecture8.tex | 14 MCMCglmm-2.22/MCMCglmm/vignettes/Lecture9.tex | 89 MCMCglmm-2.22/MCMCglmm/vignettes/Overview.Rnw | 4 MCMCglmm-2.22/MCMCglmm/vignettes/Overview.bib | 33 226 files changed, 11871 insertions(+), 9731 deletions(-)
Title: Cluster Detection with Hypothesis Free Scan Statistic
Description: Multiple scan statistic with variable window for one dimension data and scan statistic based on connected components in 2D or 3D.
Author: Robin Loche, Benoit Giron, David Abrial, Lionel Cucala, Myriam Charras-Garrido, Jocelyn De-Goer
Maintainer: David Abrial <graphscan@clermont.inra.fr>
Diff between graphscan versions 1.0 dated 2015-02-10 and 1.1 dated 2015-09-21
DESCRIPTION | 11 + MD5 | 88 +++++++-------- NAMESPACE | 17 +- R/graphscan.R | 2 R/graphscan_1d.R | 2 R/graphscan_1d_array_function.R | 4 R/graphscan_1d_barplot.cluster.1d.R | 2 R/graphscan_1d_character.R | 2 R/graphscan_1d_dnabin.R | 2 R/graphscan_1d_list.R | 2 R/graphscan_1d_plot.cluster.all.1d.R | 159 ++++++++++++++++++++-------- R/graphscan_1d_plot.cluster.one.1d.R | 2 R/graphscan_1d_plot.cluster.serie.1d.R | 2 R/graphscan_2d_plot.cluster.2d.R | 2 R/graphscan_3d_plot.cluster.3d.R | 2 R/graphscan_3d_plot.cluster.3d.projection.R | 2 R/graphscan_cluster.R | 8 - R/graphscan_get_number_proc.R | 2 R/graphscan_nd.R | 2 R/graphscan_plot.cluster.R | 2 R/graphscan_summary.R | 2 inst/NEWS.Rd |only man/france_two_clusters.Rd | 2 man/graphscan-plot.Rd | 42 +++---- man/graphscan.Rd | 7 - man/graphscan_1d.Rd | 1 man/summary.Rd |only src/2D_detection_cluster.c | 2 src/2D_detection_cluster.h | 2 src/2D_fonction_math.c | 2 src/2D_fonction_math.h | 2 src/2D_types.h | 2 src/Makevars | 2 src/cucala_methode.c | 38 +++--- src/cucala_methode.h | 2 src/detection_agregat.c | 15 +- src/detection_agregat.h | 2 src/fonction_math.c | 4 src/fonction_math.h | 2 src/get_number_proc.c | 2 src/qsort_elem.h | 2 src/rbtree.c | 2 src/rbtree.h | 2 src/types.h | 2 src/unif_aleat.c | 2 src/unif_aleat.h | 2 46 files changed, 270 insertions(+), 188 deletions(-)
Title: Genomic Region Processing using Tools Such as Bedtools, Bedops
and Tabix
Description: Genomic region processing using tools such as bedtools, bedops and tabix.
Author: Daryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between bedr versions 1.0.1 dated 2015-09-05 and 1.0.2 dated 2015-09-21
DESCRIPTION | 8 ++-- MD5 | 12 +++---- NAMESPACE | 2 - NEWS | 7 +++- R/read.vcf.R | 12 +++---- inst/doc/Using-bedr.html | 74 ++++++++++++++++++++++----------------------- man/get.example.regions.Rd | 10 +----- 7 files changed, 62 insertions(+), 63 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Description: Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ<matthias.templ@gmail.com>
Diff between simPop versions 0.2.12 dated 2015-08-31 and 0.2.13 dated 2015-09-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/simCategorical.R | 11 ++++++----- R/simContinuous.R | 31 ++++++++++++++++++++----------- R/simStructure.R | 15 +++++++++++---- data/eusilcP.RData |binary data/eusilcS.RData |binary data/ghanaS.RData |binary data/totalsRG.rda |binary data/totalsRGtab.rda |binary 11 files changed, 55 insertions(+), 34 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.5 dated 2015-09-11 and 0.5.1 dated 2015-09-21
ChangeLog | 8 ++++- DESCRIPTION | 8 ++--- MD5 | 10 +++---- NAMESPACE | 5 +++ R/fscores.R | 80 +++++++++++++++++++++++++++++++++++++++++++++------------ R/s3generics.R | 4 +- 6 files changed, 87 insertions(+), 28 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated from Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between simPH versions 1.3.2 dated 2015-05-21 and 1.3.4 dated 2015-09-21
DESCRIPTION | 16 +++---- MD5 | 30 ++++++------- NAMESPACE | 7 ++- NEWS | 27 +++++++++--- R/MinMaxLines.R | 1 R/SPInBounds.R | 91 ++++++++++++++++++++--------------------- R/SmoothSim.R | 2 R/coxsimInteract.R | 95 ++++++++++++++++++++++++------------------- R/coxsimLinear.R | 4 - R/coxsimPoly.R | 5 +- R/coxsimSpline.R | 4 - R/coxsimtvc.R | 2 README.md | 2 build/vignette.rds |binary man/coxsimInteract.Rd | 14 ++++++ vignettes/simPH-overview.Rnw | 6 +- 16 files changed, 179 insertions(+), 127 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series
from the HIS Central catalog based on geographic bounding box, server, or keyword.
GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The GetValues function can also retrieve WaterML 1 or WaterML 2.0 data
from a custom URL or from a local file. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.4.0 dated 2015-09-03 and 1.5.0 dated 2015-09-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/GetServices.R | 39 +++++++++++++++++++++++++++++++++++++-- R/GetValues.R | 2 +- 4 files changed, 44 insertions(+), 9 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst <dwbapst@gmail.com>
Diff between paleotree versions 2.4 dated 2015-05-02 and 2.5 dated 2015-09-21
CHANGELOG | 39 +++++ DESCRIPTION | 11 - MD5 | 156 ++++++++++++---------- NAMESPACE | 26 +++ R/DiversityCurves.R | 47 ++++-- R/SongZhangDicrano.R |only R/binTimeData.R | 6 R/branchClasses.R | 4 R/cal3TimePaleoPhy.R | 166 +++++++++++++++-------- R/communityEcology.R |only R/compareTimescaling.R | 20 +- R/constrainParPaleo.R | 2 R/createMrBayesConstraints.R |only R/dateNodes.R | 12 + R/degradeTree.R | 23 ++- R/depthRainbow.R | 4 R/divCurveFossilRecordSim.R |only R/durationFreq.R | 26 ++- R/equation2function.R |only R/expandTaxonTree.R | 24 ++- R/footeValues.R | 6 R/fourDateFunctions.R | 8 - R/freqRat.R | 4 R/getSampProbDisc.R | 12 - R/getSampRateCont.R | 19 +- R/horizonSampRate.R | 4 R/inverseSurv.R | 7 - R/kanto.R |only R/macroperforateForam.R |only R/makePBDBtaxonTree.R | 33 +++- R/minBranchLength.R | 10 - R/minCharChange.R | 266 +++++++++++++++++++++++++++++++++++--- R/modelMethods.R | 2 R/modifyTerminalBranches.R | 278 +++++++++++++++++++++++++++++++++++----- R/multiDiv.R | 43 ++++-- R/nearestNeighborDist.R | 2 R/occData2timeList.R | 2 R/optimPaleo.R | 2 R/paleotree-package.R | 9 + R/parentChild2taxonTree.R | 164 +++++++++++++++++++---- R/perCapitaRates.R | 28 ++-- R/perfectParsCharTree.R | 4 R/plotTraitgram.R | 5 R/probAnc.R | 14 +- R/resolveTreeChar.R | 23 ++- R/reverseList.R | 2 R/rootSplit.R | 5 R/sampleRanges.R | 22 +-- R/simFossilRecord.R |only R/simFossilRecordInternal.R |only R/simFossilRecordMethods.R |only R/simFossilTaxa.R | 42 +++--- R/simPaleoTrees.R | 11 + R/taxa2cladogram.R | 2 R/taxa2phylo.R | 190 ++++++++++++++++++++++----- R/termTaxa.R | 29 +++- R/testEdgeMat.R | 171 ++++++++++++++++++++---- R/timeLadderTree.R | 31 +++- R/timePaleoPhy.R | 116 +++++++++++----- R/timeSliceTree.R | 4 R/unitLengthTree.R | 4 README | 8 - data/SongZhangDicrano.rdata |only data/kanto.rdata |only data/macroperforateForam.rdata |only man/SongZhangDicrano.Rd |only man/cal3TimePaleoPhy.Rd | 16 +- man/communityEcology.Rd |only man/createMrBayesConstraints.Rd |only man/dateNodes.Rd | 6 man/degradeTree.Rd | 5 man/divCurveFossilRecordSim.Rd |only man/durationFreq.Rd | 7 - man/equation2function.Rd |only man/inverseSurv.Rd | 7 - man/kanto.Rd |only man/macroperforateForam.Rd |only man/makePBDBtaxonTree.Rd | 24 ++- man/minCharChange.Rd | 122 ++++++++++++++++- man/modifyTerminalBranches.Rd | 145 +++++++++++++++++++- man/multiDiv.Rd | 19 ++ man/parentChild2taxonTree.Rd | 24 +++ man/probAnc.Rd | 4 man/resolveTreeChar.Rd | 38 +++++ man/simFossilRecord.Rd |only man/simFossilRecordMethods.Rd |only man/simFossilTaxa.Rd | 7 - man/simPaleoTrees.Rd | 2 man/testEdgeMat.Rd | 5 man/timePaleoPhy.Rd | 26 +++ 90 files changed, 2061 insertions(+), 544 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms efficiently using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable matching for
two-sided markets, such as the stable marriage problem and the
college-admissions problem. Implements Irving's Algorithm for
the stable roommate problem. Implements the top trading cycle
algorithm for the indivisible goods trading problem.
Author: Jan Tilly, Nick Janetos
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.1 dated 2015-09-14 and 1.1.1 dated 2015-09-21
DESCRIPTION | 13 - MD5 | 38 ++-- NEWS.md | 27 ++ R/RcppExports.R | 19 -- R/matchingR.R | 32 +-- README.md | 110 +++++++++--- inst/doc/matchingR-intro.R | 8 inst/doc/matchingR-intro.Rmd | 15 - inst/doc/matchingR-intro.html | 47 ++--- inst/doc/matchingR-performance.R | 76 ++------ inst/doc/matchingR-performance.Rmd | 82 ++------- inst/doc/matchingR-performance.html | 325 ++++++++++-------------------------- man/checkStabilityRoommate.Rd | 6 man/galeShapleyMatching.Rd | 13 - man/pkg.env.Rd | 2 src/galeshapley.cpp | 13 - src/roommate.cpp | 41 +++- src/roommate.h | 1 vignettes/matchingR-intro.Rmd | 15 - vignettes/matchingR-performance.Rmd | 82 ++------- 20 files changed, 413 insertions(+), 552 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.6 dated 2015-06-23 and 2.1.7 dated 2015-09-21
geomorph-2.1.6/geomorph/man/define.sliders.2d.Rd |only geomorph-2.1.6/geomorph/man/define.sliders.3d.Rd |only geomorph-2.1.6/geomorph/man/pairwise.slope.test.Rd |only geomorph-2.1.6/geomorph/man/pairwiseD.test.Rd |only geomorph-2.1.7/geomorph/DESCRIPTION | 13 geomorph-2.1.7/geomorph/MD5 | 116 +-- geomorph-2.1.7/geomorph/NAMESPACE | 16 geomorph-2.1.7/geomorph/NEWS | 30 geomorph-2.1.7/geomorph/R/advanced.procD.lm.r | 84 +- geomorph-2.1.7/geomorph/R/bilat.symmetry.r | 136 ++- geomorph-2.1.7/geomorph/R/build.template.r | 4 geomorph-2.1.7/geomorph/R/compare.evol.rates.r | 7 geomorph-2.1.7/geomorph/R/compare.modular.partitions.r | 6 geomorph-2.1.7/geomorph/R/compare.multi.evol.rates.r |only geomorph-2.1.7/geomorph/R/define.links.r | 13 geomorph-2.1.7/geomorph/R/define.sliders.r | 3 geomorph-2.1.7/geomorph/R/digit.fixed.r | 2 geomorph-2.1.7/geomorph/R/digitize2d.r | 2 geomorph-2.1.7/geomorph/R/digitsurface.r | 2 geomorph-2.1.7/geomorph/R/geomorph.support.code.r | 496 +++++++------- geomorph-2.1.7/geomorph/R/globalIntegration.r | 16 geomorph-2.1.7/geomorph/R/morphol.integr.r | 86 +- geomorph-2.1.7/geomorph/R/phylo.pls.R | 77 +- geomorph-2.1.7/geomorph/R/physignal.r | 9 geomorph-2.1.7/geomorph/R/plotAllometry.r | 72 -- geomorph-2.1.7/geomorph/R/plotGMPhyloMorphoSpace.r | 117 ++- geomorph-2.1.7/geomorph/R/plotOutliers.r | 4 geomorph-2.1.7/geomorph/R/plotRefToTarget.r | 50 - geomorph-2.1.7/geomorph/R/procD.lm.r | 44 - geomorph-2.1.7/geomorph/R/procD.pgls.r | 49 - geomorph-2.1.7/geomorph/R/read.ply.r | 49 - geomorph-2.1.7/geomorph/R/readland.nts.r | 6 geomorph-2.1.7/geomorph/R/readland.tps.r | 7 geomorph-2.1.7/geomorph/R/readmulti.nts.r | 2 geomorph-2.1.7/geomorph/R/trajectory.analysis.r | 137 +-- geomorph-2.1.7/geomorph/R/two.b.pls.r | 2 geomorph-2.1.7/geomorph/R/warpRefMesh.r | 13 geomorph-2.1.7/geomorph/R/warpRefOutline.r | 10 geomorph-2.1.7/geomorph/man/advanced.procD.lm.Rd | 9 geomorph-2.1.7/geomorph/man/bilat.symmetry.Rd | 4 geomorph-2.1.7/geomorph/man/buildtemplate.Rd | 4 geomorph-2.1.7/geomorph/man/compare.evol.rates.Rd | 3 geomorph-2.1.7/geomorph/man/compare.modular.partitions.Rd | 4 geomorph-2.1.7/geomorph/man/compare.multi.evol.rates.Rd |only geomorph-2.1.7/geomorph/man/define.links.Rd | 4 geomorph-2.1.7/geomorph/man/define.sliders.Rd | 2 geomorph-2.1.7/geomorph/man/digit.fixed.Rd | 2 geomorph-2.1.7/geomorph/man/digitize2d.Rd | 2 geomorph-2.1.7/geomorph/man/digitsurface.Rd | 2 geomorph-2.1.7/geomorph/man/globalIntegration.Rd | 4 geomorph-2.1.7/geomorph/man/morphol.integr.Rd | 4 geomorph-2.1.7/geomorph/man/phylo.pls.Rd | 4 geomorph-2.1.7/geomorph/man/physignal.Rd | 3 geomorph-2.1.7/geomorph/man/plotGMPhyloMorphoSpace.Rd | 34 geomorph-2.1.7/geomorph/man/plotOutliers.Rd | 4 geomorph-2.1.7/geomorph/man/plotRefToTarget.Rd | 4 geomorph-2.1.7/geomorph/man/procD.lm.Rd | 16 geomorph-2.1.7/geomorph/man/procD.pgls.Rd | 8 geomorph-2.1.7/geomorph/man/readland.tps.Rd | 2 geomorph-2.1.7/geomorph/man/trajectory.analysis.Rd | 26 geomorph-2.1.7/geomorph/man/two.b.pls.Rd | 2 geomorph-2.1.7/geomorph/src/geomorph.c | 31 62 files changed, 1026 insertions(+), 832 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>
Diff between fitdistrplus versions 1.0-4 dated 2015-02-23 and 1.0-5 dated 2015-09-21
DESCRIPTION | 16 MD5 | 111 +++--- NAMESPACE | 159 ++++----- R/bootdist-graph.R |only R/bootdist.R | 328 ++++++++++--------- R/bootdistcens.R | 277 ++++++++-------- R/cdfcomp.R | 67 ++-- R/cdfcompcens.R | 4 R/denscomp.R | 19 - R/fitdist.R | 99 ++++- R/fitdistcens.R | 325 +++++++++++-------- R/gofstat.R | 6 R/mgedist.R | 614 +++++++++++++++++------------------- R/mledist.R | 195 ++++------- R/mmedist.R | 571 +++++++++++++++++++--------------- R/plotdist.R | 25 + R/plotdistcens.R | 6 R/ppcomp.R | 51 +-- R/qmedist.R | 527 ++++++++++++++----------------- R/qqcomp.R | 32 + R/util-checkparam.R |only R/util-startarg.R |only R/util-wtdstat.R |only build/vignette.rds |binary data/danishmulti.rda |binary data/danishuni.rda |binary data/endosulfan.rda |binary data/fluazinam.rda |binary data/groundbeef.rda |binary data/salinity.rda |binary data/smokedfish.rda |binary data/toxocara.rda |binary inst/NEWS | 16 inst/doc/paper2JSS.R | 6 inst/doc/paper2JSS.Rnw | 6 inst/doc/paper2JSS.pdf |binary man/bootdist.Rd | 335 ++++++++++---------- man/bootdistcens.Rd | 272 ++++++++-------- man/fitdist.Rd | 136 ++++---- man/fitdistcens.Rd | 525 ++++++++++++++++--------------- man/graphcomp.Rd | 43 +- man/mgedist.Rd | 26 - man/mledist.Rd | 430 ++++++++++++++----------- man/mmedist.Rd | 350 +++++++++++---------- man/qmedist.Rd | 296 +++++++++-------- tests/bootdist.R | 397 +++++++++++++---------- tests/bootdistcens.R | 120 ++++--- tests/cdfcomp.R | 377 +++++++++++----------- tests/denscomp.R | 273 ++++++++-------- tests/fitdist.R | 798 ++++++++++++++++++++++++++---------------------- tests/fitdistcens.R |only tests/mgedist.R | 164 +++++---- tests/mledist.R | 603 +++++++++++++++++++++--------------- tests/mmedist.R | 252 ++++++++++----- tests/plotdist.R | 1 tests/ppcomp.R | 20 + tests/qmedist.R | 176 ++++++---- tests/qqcomp.R | 12 vignettes/paper2JSS.Rnw | 6 59 files changed, 4981 insertions(+), 4091 deletions(-)
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed by Imai and Ratkovic (2014; JRSSB). The propensity score is estimated such that it maximizes the resulting covariate balance as well as the prediction of treatment assignment. The method, therefore, avoids an iteration between model fitting and balance checking. The package also implements several extensions of the CBPS beyond the cross-sectional, binary treatment setting. The current version implements the CBPS for longitudinal settings so that it can be used in conjunction with marginal structural models (Imai and Ratkovic, 2014), treatments with three- and four-valued treatment variables, continuous-valued treatments (Fong, Hazlett, and Imai, 2015), and the situation with multiple distinct binary treatments administered simultaneously. In the future it will be extended to other settings including the generalization of experimental and instrumental variable estimates.
Author: Christian Fong <christianfong@stanford.edu>, Marc Ratkovic <ratkovic@princeton.edu>, Chad Hazlett <chazlett@ucla.edu>, Kosuke Imai <kimai@princeton.edu>
Maintainer: Christian Fong <christianfong@stanford.edu>
Diff between CBPS versions 0.9 dated 2014-08-13 and 0.10 dated 2015-09-21
ChangeLog | 3 DESCRIPTION | 14 - MD5 | 35 +- NAMESPACE | 15 + R/BlackwellHelpCode.R | 47 +++ R/CBIV.R |only R/CBMSM.R | 88 +++++-- R/CBPSBinary.R | 594 +++++++++++++++++++++++++------------------------- R/CBPSContinuous.r | 8 R/CBPSMain.R | 457 ++++++++++++++++++++++---------------- R/CBPSMultiTreat.r | 84 ++----- R/npCBPS.R |only data/Blackwell.tab.gz |binary man/Blackwell.Rd | 2 man/CBMSM.Rd | 73 ++++-- man/CBPS.Rd | 103 +++----- man/balance.Rd | 7 man/npCBPS.Rd |only man/plot.CBMSM.Rd | 3 man/plot.CBPS.Rd | 14 - 20 files changed, 845 insertions(+), 702 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.2-0 dated 2015-09-15 and 1.2-1 dated 2015-09-21
DESCRIPTION | 8 MD5 | 37 +-- NAMESPACE | 6 R/AllGenerics.R | 2 R/abbreviate.R |only R/addComplement.R | 26 +- R/inspect.R | 2 R/interestMeasures.R | 264 ++++++++++++++++------ data/Mushroom.rda |only data/datalist | 1 inst/NEWS | 9 inst/doc/arules.pdf |binary inst/tests/test-apriori.R | 4 inst/tests/test-itemMatrix.R | 4 inst/tests/test-measures.R | 25 +- inst/tests/test-missing.R |only inst/tests/test-transactions.R | 21 + man/APappearance-class.Rd | 11 man/Mushroom.Rd |only man/abbreviate.Rd |only man/interestMeasure.Rd | 475 ++++++++++++++++++++++++++++++++--------- src/reclat.c | 10 22 files changed, 679 insertions(+), 226 deletions(-)
Title: Regularization for Variable Selection in Model-Based Clustering
and Discriminant Analysis
Description: Performs a regularization approach to variable selection in the
model-based clustering and classification frameworks.
First, the variables are arranged in order with a lasso-like procedure.
Second, the method of Maugis, Celeux, and Martin-Magniette (2009, 2011)
is adapted to define the role of variables in the two frameworks.
Author: Mohammed Sedki, Gilles Celeux, Cathy Maugis-Rabusseau
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between SelvarMix versions 1.0 dated 2014-08-27 and 1.1 dated 2015-09-20
DESCRIPTION | 20 +++--- MD5 | 20 +++--- NAMESPACE | 6 + R/ClusteringEMGlasso.R | 33 +++++----- R/DiscriminantAnalysisGlasso.R | 18 +++-- R/ModelSelectionClust.R | 4 - R/SelvarClustLasso.R | 7 -- R/SelvarLearnLasso.R | 9 -- R/VariableSelection.R | 19 ++---- src/RcppExports.cpp | 128 ++++++++++++++++------------------------- src/critClust.cpp | 109 ++++++++++++++++++---------------- 11 files changed, 177 insertions(+), 196 deletions(-)
Title: Item Response Theory via Shiny
Description: Interactive shiny application for running Item Response Theory
analysis.
Author: William Kyle Hamilton <kyle.hamilton@gmail.com>, Atsushi Mizumoto
<atsushi@mizumot.com>
Maintainer: William Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between IRTShiny versions 1.0 dated 2014-11-25 and 1.1 dated 2015-09-20
DESCRIPTION | 12 MD5 | 14 NAMESPACE | 1 NEWS |only R/IRTShiny.R | 42 - README.md |only inst/IRT/server.R | 1848 +++++++++++++++++++++++++++--------------------------- inst/IRT/ui.R | 713 +++++++++++--------- man/startIRT.Rd | 54 - 9 files changed, 1377 insertions(+), 1307 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts
('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and
supporting most output formats of R graphics including PNG, PDF and
SVG. Text glyphs will be converted into polygons or raster images,
hence after the plot has been created, it no longer relies on the font files.
No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-2 dated 2015-05-24 and 0.4-3 dated 2015-09-20
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ inst/NEWS.Rd | 14 ++++++++++---- src/util.h | 13 +++++++++---- 5 files changed, 30 insertions(+), 17 deletions(-)
Title: Tools for Selective Inference
Description: New tools for inference after selection, for use
with forward stepwise regression, least angle regression, the
lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor,
Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.0.2 dated 2015-08-21 and 1.1.0 dated 2015-09-20
DESCRIPTION | 16 ++++--- MD5 | 27 ++++++------ NAMESPACE | 3 - R/funs.common.R | 11 +++-- R/funs.fixed.R | 25 ++++++++--- R/funs.fs.R | 45 ++++++++++++++------- R/funs.inf.R | 96 +++++++++++++++++++++++++++++++++------------- R/funs.lar.R | 66 ++++++++++++++++++------------- man/estimateLambda.Rd |only man/fixedLassoInf.Rd | 20 ++++++--- man/fs.Rd | 23 ++++++----- man/fsInf.Rd | 18 ++++++-- man/lar.Rd | 6 +- man/larInf.Rd | 21 +++++++--- man/selectiveInference.Rd | 48 +++++++++++++++++++---- 15 files changed, 289 insertions(+), 136 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Convert R Graphics to Flash Animations
Description: Using the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between R2SWF versions 0.9 dated 2015-02-26 and 0.9-1 dated 2015-09-20
R2SWF-0.9-1/R2SWF/DESCRIPTION | 10 +++++----- R2SWF-0.9-1/R2SWF/MD5 | 20 ++++++++++---------- R2SWF-0.9-1/R2SWF/NAMESPACE | 3 +++ R2SWF-0.9-1/R2SWF/inst/NEWS.Rd |only R2SWF-0.9-1/R2SWF/man/dev2swf.Rd | 3 ++- R2SWF-0.9-1/R2SWF/man/file2swf.Rd | 3 ++- R2SWF-0.9-1/R2SWF/man/image2swf.Rd | 3 ++- R2SWF-0.9-1/R2SWF/man/svg2swf.Rd | 3 ++- R2SWF-0.9-1/R2SWF/man/swf.Rd | 3 ++- R2SWF-0.9-1/R2SWF/man/swf2html.Rd | 3 ++- R2SWF-0.9-1/R2SWF/src/swfFont.h | 11 ++++++++--- R2SWF-0.9/R2SWF/NEWS |only 12 files changed, 38 insertions(+), 24 deletions(-)
Title: Datasets for the R/qtl Book
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl.
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtlbook versions 0.18-1 dated 2011-11-29 and 0.18-3 dated 2015-09-20
DESCRIPTION | 13 +++++++------ MD5 | 24 +++++++++++++----------- README.md |only data/ch3a.RData |binary data/ch3b.RData |binary data/ch3c.RData |binary data/gutlength.RData |binary data/iron.RData |binary data/myocard.RData |binary data/nf1.RData |binary data/ovar.RData |binary data/trout.RData |binary inst/README.md |only inst/STATUS.txt | 36 ++++++++++++++++++++---------------- 14 files changed, 40 insertions(+), 33 deletions(-)
Title: Common Infrastructure for Extensions of Exponential Random Graph
Models
Description: Datasets and definitions of generic functions used in dependencies of the xergm package.
Author: Philip Leifeld [aut, cre]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between xergm.common versions 1.5.1 dated 2015-08-03 and 1.5.4 dated 2015-09-20
DESCRIPTION | 17 ++++++++++------- MD5 | 14 +++++++++----- NAMESPACE | 11 +++++++++++ R/preprocess.R |only R/xergm.common.R | 32 +------------------------------- data/chemnet.rda |binary data/knecht.rda |binary man/adjust.Rd |only man/handleMissings.Rd |only man/preprocess.Rd |only 10 files changed, 31 insertions(+), 43 deletions(-)
Title: Application in R for Queueing Analysis and Simulation
Description: Provides functions to compute the main characteristics of the
following queueing models: M/M/1, M/M/s, M/M/1/k, M/M/s/k, M/M/1/Inf/H, M/
M/s/Inf/H, M/M/s/Inf/H with Y replacements, M/M/Inf, Open Jackson Networks
and Closed Jackson Networks. Moreover, it is also possible to simulate
similar queueing models with any type of arrival or service distribution: G/
G/1, G/G/s, G/G/1/k, G/G/s/k, G/G/1/Inf/H, G/G/s/Inf/H, G/G/s/Inf/H with Y
replacements, Open Networks and Closed Networks. Finally, contains functions
for fit data to a statistic distribution.
Author: Borja Varela
Maintainer: Borja Varela <borja.varela.brea@gmail.com>
Diff between arqas versions 1.1 dated 2015-06-15 and 1.3 dated 2015-09-20
arqas-1.1/arqas/man/summary.MarkovianModel.Rd |only arqas-1.3/arqas/DESCRIPTION | 12 arqas-1.3/arqas/MD5 | 44 + arqas-1.3/arqas/NAMESPACE | 7 arqas-1.3/arqas/R/1_ModelsHeader.R | 56 +- arqas-1.3/arqas/R/2_SimpleModels.R | 5 arqas-1.3/arqas/R/3_ComplexModels.R | 28 - arqas-1.3/arqas/R/4_NetworkModels.R | 54 +- arqas-1.3/arqas/R/5_SimulateModels.R | 578 ++++++++++---------------- arqas-1.3/arqas/R/6_DistributionAnalysis.R | 57 +- arqas-1.3/arqas/man/ClosedJacksonNetwork.Rd | 6 arqas-1.3/arqas/man/FWq.Rd | 2 arqas-1.3/arqas/man/M_M_1.Rd | 2 arqas-1.3/arqas/man/M_M_1_INF_H.Rd | 2 arqas-1.3/arqas/man/M_M_INF.Rd | 2 arqas-1.3/arqas/man/M_M_S_INF_H_Y.Rd | 6 arqas-1.3/arqas/man/OpenJacksonNetwork.Rd | 4 arqas-1.3/arqas/man/ParallelizeSimulations.Rd |only arqas-1.3/arqas/man/denscompggplot2.Rd | 2 arqas-1.3/arqas/man/fitData.Rd | 2 arqas-1.3/arqas/man/maxCustomers.Rd | 4 arqas-1.3/arqas/man/plot.MarkovianModel.Rd |only arqas-1.3/arqas/man/plot.Rd | 10 arqas-1.3/arqas/man/summary.SimulatedModel.Rd |only arqas-1.3/arqas/man/summaryFit.Rd | 8 25 files changed, 408 insertions(+), 483 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-2 dated 2015-05-11 and 0.7-3 dated 2015-09-20
RDS-0.7-2/RDS/R/gf.R |only RDS-0.7-2/RDS/man/gf.weights.Rd |only RDS-0.7-2/RDS/man/impute.degree.Rd |only RDS-0.7-3/RDS/DESCRIPTION | 11 - RDS-0.7-3/RDS/MD5 | 61 ++++----- RDS-0.7-3/RDS/NAMESPACE | 41 +++++- RDS-0.7-3/RDS/R/LRT.trend.R | 48 +++---- RDS-0.7-3/RDS/R/RDS.compare.proportions.R | 6 RDS-0.7-3/RDS/R/bgk_kde.R | 8 - RDS-0.7-3/RDS/R/bootstrap-intervals.R | 125 ++++++++++++++----- RDS-0.7-3/RDS/R/control.rds.estimates.R | 27 +++- RDS-0.7-3/RDS/R/data-export.R | 6 RDS-0.7-3/RDS/R/data-import.R | 4 RDS-0.7-3/RDS/R/estimate-plots.R | 5 RDS-0.7-3/RDS/R/estimate-utils.R | 8 - RDS-0.7-3/RDS/R/gile-bootstrap.R | 172 +++++++++++++++++++++------ RDS-0.7-3/RDS/R/homophily.R | 8 - RDS-0.7-3/RDS/R/llmeC.R | 4 RDS-0.7-3/RDS/R/me.impute.R | 34 +++-- RDS-0.7-3/RDS/R/rds.data.frame-plots.R | 21 +-- RDS-0.7-3/RDS/R/rds.estimates.local.R | 31 +++- RDS-0.7-3/RDS/R/salganik-bootstrap.R | 4 RDS-0.7-3/RDS/R/summary.odds.R | 22 +-- RDS-0.7-3/RDS/R/weights.R | 17 +- RDS-0.7-3/RDS/R/wtd.stats.R |only RDS-0.7-3/RDS/man/RDS.bootstrap.intervals.Rd | 9 + RDS-0.7-3/RDS/man/compute.weights.Rd | 4 RDS-0.7-3/RDS/man/control.rds.estimates.Rd | 24 +++ RDS-0.7-3/RDS/man/homophily.estimates.Rd | 2 RDS-0.7-3/RDS/man/impute.visibility.Rd |only RDS-0.7-3/RDS/man/plot.rds.data.frame.Rd | 8 - RDS-0.7-3/RDS/man/reingold.tilford.plot.Rd | 6 RDS-0.7-3/RDS/src/bsC.c | 9 + RDS-0.7-3/RDS/src/bsC.h | 1 34 files changed, 495 insertions(+), 231 deletions(-)
Title: Symmetric File Encryption Using GPG
Description: Provides easy symmetric file encryption using GPG with
cryptographically strong defaults. Only symmetric encryption is
supported. GPG is pre-installed with most Linux distributions.
Windows users will need to install 'Gpg4win' (http://www.gpg4win.org/).
OS X users will need to install 'GPGTools' (https://gpgtools.org/).
Author: Brett Klamer [aut, cre]
Maintainer: Brett Klamer <rcrypt@brettklamer.com>
Diff between rcrypt versions 0.1.0 dated 2015-09-05 and 0.1.1 dated 2015-09-20
DESCRIPTION | 12 +-- MD5 | 18 ++-- NEWS | 11 ++- R/decrypt.R | 109 +++++++++++++++-------------- R/encrypt.R | 153 ++++++++++++++++++++---------------------- R/zzz.r | 40 +--------- README.md | 14 +-- man/decrypt.Rd | 4 - man/encrypt.Rd | 8 +- tests/testthat/test-decrypt.r | 4 - 10 files changed, 175 insertions(+), 198 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.500.2.0 dated 2015-09-03 and 0.5.600.2.0 dated 2015-09-19
ChangeLog | 9 DESCRIPTION | 8 MD5 | 50 inst/NEWS.Rd | 11 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 2 inst/include/armadillo_bits/Cube_bones.hpp | 7 inst/include/armadillo_bits/Cube_meat.hpp | 50 inst/include/armadillo_bits/Mat_bones.hpp | 14 inst/include/armadillo_bits/Mat_meat.hpp | 50 inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/forward_bones.hpp | 4 inst/include/armadillo_bits/glue_join_bones.hpp | 8 inst/include/armadillo_bits/glue_join_meat.hpp | 43 inst/include/armadillo_bits/operator_cube_div.hpp | 68 + inst/include/armadillo_bits/operator_cube_minus.hpp | 68 + inst/include/armadillo_bits/operator_cube_plus.hpp | 68 + inst/include/armadillo_bits/operator_cube_schur.hpp | 64 + inst/include/armadillo_bits/operator_div.hpp | 68 + inst/include/armadillo_bits/operator_minus.hpp | 68 + inst/include/armadillo_bits/operator_plus.hpp | 68 + inst/include/armadillo_bits/operator_schur.hpp | 68 + inst/include/armadillo_bits/subview_cube_each_bones.hpp |only inst/include/armadillo_bits/subview_cube_each_meat.hpp |only inst/include/armadillo_bits/subview_each_bones.hpp | 77 + inst/include/armadillo_bits/subview_each_meat.hpp | 869 ++++++++++++++-- 27 files changed, 1597 insertions(+), 149 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.12.0 dated 2015-04-07 and 1.13.0 dated 2015-09-19
ChangeLog | 9 DESCRIPTION | 12 MD5 | 55 +- NAMESPACE | 15 R/access.R | 46 + R/as.edgelist.R |only R/fileio.R | 1101 +++++++++++++++++++++++++++--------------- R/misc.R | 34 + R/plot.R | 2 R/zzz.R | 2 build/vignette.rds |binary inst/CITATION | 22 inst/doc/networkVignette.R | 80 +-- inst/doc/networkVignette.Rnw | 17 inst/doc/networkVignette.pdf |binary man/as.color.Rd |only man/as.edgelist.Rd |only man/as.matrix.network.Rd | 6 man/get.edges.Rd | 17 man/get.inducedSubgraph.Rd | 2 man/has.edges.Rd |only man/network-internal.Rd | 4 man/network-package.Rd | 4 man/network.dyadcount.Rd | 10 man/read.paj.Rd | 56 +- man/valid.eids.Rd | 4 tests/as.edgelist_tests.R |only tests/misc_tests.R |only tests/network.battery.R | 64 ++ tests/plot_tests.R | 16 tests/read.paj_tests.R |only vignettes/networkVignette.Rnw | 17 32 files changed, 1072 insertions(+), 523 deletions(-)
Title: Extension of Data.frame
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.
Author: M Dowle, A Srinivasan, T Short, S Lianoglou with contributions from R Saporta, E Antonyan
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.9.4 dated 2014-10-02 and 1.9.6 dated 2015-09-19
data.table-1.9.4/data.table/R/check_for_seq.r |only data.table-1.9.4/data.table/R/plus.R |only data.table-1.9.4/data.table/R/take.R |only data.table-1.9.4/data.table/R/trim.R |only data.table-1.9.4/data.table/R/which.first.R |only data.table-1.9.4/data.table/R/which.last.R |only data.table-1.9.6/data.table/DESCRIPTION | 22 data.table-1.9.6/data.table/MD5 | 209 data.table-1.9.6/data.table/NAMESPACE | 18 data.table-1.9.6/data.table/R/IDateTime.R | 24 data.table-1.9.6/data.table/R/between.R | 4 data.table-1.9.6/data.table/R/bmerge.R | 77 data.table-1.9.6/data.table/R/c.factor.R | 8 data.table-1.9.6/data.table/R/cedta.R | 28 data.table-1.9.6/data.table/R/data.table.R | 1031 ++-- data.table-1.9.6/data.table/R/duplicated.R | 16 data.table-1.9.6/data.table/R/fcast.R | 313 - data.table-1.9.6/data.table/R/fmelt.R | 35 data.table-1.9.6/data.table/R/foverlaps.R | 115 data.table-1.9.6/data.table/R/fread.R | 107 data.table-1.9.6/data.table/R/getdots.R | 2 data.table-1.9.6/data.table/R/last.R | 10 data.table-1.9.6/data.table/R/like.R | 2 data.table-1.9.6/data.table/R/merge.R | 118 data.table-1.9.6/data.table/R/onAttach.R | 4 data.table-1.9.6/data.table/R/onLoad.R | 16 data.table-1.9.6/data.table/R/setkey.R | 183 data.table-1.9.6/data.table/R/setops.R | 49 data.table-1.9.6/data.table/R/shift.R |only data.table-1.9.6/data.table/R/tables.R | 2 data.table-1.9.6/data.table/R/test.data.table.R | 50 data.table-1.9.6/data.table/R/transpose.R |only data.table-1.9.6/data.table/R/utils.R |only data.table-1.9.6/data.table/R/xts.R |only data.table-1.9.6/data.table/README.md | 299 + data.table-1.9.6/data.table/build/vignette.rds |binary data.table-1.9.6/data.table/inst/doc/datatable-faq.R | 55 data.table-1.9.6/data.table/inst/doc/datatable-faq.Rnw | 15 data.table-1.9.6/data.table/inst/doc/datatable-faq.pdf |binary data.table-1.9.6/data.table/inst/doc/datatable-intro-vignette.R |only data.table-1.9.6/data.table/inst/doc/datatable-intro-vignette.Rmd |only 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data.table-1.9.6/data.table/man/data.table.Rd | 32 data.table-1.9.6/data.table/man/dcast.data.table.Rd | 115 data.table-1.9.6/data.table/man/duplicated.Rd | 104 data.table-1.9.6/data.table/man/foverlaps.Rd | 22 data.table-1.9.6/data.table/man/frank.Rd |only data.table-1.9.6/data.table/man/fread.Rd | 44 data.table-1.9.6/data.table/man/like.Rd | 4 data.table-1.9.6/data.table/man/melt.data.table.Rd | 128 data.table-1.9.6/data.table/man/merge.Rd | 138 data.table-1.9.6/data.table/man/na.omit.data.table.Rd |only data.table-1.9.6/data.table/man/patterns.Rd |only data.table-1.9.6/data.table/man/rbindlist.Rd | 14 data.table-1.9.6/data.table/man/rleid.Rd |only data.table-1.9.6/data.table/man/setDF.Rd | 25 data.table-1.9.6/data.table/man/setDT.Rd | 22 data.table-1.9.6/data.table/man/setNumericRounding.Rd | 45 data.table-1.9.6/data.table/man/setattr.Rd | 77 data.table-1.9.6/data.table/man/setcolorder.Rd |only data.table-1.9.6/data.table/man/setkey.Rd | 5 data.table-1.9.6/data.table/man/setorder.Rd | 40 data.table-1.9.6/data.table/man/shift.Rd |only data.table-1.9.6/data.table/man/subset.data.table.Rd | 2 data.table-1.9.6/data.table/man/tables.Rd | 8 data.table-1.9.6/data.table/man/transpose.Rd |only data.table-1.9.6/data.table/man/truelength.Rd | 16 data.table-1.9.6/data.table/man/tstrsplit.Rd |only data.table-1.9.6/data.table/src/assign.c | 176 data.table-1.9.6/data.table/src/bmerge.c | 6 data.table-1.9.6/data.table/src/data.table.h | 17 data.table-1.9.6/data.table/src/dogroups.c | 8 data.table-1.9.6/data.table/src/fastmean.c | 1 data.table-1.9.6/data.table/src/fcast.c | 539 -- data.table-1.9.6/data.table/src/fmelt.c | 722 +- data.table-1.9.6/data.table/src/forder.c | 43 data.table-1.9.6/data.table/src/frank.c | 121 data.table-1.9.6/data.table/src/fread.c | 881 ++- data.table-1.9.6/data.table/src/gsumm.c | 84 data.table-1.9.6/data.table/src/ijoin.c | 8 data.table-1.9.6/data.table/src/init.c | 15 data.table-1.9.6/data.table/src/rbindlist.c | 68 data.table-1.9.6/data.table/src/shift.c |only data.table-1.9.6/data.table/src/transpose.c |only data.table-1.9.6/data.table/src/uniqlist.c | 51 data.table-1.9.6/data.table/src/vecseq.c | 11 data.table-1.9.6/data.table/src/wrappers.c | 20 data.table-1.9.6/data.table/tests/autoprint.R | 33 data.table-1.9.6/data.table/tests/autoprint.Rout.save | 61 data.table-1.9.6/data.table/tests/knitr.R |only data.table-1.9.6/data.table/tests/knitr.Rmd |only data.table-1.9.6/data.table/tests/knitr.Rout.save |only data.table-1.9.6/data.table/tests/tests.R | 9 data.table-1.9.6/data.table/vignettes/Makefile |only data.table-1.9.6/data.table/vignettes/css |only data.table-1.9.6/data.table/vignettes/datatable-faq.Rnw | 15 data.table-1.9.6/data.table/vignettes/datatable-intro-vignette.Rmd |only data.table-1.9.6/data.table/vignettes/datatable-keys-fast-subset.Rmd |only data.table-1.9.6/data.table/vignettes/datatable-reference-semantics.Rmd |only data.table-1.9.6/data.table/vignettes/datatable-reshape.Rmd |only data.table-1.9.6/data.table/vignettes/flights14.csv |only data.table-1.9.6/data.table/vignettes/melt_default.csv |only data.table-1.9.6/data.table/vignettes/melt_enhanced.csv |only 133 files changed, 6474 insertions(+), 2844 deletions(-)
Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@anu.edu.au>
Diff between climwin versions 0.1.1 dated 2015-07-30 and 0.1.2 dated 2015-09-19
climwin-0.1.1/climwin/DESCRIPTION |only climwin-0.1.1/climwin/MD5 |only climwin-0.1.1/climwin/R |only climwin-0.1.1/climwin/README.md |only climwin-0.1.1/climwin/build |only climwin-0.1.1/climwin/data/Mass.rda |only climwin-0.1.1/climwin/data/MassClimate.rda |only climwin-0.1.1/climwin/data/MassOutput.rda |only climwin-0.1.1/climwin/data/Offspring.rda |only climwin-0.1.1/climwin/man |only climwin-0.1.1/climwin/vignettes |only climwin-0.1.2/climwin/data/MassRand.rda |binary climwin-0.1.2/climwin/inst/doc/climwin.html | 4 ++-- 13 files changed, 2 insertions(+), 2 deletions(-)
Title: Generic Sparse Group Lasso Solver
Description: Fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. Use of multiple processors for cross validation and subsampling is supported through OpenMP. The optimization problem is solved using a coordinate gradient descent algorithm. The algorithm is applicable to a broad class of convex loss functions.Convergence of the algorithm is established (see reference). Development version is on github.
Author: Martin Vincent
Maintainer: Martin Vincent <vincent@math.ku.dk>
Diff between sglOptim versions 1.0.122.1 dated 2014-11-04 and 1.2.0 dated 2015-09-19
sglOptim-1.0.122.1/sglOptim/inst/include/sgl/AlgorithmConfigurationDefault.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/BlockVector.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/DimConfig.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/ObjectiveFunction.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/ObjectiveFunctionExpressionType.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/SglOptimizer.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/SglProblem.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/objective/sgl_algorithm_config.h |only sglOptim-1.0.122.1/sglOptim/inst/include/sgl/objective/sgl_gl_loss.h |only sglOptim-1.0.122.1/sglOptim/tests/A_lambda_sequence_test.R |only sglOptim-1.0.122.1/sglOptim/tests/F_openmp_test.R |only sglOptim-1.2.0/sglOptim/DESCRIPTION | 28 - sglOptim-1.2.0/sglOptim/MD5 | 163 +++++----- sglOptim-1.2.0/sglOptim/NAMESPACE | 29 + sglOptim-1.2.0/sglOptim/R/lambda_sequence.R | 8 sglOptim-1.2.0/sglOptim/R/prepare_args.R | 87 +++-- sglOptim-1.2.0/sglOptim/R/sgl_config.R | 15 sglOptim-1.2.0/sglOptim/R/sgl_cv.R | 1 sglOptim-1.2.0/sglOptim/R/sgl_fit.R | 12 sglOptim-1.2.0/sglOptim/R/sgl_navigate.R | 55 ++- sglOptim-1.2.0/sglOptim/R/sgl_predict.R | 8 sglOptim-1.2.0/sglOptim/R/sgl_subsampling.R | 4 sglOptim-1.2.0/sglOptim/R/startup.R |only sglOptim-1.2.0/sglOptim/inst/NEWS.Rd |only sglOptim-1.2.0/sglOptim/inst/include/rtools/get_value.h | 28 + sglOptim-1.2.0/sglOptim/inst/include/rtools/rList.h | 2 sglOptim-1.2.0/sglOptim/inst/include/rtools/rObject_decl.h | 9 sglOptim-1.2.0/sglOptim/inst/include/rtools/rObject_def.h | 68 ++++ sglOptim-1.2.0/sglOptim/inst/include/sgl.h | 27 - sglOptim-1.2.0/sglOptim/inst/include/sgl/RInterface/sgl_fit.h | 2 sglOptim-1.2.0/sglOptim/inst/include/sgl/RInterface/sgl_lambda_seq.h | 2 sglOptim-1.2.0/sglOptim/inst/include/sgl/RInterface/sgl_predict.h | 1 sglOptim-1.2.0/sglOptim/inst/include/sgl/RInterface/sgl_subsampling.h | 2 sglOptim-1.2.0/sglOptim/inst/include/sgl/algorithm_config.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/block_vector.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/config.h | 6 sglOptim-1.2.0/sglOptim/inst/include/sgl/dim_config.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/interface_basic.h | 59 ++- sglOptim-1.2.0/sglOptim/inst/include/sgl/numeric.h | 53 +++ sglOptim-1.2.0/sglOptim/inst/include/sgl/objective/linear_predictor.h | 5 sglOptim-1.2.0/sglOptim/inst/include/sgl/objective/sgl_gl_loss_base.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/objective/sgl_gl_loss_dense.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/objective/sgl_gl_loss_sparse.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/objective/sgl_matrix_data.h | 22 - sglOptim-1.2.0/sglOptim/inst/include/sgl/objective_function_type.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/sgl_optimizer.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/sgl_problem.h |only sglOptim-1.2.0/sglOptim/inst/include/sgl/simple_timer.h | 6 sglOptim-1.2.0/sglOptim/inst/include/sgl/subsampling.h | 13 sglOptim-1.2.0/sglOptim/man/Err.Rd | 62 +-- sglOptim-1.2.0/sglOptim/man/coef.sgl.Rd | 16 sglOptim-1.2.0/sglOptim/man/compute_error.Rd | 30 - sglOptim-1.2.0/sglOptim/man/create.sgldata.Rd | 49 +-- sglOptim-1.2.0/sglOptim/man/features.Rd | 15 sglOptim-1.2.0/sglOptim/man/features.sgl.Rd | 15 sglOptim-1.2.0/sglOptim/man/models.Rd | 18 - sglOptim-1.2.0/sglOptim/man/models.sgl.Rd | 18 - sglOptim-1.2.0/sglOptim/man/nmod.Rd | 14 sglOptim-1.2.0/sglOptim/man/nmod.sgl.Rd | 14 sglOptim-1.2.0/sglOptim/man/parameters.Rd | 15 sglOptim-1.2.0/sglOptim/man/parameters.sgl.Rd | 15 sglOptim-1.2.0/sglOptim/man/prepare.args.Rd | 55 +-- sglOptim-1.2.0/sglOptim/man/prepare.args.sgldata.Rd | 34 -- sglOptim-1.2.0/sglOptim/man/print_with_metric_prefix.Rd |only sglOptim-1.2.0/sglOptim/man/rearrange.Rd | 19 - sglOptim-1.2.0/sglOptim/man/rearrange.sgldata.Rd | 23 - sglOptim-1.2.0/sglOptim/man/sgl.algorithm.config.Rd | 75 +--- sglOptim-1.2.0/sglOptim/man/sgl.c.config.Rd |only sglOptim-1.2.0/sglOptim/man/sgl.standard.config.Rd | 14 sglOptim-1.2.0/sglOptim/man/sgl_cv.Rd | 86 ++--- sglOptim-1.2.0/sglOptim/man/sgl_fit.Rd | 75 +--- sglOptim-1.2.0/sglOptim/man/sgl_lambda_sequence.Rd | 52 +-- sglOptim-1.2.0/sglOptim/man/sgl_predict.Rd | 25 - sglOptim-1.2.0/sglOptim/man/sgl_print.Rd | 10 sglOptim-1.2.0/sglOptim/man/sgl_subsampling.Rd | 89 ++--- sglOptim-1.2.0/sglOptim/man/test.data.Rd | 5 sglOptim-1.2.0/sglOptim/src/Makevars | 2 sglOptim-1.2.0/sglOptim/src/only_for_testing.cpp | 16 sglOptim-1.2.0/sglOptim/src/pkg_c_config.h |only sglOptim-1.2.0/sglOptim/src/test_objective.h | 1 sglOptim-1.2.0/sglOptim/tests/A_lambda_sequence_test_1.R |only sglOptim-1.2.0/sglOptim/tests/A_lambda_sequence_test_2.R |only sglOptim-1.2.0/sglOptim/tests/B_fit_test_1.R | 7 sglOptim-1.2.0/sglOptim/tests/B_fit_test_2.R | 7 sglOptim-1.2.0/sglOptim/tests/B_fit_test_3.R | 7 sglOptim-1.2.0/sglOptim/tests/B_fit_test_4.R |only sglOptim-1.2.0/sglOptim/tests/C_grouping_test_1.R | 9 sglOptim-1.2.0/sglOptim/tests/C_grouping_test_2.R | 9 sglOptim-1.2.0/sglOptim/tests/C_grouping_test_3.R | 7 sglOptim-1.2.0/sglOptim/tests/C_grouping_test_4.R |only sglOptim-1.2.0/sglOptim/tests/D_cv_test_1.R | 4 sglOptim-1.2.0/sglOptim/tests/D_cv_test_2.R | 2 sglOptim-1.2.0/sglOptim/tests/D_cv_test_3.R | 2 sglOptim-1.2.0/sglOptim/tests/D_cv_test_4.R |only sglOptim-1.2.0/sglOptim/tests/E_subsampling_test_1.R | 2 sglOptim-1.2.0/sglOptim/tests/E_subsampling_test_2.R | 2 sglOptim-1.2.0/sglOptim/tests/E_subsampling_test_3.R | 2 sglOptim-1.2.0/sglOptim/tests/G_openmp_test.R |only 98 files changed, 902 insertions(+), 735 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. In both cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.7.0-1 dated 2015-07-18 and 2.8.0 dated 2015-09-19
rstan-2.7.0-1/rstan/inst/include/rstan/rstan_recorder.hpp |only rstan-2.8.0/rstan/DESCRIPTION | 41 rstan-2.8.0/rstan/MD5 | 94 rstan-2.8.0/rstan/NAMESPACE | 29 rstan-2.8.0/rstan/R/expose_stan_functions.R | 20 rstan-2.8.0/rstan/R/extract_sparse_parts.R |only rstan-2.8.0/rstan/R/lookup.R | 13 rstan-2.8.0/rstan/R/misc.R | 70 rstan-2.8.0/rstan/R/pairs.R | 44 rstan-2.8.0/rstan/R/plugin.R | 2 rstan-2.8.0/rstan/R/rstan.R | 47 rstan-2.8.0/rstan/R/rtools.R |only rstan-2.8.0/rstan/R/stan_csv.R | 52 rstan-2.8.0/rstan/R/stan_demo.R | 3 rstan-2.8.0/rstan/R/stan_plot.R |only rstan-2.8.0/rstan/R/stan_plot_helpers.R |only rstan-2.8.0/rstan/R/stan_plot_options.R |only rstan-2.8.0/rstan/R/stanc.R | 2 rstan-2.8.0/rstan/R/stanfit-class.R | 154 - rstan-2.8.0/rstan/R/stanmodel-class.R | 284 +- rstan-2.8.0/rstan/R/sysdata.rda |binary rstan-2.8.0/rstan/R/zzz.R | 7 rstan-2.8.0/rstan/build/vignette.rds |binary rstan-2.8.0/rstan/inst/CITATION | 6 rstan-2.8.0/rstan/inst/NEWS | 11 rstan-2.8.0/rstan/inst/doc/rstan_vignette.R | 10 rstan-2.8.0/rstan/inst/doc/rstan_vignette.Rnw | 14 rstan-2.8.0/rstan/inst/doc/rstan_vignette.pdf |binary rstan-2.8.0/rstan/inst/include/boost_not_in_BH/boost/fusion |only rstan-2.8.0/rstan/inst/include/rstan/io/rlist_ref_var_context_factory.hpp | 6 rstan-2.8.0/rstan/inst/include/rstan/rstan_writer.hpp |only rstan-2.8.0/rstan/inst/include/rstan/stan_args.hpp | 121 rstan-2.8.0/rstan/inst/include/rstan/stan_fit.hpp | 198 + rstan-2.8.0/rstan/inst/misc/stan_progress.html |only rstan-2.8.0/rstan/inst/unitTests/runit.test.extract_sparse_parts.R |only rstan-2.8.0/rstan/man/extract_sparse_parts.Rd |only rstan-2.8.0/rstan/man/lookup.Rd | 3 rstan-2.8.0/rstan/man/plotting-functions.Rd |only rstan-2.8.0/rstan/man/rstan-internal.Rd | 1 rstan-2.8.0/rstan/man/rstan.Rd | 6 rstan-2.8.0/rstan/man/stan_plot.Rd |only rstan-2.8.0/rstan/man/stan_plot_diagnostics.Rd |only rstan-2.8.0/rstan/man/stan_plot_options.Rd |only rstan-2.8.0/rstan/man/stanfit-class.Rd | 6 rstan-2.8.0/rstan/man/stanfit-method-pairs.Rd | 28 rstan-2.8.0/rstan/man/stanfit-method-plot.Rd | 103 rstan-2.8.0/rstan/man/stanfit-method-traceplot.Rd | 59 rstan-2.8.0/rstan/man/stanmodel-method-sampling.Rd | 10 rstan-2.8.0/rstan/src/Makevars | 4 rstan-2.8.0/rstan/src/Makevars.win | 2 rstan-2.8.0/rstan/src/init.cpp | 7 rstan-2.8.0/rstan/src/sparse_extractors.cpp |only rstan-2.8.0/rstan/src/stanc.cpp | 4 rstan-2.8.0/rstan/tools/stan-functions.R | 15 rstan-2.8.0/rstan/tools/stan-functions.txt | 1228 +++++----- rstan-2.8.0/rstan/vignettes/rstan_vignette.Rnw | 14 56 files changed, 1646 insertions(+), 1072 deletions(-)
Title: High Dimensional Multiclass Classification Using Sparse Group
Lasso
Description: Multinomial logistic regression with sparse group lasso penalty. Suitable for high dimensional multiclass classification with many classes. The algorithm finds the sparse group lasso penalized maximum likelihood estimator. This result in feature and parameter selection, and parameter estimation. Use of multiple processors for cross validation and subsampling is supported through OpenMP. Development version is on github.
Author: Martin Vincent
Maintainer: Martin Vincent <vincent@math.ku.dk>
Diff between msgl versions 2.0.125.1 dated 2014-11-05 and 2.2.0 dated 2015-09-19
DESCRIPTION | 24 ++----- MD5 | 85 +++++++++++++------------- NAMESPACE | 26 +++++--- R/msgl_config.R | 14 ++++ R/msgl_cv.R | 61 ++++++++++++------- R/msgl_fit.R | 109 +++++++++++++++++++++++----------- R/msgl_navigate.R | 16 +---- R/msgl_predict.R | 100 ++++++++++++++++--------------- R/msgl_subsampling.R | 63 +++++++++++++------ R/startup.R |only inst/NEWS.Rd | 21 ++++++ man/Err.msgl.Rd | 35 +++++----- man/coef.msgl.Rd | 17 ++--- man/features.msgl.Rd | 15 ++-- man/models.msgl.Rd | 18 ++--- man/msgl.Rd | 109 ++++++++++++---------------------- man/msgl.algorithm.config.Rd | 75 ++++++++++------------- man/msgl.c.config.Rd |only man/msgl.cv.Rd | 131 ++++++++++++++++------------------------- man/msgl.lambda.seq.Rd | 76 +++++++++-------------- man/msgl.standard.config.Rd | 14 ++-- man/msgl.subsampling.Rd | 137 ++++++++++++++++--------------------------- man/nmod.msgl.Rd | 14 ++-- man/parameters.msgl.Rd | 15 ++-- man/predict.msgl.Rd | 36 +++-------- man/print.msgl.Rd | 15 ++-- man/sim.data.Rd | 10 +-- src/multinomial_loss.h | 2 src/pkg_c_config.h |only src/rmsgl.cpp | 12 --- tests/msgl_cv_test_1.R | 3 tests/msgl_cv_test_2.R | 3 tests/msgl_cv_test_3.R | 1 tests/msgl_cv_test_4.R | 3 tests/msgl_grouping_test_1.R | 15 ++-- tests/msgl_grouping_test_2.R | 3 tests/msgl_grouping_test_3.R | 3 tests/msgl_grouping_test_4.R | 3 tests/msgl_predict_test_1.R | 3 tests/msgl_predict_test_2.R | 3 tests/msgl_sub_test_1.R | 3 tests/msgl_test_1.R | 3 tests/msgl_test_2.R | 3 tests/msgl_test_3.R | 3 tests/msgl_test_4.R | 3 45 files changed, 669 insertions(+), 636 deletions(-)
Title: Linear Sparse Group Lasso
Description: Linear multiple output using sparse group lasso. The algorithm finds the sparse group lasso penalized maximum likelihood estimator. This result in feature and parameter selection, and parameter estimation. Use of multiple processors for cross validation and subsampling is supported through OpenMP. Development version is on github.
Author: Martin Vincent
Maintainer: Martin Vincent <vincent@math.ku.dk>
Diff between lsgl versions 1.0.123.1 dated 2014-11-05 and 1.2.0 dated 2015-09-19
lsgl-1.0.123.1/lsgl/src/frobenius_norm_objective.h |only lsgl-1.2.0/lsgl/DESCRIPTION | 15 +- lsgl-1.2.0/lsgl/MD5 | 59 +++++----- lsgl-1.2.0/lsgl/NAMESPACE | 26 +++- lsgl-1.2.0/lsgl/R/lsgl_config.R | 14 ++ lsgl-1.2.0/lsgl/R/lsgl_cv.R | 72 ++++++++++-- lsgl-1.2.0/lsgl/R/lsgl_fit.R | 108 ++++++++++++++++--- lsgl-1.2.0/lsgl/R/lsgl_navigate.R | 101 +++++++++++------ lsgl-1.2.0/lsgl/R/lsgl_predict.R | 34 ++++-- lsgl-1.2.0/lsgl/R/startup.R |only lsgl-1.2.0/lsgl/inst |only lsgl-1.2.0/lsgl/man/Err.lsgl.Rd | 47 +++++--- lsgl-1.2.0/lsgl/man/coef.lsgl.Rd | 17 +-- lsgl-1.2.0/lsgl/man/features.lsgl.Rd | 15 +- lsgl-1.2.0/lsgl/man/lsgl.Rd | 77 +++++-------- lsgl-1.2.0/lsgl/man/lsgl.algorithm.config.Rd | 75 +++++-------- lsgl-1.2.0/lsgl/man/lsgl.c.config.Rd |only lsgl-1.2.0/lsgl/man/lsgl.cv.Rd | 77 +++++-------- lsgl-1.2.0/lsgl/man/lsgl.lambda.Rd | 56 ++++----- lsgl-1.2.0/lsgl/man/lsgl.standard.config.Rd | 14 +- lsgl-1.2.0/lsgl/man/models.lsgl.Rd | 18 +-- lsgl-1.2.0/lsgl/man/nmod.lsgl.Rd | 14 +- lsgl-1.2.0/lsgl/man/parameters.lsgl.Rd | 15 +- lsgl-1.2.0/lsgl/man/predict.lsgl.Rd | 24 +--- lsgl-1.2.0/lsgl/man/print.lsgl.Rd | 21 +-- lsgl-1.2.0/lsgl/src/Makevars | 2 lsgl-1.2.0/lsgl/src/frobenius_norm.h |only lsgl-1.2.0/lsgl/src/frobenius_norm_weighted.h |only lsgl-1.2.0/lsgl/src/lsgl.cpp | 118 ++++++++++++++++----- lsgl-1.2.0/lsgl/src/pkg_c_config.h |only lsgl-1.2.0/lsgl/tests/A_lsgl_fit_test.R | 13 ++ lsgl-1.2.0/lsgl/tests/B_lsgl_cv_test.R | 13 ++ lsgl-1.2.0/lsgl/tests/C_lsgl_omp_test.R | 5 lsgl-1.2.0/lsgl/tests/D_lsgl_grouping_test.R |only lsgl-1.2.0/lsgl/tests/E_lsgl_navigate_test.R |only 35 files changed, 666 insertions(+), 384 deletions(-)
Title: Import and Export Data
Description: Import and export data from the most common statistical formats by using
R functions that guarantee the least loss of the data information, giving special
attention to the date variables and the labelled ones.
Author: Roger Pros, Isaac Subirana, Joan Vila.
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between ImportExport versions 1.0 dated 2015-08-10 and 1.1 dated 2015-09-19
ImportExport-1.0/ImportExport/inst/Import_ExportApp/ui.r |only ImportExport-1.0/ImportExport/inst/Import_ExportApp/www/App-guide.htm |only ImportExport-1.0/ImportExport/inst/doc/shinyApp-guide.pdf |only ImportExport-1.1/ImportExport/DESCRIPTION | 8 +- ImportExport-1.1/ImportExport/MD5 | 28 ++++++---- ImportExport-1.1/ImportExport/R/ImportExportApp.R | 2 ImportExport-1.1/ImportExport/R/import_exportApp.R | 2 ImportExport-1.1/ImportExport/build/partial.rdb |binary ImportExport-1.1/ImportExport/inst/Import_ExportApp/data/date_to_char.r | 2 ImportExport-1.1/ImportExport/inst/Import_ExportApp/data/format_detector.r | 2 ImportExport-1.1/ImportExport/inst/Import_ExportApp/global.R | 2 ImportExport-1.1/ImportExport/inst/Import_ExportApp/ui.R |only ImportExport-1.1/ImportExport/inst/Import_ExportApp/www/App-guide.html |only ImportExport-1.1/ImportExport/inst/doc/links |only ImportExport-1.1/ImportExport/inst/doc/shinyApp-guide.html |only 15 files changed, 26 insertions(+), 20 deletions(-)
Title: Statistical Methods for Crime Series Linkage
Description: Statistical Methods for Crime Series Linkage. This package provides
code for criminal case linkage, crime series identification, crime series
clustering, and suspect identification.
Author: Michael Porter [aut, cre],
Brian Reich [aut]
Maintainer: Michael Porter <mporter@cba.ua.edu>
Diff between crimelinkage versions 0.0.3 dated 2015-04-18 and 0.0.4 dated 2015-09-19
crimelinkage-0.0.3/crimelinkage/man/fixDateTime.Rd |only crimelinkage-0.0.3/crimelinkage/man/getDateTime.Rd |only crimelinkage-0.0.3/crimelinkage/man/predictNB.Rd |only crimelinkage-0.0.4/crimelinkage/DESCRIPTION | 12 crimelinkage-0.0.4/crimelinkage/MD5 | 117 +-- crimelinkage-0.0.4/crimelinkage/NAMESPACE | 12 crimelinkage-0.0.4/crimelinkage/NEWS |only crimelinkage-0.0.4/crimelinkage/R/bayes_clustering.R | 154 ++-- crimelinkage-0.0.4/crimelinkage/R/caseUtils.R | 203 +---- crimelinkage-0.0.4/crimelinkage/R/compareCrimes.R | 376 +++++++--- crimelinkage-0.0.4/crimelinkage/R/crimelinkage.R | 1 crimelinkage-0.0.4/crimelinkage/R/hierclustering.R | 33 crimelinkage-0.0.4/crimelinkage/R/naivebayes.R | 211 ++++- crimelinkage-0.0.4/crimelinkage/R/seriesIDFunctions.R | 29 crimelinkage-0.0.4/crimelinkage/build/vignette.rds |binary crimelinkage-0.0.4/crimelinkage/data/crimes.rda |binary crimelinkage-0.0.4/crimelinkage/data/offenders.rda |binary crimelinkage-0.0.4/crimelinkage/inst/CITATION | 6 crimelinkage-0.0.4/crimelinkage/inst/doc/crimeclustering.R | 65 + crimelinkage-0.0.4/crimelinkage/inst/doc/crimeclustering.Rmd | 77 +- crimelinkage-0.0.4/crimelinkage/inst/doc/crimeclustering.html | 193 ++--- crimelinkage-0.0.4/crimelinkage/inst/doc/crimelinkage.R | 43 - crimelinkage-0.0.4/crimelinkage/inst/doc/crimelinkage.Rmd | 56 - crimelinkage-0.0.4/crimelinkage/inst/doc/crimelinkage.html | 109 +- crimelinkage-0.0.4/crimelinkage/man/bayesPairs.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/catLevels.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/clusterPath.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/color.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/compareCategorical.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/compareCrimes.Rd | 65 + crimelinkage-0.0.4/crimelinkage/man/compareNumeric.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/compareSpatial.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/compareTemporal.Rd | 11 crimelinkage-0.0.4/crimelinkage/man/crimeClust_bayes.Rd | 30 crimelinkage-0.0.4/crimelinkage/man/crimeClust_hier.Rd | 31 crimelinkage-0.0.4/crimelinkage/man/crimelinkage-package.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/crimes.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/dtdiff.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/expAbsDiff.Rd |only crimelinkage-0.0.4/crimelinkage/man/expAbsDiff.circ.Rd |only crimelinkage-0.0.4/crimelinkage/man/getBF.Rd | 15 crimelinkage-0.0.4/crimelinkage/man/getCrimeSeries.Rd | 4 crimelinkage-0.0.4/crimelinkage/man/getCrimes.Rd | 4 crimelinkage-0.0.4/crimelinkage/man/getCriminals.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/getD.Rd |only crimelinkage-0.0.4/crimelinkage/man/getROC.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/linkage.Rd | 4 crimelinkage-0.0.4/crimelinkage/man/make.breaks.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/makeGroups.Rd | 21 crimelinkage-0.0.4/crimelinkage/man/makePairs.Rd | 25 crimelinkage-0.0.4/crimelinkage/man/makeSeriesData.Rd | 20 crimelinkage-0.0.4/crimelinkage/man/naiveBayes.Rd | 32 crimelinkage-0.0.4/crimelinkage/man/offenders.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/plot.naiveBayes.Rd |only crimelinkage-0.0.4/crimelinkage/man/plotBF.Rd | 9 crimelinkage-0.0.4/crimelinkage/man/plotBKG.Rd | 7 crimelinkage-0.0.4/crimelinkage/man/plot_hcc.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/predict.naiveBayes.Rd |only crimelinkage-0.0.4/crimelinkage/man/predictBF.Rd | 2 crimelinkage-0.0.4/crimelinkage/man/seriesID.Rd | 17 crimelinkage-0.0.4/crimelinkage/vignettes/MCMC-results.RData |binary crimelinkage-0.0.4/crimelinkage/vignettes/crimeclustering.Rmd | 77 +- crimelinkage-0.0.4/crimelinkage/vignettes/crimelinkage.Rmd | 56 - crimelinkage-0.0.4/crimelinkage/vignettes/refs.bib | 2 64 files changed, 1229 insertions(+), 930 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey <richarddmorey@gmail.com>
Diff between BayesFactor versions 0.9.11-1 dated 2015-03-21 and 0.9.12-2 dated 2015-09-19
DESCRIPTION | 16 +-- MD5 | 155 ++++++++++++++++++------------------ NAMESPACE | 14 ++- NEWS | 13 +++ R/BayesFactorPCL-package.R | 2 R/RcppExports.R | 4 R/aaGenerics.R | 9 ++ R/anovaBF.R | 14 ++- R/common.R | 44 +++++++++- R/contingency-utility.R | 26 ++++++ R/generalTest-utility.R | 5 - R/generalTestBF.R | 12 +- R/linearReg_R2stat.R | 11 +- R/lmBF.R | 7 + R/meta-ttest-utility.R | 14 ++- R/methods-BFlinearModel-compare.R | 21 +++- R/methods-BFmodel.R | 51 +++++++---- R/methods-BFmodelSample.R | 3 R/methods-BFprobability.R | 85 ++++++++++++++----- R/nWayAOV-utility.R | 44 +++++++--- R/nWayAOV.R | 4 R/onAttach.R | 2 R/oneWayAOV_Fstat.R | 12 +- R/proportion-utility.R | 9 +- R/regressionBF-utility.R | 15 +++ R/ttestBF.R | 2 R/ttest_tstat.R | 10 +- build/vignette.rds |binary inst/doc/compare_lme4.html | 30 +++--- inst/doc/manual.R | 6 + inst/doc/manual.Rmd | 25 +++++ inst/doc/manual.html | 111 ++++++++++++++++--------- inst/doc/odds_probs.html | 2 inst/doc/priors.html | 10 +- man/BFBayesFactor-class.Rd | 2 man/BFBayesFactorList-class.Rd | 2 man/BFInfo.Rd | 2 man/BFManual.Rd | 2 man/BFodds-class.Rd | 2 man/BFprobability-class.Rd | 12 ++ man/BayesFactor-package.Rd | 4 man/anovaBF.Rd | 11 +- man/as.BFBayesFactor.Rd | 2 man/as.BFprobability.Rd | 2 man/compare-methods.Rd | 2 man/contingencyTableBF.Rd | 2 man/enumerateGeneralModels.Rd | 6 - man/extractBF-methods.Rd | 2 man/extractOdds-methods.Rd | 2 man/extractProbabilities-methods.Rd | 2 man/filterBF.Rd |only man/generalTestBF.Rd | 11 +- man/grapes-same-grapes.Rd | 2 man/grapes-termin-grapes.Rd | 2 man/linearReg.R2stat.Rd | 6 - man/lmBF.Rd | 9 +- man/logMeanExpLogs.Rd | 2 man/meta.ttestBF.Rd | 2 man/model-classes.Rd | 2 man/model.matrix-methods.Rd | 2 man/nWayAOV.Rd | 2 man/newPriorOdds.Rd | 2 man/oneWayAOV.Fstat.Rd | 6 - man/options-BayesFactor.Rd | 3 man/plot.BFBayesFactor.Rd | 2 man/plot.BFBayesFactorTop.Rd | 2 man/posterior-methods.Rd | 2 man/priorLogodds-method.Rd | 2 man/priorOdds-method.Rd | 2 man/proportionBF.Rd | 2 man/puzzles.Rd | 2 man/raceDolls.Rd | 2 man/recompute-methods.Rd | 2 man/regressionBF.Rd | 2 man/ttest.tstat.Rd | 6 - man/ttestBF.Rd | 4 src/RcppExports.cpp | 13 +++ src/dinvgamma.cpp | 6 + vignettes/manual.Rmd | 25 +++++ 79 files changed, 654 insertions(+), 316 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1247 dated 2015-05-01 and 0.95.1337 dated 2015-09-19
DESCRIPTION | 9 MD5 | 102 NAMESPACE | 16 R/Sweave_knitr.R | 54 R/animate.R | 12 R/cylinder3d.R | 3 R/device.R | 14 R/enum.R | 7 R/fonts.R | 8 R/getscene.R | 20 R/identify3d.R | 15 R/internal.R | 20 R/material.R | 6 R/matrices.R | 6 R/mesh3d.R | 9 R/obj.R | 14 R/persp3d.R | 6 R/ply.R | 13 R/r3d.rgl.R | 8 R/rgl.bringtotop.R | 4 R/scene.R | 129 R/stl.R | 9 R/subscenes.R | 21 R/triangulate.R | 2 R/webGL.R | 1097 ++-- R/webGLcontrols.R | 319 + R/zzz.R | 4 build/vignette.rds |binary inst/NEWS | 41 inst/doc/WebGL.R | 23 inst/doc/WebGL.Rmd | 44 inst/doc/WebGL.html | 6656 ++++++++++++------------- inst/doc/rgl.R | 9 inst/doc/rgl.Rmd | 12 inst/doc/rgl.html | 8741 +++++++++++++--------------------- man/ageSetter.Rd | 5 man/attributes.Rd | 12 man/bbox.Rd | 12 man/hook_rgl.Rd | 27 man/propertySetter.Rd | 91 man/webGLcontrols.Rd | 7 po |only src/BBoxDeco.cpp | 2 src/SceneNode.h | 2 src/TextSet.cpp | 22 src/api.cpp | 6 src/init.cpp | 14 vignettes/WebGL.Rmd | 44 vignettes/plotsnapshot.png |only vignettes/rgl.Rmd | 12 vignettes/rgl.md |only vignettes/setup.R | 2 vignettes/test.Rmd |only vignettes/unnamed_chunk_1snapshot.png |only vignettes/unnamed_chunk_2snapshot.png |only 55 files changed, 8234 insertions(+), 9477 deletions(-)
Title: Use Python from Within R
Description: Interact with Python from within R.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-0 dated 2015-07-09 and 0.1-1 dated 2015-09-19
DESCRIPTION | 6 +- MD5 | 24 +++++----- R/PyGet.R | 2 R/PySet.R | 111 ++++++++++++++++++++++++++++++++++++++------------ R/PySource.R | 32 ++++++-------- README.md | 5 +- src/CToR.c | 2 src/CastPyObjects.c | 58 +------------------------- src/CastPyObjects.h | 4 - src/CastRObjects.c | 2 src/PythonFunctions.c | 3 - src/PythonInR.c | 9 ---- src/PythonInR.h | 4 - 13 files changed, 131 insertions(+), 131 deletions(-)
Title: Multidimensional Iterative Proportional Fitting and Alternative
Models
Description: An implementation of the iterative proportional fitting (IPFP),
maximum likelihood, minimum chi-square and weighted least squares procedures
for updating a N-dimensional array with respect to given target marginal
distributions (which, in turn can be multi-dimensional). The package also
provides an application of the IPFP to simulate multivariate Bernoulli
distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>
Diff between mipfp versions 2.2 dated 2015-07-31 and 2.2.1 dated 2015-09-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/models.R | 43 ++++++++++++++++++++----------------------- data/Qaqish.RData |binary man/mipfp-package.Rd | 4 ++-- 5 files changed, 30 insertions(+), 33 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey <buttrey@nps.edu>
Diff between lpSolve versions 5.6.12 dated 2015-09-01 and 5.6.13 dated 2015-09-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/lusol1.h | 10 +++++----- src/myblas.c | 10 +++++----- src/myblas.h | 10 +++++----- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Calculate Solutions to the Kelvin Differential Equation using
Bessel Functions
Description: Uses Bessel functions to calculate the
fundamental and complementary analytic solutions to the
Kelvin differential equation.
Author: Andrew J Barbour
Maintainer: Andrew J Barbour <andy.barbour@gmail.com>
Diff between kelvin versions 1.2-2 dated 2013-09-04 and 2.0-0 dated 2015-09-19
kelvin-1.2-2/kelvin/demo |only kelvin-2.0-0/kelvin/DESCRIPTION | 27 ++++--- kelvin-2.0-0/kelvin/MD5 | 31 +++++--- kelvin-2.0-0/kelvin/NAMESPACE | 4 + kelvin-2.0-0/kelvin/R/Beir.R | 47 ++++++------- kelvin-2.0-0/kelvin/R/Keir.R | 74 ++++++++------------ kelvin-2.0-0/kelvin/R/kelvin-package.R | 2 kelvin-2.0-0/kelvin/R/zzz.R | 27 +------ kelvin-2.0-0/kelvin/build |only kelvin-2.0-0/kelvin/inst/InstallationNotes |only kelvin-2.0-0/kelvin/inst/NEWS.Rd | 20 +++-- kelvin-2.0-0/kelvin/inst/doc |only kelvin-2.0-0/kelvin/man/Beir.Rd | 64 ++++++++--------- kelvin-2.0-0/kelvin/man/Keir.Rd | 88 ++++++++++-------------- kelvin-2.0-0/kelvin/man/kelvin-package.Rd | 104 +++++++++++++---------------- kelvin-2.0-0/kelvin/tests |only kelvin-2.0-0/kelvin/vignettes |only 17 files changed, 224 insertions(+), 264 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.0 dated 2015-07-17 and 0.1.1 dated 2015-09-18
DESCRIPTION | 12 MD5 | 144 ++- NAMESPACE | 5 NEWS | 7 R/dependencies.R |only R/visClustering.R | 67 - R/visEdges.R | 4 R/visLayout.R | 12 R/visNetwork.R | 18 R/visNodes.R | 13 R/visOptions.R | 4 R/visPhysics.R | 6 README.md | 21 build/vignette.rds |binary inst/doc/Introduction-to-visNetwork.R | 40 inst/doc/Introduction-to-visNetwork.Rmd | 69 + inst/doc/Introduction-to-visNetwork.html | 137 ++- inst/doc/css/style.css | 444 +++++----- inst/doc/css/tipuesearch.css |only inst/doc/js/jquery.highlight.js |only inst/doc/js/jquery.url.min.js |only inst/doc/js/main.js | 188 +++- inst/doc/js/tipuesearch.config.js |only inst/doc/js/tipuesearch.js |only inst/doc/js/tipuesearch.min.js |only inst/doc/network/configure.html | 366 ++++---- inst/doc/network/edges.html | 1354 +++++++++++++++---------------- inst/doc/network/groups.html | 332 ++++--- inst/doc/network/index.html | 372 ++++---- inst/doc/network/interaction.html | 321 +++---- inst/doc/network/layout.html | 32 inst/doc/network/manipulation.html | 29 inst/doc/network/nodes.html | 68 + inst/doc/network/physics.html | 29 inst/htmlwidgets/lib/font-awesome |only inst/htmlwidgets/lib/vis/vis.map |only inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 43 inst/htmlwidgets/visNetwork.js | 43 inst/htmlwidgets/visNetwork.yaml | 2 inst/shiny/server.R | 40 man/addFontAwesome.Rd |only man/visClusteringByColor.Rd | 4 man/visClusteringByConnection.Rd | 9 man/visClusteringByGroup.Rd | 2 man/visClusteringByHubsize.Rd | 4 man/visClusteringOutliers.Rd |only man/visConfigure.Rd | 2 man/visDocumentation.Rd | 2 man/visEdges.Rd | 6 man/visEvents.Rd | 2 man/visGroups.Rd | 2 man/visHierarchicalLayout.Rd | 2 man/visInteraction.Rd | 2 man/visLayout.Rd | 12 man/visNetwork-exports.Rd | 2 man/visNetwork-shiny.Rd | 2 man/visNetwork.Rd | 20 man/visNodes.Rd | 11 man/visOptions.Rd | 6 man/visPhysics.Rd | 7 vignettes/Introduction-to-visNetwork.Rmd | 69 + 62 files changed, 2511 insertions(+), 1879 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.5 dated 2015-08-15 and 1.4.6 dated 2015-09-18
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ NEWS | 13 ++++++++++++- R/QueueFallout.R | 5 +++-- R/QueueOvertime.R | 5 +++-- R/QueuePathing.R | 5 +++-- R/QueueRanked.R | 19 ++++++++++++++----- R/QueueSummary.R | 5 +++-- R/QueueTrended.R | 17 ++++++++++++----- R/RSiteCatalyst.R | 4 ++-- R/SubmitJsonQueueReport.R | 19 +++++++++++-------- man/QueueFallout.Rd | 4 +++- man/QueueOvertime.Rd | 4 +++- man/QueuePathing.Rd | 4 +++- man/QueueRanked.Rd | 6 ++++-- man/QueueSummary.Rd | 4 +++- man/QueueTrended.Rd | 6 ++++-- man/RSiteCatalyst.Rd | 4 ++-- man/SubmitJsonQueueReport.Rd | 4 +++- 19 files changed, 110 insertions(+), 62 deletions(-)
Title: Analyzing Pointer Years and Components of Resilience
Description: Functions to calculate and plot event and pointer years as well as components of resilience. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.
Author: Marieke van der Maaten-Theunissen and Ernst van der Maaten
Maintainer: Marieke van der Maaten-Theunissen <marieketheunissen@gmail.com>
Diff between pointRes versions 1.0.2 dated 2015-03-14 and 1.1.0 dated 2015-09-18
DESCRIPTION | 10 +++++----- MD5 | 45 ++++++++++++++++++++++++--------------------- NAMESPACE | 5 ++++- R/event.plot.R | 9 +++++---- R/lowpass13.R |only R/norm.plot.R | 8 ++++---- R/pointer.norm.R | 22 +++++++++++++--------- R/pointer.plot.R | 8 +++++--- R/pointer.rgc.R | 45 ++++++++++++++++++++++++++------------------- R/res.comp.R | 4 +++- R/res.plot.R | 16 +++++++++------- R/rgc.plot.R | 10 +++++----- R/s033.R | 2 +- inst/CITATION |only inst/Changelog | 9 ++++++++- man/event.plot.Rd | 4 ++-- man/lowpass13.Rd |only man/norm.plot.Rd | 4 ++-- man/pointer.norm.Rd | 22 +++++++++++++--------- man/pointer.plot.Rd | 5 +++-- man/pointer.rgc.Rd | 10 +++++----- man/res.comp.Rd | 2 +- man/res.plot.Rd | 2 +- man/rgc.plot.Rd | 4 ++-- man/s033.Rd | 4 ++-- 25 files changed, 143 insertions(+), 107 deletions(-)
Title: A Wrapper for the Pinnacle Sports API
Description: An R interface to the Pinnaclesports.com API.
Author: Marco Blume, Nicholas Jhirad, Amine Gassem
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between pinnacle.API versions 1.81 dated 2015-09-06 and 1.89 dated 2015-09-18
pinnacle.API-1.81/pinnacle.API/man/combineFactors.Rd |only pinnacle.API-1.81/pinnacle.API/man/fixPeriods.Rd |only pinnacle.API-1.89/pinnacle.API/DESCRIPTION | 8 - pinnacle.API-1.89/pinnacle.API/MD5 | 42 +++++---- pinnacle.API-1.89/pinnacle.API/NAMESPACE | 5 - pinnacle.API-1.89/pinnacle.API/NEWS | 67 +++++++++++++++ pinnacle.API-1.89/pinnacle.API/R/Authorization.R | 4 pinnacle.API-1.89/pinnacle.API/R/GetBets.R | 8 - pinnacle.API-1.89/pinnacle.API/R/GetCurrencies.R | 2 pinnacle.API-1.89/pinnacle.API/R/GetFixtures.R | 4 pinnacle.API-1.89/pinnacle.API/R/GetInrunning.R |only pinnacle.API-1.89/pinnacle.API/R/GetLeagues.R | 4 pinnacle.API-1.89/pinnacle.API/R/GetLeaguesByID.R | 35 ++++---- pinnacle.API-1.89/pinnacle.API/R/GetOdds.R | 8 - pinnacle.API-1.89/pinnacle.API/R/PlaceParlayBet.R |only pinnacle.API-1.89/pinnacle.API/R/showOddsDF.R | 83 +++++++++++-------- pinnacle.API-1.89/pinnacle.API/R/showOddsFunctions.R | 55 +++++------- pinnacle.API-1.89/pinnacle.API/README.md | 78 ++++++++++++++++- pinnacle.API-1.89/pinnacle.API/man/GetBetsList.Rd | 9 +- pinnacle.API-1.89/pinnacle.API/man/GetInrunning.Rd |only pinnacle.API-1.89/pinnacle.API/man/GetLeaguesByID.Rd | 4 pinnacle.API-1.89/pinnacle.API/man/GetOdds.Rd | 4 pinnacle.API-1.89/pinnacle.API/man/JSONtoDF.Rd |only pinnacle.API-1.89/pinnacle.API/man/PlaceParlayBet.Rd |only pinnacle.API-1.89/pinnacle.API/man/cbindNames.Rd |only pinnacle.API-1.89/pinnacle.API/man/showOddsDF.Rd | 8 + 26 files changed, 291 insertions(+), 137 deletions(-)
Title: Access Data from the Massachusetts Bay Transit Authority (MBTA)
Web API
Description: Access to the MBTA API for R. Creates an easy-to-use bundle of
functions to work with all the built-in calls to the MBTA API. Allows users
to download realtime tracking data in dataframe format that is manipulable
in standard R analytics functions.
Author: Justin de Benedictis-Kessner [aut, cre]
Maintainer: Justin de Benedictis-Kessner <justindbk@gmail.com>
Diff between MBTAr versions 1.0.0 dated 2015-07-28 and 1.0.1 dated 2015-09-18
DESCRIPTION | 8 ++-- MD5 | 4 +- man/Troutes.Rd | 104 ++++++++++++++++++++++++++++----------------------------- 3 files changed, 58 insertions(+), 58 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Diff between laGP versions 1.2 dated 2015-09-17 and 1.2-1 dated 2015-09-18
ChangeLog | 8 +++++++- DESCRIPTION | 7 +++---- MD5 | 8 ++++---- man/optim.auglag.Rd | 8 ++++---- src/gp_sep.c | 10 +++++----- 5 files changed, 23 insertions(+), 18 deletions(-)
Title: Interpolation and Extrapolation for Species Diversity
Description: Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation of species diversity (Hill numbers) for individual-based (abundance) data or sampling-unit-based (incidence) data.
Author: T. C. Hsieh, K. H. Ma and Anne Chao
Maintainer: T. C. Hsieh <euler96@gmail.com>
Diff between iNEXT versions 2.0.3 dated 2015-06-30 and 2.0.5 dated 2015-09-18
DESCRIPTION | 18 -- MD5 | 32 ++--- NAMESPACE | 16 +- R/EstIndex.R | 83 +++++++------ R/JADE.R | 120 +++++++++---------- R/iNEXT.r | 321 ++++++++++++++++++++++++++++++--------------------- R/invChat.R |only inst/CITATION | 64 +++++----- man/ChaoEntropy.Rd | 27 ++-- man/ChaoSpecies.Rd | 21 +-- man/DataInfo.Rd | 15 +- man/EstSimpson.Rd | 24 ++- man/ant.Rd | 48 +++---- man/estimateD.Rd |only man/ggiNEXT.Rd | 55 +++++--- man/iNEXT-package.Rd | 29 ++-- man/iNEXT.Rd | 37 +++-- man/spider.Rd | 44 +++--- 18 files changed, 522 insertions(+), 432 deletions(-)
Title: Tools for the Analysis of Gutenberg-Richter Distributions of
Earthquake Magnitudes
Description: Offers functions for the comparison of Gutenberg-Richter
b-values. Several functions in GRTo are helpful for the assessment of the
quality of seismicity catalogs.
Author: Daniel Amorese, Paul A. Rydelek and Jean-Robert Grasso
Maintainer: Daniel C. Amorese <amorese@ipgp.fr>
Diff between GRTo versions 1.2 dated 2014-05-19 and 1.3 dated 2015-09-18
DESCRIPTION | 18 ++++++++--------- MD5 | 16 +++++++-------- NAMESPACE | 5 +++- R/BBootComp.R | 55 +++++++++++++++++++++++++++++++++++----------------- R/bvmed.R | 34 ++++++++++++++++++++++---------- R/fmddisc.R | 2 - man/BBootComp.Rd | 3 +- man/GRTo-package.Rd | 6 ++--- man/bvmed.Rd | 8 ++++--- 9 files changed, 94 insertions(+), 53 deletions(-)
Title: Gaussian Approximation of Bayesian Binary Regression Models
Description: The main functions compute the expectation propagation approximation of a Bayesian probit/logit models with Gaussian prior. More information can be found in Chopin and Ridgway (2015). More models and priors should follow.
Author: James Ridgway
Maintainer: James Ridgway <james.ridgway@ensae.fr>
Diff between EPGLM versions 1.0 dated 2015-07-31 and 1.1 dated 2015-09-18
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ man/EPGLM-package.Rd | 4 ++-- man/EPlogit.Rd | 26 ++++++++++++++------------ man/EPprobit.Rd | 17 ++++++++++------- src/function.cpp | 1 + src/header.h | 1 + 7 files changed, 37 insertions(+), 30 deletions(-)
Title: Acoustic Template Detection in R
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner <sdh11@cornell.edu> and Jon Katz <jonkatz4@gmail.com>, with code for the Fourier transform from the seewave package (by Jerome Sueur, Thierry Aubin, and Caroline Simonis), and code for the readMP3 function from the tuneR package (by Uwe Ligges). Therese Donovan provided creative direction and database design support.
Maintainer: Sasha D. Hafner <sdh11@cornell.edu>
Diff between monitoR versions 1.0.3 dated 2015-04-23 and 1.0.4 dated 2015-09-18
ChangeLog | 152 +++++- DESCRIPTION | 11 MD5 | 226 +++++----- NAMESPACE | 8 NEWS |only R/Classes.R | 76 +-- R/Methods-index.R | 28 - R/Methods-plot.R | 232 +++++----- R/Methods-show.R | 86 +-- R/Methods-summary.R | 6 R/batchBinMatch.R | 20 R/batchCorMatch.R | 20 R/binMatch.R | 181 ++++---- R/bindEvents.R | 34 - R/changeSampRate.R | 18 R/collapseClips.R | 20 R/combineBinTemplates.R | 14 R/combineCorTemplates.R | 14 R/compareTemplates.R | 112 ++--- R/corMatch.R | 127 ++--- R/cutWave.R |only R/cutw.R | 16 R/dbDownloadCardRecorderID.R | 77 +-- R/dbDownloadResult.R | 129 +++-- R/dbDownloadSurvey.R | 73 +-- R/dbDownloadTemplate.R | 92 ++-- R/dbSchema.R | 61 +- R/dbUploadAnno.R | 42 + R/dbUploadResult.R | 90 ++-- R/dbUploadSurvey.R | 73 +-- R/dbUploadTemplate.R | 127 +++-- R/eventEval.R | 176 ++++---- R/fileCopyRename.R | 114 ++--- R/findDetections.R | 24 - R/findPeaks.R | 68 +-- R/getClip.R | 84 +-- R/getDetections.R | 31 - R/getPeaks.R | 25 - R/getTemplates.R | 6 R/makeBinTemplate.R | 848 ++++++++++++++++++++------------------- R/makeCorTemplate.R | 288 ++++++------- R/mp3Subsamp.R | 100 ++-- R/rbindf.R | 22 - R/readBinTemplates.R | 20 R/readCorTemplates.R | 24 - R/readMP3.R | 40 - R/readOneBinTemplate.R | 50 +- R/readOneCorTemplate.R | 42 - R/showPeaks.R | 196 ++++----- R/specCols.R | 6 R/spectro.R | 24 - R/templateComment.R | 24 - R/templateCutoff.R | 26 - R/templateNames.R | 12 R/templatePath.R | 24 - R/timeAlign.R | 182 ++++---- R/viewSpec.R | 462 ++++++++++----------- R/windows.R | 32 - R/writeBinTemplates.R | 16 R/writeCorTemplates.R | 16 R/writeOneBinTemplate.R | 70 +-- R/writeOneCorTemplate.R | 64 +- README |only build/vignette.rds |binary data/btnw.rda |binary data/oven.rda |binary data/survey.rda |binary data/survey_anno.rda |binary inst/doc/monitoR_QuickStart.R | 94 ++-- inst/doc/monitoR_QuickStart.Rnw | 104 ++-- inst/doc/monitoR_QuickStart.pdf |binary man/Template-class.Rd | 6 man/TemplateList-class.Rd | 8 man/batchDetection.Rd | 13 man/bindEvents.Rd | 32 - man/btnw.Rd | 5 man/changeSampRate.Rd | 5 man/collapseClips.Rd | 6 man/combineTemplates.Rd | 38 - man/compareTemplates.Rd | 33 - man/cutWave.Rd |only man/cutw.Rd | 9 man/dbDownload.Rd | 26 - man/dbDownloadResult.Rd | 10 man/dbDownloadTemplate.Rd | 14 man/dbSchema.Rd | 9 man/dbUploadAnno.Rd | 3 man/dbUploadResult.Rd | 38 - man/dbUploadSurvey.Rd | 68 +-- man/dbUploadTemplate.Rd | 16 man/detectionList-class.Rd | 14 man/eventEval.Rd | 37 + man/fileCopyRename.Rd | 55 +- man/findPeaks.Rd | 54 +- man/getDetections.Rd | 32 - man/getTemplates.Rd | 6 man/internals.Rd | 54 +- man/makeTemplate.Rd | 87 ++-- man/monitoR-package.Rd | 71 +-- man/mp3Subsamp.Rd | 26 - man/plot-methods.Rd | 46 +- man/readTemplates.Rd | 22 - man/show-methods.Rd | 12 man/showPeaks.Rd | 49 +- man/specCols.Rd | 14 man/survey_anno.Rd | 4 man/templateComment.Rd | 30 - man/templateCutoff.Rd | 28 - man/templateMatching.Rd | 25 - man/templateNames.Rd | 28 - man/templatePath.Rd | 30 - man/templateScores-class.Rd | 2 man/timeAlign.Rd | 42 - man/viewSpec.Rd | 24 - man/writeTemplates.Rd | 22 - vignettes/monitoR_QuickStart.Rnw | 104 ++-- 116 files changed, 3512 insertions(+), 3224 deletions(-)
Title: Analyzing Combination of Proportions and Relative Risk
Description: The prop.comb.RR package analyzes combination of proportions and relative risk.
Author: Maria Alvarez and Javier Roca-Pardinas
Maintainer: Maria Alvarez <maria.alvarez@uvigo.es>
Diff between prop.comb.RR versions 1.0 dated 2015-07-08 and 1.1 dated 2015-09-18
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NAMESPACE | 5 +++++ R/print.prop.RR.R |only R/print.prop.comb.R |only R/summary.prop.RR.R | 2 +- R/summary.prop.comb.R | 2 +- man/prop.RR.Rd | 4 ++-- man/prop.comb.Rd | 10 +++++++++- man/summary.prop.comb.Rd | 11 +++++++---- 10 files changed, 38 insertions(+), 20 deletions(-)
Title: Real-Time Stock Price & Volume in China Market
Description: With this package, users can obtain the real-time price and volume information of stocks in China market, as well as the information of the stock index. This package adopted the API from Sina Finance (http://finance.sina.com.cn/).
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between StockChina versions 0.2 dated 2015-09-13 and 0.3 dated 2015-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/index.CN.R | 2 +- R/stock.CN.R | 23 +++++++++++------------ man/index.CN.Rd | 32 +++++++++++++++++++++++++------- man/stock.CN.Rd | 27 +++++++++++++++++---------- 6 files changed, 63 insertions(+), 39 deletions(-)
Title: Nonparametric Estimation of Preferential Attachment and Node
Fitness in Temporal Complex Networks
Description: A statistically sound method for estimating jointly the attachment function and node fitness in a temporal complex network by maximizing a suitable penalized log-likelihood function is implemented in this package. Tutorial can be found in the accompanying vignette. More details about the method can be found at http://dx.doi.org/10.1371/journal.pone.0137796. To cite this package in your projects, please run the command: citation("PAFit") for a list of references you should cite.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 0.7.2 dated 2015-03-27 and 0.7.5 dated 2015-09-18
DESCRIPTION | 15 ++- MD5 | 41 +++++----- NAMESPACE | 3 R/GetStatistics.R | 16 ++-- R/PAFit.R | 87 +++++++++++++-------- R/plot.pafit.r | 24 +++--- build/vignette.rds |binary inst/CITATION |only inst/doc/Tutorial.pdf |binary inst/doc/Tutorial.pdf.asis | 2 man/GenerateNet.Rd | 6 + man/GetStatistics.Rd | 4 - man/PAFit-package.Rd | 12 ++- man/PAFit.Rd | 21 ++++- man/plot.PAFit.Rd | 10 +- man/print.PAFit.Rd | 4 - man/print.PAFitData.Rd | 4 - man/summary.PAFit.Rd | 4 - man/summary.PAFitData.Rd | 4 - src/Cpp_code.cpp | 2 src/RcppExports.cpp | 176 +++++++++++++++++++------------------------- vignettes/Tutorial.pdf.asis | 4 - 22 files changed, 239 insertions(+), 200 deletions(-)
Title: Image Processing Library Based on CImg
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R.
Author: Simon Barthelme [aut, cre],
Antoine Cecchi [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Diff between imager versions 0.13 dated 2015-08-26 and 0.14 dated 2015-09-18
imager-0.13/imager/src/Makevars |only imager-0.14/imager/DESCRIPTION | 6 +++--- imager-0.14/imager/MD5 | 17 ++++++++++------- imager-0.14/imager/NEWS | 6 +++++- imager-0.14/imager/R/cimg_class.R | 13 ++++++++++--- imager-0.14/imager/README.md | 16 ++++++++++------ imager-0.14/imager/cleanup |only imager-0.14/imager/configure |only imager-0.14/imager/configure.ac |only imager-0.14/imager/man/load.image.Rd | 4 ++-- imager-0.14/imager/src/Makevars.in |only imager-0.14/imager/src/Makevars.win | 1 - 12 files changed, 40 insertions(+), 23 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus, and PHAT.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, Vincent Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan Reininghaus.
Maintainer: Jisu Kim <jisuk1@andrew.cmu.edu>
Diff between TDA versions 1.4 dated 2015-09-15 and 1.4.1 dated 2015-09-18
TDA-1.4.1/TDA/DESCRIPTION | 6 +++--- TDA-1.4.1/TDA/MD5 | 22 ++++++++++------------ TDA-1.4.1/TDA/NAMESPACE | 2 +- TDA-1.4.1/TDA/R/RcppExports.R | 4 ---- TDA-1.4.1/TDA/build/vignette.rds |binary TDA-1.4.1/TDA/inst/doc/article.pdf |binary TDA-1.4.1/TDA/man/TDA-package.Rd | 6 +++--- TDA-1.4.1/TDA/man/gridDiag.Rd | 2 +- TDA-1.4.1/TDA/man/ripsDiag.Rd | 2 +- TDA-1.4.1/TDA/src/RcppExports.cpp | 12 ------------ TDA-1.4.1/TDA/src/diag.cpp | 33 +++++++++++++++++---------------- TDA-1.4/TDA/R/alphaDiag.R |only TDA-1.4/TDA/man/alphaDiag.Rd |only 13 files changed, 36 insertions(+), 53 deletions(-)
Title: R Interface to RNG with Multiple Streams
Description: Provides an interface to the C implementation of the
random number generator with multiple independent streams
developed by L'Ecuyer et al (2002). The main purpose of this
package is to enable the use of this random number generator in
parallel R applications.
Author: Hana Sevcikova [aut, cre],
Tony Rossini [aut],
Pierre L'Ecuyer [cph] (author of the underlying C code)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between rlecuyer versions 0.3-3 dated 2012-02-02 and 0.3-4 dated 2015-09-18
ChangeLog | 4 ++++ DESCRIPTION | 24 ++++++++++++++++-------- MD5 | 8 ++++---- R/rlecuyer.R | 11 +++++++---- src/RngWrap.c | 4 +--- 5 files changed, 32 insertions(+), 19 deletions(-)
Title: Logistic Ordinal Regression Differential Item Functioning using
IRT
Description: Analysis of Differential Item Functioning (DIF) for
dichotomous and polytomous items using an iterative hybrid of
ordinal logistic regression and item response theory (IRT).
Author: Seung W. Choi, with contributions from Laura E. Gibbons and
Paul K. Crane
Maintainer: Seung W. Choi <choi.phd@gmail.com>
Diff between lordif versions 0.2-2 dated 2012-04-05 and 0.3-2 dated 2015-09-18
lordif-0.2-2/lordif/R/lordif-internal.R |only lordif-0.2-2/lordif/inst |only lordif-0.3-2/lordif/DESCRIPTION | 20 +- lordif-0.3-2/lordif/MD5 | 92 ++++----- lordif-0.3-2/lordif/NAMESPACE | 13 + lordif-0.3-2/lordif/R/DFIT.R |only lordif-0.3-2/lordif/R/calcprob.R | 34 ++- lordif-0.3-2/lordif/R/calctheta.R | 36 ++- lordif-0.3-2/lordif/R/collapse.R | 24 +- lordif-0.3-2/lordif/R/equate.R | 28 +- lordif-0.3-2/lordif/R/extract.R | 37 ++- lordif-0.3-2/lordif/R/getcutoff.R | 24 +- lordif-0.3-2/lordif/R/lordif.R | 296 +++++++++++++++++++----------- lordif-0.3-2/lordif/R/montecarlo.R | 164 ++++++++-------- lordif-0.3-2/lordif/R/permute.R | 148 +++++++-------- lordif-0.3-2/lordif/R/plot.lordif.MC.R | 64 +++--- lordif-0.3-2/lordif/R/plot.lordif.R | 186 +++++++++--------- lordif-0.3-2/lordif/R/print.lordif.MC.R | 16 - lordif-0.3-2/lordif/R/print.lordif.R | 66 ++++-- lordif-0.3-2/lordif/R/probgpcm.R |only lordif-0.3-2/lordif/R/probgrm.R | 44 ++-- lordif-0.3-2/lordif/R/recode.R | 16 - lordif-0.3-2/lordif/R/rundif.R | 124 ++++++------ lordif-0.3-2/lordif/R/runolr.R | 82 ++++---- lordif-0.3-2/lordif/R/separate.R | 36 +-- lordif-0.3-2/lordif/R/summary.lordif.MC.R | 68 +++--- lordif-0.3-2/lordif/R/summary.lordif.R | 17 + lordif-0.3-2/lordif/R/tcc.R | 26 +- lordif-0.3-2/lordif/data/Anxiety.rda |binary lordif-0.3-2/lordif/man/Anxiety.Rd | 2 lordif-0.3-2/lordif/man/DFIT.Rd |only lordif-0.3-2/lordif/man/calcprob.Rd | 36 ++- lordif-0.3-2/lordif/man/calctheta.Rd | 23 +- lordif-0.3-2/lordif/man/collapse.Rd | 10 - lordif-0.3-2/lordif/man/equate.Rd | 42 ++-- lordif-0.3-2/lordif/man/extract.Rd | 20 +- lordif-0.3-2/lordif/man/getcutoff.Rd | 21 +- lordif-0.3-2/lordif/man/lordif-package.Rd | 19 + lordif-0.3-2/lordif/man/lordif.Rd | 39 ++- lordif-0.3-2/lordif/man/montecarlo.Rd | 18 - lordif-0.3-2/lordif/man/permute.Rd | 10 - lordif-0.3-2/lordif/man/plot.lordif.MC.Rd | 15 - lordif-0.3-2/lordif/man/plot.lordif.Rd | 12 - lordif-0.3-2/lordif/man/probgpcm.Rd |only lordif-0.3-2/lordif/man/probgrm.Rd | 9 lordif-0.3-2/lordif/man/recode.Rd | 4 lordif-0.3-2/lordif/man/rundif.Rd | 2 lordif-0.3-2/lordif/man/runolr.Rd | 4 lordif-0.3-2/lordif/man/separate.Rd | 8 lordif-0.3-2/lordif/man/tcc.Rd | 35 ++- 50 files changed, 1105 insertions(+), 885 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: We efficiently approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of our calculations, we also
obtain approximate standard errors for estimated predictive errors, and for
the comparison of predictive errors between two models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.2 dated 2015-07-16 and 0.1.3 dated 2015-09-18
loo-0.1.2/loo/R/deprecated.R |only loo-0.1.2/loo/R/psisloo.R |only loo-0.1.2/loo/man/loo_and_waic.Rd |only loo-0.1.2/loo/man/psisloo.Rd |only loo-0.1.3/loo/DESCRIPTION | 14 +- loo-0.1.3/loo/MD5 | 58 ++++------ loo-0.1.3/loo/NAMESPACE | 13 +- loo-0.1.3/loo/R/compare.R | 81 ++++++++++---- loo-0.1.3/loo/R/extract_log_lik.R | 4 loo-0.1.3/loo/R/gpdfit.R | 4 loo-0.1.3/loo/R/helpers.R | 126 +++++++++++++--------- loo-0.1.3/loo/R/loo.R | 131 ++++++++++++++--------- loo-0.1.3/loo/R/loo_package.R | 4 loo-0.1.3/loo/R/print.R | 56 ++++++--- loo-0.1.3/loo/R/psislw.R | 74 ++++++++++-- loo-0.1.3/loo/R/waic.R | 39 ++++-- loo-0.1.3/loo/R/zzz.R | 10 + loo-0.1.3/loo/build/vignette.rds |binary loo-0.1.3/loo/inst/CITATION | 4 loo-0.1.3/loo/inst/doc/Example.Rmd | 4 loo-0.1.3/loo/inst/doc/Example.html | 4 loo-0.1.3/loo/man/compare.Rd | 15 +- loo-0.1.3/loo/man/extract_log_lik.Rd | 4 loo-0.1.3/loo/man/gpdfit.Rd | 4 loo-0.1.3/loo/man/loo-package.Rd | 4 loo-0.1.3/loo/man/loo.Rd | 124 +++++++++++++++------ loo-0.1.3/loo/man/print.loo.Rd | 41 ++++--- loo-0.1.3/loo/man/psislw.Rd | 19 ++- loo-0.1.3/loo/man/waic.Rd | 46 +++++++- loo-0.1.3/loo/tests/testthat/test_helpers.R | 3 loo-0.1.3/loo/tests/testthat/test_loo_and_waic.R | 31 ++++- loo-0.1.3/loo/vignettes/Example.Rmd | 4 32 files changed, 627 insertions(+), 294 deletions(-)
Title: Syntax Highlighting for R Source Code
Description: Provides syntax highlighting for R source code. Currently it
supports LaTeX and HTML output. Source code of other languages is supported
via Andre Simon's highlight package (http://www.andre-simon.de).
Author: Christopher Gandrud [ctb],
Qiang Li [ctb],
Yixuan Qiu [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between highr versions 0.5 dated 2015-04-21 and 0.5.1 dated 2015-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/highlight.R | 3 ++- R/utils.R | 10 ++++++++++ build/vignette.rds |binary 6 files changed, 22 insertions(+), 10 deletions(-)
Title: Authorize and Request Google Analytics Data
Description: The functions included are used to obtain initial authentication with Google Analytics as well as simple and organized data retrieval from the API. Allows for retrieval from multiple profiles at once.
Author: Andrew Geisler
Maintainer: Andrew Geisler <andrew.geisler@gmail.com>
Diff between GAR versions 1.0 dated 2015-03-19 and 1.1 dated 2015-09-18
DESCRIPTION | 8 - MD5 | 10 +- NAMESPACE | 5 - R/gaRequest.R | 228 ++++++++++++++++++++++++++++++++++------------------- man/GAR-package.Rd | 3 man/gaRequest.Rd | 6 + 6 files changed, 167 insertions(+), 93 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.3.1 dated 2015-06-10 and 0.4.0 dated 2015-09-18
globals-0.3.1/globals/.Rinstignore |only globals-0.4.0/globals/DESCRIPTION | 6 +-- globals-0.4.0/globals/MD5 | 13 +++---- globals-0.4.0/globals/NAMESPACE | 27 +++++++------- globals-0.4.0/globals/NEWS | 5 ++ globals-0.4.0/globals/R/findGlobals.R | 59 +++++++++++++++++++++++++++----- globals-0.4.0/globals/R/globalsOf.R | 16 ++++++++ globals-0.4.0/globals/R/utils.R | 1 globals-0.4.0/globals/tests/dotdotdot.R |only 9 files changed, 96 insertions(+), 31 deletions(-)
Title: Format R Code Automatically
Description: Provides a function tidy_source() to format R source code. Spaces
and indent will be added to the code automatically, and comments will be
preserved under certain conditions, so that R code will be more
human-readable and tidy. There is also a Shiny app as a user interface in
this package (see tidy_app()).
Author: Yihui Xie
Maintainer: Yihui Xie <xie@yihui.name>
Diff between formatR versions 1.2 dated 2015-04-21 and 1.2.1 dated 2015-09-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/tidy.R | 1 + R/utils.R | 14 +++++++++++++- build/vignette.rds |binary inst/doc/formatR.R | 2 +- inst/doc/formatR.Rmd | 6 +++--- inst/doc/formatR.html | 15 ++++++++------- vignettes/formatR.Rmd | 6 +++--- 10 files changed, 43 insertions(+), 28 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.7.2 dated 2015-08-13 and 0.8 dated 2015-09-18
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 11 ++++++----- NEWS | 5 +++++ R/eval.r | 8 ++++---- R/parse.r | 14 +++++++++++++- man/evaluate.Rd | 8 ++++---- 7 files changed, 37 insertions(+), 19 deletions(-)
Title: Double Hierarchical Generalized Linear Models
Description: Double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.
Author: Youngjo Lee, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>
Diff between dhglm versions 1.2 dated 2011-09-30 and 1.5 dated 2015-09-18
dhglm-1.2/dhglm/R/summary.dhglm.R |only dhglm-1.2/dhglm/man/summary.dhglm.Rd |only dhglm-1.5/dhglm/DESCRIPTION | 21 dhglm-1.5/dhglm/MD5 | 47 - dhglm-1.5/dhglm/NAMESPACE | 11 dhglm-1.5/dhglm/R/DHGLMMODELING.R | 1 dhglm-1.5/dhglm/R/HGLMFactorList.R | 1 dhglm-1.5/dhglm/R/HGLMFrames.R | 1 dhglm-1.5/dhglm/R/dhglmfit.R | 698 ----------------------------- dhglm-1.5/dhglm/R/dhglmfit_run.R |only dhglm-1.5/dhglm/R/expandSlash.R | 7 dhglm-1.5/dhglm/R/findbars.R | 1 dhglm-1.5/dhglm/R/findplus.R | 1 dhglm-1.5/dhglm/R/hglmfit_corr.R | 32 - dhglm-1.5/dhglm/R/nobars.R | 1 dhglm-1.5/dhglm/R/plotdhglm.R | 5 dhglm-1.5/dhglm/R/slashTerms.R | 1 dhglm-1.5/dhglm/R/subbars.R | 1 dhglm-1.5/dhglm/data/data_crack_growth.rda |binary dhglm-1.5/dhglm/data/data_epilepsy.rda |binary dhglm-1.5/dhglm/man/DHGLMMODELING.Rd | 2 dhglm-1.5/dhglm/man/crack_growth.Rd | 4 dhglm-1.5/dhglm/man/dhglm-package.Rd | 8 dhglm-1.5/dhglm/man/dhglmfit.Rd | 40 - dhglm-1.5/dhglm/man/epilepsy.Rd | 4 dhglm-1.5/dhglm/man/residual.dhglm.Rd | 2 26 files changed, 81 insertions(+), 808 deletions(-)
Title: General Purpose R Interface to Solr
Description: Provides a set of functions for querying and parsing
data from Solr endpoints (local and remote), including search, faceting,
highlighting, stats, and 'more like this'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between solr versions 0.1.4 dated 2014-03-14 and 0.1.6 dated 2015-09-17
DESCRIPTION | 16 - LICENSE | 4 MD5 | 42 ++-- NAMESPACE | 4 NEWS | 17 + R/solr-package.R | 21 +- README.md | 3 build/vignette.rds |binary man/collectargs.Rd | 5 man/is-sr.Rd | 5 man/makemultiargs.Rd | 5 man/solr-package.Rd | 11 - man/solr_all.Rd | 112 +++++------- man/solr_facet.Rd | 301 ++++++++++++++-------------------- man/solr_group.Rd | 119 +++++-------- man/solr_highlight.Rd | 361 +++++++++++++++++------------------------ man/solr_mlt.Rd | 77 +++----- man/solr_parse.Rd | 11 - man/solr_search.Rd | 112 +++++------- man/solr_stats.Rd | 31 +-- vignettes/solr_localsetup.html | 97 ++++++----- vignettes/solr_vignette.html | 100 ++++++----- 22 files changed, 665 insertions(+), 789 deletions(-)
Title: Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Description: We provide a graphical user interface for interactive Markov chain
Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
posterior sample. The interface is powered by RStudio's Shiny web application
framework and works with the output of MCMC programs written in any
programming language (and has extended functionality for Stan models fit
using the rstan package and the No-U-Turn sampler).
Author: Jonah Gabry [aut, cre],
Stan Development Team [ctb],
Michael Andreae [ctb],
Michael Betancourt [ctb],
Bob Carpenter [ctb],
Yuanjun Gao [ctb],
Andrew Gelman [ctb],
Ben Goodrich [ctb],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between shinystan versions 2.0.0 dated 2015-08-10 and 2.0.1 dated 2015-09-17
shinystan-2.0.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui/pp_yrep_from_sso.R |only shinystan-2.0.0/shinystan/inst/doc/deploying-shinystan.Rmd |only shinystan-2.0.0/shinystan/inst/doc/deploying-shinystan.html |only shinystan-2.0.0/shinystan/inst/doc/using-shinystan.Rmd |only shinystan-2.0.0/shinystan/inst/doc/using-shinystan.html |only shinystan-2.0.0/shinystan/vignettes/deploying-shinystan.Rmd |only shinystan-2.0.0/shinystan/vignettes/using-shinystan.Rmd |only shinystan-2.0.1/shinystan/DESCRIPTION | 20 +- shinystan-2.0.1/shinystan/MD5 | 81 +++++----- shinystan-2.0.1/shinystan/NAMESPACE | 2 shinystan-2.0.1/shinystan/R/deploy_shinystan.R | 9 - shinystan-2.0.1/shinystan/R/launch_shinystan.R | 5 shinystan-2.0.1/shinystan/R/launch_shinystan_demo.R | 1 shinystan-2.0.1/shinystan/R/misc.R | 18 -- shinystan-2.0.1/shinystan/R/stan2shinystan.R | 45 +++-- shinystan-2.0.1/shinystan/R/stanreg2shinystan.R |only shinystan-2.0.1/shinystan/R/zzz.R | 2 shinystan-2.0.1/shinystan/build/vignette.rds |binary shinystan-2.0.1/shinystan/data/eight_schools.rda |binary shinystan-2.0.1/shinystan/inst/ShinyStan/ggplot_fns.rda |only shinystan-2.0.1/shinystan/inst/ShinyStan/global_utils.R | 11 - shinystan-2.0.1/shinystan/inst/ShinyStan/helper_functions/gg_theme_elements.R | 2 shinystan-2.0.1/shinystan/inst/ShinyStan/helper_functions/shinystan_helpers.R | 37 ++-- shinystan-2.0.1/shinystan/inst/ShinyStan/html/accept_stat.html | 2 shinystan-2.0.1/shinystan/inst/ShinyStan/html/mcse.html | 14 - shinystan-2.0.1/shinystan/inst/ShinyStan/html/neff.html | 2 shinystan-2.0.1/shinystan/inst/ShinyStan/html/rhat.html | 7 shinystan-2.0.1/shinystan/inst/ShinyStan/server.R | 2 shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ppcheck_helpers.R | 80 ++------- shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_rep_vs_obs.R | 14 - shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_resids.R | 6 shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_test_statistics.R | 50 +++--- shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/pp_utils.R |only shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rep_vs_resid_rep.R | 10 - shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/y_vs_avg_rep.R | 6 shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui/pp_get_y_and_yrep.R |only shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/diagnostics.R | 19 +- shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/rhat_neff_mcse.R | 13 + shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/summary_stats_sampler.R | 4 shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/pages/explore/server/density.R | 20 +- shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/utilities/extract_sso.R | 26 ++- shinystan-2.0.1/shinystan/inst/ShinyStan/ui.R | 2 shinystan-2.0.1/shinystan/inst/ShinyStan/ui_files/glossary.R | 3 shinystan-2.0.1/shinystan/inst/ShinyStan/ui_files/pp_navlist.R | 9 - shinystan-2.0.1/shinystan/inst/doc/deploying-shinyStan.Rmd |only shinystan-2.0.1/shinystan/inst/doc/deploying-shinyStan.html |only shinystan-2.0.1/shinystan/inst/doc/using-shinyStan.Rmd |only shinystan-2.0.1/shinystan/inst/doc/using-shinyStan.html |only shinystan-2.0.1/shinystan/vignettes/deploying-shinyStan.Rmd |only shinystan-2.0.1/shinystan/vignettes/using-shinyStan.Rmd |only 50 files changed, 263 insertions(+), 259 deletions(-)
Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.2-0 dated 2015-08-19 and 2.2-1 dated 2015-09-17
DESCRIPTION | 8 MD5 | 92 NEWS | 10 R/commander.R | 2724 +++---- R/graphs-menu.R | 4 R/model-menu.R | 6 R/utilities.R | 598 - inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/doc/Rcmdr-manual-source.zip |binary inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/de/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/el |only inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/eu/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/gl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/id/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/it/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/ko/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/pl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/pt_BR/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/ro/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh_CN/LC_MESSAGES/R-Rcmdr.mo |binary man/AuxiliarySoftware.Rd | 8 man/Rcmdr-package.Rd | 5 man/Rcmdr.Utilities.Rd | 7 po/R-Rcmdr.pot | 32 po/R-ca.po | 9310 ++++++++++++------------ po/R-de.po | 295 po/R-el.po |only po/R-es.po | 324 po/R-eu.po | 182 po/R-fr.po | 18 po/R-gl.po | 82 po/R-id.po | 346 po/R-it.po | 9522 ++++++++++++------------- po/R-ja.po | 187 po/R-ko.po | 367 po/R-pl.po | 423 - po/R-pt_BR.po | 8684 ++++++++++++---------- po/R-ro.po | 241 po/R-sl.po | 391 - po/R-zh.po | 372 po/R-zh_CN.po | 6192 ++++++++-------- 48 files changed, 22106 insertions(+), 18324 deletions(-)
Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to https://www.quandl.com/docs/api. For more help on the package itself go to https://www.quandl.com/help/r.
Author: Raymond McTaggart [aut, cre],
Gergely Daroczi [aut],
Clement Leung [aut],
Quandl Inc. [cph]
Maintainer: Raymond McTaggart <raymond@quandl.com>
Diff between Quandl versions 2.6.0 dated 2015-04-28 and 2.7.0 dated 2015-09-17
ChangeLog | 16 + DESCRIPTION | 21 - MD5 | 39 ++- NAMESPACE | 5 R/Quandl.R | 154 ++++--------- R/Quandlapi.R | 105 +++++---- R/Quandlconfig.R |only R/Quandldatabase.R |only R/Quandlsearch.R | 85 ++----- README.md | 185 ++++++++++++---- man/Quandl.Rd | 36 +-- man/Quandl.api_key.Rd |only man/Quandl.auth.Rd | 4 man/Quandl.database.bulk_download_to_file.Rd |only man/Quandl.database.bulk_download_url.Rd |only man/Quandl.dataset.get.Rd | 18 - man/Quandl.search.Rd | 27 -- man/metaData.Rd | 10 man/quandl.api.Rd | 26 -- tests/testthat.R | 2 tests/testthat/test-api.r |only tests/testthat/test-database.r |only tests/testthat/test-get.r | 310 +++++++++++++++++++++------ tests/testthat/test-helpers.r |only tests/testthat/test-search.r |only 25 files changed, 627 insertions(+), 416 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and
Grouping Priors
Description: Algorithms for fitting penalized semiparametric Bayesian Cox models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between psbcGroup versions 1.1 dated 2015-02-09 and 1.2 dated 2015-09-17
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 ++ man/psbcEN.Rd | 5 +++-- man/psbcFL.Rd | 5 +++-- man/psbcGL.Rd | 7 ++++--- man/psbcGroup.Rd | 9 +++++---- 7 files changed, 29 insertions(+), 23 deletions(-)
Title: Calculate Multivariate Richness via UTC and sUTC
Description: Functions to calculate Unique Trait Combinations (UTC) and scaled
Unique Trait Combinations (sUTC) as measures of multivariate richness. The
package can also calculate beta-diversity for trait richness and can
partition this into nestedness-related and turnover components. The code
will also calculate several measures of overlap.
Author: Alexander Keyel
Maintainer: Alexander Keyel <skeyel@gmail.com>
Diff between multirich versions 2.0.2 dated 2015-02-06 and 2.1.1 dated 2015-09-17
DESCRIPTION | 20 - MD5 | 26 +- NAMESPACE | 14 + NEWS | 13 - R/MVR.r | 493 +++++++++++++++++++++++++++++++++++++++++++- build |only inst/doc |only man/check.breaks.Rd |only man/check.traits.Rd |only man/expand.breaks.Rd |only man/get.breaks.Rd |only man/listtotext.Rd | 4 man/make.trait.Rd |only man/multirich-package.Rd | 4 man/plot.sensitivity.Rd |only man/sensitivity.analysis.Rd |only man/sensitivity.boxplots.Rd |only man/utc.sim.Rd |only vignettes |only 19 files changed, 545 insertions(+), 29 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Diff between laGP versions 1.1-5 dated 2015-05-26 and 1.2 dated 2015-09-17
laGP-1.1-5/laGP/R/auglag.R |only laGP-1.2/laGP/ChangeLog | 16 laGP-1.2/laGP/DESCRIPTION | 8 laGP-1.2/laGP/INSTALL | 9 laGP-1.2/laGP/MD5 | 97 +- laGP-1.2/laGP/NAMESPACE | 11 laGP-1.2/laGP/R/gp.R | 134 +++- laGP-1.2/laGP/R/gp_sep.R | 471 +++++++++++++- laGP-1.2/laGP/R/laGP.R | 41 - laGP-1.2/laGP/R/laGP_sep.R |only laGP-1.2/laGP/R/optim.R |only laGP-1.2/laGP/R/prior.R | 2 laGP-1.2/laGP/R/util.R | 3 laGP-1.2/laGP/build/vignette.rds |binary laGP-1.2/laGP/demo/ALfhat.R | 13 laGP-1.2/laGP/inst/doc/laGP.R | 109 +-- laGP-1.2/laGP/inst/doc/laGP.Rnw | 97 +- laGP-1.2/laGP/inst/doc/laGP.pdf |binary laGP-1.2/laGP/man/aGP.Rd | 92 +- laGP-1.2/laGP/man/alcGP.Rd | 61 + laGP-1.2/laGP/man/darg.Rd | 6 laGP-1.2/laGP/man/deleteGP.Rd | 4 laGP-1.2/laGP/man/discrep.est.Rd | 30 laGP-1.2/laGP/man/distance.Rd | 8 laGP-1.2/laGP/man/fcalib.Rd | 58 - laGP-1.2/laGP/man/laGP.Rd | 95 +- laGP-1.2/laGP/man/llikGP.Rd | 2 laGP-1.2/laGP/man/mleGP.Rd | 59 + laGP-1.2/laGP/man/newGP.Rd | 32 laGP-1.2/laGP/man/optim.auglag.Rd | 139 ++-- laGP-1.2/laGP/man/predGP.Rd | 13 laGP-1.2/laGP/src/davies.c |only laGP-1.2/laGP/src/davies.h |only laGP-1.2/laGP/src/gamma.c | 6 laGP-1.2/laGP/src/gp.c | 266 +++++--- laGP-1.2/laGP/src/gp.h | 25 laGP-1.2/laGP/src/gp_sep.c | 1260 ++++++++++++++++++++++++++++++++++---- laGP-1.2/laGP/src/gp_sep.h | 43 - laGP-1.2/laGP/src/ieci.c | 216 ++++++ laGP-1.2/laGP/src/ieci.h | 19 laGP-1.2/laGP/src/laGP.c | 104 +-- laGP-1.2/laGP/src/laGP.h | 36 - laGP-1.2/laGP/src/laGP_sep.c |only laGP-1.2/laGP/src/laGP_sep.h |only laGP-1.2/laGP/src/matrix.c | 78 +- laGP-1.2/laGP/src/matrix.h | 2 laGP-1.2/laGP/src/rbetter.c | 2 laGP-1.2/laGP/src/rhelp.c | 32 laGP-1.2/laGP/src/rhelp.h | 10 laGP-1.2/laGP/src/util.c | 36 + laGP-1.2/laGP/src/util.h | 6 laGP-1.2/laGP/vignettes/laGP.Rnw | 97 +- laGP-1.2/laGP/vignettes/laGP.bib | 265 ++++--- 53 files changed, 3150 insertions(+), 963 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-3 dated 2015-06-10 and 0.3-4 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/ICP.R | 4 ++-- man/ICP.Rd | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.3.5 dated 2015-08-26 and 1.3.6 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/glmmLasso.r | 2 +- R/glmmLasso_RE.R | 1 + man/glmmLasso.rd | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-3 dated 2015-09-03 and 0.9-4 dated 2015-09-17
DESCRIPTION | 10 ++++---- MD5 | 44 +++++++++++++++++++++----------------- R/LOF.R | 24 ++++++++++++++++++++ R/RcppExports.R | 4 --- R/dbscan.R | 30 +++++++++++++++++++++++--- R/frNN.R | 41 +++++++++++++++++++++++++++++------ R/kNN.R | 40 +++++++++++++++++++++++++++++++--- R/kNNdist.R | 38 ++++++++++++++++++++++---------- R/optics.R | 27 +++++++++++++++++++++-- inst/NEWS | 6 +++++ inst/tests |only man/dbscan.Rd | 10 +++++--- man/frNN.Rd | 5 ++-- man/kNN.Rd | 5 ++-- man/kNNdist.Rd | 14 +----------- man/optics.Rd | 6 ++--- src/ANN/ANN.h | 4 +-- src/R_dbscan.cpp | 25 ++++++++++----------- src/R_frNN.cpp | 26 +++++++++++++++++----- src/R_kNN.cpp | 60 ++++++---------------------------------------------- src/RcppExports.cpp | 16 ------------- tests |only 22 files changed, 266 insertions(+), 169 deletions(-)
Title: Describe Data in R Using Common Descriptive Statistics
Description: Allows users to quickly and easily describe data using
common descriptive statistics.
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Diff between describer versions 0.1.0 dated 2015-09-03 and 0.2.0 dated 2015-09-17
DESCRIPTION | 8 - MD5 | 21 ++- NAMESPACE | 3 R/describe.R | 55 +++------- R/describer.R | 2 README.md | 164 ++++++++++++++++++++---------- man/describe.Rd | 23 ---- man/describe_nonnumeric.Rd | 2 man/describer.Rd | 4 tests/testthat/test-describe-dataframes.R | 4 tests/testthat/test-describe-vectors.R | 11 -- tests/testthat/test-styling.R |only 12 files changed, 163 insertions(+), 134 deletions(-)
Title: Exploring Portfolio-Based Conjectures About Financial
Instruments
Description: The backtest package provides facilities for exploring
portfolio-based conjectures about financial instruments
(stocks, bonds, swaps, options, et cetera).
Author: Jeff Enos <jeff@kanecap.com> and David Kane <dave@kanecap.com>,
with contributions from Kyle Campbell
<kyle.w.campbell@williams.edu>, Daniel Gerlanc
<daniel@gerlanc.com>, Aaron Schwartz
<Aaron.J.Schwartz@williams.edu>, Daniel Suo
<danielsuo@gmail.com>, Alexei Colin <acolin@fas.harvard.edu>,
and Luyi Zhao <luyizhao@gmail.com>
Maintainer: Daniel Gerlanc <dgerlanc@enplusadvisors.com>
Diff between backtest versions 0.3-2 dated 2013-07-09 and 0.3-4 dated 2015-09-17
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- NAMESPACE | 7 +++++++ build |only 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik <thomas.mendlik@uni-graz.at>
Diff between wux versions 2.0-2 dated 2015-06-16 and 2.1-1 dated 2015-09-17
wux-2.0-2/wux/exec/WuxModelDir.R |only wux-2.0-2/wux/exec/WuxModelDir_.R |only wux-2.0-2/wux/exec/WuxModelDir_rcp85.R |only wux-2.0-2/wux/exec/modelinput.R |only wux-2.1-1/wux/DESCRIPTION | 11 wux-2.1-1/wux/MD5 | 18 wux-2.1-1/wux/NAMESPACE | 12 wux-2.1-1/wux/R/InitModelDictionary.R | 9796 +++++++++++++-------------- wux-2.1-1/wux/R/models2wuxGetFilenames.R | 14 wux-2.1-1/wux/data/modelinput_test.rda |binary wux-2.1-1/wux/exec/cmip5_to_wux_modeldict.py | 16 wux-2.1-1/wux/man/models2wux.Rd | 4 12 files changed, 4944 insertions(+), 4927 deletions(-)
Title: Intermittent Time Series Forecasting
Description: Functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>
Diff between tsintermittent versions 1.5 dated 2014-11-20 and 1.7 dated 2015-09-17
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++++----------------- NAMESPACE | 5 ++++- R/crost.R | 12 +++++++++++- R/crost.decomp.R |only R/crost.ma.R | 11 ++++++++++- R/data.frc.R |only R/idclass.R | 2 +- R/imapa.R | 11 ++++++++++- R/sexsm.R | 13 +++++++++++-- R/simID.R | 10 +++++++--- R/tsb.R | 10 +++++++++- man/crost.Rd | 6 +++++- man/crost.decomp.Rd |only man/crost.ma.Rd | 6 +++++- man/data.frc.Rd |only man/idclass.Rd | 4 ++-- man/imapa.Rd | 8 ++++++-- man/sexsm.Rd | 6 +++++- man/simID.Rd | 2 +- man/tsb.Rd | 5 ++++- 22 files changed, 125 insertions(+), 42 deletions(-)
More information about tsintermittent at CRAN
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Title: Truncated Multivariate Normal Simulation
Description: Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator.
Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows
truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky
transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues.
Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions
for multivariate normals.
Author: Samsiddhi Bhattacjarjee <sb1@nibmg.ac.in>
Maintainer: Samsiddhi Bhattacharjee <sb1@nibmg.ac.in>
Diff between tmvnsim versions 1.0-0 dated 2015-08-19 and 1.0-1 dated 2015-09-17
tmvnsim-1.0-0/tmvnsim/man/sim.trunc.f.Rd |only tmvnsim-1.0-1/tmvnsim/DESCRIPTION | 9 ++++----- tmvnsim-1.0-1/tmvnsim/MD5 | 8 ++++---- tmvnsim-1.0-1/tmvnsim/NAMESPACE | 2 +- tmvnsim-1.0-1/tmvnsim/R/truncsimf.R | 2 +- tmvnsim-1.0-1/tmvnsim/man/tmvnsim.Rd |only 6 files changed, 10 insertions(+), 11 deletions(-)
Title: Spatial Probit Models
Description: Bayesian Estimation of Spatial Probit and Tobit Models.
Author: Stefan Wilhelm <wilhelm@financial.com> and Miguel Godinho de Matos <miguelgodinhomatos@cmu.edu>
Maintainer: Stefan Wilhelm <wilhelm@financial.com>
Diff between spatialprobit versions 0.9-10 dated 2014-05-03 and 0.9-11 dated 2015-09-17
spatialprobit-0.9-10/spatialprobit/man/summary.sarprobit.Rd |only spatialprobit-0.9-11/spatialprobit/.Rinstignore | 1 spatialprobit-0.9-11/spatialprobit/DESCRIPTION | 11 spatialprobit-0.9-11/spatialprobit/MD5 | 32 +- spatialprobit-0.9-11/spatialprobit/NAMESPACE | 28 + spatialprobit-0.9-11/spatialprobit/NEWS | 8 spatialprobit-0.9-11/spatialprobit/R/SpatialProbit-MCMC.R | 11 spatialprobit-0.9-11/spatialprobit/R/marginal.effects.R |only spatialprobit-0.9-11/spatialprobit/R/sar_base.r | 6 spatialprobit-0.9-11/spatialprobit/R/sarorderedprobit.R | 11 spatialprobit-0.9-11/spatialprobit/R/sartobit.R | 158 +++++++++- spatialprobit-0.9-11/spatialprobit/R/semprobit.R | 91 ++--- spatialprobit-0.9-11/spatialprobit/man/CKM.Rd | 4 spatialprobit-0.9-11/spatialprobit/man/fitted.Rd |only spatialprobit-0.9-11/spatialprobit/man/logLik.Rd | 2 spatialprobit-0.9-11/spatialprobit/man/marginal.effects.sarprobit.Rd | 116 ++++++- spatialprobit-0.9-11/spatialprobit/man/sarorderedprobit.Rd | 90 +++++ spatialprobit-0.9-11/spatialprobit/man/sartobit.Rd | 40 ++ spatialprobit-0.9-11/spatialprobit/man/semprobit.Rd | 12 spatialprobit-0.9-11/spatialprobit/man/summary.Rd |only 20 files changed, 505 insertions(+), 116 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.2.2 dated 2015-08-31 and 1.2.3 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/foo.R | 17 ++++++++++++----- man/spatial.pred.binomial.MCML.Rd | 2 +- man/spatial.pred.linear.MLE.Rd | 2 +- 5 files changed, 22 insertions(+), 15 deletions(-)
Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between VennDiagram versions 1.6.15 dated 2015-09-09 and 1.6.16 dated 2015-09-17
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS | 5 +++++ R/draw.triple.venn.R | 4 ++-- R/hypergeometric.test.R |only R/venn.diagram.R | 18 ++++++++++++++++-- man/venn.diagram.Rd | 4 +++- tests/testthat/testFunction.R | 9 +++++++-- 9 files changed, 45 insertions(+), 18 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.6-9 dated 2015-07-11 and 0.6-11 dated 2015-09-17
DESCRIPTION | 13 MD5 | 94 +- NEWS | 10 build/vignette.rds |binary data/Abortion.rda |binary data/Accident.RData |binary data/AirCrash.RData |binary data/Alligator.RData |binary data/Bartlett.rda |binary data/Caesar.rda |binary data/Cancer.rda |binary data/Cormorants.RData |binary data/CyclingDeaths.RData |binary data/DaytonSurvey.RData |binary data/Depends.RData |binary data/Detergent.rda |binary data/Donner.RData |binary data/Draft1970.RData |binary data/Draft1970table.RData |binary data/Dyke.rda |binary data/Fungicide.rda |binary data/GSS.rda |binary data/Geissler.RData |binary data/Gilby.rda |binary data/HairEyePlace.RData |binary data/Hauser79.RData |binary data/Heart.rda |binary data/Heckman.rda |binary data/HospVisits.RData |only data/Hoyt.rda |binary data/ICU.RData |binary data/JobSat.rda |binary data/Mammograms.RData |binary data/Mental.rda |binary data/Mice.RData |binary data/Mobility.rda |binary data/PhdPubs.RData |binary data/ShakeWords.RData |binary data/TV.rda |binary data/Titanicp.rda |binary data/Toxaemia.RData |binary data/Vietnam.RData |binary data/Vietnam.rda |binary data/Vote1980.RData |binary data/WorkerSat.RData |binary data/Yamaguchi87.RData |binary inst/doc/vcd-tutorial.R | 1524 +++++++++++++++++++++++----------------------- man/HospVisits.Rd |only man/vcdExtra-package.Rd | 4 49 files changed, 826 insertions(+), 819 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.18 dated 2015-09-02 and 0.9.19 dated 2015-09-17
DESCRIPTION | 6 - MD5 | 12 +-- NEWS | 15 +++- R/Utilities.R | 10 +++ R/manifest.R | 3 inst/doc/switchrvign.pdf |binary tests/winpath.R | 142 ++++++++++++++++++++++++----------------------- 7 files changed, 105 insertions(+), 83 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.2.0 dated 2015-09-09 and 0.2.1 dated 2015-09-17
DESCRIPTION | 8 - MD5 | 40 +++---- R/GuanTestUnif.R | 21 +--- inst/doc/spTest-vig.R | 11 -- inst/doc/spTest-vig.pdf |binary inst/doc/spTest-vig.rnw | 103 +++++++++----------- man/GuanTestUnif.Rd | 2 vignettes/figures/fig-dirsemi1-eps-converted-to.pdf |binary vignettes/figures/fig-dsvar2-eps-converted-to.pdf |binary vignettes/figures/fig-elev-eps-converted-to.pdf |binary vignettes/figures/fig-grid-eps-converted-to.pdf |binary vignettes/figures/fig-heatmap1-eps-converted-to.pdf |binary vignettes/figures/fig-iso2-eps-converted-to.pdf |binary vignettes/figures/fig-narccap-eps-converted-to.pdf |binary vignettes/figures/fig-narccap2-eps-converted-to.pdf |binary vignettes/figures/fig-precipdv-eps-converted-to.pdf |binary vignettes/figures/fig-rain-eps-converted-to.pdf |binary vignettes/figures/fig-rain1-eps-converted-to.pdf |binary vignettes/figures/fig-rain2-eps-converted-to.pdf |binary vignettes/spTest-vig.rnw | 103 +++++++++----------- vignettes/spTestReferences.bib | 13 ++ 21 files changed, 143 insertions(+), 158 deletions(-)
Title: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>
Diff between sparr versions 0.3-6 dated 2014-10-24 and 0.3-7 dated 2015-09-17
DESCRIPTION | 10 MD5 | 31 +- NAMESPACE | 8 NEWS | 8 R/bivariate.density.R | 24 + R/plot.bivden.R | 19 + R/plot.rrs.R | 147 ++++++----- R/risk.R | 4 R/rsmc.asym.R |only R/rsmc.fix.R |only R/rsmc.sym.R |only R/tolerance.R | 577 ++++++++++++++++++++++++----------------------- R/zzz.R | 2 man/bivariate.density.Rd | 2 man/plot.bivden.Rd | 148 ++++++------ man/sparr-internal.Rd | 3 man/sparr-package.Rd | 5 man/tolerance.Rd | 34 +- 18 files changed, 556 insertions(+), 466 deletions(-)
Title: R Parallel Implementation of Local Outlier Factor(LOF)
Description: R parallel implementation of Local Outlier Factor(LOF) which uses multiple CPUs to significantly speed up the LOF computation for large datasets. (Note: The overall performance depends on the computers especially the number of the cores).It also supports multiple k values to be calculated in parallel, as well as various distance measures in addition to the default Euclidean distance.
Author: Yingsong Hu, Wayne Murray and Yin Shan, Australia.
Maintainer: Yingsong Hu <yingsonghu@hotmail.com>
Diff between Rlof versions 1.1.0 dated 2015-09-11 and 1.1.1 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/distmc.Rd | 4 ++-- man/lof.Rd | 8 ++++---- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.45.0 dated 2015-09-11 and 0.45.1 dated 2015-09-17
DESCRIPTION | 10 +++-- MD5 | 16 ++++---- NEWS | 8 ++++ R/CBS.RESTRUCT.R | 10 +++-- R/PSCBS.RESTRUCT.R | 10 +++-- R/segmentByCBS.R | 8 +++- inst/doc/CBS.pdf |binary inst/doc/PairedPSCBS.pdf |binary tests/segmentByCBS,weights.R | 83 ++++++++++++++++++++++++++++++++++++++++++- 9 files changed, 123 insertions(+), 22 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4 dated 2015-09-14 and 0.4.1 dated 2015-09-17
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/miivboot.R | 75 ++-------------------------------------------- R/miive.R | 31 +++++++++---------- R/miivs.R | 96 +++++++++++++---------------------------------------------- man/miive.Rd | 2 - 6 files changed, 50 insertions(+), 170 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on
species' distributions and environmental variables as well as species' description
and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>
Diff between letsR versions 2.2 dated 2015-09-15 and 2.3 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/letsR-package.R | 4 ++-- R/lets_maplizer.R | 15 +++++++++++++-- man/lets.maplizer.Rd | 2 +- man/letsR-package.Rd | 4 ++-- tests/testthat/test-TimLucas.r | 16 ---------------- tests/testthat/test-lets_iucn.R | 2 +- 8 files changed, 30 insertions(+), 35 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation and manipulation of multistate data - the
Lexis suite of functions, which includes interfaces to mstate, etm
and cmprsk packages.
Also contains functions for Age-Period-Cohort modeling and a
function for interval censored data and some useful functions for
tabulation and plotting, as well some epidemiological datasets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <bxc@steno.dk>
Diff between Epi versions 1.1.67 dated 2014-07-23 and 1.1.71 dated 2015-09-17
Epi-1.1.67/Epi/vignettes/Follow-up.R |only Epi-1.1.67/Epi/vignettes/Follow-up.pdf |only Epi-1.1.67/Epi/vignettes/Follow-up.tex |only Epi-1.1.67/Epi/vignettes/sL-boxes.pdf |only Epi-1.1.67/Epi/vignettes/sL-comp-0.pdf |only Epi-1.1.67/Epi/vignettes/sL-mort-int.pdf |only Epi-1.1.67/Epi/vignettes/sL-pstate0.pdf |only Epi-1.1.67/Epi/vignettes/sL-pstatex.pdf |only Epi-1.1.67/Epi/vignettes/sL-pstatey.pdf |only Epi-1.1.67/Epi/vignettes/sim-Lexis.R |only Epi-1.1.67/Epi/vignettes/sim-Lexis.pdf |only Epi-1.1.67/Epi/vignettes/sim-Lexis.tex |only Epi-1.1.71/Epi/CHANGES | 35 +++++++++++ Epi-1.1.71/Epi/DESCRIPTION | 19 +++--- Epi-1.1.71/Epi/MD5 | 47 ++++++-------- Epi-1.1.71/Epi/NAMESPACE | 25 +++++++ Epi-1.1.71/Epi/R/Ns.r | 98 ++++++++++++++++++++++++------- Epi-1.1.71/Epi/R/Termplot.R |only Epi-1.1.71/Epi/R/apc.fit.R | 2 Epi-1.1.71/Epi/R/ci.cum.R | 61 +++++++------------ Epi-1.1.71/Epi/R/ci.lin.R | 94 ++++++++++++++++------------- Epi-1.1.71/Epi/R/crr.Lexis.r | 14 +--- Epi-1.1.71/Epi/R/foreign.R | 4 - Epi-1.1.71/Epi/build |only Epi-1.1.71/Epi/inst/doc/Follow-up.rnw |only Epi-1.1.71/Epi/inst/doc/sim-Lexis.pdf |binary Epi-1.1.71/Epi/inst/doc/sim-Lexis.rnw |only Epi-1.1.71/Epi/man/Ns.Rd | 87 +++++++++++++++++++-------- Epi-1.1.71/Epi/man/Termplot.Rd |only Epi-1.1.71/Epi/man/ci.cum.Rd | 23 ++++--- Epi-1.1.71/Epi/man/ci.lin.Rd | 57 ++++++++++-------- Epi-1.1.71/Epi/man/projection.ip.rd | 2 Epi-1.1.71/Epi/man/simLexis.Rd | 23 +++++-- 33 files changed, 380 insertions(+), 211 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.1 dated 2015-07-14 and 2.2.2 dated 2015-09-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 13 +++++++++++++ R/Kdhat.R | 26 ++++++++++++++++++++------ build/vignette.rds |binary man/dbmss-package.Rd | 4 ++-- src/CountNbd.cpp | 43 ++++++++++++++++++++++++------------------- 7 files changed, 69 insertions(+), 37 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-03 0.2
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.7 dated 2015-08-18 and 4.9 dated 2015-09-16
ChangeLog | 5 ++++ DESCRIPTION | 8 +++---- MD5 | 29 +++++++++++++++------------ NAMESPACE | 5 ++++ R/genMakefile.R | 48 ++++++++++++++++++++++++++++++++++++++++++--- R/seqminer.R | 12 ++++------- man/addJob.Rd |only man/isTabixRange.Rd |only man/newJob.Rd |only man/newWorkflow.Rd |only man/rvmeta.writeCovData.Rd | 2 - man/writeWorkflow.Rd |only src/bcf_index.c | 3 ++ src/bedidx.c | 3 ++ src/knetfile.c | 4 +++ src/rvMetaLoader.cpp | 7 ++++-- src/tabix_index.c | 3 ++ src/vcf.c | 3 ++ 18 files changed, 103 insertions(+), 29 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, shared objects, vignettes, or function documentation. It is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.7.0 dated 2015-07-16 and 2.8.0 dated 2015-09-16
StanHeaders-2.7.0/StanHeaders/inst/include/src/stan/interface |only StanHeaders-2.8.0/StanHeaders/DESCRIPTION | 10 StanHeaders-2.8.0/StanHeaders/MD5 | 292 ++--- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/array_var_context.hpp | 4 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/json/json_parser.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/mcmc_writer.hpp | 80 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/reader.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/ast.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/function_signatures.h | 8 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/generator.hpp | 548 ++++++---- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp | 24 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 53 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp | 41 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/model/prob_grad.hpp | 17 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/model/util.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 159 +- StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 61 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/bfgs_update.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/optimization/newton.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_delta.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_engaged.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_gamma.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_init_buffer.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_kappa.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_t0.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_term_buffer.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_adapt_window.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_bfgs.hpp | 42 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_data.hpp | 13 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_data_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_dense_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diag_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diagnose.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_diagnostic_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_engine.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_fail.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_fixed_param.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_history_size.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_hmc.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_id.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_init.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_init_alpha.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_int_time.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_iter.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_lbfgs.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_max_depth.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_method.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_metric.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_newton.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_num_samples.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_num_warmup.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_nuts.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_optimize.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_optimize_algo.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_output.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_output_file.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_random.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_refresh.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_rwm.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_sample.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_sample_algo.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_save_iterations.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_save_warmup.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_seed.hpp | 10 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_static.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_stepsize.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_stepsize_jitter.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_grad_eps.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_grad_err.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_test_gradient.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_thin.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_tolerance.hpp | 18 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_unit_e.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument_parser.hpp | 54 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/argument_probe.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/categorical_argument.hpp | 25 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/list_argument.hpp | 59 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/singleton_argument.hpp | 25 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/unvalued_argument.hpp | 19 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/valued_argument.hpp | 23 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_nuts.hpp | 11 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_static_hmc.hpp | 7 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_windowed_adapt.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/initialize_state.hpp | 39 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_error_msg.hpp | 19 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_iteration.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/io/write_stan.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/print_progress.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/run_markov_chain.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/sample.hpp | 13 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/warmup.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/optimization/do_bfgs_optimize.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/advi.hpp | 89 + StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/base_family.hpp | 20 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 56 - StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 46 StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/version.hpp | 2 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math.hpp | 9 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/quad_form_sym.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/trace_quad_form.hpp | 44 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/arr/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp | 55 - StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp | 45 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cols.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp | 1 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_u_to_z.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp | 35 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/rows.hpp | 14 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/fun/size.hpp | 12 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp | 8 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/meta/container_view.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp | 1 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf.hpp | 79 - StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_log.hpp | 16 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp | 6 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp | 7 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp | 5 StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/version.hpp | 2 145 files changed, 1647 insertions(+), 1403 deletions(-)
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on the 'htmlwidgets'
package, it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced
but can easily be added in the constructors. Complex properties (e.g.
'JavaScript' object) can be passed as named list. See examples at <http://
dataknowledge.github.io/rAmCharts/>. and <http://www.amcharts.com/> for more
information about the library. The package includes the free version of 'AmCharts'
Library. Its only limitation is that a small link to the web site will be
displayed in your charts. If you enjoy this library, do not hesitate to refer
to this page <http://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
DataKnowledge [ctb] (See official web site at http://www.datak.fr)
Maintainer: Jeffery Petit <jeff@datak.fr>
Diff between rAmCharts versions 1.1 dated 2015-09-16 and 1.1.1 dated 2015-09-16
DESCRIPTION | 31 +++++++++++++++++++++---------- MD5 | 4 +++- inst/NOTICE.Rmd |only inst/NOTICE.pdf |only 4 files changed, 24 insertions(+), 11 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.0 dated 2014-08-25 and 1.1 dated 2015-09-16
DESCRIPTION | 10 ++-- MD5 | 18 ++++--- NAMESPACE | 3 + R/aov.P.R |only R/functions.R | 68 ----------------------------- R/higgins.fisher.kruskal.test.R |only R/mood.median.test.R |only R/tukey.kruskal.test.R |only man/aov.P.Rd | 10 ++-- man/higgins.fisher.kruskal.test.Rd | 12 ++--- man/tukey.kruskal.test.Rd | 8 +-- src/aovp.f90 | 84 +++++++++++++++---------------------- 12 files changed, 70 insertions(+), 143 deletions(-)
Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MFAg versions 1.1 dated 2015-08-29 and 1.2 dated 2015-09-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/MFA.Rd | 26 +++++++++++++------------- man/MFAg-package.Rd | 4 ++-- man/Plot.MFA.Rd | 36 ++++++++++++++++++------------------ 5 files changed, 41 insertions(+), 41 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 1.2 dated 2015-08-27 and 2.0 dated 2015-09-16
hdnom-1.2/hdnom/man/glmnet.calibrate.internal.true.Rd |only hdnom-2.0/hdnom/DESCRIPTION | 10 hdnom-2.0/hdnom/MD5 | 61 - hdnom-2.0/hdnom/NAMESPACE | 10 hdnom-2.0/hdnom/NEWS.md | 12 hdnom-2.0/hdnom/R/hdnom.calibrate.R | 838 ++++++++++++--- hdnom-2.0/hdnom/R/hdnom.models.R | 471 ++++++++ hdnom-2.0/hdnom/R/hdnom.nomogram.R | 303 ++++- hdnom-2.0/hdnom/R/hdnom.validate.R | 573 ++++++++-- hdnom-2.0/hdnom/README.md | 6 hdnom-2.0/hdnom/TODO | 4 hdnom-2.0/hdnom/inst/doc/hdnom.R | 6 hdnom-2.0/hdnom/inst/doc/hdnom.Rmd | 31 hdnom-2.0/hdnom/inst/doc/hdnom.html | 68 + hdnom-2.0/hdnom/man/glmnet.basesurv.Rd | 2 hdnom-2.0/hdnom/man/glmnet.calibrate.internal.pred.Rd | 4 hdnom-2.0/hdnom/man/hdcox.aenet.Rd | 3 hdnom-2.0/hdnom/man/hdcox.alasso.Rd | 3 hdnom-2.0/hdnom/man/hdcox.enet.Rd | 3 hdnom-2.0/hdnom/man/hdcox.flasso.Rd |only hdnom-2.0/hdnom/man/hdcox.lasso.Rd | 3 hdnom-2.0/hdnom/man/hdcox.mcp.Rd |only hdnom-2.0/hdnom/man/hdcox.mnet.Rd |only hdnom-2.0/hdnom/man/hdcox.scad.Rd |only hdnom-2.0/hdnom/man/hdcox.snet.Rd |only hdnom-2.0/hdnom/man/hdnom.calibrate.Rd | 40 hdnom-2.0/hdnom/man/hdnom.calibrate.internal.true.Rd |only hdnom-2.0/hdnom/man/hdnom.nomogram.Rd | 22 hdnom-2.0/hdnom/man/hdnom.validate.Rd | 38 hdnom-2.0/hdnom/man/ncvreg.basesurv.Rd |only hdnom-2.0/hdnom/man/ncvreg.calibrate.internal.pred.Rd |only hdnom-2.0/hdnom/man/ncvreg.survcurve.Rd |only hdnom-2.0/hdnom/man/ncvreg.tune.gamma.Rd |only hdnom-2.0/hdnom/man/ncvreg.tune.gamma.alpha.Rd |only hdnom-2.0/hdnom/man/ncvreg.validate.internal.Rd |only hdnom-2.0/hdnom/man/penalized.basesurv.Rd |only hdnom-2.0/hdnom/man/penalized.calibrate.internal.pred.Rd |only hdnom-2.0/hdnom/man/penalized.survcurve.Rd |only hdnom-2.0/hdnom/man/penalized.validate.internal.Rd |only hdnom-2.0/hdnom/vignettes/hdnom.Rmd | 31 40 files changed, 2138 insertions(+), 404 deletions(-)
Title: An Algorithm to Infer Relatedness
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Diff between Relatedness versions 1.0 dated 2015-09-15 and 1.1 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/RelCoef.R | 12 ++++++++---- man/RelCoef.Rd | 2 +- man/Relatedness-package.Rd | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance, Spearman distance, Footrule distance, Hamming distance,
and Weighted-tau distance and geo-Weighted Kendall distance.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 1.1.0 dated 2015-08-19 and 1.1.1 dated 2015-09-16
DESCRIPTION | 10 ++++---- MD5 | 26 ++++++++++----------- R/class.R | 39 +++++++++++++++++++++----------- R/rankdist.R | 5 +++- man/RankControl-class.Rd | 2 - man/RankControlCayley-class.Rd | 3 ++ man/RankControlFootrule-class.Rd | 3 ++ man/RankControlHamming-class.Rd | 3 ++ man/RankControlKendall-class.Rd | 2 - man/RankControlPhiComponent-class.Rd | 2 - man/RankControlSpearman-class.Rd | 3 ++ man/RankControlWeightedKendall-class.Rd | 2 + man/RankControlWtau-class.Rd | 8 ++++++ src/utils.cpp | 2 - 14 files changed, 71 insertions(+), 39 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.33 dated 2015-07-18 and 0.2.51 dated 2015-09-16
DESCRIPTION | 8 +++--- MD5 | 18 ++++++------- R/graphics.R | 72 +++++++++++++++++++++++++++++++++--------------------- R/measures.R | 3 ++ R/read.arff.R | 2 - data/birds.rda |binary data/emotions.rda |binary data/genbase.rda |binary inst/doc/mldr.pdf |binary man/plot.mldr.Rd | 13 ++++++--- 10 files changed, 71 insertions(+), 45 deletions(-)
Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving first-order and general-order thermoluminescence glow
curves using a modified Levenberg-Marquardt algorithm. It provides the
possibility of setting constraints or fixing any of parameters. It offers
an interactive way to initialize parameters by clicking with a mouse on a
plot at positions where peak maxima should be located. The optimal estimate
is obtained by "Try-and-error". It also provides routines for simulating
first-, second-, and general-order glow peaks (or glow curves).
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Linda R. Petzold [ctb], Alan C. Hindmarsh [ctb], R. Woodrow Setzer [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between tgcd versions 1.5 dated 2015-08-05 and 1.7 dated 2015-09-16
tgcd-1.5/tgcd/src/BulirschStoer.f90 |only tgcd-1.5/tgcd/src/inverse.f90 |only tgcd-1.5/tgcd/src/numHess.f90 |only tgcd-1.7/tgcd/DESCRIPTION | 23 ++- tgcd-1.7/tgcd/MD5 | 25 ++- tgcd-1.7/tgcd/NAMESPACE | 3 tgcd-1.7/tgcd/R/simPeak.R | 182 ++++++++++++++++++++-------- tgcd-1.7/tgcd/R/simqOTOR.R |only tgcd-1.7/tgcd/R/tgcd.R | 227 +++++++++++++++++++++++++++--------- tgcd-1.7/tgcd/man/Refglow.Rd | 2 tgcd-1.7/tgcd/man/simPeak.Rd | 101 +++++++++------- tgcd-1.7/tgcd/man/simqOTOR.Rd |only tgcd-1.7/tgcd/man/tgcd.Rd | 89 +++++++------- tgcd-1.7/tgcd/src/lsoda.f |only tgcd-1.7/tgcd/src/qeOTOR.f90 |only tgcd-1.7/tgcd/src/simPeak.f90 |only tgcd-1.7/tgcd/src/tgcd.f90 | 66 +++------- tgcd-1.7/tgcd/src/tgcd1.f90 |only 18 files changed, 458 insertions(+), 260 deletions(-)
More information about TestingSimilarity at CRAN
Permanent link
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8 dated 2014-09-28 and 2.8.1 dated 2015-09-16
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 3 ++- NEWS | 3 +++ R/base64-functions.R | 12 ++++++------ R/package.R | 5 +++-- man/attributeTimeToDouble.Rd | 3 ++- man/attributeToDouble.Rd | 3 ++- man/attributeToString.Rd | 3 ++- man/base64-decode.Rd | 3 ++- man/grepNumeric.Rd | 3 ++- man/grepSubString.Rd | 3 ++- man/mzXmlHandlers.Rd | 3 ++- man/parseMzXml.Rd | 3 ++- man/readMzXmlData-defunct.Rd | 3 ++- man/readMzXmlData-package.Rd | 7 ++++--- man/readMzXmlDir.Rd | 3 ++- man/readMzXmlFile-internal.Rd | 3 ++- man/readMzXmlFile.Rd | 3 ++- man/revfregexpr.Rd | 3 ++- 20 files changed, 68 insertions(+), 49 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.12 dated 2015-06-11 and 1.13 dated 2015-09-16
MALDIquant-1.12/MALDIquant/R/calculateLabelPositions-methods.R |only MALDIquant-1.13/MALDIquant/DESCRIPTION | 23 ++-- MALDIquant-1.13/MALDIquant/MD5 | 49 ++++---- MALDIquant-1.13/MALDIquant/NAMESPACE | 32 +++++ MALDIquant-1.13/MALDIquant/NEWS | 43 +++++++ MALDIquant-1.13/MALDIquant/R/AllGenerics.R | 19 --- MALDIquant-1.13/MALDIquant/R/Deprecated.R | 56 ---------- MALDIquant-1.13/MALDIquant/R/calculateLabelPositions-functions.R |only MALDIquant-1.13/MALDIquant/R/calibrateIntensity-functions.R | 52 ++++++++- MALDIquant-1.13/MALDIquant/R/calibrateIntensity-methods.R | 32 ++--- MALDIquant-1.13/MALDIquant/R/msiSlices-functions.R | 2 MALDIquant-1.13/MALDIquant/R/plotMsiSlice-functions.R | 2 MALDIquant-1.13/MALDIquant/R/plotMsiSlice-methods.R | 2 MALDIquant-1.13/MALDIquant/build/vignette.rds |binary MALDIquant-1.13/MALDIquant/inst/doc/MALDIquant-intro.pdf |binary MALDIquant-1.13/MALDIquant/man/MALDIquant-defunct.Rd | 3 MALDIquant-1.13/MALDIquant/man/MALDIquant-deprecated.Rd | 23 +--- MALDIquant-1.13/MALDIquant/man/MALDIquant-package.Rd | 15 +- MALDIquant-1.13/MALDIquant/man/MALDIquant-parallel.Rd | 35 +++++- MALDIquant-1.13/MALDIquant/man/alignSpectra-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/binPeaks-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/calibrateIntensity-methods.Rd | 15 +- MALDIquant-1.13/MALDIquant/man/determineWarpingFunctions-functions.Rd | 2 MALDIquant-1.13/MALDIquant/man/referencePeaks-functions.Rd | 2 MALDIquant-1.13/MALDIquant/tests/testthat/test_alignSpectra-functions.R |only MALDIquant-1.13/MALDIquant/tests/testthat/test_calibrateIntensity-methods.R | 15 ++ MALDIquant-1.13/MALDIquant/tests/testthat/test_plotMsiSlice-functions.R | 8 - 27 files changed, 261 insertions(+), 173 deletions(-)
Title: Fused Lasso Latent Feature Model
Description: Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV). Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample. Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.
Author: Gen Nowak [aut, cre],
Trevor Hastie [aut],
Jonathan R. Pollack [aut],
Robert Tibshirani [aut],
Nicholas Johnson [aut]
Maintainer: Gen Nowak <gen.nowak@gmail.com>
Diff between FLLat versions 1.1 dated 2014-01-06 and 1.2 dated 2015-09-16
DESCRIPTION | 12 +-- MD5 | 48 ++++++------ NAMESPACE | 9 +- NEWS | 13 +++ R/CheckPars.R | 8 +- R/FLLat.FDR.R | 18 ++-- R/FLLat.R | 1 R/plot.FDR.R | 6 + R/plot.FLLat.R | 10 +- R/plot.PVE.R | 6 + R/predict.FLLat.R |only build/vignette.rds |binary inst/doc/FLLat_tutorial.R | 23 ++++-- inst/doc/FLLat_tutorial.pdf |binary inst/doc/FLLat_tutorial.rnw | 163 ++++++++++++++++++++++++++++--------------- man/FLLat.BIC.Rd | 43 +++++------ man/FLLat.FDR.Rd | 38 ++++------ man/FLLat.PVE.Rd | 66 ++++++++--------- man/FLLat.Rd | 75 ++++++++++--------- man/plot.FLLat.Rd | 57 +++++++-------- man/predict.FLLat.Rd |only man/simaCGH.Rd | 15 +++ src/Lat_L2.cpp | 59 ++++++++++++++- src/gen_lat_func.cpp | 6 + src/gen_lat_func.h | 4 - vignettes/FLLat_tutorial.rnw | 163 ++++++++++++++++++++++++++++--------------- 26 files changed, 522 insertions(+), 321 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto, Haruhisa Nagata
Maintainer: Kei Hirose <mail@keihirose.com>
Diff between fanc versions 1.23 dated 2015-03-27 and 1.25 dated 2015-09-16
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 4 R/fanc.R | 3 src/fanc.c | 2449 +++++++++++++++++++++++++++++------------------------------- 5 files changed, 1239 insertions(+), 1233 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, and full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 4.2 dated 2015-06-30 and 4.3 dated 2015-09-16
DESCRIPTION | 8 MD5 | 66 +- R/RcppExports.R | 28 - R/binomial.bymCAR.R | 44 + R/binomial.dissimilarityCAR.R | 46 +- R/binomial.iarCAR.R | 42 + R/binomial.independent.R | 42 + R/binomial.lerouxCAR.R | 908 ++++++++++++++++++++--------------------- R/binomial.localisedCAR.R | 5 R/gaussian.dissimilarityCAR.R | 53 +- R/gaussian.iarCAR.R | 54 +- R/gaussian.lerouxCAR.R | 46 +- R/poisson.bymCAR.R | 38 + R/poisson.dissimilarityCAR.R | 37 + R/poisson.iarCAR.R | 32 - R/poisson.independent.R | 36 + R/poisson.lerouxCAR.R | 41 + R/poisson.localisedCAR.R | 7 R/poisson.localisedCARagg.R | 7 R/print.carbayes.R | 18 build/vignette.rds |binary inst/doc/CARBayesvignette.Rnw | 16 inst/doc/CARBayesvignette.pdf |binary man/CARBayes-package.Rd | 7 man/S.CARbym.Rd | 8 man/S.CARdissimilarity.Rd | 8 man/S.CARiar.Rd | 8 man/S.CARleroux.Rd | 8 man/S.CARlocalised.Rd | 9 man/S.independent.Rd | 8 src/CARBayes.cpp | 44 - src/RcppExports.cpp | 49 +- vignettes/CARBayesvignette.Rnw | 16 vignettes/jss996.bib | 4 34 files changed, 991 insertions(+), 752 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-8 dated 2015-08-11 and 0.2-10 dated 2015-09-16
arulesSequences-0.2-10/arulesSequences/CHANGELOG | 22 + arulesSequences-0.2-10/arulesSequences/DESCRIPTION | 8 arulesSequences-0.2-10/arulesSequences/MD5 | 45 +- arulesSequences-0.2-10/arulesSequences/NAMESPACE | 5 arulesSequences-0.2-10/arulesSequences/R/02sequences.R | 81 ++-- arulesSequences-0.2-10/arulesSequences/R/03rules.R | 8 arulesSequences-0.2-10/arulesSequences/R/04parameter.R | 4 arulesSequences-0.2-10/arulesSequences/R/05read_write.R | 90 +++- arulesSequences-0.2-10/arulesSequences/R/10timed.R | 74 ++-- arulesSequences-0.2-10/arulesSequences/R/20support.R | 185 ++++++---- arulesSequences-0.2-10/arulesSequences/R/native.R | 3 arulesSequences-0.2-10/arulesSequences/data/zaki.rda |binary arulesSequences-0.2-10/arulesSequences/man/SPparameter-class.Rd | 2 arulesSequences-0.2-10/arulesSequences/man/cspade.Rd | 45 +- arulesSequences-0.2-10/arulesSequences/man/read_baskets.Rd | 29 + arulesSequences-0.2-10/arulesSequences/man/sequences-class.Rd | 1 arulesSequences-0.2-10/arulesSequences/man/support-methods.Rd | 46 +- arulesSequences-0.2-10/arulesSequences/src/cSPADE/sequence.cc | 2 arulesSequences-0.2-10/arulesSequences/src/idlists.c |only arulesSequences-0.2-10/arulesSequences/src/makebin.c | 15 arulesSequences-0.2-10/arulesSequences/tests/idlists.R |only arulesSequences-0.2-10/arulesSequences/tests/idlists.Rout.save |only arulesSequences-0.2-10/arulesSequences/tests/zaki.R | 10 arulesSequences-0.2-10/arulesSequences/tests/zaki.Rout.save | 34 + arulesSequences-0.2-8/arulesSequences/R/arules.R |only arulesSequences-0.2-8/arulesSequences/src/ptree.c |only 26 files changed, 458 insertions(+), 251 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.4 dated 2015-09-15 and 0.19.6 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/export_functions.r | 47 ++++++++++++++++++++++++++++++++++------------- inst/doc/sdcTable.pdf |binary 4 files changed, 40 insertions(+), 19 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.3.0 dated 2015-06-26 and 0.3.4 dated 2015-09-16
DESCRIPTION | 9 +++--- MD5 | 36 +++++++++++++++------------ NAMESPACE | 15 +++++++++-- R/rvertnet-package.R | 7 +++++ R/searchbyterm.R | 48 +++++++++++++++--------------------- R/vert_id.R |only R/vertmap.R | 4 ++- R/vertsearch.R | 6 ++-- R/vertsummary.R | 4 +-- R/yyy.R | 3 ++ R/zzz.R | 28 +++++++++++---------- README.md | 1 build/vignette.rds |binary man/searchbyterm.Rd | 20 +++++---------- man/vert_id.Rd |only man/vertsearch.Rd | 6 ++-- man/vertsummary.Rd | 4 +-- tests/testthat/test-searchbyterm.R | 6 ++-- tests/testthat/test-spatialsearch.R | 6 ++-- tests/testthat/test-vertmap.R |only tests/testthat/test-vertsummary.R |only 21 files changed, 109 insertions(+), 94 deletions(-)
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.5.2 dated 2015-08-05 and 0.5.4 dated 2015-09-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ build/vignette.rds |binary tests/testthat/test-fulltext.R | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.3 dated 2015-08-13 and 0.5 dated 2015-09-16
provenance-0.3/provenance/man/KS.dist.Rd |only provenance-0.3/provenance/man/SH.dist.Rd |only provenance-0.3/provenance/man/dist.Rd |only provenance-0.3/provenance/man/getKDE.Rd |only provenance-0.3/provenance/man/getKDEs.Rd |only provenance-0.3/provenance/man/getMDS.Rd |only provenance-0.3/provenance/man/getPCA.Rd |only provenance-0.3/provenance/man/plot.DZdata.Rd |only provenance-0.3/provenance/man/plot.HMdata.Rd |only provenance-0.3/provenance/man/read.DZdata.Rd |only provenance-0.3/provenance/man/read.HMdata.Rd |only provenance-0.3/provenance/man/subset.Rd |only provenance-0.3/provenance/man/ternaryplot.Rd |only provenance-0.5/provenance/DESCRIPTION | 10 provenance-0.5/provenance/MD5 | 82 - provenance-0.5/provenance/NAMESPACE | 58 provenance-0.5/provenance/R/botev.R |only provenance-0.5/provenance/R/documentation.R |only provenance-0.5/provenance/R/kde.R |only provenance-0.5/provenance/R/minsorting.R |only provenance-0.5/provenance/R/plot.R |only provenance-0.5/provenance/R/provenance.R | 1259 ++++------------- provenance-0.5/provenance/R/sircombe.R |only provenance-0.5/provenance/R/srd.R |only provenance-0.5/provenance/data |only provenance-0.5/provenance/inst/HM.csv | 34 provenance-0.5/provenance/inst/PT.csv | 34 provenance-0.5/provenance/inst/PTHM.csv |only provenance-0.5/provenance/inst/densities.csv |only provenance-0.5/provenance/inst/endmembers.csv |only provenance-0.5/provenance/man/KDE.Rd |only provenance-0.5/provenance/man/KDEs.Rd |only provenance-0.5/provenance/man/KS.diss.Rd |only provenance-0.5/provenance/man/MDS.Rd |only provenance-0.5/provenance/man/Namib.Rd |only provenance-0.5/provenance/man/PCA.Rd |only provenance-0.5/provenance/man/SH.diss.Rd |only provenance-0.5/provenance/man/amalgamate.Rd |only provenance-0.5/provenance/man/botev.Rd | 4 provenance-0.5/provenance/man/bray.diss.Rd |only provenance-0.5/provenance/man/clr.Rd | 21 provenance-0.5/provenance/man/densities.Rd |only provenance-0.5/provenance/man/diss.Rd |only provenance-0.5/provenance/man/endmembers.Rd |only provenance-0.5/provenance/man/get.n.Rd | 4 provenance-0.5/provenance/man/indscal.Rd | 9 provenance-0.5/provenance/man/minsorting.Rd |only provenance-0.5/provenance/man/plot.GPA.Rd | 10 provenance-0.5/provenance/man/plot.INDSCAL.Rd | 10 provenance-0.5/provenance/man/plot.KDE.Rd | 14 provenance-0.5/provenance/man/plot.MDS.Rd | 9 provenance-0.5/provenance/man/plot.PCA.Rd | 10 provenance-0.5/provenance/man/plot.compositional.Rd |only provenance-0.5/provenance/man/plot.distributional.Rd |only provenance-0.5/provenance/man/plot.minsorting.Rd |only provenance-0.5/provenance/man/plot.ternary.Rd |only provenance-0.5/provenance/man/procrustes.Rd | 9 provenance-0.5/provenance/man/read.compositional.Rd |only provenance-0.5/provenance/man/read.densities.Rd |only provenance-0.5/provenance/man/read.distributional.Rd |only provenance-0.5/provenance/man/restore.Rd |only provenance-0.5/provenance/man/subset.compositional.Rd |only provenance-0.5/provenance/man/subset.distributional.Rd |only provenance-0.5/provenance/man/summaryplot.Rd | 19 provenance-0.5/provenance/man/ternary.Rd |only 65 files changed, 553 insertions(+), 1043 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.5.9 dated 2015-09-08 and 0.6.0 dated 2015-09-16
PRIMsrc-0.5.9/PRIMsrc/inst/doc/PRIMsrc_0.5.9.pdf |only PRIMsrc-0.6.0/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.0/PRIMsrc/MD5 | 16 - PRIMsrc-0.6.0/PRIMsrc/R/PRIMsrc.internal.r | 54 +++--- PRIMsrc-0.6.0/PRIMsrc/R/PRIMsrc.r | 191 +++++++++-------------- PRIMsrc-0.6.0/PRIMsrc/inst/NEWS | 39 +++- PRIMsrc-0.6.0/PRIMsrc/inst/doc/PRIMsrc_0.6.0.pdf |only PRIMsrc-0.6.0/PRIMsrc/man/plot_boxtrace.Rd | 4 PRIMsrc-0.6.0/PRIMsrc/man/plot_boxtraj.Rd | 4 PRIMsrc-0.6.0/PRIMsrc/man/sbh.Rd | 22 +- 10 files changed, 159 insertions(+), 179 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Description: Evaluation of diversity in peptide libraries, including NNN, NNB,
NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined.
Metrics for evaluation include expected coverage, relative efficiency, and
the functional diversity of the library. Peptide-level inclusion
probabilities are computable for both the native and custom encoding
schemes.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Diff between peptider versions 0.2 dated 2015-04-11 and 0.2.2 dated 2015-09-16
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++++---------------------- NAMESPACE | 5 +++- R/peptider.r | 7 +++++ R/tabulate.r | 1 man/BLOSUM80.Rd | 2 - man/codons.Rd | 2 - man/coverage.Rd | 2 - man/detect.Rd | 2 - man/diversity.Rd | 2 - man/efficiency.Rd | 2 - man/encodingReduce.Rd | 2 - man/genNeighbors.Rd | 2 - man/genNeighbors_reduced.Rd | 2 - man/generateCustom.Rd | 2 - man/generateCustomLib.Rd | 2 - man/generateCustomNei.Rd | 2 - man/generateCustomProbs.Rd | 2 - man/getChoices.Rd | 2 - man/getCounts.Rd | 2 - man/getNeighbors.Rd | 2 - man/getNofNeighbors.Rd | 2 - man/libBuild.Rd | 2 - man/libscheme.Rd | 2 - man/makowski.Rd | 2 - man/ppeptide.Rd | 2 - man/scheme.Rd | 2 - man/schemes.Rd | 2 - 28 files changed, 66 insertions(+), 55 deletions(-)
Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the
'IRIS DMC MUSTANG' project. The functionality in this package
builds upon the base classes of the 'IrisSeismic' package.
Metrics include basic statistics as well as higher level
'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut, cre],
Rob Casey [aut],
Mary Templeton [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between IRISMustangMetrics versions 1.0.0 dated 2015-08-02 and 1.0.1 dated 2015-09-16
IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/PSDMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/crossCorrelationMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/R/transferFunctionMetrics.R |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/PSDMetrics.Rd |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/crossCorrelationMetrics.Rd |only IRISMustangMetrics-1.0.0/IRISMustangMetrics/man/transferFunctionMetrics.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/DESCRIPTION | 12 +++--- IRISMustangMetrics-1.0.1/IRISMustangMetrics/MD5 | 18 +++++----- IRISMustangMetrics-1.0.1/IRISMustangMetrics/NAMESPACE | 6 +-- IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/PSDMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/correlationMetric.R | 8 +--- IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/crossCorrelationMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/R/transferFunctionMetric.R |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/PSDMetric.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/crossCorrelationMetric.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/transferFunctionMetric.Rd |only 16 files changed, 21 insertions(+), 23 deletions(-)
More information about IRISMustangMetrics at CRAN
Permanent link
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Tuo Zhao, Xingguo Li, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman
Maintainer: Tuo Zhao <tzhao5@jhu.edu>
Diff between huge versions 1.2.6 dated 2014-02-28 and 1.2.7 dated 2015-09-16
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 8 ++++++-- R/huge.generator.R | 2 +- build/vignette.rds |binary man/huge-package.Rd | 6 +++--- man/huge.Rd | 24 ++++++++++++------------ man/huge.select.Rd | 4 ++-- src/SFGen.c | 18 +++++++++++------- 9 files changed, 50 insertions(+), 42 deletions(-)
Title: Create and Manipulate Discrete Random Variables
Description: Create, manipulate, transform, and simulate from discrete random
variables. The syntax is modeled after that which is used in mathematical
statistics and probability courses, but with powerful support for more
advanced probability calculations. This includes the creation of joint
random variables, and the derivation and manipulation of their conditional
and marginal distributions.
Author: Andreas Buja [aut],
Eric Hare [aut, cre],
Heike Hofmann [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Diff between discreteRV versions 1.2.1 dated 2015-05-03 and 1.2.2 dated 2015-09-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 10 ++++++++++ R/discreteRV-Probabilities.r | 14 ++++++++++++++ R/discreteRV-Simulations.r | 1 + build/vignette.rds |binary inst/doc/discreteRV.html | 14 +++++++------- 7 files changed, 41 insertions(+), 16 deletions(-)
Title: Desirability Functions for Ranking, Selecting, and Integrating
Data
Description: Functions for (1) ranking, selecting, and prioritising genes,
proteins, and metabolites from high dimensional biology experiments, (2)
multivariate hit calling in high content screens, and (3) combining data
from diverse sources.
Author: Stanley E. Lazic
Maintainer: Stanley E. Lazic <stan.lazic@cantab.net>
Diff between desiR versions 1.0 dated 2015-06-16 and 1.1 dated 2015-09-16
DESCRIPTION | 16 +++++++++------- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 1 + R/d.central.R | 9 +++++---- R/d.ends.R | 7 ++++--- R/d.high.R | 6 +++--- R/d.low.R | 6 +++--- R/des.line.R | 40 +++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/Gene_ranking.R | 14 +++++++------- inst/doc/Gene_ranking.Rmd | 22 ++++++++++------------ inst/doc/Gene_ranking.pdf |binary man/d.central.Rd | 9 +++++---- man/d.ends.Rd | 7 ++++--- man/d.high.Rd | 6 +++--- man/d.low.Rd | 6 +++--- man/des.line.Rd | 14 ++++++++++---- vignettes/Gene_ranking.Rmd | 22 ++++++++++------------ vignettes/Gene_ranking.html |only 19 files changed, 120 insertions(+), 100 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic barcode data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.2.6 dated 2015-04-18 and 0.3.0 dated 2015-09-16
DESCRIPTION | 13 LICENSE | 4 MD5 | 39 +- NAMESPACE | 3 NEWS | 11 R/bold-package.R | 39 +- R/bold_seq.R | 2 R/bold_seqspec.R | 4 R/bold_specimens.R | 8 README.md | 48 +-- build/vignette.rds |binary inst/doc/bold_vignette.Rmd | 440 +++++++++++++++++++++++++++++++ inst/doc/bold_vignette.html | 493 +++++++++++++++++------------------ man/bold-package.Rd | 29 +- man/bold_seq.Rd | 2 man/bold_seqspec.Rd | 4 man/bold_specimens.Rd | 6 man/sequences.Rd | 9 tests/test-all.R |only tests/testthat/test-bold_specimens.R | 2 vignettes/bold_vignette.Rmd | 440 +++++++++++++++++++++++++++++++ 21 files changed, 1248 insertions(+), 348 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.1-5 dated 2015-02-10 and 1.2-5 dated 2015-09-16
asbio-1.1-5/asbio/R/boostrap.r |only asbio-1.2-5/asbio/DESCRIPTION | 12 +- asbio-1.2-5/asbio/MD5 | 80 ++++++++------- asbio-1.2-5/asbio/NAMESPACE | 15 ++ asbio-1.2-5/asbio/R/book.menu.r | 144 +++++++++++++-------------- asbio-1.2-5/asbio/R/bootstrap.r |only asbio-1.2-5/asbio/R/bv.boxplot.R | 4 asbio-1.2-5/asbio/R/ci.boot.r | 4 asbio-1.2-5/asbio/R/ci.impt.R |only asbio-1.2-5/asbio/R/pairw.kw.R | 2 asbio-1.2-5/asbio/R/samp.dist.mech.tck.r | 4 asbio-1.2-5/asbio/R/see.logic.r | 12 +- asbio-1.2-5/asbio/R/sefltest.typeIISS.R |only asbio-1.2-5/asbio/R/selftest.ANOVAmixed.R |only asbio-1.2-5/asbio/R/selftest.ANOVAsiminf.R |only asbio-1.2-5/asbio/R/selftest.H0.R |only asbio-1.2-5/asbio/R/selftest.corr.R |only asbio-1.2-5/asbio/R/selftest.regapproaches.R |only asbio-1.2-5/asbio/R/selftest.regdiag.R |only asbio-1.2-5/asbio/R/selftest.stats.tck.R | 2 asbio-1.2-5/asbio/build/vignette.rds |binary asbio-1.2-5/asbio/data/mule.sel.rda |only asbio-1.2-5/asbio/data/potato.rda |binary asbio-1.2-5/asbio/man/C.isotope.rd | 2 asbio-1.2-5/asbio/man/DH.test.rd | 6 - asbio-1.2-5/asbio/man/Mode.rd | 2 asbio-1.2-5/asbio/man/PCB.rd | 2 asbio-1.2-5/asbio/man/agrostis.rd | 2 asbio-1.2-5/asbio/man/anm.mc.bvn.rd | 2 asbio-1.2-5/asbio/man/ant.dew.rd | 2 asbio-1.2-5/asbio/man/baby.walk.Rd | 6 - asbio-1.2-5/asbio/man/bayes.lm.rd | 4 asbio-1.2-5/asbio/man/bin2dec.rd | 2 asbio-1.2-5/asbio/man/bootstrap.rd | 2 asbio-1.2-5/asbio/man/bplot.rd | 2 asbio-1.2-5/asbio/man/bv.boxplot.Rd | 11 +- asbio-1.2-5/asbio/man/ci.impt.Rd |only asbio-1.2-5/asbio/man/ci.mu.Rd | 2 asbio-1.2-5/asbio/man/corn.Rd | 2 asbio-1.2-5/asbio/man/depression.rd | 2 asbio-1.2-5/asbio/man/drugs.rd | 2 asbio-1.2-5/asbio/man/moose.sel.Rd | 3 asbio-1.2-5/asbio/man/pairw.kw.rd | 7 - asbio-1.2-5/asbio/man/see.ancova.tck.rd | 2 asbio-1.2-5/asbio/man/see.mixedII.rd | 9 + asbio-1.2-5/asbio/man/selftest.se.tck1.rd | 13 ++ asbio-1.2-5/asbio/man/skew.kurt.rd | 4 47 files changed, 207 insertions(+), 163 deletions(-)
Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression', adapted to model the association between an HPO-encoded patient phenotype and binary genotype. A `no association' model is compared with one in which the log odds of having a rare genotype is linked to the semantic similarity between patient phenotype and a latent characteristic phenotype. The method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 1.1 dated 2015-08-27 and 1.2 dated 2015-09-15
DESCRIPTION | 8 - MD5 | 36 +++---- R/functions.R | 43 ++++---- R/plots.R | 4 R/simReg.R | 42 +++++--- man/get.term.term.matrix.Rd | 6 + man/hpo.plot.marginal.freqs.Rd | 8 + man/sim.reg.Rd | 9 + man/sim.reg.full.summary.Rd | 4 src/Chain.cpp | 45 ++------- src/DeltaLikelihood.cpp | 32 +++--- src/DeltaLikelihood.h | 4 src/Likelihood.cpp | 7 - src/Likelihood.h | 4 src/RcppExports.cpp | 169 +++++++++++++++++++++------------- src/RcppExports.h | 11 +- src/State.cpp | 55 ++++++++--- src/State.h | 47 +++++++-- src/Update.cpp | 203 ++++++++++++++++++++++++++++++----------- 19 files changed, 474 insertions(+), 263 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 1.1.5 dated 2015-09-03 and 2.0.0 dated 2015-09-15
RNiftyReg-1.1.5/RNiftyReg/inst/extdata/source.nii.gz |only RNiftyReg-1.1.5/RNiftyReg/inst/extdata/target.nii.gz |only RNiftyReg-1.1.5/RNiftyReg/man/convertAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/getDeformationField.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformVoxelToWorld.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformWithAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformWithControlPoints.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/xformToAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_KLdivergence.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_KLdivergence.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_aladin.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_aladin.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_blockMatching.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_blockMatching.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d_sym.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d_sym.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_femTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_femTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_globalTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_globalTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation_be.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation_jac.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_macros.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_maths.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_maths.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_mutualinformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_mutualinformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_resampling.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_resampling.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_ssd.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_ssd.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_tools.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_tools.h |only RNiftyReg-1.1.5/RNiftyReg/src/exit.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/exit.h |only RNiftyReg-1.1.5/RNiftyReg/src/index.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/index.h |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1.h |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1_io.c |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1_io.h |only RNiftyReg-1.1.5/RNiftyReg/src/niftyreg.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/niftyreg.h |only RNiftyReg-1.1.5/RNiftyReg/src/print.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/substitutions.h |only RNiftyReg-1.1.5/RNiftyReg/src/znzlib.c |only RNiftyReg-1.1.5/RNiftyReg/src/znzlib.h |only RNiftyReg-2.0.0/RNiftyReg/DESCRIPTION | 20 RNiftyReg-2.0.0/RNiftyReg/MD5 | 239 ++- RNiftyReg-2.0.0/RNiftyReg/NAMESPACE | 55 RNiftyReg-2.0.0/RNiftyReg/NEWS | 40 RNiftyReg-2.0.0/RNiftyReg/R/affine.R | 377 ++++- RNiftyReg-2.0.0/RNiftyReg/R/image.R |only RNiftyReg-2.0.0/RNiftyReg/R/nifti.R |only RNiftyReg-2.0.0/RNiftyReg/R/niftyreg.R | 725 +++++----- RNiftyReg-2.0.0/RNiftyReg/R/transform.R | 267 ++- RNiftyReg-2.0.0/RNiftyReg/R/xform.R | 110 + RNiftyReg-2.0.0/RNiftyReg/R/zzz.R | 12 RNiftyReg-2.0.0/RNiftyReg/README.md |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/affine.txt | 8 RNiftyReg-2.0.0/RNiftyReg/inst/extdata/control.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/epi_t2.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/flash_t1.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house.png |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house_colour.png |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house_colour_large.jpg |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/mni_brain.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/man/affine.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/applyTransform.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/buildAffine.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/composeTransforms.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/decomposeAffine.Rd | 69 RNiftyReg-2.0.0/RNiftyReg/man/deformationField.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/dumpNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/forward.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/halfTransform.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/internalImage.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/invertAffine.Rd | 31 RNiftyReg-2.0.0/RNiftyReg/man/isImage.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/jacobian.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/ndim.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.Rd | 132 + RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.linear.Rd | 165 +- RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.nonlinear.Rd | 188 +- RNiftyReg-2.0.0/RNiftyReg/man/pixdim.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/readAffine.Rd | 47 RNiftyReg-2.0.0/RNiftyReg/man/readNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/updateNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/voxelToWorld.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/writeAffine.Rd | 28 RNiftyReg-2.0.0/RNiftyReg/man/writeNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/xform.Rd |only RNiftyReg-2.0.0/RNiftyReg/src/AffineMatrix.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/AffineMatrix.h |only RNiftyReg-2.0.0/RNiftyReg/src/DeformationField.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/DeformationField.h |only RNiftyReg-2.0.0/RNiftyReg/src/Makevars | 20 RNiftyReg-2.0.0/RNiftyReg/src/NiftiImage.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/NiftiImage.h |only RNiftyReg-2.0.0/RNiftyReg/src/aladin.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/aladin.h |only RNiftyReg-2.0.0/RNiftyReg/src/config.h |only RNiftyReg-2.0.0/RNiftyReg/src/f3d.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/f3d.h |only RNiftyReg-2.0.0/RNiftyReg/src/main.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/niftilib |only RNiftyReg-2.0.0/RNiftyReg/src/print.h | 29 RNiftyReg-2.0.0/RNiftyReg/src/reg-lib |only RNiftyReg-2.0.0/RNiftyReg/src/zlib |only RNiftyReg-2.0.0/RNiftyReg/src/znzlib |only RNiftyReg-2.0.0/RNiftyReg/tests |only 114 files changed, 1704 insertions(+), 858 deletions(-)
Title: Simulation and Estimation of Log-GARCH Models
Description: Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between lgarch versions 0.5 dated 2014-09-01 and 0.6-2 dated 2015-09-15
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS | 25 +++++++++++++++++++++---- R/lgarch.R | 49 +++++++++++++++++++++++++++++++++++++++---------- R/lgarchSim.R | 4 ++-- R/rss.R | 11 ++++++++--- R/summary.lgarch.R | 3 ++- man/lgarch-package.Rd | 4 ++-- 9 files changed, 89 insertions(+), 36 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing
and/or imputed values are introduced, which can be used for exploring the data and the
structure of the missing and/or imputed values. Depending on this structure
of the missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.3.0 dated 2015-07-07 and 4.4.1 dated 2015-09-15
DESCRIPTION | 30 +++++++++++++++--------------- MD5 | 20 ++++++++++---------- NEWS | 3 +++ R/colormapMiss.R | 2 +- R/hotdeck.R | 17 +++++++++++++++-- data/SBS5242.rda |binary data/chorizonDL.rda |binary data/kola.background.rda |binary data/sleep.rda |binary data/tao.rda |binary data/testdata.RData |binary 11 files changed, 44 insertions(+), 28 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus, and PHAT.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, Vincent Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan Reininghaus.
Maintainer: Jisu Kim <jisuk1@andrew.cmu.edu>
Diff between TDA versions 1.3 dated 2014-12-22 and 1.4 dated 2015-09-15
TDA-1.3/TDA/R/ripsArbitDiag.R |only TDA-1.3/TDA/R/ripsL2Diag.R |only TDA-1.3/TDA/src/boost/aligned_storage.hpp |only TDA-1.3/TDA/src/boost/archive |only TDA-1.3/TDA/src/boost/array.hpp |only TDA-1.3/TDA/src/boost/assert.hpp |only TDA-1.3/TDA/src/boost/bind |only TDA-1.3/TDA/src/boost/bind.hpp |only TDA-1.3/TDA/src/boost/blank.hpp |only TDA-1.3/TDA/src/boost/blank_fwd.hpp |only TDA-1.3/TDA/src/boost/call_traits.hpp |only TDA-1.3/TDA/src/boost/checked_delete.hpp |only TDA-1.3/TDA/src/boost/compressed_pair.hpp |only TDA-1.3/TDA/src/boost/concept |only TDA-1.3/TDA/src/boost/concept_archetype.hpp |only TDA-1.3/TDA/src/boost/concept_check |only TDA-1.3/TDA/src/boost/concept_check.hpp |only TDA-1.3/TDA/src/boost/config |only TDA-1.3/TDA/src/boost/config.hpp |only TDA-1.3/TDA/src/boost/container |only TDA-1.3/TDA/src/boost/cstdint.hpp |only TDA-1.3/TDA/src/boost/current_function.hpp |only TDA-1.3/TDA/src/boost/detail |only TDA-1.3/TDA/src/boost/exception |only TDA-1.3/TDA/src/boost/foreach.hpp |only TDA-1.3/TDA/src/boost/foreach_fwd.hpp |only TDA-1.3/TDA/src/boost/function |only TDA-1.3/TDA/src/boost/function.hpp |only TDA-1.3/TDA/src/boost/function_equal.hpp |only TDA-1.3/TDA/src/boost/function_output_iterator.hpp |only TDA-1.3/TDA/src/boost/function_types |only TDA-1.3/TDA/src/boost/functional |only TDA-1.3/TDA/src/boost/get_pointer.hpp |only TDA-1.3/TDA/src/boost/graph |only TDA-1.3/TDA/src/boost/implicit_cast.hpp |only TDA-1.3/TDA/src/boost/indirect_reference.hpp |only TDA-1.3/TDA/src/boost/integer |only TDA-1.3/TDA/src/boost/integer.hpp |only TDA-1.3/TDA/src/boost/integer_fwd.hpp |only TDA-1.3/TDA/src/boost/integer_traits.hpp |only TDA-1.3/TDA/src/boost/intrusive |only TDA-1.3/TDA/src/boost/intrusive_ptr.hpp |only TDA-1.3/TDA/src/boost/io |only TDA-1.3/TDA/src/boost/io_fwd.hpp |only TDA-1.3/TDA/src/boost/iostreams |only TDA-1.3/TDA/src/boost/is_placeholder.hpp |only TDA-1.3/TDA/src/boost/iterator |only TDA-1.3/TDA/src/boost/iterator.hpp |only TDA-1.3/TDA/src/boost/iterator_adaptors.hpp |only TDA-1.3/TDA/src/boost/lambda |only TDA-1.3/TDA/src/boost/limits.hpp |only TDA-1.3/TDA/src/boost/math |only TDA-1.3/TDA/src/boost/math_fwd.hpp |only TDA-1.3/TDA/src/boost/mem_fn.hpp |only TDA-1.3/TDA/src/boost/memory_order.hpp |only TDA-1.3/TDA/src/boost/move |only TDA-1.3/TDA/src/boost/mpl |only TDA-1.3/TDA/src/boost/multi_index/composite_key.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/access_specifier.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/adl_swap.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/archive_constructed.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/auto_space.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/base_type.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/bidir_node_iterator.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/bucket_array.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/converter.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/copy_map.hpp |only 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Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing. Latest version can be found at github/DeveauP/QuantumClone .
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 0.6.15 dated 2015-06-12 and 0.9.15 dated 2015-09-15
DESCRIPTION | 6 - MD5 | 76 +++++++-------- NAMESPACE | 32 +++--- R/EM.R | 29 ++++- R/QuantumClone_v3.R | 24 ++++ man/BIC_criterion.Rd | 36 +++---- man/CellularitiesFromFreq.Rd | 76 +++++++-------- man/Cluster_plot_from_cell.Rd | 92 +++++++++--------- man/EM.algo.Rd | 54 +++++----- man/EM_clustering.Rd | 68 ++++++------- man/From_freq_to_cell.Rd | 74 +++++++------- man/FullEM.Rd | 56 +++++------ man/Multitest.Rd | 116 +++++++++++------------ man/One_D_plot.Rd | 40 ++++---- man/One_step_clustering.Rd | 153 +++++++++++++++--------------- man/Patient_schrodinger_cellularities.Rd | 56 +++++------ man/Probability.to.belong.to.clone.Rd | 64 ++++++------ man/QuantumCat.Rd | 80 ++++++++-------- man/QuantumClone.Rd | 154 +++++++++++++++---------------- man/ThreeD_plot.Rd | 68 ++++++------- man/Tree_generation.Rd | 42 ++++---- man/add_leaf_list.Rd | 52 +++++----- man/create_priors.Rd | 40 ++++---- man/e.step.Rd | 48 ++++----- man/filter_on_fik.Rd | 36 +++---- man/find_x_position.Rd | 44 ++++---- man/hard.clustering.Rd | 36 +++---- man/is_included.Rd | 40 ++++---- man/list_prod.Rd | 46 ++++----- man/longueur.Rd | 40 ++++---- man/m.step.Rd | 60 ++++++------ man/manual_plot_trees.Rd | 48 ++++----- man/multiplot_trees.Rd | 44 ++++---- man/parallelEM.Rd | 66 ++++++------- man/phylo_tree_generation.Rd | 40 ++++---- man/plot_cell_from_Return_out.Rd | 44 ++++---- man/plot_with_margins_densities.Rd | 62 ++++++------ man/statistics_on_Multitest.Rd | 122 ++++++++++++------------ man/strcount.Rd | 42 ++++---- 39 files changed, 1171 insertions(+), 1135 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implement the pathwise calibrated sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear regression, sparse logistic regression, and sparse undirected graphical model estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. Moreover, users can choose different regularizers, including L1, MCP, and SCAD regularizers. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>
Diff between picasso versions 0.3.0 dated 2014-10-18 and 0.4.7 dated 2015-09-15
picasso-0.3.0/picasso/R/glasso.R |only picasso-0.3.0/picasso/R/lasso.R |only picasso-0.3.0/picasso/R/logit.gr.orth.R |only picasso-0.3.0/picasso/R/mvr.orth.R |only picasso-0.3.0/picasso/R/picasso.mvr.R |only picasso-0.3.0/picasso/R/scio.R |only picasso-0.3.0/picasso/man/print.mvr.Rd |only picasso-0.3.0/picasso/src/mymath.c |only picasso-0.3.0/picasso/src/picasso_group_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_group_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_group_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_group_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_lasso_cyclic.c |only picasso-0.3.0/picasso/src/picasso_lasso_cyclic0.c |only picasso-0.3.0/picasso/src/picasso_lasso_greedy.c |only picasso-0.3.0/picasso/src/picasso_lasso_prox.c |only picasso-0.3.0/picasso/src/picasso_lasso_stoc.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_scio_cyclic.c |only picasso-0.3.0/picasso/src/picasso_scio_greedy.c |only picasso-0.3.0/picasso/src/picasso_scio_prox.c |only picasso-0.3.0/picasso/src/picasso_scio_stoc.c |only picasso-0.4.7/picasso/DESCRIPTION | 13 picasso-0.4.7/picasso/MD5 | 62 -- picasso-0.4.7/picasso/NAMESPACE | 6 picasso-0.4.7/picasso/R/lasso.sc.cov.R |only picasso-0.4.7/picasso/R/lasso.sc.naive.R |only picasso-0.4.7/picasso/R/logit.R | 352 +++++++-------- picasso-0.4.7/picasso/R/picasso.R | 50 +- picasso-0.4.7/picasso/R/picasso.lasso.R | 305 +++--------- picasso-0.4.7/picasso/R/picasso.logit.R | 225 ++------- picasso-0.4.7/picasso/R/picasso.scio.R | 80 +-- picasso-0.4.7/picasso/R/scio.sc.R |only picasso-0.4.7/picasso/man/picasso-package.Rd | 6 picasso-0.4.7/picasso/man/picasso.Rd | 108 +--- picasso-0.4.7/picasso/man/predict.logit.Rd | 2 picasso-0.4.7/picasso/src/lambda_max.c |only picasso-0.4.7/picasso/src/mymath.h | 63 ++ picasso-0.4.7/picasso/src/mymath1.c |only picasso-0.4.7/picasso/src/picasso_lasso_sc_cov.c |only picasso-0.4.7/picasso/src/picasso_lasso_sc_naive.c |only picasso-0.4.7/picasso/src/picasso_logit_cyclic.c | 22 picasso-0.4.7/picasso/src/picasso_scio_sc.c |only picasso-0.4.7/picasso/src/standardize_design.c |only 51 files changed, 518 insertions(+), 776 deletions(-)
Title: Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between ClusterStability versions 1.0.0 dated 2015-09-14 and 1.0.1 dated 2015-09-15
ClusterStability-1.0.0/ClusterStability/src/Makevars |only ClusterStability-1.0.1/ClusterStability/DESCRIPTION | 10 +++++----- ClusterStability-1.0.1/ClusterStability/MD5 | 6 +++--- ClusterStability-1.0.1/ClusterStability/NEWS |only ClusterStability-1.0.1/ClusterStability/man/ClusterStability-package.Rd | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
More information about ClusterStability at CRAN
Permanent link
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between BBEST versions 0.1-4 dated 2015-04-06 and 0.1-5 dated 2015-09-15
DESCRIPTION | 10 MD5 | 6 NAMESPACE | 4 README.md | 704 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 363 insertions(+), 361 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-2 dated 2015-07-01 and 1.0-4 dated 2015-09-15
DESCRIPTION | 11 MD5 | 14 - R/AAA_helpers.R | 20 - R/graph.R | 6 R/groupedmatrix.R | 677 ++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/NEWS | 8 inst/doc/arulesViz.pdf |binary 8 files changed, 368 insertions(+), 368 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.1-9 dated 2015-07-14 and 1.2-0 dated 2015-09-15
arules-1.1-9/arules/tests/associations.R |only arules-1.1-9/arules/tests/associations.Rout.save |only arules-1.1-9/arules/tests/extract.R |only arules-1.1-9/arules/tests/extract.Rout.save |only arules-1.1-9/arules/tests/interfaces.R |only arules-1.1-9/arules/tests/interfaces.Rout.save |only arules-1.1-9/arules/tests/itemMatrix.R |only arules-1.1-9/arules/tests/itemMatrix.Rout.save |only arules-1.1-9/arules/tests/matrix.R |only arules-1.1-9/arules/tests/matrix.Rout.save |only arules-1.1-9/arules/tests/measures.R |only arules-1.1-9/arules/tests/measures.Rout.save |only arules-1.1-9/arules/tests/sets.R |only arules-1.1-9/arules/tests/sets.Rout.save |only arules-1.1-9/arules/tests/transactions.R |only arules-1.1-9/arules/tests/transactions.Rout.save |only arules-1.2-0/arules/DESCRIPTION | 9 arules-1.2-0/arules/MD5 | 113 ++-- arules-1.2-0/arules/NAMESPACE | 11 arules-1.2-0/arules/R/AAADefs.R | 26 + arules-1.2-0/arules/R/AllClasses.R | 84 ++- arules-1.2-0/arules/R/Matrix.R | 34 - arules-1.2-0/arules/R/associations.R | 14 arules-1.2-0/arules/R/eclat.R | 6 arules-1.2-0/arules/R/inspect.R | 483 ++++++++++-------- arules-1.2-0/arules/R/is.superset.R | 11 arules-1.2-0/arules/R/itemCoding.R | 6 arules-1.2-0/arules/R/itemFrequency.R | 341 ++++++------- arules-1.2-0/arules/R/itemMatrix.R | 592 +++++++++++------------ arules-1.2-0/arules/R/itemsets.R | 30 - arules-1.2-0/arules/R/random.transactions.R | 10 arules-1.2-0/arules/R/read_write.R | 13 arules-1.2-0/arules/R/rules.R | 9 arules-1.2-0/arules/R/support.R | 200 ++++--- arules-1.2-0/arules/R/tidLists.R | 347 +++++++------ arules-1.2-0/arules/R/transactions.R | 97 ++- arules-1.2-0/arules/R/warm.R |only arules-1.2-0/arules/data/Adult.rda |binary arules-1.2-0/arules/data/Epub.rda |binary arules-1.2-0/arules/data/Groceries.rda |binary arules-1.2-0/arules/data/Income.rda |binary arules-1.2-0/arules/data/SunBai.rda |only arules-1.2-0/arules/data/datalist |only arules-1.2-0/arules/inst/NEWS | 41 + arules-1.2-0/arules/inst/doc/arules.R | 4 arules-1.2-0/arules/inst/doc/arules.Rnw | 8 arules-1.2-0/arules/inst/doc/arules.pdf |binary arules-1.2-0/arules/inst/tests |only arules-1.2-0/arules/man/SunBai.Rd |only arules-1.2-0/arules/man/associations-class.Rd | 6 arules-1.2-0/arules/man/hits.Rd |only arules-1.2-0/arules/man/inspect.Rd | 8 arules-1.2-0/arules/man/itemFrequency.Rd | 4 arules-1.2-0/arules/man/itemFrequencyPlot.Rd | 4 arules-1.2-0/arules/man/itemMatrix-class.Rd | 36 - arules-1.2-0/arules/man/random.transactions.Rd | 18 arules-1.2-0/arules/man/rules-class.Rd | 5 arules-1.2-0/arules/man/sort.Rd | 25 arules-1.2-0/arules/man/support.Rd | 8 arules-1.2-0/arules/man/tidLists-class.Rd | 44 + arules-1.2-0/arules/man/transactions-class.Rd | 18 arules-1.2-0/arules/man/weclat.Rd |only arules-1.2-0/arules/src/similarity.c |only arules-1.2-0/arules/src/warm.c |only arules-1.2-0/arules/tests/testthat.R |only arules-1.2-0/arules/vignettes/arules.Rnw | 8 66 files changed, 1506 insertions(+), 1167 deletions(-)
Title: Interpolation of Irregularly and Regularly Spaced Data
Description: Several cubic spline interpolation methods of H. Akima for irregular and
regular gridded data are available through this package, both for the bivariate case
(irregular data: ACM 526 and ACM 761, regular data: ACM 433) and univariate case (ACM 697).
Linear interpolation of irregular gridded data is also covered by reusing D. J. Renkas
triangulation code which is part of Akimas Fortran code.
Author: Hiroshi Akima [aut, cph] (Fortran code (TOMS 526, 761, 697 and 433)),
Albrecht Gebhardt [aut, cre, cph] (R port (interp* functions), bicubic*
functions),
Thomas Petzold [ctb, cph] (aspline function),
Martin Maechler [ctb, cph] (interp2xyz function + enhancements),
YYYY Association for Computing Machinery, Inc. [cph] (covers code from
TOMS 526, 761, 697 and 433)
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between akima versions 0.5-11 dated 2013-09-16 and 0.5-12 dated 2015-09-15
akima-0.5-11/akima/ChangeLog |only akima-0.5-11/akima/PORTING |only akima-0.5-11/akima/src/ttidbs.f |only akima-0.5-12/akima/DESCRIPTION | 42 ++++++++++++++----- akima-0.5-12/akima/MD5 | 19 +++----- akima-0.5-12/akima/NAMESPACE | 9 ++++ akima-0.5-12/akima/R/interp.R | 82 +++++++++++++++++++++++++++----------- akima-0.5-12/akima/R/interpp.R | 44 +++++++++++++++++--- akima-0.5-12/akima/README | 76 ++++++++++++++++++++++++++++++++++- akima-0.5-12/akima/cleanup | 1 akima-0.5-12/akima/man/interp.Rd | 51 ++++++++++++++++++----- akima-0.5-12/akima/man/interpp.Rd | 80 +++++++++++++++++++++++++------------ 12 files changed, 315 insertions(+), 89 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.3 dated 2015-08-13 and 0.19.4 dated 2015-09-15
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- R/export_functions.r | 49 +++++++++++-------------------------------- R/methods_class_sdcProblem.r | 3 +- build/vignette.rds |binary inst/doc/sdcTable.pdf |binary src/suppMultDimTable.cpp | 15 +++++++++---- 7 files changed, 36 insertions(+), 51 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.2 dated 2015-08-25 and 0.2.1 dated 2015-09-15
DESCRIPTION | 6 MD5 | 31 +- NAMESPACE | 2 NEWS | 17 + R/misc.R | 12 - R/rhandsontable-package.R | 1 R/rhandsontable.R | 406 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/intro_rhandsontable.R | 39 +++ inst/doc/intro_rhandsontable.Rmd | 58 ++++- inst/doc/intro_rhandsontable.html | 154 +++++++++----- inst/htmlwidgets/rhandsontable.js | 127 ++--------- man/hot_col.Rd | 11 - man/hot_context_menu.Rd |only man/hot_table.Rd | 28 -- man/rhandsontable.Rd | 12 - vignettes/intro_rhandsontable.Rmd | 58 ++++- 17 files changed, 600 insertions(+), 362 deletions(-)
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using
various projection pursuit indices.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PPtreeViz versions 1.1.0 dated 2015-06-25 and 1.3.0 dated 2015-09-15
DESCRIPTION | 16 +++++++-------- MD5 | 46 ++++++++++++++++++++++----------------------- NAMESPACE | 1 R/Huberplot.R | 4 +-- R/LDAopt.R | 4 +-- R/PDAopt.R | 2 - R/PPclassNodeViz.R | 18 ++++++++++------- R/PPclassify.R | 7 +++--- R/PPoptViz.R | 6 ++--- R/PPtreeClass.R | 12 +++++------ R/plotPPtreeclass.R | 2 - R/predictPPtreeclass.R | 3 -- R/printPPtreeclass.R | 2 - man/Huber.plot.Rd | 4 +-- man/LDAopt.Rd | 4 +-- man/PDAopt.Rd | 2 - man/PP.Tree.class.Rd | 2 - man/PP.classify.Rd | 2 - man/PPclassNode.Viz.Rd | 2 - man/PPopt.Viz.Rd | 4 +-- man/plot.PPtreeclass.Rd | 2 - man/predict.PPtreeclass.Rd | 2 - man/print.PPtreeclass.Rd | 2 - src/PPoptimize.cpp | 4 +-- 24 files changed, 78 insertions(+), 75 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.0-9 dated 2013-08-17 and 1.1-0 dated 2015-09-15
ChangeLog | 4 ++ DESCRIPTION | 18 ++++++----- MD5 | 14 ++++---- NAMESPACE | 8 ++++ R/dens.R | 98 ++++++++++++++++++++++++++++++------------------------------ R/gen.R | 40 ++++++++++++------------ R/mixsmsn.R | 26 +++++++-------- R/utils.R | 14 ++++---- 8 files changed, 118 insertions(+), 104 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on
species' distributions and environmental variables as well as species' description
and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>
Diff between letsR versions 2.1 dated 2015-04-16 and 2.2 dated 2015-09-15
letsR-2.1/letsR/man/letsR.Rd |only letsR-2.2/letsR/DESCRIPTION | 12 - letsR-2.2/letsR/MD5 | 134 ++++++++------- letsR-2.2/letsR/NAMESPACE | 19 ++ letsR-2.2/letsR/R/letsR-package.R | 15 + letsR-2.2/letsR/R/lets_correl.R | 6 letsR-2.2/letsR/R/lets_iucn_historic.R | 127 +++++++------- letsR-2.2/letsR/R/lets_iucncont.R | 8 letsR-2.2/letsR/R/lets_presab.R | 24 +- letsR-2.2/letsR/R/lets_presab_birds.R | 23 +- letsR-2.2/letsR/R/lets_presab_grid.R |only letsR-2.2/letsR/R/lets_presab_points.R | 3 letsR-2.2/letsR/R/lets_subsetPAM.R |only letsR-2.2/letsR/R/unicas.R | 2 letsR-2.2/letsR/README.md | 4 letsR-2.2/letsR/inst/CITATION |only letsR-2.2/letsR/man/IUCN.Rd | 2 letsR-2.2/letsR/man/PAM.Rd | 2 letsR-2.2/letsR/man/Phyllomedusa.Rd | 2 letsR-2.2/letsR/man/PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/lets.addpoly.Rd | 2 letsR-2.2/letsR/man/lets.addvar.Rd | 2 letsR-2.2/letsR/man/lets.classvar.Rd | 2 letsR-2.2/letsR/man/lets.correl.Rd | 2 letsR-2.2/letsR/man/lets.distmat.Rd | 2 letsR-2.2/letsR/man/lets.field.Rd | 2 letsR-2.2/letsR/man/lets.gridirizer.Rd | 2 letsR-2.2/letsR/man/lets.iucn.Rd | 2 letsR-2.2/letsR/man/lets.iucn.ha.Rd | 2 letsR-2.2/letsR/man/lets.iucn.his.Rd | 2 letsR-2.2/letsR/man/lets.iucncont.Rd | 6 letsR-2.2/letsR/man/lets.maplizer.Rd | 2 letsR-2.2/letsR/man/lets.midpoint.Rd | 2 letsR-2.2/letsR/man/lets.overlap.Rd | 2 letsR-2.2/letsR/man/lets.pamcrop.Rd | 2 letsR-2.2/letsR/man/lets.presab.Rd | 17 + letsR-2.2/letsR/man/lets.presab.birds.Rd | 16 + letsR-2.2/letsR/man/lets.presab.grid.Rd |only letsR-2.2/letsR/man/lets.presab.points.Rd | 5 letsR-2.2/letsR/man/lets.rangesize.Rd | 2 letsR-2.2/letsR/man/lets.shFilter.Rd | 2 letsR-2.2/letsR/man/lets.subsetPAM.Rd |only letsR-2.2/letsR/man/lets.summarizer.Rd | 2 letsR-2.2/letsR/man/lets.transf.Rd | 2 letsR-2.2/letsR/man/letsR-package.Rd |only letsR-2.2/letsR/man/plot.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/print.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/print.summary.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/summary.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/temp.Rd | 2 letsR-2.2/letsR/tests/testthat/test-lets_addpoly.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_addvar.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_classvar.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_correl.R | 7 letsR-2.2/letsR/tests/testthat/test-lets_distmat.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_field.R | 12 - letsR-2.2/letsR/tests/testthat/test-lets_gridirizer.R | 2 letsR-2.2/letsR/tests/testthat/test-lets_iuccont.R |only letsR-2.2/letsR/tests/testthat/test-lets_iucn.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_iucn_ha.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_iucn_his.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_maplizer.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_midpoint.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_overlap.R | 14 - letsR-2.2/letsR/tests/testthat/test-lets_pamcrop.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_presab.R | 17 + letsR-2.2/letsR/tests/testthat/test-lets_presab_birds.R | 24 ++ letsR-2.2/letsR/tests/testthat/test-lets_presab_grid.R |only letsR-2.2/letsR/tests/testthat/test-lets_presab_points.R | 10 - letsR-2.2/letsR/tests/testthat/test-lets_rangesize.R | 14 - letsR-2.2/letsR/tests/testthat/test-lets_subsetPAM.R |only letsR-2.2/letsR/tests/testthat/test-lets_summarizer.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_transf.R |only letsR-2.2/letsR/tests/testthat/test-printplotsummary.R |only 74 files changed, 385 insertions(+), 256 deletions(-)
Title: Sean Lahman's Baseball Database
Description: Provides the tables from Sean Lahman's Baseball Database as a set of R data.frames.
It uses the data on pitching, hitting and fielding performance and other tables
from 1871 through 2014, as recorded in the 2015 version of the database.
Author: Michael Friendly [aut], Dennis Murphy [ctb], Martin Monkman [ctb], Chris Dalzell [cre, ctb]
Maintainer: Chris Dalzell <cdalzell@gmail.com>
Diff between Lahman versions 3.0-1 dated 2014-09-13 and 4.0-1 dated 2015-09-15
Lahman-3.0-1/Lahman/R/sysdata.rda |only Lahman-3.0-1/Lahman/data/SchoolsPlayers.RData |only Lahman-3.0-1/Lahman/inst/scripts/README.md |only Lahman-3.0-1/Lahman/inst/scripts/lahmanData.R |only Lahman-3.0-1/Lahman/man/SchoolsPlayers.Rd |only Lahman-4.0-1/Lahman/DESCRIPTION | 29 ++-- Lahman-4.0-1/Lahman/MD5 | 128 ++++++++++----------- Lahman-4.0-1/Lahman/NEWS | 11 - Lahman-4.0-1/Lahman/R/Label.R | 2 Lahman-4.0-1/Lahman/R/battingStats.R | 2 Lahman-4.0-1/Lahman/README.md |only Lahman-4.0-1/Lahman/data/AllstarFull.RData |binary Lahman-4.0-1/Lahman/data/Appearances.RData |binary Lahman-4.0-1/Lahman/data/AwardsManagers.RData |binary Lahman-4.0-1/Lahman/data/AwardsPlayers.RData |binary Lahman-4.0-1/Lahman/data/AwardsShareManagers.RData |binary Lahman-4.0-1/Lahman/data/AwardsSharePlayers.RData |binary Lahman-4.0-1/Lahman/data/Batting.RData |binary Lahman-4.0-1/Lahman/data/BattingPost.RData |binary Lahman-4.0-1/Lahman/data/CollegePlaying.RData |only Lahman-4.0-1/Lahman/data/Fielding.RData |binary Lahman-4.0-1/Lahman/data/FieldingOF.RData |binary Lahman-4.0-1/Lahman/data/FieldingPost.RData |binary Lahman-4.0-1/Lahman/data/HallOfFame.RData |binary Lahman-4.0-1/Lahman/data/LahmanData.RData |binary Lahman-4.0-1/Lahman/data/Managers.RData |binary Lahman-4.0-1/Lahman/data/ManagersHalf.RData |binary Lahman-4.0-1/Lahman/data/Master.RData |binary Lahman-4.0-1/Lahman/data/Pitching.RData |binary Lahman-4.0-1/Lahman/data/PitchingPost.RData |binary Lahman-4.0-1/Lahman/data/Salaries.RData |binary Lahman-4.0-1/Lahman/data/Schools.RData |binary Lahman-4.0-1/Lahman/data/SeriesPost.RData |binary Lahman-4.0-1/Lahman/data/Teams.RData |binary Lahman-4.0-1/Lahman/data/TeamsFranchises.RData |binary Lahman-4.0-1/Lahman/data/TeamsHalf.RData |binary Lahman-4.0-1/Lahman/data/battingLabels.RData |binary Lahman-4.0-1/Lahman/data/datalist | 2 Lahman-4.0-1/Lahman/data/fieldingLabels.RData |binary Lahman-4.0-1/Lahman/data/pitchingLabels.RData |binary Lahman-4.0-1/Lahman/demo/batting-summstats.R | 4 Lahman-4.0-1/Lahman/inst/scripts/LahmanData.R |only Lahman-4.0-1/Lahman/inst/scripts/compress-data.R |only Lahman-4.0-1/Lahman/inst/scripts/readLahman.R | 97 ++++++++------- Lahman-4.0-1/Lahman/man/AllstarFull.Rd | 4 Lahman-4.0-1/Lahman/man/Appearances.Rd | 5 Lahman-4.0-1/Lahman/man/AwardsManagers.Rd | 4 Lahman-4.0-1/Lahman/man/AwardsPlayers.Rd | 6 Lahman-4.0-1/Lahman/man/AwardsShareManagers.Rd | 4 Lahman-4.0-1/Lahman/man/Batting.Rd | 8 - Lahman-4.0-1/Lahman/man/BattingPost.Rd | 4 Lahman-4.0-1/Lahman/man/CollegePlaying.Rd |only Lahman-4.0-1/Lahman/man/Fielding.Rd | 4 Lahman-4.0-1/Lahman/man/FieldingOF.Rd | 2 Lahman-4.0-1/Lahman/man/FieldingPost.Rd | 4 Lahman-4.0-1/Lahman/man/HallOfFame.Rd | 4 Lahman-4.0-1/Lahman/man/Label.Rd | 9 - Lahman-4.0-1/Lahman/man/Lahman-package.Rd | 10 - Lahman-4.0-1/Lahman/man/LahmanData.Rd | 4 Lahman-4.0-1/Lahman/man/Managers.Rd | 4 Lahman-4.0-1/Lahman/man/ManagersHalf.Rd | 2 Lahman-4.0-1/Lahman/man/Master.Rd | 8 - Lahman-4.0-1/Lahman/man/Pitching.Rd | 4 Lahman-4.0-1/Lahman/man/PitchingPost.Rd | 4 Lahman-4.0-1/Lahman/man/Salaries.Rd | 2 Lahman-4.0-1/Lahman/man/Schools.Rd | 35 +++-- Lahman-4.0-1/Lahman/man/SeriesPost.Rd | 4 Lahman-4.0-1/Lahman/man/Teams.Rd | 4 Lahman-4.0-1/Lahman/man/TeamsFranchises.Rd | 2 Lahman-4.0-1/Lahman/man/TeamsHalf.Rd | 2 70 files changed, 213 insertions(+), 205 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install
packages as they existed on CRAN on a specific snapshot date as if you had
a CRAN time machine. To achieve reproducibility, the checkpoint() function
installs the packages required or called by your project and scripts to a
local library exactly as they existed at the specified point in time. Only
those packages are available to your project, thereby avoiding any package
updates that came later and may have altered your results. In this way,
anyone using checkpoint's checkpoint() can ensure the reproducibility of
your scripts or projects at any time. To create the snapshot archives, once
a day (at midnight UTC) Revolution Analytics refreshes the Austria CRAN mirror, on the "Managed
R Archived Network" server (http://mran.revolutionanalytics.com/).
Immediately after completion of the rsync mirror process, the process takes a
snapshot, thus creating the archive. Snapshot archives exist starting from
2014-09-17.
Author: Revolution Analytics
Maintainer: Andrie de Vries <adevries@microsoft.com>
Diff between checkpoint versions 0.3.10 dated 2015-04-27 and 0.3.15 dated 2015-09-15
checkpoint-0.3.10/checkpoint/tests/testthat/test-2-checkpoint.R |only checkpoint-0.3.15/checkpoint/DESCRIPTION | 12 checkpoint-0.3.15/checkpoint/MD5 | 38 +- checkpoint-0.3.15/checkpoint/NAMESPACE | 10 checkpoint-0.3.15/checkpoint/NEWS |only checkpoint-0.3.15/checkpoint/R/checkpoint-package.R | 10 checkpoint-0.3.15/checkpoint/R/checkpoint.R | 66 ++--- checkpoint-0.3.15/checkpoint/R/detach.R | 7 checkpoint-0.3.15/checkpoint/R/mranUrl.R |only checkpoint-0.3.15/checkpoint/R/scanRepoPackages.R | 50 ++- checkpoint-0.3.15/checkpoint/R/setSnapshot.R | 16 - checkpoint-0.3.15/checkpoint/build/vignette.rds |binary checkpoint-0.3.15/checkpoint/inst/examples/example_setSnapshot.R | 3 checkpoint-0.3.15/checkpoint/man/checkpoint-package.Rd | 4 checkpoint-0.3.15/checkpoint/man/checkpoint.Rd | 30 +- checkpoint-0.3.15/checkpoint/man/getValidSnapshots.Rd |only checkpoint-0.3.15/checkpoint/man/setSnapshot.Rd | 5 checkpoint-0.3.15/checkpoint/tests/test-all.R | 2 checkpoint-0.3.15/checkpoint/tests/testthat/test-0-snapshots.R | 100 +++++++ checkpoint-0.3.15/checkpoint/tests/testthat/test-1-scan.R | 129 +++++++--- checkpoint-0.3.15/checkpoint/tests/testthat/test-2-snapshot-dates.R |only checkpoint-0.3.15/checkpoint/tests/testthat/test-3-checkpoint.R |only checkpoint-0.3.15/checkpoint/vignettes/checkpoint.Rmd | 8 23 files changed, 345 insertions(+), 145 deletions(-)
Title: Static R Code Analysis
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with Emacs,
Vim and Sublime Text.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 0.3.2 dated 2015-09-08 and 0.3.3 dated 2015-09-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/lint.R | 11 +++++++++-- tests/testthat/test-closed_curly_linter.R | 2 +- tests/testthat/test-exclusions.R | 5 +++-- 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Phylogenetic ANalyses of DiversificAtion
Description: Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. PLoSB (2010), Morlon et al. PNAS (2011), Condamine et al. Eco Lett (2013), Morlon et al. Eco Lett (2014), Manceau et al. (2015) and Lewitus & Morlon (submitted).
Author: Hélène Morlon [aut, cre, cph]
Maintainer: Hélène Morlon <morlon@biologie.ens.fr>
Diff between RPANDA versions 1.0 dated 2014-12-02 and 1.1 dated 2015-09-14
DESCRIPTION | 13 +++++++------ MD5 | 34 ++++++++++++++++++++++++++-------- NAMESPACE | 16 ++++++++++++---- R/BICompare.R |only R/JSDtree.R |only R/JSDtree_cluster.R |only R/plot_BICompare.R |only R/plot_spectR.R |only R/spectR.R |only README.md |only data/Phyllostomidae.rda |only data/Phyllostomidae_genera.rda |only inst |only man/BICompare.Rd |only man/Balaenopteridae.Rd | 2 +- man/JSDtree.Rd |only man/JSDtree_cluster.Rd |only man/Phyllostomidae.Rd |only man/Phyllostomidae_genera.Rd |only man/RPANDA-package.Rd | 20 ++++++++++++++------ man/fit_sgd.Rd | 13 ++++++++----- man/likelihood_sgd.Rd | 4 ++-- man/plot_BICompare.Rd |only man/plot_fit_env.Rd | 4 ++-- man/plot_spectR.Rd |only man/sim_sgd.Rd | 4 ++-- man/spectR.Rd |only 27 files changed, 74 insertions(+), 36 deletions(-)
Title: Near-Optimal and Balanced Group-Sequential Designs for Clinical
Trials with Continuous Outcomes
Description: Functions to find near-optimal multi-stage designs for continuous outcomes.
Author: James Wason [aut, cre],
John Burkardt [ctb]
Maintainer: James Wason <james.wason@mrc-bsu.cam.ac.uk>
Diff between OptGS versions 1.1 dated 2015-07-28 and 1.1.1 dated 2015-09-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/OptGS.cpp | 14 ++++++++------ 3 files changed, 14 insertions(+), 12 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.3 dated 2015-06-26 and 0.4 dated 2015-09-14
DESCRIPTION | 17 - MD5 | 21 - NAMESPACE | 5 R/MIIVsem.R | 26 - R/miivboot.R |only R/miive.R | 767 ++++++++++++++++++++++++++++++++++---------------------- R/miivs.R | 755 +++++++++++++++++++++++++++++++++++++------------------ R/print.miive.R | 89 +++--- R/print.miivs.R | 2 man/MIIVsem.Rd | 25 - man/miive.Rd | 55 +++- man/miivs.Rd | 2 12 files changed, 1119 insertions(+), 645 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms efficiently using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable matching for
two-sided markets, such as the stable marriage problem and the
college-admissions problem. Implements Irving's Algorithm for
the stable roommate problem. Implements the top trading cycle
algorithm for the indivisible goods trading problem.
Author: Jan Tilly [aut, cre],
Nick Janetos [aut]
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.0.1 dated 2015-05-13 and 1.1 dated 2015-09-14
matchingR-1.0.1/matchingR/demo |only matchingR-1.0.1/matchingR/src/main.cpp |only matchingR-1.0.1/matchingR/src/main.h |only matchingR-1.0.1/matchingR/tests/testthat/test_matching.R |only matchingR-1.1/matchingR/DESCRIPTION | 27 matchingR-1.1/matchingR/MD5 | 74 + matchingR-1.1/matchingR/NEWS.md |only matchingR-1.1/matchingR/R/RcppExports.R | 139 ++- matchingR-1.1/matchingR/R/galeshapley.R |only matchingR-1.1/matchingR/R/matchingR.R | 392 ++-------- matchingR-1.1/matchingR/R/roommate.R |only matchingR-1.1/matchingR/R/toptradingcycle.R |only matchingR-1.1/matchingR/R/utils.R | 27 matchingR-1.1/matchingR/README.md |only matchingR-1.1/matchingR/build |only matchingR-1.1/matchingR/inst/doc |only matchingR-1.1/matchingR/man/checkPreferenceOrder.Rd | 2 matchingR-1.1/matchingR/man/checkPreferenceOrderOnesided.Rd |only matchingR-1.1/matchingR/man/checkStability.Rd | 2 matchingR-1.1/matchingR/man/checkStabilityRoommate.Rd |only matchingR-1.1/matchingR/man/checkStabilityTopTradingCycle.Rd |only matchingR-1.1/matchingR/man/many2one.Rd | 6 matchingR-1.1/matchingR/man/matchingR-package.Rd | 65 + matchingR-1.1/matchingR/man/one2many.Rd | 6 matchingR-1.1/matchingR/man/one2one.Rd | 6 matchingR-1.1/matchingR/man/onesided.Rd |only matchingR-1.1/matchingR/man/pkg.env.Rd |only matchingR-1.1/matchingR/man/rankIndex.Rd | 4 matchingR-1.1/matchingR/man/set.column.major.Rd |only matchingR-1.1/matchingR/man/set.row.major.Rd |only matchingR-1.1/matchingR/man/sortIndex.Rd | 4 matchingR-1.1/matchingR/man/sortIndexOneSided.Rd |only matchingR-1.1/matchingR/man/stableRoommateMatching.Rd |only matchingR-1.1/matchingR/man/topTradingCycle.Rd |only matchingR-1.1/matchingR/man/toptrading.Rd |only matchingR-1.1/matchingR/man/validateInputs.Rd | 2 matchingR-1.1/matchingR/man/validateInputsOneSided.Rd |only matchingR-1.1/matchingR/src/RcppExports.cpp | 93 +- matchingR-1.1/matchingR/src/galeshapley.cpp |only matchingR-1.1/matchingR/src/galeshapley.h |only matchingR-1.1/matchingR/src/roommate.cpp |only matchingR-1.1/matchingR/src/roommate.h |only matchingR-1.1/matchingR/src/toptradingcycle.cpp |only matchingR-1.1/matchingR/src/toptradingcycle.h |only matchingR-1.1/matchingR/src/utils.cpp |only matchingR-1.1/matchingR/src/utils.h |only matchingR-1.1/matchingR/tests/testthat/test_galeshapley.R |only matchingR-1.1/matchingR/tests/testthat/test_helper.R | 6 matchingR-1.1/matchingR/tests/testthat/test_roommate.R |only matchingR-1.1/matchingR/tests/testthat/test_toptradingcycle.R |only matchingR-1.1/matchingR/vignettes |only 51 files changed, 395 insertions(+), 460 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-4 dated 2015-07-16 and 1.0-5 dated 2015-09-14
ChangeLog |only DESCRIPTION | 10 - MD5 | 29 ++--- NAMESPACE | 2 R/cache.R | 14 ++ R/codes.R | 19 +-- R/corpus.R | 13 +- R/dataset.R | 13 -- R/db_api.R | 12 ++ R/globals.R | 14 +- R/manifesto.R | 61 ++++++++++- inst/doc/manifestoRworkflow.pdf |binary man/corpusupdate.Rd | 10 + man/mp_cite.Rd | 11 +- vignettes/manifestoRworkflow.Rmd | 34 ++++-- vignettes/manifestoRworkflow.html | 201 ++++++++++++++++++++------------------ 16 files changed, 274 insertions(+), 169 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.16.0 dated 2015-06-13 and 0.17.0 dated 2015-09-14
ChangeLog | 344 +++++++++++++++++++++++++++ DESCRIPTION | 10 MD5 | 190 +++++++------- NAMESPACE | 5 NEWS | 16 + R/install.R | 12 R/installr-package.R |only R/os.manage.R | 6 R/updateR.R | 101 +++++-- R/zzz.R | 8 README.md | 16 + man/R_version_in_a_folder.Rd | 2 man/add.installr.GUI.Rd | 2 man/add_load_installr_on_startup_menu.Rd | 2 man/add_remove_installr_from_startup_menu.Rd | 2 man/add_to_.First_in_Rprofile.site.Rd | 2 man/ask.user.for.a.row.Rd | 2 man/ask.user.yn.question.Rd | 10 man/barplot_package_users_per_day.Rd | 2 man/browse.latest.R.NEWS.Rd | 2 man/check.for.updates.R.Rd | 6 man/check.integer.Rd | 2 man/checkMD5sums2.Rd | 2 man/copy.packages.between.libraries.Rd | 2 man/cranometer.Rd | 2 man/create.global.library.Rd | 2 man/download_RStudio_CRAN_data.Rd | 2 man/fetch_tag_from_Rd.Rd | 2 man/file.name.from.url.Rd | 2 man/format_RStudio_CRAN_data.Rd | 2 man/freegeoip.Rd | 2 man/get.installed.R.folders.Rd | 2 man/get_Rscript_PID.Rd | 2 man/get_pid.Rd | 2 man/get_tasklist.Rd | 2 man/install.7zip.Rd | 2 man/install.CMake.Rd | 2 man/install.Cygwin.Rd | 2 man/install.FFmpeg.Rd | 2 man/install.GitHub.Rd | 2 man/install.GraphicsMagick.Rd | 2 man/install.ImageMagick.Rd | 2 man/install.LaTeX2RTF.Rd | 2 man/install.LyX.Rd | 2 man/install.MikTeX.Rd | 2 man/install.R.Rd | 2 man/install.RStudio.Rd | 2 man/install.Rdevel.Rd | 2 man/install.Rtools.Rd | 6 man/install.SWFTools.Rd | 2 man/install.Texmaker.Rd | 2 man/install.URL.Rd | 2 man/install.git.Rd | 2 man/install.notepadpp.Rd | 2 man/install.npptor.Rd | 2 man/install.packages.zip.Rd | 2 man/install.pandoc.Rd | 2 man/installr-package.Rd |only man/installr.Rd | 6 man/is.RStudio.Rd | 2 man/is.Rgui.Rd | 2 man/is.empty.Rd | 2 man/is.exe.installed.Rd | 2 man/is.windows.Rd | 2 man/is_in_.First_in_Rprofile.site.Rd | 2 man/kill_all_Rscript_s.Rd | 2 man/kill_pid.Rd | 2 man/kill_process.Rd | 2 man/lineplot_package_downloads.Rd | 2 man/load_installr_on_startup.Rd | 2 man/most_downloaded_packages.Rd | 2 man/myip.Rd | 2 man/os.hibernate.Rd | 2 man/os.lock.Rd | 2 man/os.manage.Rd | 6 man/os.restart.Rd | 2 man/os.shutdown.Rd | 2 man/os.sleep.Rd | 2 man/package_authors.Rd | 2 man/pkgDNLs_worldmapcolor.Rd | 2 man/read_RStudio_CRAN_data.Rd | 2 man/remove.installr.GUI.Rd | 2 man/remove_from_.First_in_Rprofile.site.Rd | 2 man/rename_r_to_R.Rd | 2 man/require2.Rd | 2 man/restart_RGui.Rd | 2 man/rm_installr_from_startup.Rd | 2 man/source.https.Rd | 2 man/system.PATH.Rd | 2 man/turn.number.version.Rd | 2 man/turn.version.to.number.Rd | 2 man/turn.version.to.number1.Rd | 2 man/uninstall.R.Rd | 6 man/uninstall.packages.Rd | 2 man/up_folder.Rd | 2 man/updateR.Rd | 31 +- man/xlsx2csv.Rd | 2 97 files changed, 677 insertions(+), 258 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.0.0.30 dated 2015-07-22 and 3.2.0.1 dated 2015-09-14
h2o-3.0.0.30/h2o/man/h2o.getGLMModel.Rd |only h2o-3.2.0.1/h2o/DESCRIPTION | 10 h2o-3.2.0.1/h2o/MD5 | 249 ++--- h2o-3.2.0.1/h2o/NAMESPACE | 20 h2o-3.2.0.1/h2o/R/ast.R | 7 h2o-3.2.0.1/h2o/R/classes.R | 190 +++- h2o-3.2.0.1/h2o/R/communication.R | 153 ++- h2o-3.2.0.1/h2o/R/connection.R | 55 - h2o-3.2.0.1/h2o/R/constants.R | 10 h2o-3.2.0.1/h2o/R/deeplearning.R | 74 - h2o-3.2.0.1/h2o/R/exec.R | 2 h2o-3.2.0.1/h2o/R/export.R | 50 - h2o-3.2.0.1/h2o/R/frame.R | 332 +++++-- h2o-3.2.0.1/h2o/R/gbm.R | 42 h2o-3.2.0.1/h2o/R/glm.R | 60 - h2o-3.2.0.1/h2o/R/glrm.R | 83 + h2o-3.2.0.1/h2o/R/grid.R |only h2o-3.2.0.1/h2o/R/import.R | 4 h2o-3.2.0.1/h2o/R/kmeans.R | 18 h2o-3.2.0.1/h2o/R/kvstore.R | 42 h2o-3.2.0.1/h2o/R/logging.R | 10 h2o-3.2.0.1/h2o/R/models.R | 1039 ++++++++++++++++++---- h2o-3.2.0.1/h2o/R/naivebayes.R | 2 h2o-3.2.0.1/h2o/R/ops.R | 10 h2o-3.2.0.1/h2o/R/parse.R | 2 h2o-3.2.0.1/h2o/R/pca.R | 2 h2o-3.2.0.1/h2o/R/randomforest.R | 25 h2o-3.2.0.1/h2o/R/svd.R | 17 h2o-3.2.0.1/h2o/demo/00Index | 2 h2o-3.2.0.1/h2o/demo/h2o.anomaly.R |only h2o-3.2.0.1/h2o/demo/h2o.anomaly.remote.R |only h2o-3.2.0.1/h2o/inst/branch.txt | 2 h2o-3.2.0.1/h2o/inst/buildnum.txt | 2 h2o-3.2.0.1/h2o/man/H2OConnection-class.Rd | 8 h2o-3.2.0.1/h2o/man/H2OGrid-class.Rd |only h2o-3.2.0.1/h2o/man/H2OModelMetrics-class.Rd | 3 h2o-3.2.0.1/h2o/man/apply-H2OFrame-method.Rd | 3 h2o-3.2.0.1/h2o/man/as.data.frame.H2OFrame.Rd | 2 h2o-3.2.0.1/h2o/man/as.factor-H2OFrame-method.Rd | 2 h2o-3.2.0.1/h2o/man/h2o-package.Rd | 8 h2o-3.2.0.1/h2o/man/h2o.aic.Rd | 14 h2o-3.2.0.1/h2o/man/h2o.anomaly.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.anyFactor.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.auc.Rd | 11 h2o-3.2.0.1/h2o/man/h2o.betweenss.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.cbind.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.centroid_stats.Rd | 17 h2o-3.2.0.1/h2o/man/h2o.clearLog.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.clusterStatus.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.cluster_sizes.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.colnames.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.confusionMatrix.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.createFrame.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.cummax.Rd |only h2o-3.2.0.1/h2o/man/h2o.cummin.Rd |only h2o-3.2.0.1/h2o/man/h2o.cumprod.Rd |only h2o-3.2.0.1/h2o/man/h2o.cumsum.Rd |only h2o-3.2.0.1/h2o/man/h2o.cut.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.dct.Rd |only h2o-3.2.0.1/h2o/man/h2o.ddply.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.deepfeatures.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.deeplearning.Rd | 73 - h2o-3.2.0.1/h2o/man/h2o.dim.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.downloadCSV.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.download_pojo.Rd | 19 h2o-3.2.0.1/h2o/man/h2o.exportFile.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.filterNACols.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.gbm.Rd | 30 h2o-3.2.0.1/h2o/man/h2o.getGrid.Rd |only h2o-3.2.0.1/h2o/man/h2o.getModel.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.giniCoef.Rd | 13 h2o-3.2.0.1/h2o/man/h2o.glm.Rd | 24 h2o-3.2.0.1/h2o/man/h2o.glrm.Rd | 71 + h2o-3.2.0.1/h2o/man/h2o.grid.Rd |only h2o-3.2.0.1/h2o/man/h2o.head.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.hist.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.hit_ratio_table.Rd | 17 h2o-3.2.0.1/h2o/man/h2o.ifelse.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.importFile.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.impute.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.init.Rd | 19 h2o-3.2.0.1/h2o/man/h2o.insertMissingValues.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.interaction.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.is_client.Rd |only h2o-3.2.0.1/h2o/man/h2o.kmeans.Rd | 13 h2o-3.2.0.1/h2o/man/h2o.length.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.levels.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.loadModel.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.logloss.Rd | 11 h2o-3.2.0.1/h2o/man/h2o.ls.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.makeGLMModel.Rd | 7 h2o-3.2.0.1/h2o/man/h2o.match.Rd | 11 h2o-3.2.0.1/h2o/man/h2o.mean.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.mean_residual_deviance.Rd |only h2o-3.2.0.1/h2o/man/h2o.median.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.merge.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.metric.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.month.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.mse.Rd | 13 h2o-3.2.0.1/h2o/man/h2o.naiveBayes.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.nrow.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.null_deviance.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.null_dof.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.openLog.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.performance.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.quantile.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.r2.Rd | 13 h2o-3.2.0.1/h2o/man/h2o.randomForest.Rd | 17 h2o-3.2.0.1/h2o/man/h2o.rbind.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.removeAll.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.residual_deviance.Rd | 17 h2o-3.2.0.1/h2o/man/h2o.residual_dof.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.runif.Rd | 4 h2o-3.2.0.1/h2o/man/h2o.saveModel.Rd | 13 h2o-3.2.0.1/h2o/man/h2o.scale.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.sd.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.sdev.Rd |only h2o-3.2.0.1/h2o/man/h2o.setLevel.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.splitFrame.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.startGLMJob.Rd | 9 h2o-3.2.0.1/h2o/man/h2o.startLogging.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.stopLogging.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.summary.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.svd.Rd | 20 h2o-3.2.0.1/h2o/man/h2o.table.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.tabulate.Rd |only h2o-3.2.0.1/h2o/man/h2o.tot_withinss.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.totss.Rd | 16 h2o-3.2.0.1/h2o/man/h2o.transform.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.var.Rd | 2 h2o-3.2.0.1/h2o/man/h2o.which.Rd |only h2o-3.2.0.1/h2o/man/is.numeric-H2OFrame-method.Rd |only h2o-3.2.0.1/h2o/man/na.omit-H2OFrame-method.Rd |only h2o-3.2.0.1/h2o/man/range-H2OFrame-method.Rd |only h2o-3.2.0.1/h2o/man/summary-H2OGrid-method.Rd |only h2o-3.2.0.1/h2o/man/zzz.Rd | 2 136 files changed, 2348 insertions(+), 874 deletions(-)
More information about ClusterStability at CRAN
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Title: Bayesian Hierarchical Clustering Using Spike and Slab Models
Description: Builds a dendrogram using log posterior as a natural distance defined by the model and meanwhile waits the clustering variables. It is also capable to computing equivalent Bayesian discrimination probabilities. The adopted method suites small sample large dimension setting. The model parameter estimation maybe difficult, depending on data structure and the chosen distribution family.
Author: Vahid PARTOVI NIA and Anthony C. DAVISON
Maintainer: Vahid PARTOVI NIA <vpartovinia@gmail.com>
Diff between bclust versions 1.4 dated 2013-01-27 and 1.5 dated 2015-09-14
DESCRIPTION | 28 ++----- MD5 | 12 +-- NAMESPACE | 14 ++- R/bclust.R | 4 - R/zzz.R | 1 data/gaelle.rda |binary src/ClusteringvsGAL05.c | 174 +++++++++++++++++++----------------------------- 7 files changed, 100 insertions(+), 133 deletions(-)
Title: Matplotlib Default Color Map
Description: Port of the new Matplotlib default color map ('viridis') to R.
This color map is designed in such a way that it will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. It is also designed to be perceived by
readers with the most common form of color blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.1 dated 2015-07-19 and 0.2.5 dated 2015-09-14
DESCRIPTION | 29 +++++++++++++++++++++-------- MD5 | 18 +++++++++++++----- NAMESPACE | 6 ++++++ R/scales.R |only R/viridis.R | 13 +++++++++---- README.md | 14 ++++++++++++-- build |only inst |only man/scale_viridis.Rd |only man/viridis.Rd | 12 +++++++++--- man/viridis_pal.Rd |only vignettes |only 12 files changed, 70 insertions(+), 22 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.0.1-4 dated 2015-04-14 and 2.0.2-8 dated 2015-09-14
runjags-2.0.1-4/runjags/configure.win |only runjags-2.0.2-8/runjags/CHANGELOG | 41 + runjags-2.0.2-8/runjags/DESCRIPTION | 15 runjags-2.0.2-8/runjags/MD5 | 145 ++-- runjags-2.0.2-8/runjags/NAMESPACE | 10 runjags-2.0.2-8/runjags/R/autoextend.jags.R | 182 +++-- runjags-2.0.2-8/runjags/R/combine.mcmc.R | 2 runjags-2.0.2-8/runjags/R/extend.jags.R | 12 runjags-2.0.2-8/runjags/R/extract.runjags.R | 34 runjags-2.0.2-8/runjags/R/load.module.runjags.R | 82 +- runjags-2.0.2-8/runjags/R/print.methods.R | 2 runjags-2.0.2-8/runjags/R/read.jagsfile.R | 5 runjags-2.0.2-8/runjags/R/run.jags.study.R | 4 runjags-2.0.2-8/runjags/R/runjags.readin.R | 41 - runjags-2.0.2-8/runjags/R/runjags.start.R | 29 runjags-2.0.2-8/runjags/R/runjags.summaries.R | 351 +++++----- runjags-2.0.2-8/runjags/R/setup.jags.jagsfile.R | 10 runjags-2.0.2-8/runjags/R/summary.R | 44 - runjags-2.0.2-8/runjags/R/template.jags.R | 4 runjags-2.0.2-8/runjags/R/utilities.R | 16 runjags-2.0.2-8/runjags/R/utilities.invisible.R | 192 +++-- runjags-2.0.2-8/runjags/build/vignette.rds |binary runjags-2.0.2-8/runjags/configure | 18 runjags-2.0.2-8/runjags/configure.ac | 2 runjags-2.0.2-8/runjags/inst/CITATION | 4 runjags-2.0.2-8/runjags/inst/doc/UserGuide.Rtex | 2 runjags-2.0.2-8/runjags/inst/doc/UserGuide.pdf |binary runjags-2.0.2-8/runjags/inst/doc/quickjags.R | 24 runjags-2.0.2-8/runjags/inst/doc/quickjags.html | 109 +-- runjags-2.0.2-8/runjags/man/add.summary.Rd | 7 runjags-2.0.2-8/runjags/man/autorun.jags.Rd | 6 runjags-2.0.2-8/runjags/man/combine.mcmc.Rd | 2 runjags-2.0.2-8/runjags/man/extract.runjags.Rd | 36 - runjags-2.0.2-8/runjags/man/mutate.functions.Rd | 2 runjags-2.0.2-8/runjags/man/results.jags.Rd | 2 runjags-2.0.2-8/runjags/man/run.jags.Rd | 4 runjags-2.0.2-8/runjags/man/run.jags.study.Rd | 2 runjags-2.0.2-8/runjags/man/runjags-class.Rd | 2 runjags-2.0.2-8/runjags/man/runjags.printmethods.Rd | 2 runjags-2.0.2-8/runjags/man/template.jags.Rd | 2 runjags-2.0.2-8/runjags/man/write.jagsfile.Rd | 2 runjags-2.0.2-8/runjags/src/Makevars.in | 72 +- runjags-2.0.2-8/runjags/src/Makevars.win | 65 + runjags-2.0.2-8/runjags/src/distributions/DGenPar.cc | 11 runjags-2.0.2-8/runjags/src/distributions/DGenPar.h | 12 runjags-2.0.2-8/runjags/src/distributions/DHalfCauchy.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DHalfCauchy.h | 11 runjags-2.0.2-8/runjags/src/distributions/DLomax.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DLomax.h | 11 runjags-2.0.2-8/runjags/src/distributions/DMouchel.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DMouchel.h | 11 runjags-2.0.2-8/runjags/src/distributions/DPar1.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DPar1.h | 11 runjags-2.0.2-8/runjags/src/distributions/DPar2.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DPar2.h | 11 runjags-2.0.2-8/runjags/src/distributions/DPar3.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DPar3.h | 11 runjags-2.0.2-8/runjags/src/distributions/DPar4.cc | 10 runjags-2.0.2-8/runjags/src/distributions/DPar4.h | 11 runjags-2.0.2-8/runjags/src/distributions/jags/DFunction.cc | 8 runjags-2.0.2-8/runjags/src/distributions/jags/DFunction.h | 8 runjags-2.0.2-8/runjags/src/distributions/jags/DPQFunction.cc | 8 runjags-2.0.2-8/runjags/src/distributions/jags/DPQFunction.h | 8 runjags-2.0.2-8/runjags/src/distributions/jags/PFunction.cc | 8 runjags-2.0.2-8/runjags/src/distributions/jags/PFunction.h | 8 runjags-2.0.2-8/runjags/src/distributions/jags/QFunction.cc | 8 runjags-2.0.2-8/runjags/src/distributions/jags/QFunction.h | 8 runjags-2.0.2-8/runjags/src/distributions/jags/RScalarDist.cc | 8 runjags-2.0.2-8/runjags/src/distributions/jags/RScalarDist.h | 7 runjags-2.0.2-8/runjags/src/runjags.cc | 100 ++ runjags-2.0.2-8/runjags/src/testrunjags.cc | 174 ++++ runjags-2.0.2-8/runjags/tests/checkmethods.R | 5 runjags-2.0.2-8/runjags/tests/checkmodule.R | 62 - runjags-2.0.2-8/runjags/vignettes/UserGuide.Rtex | 2 74 files changed, 1519 insertions(+), 659 deletions(-)
Title: Phylogenetic Monte Carlo
Description: Monte Carlo based model choice for applied phylogenetics of
continuous traits. Method described in Carl Boettiger, Graham Coop,
Peter Ralph (2012) Is your phylogeny informative? Measuring
the power of comparative methods, Evolution 66 (7)
2240-51. doi:10.1111/j.1558-5646.2011.01574.x.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between pmc versions 1.0.0 dated 2015-06-26 and 1.0.1 dated 2015-09-14
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS | 5 ++++ R/pmc.R | 13 +++++------ inst/doc/pmc_tutorial.html | 12 +++++----- tests/testthat/test_pmc.R | 52 ++++++++++++++++++++++++++++++++++++++++----- 6 files changed, 72 insertions(+), 26 deletions(-)
More information about LinearRegressionMDE at CRAN
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Title: Models and Tests for Departure from Hardy-Weinberg Equilibrium
and Independence Between Loci
Description: Fits models for genotypic disequilibria, as described in
Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).
Contrast terms are available that account for first order interactions
between loci. Also implements, for a single locus in a single
population, a conditional exact test for Hardy-Weinberg equilibrium.
Author: John Maindonald, with \code{hwexact()} from Randall Johnson.
Maintainer: John Maindonald <John.Maindonald@anu.edu.au>
Diff between hwde versions 0.65 dated 2015-08-06 and 0.66 dated 2015-09-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 9 +++++++++ data/mendelABC.RData |binary man/MendelABC.Rd | 23 +++++++++++++++++------ 5 files changed, 34 insertions(+), 14 deletions(-)
More information about AutoregressionMDE at CRAN
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Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.14 dated 2015-09-06 and 0.5.16 dated 2015-09-13
DESCRIPTION | 8 - MD5 | 27 +++--- NAMESPACE | 2 R/vtreat.R | 170 ++++++++++++++++++++++++++++------------- README.md | 166 ++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/vtreatOverfit.R |only inst/doc/vtreatOverfit.Rmd |only inst/doc/vtreatOverfit.html |only man/designTreatmentsC.Rd | 9 +- man/designTreatmentsN.Rd | 9 +- man/vtreat-package.Rd | 4 tests/testthat/testBO.R | 4 tests/testthat/testDataTable.R |only tests/testthat/testW1.R | 8 + vignettes/vtreat.Rmd | 14 ++- vignettes/vtreatOverfit.Rmd |only 17 files changed, 295 insertions(+), 126 deletions(-)
Title: Flexible Mediation Analysis Using Natural Effect Models
Description: Run flexible mediation analyses using natural
effect models as described in Lange, Vansteelandt and Bekaert (2012),
Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet,
Buysse, Steen and Vansteelandt (2013).
Author: Johan Steen [aut, cre],
Tom Loeys [aut],
Beatrijs Moerkerke [aut],
Stijn Vansteelandt [aut],
Joris Meys [ctb] (technical support),
Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen <johan.steen@gmail.com>
Diff between medflex versions 0.5-1 dated 2015-07-01 and 0.6-0 dated 2015-09-13
medflex-0.5-1/medflex/man/weights.expData.Rd |only medflex-0.5-1/medflex/vignettes/medflex-fig2.pdf |only medflex-0.6-0/medflex/DESCRIPTION | 19 medflex-0.6-0/medflex/MD5 | 67 medflex-0.6-0/medflex/NAMESPACE | 9 medflex-0.6-0/medflex/NEWS | 9 medflex-0.6-0/medflex/R/neImpute.R | 3 medflex-0.6-0/medflex/R/neLht.R | 18 medflex-0.6-0/medflex/R/neModel.R | 184 +- medflex-0.6-0/medflex/R/neWeight.R | 7 medflex-0.6-0/medflex/R/terms-expand.R | 7 medflex-0.6-0/medflex/R/utils.R | 7 medflex-0.6-0/medflex/inst/doc/medflex.Rnw | 468 +++--- medflex-0.6-0/medflex/inst/doc/medflex.pdf |binary medflex-0.6-0/medflex/inst/doc/sandwich.Rnw | 27 medflex-0.6-0/medflex/inst/doc/sandwich.pdf |binary medflex-0.6-0/medflex/man/UPBdata.Rd | 2 medflex-0.6-0/medflex/man/expData-methods.Rd |only medflex-0.6-0/medflex/man/expData.Rd | 6 medflex-0.6-0/medflex/man/neImpute.Rd | 2 medflex-0.6-0/medflex/man/neImpute.default.Rd | 2 medflex-0.6-0/medflex/man/neImpute.formula.Rd | 2 medflex-0.6-0/medflex/man/neLht-methods.Rd | 2 medflex-0.6-0/medflex/man/neLht.Rd | 2 medflex-0.6-0/medflex/man/neModel-methods.Rd | 18 medflex-0.6-0/medflex/man/neModel.Rd | 2 medflex-0.6-0/medflex/man/neWeight.Rd | 4 medflex-0.6-0/medflex/man/neWeight.default.Rd | 2 medflex-0.6-0/medflex/man/neWeight.formula.Rd | 2 medflex-0.6-0/medflex/man/plot.neLht.Rd | 2 medflex-0.6-0/medflex/man/plot.neModel.Rd | 2 medflex-0.6-0/medflex/vignettes/bib.bib | 1656 +++++++++++++---------- medflex-0.6-0/medflex/vignettes/medflex.Rnw | 468 +++--- medflex-0.6-0/medflex/vignettes/medflex.pdf |binary medflex-0.6-0/medflex/vignettes/sandwich.Rnw | 27 medflex-0.6-0/medflex/vignettes/sandwich.pdf |binary 36 files changed, 1809 insertions(+), 1217 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.5 dated 2015-08-12 and 1.8.6 dated 2015-09-13
DESCRIPTION | 8 - MD5 | 26 +++--- R/plot.forestFloor_multiClass.R | 5 - R/plot.forestFloor_regression.R | 4 R/show3d.R | 14 +-- man/convolute_grid.Rd | 2 man/forestFloor.Rd | 171 +++++++++++++++++++++++++++++++--------- man/ggPlotForestFloor.Rd | 2 man/plot.forestFloor.Rd | 171 +++++++++++++++++++++++++++++----------- man/plot_simplex3.Rd | 4 man/show3d.Rd | 10 +- tests/stdUsage.R | 10 +- tests/testBinaryClass.R | 28 ------ tests/testMultiClass.cpp.R | 7 - 14 files changed, 311 insertions(+), 151 deletions(-)
Title: Wrapper Algorithm for All-Relevant Feature Selection
Description: An all-relevant feature selection wrapper algorithm.
It finds relevant features by comparing original attributes'
importance with importance achievable at random, estimated
using their permuted copies.
Author: Miron Bartosz Kursa [aut, cre],
Witold Remigiusz Rudnicki [aut]
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Diff between Boruta versions 4.0.0 dated 2014-12-07 and 5.0.0 dated 2015-09-13
Boruta-4.0.0/Boruta/R/TentativeRoughFix.R |only Boruta-4.0.0/Boruta/R/plot.Boruta.R |only Boruta-5.0.0/Boruta/DESCRIPTION | 24 +- Boruta-5.0.0/Boruta/MD5 | 31 +-- Boruta-5.0.0/Boruta/NAMESPACE | 8 Boruta-5.0.0/Boruta/R/Boruta.R | 198 ++++------------------- Boruta-5.0.0/Boruta/R/importance.R |only Boruta-5.0.0/Boruta/R/tools.R |only Boruta-5.0.0/Boruta/inst/NEWS | 11 + Boruta-5.0.0/Boruta/man/Boruta.Rd | 81 ++++----- Boruta-5.0.0/Boruta/man/TentativeRoughFix.Rd | 3 Boruta-5.0.0/Boruta/man/attStats.Rd | 18 -- Boruta-5.0.0/Boruta/man/getImpFerns.Rd | 5 Boruta-5.0.0/Boruta/man/getImpLegacyRf.Rd |only Boruta-5.0.0/Boruta/man/getImpRf.Rd | 20 +- Boruta-5.0.0/Boruta/man/getSelectedAttributes.Rd | 3 Boruta-5.0.0/Boruta/man/plot.Boruta.Rd | 12 - Boruta-5.0.0/Boruta/man/plotImpHistory.Rd | 9 - Boruta-5.0.0/Boruta/man/print.Boruta.Rd | 3 19 files changed, 170 insertions(+), 256 deletions(-)
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data.
The methods available closely follow those in chapter 6 of Applied Spatial
Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smacpod versions 1.2.3 dated 2015-08-29 and 1.3.0 dated 2015-09-13
smacpod-1.2.3/smacpod/man/tolenv.Rd |only smacpod-1.3.0/smacpod/DESCRIPTION | 11 - smacpod-1.3.0/smacpod/MD5 | 41 ++-- smacpod-1.3.0/smacpod/NAMESPACE | 5 smacpod-1.3.0/smacpod/R/circles.intersect.R |only smacpod-1.3.0/smacpod/R/kd.R | 2 smacpod-1.3.0/smacpod/R/kdest.R | 3 smacpod-1.3.0/smacpod/R/kdplus.test.R | 3 smacpod-1.3.0/smacpod/R/nn.R |only smacpod-1.3.0/smacpod/R/plot.kdenv.R | 21 +- smacpod-1.3.0/smacpod/R/plot.logrrenv.R | 9 - smacpod-1.3.0/smacpod/R/plot.scan.R |only smacpod-1.3.0/smacpod/R/spdensity.R | 3 smacpod-1.3.0/smacpod/R/spscan.test.R | 221 ++++++++++++++++--------- smacpod-1.3.0/smacpod/R/tolenv.R | 32 +-- smacpod-1.3.0/smacpod/man/circles.intersect.Rd |only smacpod-1.3.0/smacpod/man/kd.Rd | 2 smacpod-1.3.0/smacpod/man/kdest.Rd | 5 smacpod-1.3.0/smacpod/man/kdplus.test.Rd | 5 smacpod-1.3.0/smacpod/man/nn.Rd |only smacpod-1.3.0/smacpod/man/plot.kdenv.Rd | 10 + smacpod-1.3.0/smacpod/man/plot.logrrenv.Rd | 11 + smacpod-1.3.0/smacpod/man/plot.scan.Rd |only smacpod-1.3.0/smacpod/man/spdensity.Rd | 5 smacpod-1.3.0/smacpod/man/spscan.test.Rd | 25 +- 25 files changed, 266 insertions(+), 148 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.4.1 dated 2015-08-02 and 0.5.0 dated 2015-09-13
brms-0.4.1/brms/R/data.docu.R |only brms-0.4.1/brms/R/internal.postfit.R |only brms-0.4.1/brms/R/internal.prefit.R |only brms-0.4.1/brms/R/main.R |only brms-0.4.1/brms/R/parser.R |only brms-0.4.1/brms/R/s3.correlations.R |only brms-0.4.1/brms/R/s3.generics.R |only brms-0.4.1/brms/R/s3.methods.R |only brms-0.4.1/brms/R/support.export.R |only brms-0.4.1/brms/man/brm.data.Rd |only brms-0.4.1/brms/man/brm.pars.Rd |only brms-0.4.1/brms/man/cor.ar.Rd |only brms-0.4.1/brms/man/cor.arma.Rd |only brms-0.4.1/brms/man/cor.ma.Rd |only brms-0.4.1/brms/man/par.names.Rd |only brms-0.4.1/brms/man/posterior.samples.Rd |only brms-0.4.1/brms/tests/testthat/tests.internal.prefit.R |only brms-0.4.1/brms/tests/testthat/tests.main.R |only brms-0.4.1/brms/tests/testthat/tests.parser.R |only brms-0.4.1/brms/tests/testthat/tests.support.export.R |only brms-0.5.0/brms/DESCRIPTION | 18 brms-0.5.0/brms/MD5 | 114 + brms-0.5.0/brms/NAMESPACE | 38 brms-0.5.0/brms/R/brm.R |only brms-0.5.0/brms/R/brmsfit-helpers.R |only brms-0.5.0/brms/R/brmsfit-methods.R |only brms-0.5.0/brms/R/correlations.R |only brms-0.5.0/brms/R/data.R |only brms-0.5.0/brms/R/datasets.R |only brms-0.5.0/brms/R/deprecated.R |only brms-0.5.0/brms/R/distributions.R |only brms-0.5.0/brms/R/generics.R |only brms-0.5.0/brms/R/loglik.R |only brms-0.5.0/brms/R/misc.R | 122 + brms-0.5.0/brms/R/predict.R |only brms-0.5.0/brms/R/rename.R |only brms-0.5.0/brms/R/stan.R | 1110 ++++++++++------- brms-0.5.0/brms/R/validate.R |only brms-0.5.0/brms/README.md | 57 brms-0.5.0/brms/build |only brms-0.5.0/brms/data/kidney.rda |binary brms-0.5.0/brms/inst |only brms-0.5.0/brms/man/LOO.Rd |only brms-0.5.0/brms/man/VarCorr.Rd | 2 brms-0.5.0/brms/man/WAIC.Rd | 19 brms-0.5.0/brms/man/brm.Rd | 169 -- brms-0.5.0/brms/man/brmdata.Rd |only brms-0.5.0/brms/man/brmpars.Rd |only brms-0.5.0/brms/man/brms-package.Rd | 26 brms-0.5.0/brms/man/brmsfit-class.Rd | 10 brms-0.5.0/brms/man/cor.brms.Rd | 14 brms-0.5.0/brms/man/cor_ar.Rd |only brms-0.5.0/brms/man/cor_arma.Rd |only brms-0.5.0/brms/man/cor_ma.Rd |only brms-0.5.0/brms/man/epilepsy.Rd | 4 brms-0.5.0/brms/man/fitted.brmsfit.Rd |only brms-0.5.0/brms/man/fixef.Rd | 4 brms-0.5.0/brms/man/get_prior.Rd |only brms-0.5.0/brms/man/hypothesis.Rd | 21 brms-0.5.0/brms/man/inhaler.Rd | 6 brms-0.5.0/brms/man/kidney.Rd | 4 brms-0.5.0/brms/man/launch_shiny.Rd |only brms-0.5.0/brms/man/logLik.brmsfit.Rd |only brms-0.5.0/brms/man/macf.Rd |only brms-0.5.0/brms/man/ngrps.Rd | 2 brms-0.5.0/brms/man/parnames.Rd |only brms-0.5.0/brms/man/plot.brmsfit.Rd | 11 brms-0.5.0/brms/man/posterior_samples.Rd |only brms-0.5.0/brms/man/predict.brmsfit.Rd |only brms-0.5.0/brms/man/print.brmsfit.Rd | 2 brms-0.5.0/brms/man/prior_samples.Rd |only brms-0.5.0/brms/man/ranef.Rd | 2 brms-0.5.0/brms/man/residuals.brmsfit.Rd |only brms-0.5.0/brms/man/set_prior.Rd |only brms-0.5.0/brms/man/stancode.Rd |only brms-0.5.0/brms/man/standata.Rd |only brms-0.5.0/brms/man/summary.brmsfit.Rd | 2 brms-0.5.0/brms/man/vcov.brmsfit.Rd |only brms-0.5.0/brms/tests/testthat/tests.brm.R |only brms-0.5.0/brms/tests/testthat/tests.brmsfit-helpers.R |only brms-0.5.0/brms/tests/testthat/tests.data.R |only brms-0.5.0/brms/tests/testthat/tests.deprecated.R |only brms-0.5.0/brms/tests/testthat/tests.distributions.R |only brms-0.5.0/brms/tests/testthat/tests.misc.R |only brms-0.5.0/brms/tests/testthat/tests.rename.R |only brms-0.5.0/brms/tests/testthat/tests.stan.R | 228 +-- brms-0.5.0/brms/tests/testthat/tests.validate.R |only brms-0.5.0/brms/vignettes |only 88 files changed, 1162 insertions(+), 823 deletions(-)
Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including
sequence data from 'NCBI', plant trait data from 'BETYdb', invasive species
data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
Author: Scott Chamberlain [aut, cre],
Zachary Foster [aut],
Ignasi Bartomeus [aut],
David LeBauer [aut],
David Harris [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between traits versions 0.1.0 dated 2015-06-12 and 0.1.2 dated 2015-09-12
traits-0.1.0/traits/NEWS |only traits-0.1.2/traits/DESCRIPTION | 15 ++- traits-0.1.2/traits/MD5 | 50 ++++++------- traits-0.1.2/traits/NAMESPACE | 13 +++ traits-0.1.2/traits/R/coral.R | 10 +- traits-0.1.2/traits/R/eol_invasive.R | 14 +-- traits-0.1.2/traits/R/fe_native.R | 2 traits-0.1.2/traits/R/g_invasive.R | 2 traits-0.1.2/traits/R/is_native.R | 2 traits-0.1.2/traits/R/ncbi_byid.R | 3 traits-0.1.2/traits/R/ncbi_byname.R | 2 traits-0.1.2/traits/R/ncbi_searcher.R | 70 +++++++++++++----- traits-0.1.2/traits/R/traitbank.R | 30 +++++-- traits-0.1.2/traits/R/traits-package.r | 36 ++++++++- traits-0.1.2/traits/README.md | 114 ++++++++++++++++-------------- traits-0.1.2/traits/build/vignette.rds |binary traits-0.1.2/traits/man/coral.Rd | 10 +- traits-0.1.2/traits/man/eol_invasive_.Rd | 14 +-- traits-0.1.2/traits/man/fe_native.Rd | 2 traits-0.1.2/traits/man/g_invasive.Rd | 2 traits-0.1.2/traits/man/is_native.Rd | 2 traits-0.1.2/traits/man/ncbi_byid.Rd | 2 traits-0.1.2/traits/man/ncbi_byname.Rd | 2 traits-0.1.2/traits/man/ncbi_searcher.Rd | 19 +++-- traits-0.1.2/traits/man/traitbank.Rd | 22 +++-- traits-0.1.2/traits/man/traits-package.Rd | 32 +++++++- traits-0.1.2/traits/tests/testthat.R |only 27 files changed, 306 insertions(+), 164 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and `iDigBio`. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.3.0 dated 2015-07-04 and 0.3.2 dated 2015-09-12
DESCRIPTION | 13 +-- MD5 | 36 +++++---- NAMESPACE | 9 ++ R/as.idigbio.R |only R/inspect.R | 11 ++- R/methods.r | 17 +--- R/occ.r | 16 +++- R/occ2df.R | 15 ++-- R/occ_options.r | 22 +++--- R/plugins.r | 168 ++++++++++++++++++++++++++++++++++------------ R/spocc-package.R | 3 R/wkt_vis.r | 7 + README.md | 138 ++++++++++++++++++++++--------------- build/vignette.rds |binary man/as.idigbio.Rd |only man/inspect.Rd | 5 + man/occ.Rd | 103 +++++++++++++++++++++++++--- man/occ_options.Rd | 3 man/spocc-package.Rd | 3 tests/testthat/test-occ.R | 15 +--- 20 files changed, 404 insertions(+), 180 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.2 dated 2015-06-05 and 1.2.3 dated 2015-09-12
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/mnlogit.R | 6 ++++-- R/predict.R | 15 +++++++++++---- 6 files changed, 34 insertions(+), 16 deletions(-)
Title: Half-Normal Plots with Simulation Envelopes
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Diff between hnp versions 1.0 dated 2014-12-02 and 1.1 dated 2015-09-12
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 10 R/hnp.R | 2238 ++++++++++++++++++++++++++--------------------------- man/hnp-package.Rd | 63 - 5 files changed, 1169 insertions(+), 1158 deletions(-)
Title: Simulation of Discrete Random Variables with Given Correlation
Matrix and Marginal Distributions
Description: A gaussian copula based procedure for generating samples from discrete random variables with prescribed correlation matrix and marginal distributions.
Author: Alessandro Barbiero, Pier Alda Ferrari
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between GenOrd versions 1.3.0 dated 2015-04-01 and 1.4.0 dated 2015-09-12
DESCRIPTION | 16 ++-- MD5 | 16 ++-- NAMESPACE | 2 R/ordsample.R | 4 - man/GenOrd-package.Rd | 20 ++--- man/contord.Rd | 8 +- man/corrcheck.Rd | 6 - man/ordcont.Rd | 24 +++--- man/ordsample.Rd | 190 ++++++++++++++++++++++++++++++++++++++++++++++---- 9 files changed, 228 insertions(+), 58 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.1 dated 2015-09-09 and 1.1.2 dated 2015-09-12
gdm-1.1.1/gdm/inst/doc/gdmVignette.html |only gdm-1.1.2/gdm/DESCRIPTION | 10 ++++++---- gdm-1.1.2/gdm/MD5 | 10 +++++++--- gdm-1.1.2/gdm/build |only gdm-1.1.2/gdm/inst/doc/gdmVignette.pdf |binary gdm-1.1.2/gdm/inst/doc/gdmVignette.pdf.asis |only gdm-1.1.2/gdm/vignettes |only 7 files changed, 13 insertions(+), 7 deletions(-)
Title: Time Series Clustering with Dynamic Time Warping
Description: Time series clustering using different techniques related to the Dynamic Time Warping distance
and its corresponding lower bounds. Additionally, an implementation of k-Shape clustering is available.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 1.0.0 dated 2015-08-23 and 1.1.0 dated 2015-09-12
DESCRIPTION | 8 MD5 | 32 +-- R/DBA.R | 51 ++++- R/SBD.R | 11 + R/dtwclust-plot.R | 29 ++ R/dtwclust.R | 21 +- R/lb-improved.R | 117 +++++++++-- R/lb-keogh.R | 62 ++++-- R/shape-extraction.R | 12 - R/utils.R | 21 +- README.md | 4 man/DBA.Rd | 113 ++++++----- man/SBD.Rd | 98 +++++---- man/dtwclust.Rd | 505 ++++++++++++++++++++++++++------------------------- man/lb_improved.Rd | 125 +++++++----- man/lb_keogh.Rd | 131 +++++++------ man/plot-methods.Rd | 94 +++++---- 17 files changed, 854 insertions(+), 580 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.2.1 dated 2015-08-19 and 0.3.0 dated 2015-09-12
docopulae-0.2.1/docopulae/man/update.desigh.Rd |only docopulae-0.2.1/docopulae/man/update_reference.Rd |only docopulae-0.3.0/docopulae/DESCRIPTION | 8 docopulae-0.3.0/docopulae/MD5 | 40 - docopulae-0.3.0/docopulae/NAMESPACE | 4 docopulae-0.3.0/docopulae/R/docopulae.R | 4 docopulae-0.3.0/docopulae/R/examples/main.R | 56 + docopulae-0.3.0/docopulae/R/main.R | 704 ++++++++++++---------- docopulae-0.3.0/docopulae/R/nint.R | 3 docopulae-0.3.0/docopulae/README.md | 26 docopulae-0.3.0/docopulae/man/Defficiency.Rd | 14 docopulae-0.3.0/docopulae/man/Dsensitivity.Rd |only docopulae-0.3.0/docopulae/man/FedorovWynn.Rd | 31 docopulae-0.3.0/docopulae/man/buildf.Rd | 2 docopulae-0.3.0/docopulae/man/design.Rd |only docopulae-0.3.0/docopulae/man/docopulae.Rd | 4 docopulae-0.3.0/docopulae/man/getM.Rd | 11 docopulae-0.3.0/docopulae/man/nint_expandSpace.Rd | 2 docopulae-0.3.0/docopulae/man/nint_space.Rd | 1 docopulae-0.3.0/docopulae/man/param.Rd | 63 + docopulae-0.3.0/docopulae/man/plot.desigh.Rd | 32 - docopulae-0.3.0/docopulae/man/reduce.Rd | 9 docopulae-0.3.0/docopulae/man/update.param.Rd | 7 23 files changed, 558 insertions(+), 463 deletions(-)
Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports. Get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see http://ocrsdk.com/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between abbyyR versions 0.1 dated 2015-06-12 and 0.2 dated 2015-09-12
abbyyR-0.1/abbyyR/R/abbyy.R |only abbyyR-0.1/abbyyR/man/abbyyR.Rd |only abbyyR-0.1/abbyyR/vignettes/abbyyR-ex.Rmd |only abbyyR-0.2/abbyyR/DESCRIPTION | 8 - abbyyR-0.2/abbyyR/MD5 | 98 +++++++++++--------- abbyyR-0.2/abbyyR/NAMESPACE | 13 ++ abbyyR-0.2/abbyyR/R/abbyyR.R |only abbyyR-0.2/abbyyR/R/compareText.R |only abbyyR-0.2/abbyyR/R/deleteTask.R | 11 +- abbyyR-0.2/abbyyR/R/getAppInfo.R | 10 +- abbyyR-0.2/abbyyR/R/getResults.R | 5 - abbyyR-0.2/abbyyR/R/getTaskStatus.R | 13 +- abbyyR-0.2/abbyyR/R/listFinishedTasks.R | 9 + abbyyR-0.2/abbyyR/R/listTasks.R | 9 + abbyyR-0.2/abbyyR/R/ocrFile.R |only abbyyR-0.2/abbyyR/R/processBarcodeField.R | 13 +- abbyyR-0.2/abbyyR/R/processBusinessCard.R | 11 +- abbyyR-0.2/abbyyR/R/processCheckmarkField.R | 11 +- abbyyR-0.2/abbyyR/R/processDocument.R | 11 +- abbyyR-0.2/abbyyR/R/processFields.R | 6 - abbyyR-0.2/abbyyR/R/processImage.R | 19 ++- abbyyR-0.2/abbyyR/R/processMRZ.R | 13 +- abbyyR-0.2/abbyyR/R/processPhotoId.R | 11 +- abbyyR-0.2/abbyyR/R/processRemoteImage.R | 11 +- abbyyR-0.2/abbyyR/R/processTextField.R | 11 +- abbyyR-0.2/abbyyR/R/setapp.R | 4 abbyyR-0.2/abbyyR/R/submitImage.R | 15 +-- abbyyR-0.2/abbyyR/inst/extdata/wisc_ads |only abbyyR-0.2/abbyyR/inst/extdata/wisc_out |only abbyyR-0.2/abbyyR/man/abbyyR-package.Rd |only abbyyR-0.2/abbyyR/man/compareText.Rd |only abbyyR-0.2/abbyyR/man/deleteTask.Rd | 4 abbyyR-0.2/abbyyR/man/getAppInfo.Rd | 5 + abbyyR-0.2/abbyyR/man/getResults.Rd | 5 + abbyyR-0.2/abbyyR/man/getTaskStatus.Rd | 4 abbyyR-0.2/abbyyR/man/listFinishedTasks.Rd | 5 + abbyyR-0.2/abbyyR/man/listTasks.Rd | 5 + abbyyR-0.2/abbyyR/man/ocrFile.Rd |only abbyyR-0.2/abbyyR/man/processBarcodeField.Rd | 4 abbyyR-0.2/abbyyR/man/processBusinessCard.Rd | 4 abbyyR-0.2/abbyyR/man/processCheckmarkField.Rd | 4 abbyyR-0.2/abbyyR/man/processDocument.Rd | 4 abbyyR-0.2/abbyyR/man/processImage.Rd | 9 + abbyyR-0.2/abbyyR/man/processMRZ.Rd | 4 abbyyR-0.2/abbyyR/man/processPhotoId.Rd | 4 abbyyR-0.2/abbyyR/man/processRemoteImage.Rd | 4 abbyyR-0.2/abbyyR/man/processTextField.Rd | 4 abbyyR-0.2/abbyyR/man/setapp.Rd | 2 abbyyR-0.2/abbyyR/man/submitImage.Rd | 4 abbyyR-0.2/abbyyR/vignettes/Overview_of_abbyyR.html |only abbyyR-0.2/abbyyR/vignettes/abbyyR_example.html |only abbyyR-0.2/abbyyR/vignettes/wiscads.html |only 52 files changed, 247 insertions(+), 140 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8 dated 2015-09-10 and 0.8.1 dated 2015-09-11
DESCRIPTION | 6 MD5 | 21 - R/reflist.r | 15 R/tax.r | 4 R/tv.home.r | 3 inst/ChangeLog | 3 inst/doc/vegdata.R | 17 inst/doc/vegdata.Rnw | 981 ++++++++++++++++++++++++------------------------- inst/doc/vegdata.pdf |binary tests/testthat/obs.rds |only tests/testthat/test.R | 98 ++-- vignettes/vegdata.Rnw | 981 ++++++++++++++++++++++++------------------------- 12 files changed, 1060 insertions(+), 1069 deletions(-)
Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom
interactivity to R graphics, including 'base', 'lattice', and 'ggplot2'. The
interactivity is provided through the 'svg-pan-zoom.js' library. Various
options to the widget can tailor the pan and zoom experience to nearly any
user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library
in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom),
Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in
htmlwidgets/lib, https://github.com/hammerjs/hammer),
Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between svgPanZoom versions 0.2.0 dated 2015-07-16 and 0.3.0 dated 2015-09-11
svgPanZoom-0.2.0/svgPanZoom/NEWS |only svgPanZoom-0.3.0/svgPanZoom/DESCRIPTION | 18 + svgPanZoom-0.3.0/svgPanZoom/MD5 | 18 + svgPanZoom-0.3.0/svgPanZoom/NEWS.md |only svgPanZoom-0.3.0/svgPanZoom/R/svgPanZoom.R | 7 svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/hammer |only svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/svg-pan-zoom/LICENSE_svg-pan-zoom | 46 ++-- svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.min.js | 6 svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/svgPanZoom.js | 94 +++++++++- svgPanZoom-0.3.0/svgPanZoom/inst/htmlwidgets/svgPanZoom.yaml | 12 - svgPanZoom-0.3.0/svgPanZoom/man/svgPanZoom.Rd | 2 11 files changed, 156 insertions(+), 47 deletions(-)
Title: Forecast Verification Routines for the SPECS FP7 Project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.3-0 dated 2014-10-15 and 0.4-0 dated 2015-09-11
DESCRIPTION | 12 ++++---- MD5 | 60 +++++++++++++++++++++++------------------- NAMESPACE | 12 ++++++++ R/BrierScoreDecomposition.R | 4 +- R/ClimEns.R | 11 ++----- R/Corr.R |only R/CorrDiff.R |only R/Detrend.R | 17 +++++++++--- R/DressEnsemble.R | 6 ++-- R/EnsBrier.R | 27 +++++++++---------- R/EnsBrierDiff.R | 43 ++++++++++++++---------------- R/EnsBrierSs.R | 60 ++++++++++++++++++++++++------------------ R/EnsCrps.R | 45 +++++++++---------------------- R/EnsCrpsDiff.R | 43 +++++++++++++----------------- R/EnsCrpss.R | 61 +++++++++++++++++++++++++------------------ R/EnsRps.R | 18 ++---------- R/EnsRpsDiff.R | 23 ++++------------ R/EnsRpss.R | 21 ++++---------- R/FairBrier.R | 33 ++++++++++++++--------- R/FairBrierDiff.R | 45 +++++++++++++++---------------- R/FairBrierSs.R | 62 ++++++++++++++++++++++++-------------------- R/FairCrps.R | 46 +++++++++----------------------- R/FairCrpsDiff.R | 44 ++++++++++++++----------------- R/FairCrpss.R | 61 +++++++++++++++++++++++++------------------ R/FairRps.R | 18 ++---------- R/FairRpsDiff.R | 23 ++++------------ R/FairRpss.R | 21 ++++---------- R/FitAkdParameters.R | 11 ++----- R/Preprocess.R |only R/Rankhist.R | 12 ++++---- man/Corr.Rd |only man/CorrDiff.Rd |only man/Preprocess.Rd |only man/SpecsVerification.Rd | 3 +- 34 files changed, 404 insertions(+), 438 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework for
quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of
financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.0 dated 2014-12-02 and 0.4.1 dated 2015-09-11
ChangeLog | 40 + DESCRIPTION | 16 MD5 | 21 NAMESPACE | 41 + R/arrays.R | 91 +-- README.md | 19 demo/00Index | 1 demo/ShinyDiscountCurves.R |only inst/NEWS.Rd | 21 inst/shiny |only src/Makevars.win | 33 - src/RcppExports.cpp | 1166 ++++++++++++++++++--------------------------- 12 files changed, 674 insertions(+), 775 deletions(-)
Title: Random Subspace Method (RSM) for Linear Regression
Description: Performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.
Author: Pawel Teisseyre, Robert A. Klopotek
Maintainer: Pawel Teisseyre <teisseyrep@ipipan.waw.pl>
Diff between regRSM versions 0.4 dated 2014-04-18 and 0.5 dated 2015-09-11
DESCRIPTION | 12 +-- MD5 | 8 +- NAMESPACE | 11 +++ R/parallelRSM.R | 94 +++++++++++++++--------------- R/regRSM.r | 174 ++++++++++++++++++++++++++++++++++++-------------------- 5 files changed, 181 insertions(+), 118 deletions(-)
Title: Local Time Space Kriging
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang <dliang@umces.edu>
Diff between ltsk versions 1.0.3 dated 2015-01-26 and 1.0.4 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++++------ NAMESPACE | 5 +++++ R/check_input.R | 13 ++++++++++++- R/lnbk.R |only R/rowSplit_1.R |only R/tsbk.R |only R/vexpn.R | 14 ++++++++++++++ R/work.blk.kriging.R |only R/work.blk.kriging_2.R |only R/working.tsk.R | 2 +- man/ltsk-internal.Rd | 2 ++ man/tsbk.Rd |only 13 files changed, 51 insertions(+), 13 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl], Kathleen Gates [aut], Peter Molenaar
[aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-1 dated 2014-12-15 and 0.1-2 dated 2015-09-11
gimme-0.1-1/gimme/man/aggregate.Rd |only gimme-0.1-1/gimme/man/semigimme.Rd |only gimme-0.1-2/gimme/DESCRIPTION | 16 gimme-0.1-2/gimme/MD5 | 29 gimme-0.1-2/gimme/NAMESPACE | 24 gimme-0.1-2/gimme/R/aggSEM.R |only gimme-0.1-2/gimme/R/gimme-data.R |only gimme-0.1-2/gimme/R/gimme-pkg.R |only gimme-0.1-2/gimme/R/gimme.R | 2977 +++++++++++++++++++-------------- gimme-0.1-2/gimme/R/indSEM.R |only gimme-0.1-2/gimme/man/aggSEM.Rd |only gimme-0.1-2/gimme/man/gimme-package.Rd | 47 gimme-0.1-2/gimme/man/gimme.Rd | 119 - gimme-0.1-2/gimme/man/indSEM.Rd | 101 - gimme-0.1-2/gimme/man/ts1.Rd | 16 gimme-0.1-2/gimme/man/ts2.Rd | 16 gimme-0.1-2/gimme/man/ts3.Rd | 16 gimme-0.1-2/gimme/man/ts4.Rd | 16 gimme-0.1-2/gimme/man/ts5.Rd | 16 19 files changed, 2015 insertions(+), 1378 deletions(-)
Title: Automated Runs and Evaluations of Ecological Niche Models
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006).
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella <bob.muscarella@gmail.com>
Diff between ENMeval versions 0.1.1 dated 2014-10-05 and 0.2.0 dated 2015-09-11
DESCRIPTION | 14 +- MD5 | 52 +++---- NAMESPACE | 6 NEWS | 10 + R/ENMevaluate.R | 89 ++++++------- R/all.classes.R | 2 R/calc.aicc.R | 2 R/get.block.R | 1 R/get.checkerboard1.R | 25 ++- R/get.checkerboard2.R | 16 ++ R/get.jackknife.R | 2 R/get.randomkfold.R | 3 R/get.user.R | 3 R/make.args.R | 2 R/tuning.R | 301 +++++++++++++++++++++++++-------------------- data/enmeval_results.rda |binary inst/CITATION | 6 man/ENMeval-package.Rd | 12 + man/ENMevaluate.Rd | 19 ++ man/ENMevaluation-class.Rd | 17 +- man/calc.aicc.Rd | 2 man/calc.niche.overlap.Rd | 2 man/corrected.var.Rd | 2 man/enmeval_results.Rd | 5 man/eval.plot.Rd | 2 man/get.evaluation.bins.Rd | 6 man/make.args.Rd | 2 27 files changed, 347 insertions(+), 256 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.8.0 dated 2015-05-09 and 1.9.1 dated 2015-09-11
devtools-1.8.0/devtools/R/install-gitorious.r |only devtools-1.8.0/devtools/man/cran_env_vars.Rd |only devtools-1.8.0/devtools/man/install_gitorious.Rd |only devtools-1.8.0/devtools/tests/testthat/test-load-dir.r |only devtools-1.9.1/devtools/DESCRIPTION | 19 devtools-1.9.1/devtools/MD5 | 191 +++++----- devtools-1.9.1/devtools/NAMESPACE | 22 - devtools-1.9.1/devtools/R/build.r | 2 devtools-1.9.1/devtools/R/check-cran.r | 50 +- devtools-1.9.1/devtools/R/check-devtools.r | 6 devtools-1.9.1/devtools/R/check.r | 120 ++---- devtools-1.9.1/devtools/R/cran.r | 4 devtools-1.9.1/devtools/R/create.r | 4 devtools-1.9.1/devtools/R/deps.R | 87 ++++ devtools-1.9.1/devtools/R/dev-help.r | 2 devtools-1.9.1/devtools/R/dev-mode.r | 2 devtools-1.9.1/devtools/R/doctor.R | 40 +- devtools-1.9.1/devtools/R/document.r | 10 devtools-1.9.1/devtools/R/git.R | 46 +- devtools-1.9.1/devtools/R/imports-env.r | 27 - devtools-1.9.1/devtools/R/infrastructure-git.R | 135 ++++++- devtools-1.9.1/devtools/R/infrastructure.R | 74 ++- devtools-1.9.1/devtools/R/install-bitbucket.r | 2 devtools-1.9.1/devtools/R/install-github.r | 8 devtools-1.9.1/devtools/R/install.r | 31 + devtools-1.9.1/devtools/R/load-dll.r | 10 devtools-1.9.1/devtools/R/load.r | 19 devtools-1.9.1/devtools/R/package.r | 23 - devtools-1.9.1/devtools/R/release.r | 23 - devtools-1.9.1/devtools/R/remove-s4-class.r | 67 +++ devtools-1.9.1/devtools/R/revdep-summarise.R | 22 + devtools-1.9.1/devtools/R/revdep.R | 16 devtools-1.9.1/devtools/R/rtools.r | 5 devtools-1.9.1/devtools/R/run-source.r | 5 devtools-1.9.1/devtools/R/session-info.r | 3 devtools-1.9.1/devtools/R/show-news.r | 2 devtools-1.9.1/devtools/R/test.r | 13 devtools-1.9.1/devtools/R/uninstall.r |only devtools-1.9.1/devtools/R/upload-ftp.r |only devtools-1.9.1/devtools/R/utils.r | 8 devtools-1.9.1/devtools/R/vignettes.r | 5 devtools-1.9.1/devtools/R/with-debug.r | 5 devtools-1.9.1/devtools/R/with.r | 64 +++ devtools-1.9.1/devtools/R/zzz.r | 13 devtools-1.9.1/devtools/README.md | 5 devtools-1.9.1/devtools/build |only devtools-1.9.1/devtools/inst/doc |only devtools-1.9.1/devtools/inst/templates/travis.yml | 9 devtools-1.9.1/devtools/man/as.package.Rd | 6 devtools-1.9.1/devtools/man/build_vignettes.Rd | 6 devtools-1.9.1/devtools/man/check.Rd | 31 - devtools-1.9.1/devtools/man/check_failures.Rd |only devtools-1.9.1/devtools/man/devtools-deprecated.Rd |only devtools-1.9.1/devtools/man/dr_github.Rd | 4 devtools-1.9.1/devtools/man/infrastructure.Rd | 10 devtools-1.9.1/devtools/man/install.Rd | 14 devtools-1.9.1/devtools/man/install_bitbucket.Rd | 5 devtools-1.9.1/devtools/man/install_deps.Rd | 13 devtools-1.9.1/devtools/man/install_git.Rd | 7 devtools-1.9.1/devtools/man/install_github.Rd | 7 devtools-1.9.1/devtools/man/install_svn.Rd | 7 devtools-1.9.1/devtools/man/install_url.Rd | 7 devtools-1.9.1/devtools/man/install_version.Rd | 7 devtools-1.9.1/devtools/man/load_all.Rd | 9 devtools-1.9.1/devtools/man/package_deps.Rd | 6 devtools-1.9.1/devtools/man/release.Rd | 2 devtools-1.9.1/devtools/man/revdep.Rd | 2 devtools-1.9.1/devtools/man/revdep_check.Rd | 8 devtools-1.9.1/devtools/man/source_url.Rd | 6 devtools-1.9.1/devtools/man/submit_cran.Rd | 2 devtools-1.9.1/devtools/man/test.Rd | 6 devtools-1.9.1/devtools/man/uninstall.Rd |only devtools-1.9.1/devtools/man/use_build_ignore.Rd | 3 devtools-1.9.1/devtools/man/use_data.Rd | 3 devtools-1.9.1/devtools/man/use_data_raw.Rd | 3 devtools-1.9.1/devtools/man/use_git.Rd | 2 devtools-1.9.1/devtools/man/use_git_hook.Rd | 4 devtools-1.9.1/devtools/man/use_github.Rd | 45 ++ devtools-1.9.1/devtools/man/use_github_links.Rd |only devtools-1.9.1/devtools/man/use_package.Rd | 3 devtools-1.9.1/devtools/man/use_readme_rmd.Rd | 3 devtools-1.9.1/devtools/man/with_debug.Rd | 6 devtools-1.9.1/devtools/man/with_something.Rd | 12 devtools-1.9.1/devtools/tests/test-that.R | 6 devtools-1.9.1/devtools/tests/testthat/test-check.r | 26 - devtools-1.9.1/devtools/tests/testthat/test-dll.r | 7 devtools-1.9.1/devtools/tests/testthat/test-github-connections.R |only devtools-1.9.1/devtools/tests/testthat/test-infrastructure.r |only devtools-1.9.1/devtools/tests/testthat/test-load.r |only devtools-1.9.1/devtools/tests/testthat/test-package.R | 4 devtools-1.9.1/devtools/tests/testthat/test-remotes.r |only devtools-1.9.1/devtools/tests/testthat/test-s4-sort.r |only devtools-1.9.1/devtools/tests/testthat/test-s4-unload.r | 4 devtools-1.9.1/devtools/tests/testthat/test-test.r |only devtools-1.9.1/devtools/tests/testthat/test-uninstall.r |only devtools-1.9.1/devtools/tests/testthat/test-vignettes.r | 30 + devtools-1.9.1/devtools/tests/testthat/test-with.r | 38 + devtools-1.9.1/devtools/tests/testthat/testHelp/DESCRIPTION | 2 devtools-1.9.1/devtools/tests/testthat/testS4sort |only devtools-1.9.1/devtools/tests/testthat/testTest |only devtools-1.9.1/devtools/tests/testthat/testTestWithDepends |only devtools-1.9.1/devtools/tests/testthat/testUseData |only devtools-1.9.1/devtools/vignettes |only 103 files changed, 1087 insertions(+), 478 deletions(-)
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non-symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unina2.it>
Diff between CAvariants versions 2.1 dated 2014-07-23 and 3.0 dated 2015-09-11
CAvariants-2.1/CAvariants/R/plotcacorporateplus.R |only CAvariants-2.1/CAvariants/R/printcacorporateplus.R |only CAvariants-2.1/CAvariants/man/plotcacorporateplus.Rd |only CAvariants-2.1/CAvariants/man/printcacorporateplus.Rd |only CAvariants-3.0/CAvariants/DESCRIPTION | 21 ++---- CAvariants-3.0/CAvariants/MD5 | 34 +++++----- CAvariants-3.0/CAvariants/NAMESPACE | 18 ++++- CAvariants-3.0/CAvariants/R/CAvariants.R | 20 +++--- CAvariants-3.0/CAvariants/R/caellipse.R | 34 +++++----- CAvariants-3.0/CAvariants/R/nsca.ellipse.R | 32 +++++----- CAvariants-3.0/CAvariants/R/plot.CAvariants.R |only CAvariants-3.0/CAvariants/R/plotone.R | 4 - CAvariants-3.0/CAvariants/R/print.CAvariants.R |only CAvariants-3.0/CAvariants/R/summary.CAvariants.R |only CAvariants-3.0/CAvariants/data/asbestos.rda |binary CAvariants-3.0/CAvariants/data/shopdataM.rda |binary CAvariants-3.0/CAvariants/man/CAvariants.Rd | 56 +++++------------- CAvariants-3.0/CAvariants/man/caellipse.Rd | 12 +-- CAvariants-3.0/CAvariants/man/nsca.ellipse.Rd | 13 ++-- CAvariants-3.0/CAvariants/man/plot.CAvariants.Rd |only CAvariants-3.0/CAvariants/man/plotone.Rd | 2 CAvariants-3.0/CAvariants/man/print.CAvariants.Rd |only CAvariants-3.0/CAvariants/man/summary.CAvariants.Rd |only 23 files changed, 116 insertions(+), 130 deletions(-)
Title: Regularization Paths for Huber Loss Regression and Quantile
Regression Penalized by Lasso or Elastic-Net
Description: Efficient algorithms for fitting entire regularization paths for Huber loss regression and quantile regression penalized by lasso or elastic-net.
Author: Congrui Yi
Maintainer: Congrui Yi <congrui-yi@uiowa.edu>
Diff between hqreg versions 0.9 dated 2015-06-20 and 1.0 dated 2015-09-11
hqreg-0.9/hqreg/R/setupPsi.R |only hqreg-1.0/hqreg/DESCRIPTION | 8 hqreg-1.0/hqreg/MD5 | 23 - hqreg-1.0/hqreg/NAMESPACE | 4 hqreg-1.0/hqreg/NEWS |only hqreg-1.0/hqreg/R/cv.hqreg.R | 21 - hqreg-1.0/hqreg/R/hqreg.R | 110 ++++--- hqreg-1.0/hqreg/R/init.R |only hqreg-1.0/hqreg/R/loss.hqreg.R | 6 hqreg-1.0/hqreg/man/cv.hqreg.Rd | 2 hqreg-1.0/hqreg/man/hqreg-package.Rd | 4 hqreg-1.0/hqreg/man/hqreg.Rd | 40 +- hqreg-1.0/hqreg/man/predict.hqreg.Rd | 2 hqreg-1.0/hqreg/src/hqreg.c | 547 ++++++++++++++++++++++++++++++----- 14 files changed, 599 insertions(+), 168 deletions(-)
More information about hindexcalculator at CRAN
Permanent link
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.2 dated 2014-11-18 and 2.3 dated 2015-09-11
DESCRIPTION | 20 LICENSE |only MD5 | 32 - NAMESPACE | 33 + R/OUshifts.R | 287 +++++------ R/phyloglm.R | 1242 +++++++++++++++++++++++++----------------------- R/phylolm.R | 648 ++++++++++++------------- R/phylostep.R |only README.md |only man/OUshifts.Rd | 142 ++--- man/flowerTree.Rd | 20 man/phyloglm-methods.Rd | 74 +- man/phyloglm.Rd | 198 ++++--- man/phylolm-methods.Rd | 107 ++-- man/phylolm-package.Rd | 40 - man/phylolm.Rd | 252 ++++----- man/phylostep.Rd |only man/rbinTrait.Rd | 86 +-- src/Makevars | 3 19 files changed, 1662 insertions(+), 1522 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.4.1 dated 2015-07-29 and 0.5 dated 2015-09-11
ChangeLog | 10 DESCRIPTION | 13 MD5 | 46 - NAMESPACE | 16 R/em.R | 440 ++++++++--------- R/lms.R | 49 - R/model.R | 1085 ++++++++++++++++++++++++------------------- R/nsemm.R | 84 +-- R/qml.R | 2 R/s3generics.R | 454 +++++++++++++---- R/semm.R | 288 +++++------ man/anova.Rd | 18 man/as.data.frame.Rd | 16 man/count_free_parameters.Rd | 11 man/create_sem.Rd | 26 - man/em.Rd | 4 man/fill_model.Rd | 21 man/get_factor_scores.Rd | 7 man/nlsem-package.Rd | 36 - man/qml.Rd | 79 +-- man/simulate.Rd | 29 - man/specify_sem.Rd | 200 ++++--- tests/tests_for_model.R | 33 - tests/tests_for_semm.R | 15 24 files changed, 1674 insertions(+), 1308 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.3 dated 2015-07-12 and 1.0.4 dated 2015-09-11
DESCRIPTION | 6 - MD5 | 12 +- R/Rdsdp.R | 313 ++++++++++++++++++++++++++++---------------------------- src/Rreadsdpa.c | 2 tests/test1.R | 6 - tests/test2.R | 41 ++----- tests/test3.R | 4 7 files changed, 189 insertions(+), 195 deletions(-)
Title: Iterated Racing Procedures
Description: Iterated racing for automatic algorithm configuration.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@ulb.ac.be>
Diff between irace versions 1.06 dated 2014-11-26 and 1.07 dated 2015-09-11
irace-1.06/irace/README |only irace-1.07/irace/DESCRIPTION | 11 irace-1.07/irace/MD5 | 43 + irace-1.07/irace/NAMESPACE | 5 irace-1.07/irace/NEWS | 29 + irace-1.07/irace/R/cluster.R | 13 irace-1.07/irace/R/irace.R | 149 ++++-- irace-1.07/irace/R/main.R | 76 +++ irace-1.07/irace/R/race-wrapper.R | 325 ++++++++------- irace-1.07/irace/R/race.R | 286 ++++++------- irace-1.07/irace/R/readConfiguration.R | 184 ++++++-- irace-1.07/irace/R/readParameters.R | 19 irace-1.07/irace/R/testing.R |only irace-1.07/irace/R/utils.R | 66 ++- irace-1.07/irace/R/version.R | 2 irace-1.07/irace/README.md |only irace-1.07/irace/inst/bin/irace | 2 irace-1.07/irace/inst/examples/acotsp/default.txt |only irace-1.07/irace/inst/examples/acotsp/forbidden.txt |only irace-1.07/irace/inst/examples/acotsp/hook-run | 14 irace-1.07/irace/inst/examples/mpi/tune-main-cluster-mpi | 4 irace-1.07/irace/inst/templates/tune-conf.tmpl | 101 ++-- irace-1.07/irace/man/hook.evaluate.default.Rd | 12 irace-1.07/irace/man/hook.run.default.Rd | 10 irace-1.07/irace/man/irace-package.Rd | 13 25 files changed, 847 insertions(+), 517 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-3 dated 2015-04-29 and 2.1-4 dated 2015-09-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 18 +++++++++--------- src/logistic.cpp | 10 +++++----- 4 files changed, 21 insertions(+), 21 deletions(-)
Title: Assessing Functional Impact on Gene Expression of Mutations in
Cancer
Description: A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients;
and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.
Author: Jiarui Ding, Sohrab Shah
Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>
Diff between xseq versions 0.2.0 dated 2015-08-29 and 0.2.1 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/xseq-package.Rmd | 4 ++-- inst/doc/xseq-package.pdf |binary src/register.c | 2 +- vignettes/xseq-package.Rmd | 4 ++-- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: Basic Wireless Communications
Description: A basic wireless communications simulation package in R. The package includes
modulation functions for BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. Also included is
an AWGN noise generation function. Additionally, the package includes functions to plot
an I (in-phase) and Q (quadrature) scatter diagram, or density plot. Together these functions
enable the evaluation of respective bit error and symbol rates in an AWGN channel and for
easily viewing the respective signals and noise in a scatter plot or density plot.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.0.1 dated 2015-08-17 and 1.3 dated 2015-09-11
DESCRIPTION | 8 - MD5 | 38 ++++---- NAMESPACE | 2 R/rwirelesscom.R | 215 +++++++++++++++++++++++++++++++++++++++++-------- man/f16pskdemod.Rd |only man/f16pskmod.Rd |only man/f16qamdemod.Rd | 7 - man/f16qammod.Rd | 13 +- man/f64qamdemod.Rd | 7 - man/f64qammod.Rd | 8 - man/f8pskdemod.Rd | 5 - man/f8pskmod.Rd | 5 - man/fNo.Rd | 5 - man/fbpskdemod.Rd | 7 - man/fbpskmod.Rd | 3 man/fqpskdemod.Rd | 5 - man/fqpskmod.Rd | 3 man/iqdensityplot.Rd | 9 +- man/iqscatterplot.Rd | 5 - man/rwirelesscom.Rd | 3 tests/testthat/test1.R | 28 ++++++ 21 files changed, 287 insertions(+), 89 deletions(-)
Title: Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
Description: Rapid, simulation-based exact (restricted) likelihood ratio tests
for testing the presence of variance components/nonparametric terms for
models fit with nlme::lme(),lme4::lmer(), gamm4::gamm4(), mgcv::gamm() and
SemiPar::spm().
Author: Fabian Scheipl [aut, cre],
Ben Bolker [aut]
Maintainer: Fabian Scheipl <fabian.scheipl@stat.uni-muenchen.de>
Diff between RLRsim versions 3.0 dated 2014-08-12 and 3.1-2 dated 2015-09-11
DESCRIPTION | 19 +- MD5 | 34 +-- NAMESPACE | 23 ++ NEWS | 5 R/LRTSim.R | 252 ++++++++++++++--------------- R/RLRTSim.R | 395 +++++++++++++++++++++++----------------------- R/RLRsim-package.R | 36 +++- R/exactLRT.R | 131 +++++++-------- R/exactRLRT.R | 180 +++++++++++--------- R/extract.lmeDesign.R | 125 +++++++------- R/extract.lmerModDesign.R | 60 +++--- man/LRTSim.Rd | 3 man/RLRsim-package.Rd | 40 +++- man/exactLRT.Rd | 5 man/exactRLRT.Rd | 12 - man/extract.lmeDesign.Rd | 7 src/RLRsim.cpp | 141 ++++++++-------- src/RcppExports.cpp | 34 +-- 18 files changed, 792 insertions(+), 710 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.44.0 dated 2015-02-22 and 0.45.0 dated 2015-09-11
PSCBS-0.44.0/PSCBS/.Rinstignore |only PSCBS-0.45.0/PSCBS/DESCRIPTION | 22 +- PSCBS-0.45.0/PSCBS/MD5 | 105 +++++---- PSCBS-0.45.0/PSCBS/NAMESPACE | 108 +++------- PSCBS-0.45.0/PSCBS/NEWS | 26 ++ PSCBS-0.45.0/PSCBS/R/AbstractCBS.HCLUST.R | 5 PSCBS-0.45.0/PSCBS/R/AbstractCBS.PRUNE.R | 2 PSCBS-0.45.0/PSCBS/R/AbstractCBS.R | 14 - PSCBS-0.45.0/PSCBS/R/AbstractCBS.REPORT.R | 34 ++- PSCBS-0.45.0/PSCBS/R/CBS.CALL.R | 10 PSCBS-0.45.0/PSCBS/R/CBS.EXTS.R | 8 PSCBS-0.45.0/PSCBS/R/CBS.IO.R | 16 - PSCBS-0.45.0/PSCBS/R/CBS.PLOT,many.R | 4 PSCBS-0.45.0/PSCBS/R/CBS.PLOT.R | 2 PSCBS-0.45.0/PSCBS/R/CBS.PRUNE.R | 2 PSCBS-0.45.0/PSCBS/R/CBS.R | 4 PSCBS-0.45.0/PSCBS/R/CBS.joinSegments.R | 53 +++- PSCBS-0.45.0/PSCBS/R/DNAcopy.EXTS.R | 14 - PSCBS-0.45.0/PSCBS/R/NonPairedPSCBS.R | 2 PSCBS-0.45.0/PSCBS/R/PSCBS.R | 4 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.PLOT.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.applyByRegion.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.callGNL.R | 2 PSCBS-0.45.0/PSCBS/R/PairedPSCBS.updateMeansTogether.R | 28 +- PSCBS-0.45.0/PSCBS/R/findLargeGaps.R | 45 ++-- PSCBS-0.45.0/PSCBS/R/gapsToSegments.R | 20 + PSCBS-0.45.0/PSCBS/R/segmentByCBS.R | 45 +++- PSCBS-0.45.0/PSCBS/R/segmentByNonPairedPSCBS.R | 2 PSCBS-0.45.0/PSCBS/R/segmentByPairedPSCBS.R | 19 + PSCBS-0.45.0/PSCBS/R/writeWIG.R |only PSCBS-0.45.0/PSCBS/R/zzz.R | 1 PSCBS-0.45.0/PSCBS/build/vignette.rds |binary PSCBS-0.45.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.45.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.45.0/PSCBS/inst/templates/rsp/CBS,report.tex.rsp | 2 PSCBS-0.45.0/PSCBS/inst/templates/rsp/PairedPSCBS,report.tex.rsp | 2 PSCBS-0.45.0/PSCBS/man/AbstractCBS.Rd | 27 +- PSCBS-0.45.0/PSCBS/man/CBS.Rd | 12 - PSCBS-0.45.0/PSCBS/man/Non-documented_objects.Rd | 4 PSCBS-0.45.0/PSCBS/man/NonPairedPSCBS.Rd | 4 PSCBS-0.45.0/PSCBS/man/PSCBS.Rd | 6 PSCBS-0.45.0/PSCBS/man/PairedPSCBS.Rd | 22 +- PSCBS-0.45.0/PSCBS/man/findLargeGaps.Rd | 5 PSCBS-0.45.0/PSCBS/man/gapsToSegments.data.frame.Rd | 4 PSCBS-0.45.0/PSCBS/man/hclustCNs.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/pruneByHClust.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/report.AbstractCBS.Rd | 2 PSCBS-0.45.0/PSCBS/man/segmentByCBS.Rd | 8 PSCBS-0.45.0/PSCBS/man/segmentByPairedPSCBS.Rd | 3 PSCBS-0.45.0/PSCBS/man/writeSegments.CBS.Rd | 58 ++--- PSCBS-0.45.0/PSCBS/tests/PairedPSCBS,plot.R.HIDE |only PSCBS-0.45.0/PSCBS/tests/findLargeGaps.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,flavors.R.HIDE |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,median.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,prune.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS,weights.R |only PSCBS-0.45.0/PSCBS/tests/segmentByCBS.R | 44 +++- PSCBS-0.45.0/PSCBS/tests/segmentByNonPairedPSCBS,medianDH.R | 12 - 58 files changed, 486 insertions(+), 334 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minato-nakazawa@umin.net>
Maintainer: Minato Nakazawa <minato-nakazawa@umin.net>
Diff between fmsb versions 0.5.1 dated 2014-09-15 and 0.5.2 dated 2015-09-11
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 8 +++++++- NEWS | 5 +++++ R/demogjpn.R | 38 ++++++++++++++++++++------------------ man/Jvital.Rd | 6 ++++-- man/lifetable.Rd | 6 +++--- 7 files changed, 50 insertions(+), 35 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-7 dated 2015-08-19 and 0.1-9 dated 2015-09-11
DESCRIPTION | 8 +-- MD5 | 30 ++++++------ NAMESPACE | 2 R/AncestralStates.R | 2 R/BootstrapRep.R | 95 +++++++++++++++++++++++++++++++++------ R/CalcR2CvCorrected.R | 2 R/MantelCor.R | 12 ++-- R/MonteCarloStat.R | 21 +++++++- R/MultivDriftTest.R |only R/TestModularity.R | 10 ++-- inst/CITATION |only inst/tests/test.TestModularity.r | 6 +- man/AncestralStates.Rd | 2 man/BootstrapRep.Rd | 8 +-- man/BootstrapStat.Rd |only man/MantelCor.Rd | 6 +- man/MultivDriftTest.Rd |only man/TestModularity.Rd | 8 +-- 18 files changed, 151 insertions(+), 61 deletions(-)
Title: Censored Linear Mixture Regression Models
Description: Fit censored linear regression models where the random errors follow a finite mixture of Normal or Student-t distributions.
Author: Luis Benites Sanchez, Victor Hugo Lachos
Maintainer: Luis Benites Sanchez <lbenitesanchez@gmail.com>
Diff between CensMixReg versions 0.5 dated 2015-08-27 and 0.7 dated 2015-09-11
DESCRIPTION | 12 - MD5 | 13 - R/CensMixReg.R | 394 ++++------------------------------------------ R/CensMixRegEM.R |only R/UtilityFunctions.R | 10 - man/CensMixReg-package.Rd | 6 man/CensMixReg.Rd | 4 man/wage.rates.Rd | 62 +++++-- 8 files changed, 112 insertions(+), 389 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.0.5 dated 2015-03-23 and 2.0.6 dated 2015-09-11
DESCRIPTION | 9 +++-- MD5 | 29 +++++++++-------- NAMESPACE | 8 ++++ R/addBAMMlegend.R | 18 +++++++++-- R/colorMap.R | 75 +++++++++++++++++++++++++++++++--------------- R/plot.bammdata.R | 18 ++++++----- R/samplingProbs.R | 4 ++ R/setBAMMpriors.R | 8 ++++ R/traitDependentBAMM.R | 42 +++++++++++++++++++------ R/writeEventData.R | 4 +- inst |only man/BAMMtools-package.Rd | 14 +++++--- man/addBAMMlegend.Rd | 7 +++- man/getTipRates.Rd | 2 - man/plot.bammdata.Rd | 4 +- man/traitDependentBAMM.Rd | 19 +++++++---- 16 files changed, 180 insertions(+), 81 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.7 dated 2015-07-08 and 0.8 dated 2015-09-10
vegdata-0.7/vegdata/R/ESveg.r |only vegdata-0.7/vegdata/inst/tvdata/Data/elbaue/metainfo.txt |only vegdata-0.7/vegdata/inst/tvdata/Data/taxatest/metainfo.txt |only vegdata-0.7/vegdata/inst/tvdata/Data/taxatest/tvexport.xml |only vegdata-0.7/vegdata/man/ESveg.Rd |only vegdata-0.7/vegdata/vignettes/vegdata.bib |only vegdata-0.8/vegdata/DESCRIPTION | 10 vegdata-0.8/vegdata/MD5 | 73 +- vegdata-0.8/vegdata/NAMESPACE | 7 vegdata-0.8/vegdata/R/child.r | 18 vegdata-0.8/vegdata/R/monotypic.r | 2 vegdata-0.8/vegdata/R/reflist.r | 52 - vegdata-0.8/vegdata/R/syntab.r | 9 vegdata-0.8/vegdata/R/tax.r | 27 vegdata-0.8/vegdata/R/taxval.r | 370 +++++-------- vegdata-0.8/vegdata/R/tv.biblio.r | 7 vegdata-0.8/vegdata/R/tv.compRefl.r | 14 vegdata-0.8/vegdata/R/tv.coverperc.r | 2 vegdata-0.8/vegdata/R/tv.obs.r | 2 vegdata-0.8/vegdata/R/tv.site.r | 6 vegdata-0.8/vegdata/R/tv.traits.r | 16 vegdata-0.8/vegdata/R/tv.veg.r | 16 vegdata-0.8/vegdata/R/tv.write.r | 4 vegdata-0.8/vegdata/R/zzz.r | 2 vegdata-0.8/vegdata/inst/ChangeLog | 3 vegdata-0.8/vegdata/inst/doc/vegdata.R | 7 vegdata-0.8/vegdata/inst/doc/vegdata.Rnw | 19 vegdata-0.8/vegdata/inst/doc/vegdata.pdf |binary vegdata-0.8/vegdata/inst/tvdata/Data/elbaue/metadata.txt |only vegdata-0.8/vegdata/inst/tvdata/Data/taxatest/TvAdmin.dbf |binary vegdata-0.8/vegdata/inst/tvdata/Data/taxatest/metadata.txt |only vegdata-0.8/vegdata/inst/tvdata/Data/taxatest/tvabund.dbf |binary vegdata-0.8/vegdata/inst/tvdata/Data/taxatest/tvhabita.dbf |binary vegdata-0.8/vegdata/inst/tvdata/Data/taxatest/tvwin.set |binary vegdata-0.8/vegdata/man/taxval.Rd | 17 vegdata-0.8/vegdata/man/tv.biblio.Rd | 3 vegdata-0.8/vegdata/man/tv.site.Rd | 2 vegdata-0.8/vegdata/man/tv.write.Rd | 2 vegdata-0.8/vegdata/man/vegdata-internal.Rd | 1 vegdata-0.8/vegdata/tests/testthat/test.R | 62 +- vegdata-0.8/vegdata/vignettes/lib.bib |only vegdata-0.8/vegdata/vignettes/vegdata.Rnw | 19 42 files changed, 354 insertions(+), 418 deletions(-)
Title: Various Functions for Handling and Manipulating Remote Sensing
Data
Description: This smorgasbord provides a variety of functions which are useful
for handling, manipulating and visualizing remote sensing data.
Author: Thomas Nauss, Hanna Meyer, Florian Detsch, Tim Appelhans
Maintainer: Tim Appelhans
<admin@environmentalinformatics-marburg.de>
Diff between satellite versions 0.1.0 dated 2015-07-22 and 0.2.0 dated 2015-09-10
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++++--------- NAMESPACE | 3 +++ R/brick.R |only R/plot.R | 2 +- R/satellite-package.R | 1 + R/stack.R |only R/sysdata.rda |binary build/vignette.rds |binary data/l7.rda |binary data/l8.rda |binary inst/doc/landsat-calibration.html | 4 ++-- man/brick.Rd |only man/stack.Rd |only 14 files changed, 25 insertions(+), 17 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.0 dated 2015-07-25 and 0.12.1 dated 2015-09-10
Rcpp-0.12.0/Rcpp/inst/unitTests/testRcppClass/R/yada.R |only Rcpp-0.12.1/Rcpp/ChangeLog | 145 ++++++++ Rcpp-0.12.1/Rcpp/DESCRIPTION | 8 Rcpp-0.12.1/Rcpp/MD5 | 140 ++++---- Rcpp-0.12.1/Rcpp/R/Attributes.R | 4 Rcpp-0.12.1/Rcpp/R/loadModule.R | 6 Rcpp-0.12.1/Rcpp/build/Rcpp.pdf |binary Rcpp-0.12.1/Rcpp/build/vignette.rds |binary Rcpp-0.12.1/Rcpp/inst/NEWS.Rd | 47 ++ Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-FAQ.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-attributes.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-extending.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-modules.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-package.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-sugar.Rnw | 2 Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary Rcpp-0.12.1/Rcpp/inst/doc/Rcpp.bib | 30 + Rcpp-0.12.1/Rcpp/inst/include/Rcpp.h | 2 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/Benchmark/Timer.h | 2 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/Dimension.h | 2 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/Nullable.h |only Rcpp-0.12.1/Rcpp/inst/include/Rcpp/Reference.h | 8 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/String.h | 41 ++ Rcpp-0.12.1/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/utils/tinyformat.h | 41 ++ Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/DimNameProxy.h | 45 +- Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/Matrix.h | 164 +++++++++- Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/Subsetter.h | 30 + Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/Vector.h | 66 +++- Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/const_string_proxy.h | 7 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/converter.h | 2 Rcpp-0.12.1/Rcpp/inst/include/Rcpp/vector/string_proxy.h | 8 Rcpp-0.12.1/Rcpp/inst/include/RcppCommon.h | 1 Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/Matrix.cpp | 4 Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/Module.cpp | 141 ++++---- Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/String.cpp | 20 + Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/Subset.cpp | 46 ++ Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/Vector.cpp | 28 + Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/misc.cpp | 84 +++-- Rcpp-0.12.1/Rcpp/inst/unitTests/cpp/modref.cpp | 22 - Rcpp-0.12.1/Rcpp/inst/unitTests/runit.Matrix.R | 12 Rcpp-0.12.1/Rcpp/inst/unitTests/runit.Module.R | 12 Rcpp-0.12.1/Rcpp/inst/unitTests/runit.Module.client.package.R | 2 Rcpp-0.12.1/Rcpp/inst/unitTests/runit.String.R | 24 + Rcpp-0.12.1/Rcpp/inst/unitTests/runit.Vector.R | 26 + Rcpp-0.12.1/Rcpp/inst/unitTests/runit.misc.R | 23 + Rcpp-0.12.1/Rcpp/inst/unitTests/runit.modref.R | 8 Rcpp-0.12.1/Rcpp/inst/unitTests/runit.subset.R | 11 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppClass/NAMESPACE | 2 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppClass/R/load.R | 6 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppClass/man/Rcpp_class_examples.Rd | 6 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppClass/src/rcpp_module.cpp | 44 +- Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppModule/DESCRIPTION | 6 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppModule/R/zzz.R | 4 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppModule/src/Num.cpp | 14 Rcpp-0.12.1/Rcpp/inst/unitTests/testRcppModule/src/rcpp_module.cpp | 28 - Rcpp-0.12.1/Rcpp/src/api.cpp | 6 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-FAQ.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-attributes.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-extending.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-modules.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-package.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp-sugar.Rnw | 2 Rcpp-0.12.1/Rcpp/vignettes/Rcpp.bib | 30 + 72 files changed, 1087 insertions(+), 349 deletions(-)
Title: Request Data from the U.S. Bureau of Labor Statistics API
Description: Allows users to request data for one or multiple series through the U.S. Bureau of Labor Statistics API. Users provide parameters as specified in http://www.bls.gov/developers/api_signature.htm and the function returns a JSON string.
Author: Michael Silva <mike.a.silva@gmail.com>
Maintainer: Michael Silva <mike.a.silva@gmail.com>
Diff between blsAPI versions 0.1.1 dated 2014-12-31 and 0.1.2 dated 2015-09-10
DESCRIPTION | 7 +++---- MD5 | 4 ++-- R/blsAPI.R | 11 ++++++++++- 3 files changed, 15 insertions(+), 7 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.2 dated 2015-09-07 and 0.4.4 dated 2015-09-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/lingpg.R | 14 +++++++------- inst/NEWS | 4 ++++ man/lingpg.Rd | 2 +- man/vardpoor-package.Rd | 4 ++-- 6 files changed, 23 insertions(+), 19 deletions(-)
Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between lgcp versions 1.3-9 dated 2015-02-25 and 1.3-11 dated 2015-09-10
DESCRIPTION | 8 MD5 | 768 +++++++-------- NAMESPACE | 19 R/lgcp.R | 9 R/lgcpMethods.R | 2 build/vignette.rds |binary inst/doc/lgcp.pdf |binary man/BetaParameters.Rd | 2 man/C.diff.single.im.Rd | 2 man/CovFunction.Rd | 2 man/CovFunction.function.Rd | 2 man/CovParameters.Rd | 2 man/Cvb.Rd | 2 man/EvaluatePrior.Rd | 2 man/Extract.mstppp.Rd | 2 man/Extract.stppp.Rd | 2 man/GAfinalise.MonteCarloAverage.Rd | 2 man/GAfinalise.Rd | 2 man/GAfinalise.nullAverage.Rd | 2 man/GAinitialise.MonteCarloAverage.Rd | 2 man/GAinitialise.Rd | 2 man/GAinitialise.nullAverage.Rd | 2 man/GAreturnvalue.MonteCarloAverage.Rd | 2 man/GAreturnvalue.Rd | 2 man/GAreturnvalue.nullAverage.Rd | 2 man/GAupdate.MonteCarloAverage.Rd | 2 man/GAupdate.Rd | 2 man/GAupdate.nullAverage.Rd | 2 man/GFfinalise.Rd | 2 man/GFfinalise.dump2dir.Rd | 2 man/GFfinalise.nullFunction.Rd | 2 man/GFinitialise.Rd | 2 man/GFinitialise.dump2dir.Rd | 2 man/GFinitialise.nullFunction.Rd | 2 man/GFreturnvalue.Rd | 2 man/GFreturnvalue.dump2dir.Rd | 2 man/GFreturnvalue.nullFunction.Rd | 2 man/GFupdate.Rd | 2 man/GFupdate.dump2dir.Rd | 2 man/GFupdate.nullFunction.Rd | 2 man/GPdrv.Rd | 2 man/GPdrv2.Rd | 2 man/GPdrv2_Multitype.Rd | 2 man/GPlist2array.Rd | 2 man/GPrealisation.Rd | 2 man/GammafromY.Rd | 2 man/GaussianPrior.Rd | 2 man/K.diff.single.Rd | 2 man/K.u.Rd | 2 man/K.val.Rd | 2 man/KinhomAverage.Rd | 2 man/LogGaussianPrior.Rd | 2 man/MALAlgcp.Rd | 2 man/MALAlgcpAggregateSpatial.PlusPars.Rd | 2 man/MALAlgcpMultitypeSpatial.PlusPars.Rd | 2 man/MALAlgcpSpatial.PlusPars.Rd | 2 man/MALAlgcpSpatial.Rd | 2 man/MALAlgcpSpatioTemporal.PlusPars.Rd | 2 man/MonteCarloAverage.Rd | 2 man/PriorSpec.Rd | 2 man/PriorSpec.list.Rd | 2 man/RandomFieldsCovFct.Rd | 2 man/SpatialPolygonsDataFrame.stapp.Rd | 2 man/SpikedExponentialCovFct.Rd | 2 man/YfromGamma.Rd | 2 man/add.list.Rd | 2 man/addTemporalCovariates.Rd | 2 man/affine.SpatialPolygonsDataFrame.Rd | 2 man/affine.fromFunction.Rd | 2 man/affine.fromSPDF.Rd | 2 man/affine.fromXYZ.Rd | 2 man/affine.stppp.Rd | 2 man/aggCovInfo.ArealWeightedMean.Rd | 2 man/aggCovInfo.ArealWeightedSum.Rd | 2 man/aggCovInfo.Majority.Rd | 2 man/aggCovInfo.Rd | 2 man/aggregateCovariateInfo.Rd | 2 man/aggregateformulaList.Rd | 2 man/andrieuthomsh.Rd | 2 man/as.SpatialGridDataFrame.Rd | 2 man/as.SpatialGridDataFrame.fromXYZ.Rd | 2 man/as.SpatialPixelsDataFrame.Rd | 2 man/as.SpatialPixelsDataFrame.lgcpgrid.Rd | 2 man/as.array.lgcpgrid.Rd | 2 man/as.fromXYZ.Rd | 2 man/as.fromXYZ.fromFunction.Rd | 2 man/as.im.fromFunction.Rd | 2 man/as.im.fromSPDF.Rd | 2 man/as.im.fromXYZ.Rd | 2 man/as.list.lgcpgrid.Rd | 2 man/as.owin.stapp.Rd | 2 man/as.owinlist.Rd | 2 man/as.owinlist.SpatialPolygonsDataFrame.Rd | 2 man/as.owinlist.stapp.Rd | 2 man/as.ppp.mstppp.Rd | 2 man/as.ppp.stppp.Rd | 2 man/as.stppp.Rd | 2 man/as.stppp.stapp.Rd | 2 man/assigninterp.Rd | 2 man/at.Rd | 2 man/autocorr.Rd | 2 man/autocorrMultitype.Rd | 2 man/betavals.Rd | 2 man/blockcircbase.Rd | 2 man/blockcircbaseFunction.Rd | 2 man/bt.scalar.Rd | 2 man/checkObsWin.Rd | 2 man/chooseCellwidth.Rd | 2 man/circulant.Rd | 2 man/circulant.matrix.Rd | 2 man/circulant.numeric.Rd | 2 man/clearinterp.Rd | 2 man/computeGradtruncSpatial.Rd | 2 man/computeGradtruncSpatioTemporal.Rd | 2 man/condProbs.Rd | 2 man/constantInTime.Rd | 2 man/constantInTime.numeric.Rd | 2 man/constantInTime.stppp.Rd | 2 man/constanth.Rd | 2 man/cov.interp.fft.Rd | 2 man/covEffects.Rd | 2 man/d.func.Rd | 2 man/density.stppp.Rd | 2 man/discreteWindow.Rd | 2 man/discreteWindow.lgcpPredict.Rd | 2 man/dump2dir.Rd | 2 man/eigenfrombase.Rd | 2 man/etavals.Rd | 2 man/exceedProbs.Rd | 2 man/exceedProbsAggregated.Rd | 2 man/expectation.Rd | 2 man/expectation.lgcpPredict.Rd | 2 man/expectation.lgcpPredictSpatialOnlyPlusParameters.Rd | 2 man/exponentialCovFct.Rd | 2 man/extendspatialAtRisk.Rd | 2 man/extract.Rd | 2 man/extract.lgcpPredict.Rd | 2 man/fftgrid.Rd | 2 man/fftinterpolate.Rd | 2 man/fftinterpolate.fromFunction.Rd | 2 man/fftinterpolate.fromSPDF.Rd | 2 man/fftinterpolate.fromXYZ.Rd | 2 man/fftmultiply.Rd | 2 man/formulaList.Rd | 2 man/g.diff.single.Rd | 2 man/gOverlay.Rd | 2 man/genFFTgrid.Rd | 2 man/getCellCounts.Rd | 2 man/getCounts.Rd | 2 man/getCovParameters.GPrealisation.Rd | 2 man/getCovParameters.Rd | 2 man/getCovParameters.list.Rd | 2 man/getLHSformulaList.Rd | 2 man/getRotation.Rd | 2 man/getRotation.default.Rd | 2 man/getRotation.stppp.Rd | 2 man/getZmat.Rd | 2 man/getZmats.Rd | 2 man/getinterp.Rd | 2 man/getlgcpPredictSpatialINLA.Rd | 2 man/getpolyol.Rd | 2 man/getup.Rd | 2 man/ginhomAverage.Rd | 2 man/grid2spdf.Rd | 2 man/grid2spix.Rd | 2 man/grid2spoly.Rd | 2 man/grid2spts.Rd | 2 man/gridInWindow.Rd | 2 man/gridav.Rd | 2 man/gridav.lgcpPredict.Rd | 2 man/gridfun.Rd | 2 man/gridfun.lgcpPredict.Rd | 2 man/gu.Rd | 2 man/guessinterp.Rd | 2 man/hasNext.Rd | 2 man/hasNext.iter.Rd | 2 man/hvals.Rd | 2 man/hvals.lgcpPredict.Rd | 2 man/identify.lgcpPredict.Rd | 2 man/identifygrid.Rd | 2 man/image.lgcpgrid.Rd | 2 man/initialiseAMCMC.Rd | 2 man/initialiseAMCMC.andrieuthomsh.Rd | 2 man/initialiseAMCMC.constanth.Rd | 2 man/integerise.Rd | 2 man/integerise.mstppp.Rd | 2 man/integerise.stppp.Rd | 2 man/intens.Rd | 2 man/intens.lgcpPredict.Rd | 2 man/intens.lgcpSimMultitypeSpatialPlusParameters.Rd | 2 man/intens.lgcpSimSpatialPlusParameters.Rd | 2 man/interptypes.Rd | 2 man/inversebase.Rd | 2 man/is.SPD.Rd | 2 man/is.burnin.Rd | 2 man/is.pow2.Rd | 2 man/is.retain.Rd | 2 man/iteration.Rd | 2 man/lambdaEst.Rd | 2 man/lambdaEst.ppp.Rd | 2 man/lambdaEst.stppp.Rd | 2 man/lgcp-package.Rd | 2 man/lgcpForecast.Rd | 2 man/lgcpInits.Rd | 2 man/lgcpPredict.Rd | 2 man/lgcpPredictAggregateSpatialPlusPars.Rd | 2 man/lgcpPredictAggregated.Rd | 2 man/lgcpPredictMultitypeSpatialPlusPars.Rd | 2 man/lgcpPredictSpatial.Rd | 2 man/lgcpPredictSpatialINLA.Rd | 2 man/lgcpPredictSpatialPlusPars.Rd | 2 man/lgcpPredictSpatioTemporalPlusPars.Rd | 2 man/lgcpPrior.Rd | 2 man/lgcpSim.Rd | 2 man/lgcpSimMultitypeSpatialCovariates.Rd | 2 man/lgcpSimSpatial.Rd | 2 man/lgcpSimSpatialCovariates.Rd | 2 man/lgcpbayes.Rd | 2 man/lgcpgrid.Rd | 2 man/lgcpgrid.array.Rd | 2 man/lgcpgrid.list.Rd | 2 man/lgcpgrid.matrix.Rd | 2 man/lgcppars.Rd | 2 man/lgcpvignette.Rd | 2 man/loc2poly.Rd | 2 man/loop.mcmc.Rd | 2 man/ltar.Rd | 2 man/matchcovariance.Rd | 2 man/mcmcLoop.Rd | 2 man/mcmcProgressNone.Rd | 2 man/mcmcProgressPrint.Rd | 2 man/mcmcProgressTextBar.Rd | 2 man/mcmcProgressTk.Rd | 2 man/mcmcpars.Rd | 2 man/mcmctrace.Rd | 2 man/mcmctrace.lgcpPredict.Rd | 2 man/meanfield.Rd | 2 man/meanfield.lgcpPredict.Rd | 2 man/meanfield.lgcpPredictINLA.Rd | 2 man/minimum.contrast.Rd | 2 man/minimum.contrast.spatiotemporal.Rd | 2 man/mstppp.Rd | 2 man/mstppp.list.Rd | 2 man/mstppp.ppp.Rd | 2 man/mstppp.stppp.Rd | 2 man/muEst.Rd | 2 man/multiply.list.Rd | 2 man/my.KinhomAverage.Rd | 2 man/my.ginhomAverage.Rd | 2 man/neattable.Rd | 2 man/neigh2D.Rd | 2 man/nextStep.Rd | 2 man/nullAverage.Rd | 2 man/nullFunction.Rd | 2 man/numCases.Rd | 2 man/osppp2latlon.Rd | 2 man/osppp2merc.Rd | 2 man/paramprec.Rd | 2 man/paramprecbase.Rd | 2 man/parautocorr.Rd | 2 man/parsummary.Rd | 2 man/plot.fromSPDF.Rd | 2 man/plot.fromXYZ.Rd | 2 man/plot.lgcpAutocorr.Rd | 2 man/plot.lgcpPredict.Rd | 2 man/plot.lgcpQuantiles.Rd | 2 man/plot.lgcpZmat.Rd | 2 man/plot.lgcpgrid.Rd | 2 man/plot.mcmcdiag.Rd | 2 man/plot.mstppp.Rd | 2 man/plot.stppp.Rd | 2 man/plot.temporalAtRisk.Rd | 2 man/plotExceed.Rd | 2 man/plotExceed.array.Rd | 2 man/plotExceed.lgcpPredict.Rd | 2 man/plotit.Rd | 2 man/postcov.Rd | 2 man/postcov.lgcpPredictAggregateSpatialPlusParameters.Rd | 2 man/postcov.lgcpPredictMultitypeSpatialPlusParameters.Rd | 2 man/postcov.lgcpPredictSpatialOnlyPlusParameters.Rd | 2 man/postcov.lgcpPredictSpatioTemporalPlusParameters.Rd | 2 man/print.dump2dir.Rd | 2 man/print.fromFunction.Rd | 2 man/print.fromSPDF.Rd | 2 man/print.fromXYZ.Rd | 2 man/print.gridaverage.Rd | 2 man/print.lgcpPredict.Rd | 2 man/print.lgcpgrid.Rd | 2 man/print.mcmc.Rd | 2 man/print.mstppp.Rd | 2 man/print.stapp.Rd | 2 man/print.stppp.Rd | 2 man/print.temporalAtRisk.Rd | 2 man/priorpost.Rd | 2 man/quantile.lgcpPredict.Rd | 2 man/quantile.lgcpgrid.Rd | 2 man/raster.lgcpgrid.Rd | 2 man/rescale.mstppp.Rd | 2 man/rescale.stppp.Rd | 2 man/resetLoop.Rd | 2 man/rgauss.Rd | 2 man/roteffgain.Rd | 2 man/rotmat.Rd | 2 man/rr.Rd | 2 man/rr.lgcpPredict.Rd | 2 man/samplePosterior.Rd | 2 man/segProbs.Rd | 2 man/seintens.Rd | 2 man/seintens.lgcpPredict.Rd | 2 man/selectObsWindow.Rd | 2 man/selectObsWindow.default.Rd | 2 man/selectObsWindow.stppp.Rd | 2 man/serr.Rd | 2 man/serr.lgcpPredict.Rd | 2 man/setTxtProgressBar2.Rd | 2 man/setoutput.Rd | 2 man/showGrid.Rd | 2 man/showGrid.default.Rd | 2 man/showGrid.lgcpPredict.Rd | 2 man/showGrid.stppp.Rd | 2 man/smultiply.list.Rd | 2 man/sparsebase.Rd | 2 man/spatialAtRisk.Rd | 2 man/spatialAtRisk.SpatialGridDataFrame.Rd | 2 man/spatialAtRisk.SpatialPolygonsDataFrame.Rd | 2 man/spatialAtRisk.bivden.Rd | 2 man/spatialAtRisk.default.Rd | 2 man/spatialAtRisk.fromXYZ.Rd | 2 man/spatialAtRisk.function.Rd | 2 man/spatialAtRisk.im.Rd | 2 man/spatialAtRisk.lgcpgrid.Rd | 2 man/spatialIntensities.Rd | 2 man/spatialIntensities.fromSPDF.Rd | 2 man/spatialIntensities.fromXYZ.Rd | 2 man/spatialparsEst.Rd | 2 man/stGPrealisation.Rd | 2 man/stapp.Rd | 2 man/stapp.SpatialPolygonsDataFrame.Rd | 2 man/stapp.list.Rd | 2 man/stppp.Rd | 2 man/stppp.list.Rd | 2 man/stppp.ppp.Rd | 2 man/summary.lgcpgrid.Rd | 2 man/summary.mcmc.Rd | 2 man/target.and.grad.AggregateSpatialPlusPars.Rd | 2 man/target.and.grad.MultitypespatialPlusPars.Rd | 2 man/target.and.grad.SpatioTemporalPlusPars.Rd | 2 man/target.and.grad.spatial.Rd | 2 man/target.and.grad.spatialPlusPars.Rd | 2 man/target.and.grad.spatiotemporal.Rd | 2 man/tempRaster.Rd | 2 man/temporalAtRisk.Rd | 2 man/temporalAtRisk.function.Rd | 2 man/temporalAtRisk.numeric.Rd | 2 man/textsummary.Rd | 2 man/thetaEst.Rd | 2 man/toral.cov.mat.Rd | 2 man/touchingowin.Rd | 2 man/traceplots.Rd | 2 man/transblack.Rd | 2 man/transblue.Rd | 2 man/transgreen.Rd | 2 man/transred.Rd | 2 man/txtProgressBar2.Rd | 2 man/updateAMCMC.Rd | 2 man/updateAMCMC.andrieuthomsh.Rd | 2 man/updateAMCMC.constanth.Rd | 2 man/varfield.Rd | 2 man/varfield.lgcpPredict.Rd | 2 man/varfield.lgcpPredictINLA.Rd | 2 man/window.lgcpPredict.Rd | 2 man/xvals.Rd | 2 man/xvals.SpatialGridDataFrame.Rd | 2 man/xvals.default.Rd | 2 man/xvals.fromXYZ.Rd | 2 man/xvals.lgcpPredict.Rd | 2 man/yvals.Rd | 2 man/yvals.SpatialGridDataFrame.Rd | 2 man/yvals.default.Rd | 2 man/yvals.fromXYZ.Rd | 2 man/yvals.lgcpPredict.Rd | 2 man/zvals.Rd | 2 man/zvals.SpatialGridDataFrame.Rd | 2 man/zvals.default.Rd | 2 man/zvals.fromXYZ.Rd | 2 385 files changed, 789 insertions(+), 773 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-04 1.2-2
2009-06-18 1.2-1
2009-06-16 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-27 2.1
2009-06-16 2.0-1
Title: Text Mining Distributed Corpus Plug-In
Description: A plug-in for the text mining framework tm to support text mining
in a distributed way. The package provides a convenient interface for
handling distributed corpus objects based on distributed list objects.
Author: Ingo Feinerer [aut],
Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between tm.plugin.dc versions 0.2-7 dated 2014-06-15 and 0.2-8 dated 2015-09-10
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/corpus.R | 2 ++ man/DistributedCorpus.Rd | 7 ++++--- 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.3.0 dated 2015-09-08 and 0.3.1 dated 2015-09-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/expand.R | 2 +- inst/doc/tidy-data.html | 4 ++-- man/seq_range.Rd | 4 ++-- src/melt.cpp | 2 +- tests/testthat/test-gather.R | 8 ++++++++ 7 files changed, 23 insertions(+), 15 deletions(-)
Title: Statistical Methods for Ranking Data
Description: Functions and datasets to support Mayer Alvo and Philip L.H. Yu (2014). "Statistical Methods for Ranking Data", Springer. In this packages, smaller ranks stand for more preferred items.
Author: Li Qinglong
Maintainer: Li Qinglong <liqinglong0830@163.com>
Diff between StatMethRank versions 1.2 dated 2015-07-29 and 1.3 dated 2015-09-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/myrand.h | 8 ++++---- src/utility.h | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 0.10.0 dated 2015-05-22 and 0.11 dated 2015-09-10
mosaic-0.10.0/mosaic/man/fetchData.Rd |only mosaic-0.10.0/mosaic/man/fetchGapminder.Rd |only mosaic-0.10.0/mosaic/man/fetchGoogle.Rd |only mosaic-0.11/mosaic/DESCRIPTION | 16 mosaic-0.11/mosaic/MD5 | 192 +- mosaic-0.11/mosaic/NAMESPACE | 81 mosaic-0.11/mosaic/R/aggregatingAux.R | 160 + mosaic-0.11/mosaic/R/aggregatingMeta.R | 175 + mosaic-0.11/mosaic/R/ashplot.R |only mosaic-0.11/mosaic/R/binom.test.R | 2 mosaic-0.11/mosaic/R/confint.R | 167 + mosaic-0.11/mosaic/R/do.R | 315 +-- mosaic-0.11/mosaic/R/favstats.R | 2 mosaic-0.11/mosaic/R/fetchData.R | 217 -- mosaic-0.11/mosaic/R/fetchGapminder.R | 68 mosaic-0.11/mosaic/R/fetchGoogle.R | 90 mosaic-0.11/mosaic/R/frequencyPolygon.R | 135 + mosaic-0.11/mosaic/R/mPlots.R | 56 mosaic-0.11/mosaic/R/makeFun.R | 60 mosaic-0.11/mosaic/R/mosaic-package.R | 13 mosaic-0.11/mosaic/R/mplot.R | 21 mosaic-0.11/mosaic/R/perctable.R | 9 mosaic-0.11/mosaic/R/plotFun.R | 904 ++++++---- mosaic-0.11/mosaic/R/plotModel.R |only mosaic-0.11/mosaic/R/pqrdata.R | 1 mosaic-0.11/mosaic/R/project.R | 34 mosaic-0.11/mosaic/R/read.file.R | 2 mosaic-0.11/mosaic/R/resample.R | 86 mosaic-0.11/mosaic/R/ttest.R | 4 mosaic-0.11/mosaic/README.md | 3 mosaic-0.11/mosaic/build/vignette.rds |binary mosaic-0.11/mosaic/inst/doc/GraphicsWithMosaic.R | 4 mosaic-0.11/mosaic/inst/doc/GraphicsWithMosaic.Rmd | 4 mosaic-0.11/mosaic/inst/doc/GraphicsWithMosaic.html | 248 +- mosaic-0.11/mosaic/inst/doc/LessVolume-MoreCreativity.R | 64 mosaic-0.11/mosaic/inst/doc/LessVolume-MoreCreativity.Rmd | 6 mosaic-0.11/mosaic/inst/doc/LessVolume-MoreCreativity.html | 305 +-- mosaic-0.11/mosaic/inst/doc/MinimalR.R | 3 mosaic-0.11/mosaic/inst/doc/MinimalR.Rnw | 3 mosaic-0.11/mosaic/inst/doc/MinimalR.pdf |binary mosaic-0.11/mosaic/inst/doc/Resampling.R | 42 mosaic-0.11/mosaic/inst/doc/Resampling.Rnw | 42 mosaic-0.11/mosaic/inst/doc/Resampling.pdf |binary mosaic-0.11/mosaic/inst/doc/mosaic-resources.Rmd | 2 mosaic-0.11/mosaic/inst/doc/mosaic-resources.html | 11 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mosaic-0.11/mosaic/vignettes/GraphicsWithMosaic.Rmd | 4 mosaic-0.11/mosaic/vignettes/GraphicsWithMosaic_files |only mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity.Rmd | 6 mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/ladies5000-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-10-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-16-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-17-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-19-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-31-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-32-1.png |binary mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-37-1.png 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mosaic-0.11/mosaic/vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-9-1.png |binary mosaic-0.11/mosaic/vignettes/MinimalR.Rnw | 3 mosaic-0.11/mosaic/vignettes/Resampling.Rnw | 42 mosaic-0.11/mosaic/vignettes/mosaic-resources.Rmd | 2 92 files changed, 2227 insertions(+), 1647 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.0.4 dated 2015-08-14 and 0.1.0 dated 2015-09-10
DESCRIPTION | 12 ++-- MD5 | 12 ++-- NAMESPACE | 1 R/helpers.R | 20 +++---- R/kdecop.R | 132 +++++++++++++++++++++++++++++------------------ man/kdecop.Rd | 10 ++- man/kdecopula-package.Rd | 4 - 7 files changed, 115 insertions(+), 76 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 1.2-3 dated 2014-03-25 and 1.2-4 dated 2015-09-10
Description: Probability propagation in graphical independence networks, also known as probabilistic expert systems or Bayesian networks.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRain-1.2-3/gRain/R/Finding.R |only
gRain-1.2-3/gRain/R/GraphAlgo-misc.R |only
gRain-1.2-3/gRain/R/gRain-utilities.R |only
gRain-1.2-3/gRain/R/get_gRain.R |only
gRain-1.2-3/gRain/R/infoPrint.R |only
gRain-1.2-3/gRain/R/printlist.R |only
gRain-1.2-3/gRain/R/random_cpt.R |only
gRain-1.2-3/gRain/R/simulate-grain.R |only
gRain-1.2-3/gRain/demo/gRain.R |only
gRain-1.2-4/gRain/ChangeLog | 6
gRain-1.2-4/gRain/DESCRIPTION | 18 +
gRain-1.2-4/gRain/MD5 | 71 +++----
gRain-1.2-4/gRain/NAMESPACE | 58 +++++-
gRain-1.2-4/gRain/R/CPT-POT-compile.R | 270 +++++++---------------------
gRain-1.2-4/gRain/R/CPT-POT-extract.R | 60 ++++--
gRain-1.2-4/gRain/R/RcppExports.R |only
gRain-1.2-4/gRain/R/cptable.R | 16 +
gRain-1.2-4/gRain/R/display.R | 48 ++--
gRain-1.2-4/gRain/R/evidence.R |only
gRain-1.2-4/gRain/R/finding.R |only
gRain-1.2-4/gRain/R/grain-compile.R | 164 +++++------------
gRain-1.2-4/gRain/R/grain-main.R | 45 +++-
gRain-1.2-4/gRain/R/grain-simulate.R |only
gRain-1.2-4/gRain/R/grain-utilities.R |only
gRain-1.2-4/gRain/R/potentialList.R | 91 ++++-----
gRain-1.2-4/gRain/R/predict.R | 107 ++++++-----
gRain-1.2-4/gRain/R/propagate.R | 138 ++++++++------
gRain-1.2-4/gRain/R/querygrain.R | 257 ++++++++++++++------------
gRain-1.2-4/gRain/R/summary.R | 41 ++--
gRain-1.2-4/gRain/R/update.R | 53 -----
gRain-1.2-4/gRain/build/vignette.rds |binary
gRain-1.2-4/gRain/demo/00Index | 2
gRain-1.2-4/gRain/demo/asia.R |only
gRain-1.2-4/gRain/inst/doc/gRain-intro.R | 111 +++++------
gRain-1.2-4/gRain/inst/doc/gRain-intro.Rnw | 118 ++++++++----
gRain-1.2-4/gRain/inst/doc/gRain-intro.pdf |binary
gRain-1.2-4/gRain/man/finding.Rd |only
gRain-1.2-4/gRain/man/grain.Rd | 13 -
gRain-1.2-4/gRain/man/internal-gRain.Rd | 11 +
gRain-1.2-4/gRain/man/propagate.grain.Rd | 52 ++++-
gRain-1.2-4/gRain/man/querygrain.Rd | 50 ++---
gRain-1.2-4/gRain/src |only
gRain-1.2-4/gRain/vignettes/gRain-intro.Rnw | 118 ++++++++----
43 files changed, 1000 insertions(+), 918 deletions(-)
More information about dataonderivatives at CRAN
Permanent link
Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.2 dated 2015-07-27 and 1.0.3 dated 2015-09-09
warbleR-1.0.2/warbleR/R/Arre.aura-data.R |only warbleR-1.0.2/warbleR/R/Phae.cuvi-data.R |only warbleR-1.0.2/warbleR/data/Arre.aura.rda |only warbleR-1.0.2/warbleR/data/Phae.cuvi.rda |only warbleR-1.0.2/warbleR/data/datalist |only warbleR-1.0.2/warbleR/man/Arre.aura.Rd |only warbleR-1.0.2/warbleR/man/Phae.cuvi.Rd |only warbleR-1.0.3/warbleR/DESCRIPTION | 12 - warbleR-1.0.3/warbleR/MD5 | 65 +++++--- warbleR-1.0.3/warbleR/R/autodetec.R | 211 ++++++++++++++++++----------- warbleR-1.0.3/warbleR/R/lspec.R | 14 - warbleR-1.0.3/warbleR/R/manualoc.df-data.R | 4 warbleR-1.0.3/warbleR/R/querxc.R | 28 +++ warbleR-1.0.3/warbleR/R/sig2noise.R | 8 - warbleR-1.0.3/warbleR/R/snrspecs.R | 33 ++-- warbleR-1.0.3/warbleR/R/specreator.R | 22 +-- warbleR-1.0.3/warbleR/R/trackfreqs.R | 62 ++++---- warbleR-1.0.3/warbleR/R/warbleR-package.R | 2 warbleR-1.0.3/warbleR/build |only warbleR-1.0.3/warbleR/data/manualoc.df.rda |binary warbleR-1.0.3/warbleR/inst/CITATION | 4 warbleR-1.0.3/warbleR/inst/doc |only warbleR-1.0.3/warbleR/man/lspec.Rd | 7 warbleR-1.0.3/warbleR/man/manualoc.df.Rd | 4 warbleR-1.0.3/warbleR/man/querxc.Rd | 10 + warbleR-1.0.3/warbleR/man/sig2noise.Rd | 8 - warbleR-1.0.3/warbleR/man/snrspecs.Rd | 12 - warbleR-1.0.3/warbleR/man/specreator.Rd | 15 -- warbleR-1.0.3/warbleR/man/trackfreqs.Rd | 31 +--- warbleR-1.0.3/warbleR/man/warbleR.Rd | 12 - warbleR-1.0.3/warbleR/vignettes |only 31 files changed, 328 insertions(+), 236 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.10 dated 2015-06-15 and 1.13 dated 2015-09-09
mirt-1.10/mirt/R/read.mirt.R |only mirt-1.10/mirt/src/dgroup.c |only mirt-1.13/mirt/DESCRIPTION | 12 mirt-1.13/mirt/MD5 | 106 +++--- mirt-1.13/mirt/NAMESPACE | 7 mirt-1.13/mirt/NEWS | 24 + mirt-1.13/mirt/R/02-item_methods.R | 94 +---- mirt-1.13/mirt/R/03-estimation.R | 44 +- mirt-1.13/mirt/R/DTF.R | 6 mirt-1.13/mirt/R/Discrete-methods.R | 17 - mirt-1.13/mirt/R/EMstep.group.R | 10 mirt-1.13/mirt/R/EMstep.utils.R | 43 ++ mirt-1.13/mirt/R/LoadPars.R | 2 mirt-1.13/mirt/R/M2.R | 5 mirt-1.13/mirt/R/MHRM.group.R | 61 +-- mirt-1.13/mirt/R/MultipleGroup-methods.R | 80 +++- mirt-1.13/mirt/R/PLCI.mirt.R | 2 mirt-1.13/mirt/R/SE.methods.R | 54 ++- mirt-1.13/mirt/R/SingleGroup-methods.R | 154 ++++++--- mirt-1.13/mirt/R/boot.mirt.R | 22 - mirt-1.13/mirt/R/fscores.internal.R | 30 + mirt-1.13/mirt/R/imputeMissing.R | 39 -- mirt-1.13/mirt/R/itemGAM.R | 25 + mirt-1.13/mirt/R/itemfit.R | 74 +++- mirt-1.13/mirt/R/iteminfo.R | 11 mirt-1.13/mirt/R/itemplot.R | 32 + mirt-1.13/mirt/R/itemplot.internal.R | 38 +- mirt-1.13/mirt/R/key2binary.R | 25 + mirt-1.13/mirt/R/marginal_rxx.R | 4 mirt-1.13/mirt/R/mirt-package.R | 6 mirt-1.13/mirt/R/mirt.R | 17 - mirt-1.13/mirt/R/mixedmirt.R | 11 mirt-1.13/mirt/R/simdata.R | 68 +++- mirt-1.13/mirt/R/utils.R | 113 ++++--- mirt-1.13/mirt/build/vignette.rds |binary mirt-1.13/mirt/man/DTF.Rd | 4 mirt-1.13/mirt/man/boot.mirt.Rd | 7 mirt-1.13/mirt/man/coef-method.Rd | 2 mirt-1.13/mirt/man/imputeMissing.Rd | 11 mirt-1.13/mirt/man/itemGAM.Rd | 11 mirt-1.13/mirt/man/itemfit.Rd | 16 mirt-1.13/mirt/man/itemplot.Rd | 32 + mirt-1.13/mirt/man/key2binary.Rd | 16 mirt-1.13/mirt/man/marginal_rxx.Rd | 1 mirt-1.13/mirt/man/mirt.Rd | 17 - mirt-1.13/mirt/man/mixedmirt.Rd | 11 mirt-1.13/mirt/man/plot-method.Rd | 26 - mirt-1.13/mirt/man/simdata.Rd | 36 ++ mirt-1.13/mirt/src/Misc.h | 2 mirt-1.13/mirt/src/dpars.cpp | 337 ++++++++++++++++++++- mirt-1.13/mirt/tests/tests/test-02-mirtTwo.R | 2 mirt-1.13/mirt/tests/tests/test-04-multipleGroup.R | 4 mirt-1.13/mirt/tests/tests/test-05-confmirtOne.R | 12 mirt-1.13/mirt/tests/tests/test-06-confmirtTwo.R | 6 mirt-1.13/mirt/tests/tests/test-07-mixedmirt.R | 32 - 55 files changed, 1284 insertions(+), 537 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.0 dated 2015-03-27 and 1.1.1 dated 2015-09-09
DESCRIPTION | 6 MD5 | 30 NAMESPACE | 3 R/GDM_Table_Funcs.R | 2810 ++++++++++++++++++++++++++------------------------ data/gdm.RData |binary inst/doc |only man/createsitepair.Rd | 4 man/formatsitepair.Rd | 2 man/gdm-package.Rd | 8 man/gdm.Rd | 4 man/gdm.transform.Rd | 51 man/gdmDissim.Rd | 2 man/isplineExtract.Rd | 8 man/plot.gdm.Rd | 2 man/predict.gdm.Rd | 44 man/stackedVars.Rd | 2 16 files changed, 1599 insertions(+), 1377 deletions(-)
Title: Implements ACME Estimator of Bird and Bat Mortality by Wind
Turbines
Description: Implementation of estimator ACME, described in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran Mortality at Wind
Turbines (submitted). Unlike most other models, this estimator
supports decreasing-hazard Weibull model for persistence;
decreasing search proficiency as carcasses age; variable
bleed-through at successive searches; and interval mortality
estimates. The package provides, based on search data, functions
for estimating the mortality inflation factor in Frequentist and
Bayesian settings.
Author: Robert Wolpert [aut, cre],
Jacob Coleman [aut]
Maintainer: Robert Wolpert <wolpert@stat.duke.edu>
Diff between acmeR versions 1.0.0 dated 2015-07-24 and 1.1.0 dated 2015-09-09
acmeR-1.0.0/acmeR/man/ObjPost.Rd |only acmeR-1.1.0/acmeR/DESCRIPTION | 29 +++--- acmeR-1.1.0/acmeR/MD5 | 27 +++--- acmeR-1.1.0/acmeR/NAMESPACE | 3 acmeR-1.1.0/acmeR/R/acme_post.R | 148 +++++++++++++++++++++------------- acmeR-1.1.0/acmeR/R/acme_summary.R | 16 ++- acmeR-1.1.0/acmeR/R/acme_table.R |only acmeR-1.1.0/acmeR/R/read_data.R | 47 ++++++++-- acmeR-1.1.0/acmeR/R/sysdata.rda |binary acmeR-1.1.0/acmeR/build |only acmeR-1.1.0/acmeR/data/altamont.rda |binary acmeR-1.1.0/acmeR/inst |only acmeR-1.1.0/acmeR/man/acme.post.Rd |only acmeR-1.1.0/acmeR/man/acme.summary.Rd | 4 acmeR-1.1.0/acmeR/man/acme.table.Rd |only acmeR-1.1.0/acmeR/man/read.data.Rd | 4 acmeR-1.1.0/acmeR/vignettes |only 17 files changed, 175 insertions(+), 103 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.0 dated 2015-06-17 and 1.7.2 dated 2015-09-09
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 6 ++++-- R/TimeInstantDataFrame.R | 6 +++--- R/TimeIntervalDataFrame.R | 2 +- README | 4 ++++ man/timetools-package.Rd | 4 ++-- 7 files changed, 26 insertions(+), 20 deletions(-)
Title: Parallel Line Assays
Description: Parallel Line Assays: Completely randomized design,
Randomized Block design, and Latin squares design.
Balanced data are fitted as described in the Ph.Eur.
In the presence of missing values complete data analysis can be
performed (with computation of Fieller's confidence intervals for
the estimated potency), or imputation of values can be applied.
The package contains a script such that a pdf-document with a
report of an analysis of an assay can be produced from an input file
with data of the assay. Here no knowledge of R is needed by the user.
Author: Jens Henrik Badsberg
Maintainer: Jens Henrik Badsberg <pla2015@badsberg.eu>
Diff between pla versions 0.1 dated 2015-08-18 and 0.2 dated 2015-09-09
DESCRIPTION | 8 - MD5 | 163 ++++++++++++++++++++++++++++++++++++--- NAMESPACE | 2 R/methodsData.R | 85 ++++++++++++-------- data |only inst/scripts/Makefile |only inst/scripts/R/xtables.bak.R |only inst/vignettes |only man/AgarDiffusionAssay.Rd |only man/Corticotrophin.Rd |only man/Diphteria.Rd |only man/Erythromycin.Rd |only man/Erythropoietin.Rd |only man/FactorIX.Rd |only man/HeparinSodium.Rd |only man/HepatitisB.Rd |only man/HepatitisBvaccine.Rd |only man/HumanHepatitis.Rd |only man/IPV.Rd |only man/Nystatin.Rd |only man/Turbidimetric.Rd |only man/Vancomycin.Rd |only man/Work |only man/assayTable2frame.Rd | 8 + man/data2assayFrame.Rd | 19 ++++ man/pheur325.Rd | 2 man/pla-package.Rd | 87 +++++++++++++++++++-- man/pla.Rd | 2 man/pla.fit.Rd | 21 ++++- man/pla.plots.Rd | 28 ++++++ man/potency.Rd | 2 man/readAssayTable.Rd | 176 ++++++++++++++++++++++++++++++++++++++++++- 32 files changed, 537 insertions(+), 66 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Orthogonal Nonlinear Least-Squares Regression using Levenberg-Marquardt Minimization.
Author: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Maintainer: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Diff between onls versions 0.1-0 dated 2015-01-17 and 0.1-1 dated 2015-09-09
onls-0.1-0/onls/inst/onls-vignette.pdf |only onls-0.1-1/onls/DESCRIPTION | 10 +++++----- onls-0.1-1/onls/MD5 | 24 ++++++++++++++---------- onls-0.1-1/onls/NAMESPACE | 7 +++++++ onls-0.1-1/onls/NEWS | 7 ++++++- onls-0.1-1/onls/build |only onls-0.1-1/onls/inst/doc |only onls-0.1-1/onls/man/check_o.Rd | 2 +- onls-0.1-1/onls/man/deviance_o.Rd | 2 +- onls-0.1-1/onls/man/onls.Rd | 2 +- onls-0.1-1/onls/man/plot.onls.Rd | 4 ++-- onls-0.1-1/onls/man/print.onls.Rd | 2 +- onls-0.1-1/onls/man/summary.onls.Rd | 2 +- onls-0.1-1/onls/vignettes |only 14 files changed, 39 insertions(+), 23 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between netassoc versions 0.4.7 dated 2015-06-24 and 0.6.0 dated 2015-09-09
netassoc-0.4.7/netassoc/R/netassoc.R |only netassoc-0.4.7/netassoc/man/makenetwork.Rd |only netassoc-0.6.0/netassoc/DESCRIPTION | 11 ++++++----- netassoc-0.6.0/netassoc/MD5 | 17 +++++++++++------ netassoc-0.6.0/netassoc/NAMESPACE | 13 +++++++++++-- netassoc-0.6.0/netassoc/R/generate_nul_resample.R |only netassoc-0.6.0/netassoc/R/make_netassoc_network.R |only netassoc-0.6.0/netassoc/R/partial_correlation.R |only netassoc-0.6.0/netassoc/R/plot.R |only netassoc-0.6.0/netassoc/man/make_netassoc_network.Rd |only netassoc-0.6.0/netassoc/man/netassoc-package.Rd | 4 ++-- netassoc-0.6.0/netassoc/man/partial_correlation.Rd |only netassoc-0.6.0/netassoc/man/plot_netassoc_matrix.Rd |only netassoc-0.6.0/netassoc/man/plot_netassoc_network.Rd | 8 ++++++-- 14 files changed, 36 insertions(+), 17 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.3 dated 2015-08-21 and 1.4 dated 2015-09-09
DESCRIPTION | 14 +++++++------- MD5 | 38 +++++++++++++++++++------------------- R/CA.R | 23 +++++++++++++++++------ man/Biplot.Rd | 2 +- man/CA.Rd | 41 +++++++++++++++++++++++++---------------- man/DataFreq.Rd | 4 ++-- man/DataMix.Rd | 8 ++++---- man/DataQuali.Rd | 6 +++--- man/DataQuan.Rd | 6 +++--- man/Data_Cafes.Rd | 6 +++--- man/Data_Individuos.Rd | 6 +++--- man/GSVD.Rd | 18 +++++++++--------- man/IM.Rd | 16 ++++++++-------- man/MFA.Rd | 42 +++++++++++++++++++++--------------------- man/MVar.pt-package.Rd | 12 ++++++------ man/NormData.Rd | 12 ++++++------ man/PCA.Rd | 24 ++++++++++++------------ man/Plot.CA.Rd | 14 +++++++------- man/Plot.MFA.Rd | 32 ++++++++++++++++---------------- man/Plot.PCA.Rd | 14 +++++++------- 20 files changed, 179 insertions(+), 159 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.1.1 dated 2015-07-24 and 0.2.0 dated 2015-09-09
spTest-0.1.1/spTest/inst/CITATION |only spTest-0.2.0/spTest/DESCRIPTION | 16 +++---- spTest-0.2.0/spTest/MD5 | 62 ++++++++++++++++++++++++------ spTest-0.2.0/spTest/R/Data_Description.R |only spTest-0.2.0/spTest/R/GuanTestGrid.R | 53 ++++++++++++++----------- spTest-0.2.0/spTest/R/GuanTestUnif.R | 10 +++- spTest-0.2.0/spTest/R/GuanTestUnif_help.R | 4 - spTest-0.2.0/spTest/R/LuTest.R | 2 spTest-0.2.0/spTest/R/LuTest_help.R | 2 spTest-0.2.0/spTest/R/MaityTest.R | 9 +++- spTest-0.2.0/spTest/R/MaityTest_help.R | 4 - spTest-0.2.0/spTest/build |only spTest-0.2.0/spTest/data |only spTest-0.2.0/spTest/inst/doc |only spTest-0.2.0/spTest/man/GuanTestGrid.Rd | 24 +++++------ spTest-0.2.0/spTest/man/GuanTestUnif.Rd | 4 - spTest-0.2.0/spTest/man/WRFG.Rd |only spTest-0.2.0/spTest/vignettes |only 18 files changed, 125 insertions(+), 65 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront
data with them and analyze or visualize the results. The package supports
rules that are per-field, in-record, cross-record or cross-dataset. Rules
can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut],
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.1.2 dated 2015-09-01 and 0.1.3 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- R/compare.R | 2 +- inst/doc/intro.R | 7 +++++++ inst/doc/intro.Rmd | 12 +++++++----- inst/doc/intro.html | 36 +++++++++++++++++++++++++----------- inst/doc/rule-files.Rmd | 2 +- inst/doc/rule-files.html | 2 +- vignettes/intro.Rmd | 12 +++++++----- vignettes/rule-files.Rmd | 2 +- vignettes/rule-tour.Rmd |only vignettes/rule-tour.html |only 12 files changed, 65 insertions(+), 38 deletions(-)
Title: Package for Calculation of ARMSS, Local MSSS and Global MSSS
Description: Calculates ARMSS (age related multiple sclerosis severity), and both local and global MSSS (multiple sclerosis severity score).
Author: Helga Westerlind, Ali Manouchehrinia
Maintainer: Helga Westerlind <Helga.Westerlind@ki.se>
Diff between ms.sev versions 1.0.1 dated 2015-08-31 and 1.0.2 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ms_sev.R | 9 +++++---- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Multivariable Fractional Polynomials
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: original by Gareth Ambler <gareth@stats.ucl.ac.uk>, modified by Axel Benner <benner@dkfz.de>
Maintainer: Stephan Luecke <s.luecke@dkfz.de>
Diff between mfp versions 1.5.1 dated 2015-02-04 and 1.5.2 dated 2015-09-09
mfp-1.5.1/mfp/ChangeLog |only mfp-1.5.2/mfp/DESCRIPTION | 8 +- mfp-1.5.2/mfp/MD5 | 18 ++-- mfp-1.5.2/mfp/NAMESPACE | 13 +-- mfp-1.5.2/mfp/NEWS |only mfp-1.5.2/mfp/build/vignette.rds |binary mfp-1.5.2/mfp/data/bodyfat.rda |binary mfp-1.5.2/mfp/inst/doc/mfp_vignette.R | 120 +++++++++++++++---------------- mfp-1.5.2/mfp/inst/doc/mfp_vignette.Rnw | 2 mfp-1.5.2/mfp/inst/doc/mfp_vignette.pdf |binary mfp-1.5.2/mfp/vignettes/mfp_vignette.Rnw | 2 11 files changed, 82 insertions(+), 81 deletions(-)
Title: Discrete Laplace Mixture Inference using the EM Algorithm
Description: Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between disclapmix versions 1.6.1 dated 2015-06-12 and 1.6.2 dated 2015-09-09
disclapmix-1.6.1/disclapmix/man/haplotype_diversity.Rd |only disclapmix-1.6.1/disclapmix/man/happrobsum.Rd |only disclapmix-1.6.2/disclapmix/DESCRIPTION | 12 disclapmix-1.6.2/disclapmix/MD5 | 45 disclapmix-1.6.2/disclapmix/NAMESPACE | 7 disclapmix-1.6.2/disclapmix/NEWS | 5 disclapmix-1.6.2/disclapmix/R/RcppExports.R | 28 disclapmix-1.6.2/disclapmix/R/helper.R | 143 -- disclapmix-1.6.2/disclapmix/R/proto_functions.R |only disclapmix-1.6.2/disclapmix/man/clusterdist.Rd | 2 disclapmix-1.6.2/disclapmix/man/clusterprob.Rd | 2 disclapmix-1.6.2/disclapmix/man/contributor_pairs.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmix-package.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmix.Rd | 2 disclapmix-1.6.2/disclapmix/man/disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/generate_mixture.Rd | 2 disclapmix-1.6.2/disclapmix/man/plot.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/predict.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/print.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/rank_contributor_pairs.Rd | 2 disclapmix-1.6.2/disclapmix/man/simulate.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/man/summary.disclapmixfit.Rd | 2 disclapmix-1.6.2/disclapmix/src/RcppExports.cpp | 378 +++--- disclapmix-1.6.2/disclapmix/src/happrobsum.cpp | 804 +++++++++++++- disclapmix-1.6.2/disclapmix/src/helper.cpp | 34 25 files changed, 1120 insertions(+), 362 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.2-1 dated 2015-08-18 and 0.8.4-2 dated 2015-09-09
quanteda-0.8.2-1/quanteda/man/bigrams.Rd |only quanteda-0.8.4-2/quanteda/DESCRIPTION | 10 quanteda-0.8.4-2/quanteda/MD5 | 71 +- quanteda-0.8.4-2/quanteda/NAMESPACE | 11 quanteda-0.8.4-2/quanteda/NEWS | 37 + quanteda-0.8.4-2/quanteda/R/collocations.R | 2 quanteda-0.8.4-2/quanteda/R/corpus.R | 24 quanteda-0.8.4-2/quanteda/R/dfm-classes.R | 16 quanteda-0.8.4-2/quanteda/R/dfm-main.R | 47 - quanteda-0.8.4-2/quanteda/R/dictionaries.R | 4 quanteda-0.8.4-2/quanteda/R/encoding.R | 4 quanteda-0.8.4-2/quanteda/R/ngrams.R | 346 ++++++++++---- quanteda-0.8.4-2/quanteda/R/stopwords.R | 21 quanteda-0.8.4-2/quanteda/R/textfile.R | 73 +- quanteda-0.8.4-2/quanteda/R/textmodel-generics.R | 2 quanteda-0.8.4-2/quanteda/R/toLower.R | 4 quanteda-0.8.4-2/quanteda/R/tokenize.R | 61 +- quanteda-0.8.4-2/quanteda/R/wordstem.R | 21 quanteda-0.8.4-2/quanteda/build/vignette.rds |binary quanteda-0.8.4-2/quanteda/inst/doc/development-plans.Rmd | 3 quanteda-0.8.4-2/quanteda/inst/doc/development-plans.html | 1 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.R | 4 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.Rmd | 4 quanteda-0.8.4-2/quanteda/inst/doc/quickstart.html | 78 +-- quanteda-0.8.4-2/quanteda/man/collocations.Rd | 2 quanteda-0.8.4-2/quanteda/man/corpus.Rd | 10 quanteda-0.8.4-2/quanteda/man/dfm.Rd | 41 - quanteda-0.8.4-2/quanteda/man/dictionary.Rd | 4 quanteda-0.8.4-2/quanteda/man/encoding.Rd | 4 quanteda-0.8.4-2/quanteda/man/ngrams.Rd | 79 ++- quanteda-0.8.4-2/quanteda/man/selectFeatures.Rd | 4 quanteda-0.8.4-2/quanteda/man/textfile.Rd | 45 - quanteda-0.8.4-2/quanteda/man/textmodel.Rd | 2 quanteda-0.8.4-2/quanteda/man/toLower.Rd | 3 quanteda-0.8.4-2/quanteda/man/tokenize.Rd | 34 + quanteda-0.8.4-2/quanteda/vignettes/development-plans.Rmd | 3 quanteda-0.8.4-2/quanteda/vignettes/quickstart.Rmd | 4 37 files changed, 667 insertions(+), 412 deletions(-)
Title: Psychometric Mixture Models
Description: Psychometric mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture models
with different parameterizations of the score distribution (saturated vs. mean/variance specification)
and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without
concomitant variables. See vignette('raschmix', package = 'psychomix') for details on the Rasch mixture
models.
Author: Hannah Frick [aut, cre],
Carolin Strobl [aut],
Friedrich Leisch [aut],
Achim Zeileis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between psychomix versions 1.1-2 dated 2015-05-05 and 1.1-3 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS | 5 +++++ build/vignette.rds |binary inst/doc/raschmix.pdf |binary inst/doc/scores.pdf |binary man/btmix.Rd | 1 + tests/Examples/psychomix-Ex.Rout.save | 6 +++--- 9 files changed, 23 insertions(+), 15 deletions(-)
Title: Mesh Generation and Surface Tesselation
Description: Makes the qhull library (www.qhull.org)
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this. Currently the package only gives access to
Delaunay triangulation and convex hull computation.
Author: C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Andreas Stahel [cph, aut],
David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.3-5 dated 2014-11-08 and 0.3-6 dated 2015-09-09
DESCRIPTION | 18 +++++------ MD5 | 76 ++++++++++++++++++++++++------------------------- NAMESPACE | 6 +++ NEWS | 23 ++++++++++++++ R/convhulln.R | 8 +++-- R/delaunayn.R | 13 ++++---- R/distmesh2d.R | 6 +-- R/distmeshnd.R | 8 ++--- R/mesh.dcircle.R | 2 - R/mesh.drectangle.R | 2 - R/mesh.dsphere.R | 2 - R/surf.tri.R | 24 +++++++-------- R/tetramesh.R | 9 ++--- R/trimesh.R | 1 inst/doc/index.html | 25 ++-------------- man/Unique.Rd | 3 + man/bary2cart.Rd | 3 + man/cart2bary.Rd | 3 + man/convhulln.Rd | 3 + man/delaunayn.Rd | 8 ++--- man/distmesh2d.Rd | 5 +-- man/distmeshnd.Rd | 5 +-- man/dot.Rd | 3 + man/entry.value.Rd | 3 + man/extprod3d.Rd | 3 + man/matmax.Rd | 3 + man/mesh.dcircle.Rd | 5 +-- man/mesh.diff.Rd | 3 + man/mesh.drectangle.Rd | 5 +-- man/mesh.dsphere.Rd | 5 +-- man/mesh.hunif.Rd | 3 + man/polyarea.Rd | 3 + man/surf.tri.Rd | 27 ++++++++--------- man/tetramesh.Rd | 10 +++--- man/trimesh.Rd | 3 + man/tsearch.Rd | 3 + man/tsearchn.Rd | 3 + src/Rconvhulln.c | 4 +- src/Rdelaunayn.c | 4 +- 39 files changed, 186 insertions(+), 157 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.6-2 dated 2015-04-19 and 0.7 dated 2015-09-09
DESCRIPTION | 32 +++- MD5 | 117 +++++++++++------- NAMESPACE | 16 ++ NEWS | 35 +++++ R/blobbogram.R | 15 +- R/code.R | 2 R/deviance.R |only R/inits.R | 121 +++++++++++------- R/likelihoods.R |only R/ll-helper.counts.R |only R/ll.binom.cloglog.R | 41 ++++-- R/ll.binom.log.R |only R/ll.binom.logit.R | 42 ++++-- R/ll.call.R | 8 - R/ll.normal.identity.R | 31 +++- R/ll.poisson.log.R | 54 +++++++- R/minimum.diameter.spanning.tree.R | 8 - R/mtc.model.R | 13 +- R/mtc.model.consistency.R | 4 R/mtc.model.nodesplit.R | 20 ++- R/mtc.model.ume.R | 32 ++++ R/mtc.model.use.R | 8 - R/mtc.network.R | 119 +----------------- R/mtc.network.xml.R |only R/mtc.result.R | 35 +++-- R/mtc.run.R | 135 ++++----------------- R/relative.effect.R | 2 R/relative.effect.table.R |only data |only inst/gemtc.releffect.likelihood.r2.txt | 6 inst/gemtc.releffect.likelihood.rm.txt | 3 man/depression.Rd |only man/gemtc-package.Rd | 17 +- man/ll.call.Rd | 1 man/mtc.hy.prior.Rd | 9 - man/mtc.model.Rd | 14 +- man/mtc.network.Rd | 44 +----- man/mtc.network.xml.Rd |only man/mtc.nodesplit.Rd | 6 man/mtc.run.Rd | 22 ++- man/parkinson.Rd |only man/rank.probability.Rd | 4 man/relative.effect.Rd | 9 - man/relative.effect.table.Rd |only man/smoking.Rd |only man/thrombolytic.Rd |only tests/data/riskratio.data.txt |only tests/data/riskratio.summaries.txt |only tests/data/rr-pairwise.csv |only tests/testthat/helper-regress.R | 32 +++- tests/testthat/helper-validate.R | 10 - tests/testthat/test-regress-anohe.R | 6 tests/testthat/test-regress-models.R | 8 - tests/testthat/test-unit-ll.R | 4 tests/testthat/test-unit-ll.binom.log.R |only tests/testthat/test-unit-ll.binom.logit.R |only tests/testthat/test-unit-ll.poisson.log.R |only tests/testthat/test-unit-mtc.model.consistency.R |only tests/testthat/test-unit-mtc.model.graph.R | 2 tests/testthat/test-unit-mtc.model.nodesplit.R |only tests/testthat/test-unit-mtc.model.ume.R | 16 ++ tests/testthat/test-unit-mtc.model.use.R |only tests/testthat/test-unit-mtc.model_inits.R | 31 ++++ tests/testthat/test-unit-relative.effect.R | 2 tests/testthat/test-unit-relative.effect.table.R |only tests/testthat/test-validate-cipriani-efficacy.R | 3 tests/testthat/test-validate-luades-smoking.R | 3 tests/testthat/test-validate-luades-thrombolytic.R | 3 tests/testthat/test-validate-parkinson.R | 3 tests/testthat/test-validate-riskratio.R |only 70 files changed, 656 insertions(+), 492 deletions(-)
Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between VennDiagram versions 1.6.9 dated 2014-09-24 and 1.6.15 dated 2015-09-09
VennDiagram-1.6.15/VennDiagram/DESCRIPTION | 13 VennDiagram-1.6.15/VennDiagram/MD5 | 114 - VennDiagram-1.6.15/VennDiagram/NAMESPACE | 32 VennDiagram-1.6.15/VennDiagram/NEWS | 43 VennDiagram-1.6.15/VennDiagram/R/draw.pairwise.venn.R | 227 ++ VennDiagram-1.6.15/VennDiagram/R/draw.quad.venn.R | 157 +- VennDiagram-1.6.15/VennDiagram/R/draw.quintuple.venn.R | 189 +- VennDiagram-1.6.15/VennDiagram/R/draw.single.venn.R | 65 VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.R | 56 VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.preprocess.R |only VennDiagram-1.6.15/VennDiagram/R/draw.sp.case.scaled.R |only VennDiagram-1.6.15/VennDiagram/R/draw.triple.venn.R | 189 +- VennDiagram-1.6.15/VennDiagram/R/ellipse.R | 9 VennDiagram-1.6.15/VennDiagram/R/flip.venn.R | 3 VennDiagram-1.6.15/VennDiagram/R/partitionText.R |only VennDiagram-1.6.15/VennDiagram/R/rotate.sp.R | 71 VennDiagram-1.6.15/VennDiagram/R/venn.diagram.R | 760 +++++++--- VennDiagram-1.6.15/VennDiagram/TODO | 5 VennDiagram-1.6.15/VennDiagram/data |only VennDiagram-1.6.15/VennDiagram/inst |only VennDiagram-1.6.15/VennDiagram/man/calculate.overlap.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.pairwise.venn.Rd | 32 VennDiagram-1.6.15/VennDiagram/man/draw.quad.venn.Rd | 28 VennDiagram-1.6.15/VennDiagram/man/draw.quintuple.venn.Rd | 31 VennDiagram-1.6.15/VennDiagram/man/draw.sp.case.preprocess.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.sp.case.scaled.Rd |only VennDiagram-1.6.15/VennDiagram/man/draw.triple.venn.Rd | 34 VennDiagram-1.6.15/VennDiagram/man/get.venn.partitions.Rd |only VennDiagram-1.6.15/VennDiagram/man/make.truth.table.Rd |only VennDiagram-1.6.15/VennDiagram/man/venn.diagram.Rd | 21 VennDiagram-1.6.15/VennDiagram/man/venn.plot.Rd |only VennDiagram-1.6.15/VennDiagram/tests |only VennDiagram-1.6.9/VennDiagram/R/draw.001.R |only VennDiagram-1.6.9/VennDiagram/R/draw.010.R |only VennDiagram-1.6.9/VennDiagram/R/draw.011A.R |only VennDiagram-1.6.9/VennDiagram/R/draw.011O.R |only VennDiagram-1.6.9/VennDiagram/R/draw.012AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.021AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.022AAAO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.022AAOO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.023.R |only VennDiagram-1.6.9/VennDiagram/R/draw.032.R |only VennDiagram-1.6.9/VennDiagram/R/draw.033.R |only VennDiagram-1.6.9/VennDiagram/R/draw.100.R |only VennDiagram-1.6.9/VennDiagram/R/draw.110.R |only VennDiagram-1.6.9/VennDiagram/R/draw.111A.R |only VennDiagram-1.6.9/VennDiagram/R/draw.112AA.R |only VennDiagram-1.6.9/VennDiagram/R/draw.120.R |only VennDiagram-1.6.9/VennDiagram/R/draw.121AO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.122AAOO.R |only VennDiagram-1.6.9/VennDiagram/R/draw.130.R |only VennDiagram-1.6.9/VennDiagram/man/draw.001.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.010.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.011A.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.011O.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.012AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.021AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.022AAAO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.022AAOO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.023.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.032.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.033.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.100.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.110.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.111A.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.112AA.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.120.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.121AO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.122AAOO.Rd |only VennDiagram-1.6.9/VennDiagram/man/draw.130.Rd |only 70 files changed, 1455 insertions(+), 624 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.2-0 dated 2015-09-07 and 1.2-1 dated 2015-09-09
DESCRIPTION | 8 +-- MD5 | 18 +++--- inst/NEWS | 3 + inst/doc/stream.R | 112 +++++++++++++++++++++--------------------- inst/doc/stream.Rnw | 64 +++++++++++++----------- inst/doc/stream.pdf |binary inst/doc/stream_extension.pdf |binary inst/tests/test-DSC.R | 13 ++++ inst/tests/test-DSD.R | 1 vignettes/stream.Rnw | 64 +++++++++++++----------- 10 files changed, 155 insertions(+), 128 deletions(-)
Title: Create Dashboards with 'Shiny'
Description: Create dashboards with 'Shiny'. This package provides
a theme on top of 'Shiny', making it easy to create attractive dashboards.
Author: Winston Chang [aut, cre],
RStudio [cph],
Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinydashboard versions 0.5.0 dated 2015-06-16 and 0.5.1 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 18 +++++++++++++++++- R/dashboardSidebar.R | 4 ++++ R/deps.R | 2 +- R/tabs.R | 2 ++ R/utils.R | 8 ++++++++ inst/shinydashboard.css | 25 +++++++++++++------------ 8 files changed, 56 insertions(+), 25 deletions(-)
More information about shinydashboard at CRAN
Permanent link
Title: Adaptive Builder for Formatted Strings
Description: Provides a set of functions to facilitate building formatted strings
under various replacement rules: C-style formatting, variable-based formatting,
and number-based formatting. C-style formatting is basically identical to built-in
function 'sprintf'. Variable-based formatting allows users to put variable names
in a formatted string which will be replaced by variable values. Number-based
formatting allows users to use index numbers to represent the corresponding
argument value to appear in the string.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rprintf versions 0.1-2 dated 2014-08-15 and 0.2.1 dated 2015-09-09
rprintf-0.1-2/rprintf/inst |only rprintf-0.2.1/rprintf/DESCRIPTION | 22 ++++---- rprintf-0.2.1/rprintf/MD5 | 30 +++++----- rprintf-0.2.1/rprintf/NAMESPACE | 4 + rprintf-0.2.1/rprintf/NEWS | 4 + rprintf-0.2.1/rprintf/R/internal.R | 23 ++++---- rprintf-0.2.1/rprintf/R/rprintf.R | 55 +++++++++----------- rprintf-0.2.1/rprintf/R/rprintn.R | 36 ++++++++----- rprintf-0.2.1/rprintf/R/rprintv.R | 35 ++++++++---- rprintf-0.2.1/rprintf/README.md | 6 +- rprintf-0.2.1/rprintf/man/rprintf.Rd | 43 ++++++++------- rprintf-0.2.1/rprintf/man/rprintn.Rd | 13 ++-- rprintf-0.2.1/rprintf/man/rprintv.Rd | 11 ++-- rprintf-0.2.1/rprintf/tests/testthat/test-rprintf.R | 18 +++--- rprintf-0.2.1/rprintf/tests/testthat/test-rprintn.R | 26 ++++----- rprintf-0.2.1/rprintf/tests/testthat/test-rprintv.R | 24 ++++---- 16 files changed, 190 insertions(+), 160 deletions(-)
Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rlist versions 0.4.2.3 dated 2015-07-09 and 0.4.5.1 dated 2015-09-09
DESCRIPTION | 8 +++---- MD5 | 40 +++++++++++++++++------------------ NEWS | 5 +++- R/internal.R | 48 +++++++++++++++++++------------------------ R/lambda.R | 9 ++++---- R/list.all.R | 14 +++++++----- R/list.clean.R | 2 - R/list.count.R | 3 -- R/list.first.R | 14 ++++-------- R/list.flatten.R | 20 +++++++++++++---- R/list.map.R | 10 ++++---- R/list.order.R | 3 -- R/list.search.R | 12 ++++------ R/list.skip.R | 4 +-- R/list.take.R | 4 +-- R/utils.R | 10 +++----- README.md | 5 +++- man/list.clean.Rd | 2 - man/list.flatten.Rd | 16 +++++++++++++- tests/testthat/test-basic.R | 19 ++++++++++++++++- tests/testthat/test-search.R | 2 + 21 files changed, 144 insertions(+), 106 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written based on an accompanying 'RESTful' API.
Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more.
This package also supports experimental access to http://www.sealifebase.org data, which contains nearly
200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.2 dated 2015-09-01 and 2.0.3 dated 2015-09-09
DESCRIPTION | 6 +- MD5 | 92 +++++++++++++++++++------------------- NEWS | 6 ++ R/common_names.R | 6 +- R/distribution.R | 12 ++-- R/docs.R | 2 R/morpho_physio.R | 10 ++-- R/population_dynamics.R | 10 ++-- R/reproduction.R | 8 +-- R/species.R | 2 R/species_list.R | 2 R/synonyms.R | 2 R/trophic_ecology.R | 12 ++-- man/common_names.Rd | 2 man/common_to_sci.Rd | 2 man/diet.Rd | 2 man/distribution.Rd | 2 man/docs.Rd | 2 man/ecology.Rd | 2 man/ecosystem.Rd | 2 man/faoareas.Rd | 2 man/fecundity.Rd | 2 man/fooditems.Rd | 2 man/introductions.Rd | 2 man/length_freq.Rd | 2 man/length_length.Rd | 2 man/length_weight.Rd | 2 man/maturity.Rd | 2 man/morphology.Rd | 2 man/morphometrics.Rd | 2 man/occurrence.Rd | 2 man/oxygen.Rd | 2 man/popchar.Rd | 2 man/popgrowth.Rd | 2 man/popqb.Rd | 2 man/predators.Rd | 2 man/ration.Rd | 2 man/reproduction.Rd | 2 man/sci_to_common.Rd | 2 man/spawning.Rd | 2 man/species.Rd | 2 man/species_list.Rd | 2 man/speed.Rd | 2 man/stocks.Rd | 2 man/swimming.Rd | 2 man/synonyms.Rd | 2 tests/testthat/helper_rfishbase.R | 18 +++---- 47 files changed, 129 insertions(+), 125 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package randomForests, written by Andy Liaw.
Author: Nicolai Meinshausen, Lukas Schiesser
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between quantregForest versions 1.0 dated 2015-06-03 and 1.1 dated 2015-09-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/quantregForest.pdf |binary src/findweightsinbagfast.c | 8 ++++---- src/findweightsinbagfastimp.c | 8 ++++---- 6 files changed, 17 insertions(+), 17 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: Parametric Network Enrichment Analysis
Description: Collection of functions for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.0.1 dated 2015-08-29 and 1.1.0 dated 2015-09-09
pnea-1.0.1/pnea/man/plot.pneac.Rd |only pnea-1.0.1/pnea/man/print.pneac.Rd |only pnea-1.0.1/pnea/man/summary.pneac.Rd |only pnea-1.1.0/pnea/DESCRIPTION | 10 +- pnea-1.1.0/pnea/MD5 | 21 ++-- pnea-1.1.0/pnea/NAMESPACE | 6 - pnea-1.1.0/pnea/R/pnea.R | 149 ++++++++++++++++++++++------------- pnea-1.1.0/pnea/build/partial.rdb |binary pnea-1.1.0/pnea/data |only pnea-1.1.0/pnea/man/plot.pnea.Rd |only pnea-1.1.0/pnea/man/pnea-package.Rd | 4 pnea-1.1.0/pnea/man/pnea.Rd | 72 ++++++++++++---- pnea-1.1.0/pnea/man/print.pnea.Rd |only pnea-1.1.0/pnea/man/summary.pnea.Rd |only pnea-1.1.0/pnea/man/yeast.Rd |only 15 files changed, 169 insertions(+), 93 deletions(-)
Title: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Description: Used primarily for estimates of allele frequency surfaces from point estimates.
It can also place individuals of unknown origin back onto the geographic map with great accuracy.
Additionally, it can place admixed individuals by estimating contributing fractions at each
location on a map. Lastly, it can rank SNPs by their ability to differentiate populations.
See "Fast Spatial Ancestry via Flexible Allele Frequency Surfaces" (John Michael Ranola, John
Novembre, Kenneth Lange) in Bioinformatics 2014 for more info.
Author: John Michael O Ranola, John Novembre, and Kenneth Lange
Maintainer: John Michael O. Ranola <ranolaj@uw.edu>
Diff between OriGen versions 1.3 dated 2015-08-28 and 1.3.1 dated 2015-09-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- man/FitAdmixedModelFindUnknowns.Rd | 2 ++ man/OriGen-package.Rd | 23 +++++++++++++++-------- man/PlotAdmixedSurface.Rd | 2 ++ src/OriGen.f90 | 10 +++++----- 6 files changed, 34 insertions(+), 23 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh (2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller (2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al. (2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.6.2 dated 2015-06-10 and 0.7.1 dated 2015-09-09
DESCRIPTION | 14 - MD5 | 36 ++-- NAMESPACE | 2 NEWS | 22 ++ R/Qm.R | 8 R/af.R | 204 ++++++++++++------------- R/bglmnet.R | 245 +++++++++++++++--------------- R/glmfence.R | 30 +-- R/lmfence.R | 34 ++-- R/mplot-package.R | 145 ++++++++--------- R/mplot.R | 121 +++++++------- R/qrange.R | 30 +-- R/vis.R | 423 ++++++++++++++++++++++++++-------------------------- README.md | 43 ++++- inst/CITATION | 26 ++- man/bglmnet.Rd |only man/plot.af.Rd | 6 man/plot.bglmnet.Rd |only man/plot.vis.Rd | 4 man/vis.Rd | 9 - 20 files changed, 746 insertions(+), 656 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.2.0-3 dated 2015-09-07 and 0.2.1 dated 2015-09-09
data.tree-0.2.0-3/data.tree/inst/extdata/useR15.yaml |only data.tree-0.2.1/data.tree/DESCRIPTION | 12 data.tree-0.2.1/data.tree/MD5 | 178 data.tree-0.2.1/data.tree/NAMESPACE | 104 data.tree-0.2.1/data.tree/NEWS | 154 data.tree-0.2.1/data.tree/R/data.tree.R | 194 data.tree-0.2.1/data.tree/R/data_doc.R | 72 data.tree-0.2.1/data.tree/R/node.R | 694 +- data.tree-0.2.1/data.tree/R/node_actives.R | 152 data.tree-0.2.1/data.tree/R/node_conversion.R | 142 data.tree-0.2.1/data.tree/R/node_conversion_ape.R | 260 data.tree-0.2.1/data.tree/R/node_conversion_dataframe.R | 670 +- data.tree-0.2.1/data.tree/R/node_conversion_dendrogram.R | 258 data.tree-0.2.1/data.tree/R/node_conversion_igraph.R | 82 data.tree-0.2.1/data.tree/R/node_conversion_list.R | 408 - data.tree-0.2.1/data.tree/R/node_methods.R | 932 +-- data.tree-0.2.1/data.tree/R/node_methods_sideeffect.R | 228 data.tree-0.2.1/data.tree/R/node_methods_traversal.R | 460 - data.tree-0.2.1/data.tree/R/util.R | 410 - data.tree-0.2.1/data.tree/README.md | 58 data.tree-0.2.1/data.tree/build/vignette.rds |binary data.tree-0.2.1/data.tree/data/acme.rda |binary data.tree-0.2.1/data.tree/data/mushroom.rda |binary data.tree-0.2.1/data.tree/inst/doc/applications.R | 1542 ++--- data.tree-0.2.1/data.tree/inst/doc/applications.Rmd | 2566 ++++----- data.tree-0.2.1/data.tree/inst/doc/applications.html | 2677 ++++------ data.tree-0.2.1/data.tree/inst/doc/data.tree.R | 819 +-- data.tree-0.2.1/data.tree/inst/doc/data.tree.Rmd | 1850 +++--- data.tree-0.2.1/data.tree/inst/doc/data.tree.html | 2359 ++++---- data.tree-0.2.1/data.tree/inst/extdata/flare.json |only data.tree-0.2.1/data.tree/inst/extdata/jennylind.yaml | 60 data.tree-0.2.1/data.tree/inst/extdata/portfolio.csv | 58 data.tree-0.2.1/data.tree/inst/extdata/useR15.csv | 254 data.tree-0.2.1/data.tree/man/Aggregate.Rd | 126 data.tree-0.2.1/data.tree/man/AreNamesUnique.Rd | 54 data.tree-0.2.1/data.tree/man/Climb.Rd | 78 data.tree-0.2.1/data.tree/man/ClimbByAttribute.Rd | 68 data.tree-0.2.1/data.tree/man/Clone.Rd | 66 data.tree-0.2.1/data.tree/man/CreateRandomTree.Rd | 38 data.tree-0.2.1/data.tree/man/CreateRegularTree.Rd | 38 data.tree-0.2.1/data.tree/man/Cumulate.Rd | 72 data.tree-0.2.1/data.tree/man/DefaultPlotHeight.Rd | 50 data.tree-0.2.1/data.tree/man/Do.Rd | 40 data.tree-0.2.1/data.tree/man/FormatFixedDecimal.Rd | 48 data.tree-0.2.1/data.tree/man/FormatPercent.Rd | 62 data.tree-0.2.1/data.tree/man/Get.Rd | 128 data.tree-0.2.1/data.tree/man/GetAttribute.Rd | 70 data.tree-0.2.1/data.tree/man/GetPhyloNr.Rd | 68 data.tree-0.2.1/data.tree/man/NODE_RESERVED_NAMES_CONST.Rd | 36 data.tree-0.2.1/data.tree/man/Node.Rd | 148 data.tree-0.2.1/data.tree/man/Prune.Rd | 56 data.tree-0.2.1/data.tree/man/Revert.Rd | 50 data.tree-0.2.1/data.tree/man/Set.Rd | 76 data.tree-0.2.1/data.tree/man/SetFormat.Rd | 80 data.tree-0.2.1/data.tree/man/Sort.Rd | 86 data.tree-0.2.1/data.tree/man/ToNewick.Rd | 62 data.tree-0.2.1/data.tree/man/Traverse.Rd | 54 data.tree-0.2.1/data.tree/man/acme.Rd | 42 data.tree-0.2.1/data.tree/man/as.Node.Rd | 52 data.tree-0.2.1/data.tree/man/as.Node.data.frame.Rd | 180 data.tree-0.2.1/data.tree/man/as.Node.dendrogram.Rd | 84 data.tree-0.2.1/data.tree/man/as.Node.list.Rd | 180 data.tree-0.2.1/data.tree/man/as.Node.phylo.Rd | 86 data.tree-0.2.1/data.tree/man/as.data.frame.Node.Rd | 164 data.tree-0.2.1/data.tree/man/as.dendrogram.Node.Rd | 84 data.tree-0.2.1/data.tree/man/as.igraph.Node.Rd | 82 data.tree-0.2.1/data.tree/man/as.list.Node.Rd | 96 data.tree-0.2.1/data.tree/man/as.phylo.Node.Rd | 58 data.tree-0.2.1/data.tree/man/averageBranchingFactor.Rd | 30 data.tree-0.2.1/data.tree/man/data.tree.Rd | 228 data.tree-0.2.1/data.tree/man/isLeaf.Rd | 36 data.tree-0.2.1/data.tree/man/isNotLeaf.Rd | 36 data.tree-0.2.1/data.tree/man/isNotRoot.Rd | 36 data.tree-0.2.1/data.tree/man/isRoot.Rd | 36 data.tree-0.2.1/data.tree/man/mushroom.Rd | 50 data.tree-0.2.1/data.tree/man/print.Node.Rd | 68 data.tree-0.2.1/data.tree/tests/testthat.R | 6 data.tree-0.2.1/data.tree/tests/testthat/test-treeConstruction.R | 118 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversion.R | 272 - data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionApe.R | 202 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionDataFrame.R | 260 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionDendrogram.R | 40 data.tree-0.2.1/data.tree/tests/testthat/test-treeConversionigraph.R | 44 data.tree-0.2.1/data.tree/tests/testthat/test-treeDocu.R | 10 data.tree-0.2.1/data.tree/tests/testthat/test-treeMethods.R | 1270 ++-- data.tree-0.2.1/data.tree/tests/testthat/test-treeMethodsSideEffect.R | 114 data.tree-0.2.1/data.tree/tests/testthat/test-util.R | 88 data.tree-0.2.1/data.tree/vignettes/applications.Rmd | 2566 ++++----- data.tree-0.2.1/data.tree/vignettes/applications.banner.html | 28 data.tree-0.2.1/data.tree/vignettes/data.tree.Rmd | 1850 +++--- data.tree-0.2.1/data.tree/vignettes/intro.banner.html | 32 91 files changed, 13922 insertions(+), 13913 deletions(-)
Title: Change Point Regression
Description: Change point regression models are also called two-phase regression, break-point regression, split-point regression structural change models and threshold regression models. Hypothesis testing in change point logistic regression with or without interaction terms. Several options are provided for testing in models with interaction, including a maximum of likelihood ratios test that determines p-value through Monte Carlo. Estimation under change point model is also included, but less developed at this point.
Author: Youyi Fong
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between chngpt versions 2014.12-2 dated 2014-12-05 and 2015.9-5 dated 2015-09-09
chngpt-2014.12-2/chngpt/R/sim.sigmoid.R |only chngpt-2014.12-2/chngpt/man/sim.sigmoid.Rd |only chngpt-2015.9-5/chngpt/ChangeLog | 6 chngpt-2015.9-5/chngpt/DESCRIPTION | 12 chngpt-2015.9-5/chngpt/MD5 | 25 chngpt-2015.9-5/chngpt/NAMESPACE | 18 chngpt-2015.9-5/chngpt/R/chngpt.test.2.R |only chngpt-2015.9-5/chngpt/R/chngpt.test.R | 512 ++++---------- chngpt-2015.9-5/chngpt/R/chngptm.R | 371 ++++++---- chngpt-2015.9-5/chngpt/R/sim.chngpt.R |only chngpt-2015.9-5/chngpt/inst/unitTests/runit.chngpt.test.R | 68 + chngpt-2015.9-5/chngpt/inst/unitTests/runit.chngptm.R | 81 +- chngpt-2015.9-5/chngpt/man/chngpt.Rd | 2 chngpt-2015.9-5/chngpt/man/chngpt.test.Rd | 40 - chngpt-2015.9-5/chngpt/man/chngptm.Rd | 55 + chngpt-2015.9-5/chngpt/man/sim.chngpt.Rd |only 16 files changed, 615 insertions(+), 575 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.2 dated 2015-09-08 and 1.0.3 dated 2015-09-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/cate-vignette.R | 3 +-- inst/doc/cate-vignette.Rnw | 25 ++++++++++++++++++++++--- inst/doc/cate-vignette.pdf |binary vignettes/cate-vignette.Rnw | 25 ++++++++++++++++++++++--- 7 files changed, 56 insertions(+), 19 deletions(-)
Title: High-Speed Processing of VCF, FASTA and Alignment Data
Description: Provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Ulrich Wittelsbuerger <ulrich.wittelsbuerger@uni-duesseldorf.de>
Diff between WhopGenome versions 0.9.2 dated 2015-02-20 and 0.9.3 dated 2015-09-08
DESCRIPTION | 15 ++++++--------- MD5 | 8 ++++---- NAMESPACE | 3 +++ src/Makevars | 15 ++++++++++++++- src/tabix/razf.c | 2 +- 5 files changed, 28 insertions(+), 15 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Lei Huang [aut, cre],
Fabian Scheipl [aut],
Jeff Goldsmith [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb],
Julia Wrobel [ctb]
Maintainer: Lei Huang <huangracer@gmail.com>
Diff between refund versions 0.1-12 dated 2015-08-06 and 0.1-13 dated 2015-09-08
DESCRIPTION |only MD5 |only NAMESPACE | 7 ++++++- R |only data/DTI.RData |only data/DTI2.RData |only data/PEER.Sim.RData |binary data/Q.RData |only data/datalist |only data/sofa.RData |only man |only 11 files changed, 6 insertions(+), 1 deletion(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre],
Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.3-0 dated 2015-07-10 and 1.4-0 dated 2015-09-08
DESCRIPTION | 12 ++-- MD5 | 56 +++++++++--------- R/BIFIE.by.R | 26 +++++++- R/BIFIE.correl.R | 36 ++++++++++-- R/BIFIE.crosstab.R | 32 ++++++++++ R/BIFIE.data.jack.R | 7 +- R/BIFIE.ecdf.R | 29 ++++++++- R/BIFIE.freq.R | 39 ++++++++++--- R/BIFIE.hist.R | 21 ++++++- R/BIFIE.linreg.R | 26 ++++++++ R/BIFIE.logistreg.R | 24 +++++++- R/BIFIE.pathmodel.R | 33 +++++++++-- R/BIFIE.twolevelreg.R | 2 R/BIFIE.univar.R | 107 ++++++++++++++++++++++++++++++------ R/BIFIE_NMI_inference_parameters.R | 9 ++- R/BIFIE_multiple_groupings_helper.R |only R/BIFIE_table_multiple_groupings.R |only inst/NEWS | 23 +++++++ man/BIFIE.by.Rd | 2 man/BIFIE.correl.Rd | 4 - man/BIFIE.crosstab.Rd | 2 man/BIFIE.freq.Rd | 7 ++ man/BIFIE.hist.Rd | 6 +- man/BIFIE.linreg.Rd | 4 - man/BIFIE.logistreg.Rd | 4 - man/BIFIE.pathmodel.Rd | 9 ++- man/BIFIE.univar.Rd | 6 +- man/BIFIEsurvey-package.Rd | 5 + man/bifietable.Rd | 7 +- man/save.BIFIEdata.Rd | 18 +++--- 30 files changed, 449 insertions(+), 107 deletions(-)
Title: Anonymize Data Containing Personally Identifiable Information
Description: Allows users to quickly and easily anonymize data containing
Personally Identifiable Information (PII) through convenience functions.
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Diff between anonymizer versions 0.1.0 dated 2015-08-25 and 0.2.0 dated 2015-09-08
DESCRIPTION | 6 +- MD5 | 28 +++++---- NAMESPACE | 2 R/anonymize.R | 23 +++++--- R/anonymizer.R | 3 - R/hash.R |only R/salt.R | 24 +++++++- R/unsalt.R |only README.md | 114 +++++++++++++++++++++------------------- man/anonymize.Rd | 23 ++++++-- man/anonymizer.Rd | 3 - man/hash.Rd |only man/salt.Rd | 23 +++++++- man/unsalt.Rd |only tests/testthat/test-anonymize.R | 3 - tests/testthat/test-hash.R |only tests/testthat/test-salt.R | 5 + tests/testthat/test-unsalt.R |only 18 files changed, 163 insertions(+), 94 deletions(-)
Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses by utilizing threshold approaches under a cumulative link model, a continuation ratio model or a baseline-category logit marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between SimCorMultRes versions 1.3.0 dated 2015-01-08 and 1.3.1 dated 2015-09-08
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NAMESPACE | 3 ++- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/SCMRvin.pdf |binary man/SimCorMultRes-package.Rd | 4 ++-- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Shrinkage Covariance Matrix Estimators
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between ShrinkCovMat versions 1.1.0 dated 2015-01-08 and 1.1.1 dated 2015-09-08
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 3 +++ man/ShrinkCovMat-package.Rd | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between multgee versions 1.5.1 dated 2015-03-11 and 1.5.2 dated 2015-09-08
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/multgee.Rnw | 10 +++++----- inst/doc/multgee.pdf |binary man/multgee-package.Rd | 2 +- vignettes/multgee.Rnw | 10 +++++----- 9 files changed, 32 insertions(+), 26 deletions(-)
Title: Regression Models with Breakpoints/Changepoints Estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 0.5-1.1 dated 2015-02-18 and 0.5-1.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 13 +++++++++++++ NEWS | 8 ++++++++ R/broken.line.r | 1 + R/lines.segmented.R | 2 +- R/segmented.Arima.r | 13 ++++++++++--- R/segmented.default.r | 14 +++++++++++--- R/segmented.glm.R | 12 +++++++++--- R/segmented.lm.R | 15 +++++++++++---- R/slope.R | 2 +- data/down.rda |binary data/plant.rda |binary data/stagnant.rda |binary man/segmented-package.Rd | 4 ++-- man/segmented.Rd | 9 +++++---- 16 files changed, 91 insertions(+), 40 deletions(-)
Title: Static R Code Analysis
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with Emacs,
Vim and Sublime Text.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 0.3.1 dated 2015-09-03 and 0.3.2 dated 2015-09-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/spaces_left_parentheses_linter.R | 3 ++- README.md | 1 + tests/testthat/test-methods.R | 8 ++++---- tests/testthat/test-spaces_left_parentheses_linter.R | 10 ++++++++++ 6 files changed, 25 insertions(+), 13 deletions(-)
Title: Analyze and Gaussianize Heavy-Tailed, Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. They are based on an input/output system, where
the input random variable (RV) X ~ F, and the output Y is a non-linearly
transformed version of X with similar properties, but slightly skewed and/or
heavy-tailed. This transformed RV Y has a Lambert W x F distribution.
This package contains functions to model and analyze skewed, heavy-tailed
data the Lambert Way: simulate random samples, estimate parameters, compute
quantiles, and plot/print results nicely. Probably the most important
function is 'Gaussianize', which works similarly to 'scale', but actually
makes the data Gaussian. A do-it-yourself toolkit allows users to define
their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis
right away.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.5.1 dated 2015-04-28 and 0.6.0 dated 2015-09-08
LambertW-0.5.1/LambertW/R/H.R |only LambertW-0.5.1/LambertW/man/H.Rd |only LambertW-0.6.0/LambertW/DESCRIPTION | 12 - LambertW-0.6.0/LambertW/MD5 | 135 ++++++++++--------- LambertW-0.6.0/LambertW/NAMESPACE | 11 + LambertW-0.6.0/LambertW/NEWS | 61 ++++++++ LambertW-0.6.0/LambertW/R/0_LambertW-utils.R | 3 LambertW-0.6.0/LambertW/R/0_W.R | 90 +++++++----- LambertW-0.6.0/LambertW/R/0_loglik-LambertW-utils.R | 4 LambertW-0.6.0/LambertW/R/Gaussianize.R | 12 - LambertW-0.6.0/LambertW/R/IGMM.R | 28 ++- LambertW-0.6.0/LambertW/R/LambertW-package.R | 6 LambertW-0.6.0/LambertW/R/MLE_LambertW.R | 32 +++- LambertW-0.6.0/LambertW/R/check_beta.R | 4 LambertW-0.6.0/LambertW/R/create_LambertW_input.R | 24 ++- LambertW-0.6.0/LambertW/R/create_LambertW_output.R | 9 - LambertW-0.6.0/LambertW/R/dLambertW.R | 39 +++-- LambertW-0.6.0/LambertW/R/datasets.R | 1 LambertW-0.6.0/LambertW/R/delta_GMM.R | 41 +++++ LambertW-0.6.0/LambertW/R/delta_Taylor.R | 10 - LambertW-0.6.0/LambertW/R/deprecated_functions.R | 11 + LambertW-0.6.0/LambertW/R/deriv_W.R | 43 +++++- LambertW-0.6.0/LambertW/R/deriv_W_gamma.R | 3 LambertW-0.6.0/LambertW/R/estimate_beta.R | 8 - LambertW-0.6.0/LambertW/R/gamma_GMM.R | 6 LambertW-0.6.0/LambertW/R/gamma_Taylor.R | 5 LambertW-0.6.0/LambertW/R/get_distname_family.R | 15 +- LambertW-0.6.0/LambertW/R/get_gamma_bounds.R | 2 LambertW-0.6.0/LambertW/R/get_initial_tau.R | 3 LambertW-0.6.0/LambertW/R/get_initial_theta.R | 7 LambertW-0.6.0/LambertW/R/get_input.R | 5 LambertW-0.6.0/LambertW/R/get_output.R | 21 +- LambertW-0.6.0/LambertW/R/get_support.R | 46 ++++-- LambertW-0.6.0/LambertW/R/log_W.R | 8 - LambertW-0.6.0/LambertW/R/loglik_LambertW.R | 14 - LambertW-0.6.0/LambertW/R/loglik_penalty.R | 18 +- LambertW-0.6.0/LambertW/R/lp_norm.R | 5 LambertW-0.6.0/LambertW/R/normalize_by_tau.R |only LambertW-0.6.0/LambertW/R/pLambertW.R | 59 ++++---- LambertW-0.6.0/LambertW/R/p_m1.R | 1 LambertW-0.6.0/LambertW/R/plot.LambertW_fit.R | 60 ++++---- LambertW-0.6.0/LambertW/R/private_functions.R |only LambertW-0.6.0/LambertW/R/qLambertW.R | 121 ++++++++--------- LambertW-0.6.0/LambertW/R/rLambertW.R | 5 LambertW-0.6.0/LambertW/R/summary.LambertW_fit.R | 11 - LambertW-0.6.0/LambertW/R/test_normality.R | 14 - LambertW-0.6.0/LambertW/R/test_symmetry.R | 28 ++- LambertW-0.6.0/LambertW/R/xexp.R |only LambertW-0.6.0/LambertW/man/Gaussianize.Rd | 9 - LambertW-0.6.0/LambertW/man/LambertW-package.Rd | 2 LambertW-0.6.0/LambertW/man/LambertW-toolkit.Rd | 11 + LambertW-0.6.0/LambertW/man/LambertW-utils.Rd | 13 + LambertW-0.6.0/LambertW/man/W.Rd | 42 ++--- LambertW-0.6.0/LambertW/man/delta_GMM.Rd | 2 LambertW-0.6.0/LambertW/man/deprecated-functions.Rd | 3 LambertW-0.6.0/LambertW/man/distname-utils.Rd | 9 - LambertW-0.6.0/LambertW/man/get_output.Rd | 8 - LambertW-0.6.0/LambertW/man/get_support.Rd | 10 + LambertW-0.6.0/LambertW/man/loglik-LambertW-utils.Rd | 11 - LambertW-0.6.0/LambertW/man/tau-utils.Rd | 19 ++ LambertW-0.6.0/LambertW/man/test_symmetry.Rd | 6 LambertW-0.6.0/LambertW/man/xexp.Rd |only LambertW-0.6.0/LambertW/tests |only 63 files changed, 733 insertions(+), 453 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.3.2 dated 2015-09-05 and 1.3.3 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS | 4 ++-- R/Diversity.R | 2 +- R/Dqz.R | 2 +- R/Hqz.R | 2 +- R/HqzBeta.R | 2 +- R/Hurlbert.R | 2 +- R/HurlbertD.R | 2 +- R/PhyloBetaEntropy.R | 2 +- R/PhyloDiversity.R | 2 +- R/PhyloEntropy.R | 2 +- R/Rao.R | 2 +- R/Richness.R | 2 +- R/Shannon.R | 2 +- R/ShannonBeta.R | 2 +- R/Simpson.R | 2 +- R/SimpsonBeta.R | 2 +- R/SpeciesDistribution.R | 32 +++++++++++++++++++++++++++++--- R/Tsallis.R | 2 +- R/TsallisBeta.R | 2 +- R/rCommunity.R | 2 +- inst/doc/entropart.pdf |binary man/entropart-package.Rd | 4 ++-- 24 files changed, 78 insertions(+), 52 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.1.1 dated 2015-07-09 and 2.2.2 dated 2015-09-08
DESCRIPTION | 16 - MD5 | 56 ++++-- NAMESPACE | 42 ++++ NEWS.md |only R/RcppExports.R |only R/RcppWrappers.r |only R/error-functions.r | 15 + R/helpers.r | 163 ++++++++++++++++++ R/imputation.r |only R/learning-curve.r | 8 R/modeling.r | 1 R/preprocessing.r | 328 ++++++++++++++------------------------ R/randomForest.r | 6 R/resampling.r | 33 +++ R/reshape-result.r | 51 +++-- R/roc-curve.r | 8 man/factor_to_logical.Rd |only man/has_na.Rd |only man/impute.Rd | 2 man/is_constant.Rd |only man/mode.Rd |only man/na_index.Rd | 11 + man/pipe.Rd |only man/pre_factor_to_logical.Rd |only man/pre_impute.Rd | 2 man/pre_impute_df.Rd |only man/pre_impute_knn.Rd | 2 man/pre_log_message.Rd |only man/pre_process.Rd | 9 - man/select.Rd | 4 man/trivial_error_rate.Rd |only man/validate_data.Rd |only src |only tests/testthat/test-cppfunction.r |only tests/testthat/test-helpers.r | 37 +++- tests/testthat/test-preprocess.r | 37 ++++ 36 files changed, 553 insertions(+), 278 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 0.0.1 dated 2015-08-01 and 1.0.0 dated 2015-09-08
DESCRIPTION | 8 +-- MD5 | 25 +++++----- R/ALL.r | 116 +++++++++++++++++++++++++++++++++++++++++------- data/USAranks.rda |only man/BBFULL.Rd |only man/BBconsensus.Rd | 8 ++- man/BBconsensus2.Rd | 5 +- man/ConsRank-package.Rd | 11 ++-- man/EMCons.Rd | 4 + man/FASTcons.Rd | 7 ++ man/Penalty.Rd | 2 man/QuickCons.Rd | 7 ++ man/USAranks.Rd |only man/branches.Rd | 5 +- man/findbranches.Rd | 5 +- 15 files changed, 157 insertions(+), 46 deletions(-)
Title: Clustering of Variables Around Latent Variables
Description: Functions for the clustering of variables around Latent Variables. Each cluster of variables, which may be defined as a local or directional cluster, is associated with a latent variable.
External variables measured on the same observations or/and additional information on the variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau <evelyne.vigneau@oniris-nantes.fr>
Diff between ClustVarLV versions 1.4.0 dated 2015-06-02 and 1.4.1 dated 2015-09-08
ClustVarLV-1.4.0/ClustVarLV/R/descrip_gp.R |only ClustVarLV-1.4.0/ClustVarLV/R/summary_clv.R |only ClustVarLV-1.4.0/ClustVarLV/man/summary_clv.Rd |only ClustVarLV-1.4.1/ClustVarLV/DESCRIPTION | 8 +- ClustVarLV-1.4.1/ClustVarLV/MD5 | 27 ++++------ ClustVarLV-1.4.1/ClustVarLV/NAMESPACE | 5 + ClustVarLV-1.4.1/ClustVarLV/R/summary.clv.R |only ClustVarLV-1.4.1/ClustVarLV/build/vignette.rds |binary ClustVarLV-1.4.1/ClustVarLV/data/AUPA_psycho.rda |binary ClustVarLV-1.4.1/ClustVarLV/data/apples_sh.rda |binary ClustVarLV-1.4.1/ClustVarLV/data/authen_NMR.rda |binary ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.R | 2 ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.Rmd | 6 +- ClustVarLV-1.4.1/ClustVarLV/inst/doc/Getting_started_with_ClustVarLV.pdf |binary ClustVarLV-1.4.1/ClustVarLV/man/summary.clv.Rd |only ClustVarLV-1.4.1/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.Rmd | 6 +- ClustVarLV-1.4.1/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.html | 8 +- 17 files changed, 31 insertions(+), 31 deletions(-)
Title: Tools for Handling and Scrapping Instant Weather Forecast Feeds
Description: Handle instant weather forecasts and geographical information. It combines multiple sources of information to obtain instant weather forecasts.
Author: Stan Yip [aut, cre]
Maintainer: Stan Yip <stanyip101@gmail.com>
Diff between weatherr versions 0.1.1 dated 2015-08-26 and 0.1.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ggele.R | 2 +- man/ggele.Rd | 2 ++ man/locationforecast.Rd | 2 ++ man/weatherr-package.Rd | 4 ++-- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: Patient Rule Induction Method (PRIM)
Description: Patient Rule Induction Method (PRIM) for bump hunting in high-dimensional data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between prim versions 1.0.15 dated 2014-11-04 and 1.0.16 dated 2015-09-08
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 11 ++++++++--- build/vignette.rds |binary inst/doc/prim-2d.pdf |binary inst/doc/prim-3d.pdf |binary 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd9 versions 1.2.1 dated 2015-09-04 and 1.2.2 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- configure.ac | 12 +++++++++++- inst/doc/introduction.html | 4 ++-- src/comorbid.cpp | 4 ++-- src/local.h | 4 ++-- src/util.cpp | 6 +++--- tools/r-base-ubsan-gcc |only tools/r-devel-ubsan-clang/Dockerfile | 3 +++ 9 files changed, 36 insertions(+), 21 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong <tarn.duong@gmail.com> & Matt Wand <Matt.Wand@uts.edu.au>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.11 dated 2014-11-04 and 1.2.12 dated 2015-09-08
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NAMESPACE | 16 +++++++--------- build/vignette.rds |binary data/earthquake.RData |binary inst/doc/feature.pdf |binary man/SiZer.Rd | 2 +- 7 files changed, 22 insertions(+), 23 deletions(-)
Title: Composite Indicators Functions
Description: Contains several functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 1.0 dated 2014-09-24 and 1.1 dated 2015-09-08
DESCRIPTION | 16 ++++++---------- MD5 | 21 ++++++++++++--------- NAMESPACE | 1 + R/ci_bod.R | 8 ++++++-- R/ci_factor.R | 27 +++++++++++++++++++-------- R/ci_mean_min.R |only man/ci_bod.Rd | 5 +++++ man/ci_factor.Rd | 9 +++++++-- man/ci_mean_min.Rd |only man/ci_mpi.Rd | 4 ++-- man/ci_rbod.Rd | 2 +- man/normalise_ci.Rd | 2 +- vignettes |only 13 files changed, 60 insertions(+), 35 deletions(-)
Title: Birnbaum-Saunders Model Based on Skew-Normal Distribution
Description: It provides the density, distribution function, quantile function, random number generator, reliability function, failure rate, likelihood function,
moments and EM algorithm for Maximum Likelihood estimators, also empirical quantile and generated envelope for a given sample, all this for the three parameter
Birnbaum-Saunders model based on Skew-Normal Distribution.
Additionally, it provides the random number generator for the mixture of Birnbaum-Saunders model based on Skew-Normal distribution.
Author: Rocio Paola Maehara <rmaeharaa@gmail.com> and Luis Benites Sanchez <lbenitesanchez@gmail.com>
Maintainer: Rocio Paola Maehara <rmaeharaa@gmail.com>
Diff between bssn versions 0.5 dated 2015-08-11 and 0.6 dated 2015-09-08
bssn-0.5/bssn/R/initial.R |only bssn-0.6/bssn/DESCRIPTION | 16 ++--- bssn-0.6/bssn/MD5 | 19 +++--- bssn-0.6/bssn/NAMESPACE | 4 + bssn-0.6/bssn/R/EMbssn.R | 7 +- bssn-0.6/bssn/R/algEMbssn.R | 81 +++++++++++++++++++-------- bssn-0.6/bssn/R/functions.R | 110 ++++++++++++++++++++------------------ bssn-0.6/bssn/man/EMbssn.Rd | 10 ++- bssn-0.6/bssn/man/bssn-package.Rd | 12 ++-- bssn-0.6/bssn/man/bssn.Rd | 38 ++++++++++--- bssn-0.6/bssn/man/momentsbssn.Rd | 2 11 files changed, 182 insertions(+), 117 deletions(-)
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.2.0 dated 2014-12-05 and 0.3.0 dated 2015-09-08
DESCRIPTION | 27 MD5 | 98 +- NAMESPACE | 23 R/RcppExports.R |only R/complete.R |only R/expand.R | 80 +- R/extract.R | 36 - R/fill.R |only R/gather.R | 113 +++ R/nest.R |only R/replace_na.R |only R/separate.R | 87 +- R/spread.R | 23 R/unite.R | 2 R/unnest.R | 135 ++-- R/utils.R | 21 README.md | 4 build/vignette.rds |binary inst/doc/tidy-data.R | 6 inst/doc/tidy-data.Rmd | 22 inst/doc/tidy-data.html | 1077 +++++++++++++------------------- man/complete.Rd |only man/complete_.Rd |only man/expand.Rd | 62 + man/expand_.Rd | 3 man/extract.Rd | 13 man/extract_.Rd | 3 man/extract_numeric.Rd | 3 man/fill.Rd |only man/fill_.Rd |only man/gather.Rd | 19 man/gather_.Rd | 3 man/nest.Rd |only man/nest_.Rd |only man/pipe.Rd |only man/replace_na.Rd |only man/separate.Rd | 33 man/separate_.Rd | 22 man/seq_range.Rd | 3 man/spread.Rd | 10 man/spread_.Rd | 10 man/unite.Rd | 5 man/unite_.Rd | 3 man/unnest.Rd | 50 + man/unnest_.Rd | 7 src |only tests/testthat/test-complete.R |only tests/testthat/test-expand.R |only tests/testthat/test-extract.R | 13 tests/testthat/test-fill.R |only tests/testthat/test-gather.R | 92 ++ tests/testthat/test-matrixToDataFrame.R |only tests/testthat/test-nest.R |only tests/testthat/test-replace_na.R |only tests/testthat/test-separate.R | 54 + tests/testthat/test-spread.R | 20 tests/testthat/test-unite.R |only tests/testthat/test-unnest.R |only vignettes/tidy-data.Rmd | 22 59 files changed, 1270 insertions(+), 934 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.1-1 dated 2015-06-05 and 1.2-0 dated 2015-09-08
sp-1.1-1/sp/man/nowrapSpatialLines.Rd |only sp-1.2-0/sp/ChangeLog | 177 +++++++++++++++++++ sp-1.2-0/sp/DESCRIPTION | 17 + sp-1.2-0/sp/MD5 | 88 +++++---- sp-1.2-0/sp/NAMESPACE | 39 +++- sp-1.2-0/sp/R/Class-SpatialMultiPoints.R |only sp-1.2-0/sp/R/Class-SpatialMultiPointsDataFrame.R |only sp-1.2-0/sp/R/Class-SpatialPoints.R | 3 sp-1.2-0/sp/R/Spatial-methods.R | 41 +++- sp-1.2-0/sp/R/SpatialMultiPoints-methods.R |only sp-1.2-0/sp/R/SpatialMultiPointsDataFrame-methods.R |only sp-1.2-0/sp/R/SpatialPolygons-displayMethods.R | 4 sp-1.2-0/sp/R/aggregate.R | 28 +-- sp-1.2-0/sp/R/over.R | 24 ++ sp-1.2-0/sp/R/recenter.R | 100 ---------- sp-1.2-0/sp/R/spplot.R | 15 + sp-1.2-0/sp/build/vignette.rds |binary sp-1.2-0/sp/demo/00Index | 2 sp-1.2-0/sp/demo/depend.R | 8 sp-1.2-0/sp/demo/meuse.R | 2 sp-1.2-0/sp/demo/mp.R |only sp-1.2-0/sp/demo/webmap.R |only sp-1.2-0/sp/inst/ChangeLog | 177 +++++++++++++++++++ sp-1.2-0/sp/inst/NEWS.Rd |only sp-1.2-0/sp/inst/doc/csdacm.pdf |binary sp-1.2-0/sp/inst/doc/intro_sp.pdf |binary sp-1.2-0/sp/inst/doc/over.R | 83 ++++++++ sp-1.2-0/sp/inst/doc/over.Rnw | 115 ++++++++++++ sp-1.2-0/sp/inst/doc/over.pdf |binary sp-1.2-0/sp/inst/include/sp.h | 2 sp-1.2-0/sp/man/00sp.Rd | 2 sp-1.2-0/sp/man/CRS-class.Rd | 2 sp-1.2-0/sp/man/SpatialMultiPoints-class.Rd |only sp-1.2-0/sp/man/SpatialMultiPoints.Rd |only sp-1.2-0/sp/man/SpatialMultiPointsDataFrame-class.Rd |only sp-1.2-0/sp/man/SpatialPoints-class.Rd | 2 sp-1.2-0/sp/man/addattr.Rd | 1 sp-1.2-0/sp/man/aggregate.Rd | 8 sp-1.2-0/sp/man/coordinates-methods.Rd | 1 sp-1.2-0/sp/man/coordnames-methods.Rd | 2 sp-1.2-0/sp/man/geometry-methods.Rd | 2 sp-1.2-0/sp/man/over.Rd | 26 ++ sp-1.2-0/sp/man/spplot.Rd | 3 sp-1.2-0/sp/src/sp.h | 2 sp-1.2-0/sp/tests/fail1.Rout.save | 11 - sp-1.2-0/sp/tests/mp.R |only sp-1.2-0/sp/tests/mp.Rout.save |only sp-1.2-0/sp/tests/over.R |only sp-1.2-0/sp/tests/over.Rout.save | 57 +++--- sp-1.2-0/sp/tests/over2.R |only sp-1.2-0/sp/tests/over2.Rout.save |only sp-1.2-0/sp/tests/pass1.Rout.save | 57 ++---- sp-1.2-0/sp/vignettes/over.Rnw | 115 ++++++++++++ 53 files changed, 964 insertions(+), 252 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-18 dated 2015-08-15 and 2.4-20 dated 2015-09-08
DESCRIPTION | 15 MD5 | 18 - R/cropSpatial.R | 2 R/shift.R | 7 build/vignette.rds |binary inst/doc/Raster.R | 732 ++++++++++++++++++++++++------------------------ inst/doc/Raster.pdf |binary inst/doc/functions.R | 686 ++++++++++++++++++++++---------------------- inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary 10 files changed, 728 insertions(+), 732 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.1 dated 2015-08-27 and 1.0.2 dated 2015-09-08
DESCRIPTION | 10 ++++++---- MD5 | 24 ++++++++++++++++-------- R/cate.R | 30 ++++++++++++++++-------------- R/datasets.R |only R/factor_functions.R | 28 ++++++++++++++-------------- build |only data |only inst |only man/EigenDiff.Rd | 4 ++-- man/cate.Rd | 8 ++++---- man/est.confounder.num.Rd | 32 ++++++++++++++++---------------- man/factor.analysis.Rd | 2 +- man/gender.sm.Rd |only man/wrapper.Rd | 2 +- vignettes |only 15 files changed, 76 insertions(+), 64 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such
as calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.0 dated 2015-09-05 and 0.1.1 dated 2015-09-08
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 4 ++++ README.md | 7 ++++++- src/classQA.cpp | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.5.8 dated 2015-08-29 and 0.5.9 dated 2015-09-08
PRIMsrc-0.5.8/PRIMsrc/inst/doc/Abstract_JCB2015.pdf |only PRIMsrc-0.5.8/PRIMsrc/inst/doc/PRIMsrc_0.5.8.pdf |only PRIMsrc-0.5.8/PRIMsrc/man/plot_scatter.Rd |only PRIMsrc-0.5.9/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.5.9/PRIMsrc/MD5 | 34 +- PRIMsrc-0.5.9/PRIMsrc/NAMESPACE | 28 - PRIMsrc-0.5.9/PRIMsrc/R/PRIMsrc.internal.r | 1 PRIMsrc-0.5.9/PRIMsrc/R/PRIMsrc.r | 339 ++++++++++---------- PRIMsrc-0.5.9/PRIMsrc/inst/CITATION | 214 ++++++------ PRIMsrc-0.5.9/PRIMsrc/inst/NEWS | 26 - PRIMsrc-0.5.9/PRIMsrc/inst/doc/Abstract.JCB2016.pdf |only PRIMsrc-0.5.9/PRIMsrc/inst/doc/PRIMsrc_0.5.9.pdf |only PRIMsrc-0.5.9/PRIMsrc/man/PrimSRC-package.Rd | 19 - PRIMsrc-0.5.9/PRIMsrc/man/plot.Rd |only PRIMsrc-0.5.9/PRIMsrc/man/plot_boxtrace.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/plot_boxtraj.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/plot_profile.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/predict.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/print.Rd | 2 PRIMsrc-0.5.9/PRIMsrc/man/sbh.Rd | 4 PRIMsrc-0.5.9/PRIMsrc/man/summary.Rd | 2 21 files changed, 352 insertions(+), 333 deletions(-)
Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
Author: Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between GiANT versions 1.0 dated 2015-08-06 and 1.1 dated 2015-09-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/analysis.R | 2 +- R/hist.R | 4 ++-- build/vignette.rds |binary inst/doc/giant_package_vignette.pdf |binary man/parseGmt.Rd | 8 -------- 7 files changed, 13 insertions(+), 21 deletions(-)
Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
Description: This is a set of tools for dendrograms and
tree plots using 'ggplot2'. The 'ggplot2' philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The 'ggdendro' package resolves this by making available
functions that extract the dendrogram plot data. The package
provides implementations for tree, rpart, as well as diana and agnes
cluster diagrams.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between ggdendro versions 0.1-15 dated 2014-09-29 and 0.1-17 dated 2015-09-08
ggdendro-0.1-15/ggdendro/man/dendro_data.dendrogram.Rd |only ggdendro-0.1-17/ggdendro/DESCRIPTION | 25 +- ggdendro-0.1-17/ggdendro/MD5 | 86 ++++--- ggdendro-0.1-17/ggdendro/NAMESPACE | 22 + ggdendro-0.1-17/ggdendro/NEWS | 19 + ggdendro-0.1-17/ggdendro/R/dendro_data.R | 23 - ggdendro-0.1-17/ggdendro/R/dendro_rpart.R | 20 - ggdendro-0.1-17/ggdendro/R/dendro_tree.R | 23 - ggdendro-0.1-17/ggdendro/R/dendrogram.R | 69 ++--- ggdendro-0.1-17/ggdendro/R/ggdendro-package.R | 31 +- ggdendro-0.1-17/ggdendro/R/ggdendrogram.R | 74 ++---- ggdendro-0.1-17/ggdendro/R/rpart.R | 14 - ggdendro-0.1-17/ggdendro/build/vignette.rds |binary ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.R | 70 +++--- ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.Rmd | 98 +++++--- ggdendro-0.1-17/ggdendro/inst/doc/ggdendro.html | 116 ++++++---- ggdendro-0.1-17/ggdendro/inst/examples |only ggdendro-0.1-17/ggdendro/man/as.dendro.Rd | 3 ggdendro-0.1-17/ggdendro/man/dendro_data.Rd | 103 ++++++++ ggdendro-0.1-17/ggdendro/man/dendro_data.rpart.Rd | 27 +- ggdendro-0.1-17/ggdendro/man/dendro_data.tree.Rd | 45 ++- ggdendro-0.1-17/ggdendro/man/dendrogram_data.Rd | 19 + ggdendro-0.1-17/ggdendro/man/get_data_tree_leaf_labels.Rd | 3 ggdendro-0.1-17/ggdendro/man/ggdendro-package.Rd | 24 +- ggdendro-0.1-17/ggdendro/man/ggdendrogram.Rd | 13 - ggdendro-0.1-17/ggdendro/man/is.dendro.Rd | 5 ggdendro-0.1-17/ggdendro/man/labels.rpart.Rd | 7 ggdendro-0.1-17/ggdendro/man/rpart_labels.Rd | 12 - ggdendro-0.1-17/ggdendro/man/rpart_segments.Rd | 7 ggdendro-0.1-17/ggdendro/man/rpartco.Rd | 3 ggdendro-0.1-17/ggdendro/man/segment.Rd | 3 ggdendro-0.1-17/ggdendro/man/theme_dendro.Rd | 3 ggdendro-0.1-17/ggdendro/man/tree_labels.Rd | 3 ggdendro-0.1-17/ggdendro/man/tree_segments.Rd | 3 ggdendro-0.1-17/ggdendro/man/treeco.Rd | 3 ggdendro-0.1-17/ggdendro/tests/testthat/Rplots.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots1.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots2.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots3.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots4.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots5.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/Rplots6.pdf |only ggdendro-0.1-17/ggdendro/tests/testthat/test-1-dendrogram.R | 100 -------- ggdendro-0.1-17/ggdendro/tests/testthat/test-2-hclust.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-3-rpart.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-3-tree.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-4-clusterplots.R |only ggdendro-0.1-17/ggdendro/tests/testthat/test-6-ggdendrogram.R |only ggdendro-0.1-17/ggdendro/vignettes/ggdendro.Rmd | 102 +++++--- 49 files changed, 655 insertions(+), 523 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.0.9 dated 2015-06-14 and 1.1.2 dated 2015-09-07
DESCRIPTION | 8 +-- MD5 | 72 +++++++++++++-------------- NAMESPACE | 9 +++ R/Binary_Function.R | 5 + R/Binary_MAIN.R | 2 R/Binary_MAIN_ExactBin.R | 10 +-- R/Function.R | 1 R/Power.R | 72 +++++++++++++++++++-------- R/SKAT_EMMAX.R | 2 inst/doc/SKAT.R | 9 ++- inst/doc/SKAT.Rnw | 48 +++++++++--------- inst/doc/SKAT.pdf |binary man/Generate_SSD_SetID.rd | 13 ++-- man/Get_EffectiveNumberTest.rd | 16 ++++-- man/Get_Genotypes_SSD.rd | 6 +- man/Get_Logistic_Weights.rd | 10 ++- man/Get_RequiredSampleSize.rd | 8 +-- man/Get_Resampling_Pvalue.rd | 4 - man/Open_SSD.rd | 5 - man/Power_Continuous.rd | 36 ++++++++----- man/Power_Logistic.rd | 13 ++-- man/QQPlot_Adj.rd | 12 ++++ man/Read_Plink_FAM.rd | 9 +-- man/Read_SNP_WeightFile.rd | 17 +++--- man/Resampling_FWER.rd | 6 +- man/SKAT.SSD.All.rd | 16 +++--- man/SKAT.haplotypes.rd | 10 ++- man/SKAT.rd | 94 +++++++++++++++++++----------------- man/SKATBinary.rd | 56 +++++++++++++-------- man/SKATBinary_Single.rd | 30 ++++++----- man/SKAT_ChrX.rd | 45 ++++++----------- man/SKAT_CommonRare.rd | 12 ++-- man/SKAT_NULL_emmaX.rd | 10 +-- man/SKAT_Null_Model.rd | 12 +++- man/SKAT_Null_Model_MomentAdjust.rd | 13 +++- man/SSD_FILE_OPEN.rd | 2 vignettes/SKAT.Rnw | 48 +++++++++--------- 37 files changed, 424 insertions(+), 317 deletions(-)
Title: Replicate and Analyse InterVA4
Description: Provides an R version of the InterVA4 software for
coding cause of death from verbal autopsies. It also provides simple
graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InterVA4 versions 1.5 dated 2014-10-14 and 1.6 dated 2015-09-07
InterVA4-1.5/InterVA4/R/InterVA4_1.4-package.R |only InterVA4-1.5/InterVA4/man/InterVA.summary.Rd |only InterVA4-1.6/InterVA4/DESCRIPTION | 12 - InterVA4-1.6/InterVA4/MD5 | 27 ++-- InterVA4-1.6/InterVA4/NAMESPACE | 3 InterVA4-1.6/InterVA4/R/InterVA.R | 68 +++++++--- InterVA4-1.6/InterVA4/R/InterVA.plot.R | 120 +++++++++++++----- InterVA4-1.6/InterVA4/R/InterVA4_1.6-package.R |only InterVA4-1.6/InterVA4/man/CSMF.Rd |only InterVA4-1.6/InterVA4/man/CSMF.interVA4.Rd |only InterVA4-1.6/InterVA4/man/InterVA.Rd | 157 ++++++++++++------------ InterVA4-1.6/InterVA4/man/InterVA.plot.Rd | 47 +++---- InterVA4-1.6/InterVA4/man/InterVA4-package.Rd | 25 +-- InterVA4-1.6/InterVA4/man/Population.summary.Rd | 93 ++++---------- InterVA4-1.6/InterVA4/man/SampleInput.Rd | 11 + InterVA4-1.6/InterVA4/man/causetext.Rd | 7 - InterVA4-1.6/InterVA4/man/probbase.Rd | 7 - 17 files changed, 320 insertions(+), 257 deletions(-)
Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as
on a telephone keypad. When converting letters to numbers, a character
vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F"
becoming 3, etc. When converting numbers to letters, a character vector is
returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and
"C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between phonenumber versions 0.2.1 dated 2015-08-22 and 0.2.2 dated 2015-09-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/letterToNumber.R | 2 +- README.md | 2 +- inst/doc/phonenumber.R | 3 +++ inst/doc/phonenumber.Rmd | 9 ++++++++- inst/doc/phonenumber.html | 9 ++++++--- man/letterToNumber.Rd | 2 +- vignettes/phonenumber.Rmd | 9 ++++++++- 9 files changed, 39 insertions(+), 19 deletions(-)
Title: Use the MLS Junk Generator Algorithm to Generate a Stream of
Pseudo-Random Numbers
Description: Generate a stream of pseudo-random numbers generated using the MLS
Junk Generator algorithm. Functions exist to generate single pseudo-random
numbers as well as a vector, data frame, or matrix of pseudo-random numbers.
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between mlsjunkgen versions 0.1.0 dated 2015-08-16 and 0.1.1 dated 2015-09-07
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++-------- R/mlsjunkgend.R | 2 - R/mlsjunkgenm.R | 2 - R/mlsjunkgenv.R | 2 - README.md | 70 +++++++++++++++++++++++++---------------------- inst/doc/mlsjunkgen.R | 2 - inst/doc/mlsjunkgen.Rmd | 17 ++++++----- inst/doc/mlsjunkgen.html | 38 ++++++++++++------------- man/mlsjunkgend.Rd | 2 - man/mlsjunkgenm.Rd | 2 - man/mlsjunkgenv.Rd | 2 - vignettes/mlsjunkgen.Rmd | 17 ++++++----- 13 files changed, 98 insertions(+), 90 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: Matt Pennell <mwpennell@gmail.com>
Diff between geiger versions 2.0.5 dated 2015-09-03 and 2.0.6 dated 2015-09-07
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/gbresolve.R | 16 +++--- README.md | 37 ++++++++++++++ man/fitContinuous.Rd | 127 ++++++++++++++++++++++++--------------------------- man/fitDiscrete.Rd | 68 +++++++++++++-------------- man/gbresolve.Rd | 25 +++++----- man/subset.phylo.Rd | 5 -- 8 files changed, 165 insertions(+), 135 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.0 dated 2015-09-04 and 0.4.2 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/vardchangespoor.R | 7 ++----- R/vardcrospoor.R | 7 +++---- inst/CITATION | 2 +- inst/NEWS | 4 ++++ man/vardchangespoor.Rd | 4 ---- man/vardcrospoor.Rd | 5 ----- man/vardpoor-package.Rd | 4 ++-- man/variance_est.Rd | 42 +++++++++++++++++++++++------------------- man/variance_othstr.Rd | 40 +++++++++++++++++++++++----------------- man/varpoord.Rd | 2 ++ 12 files changed, 75 insertions(+), 72 deletions(-)
Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries
from ASCII sources and provides tools for estimating SEER second cancer risks.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>
Diff between SEERaBomb versions 2015.1 dated 2015-05-05 and 2015.2 dated 2015-09-07
DESCRIPTION | 15 +-- MD5 | 52 +++++++---- NAMESPACE | 13 ++ NEWS | 11 ++ R/getE.R | 29 +++--- R/mapCancs.R | 111 +++++++++++++++++++++---- R/mk2D.R | 10 +- R/mkDF.R |only R/mkExcel.R | 41 +++++---- R/mkSEER.R | 60 +++++++++---- R/pickFields.R | 9 +- R/plot2D.R | 28 ++++-- R/post1PYO.R | 189 ++++++++++++++++++++++++++----------------- R/print.seerSet.summary.R |only R/seerSet.R | 13 +- R/seerStats.R |only R/summary.seerSet.R |only R/tsd.R | 81 ++++++++++++------ data/nvsr.rda |only data/nvsr01.rda |only man/SEERaBomb-package.Rd | 4 man/getE.Rd | 4 man/mkDF.Rd |only man/mkExcel.Rd | 9 +- man/nvsr.Rd |only man/nvsr01.Rd |only man/plot2D.Rd | 3 man/post1PYO.Rd | 5 - man/print.seerSet.summary.Rd |only man/seerSet.Rd | 4 man/seerStats.Rd |only man/summary.seerSet.Rd |only man/tsd.Rd | 8 + 33 files changed, 472 insertions(+), 227 deletions(-)
Title: An Infra-Structure for Performance Estimation of Predictive
Models
Description: An infra-structure for estimating the predictive performance
of predictive models. In this context, it can also be used to compare and/or select among
different alternative ways of solving one or more predictive tasks. The main goal of the
package is to provide a generic infra-structure to estimate the values of different metrics
of predictive performance using different estimation procedures. These estimation tasks can be
applied to any solutions (workflows) to the predictive tasks. The package provides easy to use
standard workflows that allow the usage of any available R modeling algorithm together with
some pre-defined data pre-processing steps and also prediction post-processing methods. It also provides means for addressing issues related with the statistical significance of the observed differences.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between performanceEstimation versions 1.0.1 dated 2015-06-16 and 1.0.2 dated 2015-09-07
performanceEstimation-1.0.1/performanceEstimation/man/WFoutput-class.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/getIterationInfo.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/getIterationPreds.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/workflowInformation.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/workflowPredictions.Rd |only performanceEstimation-1.0.2/performanceEstimation/CHANGES | 14 performanceEstimation-1.0.2/performanceEstimation/DESCRIPTION | 8 performanceEstimation-1.0.2/performanceEstimation/MD5 | 47 +- performanceEstimation-1.0.2/performanceEstimation/NAMESPACE | 13 performanceEstimation-1.0.2/performanceEstimation/R/classDefs.R | 51 --- performanceEstimation-1.0.2/performanceEstimation/R/evaluationMetrics.R | 37 ++ performanceEstimation-1.0.2/performanceEstimation/R/experiments.R | 157 ++++------ performanceEstimation-1.0.2/performanceEstimation/R/methods.R | 19 - performanceEstimation-1.0.2/performanceEstimation/R/resultsManipulation.R | 23 - performanceEstimation-1.0.2/performanceEstimation/R/workflows.R | 44 +- performanceEstimation-1.0.2/performanceEstimation/inst/doc/performanceEstimation.pdf |binary performanceEstimation-1.0.2/performanceEstimation/man/Workflow-class.Rd | 4 performanceEstimation-1.0.2/performanceEstimation/man/classificationMetrics.Rd | 9 performanceEstimation-1.0.2/performanceEstimation/man/cvEstimates.Rd | 5 performanceEstimation-1.0.2/performanceEstimation/man/getIterationsInfo.Rd |only performanceEstimation-1.0.2/performanceEstimation/man/getIterationsPreds.Rd |only performanceEstimation-1.0.2/performanceEstimation/man/hldEstimates.Rd | 5 performanceEstimation-1.0.2/performanceEstimation/man/mcEstimates.Rd | 3 performanceEstimation-1.0.2/performanceEstimation/man/performanceEstimation.Rd | 2 performanceEstimation-1.0.2/performanceEstimation/man/regressionMetrics.Rd | 9 performanceEstimation-1.0.2/performanceEstimation/man/runWorkflow.Rd | 13 performanceEstimation-1.0.2/performanceEstimation/man/standardWF.Rd | 28 - performanceEstimation-1.0.2/performanceEstimation/man/timeseriesWF.Rd | 16 - 28 files changed, 237 insertions(+), 270 deletions(-)
More information about performanceEstimation at CRAN
Permanent link
Title: High-Dimensional Penalized Regression
Description: Algorithms for lasso and fused-lasso
problems: implementation of the lars algorithm [1], for the
lasso and fusion penalization and EM-based algorithms for (logistic) lasso
and fused-lasso.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between HDPenReg versions 0.91 dated 2015-02-16 and 0.92 dated 2015-09-07
DESCRIPTION | 16 +-- MD5 | 76 ++++++++--------- NAMESPACE | 9 +- NEWS | 3 R/HDPenReg-package.R | 8 + R/LarsPath.R | 19 ++-- R/cvEM.R | 4 R/lars.R | 108 ++++++++++++------------- R/predict.R | 120 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/HDPenReg.pdf |binary man/EMcvfusedlasso.Rd | 2 man/EMcvlasso.Rd | 2 man/EMfusedlasso.Rd | 2 man/EMlasso.Rd | 2 man/HDPenReg-package.Rd | 6 - man/HDcvlars.Rd | 2 man/HDfusion.Rd | 2 man/HDlars.Rd | 2 man/LarsPath-class.Rd | 2 man/coef.LarsPath.Rd | 2 man/coeff.Rd | 2 man/computeCoefficients.Rd | 2 man/plot-methods.Rd | 2 man/plot.HDcvlars.Rd | 2 man/plotCoefficient.Rd | 2 man/predict.LarsPath.Rd | 2 man/simul.Rd | 2 src/HDPenReg/lars.mk | 2 src/HDPenReg/lars/Cvlars.cpp | 12 +- src/HDPenReg/lars/Lars.cpp | 4 src/HDPenReg/lars/PathState.h | 2 src/HDPenReg/lassoModels.mk | 2 src/HDPenReg/lassoModels/EnetPenalty.h | 2 src/HDPenReg/lassoModels/IMeasure.h | 2 src/HDPenReg/lassoModels/IPenalizedSolver.h | 1 src/HDPenReg/lassoModels/IPenalty.h | 2 src/HDPenReg/lassoModels/PenalizedModels.h | 3 src/Makevars | 10 +- 39 files changed, 227 insertions(+), 216 deletions(-)
Title: Functions and Methods for Correspondence Regression
Description: A collection of tools for correspondence regression, i.e. the
correspondence analysis of the crosstabulation of a categorical variable Y
in function of another one X, where X can in turn be made up of the
combination of various categorical variables. Consequently, correspondence
regression can be used to analyze the effects for a polytomous or
multinomial outcome variable.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between corregp versions 0.1.2 dated 2015-09-02 and 0.1.3 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/corregp.r | 4 ++-- man/corregp-package.Rd | 2 +- man/plot3d.corregp.Rd | 2 +- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Perform figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotids Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, judith Peñafiel and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.0.1 dated 2015-05-12 and 3.1 dated 2015-09-07
compareGroups-3.0.1/compareGroups/inst/app/help |only compareGroups-3.0.1/compareGroups/inst/app/www/tablePDF3046.pdf |only compareGroups-3.0.1/compareGroups/man/missingTable.rd |only compareGroups-3.1/compareGroups/DESCRIPTION | 31 compareGroups-3.1/compareGroups/MD5 | 72 compareGroups-3.1/compareGroups/NAMESPACE | 10 compareGroups-3.1/compareGroups/R/export2html.R | 18 compareGroups-3.1/compareGroups/R/export2md.R |only compareGroups-3.1/compareGroups/R/export2word.R |only compareGroups-3.1/compareGroups/R/export2xls.R |only compareGroups-3.1/compareGroups/build/vignette.rds |binary compareGroups-3.1/compareGroups/inst/app/global.R |only compareGroups-3.1/compareGroups/inst/app/help.html |only compareGroups-3.1/compareGroups/inst/app/server.R | 3169 ++++------ compareGroups-3.1/compareGroups/inst/app/spss_varlist.R |only compareGroups-3.1/compareGroups/inst/app/ui.R | 457 - compareGroups-3.1/compareGroups/inst/app/www/examples |only compareGroups-3.1/compareGroups/inst/app/www/images |only compareGroups-3.1/compareGroups/inst/app/www/tablePDF6755.pdf |only compareGroups-3.1/compareGroups/inst/doc/changelog | 6 compareGroups-3.1/compareGroups/inst/exdata/predimed.csv |only compareGroups-3.1/compareGroups/inst/exdata/predimed.dat |only compareGroups-3.1/compareGroups/inst/exdata/predimed.sav |only compareGroups-3.1/compareGroups/inst/exdata/predimed.xls |only compareGroups-3.1/compareGroups/inst/exdata/predimed.xlsx |only compareGroups-3.1/compareGroups/inst/exdata/regicor.csv |only compareGroups-3.1/compareGroups/inst/exdata/regicor.dat |only compareGroups-3.1/compareGroups/inst/exdata/regicor.sav |only compareGroups-3.1/compareGroups/man/compareGroups-package.Rd | 115 compareGroups-3.1/compareGroups/man/compareGroups.Rd | 4 compareGroups-3.1/compareGroups/man/createTable.Rd | 9 compareGroups-3.1/compareGroups/man/export2csv.Rd | 113 compareGroups-3.1/compareGroups/man/export2html.Rd | 4 compareGroups-3.1/compareGroups/man/export2latex.Rd | 2 compareGroups-3.1/compareGroups/man/export2md.Rd |only compareGroups-3.1/compareGroups/man/export2pdf.Rd | 2 compareGroups-3.1/compareGroups/man/export2word.Rd |only compareGroups-3.1/compareGroups/man/export2xls.Rd |only compareGroups-3.1/compareGroups/man/missingTable.Rd |only compareGroups-3.1/compareGroups/man/varinfo.Rd | 2 compareGroups-3.1/compareGroups/vignettes/figures/bivar/age.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/bivar/sex.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/bivar/tmain.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/age.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/sex.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/tmain.pdf |binary 46 files changed, 2065 insertions(+), 1949 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso', a method to model heterogeneity in paired comparison data. Subject-specific covariates are allowed to have an influence on the attractivity/strength of the objects. An L1 penalty on the pairwise differences between the object-specific parameters allows for both clustering of objects with regard to covariates and elimination of irrelevant covariates.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1 dated 2015-09-03 and 0.1-1 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Find Biomarkers in Two-Class Discrimination Problems
Description: Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.
Author: Ron Wehrens, Pietro Franceschi
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between BioMark versions 0.4.2 dated 2014-08-06 and 0.4.5 dated 2015-09-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- man/gen.data.Rd | 6 ++---- man/get.biom.Rd | 2 -- 5 files changed, 17 insertions(+), 16 deletions(-)
Title: Phylogenetic Methods for Multiple Gene Data
Description: Toolkit for the analysis of multiple gene data. Apex implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Author: Thibaut Jombart [aut, cre],
Zhian Namir Kamvar [aut],
Klaus Schliep [aut],
Eric Archer [aut],
Rebecca Harris [aut]
Maintainer: Thibaut Jombart <t.jombart@imperial.ac.uk>
Diff between apex versions 1.0.0 dated 2015-04-15 and 1.0.1 dated 2015-09-07
apex-1.0.0/apex/R/handling.R |only apex-1.0.0/apex/man/sub-multidna-ANY-ANY-ANY-method.Rd |only apex-1.0.1/apex/DESCRIPTION | 20 - apex-1.0.1/apex/MD5 | 71 ++-- apex-1.0.1/apex/NAMESPACE | 25 + apex-1.0.1/apex/R/accessors.R | 266 +++++++++-------- apex-1.0.1/apex/R/add.gaps.R |only apex-1.0.1/apex/R/concatenate.R |only apex-1.0.1/apex/R/doc.R | 5 apex-1.0.1/apex/R/exports.R | 132 +++++++- apex-1.0.1/apex/R/internal.R | 55 +++ apex-1.0.1/apex/R/multidna.class.R | 12 apex-1.0.1/apex/R/multidna.constructor.R | 39 -- apex-1.0.1/apex/R/multiphyDat.class.R | 25 - apex-1.0.1/apex/R/multiphyDat.constructor.R | 68 +--- apex-1.0.1/apex/R/readfiles.R | 15 apex-1.0.1/apex/R/rm.gaps.R |only apex-1.0.1/apex/R/show.R | 63 +++- apex-1.0.1/apex/R/subset.R |only apex-1.0.1/apex/README.md | 248 +++------------ apex-1.0.1/apex/man/accessors.Rd |only apex-1.0.1/apex/man/add.gaps.Rd |only apex-1.0.1/apex/man/apex.Rd | 2 apex-1.0.1/apex/man/concatenate.Rd | 24 + apex-1.0.1/apex/man/dist.multidna.Rd | 2 apex-1.0.1/apex/man/getTree.Rd | 2 apex-1.0.1/apex/man/initialize-multidna-method.Rd | 8 apex-1.0.1/apex/man/initialize-multiphyDat-method.Rd | 13 apex-1.0.1/apex/man/multidna.Rd | 2 apex-1.0.1/apex/man/multidna2alignment.Rd |only apex-1.0.1/apex/man/multidna2genind.Rd | 19 - apex-1.0.1/apex/man/multidna2multiphyDat.Rd |only apex-1.0.1/apex/man/multiphyDat.Rd | 14 apex-1.0.1/apex/man/plot-multidna-ANY-method.Rd | 2 apex-1.0.1/apex/man/readfiles.Rd | 12 apex-1.0.1/apex/man/rm.gaps.Rd |only apex-1.0.1/apex/man/show-multidna-method.Rd | 2 apex-1.0.1/apex/man/show-multiphyDat-method.Rd |only apex-1.0.1/apex/man/subset.multidna.Rd |only apex-1.0.1/apex/tests/testthat/test_export.R | 6 apex-1.0.1/apex/vignettes/apex.Rmd | 18 - apex-1.0.1/apex/vignettes/figs/concat-2.png |binary apex-1.0.1/apex/vignettes/figs/plotPmlPart-1.png |binary 43 files changed, 661 insertions(+), 509 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.6 dated 2014-08-25 and 0.6.1 dated 2015-09-07
shotGroups-0.6.1/shotGroups/DESCRIPTION | 25 +-- shotGroups-0.6.1/shotGroups/MD5 | 73 +++++------ shotGroups-0.6.1/shotGroups/NAMESPACE | 5 shotGroups-0.6.1/shotGroups/R/drawTarget.R | 4 shotGroups-0.6.1/shotGroups/R/getCEP.R | 10 - shotGroups-0.6.1/shotGroups/R/getConfEll.R | 10 - shotGroups-0.6.1/shotGroups/R/getHitProb.R | 10 - shotGroups-0.6.1/shotGroups/R/getXYmat.R | 12 - shotGroups-0.6.1/shotGroups/R/groupLocation.R | 25 +-- shotGroups-0.6.1/shotGroups/R/groupShape.R | 19 +- shotGroups-0.6.1/shotGroups/R/groupSpread.R | 38 +++-- shotGroups-0.6.1/shotGroups/R/hoyt.R | 25 ++- shotGroups-0.6.1/shotGroups/R/maxwell.R | 16 -- shotGroups-0.6.1/shotGroups/R/mvnEll.R | 10 - shotGroups-0.6.1/shotGroups/R/rayleigh.R | 10 - shotGroups-0.6.1/shotGroups/R/readData.R | 39 ++++- shotGroups-0.6.1/shotGroups/R/rice.R | 119 +++--------------- shotGroups-0.6.1/shotGroups/build/vignette.rds |binary shotGroups-0.6.1/shotGroups/data/DF300BLK.rda |binary shotGroups-0.6.1/shotGroups/data/DF300BLKhl.rda |binary shotGroups-0.6.1/shotGroups/data/DFcciHV.rda |binary shotGroups-0.6.1/shotGroups/data/DFcm.rda |binary shotGroups-0.6.1/shotGroups/data/DFinch.rda |binary shotGroups-0.6.1/shotGroups/data/DFlistCm.rda |binary shotGroups-0.6.1/shotGroups/data/DFsavage.rda |binary shotGroups-0.6.1/shotGroups/data/DFscar17.rda |binary shotGroups-0.6.1/shotGroups/data/DFtalon.rda |binary shotGroups-0.6.1/shotGroups/data/targets.rda |binary shotGroups-0.6.1/shotGroups/inst/ChangeLog | 13 + shotGroups-0.6.1/shotGroups/inst/doc/shotGroups.Rnw | 10 - shotGroups-0.6.1/shotGroups/inst/doc/shotGroups.pdf |binary shotGroups-0.6.1/shotGroups/man/getCEP.Rd | 4 shotGroups-0.6.1/shotGroups/man/readDataMisc.Rd | 4 shotGroups-0.6.1/shotGroups/man/rice.Rd | 11 - shotGroups-0.6.1/shotGroups/man/shotGroups-package.Rd | 8 - shotGroups-0.6.1/shotGroups/vignettes/lit.bib | 11 + shotGroups-0.6.1/shotGroups/vignettes/shotGroups.Rnw | 10 - shotGroups-0.6/shotGroups/R/targetDef.R |only 38 files changed, 239 insertions(+), 282 deletions(-)
Title: Three-Way Component Analysis
Description: Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models.
Author: Maria Antonietta Del Ferraro, Henk A.L. Kiers, Paolo Giordani
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between ThreeWay versions 1.1.2 dated 2014-04-09 and 1.1.3 dated 2015-09-07
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- NAMESPACE | 5 ++++- 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Interface to Colombos Compendia using the Exposed REST API
Description: Provides programmatic access to Colombos, a web based
interface for exploring and analyzing comprehensive organism-specific
cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego <paolo.sonego@fmach.it>
Maintainer: Paolo Sonego <paolo.sonego@fmach.it>
Diff between Rcolombos versions 1.5.2 dated 2015-03-04 and 1.5.3 dated 2015-09-07
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/Rcolombos.R | 24 ++++++++++++------------ R/utilities.R | 12 ++++++------ 5 files changed, 27 insertions(+), 26 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.1-1 dated 2015-07-02 and 1.1-2 dated 2015-09-07
streamMOA-1.1-1/streamMOA/R/AAA.R |only streamMOA-1.1-1/streamMOA/man/saveMOA.Rd |only streamMOA-1.1-2/streamMOA/DESCRIPTION | 8 ++++---- streamMOA-1.1-2/streamMOA/MD5 | 16 +++++++--------- streamMOA-1.1-2/streamMOA/NAMESPACE | 4 +--- streamMOA-1.1-2/streamMOA/inst/NEWS | 3 +++ streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.R | 6 +++--- streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.Rnw | 6 +++--- streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.pdf |binary streamMOA-1.1-2/streamMOA/vignettes/streamMOA.Rnw | 6 +++--- 10 files changed, 24 insertions(+), 25 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-5 dated 2015-07-02 and 1.2-0 dated 2015-09-07
stream-1.1-5/stream/R/dbscan.R |only stream-1.2-0/stream/DESCRIPTION | 17 stream-1.2-0/stream/MD5 | 69 +- stream-1.2-0/stream/NAMESPACE | 25 stream-1.2-0/stream/R/DSC.R | 1 stream-1.2-0/stream/R/DSC_DBSCAN.R | 5 stream-1.2-0/stream/R/DSC_DBSTREAM.R | 162 ++-- stream-1.2-0/stream/R/DSC_DStream.R | 49 + stream-1.2-0/stream/R/DSD_Gaussians.R | 2 stream-1.2-0/stream/R/DSD_ReadCSV.R | 184 ++++- stream-1.2-0/stream/R/animation.R | 117 +-- stream-1.2-0/stream/R/description.R |only stream-1.2-0/stream/R/evaluate.R | 173 ++--- stream-1.2-0/stream/R/recluster.R | 10 stream-1.2-0/stream/R/save.R |only stream-1.2-0/stream/R/write_stream.R | 28 stream-1.2-0/stream/build/vignette.rds |binary stream-1.2-0/stream/inst/NEWS | 20 stream-1.2-0/stream/inst/doc/stream.R | 188 ++--- stream-1.2-0/stream/inst/doc/stream.Rnw | 690 +++++++++++---------- stream-1.2-0/stream/inst/doc/stream.pdf |binary stream-1.2-0/stream/inst/doc/stream_extension.R |only stream-1.2-0/stream/inst/doc/stream_extension.Rnw |only stream-1.2-0/stream/inst/doc/stream_extension.pdf |only stream-1.2-0/stream/inst/tests/test-DSC.R |only stream-1.2-0/stream/man/DSC.Rd | 8 stream-1.2-0/stream/man/DSC_DBSTREAM.Rd | 40 - stream-1.2-0/stream/man/DSD.Rd | 4 stream-1.2-0/stream/man/DSD_ReadCSV.Rd | 27 stream-1.2-0/stream/man/DSD_ReadDB.Rd | 4 stream-1.2-0/stream/man/animation.Rd | 41 - stream-1.2-0/stream/man/evaluate.Rd | 29 stream-1.2-0/stream/man/recluster.Rd | 4 stream-1.2-0/stream/man/save.Rd |only stream-1.2-0/stream/man/write_stream.Rd | 11 stream-1.2-0/stream/src/DBSTREAM.cpp | 149 +++- stream-1.2-0/stream/src/DStream.cpp | 27 stream-1.2-0/stream/vignettes/stream.Rnw | 690 +++++++++++---------- stream-1.2-0/stream/vignettes/stream.bib | 83 ++ stream-1.2-0/stream/vignettes/stream_extension.Rnw |only 40 files changed, 1673 insertions(+), 1184 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.7.0 dated 2015-07-14 and 0.8.0 dated 2015-09-07
DESCRIPTION | 6 - MD5 | 26 +++--- NEWS | 10 ++ R/availableCores.R | 2 R/plan.R | 40 ++++++++-- R/zzz.R |only build/vignette.rds |binary demo/mandelbrot.R | 51 ++++++++----- inst/doc/future.html | 5 - inst/doc/future.md.rsp | 4 - man/lazy.Rd | 179 +++++++++++++++++++++++++++-------------------- man/plan.Rd | 6 + tests/globalsOf,tweaks.R |only tests/plan.R | 43 ++++++++++- vignettes/future.md.rsp | 4 - 15 files changed, 253 insertions(+), 123 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.1.6 dated 2015-04-10 and 0.2.0-3 dated 2015-09-07
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Title: Bayesian Survival Model with Lasso Shrinkage Using Generalized
Weibull Regression
Description: Bayesian survival model using Weibull regression on both scale and shape parameters. Dependence of shape parameter on covariates permits deviation from proportional-hazard assumption, leading to dynamic - i.e. non-constant with time - hazard ratios between subjects. Bayesian Lasso shrinkage in the form of two Laplace priors - one for scale and one for shape coefficients - allows for many covariates to be included. Cross-validation helper functions can be used to tune the shrinkage parameters. Monte Carlo Markov Chain (MCMC) sampling using a Gibbs wrapper around Radford Neal's univariate slice sampler (R package MfUSampler) is used for coefficient estimation.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between BSGW versions 0.9 dated 2014-10-11 and 0.9.1 dated 2015-09-07
BSGW-0.9.1/BSGW/ChangeLog |only BSGW-0.9.1/BSGW/DESCRIPTION | 16 +-- BSGW-0.9.1/BSGW/MD5 | 22 ++-- BSGW-0.9.1/BSGW/NAMESPACE | 12 ++ BSGW-0.9.1/BSGW/R/BSGW.R | 184 +++++++++++++++++++++++++---------- BSGW-0.9.1/BSGW/R/Sample.R | 41 +++---- BSGW-0.9.1/BSGW/R/utils.R | 2 BSGW-0.9.1/BSGW/man/bsgw.Rd | 6 - BSGW-0.9.1/BSGW/man/crossval_bsgw.Rd | 10 + BSGW-0.9.1/BSGW/man/plot_bsgw.Rd | 3 BSGW-0.9.1/BSGW/man/predict_bsgw.Rd | 6 - BSGW-0.9.1/BSGW/man/summary_bsgw.Rd | 3 BSGW-0.9/BSGW/R/SliceSampler.R |only 13 files changed, 197 insertions(+), 108 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include: hiding an
element, disabling an input, resetting an input back to its original value,
delaying code execution by a few seconds, and many more useful functions.
'shinyjs' can also be used to easily run your own custom JavaScript functions
from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.1.0 dated 2015-08-13 and 0.2.0 dated 2015-09-06
shinyjs-0.1.0/shinyjs/R/onclick.R |only shinyjs-0.1.0/shinyjs/man/onclick.Rd |only shinyjs-0.1.0/shinyjs/man/resettable.Rd |only shinyjs-0.2.0/shinyjs/DESCRIPTION | 19 shinyjs-0.2.0/shinyjs/MD5 | 49 shinyjs-0.2.0/shinyjs/NAMESPACE | 3 shinyjs-0.2.0/shinyjs/NEWS.md | 42 shinyjs-0.2.0/shinyjs/R/delay.R |only shinyjs-0.2.0/shinyjs/R/jsFunc-aaa.R | 3 shinyjs-0.2.0/shinyjs/R/jsFunc-visibilityFuncs.R | 10 shinyjs-0.2.0/shinyjs/R/onevent.R |only shinyjs-0.2.0/shinyjs/R/reset.R | 23 shinyjs-0.2.0/shinyjs/R/shinyjs.R | 9 shinyjs-0.2.0/shinyjs/R/useShinyjs.R | 2 shinyjs-0.2.0/shinyjs/README.md | 167 ++- shinyjs-0.2.0/shinyjs/inst/doc/overview.Rmd | 140 ++ shinyjs-0.2.0/shinyjs/inst/doc/overview.html | 108 +- shinyjs-0.2.0/shinyjs/inst/examples/demo/helpers.R | 24 shinyjs-0.2.0/shinyjs/inst/examples/demo/ui.R | 4 shinyjs-0.2.0/shinyjs/inst/examples/sandbox/helpers.R | 3 shinyjs-0.2.0/shinyjs/inst/examples/sandbox/ui.R | 4 shinyjs-0.2.0/shinyjs/inst/srcjs/shinyjs-default-funcs.js | 734 ++++++++------ shinyjs-0.2.0/shinyjs/man/delay.Rd |only shinyjs-0.2.0/shinyjs/man/js.Rd | 2 shinyjs-0.2.0/shinyjs/man/onevent.Rd |only shinyjs-0.2.0/shinyjs/man/reset.Rd | 5 shinyjs-0.2.0/shinyjs/man/shinyjs.Rd | 9 shinyjs-0.2.0/shinyjs/man/visibilityFuncs.Rd | 12 shinyjs-0.2.0/shinyjs/vignettes/overview.Rmd | 140 ++ 29 files changed, 995 insertions(+), 517 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.2.0 dated 2015-07-12 and 0.3.0 dated 2015-09-06
DESCRIPTION | 13 - MD5 | 36 ++-- NEWS.md | 29 +++ R/ggMarginal.R | 283 ++++++++++++++++++++++++-------------- R/plotCount.R | 10 - R/removeGrid.R | 12 - R/rotateTextX.R | 10 - README.md | 3 inst/doc/overview.R | 4 inst/doc/overview.Rmd | 4 inst/doc/overview.html | 112 ++++++++------- inst/examples/ggMarginal/server.R | 2 inst/examples/ggMarginal/ui.R | 4 man/ggMarginal.Rd | 72 +++++---- man/plotCount.Rd | 10 - man/print.ggExtraPlot.Rd | 1 man/removeGrid.Rd | 12 - man/rotateTextX.Rd | 10 - vignettes/overview.Rmd | 4 19 files changed, 380 insertions(+), 251 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 1.1.1 dated 2015-05-12 and 1.1.2 dated 2015-09-06
fclust-1.1.1/fclust/R/fclust.R |only fclust-1.1.2/fclust/DESCRIPTION | 10 +++++----- fclust-1.1.2/fclust/MD5 | 8 ++++---- fclust-1.1.2/fclust/NAMESPACE | 3 +++ fclust-1.1.2/fclust/R/Fclust.R |only fclust-1.1.2/fclust/inst/CITATION | 9 +++++---- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Maximum Likelihood and Bayesian Estimation of Univariate
Probability Distributions
Description: Estimate parameters of univariate probability distributions
with maximum likelihood and Bayesian methods.
Author: Francois Aucoin
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between FAmle versions 1.3.3 dated 2015-03-12 and 1.3.4 dated 2015-09-06
DESCRIPTION | 9 +-- MD5 | 12 ++-- NAMESPACE | 5 + build/vignette.rds |binary inst/doc/FAmle.pdf |binary man/metropolis.Rd | 134 +++++++++++++++++++++++++++++++++++++++++--------- man/station01AJ010.Rd | 2 7 files changed, 128 insertions(+), 34 deletions(-)
Title: Distributions that are Sometimes Used in Hydrology
Description: Probability distributions that are sometimes useful in hydrology.
Author: Francois Aucoin
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between FAdist versions 2.1 dated 2015-03-12 and 2.2 dated 2015-09-06
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 9 insertions(+), 6 deletions(-)
More information about ExplainPrediction at CRAN
Permanent link
Title: Solid Earth Tide Computation
Description: Predicted solid earth tide displacements in the meridional,
zonal and vertical directions. Based on "Solid" from Dennis Milbert,
modified from "dehanttideinelMJD" by V. Dehant, S. Mathews, J. Gipson,
and C. Bruyninx.
Author: Jose Gama [aut, cre],
Dennis Milbert [aut, cph]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Diff between solidearthtide versions 1.0.0 dated 2015-08-08 and 1.0.2 dated 2015-09-06
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/solidearthtide.R | 2 +- man/Earthtide.Rd | 4 ++-- src/solid.f | 9 ++++----- 5 files changed, 16 insertions(+), 17 deletions(-)
More information about solidearthtide at CRAN
Permanent link
Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <http://landsat.gsfc.nasa.gov/?p=9513>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal pattern including year(s) of inflection, magnitude of change, pre- and post-inflection rates of growth or recovery. In addition, it contains routines for converting a flat map of disturbance agents to time-series disturbance maps and a graphical routine displaying the fitted trajectory of Landsat imagery.
Author: Mary C. Meyer, Xiyue Liao, Elizabeth Freeman, Gretchen G. Moisen
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeSelectForest versions 1.0 dated 2015-05-31 and 1.1 dated 2015-09-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ man/ShapeSelectForest-package.Rd | 4 ++-- man/shape.Rd | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of 'RJSONIO', but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with a web API. The implementation is
based on the mapping described in the vignette (Ooms, 2014). In addition to
converting JSON data from/to R objects, 'jsonlite' contains functions to
stream, validate, and prettify JSON data. The unit tests included with the
package verify that all edge cases are encoded and decoded consistently for
use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between jsonlite versions 0.9.16 dated 2015-04-10 and 0.9.17 dated 2015-09-06
jsonlite-0.9.16/jsonlite/R/parseTimestamp.R |only jsonlite-0.9.17/jsonlite/DESCRIPTION | 21 - jsonlite-0.9.17/jsonlite/MD5 | 77 +++--- jsonlite-0.9.17/jsonlite/NAMESPACE | 3 jsonlite-0.9.17/jsonlite/NEWS | 7 jsonlite-0.9.17/jsonlite/R/asJSON.array.R | 5 jsonlite-0.9.17/jsonlite/R/asJSON.character.R | 3 jsonlite-0.9.17/jsonlite/R/asJSON.data.frame.R | 13 - jsonlite-0.9.17/jsonlite/R/fromJSON.R | 4 jsonlite-0.9.17/jsonlite/R/print.R | 2 jsonlite-0.9.17/jsonlite/R/push_parser.R | 13 - jsonlite-0.9.17/jsonlite/R/simplifyDataFrame.R | 9 jsonlite-0.9.17/jsonlite/R/stream.R | 85 ++++--- jsonlite-0.9.17/jsonlite/R/unbox.R | 2 jsonlite-0.9.17/jsonlite/build/vignette.rds |binary jsonlite-0.9.17/jsonlite/inst/doc/json-aaquickstart.R | 2 jsonlite-0.9.17/jsonlite/inst/doc/json-aaquickstart.Rmd | 2 jsonlite-0.9.17/jsonlite/inst/doc/json-aaquickstart.html | 10 jsonlite-0.9.17/jsonlite/inst/doc/json-apis.Rmd | 164 +++++++------- jsonlite-0.9.17/jsonlite/inst/doc/json-apis.html | 166 +++++++-------- jsonlite-0.9.17/jsonlite/inst/doc/json-mapping.pdf |binary jsonlite-0.9.17/jsonlite/inst/doc/json-opencpu.pdf |binary jsonlite-0.9.17/jsonlite/inst/doc/json-paging.Rmd | 43 ++- jsonlite-0.9.17/jsonlite/inst/doc/json-paging.html | 45 ++-- jsonlite-0.9.17/jsonlite/man/flatten.Rd | 2 jsonlite-0.9.17/jsonlite/man/fromJSON.Rd | 3 jsonlite-0.9.17/jsonlite/man/prettify.Rd | 2 jsonlite-0.9.17/jsonlite/man/rbind.pages.Rd | 2 jsonlite-0.9.17/jsonlite/man/serializeJSON.Rd | 2 jsonlite-0.9.17/jsonlite/man/stream_in.Rd | 15 + jsonlite-0.9.17/jsonlite/man/unbox.Rd | 2 jsonlite-0.9.17/jsonlite/man/validate.Rd | 2 jsonlite-0.9.17/jsonlite/src/parse.c | 4 jsonlite-0.9.17/jsonlite/src/push_parser.c | 35 ++- jsonlite-0.9.17/jsonlite/vignettes/json-aaquickstart.Rmd | 2 jsonlite-0.9.17/jsonlite/vignettes/json-apis.Rmd | 164 +++++++------- jsonlite-0.9.17/jsonlite/vignettes/json-apis.Rmd.orig | 13 - jsonlite-0.9.17/jsonlite/vignettes/json-paging.Rmd | 43 ++- jsonlite-0.9.17/jsonlite/vignettes/json-paging.Rmd.orig | 8 jsonlite-0.9.17/jsonlite/vignettes/precompile.R | 3 40 files changed, 554 insertions(+), 424 deletions(-)
Title: Comparative and Population Genetic Analyses
Description: Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data. Wright-Fisher, phylogenetic tree, and statistical distribution Shiny interactive simulations for use in teaching.
Author: Heath Blackmon and Richard H. Adams
Maintainer: Heath Blackmon <coleoguy@gmail.com>
Diff between evobiR versions 1.0 dated 2013-10-21 and 1.1 dated 2015-09-06
evobiR-1.0/evobiR/R/AnalyzeAssembly.R |only evobiR-1.0/evobiR/R/CoalSim.R |only evobiR-1.0/evobiR/R/DriftSim.R |only evobiR-1.0/evobiR/R/GenomeSym.R |only evobiR-1.0/evobiR/R/GetTaxonomy.R |only evobiR-1.0/evobiR/R/HetLevels.R |only evobiR-1.0/evobiR/R/HighLevelTree.R |only evobiR-1.0/evobiR/R/MaxTips.R |only evobiR-1.0/evobiR/R/SelSim.R |only evobiR-1.0/evobiR/data/data.taxonomy.rda |only evobiR-1.0/evobiR/data/genome.rda |only evobiR-1.0/evobiR/data/mite.data.rda |only evobiR-1.0/evobiR/data/mite.tree.rda |only evobiR-1.0/evobiR/data/species.tree.rda |only evobiR-1.0/evobiR/data/taxa.table.rda |only evobiR-1.0/evobiR/data/tree.taxonomy.rda |only evobiR-1.0/evobiR/inst/assembly.fasta |only evobiR-1.0/evobiR/man/2.fasta.Rd |only evobiR-1.0/evobiR/man/3.fasta.Rd |only evobiR-1.0/evobiR/man/AnalyzeAssembly.Rd |only evobiR-1.0/evobiR/man/CoalSim.Rd |only evobiR-1.0/evobiR/man/DriftSim.Rd |only evobiR-1.0/evobiR/man/GenomeSym.Rd |only evobiR-1.0/evobiR/man/GetTaxonomy.Rd |only evobiR-1.0/evobiR/man/HetLevels.Rd |only evobiR-1.0/evobiR/man/HighLevelTree.Rd |only evobiR-1.0/evobiR/man/Max.Tips.Rd |only evobiR-1.0/evobiR/man/assembly.fasta.Rd |only evobiR-1.0/evobiR/man/data.taxonomy.Rd |only evobiR-1.0/evobiR/man/genome.Rd |only evobiR-1.0/evobiR/man/mcmc3.Rd |only evobiR-1.0/evobiR/man/mite.data.Rd |only evobiR-1.0/evobiR/man/mite.tree.Rd |only evobiR-1.0/evobiR/man/species.tree.Rd |only evobiR-1.0/evobiR/man/taxa.table.Rd |only evobiR-1.0/evobiR/man/tree.taxonomy.Rd |only evobiR-1.1/evobiR/DESCRIPTION | 16 - evobiR-1.1/evobiR/MD5 | 92 ++++------ evobiR-1.1/evobiR/NAMESPACE | 27 ++- evobiR-1.1/evobiR/R/AICc.R |only evobiR-1.1/evobiR/R/AncCond.R |only evobiR-1.1/evobiR/R/CalcD.R | 270 ++++++++++++------------------- evobiR-1.1/evobiR/R/Even.R |only evobiR-1.1/evobiR/R/Mode.R |only evobiR-1.1/evobiR/R/ReorderData.R |only evobiR-1.1/evobiR/R/ResSel.R | 11 - evobiR-1.1/evobiR/R/SlidingWindow.R |only evobiR-1.1/evobiR/R/SuperMatrix.R |only evobiR-1.1/evobiR/R/ViewEvo.R |only evobiR-1.1/evobiR/R/WinCalcD.R |only evobiR-1.1/evobiR/data/mite.trait.rda |only evobiR-1.1/evobiR/data/trees.mite.rda |only evobiR-1.1/evobiR/inst/1.fasta | 10 - evobiR-1.1/evobiR/inst/2.fasta | 11 - evobiR-1.1/evobiR/inst/bd.model |only evobiR-1.1/evobiR/inst/dist.model |only evobiR-1.1/evobiR/inst/wf.model |only evobiR-1.1/evobiR/man/1.fasta.Rd | 6 evobiR-1.1/evobiR/man/AICc.Rd |only evobiR-1.1/evobiR/man/AncCond.Rd |only evobiR-1.1/evobiR/man/CalcD.Rd | 19 -- evobiR-1.1/evobiR/man/Even.Rd |only evobiR-1.1/evobiR/man/FuzzyMatch.Rd | 4 evobiR-1.1/evobiR/man/Mode.Rd |only evobiR-1.1/evobiR/man/PPSDiscrete.Rd | 4 evobiR-1.1/evobiR/man/ReorderData.Rd |only evobiR-1.1/evobiR/man/ResSel.Rd | 3 evobiR-1.1/evobiR/man/SampleTrees.Rd | 2 evobiR-1.1/evobiR/man/SlidingWindow.Rd |only evobiR-1.1/evobiR/man/SuperMatrix.Rd |only evobiR-1.1/evobiR/man/ViewEvo.Rd |only evobiR-1.1/evobiR/man/WinCalcD.Rd |only evobiR-1.1/evobiR/man/evobiR-package.Rd | 5 evobiR-1.1/evobiR/man/mcmc2.Rd | 3 evobiR-1.1/evobiR/man/mite.trait.Rd |only evobiR-1.1/evobiR/man/trees.mite.Rd |only 76 files changed, 218 insertions(+), 265 deletions(-)
Title: Identification of Cardinal Dates in Ecological Time Series
Description: Identification of cardinal dates
(begin, time of maximum, end of mass developments)
in ecological time series using fitted Weibull functions.
Author: Susanne Rolinski [aut], René Sachse [aut], Thomas Petzoldt [aut, cre]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between cardidates versions 0.4.6 dated 2015-03-12 and 0.4.7 dated 2015-09-06
DESCRIPTION | 12 +- MD5 | 14 +- NAMESPACE | 2 build/vignette.rds |binary data/carditest.txt.gz |binary inst/doc/vignette.R | 228 +++++++++++++++++++++++----------------------- inst/doc/vignette.pdf |binary man/cardidates-package.Rd | 4 8 files changed, 132 insertions(+), 128 deletions(-)
Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between sweidnumbr versions 0.6.1 dated 2015-07-14 and 0.6.5 dated 2015-09-06
DESCRIPTION | 8 ++++---- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 2 -- R/oin.R | 4 ++-- R/oin_methods.R | 8 -------- R/pin.R | 6 +++--- R/pin_methods.R | 9 --------- build/vignette.rds |binary data/fake_pins.rda |binary man/as.oin.Rd | 2 +- man/as.pin.Rd | 2 +- tests/testthat/test-as.oin.R | 13 +++++++++++++ tests/testthat/test-as.pin.R | 11 +++++++++++ tests/testthat/test-create_S3_methods.R |only tests/testthat/test-oin_s3_methods.R | 2 ++ tests/testthat/test-pin_s3_methods.R | 3 +++ 16 files changed, 55 insertions(+), 44 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.0-6 dated 2015-08-22 and 1.0-7 dated 2015-09-06
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/AAA.R | 3 ++- R/Class-CRSx.R | 30 ++++++++++++++++++++---------- R/wrappers.R | 8 ++++++++ inst/ChangeLog | 18 ++++++++++++++++++ inst/SVN_VERSION | 2 +- inst/doc/OGR_shape_encoding.pdf |binary man/CRS-class.Rd | 4 ++-- 10 files changed, 82 insertions(+), 27 deletions(-)
Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between rasterVis versions 0.35 dated 2015-02-24 and 0.37 dated 2015-09-06
ChangeLog | 163 +++++++++++++++++++++++++++++- DESCRIPTION | 15 +- MD5 | 28 ++--- NAMESPACE | 95 ++++++++++------- R/density.R | 40 ++++--- R/gplot.R | 29 ++--- R/grid.R | 29 +++++ R/hovmoller.R | 2 R/interactRaster.R | 5 R/levelplot.R | 251 +++++++++++++++++++++++++++++------------------ R/plot3d.R | 105 +++++++++---------- R/streamplot.R | 2 R/xyplot.R | 2 man/hovmoller-methods.Rd | 4 man/levelplot-methods.Rd | 163 ++++++++++++++++-------------- 15 files changed, 619 insertions(+), 314 deletions(-)
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 2.8 dated 2015-05-18 and 2.9 dated 2015-09-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++++--- NAMESPACE | 1 + NEWS | 4 ++++ R/searchzeros.R |only man/searchzeros.Rd |only tests/xcutlip1p2.R |only tests/xcutlip1p2.Rout |only tests/xcutlip1p2.Rout.save |only tests/xsearchzeros.R |only tests/xsearchzeros.Rout |only tests/xsearchzeros.Rout.save |only 12 files changed, 20 insertions(+), 7 deletions(-)
Title: Distance Weighted Discrimination (DWD) and Kernel Methods
Description: A very efficient implementation that solves the generalized DWD under any kernel regularization. The package also handles some other general loss functions including LUM.
Author: Boxiang Wang <boxiang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between kerndwd versions 1.0.1 dated 2015-08-27 and 1.1.1 dated 2015-09-06
kerndwd-1.0.1/kerndwd/data/Haberman.rda |only kerndwd-1.0.1/kerndwd/man/Haberman.Rd |only kerndwd-1.1.1/kerndwd/DESCRIPTION | 10 - kerndwd-1.1.1/kerndwd/MD5 | 42 ++-- kerndwd-1.1.1/kerndwd/NAMESPACE | 3 kerndwd-1.1.1/kerndwd/R/cv.kerndwd.R | 64 +++--- kerndwd-1.1.1/kerndwd/R/kerndwd.R | 267 +++++++++++++++++++++++++-- kerndwd-1.1.1/kerndwd/R/plot.cv.kerndwd.R | 6 kerndwd-1.1.1/kerndwd/R/utilities.R | 10 - kerndwd-1.1.1/kerndwd/data/BUPA.rda |only kerndwd-1.1.1/kerndwd/man/BUPA.Rd |only kerndwd-1.1.1/kerndwd/man/cv.kerndwd.Rd | 48 ++-- kerndwd-1.1.1/kerndwd/man/dots.Rd | 44 ++-- kerndwd-1.1.1/kerndwd/man/kerndwd-package.Rd | 8 kerndwd-1.1.1/kerndwd/man/kerndwd.Rd | 74 +++++-- kerndwd-1.1.1/kerndwd/man/plot.cv.kerndwd.Rd | 14 - kerndwd-1.1.1/kerndwd/man/plot.kerndwd.Rd | 10 - kerndwd-1.1.1/kerndwd/man/predict.kerndwd.Rd | 13 - kerndwd-1.1.1/kerndwd/src/kdwd.f90 | 53 ++--- kerndwd-1.1.1/kerndwd/src/klum.f90 |only kerndwd-1.1.1/kerndwd/src/ldwd.f90 | 16 - kerndwd-1.1.1/kerndwd/src/llum.f90 |only kerndwd-1.1.1/kerndwd/src/wkdwd.f90 | 46 ++-- kerndwd-1.1.1/kerndwd/src/wklum.f90 |only kerndwd-1.1.1/kerndwd/src/wldwd.f90 | 20 +- kerndwd-1.1.1/kerndwd/src/wllum.f90 |only 26 files changed, 512 insertions(+), 236 deletions(-)
Title: A Package for Graphical Modelling in R
Diff between gRbase versions 1.7-1 dated 2015-08-21 and 1.7-2 dated 2015-09-06
Description: The gRbase package provides general features
which are used by other graphical modelling packages, in particular
by the packages gRain, gRim and gRc.
gRbase contains several datasets relevant for use in connection with
graphical models. Almost all datasets used in the book Graphical
Models with R (2012) are contained in gRbase.
gRbase implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph
algorithms are:
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junctionTree.
gRbase facilitates array operations,
gRbase implements functions for testing for conditional independence.
gRbase illustrates how hierarchical log-linear models (hllm) may be
implemented and describes concept of gmData (graphical meta
data). These features, however, are not maintained anymore and
remains in gRbase only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The gRbase Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE Proper functionality of gRbase requires that the packages graph,
Rgraphviz and RBGL are installed from bioconductor; for
installation instructions please refer to the webpage given below.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 11 +++
DESCRIPTION | 6 +-
MD5 | 32 +++++------
R/RcppExports.R | 4 +
R/graph-coerce.R | 45 +++++++++++++++
inst/doc/gRbase-arrayops.pdf |binary
inst/doc/gRbase-graphs.pdf |binary
inst/include/gRbase_RcppExports.h | 19 ++++++
man/GraphAlgo-coerce.Rd | 17 ++++-
man/GraphAlgo-edgeList.Rd | 6 +-
man/GraphAlgo-mcs.Rd | 2
man/GraphAlgo-operations1.Rd | 15 ++---
man/gRbase-utilities.Rd | 1
src/RcppExports.cpp | 34 +++++++++++
src/_m_isadjMAT.cpp | 4 -
src/_u_utility.cpp | 94 +++++++++++++++++++++++++++++++-
src/c-combnPrimC.c | 110 +++++++++++++++++++-------------------
17 files changed, 303 insertions(+), 97 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: A high performance package estimating Cox Model when an even have more than one causes, which also supports random and fixed effects, tied events, and time-varying variables.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between CoxPlus versions 1.0.2 dated 2015-09-05 and 1.1.0 dated 2015-09-06
CoxPlus-1.0.2/CoxPlus/src/ldl.h |only CoxPlus-1.1.0/CoxPlus/DESCRIPTION | 10 ++-- CoxPlus-1.1.0/CoxPlus/MD5 | 9 +--- CoxPlus-1.1.0/CoxPlus/R/fastCox.R | 28 +++++++++---- CoxPlus-1.1.0/CoxPlus/man/CoxPlus.Rd | 9 +--- CoxPlus-1.1.0/CoxPlus/src/coxReg.cpp | 73 ++++------------------------------- 6 files changed, 41 insertions(+), 88 deletions(-)
Title: Read CDISC Data Files
Description: CDISC Dataset-XML and Define-XML are used as file format for clinical trial data and metadata respectively. This functions supports reading both Dataset-XML and Define-XML. The Clinical Data Interchange Standards Consortium (CDISC, http://www.cdisc.org/) is a standards developing organization (SDO) to develop global standards and innovations regarding medical research and healthcare.
Author: Ippei Akiya
Maintainer: Ippei Akiya <ippei.aki@datadriven.jp>
Diff between R4CDISC versions 0.3 dated 2014-12-29 and 0.4 dated 2015-09-05
R4CDISC-0.3/R4CDISC/R/getVarName.R |only R4CDISC-0.3/R4CDISC/inst/tests |only R4CDISC-0.4/R4CDISC/DESCRIPTION | 13 +- R4CDISC-0.4/R4CDISC/MD5 | 23 ++-- R4CDISC-0.4/R4CDISC/NAMESPACE | 2 R4CDISC-0.4/R4CDISC/R/getCT.R | 72 +----------- R4CDISC-0.4/R4CDISC/R/getCTasDataFrame.R |only R4CDISC-0.4/R4CDISC/R/getCodeListItem.R | 170 +++++++++++++++--------------- R4CDISC-0.4/R4CDISC/R/getEnumeratedItem.R | 155 ++++++++++++--------------- R4CDISC-0.4/R4CDISC/R/getSDS.R | 16 +- R4CDISC-0.4/R4CDISC/man/getCT.Rd | 3 R4CDISC-0.4/R4CDISC/tests |only 12 files changed, 191 insertions(+), 263 deletions(-)
Title: Qualitative Validation Methods
Description: Qualitative methods for the validation of dynamic models.
It contains (i) an orthogonal set of deviance measures for absolute,
relative and ordinal scale and (ii) approaches accounting for time
shifts. The first approach transforms time to take time delays and speed
differences into account. The second divides the time series into
interval units according to their main features and finds the longest
common subsequence (LCS) using a dynamic programming algorithm.
Author: K. Gerald van den Boogaart [aut, ths],
Stefanie Rost [aut],
Thomas Petzoldt [aut, ths, cre]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between qualV versions 0.3-1 dated 2015-03-12 and 0.3-2 dated 2015-09-05
DESCRIPTION | 20 +++++++++++++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- data/phyto.rda |binary inst/NEWS | 13 ++++--------- man/LCS.Rd | 7 ++++--- man/qualV.Rd | 6 +++--- man/quantV.Rd | 10 +++++----- man/qvalLCS.Rd | 4 ++-- man/timeTransME.Rd | 14 +++++++------- 10 files changed, 50 insertions(+), 44 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between OUwie versions 1.45 dated 2015-03-09 and 1.46 dated 2015-09-05
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + R/OUwie.R | 1 - R/OUwie.boot.R | 6 +++++- R/OUwie.slice.R | 3 +-- R/varcov.ou.R | 1 - man/OUwie.slice.Rd | 2 ++ 8 files changed, 22 insertions(+), 17 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.3.1 dated 2015-09-04 and 1.3.2 dated 2015-09-05
DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS | 7 ++++++- R/Diversity.R | 2 +- R/Dqz.R | 2 +- R/Hqz.R | 27 +++++++++++++++++++-------- R/HqzBeta.R | 2 +- R/Hurlbert.R | 2 +- R/HurlbertD.R | 2 +- R/PhyloBetaEntropy.R | 2 +- R/PhyloDiversity.R | 2 +- R/PhyloEntropy.R | 2 +- R/Preprocess.Tree.R | 2 +- R/Rao.R | 24 +++++++++++++++++++----- R/Richness.R | 2 +- R/Shannon.R | 20 ++++++++++++++++---- R/ShannonBeta.R | 2 +- R/Simpson.R | 19 ++++++++++++++++--- R/SimpsonBeta.R | 2 +- R/Tsallis.R | 19 +++++++++++++++---- R/TsallisBeta.R | 2 +- R/rCommunity.R | 2 +- inst/doc/entropart.pdf |binary man/entropart-package.Rd | 4 ++-- 24 files changed, 134 insertions(+), 68 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: A high performance package estimating Proportional Hazards Model when an even can have more than one causes, including support for random and fixed effects, tied events, and time-varying variables.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between CoxPlus versions 1.0.1 dated 2015-09-05 and 1.0.2 dated 2015-09-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Makevars | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Genomic Region Processing using Tools Such as Bedtools, Bedops
and Tabix
Description: Genomic region processing using tools such as bedtools, bedops and tabix.
Author: Daryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros
Maintainer: Paul Boutros <Paul.Boutros@oicr.on.ca>
Diff between bedr versions 1.0.0 dated 2015-09-04 and 1.0.1 dated 2015-09-05
DESCRIPTION | 8 ++--- MD5 | 8 ++--- NEWS | 7 +++- R/bedr.sort.region.R | 12 ++++++- inst/doc/Using-bedr.html | 74 +++++++++++++++++++++++------------------------ 5 files changed, 62 insertions(+), 47 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.7 dated 2015-08-24 and 0.8 dated 2015-09-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ configure | 5 ++--- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.5 dated 2015-08-25 and 0.10.6 dated 2015-09-05
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine Mullen,
Brian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by Rainer Storn)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.3 dated 2015-08-23 and 0.1.4 dated 2015-09-05
ChangeLog | 13 + DESCRIPTION | 8 MD5 | 26 +- R/DEoptim.R | 2 R/RcppExports.R |only build/vignette.rds |binary inst/doc/RcppDE.Rnw | 7 inst/doc/RcppDE.pdf |binary src/Makevars | 2 src/RcppExports.cpp |only src/deoptim.cpp | 148 +++++++--------- src/devol.cpp | 450 +++++++++++++++++++++++++-------------------------- src/evaluate.h | 172 +++++++++---------- src/permute.cpp | 18 -- vignettes/RcppDE.Rnw | 7 15 files changed, 427 insertions(+), 426 deletions(-)
Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.1.0 dated 2015-07-27 and 1.2.0 dated 2015-09-05
DESCRIPTION | 10 +- MD5 | 28 ++--- NAMESPACE | 2 NEWS | 18 +++ R/WiSEConfidenceRegion.R | 19 ++- R/WiSEHypothesisTest.R | 17 ++- R/smoothTimeSeries.R | 25 +++-- build/vignette.rds |binary inst/doc/WiSEBoot_Examples_Vignette.R | 154 +++++++++++++++---------------- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 9 + inst/doc/WiSEBoot_Examples_Vignette.pdf |binary man/WiSEConfidenceRegion.Rd | 5 - man/WiSEHypothesisTest.Rd | 5 - man/smoothTimeSeries.Rd | 5 - vignettes/WiSEBoot_Examples_Vignette.Rnw | 9 + 15 files changed, 177 insertions(+), 129 deletions(-)
Title: Data Analysis Using Rough Set and Fuzzy Rough Set Theories
Description: Implementations of algorithms for data analysis
based on the rough set theory (RST) and the fuzzy rough set theory (FRST). We
not only provide implementations for the basic concepts of RST and FRST but also
popular algorithms that derive from those theories. The methods included in the
package can be divided into several categories based on their functionality:
discretization, feature selection, instance selection, rule induction and classification
based on nearest neighbors. RST was introduced by Zdzisław Pawlak in 1982
as a sophisticated mathematical tool to
model and process imprecise or incomplete information. By using
the indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST. The
FRST combines concepts of vagueness and indiscernibility that are expressed
with fuzzy sets (as proposed by Zadeh, in 1965) and RST.
Author: Lala Septem Riza [aut],
Andrzej Janusz [aut],
Dominik Ślęzak [ctb],
Chris Cornelis [ctb],
Francisco Herrera [ctb],
Jose Manuel Benitez [ctb],
Christoph Bergmeir [ctb, cre],
Sebastian Stawicki [ctb]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RoughSets versions 1.2-1 dated 2015-03-24 and 1.3-0 dated 2015-09-05
RoughSets-1.2-1/RoughSets/demo/D.local.discernibility.matrix.RST.R |only RoughSets-1.2-1/RoughSets/demo/D.max.discernibility.matrix.RST.R |only RoughSets-1.2-1/RoughSets/man/D.local.discernibility.matrix.RST.Rd |only RoughSets-1.2-1/RoughSets/man/D.max.discernibility.matrix.RST.Rd |only RoughSets-1.3-0/RoughSets/DESCRIPTION | 23 RoughSets-1.3-0/RoughSets/MD5 | 245 RoughSets-1.3-0/RoughSets/NAMESPACE | 14 RoughSets-1.3-0/RoughSets/R/BasicFuzzyRoughSets.R | 3344 +++++----- RoughSets-1.3-0/RoughSets/R/BasicRoughSets.OtherFuncCollections.R | 2596 +++---- RoughSets-1.3-0/RoughSets/R/BasicRoughSets.R | 804 +- RoughSets-1.3-0/RoughSets/R/Discretization.OtherFuncCollections.R | 547 - RoughSets-1.3-0/RoughSets/R/Discretization.R | 632 - RoughSets-1.3-0/RoughSets/R/FeatureSelection.OtherFuncCollections.R | 1938 ++--- RoughSets-1.3-0/RoughSets/R/FeatureSelection.R | 3224 ++++----- RoughSets-1.3-0/RoughSets/R/FuzzyRoughSets-introduction.R | 274 RoughSets-1.3-0/RoughSets/R/IOFunctions.R | 1789 ++--- RoughSets-1.3-0/RoughSets/R/InstanceSelection.OtherFuncCollections.R | 126 RoughSets-1.3-0/RoughSets/R/InstanceSelection.R | 658 - RoughSets-1.3-0/RoughSets/R/MissingValue.R | 814 +- RoughSets-1.3-0/RoughSets/R/NearestNeigbour.OtherFuncCollections.R | 480 - RoughSets-1.3-0/RoughSets/R/NearestNeigbour.R | 674 +- RoughSets-1.3-0/RoughSets/R/RcppExports.R | 22 RoughSets-1.3-0/RoughSets/R/RoughSets-introduction.R | 232 RoughSets-1.3-0/RoughSets/R/RoughSets-package.R | 1084 +-- RoughSets-1.3-0/RoughSets/R/RuleInduction.OtherFuncCollections.R | 955 +- RoughSets-1.3-0/RoughSets/R/RuleInduction.R | 2191 +++--- RoughSets-1.3-0/RoughSets/R/docData.R | 288 RoughSets-1.3-0/RoughSets/demo/00Index | 60 RoughSets-1.3-0/RoughSets/demo/BasicConcept.FRST.R | 94 RoughSets-1.3-0/RoughSets/demo/BasicConcept.RST.R | 50 RoughSets-1.3-0/RoughSets/demo/D.discretize.equal.intervals.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/D.discretize.quantiles.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/D.global.discernibility.heuristic.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/DiscernibilityMatrix.FRST.R | 56 RoughSets-1.3-0/RoughSets/demo/DiscernibilityMatrix.RST.R | 22 RoughSets-1.3-0/RoughSets/demo/FRNN.O.iris.R | 66 RoughSets-1.3-0/RoughSets/demo/FRNN.iris.R | 76 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.FRST.Ex1.R | 112 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.FRST.Ex2.R | 102 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.FRST.Ex3.R | 102 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.FRST.Ex4.R | 108 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.FRST.Ex5.R | 114 RoughSets-1.3-0/RoughSets/demo/FS.QuickReduct.RST.R | 20 RoughSets-1.3-0/RoughSets/demo/FS.greedy.heuristic.reduct.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/FS.greedy.heuristic.superreduct.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/FS.nearOpt.fvprs.FRST.R | 18 RoughSets-1.3-0/RoughSets/demo/FS.permutation.heuristic.reduct.RST.R | 28 RoughSets-1.3-0/RoughSets/demo/GettingStarted.A.R | 206 RoughSets-1.3-0/RoughSets/demo/GettingStarted.B.R | 272 RoughSets-1.3-0/RoughSets/demo/IS.FRIS.FRST.R | 38 RoughSets-1.3-0/RoughSets/demo/IS.FRPS.FRST.R | 30 RoughSets-1.3-0/RoughSets/demo/MV.simpleData.R | 60 RoughSets-1.3-0/RoughSets/demo/POSNN.iris.R | 64 RoughSets-1.3-0/RoughSets/demo/RI.classification.FRST.R | 62 RoughSets-1.3-0/RoughSets/demo/RI.indiscernibilityBasedRules.RST.R | 38 RoughSets-1.3-0/RoughSets/demo/RI.regression.FRST.R | 38 RoughSets-1.3-0/RoughSets/demo/SimulationDataAnalysisWine.R | 296 RoughSets-1.3-0/RoughSets/man/A.Introduction-RoughSets.Rd | 202 RoughSets-1.3-0/RoughSets/man/B.Introduction-FuzzyRoughSets.Rd | 246 RoughSets-1.3-0/RoughSets/man/BC.IND.relation.FRST.Rd | 634 - RoughSets-1.3-0/RoughSets/man/BC.IND.relation.RST.Rd | 132 RoughSets-1.3-0/RoughSets/man/BC.LU.approximation.FRST.Rd | 796 +- RoughSets-1.3-0/RoughSets/man/BC.LU.approximation.RST.Rd | 116 RoughSets-1.3-0/RoughSets/man/BC.discernibility.mat.FRST.Rd | 434 - RoughSets-1.3-0/RoughSets/man/BC.discernibility.mat.RST.Rd | 132 RoughSets-1.3-0/RoughSets/man/BC.positive.reg.FRST.Rd | 224 RoughSets-1.3-0/RoughSets/man/BC.positive.reg.RST.Rd | 122 RoughSets-1.3-0/RoughSets/man/C.FRNN.FRST.Rd | 270 RoughSets-1.3-0/RoughSets/man/C.FRNN.O.FRST.Rd | 166 RoughSets-1.3-0/RoughSets/man/C.POSNN.FRST.Rd | 162 RoughSets-1.3-0/RoughSets/man/D.discretization.RST.Rd | 164 RoughSets-1.3-0/RoughSets/man/D.discretize.equal.intervals.RST.Rd | 111 RoughSets-1.3-0/RoughSets/man/D.discretize.quantiles.RST.Rd | 113 RoughSets-1.3-0/RoughSets/man/D.global.discernibility.heuristic.RST.Rd | 167 RoughSets-1.3-0/RoughSets/man/D.local.discernibility.heuristic.RST.Rd |only RoughSets-1.3-0/RoughSets/man/FS.DAAR.heuristic.RST.Rd | 194 RoughSets-1.3-0/RoughSets/man/FS.all.reducts.computation.Rd | 132 RoughSets-1.3-0/RoughSets/man/FS.feature.subset.computation.Rd | 142 RoughSets-1.3-0/RoughSets/man/FS.greedy.heuristic.reduct.RST.Rd | 213 RoughSets-1.3-0/RoughSets/man/FS.greedy.heuristic.superreduct.RST.Rd | 149 RoughSets-1.3-0/RoughSets/man/FS.nearOpt.fvprs.FRST.Rd | 150 RoughSets-1.3-0/RoughSets/man/FS.one.reduct.computation.Rd | 138 RoughSets-1.3-0/RoughSets/man/FS.permutation.heuristic.reduct.RST.Rd | 158 RoughSets-1.3-0/RoughSets/man/FS.quickreduct.FRST.Rd | 582 - RoughSets-1.3-0/RoughSets/man/FS.quickreduct.RST.Rd | 136 RoughSets-1.3-0/RoughSets/man/FS.reduct.computation.Rd | 140 RoughSets-1.3-0/RoughSets/man/IS.FRIS.FRST.Rd | 168 RoughSets-1.3-0/RoughSets/man/IS.FRPS.FRST.Rd | 152 RoughSets-1.3-0/RoughSets/man/MV.conceptClosestFit.Rd | 100 RoughSets-1.3-0/RoughSets/man/MV.deletionCases.Rd | 90 RoughSets-1.3-0/RoughSets/man/MV.globalClosestFit.Rd | 108 RoughSets-1.3-0/RoughSets/man/MV.missingValueCompletion.Rd | 120 RoughSets-1.3-0/RoughSets/man/MV.mostCommonVal.Rd | 90 RoughSets-1.3-0/RoughSets/man/MV.mostCommonValResConcept.Rd | 90 RoughSets-1.3-0/RoughSets/man/RI.AQRules.RST.Rd | 148 RoughSets-1.3-0/RoughSets/man/RI.CN2Rules.RST.Rd | 138 RoughSets-1.3-0/RoughSets/man/RI.GFRS.FRST.Rd | 174 RoughSets-1.3-0/RoughSets/man/RI.LEM2Rules.RST.Rd | 134 RoughSets-1.3-0/RoughSets/man/RI.hybridFS.FRST.Rd | 144 RoughSets-1.3-0/RoughSets/man/RI.indiscernibilityBasedRules.RST.Rd | 139 RoughSets-1.3-0/RoughSets/man/RI.laplace.Rd |only RoughSets-1.3-0/RoughSets/man/RoughSetData.Rd | 260 RoughSets-1.3-0/RoughSets/man/RoughSets-package.Rd | 1050 +-- RoughSets-1.3-0/RoughSets/man/SF.applyDecTable.Rd | 223 RoughSets-1.3-0/RoughSets/man/SF.asDecisionTable.Rd | 140 RoughSets-1.3-0/RoughSets/man/SF.asFeatureSubset.Rd | 104 RoughSets-1.3-0/RoughSets/man/SF.read.DecisionTable.Rd | 98 RoughSets-1.3-0/RoughSets/man/X.entropy.Rd | 50 RoughSets-1.3-0/RoughSets/man/X.gini.Rd | 52 RoughSets-1.3-0/RoughSets/man/X.laplace.Rd | 48 RoughSets-1.3-0/RoughSets/man/X.nOfConflicts.Rd | 42 RoughSets-1.3-0/RoughSets/man/X.ruleStrength.Rd | 50 RoughSets-1.3-0/RoughSets/man/X.rulesCounting.Rd | 50 RoughSets-1.3-0/RoughSets/man/as.character.RuleSetRST.Rd |only RoughSets-1.3-0/RoughSets/man/as.list.RuleSetRST.Rd |only RoughSets-1.3-0/RoughSets/man/predict.RuleSetFRST.Rd | 136 RoughSets-1.3-0/RoughSets/man/predict.RuleSetRST.Rd | 182 RoughSets-1.3-0/RoughSets/man/print.FeatureSubset.Rd | 66 RoughSets-1.3-0/RoughSets/man/print.RuleSetRST.Rd | 75 RoughSets-1.3-0/RoughSets/man/sub-.RuleSetRST.Rd |only RoughSets-1.3-0/RoughSets/man/summary.IndiscernibilityRelation.Rd | 92 RoughSets-1.3-0/RoughSets/man/summary.LowerUpperApproximation.Rd | 80 RoughSets-1.3-0/RoughSets/man/summary.PositiveRegion.Rd | 82 RoughSets-1.3-0/RoughSets/man/summary.RuleSetFRST.Rd | 120 RoughSets-1.3-0/RoughSets/man/summary.RuleSetRST.Rd | 88 RoughSets-1.3-0/RoughSets/src/RcppExports.cpp | 41 RoughSets-1.3-0/RoughSets/src/discretization.cc | 37 RoughSets-1.3-0/RoughSets/src/indiscernibility.cpp | 109 128 files changed, 18431 insertions(+), 18190 deletions(-)
Title: Minimal Protein Set Explaining Peptide Spectrum Matches
Description: Determine minimal protein set explaining peptide spectrum matches.
Author: Witold Wolski
Maintainer: Witold Wolski <wewolski@gmail.com>
Diff between prozor versions 0.1 dated 2015-09-04 and 0.1.1 dated 2015-09-05
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/annotatePeptides.R | 31 +++++++++++++++++++++++-------- R/greedy.R | 19 +++++++++---------- 4 files changed, 40 insertions(+), 26 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.6 dated 2015-08-11 and 0.4.0 dated 2015-09-04
vardpoor-0.3.6/vardpoor/R/linrmi.R |only vardpoor-0.3.6/vardpoor/man/linrmi.Rd |only vardpoor-0.4.0/vardpoor/DESCRIPTION | 8 +- vardpoor-0.4.0/vardpoor/MD5 | 44 ++++++++-------- vardpoor-0.4.0/vardpoor/NAMESPACE | 2 vardpoor-0.4.0/vardpoor/R/linrmir.R |only vardpoor-0.4.0/vardpoor/R/vardchangespoor.R | 2 vardpoor-0.4.0/vardpoor/R/vardcrospoor.R | 16 ++--- vardpoor-0.4.0/vardpoor/R/vardomh.R | 14 +++-- vardpoor-0.4.0/vardpoor/R/varpoord.R | 39 +++++++------- vardpoor-0.4.0/vardpoor/inst/CITATION | 4 - vardpoor-0.4.0/vardpoor/inst/NEWS | 6 ++ vardpoor-0.4.0/vardpoor/man/linarpr.Rd | 2 vardpoor-0.4.0/vardpoor/man/lingini.Rd | 3 - vardpoor-0.4.0/vardpoor/man/lingini2.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linpoormed.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linqsr.Rd | 3 - vardpoor-0.4.0/vardpoor/man/linrmir.Rd |only vardpoor-0.4.0/vardpoor/man/linrmpg.Rd | 3 - vardpoor-0.4.0/vardpoor/man/vardchangespoor.Rd | 2 vardpoor-0.4.0/vardpoor/man/vardcrospoor.Rd | 4 - vardpoor-0.4.0/vardpoor/man/vardomh.Rd | 40 ++++++++++++-- vardpoor-0.4.0/vardpoor/man/vardpoor-package.Rd | 4 - vardpoor-0.4.0/vardpoor/man/variance_est.Rd | 10 +++ vardpoor-0.4.0/vardpoor/man/varpoord.Rd | 66 ++++++++++++++++++------ 25 files changed, 179 insertions(+), 99 deletions(-)
Title: Model Selection for Index of Asymmetry Distribution
Description: Calculate AIC's and AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of two normal distributions) which fit the distribution of indices of asymmetry (IAS), and plot their density, to help determine IAS distribution is unimodal or bimodal.
Author: Satoshi Takahashi
Maintainer: Satoshi Takahashi <takahasi@lisboa.ics.nara-wu.ac.jp>
Diff between IASD versions 1.0.7 dated 2013-08-07 and 1.1 dated 2015-09-04
DESCRIPTION | 12 +- MD5 | 10 - NAMESPACE | 6 + R/IASD.R | 304 ++++++++++++++++++++++++++++------------------------ man/IASD-package.Rd | 5 man/IASD.Rd | 75 +++++++++--- 6 files changed, 241 insertions(+), 171 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.2.1 dated 2014-11-13 and 1.3.1 dated 2015-09-04
entropart-1.2.1/entropart/R/bcDiversity.R |only entropart-1.2.1/entropart/R/bcDqz.R |only entropart-1.2.1/entropart/R/bcHqz.R |only entropart-1.2.1/entropart/R/bcHqzBeta.R |only entropart-1.2.1/entropart/R/bcPhyloBetaEntropy.R |only entropart-1.2.1/entropart/R/bcPhyloDiversity.R |only entropart-1.2.1/entropart/R/bcPhyloEntropy.R |only entropart-1.2.1/entropart/R/bcRao.R |only entropart-1.2.1/entropart/R/bcShannon.R |only entropart-1.2.1/entropart/R/bcShannonBeta.R |only entropart-1.2.1/entropart/R/bcSimpson.R |only entropart-1.2.1/entropart/R/bcSimpsonBeta.R |only entropart-1.2.1/entropart/R/bcTsallis.R |only entropart-1.2.1/entropart/R/bcTsallisBeta.R |only entropart-1.2.1/entropart/R/is.MCdiversity.R |only entropart-1.2.1/entropart/R/is.MCentropy.R |only entropart-1.2.1/entropart/R/is.MetaCommunity.R |only entropart-1.2.1/entropart/R/is.PPtree.R |only entropart-1.2.1/entropart/R/is.PhyloDiversity.R |only entropart-1.2.1/entropart/R/is.PhyloEntropy.R |only entropart-1.2.1/entropart/R/is.PhyloValue.R |only entropart-1.2.1/entropart/R/is.SimTest.R |only entropart-1.2.1/entropart/R/plot.DivEst.R |only entropart-1.2.1/entropart/R/plot.DivPart.R |only entropart-1.2.1/entropart/R/plot.DivProfile.R |only entropart-1.2.1/entropart/R/plot.MCdiversity.R |only entropart-1.2.1/entropart/R/plot.MCentropy.R |only entropart-1.2.1/entropart/R/plot.MetaCommunity.R |only entropart-1.2.1/entropart/R/plot.PPtree.R |only entropart-1.2.1/entropart/R/plot.PhyloValue.R |only entropart-1.2.1/entropart/R/plot.SimTest.R |only entropart-1.2.1/entropart/R/summary.DivEst.R |only entropart-1.2.1/entropart/R/summary.DivPart.R |only entropart-1.2.1/entropart/R/summary.DivProfile.R |only entropart-1.2.1/entropart/R/summary.MCdiversity.R |only entropart-1.2.1/entropart/R/summary.MCentropy.R |only entropart-1.2.1/entropart/R/summary.MetaCommunity.R |only entropart-1.2.1/entropart/R/summary.PhyloDiversity.R |only entropart-1.2.1/entropart/R/summary.PhyloEntropy.R |only entropart-1.2.1/entropart/R/summary.PhyloValue.R |only entropart-1.2.1/entropart/R/summary.SimTest.R |only entropart-1.2.1/entropart/vignettes/entropart-MCPlot.pdf |only entropart-1.2.1/entropart/vignettes/entropart-lnq.pdf |only entropart-1.3.1/entropart/DESCRIPTION | 11 entropart-1.3.1/entropart/MD5 | 207 +++++------ entropart-1.3.1/entropart/NAMESPACE | 104 +++++ entropart-1.3.1/entropart/NEWS | 18 + entropart-1.3.1/entropart/R/AbdFreqCount.R |only entropart-1.3.1/entropart/R/AllenH.R | 4 entropart-1.3.1/entropart/R/CEnvelope.R |only entropart-1.3.1/entropart/R/ChaoPD.R | 2 entropart-1.3.1/entropart/R/CheckentropartArguments.R | 269 +++++++++++---- entropart-1.3.1/entropart/R/CommunityProfile.R | 106 +++++ entropart-1.3.1/entropart/R/DivEst.R | 75 ++++ entropart-1.3.1/entropart/R/DivPart.R | 45 ++ entropart-1.3.1/entropart/R/DivProfile.R | 70 +++ entropart-1.3.1/entropart/R/Diversity.R | 69 +++ entropart-1.3.1/entropart/R/Dqz.R | 72 +++- entropart-1.3.1/entropart/R/EntropyCI.R | 10 entropart-1.3.1/entropart/R/Hqz.R | 162 ++++++++- entropart-1.3.1/entropart/R/HqzBeta.R | 98 +++++ entropart-1.3.1/entropart/R/Hurlbert.R |only entropart-1.3.1/entropart/R/HurlbertD.R |only entropart-1.3.1/entropart/R/MCdiversity.R |only entropart-1.3.1/entropart/R/MCentropy.R |only entropart-1.3.1/entropart/R/MetaCommunity.R | 40 ++ entropart-1.3.1/entropart/R/Optimal.Similarity.R |only entropart-1.3.1/entropart/R/Originality.Species.R | 9 entropart-1.3.1/entropart/R/PPtree.R |only entropart-1.3.1/entropart/R/PhyloApply.R | 6 entropart-1.3.1/entropart/R/PhyloBetaEntropy.R | 103 +++++ entropart-1.3.1/entropart/R/PhyloDiversity.R | 114 ++++++ entropart-1.3.1/entropart/R/PhyloEntropy.R | 106 +++++ entropart-1.3.1/entropart/R/PhyloValue.R |only entropart-1.3.1/entropart/R/Preprocess.Tree.R | 2 entropart-1.3.1/entropart/R/Rao.R | 72 +++- entropart-1.3.1/entropart/R/Richness.R | 172 +++++++++ entropart-1.3.1/entropart/R/Shannon.R | 172 +++++++++ entropart-1.3.1/entropart/R/ShannonBeta.R | 112 ++++++ entropart-1.3.1/entropart/R/SimTest.R | 35 + entropart-1.3.1/entropart/R/Simpson.R | 72 +++- entropart-1.3.1/entropart/R/SimpsonBeta.R | 85 ++++ entropart-1.3.1/entropart/R/SpeciesDistribution.R |only entropart-1.3.1/entropart/R/Tsallis.R | 175 +++++++++ entropart-1.3.1/entropart/R/TsallisBeta.R | 117 ++++++ entropart-1.3.1/entropart/R/expq.R | 17 entropart-1.3.1/entropart/R/lnq.R | 17 entropart-1.3.1/entropart/R/rCommunity.R |only entropart-1.3.1/entropart/build/vignette.rds |binary entropart-1.3.1/entropart/inst/CITATION | 10 entropart-1.3.1/entropart/inst/doc/entropart.R | 152 ++++++-- entropart-1.3.1/entropart/inst/doc/entropart.Rnw | 177 +++++++-- entropart-1.3.1/entropart/inst/doc/entropart.pdf |binary entropart-1.3.1/entropart/man/AbdFreqCount.Rd |only entropart-1.3.1/entropart/man/AllenH.Rd | 7 entropart-1.3.1/entropart/man/AlphaDiversity.Rd | 4 entropart-1.3.1/entropart/man/AlphaEntropy.Rd | 4 entropart-1.3.1/entropart/man/BetaDiversity.Rd | 4 entropart-1.3.1/entropart/man/BetaEntropy.Rd | 4 entropart-1.3.1/entropart/man/ChaoPD.Rd | 3 entropart-1.3.1/entropart/man/CommunityProfile.Rd | 84 ++++ entropart-1.3.1/entropart/man/DivEst.Rd | 8 entropart-1.3.1/entropart/man/DivPart.Rd | 8 entropart-1.3.1/entropart/man/DivProfile.Rd | 6 entropart-1.3.1/entropart/man/Diversity.Rd | 39 +- entropart-1.3.1/entropart/man/Dqz.Rd | 24 + entropart-1.3.1/entropart/man/EntropyCI.Rd | 16 entropart-1.3.1/entropart/man/GammaDiversity.Rd | 4 entropart-1.3.1/entropart/man/GammaEntropy.Rd | 4 entropart-1.3.1/entropart/man/Hqz.Rd | 27 + entropart-1.3.1/entropart/man/HqzBeta.Rd | 34 + entropart-1.3.1/entropart/man/Hurlbert.Rd |only entropart-1.3.1/entropart/man/Optimal.Similarity.Rd |only entropart-1.3.1/entropart/man/Paracou618.Functional.Rd | 2 entropart-1.3.1/entropart/man/Paracou618.dist.Rd | 2 entropart-1.3.1/entropart/man/PhyloApply.Rd | 2 entropart-1.3.1/entropart/man/PhyloBetaEntropy.Rd | 44 +- entropart-1.3.1/entropart/man/PhyloDiversity.Rd | 26 + entropart-1.3.1/entropart/man/PhyloEntropy.Rd | 28 + entropart-1.3.1/entropart/man/Rao.Rd | 37 +- entropart-1.3.1/entropart/man/Richness.Rd | 76 +++- entropart-1.3.1/entropart/man/Shannon.Rd | 47 +- entropart-1.3.1/entropart/man/ShannonBeta.Rd | 32 + entropart-1.3.1/entropart/man/Simpson.Rd | 32 + entropart-1.3.1/entropart/man/SimpsonBeta.Rd | 34 + entropart-1.3.1/entropart/man/SpeciesDistribution.Rd |only entropart-1.3.1/entropart/man/Tsallis.Rd | 50 ++ entropart-1.3.1/entropart/man/TsallisBeta.Rd | 23 + entropart-1.3.1/entropart/man/entropart-package.Rd | 11 entropart-1.3.1/entropart/man/expq.Rd | 9 entropart-1.3.1/entropart/man/lnq.Rd | 9 entropart-1.3.1/entropart/man/rCommunity.Rd |only entropart-1.3.1/entropart/vignettes/entropart.Rnw | 177 +++++++-- entropart-1.3.1/entropart/vignettes/entropart.bib | 101 ++++- 134 files changed, 3544 insertions(+), 565 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug-Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding
the maximum tolerated dose (MTD). It can be used to design both single-agent and
drug-combination trials. The BOIN design is motivated by the top priority and concern of
clinicians when testing a new drug, which is to effectively treat patients and minimize the chance
of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same time.
The BOIN design is algorithm-based and can be implemented in a simple way similar to the
traditional 3+3 design. The BOIN design yields an average performance that is comparable to
that of the continual reassessment method (CRM, one of the best model-based designs) in terms of
selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic
or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 1.2 dated 2015-07-27 and 2.0 dated 2015-09-04
DESCRIPTION | 24 ++++++++++++++++------ MD5 | 22 +++++++++++++------- R/conduct.comb.R |only R/get.boundary.R | 45 +++++++++++------------------------------- R/get.oc.R | 8 +++---- R/get.oc.comb.R |only R/select.mtd.R | 3 +- R/select.mtd.comb.R |only man/BOIN-package.Rd | 52 ++++++++++++++++++++++++++++++++++++------------- man/conduct.comb.Rd |only man/get.boundary.Rd | 18 ++++++---------- man/get.oc.Rd | 19 +++++++---------- man/get.oc.comb.Rd |only man/select.mtd.Rd | 24 +++++++++++----------- man/select.mtd.comb.Rd |only 15 files changed, 116 insertions(+), 99 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant <bjgrant@umich.edu>
Diff between bio3d versions 2.2-2 dated 2015-03-03 and 2.2-3 dated 2015-09-04
DESCRIPTION | 8 +++--- MD5 | 52 +++++++++++++++++++++--------------------- NAMESPACE | 4 +++ R/as.pdb.prmtop.R | 6 ++-- R/atom.select.prmtop.R | 2 - R/binding.site.R | 35 ++++++++++++++-------------- R/cnapath.R | 10 ++++---- R/filter.dccm.R | 2 - R/hmmer.R | 4 +-- R/orient.pdb.R | 25 +++++++++++--------- R/pdbaln.R | 12 ++++++++- R/plot.fluct.R | 5 ++-- R/plotb3.R | 4 +-- R/read.pdb.R | 6 ++-- R/seqaln.R | 10 +++++++- R/trim.pdbs.R | 1 R/trim.xyz.R | 3 -- build/vignette.rds |binary inst/doc/bio3d_vignettes.html | 11 ++++++++ man/hmmer.Rd | 4 +-- man/pfam.Rd | 2 - man/plot.hmmer.Rd | 2 - man/read.ncdf.Rd | 2 - man/uniprot.Rd | 2 - man/write.ncdf.Rd | 2 - tests/testthat/test-dssp.R | 4 +++ tests/testthat/test-fitting.R | 10 +++++++- 27 files changed, 138 insertions(+), 90 deletions(-)
Title: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Description: The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker
Maintainer: Katharine M. Mullen <mullenkate@gmail.com>
Diff between minpack.lm versions 1.1-8 dated 2013-08-31 and 1.1-9 dated 2015-09-04
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 5 ++++- NEWS | 2 ++ man/nls.lm.Rd | 2 +- 5 files changed, 17 insertions(+), 11 deletions(-)
Title: Tools for Aquatic Sciences
Description: Datasets, constants, conversion factors, utilities for MArine, Riverine,
Estuarine, LAcustrine and Coastal science.
The package contains among others: (1) chemical and
physical constants and datasets, e.g. atomic weights, gas
constants, the earths bathymetry; (2) conversion factors
(e.g. gram to mol to liter, barometric units,
temperature, salinity); (3) physical functions, e.g. to
estimate concentrations of conservative substances, gas
transfer and diffusion coefficients, the Coriolis force
and gravity; (4) thermophysical properties of the
seawater, as from the UNESCO polynomial or from the more
recent derivation based on a Gibbs function.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>,
Filip Meysman <filip.meysman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between marelac versions 2.1.4 dated 2014-11-04 and 2.1.5 dated 2015-09-04
DESCRIPTION | 11 - MD5 | 31 ++-- NAMESPACE | 3 R/diffcoeff.R | 44 ++++-- R/earth_surf.R | 12 - R/sw_dens.R | 4 R/xcbind.R |only build/vignette.rds |binary data/AtomicWeight.rda |binary data/Bathymetry.rda |binary data/Constants.rda |binary data/Oceans.rda |binary data/sw_sfac.rda |binary man/AtomicWeight.Rd | 8 - man/convert_p.Rd | 2 man/diffcoeff.Rd | 315 ++++++++++++++++++++++++++------------------------ man/molvol.Rd | 185 ++++++++++++++--------------- 17 files changed, 327 insertions(+), 288 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd9 versions 1.2 dated 2015-04-21 and 1.2.1 dated 2015-09-04
icd9-1.2.1/icd9/DESCRIPTION | 10 - icd9-1.2.1/icd9/MD5 | 97 ++++++++------- icd9-1.2.1/icd9/NAMESPACE | 11 + icd9-1.2.1/icd9/R/RcppExports.R | 32 ++--- icd9-1.2.1/icd9/R/benchmark.R | 27 ++-- icd9-1.2.1/icd9/R/convert.R | 1 icd9-1.2.1/icd9/R/datadocs.R | 2 icd9-1.2.1/icd9/R/ranges.R | 28 ++++ icd9-1.2.1/icd9/R/score.R | 2 icd9-1.2.1/icd9/R/util.R | 9 - icd9-1.2.1/icd9/R/zzz.R | 6 icd9-1.2.1/icd9/README.md | 14 +- icd9-1.2.1/icd9/build/vignette.rds |binary icd9-1.2.1/icd9/data/icd9Chapters.rda |binary icd9-1.2.1/icd9/data/mappingNames.rda |binary icd9-1.2.1/icd9/inst/doc/introduction.R | 1 icd9-1.2.1/icd9/inst/doc/introduction.Rmd | 5 icd9-1.2.1/icd9/inst/doc/introduction.html | 8 - icd9-1.2.1/icd9/inst/include/icd9_RcppExports.h | 102 ++++++++-------- icd9-1.2.1/icd9/man/convert.Rd | 25 ---- icd9-1.2.1/icd9/man/expandRangeWorker.Rd |only icd9-1.2.1/icd9/man/icd9AddLeadingZeroes.Rd | 8 - icd9-1.2.1/icd9/man/icd9ChaptersToMap.Rd | 5 icd9-1.2.1/icd9/man/icd9DropLeadingZeroes.Rd | 5 icd9-1.2.1/icd9/man/icd9ExpandMinor.Rd | 2 icd9-1.2.1/icd9/man/icd9Hierarchy.Rd | 2 icd9-1.2.1/icd9/man/icd9LongToWide.Rd | 5 icd9-1.2.1/icd9/man/icd9WideToLong.Rd | 5 icd9-1.2.1/icd9/man/logicalToBinary.Rd | 5 icd9-1.2.1/icd9/man/randomShortIcd9.Rd |only icd9-1.2.1/icd9/man/strMultiMatch.Rd | 5 icd9-1.2.1/icd9/man/zip_single.Rd |only icd9-1.2.1/icd9/src/RcppExports.cpp | 148 ++++++++++++------------ icd9-1.2.1/icd9/src/comorbid.cpp | 4 icd9-1.2.1/icd9/src/convert.cpp | 133 +++++++++++---------- icd9-1.2.1/icd9/src/convert.h | 4 icd9-1.2.1/icd9/src/longToWide.cpp | 6 icd9-1.2.1/icd9/src/manip.cpp | 20 +-- icd9-1.2.1/icd9/src/manip.h | 4 icd9-1.2.1/icd9/src/ranges.cpp | 22 +-- icd9-1.2.1/icd9/src/util.cpp | 3 icd9-1.2.1/icd9/tests/testthat/helper-base.R | 2 icd9-1.2.1/icd9/tests/testthat/test-comorbid.R | 8 + icd9-1.2.1/icd9/tests/testthat/test-condense.R | 2 icd9-1.2.1/icd9/tests/testthat/test-convert.R | 10 - icd9-1.2.1/icd9/tests/testthat/test-score.R | 2 icd9-1.2.1/icd9/tools/docker-ubsan-clang.sh |only icd9-1.2.1/icd9/tools/r-devel-ubsan-clang |only icd9-1.2.1/icd9/tools/rocker-devel.sh |only icd9-1.2.1/icd9/tools/rocker-san.sh |only icd9-1.2.1/icd9/tools/rocker-ubsan-clang.sh |only icd9-1.2.1/icd9/tools/rocker-vanilla.sh |only icd9-1.2.1/icd9/vignettes/introduction.Rmd | 5 icd9-1.2/icd9/R/RcppExportsShim.R |only 54 files changed, 409 insertions(+), 386 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.5 dated 2015-05-29 and 1.1.6 dated 2015-09-04
ExomeDepth-1.1.5/ExomeDepth/vignettes/.install_extras |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.R |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.pdf |only ExomeDepth-1.1.6/ExomeDepth/DESCRIPTION | 8 +- ExomeDepth-1.1.6/ExomeDepth/MD5 | 27 +++++----- ExomeDepth-1.1.6/ExomeDepth/NAMESPACE | 3 + ExomeDepth-1.1.6/ExomeDepth/R/class_definition.R | 2 ExomeDepth-1.1.6/ExomeDepth/R/plot_CNVs_method.R | 2 ExomeDepth-1.1.6/ExomeDepth/build/vignette.rds |binary ExomeDepth-1.1.6/ExomeDepth/data/Conrad.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/ExomeCount.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/exons.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/exons.hg19.X.RData |binary ExomeDepth-1.1.6/ExomeDepth/data/genes.hg19.RData |binary ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.R |only ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.6/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary ExomeDepth-1.1.6/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw |only 18 files changed, 23 insertions(+), 19 deletions(-)
Title: Differential Exon Usage Test for RNA-Seq Data via Empirical
Bayes Shrinkage of the Dispersion Parameter
Description: Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.
Author: Sean Ruddy
Maintainer: Sean Ruddy <s.ruddy@yahoo.com>
Diff between DoubleExpSeq versions 1.0 dated 2014-05-14 and 1.1 dated 2015-09-04
DESCRIPTION | 15 ++++---- MD5 | 14 ++++---- NAMESPACE | 5 ++ R/DBGLM1.R | 6 ++- R/DoubleExpSeq-internal.R | 77 ++++++++++++++++++++++++++++++++++++++++++++-- R/EstimateDEBDisp.R | 21 +++++++++--- data/exon.RData |binary man/EstimateDEBDisp.Rd | 8 +++- 8 files changed, 119 insertions(+), 27 deletions(-)
Title: Multi-Resolution Estimation of the Hazard Rate
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times. Can accommodate covariates under the proportional and non-proportional hazards setting, and is ideal for analysis of survival data with long-term follow-up.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar <yolanda.hagar@colorado.edu>
Diff between MRH versions 2.0 dated 2015-01-13 and 2.1 dated 2015-09-04
MRH-2.0/MRH/man/Prune.Rd |only MRH-2.0/MRH/man/find.Rmp.Rd |only MRH-2.1/MRH/DESCRIPTION | 8 ++++---- MRH-2.1/MRH/MD5 | 24 +++++++++++------------- MRH-2.1/MRH/NAMESPACE | 10 +++++++++- MRH-2.1/MRH/R/S3functions_BA.r | 9 +++++---- MRH-2.1/MRH/inst/doc/MRH.pdf |binary MRH-2.1/MRH/man/AnalyzeMultiple.Rd | 6 ++++++ MRH-2.1/MRH/man/CalcFunction.Rd | 6 +++--- MRH-2.1/MRH/man/DIC.Rd | 10 ++++++---- MRH-2.1/MRH/man/MRH-package.Rd | 4 ++-- MRH-2.1/MRH/man/MRH.Rd | 2 +- MRH-2.1/MRH/man/estimateMRH.Rd | 18 +++++++++++++++--- MRH-2.1/MRH/man/summary.MRH.Rd | 2 ++ 14 files changed, 64 insertions(+), 35 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train supervised and self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 2.0.18 dated 2015-03-25 and 2.0.19 dated 2015-09-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 7 +++++++ NEWS | 6 ++++++ R/plot.kohonen.R | 4 ++-- 5 files changed, 22 insertions(+), 9 deletions(-)
Title: Predict Gender from Names Using Historical Data
Description: Encodes gender based on names and dates of birth using historical
datasets. By using these datasets instead of lists of male and female names,
this package is able to more accurately guess the gender of a name, and it
is able to report the probability that a name was male or female.
Author: Lincoln Mullen [aut, cre],
Cameron Blevins [ctb],
Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between gender versions 0.5.0 dated 2015-08-22 and 0.5.1 dated 2015-09-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 +++++ R/install-genderdata-package.R | 8 +++++--- README.md | 12 ++++++++++-- 5 files changed, 28 insertions(+), 13 deletions(-)
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
Diff between FRESA.CAD versions 2.0.2 dated 2015-02-22 and 2.1.3 dated 2015-09-04
FRESA.CAD-2.0.2/FRESA.CAD/R/NeRIBasedFRESA.Model.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/ReclassificationFRESA.Model.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/backVarElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/backVarNeRIElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapValidation.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapValidationNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapVarElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/bootstrapVarNeRIElimination.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/crossValidationFeatureSelection.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/crossValidationNeRIFeatureSelection.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/getKNNpredictionFromFormula.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/getVarNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/getVarReclassification.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/medianPredict.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/plot.bootstrapValidation.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/plot.bootstrapValidationNeRI.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/residualtForNeRIs.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/summaryReport.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/uniRankVar.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/update.uniRankVar.r |only FRESA.CAD-2.0.2/FRESA.CAD/R/updateModel.R |only FRESA.CAD-2.0.2/FRESA.CAD/R/updateNeRImodel.R |only FRESA.CAD-2.0.2/FRESA.CAD/man/NeRIBasedFRESA.Model.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/ReclassificationFRESA.Model.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/backVarElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/backVarNeRIElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapValidation.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapValidationNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapVarElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/bootstrapVarNeRIElimination.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/crossValidationFeatureSelection.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/crossValidationNeRIFeatureSelection.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/getVarNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/getVarReclassification.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/plot.bootstrapValidation.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/plot.bootstrapValidationNeRI.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/residualForNeRIs.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/updateModel.Rd |only FRESA.CAD-2.0.2/FRESA.CAD/man/updateNeRImodel.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/DESCRIPTION | 11 FRESA.CAD-2.1.3/FRESA.CAD/MD5 | 132 +- FRESA.CAD-2.1.3/FRESA.CAD/NAMESPACE | 14 FRESA.CAD-2.1.3/FRESA.CAD/NEWS | 72 - FRESA.CAD-2.1.3/FRESA.CAD/R/FRESA.Model.R | 119 + FRESA.CAD-2.1.3/FRESA.CAD/R/ForwardSelection.Model.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/ForwardSelection.Model.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/backVarElimination.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/backVarElimination.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapValidation.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapValidation.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapVarElimination.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/bootstrapVarElimination.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/crossValidationFeatureSelection.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/crossValidationFeatureSelection.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getKNNpredictionFromFormula.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getVar.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/getVar.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/medianPredict.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/modelFitting.R | 14 FRESA.CAD-2.1.3/FRESA.CAD/R/plot.bootstrapValidation.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/plot.bootstrapValidation.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/plotModels.ROC.R | 10 FRESA.CAD-2.1.3/FRESA.CAD/R/reportEquivalentVariables.R | 45 FRESA.CAD-2.1.3/FRESA.CAD/R/residualtForFRESA.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/summary.bootstrapValidation.R | 4 FRESA.CAD-2.1.3/FRESA.CAD/R/summaryReport.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/timeSerieAnalysis.R | 86 + FRESA.CAD-2.1.3/FRESA.CAD/R/uniRankVar.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/univariateRankVariables.R | 4 FRESA.CAD-2.1.3/FRESA.CAD/R/update.uniRankVar.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/updateModel.Bin.R |only FRESA.CAD-2.1.3/FRESA.CAD/R/updateModel.Res.R |only FRESA.CAD-2.1.3/FRESA.CAD/man/FRESA.CAD-package.Rd | 24 FRESA.CAD-2.1.3/FRESA.CAD/man/FRESA.Model.Rd | 10 FRESA.CAD-2.1.3/FRESA.CAD/man/ForwardModel.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/ForwardModel.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/backVarElimination.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/backVarElimination.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapValidation.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapValidation.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapVarElimination.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/bootstrapVarElimination.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/crossValidationFeatureSelection.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/crossValidationFeatureSelection.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/getVar.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/getVar.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/heatMaps.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/improvedResiduals.Rd | 6 FRESA.CAD-2.1.3/FRESA.CAD/man/medianPredict.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/plot.bootstrapValidation.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/plot.bootstrapValidation.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/plotModels.ROC.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/predictForFresa.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/reportEquivalentVariables.Rd | 2 FRESA.CAD-2.1.3/FRESA.CAD/man/residualForFRESA.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/summary.bootstrapValidation.Rd | 16 FRESA.CAD-2.1.3/FRESA.CAD/man/summaryReport.Rd | 10 FRESA.CAD-2.1.3/FRESA.CAD/man/uniRankVar.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/univariateRankVariables.Rd | 4 FRESA.CAD-2.1.3/FRESA.CAD/man/updateModel.Bin.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/man/updateModel.Res.Rd |only FRESA.CAD-2.1.3/FRESA.CAD/src/FRESAcommons.cpp | 658 ++++++---- FRESA.CAD-2.1.3/FRESA.CAD/src/FRESAcommons.h | 40 FRESA.CAD-2.1.3/FRESA.CAD/src/binaryFeatureSelectionCpp.cpp | 262 ++- FRESA.CAD-2.1.3/FRESA.CAD/src/regresionFeatureSelectionCpp.cpp | 220 ++- 106 files changed, 1120 insertions(+), 659 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R
interface. It contains several machine learning model learning techniques in
classification and regression, for example classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with ExplainPrediction package.
The package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for example to discretize
numeric attributes.
Its additional feature is OrdEval algorithm and its visualization used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 0.9.46 dated 2015-06-03 and 1.47.1 dated 2015-09-04
ChangeLog | 2 DESCRIPTION | 32 MD5 | 54 - NAMESPACE | 15 R/Rinterface.R | 1888 ++++++++++++++++++++++++----------------------- R/util.R | 50 - man/CORElearn-package.Rd | 40 man/CoreModel.Rd | 20 man/discretize.Rd | 60 + man/helpCore.Rd | 10 man/modelEval.Rd | 8 man/predict.CoreModel.Rd | 1 man/rfClustering.Rd | 2 man/saveRF.Rd | 4 src/Rfront.cpp | 86 +- src/Rfront.h | 5 src/binarize.cpp | 47 + src/binarizeReg.cpp | 240 +++++ src/dataStore.h | 2 src/estimator.h | 1 src/estimatorReg.cpp | 3 src/estimatorReg.h | 3 src/expr.cpp | 7 src/frontend.cpp | 2 src/options.cpp | 18 src/options.h | 2 src/treenodeReg.cpp | 2 src/trutilReg.cpp | 112 -- 28 files changed, 1530 insertions(+), 1186 deletions(-)
Title: Chemometrics with R - Multivariate Data Analysis in the Natural
Sciences and Life Sciences
Description: Functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
Author: Ron Wehren9
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ChemometricsWithR versions 0.1.8 dated 2014-08-04 and 0.1.9 dated 2015-09-04
ChemometricsWithR-0.1.8/ChemometricsWithR/R/classvec2classmat.R |only ChemometricsWithR-0.1.8/ChemometricsWithR/man/classvec2classmat.Rd |only ChemometricsWithR-0.1.9/ChemometricsWithR/DESCRIPTION | 14 +++---- ChemometricsWithR-0.1.9/ChemometricsWithR/MD5 | 6 +-- ChemometricsWithR-0.1.9/ChemometricsWithR/NAMESPACE | 18 +++++++++- 5 files changed, 26 insertions(+), 12 deletions(-)
More information about ChemometricsWithR at CRAN
Permanent link
Title: Medical Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported.
Author: Jon Clayden, based on original code by Marc Modat and Pankaj Daga
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 1.1.3 dated 2015-02-18 and 1.1.5 dated 2015-09-03
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 4 ++++ NEWS | 19 ++++++++++++++++++- R/transform.R | 4 ++-- R/xform.R | 4 ++-- src/_reg_f3d.cpp | 11 ++--------- src/_reg_f3d_sym.cpp | 9 ++------- src/_reg_localTransformation_jac.cpp | 14 +++----------- src/_reg_resampling.cpp | 28 ++++++++-------------------- 10 files changed, 56 insertions(+), 67 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.3.1 dated 2015-07-29 and 0.3.2 dated 2015-09-03
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NEWS | 7 +++ R/qic.R | 106 +++++++++++++++++++++++++++++------------------------ build/vignette.rds |binary man/qic.Rd | 28 ++++++++------ 6 files changed, 90 insertions(+), 69 deletions(-)
Title: Bayesian Inference for Zero-Inflated Count Models
Description: Provides MCMC algorithms for the analysis of
zero-inflated count models. The case of stochastic search
variable selection (SVS) is also considered. All MCMC samplers
are coded in C++ for improved efficiency. A data set
considering the demand for health care is provided.
Author: Markus Jochmann <markus.jochmann@ncl.ac.uk>
Maintainer: Markus Jochmann <markus.jochmann@ncl.ac.uk>
Diff between zic versions 0.8.1 dated 2013-12-08 and 0.9 dated 2015-09-03
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +++ man/zic.Rd | 8 ++++++++ man/zic.svs.Rd | 9 +++++++++ 5 files changed, 31 insertions(+), 10 deletions(-)
Title: Skewed Generalized T Distribution Tree
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis
Maintainer: Carter Davis <cdavis40@chicagobooth.edu>
Diff between sgt versions 1.1 dated 2015-02-25 and 2.0 dated 2015-09-03
sgt-1.1/sgt/man/summaryMLE.Rd |only sgt-2.0/sgt/DESCRIPTION | 14 +- sgt-2.0/sgt/MD5 | 28 +++-- sgt-2.0/sgt/NAMESPACE | 22 +++- sgt-2.0/sgt/R/InternalSGED.R |only sgt-2.0/sgt/R/InternalSGT.R |only sgt-2.0/sgt/R/InternalUNIF.R |only sgt-2.0/sgt/R/SGT.R | 106 ++++++++++++------- sgt-2.0/sgt/R/SGTMLE.R | 187 ++++++++++++++--------------------- sgt-2.0/sgt/README.md |only sgt-2.0/sgt/build |only sgt-2.0/sgt/inst |only sgt-2.0/sgt/man/sgt.Rd | 72 ++++++------- sgt-2.0/sgt/man/sgtmle.Rd | 207 +++++++++++++-------------------------- sgt-2.0/sgt/man/summarysgtest.Rd |only sgt-2.0/sgt/vignettes |only 16 files changed, 300 insertions(+), 336 deletions(-)
Title: Generator of Semi-Artificial Data
Description: Package semiArtificial contains methods to generate and evaluate semi-artificial data sets.
Based on a given data set different methods learn data properties using machine learning algorithms and
generate new data with the same properties.
The package currently includes the following data generator:
-a RBF network based generator using rbfDDA from RSNNS package,
-a Random Forest based generator for both classification and regression problems
-a density forest based generator for unsupervised data
Data evaluation support tools include:
-single attribute based statistical evaluation: mean, median, standard deviation, skewness, kurtosis, medcouple, L/RMC, KS test, Hellinger distance
-evaluation based on clustering using Adjusted Rand Index (ARI) and FM
-evaluation based on classification performance with various learning models, eg, random forests.
Author: Marko Robnik-Sikonja
Maintainer: Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>
Diff between semiArtificial versions 1.2.0 dated 2014-03-17 and 2.0.1 dated 2015-09-03
semiArtificial-1.2.0/semiArtificial/R/semiArt.R |only semiArtificial-1.2.0/semiArtificial/man/newdata.RBFgenerator.Rd |only semiArtificial-2.0.1/semiArtificial/ChangeLog | 2 semiArtificial-2.0.1/semiArtificial/DESCRIPTION | 21 semiArtificial-2.0.1/semiArtificial/MD5 | 28 semiArtificial-2.0.1/semiArtificial/NAMESPACE | 24 semiArtificial-2.0.1/semiArtificial/R/dataQuality.R | 316 ++++++---- semiArtificial-2.0.1/semiArtificial/R/densityTree.R |only semiArtificial-2.0.1/semiArtificial/R/forestDataGen.R |only semiArtificial-2.0.1/semiArtificial/R/misc.R | 64 +- semiArtificial-2.0.1/semiArtificial/R/rbfDataGen.R |only semiArtificial-2.0.1/semiArtificial/R/rndtrees.R |only semiArtificial-2.0.1/semiArtificial/man/ariCompare.Rd | 24 semiArtificial-2.0.1/semiArtificial/man/dataSimilarity.Rd | 3 semiArtificial-2.0.1/semiArtificial/man/newdata.Rd |only semiArtificial-2.0.1/semiArtificial/man/performanceCompare.Rd | 15 semiArtificial-2.0.1/semiArtificial/man/rbfDataGen.Rd | 7 semiArtificial-2.0.1/semiArtificial/man/semiArtificial-package.Rd | 16 semiArtificial-2.0.1/semiArtificial/man/treeEnsemble.Rd |only 19 files changed, 355 insertions(+), 165 deletions(-)
More information about semiArtificial at CRAN
Permanent link
More information about ICC.Sample.Size at CRAN
Permanent link
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the system
clipboards of Windows, OS X, and Linux.
Author: Matthew Lincoln [aut, cre],
Louis Maddox [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.1.0 dated 2015-09-02 and 0.1.1 dated 2015-09-03
DESCRIPTION | 7 +++---- MD5 | 9 +++++---- NEWS.md |only R/clipboard.R | 6 ++---- R/linux_clipboard.R | 30 ++++++++++++++++++++---------- README.md | 6 ++++-- 6 files changed, 34 insertions(+), 24 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series
from the HIS Central catalog based on geographic bounding box, server, or keyword.
GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The GetValues function can also retrieve WaterML 1 or WaterML 2.0 data
from a custom URL or from a local file. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.3.2 dated 2015-07-12 and 1.4.0 dated 2015-09-03
DESCRIPTION | 10 ++--- MD5 | 12 +++--- NAMESPACE | 1 R/GetValues.R | 92 ++++++++++++++++++++++++++++-------------------- R/MakeSOAPEnvelope.R | 2 - build/vignette.rds |binary man/MakeSOAPEnvelope.Rd | 2 - 7 files changed, 68 insertions(+), 51 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.400.2.0 dated 2015-08-17 and 0.5.500.2.0 dated 2015-09-03
ChangeLog | 17 DESCRIPTION | 10 MD5 | 106 - build/vignette.rds |binary inst/NEWS.Rd | 12 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo_bits/BaseCube_bones.hpp | 4 inst/include/armadillo_bits/Base_bones.hpp | 4 inst/include/armadillo_bits/Col_bones.hpp | 4 inst/include/armadillo_bits/Col_meat.hpp | 27 inst/include/armadillo_bits/Cube_bones.hpp | 19 inst/include/armadillo_bits/Cube_meat.hpp | 130 ++ inst/include/armadillo_bits/GenCube_bones.hpp | 6 inst/include/armadillo_bits/GenCube_meat.hpp | 22 inst/include/armadillo_bits/Gen_bones.hpp | 8 inst/include/armadillo_bits/Gen_meat.hpp | 46 inst/include/armadillo_bits/Mat_bones.hpp | 19 inst/include/armadillo_bits/Mat_meat.hpp | 135 ++ inst/include/armadillo_bits/Row_bones.hpp | 4 inst/include/armadillo_bits/Row_meat.hpp | 27 inst/include/armadillo_bits/SizeCube_bones.hpp | 20 inst/include/armadillo_bits/SizeCube_meat.hpp | 116 + inst/include/armadillo_bits/SizeMat_bones.hpp | 20 inst/include/armadillo_bits/SizeMat_meat.hpp | 110 + inst/include/armadillo_bits/SpBase_bones.hpp | 8 inst/include/armadillo_bits/SpMat_bones.hpp | 20 inst/include/armadillo_bits/SpMat_meat.hpp | 123 ++ inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/field_bones.hpp | 14 inst/include/armadillo_bits/field_meat.hpp | 52 inst/include/armadillo_bits/fn_eye.hpp | 76 + inst/include/armadillo_bits/fn_max.hpp | 22 inst/include/armadillo_bits/fn_min.hpp | 22 inst/include/armadillo_bits/fn_ones.hpp | 84 + inst/include/armadillo_bits/fn_randg.hpp | 48 inst/include/armadillo_bits/fn_randi.hpp | 52 inst/include/armadillo_bits/fn_randn.hpp | 52 inst/include/armadillo_bits/fn_randu.hpp | 52 inst/include/armadillo_bits/fn_reshape.hpp | 38 inst/include/armadillo_bits/fn_resize.hpp | 36 inst/include/armadillo_bits/fn_size.hpp | 46 inst/include/armadillo_bits/fn_speye.hpp | 30 inst/include/armadillo_bits/fn_sprandn.hpp | 30 inst/include/armadillo_bits/fn_sprandu.hpp | 28 inst/include/armadillo_bits/fn_zeros.hpp | 74 + inst/include/armadillo_bits/forward_bones.hpp | 14 inst/include/armadillo_bits/op_clamp_meat.hpp | 35 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 1 inst/include/armadillo_bits/span.hpp | 7 inst/include/armadillo_bits/subview_bones.hpp | 29 inst/include/armadillo_bits/subview_elem1_meat.hpp | 152 +- inst/include/armadillo_bits/subview_elem2_meat.hpp | 98 - inst/include/armadillo_bits/subview_meat.hpp | 1233 ++++++--------------- 54 files changed, 1995 insertions(+), 1351 deletions(-)
Title: Multivariate Probit Models
Description: Tools for estimating multivariate probit models,
calculating conditional and unconditional expectations,
and calculating marginal effects on conditional and unconditional
expectations.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between mvProbit versions 0.1-0 dated 2011-11-13 and 0.1-4 dated 2015-09-03
DESCRIPTION | 18 MD5 | 28 NAMESPACE | 13 R/mvProbitExpInternal.R | 6 R/pmvnormWrap.R | 3 R/print.summary.mvProbitMargEff.R | 7 tests/mvProbitEst.R | 207 + tests/mvProbitEst.Rout.save | 4012 ++++++++++++++----------- tests/mvProbitMargEff2.R |only tests/mvProbitMargEff2.Rout.save |only tests/mvProbitTest.R | 177 - tests/mvProbitTest.Rout.save | 5969 ++++++++++++++++---------------------- tests/mvProbitTest5.R | 71 tests/mvProbitTest5.Rout.save | 4855 ++++++++++++++---------------- tests/pmvnormWrapTest.R | 32 tests/pmvnormWrapTest.Rout.save | 86 16 files changed, 7470 insertions(+), 8014 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it is possible to create and manipulate multivariate network
data with different formats, and there are effective ways available to treat multiple networks
with routines that combine algebraic systems like the partially ordered semigroup or the
semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. As well an algebraic approach for two-mode networks is made
through Galois derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.7 dated 2015-09-01 and 1.7.1 dated 2015-09-03
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ inst/CHANGELOG | 5 +++++ inst/doc/TwoModeNetworks.R | 2 +- inst/doc/TwoModeNetworks.Rnw | 5 +++-- inst/doc/TwoModeNetworks.pdf |binary man/as.signed.Rd | 2 +- man/expos.Rd | 2 +- man/fltr.Rd | 2 +- man/incubs.Rd | 1 + man/multiplex-package.Rd | 4 ++-- man/rel.sys.Rd | 2 +- vignettes/TwoModeNetworks.Rnw | 5 +++-- 13 files changed, 35 insertions(+), 27 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Diff between ggmcmc versions 0.7.1 dated 2015-07-29 and 0.7.2 dated 2015-09-03
DESCRIPTION | 12 +++++++----- MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 19 +++++++++++++++++-- NEWS | 23 +++++++++++++++++++++++ R/functions.R | 6 +++--- R/ggs.R | 17 +++++++++-------- R/ggs_Rhat.R | 12 ++++++------ R/ggs_autocorrelation.R | 4 ++-- R/ggs_caterpillar.R | 5 +++-- R/ggs_compare_partial.R | 2 +- R/ggs_geweke.R | 10 +++++----- R/ggs_histogram.R | 4 ++-- R/ggs_pairs.R | 3 ++- R/ggs_ppmean.R | 2 +- R/ggs_ppsd.R | 2 +- R/ggs_rocplot.R | 4 ++-- R/ggs_running.R | 4 ++-- R/ggs_separation.R | 8 ++++---- R/ggs_traceplot.R | 2 +- R/globals.R | 2 ++ R/help.R | 4 +++- inst/CITATION | 4 ++-- 22 files changed, 119 insertions(+), 72 deletions(-)
Title: Experience Life Tables
Description: Build experience life tables.
Author: Julien Tomas, Frederic Planchet, Wassim Youssef
Maintainer: Wassim Youssef <Wassim.G.Youssef@gmail.com>
Diff between ELT versions 1.3 dated 2014-08-16 and 1.4 dated 2015-09-03
DESCRIPTION | 14 - MD5 | 53 ++--- NAMESPACE | 5 R/S01.R | 210 +++++++++++++-------- R/S11.R | 440 +++++++++++++++++++++++----------------------- R/SDirectory.R | 38 ++- man/AddReference.Rd | 3 man/ComparisonMethods.Rd | 3 man/CompletionA.Rd | 3 man/CompletionB.Rd | 3 man/Dispersion.Rd | 12 - man/ELT-package.Rd | 8 man/FctMethod1.Rd | 3 man/FctMethod2.Rd | 3 man/FctMethod3.Rd | 3 man/FctMethod4_1stPart.Rd | 3 man/FctMethod4_2ndPart.Rd | 3 man/Method1.Rd | 3 man/Method2.Rd | 3 man/Method3.Rd | 3 man/Method4A.Rd | 3 man/Method4B.Rd | 3 man/NoCompletion.Rd |only man/ReadHistory.Rd | 3 man/SurfacePlot.Rd | 3 man/ValidationLevel1.Rd | 3 man/ValidationLevel2.Rd | 3 man/ValidationLevel3.Rd | 3 28 files changed, 456 insertions(+), 381 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-2 dated 2015-08-11 and 0.9-3 dated 2015-09-03
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/dbscan.R | 5 +++-- inst/NEWS | 5 ++++- man/dbscan.Rd | 34 ++++++++++++++++++---------------- src/R_dbscan.cpp | 51 +++++++++++++++++++++++++++++++++++++++------------ src/RcppExports.cpp | 7 ++++--- 8 files changed, 81 insertions(+), 47 deletions(-)
Title: Simulation of Ecological (and Other) Dynamic Systems
Description: An object oriented framework to simulate
ecological (and other) dynamic systems. It can be used for
differential equations, individual-based (or agent-based) and other
models as well. The package helps to organize scenarios (to avoid copy
and paste) and aims to improve readability and usability of code.
Author: Thomas Petzoldt
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between simecol versions 0.8-6 dated 2015-03-19 and 0.8-7 dated 2015-09-03
simecol-0.8-6/simecol/inst/doc/examples/competition.R |only simecol-0.8-7/simecol/DESCRIPTION | 14 simecol-0.8-7/simecol/MD5 | 52 simecol-0.8-7/simecol/NAMESPACE | 91 simecol-0.8-7/simecol/R/aaa_classes.R | 118 simecol-0.8-7/simecol/R/fitOdeModel.R | 149 - simecol-0.8-7/simecol/R/modelFit.R |only simecol-0.8-7/simecol/R/ssqOdeModel.R | 12 simecol-0.8-7/simecol/build/vignette.rds |binary simecol-0.8-7/simecol/data/CA.rda |binary simecol-0.8-7/simecol/data/chemostat.rda |binary simecol-0.8-7/simecol/data/conway.rda |binary simecol-0.8-7/simecol/data/diffusion.rda |binary simecol-0.8-7/simecol/data/lv.rda |binary simecol-0.8-7/simecol/data/lv3.rda |binary simecol-0.8-7/simecol/data/upca.rda |binary simecol-0.8-7/simecol/inst/NEWS | 4 simecol-0.8-7/simecol/inst/doc/a-simecol-introduction.R | 622 ++-- simecol-0.8-7/simecol/inst/doc/a-simecol-introduction.pdf |binary simecol-0.8-7/simecol/inst/doc/b-simecol-howtos.R | 986 +++---- simecol-0.8-7/simecol/inst/doc/b-simecol-howtos.Rnw | 48 simecol-0.8-7/simecol/inst/doc/b-simecol-howtos.pdf |binary simecol-0.8-7/simecol/inst/doc/examples/fitOdeModel/initval.R | 91 simecol-0.8-7/simecol/man/fitOdeModel.Rd | 418 +-- simecol-0.8-7/simecol/man/iteration.Rd | 32 simecol-0.8-7/simecol/man/modelFit-methods.Rd |only simecol-0.8-7/simecol/man/modelFit.Rd |only simecol-0.8-7/simecol/vignettes/b-simecol-howtos.Rnw | 48 simecol-0.8-7/simecol/vignettes/simecol.bib | 1277 +++++----- 29 files changed, 2061 insertions(+), 1901 deletions(-)
Title: Companion to Applied Regression
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 2.0-26 dated 2015-08-06 and 2.1-0 dated 2015-09-03
car-2.0-26/car/man/estimateTransform.Rd |only car-2.1-0/car/DESCRIPTION | 13 - car-2.1-0/car/MD5 | 135 +++++------ car-2.1-0/car/NAMESPACE | 28 +- car-2.1-0/car/NEWS | 6 car-2.1-0/car/R/Anova.R | 3 car-2.1-0/car/R/boxCox.R | 171 ++++++++------ car-2.1-0/car/R/powerTransform.R | 136 ++++++----- car-2.1-0/car/R/skewPower.R |only car-2.1-0/car/build/vignette.rds |binary car-2.1-0/car/data/AMSsurvey.rda |binary car-2.1-0/car/data/Adler.rda |binary car-2.1-0/car/data/Angell.rda |binary car-2.1-0/car/data/Anscombe.rda |binary car-2.1-0/car/data/Baumann.rda |binary car-2.1-0/car/data/Bfox.rda |binary car-2.1-0/car/data/Blackmore.rda |binary car-2.1-0/car/data/Burt.rda |binary car-2.1-0/car/data/CanPop.rda |binary car-2.1-0/car/data/Chile.rda |binary car-2.1-0/car/data/Chirot.rda |binary car-2.1-0/car/data/Cowles.rda |binary car-2.1-0/car/data/Davis.rda |binary car-2.1-0/car/data/DavisThin.rda |binary car-2.1-0/car/data/Depredations.rda |binary car-2.1-0/car/data/Duncan.rda |binary car-2.1-0/car/data/Ericksen.rda |binary car-2.1-0/car/data/Florida.rda |binary car-2.1-0/car/data/Freedman.rda |binary car-2.1-0/car/data/Friendly.rda |binary car-2.1-0/car/data/Ginzberg.rda |binary car-2.1-0/car/data/Greene.rda |binary car-2.1-0/car/data/Guyer.rda |binary car-2.1-0/car/data/Hartnagel.rda |binary car-2.1-0/car/data/Highway1.rda |binary car-2.1-0/car/data/KosteckiDillon.rda |binary car-2.1-0/car/data/Leinhardt.rda |binary car-2.1-0/car/data/LoBD.rda |only car-2.1-0/car/data/Mandel.rda |binary car-2.1-0/car/data/Migration.rda |binary car-2.1-0/car/data/Moore.rda |binary car-2.1-0/car/data/Mroz.rda |binary car-2.1-0/car/data/OBrienKaiser.rda |binary car-2.1-0/car/data/Ornstein.rda |binary car-2.1-0/car/data/Pottery.rda |binary car-2.1-0/car/data/Prestige.rda |binary car-2.1-0/car/data/Quartet.rda |binary car-2.1-0/car/data/Robey.rda |binary car-2.1-0/car/data/SLID.rda |binary car-2.1-0/car/data/Sahlins.rda |binary car-2.1-0/car/data/Salaries.rda |binary car-2.1-0/car/data/Soils.rda |binary car-2.1-0/car/data/States.rda |binary car-2.1-0/car/data/Transact.rda |binary car-2.1-0/car/data/UN.rda |binary car-2.1-0/car/data/USPop.rda |binary car-2.1-0/car/data/Vocab.rda |binary car-2.1-0/car/data/WeightLoss.rda |binary car-2.1-0/car/data/Womenlf.rda |binary car-2.1-0/car/data/Wong.rda |binary car-2.1-0/car/data/Wool.rda |binary car-2.1-0/car/inst/doc/embedding.R | 382 ++++++++++++++++---------------- car-2.1-0/car/inst/doc/embedding.pdf |binary car-2.1-0/car/man/LoBD.Rd |only car-2.1-0/car/man/bcPower.Rd | 40 +-- car-2.1-0/car/man/boxCox.Rd | 171 +++++++------- car-2.1-0/car/man/car-package.Rd | 4 car-2.1-0/car/man/hccm.Rd | 3 car-2.1-0/car/man/powerTransform.Rd | 138 ++++++----- car-2.1-0/car/man/skewPower.Rd |only car-2.1-0/car/man/testTransform.Rd | 15 - 71 files changed, 678 insertions(+), 567 deletions(-)
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Jeffrey Horner [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.3 dated 2015-03-29 and 0.4 dated 2015-09-03
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 11 +++++++++++ R/mime.R | 11 +++++++++++ R/mimemap.R | 27 ++++++++++++++++++--------- README.md | 2 +- 7 files changed, 53 insertions(+), 21 deletions(-)
Title: Static R Code Analysis
Description: Checks adherence to a given style, syntax errors and possible
semantic issues. Supports on the fly checking of R code edited with Emacs,
Vim and Sublime Text.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between lintr versions 0.2.0 dated 2014-12-01 and 0.3.1 dated 2015-09-03
lintr-0.2.0/lintr/inst/flycheck |only lintr-0.3.1/lintr/DESCRIPTION | 16 - lintr-0.3.1/lintr/LICENSE | 2 lintr-0.3.1/lintr/MD5 | 133 +++++--- lintr-0.3.1/lintr/NAMESPACE | 18 - lintr-0.3.1/lintr/R/absolute_paths_linter.R | 3 lintr-0.3.1/lintr/R/assignment_linter.R | 3 lintr-0.3.1/lintr/R/cache.R | 51 ++- lintr-0.3.1/lintr/R/closed_curly_linter.R | 77 ++--- lintr-0.3.1/lintr/R/commas_linter.R | 6 lintr-0.3.1/lintr/R/commented_code_linter.R |only lintr-0.3.1/lintr/R/comments.R |only lintr-0.3.1/lintr/R/exclude.R |only lintr-0.3.1/lintr/R/expect_lint.R | 40 ++ lintr-0.3.1/lintr/R/extract.R |only lintr-0.3.1/lintr/R/get_source_expressions.R | 37 +- lintr-0.3.1/lintr/R/infix_spaces_linter.R | 3 lintr-0.3.1/lintr/R/line_length_linter.R | 3 lintr-0.3.1/lintr/R/lint.R | 149 ++++++---- lintr-0.3.1/lintr/R/methods.R |only lintr-0.3.1/lintr/R/no_tab_linter.R | 3 lintr-0.3.1/lintr/R/object_usage_linter.R | 101 +++--- lintr-0.3.1/lintr/R/objects_linter.R | 98 ++++-- lintr-0.3.1/lintr/R/open_curly_linter.R | 78 ++--- lintr-0.3.1/lintr/R/settings.R |only lintr-0.3.1/lintr/R/single_quotes_linter.R | 5 lintr-0.3.1/lintr/R/spaces_inside_linter.R | 3 lintr-0.3.1/lintr/R/spaces_left_parentheses_linter.R | 3 lintr-0.3.1/lintr/R/trailing_blank_lines_linter.R | 26 - lintr-0.3.1/lintr/R/trailing_whitespace_linter.R | 10 lintr-0.3.1/lintr/R/utils.R | 29 + lintr-0.3.1/lintr/R/zzz.R | 40 ++ lintr-0.3.1/lintr/README.md | 122 ++++++-- lintr-0.3.1/lintr/build/vignette.rds |binary lintr-0.3.1/lintr/inst/doc/creating_linters.html | 4 lintr-0.3.1/lintr/inst/example |only lintr-0.3.1/lintr/inst/syntastic/lintr.vim | 2 lintr-0.3.1/lintr/man/Lint.Rd | 7 lintr-0.3.1/lintr/man/clear_cache.Rd | 4 lintr-0.3.1/lintr/man/default_linters.Rd | 6 lintr-0.3.1/lintr/man/default_settings.Rd |only lintr-0.3.1/lintr/man/exclude.Rd |only lintr-0.3.1/lintr/man/expect_lint.Rd | 6 lintr-0.3.1/lintr/man/expect_lint_free.Rd |only lintr-0.3.1/lintr/man/get_source_expressions.Rd | 2 lintr-0.3.1/lintr/man/lint_file.Rd | 8 lintr-0.3.1/lintr/man/lint_package.Rd | 4 lintr-0.3.1/lintr/man/linters.Rd | 35 +- lintr-0.3.1/lintr/man/lintr.Rd | 6 lintr-0.3.1/lintr/man/parse_exclusions.Rd |only lintr-0.3.1/lintr/man/read_settings.Rd |only lintr-0.3.1/lintr/man/with_defaults.Rd | 7 lintr-0.3.1/lintr/tests/testthat.Rout |only lintr-0.3.1/lintr/tests/testthat/exclusions-test |only lintr-0.3.1/lintr/tests/testthat/knitr_formats |only lintr-0.3.1/lintr/tests/testthat/test-absolute_paths_linter.R | 20 - lintr-0.3.1/lintr/tests/testthat/test-cache.R |only lintr-0.3.1/lintr/tests/testthat/test-closed_curly_linter.R | 22 + lintr-0.3.1/lintr/tests/testthat/test-commas_linter.R | 2 lintr-0.3.1/lintr/tests/testthat/test-commented_code_linter.R |only lintr-0.3.1/lintr/tests/testthat/test-comments.R |only lintr-0.3.1/lintr/tests/testthat/test-error.R | 5 lintr-0.3.1/lintr/tests/testthat/test-exclusions.R |only lintr-0.3.1/lintr/tests/testthat/test-infix_spaces_linter.R | 1 lintr-0.3.1/lintr/tests/testthat/test-knitr_formats.R |only lintr-0.3.1/lintr/tests/testthat/test-methods.R |only lintr-0.3.1/lintr/tests/testthat/test-multiple_dots_linter.R | 10 lintr-0.3.1/lintr/tests/testthat/test-object_camel_case_linter.R | 16 - lintr-0.3.1/lintr/tests/testthat/test-object_snake_case_linter.R | 16 - lintr-0.3.1/lintr/tests/testthat/test-object_usage_linter.R | 11 lintr-0.3.1/lintr/tests/testthat/test-open_curly_linter.R | 23 - lintr-0.3.1/lintr/tests/testthat/test-rstudio_markers.R |only lintr-0.3.1/lintr/tests/testthat/test-settings.R |only lintr-0.3.1/lintr/tests/testthat/test-single_quotes_linter.R | 3 lintr-0.3.1/lintr/tests/testthat/test-spaces_inside_linter.R | 1 lintr-0.3.1/lintr/tests/testthat/test-spaces_left_parentheses_linter.R | 2 lintr-0.3.1/lintr/tests/testthat/test-trailing_whitespace_linter.R | 9 77 files changed, 854 insertions(+), 437 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 4.3-5 dated 2015-07-03 and 4.3-6 dated 2015-09-03
gamlss-4.3-5/gamlss/R/stepGAICall-03-10-13.R |only gamlss-4.3-6/gamlss/DESCRIPTION | 8 +- gamlss-4.3-6/gamlss/MD5 | 25 +++---- gamlss-4.3-6/gamlss/NAMESPACE | 2 gamlss-4.3-6/gamlss/R/DropAddStepGAIC-Parallel.R | 76 ++++++++++++++------- gamlss-4.3-6/gamlss/R/gamlss.R | 21 +++++- gamlss-4.3-6/gamlss/R/pb_goingtozero.R |only gamlss-4.3-6/gamlss/R/re_gamlss_lme.R | 3 gamlss-4.3-6/gamlss/R/stepGAICAll-A-parallel.R |only gamlss-4.3-6/gamlss/R/term.plot-new.R | 72 ++++++++++++++++---- gamlss-4.3-6/gamlss/inst/doc/NEWS.txt | 12 +++ gamlss-4.3-6/gamlss/man/gamlss.ps.Rd | 3 gamlss-4.3-6/gamlss/man/ps.Rd | 80 ++++++++++++++++++++--- gamlss-4.3-6/gamlss/man/random.Rd | 2 gamlss-4.3-6/gamlss/man/stepGAIC.Rd | 4 - 15 files changed, 240 insertions(+), 68 deletions(-)
Title: Data Analysis and Graphics Data and Functions
Description: Various data sets used in examples and exercises in the
book Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data
Analysis and Graphics Using R".
Author: John H. Maindonald and W. John Braun
Maintainer: W. John Braun <braun@stats.uwo.ca>
Diff between DAAG versions 1.20 dated 2014-04-30 and 1.22 dated 2015-09-03
DAAG-1.20/DAAG/man/bomregions2012.Rd |only DAAG-1.20/DAAG/man/cps2.Rd |only DAAG-1.20/DAAG/man/cps3.Rd |only DAAG-1.20/DAAG/man/overlap.density.Rd |only DAAG-1.22/DAAG/DESCRIPTION | 13 +- DAAG-1.22/DAAG/MD5 | 97 ++++++++--------- DAAG-1.22/DAAG/NAMESPACE | 17 ++ DAAG-1.22/DAAG/NEWS | 16 ++ DAAG-1.22/DAAG/R/CVlm.R | 48 ++++---- DAAG-1.22/DAAG/R/bestset.noise.R | 4 DAAG-1.22/DAAG/R/bestsetNoise.R | 4 DAAG-1.22/DAAG/R/bsnCV.R | 4 DAAG-1.22/DAAG/R/bsnOpt.R | 4 DAAG-1.22/DAAG/R/bsnVaryNvar.R | 12 +- DAAG-1.22/DAAG/R/compareTreecalcs.R | 15 +- DAAG-1.22/DAAG/R/cv.lm.R | 48 ++++---- DAAG-1.22/DAAG/R/datafile.R | 4 DAAG-1.22/DAAG/R/errorsINseveral.R | 10 - DAAG-1.22/DAAG/R/errorsINx.R | 28 ++-- DAAG-1.22/DAAG/R/excessRisk.R | 2 DAAG-1.22/DAAG/R/multilap.R | 32 ++--- DAAG-1.22/DAAG/R/onet.R | 44 +++---- DAAG-1.22/DAAG/R/onetPermutation.R | 44 +++---- DAAG-1.22/DAAG/R/overlap.density.R | 131 +++++++++++++++------- DAAG-1.22/DAAG/R/overlapDensity.R | 188 ++++++++++++++++++--------------- DAAG-1.22/DAAG/R/plotSimDiags.R | 30 ++--- DAAG-1.22/DAAG/R/qreference.R | 4 DAAG-1.22/DAAG/R/sampdist.R | 16 +- DAAG-1.22/DAAG/R/show.colors.R | 7 - DAAG-1.22/DAAG/R/twot.R | 48 ++++---- DAAG-1.22/DAAG/R/twotPermutation.R | 2 DAAG-1.22/DAAG/build/vignette.rds |binary DAAG-1.22/DAAG/data/cps3.rda |only DAAG-1.22/DAAG/data/hurricNamed.rda |only DAAG-1.22/DAAG/man/CVlm.Rd | 38 +++--- DAAG-1.22/DAAG/man/bomregions.Rd | 54 ++++----- DAAG-1.22/DAAG/man/compareTreecalcs.Rd | 4 DAAG-1.22/DAAG/man/cps1.Rd | 9 + DAAG-1.22/DAAG/man/datafile.Rd | 5 DAAG-1.22/DAAG/man/excessRisk.Rd | 7 - DAAG-1.22/DAAG/man/greatLakes.Rd | 4 DAAG-1.22/DAAG/man/grog.Rd | 7 - DAAG-1.22/DAAG/man/hurricNamed.Rd |only DAAG-1.22/DAAG/man/moths.Rd | 11 + DAAG-1.22/DAAG/man/multilap.Rd | 4 DAAG-1.22/DAAG/man/nassCDS.Rd | 5 DAAG-1.22/DAAG/man/nasshead.Rd | 10 - DAAG-1.22/DAAG/man/nihills.Rd | 10 - DAAG-1.22/DAAG/man/onet.permutation.Rd | 3 DAAG-1.22/DAAG/man/onetPermutation.Rd | 3 DAAG-1.22/DAAG/man/overlapDensity.Rd | 44 +++++-- DAAG-1.22/DAAG/man/twot.permutation.Rd | 3 DAAG-1.22/DAAG/man/twotPermutation.Rd | 3 53 files changed, 615 insertions(+), 481 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 0.10-6 dated 2015-01-27 and 0.11-0 dated 2015-09-03
unmarked-0.10-6/unmarked/data/Switzerland.txt.gz |only unmarked-0.11-0/unmarked/DESCRIPTION | 16 +- unmarked-0.11-0/unmarked/MD5 | 87 ++++++----- unmarked-0.11-0/unmarked/NAMESPACE | 16 +- unmarked-0.11-0/unmarked/NEWS | 21 ++ unmarked-0.11-0/unmarked/R/boot.R | 120 ++++++++++++++++ unmarked-0.11-0/unmarked/R/gdistsamp.R | 2 unmarked-0.11-0/unmarked/R/getDesign.R | 76 +++++----- unmarked-0.11-0/unmarked/R/gmultmix.R | 1 unmarked-0.11-0/unmarked/R/occuPEN.R |only unmarked-0.11-0/unmarked/R/pcountOpen.R | 22 +- unmarked-0.11-0/unmarked/R/ranef.R | 30 +++- unmarked-0.11-0/unmarked/R/unmarkedFit.R | 105 ++++++++------ unmarked-0.11-0/unmarked/R/unmarkedFrame.R | 6 unmarked-0.11-0/unmarked/build/vignette.rds |binary unmarked-0.11-0/unmarked/data/Switzerland.RData |only unmarked-0.11-0/unmarked/data/birds.RData |binary unmarked-0.11-0/unmarked/data/crossbill.rda |binary unmarked-0.11-0/unmarked/data/cruz.rda |binary unmarked-0.11-0/unmarked/data/frogs.RData |binary unmarked-0.11-0/unmarked/data/gf.RData |binary unmarked-0.11-0/unmarked/data/issj.rda |binary unmarked-0.11-0/unmarked/data/jay.rda |only unmarked-0.11-0/unmarked/data/linetran.RData |binary unmarked-0.11-0/unmarked/data/mallard.RData |binary unmarked-0.11-0/unmarked/data/masspcru.RData |binary unmarked-0.11-0/unmarked/data/ovendata.RData |binary unmarked-0.11-0/unmarked/data/pointtran.RData |binary unmarked-0.11-0/unmarked/inst/doc/cap-recap.pdf |binary unmarked-0.11-0/unmarked/inst/doc/colext.pdf |binary unmarked-0.11-0/unmarked/inst/doc/distsamp.pdf |binary unmarked-0.11-0/unmarked/inst/doc/spp-dist.Rnw | 4 unmarked-0.11-0/unmarked/inst/doc/spp-dist.pdf |binary unmarked-0.11-0/unmarked/inst/doc/unmarked.pdf |binary unmarked-0.11-0/unmarked/inst/unitTests/runit.occuPEN.R |only unmarked-0.11-0/unmarked/man/computeMPLElambdas.Rd |only unmarked-0.11-0/unmarked/man/jay.Rd |only unmarked-0.11-0/unmarked/man/linearComb-methods.Rd | 2 unmarked-0.11-0/unmarked/man/multinomPois.Rd | 2 unmarked-0.11-0/unmarked/man/nonparboot-methods.Rd | 10 + unmarked-0.11-0/unmarked/man/occuPEN.Rd |only unmarked-0.11-0/unmarked/man/occuPEN_CV.Rd |only unmarked-0.11-0/unmarked/man/ranef-methods.Rd | 4 unmarked-0.11-0/unmarked/man/unmarked-package.Rd | 5 unmarked-0.11-0/unmarked/man/unmarkedFit-class.Rd | 8 - unmarked-0.11-0/unmarked/src/Makevars.win | 14 - unmarked-0.11-0/unmarked/src/nll_occuPEN.cpp |only unmarked-0.11-0/unmarked/src/nll_occuPEN.h |only unmarked-0.11-0/unmarked/src/nll_pcountOpen.cpp | 8 - unmarked-0.11-0/unmarked/vignettes/spp-dist.Rnw | 4 50 files changed, 384 insertions(+), 179 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: Matt Pennell <mwpennell@gmail.com>
Diff between geiger versions 2.0.3 dated 2014-05-16 and 2.0.5 dated 2015-09-03
ChangeLog | 12 DESCRIPTION | 17 MD5 | 40 - NAMESPACE | 34 + R/TESTING.R | 1202 ++++++++++++++++++++++++------------------------- R/congruify.R | 110 ++-- R/diversitree.R | 22 R/gbresolve.R | 144 ++--- R/mecca.R | 851 +++++++++++++++++----------------- R/medusa.R | 190 +++---- R/plotting.R | 218 ++++---- R/simulation.R | 2 R/traits.R | 318 ++++++------ R/utilities-misc.R | 279 +++++------ R/utilities-phylo.R | 437 +++++++++-------- man/drop.extinct.Rd | 32 - man/fitContinuous.Rd | 10 man/fitDiscrete.Rd | 12 man/geiger-internal.Rd | 7 man/mecca.Rd | 7 man/sim.char.Rd | 2 21 files changed, 1993 insertions(+), 1953 deletions(-)
Title: Tools for Assessing Estimability of Linear Predictions
Description: Provides tools for determining estimability of linear functions of regression coefficients,
and 'epredict' methods that handle non-estimable cases correctly.
Author: Russell V. Lenth
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between estimability versions 1.1 dated 2015-02-12 and 1.1-1 dated 2015-09-03
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 11 +++++++++++ inst/NEWS | 3 +++ 4 files changed, 22 insertions(+), 8 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-2 dated 2015-06-30 and 1.1-3 dated 2015-09-03
DESCRIPTION | 8 - MD5 | 18 +-- R/tsp_two_opt.R | 3 build/vignette.rds |binary data/USCA312.rda |binary data/USCA312_map.rda |binary data/USCA50.rda |binary inst/NEWS | 8 + inst/doc/TSP.pdf |binary src/two_opt.c | 281 ++++++++++++++++++++++++++++++++++++--------------- 10 files changed, 220 insertions(+), 98 deletions(-)
Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth <russell-lenth@uiowa.edu>
Diff between rsm versions 2.7-2 dated 2015-05-12 and 2.7-3 dated 2015-09-03
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 32 ++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary 8 files changed, 47 insertions(+), 11 deletions(-)
Title: Parametric Frailty Models
Description: Fits Parametric Frailty Models by maximum marginal likelihood.
Possible baseline hazards: Weibull, inverse Weibull, exponential, Gompertz, lognormal and loglogistic.
Possible Frailty distributions: gamma, inverse Gaussian, positive stable and lognormal.
Author: Federico Rotolo <federico.rotolo@gustaveroussy.fr>
and Marco Munda <marco.munda@arlenda.com>
Maintainer: Federico Rotolo <federico.rotolo@gustaveroussy.fr>
Diff between parfm versions 2.5.8 dated 2015-06-08 and 2.5.10 dated 2015-09-03
parfm-2.5.10/parfm/DESCRIPTION | 15 parfm-2.5.10/parfm/MD5 | 37 - parfm-2.5.10/parfm/NAMESPACE | 7 parfm-2.5.10/parfm/NEWS | 5 parfm-2.5.10/parfm/R/frailtydistros.R | 525 +++++++++++++-------------- parfm-2.5.10/parfm/R/parfm.R | 6 parfm-2.5.10/parfm/data/asthma.RData |binary parfm-2.5.10/parfm/data/culling.RData |binary parfm-2.5.10/parfm/data/datalist | 16 parfm-2.5.10/parfm/data/diagnosis.RData |binary parfm-2.5.10/parfm/data/ecf.RData |binary parfm-2.5.10/parfm/data/insem.RData |binary parfm-2.5.10/parfm/data/insemtvc.RData |binary parfm-2.5.10/parfm/data/mastitis.RData |binary parfm-2.5.10/parfm/data/reconstitution.RData |binary parfm-2.5.10/parfm/man/ci.parfm.Rd | 2 parfm-2.5.10/parfm/man/predict.parfm.Rd | 2 parfm-2.5.10/parfm/man/select.parfm.Rd | 3 parfm-2.5.10/parfm/man/tau.Rd | 2 parfm-2.5.8/parfm/tests/Rplots.pdf |only 20 files changed, 316 insertions(+), 304 deletions(-)
Title: Factors with Levels
Description: Provides an extension to factors called 'lfactor' that are similar to factors but allow users to refer to 'lfactor' levels by either the level or the label.
Author: Paul Bailey [aut, cre]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between lfactors versions 0.4.0 dated 2015-04-27 and 0.5.3 dated 2015-09-03
DESCRIPTION | 11 ++++++----- MD5 | 20 +++++++++++++------- NAMESPACE | 5 +++++ R/Ops.lfactor.R | 2 -- R/all.R | 2 ++ R/assign.R |only R/droplevels.R |only R/lfactor.R | 1 + R/relevel.R |only R/subset.R | 11 +++++++++-- R/zzz.R | 25 +++++++++++++++---------- inst |only tests |only 13 files changed, 51 insertions(+), 26 deletions(-)
Title: Simple Component Analysis
Description: Simple Component Analysis (SCA) often provides much more
interpretable components than Principal Components (PCA) while still
representing much of the variability in the data.
Author: Valentin Rousson <rousson@ifspm.unizh.ch> and Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sca versions 0.8-9 dated 2012-09-01 and 0.9-0 dated 2015-09-02
sca-0.8-9/sca/Done-MM |only sca-0.8-9/sca/INDEX |only sca-0.8-9/sca/INDEX-manual |only sca-0.9-0/sca/DESCRIPTION | 15 ++++++++------- sca-0.9-0/sca/MD5 | 8 +++----- sca-0.9-0/sca/NAMESPACE | 4 ++++ sca-0.9-0/sca/tests/artif3.Rout-64b |only 7 files changed, 15 insertions(+), 12 deletions(-)
Title: Computing, Fitting and Validating the PPS Distribution
Description: Statistical functions to describe a Pareto Positive Stable (PPS)
distribution and fit it to real data. Graphical and statistical tools to
validate the fits are included.
Author: Antonio Jose Saez-Castillo [aut, cre],
Faustino Prieto [aut],
Jose Maria Sarabia [aut]
Maintainer: Antonio Jose Saez-Castillo <ajsaez@ujaen.es>
Diff between ParetoPosStable versions 1.0.3 dated 2014-10-22 and 1.1 dated 2015-09-02
ParetoPosStable-1.0.3/ParetoPosStable/inst |only ParetoPosStable-1.0.3/ParetoPosStable/man/ParetoPosStable-package.Rd |only ParetoPosStable-1.1/ParetoPosStable/DESCRIPTION | 15 ParetoPosStable-1.1/ParetoPosStable/MD5 | 43 ParetoPosStable-1.1/ParetoPosStable/NAMESPACE | 49 ParetoPosStable-1.1/ParetoPosStable/R/PPS.fit.R |only ParetoPosStable-1.1/ParetoPosStable/R/ParetoPosStable.R | 583 ---------- ParetoPosStable-1.1/ParetoPosStable/R/coef.PPSfit.R |only ParetoPosStable-1.1/ParetoPosStable/R/forbes400.R |only ParetoPosStable-1.1/ParetoPosStable/R/logLik.PPSfit.R |only ParetoPosStable-1.1/ParetoPosStable/R/managing.R |only ParetoPosStable-1.1/ParetoPosStable/R/pareto.fit.R |only ParetoPosStable-1.1/ParetoPosStable/R/plot.PPSfit.R |only ParetoPosStable-1.1/ParetoPosStable/R/print.PPSfit.R |only ParetoPosStable-1.1/ParetoPosStable/R/se.R |only ParetoPosStable-1.1/ParetoPosStable/R/turkey.R |only ParetoPosStable-1.1/ParetoPosStable/R/validation.R |only ParetoPosStable-1.1/ParetoPosStable/man/GoF.Rd | 38 ParetoPosStable-1.1/ParetoPosStable/man/PPS.fit.Rd | 54 ParetoPosStable-1.1/ParetoPosStable/man/ParetoPosStable.Rd |only ParetoPosStable-1.1/ParetoPosStable/man/coef.PPSfit.Rd | 24 ParetoPosStable-1.1/ParetoPosStable/man/dPPS.Rd | 63 - ParetoPosStable-1.1/ParetoPosStable/man/forbes400.Rd | 33 ParetoPosStable-1.1/ParetoPosStable/man/logLik.PPSfit.Rd | 28 ParetoPosStable-1.1/ParetoPosStable/man/pareto.fit.Rd | 27 ParetoPosStable-1.1/ParetoPosStable/man/plot.PPSfit.Rd | 48 ParetoPosStable-1.1/ParetoPosStable/man/print.PPSfit.Rd | 27 ParetoPosStable-1.1/ParetoPosStable/man/se.Rd | 42 ParetoPosStable-1.1/ParetoPosStable/man/turkey.Rd | 35 29 files changed, 322 insertions(+), 787 deletions(-)
More information about ParetoPosStable at CRAN
Permanent link
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.3.4 dated 2015-08-09 and 1.4 dated 2015-09-02
NAM-1.3.4/NAM/R/report.R |only NAM-1.3.4/NAM/man/report.Rd |only NAM-1.4/NAM/DESCRIPTION | 8 NAM-1.4/NAM/MD5 | 30 +- NAM-1.4/NAM/R/RcppExports.R | 70 ++--- NAM-1.4/NAM/R/gibbs.R | 533 ++++++++++++++++++++-------------------- NAM-1.4/NAM/R/gwas.R | 52 +++ NAM-1.4/NAM/R/gwas2.R | 50 ++- NAM-1.4/NAM/R/manhattan.R | 84 ++++-- NAM-1.4/NAM/R/snpQC.R | 111 ++++++++ NAM-1.4/NAM/inst |only NAM-1.4/NAM/man/Internals.Rd | 1 NAM-1.4/NAM/man/Manhattan.Rd |only NAM-1.4/NAM/man/NAM-package.Rd | 66 ++-- NAM-1.4/NAM/man/gibbs.Rd | 178 ++++++------- NAM-1.4/NAM/man/gwas.Rd | 15 - NAM-1.4/NAM/man/snpQC.Rd | 2 NAM-1.4/NAM/src/RcppExports.cpp | 150 ++++------- 18 files changed, 777 insertions(+), 573 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.20 dated 2015-08-29 and 2.20-2 dated 2015-09-02
DESCRIPTION | 7 +++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ R/aovlist-support.R | 26 ++++++++++++++++++-------- R/rbind.R | 9 +++++++++ R/ref.grid.R | 3 +++ inst/NEWS | 6 ++++++ inst/doc/extending.R | 1 - inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 1 - inst/doc/using-lsmeans.pdf |binary man/lsmeans-package.Rd | 1 + tests/tests1.Rout.save | 11 +++++++++-- 13 files changed, 63 insertions(+), 28 deletions(-)
More information about IalsaSynthesis at CRAN
Permanent link
Title: Robust Geostatistical Analysis of Spatial Data
Description: The georob package provides functions for efficiently fitting
linear models with spatially correlated errors by robust and
Gaussian (Restricted) Maximum Likelihood and for computing robust
and customary point and block external-drift kriging predictions,
along with utility functions for variogram modelling
in ad-hoc geostatistical analyses, model building, model evaluation
by cross-validation and for unbiased back-transformation of kriging
predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.1-5 dated 2014-08-28 and 0.2-1 dated 2015-09-02
georob-0.1-5/georob/man/georob.control.Rd |only georob-0.2-1/georob/ChangeLog | 105 georob-0.2-1/georob/DESCRIPTION | 26 georob-0.2-1/georob/MD5 | 57 georob-0.2-1/georob/NAMESPACE | 101 georob-0.2-1/georob/NEWS | 1 georob-0.2-1/georob/R/georob.S3methods.R | 874 +++-- georob-0.2-1/georob/R/georob.cv.R | 320 +- georob-0.2-1/georob/R/georob.exported.functions.R | 687 ++-- georob-0.2-1/georob/R/georob.lgnpp.R | 24 georob-0.2-1/georob/R/georob.predict.R | 1974 +++++++----- georob-0.2-1/georob/R/georob.private.functions.R | 3520 +++++++++++----------- georob-0.2-1/georob/R/variogram.R | 133 georob-0.2-1/georob/demo/georob_example.R | 24 georob-0.2-1/georob/man/S3methods.georob.Rd | 17 georob-0.2-1/georob/man/compress.Rd | 2 georob-0.2-1/georob/man/control.georob.Rd |only georob-0.2-1/georob/man/cv.georob.Rd | 34 georob-0.2-1/georob/man/fit.variogram.model.Rd | 68 georob-0.2-1/georob/man/georob-package.Rd | 128 georob-0.2-1/georob/man/georob.Rd | 162 - georob-0.2-1/georob/man/georobModelBuilding.Rd | 24 georob-0.2-1/georob/man/georobObject.Rd | 149 georob-0.2-1/georob/man/internal.functions.Rd | 103 georob-0.2-1/georob/man/lgnpp.Rd | 112 georob-0.2-1/georob/man/plot.georob.Rd | 6 georob-0.2-1/georob/man/pmm.Rd | 42 georob-0.2-1/georob/man/predict.georob.Rd | 33 georob-0.2-1/georob/man/profilelogLik.Rd |only georob-0.2-1/georob/man/sample.variogram.Rd | 22 georob-0.2-1/georob/man/validate.predictions.Rd | 55 31 files changed, 5203 insertions(+), 3600 deletions(-)
Title: Functional Programming in R
Description: Extends functional programming in R by
providing support to the usual higher order functional
suspects (Map, Reduce, Filter, etc.).
Author: Paul Hendricks [aut, cre]
Maintainer: Paul Hendricks <paul.hendricks.2013@owu.edu>
Diff between functools versions 0.1.0 dated 2015-07-23 and 0.2.0 dated 2015-09-02
functools-0.1.0/functools/R/Failwith.R |only functools-0.1.0/functools/R/Finder.R |only functools-0.1.0/functools/R/IterateUntil.R |only functools-0.1.0/functools/man/Failwith.Rd |only functools-0.1.0/functools/man/Finder.Rd |only functools-0.1.0/functools/man/IterateUntil.Rd |only functools-0.1.0/functools/tests/testthat/test-Curry.R |only functools-0.1.0/functools/tests/testthat/test-Failwith.R |only functools-0.1.0/functools/tests/testthat/test-False.R |only functools-0.1.0/functools/tests/testthat/test-Finder.R |only functools-0.1.0/functools/tests/testthat/test-Identity.R |only functools-0.1.0/functools/tests/testthat/test-IterateUntil.R |only functools-0.1.0/functools/tests/testthat/test-LogicalOperators.R |only functools-0.1.0/functools/tests/testthat/test-Max.R |only functools-0.1.0/functools/tests/testthat/test-Min.R |only functools-0.1.0/functools/tests/testthat/test-Na.R |only functools-0.1.0/functools/tests/testthat/test-Null.R |only functools-0.1.0/functools/tests/testthat/test-Plucker.R |only functools-0.1.0/functools/tests/testthat/test-Repeat.R |only functools-0.1.0/functools/tests/testthat/test-Repeatedly.R |only functools-0.1.0/functools/tests/testthat/test-Splat.R |only functools-0.1.0/functools/tests/testthat/test-True.R |only functools-0.1.0/functools/tests/testthat/test-Withdraw.R |only functools-0.2.0/functools/DESCRIPTION | 12 functools-0.2.0/functools/MD5 | 132 +++++----- functools-0.2.0/functools/NAMESPACE | 11 functools-0.2.0/functools/R/All.R | 42 +-- functools-0.2.0/functools/R/Always.R | 12 functools-0.2.0/functools/R/Andify.R | 9 functools-0.2.0/functools/R/Any.R | 42 +-- functools-0.2.0/functools/R/Apply.R | 12 functools-0.2.0/functools/R/Best.R | 25 - functools-0.2.0/functools/R/Compact.R | 11 functools-0.2.0/functools/R/Compose.R | 19 - functools-0.2.0/functools/R/Existy.R | 6 functools-0.2.0/functools/R/Fail-With.R |only functools-0.2.0/functools/R/Lapply.R | 10 functools-0.2.0/functools/R/Mapply.R |only functools-0.2.0/functools/R/Memoise.R |only functools-0.2.0/functools/R/Orify.R | 13 functools-0.2.0/functools/R/Partial.R |only functools-0.2.0/functools/R/Reduce-Right.R |only functools-0.2.0/functools/R/Sapply.R |only functools-0.2.0/functools/R/Tapply.R |only functools-0.2.0/functools/R/Truthy.R | 6 functools-0.2.0/functools/R/Vapply.R |only functools-0.2.0/functools/R/functools.R | 4 functools-0.2.0/functools/README.md | 22 - functools-0.2.0/functools/man/All.Rd | 38 +- functools-0.2.0/functools/man/Always.Rd | 10 functools-0.2.0/functools/man/Andify.Rd | 4 functools-0.2.0/functools/man/Any.Rd | 38 +- functools-0.2.0/functools/man/Apply.Rd | 14 - functools-0.2.0/functools/man/Best.Rd | 24 - functools-0.2.0/functools/man/Compact.Rd | 11 functools-0.2.0/functools/man/Compose.Rd | 16 - functools-0.2.0/functools/man/Existy.Rd | 4 functools-0.2.0/functools/man/Fail_With.Rd |only functools-0.2.0/functools/man/Lapply.Rd | 12 functools-0.2.0/functools/man/Mapply.Rd |only functools-0.2.0/functools/man/Memoise.Rd |only functools-0.2.0/functools/man/Orify.Rd | 8 functools-0.2.0/functools/man/Partial.Rd |only functools-0.2.0/functools/man/Reduce_Right.Rd |only functools-0.2.0/functools/man/Sapply.Rd |only functools-0.2.0/functools/man/Tapply.Rd |only functools-0.2.0/functools/man/Truthy.Rd | 4 functools-0.2.0/functools/man/Vapply.Rd |only functools-0.2.0/functools/man/functools.Rd | 4 functools-0.2.0/functools/tests/testthat/test-All.R | 30 +- functools-0.2.0/functools/tests/testthat/test-Always.R | 15 - functools-0.2.0/functools/tests/testthat/test-Andify.R | 31 ++ functools-0.2.0/functools/tests/testthat/test-Any.R | 31 +- functools-0.2.0/functools/tests/testthat/test-Apply.R | 21 + functools-0.2.0/functools/tests/testthat/test-Best.R | 19 + functools-0.2.0/functools/tests/testthat/test-Compact.R | 28 +- functools-0.2.0/functools/tests/testthat/test-Compose.R | 21 + functools-0.2.0/functools/tests/testthat/test-Constants.R |only functools-0.2.0/functools/tests/testthat/test-Existy.R | 22 + functools-0.2.0/functools/tests/testthat/test-Fail-With.R |only functools-0.2.0/functools/tests/testthat/test-Lapply.R | 21 + functools-0.2.0/functools/tests/testthat/test-Mapply.R |only functools-0.2.0/functools/tests/testthat/test-Memoise.R |only functools-0.2.0/functools/tests/testthat/test-Orify.R | 15 - functools-0.2.0/functools/tests/testthat/test-Partial.R |only functools-0.2.0/functools/tests/testthat/test-Reduce-Right.R |only functools-0.2.0/functools/tests/testthat/test-Reject.R | 18 + functools-0.2.0/functools/tests/testthat/test-Sapply.R |only functools-0.2.0/functools/tests/testthat/test-Tapply.R |only functools-0.2.0/functools/tests/testthat/test-Truthy.R | 23 + functools-0.2.0/functools/tests/testthat/test-Vapply.R |only 91 files changed, 525 insertions(+), 345 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.6 dated 2015-05-22 and 1.7 dated 2015-09-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/coneproj.R | 2 +- man/coneA.Rd | 1 + src/coneproj.cpp | 9 ++++++--- 6 files changed, 19 insertions(+), 13 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.10 dated 2015-07-01 and 0.9.18 dated 2015-09-02
DESCRIPTION | 7 +- MD5 | 76 +++++++++++++++-------------- NAMESPACE | 4 + NEWS | 108 +++++++++++++++++++++++++++--------------- R/AllClasses.R | 5 + R/GitFunctions.R | 51 +++++++++++++++++-- R/SwitchrParam.R | 8 +-- R/Utilities.R | 88 +++++++++++++++++++++++++++------- R/accessors.R | 34 +++++++++++++ R/annotateDESCs.R | 70 +++++++++++++-------------- R/biocManifest.R | 13 +++-- R/biocversion.R | 8 ++- R/conditionalCode.R | 9 +-- R/crandbtmp.R | 5 - R/flushSession.R | 49 +++++++++++++++---- R/lazyRepo.R | 12 +--- R/loadManifest.R | 8 ++- R/makeCheckout.R |only R/makePkgSourceDir-methods.R | 53 ++++++++++++-------- R/methods.R | 10 +-- R/retrievePkgVersion.R | 57 +++++++++++++++++----- R/saveManifest.R | 10 +-- build/vignette.rds |binary inst/doc/switchrvign.R | 35 +++++++------ inst/doc/switchrvign.Rnw | 15 +++-- inst/doc/switchrvign.pdf |binary inst/examples/localcheckout.R |only inst/examples/sessionInfo.R | 10 +-- inst/gamvsmgcvtest.R | 4 + inst/localcheckoutest.R | 17 ++++++ inst/talks/JSM2015.org |only inst/talks/JSM2015.pdf |only man/BiocSVNManifest.Rd | 4 - man/SwitchrParam.Rd | 5 + man/findPkgDir.Rd | 4 - man/gotoVersCommit.Rd | 5 + man/makePkgCheckout.Rd |only man/normalizePath2.Rd | 5 + man/shell_timing.Rd |only man/switchrDontUnload.Rd | 3 - tests/winpath.R | 100 ++++++++++++++++++++++++++++++++++++++ vignettes/switchrvign.Rnw | 15 +++-- 42 files changed, 644 insertions(+), 263 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written based on an accompanying 'RESTful' API.
Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more.
This package also supports experimental access to http://www.sealifebase.org data, which contains nearly
200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.1 dated 2015-08-15 and 2.0.2 dated 2015-09-01
DESCRIPTION | 6 - MD5 | 109 ++++++++++++------------ NAMESPACE | 2 NEWS | 5 + build/vignette.rds |binary inst/doc/tutorial.R |only inst/doc/tutorial.Rmd | 128 ++++++++++++++++++++++++++++ inst/doc/tutorial.html | 133 +++++++++++++++++++++++++++++- man/common_names.Rd | 2 man/common_to_sci.Rd | 2 man/diet.Rd | 2 man/distribution.Rd | 2 man/docs.Rd | 2 man/ecology.Rd | 2 man/ecosystem.Rd | 2 man/faoareas.Rd | 2 man/fecundity.Rd | 2 man/fishbase.Rd | 2 man/fooditems.Rd | 2 man/heartbeat.Rd | 2 man/introductions.Rd | 2 man/length_freq.Rd | 2 man/length_length.Rd | 2 man/length_weight.Rd | 2 man/list_fields.Rd | 2 man/load_taxa.Rd | 2 man/maturity.Rd | 2 man/morphology.Rd | 2 man/morphometrics.Rd | 2 man/occurrence.Rd | 2 man/oxygen.Rd | 2 man/ping.Rd | 2 man/popchar.Rd | 2 man/popgrowth.Rd | 2 man/popqb.Rd | 2 man/predators.Rd | 2 man/ration.Rd | 2 man/reproduction.Rd | 2 man/rfishbase-package.Rd | 2 man/sci_to_common.Rd | 2 man/sealifebase.Rd | 2 man/spawning.Rd | 2 man/species.Rd | 2 man/species_fields.Rd | 2 man/species_list.Rd | 2 man/species_names.Rd | 2 man/speed.Rd | 2 man/stocks.Rd | 2 man/swimming.Rd | 2 man/synonyms.Rd | 2 man/validate_names.Rd | 2 tests/testthat/helper_rfishbase.R | 2 tests/testthat/test_list_fields.R | 3 tests/testthat/test_load_taxa.R | 2 tests/testthat/test_population_dynamics.R | 3 vignettes/tutorial.Rmd | 2 56 files changed, 374 insertions(+), 107 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7 dated 2015-08-01 and 1.7.1 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/rcbalance-internal.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.4 dated 2015-08-27 and 0.5 dated 2015-09-01
nhanesA-0.4/nhanesA/R/sysdata.rda |only nhanesA-0.5/nhanesA/DESCRIPTION | 10 - nhanesA-0.5/nhanesA/INDEX | 2 nhanesA-0.5/nhanesA/MD5 | 19 +- nhanesA-0.5/nhanesA/NAMESPACE | 6 nhanesA-0.5/nhanesA/R/nhanes.R | 199 +++++++++++++++++------------ nhanesA-0.5/nhanesA/man/nhanes.Rd | 21 +-- nhanesA-0.5/nhanesA/man/nhanesAttr.Rd | 13 - nhanesA-0.5/nhanesA/man/nhanesTableVars.Rd | 19 +- nhanesA-0.5/nhanesA/man/nhanesTables.Rd | 19 +- nhanesA-0.5/nhanesA/man/nhanesTranslate.Rd | 25 +-- 11 files changed, 186 insertions(+), 147 deletions(-)
Title: Multi-Group Sparse Discriminant Analysis
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of 'I.Gaynanova, J.Booth and M.Wells (2015), Simultaneous sparse estimation of canonical vectors in the p>>N setting'.
Author: Irina Gaynanova
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between MGSDA versions 1.1 dated 2014-08-28 and 1.2 dated 2015-09-01
MGSDA-1.1/MGSDA/R/constructD.R |only MGSDA-1.1/MGSDA/R/solveVcoordf2.R |only MGSDA-1.1/MGSDA/R/solveVcoordf2C.R |only MGSDA-1.2/MGSDA/DESCRIPTION | 14 +- MGSDA-1.2/MGSDA/MD5 | 22 +-- MGSDA-1.2/MGSDA/NAMESPACE | 2 MGSDA-1.2/MGSDA/R/SolveMyLasso.R |only MGSDA-1.2/MGSDA/R/SolveMyLassoF.R |only MGSDA-1.2/MGSDA/R/createY.R |only MGSDA-1.2/MGSDA/R/cv.dLDA.R | 88 ++++++++------- MGSDA-1.2/MGSDA/R/dLDA.R | 40 +++--- MGSDA-1.2/MGSDA/man/MGSDA-package.Rd | 10 - MGSDA-1.2/MGSDA/man/cv.dLDA.Rd | 4 MGSDA-1.2/MGSDA/man/dLDA.Rd | 5 MGSDA-1.2/MGSDA/src/solveVcoordf2st.c | 199 ++++++++++++++++++++-------------- 15 files changed, 216 insertions(+), 168 deletions(-)
Title: Functions for Analysis of Data with General Recognition Theory
Description: Tools associated with General
Recognition Theory (Townsend & Ashby, 1986), including Gaussian model fitting of 4x4 and more
general confusion matrices, associated plotting and model comparison tools,
and tests of marginal response invariance and report independence.
Author: Robert X.D. Hawkins <rxdh@stanford.edu>, Joe Houpt
<joseph.houpt@wright.edu>, Noah Silbert <noahpoah@gmail.com>, Leslie
Blaha <Leslie.Blaha@wpafb.af.mil>, Thomas D. Wickens
<twickens@socrates.berkeley.edu>
Maintainer: Robert X.D. Hawkins <rxdh@stanford.edu>
Diff between mdsdt versions 1.0 dated 2014-09-30 and 1.1 dated 2015-09-01
DESCRIPTION | 10 ++-- MD5 | 35 +++++++------- NAMESPACE | 35 +++++++++++--- R/grt_base.R | 128 ++++++++++++++++++++++++++++++++++------------------- README.md | 9 +-- man/GOF.Rd | 29 ++++++------ man/anova.grt.Rd |only man/fit.grt.Rd | 41 ++++++---------- man/mriTest.Rd | 36 +++++--------- man/plot.grt.Rd | 21 +++----- man/print.grt.Rd | 13 ++--- man/riTest.Rd | 33 ++++--------- man/silbert09a.Rd | 17 +++---- man/silbert09b.Rd | 17 +++---- man/silbert12.Rd | 16 +++--- man/summary.grt.Rd | 13 ++--- man/thomasA.Rd | 20 +++----- man/thomasB.Rd | 20 +++----- man/wo89xt.Rd | 21 ++++---- 19 files changed, 266 insertions(+), 248 deletions(-)
Title: Efficient Approximate Bayesian Computation Sampling Schemes
Description: Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot, Thierry Faure, Nicolas Dumoulin, Carlo Albert.
Maintainer: Nicolas Dumoulin <nicolas.dumoulin@irstea.fr>
Diff between EasyABC versions 1.4 dated 2014-12-17 and 1.5 dated 2015-09-01
CHANGELOG | 6 + DESCRIPTION | 16 +-- MD5 | 23 ++-- NAMESPACE | 5 - R/EasyABC-internal.R | 224 ++++++++++++++++++++++-------------------------- R/SABC-internal.R |only R/SABC.R |only build/vignette.rds |binary inst/doc/EasyABC.pdf |binary man/ABC_mcmc.Rd | 7 + man/ABC_sequential.Rd | 7 + man/EasyABC-internal.Rd | 3 man/EasyABC-package.Rd | 28 +++--- man/SABC.Rd |only 14 files changed, 162 insertions(+), 157 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-19 2.0.4
2013-04-26 2.0.3
2012-12-10 2.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-04 1.03
2012-09-20 1.02
2012-07-22 1.01
2012-06-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 1.0.5
2014-08-07 1.0.3
2014-08-02 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-05 0.0.4
2014-02-16 0.0.3
2013-11-23 0.0.2
2013-11-18 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-28 1.4.7
2014-02-27 1.4.6
2014-01-23 1.4.5
2013-09-24 1.4.4
2013-08-27 1.4.3
2013-07-31 1.4.2
2013-01-11 1.4
2012-10-01 1.3.1
2012-07-20 1.3
2012-05-14 1.2
2012-04-11 1.1
2011-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 1.6.2
2014-01-16 1.6.1
2013-09-06 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-20 1.1-5
2014-12-05 1.1-4
2014-05-08 1.1-3
2014-04-28 1.1-2
2013-12-30 1.1-1
2013-12-13 1.1-0
2013-06-05 1.0-1
2013-02-19 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-10 0.4
2014-05-25 0.3
2013-07-21 0.2
2013-02-06 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-04 9.5
2012-08-17 9.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-16 0.6.0
Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on
top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre],
Jeroen Ooms [ctb],
RStudio [cph],
R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between xml2 versions 0.1.1 dated 2015-06-02 and 0.1.2 dated 2015-09-01
xml2-0.1.1/xml2/src/Makevars |only xml2-0.1.2/xml2/DESCRIPTION | 8 +- xml2-0.1.2/xml2/MD5 | 17 ++-- xml2-0.1.2/xml2/R/RcppExports.R | 4 + xml2-0.1.2/xml2/configure | 85 ++++++++++++++++-------- xml2-0.1.2/xml2/src/Makevars.in |only xml2-0.1.2/xml2/src/RcppExports.cpp | 10 ++ xml2-0.1.2/xml2/src/xml2_init.cpp | 7 + xml2-0.1.2/xml2/src/xml2_url.cpp | 12 +++ xml2-0.1.2/xml2/tests/testthat/helper-version.R |only xml2-0.1.2/xml2/tools/winlibs.R | 2 11 files changed, 105 insertions(+), 40 deletions(-)
Title: Triangulation of Irregularly Spaced Data
Description: A constrained two-dimensional Delaunay triangulation package
providing both triangulation and generation of voronoi mosaics of
irregular spaced data.
Author: Fortran code by R. J. Renka.
R functions by Albrecht Gebhardt <albrecht.gebhardt@aau.at>.
With contributions from Stephen Eglen <stephen@anc.ed.ac.uk>,
Sergei Zuyev <sergei@stams.strath.ac.uk> and
Denis White <white.denis@epamail.epa.gov>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between tripack versions 1.3-6 dated 2013-09-16 and 1.3-7 dated 2015-09-01
tripack-1.3-6/tripack/ChangeLog |only tripack-1.3-7/tripack/DESCRIPTION | 16 +++++++++------- tripack-1.3-7/tripack/LICENSE | 2 +- tripack-1.3-7/tripack/MD5 | 7 +++---- tripack-1.3-7/tripack/NAMESPACE | 10 ++++++++++ 5 files changed, 23 insertions(+), 12 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey <buttrey@nps.edu>
Diff between lpSolve versions 5.6.11 dated 2015-04-06 and 5.6.12 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/lp_lib.c | 2 +- src/lusol1.h | 6 +++--- src/myblas.c | 4 ++-- src/myblas.h | 4 ++-- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Reliable Comparison of Floating Point Numbers
Description: Comparisons of floating point numbers are problematic due to errors
associated with the binary representation of decimal numbers.
Despite being aware of these problems, people still use numerical methods
that fail to account for these and other rounding errors (this pitfall is
the first to be highlighted in Circle 1 of Burns (2012)
[The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
This package provides new relational operators useful for performing
floating point number comparisons with a set tolerance.
Author: Alex M Chubaty [aut, cre],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between fpCompare versions 0.2.0 dated 2015-05-16 and 0.2.1 dated 2015-09-01
fpCompare-0.2.0/fpCompare/inst/doc/fpCompare.html |only fpCompare-0.2.1/fpCompare/DESCRIPTION | 14 +++---- fpCompare-0.2.1/fpCompare/MD5 | 16 ++++---- fpCompare-0.2.1/fpCompare/NEWS | 6 +++ fpCompare-0.2.1/fpCompare/README.md | 4 +- fpCompare-0.2.1/fpCompare/build/vignette.rds |binary fpCompare-0.2.1/fpCompare/inst/doc/fpCompare.Rmd | 12 +++--- fpCompare-0.2.1/fpCompare/inst/doc/fpCompare.pdf |only fpCompare-0.2.1/fpCompare/tests/testthat/test-numerical-comparisons.R | 18 +++++----- fpCompare-0.2.1/fpCompare/vignettes/fpCompare.Rmd | 12 +++--- 10 files changed, 44 insertions(+), 38 deletions(-)
Title: Bindings to the 'CommonMark' Reference Implementation
Description: The 'CommonMark' spec is a rationalized version of markdown syntax.
This package converts markdown text to various formats including html, latex
and 'groff' man. In addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.4 dated 2015-05-30 and 0.5 dated 2015-09-01
commonmark-0.4/commonmark/src/cmark/COPYING |only commonmark-0.4/commonmark/src/cmark/debug.h |only commonmark-0.4/commonmark/src/cmark/html_unescape.h |only commonmark-0.5/commonmark/DESCRIPTION | 14 commonmark-0.5/commonmark/MD5 | 84 commonmark-0.5/commonmark/NAMESPACE | 1 commonmark-0.5/commonmark/NEWS |only commonmark-0.5/commonmark/R/markdown.R | 12 commonmark-0.5/commonmark/man/commonmark.Rd | 8 commonmark-0.5/commonmark/src/Makevars | 9 commonmark-0.5/commonmark/src/cmark/bench.h | 16 commonmark-0.5/commonmark/src/cmark/blocks.c | 1795 commonmark-0.5/commonmark/src/cmark/buffer.c | 492 commonmark-0.5/commonmark/src/cmark/buffer.h | 102 commonmark-0.5/commonmark/src/cmark/chunk.h | 204 commonmark-0.5/commonmark/src/cmark/cmark.c | 21 commonmark-0.5/commonmark/src/cmark/cmark.h | 292 commonmark-0.5/commonmark/src/cmark/cmark_ctype.c | 59 commonmark-0.5/commonmark/src/cmark/cmark_version.h | 4 commonmark-0.5/commonmark/src/cmark/commonmark.c | 994 commonmark-0.5/commonmark/src/cmark/entities.inc |only commonmark-0.5/commonmark/src/cmark/houdini.h | 43 commonmark-0.5/commonmark/src/cmark/houdini_href_e.c | 121 commonmark-0.5/commonmark/src/cmark/houdini_html_e.c | 95 commonmark-0.5/commonmark/src/cmark/houdini_html_u.c | 247 commonmark-0.5/commonmark/src/cmark/html.c | 587 commonmark-0.5/commonmark/src/cmark/inlines.c | 1973 commonmark-0.5/commonmark/src/cmark/inlines.h | 6 commonmark-0.5/commonmark/src/cmark/iterator.c | 244 commonmark-0.5/commonmark/src/cmark/iterator.h | 10 commonmark-0.5/commonmark/src/cmark/latex.c |only commonmark-0.5/commonmark/src/cmark/main.c | 327 commonmark-0.5/commonmark/src/cmark/man.c | 486 commonmark-0.5/commonmark/src/cmark/node.c | 1591 commonmark-0.5/commonmark/src/cmark/node.h | 94 commonmark-0.5/commonmark/src/cmark/parser.h | 22 commonmark-0.5/commonmark/src/cmark/references.c | 202 commonmark-0.5/commonmark/src/cmark/references.h | 18 commonmark-0.5/commonmark/src/cmark/render.c |only commonmark-0.5/commonmark/src/cmark/render.h |only commonmark-0.5/commonmark/src/cmark/scanners.c |42924 ++++++++++++------- commonmark-0.5/commonmark/src/cmark/scanners.h | 47 commonmark-0.5/commonmark/src/cmark/utf8.c | 682 commonmark-0.5/commonmark/src/cmark/utf8.h | 12 commonmark-0.5/commonmark/src/cmark/xml.c | 274 commonmark-0.5/commonmark/src/config.h | 14 commonmark-0.5/commonmark/src/wrapper.c | 13 47 files changed, 33105 insertions(+), 21034 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, generalized accelerated failure time frailty models, and standard semiparametric frailty models within the context of proportional hazards, proportional odds and accelerated failure time.
Author: Haiming Zhou <zhouh@niu.edu> and Tim Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.0.2 dated 2014-12-19 and 1.0.3 dated 2015-09-01
DESCRIPTION | 16 MD5 | 63 +- NAMESPACE | 19 R/GetCurves.R | 31 - R/anovaDDP.R | 24 - R/frailtyGAFT.R | 899 +++++++++++++++++++++++------------------ R/indeptCoxph.R | 319 +++++++------- R/spCopulaCoxph.R | 392 ++++++++--------- R/spCopulaDDP.R | 33 - R/survregbayes.R |only R/wrappers.R | 17 man/GetCurves.Rd | 93 +--- man/anovaDDP.Rd | 591 +++++++++++++------------- man/baseline.Rd |only man/frailtyGAFT.Rd | 462 +++++++++------------ man/indeptCoxph.Rd | 514 +++++++++++------------ man/spBayesSurv-package.Rd | 65 +- man/spCopulaCoxph.Rd | 527 +++++++++++------------- man/spCopulaDDP.Rd | 29 - man/survregbayes.Rd |only src/spSurv_AFT.cpp |only src/spSurv_AH.cpp |only src/spSurv_Coxph_tools.cpp | 8 src/spSurv_DDP_tools.cpp | 4 src/spSurv_LDTFP_tools.cpp | 190 ++------ src/spSurv_LDTFP_tools.h | 6 src/spSurv_MPT_tools.cpp |only src/spSurv_MPT_tools.h |only src/spSurv_PH.cpp |only src/spSurv_PO.cpp |only src/spSurv_anovaDDP.cpp | 6 src/spSurv_common.h | 1 src/spSurv_frailtyLDTFP.cpp | 6 src/spSurv_indeptCoxph.cpp | 4 src/spSurv_nonfrailtyLDTFP.cpp | 8 src/spSurv_spCopulaCoxph.cpp | 4 src/spSurv_spCopulaDDP.cpp | 4 37 files changed, 2137 insertions(+), 2198 deletions(-)
Title: An Object-Oriented Framework for Geostatistical Modeling in S+
Description: An Object-oriented Framework for Geostatistical Modeling in S+
containing functions for variogram estimation, variogram fitting and kriging
as well as some plot functions. Written entirely in S, therefore works only
for small data sets in acceptable computing time.
Author: S original by James J. Majure <majure@iastate.edu> Iowa State University, R port + extensions by Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between sgeostat versions 1.0-25 dated 2013-03-01 and 1.0-26 dated 2015-09-01
sgeostat-1.0-25/sgeostat/ChangeLog |only sgeostat-1.0-25/sgeostat/LICENSE |only sgeostat-1.0-25/sgeostat/digi.R |only sgeostat-1.0-25/sgeostat/maas.dig |only sgeostat-1.0-25/sgeostat/makefile |only sgeostat-1.0-25/sgeostat/www-SGeoStat |only sgeostat-1.0-25/sgeostat/zn_map.eps |only sgeostat-1.0-25/sgeostat/zn_map.gif |only sgeostat-1.0-25/sgeostat/zn_map.ps |only sgeostat-1.0-26/sgeostat/DESCRIPTION | 21 ++++++------ sgeostat-1.0-26/sgeostat/MD5 | 44 +------------------------- sgeostat-1.0-26/sgeostat/README | 42 ++++++++++++++++++++++++ sgeostat-1.0-26/sgeostat/man/fit.variogram.Rd | 5 +- 13 files changed, 59 insertions(+), 53 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.0 dated 2015-02-07 and 2.2 dated 2015-09-01
SemiCompRisks-2.0/SemiCompRisks/R/BayesIDcor.R |only SemiCompRisks-2.0/SemiCompRisks/R/BayesSurvcor.R |only SemiCompRisks-2.0/SemiCompRisks/R/ehr.R |only SemiCompRisks-2.0/SemiCompRisks/data/scrCorData.rda |only SemiCompRisks-2.0/SemiCompRisks/man/BayesIDcor.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/BayesSurvcor.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/ehr.Rd |only SemiCompRisks-2.0/SemiCompRisks/man/scrCorData.Rd |only SemiCompRisks-2.2/SemiCompRisks/DESCRIPTION | 16 SemiCompRisks-2.2/SemiCompRisks/MD5 | 120 SemiCompRisks-2.2/SemiCompRisks/NAMESPACE | 41 SemiCompRisks-2.2/SemiCompRisks/R/BayesID.R | 3513 +++++- SemiCompRisks-2.2/SemiCompRisks/R/BayesSurv.R | 1003 + SemiCompRisks-2.2/SemiCompRisks/R/FreqID.R |only SemiCompRisks-2.2/SemiCompRisks/R/FreqSurv.R |only SemiCompRisks-2.2/SemiCompRisks/R/initiate.startValues.R |only SemiCompRisks-2.2/SemiCompRisks/R/internalFunc.R | 160 SemiCompRisks-2.2/SemiCompRisks/R/methods.R | 5408 ++++------ SemiCompRisks-2.2/SemiCompRisks/R/simID.R | 138 SemiCompRisks-2.2/SemiCompRisks/R/simSurv.R | 69 SemiCompRisks-2.2/SemiCompRisks/data/scrData.rda |binary SemiCompRisks-2.2/SemiCompRisks/data/survData.rda |binary SemiCompRisks-2.2/SemiCompRisks/man/BMT.Rd | 42 SemiCompRisks-2.2/SemiCompRisks/man/BayesID.Rd | 590 - SemiCompRisks-2.2/SemiCompRisks/man/BayesSurv.Rd | 448 SemiCompRisks-2.2/SemiCompRisks/man/FreqID.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/FreqSurv.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/SemiCompRisks-package.Rd | 28 SemiCompRisks-2.2/SemiCompRisks/man/initiate.startValues.Rd |only SemiCompRisks-2.2/SemiCompRisks/man/methods.Rd | 103 SemiCompRisks-2.2/SemiCompRisks/man/scrData.Rd | 68 SemiCompRisks-2.2/SemiCompRisks/man/simID.Rd | 137 SemiCompRisks-2.2/SemiCompRisks/man/simSurv.Rd | 65 SemiCompRisks-2.2/SemiCompRisks/man/survData.Rd | 37 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScr.c | 27 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScrSM.c | 27 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScrSM_Updates.c | 321 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorScr_Updates.c | 324 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorSurv.c | 15 SemiCompRisks-2.2/SemiCompRisks/src/BpeDpCorSurv_Updates.c | 11 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScr.c | 23 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScrSM.c | 25 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScrSM_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorScr_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorSurv.c | 10 SemiCompRisks-2.2/SemiCompRisks/src/BpeMvnCorSurv_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeScr.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BpeScrSM.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BpeScrSM_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeScr_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BpeSurv.c | 8 SemiCompRisks-2.2/SemiCompRisks/src/BpeSurv_Updates.c | 4 SemiCompRisks-2.2/SemiCompRisks/src/BweibCorSurv.c | 9 SemiCompRisks-2.2/SemiCompRisks/src/BweibCorSurv_Updates.c | 2 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScr.c | 34 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScrSM.c | 34 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScrSM_Updates.c | 244 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorScr_Updates.c | 249 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorSurv.c | 25 SemiCompRisks-2.2/SemiCompRisks/src/BweibDpCorSurv_Updates.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScr.c | 29 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScrSM.c | 28 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScrSM_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BweibMvnCorScr_Updates.c | 20 SemiCompRisks-2.2/SemiCompRisks/src/BweibScr.c | 6 SemiCompRisks-2.2/SemiCompRisks/src/BweibScrSM.c | 5 SemiCompRisks-2.2/SemiCompRisks/src/BweibSurv.c | 49 SemiCompRisks-2.2/SemiCompRisks/src/Utilities.c | 132 68 files changed, 8812 insertions(+), 4929 deletions(-)
Title: Convert Text into Speech
Description: Convert text into speech (voice file in 'mp3' or 'wav' format) with APIs offered by Google Translate and ITRI TTS (Text-To-Speech service, Industrial Technology Research Institute, Taiwan. http://tts.itri.org.tw/). Two main functions are given corresponding these two APIs, tts_google() and tts_ITRI(). For tts_google(), only English is supported. For tts_ITRI(), English and Chinese (both traditional and simplified) are supported, and user can specify the speaker accent, speed and volume. Both functions require internet connection.
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between Rtts versions 0.3.1 dated 2015-06-03 and 0.3.2 dated 2015-09-01
DESCRIPTION | 8 ++-- MD5 | 11 +++-- NEWS |only R/tts_ITRI.R | 25 +++++++++++-- R/tts_ITRI_getID.R | 90 ++++++++++++++++++++++++++++--------------------- R/tts_ITRI_getStatus.R | 7 +++ R/tts_ITRI_getURL.R | 7 +++ 7 files changed, 97 insertions(+), 51 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-176 dated 2015-06-25 and 0.15-244 dated 2015-09-01
ChangeLog | 15 ++ DESCRIPTION | 8 - MD5 | 32 +++--- R/RhpcExt.R | 113 ++++++++++++++++++++++ R/RhpcOp.R | 16 --- man/Rhpc-package.Rd | 35 ++++++ src/Makevars.win | 2 src/RhpcMPI.c | 43 -------- src/RhpcMPIWorkerCall.h | 56 ++-------- src/RhpcMPIlapplyLB.h | 111 +++++---------------- src/RhpcMPIlapplyseq.h | 112 ++++++--------------- src/common/Rhpc.h | 2 src/worker/Rhpc.cmd.in | 14 +- src/worker/RhpcWorker.c | 10 - src/worker/RhpcWorker_LapplyLB.h | 107 ++++---------------- src/worker/RhpcWorker_Lapplyseq.h | 189 ++++++++++++++----------------------- src/worker/RhpcWorker_WorkerCall.h | 52 ++-------- 17 files changed, 380 insertions(+), 537 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-11 dated 2015-05-29 and 0.3-12 dated 2015-09-01
ChangeLog | 86 +++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++-- MD5 | 35 ++++++++-------- NAMESPACE | 6 ++ R/AAA.R | 8 +++ R/over.R | 64 ++++++++++++++++++++++-------- configure | 22 +++++----- configure.ac | 2 inst/ChangeLog | 86 +++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 man/misc-over.Rd |only man/pred-binary-gContains.Rd | 2 man/pred-binary-gCrosses.Rd | 2 man/pred-binary-gEquals.Rd | 2 man/pred-binary-gIntersects.Rd | 2 man/pred-binary-gRelate.Rd | 2 man/pred-binary-gTouches.Rd | 2 src/rgeos_R2geos.c | 16 +++---- src/rgeos_predicate_binary.c | 16 ++++--- 19 files changed, 294 insertions(+), 71 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it is possible to create and manipulate multivariate network
data with different formats, and there are effective ways available to treat multiple networks
with routines that combine algebraic systems like the partially ordered semigroup or the
semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. As well an algebraic approach for two-mode networks is made
through Galois derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.6 dated 2015-05-19 and 1.7 dated 2015-09-01
multiplex-1.6/multiplex/R/slc.R |only multiplex-1.6/multiplex/inst/doc/TwoMode.R |only multiplex-1.6/multiplex/inst/doc/TwoMode.Rnw |only multiplex-1.6/multiplex/inst/doc/TwoMode.pdf |only multiplex-1.6/multiplex/man/incubA.Rd |only multiplex-1.6/multiplex/man/slc.Rd |only multiplex-1.6/multiplex/vignettes/TwoMode.Rnw |only multiplex-1.7/multiplex/DESCRIPTION | 27 - multiplex-1.7/multiplex/MD5 | 117 ++--- multiplex-1.7/multiplex/R/as.signed.R |only multiplex-1.7/multiplex/R/bundle.census.R | 90 ++-- multiplex-1.7/multiplex/R/bundles.R | 82 +-- multiplex-1.7/multiplex/R/decomp.R | 8 multiplex-1.7/multiplex/R/dhc.R | 25 - multiplex-1.7/multiplex/R/diagram.R | 32 - multiplex-1.7/multiplex/R/diagram.levels.R | 18 multiplex-1.7/multiplex/R/dichot.R | 12 multiplex-1.7/multiplex/R/expos.R | 377 +++++++++--------- multiplex-1.7/multiplex/R/flt.R |only multiplex-1.7/multiplex/R/fltr.R | 66 ++- multiplex-1.7/multiplex/R/galois.R | 164 +++---- multiplex-1.7/multiplex/R/iinc.R | 2 multiplex-1.7/multiplex/R/jnt.R | 68 ++- multiplex-1.7/multiplex/R/neighb.R |only multiplex-1.7/multiplex/R/ngbs.R | 57 ++ multiplex-1.7/multiplex/R/pacnet.R | 76 +-- multiplex-1.7/multiplex/R/prev.R | 41 + multiplex-1.7/multiplex/R/rbox.R | 68 +-- multiplex-1.7/multiplex/R/read.gml.R | 104 ++-- multiplex-1.7/multiplex/R/read.srt.R | 95 ++-- multiplex-1.7/multiplex/R/rel.sys.R | 127 ++++-- multiplex-1.7/multiplex/R/rm.isol.R | 40 - multiplex-1.7/multiplex/R/semiring.R | 6 multiplex-1.7/multiplex/R/signed.R | 38 - multiplex-1.7/multiplex/R/strings.R | 201 ++++----- multiplex-1.7/multiplex/R/summaryBundles.R | 178 +++++--- multiplex-1.7/multiplex/R/write.dat.R | 4 multiplex-1.7/multiplex/R/write.gml.R | 6 multiplex-1.7/multiplex/R/write.srt.R | 29 - multiplex-1.7/multiplex/build/vignette.rds |binary multiplex-1.7/multiplex/data/incubA.RData |binary multiplex-1.7/multiplex/data/incubB.RData |binary multiplex-1.7/multiplex/data/incubC.RData |binary multiplex-1.7/multiplex/data/incubD.RData |binary multiplex-1.7/multiplex/data/incubs.RData |only multiplex-1.7/multiplex/inst/CHANGELOG | 25 + multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.R |only multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.Rnw |only multiplex-1.7/multiplex/inst/doc/TwoModeNetworks.pdf |only multiplex-1.7/multiplex/man/as.signed.Rd |only multiplex-1.7/multiplex/man/bundles.Rd | 2 multiplex-1.7/multiplex/man/diagram.Rd | 4 multiplex-1.7/multiplex/man/diagram.levels.Rd | 2 multiplex-1.7/multiplex/man/dichot.Rd | 8 multiplex-1.7/multiplex/man/expos.Rd | 48 +- multiplex-1.7/multiplex/man/flt.Rd |only multiplex-1.7/multiplex/man/fltr.Rd | 36 - multiplex-1.7/multiplex/man/galois.Rd | 6 multiplex-1.7/multiplex/man/iinc.Rd | 2 multiplex-1.7/multiplex/man/incubs.Rd |only multiplex-1.7/multiplex/man/multiplex-package.Rd | 4 multiplex-1.7/multiplex/man/neighb.Rd |only multiplex-1.7/multiplex/man/partial.order.Rd | 4 multiplex-1.7/multiplex/man/perm.Rd | 1 multiplex-1.7/multiplex/man/rel.sys.Rd | 28 + multiplex-1.7/multiplex/man/semiring.Rd | 2 multiplex-1.7/multiplex/man/signed.Rd | 4 multiplex-1.7/multiplex/man/summaryBundles.Rd | 5 multiplex-1.7/multiplex/vignettes/TwoModeNetworks.Rnw |only 69 files changed, 1353 insertions(+), 986 deletions(-)
Title: Multidimensional Projection Techniques
Description: Multidimensional projection techniques are used to create two dimensional representations of multidimensional data sets.
Author: Francisco M. Fatore,
Samuel G. Fadel
Maintainer: Francisco M. Fatore <fmfatore@gmail.com>
Diff between mp versions 0.3 dated 2015-08-16 and 0.3.1 dated 2015-09-01
mp-0.3.1/mp/DESCRIPTION | 8 +- mp-0.3.1/mp/MD5 | 23 +++----- mp-0.3.1/mp/NAMESPACE | 24 ++++---- mp-0.3.1/mp/R/RcppExports.R | 30 +++++----- mp-0.3.1/mp/man/forceScheme.Rd | 112 ++++++++++++++++++++-------------------- mp-0.3.1/mp/man/is.symmetric.Rd | 36 ++++++------ mp-0.3.1/mp/man/lamp.Rd | 78 +++++++++++++-------------- mp-0.3.1/mp/man/lsp.Rd | 80 ++++++++++++++-------------- mp-0.3.1/mp/man/mp.Rd | 22 +++---- mp-0.3.1/mp/man/plmp.Rd | 74 +++++++++++++------------- mp-0.3.1/mp/man/tSNE.Rd | 84 +++++++++++++++--------------- mp-0.3.1/mp/src/lamp.cpp | 2 mp-0.3/mp/README.md |only 13 files changed, 287 insertions(+), 286 deletions(-)
Title: MOdelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of bioassay data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut, cre], Philippe Ruiz [aut, cre], Sandrine Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon-Kam-king [ctb], Philippe Veber [ctb]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>
Diff between morse versions 1.0.2 dated 2014-07-03 and 2.0.0 dated 2015-09-01
morse-1.0.2/morse/R/plot.repro.fit.R |only morse-1.0.2/morse/R/print.repro.check.data.R |only morse-1.0.2/morse/R/print.repro.data.R |only morse-1.0.2/morse/R/print.repro.fit.R |only morse-1.0.2/morse/R/repro.check.data.R |only morse-1.0.2/morse/R/repro.convergence.R |only morse-1.0.2/morse/R/repro.cumulplot.R |only morse-1.0.2/morse/R/repro.data.R |only morse-1.0.2/morse/R/repro.fit.R |only morse-1.0.2/morse/R/repro.fullsurvplot.R |only morse-1.0.2/morse/R/repro.parfit.R |only morse-1.0.2/morse/R/repro.survplot.R |only morse-1.0.2/morse/R/summary.repro.data.R |only morse-1.0.2/morse/R/summary.repro.fit.R |only morse-1.0.2/morse/man/repro.check.data.Rd |only morse-1.0.2/morse/man/repro.convergence.Rd |only morse-1.0.2/morse/man/repro.cumulplot.Rd |only morse-1.0.2/morse/man/repro.data.Rd |only morse-1.0.2/morse/man/repro.fit.Rd |only morse-1.0.2/morse/man/repro.fullsurvplot.Rd |only morse-1.0.2/morse/man/repro.survplot.Rd |only morse-2.0.0/morse/DESCRIPTION | 23 morse-2.0.0/morse/MD5 | 90 +- morse-2.0.0/morse/NAMESPACE | 78 + morse-2.0.0/morse/NEWS | 44 - morse-2.0.0/morse/R/as.survData.R |only morse-2.0.0/morse/R/errorTable.R |only morse-2.0.0/morse/R/morse-internal.R | 1140 ++++----------------------- morse-2.0.0/morse/R/morse.R |only morse-2.0.0/morse/R/plot.reproData.R |only morse-2.0.0/morse/R/plot.reproFitTT.R |only morse-2.0.0/morse/R/plot.survData.R |only morse-2.0.0/morse/R/plot.survFitTT.R |only morse-2.0.0/morse/R/print.reproFitTT.R |only morse-2.0.0/morse/R/print.survFitTT.R |only morse-2.0.0/morse/R/reproData.R |only morse-2.0.0/morse/R/reproDataCheck.R |only morse-2.0.0/morse/R/reproFitTT.R |only morse-2.0.0/morse/R/summary.reproData.R |only morse-2.0.0/morse/R/summary.reproFitTT.R |only morse-2.0.0/morse/R/summary.survData.R |only morse-2.0.0/morse/R/summary.survFitTT.R |only morse-2.0.0/morse/R/survData.R |only morse-2.0.0/morse/R/survDataCheck.R |only morse-2.0.0/morse/R/survFitTT.R |only morse-2.0.0/morse/README.md |only morse-2.0.0/morse/build |only morse-2.0.0/morse/inst |only morse-2.0.0/morse/man/as.survData.Rd |only morse-2.0.0/morse/man/cadmium1.Rd | 73 - morse-2.0.0/morse/man/cadmium2.Rd | 67 - morse-2.0.0/morse/man/chlordan.Rd | 69 - morse-2.0.0/morse/man/copper.Rd | 71 - morse-2.0.0/morse/man/morse-package.Rd | 122 +- morse-2.0.0/morse/man/plot.reproData.Rd |only morse-2.0.0/morse/man/plot.reproFitTT.Rd |only morse-2.0.0/morse/man/plot.survData.Rd |only morse-2.0.0/morse/man/plot.survFitTT.Rd |only morse-2.0.0/morse/man/print.reproFitTT.Rd |only morse-2.0.0/morse/man/print.survFitTT.Rd |only morse-2.0.0/morse/man/reproData.Rd |only morse-2.0.0/morse/man/reproDataCheck.Rd |only morse-2.0.0/morse/man/reproFitTT.Rd |only morse-2.0.0/morse/man/summary.reproData.Rd |only morse-2.0.0/morse/man/summary.reproFitTT.Rd |only morse-2.0.0/morse/man/summary.survData.Rd |only morse-2.0.0/morse/man/summary.survFitTT.Rd |only morse-2.0.0/morse/man/survData.Rd |only morse-2.0.0/morse/man/survDataCheck.Rd |only morse-2.0.0/morse/man/survFitTT.Rd |only morse-2.0.0/morse/man/zinc.Rd | 70 - morse-2.0.0/morse/tests |only morse-2.0.0/morse/vignettes |only 73 files changed, 550 insertions(+), 1297 deletions(-)
Title: Functions to Fit Monotone Polynomials
Description: Functions for fitting monotone polynomials to data.
Author: Berwin A. Turlach [aut, cre],
Kevin Murray [ctb]
Maintainer: Berwin A. Turlach <Berwin.Turlach@gmail.com>
Diff between MonoPoly versions 0.2-8 dated 2013-11-03 and 0.2-10 dated 2015-09-01
DESCRIPTION | 19 +++++++++---------- MD5 | 22 ++++++++++++---------- NAMESPACE | 8 ++++++++ R/00MonPol.R | 26 ++++++++++++++------------ R/Nointercept.R |only R/ismonotone.R |only R/util.R | 8 +++++--- inst/CITATION | 2 +- inst/doc/MonoPoly-manual.pdf |binary man/monpol.Rd | 11 ++++++----- man/monpol.fit.Rd | 7 ++++--- man/w0.Rd | 7 ++++--- man/w2.Rd | 7 ++++--- 13 files changed, 67 insertions(+), 50 deletions(-)
More information about interactionTest at CRAN
Permanent link
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood
estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated
random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of
clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events
with terminal event for clustered data or not.
5) Joint General frailty models in the context of a joint modelling for recurrent
events with terminal event data with two independent frailty terms.
Prediction values are available. Left-truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional hazard
and shared frailty model) and strata are allowed. In each model,
the random effects have a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying covariates
effects in Cox, shared and joint models. The package includes concordance measures
for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.7.5 dated 2015-03-06 and 2.7.6.1 dated 2015-09-01
DESCRIPTION | 14 MD5 | 45 NAMESPACE | 9 NEWS | 4 R/frailtyPenal.R | 4005 +++++++++++++++++++-------------------- R/print.jointPenal.R | 709 +++--- R/waldtest.R | 13 demo/00Index | 2 demo/frailtypack_additivePenal.R | 4 demo/frailtypack_frailtyPenal.R | 4 demo/frailtypack_jointPenal.R | 52 demo/frailtypack_multivPenal.R | 6 demo/frailtypack_nestedPenal.R | 4 man/frailtyPenal.Rd | 67 man/frailtypack-package.Rd | 16 man/prediction.Rd | 496 ++-- src/AparamMultive.f90 | 56 src/Aparameters.f90 | 86 src/Makevars | 5 src/aaOptim.f90 | 493 ++-- src/aaOptimres.f90 | 2 src/funcpaMultivSplines.f90 | 1 src/funcpajgeneral.f90 |only src/joint.f90 | 974 ++++++--- 24 files changed, 3765 insertions(+), 3302 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.1 dated 2015-08-21 and 0.0.2 dated 2015-09-01
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ NEWS | 15 +++++++++++++-- R/epifit.R | 49 +++++++++++++++++++++++++++++++++---------------- R/modules.R | 40 +++++++++++++++------------------------- R/print.epifit.R | 8 ++++---- man/epifit.Rd | 35 ++++++++++++++++++++++++++++------- 7 files changed, 107 insertions(+), 67 deletions(-)
Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino <toni.giorgino@gmail.com>,
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>
Diff between dtw versions 1.17-1 dated 2013-12-11 and 1.18-1 dated 2015-09-01
dtw-1.17-1/dtw/vignettes/alignMVM.pdf |only dtw-1.17-1/dtw/vignettes/mvmSP.pdf |only dtw-1.17-1/dtw/vignettes/object-diagram.pdf |only dtw-1.17-1/dtw/vignettes/plot-conventions.pdf |only dtw-1.18-1/dtw/DESCRIPTION | 15 ++++++----- dtw-1.18-1/dtw/MD5 | 34 +++++++++++++------------- dtw-1.18-1/dtw/NAMESPACE | 9 ++++++ dtw-1.18-1/dtw/R/backtrack.R | 14 +++++++--- dtw-1.18-1/dtw/R/dtw.R | 4 ++- dtw-1.18-1/dtw/R/zzz.R | 5 ++- dtw-1.18-1/dtw/build/vignette.rds |binary dtw-1.18-1/dtw/inst/ChangeLog | 7 +++++ dtw-1.18-1/dtw/inst/doc/dtw.Rnw | 8 +++--- dtw-1.18-1/dtw/inst/doc/dtw.pdf |binary dtw-1.18-1/dtw/man/dtw.Rd | 15 +++++++---- dtw-1.18-1/dtw/tests/dtw_test.R | 2 - dtw-1.18-1/dtw/tests/dtw_test.Rout.save | 12 --------- dtw-1.18-1/dtw/vignettes/dtw.Rnw | 8 +++--- dtw-1.18-1/dtw/vignettes/figures |only 19 files changed, 76 insertions(+), 57 deletions(-)
Title: Extended Empirical Likelihood
Description: Compute the extended empirical log likelihood ratio (Tsao & Wu, 2014) for the mean and parameters defined by estimating equations.
Author: Fan Wu and Yu Zhang
Maintainer: Yu Zhang <yuz@uvic.ca>
Diff between eel versions 1.0 dated 2015-08-19 and 1.1 dated 2015-09-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/eel.R | 20 ++++++-------------- R/eel_est.R | 15 ++++++--------- build/partial.rdb |binary man/eel-package.Rd | 2 -- 6 files changed, 21 insertions(+), 34 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.4.2 dated 2015-06-16 and 0.4.3 dated 2015-09-01
dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Name.h |only dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Reducer.h |only dplyr-0.4.2/dplyr/inst/include/dplyr/Result/TypedProcessor.h |only dplyr-0.4.2/dplyr/inst/include/tools/StrictListOf.h |only dplyr-0.4.3/dplyr/DESCRIPTION | 30 dplyr-0.4.3/dplyr/MD5 | 295 ++-- dplyr-0.4.3/dplyr/NAMESPACE | 6 dplyr-0.4.3/dplyr/R/RcppExports.R | 13 dplyr-0.4.3/dplyr/R/colwise.R | 13 dplyr-0.4.3/dplyr/R/compute-collect.r | 2 dplyr-0.4.3/dplyr/R/data-lahman.r | 4 dplyr-0.4.3/dplyr/R/data-nycflights13.r | 2 dplyr-0.4.3/dplyr/R/dataframe.R | 18 dplyr-0.4.3/dplyr/R/dbi-s3.r | 2 dplyr-0.4.3/dplyr/R/dplyr.r | 3 dplyr-0.4.3/dplyr/R/explain.r | 4 dplyr-0.4.3/dplyr/R/frame-data.R |only dplyr-0.4.3/dplyr/R/glimpse.R | 6 dplyr-0.4.3/dplyr/R/grouped-df.r | 4 dplyr-0.4.3/dplyr/R/join.r | 32 dplyr-0.4.3/dplyr/R/manip.r | 10 dplyr-0.4.3/dplyr/R/progress.R | 10 dplyr-0.4.3/dplyr/R/rank.R | 4 dplyr-0.4.3/dplyr/R/rbind.r | 39 dplyr-0.4.3/dplyr/R/rowwise.r | 4 dplyr-0.4.3/dplyr/R/src-local.r | 2 dplyr-0.4.3/dplyr/R/src-mysql.r | 4 dplyr-0.4.3/dplyr/R/src-postgres.r | 8 dplyr-0.4.3/dplyr/R/src-sqlite.r | 8 dplyr-0.4.3/dplyr/R/tally.R | 2 dplyr-0.4.3/dplyr/R/tbl-cube.r | 2 dplyr-0.4.3/dplyr/R/tbl-df.r | 9 dplyr-0.4.3/dplyr/R/tbl-dt.r | 2 dplyr-0.4.3/dplyr/R/tbl-sql.r | 7 dplyr-0.4.3/dplyr/R/translate-sql-base.r | 19 dplyr-0.4.3/dplyr/R/utils-format.r | 31 dplyr-0.4.3/dplyr/R/utils.r | 2 dplyr-0.4.3/dplyr/R/zzz.r | 3 dplyr-0.4.3/dplyr/README.md | 65 - dplyr-0.4.3/dplyr/build/vignette.rds |binary dplyr-0.4.3/dplyr/inst/doc/data_frames.R | 7 dplyr-0.4.3/dplyr/inst/doc/data_frames.Rmd | 67 - dplyr-0.4.3/dplyr/inst/doc/data_frames.html | 142 +- dplyr-0.4.3/dplyr/inst/doc/databases.Rmd | 2 dplyr-0.4.3/dplyr/inst/doc/databases.html | 114 - dplyr-0.4.3/dplyr/inst/doc/hybrid-evaluation.Rmd | 2 dplyr-0.4.3/dplyr/inst/doc/hybrid-evaluation.html | 6 dplyr-0.4.3/dplyr/inst/doc/introduction.Rmd | 114 - dplyr-0.4.3/dplyr/inst/doc/introduction.html | 378 +++-- dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.R | 2 dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.Rmd | 4 dplyr-0.4.3/dplyr/inst/doc/new-sql-backend.html | 8 dplyr-0.4.3/dplyr/inst/doc/nse.html | 4 dplyr-0.4.3/dplyr/inst/doc/two-table.Rmd | 4 dplyr-0.4.3/dplyr/inst/doc/two-table.html | 236 ++- dplyr-0.4.3/dplyr/inst/doc/window-functions.html | 78 - dplyr-0.4.3/dplyr/inst/include/dplyr.h | 32 dplyr-0.4.3/dplyr/inst/include/dplyr/CharacterVectorOrderer.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/Collecter.h | 325 ++--- dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameAble.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameColumnSubsetVisitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameColumnVisitor.h | 54 dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameSubsetVisitors.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/DataFrameVisitors.h | 104 - dplyr-0.4.3/dplyr/inst/include/dplyr/Gatherer.h | 211 --- dplyr-0.4.3/dplyr/inst/include/dplyr/GroupedDataFrame.h | 105 - dplyr-0.4.3/dplyr/inst/include/dplyr/JoinVisitor.h | 3 dplyr-0.4.3/dplyr/inst/include/dplyr/JoinVisitorImpl.h | 129 + dplyr-0.4.3/dplyr/inst/include/dplyr/MatrixColumnSubsetVectorVisitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/MatrixColumnVisitor.h | 128 - dplyr-0.4.3/dplyr/inst/include/dplyr/NamedListAccumulator.h | 63 dplyr-0.4.3/dplyr/inst/include/dplyr/OrderVisitorImpl.h | 163 +- dplyr-0.4.3/dplyr/inst/include/dplyr/Replicator.h | 139 -- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallElementProxy.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallProxy.h | 150 -- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/CallbackProcessor.h | 67 - dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Count_Distinct.h | 29 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/DelayedProcessor.h | 204 +-- dplyr-0.4.3/dplyr/inst/include/dplyr/Result/First.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/GroupedCallProxy.h | 9 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/GroupedHybridCall.h | 40 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Lag.h | 85 - dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Last.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/LazyGroupedSubsets.h | 80 - dplyr-0.4.3/dplyr/inst/include/dplyr/Result/LazyRowwiseSubsets.h | 2 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/LazySubsets.h | 61 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Lead.h | 110 - dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Mean.h | 6 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Nth.h | 4 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Processor.h | 27 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/RowwiseSubset.h | 42 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Sd.h | 6 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Sum.h | 8 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Var.h | 14 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/all.h | 3 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/max.h | 12 dplyr-0.4.3/dplyr/inst/include/dplyr/Result/min.h | 13 dplyr-0.4.3/dplyr/inst/include/dplyr/SubsetVectorVisitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/SubsetVectorVisitorImpl.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/VectorVisitor.h | 44 dplyr-0.4.3/dplyr/inst/include/dplyr/VectorVisitorImpl.h | 234 +-- dplyr-0.4.3/dplyr/inst/include/dplyr/subset_visitor.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/tbl_cpp.h | 59 dplyr-0.4.3/dplyr/inst/include/dplyr/workarounds.h | 15 dplyr-0.4.3/dplyr/inst/include/tools/DotsOf.h | 88 + dplyr-0.4.3/dplyr/inst/include/tools/SymbolMap.h |only dplyr-0.4.3/dplyr/inst/include/tools/tools.h | 2 dplyr-0.4.3/dplyr/man/add_rownames.Rd | 7 dplyr-0.4.3/dplyr/man/bind.Rd | 17 dplyr-0.4.3/dplyr/man/compute.Rd | 2 dplyr-0.4.3/dplyr/man/dplyr-formatting.Rd | 2 dplyr-0.4.3/dplyr/man/dplyr.Rd | 2 dplyr-0.4.3/dplyr/man/explain.Rd | 4 dplyr-0.4.3/dplyr/man/filter.Rd | 7 dplyr-0.4.3/dplyr/man/frame_data.Rd |only dplyr-0.4.3/dplyr/man/glimpse.Rd | 2 dplyr-0.4.3/dplyr/man/join.Rd | 30 dplyr-0.4.3/dplyr/man/lahman.Rd | 2 dplyr-0.4.3/dplyr/man/n_distinct.Rd | 4 dplyr-0.4.3/dplyr/man/progress_estimated.Rd | 4 dplyr-0.4.3/dplyr/man/select.Rd | 3 dplyr-0.4.3/dplyr/man/src_postgres.Rd | 2 dplyr-0.4.3/dplyr/man/summarise_each.Rd | 8 dplyr-0.4.3/dplyr/man/tally.Rd | 2 dplyr-0.4.3/dplyr/src/RcppExports.cpp | 39 dplyr-0.4.3/dplyr/src/api.cpp |only dplyr-0.4.3/dplyr/src/arrange.cpp | 15 dplyr-0.4.3/dplyr/src/bind.cpp | 78 - 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dplyr-0.4.3/dplyr/vignettes/databases.Rmd | 2 dplyr-0.4.3/dplyr/vignettes/hybrid-evaluation.Rmd | 2 dplyr-0.4.3/dplyr/vignettes/introduction.Rmd | 114 - dplyr-0.4.3/dplyr/vignettes/new-sql-backend.Rmd | 4 dplyr-0.4.3/dplyr/vignettes/two-table.Rmd | 4 157 files changed, 3771 insertions(+), 3150 deletions(-)
Title: Statistical Tests for Cryptographic Randomness
Description: Performs cryptographic randomness tests on a sequence of random integers or bits. Most of the included tests are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests. Additionally, it includes functions for the calculation of greatest common divisor, the Stirling numbers of the second kind, critical value of the topological binary test, and base conversions from base 2 to 10 and vice versa.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>
Diff between CryptRndTest versions 1.0.5 dated 2015-06-16 and 1.1.5 dated 2015-09-01
DESCRIPTION | 14 - MD5 | 62 +++++--- NAMESPACE | 24 ++- R/GCD.R | 38 +---- R/GCD.big.R |only R/GCD.q.R |only R/GCD.test.R | 111 ++++++++------- R/KSADCHRY.R | 32 +--- R/KSADdga.R | 40 ++--- R/Random.walk.D.R | 27 +-- R/Random.walk.G.R | 27 +-- R/Random.walk.Y.R | 17 -- R/Strlng2.R | 5 R/TBT.criticalValue.R |only R/adaptive.chi.square.R | 77 ++++------ R/birthday.spacings.R | 5 R/book.stack.R | 24 +-- R/dogumGunuAraliklari.R | 9 - R/random.walk.tests.R | 10 - R/toBaseTen.R |only R/toBaseTwo.R |only R/topological.binary.R | 23 +-- man/CryptRndTest-internal.Rd | 8 - man/CryptRndTest-package.Rd | 203 ++++++++++++++-------------- man/GCD.Rd | 18 +- man/GCD.big.Rd |only man/GCD.q.Rd |only man/GCD.test.Rd | 233 ++++++++++++++++----------------- man/Strlng2.Rd | 18 +- man/TBT.criticalValue.Rd |only man/adaptive.chi.square.Rd | 151 ++++++++++----------- man/birthday.spacings.Rd | 18 +- man/book.stack.Rd | 18 +- man/random.walk.tests.Rd | 302 +++++++++++++++++++++---------------------- man/toBaseTen.Rd |only man/toBaseTwo.Rd |only man/topological.binary.Rd | 131 +++++++++--------- 37 files changed, 805 insertions(+), 840 deletions(-)
Title: COnstrained B-Splines (Sparse Matrix Based)
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng <Pin.Ng@nau.edu> and Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cobs versions 1.3-0 dated 2015-01-06 and 1.3-1 dated 2015-09-01
ChangeLog | 5 +++++ DESCRIPTION | 16 ++++++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 17 +++++++++++------ R/concaveRegr.R | 4 ++-- R/l1Design.R | 2 +- R/looDesign.R | 6 +++--- R/qbsks.R | 2 +- R/scobs.R | 2 +- man/exHe.Rd | 5 +++-- 10 files changed, 44 insertions(+), 33 deletions(-)
Title: Construct Graphs of S4 Class Hierarchies
Description: Construct directed graphs of S4 class hierarchies and
visualize them. In general, these graphs typically are DAGs (directed
acyclic graphs), often simple trees in practice.
Author: Martin Maechler partly based on code from Robert Gentleman
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between classGraph versions 0.7-4 dated 2010-08-11 and 0.7-5 dated 2015-09-01
ChangeLog | 5 +++++ DESCRIPTION | 17 +++++++++-------- MD5 |only NAMESPACE | 27 ++++++++++++++++++++++----- R/S4classes-MM.R | 4 ++-- man/bGraph.Rd | 2 ++ man/classTree.Rd | 3 +-- man/mRagraph.Rd | 2 +- man/numOutEdges.Rd | 2 +- man/plotRag.Rd | 3 ++- tests/Matrix-ex.R | 3 ++- 11 files changed, 47 insertions(+), 21 deletions(-)
Title: Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures.
These are useful when data is heterogeneous, e.g. in
pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms
(flexible support size) and EM algorithms (fixed support size)
are provided for univariate and bivariate data.
Author: Peter Schlattmann <peter.schlattmann@mti.uni-jena.de>, Johannes
Hoehne, Maryna Verba
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>
Diff between CAMAN versions 0.72 dated 2014-10-23 and 0.73 dated 2015-09-01
DESCRIPTION | 17 +++++++---------- MD5 | 12 ++++++------ NAMESPACE | 10 +++++++++- R/CAMAN.R | 2 +- R/covariate_CAMAN.r | 1 + man/mixcov.Rd | 6 +++--- src/vemema_vem.cpp | 12 ++++++------ 7 files changed, 33 insertions(+), 27 deletions(-)
Title: David Scott's ASH Routines
Description: David Scott's ASH routines ported from S-PLUS to R.
Author: S original by David W. Scott
R port by Albrecht Gebhardt <albrecht.gebhardt@aau.at>
adopted to recent S-PLUS by Stephen Kaluzny <spk@insightful.com>
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between ash versions 1.0-14 dated 2013-02-11 and 1.0-15 dated 2015-09-01
ash-1.0-14/ash/ChangeLog |only ash-1.0-15/ash/DESCRIPTION | 22 +++++++++++----------- ash-1.0-15/ash/MD5 | 3 +-- 3 files changed, 12 insertions(+), 13 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.18 dated 2015-08-16 and 5.19 dated 2015-08-31
DESCRIPTION | 6 +- MD5 | 12 ++--- R/crq.R | 120 +++++++++++++++++++++++++++++++++++++++++++++++++-------- R/quantreg.R | 2 inst/ChangeLog | 18 ++++++++ man/crq.Rd | 7 +++ tests/rq.R | 7 +-- 7 files changed, 143 insertions(+), 29 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user-specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Diff between markophylo versions 1.0.1 dated 2015-07-07 and 1.0.2 dated 2015-08-31
DESCRIPTION | 14 - MD5 | 23 +- NAMESPACE | 14 + NEWS |only R/custom-general14.R | 197 +++++++++++++++++++---- build/vignette.rds |binary inst/doc/estimaterates.R | 67 +++++++ inst/doc/estimaterates.Rmd | 117 +++++++++++-- inst/doc/estimaterates.html | 370 +++++++++++++++++++++++++++++++++++++------- man/estimaterates.Rd | 72 ++++++-- man/markophylo-package.Rd | 4 tests |only vignettes/estimaterates.Rmd | 117 +++++++++++-- 13 files changed, 825 insertions(+), 170 deletions(-)
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.5.0 dated 2015-06-09 and 1.5.2 dated 2015-08-31
DESCRIPTION | 10 MD5 | 392 +++++++++++++++++++-------------------- NAMESPACE | 46 ++++ NEWS | 34 +++ R/addColor.r | 3 R/addData_gui.r | 7 R/addDye_gui.r | 5 R/addMarker.r | 4 R/addMarker_gui.r | 5 R/addSize.r | 3 R/addSize_gui.r | 5 R/blockAT.r | 11 - R/calculateAT.r | 146 ++++++++++---- R/calculateAT6.r | 49 +++- R/calculateAT6_gui.r | 110 ++-------- R/calculateAT_gui.r | 9 R/calculateBalance.r | 6 R/calculateBalance_gui.r | 12 - R/calculateCapillary.r | 4 R/calculateCapillary_gui.r | 5 R/calculateConcordance.r | 3 R/calculateConcordance_gui.r | 5 R/calculateDropout.r | 10 R/calculateDropout_gui.r | 8 R/calculateHeight_gui.r | 5 R/calculateHeterozygous_gui.r | 5 R/calculateMixture_gui.r | 6 R/calculateOL.r | 3 R/calculateOL_gui.r | 3 R/calculateOverlap.r | 4 R/calculateOverlap_gui.r | 3 R/calculatePeaks.r | 3 R/calculatePeaks_gui.r | 5 R/calculatePullup.r | 3 R/calculatePullup_gui.r | 7 R/calculateResultType.r | 3 R/calculateResultType_gui.r | 5 R/calculateStutter_gui.r | 10 R/checkSubset_gui.r | 8 R/colNames.r | 5 R/columns.r | 3 R/columns_gui.r | 5 R/combine_gui.r | 7 R/compact.r | 3 R/cropData_gui.r | 5 R/editData_gui.r | 5 R/export.r | 5 R/export_gui.r | 7 R/filterProfile.r | 5 R/filterProfile_gui.r | 8 R/generateEPG.r | 5 R/generateEPG_gui.r | 5 R/getDb.r | 3 R/getKit.r | 25 +- R/ggsave_gui.r | 6 R/guessProfile.r | 5 R/guessProfile_gui.r | 2 R/heightToPeak.r | 5 R/import.r | 41 +--- R/import_gui.r | 5 R/listObjects.r | 21 +- R/makeKit_gui.r | 5 R/modelDropout_gui.r | 106 +++++++--- R/plotAT_gui.r | 12 - R/plotBalance_gui.r | 15 - R/plotCapillary_gui.r | 7 R/plotDistribution_gui.r | 28 +- R/plotDropout_gui.r | 11 - R/plotKit_gui.r | 6 R/plotPeaks_gui.r | 9 R/plotPrecision_gui.r | 14 - R/plotPullup_gui.r | 8 R/plotResultType_gui.r | 10 R/plotStutter_gui.r | 16 - R/slim.r | 291 +++++++++++++++++----------- R/slim_gui.r | 7 R/strvalidator.r | 11 - R/tableBalance.r | 5 R/tableBalance_gui.r | 7 R/tableCapillary.r | 7 R/tableCapillary_gui.r | 7 R/tablePrecision.r | 6 R/tablePrecision_gui.r | 8 R/tableStutter.r | 5 R/tableStutter_gui.r | 7 R/trim.r | 5 R/trim_gui.r | 8 README.md | 9 man/addColor.Rd | 2 man/addData.Rd | 2 man/addData_gui.Rd | 2 man/addDye_gui.Rd | 2 man/addMarker.Rd | 2 man/addMarker_gui.Rd | 2 man/addSize.Rd | 2 man/addSize_gui.Rd | 2 man/blockAT.Rd | 5 man/calculateAT.Rd | 9 man/calculateAT6.Rd | 2 man/calculateAT6_gui.Rd | 2 man/calculateAT_gui.Rd | 2 man/calculateBalance.Rd | 4 man/calculateBalance_gui.Rd | 2 man/calculateCapillary.Rd | 2 man/calculateCapillary_gui.Rd | 2 man/calculateConcordance.Rd | 2 man/calculateConcordance_gui.Rd | 2 man/calculateDropout.Rd | 2 man/calculateDropout_gui.Rd | 2 man/calculateHeight.Rd | 2 man/calculateHeight_gui.Rd | 2 man/calculateHeterozygous.Rd | 2 man/calculateHeterozygous_gui.Rd | 2 man/calculateMixture.Rd | 2 man/calculateMixture_gui.Rd | 2 man/calculateOL.Rd | 2 man/calculateOL_gui.Rd | 2 man/calculateOverlap.Rd | 2 man/calculateOverlap_gui.Rd | 2 man/calculatePeaks.Rd | 2 man/calculatePeaks_gui.Rd | 2 man/calculatePullup.Rd | 2 man/calculatePullup_gui.Rd | 2 man/calculateResultType.Rd | 2 man/calculateResultType_gui.Rd | 2 man/calculateStutter.Rd | 2 man/calculateStutter_gui.Rd | 2 man/checkDataset.Rd | 2 man/checkSubset.Rd | 2 man/checkSubset_gui.Rd | 2 man/colNames.Rd | 2 man/columns.Rd | 2 man/columns_gui.Rd | 2 man/combineBinsAndPanels.Rd | 2 man/combine_gui.Rd | 2 man/compact.Rd | 2 man/cropData_gui.Rd | 2 man/detectKit.Rd | 2 man/editData_gui.Rd | 2 man/export.Rd | 2 man/export_gui.Rd | 2 man/filterProfile.Rd | 2 man/filterProfile_gui.Rd | 2 man/generateEPG.Rd | 2 man/generateEPG_gui.Rd | 2 man/getDb.Rd | 2 man/getKit.Rd | 8 man/ggsave_gui.Rd | 2 man/guessProfile.Rd | 2 man/guessProfile_gui.Rd | 2 man/heightToPeak.Rd | 2 man/import.Rd | 2 man/import_gui.Rd | 2 man/listObjects.Rd | 10 man/makeKit_gui.Rd | 2 man/modelDropout_gui.Rd | 87 ++++++-- man/plotAT_gui.Rd | 2 man/plotBalance_gui.Rd | 2 man/plotCapillary_gui.Rd | 2 man/plotDistribution_gui.Rd | 2 man/plotDropout_gui.Rd | 2 man/plotKit_gui.Rd | 2 man/plotPeaks_gui.Rd | 2 man/plotPrecision_gui.Rd | 2 man/plotPullup_gui.Rd | 2 man/plotResultType_gui.Rd | 2 man/plotStutter_gui.Rd | 2 man/readBinsFile.Rd | 2 man/readPanelsFile.Rd | 2 man/ref1.Rd | 2 man/ref11.Rd | 2 man/ref2.Rd | 2 man/ref3.Rd | 2 man/ref4.Rd | 2 man/ref51.Rd | 2 man/ref52.Rd | 2 man/saveObject.Rd | 2 man/set1.Rd | 2 man/set2.Rd | 2 man/set3.Rd | 2 man/set4.Rd | 2 man/set5.Rd | 2 man/slim.Rd | 2 man/slim_gui.Rd | 2 man/sortMarker.Rd | 2 man/strValidator-package.Rd | 2 man/strvalidator.Rd | 4 man/tableBalance.Rd | 2 man/tableBalance_gui.Rd | 2 man/tableCapillary.Rd | 2 man/tableCapillary_gui.Rd | 2 man/tablePrecision.Rd | 2 man/tablePrecision_gui.Rd | 2 man/tableStutter.Rd | 2 man/tableStutter_gui.Rd | 2 man/trim.Rd | 2 man/trim_gui.Rd | 2 197 files changed, 1300 insertions(+), 807 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph],
Matthew Collins [aut, cre],
Scott Chamberlain [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>
Diff between ridigbio versions 0.3 dated 2015-07-14 and 0.3.1 dated 2015-08-31
DESCRIPTION | 8 +++--- MD5 | 6 ++--- tests/testthat/test-idig_count_media.R | 38 ++++++++++++++++---------------- tests/testthat/test-idig_search_media.R | 2 - 4 files changed, 27 insertions(+), 27 deletions(-)
Title: Clustering using Mixture Models
Description: Algorithms and methods for estimating parametric mixture models with missing data.
Author: Serge Iovleff [aut, cre]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between MixAll versions 1.0.2 dated 2015-04-04 and 1.1.1 dated 2015-08-31
DESCRIPTION | 16 - MD5 | 155 ++++++----- NAMESPACE | 11 R/ClusterAlgo.R | 47 ++- R/ClusterCategorical.R | 34 +- R/ClusterDiagGaussian.R | 32 +- R/ClusterGamma.R | 28 +- R/ClusterHeterogeneous.R | 8 R/ClusterInit.R | 44 ++- R/ClusterKernel.R |only R/ClusterModelNames.R | 162 ++++++++--- R/ClusterPoisson.R | 5 R/ClusterStrategy.R | 8 R/IClusterModel.R | 2 R/MixAll.R | 29 +- R/global.R | 13 R/missingValues.R | 18 + build/vignette.rds |binary data/bullsEye.rda |only inst/doc/Introduction-Mixtures.R | 57 ++-- inst/doc/Introduction-Mixtures.Rnw | 406 +++++++++++++++++++++--------- inst/doc/Introduction-Mixtures.pdf |binary man/ClusterAlgo-class.Rd | 8 man/ClusterCategorical-class.Rd | 4 man/ClusterCategoricalComponent-class.Rd | 6 man/ClusterDiagGaussian-class.Rd | 2 man/ClusterDiagGaussianComponent-class.Rd | 4 man/ClusterGamma-class.Rd | 6 man/ClusterGammaComponent-class.Rd | 6 man/ClusterHeterogeneous-class.Rd | 2 man/ClusterInit-class.Rd | 2 man/ClusterKernel-class.Rd |only man/ClusterKernelComponent-class.Rd |only man/ClusterModels-class.Rd | 2 man/ClusterPoisson-class.Rd | 2 man/ClusterStrategy-class.Rd | 2 man/DebTrivedi.Rd | 2 man/HeartDisease.Rd | 2 man/IClusterComponent-class.Rd | 2 man/MixAll-package.Rd | 18 - man/birds.Rd | 2 man/bullsEye.Rd |only man/car.Rd | 2 man/clusterAlgo.Rd | 13 man/clusterCategorical.Rd | 23 - man/clusterCategoricalNames.Rd | 9 man/clusterDiagGaussian.Rd | 16 - man/clusterDiagGaussianNames.Rd | 28 +- man/clusterGamma.Rd | 13 man/clusterGammaNames.Rd | 23 - man/clusterHeterogeneous.Rd | 6 man/clusterInit.Rd | 5 man/clusterKernel.Rd |only man/clusterKernelNames.Rd |only man/clusterPoisson.Rd | 4 man/clusterPoissonNames.Rd | 9 man/clusterStrategy.Rd | 2 man/extract-methods.Rd | 7 man/geyser.Rd | 2 man/initialize-methods.Rd | 21 + man/missingValues-methods.Rd | 19 + man/plot-ClusterCategorical-method.Rd | 4 man/plot-ClusterDiagGaussian-method.Rd | 4 man/plot-ClusterGamma-method.Rd | 4 man/plot-ClusterHeterogeneous-method.Rd | 2 man/plot-ClusterKernel-method.Rd |only man/plot-ClusterPoisson-method.Rd | 4 man/print-methods.Rd | 10 man/show-methods.Rd | 12 man/summary-methods.Rd | 7 man/titanic.Rd | 2 src/ClusterFacade.cpp | 23 - src/ClusterFacade.h | 4 src/ClusterLauncher.cpp | 151 +++++++---- src/ClusterLauncher.h | 41 ++- src/RDataHandler.cpp | 5 src/RDataHandler.h | 24 - src/RankMixture |only src/clusterMixture.cpp | 76 +++++ tests/simulHeterogeneous.R |only vignettes/Introduction-Mixtures.Rnw | 406 +++++++++++++++++++++--------- vignettes/MixAll.bib | 26 + 82 files changed, 1460 insertions(+), 694 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related mathematical operations oriented around the oft cited and fundamental bicopula theory described by Nelsen (2006), Joe (2014), and other selected works. The lower, upper, product, and a few select other bicopula are implemented. Individual copula support is deliberately limited to keep the package focused on an educational API to major bicopula theory. Expressions for an arbitrary bicopula include the diagonal, survival copula, the dual of a copula, co-copula, and numerical bicopula density. Level curves (sets) as well as horizontal and vertical sections and derivatives of such sections also are supported. The numerical derivatives of a bicopula are provided as well as inverses; simulation by the conditional distribution method thus are supported. Composition, convex combination, and products of bicopula are provided. Copula properties include Kendall Function and L-moments thereof, Kendall Tau, Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-Wolff Sigma, tail dependency and order, and skewness. Evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing are available. Kullback-Leibler divergence, Vuong's procedure, and L-comoments for copula inference are available. Quantile and median regressions for V with respect to U and U with respect to V are available. Empirical copulas (EC) are supported.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 1.7.1 dated 2015-01-30 and 2.0.1 dated 2015-08-31
ChangeLog | 125 ++++++++++-- DESCRIPTION | 12 - MD5 | 273 ++++++++++++++++------------ NAMESPACE | 41 +++- R/COP.R | 21 +- R/COPinv.R | 20 +- R/COPinv2.R | 18 + R/EMPIRcop.R | 69 +++---- R/EMPIRsim.R | 54 ++++- R/FRECHETcop.R | 17 - R/GHcop.R | 40 +++- R/GLcop.R |only R/HRcop.R |only R/P.R | 2 R/PARETOcop.R |only R/PSP.R | 8 R/W.R | 2 R/blomCOP.R | 6 R/composite1COP.R | 4 R/composite2COP.R | 5 R/composite3COP.R | 3 R/convex2COP.R |only R/copBasic.fitpara.R |only R/densityCOP.R | 25 +- R/derCOPinv.R | 9 R/derCOPinv2.R | 9 R/diagCOPatf.R | 46 +++- R/footCOP.R |only R/giniCOP.R | 24 ++ R/hoefCOP.R | 93 +++++++-- R/isfuncCOP.R |only R/joeskewCOP.R |only R/joint.curvesCOP.R |only R/joint.curvesCOP2.R |only R/jointCOP.R |only R/kfuncCOP.R |only R/kfuncCOPinv.R |only R/kfuncCOPlmoms.R |only R/kullCOP.R | 102 +++++++++- R/lcomCOPpv.R | 132 +++++++------ R/prod2COP.R |only R/qua.regressCOP.draw.R | 8 R/rhoCOP.R | 22 +- R/rhobevCOP.R |only R/semicorCOP.R | 12 - R/simCOP.R | 12 - R/simCOPmicro.R | 20 +- R/statTn.R |only R/tailconCOP.R |only R/tauCOP.R | 73 +++++-- R/uvlmoms.R | 10 - R/vuongCOP.R | 79 ++++++-- R/wolfCOP.R | 45 +++- inst/CITATION | 2 inst/doc/CopulaRelations_BaseFigure_inR.txt |only man/COP.Rd | 43 ++++ man/COPinv.Rd | 13 + man/COPinv2.Rd | 13 + man/EMPIRcop.Rd | 143 ++++++++++---- man/EMPIRcopdf.Rd | 5 man/EMPIRgrid.Rd | 4 man/EMPIRgridder.Rd | 2 man/EMPIRgridder2.Rd | 2 man/EMPIRgridderinv.Rd | 2 man/EMPIRgridderinv2.Rd | 2 man/EMPIRmed.regress.Rd | 2 man/EMPIRmed.regress2.Rd | 2 man/EMPIRqua.regress.Rd | 4 man/EMPIRqua.regress2.Rd | 4 man/EMPIRsim.Rd | 39 +++- man/EMPIRsimv.Rd | 35 +-- man/FRECHETcop.Rd | 44 +++- man/GHcop.Rd | 236 ++++++++++++++++++++---- man/GLcop.Rd |only man/HRcop.Rd |only man/M.Rd | 3 man/N4212cop.Rd | 15 - man/P.Rd | 8 man/PARETOcop.Rd |only man/PLACKETTcop.Rd | 23 +- man/PLACKETTpar.Rd | 40 ++-- man/PLACKETTsim.Rd | 4 man/PSP.Rd | 8 man/PlackettPlackettABKGtest.Rd | 20 +- man/PlackettPlackettNP.Rd | 16 - man/ReineckeWell266.Rd | 3 man/ReineckeWells.Rd | 3 man/W.Rd | 3 man/asCOP.Rd | 12 - man/blomCOP.Rd | 28 +- man/coCOP.Rd | 17 + man/composite1COP.Rd | 6 man/composite2COP.Rd | 12 - man/composite3COP.Rd | 18 + man/convex2COP.Rd |only man/copBasic-package.Rd | 174 +++++++++++------ man/copBasic.fitpara.Rd |only man/densityCOP.Rd | 21 +- man/densityCOPplot.Rd | 28 +- man/derCOP.Rd | 23 +- man/derCOP2.Rd | 18 - man/derCOPinv.Rd | 121 ++++++++++-- man/derCOPinv2.Rd | 42 ++-- man/diagCOP.Rd | 21 +- man/diagCOPatf.Rd | 40 ++-- man/duCOP.Rd | 93 ++++++++- man/figures |only man/footCOP.Rd |only man/giniCOP.Rd | 88 ++++++--- man/gridCOP.Rd | 17 + man/hoefCOP.Rd | 102 +++++++--- man/isCOP.LTD.Rd | 6 man/isCOP.PQD.Rd | 56 +++-- man/isCOP.RTI.Rd | 9 man/isCOP.permsym.Rd | 10 - man/isCOP.radsym.Rd | 34 +-- man/isfuncCOP.Rd |only man/joeskewCOP.Rd |only man/joint.curvesCOP.Rd |only man/joint.curvesCOP2.Rd |only man/jointCOP.Rd |only man/kfuncCOP.Rd |only man/kfuncCOPinv.Rd |only man/kfuncCOPlmoms.Rd |only man/kullCOP.Rd | 93 +++++---- man/lcomCOPpv.Rd | 24 +- man/lcomoms2.ABKGcop2parameter.Rd | 13 - man/lcomoms2.ABcop2parameter.Rd | 20 -- man/level.curvesCOP.Rd | 25 +- man/level.curvesCOP2.Rd | 15 - man/level.setCOP.Rd | 13 - man/level.setCOP2.Rd | 16 - man/med.regressCOP.Rd | 21 -- man/med.regressCOP2.Rd | 9 man/prod2COP.Rd |only man/qua.regressCOP.Rd | 27 +- man/qua.regressCOP.draw.Rd | 6 man/qua.regressCOP2.Rd | 4 man/rhoCOP.Rd | 25 +- man/rhobevCOP.Rd |only man/sectionCOP.Rd | 15 - man/semicorCOP.Rd | 29 +- man/simCOP.Rd | 29 +- man/simCOPmicro.Rd | 82 ++++++++ man/simcomposite3COP.Rd | 13 - man/simcompositeCOP.Rd | 21 -- man/statTn.Rd |only man/surCOP.Rd | 13 - man/surfuncCOP.Rd | 14 + man/tailconCOP.Rd |only man/taildepCOP.Rd | 54 +++-- man/tailordCOP.Rd | 34 +-- man/tauCOP.Rd | 65 ++++-- man/uvlmoms.Rd | 40 ++-- man/vuongCOP.Rd | 165 +++++++++------- man/wolfCOP.Rd | 44 +++- 156 files changed, 2754 insertions(+), 1355 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Bayesian inference for structure learning in undirected graphical models. The main target is to uncover complicated patterns in multivariate data wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.21 dated 2015-08-23 and 2.22 dated 2015-08-31
DESCRIPTION | 8 +- MD5 | 24 +++---- NAMESPACE | 1 R/bdgraph.R | 124 ++++++++++++++++++++------------------ R/plotcoda.R | 5 - R/select.R | 2 R/traceplot.R | 57 +++++++++-------- build/vignette.rds |binary man/BDgraph-package.Rd | 2 man/bdgraph.Rd | 15 +--- man/plotcoda.Rd | 2 man/traceplot.Rd | 4 - src/BDgraph.cpp | 157 +++++++++++++++++++++++++++---------------------- 13 files changed, 214 insertions(+), 187 deletions(-)
Title: Asymmetric Price Transmission
Description: Asymmetric price transmission between two time series is assessed. Several functions are available for linear and nonlinear threshold cointegration, and furthermore, symmetric and asymmetric error correction model. A graphical user interface is also included for major functions included in the package, so users can also use these functions in a more intuitive way.
Author: Changyou Sun <cs258@msstate.edu>
Maintainer: Changyou Sun <cs258@msstate.edu>
Diff between apt versions 2.3 dated 2014-11-27 and 2.4 dated 2015-08-31
apt-2.3/apt/inst/doc/ERERchapter17SampleStudyAPT.pdf |only apt-2.4/apt/DESCRIPTION | 12 ++--- apt-2.4/apt/MD5 | 14 +++--- apt-2.4/apt/NAMESPACE | 43 +++++++++++++++++-- apt-2.4/apt/build/vignette.rds |binary apt-2.4/apt/inst/doc/ERERchapter17smallSize.pdf |only apt-2.4/apt/inst/doc/apt.pdf |binary apt-2.4/apt/man/apt-package.Rd | 8 +-- apt-2.4/apt/man/daVich.Rd | 2 9 files changed, 58 insertions(+), 21 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.3 dated 2015-07-27 and 0.2.4 dated 2015-08-31
RGA-0.2.3/RGA/R/rt.R |only RGA-0.2.3/RGA/R/shiny.R |only RGA-0.2.3/RGA/man/RGA.Rd |only RGA-0.2.3/RGA/man/dimsmets.Rd |only RGA-0.2.3/RGA/man/get_rt.Rd |only RGA-0.2.3/RGA/man/list_metadata.Rd |only RGA-0.2.4/RGA/DESCRIPTION | 19 +-- RGA-0.2.4/RGA/MD5 | 84 +++++++-------- RGA-0.2.4/RGA/NAMESPACE | 15 -- RGA-0.2.4/RGA/R/auth.R | 33 +++++- RGA-0.2.4/RGA/R/convert.R | 12 -- RGA-0.2.4/RGA/R/firstdate.R | 5 RGA-0.2.4/RGA/R/ga.R | 10 - RGA-0.2.4/RGA/R/get-data.R | 10 - RGA-0.2.4/RGA/R/mcf.R | 8 - RGA-0.2.4/RGA/R/metadata.R | 21 ++- RGA-0.2.4/RGA/R/mgmt.R | 1 RGA-0.2.4/RGA/R/package.R | 6 - RGA-0.2.4/RGA/R/query.R | 4 RGA-0.2.4/RGA/R/realtime.R |only RGA-0.2.4/RGA/R/report.R | 26 ++-- RGA-0.2.4/RGA/R/request.R | 25 +++- RGA-0.2.4/RGA/R/url.R | 25 ---- RGA-0.2.4/RGA/R/utils.R | 3 RGA-0.2.4/RGA/R/zzz.R | 1 RGA-0.2.4/RGA/README.md | 33 ++++-- RGA-0.2.4/RGA/build/vignette.rds |binary RGA-0.2.4/RGA/data/ga.rda |binary RGA-0.2.4/RGA/inst/NEWS.Rd | 144 ++++++++++++++------------- RGA-0.2.4/RGA/inst/doc/authorize.Rmd | 15 ++ RGA-0.2.4/RGA/inst/doc/authorize.html | 9 + RGA-0.2.4/RGA/inst/doc/metadata-api.Rmd | 12 -- RGA-0.2.4/RGA/inst/doc/metadata-api.html | 8 - RGA-0.2.4/RGA/inst/doc/reporting-api.Rmd | 21 ++- RGA-0.2.4/RGA/inst/doc/reporting-api.html | 21 ++- RGA-0.2.4/RGA/man/RGA-package.Rd |only RGA-0.2.4/RGA/man/authorize.Rd | 9 + RGA-0.2.4/RGA/man/firstdate.Rd | 8 + RGA-0.2.4/RGA/man/ga.Rd | 4 RGA-0.2.4/RGA/man/get_ga.Rd | 9 - RGA-0.2.4/RGA/man/get_mcf.Rd | 7 - RGA-0.2.4/RGA/man/get_realtime.Rd |only RGA-0.2.4/RGA/man/list_dimsmets.Rd |only RGA-0.2.4/RGA/tests/testthat/test-metadata.R | 2 RGA-0.2.4/RGA/tests/testthat/test-url.R | 7 - RGA-0.2.4/RGA/vignettes/authorize.Rmd | 15 ++ RGA-0.2.4/RGA/vignettes/metadata-api.Rmd | 12 -- RGA-0.2.4/RGA/vignettes/reporting-api.Rmd | 21 ++- 48 files changed, 360 insertions(+), 305 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.2.1 dated 2015-08-13 and 1.2.2 dated 2015-08-31
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 1 + R/foo.R | 37 ++++++++++++++++++++++++++++++++++++- man/binomial.logistic.MCML.Rd | 2 ++ man/trace.plot.MCML.Rd |only 6 files changed, 48 insertions(+), 9 deletions(-)
Title: Hierarchical Generalized Linear Models
Description: Procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Moudud Alam, Lars Ronnegard, Xia Shen
Maintainer: Xia Shen <xia.shen@ki.se>
Diff between hglm versions 2.1-0 dated 2015-05-19 and 2.1-1 dated 2015-08-31
hglm-2.1-0/hglm/build |only hglm-2.1-1/hglm/ChangeLog | 10 +++++ hglm-2.1-1/hglm/DESCRIPTION | 10 ++--- hglm-2.1-1/hglm/MD5 | 28 +++++++------- hglm-2.1-1/hglm/NAMESPACE | 14 ++++++- hglm-2.1-1/hglm/R/GLM.MME.R | 7 ++- hglm-2.1-1/hglm/R/hglm.default.R | 2 - hglm-2.1-1/hglm/R/hglm.formula.R | 2 - hglm-2.1-1/hglm/R/hglm2.formula.R | 3 + hglm-2.1-1/hglm/inst/doc/hglm.R |only hglm-2.1-1/hglm/inst/doc/hglm.Rnw | 2 - hglm-2.1-1/hglm/inst/doc/hglm.pdf |binary hglm-2.1-1/hglm/man/hglm-package.Rd | 4 +- hglm-2.1-1/hglm/man/inverse.gamma.Rd |only hglm-2.1-1/hglm/man/inverse.sqrt.Rd |only hglm-2.1-1/hglm/vignettes/hglm-knitr-knitr-compressed.pdf |binary hglm-2.1-1/hglm/vignettes/hglm.Rnw | 2 - 17 files changed, 54 insertions(+), 30 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei (Wayne) Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [aut],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.1 dated 2015-07-11 and 0.2.2 dated 2015-08-31
DESCRIPTION | 14 +- MD5 | 41 ++++- NAMESPACE | 15 +- NEWS | 13 + R/MultiChainLadder.R | 2 R/glmReserve.R | 69 ++++++++-- build/vignette.rds |binary inst/doc/ChainLadder.R | 16 +- inst/doc/ChainLadder.Rnw | 11 - inst/doc/ChainLadder.pdf |binary man/glmReserve.Rd | 31 +++- vignettes/ChainLadder.Rnw | 11 - vignettes/Log-incremental/Log-incremental-019.pdf |only vignettes/Log-incremental/Log-incremental-025.pdf |only vignettes/Log-incremental/Log-incremental-028.pdf |only vignettes/Log-incremental/Log-incremental-031.pdf |only vignettes/Log-incremental/Log-incremental-concordance.tex |only vignettes/Log-incremental/Log-incremental-linerregressionplot.pdf |only vignettes/Log-incremental/Log-incremental-triangleplotinteractionplot.pdf |only vignettes/Log-incremental/Log-incremental-triangleplotlattice.pdf |only vignettes/Log-incremental/Log-incremental-trianglestructure.pdf |only vignettes/Log-incremental/Log-incremental.Rnw | 7 - vignettes/Log-incremental/Log-incremental.bbl |only vignettes/Log-incremental/Log-incremental.log |only vignettes/Log-incremental/Log-incremental.pdf |only vignettes/Log-incremental/Log-incremental.synctex.gz |only vignettes/Log-incremental/Log-incremental.tex |only vignettes/Log-incremental/Log-incremental.toc |only vignettes/Log-incremental/Rplots.pdf |only vignettes/glmReservePlot.png |only 30 files changed, 172 insertions(+), 58 deletions(-)
Title: Dynamic Plots for Time Series Forecasting
Description: Combines a forecast of a time series, using the function forecast(), with the dynamic plots from dygraphs.
Author: David Beiner
Maintainer: David Beiner <zra.r.package@gmail.com>
Diff between ZRA versions 0.1 dated 2015-08-23 and 0.2 dated 2015-08-31
DESCRIPTION | 8 +-- MD5 | 6 +- R/ZRA.R | 126 +++++++++++++++++++++++++++++++----------------------------- man/ZRA.Rd | 6 +- 4 files changed, 76 insertions(+), 70 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb],
Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.2.0 dated 2015-06-19 and 1.2.1 dated 2015-08-31
DESCRIPTION | 11 +- MD5 | 16 ++-- NAMESPACE | 1 NEWS | 16 +++- R/suffix.R | 157 ++++++++++++++++++++++++++--------------- man/suffix_extract.Rd | 14 +-- src/compose.h | 35 +++++++++ src/parsing.h | 9 ++ tests/testthat/test_suffixes.R | 40 ++++++++-- 9 files changed, 214 insertions(+), 85 deletions(-)
Title: Specific Correspondence Analysis for the Social Sciences
Description: Specific and class specific multiple correspondence analysis on survey-like data. Soc.ca is optimized to the needs of the social
scientist and presents easily interpretable results in near publication ready quality.
Author: Anton Grau Larsen, with contributions from Christoph Ellersgaard and
Stefan Andrade
Maintainer: Anton Grau Larsen <alar@soc.ku.dk>
Diff between soc.ca versions 0.7.1 dated 2014-02-08 and 0.7.2 dated 2015-08-31
DESCRIPTION | 18 +--- MD5 | 92 ++++++++++++------------ NAMESPACE | 6 + R/data_documentation.r | 2 R/functions_analysis.r | 101 ++++++++++++++++++++++++++ R/functions_array.r | 10 +- R/functions_description.r | 11 +- R/functions_ellipse.r | 109 ++++++++++++++++------------ R/functions_label.r | 2 R/functions_plot.r | 44 +++++++++-- R/zzz.r |only man/add.count.Rd | 18 ++-- man/add.to.label.Rd | 24 ++---- man/assign.label.Rd | 37 ++++----- man/average.coord.Rd | 15 +-- man/balance.Rd | 18 ++-- man/contribution.Rd | 45 +++++------ man/create.quadrant.Rd | 19 ++--- man/csa.all.Rd | 23 ++---- man/csa.measures.Rd | 26 ++---- man/directors.Rd | 71 ++++++++---------- man/export.Rd | 9 +- man/export.label.Rd | 33 +++----- man/indicator.Rd | 13 +-- man/invert.Rd | 15 +-- man/map.active.Rd | 111 ++++++++++++++--------------- man/map.add.Rd | 147 ++++++++++++++++++--------------------- man/map.array.Rd | 23 ++---- man/map.csa.all.Rd | 32 +++----- man/map.csa.mca.Rd | 14 +-- man/map.csa.mca.array.Rd | 13 +-- man/map.ctr.Rd | 88 +++++++++++------------ man/map.density.Rd | 38 ++++------ man/map.ellipse.Rd | 32 ++++---- man/map.ellipse.array.Rd | 33 ++++---- man/map.ind.Rd | 78 +++++++++----------- man/map.mod.Rd | 112 ++++++++++++++--------------- man/map.path.Rd | 33 ++++---- man/map.select.Rd | 143 ++++++++++++++++++------------------- man/map.sup.Rd | 111 ++++++++++++++--------------- man/min_cut.Rd | 20 ++--- man/print.soc.mca.Rd | 31 ++++---- man/soc.ca.Rd | 36 ++++----- man/soc.csa.Rd | 85 ++++++++-------------- man/soc.mca.Rd | 82 ++++++++------------- man/supplementary.individuals.Rd |only man/taste.Rd | 24 ++---- man/variance.Rd | 18 ++-- 48 files changed, 1045 insertions(+), 1020 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Description: Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ<matthias.templ@gmail.com>
Diff between simPop versions 0.2.9 dated 2015-01-26 and 0.2.12 dated 2015-08-31
DESCRIPTION | 12 - MD5 | 35 ++--- NAMESPACE | 10 + NEWS | 13 + R/ipu.r | 153 +++++++++++++++++++++ R/simCategorical.R | 148 +++++++++++++-------- R/simContinuous.R | 307 ++++++++++++++++++++++++++++---------------- R/utils.R | 304 +++++++++++++++++++++++++++++++++++++++++-- data/eusilcP.RData |binary data/eusilcS.RData |binary data/ghanaS.RData |binary data/totalsRG.rda |binary data/totalsRGtab.rda |binary man/set_get-methods.Rd |only man/simCategorical.Rd | 14 +- man/simContinuous.Rd | 16 +- tests/cpp_sa.r |only tests/debug_ipu.r |only tests/mosaicplots.r |only tests/test_simCategorical.r |only tests/test_sprague.R | 274 --------------------------------------- 21 files changed, 809 insertions(+), 477 deletions(-)
Title: Package for Calculation of ARMSS, Local MSSS and Global MSSS
Description: Calculates ARMSS, age related multiple sclerosis severity score, and both local and global msss.
Author: Helga Westerlind, Ali Manouchehrinia
Maintainer: Helga Westerlind <Helga.Westerlind@ki.se>
Diff between ms.sev versions 1.0 dated 2015-08-26 and 1.0.1 dated 2015-08-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ms_sev.R | 30 ++++++++++++++---------------- 3 files changed, 19 insertions(+), 21 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Description: Functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre],
Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between gMCP versions 0.8-9 dated 2015-08-10 and 0.8-10 dated 2015-08-31
gMCP-0.8-10/gMCP/DESCRIPTION | 6 gMCP-0.8-10/gMCP/MD5 | 97 gMCP-0.8-10/gMCP/NAMESPACE | 2 gMCP-0.8-10/gMCP/NEWS | 23 gMCP-0.8-10/gMCP/R/calcPower.R | 141 gMCP-0.8-10/gMCP/R/exampleGraphs.R | 3 gMCP-0.8-10/gMCP/R/gACT-internal.R | 17 gMCP-0.8-10/gMCP/R/gMCP.R | 40 gMCP-0.8-10/gMCP/R/gMCP.extended.R | 6 gMCP-0.8-10/gMCP/R/graphTest.R | 63 gMCP-0.8-10/gMCP/R/onLoad.R | 3 gMCP-0.8-10/gMCP/R/sampSize.R | 12 gMCP-0.8-10/gMCP/R/subVariables.R | 45 gMCP-0.8-10/gMCP/TODO | 73 gMCP-0.8-10/gMCP/inst/doc/AQuickStart.pdf |binary gMCP-0.8-10/gMCP/inst/doc/gMCP.R | 4336 ---------- gMCP-0.8-10/gMCP/inst/doc/gMCP.Rnw | 30 gMCP-0.8-10/gMCP/inst/doc/gMCP.pdf |binary gMCP-0.8-10/gMCP/inst/doc/parametric.pdf |binary gMCP-0.8-10/gMCP/inst/java/gsrmtp.jar |binary gMCP-0.8-10/gMCP/inst/unitTests/runit.sampSize.R | 28 gMCP-0.8-10/gMCP/java/org/af/gMCP/config/GeneralConfig.java | 11 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/CreateGraphGUI.java | 50 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/MenuBarMGraph.java | 8 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/graph/GraphView.java | 13 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/graph/NetList.java | 3 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/graph/PView.java | 3 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/options/MiscPanel.java | 63 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/options/OptionsDialog.java | 27 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/CVPanel.java | 4 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/NCPCalculatorDialog.java | 2 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/PDialog.java | 4 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/PowerDialog.java | 124 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/PowerReq.java | 4 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/PowerResultDialog.java | 130 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/PowerResultTableModel.java |only gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/RandomizationPanel.java | 2 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/SampSizeResultTableModel.java |only gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/SampleSizeDialog.java | 21 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/Scenario.java | 4 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/ScenarioPanel.java | 9 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/UserDefinedPanel.java | 4 gMCP-0.8-10/gMCP/java/org/af/gMCP/gui/power/VariablePanel.java |only gMCP-0.8-10/gMCP/man/exampleGraphs.Rd | 2 gMCP-0.8-10/gMCP/man/gMCP.Rd | 2 gMCP-0.8-10/gMCP/man/rejectNode.Rd | 7 gMCP-0.8-10/gMCP/man/replaceVariables.Rd | 19 gMCP-0.8-10/gMCP/man/sampSize.Rd | 8 gMCP-0.8-10/gMCP/vignettes/gMCP.Rnw | 30 gMCP-0.8-10/gMCP/vignettes/pictures/ImportTextLibreOffice.png |only gMCP-0.8-10/gMCP/vignettes/pictures/PowerResults.png |only gMCP-0.8-10/gMCP/vignettes/pvals.RData |only gMCP-0.8-9/gMCP/vignettes/childs |only 53 files changed, 780 insertions(+), 4699 deletions(-)
Title: Empirical Research in Economics with R
Description: Functions, datasets, and sample codes related to the book of 'Empirical Research in Economics: Growing up with R' by Dr. Changyou Sun are included. Marginal effects for binary or ordered choice models can be calculated. Static and dynamic Almost Ideal Demand System (AIDS) models can be estimated. A typical event analysis in finance can be conducted with several functions included.
Author: Changyou Sun <cs258@msstate.edu>
Maintainer: Changyou Sun <cs258@msstate.edu>
Diff between erer versions 2.3 dated 2014-11-27 and 2.4 dated 2015-08-31
erer-2.3/erer/inst/doc/r119Amemo.r |only erer-2.3/erer/inst/doc/r119Bdemand.r |only erer-2.3/erer/inst/doc/r166mapGgplot.r |only erer-2.4/erer/DESCRIPTION | 10 - erer-2.4/erer/MD5 | 118 +++++++++--------- erer-2.4/erer/NAMESPACE | 48 ++++++- erer-2.4/erer/R/ocME.r | 2 erer-2.4/erer/inst/doc/r073curlybrace.r | 2 erer-2.4/erer/inst/doc/r085sample.r | 2 erer-2.4/erer/inst/doc/r086excel.r | 14 +- erer-2.4/erer/inst/doc/r087export.r | 6 erer-2.4/erer/inst/doc/r091operator.r | 2 erer-2.4/erer/inst/doc/r092string.r | 6 erer-2.4/erer/inst/doc/r094string_app.r | 3 erer-2.4/erer/inst/doc/r101index.r | 3 erer-2.4/erer/inst/doc/r102dataframe.r | 2 erer-2.4/erer/inst/doc/r103dataframeSummary.r | 2 erer-2.4/erer/inst/doc/r104dataframeApply.r | 5 erer-2.4/erer/inst/doc/r105callingFunction.r | 4 erer-2.4/erer/inst/doc/r114multiplepages.r | 16 +- erer-2.4/erer/inst/doc/r115multiplegraphs.r | 35 ++++- erer-2.4/erer/inst/doc/r116highlow.r | 12 - erer-2.4/erer/inst/doc/r117region.r | 16 +- erer-2.4/erer/inst/doc/r119Ademand.r |only erer-2.4/erer/inst/doc/r119Bmemo.r |only erer-2.4/erer/inst/doc/r121wanJAAE.r | 24 ++- erer-2.4/erer/inst/doc/r131conditional.r | 2 erer-2.4/erer/inst/doc/r134stop.r | 2 erer-2.4/erer/inst/doc/r136elasticity.r | 4 erer-2.4/erer/inst/doc/r142inversion.r | 2 erer-2.4/erer/inst/doc/r145meBinary.r | 4 erer-2.4/erer/inst/doc/r153return.r | 8 - erer-2.4/erer/inst/doc/r154environment.r | 18 +- erer-2.4/erer/inst/doc/r155s34need.r | 6 erer-2.4/erer/inst/doc/r156s3.r | 23 ++- erer-2.4/erer/inst/doc/r159Boptimize.r | 4 erer-2.4/erer/inst/doc/r159Coptim.r | 4 erer-2.4/erer/inst/doc/r161gridBasic.r | 29 ++-- erer-2.4/erer/inst/doc/r162gridHunt.r | 5 erer-2.4/erer/inst/doc/r163gridMemo.r | 13 + erer-2.4/erer/inst/doc/r164ggplotHunt.r | 9 - erer-2.4/erer/inst/doc/r165ggplotAids.r | 21 +-- erer-2.4/erer/inst/doc/r166map.r | 5 erer-2.4/erer/inst/doc/r172sunBedsGraph.r | 24 +-- erer-2.4/erer/inst/doc/r181debug.r | 7 - erer-2.4/erer/inst/doc/r181missFunction.r |only erer-2.4/erer/inst/doc/r182time.r | 10 - erer-2.4/erer/inst/doc/r191skeleton.r | 6 erer-2.4/erer/inst/doc/r192ciTarFit.r | 13 - erer-2.4/erer/inst/doc/r193namespace.r | 2 erer-2.4/erer/inst/doc/r201chess.r | 6 erer-2.4/erer/inst/doc/r202tax.r | 10 - erer-2.4/erer/inst/doc/r203guiCor.r | 7 - erer-2.4/erer/inst/doc/rAppendixShowbox3mosaic.r | 13 + erer-2.4/erer/inst/doc/rAppendixShowbox4diagram.r | 8 - erer-2.4/erer/inst/doc/rAppendixShowbox5correlation.r | 7 - erer-2.4/erer/inst/doc/rAppendixShowbox6face.r | 10 - erer-2.4/erer/inst/doc/rAppendixocME.r | 17 +- erer-2.4/erer/inst/doc/rAppendixocProb.r | 16 +- erer-2.4/erer/man/daBed.Rd | 2 erer-2.4/erer/man/daBedRaw.Rd | 2 erer-2.4/erer/man/erer-package.Rd | 10 - erer-2.4/erer/man/ocME.Rd | 5 63 files changed, 388 insertions(+), 278 deletions(-)
Title: Discriminant Analysis with Additional Information
Description: In applications it is usual that some additional information is available. This package dawai (an acronym for Discriminant Analysis With Additional Information) performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means. It also computes several estimations of the true error rate.
Author: David Conde, Miguel A. Fernandez, Bonifacio Salvador
Maintainer: David Conde <dconde@eio.uva.es>
Diff between dawai versions 1.2 dated 2015-08-13 and 1.2.1 dated 2015-08-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/dawai-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>
Diff between clusterCrit versions 1.2.5 dated 2015-06-04 and 1.2.6 dated 2015-08-31
clusterCrit-1.2.5/clusterCrit/inst/unitTests/extCriteria/runit_all_ext.R |only clusterCrit-1.2.5/clusterCrit/inst/unitTests/intCriteria/runit_all_int.R |only clusterCrit-1.2.6/clusterCrit/DESCRIPTION | 8 clusterCrit-1.2.6/clusterCrit/MD5 | 124 ++++------ clusterCrit-1.2.6/clusterCrit/build/clusterCrit.pdf |binary clusterCrit-1.2.6/clusterCrit/build/partial.rdb |binary clusterCrit-1.2.6/clusterCrit/inst/unitTests/Makefile | 2 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_czekanowski_dice.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_folkes_mallows.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_hubert.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_jaccard.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_kulczynski.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_mcnemar.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_phi.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_precision.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_rand.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_recall.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_rogers_tanimoto.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_russel_rao.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_sokal_sneath1.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/extCriteria/runit_sokal_sneath2.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_ball_hall.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_banfeld_raftery.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_c_index.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_calinski_harabasz.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_davies_bouldin.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_det_ratio.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_dunn.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_g_plus.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gamma.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi11.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi12.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi13.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi21.R | 7 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi22.R | 7 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi23.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi31.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi32.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi33.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi41.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi42.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi43.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi51.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi52.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_gdi53.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_ksq_detw.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_log_det_ratio.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_log_ss_ratio.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_mcclain_rao.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_pbm.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_point_biserial.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_ratkowsky_lance.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_ray_turi.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_s_dbw.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_scott_symons.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_sd_dis.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_sd_scat.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_silhouette.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_tau.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_trace_w.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_trace_wib.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_wemmert_gancarski.R | 9 clusterCrit-1.2.6/clusterCrit/inst/unitTests/intCriteria/runit_xie_beni.R | 9 clusterCrit-1.2.6/clusterCrit/src/indices.f95 | 30 +- 64 files changed, 359 insertions(+), 305 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.7 dated 2015-06-13 and 0.8 dated 2015-08-30
DESCRIPTION | 14 +- MD5 | 41 +++--- NAMESPACE | 1 NEWS | 22 +++ R/draft.R | 4 R/html_dependencies.R | 53 +++++--- R/html_resources.R | 62 +++++++--- R/output_format.R | 10 - R/pandoc.R | 4 R/params.R |only R/relative_to.R | 2 R/render.R | 33 ----- R/slidy_presentation.R | 10 - R/util.R | 2 R/word_document.R | 4 inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 4 man/knit_params_ask.Rd |only man/relative_to.Rd | 6 man/render.Rd | 3 man/word_document.Rd | 6 tests/testthat/resources/readcsv-source.R |only tests/testthat/resources/readcsv.R |only tests/testthat/resources/readcsv.Rmd |only tests/testthat/test-resources.R | 16 ++ 24 files changed, 186 insertions(+), 111 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis <arelli4@uky.edu>
Diff between npmv versions 2.2 dated 2015-02-25 and 2.3.0 dated 2015-08-30
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 ++++ R/nonpartest.R | 12 +++++++++--- R/ssnonpartest.R | 52 +++++++++++++++++++++++++++++++++++++++------------- man/npmv-package.Rd | 4 ++-- 6 files changed, 64 insertions(+), 28 deletions(-)
Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices
The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data
structures and R using concepts from 'Rcpp' which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses 'Rcpp' to connect to another third-party library. The 'autoconf'
script, 'inline' plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGSL versions 0.2.5 dated 2015-07-07 and 0.3.0 dated 2015-08-30
RcppGSL-0.2.5/RcppGSL/inst/examples/bSpline/plotHelper.R |only RcppGSL-0.2.5/RcppGSL/inst/include/macros |only RcppGSL-0.3.0/RcppGSL/ChangeLog | 65 + RcppGSL-0.3.0/RcppGSL/DESCRIPTION | 10 RcppGSL-0.3.0/RcppGSL/MD5 | 52 - RcppGSL-0.3.0/RcppGSL/R/RcppExports.R | 4 RcppGSL-0.3.0/RcppGSL/build/vignette.rds |binary RcppGSL-0.3.0/RcppGSL/cleanup | 2 RcppGSL-0.3.0/RcppGSL/inst/NEWS.Rd | 22 RcppGSL-0.3.0/RcppGSL/inst/doc/RcppGSL-intro.R | 20 RcppGSL-0.3.0/RcppGSL/inst/doc/RcppGSL-intro.Rnw | 416 ++++++---- RcppGSL-0.3.0/RcppGSL/inst/doc/RcppGSL-intro.pdf |binary RcppGSL-0.3.0/RcppGSL/inst/doc/RcppGSL-unitTests.pdf |binary RcppGSL-0.3.0/RcppGSL/inst/examples/RcppGSLExample/R/RcppExports.R | 12 RcppGSL-0.3.0/RcppGSL/inst/examples/RcppGSLExample/src/RcppExports.cpp | 30 RcppGSL-0.3.0/RcppGSL/inst/examples/RcppGSLExample/src/colNorm.cpp | 33 RcppGSL-0.3.0/RcppGSL/inst/examples/bSpline/bSpline.cpp | 82 - RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL.h | 8 RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSLForward.h | 369 ++++---- RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_matrix.h | 317 +++---- RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_matrix_view.h | 72 - RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_typedef.h |only RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_types.h |only RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_vector.h | 108 +- RcppGSL-0.3.0/RcppGSL/inst/include/RcppGSL_vector_view.h | 72 - RcppGSL-0.3.0/RcppGSL/inst/unitTests/cpp/gsl.cpp | 10 RcppGSL-0.3.0/RcppGSL/src/RcppExports.cpp | 10 RcppGSL-0.3.0/RcppGSL/src/fastLm.cpp | 50 - RcppGSL-0.3.0/RcppGSL/vignettes/RcppGSL-intro.Rnw | 416 ++++++---- 29 files changed, 1234 insertions(+), 946 deletions(-)
Title: R Wrapper for the 'Wufoo.com' - The Form Building Service
Description: Allows form managers to download entries from their respondents using Wufoo JSON API. Additionally, the Wufoo reports - when public - can be also acquired programmatically. Note that building new forms within this package is not supported.
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>
Diff between WufooR versions 0.5.5 dated 2015-07-17 and 0.5.7 dated 2015-08-30
DESCRIPTION | 12 - MD5 | 18 - NEWS | 3 R/API.R | 19 + R/Fields.R | 2 R/Form.R | 6 build/vignette.rds |binary inst/doc/Tutorial.R | 62 ++--- inst/doc/Tutorial.html | 524 ++++++++++++++++++++++++------------------------- man/fields_info.Rd | 2 10 files changed, 329 insertions(+), 319 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between spatial versions 7.3-10 dated 2015-06-29 and 7.3-11 dated 2015-08-30
DESCRIPTION | 8 ++++---- LICENCE.note | 4 ++-- MD5 | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.7-4 dated 2015-07-14 and 1.7-6 dated 2015-08-30
DESCRIPTION | 11 +- MD5 | 40 +++---- NAMESPACE | 3 R/DAS-scale.R | 12 +- R/accessors.R | 49 +++++---- R/rlmer.R | 1 build/vignette.rds |binary inst/doc/rlmer.pdf |binary man/getME.Rd | 45 ++++---- man/rlmer.Rd | 1 tests/compare-methods.Rout.save | 25 +--- tests/getME.R | 4 tests/getME.Rout.save | 87 +++++++++++++--- tests/tau.R | 15 ++ vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary vignettes/figs/fig-ex-penicillin-raw.pdf |binary vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary vignettes/figs/fig-ex-penicillin-ta.pdf |binary vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary vignettes/figs/fig-ex-smoothedHuber.pdf |binary 21 files changed, 196 insertions(+), 97 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometrics and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 1.5.6 dated 2015-07-08 and 1.5.8 dated 2015-08-30
DESCRIPTION | 8 +- MD5 | 44 ++++++------ NAMESPACE | 2 R/alpha.R | 4 - R/cosinor.R | 2 R/df2latex.R | 10 +- R/fa.R | 81 +++++++++++++++------- R/principal.R | 2 R/test.psych.r | 121 ++++++++++++++++++++++----------- inst/CITATION | 4 - inst/NEWS.Rd | 25 ++++++ inst/doc/overview.R | 160 ++++++++++++++++++++++---------------------- inst/doc/overview.Rnw | 37 +++++----- inst/doc/overview.pdf |binary inst/doc/psych_for_sem.Rnw | 16 ++-- inst/doc/psych_for_sem.pdf |binary man/cosinor.Rd | 11 +-- man/fa.Rd | 14 ++- man/msq.Rd | 15 +++- man/principal.Rd | 9 +- man/test.psych.Rd | 3 vignettes/overview.Rnw | 37 +++++----- vignettes/psych_for_sem.Rnw | 16 ++-- 23 files changed, 373 insertions(+), 248 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between nnet versions 7.3-10 dated 2015-06-29 and 7.3-11 dated 2015-08-30
DESCRIPTION | 8 ++++---- LICENCE.note | 4 ++-- MD5 | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.1.0.1 dated 2015-07-28 and 0.2.0.0 dated 2015-08-30
dotwhisker-0.1.0.1/dotwhisker/inst/doc/dwplot-vignette.R |only dotwhisker-0.1.0.1/dotwhisker/inst/doc/dwplot-vignette.Rmd |only dotwhisker-0.1.0.1/dotwhisker/inst/doc/dwplot-vignette.html |only dotwhisker-0.1.0.1/dotwhisker/vignettes/dwplot-vignette.Rmd |only dotwhisker-0.1.0.1/dotwhisker/vignettes/vignette_dwplot.bib |only dotwhisker-0.2.0.0/dotwhisker/DESCRIPTION | 20 dotwhisker-0.2.0.0/dotwhisker/MD5 | 44 +- dotwhisker-0.2.0.0/dotwhisker/NAMESPACE | 8 dotwhisker-0.2.0.0/dotwhisker/R/add_brackets.R | 142 +++--- dotwhisker-0.2.0.0/dotwhisker/R/by_2sd.R | 25 - dotwhisker-0.2.0.0/dotwhisker/R/dwplot.R | 208 +++++++--- dotwhisker-0.2.0.0/dotwhisker/R/relabel_predictors.R |only dotwhisker-0.2.0.0/dotwhisker/R/relabel_y_axis.R |only dotwhisker-0.2.0.0/dotwhisker/R/secret_weapon.R |only dotwhisker-0.2.0.0/dotwhisker/R/small_multiple.R |only dotwhisker-0.2.0.0/dotwhisker/README.md | 7 dotwhisker-0.2.0.0/dotwhisker/build/vignette.rds |binary dotwhisker-0.2.0.0/dotwhisker/inst/CITATION | 4 dotwhisker-0.2.0.0/dotwhisker/inst/doc/dotwhisker-vignette.R |only dotwhisker-0.2.0.0/dotwhisker/inst/doc/dotwhisker-vignette.Rmd |only dotwhisker-0.2.0.0/dotwhisker/inst/doc/dotwhisker-vignette.html |only dotwhisker-0.2.0.0/dotwhisker/inst/doc/kl2007_examples.R |only dotwhisker-0.2.0.0/dotwhisker/inst/doc/kl2007_examples.Rmd |only dotwhisker-0.2.0.0/dotwhisker/inst/doc/kl2007_examples.html |only dotwhisker-0.2.0.0/dotwhisker/man/add_brackets.Rd | 3 dotwhisker-0.2.0.0/dotwhisker/man/by_2sd.Rd | 1 dotwhisker-0.2.0.0/dotwhisker/man/dwplot.Rd | 25 - dotwhisker-0.2.0.0/dotwhisker/man/relabel_predictors.Rd |only dotwhisker-0.2.0.0/dotwhisker/man/relabel_y_axis.Rd |only dotwhisker-0.2.0.0/dotwhisker/man/secret_weapon.Rd |only dotwhisker-0.2.0.0/dotwhisker/man/small_multiple.Rd |only dotwhisker-0.2.0.0/dotwhisker/vignettes/dotwhisker-vignette.Rmd |only dotwhisker-0.2.0.0/dotwhisker/vignettes/kl2007_examples.Rmd |only dotwhisker-0.2.0.0/dotwhisker/vignettes/vignette.bib |only 34 files changed, 308 insertions(+), 179 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-13 dated 2015-06-29 and 7.3-14 dated 2015-08-30
DESCRIPTION | 8 ++++---- LICENCE.note | 4 ++-- MD5 | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.12-0 dated 2015-08-27 and 1.13-0 dated 2015-08-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/TAM.itempartable.R | 13 +++++++++++-- R/tam.mml.R | 2 +- inst/NEWS | 22 ++++++++++++++++++++++ man/TAM-package.Rd | 2 +- man/tam.mml.Rd | 44 ++++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 89 insertions(+), 14 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.5.7 dated 2015-07-28 and 0.5.8 dated 2015-08-29
PRIMsrc-0.5.7/PRIMsrc/inst/doc/PRIMsrc_0.5.7.pdf |only PRIMsrc-0.5.8/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.5.8/PRIMsrc/MD5 | 56 +-- PRIMsrc-0.5.8/PRIMsrc/NAMESPACE | 1 PRIMsrc-0.5.8/PRIMsrc/R/PRIMsrc.internal.r | 218 ++++++++++---- PRIMsrc-0.5.8/PRIMsrc/R/PRIMsrc.r | 348 +++++++++++++---------- PRIMsrc-0.5.8/PRIMsrc/data/Real.1.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/Real.2.rda |only PRIMsrc-0.5.8/PRIMsrc/data/Synthetic.1.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/Synthetic.2.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/Synthetic.3.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/Synthetic.4.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/Synthetic.5.rda |binary PRIMsrc-0.5.8/PRIMsrc/data/datalist |only PRIMsrc-0.5.8/PRIMsrc/inst/NEWS | 28 + PRIMsrc-0.5.8/PRIMsrc/inst/doc/PRIMsrc_0.5.8.pdf |only PRIMsrc-0.5.8/PRIMsrc/man/PrimSRC-package.Rd | 33 +- PRIMsrc-0.5.8/PRIMsrc/man/Real.1-data.Rd | 8 PRIMsrc-0.5.8/PRIMsrc/man/Real.2-data.Rd |only PRIMsrc-0.5.8/PRIMsrc/man/Synthetic.1-data.Rd | 2 PRIMsrc-0.5.8/PRIMsrc/man/Synthetic.2-data.Rd | 2 PRIMsrc-0.5.8/PRIMsrc/man/Synthetic.3-data.Rd | 2 PRIMsrc-0.5.8/PRIMsrc/man/Synthetic.4-data.Rd | 4 PRIMsrc-0.5.8/PRIMsrc/man/Synthetic.5-data.Rd | 4 PRIMsrc-0.5.8/PRIMsrc/man/plot_boxkm.Rd | 19 - PRIMsrc-0.5.8/PRIMsrc/man/plot_boxtrace.Rd | 11 PRIMsrc-0.5.8/PRIMsrc/man/plot_boxtraj.Rd | 11 PRIMsrc-0.5.8/PRIMsrc/man/plot_profile.Rd | 9 PRIMsrc-0.5.8/PRIMsrc/man/plot_scatter.Rd | 15 PRIMsrc-0.5.8/PRIMsrc/man/print.Rd |only PRIMsrc-0.5.8/PRIMsrc/man/sbh.Rd | 76 ++--- PRIMsrc-0.5.8/PRIMsrc/man/summary.Rd | 4 32 files changed, 539 insertions(+), 320 deletions(-)
Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MFAg versions 1.0 dated 2015-08-21 and 1.1 dated 2015-08-29
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/IM.Rd | 2 +- man/MFA.Rd | 2 +- man/MFAg-package.Rd | 8 ++++---- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data.
The methods available closely follow those in chapter 6 of Applied Spatial
Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smacpod versions 1.1.1 dated 2014-11-18 and 1.2.3 dated 2015-08-29
smacpod-1.1.1/smacpod/R/confenv.kdenv.R |only smacpod-1.1.1/smacpod/R/lines.cienv.R |only smacpod-1.1.1/smacpod/R/tolenv.renv.R |only smacpod-1.1.1/smacpod/man/confenv.Rd |only smacpod-1.1.1/smacpod/man/lines.Rd |only smacpod-1.2.3/smacpod/DESCRIPTION | 8 +-- smacpod-1.2.3/smacpod/MD5 | 50 ++++++++++----------- smacpod-1.2.3/smacpod/NAMESPACE | 16 ++++-- smacpod-1.2.3/smacpod/R/kd.R | 6 +- smacpod-1.2.3/smacpod/R/kdest.R | 24 +++++++--- smacpod-1.2.3/smacpod/R/kdplus.test.R | 9 ++- smacpod-1.2.3/smacpod/R/logrr.R | 68 ++++++++++++++++++++--------- smacpod-1.2.3/smacpod/R/logrr.test.R | 2 smacpod-1.2.3/smacpod/R/plot.kdenv.R |only smacpod-1.2.3/smacpod/R/plot.logrrenv.R |only smacpod-1.2.3/smacpod/R/qnn.test.R | 6 +- smacpod-1.2.3/smacpod/R/spdensity.R | 4 - smacpod-1.2.3/smacpod/R/spscan.test.R | 7 +- smacpod-1.2.3/smacpod/R/tolenv.R |only smacpod-1.2.3/smacpod/man/grave.Rd | 3 - smacpod-1.2.3/smacpod/man/kd.Rd | 3 - smacpod-1.2.3/smacpod/man/kdest.Rd | 13 +++-- smacpod-1.2.3/smacpod/man/kdplus.test.Rd | 5 +- smacpod-1.2.3/smacpod/man/logrr.Rd | 29 ++++++++---- smacpod-1.2.3/smacpod/man/logrr.test.Rd | 3 - smacpod-1.2.3/smacpod/man/plot.kdenv.Rd |only smacpod-1.2.3/smacpod/man/plot.logrrenv.Rd |only smacpod-1.2.3/smacpod/man/qnn.test.Rd | 3 - smacpod-1.2.3/smacpod/man/spdensity.Rd | 3 - smacpod-1.2.3/smacpod/man/spscan.test.Rd | 9 ++- smacpod-1.2.3/smacpod/man/tolenv.Rd | 24 ++-------- 31 files changed, 178 insertions(+), 117 deletions(-)
Title: Talk to the NCBI EUtils
Description: An interface to NCBI databases such as PubMed, GenBank, or GEO
powered by the Entrez Programming Utilities (EUtils). The nine EUtils
provide programmatic access to the NCBI Entrez query and database
system for searching and retrieving biological data.
Author: Gerhard Schöfl <gerhard.schofl@gmail.com>
Maintainer: Gerhard Schöfl <gerhard.schofl@gmail.com>
Diff between reutils versions 0.1.2 dated 2014-02-26 and 0.2.1 dated 2015-08-29
reutils-0.1.2/reutils/man/efetch-methods.Rd |only reutils-0.1.2/reutils/man/einfo-methods.Rd |only reutils-0.1.2/reutils/man/elink-methods.Rd |only reutils-0.1.2/reutils/man/esearch-methods.Rd |only reutils-0.1.2/reutils/man/esummary-methods.Rd |only reutils-0.2.1/reutils/DESCRIPTION | 26 - reutils-0.2.1/reutils/LICENSE | 2 reutils-0.2.1/reutils/MD5 | 125 ++++---- reutils-0.2.1/reutils/NAMESPACE | 43 +- reutils-0.2.1/reutils/NEWS | 17 - reutils-0.2.1/reutils/R/ecitmatch.R | 36 +- reutils-0.2.1/reutils/R/efetch.R | 144 ++++++--- reutils-0.2.1/reutils/R/egquery.R | 23 - reutils-0.2.1/reutils/R/einfo.R | 170 ++++++----- reutils-0.2.1/reutils/R/elink.R | 89 ++--- reutils-0.2.1/reutils/R/epost.R | 54 +-- reutils-0.2.1/reutils/R/esearch.R | 145 ++++++--- reutils-0.2.1/reutils/R/espell.R | 30 + reutils-0.2.1/reutils/R/esummary.R | 56 ++- reutils-0.2.1/reutils/R/eutil-error.R | 40 +- reutils-0.2.1/reutils/R/eutil.R | 149 +++++---- reutils-0.2.1/reutils/R/parse-docsum.R | 48 +-- reutils-0.2.1/reutils/R/parse-params.R | 12 reutils-0.2.1/reutils/R/reutils-package.R | 6 reutils-0.2.1/reutils/R/utils.R | 114 +++---- reutils-0.2.1/reutils/man/content.Rd | 99 +++++- reutils-0.2.1/reutils/man/database.Rd | 15 reutils-0.2.1/reutils/man/ecitmatch.Rd | 20 - reutils-0.2.1/reutils/man/efetch.Rd | 137 ++++---- reutils-0.2.1/reutils/man/egquery.Rd | 7 reutils-0.2.1/reutils/man/einfo.Rd | 47 ++- reutils-0.2.1/reutils/man/elink.Rd | 58 +-- reutils-0.2.1/reutils/man/entrez_linkset-class.Rd | 3 reutils-0.2.1/reutils/man/entrez_uid-class.Rd | 3 reutils-0.2.1/reutils/man/epost.Rd | 30 - reutils-0.2.1/reutils/man/esearch.Rd | 112 +++---- reutils-0.2.1/reutils/man/espell.Rd | 12 reutils-0.2.1/reutils/man/esummary.Rd | 71 ++-- reutils-0.2.1/reutils/man/eutil-class.Rd | 46 +- reutils-0.2.1/reutils/man/eutil_error-class.Rd | 15 reutils-0.2.1/reutils/man/extract-efetch.Rd |only reutils-0.2.1/reutils/man/extract-einfo.Rd |only reutils-0.2.1/reutils/man/extract-elink.Rd |only reutils-0.2.1/reutils/man/extract-esearch.Rd |only reutils-0.2.1/reutils/man/getError.Rd | 11 reutils-0.2.1/reutils/man/getUrl.Rd | 11 reutils-0.2.1/reutils/man/linkset.Rd | 20 - reutils-0.2.1/reutils/man/make_flattener.Rd | 8 reutils-0.2.1/reutils/man/ncbi_retrieval_type.Rd | 9 reutils-0.2.1/reutils/man/performQuery.Rd | 9 reutils-0.2.1/reutils/man/querykey.Rd | 15 reutils-0.2.1/reutils/man/retmode.Rd | 13 reutils-0.2.1/reutils/man/rettype.Rd | 13 reutils-0.2.1/reutils/man/reutils.Rd | 138 ++++---- reutils-0.2.1/reutils/man/sub-esummary.Rd |only reutils-0.2.1/reutils/man/uid.Rd | 17 - reutils-0.2.1/reutils/man/webenv.Rd | 15 reutils-0.2.1/reutils/man/xattr.Rd | 18 - reutils-0.2.1/reutils/man/xname.Rd | 16 - reutils-0.2.1/reutils/man/xset.Rd | 11 reutils-0.2.1/reutils/man/xvalue.Rd | 16 - reutils-0.2.1/reutils/tests/testthat/test-01-helpers.R | 6 reutils-0.2.1/reutils/tests/testthat/test-02-eutil-methods.R | 20 - reutils-0.2.1/reutils/tests/testthat/test-03-einfo.R | 20 - reutils-0.2.1/reutils/tests/testthat/test-04-esearch.R | 63 +++- reutils-0.2.1/reutils/tests/testthat/test-05-esummary.R | 10 reutils-0.2.1/reutils/tests/testthat/test-06-epost.R | 4 reutils-0.2.1/reutils/tests/testthat/test-07-efetch.R | 36 ++ reutils-0.2.1/reutils/tests/testthat/test-09-ecitmatch.R |only 69 files changed, 1476 insertions(+), 1027 deletions(-)
Title: Tools to Fit Flexible Parametric Curves
Description: Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
Author: Stephen Oswald [aut, cre]
Maintainer: Stephen Oswald <steve.oswald@psu.edu>
Diff between FlexParamCurve versions 1.5-2 dated 2015-04-01 and 1.5-3 dated 2015-08-29
DESCRIPTION | 11 ++- MD5 | 34 +++++------ NAMESPACE | 2 NEWS | 31 ++++++++++ R/SSposnegRichards.R | 126 ++++++++++++++++++++++++------------------ R/get.mod.R | 25 ++++---- R/modpar.R | 49 ++++++++++------ R/pn.mod.compare.R | 7 +- R/pn.modselect.step.R | 21 ++++--- man/FlexParamCurve-package.Rd | 8 ++ man/SSposnegRichards.Rd | 10 +-- man/get.mod.Rd | 23 ++++--- man/logist.data.Rd | 1 man/modpar.Rd | 11 +++ man/penguin.data.Rd | 1 man/posneg.data.Rd | 1 man/posnegRichards.calls.Rd | 8 +- man/tern.data.Rd | 1 18 files changed, 231 insertions(+), 139 deletions(-)
More information about FlexParamCurve at CRAN
Permanent link
Title: Partial Linear Least-Squares Regression using Constrained
Splines
Description: Given response y, continuous predictor x, and covariate matrix, the relationship between E(y) and x is estimated with a shape constrained regression spline. Function outputs fits and various types of inference.
Author: Mary C Meyer
Maintainer: Mary C Meyer <meyer@stat.colostate.edu>
Diff between ConSpline versions 1.0 dated 2015-03-30 and 1.1 dated 2015-08-29
DESCRIPTION | 10 ++++---- MD5 | 14 ++++++----- R/conspline.R | 47 +++++++++++++++++++++++--------------- data/GAVoting.rda |only data/WhiteSpruce.rda |binary man/ConSpline-package.Rd | 20 +++++++++------- man/GAVoting.Rd |only man/WhiteSpruce.Rd | 6 +++- man/conspline.Rd | 57 +++++++++++++++++------------------------------ 9 files changed, 79 insertions(+), 75 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between CDM versions 4.4-1 dated 2015-07-01 and 4.5-0 dated 2015-08-29
DESCRIPTION | 12 +++---- MD5 | 59 +++++++++++++++++++------------------ NAMESPACE | 2 - R/IRT.jackknife.gdina.R | 1 R/din.R | 4 +- R/gdina.R | 5 ++- R/gdina_designmatrices.R | 74 +++++++++++++++++++++++++++++++++++++++++++---- R/gdm.R | 5 ++- R/gdm_algorithm.R | 5 +-- R/gdm_postproc.R | 6 ++- R/itemfit.rmsea.R | 7 ++++ R/mcdina.R | 2 - R/print.summary.din.R | 8 ++++- R/slca.R | 1 R/summary.din.R | 6 +-- R/summary.gdina.R | 8 +++-- R/summary.gdm.R | 6 ++- R/summary.mcdina.R | 4 +- R/summary.slca.R | 5 ++- R/vcov.din.R | 33 -------------------- R/vcov.loglike.din.R |only inst/NEWS | 17 +++++++++- man/CDM-package.Rd | 53 +++++++++++++++++---------------- man/IRT.itemfit.Rd | 2 - man/din.Rd | 1 man/gdina.Rd | 3 + man/gdm.Rd | 1 man/itemfit.sx2.Rd | 15 +++++---- man/mcdina.Rd | 1 man/modelfit.cor.Rd | 2 - man/slca.Rd | 1 31 files changed, 218 insertions(+), 131 deletions(-)
Title: The Bee Swarm Plot, an Alternative to Stripchart
Description: The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.
Author: Aron Eklund
Maintainer: Aron Eklund <eklund@cbs.dtu.dk>
Diff between beeswarm versions 0.2.0 dated 2015-05-04 and 0.2.1 dated 2015-08-29
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- NAMESPACE | 4 ++++ NEWS | 5 +++++ README.md |only 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Debugging with Restore Points
Description: Debugging with restore points instead of break points. A restore
point stores all local variables when called inside a function. The stored
values can later be retrieved and evaluated in a modified R console that
replicates the function's environment. To debug step by step, one can
simply copy & paste the function body from the R script. Particularly
convenient in combination with RStudio. See the github page for a tutorial.
Author: Sebastian Kranz
Maintainer: Sebastian Kranz <sebastian.kranz@uni-ulm.de>
Diff between restorepoint versions 0.1.5 dated 2014-02-20 and 0.1.7 dated 2015-08-29
restorepoint-0.1.5/restorepoint/man/set.restore.point.options.Rd |only restorepoint-0.1.7/restorepoint/DESCRIPTION | 10 restorepoint-0.1.7/restorepoint/MD5 | 46 +- restorepoint-0.1.7/restorepoint/NAMESPACE | 6 restorepoint-0.1.7/restorepoint/R/restorepoint.R | 138 +++++- restorepoint-0.1.7/restorepoint/inst/examples/restorepoint_examples.R | 77 +++ restorepoint-0.1.7/restorepoint/man/add.restore.point.test.Rd |only restorepoint-0.1.7/restorepoint/man/assert.Rd | 8 restorepoint-0.1.7/restorepoint/man/break.point.Rd |only restorepoint-0.1.7/restorepoint/man/calls.to.trace.Rd | 14 restorepoint-0.1.7/restorepoint/man/can.parse.multi.line.Rd | 12 restorepoint-0.1.7/restorepoint/man/clone.environment.Rd | 12 restorepoint-0.1.7/restorepoint/man/copy.into.env.Rd | 32 - restorepoint-0.1.7/restorepoint/man/default.error.string.fun.Rd | 10 restorepoint-0.1.7/restorepoint/man/env.console.Rd | 59 -- restorepoint-0.1.7/restorepoint/man/eval.with.error.trace.Rd | 31 - restorepoint-0.1.7/restorepoint/man/get.restore.point.options.Rd | 6 restorepoint-0.1.7/restorepoint/man/get.stored.dots.Rd | 12 restorepoint-0.1.7/restorepoint/man/get.stored.object.list.Rd | 7 restorepoint-0.1.7/restorepoint/man/is.storing.Rd | 6 restorepoint-0.1.7/restorepoint/man/restore.objects.Rd | 29 - restorepoint-0.1.7/restorepoint/man/restore.point.Rd | 227 ++++++---- restorepoint-0.1.7/restorepoint/man/restore.point.browser.Rd | 52 +- restorepoint-0.1.7/restorepoint/man/restore.point.options.Rd |only restorepoint-0.1.7/restorepoint/man/set.storing.Rd | 10 restorepoint-0.1.7/restorepoint/man/store.objects.Rd | 65 +- 26 files changed, 549 insertions(+), 320 deletions(-)
Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')
to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and
q variables are measured on the same samples or individuals n. These data may come from high throughput
technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other
large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with
the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting
the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent
Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration
of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found
on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 5.1.1 dated 2015-07-30 and 5.1.2 dated 2015-08-29
DESCRIPTION | 6 MD5 | 24 NAMESPACE | 12 NEWS | 21 R/helpers.R | 6 R/perf.R | 2 R/plotIndiv.R | 388 +++++---- R/plotVar.R | 2179 ++++++++++++------------------------------------------- R/spls.R | 4 man/plotIndiv.Rd | 89 +- man/plotVar.Rd | 238 +++--- man/sipca.Rd | 2 man/spca.Rd | 7 13 files changed, 962 insertions(+), 2016 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.19 dated 2015-07-26 and 2.20 dated 2015-08-29
DESCRIPTION | 22 +++--- MD5 | 30 ++++---- NAMESPACE | 4 + R/helpers.R | 22 +++--- R/lsmip.R | 12 +-- R/multinom-support.R |only R/rbind.R |only build/vignette.rds |binary inst/NEWS | 11 +++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 158 +++++++++++++++++++++++--------------------- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 16 ++++ man/lsmip.Rd | 7 + man/models.Rd | 12 ++- man/summary.Rd | 23 +++++- vignettes/using-lsmeans.rnw | 16 ++++ 17 files changed, 215 insertions(+), 118 deletions(-)
Title: An Implementation of Common Response Time Trimming Methods
Description: Provides various commonly-used response time trimming
methods, including the recursive / moving-criterion methods reported by
Van Selst and Jolicoeur (1994). By passing trimming functions raw data files,
the package will return trimmed data ready for inferential testing.
Author: James Grange [aut, cre]
Maintainer: James Grange <grange.jim@gmail.com>
Diff between trimr versions 1.0.0 dated 2015-08-02 and 1.0.1 dated 2015-08-28
DESCRIPTION | 6 - MD5 | 20 ++-- R/datasets.R | 2 R/modifiedRecursive.R | 16 ++- README.md | 34 +++++-- data/linearInterpolation.rda |binary inst/doc/trimr-vignette.R | 40 ++++++++ inst/doc/trimr-vignette.Rmd | 68 ++++++++++++++ inst/doc/trimr-vignette.html | 203 ++++++++++++++++++++++++++++++------------- man/linearInterpolation.Rd | 2 vignettes/trimr-vignette.Rmd | 68 ++++++++++++++ 11 files changed, 377 insertions(+), 82 deletions(-)
Title: Analysis of Kin-Cohort Studies
Description: Analysis of kin-cohort studies. kin.cohort provides estimates of age-specific
cumulative risk of a disease for carriers and noncarriers of a mutation. The cohorts are
retrospectively built from relatives of probands for whom the genotype is known. Currently
the method of moments and marginal maximum likelihood are implemented. Confidence intervals
are calculated from bootstrap samples.
Most of the code is a translation from previous 'MATLAB' code by N. Chatterjee.
Author: Victor Moreno, Nilanjan Chatterjee, Bhramar Mukherjee
Maintainer: Victor Moreno <v.moreno@iconcologia.net>
Diff between kin.cohort versions 0.6 dated 2009-01-29 and 0.7 dated 2015-08-28
DESCRIPTION | 35 ++++---- MD5 |only NAMESPACE | 19 ++-- inst/ChangeLog | 7 + man/kc.marginal.Rd | 118 +++++++++++++-------------- man/kc.moments.Rd | 110 +++++++++++++------------ man/kin.cohort.Rd | 146 +++++++++++++++++---------------- man/simulations.Rd | 228 ++++++++++++++++++++++++++--------------------------- 8 files changed, 341 insertions(+), 322 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.1 dated 2015-05-29 and 1.2 dated 2015-08-28
DESCRIPTION | 10 - MD5 | 8 - NAMESPACE | 1 R/GEE.var.fg.R | 294 ++++++++++++++++++++++++++++----------------------------- R/GEE.var.kc.R | 2 5 files changed, 158 insertions(+), 157 deletions(-)
Title: Nonparametric Multiple Expectile Regression via ER-Boost
Description: Expectile regression is a nice tool for estimating the conditional expectiles of a response variable given a set of covariates. This package implements a regression tree based gradient boosting estimator for nonparametric multiple expectile regression.
Author: Yi Yang <yiyang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Yi Yang <yiyang@umn.edu>
Diff between erboost versions 1.2 dated 2013-10-28 and 1.3 dated 2015-08-28
ChangeLog | 3 +++ DESCRIPTION | 13 +++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 14 ++++++++++++++ R/erboost.R | 10 +++++----- man/erboost.Rd | 30 ++++++++++++++++++------------ man/erboost.perf.Rd | 8 ++------ man/plot.erboost.Rd | 6 +++--- man/relative.influence.Rd | 8 ++++---- man/summary.erboost.Rd | 8 ++++---- 10 files changed, 67 insertions(+), 51 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 2.0.1 dated 2015-06-16 and 3.0.1 dated 2015-08-28
DESCRIPTION | 10 +- MD5 | 8 - NAMESPACE | 2 R/CMplot.r | 204 +++++++++++++++++++++++++++++++++++--------------- man/CMplot-package.Rd | 65 ++++++++++++--- 5 files changed, 206 insertions(+), 83 deletions(-)
Title: Optimal Experimental Designs for Accelerated Life Testing
Description: Creates the optimal (D, U and I) designs for the accelerated life
testing with right censoring or interval censoring. It uses generalized
linear model (GLM) approach to derive the asymptotic variance-covariance
matrix of regression coefficients. The failure time distribution is assumed
to follow Weibull distribution with a known shape parameter and log-linear
link functions are used to model the relationship between failure time
parameters and stress variables. The acceleration model may have multiple
stress factors, although most ALTs involve only two or less stress factors.
ALTopt package also provides several plotting functions including contour plot,
Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space
(VDUS) plot.
Author: Kangwon Seo [aut, cre],
Rong Pan [aut]
Maintainer: Kangwon Seo <kseo7@asu.edu>
Diff between ALTopt versions 0.1.0 dated 2015-01-17 and 0.1.1 dated 2015-08-27
DESCRIPTION | 30 ++++++++++----------- MD5 | 55 +++++++++++++++++++-------------------- NAMESPACE | 15 +++++++++- R/ALTopt.R | 62 +++++++++++++++++++++++++++++++++++++++++++- build |only man/ALTopt-package.Rd | 24 +++++------------ man/Dobj.ic.Rd | 2 - man/Dobj.rc.Rd | 2 - man/ExtendedForm.Rd | 2 - man/Iobj.ic.Rd | 2 - man/Iobj.rc.Rd | 2 - man/PreVar.Rd | 2 - man/Uobj.ic.Rd | 2 - man/Uobj.rc.Rd | 2 - man/alteval.ic.Rd | 2 - man/alteval.rc.Rd | 2 - man/altopt.ic.Rd | 4 ++ man/altopt.rc.Rd | 4 ++ man/compare.fus.Rd | 2 - man/compare.vdus.Rd | 2 - man/convert.stress.level.Rd | 2 - man/design.plot.Rd | 2 - man/kmeansCls.Rd | 2 - man/pv.contour.ic.Rd | 2 - man/pv.contour.rc.Rd | 2 - man/pv.fus.ic.Rd | 2 - man/pv.fus.rc.Rd | 2 - man/pv.vdus.ic.Rd | 2 - man/pv.vdus.rc.Rd | 2 - 29 files changed, 153 insertions(+), 83 deletions(-)
Title: Truncated Multivariate Normal and Student t Distribution
Description: Random number generation for the truncated multivariate normal and Student t distribution.
Computes probabilities, quantiles and densities,
including one-dimensional and bivariate marginal densities. Computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.
Author: Stefan Wilhelm <wilhelm@financial.com> with contributions from Manjunath B G <bgmanjunath@gmail.com>
Maintainer: Stefan Wilhelm <wilhelm@financial.com>
Diff between tmvtnorm versions 1.4-9 dated 2014-03-03 and 1.4-10 dated 2015-08-27
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS | 3 +++ R/dtmvnorm-marginal.R | 4 ++-- build/vignette.rds |binary inst/doc/GibbsSampler.pdf |binary src/Makevars | 2 ++ 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Multinomial Processing Tree Models
Description: Fitting and testing multinomial processing tree (MPT) models, a
class of statistical models for categorical data. The parameters are the
link probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer &
Batchelder, 1988).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between mpt versions 0.5-1 dated 2015-02-03 and 0.5-2 dated 2015-08-27
ChangeLog | 9 +++++++++ DESCRIPTION | 19 ++++++++++--------- MD5 | 10 +++++----- NAMESPACE | 7 ++++--- R/mpt.R | 42 +++++++++++++++++++++++++----------------- R/mptspec.R | 2 +- 6 files changed, 54 insertions(+), 35 deletions(-)
Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between extRemes versions 2.0-5 dated 2015-01-21 and 2.0-6 dated 2015-08-27
DESCRIPTION | 9 ++- MD5 | 28 +++++------ NAMESPACE | 76 ++++++++++++++++++++++++++++++ R/fitdiagnostics.R | 104 +++++++++++++++++++++++++++++++++++------- R/fitfuns.R | 53 ++++++++++++++------- R/quantiles.R | 2 man/Denmint.Rd | 2 man/FCwx.Rd | 2 man/Fort.Rd | 2 man/Ozone4H.Rd | 2 man/Rsum.Rd | 13 ++++- man/ci.rl.ns.fevd.bayesian.Rd | 2 man/damage.Rd | 4 - man/ftcanmax.Rd | 2 man/make.qcov.Rd | 2 15 files changed, 240 insertions(+), 63 deletions(-)
Title: Classification Accuracy and Consistency under Item Response
Theory
Description: Computes classification accuracy and consistency indices under Item Response Theory. Implements the total score IRT-based methods in Lee, Hanson & Brennen (2002) and Lee (2010), the IRT-based methods in Rudner (2001, 2005), and the total score nonparametric methods in Lathrop & Cheng (2014). For dichotomous and polytomous tests.
Author: Quinn N. Lathrop
Maintainer: Quinn N. Lathrop <quinn.lathrop@gmail.com>
Diff between cacIRT versions 1.3 dated 2014-01-28 and 1.4 dated 2015-08-27
cacIRT-1.3/cacIRT/R/TOtable.F.R |only cacIRT-1.3/cacIRT/man/TOtable.F.Rd |only cacIRT-1.4/cacIRT/DESCRIPTION | 17 +- cacIRT-1.4/cacIRT/MD5 | 47 +++---- cacIRT-1.4/cacIRT/NAMESPACE | 6 cacIRT-1.4/cacIRT/R/Lee.D.R | 119 +++++++++--------- cacIRT-1.4/cacIRT/R/Lee.P.R | 123 +++++++++---------- cacIRT-1.4/cacIRT/R/Lee.pnr.R |only cacIRT-1.4/cacIRT/R/Lee.poly.D.R |only cacIRT-1.4/cacIRT/R/Lee.poly.P.R | 115 ++++++++--------- cacIRT-1.4/cacIRT/R/MLE.R | 33 ++--- cacIRT-1.4/cacIRT/R/Rud.D.R | 92 +++++++------- cacIRT-1.4/cacIRT/R/Rud.P.R | 82 ++++++------ cacIRT-1.4/cacIRT/R/SEM.R | 16 +- cacIRT-1.4/cacIRT/R/class.Lee.R | 43 +++--- cacIRT-1.4/cacIRT/R/class.Rud.R | 47 +++---- cacIRT-1.4/cacIRT/R/gen.rec.raw.R | 102 +++++++-------- cacIRT-1.4/cacIRT/R/iif.R | 35 ++--- cacIRT-1.4/cacIRT/R/irf.R | 17 +- cacIRT-1.4/cacIRT/R/pnr.R |only cacIRT-1.4/cacIRT/R/recursive.raw.R | 63 ++++----- cacIRT-1.4/cacIRT/man/IRT.Rd | 146 +++++++++++----------- cacIRT-1.4/cacIRT/man/Lee.ploy.Rd |only cacIRT-1.4/cacIRT/man/cacIRT-package.Rd | 98 ++++++++------- cacIRT-1.4/cacIRT/man/cacNP.Rd |only cacIRT-1.4/cacIRT/man/class.Lee.Rd | 207 ++++++++++++++------------------ cacIRT-1.4/cacIRT/man/class.Rud.Rd | 194 ++++++++++++++--------------- cacIRT-1.4/cacIRT/man/recursive.raw.Rd | 160 +++++++++++++----------- 28 files changed, 895 insertions(+), 867 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.3 dated 2015-08-26 and 1.5 dated 2015-08-27
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- inst/doc/Anthropometry.Rnw | 2 +- inst/doc/Anthropometry.pdf |binary man/Anthropometry-package.Rd | 4 ++-- man/getDistMatrix.Rd | 2 ++ man/hipamAnthropom.Rd | 2 ++ man/preprocessing.Rd | 4 +--- man/projShapes.Rd | 1 - man/trimmedoid.Rd | 2 ++ vignettes/Anthropometry.Rnw | 2 +- 11 files changed, 25 insertions(+), 22 deletions(-)
Title: Random Walks in the Intersection of Hyperplanes and the
N-Simplex
Description: Consider the intersection of two spaces: the complete solution space
to Ax = b and the N-simplex. The intersection of these two spaces is
a non-negative convex polytope. The package walkr samples from this
intersection using two Monte-Carlo Markov Chain (MCMC) methods:
hit-and-run and Dikin walk. walkr also provide tools to examine sample
quality.
Author: as.person(c(
"Andy Yao <andy.yao17@gmail.com> [aut]",
"David Kane <dave.kane@gmail.com> [aut]"
))
Maintainer: Andy Yao <andy.yao17@gmail.com>
Diff between walkr versions 0.3-2 dated 2015-08-13 and 0.3.3 dated 2015-08-27
walkr-0.3-2/walkr/vignettes/img/dikintrap.png |only walkr-0.3-2/walkr/vignettes/img/hartrap.png |only walkr-0.3-2/walkr/vignettes/img/pics |only walkr-0.3.3/walkr/DESCRIPTION | 23 walkr-0.3.3/walkr/MD5 | 56 walkr-0.3.3/walkr/NEWS |only walkr-0.3.3/walkr/R/complete_solution.R | 2 walkr-0.3.3/walkr/R/dikin_walk.R | 20 walkr-0.3.3/walkr/R/hit_and_run.R | 19 walkr-0.3.3/walkr/R/walkr.R | 6 walkr-0.3.3/walkr/build/vignette.rds |binary walkr-0.3.3/walkr/inst/CITATION |only walkr-0.3.3/walkr/inst/doc/walkr.R | 124 + walkr-0.3.3/walkr/inst/doc/walkr.Rnw | 1065 +++++++++----- walkr-0.3.3/walkr/inst/doc/walkr.pdf |binary walkr-0.3.3/walkr/man/walkr.Rd | 2 walkr-0.3.3/walkr/tests/testthat/test.hitandrun.uniform.R | 17 walkr-0.3.3/walkr/vignettes/img/exp_dikin2.png |only walkr-0.3.3/walkr/vignettes/img/exp_dikin3.png |only walkr-0.3.3/walkr/vignettes/img/exp_dikin41.png |only walkr-0.3.3/walkr/vignettes/img/exp_dikin42.png |only walkr-0.3.3/walkr/vignettes/img/exp_dikin5.png |only walkr-0.3.3/walkr/vignettes/img/exp_dikin6.png |only walkr-0.3.3/walkr/vignettes/img/exp_hitandrun2.png |only walkr-0.3.3/walkr/vignettes/img/exp_hitandrun3.png |only walkr-0.3.3/walkr/vignettes/img/exp_hitandrun4.png |only walkr-0.3.3/walkr/vignettes/img/exp_hitandrun5.png |only walkr-0.3.3/walkr/vignettes/img/exp_trapezoid1.png |only walkr-0.3.3/walkr/vignettes/img/simplex3D.png |binary walkr-0.3.3/walkr/vignettes/img/traceplot.png |only walkr-0.3.3/walkr/vignettes/walkr-concordance.tex |only walkr-0.3.3/walkr/vignettes/walkr.Rnw | 1065 +++++++++----- walkr-0.3.3/walkr/vignettes/walkr.bib | 59 33 files changed, 1650 insertions(+), 808 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.11-0 dated 2015-08-11 and 1.12-0 dated 2015-08-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/tam.mml.3pl.est.guessing.R | 18 ++++++++++-------- R/tam.mml.R | 5 ++++- inst/NEWS | 24 +++++++++++++++++++++++- man/TAM-package.Rd | 2 +- 6 files changed, 47 insertions(+), 20 deletions(-)
Title: Sparse Group Partial Least Square Methods
Description: The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.
Author: Benoit Liquet and Pierre Lafaye de Micheaux
Maintainer: Benoit Liquet <b.liquet@uq.edu.au>
Diff between sgPLS versions 1.2 dated 2015-04-30 and 1.3 dated 2015-08-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/sgPLS-internal.R | 17 +++++++++++------ man/sgPLS.Rd | 2 +- 5 files changed, 22 insertions(+), 15 deletions(-)
Title: Estimating Systems of Simultaneous Equations
Description: Fitting simultaneous
systems of linear and nonlinear equations using Ordinary Least
Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated
Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted
Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS).
Author: Arne Henningsen and Jeff D. Hamann
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between systemfit versions 1.1-16 dated 2015-06-09 and 1.1-18 dated 2015-08-27
DESCRIPTION | 10 +- MD5 | 50 +++++----- NAMESPACE | 27 +++++ NEWS | 12 ++ R/logLik.R | 9 + build/vignette.rds |binary man/logLik.systemfit.Rd | 21 ++++ man/systemfit.Rd | 5 - tests/KleinI.R | 20 +++- tests/KleinI.Rout.save | 69 +++++++++++++ tests/KleinI_noMat.R | 18 +++ tests/KleinI_noMat.Rout.save | 69 +++++++++++++ tests/test_2sls.R | 7 + tests/test_2sls.Rout.save | 18 +++ tests/test_3sls.R | 10 ++ tests/test_3sls.Rout.save | 24 ++++ tests/test_ols.R | 28 +++++ tests/test_ols.Rout.save | 45 ++++++++- tests/test_panel.R | 6 + tests/test_panel.Rout.save | 214 ++++++++++++++++++++++--------------------- tests/test_sur.R | 16 +++ tests/test_sur.Rout.save | 34 ++++++ tests/test_w2sls.R | 8 + tests/test_w2sls.Rout.save | 20 +++- tests/test_wls.R | 27 +++++ tests/test_wls.Rout.save | 46 ++++++++- 26 files changed, 659 insertions(+), 154 deletions(-)
Title: Quantitative Linkage Analysis Tools using the Variance
Components Approach
Description:
Calculate the polygenic and major gene models for quantitative trait
linkage analysis using variance components approach. The 0.2.2
release includes bug fixes that allow 'multic' to run properly
on 64-bit systems. The 0.3.0 release includes a fully implemented
sw2mloci() function. As of 0.3.8, Splus version is no longer
supported. Additional documentation and examples can be found
in the inst directory.
Author: Eric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Maintainer: Pat Votruba <votruba.patrick@mayo.edu>
Diff between multic versions 0.4.2 dated 2015-08-21 and 0.4.3 dated 2015-08-27
CHANGES | 5 +++ DESCRIPTION | 8 ++--- MD5 | 6 +-- R/load.effects.q | 87 ++++++++++++++++++++++++++++++++++++------------------- 4 files changed, 69 insertions(+), 37 deletions(-)
Title: Tools for Working with Points and Intervals
Description: Tools for working with and comparing sets of points and intervals.
Author: Richard Bourgon <bourgon.richard@gene.com>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between intervals versions 0.15.0 dated 2014-09-19 and 0.15.1 dated 2015-08-27
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NAMESPACE | 1 + README.md |only build/vignette.rds |binary inst/doc/intervals_overview.pdf |binary src/which_nearest.cpp | 12 ++++++++++-- 7 files changed, 23 insertions(+), 13 deletions(-)
Title: Performance Analysis and Companion Functions for Accuracy
Improvement for Binary Classification Problems
Description: Provides companion function for analysing the performance of classification models. Also, provides function to optimise probability cut-off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, etc to aid accuracy improvement in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>
Diff between InformationValue versions 1.1.0 dated 2015-08-04 and 1.1.1 dated 2015-08-27
DESCRIPTION | 9 + MD5 | 18 ++- NAMESPACE | 4 R/Main.R | 10 +- README.md | 207 +++++++++++++++++++++++++++++++++++++++++++- build |only data/ActualsAndScores.RData |binary inst |only man/optimalCutoff.Rd | 4 vignettes |only 10 files changed, 234 insertions(+), 18 deletions(-)
More information about InformationValue at CRAN
Permanent link
Title: Basic Functions for Supporting an Implementation of Choice
Experiments
Description: Provides seven basic functions that support an implementation of choice experiments.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.CEs versions 0.3-3 dated 2015-04-27 and 0.4-1 dated 2015-08-27
DESCRIPTION | 12 ++--- MD5 | 14 ++++- NAMESPACE | 57 +++++++++++++++--------- NEWS | 121 ++++++++++++++++++++++++++------------------------- R/print.sb.R |only R/print.summary.sb.R |only R/sb.check.args.R |only R/sb.design.R |only R/sb.extract.R |only R/sb.submit.R |only R/summary.sb.R |only man/sb.design.Rd |only 12 files changed, 117 insertions(+), 87 deletions(-)
Title: A GUI to View, Design and Export Various Graphs of Data
Description: Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>
Diff between plfMA versions 1.0 dated 2015-08-19 and 1.0.1 dated 2015-08-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/plfMA.R | 15 ++++++++++++++- man/plfMA.Rd | 6 +++--- 5 files changed, 26 insertions(+), 12 deletions(-)
Title: Modern Measures of Population Differentiation
Description: Provides functions for measuring
population divergence from genotypic data.
Author: David Winter [aut, cre],
Peter Green [ctb],
Zhian Kamvar [ctb],
Thierry Gosselin [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between mmod versions 1.3.0 dated 2015-07-11 and 1.3.1 dated 2015-08-27
DESCRIPTION | 12 +++++++----- MD5 | 9 +++++---- NEWS | 5 +++++ R/pairwise.R | 2 +- build/vignette.rds |binary vignettes/new.md |only 6 files changed, 18 insertions(+), 10 deletions(-)
Title: A Simple Wrapper for the LASVM Solver
Description: This is a simple wrapper for the LASVM Solver (see http://leon.bottou.org/projects/lasvm). LASVM is basically an online variant of the SMO solver.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>
Diff between lasvmR versions 0.1.1 dated 2015-08-26 and 0.1.2 dated 2015-08-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/la_svm.cpp | 8 ++------ 3 files changed, 8 insertions(+), 12 deletions(-)
Title: The Irvine Robustness Assessment for Qualitative Comparative
Analysis
Description: Test the robustness of a user's QCA solutions to randomness, using iraQCA. iaQCA is packaged with the irrQCA function, which provides recommendations for improving QCA solutions to reach typical significance levels.
Author: C. Ben Gibson [aut, cre],
Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>
Diff between iaQCA versions 0.8.0.0 dated 2015-08-06 and 0.8.7.0 dated 2015-08-27
iaQCA-0.8.0.0/iaQCA/R/iaQCA.R |only iaQCA-0.8.0.0/iaQCA/R/irQCA.R |only iaQCA-0.8.0.0/iaQCA/R/sim.iaQCA.R |only iaQCA-0.8.0.0/iaQCA/man/irQCA.Rd |only iaQCA-0.8.0.0/iaQCA/man/sim.iaQCA.Rd |only iaQCA-0.8.7.0/iaQCA/DESCRIPTION | 15 +++-- iaQCA-0.8.7.0/iaQCA/MD5 | 21 ++++---- iaQCA-0.8.7.0/iaQCA/NAMESPACE | 6 +- iaQCA-0.8.7.0/iaQCA/R/configuration.table.R | 2 iaQCA-0.8.7.0/iaQCA/R/iraQCA.R |only iaQCA-0.8.7.0/iaQCA/R/irrQCA.R |only iaQCA-0.8.7.0/iaQCA/R/sim.iraQCA.R |only iaQCA-0.8.7.0/iaQCA/man/conf.table.Rd | 2 iaQCA-0.8.7.0/iaQCA/man/iaQCA.Rd | 71 +++++++++++++++------------- iaQCA-0.8.7.0/iaQCA/man/iraQCA.Rd |only iaQCA-0.8.7.0/iaQCA/man/irrQCA.Rd |only iaQCA-0.8.7.0/iaQCA/man/sim.iraQCA.Rd |only 17 files changed, 65 insertions(+), 52 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.2.4 dated 2015-08-25 and 1.2.5 dated 2015-08-27
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- inst/doc/cgdsr.R | 2 +- inst/doc/cgdsr.Rnw | 4 ++-- inst/tests/test_cgdsr.R | 12 ++++++------ man/cgdsr-CGDS.Rd | 2 +- man/cgdsr-getCancerStudies.Rd | 2 +- man/cgdsr-getCaseLists.Rd | 2 +- man/cgdsr-getClinicalData.Rd | 2 +- man/cgdsr-getGeneticProfiles.Rd | 2 +- man/cgdsr-getMutationData.Rd | 2 +- man/cgdsr-getProfileData.Rd | 2 +- man/cgdsr-package.Rd | 4 ++-- man/cgdsr-plot.Rd | 2 +- man/cgdsr-setPlotErrorMsg.Rd | 4 ++-- man/cgdsr-setVerbose.Rd | 4 ++-- man/cgdsr-test.Rd | 4 ++-- vignettes/cgdsr.Rnw | 4 ++-- 18 files changed, 47 insertions(+), 47 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.2 dated 2015-07-01 and 1.8.3 dated 2015-08-26
DESCRIPTION | 14 MD5 | 167 - NAMESPACE | 282 +-- NEWS | 1242 ++++++------- R/helpfunctions.R | 1499 ++++++++-------- R/sjPlotAncovaLSMeans.R | 51 R/sjPlotAnova.R | 32 R/sjPlotClusterAnalysis.R | 1769 +++++++++---------- R/sjPlotCorr.R | 712 +++---- R/sjPlotDist.R | 1066 +++++------ R/sjPlotFrequencies.R | 53 R/sjPlotGLME.R | 4184 ++++++++++++++++++++++----------------------- R/sjPlotGroupFrequencies.R | 2368 ++++++++++++------------- R/sjPlotGroupPropTable.R |only R/sjPlotInteractions.R | 2930 +++++++++++++++---------------- R/sjPlotLikert.R | 1318 +++++++------- R/sjPlotLinreg.R | 2568 ++++++++++++++------------- R/sjPlotLinregMultiple.R | 817 ++++---- R/sjPlotOdds.R | 1786 +++++++++---------- R/sjPlotOddsMultiple.R | 117 - R/sjPlotPCA.R | 933 +++++----- R/sjPlotPearsonsChi2Test.R | 4 R/sjPlotPolynomials.R | 66 R/sjPlotPropTable.R | 1290 ++++++------- R/sjPlotScatter.R | 14 R/sjPlotSetTheme.R | 1791 ++++++++++--------- R/sjPlotStackFrequencies.R | 1007 +++++----- R/sjTabCorr.R | 1023 +++++------ R/sjTabDataFrame.R | 118 - R/sjTabFrequencies.R | 87 R/sjTabGrpmean.R | 31 R/sjTabItemAnalysis.R | 5 R/sjTabLinReg.R | 3035 ++++++++++++++++---------------- R/sjTabMannWhitney.R | 172 - R/sjTabOdds.R | 2769 ++++++++++++++--------------- R/sjTabPCA.R | 1189 ++++++------ R/sjTabPropTable.R | 1577 ++++++++-------- R/sjTabSPSS.R | 762 ++++---- R/sjTabStackFrq.R | 1040 +++++------ R/zzz.R | 2 README.md | 42 man/dist_chisq.Rd | 7 man/dist_f.Rd | 7 man/dist_norm.Rd | 5 man/dist_t.Rd | 7 man/save_plot.Rd |only man/sjPlot-package.Rd | 4 man/sjc.cluster.Rd | 176 - man/sjc.dend.Rd | 102 - man/sjc.elbow.Rd | 2 man/sjc.kgap.Rd | 133 - man/sjc.qclus.Rd | 368 +-- man/sjp.aov1.Rd | 295 +-- man/sjp.chi2.Rd | 2 man/sjp.corr.Rd | 274 +- man/sjp.frq.Rd | 644 +++--- man/sjp.glm.Rd | 471 ++--- man/sjp.glmer.Rd | 429 ++-- man/sjp.glmm.Rd | 346 ++- man/sjp.gpt.Rd |only man/sjp.grpfrq.Rd | 594 +++--- man/sjp.int.Rd | 780 ++++---- man/sjp.likert.Rd | 460 ++-- man/sjp.lm.Rd | 478 ++--- man/sjp.lmer.Rd | 507 ++--- man/sjp.lmm.Rd | 330 +-- man/sjp.pca.Rd | 11 man/sjp.poly.Rd | 279 +-- man/sjp.scatter.Rd | 350 +-- man/sjp.setTheme.Rd | 32 man/sjp.stackfrq.Rd | 7 man/sjp.xtab.Rd | 470 ++--- man/sjt.corr.Rd | 360 +-- man/sjt.df.Rd | 313 +-- man/sjt.frq.Rd | 498 ++--- man/sjt.glm.Rd | 667 +++---- man/sjt.glmer.Rd | 448 ++-- man/sjt.grpmean.Rd | 184 - man/sjt.itemanalysis.Rd | 371 +-- man/sjt.lm.Rd | 825 ++++---- man/sjt.lmer.Rd | 450 ++-- man/sjt.mwu.Rd | 142 - man/sjt.pca.Rd | 369 +-- man/sjt.stackfrq.Rd | 402 ++-- man/sjt.xtab.Rd | 426 ++-- man/view_df.Rd | 262 +- 86 files changed, 26961 insertions(+), 26258 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/or who are new to R), supporting following common tasks:
1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc.
2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values.
3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.0.3 dated 2015-06-20 and 1.1 dated 2015-08-26
sjmisc-1.0.3/sjmisc/R/sjImportSPSS.R |only sjmisc-1.0.3/sjmisc/R/sjRecode.R |only sjmisc-1.0.3/sjmisc/man/get_val_labels.Rd |only sjmisc-1.0.3/sjmisc/man/get_var_labels.Rd |only sjmisc-1.0.3/sjmisc/man/set_val_labels.Rd |only sjmisc-1.0.3/sjmisc/man/set_var_labels.Rd |only sjmisc-1.0.3/sjmisc/man/std_e.Rd |only sjmisc-1.0.3/sjmisc/man/to_fac.Rd |only sjmisc-1.1/sjmisc/DESCRIPTION | 28 sjmisc-1.1/sjmisc/MD5 | 193 ++- sjmisc-1.1/sjmisc/NAMESPACE | 49 + sjmisc-1.1/sjmisc/NEWS | 136 +- sjmisc-1.1/sjmisc/R/S3-methods.R |only sjmisc-1.1/sjmisc/R/add_labels.R |only sjmisc-1.1/sjmisc/R/as_labelled.R |only sjmisc-1.1/sjmisc/R/copy_labels.R |only sjmisc-1.1/sjmisc/R/cramer.R |only sjmisc-1.1/sjmisc/R/cronb.R |only sjmisc-1.1/sjmisc/R/cv.R |only sjmisc-1.1/sjmisc/R/dicho.R |only sjmisc-1.1/sjmisc/R/efc.R | 66 - sjmisc-1.1/sjmisc/R/eta_sq.R |only sjmisc-1.1/sjmisc/R/fill_labels.R |only sjmisc-1.1/sjmisc/R/frq.R |only sjmisc-1.1/sjmisc/R/get_label.R |only sjmisc-1.1/sjmisc/R/get_labels.R |only sjmisc-1.1/sjmisc/R/get_na.R |only sjmisc-1.1/sjmisc/R/get_na_flags.R |only sjmisc-1.1/sjmisc/R/get_values.R |only sjmisc-1.1/sjmisc/R/gof.R |only sjmisc-1.1/sjmisc/R/group_str.R |only sjmisc-1.1/sjmisc/R/group_var.R |only sjmisc-1.1/sjmisc/R/helpfunctions.R | 257 ++--- sjmisc-1.1/sjmisc/R/icc.R |only sjmisc-1.1/sjmisc/R/is_crossed.R |only sjmisc-1.1/sjmisc/R/is_empty.R |only sjmisc-1.1/sjmisc/R/is_even.R |only sjmisc-1.1/sjmisc/R/is_labelled.R |only sjmisc-1.1/sjmisc/R/is_nested.R |only sjmisc-1.1/sjmisc/R/is_num_fac.R |only sjmisc-1.1/sjmisc/R/is_odd.R |only sjmisc-1.1/sjmisc/R/labelled.R |only sjmisc-1.1/sjmisc/R/mean_n.R |only sjmisc-1.1/sjmisc/R/mic.R |only sjmisc-1.1/sjmisc/R/mwu.R |only sjmisc-1.1/sjmisc/R/phi.R |only sjmisc-1.1/sjmisc/R/pseudo_r2.R |only sjmisc-1.1/sjmisc/R/read_write.R |only sjmisc-1.1/sjmisc/R/rec.R |only sjmisc-1.1/sjmisc/R/reliab_test.R |only sjmisc-1.1/sjmisc/R/remove_labels.R |only sjmisc-1.1/sjmisc/R/replace_na.R |only sjmisc-1.1/sjmisc/R/rmse.R |only sjmisc-1.1/sjmisc/R/se.R |only sjmisc-1.1/sjmisc/R/set_label.R |only sjmisc-1.1/sjmisc/R/set_labels.R |only sjmisc-1.1/sjmisc/R/set_na.R |only sjmisc-1.1/sjmisc/R/sjStatistics.R | 1464 ++---------------------------- sjmisc-1.1/sjmisc/R/std_b.R |only sjmisc-1.1/sjmisc/R/str_pos.R |only sjmisc-1.1/sjmisc/R/to_factor.R |only sjmisc-1.1/sjmisc/R/to_label.R |only sjmisc-1.1/sjmisc/R/to_na.R |only sjmisc-1.1/sjmisc/R/to_value.R |only sjmisc-1.1/sjmisc/R/trim.R |only sjmisc-1.1/sjmisc/R/unlabel.R |only sjmisc-1.1/sjmisc/R/weight.R |only sjmisc-1.1/sjmisc/R/word_wrap.R |only sjmisc-1.1/sjmisc/R/zap_labels.R |only sjmisc-1.1/sjmisc/README.md | 61 - sjmisc-1.1/sjmisc/man/add_labels.Rd | 63 - sjmisc-1.1/sjmisc/man/as_labelled.Rd |only sjmisc-1.1/sjmisc/man/chisq_gof.Rd | 14 sjmisc-1.1/sjmisc/man/cod.Rd | 6 sjmisc-1.1/sjmisc/man/copy_labels.Rd |only sjmisc-1.1/sjmisc/man/cramer.Rd | 7 sjmisc-1.1/sjmisc/man/cronb.Rd | 4 sjmisc-1.1/sjmisc/man/cv.Rd | 8 sjmisc-1.1/sjmisc/man/dicho.Rd | 48 sjmisc-1.1/sjmisc/man/efc.Rd | 6 sjmisc-1.1/sjmisc/man/eta_sq.Rd | 4 sjmisc-1.1/sjmisc/man/fill_labels.Rd |only sjmisc-1.1/sjmisc/man/frq.Rd |only sjmisc-1.1/sjmisc/man/get_label.Rd |only sjmisc-1.1/sjmisc/man/get_labels.Rd |only sjmisc-1.1/sjmisc/man/get_na.Rd |only sjmisc-1.1/sjmisc/man/get_na_flags.Rd |only sjmisc-1.1/sjmisc/man/get_values.Rd | 35 sjmisc-1.1/sjmisc/man/group_labels.Rd | 47 sjmisc-1.1/sjmisc/man/group_str.Rd | 33 sjmisc-1.1/sjmisc/man/group_var.Rd | 40 sjmisc-1.1/sjmisc/man/hoslem_gof.Rd | 8 sjmisc-1.1/sjmisc/man/icc.Rd | 4 sjmisc-1.1/sjmisc/man/is_crossed.Rd | 6 sjmisc-1.1/sjmisc/man/is_empty.Rd | 4 sjmisc-1.1/sjmisc/man/is_even.Rd | 4 sjmisc-1.1/sjmisc/man/is_labelled.Rd |only sjmisc-1.1/sjmisc/man/is_nested.Rd | 6 sjmisc-1.1/sjmisc/man/is_num_fac.Rd | 4 sjmisc-1.1/sjmisc/man/is_odd.Rd | 4 sjmisc-1.1/sjmisc/man/labelled.Rd |only sjmisc-1.1/sjmisc/man/levene_test.Rd | 6 sjmisc-1.1/sjmisc/man/mean_n.Rd | 6 sjmisc-1.1/sjmisc/man/mic.Rd | 6 sjmisc-1.1/sjmisc/man/mwu.Rd | 21 sjmisc-1.1/sjmisc/man/phi.Rd | 7 sjmisc-1.1/sjmisc/man/pseudo_r2.Rd | 6 sjmisc-1.1/sjmisc/man/read_sas.Rd | 16 sjmisc-1.1/sjmisc/man/read_spss.Rd | 52 - sjmisc-1.1/sjmisc/man/read_stata.Rd | 14 sjmisc-1.1/sjmisc/man/rec.Rd | 32 sjmisc-1.1/sjmisc/man/recode_to.Rd | 16 sjmisc-1.1/sjmisc/man/reliab_test.Rd | 12 sjmisc-1.1/sjmisc/man/remove_labels.Rd | 8 sjmisc-1.1/sjmisc/man/replace_na.Rd | 10 sjmisc-1.1/sjmisc/man/rmse.Rd | 6 sjmisc-1.1/sjmisc/man/se.Rd |only sjmisc-1.1/sjmisc/man/set_label.Rd |only sjmisc-1.1/sjmisc/man/set_labels.Rd |only sjmisc-1.1/sjmisc/man/set_na.Rd | 67 + sjmisc-1.1/sjmisc/man/sjmisc-package.Rd | 71 - sjmisc-1.1/sjmisc/man/std_beta.Rd | 40 sjmisc-1.1/sjmisc/man/str_pos.Rd | 12 sjmisc-1.1/sjmisc/man/table_values.Rd | 6 sjmisc-1.1/sjmisc/man/to_factor.Rd |only sjmisc-1.1/sjmisc/man/to_label.Rd | 62 + sjmisc-1.1/sjmisc/man/to_na.Rd |only sjmisc-1.1/sjmisc/man/to_sjPlot.Rd | 16 sjmisc-1.1/sjmisc/man/to_value.Rd | 26 sjmisc-1.1/sjmisc/man/trim.Rd | 4 sjmisc-1.1/sjmisc/man/weight.Rd | 18 sjmisc-1.1/sjmisc/man/weight2.Rd | 24 sjmisc-1.1/sjmisc/man/word_wrap.Rd | 8 sjmisc-1.1/sjmisc/man/write_spss.Rd | 15 sjmisc-1.1/sjmisc/man/write_stata.Rd | 13 sjmisc-1.1/sjmisc/man/zap_labels.Rd |only sjmisc-1.1/sjmisc/man/zap_unlabelled.Rd |only 137 files changed, 1144 insertions(+), 2065 deletions(-)
Title: Some Invalid Some Valid Instrumental Variables Estimator
Description: Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome.
Author: Hyunseung Kang <hskang@stanford.edu>
Maintainer: Hyunseung Kang <hskang@stanford.edu>
Diff between sisVIVE versions 1.1 dated 2015-05-05 and 1.2 dated 2015-08-26
sisVIVE-1.1/sisVIVE/man/plot.sisVIVE.Rd |only sisVIVE-1.2/sisVIVE/DESCRIPTION | 12 +-- sisVIVE-1.2/sisVIVE/MD5 | 13 +--- sisVIVE-1.2/sisVIVE/NAMESPACE | 6 - sisVIVE-1.2/sisVIVE/R/sisVIVE.R | 94 ++++++++++++----------------- sisVIVE-1.2/sisVIVE/man/predict.sisVIVE.Rd | 2 sisVIVE-1.2/sisVIVE/man/sisVIVE.Rd | 3 sisVIVE-1.2/sisVIVE/man/summary.sisVIVE.Rd | 2 8 files changed, 60 insertions(+), 72 deletions(-)
Title: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome
Similarity Networks
Description: Compares the evolution of an original network X to an augmented network Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal paths and disconnected nodes.
Author: Etienne Lord, Margaux Le Cam, Eric Bapteste, Vladimir Makarenkov and Francois-Joseph Lapointe
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between SDDE versions 1.0.0 dated 2015-03-06 and 1.0.1 dated 2015-08-26
DESCRIPTION | 11 ++-- MD5 | 36 ++++++++------ NAMESPACE | 4 + NEWS |only R/complete_network.R | 7 ++ R/complete_network_trace.R | 2 R/info_network.R | 10 +++- R/random_network.R | 79 ++++++++++++++++++++++--------- R/sample_network.R | 2 R/save_network.R | 109 +++++++++++++++++++++++++++++++------------- R/version.R |only data/Eukaryote_nonphoto.rda |binary data/Eukaryote_photo.rda |binary data/Plasmids.rda |binary data/Sample_1.rda |binary data/Sample_2.rda |binary data/Viruses.rda |binary man/SDDE-package.Rd | 7 +- man/Version.Rd |only man/plot_network.Rd |only man/random_network.Rd | 11 +++- 21 files changed, 189 insertions(+), 89 deletions(-)
Title: Rank Estimation for Linear Models
Description: R estimation and inference for linear models. Estimation
is for general scores and a library of commonly used score
functions is included.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke <kloke@biostat.wisc.edu>
Diff between Rfit versions 0.21 dated 2014-11-07 and 0.22.0 dated 2015-08-26
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 19 +++++++++++++++++++ R/drop.test.R | 5 +++-- R/oneway.rfit.R | 10 +++++++--- R/rfit.default.R | 25 +++++++++++++++++++++---- R/rstudent.rfit.R | 2 +- tests |only 8 files changed, 64 insertions(+), 20 deletions(-)
Title: Component Models for Multi-Way Data
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints (orthogonality and non-negativity). Fit models include Individual Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between multiway versions 1.0-0 dated 2015-04-15 and 1.0-1 dated 2015-08-26
multiway-1.0-0/multiway/man/nrescale.Rd |only multiway-1.0-1/multiway/ChangeLog |only multiway-1.0-1/multiway/DESCRIPTION | 8 - multiway-1.0-1/multiway/MD5 | 70 +++++++++----- multiway-1.0-1/multiway/NAMESPACE | 22 ++++ multiway-1.0-1/multiway/R/congru.R |only multiway-1.0-1/multiway/R/indscal.R | 51 +++++++--- multiway-1.0-1/multiway/R/ncenter.R | 22 ++-- multiway-1.0-1/multiway/R/nrescale.R | 72 --------------- multiway-1.0-1/multiway/R/nscale.R |only multiway-1.0-1/multiway/R/parafac.R | 33 ++++--- multiway-1.0-1/multiway/R/parafac2.R | 58 +++++++----- multiway-1.0-1/multiway/R/parafac2_3way.R | 104 +++++++++++----------- multiway-1.0-1/multiway/R/parafac2_4way.R | 127 +++++++++++++-------------- multiway-1.0-1/multiway/R/parafac_3way.R | 76 +++++++--------- multiway-1.0-1/multiway/R/parafac_4way.R | 103 ++++++++++----------- multiway-1.0-1/multiway/R/reorder.indscal.R |only multiway-1.0-1/multiway/R/reorder.parafac.R |only multiway-1.0-1/multiway/R/reorder.parafac2.R |only multiway-1.0-1/multiway/R/reorder.sca.R |only multiway-1.0-1/multiway/R/reorder.tucker.R |only multiway-1.0-1/multiway/R/rescale.R |only multiway-1.0-1/multiway/R/rescale.indscal.R |only multiway-1.0-1/multiway/R/rescale.parafac.R |only multiway-1.0-1/multiway/R/rescale.parafac2.R |only multiway-1.0-1/multiway/R/rescale.sca.R |only multiway-1.0-1/multiway/R/rescale.tucker.R |only multiway-1.0-1/multiway/R/resign.R |only multiway-1.0-1/multiway/R/resign.indscal.R |only multiway-1.0-1/multiway/R/resign.parafac.R |only multiway-1.0-1/multiway/R/resign.parafac2.R |only multiway-1.0-1/multiway/R/resign.sca.R |only multiway-1.0-1/multiway/R/resign.tucker.R |only multiway-1.0-1/multiway/R/sca.R | 22 ++-- multiway-1.0-1/multiway/R/tucker.R | 32 ++++-- multiway-1.0-1/multiway/R/tucker_3way.R | 7 - multiway-1.0-1/multiway/R/tucker_4way.R | 9 + multiway-1.0-1/multiway/man/congru.Rd |only multiway-1.0-1/multiway/man/indscal.Rd | 32 +++++- multiway-1.0-1/multiway/man/ncenter.Rd | 28 ++--- multiway-1.0-1/multiway/man/nscale.Rd |only multiway-1.0-1/multiway/man/parafac.Rd | 39 ++++++-- multiway-1.0-1/multiway/man/parafac2.Rd | 47 ++++++++- multiway-1.0-1/multiway/man/reorder.Rd |only multiway-1.0-1/multiway/man/rescale.Rd |only multiway-1.0-1/multiway/man/resign.Rd |only multiway-1.0-1/multiway/man/sca.Rd | 105 ++++++++++++++++++++-- multiway-1.0-1/multiway/man/smpower.Rd | 2 multiway-1.0-1/multiway/man/tucker.Rd | 42 +++++++- 49 files changed, 662 insertions(+), 449 deletions(-)
Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users
to create interactive charts based on data frames. Charts
are displayed locally via the R HTTP help server. A modern
browser with Internet connection is required and for some
charts a Flash player. The data remains local and is not
uploaded to Google.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between googleVis versions 0.5.9 dated 2015-07-04 and 0.5.10 dated 2015-08-26
DESCRIPTION |only MD5 |only NEWS | 13 R/gvis.R | 1 README.md |only THANKS |only build |only inst/doc/Using_Roles_via_googleVis.html | 220 +++--- inst/doc/Using_Trendlines_with_googleVis.html | 80 +- inst/doc/Using_googleVis_with_knitr.html | 76 +- inst/doc/googleVis.pdf |binary inst/doc/googleVis_examples.Rmd | 2 inst/doc/googleVis_examples.html | 732 +++++++++++----------- man |only vignettes/Ideas |only vignettes/Using_Roles_via_googleVis.Rmd |only vignettes/Using_Trendlines_with_googleVis.Rmd |only vignettes/Using_googleVis_with_knitr.Rmd |only vignettes/figures/Apostrophe.pdf |only vignettes/figures/CambR_googleVis_29_May_2012.pdf |only vignettes/figures/CreatePost.pdf |only vignettes/figures/MarkdownExample.pdf |binary vignettes/figures/MotionChart.pdf |only vignettes/figures/Options.pdf |only vignettes/figures/googleVisDemoPlots.pdf |only vignettes/googleVis.bib |only vignettes/googleVis_examples.Rmd |only vignettes/mystyle.css |only 28 files changed, 567 insertions(+), 557 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.4.0 dated 2015-08-26 and 0.4.1 dated 2015-08-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/Makevars | 2 +- src/Makevars.win | 2 +- src/fcnn/level1_impl.h | 5 +++++ 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.1.0 dated 2015-05-05 and 3.2.0 dated 2015-08-26
DESCRIPTION | 6 +-- MD5 | 60 +++++++++++++++++---------------- NAMESPACE | 3 + NEWS | 6 +++ R/acs.R | 1 R/choropleth.R | 27 ++++++++------ R/data.R | 9 ++++ R/get_state_demograhpics.R | 1 R/usa.R | 6 ++- README.md | 5 ++ build/vignette.rds |binary data/continental_us_states.rdata |only inst/doc/a-introduction.html | 2 - inst/doc/b-state-choropleth.html | 6 +-- inst/doc/c-county-choropleth.html | 8 ++-- inst/doc/d-country-choropleth.html | 6 +-- inst/doc/e-mapping-us-census-data.Rmd | 2 - inst/doc/e-mapping-us-census-data.html | 2 - inst/doc/f-world-bank-data.html | 6 +-- inst/doc/h-creating-your-own-maps.html | 2 - inst/doc/i-creating-admin1-maps.Rmd | 2 - inst/doc/i-creating-admin1-maps.html | 6 +-- man/Admin1Choropleth.Rd | 2 - man/Choropleth.Rd | 2 - man/CountryChoropleth.Rd | 2 - man/CountyChoropleth.Rd | 2 - man/CountyZoomChoropleth.Rd | 2 - man/StateChoropleth.Rd | 2 - man/USAChoropleth.Rd | 2 - man/continental_us_states.Rd |only vignettes/e-mapping-us-census-data.Rmd | 2 - vignettes/i-creating-admin1-maps.Rmd | 2 - 32 files changed, 107 insertions(+), 77 deletions(-)
Title: Wrap Around Time Series Graphics
Description: Wrap-around Time Series (WATS) plots for interrupted time series
designs with seasonal patterns.
Author: Will Beasley [aut, cre], Joe Rodgers [aut], Matthew Schuelke [ctb],
Ronnie Coleman [ctb], Mark Joseph Lachowicz [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between Wats versions 0.2-16 dated 2014-05-21 and 0.10.1 dated 2015-08-26
Wats-0.10.1/Wats/DESCRIPTION | 20 +- Wats-0.10.1/Wats/LICENSE | 4 Wats-0.10.1/Wats/MD5 | 100 ++++------ Wats-0.10.1/Wats/NAMESPACE | 2 Wats-0.10.1/Wats/NEWS | 7 Wats-0.10.1/Wats/R/AnnotateData.R | 4 Wats-0.10.1/Wats/R/AugmentData.R | 14 - Wats-0.10.1/Wats/R/CartesianPeriodic.R | 2 Wats-0.10.1/Wats/R/CartesianRolling.R | 2 Wats-0.10.1/Wats/R/CountyMonthBirthRateDoc.R | 6 Wats-0.10.1/Wats/R/PolarPeriodic.R | 8 Wats-0.10.1/Wats/R/PolarizeCartesian.R | 8 Wats-0.10.1/Wats/R/Wats-package.r | 38 +++ Wats-0.10.1/Wats/README.md | 42 +++- Wats-0.10.1/Wats/build/vignette.rds |binary Wats-0.10.1/Wats/inst/CITATION | 17 + Wats-0.10.1/Wats/inst/doc/MbrFigures.R | 38 +-- Wats-0.10.1/Wats/inst/doc/MbrFigures.Rmd | 1 Wats-0.10.1/Wats/inst/doc/MbrFigures.html | 72 ++++--- Wats-0.10.1/Wats/inst/doc/OkFertilityWithIntercensalEstimates.R | 26 -- Wats-0.10.1/Wats/inst/doc/OkFertilityWithIntercensalEstimates.Rmd | 1 Wats-0.10.1/Wats/inst/doc/OkFertilityWithIntercensalEstimates.html | 97 +++++---- Wats-0.10.1/Wats/man/AnnotateData.Rd | 5 Wats-0.10.1/Wats/man/AugmentCycleData.Rd | 11 - Wats-0.10.1/Wats/man/CartesianPeriodic.Rd | 5 Wats-0.10.1/Wats/man/CartesianRolling.Rd | 5 Wats-0.10.1/Wats/man/CountyMonthBirthRate.Rd | 9 Wats-0.10.1/Wats/man/PolarPeriodic.Rd | 11 - Wats-0.10.1/Wats/man/PolarizeCartesian.Rd | 7 Wats-0.10.1/Wats/man/Wats-package.Rd |only Wats-0.10.1/Wats/tests/testthat/MasterTestRunner.R | 6 Wats-0.10.1/Wats/tests/testthat/test.Annotate.R | 2 Wats-0.10.1/Wats/tests/testthat/test.Augment.R | 2 Wats-0.10.1/Wats/tests/testthat/test.Linear.R | 2 Wats-0.10.1/Wats/vignettes/MbrFigures.Rmd | 1 Wats-0.10.1/Wats/vignettes/OkFertilityWithIntercensalEstimates.Rmd | 1 Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure2IndividualBasic-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure2Stylized-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure4Basic-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure4Stylized-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure5-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure6-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure7-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure7AllCounties-1.png |only Wats-0.10.1/Wats/vignettes/figure_mbr_rmd/Figure8-1.png |only Wats-0.10.1/Wats/vignettes/figure_okc_fertility_intercensal_rmd/CartesianPeriodic-1.png |only Wats-0.10.1/Wats/vignettes/figure_okc_fertility_intercensal_rmd/CartesianRolling-1.png |only Wats-0.10.1/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryFrequentist-1.png |only Wats-0.10.1/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryFrequentist-2.png |only Wats-0.10.1/Wats/vignettes/figure_okc_fertility_intercensal_rmd/PolarPeriodic-1.png |only Wats-0.2-16/Wats/man/Wats.Rd |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure2IndividualBasic.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure2Stylized.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure4Basic.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure4Stylized.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure5.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure6.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure7.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure7AllCounties.png |only Wats-0.2-16/Wats/vignettes/figure_mbr_rmd/Figure8.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/CartesianPeriodic.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/CartesianRolling.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryFrequentist1.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryFrequentist2.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryUnsmoothed1.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/ConfirmatoryUnsmoothed2.png |only Wats-0.2-16/Wats/vignettes/figure_okc_fertility_intercensal_rmd/PolarPeriodic.png |only 67 files changed, 317 insertions(+), 259 deletions(-)
Title: STK++ Integration to R using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp.
The rtkpp package includes the header files from the STK++
library (currently version 0.8.99). Thus users do not need to
install STK++ itself in order to use it.
STK++ is licensed under the GNU LGPL version 2 or later. rtkpp
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre],
Vincent Kubicki [ctb],
Quentin Grimonprez [ctb],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff <serge.iovleff@stkpp.org>
Diff between rtkpp versions 0.8.6 dated 2015-03-11 and 0.9.2 dated 2015-08-26
rtkpp-0.8.6/rtkpp/inst/projects/AAModels/src/STK_GaussianAAModel.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/AAModels/src/STK_IAAModel.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/AAModels/src/STK_LinearAAModel.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/AAModels/src/makevars.local |only rtkpp-0.8.6/rtkpp/inst/projects/Algebra/src/STK_Qr.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Algebra/src/STK_Svd.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Algebra/src/STK_SymEigen.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Algebra/src/STK_lapack_SymEigen.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Algebra/src/makevars.local |only rtkpp-0.8.6/rtkpp/inst/projects/Analysis/include/STK_Funct_poisson_raw.h |only rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_IArrayBase.h |only rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/products/STK_ProductImpl.h |only rtkpp-0.8.6/rtkpp/inst/projects/Arrays/src/STK_Arrays_Util.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalParameters.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_DiagGaussianParameters.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaParameters.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/KernelMixtureModels/STK_KernelGaussianParameters.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/KernelMixtureModels/STK_KernelMixtureBridge.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonParameters.h |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/src/STK_IMixtureManager.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Clustering/src/makevars.local |only rtkpp-0.8.6/rtkpp/inst/projects/DManager/src/STK_ExportToCsv.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/DManager/src/STK_IDataHandler.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Reduct/include/STK_IReduct.h |only rtkpp-0.8.6/rtkpp/inst/projects/Reduct/src/STK_ILinearReduct.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Reduct/src/STK_IReduct.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Reduct/src/STK_LocalVariance.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Reduct/src/STK_ProjectedVariance.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegression.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Regress/src/STK_BSplineRegression.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Regress/src/STK_MultidimRegression.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/Rtkpp/include/STK_ClusterFacade.h |only rtkpp-0.8.6/rtkpp/inst/projects/Rtkpp/include/STK_ClusterLauncher.h |only rtkpp-0.8.6/rtkpp/inst/projects/Rtkpp/include/STK_RDataHandler.h |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/include/STK_Global.h |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Binary.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Chrono.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Exceptions.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Global.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Integer.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Range.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Real.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STKernel/src/STK_Sign.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_IMultiLaw.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_JointBernoulli.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_JointCauchy.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_JointGamma.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_JointNormal.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_MultiNormal.h |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/src/STK_Law_Bernoulli.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/src/STK_Law_Categorical.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/src/STK_Law_Uniform.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/StatModels/src/STK_GaussianModel.cpp |only rtkpp-0.8.6/rtkpp/inst/projects/StatModels/src/STK_IGaussianModel.cpp |only rtkpp-0.9.2/rtkpp/DESCRIPTION | 12 rtkpp-0.9.2/rtkpp/MD5 | 549 ++-- rtkpp-0.9.2/rtkpp/R/rtkppFlags.R | 9 rtkpp-0.9.2/rtkpp/build/vignette.rds |binary rtkpp-0.9.2/rtkpp/cleanup | 2 rtkpp-0.9.2/rtkpp/inst/NEWS.Rd | 18 rtkpp-0.9.2/rtkpp/inst/doc/rtkpp-introduction.R | 2 rtkpp-0.9.2/rtkpp/inst/doc/rtkpp-introduction.Rnw | 96 rtkpp-0.9.2/rtkpp/inst/doc/rtkpp-introduction.pdf |binary rtkpp-0.9.2/rtkpp/inst/include/Algebra.h | 18 rtkpp-0.9.2/rtkpp/inst/include/Analysis.h | 2 rtkpp-0.9.2/rtkpp/inst/include/Arrays.h | 11 rtkpp-0.9.2/rtkpp/inst/include/Clustering.h | 70 rtkpp-0.9.2/rtkpp/inst/include/DManager.h | 4 rtkpp-0.9.2/rtkpp/inst/include/RTKpp.h | 4 rtkpp-0.9.2/rtkpp/inst/include/RTKppForward.h | 1 rtkpp-0.9.2/rtkpp/inst/include/Reduct.h | 4 rtkpp-0.9.2/rtkpp/inst/include/STKpp.h | 6 rtkpp-0.9.2/rtkpp/inst/include/STatistiK.h | 86 rtkpp-0.9.2/rtkpp/inst/makefile | 466 +-- rtkpp-0.9.2/rtkpp/inst/projects/AAModels/include/STK_GaussianAAModel.h | 215 + rtkpp-0.9.2/rtkpp/inst/projects/AAModels/include/STK_IAAModel.h | 410 ++- rtkpp-0.9.2/rtkpp/inst/projects/AAModels/include/STK_LinearAAModel.h | 235 + rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_Algebra_Util.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_CG.h | 135 - rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_GinvSymmetric.h | 7 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_Givens.h | 4 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_Householder.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_ILeastSquare.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_IQr.h | 118 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_ISvd.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_ISymEigen.h | 106 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_MultiLeastSquare.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_Qr.h | 80 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_Svd.h | 722 ++++- rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_SymEigen.h | 340 ++ rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_WeightedSvd.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_lapack_MultiLeastSquare.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_lapack_Qr.h | 70 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_lapack_Svd.h |only rtkpp-0.9.2/rtkpp/inst/projects/Algebra/include/STK_lapack_SymEigen.h | 323 +- rtkpp-0.9.2/rtkpp/inst/projects/Algebra/src/STK_lapack_Qr.cpp | 85 rtkpp-0.9.2/rtkpp/inst/projects/Algebra/src/STK_lapack_Svd.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/Analysis/include/STK_Funct_Util.h | 9 rtkpp-0.9.2/rtkpp/inst/projects/Analysis/include/STK_Funct_betaRatio.h | 20 rtkpp-0.9.2/rtkpp/inst/projects/Analysis/include/STK_Funct_raw.h | 123 - rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_b1.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_betaRatio.cpp | 70 rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_beta_raw.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_binomial_raw.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_gamma.cpp | 8 rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_gammaRatio.cpp | 1 rtkpp-0.9.2/rtkpp/inst/projects/Analysis/src/STK_Funct_poisson_raw.cpp | 12 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_AllocatorBase.h | 246 +- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array1D.h | 93 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2D.h | 18 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DDiagonal.h | 20 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DLowerTriangular.h | 14 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DNumber.h | 9 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DPoint.h | 12 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DSquare.h | 18 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DUpperTriangular.h | 14 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2DVector.h | 18 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Array2D_Functors.h | 48 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ArrayBase.h | 259 +- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseApplier.h | 20 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseAssign.h | 354 +- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseInitializer.h | 8 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Arrays_Util.h | 32 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CAllocator.h | 1211 +++------- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CArray.h | 49 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CArrayNumber.h | 34 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CArrayPoint.h | 55 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CArraySquare.h | 38 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_CArrayVector.h | 54 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Const_Arrays.h | 121 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_Display.h | 38 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ExprBase.h | 115 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ExprBaseDot.h | 13 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ExprBaseFunctors.h | 12 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ExprBaseProduct.h | 8 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ExprBaseVisitor.h | 134 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_IArray1D.h | 76 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_IArray2D.h | 38 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_IArray2DBase.h | 104 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ICArray.h | 208 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_IContainerRef.h | 14 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ITContainer.h | 142 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ITContainer1D.h | 165 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_ITContainer2D.h |only rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/STK_SparseMatrix.h |only rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_BinaryOperators.h | 27 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_DiagonalOperator.h | 146 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_DotOperators.h | 18 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_SlicingOperators.h | 263 -- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_TransposeOperator.h | 55 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/operators/STK_UnaryOperators.h | 77 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByArrayProduct.h | 394 +-- rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByVectorProduct.h | 181 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/products/STK_ProductDispatcher.h |only rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/products/STK_ProductOperators.h | 129 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/products/STK_ProductRaw.h |only rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/visitors/STK_SlicingVisitors.h | 58 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorSelector.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/visitors/STK_Visitors.h | 142 - rtkpp-0.9.2/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorsImpl.h | 54 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBase.h | 138 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBridge.h | 72 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalMixtureManager.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pjk.h | 130 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pk.h | 112 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_DiagGaussianBase.h | 115 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_DiagGaussianBridge.h | 97 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_DiagGaussianMixtureManager.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_Gaussian_s.h | 158 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_Gaussian_sj.h | 159 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_Gaussian_sjk.h | 114 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels/STK_Gaussian_sk.h | 121 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBase.h | 190 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBridge.h | 187 + rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaMixtureManager.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bjk.h | 175 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bk.h | 178 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bjk.h | 180 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bk.h | 179 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_b.h | 182 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bj.h | 185 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bjk.h | 141 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bk.h | 135 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_b.h | 172 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bj.h | 184 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bjk.h | 128 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bk.h | 127 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/KernelMixtureModels/STK_KernelGaussian.h | 361 ++ rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/KernelMixtureModels/STK_KernelGaussianBridge.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/KernelMixtureModels/STK_KernelMixtureManager.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonBase.h | 94 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonBridge.h | 78 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonMixtureManager.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_ljk.h | 105 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_ljlk.h | 138 - rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_lk.h | 98 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_Clust_Util.h | 82 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_IMixture.h | 12 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_IMixtureBridge.h | 70 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_IMixtureManager.h | 188 + rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_IMixtureModel.h | 120 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureAlgo.h | 104 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureComposer.h | 87 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureInit.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureManager.h | 226 + rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureParameters.h |only rtkpp-0.9.2/rtkpp/inst/projects/Clustering/include/STK_MixtureStrategy.h | 5 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_Clust_Util.cpp | 20 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_IMixture.cpp | 2 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_IMixtureComposer.cpp | 8 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_MixtureAlgo.cpp | 283 +- rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp | 35 rtkpp-0.9.2/rtkpp/inst/projects/Clustering/src/STK_MixtureStrategy.cpp | 201 + rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_Cell.h | 4 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_DataFrame.h | 39 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_DataHandler.h | 63 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_DataHandlerBase.h |only rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_ExportToCsv.h | 222 + rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_IDataHandler.h | 45 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_IVariable.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_List1D.h | 38 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_ReadWriteCsv.h | 30 rtkpp-0.9.2/rtkpp/inst/projects/DManager/include/STK_Variable.h | 14 rtkpp-0.9.2/rtkpp/inst/projects/DManager/src/STK_DataFrame.cpp | 12 rtkpp-0.9.2/rtkpp/inst/projects/DManager/src/STK_IPage.cpp | 4 rtkpp-0.9.2/rtkpp/inst/projects/DManager/src/STK_Option.cpp | 2 rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_ILinearReduct.h | 165 + rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_IReducer.h |only rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_LocalVariance.h | 421 +++ rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_LocalVariancePage.h | 12 rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_ProjectedVariance.h | 105 rtkpp-0.9.2/rtkpp/inst/projects/Reduct/include/STK_Reduct_Util.h | 27 rtkpp-0.9.2/rtkpp/inst/projects/Reduct/src/STK_LocalVariancePage.cpp | 12 rtkpp-0.9.2/rtkpp/inst/projects/Reduct/src/STK_Reduct_Util.cpp | 32 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineCoefficients.h | 48 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegression.h | 202 + rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegressionPage.h | 6 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_BSplineCoefficients.h | 97 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_BSplineRegression.h | 153 - rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_IRegression.h | 89 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_MultidimRegression.h | 80 rtkpp-0.9.2/rtkpp/inst/projects/Regress/include/STK_Regress_Util.h | 19 rtkpp-0.9.2/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegressionPage.cpp | 6 rtkpp-0.9.2/rtkpp/inst/projects/Regress/src/STK_Regress_Util.cpp | 17 rtkpp-0.9.2/rtkpp/inst/projects/Rtkpp/include/STK_RMatrix.h | 21 rtkpp-0.9.2/rtkpp/inst/projects/Rtkpp/include/STK_RVector.h | 24 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Arithmetic.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Binary.h | 59 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Chrono.h | 20 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Constants.h | 15 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Exceptions.h | 48 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Functors.h | 288 +- rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Integer.h | 51 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Proxy.h | 5 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Range.h | 366 +-- rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Real.h | 35 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_Sign.h | 61 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/include/STK_String.h | 63 rtkpp-0.9.2/rtkpp/inst/projects/STKernel/src/STK_String.cpp | 59 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_Exponential.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_Gaussian.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_IKernelBase.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_Linear.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_Polynomial.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_RationalQuadratic.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Kernel_Util.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Bernoulli.h | 125 - rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Beta.h | 91 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Binomial.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Categorical.h | 77 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Cauchy.h | 117 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_ChiSquared.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Exponential.h | 69 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_FisherSnedecor.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Gamma.h | 106 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Geometric.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_HyperGeometric.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_ILawBase.h | 4 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_IUnivLaw.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_LogNormal.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Logistic.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_NegativeBinomial.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Normal.h | 95 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Poisson.h | 52 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Student.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Uniform.h | 164 + rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_UniformDiscrete.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Util.h | 6 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Law_Weibull.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_IMultiLaw.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_JointBernoulli.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_JointCauchy.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_JointGamma.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_JointNormal.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_MultiLaw_Normal.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_RandBase.h | 6 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Stat_Functors.h | 48 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Stat_MultivariateReal.h | 129 - rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/include/STK_Stat_Online.h |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Beta.cpp | 130 - rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Binomial.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Cauchy.cpp | 109 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_ChiSquared.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Exponential.cpp | 142 - rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_FisherSnedecor.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Gamma.cpp | 54 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Geometric.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_HyperGeometric.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_LogNormal.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Logistic.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_NegativeBinomial.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Normal.cpp | 220 + rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Poisson.cpp | 45 rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Student.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/STatistiK/src/STK_Law_Weibull.cpp |only rtkpp-0.9.2/rtkpp/inst/projects/Sdk/include/STK_Macros.h | 4 rtkpp-0.9.2/rtkpp/inst/projects/Sdk/include/STK_MetaTemplate.h | 29 rtkpp-0.9.2/rtkpp/inst/projects/Sdk/include/STK_StaticAssert.h | 80 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_Gaussian2BlocksModel.h | 6 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_GaussianModel.h | 106 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_IGaussianModel.h | 41 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_IMultiStatModel.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_IStatModel.h | 4 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_JointBernoulliModel.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_JointGammaModel.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/include/STK_JointGaussianModel.h | 2 rtkpp-0.9.2/rtkpp/inst/projects/StatModels/src/STK_Gaussian2BlocksModel.cpp | 18 rtkpp-0.9.2/rtkpp/man/rtkpp-package.Rd | 3 rtkpp-0.9.2/rtkpp/man/rtkppFlags.Rd | 3 rtkpp-0.9.2/rtkpp/src/Makevars | 13 rtkpp-0.9.2/rtkpp/vignettes/rtkpp-introduction.Rnw | 96 rtkpp-0.9.2/rtkpp/vignettes/rtkpp.bib | 515 ---- 332 files changed, 13213 insertions(+), 8278 deletions(-)
Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes multivariate methods and data visualization tools
to implement profile analysis and cross-validation techniques described
in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins <cddesjardins@gmail.com>,
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.2-1 dated 2013-12-20 and 0.3 dated 2015-08-26
profileR-0.2-1/profileR/R/cp.R |only profileR-0.2-1/profileR/R/pc.R |only profileR-0.2-1/profileR/man/cp.Rd |only profileR-0.2-1/profileR/man/pc.Rd |only profileR-0.3/profileR/DESCRIPTION | 21 +++++++-------- profileR-0.3/profileR/MD5 | 36 ++++++++++++++++++--------- profileR-0.3/profileR/NAMESPACE | 17 ++++++++---- profileR-0.3/profileR/NEWS | 6 ++++ profileR-0.3/profileR/R/cpa.R |only profileR-0.3/profileR/R/mpa.R |only profileR-0.3/profileR/R/paos.R |only profileR-0.3/profileR/R/pbg.R | 25 ++++++++++++++++++ profileR-0.3/profileR/R/pcv.R |only profileR-0.3/profileR/R/plot.critpat.R | 13 +++++++-- profileR-0.3/profileR/R/profileplot.R | 25 ++++++++++++++++++ profileR-0.3/profileR/R/summary.critpat.R | 13 ++++++--- profileR-0.3/profileR/R/wprifm.R |only profileR-0.3/profileR/data/mod_data.rda |only profileR-0.3/profileR/data/nutrient.rda |only profileR-0.3/profileR/man/cpa.Rd |only profileR-0.3/profileR/man/mod_data.Rd |only profileR-0.3/profileR/man/mpa.Rd |only profileR-0.3/profileR/man/nutrient.Rd |only profileR-0.3/profileR/man/pams.Rd | 2 - profileR-0.3/profileR/man/paos.Rd |only profileR-0.3/profileR/man/pcv.Rd |only profileR-0.3/profileR/man/plot.critpat.Rd |only profileR-0.3/profileR/man/summary.critpat.Rd |only profileR-0.3/profileR/man/wprifm.Rd |only 29 files changed, 121 insertions(+), 37 deletions(-)
Title: Selection of Linear Estimators
Description: Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Author: Yannick Baraud, Christophe Giraud, Sylvie Huet
Maintainer: Annie Bouvier <Annie.Bouvier@jouy.inra.fr>
Diff between LINselect versions 0.0-1 dated 2013-12-20 and 0.0-2 dated 2015-08-26
LINselect-0.0-1/LINselect/tests/tuneLasso.Rout |only LINselect-0.0-2/LINselect/DESCRIPTION | 14 LINselect-0.0-2/LINselect/MD5 | 23 - LINselect-0.0-2/LINselect/NAMESPACE | 7 LINselect-0.0-2/LINselect/R/VARselect.R | 20 LINselect-0.0-2/LINselect/R/simulData.R | 2 LINselect-0.0-2/LINselect/R/tuneLasso.R | 2 LINselect-0.0-2/LINselect/inst/doc/Notice.pdf |binary LINselect-0.0-2/LINselect/man/VARselect.Rd | 2 LINselect-0.0-2/LINselect/tests/TestVARselect.R | 97 ++-- LINselect-0.0-2/LINselect/tests/TestVARselect.Rout.save | 346 ++-------------- LINselect-0.0-2/LINselect/tests/TesttuneLasso.R | 25 - LINselect-0.0-2/LINselect/tests/TesttuneLasso.Rout.save | 56 -- 13 files changed, 168 insertions(+), 426 deletions(-)
Title: Rigorous Data Reduction and Error Propagation of Ar40 / Ar39
Data
Description: Processes noble gas mass spectrometer data to determine the isotopic composition of argon (comprised of Ar36, Ar37, Ar38, Ar39 and Ar40) released from neutron-irradiated potassium-bearing minerals. Then uses these compositions to calculate precise and accurate geochronological ages for multiple samples as well as the covariances between them. Error propagation is done in matrix form, which jointly treats all samples and all isotopes simultaneously at every step of the data reduction process. Includes methods for regression of the time-resolved mass spectrometer signals to t=0 ('time zero') for both single- and multi-collector instruments, blank correction, mass fractionation correction, detector intercalibration, decay corrections, interference corrections, interpolation of the irradiation parameter between neutron fluence monitors, and (weighted mean) age calculation. All operations are performed on the logs of the ratios between the different argon isotopes so as to properly treat them as 'compositional data', sensu Aitchison [1986, The Statistics of Compositional Data, Chapman and Hall].
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between ArArRedux versions 0.1 dated 2015-04-29 and 0.2 dated 2015-08-26
DESCRIPTION | 15 MD5 | 40 R/ArArRedux.R | 3591 +++++++++++++++++++++++------------------------ R/documentation.R | 2 data/Melbourne.rda |binary man/Melbourne.Rd | 2 man/average.Rd | 2 man/averagebyday.Rd | 2 man/blankcorr.Rd | 2 man/calibration.Rd | 2 man/clcorrection.Rd | 2 man/decaycorrection.Rd | 2 man/fitlogratios.Rd | 2 man/get4039.Rd | 2 man/getJfactors.Rd | 2 man/getages.Rd | 2 man/getmasses.Rd | 2 man/massfractionation.Rd | 2 man/plotcorr.Rd | 6 man/read.Rd | 2 man/subset.Rd | 2 21 files changed, 1877 insertions(+), 1807 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.2 dated 2015-05-14 and 1.3 dated 2015-08-26
Anthropometry-1.2/Anthropometry/R/stepArchetypesMod.R |only Anthropometry-1.2/Anthropometry/man/stepArchetypesMod.Rd |only Anthropometry-1.3/Anthropometry/DESCRIPTION | 8 Anthropometry-1.3/Anthropometry/MD5 | 114 - Anthropometry-1.3/Anthropometry/NAMESPACE | 16 Anthropometry-1.3/Anthropometry/NEWS | 21 Anthropometry-1.3/Anthropometry/R/Anthropometry-internalArchetypoids.R | 4 Anthropometry-1.3/Anthropometry/R/HartiganShapes.R | 6 Anthropometry-1.3/Anthropometry/R/LloydShapes.R | 6 Anthropometry-1.3/Anthropometry/R/TDDclust.R | 12 Anthropometry-1.3/Anthropometry/R/anthrCases.R | 92 - Anthropometry-1.3/Anthropometry/R/archetypesBoundary.R | 2 Anthropometry-1.3/Anthropometry/R/hipamAnthropom.R | 2 Anthropometry-1.3/Anthropometry/R/stepArchetypesRawData.R |only Anthropometry-1.3/Anthropometry/R/stepArchetypoids.R | 4 Anthropometry-1.3/Anthropometry/R/trimmOutl.R | 85 - Anthropometry-1.3/Anthropometry/R/trimmedLloydShapes.R | 9 Anthropometry-1.3/Anthropometry/R/trimowa.R | 2 Anthropometry-1.3/Anthropometry/build/vignette.rds |binary Anthropometry-1.3/Anthropometry/inst/doc/Anthropometry.R | 132 - Anthropometry-1.3/Anthropometry/inst/doc/Anthropometry.Rnw | 777 +++++----- Anthropometry-1.3/Anthropometry/inst/doc/Anthropometry.pdf |binary Anthropometry-1.3/Anthropometry/man/Anthropometry-internalArchetypoids.Rd | 4 Anthropometry-1.3/Anthropometry/man/Anthropometry-package.Rd | 10 Anthropometry-1.3/Anthropometry/man/HartiganShapes.Rd | 6 Anthropometry-1.3/Anthropometry/man/LloydShapes.Rd | 5 Anthropometry-1.3/Anthropometry/man/TDDclust.Rd | 8 Anthropometry-1.3/Anthropometry/man/anthrCases.Rd | 57 Anthropometry-1.3/Anthropometry/man/archetypesBoundary.Rd | 4 Anthropometry-1.3/Anthropometry/man/archetypoids.Rd | 16 Anthropometry-1.3/Anthropometry/man/array3Dlandm.Rd | 2 Anthropometry-1.3/Anthropometry/man/bustSizesStandard.Rd | 2 Anthropometry-1.3/Anthropometry/man/cdfDissWomenPrototypes.Rd | 10 Anthropometry-1.3/Anthropometry/man/descrDissTrunks.Rd | 2 Anthropometry-1.3/Anthropometry/man/getDistMatrix.Rd | 5 Anthropometry-1.3/Anthropometry/man/hipamAnthropom.Rd | 20 Anthropometry-1.3/Anthropometry/man/matPercs.Rd | 4 Anthropometry-1.3/Anthropometry/man/percentilsArchetypoid.Rd | 2 Anthropometry-1.3/Anthropometry/man/plotPrototypes.Rd | 20 Anthropometry-1.3/Anthropometry/man/plotTrimmOutl.Rd | 12 Anthropometry-1.3/Anthropometry/man/projShapes.Rd | 2 Anthropometry-1.3/Anthropometry/man/screeArchetypal.Rd | 2 Anthropometry-1.3/Anthropometry/man/shapes3dShapes.Rd | 2 Anthropometry-1.3/Anthropometry/man/skeletonsArchetypal.Rd | 2 Anthropometry-1.3/Anthropometry/man/stepArchetypesRawData.Rd |only Anthropometry-1.3/Anthropometry/man/stepArchetypoids.Rd | 6 Anthropometry-1.3/Anthropometry/man/trimmOutl.Rd | 57 Anthropometry-1.3/Anthropometry/man/trimmedLloydShapes.Rd | 10 Anthropometry-1.3/Anthropometry/man/trimmedoid.Rd | 4 Anthropometry-1.3/Anthropometry/man/trimowa.Rd | 6 Anthropometry-1.3/Anthropometry/man/weightsMixtureUB.Rd | 2 Anthropometry-1.3/Anthropometry/vignettes/Anthropometry.Rnw | 777 +++++----- Anthropometry-1.3/Anthropometry/vignettes/decisionTree_1.png |binary Anthropometry-1.3/Anthropometry/vignettes/hipam1.pdf |binary Anthropometry-1.3/Anthropometry/vignettes/hipam2.pdf |binary Anthropometry-1.3/Anthropometry/vignettes/prendas_1.png |binary Anthropometry-1.3/Anthropometry/vignettes/prendas_2.png |binary Anthropometry-1.3/Anthropometry/vignettes/prendas_3.png |binary Anthropometry-1.3/Anthropometry/vignettes/trimowa1.pdf |binary Anthropometry-1.3/Anthropometry/vignettes/trimowa2.pdf |binary 60 files changed, 1200 insertions(+), 1151 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
Author: David I. Hastie <david.hastie@rsimony.com>, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson <sylvia.richardson@mrc-bsu.cam.ac.uk> with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.1.1 dated 2015-06-12 and 3.1.2 dated 2015-08-26
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 4 ++++ R/postProcess.R | 2 +- man/PReMiuM-package.Rd | 4 ++-- src/PReMiuM.cpp | 1 - src/include/PReMiuMProposals.h | 15 ++++++--------- 8 files changed, 31 insertions(+), 24 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.3.2 dated 2015-07-16 and 1.4.0 dated 2015-08-26
DESCRIPTION | 16 ++++++------- MD5 | 32 +++++++++++++------------- R/colourScale.R | 59 ++++++++++++++++++++++++++++++++++-------------- R/insetMap.R | 28 ++++++++++++++-------- R/map.new.R | 5 +--- R/openmap.R | 40 ++++++++++++++++++++++++++------ R/utils.R | 4 +-- build/vignette.rds |binary inst/doc/mapLayers.pdf |binary inst/doc/mapLayers.rnw | 3 -- inst/doc/mapmisc.pdf |binary inst/doc/mapmisc.rnw | 6 ++-- man/openmap.Rd | 6 ++++ tests/north.R | 6 ++-- tests/openmap.R | 2 - vignettes/mapLayers.rnw | 3 -- vignettes/mapmisc.rnw | 6 ++-- 17 files changed, 137 insertions(+), 79 deletions(-)
Title: A Simple Wrapper for the LASVM Solver
Description: This is a simple wrapper for the LASVM Solver (see http://leon.bottou.org/projects/lasvm). LASVM is basically an online variant of the SMO solver.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>
Diff between lasvmR versions 0.1 dated 2015-08-21 and 0.1.1 dated 2015-08-26
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ cleanup | 1 + inst/doc/lasvmR-vignette.html | 4 ++-- src/la_svm.cpp | 8 ++++---- src/la_test.cpp | 1 - src/lasvm_wrapper.cpp | 13 ++++++++----- 7 files changed, 27 insertions(+), 23 deletions(-)
Title: Gaussian Graphs Models Selection
Description: Graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier <Annie.Bouvier@jouy.inra.fr>
Diff between GGMselect versions 0.1-9 dated 2014-09-10 and 0.1-10 dated 2015-08-26
GGMselect-0.1-10/GGMselect/DESCRIPTION | 17 ++-- GGMselect-0.1-10/GGMselect/MD5 | 66 +++++++------------ GGMselect-0.1-10/GGMselect/NAMESPACE | 1 GGMselect-0.1-10/GGMselect/NEWS | 7 ++ GGMselect-0.1-10/GGMselect/R/EW.R | 7 -- GGMselect-0.1-10/GGMselect/R/GGMselect.R | 20 ++--- GGMselect-0.1-10/GGMselect/R/MyFamily.R | 4 - GGMselect-0.1-10/GGMselect/R/QE.R | 18 ++--- GGMselect-0.1-10/GGMselect/R/convertGraph.R | 2 GGMselect-0.1-10/GGMselect/R/penalty.R | 4 - GGMselect-0.1-10/GGMselect/build/vignette.rds |binary GGMselect-0.1-10/GGMselect/inst/doc/Notice.pdf |binary GGMselect-0.1-10/GGMselect/inst/extdata |only GGMselect-0.1-10/GGMselect/tests/bsch.R | 4 - GGMselect-0.1-10/GGMselect/tests/bsch.Rout.save | 16 +--- GGMselect-0.1-10/GGMselect/tests/penInf.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/sh9.2012.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/shPUR.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test1Fast.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test1QE.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test2Fast.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test2QE.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test3Fast.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test3QE.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test5Fast.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/test7Fast.Rout.save | 12 +-- GGMselect-0.1-10/GGMselect/tests/testMyFam.Rout.save | 12 +-- GGMselect-0.1-9/GGMselect/tests/G3simone.Rdata |only GGMselect-0.1-9/GGMselect/tests/GaussianData.txt |only GGMselect-0.1-9/GGMselect/tests/genes.lm.Rdata |only GGMselect-0.1-9/GGMselect/tests/raj.R |only GGMselect-0.1-9/GGMselect/tests/raj.Rout.save |only GGMselect-0.1-9/GGMselect/tests/test4Fast.R |only GGMselect-0.1-9/GGMselect/tests/test4Fast.Rout.save |only GGMselect-0.1-9/GGMselect/tests/test4QE.R |only GGMselect-0.1-9/GGMselect/tests/test4QE.Rout.save |only GGMselect-0.1-9/GGMselect/tests/test5QE.R.sv |only GGMselect-0.1-9/GGMselect/tests/test6Fast.R |only GGMselect-0.1-9/GGMselect/tests/test6Fast.Rout.save |only GGMselect-0.1-9/GGMselect/tests/test6QE.R.sv |only GGMselect-0.1-9/GGMselect/tests/test7QE.R.sv |only 41 files changed, 124 insertions(+), 186 deletions(-)
Title: Fast Estimation of a Covariance Matrix by Banding the Cholesky
Factor
Description: Fast and numerically stable estimation of a covariance matrix by banding the Cholesky factor using a modified Gram-Schmidt algorithm implemented in RcppArmadilo. See <http://stat.umn.edu/~molst029> for details on the algorithm.
Author: Aaron Molstad <molst029@umn.edu>
Maintainer: Aaron Molstad <molst029@umn.edu>
Diff between FastBandChol versions 0.1.0 dated 2015-08-24 and 0.1.1 dated 2015-08-26
FastBandChol-0.1.0/FastBandChol/src/Makevars.win |only FastBandChol-0.1.1/FastBandChol/DESCRIPTION | 6 +-- FastBandChol-0.1.1/FastBandChol/MD5 | 24 ++++++------ FastBandChol-0.1.1/FastBandChol/NAMESPACE | 8 ++-- FastBandChol-0.1.1/FastBandChol/R/Banded_Chol.R | 2 - FastBandChol-0.1.1/FastBandChol/R/Banded_Chol_CV.R | 6 +-- FastBandChol-0.1.1/FastBandChol/R/Banded_Sample.R | 2 - FastBandChol-0.1.1/FastBandChol/R/Banded_Sample_CV.R | 6 +-- FastBandChol-0.1.1/FastBandChol/man/Banded.Chol.CV.Rd | 23 ++++++----- FastBandChol-0.1.1/FastBandChol/man/Banded.Chol.Rd | 16 ++++---- FastBandChol-0.1.1/FastBandChol/man/Banded.Sample.CV.Rd | 22 ++++++----- FastBandChol-0.1.1/FastBandChol/man/Banded.Sample.Rd | 16 ++++---- FastBandChol-0.1.1/FastBandChol/man/FastBandChol-package.Rd | 4 +- FastBandChol-0.1.1/FastBandChol/src/Makevars |only 14 files changed, 69 insertions(+), 66 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 0.94-1 dated 2015-06-03 and 0.94-3 dated 2015-08-26
DESCRIPTION | 18 +- MD5 | 39 +++-- NAMESPACE | 3 R/RSAGA-core.R | 15 +- R/RSAGA-modules.R | 323 +++++++++++++++++++++++++------------------- R/RSAGA-package.R | 4 R/gridtools.R | 38 ++--- R/landslides.R |only build |only data |only inst/doc |only man/RSAGA-package.Rd | 4 man/focal.function.Rd | 2 man/grid.predict.Rd | 2 man/landslides.Rd |only man/multi.focal.function.Rd | 4 man/pick.from.points.Rd | 2 man/rsaga.grid.calculus.Rd | 36 ++-- man/rsaga.import.gdal.Rd | 211 ++++++++++++++++------------ man/rsaga.wetness.index.Rd | 2 vignettes |only 21 files changed, 406 insertions(+), 297 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre],
David Bard [ctb],
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb],
Benjamin Nutter [ctb],
Andrew Peters [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 0.9.0 dated 2015-08-15 and 0.9.3 dated 2015-08-26
REDCapR-0.9.0/REDCapR/man/REDCapR.Rd |only REDCapR-0.9.3/REDCapR/DESCRIPTION | 8 REDCapR-0.9.3/REDCapR/MD5 | 156 REDCapR-0.9.3/REDCapR/NAMESPACE | 38 REDCapR-0.9.3/REDCapR/NEWS | 181 REDCapR-0.9.3/REDCapR/R/REDCapR-package.R | 44 REDCapR-0.9.3/REDCapR/R/create_batch_glossary.R | 132 REDCapR-0.9.3/REDCapR/R/metadata_utilities.R | 188 REDCapR-0.9.3/REDCapR/R/project_simple.R | 208 REDCapR-0.9.3/REDCapR/R/redcap_column_sanitize.R | 96 REDCapR-0.9.3/REDCapR/R/redcap_download_file_oneshot.R | 330 REDCapR-0.9.3/REDCapR/R/redcap_metadata_read.R | 304 REDCapR-0.9.3/REDCapR/R/redcap_project.R | 246 REDCapR-0.9.3/REDCapR/R/redcap_read.R | 441 REDCapR-0.9.3/REDCapR/R/redcap_read_oneshot.R | 438 REDCapR-0.9.3/REDCapR/R/redcap_upload_file_oneshot.R | 290 REDCapR-0.9.3/REDCapR/R/redcap_write.R | 322 REDCapR-0.9.3/REDCapR/R/redcap_write_oneshot.R | 378 REDCapR-0.9.3/REDCapR/R/retrieve_token.R | 222 REDCapR-0.9.3/REDCapR/R/utilities.R | 92 REDCapR-0.9.3/REDCapR/R/validate_for_write.R | 162 REDCapR-0.9.3/REDCapR/README.md | 200 REDCapR-0.9.3/REDCapR/build/vignette.rds |binary REDCapR-0.9.3/REDCapR/inst/doc/BasicREDCapROperations.R | 208 REDCapR-0.9.3/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 316 REDCapR-0.9.3/REDCapR/inst/doc/BasicREDCapROperations.html | 726 REDCapR-0.9.3/REDCapR/inst/doc/SecurityDatabase.Rmd | 354 REDCapR-0.9.3/REDCapR/inst/doc/SecurityDatabase.html | 472 REDCapR-0.9.3/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 762 REDCapR-0.9.3/REDCapR/inst/doc/TroubleshootingApiCalls.html | 1128 - REDCapR-0.9.3/REDCapR/inst/misc/vignette.css | 72 REDCapR-0.9.3/REDCapR/inst/ssl_certs/Readme.md | 6 REDCapR-0.9.3/REDCapR/inst/ssl_certs/mozilla_ca_root.crt | 7976 +++++----- REDCapR-0.9.3/REDCapR/inst/test_data/project_color_boxes/Readme.md | 106 REDCapR-0.9.3/REDCapR/inst/test_data/project_color_boxes/color_boxes_data.csv | 8 REDCapR-0.9.3/REDCapR/inst/test_data/project_color_boxes/color_boxes_data_dictionary.csv | 6 REDCapR-0.9.3/REDCapR/inst/test_data/project_longitudinal/longitudinal_data.csv | 38 REDCapR-0.9.3/REDCapR/inst/test_data/project_longitudinal/longitudinal_data_dictionary.csv | 192 REDCapR-0.9.3/REDCapR/inst/test_data/project_russian/russian_data.csv | 8 REDCapR-0.9.3/REDCapR/inst/test_data/project_simple/simple_data.csv | 32 REDCapR-0.9.3/REDCapR/inst/test_data/project_simple/simple_data_dictionary.csv | 34 REDCapR-0.9.3/REDCapR/inst/test_data/project_simple/simple_metadata.csv | 34 REDCapR-0.9.3/REDCapR/man/REDCapR-package.Rd |only REDCapR-0.9.3/REDCapR/man/create_batch_glossary.Rd | 106 REDCapR-0.9.3/REDCapR/man/metadata_utilities.Rd | 148 REDCapR-0.9.3/REDCapR/man/redcap_column_sanitize.Rd | 94 REDCapR-0.9.3/REDCapR/man/redcap_download_file_oneshot.Rd | 182 REDCapR-0.9.3/REDCapR/man/redcap_metadata_read.Rd | 136 REDCapR-0.9.3/REDCapR/man/redcap_project.Rd | 114 REDCapR-0.9.3/REDCapR/man/redcap_read.Rd | 201 REDCapR-0.9.3/REDCapR/man/redcap_read_oneshot.Rd | 258 REDCapR-0.9.3/REDCapR/man/redcap_upload_file_oneshot.Rd | 176 REDCapR-0.9.3/REDCapR/man/redcap_write.Rd | 210 REDCapR-0.9.3/REDCapR/man/redcap_write_oneshot.Rd | 174 REDCapR-0.9.3/REDCapR/man/replace_nas_with_explicit.Rd | 74 REDCapR-0.9.3/REDCapR/man/retrieve_token.Rd | 156 REDCapR-0.9.3/REDCapR/man/validate_for_write.Rd | 96 REDCapR-0.9.3/REDCapR/tests/manual/README.md | 8 REDCapR-0.9.3/REDCapR/tests/manual/test-could-not-connect-rate.R | 104 REDCapR-0.9.3/REDCapR/tests/manual/test-stress_test_serial.R | 226 REDCapR-0.9.3/REDCapR/tests/test-all.R | 10 REDCapR-0.9.3/REDCapR/tests/testthat/test-column-sanitize.R | 80 REDCapR-0.9.3/REDCapR/tests/testthat/test-create_batch_glossary.R | 162 REDCapR-0.9.3/REDCapR/tests/testthat/test-file_oneshot.R | 436 REDCapR-0.9.3/REDCapR/tests/testthat/test-metadata_read.R | 550 REDCapR-0.9.3/REDCapR/tests/testthat/test-metadata_utilities.R | 68 REDCapR-0.9.3/REDCapR/tests/testthat/test-project.R | 146 REDCapR-0.9.3/REDCapR/tests/testthat/test-read_batch_longitudinal.R | 176 REDCapR-0.9.3/REDCapR/tests/testthat/test-read_batch_simple.R | 786 REDCapR-0.9.3/REDCapR/tests/testthat/test-read_errors.R | 164 REDCapR-0.9.3/REDCapR/tests/testthat/test-read_oneshot.R | 524 REDCapR-0.9.3/REDCapR/tests/testthat/test-read_russian.R | 92 REDCapR-0.9.3/REDCapR/tests/testthat/test-retrieve_token.R | 236 REDCapR-0.9.3/REDCapR/tests/testthat/test-utilities.R | 148 REDCapR-0.9.3/REDCapR/tests/testthat/test-validate_for_write.R | 82 REDCapR-0.9.3/REDCapR/tests/testthat/test-write_batch.R | 364 REDCapR-0.9.3/REDCapR/tests/testthat/test-write_oneshot.R | 364 REDCapR-0.9.3/REDCapR/vignettes/BasicREDCapROperations.Rmd | 316 REDCapR-0.9.3/REDCapR/vignettes/SecurityDatabase.Rmd | 354 REDCapR-0.9.3/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 762 80 files changed, 12652 insertions(+), 12585 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo, ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.29 dated 2015-07-08 and 1.30 dated 2015-08-26
DESCRIPTION | 12 MD5 | 22 NEWS | 8 R/EZR.R | 71 + inst/CHANGES | 8 inst/doc/EZR.htm | 4 inst/doc/EZR.pdf |binary inst/etc/menus.txt | 1195 +++++++++++++--------------- inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary man/EZR.Rd | 4 man/EZR.dialogs.Rd | 1 po/R-RcmdrPlugin.EZR.po | 16 12 files changed, 707 insertions(+), 634 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.2-08 dated 2015-07-10 and 1.2-09 dated 2015-08-26
DESCRIPTION | 8 ++--- MD5 | 27 ++++++++++-------- NAMESPACE | 5 ++- NEWS | 11 +++++++ R/Fieller.R | 4 ++ R/OwensQ.R | 4 +- R/OwensQOwen.R | 46 +++++++++++++++++-------------- R/SampleSize.R | 6 ++-- R/power.R | 74 +++++++++++++++++++++++++++++++++++++++++--------- R/power_PASS.R |only R/power_TOST_sim.R |only R/samplesize_scABEL.R | 20 ++++++------- man/power.TOST.Rd | 27 +++++++++++------- man/power.TOST.sim.Rd |only man/power.dp.Rd | 3 +- man/sampleN.TOST.Rd | 14 ++++++--- 16 files changed, 166 insertions(+), 83 deletions(-)
Title: Mixed-Effects Ordinal Regression Analysis
Description: Provides the function 'mixord' for fitting a mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and variance-covariance matrix, and estimating contrasts for the fitted models.
Author: Donald Hedeker <DHedeker@health.bsd.uchicago.edu>, Kellie J. Archer, Rachel Nordgren, Robert D. Gibbons
Maintainer: Kellie J. Archer <kjarcher@vcu.edu>
Diff between mixor versions 1.0.2 dated 2015-01-13 and 1.0.3 dated 2015-08-26
DESCRIPTION | 10 - MD5 | 77 +++++++------ NAMESPACE | 17 ++- R/AIC.mixor.R |only R/BIC.mixor.R |only R/Contrasts.R | 9 + R/deviance.mixor.R |only R/logLik.mixor.R |only R/mixor.R |only R/mixord.R | 198 ---------------------------------- R/predict.mixor.R |only R/summary.mixor.R | 4 R/vcov.mixor.R | 3 build/vignette.rds |binary data/SmokeOnset.rda |binary data/SmokingPrevention.rda |binary data/concen.rda |binary data/irt.data.rda |binary data/norcag.rda |binary data/schizophrenia.rda |binary inst/doc/mixor.R | 153 ++++++++++++++++----------- inst/doc/mixor.Rnw | 255 +++++++++++++++++++++++++++------------------ inst/doc/mixor.pdf |binary man/AIC.mixor.Rd |only man/BIC.mixor.Rd |only man/Contrasts.Rd | 37 +++--- man/Mixor-deprecated.Rd |only man/Mixor-package.Rd | 22 +-- man/SmokeOnset.Rd | 36 ++---- man/SmokingPrevention.Rd | 7 - man/coef.mixor.Rd | 10 - man/concen.Rd | 7 - man/deviance.mixor.Rd |only man/irt.data.Rd | 7 - man/logLik.mixor.Rd |only man/mixor.Rd |only man/mixord.Rd | 131 ----------------------- man/norcag.Rd | 9 - man/plot.mixor.Rd | 9 - man/predict.mixor.Rd |only man/print.mixor.Rd | 11 - man/schizophrenia.Rd | 9 - man/summary.mixor.Rd | 15 +- man/vcov.mixor.Rd | 14 -- vignettes/mixor.Rnw | 255 +++++++++++++++++++++++++++------------------ vignettes/mixor.bib | 27 ++-- 46 files changed, 586 insertions(+), 746 deletions(-)
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.10 dated 2015-06-16 and 0.0.11 dated 2015-08-26
MCDA-0.0.10/MCDA/R/MRSortInference.R |only MCDA-0.0.10/MCDA/inst/extdata/MRSortIdentifyIncompatibleAssignmentsModel.gmpl |only MCDA-0.0.10/MCDA/man/MRSortInference.Rd |only MCDA-0.0.10/MCDA/tests/MRSortInference.R |only MCDA-0.0.11/MCDA/DESCRIPTION | 10 MCDA-0.0.11/MCDA/MD5 | 114 ++ MCDA-0.0.11/MCDA/NAMESPACE | 10 MCDA-0.0.11/MCDA/R/LPDMRSort.R |only MCDA-0.0.11/MCDA/R/LPDMRSortIdentifyIncompatibleAssignments.R |only MCDA-0.0.11/MCDA/R/LPDMRSortInferenceExact.R |only MCDA-0.0.11/MCDA/R/MRSort.R | 10 MCDA-0.0.11/MCDA/R/MRSortIdentifyIncompatibleAssignments.R | 392 +++++----- MCDA-0.0.11/MCDA/R/MRSortInferenceApprox.R |only MCDA-0.0.11/MCDA/R/MRSortInferenceExact.R |only MCDA-0.0.11/MCDA/R/operators.R |only MCDA-0.0.11/MCDA/README | 7 MCDA-0.0.11/MCDA/inst/extdata/MRSortDIdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDIdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDInferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1IdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1IdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV1InferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2IdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2IdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV2InferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3IdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3IdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV3InferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4IdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4IdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV4InferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5IdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5IdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortDV5InferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortIdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortIdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortInferenceLW.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortInferenceModel.gmpl | 22 MCDA-0.0.11/MCDA/inst/extdata/MRSortInferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortInferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortInferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVIdentifyInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVIdentifyMinimalInvalidAssignmentsSet.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModel.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadWeights.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadWeightsLPD.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadWeightsProfiles.gmpl |only MCDA-0.0.11/MCDA/inst/extdata/MRSortVInferenceModelSpreadWeightsProfilesLPD.gmpl |only MCDA-0.0.11/MCDA/man/LPDMRSort.Rd |only MCDA-0.0.11/MCDA/man/LPDMRSortIdentifyIncompatibleAssignments.Rd |only MCDA-0.0.11/MCDA/man/LPDMRSortInferenceExact.Rd |only MCDA-0.0.11/MCDA/man/MRSort.Rd | 34 MCDA-0.0.11/MCDA/man/MRSortIdentifyIncompatibleAssignments.Rd | 156 +-- MCDA-0.0.11/MCDA/man/MRSortInferenceApprox.Rd |only MCDA-0.0.11/MCDA/man/MRSortInferenceExact.Rd |only MCDA-0.0.11/MCDA/tests/LPDMRSort.R |only MCDA-0.0.11/MCDA/tests/LPDMRSortIdentifyIncompatibleAssignments.R |only MCDA-0.0.11/MCDA/tests/LPDMRSortInferenceExact.R |only MCDA-0.0.11/MCDA/tests/MRSortIdentifyIncompatibleAssignments.R | 74 - MCDA-0.0.11/MCDA/tests/MRSortInferenceApprox.R |only MCDA-0.0.11/MCDA/tests/MRSortInferenceExact.R |only 106 files changed, 484 insertions(+), 345 deletions(-)
Title: Functions for Plotting HPO Terms
Description: Collection of functions for manipulating sets of HPO terms and plotting them with a various options.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between hpoPlot versions 2.0 dated 2015-01-12 and 2.2 dated 2015-08-26
DESCRIPTION | 12 MD5 | 122 +++---- NAMESPACE | 7 R/graphs.R | 37 +- R/sets.R | 15 build/vignette.rds |binary data/hpo.terms.RData |binary data/mpo.terms.RData |binary data/mpo.to.hpo.RData |binary inst/doc/hpoPlot-guide.Rmd | 2 inst/doc/hpoPlot-guide.html | 360 ++++++++++++++++------- man/apply.term.filters.Rd | 2 man/calibrate.sizes.Rd | 2 man/clean.terms.Rd | 2 man/exclude.branch.Rd | 2 man/get.ancestors.Rd | 2 man/get.case.based.colours.Rd | 2 man/get.case.based.labels.Rd | 2 man/get.case.term.matrix.Rd | 2 man/get.code.node.labels.Rd | 2 man/get.descendants.Rd | 2 man/get.frequency.based.colours.Rd | 2 man/get.frequency.based.labels.Rd | 2 man/get.frequency.based.sizes.Rd | 2 man/get.full.labels.Rd | 2 man/get.grey.borders.Rd | 2 man/get.hpo.graph.Rd | 2 man/get.hpo.terms.Rd | 2 man/get.informative.node.labels.Rd | 2 man/get.mpo.to.hpo.Rd | 2 man/get.no.borders.Rd | 2 man/get.node.friendly.long.names.Rd | 2 man/get.ontology.Rd | 2 man/get.pop.frequency.based.colours.Rd | 2 man/get.shortened.names.Rd | 2 man/get.significance.based.sizes.Rd | 2 man/get.simple.node.labels.Rd | 2 man/get.standard.sizes.Rd | 2 man/get.term.adjacency.matrix.Rd | 2 man/get.term.descendancy.matrix.Rd | 2 man/get.term.frequencies.Rd | 2 man/get.term.info.content.Rd | 2 man/get.term.pseudo.adjacency.matrix.Rd | 2 man/get.white.nodes.Rd | 2 man/hpo.plot.Rd | 22 - man/hpo.terms.Rd | 2 man/intersection.with.branches.Rd | 2 man/mpo.terms.Rd | 2 man/mpo.to.hpo.Rd | 2 man/n.most.frequent.terms.Rd | 2 man/p.values.for.occurrence.of.term.in.group.Rd | 2 man/prune.branch.Rd | 2 man/remove.links.Rd | 2 man/remove.non.pa.terms.Rd | 2 man/remove.terms.with.less.than.n.occurrences.Rd | 2 man/remove.uninformative.for.plot.Rd | 2 man/remove.uninformative.terms.Rd | 2 man/setDimNames.Rd | 2 man/simpleCap.Rd | 2 man/swap.out.alt.ids.Rd | 2 man/term.set.list.from.character.Rd | 2 vignettes/hpoPlot-guide.Rmd | 2 62 files changed, 433 insertions(+), 244 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.3.4 dated 2015-04-30 and 1.3.5 dated 2015-08-26
DESCRIPTION | 8 MD5 | 14 NAMESPACE | 3 R/glmmLasso.r | 5071 +-------------------------------------------- R/glmmLasso_RE.R |only R/glmmLasso_noRE.R |only R/glmm_final.smooth_noRE.R |only R/glmm_final_noRE.R |only R/logLik.glmmLasso.r | 16 man/glmmLasso.rd | 20 10 files changed, 150 insertions(+), 4982 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.2.7 dated 2015-07-31 and 0.2.8 dated 2015-08-26
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 8 ++++++++ R/kde.R | 2 ++ R/telemetry.R | 11 +++++++++-- R/variogram.R | 20 +++++++++++--------- TODO | 2 ++ data/buffalo.rda |binary inst/doc/akde.html | 4 ++-- inst/doc/variogram.html | 6 +++--- man/as.telemetry.Rd | 10 ++++++++-- man/ctmm-package.Rd | 4 ++-- man/ctmm.fit.Rd | 2 +- 13 files changed, 64 insertions(+), 37 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) prior distributions. A number of different random effects structures are available, and full details are given in the vignette accompanying this package and the references below. The creation of this package was supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 2.0 dated 2015-07-06 and 2.1 dated 2015-08-26
DESCRIPTION | 10 MD5 | 40 NAMESPACE | 3 R/RcppExports.R | 36 R/ST.CARadaptive.R | 52 - R/ST.CARlocalised.R | 2 R/ST.CARsepspatial.R |only R/binomial.CARadaptive.R | 1081 +++++++++++++-------------- R/binomial.CARsepspatial.R |only R/gaussian.CARadaptive.R | 1062 +++++++++++++------------- R/poisson.CARadaptive.R | 1006 ++++++++++++------------- R/poisson.CARsepspatial.R |only build/vignette.rds |binary inst/doc/CARBayesSTvignette.R | 2 inst/doc/CARBayesSTvignette.Rnw | 35 inst/doc/CARBayesSTvignette.pdf |binary man/CARBayesST-package.Rd | 17 man/ST.CARadaptive.Rd | 350 ++++---- man/ST.CARsepspatial.Rd |only src/CARBayesST.cpp | 433 ++++++++++ src/RcppExports.cpp | 144 +++ vignettes/CARBayesSTvignette-concordance.tex |only vignettes/CARBayesSTvignette.Rnw | 35 vignettes/CARBayesSTvignette.tex |only 24 files changed, 2492 insertions(+), 1816 deletions(-)
Title: Tools for Handling and Scrapping Instant Weather Forecast Feeds
Description: Handle instant weather forecasts and geographical information. It combines multiple sources of information to obtain instant weather forecasts.
Author: Stan Yip [aut, cre]
Maintainer: Stan Yip <stanyip101@gmail.com>
Diff between weatherr versions 0.1 dated 2015-07-16 and 0.1.1 dated 2015-08-26
weatherr-0.1.1/weatherr/DESCRIPTION | 8 ++++---- weatherr-0.1.1/weatherr/MD5 | 11 ++++++----- weatherr-0.1.1/weatherr/R/ggele.R |only weatherr-0.1.1/weatherr/R/locationforecast.R | 7 +++---- weatherr-0.1.1/weatherr/man/ggele.Rd |only weatherr-0.1.1/weatherr/man/locationforecast.Rd | 4 ++-- weatherr-0.1.1/weatherr/man/weatherr-package.Rd | 4 ++-- weatherr-0.1/weatherr/INDEX |only 8 files changed, 17 insertions(+), 17 deletions(-)
Title: Robust Regression Functions
Description: Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.
Author: Ian M. Johnson <ian@alpha-analysis.com>
Maintainer: Ian M. Johnson <ian@alpha-analysis.com>
Diff between robustreg versions 0.1-8 dated 2015-07-30 and 0.1-9 dated 2015-08-26
robustreg-0.1-8/robustreg/man/fit.Rd |only robustreg-0.1-9/robustreg/DESCRIPTION | 8 +-- robustreg-0.1-9/robustreg/MD5 | 28 +++++++---- robustreg-0.1-9/robustreg/NAMESPACE | 4 + robustreg-0.1-9/robustreg/R/RcppExports.R | 16 ++++++ robustreg-0.1-9/robustreg/R/robustRegBS.R | 17 +----- robustreg-0.1-9/robustreg/R/robustRegH.R | 26 +++++----- robustreg-0.1-9/robustreg/man/fit_rcpp.Rd |only robustreg-0.1-9/robustreg/man/mad_rcpp.Rd |only robustreg-0.1-9/robustreg/man/median_rcpp.Rd |only robustreg-0.1-9/robustreg/man/psiBS_rcpp.Rd |only robustreg-0.1-9/robustreg/man/psiHuber_rcpp.Rd |only robustreg-0.1-9/robustreg/man/robustRegBS.Rd | 4 - robustreg-0.1-9/robustreg/man/robustRegH.Rd | 10 +-- robustreg-0.1-9/robustreg/src/Makevars.win |only robustreg-0.1-9/robustreg/src/RcppExports.cpp | 63 +++++++++++++++++++++++++ robustreg-0.1-9/robustreg/src/fit.cpp | 2 robustreg-0.1-9/robustreg/src/median.cpp |only robustreg-0.1-9/robustreg/src/psiBS.cpp |only robustreg-0.1-9/robustreg/src/psiHuber.cpp |only 20 files changed, 131 insertions(+), 47 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-25 dated 2015-06-19 and 1.0-26 dated 2015-08-26
DESCRIPTION | 12 +++--- MD5 | 61 ++++++++++++++++---------------- NAMESPACE | 6 +++ R/krige0.R | 4 +- R/variogramST.R | 2 - build/vignette.rds |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.Rnw | 35 +++++++++--------- inst/doc/spatio-temporal-kriging.bib |only inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.R | 64 +++++++++++++++++----------------- inst/doc/st.Rnw | 7 +-- inst/doc/st.pdf |binary tests/unproj.Rout.save | 15 +++++-- tests/windst.Rout.save | 10 ++--- vignettes/.install_extras |only vignettes/spatio-temporal-kriging.Rnw | 35 +++++++++--------- vignettes/st.Rnw | 7 +-- 33 files changed, 134 insertions(+), 124 deletions(-)
Title: Gamma Lasso Regression
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization, http://arxiv.org/abs/1308.5623.
Author: Matt Taddy <taddy@chicagobooth.edu>
Maintainer: Matt Taddy <taddy@chicagobooth.edu>
Diff between gamlr versions 1.13-2 dated 2015-08-18 and 1.13-3 dated 2015-08-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/gamlr.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.4 dated 2015-07-25 and 0.4.0 dated 2015-08-26
DESCRIPTION | 8 MD5 | 35 +-- NAMESPACE | 3 R/mlp_net.R | 252 +++++++++++++++++++++---- R/mlp_prune.R | 7 man/mlp_net-MSE-gradients.Rd | 13 + man/mlp_net-combining-two-networks.Rd |only src/Makevars | 4 src/Makevars.win | 4 src/fcnn/level1.h | 123 ++++++++++-- src/fcnn/level1_impl.h | 215 ++++++++++++++++----- src/fcnn/level2.cpp | 88 ++++++-- src/fcnn/level2.h | 11 + src/fcnn/level3.cpp | 334 +++++++++++++++++++++++++++++++--- src/fcnn/level3.h | 18 + src/fcnn/report.cpp | 4 src/fcnn/struct.cpp | 251 +++++++++++++++++++++++++ src/fcnn/struct.h | 28 ++ src/interface.cpp | 250 ++++++++++++++++++++++--- 19 files changed, 1427 insertions(+), 221 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 1.35 dated 2015-05-20 and 2.0 dated 2015-08-26
DLMtool-1.35/DLMtool/R/DLM_quota.R |only DLMtool-1.35/DLMtool/R/DLM_size.R |only DLMtool-1.35/DLMtool/R/DLM_space.R |only DLMtool-1.35/DLMtool/man/DLM-class.Rd |only DLMtool-1.35/DLMtool/man/area1MPA.Rd |only DLMtool-1.35/DLMtool/man/getQuota.Rd |only DLMtool-1.35/DLMtool/man/matsizlim.Rd |only DLMtool-2.0/DLMtool/DESCRIPTION | 10 DLMtool-2.0/DLMtool/MD5 | 192 +-- DLMtool-2.0/DLMtool/NAMESPACE | 24 DLMtool-2.0/DLMtool/R/DLM_input.R |only DLMtool-2.0/DLMtool/R/DLM_output.R |only DLMtool-2.0/DLMtool/R/MSE_source.R | 984 ++++++++++-------- DLMtool-2.0/DLMtool/R/Source.r | 364 +++--- DLMtool-2.0/DLMtool/build/vignette.rds |binary DLMtool-2.0/DLMtool/data/DLMdat.RData |binary DLMtool-2.0/DLMtool/inst/doc/DLMtool.R | 153 +- DLMtool-2.0/DLMtool/inst/doc/DLMtool.Rnw | 368 +++--- DLMtool-2.0/DLMtool/inst/doc/DLMtool.pdf |binary DLMtool-2.0/DLMtool/man/BK.Rd | 16 DLMtool-2.0/DLMtool/man/BK_CC.Rd | 8 DLMtool-2.0/DLMtool/man/BK_ML.Rd | 8 DLMtool-2.0/DLMtool/man/CC1.Rd | 11 DLMtool-2.0/DLMtool/man/CC4.Rd | 12 DLMtool-2.0/DLMtool/man/Can.Rd | 8 DLMtool-2.0/DLMtool/man/Cant.Rd | 6 DLMtool-2.0/DLMtool/man/CompSRA.Rd | 12 DLMtool-2.0/DLMtool/man/CompSRA4010.Rd |only DLMtool-2.0/DLMtool/man/DBSRA.Rd | 16 DLMtool-2.0/DLMtool/man/DBSRA4010.Rd | 8 DLMtool-2.0/DLMtool/man/DBSRA_40.Rd | 8 DLMtool-2.0/DLMtool/man/DBSRA_ML.Rd | 4 DLMtool-2.0/DLMtool/man/DCAC.Rd | 8 DLMtool-2.0/DLMtool/man/DCAC4010.Rd | 8 DLMtool-2.0/DLMtool/man/DCAC_40.Rd | 8 DLMtool-2.0/DLMtool/man/DCAC_ML.Rd | 6 DLMtool-2.0/DLMtool/man/DD.Rd | 12 DLMtool-2.0/DLMtool/man/DD4010.Rd | 12 DLMtool-2.0/DLMtool/man/DLMDataDir.Rd | 4 DLMtool-2.0/DLMtool/man/DLM_data-class.Rd |only DLMtool-2.0/DLMtool/man/DLMdat.Rd | 2 DLMtool-2.0/DLMtool/man/DLMtool-package.Rd | 10 DLMtool-2.0/DLMtool/man/DepF.Rd | 10 DLMtool-2.0/DLMtool/man/DynF.Rd | 14 DLMtool-2.0/DLMtool/man/FMSYref.Rd | 8 DLMtool-2.0/DLMtool/man/FMSYref50.Rd | 8 DLMtool-2.0/DLMtool/man/FMSYref75.Rd | 6 DLMtool-2.0/DLMtool/man/Fadapt.Rd | 4 DLMtool-2.0/DLMtool/man/Fdem.Rd | 6 DLMtool-2.0/DLMtool/man/Fdem_CC.Rd | 8 DLMtool-2.0/DLMtool/man/Fdem_ML.Rd | 6 DLMtool-2.0/DLMtool/man/Fleet-class.Rd | 18 DLMtool-2.0/DLMtool/man/Fratio.Rd | 10 DLMtool-2.0/DLMtool/man/Fratio4010.Rd | 6 DLMtool-2.0/DLMtool/man/Fratio_CC.Rd | 6 DLMtool-2.0/DLMtool/man/Fratio_ML.Rd | 8 DLMtool-2.0/DLMtool/man/GB_CC.Rd | 10 DLMtool-2.0/DLMtool/man/GB_slope.Rd | 8 DLMtool-2.0/DLMtool/man/GB_target.Rd | 10 DLMtool-2.0/DLMtool/man/Gcontrol.Rd | 10 DLMtool-2.0/DLMtool/man/Islope1.Rd | 6 DLMtool-2.0/DLMtool/man/Islope4.Rd | 4 DLMtool-2.0/DLMtool/man/Itarget1.Rd | 8 DLMtool-2.0/DLMtool/man/Itarget4.Rd | 8 DLMtool-2.0/DLMtool/man/Kplot.Rd | 8 DLMtool-2.0/DLMtool/man/LstepCC1.Rd | 6 DLMtool-2.0/DLMtool/man/LstepCC4.Rd | 6 DLMtool-2.0/DLMtool/man/Ltarget1.Rd | 6 DLMtool-2.0/DLMtool/man/Ltarget4.Rd | 6 DLMtool-2.0/DLMtool/man/MCD.Rd |only DLMtool-2.0/DLMtool/man/MCD4010.Rd |only DLMtool-2.0/DLMtool/man/MRnoreal.Rd |only DLMtool-2.0/DLMtool/man/MRreal.Rd |only DLMtool-2.0/DLMtool/man/MSE-class.Rd | 96 + DLMtool-2.0/DLMtool/man/Needed.Rd | 8 DLMtool-2.0/DLMtool/man/OM-class.Rd | 10 DLMtool-2.0/DLMtool/man/Observation-class.Rd | 70 - DLMtool-2.0/DLMtool/man/Pplot.Rd | 5 DLMtool-2.0/DLMtool/man/Rcontrol.Rd | 8 DLMtool-2.0/DLMtool/man/Rcontrol2.Rd | 12 DLMtool-2.0/DLMtool/man/SBT1.Rd | 10 DLMtool-2.0/DLMtool/man/SBT2.Rd | 10 DLMtool-2.0/DLMtool/man/SPMSY.Rd | 12 DLMtool-2.0/DLMtool/man/SPSRA.Rd | 6 DLMtool-2.0/DLMtool/man/SPSRA_ML.Rd | 6 DLMtool-2.0/DLMtool/man/SPmod.Rd | 12 DLMtool-2.0/DLMtool/man/SPslope.Rd | 14 DLMtool-2.0/DLMtool/man/Sam.Rd | 6 DLMtool-2.0/DLMtool/man/Sense.Rd | 18 DLMtool-2.0/DLMtool/man/Stock-class.Rd | 54 DLMtool-2.0/DLMtool/man/TAC.Rd |only DLMtool-2.0/DLMtool/man/Tplot.Rd | 5 DLMtool-2.0/DLMtool/man/VOI.Rd |only DLMtool-2.0/DLMtool/man/YPR.Rd | 10 DLMtool-2.0/DLMtool/man/YPR_CC.Rd | 6 DLMtool-2.0/DLMtool/man/YPR_ML.Rd | 8 DLMtool-2.0/DLMtool/man/comp.Rd | 4 DLMtool-2.0/DLMtool/man/curE.Rd |only DLMtool-2.0/DLMtool/man/curE75.Rd |only DLMtool-2.0/DLMtool/man/initialize-methods.Rd | 2 DLMtool-2.0/DLMtool/man/matagelim.Rd |only DLMtool-2.0/DLMtool/man/plot-methods.Rd | 4 DLMtool-2.0/DLMtool/man/replic8.Rd | 4 DLMtool-2.0/DLMtool/man/runMSE.Rd | 6 DLMtool-2.0/DLMtool/man/summary-methods.Rd | 2 DLMtool-2.0/DLMtool/vignettes/DLMtool-concordance.tex |only DLMtool-2.0/DLMtool/vignettes/DLMtool.Rnw | 368 +++--- DLMtool-2.0/DLMtool/vignettes/framed.sty |only 108 files changed, 1814 insertions(+), 1458 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.36-6 dated 2015-03-05 and 1.37-11 dated 2015-08-25
DESCRIPTION | 12 +++--- MD5 | 68 +++++++++++++++++++------------------- NAMESPACE | 82 +++++++++++++++++++++++++++++++++++++++++++++- R/add_threshold.R | 2 - R/plot.R | 89 +++++++++++++++----------------------------------- R/read.cross.csv.R | 11 +++--- R/read.cross.csvs.R | 11 +++--- R/read.cross.mm.R | 11 ++++-- R/read.cross.tidy.R | 9 +++-- R/refineqtl.R | 8 ++-- R/scantwo.R | 15 ++++++-- R/scantwopermhk.R | 9 +++++ R/stepwiseqtl.R | 11 +++++- R/summary.cross.R | 5 ++ R/util.R | 11 +++++- R/write.cross.mq.R | 7 ++- build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/CITATION | 14 +++---- inst/INSTALL_ME.txt | 16 ++++---- inst/README.md | 2 - inst/STATUS.txt | 35 +++++++++++++++++++ inst/doc/rqtltour.pdf |binary man/sim.cross.Rd | 24 ++++++------- 35 files changed, 294 insertions(+), 158 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.2.3 dated 2015-08-19 and 1.2.4 dated 2015-08-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/cgdsr-getCaseLists.Rd | 2 +- man/cgdsr-getGeneticProfiles.Rd | 2 +- man/cgdsr-getProfileData.Rd | 6 +++--- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-3 dated 2015-07-16 and 1.2-4 dated 2015-08-25
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ NEWS | 19 ++++++++---- R/sn-funct.R | 73 ++++++++++++++++++++++++++++++------------------ man/dst.Rd | 13 +++++--- man/makeSECdistr.Rd | 6 ++- man/plot.SECdistr.Rd | 14 ++++++++- man/selm.Rd | 4 +- man/sn-package.Rd | 1 man/summary.SECdistr.Rd | 10 +++--- 10 files changed, 106 insertions(+), 60 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package
offers an approach for the determination of the best
stratification of a sampling frame, the one that ensures the
minimum sample cost under the condition to satisfy precision
constraints in a multivariate and multidomain case. This
approach is based on the use of the genetic algorithm: each
solution (i.e. a particular partition in strata of the sampling
frame) is considered as an individual in a population; the
fitness of all individuals is evaluated applying the
Bethel-Chromy algorithm to calculate the sampling size
satisfying precision constraints on the target estimates.
Functions in the package allows to: (a) analyse the obtained
results of the optimisation step; (b) assign the new strata
labels to the sampling frame; (c) select a sample from the new
frame accordingly to the best allocation.
Functions for the execution of the genetic algorithm are a modified
version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Daniela Pagliuca and Egon Willighagen
Maintainer: Giulio Barcaroli <barcarol@istat.it>
Diff between SamplingStrata versions 1.0-3 dated 2014-10-21 and 1.0-4 dated 2015-08-25
DESCRIPTION | 12 +- MD5 | 28 ++--- NAMESPACE | 4 NEWS | 4 R/buildStrataDF.R | 1 R/evalSolution.r | 188 +++++++++++++++++------------------- R/optimizeStrata.R | 122 ++++++++++++++--------- R/strataGenalg.R | 2 R/updateFrame.R | 1 build/vignette.rds |binary data/swissframe.rda |binary data/swissmunicipalities.rda |binary data/swissstrata.rda |binary inst/doc/SamplingStrataVignette.pdf |binary man/evalSolution.Rd | 19 +-- 15 files changed, 208 insertions(+), 173 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: R Interface to the Protocol Buffers API
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal RPC protocols and file formats. Additional
documentation is available in the arXiv.org preprint "RProtoBuf:
Efficient Cross-Language Data Serialization in R" by Eddelbuettel,
Stokely, and Ooms (2014) at <http://arxiv.org/abs/1401.7372>.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.2 dated 2014-12-11 and 0.4.3 dated 2015-08-25
ChangeLog | 52 ++++++++++++++++++++++++++++++++- DESCRIPTION | 25 ++++++--------- MD5 | 26 ++++++++-------- NAMESPACE | 2 - README.md | 4 -- build/vignette.rds |binary inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/doc/RProtoBuf-unitTests.pdf |binary inst/unitTests/runit.FieldDescriptor.R | 43 +++++++++++++-------------- inst/unitTests/runit.serialize.R | 9 ++--- man/RProtoBuf-package.Rd | 37 +++-------------------- src/Makevars.win | 32 ++++++++++---------- tools/winlibs.R | 12 +++---- 14 files changed, 130 insertions(+), 112 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.4 dated 2015-07-28 and 0.10.5 dated 2015-08-25
DESCRIPTION | 12 +-- MD5 | 7 + configure | 205 ++++++++++++++++++++------------------------------------ src/Makevars.in |only tools/winlibs.R | 2 5 files changed, 86 insertions(+), 140 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kent Russel [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.1.8 dated 2015-07-11 and 0.2.1 dated 2015-08-25
networkD3-0.1.8/networkD3/R/treeNetwork.R |only networkD3-0.1.8/networkD3/inst/htmlwidgets/treeNetwork.js |only networkD3-0.1.8/networkD3/inst/htmlwidgets/treeNetwork.yaml |only networkD3-0.1.8/networkD3/man/as.treeNetwork.Rd |only networkD3-0.1.8/networkD3/man/treeNetwork.Rd |only networkD3-0.2.1/networkD3/DESCRIPTION | 14 +-- networkD3-0.2.1/networkD3/MD5 | 40 +++++---- networkD3-0.2.1/networkD3/NAMESPACE | 16 ++- networkD3-0.2.1/networkD3/NEWS | 24 +++++ networkD3-0.2.1/networkD3/R/dendroNetwork.R |only networkD3-0.2.1/networkD3/R/diagonalNetwork.R |only networkD3-0.2.1/networkD3/R/forceNetwork.R | 2 networkD3-0.2.1/networkD3/R/radialNetwork.R |only networkD3-0.2.1/networkD3/R/sankeyNetwork.R | 7 - networkD3-0.2.1/networkD3/R/simpleNetwork.R | 2 networkD3-0.2.1/networkD3/README.md | 2 networkD3-0.2.1/networkD3/inst/examples/examples.R | 42 +++++----- networkD3-0.2.1/networkD3/inst/examples/examples.Rmd | 17 +++- networkD3-0.2.1/networkD3/inst/htmlwidgets/dendroNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/dendroNetwork.yaml |only networkD3-0.2.1/networkD3/inst/htmlwidgets/diagonalNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/diagonalNetwork.yaml |only networkD3-0.2.1/networkD3/inst/htmlwidgets/forceNetwork.js | 4 networkD3-0.2.1/networkD3/inst/htmlwidgets/radialNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/radialNetwork.yaml |only networkD3-0.2.1/networkD3/man/as.radialNetwork.Rd |only networkD3-0.2.1/networkD3/man/dendroNetwork.Rd |only networkD3-0.2.1/networkD3/man/diagonalNetwork.Rd |only networkD3-0.2.1/networkD3/man/networkD3-shiny.Rd | 28 ++++-- networkD3-0.2.1/networkD3/man/radialNetwork.Rd |only 30 files changed, 133 insertions(+), 65 deletions(-)
Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <http://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos="http://www.math.ntnu.no/inla/R/testing").
Author: Jingyi Guo <jingyi.guo@math.ntnu.no> and Andrea Riebler <andrea.riebler@math.ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@math.ntnu.no>
Diff between meta4diag versions 1.0.19 dated 2015-08-23 and 1.0.20 dated 2015-08-25
DESCRIPTION | 15 +++++++++------ MD5 | 16 ++++++++-------- R/meta4diagGUI.R | 4 ++-- data/Catheter.rda |binary data/Scheidler.rda |binary data/Telomerase.rda |binary data/table_cor.rda |binary data/table_var.rda |binary inst/etc/welcometext.txt | 4 ++-- 9 files changed, 21 insertions(+), 18 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9.2 dated 2015-08-08 and 0.9.3 dated 2015-08-25
curl-0.9.2/curl/src/options.c |only curl-0.9.2/curl/src/options.h |only curl-0.9.3/curl/DESCRIPTION | 6 +- curl-0.9.3/curl/MD5 | 22 ++++----- curl-0.9.3/curl/NAMESPACE | 1 curl-0.9.3/curl/NEWS | 5 ++ curl-0.9.3/curl/R/utilities.R | 11 +--- curl-0.9.3/curl/build/vignette.rds |binary curl-0.9.3/curl/configure | 83 +++++++++++++++++++++++++++--------- curl-0.9.3/curl/man/curl_options.Rd | 5 +- curl-0.9.3/curl/src/Makevars.in |only curl-0.9.3/curl/src/Makevars.win | 3 - curl-0.9.3/curl/tools/options.R |only curl-0.9.3/curl/tools/winlibs.R | 2 14 files changed, 92 insertions(+), 46 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.1 dated 2015-06-24 and 0.2 dated 2015-08-25
DESCRIPTION | 20 LICENSE | 2 LICENSE.note | 56 MD5 | 63 NAMESPACE | 1 NEWS | 36 R/misc.R | 32 R/rhandsontable-package.R | 8 R/rhandsontable.R | 107 build/vignette.rds |binary inst/doc/intro_rhandsontable.R | 270 inst/doc/intro_rhandsontable.Rmd | 426 inst/doc/intro_rhandsontable.html | 476 inst/htmlwidgets/lib/handsontable/handsontable.full.css | 358 inst/htmlwidgets/lib/handsontable/handsontable.full.js |46985 ++++++++-------- inst/htmlwidgets/lib/jquery |only inst/htmlwidgets/lib/moment/moment.js | 5036 - inst/htmlwidgets/lib/sparkline |only inst/htmlwidgets/rhandsontable.css | 15 inst/htmlwidgets/rhandsontable.js | 121 inst/htmlwidgets/rhandsontable.yaml | 14 man/hot_cell.Rd | 3 man/hot_col.Rd | 8 man/hot_cols.Rd | 7 man/hot_rows.Rd | 3 man/hot_table.Rd | 19 man/hot_to_r.Rd | 3 man/hot_validate_character.Rd | 5 man/hot_validate_numeric.Rd | 5 man/rHandsontableOutput.Rd | 10 man/renderRHandsontable.Rd | 3 man/rhandsontable-package.Rd |only man/rhandsontable.Rd | 6 vignettes/intro_rhandsontable.Rmd | 426 34 files changed, 29278 insertions(+), 25246 deletions(-)
Title: Approximation of First-Passage-Time Densities for Diffusion
Processes
Diff between fptdApprox versions 2.0 dated 2013-12-27 and 2.1 dated 2015-08-25
Description: Efficient approximation of first-passage-time densities for diffusion processes based on the First-Passage-Time Location (FPTL) function.
Author: Patricia Román-Román, Juan J. Serrano-Pérez and Francisco Torres-Ruiz.
Maintainer: Juan J. Serrano-Pérez
DESCRIPTION | 20 ++++++++------------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 13 +++++++++++++
R/is.fptl.R | 2 +-
R/plot.fpt.density.R | 5 ++---
man/Approx.cfpt.density.rd | 8 ++++----
man/Approx.fpt.density.rd | 8 ++++----
man/FPTL.Rd | 8 ++++----
man/Integration.Steps.Rd | 8 ++++----
man/diffproc.Rd | 5 +++++
man/fptdApprox-package.Rd | 12 ++++++------
man/growth.intervals.Rd | 6 ++----
man/is.fpt.density.rd | 5 +++++
man/plot.fpt.density.Rd | 15 ++++++++-------
man/plot.fptl.Rd | 17 +++++++----------
man/print.fpt.density.rd | 9 ++++++---
man/report.Rd | 3 +--
man/report.fpt.density.Rd | 8 ++++++--
man/report.summary.fptl.Rd | 5 +++++
man/summary.fptl.Rd | 8 ++++----
20 files changed, 114 insertions(+), 89 deletions(-)
Title: Contouring of Non-Regular Three-Dimensional Data
Description: Create contour lines for a non regular series of points, potentially from a non-regular canvas.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton <n.hamilton@unsw.edu.au>
Diff between contoureR versions 1.0.1 dated 2015-08-22 and 1.0.5 dated 2015-08-25
DESCRIPTION | 6 - MD5 | 38 +++--- NEWS | 6 + R/RcppExports-Doc.R | 29 +++++ R/RcppExports.R | 12 +- R/contourLines.R | 22 ++- R/contoureR-package.R | 1 R/convexHull.R | 32 +++-- README.md |only man/contourLinesR.Rd | 6 - man/contoureR.Rd | 1 man/convexHullAM.Rd |only man/getContourLines.Rd | 7 + man/getConvexHull.Rd | 28 +++- src/Makevars.win |only src/RcppExports.cpp | 34 +++++ src/contourWalker.cpp | 112 ++++++++++++------- src/convexHull_Monotone.cpp |only src/convexHull_Monotone.h |only src/functions.cpp | 39 +++--- src/functions.h | 18 ++- src/structs.h | 253 +++++++++++++++++++++++++------------------- src/templates.h |only 23 files changed, 423 insertions(+), 221 deletions(-)
Title: Comparing Objects for Differences
Description: Functions to compare a model object to a comparison object.
If the objects are not identical, the functions can be instructed to
explore various modifications of the objects (e.g., sorting rows,
dropping names) to see if the modified versions are identical.
Author: Paul Murrell
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between compare versions 0.2-5 dated 2014-12-16 and 0.2-6 dated 2015-08-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/same.R | 8 ++------ build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/compare-intro.pdf |binary inst/doc/fundamentals.pdf |binary 7 files changed, 20 insertions(+), 15 deletions(-)
Title: Central Limit Theorem Experiments (Theoretical and Simulation)
Description: Central limit theorem experiments presented by data frames or plots. Functions include generating theoretical sample space, corresponding probability, and simulated results as well.
Author: Simiao Ye, Jingning Mei
Maintainer: Simiao Ye <simiao.ye@gmail.com>
Diff between clttools versions 1.0 dated 2015-08-23 and 1.1 dated 2015-08-25
DESCRIPTION | 6 +-- MD5 | 30 ++++++++--------- R/clttools.R | 86 +++++++++----------------------------------------- man/coin.Rd | 3 - man/coin.plot.Rd | 3 - man/coin.simu.Rd | 3 - man/coin.simu.plot.Rd | 3 - man/dice.Rd | 3 - man/dice.plot.Rd | 3 - man/dice.simu.Rd | 3 - man/dice.simu.plot.Rd | 3 - man/expt.Rd | 3 - man/expt.mse.Rd | 3 - man/expt.plot.Rd | 3 - man/expt.simu.Rd | 3 - man/expt.simu.plot.Rd | 3 - 16 files changed, 47 insertions(+), 114 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-61 dated 2015-06-11 and 0.1-62 dated 2015-08-24
DESCRIPTION | 12 ++++----- MD5 | 34 +++++++++++++++++--------- NAMESPACE | 53 ++++++++++++++++++++++++++++++++++------- NEWS | 4 +++ R/BifixedContCont.R | 3 +- R/MixedContContIT.R | 4 +-- R/SummaryTrialLevelContCont.R |only R/TrialLevelContCont.R |only R/TwoStageSurvSurv.R |only R/UnimixedContCont.R | 20 +++++++-------- R/plot.TrialLevelContCont.R |only R/plot.TwoStageSurvSurv.R |only R/summary.TwoStageSurvSurv.R |only data/Ovarian.rda |only man/BifixedContCont.Rd | 2 - man/BimixedContCont.Rd | 2 - man/Ovarian.Rd |only man/TrialLevelContCont.Rd |only man/TwoStageSurvSurv.Rd |only man/UnifixedContCont.Rd | 2 - man/UnimixedContCont.Rd | 2 - man/plot.TrialLevelContCont.Rd |only man/plot.TwoStageSurvSurv.Rd |only man/summary.gen.Rd | 4 +++ 24 files changed, 100 insertions(+), 42 deletions(-)
Title: Incremental Decomposition Methods
Description: Principal Component Analysis and Multiple Correspondence Analysis using incremental eigenvalue decomposition methods.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.0 dated 2015-06-03 and 1.2 dated 2015-08-24
idm-1.0/idm/R/add_svd.r |only idm-1.2/idm/DESCRIPTION | 10 +- idm-1.2/idm/MD5 | 40 +++++----- idm-1.2/idm/NAMESPACE | 2 idm-1.2/idm/R/add_eig.r | 166 +++++++++++++++++++++--------------------- idm-1.2/idm/R/add_svd.R |only idm-1.2/idm/R/do_eig.r | 90 +++------------------- idm-1.2/idm/R/h_exact_mca.r | 45 ++++------- idm-1.2/idm/R/i_mca.r | 9 +- idm-1.2/idm/R/i_pca.r | 11 +- idm-1.2/idm/R/r_live_mca.r | 62 ++++++--------- idm-1.2/idm/R/update_mca.R | 41 +++------- idm-1.2/idm/R/update_pca.R | 41 +++++----- idm-1.2/idm/man/add_eig.Rd | 34 ++++---- idm-1.2/idm/man/add_svd.Rd | 67 +++++++++++----- idm-1.2/idm/man/do_eig.Rd | 5 - idm-1.2/idm/man/i_mca.Rd | 27 +++--- idm-1.2/idm/man/i_pca.Rd | 7 + idm-1.2/idm/man/idm.Rd | 10 +- idm-1.2/idm/man/plot.i_mca.Rd | 2 idm-1.2/idm/man/update_mca.Rd | 11 +- idm-1.2/idm/man/update_pca.Rd | 25 +++--- 22 files changed, 322 insertions(+), 383 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide
methods for automatically determining breaks and labels
for axes and legends.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 0.2.5 dated 2015-06-12 and 0.3.0 dated 2015-08-24
DESCRIPTION | 6 +-- MD5 | 67 +++++++++++++++++++++--------------------- NAMESPACE | 16 +++++++--- NEWS | 12 ++++++- R/bounds.r | 6 ++- R/colour-manip.r | 49 +++++++++++++++--------------- R/colour-mapping.r | 10 +++--- R/date-time.r | 2 - R/formatter.r | 6 +-- R/pal-brewer.r | 4 +- R/pal-dichromat.r | 2 - R/pal-gradient.r | 53 ++++++++++++++------------------- R/pal-grey.r | 2 - R/pal-hue.r | 2 - R/scale-continuous.r | 24 ++++++++------- R/scale-discrete.r | 14 ++++++-- R/scales.r | 4 +- R/trans-date.r | 22 ++++++------- R/trans.r | 2 - README.md | 2 - build/partial.rdb |binary man/alpha.Rd | 2 - man/brewer_pal.Rd | 4 +- man/date_trans.Rd | 4 +- man/dichromat_pal.Rd | 2 - man/div_gradient_pal.Rd | 12 +++---- man/gradient_n_pal.Rd | 4 +- man/rescale.Rd | 2 - man/seq_gradient_pal.Rd | 6 +-- man/time_trans.Rd | 4 +- man/train_continuous.Rd |only man/train_discrete.Rd |only tests/testthat/test-alpha.r | 4 +- tests/testthat/test-range.r | 25 --------------- tests/testthat/test-rescale.R |only tests/testthat/test-scale.r | 2 - 36 files changed, 190 insertions(+), 186 deletions(-)
Title: Efficient Authenticated Interaction with the O*NET API
Description: Provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API <www.onetonline.org>. The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Author: Eric Knudsen
Maintainer: Eric Knudsen <eknudsen@gc.cuny.edu>
Diff between ONETr versions 1.0.2 dated 2015-01-23 and 1.0.3 dated 2015-08-24
ONETr-1.0.2/ONETr/README.md |only ONETr-1.0.3/ONETr/DESCRIPTION | 12 +-- ONETr-1.0.3/ONETr/MD5 | 89 ++++++++++++++-------------- ONETr-1.0.3/ONETr/NAMESPACE | 2 ONETr-1.0.3/ONETr/R/abilities.R | 10 --- ONETr-1.0.3/ONETr/R/education.R | 15 ---- ONETr-1.0.3/ONETr/R/interests.R | 18 +---- ONETr-1.0.3/ONETr/R/jobTitles.R | 10 --- ONETr-1.0.3/ONETr/R/jobZone.R | 10 --- ONETr-1.0.3/ONETr/R/keySearch.R | 2 ONETr-1.0.3/ONETr/R/knowledge.R | 10 --- ONETr-1.0.3/ONETr/R/occupation.R | 12 +-- ONETr-1.0.3/ONETr/R/relatedOccupations.R | 14 ---- ONETr-1.0.3/ONETr/R/sim.index.R |only ONETr-1.0.3/ONETr/R/skills.R | 10 --- ONETr-1.0.3/ONETr/R/socSearch.R | 4 - ONETr-1.0.3/ONETr/R/tasks.R | 10 --- ONETr-1.0.3/ONETr/R/technology.R | 10 --- ONETr-1.0.3/ONETr/R/tools.R | 11 +-- ONETr-1.0.3/ONETr/R/workActivities.R | 10 --- ONETr-1.0.3/ONETr/R/workContext.R | 10 --- ONETr-1.0.3/ONETr/R/workStyles.R | 10 --- ONETr-1.0.3/ONETr/R/workValues.R | 10 --- ONETr-1.0.3/ONETr/data/jobData2.rda |only ONETr-1.0.3/ONETr/man/ONETr-package.Rd | 64 ++++++++++---------- ONETr-1.0.3/ONETr/man/abilities.Rd | 78 ++++++++++++------------ ONETr-1.0.3/ONETr/man/cacheEnv.Rd | 16 ++--- ONETr-1.0.3/ONETr/man/education.Rd | 74 +++++++++++------------ ONETr-1.0.3/ONETr/man/interests.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/jobData.Rd | 26 ++++---- ONETr-1.0.3/ONETr/man/jobData2.Rd |only ONETr-1.0.3/ONETr/man/jobTitles.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/jobZone.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/keySearch.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/knowledge.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/occupation.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/relatedOccupations.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/setCreds.Rd | 72 +++++++++++----------- ONETr-1.0.3/ONETr/man/sim.index.Rd |only ONETr-1.0.3/ONETr/man/skills.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/socSearch.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/tasks.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/technology.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/tools.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workActivities.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workContext.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workStyles.Rd | 76 +++++++++++------------ ONETr-1.0.3/ONETr/man/workValues.Rd | 76 +++++++++++------------ 48 files changed, 882 insertions(+), 953 deletions(-)
Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard
errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE
computation for expectation and quantile estimators is
supported as well as multivariate estimations. The package also provides
functions for computing effective sample size and for plotting
Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes
<hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>
Diff between mcmcse versions 1.1-1 dated 2015-07-31 and 1.1-2 dated 2015-08-24
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- R/confRegion.R | 3 +-- R/multiESS.R | 10 ++++++++-- build/vignette.rds |binary inst/doc/mcmcse_vignette.pdf |binary man/confRegion.Rd | 18 ++++++++---------- man/ess.Rd | 2 +- man/mcmcse-package.Rd | 8 +++++--- man/mcse.mat.Rd | 2 +- man/mcse.multi.Rd | 8 ++++++++ man/multiESS.Rd | 2 +- vignettes/mcmcse_vignette.fdb_latexmk |only 13 files changed, 49 insertions(+), 35 deletions(-)
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (http://turfjs.org/) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.1.0 dated 2015-05-16 and 0.1.4 dated 2015-08-24
lawn-0.1.0/lawn/inst/ignore |only lawn-0.1.4/lawn/DESCRIPTION | 13 - lawn-0.1.4/lawn/MD5 | 47 ++--- lawn-0.1.4/lawn/NAMESPACE | 22 ++ lawn-0.1.4/lawn/NEWS | 18 + lawn-0.1.4/lawn/R/as_feature.R | 2 lawn-0.1.4/lawn/R/centroid.R | 2 lawn-0.1.4/lawn/R/flip.R | 2 lawn-0.1.4/lawn/R/hex_grid.R | 1 lawn-0.1.4/lawn/R/lawn-package.R | 3 lawn-0.1.4/lawn/R/print_methods.R |only lawn-0.1.4/lawn/R/random.R | 2 lawn-0.1.4/lawn/R/tbldf.R |only lawn-0.1.4/lawn/README.md | 195 +++++++-------------- lawn-0.1.4/lawn/build/vignette.rds |binary lawn-0.1.4/lawn/data/lawn_data.rda |binary lawn-0.1.4/lawn/inst/doc/lawn_vignette.Rmd | 1 lawn-0.1.4/lawn/inst/doc/lawn_vignette.html | 228 +++++++------------------ lawn-0.1.4/lawn/man/as_feature.Rd | 2 lawn-0.1.4/lawn/man/lawn_flip.Rd | 2 lawn-0.1.4/lawn/man/lawn_hex_grid.Rd | 1 lawn-0.1.4/lawn/man/lawn_random.Rd | 2 lawn-0.1.4/lawn/man/print-methods.Rd |only lawn-0.1.4/lawn/man/type_sum.Rd |only lawn-0.1.4/lawn/tests/testthat/test-centroid.R | 4 lawn-0.1.4/lawn/tests/testthat/test-onload.R | 6 lawn-0.1.4/lawn/vignettes/lawn_vignette.Rmd | 1 27 files changed, 221 insertions(+), 333 deletions(-)
Title: Independent Component Analysis
Description: Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between ica versions 1.0-0 dated 2014-09-02 and 1.0-1 dated 2015-08-24
ica-1.0-0/ica/R/acyidx.R |only ica-1.0-0/ica/man/acyidx.Rd |only ica-1.0-1/ica/ChangeLog |only ica-1.0-1/ica/DESCRIPTION | 8 - ica-1.0-1/ica/MD5 | 39 ++--- ica-1.0-1/ica/NAMESPACE | 6 ica-1.0-1/ica/R/acy.R |only ica-1.0-1/ica/R/congru.R | 31 +++- ica-1.0-1/ica/R/icafast.R | 159 ++++++++++++--------- ica-1.0-1/ica/R/icaimax.R | 140 ++++++++++-------- ica-1.0-1/ica/R/icajade.R | 119 ++++++++------- ica-1.0-1/ica/R/icaplot.R | 20 +- ica-1.0-1/ica/R/icasamp.R | 285 +++++++++++++++++++++----------------- ica-1.0-1/ica/R/sdiag.R | 2 ica-1.0-1/ica/man/acy.Rd |only ica-1.0-1/ica/man/congru.Rd | 35 +++- ica-1.0-1/ica/man/ica-internal.Rd | 2 ica-1.0-1/ica/man/ica-package.Rd | 2 ica-1.0-1/ica/man/icafast.Rd | 47 ++---- ica-1.0-1/ica/man/icaimax.Rd | 47 ++---- ica-1.0-1/ica/man/icajade.Rd | 45 ++---- ica-1.0-1/ica/man/icaplot.Rd | 13 + ica-1.0-1/ica/man/icasamp.Rd | 10 - 23 files changed, 561 insertions(+), 449 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.12 dated 2015-08-21 and 0.99.13 dated 2015-08-24
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 3 NEWS | 17 ++ R/DescTools.r | 206 ----------------------------------- R/FastDesc.R | 274 +++++++++++++++++++++++++++++------------------ man/DescTools-package.Rd | 2 man/GCD.Rd | 2 man/StrTrim.Rd | 10 - src/aux_fct.cpp | 74 +++++++----- 10 files changed, 250 insertions(+), 366 deletions(-)
Title: Variational Bayesian Mixture Models
Description: Variational algorithms and methods for fitting mixture
models. Main functions are varbayes, vbcomp, vbconstr, mppca,
mmppca and gmmkmsock.
Author: Pierrick Bruneau
Maintainer: Pierrick Bruneau <pbruneau@gmail.com>
Diff between VBmix versions 0.2.17 dated 2014-05-06 and 0.3.1 dated 2015-08-24
VBmix-0.2.17/VBmix/R/classicEM.R |only VBmix-0.2.17/VBmix/configure.win |only VBmix-0.2.17/VBmix/man/Rdct.Rd |only VBmix-0.2.17/VBmix/man/Rdct2D.Rd |only VBmix-0.2.17/VBmix/man/RinvDct2D.Rd |only VBmix-0.2.17/VBmix/man/classicEM.Rd |only VBmix-0.2.17/VBmix/man/readLabelFile.Rd |only VBmix-0.2.17/VBmix/man/readPixmapFile.Rd |only VBmix-0.2.17/VBmix/src/config.h.win |only VBmix-0.2.17/VBmix/src/readDataFile.cpp |only VBmix-0.3.1/VBmix/DESCRIPTION | 14 VBmix-0.3.1/VBmix/MD5 | 63 +- VBmix-0.3.1/VBmix/NAMESPACE | 3 VBmix-0.3.1/VBmix/R/Rutils.R | 21 VBmix-0.3.1/VBmix/R/displayScatter.R | 7 VBmix-0.3.1/VBmix/R/interfaces.R | 94 ++- VBmix-0.3.1/VBmix/README | 3 VBmix-0.3.1/VBmix/configure | 932 +++--------------------------- VBmix-0.3.1/VBmix/configure.ac | 16 VBmix-0.3.1/VBmix/data/VBmix.RData |binary VBmix-0.3.1/VBmix/inst/lowerpack.pdf |only VBmix-0.3.1/VBmix/inst/suffstats.pdf |only VBmix-0.3.1/VBmix/man/EM.Rd |only VBmix-0.3.1/VBmix/man/gdist.Rd |only VBmix-0.3.1/VBmix/man/getCouple.Rd | 3 VBmix-0.3.1/VBmix/man/getLabels.Rd | 2 VBmix-0.3.1/VBmix/man/mkmeans.Rd |only VBmix-0.3.1/VBmix/man/mvndensity.Rd | 5 VBmix-0.3.1/VBmix/man/mvnradiusdensity.Rd |only VBmix-0.3.1/VBmix/man/varbayes.Rd | 2 VBmix-0.3.1/VBmix/src/EM.c |only VBmix-0.3.1/VBmix/src/EM.h |only VBmix-0.3.1/VBmix/src/config.h |only VBmix-0.3.1/VBmix/src/config.h.in | 33 - VBmix-0.3.1/VBmix/src/getLabels.c | 9 VBmix-0.3.1/VBmix/src/mkmeans.c |only VBmix-0.3.1/VBmix/src/mkmeans.h |only VBmix-0.3.1/VBmix/src/mppca.cpp | 41 - VBmix-0.3.1/VBmix/src/mppca.h | 5 VBmix-0.3.1/VBmix/src/test.c |only VBmix-0.3.1/VBmix/src/test.h |only VBmix-0.3.1/VBmix/src/utils.c | 459 +++++++++++--- VBmix-0.3.1/VBmix/src/utils.h | 40 + VBmix-0.3.1/VBmix/src/varbayes.c | 8 44 files changed, 661 insertions(+), 1099 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.6 dated 2015-04-03 and 0.7 dated 2015-08-24
DESCRIPTION | 18 +++---- MD5 | 23 +++++---- NAMESPACE | 7 ++ NEWS | 7 ++ R/V8.R | 12 +++- build/vignette.rds |binary configure | 133 +++++++++++++++++++++++++++++------------------------ man/JS.Rd | 2 man/new_context.Rd | 2 src/Makevars.in |only src/Makevars.win | 20 ++++--- tools/v8-315.rb |only tools/version.cpp |only tools/winlibs.R | 17 +++++- 14 files changed, 146 insertions(+), 95 deletions(-)
Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using
structural equations, with emphasis on problems in causal inference.
Specify interventions and simulate from intervened data generating
distributions. Define and evaluate treatment-specific means, the average
treatment effects and coefficients from working marginal structural models.
User interface designed to facilitate the conduct of transparent and
reproducible simulation studies, and allows concise expression of complex
functional dependencies for a large number of time-varying nodes. See the
package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between simcausal versions 0.2.0 dated 2015-06-12 and 0.3.0 dated 2015-08-24
DESCRIPTION | 10 MD5 | 72 NAMESPACE | 24 NEWS | 19 R/DAG_node_R6.R |only R/distributions.R | 31 R/interface.r | 14 R/network.R |only R/node.R | 299 --- R/parserfunctions.r | 571 +++--- R/parserfunctions_R6.r |only R/simcausal-package.r | 6 R/simcausal.r | 513 +++-- R/simulation.r | 1213 ++++++------- R/targetparam.r | 800 ++++----- R/zzz.R | 29 README.md | 6 inst/doc/simcausal_vignette.R | 2 inst/doc/simcausal_vignette.Rnw | 2 inst/doc/simcausal_vignette.pdf |binary man/DAG_Class.Rd |only man/Define_sVar.Rd |only man/NetInd.to.sparseAdjMat.Rd |only man/NetIndClass.Rd |only man/Node_Class.Rd |only man/doLTCF.Rd | 2 man/eval.target.Rd | 5 man/igraph.to.sparseAdjMat.Rd |only man/network.Rd |only man/node.Rd | 13 man/plotDAG.Rd | 5 man/plotSurvEst.Rd | 14 man/set.DAG.Rd | 4 man/sim.Rd | 9 man/simfull.Rd | 5 man/simobs.Rd | 7 man/sparseAdjMat.to.NetInd.Rd |only man/sparseAdjMat.to.igraph.Rd |only tests/RUnit/example.simnets.R |only tests/RUnit/runit.simnets.R |only tests/RUnit/runittests.R | 3197 +++++++++++++++++++----------------- tests/RUnit/sim.impute.examples12.R | 2 tests/test-all.R | 4 vignettes/simcausal_vignette.Rnw | 2 44 files changed, 3528 insertions(+), 3352 deletions(-)
Title: Semiparametric Bivariate Regression Models
Description: Routine for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.5 dated 2015-07-22 and 3.6 dated 2015-08-24
ChangeLog | 4 DESCRIPTION | 9 MD5 | 84 ++--- NAMESPACE | 11 R/AT.r | 176 ++++++++-- R/LM.bpm.r | 2 R/OR.r | 49 ++ R/RR.r | 47 ++ R/S.m.r | 12 R/SemiParBIVProbit.fit.R | 24 - R/SemiParBIVProbit.fit.post.r | 28 + R/SemiParBIVProbit.r | 359 +++++++++++++++------ R/adjCov.r | 26 + R/adjCovSD.r | 27 + R/bprobgHs.r | 189 +++++------ R/bprobgHsCont.r | 49 +- R/bprobgHsCont3.r |only R/bprobgHsContUniv.r | 22 - R/bprobgHsContUniv3.r |only R/bprobgHsPO.r | 109 ++---- R/bprobgHsPO0.r | 46 +- R/bprobgHsSS.r | 120 +++---- R/conv.check.r | 4 R/copgHs.r | 2 R/copgHs2.r | 2 R/copgHsAT.r | 4 R/copgHsCont.r | 7 R/distrHs.r | 609 ++++++++++++++++++++++++------------- R/distrHsAT.r | 33 +- R/gt.bpm.R | 12 R/logLik.SemiParBIVProbit.r | 2 R/pen.r | 57 ++- R/polys.setup.r |only R/post.check.R |only R/print.SemiParBIVProbit.r | 35 +- R/print.summary.SemiParBIVProbit.r | 70 +++- R/resp.check.R | 61 +++ R/summary.SemiParBIVProbit.r | 304 ++++++++++++------ R/working.comp.r | 20 + man/SemiParBIVProbit.Rd | 10 man/bprobgHsCont3.Rd |only man/bprobgHsContUniv3.Rd |only man/hiv.Rd | 57 +++ man/polys.setup.Rd |only man/post.check.Rd |only man/prev.Rd | 3 man/resp.check.Rd | 7 47 files changed, 1804 insertions(+), 888 deletions(-)
More information about SemiParBIVProbit at CRAN
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Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.0.5 dated 2015-05-03 and 1.0.6 dated 2015-08-24
DESCRIPTION | 12 ++-- MD5 | 45 ++++++++++------ NAMESPACE | 2 R/fun.r | 49 +++++++++++++---- R/mvBM.r | 38 +++++++++---- R/mvEB.r | 26 ++++++--- R/mvLLIK.r | 120 +++++++++++++++++++++++++++++++------------- R/mvOU.r | 24 ++++++-- R/mvSHIFT.r | 35 ++++++++---- R/mvSIM.r | 6 +- R/mvmorphPrecalc.r | 20 +++++-- README.md |only build |only inst |only man/mvBM.Rd | 10 ++- man/mvEB.Rd | 5 + man/mvLL.Rd | 7 +- man/mvMORPH-package.Rd | 4 - man/mvOU.Rd | 12 ++-- man/mvSHIFT.Rd | 2 src/weight-matrix-mvmorph.c | 1 tests |only vignettes |only 23 files changed, 290 insertions(+), 128 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.4 dated 2015-08-03 and 0.4.2 dated 2015-08-24
DESCRIPTION | 10 - MD5 | 53 +++--- NAMESPACE | 2 NEWS | 5 R/0_higherOrder.R |only R/1_functions4Fitting.R | 2 R/1_supplementaryPlot.R | 7 R/5_statisticalTests.R | 144 +++++++++++------- R/RcppExports.R | 8 + inst/doc/BayesianInference.pdf |binary inst/doc/CTMC.pdf |binary inst/doc/an_introduction_to_markovchain_package.R | 100 +++++++++--- inst/doc/an_introduction_to_markovchain_package.Rnw | 147 +++++++++++++++++-- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.pdf |binary man/HigherOrderMarkovChain-class.Rd |only man/fitHigherOrderMarkovChain.Rd |only man/markovchain-package.Rd | 4 man/verifyMarkovProperty.Rd | 25 +-- src/0_classesAndMethods.cpp | 1 src/1_ctmcFunctions4Fitting.cpp | 2 src/1_fitHigherOrder.cpp |only src/1_functions4Fitting.cpp | 12 + src/2_probabilistic.cpp | 7 src/3_multinomCI.cpp | 8 - src/RcppExports.cpp | 23 ++ tests/testthat/testHigerOrder.R |only tests/testthat/testInference.R | 16 -- vignettes/an_introduction_to_markovchain_package.Rnw | 147 +++++++++++++++++-- vignettes/markovchainBiblio.bib | 44 +++++ 30 files changed, 580 insertions(+), 187 deletions(-)
Title: Estimation of Meiotic Recombination Rates Using Marey Maps
Description: Local recombination rates are graphically estimated across a genome using marey maps.
Author: Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between MareyMap versions 1.3.0 dated 2015-07-08 and 1.3.1 dated 2015-08-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/mmspline3.R | 5 +++-- build/vignette.rds |binary inst/doc/vignette.pdf |binary 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-629 dated 2015-04-18 and 0.1-630 dated 2015-08-24
cheddar-0.1-629/cheddar/build |only cheddar-0.1-630/cheddar/DESCRIPTION | 10 cheddar-0.1-630/cheddar/MD5 | 20 - cheddar-0.1-630/cheddar/NAMESPACE | 7 cheddar-0.1-630/cheddar/inst/doc/CheddarQuickstart.pdf |binary cheddar-0.1-630/cheddar/inst/doc/Collections.pdf |binary cheddar-0.1-630/cheddar/inst/doc/Community.pdf |binary cheddar-0.1-630/cheddar/inst/doc/ImportExport.pdf |binary cheddar-0.1-630/cheddar/inst/doc/PlotsAndStats.pdf |binary cheddar-0.1-630/cheddar/man/cheddar.Rd | 6 cheddar-0.1-630/cheddar/src/trophic_chains.cpp | 174 ++++++++--------- cheddar-0.1-630/cheddar/tests/graph_tests.R |only 12 files changed, 112 insertions(+), 105 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.5 dated 2015-04-18 and 1.1.6 dated 2015-08-23
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 9 +++++++++ R/residuals.glmssn.R | 2 +- build/vignette.rds |binary data/datalist | 2 +- data/mf04.rda |binary data/mf04p.rda |binary data/modelFits.rda |binary inst/doc/STARS.pdf |binary man/createSSN.Rd | 1 + man/plot.influenceSSN.Rd | 2 +- man/residuals.glmssn.Rd | 6 +++--- 13 files changed, 33 insertions(+), 23 deletions(-)
Title: Infrastructure for Seriation
Description: Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.1-1 dated 2015-06-30 and 1.1-2 dated 2015-08-23
DESCRIPTION | 9 +- MD5 | 48 +++++++------- NAMESPACE | 8 +- R/AAAparameter.R | 16 ++-- R/dissimilartiy.R | 154 +++++++++++++++++++++++++--------------------- R/permutation.R | 3 R/permutation_vector.R | 7 +- build/vignette.rds |binary data/Chameleon.rda |binary data/Irish.rda |binary data/Munsingen.rda |binary data/Psych24.rda |binary data/Townships.rda |binary data/Wood.rda |binary data/Zoo.rda |binary inst/NEWS | 12 ++- inst/doc/seriation.R | 127 ++++++++++++++++--------------------- inst/doc/seriation.Rnw | 88 ++++++++++++++------------ inst/doc/seriation.pdf |binary man/dissimilarity.Rd | 99 +++++++++++++++-------------- man/get_order.Rd | 29 +++++--- man/hmap.Rd | 3 man/permutation.Rd | 4 - man/permutation_vector.Rd | 26 +++++-- vignettes/seriation.Rnw | 88 ++++++++++++++------------ 25 files changed, 377 insertions(+), 344 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-19 dated 2015-06-12 and 3.1-21 dated 2015-08-23
DESCRIPTION | 12 +- MD5 | 28 +++--- NAMESPACE | 27 ++++- NEWS | 30 ++++++ R/ancova.R | 2 R/formatHex.R |only R/normal.and.t.R | 63 +++++++++---- R/showHex.R | 198 +++++++++++++++++++++++++++++++------------ inst/scripts/hh2/PrcnApx.R | 45 ++++----- inst/scripts/hh2/RApx.R | 43 ++++----- inst/scripts/hh2/RExcelApx.R | 2 inst/scripts/hh2/conc.R | 32 +++--- inst/scripts/hh2/oway.R | 30 +++--- inst/scripts/hh2/regb.R | 6 - man/formatHex.Rd |only man/showHex.Rd | 102 ++++++++++++---------- 16 files changed, 404 insertions(+), 216 deletions(-)
Title: Fit a Spatial Occupancy Model via Gibbs Sampling
Description: Fit a spatial-temporal occupancy models using
a probit formulation instead of a traditional logit
model.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between stocc versions 1.23 dated 2014-07-29 and 1.30 dated 2015-08-23
DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 14 +++++++++++++- R/spatial.occupancy.R | 27 +++++++++------------------ R/stocc-package.R | 8 +++++--- man/habData.Rd | 3 ++- man/icar.Q.Rd | 3 ++- man/make.so.data.Rd | 3 ++- man/occupancyData.Rd | 3 ++- man/spatial.occupancy.Rd | 9 ++++----- man/stocc-package.Rd | 7 ++++--- man/visitData.Rd | 3 ++- 12 files changed, 63 insertions(+), 53 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-0 dated 2015-03-11 and 0.1-2 dated 2015-08-23
ChangeLog | 222 ++++++++++++++++++++++---------------------- DESCRIPTION | 23 ++-- MD5 | 15 +- NAMESPACE | 4 R/bin_link.R | 4 R/vect_link.R | 282 +++++++++++++++++++++++++++++++++++++++++++------------- R/xml1.R | 2 inst |only man/readVECT.Rd | 35 +++++- 9 files changed, 387 insertions(+), 200 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine Mullen,
Brian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by Rainer Storn)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.2 dated 2013-12-12 and 0.1.3 dated 2015-08-23
RcppDE-0.1.2/RcppDE/demo/CompiledBenchmark.R |only RcppDE-0.1.2/RcppDE/demo/LargeBenchmark.R |only RcppDE-0.1.2/RcppDE/demo/SmallBenchmark.R |only RcppDE-0.1.3/RcppDE/ChangeLog | 32 +++++++++++++++++++++++++++ RcppDE-0.1.3/RcppDE/DESCRIPTION | 30 ++++++++++++------------- RcppDE-0.1.3/RcppDE/MD5 | 31 +++++++++++++------------- RcppDE-0.1.3/RcppDE/NAMESPACE | 11 +++++---- RcppDE-0.1.3/RcppDE/README.md | 10 +++++--- RcppDE-0.1.3/RcppDE/build/vignette.rds |binary RcppDE-0.1.3/RcppDE/demo/00Index | 10 ++++---- RcppDE-0.1.3/RcppDE/demo/c++ |only RcppDE-0.1.3/RcppDE/demo/compiled.R |only RcppDE-0.1.3/RcppDE/demo/large.R |only RcppDE-0.1.3/RcppDE/demo/small.R |only RcppDE-0.1.3/RcppDE/inst/doc/RcppDE.R | 2 - RcppDE-0.1.3/RcppDE/inst/doc/RcppDE.Rnw | 4 +-- RcppDE-0.1.3/RcppDE/inst/doc/RcppDE.pdf |binary RcppDE-0.1.3/RcppDE/man/DEoptim.Rd | 2 - RcppDE-0.1.3/RcppDE/src/devol.cpp | 2 - RcppDE-0.1.3/RcppDE/vignettes/RcppDE.Rnw | 4 +-- 20 files changed, 88 insertions(+), 50 deletions(-)
Title: Time Series Clustering with Dynamic Time Warping
Description: Time series clustering using different techniques related to the Dynamic Time Warping distance
and its corresponding lower bounds. Additionally, an implementation of k-Shape clustering is available.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 0.1.0 dated 2015-08-02 and 1.0.0 dated 2015-08-23
dtwclust-0.1.0/dtwclust/inst/dtwclust.pdf |only dtwclust-1.0.0/dtwclust/DESCRIPTION | 12 dtwclust-1.0.0/dtwclust/MD5 | 60 +-- dtwclust-1.0.0/dtwclust/NAMESPACE | 61 +-- dtwclust-1.0.0/dtwclust/R/DBA.R | 35 - dtwclust-1.0.0/dtwclust/R/NCCc.R | 6 dtwclust-1.0.0/dtwclust/R/SBD.R | 4 dtwclust-1.0.0/dtwclust/R/TADPole.R | 24 - dtwclust-1.0.0/dtwclust/R/dtw-lb.R | 20 - dtwclust-1.0.0/dtwclust/R/dtw2.R | 3 dtwclust-1.0.0/dtwclust/R/dtwclust-classes.R | 12 dtwclust-1.0.0/dtwclust/R/dtwclust-plot.R | 105 ++++- dtwclust-1.0.0/dtwclust/R/dtwclust.R | 237 +++++++++---- dtwclust-1.0.0/dtwclust/R/kcca-list.R |only dtwclust-1.0.0/dtwclust/R/lb-improved.R | 401 +++++++++------------- dtwclust-1.0.0/dtwclust/R/lb-keogh.R | 148 ++------ dtwclust-1.0.0/dtwclust/R/pkg.R | 235 ++++++------ dtwclust-1.0.0/dtwclust/R/reinterpolate.R | 2 dtwclust-1.0.0/dtwclust/R/shape-extraction.R | 2 dtwclust-1.0.0/dtwclust/R/utils.R | 342 ++++++++++++------ dtwclust-1.0.0/dtwclust/README.md | 36 + dtwclust-1.0.0/dtwclust/man/DBA.Rd | 8 dtwclust-1.0.0/dtwclust/man/SBD.Rd | 2 dtwclust-1.0.0/dtwclust/man/TADPole.Rd | 2 dtwclust-1.0.0/dtwclust/man/dtw_lb.Rd | 148 ++++---- dtwclust-1.0.0/dtwclust/man/dtwclust-class.Rd | 8 dtwclust-1.0.0/dtwclust/man/dtwclust-package.Rd | 13 dtwclust-1.0.0/dtwclust/man/dtwclust.Rd | 437 +++++++++++++----------- dtwclust-1.0.0/dtwclust/man/lb_improved.Rd | 3 dtwclust-1.0.0/dtwclust/man/lb_keogh.Rd | 3 dtwclust-1.0.0/dtwclust/man/plot-methods.Rd | 16 dtwclust-1.0.0/dtwclust/man/shape_extraction.Rd | 2 32 files changed, 1309 insertions(+), 1078 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 0.5 dated 2015-03-20 and 0.6 dated 2015-08-23
DESCRIPTION | 10 +- MD5 | 54 ++++++------- NAMESPACE | 6 + NEWS | 18 +++- R/base-pref-macros.R | 76 +++++++++---------- R/base-pref.r | 95 ++++++++++++++++-------- R/complex-pref.r | 35 ++++---- R/pred-succ.r | 29 +++---- R/pref-classes.r | 185 ++++++++++++++++++++++++++++++++++------------- R/pref-eval.r | 84 +++++++++++---------- R/rPref.r | 24 +++--- R/show-pref.r | 53 ++++++++----- R/visualize.r | 87 ++++++++++++++++------ inst/test/test-hasse.R | 8 +- inst/test/test-pref.r | 80 ++++++++++++++++++++ inst/test/test-strings.R | 3 man/base_pref.Rd | 86 +++++++++++++++------ man/base_pref_macros.Rd | 39 ++++++--- man/complex_pref.Rd | 27 +++--- man/get_btg.Rd | 56 ++++++++++---- man/get_hasse_diag.Rd | 8 +- man/plot_front.Rd | 10 +- man/pred_succ.Rd | 31 ++++--- man/psel.Rd | 74 +++++++++--------- man/rPref.Rd | 26 +++--- man/show.pref.Rd | 20 ++--- man/show.query.Rd | 6 - src/scalagon.h | 2 28 files changed, 786 insertions(+), 446 deletions(-)
Title: Stabilized Nearest Neighbor Classifier
Description: Implement K-nearest neighbor classifier, weighted nearest neighbor classifier, bagged nearest neighbor classifier, optimal weighted nearest neighbor classifier and stabilized nearest neighbor classifier, and perform model selection via 5 fold cross-validation for them. This package also provides functions for computing the classification error and classification instability of a classification procedure.
Author: Wei Sun, Xingye Qiao, and Guang Cheng
Maintainer: Wei Sun <sunweisurrey8@gmail.com>
Diff between snn versions 1.0 dated 2015-07-28 and 1.1 dated 2015-08-23
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/mybnn.R | 23 +++++++++++++++-------- R/myknn.R | 13 ++++++++++--- R/myownn.R | 23 +++++++++++++++-------- R/mysnn.R | 24 ++++++++++++++++-------- man/cv.tune.Rd | 2 +- man/mybnn.Rd | 2 +- man/myknn.Rd | 2 +- man/myownn.Rd | 2 +- man/mysnn.Rd | 2 +- man/mywnn.Rd | 2 +- man/snn-package.Rd | 2 +- 13 files changed, 79 insertions(+), 50 deletions(-)
Title: Using R to Run 'JAGS'
Description: Providing wrapper functions to implement Bayesian analysis in JAGS. Some major features include monitoring convergence of a MCMC model using Rubin and Gelman Rhat statistics, automatically running a MCMC model till it converges, and implementing parallel processing of a MCMC model for multiple chains.
Author: Yu-Sung Su <suyusung@tsinghua.edu.cn>,
Masanao Yajima <yajima@stat.ucla.edu>,
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between R2jags versions 0.5-6 dated 2015-04-21 and 0.5-7 dated 2015-08-23
CHANGELOG | 6 +++++ DESCRIPTION | 11 +++++---- MD5 | 10 ++++---- NAMESPACE | 9 +++++++ R/jags2.R | 62 +++++++++++++++++++++++++++---------------------------- R/jagsParallel.R | 38 +++++++++++++++++++++++++++++++-- 6 files changed, 92 insertions(+), 44 deletions(-)
Title: Graphical User Interface for Rprof()
Description: Show graphically the results of profiling R functions by tracking their execution time.
Author: Fernando de Villar<fdevillar@gmail.com> and Angel Rubio <arubio@ceit.es>
Maintainer: Fernando de Villar<fdevillar@gmail.com>
Diff between GUIProfiler versions 0.1.2 dated 2014-11-15 and 2.0.1 dated 2015-08-23
GUIProfiler-0.1.2/GUIProfiler/R/RRprofReport.r |only GUIProfiler-2.0.1/GUIProfiler/DESCRIPTION | 15 ++++++++------- GUIProfiler-2.0.1/GUIProfiler/MD5 | 14 +++++++------- GUIProfiler-2.0.1/GUIProfiler/NAMESPACE | 10 ++++++++-- GUIProfiler-2.0.1/GUIProfiler/R/RRprofReport.R |only GUIProfiler-2.0.1/GUIProfiler/man/GUIProfiler-package.Rd | 12 ++++++------ GUIProfiler-2.0.1/GUIProfiler/man/RRprofReport.Rd | 6 ++++-- GUIProfiler-2.0.1/GUIProfiler/man/RRprofStart.Rd | 2 +- GUIProfiler-2.0.1/GUIProfiler/man/RRprofStop.Rd | 2 +- 9 files changed, 35 insertions(+), 26 deletions(-)
Title: Empirical Likelihood Ratio for Censored/Truncated Data
Description: Empirical likelihood ratio tests for means/quantiles/hazards
from possibly censored and/or truncated data. Now does regression too.
This version contains some C code.
Author: Mai Zhou. (Art Owen for el.test(). Yifan Yang for C code.)
Maintainer: Mai Zhou <mai@ms.uky.edu>
Diff between emplik versions 1.0-1 dated 2015-04-28 and 1.0-2 dated 2015-08-23
DESCRIPTION | 6 - MD5 | 60 ++++++------- NAMESPACE | 3 man/BJnoint.Rd | 111 ++++++++++++------------- man/ROCnp.Rd | 6 + man/ROCnp2.Rd | 5 - man/RankRegTest.Rd | 150 +++++++++++++++++----------------- man/RankRegTestH.Rd | 4 man/WRegEst.Rd | 12 +- man/WRegTest.Rd | 7 + man/bjtest.Rd | 117 +++++++++++++------------- man/bjtest1d.Rd | 107 ++++++++++++------------ man/bjtestII.Rd | 6 - man/el.cen.EM.Rd | 9 -- man/el.cen.EM2.Rd | 6 + man/el.cen.test.Rd | 205 ++++++++++++++++++++++++----------------------- man/el.ltrc.EM.Rd | 213 +++++++++++++++++++++++++------------------------ man/el.test.Rd | 112 ++++++++++++------------- man/el.test.wt.Rd | 140 ++++++++++++++++---------------- man/el.test.wt2.Rd | 163 +++++++++++++++++++------------------ man/el.trun.test.Rd | 185 +++++++++++++++++++++--------------------- man/emplik-internal.Rd | 2 man/emplikH.disc.Rd | 3 man/emplikH.disc2.Rd | 6 - man/emplikH1.test.Rd | 162 ++++++++++++++++++------------------- man/emplikH2.test.Rd | 194 ++++++++++++++++++++++---------------------- man/emplikHs.disc2.Rd | 4 man/emplikHs.test2.Rd | 2 man/findUL.Rd | 5 - man/myeloma.Rd | 2 src/cumsumsurv.c | 2 31 files changed, 1023 insertions(+), 986 deletions(-)
Title: Dive Analysis and Calibration
Description: Utilities to represent, visualize, filter, analyse, and summarize
time-depth recorder (TDR) data. Miscellaneous functions for
handling location data are also provided.
Author: Sebastian P. Luque <spluque@gmail.com>
Maintainer: Sebastian P. Luque <spluque@gmail.com>
Diff between diveMove versions 1.3.9 dated 2014-02-20 and 1.4.0 dated 2015-08-23
diveMove-1.3.9/diveMove/README |only diveMove-1.4.0/diveMove/ChangeLog | 2 diveMove-1.4.0/diveMove/DESCRIPTION | 8 - diveMove-1.4.0/diveMove/MD5 | 108 +++++++++--------- diveMove-1.4.0/diveMove/NAMESPACE | 12 +- diveMove-1.4.0/diveMove/NEWS | 6 + diveMove-1.4.0/diveMove/R/AllClass.R | 2 diveMove-1.4.0/diveMove/R/AllGenerics.R | 2 diveMove-1.4.0/diveMove/R/AllMethod.R | 7 - diveMove-1.4.0/diveMove/R/austFilter.R | 2 diveMove-1.4.0/diveMove/R/bouts.R | 27 ++-- diveMove-1.4.0/diveMove/R/calibrate.R | 2 diveMove-1.4.0/diveMove/R/detDive.R | 2 diveMove-1.4.0/diveMove/R/detPhase.R | 2 diveMove-1.4.0/diveMove/R/distSpeed.R | 2 diveMove-1.4.0/diveMove/R/diveStats.R | 2 diveMove-1.4.0/diveMove/R/oneDiveStats.R | 2 diveMove-1.4.0/diveMove/R/plotTDR.R | 5 diveMove-1.4.0/diveMove/R/readLocs.R | 2 diveMove-1.4.0/diveMove/R/readTDR.R | 2 diveMove-1.4.0/diveMove/R/speedStats.R | 2 diveMove-1.4.0/diveMove/R/stampDive.R | 2 diveMove-1.4.0/diveMove/R/zoc.R | 2 diveMove-1.4.0/diveMove/R/zzz.R | 2 diveMove-1.4.0/diveMove/README.md |only diveMove-1.4.0/diveMove/build/vignette.rds |binary diveMove-1.4.0/diveMove/inst/doc/diveMove.Rnw | 2 diveMove-1.4.0/diveMove/inst/doc/diveMove.pdf |binary diveMove-1.4.0/diveMove/man/TDR-accessors.Rd | 11 + diveMove-1.4.0/diveMove/man/TDR-class.Rd | 2 diveMove-1.4.0/diveMove/man/TDRcalibrate-accessors.Rd | 2 diveMove-1.4.0/diveMove/man/TDRcalibrate-class.Rd | 2 diveMove-1.4.0/diveMove/man/austFilter.Rd | 2 diveMove-1.4.0/diveMove/man/bout-methods.Rd | 2 diveMove-1.4.0/diveMove/man/bout-misc.Rd | 2 diveMove-1.4.0/diveMove/man/bouts2MLE.Rd | 2 diveMove-1.4.0/diveMove/man/bouts2NLS.Rd | 2 diveMove-1.4.0/diveMove/man/calibrateDepth.Rd | 2 diveMove-1.4.0/diveMove/man/calibrateSpeed.Rd | 2 diveMove-1.4.0/diveMove/man/detDive-internal.Rd | 2 diveMove-1.4.0/diveMove/man/detPhase-internal.Rd | 2 diveMove-1.4.0/diveMove/man/distSpeed.Rd | 2 diveMove-1.4.0/diveMove/man/diveMove-internal.Rd | 2 diveMove-1.4.0/diveMove/man/diveMove-package.Rd | 2 diveMove-1.4.0/diveMove/man/diveStats.Rd | 2 diveMove-1.4.0/diveMove/man/dives.Rd | 2 diveMove-1.4.0/diveMove/man/extractDive-methods.Rd | 2 diveMove-1.4.0/diveMove/man/labDive-internal.Rd | 2 diveMove-1.4.0/diveMove/man/plotTDR-methods.Rd | 2 diveMove-1.4.0/diveMove/man/readLocs.Rd | 2 diveMove-1.4.0/diveMove/man/readTDR.Rd | 2 diveMove-1.4.0/diveMove/man/rqPlot.Rd | 2 diveMove-1.4.0/diveMove/man/sealLocs.Rd | 2 diveMove-1.4.0/diveMove/man/timeBudget-methods.Rd | 2 diveMove-1.4.0/diveMove/vignettes/Makefile | 2 diveMove-1.4.0/diveMove/vignettes/diveMove.Rnw | 2 56 files changed, 145 insertions(+), 127 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Bayesian inference for structure learning in undirected graphical models. The main target is to uncover complicated patterns in multivariate data wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.20 dated 2015-08-21 and 2.21 dated 2015-08-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 13 +++++++------ src/BDgraph.cpp | 18 ++++++++++-------- 4 files changed, 24 insertions(+), 21 deletions(-)
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files.
This attempts to provide a cleaner alternative to options().
Author: Sahil Seth [aut, cre],
Yihui Xie [ctb] (kable from knitr R/table.R)
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between params versions 0.2.4 dated 2015-08-14 and 0.2.5 dated 2015-08-22
params-0.2.4/params/build |only params-0.2.5/params/DESCRIPTION | 19 ++-- params-0.2.5/params/MD5 | 21 ++--- params-0.2.5/params/NAMESPACE | 3 params-0.2.5/params/NEWS.md | 5 + params-0.2.5/params/R/conf.R | 9 +- params-0.2.5/params/R/kable.R |only params-0.2.5/params/R/opts.R | 6 - params-0.2.5/params/R/pkg-opts.R | 15 ++- params-0.2.5/params/README.md | 156 +++++++++++++++----------------------- params-0.2.5/params/man/kable.Rd |only params-0.2.5/params/man/opts.Rd | 2 params-0.2.5/params/man/params.Rd | 18 +++- 13 files changed, 127 insertions(+), 127 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.3.2 dated 2015-07-15 and 1.3.3 dated 2015-08-22
DESCRIPTION | 6 ++--- MD5 | 21 +++++++++--------- NEWS | 7 ++++-- R/get_dataset.R | 15 +++++++++++-- R/get_download.R | 10 +++++++- R/print.dataset_list.R | 5 ++++ R/sysdata.rda |binary README.md | 3 +- inst/crystal.tlx |only man/get_dataset.Rd | 3 +- tests/testthat/test_neotoma.R | 42 ++++++++++++++++++------------------- tests/testthat/test_simple_paper.R | 6 ++--- 12 files changed, 74 insertions(+), 44 deletions(-)
Title: Modelling with Sparse And Dense Matrices
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between MatrixModels versions 0.4-0 dated 2015-01-14 and 0.4-1 dated 2015-08-22
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 11 ++++++----- R/modelMatrix.R | 14 ++++++-------- 4 files changed, 21 insertions(+), 22 deletions(-)
Title: Linear Time Series Analysis
Description: Methods of developing linear time series modelling.
Methods are given for loglikelihood computation, forecasting
and simulation.
Author: A.I. McLeod, Hao Yu, Zinovi Krougly
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between ltsa versions 1.4.4 dated 2012-12-14 and 1.4.5 dated 2015-08-22
DESCRIPTION | 15 ++++++++------- MD5 | 10 ++++++---- NAMESPACE | 3 ++- NEWS | 4 ++++ R/exactLoglikelihood.R |only man/exactLoglikelihood.Rd |only man/ltsa-package.Rd | 7 ++++--- 7 files changed, 24 insertions(+), 15 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.3 dated 2015-07-24 and 3.3.4 dated 2015-08-22
DESCRIPTION | 8 +- MD5 | 66 ++++++++++---------- NEWS | 46 +++++++++++++- R/ANOVAz2.R | 1 R/BoxPlot.R | 23 ++++--- R/CountAll.R | 9 +- R/Density.R | 24 ++++--- R/Help.R | 6 - R/Histogram.R | 24 ++++--- R/Merge.R | 7 +- R/Nest.R | 2 R/Read.R | 37 ++++++++--- R/Recode.R | 5 - R/Regression.R | 9 +- R/Subset.R | 6 + R/SummaryStats.R | 143 +++++++++++++++++++++----------------------- R/corCFA.R | 2 R/details.R | 85 ++++++++++++++------------ R/plt.zmain.R | 2 R/print.outall.r | 11 +++ R/reg.z1modelBasic.R | 7 +- R/reg.z3resfitResidual.R | 1 R/reg.z5Plot.R | 2 R/reg.zknitr.R | 152 ++++++++++++++++++++++++++++++++--------------- R/set.R | 14 ++++ R/ss.zfactor.R | 2 R/ss.znumeric.R | 16 +--- R/xP.R | 6 - R/zzz.R | 27 +++++--- man/ANOVA.Rd | 10 +-- man/Read.Rd | 9 +- man/Regression.Rd | 37 +++++++---- man/Write.Rd | 2 man/set.Rd | 18 +++++ 34 files changed, 509 insertions(+), 310 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-08 1.0.0
Title: Data Files and Functions Accompanying the Book "Bayesian Data
Analysis in Ecology using R, BUGS and Stan"
Description: Data files and functions accompanying the book Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt (2015) "Bayesian Data Analysis in Ecology using R, BUGS and Stan", Elsevier, New York.
Author: Fraenzi Korner-Nievergelt, Tobias Roth, Stefanie von Felten, Jerome Guelat, Bettina Almasi, Pius Korner-Nievergelt
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between blmeco versions 1.0 dated 2015-02-04 and 1.1 dated 2015-08-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 10 ++++++++-- 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.0-5 dated 2015-08-18 and 1.0-6 dated 2015-08-22
ChangeLog | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/ChangeLog | 13 +++++++++++++ inst/SVN_VERSION | 2 +- inst/doc/OGR_shape_encoding.pdf |binary man/writeOGR.Rd | 4 ++++ src/OGR_write.cpp | 19 ++++++++++++------- src/gdal-bindings.cpp | 9 +++++++++ 9 files changed, 64 insertions(+), 20 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 1.1 dated 2015-03-23 and 1.2 dated 2015-08-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 2 +- inst/NEWS.Rd | 9 ++++++++- inst/doc/PMCMR.Rnw | 6 +++--- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 4 ++-- vignettes/PMCMR.Rnw | 6 +++--- 8 files changed, 28 insertions(+), 21 deletions(-)
Title: Partial Least Squares and Principal Component Regression
Diff between pls versions 2.4-3 dated 2013-08-10 and 2.5-0 dated 2015-08-22
Description: Multivariate regression methods
Partial Least Squares Regression (PLSR), Principal Component
Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Author: Bjørn-Helge Mevik, Ron Wehrens and Kristian Hovde Liland
Maintainer: Bjørn-Helge Mevik
pls-2.4-3/pls/CHANGES |only
pls-2.5-0/pls/DESCRIPTION | 13 ++++-----
pls-2.5-0/pls/MD5 | 25 +++++++++++------
pls-2.5-0/pls/NAMESPACE | 14 +++++++--
pls-2.5-0/pls/R/crossval.R | 15 ++++------
pls-2.5-0/pls/R/cvsegments.R | 47 +++++++++++++++++++++++++++------
pls-2.5-0/pls/R/plots.R | 10 +++----
pls-2.5-0/pls/R/widekernelpls_NA.fit.R |only
pls-2.5-0/pls/build |only
pls-2.5-0/pls/inst |only
pls-2.5-0/pls/man/crossval.Rd | 4 +-
pls-2.5-0/pls/man/cvsegments.Rd | 28 ++++++++++++++++---
pls-2.5-0/pls/man/validationplot.Rd | 8 ++---
pls-2.5-0/pls/vignettes |only
14 files changed, 114 insertions(+), 50 deletions(-)
Title: Cross-Entropy R Package for Optimization
Description: Optimization solver based on the Cross-Entropy method.
Author: Tim Benham and Qibin Duan and Dirk P. Kroese and Benoit Liquet
Maintainer: Benoit Liquet <b.liquet@uq.edu.au>
Diff between CEoptim versions 1.0 dated 2015-02-26 and 1.1 dated 2015-08-22
DESCRIPTION | 10 - MD5 | 20 +-- NAMESPACE | 2 R/CEoptim.R | 86 ++++++++++----- R/print.CEoptim.R | 62 +++++++---- man/CEoptim.Rd | 281 +++++++++++++++++++++++++-------------------------- man/FitzHugh.Rd | 9 + man/dirichletrnd.Rd | 11 + man/lesmis.Rd | 6 + man/print.CEoptim.Rd | 24 ++++ man/yt.Rd | 6 + 11 files changed, 315 insertions(+), 202 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-17 0.9.7.5
Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as
on a telephone keypad. When converting letters to numbers, a character
vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F"
becoming 3, etc. When converting numbers to letters, a character vector is
returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and
"C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between phonenumber versions 0.2.0 dated 2015-08-01 and 0.2.1 dated 2015-08-22
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/letterToNumber.R | 45 ++++++++++++-------------- R/numberToLetter.R | 57 ++++++++++++++------------------- README.md | 60 ++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/phonenumber.Rmd | 3 + inst/doc/phonenumber.html | 4 +- tests/testthat/test-numberToLetter.R | 1 vignettes/phonenumber.Rmd | 3 + 10 files changed, 95 insertions(+), 102 deletions(-)
Title: Predict Gender from Names Using Historical Data
Description: Encodes gender based on names and dates of birth using historical
datasets. By using these datasets instead of lists of male and female names,
this package is able to more accurately guess the gender of a name, and it
is able to report the probability that a name was male or female.
Author: Lincoln Mullen [aut, cre],
Cameron Blevins [ctb],
Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between gender versions 0.4.3 dated 2014-12-23 and 0.5.0 dated 2015-08-22
gender-0.4.3/gender/man/gender_demo.Rd |only gender-0.4.3/gender/man/gender_genderize.Rd |only gender-0.4.3/gender/man/gender_ipums_usa.Rd |only gender-0.4.3/gender/man/gender_kantrowitz.Rd |only gender-0.4.3/gender/man/gender_ssa.Rd |only gender-0.4.3/gender/man/get_correction_factors.Rd |only gender-0.5.0/gender/DESCRIPTION | 22 gender-0.5.0/gender/MD5 | 72 gender-0.5.0/gender/NAMESPACE | 8 gender-0.5.0/gender/NEWS | 10 gender-0.5.0/gender/R/gender-demo.R | 108 - gender-0.5.0/gender/R/gender-genderize.R | 42 gender-0.5.0/gender/R/gender-ipums-usa.R | 108 - gender-0.5.0/gender/R/gender-kantrowitz.R | 33 gender-0.5.0/gender/R/gender-napp.R |only gender-0.5.0/gender/R/gender-package.r | 10 gender-0.5.0/gender/R/gender-ssa.R | 158 - gender-0.5.0/gender/R/gender.R | 137 + gender-0.5.0/gender/R/gender_df.R |only gender-0.5.0/gender/R/install-genderdata-package.R | 44 gender-0.5.0/gender/R/sysdata.rda |binary gender-0.5.0/gender/README.md | 236 -- gender-0.5.0/gender/build/vignette.rds |binary gender-0.5.0/gender/inst/CITATION | 28 gender-0.5.0/gender/inst/doc/predicting-gender.R | 92 - gender-0.5.0/gender/inst/doc/predicting-gender.Rmd | 178 +- gender-0.5.0/gender/inst/doc/predicting-gender.html | 801 ++-------- gender-0.5.0/gender/man/check_genderdata_package.Rd | 2 gender-0.5.0/gender/man/gender-package.Rd |only gender-0.5.0/gender/man/gender.Rd | 81 - gender-0.5.0/gender/man/gender_df.Rd |only gender-0.5.0/gender/man/install_genderdata_package.Rd | 2 gender-0.5.0/gender/tests/run-all.R | 2 gender-0.5.0/gender/tests/testthat/sample-data.r | 7 gender-0.5.0/gender/tests/testthat/test-argument-validation.r | 20 gender-0.5.0/gender/tests/testthat/test-demo.r | 2 gender-0.5.0/gender/tests/testthat/test-gender_df.R |only gender-0.5.0/gender/tests/testthat/test-genderize.R | 15 gender-0.5.0/gender/tests/testthat/test-ipums.r | 8 gender-0.5.0/gender/tests/testthat/test-kantrowitz.r | 12 gender-0.5.0/gender/tests/testthat/test-napp.r |only gender-0.5.0/gender/tests/testthat/test-ssa.r | 5 gender-0.5.0/gender/vignettes/predicting-gender.Rmd | 180 +- 43 files changed, 981 insertions(+), 1442 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.8 dated 2015-07-22 and 0.9 dated 2015-08-22
DESCRIPTION | 8 - MD5 | 46 +++---- NAMESPACE | 5 R/auxilaryfunctions.R | 255 +++++++++++++++++++++++++---------------- R/boral.jags.R | 195 ++++++++++++++----------------- inst/NEWS.Rd | 93 +++++++------- man/boral-package.Rd | 23 --- man/boral.Rd | 55 ++++---- man/calc.condlogLik.Rd | 23 +-- man/calc.logLik.lv0.Rd | 23 +-- man/calc.marglogLik.Rd | 26 +--- man/create.life.Rd | 69 +++++++---- man/ds.residuals.Rd | 3 man/fitted.boral.Rd | 3 man/get.enviro.cor.Rd | 23 ++- man/get.hpdintervals.Rd | 10 - man/get.measures.Rd | 8 - man/get.more.measures.Rd | 11 - man/get.residual.cor.Rd | 17 +- man/lvsplot.Rd | 37 +++-- man/make.jagsboralmodel.Rd | 37 ++--- man/make.jagsboralnullmodel.Rd | 19 +-- man/plot.boral.Rd | 18 +- man/summary.boral.Rd | 3 24 files changed, 529 insertions(+), 481 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett@lshtm.ac.uk>
Diff between smcfcs versions 1.0.0 dated 2015-05-12 and 1.1.0 dated 2015-08-21
DESCRIPTION | 8 +- MD5 | 24 +++--- NAMESPACE | 1 R/smcfcs.r | 147 +++++++++++++++++++++++++++++++++--------- build/vignette.rds |binary data/ex_compet.rda |binary data/ex_coxquad.rda |binary data/ex_lininter.rda |binary data/ex_linquad.rda |binary data/ex_logisticquad.rda |binary man/ex_lininter.Rd | 1 man/smcfcs.Rd | 30 ++++---- vignettes/smcfcs-vignette.Rmd | 4 - 13 files changed, 154 insertions(+), 61 deletions(-)
Title: Option Pricing and Estimation of Financial Models in R
Description: Companion package to the book Option Pricing and
Estimation of Financial Models in R, Wiley, Chichester. ISBN:
978-0-470-74584-7.
Author: Stefano Maria Iacus
Maintainer: Stefano Maria Iacus <stefano.iacus@unimi.it>
Diff between opefimor versions 1.1 dated 2012-12-30 and 1.2 dated 2015-08-21
DESCRIPTION | 11 ++++++----- MD5 | 4 +++- build |only inst/doc/opefimor.R |only 4 files changed, 9 insertions(+), 6 deletions(-)
Title: Nash Optimal Party Positions
Description: Estimation of party/candidate ideological positions
that correspond to a Nash equilibrium along a
one-dimensional space.
Author: Luigi Curini, Stefano M. Iacus
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between nopp versions 1.0.4 dated 2014-08-25 and 1.0.6 dated 2015-08-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 4 ++++ R/zzz.R | 1 - 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Iterated Function Systems
Description: Iterated Function Systems Estimator.
Author: S. M. Iacus
Maintainer: S. M. Iacus <stefano.iacus@unimi.it>
Diff between ifs versions 0.1.4 dated 2012-12-10 and 0.1.5 dated 2015-08-21
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- NAMESPACE | 4 +++- 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Tools for Selective Inference
Description: New tools for inference after selection, for use with forward stepwise regression, least angle regression, the lasso, and the many normal means problem. This R code was developed in coordination with an analogous Python package developed by Jonathan Taylor and others, see http://github.com/selective-inference/selective-inference.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.0.1 dated 2015-08-21 and 1.0.2 dated 2015-08-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/funs.fixed.R | 12 ++++++------ man/fixedLassoInf.Rd | 22 +++++++++------------- man/fsInf.Rd | 10 +++++----- man/larInf.Rd | 10 +++++----- 6 files changed, 33 insertions(+), 37 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Analise Multivariada (Brazilian Portuguese)
Description: Pacote para Analise Multivariada, que possui funcoes que executam Analise de Correspondencia Simples (CA) e Multipla (MCA), Analise de Componentes Principais (PCA), Analise de Multiplos Fatores (MFA) para dados Quantitativos, Qualitativos, Frequencia (MFACT) e dados Mistos. Tambem possui outras funcoes uteis para a Analise Multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.2 dated 2015-06-23 and 1.3 dated 2015-08-21
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 6 +++++- R/Biplot.R | 18 ++++++++++++------ R/LocLab.R |only R/Plot.CA.R | 12 ++++++++---- R/Plot.MFA.R | 15 ++++++++++----- R/Plot.PCA.R | 8 +++++--- man/LocLab.Rd |only man/MVar.pt-package.Rd | 2 +- man/NormData.Rd | 4 ++-- man/Plot.CA.Rd | 4 ++-- man/Plot.MFA.Rd | 4 ++-- man/Plot.PCA.Rd | 4 ++-- 14 files changed, 67 insertions(+), 44 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Package DoE.base creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 0.27 dated 2015-03-28 and 0.27-1 dated 2015-08-21
DESCRIPTION | 12 ++++---- MD5 | 21 ++++++++------ NAMESPACE | 3 +- R/GRind.R | 16 +++++++---- R/SCFTs.R |only R/planor2design.r | 2 - R/print.GRind.R |only inst/NEWS | 9 ++++++ man/DoE.base-package.Rd | 8 ++--- man/GRind.Rd |only man/generalized.word.length.Rd | 59 ++++------------------------------------- man/show.oas.Rd | 6 ++-- tests/test_colorder.Rout.save | 16 +++++++++-- 13 files changed, 68 insertions(+), 84 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Bayesian inference for structure learning in undirected graphical models. The main target is to uncover complicated patterns in multivariate data wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.19 dated 2015-06-16 and 2.20 dated 2015-08-21
DESCRIPTION | 10 - MD5 | 40 ++-- NAMESPACE | 12 - NEWS | 3 R/bdgraph.R | 44 +++- R/bdgraph.npn.R | 10 - R/bdgraph.sim.R | 14 - R/compare.R | 2 R/phat.R | 6 R/plotcoda.R | 4 R/plotroc.R | 14 - R/prob.R | 28 +-- build/vignette.rds |binary man/bdgraph.Rd | 12 - man/bdgraph.sim.Rd | 2 man/compare.Rd | 2 man/plot.simulate.Rd | 10 - man/plotroc.Rd | 2 man/print.simulate.Rd | 10 - man/prob.Rd | 2 src/BDgraph.cpp | 458 ++++++++++++++++++++++++++++++++++++++++++++++++-- 21 files changed, 579 insertions(+), 106 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1 dated 2015-05-04 and 1.1.1 dated 2015-08-21
DESCRIPTION | 16 +++++++------- MD5 | 18 ++++++++-------- NAMESPACE | 11 +++++++++ R/vdg-package.R | 4 +++ build/vignette.rds |binary inst/doc/vdg.R | 26 +++++++++++------------ inst/doc/vdg.Rnw | 59 ++++++++++++++++++++++++++--------------------------- inst/doc/vdg.pdf |binary vignettes/vdg.Rnw | 59 ++++++++++++++++++++++++++--------------------------- vignettes/vdg.bib | 34 ++++++++++++++++++------------ 10 files changed, 124 insertions(+), 103 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams
(q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler).
An implementation of soundex is provided as well. Distances can be computed
between character vectors while taking proper care of encoding or between
integer vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.2 dated 2015-06-24 and 0.9.3 dated 2015-08-21
DESCRIPTION | 14 +- MD5 | 64 ++++++------ NAMESPACE | 8 + NEWS | 9 + R/amatch.R | 202 ++++++++++++++++++++++++++++++-------- R/doc_metrics.R | 47 +++++--- R/doc_parallel.R | 31 +++-- R/qgrams.R | 55 ++++++++-- R/seqdist.R |only R/stringdist.R | 188 +++++++++++++++++++++++------------ R/stringsim.R | 65 +++++++++++- R/utils.R | 25 ++++ man/amatch.Rd | 84 +++++++++------ man/qgrams.Rd | 2 man/seq_amatch.Rd |only man/seq_dist.Rd |only man/seq_qgrams.Rd |only man/seq_sim.Rd |only man/stringdist-metrics.Rd | 47 +++++--- man/stringdist-package.Rd | 41 +++++-- man/stringdist-parallelization.Rd | 29 +++-- man/stringdist.Rd | 85 +++++++++------ man/stringsim.Rd | 2 src/Rstringdist.c | 78 ++++++++++++-- src/dl.c | 8 - src/lv.c | 13 +- src/osa.c | 8 - src/qgram.c | 14 -- src/soundex.c | 4 src/utf8ToInt.c | 91 ++++++++++++----- src/utils.h | 5 tests/testthat/testAmatch.R | 22 ++++ tests/testthat/testQgrams.R | 11 ++ tests/testthat/testSeqDist.R |only tests/testthat/testStringdist.R | 35 ++++++ tests/testthat/testStringsim.R | 30 ++++- 36 files changed, 949 insertions(+), 368 deletions(-)
Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for
Stochastic Differential Equations With R Examples, ISBN
978-0-387-75838-1, Springer, NY.
Author: Stefano Maria Iacus
Maintainer: Stefano Maria Iacus <stefano.iacus@unimi.it>
Diff between sde versions 2.0.13 dated 2014-08-25 and 2.0.14 dated 2015-08-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- build/vignette.rds |binary inst/doc/sde.errata.pdf |binary 5 files changed, 14 insertions(+), 9 deletions(-)
More information about searchConsoleR at CRAN
Permanent link
Title: Analysis of Health-Related Quality of Life in Oncology
Description: To generate the scores of the EORTC QLQ-C30 questionnaire and supplementary modules and to determine the time to health-related quality of life score deterioration in longitudinal analysis.
Author: Amelie Anota
Maintainer: Amelie Anota <aanota@chu-besancon.fr>
Diff between QoLR versions 1.0.1 dated 2015-07-28 and 1.0.2 dated 2015-08-21
DESCRIPTION | 8 +-- MD5 | 30 ++++++----- R/TTD.R | 20 +++---- R/TUDD.R | 20 +++---- build/vignette.rds |binary data/dataqol.rda |binary data/dataqol1.rda |only data/dataqol2.rda |only inst/doc/QoLR.Rmd | 138 +++++++++++++++++----------------------------------- inst/doc/QoLR.html | 75 +++++++++++++++------------- man/QoLR-package.Rd | 4 - man/TTD.Rd | 49 ++++++------------ man/TUDD.Rd | 49 ++++++------------ man/dataqol1.Rd |only man/dataqol2.Rd |only man/plotTTD.Rd | 43 ++++------------ man/write.TTD.Rd | 26 +-------- vignettes/QoLR.Rmd | 138 +++++++++++++++++----------------------------------- 18 files changed, 227 insertions(+), 373 deletions(-)
Title: Parametric Time Warping
Description: Parametric Time Warping aligns patterns, i.e. it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation). Both
warping of peak profiles and of peak lists are supported.
Author: Jan Gerretzen <j.gerretzen@science.ru.nl>, Paul Eilers
<p.eilers@erasmusmc.nl>, Hans Wouters, Tom Bloemberg
<t.bloemberg@science.ru.nl>, Ron Wehrens <ron.wehrens@gmail.com>
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ptw versions 1.9-10 dated 2015-07-01 and 1.9-11 dated 2015-08-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/stickPTW.Rnw | 2 +- inst/doc/stickPTW.pdf |binary vignettes/stickPTW.Rnw | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-)
Title: A Package for Graphical Modelling in R
Diff between gRbase versions 1.7-0.1 dated 2014-03-23 and 1.7-1 dated 2015-08-21
Description: The gRbase package provides general features
which are used by other graphical modelling packages, in particular
by the packages gRain, gRim and gRc.
gRbase contains several datasets relevant for use in connection with
graphical models. Almost all datasets used in the book Graphical
Models with R (2012) are contained in gRbase.
gRbase implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph
algorithms are:
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junctionTree.
gRbase facilitates array operations,
gRbase implements functions for testing for conditional independence.
gRbase illustrates how hierarchical log-linear models (hllm) may be
implemented and describes concept of gmData (graphical meta
data). These features, however, are not maintained anymore and
remains in gRbase only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The gRbase Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE Proper functionality of gRbase requires that the packages graph,
Rgraphviz and RBGL are installed from bioconductor; for
installation instructions please refer to the webpage given below.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRbase-1.7-0.1/gRbase/R/ZZOLD-gRbase.R |only
gRbase-1.7-0.1/gRbase/R/graph-representations.R |only
gRbase-1.7-0.1/gRbase/gRbase-Ex.R |only
gRbase-1.7-0.1/gRbase/inst/doc/gRbase-arrayops1.R |only
gRbase-1.7-0.1/gRbase/inst/doc/gRbase-arrayops1.Rnw |only
gRbase-1.7-0.1/gRbase/inst/doc/gRbase-arrayops1.pdf |only
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gRbase-1.7-0.1/gRbase/src/arrayBasic.cpp |only
gRbase-1.7-0.1/gRbase/src/arrayOps.cpp |only
gRbase-1.7-0.1/gRbase/src/arrayOps.h |only
gRbase-1.7-0.1/gRbase/src/arrayPerm.cpp |only
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gRbase-1.7-0.1/gRbase/src/propagate.cpp |only
gRbase-1.7-0.1/gRbase/src/rowmat2list.cpp |only
gRbase-1.7-0.1/gRbase/src/sparseM-utilities.cpp |only
gRbase-1.7-0.1/gRbase/src/topoSortMAT.cpp |only
gRbase-1.7-0.1/gRbase/src/triangulateMAT.cpp |only
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gRbase-1.7-0.1/gRbase/vignettes/gRbase-arrayops2b.Rnw |only
gRbase-1.7-1/gRbase/ChangeLog | 239 +-
gRbase-1.7-1/gRbase/DESCRIPTION | 26
gRbase-1.7-1/gRbase/MD5 | 143 -
gRbase-1.7-1/gRbase/NAMESPACE | 107 -
gRbase-1.7-1/gRbase/R/RcppExports.R | 248 +-
gRbase-1.7-1/gRbase/R/array-addon.R |only
gRbase-1.7-1/gRbase/R/array-parray.R | 69
gRbase-1.7-1/gRbase/R/array-table-operations.R | 252 +-
gRbase-1.7-1/gRbase/R/c-arrayops.R | 110 -
gRbase-1.7-1/gRbase/R/c-combnPrimR.R | 4
gRbase-1.7-1/gRbase/R/c-setops.R | 4
gRbase-1.7-1/gRbase/R/gRbase-utilities-FIXME-cleanup.R | 55
gRbase-1.7-1/gRbase/R/graph-algo-mcs.R | 749 -------
gRbase-1.7-1/gRbase/R/graph-algo-moralize.R | 42
gRbase-1.7-1/gRbase/R/graph-algo-rip.R | 21
gRbase-1.7-1/gRbase/R/graph-algo-triangulate.R | 47
gRbase-1.7-1/gRbase/R/graph-coerce.R | 427 +++
gRbase-1.7-1/gRbase/R/graph-create-ugdag.R | 171 -
gRbase-1.7-1/gRbase/R/graph-properties.R | 229 +-
gRbase-1.7-1/gRbase/R/graph-querygraph.R | 28
gRbase-1.7-1/gRbase/R/graph-utilities.R | 161 -
gRbase-1.7-1/gRbase/R/processFormula.R | 38
gRbase-1.7-1/gRbase/R/tableInterface.R |only
gRbase-1.7-1/gRbase/R/yyOLD-gRbase.R |only
gRbase-1.7-1/gRbase/build/vignette.rds |binary
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gRbase-1.7-1/gRbase/inst/doc/gRbase-graphs.Rnw | 302 +-
gRbase-1.7-1/gRbase/inst/doc/gRbase-graphs.pdf |binary
gRbase-1.7-1/gRbase/inst/include/gRbase.h | 13
gRbase-1.7-1/gRbase/inst/include/gRbase_RcppExports.h | 617 +++++
gRbase-1.7-1/gRbase/inst/include/gRbase_typedefs.h | 1
gRbase-1.7-1/gRbase/man/GraphAlgo-coerce.Rd | 62
gRbase-1.7-1/gRbase/man/GraphAlgo-is-graph.Rd | 30
gRbase-1.7-1/gRbase/man/GraphAlgo-triangulate.Rd | 5
gRbase-1.7-1/gRbase/man/arraypack-internal.Rd |only
gRbase-1.7-1/gRbase/man/gRbase-internal.Rd | 42
gRbase-1.7-1/gRbase/man/gRbase-utilities.Rd | 2
gRbase-1.7-1/gRbase/man/gRbase.Rd | 20
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gRbase-1.7-1/gRbase/man/tabMult.Rd |only
gRbase-1.7-1/gRbase/man/table-operations.Rd | 73
gRbase-1.7-1/gRbase/man/ugdag.Rd | 77
gRbase-1.7-1/gRbase/src/RcppExports.cpp | 1815 +++++++++++------
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gRbase-1.7-1/gRbase/src/allSubsets.cpp | 65
gRbase-1.7-1/gRbase/src/c-setops.c | 4
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gRbase-1.7-1/gRbase/src/mcsMAT2.h |only
gRbase-1.7-1/gRbase/src/names2pairsM.cpp |only
gRbase-1.7-1/gRbase/src/solveSPD.cpp | 14
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104 files changed, 3954 insertions(+), 2862 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each set of
nested blocks optimized within the levels of any existing higher-level blocks.
Block sizes are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.6 dated 2015-05-06 and 1.7 dated 2015-08-21
DESCRIPTION | 8 MD5 | 12 - NAMESPACE | 2 R/blocks.r | 525 ++++++++++++++++++++++++++++------------------------- R/upper_bounds.r | 10 - build/vignette.rds |binary man/blocks.Rd | 28 +- 7 files changed, 314 insertions(+), 271 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.11 dated 2015-05-15 and 0.99.12 dated 2015-08-21
DescTools-0.99.11/DescTools/R/AUC.R |only DescTools-0.99.11/DescTools/R/AddMonths.R |only DescTools-0.99.11/DescTools/R/Agree.R |only DescTools-0.99.11/DescTools/R/AllDuplicated.R |only DescTools-0.99.11/DescTools/R/AndersonDarlingTest.R |only DescTools-0.99.11/DescTools/R/AscToChar.R |only DescTools-0.99.11/DescTools/R/Assocs.R |only DescTools-0.99.11/DescTools/R/Atkinson.R |only DescTools-0.99.11/DescTools/R/AxisBreak.R |only DescTools-0.99.11/DescTools/R/BartelsRankTest.R |only DescTools-0.99.11/DescTools/R/BinToDec.R |only DescTools-0.99.11/DescTools/R/BinomCI.R |only DescTools-0.99.11/DescTools/R/BinomDiffCI.R |only DescTools-0.99.11/DescTools/R/BinomRatioCI.R |only DescTools-0.99.11/DescTools/R/BoxCox.R |only DescTools-0.99.11/DescTools/R/BoxCoxInv.R |only DescTools-0.99.11/DescTools/R/BoxCoxLambda.R |only DescTools-0.99.11/DescTools/R/BoxedText.R |only DescTools-0.99.11/DescTools/R/BreslowDayTest.R |only DescTools-0.99.11/DescTools/R/BubbleLegend.R |only DescTools-0.99.11/DescTools/R/CCC.R |only DescTools-0.99.11/DescTools/R/Canvas.R |only DescTools-0.99.11/DescTools/R/CartToPol.R |only DescTools-0.99.11/DescTools/R/CartToSph.R |only DescTools-0.99.11/DescTools/R/CatTable.R |only DescTools-0.99.11/DescTools/R/CharToAsc.R |only DescTools-0.99.11/DescTools/R/ChooseColorDlg.R |only DescTools-0.99.11/DescTools/R/ClipToVect.R |only DescTools-0.99.11/DescTools/R/Clockwise.R |only DescTools-0.99.11/DescTools/R/Closest.R |only DescTools-0.99.11/DescTools/R/Coalesce.R |only DescTools-0.99.11/DescTools/R/CochranArmitageTest.R |only DescTools-0.99.11/DescTools/R/CochranQTest.R |only DescTools-0.99.11/DescTools/R/CochranQTest.default.R |only DescTools-0.99.11/DescTools/R/CochranQTest.formula.R |only DescTools-0.99.11/DescTools/R/CoefVar.R |only DescTools-0.99.11/DescTools/R/CohenD.R |only DescTools-0.99.11/DescTools/R/CohenKappa.R |only DescTools-0.99.11/DescTools/R/ColToGray.R |only DescTools-0.99.11/DescTools/R/ColToGrey.R |only 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DescTools-0.99.11/DescTools/R/WrdPlot.R |only DescTools-0.99.11/DescTools/R/WrdR.R |only DescTools-0.99.11/DescTools/R/WrdSetFont.R |only DescTools-0.99.11/DescTools/R/WrdTable.Freq.R |only DescTools-0.99.11/DescTools/R/WrdTable.R |only DescTools-0.99.11/DescTools/R/WrdTable.default.R |only DescTools-0.99.11/DescTools/R/WrdTable.ftable.R |only DescTools-0.99.11/DescTools/R/WrdText.R |only DescTools-0.99.11/DescTools/R/WrdUpdateBookmark.R |only DescTools-0.99.11/DescTools/R/XLGetRange.R |only DescTools-0.99.11/DescTools/R/XLGetWorkbook.R |only DescTools-0.99.11/DescTools/R/XLKill.R |only DescTools-0.99.11/DescTools/R/XLView.R |only DescTools-0.99.11/DescTools/R/Year.R |only DescTools-0.99.11/DescTools/R/YearDay.R |only DescTools-0.99.11/DescTools/R/YearMonth.R |only DescTools-0.99.11/DescTools/R/YuenTTest.R |only DescTools-0.99.11/DescTools/R/YuenTTest.default.R |only DescTools-0.99.11/DescTools/R/YuenTTest.formula.R |only DescTools-0.99.11/DescTools/R/YuleQ.R |only 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DescTools-0.99.11/DescTools/R/pRevGumbel.R |only DescTools-0.99.11/DescTools/R/plot.Conf.R |only DescTools-0.99.11/DescTools/R/plot.Lc.R |only DescTools-0.99.11/DescTools/R/plot.Lclist.R |only DescTools-0.99.11/DescTools/R/plot.PostHocTest.R |only DescTools-0.99.11/DescTools/R/plot.bagplot.R |only DescTools-0.99.11/DescTools/R/power.chisq.test.R |only DescTools-0.99.11/DescTools/R/print.Assocs.R |only DescTools-0.99.11/DescTools/R/print.Conf.R |only DescTools-0.99.11/DescTools/R/print.CorPolychor.R |only DescTools-0.99.11/DescTools/R/print.DunnTest.R |only DescTools-0.99.11/DescTools/R/print.Freq.R |only DescTools-0.99.11/DescTools/R/print.HoeffD.R |only DescTools-0.99.11/DescTools/R/print.ICC.R |only DescTools-0.99.11/DescTools/R/print.PostHocTest.R |only DescTools-0.99.11/DescTools/R/print.mtest.R |only DescTools-0.99.11/DescTools/R/qBenf.R |only DescTools-0.99.11/DescTools/R/qRevGumbel.R |only DescTools-0.99.11/DescTools/R/qRevGumbelExp.R |only DescTools-0.99.11/DescTools/R/rBenf.R |only DescTools-0.99.11/DescTools/R/rRevGumbel.R |only DescTools-0.99.11/DescTools/R/reorder.factor.R |only DescTools-0.99.11/DescTools/R/split.formula.R |only DescTools-0.99.11/DescTools/R/z%()%.R |only DescTools-0.99.11/DescTools/R/z%(]%.R |only DescTools-0.99.11/DescTools/R/z%)(%.R |only DescTools-0.99.11/DescTools/R/z%)[%.R |only DescTools-0.99.11/DescTools/R/z%[)%.R |only DescTools-0.99.11/DescTools/R/z%[]%.R |only DescTools-0.99.11/DescTools/R/z%](%.R |only DescTools-0.99.11/DescTools/R/z%][%.R |only DescTools-0.99.11/DescTools/R/z%c%.R |only DescTools-0.99.11/DescTools/R/z%like%.R |only DescTools-0.99.11/DescTools/R/z%nin%.R |only DescTools-0.99.11/DescTools/R/z%overlaps%.R |only DescTools-0.99.11/DescTools/inst/doc/DescTools.Rnw |only DescTools-0.99.11/DescTools/inst/doc/DescTools.pdf |only DescTools-0.99.11/DescTools/man/DescTools-internal.Rd |only DescTools-0.99.11/DescTools/man/Explore.Rd |only DescTools-0.99.11/DescTools/man/GetAllSubsets.Rd |only DescTools-0.99.11/DescTools/man/GetPairs.Rd |only DescTools-0.99.11/DescTools/man/Mbind.Rd |only DescTools-0.99.11/DescTools/man/PlotDotCI.Rd |only DescTools-0.99.11/DescTools/man/PlotDotCIp.Rd |only DescTools-0.99.11/DescTools/vignettes/DescTools.Rnw |only DescTools-0.99.12/DescTools/DESCRIPTION | 14 DescTools-0.99.12/DescTools/MD5 | 709 +--------- DescTools-0.99.12/DescTools/NAMESPACE | 44 DescTools-0.99.12/DescTools/NEWS | 186 +- DescTools-0.99.12/DescTools/R/DescTools.r |only DescTools-0.99.12/DescTools/R/FastDesc.R |only DescTools-0.99.12/DescTools/R/PageDF.r |only DescTools-0.99.12/DescTools/R/RcppExports.R |only DescTools-0.99.12/DescTools/R/test.DescTools.r |only DescTools-0.99.12/DescTools/build/vignette.rds |binary DescTools-0.99.12/DescTools/data/day.abb.rda |binary DescTools-0.99.12/DescTools/data/day.name.rda |binary DescTools-0.99.12/DescTools/data/hblue.rda |binary DescTools-0.99.12/DescTools/data/hecru.rda |binary DescTools-0.99.12/DescTools/data/hgreen.rda |binary DescTools-0.99.12/DescTools/data/horange.rda |binary DescTools-0.99.12/DescTools/data/hred.rda |binary DescTools-0.99.12/DescTools/data/hyellow.rda |binary DescTools-0.99.12/DescTools/data/wdConst.rda |binary DescTools-0.99.12/DescTools/inst/doc/Combinatorics.Rnw |only DescTools-0.99.12/DescTools/inst/doc/Combinatorics.pdf |only DescTools-0.99.12/DescTools/inst/doc/DescToolsCompanion.pdf |binary DescTools-0.99.12/DescTools/inst/doc/TablesInR.Rnw |only DescTools-0.99.12/DescTools/inst/doc/TablesInR.pdf |only DescTools-0.99.12/DescTools/man/Abind.Rd |only DescTools-0.99.12/DescTools/man/AscToChar.Rd | 2 DescTools-0.99.12/DescTools/man/BinTree.Rd |only DescTools-0.99.12/DescTools/man/BinomCI.Rd | 85 - DescTools-0.99.12/DescTools/man/CombPairs.Rd |only DescTools-0.99.12/DescTools/man/Conf.Rd | 30 DescTools-0.99.12/DescTools/man/CorPolychor.Rd | 8 DescTools-0.99.12/DescTools/man/Desc.Date.Rd | 18 DescTools-0.99.12/DescTools/man/Desc.data.frame.Rd | 9 DescTools-0.99.12/DescTools/man/Desc.factor.Rd | 30 DescTools-0.99.12/DescTools/man/Desc.integer.Rd | 40 DescTools-0.99.12/DescTools/man/Desc.logical.Rd | 12 DescTools-0.99.12/DescTools/man/Desc.numeric.Rd | 34 DescTools-0.99.12/DescTools/man/Desc.table.Rd | 45 DescTools-0.99.12/DescTools/man/DescTools-package.Rd | 45 DescTools-0.99.12/DescTools/man/DescWrd.Rd | 51 DescTools-0.99.12/DescTools/man/DoCall.Rd |only DescTools-0.99.12/DescTools/man/DunnTest.Rd | 5 DescTools-0.99.12/DescTools/man/DunnettTest.Rd | 9 DescTools-0.99.12/DescTools/man/Eps.Rd |only DescTools-0.99.12/DescTools/man/ErrBars.Rd | 16 DescTools-0.99.12/DescTools/man/Format.Rd | 73 - DescTools-0.99.12/DescTools/man/Frac.Rd | 9 DescTools-0.99.12/DescTools/man/Freq.Rd | 30 DescTools-0.99.12/DescTools/man/GCD.Rd | 26 DescTools-0.99.12/DescTools/man/Gini.Rd | 48 DescTools-0.99.12/DescTools/man/HotellingsT.Rd | 23 DescTools-0.99.12/DescTools/man/HuberM.Rd | 10 DescTools-0.99.12/DescTools/man/Label.Rd | 10 DescTools-0.99.12/DescTools/man/Large.Rd | 2 DescTools-0.99.12/DescTools/man/Logit.Rd | 2 DescTools-0.99.12/DescTools/man/MosesTest.Rd | 28 DescTools-0.99.12/DescTools/man/NemenyiTest.Rd | 3 DescTools-0.99.12/DescTools/man/OddsRatio.Rd | 7 DescTools-0.99.12/DescTools/man/PDFManual.Rd |only DescTools-0.99.12/DescTools/man/PairApply.Rd | 2 DescTools-0.99.12/DescTools/man/PercTable.Rd | 56 DescTools-0.99.12/DescTools/man/Permn.Rd | 46 DescTools-0.99.12/DescTools/man/PlotArea.Rd | 10 DescTools-0.99.12/DescTools/man/PlotDesc.Rd | 48 DescTools-0.99.12/DescTools/man/PlotDot.Rd | 16 DescTools-0.99.12/DescTools/man/PlotECDF.Rd |only DescTools-0.99.12/DescTools/man/PlotFdist.Rd | 20 DescTools-0.99.12/DescTools/man/PlotHorizBar.Rd | 11 DescTools-0.99.12/DescTools/man/PlotMosaic.Rd |only DescTools-0.99.12/DescTools/man/PlotMultiDens.Rd | 3 DescTools-0.99.12/DescTools/man/PlotViolin.Rd | 5 DescTools-0.99.12/DescTools/man/RndPairs.Rd | 20 DescTools-0.99.12/DescTools/man/SetRowNames.Rd |only DescTools-0.99.12/DescTools/man/Stamp.Rd | 11 DescTools-0.99.12/DescTools/man/StrAlign.Rd |only DescTools-0.99.12/DescTools/man/StrPad.Rd | 8 DescTools-0.99.12/DescTools/man/StrTrim.Rd | 4 DescTools-0.99.12/DescTools/man/SysInfo.Rd | 8 DescTools-0.99.12/DescTools/man/TOne.Rd |only DescTools-0.99.12/DescTools/man/TextToTable.Rd |only DescTools-0.99.12/DescTools/man/Winsorize.Rd | 7 DescTools-0.99.12/DescTools/man/XLDateToPOSIXct.Rd |only DescTools-0.99.12/DescTools/man/XLGetRange.Rd | 38 DescTools-0.99.12/DescTools/man/XLView.Rd | 15 DescTools-0.99.12/DescTools/man/Xplore.Rd |only DescTools-0.99.12/DescTools/man/ZTest.Rd | 18 DescTools-0.99.12/DescTools/man/Zodiac.Rd | 6 DescTools-0.99.12/DescTools/man/as.matrix.Rd | 9 DescTools-0.99.12/DescTools/man/axTicks.POSIXct.Rd |only DescTools-0.99.12/DescTools/man/power.chisq.test.Rd | 45 DescTools-0.99.12/DescTools/src/RcppExports.cpp |only DescTools-0.99.12/DescTools/src/aux_fct.cpp |only DescTools-0.99.12/DescTools/src/moments.c | 2 DescTools-0.99.12/DescTools/src/ranksort.c | 1 DescTools-0.99.12/DescTools/vignettes/Combinatorics.Rnw |only DescTools-0.99.12/DescTools/vignettes/TablesInR.Rnw |only 643 files changed, 903 insertions(+), 1169 deletions(-)
Title: Time Value of Money Functions
Description: Functions for managing cashflows and interest rate curves.
Author: Juan Manuel Truppia
Maintainer: Juan Manuel Truppia <jmtruppia@gmail.com>
Diff between tvm versions 0.2 dated 2014-04-28 and 0.3.0 dated 2015-08-21
tvm-0.2/tvm/README |only tvm-0.3.0/tvm/DESCRIPTION | 12 tvm-0.3.0/tvm/LICENSE | 2 tvm-0.3.0/tvm/MD5 | 56 +-- tvm-0.3.0/tvm/NAMESPACE | 47 +- tvm-0.3.0/tvm/NEWS.md |only tvm-0.3.0/tvm/R/CfFuncs.R | 441 +++++++++++++------------- tvm-0.3.0/tvm/R/CurveFuncs.R | 346 ++++++++++---------- tvm-0.3.0/tvm/R/tvm-package.R |only tvm-0.3.0/tvm/README.md |only tvm-0.3.0/tvm/build |only tvm-0.3.0/tvm/inst |only tvm-0.3.0/tvm/man/adjust_disc.Rd | 39 +- tvm-0.3.0/tvm/man/cashflow.Rd | 37 +- tvm-0.3.0/tvm/man/cft.Rd | 63 +-- tvm-0.3.0/tvm/man/disc_cf.Rd | 38 +- tvm-0.3.0/tvm/man/find_rate.Rd | 56 +-- tvm-0.3.0/tvm/man/irr.Rd | 48 +- tvm-0.3.0/tvm/man/loan.Rd | 59 +-- tvm-0.3.0/tvm/man/npv.Rd | 49 +- tvm-0.3.0/tvm/man/plot.rate_curve.Rd | 53 +-- tvm-0.3.0/tvm/man/pmt.Rd | 50 +- tvm-0.3.0/tvm/man/rate.Rd | 61 +-- tvm-0.3.0/tvm/man/rate_curve.Rd | 81 ++-- tvm-0.3.0/tvm/man/rem.Rd | 44 +- tvm-0.3.0/tvm/man/sub-.rate_curve.Rd | 55 +-- tvm-0.3.0/tvm/man/tvm.Rd |only tvm-0.3.0/tvm/man/xirr.Rd |only tvm-0.3.0/tvm/man/xnpv.Rd |only tvm-0.3.0/tvm/tests/test-all.R | 2 tvm-0.3.0/tvm/tests/testthat/test_cashflows.R | 32 - tvm-0.3.0/tvm/tests/testthat/test_curves.R | 90 ++--- tvm-0.3.0/tvm/vignettes |only 33 files changed, 911 insertions(+), 850 deletions(-)
Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet'
software.
Author: Emily Beylerian [cre, aut],
Kirk Li [ctb],
Samuel Jenness [ctb],
Martina Morris [ctb]
Maintainer: Emily Beylerian <ebey@uw.edu>
Diff between statnetWeb versions 0.3.5 dated 2015-08-20 and 0.3.6 dated 2015-08-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/run_sw.R | 5 ++--- inst/shiny/server.R | 1 - 4 files changed, 9 insertions(+), 11 deletions(-)
Title: Tools for Selective Inference
Description: New tools for inference after selection, for use with forward stepwise regression, least angle regression, the lasso, and the many normal means problem. This R code was developed in coordination with an analogous Python package developed by Jonathan Taylor and others, see http://github.com/selective-inference/selective-inference.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.0 dated 2015-08-14 and 1.0.1 dated 2015-08-21
selectiveInference-1.0.1/selectiveInference/DESCRIPTION | 6 selectiveInference-1.0.1/selectiveInference/MD5 | 25 +-- selectiveInference-1.0.1/selectiveInference/NAMESPACE | 2 selectiveInference-1.0.1/selectiveInference/R/funs.fixed.R | 45 +++--- selectiveInference-1.0.1/selectiveInference/R/funs.fs.R | 72 +++++----- selectiveInference-1.0.1/selectiveInference/R/funs.inf.R | 38 ++++- selectiveInference-1.0.1/selectiveInference/R/funs.lar.R | 71 +++++---- selectiveInference-1.0.1/selectiveInference/man/fixedLassoInf.Rd | 9 - selectiveInference-1.0.1/selectiveInference/man/fsInf.Rd | 2 selectiveInference-1.0.1/selectiveInference/man/larInf.Rd | 2 selectiveInference-1.0.1/selectiveInference/man/plot.fs.Rd | 21 -- selectiveInference-1.0.1/selectiveInference/man/plot.lar.Rd | 23 +-- selectiveInference-1.0.1/selectiveInference/man/selectiveInference.Rd | 2 selectiveInference-1.0/selectiveInference/R/forlater |only 14 files changed, 178 insertions(+), 140 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using a Markov Chain Monte Carlo algorithm. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. The algorithm also can be used in combination with efficient simulation methods such as simulated and parallel tempering algorithms. Tools for analysis such as inverse probability reweighting and plotting functionality are included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2015) ``A New Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper available at <http://http://imai.princeton.edu/research/files/redist.pdf>.
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins <mjh5@princeton.edu>, and Kosuke Imai <kimai@princeton.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>
Diff between redist versions 1.1 dated 2015-05-19 and 1.2 dated 2015-08-21
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 4 +++- data/algdat.p10.rda |binary data/algdat.p20.rda |binary data/algdat.pfull.rda |binary man/redist.rsg.Rd | 5 ++--- src/sw_mh_helper.cpp | 45 +++++++++++++++++++++++---------------------- 9 files changed, 41 insertions(+), 38 deletions(-)
Title: Calculate Design Parameters for Biomarker Validation Studies
Description: Helps a clinical trial team discuss
the clinical goals of a well-defined biomarker with a diagnostic,
staging, prognostic, or predictive purpose. From this discussion will
come a statistical plan for a (non-randomized) validation trial.
Both prospective and retrospective trials are supported. In a specific
focused discussion, investigators should determine the range of
"discomfort" for the NNT, number needed to treat. The meaning of
the discomfort range, [NNTlower, NNTupper], is that within this range
most physicians would feel discomfort either in treating or withholding
treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg,
become the targets of the study's design. If the trial can demonstrate
that a positive biomarker test yields an NNT less than NNTlower,
and that a negative biomarker test yields an NNT less than NNTlower,
then the biomarker may be useful for patients. A highlight of the package
is visualization of a "contra-Bayes" theorem, which produces criteria for
retrospective case-controls studies.
Author: Roger Day
Maintainer: Roger Day <day01@pitt.edu>
Diff between NNTbiomarker versions 0.28 dated 2015-05-05 and 0.29.11 dated 2015-08-21
NNTbiomarker-0.28/NNTbiomarker/inst/shinyCombinePlots/www/Using_the_NNTbiomarker_package.html |only NNTbiomarker-0.28/NNTbiomarker/inst/shinyCombinePlots/www/information.html |only NNTbiomarker-0.28/NNTbiomarker/inst/shinyElicit/www/Using_the_NNTbiomarker_package.html |only NNTbiomarker-0.28/NNTbiomarker/inst/shinyElicit/www/information.html |only NNTbiomarker-0.29.11/NNTbiomarker/DESCRIPTION | 14 NNTbiomarker-0.29.11/NNTbiomarker/MD5 | 88 ++- NNTbiomarker-0.29.11/NNTbiomarker/NAMESPACE | 10 NNTbiomarker-0.29.11/NNTbiomarker/R/NNTintervals.R | 4 NNTbiomarker-0.29.11/NNTbiomarker/R/ROCplots.R |only NNTbiomarker-0.29.11/NNTbiomarker/R/aaa.R | 7 NNTbiomarker-0.29.11/NNTbiomarker/R/achievable.se.sp.R | 6 NNTbiomarker-0.29.11/NNTbiomarker/R/argmin.R |only NNTbiomarker-0.29.11/NNTbiomarker/R/sesp-pv-NNT.R | 24 NNTbiomarker-0.29.11/NNTbiomarker/R/zzz.R |only NNTbiomarker-0.29.11/NNTbiomarker/build/vignette.rds |binary NNTbiomarker-0.29.11/NNTbiomarker/inst/Janes-fit.R |only NNTbiomarker-0.29.11/NNTbiomarker/inst/NOTUSED |only NNTbiomarker-0.29.11/NNTbiomarker/inst/ROCplots-Using-ggplot2.R |only NNTbiomarker-0.29.11/NNTbiomarker/inst/ToDo.txt |only NNTbiomarker-0.29.11/NNTbiomarker/inst/debugTools.R | 285 +++++----- NNTbiomarker-0.29.11/NNTbiomarker/inst/doc/The_Biomarker_Crisis.html | 215 +------ NNTbiomarker-0.29.11/NNTbiomarker/inst/doc/Using_the_NNTbiomarker_package.html | 280 ++------- NNTbiomarker-0.29.11/NNTbiomarker/inst/doc/debugTools.html | 207 +------ NNTbiomarker-0.29.11/NNTbiomarker/inst/human.html.R |only NNTbiomarker-0.29.11/NNTbiomarker/inst/oncotypeDX-risk-functions.jpg.xml |only NNTbiomarker-0.29.11/NNTbiomarker/inst/pageOpenTest.R |only NNTbiomarker-0.29.11/NNTbiomarker/inst/plot_digitizer_Figure_7_example.xml |only NNTbiomarker-0.29.11/NNTbiomarker/inst/rasterImages |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyAE |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyCombinePlots/debugTools.R | 285 +++++----- NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyCombinePlots/plotDiscomfort.R | 22 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyCombinePlots/server.R | 5 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyCombinePlots/shinyapps/trials/shinyCombinePlots.dcf | 4 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyCombinePlots/ui.R | 172 +++--- NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/Steps-example.Rmd |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/Steps-example.docx |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/Steps.md |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/debugTools.R | 285 +++++----- NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/global.R | 14 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/plotDiscomfort.R | 20 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/report.R |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/rsconnect |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/server.R | 123 +++- NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/shinyapps/trials/shinyElicit.dcf | 4 NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/stepsTableInitial.R | 34 - NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/ui.R | 192 ++++-- NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/www/Steps.Rmd |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyElicit/www/Steps.html |only NNTbiomarker-0.29.11/NNTbiomarker/inst/shinyROC |only NNTbiomarker-0.29.11/NNTbiomarker/inst/temp |only NNTbiomarker-0.29.11/NNTbiomarker/inst/testing_ggplot_guides.R |only NNTbiomarker-0.29.11/NNTbiomarker/man/ROCplots.Rd |only NNTbiomarker-0.29.11/NNTbiomarker/man/argmin.Rd |only NNTbiomarker-0.29.11/NNTbiomarker/man/grapes-and-grapes.Rd |only 54 files changed, 1106 insertions(+), 1194 deletions(-)
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Description: Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes.
Directional and other multivariate histograms are provided.
Author: John P. Nolan
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvmesh versions 1.0 dated 2015-04-10 and 1.1 dated 2015-08-21
DESCRIPTION | 14 +- MD5 | 19 ++- NAMESPACE | 8 + R/mvhist.R | 32 ++++++ R/mvmesh-methods.R | 12 +- R/mvmesh.R | 244 ++++++++++++++++++++++++++++++++++++++++++++++---- demo/mvmesh.R | 13 ++ man/HollowTube.Rd |only man/mvhist.Rd | 54 +++++++++-- man/mvmesh-geom.Rd | 30 ++++-- man/mvmesh-package.Rd | 93 +++++++++++-------- 11 files changed, 427 insertions(+), 92 deletions(-)
Title: Quantitative Linkage Analysis Tools using the Variance
Components Approach
Description:
Calculate the polygenic and major gene models for quantitative trait
linkage analysis using variance components approach. The 0.2.2
release includes bug fixes that allow 'multic' to run properly
on 64-bit systems. The 0.3.0 release includes a fully implemented
sw2mloci() function. As of 0.3.8, Splus version is no longer
supported. Additional documentation and examples can be found
in the inst directory.
Author: Eric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Maintainer: Pat Votruba <votruba.patrick@mayo.edu>
Diff between multic versions 0.3.8.1 dated 2014-01-07 and 0.4.2 dated 2015-08-21
multic-0.3.8.1/multic/INSTALL |only multic-0.3.8.1/multic/docs |only multic-0.3.8.1/multic/examples |only multic-0.4.2/multic/CHANGES | 18 ++++ multic-0.4.2/multic/DESCRIPTION | 30 +++--- multic-0.4.2/multic/MD5 | 89 ++++++++++---------- multic-0.4.2/multic/NAMESPACE | 13 +- multic-0.4.2/multic/R/load.effects.q | 5 - multic-0.4.2/multic/R/multic.q | 12 +- multic-0.4.2/multic/R/residuals.multic.q | 16 +-- multic-0.4.2/multic/R/t.rank.q | 2 multic-0.4.2/multic/inst |only multic-0.4.2/multic/man/plot.family.lods.Rd | 2 multic-0.4.2/multic/man/sw2mloci.Rd | 6 - multic-0.4.2/multic/src/Maxfun_source.cpp | 122 ++++++++++++++-------------- multic-0.4.2/multic/src/multic.cpp | 2 16 files changed, 170 insertions(+), 147 deletions(-)
Title: Expand Short URLs Using the 'LongURL' API
Description: Interface to the 'LongURL' API to identify known URL shortener services
and expand vectors of short URLs with optional error checking and
URL validation. See <http://longurl.org/> for more information about
'LongURL'.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between longurl versions 0.1.0 dated 2015-06-23 and 0.1.1 dated 2015-08-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/longurl.r | 29 +++++++++++++++++++++-------- man/expand_urls.Rd | 4 ++-- man/known_services.Rd | 4 +++- 5 files changed, 33 insertions(+), 18 deletions(-)
Title: Variations of Parallel Coordinate Plots for Categorical Data
Description: Create hammock plots, parallel sets, and common angle plots
with ggplot2.
Author: Heike Hofmann, Marie Vendettuoli
Maintainer: Heike Hofmann <hofmann@iastate.edu>
Diff between ggparallel versions 0.1.1 dated 2012-09-09 and 0.1.2 dated 2015-08-21
ggparallel-0.1.1/ggparallel/ggparallel.Rproj |only ggparallel-0.1.1/ggparallel/ggparallel_0.1.tar.gz |only ggparallel-0.1.2/ggparallel/DESCRIPTION | 21 - ggparallel-0.1.2/ggparallel/LICENSE |only ggparallel-0.1.2/ggparallel/MD5 | 23 - ggparallel-0.1.2/ggparallel/NAMESPACE | 5 ggparallel-0.1.2/ggparallel/NEWS | 5 ggparallel-0.1.2/ggparallel/R/genes.R | 72 ++-- ggparallel-0.1.2/ggparallel/R/help.R | 7 ggparallel-0.1.2/ggparallel/R/parallel.R | 290 ++++++++---------- ggparallel-0.1.2/ggparallel/inst/examples |only ggparallel-0.1.2/ggparallel/inst/references.bib |only ggparallel-0.1.2/ggparallel/man/genes.Rd | 101 ++++-- ggparallel-0.1.2/ggparallel/man/ggparallel.Rd | 175 +++------- ggparallel-0.1.2/ggparallel/man/package-ggparallel.Rd | 9 15 files changed, 345 insertions(+), 363 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models on top of static maps
from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those
tasks, including functions for geolocation and routing.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between ggmap versions 2.4 dated 2015-03-05 and 2.5.2 dated 2015-08-21
DESCRIPTION | 17 - MD5 | 113 ++++++------ NAMESPACE | 12 + NEWS | 42 ++++ R/bb2bbox.R | 2 R/geocode.R | 441 ++++++++++++++++++++++++++++------------------- R/get_cloudmademap.R | 12 + R/get_googlemap.R | 103 ++++++++-- R/get_map.R | 41 ++-- R/get_navermap.R | 5 R/get_openstreetmap.R | 5 R/get_stamenmap.R | 29 ++- R/ggmap.R | 365 +++++++++++++++----------------------- R/ggplot2.R | 7 R/help.R | 5 R/helpers.R |only R/mapdist.R | 78 ++++---- R/mutate_geocode.R |only R/print.R |only R/qmap.R | 44 ---- R/qmplot.R | 195 +++++++++++--------- R/revgeocode.R | 3 R/route.R | 141 +++++++-------- man/LonLat2XY.Rd | 2 man/OSM_scale_lookup.Rd | 2 man/XY2LonLat.Rd | 2 man/bb2bbox.Rd | 4 man/calc_zoom.Rd | 2 man/crime.Rd | 2 man/distQueryCheck.Rd | 2 man/file_drawer.Rd | 2 man/geocode.Rd | 86 +++++---- man/geom_leg.Rd | 14 - man/get_cloudmademap.Rd | 2 man/get_googlemap.Rd | 71 ++++--- man/get_map.Rd | 39 ++-- man/get_navermap.Rd | 2 man/get_openstreetmap.Rd | 2 man/get_stamenmap.Rd | 12 - man/ggimage.Rd | 2 man/gglocator.Rd | 2 man/ggmap.Rd | 285 +++++++++++------------------- man/ggmapplot.Rd | 2 man/hadley.Rd | 2 man/inset.Rd | 2 man/inset_raster.Rd | 2 man/legs2route.Rd | 22 +- man/make_bbox.Rd | 2 man/mapdist.Rd | 26 +- man/mutate_geocode.Rd |only man/print.ggmap.Rd |only man/qmap.Rd | 2 man/qmplot.Rd | 194 +++++++++++--------- man/revgeocode.Rd | 6 man/route.Rd | 34 +-- man/routeQueryCheck.Rd | 2 man/theme_inset.Rd | 2 man/theme_nothing.Rd | 2 man/wind.Rd | 2 man/zips.Rd | 2 60 files changed, 1347 insertions(+), 1152 deletions(-)
Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models.
Author: Yanwei (Wayne) Zhang
Maintainer: Yanwei (Wayne) Zhang <actuary_zhang@hotmail.com>
Diff between cplm versions 0.7-3 dated 2015-07-12 and 0.7-4 dated 2015-08-21
DESCRIPTION | 10 MD5 | 42 - NAMESPACE | 5 NEWS | 16 R/amer.R | 5 R/bcplm.R | 368 +++++------ R/classMethods.R | 12 R/utilities.R | 660 ++++++++++----------- inst/CITATION |only inst/doc/TweediePaper.pdf |only inst/doc/cplm.Rnw | 1441 +++++++++++++++++++++++----------------------- inst/doc/cplm.pdf |binary man/bcplm.Rd | 4 man/cpglm.Rd | 210 +++--- man/cpglmm.Rd | 7 man/cplm-package.Rd | 2 man/getF.Rd | 6 man/gini.Rd | 2 man/sp2d.Rd | 8 man/tp.Rd | 3 man/zcpglm.Rd | 2 src/cpglmm.c | 9 vignettes/cplm.Rnw | 1441 +++++++++++++++++++++++----------------------- 23 files changed, 2158 insertions(+), 2095 deletions(-)
Title: Self Calibrating Quantile-Quantile Plots for Visual Testing
Description: Provides the function qqtest which incorporates uncertainty in its
qqplot display(s) so that the user might have a better sense of the
evidence against the specified distributional hypothesis. qqtest draws a
quantile quantile plot for visually assessing whether the data come from a
test distribution that has been defined in one of many ways. The vertical
axis plots the data quantiles, the horizontal those of a test distribution.
The default behaviour generates 1000 samples from the test distribution and
overlays the plot with shaded pointwise interval estimates for the ordered
quantiles from the test distribution. A small number of independently
generated exemplar quantile plots can also be overlaid. Both the interval
estimates and the exemplars provide different comparative information to
assess the evidence provided by the qqplot for or against the hypothesis
that the data come from the test distribution (default is normal or
gaussian). Finally, a visual test of significance (a lineup plot) can also
be displayed to test the null hypothesis that the data come from the test
distribution.
Author: Wayne Oldford [aut, cre]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between qqtest versions 1.0 dated 2014-12-13 and 1.1 dated 2015-08-20
qqtest-1.0/qqtest/R/qqplot.R |only qqtest-1.0/qqtest/data/penicillin.RData |only qqtest-1.1/qqtest/DESCRIPTION | 19 +- qqtest-1.1/qqtest/MD5 | 41 +++-- qqtest-1.1/qqtest/NAMESPACE | 28 +++ qqtest-1.1/qqtest/R/WachusettReservoir.R |only qqtest-1.1/qqtest/R/bacteria.R |only qqtest-1.1/qqtest/R/penicillin.R |only qqtest-1.1/qqtest/R/primer.R |only qqtest-1.1/qqtest/R/pullstrength.R |only qqtest-1.1/qqtest/R/qkay.R | 6 qqtest-1.1/qqtest/R/qqtest.R |only qqtest-1.1/qqtest/R/sittingHeights.R |only qqtest-1.1/qqtest/R/stacklossDistances.R |only qqtest-1.1/qqtest/data/WachusettReservoir.rda |only qqtest-1.1/qqtest/data/bacteria.rda |only qqtest-1.1/qqtest/data/penicillin.rda |only qqtest-1.1/qqtest/data/primer.rda |only qqtest-1.1/qqtest/data/pullstrength.rda |only qqtest-1.1/qqtest/data/sittingHeights.rda |only qqtest-1.1/qqtest/data/stacklossDistances.rda |only qqtest-1.1/qqtest/man/WachusettReservoir.Rd |only qqtest-1.1/qqtest/man/bacteria.Rd |only qqtest-1.1/qqtest/man/dkay.Rd | 3 qqtest-1.1/qqtest/man/penicillin.Rd | 47 ++--- qqtest-1.1/qqtest/man/pkay.Rd | 3 qqtest-1.1/qqtest/man/primer.Rd |only qqtest-1.1/qqtest/man/pullstrength.Rd |only qqtest-1.1/qqtest/man/qkay.Rd | 4 qqtest-1.1/qqtest/man/qqtest.Rd | 210 ++++++++++++++++---------- qqtest-1.1/qqtest/man/rkay.Rd | 3 qqtest-1.1/qqtest/man/sittingHeights.Rd |only qqtest-1.1/qqtest/man/stacklossDistances.Rd |only 33 files changed, 237 insertions(+), 127 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut], Martin Maechler [aut],
Ben Bolker [aut, cre], Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb], Bin Dai [ctb],
Gabor Grothendieck [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-8 dated 2015-06-22 and 1.1-9 dated 2015-08-20
DESCRIPTION | 8 - MD5 | 64 ++++----- NAMESPACE | 44 ++++-- R/AllClass.R | 120 ++--------------- R/hooks.R | 6 R/lmList.R | 46 ++++-- R/lmer.R | 281 ++++++++++++++++++++++++++---------------- R/modular.R | 42 ++++-- R/nbinom.R | 116 ++++++++++------- R/plot.R | 48 ++----- R/predict.R | 80 ++++++++--- R/profile.R | 55 +++++--- R/utilities.R | 112 +++++++--------- README.md | 2 inst/CITATION | 2 inst/NEWS.Rd | 87 +++++++++---- inst/testdata/badprof.rds |only inst/tests/test-formulaEval.R | 17 ++ inst/tests/test-glmer.R | 11 - inst/tests/test-glmernb.R |only inst/tests/test-methods.R | 150 ++++++++++++++++------ man/getME.Rd | 123 +++++++++--------- man/glmer.Rd | 8 - man/glmer.nb.Rd | 84 ++++++++++-- man/lmResp-class.Rd | 15 +- man/lmer.Rd | 2 man/merMod-class.Rd | 43 +++--- man/mkMerMod.Rd | 26 ++- man/mkReTrms.Rd | 29 +++- tests/boundary.R | 55 ++++---- tests/getME.R | 2 tests/lmList-tst.R | 15 ++ tests/nbinom.R | 16 +- tests/testOptControl.R | 13 + 34 files changed, 1041 insertions(+), 681 deletions(-)
Title: A Hydraulics Package to Compute Open-Channel Flow over Weirs
Description: Provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between weirs versions 0.24 dated 2015-04-20 and 0.25 dated 2015-08-20
ChangeLog | 6 ++++++ DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 ++ 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 0.65-1 dated 2015-06-01 and 1.1.1.1 dated 2015-08-20
pomp-0.65-1/pomp/build/pomp.pdf |only pomp-0.65-1/pomp/inst/TODO |only pomp-0.65-1/pomp/inst/examples/ewmeas.csv |only pomp-0.65-1/pomp/man/LondonYorke.Rd |only pomp-0.65-1/pomp/man/pomp-package.Rd |only pomp-1.1.1.1/pomp/DESCRIPTION | 41 ++- pomp-1.1.1.1/pomp/MD5 | 191 ++++++++--------- pomp-1.1.1.1/pomp/NAMESPACE | 27 +- pomp-1.1.1.1/pomp/R/abc-methods.R | 4 pomp-1.1.1.1/pomp/R/abc.R | 44 +-- pomp-1.1.1.1/pomp/R/bake.R |only pomp-1.1.1.1/pomp/R/bsmc.R | 38 +-- pomp-1.1.1.1/pomp/R/bsmc2.R | 46 +--- pomp-1.1.1.1/pomp/R/builder.R | 108 ++++++--- pomp-1.1.1.1/pomp/R/covmat.R |only pomp-1.1.1.1/pomp/R/generics.R | 8 pomp-1.1.1.1/pomp/R/init-state-pomp.R | 7 pomp-1.1.1.1/pomp/R/load.R | 29 +- pomp-1.1.1.1/pomp/R/logmeanexp.R | 7 pomp-1.1.1.1/pomp/R/mif-methods.R | 18 - pomp-1.1.1.1/pomp/R/mif.R | 120 +++++----- pomp-1.1.1.1/pomp/R/mif2-methods.R |only pomp-1.1.1.1/pomp/R/mif2.R |only pomp-1.1.1.1/pomp/R/minim.R | 6 pomp-1.1.1.1/pomp/R/nlf-guts.R | 6 pomp-1.1.1.1/pomp/R/nlf-objfun.R | 2 pomp-1.1.1.1/pomp/R/nlf.R | 28 -- pomp-1.1.1.1/pomp/R/parmat.R | 5 pomp-1.1.1.1/pomp/R/pfilter-methods.R | 10 pomp-1.1.1.1/pomp/R/pfilter.R | 222 ++++++++++++------- pomp-1.1.1.1/pomp/R/pmcmc-methods.R | 4 pomp-1.1.1.1/pomp/R/pmcmc.R | 161 ++++++++------ pomp-1.1.1.1/pomp/R/pomp-class.R | 29 -- pomp-1.1.1.1/pomp/R/pomp-methods.R | 17 - pomp-1.1.1.1/pomp/R/pomp.R | 53 +++- pomp-1.1.1.1/pomp/R/probe-match.R | 4 pomp-1.1.1.1/pomp/R/profile-design.R | 1 pomp-1.1.1.1/pomp/R/proposals.R | 113 +++++++++- pomp-1.1.1.1/pomp/R/sannbox.R | 1 pomp-1.1.1.1/pomp/R/simulate-pomp.R | 24 -- pomp-1.1.1.1/pomp/R/spect.R | 18 - pomp-1.1.1.1/pomp/R/traj-match.R | 4 pomp-1.1.1.1/pomp/build/partial.rdb |only pomp-1.1.1.1/pomp/data/LondonYorke.rda |binary pomp-1.1.1.1/pomp/data/ewcitmeas.rda |only pomp-1.1.1.1/pomp/data/ewmeas.rda |only pomp-1.1.1.1/pomp/demo/gompertz.R | 24 +- pomp-1.1.1.1/pomp/demo/sir.R | 48 ++-- pomp-1.1.1.1/pomp/inst/NEWS | 144 ++++++++++++ pomp-1.1.1.1/pomp/inst/NEWS.Rd | 123 ++++++++++ pomp-1.1.1.1/pomp/inst/doc/index.html | 17 - pomp-1.1.1.1/pomp/inst/examples/bbs.R | 20 - pomp-1.1.1.1/pomp/inst/examples/dacca.R | 1 pomp-1.1.1.1/pomp/inst/examples/dacca2.R |only pomp-1.1.1.1/pomp/inst/examples/ebola.R |only pomp-1.1.1.1/pomp/inst/examples/euler.sir.R | 20 - pomp-1.1.1.1/pomp/inst/examples/gillespie.sir.R | 10 pomp-1.1.1.1/pomp/inst/examples/gompertz.R | 1 pomp-1.1.1.1/pomp/inst/examples/ou2.R | 1 pomp-1.1.1.1/pomp/inst/examples/ricker.R | 1 pomp-1.1.1.1/pomp/man/abc.Rd | 26 +- pomp-1.1.1.1/pomp/man/bake.Rd |only pomp-1.1.1.1/pomp/man/bsmc.Rd | 15 - pomp-1.1.1.1/pomp/man/bsplines.Rd | 2 pomp-1.1.1.1/pomp/man/builder.Rd | 4 pomp-1.1.1.1/pomp/man/csnippet.Rd | 21 + pomp-1.1.1.1/pomp/man/design.Rd | 2 pomp-1.1.1.1/pomp/man/eulermultinom.Rd | 2 pomp-1.1.1.1/pomp/man/example.Rd | 2 pomp-1.1.1.1/pomp/man/gompertz.Rd | 2 pomp-1.1.1.1/pomp/man/logmeanexp.Rd | 6 pomp-1.1.1.1/pomp/man/lowlevel.Rd | 2 pomp-1.1.1.1/pomp/man/measles.Rd |only pomp-1.1.1.1/pomp/man/mif.Rd | 37 ++- pomp-1.1.1.1/pomp/man/mif2.Rd |only pomp-1.1.1.1/pomp/man/nlf.Rd | 13 - pomp-1.1.1.1/pomp/man/package.Rd |only pomp-1.1.1.1/pomp/man/parmat.Rd | 2 pomp-1.1.1.1/pomp/man/particles-mif.Rd | 2 pomp-1.1.1.1/pomp/man/pfilter.Rd | 31 +- pomp-1.1.1.1/pomp/man/plugins.Rd | 20 - pomp-1.1.1.1/pomp/man/pmcmc.Rd | 68 ++++-- pomp-1.1.1.1/pomp/man/pomp-fun.Rd | 2 pomp-1.1.1.1/pomp/man/pomp-methods.Rd | 5 pomp-1.1.1.1/pomp/man/pomp.Rd | 36 +-- pomp-1.1.1.1/pomp/man/probe.Rd | 2 pomp-1.1.1.1/pomp/man/proposals.Rd | 25 +- pomp-1.1.1.1/pomp/man/ricker.Rd | 2 pomp-1.1.1.1/pomp/man/sannbox.Rd | 4 pomp-1.1.1.1/pomp/man/simulate-pomp.Rd | 2 pomp-1.1.1.1/pomp/man/sir.Rd | 4 pomp-1.1.1.1/pomp/man/spect.Rd | 2 pomp-1.1.1.1/pomp/src/cholmodel.c | 4 pomp-1.1.1.1/pomp/src/dmeasure.c | 5 pomp-1.1.1.1/pomp/src/dprior.c | 3 pomp-1.1.1.1/pomp/src/euler.c | 14 - pomp-1.1.1.1/pomp/src/initstate.c | 269 +++++++++++++++++------- pomp-1.1.1.1/pomp/src/mif2.c |only pomp-1.1.1.1/pomp/src/partrans.c | 2 pomp-1.1.1.1/pomp/src/pfilter.c | 33 ++ pomp-1.1.1.1/pomp/src/pomp_fun.c | 8 pomp-1.1.1.1/pomp/src/pomp_internal.h | 2 pomp-1.1.1.1/pomp/src/rmeasure.c | 4 pomp-1.1.1.1/pomp/src/rprior.c | 2 pomp-1.1.1.1/pomp/src/simulate.c | 3 pomp-1.1.1.1/pomp/src/sir.c | 12 + 106 files changed, 1591 insertions(+), 917 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between marked versions 1.1.9 dated 2015-08-19 and 1.1.10 dated 2015-08-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 - NEWS | 6 ++++++ R/crm.R | 2 +- R/crm.wrapper.R | 2 +- inst/doc/markedVignette.pdf |binary 7 files changed, 18 insertions(+), 13 deletions(-)
Title: Baseline Correction for Copy Number Data from Cancer Samples
Description: The 450k arrays are frequently used in the epigenetic studies, the copy number calling from the 450k data is possible but it faces some difficulties in cancer samples regarding the determination of the copy number status due to the false sample centering and baseline shifting. Without solving this issue the CN calling will be inaccurate. CopyNumber450kCancer-package was designed to correct the baseline in cancer samples using the Maximum Density Peak Estimation (MDPE) method.
The main advantages for CopyNumber450kCancer-package are: Fast (few seconds per sample), high accuracy rate, in-sample correction, no input parameters needed, low computer sources required, and adaptable for 450k-similar technologies.
Author: Nour-al-dain Marzouka [aut, cre]
Maintainer: Nour-al-dain Marzouka <nour.marzouka@medsci.uu.se>
Diff between CopyNumber450kCancer versions 1.0.3 dated 2015-06-18 and 1.0.4 dated 2015-08-20
DESCRIPTION | 9 ++-- MD5 | 23 +++++----- NAMESPACE | 8 +++ R/CopyNumber450kCancer.R | 72 +++++++++++++++------------------ man/AutoCorrectPeak.Rd | 27 +++++------- man/CopyNumber450kCancer-package.Rd | 11 ++--- man/PlotCNV.Rd | 10 ---- man/PlotMerged.Rd | 12 +---- man/ReadData.Rd | 45 ++++++++++---------- man/ReviewPlot.Rd | 16 +------ man/plotRegions.Rd | 12 ----- man/print.CopyNumber450kCancer_data.Rd | 2 vignettes |only 13 files changed, 106 insertions(+), 141 deletions(-)
More information about CopyNumber450kCancer at CRAN
Permanent link
Title: Collocation Inference for Dynamic Systems
Description: These functions implement collocation-inference
for continuous-time and discrete-time stochastic processes.
They provide model-based smoothing, gradient-matching,
generalized profiling and forwards prediction error methods.
Author: Giles Hooker <gjh27@cornell.edu>,
Luo Xiao <lx42@cornell.edu>,
James Ramsay <ramsay@psych.mcgill.ca>
Maintainer: Giles Hooker <gjh27@cornell.edu>
Diff between CollocInfer versions 1.0.1 dated 2014-05-07 and 1.0.2 dated 2015-08-20
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NAMESPACE | 9 ++++++++- R/FitMatchOptimization.R | 4 ++-- R/InnerOptimization.R | 4 ++-- R/OuterOptimization.R | 4 ++-- R/ParsMatchOptimization.R | 4 ++-- R/ls.shortcut.r | 4 ++-- 8 files changed, 32 insertions(+), 25 deletions(-)
Title: Blaker's Binomial Confidence Limits
Description: Fast and accurate calculation of Blaker's binomial confidence limits (and some related stuff).
Author: Jan Klaschka
Maintainer: Jan Klaschka <klaschka@cs.cas.cz>
Diff between BlakerCI versions 1.0-4 dated 2014-05-07 and 1.0-5 dated 2015-08-20
ChangeLog | 5 +++ DESCRIPTION | 16 +++++------ MD5 | 19 ++++++++----- NAMESPACE | 4 ++ R/binom.blaker.VHadj.acc.R |only R/binom.blaker.VHadj.limits.R |only R/binom.blaker.VHadj.lower.limit.R |only man/BlakerCI-internal.Rd | 36 +++++++++++++++++++++----- man/BlakerCI-package.Rd | 8 ++--- man/binom.blaker.VHadj.acc.Rd |only man/binom.blaker.VHadj.limits.Rd |only man/binom.blaker.acc.Rd | 21 +++++++-------- man/binom.blaker.limits.Rd | 51 +++++++++++++++++++++++-------------- 13 files changed, 103 insertions(+), 57 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.1.7 dated 2015-02-11 and 0.2.0 dated 2015-08-20
DESCRIPTION | 15 MD5 | 42 NAMESPACE | 13 NEWS | 12 R/SeqFeatR_GUI.R | 121 + R/assocpairfeat.R | 6 R/assocpoint.R | 2310 ++++++++++++++++--------------- R/assocpointhierarchical.R |only R/tartan.R | 30 build/vignette.rds |binary inst/doc/SeqFeatR_tutorial.Rnw | 65 inst/doc/SeqFeatR_tutorial.pdf |binary inst/extdata/Example_model_for_bayes.txt |only inst/extdata/config.cfg | 6 inst/extdata/tart_1.csv |only inst/extdata/tart_2.csv |only man/assocpair.Rd | 5 man/assocpoint.Rd | 89 - man/assocpointhierarchical.Rd |only vignettes/SeqFeatR_tutorial.Rnw | 65 vignettes/log.pdf |binary vignettes/log.pdf_tex | 2 vignettes/phylo_ex.pdf |only vignettes/phylo_ex.pdf_tex |only vignettes/phylo_ex.svg |only vignettes/tart.pdf |only vignettes/tart.pdf_tex |only 27 files changed, 1632 insertions(+), 1149 deletions(-)
Title: Various Similarity and Distance Metrics for Marked Point
Processes
Description: Compute similarities and distances between marked point processes.
Author: Hideitsu Hino, Ken Takano, Yuki Yoshikawa, and Noboru Murata
Maintainer: Hideitsu Hino <hinohide@cs.tsukuba.ac.jp>
Diff between mmpp versions 0.1 dated 2015-02-20 and 0.4 dated 2015-08-20
mmpp-0.1/mmpp/man/mmpp.Rd |only mmpp-0.4/mmpp/DESCRIPTION | 8 - mmpp-0.4/mmpp/MD5 | 38 ++++---- mmpp-0.4/mmpp/NAMESPACE | 3 mmpp-0.4/mmpp/NEWS | 14 +++ mmpp-0.4/mmpp/R/coocmetric.r | 24 ++--- mmpp-0.4/mmpp/R/fmetric.r | 19 ++-- mmpp-0.4/mmpp/R/ieimetric.r | 110 ++++++++++++++++--------- mmpp-0.4/mmpp/R/iipmetric.r | 22 ++--- mmpp-0.4/mmpp/R/k2d.r | 8 - mmpp-0.4/mmpp/R/mmpp.r | 156 +++++++++++++++++++++++++++++++++--- mmpp-0.4/mmpp/R/splitData.r | 71 +++++++++------- mmpp-0.4/mmpp/R/utils.r | 5 - mmpp-0.4/mmpp/man/Miyagi20030626.Rd | 16 +-- mmpp-0.4/mmpp/man/coocmetric.Rd | 24 ++--- mmpp-0.4/mmpp/man/fmetric.Rd | 21 ++-- mmpp-0.4/mmpp/man/ieimetric.Rd | 18 ++-- mmpp-0.4/mmpp/man/iipmetric.Rd | 23 ++--- mmpp-0.4/mmpp/man/k2d.Rd | 8 - mmpp-0.4/mmpp/man/mmpp-package.Rd |only mmpp-0.4/mmpp/man/splitMPP.Rd | 31 ++++--- 21 files changed, 411 insertions(+), 208 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-17 0.91
Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet'
software.
Author: Emily Beylerian [cre, aut],
Kirk Li [ctb],
Samuel Jenness [ctb],
Martina Morris [ctb]
Maintainer: Emily Beylerian <ebey@uw.edu>
Diff between statnetWeb versions 0.3.4 dated 2015-06-17 and 0.3.5 dated 2015-08-20
DESCRIPTION | 9 + MD5 | 16 +-- R/run_sw.R | 3 README.md | 12 +- inst/shiny/global.R | 38 ++++---- inst/shiny/server.R | 200 +++++++++++++++++++++++++++---------------- inst/shiny/ui.R | 217 ++++++++++++++++++++++++++--------------------- inst/shiny/www/alert.js | 16 +++ inst/shiny/www/style.css | 5 + 9 files changed, 312 insertions(+), 204 deletions(-)
Title: ARMA-GARCH/APARCH Models with GEV and Stable Distributions
Description: Package for simulation and estimation of ARMA-GARCH/APARCH models with GEV and stable distributions.
Author: Thiago Sousa [aut, cre],
Cira Otiniano [ctb],
Silvia Lopes [ctb],
Diethelm Wuertz [ctb, cph]
Maintainer: Thiago Sousa <thiagoestatistico@gmail.com>
Diff between GEVStableGarch versions 1.0 dated 2014-03-16 and 1.1 dated 2015-08-20
GEVStableGarch-1.0/GEVStableGarch/R/GEVStableGarch.r |only GEVStableGarch-1.0/GEVStableGarch/man/GSgarch.Fit.Rd |only GEVStableGarch-1.0/GEVStableGarch/man/GSgarch.FitAIC.Rd |only GEVStableGarch-1.0/GEVStableGarch/man/GSgarch.Sim.Rd |only GEVStableGarch-1.1/GEVStableGarch/ChangeLog |only GEVStableGarch-1.1/GEVStableGarch/DESCRIPTION | 27 - GEVStableGarch-1.1/GEVStableGarch/MD5 | 42 ++ GEVStableGarch-1.1/GEVStableGarch/NAMESPACE | 97 ++++- GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-armaGarchDist.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-filter.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-fit.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-getFormula.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-getOrder.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-getStart.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-onAttach.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-package.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-select.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-sim.R |only GEVStableGarch-1.1/GEVStableGarch/R/GEVStableGarch-stationarityAparch.R |only GEVStableGarch-1.1/GEVStableGarch/R/class-GEVSTABLEGARCH.R |only GEVStableGarch-1.1/GEVStableGarch/R/class-GEVSTABLEGARCHSPEC.R |only GEVStableGarch-1.1/GEVStableGarch/R/dist-gat.R |only GEVStableGarch-1.1/GEVStableGarch/R/dist-skstd.R |only GEVStableGarch-1.1/GEVStableGarch/R/gevStableGarch-spec.R |only GEVStableGarch-1.1/GEVStableGarch/R/methods-show.R |only GEVStableGarch-1.1/GEVStableGarch/data |only GEVStableGarch-1.1/GEVStableGarch/inst/doc |only GEVStableGarch-1.1/GEVStableGarch/man/GEVStableGarch-package.Rd | 173 ++++++---- GEVStableGarch-1.1/GEVStableGarch/man/class-GEVSTABLEGARCH.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/class-GEVSTABLEGARCHSPEC.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/data.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/dist-gat.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/dist-skstd.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/gsFit.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/gsMomentAparch.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/gsSelect.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/gsSim.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/gsSpec.Rd |only GEVStableGarch-1.1/GEVStableGarch/man/show-methods.Rd |only 39 files changed, 244 insertions(+), 95 deletions(-)
More information about GEVStableGarch at CRAN
Permanent link
Title: Functions and Data for a Course on Modern Regression and
Classification
Description: Functions and data are provided that support a course that emphasizes statistical
issues of inference and generalizability. Attention is restricted to a relatively small
number of methods, often (misleadingly in my view) referred to as algorithms.
Author: John Maindonald
Maintainer: John Maindonald <john.maindonald@anu.edu.au>
Diff between gamclass versions 0.55 dated 2014-08-23 and 0.56 dated 2015-08-20
gamclass-0.55/gamclass/vignettes/figs2.Rmw |only gamclass-0.56/gamclass/DESCRIPTION | 18 gamclass-0.56/gamclass/MD5 | 323 +++++++++++++--- gamclass-0.56/gamclass/NAMESPACE | 7 gamclass-0.56/gamclass/build/vignette.rds |binary gamclass-0.56/gamclass/inst/doc/figs1.R | 113 ++--- gamclass-0.56/gamclass/inst/doc/figs1.Rnw | 122 ++---- gamclass-0.56/gamclass/inst/doc/figs1.pdf |binary gamclass-0.56/gamclass/inst/doc/figs10.R | 15 gamclass-0.56/gamclass/inst/doc/figs10.Rnw | 16 gamclass-0.56/gamclass/inst/doc/figs10.pdf |binary gamclass-0.56/gamclass/inst/doc/figs11.R | 66 +-- gamclass-0.56/gamclass/inst/doc/figs11.Rnw | 70 +-- gamclass-0.56/gamclass/inst/doc/figs11.pdf |binary gamclass-0.56/gamclass/inst/doc/figs2.R | 84 ++-- gamclass-0.56/gamclass/inst/doc/figs2.Rnw | 96 ++-- gamclass-0.56/gamclass/inst/doc/figs2.pdf |binary gamclass-0.56/gamclass/inst/doc/figs3.R | 188 ++++----- gamclass-0.56/gamclass/inst/doc/figs3.Rnw | 199 +++++---- gamclass-0.56/gamclass/inst/doc/figs3.pdf |binary gamclass-0.56/gamclass/inst/doc/figs4.R | 179 ++++---- gamclass-0.56/gamclass/inst/doc/figs4.Rnw | 171 ++++---- gamclass-0.56/gamclass/inst/doc/figs4.pdf |binary gamclass-0.56/gamclass/inst/doc/figs5.R | 36 - gamclass-0.56/gamclass/inst/doc/figs5.Rnw | 40 - gamclass-0.56/gamclass/inst/doc/figs5.pdf |binary gamclass-0.56/gamclass/inst/doc/figs6.R | 97 ++-- gamclass-0.56/gamclass/inst/doc/figs6.Rnw | 168 +++----- gamclass-0.56/gamclass/inst/doc/figs6.pdf |binary gamclass-0.56/gamclass/inst/doc/figs7.R | 31 - gamclass-0.56/gamclass/inst/doc/figs7.Rnw | 35 - gamclass-0.56/gamclass/inst/doc/figs7.pdf |binary gamclass-0.56/gamclass/inst/doc/figs8.R | 40 - gamclass-0.56/gamclass/inst/doc/figs8.Rnw | 90 +--- gamclass-0.56/gamclass/inst/doc/figs8.pdf |binary gamclass-0.56/gamclass/inst/doc/figs9.R | 104 ++--- gamclass-0.56/gamclass/inst/doc/figs9.Rnw | 112 ++--- gamclass-0.56/gamclass/inst/doc/figs9.pdf |binary gamclass-0.56/gamclass/man/CVcluster.Rd | 2 gamclass-0.56/gamclass/man/CVgam.Rd | 2 gamclass-0.56/gamclass/man/FARS.Rd | 2 gamclass-0.56/gamclass/man/FARSmiss.Rd | 2 gamclass-0.56/gamclass/man/RFcluster.Rd | 2 gamclass-0.56/gamclass/man/fars2007.Rd | 2 gamclass-0.56/gamclass/man/modregR-package.Rd | 4 gamclass-0.56/gamclass/man/simreg.Rd | 4 gamclass-0.56/gamclass/vignettes/figs |only gamclass-0.56/gamclass/vignettes/figs1-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs1.Rnw | 122 ++---- gamclass-0.56/gamclass/vignettes/figs10-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs10.Rnw | 16 gamclass-0.56/gamclass/vignettes/figs11-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs11.Rnw | 70 +-- gamclass-0.56/gamclass/vignettes/figs2-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs2.Rnw | 96 ++-- gamclass-0.56/gamclass/vignettes/figs3-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs3.Rnw | 199 +++++---- gamclass-0.56/gamclass/vignettes/figs4-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs4.Rnw | 171 ++++---- gamclass-0.56/gamclass/vignettes/figs5-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs5.Rnw | 40 - gamclass-0.56/gamclass/vignettes/figs6-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs6.Rnw | 168 +++----- gamclass-0.56/gamclass/vignettes/figs7-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs7.Rnw | 35 - gamclass-0.56/gamclass/vignettes/figs8-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs8.Rnw | 90 +--- gamclass-0.56/gamclass/vignettes/figs9-concordance.tex |only gamclass-0.56/gamclass/vignettes/figs9.Rnw | 112 ++--- 69 files changed, 1833 insertions(+), 1726 deletions(-)
Title: Fit Continuous-Time Correlated Random Walk Models to Animal
Movement Data
Description: The (C)orrelated (RA)ndom (W)alk (L)ibrary of
R functions was designed for fitting continuous-time
correlated random walk (CTCRW) models with time indexed
covariates. The model is fit using the Kalman-Filter on
a state space version of the continuous-time stochastic
movement process.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between crawl versions 1.4-1 dated 2013-07-26 and 1.5 dated 2015-08-20
DESCRIPTION | 19 -- MD5 | 60 +++---- NAMESPACE | 22 ++ R/AllMethod.R | 3 R/crawl-package.R | 12 + R/crwMLE.R | 47 +++-- R/crwPredictPlot.R | 12 - R/crwUseGrid.R | 4 demo/northernFurSeal.R | 1 man/aic.crw.Rd | 32 +-- man/as.flat.Rd | 18 +- man/crawl-package.Rd | 33 +--- man/crwMLE.Rd | 313 +++++++++++++++++--------------------- man/crwN2ll.Rd | 92 +++++------ man/crwPostIS.Rd | 88 ++++------ man/crwPredict.Rd | 103 +++++------- man/crwPredictPlot.Rd | 25 +-- man/crwSamplePar.Rd | 120 ++++++-------- man/crwSimulator.Rd | 144 +++++++---------- man/crwUseGrid.Rd | 29 +-- man/displayPar.Rd | 72 +++----- man/expandPred.Rd | 28 +-- man/fillCols.Rd | 15 - man/harborSeal.Rd | 20 +- man/intToPOSIX.Rd | 27 +-- man/logSpeed.Rd | 30 +-- man/mergeTrackStop.Rd | 53 +++--- man/northernFurSeal.Rd | 33 ---- src/crwDriftSimulate.f90 | 378 +++++++++++++++++++++++------------------------ src/crwN2ll.f90 | 128 +++++++-------- src/crwSimulate.f90 | 66 ++++---- 31 files changed, 974 insertions(+), 1053 deletions(-)
Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box'
(https://www.box.com/). In addition to uploading and downloading files, this
package includes functions which mirror base R operations for local files,
(e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git'
style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <rocks.brendan@gmail.com>
Diff between boxr versions 0.2.6 dated 2015-05-26 and 0.2.9 dated 2015-08-20
DESCRIPTION | 8 MD5 | 18 R/boxr__internal_dir_comparison.R | 732 +++++++++++++++++++------------------- R/boxr__internal_misc.R | 2 R/boxr_auth.R | 4 build/vignette.rds |binary inst/doc/boxr.Rmd | 6 inst/doc/boxr.html | 356 +++++------------- man/box_auth.Rd | 2 vignettes/boxr.Rmd | 6 10 files changed, 492 insertions(+), 642 deletions(-)
Title: Bootstrap Subsamplings of Sparse Partial Least Squares -
Discriminant Analysis for Classification and Signature
Identification
Description: Applicable to any classification problem with more than 2 classes. It relies on bootstrap subsamplings of sPLS-DA and provides tools to select the most stable variables (defined as the ones consistently selected over the bootstrap subsamplings) and to predict the class of test samples.
Author: Florian Rohart [aut, cre], Kim-Anh Le Cao [boss], Christine Wells [boss]
Maintainer: Florian Rohart <florian.rohart@gmail.com>
Diff between bootsPLS versions 1.0.2 dated 2015-03-23 and 1.0.3 dated 2015-08-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/prediction.R | 12 ++++++------ R/spls.hybrid.R | 19 +++++++++++++++---- 5 files changed, 33 insertions(+), 18 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between marked versions 1.1.8 dated 2015-03-16 and 1.1.9 dated 2015-08-19
DESCRIPTION | 12 ++++---- MD5 | 49 +++++++++++++++++--------------- NAMESPACE | 23 ++++++++++++++- NEWS | 14 +++++++++ R/HMMLikelihood.r | 5 ++- R/HMMutilities.r | 18 ++++++++---- R/Observation_functions.r | 56 ++++++++++++++++++++++++++++++++----- R/compute.real.R | 2 - R/create.dm.R | 33 +++++++++++++++------- R/crm.R | 32 +++++++++++++++++++-- R/marked-package.R | 66 ++++++++++++++++++++++++++++++++++++++++++++ R/omega.r | 11 ++++++- R/probitCJS.R | 18 ++++++------ R/setup.parameters.R | 13 ++++++-- R/simHMM.r | 4 +- R/simplify.r |only build/vignette.rds |binary data/sealions.rda |only inst/cjs.tpl | 6 ++-- inst/cjs_reml.tpl | 6 ++-- inst/cjsre.tpl | 8 ++--- inst/doc/markedVignette.pdf |binary man/create.dm.Rd | 4 ++ man/crm.Rd | 5 ++- man/omega.Rd | 2 - man/sealions.Rd |only src/mvmsdmat.f | 4 ++ 27 files changed, 302 insertions(+), 89 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-6 dated 2015-08-03 and 0.1-7 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/MultiMahalanobis.R | 2 +- inst/tests/test.MultiMahalanobis.r | 20 ++++++++++---------- 4 files changed, 18 insertions(+), 18 deletions(-)
Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. Ongoing developments of the package
focus on offering easy to use tools for creating other spatio-dynamic
models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.1 dated 2015-07-16 and 1.1.1 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 2 +- R/animate_bs.R | 2 +- R/animate_model.R | 8 ++++---- R/animate_rb.R | 2 +- R/animate_sm.R | 2 +- R/animate_ss.R | 2 +- R/mrgf.R | 10 +++++----- R/plot_maps.R | 8 ++++---- build/vignette.rds |binary inst/doc/isem2013_jml.pdf |binary man/animate_bs.Rd | 2 +- man/animate_model.Rd | 2 +- man/animate_rb.Rd | 2 +- man/animate_sm.Rd | 2 +- man/animate_ss.Rd | 2 +- man/mrgf.Rd | 12 ++++++------ man/neigh_cell.Rd | 2 +- man/plot_maps.Rd | 2 +- man/run_model.Rd | 2 +- man/spdynmod.Rd | 2 +- 22 files changed, 58 insertions(+), 58 deletions(-)
Title: Basic Symbolic Expression Simplification
Description: Basic tools for symbolic expression simplification, e.g. simplify(x*1) => x, or simplify(sin(x)^2+cos(x)^2) => 1. Based on the "Expression v3" (Ev3) 1.0 system by Leo Liberti.
Author: Oliver Flasch [aut, cre], Felix Gorschlueter [aut], Leo Liberti [ctb]
Maintainer: Oliver Flasch <of@sourcewerk.de>
Diff between simplr versions 0.1-0 dated 2015-08-19 and 0.1-1 dated 2015-08-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/expression.cpp | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Graphical Integrated Text Mining Solution
Description: An R Commander plug-in providing an integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, vocabulary tables, terms
co-occurrences and documents similarity measures, time series analysis,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files, Twitter queries,
as well as from Dow Jones Factiva, LexisNexis, Europresse and Alceste files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between RcmdrPlugin.temis versions 0.7.3 dated 2015-01-23 and 0.7.4 dated 2015-08-19
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 7 ++++++- NEWS | 3 +++ R/corpusCa.R | 2 +- R/corpusClustering.R | 2 +- 6 files changed, 21 insertions(+), 13 deletions(-)
More information about RcmdrPlugin.temis at CRAN
Permanent link
Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better printing of large matrices via a new generic function
for "pretty" printing, and (iii) a number of convenience functions for users
more familiar with other scientific languages like 'Julia', 'Matlab'/'Octave',
or 'Python'+'NumPy'.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between ramify versions 0.3.1 dated 2015-07-08 and 0.3.2 dated 2015-08-19
DESCRIPTION | 15 ++++++++------- MD5 | 21 +++++++++++++-------- NAMESPACE | 1 + NEWS | 5 +++++ R/convenience.R | 18 ++++++++++++++++++ R/ramify.R | 49 ++++++++++++------------------------------------- R/utils.R | 13 ------------- build |only inst |only man/atleast_2d.Rd | 18 ++++++++++++++---- man/ramify.Rd | 45 ++++++++++----------------------------------- vignettes |only 12 files changed, 81 insertions(+), 104 deletions(-)
Title: Sensitivity Analysis in Observational Studies
Description: Sensitivity analysis in observational studies, including evidence factors and amplification, using the permutation distribution of Huber-Maritz M-statistics, including the permutational t-test.
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>
Diff between sensitivitymv versions 1.2 dated 2013-11-20 and 1.3 dated 2015-08-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + R/senmv.R | 20 ++++++++++---------- 4 files changed, 19 insertions(+), 18 deletions(-)
Title: Meta Analysis for SNP-Set (Sequence) Kernel Association Test
Description: Functions for Meta-analysis Burden test, SKAT and SKAT-O. These methods use summary-level score statistics to carry out gene-based meta-analysis for rare variants.
Author: Seunggeun (Shawn) Lee
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between MetaSKAT versions 0.40 dated 2014-03-27 and 0.60 dated 2015-08-19
DESCRIPTION | 14 +- MD5 | 49 ++++---- NAMESPACE | 7 - R/Meta_Null_Model.R | 18 +-- R/Meta_Permutation.R |only R/Meta_SKAT.R | 134 ++++++++++++++++++++++-- R/Meta_SSD_Read.R | 242 +++++++------------------------------------- R/Meta_SSD_Write.R | 42 +++++-- R/Meta_SaveData.R | 4 inst/doc/MetaSKAT.Rnw | 37 +++--- inst/doc/MetaSKAT.pdf |binary man/Example.rd | 6 - man/Generate_Meta_Files.rd | 46 ++++++-- man/MetaSKAT_MSSD_OneSet.rd | 41 +++---- man/MetaSKAT_wZ.rd | 45 +++++--- man/Meta_Null_Model.rd | 24 ++-- man/Open_MSSD_File_2Read.rd | 4 src/Interface_Meta.cpp | 8 - src/MatFile.cpp | 30 +++-- src/MatFile.h | 15 +- src/Meta.cpp | 14 ++ src/Meta.h | 4 src/Read_Dosage.cpp | 55 +++++++--- src/Read_Dosage.h | 3 src/error_messages.h | 1 vignettes/MetaSKAT.Rnw | 37 +++--- 26 files changed, 476 insertions(+), 404 deletions(-)
Title: Classes and Methods for Trajectory Data
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut],
Benedikt Klus [aut],
Benedikt Graeler [ctb],
Nikolai Gorte [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between trajectories versions 0.1-3 dated 2015-05-21 and 0.1-4 dated 2015-08-19
trajectories-0.1-3/trajectories/demo/Tracks.R |only trajectories-0.1-3/trajectories/demo/geolife.R |only trajectories-0.1-4/trajectories/DESCRIPTION | 18 trajectories-0.1-4/trajectories/MD5 | 45 - trajectories-0.1-4/trajectories/NAMESPACE | 40 - trajectories-0.1-4/trajectories/R/Class-Tracks.R | 50 - trajectories-0.1-4/trajectories/R/Tracks-methods.R | 407 ++---------- trajectories-0.1-4/trajectories/R/difftrack.R | 16 trajectories-0.1-4/trajectories/R/generalize.R |only trajectories-0.1-4/trajectories/R/stcube.R |only trajectories-0.1-4/trajectories/README.md | 2 trajectories-0.1-4/trajectories/build/vignette.rds |binary trajectories-0.1-4/trajectories/data/storms.rda |only trajectories-0.1-4/trajectories/demo/00Index | 10 trajectories-0.1-4/trajectories/demo/Geolife.R |only trajectories-0.1-4/trajectories/demo/enviroCaR.R | 10 trajectories-0.1-4/trajectories/demo/google.R |only trajectories-0.1-4/trajectories/demo/stcube.R | 3 trajectories-0.1-4/trajectories/demo/storms.R | 23 trajectories-0.1-4/trajectories/inst/doc/tracks.R | 50 - trajectories-0.1-4/trajectories/inst/doc/tracks.Rnw | 13 trajectories-0.1-4/trajectories/inst/doc/tracks.pdf |binary trajectories-0.1-4/trajectories/inst/history-06-09-2015.kml |only trajectories-0.1-4/trajectories/man/Track-class.Rd | 67 + trajectories-0.1-4/trajectories/man/stcube.Rd | 11 trajectories-0.1-4/trajectories/man/storms.Rd |only trajectories-0.1-4/trajectories/tests/tracks.Rout.save | 17 trajectories-0.1-4/trajectories/vignettes/tracks.Rnw | 13 28 files changed, 324 insertions(+), 471 deletions(-)
Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.1-7 dated 2015-02-22 and 2.2-0 dated 2015-08-19
DESCRIPTION | 20 MD5 | 52 NAMESPACE | 25 NEWS | 22 R/cluster.R | 4 R/commander.R | 2708 ++++--- R/data-menu.R | 611 + R/file-menu.R | 2036 +++-- R/globals.R | 110 R/graphs-menu.R | 2157 +++--- R/model-menu.R | 46 R/startup.R | 23 R/utilities.R | 716 +- inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/doc/Rcmdr-manual-source.zip |binary inst/etc/Rcmdr-RMarkdown-Template.Rmd |only inst/etc/Rcmdr-menus.txt | 12 inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary man/AuxiliarySoftware.Rd |only man/Commander.Rd | 5 man/Confint.Rd | 1 man/Rcmdr-package.Rd | 19 man/Rcmdr.Utilities.Rd | 18 po/R-Rcmdr.pot | 158 po/R-fr.po | 9503 ++++++++++++++-------------- po/R-ru.po | 153 src/Makevars.win | 2 28 files changed, 9685 insertions(+), 8716 deletions(-)
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived
supra-threshold differences. The package contains functions that
allow the user to design and run a difference scaling experiment,
to fit the resulting data by maximum likelihood and test the
internal validity of the estimated scale.
Author: Kenneth Knoblauch and Laurence T. Maloney,
based in part on C code written by Laurence T. Maloney
and J. N. Yang
Maintainer: Ken Knoblauch <ken.knoblauch@inserm.fr>
Diff between MLDS versions 0.4.3 dated 2014-01-20 and 0.4.5 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 9 +++++++++ build/vignette.rds |binary data/AutumnLab.rda |binary data/Transparency.rda |binary data/kk1.rda |binary data/kk2.rda |binary data/kk3.rda |binary data/kktriad.rda |binary inst/NEWS | 6 +++++- inst/doc/MLDS.Stex | 10 +++++----- inst/doc/MLDS.pdf |binary vignettes/MLDS.Stex | 10 +++++----- 14 files changed, 41 insertions(+), 28 deletions(-)
Title: Interactive Q-Learning
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn <kalinn@ncsu.edu>
Diff between iqLearn versions 1.3 dated 2015-02-25 and 1.4 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 +++- inst/doc/iqLearn.Rnw | 10 +++++----- vignettes/iqLearn.Rnw | 10 +++++----- 5 files changed, 21 insertions(+), 19 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now
uses and relies on grid graphics and formal (S4) classes and
methods.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas
Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>,
contains copies of lattice functions written by Deepayan Sarkar
<deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.27.0 dated 2014-08-09 and 1.27.1 dated 2015-08-19
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++++----------- R/hdiffplot.R | 2 +- R/hexPlotMA.R | 37 +++++++++++++++++++++---------------- R/hexViewport.R | 9 ++++++--- R/lattice.R | 12 ++++++------ README.md |only TODO | 5 +++++ build/vignette.rds |binary man/erode.hexbin.Rd | 2 +- man/gplot.hexbin.Rd | 2 +- man/grid.hexagons.Rd | 2 +- tests/hray.Rout.save |only tests/large.Rout.save |only tests/viewp-ex.Rout.save |only vignettes/hexagon_binning.Rnw | 15 +++++++++------ 16 files changed, 73 insertions(+), 52 deletions(-)
Title: Easy Authentication with Google OAuth2 APIs
Description: Create R functions that interact with OAuth2 Google APIs easily,
with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAuthR versions 0.1.0 dated 2015-08-18 and 0.1.1 dated 2015-08-19
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/googleAuthR.R | 2 ++ R/googleAuthR_generator.R | 20 ++++++++++++-------- README.md | 8 ++++++++ inst/doc/googleAuthR.Rmd | 2 +- inst/doc/googleAuthR.html | 6 +++--- man/Authentication.Rd | 2 +- man/googleAuthR.Rd | 3 +++ vignettes/googleAuthR.Rmd | 2 +- 10 files changed, 43 insertions(+), 26 deletions(-)
Title: Print Nicely Formatted Comments for Use in Script Files
Description: Functions to
produce nicely formatted comments to use in R-scripts (or
Latex/HTML/markdown etc). A comment with formatting is printed to the
console and can then be copied to a script.
Author: Erik Bulow
Maintainer: Erik Bulow <erik.bulow@rccvast.se>
Diff between commentr versions 0.1 dated 2014-10-20 and 1.0.1 dated 2015-08-19
commentr-0.1/commentr/R/comment_line.R |only commentr-0.1/commentr/tests/testthat/test-comment_line.R |only commentr-1.0.1/commentr/DESCRIPTION | 10 commentr-1.0.1/commentr/MD5 | 37 +-- commentr-1.0.1/commentr/NAMESPACE | 3 commentr-1.0.1/commentr/NEWS |only commentr-1.0.1/commentr/R/block_comment.R | 43 +-- commentr-1.0.1/commentr/R/commentr.R | 74 +++--- commentr-1.0.1/commentr/R/header_comment.R | 73 +++--- commentr-1.0.1/commentr/R/help_functions.R | 38 ++- commentr-1.0.1/commentr/R/line_comment.R | 24 + commentr-1.0.1/commentr/README.md | 146 ++++++------ commentr-1.0.1/commentr/inst |only commentr-1.0.1/commentr/man/comment.Rd | 89 ++++--- commentr-1.0.1/commentr/man/comment_end.Rd | 4 commentr-1.0.1/commentr/man/comment_start.Rd | 4 commentr-1.0.1/commentr/man/comment_width.Rd | 3 commentr-1.0.1/commentr/man/empty_line.Rd | 4 commentr-1.0.1/commentr/man/full_line.Rd | 4 commentr-1.0.1/commentr/man/out.Rd |only commentr-1.0.1/commentr/tests/testthat/test-header_coment.R | 1 21 files changed, 339 insertions(+), 218 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.1.33 dated 2015-01-02 and 1.2.3 dated 2015-08-19
cgdsr-1.1.33/cgdsr/ChangeLog |only cgdsr-1.2.3/cgdsr/DESCRIPTION | 25 +++++++++++++----------- cgdsr-1.2.3/cgdsr/MD5 | 11 +++++----- cgdsr-1.2.3/cgdsr/NAMESPACE | 28 +++++++++++++++++++++------ cgdsr-1.2.3/cgdsr/R/cgdsr.R | 36 +++++++++++++++-------------------- cgdsr-1.2.3/cgdsr/inst/doc/cgdsr.pdf |binary cgdsr-1.2.3/cgdsr/inst/tests |only cgdsr-1.2.3/cgdsr/tests |only 8 files changed, 58 insertions(+), 42 deletions(-)
Title: Coarsened Exact Matching
Description: Implementation of the Coarsened Exact Matching algorithm.
Author: Iacus, Stefano M., King, Gary, Porro, Giuseppe
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between cem versions 1.1.16 dated 2015-06-04 and 1.1.17 dated 2015-08-19
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NAMESPACE | 6 ++++-- build/vignette.rds |binary inst/doc/JSSstyle/jss.pdf |binary inst/doc/cem.Rnw | 3 ++- inst/doc/coarsen1.pdf |binary inst/doc/teff.pdf |binary man/att.Rd | 27 +++++++++++++++------------ man/cem.Rd | 2 ++ man/imbalance.Rd | 2 ++ man/pscoreSelect.Rd | 4 +++- vignettes/cem.Rnw | 7 ++++--- 13 files changed, 47 insertions(+), 34 deletions(-)
Title: Streams of Random Numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.
Author: Josef Leydold <josef.leydold@wu.ac.at>
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between rstream versions 1.3.3 dated 2015-07-17 and 1.3.4 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS | 7 ++++++- inst/doc/rstream.pdf |binary man/rstream-package.Rd | 4 ++-- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Libreria Del Laboratorio Di Statistica Con R
Description: Insieme di funzioni di supporto al volume "Laboratorio di
Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006.
This package contains sets of functions defined in "Laboratorio
di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia,
2006. Function names and docs are in italian as well.
Author: Stefano M.Iacus <stefano.iacus@unimi.it> and Guido Masarotto
<guido@sirio.stat.unipd.it>
Maintainer: Stefano M.Iacus <stefano.iacus@unimi.it>
Diff between labstatR versions 1.0.7 dated 2012-08-21 and 1.0.8 dated 2015-08-19
labstatR-1.0.7/labstatR/man/hist.pf.Rd |only labstatR-1.0.7/labstatR/man/mean.a.Rd |only labstatR-1.0.7/labstatR/man/mean.g.Rd |only labstatR-1.0.8/labstatR/DESCRIPTION | 13 +++++++------ labstatR-1.0.8/labstatR/MD5 | 14 +++++++------- labstatR-1.0.8/labstatR/NAMESPACE | 4 ++++ labstatR-1.0.8/labstatR/R/labstatR.R | 2 +- labstatR-1.0.8/labstatR/R/zzz.R | 5 ++++- labstatR-1.0.8/labstatR/man/histpf.Rd |only labstatR-1.0.8/labstatR/man/meana.Rd |only labstatR-1.0.8/labstatR/man/meang.Rd |only 11 files changed, 23 insertions(+), 15 deletions(-)
Title: Boosting Methods for GAMLSS
Description: Boosting models for fitting generalized additive models for
location, shape and scale (GAMLSS) to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between gamboostLSS versions 1.1-3 dated 2015-01-12 and 1.2-0 dated 2015-08-19
ChangeLog | 223 ++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 15 +- MD5 | 53 +++++---- NAMESPACE | 19 ++- R/as.families.R | 161 ++++++++++++----------------- R/cvrisk.R | 6 - R/families.R | 231 ++++++++++++++++-------------------------- R/helpers.R | 66 +++++++++++- R/mboostLSS.R | 10 + R/methods.R | 75 +++++++++++++ build |only data/india.RData |binary data/india.bnd.RData |binary inst/CITATION | 25 ++++ inst/NEWS.Rd | 47 +++++++- inst/doc |only man/as.families.Rd | 25 +++- man/cvrisk.Rd | 25 +++- man/families.Rd | 66 ++++++++---- man/gamboostLSS-package.Rd | 26 ++-- man/india.Rd | 12 +- man/mboostLSS.Rd | 50 +++------ man/methods.Rd | 73 ++++++++----- man/weighted_median.Rd |only tests/regtest-families.R | 48 ++++++++ tests/regtest-mstop.R | 3 tests/regtest-stabilization.R |only vignettes |only 28 files changed, 880 insertions(+), 379 deletions(-)
Title: Comprehensive Research Synthesis Tools for Systematic Reviews
and Meta-Analysis
Description: Functionalities for facilitating systematic reviews, data extractions, and meta-analyses. It includes a GUI (graphical user interface) to help screen the abstracts and titles of bibliographic data; tools to assign screening effort across multiple collaborators/reviewers and to assess inter-reviewer reliability; tools to help automate the download and retrieval of journal PDF articles from online databases; automated and manual data extraction from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random effects sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g., effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software. Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031.
Author: Marc J. Lajeunesse [aut, cre]
Maintainer: Marc J. Lajeunesse <lajeunesse@usf.edu>
Diff between metagear versions 0.1 dated 2015-05-21 and 0.2 dated 2015-08-19
DESCRIPTION | 14 ++--- MD5 | 84 +++++++++++++++++++--------------- NAMESPACE | 25 ++++++++++ NEWS.md |only R/MA_effectsTable.R | 1 R/PDF_download.R | 1 R/PDFs_collect.R | 3 - R/abstract_screener.R | 9 ++- R/browse_DOI.R | 1 R/covariance_commonControl.R | 2 R/effort_initialize.R | 2 R/effort_merge.R | 1 R/effort_redistribute.R | 2 R/effort_summary.R | 5 +- R/figure_add.R |only R/figure_barPlot.R |only R/figure_display.R |only R/figure_displayDetectedPoints.R | 1 R/figure_displayDetections.R | 1 R/figure_extractDetectedPoints.R | 1 R/figure_removeOutlyingPoints.R | 10 ++-- R/figure_scatterPlot.R | 3 - R/figure_utils.R | 4 + R/impute_missingness.R | 2 R/isPDF.R | 2 R/metagear_data.R | 13 +++++ R/random_N.R | 1 R/random_RR.R | 1 R/random_d.R | 1 R/random_pairedN.R | 3 - R/random_r.R | 1 R/replicate_MetaWin2.0.R | 5 +- data/Kortum_and_Acymyan_2013_Fig4.rda |only inst/CITATION | 10 ++-- man/Kortum_and_Acymyan_2013_Fig4.Rd |only man/abstract_screener.Rd | 6 +- man/effort_initialize.Rd | 2 man/effort_summary.Rd | 2 man/figure_add.Rd |only man/figure_barPlot.Rd |only man/figure_display.Rd |only man/figure_removeOutlyingPoints.Rd | 10 ++-- man/figure_scatterPlot.Rd | 2 man/impute_missingness.Rd | 2 man/isPDF.Rd | 2 man/random_pairedN.Rd | 2 man/replicate_MetaWin2.0.Rd | 3 - vignettes |only 48 files changed, 155 insertions(+), 85 deletions(-)
Title: Learning Causal Cyclic Graphs from Unknown Shift Interventions
Description: Code for 'backShift', an algorithm to estimate the connectivity
matrix of a directed (possibly cyclic) graph with hidden variables. The
underlying system is required to be linear and we assume that observations
under different shift interventions are available. For more details,
see <http://arxiv.org/abs/1506.02494>.
Author: Christina Heinze <heinze@stat.math.ethz.ch>
Maintainer: Christina Heinze <heinze@stat.math.ethz.ch>
Diff between backShift versions 0.1.1 dated 2015-06-09 and 0.1.2 dated 2015-08-19
backShift-0.1.1/backShift/demo |only backShift-0.1.2/backShift/DESCRIPTION | 14 +++++--- backShift-0.1.2/backShift/MD5 | 29 +++++++++++------- backShift-0.1.2/backShift/NAMESPACE | 6 ++- backShift-0.1.2/backShift/R/checkDiagonalization.R |only backShift-0.1.2/backShift/R/computeVarEnv.R | 2 - backShift-0.1.2/backShift/R/edgeRetention.R | 14 +++----- backShift-0.1.2/backShift/R/edgeSelection.R | 11 ++++-- backShift-0.1.2/backShift/R/plotGraph.R | 6 +-- backShift-0.1.2/backShift/R/plotInterventionVar.R |only backShift-0.1.2/backShift/R/simulate.R | 12 +++++-- backShift-0.1.2/backShift/build |only backShift-0.1.2/backShift/inst |only backShift-0.1.2/backShift/man/backShift.Rd | 21 ++++++++----- backShift-0.1.2/backShift/man/plotDiagonalization.Rd |only backShift-0.1.2/backShift/man/plotGraphEdgeAttr.Rd | 4 +- backShift-0.1.2/backShift/man/plotInterventionVars.Rd |only backShift-0.1.2/backShift/vignettes |only 18 files changed, 72 insertions(+), 47 deletions(-)
Title: R Interface to the UNU.RAN Random Variate Generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.22.0 dated 2015-07-17 and 0.23.0 dated 2015-08-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS | 5 +++++ inst/doc/Runuran.pdf |binary man/Runuran-package.Rd | 4 ++-- src/Makevars.in | 2 +- vignettes/inputs/version.tex | 2 +- 8 files changed, 21 insertions(+), 15 deletions(-)
Title: Basic Functions for Power Analysis
Description: Power analysis functions along the lines of Cohen (1988).
Author: Stephane Champely [aut],
Claus Ekstrom [ctb],
Peter Dalgaard [ctb],
Jeffrey Gill [ctb],
Jan Wunder [ctb],
Helios De Rosario [cre]
Maintainer: Helios De Rosario <helios.derosario@gmail.com>
Diff between pwr versions 1.1-2 dated 2015-02-27 and 1.1-3 dated 2015-08-19
ChangeLog | 8 ++++++++ DESCRIPTION | 13 ++++++++----- MD5 | 10 +++++----- NAMESPACE | 3 +++ R/pwr.t2n.test.R | 5 ++--- man/pwr-package.Rd | 6 +++--- 6 files changed, 29 insertions(+), 16 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-121 dated 2015-06-29 and 3.1-122 dated 2015-08-19
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/nlmefit.c | 15 ++++++++++----- 4 files changed, 27 insertions(+), 12 deletions(-)
Title: Land Use Change Modelling in R
Description: Classes and methods for spatially explicit land use change
modelling in R.
Author: Simon Moulds <simon.moulds10@imperial.ac.uk>
Maintainer: Simon Moulds <simon.moulds10@imperial.ac.uk>
Diff between lulcc versions 1.0.0 dated 2015-07-30 and 1.0.1 dated 2015-08-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/allocateclues.c | 8 ++++---- src/allow.c | 1 - src/total.c | 4 ++-- 5 files changed, 13 insertions(+), 14 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-65 dated 2015-07-02 and 0.8-66 dated 2015-08-19
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/spss.c | 3 ++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance, Spearman distance, Footrule distance, Hamming distance,
and Weigthed-tau distance and geo-Weighted Kendall distance.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 1.0.0 dated 2015-07-12 and 1.1.0 dated 2015-08-19
rankdist-1.0.0/rankdist/README.md |only rankdist-1.1.0/rankdist/DESCRIPTION | 11 rankdist-1.1.0/rankdist/MD5 | 64 +- rankdist-1.1.0/rankdist/NAMESPACE | 7 rankdist-1.1.0/rankdist/R/RcppExports.R | 16 rankdist-1.1.0/rankdist/R/class.R | 58 ++ rankdist-1.1.0/rankdist/R/method.R | 240 +++++++--- rankdist-1.1.0/rankdist/R/rankdist.R | 95 ++- rankdist-1.1.0/rankdist/R/utils.R | 59 ++ rankdist-1.1.0/rankdist/man/DistanceBlock.Rd | 6 rankdist-1.1.0/rankdist/man/DistanceMatrix.Rd | 5 rankdist-1.1.0/rankdist/man/DistancePair.Rd | 6 rankdist-1.1.0/rankdist/man/GenerateExample.Rd | 12 rankdist-1.1.0/rankdist/man/GenerateExampleTopQ.Rd | 15 rankdist-1.1.0/rankdist/man/HashtoRank.Rd | 4 rankdist-1.1.0/rankdist/man/ModelSummary.Rd | 2 rankdist-1.1.0/rankdist/man/MomentsEst.Rd | 2 rankdist-1.1.0/rankdist/man/OrderingToRanking.Rd | 2 rankdist-1.1.0/rankdist/man/RankControl-class.Rd | 2 rankdist-1.1.0/rankdist/man/RankControlCayley-class.Rd |only rankdist-1.1.0/rankdist/man/RankControlFootrule-class.Rd |only rankdist-1.1.0/rankdist/man/RankControlHamming-class.Rd |only rankdist-1.1.0/rankdist/man/RankControlKendall-class.Rd | 2 rankdist-1.1.0/rankdist/man/RankControlPhiComponent-class.Rd | 2 rankdist-1.1.0/rankdist/man/RankControlSpearman-class.Rd |only rankdist-1.1.0/rankdist/man/RankControlWeightedKendall-class.Rd | 2 rankdist-1.1.0/rankdist/man/RankControlWtau-class.Rd |only rankdist-1.1.0/rankdist/man/RankData-class.Rd | 10 rankdist-1.1.0/rankdist/man/RankDistanceModel.Rd | 8 rankdist-1.1.0/rankdist/man/RankInit-class.Rd | 2 rankdist-1.1.0/rankdist/man/RanktoHash.Rd | 5 rankdist-1.1.0/rankdist/man/apa_obj.Rd | 2 rankdist-1.1.0/rankdist/man/apa_partial_obj.Rd | 2 rankdist-1.1.0/rankdist/src/RcppExports.cpp | 150 ++++-- rankdist-1.1.0/rankdist/src/utils.cpp | 83 +++ rankdist-1.1.0/rankdist/tests/testthat/test_FindCayley.R |only rankdist-1.1.0/rankdist/tests/testthat/test_breaktie.R |only 37 files changed, 660 insertions(+), 214 deletions(-)
Title: Inverse Regression for Text Analysis
Description: Multinomial [inverse] regression inference for text documents and associated attributes. Provides fast sparse multinomial logistic regression for phrase counts. A minimalist partial least squares routine is also included. Note that the topic modeling capability of textir is now a separate package, maptpx.
Author: Matt Taddy <taddy@chicagobooth.edu>
Maintainer: Matt Taddy <taddy@chicagobooth.edu>
Diff between textir versions 2.0-3 dated 2015-04-01 and 2.0-4 dated 2015-08-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.5 dated 2015-06-29 and 4.7 dated 2015-08-18
ChangeLog | 12 ++ DESCRIPTION | 8 - MD5 | 17 ++-- R/genMakefile.R |only R/seqminer.R | 86 +++++++++++++++++++- README.md | 1 inst/CITATION | 8 - src/RangeList.cpp | 8 + src/StringUtil.h | 219 ++++++++++++++++++++++++++-------------------------- src/tabixLoader.cpp | 4 10 files changed, 235 insertions(+), 128 deletions(-)
Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference
semantics, similar to R's built-in reference classes. Compared to reference
classes, R6 classes are simpler and lighter-weight, and they are not built
on S4 classes so they do not require the methods package. These classes
allow public and private members, and they support inheritance, even when
the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.1.0 dated 2015-07-03 and 2.1.1 dated 2015-08-18
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS | 9 ++ R/clone.R | 14 ++-- R/print.R | 2 README.md | 7 +- build/vignette.rds |binary inst/doc/Introduction.html | 6 - inst/doc/Performance.html | 143 ++++++++++++++++++++++---------------------- tests/testthat/test-clone.R | 25 +++++++ 10 files changed, 136 insertions(+), 94 deletions(-)
Title: Two-Parameter HMD Model Life Table System
Description: Functions supplied in this package will implement
discriminant analysis to select an appropriate life table
family, select an appropriate alpha level based on a desired
life expectancy at birth, produce a model mortality pattern
based on family and level as well as plot the results.
Author: David J. Sharrow, GUI by Hana Sevcikova
Maintainer: David J. Sharrow <dsharrow@uw.edu>
Diff between LifeTables versions 0.2 dated 2012-08-22 and 1.0 dated 2015-08-18
DESCRIPTION | 16 ++-- MD5 | 43 ++++++------ NAMESPACE | 21 ++++-- R/alpha.e0.R | 2 R/gui.R | 149 ++++++++++++++++++++++----------------------- R/hmd.DA.R | 34 +++++----- R/hmd.DA.mx.R | 23 ++++-- R/lt.mx.R | 108 ++++++++++++++++---------------- R/mod.lt.R | 2 R/mortmod.R | 9 +- data/MLTobs.RData |binary inst |only man/LifeTables-internal.Rd | 6 - man/LifeTables-package.Rd | 10 +-- man/MLTobs.Rd | 32 ++++----- man/alpha.e0.Rd | 4 - man/hmd.DA.Rd | 12 +-- man/hmd.DA.mx.Rd | 42 ++++++++---- man/lt.mx.Rd | 24 ++++--- man/mod.lt.Rd | 21 +++--- man/modelLT.gui.Rd | 2 man/mortmod.Rd | 12 +-- man/plotMLT.Rd | 6 - 23 files changed, 309 insertions(+), 269 deletions(-)
Title: Local Fisher Discriminant Analysis
Description: Functions for performing and visualizing Local Fisher Discriminant Analysis(LFDA), Kernel Fisher Discriminant Analysis(KLFDA), and Semi-supervised Local Fisher Discriminant Analysis(SELF).
Author: Yuan Tang <terrytangyuan@gmail.com> with great contributions from Zachary Deane-Mayer.
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between lfda versions 1.0.0 dated 2015-08-13 and 1.1.0 dated 2015-08-18
DESCRIPTION | 8 +-- MD5 | 25 +++++++---- NAMESPACE | 7 +++ R/helpers.R | 69 ++++++++++++++++++++++++++------ R/klfda.R | 73 +++++++++++++--------------------- R/lfda.R | 77 +++++++++++++++++++++++------------- R/lfda_visualization.R | 5 ++ R/self.R |only README.md | 50 ++++++++++++++++++++++- man/getAffinityMatrix.Rd |only man/getMetricOfType.Rd |only man/predict.lfda.Rd |only man/print.lfda.Rd |only man/self.Rd |only tests/testthat/test_lfda.R | 6 ++ tests/testthat/test_self.R |only tests/testthat/test_visualization.R | 11 +++++ 17 files changed, 234 insertions(+), 97 deletions(-)
Title: Gamma Lasso Regression
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization, http://arxiv.org/abs/1308.5623.
Author: Matt Taddy <taddy@chicagobooth.edu>
Maintainer: Matt Taddy <taddy@chicagobooth.edu>
Diff between gamlr versions 1.13-1 dated 2015-04-14 and 1.13-2 dated 2015-08-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 4 ++++ R/cv.gamlr.R | 6 +++--- R/gamlr.R | 2 +- man/hockey.Rd | 2 +- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: Distributed Multinomial Regression
Description: Estimation for a multinomial logistic regression factorized into independent Poisson log regressions. See the textir package for applications in multinomial inverse regression analysis of text.
Author: Matt Taddy <taddy@chicagobooth.edu>
Maintainer: Matt Taddy <taddy@chicagobooth.edu>
Diff between distrom versions 0.3-2 dated 2015-04-01 and 0.3-3 dated 2015-08-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/dmr.R | 11 +++++++---- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Circular Visualization in R
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.0 dated 2015-08-01 and 0.3.1 dated 2015-08-18
circlize-0.3.0/circlize/vignettes/Output |only circlize-0.3.1/circlize/DESCRIPTION | 11 circlize-0.3.1/circlize/MD5 | 147 ++++------ circlize-0.3.1/circlize/NAMESPACE | 9 circlize-0.3.1/circlize/NEWS | 9 circlize-0.3.1/circlize/R/chordDiagram.R | 107 +++++-- circlize-0.3.1/circlize/R/link.R | 33 +- circlize-0.3.1/circlize/R/utils.R | 125 +++++--- circlize-0.3.1/circlize/inst/doc/circlize.pdf |binary circlize-0.3.1/circlize/inst/doc/circular_phylogenetic_tree.pdf |binary circlize-0.3.1/circlize/inst/doc/circular_visualization_of_matrix.pdf |binary circlize-0.3.1/circlize/inst/doc/genomic_plot.pdf |binary circlize-0.3.1/circlize/inst/doc/interesting_graphics.pdf |binary circlize-0.3.1/circlize/inst/doc/visualize_relations_by_chord_diagram.pdf |binary circlize-0.3.1/circlize/man/adjacencyList2Matrix.rd | 29 + circlize-0.3.1/circlize/man/chordDiagram.rd | 23 - circlize-0.3.1/circlize/man/chordDiagramFromDataFrame.rd | 20 - circlize-0.3.1/circlize/man/chordDiagramFromMatrix.rd | 17 - circlize-0.3.1/circlize/man/circlize-package.rd | 33 +- circlize-0.3.1/circlize/man/circlize.rd | 8 circlize-0.3.1/circlize/man/circos.axis.rd | 15 - circlize-0.3.1/circlize/man/circos.clear.rd | 18 - circlize-0.3.1/circlize/man/circos.dendrogram.rd | 11 circlize-0.3.1/circlize/man/circos.genomicDensity.rd | 57 ++- circlize-0.3.1/circlize/man/circos.genomicInitialize.rd | 81 ++--- circlize-0.3.1/circlize/man/circos.genomicLines.rd | 117 ++++--- circlize-0.3.1/circlize/man/circos.genomicLink.rd | 55 +-- circlize-0.3.1/circlize/man/circos.genomicPoints.rd | 21 - circlize-0.3.1/circlize/man/circos.genomicPosTransformLines.rd | 21 - circlize-0.3.1/circlize/man/circos.genomicRainfall.rd | 61 ++-- circlize-0.3.1/circlize/man/circos.genomicRect.rd | 21 - circlize-0.3.1/circlize/man/circos.genomicText.rd | 55 +-- circlize-0.3.1/circlize/man/circos.genomicTrack.rd | 13 circlize-0.3.1/circlize/man/circos.genomicTrackPlotRegion.rd | 29 + circlize-0.3.1/circlize/man/circos.info.rd | 51 +-- circlize-0.3.1/circlize/man/circos.initialize.rd | 47 +-- circlize-0.3.1/circlize/man/circos.initializeWithIdeogram.rd | 103 +++---- circlize-0.3.1/circlize/man/circos.lines.rd | 91 +++--- circlize-0.3.1/circlize/man/circos.link.rd | 89 +++--- circlize-0.3.1/circlize/man/circos.par.rd | 21 - circlize-0.3.1/circlize/man/circos.points.rd | 11 circlize-0.3.1/circlize/man/circos.polygon.rd | 59 ++-- circlize-0.3.1/circlize/man/circos.rect.rd | 11 circlize-0.3.1/circlize/man/circos.segments.rd | 6 circlize-0.3.1/circlize/man/circos.text.rd | 95 +++--- circlize-0.3.1/circlize/man/circos.track.rd | 7 circlize-0.3.1/circlize/man/circos.trackHist.rd | 49 +-- circlize-0.3.1/circlize/man/circos.trackLines.rd | 11 circlize-0.3.1/circlize/man/circos.trackPlotRegion.rd | 11 circlize-0.3.1/circlize/man/circos.trackPoints.rd | 11 circlize-0.3.1/circlize/man/circos.trackText.rd | 11 circlize-0.3.1/circlize/man/circos.update.rd | 7 circlize-0.3.1/circlize/man/circos.updatePlotRegion.rd | 13 circlize-0.3.1/circlize/man/colorRamp2.rd | 45 ++- circlize-0.3.1/circlize/man/cytoband.col.rd | 27 + circlize-0.3.1/circlize/man/draw.sector.rd | 89 +++--- circlize-0.3.1/circlize/man/generateRandomBed.rd | 25 - circlize-0.3.1/circlize/man/genomicDensity.rd | 32 +- circlize-0.3.1/circlize/man/get.all.sector.index.rd | 34 +- circlize-0.3.1/circlize/man/get.all.track.index.rd | 34 +- circlize-0.3.1/circlize/man/get.cell.meta.data.rd | 41 +- circlize-0.3.1/circlize/man/get.current.chromosome.rd | 34 +- circlize-0.3.1/circlize/man/getI.rd | 21 - circlize-0.3.1/circlize/man/highlight.chromosome.rd | 21 - circlize-0.3.1/circlize/man/highlight.sector.rd | 43 +- circlize-0.3.1/circlize/man/posTransform.default.rd | 23 - circlize-0.3.1/circlize/man/posTransform.text.rd | 17 - circlize-0.3.1/circlize/man/rainfallTransform.rd | 29 + circlize-0.3.1/circlize/man/rand_color.rd | 7 circlize-0.3.1/circlize/man/read.chromInfo.rd | 18 - circlize-0.3.1/circlize/man/read.cytoband.rd | 32 +- circlize-0.3.1/circlize/man/reverse.circlize.rd | 30 +- circlize-0.3.1/circlize/man/show.index.rd | 16 - 73 files changed, 1338 insertions(+), 1130 deletions(-)
Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark
shapes, including Procrustes analysis, graphical displays, principal
components analysis, permutation and bootstrap tests, thin-plate
spline transformation grids and comparing covariance matrices.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>
Diff between shapes versions 1.1-10 dated 2014-09-20 and 1.1-11 dated 2015-08-18
shapes-1.1-10/shapes/man/sooty.dat.Rd |only shapes-1.1-11/shapes/DESCRIPTION | 22 +++---- shapes-1.1-11/shapes/MD5 | 69 +++++++++++++----------- shapes-1.1-11/shapes/NAMESPACE | 6 ++ shapes-1.1-11/shapes/R/shapes.R | 51 +++++++++++++++++ shapes-1.1-11/shapes/data/apes.rda |binary shapes-1.1-11/shapes/data/brains.rda |binary shapes-1.1-11/shapes/data/cortical.rda |only shapes-1.1-11/shapes/data/digit3.dat.rda |binary shapes-1.1-11/shapes/data/dna.dat.rda |binary shapes-1.1-11/shapes/data/gels.rda |only shapes-1.1-11/shapes/data/gorf.dat.rda |binary shapes-1.1-11/shapes/data/gorm.dat.rda |binary shapes-1.1-11/shapes/data/humanmove.rda |only shapes-1.1-11/shapes/data/macaques.rda |binary shapes-1.1-11/shapes/data/macf.dat.rda |binary shapes-1.1-11/shapes/data/macm.dat.rda |binary shapes-1.1-11/shapes/data/mice.rda |binary shapes-1.1-11/shapes/data/nsa.rda |binary shapes-1.1-11/shapes/data/panf.dat.rda |binary shapes-1.1-11/shapes/data/panm.dat.rda |binary shapes-1.1-11/shapes/data/pongof.dat.rda |binary shapes-1.1-11/shapes/data/pongom.dat.rda |binary shapes-1.1-11/shapes/data/protein.rda |binary shapes-1.1-11/shapes/data/qcet2.dat.rda |binary shapes-1.1-11/shapes/data/qlet2.dat.rda |binary shapes-1.1-11/shapes/data/qset2.dat.rda |binary shapes-1.1-11/shapes/data/rats.rda |only shapes-1.1-11/shapes/data/sand.rda |binary shapes-1.1-11/shapes/data/schizophrenia.dat.rda |binary shapes-1.1-11/shapes/data/schizophrenia.rda |binary shapes-1.1-11/shapes/data/shells.rda |only shapes-1.1-11/shapes/data/sooty.dat.rda |binary shapes-1.1-11/shapes/data/sooty.rda |only shapes-1.1-11/shapes/data/steroids.rda |binary shapes-1.1-11/shapes/man/cortical.Rd |only shapes-1.1-11/shapes/man/gels.Rd |only shapes-1.1-11/shapes/man/humanmove.Rd |only shapes-1.1-11/shapes/man/rats.Rd |only shapes-1.1-11/shapes/man/shapes-internal.Rd | 2 shapes-1.1-11/shapes/man/shells.Rd |only shapes-1.1-11/shapes/man/sooty.Rd |only 42 files changed, 108 insertions(+), 42 deletions(-)
Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation
and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GlobalOptions versions 0.0.7 dated 2015-07-07 and 0.0.8 dated 2015-08-18
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------ NAMESPACE | 6 +-- NEWS | 6 +++ R/setGlobalOptions.R | 31 +++++++++++++++++ inst/doc/GlobalOptions.R | 3 + inst/doc/GlobalOptions.Rnw | 3 + inst/doc/GlobalOptions.pdf |binary inst/tests/test.R | 4 ++ man/Assign.GlobalOptionsFun.rd |only man/Subset.GlobalOptionsFun.rd |only man/setGlobalOptions.rd | 72 +++++++++++++++++++---------------------- vignettes/GlobalOptions.Rnw | 3 + 13 files changed, 103 insertions(+), 55 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.5.9 dated 2015-01-30 and 0.6.0 dated 2015-08-18
DESCRIPTION | 8 - MD5 | 58 +++++++----- NAMESPACE | 16 +++ NEWS | 18 +++ R/assign.plot.colors.R | 16 +-- R/classify.R | 19 ++- R/dist.argamon.R |only R/dist.cosine.R |only R/dist.delta.R |only R/dist.eder.R |only R/dist.simple.R |only R/gui.classify.R | 24 ++--- R/gui.stylo.R | 23 ++-- R/make.frequency.list.R |only R/oppose.R | 32 +++++- R/parse.pos.tags.R |only R/perform.delta.R | 97 +++++++++++--------- R/perform.nsc.R | 16 ++- R/rolling.classify.r | 108 +++++++++++++++++----- R/stylo.R | 187 +++++++++++++++++++++++---------------- R/stylo.default.settings.R | 58 +++++++++--- R/txt.to.words.R | 4 R/txt.to.words.ext.R | 23 ++-- man/delete.stop.words.Rd | 12 ++ man/dist.cosine.Rd |only man/dist.delta.Rd |only man/dist.simple.Rd |only man/make.frequency.list.Rd |only man/make.table.of.frequencies.Rd | 6 - man/parse.pos.tags.Rd |only man/perform.delta.Rd | 16 +-- man/perform.nsc.Rd | 8 + man/rolling.classify.Rd | 23 +++- man/rolling.delta.Rd | 10 +- man/stylo.Rd | 2 man/txt.to.words.Rd | 4 36 files changed, 527 insertions(+), 261 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.0-4 dated 2015-06-23 and 1.0-5 dated 2015-08-18
ChangeLog | 24 ++++++++++++++++++++++++ DESCRIPTION | 9 +++++---- MD5 | 28 +++++++++++++++------------- NAMESPACE | 6 +++++- R/ogr_sp.R | 7 +++++++ build/vignette.rds |binary configure | 18 +++++++++--------- data/GridsDatums.rda |only inst/ChangeLog | 24 ++++++++++++++++++++++++ inst/SVN_VERSION | 2 +- inst/doc/OGR_shape_encoding.pdf |binary man/GridsDatums.Rd |only man/showWKT.Rd | 6 +++++- src/init.c | 1 + src/ogr_proj.cpp | 33 +++++++++++++++++++++++++++++++++ src/rgdal.h | 1 + 16 files changed, 130 insertions(+), 29 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics are also available. polysat can assist the user in estimating the
ploidy of samples, and it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also
included for assigning alleles to isoloci in cases where one pair of
microsatellite primers amplifies alleles from two or more independently
segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.4-0 dated 2015-06-13 and 1.4-1 dated 2015-08-18
DESCRIPTION | 20 - MD5 | 38 +- NAMESPACE | 2 NEWS | 65 ++-- R/classes_generics_methods.R | 42 ++ R/dataimport.R | 13 build/vignette.rds |binary inst/doc/polysattutorial.R | 616 ++++++++++++++++++++--------------------- inst/doc/polysattutorial.pdf |binary inst/extdata/STRandExample.txt | 18 - man/alleleDiversity.Rd | 148 ++++----- man/catalanAlleles.Rd | 288 +++++++++---------- man/freq.to.genpop.Rd | 2 man/gendata.to.genind.Rd | 148 ++++----- man/mergeAlleleAssignments.Rd | 164 +++++----- man/pld.Rd | 206 ++++++------- man/ploidysuper-class.Rd | 146 ++++----- man/read.STRand.Rd | 174 +++++------ man/reformatPloidies.Rd | 224 +++++++------- vignettes/STRandExample.txt | 18 - 20 files changed, 1195 insertions(+), 1137 deletions(-)
Title: Longitudinal Data
Description: Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Dai Fang [ctb],
Luke Tierney [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between longitudinalData versions 2.3 dated 2015-05-19 and 2.4 dated 2015-08-18
longitudinalData-2.3/longitudinalData/R/longDataPlot.r |only longitudinalData-2.3/longitudinalData/man/plotTraj.Rd |only longitudinalData-2.3/longitudinalData/man/plotTraj3d.Rd |only longitudinalData-2.4/longitudinalData/DESCRIPTION | 10 longitudinalData-2.4/longitudinalData/MD5 | 72 longitudinalData-2.4/longitudinalData/NAMESPACE | 22 longitudinalData-2.4/longitudinalData/R/function.r | 20 longitudinalData-2.4/longitudinalData/R/global.r | 8 longitudinalData-2.4/longitudinalData/R/imputCopyMean.R | 100 longitudinalData-2.4/longitudinalData/R/imputCross.R | 172 - longitudinalData-2.4/longitudinalData/R/imputLinearInterpol.R | 76 longitudinalData-2.4/longitudinalData/R/imputTraj.R | 280 +- longitudinalData-2.4/longitudinalData/R/imputation.r | 246 +- longitudinalData-2.4/longitudinalData/R/listPartition.r | 759 +++--- longitudinalData-2.4/longitudinalData/R/longData.r | 39 longitudinalData-2.4/longitudinalData/R/longData3d.r | 88 longitudinalData-2.4/longitudinalData/R/newPlot.r |only longitudinalData-2.4/longitudinalData/R/parLongData.r | 317 +- longitudinalData-2.4/longitudinalData/R/parWindows.r | 252 +- longitudinalData-2.4/longitudinalData/R/partition.r | 1110 +++++----- longitudinalData-2.4/longitudinalData/man/ListPartition-class.Rd | 1 longitudinalData-2.4/longitudinalData/man/LongData-class.Rd | 27 longitudinalData-2.4/longitudinalData/man/LongData3d-class.Rd | 13 longitudinalData-2.4/longitudinalData/man/ParLongData-class.Rd | 2 longitudinalData-2.4/longitudinalData/man/Partition-class.Rd | 1 longitudinalData-2.4/longitudinalData/man/expandParLongData.Rd | 6 longitudinalData-2.4/longitudinalData/man/initializePartition.Rd | 12 longitudinalData-2.4/longitudinalData/man/longData-internal.Rd | 1 longitudinalData-2.4/longitudinalData/man/longData.Rd | 2 longitudinalData-2.4/longitudinalData/man/longData3d.Rd | 10 longitudinalData-2.4/longitudinalData/man/longitudinalData-package.Rd | 10 longitudinalData-2.4/longitudinalData/man/makeLatexFile.Rd | 6 longitudinalData-2.4/longitudinalData/man/parLongData.Rd | 11 longitudinalData-2.4/longitudinalData/man/plot3dPdf.Rd | 2 longitudinalData-2.4/longitudinalData/man/plotTrajMeans.Rd |only longitudinalData-2.4/longitudinalData/man/plotTrajMeans3d.Rd |only longitudinalData-2.4/longitudinalData/man/qualityCriterion.Rd | 6 longitudinalData-2.4/longitudinalData/man/restoreRealData.Rd | 6 longitudinalData-2.4/longitudinalData/man/saveTrianglesAsASY.Rd | 8 longitudinalData-2.4/longitudinalData/man/scale.Rd | 8 40 files changed, 1829 insertions(+), 1874 deletions(-)
More information about longitudinalData at CRAN
Permanent link
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml versions 2.3.1 dated 2015-06-04 and 2.4 dated 2015-08-18
DESCRIPTION | 10 MD5 | 30 - NAMESPACE | 22 - R/clusterLongData.R | 783 ++++++++++++++++---------------------- R/global.R | 20 R/kml.R | 163 +++++-- R/parKml.R | 2 man/ClusterLongData-class.Rd | 6 man/ParKml-class.Rd | 2 man/choice.Rd | 4 man/generateArtificialLongData.Rd | 11 man/kml-internal.Rd | 4 man/kml-package.Rd | 4 man/parKml.Rd | 4 man/plot.Rd | 16 man/plotMeans.Rd |only man/plotTraj.Rd |only 17 files changed, 546 insertions(+), 535 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and
pedigree-based partitioning of individual variation into a range of
environmental and genetic variance components for individual and
maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 1.6-2 dated 2015-06-27 and 1.6-3 dated 2015-08-18
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/warcolak.convert.R | 2 +- inst/doc/dmmOverview.pdf |binary inst/doc/mods.txt | 5 +++++ man/warcolak.convert.Rd | 11 +++++++++-- 7 files changed, 29 insertions(+), 13 deletions(-)
Title: Hybrid Simulation and Genome Scan for Dominant Markers
Description: Hybrid simulation functions for dominant genetic data and genome scan methods.
Author: Francisco Balao [aut, cre],
Juan Luis García-Castaño [aut]
Maintainer: Francisco Balao <fbalao@us.es>
Diff between AFLPsim versions 0.3-4 dated 2014-12-24 and 0.4-2 dated 2015-08-18
DESCRIPTION | 16 +++++++++------- MD5 | 14 +++++++++----- NAMESPACE | 9 +++++++-- R/sim2genind.R | 2 +- README.md | 7 ++++--- build |only inst/doc |only man/AFLPsim-package.Rd | 8 ++++---- vignettes |only 9 files changed, 34 insertions(+), 22 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.4.10 dated 2015-07-01 and 1.4.11 dated 2015-08-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 +- R/ABplot.R | 7 ++++--- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Spatio-Temporal Bayesian Modelling Using R
Description: Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTimer versions 2.0-0 dated 2015-01-19 and 2.0-1 dated 2015-08-18
DESCRIPTION | 13 MD5 | 14 NAMESPACE | 24 + inst/ChangeLog | 44 ++ src/equation_xb_ar.c | 12 src/equation_xb_gp.c | 35 -- src/equation_xb_gpp.c | 27 - src/prediction_xb_gpp.c | 827 ------------------------------------------------ 8 files changed, 118 insertions(+), 878 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.2-0 dated 2015-07-31 and 0.8.2-1 dated 2015-08-18
DESCRIPTION | 10 +-- MD5 | 23 ++++---- NAMESPACE | 4 + NEWS | 19 ++++++ R/corpus.R | 128 ++++++++++++++++++++++------------------------- R/dfm-methods.R | 45 ++++++++++++++-- README.md | 124 +++++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/quickstart.html | 42 ++++++++------- man/removeFeatures.Rd | 4 + man/sample.Rd |only man/subset.corpus.Rd | 14 +++-- man/trim.Rd | 6 +- 13 files changed, 295 insertions(+), 124 deletions(-)
Title: Utilities and Kinship Information for Research with the NLSY
Description: Utilities and kinship information for behavior genetics and
developmental research using the National Longitudinal Survey of Youth
(NLSY; <http://www.bls.gov/nls/>).
Author: Will Beasley, Joe Rodgers, David Bard, Michael Hunter, S. Mason Garrison, and Kelly
Meredith
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between NlsyLinks versions 1.302 dated 2013-12-06 and 2.0.1 dated 2015-08-18
NlsyLinks-1.302/NlsyLinks/inst/tests |only NlsyLinks-1.302/NlsyLinks/tests/DatasetsFixture.R |only NlsyLinks-2.0.1/NlsyLinks/DESCRIPTION | 32 - NlsyLinks-2.0.1/NlsyLinks/MD5 | 150 +++---- NlsyLinks-2.0.1/NlsyLinks/NAMESPACE | 5 NlsyLinks-2.0.1/NlsyLinks/NEWS | 15 NlsyLinks-2.0.1/NlsyLinks/R/AceEstimate.R | 43 -- NlsyLinks-2.0.1/NlsyLinks/R/AceLavaanGroup.R | 40 + NlsyLinks-2.0.1/NlsyLinks/R/AceUnivariate.R | 9 NlsyLinks-2.0.1/NlsyLinks/R/CleanSemAceDataset.R | 12 NlsyLinks-2.0.1/NlsyLinks/R/ColumnUtilities.R | 6 NlsyLinks-2.0.1/NlsyLinks/R/CreateAceEstimate.R | 12 NlsyLinks-2.0.1/NlsyLinks/R/CreatePairLinksDoubleEntered.R | 55 +- NlsyLinks-2.0.1/NlsyLinks/R/CreatePairLinksDoubleEnteredWithNoOutcomes.R | 17 NlsyLinks-2.0.1/NlsyLinks/R/CreatePairLinksSingleEntered.R | 23 - NlsyLinks-2.0.1/NlsyLinks/R/CreateSpatialNeighbours.R | 23 - NlsyLinks-2.0.1/NlsyLinks/R/CreateSubjectTag.R | 15 NlsyLinks-2.0.1/NlsyLinks/R/DeFriesFulker.R | 30 - NlsyLinks-2.0.1/NlsyLinks/R/ExtraOutcomes79Doc.R | 4 NlsyLinks-2.0.1/NlsyLinks/R/Links79PairDoc.R | 2 NlsyLinks-2.0.1/NlsyLinks/R/NlsyLinks.R | 21 NlsyLinks-2.0.1/NlsyLinks/R/RGroupSummary.R | 29 - NlsyLinks-2.0.1/NlsyLinks/R/ReadCsvNlsy79.R | 14 NlsyLinks-2.0.1/NlsyLinks/R/SurveyDateDoc.R |only NlsyLinks-2.0.1/NlsyLinks/R/ValidateOutcomeDataset.R | 26 - NlsyLinks-2.0.1/NlsyLinks/R/ValidatePairLinks.R | 24 - NlsyLinks-2.0.1/NlsyLinks/R/ValidatePairLinksAreSymmetric.R | 11 NlsyLinks-2.0.1/NlsyLinks/README.md |only NlsyLinks-2.0.1/NlsyLinks/build/vignette.rds |binary NlsyLinks-2.0.1/NlsyLinks/data/ExtraOutcomes79.rda |binary NlsyLinks-2.0.1/NlsyLinks/data/Links79Pair.rda |binary NlsyLinks-2.0.1/NlsyLinks/data/Links79PairExpanded.rda |binary NlsyLinks-2.0.1/NlsyLinks/data/SubjectDetails79.rda |binary NlsyLinks-2.0.1/NlsyLinks/data/SurveyDate.rda |only NlsyLinks-2.0.1/NlsyLinks/data/datalist |only NlsyLinks-2.0.1/NlsyLinks/inst/doc/Faq.R | 91 +--- NlsyLinks-2.0.1/NlsyLinks/inst/doc/Faq.Rnw | 56 +- NlsyLinks-2.0.1/NlsyLinks/inst/doc/Faq.pdf |binary NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsInvestigator.R | 13 NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsInvestigator.Rnw | 4 NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsInvestigator.pdf |binary NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsyAce.R | 127 ++--- NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsyAce.Rnw | 134 +++--- NlsyLinks-2.0.1/NlsyLinks/inst/doc/NlsyAce.pdf |binary NlsyLinks-2.0.1/NlsyLinks/man/Ace.Rd | 78 +-- NlsyLinks-2.0.1/NlsyLinks/man/AceEstimate-class.Rd | 26 - NlsyLinks-2.0.1/NlsyLinks/man/AceLavaanGroup.Rd | 67 --- NlsyLinks-2.0.1/NlsyLinks/man/CleanSemAceDataset.Rd | 66 +-- NlsyLinks-2.0.1/NlsyLinks/man/ColumnUtilities.Rd | 52 -- NlsyLinks-2.0.1/NlsyLinks/man/CreateAceEstimate.Rd | 43 -- NlsyLinks-2.0.1/NlsyLinks/man/CreatePairLinks.Rd | 86 +--- NlsyLinks-2.0.1/NlsyLinks/man/CreateSpatialNeighbours.Rd | 91 +--- NlsyLinks-2.0.1/NlsyLinks/man/CreateSubjectTag.Rd | 34 - NlsyLinks-2.0.1/NlsyLinks/man/ExtraOutcomes79.Rd | 58 +- NlsyLinks-2.0.1/NlsyLinks/man/GetDetails-methods.Rd | 7 NlsyLinks-2.0.1/NlsyLinks/man/Links79Pair.Rd | 213 ++++------ NlsyLinks-2.0.1/NlsyLinks/man/Links79PairExpanded.Rd | 128 ++---- NlsyLinks-2.0.1/NlsyLinks/man/NlsyLinks-package.Rd | 141 +++--- NlsyLinks-2.0.1/NlsyLinks/man/RGroupSummary.Rd | 95 +--- NlsyLinks-2.0.1/NlsyLinks/man/ReadCsvNlsy79.Rd | 44 -- NlsyLinks-2.0.1/NlsyLinks/man/SubjectDetails79.Rd | 20 NlsyLinks-2.0.1/NlsyLinks/man/SurveyDate.Rd |only NlsyLinks-2.0.1/NlsyLinks/man/ValidateOutcomeDataset.Rd | 49 +- NlsyLinks-2.0.1/NlsyLinks/man/ValidatePairLinks.Rd | 40 - NlsyLinks-2.0.1/NlsyLinks/man/ValidatePairLinksAreSymmetric.Rd | 29 - NlsyLinks-2.0.1/NlsyLinks/tests/test-all.R |only NlsyLinks-2.0.1/NlsyLinks/tests/testthat |only NlsyLinks-2.0.1/NlsyLinks/vignettes/Faq-concordance.tex |only NlsyLinks-2.0.1/NlsyLinks/vignettes/Faq.Rnw | 56 +- NlsyLinks-2.0.1/NlsyLinks/vignettes/NlsInvestigator.Rnw | 4 NlsyLinks-2.0.1/NlsyLinks/vignettes/NlsyAce.Rnw | 134 +++--- 71 files changed, 1182 insertions(+), 1422 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.3.4 dated 2015-07-07 and 1.3.5 dated 2015-08-17
DESCRIPTION | 12 ++-- MD5 | 44 +++++++-------- R/0gm.R | 133 ++++++++++++++++++++++++++++++++++++++++++------ R/excProb.R | 4 - R/glgm.R | 2 R/lgcp.R | 6 +- R/loglikLgm.R | 51 ++++++++++++++++-- R/maternGmrfPrec.R | 10 ++- R/spdfToBrick.R | 2 data/gambiaUTM.RData |binary data/loaloa.RData |binary data/murder.RData |binary data/nn32.RData |binary data/rongelapUTM.RData |binary data/swissRain.RData |binary data/swissRainR.RData |binary data/torontoPop.RData |binary data/wheat.RData |binary src/Makevars | 1 src/gmrfLik.c | 2 tests/lgcp.R | 21 +++---- tests/lgm.R | 3 - tests/stackRasterList.R | 2 23 files changed, 219 insertions(+), 74 deletions(-)
Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within
(i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in
long format (i.e., one observation per row), potentially aggregating multiple
observations per individual and cell of the design. mixed() fits mixed models using
lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger
approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs),
or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default
(imitating commercial statistical software).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.13-145 dated 2015-01-12 and 0.14-2 dated 2015-08-17
afex-0.13-145/afex/R/aov.car.R |only afex-0.13-145/afex/R/nice.anova.R |only afex-0.13-145/afex/man/aov.car.Rd |only afex-0.13-145/afex/man/nice.anova.Rd |only afex-0.13-145/afex/tests/testthat/test-all.R |only afex-0.13-145/afex/tests/testthat/test-aov.car-basic.R |only afex-0.13-145/afex/tests/testthat/test-aov.car-bugs.R |only afex-0.13-145/afex/tests/testthat/test-aov.car-structural.R |only afex-0.14-2/afex/DESCRIPTION | 62 afex-0.14-2/afex/MD5 | 99 - afex-0.14-2/afex/NAMESPACE | 144 +- afex-0.14-2/afex/NEWS | 71 + afex-0.14-2/afex/R/afex-package.R | 44 afex-0.14-2/afex/R/allFit.R | 1 afex-0.14-2/afex/R/aov_car.R |only afex-0.14-2/afex/R/compare.2.vectors.R | 15 afex-0.14-2/afex/R/deprecated.R |only afex-0.14-2/afex/R/helpers.R |only afex-0.14-2/afex/R/ks2013.3-data.R |only afex-0.14-2/afex/R/md_12.1-data.R | 2 afex-0.14-2/afex/R/md_15.1-data.R | 2 afex-0.14-2/afex/R/methods.afex_aov.R |only afex-0.14-2/afex/R/mixed.R | 261 +++- afex-0.14-2/afex/R/nice.R |only afex-0.14-2/afex/R/obk.long-data.R | 1 afex-0.14-2/afex/R/sk2011.1-data.R |only afex-0.14-2/afex/R/sk2011.2-data.R |only afex-0.14-2/afex/R/zzz.R | 36 afex-0.14-2/afex/build |only afex-0.14-2/afex/data/ks2013.3.rda |only afex-0.14-2/afex/data/md_12.1.rda |binary afex-0.14-2/afex/data/md_15.1.rda |binary afex-0.14-2/afex/data/md_16.1.rda |binary afex-0.14-2/afex/data/md_16.4.rda |binary afex-0.14-2/afex/data/obk.long.rda |binary afex-0.14-2/afex/data/sk2011.1.rda |only afex-0.14-2/afex/data/sk2011.2.rda |only afex-0.14-2/afex/inst |only afex-0.14-2/afex/man/afex-package.Rd | 55 afex-0.14-2/afex/man/afex_aov-methods.Rd |only afex-0.14-2/afex/man/afex_options.Rd |only afex-0.14-2/afex/man/allFit.Rd | 121 - afex-0.14-2/afex/man/aov_car.Rd |only afex-0.14-2/afex/man/compare.2.vectors.Rd | 163 +- afex-0.14-2/afex/man/deprecated.Rd |only afex-0.14-2/afex/man/ems.Rd | 91 - afex-0.14-2/afex/man/ks2013.3.Rd |only afex-0.14-2/afex/man/md_12.1.Rd | 97 - afex-0.14-2/afex/man/md_15.1.Rd | 137 +- afex-0.14-2/afex/man/md_16.1.Rd | 77 - afex-0.14-2/afex/man/md_16.4.Rd | 75 - afex-0.14-2/afex/man/mixed.Rd | 634 +++++----- afex-0.14-2/afex/man/nice.Rd |only afex-0.14-2/afex/man/obk.long.Rd | 102 - afex-0.14-2/afex/man/round_ps.Rd | 61 afex-0.14-2/afex/man/set_sum_contrasts.Rd | 59 afex-0.14-2/afex/man/sk2011.1.Rd |only afex-0.14-2/afex/man/sk2011.2.Rd |only afex-0.14-2/afex/tests/testthat.R |only afex-0.14-2/afex/tests/testthat/test-afex_aov.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-basic.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-bugs.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-structural.R |only afex-0.14-2/afex/tests/testthat/test-compare_2_vectors.R |only afex-0.14-2/afex/tests/testthat/test-lsmeans-interface.R |only afex-0.14-2/afex/tests/testthat/test-mixed-mw.R | 12 afex-0.14-2/afex/tests/testthat/test-mixed-structure.R | 64 - afex-0.14-2/afex/vignettes |only 68 files changed, 1460 insertions(+), 1026 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-25 1.0-1
2012-06-13 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-30 1.2
2014-02-21 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-18 1.0.1
Title: K-Means for Joint Longitudinal Data
Description: An implementation of k-means specifically design
to cluster joint trajectories (longitudinal data on
several variable-trajectories).
Like 'kml', it provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical
interface for choosing the 'best' number of clusters. In addition, the 3D graph
representing the mean joint-trajectories of each cluster can be exported through
LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml3d versions 2.3 dated 2015-05-21 and 2.4 dated 2015-08-17
kml3d-2.3/kml3d/man/choice.Rd |only kml3d-2.3/kml3d/tests/fromLongitudinalData.r |only kml3d-2.3/kml3d/tests/testClusterLongData3d.r |only kml3d-2.3/kml3d/tests/testDistance3d.r |only kml3d-2.3/kml3d/tests/testKml3d.r |only kml3d-2.4/kml3d/DESCRIPTION | 10 kml3d-2.4/kml3d/MD5 | 41 - kml3d-2.4/kml3d/NAMESPACE | 8 kml3d-2.4/kml3d/R/clusterLongData3d.r | 784 +++++++++----------- kml3d-2.4/kml3d/R/global.r | 10 kml3d-2.4/kml3d/R/kml3d.r | 41 - kml3d-2.4/kml3d/man/ClusterLongData3d-class.Rd | 3 kml3d-2.4/kml3d/man/affectIndiv3d.Rd | 8 kml3d-2.4/kml3d/man/calculTrajMean3d.Rd | 8 kml3d-2.4/kml3d/man/generateArtificialLongData3d.Rd | 9 kml3d-2.4/kml3d/man/kml3d-package.Rd | 10 kml3d-2.4/kml3d/man/kml3d.Rd | 2 kml3d-2.4/kml3d/man/plot.Rd | 36 kml3d-2.4/kml3d/man/plot3d.Rd | 24 kml3d-2.4/kml3d/man/plot3dPdf.Rd | 2 kml3d-2.4/kml3d/man/plotMean3d.Rd |only kml3d-2.4/kml3d/man/plotTraj3d.Rd |only kml3d-2.4/kml3d/tests/01_testDistance3d.r |only kml3d-2.4/kml3d/tests/02_fromLongitudinalData.r |only kml3d-2.4/kml3d/tests/03_testClusterLongData3d.r |only kml3d-2.4/kml3d/tests/04_testKml3d.r |only kml3d-2.4/kml3d/tests/CLD3.Rdata |binary 27 files changed, 470 insertions(+), 526 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits a stable isotope mixing model via JAGS in R. The package allows for any number of isotopes or sources, as well as concentration dependencies.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@ucd.ie>
Diff between simmr versions 0.1 dated 2015-08-06 and 0.2 dated 2015-08-17
simmr-0.1/simmr/vignettes/simmr_files |only simmr-0.2/simmr/DESCRIPTION | 8 simmr-0.2/simmr/MD5 | 41 +-- simmr-0.2/simmr/R/compare_groups.R |only simmr-0.2/simmr/R/plot.simmr_input.R | 41 ++- simmr-0.2/simmr/R/plot.simmr_output.R | 8 simmr-0.2/simmr/R/print.simmr_input.R | 1 simmr-0.2/simmr/R/print.simmr_output.R | 3 simmr-0.2/simmr/R/simmr_load.R | 17 + simmr-0.2/simmr/R/simmr_mcmc.R | 63 ++-- simmr-0.2/simmr/R/summary.simmr_output.R | 79 +++--- simmr-0.2/simmr/build/partial.rdb |binary simmr-0.2/simmr/inst/doc/simmr.R | 127 +++++++++ simmr-0.2/simmr/inst/doc/simmr.Rmd | 246 +++++++++++++++---- simmr-0.2/simmr/inst/doc/simmr.html | 362 +++++++++++++++++++++++----- simmr-0.2/simmr/man/compare_groups.Rd |only simmr-0.2/simmr/man/plot.simmr_input.Rd | 104 +++++++- simmr-0.2/simmr/man/plot.simmr_output.Rd | 8 simmr-0.2/simmr/man/simmr_load.Rd | 26 +- simmr-0.2/simmr/man/simmr_mcmc.Rd | 118 +++++++++ simmr-0.2/simmr/man/summary.simmr_output.Rd | 8 simmr-0.2/simmr/vignettes/simmr.Rmd | 246 +++++++++++++++---- 22 files changed, 1238 insertions(+), 268 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.300.4 dated 2015-08-04 and 0.5.400.2.0 dated 2015-08-17
ChangeLog | 24 +++ DESCRIPTION | 8 - MD5 | 79 ++++++---- NAMESPACE | 2 R/RcppArmadillo.package.skeleton.R | 12 - inst/NEWS.Rd | 18 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/examples/varSimulation.r | 3 inst/include/armadillo | 9 + inst/include/armadillo_bits/Op_bones.hpp | 76 ++++++++-- inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/auxlib_meat.hpp | 4 inst/include/armadillo_bits/fn_cumprod.hpp |only inst/include/armadillo_bits/fn_cumsum.hpp | 96 ++----------- inst/include/armadillo_bits/fn_diff.hpp |only inst/include/armadillo_bits/fn_eye.hpp | 4 inst/include/armadillo_bits/fn_find_unique.hpp |only inst/include/armadillo_bits/fn_interp1.hpp | 58 +++---- inst/include/armadillo_bits/fn_misc.hpp | 34 ++++ inst/include/armadillo_bits/fn_normalise.hpp | 35 ---- inst/include/armadillo_bits/fn_repmat.hpp | 11 + inst/include/armadillo_bits/fn_unique.hpp | 20 +- inst/include/armadillo_bits/forward_bones.hpp | 10 - inst/include/armadillo_bits/gmm_diag_meat.hpp | 14 + inst/include/armadillo_bits/mtOp_bones.hpp | 3 inst/include/armadillo_bits/op_cumprod_bones.hpp |only inst/include/armadillo_bits/op_cumprod_meat.hpp |only inst/include/armadillo_bits/op_cumsum_bones.hpp | 13 - inst/include/armadillo_bits/op_cumsum_meat.hpp | 138 +++++++++---------- inst/include/armadillo_bits/op_diff_bones.hpp |only inst/include/armadillo_bits/op_diff_meat.hpp |only inst/include/armadillo_bits/op_find_unique_bones.hpp |only inst/include/armadillo_bits/op_find_unique_meat.hpp |only inst/include/armadillo_bits/op_flip_meat.hpp | 32 ++-- inst/include/armadillo_bits/op_misc_bones.hpp | 10 + inst/include/armadillo_bits/op_misc_meat.hpp | 63 ++++++++ inst/include/armadillo_bits/op_normalise_bones.hpp | 17 -- inst/include/armadillo_bits/op_normalise_meat.hpp | 29 --- inst/include/armadillo_bits/op_repmat_bones.hpp | 7 inst/include/armadillo_bits/op_repmat_meat.hpp | 52 +++++-- inst/include/armadillo_bits/op_sum_meat.hpp | 7 inst/include/armadillo_bits/op_unique_bones.hpp | 38 ++++- inst/include/armadillo_bits/op_unique_meat.hpp | 122 ++++++++-------- inst/include/armadillo_bits/unwrap.hpp | 30 +++- 45 files changed, 630 insertions(+), 454 deletions(-)
Title: Classical, Reloaded and Adaptive FastICA Algorithms
Description: Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>
Diff between fICA versions 1.0-2 dated 2014-10-27 and 1.0-3 dated 2015-08-17
DESCRIPTION | 10 +-- MD5 | 24 ++++---- NAMESPACE | 4 + R/adapt_fICA.R | 116 ++++++++++++++++++--------------------- R/compute_alphas.R | 29 ++++----- R/fICA.R | 146 ++++++++++++++++++++++++++++++++------------------ R/internals.R | 57 +++++++------------ R/reloaded_fICA.R | 145 ++++++++++++++++++++++++------------------------- inst/ChangeLog | 4 + man/adapt_fICA.Rd | 5 + man/compute_alphas.Rd | 2 man/fICA-package.Rd | 4 - man/fICA.Rd | 9 ++- 13 files changed, 295 insertions(+), 260 deletions(-)
Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between cp4p versions 0.3 dated 2015-07-21 and 0.3.1 dated 2015-08-17
DESCRIPTION | 6 +-- MD5 | 12 +++---- R/estim_pi0.R | 82 +++++++++++++++++++++++++++++++++--------------- man/LFQRatio2.Rd | 8 ++-- man/LFQRatio25.Rd | 8 ++-- man/calibration.plot.Rd | 4 +- man/cp4p-package.Rd | 2 - 7 files changed, 78 insertions(+), 44 deletions(-)
Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric and squared symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>
Diff between BSSasymp versions 1.1-0 dated 2014-10-28 and 1.1-1 dated 2015-08-17
DESCRIPTION | 12 - MD5 | 40 +-- NAMESPACE | 4 R/CRB.R | 32 +- R/FOBI_ascov.R | 131 +++++------ R/FastICA_ascov.R | 502 +++++++++++++++++++++++++------------------ R/JADE_ascov.R | 136 +++++------ R/SOBI_ascov.R | 231 +++++++++---------- R/SOBIdefl_ascov.R | 244 +++++++++----------- inst/ChangeLog | 7 man/ASCOV_FastICAdefl.Rd | 2 man/ASCOV_FastICAdefl_est.Rd | 2 man/ASCOV_FastICAsym.Rd | 15 - man/ASCOV_FastICAsym_est.Rd | 6 man/ASCOV_JADE.Rd | 6 man/ASCOV_JADE_est.Rd | 4 man/ASCOV_SOBI.Rd | 2 man/ASCOV_SOBI_est.Rd | 10 man/BSSasymp-package.Rd | 6 man/CRB.Rd | 2 man/alphas.Rd | 2 21 files changed, 710 insertions(+), 686 deletions(-)
Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate
Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM). The package includes a vignette which can be accessed via vignette(‘Bchron’).
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>
Diff between Bchron versions 4.1.1 dated 2014-04-22 and 4.1.2 dated 2015-08-17
Bchron-4.1.1/Bchron/R/zzz.R |only Bchron-4.1.2/Bchron/DESCRIPTION | 19 +++++----- Bchron-4.1.2/Bchron/MD5 | 34 ++++++++++-------- Bchron-4.1.2/Bchron/NAMESPACE | 7 +++ Bchron-4.1.2/Bchron/R/BchronCalibrate.R | 8 ++-- Bchron-4.1.2/Bchron/R/BchronDensity.R | 20 +++++----- Bchron-4.1.2/Bchron/R/Bchronology.R | 18 ++++----- Bchron-4.1.2/Bchron/R/plot.BchronCalibratedDates.R | 16 ++++---- Bchron-4.1.2/Bchron/R/plot.BchronDensityRun.R | 12 +++--- Bchron-4.1.2/Bchron/R/plot.BchronDensityRunFast.R | 16 ++++---- Bchron-4.1.2/Bchron/R/plot.BchronRSLRun.R | 10 ++--- Bchron-4.1.2/Bchron/R/plot.BchronologyRun.R | 14 +++---- Bchron-4.1.2/Bchron/R/predict.BchronologyRun.R | 2 - Bchron-4.1.2/Bchron/R/summary.BchronCalibratedDates.R | 9 ++++ Bchron-4.1.2/Bchron/R/summary.BchronologyRun.R | 4 +- Bchron-4.1.2/Bchron/build |only Bchron-4.1.2/Bchron/inst |only Bchron-4.1.2/Bchron/man/plot.BchronCalibratedDates.Rd | 16 +++++++- Bchron-4.1.2/Bchron/vignettes |only 19 files changed, 120 insertions(+), 85 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 0.4-4 dated 2015-06-26 and 0.4-5 dated 2015-08-17
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 6 +++++- R/mstmap10.R | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 3 +++ inst/doc/asmapvignette.Rnw | 19 +++++++++++++------ inst/doc/asmapvignette.pdf |binary man/heatMap.Rd | 14 +++++++------- vignettes/asmapvignette.Rnw | 19 +++++++++++++------ vignettes/heatmap.png |binary vignettes/heatmapDH.png |binary 12 files changed, 58 insertions(+), 37 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-6 dated 2015-04-28 and 0.1-7 dated 2015-08-17
DESCRIPTION | 8 ++-- MD5 | 10 ++--- R/allPerm.R | 22 +++++-------- R/initMC.r | 91 +++++++++++++++++++++++++++--------------------------- R/nextPerm.R | 23 +++++-------- src/multicool.cpp | 1 6 files changed, 76 insertions(+), 79 deletions(-)
Title: Tools for Discrete Multivariate Mixed Membership Models
Description: Fits mixed membership models with discrete multivariate data (with
or without repeated measures) following the general framework of Erosheva et al
(2004). This package uses a Variational EM approach by approximating the
posterior distribution of latent memberships and selecting hyperparameters
through a pseudo-MLE procedure. Currently supported data types are
Bernoulli, multinomial and rank (Plackett-Luce). The extended GoM model with fixed stayers from Erosheva et al (2007) is now also supported. See Airoldi et al (2014) for other examples of mixed membership models.
Author: Y. Samuel Wang [aut, cre],
Elena A. Erosheva [aut]
Maintainer: Y. Samuel Wang <ysamwang@uw.edu>
Diff between mixedMem versions 1.0.2 dated 2015-04-30 and 1.1.0 dated 2015-08-16
DESCRIPTION | 18 +-- MD5 | 96 +++++++++++------- NAMESPACE | 1 R/ANES.R | 17 +-- R/RcppExports.R | 30 +++-- R/bic_calculator.R | 11 -- R/check_model.r | 25 ++++ R/findLabels.R | 70 +++++++------ R/mixedMemModel.R | 166 ++++++++++++++++---------------- R/mmVarFit.R | 187 +++++++++++++++++++------------------ R/rmixedMem.R | 54 +++++----- R/viz_functions.R | 146 +++++++++++++++------------- build/vignette.rds |binary inst/doc/mixedMem.R | 4 inst/doc/mixedMem.Rnw | 20 +-- inst/doc/mixedMem.pdf |binary man/ANES.Rd | 8 - man/computeBIC.Rd | 14 +- man/computeELBO.Rd | 16 +-- man/findLabels.Rd | 44 ++++---- man/gmv_theta.Rd | 15 +- man/mixedMem-package.Rd | 44 ++++---- man/mixedMemModel.Rd | 95 ++++++++++-------- man/mmVarFit.Rd | 136 +++++++++++++------------- man/permuteLabels.Rd | 20 ++- man/plot.mixedMemModel.Rd | 34 +++--- man/rmixedMem.Rd | 57 +++++------ man/summary.mixedMemModel.Rd | 9 - man/vizMem.Rd | 32 +++--- man/vizTheta.Rd | 28 +++-- src/RcppExports.cpp | 106 +++++++++++++------- src/eStep.h | 3 src/eStepExt.cpp |only src/eStepExt.h |only src/extended.cpp |only src/extended.h |only src/mStep.h | 3 src/mStepExt.cpp |only src/mStepExt.h |only src/mm_model.cpp | 47 +++++---- src/mm_model.h | 4 src/mm_modelExt.cpp |only src/mm_modelExt.h |only src/rFunc.cpp | 30 +++++ src/settings.h | 1 src/varInf.cpp | 9 - src/varInf.h | 2 src/varInfExt.cpp |only src/varInfExt.h |only vignettes/figure |only vignettes/framed.sty |only vignettes/mixedMem-concordance.tex |only vignettes/mixedMem.Rnw | 20 +-- 53 files changed, 902 insertions(+), 720 deletions(-)
Title: The Gauss Hypergeometric Function
Description: The Gaussian hypergeometric function for complex numbers.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hypergeo versions 1.2-9 dated 2014-11-06 and 1.2-11 dated 2015-08-16
DESCRIPTION | 12 ++++++------ MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + R/hypergeo.R | 14 +++++++------- R/hypergeo_ODE.R |only build/vignette.rds |binary inst/doc/hypergeometric.Rnw | 4 ++-- inst/doc/hypergeometric.pdf |binary man/f15.3.1.Rd | 2 +- man/f15.5.1.Rd |only man/genhypergeo.Rd | 2 +- man/hypergeo-package.Rd | 3 ++- man/hypergeo.Rd | 17 ++++++++++------- vignettes/hypergeometric.Rnw | 4 ++-- 14 files changed, 45 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-05-22 0.1-0
Title: Multidimensional Projection Techniques
Description: Multidimensional projection techniques are used to create two-dimensional representations of multidimensional data sets.
Author: Francisco M. Fatore,
Samuel G. Fadel
Maintainer: Francisco M. Fatore <fmfatore@gmail.com>
Diff between mp versions 0.2.0 dated 2014-11-14 and 0.3 dated 2015-08-16
DESCRIPTION | 12 +-- MD5 | 36 +++++++---- NAMESPACE | 9 ++ R/RcppExports.R | 12 ++- R/forceScheme.R | 130 +++++++++++++++++++--------------------- R/is_symmetric.R |only R/lamp.R | 167 +++++++++++++++++++++++++++------------------------- R/lsp.R |only R/mp.R | 13 +--- R/plmp.R |only R/tSNE.R |only README.md |only man/forceScheme.Rd | 33 +++++----- man/is.symmetric.Rd |only man/lamp.Rd | 22 ++++-- man/lsp.Rd |only man/mp.Rd | 3 man/plmp.Rd |only man/tSNE.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 67 +++++++++++--------- src/forceScheme.cpp | 71 ++++++---------------- src/lamp.cpp | 36 ++++++----- src/tSNE.cpp |only 24 files changed, 318 insertions(+), 295 deletions(-)
Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate georeferenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek <jstachel@sfwmd.gov>
Maintainer: Joseph Stachelek <jstachel@sfwmd.gov>
Diff between ipdw versions 0.2-2 dated 2015-03-11 and 0.2-3 dated 2015-08-16
ipdw-0.2-2/ipdw/R/df2spdf.R |only ipdw-0.2-3/ipdw/DESCRIPTION | 15 ++++++------ ipdw-0.2-3/ipdw/MD5 | 34 ++++++++++++++--------------- ipdw-0.2-3/ipdw/NAMESPACE | 3 +- ipdw-0.2-3/ipdw/R/costrasterGen.R | 19 ++++++++-------- ipdw-0.2-3/ipdw/R/errorGen.R | 15 ++++++------ ipdw-0.2-3/ipdw/R/ipdwInterp.R | 34 ++++++++++++++--------------- ipdw-0.2-3/ipdw/R/pathdistGen.R | 34 +++++++++++++++++++---------- ipdw-0.2-3/ipdw/README.md |only ipdw-0.2-3/ipdw/TODO | 8 ++++++ ipdw-0.2-3/ipdw/build/vignette.rds |binary ipdw-0.2-3/ipdw/inst/CITATION | 4 +-- ipdw-0.2-3/ipdw/inst/doc/ipdw.Rnw | 1 ipdw-0.2-3/ipdw/man/costrasterGen.Rd | 26 +++++++--------------- ipdw-0.2-3/ipdw/man/errorGen.Rd | 12 +++++----- ipdw-0.2-3/ipdw/man/ipdw.Rd | 41 +++++++++++++---------------------- ipdw-0.2-3/ipdw/man/ipdwInterp.Rd | 18 +++++---------- ipdw-0.2-3/ipdw/man/pathdistGen.Rd | 12 ++++------ ipdw-0.2-3/ipdw/vignettes/ipdw.Rnw | 1 19 files changed, 138 insertions(+), 139 deletions(-)
Title: Readable Regular Expressions
Description: An R framework for constructing and managing human
readable regular expressions. It aims to provide tools that
enable the user to write regular expressions in a way that is
similar to the ways R code is written. The tools allow the user
to (1) write in smaller, modular, named, sub-expressions, (2)
write top to bottom, rather than a single string (3) comment
individual chunks, (4) indent expressions to clearly present
regular expression groups, (5) add vertical line spaces and R
comments (i.e., #), and (6) test the validity of the
concatenated expression and the modular sub-expressions.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between regexr versions 1.0.2 dated 2015-01-11 and 1.1.0 dated 2015-08-16
DESCRIPTION | 31 +++++++------- MD5 | 71 ++++++++++++++++----------------- NAMESPACE | 2 NEWS | 13 ++++++ R/as.regexr.R | 34 ++++++++++++--- R/construct.R | 6 +- README.md | 43 +++++++------------ inst/CITATION | 6 +- inst/regexr_logo/Thumbs.db |only man/add_comments.Rd | 3 - man/as.regexr.Rd | 18 ++++++-- man/as.regexr.character.Rd | 3 - man/as.regexr.default.Rd | 3 - man/comments-set-.regexr.Rd | 3 - man/comments.Rd | 3 - man/comments.regexr.Rd | 3 - man/construct.Rd | 9 ++-- man/get_construct.Rd | 5 +- man/get_construct.reverse_construct.Rd | 3 - man/names-set-.regexr.Rd | 3 - man/names.regexr.Rd | 3 - man/print.regexr.Rd | 3 - man/print.reverse_construct.Rd | 3 - man/print.subcom.Rd | 3 - man/print.summary_regexr.Rd | 3 - man/print.unglued.Rd | 3 - man/regexr.Rd | 3 - man/set_names.Rd | 3 - man/subs-set-.regexr.Rd | 3 - man/subs.Rd | 3 - man/subs.regexr.Rd | 3 - man/summary.regexr.Rd | 3 - man/test.Rd | 3 - man/test.regexr.Rd | 3 - man/unglue.Rd | 3 - man/unglue.regexr.Rd | 3 - tests/testthat/test-as.regexr.R | 16 +++---- 37 files changed, 191 insertions(+), 135 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.11 dated 2015-01-11 and 5.18 dated 2015-08-16
DESCRIPTION | 21 ++++++--- MD5 | 55 +++++++++++++++---------- NAMESPACE | 93 ++++++++++++++++++++++++++++++++++++++++++- R/anova.R | 32 +++++++++++--- R/crq.R | 27 ++++++++++-- R/dynrq.R | 44 ++++++++++---------- R/qrisk.R | 1 R/quantreg.R | 19 ++++++-- R/rqss.R | 44 ++++++++++---------- R/sfn.R | 2 data/gasprice.rda |only inst/ChangeLog | 43 +++++++++++++++++++ inst/TODO | 3 + inst/doc/abbrev.bib |only inst/doc/book.bib |only inst/doc/engelcoef.pdf |only inst/doc/rq-Frankplot.pdf |only inst/doc/rq-cobar.pdf |only inst/doc/rq-engellogplot.pdf |only inst/doc/rq-engelplot.pdf |only inst/doc/rq-eqfs.pdf |only inst/doc/rq-mammals.pdf |only inst/doc/rq-mcycle1.pdf |only inst/doc/rq-regspline.pdf |only inst/doc/rq.R | 2 inst/doc/rq.Rnw | 4 + inst/doc/rq.pdf |binary man/anova.rq.Rd | 15 +++++- man/crq.Rd | 4 - man/dynrq.Rd | 1 man/gasprice.Rd |only man/predict.rqss.Rd | 2 man/rq.Rd | 2 man/rqss.object.Rd | 1 man/summary.rq.Rd | 15 ++++-- 35 files changed, 327 insertions(+), 103 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with
the 'qdap' package that may be useful outside of the context of
discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar
amounts, email addresses, hash tags, numbers, percentages,
citations, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.4.0 dated 2015-07-18 and 0.5.0 dated 2015-08-16
DESCRIPTION | 24 +- MD5 | 111 ++++++------ NAMESPACE | 3 NEWS | 50 +++++ R/explain.R | 87 +++++----- R/qdapRegex-package.R | 22 ++ R/rm_between.R | 93 ++++++++-- R/rm_nchar_words.R | 7 R/rm_number.R | 4 R/rm_tag.R | 18 -- R/rm_time.R | 107 ++++++++++++ R/rm_url.R | 5 README.md | 260 +++++++++++++++++------------- data/regex_cheat.rda |binary data/regex_supplement.rda |binary data/regex_usa.rda |binary inst/CITATION | 4 man/explain.Rd | 16 - man/regex_supplement.Rd | 15 + man/regex_usa.Rd | 7 man/rm_abbreviation.Rd | 4 man/rm_between.Rd | 26 ++- man/rm_bracket.Rd | 4 man/rm_caps.Rd | 4 man/rm_caps_phrase.Rd | 4 man/rm_citation.Rd | 4 man/rm_citation_tex.Rd | 4 man/rm_city_state.Rd | 4 man/rm_city_state_zip.Rd | 4 man/rm_date.Rd | 4 man/rm_default.Rd | 4 man/rm_dollar.Rd | 4 man/rm_email.Rd | 4 man/rm_emoticon.Rd | 4 man/rm_endmark.Rd | 4 man/rm_hash.Rd | 4 man/rm_nchar_words.Rd | 11 - man/rm_non_ascii.Rd | 4 man/rm_non_words.Rd | 4 man/rm_number.Rd | 13 - man/rm_percent.Rd | 4 man/rm_phone.Rd | 4 man/rm_postal_code.Rd | 4 man/rm_repeated_characters.Rd | 4 man/rm_repeated_phrases.Rd | 4 man/rm_repeated_words.Rd | 4 man/rm_tag.Rd | 22 +- man/rm_time.Rd | 95 ++++++++++ man/rm_title_name.Rd | 7 man/rm_url.Rd | 11 - man/rm_white.Rd | 4 man/rm_zip.Rd | 4 tests/testthat/test-as_time.R |only tests/testthat/test-explain.R | 2 tests/testthat/test-rm_between.R | 35 +++- tests/testthat/test-rm_between_multiple.R | 24 ++ tests/testthat/test-rm_time.R | 38 ++++ 57 files changed, 882 insertions(+), 335 deletions(-)
Title: Accurate, Adaptable, and Accessible Error Metrics for Predictive
Models
Description: Supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.
Author: Scott Fortmann-Roe
Maintainer: Scott Fortmann-Roe <scottfr@berkeley.edu>
Diff between A3 versions 0.9.2 dated 2013-07-15 and 1.0.0 dated 2015-08-16
A3-0.9.2/A3/man/plot.a3.Rd |only A3-0.9.2/A3/man/print.a3.Rd |only A3-0.9.2/A3/man/xtable.a3.Rd |only A3-0.9.2/A3/xtable.html |only A3-0.9.2/A3/xtable.tex |only A3-1.0.0/A3/DESCRIPTION | 19 +++----- A3-1.0.0/A3/MD5 | 36 ++++++++--------- A3-1.0.0/A3/NAMESPACE | 7 ++- A3-1.0.0/A3/NEWS | 9 ++++ A3-1.0.0/A3/R/A3.R | 66 ++++++++++++++++++++++--------- A3-1.0.0/A3/inst/CITATION | 30 +++++++------- A3-1.0.0/A3/man/a3.Rd | 30 ++++++-------- A3-1.0.0/A3/man/a3.base.Rd | 72 +++++++++++++--------------------- A3-1.0.0/A3/man/a3.gen.default.Rd | 41 +++++++------------ A3-1.0.0/A3/man/a3.lm.Rd | 25 ++++------- A3-1.0.0/A3/man/a3.r2.Rd | 27 +++++------- A3-1.0.0/A3/man/housing.Rd | 54 +++++++++++-------------- A3-1.0.0/A3/man/multifunctionality.Rd | 32 +++++++-------- A3-1.0.0/A3/man/plot.A3.Rd |only A3-1.0.0/A3/man/plotPredictions.Rd | 23 +++++----- A3-1.0.0/A3/man/plotSlopes.Rd | 19 ++++---- A3-1.0.0/A3/man/print.A3.Rd |only A3-1.0.0/A3/man/xtable.A3.Rd |only 23 files changed, 243 insertions(+), 247 deletions(-)
Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rugarch versions 1.3-4 dated 2014-11-08 and 1.3-6 dated 2015-08-16
ChangeLog | 19 DESCRIPTION | 14 MD5 | 123 - NAMESPACE | 12 R/arfima-classes.R | 2 R/arfima-main.R | 2 R/arfima-methods.R | 23 R/arfima-multi.R | 2 R/rugarch-aparch.R | 2 R/rugarch-armafor.R | 2 R/rugarch-benchmarks.R | 10 R/rugarch-bootstrap.R | 2 R/rugarch-classes.R | 2 R/rugarch-csgarch.R | 2 R/rugarch-cv.R |only R/rugarch-cwrappers.R | 2 R/rugarch-distributions.R | 36 R/rugarch-egarch.R | 2 R/rugarch-fgarch.R | 2 R/rugarch-gjrgarch.R | 2 R/rugarch-graphs.R | 2 R/rugarch-helperfn.R | 2 R/rugarch-igarch.R | 4 R/rugarch-imports.R | 2 R/rugarch-kappa.R | 2 R/rugarch-lossfn.R | 2 R/rugarch-mcsgarch.R | 2 R/rugarch-methods.R | 791 +++---- R/rugarch-multi.R | 2 R/rugarch-numderiv.R | 370 +-- R/rugarch-plots.R | 126 - R/rugarch-realgarch.R | 2 R/rugarch-rolling.R | 2 R/rugarch-series.R | 2 R/rugarch-sgarch.R | 2 R/rugarch-solvers.R | 2 R/rugarch-startpars.R | 2 R/rugarch-tests.R | 2475 +++++++++++------------ R/rugarch-uncertainty.R | 2 R/zzz.R | 2 README.md | 3 build/vignette.rds |binary inst/COPYRIGHTS | 20 inst/doc/Introduction_to_the_rugarch_package.pdf |binary inst/rugarch.tests/rugarch.test1.R | 18 man/ARFIMAfit-class.Rd | 10 man/BerkowitzTest.Rd | 13 man/arfimacv.Rd |only man/dmbp.Rd | 1 man/mcs.Rd |only man/rugarch-package.Rd | 6 man/uGARCHfit-class.Rd | 9 src/distributions.c | 2 src/distributions.h | 2 src/filters.c | 2 src/filters.h | 2 src/fracdiff.c | 2 src/fracdiff.h | 2 src/garchmodels.c | 2 src/garchsim.cpp | 2 src/garchsim.h | 2 src/rugarch.h | 2 vignettes/rugarch.tex | 49 vignettes/rugarchbib.bib | 1472 +++++++------ 64 files changed, 2938 insertions(+), 2740 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.0-22 dated 2015-07-28 and 1.0-23 dated 2015-08-16
DESCRIPTION | 10 - MD5 | 40 +++--- NAMESPACE | 12 + R/internals.R |only build/vignette.rds |binary inst/NEWS | 6 inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary man/party_intern.Rd |only tests/Distributions.Rout.save | 20 +-- tests/Examples/party-Ex.Rout.save | 195 +++++++++++++++---------------- tests/IndependenceTest-regtest.Rout.save | 8 - tests/LinearStatistic-regtest.Rout.save | 19 +-- tests/Node-regtest.Rout.save | 19 +-- tests/Predict-regtest.Rout.save | 20 +-- tests/RandomForest-regtest.Rout.save | 52 ++++---- tests/Splits-regtest.Rout.save | 34 ++--- tests/TestStatistic-regtest.Rout.save | 19 +-- tests/TreeGrow-regtest.Rout.save | 58 ++++----- tests/Utils-regtest.Rout.save | 19 +-- tests/bugfixes.Rout.save | 20 +-- tests/mob.Rout.save | 15 +- 22 files changed, 293 insertions(+), 273 deletions(-)
Title: Simple Key-Value Database
Description: Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple interface is provided for inserting,
retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be
treated much like environments and lists are already used in R. These utilities are provided to encourage
interactive and exploratory analysis on large datasets. Three different file formats for representing the
database are currently available and new formats can easily be incorporated by third parties for use in the
'filehash' framework.
Author: Roger D. Peng <rdpeng@jhu.edu>
Maintainer: Roger D. Peng <rdpeng@jhu.edu>
Diff between filehash versions 2.2-2 dated 2014-02-10 and 2.3 dated 2015-08-16
DESCRIPTION | 22 ++++++++++++++-------- MD5 | 10 +++++----- R/filehash-DB1.R | 21 ++++++++++++++++++--- R/filehash-RDS.R | 25 ++++++++++++++++--------- build/vignette.rds |binary inst/doc/filehash.pdf |binary 6 files changed, 53 insertions(+), 25 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.0-24 dated 2014-09-17 and 1.1-0 dated 2015-08-16
coin-1.0-24/coin/R/AdditionalClasses.R |only coin-1.0-24/coin/R/ClassicalTests.R |only coin-1.0-24/coin/inst/README |only coin-1.0-24/coin/man/Distribution.Rd |only coin-1.0-24/coin/man/ExactNullDistribution-methods.Rd |only coin-1.0-24/coin/man/MarginalHomogeneityTest.Rd |only coin-1.0-24/coin/man/MaxTypeIndependenceTestStatistic-class.Rd |only coin-1.0-24/coin/man/MaxstatTest.Rd |only coin-1.0-24/coin/man/PermutationDistribution.Rd |only coin-1.0-24/coin/man/QuadTypeIndependenceTestStatistic-class.Rd |only coin-1.0-24/coin/man/ScalarIndependenceTestStatistic-class.Rd |only coin-1.0-24/coin/man/SpearmanTest.Rd |only coin-1.0-24/coin/man/SurvTest.Rd |only coin-1.0-24/coin/man/coin.Rd |only coin-1.0-24/coin/man/initialize-methods.Rd |only coin-1.0-24/coin/man/show-methods.Rd |only coin-1.0-24/coin/tests/oral_contraceptives.rda |only coin-1.1-0/coin/DESCRIPTION | 21 coin-1.1-0/coin/MD5 | 284 coin-1.1-0/coin/NAMESPACE | 147 coin-1.1-0/coin/R/AAA.R | 8 coin-1.1-0/coin/R/Classes.R | 209 coin-1.1-0/coin/R/Confints.R | 476 coin-1.1-0/coin/R/ContingencyTests.R |only coin-1.1-0/coin/R/ContrastTest.R |only coin-1.1-0/coin/R/CorrelationTests.R |only coin-1.1-0/coin/R/ExactDistributions.R | 494 coin-1.1-0/coin/R/IndependenceTest.R | 142 coin-1.1-0/coin/R/InitMethods.R | 323 coin-1.1-0/coin/R/LocationTests.R |only coin-1.1-0/coin/R/MTP.R | 457 coin-1.1-0/coin/R/MarginalHomogeneityTests.R |only coin-1.1-0/coin/R/MaximallySelectedStatisticsTests.R |only coin-1.1-0/coin/R/Methods.R | 687 - coin-1.1-0/coin/R/MonteCarloDistributions.R |only coin-1.1-0/coin/R/Print.R | 217 coin-1.1-0/coin/R/ScaleTests.R |only coin-1.1-0/coin/R/SurvivalTests.R |only coin-1.1-0/coin/R/SymmetryTest.R |only coin-1.1-0/coin/R/SymmetryTests.R |only coin-1.1-0/coin/R/Transformations.R | 429 coin-1.1-0/coin/R/helpers.R | 510 - coin-1.1-0/coin/R/zAccess.R | 540 - coin-1.1-0/coin/build/vignette.rds |binary coin-1.1-0/coin/data/CWD.rda |binary coin-1.1-0/coin/data/GTSG.rda |only coin-1.1-0/coin/data/alpha.rda |binary coin-1.1-0/coin/data/alzheimer.rda |binary coin-1.1-0/coin/data/asat.rda |binary coin-1.1-0/coin/data/glioma.rda |binary coin-1.1-0/coin/data/hohnloser.rda |binary coin-1.1-0/coin/data/jobsatisfaction.rda |binary coin-1.1-0/coin/data/malformations.rda |only coin-1.1-0/coin/data/mercuryfish.rda |binary coin-1.1-0/coin/data/neuropathy.rda |binary coin-1.1-0/coin/data/ocarcinoma.rda |binary coin-1.1-0/coin/data/photocar.rda |binary coin-1.1-0/coin/data/rotarod.rda |binary coin-1.1-0/coin/data/treepipit.rda |binary coin-1.1-0/coin/data/vision.rda |only coin-1.1-0/coin/inst/CITATION | 22 coin-1.1-0/coin/inst/NEWS.Rd | 574 - coin-1.1-0/coin/inst/doc/LegoCondInf.R | 44 coin-1.1-0/coin/inst/doc/LegoCondInf.Rnw | 362 coin-1.1-0/coin/inst/doc/LegoCondInf.pdf |binary coin-1.1-0/coin/inst/doc/MAXtest.R | 746 - coin-1.1-0/coin/inst/doc/MAXtest.Rnw | 1122 +- coin-1.1-0/coin/inst/doc/MAXtest.pdf |binary coin-1.1-0/coin/inst/doc/coin.R | 38 coin-1.1-0/coin/inst/doc/coin.Rnw | 154 coin-1.1-0/coin/inst/doc/coin.pdf |binary coin-1.1-0/coin/inst/doc/coin_implementation.R | 107 coin-1.1-0/coin/inst/doc/coin_implementation.Rnw | 378 coin-1.1-0/coin/inst/doc/coin_implementation.pdf |binary coin-1.1-0/coin/inst/doxygen.cfg |only coin-1.1-0/coin/man/CWD.Rd | 111 coin-1.1-0/coin/man/ContingencyTests.Rd | 371 coin-1.1-0/coin/man/CorrelationTests.Rd |only coin-1.1-0/coin/man/ExpectCovar-class.Rd | 42 coin-1.1-0/coin/man/ExpectCovarInfluence-class.Rd | 45 coin-1.1-0/coin/man/GTSG.Rd |only coin-1.1-0/coin/man/IndependenceLinearStatistic-class.Rd | 103 coin-1.1-0/coin/man/IndependenceProblem-class.Rd | 54 coin-1.1-0/coin/man/IndependenceTest-class.Rd | 176 coin-1.1-0/coin/man/IndependenceTest.Rd | 345 coin-1.1-0/coin/man/IndependenceTestProblem-class.Rd | 70 coin-1.1-0/coin/man/IndependenceTestStatistic-class.Rd | 203 coin-1.1-0/coin/man/LocationTests.Rd | 477 coin-1.1-0/coin/man/MarginalHomogeneityTests.Rd |only coin-1.1-0/coin/man/MaximallySelectedStatisticsTests.Rd |only coin-1.1-0/coin/man/NullDistribution-class.Rd | 138 coin-1.1-0/coin/man/NullDistribution-methods.Rd |only coin-1.1-0/coin/man/NullDistribution.Rd |only coin-1.1-0/coin/man/PValue-class.Rd | 38 coin-1.1-0/coin/man/PermutationDistribution-methods.Rd |only coin-1.1-0/coin/man/ScaleTests.Rd | 333 coin-1.1-0/coin/man/SurvivalTests.Rd |only coin-1.1-0/coin/man/SymmetryProblem-class.Rd | 40 coin-1.1-0/coin/man/SymmetryTest.Rd | 268 coin-1.1-0/coin/man/SymmetryTests.Rd | 416 coin-1.1-0/coin/man/Transformations.Rd | 317 coin-1.1-0/coin/man/VarCovar-class.Rd |only coin-1.1-0/coin/man/alpha.Rd | 60 coin-1.1-0/coin/man/alzheimer.Rd | 72 coin-1.1-0/coin/man/asat.Rd | 67 coin-1.1-0/coin/man/coin-package.Rd |only coin-1.1-0/coin/man/expectation-methods.Rd | 103 coin-1.1-0/coin/man/glioma.Rd | 133 coin-1.1-0/coin/man/hohnloser.Rd | 62 coin-1.1-0/coin/man/jobsatisfaction.Rd | 46 coin-1.1-0/coin/man/malformations.Rd |only coin-1.1-0/coin/man/mercuryfish.Rd | 137 coin-1.1-0/coin/man/neuropathy.Rd | 70 coin-1.1-0/coin/man/ocarcinoma.Rd | 74 coin-1.1-0/coin/man/photocar.Rd | 130 coin-1.1-0/coin/man/pvalue-methods.Rd | 265 coin-1.1-0/coin/man/rotarod.Rd | 73 coin-1.1-0/coin/man/statistic-methods.Rd | 85 coin-1.1-0/coin/man/treepipit.Rd | 105 coin-1.1-0/coin/man/vision.Rd |only coin-1.1-0/coin/src/Classes.c | 9 coin-1.1-0/coin/src/Classes.h | 1 coin-1.1-0/coin/src/Helpers.c | 75 coin-1.1-0/coin/src/Helpers.h | 1 coin-1.1-0/coin/src/LinearStatistic.c | 185 coin-1.1-0/coin/src/LinearStatistic.h | 1 coin-1.1-0/coin/src/Makevars | 2 coin-1.1-0/coin/src/StreitbergRoehmel.c | 127 coin-1.1-0/coin/src/coin_common.h | 1 coin-1.1-0/coin/src/vandeWiel.c | 179 coin-1.1-0/coin/tests/AIDS.rda |binary coin-1.1-0/coin/tests/Examples/coin-Ex.Rout.save | 5097 +++++----- coin-1.1-0/coin/tests/FAILURE.rda |only coin-1.1-0/coin/tests/LANCET.rda |only coin-1.1-0/coin/tests/army.rda |binary coin-1.1-0/coin/tests/asthma.rda |binary coin-1.1-0/coin/tests/bloodp.rda |binary coin-1.1-0/coin/tests/bugfixes.R | 318 coin-1.1-0/coin/tests/bugfixes.Rout.save | 557 - coin-1.1-0/coin/tests/comparisons.R | 451 coin-1.1-0/coin/tests/comparisons.Rout.save | 490 coin-1.1-0/coin/tests/employment.rda |binary coin-1.1-0/coin/tests/lungcancer.rda |binary coin-1.1-0/coin/tests/regtest_2sample.R | 276 coin-1.1-0/coin/tests/regtest_2sample.Rout.save | 621 + coin-1.1-0/coin/tests/regtest_Ksample.R | 260 coin-1.1-0/coin/tests/regtest_Ksample.Rout.save | 585 + coin-1.1-0/coin/tests/regtest_MTP.R | 203 coin-1.1-0/coin/tests/regtest_MTP.Rout.save | 346 coin-1.1-0/coin/tests/regtest_contingency.R | 23 coin-1.1-0/coin/tests/regtest_contingency.Rout.save | 68 coin-1.1-0/coin/tests/regtest_correlation.R | 45 coin-1.1-0/coin/tests/regtest_correlation.Rout.save | 89 coin-1.1-0/coin/tests/regtest_distribution.R |only coin-1.1-0/coin/tests/regtest_distribution.Rout.save |only coin-1.1-0/coin/tests/regtest_helpers.R |only coin-1.1-0/coin/tests/regtest_helpers.Rout.save |only coin-1.1-0/coin/tests/regtest_midpvalue.R |only coin-1.1-0/coin/tests/regtest_midpvalue.Rout.save |only coin-1.1-0/coin/tests/regtest_trafo.R |only coin-1.1-0/coin/tests/regtest_trafo.Rout.save |only coin-1.1-0/coin/vignettes/LegoCondInf.Rnw | 362 coin-1.1-0/coin/vignettes/LegoCondInf.Rout.save |only coin-1.1-0/coin/vignettes/LegoCondInf.bib | 525 - coin-1.1-0/coin/vignettes/MAXtest.Rnw | 1122 +- coin-1.1-0/coin/vignettes/MAXtest.Rout.save |only coin-1.1-0/coin/vignettes/coin.Rnw | 154 coin-1.1-0/coin/vignettes/coin.Rout.save |only coin-1.1-0/coin/vignettes/coin.bib | 700 - coin-1.1-0/coin/vignettes/coin_implementation.Rnw | 378 coin-1.1-0/coin/vignettes/coin_implementation.Rout.save |only coin-1.1-0/coin/vignettes/references.bib | 691 - 172 files changed, 17158 insertions(+), 10304 deletions(-)
Title: A Gallery of Animations in Statistics and Utilities to Create
Animations
Description: Provides functions for animations in statistics, covering topics in
probability theory, mathematical statistics, multivariate statistics,
nonparametric statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning. These functions
may be helpful in teaching statistics and data analysis. Also provided in
this package are a series of functions to save animations to various formats,
e.g. Flash, GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(),
saveHTML(), saveLatex(), and saveVideo() respectively). PDF animations can
be inserted into Sweave/knitr easily.
Author: Yihui Xie [cre, aut],
Christian Mueller [ctb],
Lijia Yu [ctb],
Weicheng Zhu [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between animation versions 2.3 dated 2014-07-25 and 2.4 dated 2015-08-16
DESCRIPTION | 50 +++++++------ MD5 | 148 +++++++++++++++++++-------------------- NAMESPACE | 5 + NEWS | 11 ++ R/BM.circle.R | 2 R/MC.samplemean.R | 2 R/animation-package.R | 4 - R/boot.iid.R | 1 R/boot.lowess.R | 4 - R/cv.nfeaturesLDA.R | 2 R/g.brownian.motion.R | 2 R/grad.desc.R | 4 - R/im.convert.R | 3 R/lln.ani.R | 2 R/saveGIF.R | 2 R/saveSWF.R | 2 R/saveVideo.R | 19 ++--- R/zzz.R | 18 ++++ README.md | 4 - inst/misc/scianimator/index.html | 6 - man/BM.circle.Rd | 3 man/CLELAL09.Rd | 1 man/HuSpeech.Rd | 1 man/MC.hitormiss.Rd | 5 - man/MC.samplemean.Rd | 4 - man/ObamaSpeech.Rd | 1 man/Rosling.bubbles.Rd | 9 +- man/ani.options.Rd | 1 man/ani.pause.Rd | 1 man/ani.record.Rd | 1 man/ani.start.Rd | 1 man/animation-package.Rd | 5 - man/bisection.method.Rd | 3 man/boot.iid.Rd | 5 - man/boot.lowess.Rd | 3 man/brownian.motion.Rd | 3 man/buffon.needle.Rd | 3 man/clt.ani.Rd | 5 - man/conf.int.Rd | 1 man/convert.Rd | 1 man/cv.ani.Rd | 1 man/cv.nfeaturesLDA.Rd | 1 man/ecol.death.sim.Rd | 7 + man/flip.coin.Rd | 3 man/g.brownian.motion.Rd | 5 - man/grad.desc.Rd | 5 - man/iatemp.Rd | 1 man/kfcv.Rd | 1 man/kmeans.ani.Rd | 9 +- man/knn.ani.Rd | 3 man/least.squares.Rd | 9 +- man/lln.ani.Rd | 3 man/moving.block.Rd | 1 man/mwar.ani.Rd | 3 man/newton.method.Rd | 3 man/pageview.Rd | 1 man/pdftk.Rd | 1 man/pollen.Rd | 3 man/price.ani.Rd | 7 + man/qpdf.Rd | 1 man/quincunx.Rd | 9 +- man/sample.cluster.Rd | 3 man/sample.ratio.Rd | 3 man/sample.simple.Rd | 3 man/sample.strat.Rd | 3 man/sample.system.Rd | 3 man/saveGIF.Rd | 1 man/saveHTML.Rd | 1 man/saveLatex.Rd | 9 +- man/saveSWF.Rd | 5 - man/saveVideo.Rd | 28 ++++--- man/sim.qqnorm.Rd | 1 man/vanke1127.Rd | 26 +++--- man/vi.grid.illusion.Rd | 1 man/vi.lilac.chaser.Rd | 1 75 files changed, 305 insertions(+), 208 deletions(-)
Title: Sparse Linear Algebra
Description: Some basic linear algebra functionality for sparse matrices is
provided: including Cholesky decomposition and backsolving as well as
standard R subsetting and Kronecker products.
Author: Roger Koenker <rkoenker@uiuc.edu> and Pin Ng <Pin.Ng@NAU.EDU>
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between SparseM versions 1.6 dated 2015-01-05 and 1.7 dated 2015-08-15
SparseM-1.6/SparseM/inst/Changelog |only SparseM-1.7/SparseM/DESCRIPTION | 12 +++++++----- SparseM-1.7/SparseM/MD5 | 6 +++--- SparseM-1.7/SparseM/NAMESPACE | 22 ++++++++++++++++++---- SparseM-1.7/SparseM/inst/ChangeLog |only 5 files changed, 28 insertions(+), 12 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-15 dated 2015-07-01 and 2.4-18 dated 2015-08-15
ChangeLog | 11 DESCRIPTION | 13 MD5 | 136 ++++---- NAMESPACE | 10 R/VectorLayer.R | 12 R/aggregate_sp.R | 21 - R/as.spatial.R | 4 R/bind.R | 16 R/brick.R | 8 R/click.R | 4 R/coerce.R | 14 R/corLocal.R | 4 R/cropSpatial.R | 4 R/dataType.R | 6 R/destair.R | 4 R/erase.R | 2 R/extension.R | 6 R/extractPoints_sp.R | 2 R/fixDBFnames.R | 2 R/focalWeight.R | 4 R/geom.R | 4 R/getData.R | 72 ++-- R/getValuesRows.R | 6 R/hdr.R | 2 R/imageplot.R | 6 R/indexReplaceBrick.R | 2 R/inifile.R | 4 R/isLonLat.R | 4 R/kml.R | 12 R/labels.R |only R/makeProjString.R | 2 R/nchar.R |only R/newPLot.R | 4 R/plot.R | 4 R/plotRaster.R | 2 R/plotRaster2.R | 2 R/print.R | 2 R/project.R | 4 R/quad.R | 2 R/raster.R | 18 - R/rasterFromASCII.R | 2 R/rasterFromIDRISI.R | 2 R/rasterFromRasterFile.R | 6 R/rasterFromSAGA.R | 2 R/rasterOptions.R | 12 R/rasterize.R | 2 R/rasterizeLines.R | 2 R/select.R | 14 R/shift.R | 12 R/show.R | 12 R/shp.R | 4 R/simplifyPols.R | 2 R/spplot.R | 4 R/stack.R | 4 R/subset.R | 21 - R/text.R | 54 ++- R/tmpFile.R | 4 R/union_sp.R | 2 R/zoom.R | 6 build/vignette.rds |binary inst/doc/Raster.R | 732 ++++++++++++++++++++++---------------------- inst/doc/Raster.pdf |binary inst/doc/functions.R | 686 ++++++++++++++++++++--------------------- inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary inst/external/countries.csv | 511 +++++++++++++++--------------- man/Arith-methods.Rd | 1 man/aggregate.Rd | 3 man/corLocal.Rd | 2 man/text.Rd | 20 - 70 files changed, 1325 insertions(+), 1232 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Description: This is an implementation of constrained dual scaling for detecting response
styles in categorical data, including utility functions. The procedure involves adding
additional columns to the data matrix representing the boundaries between the rating categories.
The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are
sought which provide optimal scores for the rating categories. These optimal scores are
constrained to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can be diagnosed
from the optimal scores for said cluster, and this can be used to construct an
imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between cds versions 1.0.1 dated 2015-02-24 and 1.0.2 dated 2015-08-15
DESCRIPTION | 13 ++++---- MD5 | 72 ++++++++++++++++++++++++------------------------- NAMESPACE | 18 +++++++++++- R/cds.R | 3 ++ man/G.start.Rd | 2 - man/Lfun.G.upd.Rd | 2 - man/Lfun.Rd | 2 - man/addbounds.Rd | 2 - man/approxloads.Rd | 2 - man/calc.wt.bubbles.Rd | 2 - man/cds-package.Rd | 2 - man/cds.Rd | 2 - man/cds.sim.Rd | 2 - man/cdstoclue.Rd | 2 - man/clean.scales.Rd | 2 - man/create.ind.Rd | 2 - man/create.rs.Rd | 2 - man/createcdsdata.Rd | 2 - man/datsim.Rd | 2 - man/gen.cop.Rd | 2 - man/genPCA.Rd | 2 - man/group.ALS.Rd | 2 - man/indmat.Rd | 2 - man/ispline.Rd | 2 - man/orthprocr.Rd | 2 - man/plot.cds.Rd | 2 - man/plot.cdslist.Rd | 2 - man/print.cds.Rd | 2 - man/print.cdsdata.Rd | 2 - man/rcormat.Rd | 2 - man/rcovmat.Rd | 2 - man/sensory.Rd | 2 - man/sensory.aux.Rd | 2 - man/simpca.Rd | 2 - man/trQnorm.Rd | 2 - man/trRnorm.Rd | 2 - man/updateG.Rd | 2 - 37 files changed, 96 insertions(+), 76 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.5 dated 2015-07-01 and 1.6 dated 2015-08-15
DESCRIPTION | 6 ++-- MD5 | 65 ++++++++++++++++++++++++----------------------- NAMESPACE | 1 R/archivistOptions.R |only R/aread.R | 20 +++++++++----- R/createEmptyRepo.R | 8 +++++ R/saveToRepo.R | 3 +- R/zzz.R | 4 ++ demo/00Index | 1 demo/archivist_jss.r |only man/Repository.Rd | 2 - man/Tags.Rd | 6 ++-- man/addTagsRepo.Rd | 6 ++-- man/ahistory.Rd | 4 +- man/archivist-package.Rd | 6 ++-- man/archivistOptions.Rd |only man/aread.Rd | 2 - man/asearch.Rd | 2 - man/cache.Rd | 2 - man/copyToRepo.Rd | 2 - man/createEmptyRepo.Rd | 6 ++-- man/deleteRepo.Rd | 2 - man/getTags.Rd | 4 +- man/loadFromRepo.Rd | 2 - man/magrittr.Rd | 6 ++-- man/md5hash.Rd | 2 - man/rmFromRepo.Rd | 2 - man/saveSetToRepo.Rd | 2 - man/saveToRepo.Rd | 4 +- man/searchInRepo.Rd | 2 - man/setRepo.Rd | 4 +- man/shinySearchInRepo.Rd | 2 - man/showRepo.Rd | 2 - man/summaryRepo.Rd | 2 - man/zipRepo.Rd | 4 +- 35 files changed, 104 insertions(+), 82 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, quite a few related to graphics; many ported from S-plus times.
Author: Martin Maechler et al.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.0-27 dated 2015-01-07 and 1.0-28 dated 2015-08-15
DESCRIPTION | 16 +++++++------- MD5 | 57 +++++++++++++++++++++++++------------------------- NAMESPACE | 29 +++++++++++++++++++------ R/Defunct.R | 7 ------ R/misc-goodies.R | 8 +++---- R/prettylab.R | 6 +++-- R/prime-numbers-fn.R | 12 +++++----- R/ps.goodies.R |binary R/tkdensity.R | 52 +++++++++++++++++++++++++-------------------- R/u.goodies.R | 19 ++++++++++++++++ R/unix/Sys.ps.R | 17 -------------- demo/00Index | 1 demo/pretty-lab.R |only inst/NEWS.Rd | 24 ++++++++++++++++++++- man/ecdf.ksCI.Rd | 10 +++----- man/ellipsePoints.Rd | 2 - man/empty.dimnames.Rd | 6 ++--- man/errbar.Rd | 4 --- man/factorize.Rd | 4 --- man/histBxp.Rd | 4 +-- man/inv.seq.Rd | 4 --- man/last.Rd | 2 - man/missingCh.Rd | 4 --- man/p.tachoPlot.Rd | 4 --- man/p.ts.Rd | 3 -- man/plotStep.Rd | 3 -- man/primes.Rd | 3 -- man/tkdensity.Rd | 6 +---- man/u.sys.Rd | 21 ++++++++++++++---- man/unix/Sys.ps.Rd | 11 +++++---- 30 files changed, 190 insertions(+), 149 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.4 dated 2015-07-11 and 1.4.5 dated 2015-08-15
DESCRIPTION | 8 ++-- MD5 | 52 +++++++++++++++++++------------ NAMESPACE | 4 ++ NEWS | 8 ++++ R/GetFunctions.R |only R/GetPrivacySettings.R |only R/GetTemplate.R |only R/ParseSummary.R |only R/QueueSummary.R |only R/QueueTrended.R | 23 +++++++------ R/RSiteCatalyst.R | 4 +- R/SCAuth.R | 24 +++++++------- R/SubmitJsonQueueReport.R | 3 + man/GetEndpoint.Rd | 2 - man/GetFunctions.Rd |only man/GetPrivacySettings.Rd |only man/GetTemplate.Rd |only man/GetUsageLog.Rd | 2 - man/ParseFallout.Rd | 2 - man/ParseOvertime.Rd | 2 - man/ParsePathing.Rd | 2 - man/ParseRanked.Rd | 2 - man/ParseSummary.Rd |only man/ParseTrended.Rd | 2 - man/QueueSummary.Rd |only man/QueueTrended.Rd | 2 - man/RSiteCatalyst.Rd | 4 +- man/SCAuth.Rd | 18 +++++----- tests/testthat/test-QueueSummary.R |only tests/testthat/test-getfunctions.R |only tests/testthat/test-getprivacysettings.R |only tests/testthat/test-gettemplate.R |only tests/testthat/test-queueranked.R | 25 ++++++++++++++ tests/testthat/test-queuetrended.R | 30 +++++++++++++++++ 34 files changed, 151 insertions(+), 68 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written based on an accompanying 'RESTful' API.
Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more.
This package also supports experimental access to http://www.sealifebase.org data, which contains nearly
200,000 species records for all types of aquatic life not covered by 'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 0.2-2 dated 2014-01-07 and 2.0.1 dated 2015-08-15
rfishbase-0.2-2/rfishbase/R/analysis.R |only rfishbase-0.2-2/rfishbase/R/cacheFB.R |only rfishbase-0.2-2/rfishbase/R/clean_data.R |only rfishbase-0.2-2/rfishbase/R/ecology_from_html.R |only rfishbase-0.2-2/rfishbase/R/enviro-climate-range.R |only rfishbase-0.2-2/rfishbase/R/length-weight-table.R |only rfishbase-0.2-2/rfishbase/R/metabolism.R |only rfishbase-0.2-2/rfishbase/R/pictures.R |only rfishbase-0.2-2/rfishbase/R/zzz.R |only rfishbase-0.2-2/rfishbase/data/datalist |only rfishbase-0.2-2/rfishbase/data/labridtree.rda |only rfishbase-0.2-2/rfishbase/inst/doc/rfishbase |only rfishbase-0.2-2/rfishbase/inst/tests |only rfishbase-0.2-2/rfishbase/man/clean_data.Rd |only rfishbase-0.2-2/rfishbase/man/drop_nonascii.Rd |only rfishbase-0.2-2/rfishbase/man/familySearch.Rd |only rfishbase-0.2-2/rfishbase/man/findSpecies.Rd |only rfishbase-0.2-2/rfishbase/man/fish.data.Rd |only rfishbase-0.2-2/rfishbase/man/fish_names.Rd |only rfishbase-0.2-2/rfishbase/man/getData.Rd |only rfishbase-0.2-2/rfishbase/man/getDepth.Rd |only rfishbase-0.2-2/rfishbase/man/getEnviroClimateRange.Rd |only rfishbase-0.2-2/rfishbase/man/getIds.Rd |only rfishbase-0.2-2/rfishbase/man/getLengthWeight.Rd |only rfishbase-0.2-2/rfishbase/man/getMetabolism.Rd |only rfishbase-0.2-2/rfishbase/man/getPictures.Rd |only rfishbase-0.2-2/rfishbase/man/getQuantTraits.Rd |only rfishbase-0.2-2/rfishbase/man/getRefs.Rd |only rfishbase-0.2-2/rfishbase/man/getSize.Rd |only rfishbase-0.2-2/rfishbase/man/getTrophicLevel.Rd |only rfishbase-0.2-2/rfishbase/man/habitatSearch.Rd |only rfishbase-0.2-2/rfishbase/man/labridtree.Rd |only rfishbase-0.2-2/rfishbase/man/loadCache.Rd |only rfishbase-0.2-2/rfishbase/man/updateCache.Rd |only rfishbase-0.2-2/rfishbase/man/which_fish.Rd |only rfishbase-2.0.1/rfishbase/DESCRIPTION | 39 +-- rfishbase-2.0.1/rfishbase/MD5 | 150 +++++++----- rfishbase-2.0.1/rfishbase/NAMESPACE | 72 ++++- rfishbase-2.0.1/rfishbase/NEWS | 80 ++---- rfishbase-2.0.1/rfishbase/R/00-endpoint.R |only rfishbase-2.0.1/rfishbase/R/check_and_parse.R |only rfishbase-2.0.1/rfishbase/R/common_names.R |only rfishbase-2.0.1/rfishbase/R/distribution.R |only rfishbase-2.0.1/rfishbase/R/docs.R |only rfishbase-2.0.1/rfishbase/R/fishbase.R | 189 --------------- rfishbase-2.0.1/rfishbase/R/heartbeat.R |only rfishbase-2.0.1/rfishbase/R/list_fields.R |only rfishbase-2.0.1/rfishbase/R/load_taxa.R |only rfishbase-2.0.1/rfishbase/R/morpho_physio.R |only rfishbase-2.0.1/rfishbase/R/population_dynamics.R |only rfishbase-2.0.1/rfishbase/R/reproduction.R |only rfishbase-2.0.1/rfishbase/R/species.R |only rfishbase-2.0.1/rfishbase/R/species_list.R |only rfishbase-2.0.1/rfishbase/R/species_names.R |only rfishbase-2.0.1/rfishbase/R/synonyms.R |only rfishbase-2.0.1/rfishbase/R/trophic_ecology.R |only rfishbase-2.0.1/rfishbase/README.md | 206 +++++++++++++---- rfishbase-2.0.1/rfishbase/build |only rfishbase-2.0.1/rfishbase/data/fields.R |only rfishbase-2.0.1/rfishbase/data/fishbase.rda |binary rfishbase-2.0.1/rfishbase/data/sealifebase.rda |only rfishbase-2.0.1/rfishbase/inst/doc/tutorial.Rmd |only rfishbase-2.0.1/rfishbase/inst/doc/tutorial.html |only rfishbase-2.0.1/rfishbase/inst/examples |only rfishbase-2.0.1/rfishbase/inst/metadata |only rfishbase-2.0.1/rfishbase/man/common_names.Rd |only rfishbase-2.0.1/rfishbase/man/common_to_sci.Rd |only rfishbase-2.0.1/rfishbase/man/diet.Rd |only rfishbase-2.0.1/rfishbase/man/distribution.Rd |only rfishbase-2.0.1/rfishbase/man/docs.Rd |only rfishbase-2.0.1/rfishbase/man/ecology.Rd |only rfishbase-2.0.1/rfishbase/man/ecosystem.Rd |only rfishbase-2.0.1/rfishbase/man/faoareas.Rd |only rfishbase-2.0.1/rfishbase/man/fecundity.Rd |only rfishbase-2.0.1/rfishbase/man/fishbase.Rd | 46 +-- rfishbase-2.0.1/rfishbase/man/fooditems.Rd |only rfishbase-2.0.1/rfishbase/man/heartbeat.Rd |only rfishbase-2.0.1/rfishbase/man/introductions.Rd |only rfishbase-2.0.1/rfishbase/man/length_freq.Rd |only rfishbase-2.0.1/rfishbase/man/length_length.Rd |only rfishbase-2.0.1/rfishbase/man/length_weight.Rd |only rfishbase-2.0.1/rfishbase/man/list_fields.Rd |only rfishbase-2.0.1/rfishbase/man/load_taxa.Rd |only rfishbase-2.0.1/rfishbase/man/maturity.Rd |only rfishbase-2.0.1/rfishbase/man/morphology.Rd |only rfishbase-2.0.1/rfishbase/man/morphometrics.Rd |only rfishbase-2.0.1/rfishbase/man/occurrence.Rd |only rfishbase-2.0.1/rfishbase/man/oxygen.Rd |only rfishbase-2.0.1/rfishbase/man/ping.Rd |only rfishbase-2.0.1/rfishbase/man/popchar.Rd |only rfishbase-2.0.1/rfishbase/man/popgrowth.Rd |only rfishbase-2.0.1/rfishbase/man/popqb.Rd |only rfishbase-2.0.1/rfishbase/man/predators.Rd |only rfishbase-2.0.1/rfishbase/man/ration.Rd |only rfishbase-2.0.1/rfishbase/man/reproduction.Rd |only rfishbase-2.0.1/rfishbase/man/rfishbase-package.Rd |only rfishbase-2.0.1/rfishbase/man/sci_to_common.Rd |only rfishbase-2.0.1/rfishbase/man/sealifebase.Rd |only rfishbase-2.0.1/rfishbase/man/spawning.Rd |only rfishbase-2.0.1/rfishbase/man/species.Rd |only rfishbase-2.0.1/rfishbase/man/species_fields.Rd |only rfishbase-2.0.1/rfishbase/man/species_list.Rd |only rfishbase-2.0.1/rfishbase/man/species_names.Rd |only rfishbase-2.0.1/rfishbase/man/speed.Rd |only rfishbase-2.0.1/rfishbase/man/stocks.Rd |only rfishbase-2.0.1/rfishbase/man/swimming.Rd |only rfishbase-2.0.1/rfishbase/man/synonyms.Rd |only rfishbase-2.0.1/rfishbase/man/validate_names.Rd |only rfishbase-2.0.1/rfishbase/tests |only rfishbase-2.0.1/rfishbase/vignettes |only 110 files changed, 381 insertions(+), 401 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong <ykong@cuhk.edu.hk>
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.3.0 dated 2015-04-22 and 1.3.1 dated 2015-08-15
DESCRIPTION | 14 ++-- MD5 | 132 ++++++++++++++++++++-------------------- NAMESPACE | 3 R/fixed.R | 33 +++++++--- R/fixed0.R | 32 +++++++-- R/fixed01.R | 43 ++++++++++--- R/fixed1.R | 35 ++++++++-- R/joint.1z.R | 50 ++++++++++----- R/joint.1z0.R | 57 +++++++++++++---- R/joint.1z01.R | 64 ++++++++++++++----- R/joint.1z1.R | 52 ++++++++++++--- R/joint.2z.R | 118 ++++++++++++++++++++++++++--------- R/joint.2z0.R | 133 ++++++++++++++++++++++++++++++---------- R/joint.2z01.R | 140 ++++++++++++++++++++++++++++++++---------- R/joint.2z1.R | 134 ++++++++++++++++++++++++++++++---------- R/sep.1z.R | 49 ++++++++++---- R/sep.1z0.R | 57 +++++++++++++---- R/sep.1z01.R | 70 ++++++++++++++++----- R/sep.1z1.R | 50 +++++++++++---- R/sep.2z.R | 93 ++++++++++++++++++++++------ R/sep.2z0.R | 99 +++++++++++++++++++++++------- R/sep.2z01.R | 111 ++++++++++++++++++++++++++------- R/sep.2z1.R | 94 +++++++++++++++++++++++----- R/zoib.R | 155 +++++++++++++++++++++++++++-------------------- inst/bugs/fixed.bug | 28 ++++---- inst/bugs/fixed0.bug | 37 +++++------ inst/bugs/fixed01.bug | 48 +++++++------- inst/bugs/fixed1.bug | 30 ++++----- inst/bugs/joint_1z.bug | 38 +++++------ inst/bugs/joint_1z0.bug | 52 ++++++++------- inst/bugs/joint_1z01.bug | 66 ++++++++++---------- inst/bugs/joint_1z1.bug | 50 +++++++-------- inst/bugs/joint_2z.bug | 40 ++++++------ inst/bugs/joint_2z0.bug | 51 ++++++++------- inst/bugs/joint_2z01.bug | 68 +++++++++++--------- inst/bugs/joint_2z1.bug | 52 ++++++++------- inst/bugs/sep_1z.bug | 34 +++++----- inst/bugs/sep_1z0.bug | 45 ++++++------- inst/bugs/sep_1z01.bug | 59 +++++++++-------- inst/bugs/sep_1z1.bug | 47 +++++++------- inst/bugs/sep_2z.bug | 31 ++++----- inst/bugs/sep_2z0.bug | 46 +++++++------ inst/bugs/sep_2z01.bug | 56 +++++++++------- inst/bugs/sep_2z1.bug | 46 +++++++------ man/fixed.Rd | 5 + man/fixed0.Rd | 5 + man/fixed01.Rd | 5 + man/fixed1.Rd | 5 + man/joint.1z.Rd | 5 + man/joint.1z0.Rd | 5 + man/joint.1z01.Rd | 7 +- man/joint.1z1.Rd | 5 + man/joint.2z.Rd | 5 + man/joint.2z0.Rd | 5 + man/joint.2z01.Rd | 5 + man/joint.2z1.Rd | 5 + man/sep.1z.Rd | 5 + man/sep.1z0.Rd | 5 + man/sep.1z01.Rd | 5 + man/sep.1z1.Rd | 5 + man/sep.2z.Rd | 5 + man/sep.2z0.Rd | 5 + man/sep.2z01.Rd | 5 + man/sep.2z1.Rd | 5 + man/zoib-package.Rd | 10 +-- man/zoib.Rd | 109 ++++++++++++++++++--------------- tests/test2.R | 2 67 files changed, 1968 insertions(+), 997 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre],
David Bard [ctb],
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb],
Benjamin Nutter [ctb],
Andrew Peters [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 0.7-1 dated 2014-12-18 and 0.9.0 dated 2015-08-15
REDCapR-0.7-1/REDCapR/R/auxiliary.R |only REDCapR-0.7-1/REDCapR/tests/manual/test-read_errors.R |only REDCapR-0.7-1/REDCapR/tests/testthat/test-read_batch.R |only REDCapR-0.7-1/REDCapR/vignettes/images/ApiPrivilegeDashboard.PNG |only REDCapR-0.7-1/REDCapR/vignettes/images/EmailVerified.PNG |only REDCapR-0.7-1/REDCapR/vignettes/images/MagnifyingGlass.PNG |only REDCapR-0.9.0/REDCapR/DESCRIPTION | 17 REDCapR-0.9.0/REDCapR/MD5 | 153 REDCapR-0.9.0/REDCapR/NAMESPACE | 38 REDCapR-0.9.0/REDCapR/NEWS | 164 REDCapR-0.9.0/REDCapR/R/REDCapR-package.R | 24 REDCapR-0.9.0/REDCapR/R/create_batch_glossary.R | 126 REDCapR-0.9.0/REDCapR/R/metadata_utilities.R | 188 REDCapR-0.9.0/REDCapR/R/project_simple.R | 199 REDCapR-0.9.0/REDCapR/R/redcap_column_sanitize.R | 88 REDCapR-0.9.0/REDCapR/R/redcap_download_file_oneshot.R | 327 REDCapR-0.9.0/REDCapR/R/redcap_metadata_read.R | 295 REDCapR-0.9.0/REDCapR/R/redcap_project.R | 248 REDCapR-0.9.0/REDCapR/R/redcap_read.R | 404 REDCapR-0.9.0/REDCapR/R/redcap_read_oneshot.R | 430 REDCapR-0.9.0/REDCapR/R/redcap_upload_file_oneshot.R | 288 REDCapR-0.9.0/REDCapR/R/redcap_write.R | 307 REDCapR-0.9.0/REDCapR/R/redcap_write_oneshot.R | 376 REDCapR-0.9.0/REDCapR/R/retrieve_token.R |only REDCapR-0.9.0/REDCapR/R/utilities.R |only REDCapR-0.9.0/REDCapR/R/validate_for_write.R | 158 REDCapR-0.9.0/REDCapR/README.md | 172 REDCapR-0.9.0/REDCapR/build/vignette.rds |binary REDCapR-0.9.0/REDCapR/inst/doc/BasicREDCapROperations.R | 208 REDCapR-0.9.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 314 REDCapR-0.9.0/REDCapR/inst/doc/BasicREDCapROperations.html | 899 - REDCapR-0.9.0/REDCapR/inst/doc/SecurityDatabase.Rmd | 350 REDCapR-0.9.0/REDCapR/inst/doc/SecurityDatabase.html | 588 REDCapR-0.9.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 759 REDCapR-0.9.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 1148 - REDCapR-0.9.0/REDCapR/inst/misc/vignette.css | 72 REDCapR-0.9.0/REDCapR/inst/ssl_certs/Readme.md | 6 REDCapR-0.9.0/REDCapR/inst/ssl_certs/mozilla_ca_root.crt | 7882 +++++----- REDCapR-0.9.0/REDCapR/inst/test_data/levon_and_barry.jpg |only REDCapR-0.9.0/REDCapR/inst/test_data/project_color_boxes/Readme.md | 106 REDCapR-0.9.0/REDCapR/inst/test_data/project_color_boxes/color_boxes_data.csv | 8 REDCapR-0.9.0/REDCapR/inst/test_data/project_color_boxes/color_boxes_data_dictionary.csv | 6 REDCapR-0.9.0/REDCapR/inst/test_data/project_longitudinal |only REDCapR-0.9.0/REDCapR/inst/test_data/project_russian |only REDCapR-0.9.0/REDCapR/inst/test_data/project_simple/simple_data.csv | 32 REDCapR-0.9.0/REDCapR/inst/test_data/project_simple/simple_data_dictionary.csv | 34 REDCapR-0.9.0/REDCapR/inst/test_data/project_simple/simple_metadata.csv | 34 REDCapR-0.9.0/REDCapR/man/REDCapR.Rd | 36 REDCapR-0.9.0/REDCapR/man/create_batch_glossary.Rd | 119 REDCapR-0.9.0/REDCapR/man/metadata_utilities.Rd | 164 REDCapR-0.9.0/REDCapR/man/redcap_column_sanitize.Rd | 99 REDCapR-0.9.0/REDCapR/man/redcap_download_file_oneshot.Rd | 212 REDCapR-0.9.0/REDCapR/man/redcap_metadata_read.Rd | 164 REDCapR-0.9.0/REDCapR/man/redcap_project.Rd | 116 REDCapR-0.9.0/REDCapR/man/redcap_read.Rd | 236 REDCapR-0.9.0/REDCapR/man/redcap_read_oneshot.Rd | 304 REDCapR-0.9.0/REDCapR/man/redcap_upload_file_oneshot.Rd | 203 REDCapR-0.9.0/REDCapR/man/redcap_write.Rd | 228 REDCapR-0.9.0/REDCapR/man/redcap_write_oneshot.Rd | 201 REDCapR-0.9.0/REDCapR/man/replace_nas_with_explicit.Rd |only REDCapR-0.9.0/REDCapR/man/retrieve_token.Rd | 187 REDCapR-0.9.0/REDCapR/man/validate_for_write.Rd | 99 REDCapR-0.9.0/REDCapR/tests/manual/README.md | 8 REDCapR-0.9.0/REDCapR/tests/manual/test-could-not-connect-rate.R |only REDCapR-0.9.0/REDCapR/tests/manual/test-stress_test_serial.R |only REDCapR-0.9.0/REDCapR/tests/test-all.R | 25 REDCapR-0.9.0/REDCapR/tests/testthat/test-column-sanitize.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-create_batch_glossary.R | 162 REDCapR-0.9.0/REDCapR/tests/testthat/test-file_oneshot.R | 376 REDCapR-0.9.0/REDCapR/tests/testthat/test-metadata_read.R | 550 REDCapR-0.9.0/REDCapR/tests/testthat/test-metadata_utilities.R | 68 REDCapR-0.9.0/REDCapR/tests/testthat/test-project.R | 146 REDCapR-0.9.0/REDCapR/tests/testthat/test-read_batch_longitudinal.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-read_batch_simple.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-read_errors.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-read_oneshot.R | 524 REDCapR-0.9.0/REDCapR/tests/testthat/test-read_russian.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-retrieve_token.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-utilities.R |only REDCapR-0.9.0/REDCapR/tests/testthat/test-validate_for_write.R | 82 REDCapR-0.9.0/REDCapR/tests/testthat/test-write_batch.R | 364 REDCapR-0.9.0/REDCapR/tests/testthat/test-write_oneshot.R | 364 REDCapR-0.9.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 314 REDCapR-0.9.0/REDCapR/vignettes/SecurityDatabase.Rmd | 350 REDCapR-0.9.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 759 REDCapR-0.9.0/REDCapR/vignettes/images/ApiPrivilegeDashboard.png |only REDCapR-0.9.0/REDCapR/vignettes/images/EmailVerified.png |only REDCapR-0.9.0/REDCapR/vignettes/images/MagnifyingGlass.png |only 88 files changed, 11295 insertions(+), 11613 deletions(-)
Title: Beta-Diversity Within a Metaweb of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between betalink versions 2.0.2 dated 2015-07-15 and 2.1.0 dated 2015-08-15
DESCRIPTION | 4 +-- MD5 | 8 +++---- NEWS | 6 +++++ R/network_betadiversity.R | 46 ++++++++++++++++++++++++++----------------- man/network_betadiversity.Rd | 4 ++- 5 files changed, 43 insertions(+), 25 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
Author: Eduard Szoecs [aut, cre],
Daniel Muench [ctb]
Maintainer: Eduard Szoecs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.1 dated 2015-03-06 and 0.0.2 dated 2015-08-14
DESCRIPTION | 23 ++++++++----- MD5 | 40 +++++++++++++++-------- NAMESPACE | 8 +++- NEWS |only R/allanwood.R |only R/chemspider.R | 83 ++++++++++++++++++++++++++---------------------- R/cir.R | 32 ++++++++++++------ R/cts.R | 77 ++++++++++++++++++++++++++++++-------------- R/pan.R |only R/pubchem.R | 66 +++++++++++++++++++++++--------------- man/allanwood.Rd |only man/cid_compinfo.Rd | 16 ++++++--- man/cir_query.Rd | 8 ++++ man/csid_compinfo.Rd | 12 ++++-- man/csid_extcompinfo.Rd | 11 ++++-- man/cts_compinfo.Rd | 17 +++++++-- man/cts_convert.Rd | 12 +++++- man/get_cid.Rd | 9 ++++- man/get_csid.Rd | 4 +- man/pan.Rd |only tests |only 21 files changed, 272 insertions(+), 146 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between lsbclust versions 1.0.2 dated 2015-03-11 and 1.0.3 dated 2015-08-14
DESCRIPTION | 12 +++---- MD5 | 70 ++++++++++++++++++++++---------------------- NAMESPACE | 5 ++- R/RcppExports.R | 40 +++++++++++++++++++++++++ R/lsbclust.R | 3 + data/dcars.rda |binary data/lov.rda |binary data/supermarkets.rda |binary man/ClustMeans.Rd | 2 - man/KMeansW.Rd |only man/LossMat.Rd | 2 - man/bicomp.Rd | 2 - man/cmat.Rd | 2 - man/dcars.Rd | 2 - man/genproc.Rd | 2 - man/indarr.Rd | 2 - man/int.lsbclust.Rd | 2 - man/lov.Rd | 2 - man/lsbclust-package.Rd | 2 - man/lsbclust.Rd | 2 - man/lsbclusttoclue.Rd | 2 - man/orc.lsbclust.Rd | 2 - man/plot.bicomp.Rd | 2 - man/plot.col.kmeans.Rd | 2 - man/plot.int.lsbclust.Rd | 2 - man/plot.lsbclust.Rd | 2 - man/plot.ovl.kmeans.Rd | 2 - man/plot.row.kmeans.Rd | 2 - man/plot.step.lsbclust.Rd | 2 - man/print.lsbclust.Rd | 2 - man/sim.lsbclust.Rd | 2 - man/step.lsbclust.Rd | 2 - man/summary.int.lsbclust.Rd | 2 - man/summary.lsbclust.Rd | 2 - man/supermarkets.Rd | 2 - src/KMeansW.cpp |only src/RcppExports.cpp | 44 +++++++++++++++++++++++++++ 37 files changed, 159 insertions(+), 67 deletions(-)
Title: Generalized Elastic Nets
Description: Implements several extensions of the elastic net regularization scheme. These extensions include individual feature penalties for the L1 term, feature-feature penalties for the L2 term, as well as translation coefficients for the latter.
Author: Artem Sokolov
Maintainer: Artem Sokolov <artem.sokolov@gmail.com>
Diff between gelnet versions 1.1 dated 2015-05-14 and 1.2 dated 2015-08-14
CHANGES | 10 + DESCRIPTION | 8 - MD5 | 31 +++-- NAMESPACE | 4 R/gelnet.R | 254 ++++++++++++++++++++++++++++++++++++++++----- man/L1.ceiling.Rd | 2 man/adj2lapl.Rd | 4 man/adj2nlapl.Rd | 4 man/gelnet.L1bin.Rd | 4 man/gelnet.klr.Rd | 8 - man/gelnet.kor.Rd |only man/gelnet.krr.Rd | 9 + man/gelnet.lin.Rd | 2 man/gelnet.lin.obj.Rd | 10 - man/gelnet.logreg.Rd | 2 man/gelnet.logreg.obj.Rd | 8 - man/gelnet.oneclass.Rd |only man/gelnet.oneclass.obj.Rd |only 18 files changed, 292 insertions(+), 68 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 0.90.0 dated 2015-05-08 and 1.0.0 dated 2015-08-14
DESCRIPTION | 8 +- MD5 | 57 ++++++++------- NAMESPACE | 7 + NEWS | 182 +++++++++++++++++++++++++++++++-------------------- R/base.methods.R | 4 - R/checkX13.R | 28 +++++-- R/deparse.R | 4 - R/detect.R | 82 ---------------------- R/extractors.R | 1 R/import.spc.R |only R/inspect-sub.R | 65 ++++++++++++++++++ R/inspect.R | 10 +- R/out.R | 3 R/parse_spc.R |only R/plot.R | 21 +++++ R/read_mdl.R | 40 ----------- R/read_series.R | 25 ++++--- R/read_udg.R | 2 R/seas.R | 128 ++++++++++++++++++++++------------- R/spclist.R | 4 - R/static.R | 12 +-- R/summary.R | 5 - R/x13messages.R |only README.md | 73 +++++++++++++++----- build/vignette.rds |binary inst/doc/seas.pdf |binary man/import.spc.Rd |only man/import.ts.Rd |only man/inspect.Rd | 2 man/seas.Rd | 20 ++++- man/static.Rd | 7 + vignettes/README.tex | 102 ++++++++++++++++++++-------- 32 files changed, 532 insertions(+), 360 deletions(-)
Title: Analysis of Data Acquired Using the Receiver Operating
Characteristic Paradigm and Its Extensions
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software. In addition to open-source access to the functions, the package includes a graphical interface for users already familiar with the Windows software, who simply wish to run the program.
Author: Xuetong Zhai [aut, cre],
Dev Chakraborty [aut, ths]
Maintainer: Xuetong Zhai <xuetong.zhai@gmail.com>
Diff between RJafroc versions 0.1.0 dated 2015-07-30 and 0.1.1 dated 2015-08-14
DESCRIPTION | 10 +- MD5 | 63 ++++++++-------- R/CalculateAFROCPoints.R | 2 R/CalculateAvgAFROCPoints.R | 2 R/CalculateAvgFROCPoints.R | 2 R/CalculateAvgROCPoints.R | 2 R/CalculateFROCPoints.R | 2 R/CalculateROCPoints.R | 2 R/DBMHAnalysis.R | 12 +-- R/EmpiricalOpCharac.R | 6 - R/FigureOfMerit.R | 18 ++-- R/ORHAnalysis.R | 12 +-- R/OutputReport.R | 10 ++ R/PowerGivenJK.R | 2 R/PowerTable.R | 2 R/ReadDataFile.R | 8 +- R/SampleSizeGivenJ.R | 2 R/SaveDataFile.R | 2 inst/doc/RJafroc.R | 4 - inst/doc/RJafroc.Rnw | 168 ++++++++++++++++++++++---------------------- inst/doc/RJafroc.pdf |binary man/DBMHAnalysis.Rd | 4 - man/EmpiricalOpCharac.Rd | 6 - man/FigureOfMerit.Rd | 18 ++-- man/ORHAnalysis.Rd | 4 - man/OutputReport.Rd | 10 ++ man/PowerGivenJK.Rd | 2 man/PowerTable.Rd | 2 man/ReadDataFile.Rd | 8 +- man/SampleSizeGivenJ.Rd | 2 man/SaveDataFile.Rd | 2 vignettes/RJafroc.Rnw | 168 ++++++++++++++++++++++---------------------- vignettes/jsslogo.jpg |only 33 files changed, 285 insertions(+), 272 deletions(-)
Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.0-5 dated 2015-05-28 and 2.0-6 dated 2015-08-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 7 +++++++ R/rformulate.r | 4 +++- R/rsdiff.r | 32 +++++++++++++++++++------------- 5 files changed, 37 insertions(+), 22 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.0-2 dated 2015-07-28 and 1.0-3 dated 2015-08-14
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/ctree.R | 29 ++++++++++++++++------------- build/vignette.rds |binary inst/NEWS.Rd | 17 +++++++++++------ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary 9 files changed, 41 insertions(+), 33 deletions(-)
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files.
This attempts to provide a cleaner alternative to options().
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between params versions 0.2 dated 2015-07-27 and 0.2.4 dated 2015-08-14
params-0.2.4/params/DESCRIPTION | 8 ++-- params-0.2.4/params/MD5 | 21 ++++++---- params-0.2.4/params/NAMESPACE | 6 ++- params-0.2.4/params/NEWS.md |only params-0.2.4/params/R/conf.R | 50 +++++++++++++------------ params-0.2.4/params/R/opts.R | 65 ++++++++++++++------------------ params-0.2.4/params/R/pkg-opts.R |only params-0.2.4/params/R/zzz.R | 2 - params-0.2.4/params/README.md | 16 ++++++-- params-0.2.4/params/build |only params-0.2.4/params/man/opts.Rd |only params-0.2.4/params/man/params.Rd | 68 ++++++++++++++++++++++++++++++---- params-0.2.4/params/man/parse_opts.Rd |only params-0.2/params/man/load_conf.Rd |only params-0.2/params/man/parse_conf.Rd |only 15 files changed, 148 insertions(+), 88 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.0.3 dated 2015-07-21 and 0.0.4 dated 2015-08-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/helpers.R | 2 +- man/kdecopula-package.Rd | 6 +++--- src/interp.cpp | 2 +- src/renorm.cpp | 5 +++-- 6 files changed, 17 insertions(+), 16 deletions(-)
Title: Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria
Description: Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between JADE versions 1.9-92 dated 2014-10-23 and 1.9-93 dated 2015-08-14
JADE-1.9-92/JADE/src/Fortran_JADE.f |only JADE-1.9-93/JADE/DESCRIPTION | 16 +++---- JADE-1.9-93/JADE/MD5 | 80 +++++++++++++++++++++-------------- JADE-1.9-93/JADE/NAMESPACE | 3 - JADE-1.9-93/JADE/R/AMUSE.R | 10 ++-- JADE-1.9-93/JADE/R/ComonGAP.R | 27 ++++++----- JADE-1.9-93/JADE/R/FG.R | 67 ++++++++++++++++------------- JADE-1.9-93/JADE/R/FOBI.R | 13 +++-- JADE-1.9-93/JADE/R/JADE.R | 75 ++++++++++++++++---------------- JADE-1.9-93/JADE/R/MD.R | 38 ++++++++++------ JADE-1.9-93/JADE/R/NSSJD.R | 8 +-- JADE-1.9-93/JADE/R/NSSSD.R | 8 +-- JADE-1.9-93/JADE/R/NSSTDJD.R | 6 +- JADE-1.9-93/JADE/R/SIR.R | 24 +++++----- JADE-1.9-93/JADE/R/SOBI.R | 18 +++---- JADE-1.9-93/JADE/R/amari.error.R | 8 +-- JADE-1.9-93/JADE/R/cjd.R | 36 +++++++-------- JADE-1.9-93/JADE/R/djd.R | 43 ++++++++++-------- JADE-1.9-93/JADE/R/frjd.R |only JADE-1.9-93/JADE/R/internals.R | 14 +++--- JADE-1.9-93/JADE/R/k_JADE.R | 35 +++++++-------- JADE-1.9-93/JADE/R/multscatter.R | 2 JADE-1.9-93/JADE/R/rjd.R | 72 +++++++++++++++---------------- JADE-1.9-93/JADE/R/rjd.fortran.R | 41 ++--------------- JADE-1.9-93/JADE/build |only JADE-1.9-93/JADE/inst/ChangeLog | 8 +++ JADE-1.9-93/JADE/inst/doc |only JADE-1.9-93/JADE/inst/vignette |only JADE-1.9-93/JADE/man/FG.Rd | 5 +- JADE-1.9-93/JADE/man/JADE-package.Rd | 8 +-- JADE-1.9-93/JADE/man/JADE.Rd | 5 -- JADE-1.9-93/JADE/man/NSS.JD.Rd | 6 +- JADE-1.9-93/JADE/man/NSS.TD.JD.Rd | 6 +- JADE-1.9-93/JADE/man/SOBI.Rd | 4 - JADE-1.9-93/JADE/man/k_JADE.Rd | 6 +- JADE-1.9-93/JADE/man/rjd.Rd | 22 +++++---- JADE-1.9-93/JADE/src/cJADE.cpp |only JADE-1.9-93/JADE/vignettes |only 38 files changed, 369 insertions(+), 345 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap; all of which have detailed examples in doc/manualHaploStats.pdf.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.6.11 dated 2014-09-04 and 1.7.1 dated 2015-08-14
DESCRIPTION | 15 +++++---- MD5 | 66 +++++++++++++++++++++--------------------- NAMESPACE | 9 +++++ R/Ginv.R | 2 - R/geno.count.pairs.q | 2 - R/haplo.design.q | 2 - R/haplo.em.control.q | 2 - R/haplo.em.fitter.q | 2 - R/haplo.em.q | 2 - R/haplo.enum.q | 2 - R/haplo.group.q | 2 - R/haplo.hash.q | 2 - R/haplo.score.glm.q | 2 - R/haplo.score.merge.q | 2 - R/haplo.score.podds.q | 2 - R/haplo.score.q | 4 +- R/haplo.score.slide.q | 2 - R/locator.haplo.q | 2 - R/plot.haplo.score.q | 2 - R/plot.haplo.score.slide.q | 2 - R/plot.seqhap.q | 2 - R/print.haplo.em.q | 2 - R/print.haplo.glm.q | 3 - R/print.haplo.group.q | 2 - R/print.haplo.score.merge.q | 2 - R/print.haplo.score.q | 2 - R/print.haplo.score.slide.q | 2 - R/print.seqhap.q | 2 - R/printBanner.q | 2 - R/score.sim.control.q | 2 - R/seqhap.q | 2 - R/summary.haplo.em.q | 2 - R/summaryGeno.q | 2 - inst/doc/manualHaploStats.pdf |binary 34 files changed, 81 insertions(+), 72 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.3.0 dated 2015-07-07 and 2.3.1 dated 2015-08-14
DESCRIPTION | 9 +++--- MD5 | 28 +++++++++---------- R/importWaterML1.r | 9 +++--- R/readNWISdv.r | 1 R/renameColumns.R | 3 -- R/whatWQPsites.R | 4 +- README.md | 3 ++ inst/doc/dataRetrieval.R | 60 +++++++++++++++++++---------------------- inst/doc/dataRetrieval.Rnw | 34 +++++------------------ inst/doc/dataRetrieval.pdf |binary man/importWaterML1.Rd | 9 +++--- man/readNWISdv.Rd | 1 man/renameNWISColumns.Rd | 3 -- tests/testthat/tests_imports.R | 19 ++++++------ vignettes/dataRetrieval.Rnw | 32 ++++----------------- 15 files changed, 89 insertions(+), 126 deletions(-)
Title: Bootstrap Effect Sizes
Description: Calculate robust measures of effect sizes using the bootstrap.
Author: Daniel Gerlanc <dgerlanc@enplusadvisors.com> and Kris Kirby <kkirby@williams.edu>
Maintainer: Daniel Gerlanc <dgerlanc@enplusadvisors.com>
Diff between bootES versions 1.01 dated 2013-01-02 and 1.2 dated 2015-08-14
ChangeLog |only DESCRIPTION | 16 +++++++------- MD5 | 18 ++++++++++------ NAMESPACE | 7 ++++++ R/bootES.R | 29 ++++++++++++++++++++++++++- R/cohensd.R | 2 + R/univariate.R | 19 ++++++++++++++++- README.md |only inst/robust_d_test.csv |only inst/tests/runit.akpRobustD.R |only inst/tests/runit.bootES.R | 45 ++++++++++++++++++++++++++++++++++++++++-- man/bootES.Rd | 4 +++ 12 files changed, 121 insertions(+), 19 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mboost versions 2.4-2 dated 2015-02-12 and 2.5-0 dated 2015-08-14
DESCRIPTION | 17 ++-- MD5 | 59 ++++++++-------- NAMESPACE | 2 R/AAA.R | 29 -------- R/bkronecker.R | 24 +++--- R/bl.R | 132 +++++++++++++++++++++++++++----------- R/bmono.R | 30 ++++---- R/bmrf.R | 8 -- R/crossvalidation.R | 30 ++++++-- R/family.R | 32 +++++---- R/helpers.R | 24 ++++++ R/mboost.R | 6 - R/methods.R | 17 ++-- R/plot.R | 16 +++- build/vignette.rds |binary inst/CITATION | 76 +++++++++++++-------- inst/NEWS.Rd | 66 ++++++++++++++++++- inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.pdf |binary man/Family.Rd | 120 ++++++++++++++++++++++++---------- man/baselearners.Rd | 48 ++++++++++--- man/confint.Rd | 4 + man/cvrisk.Rd | 9 ++ man/glmboost.Rd | 19 +---- man/mboost.Rd | 17 ---- man/mboost_package.Rd | 4 - man/methods.Rd | 16 +++- man/plot.Rd |only man/stabsel.Rd | 7 ++ 31 files changed, 532 insertions(+), 280 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.10.5 dated 2015-05-06 and 1.11 dated 2015-08-14
DESCRIPTION | 28 ++-- MD5 | 75 ++++++------ NAMESPACE | 9 + R/block.R | 15 -- R/citation.R | 3 R/engine.R | 11 - R/hooks-extra.R | 67 ----------- R/hooks-html.R | 2 R/output.R | 6 R/package.R | 1 R/params.R | 207 +++++++++++++--------------------- R/plot.R | 26 +++- R/table.R | 23 ++- R/template.R | 2 R/utils-conversion.R | 6 R/utils.R | 7 + README.md | 7 - build/knitr.pdf |binary build/vignette.rds |binary inst/CITATION | 9 - inst/doc/docco-classic.html | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 inst/doc/knit_print.html | 6 inst/doc/knitr-html.html | 2 inst/doc/knitr-intro.html | 12 - inst/doc/knitr-markdown.html | 4 inst/doc/knitr-refcard.pdf |binary man/chunk_hook.Rd | 30 +--- man/kable.Rd | 8 + man/knit2html.Rd | 6 man/knit_params.Rd | 61 +--------- man/knit_params_yaml.Rd |only man/plot_crop.Rd | 5 man/rst2pdf.Rd | 2 man/write_bib.Rd | 3 tests/testit/test-params.R | 97 +++++++++++---- tests/testit/test-plot.R | 6 vignettes/assets/template-refcard.tex | 2 39 files changed, 364 insertions(+), 392 deletions(-)
Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig <c.hennig@ucl.ac.uk>
Maintainer: Christian Hennig <c.hennig@ucl.ac.uk>
Diff between fpc versions 2.1-9 dated 2014-10-02 and 2.1-10 dated 2015-08-14
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 37 +++++++++++++++++++++++++++++++++++++ R/clusterboot.R | 4 ++-- man/cluster.stats.Rd | 17 ++++++----------- man/distancefactor.Rd | 17 +++++++---------- man/distcritmulti.Rd | 14 +++++--------- man/flexmixedruns.Rd | 12 ++++-------- man/lcmixed.Rd | 12 ++++-------- man/pamk.Rd | 11 ++++++++++- tests/Examples/fpc-Ex.Rout.save | 17 ++++++++--------- tests/fpctests.Rout.save | 22 ++++++++++++---------- 12 files changed, 113 insertions(+), 85 deletions(-)
Title: CRISPR AnalyzeR for Pooled CRISPR Screens
Description: CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <https://en.wikipedia.org/wiki/CRISPR> for more information on
CRISPR.
Author: Jan Winter, Florian Heigwer
Maintainer: Jan Winter <jan.winter@dkfz-heidelberg.de>
Diff between caRpools versions 0.82 dated 2015-08-10 and 0.82.3 dated 2015-08-14
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/compare.analysis.R | 15 ++++---- R/get.gene.info.R | 82 +++++++++++++++++++++++++----------------------- R/load.packages.R | 2 - inst/doc/CaRpools.R | 2 - inst/doc/CaRpools.Rmd | 2 - inst/doc/CaRpools.html | 10 ++--- man/compare.analysis.Rd | 2 - vignettes/CaRpools.Rmd | 2 - 10 files changed, 71 insertions(+), 70 deletions(-)
Title: Discriminant Analysis with Additional Information
Description: In applications it is usual that some additional information is available. This package dawai (an acronym for Discriminant Analysis With Additional Information) performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means. It also computes several estimations of the true error rate.
Author: David Conde, Miguel A. Fernandez, Bonifacio Salvador
Maintainer: David Conde <dconde@eio.uva.es>
Diff between dawai versions 1.1 dated 2014-10-02 and 1.2 dated 2015-08-13
DESCRIPTION | 12 ++++++------ MD5 | 19 ++++++++++--------- NAMESPACE | 3 ++- inst/CITATION |only man/dawai-package.Rd | 2 ++ man/err.est.rlda.Rd | 2 ++ man/err.est.rqda.Rd | 2 ++ man/predict.rlda.Rd | 2 ++ man/predict.rqda.Rd | 2 ++ man/rlda.Rd | 2 ++ man/rqda.Rd | 2 ++ 11 files changed, 32 insertions(+), 16 deletions(-)
Title: Diffusion IRT Models for Response and Response Time Data
Description: Package to fit diffusion-based IRT models to response and
response time data. Models are fit using marginal maximum
likelihood. Parameter restrictions (fixed value and equality
constraints) are possible. In addition, factor scores (person drift
rate and person boundary separation) can be estimated. Model fit
assessment tools are also available. The traditional diffusion model
can be estimated as well.
Author: Dylan Molenaar
Maintainer: Dylan Molenaar <d.molenaar@uva.nl>
Diff between diffIRT versions 1.4 dated 2014-06-05 and 1.5 dated 2015-08-13
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- NAMESPACE | 9 ++++++--- inst |only man/RespFit.Rd | 4 ++-- man/brightness.Rd | 11 ++++++----- man/diffIRT.Rd | 4 ++-- man/extraversion.Rd | 5 +++-- man/rotation.Rd | 5 +++-- man/simdiffT.Rd | 4 ++-- 10 files changed, 39 insertions(+), 32 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.1 dated 2015-07-21 and 0.19.3 dated 2015-08-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/classes.r | 4 ++-- R/generics_problemInstance.r | 2 +- R/methods_class_sdcProblem.r | 25 ++++++++++++++++++------- inst/doc/sdcTable.pdf |binary man/get.problemInstance-method.Rd | 2 +- src/suppMultDimTable.cpp | 17 +++++++++++++---- 8 files changed, 46 insertions(+), 26 deletions(-)
Title: Rough - Enhanced - Bayesian Finite Mixture Modeling
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.7.1 dated 2015-04-04 and 2.7.2 dated 2015-08-13
rebmix-2.7.1/rebmix/src/Rrebmix.c |only rebmix-2.7.1/rebmix/src/rebmix.c |only rebmix-2.7.1/rebmix/src/rebmixf.c |only rebmix-2.7.1/rebmix/src/rngmixf.c |only rebmix-2.7.1/rebmix/vignettes/algorithm.pdf |only rebmix-2.7.2/rebmix/DESCRIPTION | 7 rebmix-2.7.2/rebmix/MD5 | 67 - rebmix-2.7.2/rebmix/NAMESPACE | 2 rebmix-2.7.2/rebmix/R/IC.R | 148 +-- rebmix-2.7.2/rebmix/R/RCLSMIX.R | 48 - rebmix-2.7.2/rebmix/R/REBMIX.R | 174 ++-- rebmix-2.7.2/rebmix/R/RNGMIX.R | 18 rebmix-2.7.2/rebmix/R/demix.R | 8 rebmix-2.7.2/rebmix/inst/CITATION | 17 rebmix-2.7.2/rebmix/inst/NEWS.Rd | 8 rebmix-2.7.2/rebmix/inst/doc/rebmix.Rnw | 330 ------- rebmix-2.7.2/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.7.2/rebmix/man/AIC.Rd | 20 rebmix-2.7.2/rebmix/man/AWE.Rd | 4 rebmix-2.7.2/rebmix/man/BIC.Rd | 4 rebmix-2.7.2/rebmix/man/CLC.Rd | 4 rebmix-2.7.2/rebmix/man/HQC.Rd | 4 rebmix-2.7.2/rebmix/man/ICL.Rd | 4 rebmix-2.7.2/rebmix/man/ICLBIC.Rd | 4 rebmix-2.7.2/rebmix/man/MDL.Rd | 6 rebmix-2.7.2/rebmix/man/PC.Rd | 4 rebmix-2.7.2/rebmix/man/PRD.Rd | 4 rebmix-2.7.2/rebmix/man/RCLSMIX.Rd | 4 rebmix-2.7.2/rebmix/man/SSE.Rd | 4 rebmix-2.7.2/rebmix/man/logL.Rd | 4 rebmix-2.7.2/rebmix/src/Rrebmix.cpp |only rebmix-2.7.2/rebmix/src/base.cpp |only rebmix-2.7.2/rebmix/src/base.h |only rebmix-2.7.2/rebmix/src/rebmix.cpp |only rebmix-2.7.2/rebmix/src/rebmixf.cpp |only rebmix-2.7.2/rebmix/src/rebmixf.h | 416 ++-------- rebmix-2.7.2/rebmix/src/rngmixf.cpp |only rebmix-2.7.2/rebmix/src/rngmixf.h | 95 -- rebmix-2.7.2/rebmix/vignettes/rebmix.Rnw | 330 ------- rebmix-2.7.2/rebmix/vignettes/rebmix.bib | 1162 ++++++++++++++-------------- 40 files changed, 1067 insertions(+), 1833 deletions(-)
Title: Estimation of Conditional Quantiles using Optimal Quantization
Description: Estimation of conditional quantiles using optimal quantization.
Construction of an optimal grid of N quantizers, estimation of conditional
quantiles and data driven selection of the size N of the grid. Graphical
illustrations for the selection of N and of resulting estimated curves or
surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier <ischarli@ulb.ac.be>
Diff between QuantifQuantile versions 2.1 dated 2015-04-27 and 2.2 dated 2015-08-13
DESCRIPTION | 8 ++++---- MD5 | 21 ++++++++++++--------- NAMESPACE | 16 ++++++++++++++-- R/QuantifQuantile.R | 22 ++++++++++++++++++++-- R/QuantifQuantile.d.R | 15 ++++++++++++++- R/QuantifQuantile.d2.R | 16 ++++++++++++++-- R/gironde.R |only R/plot.QuantifQuantile.R | 14 +++++++++++--- R/print.QuantifQuantile.R | 5 ++--- R/summary.QuantifQuantile.R | 4 +--- data |only man/QuantifQuantile.Rd | 6 ++++++ man/gironde.Rd |only 13 files changed, 98 insertions(+), 29 deletions(-)
More information about QuantifQuantile at CRAN
Permanent link
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.2 dated 2015-06-05 and 0.3 dated 2015-08-13
DESCRIPTION | 10 - MD5 | 58 +++++------ NAMESPACE | 2 R/provenance.R | 265 +++++++++++++++++++++++++++++----------------------- man/KS.dist.Rd | 2 man/SH.dist.Rd | 2 man/botev.Rd | 2 man/clr.Rd | 2 man/dist.Rd | 2 man/get.f.Rd | 2 man/get.n.Rd | 2 man/get.p.Rd | 2 man/getKDE.Rd | 2 man/getKDEs.Rd | 2 man/getMDS.Rd | 2 man/getPCA.Rd | 2 man/indscal.Rd | 2 man/plot.DZdata.Rd | 10 + man/plot.GPA.Rd | 2 man/plot.HMdata.Rd | 10 + man/plot.INDSCAL.Rd | 2 man/plot.KDE.Rd | 2 man/plot.MDS.Rd | 2 man/plot.PCA.Rd | 2 man/procrustes.Rd | 2 man/read.DZdata.Rd | 8 + man/read.HMdata.Rd | 8 + man/subset.Rd | 2 man/summaryplot.Rd | 2 man/ternaryplot.Rd | 2 30 files changed, 229 insertions(+), 186 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.2 dated 2015-08-05 and 1.2.1 dated 2015-08-13
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NAMESPACE | 13 ++----- R/foo.R | 79 +++++++++++++++++++++++++++++--------------- man/contour.pred.PrevMap.Rd | 2 - man/plot.pred.PrevMap.Rd | 4 +- 6 files changed, 71 insertions(+), 47 deletions(-)
Title: Multivariate-from-Univariate (MfU) MCMC Sampler
Description: Convenience functions for multivariate MCMC using univariate samplers including:
slice sampler with stepout and shrinkage (Neal, 2003),
adaptive rejection sampler (Gilks and Wild, 1992),
adaptive rejection Metropolis (Gilks et al 1995), and
univariate Metropolis with Gaussian proposal.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between MfUSampler versions 0.9.1 dated 2014-12-26 and 1.0.0 dated 2015-08-13
MfUSampler-0.9.1/MfUSampler/vignettes/fig_logistic_dag.jpg |only MfUSampler-1.0.0/MfUSampler/ChangeLog | 6 MfUSampler-1.0.0/MfUSampler/DESCRIPTION | 18 MfUSampler-1.0.0/MfUSampler/MD5 | 35 MfUSampler-1.0.0/MfUSampler/NAMESPACE | 18 MfUSampler-1.0.0/MfUSampler/R/MfUSampler.R | 150 ++ MfUSampler-1.0.0/MfUSampler/R/UniMetrop.R |only MfUSampler-1.0.0/MfUSampler/build/vignette.rds |binary MfUSampler-1.0.0/MfUSampler/inst/doc/MfUSampler.R | 454 +++++-- MfUSampler-1.0.0/MfUSampler/inst/doc/MfUSampler.Rnw | 600 ++++++---- MfUSampler-1.0.0/MfUSampler/inst/doc/MfUSampler.pdf |binary MfUSampler-1.0.0/MfUSampler/man/MfU.Control.Rd | 29 MfUSampler-1.0.0/MfUSampler/man/MfU.Sample.Rd | 76 - MfUSampler-1.0.0/MfUSampler/man/predict.MfU.Rd |only MfUSampler-1.0.0/MfUSampler/man/summary.MfU.Rd |only MfUSampler-1.0.0/MfUSampler/vignettes/MfUSampler.Rnw | 600 ++++++---- MfUSampler-1.0.0/MfUSampler/vignettes/MfUSampler.bib | 180 ++- MfUSampler-1.0.0/MfUSampler/vignettes/MfUSampler_process_diagram.pdf |only MfUSampler-1.0.0/MfUSampler/vignettes/summ.ars |only MfUSampler-1.0.0/MfUSampler/vignettes/summ.slice |only MfUSampler-1.0.0/MfUSampler/vignettes/t.naive |only MfUSampler-1.0.0/MfUSampler/vignettes/t.parallel |only MfUSampler-1.0.0/MfUSampler/vignettes/t.rcpp |only MfUSampler-1.0.0/MfUSampler/vignettes/t.revised |only 24 files changed, 1488 insertions(+), 678 deletions(-)
Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics
interface to visualize backtest results of different financial
instruments, such as equities, futures, and credit default swaps.
The package does not run backtests on the given data set but
displays a graphical explanation of the backtest results. Users can
look at backtest graphics for different instruments, investment
strategies, and portfolios. Summary statistics of different
portfolio holdings are shown in the left panel, and interactive
plots of profit and loss (P\&L), net market value (NMV) and
gross market value (GMV) are displayed in the right panel.
Author: as.person(c(
"David Kane <dave.kane@gmail.com> [aut]",
"Ziqi Lu <ziqi.lu@williams.edu> [aut]",
"Fan Zhang <fan.zhang@williams.edu> [aut]",
"Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]"
))
Maintainer: Miller Zijie Zhu <zijie.miller.zhu@gmail.com>
Diff between backtestGraphics versions 0.1.4 dated 2015-08-12 and 0.1.5 dated 2015-08-13
backtestGraphics-0.1.4/backtestGraphics/tests/testthat/test_slice_data.R |only backtestGraphics-0.1.4/backtestGraphics/tests/testthat/test_slice_data.RData |only backtestGraphics-0.1.4/backtestGraphics/tests/testthat/test_sum_data.R |only backtestGraphics-0.1.4/backtestGraphics/tests/testthat/test_sum_data.RData |only backtestGraphics-0.1.5/backtestGraphics/DESCRIPTION | 8 ++++---- backtestGraphics-0.1.5/backtestGraphics/MD5 | 8 ++------ backtestGraphics-0.1.5/backtestGraphics/inst/doc/backtestGraphics.pdf |binary 7 files changed, 6 insertions(+), 10 deletions(-)
More information about backtestGraphics at CRAN
Permanent link
Title: Statistical Procedures for Agricultural Research
Description: Agricolae was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, mention Systems Engineering, Faculty of Industrial and Systems Engineering, National Engineering University (UNI), Lima-Peru. Original idea, support and data sets came from CIP (International Potato Center). Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>
Diff between agricolae versions 1.2-1 dated 2014-09-01 and 1.2-2 dated 2015-08-13
agricolae-1.2-1/agricolae/vignettes/lattice3X3.txt |only agricolae-1.2-2/agricolae/DESCRIPTION | 10 agricolae-1.2-2/agricolae/MD5 | 79 ++--- agricolae-1.2-2/agricolae/NAMESPACE | 13 agricolae-1.2-2/agricolae/NEWS | 8 agricolae-1.2-2/agricolae/R/BIB.test.R | 2 agricolae-1.2-2/agricolae/R/DAU.test.R | 2 agricolae-1.2-2/agricolae/R/HSD.test.R | 2 agricolae-1.2-2/agricolae/R/LSD.test.R | 2 agricolae-1.2-2/agricolae/R/PBIB.test.r | 2 agricolae-1.2-2/agricolae/R/SNK.test.R | 2 agricolae-1.2-2/agricolae/R/design.bib.R | 46 ++- agricolae-1.2-2/agricolae/R/design.graeco.R | 2 agricolae-1.2-2/agricolae/R/design.lsd.R | 2 agricolae-1.2-2/agricolae/R/design.rcbd.R | 2 agricolae-1.2-2/agricolae/R/design.youden.r | 2 agricolae-1.2-2/agricolae/R/duncan.test.r | 2 agricolae-1.2-2/agricolae/R/durbin.test.R | 2 agricolae-1.2-2/agricolae/R/friedman.R | 2 agricolae-1.2-2/agricolae/R/graph.freq.R | 1 agricolae-1.2-2/agricolae/R/intervals.freq.R | 6 agricolae-1.2-2/agricolae/R/kruskal.R | 2 agricolae-1.2-2/agricolae/R/median.test.r | 2 agricolae-1.2-2/agricolae/R/scheffe.test.R | 2 agricolae-1.2-2/agricolae/R/summary.graph.freq.R | 10 agricolae-1.2-2/agricolae/R/table.freq.R | 8 agricolae-1.2-2/agricolae/R/waerden.test.R | 2 agricolae-1.2-2/agricolae/R/waller.test.R | 2 agricolae-1.2-2/agricolae/build/vignette.rds |binary agricolae-1.2-2/agricolae/inst/doc/tutorial.R | 300 +++++++++----------- agricolae-1.2-2/agricolae/inst/doc/tutorial.Rnw | 57 +-- agricolae-1.2-2/agricolae/inst/doc/tutorial.pdf |binary agricolae-1.2-2/agricolae/man/agricolae-package.Rd | 4 agricolae-1.2-2/agricolae/man/design.bib.Rd | 38 ++ agricolae-1.2-2/agricolae/man/design.graeco.Rd | 12 agricolae-1.2-2/agricolae/man/design.lsd.Rd | 7 agricolae-1.2-2/agricolae/man/design.rcbd.Rd | 4 agricolae-1.2-2/agricolae/man/design.youden.rd | 12 agricolae-1.2-2/agricolae/man/summary.graph.freq.Rd | 10 agricolae-1.2-2/agricolae/man/table.freq.Rd | 10 agricolae-1.2-2/agricolae/vignettes/tutorial.Rnw | 57 +-- 41 files changed, 402 insertions(+), 326 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
'shinyjs' can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.8.3 dated 2015-07-31 and 0.1.0 dated 2015-08-13
DESCRIPTION | 8 +++--- MD5 | 39 ++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 10 ++++++++ R/colourInput.R | 42 ++++++++++++++++++++------------- R/disabled.R |only R/extendShinyjs.R | 26 ++++++++++++++++++++ R/globals.R |only R/inlineCSS.R | 2 - R/jsFunc-stateFuncs.R | 1 R/useShinyjs.R | 8 +++++- R/utils.R | 21 +++++++++++++++- README.md | 32 ++++++++++++++++++++++++- inst/doc/overview.Rmd | 25 ++++++++++++++++++++ inst/doc/overview.html | 45 ++++++++++++++++++++++++++---------- inst/srcjs/shinyjs-default-funcs.js | 22 ++++++++++++++++- man/disabled.Rd |only man/extendShinyjs.Rd | 28 ++++++++++++++++++++++ man/js.Rd | 2 - man/stateFuncs.Rd | 1 man/useShinyjs.Rd | 7 ++++- vignettes/overview.Rmd | 25 ++++++++++++++++++++ 22 files changed, 286 insertions(+), 59 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.6 dated 2015-07-27 and 1.3.7 dated 2015-08-13
SciencesPo-1.3.6/SciencesPo/R/geary.test.R |only SciencesPo-1.3.6/SciencesPo/R/weighted.var.R |only SciencesPo-1.3.6/SciencesPo/man/geary.test.Rd |only SciencesPo-1.3.6/SciencesPo/man/head.Rd |only SciencesPo-1.3.6/SciencesPo/man/weighted.var.Rd |only SciencesPo-1.3.7/SciencesPo/DESCRIPTION | 8 +- SciencesPo-1.3.7/SciencesPo/MD5 | 77 ++++++++++++++------ SciencesPo-1.3.7/SciencesPo/NAMESPACE | 26 +++++- SciencesPo-1.3.7/SciencesPo/R/DEPRECATED.R | 9 +- SciencesPo-1.3.7/SciencesPo/R/Themes.R | 13 ++- SciencesPo-1.3.7/SciencesPo/R/agostino.R |only SciencesPo-1.3.7/SciencesPo/R/anderson.darling.R |only SciencesPo-1.3.7/SciencesPo/R/anscombe.glynn.R |only SciencesPo-1.3.7/SciencesPo/R/bonett.seier.R |only SciencesPo-1.3.7/SciencesPo/R/compute.R | 10 +- SciencesPo-1.3.7/SciencesPo/R/countNAs.R |only SciencesPo-1.3.7/SciencesPo/R/crosstable.R | 5 - SciencesPo-1.3.7/SciencesPo/R/dHondt.R | 8 +- SciencesPo-1.3.7/SciencesPo/R/database.R | 30 ------- SciencesPo-1.3.7/SciencesPo/R/describe.R |only SciencesPo-1.3.7/SciencesPo/R/electoralTool.R | 4 - SciencesPo-1.3.7/SciencesPo/R/freq.R | 62 +++++++++++++++- SciencesPo-1.3.7/SciencesPo/R/geary.R |only SciencesPo-1.3.7/SciencesPo/R/ggMultiplot.R | 8 ++ SciencesPo-1.3.7/SciencesPo/R/hamilton.R |only SciencesPo-1.3.7/SciencesPo/R/james.stein.R |only SciencesPo-1.3.7/SciencesPo/R/jarque.bera.R |only SciencesPo-1.3.7/SciencesPo/R/levy.flight.R |only SciencesPo-1.3.7/SciencesPo/R/lilliefors.R |only SciencesPo-1.3.7/SciencesPo/R/odds.ratio.R |only SciencesPo-1.3.7/SciencesPo/R/package.R |only SciencesPo-1.3.7/SciencesPo/R/roc.R |only SciencesPo-1.3.7/SciencesPo/R/rounded.R |only SciencesPo-1.3.7/SciencesPo/R/utils.R | 1 SciencesPo-1.3.7/SciencesPo/R/wtd.var.R |only SciencesPo-1.3.7/SciencesPo/demo/SciencesPo.R | 53 +++++++++++++ SciencesPo-1.3.7/SciencesPo/man/NAasMissing.Rd |only SciencesPo-1.3.7/SciencesPo/man/agostino.Rd |only SciencesPo-1.3.7/SciencesPo/man/anderson.darling.Rd |only SciencesPo-1.3.7/SciencesPo/man/anscombe.glynn.Rd |only SciencesPo-1.3.7/SciencesPo/man/bonett.seier.Rd |only SciencesPo-1.3.7/SciencesPo/man/compute.Rd | 8 +- SciencesPo-1.3.7/SciencesPo/man/countNAs.Rd |only SciencesPo-1.3.7/SciencesPo/man/dHondt.Rd | 6 + SciencesPo-1.3.7/SciencesPo/man/describe.Rd |only SciencesPo-1.3.7/SciencesPo/man/freq.Rd | 4 - SciencesPo-1.3.7/SciencesPo/man/geary.Rd |only SciencesPo-1.3.7/SciencesPo/man/ggplotArrange.Rd |only SciencesPo-1.3.7/SciencesPo/man/hamilton-methods.Rd |only SciencesPo-1.3.7/SciencesPo/man/james.stein.Rd |only SciencesPo-1.3.7/SciencesPo/man/jarque.bera.Rd |only SciencesPo-1.3.7/SciencesPo/man/levy.flight.Rd |only SciencesPo-1.3.7/SciencesPo/man/lilliefors.Rd |only SciencesPo-1.3.7/SciencesPo/man/odds.ratio.Rd |only SciencesPo-1.3.7/SciencesPo/man/package.Rd |only SciencesPo-1.3.7/SciencesPo/man/roc.Rd |only SciencesPo-1.3.7/SciencesPo/man/rounded.Rd |only SciencesPo-1.3.7/SciencesPo/man/smallAsMissing.Rd |only SciencesPo-1.3.7/SciencesPo/man/tab.Rd | 5 + SciencesPo-1.3.7/SciencesPo/man/wtd.var.Rd |only SciencesPo-1.3.7/SciencesPo/src/wcorr.c |only 61 files changed, 249 insertions(+), 88 deletions(-)
Title: Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks
Diff between geospt versions 1.0-1 dated 2015-02-08 and 1.0-2 dated 2015-08-13
Description: Estimation of the variogram through trimmed mean, radial basis
functions (optimization, prediction and cross-validation), summary
statistics from cross-validation, pocket plot, and design of
optimal sampling networks through sequential and simultaneous
points methods.
Author: Carlos Melo
Maintainer: Alí Santacruz
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
NAMESPACE | 7 ++++++-
man/geospt-package.Rd | 4 ++--
man/seqPtsOptNet.Rd | 5 ++---
5 files changed, 20 insertions(+), 15 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.7 dated 2015-04-21 and 0.7.2 dated 2015-08-13
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NAMESPACE | 4 ++++ NEWS | 5 +++++ R/eval.r | 2 +- R/output.r | 2 +- R/replay.r | 5 +++++ tests/test-replay.R |only 8 files changed, 28 insertions(+), 13 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 2.3.0 dated 2015-07-07 and 2.3.1 dated 2015-08-13
EGRET-2.3.0/EGRET/inst/doc/SeasonalFraction.R |only EGRET-2.3.0/EGRET/inst/doc/SeasonalFraction.Rmd |only EGRET-2.3.0/EGRET/inst/doc/SeasonalFraction.html |only EGRET-2.3.0/EGRET/inst/doc/vignetteFlowWeighted.R |only EGRET-2.3.0/EGRET/inst/doc/vignetteFlowWeighted.Rmd |only EGRET-2.3.0/EGRET/inst/doc/vignetteFlowWeighted.html |only EGRET-2.3.0/EGRET/man/estFNsegs.Rd |only EGRET-2.3.0/EGRET/man/flexFN.Rd |only EGRET-2.3.1/EGRET/DESCRIPTION | 8 - EGRET-2.3.1/EGRET/MD5 | 18 -- EGRET-2.3.1/EGRET/NAMESPACE | 2 EGRET-2.3.1/EGRET/NEWS | 4 EGRET-2.3.1/EGRET/R/modelEstimation.R | 152 ------------------- EGRET-2.3.1/EGRET/inst/doc/EGRET.pdf |binary 14 files changed, 13 insertions(+), 171 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.4 dated 2015-08-12 and 1.8.5 dated 2015-08-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- tests/ggplotUsage.R | 2 +- tests/stdUsage.R | 2 +- tests/testBinaryClass.R | 2 +- tests/testMultiClass.cpp.R | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.10.1 dated 2015-05-07 and 0.11.0 dated 2015-08-12
git2r-0.10.1/git2r/src/libgit2/include/git2/push.h |only git2r-0.11.0/git2r/DESCRIPTION | 24 git2r-0.11.0/git2r/MD5 | 529 ++-- git2r-0.11.0/git2r/NAMESPACE | 12 git2r-0.11.0/git2r/NEWS | 53 git2r-0.11.0/git2r/R/S4_classes.r | 37 git2r-0.11.0/git2r/R/blob.r | 6 git2r-0.11.0/git2r/R/branch.r | 22 git2r-0.11.0/git2r/R/bundle_r_package.r | 2 git2r-0.11.0/git2r/R/checkout.r | 103 git2r-0.11.0/git2r/R/commit.r | 83 git2r-0.11.0/git2r/R/contributions.r | 17 git2r-0.11.0/git2r/R/credential.r | 43 git2r-0.11.0/git2r/R/fetch.r | 4 git2r-0.11.0/git2r/R/git2r.r | 2 git2r-0.11.0/git2r/R/index.r | 12 git2r-0.11.0/git2r/R/libgit2.r | 2 git2r-0.11.0/git2r/R/merge.r | 3 git2r-0.11.0/git2r/R/note.r | 2 git2r-0.11.0/git2r/R/plot.r | 18 git2r-0.11.0/git2r/R/pull.r | 4 git2r-0.11.0/git2r/R/punch_card.r |only git2r-0.11.0/git2r/R/push.r | 30 git2r-0.11.0/git2r/R/reference.r | 21 git2r-0.11.0/git2r/R/reflog.r | 2 git2r-0.11.0/git2r/R/refspec.r |only git2r-0.11.0/git2r/R/remote.r | 20 git2r-0.11.0/git2r/R/repository.r | 149 - git2r-0.11.0/git2r/R/reset.r | 2 git2r-0.11.0/git2r/R/revparse.r | 4 git2r-0.11.0/git2r/R/stash.r | 36 git2r-0.11.0/git2r/R/status.r | 25 git2r-0.11.0/git2r/R/tag.r | 38 git2r-0.11.0/git2r/R/tree.r | 4 git2r-0.11.0/git2r/R/when.r | 10 git2r-0.11.0/git2r/configure | 107 git2r-0.11.0/git2r/configure.win | 121 + git2r-0.11.0/git2r/inst/AUTHORS | 6 git2r-0.11.0/git2r/inst/COPYRIGHTS | 5 git2r-0.11.0/git2r/man/add-methods.Rd | 8 git2r-0.11.0/git2r/man/add_session_info.Rd |only git2r-0.11.0/git2r/man/branches-methods.Rd | 9 git2r-0.11.0/git2r/man/clone-methods.Rd | 8 git2r-0.11.0/git2r/man/commits-methods.Rd | 8 git2r-0.11.0/git2r/man/contributions-methods.Rd | 9 git2r-0.11.0/git2r/man/cred_env-class.Rd |only git2r-0.11.0/git2r/man/cred_env-methods.Rd |only git2r-0.11.0/git2r/man/cred_ssh_key-methods.Rd | 3 git2r-0.11.0/git2r/man/get_refspec.Rd |only git2r-0.11.0/git2r/man/is_bare-methods.Rd | 6 git2r-0.11.0/git2r/man/is_detached-methods.Rd | 6 git2r-0.11.0/git2r/man/is_empty-methods.Rd | 6 git2r-0.11.0/git2r/man/is_shallow-methods.Rd | 6 git2r-0.11.0/git2r/man/lookup_repository.Rd |only git2r-0.11.0/git2r/man/merge-methods.Rd | 2 git2r-0.11.0/git2r/man/punch_card-methods.Rd |only git2r-0.11.0/git2r/man/references-methods.Rd | 9 git2r-0.11.0/git2r/man/remotes-methods.Rd | 9 git2r-0.11.0/git2r/man/stash_list-methods.Rd | 9 git2r-0.11.0/git2r/man/status-methods.Rd | 14 git2r-0.11.0/git2r/man/tags-methods.Rd | 9 git2r-0.11.0/git2r/man/workdir-methods.Rd | 9 git2r-0.11.0/git2r/src/Makevars.in | 61 git2r-0.11.0/git2r/src/Makevars.win | 94 git2r-0.11.0/git2r/src/git2r.c | 7 git2r-0.11.0/git2r/src/git2r_arg.c | 8 git2r-0.11.0/git2r/src/git2r_blame.c | 10 git2r-0.11.0/git2r/src/git2r_blob.c | 54 git2r-0.11.0/git2r/src/git2r_branch.c | 203 - git2r-0.11.0/git2r/src/git2r_checkout.c | 14 git2r-0.11.0/git2r/src/git2r_clone.c | 73 git2r-0.11.0/git2r/src/git2r_clone.h | 1 git2r-0.11.0/git2r/src/git2r_commit.c | 66 git2r-0.11.0/git2r/src/git2r_config.c | 139 + git2r-0.11.0/git2r/src/git2r_config.h | 2 git2r-0.11.0/git2r/src/git2r_cred.c | 199 + git2r-0.11.0/git2r/src/git2r_diff.c | 96 git2r-0.11.0/git2r/src/git2r_error.c | 79 git2r-0.11.0/git2r/src/git2r_error.h | 20 git2r-0.11.0/git2r/src/git2r_graph.c | 22 git2r-0.11.0/git2r/src/git2r_index.c | 35 git2r-0.11.0/git2r/src/git2r_index.h | 2 git2r-0.11.0/git2r/src/git2r_merge.c | 78 git2r-0.11.0/git2r/src/git2r_note.c | 99 git2r-0.11.0/git2r/src/git2r_object.c | 14 git2r-0.11.0/git2r/src/git2r_odb.c | 52 git2r-0.11.0/git2r/src/git2r_push.c | 53 git2r-0.11.0/git2r/src/git2r_reference.c | 62 git2r-0.11.0/git2r/src/git2r_reference.h | 1 git2r-0.11.0/git2r/src/git2r_reflog.c | 10 git2r-0.11.0/git2r/src/git2r_remote.c | 131 - git2r-0.11.0/git2r/src/git2r_repository.c | 74 git2r-0.11.0/git2r/src/git2r_reset.c | 12 git2r-0.11.0/git2r/src/git2r_revparse.c | 18 git2r-0.11.0/git2r/src/git2r_revwalk.c | 46 git2r-0.11.0/git2r/src/git2r_signature.c | 8 git2r-0.11.0/git2r/src/git2r_stash.c | 38 git2r-0.11.0/git2r/src/git2r_status.c | 20 git2r-0.11.0/git2r/src/git2r_tag.c | 178 + git2r-0.11.0/git2r/src/git2r_transfer.h | 12 git2r-0.11.0/git2r/src/libgit2/attr.c | 9 git2r-0.11.0/git2r/src/libgit2/attr_file.c | 70 git2r-0.11.0/git2r/src/libgit2/attr_file.h | 4 git2r-0.11.0/git2r/src/libgit2/blame.c | 4 git2r-0.11.0/git2r/src/libgit2/blame_git.c | 25 git2r-0.11.0/git2r/src/libgit2/blob.c | 13 git2r-0.11.0/git2r/src/libgit2/branch.c | 22 git2r-0.11.0/git2r/src/libgit2/buf_text.c | 10 git2r-0.11.0/git2r/src/libgit2/buf_text.h | 3 git2r-0.11.0/git2r/src/libgit2/buffer.c | 14 git2r-0.11.0/git2r/src/libgit2/buffer.h | 2 git2r-0.11.0/git2r/src/libgit2/cache.c | 9 git2r-0.11.0/git2r/src/libgit2/checkout.c | 96 git2r-0.11.0/git2r/src/libgit2/clone.c | 62 git2r-0.11.0/git2r/src/libgit2/commit.c | 65 git2r-0.11.0/git2r/src/libgit2/common.h | 22 git2r-0.11.0/git2r/src/libgit2/config.c | 31 git2r-0.11.0/git2r/src/libgit2/config.h | 6 git2r-0.11.0/git2r/src/libgit2/config_file.c | 1006 ++++----- git2r-0.11.0/git2r/src/libgit2/crlf.c | 56 git2r-0.11.0/git2r/src/libgit2/curl_stream.c |only git2r-0.11.0/git2r/src/libgit2/curl_stream.h |only git2r-0.11.0/git2r/src/libgit2/describe.c | 2 git2r-0.11.0/git2r/src/libgit2/diff.c | 358 ++- git2r-0.11.0/git2r/src/libgit2/diff.h | 22 git2r-0.11.0/git2r/src/libgit2/diff_driver.c | 2 git2r-0.11.0/git2r/src/libgit2/diff_file.c | 36 git2r-0.11.0/git2r/src/libgit2/diff_file.h | 6 git2r-0.11.0/git2r/src/libgit2/diff_patch.c | 337 ++- git2r-0.11.0/git2r/src/libgit2/diff_patch.h | 36 git2r-0.11.0/git2r/src/libgit2/diff_print.c | 282 +- git2r-0.11.0/git2r/src/libgit2/diff_tform.c | 88 git2r-0.11.0/git2r/src/libgit2/errors.c | 115 - git2r-0.11.0/git2r/src/libgit2/fetch.c | 37 git2r-0.11.0/git2r/src/libgit2/fetch.h | 11 git2r-0.11.0/git2r/src/libgit2/filebuf.c | 9 git2r-0.11.0/git2r/src/libgit2/filebuf.h | 2 git2r-0.11.0/git2r/src/libgit2/fileops.c | 8 git2r-0.11.0/git2r/src/libgit2/filter.c | 67 git2r-0.11.0/git2r/src/libgit2/fnmatch.c | 10 git2r-0.11.0/git2r/src/libgit2/global.c | 82 git2r-0.11.0/git2r/src/libgit2/global.h | 5 git2r-0.11.0/git2r/src/libgit2/ident.c | 4 git2r-0.11.0/git2r/src/libgit2/ignore.c | 57 git2r-0.11.0/git2r/src/libgit2/ignore.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/blob.h | 10 git2r-0.11.0/git2r/src/libgit2/include/git2/checkout.h | 11 git2r-0.11.0/git2r/src/libgit2/include/git2/clone.h | 13 git2r-0.11.0/git2r/src/libgit2/include/git2/commit.h | 11 git2r-0.11.0/git2r/src/libgit2/include/git2/cred_helpers.h | 4 git2r-0.11.0/git2r/src/libgit2/include/git2/describe.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/diff.h | 105 git2r-0.11.0/git2r/src/libgit2/include/git2/errors.h | 18 git2r-0.11.0/git2r/src/libgit2/include/git2/filter.h | 53 git2r-0.11.0/git2r/src/libgit2/include/git2/index.h | 51 git2r-0.11.0/git2r/src/libgit2/include/git2/merge.h | 3 git2r-0.11.0/git2r/src/libgit2/include/git2/notes.h | 4 git2r-0.11.0/git2r/src/libgit2/include/git2/odb.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/odb_backend.h | 4 git2r-0.11.0/git2r/src/libgit2/include/git2/pack.h | 12 git2r-0.11.0/git2r/src/libgit2/include/git2/rebase.h | 52 git2r-0.11.0/git2r/src/libgit2/include/git2/remote.h | 523 ++-- git2r-0.11.0/git2r/src/libgit2/include/git2/repository.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/reset.h | 5 git2r-0.11.0/git2r/src/libgit2/include/git2/revwalk.h | 18 git2r-0.11.0/git2r/src/libgit2/include/git2/stash.h | 139 + git2r-0.11.0/git2r/src/libgit2/include/git2/status.h | 1 git2r-0.11.0/git2r/src/libgit2/include/git2/submodule.h | 132 - git2r-0.11.0/git2r/src/libgit2/include/git2/sys/config.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/diff.h | 8 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/filter.h | 5 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/odb_backend.h | 4 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/refdb_backend.h | 7 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/stream.h | 2 git2r-0.11.0/git2r/src/libgit2/include/git2/sys/transport.h | 38 git2r-0.11.0/git2r/src/libgit2/include/git2/transport.h | 62 git2r-0.11.0/git2r/src/libgit2/include/git2/types.h | 31 git2r-0.11.0/git2r/src/libgit2/include/git2/version.h | 6 git2r-0.11.0/git2r/src/libgit2/index.c | 509 +++- git2r-0.11.0/git2r/src/libgit2/index.h | 5 git2r-0.11.0/git2r/src/libgit2/indexer.c | 24 git2r-0.11.0/git2r/src/libgit2/iterator.c | 276 ++ git2r-0.11.0/git2r/src/libgit2/iterator.h | 25 git2r-0.11.0/git2r/src/libgit2/merge.c | 208 - git2r-0.11.0/git2r/src/libgit2/merge.h | 18 git2r-0.11.0/git2r/src/libgit2/netops.c | 6 git2r-0.11.0/git2r/src/libgit2/netops.h | 4 git2r-0.11.0/git2r/src/libgit2/notes.c | 61 git2r-0.11.0/git2r/src/libgit2/odb.c | 26 git2r-0.11.0/git2r/src/libgit2/odb.h | 2 git2r-0.11.0/git2r/src/libgit2/odb_loose.c | 4 git2r-0.11.0/git2r/src/libgit2/odb_pack.c | 2 git2r-0.11.0/git2r/src/libgit2/openssl_stream.c | 159 + git2r-0.11.0/git2r/src/libgit2/pack-objects.c | 64 git2r-0.11.0/git2r/src/libgit2/pack-objects.h | 1 git2r-0.11.0/git2r/src/libgit2/pack.c | 28 git2r-0.11.0/git2r/src/libgit2/path.c | 461 ++-- git2r-0.11.0/git2r/src/libgit2/path.h | 201 + git2r-0.11.0/git2r/src/libgit2/posix.h | 1 git2r-0.11.0/git2r/src/libgit2/push.c | 87 git2r-0.11.0/git2r/src/libgit2/push.h | 35 git2r-0.11.0/git2r/src/libgit2/rebase.c | 264 +- git2r-0.11.0/git2r/src/libgit2/refdb_fs.c | 7 git2r-0.11.0/git2r/src/libgit2/reflog.c | 2 git2r-0.11.0/git2r/src/libgit2/refs.c | 10 git2r-0.11.0/git2r/src/libgit2/refspec.c | 9 git2r-0.11.0/git2r/src/libgit2/remote.c | 689 +++--- git2r-0.11.0/git2r/src/libgit2/remote.h | 4 git2r-0.11.0/git2r/src/libgit2/repository.c | 60 git2r-0.11.0/git2r/src/libgit2/repository.h | 1 git2r-0.11.0/git2r/src/libgit2/reset.c | 7 git2r-0.11.0/git2r/src/libgit2/revwalk.c | 28 git2r-0.11.0/git2r/src/libgit2/settings.c | 6 git2r-0.11.0/git2r/src/libgit2/stash.c | 455 ++++ git2r-0.11.0/git2r/src/libgit2/status.c | 6 git2r-0.11.0/git2r/src/libgit2/stransport_stream.c |only git2r-0.11.0/git2r/src/libgit2/stransport_stream.h |only git2r-0.11.0/git2r/src/libgit2/stream.h | 15 git2r-0.11.0/git2r/src/libgit2/submodule.c | 1094 +++------- git2r-0.11.0/git2r/src/libgit2/submodule.h | 24 git2r-0.11.0/git2r/src/libgit2/sysdir.c | 30 git2r-0.11.0/git2r/src/libgit2/thread-utils.c | 2 git2r-0.11.0/git2r/src/libgit2/tls_stream.c |only git2r-0.11.0/git2r/src/libgit2/tls_stream.h |only git2r-0.11.0/git2r/src/libgit2/transaction.c | 1 git2r-0.11.0/git2r/src/libgit2/transport.c | 8 git2r-0.11.0/git2r/src/libgit2/transports/cred.c | 56 git2r-0.11.0/git2r/src/libgit2/transports/git.c | 6 git2r-0.11.0/git2r/src/libgit2/transports/http.c | 39 git2r-0.11.0/git2r/src/libgit2/transports/local.c | 122 - git2r-0.11.0/git2r/src/libgit2/transports/smart.c | 2 git2r-0.11.0/git2r/src/libgit2/transports/smart.h | 2 git2r-0.11.0/git2r/src/libgit2/transports/smart_pkt.c | 2 git2r-0.11.0/git2r/src/libgit2/transports/smart_protocol.c | 22 git2r-0.11.0/git2r/src/libgit2/transports/ssh.c | 65 git2r-0.11.0/git2r/src/libgit2/transports/winhttp.c | 73 git2r-0.11.0/git2r/src/libgit2/tree.c | 4 git2r-0.11.0/git2r/src/libgit2/unix/posix.h | 6 git2r-0.11.0/git2r/src/libgit2/util.c | 66 git2r-0.11.0/git2r/src/libgit2/util.h | 134 + git2r-0.11.0/git2r/src/libgit2/win32/path_w32.c | 75 git2r-0.11.0/git2r/src/libgit2/win32/path_w32.h | 3 git2r-0.11.0/git2r/src/libgit2/win32/posix.h | 7 git2r-0.11.0/git2r/src/libgit2/win32/posix_w32.c | 160 - git2r-0.11.0/git2r/src/libgit2/win32/pthread.c | 2 git2r-0.11.0/git2r/src/libgit2/win32/utf-conv.c | 4 git2r-0.11.0/git2r/src/libgit2/win32/utf-conv.h | 4 git2r-0.11.0/git2r/src/libgit2/win32/w32_buffer.c |only git2r-0.11.0/git2r/src/libgit2/win32/w32_buffer.h |only git2r-0.11.0/git2r/src/libgit2/win32/w32_util.h | 82 git2r-0.11.0/git2r/src/libgit2/xdiff/xdiff.h | 16 git2r-0.11.0/git2r/src/libgit2/xdiff/xdiffi.c | 50 git2r-0.11.0/git2r/src/libgit2/xdiff/xdiffi.h | 1 git2r-0.11.0/git2r/src/libgit2/xdiff/xemit.c | 49 git2r-0.11.0/git2r/src/libgit2/xdiff/xemit.h | 2 git2r-0.11.0/git2r/src/libgit2/xdiff/xhistogram.c | 2 git2r-0.11.0/git2r/src/libgit2/xdiff/xmerge.c | 4 git2r-0.11.0/git2r/src/libgit2/xdiff/xpatience.c | 2 git2r-0.11.0/git2r/src/libgit2/xdiff/xprepare.c | 21 git2r-0.11.0/git2r/src/libgit2/xdiff/xutils.c | 42 git2r-0.11.0/git2r/src/libgit2/xdiff/xutils.h | 1 git2r-0.11.0/git2r/tests/add-force.R |only git2r-0.11.0/git2r/tests/branch.R | 35 git2r-0.11.0/git2r/tests/checkout_branch.R | 26 git2r-0.11.0/git2r/tests/clone_branch.R |only git2r-0.11.0/git2r/tests/merge.R | 4 git2r-0.11.0/git2r/tests/merge_named_branch.R | 4 git2r-0.11.0/git2r/tests/pull.R | 6 git2r-0.11.0/git2r/tests/push.R | 25 git2r-0.11.0/git2r/tests/reference.R |only git2r-0.11.0/git2r/tests/refspec.R |only git2r-0.11.0/git2r/tests/remove.R |only git2r-0.11.0/git2r/tests/repository.R | 5 git2r-0.11.0/git2r/tests/stash.R | 6 git2r-0.11.0/git2r/tests/tag.R | 8 git2r-0.11.0/git2r/tools/missing |only 277 files changed, 9304 insertions(+), 5098 deletions(-)
Title: Convert Data from and to 'geoJSON' or 'topoJSON'
Description: Convert data to 'geoJSON' or 'topoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial
classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'geoJSON' and 'topoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.1.0 dated 2015-04-30 and 0.1.4 dated 2015-08-12
geojsonio-0.1.0/geojsonio/R/file_to_geojson.R |only geojsonio-0.1.0/geojsonio/R/geojson_write.R |only geojsonio-0.1.0/geojsonio/R/zzz.R |only geojsonio-0.1.0/geojsonio/inst/doc/geojson_spec.R |only geojsonio-0.1.0/geojsonio/inst/doc/geojsonio_vignette.R |only geojsonio-0.1.0/geojsonio/inst/vign/figure/unnamed-chunk-12-1.png |only geojsonio-0.1.0/geojsonio/inst/vign/figure/unnamed-chunk-15-1.png |only geojsonio-0.1.0/geojsonio/inst/vign/figure/unnamed-chunk-22-1.png |only geojsonio-0.1.0/geojsonio/tests/testthat/myfile.geojson |only geojsonio-0.1.4/geojsonio/DESCRIPTION | 15 geojsonio-0.1.4/geojsonio/MD5 | 114 ++-- geojsonio-0.1.4/geojsonio/NAMESPACE | 22 geojsonio-0.1.4/geojsonio/NEWS | 28 + geojsonio-0.1.4/geojsonio/R/as.json.R | 3 geojsonio-0.1.4/geojsonio/R/as_spatial_methods.R | 15 geojsonio-0.1.4/geojsonio/R/construction.R | 24 geojsonio-0.1.4/geojsonio/R/file_to_geojson.r |only geojsonio-0.1.4/geojsonio/R/geojson_json.R | 3 geojsonio-0.1.4/geojsonio/R/geojson_list.R | 9 geojsonio-0.1.4/geojsonio/R/geojson_read.R | 72 ++ geojsonio-0.1.4/geojsonio/R/geojson_write.r |only geojsonio-0.1.4/geojsonio/R/geojsonio-package.R | 46 + geojsonio-0.1.4/geojsonio/R/mapleaflet.R |only geojsonio-0.1.4/geojsonio/R/onLoad.R | 4 geojsonio-0.1.4/geojsonio/R/projections.R | 15 geojsonio-0.1.4/geojsonio/R/zzz.r |only geojsonio-0.1.4/geojsonio/README.md | 86 ++- geojsonio-0.1.4/geojsonio/build/vignette.rds |binary geojsonio-0.1.4/geojsonio/inst/doc/geojson_spec.Rmd | 10 geojsonio-0.1.4/geojsonio/inst/doc/geojson_spec.html | 98 ++- geojsonio-0.1.4/geojsonio/inst/doc/geojsonio_vignette.Rmd | 260 +++++----- geojsonio-0.1.4/geojsonio/inst/doc/geojsonio_vignette.html | 242 ++++----- geojsonio-0.1.4/geojsonio/inst/doc/maps.Rmd |only geojsonio-0.1.4/geojsonio/inst/doc/maps.html |only geojsonio-0.1.4/geojsonio/inst/examples/feature_collection.geojson |only geojsonio-0.1.4/geojsonio/inst/ignore/postgis-play.R |only geojsonio-0.1.4/geojsonio/inst/ignore/postgis.R |only geojsonio-0.1.4/geojsonio/inst/ignore/postgis_code.R |only geojsonio-0.1.4/geojsonio/inst/img/unnamed-chunk-18-1.png |only geojsonio-0.1.4/geojsonio/inst/img/unnamed-chunk-20-1.png |only geojsonio-0.1.4/geojsonio/inst/js/turf_extent.js |only geojsonio-0.1.4/geojsonio/inst/vign/figure/leafletmap1.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/leafletmap2.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/map_leaf1.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/map_leaf2.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/maps_dataframe.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/maps_sppixels.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/maps_sppts.png |only geojsonio-0.1.4/geojsonio/inst/vign/figure/unnamed-chunk-17-1.png |binary geojsonio-0.1.4/geojsonio/inst/vign/geojson_spec.Rmd | 1 geojsonio-0.1.4/geojsonio/inst/vign/geojson_spec.md | 1 geojsonio-0.1.4/geojsonio/inst/vign/geojsonio_vignette.Rmd | 51 - geojsonio-0.1.4/geojsonio/inst/vign/geojsonio_vignette.md | 89 +-- geojsonio-0.1.4/geojsonio/inst/vign/maps.Rmd |only geojsonio-0.1.4/geojsonio/inst/vign/maps.md |only geojsonio-0.1.4/geojsonio/man/file_to_geojson.Rd | 13 geojsonio-0.1.4/geojsonio/man/geojson-add.Rd | 2 geojsonio-0.1.4/geojsonio/man/geojson_read.Rd | 43 + geojsonio-0.1.4/geojsonio/man/geojson_write.Rd | 28 - geojsonio-0.1.4/geojsonio/man/geojsonio.Rd | 38 + geojsonio-0.1.4/geojsonio/man/map_leaf.Rd |only geojsonio-0.1.4/geojsonio/man/pipe.Rd | 2 geojsonio-0.1.4/geojsonio/tests/test-all.R |only geojsonio-0.1.4/geojsonio/tests/testthat/helper-geojsonio.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-as.json.R | 2 geojsonio-0.1.4/geojsonio/tests/testthat/test-as.location.R | 9 geojsonio-0.1.4/geojsonio/tests/testthat/test-construction.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-file_to_geojson.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-geojson_json.R | 16 geojsonio-0.1.4/geojsonio/tests/testthat/test-geojson_list.R | 15 geojsonio-0.1.4/geojsonio/tests/testthat/test-geojson_read.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-geojson_write.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-lint.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-map_gist.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-onload.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-projections.R |only geojsonio-0.1.4/geojsonio/tests/testthat/test-rbind_fill.R |only geojsonio-0.1.4/geojsonio/vignettes/geojson_spec.Rmd | 10 geojsonio-0.1.4/geojsonio/vignettes/geojsonio_vignette.Rmd | 260 +++++----- geojsonio-0.1.4/geojsonio/vignettes/maps.Rmd |only 80 files changed, 984 insertions(+), 662 deletions(-)
Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics
interface to visualize backtest results of different financial
instruments, such as equities, futures, and credit default swaps.
The package does not run backtests on the given data set but
displays a graphical explanation of the backtest results. Users can
look at backtest graphics for different instruments, investment
strategies, and portfolios. Summary statistics of different
portfolio holdings are shown in the left panel, and interactive
plots of profit and loss (P\&L), net market value (NMV) and
gross market value (GMV) are displayed in the right panel.
Author: as.person(c(
"David Kane <dave.kane@gmail.com> [aut]",
"Ziqi Lu <ziqi.lu@williams.edu> [aut]",
"Fan Zhang <fan.zhang@williams.edu> [aut]",
"Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]"
))
Maintainer: Miller Zijie Zhu <zijie.miller.zhu@gmail.com>
Diff between backtestGraphics versions 0.1-3 dated 2015-08-11 and 0.1.4 dated 2015-08-12
DESCRIPTION | 8 - MD5 | 12 +- R/backtestGraphics.R | 175 +++++++++++++++++++-------------------- inst/doc/backtestGraphics.pdf |binary man/backtestGraphics.Rd | 104 +++++++++++------------ tests/testthat/test_slice_data.R | 24 +++-- tests/testthat/test_sum_data.R | 6 - 7 files changed, 172 insertions(+), 157 deletions(-)
More information about backtestGraphics at CRAN
Permanent link
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between mvSLOUCH versions 1.2 dated 2015-07-26 and 1.2.1 dated 2015-08-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/evolmodelest.R | 20 ++++++++++---------- man/estimate.evolutionary.model.Rd | 9 +++++---- 4 files changed, 21 insertions(+), 20 deletions(-)
Title: Design and Analysis of Mixture Experiments
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson [aut, cre],
Cameron Willden [aut],
Greg Piepel [ctb]
Maintainer: John Lawson <lawson@byu.edu>
Diff between mixexp versions 1.2.1 dated 2015-03-16 and 1.2.3 dated 2015-08-12
DESCRIPTION | 25 +++++++++++-------------- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ R/MixModel.R | 2 +- data/Burn.rda |binary data/SneeMq.rda |binary data/conmx.rda |binary data/etch.rda |binary data/fishp.rda |binary man/MixModel.Rd | 17 +++++++++-------- man/mixexp-package.Rd | 2 -- 11 files changed, 35 insertions(+), 35 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.3 dated 2015-08-02 and 1.8.4 dated 2015-08-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- tests/ggplotUsage.R | 2 +- tests/stdUsage.R | 1 + tests/testBinaryClass.R | 1 + tests/testMultiClass.cpp.R | 1 + 6 files changed, 12 insertions(+), 9 deletions(-)
Title: Climate Classification According to Several Indices
Description: Classification of climate according to Koeppen - Geiger, of aridity
indices, of continentality indices, of water balance after Thornthwaite, of
viticultural bioclimatic indices. Drawing climographs: Thornthwaite, Peguy,
Bagnouls-Gaussen.
Author: Emanuele Eccel [aut, cre],
Emanuele Cordano [aut],
Giambattista Toller [aut],
Fabio Zottele [ctb]
Maintainer: Emanuele Eccel <emanuele.eccel@fmach.it>
Diff between ClimClass versions 1.0 dated 2014-12-03 and 2.0.1 dated 2015-08-12
ClimClass-1.0/ClimClass/README.md |only ClimClass-1.0/ClimClass/inst/stuff |only ClimClass-1.0/ClimClass/man/ClimClass-package.Rd |only ClimClass-2.0.1/ClimClass/DESCRIPTION | 32 - ClimClass-2.0.1/ClimClass/MD5 | 67 +- ClimClass-2.0.1/ClimClass/NAMESPACE | 19 ClimClass-2.0.1/ClimClass/R/Bagn_Gau.R | 233 +++++----- ClimClass-2.0.1/ClimClass/R/ClimClass.R |only ClimClass-2.0.1/ClimClass/R/RDI.R |only ClimClass-2.0.1/ClimClass/R/Trent_climate.R |only ClimClass-2.0.1/ClimClass/R/as.datcli.R | 186 ++++---- ClimClass-2.0.1/ClimClass/R/climate.R | 105 ++-- ClimClass-2.0.1/ClimClass/R/contin.R | 26 - ClimClass-2.0.1/ClimClass/R/koeppen_geiger.R | 359 +++++++++------- ClimClass-2.0.1/ClimClass/R/oiv_ind.R |only ClimClass-2.0.1/ClimClass/R/peguy.R | 296 ++++++------- ClimClass-2.0.1/ClimClass/R/plot_quant.R | 235 +++++----- ClimClass-2.0.1/ClimClass/data/Trent_climate.RData |binary ClimClass-2.0.1/ClimClass/data/datalist |only ClimClass-2.0.1/ClimClass/man/ClimClass.Rd |only ClimClass-2.0.1/ClimClass/man/ExAtRa.Rd | 29 - ClimClass-2.0.1/ClimClass/man/P.Rd |only ClimClass-2.0.1/ClimClass/man/RDI.Rd |only ClimClass-2.0.1/ClimClass/man/Tm.Rd |only ClimClass-2.0.1/ClimClass/man/Tn.Rd |only ClimClass-2.0.1/ClimClass/man/Trent_climate.Rd | 63 -- ClimClass-2.0.1/ClimClass/man/Tx.Rd |only ClimClass-2.0.1/ClimClass/man/W_balance.Rd |only ClimClass-2.0.1/ClimClass/man/arid.Rd | 119 +---- ClimClass-2.0.1/ClimClass/man/arid_ind_tables.Rd |only ClimClass-2.0.1/ClimClass/man/as.datcli.Rd | 41 - ClimClass-2.0.1/ClimClass/man/bagn_gau.Rd | 64 -- ClimClass-2.0.1/ClimClass/man/clima_81_10.Rd |only ClimClass-2.0.1/ClimClass/man/climate.Rd | 35 - ClimClass-2.0.1/ClimClass/man/coeff_rad.Rd |only ClimClass-2.0.1/ClimClass/man/contin.Rd | 79 +-- ClimClass-2.0.1/ClimClass/man/continental_ind_tables.Rd |only ClimClass-2.0.1/ClimClass/man/coord_elev.Rd |only ClimClass-2.0.1/ClimClass/man/koeppen_geiger.Rd | 105 ++-- ClimClass-2.0.1/ClimClass/man/lista_cli.Rd |only ClimClass-2.0.1/ClimClass/man/oiv_ind.Rd |only ClimClass-2.0.1/ClimClass/man/peguy.Rd | 46 -- ClimClass-2.0.1/ClimClass/man/plot.thornthwaite.Rd | 78 +-- ClimClass-2.0.1/ClimClass/man/quantiles.Rd |only ClimClass-2.0.1/ClimClass/man/thornt_lst.Rd |only ClimClass-2.0.1/ClimClass/man/thornthwaite.Rd | 124 +---- 46 files changed, 1103 insertions(+), 1238 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.7.0 dated 2015-08-10 and 0.7.1 dated 2015-08-12
DESCRIPTION | 8 - MD5 | 16 +- NEWS | 11 + R/modules-smd.R | 4 build/vignette.rds |binary inst/doc/smd.Rmd | 2 inst/doc/smd.html | 268 +++++++++++++++++++------------------- tests/testthat/test-modules-smd.R | 32 +++- vignettes/smd.Rmd | 2 9 files changed, 185 insertions(+), 158 deletions(-)
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2S versions 1.0.2 dated 2015-07-08 and 1.0.3 dated 2015-08-12
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++++----- NEWS | 6 ++++++ README | 28 +++++++++++++++++++++++++++- build |only inst/doc/MM2S.R |only inst/doc/MM2S.Rnw |only inst/doc/MM2S.pdf |binary inst/doc/MM2S_Vignette_FrozenCapture.pdf |only vignettes/MM2S.Rnw | 5 +++-- 10 files changed, 51 insertions(+), 13 deletions(-)
Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation, incremental, and stochastic gradient methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@depaul.edu>
Diff between onlinePCA versions 1.0-1 dated 2015-01-21 and 1.2 dated 2015-08-12
onlinePCA-1.0-1/onlinePCA/src/sgapca.cpp |only onlinePCA-1.2/onlinePCA/DESCRIPTION | 14 ++-- onlinePCA-1.2/onlinePCA/MD5 | 71 +++++++++++--------- onlinePCA-1.2/onlinePCA/NAMESPACE | 7 +- onlinePCA-1.2/onlinePCA/NEWS | 27 +++++++ onlinePCA-1.2/onlinePCA/R/RcppExports.R | 16 +++- onlinePCA-1.2/onlinePCA/R/batchpca.R | 12 +-- onlinePCA-1.2/onlinePCA/R/ccipca.R |only onlinePCA-1.2/onlinePCA/R/coef2fd.R | 9 +- onlinePCA-1.2/onlinePCA/R/create.basis.R | 48 +++++++------ onlinePCA-1.2/onlinePCA/R/fd2coef.R | 11 +-- onlinePCA-1.2/onlinePCA/R/ghapca.R |only onlinePCA-1.2/onlinePCA/R/impute.R |only onlinePCA-1.2/onlinePCA/R/incRpca.R | 70 +++++++++----------- onlinePCA-1.2/onlinePCA/R/incRpca.rc.R |only onlinePCA-1.2/onlinePCA/R/perturbationRpca.R | 64 +++++++----------- onlinePCA-1.2/onlinePCA/R/secularRpca.R | 77 +++++++++------------- onlinePCA-1.2/onlinePCA/R/sgapca.R | 61 +++++++++-------- onlinePCA-1.2/onlinePCA/R/snlpca.R | 75 +++++++++++---------- onlinePCA-1.2/onlinePCA/R/updateCovariance.R | 24 +++--- onlinePCA-1.2/onlinePCA/R/updateMean.R | 37 +++++----- onlinePCA-1.2/onlinePCA/man/batchpca.Rd | 24 +++--- onlinePCA-1.2/onlinePCA/man/ccipca.Rd |only onlinePCA-1.2/onlinePCA/man/coef2fd.Rd | 27 +++---- onlinePCA-1.2/onlinePCA/man/create.basis.Rd | 30 ++++---- onlinePCA-1.2/onlinePCA/man/fd2coef.Rd | 31 ++++----- onlinePCA-1.2/onlinePCA/man/ghapca.Rd |only onlinePCA-1.2/onlinePCA/man/impute.Rd |only onlinePCA-1.2/onlinePCA/man/incRpca.Rd | 51 +++++++------- onlinePCA-1.2/onlinePCA/man/incRpca.rc.Rd |only onlinePCA-1.2/onlinePCA/man/onlinePCA-package.Rd | 13 ++- onlinePCA-1.2/onlinePCA/man/perturbationRpca.Rd | 33 ++++----- onlinePCA-1.2/onlinePCA/man/secularRpca.Rd | 45 ++++++------- onlinePCA-1.2/onlinePCA/man/sgapca.Rd | 54 ++++++++------- onlinePCA-1.2/onlinePCA/man/snlpca.Rd | 67 ++++++++++--------- onlinePCA-1.2/onlinePCA/man/updateCovariance.Rd | 25 +++---- onlinePCA-1.2/onlinePCA/man/updateMean.Rd | 41 +++++------ onlinePCA-1.2/onlinePCA/src/Makevars | 30 ++++++++ onlinePCA-1.2/onlinePCA/src/Makevars.win | 4 - onlinePCA-1.2/onlinePCA/src/RcppExports.cpp | 79 ++++++++++++++--------- onlinePCA-1.2/onlinePCA/src/ccipca.cpp |only onlinePCA-1.2/onlinePCA/src/sga_ghapca.cpp |only 42 files changed, 627 insertions(+), 550 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.3.2 dated 2015-07-28 and 0.3.3 dated 2015-08-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/latex2exp.R | 7 +++---- vignettes/latex2exp.Rmd | 6 ++++++ 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Higher Order Likelihood Inference
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>
Diff between hoa versions 2.1.2 dated 2015-07-14 and 2.1.4 dated 2015-08-11
CHANGES | 10 +++++++++- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/tem.R | 19 +++++++++++++------ 4 files changed, 29 insertions(+), 14 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-1 dated 2015-07-23 and 0.9-2 dated 2015-08-11
dbscan-0.9-1/dbscan/R/kNNdistplot.R |only dbscan-0.9-1/dbscan/man/kNNdistplot.Rd |only dbscan-0.9-1/dbscan/src/dbscan.cpp |only dbscan-0.9-1/dbscan/src/kNNdist.cpp |only dbscan-0.9-2/dbscan/DESCRIPTION | 18 ++++---- dbscan-0.9-2/dbscan/MD5 | 40 ++++++++++++------- dbscan-0.9-2/dbscan/NAMESPACE | 13 +++++- dbscan-0.9-2/dbscan/R/LOF.R |only dbscan-0.9-2/dbscan/R/RcppExports.R | 12 +++++ dbscan-0.9-2/dbscan/R/dbscan.R | 18 ++++++++ dbscan-0.9-2/dbscan/R/frNN.R |only dbscan-0.9-2/dbscan/R/kNN.R |only dbscan-0.9-2/dbscan/R/kNNdist.R |only dbscan-0.9-2/dbscan/R/optics.R |only dbscan-0.9-2/dbscan/inst/NEWS | 12 ++++- dbscan-0.9-2/dbscan/man/dbscan.Rd | 53 +++++++++++++------------- dbscan-0.9-2/dbscan/man/frNN.Rd |only dbscan-0.9-2/dbscan/man/kNN.Rd |only dbscan-0.9-2/dbscan/man/kNNdist.Rd |only dbscan-0.9-2/dbscan/man/lof.Rd |only dbscan-0.9-2/dbscan/man/optics.Rd |only dbscan-0.9-2/dbscan/src/ANN/ANN.h | 9 ++-- dbscan-0.9-2/dbscan/src/R_dbscan.cpp |only dbscan-0.9-2/dbscan/src/R_frNN.cpp |only dbscan-0.9-2/dbscan/src/R_kNN.cpp |only dbscan-0.9-2/dbscan/src/R_optics.cpp |only dbscan-0.9-2/dbscan/src/R_regionQuery.cpp |only dbscan-0.9-2/dbscan/src/R_regionQuery.h |only dbscan-0.9-2/dbscan/src/RcppExports.cpp | 49 ++++++++++++++++++++++++ dbscan-0.9-2/dbscan/src/brute.cpp | 6 +- dbscan-0.9-2/dbscan/src/kd_fix_rad_search.cpp | 9 ++-- 31 files changed, 178 insertions(+), 61 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.0.10 dated 2015-05-18 and 1.0.11 dated 2015-08-11
CHANGES | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/jonkheere.R | 8 +++++++- 4 files changed, 17 insertions(+), 7 deletions(-)
Title: Distances and Routes on Geographical Grids
Description: Calculate distances and routes on geographic grids.
Author: Jacob van Etten
Maintainer: Jacob van Etten <jacobvanetten@yahoo.com>
Diff between gdistance versions 1.1-7 dated 2015-03-11 and 1.1-9 dated 2015-08-11
gdistance-1.1-7/gdistance/man/gdistance-internal.Rd |only gdistance-1.1-9/gdistance/ChangeLog | 4 gdistance-1.1-9/gdistance/DESCRIPTION | 15 gdistance-1.1-9/gdistance/MD5 | 23 gdistance-1.1-9/gdistance/NAMESPACE | 1 gdistance-1.1-9/gdistance/build/vignette.rds |binary gdistance-1.1-9/gdistance/data/genDist.RData |binary gdistance-1.1-9/gdistance/data/popCoord.RData |binary gdistance-1.1-9/gdistance/inst/doc/gdistance1.R | 668 ++++++++++---------- gdistance-1.1-9/gdistance/inst/doc/gdistance1.Rnw | 254 ++++--- gdistance-1.1-9/gdistance/inst/doc/gdistance1.pdf |binary gdistance-1.1-9/gdistance/vignettes/gdistance1.Rnw | 254 ++++--- gdistance-1.1-9/gdistance/vignettes/gdistance1.bib | 20 13 files changed, 679 insertions(+), 560 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.4 dated 2015-07-10 and 0.3.6 dated 2015-08-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/varpoord.R | 3 +-- inst/CITATION | 2 +- inst/NEWS | 4 ++++ man/vardpoor-package.Rd | 4 ++-- man/varpoord.Rd | 19 +++++++++++++++++-- 7 files changed, 35 insertions(+), 17 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.10-0 dated 2015-07-25 and 1.11-0 dated 2015-08-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/tam.mml.2pl.R | 7 ++++--- R/tam.mml.3pl.R | 12 ++++++++++-- R/tam.mml.3pl.est.guessing.R | 27 +++++++++++++++++---------- R/tam.mml.R | 15 ++++----------- R/tam.mml.mfr.R | 4 +++- inst/NEWS | 26 ++++++++++++++++++++++++++ man/TAM-package.Rd | 2 +- man/tam.mml.3pl.Rd | 4 ++++ man/tam.modelfit.Rd | 2 +- 11 files changed, 84 insertions(+), 43 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.28 dated 2015-01-06 and 0.4.29 dated 2015-08-11
RUnit-0.4.28/RUnit/INDEX |only RUnit-0.4.29/RUnit/DESCRIPTION | 19 +++----- RUnit-0.4.29/RUnit/MD5 | 27 +++++------- RUnit-0.4.29/RUnit/NAMESPACE | 1 RUnit-0.4.29/RUnit/NEWS | 5 ++ RUnit-0.4.29/RUnit/R/00Init.r | 2 RUnit-0.4.29/RUnit/R/checkFuncs.r | 22 ++++----- RUnit-0.4.29/RUnit/R/runit.r | 40 +++++++++--------- RUnit-0.4.29/RUnit/R/testLogger.r | 4 - RUnit-0.4.29/RUnit/build/RUnit.pdf |binary RUnit-0.4.29/RUnit/build/vignette.rds |binary RUnit-0.4.29/RUnit/inst/doc/RUnit.pdf |binary RUnit-0.4.29/RUnit/inst/unitTests/runitHTMLProtocol.r | 4 - RUnit-0.4.29/RUnit/inst/unitTests/runitTextProtocol.r | 4 - RUnit-0.4.29/RUnit/man/RUnit-intro.Rd | 8 --- 15 files changed, 66 insertions(+), 70 deletions(-)
Title: Robust Estimation of Location and Scatter
Description: The restlos package provides algorithms for robust estimation of location (mean and mode) and scatter based on minimum spanning trees (pMST), self-organizing maps (Flood Algorithm), Delaunay triangulations (RDELA), and nested minimum volume convex sets (MVCH). The functions are also suitable for outlier detection.
Author: Steffen Liebscher and Thomas Kirschstein
Maintainer: Steffen Liebscher <steffen.liebscher@wiwi.uni-halle.de>
Diff between restlos versions 0.1-3 dated 2014-10-20 and 0.2-2 dated 2015-08-11
restlos-0.1-3/restlos/R/rdela.R |only restlos-0.2-2/restlos/DESCRIPTION | 16 +-- restlos-0.2-2/restlos/MD5 | 32 +++--- restlos-0.2-2/restlos/NAMESPACE | 19 ++- restlos-0.2-2/restlos/R/MVCH.r |only restlos-0.2-2/restlos/R/flood.R | 134 +++++++++++++------------- restlos-0.2-2/restlos/R/pMST.r | 8 - restlos-0.2-2/restlos/R/plot.rdela.R | 4 restlos-0.2-2/restlos/R/rdela.r |only restlos-0.2-2/restlos/man/MVCH.Rd |only restlos-0.2-2/restlos/man/flood.Rd | 2 restlos-0.2-2/restlos/man/halle.Rd | 4 restlos-0.2-2/restlos/man/pMST.Rd | 30 +++-- restlos-0.2-2/restlos/man/plot.flood.Rd | 2 restlos-0.2-2/restlos/man/plot.pMST.Rd | 6 - restlos-0.2-2/restlos/man/plot.rdela.Rd | 2 restlos-0.2-2/restlos/man/rdela.Rd | 18 ++- restlos-0.2-2/restlos/man/restlos-internal.Rd | 1 restlos-0.2-2/restlos/man/restlos-package.Rd | 10 + 19 files changed, 157 insertions(+), 131 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between poweRlaw versions 0.30.2 dated 2015-04-16 and 0.50.0 dated 2015-08-11
DESCRIPTION | 20 +++--- MD5 | 104 +++++++++++++++++---------------- NAMESPACE | 9 ++ NEWS | 20 +++--- R/AllGenerics.R | 27 +------- R/aaa_all_classes.R | 31 +++++++++ R/bootstrap.R | 4 - R/bootstrap_p.R | 31 +++++---- R/data_help_files.R | 3 R/def_dispois.R | 10 +++ R/dist_data_cdf_methods.R | 8 -- R/estimate_xmin.R | 28 ++++---- R/get_n.R |only R/get_ntail.R |only R/plot_methods.R | 4 - build/vignette.rds |binary data/bootstrap_moby.RData |binary data/bootstrap_p_moby.RData |binary inst/doc/a_introduction.R | 14 +--- inst/doc/a_introduction.Rnw | 63 ++++++++++--------- inst/doc/a_introduction.pdf |binary inst/doc/b_powerlaw_examples.R | 27 ++++++++ inst/doc/b_powerlaw_examples.Rnw | 75 +++++++++++++++++++++-- inst/doc/b_powerlaw_examples.pdf |binary inst/doc/c_comparing_distributions.pdf |binary inst/doc/d_jss_paper.pdf |binary man/bootstrap_moby.Rd | 2 man/compare_distributions.Rd | 2 man/displ.Rd | 2 man/dist_cdf-methods.Rd | 2 man/dist_data_cdf-methods.Rd | 13 +--- man/dist_ll-methods.Rd | 4 - man/dist_pdf-methods.Rd | 7 +- man/dist_rand-methods.Rd | 12 ++- man/dplcon.Rd | 2 man/dpldis.Rd | 2 man/estimate_pars.Rd | 2 man/estimate_xmin.Rd | 8 +- man/get_n.Rd |only man/get_ntail.Rd |only man/moby.Rd | 2 man/native_american.Rd | 2 man/plot-distribution-ANY-method.Rd | 2 man/plot.bs_xmin.Rd | 2 man/population.Rd | 2 man/poweRlaw-package.Rd | 2 man/show-distribution-method.Rd | 2 man/swiss_prot.Rd | 6 + vignettes/a_introduction.Rnw | 63 ++++++++++--------- vignettes/b_powerlaw_examples.Rnw | 75 +++++++++++++++++++++-- vignettes/examples1.rds |binary vignettes/knitr_figure_poweRlaw |only vignettes/plfit_res.rds |binary vignettes/poweRlaw.bib | 20 ++++++ 54 files changed, 464 insertions(+), 250 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.2 dated 2015-08-01 and 0.9.3 dated 2015-08-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS.Rd | 7 +++++++ src/Dataset.cpp | 2 +- src/Helpers.cpp | 2 -- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Grain-Size Statistics and Description of Sediment
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves.
Author: Regis K. Gallon (MNHN), Jerome Fournier (CNRS|MNHN)
Maintainer: Regis K. Gallon <reg.gallon@gmail.com>
Diff between G2Sd versions 2.1.3 dated 2015-03-12 and 2.1.4 dated 2015-08-11
G2Sd |only 1 file changed
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.2 dated 2015-05-15 and 0.4 dated 2015-08-11
dynRB-0.2/dynRB/R/dynRB_Pnc.R |only dynRB-0.2/dynRB/R/dynRB_VPac.R |only dynRB-0.2/dynRB/R/dynRB_Vnc.R |only dynRB-0.2/dynRB/R/funclist4.R |only dynRB-0.2/dynRB/man/dynRB_Pnc.Rd |only dynRB-0.2/dynRB/man/dynRB_VPac.Rd |only dynRB-0.2/dynRB/man/dynRB_Vnc.Rd |only dynRB-0.2/dynRB/man/funclist4.Rd |only dynRB-0.4/dynRB/DESCRIPTION | 14 - dynRB-0.4/dynRB/MD5 | 34 +- dynRB-0.4/dynRB/NAMESPACE | 3 dynRB-0.4/dynRB/R/dynRB_Pn.R | 64 +++-- dynRB-0.4/dynRB/R/dynRB_VPa.R | 131 +++++----- dynRB-0.4/dynRB/R/dynRB_Vn.R | 45 ++- dynRB-0.4/dynRB/R/funclist1.R | 291 +---------------------- dynRB-0.4/dynRB/R/funclist2.R | 441 +++++------------------------------ dynRB-0.4/dynRB/R/funclist3.R | 116 +-------- dynRB-0.4/dynRB/R/overview.R |only dynRB-0.4/dynRB/man/dynRB-package.Rd | 16 - dynRB-0.4/dynRB/man/dynRB_Pn.Rd | 16 - dynRB-0.4/dynRB/man/dynRB_VPa.Rd | 19 + dynRB-0.4/dynRB/man/dynRB_Vn.Rd | 15 - dynRB-0.4/dynRB/man/overview.Rd |only 23 files changed, 326 insertions(+), 879 deletions(-)
Title: Performing Multivariate Dose-Response Meta-Analysis
Description: It estimates a dose-response relation from either a single or
multiple summarized data. The trend estimation takes into account the
correlation among sets of log relative risks and use it to efficiently
estimate the dose-response relation. To obtain a pooled functional
relation, the study-specific trends are combined according to principles of
multivariate random-effects meta-analysis.
Author: Alessio Crippa
Maintainer: Alessio Crippa <alessio.crippa@ki.se>
Diff between dosresmeta versions 1.3.0 dated 2014-01-17 and 1.3.2 dated 2015-08-11
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 13 + R/coef.dosresmeta.R | 100 ++++++------ R/dosresmeta-package.R | 9 - R/dosresmeta.R | 32 +-- R/predict.dosresmeta.R | 238 ++++++++++++++--------------- R/summary.dosresmeta.R | 372 ++++++++++++++++++++++------------------------ man/alcohol_crc.Rd | 60 +++---- man/alcohol_cvd.Rd | 64 +++---- man/cc_ex.Rd | 70 ++++---- man/coef.dosresmeta.Rd | 97 +++++------ man/dosresmeta-package.Rd | 105 +++++------- man/dosresmeta.Rd | 328 +++++++++++++++------------------------- man/grl.Rd | 171 ++++++++------------- man/hamling.Rd | 166 ++++++++------------ man/predict.dosresmeta.Rd | 217 +++++++++++--------------- man/summary.dosresmeta.Rd | 147 +++++++----------- 18 files changed, 1004 insertions(+), 1229 deletions(-)
Title: Binarization and Trinarization of One-Dimensional Data
Description: Provides methods for the binarization and trinarization of one-dimensional data and some visualization functions.
Author: Stefan Mundus, Christoph Müssel, Florian Schmid, Ludwig Lausser, Tamara J. Blätte, Martin Hopfensitz, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between BiTrinA versions 1.0 dated 2015-08-05 and 1.1 dated 2015-08-11
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 3 ++- R/binarizeMatrix.R | 9 +++++++-- R/result_TASC.R | 3 ++- R/trinarizeKMeans.R |only inst/doc/Vignette.Rnw | 2 +- inst/doc/Vignette.pdf |binary man/trinarizeKMeans.Rd |only man/trinarizeMatrix.Rd | 8 ++++---- vignettes/Vignette.Rnw | 2 +- 11 files changed, 31 insertions(+), 22 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-6 dated 2014-01-17 and 0.2-8 dated 2015-08-11
CHANGELOG | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 4 ++++ data/zaki.rda |binary src/TPOSE/exttpose.cc | 2 +- src/cSPADE/partition.cc | 2 +- src/cSPADE/sequence.cc | 2 +- 8 files changed, 27 insertions(+), 14 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.45 dated 2015-05-26 and 0.48 dated 2015-08-11
DESCRIPTION | 12 +-- MD5 | 160 +++++++++++++++++++++---------------------- NAMESPACE | 3 R/diagnose.R | 2 R/util.R | 6 + README.md | 2 build/vignette.rds |binary inst/doc/diagnostics.R | 6 - inst/doc/diagnostics.html | 58 +++++++-------- inst/doc/flexmirt-plots.R | 10 +- inst/doc/flexmirt-plots.html | 2 inst/tests/test-ld.R | 34 ++++++--- man/ChenThissen1997.Rd | 3 man/EAPscores.Rd | 3 man/LSAT6.Rd | 3 man/LSAT7.Rd | 3 man/SitemFit.Rd | 3 man/SitemFit1.Rd | 3 man/as.IFAgroup.Rd | 3 man/bestToOmit.Rd | 3 man/compressDataFrame.Rd | 3 man/crosstabTest.Rd | 3 man/expandDataFrame.Rd | 3 man/fromFactorLoading.Rd | 3 man/fromFactorThreshold.Rd | 3 man/itemOutcomeBySumScore.Rd | 3 man/kct.Rd | 3 man/logit.Rd | 3 man/multinomialFit.Rd | 3 man/observedSumScore.Rd | 3 man/omitItems.Rd | 3 man/omitMostMissing.Rd | 3 man/orderCompletely.Rd | 3 man/ordinal.gamma.Rd | 3 man/ptw2011.gof.test.Rd | 3 man/read.flexmirt.Rd | 3 man/rpf.1dim-class.Rd | 3 man/rpf.1dim.drm-class.Rd | 3 man/rpf.1dim.fit.Rd | 3 man/rpf.1dim.graded-class.Rd | 3 man/rpf.1dim.grm-class.Rd | 3 man/rpf.1dim.moment.Rd | 3 man/rpf.1dim.residual.Rd | 3 man/rpf.1dim.stdresidual.Rd | 3 man/rpf.base-class.Rd | 3 man/rpf.dLL.Rd | 3 man/rpf.dTheta.Rd | 3 man/rpf.drm.Rd | 3 man/rpf.grm.Rd | 3 man/rpf.id_of.Rd | 3 man/rpf.info.Rd | 3 man/rpf.introduction.Rd | 3 man/rpf.logprob.Rd | 3 man/rpf.mcm.Rd | 3 man/rpf.mdim-class.Rd | 3 man/rpf.mdim.drm-class.Rd | 3 man/rpf.mdim.graded-class.Rd | 3 man/rpf.mdim.grm-class.Rd | 3 man/rpf.mdim.mcm-class.Rd | 3 man/rpf.mdim.nrm-class.Rd | 3 man/rpf.mean.info.Rd | 3 man/rpf.mean.info1.Rd | 3 man/rpf.modify.Rd | 3 man/rpf.nrm.Rd | 3 man/rpf.numParam.Rd | 3 man/rpf.numSpec.Rd | 3 man/rpf.ogive.Rd | 3 man/rpf.paramInfo.Rd | 3 man/rpf.prob.Rd | 3 man/rpf.rescale.Rd | 3 man/rpf.rparam.Rd | 3 man/rpf.sample.Rd | 3 man/science.Rd | 3 man/stripData.Rd | 3 man/sumScoreEAP.Rd | 3 man/sumScoreEAPTest.Rd | 3 man/tabulateRows.Rd | 3 man/toFactorLoading.Rd | 12 ++- man/toFactorThreshold.Rd | 3 man/write.flexmirt.Rd | 3 src/diagnose.cpp | 2 81 files changed, 305 insertions(+), 205 deletions(-)
More information about RateDistortion at CRAN
Permanent link
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis Hastings with exponential down weighting.
Author: Matthew J. Denny <mzd5530@psu.edu>, James D. Wilson <jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A. Desmarais <bbd5087@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mzd5530@psu.edu>
Diff between GERGM versions 0.3.1 dated 2015-08-09 and 0.3.2 dated 2015-08-11
GERGM-0.3.1/GERGM/build |only GERGM-0.3.2/GERGM/DESCRIPTION | 6 - GERGM-0.3.2/GERGM/MD5 | 21 ++-- GERGM-0.3.2/GERGM/R/Estimate_Plot.R | 8 + GERGM-0.3.2/GERGM/R/RcppExports.R | 4 GERGM-0.3.2/GERGM/R/Simulate_GERGM.R | 5 - GERGM-0.3.2/GERGM/R/gergm.R | 70 +++++++------- GERGM-0.3.2/GERGM/README.md | 85 +++++++++--------- GERGM-0.3.2/GERGM/man/GERGM-package.Rd | 12 -- GERGM-0.3.2/GERGM/man/gergm.Rd | 4 GERGM-0.3.2/GERGM/src/Metropolis_Hastings_Sampler.cpp | 27 ++--- GERGM-0.3.2/GERGM/src/RcppExports.cpp | 7 - 12 files changed, 133 insertions(+), 116 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Functions for Bayesian meta-analysis of diagnostic test data which are based on a scale mixtures bivariate random-effects model.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 2.0 dated 2015-06-16 and 2.0.1 dated 2015-08-11
ChangeLog | 8 DESCRIPTION | 10 - MD5 | 16 - NAMESPACE | 35 ++-- R/bsroc.R | 393 ++++++++++++++++++++++++------------------------ R/plotcompare.R | 455 ++++++++++++++++++++++++++++---------------------------- R/plotcont.R | 291 +++++++++++++++++------------------ R/plotsesp.R | 165 ++++++++++---------- R/plotw.R | 185 +++++++++++----------- 9 files changed, 788 insertions(+), 770 deletions(-)
More information about backtestGraphics at CRAN
Permanent link
Title: Implements the MixMAP Algorithm
Description: A collection of functions to implement the MixMAP algorithm, which performs gene
level tests of association using data from a previous GWAS or data from a
meta-analysis of several GWAS. Conceptually, genes are detected as
significant if the collection of p-values within a gene are determined to
be collectively smaller than would be observed by chance.
Author: Gregory J. Matthews
Maintainer: Gregory J. Matthews <gjm112@gmail.com>
Diff between MixMAP versions 1.3.1 dated 2014-03-10 and 1.3.4 dated 2015-08-10
DESCRIPTION | 18 +++++++++--------- MD5 | 25 +++++++++++++------------ NAMESPACE | 3 +++ R/mixmapTest.R | 7 +++++-- README.md | 4 +++- data/MixMAP_example.RData |binary inst |only man/MixMAPclass.Rd | 8 ++++---- man/MixMAPexample.Rd | 4 +++- man/MixMAPpackage.Rd | 4 +++- man/mixmapPI.Rd | 22 +++++++++++----------- man/mixmapTest.Rd | 18 +++++++++--------- man/plot.MixMAP.Rd | 10 ++++++---- man/summary.MixMAP.Rd | 10 ++++++---- 14 files changed, 75 insertions(+), 58 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters and a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.1.9425 dated 2015-06-12 and 0.0.1.9525 dated 2015-08-10
DESCRIPTION | 8 +-- MD5 | 40 +++++++++--------- NAMESPACE | 2 R/AQSearch.CAS.R | 25 ++++++----- R/AQSearch.R | 37 +++++++++-------- R/AQSearchUtils.R | 8 +++ R/AQSys.R | 33 +++++++++++---- R/AQSys.err.R | 1 R/AQSys.gsnchk.R | 53 ++++++++++++++----------- R/AQSys.mathDesc.R | 51 ++++++++++++++---------- R/AQSys.mrchk.R | 82 +++++++++++++++++++++++--------------- R/AQSys.mrgsn.R | 36 ++++++++++------- R/AQSysCurve.R | 26 +++++++----- R/AQSysDB.R | 91 ++++++++++++++++++++++++++++--------------- R/AQSysFormulas.R | 49 +++++++++++++---------- R/AQSysUtils.R | 51 ++++++++++++++---------- R/LLSRxy.R | 8 ++- man/AQSearch.Rd | 2 man/AQSysBancroft.Rd | 4 - man/AQSysOthmer.Rd | 4 - tests/testthat/testMainFns.R | 5 +- 21 files changed, 378 insertions(+), 238 deletions(-)
Title: Cooperative Game Theory
Description: Implementation of a common set of punctual solutions for Cooperative Game Theory.
Author: Sebastian Cano-Berlanga
Maintainer: Sebastian Cano-Berlanga <cano.berlanga@gmail.com>
Diff between GameTheory versions 1.0 dated 2015-03-08 and 2.0 dated 2015-08-10
GameTheory-1.0/GameTheory/R/NucleolusCost.R |only GameTheory-1.0/GameTheory/R/PlotAll.R |only GameTheory-1.0/GameTheory/man/NucleolusCost.Rd |only GameTheory-1.0/GameTheory/man/PlotAll.Rd |only GameTheory-2.0/GameTheory/DESCRIPTION | 8 - GameTheory-2.0/GameTheory/MD5 | 62 ++++++---- GameTheory-2.0/GameTheory/NAMESPACE | 9 + GameTheory-2.0/GameTheory/R/AdjustedProportional.R |only GameTheory-2.0/GameTheory/R/AllRules.R | 2 GameTheory-2.0/GameTheory/R/CEA.R | 4 GameTheory-2.0/GameTheory/R/CEL.R | 4 GameTheory-2.0/GameTheory/R/DefineGame.R |only GameTheory-2.0/GameTheory/R/Nucleolus.R | 97 +++++++++++++---- GameTheory-2.0/GameTheory/R/NucleolusCapita.R |only GameTheory-2.0/GameTheory/R/Proportional.R | 4 GameTheory-2.0/GameTheory/R/RandomArrival.R | 4 GameTheory-2.0/GameTheory/R/ShapleyShubick.R | 8 + GameTheory-2.0/GameTheory/R/ShapleyValue.R | 11 + GameTheory-2.0/GameTheory/R/Talmud.R | 8 - GameTheory-2.0/GameTheory/R/plot.ClaimsRules.R |only GameTheory-2.0/GameTheory/R/summary.ClaimsRule.R |only GameTheory-2.0/GameTheory/R/summary.ClaimsRules.R |only GameTheory-2.0/GameTheory/R/summary.Game.R |only GameTheory-2.0/GameTheory/R/summary.Nucleolus.R |only GameTheory-2.0/GameTheory/R/summary.ShapleyShubik.R |only GameTheory-2.0/GameTheory/R/summary.ShapleyValue.R |only GameTheory-2.0/GameTheory/build/vignette.rds |binary GameTheory-2.0/GameTheory/inst/doc/GameTheory.pdf |binary GameTheory-2.0/GameTheory/man/AdjustedProportional.Rd |only GameTheory-2.0/GameTheory/man/AllRules.Rd | 5 GameTheory-2.0/GameTheory/man/DefineGame.Rd |only GameTheory-2.0/GameTheory/man/GameTheory-package.Rd | 66 ++++------- GameTheory-2.0/GameTheory/man/LorenzRules.Rd | 4 GameTheory-2.0/GameTheory/man/Nucleolus.Rd | 57 +++++---- GameTheory-2.0/GameTheory/man/NucleolusCapita.Rd |only GameTheory-2.0/GameTheory/man/ShapleyShubik.Rd | 17 -- GameTheory-2.0/GameTheory/man/ShapleyValue.Rd | 15 ++ GameTheory-2.0/GameTheory/man/plot.ClaimsRules.Rd |only GameTheory-2.0/GameTheory/man/summary.ClaimsRule.Rd |only GameTheory-2.0/GameTheory/man/summary.ClaimsRules.Rd |only GameTheory-2.0/GameTheory/man/summary.Game.Rd |only GameTheory-2.0/GameTheory/man/summary.Nucleolus.Rd |only GameTheory-2.0/GameTheory/man/summary.ShapleyShubik.Rd |only GameTheory-2.0/GameTheory/man/summary.ShapleyValue.Rd |only 44 files changed, 241 insertions(+), 144 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.6.3 dated 2014-12-29 and 0.7.0 dated 2015-08-10
tableone-0.6.3/tableone/R/modules.R |only tableone-0.7.0/tableone/DESCRIPTION | 30 tableone-0.7.0/tableone/MD5 | 94 +- tableone-0.7.0/tableone/NAMESPACE | 26 tableone-0.7.0/tableone/NEWS | 57 + tableone-0.7.0/tableone/R/CreateCatTable.R | 121 +-- tableone-0.7.0/tableone/R/CreateContTable.R | 72 +- tableone-0.7.0/tableone/R/CreateTableOne.R | 348 ++++------ tableone-0.7.0/tableone/R/ExtractSmd.R |only tableone-0.7.0/tableone/R/ShowRegTable.R | 45 - tableone-0.7.0/tableone/R/modules-constructors.R |only tableone-0.7.0/tableone/R/modules-print.R |only tableone-0.7.0/tableone/R/modules-smd.R |only tableone-0.7.0/tableone/R/modules-svy.R |only tableone-0.7.0/tableone/R/print.CatTable.R | 276 +------ tableone-0.7.0/tableone/R/print.ContTable.R | 131 +-- tableone-0.7.0/tableone/R/print.TableOne.R | 274 ++----- tableone-0.7.0/tableone/R/print.svyCatTable.R |only tableone-0.7.0/tableone/R/print.svyContTable.R |only tableone-0.7.0/tableone/R/summary.CatTable.R | 36 - tableone-0.7.0/tableone/R/summary.ContTable.R | 36 - tableone-0.7.0/tableone/R/summary.TableOne.R | 75 -- tableone-0.7.0/tableone/R/summary.svyCatTable.R |only tableone-0.7.0/tableone/R/summary.svyContTable.R |only tableone-0.7.0/tableone/R/svyCreateCatTable.R |only tableone-0.7.0/tableone/R/svyCreateContTable.R |only tableone-0.7.0/tableone/R/svyCreateTableOne.R |only tableone-0.7.0/tableone/R/tableone-package.R | 81 -- tableone-0.7.0/tableone/build/vignette.rds |binary tableone-0.7.0/tableone/inst/doc/introduction.R | 6 tableone-0.7.0/tableone/inst/doc/introduction.Rmd | 8 tableone-0.7.0/tableone/inst/doc/introduction.html | 112 +-- tableone-0.7.0/tableone/inst/doc/smd.R |only tableone-0.7.0/tableone/inst/doc/smd.Rmd |only tableone-0.7.0/tableone/inst/doc/smd.html |only tableone-0.7.0/tableone/man/CreateCatTable.Rd | 34 tableone-0.7.0/tableone/man/CreateContTable.Rd | 19 tableone-0.7.0/tableone/man/CreateTableOne.Rd | 64 + tableone-0.7.0/tableone/man/ExtractSmd.Rd |only tableone-0.7.0/tableone/man/ShowRegTable.Rd | 6 tableone-0.7.0/tableone/man/print.CatTable.Rd | 23 tableone-0.7.0/tableone/man/print.ContTable.Rd | 22 tableone-0.7.0/tableone/man/print.TableOne.Rd | 75 -- tableone-0.7.0/tableone/man/print.svyCatTable.Rd |only tableone-0.7.0/tableone/man/print.svyContTable.Rd |only tableone-0.7.0/tableone/man/summary.CatTable.Rd | 32 tableone-0.7.0/tableone/man/summary.ContTable.Rd | 32 tableone-0.7.0/tableone/man/summary.TableOne.Rd | 43 - tableone-0.7.0/tableone/man/summary.svyCatTable.Rd |only tableone-0.7.0/tableone/man/summary.svyContTable.Rd |only tableone-0.7.0/tableone/man/svyCreateCatTable.Rd |only tableone-0.7.0/tableone/man/svyCreateContTable.Rd |only tableone-0.7.0/tableone/man/svyCreateTableOne.Rd |only tableone-0.7.0/tableone/man/tableone-package.Rd | 79 -- tableone-0.7.0/tableone/tests/testthat/test-CreateTableOne.R | 266 +++++++ tableone-0.7.0/tableone/tests/testthat/test-ExtractSmd.R |only tableone-0.7.0/tableone/tests/testthat/test-ShowRegTable.R |only tableone-0.7.0/tableone/tests/testthat/test-modules-smd.R |only tableone-0.7.0/tableone/tests/testthat/test-modules-svy.R |only tableone-0.7.0/tableone/tests/testthat/test-modules.R | 1 tableone-0.7.0/tableone/tests/testthat/test-svyCreateTableOne.R |only tableone-0.7.0/tableone/vignettes/introduction.Rmd | 8 tableone-0.7.0/tableone/vignettes/smd.Rmd |only 63 files changed, 1187 insertions(+), 1345 deletions(-)
Title: Threshold Regression
Description: Fit a threshold regression model based on the first-hitting-time of a boundary by the sample path of a Wiener diffusion process. The threshold regression methodology is well suited to applications involving survival and time-to-event data.
Author: Tao Xiao
Maintainer: Tao Xiao <taoxiao1@gmail.com>
Diff between threg versions 1.0.2 dated 2013-04-18 and 1.0.3 dated 2015-08-10
threg-1.0.2/threg/inst/doc |only threg-1.0.3/threg/DESCRIPTION | 17 threg-1.0.3/threg/MD5 | 22 threg-1.0.3/threg/NAMESPACE | 19 threg-1.0.3/threg/R/hr.threg.R |only threg-1.0.3/threg/R/plot.threg.R |only threg-1.0.3/threg/R/predict.threg.R |only threg-1.0.3/threg/R/print.threg.R |only threg-1.0.3/threg/R/threg.R | 905 +-------------------------------- threg-1.0.3/threg/data/bmt.RData |binary threg-1.0.3/threg/data/lkr.RData |binary threg-1.0.3/threg/inst/CITATION |only threg-1.0.3/threg/man/hr.threg.Rd |only threg-1.0.3/threg/man/plot.threg.Rd |only threg-1.0.3/threg/man/predict.threg.Rd |only threg-1.0.3/threg/man/print.threg.Rd |only threg-1.0.3/threg/man/threg.Rd | 67 -- 17 files changed, 94 insertions(+), 936 deletions(-)
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System. These tools address common challenges
associated with continuous time series data for environmental decision
making.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between SWMPr versions 2.0.0 dated 2015-04-01 and 2.1.0 dated 2015-08-10
DESCRIPTION | 10 - MD5 | 87 +++++---- NAMESPACE | 30 +++ R/gradcols.R |only R/swmpr_analyze.R | 408 +++++++++++++++++++++++++++++++++++++++++++--- R/swmpr_misc.R | 146 ---------------- R/swmpr_organize.R | 223 +++++++++++++++++++------ R/swmpr_retrieval.R | 418 +++++++++++++++++++++++++++++++++--------------- man/aggremetab.Rd | 7 man/aggreswmp.Rd | 11 + man/all_params.Rd | 15 + man/all_params_dtrng.Rd | 19 +- man/apacpnut.Rd | 2 man/apacpwq.Rd | 2 man/apadbwq.Rd | 2 man/apaebmet.Rd | 2 man/calckl.Rd | 2 man/comb.Rd | 21 ++ man/decomp.Rd | 27 ++- man/decomp_cj.Rd | 26 ++ man/ecometab.Rd | 9 - man/gradcols.Rd |only man/hist.swmpr.Rd | 5 man/import_local.Rd | 17 + man/import_remote.Rd | 7 man/map_reserve.Rd | 7 man/metab_day.Rd | 2 man/na.approx.swmpr.Rd | 5 man/overplot.Rd |only man/param_names.Rd | 2 man/parser.Rd | 2 man/plot.swmpr.Rd | 7 man/plot_metab.Rd | 9 - man/plot_summary.Rd | 7 man/qaqc.Rd | 20 +- man/qaqcchk.Rd | 7 man/rem_reps.Rd | 7 man/setstep.Rd | 27 ++- man/single_param.Rd | 11 - man/site_codes.Rd | 7 man/site_codes_ind.Rd | 7 man/smoother.Rd | 9 - man/stat_locs.Rd | 2 man/subset.swmpr.Rd | 5 man/swmpr.Rd | 2 man/time_vec.Rd | 2 46 files changed, 1170 insertions(+), 473 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.2.0 dated 2015-07-17 and 1.2.1 dated 2015-08-10
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 9 +++++++++ R/es.R | 6 +++--- README.md | 2 ++ man/es.Rd | 2 +- tests/testthat/test-05-ore.R | 2 +- tests/testthat/test-25-es.R | 1 + 8 files changed, 29 insertions(+), 17 deletions(-)
Title: Cusp-Catastrophe Model Fitting Using Maximum Likelihood
Description: Cobb's maximum likelihood method for cusp-catastrophe modeling
(Grasman, van der Maas, & Wagenmakers, 2009, JSS, 32:8;
Cobb, L, 1981, Behavioral Science, 26:1, 75--78).
Includes a cusp() function for model fitting, and several
utility functions for plotting, and for comparing the
model to linear regression and logistic curve models.
Author: Raoul P. P. P. Grasman [aut, cre, cph]
Maintainer: Raoul Grasman <rgrasman@uva.nl>
Diff between cusp versions 2.3.1 dated 2015-06-26 and 2.3.3 dated 2015-08-10
DESCRIPTION | 11 +++--- MD5 | 18 +++++----- NAMESPACE | 5 ++ R/cusp.fit.R | 35 ++++++++++--------- R/predict.cusp.R |only inst/doc/Cusp-JSS.Rnw | 30 ++++++++-------- inst/doc/cusp-hands-on-examples.pdf |binary man/cusp.logist.Rd | 64 ++++++++++++++++++------------------ man/predict.cusp.Rd |only man/summary.cusp.Rd | 2 - vignettes/Cusp-JSS.Rnw | 30 ++++++++-------- 11 files changed, 103 insertions(+), 92 deletions(-)
Title: Flexible Tree Taper Curves Based on Semiparametric Mixed Models
Description: Implementation of functions for fitting taper curves (a semiparametric linear mixed effects taper model) to diameter measurements along stems. Further functions are provided to estimate the uncertainty around the predicted curves, to calculate timber volume (also by sections) and marginal (e.g., upper) diameters. For cases where tree
heights are not measured, methods for estimating
additional variance in volume predictions resulting from uncertainties in
tree height models (tariffs) are provided. The example data include the taper curve parameters for Norway spruce used in the 3rd German NFI fitted to 380 trees and a subset of section-wise diameter measurements of these trees. The functions implemented here are detailed in the following publication: Kublin, E., Breidenbach, J., Kaendler, G. (2013) A flexible stem taper and volume prediction method based on mixed-effects B-spline regression, Eur J For Res, 132:983-997.
Author: Edgar Kublin [aut],
Johannes Breidenbach [ctb, cre]
Maintainer: Johannes Breidenbach <job@nibio.no>
Diff between TapeR versions 0.3.2 dated 2013-12-14 and 0.3.3 dated 2015-08-10
DESCRIPTION | 19 +-- MD5 | 28 ++-- NAMESPACE | 6 + R/CdN_DHxHt.f.R | 2 R/EYx_ssp.f.R | 4 R/E_DHx_HmDm_HT_CIdHt.f.R | 14 +- R/E_VOL_AB_HmDm_Ht.f.R | 6 - R/Int_E_VOL_AB_HmDm_HT_dHt.f.R | 2 R/SK_EBLUP_LME.f.R | 8 - R/SK_VOLab_EBLUP_LME.f.R | 6 - R/e_vol_ab_hmdm_ht.f_1.R | 8 - build/vignette.rds |binary inst/doc/TapeR.Rnw | 244 ++++++++++++++++++++--------------------- inst/doc/TapeR.pdf |binary vignettes/TapeR.Rnw | 244 ++++++++++++++++++++--------------------- 15 files changed, 298 insertions(+), 293 deletions(-)
Title: Multidimensional Scaling
Description: Provides the following approaches for multidimensional
scaling (MDS) based on stress minimization by means of majorization
(smacof): basic MDS on symmetric dissimilarity matrices,
MDS with external constraints on the configuration, individual difference scaling (idioscal, indscal, and friends),
MDS with spherical restrictions, and unfolding. The MDS type can be ratio, interval, ordinal, and monotone splines.
Various tools and extensiosn like jackknife MDS, permutation tests, gravity models, inverse MDS, unidimensional scaling,
classical scaling, and Procrustes.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Ingwer Borg [ctb], Patrick
J. F. Groenen [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between smacof versions 1.6-2 dated 2015-01-27 and 1.7-0 dated 2015-08-10
smacof-1.6-2/smacof/COPYING |only smacof-1.6-2/smacof/R/mds.R |only smacof-1.6-2/smacof/R/plot3d.smacof.r |only smacof-1.6-2/smacof/R/plot3d.smacofID.r |only smacof-1.6-2/smacof/R/plot3d.smacofR.r |only smacof-1.6-2/smacof/R/plot3dstatic.r |only smacof-1.6-2/smacof/R/plot3dstatic.smacof.r |only smacof-1.6-2/smacof/R/plot3dstatic.smacofID.r |only smacof-1.6-2/smacof/R/plot3dstatic.smacofR.r |only smacof-1.6-2/smacof/inst/COPYRIGHTS |only smacof-1.6-2/smacof/man/plot3d.smacof.rd |only smacof-1.6-2/smacof/man/smacof-package.Rd |only smacof-1.7-0/smacof/DESCRIPTION | 33 +++---- smacof-1.7-0/smacof/MD5 | 111 ++++++++++++++++---------- smacof-1.7-0/smacof/NAMESPACE | 25 ++--- smacof-1.7-0/smacof/R/Procrustes.R |only smacof-1.7-0/smacof/R/checkdiss.R |only smacof-1.7-0/smacof/R/initConf.R |only smacof-1.7-0/smacof/R/initWeights.R | 21 +++- smacof-1.7-0/smacof/R/inverseMDS.R |only smacof-1.7-0/smacof/R/inverseUtilities.R |only smacof-1.7-0/smacof/R/nextperm.R |only smacof-1.7-0/smacof/R/normDissN.R | 4 smacof-1.7-0/smacof/R/permtest.R | 2 smacof-1.7-0/smacof/R/permtest.smacof.R | 3 smacof-1.7-0/smacof/R/permtest.smacofR.R | 3 smacof-1.7-0/smacof/R/plot.procr.R |only smacof-1.7-0/smacof/R/plot.smacof.R | 89 ++++++++++---------- smacof-1.7-0/smacof/R/plot.smacofID.r | 4 smacof-1.7-0/smacof/R/plot.smacofR.R | 22 +++-- smacof-1.7-0/smacof/R/plot.uniscale.R |only smacof-1.7-0/smacof/R/print.procr.R |only smacof-1.7-0/smacof/R/print.smacofPerm.R | 2 smacof-1.7-0/smacof/R/print.smacofR.R | 2 smacof-1.7-0/smacof/R/print.uniscale.R |only smacof-1.7-0/smacof/R/randomstress.R |only smacof-1.7-0/smacof/R/residuals.smacof.R | 2 smacof-1.7-0/smacof/R/residuals.smacofID.R | 4 smacof-1.7-0/smacof/R/smacofConstraint.R | 20 +++- smacof-1.7-0/smacof/R/smacofIndDiff.R | 19 ++-- smacof-1.7-0/smacof/R/smacofRect.R | 6 + smacof-1.7-0/smacof/R/smacofSphere.R | 40 ++++++--- smacof-1.7-0/smacof/R/smacofSym.R | 36 +++++--- smacof-1.7-0/smacof/R/spp.R |only smacof-1.7-0/smacof/R/summary.smacofB.R | 10 +- smacof-1.7-0/smacof/R/summary.smacofID.R | 5 - smacof-1.7-0/smacof/R/torgerson.R | 11 +- smacof-1.7-0/smacof/R/uniscale.R |only smacof-1.7-0/smacof/build |only smacof-1.7-0/smacof/data/Duration.rda |only smacof-1.7-0/smacof/data/DurationRaw.rda |only smacof-1.7-0/smacof/data/Guerry.rda |only smacof-1.7-0/smacof/data/Lawler.rda |only smacof-1.7-0/smacof/data/OCP.rda |only smacof-1.7-0/smacof/data/PVQ40.rda |only smacof-1.7-0/smacof/data/Plato7.rda |only smacof-1.7-0/smacof/data/RockHard.rda |only smacof-1.7-0/smacof/data/intelligence.rda |only smacof-1.7-0/smacof/inst/NEWS.Rd | 15 +++ smacof-1.7-0/smacof/inst/doc |only smacof-1.7-0/smacof/man/Duration.Rd |only smacof-1.7-0/smacof/man/Guerry.Rd |only smacof-1.7-0/smacof/man/Lawler.Rd |only smacof-1.7-0/smacof/man/OCP.Rd |only smacof-1.7-0/smacof/man/PVQ40.Rd |only smacof-1.7-0/smacof/man/Plato7.Rd |only smacof-1.7-0/smacof/man/Procrustes.Rd |only smacof-1.7-0/smacof/man/RockHard.Rd |only smacof-1.7-0/smacof/man/intelligence.Rd |only smacof-1.7-0/smacof/man/inverseMDS.Rd |only smacof-1.7-0/smacof/man/permtest.smacof.Rd | 7 - smacof-1.7-0/smacof/man/plot.smacof.rd | 17 ++- smacof-1.7-0/smacof/man/randomstress.Rd |only smacof-1.7-0/smacof/man/sim2diss.Rd | 2 smacof-1.7-0/smacof/man/smacofConstraint.rd | 43 ++++------ smacof-1.7-0/smacof/man/smacofSym.Rd | 16 ++- smacof-1.7-0/smacof/man/torgerson.Rd |only smacof-1.7-0/smacof/man/uniscale.Rd |only smacof-1.7-0/smacof/src/nextperm.c |only smacof-1.7-0/smacof/vignettes |only 80 files changed, 338 insertions(+), 236 deletions(-)
Title: Tools for Fitting Sparse Latent Factor Model
Description: Set of tools to find coherent patterns in microarray data
using a Bayesian sparse latent factor model (Duarte and Mayrink 2015 -
http://link.springer.com/chapter/10.1007%2F978-3-319-12454-4_15).
Considerable effort has been put into making slfm fast and memory efficient,
turning it an interesting alternative to simpler methods in terms
of execution time. It implements versions of the SLFM using both type
of mixtures: using a degenerate distribution or a very concentrated
normal distribution for the spike part of the mixture. It also implements
additional functions to help pre-process the data and fit the model
for a large number of arrays.
Author: Joao Duarte and Vinicius Mayrink
Maintainer: Joao Duarte <jdanielnd@gmail.com>
Diff between slfm versions 0.2.1 dated 2015-08-08 and 0.2.2 dated 2015-08-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 +++++ R/slfm.r | 11 ++++++----- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: A Graphical User Interface for the MuToss Project
Description: The mutossGUI package provides a graphical user interface for the MuToss Project.
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between mutossGUI versions 0.1-9 dated 2014-08-25 and 0.1-10 dated 2015-08-10
mutossGUI-0.1-10/mutossGUI/DESCRIPTION | 10 ++-- mutossGUI-0.1-10/mutossGUI/MD5 | 22 +++++----- mutossGUI-0.1-10/mutossGUI/NAMESPACE | 2 mutossGUI-0.1-10/mutossGUI/R/onLoad.R | 10 ++++ mutossGUI-0.1-10/mutossGUI/inst/java/mutossgui.jar |binary mutossGUI-0.1-10/mutossGUI/java/af/statguitoolkit/errorhandling/ErrorDialogChooseLevelBase.java |only mutossGUI-0.1-10/mutossGUI/java/af/statguitoolkit/errorhandling/ErrorDialogChooseLevelMutoss.java |only mutossGUI-0.1-10/mutossGUI/java/af/statguitoolkit/io/datasets/DataSetLoader.java | 11 ++--- mutossGUI-0.1-10/mutossGUI/java/build.xml | 6 +- mutossGUI-0.1-10/mutossGUI/java/org/mutoss/MuTossControl.java | 1 mutossGUI-0.1-10/mutossGUI/java/org/mutoss/gui/MuTossGUI.java | 8 ++- mutossGUI-0.1-10/mutossGUI/java/org/mutoss/gui/dialogs/MethodDialog.java | 1 mutossGUI-0.1-9/mutossGUI/java/af/statguitoolkit/errorhandling/ErrorDialogSGTK.java |only mutossGUI-0.1-9/mutossGUI/java/af/statguitoolkit/io/datasets/XLSToolkit.java |only 14 files changed, 42 insertions(+), 29 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.4 dated 2015-05-19 and 0.4.5 dated 2015-08-10
DESCRIPTION | 104 - MD5 | 271 ++-- NAMESPACE | 75 - NEWS | 1499 +++---------------------- R/Analyse_SAR.OSLdata.R | 4 R/CW2pHMi.R | 128 +- R/CW2pLM.R | 4 R/CW2pLMi.R | 114 - R/CW2pPMi.R | 110 - R/Luminescence-package.R | 457 +------ R/RLum-class.R | 40 R/RLum.Analysis-class.R | 351 +++--- R/RLum.Data-class.R | 41 R/RLum.Data.Curve-class.R | 232 ++- R/RLum.Data.Image-class.R | 199 ++- R/RLum.Data.Spectrum-class.R | 316 +++-- R/RLum.Results-class.R | 402 +++--- R/Risoe.BINfileData2RLum.Analysis.R | 6 R/Risoe.BINfileData2RLum.Data.Curve.R | 37 R/RisoeBINfileData-class.R | 202 +++ R/Second2Gray.R | 87 + R/analyse_IRSAR.RF.R | 1811 +++++++++++++++++-------------- R/analyse_SAR.CWOSL.R | 51 R/analyse_SAR.TL.R | 24 R/analyse_pIRIRSequence.R | 76 - R/apply_CosmicRayRemoval.R | 150 +- R/apply_EfficiencyCorrection.R | 8 R/calc_AliquotSize.R | 5 R/calc_CentralDose.R | 28 R/calc_CommonDose.R | 74 - R/calc_CosmicDoseRate.R | 15 R/calc_FadingCorr.R | 128 +- R/calc_FiniteMixture.R | 9 R/calc_FuchsLang2001.R | 5 R/calc_HomogeneityTest.R | 7 R/calc_IEU.R | 27 R/calc_MinDose.R | 9 R/calc_OSLLxTxRatio.R | 17 R/calc_SourceDoseRate.R | 53 R/calc_Statistics.R | 33 R/calc_TLLxTxRatio.R | 60 - R/extract_IrradiationTimes.R | 32 R/fit_CWCurve.R | 28 R/fit_LMCurve.R | 5 R/get_Quote.R |only R/get_RLum.R | 95 - R/get_Risoe.BINfileData.R |only R/length_RLum.R |only R/merge_RLum.Analysis.R | 5 R/merge_RLum.Data.Curve.R | 50 R/merge_RLum.R | 113 + R/merge_Risoe.BINfileData.R | 28 R/plot_AbanicoPlot.R | 643 +++++------ R/plot_DRTResults.R | 2 R/plot_GrowthCurve.R | 6 R/plot_Histogram.R | 88 - R/plot_KDE.R | 12 R/plot_RLum.Analysis.R | 71 - R/plot_RLum.Data.Curve.R | 295 +++-- R/plot_RLum.Data.Image.R | 22 R/plot_RLum.Data.Spectrum.R | 24 R/plot_RLum.R | 81 + R/plot_RadialPlot.R | 70 - R/readBIN2R.R | 59 - R/readSPE2R.R | 25 R/readXSYG2R.R | 429 ++++--- R/set_RLum.R |only R/set_Risoe.BINfileData.R |only R/structure_RLum.R |only R/writeR2BIN.R | 52 R/zzz.R | 274 ++-- data/ExampleData.BINfileData.RData |binary data/ExampleData.RLum.Data.Image.RData |binary inst/NEWS.Rd | 1500 ++----------------------- man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/ExampleData.BINfileData.Rd | 5 man/ExampleData.XSYG.Rd | 2 man/Luminescence-package.Rd | 9 man/RLum-class.Rd | 11 man/RLum.Analysis-class.Rd | 102 + man/RLum.Data-class.Rd | 11 man/RLum.Data.Curve-class.Rd | 64 - man/RLum.Data.Image-class.Rd | 63 - man/RLum.Data.Spectrum-class.Rd | 65 - man/RLum.Results-class.Rd | 64 - man/Risoe.BINfileData-class.Rd | 47 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Risoe.BINfileData2RLum.Data.Curve.Rd | 4 man/Second2Gray.Rd | 16 man/analyse_IRSAR.RF.Rd | 279 ++-- man/analyse_SAR.CWOSL.Rd | 23 man/analyse_SAR.TL.Rd | 6 man/analyse_pIRIRSequence.Rd | 10 man/apply_CosmicRayRemoval.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/calc_AliquotSize.Rd | 4 man/calc_CentralDose.Rd | 4 man/calc_CommonDose.Rd | 4 man/calc_CosmicDoseRate.Rd | 6 man/calc_FadingCorr.Rd | 6 man/calc_FiniteMixture.Rd | 6 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 4 man/calc_IEU.Rd | 7 man/calc_MinDose.Rd | 8 man/calc_OSLLxTxRatio.Rd | 6 man/calc_SourceDoseRate.Rd | 14 man/calc_Statistics.Rd | 6 man/calc_TLLxTxRatio.Rd | 30 man/extract_IrradiationTimes.Rd | 8 man/fit_CWCurve.Rd | 4 man/fit_LMCurve.Rd | 2 man/get_Quote.Rd |only man/get_RLum.Rd | 45 man/get_Risoe.BINfileData.Rd |only man/length_RLum.Rd |only man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 4 man/merge_RLum.Rd | 10 man/merge_RLum.Results.Rd |only man/merge_Risoe.BINfileData.Rd | 2 man/plot_AbanicoPlot.Rd | 125 +- man/plot_DRTResults.Rd | 2 man/plot_GrowthCurve.Rd | 6 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 4 man/plot_RLum.Analysis.Rd | 17 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 8 man/plot_RLum.Data.Spectrum.Rd | 6 man/plot_RLum.Rd | 6 man/plot_RadialPlot.Rd | 8 man/readBIN2R.Rd | 15 man/readSPE2R.Rd | 13 man/readXSYG2R.Rd | 16 man/set_RLum.Rd |only man/set_Risoe.BINfileData.Rd |only man/structure_RLum.Rd |only man/writeR2BIN.Rd | 4 143 files changed, 5761 insertions(+), 6732 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Description: Functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre],
Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between gMCP versions 0.8-8 dated 2014-10-02 and 0.8-9 dated 2015-08-10
gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/power/Group.java |only gMCP-0.8-8/gMCP/java/org/af/gMCP/gui/power/GroupPanel.java |only gMCP-0.8-8/gMCP/vignettes/pictures/power.png |only gMCP-0.8-9/gMCP/DESCRIPTION | 10 gMCP-0.8-9/gMCP/MD5 | 233 gMCP-0.8-9/gMCP/NAMESPACE | 7 gMCP-0.8-9/gMCP/NEWS | 140 gMCP-0.8-9/gMCP/R/calcPower.R | 86 gMCP-0.8-9/gMCP/R/doRUnitTests.R | 12 gMCP-0.8-9/gMCP/R/exampleGraphs.R | 16 gMCP-0.8-9/gMCP/R/gACT-internal.R | 17 gMCP-0.8-9/gMCP/R/gMCP.R | 10 gMCP-0.8-9/gMCP/R/gMCP.extended.R |only gMCP-0.8-9/gMCP/R/generateTest.R | 9 gMCP-0.8-9/gMCP/R/graph2latex.R | 17 gMCP-0.8-9/gMCP/R/graphMCP.R | 6 gMCP-0.8-9/gMCP/R/graphTest.R | 3 gMCP-0.8-9/gMCP/R/onLoad.R | 10 gMCP-0.8-9/gMCP/R/sampSize.R | 135 gMCP-0.8-9/gMCP/R/startGUIs.R | 47 gMCP-0.8-9/gMCP/TODO | 72 gMCP-0.8-9/gMCP/build/vignette.rds |binary gMCP-0.8-9/gMCP/inst/doc/AQuickStart.pdf |binary gMCP-0.8-9/gMCP/inst/doc/gMCP.R | 4411 +++++++++- gMCP-0.8-9/gMCP/inst/doc/gMCP.Rnw | 515 - gMCP-0.8-9/gMCP/inst/doc/gMCP.pdf |binary gMCP-0.8-9/gMCP/inst/doc/parametric.pdf |binary gMCP-0.8-9/gMCP/inst/java/gsrmtp.jar |binary gMCP-0.8-9/gMCP/inst/unitTests/runit.cover.everything.R | 8 gMCP-0.8-9/gMCP/inst/unitTests/runit.gMCP.extended.R |only gMCP-0.8-9/gMCP/inst/unitTests/runit.power.R | 19 gMCP-0.8-9/gMCP/inst/unitTests/runit.sampSize.R |only gMCP-0.8-9/gMCP/java/org/af/gMCP/config/Configuration.java | 25 gMCP-0.8-9/gMCP/java/org/af/gMCP/config/VersionComparator.java | 2 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/CreateGraphGUI.java | 23 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/ErrorDialogChooseLevel.java | 111 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/ErrorDialogChooseLevelBase.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/ErrorDialogGMCP.java | 71 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/MenuBarMGraph.java | 67 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/RControl.java | 2 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/GraphSaveDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java | 4 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/ImageExportDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/ImagePanel.java | 22 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java | 25 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/PowerOptionsPanel.java | 12 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/RejectedDialog.java | 21 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/dialogs/VariableNameDialog.java | 2 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/Edge.java | 57 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/GraphMCP.java | 21 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/GraphView.java | 36 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/LaTeXTool.java | 12 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/NetList.java | 44 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/NetListPanel.java | 26 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/Node.java | 102 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/PPanel.java | 17 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/PView.java | 35 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/UpdateEdge.java | 2 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/UpdateNode.java | 92 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/images/questionmark.png |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/images/questionmark32.png |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/graph/images/questionmark64.png |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/options/GeneralPanel.java | 61 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/options/MiscPanel.java | 86 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/options/NumericPanel.java | 15 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/options/OptionsDialog.java | 81 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/Arm.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/CVPanel.java | 20 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/EndpointDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/HorizontalButtonPane.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/KoutofNDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/MarginalPowerPanel.java | 1 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/NCPCalculatorDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/NCPRequestor.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PDialog.java | 34 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PopulationDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PowerDialog.java | 67 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PowerReq.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PowerReqPanel.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/PowerResultDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/RandomizationPanel.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/SampleSizeDialog.java | 139 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/Scenario.java | 52 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/Scenario2.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/ScenarioPanel.java | 15 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/ScenarioPanel2.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/ScenarioPanelInterface.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/SettingsToXML.java | 1 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/UserDefinedDialog.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/UserDefinedPanel.java | 102 gMCP-0.8-9/gMCP/java/org/af/gMCP/gui/power/XMLIO.java |only gMCP-0.8-9/gMCP/java/org/af/gMCP/poi/GraphDocXWriter.java | 2 gMCP-0.8-9/gMCP/man/bdiagNA.Rd | 3 gMCP-0.8-9/gMCP/man/bonferroni.test.Rd |only gMCP-0.8-9/gMCP/man/bonferroni.trimmed.simes.test.Rd |only gMCP-0.8-9/gMCP/man/calcPower.Rd | 52 gMCP-0.8-9/gMCP/man/corMatWizard.Rd | 19 gMCP-0.8-9/gMCP/man/doInterim.Rd | 3 gMCP-0.8-9/gMCP/man/exampleGraphs.Rd | 19 gMCP-0.8-9/gMCP/man/extractPower.Rd | 6 gMCP-0.8-9/gMCP/man/gMCP-package.Rd | 9 gMCP-0.8-9/gMCP/man/gMCP.Rd | 14 gMCP-0.8-9/gMCP/man/gMCP.extended.Rd |only gMCP-0.8-9/gMCP/man/gMCPReport.Rd | 5 gMCP-0.8-9/gMCP/man/generateBounds.Rd | 3 gMCP-0.8-9/gMCP/man/generatePvals.Rd | 3 gMCP-0.8-9/gMCP/man/generateTest.Rd | 11 gMCP-0.8-9/gMCP/man/generateWeights.Rd | 3 gMCP-0.8-9/gMCP/man/getJavaInfo.Rd | 3 gMCP-0.8-9/gMCP/man/graph2latex.Rd | 15 gMCP-0.8-9/gMCP/man/graphAnalysis.Rd | 3 gMCP-0.8-9/gMCP/man/graphGUI.Rd | 3 gMCP-0.8-9/gMCP/man/graphTest.Rd | 9 gMCP-0.8-9/gMCP/man/joinGraphs.Rd | 3 gMCP-0.8-9/gMCP/man/matrix2graph.Rd | 3 gMCP-0.8-9/gMCP/man/parametric.test.Rd |only gMCP-0.8-9/gMCP/man/placeNodes.Rd | 3 gMCP-0.8-9/gMCP/man/plotSimCI.Rd | 3 gMCP-0.8-9/gMCP/man/rejectNode.Rd | 3 gMCP-0.8-9/gMCP/man/replaceVariables.Rd | 3 gMCP-0.8-9/gMCP/man/rqmvnorm.Rd | 3 gMCP-0.8-9/gMCP/man/sampSize.Rd | 86 gMCP-0.8-9/gMCP/man/sampSizeCore.Rd |only gMCP-0.8-9/gMCP/man/secondStageTest.Rd | 3 gMCP-0.8-9/gMCP/man/simes.on.subsets.test.Rd |only gMCP-0.8-9/gMCP/man/simes.test.Rd |only gMCP-0.8-9/gMCP/man/subgraph.Rd | 3 gMCP-0.8-9/gMCP/man/substituteEps.Rd | 3 gMCP-0.8-9/gMCP/man/unitTestsGMCP.Rd | 5 gMCP-0.8-9/gMCP/man/weighted.test.functions.Rd |only gMCP-0.8-9/gMCP/vignettes/childs |only gMCP-0.8-9/gMCP/vignettes/gMCP.Rnw | 515 - gMCP-0.8-9/gMCP/vignettes/literatur.bib | 31 gMCP-0.8-9/gMCP/vignettes/pictures/arm.png |only gMCP-0.8-9/gMCP/vignettes/pictures/corMat2.png |only gMCP-0.8-9/gMCP/vignettes/pictures/exportPNG.png |only gMCP-0.8-9/gMCP/vignettes/pictures/power_requirements.png |only gMCP-0.8-9/gMCP/vignettes/pictures/udpf.png |only gMCP-0.8-9/gMCP/vignettes/pictures/udpf2.png |only 139 files changed, 6997 insertions(+), 1143 deletions(-)
Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac <hlavac@fas.harvard.edu>
Maintainer: Marek Hlavac <hlavac@fas.harvard.edu>
Diff between ExtremeBounds versions 0.1.5 dated 2015-02-28 and 0.1.5.1 dated 2015-08-10
DESCRIPTION | 10 MD5 | 24 - NAMESPACE | 2 R/ExtremeBounds-internal.R | 2 build/vignette.rds |binary inst/CITATION | 4 inst/ChangeLog | 3 inst/doc/ExtremeBounds.pdf |binary man/ExtremeBounds.Rd | 2 man/eba.Rd | 2 man/hist.eba.Rd | 2 man/print.eba.Rd | 2 vignettes/ExtremeBounds.bib | 1038 ++++++++++++++++++++++---------------------- 13 files changed, 547 insertions(+), 544 deletions(-)
Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2015' (or 2012, 2010) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 1.6-2 dated 2015-05-29 and 1.7-1 dated 2015-08-09
wppExplorer-1.6-2/wppExplorer/tests/run_tests.R |only wppExplorer-1.6-2/wppExplorer/tests/test_functions.R |only wppExplorer-1.7-1/wppExplorer/ChangeLog | 10 ++++ wppExplorer-1.7-1/wppExplorer/DESCRIPTION | 16 +++---- wppExplorer-1.7-1/wppExplorer/MD5 | 31 +++++++------ wppExplorer-1.7-1/wppExplorer/NAMESPACE | 5 +- wppExplorer-1.7-1/wppExplorer/R/global.R | 4 - wppExplorer-1.7-1/wppExplorer/R/wpp.R | 34 ++++++++------- wppExplorer-1.7-1/wppExplorer/data/iso3166.R | 10 +++- wppExplorer-1.7-1/wppExplorer/data/iso3166ud.R | 2 wppExplorer-1.7-1/wppExplorer/inst/explore/server.R | 4 - wppExplorer-1.7-1/wppExplorer/inst/explore/ui.R | 6 +- wppExplorer-1.7-1/wppExplorer/man/wpp.explore.Rd | 6 +- wppExplorer-1.7-1/wppExplorer/man/wpp.indicator.Rd | 22 ++++----- wppExplorer-1.7-1/wppExplorer/man/wppExplorer-package.Rd | 14 ++---- wppExplorer-1.7-1/wppExplorer/man/wpp_year.Rd | 4 - wppExplorer-1.7-1/wppExplorer/tests/testthat |only wppExplorer-1.7-1/wppExplorer/tests/testthat.R |only 18 files changed, 96 insertions(+), 72 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.3.3 dated 2015-07-16 and 1.3.4 dated 2015-08-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/report.R | 4 ++-- data/tpod.RData |binary man/NAM-package.Rd | 4 ++-- man/report.Rd | 2 ++ 6 files changed, 15 insertions(+), 13 deletions(-)
Title: Smoothing Splines for Large Samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between bigsplines versions 1.0-6 dated 2015-03-17 and 1.0-7 dated 2015-08-09
ChangeLog | 56 +++++++----- DESCRIPTION | 11 +- MD5 | 71 ++++++++------- NAMESPACE | 18 +++- R/bigssa.R | 9 +- R/bigssg.R | 4 R/bigssp.R | 9 +- R/getRandom.R |only R/makeZtX.R | 115 +++++++++++++++++++------ R/makeZtZ.R | 202 +++++++++++++++++++++++++++++++++++++++------ R/makessa.R | 51 +++-------- R/makessp.R | 51 +++-------- R/pinvsm.R | 4 R/remlri.R | 117 +++++++++++++++++--------- R/remlvc.R | 145 ++++++++++++++++++++++---------- R/ssawork.R | 67 ++++++++++---- R/sspwork.R | 63 +++++++++----- R/summary.bigspline.R | 4 R/summary.bigssa.R | 4 R/summary.bigssg.R | 4 R/summary.bigssp.R | 4 R/summary.bigtps.R | 4 man/bigspline.Rd | 21 ++++ man/bigsplines-internal.Rd | 1 man/bigsplines-package.Rd | 6 - man/bigssa.Rd | 31 ++++-- man/bigssg.Rd | 8 + man/bigssp.Rd | 29 ++++-- man/bigtps.Rd | 4 man/makessa.Rd | 17 ++- man/makessg.Rd | 4 man/makessp.Rd | 17 ++- man/predict.bigspline.Rd | 4 man/predict.bigssa.Rd | 4 man/predict.bigssg.Rd | 4 man/predict.bigssp.Rd | 4 man/predict.bigtps.Rd | 4 37 files changed, 789 insertions(+), 382 deletions(-)
Title: Permutation of Species During Turnover Events
Description: Provides a robust framework for analyzing the extent to which differential survival with respect to higher level trait variation is reducible to lower level variation. In addition to its primary test, it also provides functions for simulation-based power analysis, reading in common data set formats, and visualizing results. Temporarily contains an edited version of function hr.mcp() from package 'wild1', written by Glen Sargeant. For tutorial see: http://evolve.zoo.ox.ac.uk/Evolve/Perspectev.html.
Author: Kenneth B. Hoehn [aut, cre],
Glen A. Sargeant [ctb]
Maintainer: Kenneth B. Hoehn <perspectev@gmail.com>
Diff between perspectev versions 1.0 dated 2015-05-13 and 1.1 dated 2015-08-09
DESCRIPTION | 13 - MD5 | 24 +- NAMESPACE | 3 R/hr.mcp.R |only R/perspectev.R | 502 +++++++++++++++++++++++++++------------------ data/occurrence_data.rda |binary inst |only man/perspectev-datasets.Rd | 2 man/perspectev-internal.Rd | 4 man/perspectev-package.Rd | 8 man/perspectev.calc.Rd | 5 man/perspectev.read.Rd | 92 +++++--- man/perspectev.simulate.Rd | 11 man/perspectev.test.Rd | 11 14 files changed, 423 insertions(+), 252 deletions(-)
Title: Functions for some Unit-Level Small Area Estimators and their
Variances
Description: Implementation of some unit level EBLUP and GREG estimators as well as the estimate of their variances to further document the publication of Breidenbach and Astrup (2011). The vignette further explains the use of the implemented functions.
Author: Johannes Breidenbach
Maintainer: Johannes Breidenbach <job@nibio.no>
Diff between JoSAE versions 0.2.2 dated 2013-12-14 and 0.2.3 dated 2015-08-09
DESCRIPTION | 16 - MD5 | 24 - NAMESPACE | 19 - build/vignette.rds |binary data/nfi.rdata |only inst/CHANGES | 6 inst/doc/JoSAE.R | 86 ++++- inst/doc/JoSAE.Rnw | 730 ++++++++++++++++++++++++++---------------------- inst/doc/JoSAE.pdf |binary man/JoSAE-package.Rd | 30 - man/landsat.Rd | 22 - man/nfi.Rd |only vignettes/JoSAE-004.pdf |only vignettes/JoSAE-009.pdf |only vignettes/JoSAE.Rnw | 730 ++++++++++++++++++++++++++---------------------- 15 files changed, 945 insertions(+), 718 deletions(-)
Title: 'Correctly Analyse Disease Recurrence with Missing at Risk
Information using Population Mortality'
Description: Implements two methods: a nonparametric risk adjustment and a data imputation method that use general population mortality tables to allow a correct analysis of time to disease recurrence.
Author: Tomaz Stupnik [aut, cre],
Maja Pohar Perme [aut]
Maintainer: Tomaz Stupnik <tomaz.stupnik@guest.arnes.si>
Diff between missDeaths versions 1.0 dated 2015-06-21 and 1.2 dated 2015-08-09
missDeaths-1.0/missDeaths/src/Xsimcensor.cpp |only missDeaths-1.2/missDeaths/DESCRIPTION | 10 ++++----- missDeaths-1.2/missDeaths/MD5 | 17 +++++++-------- missDeaths-1.2/missDeaths/NAMESPACE | 3 +- missDeaths-1.2/missDeaths/R/RcppExports.R | 28 -------------------------- missDeaths-1.2/missDeaths/man/md.impute.Rd | 2 - missDeaths-1.2/missDeaths/man/md.survcox.Rd | 4 +-- missDeaths-1.2/missDeaths/src/RcppExports.cpp | 19 ----------------- missDeaths-1.2/missDeaths/src/simcensor.cpp | 12 +++++------ missDeaths-1.2/missDeaths/src/simulate.cpp | 4 +-- 10 files changed, 25 insertions(+), 74 deletions(-)
Title: Multivariate Survival Trees
Description: Constructs trees for multivariate survival data using marginal and frailty models.
Author: Xiaogang Su, Peter Calhoun, and Juanjuan Fan
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between MST versions 1.0 dated 2014-09-20 and 1.1 dated 2015-08-08
MST-1.0/MST/R/ordinalize.R |only MST-1.1/MST/DESCRIPTION | 12 ++-- MST-1.1/MST/MD5 | 44 ++++++++-------- MST-1.1/MST/NAMESPACE | 7 ++ MST-1.1/MST/R/MST-internal.R |only MST-1.1/MST/R/MST.R | 88 ++++++++++++++++++++++++++------ MST-1.1/MST/R/MST.plot.R | 43 ++++++++++----- MST-1.1/MST/R/MST.plot.latex.R |only MST-1.1/MST/R/bootstrap.grow.prune.R | 13 ++-- MST-1.1/MST/R/bootstrap.size.R | 4 - MST-1.1/MST/R/de.R | 3 - MST-1.1/MST/R/grow.MST.R | 13 ++-- MST-1.1/MST/R/ordinalizeFunc.R |only MST-1.1/MST/R/partition.MST.R | 21 ++++--- MST-1.1/MST/R/rmultime.R | 5 + MST-1.1/MST/R/sortTree.R |only MST-1.1/MST/R/splitting.stat.MST1.R | 4 - MST-1.1/MST/R/splitting.stat.MST2.R | 7 +- MST-1.1/MST/man/MST-package.Rd | 9 +-- MST-1.1/MST/man/MST.Rd | 57 ++++++++++---------- MST-1.1/MST/man/MST.plot.Rd | 22 ++++---- MST-1.1/MST/man/MST.plot.latex.Rd |only MST-1.1/MST/man/bootstrap.grow.prune.Rd | 14 ++--- MST-1.1/MST/man/bootstrap.size.Rd | 4 - MST-1.1/MST/man/grow.MST.Rd | 16 ++--- MST-1.1/MST/man/rmultime.Rd | 11 +--- 26 files changed, 246 insertions(+), 151 deletions(-)
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Mantel's permutation test can be found in this package. A new approach for calculating its
power is implemented. biotools also contains the new tests for genetic covariance components.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between biotools versions 2.1 dated 2015-05-09 and 2.2 dated 2015-08-08
biotools-2.1/biotools/R/coph.tocher.R |only biotools-2.1/biotools/R/indicate.signif.r |only biotools-2.1/biotools/R/onload.R |only biotools-2.1/biotools/R/simpval.R |only biotools-2.1/biotools/man/coph.tocher.Rd |only biotools-2.1/biotools/man/predict.D2.disc.Rd |only biotools-2.2/biotools/DESCRIPTION | 13 ++-- biotools-2.2/biotools/MD5 | 39 ++++++------- biotools-2.2/biotools/NAMESPACE | 15 ++++- biotools-2.2/biotools/NEWS | 17 +++++ biotools-2.2/biotools/R/D2.disc.R | 66 +++++++++++++++------- biotools-2.2/biotools/R/boxM.R | 2 biotools-2.2/biotools/R/confusionmatrix.R | 1 biotools-2.2/biotools/R/gencovtest.r |only biotools-2.2/biotools/R/singh.R | 27 +++++---- biotools-2.2/biotools/R/tocher.R | 77 ++++++++++++++++++++++++-- biotools-2.2/biotools/R/zz.R |only biotools-2.2/biotools/data/maize.rda |only biotools-2.2/biotools/man/D2.disc.Rd | 20 ++++++ biotools-2.2/biotools/man/biotools-package.Rd | 12 ++-- biotools-2.2/biotools/man/gencovtest.Rd |only biotools-2.2/biotools/man/maize.Rd |only biotools-2.2/biotools/man/mantelPower.Rd | 2 biotools-2.2/biotools/man/mantelTest.Rd | 2 biotools-2.2/biotools/man/singh.Rd | 14 ++-- biotools-2.2/biotools/man/tocher.Rd | 22 ++++++- 26 files changed, 245 insertions(+), 84 deletions(-)
More information about solidearthtide at CRAN
Permanent link
Title: Tools for Fitting Sparse Latent Factor Model
Description: Set of tools to find coherent patterns in microarray data
using a Bayesian sparse latent factor model (Duarte and Mayrink 2015 -
http://link.springer.com/chapter/10.1007%2F978-3-319-12454-4_15).
Considerable effort has been put into making slfm fast and memory efficient,
turning it an interesting alternative to simpler methods in terms
of execution time. It implements versions of the SLFM using both type
of mixtures: using a degenerate distribution or a very concentrated
normal distribution for the spike part of the mixture. It also implements
additional functions to help pre-process the data and fit the model
for a large number of arrays.
Author: Joao Duarte and Vinicius Mayrink
Maintainer: Joao Duarte <jdanielnd@gmail.com>
Diff between slfm versions 0.2.0 dated 2015-07-29 and 0.2.1 dated 2015-08-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 7 +++++++ R/class_interval.r | 12 ++++++------ R/slfm.r | 4 ++-- R/slfm_list.r | 13 +++++++++---- 6 files changed, 32 insertions(+), 20 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions allow to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>;
Yulia R. Gel <ygl@utdallas.edu>;
Xingyu Wang <x263wang@uwaterloo.ca>
Maintainer: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>
Diff between funtimes versions 1.1 dated 2015-06-07 and 2.0 dated 2015-08-08
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++++++++------ NAMESPACE | 1 + R/CExpandSlideCluster.R |only R/CExpandWindowCluster.R |only R/CHomogeneity.R |only R/CNeighbor.R |only R/CSlideCluster.R |only R/CWindowCluster.R |only R/i.tails.R |only R/q.tails.R |only man/CExpandSlideCluster.Rd |only man/CExpandWindowCluster.Rd |only man/CHomogeneity.Rd |only man/CNeighbor.Rd |only man/CSlideCluster.Rd |only man/CWindowCluster.Rd |only man/HVK.Rd | 2 +- man/WAVK.Rd | 6 +++--- man/i.tails.Rd |only man/q.tails.Rd |only man/sync.test.Rd | 10 +++++----- man/wavk.test.Rd | 10 +++++----- 23 files changed, 41 insertions(+), 24 deletions(-)
Title: Drat R Archive Template
Description: Creation and Use of R Repositories via two helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Sebastian
Gibb, Colin Gillespie, Matt Jones, Thomas Leeper, Steven Pav and Jan Schulz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.0.4 dated 2015-05-26 and 0.1.0 dated 2015-08-08
drat-0.0.4/drat/man/getPathForPackageType.Rd |only drat-0.1.0/drat/ChangeLog | 57 ++++++++ drat-0.1.0/drat/DESCRIPTION | 12 + drat-0.1.0/drat/MD5 | 42 +++--- drat-0.1.0/drat/NAMESPACE | 6 drat-0.1.0/drat/R/archivePackages.R |only drat-0.1.0/drat/R/insertPackage.R | 111 ++++++++++++---- drat-0.1.0/drat/R/pruneRepo.R | 9 + drat-0.1.0/drat/README.md | 34 +++- drat-0.1.0/drat/build/vignette.rds |binary drat-0.1.0/drat/inst/doc/CombiningDratAndTravis.Rmd | 6 drat-0.1.0/drat/inst/doc/CombiningDratAndTravis.html | 6 drat-0.1.0/drat/inst/doc/DratFAQ.Rmd | 41 +++++ drat-0.1.0/drat/inst/doc/DratFAQ.html | 17 ++ drat-0.1.0/drat/inst/doc/DratForPackageAuthors.Rmd | 4 drat-0.1.0/drat/inst/doc/DratForPackageAuthors.html | 4 drat-0.1.0/drat/inst/scripts/getCommitMessageForDrat.sh |only drat-0.1.0/drat/man/archivePackages.Rd |only drat-0.1.0/drat/man/getPackageInfo.Rd |only drat-0.1.0/drat/man/getPathForPackage.Rd |only drat-0.1.0/drat/man/insertPackage.Rd | 12 + drat-0.1.0/drat/man/pruneRepo.Rd | 8 - drat-0.1.0/drat/vignettes/CombiningDratAndTravis.Rmd | 6 drat-0.1.0/drat/vignettes/DratFAQ.Rmd | 41 +++++ drat-0.1.0/drat/vignettes/DratForPackageAuthors.Rmd | 4 25 files changed, 327 insertions(+), 93 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that can be indexed similarly to lists, e.g. 'x <- listenv(); x[[2]] <- "b"; names(x)[2] <- "B"; print(x$B)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.3.0 dated 2015-05-28 and 0.4.0 dated 2015-08-08
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 45 +++++--- NEWS | 10 + R/get_variable.R | 1 R/listenv.R | 210 +++++++++++++++++++++++++++++++++++++++-- R/parse_env_subset.R | 1 man/listenv.Rd | 5 tests/as.listenv.R |only tests/listenv.R | 257 +++++++++++++++++++++++++++++++++++++++++++++++++++ tests/utils.R |only 11 files changed, 511 insertions(+), 44 deletions(-)
Title: Genetic Association Studies
Description: Some procedures including EIGENSTRAT (a procedure for
detecting and correcting for population stratification through
searching for the eigenvectors in genetic association studies),
PCoC (a procedure for correcting for population stratification
through calculating the principal coordinates and the clustering
of the subjects), Tracy-Wisdom test (a procedure for detecting
the significant eigenvalues of a matrix), distance regression (a
procedure for detecting the association between a distance matrix
and some independent variants of interest), single-marker test (a
procedure for identifying the association between the genotype at
a biallelic marker and a trait using the Wald test or the Fisher
exact test), MAX3 (a procedure for testing for the association
between a single nucleotide polymorphism and a binary phenotype
using the maximum value of the three test statistics derived for
the recessive, additive, and dominant models), nonparametric trend
test (a procedure for testing for the association between a genetic
variant and a non-normal distributed quantitative trait based on the
nonparametric risk), and nonparametric MAX3 (a procedure for testing
for the association between a biallelic single nucleotide polymorphism
and a quantitative trait using the maximum value of the three
nonparametric trend tests derived for the recessive, additive, and
dominant models), which are commonly used in genetic association studies.
Author: Lin Wang [aut],
Wei Zhang [aut],
Qizhai Li [aut],
Weicheng Zhu [ctb]
Maintainer: Lin Wang <wanglin2009@amss.ac.cn>
Diff between AssocTests versions 0.0-2 dated 2015-06-26 and 0.0-3 dated 2015-08-08
DESCRIPTION | 8 ++-- MD5 | 38 +++++++++---------- NAMESPACE | 6 ++- R/DR_main.R | 59 ++++++++++++++++++++---------- R/EigenStrat_main.R | 42 ++++++++++----------- R/MAX3_main.R | 67 ++++++++++++++++++++++------------ R/MDS.R | 2 - R/NMAX3_main.R | 52 ++++++++++++++++++-------- R/NPT_main.R | 49 +++++++++++++++++------- R/PCoC_main.R | 14 +++---- R/SMT_main.R | 102 +++++++++++++++++++++++++++++++++++++--------------- R/TW_main.R | 41 ++++++++++++++------ man/dr.Rd | 44 +++++++++++++--------- man/eigenstrat.Rd | 36 +++++++++--------- man/max3.Rd | 54 ++++++++++++++++----------- man/nmax3.Rd | 38 ++++++++++++------- man/npt.Rd | 36 +++++++++++------- man/pcoc.Rd | 14 +++---- man/smt.Rd | 62 ++++++++++++++++++------------- man/tw.Rd | 27 +++++++++---- 20 files changed, 502 insertions(+), 289 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9.1 dated 2015-07-04 and 0.9.2 dated 2015-08-08
curl-0.9.1/curl/man/ie_proxy_info.Rd |only curl-0.9.2/curl/DESCRIPTION | 6 - curl-0.9.2/curl/MD5 | 30 +++---- curl-0.9.2/curl/NAMESPACE | 2 curl-0.9.2/curl/NEWS | 11 ++ curl-0.9.2/curl/R/handle.R | 5 - curl-0.9.2/curl/R/proxy.R | 38 ++++++++- curl-0.9.2/curl/data/curl_symbols.rda |binary curl-0.9.2/curl/man/ie_proxy.Rd |only curl-0.9.2/curl/src/Makevars.win | 11 -- curl-0.9.2/curl/src/ieproxy.c | 120 +++++++++++++++++++++++++++++- curl-0.9.2/curl/src/utils.c | 9 +- curl-0.9.2/curl/src/winhttp32.def | 27 ++++++ curl-0.9.2/curl/src/winhttp64.def | 27 ++++++ curl-0.9.2/curl/tools/symbols-in-versions | 7 + curl-0.9.2/curl/tools/symbols.R | 10 +- curl-0.9.2/curl/tools/winlibs.R | 4 - 17 files changed, 266 insertions(+), 41 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-45-2 dated 2015-03-14 and 0.9-50 dated 2015-08-08
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
RVAideMemoire-0.9-45-2/RVAideMemoire/R/DA.confusion.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/DA.valid.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/DA.var.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/PLSDA.ncomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/PLSDA.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/byf.normhist.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/cor.sparse.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/fc.multcomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/friedman.rating.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/kruskal.rating.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.manova.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.wilcox.rating.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/plot1comp.ind.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/plot1comp.var.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/s.corcircle2.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/scat.mix.categorical.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/scat.mix.numeric.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/scatter.coa2.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.paired.rating.multcomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.rating.signtest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.rating.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/DA.confusion.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/DA.valid.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/LDA.format.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/PLSDA.ncomp.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/PLSDA.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cor.sparse.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plot1comp.ind.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plot1comp.var.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/s.corcircle2.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scat.mix.categorical.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scat.mix.numeric.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scatter.coa2.Rd |only
RVAideMemoire-0.9-50/RVAideMemoire/DESCRIPTION | 15
RVAideMemoire-0.9-50/RVAideMemoire/MD5 | 143 +-
RVAideMemoire-0.9-50/RVAideMemoire/NAMESPACE | 58 -
RVAideMemoire-0.9-50/RVAideMemoire/NEWS | 23
RVAideMemoire-0.9-50/RVAideMemoire/R/CvM.test.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.anova.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.biplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.cmv.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.cor.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.corplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.cv.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.ident.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.load.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.loadplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.pairplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.plot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.scoreplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.scores.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.synt.R | 482 ++++++----
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.test.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/MVA.trajplot.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/PLSDA.VIP.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/adonis.II.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/back.lsmeans.R | 5
RVAideMemoire-0.9-50/RVAideMemoire/R/bootstrap.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/cor.2comp.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/cor.conf.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/cramer.test.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/deprecated.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/dhist.R | 26
RVAideMemoire-0.9-50/RVAideMemoire/R/inertia.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/overdisp.glmer.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/pairwise.perm.manova.R | 1
RVAideMemoire-0.9-50/RVAideMemoire/R/pairwise.to.groups.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/pcor.test.R | 7
RVAideMemoire-0.9-50/RVAideMemoire/R/perm.bartlett.test.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/perm.cor.test.R | 4
RVAideMemoire-0.9-50/RVAideMemoire/R/perm.t.test.R | 4
RVAideMemoire-0.9-50/RVAideMemoire/R/perm.var.test.R | 4
RVAideMemoire-0.9-50/RVAideMemoire/R/plotresid.R | 3
RVAideMemoire-0.9-50/RVAideMemoire/R/predict.MVA.cv.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/predict.coadisc.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/prop.multinom.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/prop.multinom.test.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/spearman.ci.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/R/splitf.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/wald.ptheo.test.R | 63 +
RVAideMemoire-0.9-50/RVAideMemoire/R/wmean.R |only
RVAideMemoire-0.9-50/RVAideMemoire/R/zzz.R | 2
RVAideMemoire-0.9-50/RVAideMemoire/man/G.test.Rd | 2
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RVAideMemoire-0.9-50/RVAideMemoire/man/MVA.trajplot.Rd |only
RVAideMemoire-0.9-50/RVAideMemoire/man/PLSDA.VIP.Rd | 2
RVAideMemoire-0.9-50/RVAideMemoire/man/RVAideMemoire-package.Rd | 4
RVAideMemoire-0.9-50/RVAideMemoire/man/back.lsmeans.Rd | 10
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RVAideMemoire-0.9-50/RVAideMemoire/man/multinomial.test.Rd | 2
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RVAideMemoire-0.9-50/RVAideMemoire/man/wmean.Rd |only
107 files changed, 661 insertions(+), 331 deletions(-)
Title: Empirical Likelihood Analysis for the Cox Model and
Yang-Prentice (2005) Model
Description: Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) models.
Empirical likelihood tests within a Cox model, for parameters defined via
both baseline hazard function and regression parameters.
Author: Mai Zhou
Maintainer: Mai Zhou <mai@ms.uky.edu>
Diff between ELYP versions 0.7-2 dated 2015-04-27 and 0.7-3 dated 2015-08-07
DESCRIPTION | 6 ++--- MD5 | 56 +++++++++++++++++++++++++-------------------------- NAMESPACE | 3 +- R/ELrange.R | 6 ++--- inst/doc/FAQ.txt | 13 ++++++----- man/BJfindL2.Rd | 2 - man/BJfindU2.Rd | 4 +-- man/CoxEL.Rd | 13 ++++++----- man/CoxFindL2.Rd | 8 +++---- man/CoxFindL3.Rd | 8 +++---- man/CoxFindU2.Rd | 8 +++---- man/CoxFindU3.Rd | 4 +-- man/ELrange.Rd | 6 ++--- man/GastricCancer.Rd | 2 - man/Pfun.Rd | 2 - man/Pfun2.Rd | 4 +-- man/findL2d.Rd | 10 ++++----- man/findL3.Rd | 4 ++- man/findL4.Rd | 4 +-- man/findU2d.Rd | 8 +++---- man/findU3.Rd | 8 +++---- man/findU32.Rd | 4 +-- man/findU4.Rd | 4 +-- man/fitYP3.Rd | 4 +-- man/fitYP4.Rd | 4 +-- man/fitYP41.Rd | 4 +-- man/myLLfun.Rd | 4 +-- man/myLLfun2.Rd | 3 +- man/simuDataYP.Rd | 7 +++--- 29 files changed, 110 insertions(+), 103 deletions(-)
Title: Functional Annotation and Biological Data Retrieval with R
Description: Performing biological data retrieval and functional annotation with R.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>
Diff between biomartr versions 0.0.1 dated 2015-07-22 and 0.0.2 dated 2015-08-07
DESCRIPTION | 23 +++++++------- MD5 | 49 ++++++++++++++++++------------ R/listDatabases.R | 2 - README.md | 19 ++++++++++- build |only inst/doc |only man/listDatabases.Rd | 2 - tests/testthat/test-biomart.R | 7 ++-- tests/testthat/test-getAttributes.R | 2 + tests/testthat/test-getCDS.R | 23 +++++++------- tests/testthat/test-getDatasets.R | 2 + tests/testthat/test-getFilters.R | 3 + tests/testthat/test-getGO.R | 6 +-- tests/testthat/test-getGenome.R | 23 +++++++------- tests/testthat/test-getMarts.R | 2 + tests/testthat/test-getProteome.R | 23 +++++++------- tests/testthat/test-is.genome.available.R | 2 + tests/testthat/test-organismAttributes.R | 2 + tests/testthat/test-organismBM.R | 2 + tests/testthat/test-organismFilters.R | 2 + vignettes/Sequence_Retrieval.Rmd | 4 +- 21 files changed, 127 insertions(+), 71 deletions(-)
Title: ABC-SMC Inference of STEPCAM
Description: STEPwise Community Assembly Model collection, applying ABC-SMC in order to infer different community assembly processes. Also includes several plotting functions in order to visualize found estimates.
Author: Thijs Janzen & Fons van der Plas
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between STEPCAM versions 1.0 dated 2014-06-27 and 1.1 dated 2015-08-07
DESCRIPTION | 15 +++++++-------- MD5 | 23 ++++++++++++----------- NAMESPACE | 10 +++++++++- R/ABC_SMC.R | 15 ++++++++------- R/main.R | 21 +++++++++++++-------- R/modified_dbFD.R |only R/ternPlot.R | 4 ++-- man/STEPCAM-internal.Rd | 4 +++- man/STEPCAM-package.Rd | 27 +++++++++++++++++++-------- man/STEPCAM_ABC.Rd | 18 +++++++++--------- man/TernPlot.Rd | 16 +++++----------- man/generate.Artificial.Data.Rd | 4 ---- man/plotSTEPCAM.Rd | 15 +++++---------- 13 files changed, 92 insertions(+), 80 deletions(-)
Title: Import Stata 13 and 14 Data Files
Description: Function to read and write the Stata 13 (and newer) file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.7 dated 2015-05-11 and 0.7.1 dated 2015-08-07
readstata13-0.7.1/readstata13/DESCRIPTION | 6 +++--- readstata13-0.7.1/readstata13/MD5 | 15 +++++++-------- readstata13-0.7.1/readstata13/NAMESPACE | 6 ++++++ readstata13-0.7.1/readstata13/NEWS | 3 +++ readstata13-0.7.1/readstata13/R/save.R | 6 ++++-- readstata13-0.7.1/readstata13/README.md | 6 +++--- readstata13-0.7.1/readstata13/src/rcpp_readstata.cpp | 2 +- readstata13-0.7.1/readstata13/src/rcpp_savestata.cpp | 18 +++++++++++++++--- readstata13-0.7/readstata13/CHANGELOG |only 9 files changed, 42 insertions(+), 20 deletions(-)
Title: Data Sets for Econometrics
Description: Data sets for econometrics.
Author: Yves Croissant <yves.croissant@let.ish-lyon.cnrs.fr>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecdat versions 0.2-7 dated 2014-09-04 and 0.2-9 dated 2015-08-07
DESCRIPTION | 20 +- MD5 | 338 +++++++++++++++++++------------------- data/Accident.rda |binary data/Airline.rda |binary data/Airq.rda |binary data/Benefits.rda |binary data/Bids.rda |binary data/BudgetFood.rda |binary data/BudgetItaly.rda |binary data/BudgetUK.rda |binary data/Bwages.rda |binary data/CPSch3.rda |binary data/CRANpackages.rda |binary data/CRSPday.rda |binary data/CRSPmon.rda |binary data/Capm.rda |binary data/Car.rda |binary data/Caschool.rda |binary data/Catsup.rda |binary data/Cigar.rda |binary data/Cigarette.rda |binary data/Clothing.rda |binary data/Computers.rda |binary data/Consumption.rda |binary data/Cracker.rda |binary data/Crime.rda |binary data/DM.rda |binary data/Diamond.rda |binary data/Doctor.rda |binary data/DoctorAUS.rda |binary data/DoctorContacts.rda |binary data/Earnings.rda |binary data/Electricity.rda |binary data/Fair.rda |binary data/Fatality.rda |binary data/FinancialCrisisFiles.rda |binary data/Fishing.rda |binary data/Forward.rda |binary data/FriendFoe.rda |binary data/Garch.rda |binary data/Gasoline.rda |binary data/Griliches.rda |binary data/Grunfeld.rda |binary data/HC.rda |binary data/HHSCyberSecurityBreaches.rda |only data/HI.rda |binary data/Hdma.rda |binary data/Heating.rda |binary data/Hedonic.rda |binary data/Housing.rda |binary data/Hstarts.rda |binary data/Icecream.rda |binary data/IncomeUK.rda |binary data/Irates.rda |binary data/Journals.rda |binary data/Kakadu.rda |binary data/Ketchup.rda |binary data/Klein.rda |binary data/LT.rda |binary data/LaborSupply.rda |binary data/Labour.rda |binary data/Longley.rda |binary data/MCAS.rda |binary data/MW.rda |binary data/Macrodat.rda |binary data/Males.rda |binary data/ManufCost.rda |binary data/Mathlevel.rda |binary data/MedExp.rda |binary data/Metal.rda |binary data/Mishkin.rda |binary data/Mode.rda |binary data/ModeChoice.rda |binary data/Mofa.rda |binary data/Money.rda |binary data/MoneyUS.rda |binary data/Mpyr.rda |binary data/Mroz.rda |binary data/MunExp.rda |binary data/NaturalPark.rda |binary data/Nerlove.rda |binary data/OFP.rda |binary data/Oil.rda |binary data/Orange.rda |binary data/PE.rda |binary data/PPP.rda |binary data/PSID.rda |binary data/Participation.rda |binary data/PatentsHGH.rda |binary data/PatentsRD.rda |binary data/Pound.rda |binary data/Pricing.rda |binary data/Produc.rda |binary data/RetSchool.rda |binary data/SP500.rda |binary data/Schooling.rda |binary data/Solow.rda |binary data/Somerville.rda |binary data/Star.rda |binary data/Strike.rda |binary data/StrikeDur.rda |binary data/StrikeNb.rda |binary data/SumHes.rda |binary data/Tbrate.rda |binary data/Tobacco.rda |binary data/Train.rda |binary data/TranspEq.rda |binary data/Treatment.rda |binary data/Tuna.rda |binary data/USFinanceIndustry.rda |binary data/USclassifiedDocuments.rda |binary data/USstateAbbreviations.rda |binary data/UStaxWords.rda |binary data/UnempDur.rda |binary data/Unemployment.rda |binary data/University.rda |binary data/VietNamH.rda |binary data/VietNamI.rda |binary data/Wages.rda |binary data/Wages1.rda |binary data/Workinghours.rda |binary data/Yen.rda |binary data/Yogurt.rda |binary data/bankingCrises.rda |binary data/breaches.rda |only data/datalist | 2 data/incomeInequality.rda |binary data/nonEnglishNames.rda |binary data/politicalKnowledge.rda |binary man/Airq.Rd | 3 man/Benefits.Rd | 2 man/Bwages.Rd | 2 man/Capm.Rd | 5 man/Clothing.Rd | 2 man/DM.Rd | 3 man/Diamond.Rd | 3 man/Electricity.Rd | 2 man/Forward.Rd | 2 man/FriendFoe.Rd | 3 man/Garch.Rd | 2 man/Griliches.Rd | 2 man/HHSCyberSecurityBreaches.Rd |only man/Housing.Rd | 2 man/Icecream.Rd | 2 man/IncomeUK.Rd | 3 man/Index.Source.Rd | 7 man/Irates.Rd | 2 man/LT.Rd | 2 man/Labour.Rd | 2 man/Males.Rd | 2 man/Mishkin.Rd | 2 man/MoneyUS.Rd | 2 man/Mpyr.Rd | 2 man/NaturalPark.Rd | 2 man/Nerlove.Rd | 2 man/PE.Rd | 2 man/PPP.Rd | 2 man/PatentsRD.Rd | 2 man/Pound.Rd | 2 man/Pricing.Rd | 2 man/SP500.Rd | 2 man/Schooling.Rd | 2 man/SumHes.Rd | 2 man/Tobacco.Rd | 2 man/USclassifiedDocuments.Rd | 153 ++++++++--------- man/USstateAbbreviations.Rd | 4 man/Wages1.Rd | 2 man/Yen.Rd | 2 man/bankingCrises.Rd | 129 +++++++------- man/breaches.Rd |only man/nonEnglishNames.Rd | 84 ++++----- man/politicalKnowledge.Rd | 2 172 files changed, 417 insertions(+), 400 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.7.2 dated 2015-05-25 and 2.8.0 dated 2015-08-07
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NAMESPACE | 7 +++++++ NEWS | 14 +++++++++++++- R/GenericDataFileSet.R | 38 +++++++++++++++++++++++++++++++------- R/TabularTextFile.R | 12 ++++++++++-- man/sortBy.GenericDataFileSet.Rd | 10 ++++++---- tests/GenericDataFileSet,sortBy.R | 8 ++++++-- 8 files changed, 87 insertions(+), 30 deletions(-)
Title: Loading Google Adwords Data into R
Description: Aims at loading Google Adwords data into R. Adwords is an online
advertising service that enables advertisers to display advertising copy to web users.
Therefore the package implements three main features. First, the package provides an
authentication process for R with the Google Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>, Matthias Bannert
<matthias.bannert@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Diff between RAdwords versions 0.1.4 dated 2015-04-16 and 0.1.6 dated 2015-08-07
DESCRIPTION | 8 +++--- MD5 | 65 +++++++++++++++++++++++++++++++++++++++---------- NAMESPACE | 3 ++ NEWS | 14 ++++++++++ R/getAuth.R | 4 ++- R/getData.R | 7 +++-- R/metrics.R | 12 ++++++--- R/reports.R | 12 ++++++--- R/transformData.R | 41 +++++++++++++++++++++++------- inst/extdata/api201506 |only man/getData.Rd | 4 +-- man/metrics.Rd | 4 +-- man/reports.Rd | 4 +-- man/transformData.Rd | 4 +-- 14 files changed, 138 insertions(+), 44 deletions(-)
Title: Bayesian Models for Cost-Effectiveness Analysis in the Presence
of Structural Zero Costs
Description: Implements a full Bayesian cost-effectiveness analysis in the case where the cost variable is characterised by structural zeros. The package implements the Gamma, log-Normal and Normal models for the cost variable and the Gamma, Beta, Bernoulli and Normal models for the measure of clinical effectiveness.
Author: Gianluca Baio
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between BCEs0 versions 1.1 dated 2013-11-15 and 1.1-1 dated 2015-08-07
DESCRIPTION | 12 ++--- MD5 | 10 ++-- NAMESPACE | 7 +++ R/bces0.R | 106 ++++++++++++++++++++++++------------------------- data/acupuncture.RData |binary man/BCEs0-package.Rd | 4 - 6 files changed, 74 insertions(+), 65 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.0 dated 2015-06-13 and 0.6.2 dated 2015-08-07
taxize-0.6.0/taxize/NEWS |only taxize-0.6.0/taxize/man/ifelsedata.Rd |only taxize-0.6.0/taxize/tests/testthat/test-itis_phymat_format.R |only taxize-0.6.2/taxize/DESCRIPTION | 12 taxize-0.6.2/taxize/MD5 | 251 ++++---- taxize-0.6.2/taxize/NAMESPACE | 66 +- taxize-0.6.2/taxize/R/children.R | 50 - taxize-0.6.2/taxize/R/class2tree.R | 1 taxize-0.6.2/taxize/R/classification.R | 149 ++-- taxize-0.6.2/taxize/R/col_children.R | 30 taxize-0.6.2/taxize/R/col_classification.R | 2 taxize-0.6.2/taxize/R/col_downstream.R | 7 taxize-0.6.2/taxize/R/col_search.R | 189 ++++-- taxize-0.6.2/taxize/R/comm2sci.R | 2 taxize-0.6.2/taxize/R/downstream.R | 48 + taxize-0.6.2/taxize/R/eol_dataobjects.R | 2 taxize-0.6.2/taxize/R/eol_hierarchy.R | 3 taxize-0.6.2/taxize/R/eol_invasive.R | 6 taxize-0.6.2/taxize/R/eol_pages.R | 2 taxize-0.6.2/taxize/R/eol_search.R | 4 taxize-0.6.2/taxize/R/gbif_parse.R | 8 taxize-0.6.2/taxize/R/get_boldid.R | 3 taxize-0.6.2/taxize/R/get_colid.R | 45 - taxize-0.6.2/taxize/R/get_eolid.R | 4 taxize-0.6.2/taxize/R/get_gbifid.R | 7 taxize-0.6.2/taxize/R/get_tpsid.R | 3 taxize-0.6.2/taxize/R/get_tsn.R | 1 taxize-0.6.2/taxize/R/get_ubioid.R | 3 taxize-0.6.2/taxize/R/get_uid.R | 102 ++- taxize-0.6.2/taxize/R/gni_details.R | 46 - taxize-0.6.2/taxize/R/gni_helpers.R |only taxize-0.6.2/taxize/R/gni_parse.R | 25 taxize-0.6.2/taxize/R/gni_search.R | 42 - taxize-0.6.2/taxize/R/gnr_datasources.R | 2 taxize-0.6.2/taxize/R/gnr_resolve.R | 110 ++- taxize-0.6.2/taxize/R/iplant_resolve.R | 21 taxize-0.6.2/taxize/R/ipni_search.R | 2 taxize-0.6.2/taxize/R/itis.R | 4 taxize-0.6.2/taxize/R/itis_downstream.R | 1 taxize-0.6.2/taxize/R/iucn_summary.R | 10 taxize-0.6.2/taxize/R/nbn_search.R | 4 taxize-0.6.2/taxize/R/phylomatic_format.R | 1 taxize-0.6.2/taxize/R/phylomatic_tree.R | 91 +- taxize-0.6.2/taxize/R/plantminer.R | 3 taxize-0.6.2/taxize/R/rankagg.R | 17 taxize-0.6.2/taxize/R/resolve.R | 95 +-- taxize-0.6.2/taxize/R/sci2comm.R | 16 taxize-0.6.2/taxize/R/scrapenames.r | 116 ++- taxize-0.6.2/taxize/R/synonyms.R | 71 +- taxize-0.6.2/taxize/R/tax_agg.R | 3 taxize-0.6.2/taxize/R/taxize-package.R | 32 - taxize-0.6.2/taxize/R/taxize_cite.R | 8 taxize-0.6.2/taxize/R/tnrs.R | 190 +++--- taxize-0.6.2/taxize/R/tnrs_sources.r | 36 - taxize-0.6.2/taxize/R/tp_accnames.R | 2 taxize-0.6.2/taxize/R/tp_classification.R | 2 taxize-0.6.2/taxize/R/tp_dist.R | 2 taxize-0.6.2/taxize/R/tp_refs.R | 2 taxize-0.6.2/taxize/R/tp_search.R | 2 taxize-0.6.2/taxize/R/tp_summary.R | 2 taxize-0.6.2/taxize/R/tp_synonyms.R | 2 taxize-0.6.2/taxize/R/tpl_search.r | 28 taxize-0.6.2/taxize/R/ubio_classification.R | 49 - taxize-0.6.2/taxize/R/ubio_classification_search.R | 18 taxize-0.6.2/taxize/R/ubio_id.R | 62 +- taxize-0.6.2/taxize/R/ubio_search.R | 14 taxize-0.6.2/taxize/R/ubio_synonyms.R | 35 - taxize-0.6.2/taxize/R/upstream.R | 32 - taxize-0.6.2/taxize/R/vascan_search.r | 1 taxize-0.6.2/taxize/R/zzz.R | 43 - taxize-0.6.2/taxize/README.md | 20 taxize-0.6.2/taxize/build/vignette.rds |binary taxize-0.6.2/taxize/inst/NEWS.Rd |only taxize-0.6.2/taxize/inst/doc/taxize_vignette.Rmd | 308 ++++++++-- taxize-0.6.2/taxize/inst/doc/taxize_vignette.html | 306 ++++++++- taxize-0.6.2/taxize/inst/examples |only taxize-0.6.2/taxize/inst/vign/taxize_vignette.md | 308 ++++++++-- taxize-0.6.2/taxize/man/children.Rd | 9 taxize-0.6.2/taxize/man/classification.Rd | 16 taxize-0.6.2/taxize/man/col_search.Rd | 14 taxize-0.6.2/taxize/man/downstream.Rd | 9 taxize-0.6.2/taxize/man/get_boldid.Rd | 1 taxize-0.6.2/taxize/man/get_colid.Rd | 25 taxize-0.6.2/taxize/man/get_gbifid.Rd | 1 taxize-0.6.2/taxize/man/get_tpsid.Rd | 1 taxize-0.6.2/taxize/man/get_ubioid.Rd | 1 taxize-0.6.2/taxize/man/get_uid.Rd | 65 +- taxize-0.6.2/taxize/man/gni_details.Rd | 16 taxize-0.6.2/taxize/man/gni_parse.Rd | 8 taxize-0.6.2/taxize/man/gni_search.Rd | 17 taxize-0.6.2/taxize/man/iplant_resolve.Rd | 8 taxize-0.6.2/taxize/man/iucn_summary.Rd | 2 taxize-0.6.2/taxize/man/phylomatic_tree-deprecated.Rd | 4 taxize-0.6.2/taxize/man/rankagg.Rd | 1 taxize-0.6.2/taxize/man/resolve.Rd | 53 + taxize-0.6.2/taxize/man/scrapenames.Rd | 46 - taxize-0.6.2/taxize/man/synonyms.Rd | 9 taxize-0.6.2/taxize/man/taxize-defunct.Rd | 2 taxize-0.6.2/taxize/man/taxize-package.Rd | 16 taxize-0.6.2/taxize/man/taxize_cite.Rd | 3 taxize-0.6.2/taxize/man/tnrs.Rd | 29 taxize-0.6.2/taxize/man/tnrs_sources.Rd | 10 taxize-0.6.2/taxize/man/tpl_search-defunct.Rd | 22 taxize-0.6.2/taxize/man/ubio_classification.Rd | 4 taxize-0.6.2/taxize/man/ubio_classification_search.Rd | 4 taxize-0.6.2/taxize/man/ubio_id.Rd | 4 taxize-0.6.2/taxize/man/ubio_synonyms.Rd | 8 taxize-0.6.2/taxize/man/upstream.Rd | 2 taxize-0.6.2/taxize/tests/testthat/test-classification.R | 54 + taxize-0.6.2/taxize/tests/testthat/test-col_search.R | 28 taxize-0.6.2/taxize/tests/testthat/test-comm2sci.R | 14 taxize-0.6.2/taxize/tests/testthat/test-eol_dataobjects.R | 2 taxize-0.6.2/taxize/tests/testthat/test-eol_pages.R | 10 taxize-0.6.2/taxize/tests/testthat/test-get_uid.R | 46 + taxize-0.6.2/taxize/tests/testthat/test-gnr_resolve.R | 22 taxize-0.6.2/taxize/tests/testthat/test-iucn_getname.R | 6 taxize-0.6.2/taxize/tests/testthat/test-ncbi_children.R |only taxize-0.6.2/taxize/tests/testthat/test-ncbi_get_taxon_summary.R |only taxize-0.6.2/taxize/tests/testthat/test-phylomatic_format.R |only taxize-0.6.2/taxize/tests/testthat/test-phylomatic_tree.R | 2 taxize-0.6.2/taxize/tests/testthat/test-ping.R |only taxize-0.6.2/taxize/tests/testthat/test-plantminer.R | 2 taxize-0.6.2/taxize/tests/testthat/test-tnrs.R | 8 taxize-0.6.2/taxize/tests/testthat/test-tnrs_sources.R | 4 taxize-0.6.2/taxize/tests/testthat/test-tp_accnames.R | 2 taxize-0.6.2/taxize/tests/testthat/test-tp_dist.R | 2 taxize-0.6.2/taxize/tests/testthat/test-tp_refs.R | 2 taxize-0.6.2/taxize/tests/testthat/test-tp_search.R | 4 taxize-0.6.2/taxize/tests/testthat/test-tp_summary.R | 2 taxize-0.6.2/taxize/tests/testthat/test-tp_synonyms.R | 2 taxize-0.6.2/taxize/tests/testthat/test-ubio_classification.R |only taxize-0.6.2/taxize/vignettes/taxize_vignette.Rmd | 308 ++++++++-- 132 files changed, 2694 insertions(+), 1420 deletions(-)
Title: Access to Facebook API via R
Description: Provides an interface to the Facebook API.
Author: Pablo Barbera <pablo.barbera@nyu.edu>, Michael Piccirilli
<mrp2181@columbia.edu>
Maintainer: Pablo Barbera <pablo.barbera@nyu.edu>
Diff between Rfacebook versions 0.5 dated 2015-01-09 and 0.6 dated 2015-08-07
ChangeLog | 10 ++++++- DESCRIPTION | 10 +++---- MD5 | 57 ++++++++++++++++++++++--------------------- NAMESPACE | 5 +++ R/fbOAuth.R | 23 ++++++++++------- R/getGroup.R |only R/getInsights.R | 62 ++++++++++++++++++++++++++++++++--------------- R/getLikes.R | 7 ++++- R/getNetwork.R | 4 +-- R/getPage.R | 10 +++---- R/getUsers.R | 8 +++--- R/searchFacebook.R | 2 - R/searchPages.R | 4 +-- R/utils.R | 59 +++++++++++++++++++++++++++++++++++++------- man/Rfacebook-package.Rd | 2 - man/fbOAuth.Rd | 2 - man/getCheckins.Rd | 2 - man/getFQL.Rd | 2 - man/getFriends.Rd | 2 - man/getGroup.Rd |only man/getInsights.Rd | 31 ++++++++++++++++++----- man/getLikes.Rd | 6 +++- man/getNetwork.Rd | 2 - man/getNewsfeed.Rd | 2 - man/getPage.Rd | 10 +++---- man/getPost.Rd | 2 - man/getUsers.Rd | 2 - man/searchFacebook.Rd | 2 - man/searchGroup.Rd |only man/searchPages.Rd | 4 +-- man/updateStatus.Rd | 2 - 31 files changed, 221 insertions(+), 113 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data". The package contains code for designed
experiments, data sets and other convenience functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kevin.dunn@mcmaster.ca>
Diff between pid versions 0.32 dated 2015-07-23 and 0.36 dated 2015-08-07
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/contourPlot.R | 2 +- inst/trade-off-table.pdf |binary inst/trade-off-table.png |binary man/contourPlot.Rd | 5 +++-- man/figures/trade-off-table.pdf |binary man/figures/trade-off-table.png |binary man/pollutant.Rd | 2 +- man/tradeOffTable.Rd | 5 ++++- man/tradeoff.Rd | 3 ++- 11 files changed, 25 insertions(+), 20 deletions(-)
Title: Tools for Ecological Network Analysis
Description: Provides algorithms for the analysis of ecological networks.
Author: M.K. Lau, S.R. Borrett, D.E. Hines, P. Singh
Maintainer: Matthew K. Lau <enaR.maintainer@gmail.com>
Diff between enaR versions 2.9 dated 2015-07-21 and 2.9.1 dated 2015-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- R/as.bipartite.R |only inst/doc/enaR-vignette.pdf |binary man/as.bipartite.Rd |only man/enaR-package.Rd | 8 ++------ 6 files changed, 11 insertions(+), 13 deletions(-)
Title: Companion to Applied Regression
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 2.0-25 dated 2015-03-03 and 2.0-26 dated 2015-08-06
DESCRIPTION | 18 MD5 | 128 ++-- NAMESPACE | 557 ++++++++++---------- NEWS | 1306 ++++++++++++++++++++++++------------------------ R/Anova.R | 194 +++---- R/scatterplot.R | 26 build/vignette.rds |binary data/AMSsurvey.rda |binary data/Adler.rda |binary data/Angell.rda |binary data/Anscombe.rda |binary data/Baumann.rda |binary data/Bfox.rda |binary data/Blackmore.rda |binary data/Burt.rda |binary data/CanPop.rda |binary data/Chile.rda |binary data/Chirot.rda |binary data/Cowles.rda |binary data/Davis.rda |binary data/DavisThin.rda |binary data/Depredations.rda |binary data/Duncan.rda |binary data/Ericksen.rda |binary data/Florida.rda |binary data/Freedman.rda |binary data/Friendly.rda |binary data/Ginzberg.rda |binary data/Greene.rda |binary data/Guyer.rda |binary data/Hartnagel.rda |binary data/Highway1.rda |binary data/KosteckiDillon.rda |binary data/Leinhardt.rda |binary data/Mandel.rda |binary data/Migration.rda |binary data/Moore.rda |binary data/Mroz.rda |binary data/OBrienKaiser.rda |binary data/Ornstein.rda |binary data/Pottery.rda |binary data/Prestige.rda |binary data/Quartet.rda |binary data/Robey.rda |binary data/SLID.rda |binary data/Sahlins.rda |binary data/Salaries.rda |binary data/Soils.rda |binary data/States.rda |binary data/Transact.rda |binary data/UN.rda |binary data/USPop.rda |binary data/Vocab.rda |binary data/WeightLoss.rda |binary data/Womenlf.rda |binary data/Wong.rda |binary data/Wool.rda |binary inst/doc/embedding.R | 382 +++++++------- inst/doc/embedding.pdf |binary man/AMSsurvey.Rd | 2 man/Anova.Rd | 7 man/Depredations.Rd | 64 +- man/car-package.Rd | 72 +- man/hccm.Rd | 4 man/scatterplot.Rd | 10 65 files changed, 1414 insertions(+), 1356 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations, such as erosion and dilation, on data of arbitrary dimensionality. Can also be used for resampling, filtering, smoothing and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.1.0 dated 2014-09-24 and 1.2.0 dated 2015-08-06
DESCRIPTION | 14 +- MD5 | 50 +++++----- NAMESPACE | 56 ++++++++++- NEWS | 10 ++ R/automata.R | 51 ++++++++++ R/display.R | 84 ++++++++++++++++- R/kernels.R | 159 ++++++++++++++++++++++++++++++-- R/morph.R | 201 +++++++++++++++++++++++++++++++++++++++++ R/resample.R | 53 ++++++++++ R/zzz.R |only README.md | 4 man/binarise.Rd | 25 ++--- man/binary.Rd | 23 ++-- man/display.Rd | 68 ++++++++++--- man/filters.Rd | 36 ++++--- man/gameOfLife.Rd | 87 +++++++++++------ man/gaussianSmooth.Rd | 32 ++++-- man/kernels.Rd | 164 +++++++++++++++++++++++---------- man/morph.Rd | 79 +++++++++++----- man/morphology.Rd | 66 ++++++++----- man/neighbourhood.Rd | 35 ++++--- man/resample.Rd | 56 +++++++---- man/sampleKernelFunction.Rd | 62 +++++++----- man/threshold.Rd |only src/Morpher.cpp | 18 ++- src/main.cpp | 4 tests/testthat/test-10-morph.R | 9 + 27 files changed, 1140 insertions(+), 306 deletions(-)
Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. It provides an
interface to S4 reference classes and two alternative new implementations. One
is an experimental version built around S4 (defineClass) and the other one
(retList) makes it more convenient to work with lists returned from functions
and uses only S3.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between aoos versions 0.2.0 dated 2015-04-21 and 0.3.0 dated 2015-08-06
aoos-0.2.0/aoos/R/Class.R |only aoos-0.2.0/aoos/man/Class.Rd |only aoos-0.3.0/aoos/DESCRIPTION | 19 aoos-0.3.0/aoos/LICENSE | 687 ------------------ aoos-0.3.0/aoos/MD5 | 103 +- aoos-0.3.0/aoos/NAMESPACE | 65 + aoos-0.3.0/aoos/NEWS | 151 ++- aoos-0.3.0/aoos/R/Accessor.R | 104 +- aoos-0.3.0/aoos/R/Binary.R | 163 ++-- aoos-0.3.0/aoos/R/Infix.R |only aoos-0.3.0/aoos/R/NAMESPACE.R |only aoos-0.3.0/aoos/R/Private.R | 146 +-- aoos-0.3.0/aoos/R/Show.R | 46 - aoos-0.3.0/aoos/R/aoos.R | 221 ++--- aoos-0.3.0/aoos/R/defineClass.R | 258 +++--- aoos-0.3.0/aoos/R/defineRefClass.R |only aoos-0.3.0/aoos/R/helper.R |only aoos-0.3.0/aoos/R/packageStartupMessage.R | 4 aoos-0.3.0/aoos/R/public-interfaces.R | 184 ++-- aoos-0.3.0/aoos/R/retList.R |only aoos-0.3.0/aoos/build/vignette.rds |binary aoos-0.3.0/aoos/inst/doc/Introduction.R | 15 aoos-0.3.0/aoos/inst/doc/Introduction.Rmd | 58 - aoos-0.3.0/aoos/inst/doc/Introduction.html | 160 ++-- aoos-0.3.0/aoos/inst/doc/aoosClasses.R | 212 ++--- aoos-0.3.0/aoos/inst/doc/aoosClasses.Rmd | 336 ++++---- aoos-0.3.0/aoos/inst/doc/aoosClasses.html | 497 ++++++------- aoos-0.3.0/aoos/inst/doc/performance.R |only aoos-0.3.0/aoos/inst/doc/performance.Rmd |only aoos-0.3.0/aoos/inst/doc/performance.html |only aoos-0.3.0/aoos/inst/doc/referenceClasses.R | 142 +-- aoos-0.3.0/aoos/inst/doc/referenceClasses.Rmd | 184 ++-- aoos-0.3.0/aoos/inst/doc/referenceClasses.html | 320 ++++---- aoos-0.3.0/aoos/inst/doc/retListClasses.R |only aoos-0.3.0/aoos/inst/doc/retListClasses.Rmd |only aoos-0.3.0/aoos/inst/doc/retListClasses.html |only aoos-0.3.0/aoos/man/Accessor.Rd | 48 - aoos-0.3.0/aoos/man/Binary.Rd | 106 +- aoos-0.3.0/aoos/man/Infix.Rd |only aoos-0.3.0/aoos/man/Private.Rd | 112 +- aoos-0.3.0/aoos/man/Show.Rd | 54 - aoos-0.3.0/aoos/man/aoos.Rd | 71 - aoos-0.3.0/aoos/man/defineClass.Rd | 156 ++-- aoos-0.3.0/aoos/man/defineRefClass.Rd |only aoos-0.3.0/aoos/man/envHelper.Rd |only aoos-0.3.0/aoos/man/publicInterface.Rd | 56 - aoos-0.3.0/aoos/man/retList.Rd |only aoos-0.3.0/aoos/tests/testthat.R | 8 aoos-0.3.0/aoos/tests/testthat/test-Accessor.R | 60 - aoos-0.3.0/aoos/tests/testthat/test-Binary.R | 130 +-- aoos-0.3.0/aoos/tests/testthat/test-Class.R | 216 ++--- aoos-0.3.0/aoos/tests/testthat/test-Infix.R |only aoos-0.3.0/aoos/tests/testthat/test-basics.R | 306 ++++---- aoos-0.3.0/aoos/tests/testthat/test-inheritance.R | 180 ++-- aoos-0.3.0/aoos/tests/testthat/test-publicInterface.R | 230 +++--- aoos-0.3.0/aoos/tests/testthat/test-retList.R |only aoos-0.3.0/aoos/tests/testthat/test-self.R | 94 +- aoos-0.3.0/aoos/tests/testthat/test-summary.R | 40 - aoos-0.3.0/aoos/vignettes/Introduction.Rmd | 58 - aoos-0.3.0/aoos/vignettes/aoosClasses.Rmd | 336 ++++---- aoos-0.3.0/aoos/vignettes/performance.Rmd |only aoos-0.3.0/aoos/vignettes/referenceClasses.Rmd | 184 ++-- aoos-0.3.0/aoos/vignettes/retListClasses.Rmd |only 63 files changed, 2978 insertions(+), 3542 deletions(-)
Title: Confidence Intervals for Two Sample Comparisons
Description: Calculation of the parametric, nonparametric confidence intervals
for the difference or ratio of location parameters, nonparametric confidence interval
for the Behrens-Fisher problem and for the difference, ratio and odds-ratio of binomial
proportions for comparison of independent samples. Common wrapper functions to split
data sets and apply confidence intervals or tests to these subsets.
A by-statement allows calculation of CI separately for the levels of further factors.
CI are not adjusted for multiplicity.
Author: Frank Schaarschmidt [aut, cre], Daniel Gerhard [aut]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between pairwiseCI versions 0.1-22 dated 2013-10-23 and 0.1-25 dated 2015-08-06
DESCRIPTION | 18 - MD5 | 26 +- NAMESPACE | 10 R/RRODpairwiseCI.R |only R/pairwiseCI.R | 7 R/pairwiseCIProp.R | 4 R/plot.pairwiseCI.R | 428 +++++------------------------------- R/print.pairwiseCI.R | 2 data/Oats.rda |binary data/behenic.rda |binary man/MOVERR.Rd |only man/Overdispersed.binomial.ratio.Rd |only man/QBmover.Rd |only man/as.data.frame.pairwiseMEP.Rd | 26 -- man/pairwiseMEP.Rd | 22 + man/plot.pairwiseCI.Rd | 3 16 files changed, 123 insertions(+), 423 deletions(-)
Title: IBM in-Database Analytics for R
Description: Functionality required to efficiently use R with
IBM DB2(C) for Linux, Unix and Windows as well as IBM dashDB(C).
Many basic and complex R operations are pushed down into the database, which removes
the main memory boundary of R and allows to make full use of parallel processing in
the underlying database.
Author: IBM Corporation
Maintainer: Michael Wurst <inza@de.ibm.com>
Diff between ibmdbR versions 1.36.7 dated 2015-03-08 and 1.42.2 dated 2015-08-06
DESCRIPTION | 8 +++--- MD5 | 48 +++++++++++++++++++++------------------ NAMESPACE | 21 ++++++++++------- R/aggregate.R |only R/connect.R | 14 +++++------ R/connection.R | 59 ++++++++++++++++++++++++++++++++++++++++--------- R/data.frame.R | 20 +++++++++------- R/data.frame.methods.R | 4 +-- R/kMeans.R | 4 +-- R/list.R | 36 ++++++++++++++++------------- R/lm.R | 9 +++++-- R/model.management.R | 34 +++++++++++++--------------- R/nb.R | 2 - R/parse.formula.R | 2 - R/rules.R |only R/sample.R | 11 ++++----- R/save.R | 4 +-- R/sql.R | 4 +-- R/update.R | 4 +-- build/vignette.rds |binary inst/doc/ibmdbR.pdf |binary man/ida.list.Rd | 6 ++-- man/idaArule.Rd |only man/idaGetModelName.Rd |only man/idaKMeans.Rd | 25 ++++++++++++-------- man/idaLm.Rd | 11 ++++----- man/idaNb.Rd | 9 ++++++- 27 files changed, 203 insertions(+), 132 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre],
Achim Zeileis [aut]
Maintainer: Jakob Messner <Jakob.Messner@uibk.ac.at>
Diff between crch versions 0.9-0 dated 2015-06-27 and 0.9-1 dated 2015-08-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 3 +++ NEWS | 8 ++++++++ R/crch.R | 20 ++++++++++++++++---- inst/doc/crch.pdf |binary man/coef.crch.Rd | 2 ++ 7 files changed, 39 insertions(+), 14 deletions(-)
Title: Data Sets, Etc. for the Text "Using R for Introductory
Statistics", Second Edition
Description: A collection of data sets to accompany the
textbook "Using R for Introductory Statistics," second
edition.
Author: John Verzani <verzani@math.csi.cuny.edu>
Maintainer: John Verzani <verzani@math.csi.cuny.edu>
Diff between UsingR versions 2.0-4 dated 2015-01-22 and 2.0-5 dated 2015-08-06
UsingR-2.0-4/UsingR/ChangeLog |only UsingR-2.0-4/UsingR/DESCRIPTION |only UsingR-2.0-4/UsingR/MD5 |only UsingR-2.0-4/UsingR/R |only UsingR-2.0-4/UsingR/data/SAT.txt.gz |only UsingR-2.0-4/UsingR/data/babyboom.rda |only UsingR-2.0-4/UsingR/data/batting.rda |only UsingR-2.0-4/UsingR/data/cabinet.rda |only UsingR-2.0-4/UsingR/data/firstchi.rda |only UsingR-2.0-4/UsingR/data/google.rda |only UsingR-2.0-4/UsingR/data/movie_data_2011.rda |only UsingR-2.0-4/UsingR/data/movies.rda |only UsingR-2.0-4/UsingR/data/primes.txt.xz |only UsingR-2.0-4/UsingR/data/tempsalinity.rda |only UsingR-2.0-4/UsingR/man |only UsingR-2.0-5/UsingR/NAMESPACE | 50 +++++++ UsingR-2.0-5/UsingR/data/BushApproval.rda |binary UsingR-2.0-5/UsingR/data/HUMMER.rda |binary UsingR-2.0-5/UsingR/data/KSI.rda |binary UsingR-2.0-5/UsingR/data/MLBattend.rda |binary UsingR-2.0-5/UsingR/data/Medicare.rda |binary UsingR-2.0-5/UsingR/data/OBP.rda |binary UsingR-2.0-5/UsingR/data/ObamaApproval.rda |binary 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Title: Udunits-2 Bindings for R
Description: Provides simple bindings to version 2 of Unidata's udunits library.
Author: James Hiebert <hiebert@uvic.ca>
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between udunits2 versions 0.6 dated 2012-02-07 and 0.8 dated 2015-08-06
udunits2-0.6/udunits2/R/load.R.in |only udunits2-0.6/udunits2/configure.in |only udunits2-0.6/udunits2/src/Makefile.in |only udunits2-0.6/udunits2/src/Makevars |only udunits2-0.6/udunits2/test.script.R |only udunits2-0.8/udunits2/CHANGELOG |only udunits2-0.8/udunits2/COPYING |only udunits2-0.8/udunits2/DESCRIPTION | 14 udunits2-0.8/udunits2/MD5 | 32 udunits2-0.8/udunits2/R/windows/load.R | 1 udunits2-0.8/udunits2/configure | 1780 ++++-------------------- udunits2-0.8/udunits2/configure.ac |only udunits2-0.8/udunits2/inst |only udunits2-0.8/udunits2/man/ud.are.convertible.Rd | 2 udunits2-0.8/udunits2/man/ud.convert.Rd | 2 udunits2-0.8/udunits2/man/ud.get.name.Rd | 4 udunits2-0.8/udunits2/man/ud.is.parseable.Rd | 2 udunits2-0.8/udunits2/man/ud.set.encoding.Rd | 2 udunits2-0.8/udunits2/src/Makevars.in | 4 19 files changed, 377 insertions(+), 1466 deletions(-)
Title: Tumor Growth Rate Analysis
Description: A tool to obtain tumor growth rates from clinical trial patient data. Output includes individual and summary data for tumor growth rate estimates as well as optional plots of the observed and predicted tumor quantity over time.
Author: Julia Wilkerson
Maintainer: Julia Wilkerson <wilkersj@mail.nih.gov>
Diff between tumgr versions 0.0.2 dated 2015-07-08 and 0.0.3 dated 2015-08-06
DESCRIPTION | 14 +++++--- MD5 | 9 +++-- NEWS |only R/gdrate.R | 46 ++++++++++++++++++----------- man/gdrate.Rd | 79 +++++++++++++++++++++++++++++++++++++------------- tests/testthat/test.R | 68 +++++++++++++++++++++---------------------- 6 files changed, 135 insertions(+), 81 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Lei Huang [aut, cre],
Fabian Scheipl [aut],
Jeff Goldsmith [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb]
Maintainer: Lei Huang <huangracer@gmail.com>
Diff between refund versions 0.1-11 dated 2014-06-28 and 0.1-12 dated 2015-08-06
refund-0.1-11/refund/DESCRIPTION |only refund-0.1-11/refund/MD5 |only refund-0.1-11/refund/R |only refund-0.1-11/refund/data/DTI.RData |only refund-0.1-11/refund/data/DTI2.RData |only refund-0.1-11/refund/data/PEER.Sim.rda |only refund-0.1-11/refund/data/Q.rda |only refund-0.1-11/refund/data/datalist |only refund-0.1-11/refund/man |only refund-0.1-12/refund/NAMESPACE | 233 ++++++++++++++++++++++++++++--- refund-0.1-12/refund/data/PEER.Sim.RData |only refund-0.1-12/refund/data/gasoline.RData |binary 12 files changed, 216 insertions(+), 17 deletions(-)
Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('pez.shape', 'pez.evenness',
'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation
of Cavender-Bares (2004) correlation of phylogenetic and
ecological matrices ('fingerprint.regression'). Phylogenetic
Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives &
Helmus (2011) and Rafferty & Ives (2013). Simulation of null
assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between pez versions 1.0-0 dated 2015-02-11 and 1.1-0 dated 2015-08-06
pez-1.0-0/pez/R/laja.r |only pez-1.0-0/pez/R/scape.r |only pez-1.0-0/pez/inst/tests/test_dispersion.R |only pez-1.0-0/pez/inst/tests/test_dissimilarity.R |only pez-1.0-0/pez/inst/tests/test_evenness.R |only pez-1.0-0/pez/inst/tests/test_shape.R |only pez-1.0-0/pez/man/dispersion.Rd |only pez-1.0-0/pez/man/dissimilarity.Rd |only pez-1.0-0/pez/man/evenness.Rd |only pez-1.0-0/pez/man/shape.Rd |only pez-1.1-0/pez/DESCRIPTION | 28 - pez-1.1-0/pez/MD5 | 124 +++--- pez-1.1-0/pez/NAMESPACE | 105 ++++- pez-1.1-0/pez/NEWS | 7 pez-1.1-0/pez/R/comparative.comm.R | 67 ++- pez-1.1-0/pez/R/dispersion.R | 158 +------ pez-1.1-0/pez/R/dissimilarity.R | 66 +-- pez-1.1-0/pez/R/dist.matrix.R | 8 pez-1.1-0/pez/R/eco.env.regression.R | 2 pez-1.1-0/pez/R/eco.phy.regression.R | 4 pez-1.1-0/pez/R/eco.scape.R |only pez-1.1-0/pez/R/eco.trait.regression.R | 3 pez-1.1-0/pez/R/evenness.R | 481 +++--------------------- pez-1.1-0/pez/R/fingerprint.regression.R | 10 pez-1.1-0/pez/R/laja.R |only pez-1.1-0/pez/R/metapop.sim.R | 48 +- pez-1.1-0/pez/R/metric.null.R |only pez-1.1-0/pez/R/metrics.R |only pez-1.1-0/pez/R/pez-package.R | 10 pez-1.1-0/pez/R/pglmm.R | 177 ++++---- pez-1.1-0/pez/R/phy.signal.R | 1 pez-1.1-0/pez/R/phy.sim.R | 12 pez-1.1-0/pez/R/plotting.R | 3 pez-1.1-0/pez/R/scape.R |only pez-1.1-0/pez/R/shape.R | 310 +++++---------- pez-1.1-0/pez/R/traits.R | 47 +- pez-1.1-0/pez/R/utility.R | 145 ------- pez-1.1-0/pez/build/vignette.rds |binary pez-1.1-0/pez/inst/CITATION |only pez-1.1-0/pez/inst/doc/pez-intro.R | 55 +- pez-1.1-0/pez/inst/doc/pez-intro.Rnw | 171 +++++--- pez-1.1-0/pez/inst/doc/pez-intro.pdf |binary pez-1.1-0/pez/inst/tests/test_metapop.sim.R | 148 ------- pez-1.1-0/pez/inst/tests/test_metric_wrappers.R |only pez-1.1-0/pez/inst/tests/test_metrics.R |only pez-1.1-0/pez/inst/tests/test_pglmm.R |only pez-1.1-0/pez/inst/tests/test_plots.R |only pez-1.1-0/pez/inst/tests/test_scape.R |only pez-1.1-0/pez/inst/tests/test_traits.R | 13 pez-1.1-0/pez/man/ConDivSim.Rd | 10 pez-1.1-0/pez/man/cc.manip.Rd | 27 - pez-1.1-0/pez/man/comparative.comm.Rd | 9 pez-1.1-0/pez/man/dist.xxx.Rd | 7 pez-1.1-0/pez/man/drop_tip.Rd | 3 pez-1.1-0/pez/man/eco.scape.Rd |only pez-1.1-0/pez/man/eco.xxx.regression.Rd | 5 pez-1.1-0/pez/man/eco.xxx.regression.list.Rd | 3 pez-1.1-0/pez/man/fingerprint.regression.Rd | 17 pez-1.1-0/pez/man/generic.metrics.Rd |only pez-1.1-0/pez/man/laja.Rd | 3 pez-1.1-0/pez/man/pez-internal.Rd | 14 pez-1.1-0/pez/man/pez.Rd | 13 pez-1.1-0/pez/man/pez.dispersion.Rd |only pez-1.1-0/pez/man/pez.dissimilarity.Rd |only pez-1.1-0/pez/man/pez.evenness.Rd |only pez-1.1-0/pez/man/pez.metrics.Rd |only pez-1.1-0/pez/man/pez.shape.Rd |only pez-1.1-0/pez/man/pglmm.Rd | 65 +-- pez-1.1-0/pez/man/phy.build.Rd | 3 pez-1.1-0/pez/man/phy.signal.Rd | 3 pez-1.1-0/pez/man/plot.comparative.comm.Rd | 9 pez-1.1-0/pez/man/scape.Rd | 84 ++-- pez-1.1-0/pez/man/sim.meta.Rd | 34 - pez-1.1-0/pez/man/sim.phy.Rd | 14 pez-1.1-0/pez/man/trait.asm.Rd | 3 pez-1.1-0/pez/man/traitgram.cc.Rd | 5 pez-1.1-0/pez/vignettes/pez-intro.Rnw | 171 +++++--- 77 files changed, 1100 insertions(+), 1605 deletions(-)
Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also
given. Set partitions are now included.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.9-15 dated 2013-12-08 and 1.9-18 dated 2015-08-06
partitions-1.9-15/partitions/DESCRIPTION |only partitions-1.9-15/partitions/MD5 |only partitions-1.9-15/partitions/NAMESPACE |only partitions-1.9-15/partitions/R |only partitions-1.9-15/partitions/build |only partitions-1.9-15/partitions/inst/doc/partitionspaper.R |only partitions-1.9-15/partitions/inst/doc/scrabble.R |only partitions-1.9-15/partitions/man |only partitions-1.9-15/partitions/src |only partitions-1.9-15/partitions/tests |only partitions-1.9-15/partitions/vignettes |only partitions-1.9-18/partitions/inst/doc/partitionspaper.pdf |binary partitions-1.9-18/partitions/inst/doc/scrabble.pdf |binary partitions-1.9-18/partitions/inst/doc/setpartitions.pdf |binary 14 files changed
Title: Models and Tests for Departure from Hardy-Weinberg Equilibrium
and Independence Between Loci
Description: Fits models for genotypic disequilibria, as described in
Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).
Contrast terms are available that account for first order interactions
between loci. Also implements, for a single locus in a single
population, a conditional exact test for Hardy-Weinberg equilibrium.
Author: John Maindonald, with \code{hwexact()} from Randall Johnson.
Maintainer: John Maindonald <John.Maindonald@anu.edu.au>
Diff between hwde versions 0.64 dated 2013-11-28 and 0.65 dated 2015-08-06
DESCRIPTION | 25 ++++++++++++------------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/hwde.R | 2 +- build/vignette.rds |binary data/IndianIrish.RData |binary data/mendelABC.RData |binary man/hwde.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multi-variate clustering (MVC), cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 1.2.2 dated 2015-07-22 and 1.2.3 dated 2015-08-06
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/HiClimR.R | 3 ++- R/coarseR.R | 8 +++++++- R/fastCor.R | 3 ++- R/geogMask.R | 18 +++++++++++------- R/grid2D.R | 3 ++- R/minSigCor.R | 3 ++- R/validClimR.R | 3 ++- README.md | 21 ++++++++++++++++++++- man/HiClimR.Rd | 2 +- man/coarseR.Rd | 17 ++++++++++------- src/HiClimR.f90 | 1 + 13 files changed, 76 insertions(+), 38 deletions(-)
Title: PCM for Hybridization
Description: The BMhyd package analyzes the phenotypic evolution of species of hybrid origin on a phylogenetic network. This package can detect the hybrid vigor effect, a burst of variation at formation, and the relative portion of heritability from its parents. Parameters are estimated by maximum likelihood. Users need to enter a comparative data set, a phylogeny, and information on gene flow leading to hybrids.
Author: Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu> and Brian O'Meara <omeara.brian@gmail.com>
Maintainer: Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu>
Diff between BMhyd versions 1.2-2 dated 2014-02-15 and 1.2-8 dated 2015-08-06
DESCRIPTION | 20 MD5 | 31 NAMESPACE | 12 R/bmhyd.r | 1784 +++++++++++------------------- data |only man/AICc.Rd |only man/AdaptiveConfidenceIntervalSampling.Rd |only man/AdjustForDet.Rd |only man/AkaikeWeight.Rd |only man/AttachHybridsToDonor.Rd |only man/CalculateLikelihood.Rd |only man/ContourFromAdaptiveSampling.Rd |only man/DetPass.Rd |only man/GenerateValues.Rd |only man/GetAncestor.Rd |only man/GetClade.Rd |only man/GetMeansModified.Rd |only man/GetVModified.Rd |only man/LumpIntoClades.Rd |only man/PlotNetwork.Rd |only man/Plot_ConvexHull.Rd |only man/SimulateNetwork.Rd |only man/SimulateTipData.Rd |only man/bmhyd.Rd | 119 +- man/cichlid.Rd | 14 man/nicotiana.Rd |only 26 files changed, 826 insertions(+), 1154 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre],
Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>
Diff between alineR versions 1.1 dated 2015-07-27 and 1.1.1 dated 2015-08-06
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NAMESPACE | 3 +-- man/aline-package.Rd | 10 +++------- man/aline.Rd | 4 ++-- man/optimization.GA.Rd |only 6 files changed, 14 insertions(+), 18 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.12.1 dated 2015-06-12 and 0.12.2 dated 2015-08-05
shiny-0.12.1/shiny/R/slider.R |only shiny-0.12.1/shiny/man/imageOutput.Rd |only shiny-0.12.2/shiny/DESCRIPTION | 30 shiny-0.12.2/shiny/LICENSE | 26 shiny-0.12.2/shiny/MD5 | 122 - shiny-0.12.2/shiny/NAMESPACE | 3 shiny-0.12.2/shiny/NEWS | 31 shiny-0.12.2/shiny/R/app.R | 2 shiny-0.12.2/shiny/R/bootstrap.R | 1127 ---------- shiny-0.12.2/shiny/R/fileupload.R | 34 shiny-0.12.2/shiny/R/graph.R | 4 shiny-0.12.2/shiny/R/imageutils.R | 12 shiny-0.12.2/shiny/R/input-action.R |only shiny-0.12.2/shiny/R/input-checkbox.R |only shiny-0.12.2/shiny/R/input-checkboxgroup.R |only shiny-0.12.2/shiny/R/input-date.R |only shiny-0.12.2/shiny/R/input-daterange.R |only shiny-0.12.2/shiny/R/input-file.R |only shiny-0.12.2/shiny/R/input-numeric.R |only shiny-0.12.2/shiny/R/input-password.R |only shiny-0.12.2/shiny/R/input-radiobuttons.R |only shiny-0.12.2/shiny/R/input-select.R |only shiny-0.12.2/shiny/R/input-slider.R |only shiny-0.12.2/shiny/R/input-submit.R |only shiny-0.12.2/shiny/R/input-text.R |only shiny-0.12.2/shiny/R/input-utils.R |only shiny-0.12.2/shiny/R/map.R | 3 shiny-0.12.2/shiny/R/middleware.R | 27 shiny-0.12.2/shiny/R/progress.R | 2 shiny-0.12.2/shiny/R/reactives.R | 4 shiny-0.12.2/shiny/R/render-plot.R | 97 shiny-0.12.2/shiny/R/run-url.R | 8 shiny-0.12.2/shiny/R/server-input-handlers.R |only shiny-0.12.2/shiny/R/server.R | 107 shiny-0.12.2/shiny/R/shiny.R | 24 shiny-0.12.2/shiny/R/shinyui.R | 5 shiny-0.12.2/shiny/R/shinywrappers.R | 18 shiny-0.12.2/shiny/R/tar.R | 2 shiny-0.12.2/shiny/R/update-input.R | 49 shiny-0.12.2/shiny/R/utils.R | 26 shiny-0.12.2/shiny/inst/examples/01_hello/rsconnect |only shiny-0.12.2/shiny/inst/staticdocs/index.r | 12 shiny-0.12.2/shiny/inst/tests/test-utils.R | 17 shiny-0.12.2/shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.js | 224 + shiny-0.12.2/shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 5 shiny-0.12.2/shiny/inst/www/shared/shiny.js | 141 - shiny-0.12.2/shiny/inst/www/shared/shiny.js.map | 2 shiny-0.12.2/shiny/inst/www/shared/shiny.min.js | 6 shiny-0.12.2/shiny/inst/www/shared/shiny.min.js.map | 2 shiny-0.12.2/shiny/inst/www/shared/strftime |only shiny-0.12.2/shiny/man/actionButton.Rd | 10 shiny-0.12.2/shiny/man/checkboxGroupInput.Rd | 8 shiny-0.12.2/shiny/man/checkboxInput.Rd | 7 shiny-0.12.2/shiny/man/dateInput.Rd | 7 shiny-0.12.2/shiny/man/dateRangeInput.Rd | 7 shiny-0.12.2/shiny/man/fileInput.Rd | 7 shiny-0.12.2/shiny/man/navbarPage.Rd | 3 shiny-0.12.2/shiny/man/navlistPanel.Rd | 3 shiny-0.12.2/shiny/man/numericInput.Rd | 8 shiny-0.12.2/shiny/man/passwordInput.Rd | 7 shiny-0.12.2/shiny/man/plotOutput.Rd |only shiny-0.12.2/shiny/man/radioButtons.Rd | 16 shiny-0.12.2/shiny/man/registerInputHandler.Rd | 2 shiny-0.12.2/shiny/man/removeInputHandler.Rd | 2 shiny-0.12.2/shiny/man/repeatable.Rd | 2 shiny-0.12.2/shiny/man/selectInput.Rd | 6 shiny-0.12.2/shiny/man/shiny-options.Rd | 4 shiny-0.12.2/shiny/man/sliderInput.Rd | 36 shiny-0.12.2/shiny/man/submitButton.Rd | 7 shiny-0.12.2/shiny/man/textInput.Rd | 7 shiny-0.12.2/shiny/man/updateSliderInput.Rd | 4 shiny-0.12.2/shiny/man/updateTabsetPanel.Rd | 6 72 files changed, 895 insertions(+), 1436 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo <cepardot@unal.edu.co>, Pedro Cesar del Campo
<pcdelcampon@unal.edu.co> and Camilo Jose Torres
<cjtorresj@unal.edu.co>, with the contributions from Ivan Diaz
<ildiazm@unal.edu.co>, Mauricio Sadinle
<msadinleg@unal.edu.co>.
Maintainer: Campo Elias Pardo <cepardot@unal.edu.co>
Diff between FactoClass versions 1.1.1 dated 2015-02-03 and 1.1.2 dated 2015-08-05
DESCRIPTION | 8 - MD5 | 26 ++-- NAMESPACE | 6 R/cluster.carac.R | 326 ++++++++++++++++++++++++--------------------------- R/plotct.R | 18 ++ R/supqual.R |only R/ward.cluster.R | 188 ++++++++++++++--------------- data/BreedsDogs.rda |binary data/admi.rda |only data/cafe.rda |only data/icfes08.rda |only man/admi.Rd |only man/cafe.Rd |only man/cluster.carac.Rd | 123 +++++++++---------- man/icfes08.Rd |only man/plotct.Rd | 69 ++++++---- man/stableclus.Rd | 1 man/supqual.Rd |only 18 files changed, 396 insertions(+), 369 deletions(-)
Title: Total Operating Characteristic Curve and ROC Curve
Diff between TOC versions 0.0-2 dated 2015-06-05 and 0.0-3 dated 2015-08-05
Description: Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating characteristic to measure diagnostic ability for multiple thresholds. Int. J. Geogr. Inf. Sci. 28 (3), 570-583).
Author: Robert G. Pontius
Maintainer: Alí Santacruz
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
NAMESPACE | 5 ++++-
man/TOC-package.Rd | 4 ++--
4 files changed, 14 insertions(+), 10 deletions(-)
Title: Sparse Distance Weighted Discrimination
Description: Formulates a sparse distance weighted discrimination (SDWD) for high-dimensional classification and implements a very fast algorithm for computing its solution path with the L1, the elastic-net, and the adaptive elastic-net penalties.
Author: Boxiang Wang and Hui Zou
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between sdwd versions 1.0.1 dated 2015-01-05 and 1.0.2 dated 2015-08-05
ChangeLog | 6 - DESCRIPTION | 14 +- MD5 | 38 +++--- NAMESPACE | 16 +- R/coef.sdwd.R | 10 - R/cv.sdwd.R | 38 +++--- R/p.sdwd.R | 26 ++-- R/sdwd.R | 10 - R/utilities.R | 294 ++++++++++++++++++++++++------------------------- man/coef.cv.sdwd.Rd | 6 - man/coef.sdwd.Rd | 6 - man/cv.sdwd.Rd | 6 - man/plot.cv.sdwd.Rd | 6 - man/plot.sdwd.Rd | 12 +- man/predict.cv.sdwd.Rd | 9 - man/predict.sdwd.Rd | 11 + man/print.sdwd.Rd | 14 +- man/sdwd-internal.Rd | 11 + man/sdwd-package.Rd | 18 +-- man/sdwd.Rd | 12 +- 20 files changed, 283 insertions(+), 280 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.1.5 dated 2015-06-09 and 1.2 dated 2015-08-05
DESCRIPTION | 10 MD5 | 15 NAMESPACE | 10 R/foo.R | 791 ++++++++++++++++++++++++++++++++----- man/binary.probit.Bayes.Rd |only man/control.mcmc.Bayes.Rd | 10 man/plot.pred.PrevMap.Rd | 4 man/spatial.pred.binomial.Bayes.Rd | 16 man/summary.Bayes.PrevMap.Rd | 4 9 files changed, 740 insertions(+), 120 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods kernlab
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexis@ci.tuwien.ac.at>
Diff between kernlab versions 0.9-20 dated 2015-01-10 and 0.9-22 dated 2015-08-05
DESCRIPTION | 13 ++++++----- MD5 | 58 +++++++++++++++++++++++++------------------------- NAMESPACE | 8 +++++- R/gausspr.R | 13 +++++++---- R/kmmd.R | 4 +-- R/kqr.R | 13 +++-------- R/ksvm.R | 8 +++--- R/lssvm.R | 20 +++++++++++------ R/onlearn.R | 6 ++--- R/rvm.R | 30 ++++++------------------- R/specc.R | 4 +-- build/vignette.rds |binary data/income.rda |binary data/musk.rda |binary data/promotergene.rda |binary data/reuters.rda |binary data/spam.rda |binary data/spirals.rda |binary data/ticdata.rda |binary inst/doc/kernlab.pdf |binary man/csi.Rd | 2 - man/gausspr.Rd | 8 +++--- man/ipop.Rd | 2 - man/kkmeans.Rd | 2 - man/kmmd.Rd | 2 - man/kpca.Rd | 2 - man/ksvm.Rd | 6 ++--- man/onlearn.Rd | 2 - man/predict.ksvm.Rd | 2 - man/specc.Rd | 2 - 30 files changed, 101 insertions(+), 106 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.6-6 dated 2015-07-17 and 1.6-7 dated 2015-08-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/svm.R | 20 +++++++++++--------- inst/NEWS.Rd | 5 +++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary 6 files changed, 24 insertions(+), 17 deletions(-)
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)). Procedures are included for use with GLM, ivreg, plm (fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>
Diff between clusterSEs versions 2.0.1 dated 2015-07-14 and 2.1 dated 2015-08-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/clusterIM.glm.R | 34 +++++++++++++++++++++++++++++++--- man/cluster.im.glm.Rd | 6 ++++-- 4 files changed, 41 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-22 1.0.1
2010-04-17 1.0.0
2010-02-16 0.02.1
2009-12-01 0.02
2009-05-11 0.01-2
2009-02-23 0.01.1
2008-09-30 0.01
Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving first-order thermoluminescence glow curves using a modified Levenberg-Marquardt algorithm. It provides the possibility of setting constraints or fixing any of parameters. It offers an interactive way to initialize parameters by clicking with a mouse on a plot at positions where peak maxima should be located. Glow peaks can be simulated according to the Randall-Wilkins model.
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between tgcd versions 1.4 dated 2015-06-07 and 1.5 dated 2015-08-05
DESCRIPTION | 20 ++++++++------- MD5 | 13 ++++++---- NAMESPACE | 5 +++ R/simPeak.R |only R/tgcd.R | 63 ++++++++++++++++++++++++++++++-------------------- man/Refglow.Rd | 8 ++++-- man/simPeak.Rd |only man/tgcd.Rd | 22 ++++++++++------- src/BulirschStoer.f90 |only 9 files changed, 82 insertions(+), 49 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between statnet.common versions 3.2.2 dated 2014-12-09 and 3.2.3 dated 2015-08-05
DESCRIPTION | 13 ++++++------ LICENSE | 2 - MD5 | 24 ++++++++++++----------- NAMESPACE | 6 ++++- NEWS |only R/cite.utilities.R | 50 +++++++++++++++++++++++++++++++++---------------- R/control.utilities.R | 3 +- R/misc.utilities.R | 7 ++++++ R/startup.utilities.R | 2 - inst/CITATION | 46 ++++++++++++++++++++++++++++++++++++++++++++- man/ERRVL.Rd |only man/NVL.Rd | 2 - man/sort.data.frame.Rd | 2 - man/statnet.cite.Rd | 3 +- 14 files changed, 119 insertions(+), 41 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <abilgrau@math.aau.dk>
Diff between GMCM versions 1.2.1 dated 2015-04-20 and 1.2.2 dated 2015-08-05
DESCRIPTION | 7 ++-- MD5 | 60 ++++++++++++++++++++-------------------- NAMESPACE | 11 ++++++- R/GMCM-package.R | 12 ++++---- inst/doc/GMCM-JStatSoft.Rnw | 2 - inst/doc/GMCM-JStatSoft.pdf |binary inst/tests/test-colSds-rowSds.R | 8 ++--- man/EMAlgorithm.Rd | 2 - man/EStep.Rd | 2 - man/GMCM-package.Rd | 12 ++++---- man/PseudoEMAlgorithm.Rd | 2 - man/SimulateGMCMData.Rd | 2 - man/Uhat.Rd | 2 - man/choose.theta.Rd | 2 - man/colSds.Rd | 2 - man/cummean.Rd | 2 - man/dgmcm.loglik.Rd | 2 - man/dmvnormal.Rd | 2 - man/fit.full.GMCM.Rd | 2 - man/fit.meta.GMCM.Rd | 2 - man/freshVsFrozen.Rd | 2 - man/full2meta.Rd | 2 - man/get.IDR.Rd | 2 - man/is.theta.Rd | 2 - man/logit.Rd | 2 - man/rho.transform.Rd | 2 - man/rtheta.Rd | 2 - man/tt.Rd | 2 - man/u133VsExon.Rd | 2 - tests/test-all.R | 6 ++++ vignettes/GMCM-JStatSoft.Rnw | 2 - 31 files changed, 88 insertions(+), 74 deletions(-)
Title: Camera Trap Photograph Management and Preparation of Occupancy
Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy analysis with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can plot activity data using various functions (using package overlap and adapting function from the plotrix package).
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut]
Rahel Sollmann [aut]
Andreas Wilting [ctb, ths]
John Mathai [ctb]
Seth Timothy Wong [ctb]
An The Truong Nguyen [ctb]
Azlan bin Mohamed [ctb]
Andrew Tilker [ctb]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.97.0 dated 2015-07-29 and 0.97.1 dated 2015-08-05
camtrapR-0.97.0/camtrapR/R/TimeShiftImages.R |only camtrapR-0.97.0/camtrapR/man/TimeShiftImages.Rd |only camtrapR-0.97.1/camtrapR/DESCRIPTION | 17 - camtrapR-0.97.1/camtrapR/MD5 | 43 +-- camtrapR-0.97.1/camtrapR/NAMESPACE | 2 camtrapR-0.97.1/camtrapR/NEWS |only camtrapR-0.97.1/camtrapR/R/cameraOperation.r | 61 ++-- camtrapR-0.97.1/camtrapR/R/surveyReport.R | 241 ++++++++++--------- camtrapR-0.97.1/camtrapR/R/timeShiftImages.R |only camtrapR-0.97.1/camtrapR/data/camtraps.rda |binary camtrapR-0.97.1/camtrapR/man/activityDensity.Rd | 2 camtrapR-0.97.1/camtrapR/man/appendSpeciesNames.Rd | 8 camtrapR-0.97.1/camtrapR/man/camtrapR-package.Rd | 58 ++-- camtrapR-0.97.1/camtrapR/man/camtraps.Rd | 4 camtrapR-0.97.1/camtrapR/man/checkSpeciesFolders.Rd | 12 camtrapR-0.97.1/camtrapR/man/createSpeciesFolders.Rd | 12 camtrapR-0.97.1/camtrapR/man/detectionHistory.Rd | 2 camtrapR-0.97.1/camtrapR/man/detectionMaps.Rd | 10 camtrapR-0.97.1/camtrapR/man/exifTagNames.Rd | 9 camtrapR-0.97.1/camtrapR/man/getSpeciesImages.Rd | 10 camtrapR-0.97.1/camtrapR/man/imageRename.Rd | 18 - camtrapR-0.97.1/camtrapR/man/recordDatabase.Rd | 4 camtrapR-0.97.1/camtrapR/man/surveyReport.Rd | 35 +- camtrapR-0.97.1/camtrapR/man/timeShiftImages.Rd |only camtrapR-0.97.1/camtrapR/man/timeShiftTable.Rd | 2 25 files changed, 304 insertions(+), 246 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files,
calculate DVH metrics, gEUD, BED, EQD2, NTCP, TCP, show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3 dated 2015-05-04 and 0.3.1 dated 2015-08-05
DESCRIPTION | 11 +++++---- MD5 | 50 +++++++++++++++++++++++--------------------- NAMESPACE | 4 ++- R/convertDVH.R | 30 +++++++++++++++++++++++--- R/parseCadplan.R | 2 - R/parseEclipse.R | 13 ++++++++--- R/parseHiArt.R |only R/parseMasterplan.R | 6 ++--- R/parseMonaco.R |only R/parsePinnacleDVH.R | 4 +-- R/readDVH.R | 40 +++++++++++++++++++++++++++++++---- R/showDVH.R | 52 ++++++++++++++++++++++++++++++++++++++-------- R/unix/parseDVH.R | 10 +++++++- R/windows/parseDVH.R | 10 +++++++- inst/ChangeLog | 18 +++++++++++++++ inst/DVHshiny/ABOUT.md | 8 +++---- inst/DVHshiny/server.R | 9 +++++-- inst/DVHshiny/ui.R | 7 ++++-- inst/doc/DVHmetrics.Rnw | 8 +++---- inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 18 +++++++++++++++ inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 +-- man/readDVH.Rd | 22 +++++++++++++------ vignettes/DVHmetrics.Rnw | 8 +++---- vignettes/DVHshiny.Rnw | 18 +++++++++++++++ vignettes/lit.bib | 36 ++++++++++++++++++++----------- 27 files changed, 286 insertions(+), 102 deletions(-)
Title: A Graphical Tool for Wavelet (Cross) Correlation and Wavelet
Multiple (Cross) Correlation Analysis
Description: Set of functions that improves the graphical presentations of the functions 'wave.correlation' and 'spin.correlation' (waveslim package, Whitcher 2012) and the 'wave.multiple.correlation' and 'wave.multiple.cross.correlation' (wavemulcor package, Fernandez-Macho 2012b). The plot outputs (heatmaps) can be displayed in the screen or can be saved as PNG or JPG images or as PDF or EPS formats. The W2CWM2C package also helps to handle the (input data) multivariate time series easily as a list of N elements (times series) and provides a multivariate data set (dataexample) to exemplify its use. A description of the package was published in Computing in Science & Engineering (Volume:16, Issue: 6) on Sep. 09, 2014, doi:10.1109/MCSE.2014.96.
Author: Josue M. Polanco-Martinez
Maintainer: Josue M. Polanco-Martinez <josue.m.polanco@gmail.com>
Diff between W2CWM2C versions 1.0 dated 2012-11-24 and 2.0 dated 2015-08-05
W2CWM2C-1.0/W2CWM2C/doc |only W2CWM2C-2.0/W2CWM2C/DESCRIPTION | 28 ++---- W2CWM2C-2.0/W2CWM2C/MD5 | 25 ++--- W2CWM2C-2.0/W2CWM2C/NAMESPACE | 8 + W2CWM2C-2.0/W2CWM2C/R/WC.R | 129 ++++++++++++++++----------- W2CWM2C-2.0/W2CWM2C/R/WCC.R | 135 +++++++++++++++-------------- W2CWM2C-2.0/W2CWM2C/R/WMC.R | 29 +++++- W2CWM2C-2.0/W2CWM2C/R/WMCC.R | 99 +++++++++++---------- W2CWM2C-2.0/W2CWM2C/man/W2CWM2C-package.Rd | 104 +++++++++++----------- W2CWM2C-2.0/W2CWM2C/man/WC.Rd | 107 +++++++++++++--------- W2CWM2C-2.0/W2CWM2C/man/WCC.Rd | 106 +++++++++++++--------- W2CWM2C-2.0/W2CWM2C/man/WMC.Rd | 85 +++++++++++------- W2CWM2C-2.0/W2CWM2C/man/WMCC.Rd | 112 ++++++++++++++---------- W2CWM2C-2.0/W2CWM2C/man/dataexample.Rd | 13 +- 14 files changed, 570 insertions(+), 410 deletions(-)
Title: Dataframe Summaries, Frequency Tables and Numerical Summaries
with Customizable Output
Description: Generates formatted summary tables for vectors and dataframes.
Three summarizing functions: 1) 'freq' generates frequency tables
reporting counts and proportions (including cumulative); 2) 'descr'
gives common central tendency statistics and measures of dispersion
for numerical data; 3) 'dfSummary' gives as much information
as possible about a dataframe and its components in a clear,
legible table. All three functions can either display plain text tables
in the console or write markdown, text or html files to disk. An
additional misc function, 'what.is', extends base 'is' function,
checking the object against all 'is' functions and gives a variety
of other information about the object.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.3 dated 2015-03-11 and 0.4 dated 2015-08-05
summarytools-0.3/summarytools/man/desc.Rd |only summarytools-0.4/summarytools/DESCRIPTION | 17 summarytools-0.4/summarytools/MD5 | 42 summarytools-0.4/summarytools/NAMESPACE | 3 summarytools-0.4/summarytools/NEWS | 4 summarytools-0.4/summarytools/R/descr.R | 27 summarytools-0.4/summarytools/R/dfSummary.R | 23 summarytools-0.4/summarytools/R/freq.R | 18 summarytools-0.4/summarytools/R/misc.R | 2 summarytools-0.4/summarytools/R/print.summarytools.R | 27 summarytools-0.4/summarytools/R/what.is.R | 61 summarytools-0.4/summarytools/data |only summarytools-0.4/summarytools/inst/includes/stylesheets/bootstrap-theme.css | 261 summarytools-0.4/summarytools/inst/includes/stylesheets/bootstrap-theme.min.css | 11 summarytools-0.4/summarytools/inst/includes/stylesheets/bootstrap.css | 6697 ++++++++-- summarytools-0.4/summarytools/inst/includes/stylesheets/bootstrap.min.css | 27 summarytools-0.4/summarytools/man/descr.Rd |only summarytools-0.4/summarytools/man/dfSummary.Rd | 5 summarytools-0.4/summarytools/man/examens.Rd |only summarytools-0.4/summarytools/man/exams.Rd |only summarytools-0.4/summarytools/man/freq.Rd | 10 summarytools-0.4/summarytools/man/fumeurs.Rd |only summarytools-0.4/summarytools/man/print.summarytools.Rd | 3 summarytools-0.4/summarytools/man/smokers.Rd |only 24 files changed, 6246 insertions(+), 992 deletions(-)
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.5.0 dated 2015-07-01 and 0.5.2 dated 2015-08-05
rplos-0.5.0/rplos/R/utils.r |only rplos-0.5.2/rplos/DESCRIPTION | 8 +- rplos-0.5.2/rplos/MD5 | 28 +++++---- rplos-0.5.2/rplos/NAMESPACE | 1 rplos-0.5.2/rplos/NEWS.md | 64 +++++++++++++--------- rplos-0.5.2/rplos/R/crossref.R | 5 - rplos-0.5.2/rplos/R/facetplos.r | 8 +- rplos-0.5.2/rplos/R/fulltext.R | 3 - rplos-0.5.2/rplos/R/highbrow.r | 28 +++++---- rplos-0.5.2/rplos/R/rplos-package.R | 2 rplos-0.5.2/rplos/R/zzz.R | 15 +++++ rplos-0.5.2/rplos/README.md | 2 rplos-0.5.2/rplos/man/facetplos.Rd | 2 rplos-0.5.2/rplos/tests/testthat/test-crossref.R |only rplos-0.5.2/rplos/tests/testthat/test-facetplos.R |only rplos-0.5.2/rplos/tests/testthat/test-fulltext.R |only rplos-0.5.2/rplos/tests/testthat/test-highbrow.R |only rplos-0.5.2/rplos/tests/testthat/test-highplos.R |only 18 files changed, 102 insertions(+), 64 deletions(-)
Title: Transforms Input Data from a PMML Perspective
Description: Allows for data to be transformed before using
it to construct models. Builds structures to allow functions in
the PMML package to output transformation details in
addition to the model in the resulting PMML file.
Author: Tridivesh Jena, Wen Ching Lin, Dmitriy Bolotov (Zementis, Inc.)
Maintainer: Tridivesh Jena <rpmmlsupport@zementis.net>
Diff between pmmlTransformations versions 1.2.2 dated 2014-06-17 and 1.3.0 dated 2015-08-05
DESCRIPTION | 23 + MD5 | 45 ++- NAMESPACE | 2 R/DiscretizeXform.R | 22 + R/FunctionXform.R |only R/Initialize.R | 24 +- R/MapXform.R | 54 +++- R/MinMaxXform.R | 34 +- R/NormDiscreteXform.R | 20 + R/RenameVar.R | 4 R/WrapData.R | 27 +- R/ZScoreXform.R | 314 +++++++++++++-------------- build |only inst/ChangeLog | 10 inst/doc |only man/FunctionXform.Rd |only man/pmmlTransformations-package.Rd | 26 +- man/pmmlTransformations.DiscretizeXform.Rd | 108 +++++---- man/pmmlTransformations.MapXform.Rd | 53 ++-- man/pmmlTransformations.MinMaxXform.Rd | 30 +- man/pmmlTransformations.NormDiscreteXform.Rd | 24 +- man/pmmlTransformations.RenameVar.Rd | 3 man/pmmlTransformations.WrapData.Rd | 7 man/pmmlTransformations.ZScoreXform.Rd | 28 +- vignettes |only 25 files changed, 492 insertions(+), 366 deletions(-)
More information about pmmlTransformations at CRAN
Permanent link
Title: Generate PMML for Various Models
Description:
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org.
The generated PMML can be imported into any PMML consuming application,
such as the Zementis ADAPA and UPPI scoring engines which allow for
predictive models built in R to be deployed and executed on site, in
the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza, Pivotal,
Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler (arules),
Zementis Inc, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha, Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@zementis.net>
Diff between pmml versions 1.4.2 dated 2014-06-17 and 1.5.0 dated 2015-08-05
DESCRIPTION | 26 ++--- MD5 | 94 ++++++++++++-------- NAMESPACE | 22 ++++ R/AddAttributes.R |only R/addDDAttributes.R |only R/addDFChildren.R |only R/addLT.R | 3 R/addOutputField.R |only R/functionToPMML.R |only R/makeIntervals.R |only R/makeOutputNodes.R |only R/makeValues.R |only R/pmml.R | 170 ++++++++++++++++++++++++++++++++----- R/pmml.coxph.R | 16 +-- R/pmml.datadictionary.R | 105 ++++++++--------------- R/pmml.itemsets.R | 10 +- R/pmml.ksvm.R | 8 - R/pmml.lm.R | 2 R/pmml.miningschema.R | 213 +++++++++++++++++------------------------------ R/pmml.multinom.R | 2 R/pmml.naiveBayes.R | 29 ------ R/pmml.randomForest.R | 168 +------------------------------------ R/pmml.rfsrc.R | 2 R/pmml.rpart.R | 110 ------------------------ R/pmml.rules.R | 30 +++--- data/houseVotes84.rda |only inst/ChangeLog | 7 + man/AddAttributes.Rd |only man/addDDAttributes.Rd |only man/addDFChildren.Rd |only man/addLT.Rd | 14 +-- man/addMSAttributes.Rd | 35 ++++--- man/addOutputField.Rd |only man/fileToXMLNode.Rd | 3 man/functionToPMML.Rd |only man/houseVotes84.Rd |only man/makeIntervals.Rd |only man/makeOutputNodes.Rd |only man/makeValues.Rd |only man/pmml.Rd | 60 +++++++------ man/pmml.ada.Rd | 11 +- man/pmml.arules.Rd | 14 +-- man/pmml.coxph.Rd | 11 +- man/pmml.cv.glmnet.Rd | 20 ++-- man/pmml.glm.Rd | 13 +- man/pmml.hclust.Rd | 16 +-- man/pmml.kmeans.Rd | 8 - man/pmml.ksvm.Rd | 28 +++--- man/pmml.lm.Rd | 10 +- man/pmml.multinom.Rd | 4 man/pmml.naiveBayes.Rd | 16 +-- man/pmml.nnet.Rd | 12 +- man/pmml.randomForest.Rd | 11 +- man/pmml.rfsrc.Rd | 12 +- man/pmml.rpart.Rd | 12 +- man/pmml.svm.Rd | 12 +- man/pmmltoc.Rd | 3 57 files changed, 592 insertions(+), 750 deletions(-)
Title: Meta Analysis via Shiny
Description: Interactive shiny application for running a meta-analysis,
provides support for both random effects and fixed effects models with the 'metafor' package.
Additional support is included for calculating effect sizes plus
support for single case designs, graphical output, and detecting publication bias.
Author: William Kyle Hamilton [aut, cre],
Atsushi Mizumoto [aut],
Burak Aydin [ctb, trl],
Kathleen Coburn [ctb]
Maintainer: William Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between MAVIS versions 1.1 dated 2015-04-30 and 1.1.1 dated 2015-08-05
DESCRIPTION | 17 ++++++++++------- MD5 | 19 +++++++++++-------- NAMESPACE | 6 ++++-- NEWS | 6 ++++++ R/MAVIS.R | 31 +++++++++++++++++++++++++------ README.md | 18 +++++++++++------- inst/aRma |only inst/shiny/server.R | 16 ++++++++++++++++ inst/shiny/ui.R | 44 ++++++++++++++++++++++++++++++++++++++++++-- man/startaRma.Rd |only man/startmavis.Rd | 2 +- 11 files changed, 126 insertions(+), 33 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for displaying and analyzing functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.3 dated 2015-03-30 and 4.4 dated 2015-08-05
ChangeLog | 327 +++++++++++++++++++------------------ DESCRIPTION | 15 - MD5 | 24 +- NAMESPACE | 15 + R/T_stationary.R |only R/dynupdate.R | 262 ++++++++++++++--------------- R/farforecast.R |only R/forecast.ftsm.R | 455 +++++++++++++++++++++++++--------------------------- R/ftsmPI.r | 106 +++++++----- build/vignette.rds |binary data |only inst/CITATION |only man/T_stationary.Rd |only man/dynupdate.Rd | 10 - man/farforecast.Rd |only man/pm_10_GR.Rd |only 16 files changed, 630 insertions(+), 584 deletions(-)
Title: Credit Default Swap Functions
Description: It provides functions to bootstrap Credit Curves from market quotes (Credit Default Swap - CDS - spreads) and price Credit Default Swaps - CDS.
Author: Bertrand Le Nezet [cre, aut, cph],
Richard Brent [ctb, cph],
John Burkardt [ctb, cph]
Maintainer: Bertrand Le Nezet <bertrand.lenezet@gmail.com>
Diff between credule versions 0.1.2 dated 2015-07-27 and 0.1.3 dated 2015-08-05
DESCRIPTION | 14 +++++++++----- MD5 | 13 +++++++++---- build |only inst |only man/bootstrapCDS.Rd | 17 ++++++++++++++++- man/credule-package.Rd | 28 +++++++++++++++++++++++----- man/priceCDS.Rd | 32 +++++++++++++++++++++----------- vignettes |only 8 files changed, 78 insertions(+), 26 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.55-2 dated 2015-04-22 and 0.59-5 dated 2015-08-05
broman-0.55-2/broman/R/errors2pushbullet.R |only broman-0.55-2/broman/R/note.R |only broman-0.59-5/broman/DESCRIPTION | 8 broman-0.59-5/broman/MD5 | 166 ++++++++-------- broman-0.59-5/broman/NAMESPACE | 30 ++ broman-0.59-5/broman/R/add_commas.R |only broman-0.59-5/broman/R/arrowlocator.R | 1 broman-0.59-5/broman/R/brocolors.R | 42 ++-- broman-0.59-5/broman/R/colwalpha.R | 2 broman-0.59-5/broman/R/compare_rows.R |only broman-0.59-5/broman/R/excel_fig.R |only broman-0.59-5/broman/R/fisher.R | 1 broman-0.59-5/broman/R/grayplot.R | 6 broman-0.59-5/broman/R/help.R | 3 broman-0.59-5/broman/R/histlines.R | 1 broman-0.59-5/broman/R/holmans_triangle.R | 2 broman-0.59-5/broman/R/mypairs.R | 2 broman-0.59-5/broman/R/objectsizes.R | 3 broman-0.59-5/broman/R/openfile.R |only broman-0.59-5/broman/R/pushbullet.R |only broman-0.59-5/broman/R/qqline2.R | 3 broman-0.59-5/broman/R/quantileSE.R | 2 broman-0.59-5/broman/R/revrainbow.R | 2 broman-0.59-5/broman/R/rmvn.R | 2 broman-0.59-5/broman/R/strwidth2lines.R | 1 broman-0.59-5/broman/R/strwidth2xlim.R | 1 broman-0.59-5/broman/R/switchv.R |only broman-0.59-5/broman/R/theme_karl.R | 1 broman-0.59-5/broman/R/util.R | 2 broman-0.59-5/broman/R/venn_diagram.R | 1 broman-0.59-5/broman/R/winsorize.R | 5 broman-0.59-5/broman/R/xlimlabel.R | 1 broman-0.59-5/broman/inst/STATUS.txt | 45 ++++ broman-0.59-5/broman/man/add_commas.Rd |only broman-0.59-5/broman/man/arrowlocator.Rd | 2 broman-0.59-5/broman/man/attachfile.Rd | 2 broman-0.59-5/broman/man/attrnames.Rd | 2 broman-0.59-5/broman/man/brocolors.Rd | 35 +-- broman-0.59-5/broman/man/bromanversion.Rd | 2 broman-0.59-5/broman/man/cf.Rd | 2 broman-0.59-5/broman/man/chisq.Rd | 2 broman-0.59-5/broman/man/colwalpha.Rd | 2 broman-0.59-5/broman/man/compare_rows.Rd |only broman-0.59-5/broman/man/convert2hex.Rd | 2 broman-0.59-5/broman/man/done.Rd | 4 broman-0.59-5/broman/man/errors2pushbullet.Rd | 7 broman-0.59-5/broman/man/excel_fig.Rd |only broman-0.59-5/broman/man/exit.Rd | 2 broman-0.59-5/broman/man/fisher.Rd | 2 broman-0.59-5/broman/man/grayplot.Rd | 2 broman-0.59-5/broman/man/h.Rd | 2 broman-0.59-5/broman/man/hex2dec.Rd | 2 broman-0.59-5/broman/man/histlines.Rd | 2 broman-0.59-5/broman/man/kbdate.Rd | 2 broman-0.59-5/broman/man/lenuniq.Rd | 2 broman-0.59-5/broman/man/loadfile.Rd | 2 broman-0.59-5/broman/man/make.Rd | 2 broman-0.59-5/broman/man/manyboxplot.Rd | 2 broman-0.59-5/broman/man/mypairs.Rd | 2 broman-0.59-5/broman/man/myround.Rd | 2 broman-0.59-5/broman/man/normalize.Rd | 2 broman-0.59-5/broman/man/note.Rd | 4 broman-0.59-5/broman/man/objectsizes.Rd | 2 broman-0.59-5/broman/man/openfile.Rd |only broman-0.59-5/broman/man/paired.perm.test.Rd | 2 broman-0.59-5/broman/man/paste..Rd | 2 broman-0.59-5/broman/man/paste00.Rd | 2 broman-0.59-5/broman/man/perm.test.Rd | 2 broman-0.59-5/broman/man/plot_crayons.Rd | 2 broman-0.59-5/broman/man/pushbullet_devices.Rd |only broman-0.59-5/broman/man/qqline2.Rd | 2 broman-0.59-5/broman/man/qr2.Rd | 2 broman-0.59-5/broman/man/quantileSE.Rd | 2 broman-0.59-5/broman/man/revrainbow.Rd | 2 broman-0.59-5/broman/man/rmvn.Rd | 2 broman-0.59-5/broman/man/runningmean.Rd | 2 broman-0.59-5/broman/man/runningratio.Rd | 2 broman-0.59-5/broman/man/simp.Rd | 2 broman-0.59-5/broman/man/stop_sending_errors.Rd |only broman-0.59-5/broman/man/strwidth2lines.Rd | 2 broman-0.59-5/broman/man/strwidth2xlim.Rd | 2 broman-0.59-5/broman/man/switchv.Rd |only broman-0.59-5/broman/man/triarrow.Rd | 2 broman-0.59-5/broman/man/trilines.Rd | 2 broman-0.59-5/broman/man/triplot.Rd | 2 broman-0.59-5/broman/man/tripoints.Rd | 2 broman-0.59-5/broman/man/venn.Rd | 2 broman-0.59-5/broman/man/winsorize.Rd | 2 broman-0.59-5/broman/man/xlimlabel.Rd | 2 broman-0.59-5/broman/src/compare_rows.c |only broman-0.59-5/broman/src/compare_rows.h |only broman-0.59-5/broman/tests/testthat/test-add_commas.R |only broman-0.59-5/broman/tests/testthat/test-compare_rows.R |only broman-0.59-5/broman/tests/testthat/test-switchv.R |only 94 files changed, 291 insertions(+), 182 deletions(-)
Title: Tools for Electromyogram Signals (EMG) Analysis
Description: Data processing tools to compute the rectified, integrated and the averaged EMG. Routines for automatic detection of activation phases. A routine to compute and plot the ensemble average of the EMG. An EMG signal simulator for general purposes.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>
Diff between biosignalEMG versions 1.0.3 dated 2015-07-05 and 2.0.0 dated 2015-08-05
biosignalEMG-1.0.3/biosignalEMG/R/synthetic.emg.R |only biosignalEMG-1.0.3/biosignalEMG/man/synthetic.emg.Rd |only biosignalEMG-2.0.0/biosignalEMG/DESCRIPTION | 15 - biosignalEMG-2.0.0/biosignalEMG/MD5 | 86 +++-- biosignalEMG-2.0.0/biosignalEMG/NAMESPACE | 11 biosignalEMG-2.0.0/biosignalEMG/NEWS | 27 + biosignalEMG-2.0.0/biosignalEMG/R/ANDP.R |only biosignalEMG-2.0.0/biosignalEMG/R/MNChPD.R |only biosignalEMG-2.0.0/biosignalEMG/R/PCE.R |only biosignalEMG-2.0.0/biosignalEMG/R/PR.R |only biosignalEMG-2.0.0/biosignalEMG/R/TD.R |only biosignalEMG-2.0.0/biosignalEMG/R/as.emg.R |only biosignalEMG-2.0.0/biosignalEMG/R/as.emg.data.frame.R |only biosignalEMG-2.0.0/biosignalEMG/R/as.emg.default.R |only biosignalEMG-2.0.0/biosignalEMG/R/as.emg.matrix.R |only biosignalEMG-2.0.0/biosignalEMG/R/as.emg.numeric.R |only biosignalEMG-2.0.0/biosignalEMG/R/biosignalEMG-internal.R |only biosignalEMG-2.0.0/biosignalEMG/R/dcbiasremoval.R | 16 - biosignalEMG-2.0.0/biosignalEMG/R/eaemg.R | 19 - biosignalEMG-2.0.0/biosignalEMG/R/emg.R | 23 + biosignalEMG-2.0.0/biosignalEMG/R/envelope.R | 26 - biosignalEMG-2.0.0/biosignalEMG/R/extractchannel.R |only biosignalEMG-2.0.0/biosignalEMG/R/highpass.R |only biosignalEMG-2.0.0/biosignalEMG/R/iemg.R | 3 biosignalEMG-2.0.0/biosignalEMG/R/integration.R | 19 - biosignalEMG-2.0.0/biosignalEMG/R/is.emg.R |only biosignalEMG-2.0.0/biosignalEMG/R/loadABF1.R |only biosignalEMG-2.0.0/biosignalEMG/R/movingaverage.R | 16 - biosignalEMG-2.0.0/biosignalEMG/R/onoff_bonato.R |only biosignalEMG-2.0.0/biosignalEMG/R/onoff_singlethres.R |only biosignalEMG-2.0.0/biosignalEMG/R/plot.emg.R | 150 +++++++++- biosignalEMG-2.0.0/biosignalEMG/R/print.summary.emg.R | 36 +- biosignalEMG-2.0.0/biosignalEMG/R/rectification.R | 21 - biosignalEMG-2.0.0/biosignalEMG/R/summary.emg.R | 14 biosignalEMG-2.0.0/biosignalEMG/R/syntheticemg.R |only biosignalEMG-2.0.0/biosignalEMG/R/whitening.R |only biosignalEMG-2.0.0/biosignalEMG/data |only biosignalEMG-2.0.0/biosignalEMG/inst |only biosignalEMG-2.0.0/biosignalEMG/man/as.emg.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/biosignalEMG-internal.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/biosignalEMG-package.Rd | 48 +-- biosignalEMG-2.0.0/biosignalEMG/man/dcbiasremoval.Rd | 35 +- biosignalEMG-2.0.0/biosignalEMG/man/eaemg.Rd | 58 ++- biosignalEMG-2.0.0/biosignalEMG/man/emg.Rd | 44 +- biosignalEMG-2.0.0/biosignalEMG/man/emg95306000.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/emg96627009.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/envelope.Rd | 66 ++-- biosignalEMG-2.0.0/biosignalEMG/man/extractchannel.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/highpass.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/iemg.Rd | 30 +- biosignalEMG-2.0.0/biosignalEMG/man/integration.Rd | 64 ++-- biosignalEMG-2.0.0/biosignalEMG/man/loadABF1.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/movingaverage.Rd | 43 +- biosignalEMG-2.0.0/biosignalEMG/man/onoff_bonato.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/onoff_quality-measures.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/onoff_singlethres.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/print.summary.eaemg.Rd | 19 - biosignalEMG-2.0.0/biosignalEMG/man/print.summary.emg.Rd | 12 biosignalEMG-2.0.0/biosignalEMG/man/rectification.Rd | 53 +-- biosignalEMG-2.0.0/biosignalEMG/man/syntheticemg.Rd |only biosignalEMG-2.0.0/biosignalEMG/man/whitening.Rd |only 61 files changed, 607 insertions(+), 347 deletions(-)
Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.3 dated 2015-06-24 and 0.4 dated 2015-08-04
DESCRIPTION | 10 - MD5 | 28 +-- NAMESPACE | 9 - R/MetaLandSim.GUI.R | 2 R/range_raster.R | 128 ++++++--------- inst/CITATION | 9 - inst/doc/MetaLandSim.pdf |binary inst/doc/landscape_simulation.pdf |binary inst/doc/parametrization.pdf |binary inst/doc/range_expansion.Rnw | 5 inst/doc/range_expansion.pdf |binary inst/examples/landmask.asc | 318 +++++++++++++++----------------------- man/MetaLandSim-package.Rd | 4 man/range_raster.Rd | 12 - vignettes/range_expansion.Rnw | 5 15 files changed, 234 insertions(+), 296 deletions(-)
Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <agnieszka.krol@isped.u-bordeaux2.fr>
Diff between SemiMarkov versions 1.4.1 dated 2015-04-10 and 1.4.2 dated 2015-08-04
DESCRIPTION | 11 - MD5 | 15 +- NAMESPACE | 3 R/SemiMarkov.r | 325 +++++++++++++++++++++++++++++++++++++++++------------ inst |only man/hazard.Rd | 48 ++++--- man/param.init.Rd | 9 - man/plot.hazard.Rd | 38 +++--- man/semiMarkov.Rd | 58 +++++---- 9 files changed, 356 insertions(+), 151 deletions(-)
Title: Hierarchical Modeling and Frequency Method Checking on
Overdispersed Gaussian, Poisson, and Binomial Data
Description: We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>
Diff between Rgbp versions 1.0.9 dated 2015-07-27 and 1.1.0 dated 2015-08-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/br.R | 18 +++++++++--------- R/coverage.R | 1 + R/pr.R | 10 +++++----- man/coverage.Rd | 6 ++++++ 6 files changed, 30 insertions(+), 23 deletions(-)
Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre],
Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>
Diff between rDEA versions 1.2-1 dated 2015-06-20 and 1.2-2 dated 2015-08-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + inst/CHANGELOG | 4 ++++ man/dea_env_robust.Rd | 2 +- man/dea_robust.Rd | 2 +- man/rts_test.Rd | 2 +- 7 files changed, 17 insertions(+), 12 deletions(-)
Title: R Commander Miscellaneous Functions
Description:
Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between RcmdrMisc versions 1.0-2 dated 2014-09-04 and 1.0-3 dated 2015-08-04
DESCRIPTION | 15 ++++---- MD5 | 14 +++++-- NAMESPACE | 13 +++++-- NEWS | 13 ++++++- R/Barplot.R |only R/Dotplot.R |only R/rcorr.adjust.R | 100 ++++++++++++++++++++++++++++--------------------------- R/readXL.R |only man/Barplot.Rd |only man/Dotplot.Rd |only man/readXL.Rd |only 11 files changed, 92 insertions(+), 63 deletions(-)
Title: Performance Analysis and Companion Functions for Accuracy
Improvement for Binary Classification Problems
Description: Provides companion function for analysing the performance of classification models. Also, provides function to optimise probability cut-off score based on used specified objectives, Plot 'ROC' Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, etc to aid accuracy improvement in binary classification models.
Author: Selva Prabhakaran
Maintainer: Selva Prabhakaran <selva86@gmail.com>
Diff between InformationValue versions 1.0.1 dated 2015-07-31 and 1.1.0 dated 2015-08-04
DESCRIPTION | 16 ++++++------ MD5 | 11 +++++--- NAMESPACE | 2 + R/Main.R | 67 +++++++++++++++++++++++++++++++++++++++++++++++---- R/StandAloneFuncs.R |only README.md |only man/misClassError.Rd | 2 - man/optimalCutoff.Rd |only 8 files changed, 81 insertions(+), 17 deletions(-)
More information about InformationValue at CRAN
Permanent link
Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.7 dated 2014-05-29 and 0.9.4 dated 2015-08-04
DESCRIPTION | 13 - MD5 | 49 +++- NAMESPACE | 9 R/internal.R |only R/matchtools.R | 134 +++++++++++++ R/memtools.R | 233 ++++++++++++++++++++++- R/mixtools.R | 4 R/plottools.R | 502 +++++++++++++++++++++++++++++++++++++++++++++++--- build |only data/orxlong.rda |only data/orxwide.rda |only data/vcaplong.rda |binary inst |only man/figures |only man/hamlet-package.Rd | 15 - man/hmap.Rd | 136 ++++++++++++- man/hmap.annotate.Rd |only man/hmap.key.Rd |only man/match.allocate.Rd | 2 man/match.bb.Rd | 2 man/match.dummy.Rd | 2 man/match.ga.Rd |only man/mem.powersimu.Rd |only man/mixplot.Rd | 22 +- man/orxlong.Rd |only man/orxwide.Rd |only man/vcaplong.Rd | 6 man/vcapwide.Rd | 3 vignettes |only 29 files changed, 1038 insertions(+), 94 deletions(-)
Title: Testing Goodness-of-Fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on a kernel smoothing of the data.
Author: Jose M. Pavia
Maintainer: Jose M. Pavia <Jose.M.Pavia@uv.es>
Diff between GoFKernel versions 2.0-5 dated 2014-12-03 and 2.0-6 dated 2015-08-04
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 2 +- R/GoFKernel.r | 4 ++-- inst |only man/GoFKernel-package.Rd | 6 +++--- man/dgeometric.test.Rd | 2 +- man/fan.test.Rd | 3 ++- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.3.2 dated 2015-06-18 and 1.4.2 dated 2015-08-04
crunch-1.3.2/crunch/R/graft.R |only crunch-1.3.2/crunch/man/cloneDataset.Rd |only crunch-1.3.2/crunch/man/graftDataset.Rd |only crunch-1.3.2/crunch/tests/testthat/test-appending.R.orig |only crunch-1.3.2/crunch/tests/testthat/test-graft.R |only crunch-1.4.2/crunch/DESCRIPTION | 10 crunch-1.4.2/crunch/MD5 | 119 +++--- crunch-1.4.2/crunch/NAMESPACE | 22 - crunch-1.4.2/crunch/R/AllClasses.R | 2 crunch-1.4.2/crunch/R/AllGenerics.R | 7 crunch-1.4.2/crunch/R/api.R | 24 - crunch-1.4.2/crunch/R/append-dataset.R | 2 crunch-1.4.2/crunch/R/auth.R | 19 crunch-1.4.2/crunch/R/batches.R | 16 crunch-1.4.2/crunch/R/category.R | 25 - crunch-1.4.2/crunch/R/crest.R | 6 crunch-1.4.2/crunch/R/cube-query.R | 1 crunch-1.4.2/crunch/R/cube-result.R | 1 crunch-1.4.2/crunch/R/dataset-catalog.R | 2 crunch-1.4.2/crunch/R/dataset-extract.R | 10 crunch-1.4.2/crunch/R/dataset.R | 4 crunch-1.4.2/crunch/R/join-dataset.R | 4 crunch-1.4.2/crunch/R/misc.R | 10 crunch-1.4.2/crunch/R/new-dataset.R | 1 crunch-1.4.2/crunch/R/shoji.R | 15 crunch-1.4.2/crunch/R/show.R | 192 ++++++---- crunch-1.4.2/crunch/R/subvariables.R | 2 crunch-1.4.2/crunch/R/teams.R | 2 crunch-1.4.2/crunch/R/univariate.R | 10 crunch-1.4.2/crunch/R/user.R | 17 crunch-1.4.2/crunch/R/variable-order.R | 40 -- crunch-1.4.2/crunch/R/variable-summary.R | 13 crunch-1.4.2/crunch/R/variable-to-R.R | 13 crunch-1.4.2/crunch/R/variable-type.R | 41 -- crunch-1.4.2/crunch/R/versions.R |only crunch-1.4.2/crunch/build/vignette.rds |binary crunch-1.4.2/crunch/inst/doc/analyze.html | 6 crunch-1.4.2/crunch/inst/doc/variables.html | 6 crunch-1.4.2/crunch/man/describe-catalog.Rd | 12 crunch-1.4.2/crunch/man/restoreVersion.Rd |only crunch-1.4.2/crunch/man/saveVersion.Rd |only crunch-1.4.2/crunch/man/show-crunch.Rd | 20 - crunch-1.4.2/crunch/man/versions.Rd |only crunch-1.4.2/crunch/tests/testthat/api/accounts/account1/users.json | 12 crunch-1.4.2/crunch/tests/testthat/api/datasets/dataset1.json | 1 crunch-1.4.2/crunch/tests/testthat/api/datasets/dataset1/savepoints.json |only crunch-1.4.2/crunch/tests/testthat/api/teams/team1/members.json | 4 crunch-1.4.2/crunch/tests/testthat/helper.R | 63 ++- crunch-1.4.2/crunch/tests/testthat/test-api.R | 10 crunch-1.4.2/crunch/tests/testthat/test-append-arrays.R | 8 crunch-1.4.2/crunch/tests/testthat/test-append-conflicts.R | 24 - crunch-1.4.2/crunch/tests/testthat/test-appending.R | 12 crunch-1.4.2/crunch/tests/testthat/test-auth.R | 17 crunch-1.4.2/crunch/tests/testthat/test-dataset.R | 19 crunch-1.4.2/crunch/tests/testthat/test-get-datasets.R | 6 crunch-1.4.2/crunch/tests/testthat/test-make-array.R | 6 crunch-1.4.2/crunch/tests/testthat/test-misc.R | 26 - crunch-1.4.2/crunch/tests/testthat/test-new-dataset.R | 20 - crunch-1.4.2/crunch/tests/testthat/test-subvariables.R | 33 + crunch-1.4.2/crunch/tests/testthat/test-teams.R | 2 crunch-1.4.2/crunch/tests/testthat/test-update-array.R |only crunch-1.4.2/crunch/tests/testthat/test-update-errors.R |only crunch-1.4.2/crunch/tests/testthat/test-update.R | 52 -- crunch-1.4.2/crunch/tests/testthat/test-user.R | 29 + crunch-1.4.2/crunch/tests/testthat/test-variable-type.R | 2 crunch-1.4.2/crunch/tests/testthat/test-variables.R | 14 crunch-1.4.2/crunch/tests/testthat/test-versioning.R |only 67 files changed, 505 insertions(+), 529 deletions(-)
Title: Statistical Tests for Evaluating Conformity to Benford's Law
Description: Several specialized statistical tests and support functions
for determining if numerical data could conform to Benford's law.
Author: Dieter William Joenssen [aut, cre, cph],
Thomas Muellerleile [ctb]
Maintainer: Dieter William Joenssen <Dieter.Joenssen@googlemail.com>
Diff between BenfordTests versions 1.1.1 dated 2013-11-04 and 1.2.0 dated 2015-08-04
DESCRIPTION | 21 +++---- MD5 | 41 +++++++------- NAMESPACE | 4 + NEWS | 35 ++++++++---- R/Benford_tests.R | 123 +++++++++++++++++++++++++++++++++++++++++++- man/BenfordTests-package.Rd | 30 +++++----- man/chisq.benftest.Rd | 2 man/edist.benftest.Rd | 4 - man/jointdigit.benftest.Rd |only man/jpsq.benftest.Rd | 4 - man/ks.benftest.Rd | 2 man/mdist.benftest.Rd | 4 - man/meandigit.benftest.Rd | 2 man/pbenf.Rd | 2 man/qbenf.Rd | 2 man/rbenf.Rd | 2 man/signifd.Rd | 2 man/signifd.analysis.Rd | 2 man/signifd.seq.Rd | 2 man/simulateH0.Rd | 2 man/usq.benftest.Rd | 4 - src/NULLH_BfT.c | 29 ++++++---- 22 files changed, 231 insertions(+), 88 deletions(-)
Title: A Simple Wrapper for the k-Means Library Yakmo
Description: This is a simple wrapper for the yakmo K-Means library (developed by Naoki Yoshinaga, see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/). It performs fast and robust (orthogonal) K-Means.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>
Diff between yakmoR versions 0.1.0 dated 2015-08-03 and 0.1.1 dated 2015-08-04
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/yakmo.h | 10 +++++++++- 3 files changed, 15 insertions(+), 7 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.200.1.0 dated 2015-06-05 and 0.5.300.4 dated 2015-08-04
ChangeLog | 33 + DESCRIPTION | 10 MD5 | 187 +++--- NAMESPACE | 2 R/RcppArmadillo.package.skeleton.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 24 inst/doc/RcppArmadillo-intro.Rnw | 2 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/examples/kalman/benchmark.R | 2 inst/include/armadillo | 1 inst/include/armadillo_bits/Cube_bones.hpp | 15 inst/include/armadillo_bits/Cube_meat.hpp | 159 +++-- inst/include/armadillo_bits/Mat_bones.hpp | 3 inst/include/armadillo_bits/Mat_meat.hpp | 102 ++- inst/include/armadillo_bits/SpMat_bones.hpp | 45 - inst/include/armadillo_bits/SpMat_meat.hpp | 423 ++++++++++----- inst/include/armadillo_bits/SpSubview_bones.hpp | 38 - inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 6 inst/include/armadillo_bits/arma_boost.hpp | 12 inst/include/armadillo_bits/arma_cmath.hpp | 4 inst/include/armadillo_bits/arma_ostream_meat.hpp | 13 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/arpack_wrapper.hpp | 24 inst/include/armadillo_bits/arrayops_bones.hpp | 14 inst/include/armadillo_bits/arrayops_meat.hpp | 54 + inst/include/armadillo_bits/atlas_wrapper.hpp | 56 - inst/include/armadillo_bits/auxlib_bones.hpp | 12 inst/include/armadillo_bits/auxlib_meat.hpp | 241 ++++++++ inst/include/armadillo_bits/blas_wrapper.hpp | 30 - inst/include/armadillo_bits/constants.hpp | 54 - inst/include/armadillo_bits/constants_compat.hpp | 46 - inst/include/armadillo_bits/debug.hpp | 27 inst/include/armadillo_bits/diagview_meat.hpp | 10 inst/include/armadillo_bits/diskio_meat.hpp | 182 +++--- inst/include/armadillo_bits/fn_as_scalar.hpp | 58 +- inst/include/armadillo_bits/fn_cor.hpp | 4 inst/include/armadillo_bits/fn_cov.hpp | 4 inst/include/armadillo_bits/fn_diagmat.hpp | 16 inst/include/armadillo_bits/fn_elem.hpp | 84 ++ inst/include/armadillo_bits/fn_histc.hpp | 22 inst/include/armadillo_bits/fn_interp1.hpp | 137 ++-- inst/include/armadillo_bits/fn_qz.hpp |only inst/include/armadillo_bits/fn_reshape.hpp | 20 inst/include/armadillo_bits/fn_resize.hpp | 16 inst/include/armadillo_bits/fn_sort_index.hpp | 4 inst/include/armadillo_bits/fn_vectorise.hpp | 2 inst/include/armadillo_bits/glue_histc_bones.hpp | 12 inst/include/armadillo_bits/glue_histc_meat.hpp | 191 ++---- inst/include/armadillo_bits/glue_mixed_meat.hpp | 52 - inst/include/armadillo_bits/lapack_bones.hpp | 18 inst/include/armadillo_bits/lapack_wrapper.hpp | 227 +++++--- inst/include/armadillo_bits/op_all_meat.hpp | 4 inst/include/armadillo_bits/op_any_meat.hpp | 4 inst/include/armadillo_bits/op_cumsum_meat.hpp | 6 inst/include/armadillo_bits/op_max_bones.hpp | 12 inst/include/armadillo_bits/op_max_meat.hpp | 163 ++++- inst/include/armadillo_bits/op_mean_bones.hpp | 10 inst/include/armadillo_bits/op_mean_meat.hpp | 193 +++++- inst/include/armadillo_bits/op_median_meat.hpp | 214 ++++--- inst/include/armadillo_bits/op_min_bones.hpp | 11 inst/include/armadillo_bits/op_min_meat.hpp | 169 ++++- inst/include/armadillo_bits/op_normalise_meat.hpp | 8 inst/include/armadillo_bits/op_prod_meat.hpp | 2 inst/include/armadillo_bits/op_shuffle_meat.hpp | 2 inst/include/armadillo_bits/op_sort_index_meat.hpp | 24 inst/include/armadillo_bits/op_sort_meat.hpp | 12 inst/include/armadillo_bits/op_stddev_meat.hpp | 50 - inst/include/armadillo_bits/op_sum_bones.hpp | 15 inst/include/armadillo_bits/op_sum_meat.hpp | 204 ++++--- inst/include/armadillo_bits/op_var_meat.hpp | 56 + inst/include/armadillo_bits/spdiagview_meat.hpp | 10 inst/include/armadillo_bits/spglue_minus_meat.hpp | 2 inst/include/armadillo_bits/spglue_plus_meat.hpp | 2 inst/include/armadillo_bits/spglue_times_meat.hpp | 11 inst/include/armadillo_bits/spop_htrans_meat.hpp | 2 inst/include/armadillo_bits/spop_max_bones.hpp | 6 inst/include/armadillo_bits/spop_max_meat.hpp | 380 ++++--------- inst/include/armadillo_bits/spop_mean_bones.hpp | 7 inst/include/armadillo_bits/spop_mean_meat.hpp | 199 ++++--- inst/include/armadillo_bits/spop_min_bones.hpp | 6 inst/include/armadillo_bits/spop_min_meat.hpp | 362 +++++------- inst/include/armadillo_bits/spop_misc_bones.hpp | 64 ++ inst/include/armadillo_bits/spop_misc_meat.hpp | 247 +++++++- inst/include/armadillo_bits/spop_strans_meat.hpp | 8 inst/include/armadillo_bits/spop_sum_bones.hpp | 3 inst/include/armadillo_bits/spop_sum_meat.hpp | 70 +- inst/include/armadillo_bits/spop_var_meat.hpp | 57 +- inst/include/armadillo_bits/subview_bones.hpp | 3 inst/include/armadillo_bits/subview_cube_bones.hpp | 5 inst/include/armadillo_bits/subview_cube_meat.hpp | 88 ++- inst/include/armadillo_bits/subview_meat.hpp | 52 + inst/include/armadillo_bits/unwrap_spmat.hpp | 18 vignettes/RcppArmadillo-intro.Rnw | 2 95 files changed, 3503 insertions(+), 1966 deletions(-)
Title: Data Management for Hydrology and Beyond Using the Observations
Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>
Diff between RObsDat versions 15.02 dated 2015-02-27 and 15.08 dated 2015-08-03
RObsDat-15.02/RObsDat/man/restructureDataResult.Rd |only RObsDat-15.08/RObsDat/DESCRIPTION | 10 +++++----- RObsDat-15.08/RObsDat/MD5 | 11 +++++------ RObsDat-15.08/RObsDat/NAMESPACE | 4 ++++ RObsDat-15.08/RObsDat/build/vignette.rds |binary RObsDat-15.08/RObsDat/inst/doc/RObsDat_Einstiegstutorial.pdf |binary RObsDat-15.08/RObsDat/vignettes/RObsDat.bib | 2 +- 7 files changed, 15 insertions(+), 12 deletions(-)
Title: Package Provides Access to Fake User Data
Description: Generates random names with additional information including fake SSNs, gender, location, zip, age, address, and nationality.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>
Diff between randNames versions 0.2 dated 2015-04-28 and 0.2.1 dated 2015-08-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/rand_names.R | 6 +++--- README.md | 6 ++++++ man/rand_names.Rd | 4 ++-- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.3.1 dated 2015-07-07 and 0.4 dated 2015-08-03
ChangeLog | 12 - DESCRIPTION | 12 - MD5 | 75 ++++--- NAMESPACE | 10 - NEWS | 11 - R/0_classesAndMethods.R | 127 ++++++++---- R/1_functions4Fitting.R | 187 ++++++++++--------- R/1_supplementaryPlot.R |only R/2_probabilistic.R | 1 R/5_statisticalTests.R |only R/RcppExports.R | 8 README.md | 3 inst/doc/BayesianInference.pdf |binary inst/doc/CTMC.R | 4 inst/doc/CTMC.Rmd | 6 inst/doc/CTMC.pdf |binary inst/doc/an_introduction_to_markovchain_package.R | 169 ++++++++++------- inst/doc/an_introduction_to_markovchain_package.Rnw | 89 ++++++++- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.Rmd | 6 inst/doc/markovchainCrashIntro.pdf |binary man/ctmcFit.Rd |only man/markovchain-class.Rd | 4 man/markovchain-package.Rd | 4 man/markovchainListFit.Rd | 2 man/multinomialConfidenceIntervals.Rd |only man/verifyMarkovProperty.Rd |only src/1_ctmcFunctions4Fitting.cpp |only src/1_functions4Fitting.cpp | 25 +- src/2_probabilistic.cpp | 4 src/3_multinomCI.cpp | 134 ++++++++++++- src/RcppExports.cpp | 26 ++ tests/testthat/testBasic1.R | 5 tests/testthat/testInference.R |only tests/testthat/testMultinomCI.R | 5 tests/testthat/testPlot.R | 66 ++++-- tests/testthat/testRecurrentClasses.R | 1 tests/testthat/testetm.R |only tests/testthat/testmsm.R |only vignettes/CTMC.Rmd | 6 vignettes/an_introduction_to_markovchain_package.Rnw | 89 ++++++++- vignettes/markovchainBiblio.bib | 27 ++ vignettes/markovchainCrashIntro.Rmd | 6 43 files changed, 799 insertions(+), 325 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between httpuv versions 1.3.2 dated 2014-10-23 and 1.3.3 dated 2015-08-03
DESCRIPTION | 14 +-- MD5 | 36 +++---- NAMESPACE | 3 NEWS | 8 + R/httpuv.R | 8 + man/WebSocket-class.Rd | 3 man/encodeURI.Rd | 3 man/httpuv-package.Rd | 3 man/interrupt.Rd | 3 man/rawToBase64.Rd | 3 man/runServer.Rd | 3 man/service.Rd | 3 man/startDaemonizedServer.Rd | 3 man/startServer.Rd | 3 man/stopDaemonizedServer.Rd | 3 man/stopServer.Rd | 3 src/Makevars | 3 src/RcppExports.cpp | 196 ++++++++++++++++--------------------------- src/http.cpp | 10 +- 19 files changed, 149 insertions(+), 162 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-5 dated 2015-05-22 and 0.1-6 dated 2015-08-03
DESCRIPTION | 11 +++-- MD5 | 14 +++---- NAMESPACE | 33 ++++++++++++++++ R/EvolQG.R | 5 ++ R/ExtendMatrix.R | 2 - R/MatrixStatistics.R | 74 +++++++++++++++++++++++++++++++++---- R/PCAsimilarity.R | 2 - inst/tests/test.MatrixStatistics.r | 28 ++++++++++---- 8 files changed, 139 insertions(+), 30 deletions(-)
Title: Methods for Dimension Reduction for Regression
Description: Functions, methods, and datasets for fitting dimension
reduction regression, using slicing (methods SAVE and SIR), Principal
Hessian Directions (phd, using residuals and the response), and an
iterative IRE. Partial methods, that condition on categorical
predictors are also available. A variety of tests, and stepwise
deletion of predictors, is also included. Also included is
code for computing permutation tests of dimension. Adding additional
methods of estimating dimension is straightforward.
For documentation, see the vignette in the package. With version 3.0.4,
the arguments for dr.step have been modified.
Author: Sanford Weisberg <sandy@umn.edu>,
Maintainer: Sanford Weisberg <sandy@umn.edu>
Diff between dr versions 3.0.9 dated 2014-11-30 and 3.0.10 dated 2015-08-03
DESCRIPTION | 13 +- MD5 | 12 +- NAMESPACE | 9 + NEWS | 4 build/vignette.rds |binary inst/doc/overview.R | 294 +++++++++++++++++++++++++------------------------- inst/doc/overview.pdf |binary 7 files changed, 173 insertions(+), 159 deletions(-)
Title: Split and Recombine Your Data
Description: Sometimes you need to split your data and work on the two chunks independently before bringing them back together. 'Taber' allows you to do that with its two functions.
Author: Seth Wenchel [aut, cre, cph]
Maintainer: Seth Wenchel <seth@wenchel.com>
Diff between taber versions 0.0.1 dated 2015-07-04 and 0.1.0 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++++------ NAMESPACE | 2 ++ NEWS |only R/tabe.R | 50 ++++++++++++++++++++++++++++---------------------- R/zzz.R | 14 +++++++++++++- README.md |only data |only man/clear_stack.Rd |only man/graft.Rd | 20 +++++++++++--------- man/scion.Rd | 13 +++++++------ man/stack_view.Rd |only 12 files changed, 77 insertions(+), 49 deletions(-)
Title: Microsoft Word, Microsoft Powerpoint and HTML Documents
Generation
Description: Create Microsoft Word document (>=2007),
Microsoft Powerpoint document (>=2007) and HTML documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document (*.docx and *.pptx). You can use the package as a tool
for fast reporting and as a tool for reporting automation. The package does
not require any installation of Microsoft product to be able to write
Microsoft files (docx and pptx).
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation),
Dmitry Baranovskiy [ctb, cph] (raphael javascript
libraries)
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between ReporteRs versions 0.7.8 dated 2015-03-06 and 0.8.2 dated 2015-08-03
ReporteRs-0.7.8/ReporteRs/inst/java/ReporteRs-0.7.jar |only ReporteRs-0.7.8/ReporteRs/java/ReporteRs-0.7-src.jar |only ReporteRs-0.8.2/ReporteRs/DESCRIPTION | 10 ReporteRs-0.8.2/ReporteRs/MD5 | 401 +++++----- ReporteRs-0.8.2/ReporteRs/NAMESPACE | 26 ReporteRs-0.8.2/ReporteRs/NEWS | 97 ++ ReporteRs-0.8.2/ReporteRs/R/00_AllGeneric.R | 21 ReporteRs-0.8.2/ReporteRs/R/01_tools.R | 79 + ReporteRs-0.8.2/ReporteRs/R/CodeBlock.R |only ReporteRs-0.8.2/ReporteRs/R/FlexCell.R | 2 ReporteRs-0.8.2/ReporteRs/R/FlexRow.R | 23 ReporteRs-0.8.2/ReporteRs/R/FlexTable.R | 10 ReporteRs-0.8.2/ReporteRs/R/FlexTablePublicAPI.R | 23 ReporteRs-0.8.2/ReporteRs/R/FlexTable_theme.R | 14 ReporteRs-0.8.2/ReporteRs/R/FontMetric.R | 14 ReporteRs-0.8.2/ReporteRs/R/ReporteRs.R | 4 ReporteRs-0.8.2/ReporteRs/R/add.plot.interactivity.R | 153 ++- ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.bsdoc.R |only ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.docx.R |only ReporteRs-0.8.2/ReporteRs/R/addCodeBlock.pptx.R |only 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ReporteRs-0.8.2/ReporteRs/java/ReporteRs-0.8-src.jar |only ReporteRs-0.8.2/ReporteRs/man/BootstrapMenu.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/CodeBlock.Rd |only ReporteRs-0.8.2/ReporteRs/man/DropDownMenu.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/FlexCell.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/FlexRow-alter.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/FlexRow.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/FlexTable-alter.Rd | 4 ReporteRs-0.8.2/ReporteRs/man/FlexTable.Rd | 4 ReporteRs-0.8.2/ReporteRs/man/FontMetric.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/Footnote.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/RScript.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/ReporteRs-package.Rd | 6 ReporteRs-0.8.2/ReporteRs/man/add.plot.interactivity.Rd | 9 ReporteRs-0.8.2/ReporteRs/man/add.pot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addBootstrapMenu.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addCodeBlock.Rd |only ReporteRs-0.8.2/ReporteRs/man/addCodeBlock.bsdoc.Rd |only ReporteRs-0.8.2/ReporteRs/man/addCodeBlock.docx.Rd |only ReporteRs-0.8.2/ReporteRs/man/addCodeBlock.pptx.Rd |only ReporteRs-0.8.2/ReporteRs/man/addColumnBreak.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addColumnBreak.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addDate.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addDate.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addDocument.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addDocument.docx.Rd | 28 ReporteRs-0.8.2/ReporteRs/man/addFlexTable.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFlexTable.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFlexTable.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFlexTable.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFooter.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFooter.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFooter.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addFooterRow.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addHeaderRow.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addIframe.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addIframe.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addImage.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addImage.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addImage.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addImage.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addJavascript.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addLinkItem.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addMarkdown.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addMarkdown.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addMarkdown.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addMarkdown.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPageBreak.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPageBreak.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPageNumber.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPageNumber.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addParagraph.Footnote.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addParagraph.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addParagraph.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addParagraph.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addParagraph.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPlot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPlot.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPlot.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPlot.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addPostCommand.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addRScript.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addRScript.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addRScript.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addRScript.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addSection.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addSection.docx.Rd | 6 ReporteRs-0.8.2/ReporteRs/man/addSlide.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addSlide.pptx.Rd | 6 ReporteRs-0.8.2/ReporteRs/man/addSubtitle.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addSubtitle.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTOC.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTOC.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTOC.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTitle.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTitle.bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTitle.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/addTitle.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.FlexTable.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.FlexTable.sessionInfo.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.html.FlexTable.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.html.RScript.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.html.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/as.html.bsdoc.Rd |only ReporteRs-0.8.2/ReporteRs/man/as.html.pot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/borderDashed.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/borderDotted.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/borderNone.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/borderProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/borderSolid.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/bsdoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/cellProperties.Rd | 8 ReporteRs-0.8.2/ReporteRs/man/chprop.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/chprop.borderProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/chprop.cellProperties.Rd | 8 ReporteRs-0.8.2/ReporteRs/man/chprop.parProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/chprop.textProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/declareTitlesStyles.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/declareTitlesStyles.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/deleteBookmark.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/deleteBookmarkNextContent.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/dim.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/dim.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/doc-list-settings.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/docx-bookmark.Rd | 4 ReporteRs-0.8.2/ReporteRs/man/docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/is.color.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/light.table.Rd | 7 ReporteRs-0.8.2/ReporteRs/man/list_bookmarks.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/parCenter.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/parJustify.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/parLeft.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/parProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/parRight.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/plus-.pot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/pot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/pot_img.Rd |only ReporteRs-0.8.2/ReporteRs/man/pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.FlexTable.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.Footnote.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.bsdoc.Rd | 13 ReporteRs-0.8.2/ReporteRs/man/print.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.pot.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/print.textProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/raphael.html.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/raphael_clicks.Rd |only ReporteRs-0.8.2/ReporteRs/man/raphael_dbclicks.Rd |only ReporteRs-0.8.2/ReporteRs/man/raphael_tooltips.Rd |only ReporteRs-0.8.2/ReporteRs/man/raphael_tracer_off.Rd |only ReporteRs-0.8.2/ReporteRs/man/raphael_tracer_on.Rd |only ReporteRs-0.8.2/ReporteRs/man/registerRaphaelGraph.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/reporters_str_width.Rd |only ReporteRs-0.8.2/ReporteRs/man/setColumnsColors.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/setFlexTableBackgroundColors.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/setFlexTableBorders.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/setFlexTableWidths.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/setRowsColors.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/setZebraStyle.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/set_of_paragraphs.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/slide.layouts.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/slide.layouts.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/spanFlexTableColumns.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/spanFlexTableRows.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/styles.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/styles.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/textBold.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/textBoldItalic.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/textItalic.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/textNormal.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/textProperties.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/text_extract.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/toc.options.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/toc.options.docx.Rd | 4 ReporteRs-0.8.2/ReporteRs/man/triggerPostCommand.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/vanilla.table.Rd | 7 ReporteRs-0.8.2/ReporteRs/man/writeDoc.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/writeDoc.bsdoc.Rd | 8 ReporteRs-0.8.2/ReporteRs/man/writeDoc.docx.Rd | 2 ReporteRs-0.8.2/ReporteRs/man/writeDoc.pptx.Rd | 2 ReporteRs-0.8.2/ReporteRs/src/DOCX.cpp | 222 +++-- ReporteRs-0.8.2/ReporteRs/src/DOCX.h | 3 ReporteRs-0.8.2/ReporteRs/src/PPTX.cpp | 195 +++- ReporteRs-0.8.2/ReporteRs/src/PPTX.h | 3 ReporteRs-0.8.2/ReporteRs/src/RAPHAEL.cpp | 221 ++++- ReporteRs-0.8.2/ReporteRs/src/RAPHAEL.h | 3 ReporteRs-0.8.2/ReporteRs/src/common.cpp | 148 +++ ReporteRs-0.8.2/ReporteRs/src/common.h | 9 ReporteRs-0.8.2/ReporteRs/src/dml_utils.cpp | 37 ReporteRs-0.8.2/ReporteRs/src/dml_utils.h | 4 ReporteRs-0.8.2/ReporteRs/src/raphael_utils.cpp | 17 ReporteRs-0.8.2/ReporteRs/src/raphael_utils.h | 1 ReporteRs-0.8.2/ReporteRs/src/utils.cpp | 59 + 213 files changed, 1722 insertions(+), 804 deletions(-)
Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.1 dated 2014-06-24 and 2.7 dated 2015-08-03
DESCRIPTION | 21 ++++++++++++--------- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/pedgene.R | 32 +++++++++++++++++++++++++++----- R/pedgene.stats.R | 13 ++++++++++--- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ man/pedgene.Rd | 14 +++++++++++--- tests/test.pedgene.expanded.R | 10 ++++++++++ tests/test.pedgene.expanded.Rout.save | 26 ++++++++++++++++++++++---- 10 files changed, 111 insertions(+), 33 deletions(-)
Title: Pedigree Functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe
family relationships such as kinship and identity-by-descent, which
can be used to model family data in mixed effects models, such as in the
coxme function. Also includes a tool for pedigree drawing which is
focused on producing compact layouts without intervention. Recent additions
include utilities to trim the pedigree object with various criteria, and
kinship for the X chromosome.
Author: Terry M Therneau [aut],
Schaid Daniel [ctb],
Jason Sinnwell [aut, cre],
Elizabeth Atkinson [ctb]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between kinship2 versions 1.6.0 dated 2014-07-22 and 1.6.4 dated 2015-08-03
kinship2-1.6.0/kinship2/noweb/all.pdf |only kinship2-1.6.4/kinship2/DESCRIPTION | 29 kinship2-1.6.4/kinship2/MD5 | 33 kinship2-1.6.4/kinship2/NAMESPACE | 9 kinship2-1.6.4/kinship2/R/kinship.R | 7 kinship2-1.6.4/kinship2/R/pedigree.R | 63 + kinship2-1.6.4/kinship2/build/vignette.rds |binary kinship2-1.6.4/kinship2/inst/NEWS.Rd | 8 kinship2-1.6.4/kinship2/man/pedigree.Rd | 15 kinship2-1.6.4/kinship2/noweb/all.aux | 19 kinship2-1.6.4/kinship2/noweb/all.log | 586 +++++++++++++-- kinship2-1.6.4/kinship2/noweb/all.nw | 86 +- kinship2-1.6.4/kinship2/noweb/all.tex | 1036 +++++++++++++++++---------- kinship2-1.6.4/kinship2/noweb/kinship.R |only kinship2-1.6.4/kinship2/noweb/kinship.Rnw | 7 kinship2-1.6.4/kinship2/noweb/pedigree.R |only kinship2-1.6.4/kinship2/noweb/pedigree.Rnw | 79 +- kinship2-1.6.4/kinship2/tests/kin1.Rout.save | 20 kinship2-1.6.4/kinship2/tests/twin.Rout.save | 8 19 files changed, 1447 insertions(+), 558 deletions(-)
Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>
Diff between D3M versions 0.40 dated 2015-08-02 and 0.41 dated 2015-08-03
DESCRIPTION | 8 +- MD5 | 20 ++--- R/RcppExports.R | 4 - R/d3m_main.R | 12 +-- R/d3m_parallel.R | 5 - R/wasser_test.R | 15 +++- man/D3M.Rd | 5 + man/d3m.parallel.Rd | 5 + man/wasser.test.Rd | 10 ++ src/RcppExports.cpp | 7 + src/funcs.cpp | 184 ++++++++++------------------------------------------ 11 files changed, 96 insertions(+), 179 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.36 dated 2015-07-28 and 1.37 dated 2015-08-03
aSPU-1.36/aSPU/R/aSPUM.R |only aSPU-1.36/aSPU/R/aSPUMpath.r |only aSPU-1.36/aSPU/man/aSPUM.Rd |only aSPU-1.36/aSPU/man/aSPUMpath.Rd |only aSPU-1.37/aSPU/DESCRIPTION | 8 +- aSPU-1.37/aSPU/MD5 | 24 ++++---- aSPU-1.37/aSPU/NAMESPACE | 4 - aSPU-1.37/aSPU/R/aSPUs.R |only aSPU-1.37/aSPU/R/aSPUsPath.r |only aSPU-1.37/aSPU/R/aSPUwpermC.R | 1 aSPU-1.37/aSPU/build/vignette.rds |binary aSPU-1.37/aSPU/inst/doc/aSPUstat.R | 6 +- aSPU-1.37/aSPU/inst/doc/aSPUstat.Rmd | 33 +++++------- aSPU-1.37/aSPU/inst/doc/aSPUstat.html | 93 ++++++++++++++-------------------- aSPU-1.37/aSPU/man/aSPUs.Rd |only aSPU-1.37/aSPU/man/aSPUsPath.Rd |only aSPU-1.37/aSPU/vignettes/aSPUstat.Rmd | 33 +++++------- 17 files changed, 94 insertions(+), 108 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-9 dated 2015-08-02 and 1.0-10 dated 2015-08-03
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/ModisDownload.R | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 2.3-10 dated 2015-07-09 and 2.3-11 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapproj versions 1.2-3 dated 2015-07-09 and 1.2-4 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or
higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapdata versions 2.2-4 dated 2015-07-09 and 2.2-5 dated 2015-08-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Miscellaneous Functions for Math, Plotting, Printing,
Statistics, Strings, and Tools
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
Author: Christian W. Hoffmann <christian@echoffmann.ch> <http://www.echoffmann.ch>
Maintainer: Christian W. Hoffmann <christian@echoffmann.ch>
Diff between cwhmisc versions 5.0 dated 2014-10-15 and 6.0 dated 2015-08-03
cwhmisc-5.0/cwhmisc/R/SetPPT.R |only cwhmisc-5.0/cwhmisc/R/dim.R |only cwhmisc-5.0/cwhmisc/R/heading.R |only cwhmisc-5.0/cwhmisc/R/paste.infix.R |only cwhmisc-5.0/cwhmisc/R/rotL.R |only cwhmisc-5.0/cwhmisc/R/vector.R |only cwhmisc-5.0/cwhmisc/inst/doc/cwhmisc.R |only cwhmisc-5.0/cwhmisc/man/SetPPT.Rd |only cwhmisc-5.0/cwhmisc/man/dim.Rd |only cwhmisc-5.0/cwhmisc/man/figures |only cwhmisc-5.0/cwhmisc/man/heading.Rd |only cwhmisc-5.0/cwhmisc/man/numeric.Rd |only cwhmisc-5.0/cwhmisc/man/paste.infix.Rd |only cwhmisc-5.0/cwhmisc/man/plotSymbol.Rd |only cwhmisc-5.0/cwhmisc/man/rotL.Rd |only cwhmisc-5.0/cwhmisc/man/vector.Rd |only cwhmisc-6.0/cwhmisc/ChangeLog |only cwhmisc-6.0/cwhmisc/DESCRIPTION | 15 - cwhmisc-6.0/cwhmisc/MD5 | 110 ++++++------ cwhmisc-6.0/cwhmisc/NAMESPACE | 4 cwhmisc-6.0/cwhmisc/R/Ddim.R |only cwhmisc-6.0/cwhmisc/R/RCA.R | 63 +++---- cwhmisc-6.0/cwhmisc/R/clocksense.R | 9 - cwhmisc-6.0/cwhmisc/R/const.R | 7 cwhmisc-6.0/cwhmisc/R/coords.R | 98 +++++++++-- cwhmisc-6.0/cwhmisc/R/date.R |only cwhmisc-6.0/cwhmisc/R/dcmpf.R | 2 cwhmisc-6.0/cwhmisc/R/ellipse.R | 15 + cwhmisc-6.0/cwhmisc/R/factor.R | 2 cwhmisc-6.0/cwhmisc/R/frac.R | 8 cwhmisc-6.0/cwhmisc/R/functions.R | 18 +- cwhmisc-6.0/cwhmisc/R/lpr.R | 7 cwhmisc-6.0/cwhmisc/R/n2c.R | 8 cwhmisc-6.0/cwhmisc/R/operators.R |only cwhmisc-6.0/cwhmisc/R/plt.R | 4 cwhmisc-6.0/cwhmisc/README | 3 cwhmisc-6.0/cwhmisc/build/vignette.rds |binary cwhmisc-6.0/cwhmisc/inst/doc/SplomT.pdf |only cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc-Scw.pdf |only cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc.Rnw | 228 ++++++++++++-------------- cwhmisc-6.0/cwhmisc/inst/doc/cwhmisc.pdf |binary cwhmisc-6.0/cwhmisc/man/Ddim.Rd |only cwhmisc-6.0/cwhmisc/man/FinneyCorr.Rd | 2 cwhmisc-6.0/cwhmisc/man/RCA.Rd | 27 +-- cwhmisc-6.0/cwhmisc/man/astroC.Rd | 4 cwhmisc-6.0/cwhmisc/man/astroGeo.Rd | 2 cwhmisc-6.0/cwhmisc/man/const.Rd | 18 +- cwhmisc-6.0/cwhmisc/man/coords.Rd | 102 +++++++++-- cwhmisc-6.0/cwhmisc/man/cwhmisc-internal.Rd |only cwhmisc-6.0/cwhmisc/man/cwhmisc-package.Rd | 27 ++- cwhmisc-6.0/cwhmisc/man/date.Rd |only cwhmisc-6.0/cwhmisc/man/dcmpf.Rd | 4 cwhmisc-6.0/cwhmisc/man/delayt.Rd | 2 cwhmisc-6.0/cwhmisc/man/digits.Rd | 5 cwhmisc-6.0/cwhmisc/man/ellipse.Rd | 22 +- cwhmisc-6.0/cwhmisc/man/f.log.Rd | 6 cwhmisc-6.0/cwhmisc/man/factor.Rd | 3 cwhmisc-6.0/cwhmisc/man/format.fix.Rd | 1 cwhmisc-6.0/cwhmisc/man/functions.Rd | 23 ++ cwhmisc-6.0/cwhmisc/man/grepnot.Rd | 19 -- cwhmisc-6.0/cwhmisc/man/int2.Rd | 5 cwhmisc-6.0/cwhmisc/man/lpr.Rd | 11 - cwhmisc-6.0/cwhmisc/man/n2c.Rd | 3 cwhmisc-6.0/cwhmisc/man/numer.Rd |only cwhmisc-6.0/cwhmisc/man/operators.Rd |only cwhmisc-6.0/cwhmisc/man/plotSymbols.Rd |only cwhmisc-6.0/cwhmisc/man/plt.Rd | 7 cwhmisc-6.0/cwhmisc/man/replacechar.Rd | 3 cwhmisc-6.0/cwhmisc/vignettes/SplomT.pdf |only cwhmisc-6.0/cwhmisc/vignettes/cwhmisc-Scw.pdf |only cwhmisc-6.0/cwhmisc/vignettes/cwhmisc.Rnw | 228 ++++++++++++-------------- 71 files changed, 633 insertions(+), 492 deletions(-)
Title: Multivariate Curve Resolution Alternating Least Squares
(MCR-ALS)
Description: Alternating least squares is often used to resolve
components contributing to data with a bilinear structure; the
basic technique may be extended to alternating constrained
least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components.
Several data matrices may be decomposed simultaneously by
assuming that one of the two matrices in the bilinear
decomposition is shared between datasets.
Author: Katharine M. Mullen
Maintainer: Katharine Mullen <mullenkate@gmail.com>
Diff between ALS versions 0.0.5 dated 2012-07-02 and 0.0.6 dated 2015-08-03
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 8 ++++++++ NEWS | 4 ++++ R/getC.R | 4 ++-- R/getCList.R | 4 ++-- R/getS.R | 4 ++-- inst |only man/als.Rd | 4 ++-- 9 files changed, 33 insertions(+), 19 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.5.0 dated 2015-04-15 and 1.0.6.0 dated 2015-08-03
ggtern-1.0.5.0/ggtern/R/geom-density2d.R |only ggtern-1.0.5.0/ggtern/R/stat-density-2d.R |only ggtern-1.0.5.0/ggtern/man/geom_density2d.Rd |only ggtern-1.0.5.0/ggtern/man/geom_smooth.Rd |only ggtern-1.0.5.0/ggtern/man/stat_density2d.Rd |only ggtern-1.0.5.0/ggtern/man/stat_smooth.Rd |only ggtern-1.0.6.0/ggtern/DESCRIPTION | 29 +- ggtern-1.0.6.0/ggtern/MD5 | 180 +++++++++-------- ggtern-1.0.6.0/ggtern/NAMESPACE | 18 + ggtern-1.0.6.0/ggtern/NEWS | 11 + ggtern-1.0.6.0/ggtern/R/clip-polygons.R |only ggtern-1.0.6.0/ggtern/R/coord-tern.R | 110 +++++----- ggtern-1.0.6.0/ggtern/R/geom-confidence.R | 52 +--- ggtern-1.0.6.0/ggtern/R/geom-density-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-errorbarT.R | 6 ggtern-1.0.6.0/ggtern/R/geom-interpolate-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-polygon-tern.R |only ggtern-1.0.6.0/ggtern/R/geom-smooth.R | 10 ggtern-1.0.6.0/ggtern/R/gg-internal.R | 4 ggtern-1.0.6.0/ggtern/R/ggtern-build.R | 26 +- ggtern-1.0.6.0/ggtern/R/onLoad.R | 6 ggtern-1.0.6.0/ggtern/R/panel.R | 1 ggtern-1.0.6.0/ggtern/R/plot-construction.R | 36 +-- ggtern-1.0.6.0/ggtern/R/scales.R | 15 + ggtern-1.0.6.0/ggtern/R/stat-density-tern.R |only ggtern-1.0.6.0/ggtern/R/stat-interpolate-tern.R |only ggtern-1.0.6.0/ggtern/R/stat-smooth.R | 10 ggtern-1.0.6.0/ggtern/R/statnew.R | 12 - ggtern-1.0.6.0/ggtern/R/strip-unapproved.R | 26 +- ggtern-1.0.6.0/ggtern/R/tern-render.R | 114 ++++++---- ggtern-1.0.6.0/ggtern/R/theme-defaults.R | 117 +++++------ ggtern-1.0.6.0/ggtern/R/theme-novar-tern.R |only ggtern-1.0.6.0/ggtern/R/theme.R | 1 ggtern-1.0.6.0/ggtern/R/utilities-help.R | 8 ggtern-1.0.6.0/ggtern/R/utilities.R | 123 ++++++++++- ggtern-1.0.6.0/ggtern/build/partial.rdb |binary ggtern-1.0.6.0/ggtern/man/aes.Rd | 17 - ggtern-1.0.6.0/ggtern/man/approved_geometries.Rd | 10 ggtern-1.0.6.0/ggtern/man/clipPolygons.Rd |only ggtern-1.0.6.0/ggtern/man/convenience_functions.Rd | 52 ++-- ggtern-1.0.6.0/ggtern/man/coord.Rd | 32 +-- ggtern-1.0.6.0/ggtern/man/coord_tern.Rd | 74 +++--- ggtern-1.0.6.0/ggtern/man/data.Rd | 9 ggtern-1.0.6.0/ggtern/man/data_Feldspar.Rd | 5 ggtern-1.0.6.0/ggtern/man/data_USDA.Rd | 12 - ggtern-1.0.6.0/ggtern/man/element_ternary.Rd | 61 ++--- ggtern-1.0.6.0/ggtern/man/enforceTernaryCoordinates.Rd |only ggtern-1.0.6.0/ggtern/man/expandRange.Rd |only ggtern-1.0.6.0/ggtern/man/expandTern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_TLRline.Rd | 85 +++----- ggtern-1.0.6.0/ggtern/man/geom_density_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_errorbarTLR.Rd | 63 ++--- ggtern-1.0.6.0/ggtern/man/geom_interpolate_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_polygon_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geom_segment.Rd | 48 ++-- ggtern-1.0.6.0/ggtern/man/geom_smooth_tern.Rd |only ggtern-1.0.6.0/ggtern/man/geomconfidence.Rd | 57 ++--- ggtern-1.0.6.0/ggtern/man/ggplot_build.Rd | 17 - ggtern-1.0.6.0/ggtern/man/ggplot_gtable.Rd | 22 +- ggtern-1.0.6.0/ggtern/man/ggsave.Rd | 51 ++-- ggtern-1.0.6.0/ggtern/man/ggtern-labels.Rd | 65 ++---- ggtern-1.0.6.0/ggtern/man/ggtern-package.Rd | 133 +++++------- ggtern-1.0.6.0/ggtern/man/ggtern.Rd | 21 - ggtern-1.0.6.0/ggtern/man/ggtern.multi.Rd | 39 +-- ggtern-1.0.6.0/ggtern/man/iflasttern.Rd | 10 ggtern-1.0.6.0/ggtern/man/kde2d.weighted.Rd | 36 ++- ggtern-1.0.6.0/ggtern/man/logratio.Rd | 28 +- ggtern-1.0.6.0/ggtern/man/mahalanobis.Rd | 15 - ggtern-1.0.6.0/ggtern/man/notransform.Rd | 11 - ggtern-1.0.6.0/ggtern/man/overloaded.Rd | 157 ++++++-------- ggtern-1.0.6.0/ggtern/man/point.in.sequence.Rd | 42 +-- ggtern-1.0.6.0/ggtern/man/print.Rd | 16 - ggtern-1.0.6.0/ggtern/man/scale_TLR_continuous.Rd | 39 +-- ggtern-1.0.6.0/ggtern/man/showhidegrid.Rd | 41 +-- ggtern-1.0.6.0/ggtern/man/stat_density_tern.Rd |only ggtern-1.0.6.0/ggtern/man/stat_interpolate_tern.Rd |only ggtern-1.0.6.0/ggtern/man/stat_smooth_tern.Rd |only ggtern-1.0.6.0/ggtern/man/strip_unapproved.Rd | 15 - ggtern-1.0.6.0/ggtern/man/suffix_arrow.Rd | 31 +- ggtern-1.0.6.0/ggtern/man/suppressColours.Rd |only ggtern-1.0.6.0/ggtern/man/ternLimitsForCoord.Rd |only ggtern-1.0.6.0/ggtern/man/tern_dep.Rd | 43 +--- ggtern-1.0.6.0/ggtern/man/tern_limits.Rd | 26 -- ggtern-1.0.6.0/ggtern/man/tern_stop.Rd | 9 ggtern-1.0.6.0/ggtern/man/ternary_transformations.Rd | 106 +++------- ggtern-1.0.6.0/ggtern/man/theme_arrowbaseline.Rd | 16 - ggtern-1.0.6.0/ggtern/man/theme_bw.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_classic.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_clockwise.Rd | 10 ggtern-1.0.6.0/ggtern/man/theme_complete.Rd | 22 -- ggtern-1.0.6.0/ggtern/man/theme_custom.Rd | 20 - ggtern-1.0.6.0/ggtern/man/theme_elements.Rd | 49 +--- ggtern-1.0.6.0/ggtern/man/theme_gray.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_minimal.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_novar_tern.Rd |only ggtern-1.0.6.0/ggtern/man/theme_rgbg.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_rgbw.Rd | 9 ggtern-1.0.6.0/ggtern/man/theme_showlabels.Rd | 12 - ggtern-1.0.6.0/ggtern/man/theme_showprimary.Rd | 56 +---- ggtern-1.0.6.0/ggtern/man/theme_showtitles.Rd | 10 ggtern-1.0.6.0/ggtern/man/themearrowlength.Rd | 79 ++----- ggtern-1.0.6.0/ggtern/man/themeshowhidearrows.Rd | 11 - ggtern-1.0.6.0/ggtern/man/themeticksoutside.Rd | 9 ggtern-1.0.6.0/ggtern/man/undoCartesian.Rd |only ggtern-1.0.6.0/ggtern/man/undocumented.Rd | 128 ++++-------- 105 files changed, 1392 insertions(+), 1497 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for z-identifiability, transportability, z-transportability and meta-transportability of causal effects by Elias Bareinboim and Judea Pearl. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.1.3 dated 2015-06-30 and 1.2.0 dated 2015-08-03
causaleffect-1.1.3/causaleffect/R/getNonIgnorableNodes.probability.R |only causaleffect-1.1.3/causaleffect/R/organizeTerms.probability.R |only causaleffect-1.2.0/causaleffect/DESCRIPTION | 14 +- causaleffect-1.2.0/causaleffect/MD5 | 48 ++++++--- causaleffect-1.2.0/causaleffect/NAMESPACE | 2 causaleffect-1.2.0/causaleffect/NEWS | 5 - causaleffect-1.2.0/causaleffect/R/activate.interventions.R |only causaleffect-1.2.0/causaleffect/R/causal.effect.R | 17 ++- causaleffect-1.2.0/causaleffect/R/get.expression.R | 29 +++-- causaleffect-1.2.0/causaleffect/R/getNonIgnorableNodes.R | 8 + causaleffect-1.2.0/causaleffect/R/id.R | 7 - causaleffect-1.2.0/causaleffect/R/idc.R | 4 causaleffect-1.2.0/causaleffect/R/meta.transport.R |only causaleffect-1.2.0/causaleffect/R/observed.graph.R | 2 causaleffect-1.2.0/causaleffect/R/organizeTerms.R | 17 +++ causaleffect-1.2.0/causaleffect/R/probability.R | 4 causaleffect-1.2.0/causaleffect/R/sc.components.R |only causaleffect-1.2.0/causaleffect/R/sid.R |only causaleffect-1.2.0/causaleffect/R/simplify.expression.R |only causaleffect-1.2.0/causaleffect/R/simplify.meta.expression.R |only causaleffect-1.2.0/causaleffect/R/transport.R |only causaleffect-1.2.0/causaleffect/R/trz.R |only causaleffect-1.2.0/causaleffect/R/unobserved.graph.R | 4 causaleffect-1.2.0/causaleffect/R/usid.R |only causaleffect-1.2.0/causaleffect/R/zid.R |only causaleffect-1.2.0/causaleffect/R/zzaux.effect.R |only causaleffect-1.2.0/causaleffect/man/causal.effect.Rd | 9 + causaleffect-1.2.0/causaleffect/man/causaleffect-package.Rd | 50 +++++++--- causaleffect-1.2.0/causaleffect/man/get.expression.Rd | 7 - causaleffect-1.2.0/causaleffect/man/meta.transport.Rd |only causaleffect-1.2.0/causaleffect/man/parse.graphml.Rd | 8 - causaleffect-1.2.0/causaleffect/man/transport.Rd |only causaleffect-1.2.0/causaleffect/man/zzaux.effect.Rd |only 33 files changed, 151 insertions(+), 84 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.5 dated 2015-06-30 and 1.8.3 dated 2015-08-02
forestFloor-1.5/forestFloor/man/show3d_new.Rd |only forestFloor-1.8.3/forestFloor/DESCRIPTION | 12 forestFloor-1.8.3/forestFloor/MD5 | 54 forestFloor-1.8.3/forestFloor/NAMESPACE | 47 forestFloor-1.8.3/forestFloor/R/RcppExports.R | 4 forestFloor-1.8.3/forestFloor/R/append.overwrite.alists.R |only forestFloor-1.8.3/forestFloor/R/as.numeric.factor.R |only forestFloor-1.8.3/forestFloor/R/box.outliers.R |only forestFloor-1.8.3/forestFloor/R/convolute_ff.R |only forestFloor-1.8.3/forestFloor/R/convolute_ff2.R |only forestFloor-1.8.3/forestFloor/R/fcol.R |only forestFloor-1.8.3/forestFloor/R/forestFloor_multiClass.R |only forestFloor-1.8.3/forestFloor/R/forestFloor_source.R | 804 +--------- forestFloor-1.8.3/forestFloor/R/ggPlotForestFloor.R |only forestFloor-1.8.3/forestFloor/R/plot.forestFloor_multiClass.R |only forestFloor-1.8.3/forestFloor/R/plot.forestFloor_regression.R |only forestFloor-1.8.3/forestFloor/R/plot_simplex3.R |only forestFloor-1.8.3/forestFloor/R/print.forestFloor_regression.R |only forestFloor-1.8.3/forestFloor/R/show3d.R |only forestFloor-1.8.3/forestFloor/R/vec.plot.R |only forestFloor-1.8.3/forestFloor/man/as.numeric.factor.Rd |only forestFloor-1.8.3/forestFloor/man/convolute_ff.Rd | 2 forestFloor-1.8.3/forestFloor/man/convolute_ff2.Rd | 12 forestFloor-1.8.3/forestFloor/man/convolute_grid.Rd | 18 forestFloor-1.8.3/forestFloor/man/fcol.Rd | 2 forestFloor-1.8.3/forestFloor/man/forestFloor-package.Rd | 52 forestFloor-1.8.3/forestFloor/man/forestFloor.Rd | 51 forestFloor-1.8.3/forestFloor/man/ggPlotForestFloor.Rd |only forestFloor-1.8.3/forestFloor/man/ggplotGrob.Rd |only forestFloor-1.8.3/forestFloor/man/plot.forestFloor.Rd | 87 - forestFloor-1.8.3/forestFloor/man/plot_simplex3.Rd |only forestFloor-1.8.3/forestFloor/man/print.forestFloor.Rd | 6 forestFloor-1.8.3/forestFloor/man/show3d.Rd |only forestFloor-1.8.3/forestFloor/src/RcppExports.cpp | 25 forestFloor-1.8.3/forestFloor/src/multiClass.cpp |only forestFloor-1.8.3/forestFloor/src/testcpp_rec6.cpp | 346 ++++ forestFloor-1.8.3/forestFloor/tests/ggplotUsage.R |only forestFloor-1.8.3/forestFloor/tests/stdUsage.R | 37 forestFloor-1.8.3/forestFloor/tests/testBinaryClass.R |only forestFloor-1.8.3/forestFloor/tests/testMultiClass.cpp.R |only 40 files changed, 692 insertions(+), 867 deletions(-)
Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>
Diff between D3M versions 0.31 dated 2015-07-29 and 0.40 dated 2015-08-02
D3M-0.31/D3M/R/D3M_main.R |only D3M-0.31/D3M/R/top_D3M.R |only D3M-0.31/D3M/R/wasserMetric_vec.R |only D3M-0.31/D3M/man/d3m.Rd |only D3M-0.40/D3M/DESCRIPTION | 11 - D3M-0.40/D3M/MD5 | 36 ++-- D3M-0.40/D3M/NAMESPACE | 2 D3M-0.40/D3M/R/RcppExports.R | 10 - D3M-0.40/D3M/R/d3m.R |only D3M-0.40/D3M/R/d3m_main.R |only D3M-0.40/D3M/R/d3m_parallel.R | 4 D3M-0.40/D3M/R/top_d3m.R |only D3M-0.40/D3M/R/wasser.R | 4 D3M-0.40/D3M/R/wasser_test.R | 4 D3M-0.40/D3M/R/wasser_vec.R |only D3M-0.40/D3M/man/D3M-package.Rd |only D3M-0.40/D3M/man/D3M.Rd |only D3M-0.40/D3M/man/d3m.parallel.Rd | 4 D3M-0.40/D3M/man/topD3M.Rd | 8 D3M-0.40/D3M/man/wasser.test.Rd | 4 D3M-0.40/D3M/man/wasserMetric.Rd | 4 D3M-0.40/D3M/man/wasserMetric.v.Rd | 6 D3M-0.40/D3M/src/RcppExports.cpp | 23 -- D3M-0.40/D3M/src/funcs.cpp | 306 ++++++++++++++++++++++++++++--------- 24 files changed, 293 insertions(+), 133 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.4.0 dated 2015-07-23 and 0.4.1 dated 2015-08-02
DESCRIPTION | 8 - MD5 | 28 +-- R/internal.postfit.R | 44 +++++ R/internal.prefit.R | 19 +- R/main.R | 35 ++-- R/s3.generics.R | 13 + R/s3.methods.R | 23 +- R/stan.R | 257 +++++++++++++++++++-------------- R/support.export.R | 86 +++++------ man/brm.Rd | 14 + man/brm.pars.Rd | 7 man/brmsfit-class.Rd | 2 man/hypothesis.Rd | 8 - tests/testthat/tests.internal.prefit.R | 6 tests/testthat/tests.stan.R | 41 ++++- 15 files changed, 372 insertions(+), 219 deletions(-)
Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between GeneNet versions 1.2.12 dated 2015-01-20 and 1.2.13 dated 2015-08-02
GeneNet-1.2.12/GeneNet/R/ggm.make.dot.R |only GeneNet-1.2.12/GeneNet/R/ggm.make.igraph.R |only GeneNet-1.2.12/GeneNet/R/ggm.test.edges.R |only GeneNet-1.2.12/GeneNet/man/ggm.make.igraph.Rd |only GeneNet-1.2.12/GeneNet/man/ggm.test.edges.Rd |only GeneNet-1.2.13/GeneNet/DESCRIPTION | 17 +++--- GeneNet-1.2.13/GeneNet/MD5 | 28 ++++----- GeneNet-1.2.13/GeneNet/NAMESPACE | 15 ++--- GeneNet-1.2.13/GeneNet/NEWS | 15 ++++- GeneNet-1.2.13/GeneNet/R/network.make.dot.R |only GeneNet-1.2.13/GeneNet/R/network.make.graph.R |only GeneNet-1.2.13/GeneNet/R/network.test.edges.R |only GeneNet-1.2.13/GeneNet/data/ecoli.rda |binary GeneNet-1.2.13/GeneNet/inst/doc/arabidopsis-net.R | 62 ++++++++++++++++++---- GeneNet-1.2.13/GeneNet/inst/doc/ecoli-net.R | 42 ++++++++------ GeneNet-1.2.13/GeneNet/inst/doc/tcell-net.R | 46 +++++++++++----- GeneNet-1.2.13/GeneNet/man/arth800.Rd | 44 +++++++-------- GeneNet-1.2.13/GeneNet/man/ggm.estimate.pcor.Rd | 2 GeneNet-1.2.13/GeneNet/man/network.make.graph.Rd |only GeneNet-1.2.13/GeneNet/man/network.test.edges.Rd |only 20 files changed, 175 insertions(+), 96 deletions(-)
Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create,
manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.1-4 dated 2015-01-27 and 0.1-6 dated 2015-08-02
DESCRIPTION | 14 MD5 | 30 - NAMESPACE | 73 ++- R/readCookPVI.R | 202 ++++----- R/readUSsenate.R | 180 ++++---- R/readUSstateAbbreviations.R | 178 ++++---- R/testURLs.R | 230 +++++----- man/Interp.Rd | 884 ++++++++++++++++++++-------------------- man/classIndex.Rd | 248 +++++------ man/matchQuote.Rd | 192 ++++---- man/readCookPVI.Rd | 228 +++++----- man/readUSsenate.Rd | 208 ++++----- man/readUSstateAbbreviations.Rd | 120 ++--- man/strsplit1.Rd | 176 +++---- man/subNonStandardCharacters.Rd | 6 man/truncdist.Rd | 585 +++++++++++++------------- 16 files changed, 1800 insertions(+), 1754 deletions(-)
Title: Implementation of the Fourier Amplitude Sensitivity Test (FAST)
Description: The Fourier Amplitude Sensitivity Test (FAST) is a method to determine global sensitivities of a model on parameter changes with relatively few model runs. This package implements this sensitivity analysis method.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>
Diff between fast versions 0.63 dated 2013-07-08 and 0.64 dated 2015-08-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 ++ R/sensitivity.R | 4 ++-- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an
efficient implementation of gradient boosting framework.
This package is its R interface. The package includes efficient
linear model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10 times faster
than existing gradient boosting packages. It supports various
objective functions, including regression, classification and ranking. The
package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen <tianqi.tchen@gmail.com>, Tong He <hetong007@gmail.com>, Michael Benesty <michael@benesty.fr>
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 0.4-1 dated 2015-08-01 and 0.4-2 dated 2015-08-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/discoverYourData.html | 2 +- inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.html | 4 ++-- src/xgboost_R.cpp | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Color-Based Plots for Multivariate Visualization
Description: Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, display a matrix as an array of colors, and draw color keys. Higher-level plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.
Author: Aron C. Eklund
Maintainer: Aron C. Eklund <eklund@cbs.dtu.dk>
Diff between squash versions 1.0.6 dated 2014-08-04 and 1.0.7 dated 2015-08-02
DESCRIPTION | 18 +++++++++--------- MD5 | 11 ++++++----- NAMESPACE | 7 +++---- NEWS | 6 ++++++ README.md |only man/colorgram.Rd | 2 +- man/hist2.Rd | 2 +- 7 files changed, 26 insertions(+), 20 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-3 dated 2012-11-26 and 1.0-9 dated 2015-08-02
DESCRIPTION | 25 +-- MD5 | 42 ++--- NAMESPACE | 17 +- R/ModisDownload.R |only R/extract.R | 314 +++++++++++++++++++++--------------------- R/index.R | 29 ++- R/plot.R | 120 +++++++--------- R/subset.R | 66 ++++---- man/ModisDownload.Rd |only man/RasterStackBrick-class.Rd | 96 ++++++------ man/apply.monthly.Rd | 120 ++++++++-------- man/cellFromXY.Rd | 100 ++++++------- man/endpoints.Rd | 118 +++++++-------- man/extract.Rd | 188 ++++++++++++------------- man/extractIndex.Rd | 186 ++++++++++++------------ man/index.Rd | 92 ++++++------ man/period.apply.Rd | 108 ++++++++------ man/plot.Rd | 209 ++++++++++++++------------- man/read.rts.Rd | 98 ++++++------- man/rts.Rd | 136 +++++++++--------- man/subset.Rd | 136 +++++++++--------- man/subsetIndex.Rd | 110 +++++++------- man/write.rts.Rd | 130 ++++++++--------- 23 files changed, 1238 insertions(+), 1202 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 4.1-1 dated 2015-07-28 and 4.2 dated 2015-08-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++-- R/getProfiles.R | 6 +++++- 4 files changed, 17 insertions(+), 10 deletions(-)
More information about IRISMustangMetrics at CRAN
Permanent link
Title: Forecasting Time Series by Theta Method
Description: Routines for forecasting univariate time series using Theta Method and Optimised Theta Method (Fioruci et al, 2015). Contains several cross-validation routines.
Author: Jose Augusto Fioruci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fioruci <jafioruci@gmail.com>
Diff between forecTheta versions 1.0 dated 2015-04-15 and 1.1 dated 2015-08-02
ChangeLog |only DESCRIPTION | 12 +++++++----- MD5 | 11 ++++++----- NAMESPACE | 1 + R/forecastFunctions.R | 33 +++++++++++++++++++++++++++------ man/forecTheta-package.Rd | 4 ++-- man/forecastFunctions.Rd | 39 ++++++++++++++++++++++----------------- 7 files changed, 65 insertions(+), 35 deletions(-)
Title: Descriptive Statistics
Description: Weighted frequency and contingency tables of categorical
variables and of the comparison of the mean value of a numerical
variable by the levels of a factor, and methods to produce xtable
objects of the tables and to plot them. There are also functions to
facilitate the character encoding conversion of objects, to quickly
convert fixed width files into csv ones, and to export a data.frame to
a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation
written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan
Kraft
Maintainer: Jakson Aquino <jalvesaq@gmail.com>
Diff between descr versions 1.1.1 dated 2015-05-06 and 1.1.2 dated 2015-08-02
DESCRIPTION | 10 MD5 | 28 - NAMESPACE | 9 NEWS | 13 R/CrossTable.R | 922 +++++++++++++++++++---------------- R/crosstab.R | 46 + R/forODFTable.R | 10 R/xtable.R | 169 +----- inst/po/pt_BR/LC_MESSAGES/R-descr.mo |binary man/CrossTable.Rd | 51 + man/crosstab.Rd | 53 +- man/xtable.CrossTable.Rd | 9 po/R-descr.pot | 145 +++-- po/R-pt_BR.po | 156 +++-- po/descr.pot | 2 15 files changed, 919 insertions(+), 704 deletions(-)
Title: Tools for the 'Parallel' Package
Description: Miscellaneous utilities for the 'parallel' package,
cluster-oriented section; "Snowdoop" alternative to MapReduce;
file splitting and distributed operations such as sort and aggregate.
"Software Alchemy" method for parallelizing most statistical methods,
presented in N. Matloff, Parallel Computation for Data Science,
Chapman and Hall, 2015. Includes a debugging aid.
Author: Norm Matloff <normmatloff@gmail.com> [aut],
Alex Rumbaugh <aprumbaugh@ucdavis.edu> [ctb]
Maintainer: Norm Matloff <normmatloff@gmail.com>
Diff between partools versions 1.1.1 dated 2015-07-21 and 1.1.3 dated 2015-08-01
DESCRIPTION | 9 +--- MD5 | 22 +++++----- R/CA.R | 53 +++++++++++++++----------- R/DebugSnow.R | 7 +++ R/SnowUtils.R | 11 +++-- R/Snowdoop.R | 50 +++++++++++++----------- build/vignette.rds |binary inst/doc/partools.pdf |binary man/ca.Rd | 101 ++++++++++++++++++++++++++++---------------------- man/dbs.Rd | 2 man/formrowchunks.Rd | 2 man/snowdoop.Rd | 46 ++++++++++++++-------- 12 files changed, 179 insertions(+), 124 deletions(-)
Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. nplr can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre],
Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>
Diff between nplr versions 0.1-3 dated 2015-07-11 and 0.1-4 dated 2015-08-01
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++--------- NEWS | 10 ++++++- R/helpers.R | 60 +++++++++++++++++++++++++++++++++------------ R/nplr.R | 2 + R/overlay.R | 4 +-- R/plot.nplr.R | 6 +++- inst/doc/nplr.R | 27 ++++++++------------ inst/doc/nplr.Rnw | 50 ++++++++++++++++++++++--------------- inst/doc/nplr.pdf |binary inst/extdata/multicell.tsv |only man/overlay.Rd | 27 ++++++++------------ man/plot.nplr.Rd | 7 +++-- vignettes/nplr.Rnw | 50 ++++++++++++++++++++++--------------- vignettes/nplrApp.png |only 15 files changed, 166 insertions(+), 111 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.1 dated 2015-05-10 and 0.9.2 dated 2015-08-01
h5-0.9.1/h5/NEWS |only h5-0.9.2/h5/DESCRIPTION | 15 h5-0.9.2/h5/INSTALL | 2 h5-0.9.2/h5/MD5 | 104 +- h5-0.9.2/h5/NAMESPACE | 11 h5-0.9.2/h5/R/CommonFG-DataSet.R | 197 ++++- h5-0.9.2/h5/R/CommonFG-Group.R | 45 + h5-0.9.2/h5/R/CommonFG.R | 86 +- h5-0.9.2/h5/R/DataSet.R | 51 - h5-0.9.2/h5/R/DataSpace.R | 13 h5-0.9.2/h5/R/Dataset-Extend.R | 152 +-- h5-0.9.2/h5/R/Dataset-Subset.R | 373 +++++---- h5-0.9.2/h5/R/H5File.R | 48 - h5-0.9.2/h5/R/H5Group.R | 5 h5-0.9.2/h5/R/H5Location-Attribute.R | 43 - h5-0.9.2/h5/R/Helpers.R | 41 - h5-0.9.2/h5/R/RcppExports.R | 32 h5-0.9.2/h5/R/h5-package.R | 14 h5-0.9.2/h5/configure | 58 - h5-0.9.2/h5/configure.ac | 55 - h5-0.9.2/h5/inst/NEWS.Rd | 19 h5-0.9.2/h5/inst/benchmark/benchmark-BigSet.R | 8 h5-0.9.2/h5/man/CommonFG-DataSet.Rd | 48 - h5-0.9.2/h5/man/CommonFG-Group.Rd | 15 h5-0.9.2/h5/man/CommonFG.Rd | 27 h5-0.9.2/h5/man/DataSet-Subset.Rd | 22 h5-0.9.2/h5/man/H5File.Rd | 14 h5-0.9.2/h5/man/H5Location-Attribute.Rd | 26 h5-0.9.2/h5/man/h5-package.Rd | 14 h5-0.9.2/h5/src/Attribute.cpp | 66 - h5-0.9.2/h5/src/Attribute.h | 1 h5-0.9.2/h5/src/Dataset.cpp | 120 +-- h5-0.9.2/h5/src/Dataset.h | 1 h5-0.9.2/h5/src/Dataspace.cpp | 31 h5-0.9.2/h5/src/Dataspace.h | 6 h5-0.9.2/h5/src/File.cpp | 14 h5-0.9.2/h5/src/Group.cpp | 119 ++- h5-0.9.2/h5/src/Group.h | 8 h5-0.9.2/h5/src/Helpers.cpp | 495 +++++++++++-- h5-0.9.2/h5/src/Helpers.h | 22 h5-0.9.2/h5/src/RcppExports.cpp | 84 +- h5-0.9.2/h5/tests/testthat.R | 2 h5-0.9.2/h5/tests/testthat/test-Attribute.R | 58 + h5-0.9.2/h5/tests/testthat/test-DataSet-IO.R | 80 +- h5-0.9.2/h5/tests/testthat/test-DataSet-Select-Elem.R | 20 h5-0.9.2/h5/tests/testthat/test-DataSet-Select-Hyperslab.R | 21 h5-0.9.2/h5/tests/testthat/test-DataSet-Select-Subset.R | 84 +- h5-0.9.2/h5/tests/testthat/test-DataSet-extend.R | 56 - h5-0.9.2/h5/tests/testthat/test-DataSet.R | 103 ++ h5-0.9.2/h5/tests/testthat/test-H5File-Subset.R | 35 h5-0.9.2/h5/tests/testthat/test-H5File.R | 63 + h5-0.9.2/h5/tests/testthat/test-H5Group.R | 54 + h5-0.9.2/h5/tests/testthat/test-io.R | 10 h5-0.9.2/h5/tests/testthat/test-vlen.R |only 54 files changed, 2124 insertions(+), 967 deletions(-)
Title: Circular Visualization in R
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.2.5 dated 2015-07-08 and 0.3.0 dated 2015-08-01
circlize |only 1 file changed
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.6 dated 2015-05-23 and 1.7 dated 2015-08-01
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NAMESPACE | 2 + R/build.dist.struct.R | 32 ++++++++++++----- R/rcbalance-internal.R | 16 +++++++- R/rcbalance.R | 85 ++++++++++++++++++++++++++++++++++------------- man/rcbalance-package.Rd | 4 +- man/rcbalance.Rd | 4 +- 8 files changed, 117 insertions(+), 48 deletions(-)
Title: Uncertainty Analysis for Species Distribution Models
Description: This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between usdm versions 1.1-12 dated 2013-07-23 and 1.1-15 dated 2015-08-01
DESCRIPTION | 20 +++--- MD5 | 6 +- NAMESPACE | 10 ++- R/exclude.R | 172 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 106 insertions(+), 102 deletions(-)
Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as
on a telephone keypad. When converting letters to numbers, a character
vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F"
becoming 3, etc. When converting numbers to letters, a character vector is
returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and
"C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between phonenumber versions 0.1.0 dated 2015-07-10 and 0.2.0 dated 2015-08-01
DESCRIPTION | 9 ++-- MD5 | 26 ++++++------ R/letterToNumber.R | 47 ++++++++++++++++------ R/numberToLetter.R | 57 ++++++++++++++++++++------- R/phonenumber.R |only README.md | 72 +++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/phonenumber.Rmd | 57 +++++++++++++++++++-------- inst/doc/phonenumber.html | 39 +++++++++++++++--- man/letterToNumber.Rd | 25 ++++++++++-- man/numberToLetter.Rd | 26 ++++++++++-- man/phonenumber.Rd |only tests/testthat/test-letterToNumber.R | 5 ++ tests/testthat/test-numberToLetter.R | 8 +++ vignettes/phonenumber.Rmd | 57 +++++++++++++++++++-------- 15 files changed, 325 insertions(+), 103 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future. Web applications are provided
(via 'shiny') for the implemented methods to help in designing and deploying the
computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 0.25.2 dated 2015-07-14 and 0.25.3 dated 2015-08-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/coxstuff.R | 9 ++++++--- R/distcomp.R | 8 +++++--- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 0.0 dated 2015-07-22 and 0.0.1 dated 2015-08-01
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ALL.r | 33 ++++++++++++++++++++++++++++++--- man/ConsRank-package.Rd | 2 -- 4 files changed, 37 insertions(+), 12 deletions(-)
Title: OCI Based Oracle Database Interface for R
Description: Oracle database interface (DBI) driver for R.
This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Rajendra S. Pingte <rajendra.pingte@oracle.com>
Diff between ROracle versions 1.1-12 dated 2014-11-20 and 1.2-1 dated 2015-07-31
DESCRIPTION | 12 INSTALL | 156 +++++---- MD5 | 176 +++++------ NAMESPACE | 2 NEWS | 26 + R/dbi.R | 16 - R/oci.R | 245 +++++++++++++-- configure | 18 - configure.ac | 2 inst/Copyrights | 2 inst/doc/man/de/OraConnection-class.Rd | 4 inst/doc/man/de/Oracle.Rd | 50 ++- inst/doc/man/de/dbConnect-methods.Rd | 102 +++--- inst/doc/man/de/dbDriver-methods.Rd | 50 +-- inst/doc/man/de/dbGetInfo-methods.Rd | 237 ++++++++++++++ inst/doc/man/de/dbReadTable-methods.Rd | 374 +++++++++++++++++++---- inst/doc/man/de/dbSendQuery-methods.Rd | 65 ++-- inst/doc/man/en/Oracle.Rd | 47 ++ inst/doc/man/en/dbDriver-methods.Rd | 46 +- inst/doc/man/en/dbGetInfo-methods.Rd | 26 + inst/doc/man/en/dbReadTable-methods.Rd | 166 +++++++++- inst/doc/man/en/dbSendQuery-methods.Rd | 64 ++-- inst/doc/man/es/OraConnection-class.Rd | 4 inst/doc/man/es/Oracle.Rd | 53 ++- inst/doc/man/es/dbConnect-methods.Rd | 93 +++-- inst/doc/man/es/dbDriver-methods.Rd | 44 +- inst/doc/man/es/dbGetInfo-methods.Rd | 237 ++++++++++++++ inst/doc/man/es/dbReadTable-methods.Rd | 342 ++++++++++++++++++--- inst/doc/man/es/dbSendQuery-methods.Rd | 68 ++-- inst/doc/man/fr/OraConnection-class.Rd | 4 inst/doc/man/fr/Oracle.Rd | 45 ++ inst/doc/man/fr/dbConnect-methods.Rd | 100 +++--- inst/doc/man/fr/dbDriver-methods.Rd | 46 +- inst/doc/man/fr/dbGetInfo-methods.Rd | 239 ++++++++++++++- inst/doc/man/fr/dbReadTable-methods.Rd | 344 ++++++++++++++++++--- inst/doc/man/fr/dbSendQuery-methods.Rd | 75 ++-- inst/doc/man/it/OraConnection-class.Rd | 4 inst/doc/man/it/Oracle.Rd | 43 ++ inst/doc/man/it/dbConnect-methods.Rd | 94 +++-- inst/doc/man/it/dbDriver-methods.Rd | 30 + inst/doc/man/it/dbGetInfo-methods.Rd | 237 ++++++++++++++ inst/doc/man/it/dbReadTable-methods.Rd | 358 +++++++++++++++++++--- inst/doc/man/it/dbSendQuery-methods.Rd | 65 ++-- inst/doc/man/ja/OraConnection-class.Rd | 4 inst/doc/man/ja/Oracle.Rd | 61 ++- inst/doc/man/ja/dbConnect-methods.Rd | 131 ++++---- inst/doc/man/ja/dbDriver-methods.Rd | 47 +- inst/doc/man/ja/dbGetInfo-methods.Rd | 231 ++++++++++++++ inst/doc/man/ja/dbReadTable-methods.Rd | 359 +++++++++++++++++++--- inst/doc/man/ja/dbSendQuery-methods.Rd | 61 ++- inst/doc/man/ko/OraConnection-class.Rd | 4 inst/doc/man/ko/Oracle.Rd | 52 ++- inst/doc/man/ko/dbConnect-methods.Rd | 114 ++++--- inst/doc/man/ko/dbDriver-methods.Rd | 38 +- inst/doc/man/ko/dbGetInfo-methods.Rd | 235 ++++++++++++++ inst/doc/man/ko/dbReadTable-methods.Rd | 380 +++++++++++++++++++----- inst/doc/man/ko/dbSendQuery-methods.Rd | 55 ++- inst/doc/man/pt_BR/OraConnection-class.Rd | 4 inst/doc/man/pt_BR/Oracle.Rd | 60 ++- inst/doc/man/pt_BR/dbConnect-methods.Rd | 128 ++++---- inst/doc/man/pt_BR/dbDriver-methods.Rd | 50 +-- inst/doc/man/pt_BR/dbGetInfo-methods.Rd | 241 ++++++++++++++- inst/doc/man/pt_BR/dbReadTable-methods.Rd | 376 +++++++++++++++++++---- inst/doc/man/pt_BR/dbSendQuery-methods.Rd | 85 +++-- inst/doc/man/zh_CN/OraConnection-class.Rd | 4 inst/doc/man/zh_CN/Oracle.Rd | 51 ++- inst/doc/man/zh_CN/dbConnect-methods.Rd | 104 +++--- inst/doc/man/zh_CN/dbDriver-methods.Rd | 44 +- inst/doc/man/zh_CN/dbGetInfo-methods.Rd | 231 ++++++++++++++ inst/doc/man/zh_CN/dbReadTable-methods.Rd | 340 ++++++++++++++++++--- inst/doc/man/zh_CN/dbSendQuery-methods.Rd | 57 ++- inst/doc/man/zh_TW/OraConnection-class.Rd | 4 inst/doc/man/zh_TW/Oracle.Rd | 59 ++- inst/doc/man/zh_TW/dbConnect-methods.Rd | 140 ++++---- inst/doc/man/zh_TW/dbDriver-methods.Rd | 46 +- inst/doc/man/zh_TW/dbGetInfo-methods.Rd | 239 ++++++++++++++- inst/doc/man/zh_TW/dbListConnections-methods.Rd | 2 inst/doc/man/zh_TW/dbReadTable-methods.Rd | 380 +++++++++++++++++++----- inst/doc/man/zh_TW/dbSendQuery-methods.Rd | 87 +++-- inst/doc/man/zh_TW/summary-methods.Rd | 2 man/Oracle.Rd | 47 ++ man/dbDriver-methods.Rd | 46 +- man/dbGetInfo-methods.Rd | 26 + man/dbReadTable-methods.Rd | 166 +++++++++- man/dbSendQuery-methods.Rd | 64 ++-- src/rodbi.c | 285 +++++++++++++++--- src/rodbi.h | 7 src/rooci.c | 159 ++++++---- src/rooci.h | 6 89 files changed, 7679 insertions(+), 2044 deletions(-)
Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>
Diff between oglmx versions 1.0.2 dated 2015-06-01 and 1.0.3 dated 2015-07-31
DESCRIPTION | 10 +- MD5 | 20 ++-- R/oglmx-functions.R | 182 +++++++++++++++++++++++++++++++++----------- R/oglmx.margins-functions.R | 2 build/partial.rdb |binary man/logit.reg.Rd | 10 +- man/oglmx.Rd | 19 +++- man/ologit.reg.Rd | 10 +- man/oprobit.reg.Rd | 11 ++ man/probit.reg.Rd | 10 +- man/summary.oglmx.Rd | 2 11 files changed, 202 insertions(+), 74 deletions(-)
Title: Visualizations of Paired Comparisons
Description: Convert a logical vector or a vector of
p-values or a correlation, difference, or distance
matrix into a display identifying the pairs for
which the differences were not significantly
different. Designed for use in conjunction with
the output of functions like TukeyHSD, dist{stats},
simint, simtest, csimint, csimtest{multcomp},
friedmanmc, kruskalmc{pgirmess}.
Author: Spencer Graves, Hans-Peter Piepho and Luciano Selzer with
help from Sundar Dorai-Raj
Maintainer: Luciano Selzer <luciano.selzer@gmail.com>
Diff between multcompView versions 0.1-5 dated 2012-05-26 and 0.1-7 dated 2015-07-31
multcompView-0.1-5/multcompView/NEWS |only multcompView-0.1-5/multcompView/man/multcompView.package.Rd |only multcompView-0.1-5/multcompView/man/plot.multcomp.Rd |only multcompView-0.1-5/multcompView/man/plotDisplay.Rd |only multcompView-0.1-7/multcompView/DESCRIPTION | 30 multcompView-0.1-7/multcompView/MD5 | 53 - multcompView-0.1-7/multcompView/NAMESPACE | 53 + multcompView-0.1-7/multcompView/R/extract_p.R | 83 +- multcompView-0.1-7/multcompView/R/multcompBoxplot.R | 378 +++++++---- multcompView-0.1-7/multcompView/R/multcompLetters.R | 243 +++++++ multcompView-0.1-7/multcompView/R/multcompTs.R | 117 +++ multcompView-0.1-7/multcompView/R/multcompView-package.R |only multcompView-0.1-7/multcompView/R/plot.multcompLetters.R | 125 +++ multcompView-0.1-7/multcompView/R/plot.multcompTs.R | 133 +++ multcompView-0.1-7/multcompView/R/plotBoxes.R | 90 ++ multcompView-0.1-7/multcompView/R/plotLetters.R | 131 +++ multcompView-0.1-7/multcompView/R/plotTs.R | 91 ++ multcompView-0.1-7/multcompView/R/print.multcompLetters.R | 28 multcompView-0.1-7/multcompView/R/vec2mat.R | 64 + multcompView-0.1-7/multcompView/R/vec2mat2.R | 36 + multcompView-0.1-7/multcompView/man/extract_p.Rd | 54 - multcompView-0.1-7/multcompView/man/multcompBoxplot.Rd | 196 ++--- multcompView-0.1-7/multcompView/man/multcompLetters.Rd | 231 ++---- multcompView-0.1-7/multcompView/man/multcompTs.Rd | 164 +--- multcompView-0.1-7/multcompView/man/multcompView-package.Rd |only multcompView-0.1-7/multcompView/man/plot.multcompLetters.Rd |only multcompView-0.1-7/multcompView/man/plot.multcompTs.Rd |only multcompView-0.1-7/multcompView/man/plotBoxes.Rd |only multcompView-0.1-7/multcompView/man/plotLetters.Rd |only multcompView-0.1-7/multcompView/man/plotTs.Rd |only multcompView-0.1-7/multcompView/man/print.multcompLetters.Rd | 59 - multcompView-0.1-7/multcompView/man/vec2mat.Rd | 75 -- multcompView-0.1-7/multcompView/man/vec2mat2.Rd | 60 - 33 files changed, 1805 insertions(+), 689 deletions(-)
Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard
errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE
computation for expectation and quantile estimators is
supported as well as multivariate estimations. The package also provides
functions for computing effective sample size and for plotting
Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes
<hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>
Diff between mcmcse versions 1.0-1 dated 2012-08-06 and 1.1-1 dated 2015-07-31
DESCRIPTION | 30 +++++++++++--------- MD5 | 36 +++++++++++++++++++----- NAMESPACE | 16 ++++++++++ R/RcppExports.R |only R/confRegion.R |only R/mcmcse.R | 74 ++++++++++++++++++++++++++++++-------------------- R/mcse_multi.R |only R/multiESS.R |only R/qq_test.R |only R/zzz.R | 7 ++-- build |only inst/CITATION | 11 ++++--- inst/doc |only man/confRegion.Rd |only man/ess.Rd | 48 ++++++++++++++++---------------- man/mcmcse-package.Rd |only man/mcse.Rd | 2 + man/mcse.multi.Rd |only man/multiESS.Rd |only man/qqTest.Rd |only src |only tests |only vignettes |only 23 files changed, 143 insertions(+), 81 deletions(-)
Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb],
Tengfei Yin [ctb],
Nan Xiao [aut, cre]
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between liftr versions 0.1 dated 2015-07-15 and 0.2 dated 2015-07-31
liftr-0.1/liftr/NEWS |only liftr-0.2/liftr/DESCRIPTION | 20 + liftr-0.2/liftr/MD5 | 25 - liftr-0.2/liftr/NAMESPACE | 1 liftr-0.2/liftr/NEWS.md |only liftr-0.2/liftr/R/lift.R | 26 + liftr-0.2/liftr/R/liftr-package.R | 1 liftr-0.2/liftr/R/utils.R | 10 liftr-0.2/liftr/README.md | 21 - liftr-0.2/liftr/inst/Dockerfile.Rmd | 11 liftr-0.2/liftr/inst/doc/liftr-intro.Rmd | 2 liftr-0.2/liftr/inst/doc/liftr-intro.html | 405 ++++++++++-------------------- liftr-0.2/liftr/inst/pandoc.Rmd |only liftr-0.2/liftr/man/liftr-package.Rd | 1 liftr-0.2/liftr/vignettes/liftr-intro.Rmd | 2 15 files changed, 218 insertions(+), 307 deletions(-)
Title: Order Restricted Clustering for Microarray Experiments
Description: Provides clustering of genes with similar
dose response (or time course) profiles. It implements the method
described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between ORCME versions 2.0.1 dated 2014-07-16 and 2.0.2 dated 2015-07-31
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- NAMESPACE | 4 +++- data/doseData.rda |binary data/geneData.rda |binary 5 files changed, 16 insertions(+), 14 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different
degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large
for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional
parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>
Diff between Kernelheaping versions 0.9 dated 2015-06-13 and 1.0 dated 2015-07-31
DESCRIPTION | 8 +- MD5 | 14 ++-- NAMESPACE | 19 +++++ R/functions.R | 154 ++++++++++++++++++++++++----------------------- data/students.rda |binary man/dbivr.Rd | 9 +- man/dheaping.Rd | 17 +++-- man/sim.Kernelheaping.Rd | 2 8 files changed, 126 insertions(+), 97 deletions(-)
Title: Order-Restricted Inference for Microarray Experiments
Description: Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
Author: Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between IsoGene versions 1.0-23 dated 2014-12-18 and 1.0-24 dated 2015-07-31
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NAMESPACE | 2 ++ data/dopamine.rda |binary data/exampleData.rda |binary inst/doc/IsoGene.pdf |binary 6 files changed, 15 insertions(+), 13 deletions(-)
Title: Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Description: Functions to compare two or more survival curves with:
a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>
Diff between FHtest versions 1.2 dated 2015-05-27 and 1.3 dated 2015-07-31
FHtest-1.2/FHtest/R/FHtest-internal.R |only FHtest-1.3/FHtest/DESCRIPTION | 8 ++--- FHtest-1.3/FHtest/MD5 | 43 +++++++++++++++----------------- FHtest-1.3/FHtest/NAMESPACE | 4 +- FHtest-1.3/FHtest/R/FHtesticp.R | 2 - FHtest-1.3/FHtest/R/FHtesticp.formula.R | 22 ++++++++-------- FHtest-1.3/FHtest/R/FHtestics.R | 2 - FHtest-1.3/FHtest/R/FHtestics.formula.R | 30 +++++++++++----------- FHtest-1.3/FHtest/R/FHtestrcc.R | 5 +-- FHtest-1.3/FHtest/R/FHtestrcc.formula.R | 30 +++++++++++----------- FHtest-1.3/FHtest/R/FHtestrcp.R | 5 +-- FHtest-1.3/FHtest/R/FHtestrcp.formula.R | 30 +++++++++++----------- FHtest-1.3/FHtest/R/rcc.R | 37 ++++++++++++++------------- FHtest-1.3/FHtest/R/rcp.R | 26 ++++++++----------- FHtest-1.3/FHtest/man/FHtest-package.Rd | 6 ++-- FHtest-1.3/FHtest/man/FHtesticp.Rd | 8 ++--- FHtest-1.3/FHtest/man/FHtestics.Rd | 9 ++---- FHtest-1.3/FHtest/man/FHtestrcc.Rd | 7 ++--- FHtest-1.3/FHtest/man/FHtestrcp.Rd | 9 ++---- FHtest-1.3/FHtest/man/ics.Rd | 2 - FHtest-1.3/FHtest/man/illust3.Rd | 37 +++++++++++---------------- FHtest-1.3/FHtest/man/rcc.Rd | 2 - FHtest-1.3/FHtest/man/rcp.Rd | 2 - 23 files changed, 155 insertions(+), 171 deletions(-)
Title: Tools for Making and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games.
This package is an alternative to the earlier sudoku-solver package,
'sudoku'. The present package uses a slightly different algorithm, has a
simpler coding and presents a few more sugar tools, such as plot and print
methods. Solved sudoku games are of some interest in Experimental Design
as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between sudokuAlt versions 0.1-5 dated 2015-07-24 and 0.1-6 dated 2015-07-31
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/sudokuAlt.R | 21 +++++++++++++-------- man/fetchAUGame.Rd | 13 ++++++------- man/fetchUKGame.Rd | 5 +++++ 5 files changed, 33 insertions(+), 24 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
'shinyjs' can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.7.0 dated 2015-06-24 and 0.0.8.3 dated 2015-07-31
DESCRIPTION | 6 MD5 | 90 ++++----- NEWS.md | 24 ++ R/colourInput.R | 47 +++- R/extendShinyjs.R | 20 +- R/hidden.R | 2 R/inlineCSS.R | 6 R/jsFunc-aaa.R | 7 R/jsFunc-classFuncs.R | 4 R/jsFunc-messageFuncs.R | 2 R/jsFunc-runjs.R | 2 R/jsFunc-stateFuncs.R | 4 R/jsFunc-text.R | 2 R/jsFunc-visibilityFuncs.R | 4 R/onclick.R | 6 R/reset.R | 6 R/useShinyjs.R | 9 R/utils.R | 25 -- README.md | 23 +- inst/doc/overview.Rmd | 21 -- inst/doc/overview.html | 38 +-- inst/examples/basic/app.R | 2 inst/examples/colourInput/app.R | 41 +++- inst/examples/demo/server.R | 2 inst/srcjs/input_binding_colour.js | 21 +- inst/srcjs/shinyjs-default-funcs.js | 16 + inst/www/shared/colourpicker/css/colourpicker.css | 49 +++- inst/www/shared/colourpicker/css/colourpicker.min.css | 2 inst/www/shared/colourpicker/js/colourpicker.js | 179 ++++++++++++------ inst/www/shared/colourpicker/js/colourpicker.min.js | 2 man/classFuncs.Rd | 4 man/colourInput.Rd | 19 + man/extendShinyjs.Rd | 18 + man/hidden.Rd | 2 man/inlineCSS.Rd | 6 man/js.Rd | 2 man/messageFuncs.Rd | 2 man/onclick.Rd | 2 man/reset.Rd | 2 man/runjs.Rd | 2 man/stateFuncs.Rd | 4 man/text.Rd | 2 man/updateColourInput.Rd | 8 man/useShinyjs.Rd | 11 - man/visibilityFuncs.Rd | 4 vignettes/overview.Rmd | 21 -- 46 files changed, 489 insertions(+), 282 deletions(-)
Title: Tools for Nonlinear Regression Analysis
Description: Several tools for assessing the quality of fit of a
gaussian nonlinear model are provided.
Author: Florent Baty <florent.baty@gmail.com> and Marie-Laure
Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>,
with contributions from Sandrine Charles, Jean-Pierre Flandrois,
and Christian Ritz
Maintainer: Florent Baty <florent.baty@gmail.com>
Diff between nlstools versions 1.0-1 dated 2015-02-26 and 1.0-2 dated 2015-07-31
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 4 +++- inst/CITATION | 40 ++++++++++++++++++++++++---------------- inst/NEWS | 8 ++++++++ man/nlstools.Rd | 3 ++- 7 files changed, 50 insertions(+), 28 deletions(-)
Title: Multidimensional Iterative Proportional Fitting and Alternative
Models
Description: An implementation of the iterative proportional fitting (IPFP),
maximum likelihood, minimum chi-square and weighted least squares procedures
for updating a N-dimensional array with respect to given target marginal
distributions (which, in turn can be multi-dimensional). The package also
provides an application of the IPFP to simulate multivariate Bernoulli
distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>
Diff between mipfp versions 2.0 dated 2015-03-30 and 2.2 dated 2015-07-31
DESCRIPTION | 13 + MD5 | 40 +++--- NAMESPACE | 2 R/binary.R | 97 ++++++++++---- R/ipfp_multi_dim.R | 24 ++- R/models.R | 173 ++++++++++++++++---------- R/utils.R | 125 ++++++++++++++++++ data |only man/Array2Vector.Rd | 1 man/Corr2Odds.Rd | 4 man/Corr2PairProbs.Rd | 2 man/GetConfInt.Rd |only man/GetLinInd.Rd |only man/Ipfp.Rd | 37 ++++- man/IpfpCov.Rd | 12 - man/ObtainModelEstimates.Rd | 76 +++++++---- man/ObtainMultBinaryDist.Rd | 15 +- man/Odds2Corr.Rd | 4 man/Odds2PairProbs.Rd | 2 man/Qaqish.Rd |only man/RMultBinary.Rd | 40 +++--- man/mipfp-package.Rd | 292 ++++++++++++++++++++++---------------------- man/spnamur.Rd |only 23 files changed, 623 insertions(+), 336 deletions(-)
More information about InformationValue at CRAN
Permanent link
Title: Optimization of Sample Configurations using Spatial Simulated
Annealing
Description: Methods to optimize sample configurations using spatial simulated
annealing. Multiple objective functions are implemented for various
purposes, such as variogram estimation, trend estimation, and spatial
interpolation. A general purpose spatial simulated annealing function
enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre],
Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths],
Gerard B M Heuvelink [ths],
Edzer Pebesma [ctb],
Jon Skoien [ctb],
Joshua French [ctb],
Pierre Roudier [ctb],
Dick Brus [ctb],
Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between spsann versions 1.0.0 dated 2015-07-15 and 1.0.1 dated 2015-07-31
DESCRIPTION | 50 ++++++++++++++++++++++++--------------------- MD5 | 45 ++++++++++++++++++++-------------------- R/AAA.R | 5 ---- R/SPSANNtools.R | 2 - R/check-spsann-arguments.R | 2 - R/check-suggests.R |only R/optimACDC.R | 4 +-- R/optimMKV.R | 12 +++++++++- R/optimMSSD.R | 28 ++++++++++++++++++------- R/plot-and-jitter.R | 2 - R/plotting-options.R | 2 - R/prepare-acdc-covars.R | 4 +-- R/prepare-points.R | 2 - R/spsann.R | 2 - README.md | 17 ++++++++++++++- man/optimACDC.Rd | 16 +++++++------- man/optimCORR.Rd | 10 ++++----- man/optimDIST.Rd | 10 ++++----- man/optimMKV.Rd | 4 +-- man/optimMSSD.Rd | 4 +-- man/optimPPL.Rd | 4 +-- man/optimSPAN.Rd | 16 +++++++------- man/optimUSER.Rd | 4 +-- man/spsann-package.Rd | 2 - 24 files changed, 141 insertions(+), 106 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.0-4 dated 2015-07-13 and 0.8.2-0 dated 2015-07-31
quanteda-0.8.0-4/quanteda/R/clean.R |only quanteda-0.8.0-4/quanteda/inst/doc/corpus-sources.R |only quanteda-0.8.0-4/quanteda/inst/doc/corpus-sources.Rmd |only quanteda-0.8.0-4/quanteda/inst/doc/corpus-sources.html |only quanteda-0.8.0-4/quanteda/inst/doc/design-and-workflow.R |only quanteda-0.8.0-4/quanteda/inst/doc/design-and-workflow.Rmd |only quanteda-0.8.0-4/quanteda/inst/doc/design-and-workflow.html |only quanteda-0.8.0-4/quanteda/man/clean.Rd |only quanteda-0.8.0-4/quanteda/vignettes/corpus-sources.Rmd |only quanteda-0.8.0-4/quanteda/vignettes/corpus-sources.md |only quanteda-0.8.0-4/quanteda/vignettes/design-and-workflow.Rmd |only quanteda-0.8.0-4/quanteda/vignettes/design-and-workflow.md |only quanteda-0.8.0-4/quanteda/vignettes/development-plans.md |only quanteda-0.8.0-4/quanteda/vignettes/quickstart.md |only quanteda-0.8.2-0/quanteda/DESCRIPTION | 12 quanteda-0.8.2-0/quanteda/MD5 | 87 quanteda-0.8.2-0/quanteda/NAMESPACE | 13 quanteda-0.8.2-0/quanteda/NEWS | 39 quanteda-0.8.2-0/quanteda/R/corpus.R | 13 quanteda-0.8.2-0/quanteda/R/dataDocs.R | 4 quanteda-0.8.2-0/quanteda/R/dfm-main.R | 142 + quanteda-0.8.2-0/quanteda/R/dfm-methods.R | 18 quanteda-0.8.2-0/quanteda/R/dictionaries.R | 142 + quanteda-0.8.2-0/quanteda/R/readability.R | 246 ++ quanteda-0.8.2-0/quanteda/R/stopwords.R | 134 + quanteda-0.8.2-0/quanteda/R/textfile.R | 85 quanteda-0.8.2-0/quanteda/R/tokenize.R | 223 +- quanteda-0.8.2-0/quanteda/R/wordstem.R | 60 quanteda-0.8.2-0/quanteda/README.md | 108 - quanteda-0.8.2-0/quanteda/build/vignette.rds |binary quanteda-0.8.2-0/quanteda/demo/quanteda.R | 3 quanteda-0.8.2-0/quanteda/inst/doc/development-plans.R |only quanteda-0.8.2-0/quanteda/inst/doc/development-plans.Rmd | 314 +++ quanteda-0.8.2-0/quanteda/inst/doc/development-plans.html | 387 ++++ quanteda-0.8.2-0/quanteda/inst/doc/quickstart.R | 274 +- quanteda-0.8.2-0/quanteda/inst/doc/quickstart.Rmd | 580 ++++-- quanteda-0.8.2-0/quanteda/inst/doc/quickstart.html | 1119 ++++++++---- quanteda-0.8.2-0/quanteda/man/applyDictionary.Rd |only quanteda-0.8.2-0/quanteda/man/dfm.Rd | 23 quanteda-0.8.2-0/quanteda/man/exampleString.Rd | 2 quanteda-0.8.2-0/quanteda/man/readability.Rd | 25 quanteda-0.8.2-0/quanteda/man/removeFeatures.Rd | 18 quanteda-0.8.2-0/quanteda/man/scrabble.Rd |only quanteda-0.8.2-0/quanteda/man/segment.Rd | 4 quanteda-0.8.2-0/quanteda/man/selectFeatures.Rd |only quanteda-0.8.2-0/quanteda/man/show-dictionary-method.Rd |only quanteda-0.8.2-0/quanteda/man/syllables.Rd | 2 quanteda-0.8.2-0/quanteda/man/textfile.Rd | 71 quanteda-0.8.2-0/quanteda/man/tokenize.Rd | 21 quanteda-0.8.2-0/quanteda/man/trim.Rd | 19 quanteda-0.8.2-0/quanteda/man/wordstem.Rd | 6 quanteda-0.8.2-0/quanteda/tests/testthat/testDfm.R |only quanteda-0.8.2-0/quanteda/tests/testthat/testDictionaries.R |only quanteda-0.8.2-0/quanteda/vignettes/development-plans.Rmd | 314 +++ quanteda-0.8.2-0/quanteda/vignettes/quickstart.Rmd | 580 ++++-- 55 files changed, 3865 insertions(+), 1223 deletions(-)
Title: Programmatic Interface to the 'Dropbox' API
Description: Provides full programmatic access to the Dropbox file hosting platform (dropbox.com), including support for all standard file operations.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>
Diff between rdrop2 versions 0.6 dated 2015-04-15 and 0.7.0 dated 2015-07-30
rdrop2-0.6/rdrop2/R/drop_mime.R |only rdrop2-0.6/rdrop2/man/drop_mime.Rd |only rdrop2-0.6/rdrop2/tests |only rdrop2-0.7.0/rdrop2/DESCRIPTION | 11 +++-- rdrop2-0.7.0/rdrop2/MD5 | 53 +++++++++++++-------------- rdrop2-0.7.0/rdrop2/NAMESPACE | 4 +- rdrop2-0.7.0/rdrop2/R/drop_delta.R |only rdrop2-0.7.0/rdrop2/R/drop_dir.R | 53 ++++++++++++++++++++------- rdrop2-0.7.0/rdrop2/R/drop_file_ops.R | 11 ++++- rdrop2-0.7.0/rdrop2/R/drop_get.R | 42 ++++++++++++--------- rdrop2-0.7.0/rdrop2/R/drop_read_csv.R | 6 ++- rdrop2-0.7.0/rdrop2/R/drop_utils.R | 5 ++ rdrop2-0.7.0/rdrop2/man/drop_acc.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_auth.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_copy.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_create.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_delete.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_delta.Rd |only rdrop2-0.7.0/rdrop2/man/drop_dir.Rd | 6 ++- rdrop2-0.7.0/rdrop2/man/drop_exists.Rd | 10 ++++- rdrop2-0.7.0/rdrop2/man/drop_get.Rd | 12 +++--- rdrop2-0.7.0/rdrop2/man/drop_history.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_media.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_move.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_read_csv.Rd | 10 ++++- rdrop2-0.7.0/rdrop2/man/drop_search.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_share.Rd | 2 - rdrop2-0.7.0/rdrop2/man/drop_upload.Rd | 2 - rdrop2-0.7.0/rdrop2/man/get_dropbox_token.Rd | 2 - rdrop2-0.7.0/rdrop2/man/pipe.Rd | 2 - 30 files changed, 156 insertions(+), 93 deletions(-)
Title: Tools for Phonetic and Acoustic Analyses
Description: Contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.
Author: Santiago Barreda
Maintainer: Santiago Barreda <sbarreda@ucdavis.edu>
Diff between phonTools versions 0.2-2.0 dated 2014-08-04 and 0.2-2.1 dated 2015-07-30
DESCRIPTION | 12 +-- LICENSE | 2 MD5 | 172 ++++++++++++++++++++++++----------------------- NAMESPACE | 33 ++++++++- R/FIRfilter.R | 2 R/Ffilter.R | 138 +++++++++++++++++++------------------ R/PSTM.R | 2 R/anova.rcr.R | 7 + R/combocalc.R | 2 R/createtemplate.R | 2 R/errorbar.R | 10 ++ R/fastacf.R | 2 R/findformants.R | 2 R/formanttrack.R | 19 +++-- R/freqresponse.R | 2 R/hotelling.test.R | 3 R/imputeformants.R | 2 R/interpolate.R | 3 R/ipainfo.R | 2 R/iplot.R |only R/ldaclassify.R | 29 ++++--- R/ldboundary.R | 2 R/loadsound.R | 2 R/loadtable.R | 2 R/lpc.R | 2 R/makeFIR.R | 53 +++++++------- R/makesound.R | 2 R/mscohere.R | 2 R/multiplot.R | 2 R/normalize.R | 6 - R/normalize.compare.R | 4 - R/ntypes.R | 4 - R/outlier.plot.R |only R/peakfind.R | 2 R/phasor.R | 2 R/pickIPA.R | 2 R/pitchtrack.R | 7 - R/playsound.R |only R/plot.rcr.R | 7 + R/plot.sound.R | 2 R/plot.spectrogram.R | 2 R/plot.template.R | 2 R/polezero.R | 2 R/powertrack.R | 2 R/preemphasis.R | 2 R/print.anova.rcr.R | 2 R/print.hotelling.test.R | 2 R/print.rcr.R | 2 R/print.sound.R | 2 R/print.spectrogram.R | 2 R/print.summary.rcr.R | 2 R/print.template.R | 2 R/pwelch.R | 2 R/rcr.R | 2 R/reduce.fraction.R | 2 R/resample.R | 2 R/rmvtnorm.R | 2 R/rotate.R | 2 R/sdellipse.R | 17 +++- R/selectslice.R | 2 R/sinc.R | 2 R/sinusoid.R | 4 - R/snip.R | 69 +++++++++--------- R/spectralslice.R | 21 ++++- R/spectrogram.R | 4 - R/summary.rcr.R | 2 R/synthfilter.R | 7 + R/territorialmap.R | 2 R/vowelplot.R | 2 R/vowelsynth.R | 26 ++++--- R/vplot.R | 7 - R/windowfunc.R | 2 R/writesound.R | 9 +- R/xsampatoIPA.R | 9 +- R/zeros.R | 2 data/h95.rda |binary man/Ffilter.Rd | 3 man/PSTM.Rd | 2 man/errorbars.Rd | 1 man/formanttrack.Rd | 5 - man/ldclassify.Rd | 13 ++- man/playsound.Rd |only man/sdellipse.Rd | 3 man/snip.Rd | 2 man/spectralslice.Rd | 1 man/spectrogram.Rd | 2 man/synthfilter.Rd | 3 man/vowelsynth.Rd | 11 +-- man/writesound.Rd | 4 - 89 files changed, 468 insertions(+), 354 deletions(-)
Title: Functions for Optimal Matching
Description: Provides routines for distance based bipartite matching to reduce
covariate imbalance between treatment and control groups in observational
studies. Routines are provided to generate distances from GLM models (propensity
score matching) and formulas (Euclidean and Mahalanobis matching), stratified
matching (exact matching), and calipers. Results of the fullmatch routine are
guaranteed to provide minimum average within matched set distance.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson
<mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, and Peter
Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas
<dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>
Diff between optmatch versions 0.9-3 dated 2014-08-12 and 0.9-5 dated 2015-07-30
optmatch-0.9-3/optmatch/R/boxplot-methods.R |only optmatch-0.9-3/optmatch/demo |only optmatch-0.9-3/optmatch/man/caliperSize.Rd |only optmatch-0.9-3/optmatch/man/caliperUpperBound.Rd |only optmatch-0.9-3/optmatch/man/dist_digest.Rd |only optmatch-0.9-3/optmatch/man/fmla2treatedblocking.Rd |only optmatch-0.9-3/optmatch/man/makeInfinitySparseMatrix.Rd |only optmatch-0.9-3/optmatch/man/makeOptmatch.Rd |only optmatch-0.9-3/optmatch/man/scoreCaliper.Rd |only optmatch-0.9-3/optmatch/man/setFeasibilityConstants.Rd |only optmatch-0.9-3/optmatch/man/setTryRecovery.Rd |only optmatch-0.9-3/optmatch/man/validDistanceSpecification.Rd |only optmatch-0.9-3/optmatch/src/cuseful.c |only optmatch-0.9-3/optmatch/src/distances.c |only optmatch-0.9-3/optmatch/src/map.c |only optmatch-0.9-3/optmatch/src/r_smahal.c |only optmatch-0.9-3/optmatch/src/register.c |only optmatch-0.9-3/optmatch/src/smahal.c |only optmatch-0.9-3/optmatch/src/subsetInfSparseMatrix.c |only optmatch-0.9-5/optmatch/DESCRIPTION | 41 optmatch-0.9-5/optmatch/MD5 | 166 +- optmatch-0.9-5/optmatch/NAMESPACE | 18 optmatch-0.9-5/optmatch/NEWS | 20 optmatch-0.9-5/optmatch/R/InfinitySparseMatrix.R | 159 +- optmatch-0.9-5/optmatch/R/Optmatch.R | 35 optmatch-0.9-5/optmatch/R/boxplotMethods.R |only optmatch-0.9-5/optmatch/R/deprecated.R | 3 optmatch-0.9-5/optmatch/R/feasible.R | 77 - optmatch-0.9-5/optmatch/R/fill.NAs.R | 119 +- optmatch-0.9-5/optmatch/R/fmatch.R | 8 optmatch-0.9-5/optmatch/R/fullmatch.R | 14 optmatch-0.9-5/optmatch/R/match_on.R | 576 ++++++---- optmatch-0.9-5/optmatch/R/pairmatch.R | 7 optmatch-0.9-5/optmatch/R/scores.R | 138 +- optmatch-0.9-5/optmatch/R/stratumStructure.R | 7 optmatch-0.9-5/optmatch/R/summary.optmatch.R | 7 optmatch-0.9-5/optmatch/R/utilities.R | 55 optmatch-0.9-5/optmatch/R/zzz.R | 11 optmatch-0.9-5/optmatch/R/zzzDistanceSpecification.R | 14 optmatch-0.9-5/optmatch/data/plantdist.rda |binary optmatch-0.9-5/optmatch/inst/examples/caliper.R | 4 optmatch-0.9-5/optmatch/inst/tests/test.RItools.R | 60 - optmatch-0.9-5/optmatch/inst/tests/test.fill.NAs.R | 98 + optmatch-0.9-5/optmatch/inst/tests/test.fmatch.R | 1 optmatch-0.9-5/optmatch/inst/tests/test.fullmatch.R | 92 + optmatch-0.9-5/optmatch/inst/tests/test.fullmatch.infeasible.recovery.R | 12 optmatch-0.9-5/optmatch/inst/tests/test.match_on.R | 219 +++ optmatch-0.9-5/optmatch/inst/tests/test.scores.R | 198 ++- optmatch-0.9-5/optmatch/man/InfinitySparseMatrix-class.Rd |only optmatch-0.9-5/optmatch/man/antiExactMatch.Rd | 49 optmatch-0.9-5/optmatch/man/caliper-methods.Rd | 132 +- optmatch-0.9-5/optmatch/man/compare_optmatch.Rd | 28 optmatch-0.9-5/optmatch/man/dimnames-InfinitySparseMatrix.Rd |only optmatch-0.9-5/optmatch/man/distUnion.Rd | 55 optmatch-0.9-5/optmatch/man/effectiveSampleSize.Rd | 29 optmatch-0.9-5/optmatch/man/fill.NAs.rd | 6 optmatch-0.9-5/optmatch/man/fullmatch.Rd | 339 ++--- optmatch-0.9-5/optmatch/man/getMaxProblemSize.Rd | 22 optmatch-0.9-5/optmatch/man/ismBinaryOps.Rd |only optmatch-0.9-5/optmatch/man/match_on-methods.Rd | 406 +++---- optmatch-0.9-5/optmatch/man/maxCaliper.Rd | 53 optmatch-0.9-5/optmatch/man/mdist.Rd | 58 - optmatch-0.9-5/optmatch/man/minExactMatch.Rd | 50 optmatch-0.9-5/optmatch/man/num_eligible_matches-methods.Rd | 28 optmatch-0.9-5/optmatch/man/optmatch-defunct.Rd | 36 optmatch-0.9-5/optmatch/man/optmatch.Rd | 113 - optmatch-0.9-5/optmatch/man/optmatch_restrictions.Rd | 27 optmatch-0.9-5/optmatch/man/optmatch_same_distance.Rd | 31 optmatch-0.9-5/optmatch/man/pairmatch.Rd | 136 +- optmatch-0.9-5/optmatch/man/print.optmatch.Rd | 29 optmatch-0.9-5/optmatch/man/scores.Rd | 68 - optmatch-0.9-5/optmatch/man/subdim-methods.Rd | 26 optmatch-0.9-5/optmatch/man/subproblemSuccess.Rd | 22 optmatch-0.9-5/optmatch/man/update.optmatch.Rd | 27 optmatch-0.9-5/optmatch/src/Makevars | 11 optmatch-0.9-5/optmatch/src/cuseful.cc |only optmatch-0.9-5/optmatch/src/cuseful.h | 5 optmatch-0.9-5/optmatch/src/distances.cc |only optmatch-0.9-5/optmatch/src/distances.h | 5 optmatch-0.9-5/optmatch/src/ism.cc |only optmatch-0.9-5/optmatch/src/ism.h |only optmatch-0.9-5/optmatch/src/map.cc |only optmatch-0.9-5/optmatch/src/map.h | 4 optmatch-0.9-5/optmatch/src/r_smahal.cc |only optmatch-0.9-5/optmatch/src/r_smahal.h |only optmatch-0.9-5/optmatch/src/register.cc |only optmatch-0.9-5/optmatch/src/register.h | 9 optmatch-0.9-5/optmatch/src/smahal.cc |only optmatch-0.9-5/optmatch/src/smahal.h | 9 optmatch-0.9-5/optmatch/src/subsetInfSparseMatrix.cc |only optmatch-0.9-5/optmatch/src/subsetInfSparseMatrix.h | 5 optmatch-0.9-5/optmatch/tests/Examples/optmatch-Ex.Rout.save | 239 ---- optmatch-0.9-5/optmatch/tests/fullmatch.Rout.save | 21 optmatch-0.9-5/optmatch/tests/mahal-dist.Rout.save | 21 optmatch-0.9-5/optmatch/tests/maxcontrolscap-tests.Rout.save | 32 optmatch-0.9-5/optmatch/tests/mdist.Rout.save | 29 optmatch-0.9-5/optmatch/tests/moremethods.optmatch-tests.Rout.save | 19 optmatch-0.9-5/optmatch/tests/pairmatch-tests.Rout.save | 17 optmatch-0.9-5/optmatch/tests/stratumStructure-tests.Rout.save | 42 optmatch-0.9-5/optmatch/tests/summary.optmatch-tests.Rout.save | 23 100 files changed, 2392 insertions(+), 2028 deletions(-)
Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological processes to capture evolutionary signals in transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>
Diff between myTAI versions 0.2.1 dated 2015-07-23 and 0.3.0 dated 2015-07-30
DESCRIPTION | 9 - MD5 | 46 ++++---- NAMESPACE | 2 R/DiffGenes.R | 2 R/PlotBarRE.R | 2 R/PlotCategoryExpr.R |only R/PlotEnrichment.R | 1 R/PlotReplicateQuality.R |only README.md | 36 ++++-- inst/doc/Advanced.R | 104 ++++++++++++++++-- inst/doc/Advanced.Rmd | 232 ++++++++++++++++++++++++++++++++++++++--- inst/doc/Advanced.html | 159 +++++++++++++++++++++++++--- inst/doc/Enrichment.Rmd | 6 - inst/doc/Enrichment.html | 10 - inst/doc/Expression.R | 23 ++++ inst/doc/Expression.Rmd | 47 ++++++++ inst/doc/Expression.html | 30 ++++- inst/doc/Intermediate.html | 4 inst/doc/Introduction.html | 4 inst/doc/Taxonomy.html | 4 man/PlotCategoryExpr.Rd |only man/PlotReplicateQuality.Rd |only tests/testthat/test-taxonomy.R | 112 ++++++++++--------- vignettes/Advanced.Rmd | 232 ++++++++++++++++++++++++++++++++++++++--- vignettes/Enrichment.Rmd | 6 - vignettes/Expression.Rmd | 47 ++++++++ 26 files changed, 953 insertions(+), 165 deletions(-)
Title: Harvest the Classification Tree
Description: Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.
Author: Bingyuan Liu/Yan Yuan/Qian Shi
Maintainer: Bingyuan Liu <adler1016@gmail.com>
Diff between Harvest.Tree versions 1.0 dated 2015-07-10 and 1.1 dated 2015-07-30
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- R/harfunc.R | 2 +- R/harvest.R | 9 +++++++-- R/predict.harfunc.R | 10 +++++++--- man/Harvest.Tree-package.Rd | 13 +++++++------ man/harfunc.Rd | 2 +- man/harvest.Rd | 15 +++++++++++++-- man/predict.Rd | 15 ++++++++++++--- 9 files changed, 63 insertions(+), 33 deletions(-)
Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.0.1 dated 2015-06-28 and 1.1.0 dated 2015-07-30
ChangeLog | 187 ++++++++++++++++++++++++++++ DESCRIPTION | 26 ++- MD5 | 80 ++++++------ NAMESPACE | 4 NEWS | 38 +++++ R/attr_access.R | 11 + R/circlize.R |only R/color_branches.R | 19 ++ R/ggdend.R | 11 + R/labels_colors.R | 59 ++++++++ R/set.dendrogram.R | 13 + R/untangle.R | 11 + R/zzz.R | 3 README.md | 13 + TODO | 8 + build/vignette.rds |binary inst/CITATION |only inst/doc/Cluster_Analysis.R | 42 ++++-- inst/doc/Cluster_Analysis.Rmd | 169 ++++++++++++++----------- inst/doc/Cluster_Analysis.html | 226 ++++++++++++++++++---------------- inst/doc/FAQ.R | 69 +++++++++- inst/doc/FAQ.Rmd | 139 +++++++++++++++++++- inst/doc/FAQ.html | 118 +++++++++++++++-- inst/doc/Quick_Introduction.R |only inst/doc/Quick_Introduction.Rmd |only inst/doc/Quick_Introduction.html |only inst/doc/introduction.R | 63 ++++++++- inst/doc/introduction.Rmd | 85 ++++++++++++ inst/doc/introduction.html | 225 +++++++++++++++++++++------------ man/assign_values_to_nodes_nodePar.Rd | 7 + man/circlize_dendrogram.Rd |only man/color_branches.Rd | 3 man/color_labels.Rd | 3 man/get_leaves_branches_col.Rd | 2 man/ggdend.Rd | 5 man/labels_cex.Rd |only man/labels_colors.Rd | 8 + man/set.Rd | 7 - man/untangle.Rd | 1 man/untangle_step_rotate_1side.Rd | 2 man/untangle_step_rotate_2side.Rd | 8 + vignettes/Cluster_Analysis.Rmd | 169 ++++++++++++++----------- vignettes/FAQ.Rmd | 139 +++++++++++++++++++- vignettes/Quick_Introduction.Rmd |only vignettes/introduction.Rmd | 85 ++++++++++++ 45 files changed, 1596 insertions(+), 462 deletions(-)
Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@anu.edu.au>
Diff between climwin versions 0.1.0 dated 2015-07-19 and 0.1.1 dated 2015-07-30
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/otherfunctions.R | 4 ++-- R/zzz.R | 2 +- inst/doc/climwin.html | 4 ++-- tests/testthat/testplotall.R | 36 +++++++++++++++++++++++++----------- tests/testthat/testplotbest.R | 6 +++++- tests/testthat/testplotbetas.R | 21 +++++++++++++-------- tests/testthat/testplotdelta.R | 10 ++++++++-- tests/testthat/testplothist.R | 17 +++++++++++++---- tests/testthat/testplotweights.R | 10 ++++++++-- tests/testthat/testplotwin.R | 10 ++++++++-- 12 files changed, 99 insertions(+), 49 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.1.3 dated 2015-06-24 and 3.1.4 dated 2015-07-30
DESCRIPTION | 6 +- MD5 | 76 ++++++++++++++++---------------- NAMESPACE | 12 ++++- NEWS | 9 +++ R/as.char.R | 9 +++ R/dotlib.R | 5 +- R/lib.R | 2 R/meta.R | 3 - R/methods.R | 24 ++++++++++ R/plotmo.R | 6 +- R/plotresids.R | 2 R/xy.R | 2 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/Rplots.ps |only inst/slowtests/test.center.bat | 2 inst/slowtests/test.dots.R | 18 +++---- inst/slowtests/test.dots.Rout.save | 22 ++++----- inst/slowtests/test.dots.bat | 2 inst/slowtests/test.emma.Rout.save | 2 inst/slowtests/test.emma.bat | 2 inst/slowtests/test.fac.bat | 2 inst/slowtests/test.glmnet.bat | 2 inst/slowtests/test.ltut.R | 26 +++------- inst/slowtests/test.ltut.Rout.save | 31 +++++-------- inst/slowtests/test.ltut.bat | 2 inst/slowtests/test.non.earth.Rout.save | 6 +- inst/slowtests/test.non.earth.bat | 2 inst/slowtests/test.plotmo.Rout |only inst/slowtests/test.plotmo.Rout.save | 2 inst/slowtests/test.plotmo.args.bat | 2 inst/slowtests/test.plotmo.bat | 2 inst/slowtests/test.plotmo.dots.bat | 2 inst/slowtests/test.plotmo.x.bat | 2 inst/slowtests/test.plotmo3.Rout.save | 2 inst/slowtests/test.plotmo3.bat | 2 inst/slowtests/test.plotres.Rout.save | 2 inst/slowtests/test.plotres.bat | 2 inst/slowtests/test.printcall.bat | 2 40 files changed, 171 insertions(+), 124 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
A Windows binary file and scripts for an easy application of the functions are
provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.4 dated 2015-06-26 and 1.5 dated 2015-07-30
DESCRIPTION | 17 +++++++++------ MD5 | 56 ++++++++++++++++++++++++++------------------------- NAMESPACE | 5 ++-- R/box_mergetime.R | 4 +-- R/dayrange.R | 3 -- R/divdpm.R | 3 -- R/extract.period.R | 3 -- R/get_time.R |only R/levbox_mergetime.R | 4 +-- R/mon.anomaly.R | 3 -- R/monmean.R | 3 -- R/monsum.R | 3 -- R/muldpm.R | 3 -- R/multimonmean.R | 3 -- R/multimonsum.R | 3 -- R/ncinfo.R | 2 - R/seas.anomaly.R | 3 -- R/seasmean.R | 3 -- R/selmon.R | 3 -- R/selperiod.R | 3 -- R/seltime.R | 3 -- R/selyear.R | 3 -- R/year.anomaly.R | 3 -- R/yearmean.R | 3 -- R/yearsum.R | 3 -- R/ymonmean.R | 3 -- R/ymonsum.R | 3 -- R/yseasmean.R | 3 -- man/cmsaf-package.Rd | 7 +++--- man/get_time.Rd |only 30 files changed, 72 insertions(+), 86 deletions(-)
Title: Toolbox for Pseudo and Quasi Random Number Generation and RNG
Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some RNG tests - the gap test, the serial test, the poker test. The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package. A number of RNGs and tests for RNGs are also provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between randtoolbox versions 1.16 dated 2014-12-05 and 1.17 dated 2015-07-30
DESCRIPTION | 12 ++++++------ LICENSE | 6 +++--- MD5 | 27 ++++++++++++++------------- NAMESPACE | 7 +++++-- R/quasiRNG.R | 12 ++++-------- build/vignette.rds |binary configure.ac | 4 ++-- inst/NEWS | 15 +++++++++++++++ inst/doc/fullpres.R | 2 +- inst/doc/fullpres.pdf |binary inst/doc/shortintro.R | 2 +- inst/doc/shortintro.pdf |binary man/overall-doc.Rd | 17 ++++++++--------- man/pseudoRNG.Rd | 2 +- tests/test-sobol-scram.R |only 15 files changed, 60 insertions(+), 46 deletions(-)
Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine)
and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate
as well as vine copula selection are provided. Models can be estimated
either sequentially or by joint maximum likelihood estimation.
Sampling algorithms and plotting methods are also included.
Data is assumed to lie in the unit hypercube (so-called copula
data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt
<tobias.erhardt@tum.de>
Diff between CDVine versions 1.2 dated 2014-03-27 and 1.3 dated 2015-07-30
DESCRIPTION | 23 MD5 | 62 +- NAMESPACE | 73 +-- R/BiCopCDF.r | 148 +++--- R/BiCopChiPlot.r | 255 +++++----- R/BiCopEst.R | 1178 ++++++++++++++++++++++++-------------------------- R/BiCopGofKendall.r | 498 ++++++++++----------- R/BiCopHfunc.r | 145 +++--- R/BiCopIndTest.r | 36 - R/BiCopLambda.r | 511 ++++++++++----------- R/BiCopMetaContour.r | 848 +++++++++++++++++------------------ R/BiCopName.r | 232 ++++----- R/BiCopPDF.r | 109 +++- R/BiCopPar2TailDep.r | 220 ++++----- R/BiCopPar2Tau.r | 305 ++++++------ R/BiCopSelect.r | 689 ++++++++++++++--------------- R/BiCopSim.R | 10 R/BiCopTau2Par.r | 74 +-- R/BiCopVuongClarke.r | 384 +++++++--------- R/CDVineAIC.R | 300 +++++++----- R/CDVineClarkeTest.r | 369 +++++++++------ R/CDVineCopSelect.R | 272 +++++------ R/CDVineLogLik.R | 211 ++++---- R/CDVineMLE.R | 690 +++++++++++++++-------------- R/CDVinePar2Tau.r | 127 +++-- R/CDVineSeqEst.R | 507 ++++++++++----------- R/CDVineSim.R | 487 ++++++++++---------- R/CDVineTreePlot.R | 642 +++++++++++++-------------- R/CDVineVuongTest.r | 376 +++++++++------ R/zzz.R | 5 inst/ChangeLog | 8 man/CDVine-package.Rd | 11 32 files changed, 5087 insertions(+), 4718 deletions(-)
Title: A Simple Approach to Scale Gene Expression Data Derived from
Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene
expression generated across different experiments, and on
different platforms; that does not require global
renormalization, and is not restricted to comparison of
identical probes. YuGene works on a range of microarray dataset
distributions, such as between manufacturers. The resulting
output allows direct comparisons of gene expression between
experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>
Diff between YuGene versions 1.1.2 dated 2014-07-13 and 1.1.4 dated 2015-07-30
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 2 ++ NEWS |only data/array.rda |binary data/ascorbate.rda |binary man/YuGene-package.Rd | 4 ++-- man/pca.YuGene.Rd | 30 ++++++++++++++++-------------- 8 files changed, 34 insertions(+), 29 deletions(-)
Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')
to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and
q variables are measured on the same samples or individuals n. These data may come from high throughput
technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other
large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with
the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting
the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent
Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration
of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found
on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 5.0-4 dated 2015-04-28 and 5.1.1 dated 2015-07-30
mixOmics-5.0-4/mixOmics/R/cim.pls.R |only mixOmics-5.0-4/mixOmics/R/cim.rcc.R |only mixOmics-5.0-4/mixOmics/R/cim.spls.R |only mixOmics-5.0-4/mixOmics/R/wrapper.rgcca.R |only mixOmics-5.0-4/mixOmics/R/wrapper.sgcca.R |only mixOmics-5.0-4/mixOmics/README |only mixOmics-5.0-4/mixOmics/man/color.jet.Rd |only mixOmics-5.0-4/mixOmics/man/valid.Rd |only mixOmics-5.0-4/mixOmics/man/wrapper.rgcca.Rd |only mixOmics-5.0-4/mixOmics/man/wrapper.sgcca.Rd |only mixOmics-5.1.1/mixOmics/DESCRIPTION | 12 mixOmics-5.1.1/mixOmics/MD5 | 104 - mixOmics-5.1.1/mixOmics/NAMESPACE | 62 mixOmics-5.1.1/mixOmics/NEWS | 36 mixOmics-5.1.1/mixOmics/R/cim.R | 2031 +++++++++++++++------- mixOmics-5.1.1/mixOmics/R/helpers.R |only mixOmics-5.1.1/mixOmics/R/imgCor.R | 124 - mixOmics-5.1.1/mixOmics/R/perf.R | 4 mixOmics-5.1.1/mixOmics/R/plotContrib.R |only mixOmics-5.1.1/mixOmics/R/plotIndiv.R | 722 +++---- mixOmics-5.1.1/mixOmics/R/plotVar.R | 128 - mixOmics-5.1.1/mixOmics/R/pls.R | 159 + mixOmics-5.1.1/mixOmics/R/predict.R | 3 mixOmics-5.1.1/mixOmics/R/print.methods.R | 53 mixOmics-5.1.1/mixOmics/R/selectVar.R | 20 mixOmics-5.1.1/mixOmics/R/spls.R | 61 mixOmics-5.1.1/mixOmics/R/splsda.R | 2 mixOmics-5.1.1/mixOmics/R/srgcca.R |only mixOmics-5.1.1/mixOmics/R/tau.estim.R | 2 mixOmics-5.1.1/mixOmics/R/unmap.R | 82 mixOmics-5.1.1/mixOmics/R/withinVariation.R | 2 mixOmics-5.1.1/mixOmics/R/wrappers.R |only mixOmics-5.1.1/mixOmics/data/breast.tumors.rda |binary mixOmics-5.1.1/mixOmics/data/linnerud.rda |binary mixOmics-5.1.1/mixOmics/data/liver.toxicity.rda |binary mixOmics-5.1.1/mixOmics/data/multidrug.rda |binary mixOmics-5.1.1/mixOmics/data/nutrimouse.rda |binary mixOmics-5.1.1/mixOmics/data/prostate.rda |binary mixOmics-5.1.1/mixOmics/data/srbct.rda |binary mixOmics-5.1.1/mixOmics/data/vac18.rda |binary mixOmics-5.1.1/mixOmics/data/vac18.simulated.rda |binary mixOmics-5.1.1/mixOmics/data/yeast.rda |binary mixOmics-5.1.1/mixOmics/man/cim.Rd | 439 +++- mixOmics-5.1.1/mixOmics/man/colors.Rd |only mixOmics-5.1.1/mixOmics/man/imgCor.Rd | 46 mixOmics-5.1.1/mixOmics/man/internal-functions.Rd | 13 mixOmics-5.1.1/mixOmics/man/ipca.Rd | 4 mixOmics-5.1.1/mixOmics/man/multilevel.Rd | 39 mixOmics-5.1.1/mixOmics/man/pca.Rd | 4 mixOmics-5.1.1/mixOmics/man/plotContrib.Rd |only mixOmics-5.1.1/mixOmics/man/plotIndiv.Rd | 249 +- mixOmics-5.1.1/mixOmics/man/plotVar.Rd | 86 mixOmics-5.1.1/mixOmics/man/plsda.Rd | 14 mixOmics-5.1.1/mixOmics/man/rcc.Rd | 5 mixOmics-5.1.1/mixOmics/man/selectVar.Rd | 20 mixOmics-5.1.1/mixOmics/man/sipca.Rd | 4 mixOmics-5.1.1/mixOmics/man/spca.Rd | 4 mixOmics-5.1.1/mixOmics/man/splsda.Rd | 10 mixOmics-5.1.1/mixOmics/man/tau.estimate.Rd | 17 mixOmics-5.1.1/mixOmics/man/unmap.Rd |only mixOmics-5.1.1/mixOmics/man/withinVariation.Rd | 4 mixOmics-5.1.1/mixOmics/man/wrappers.Rd |only 62 files changed, 2866 insertions(+), 1699 deletions(-)
Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from
environmental monitoring programs. The package name stands for "water quality"
and reflects the original focus on time series data for physical and
chemical properties of water, as well as the plankton. Intended for programs
that sample approximately monthly at discrete stations, a feature of many
legacy data sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>
Diff between wq versions 0.4.3 dated 2015-04-03 and 0.4.4 dated 2015-07-30
wq-0.4.3/wq/R/wq-internal.R |only wq-0.4.3/wq/man/wq-internal.Rd |only wq-0.4.4/wq/DESCRIPTION | 14 ++-- wq-0.4.4/wq/MD5 | 22 +++---- wq-0.4.4/wq/NAMESPACE | 10 ++- wq-0.4.4/wq/NEWS | 8 ++ wq-0.4.4/wq/R/WqData-class.R | 3 wq-0.4.4/wq/build/vignette.rds |binary wq-0.4.4/wq/inst/doc/wq-package.R | 106 +++++++++++++++++------------------ wq-0.4.4/wq/inst/doc/wq-package.Rnw | 4 - wq-0.4.4/wq/inst/doc/wq-package.pdf |binary wq-0.4.4/wq/man/wq-package.Rd | 8 +- wq-0.4.4/wq/vignettes/wq-package.Rnw | 4 - 13 files changed, 98 insertions(+), 81 deletions(-)
Title: Robust Regression Functions
Description: Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.
Author: Ian M. Johnson <ian@alpha-analysis.com>
Maintainer: Ian M. Johnson <ian@alpha-analysis.com>
Diff between robustreg versions 0.1-7 dated 2014-10-28 and 0.1-8 dated 2015-07-30
robustreg-0.1-7/robustreg/src/Makevars |only robustreg-0.1-8/robustreg/DESCRIPTION | 14 +++++++------- robustreg-0.1-8/robustreg/MD5 | 11 +++++------ robustreg-0.1-8/robustreg/NAMESPACE | 8 +++++--- robustreg-0.1-8/robustreg/man/fit.Rd | 4 ++-- robustreg-0.1-8/robustreg/man/robustRegBS.Rd | 2 +- robustreg-0.1-8/robustreg/man/robustRegH.Rd | 2 +- 7 files changed, 21 insertions(+), 20 deletions(-)
Title: Analysis of Data Acquired Using the Receiver Operating
Characteristic Paradigm and Its Extensions
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software.
Author: Xuetong Zhai [aut, cre],
Dev Chakraborty [aut, ths]
Maintainer: Xuetong Zhai <xuetong.zhai@gmail.com>
Diff between RJafroc versions 0.0.1 dated 2015-04-24 and 0.1.0 dated 2015-07-30
DESCRIPTION | 12 MD5 | 103 ++-- NAMESPACE | 12 R/CalculateAFROCPoints.R | 6 R/CalculateAvgAFROCPoints.R | 6 R/CalculateAvgFROCPoints.R | 1 R/CalculateAvgROCPoints.R | 13 R/CalculateFROCPoints.R | 1 R/CalculateROCPoints.R | 13 R/DBMHAnalysis.R | 2 R/EmpiricalOpCharac.R | 2 R/EstimateVarCov.R | 41 + R/FROC2HrROC.R |only R/ORHAnalysis.R | 1 R/PlotAFROC.R | 80 ++- R/PlotFROC.R | 84 +++ R/PlotROC.R | 80 ++- R/PowerGivenJK.R | 1 R/PowerTable.R | 2 R/RJafrocGui.R |only R/ReadDataFile.R | 31 - R/ReadJAFROC.R | 30 + R/ReadOrDbmMrmc.R | 1 R/ResamplingEstimateVarCovs.R | 1 R/SampleSizeGivenJ.R | 5 R/SaveJAFROC.R | 12 build/vignette.rds |binary inst/GUI |only inst/doc/RJafroc.R | 193 ++++---- inst/doc/RJafroc.Rnw | 941 +++++++++++++++++++++++------------------- inst/doc/RJafroc.pdf |binary inst/tests |only man/DBMHAnalysis.Rd | 2 man/EmpiricalOpCharac.Rd | 4 man/FROC2HrROC.Rd |only man/FigureOfMerit.Rd | 2 man/ORHAnalysis.Rd | 2 man/OutputReport.Rd | 2 man/PowerGivenJK.Rd | 2 man/PowerTable.Rd | 2 man/RJafroc-package.Rd | 1 man/RJafrocGui.Rd |only man/ReadDataFile.Rd | 33 - man/SampleSizeGivenJ.Rd | 2 man/SaveDataFile.Rd | 2 man/frocData.Rd | 2 man/rocData.Rd | 2 man/roiData.Rd | 2 vignettes/Analysis.png |only vignettes/DataViewer.png |only vignettes/Opening.png |only vignettes/RJafroc.Rnw | 941 +++++++++++++++++++++++------------------- vignettes/RJafroc.bib | 493 ++++++++++++++-------- vignettes/Report.png |only vignettes/SelectFile.png |only 55 files changed, 1885 insertions(+), 1283 deletions(-)
Title: Integrates R and Essentia
Description: Contains two functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.udb' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>
Diff between RESS versions 1.1 dated 2015-06-09 and 1.2 dated 2015-07-30
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + R/essquery.R | 10 ++++++---- R/readudb.R | 8 +++++--- man/RESS-package.Rd | 4 ++-- man/essQuery.Rd | 26 +++++++++++++------------- man/read.udb.Rd | 32 ++++++++++++++++---------------- 8 files changed, 55 insertions(+), 49 deletions(-)
Title: Statistical Inference and Sensitivity Analysis for Instrumental
Variables Model
Description: Contains functions for carrying out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics.
Author: Yang Jiang, Hyunseung Kang, and Dylan Small
Maintainer: Hyunseung Kang <hskang@stanford.edu>
Diff between ivmodel versions 1.0 dated 2015-05-03 and 1.1 dated 2015-07-30
ivmodel-1.0/ivmodel/man/print.ivmodel.Rd |only ivmodel-1.1/ivmodel/DESCRIPTION | 17 +-- ivmodel-1.1/ivmodel/MD5 | 44 ++++---- ivmodel-1.1/ivmodel/NAMESPACE | 18 +-- ivmodel-1.1/ivmodel/R/function.r | 38 ++++++- ivmodel-1.1/ivmodel/R/method.r | 10 + ivmodel-1.1/ivmodel/build |only ivmodel-1.1/ivmodel/man/AR.power.Rd | 132 +++++++++---------------- ivmodel-1.1/ivmodel/man/AR.size.Rd | 136 +++++++++---------------- ivmodel-1.1/ivmodel/man/AR.test.Rd | 84 +++++---------- ivmodel-1.1/ivmodel/man/ARsens.power.Rd | 153 ++++++++++------------------- ivmodel-1.1/ivmodel/man/ARsens.size.Rd | 141 ++++++++++---------------- ivmodel-1.1/ivmodel/man/ARsens.test.Rd | 81 ++++----------- ivmodel-1.1/ivmodel/man/CLR.test.Rd | 29 ++--- ivmodel-1.1/ivmodel/man/FullerEst.Rd | 34 +++--- ivmodel-1.1/ivmodel/man/LIMLEst.Rd | 27 ++--- ivmodel-1.1/ivmodel/man/TSLS.power.Rd |only ivmodel-1.1/ivmodel/man/TSLS.size.Rd |only ivmodel-1.1/ivmodel/man/card.data.Rd | 16 --- ivmodel-1.1/ivmodel/man/coef.ivmodel.Rd | 67 ++++-------- ivmodel-1.1/ivmodel/man/confint.ivmodel.Rd | 71 ++++--------- ivmodel-1.1/ivmodel/man/ivmodel-package.Rd | 71 ++++++------- ivmodel-1.1/ivmodel/man/ivmodel.Rd | 46 ++++---- ivmodel-1.1/ivmodel/man/kClassEst.Rd | 36 +++--- ivmodel-1.1/ivmodel/man/para.Rd |only ivmodel-1.1/ivmodel/man/summary.ivmodel.Rd |only 26 files changed, 531 insertions(+), 720 deletions(-)
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output
Description: Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.5-7 dated 2015-07-28 and 1.5-8 dated 2015-07-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 +++++ src/cairogd.h | 2 +- src/img-backend.c | 2 +- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: The Bayesian Dynamic Conditional Correlation GARCH Model
Description: Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635).
Author: Jose A Fioruci <jafioruci@gmail.com>, Ricardo S Ehlers <ehlers@icmc.usp.br>, Francisco Louzada <louzada@icmc.usp.br>
Maintainer: Jose A Fioruci <jafioruci@gmail.com>
Diff between bayesDccGarch versions 1.1 dated 2015-06-03 and 1.2 dated 2015-07-30
ChangeLog | 13 +++++++++---- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/mainFunctions.R | 2 +- man/bayesDccGarch-package.Rd | 6 +++--- man/bayesDccGarch.Rd | 2 +- 7 files changed, 26 insertions(+), 19 deletions(-)
Title: Signal Processing
Description: A set of signal processing functions originally written for 'Matlab' and 'Octave'.
Includes filter generation utilities, filtering functions,
resampling routines, and visualization of filter models. It also
includes interpolation functions.
Author: Uwe Ligges [aut, cre] (new maintainer),
Tom Short [aut] (port to R),
Paul Kienzle [aut] (majority of the original sources),
Sarah Schnackenberg [ctb] (various test cases and bug fixes),
David Billinghurst [ctb],
Hans-Werner Borchers [ctb],
Andre Carezia [ctb],
Pascal Dupuis [ctb],
John W. Eaton [ctb],
E. Farhi [ctb],
Kai Habel [ctb],
Kurt Hornik [ctb],
Sebastian Krey [ctb],
Bill Lash [ctb],
Friedrich Leisch [ctb],
Olaf Mersmann [ctb],
Paulo Neis [ctb],
Jaakko Ruohio [ctb],
Julius O. Smith III [ctb],
Doug Stewart [ctb],
Andreas Weingessel [ctb]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between signal versions 0.7-5 dated 2015-05-31 and 0.7-6 dated 2015-07-29
ChangeLog | 3 +++ DESCRIPTION | 18 +++++++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ R/chebwin.R | 8 ++++---- R/sftrans.R | 12 ++++++------ man/chebwin.Rd | 2 +- man/resample.Rd | 2 +- man/signal.package.Rd | 2 +- 9 files changed, 35 insertions(+), 30 deletions(-)
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between scatterplot3d versions 0.3-35 dated 2014-02-11 and 0.3-36 dated 2015-07-29
CHANGES | 3 ++- DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NAMESPACE | 3 +++ build/vignette.rds |binary inst/doc/s3d.pdf |binary 6 files changed, 15 insertions(+), 10 deletions(-)
Title: R Interface to WinEdt
Description: A plug in for using WinEdt as an editor for R.
Author: Uwe Ligges <Uwe.Ligges@R-project.org>
with contributions (the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller
Maintainer: Uwe Ligges <Uwe.Ligges@R-project.org>
Diff between RWinEdt versions 2.0-4 dated 2015-06-17 and 2.0-5 dated 2015-07-29
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 1 + inst/doc/RWinEdt.pdf |binary src/Makevars.win | 2 +- 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
Description: Invoke a 'BUGS' model in 'OpenBUGS' or 'WinBUGS', a class "bugs" for 'BUGS'
results and functions to work with that class.
Function write.model() allows a 'BUGS' model file to be written.
The class and auxiliary functions could be used with other MCMC programs, including 'JAGS'.
Author: originally written by Andrew Gelman <gelman@stat.columbia.edu>;
changes and packaged by Sibylle Sturtz <sturtz@statistik.tu-dortmund.de>
and Uwe Ligges <ligges@statistik.tu-dortmund.de>.
With considerable contributions by Gregor Gorjanc <gregor.gorjanc@bfro.uni-lj.si>
and Jouni Kerman <kerman@stat.columbia.edu>.
Ported to S-PLUS by Insightful Corp.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between R2WinBUGS versions 2.1-20 dated 2015-05-31 and 2.1-21 dated 2015-07-29
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/attach.all.R | 2 +- inst/NEWS | 4 ++++ 5 files changed, 18 insertions(+), 9 deletions(-)
Title: Tests for Normality
Description: Five omnibus tests for testing the composite hypothesis of
normality.
Author: Juergen Gross [aut],
Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between nortest versions 1.0-3 dated 2015-02-26 and 1.0-4 dated 2015-07-29
ChangeLog | 3 +++ DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 1 + 4 files changed, 13 insertions(+), 8 deletions(-)
More information about googlePublicData at CRAN
Permanent link
Title: Interface to the 'OpenBUGS' MCMC Software
Description: Fully-interactive R interface to the 'OpenBUGS' software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between BRugs versions 0.8-4 dated 2015-05-31 and 0.8-5 dated 2015-07-29
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NAMESPACE | 6 +++++- NEWS | 3 +++ man/BRugs.Rd | 4 ++-- man/model.factory.Rd | 2 +- 6 files changed, 24 insertions(+), 17 deletions(-)
Title: Advanced Data Analysis of T Cell Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.1 dated 2015-07-28 and 2.1.1 dated 2015-07-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/input.R | 8 ++++---- README.md | 2 +- inst/doc/tcrvignette.html | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 1.7 dated 2015-06-15 and 1.9.2 dated 2015-07-29
DESCRIPTION | 16 ++++++++-------- MD5 | 35 +++++++++++++++++++---------------- NAMESPACE | 20 ++++++++++++++++++++ NEWS.md |only R/calc.imp.pval.R | 17 +++++++++++------ R/clean.rf.data.R | 2 ++ R/exptd.err.rate.R |only R/plot.rfPermute.R | 3 +++ R/plot.rp.importance.r | 30 +++++++++++++++++++++++------- R/proximity.plot.r | 11 +++++++++++ R/rfPermute.R | 31 +++++++++++++++++++++++++------ R/rfPermute.default.R | 27 ++++++++++++++++++++++----- R/rfPermute.formula.R | 1 + R/rp.combine.R | 3 ++- inst/NEWS.rd | 6 ++++++ man/calc.imp.pval.Rd | 6 ++++-- man/exptd.err.rate.Rd |only man/plot.rp.importance.Rd | 8 ++++++-- man/proximity.plot.Rd | 6 ++++++ man/rfPermute.Rd | 19 ++++++++++++++----- 20 files changed, 183 insertions(+), 58 deletions(-)
Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and
techniques used in the field of pedometrics (see
http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics).
These functions were developed to fulfil the demands created by the PhD
research project (2012-2016) entitled "Contribution to the Construction of
Models for Predicting Soil Properties", developed by Alessandro Samuel-Rosa
under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do
Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and
Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands).
The project is supported by the CAPES, Ministério da Educação, BrasÃlia -
DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions
simply extend the functionalities of other functions
commonly used for the analysis of pedometric data. It should be noted that
changes are likely to occur quite often and the use of this package as a
dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre],
Lúcia Anjos [ths],
Gustavo Vasques [ths],
Gerard Heuvelink [ths],
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb],
Frank Harrell Jr [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-2 dated 2015-06-02 and 0.6-3 dated 2015-07-29
pedometrics-0.6-2/pedometrics/man/is.numint.Rd |only pedometrics-0.6-3/pedometrics/DESCRIPTION | 96 ++++--- pedometrics-0.6-3/pedometrics/MD5 | 83 +++--- pedometrics-0.6-3/pedometrics/NAMESPACE | 42 +-- pedometrics-0.6-3/pedometrics/R/AAAA.R |only pedometrics-0.6-3/pedometrics/R/adjR2.R | 24 - pedometrics-0.6-3/pedometrics/R/bbox2sp.R | 65 ++--- pedometrics-0.6-3/pedometrics/R/buildMS.R | 54 +--- pedometrics-0.6-3/pedometrics/R/cdfPlot.R | 97 +++---- pedometrics-0.6-3/pedometrics/R/cdfStats.R | 18 - pedometrics-0.6-3/pedometrics/R/cdfTable.R | 24 - pedometrics-0.6-3/pedometrics/R/cont2cat.R | 182 ++++++++++++--- pedometrics-0.6-3/pedometrics/R/coordenadas.R | 31 -- pedometrics-0.6-3/pedometrics/R/cramer.R | 4 pedometrics-0.6-3/pedometrics/R/gcpDiff.R | 21 - pedometrics-0.6-3/pedometrics/R/numint.R | 120 +++++++-- pedometrics-0.6-3/pedometrics/R/pedometrics.R | 35 +- pedometrics-0.6-3/pedometrics/R/plotESDA.R | 52 ++-- pedometrics-0.6-3/pedometrics/R/plotHD.R | 110 ++++----- pedometrics-0.6-3/pedometrics/R/plotMS.R | 69 ++--- pedometrics-0.6-3/pedometrics/R/statsMS.R | 65 ++--- pedometrics-0.6-3/pedometrics/R/stepVIF.R | 49 +--- pedometrics-0.6-3/pedometrics/R/trend.R |only pedometrics-0.6-3/pedometrics/R/vgmLags.R |only pedometrics-0.6-3/pedometrics/man/adjR2.Rd | 4 pedometrics-0.6-3/pedometrics/man/bbox2sp.Rd | 5 pedometrics-0.6-3/pedometrics/man/buildMS.Rd | 4 pedometrics-0.6-3/pedometrics/man/cdfPlot.Rd | 2 pedometrics-0.6-3/pedometrics/man/cdfStats.Rd | 2 pedometrics-0.6-3/pedometrics/man/cdfTable.Rd | 2 pedometrics-0.6-3/pedometrics/man/cont2cat.Rd | 59 +++- pedometrics-0.6-3/pedometrics/man/coordenadas.Rd | 4 pedometrics-0.6-3/pedometrics/man/cramer.Rd | 2 pedometrics-0.6-3/pedometrics/man/gcpDiff.Rd | 6 pedometrics-0.6-3/pedometrics/man/gcpVector.Rd | 2 pedometrics-0.6-3/pedometrics/man/numint.Rd |only pedometrics-0.6-3/pedometrics/man/pedometrics-package.Rd | 37 +-- pedometrics-0.6-3/pedometrics/man/plotESDA.Rd | 12 pedometrics-0.6-3/pedometrics/man/plotHD.Rd | 6 pedometrics-0.6-3/pedometrics/man/plotMS.Rd | 4 pedometrics-0.6-3/pedometrics/man/rowMinCpp.Rd | 2 pedometrics-0.6-3/pedometrics/man/statsMS.Rd | 4 pedometrics-0.6-3/pedometrics/man/stepVIF.Rd | 8 pedometrics-0.6-3/pedometrics/man/trend.Rd |only pedometrics-0.6-3/pedometrics/man/vgmLags.Rd |only pedometrics-0.6-3/pedometrics/src/RcppExports.cpp | 14 - 46 files changed, 764 insertions(+), 656 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 0.1-3 dated 2015-07-01 and 0.1-4 dated 2015-07-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS.Rd | 8 ++++++++ man/Pade.Rd | 2 +- 4 files changed, 16 insertions(+), 8 deletions(-)
More information about HistogramTools at CRAN
Permanent link
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tool for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Diff between ggmcmc versions 0.6 dated 2014-12-30 and 0.7.1 dated 2015-07-29
DESCRIPTION | 20 ++++----- MD5 | 94 ++++++++++++++++++++++---------------------- NAMESPACE | 4 + NEWS | 30 ++++++++++++++ R/functions.R | 8 +-- R/ggs.R | 63 +++++++++++++++++++++-------- R/ggs_Rhat.R | 16 +++---- R/ggs_caterpillar.R | 2 R/ggs_compare_partial.R | 4 - R/ggs_crosscorrelation.R | 3 - R/ggs_geweke.R | 12 ++--- R/ggs_pairs.R |only R/ggs_ppmean.R | 2 R/ggs_ppsd.R | 2 R/ggs_rocplot.R | 6 +- R/ggs_running.R | 6 +- R/ggs_separation.R | 8 +-- R/globals.R | 5 +- man/ac.Rd | 2 man/calc_bin.Rd | 2 man/ci.Rd | 4 - man/get_family.Rd | 2 man/ggmcmc.Rd | 2 man/ggs.Rd | 5 +- man/ggs_Rhat.Rd | 2 man/ggs_autocorrelation.Rd | 2 man/ggs_caterpillar.Rd | 2 man/ggs_chain.Rd | 2 man/ggs_compare_partial.Rd | 2 man/ggs_crosscorrelation.Rd | 2 man/ggs_density.Rd | 2 man/ggs_geweke.Rd | 2 man/ggs_histogram.Rd | 2 man/ggs_pairs.Rd |only man/ggs_ppmean.Rd | 2 man/ggs_ppsd.Rd | 2 man/ggs_rocplot.Rd | 2 man/ggs_running.Rd | 2 man/ggs_separation.Rd | 2 man/ggs_traceplot.Rd | 2 man/gl_unq.Rd | 2 man/radon.Rd | 2 man/roc_calc.Rd | 2 man/s.Rd | 2 man/s.binary.Rd | 2 man/s.y.rep.Rd | 2 man/sde0f.Rd | 2 man/y.Rd | 2 man/y.binary.Rd | 2 49 files changed, 210 insertions(+), 140 deletions(-)
Title: Density Surface Modelling of Distance Sampling Data
Description: Density surface modelling of line transect data. A Generalized Additive Model-based approach is used to calculate spatially-explicit estimates of animal abundance from distance sampling (also presence/absence and strip transect) data. Several utility functions are provided for model checking, plotting and variance estimation.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley.
Maintainer: David Lawrence Miller <dave@ninepointeightone.net>
Diff between dsm versions 2.2.5 dated 2014-09-15 and 2.2.9 dated 2015-07-29
DESCRIPTION | 29 ++--------- MD5 | 106 ++++++++++++++++++++--------------------- NAMESPACE | 37 +++++++++++++- NEWS | 16 ++++++ R/check.cols.R | 2 R/dsm-package.R | 9 ++- R/dsm.R | 40 ++++++++------- R/dsm.cor.R | 6 +- R/dsm.var.gam.R | 72 +++++++++++++-------------- R/dsm.var.movblk.R | 15 +++-- R/dsm.var.prop.R | 43 +++++----------- R/generate.ds.uncertainty.R | 1 R/make.data.R | 6 ++ R/plot.dsm.R | 4 - R/plot.dsm.var.R | 23 ++++---- R/predict.dsm.R | 17 ++---- R/print.dsm.R | 4 - R/print.dsm.var.R | 27 ---------- R/print.summary.dsm.var.R | 19 ++++--- R/rqgam.check.R | 46 +++++++++++++---- R/summary.dsm.R | 4 - R/summary.dsm.var.R | 64 +++++++++++++----------- R/trim.var.R | 5 + README.md | 5 + data/mexdolphins.rda |binary man/block.info.per.su.Rd | 3 - man/check.cols.Rd | 3 - man/dsm-data.Rd | 3 - man/dsm-package.Rd | 10 +++ man/dsm.Rd | 17 ++++-- man/dsm.cor.Rd | 11 ++-- man/dsm.var.gam.Rd | 31 +++-------- man/dsm.var.movblk.Rd | 11 +--- man/dsm.var.prop.Rd | 30 +++-------- man/generate.ds.uncertainty.Rd | 3 - man/generate.mb.sample.Rd | 3 - man/latlong2km.Rd | 3 - man/make.soapgrid.Rd | 3 - man/matrixnotposdef.handler.Rd | 3 - man/mexdolphins.Rd | 5 + man/offsets.Rd | 3 - man/plot.dsm.Rd | 3 - man/plot.dsm.var.Rd | 3 - man/predict.dsm.Rd | 16 +++--- man/print.dsm.Rd | 3 - man/print.dsm.var.Rd | 3 - man/print.summary.dsm.var.Rd | 3 - man/rqgam.check.Rd | 13 +++-- man/summary.dsm.Rd | 3 - man/summary.dsm.var.Rd | 3 - man/trim.var.Rd | 3 - tests/testthat/test_input.R | 38 +++++++++++++- tests/testthat/test_mex.R | 3 - tests/testthat/test_movblk.R | 29 +++++++++-- 54 files changed, 486 insertions(+), 379 deletions(-)
Title: R Binder for the Yhat API
Description: Deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp <greg@yhathq.com>, Eric Chiang <eric@yhathq.com>
Maintainer: Greg Lamp <greg@yhathq.com>
Diff between yhatr versions 0.13.6 dated 2015-06-19 and 0.13.7 dated 2015-07-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 ++ R/yhatR.R | 32 +++++++++++++++++++++----------- 4 files changed, 30 insertions(+), 18 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: David Miller <dave@ninepointeightone.net>
Diff between mrds versions 2.1.12 dated 2015-02-04 and 2.1.14 dated 2015-07-29
mrds-2.1.12/mrds/R/errors.R |only mrds-2.1.12/mrds/man/errors.Rd |only mrds-2.1.14/mrds/DESCRIPTION | 13 mrds-2.1.14/mrds/MD5 | 354 ++++++++++---------- mrds-2.1.14/mrds/NAMESPACE | 43 ++ mrds-2.1.14/mrds/NEWS | 18 + mrds-2.1.14/mrds/R/DeltaMethod.R | 33 - mrds-2.1.14/mrds/R/NCovered.io.fi.R | 2 mrds-2.1.14/mrds/R/NCovered.rem.R | 3 mrds-2.1.14/mrds/R/NCovered.trial.R | 1 mrds-2.1.14/mrds/R/cdf.ds.R | 8 mrds-2.1.14/mrds/R/check.bounds.R | 43 +- mrds-2.1.14/mrds/R/check.mono.R | 15 mrds-2.1.14/mrds/R/coef.ds.R | 1 mrds-2.1.14/mrds/R/compute.Nht.R | 4 mrds-2.1.14/mrds/R/create.ddfobj.R | 12 mrds-2.1.14/mrds/R/create.varstructure.R | 4 mrds-2.1.14/mrds/R/ddf.ds.R | 24 - mrds-2.1.14/mrds/R/ddf.gof.R | 13 mrds-2.1.14/mrds/R/ddf.io.R | 4 mrds-2.1.14/mrds/R/ddf.io.fi.R | 1 mrds-2.1.14/mrds/R/ddf.rem.R | 2 mrds-2.1.14/mrds/R/detfct.fit.R | 90 ++--- mrds-2.1.14/mrds/R/detfct.fit.mono.R | 15 mrds-2.1.14/mrds/R/detfct.fit.opt.R | 174 ++++++--- mrds-2.1.14/mrds/R/dht.R | 26 - mrds-2.1.14/mrds/R/dht.se.R | 22 - mrds-2.1.14/mrds/R/flnl.R | 10 mrds-2.1.14/mrds/R/flpt.lnl.r | 2 mrds-2.1.14/mrds/R/g0.R | 2 mrds-2.1.14/mrds/R/gof.ds.R | 1 mrds-2.1.14/mrds/R/gstdint.R | 3 mrds-2.1.14/mrds/R/histline.R | 6 mrds-2.1.14/mrds/R/integratelogisticdup.R | 26 + mrds-2.1.14/mrds/R/integratepdf.r | 1 mrds-2.1.14/mrds/R/io.glm.R | 17 mrds-2.1.14/mrds/R/is.linear.logistic.R | 10 mrds-2.1.14/mrds/R/is.logistic.constant.R | 6 mrds-2.1.14/mrds/R/logisticbyx.R | 4 mrds-2.1.14/mrds/R/logisticbyz.R | 4 mrds-2.1.14/mrds/R/logisticdupbyx.R | 13 mrds-2.1.14/mrds/R/logisticdupbyx_fast.R |only mrds-2.1.14/mrds/R/mrds-package.R | 4 mrds-2.1.14/mrds/R/nlminb_wrapper.R |only mrds-2.1.14/mrds/R/optimx.setup.R |only mrds-2.1.14/mrds/R/p.det.R | 48 +- mrds-2.1.14/mrds/R/parse.optimx.R |only mrds-2.1.14/mrds/R/pdot.dsr.integrate.logistic.R | 22 - mrds-2.1.14/mrds/R/plot.det.tables.R | 2 mrds-2.1.14/mrds/R/plot.ds.R | 25 - mrds-2.1.14/mrds/R/plot.layout.R | 1 mrds-2.1.14/mrds/R/plot_uncond.R | 1 mrds-2.1.14/mrds/R/predict.ds.R | 5 mrds-2.1.14/mrds/R/predict.io.fi.R | 10 mrds-2.1.14/mrds/R/print.dht.R | 92 ++--- mrds-2.1.14/mrds/R/prob.se.R | 2 mrds-2.1.14/mrds/R/process.data.R | 2 mrds-2.1.14/mrds/R/qqplot.ddf.R | 6 mrds-2.1.14/mrds/R/rescale_pars.R |only mrds-2.1.14/mrds/R/scalecheck.R |only mrds-2.1.14/mrds/R/setcov.R | 8 mrds-2.1.14/mrds/R/setinitial.ds.R | 12 mrds-2.1.14/mrds/R/summary.ds.R | 12 mrds-2.1.14/mrds/R/survey.region.dht.R | 7 mrds-2.1.14/mrds/R/test.breaks.R | 14 mrds-2.1.14/mrds/README.md | 9 mrds-2.1.14/mrds/data/book.tee.data.rda |binary mrds-2.1.14/mrds/man/DeltaMethod.Rd | 36 -- mrds-2.1.14/mrds/man/NCovered.Rd | 3 mrds-2.1.14/mrds/man/adj.check.order.Rd | 3 mrds-2.1.14/mrds/man/apex.gamma.Rd | 3 mrds-2.1.14/mrds/man/assign.default.values.Rd | 3 mrds-2.1.14/mrds/man/assign.par.Rd | 3 mrds-2.1.14/mrds/man/average.line.Rd | 3 mrds-2.1.14/mrds/man/average.line.cond.Rd | 3 mrds-2.1.14/mrds/man/book.tee.data.Rd | 3 mrds-2.1.14/mrds/man/calc.se.Np.Rd | 3 mrds-2.1.14/mrds/man/cdf.ds.Rd | 3 mrds-2.1.14/mrds/man/cds.Rd | 3 mrds-2.1.14/mrds/man/check.bounds.Rd | 11 mrds-2.1.14/mrds/man/check.mono.Rd | 5 mrds-2.1.14/mrds/man/coef.ds.Rd | 3 mrds-2.1.14/mrds/man/compute.Nht.Rd | 3 mrds-2.1.14/mrds/man/covered.region.dht.Rd | 3 mrds-2.1.14/mrds/man/create.ddfobj.Rd | 3 mrds-2.1.14/mrds/man/create.model.frame.Rd | 3 mrds-2.1.14/mrds/man/create.varstructure.Rd | 3 mrds-2.1.14/mrds/man/ddf.Rd | 3 mrds-2.1.14/mrds/man/ddf.ds.Rd | 3 mrds-2.1.14/mrds/man/ddf.gof.Rd | 12 mrds-2.1.14/mrds/man/ddf.io.Rd | 3 mrds-2.1.14/mrds/man/ddf.io.fi.Rd | 3 mrds-2.1.14/mrds/man/ddf.rem.Rd | 3 mrds-2.1.14/mrds/man/ddf.rem.fi.Rd | 3 mrds-2.1.14/mrds/man/ddf.trial.Rd | 3 mrds-2.1.14/mrds/man/ddf.trial.fi.Rd | 3 mrds-2.1.14/mrds/man/det.tables.Rd | 3 mrds-2.1.14/mrds/man/detfct.fit.Rd | 4 mrds-2.1.14/mrds/man/detfct.fit.opt.Rd | 4 mrds-2.1.14/mrds/man/dht.Rd | 26 - mrds-2.1.14/mrds/man/dht.deriv.Rd | 3 mrds-2.1.14/mrds/man/dht.se.Rd | 3 mrds-2.1.14/mrds/man/distpdf.Rd | 3 mrds-2.1.14/mrds/man/ds.function.Rd | 3 mrds-2.1.14/mrds/man/flnl.Rd | 3 mrds-2.1.14/mrds/man/flt.var.Rd | 3 mrds-2.1.14/mrds/man/g0.Rd | 3 mrds-2.1.14/mrds/man/getpar.Rd | 3 mrds-2.1.14/mrds/man/gof.ds.Rd | 3 mrds-2.1.14/mrds/man/gstdint.Rd | 3 mrds-2.1.14/mrds/man/histline.Rd | 3 mrds-2.1.14/mrds/man/integratedetfct.logistic.Rd | 3 mrds-2.1.14/mrds/man/integratelogistic.analytic.Rd | 3 mrds-2.1.14/mrds/man/integratepdf.Rd | 3 mrds-2.1.14/mrds/man/io.glm.Rd | 3 mrds-2.1.14/mrds/man/is.linear.logistic.Rd | 3 mrds-2.1.14/mrds/man/is.logistic.constant.Rd | 3 mrds-2.1.14/mrds/man/keyfct.th1.Rd | 3 mrds-2.1.14/mrds/man/keyfct.th2.Rd | 3 mrds-2.1.14/mrds/man/lfbcvi.Rd | 3 mrds-2.1.14/mrds/man/lfgcwa.Rd | 3 mrds-2.1.14/mrds/man/logisticbyx.Rd | 3 mrds-2.1.14/mrds/man/logisticbyz.Rd | 3 mrds-2.1.14/mrds/man/logisticdetfct.Rd | 3 mrds-2.1.14/mrds/man/logisticdupbyx.Rd | 3 mrds-2.1.14/mrds/man/logisticdupbyx_fast.Rd |only mrds-2.1.14/mrds/man/logit.Rd | 3 mrds-2.1.14/mrds/man/mcds.Rd | 3 mrds-2.1.14/mrds/man/mrds-opt.Rd | 3 mrds-2.1.14/mrds/man/mrds-package.Rd | 8 mrds-2.1.14/mrds/man/nlminb_wrapper.Rd |only mrds-2.1.14/mrds/man/p.det.Rd | 5 mrds-2.1.14/mrds/man/parse.optimx.Rd |only mrds-2.1.14/mrds/man/pdot.dsr.integrate.logistic.Rd | 3 mrds-2.1.14/mrds/man/plot.det.tables.Rd | 3 mrds-2.1.14/mrds/man/plot.ds.Rd | 3 mrds-2.1.14/mrds/man/plot.io.Rd | 3 mrds-2.1.14/mrds/man/plot.io.fi.Rd | 3 mrds-2.1.14/mrds/man/plot.layout.Rd | 3 mrds-2.1.14/mrds/man/plot.rem.Rd | 3 mrds-2.1.14/mrds/man/plot.rem.fi.Rd | 3 mrds-2.1.14/mrds/man/plot.trial.Rd | 3 mrds-2.1.14/mrds/man/plot.trial.fi.Rd | 3 mrds-2.1.14/mrds/man/plot_cond.Rd | 3 mrds-2.1.14/mrds/man/plot_uncond.Rd | 3 mrds-2.1.14/mrds/man/predict.ds.Rd | 3 mrds-2.1.14/mrds/man/print.ddf.Rd | 3 mrds-2.1.14/mrds/man/print.ddf.gof.Rd | 3 mrds-2.1.14/mrds/man/print.det.tables.Rd | 3 mrds-2.1.14/mrds/man/print.dht.Rd | 9 mrds-2.1.14/mrds/man/print.summary.ds.Rd | 3 mrds-2.1.14/mrds/man/print.summary.io.Rd | 3 mrds-2.1.14/mrds/man/print.summary.io.fi.Rd | 3 mrds-2.1.14/mrds/man/print.summary.rem.Rd | 3 mrds-2.1.14/mrds/man/print.summary.rem.fi.Rd | 3 mrds-2.1.14/mrds/man/print.summary.trial.Rd | 3 mrds-2.1.14/mrds/man/print.summary.trial.fi.Rd | 3 mrds-2.1.14/mrds/man/prob.deriv.Rd | 3 mrds-2.1.14/mrds/man/prob.se.Rd | 3 mrds-2.1.14/mrds/man/process.data.Rd | 3 mrds-2.1.14/mrds/man/pronghorn.Rd | 3 mrds-2.1.14/mrds/man/ptdata.distance.Rd | 3 mrds-2.1.14/mrds/man/ptdata.dual.Rd | 3 mrds-2.1.14/mrds/man/ptdata.removal.Rd | 3 mrds-2.1.14/mrds/man/ptdata.single.Rd | 3 mrds-2.1.14/mrds/man/qqplot.ddf.Rd | 3 mrds-2.1.14/mrds/man/rem.glm.Rd | 3 mrds-2.1.14/mrds/man/rescale_pars.Rd |only mrds-2.1.14/mrds/man/setbounds.Rd | 3 mrds-2.1.14/mrds/man/setcov.Rd | 3 mrds-2.1.14/mrds/man/setinitial.ds.Rd | 3 mrds-2.1.14/mrds/man/sim.mix.Rd | 3 mrds-2.1.14/mrds/man/stake77.Rd | 3 mrds-2.1.14/mrds/man/stake78.Rd | 3 mrds-2.1.14/mrds/man/summary.ds.Rd | 3 mrds-2.1.14/mrds/man/summary.io.Rd | 3 mrds-2.1.14/mrds/man/summary.io.fi.Rd | 3 mrds-2.1.14/mrds/man/summary.rem.Rd | 3 mrds-2.1.14/mrds/man/summary.rem.fi.Rd | 3 mrds-2.1.14/mrds/man/summary.trial.Rd | 3 mrds-2.1.14/mrds/man/summary.trial.fi.Rd | 3 mrds-2.1.14/mrds/man/survey.region.dht.Rd | 3 mrds-2.1.14/mrds/man/test.breaks.Rd | 3 mrds-2.1.14/mrds/man/varn.Rd | 3 184 files changed, 998 insertions(+), 743 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: David Lawrence Miller <dave@ninepointeightone.net>
Diff between Distance versions 0.9.3 dated 2015-02-04 and 0.9.4 dated 2015-07-29
DESCRIPTION | 9 +-- MD5 | 38 +++++++------ NAMESPACE | 6 +- NEWS | 8 ++ R/Distance-package.R | 4 + R/checkdata.R | 25 ++++++++ R/ds.R | 120 +++++++++++++++++++++++++------------------ R/ds.gof.R |only R/plot.dsmodel.R | 1 README.md | 1 man/Distance-package.Rd | 7 ++ man/checkdata.Rd | 7 +- man/create.bins.Rd | 3 - man/ds.Rd | 25 ++++---- man/ds.gof.Rd |only man/flatfile.Rd | 3 - man/minke.Rd | 3 - man/plot.dsmodel.Rd | 3 - man/print.dsmodel.Rd | 3 - man/print.summary.dsmodel.Rd | 3 - man/summary.dsmodel.Rd | 3 - 21 files changed, 173 insertions(+), 99 deletions(-)
Title: Density Estimation for Grouped Data
Description: Functions for density estimation based on grouped (or pre-binned)
data.
Author: Bin Wang <bwang@southalabama.edu>.
Maintainer: Bin Wang <bwang@southalabama.edu>
Diff between bda versions 5.1.3 dated 2015-04-04 and 5.1.6 dated 2015-07-29
DESCRIPTION | 8 +-- MD5 | 16 ++++--- NAMESPACE | 12 +++++ PORTING | 2 R/bde.R | 15 ++---- R/histospline.R |only R/smkde.R |only data/ofc.tab.gz |only man/ofc.Rd |only src/Fkernel.f | 126 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ src/init.c | 14 +++++- 11 files changed, 173 insertions(+), 20 deletions(-)
Title: Import Stata 'webuse' Datasets
Description: A Stata-style `webuse()` function for importing named datasets from Stata's online collection.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between webuse versions 0.1.1 dated 2015-07-28 and 0.1.2 dated 2015-07-29
DESCRIPTION | 15 ++++++++------- MD5 | 12 +++++++----- NAMESPACE | 2 +- NEWS | 5 +++++ R/webuse.R | 2 +- man/webuse.Rd | 5 ++--- tests |only 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Analysis and Search of Crossover Designs
Description: Package Crossover provides different crossover designs from combinatorial or search algorithms as well as from literature and a GUI to access them.
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between Crossover versions 0.1-14 dated 2015-03-26 and 0.1-15 dated 2015-07-29
DESCRIPTION | 6 +-- MD5 | 22 ++++++------ NAMESPACE | 5 ++ NEWS | 18 ++++++++- R/crossoverS4.R | 2 - R/onLoad.R | 5 +- inst/doc/Crossover.pdf |binary inst/java/crossover.jar |binary java/org/mutoss/gui/AlgorithmPanel.java | 22 ++++++------ java/org/mutoss/gui/CrossoverGUI.java | 19 ++++++++-- java/org/mutoss/gui/RControl.java | 3 + java/org/mutoss/gui/dialogs/ErrorDialogChooseLevel.java |only java/org/mutoss/gui/dialogs/ErrorDialogChooseLevelBase.java |only 13 files changed, 69 insertions(+), 33 deletions(-)
Title: Analyze Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.0.1 dated 2015-05-28 and 1.1.0 dated 2015-07-29
ChangeLog | 499 ++++++++++++++++++++++++++++++++++++++++++------- DESCRIPTION | 13 - MD5 | 94 +++++---- NAMESPACE | 2 NEWS |only R/calcCOD.R | 14 - R/checkArgClassValue.R |only R/cumBg.R | 360 ++++++++++++++++++++--------------- R/interp.R | 65 +++--- R/mass2vol.R | 151 ++++++++------ R/molMass.R | 44 ++-- R/partCO2.R | 95 +++++---- R/predBg.R | 144 +++++++------- R/rbindf.R | 24 +- R/readFormula.R | 52 +++-- R/stdVol.R | 75 ++++--- R/summBg.R | 207 ++++++++++++-------- R/unitConvert.R | 47 ++-- R/vol2mass.R | 84 +++++--- R/watVap.R |only build |only data/comp.rda |binary data/comp2.rda |binary data/mass.rda |binary data/massw.rda |binary data/oldcomp.rda |only data/setup.rda |binary data/setup2.rda |binary data/vol.rda |binary data/vol2.rda |binary inst |only man/biogas-package.Rd | 114 ++++------- man/calcCOD.Rd | 8 man/comp.Rd | 6 man/comp2.Rd | 2 man/cumBg.Rd | 267 +++++++++++++++++++------- man/interp.Rd | 35 +-- man/mass.Rd | 3 man/mass2vol.Rd | 75 +++++-- man/massw.Rd | 4 man/molMass.Rd | 6 man/predBg.Rd | 50 ++-- man/setup.Rd | 19 + man/setup2.Rd | 2 man/stdVol.Rd | 65 +++--- man/summBg.Rd | 89 ++++---- man/vol.Rd | 8 man/vol2mass.Rd | 64 ++++-- tests |only vignettes |only 50 files changed, 1803 insertions(+), 984 deletions(-)
Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and
plotting functions. Used to support packages and code written by
researchers at the Southwest Fisheries Science Center of the National
Oceanic and Atmospheric Administration.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between swfscMisc versions 1.0.3 dated 2014-12-31 and 1.0.6 dated 2015-07-29
swfscMisc-1.0.3/swfscMisc/R/invLogOdds.R |only swfscMisc-1.0.3/swfscMisc/R/invOdds.R |only swfscMisc-1.0.3/swfscMisc/R/logOdds.R |only swfscMisc-1.0.3/swfscMisc/R/scatterhist.R |only swfscMisc-1.0.6/swfscMisc/DESCRIPTION | 16 +- swfscMisc-1.0.6/swfscMisc/MD5 | 145 ++++++++++---------- swfscMisc-1.0.6/swfscMisc/NAMESPACE | 41 +++++ swfscMisc-1.0.6/swfscMisc/NEWS.md |only swfscMisc-1.0.6/swfscMisc/R/affin.prop.R | 7 swfscMisc-1.0.6/swfscMisc/R/bearing.R | 7 swfscMisc-1.0.6/swfscMisc/R/box.area.R | 8 - swfscMisc-1.0.6/swfscMisc/R/braces.R | 7 swfscMisc-1.0.6/swfscMisc/R/central.quantile.R | 7 swfscMisc-1.0.6/swfscMisc/R/circle.polygon.R | 6 swfscMisc-1.0.6/swfscMisc/R/color.name.R | 7 swfscMisc-1.0.6/swfscMisc/R/convert.angle.R | 6 swfscMisc-1.0.6/swfscMisc/R/convert.distance.R | 6 swfscMisc-1.0.6/swfscMisc/R/copy.tri.R | 6 swfscMisc-1.0.6/swfscMisc/R/crossing.point.R |only swfscMisc-1.0.6/swfscMisc/R/das.map.R | 12 - swfscMisc-1.0.6/swfscMisc/R/das.merge.acoustic.R | 7 swfscMisc-1.0.6/swfscMisc/R/das.read.R | 6 swfscMisc-1.0.6/swfscMisc/R/das.spp.freq.R | 6 swfscMisc-1.0.6/swfscMisc/R/datum.R | 6 swfscMisc-1.0.6/swfscMisc/R/destination.R | 14 - swfscMisc-1.0.6/swfscMisc/R/distance.R | 57 ++++--- swfscMisc-1.0.6/swfscMisc/R/diversity.R |only swfscMisc-1.0.6/swfscMisc/R/fisher.method.p.R |only swfscMisc-1.0.6/swfscMisc/R/geometric.mean.R | 7 swfscMisc-1.0.6/swfscMisc/R/harmonic.mean.R | 7 swfscMisc-1.0.6/swfscMisc/R/isBetween.R |only swfscMisc-1.0.6/swfscMisc/R/lab.wid.R | 7 swfscMisc-1.0.6/swfscMisc/R/lat.lon.axes.R | 7 swfscMisc-1.0.6/swfscMisc/R/na.count.R | 6 swfscMisc-1.0.6/swfscMisc/R/normalize.R | 7 swfscMisc-1.0.6/swfscMisc/R/odds.R | 23 ++- swfscMisc-1.0.6/swfscMisc/R/one.arg.R | 8 - swfscMisc-1.0.6/swfscMisc/R/pVal.R |only swfscMisc-1.0.6/swfscMisc/R/row.col.page.fit.r | 6 swfscMisc-1.0.6/swfscMisc/R/sample.map.R | 12 - swfscMisc-1.0.6/swfscMisc/R/scatterdens.R | 30 +++- swfscMisc-1.0.6/swfscMisc/R/sex.symbols.R | 7 swfscMisc-1.0.6/swfscMisc/R/uniform.test.R | 7 swfscMisc-1.0.6/swfscMisc/R/zero.pad.R | 8 - swfscMisc-1.0.6/swfscMisc/man/affin.prop.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/bearing.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/box.area.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/braces.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/central.quantile.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/circle.polygon.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/color.name.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/convert.angle.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/convert.distance.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/copy.tri.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/crossing.point.Rd |only swfscMisc-1.0.6/swfscMisc/man/das.map.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/das.merge.acoustic.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/das.read.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/das.spp.freq.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/datum.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/destination.Rd | 8 - swfscMisc-1.0.6/swfscMisc/man/distance.Rd | 32 ++-- swfscMisc-1.0.6/swfscMisc/man/diversity.Rd |only swfscMisc-1.0.6/swfscMisc/man/fisher.method.p.Rd |only swfscMisc-1.0.6/swfscMisc/man/geometric.mean.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/harmonic.mean.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/isBetween.Rd |only swfscMisc-1.0.6/swfscMisc/man/lab.wid.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/lat.lon.axes.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/na.count.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/normalize.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/odds.Rd | 13 - swfscMisc-1.0.6/swfscMisc/man/one.arg.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/pVal.Rd |only swfscMisc-1.0.6/swfscMisc/man/row.col.page.fit.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/sample.map.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/scatterdens.Rd | 6 swfscMisc-1.0.6/swfscMisc/man/sex.symbols.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/uniform.test.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/which.nearest.Rd | 3 swfscMisc-1.0.6/swfscMisc/man/zero.pad.Rd | 3 81 files changed, 403 insertions(+), 259 deletions(-)
Title: Stochastic Newton Sampler (SNS)
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability density functions (PDFs) where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A Boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the PDF (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle. Numerical differentiation is available when analytical expressions for gradient and Hessian are not available. Facilities for validation and numerical differentiation of log-density are provided.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani <alireza.mahani@sentrana.com>
Diff between sns versions 1.0.0 dated 2015-02-07 and 1.1.0 dated 2015-07-29
sns-1.0.0/sns/NEWS |only sns-1.0.0/sns/vignettes/figs.pdf |only sns-1.0.0/sns/vignettes/summs |only sns-1.0.0/sns/vignettes/summs.pred |only sns-1.1.0/sns/ChangeLog | 36 sns-1.1.0/sns/DESCRIPTION | 14 sns-1.1.0/sns/MD5 | 49 sns-1.1.0/sns/NAMESPACE | 13 sns-1.1.0/sns/R/ess.R | 4 sns-1.1.0/sns/R/sns.R | 52 sns-1.1.0/sns/R/sns.methods.R | 196 ++ sns-1.1.0/sns/R/zzz.R | 17 sns-1.1.0/sns/build/vignette.rds |binary sns-1.1.0/sns/inst/doc/SNS.R | 264 ++- sns-1.1.0/sns/inst/doc/SNS.Rnw | 1175 +++++++++++------ sns-1.1.0/sns/inst/doc/SNS.pdf |binary sns-1.1.0/sns/man/ess.Rd | 6 sns-1.1.0/sns/man/plot.sns.Rd | 2 sns-1.1.0/sns/man/predict.sns.Rd | 48 sns-1.1.0/sns/man/sns.Rd | 160 +- sns-1.1.0/sns/man/sns.check.logdensity.Rd |only sns-1.1.0/sns/man/sns.fghEval.numaug.Rd |only sns-1.1.0/sns/man/sns.run.Rd |only sns-1.1.0/sns/man/summary.sns.Rd | 4 sns-1.1.0/sns/vignettes/SNS.Rnw | 1175 +++++++++++------ sns-1.1.0/sns/vignettes/SNS.bib | 518 ++++--- sns-1.1.0/sns/vignettes/fig_bench_N_binomial.pdf |only sns-1.1.0/sns/vignettes/fig_bench_N_exponential.pdf |only sns-1.1.0/sns/vignettes/fig_bench_N_poisson.pdf |only sns-1.1.0/sns/vignettes/fig_bench_corr_binomial.pdf |only sns-1.1.0/sns/vignettes/fig_bench_corr_exponential.pdf |only sns-1.1.0/sns/vignettes/fig_bench_corr_poisson.pdf |only 32 files changed, 2515 insertions(+), 1218 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high
dimensional data. Ensembles of classification, regression, survival and
probability prediction trees are supported. Data from genome-wide
association studies can be analyzed efficiently. In addition to data
frames, datasets of class 'gwaa.data' (R package GenABEL) can be directly
analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.2.6 dated 2015-07-28 and 0.2.7 dated 2015-07-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/ForestClassification.cpp | 4 ++-- src/ForestProbability.cpp | 4 ++-- src/ForestRegression.cpp | 4 ++-- src/ForestSurvival.cpp | 4 ++-- src/version.h | 2 +- 7 files changed, 19 insertions(+), 19 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.2.0 dated 2015-06-27 and 0.3.1 dated 2015-07-29
DESCRIPTION | 10 - MD5 | 27 ++-- NAMESPACE | 4 NEWS | 25 ++- R/qic.R | 287 ++++++++++++++++++++++++++------------------ R/trc.R | 6 README.md | 50 +++---- build/vignette.rds |binary inst/doc/controlcharts.R |only inst/doc/controlcharts.Rmd |only inst/doc/controlcharts.html |only inst/doc/runcharts.Rmd | 21 +-- inst/doc/runcharts.html | 26 +-- man/plot.qic.Rd |only man/qic.Rd | 58 +++++--- vignettes/controlcharts.Rmd |only vignettes/runcharts.Rmd | 21 +-- 17 files changed, 313 insertions(+), 222 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.3 dated 2015-03-11 and 0.4.1 dated 2015-07-29
ChangeLog | 17 ++++- DESCRIPTION | 10 +- MD5 | 30 ++++---- NAMESPACE | 3 R/em.R | 31 +++++---- R/fscores.R |only R/lms.R | 4 - R/model.R | 16 +--- R/qml.R | 117 ++++++++++++++++++++++------------ R/s3generics.R | 46 +++++++------ R/semm.R | 46 ++++++++----- man/em.Rd | 159 +++++++++++++++++++++++++---------------------- man/get_factor_scores.Rd |only man/nlsem-package.Rd | 4 - man/qml.Rd | 7 -- man/specify_sem.Rd | 2 man/summary.Rd | 26 ++++--- 17 files changed, 293 insertions(+), 225 deletions(-)
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Description: Functions, data sets, analyses and examples from the
third edition of the book
`A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides).
Author: Torsten Hothorn and Brian S. Everitt
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR3 versions 1.0-4 dated 2015-03-09 and 1.0-5 dated 2015-07-29
DESCRIPTION | 10 +- MD5 | 110 +++++++++++++------------- NAMESPACE | 1 build/vignette.rds |binary data/BCG.rda |binary data/CYGOB1.rda |binary data/Lanza.rda |binary data/birthdeathrates.rda |binary data/bladdercancer.rda |binary data/epilepsy.rda |binary data/foster.rda |binary data/heptathlon.rda |binary data/meteo.rda |binary data/orallesions.rda |binary data/phosphate.rda |binary data/pistonrings.rda |binary data/planets.rda |binary data/plasma.rda |binary data/polyps.rda |binary data/rearrests.rda |binary data/roomwidth.rda |binary data/schizophrenia.rda |binary data/schizophrenia2.rda |binary data/smoking.rda |binary data/students.rda |binary data/suicides.rda |binary data/toothpaste.rda |binary data/voting.rda |binary data/water.rda |binary data/watervoles.rda |binary data/waves.rda |binary data/weightgain.rda |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_bayesian_inference.pdf |binary inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.pdf |binary inst/doc/Ch_gam.pdf |binary inst/doc/Ch_graphical_display.pdf |binary inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_missing_values.pdf |binary inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_quantile_regression.pdf |binary inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_simultaneous_inference.pdf |binary inst/doc/Ch_survival_analysis.pdf |binary vignettes/tables/rec.tex | 10 +- 56 files changed, 70 insertions(+), 65 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank ordering statistics method is presented to search for
differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
This method may be useful for high-throughput biological data (microarray, sequencing, ...).
Probabilities are associated with genes/probes in the dataset and there is no problem of
multiple tests when using this method. For aCGH data, segmentation results are obtained by
merging the significant probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.3 dated 2014-11-27 and 1.4 dated 2015-07-29
DESCRIPTION | 20 +++++++++++--------- MD5 | 40 ++++++++++++++++++++++++++-------------- NAMESPACE | 6 +++++- R/fcrosChrPlot.R |only R/fcrosChrPlot2.R |only R/fcrosChrSegment.R |only R/fcrosChrSummary.R |only data/cghData.rda |only data/cghInfo.rda |only data/datalist | 2 ++ man/cghData.Rd |only man/cghInfo.Rd |only man/fcros-package.Rd | 39 ++++++++++++++++++++++++--------------- man/fcros.Rd | 6 +++--- man/fcros2.Rd | 23 +++++++++++++---------- man/fcrosChrPlot.Rd |only man/fcrosChrPlot2.Rd |only man/fcrosChrSegment.Rd |only man/fcrosChrSummary.Rd |only man/fcrosFCmat.Rd | 12 +++++------- man/fcrosHistoPlot.Rd | 9 +++++---- man/fcrosMod.Rd | 12 +++++------- man/fcrosRead.Rd | 4 +++- man/fcrosTopN.Rd | 11 ++++++----- man/fcrosVolcanoPlot.Rd | 6 +++--- man/fcrosWrite.Rd | 15 +++++++-------- man/fdata.Rd | 2 +- 27 files changed, 119 insertions(+), 88 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-6 dated 2013-12-23 and 0.9-7 dated 2015-07-29
DESCRIPTION | 11 MD5 | 195 ++++++---- NAMESPACE | 2 NEWS | 15 R/call.R | 2 R/jinit.R | 2 R/reflection.R | 6 R/windows/FirstLib.R | 3 configure | 4 configure.ac | 4 inst/java/RJavaArrayTools$ArrayDimensionMismatchException.class |binary inst/java/RJavaArrayTools.class |binary inst/java/RJavaArrayTools.java | 1 inst/java/RJavaImport.java | 2 inst/java/RJavaTools.java | 2 inst/java/boot/RJavaClassLoader.java | 4 inst/javadoc/ArrayDimensionException.html | 4 inst/javadoc/ArrayWrapper.html | 4 inst/javadoc/ArrayWrapper_Test.html | 4 inst/javadoc/DummyPoint.html | 4 inst/javadoc/FlatException.html | 4 inst/javadoc/NotAnArrayException.html | 4 inst/javadoc/NotComparableException.html | 4 inst/javadoc/ObjectArrayException.html | 4 inst/javadoc/PrimitiveArrayException.html | 4 inst/javadoc/RJavaArrayIterator.html | 4 inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 inst/javadoc/RJavaArrayTools.html | 8 inst/javadoc/RJavaArrayTools_Test.html | 4 inst/javadoc/RJavaClassLoader.html | 8 inst/javadoc/RJavaComparator.html | 4 inst/javadoc/RJavaImport.html | 6 inst/javadoc/RJavaTools.html | 6 inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 inst/javadoc/RJavaTools_Test.TestException.html | 4 inst/javadoc/RJavaTools_Test.html | 4 inst/javadoc/RectangularArrayBuilder.html | 4 inst/javadoc/RectangularArrayBuilder_Test.html | 4 inst/javadoc/RectangularArrayExamples.html | 4 inst/javadoc/RectangularArraySummary.html | 4 inst/javadoc/TestException.html | 4 inst/javadoc/allclasses-frame.html | 4 inst/javadoc/allclasses-noframe.html | 4 inst/javadoc/constant-values.html | 4 inst/javadoc/deprecated-list.html | 4 inst/javadoc/help-doc.html | 4 inst/javadoc/index-all.html | 4 inst/javadoc/index.html | 2 inst/javadoc/overview-tree.html | 4 inst/javadoc/package-frame.html | 4 inst/javadoc/package-summary.html | 4 inst/javadoc/package-tree.html | 4 inst/javadoc/serialized-form.html | 4 inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary jri/NEWS | 1 jri/REngine |only jri/src/Makefile.all | 2 man/jsimplify.Rd | 9 src/Rglue.c | 68 ++- src/java/RJavaArrayTools$ArrayDimensionMismatchException.class |binary src/java/RJavaArrayTools.class |binary src/java/RJavaArrayTools.java | 1 src/java/RJavaClassLoader.java | 4 src/java/RJavaImport.java | 2 src/java/RJavaTools.java | 2 src/rJava.h | 2 67 files changed, 304 insertions(+), 198 deletions(-)
Title: Fast Interactive Framework for Web Scripting Using R
Description: Infrastrcture for creating rich, dynamic web content using R scripts while maintaining very fast response time.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeffrey.horner@gmail.com>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between FastRWeb versions 1.1-0 dated 2012-12-15 and 1.1-1 dated 2015-07-29
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NAMESPACE | 5 +++++ NEWS | 10 ++++++++++ R/plots.R | 5 ++++- R/run.R | 40 ++++++++++++++++++++++++++++++++-------- man/WebResult.Rd | 3 ++- src/Rcgi/Makefile.in | 4 +--- 8 files changed, 69 insertions(+), 28 deletions(-)
More information about TipDatingBeast at CRAN
Permanent link
Title: Statistical Methods for Ranking Data
Description: Functions and datasets to support Statistical Methods for Ranking Data by Mayer Alvo and Philip L.H. Yu(2014). In this packages, smaller ranks stand for more preferred items.
Author: Li Qinglong
Maintainer: Li Qinglong <liqinglong0830@163.com>
Diff between StatMethRank versions 1.0 dated 2014-07-10 and 1.2 dated 2015-07-29
StatMethRank-1.0/StatMethRank/R/summary.trace.R |only StatMethRank-1.2/StatMethRank/DESCRIPTION | 18 +- StatMethRank-1.2/StatMethRank/MD5 | 101 ++++++++------ StatMethRank-1.2/StatMethRank/NAMESPACE | 19 ++ StatMethRank-1.2/StatMethRank/R/APA.R | 2 StatMethRank-1.2/StatMethRank/R/Croon.R | 1 StatMethRank-1.2/StatMethRank/R/RcppExports.R |only StatMethRank-1.2/StatMethRank/R/big4year.R | 4 StatMethRank-1.2/StatMethRank/R/compatible.rankings.R | 2 StatMethRank-1.2/StatMethRank/R/convertNodeId.R |only StatMethRank-1.2/StatMethRank/R/decTreeImpFunc.R |only StatMethRank-1.2/StatMethRank/R/freq2case.R | 3 StatMethRank-1.2/StatMethRank/R/generate.perms.R | 10 - StatMethRank-1.2/StatMethRank/R/interaction.test.R | 2 StatMethRank-1.2/StatMethRank/R/is.compatible.R | 2 StatMethRank-1.2/StatMethRank/R/mvnos.model.R | 8 - StatMethRank-1.2/StatMethRank/R/mwdbm.R | 5 StatMethRank-1.2/StatMethRank/R/myformatg.R |only StatMethRank-1.2/StatMethRank/R/mylabels.rpart.R |only StatMethRank-1.2/StatMethRank/R/mypart.branch.R |only StatMethRank-1.2/StatMethRank/R/myplot.rpart.r |only StatMethRank-1.2/StatMethRank/R/myrpartco.R |only StatMethRank-1.2/StatMethRank/R/mystring.bounding.box.R |only StatMethRank-1.2/StatMethRank/R/mytext.R |only StatMethRank-1.2/StatMethRank/R/mytext.rpart.R |only StatMethRank-1.2/StatMethRank/R/mytree.depth.R |only StatMethRank-1.2/StatMethRank/R/plotDecROC.R |only StatMethRank-1.2/StatMethRank/R/plotDecTree.R |only StatMethRank-1.2/StatMethRank/R/summary_trace.R |only StatMethRank-1.2/StatMethRank/R/visitNodePreorder.R |only StatMethRank-1.2/StatMethRank/R/wdmat.R | 4 StatMethRank-1.2/StatMethRank/man/APA.Rd | 5 StatMethRank-1.2/StatMethRank/man/Croon.Rd | 4 StatMethRank-1.2/StatMethRank/man/HKPOS.Rd | 3 StatMethRank-1.2/StatMethRank/man/Scores.Rd | 3 StatMethRank-1.2/StatMethRank/man/Song.Rd | 3 StatMethRank-1.2/StatMethRank/man/StatMethRank-package.Rd | 2 StatMethRank-1.2/StatMethRank/man/Sutton.Rd | 3 StatMethRank-1.2/StatMethRank/man/agreement.test.Rd | 3 StatMethRank-1.2/StatMethRank/man/big4year.Rd | 7 StatMethRank-1.2/StatMethRank/man/case2freq.Rd | 3 StatMethRank-1.2/StatMethRank/man/compatible.rankings.Rd | 5 StatMethRank-1.2/StatMethRank/man/decTreeImpFunc.Rd |only StatMethRank-1.2/StatMethRank/man/freq2case.Rd | 7 StatMethRank-1.2/StatMethRank/man/generate.combs.Rd | 3 StatMethRank-1.2/StatMethRank/man/generate.perms.Rd | 7 StatMethRank-1.2/StatMethRank/man/incomplete.rankings.Rd | 3 StatMethRank-1.2/StatMethRank/man/independence.test.Rd | 3 StatMethRank-1.2/StatMethRank/man/interaction.test.Rd | 3 StatMethRank-1.2/StatMethRank/man/is.compatible.Rd | 5 StatMethRank-1.2/StatMethRank/man/msci.Rd | 3 StatMethRank-1.2/StatMethRank/man/mvnos.model.Rd | 5 StatMethRank-1.2/StatMethRank/man/mwdbm.Rd | 8 - StatMethRank-1.2/StatMethRank/man/plotDecROC.Rd |only StatMethRank-1.2/StatMethRank/man/plotDecTree.Rd |only StatMethRank-1.2/StatMethRank/man/repmat.Rd | 3 StatMethRank-1.2/StatMethRank/man/wdmat.Rd | 7 StatMethRank-1.2/StatMethRank/src |only 58 files changed, 177 insertions(+), 102 deletions(-)
Title: Tools for Fitting Sparse Latent Factor Model
Description: Set of tools to find coherent patterns in microarray data
using a Bayesian sparse latent factor model (Duarte and Mayrink 2015 -
http://link.springer.com/chapter/10.1007%2F978-3-319-12454-4_15).
Considerable effort has been put into making slfm fast and memory efficient,
turning it an interesting alternative to simpler methods in terms
of execution time. It implements versions of the SLFM using both type
of mixtures: using a degenerate distribution or a very concentrated
normal distribution for the spike part of the mixture. It also implements
additional functions to help pre-process the data and fit the model
for a large number of arrays.
Author: Joao Duarte and Vinicius Mayrink
Maintainer: Joao Duarte <jdanielnd@gmail.com>
Diff between slfm versions 0.1 dated 2014-05-08 and 0.2.0 dated 2015-07-29
slfm-0.1/slfm/README.md |only slfm-0.2.0/slfm/DESCRIPTION | 22 ++++++--- slfm-0.2.0/slfm/MD5 | 38 ++++++++------- slfm-0.2.0/slfm/NAMESPACE | 13 +++++ slfm-0.2.0/slfm/NEWS | 13 ++++- slfm-0.2.0/slfm/R/RcppExports.R | 12 ++++ slfm-0.2.0/slfm/R/class_interval.r | 6 ++ slfm-0.2.0/slfm/R/plot_matrix.r |only slfm-0.2.0/slfm/R/process_matrix.r | 3 + slfm-0.2.0/slfm/R/slfm-package.r | 15 ++++-- slfm-0.2.0/slfm/R/slfm.r | 83 +++++++++++++++++++++++++--------- slfm-0.2.0/slfm/R/slfm_list.r | 26 ++++------ slfm-0.2.0/slfm/man/plot_matrix.Rd |only slfm-0.2.0/slfm/man/process_matrix.Rd | 14 ++--- slfm-0.2.0/slfm/man/slfm-package.Rd | 23 ++++++--- slfm-0.2.0/slfm/man/slfm.Rd | 43 ++++++++++------- slfm-0.2.0/slfm/man/slfm_list.Rd | 36 ++++++++------ slfm-0.2.0/slfm/src/Makevars |only slfm-0.2.0/slfm/src/Makevars.win | 5 -- slfm-0.2.0/slfm/src/RcppExports.cpp | 72 ++++++++++++++++++++++------- slfm-0.2.0/slfm/src/gibbs.cpp | 28 +++++++---- slfm-0.2.0/slfm/src/slfm_MDN.cpp |only slfm-0.2.0/slfm/src/slfm_MNN.cpp |only 23 files changed, 308 insertions(+), 144 deletions(-)
Title: Access to Cryptsy Crypto-Currency Exchange Public Information
API via R
Description: Basic access to market infomation from the public API for the Crypto-Currency exchange Cryptsy.
Author: William Kyle Hamilton <kyle.hamilton@gmail.com>
Maintainer: William Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between RCryptsy versions 0.2 dated 2014-11-23 and 0.4 dated 2015-07-29
DESCRIPTION | 17 ++-- MD5 | 60 +++++++-------- NAMESPACE | 4 - NEWS | 17 +++- R/RCryptsy.R | 151 +++++++++++++++++++++++++-------------- README.md | 8 ++ man/GeneralMarketData_42CBTC.Rd | 5 - man/GeneralMarketData_ADTLTC.Rd | 4 - man/GeneralMarketData_ANCLTC.Rd | 4 - man/GeneralMarketData_ASCLTC.Rd | 6 + man/GeneralMarketData_AURLTC.Rd | 4 - man/GeneralMarketData_BATLTC.Rd | 4 - man/GeneralMarketData_BCLTC.Rd | 4 - man/GeneralMarketData_BTCUSD.Rd | 4 - man/GeneralMarketData_CAIxLTC.Rd | 4 - man/GeneralMarketData_CGBLTC.Rd | 4 - man/GeneralMarketData_DOGEBTC.Rd | 4 - man/GeneralMarketData_DOGELTC.Rd | 4 - man/GeneralMarketData_DOGEUSD.Rd | 4 - man/GeneralMarketData_DRKBTC.Rd | 4 - man/GeneralMarketData_DRKUSD.Rd | 4 - man/GeneralMarketData_FTCBTC.Rd | 4 - man/GeneralMarketData_FTCUSD.Rd | 4 - man/GeneralMarketData_LTCBTC.Rd | 4 - man/GeneralMarketData_LTCUSD.Rd | 4 - man/GeneralMarketData_NXTBTC.Rd | 4 - man/GeneralMarketData_PCCUSD.Rd | 4 - man/GeneralMarketData_RDDUSD.Rd | 4 - man/GeneralMarketData_UNOBTC.Rd | 4 - man/GeneralMarketData_XRPUSD.Rd | 4 - man/RCryptsy-package.Rd | 4 - 31 files changed, 238 insertions(+), 122 deletions(-)
Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely
used simulator of agricultural systems. This package includes
functions to create, edit and run APSIM simulations from R. It
also includes functions to visualize the results of an APSIM simulation
and perform sensitivity/uncertainty analysis of APSIM either via functions
in the sensitivity package or by novel emulator-based functions.
For more on APSIM including download instructions go to
\url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill <bryan.stanfill@csiro.au>
Diff between apsimr versions 1.0 dated 2015-05-04 and 1.1 dated 2015-07-29
DESCRIPTION | 8 ++--- MD5 | 40 ++++++++++++------------- NAMESPACE | 3 + NEWS | 28 +++++++++++++++++ R/editAPSIM.R | 41 ++++++++++++++++---------- R/emulateAPSIM.R | 6 ++- R/runAPSIM.R | 69 ++++++++++++++++++++++++++++---------------- R/sensitivityAPSIM.R | 8 ++--- build/vignette.rds |binary inst/doc/apsimr-basics.R | 6 +-- inst/doc/apsimr-basics.Rnw | 31 +++++++++---------- inst/doc/apsimr-basics.pdf |binary man/apsim.Rd | 8 ++--- man/apsim_emul_sa.Rd | 4 +- man/apsim_vector.Rd | 8 ++--- man/apsimr-package.Rd | 2 - man/edit_apsim.Rd | 5 +-- man/edit_sim_file.Rd | 7 ++-- man/example_apsim.Rd | 5 +-- man/plot.gamSA.Rd | 2 - vignettes/apsimr-basics.Rnw | 31 +++++++++---------- 21 files changed, 188 insertions(+), 124 deletions(-)
Title: Computes Weight of Evidence and Information Values
Description: Shows the relationship between an independent and dependent variable through Weight of Evidence and Information Value.
Author: Sudarson Mothilal Thoppay <sudarson@outlook.com>
Maintainer: Sudarson Mothilal Thoppay <sudarson@outlook.com>
Diff between woe versions 0.1 dated 2015-07-14 and 0.2 dated 2015-07-28
woe-0.1/woe/inst/tests/Rplots.pdf |only woe-0.2/woe/DESCRIPTION | 6 +++--- woe-0.2/woe/MD5 | 9 ++++----- woe-0.2/woe/R/woe.R | 28 +++++++++++++++++++++++----- woe-0.2/woe/inst/tests/testwoe.R | 8 ++++---- woe-0.2/woe/man/woe.Rd | 23 +++++++++++++++++++---- 6 files changed, 53 insertions(+), 21 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design,
along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 0.0.4 dated 2015-07-15 and 0.0.5 dated 2015-07-28
DESCRIPTION | 25 ++++++++++++-------- MD5 | 36 ++++++++++++++++++++--------- NEWS | 13 ++++++++++ R/Boxplot.R | 7 +++-- R/Element.queries.R | 42 ++++++++++++++++++++++++++++++++++ R/Helper.funcs.R | 8 ++++++ R/MainBar.R | 47 ++++++++++++++++++++++++++++---------- R/SizeBar.R | 2 - R/UpSet.plot.R | 64 +++++++++++++++++++++++++++++++++++++++------------- R/upset.R | 29 +++++++++++++---------- README.md | 29 +++++++++++++++++------ build |only inst/doc |only man/upset.Rd | 22 ++++++++--------- vignettes |only 15 files changed, 241 insertions(+), 83 deletions(-)
Title: R Based Twitter Client
Description: Provides an interface to the Twitter web API.
Author: Jeff Gentry <geoffjentry@gmail.com>
Maintainer: Jeff Gentry <geoffjentry@gmail.com>
Diff between twitteR versions 1.1.8 dated 2015-02-10 and 1.1.9 dated 2015-07-28
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 2 ++ R/db.R | 4 ++-- R/followers.R | 9 ++++----- R/oauth.R | 20 ++++++++++++++------ R/statuses.R | 5 +++-- README.md | 9 +++++---- man/favorites.Rd | 2 +- man/updateStatus.Rd | 4 +++- man/use_oauth_token.Rd |only 11 files changed, 48 insertions(+), 34 deletions(-)
Title: Import Articles from 'Europresse' Using the 'tm' Text Mining
Framework
Description: Provides a 'tm' Source to create corpora from
articles exported from the 'Europresse' content provider as
HTML files. It is able to read both text content and meta-data
information (including source, date, title, author and pages).
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between tm.plugin.europresse versions 1.2 dated 2015-03-27 and 1.3 dated 2015-07-28
tm.plugin.europresse-1.2/tm.plugin.europresse/inst/texts/europresse_test.html |only tm.plugin.europresse-1.3/tm.plugin.europresse/DESCRIPTION | 12 - tm.plugin.europresse-1.3/tm.plugin.europresse/MD5 | 17 - tm.plugin.europresse-1.3/tm.plugin.europresse/NAMESPACE | 3 tm.plugin.europresse-1.3/tm.plugin.europresse/NEWS | 3 tm.plugin.europresse-1.3/tm.plugin.europresse/R/EuropresseSource.R | 17 + tm.plugin.europresse-1.3/tm.plugin.europresse/R/readEuropresseHTML.R | 103 +++++++++- tm.plugin.europresse-1.3/tm.plugin.europresse/inst/texts/europresse_test1.html |only tm.plugin.europresse-1.3/tm.plugin.europresse/inst/texts/europresse_test2.html |only tm.plugin.europresse-1.3/tm.plugin.europresse/man/EuropresseSource.Rd | 10 tm.plugin.europresse-1.3/tm.plugin.europresse/man/readEuropresse.Rd | 11 - 11 files changed, 150 insertions(+), 26 deletions(-)
More information about tm.plugin.europresse at CRAN
Permanent link
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression and as
predictors in a linear regression. For simulation and bootstrap purposes,
RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>
Diff between RRreg versions 0.3.0 dated 2015-02-23 and 0.4.1 dated 2015-07-28
RRreg-0.3.0/RRreg/vignettes/figure |only RRreg-0.4.1/RRreg/DESCRIPTION | 10 +- RRreg-0.4.1/RRreg/MD5 | 75 +++++++++---------- RRreg-0.4.1/RRreg/NAMESPACE | 6 + RRreg-0.4.1/RRreg/NEWS | 8 ++ RRreg-0.4.1/RRreg/R/RRlin.R | 2 RRreg-0.4.1/RRreg/R/RRlog.CDM.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.FR.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.Mangat.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.R | 93 +++++++++++++++++++++--- RRreg-0.4.1/RRreg/R/RRlog.SLD.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.UQTknown.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.UQTunknown.R | 4 - RRreg-0.4.1/RRreg/R/RRlog.Warner.R | 4 - RRreg-0.4.1/RRreg/R/RRreg-package.R | 5 - RRreg-0.4.1/RRreg/build/vignette.rds |binary RRreg-0.4.1/RRreg/inst/doc/RRreg.Rmd | 20 ++--- RRreg-0.4.1/RRreg/inst/doc/RRreg.html | 124 ++++++++++++++++---------------- RRreg-0.4.1/RRreg/man/RRcor.Rd | 2 RRreg-0.4.1/RRreg/man/RRgen.Rd | 2 RRreg-0.4.1/RRreg/man/RRlin.Rd | 4 - RRreg-0.4.1/RRreg/man/RRlog.Rd | 6 - RRreg-0.4.1/RRreg/man/RRreg-package.Rd | 6 - RRreg-0.4.1/RRreg/man/RRsimu.Rd | 2 RRreg-0.4.1/RRreg/man/RRuni.Rd | 2 RRreg-0.4.1/RRreg/man/plot.RRlog.Rd |only RRreg-0.4.1/RRreg/man/plot.powerplot.Rd | 2 RRreg-0.4.1/RRreg/man/powerplot.Rd | 2 RRreg-0.4.1/RRreg/man/predict.RRlog.Rd | 2 RRreg-0.4.1/RRreg/vignettes/RRreg.Rmd | 20 ++--- RRreg-0.4.1/RRreg/vignettes/figures |only 31 files changed, 261 insertions(+), 160 deletions(-)
Title: Read and Analyze 'PLEXOS' Solutions
Description: Efficiently read and analyze 'PLEXOS' solutions by converting them
into 'SQLite' databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios. 'PLEXOS' is a power systems
production cost model, created and distributed by Energy Exemplar
(see URL below for more information).
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez <edu.ibanez@gmail.com>
Diff between rplexos versions 1.1.1 dated 2015-06-11 and 1.1.4 dated 2015-07-28
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/debug.R | 1 + R/globalVariables.R | 2 +- R/plexos_open.R | 1 + R/process_solution.R | 2 ++ build/vignette.rds |binary 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.3 dated 2015-04-21 and 0.10.4 dated 2015-07-28
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/driver.R | 1 + R/table.R | 1 + configure | 20 +++++++++++++++----- tools/mysql-connector-c.rb | 31 ++++++++++++++++++++----------- 7 files changed, 54 insertions(+), 30 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.6 dated 2015-07-20 and 1.5.8 dated 2015-07-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/data_frame.h | 5 +++-- src/refGenome.cpp | 4 +++- tests/test-all.R | 3 ++- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Analysis of Health-Related Quality of Life in Oncology
Description: To generate the scores of the EORTC QLQ-C30 questionnaire and supplementary modules and to determine the time to health-related quality of life score deterioration in longitudinal analysis.
Author: Amelie Anota
Maintainer: Amelie Anota <aanota@chu-besancon.fr>
Diff between QoLR versions 1.0 dated 2014-07-13 and 1.0.1 dated 2015-07-28
QoLR-1.0.1/QoLR/DESCRIPTION | 17 +++-- QoLR-1.0.1/QoLR/MD5 | 97 +++++++++++++++++------------- QoLR-1.0.1/QoLR/NAMESPACE | 12 +++ QoLR-1.0.1/QoLR/R/TTD.R | 35 ++++++++-- QoLR-1.0.1/QoLR/R/TUDD.R | 27 +++++++- QoLR-1.0.1/QoLR/R/scoring.INPATSAT32.R |only QoLR-1.0.1/QoLR/R/scoring.QLQBN20.R | 38 ++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQBR23.R | 45 ++++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQC15PAL.R |only QoLR-1.0.1/QoLR/R/scoring.QLQC30.R | 47 ++++++++++++-- QoLR-1.0.1/QoLR/R/scoring.QLQCR29.R | 44 ++++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQCX24.R | 44 ++++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQELD14.R |only QoLR-1.0.1/QoLR/R/scoring.QLQEN24.R | 43 +++++++++++-- QoLR-1.0.1/QoLR/R/scoring.QLQHCC18.R |only QoLR-1.0.1/QoLR/R/scoring.QLQHN35.R | 48 +++++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQINFO25.R |only QoLR-1.0.1/QoLR/R/scoring.QLQLC13.R | 41 +++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQLMC21.R |only QoLR-1.0.1/QoLR/R/scoring.QLQMY20.R | 42 +++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQOES18.R | 42 +++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQOG25.R | 41 +++++++++++- QoLR-1.0.1/QoLR/R/scoring.QLQOV28.R |only QoLR-1.0.1/QoLR/R/scoring.QLQPR25.R | 49 ++++++++++++--- QoLR-1.0.1/QoLR/R/scoring.QLQSTO22.R | 44 ++++++++++++- QoLR-1.0.1/QoLR/build |only QoLR-1.0.1/QoLR/data/dataqol.rda |only QoLR-1.0.1/QoLR/inst |only QoLR-1.0.1/QoLR/man/QoLR-package.Rd | 37 +---------- QoLR-1.0.1/QoLR/man/TTD.Rd | 26 ++++++-- QoLR-1.0.1/QoLR/man/TUDD.Rd | 25 ++++++- QoLR-1.0.1/QoLR/man/dataqol.Rd |only QoLR-1.0.1/QoLR/man/plotTTD.Rd | 43 +++++++++---- QoLR-1.0.1/QoLR/man/scoring.INPATSAT32.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQBN20.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQBR23.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQC15PAL.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQC30.Rd | 12 +-- QoLR-1.0.1/QoLR/man/scoring.QLQCR29.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQCX24.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQELD14.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQEN24.Rd | 9 +- QoLR-1.0.1/QoLR/man/scoring.QLQHCC18.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQHN35.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQINFO25.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQLC13.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQLMC21.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQMY20.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQOES18.Rd | 6 - QoLR-1.0.1/QoLR/man/scoring.QLQOG25.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQOV28.Rd |only QoLR-1.0.1/QoLR/man/scoring.QLQPR25.Rd | 8 +- QoLR-1.0.1/QoLR/man/scoring.QLQSTO22.Rd | 8 +- QoLR-1.0.1/QoLR/man/write.TTD.Rd | 28 ++++++-- QoLR-1.0.1/QoLR/man/write.TUDD.Rd | 15 ---- QoLR-1.0.1/QoLR/vignettes |only QoLR-1.0/QoLR/data/dataqol1.rda |only QoLR-1.0/QoLR/data/dataqol2.rda |only QoLR-1.0/QoLR/man/dataqol1.Rd |only QoLR-1.0/QoLR/man/dataqol2.Rd |only 60 files changed, 786 insertions(+), 251 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.0-21 dated 2015-06-06 and 1.0-22 dated 2015-07-28
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 9 ++++++++- R/Predict.R | 3 +-- build/vignette.rds |binary data/readingSkills.rda |binary inst/NEWS | 6 +++++- inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary tests/Examples/party-Ex.Rout.save | 16 ++++++++-------- tests/RandomForest-regtest.Rout.save | 24 ++++++++++++------------ tests/TreeGrow-regtest.Rout.save | 33 ++++++++++++++------------------- vignettes/party.Rout.save | 18 +++++++++--------- 13 files changed, 73 insertions(+), 68 deletions(-)
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two tissues.
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between lineup versions 0.34-1 dated 2012-10-15 and 0.37-6 dated 2015-07-28
lineup-0.34-1/lineup/README.txt |only lineup-0.34-1/lineup/inst/README.txt |only lineup-0.34-1/lineup/inst/STATUS.txt |only lineup-0.34-1/lineup/man/lineup-internal.Rd |only lineup-0.37-6/lineup/ChangeLog |only lineup-0.37-6/lineup/DESCRIPTION | 25 lineup-0.37-6/lineup/MD5 | 112 ++-- lineup-0.37-6/lineup/NAMESPACE | 56 +- lineup-0.37-6/lineup/NEWS |only lineup-0.37-6/lineup/R/calc.locallod.R | 205 ++++--- lineup-0.37-6/lineup/R/combinedist.R | 194 ++++--- lineup-0.37-6/lineup/R/corbetw2mat.R | 265 +++++----- lineup-0.37-6/lineup/R/distee.R | 274 +++++----- lineup-0.37-6/lineup/R/disteg.R | 541 +++++++++++---------- lineup-0.37-6/lineup/R/expr1-data.R |only lineup-0.37-6/lineup/R/f2cross-data.R |only lineup-0.37-6/lineup/R/find.gene.pseudomarker.R | 152 +++-- lineup-0.37-6/lineup/R/findCommonID.R | 136 ++--- lineup-0.37-6/lineup/R/fscale.R | 81 +-- lineup-0.37-6/lineup/R/genepos-data.R |only lineup-0.37-6/lineup/R/omitdiag.R | 81 +-- lineup-0.37-6/lineup/R/plot.lineupdist.R | 133 ++--- lineup-0.37-6/lineup/R/plot2dist.R | 273 +++++----- lineup-0.37-6/lineup/R/plotEGclass.R | 489 ++++++++++-------- lineup-0.37-6/lineup/R/pmap-data.R |only lineup-0.37-6/lineup/R/pulldiag.R | 69 +- lineup-0.37-6/lineup/R/subset.lineupdist.R | 101 ++- lineup-0.37-6/lineup/R/summary.lineupdist.R | 276 +++++----- lineup-0.37-6/lineup/R/util.R | 53 -- lineup-0.37-6/lineup/build |only lineup-0.37-6/lineup/data |only lineup-0.37-6/lineup/inst/doc |only lineup-0.37-6/lineup/man/calc.locallod.Rd | 163 ++---- lineup-0.37-6/lineup/man/combinedist.Rd | 124 ++-- lineup-0.37-6/lineup/man/corbetw2mat.Rd | 137 ++--- lineup-0.37-6/lineup/man/distee.Rd | 108 +--- lineup-0.37-6/lineup/man/disteg.Rd | 248 ++++----- lineup-0.37-6/lineup/man/expr-data.Rd |only lineup-0.37-6/lineup/man/f2cross.Rd |only lineup-0.37-6/lineup/man/find.gene.pseudomarker.Rd | 161 ++---- lineup-0.37-6/lineup/man/findCommonID.Rd | 81 +-- lineup-0.37-6/lineup/man/fscale.Rd | 50 - lineup-0.37-6/lineup/man/genepos.Rd |only lineup-0.37-6/lineup/man/lineupversion.Rd | 32 - lineup-0.37-6/lineup/man/omitdiag.Rd | 100 +-- lineup-0.37-6/lineup/man/plot.lineupdist.Rd | 121 +--- lineup-0.37-6/lineup/man/plot2dist.Rd | 128 +--- lineup-0.37-6/lineup/man/plotEGclass.Rd | 159 ++---- lineup-0.37-6/lineup/man/pmap.Rd |only lineup-0.37-6/lineup/man/pulldiag.Rd | 97 +-- lineup-0.37-6/lineup/man/subset.lineupdist.Rd | 64 +- lineup-0.37-6/lineup/man/summary.lineupdist.Rd | 122 +--- lineup-0.37-6/lineup/src/corbetw2mat.c | 448 ++++++++--------- lineup-0.37-6/lineup/src/corbetw2mat.h | 74 +- lineup-0.37-6/lineup/src/fscale.c | 72 +- lineup-0.37-6/lineup/src/propmismatch.c | 64 +- lineup-0.37-6/lineup/src/propmismatch.h | 14 lineup-0.37-6/lineup/src/rmsd.c | 90 +-- lineup-0.37-6/lineup/src/rmsd.h | 14 lineup-0.37-6/lineup/src/util.c | 34 - lineup-0.37-6/lineup/tests |only lineup-0.37-6/lineup/vignettes |only 62 files changed, 3092 insertions(+), 3129 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.3.1 dated 2015-07-05 and 0.3.2 dated 2015-07-28
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/latex2exp.R | 36 ++++++++++++++++++++++++++++++------ man/print.latextoken.Rd |only tests/testthat/Rplots.pdf |binary 5 files changed, 38 insertions(+), 13 deletions(-)
Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA and PIAAC).
Author: Daniel Caro <daniel.caro@education.ox.ac.uk>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <daniel.caro@education.ox.ac.uk>
Diff between intsvy versions 1.6 dated 2014-12-08 and 1.7 dated 2015-07-28
DESCRIPTION | 15 - MD5 | 103 +++++---- NAMESPACE | 24 ++ R/my.methods.R |only R/piaac.ben.pv.R | 133 ++++++----- R/piaac.mean.R | 75 +++--- R/piaac.reg.R | 99 ++++---- R/piaac.reg.pv.R | 7 R/pirls.ben.pv.R | 95 ++++---- R/pirls.log.R |only R/pirls.log.pv.R |only R/pirls.mean.R | 57 ++--- R/pirls.mean.pv.R | 111 +++++---- R/pirls.per.pv.R |only R/pirls.reg.R | 37 +-- R/pirls.reg.pv.R | 111 +++++---- R/pirls.select.merge.R | 484 +++++++++++++++++++++--------------------- R/pirls.table.R | 88 +++---- R/pisa.ben.pv.R | 137 ++++++------ R/pisa.log.R |only R/pisa.log.pv.R |only R/pisa.mean.R | 76 +++--- R/pisa.mean.pv.R | 170 +++++++------- R/pisa.per.pv.R |only R/pisa.reg.R | 38 +-- R/pisa.reg.pv.R | 50 ++-- R/pisa.rho.R |only R/pisa.select.merge.R | 350 +++++++++++++++--------------- R/pisa.table.R | 2 R/plot.intsvy.reg.R | 78 +++--- R/timss.ben.pv.R | 95 ++++---- R/timss.log.R |only R/timss.log.pv.R |only R/timss.mean.R | 59 ++--- R/timss.mean.pv.R | 113 +++++---- R/timss.per.pv.R |only R/timss.reg.R | 43 ++- R/timss.reg.pv.R | 109 +++++---- R/timss.table.R | 88 +++---- R/timssg4.select.merge.R | 499 +++++++++++++++++++++----------------------- R/timssg8.select.merge.R | 397 +++++++++++++++++------------------ man/intsvy-package.Rd | 40 +-- man/pirls.log.Rd |only man/pirls.log.pv.Rd |only man/pirls.per.pv.Rd |only man/pirls.reg.Rd | 121 +++++----- man/pirls.reg.pv.Rd | 113 +++++---- man/pirls.select.merge.Rd | 103 ++++----- man/pisa.log.Rd |only man/pisa.log.pv.Rd |only man/pisa.per.pv.Rd |only man/pisa.reg.Rd | 107 +++++---- man/pisa.reg.pv.Rd | 107 ++++----- man/pisa.rho.Rd |only man/plot.intsvy.reg.Rd | 107 ++++----- man/timss.log.Rd |only man/timss.log.pv.Rd |only man/timss.per.pv.Rd |only man/timss.reg.Rd | 100 ++++---- man/timss.reg.pv.Rd | 109 ++++----- man/timssg4.select.merge.Rd | 107 +++++---- man/timssg8.select.merge.Rd | 99 ++++---- vignettes/piaac.Rmd | 375 ++++++++++++++++----------------- 63 files changed, 2715 insertions(+), 2516 deletions(-)
Title: Renewable Energy Probability Resource Assessment Tool (REPRA)
Description: Methods to calculate resource adequacy
metrics in power systems, which are based on the notion of
loss-of-load probability (LOLP) and include the treatment of conventional
and variable renewable generators.
Author: Eduardo Ibanez [aut, cre],
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez <edu.ibanez@gmail.com>
Diff between repra versions 0.4.2 dated 2014-10-06 and 0.4.4 dated 2015-07-28
DESCRIPTION | 24 LICENSE | 4 MD5 | 66 +- NAMESPACE | 49 - R/RcppExports.R | 14 R/auxiliary.R | 232 ++++---- R/calculate_elcc.R | 430 ++++++++-------- R/calculate_metrics.R | 197 +++---- R/capacity_value.R | 286 +++++----- R/globalVariables.R | 10 R/help.R | 106 ++-- R/outage_table.R | 287 +++++------ R/sliding_window.R | 441 ++++++++-------- R/timedata.R | 284 +++++----- README.md | 16 build/vignette.rds |binary inst/doc/repra.R | 150 ++--- inst/doc/repra.html | 990 ++++++++++++++++++++------------------ inst/doc/sliding_window.R | 146 ++--- inst/doc/sliding_window.Rmd | 2 inst/doc/sliding_window.html | 676 ++++++++++++------------- man/calculate_elcc.Rd | 155 ++--- man/calculate_metrics.Rd | 127 ++-- man/capacity_value.Rd | 159 +++--- man/format_timedata.Rd | 161 +++--- man/outage_table.Rd | 177 +++--- man/repra-package.Rd | 45 - man/repra.data.Rd | 85 +-- man/sliding_window.Rd | 249 ++++----- src/RcppExports.cpp | 18 tests/test-all.R | 4 tests/testthat/test-outagetable.R | 44 - tests/testthat/test-timedata.R | 52 - vignettes/sliding_window.Rmd | 2 34 files changed, 2907 insertions(+), 2781 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.0-1 dated 2015-04-08 and 1.0-2 dated 2015-07-28
DESCRIPTION | 10 MD5 | 42 +-- NAMESPACE | 2 R/cforest.R | 3 R/glmtree.R | 5 R/lmtree.R | 7 R/modelparty.R | 5 R/node.R | 8 R/party.R | 50 +++- R/plot.R | 18 - R/split.R | 8 build/vignette.rds |binary inst/NEWS.Rd | 13 + inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary man/HuntingSpiders.Rd | 2 man/party-predict.Rd | 6 man/partysplit.Rd | 14 - tests/regtest-party.Rout.save | 464 ++++++++++++++++++++---------------------- vignettes/ctree.Rout.save | 20 - 22 files changed, 355 insertions(+), 322 deletions(-)
Title: Near-Optimal and Balanced Group-Sequential Designs for Clinical
Trials with Continuous Outcomes
Description: Functions to find near-optimal multi-stage designs for continuous outcomes.
Author: James Wason [aut, cre],
John Burkardt [ctb]
Maintainer: James Wason <james.wason@mrc-bsu.cam.ac.uk>
Diff between OptGS versions 1.0 dated 2015-07-27 and 1.1 dated 2015-07-28
DESCRIPTION | 8 +-- MD5 | 14 +++--- R/powerfamily.R | 3 - src/OptGS.cpp | 29 ++++++------- src/multistagefunctions_v3.cpp | 4 - src/multistagefunctions_v3.h | 2 src/normaldistribution.cpp | 88 ++--------------------------------------- src/normaldistribution.h | 2 8 files changed, 34 insertions(+), 116 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.4.2 dated 2015-07-27 and 0.4.3 dated 2015-07-28
DESCRIPTION | 8 +++---- MD5 | 6 ++--- R/cv.ses.R | 56 +++++++++++++++++++++++++++++++++++++---------------- man/MXM-package.Rd | 4 +-- 4 files changed, 49 insertions(+), 25 deletions(-)
Title: An Introduction to Applied Multivariate Analysis with R
Description: Functions, data sets, analyses and examples from the book
`An Introduction to Applied Multivariate Analysis with R'
(Brian S. Everitt and Torsten Hothorn, Springer, 2011).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between MVA versions 1.0-5 dated 2014-03-12 and 1.0-6 dated 2015-07-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 4 ++++ build/vignette.rds |binary inst/doc/Ch-Errata.R | 1 + inst/doc/Ch-Errata.pdf |binary 6 files changed, 14 insertions(+), 9 deletions(-)
Title: Improved Predictors
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems
as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut],
Torsten Hothorn [aut, cre],
Brian D. Ripley [ctb],
Terry Therneau [ctb],
Beth Atkinson [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between ipred versions 0.9-4 dated 2015-02-21 and 0.9-5 dated 2015-07-28
DESCRIPTION | 10 ++++---- MD5 | 14 +++++------ NAMESPACE | 6 ++++ build/vignette.rds |binary inst/NEWS | 4 +++ inst/doc/ipred-examples.pdf |binary tests/Examples/ipred-Ex.Rout.save | 42 ++++++++++++++------------------- tests/ipred-segfault.Rout.save | 47 ++++++++++++++++++-------------------- 8 files changed, 63 insertions(+), 60 deletions(-)
Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Description: Functions, data sets, analyses and examples from the
second edition of the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2008). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
the package contains Sweave code for producing slides for selected
chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR2 versions 1.1-13 dated 2015-01-09 and 1.1-14 dated 2015-07-28
DESCRIPTION | 8 - MD5 | 180 ++++++++++++------------- NAMESPACE | 1 build/vignette.rds |binary data/BCG.rda |binary data/CYGOB1.rda |binary data/Lanza.rda |binary data/birthdeathrates.rda |binary data/bladdercancer.rda |binary data/epilepsy.rda |binary data/foster.rda |binary data/heptathlon.rda |binary data/meteo.rda |binary data/orallesions.rda |binary data/phosphate.rda |binary data/pistonrings.rda |binary data/planets.rda |binary data/plasma.rda |binary data/polyps.rda |binary data/rearrests.rda |binary data/roomwidth.rda |binary data/schizophrenia.rda |binary data/schizophrenia2.rda |binary data/smoking.rda |binary data/students.rda |binary data/suicides.rda |binary data/toothpaste.rda |binary data/voting.rda |binary data/water.rda |binary data/watervoles.rda |binary data/waves.rda |binary data/weightgain.rda |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.Rnw | 13 + inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.Rnw | 13 + inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.Rnw | 13 + inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_cluster_analysis.Rnw | 13 + inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.Rnw | 13 + inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.Rnw | 13 + inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.Rnw | 13 + inst/doc/Ch_errata.pdf |binary inst/doc/Ch_gam.Rnw | 13 + inst/doc/Ch_gam.pdf |binary inst/doc/Ch_graphical_display.Rnw | 13 + inst/doc/Ch_graphical_display.pdf |binary inst/doc/Ch_introduction_to_R.Rnw | 13 + inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.Rnw | 13 + inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.Rnw | 13 + inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_multidimensional_scaling.Rnw | 13 + inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.Rnw | 16 +- inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.Rnw | 13 + inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_recursive_partitioning.Rnw | 14 + inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.Rnw | 13 + inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_simultaneous_inference.Rnw | 13 + inst/doc/Ch_simultaneous_inference.pdf |binary inst/doc/Ch_survival_analysis.Rnw | 13 + inst/doc/Ch_survival_analysis.pdf |binary vignettes/Ch_analysing_longitudinal_dataI.Rnw | 13 + vignettes/Ch_analysing_longitudinal_dataII.Rnw | 13 + vignettes/Ch_analysis_of_variance.Rnw | 13 + vignettes/Ch_cluster_analysis.Rnw | 13 + vignettes/Ch_conditional_inference.Rnw | 13 + vignettes/Ch_density_estimation.Rnw | 13 + vignettes/Ch_errata.Rnw | 13 + vignettes/Ch_gam.Rnw | 13 + vignettes/Ch_graphical_display.Rnw | 13 + vignettes/Ch_introduction_to_R.Rnw | 13 + vignettes/Ch_logistic_regression_glm.Rnw | 13 + vignettes/Ch_meta_analysis.Rnw | 13 + vignettes/Ch_multidimensional_scaling.Rnw | 13 + vignettes/Ch_multiple_linear_regression.Rnw | 16 +- vignettes/Ch_principal_components_analysis.Rnw | 13 + vignettes/Ch_recursive_partitioning.Rnw | 14 + vignettes/Ch_simple_inference.Rnw | 13 + vignettes/Ch_simultaneous_inference.Rnw | 13 + vignettes/Ch_survival_analysis.Rnw | 13 + vignettes/tables/rec.tex | 10 - 91 files changed, 598 insertions(+), 107 deletions(-)
Title: A Handbook of Statistical Analyses Using R (1st Edition)
Description: Functions, data sets, analyses and examples from the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2006). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available.
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between HSAUR versions 1.3-6 dated 2015-01-09 and 1.3-7 dated 2015-07-28
DESCRIPTION | 8 - MD5 | 140 ++++++++++++------------- NAMESPACE | 1 build/vignette.rds |binary inst/NEWS | 4 inst/doc/Ch_analysing_longitudinal_dataI.R | 9 + inst/doc/Ch_analysing_longitudinal_dataI.Rnw | 22 +++ inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary inst/doc/Ch_analysing_longitudinal_dataII.R | 4 inst/doc/Ch_analysing_longitudinal_dataII.Rnw | 20 +++ inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary inst/doc/Ch_analysis_of_variance.R | 4 inst/doc/Ch_analysis_of_variance.Rnw | 18 +++ inst/doc/Ch_analysis_of_variance.pdf |binary inst/doc/Ch_cluster_analysis.R | 4 inst/doc/Ch_cluster_analysis.Rnw | 17 +++ inst/doc/Ch_cluster_analysis.pdf |binary inst/doc/Ch_conditional_inference.R | 4 inst/doc/Ch_conditional_inference.Rnw | 17 +++ inst/doc/Ch_conditional_inference.pdf |binary inst/doc/Ch_density_estimation.R | 4 inst/doc/Ch_density_estimation.Rnw | 18 +++ inst/doc/Ch_density_estimation.pdf |binary inst/doc/Ch_errata.R | 4 inst/doc/Ch_errata.Rnw | 17 +++ inst/doc/Ch_errata.pdf |binary inst/doc/Ch_introduction_to_R.R | 4 inst/doc/Ch_introduction_to_R.Rnw | 17 +++ inst/doc/Ch_introduction_to_R.pdf |binary inst/doc/Ch_logistic_regression_glm.R | 4 inst/doc/Ch_logistic_regression_glm.Rnw | 17 +++ inst/doc/Ch_logistic_regression_glm.pdf |binary inst/doc/Ch_meta_analysis.R | 4 inst/doc/Ch_meta_analysis.Rnw | 17 +++ inst/doc/Ch_meta_analysis.pdf |binary inst/doc/Ch_multidimensional_scaling.R | 4 inst/doc/Ch_multidimensional_scaling.Rnw | 17 +++ inst/doc/Ch_multidimensional_scaling.pdf |binary inst/doc/Ch_multiple_linear_regression.R | 4 inst/doc/Ch_multiple_linear_regression.Rnw | 17 +++ inst/doc/Ch_multiple_linear_regression.pdf |binary inst/doc/Ch_principal_components_analysis.R | 4 inst/doc/Ch_principal_components_analysis.Rnw | 17 +++ inst/doc/Ch_principal_components_analysis.pdf |binary inst/doc/Ch_recursive_partitioning.R | 4 inst/doc/Ch_recursive_partitioning.Rnw | 18 +++ inst/doc/Ch_recursive_partitioning.pdf |binary inst/doc/Ch_simple_inference.R | 4 inst/doc/Ch_simple_inference.Rnw | 17 +++ inst/doc/Ch_simple_inference.pdf |binary inst/doc/Ch_survival_analysis.R | 4 inst/doc/Ch_survival_analysis.Rnw | 17 +++ inst/doc/Ch_survival_analysis.pdf |binary inst/doc/preface.pdf |binary vignettes/Ch_analysing_longitudinal_dataI.Rnw | 22 +++ vignettes/Ch_analysing_longitudinal_dataII.Rnw | 20 +++ vignettes/Ch_analysis_of_variance.Rnw | 18 +++ vignettes/Ch_cluster_analysis.Rnw | 17 +++ vignettes/Ch_conditional_inference.Rnw | 17 +++ vignettes/Ch_density_estimation.Rnw | 18 +++ vignettes/Ch_errata.Rnw | 17 +++ vignettes/Ch_introduction_to_R.Rnw | 17 +++ vignettes/Ch_logistic_regression_glm.Rnw | 17 +++ vignettes/Ch_meta_analysis.Rnw | 17 +++ vignettes/Ch_multidimensional_scaling.Rnw | 17 +++ vignettes/Ch_multiple_linear_regression.Rnw | 17 +++ vignettes/Ch_principal_components_analysis.Rnw | 17 +++ vignettes/Ch_recursive_partitioning.Rnw | 18 +++ vignettes/Ch_simple_inference.Rnw | 17 +++ vignettes/Ch_survival_analysis.Rnw | 17 +++ vignettes/tables/rec.tex | 10 - 71 files changed, 698 insertions(+), 100 deletions(-)
Title: Advanced Data Analysis of T Cell Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.0 dated 2015-05-14 and 2.1 dated 2015-07-28
DESCRIPTION | 12 - MD5 | 41 ++-- NAMESPACE | 6 R/dataproc.R | 5 R/datatools.R | 20 +- R/docdata.R | 66 ++++-- R/input.R | 453 +++++++++++++++++++++++++++++++++++++++++++--- R/plots.R | 2 R/segments.R | 25 +- R/shared.R | 4 R/spectrum.R | 4 R/stats.R | 4 README.md | 16 + data/twa.rda |binary inst/CITATION | 12 - inst/doc/tcrvignette.Rmd | 20 +- inst/doc/tcrvignette.html | 66 ++++-- man/fix.alleles.Rd |only man/parse.folder.Rd | 40 +++- man/pca.segments.Rd | 6 man/segments.alphabets.Rd | 6 vignettes/tcrvignette.Rmd | 20 +- 22 files changed, 698 insertions(+), 130 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb]
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb]
Amandine Gasc [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.0.1 dated 2015-07-08 and 2.0.2 dated 2015-07-28
DESCRIPTION | 8 +- MD5 | 23 ++++---- NEWS | 15 ++++- R/seewave.r | 119 ++++++++++++++++++++++++------------------ demo/seewave.R | 6 -- inst/doc/seewave_IO.pdf |binary inst/doc/seewave_analysis.pdf |binary man/ACI.Rd | 4 - man/ama.Rd | 3 - man/duration.Rd |only man/ffilter.Rd | 2 man/seewave.package.Rd | 4 - man/synth.Rd | 3 - 13 files changed, 109 insertions(+), 78 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 4.0-5 dated 2015-05-20 and 4.1-1 dated 2015-07-28
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 5 +++++ NEWS | 3 +++ R/GLMM_MCMC.R | 6 +++--- R/GLMM_MCMCifit.R | 32 ++++++++++++++++---------------- R/NMixMCMC.R | 6 +++--- data/Acidity.rda |binary data/Enzyme.rda |binary data/Galaxy.rda |binary man/GLMMMCMC.Rd | 8 ++++++-- man/NMixMCMC.Rd | 7 +++++-- 12 files changed, 57 insertions(+), 42 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.2.1 dated 2015-06-19 and 0.3.0 dated 2015-07-28
ChangeLog | 33 ++++++ DESCRIPTION | 12 +- MD5 | 74 ++++++++------- NAMESPACE | 4 R/AAAClasses.R | 40 +++++++- R/PROSAIL.R | 2 R/PROSPECT.R | 2 R/Spectra-class.R |only R/blockwise_functions.R |only R/continuum_transform.R | 47 +++++---- R/distance.R | 3 R/hsdardocs.R | 10 ++ R/raster-methods.R |only R/rededge.R | 3 R/smgm.R | 2 R/soilindex.R | 2 R/speclib.R | 120 +++++++++++++++++------- R/speclib_differenciate.R | 5 - R/speclib_dim.R | 3 R/speclib_index.R | 22 +++- R/speclib_mask.R | 3 R/speclib_plot.R | 12 ++ R/speclib_print.R | 10 ++ R/speclib_smooth.R | 16 ++- R/speclib_spectra.R | 47 +++++++-- R/spectral_resampling.R | 4 R/spectral_resampling_response.R | 3 R/unmix.R | 29 ++++-- R/vegindex.R | 14 ++ data/endmember_spectra.RData |binary data/spectral_data.RData |binary inst/doc/References.pdf |binary inst/doc/hsdar-intro.pdf |binary man/Speclib-class.Rd | 11 +- man/raster-methods.Rd |only man/smooth_speclib.Rd | 9 + man/speclib.Rd | 17 ++- man/spectra.Rd | 9 + man/unmix.Rd | 5 - vignettes/hsdar-intro.tex | 188 ++++++++++++++++++++++++++++++++++++--- 40 files changed, 606 insertions(+), 155 deletions(-)
Title: Fitting Mixture Distributions with GAMLSS
Description: The main purpose of this package is to allow fitting of
mixture distributions with GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.mx versions 4.3-1 dated 2015-02-04 and 4.3-2 dated 2015-07-28
DESCRIPTION | 12 +++--- MD5 | 8 ++-- NAMESPACE | 107 ++++++++++++++++++++++++++++---------------------------- data/brains.rda |binary data/enzyme.rda |binary 5 files changed, 65 insertions(+), 62 deletions(-)
Title: Tools for generating and handling of UUIDs
Description: Tools for generating and handling of UUIDs (Universally Unique Identifiers).
Author: Simon Urbanek <Simon.Urbanek@r-project.org> (R package), Theodore Ts'o <tytso@thunk.org> (libuuid)
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between uuid versions 0.1-1 dated 2013-09-04 and 0.1-2 dated 2015-07-28
DESCRIPTION | 10 LICENSE |only MD5 | 16 NEWS |only configure | 4420 +++++++++++++++++++++++++--------------------------- configure.ac | 5 man/UUIDgenerate.Rd | 4 src/config.h.in | 6 src/gen_uuid.c | 7 src/win32/config.h | 3 10 files changed, 2207 insertions(+), 2264 deletions(-)
Title: Set of Common Tools for Model Diagnostics
Description: Set of tools to assess the performance of a model through the computation of typical prediction scores against one or more observational datasets or reanalyses (a reanalysis being a physical extrapolation of observations that relies on the equations from a model, not a pure observational dataset).
Author: Virginie Guemas <virginie.guemas@ic3.cat>, Nicolau Manubens Gil <nicolau.manubens@ic3.cat>, Isabel Andreu-Burillo <isabel.andreu-burillo@ic3.cat>, Fabian Lienert <fabian.lienert@ic3.cat>, Javier Garcia-Serrano <jgarcia@ic3.cat>, Ludovic Auger <ludovic.auger@meteo.fr>, Chloé Prodhomme <chloe.prodhomme@ic3.cat>, Martin Ménégoz <martin.menegoz@ic3.cat>
Maintainer: Nicolau Manubens <nicolau.manubens@ic3.cat>
Diff between s2dverification versions 2.1.1 dated 2014-06-13 and 2.4.0 dated 2015-07-28
s2dverification-2.1.1/s2dverification/data/datalist |only s2dverification-2.4.0/s2dverification/DESCRIPTION | 17 s2dverification-2.4.0/s2dverification/MD5 | 525 ++++- s2dverification-2.4.0/s2dverification/NAMESPACE | 8 s2dverification-2.4.0/s2dverification/R/ACC.R | 266 ++ s2dverification-2.4.0/s2dverification/R/Alpha.R | 17 s2dverification-2.4.0/s2dverification/R/Ano.R | 20 s2dverification-2.4.0/s2dverification/R/Ano_CrossValid.R | 20 s2dverification-2.4.0/s2dverification/R/CRPS.R |only s2dverification-2.4.0/s2dverification/R/Clim.R | 21 s2dverification-2.4.0/s2dverification/R/ColorBar.R | 27 s2dverification-2.4.0/s2dverification/R/ConfigAddEntry.R |only s2dverification-2.4.0/s2dverification/R/ConfigAddVar.R |only s2dverification-2.4.0/s2dverification/R/ConfigApplyMatchingEntries.R |only s2dverification-2.4.0/s2dverification/R/ConfigEditDefinition.R |only s2dverification-2.4.0/s2dverification/R/ConfigEditEntry.R |only s2dverification-2.4.0/s2dverification/R/ConfigFileCreate.R |only s2dverification-2.4.0/s2dverification/R/ConfigFileOpen.R |only s2dverification-2.4.0/s2dverification/R/ConfigFileSave.R |only s2dverification-2.4.0/s2dverification/R/ConfigMatchingVars.R |only s2dverification-2.4.0/s2dverification/R/ConfigRemoveDefinition.R |only s2dverification-2.4.0/s2dverification/R/ConfigRemoveEntry.R |only s2dverification-2.4.0/s2dverification/R/ConfigRemoveVar.R |only s2dverification-2.4.0/s2dverification/R/ConfigShowDefinitions.R |only s2dverification-2.4.0/s2dverification/R/ConfigShowSimilarEntries.R |only s2dverification-2.4.0/s2dverification/R/ConfigShowSimilarVars.R |only s2dverification-2.4.0/s2dverification/R/ConfigShowTable.R |only s2dverification-2.4.0/s2dverification/R/ConfigShowVars.R |only s2dverification-2.4.0/s2dverification/R/Consist_Trend.R | 30 s2dverification-2.4.0/s2dverification/R/Corr.R | 62 s2dverification-2.4.0/s2dverification/R/Enlarge.R | 13 s2dverification-2.4.0/s2dverification/R/Eno.R | 16 s2dverification-2.4.0/s2dverification/R/EnoNew.R | 17 s2dverification-2.4.0/s2dverification/R/Filter.R | 17 s2dverification-2.4.0/s2dverification/R/FitAcfCoef.R | 21 s2dverification-2.4.0/s2dverification/R/FitAutocor.R | 19 s2dverification-2.4.0/s2dverification/R/GenSeries.R | 16 s2dverification-2.4.0/s2dverification/R/Histo2Hindcast.R | 22 s2dverification-2.4.0/s2dverification/R/IniListDims.R | 22 s2dverification-2.4.0/s2dverification/R/InsertDim.R | 14 s2dverification-2.4.0/s2dverification/R/LeapYear.R | 11 s2dverification-2.4.0/s2dverification/R/Load.R | 910 ++++++---- s2dverification-2.4.0/s2dverification/R/Mean1Dim.R | 15 s2dverification-2.4.0/s2dverification/R/MeanListDim.R | 14 s2dverification-2.4.0/s2dverification/R/Plot2VarsVsLTime.R | 41 s2dverification-2.4.0/s2dverification/R/PlotACC.R | 48 s2dverification-2.4.0/s2dverification/R/PlotAno.R | 42 s2dverification-2.4.0/s2dverification/R/PlotClim.R | 30 s2dverification-2.4.0/s2dverification/R/PlotEquiMap.R | 84 s2dverification-2.4.0/s2dverification/R/PlotSection.R | 23 s2dverification-2.4.0/s2dverification/R/PlotStereoMap.R |only s2dverification-2.4.0/s2dverification/R/PlotVsLTime.R | 38 s2dverification-2.4.0/s2dverification/R/ProbBins.R |only s2dverification-2.4.0/s2dverification/R/RMS.R | 30 s2dverification-2.4.0/s2dverification/R/RMSSS.R | 24 s2dverification-2.4.0/s2dverification/R/RatioRMS.R | 20 s2dverification-2.4.0/s2dverification/R/RatioSDRMS.R | 25 s2dverification-2.4.0/s2dverification/R/Regression.R | 24 s2dverification-2.4.0/s2dverification/R/Season.R | 21 s2dverification-2.4.0/s2dverification/R/SelIndices.R | 16 s2dverification-2.4.0/s2dverification/R/Smoothing.R | 37 s2dverification-2.4.0/s2dverification/R/Spectrum.R | 16 s2dverification-2.4.0/s2dverification/R/Spread.R | 24 s2dverification-2.4.0/s2dverification/R/Trend.R | 23 s2dverification-2.4.0/s2dverification/R/Utils.R |only s2dverification-2.4.0/s2dverification/data/sampleDepthData.RData |binary s2dverification-2.4.0/s2dverification/data/sampleMap.RData |binary s2dverification-2.4.0/s2dverification/data/sampleTimeSeries.RData |binary s2dverification-2.4.0/s2dverification/inst/config |only s2dverification-2.4.0/s2dverification/inst/doc/masks |only s2dverification-2.4.0/s2dverification/inst/doc/plot_timeseries.R | 23 s2dverification-2.4.0/s2dverification/inst/sample_data |only s2dverification-2.4.0/s2dverification/man/ACC.Rd | 124 - s2dverification-2.4.0/s2dverification/man/Alpha.Rd | 18 s2dverification-2.4.0/s2dverification/man/Ano.Rd | 68 s2dverification-2.4.0/s2dverification/man/Ano_CrossValid.Rd | 44 s2dverification-2.4.0/s2dverification/man/CRPS.Rd |only s2dverification-2.4.0/s2dverification/man/Clim.Rd | 67 s2dverification-2.4.0/s2dverification/man/ColorBar.Rd | 34 s2dverification-2.4.0/s2dverification/man/ConfigAddVar.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigApplyMatchingEntries.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigEditDefinition.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigEditEntry.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigFileOpen.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigMatchingVars.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigShowSimilarEntries.Rd |only s2dverification-2.4.0/s2dverification/man/ConfigShowTable.Rd |only s2dverification-2.4.0/s2dverification/man/Consist_Trend.Rd | 97 - s2dverification-2.4.0/s2dverification/man/Corr.Rd | 118 - s2dverification-2.4.0/s2dverification/man/Enlarge.Rd | 23 s2dverification-2.4.0/s2dverification/man/Eno.Rd | 67 s2dverification-2.4.0/s2dverification/man/EnoNew.Rd | 56 s2dverification-2.4.0/s2dverification/man/Filter.Rd | 31 s2dverification-2.4.0/s2dverification/man/FitAcfCoef.Rd | 12 s2dverification-2.4.0/s2dverification/man/FitAutocor.Rd | 12 s2dverification-2.4.0/s2dverification/man/GenSeries.Rd | 8 s2dverification-2.4.0/s2dverification/man/Histo2Hindcast.Rd | 91 - s2dverification-2.4.0/s2dverification/man/IniListDims.Rd | 35 s2dverification-2.4.0/s2dverification/man/InsertDim.Rd | 29 s2dverification-2.4.0/s2dverification/man/LeapYear.Rd | 22 s2dverification-2.4.0/s2dverification/man/Load.Rd | 627 +++--- s2dverification-2.4.0/s2dverification/man/LoadDataFile.Rd |only s2dverification-2.4.0/s2dverification/man/Mean1Dim.Rd | 29 s2dverification-2.4.0/s2dverification/man/MeanListDim.Rd | 29 s2dverification-2.4.0/s2dverification/man/Plot2VarsVsLTime.Rd | 121 - s2dverification-2.4.0/s2dverification/man/PlotACC.Rd | 115 - s2dverification-2.4.0/s2dverification/man/PlotAno.Rd | 98 - s2dverification-2.4.0/s2dverification/man/PlotClim.Rd | 67 s2dverification-2.4.0/s2dverification/man/PlotEquiMap.Rd | 135 - s2dverification-2.4.0/s2dverification/man/PlotSection.Rd | 48 s2dverification-2.4.0/s2dverification/man/PlotStereoMap.Rd |only s2dverification-2.4.0/s2dverification/man/PlotVsLTime.Rd | 144 - s2dverification-2.4.0/s2dverification/man/ProbBins.Rd |only s2dverification-2.4.0/s2dverification/man/RMS.Rd | 100 - s2dverification-2.4.0/s2dverification/man/RMSSS.Rd | 71 s2dverification-2.4.0/s2dverification/man/RatioRMS.Rd | 101 - s2dverification-2.4.0/s2dverification/man/RatioSDRMS.Rd | 64 s2dverification-2.4.0/s2dverification/man/Regression.Rd | 84 s2dverification-2.4.0/s2dverification/man/Season.Rd | 56 s2dverification-2.4.0/s2dverification/man/SelIndices.Rd | 34 s2dverification-2.4.0/s2dverification/man/Smoothing.Rd | 51 s2dverification-2.4.0/s2dverification/man/Spectrum.Rd | 30 s2dverification-2.4.0/s2dverification/man/Spread.Rd | 102 - s2dverification-2.4.0/s2dverification/man/Trend.Rd | 59 s2dverification-2.4.0/s2dverification/man/s2dverification-package.Rd | 20 s2dverification-2.4.0/s2dverification/man/sampleDepthData.Rd | 28 s2dverification-2.4.0/s2dverification/man/sampleMap.Rd | 74 s2dverification-2.4.0/s2dverification/man/sampleTimeSeries.Rd | 76 128 files changed, 3129 insertions(+), 2919 deletions(-)
More information about s2dverification at CRAN
Permanent link
Title: Client for Rserve
Description: Client for Rserve, allowing to connect to Rserve instances and issue commands.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between RSclient versions 0.7-2 dated 2013-08-02 and 0.7-3 dated 2015-07-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 4 +++- NEWS | 6 ++++++ src/cli.c | 10 ++++++---- 5 files changed, 22 insertions(+), 12 deletions(-)
Title: Predict Protein-Protein Interactions Based on Functional and
Topological Similarities
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions to calculate GO semantic similarities are re-used from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng <anfdeng@163.com>
Diff between ppiPre versions 1.8 dated 2015-07-01 and 1.9 dated 2015-07-28
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NEWS |only R/GOKEGGSims.r | 12 ++++++------ man/GOKEGGSims.Rd | 2 +- man/ppiPre-package.Rd | 8 ++++---- 6 files changed, 21 insertions(+), 20 deletions(-)
Title: Public Key Infrastucture for R Based on the X.509 Standard
Description: PKI functions such as verifying certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between PKI versions 0.1-1 dated 2013-02-20 and 0.1-3 dated 2015-07-28
DESCRIPTION | 14 +- LICENSE |only MD5 | 36 +++--- NAMESPACE | 5 NEWS | 39 ++++++ R/crypt.R | 4 R/digest.R | 4 R/rsa.R | 35 +++--- R/signR.R | 87 ++++++++++++++ R/x509.R | 13 +- man/ASN1.Rd | 8 - man/BIGNUMint.Rd | 2 man/PKI.crypt.Rd | 34 ++++- man/PKI.digest.Rd | 4 man/PKI.sign.Rd | 9 - man/PKI.sign.tar.Rd |only man/RSA.Rd | 30 +++-- man/X509.Rd | 14 ++ src/pki-x509.c | 303 +++++++++++++++++++++++++++++++++++++++++++++------- src/pki.h | 2 20 files changed, 520 insertions(+), 123 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using capture-recapture data consisting of a single conventional mark or multiple non-invasive marks.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 1.2.0 dated 2015-06-23 and 1.3.0 dated 2015-07-28
DESCRIPTION | 14 +- MD5 | 26 ++- NAMESPACE | 17 +- NEWS | 17 ++ R/CJS.R | 320 ++++++++++++++++++++++++++++++++++-------------- R/Closed.R | 207 +++++++++++++++++++++++-------- R/multimark_functions.R | 14 +- man/markCJS.Rd |only man/markClosed.Rd |only man/multimarkCJS.Rd | 20 ++- man/multimarkClosed.Rd | 3 man/multimodelCJS.Rd | 17 +- man/multimodelClosed.Rd | 14 -- src/Closed.c | 85 ++++++------ src/ProbitCJS.c | 174 +++++++++++++------------- 15 files changed, 598 insertions(+), 330 deletions(-)
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output
Description: This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.5-6 dated 2014-06-26 and 1.5-7 dated 2015-07-28
DESCRIPTION | 9 +++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS | 16 ++++++++++++++++ R/Cairo.R | 10 ++++++++++ man/Cairo.Rd | 5 +++-- man/Cairo.capture.Rd | 16 ++++++++++++++-- src/cairogd.c | 15 ++++++++------- src/cairogd.h | 2 +- src/cairotalk.c | 21 +++++++++++++++++++-- src/img-backend.c | 35 ++++++++++++++++++++++++++++++++++- src/img-backend.h | 3 ++- 12 files changed, 125 insertions(+), 31 deletions(-)
Title: Tools for base64 encoding
Description: This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between base64enc versions 0.1-2 dated 2014-06-26 and 0.1-3 dated 2015-07-28
DESCRIPTION | 6 +++--- MD5 | 9 ++++++--- NAMESPACE | 4 ++-- NEWS | 5 +++++ R/UTF8.R |only man/checkUTF8.Rd |only src/utf8.c |only 7 files changed, 16 insertions(+), 8 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.35 dated 2015-06-04 and 1.36 dated 2015-07-28
DESCRIPTION | 11 +++++++---- MD5 | 32 ++++++++++++++++++++++---------- NAMESPACE | 5 +++++ R/GATES2.R | 7 +++++-- R/aSPUM.R |only R/aSPUMpath.r |only R/aSPUpath.r | 11 +++++++++-- R/aSPUw.R | 8 ++++++-- R/aSPUwboot.R |only R/aSPUwperm.R | 4 ++-- R/aSPUwpermC.R | 13 ++++++------- R/aSPUwsim.R | 25 +++++++++++++------------ build |only data/kegg9.rda |only inst |only man/GATES2.Rd | 7 +++++-- man/aSPUM.Rd |only man/aSPUMpath.Rd |only man/aSPUw.Rd | 6 +++--- man/kegg9.Rd |only vignettes |only 21 files changed, 83 insertions(+), 46 deletions(-)
Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.0.0 dated 2015-07-06 and 1.1.0 dated 2015-07-27
DESCRIPTION | 10 +- MD5 | 15 +-- NEWS |only R/WiSEHypothesisTest.R | 17 +-- build/vignette.rds |binary inst/doc/WiSEBoot_Examples_Vignette.R | 154 +++++++++++++++---------------- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 2 inst/doc/WiSEBoot_Examples_Vignette.pdf |binary vignettes/WiSEBoot_Examples_Vignette.Rnw | 2 9 files changed, 100 insertions(+), 100 deletions(-)
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.0.8 dated 2014-11-07 and 1.1.0 dated 2015-07-27
stm-1.0.8/stm/R/STMln.R |only stm-1.1.0/stm/DESCRIPTION | 19 stm-1.1.0/stm/LICENSE | 2 stm-1.1.0/stm/MD5 | 101 ++-- stm-1.1.0/stm/NAMESPACE | 25 - stm-1.1.0/stm/R/RcppExports.R |only stm-1.1.0/stm/R/STMestep.R | 15 stm-1.1.0/stm/R/STMinit.R | 54 +- stm-1.1.0/stm/R/STMlncpp.R |only stm-1.1.0/stm/R/STMmnreg.R | 44 + stm-1.1.0/stm/R/STMmu.R | 86 ++- stm-1.1.0/stm/R/estimateEffect.R | 27 - stm-1.1.0/stm/R/findThoughts.R | 5 stm-1.1.0/stm/R/findTopic.R |only stm-1.1.0/stm/R/heldout.R | 4 stm-1.1.0/stm/R/labelTopics.R | 32 - stm-1.1.0/stm/R/parseFormulas.R | 6 stm-1.1.0/stm/R/plot.STM.R | 5 stm-1.1.0/stm/R/plot.estimateEffect.R | 2 stm-1.1.0/stm/R/plot.searchK.R | 8 stm-1.1.0/stm/R/prepDocuments.R | 4 stm-1.1.0/stm/R/produce_cmatrix.R | 3 stm-1.1.0/stm/R/readCorpus.R | 12 stm-1.1.0/stm/R/spectral.R | 96 +++- stm-1.1.0/stm/R/stm.R | 46 + stm-1.1.0/stm/R/stm.control.R | 4 stm-1.1.0/stm/R/textProcessor.R | 58 +- stm-1.1.0/stm/R/thetaPosterior.R | 8 stm-1.1.0/stm/R/toLDAvis.R |only stm-1.1.0/stm/R/topicLasso.R |only stm-1.1.0/stm/build/vignette.rds |binary stm-1.1.0/stm/data/gadarian.RData |binary stm-1.1.0/stm/data/gadarianFit.RData |binary stm-1.1.0/stm/data/poliblog5k.RData |binary stm-1.1.0/stm/inst/CITATION | 4 stm-1.1.0/stm/inst/NEWS.Rd | 25 + stm-1.1.0/stm/inst/doc/stmVignette.R | 225 +++++---- stm-1.1.0/stm/inst/doc/stmVignette.Rnw | 632 ++++++++++++++++----------- stm-1.1.0/stm/inst/doc/stmVignette.pdf |binary stm-1.1.0/stm/man/estimateEffect.Rd | 9 stm-1.1.0/stm/man/findThoughts.Rd | 12 stm-1.1.0/stm/man/findTopic.Rd |only stm-1.1.0/stm/man/multiSTM.Rd | 4 stm-1.1.0/stm/man/plot.MultimodDiagnostic.Rd | 5 stm-1.1.0/stm/man/plot.estimateEffect.Rd | 3 stm-1.1.0/stm/man/searchK.Rd | 2 stm-1.1.0/stm/man/stm-package.Rd | 4 stm-1.1.0/stm/man/stm.Rd | 23 stm-1.1.0/stm/man/textProcessor.Rd | 14 stm-1.1.0/stm/man/toLDAvis.Rd |only stm-1.1.0/stm/man/topicLasso.Rd |only stm-1.1.0/stm/src |only stm-1.1.0/stm/vignettes/Flowchart.pdf |only stm-1.1.0/stm/vignettes/jsslogo.jpg |only stm-1.1.0/stm/vignettes/stmVignette.Rnw | 632 ++++++++++++++++----------- stm-1.1.0/stm/vignettes/vignetteBib.bib | 415 ++++++++++++----- 56 files changed, 1781 insertions(+), 894 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit
a regression model with possibly right, left or interval
censored observations and with the error distribution
expressed as a mixture of G-splines. Core part
of the computation is done in compiled C++ written
using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between smoothSurv versions 1.5-2 dated 2015-05-21 and 1.6 dated 2015-07-27
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 5 +++++ NEWS | 4 ++++ 4 files changed, 18 insertions(+), 8 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.5 dated 2015-07-15 and 1.3.6 dated 2015-07-27
SciencesPo-1.3.5/SciencesPo/R/add.ellipses.R |only SciencesPo-1.3.5/SciencesPo/R/between.R |only SciencesPo-1.3.5/SciencesPo/R/by.data.frame.R |only SciencesPo-1.3.5/SciencesPo/R/formatPercent.R |only SciencesPo-1.3.5/SciencesPo/R/legendPlotMinimalist.R |only SciencesPo-1.3.5/SciencesPo/R/name.slicer.R |only SciencesPo-1.3.5/SciencesPo/R/posixify.R |only SciencesPo-1.3.5/SciencesPo/R/roman.numeral.R |only SciencesPo-1.3.5/SciencesPo/R/use.R |only SciencesPo-1.3.5/SciencesPo/R/var_order.R |only SciencesPo-1.3.5/SciencesPo/R/weighted.variance.R |only SciencesPo-1.3.5/SciencesPo/man/add.ellipses.Rd |only SciencesPo-1.3.5/SciencesPo/man/as.data.frame.by.Rd |only SciencesPo-1.3.5/SciencesPo/man/bin.Rd |only SciencesPo-1.3.5/SciencesPo/man/formatPercent.Rd |only SciencesPo-1.3.5/SciencesPo/man/legendPlotMinimalist.Rd |only SciencesPo-1.3.5/SciencesPo/man/name.slicer.Rd |only SciencesPo-1.3.5/SciencesPo/man/posixify.Rd |only SciencesPo-1.3.5/SciencesPo/man/roman.numeral.Rd |only SciencesPo-1.3.5/SciencesPo/man/use.Rd |only SciencesPo-1.3.5/SciencesPo/man/varOrder.Rd |only SciencesPo-1.3.5/SciencesPo/man/weighted.variance.Rd |only SciencesPo-1.3.5/SciencesPo/man/zScores.Rd |only SciencesPo-1.3.6/SciencesPo/DESCRIPTION | 14 - SciencesPo-1.3.6/SciencesPo/MD5 | 107 +++++---- SciencesPo-1.3.6/SciencesPo/NAMESPACE | 60 +++-- SciencesPo-1.3.6/SciencesPo/R/DATA.R | 93 ++++---- SciencesPo-1.3.6/SciencesPo/R/MANIPULATION.R | 113 ---------- SciencesPo-1.3.6/SciencesPo/R/Themes.R |only SciencesPo-1.3.6/SciencesPo/R/add.R |only SciencesPo-1.3.6/SciencesPo/R/allocation.R |only SciencesPo-1.3.6/SciencesPo/R/as.percent.R |only SciencesPo-1.3.6/SciencesPo/R/as.roman.R |only SciencesPo-1.3.6/SciencesPo/R/build.R |only SciencesPo-1.3.6/SciencesPo/R/ci.R | 4 SciencesPo-1.3.6/SciencesPo/R/crosstable.R | 135 ++++++++---- SciencesPo-1.3.6/SciencesPo/R/dHondt.R | 30 +- SciencesPo-1.3.6/SciencesPo/R/database.R |only SciencesPo-1.3.6/SciencesPo/R/electoralTool.R | 175 ++++++++++++++++ SciencesPo-1.3.6/SciencesPo/R/ellipses.R |only SciencesPo-1.3.6/SciencesPo/R/footnote.R |only SciencesPo-1.3.6/SciencesPo/R/lookup.R | 3 SciencesPo-1.3.6/SciencesPo/R/mode.R | 4 SciencesPo-1.3.6/SciencesPo/R/normalize.R |only SciencesPo-1.3.6/SciencesPo/R/recode.R |only SciencesPo-1.3.6/SciencesPo/R/rename.R | 105 --------- SciencesPo-1.3.6/SciencesPo/R/svTransform.R |only SciencesPo-1.3.6/SciencesPo/R/tabulate.R |only SciencesPo-1.3.6/SciencesPo/R/utils.R | 11 - SciencesPo-1.3.6/SciencesPo/R/var.order.R |only SciencesPo-1.3.6/SciencesPo/R/weighted.var.R |only SciencesPo-1.3.6/SciencesPo/R/z.scores.R |only SciencesPo-1.3.6/SciencesPo/README.md | 2 SciencesPo-1.3.6/SciencesPo/demo/SciencesPo.R | 52 +++- SciencesPo-1.3.6/SciencesPo/inst/NEWS.Rd | 10 SciencesPo-1.3.6/SciencesPo/man/add-methods.Rd |only SciencesPo-1.3.6/SciencesPo/man/allocation.Rd |only SciencesPo-1.3.6/SciencesPo/man/as.percent.Rd |only SciencesPo-1.3.6/SciencesPo/man/as.roman.Rd |only SciencesPo-1.3.6/SciencesPo/man/build-methods.Rd |only SciencesPo-1.3.6/SciencesPo/man/cox.shugart.Rd |only SciencesPo-1.3.6/SciencesPo/man/dHondt.Rd | 18 + SciencesPo-1.3.6/SciencesPo/man/database.Rd |only SciencesPo-1.3.6/SciencesPo/man/dbTempTable.Rd |only SciencesPo-1.3.6/SciencesPo/man/ellipses.Rd |only SciencesPo-1.3.6/SciencesPo/man/farina.Rd |only SciencesPo-1.3.6/SciencesPo/man/footnote.Rd |only SciencesPo-1.3.6/SciencesPo/man/gallagher.Rd |only SciencesPo-1.3.6/SciencesPo/man/grofman.Rd |only SciencesPo-1.3.6/SciencesPo/man/head.Rd |only SciencesPo-1.3.6/SciencesPo/man/lijphart.Rd |only SciencesPo-1.3.6/SciencesPo/man/lookup.Rd | 3 SciencesPo-1.3.6/SciencesPo/man/normalize.Rd | 2 SciencesPo-1.3.6/SciencesPo/man/recode.Rd |only SciencesPo-1.3.6/SciencesPo/man/rename.Rd | 30 -- SciencesPo-1.3.6/SciencesPo/man/scale_colour_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/scale_fill_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/svTransform.Rd | 2 SciencesPo-1.3.6/SciencesPo/man/tab.Rd | 29 ++ SciencesPo-1.3.6/SciencesPo/man/tabulate.Rd |only SciencesPo-1.3.6/SciencesPo/man/theme_pub.Rd |only SciencesPo-1.3.6/SciencesPo/man/var.order.Rd |only SciencesPo-1.3.6/SciencesPo/man/weighted.var.Rd |only SciencesPo-1.3.6/SciencesPo/man/z.scores.Rd |only SciencesPo-1.3.6/SciencesPo/tests/testthat/test-cv.R |only SciencesPo-1.3.6/SciencesPo/tests/testthat/test-se.R | 6 86 files changed, 545 insertions(+), 463 deletions(-)
Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between RcmdrPlugin.NMBU versions 1.8.0.4 dated 2015-03-12 and 1.8.3 dated 2015-07-27
DESCRIPTION | 10 MD5 | 18 NAMESPACE | 15 R/NMBU.GUI.Models.R | 10 R/NMBU.GUI.Statistics.R | 425 ++++++++++------- R/NMBU.RcmdrPlugin.NMBU.R | 2 R/NMBU.Utilities.R | 989 ++++++++++++++++++++++++---------------- R/globals.R | 3 inst/etc/menus.txt | 42 + man/RcmdrPlugin.NMBU-package.Rd | 8 10 files changed, 926 insertions(+), 596 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: An Extension (for Package 'SigTree') of Some of the Classes in
Package 'phylobase'
Description: Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
Author: J. Conrad Stack
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Diff between phyext2 versions 0.0.3 dated 2015-07-17 and 0.0.4 dated 2015-07-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 9 +++++++++ R/phyext2.R | 3 ++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>
Diff between MPTinR versions 1.9.2 dated 2015-06-13 and 1.10.3 dated 2015-07-27
DESCRIPTION | 10 MD5 | 31 NAMESPACE | 3 NEWS | 27 R/fit.mptinr.R | 6 R/get.mpt.fia.R | 316 ++++----- R/select.mpt.R | 10 data/roc6.rda |only data/roc8.rda |only inst/doc/mptinr_introduction.R | 383 ++++++----- inst/doc/mptinr_introduction.Rnw | 1239 +++++++++++++++++++------------------- inst/doc/mptinr_introduction.pdf |binary man/fit.model.Rd | 8 man/rocs.Rd |only man/select.mpt.Rd | 21 src/RcppExports.cpp | 18 vignettes/MPT.bib | 25 vignettes/mptinr_introduction.Rnw | 1239 +++++++++++++++++++------------------- 18 files changed, 1721 insertions(+), 1615 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.0 dated 2015-07-23 and 1.1 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/invert_toeplitz.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Query Team Cymru IP Address, Autonomous System Number (ASN),
Border Gateway Protocol (BGP), Bogon and Malware Hash Data
Services
Description: A toolkit for querying Team Cymru <http://team-cymru.org> IP address,
Autonomous System Number (ASN), Border Gateway Protocol (BGP), Bogon
and Malware Hash Data Services.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between cymruservices versions 0.1.0 dated 2015-07-23 and 0.1.1 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bogons.R | 34 ++++++++++++++++++++++++++++------ man/ipv4_bogons.Rd | 2 +- man/ipv6_bogons.Rd | 2 +- 5 files changed, 37 insertions(+), 15 deletions(-)
Title: Credit Default Swap Functions
Description: One function to bootstrap a credit curve from market quotes (Credit Default Swap spreads) and another function to price Credit Default Swaps from a credit curve.
Author: Bertrand Le Nezet [cre, aut, cph],
Richard Brent [ctb, cph],
John Burkardt [ctb, cph]
Maintainer: Bertrand Le Nezet <bertrand.lenezet@gmail.com>
Diff between credule versions 0.1 dated 2015-07-25 and 0.1.2 dated 2015-07-27
credule-0.1.2/credule/DESCRIPTION | 16 - credule-0.1.2/credule/MD5 | 12 credule-0.1.2/credule/man/bootstrapCDS.Rd | 2 credule-0.1.2/credule/man/credule-package.Rd | 6 credule-0.1.2/credule/man/priceCDS.Rd | 2 credule-0.1.2/credule/src/credule.c | 380 +++++---------------------- credule-0.1.2/credule/src/credule.h |only credule-0.1/credule/R/credule-Ex.R |only 8 files changed, 106 insertions(+), 312 deletions(-)
Title: Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>
Diff between cpm versions 2.1 dated 2015-07-12 and 2.2 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/CITATION | 34 +++++++++++++++++++--------------- man/cpmPackage.Rd | 2 +- 4 files changed, 26 insertions(+), 22 deletions(-)
Title: Bayesian Optimal Interval Design for Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 1.1 dated 2015-02-15 and 1.2 dated 2015-07-27
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/get.boundary.R | 8 ++++++-- R/get.oc.R | 4 ++-- R/select.mtd.R | 8 ++++++-- man/BOIN-package.Rd | 13 +++++++------ man/get.boundary.Rd | 30 +++++++++++++++--------------- man/get.oc.Rd | 30 +++++++++++++++--------------- man/select.mtd.Rd | 23 ++++++++++++++++------- 10 files changed, 83 insertions(+), 63 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Description: Contains Bayesian implementations of Mixed-Effects Accelerated Failure Time (MEAFT) models
for censored data. Those can be not only right-censored but also interval-censored,
doubly-interval-censored or misclassified interval-censored.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between bayesSurv versions 2.4 dated 2015-02-05 and 2.6 dated 2015-07-27
CHANGES | 12 +++++++++++- DESCRIPTION | 13 ++++++++----- MD5 | 14 ++++++++------ NAMESPACE | 15 +++++++++++++++ R/bayessurvreg3.R | 4 ++-- R/bayessurvreg3Para.R |only R/predictive2Para.R |only man/bayessurvreg3.Rd | 26 ++++++++++++++++++++++++++ man/predictive2.Rd | 10 ++++++++++ 9 files changed, 80 insertions(+), 14 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.0.2 dated 2015-04-21 and 1.0.3 dated 2015-07-27
sitar-1.0.2/sitar/R/predict.R |only sitar-1.0.3/sitar/DESCRIPTION | 8 - sitar-1.0.3/sitar/MD5 | 35 +++-- sitar-1.0.3/sitar/NAMESPACE | 33 +++- sitar-1.0.3/sitar/NEWS | 21 +++ sitar-1.0.3/sitar/R/anova.sitar.R |only sitar-1.0.3/sitar/R/ifun.R |only sitar-1.0.3/sitar/R/mplot.R | 10 - sitar-1.0.3/sitar/R/plot.sitar.R | 195 ++++++++++++++++------------ sitar-1.0.3/sitar/R/predict.sitar.R |only sitar-1.0.3/sitar/R/sitar.R | 13 + sitar-1.0.3/sitar/R/sitarlib.R | 33 ---- sitar-1.0.3/sitar/R/xyadj.R |only sitar-1.0.3/sitar/data/heights.rda |binary sitar-1.0.3/sitar/man/anova.sitar.Rd |only sitar-1.0.3/sitar/man/getCovariate.sitar.Rd |only sitar-1.0.3/sitar/man/heights.Rd | 5 sitar-1.0.3/sitar/man/ifun.Rd |only sitar-1.0.3/sitar/man/mplot.Rd | 2 sitar-1.0.3/sitar/man/plot.sitar.Rd | 65 ++++++--- sitar-1.0.3/sitar/man/predict.sitar.Rd | 23 ++- sitar-1.0.3/sitar/man/sitar.Rd | 14 +- sitar-1.0.3/sitar/man/xyadj.Rd |only 23 files changed, 280 insertions(+), 177 deletions(-)
Title: Discrete Laplace Distributions
Description: Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
Author: Alessandro Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo <riccardo.arner@libero.it>
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteLaplace versions 1.0 dated 2012-02-02 and 1.1 dated 2015-07-27
DiscreteLaplace-1.0/DiscreteLaplace/R/pdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/R/qdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/R/rdlaplace.R |only DiscreteLaplace-1.0/DiscreteLaplace/doc |only DiscreteLaplace-1.0/DiscreteLaplace/man/pdlaplace.Rd |only DiscreteLaplace-1.0/DiscreteLaplace/man/qdlaplace.Rd |only DiscreteLaplace-1.0/DiscreteLaplace/man/rdlaplace.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/DESCRIPTION | 20 +-- DiscreteLaplace-1.1/DiscreteLaplace/MD5 | 39 +++-- DiscreteLaplace-1.1/DiscreteLaplace/NAMESPACE | 3 DiscreteLaplace-1.1/DiscreteLaplace/R/Edlaplace.R | 2 DiscreteLaplace-1.1/DiscreteLaplace/R/Edlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/ddlaplace.R | 45 +++++- DiscreteLaplace-1.1/DiscreteLaplace/R/ddlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/dlaplacelike2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/estdlaplace2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/iFI.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/iFI2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/ioFI2.R |only DiscreteLaplace-1.1/DiscreteLaplace/R/loss.R |only DiscreteLaplace-1.1/DiscreteLaplace/man/DiscreteLaplace-package.Rd | 16 +- DiscreteLaplace-1.1/DiscreteLaplace/man/Edlaplace.Rd | 8 - DiscreteLaplace-1.1/DiscreteLaplace/man/Edlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/ddlaplace.Rd | 66 ++++++++-- DiscreteLaplace-1.1/DiscreteLaplace/man/ddlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/dlaplacelike.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/estdlaplace.Rd | 11 - DiscreteLaplace-1.1/DiscreteLaplace/man/estdlaplace2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/iFI.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/iFI2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/ioFI2.Rd |only DiscreteLaplace-1.1/DiscreteLaplace/man/loss.Rd |only 32 files changed, 145 insertions(+), 65 deletions(-)
More information about DiscreteLaplace at CRAN
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Title: An R Package for Changepoint Analysis
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean, cpt.var, cpt.meanvar functions should be your first point of call.
Author: Rebecca Killick [aut, cre],
Kaylea Haynes [aut],
Idris Eckley [aut],
Paul Fearnhead [ctb],
Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between changepoint versions 1.1.5 dated 2014-06-25 and 2.0.1 dated 2015-07-27
changepoint-1.1.5/changepoint/man/PELT.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/PELT.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/PELT.var.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/binseg.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/binseg.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/binseg.var.css.Rd |only changepoint-1.1.5/changepoint/man/binseg.var.norm.Rd |only changepoint-1.1.5/changepoint/man/decision.Rd |only changepoint-1.1.5/changepoint/man/multiple.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/multiple.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/multiple.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/multiple.var.css.Rd |only changepoint-1.1.5/changepoint/man/multiple.var.norm.Rd |only changepoint-1.1.5/changepoint/man/print-methods.Rd |only changepoint-1.1.5/changepoint/man/segneigh.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/segneigh.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/segneigh.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/segneigh.var.css.Rd |only changepoint-1.1.5/changepoint/man/segneigh.var.norm.Rd |only changepoint-1.1.5/changepoint/man/single.mean.cusum.Rd |only changepoint-1.1.5/changepoint/man/single.mean.cusum.calc.Rd |only changepoint-1.1.5/changepoint/man/single.mean.norm.Rd |only changepoint-1.1.5/changepoint/man/single.mean.norm.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.exp.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.exp.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.gamma.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.gamma.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.norm.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.norm.calc.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.poisson.Rd |only changepoint-1.1.5/changepoint/man/single.meanvar.poisson.calc.Rd |only changepoint-1.1.5/changepoint/man/single.var.css.Rd |only changepoint-1.1.5/changepoint/man/single.var.css.calc.Rd |only changepoint-1.1.5/changepoint/man/single.var.norm.Rd |only changepoint-1.1.5/changepoint/man/single.var.norm.calc.Rd |only changepoint-1.1.5/changepoint/src/PELT.c |only changepoint-2.0.1/changepoint/DESCRIPTION | 22 changepoint-2.0.1/changepoint/MD5 | 122 changepoint-2.0.1/changepoint/NAMESPACE | 26 changepoint-2.0.1/changepoint/NEWS | 33 changepoint-2.0.1/changepoint/R/BinSeg_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/CROPS.R |only changepoint-2.0.1/changepoint/R/PELT_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/SegNeigh_one_func_minseglen.R |only changepoint-2.0.1/changepoint/R/class_input.R |only changepoint-2.0.1/changepoint/R/cpt.R | 364 +- changepoint-2.0.1/changepoint/R/cpt.class.R | 230 + changepoint-2.0.1/changepoint/R/data_input.R |only changepoint-2.0.1/changepoint/R/decision.R | 62 changepoint-2.0.1/changepoint/R/exp.R | 624 ++-- changepoint-2.0.1/changepoint/R/gamma.R | 407 +-- changepoint-2.0.1/changepoint/R/multiple.nonparametric.R | 615 ++-- changepoint-2.0.1/changepoint/R/multiple.norm.R | 1256 +++++----- changepoint-2.0.1/changepoint/R/penalty_decision.R |only changepoint-2.0.1/changepoint/R/poisson.R | 409 +-- changepoint-2.0.1/changepoint/R/range_of_penalties.R |only changepoint-2.0.1/changepoint/R/single.nonparametric.R | 406 +-- changepoint-2.0.1/changepoint/R/single.norm.R | 328 +- changepoint-2.0.1/changepoint/R/zzz.R | 4 changepoint-2.0.1/changepoint/inst/CITATION | 48 changepoint-2.0.1/changepoint/man/changepoint-package.Rd | 4 changepoint-2.0.1/changepoint/man/cpt-class.Rd | 7 changepoint-2.0.1/changepoint/man/cpt.mean.Rd | 29 changepoint-2.0.1/changepoint/man/cpt.meanvar.Rd | 28 changepoint-2.0.1/changepoint/man/cpt.range-class.Rd |only changepoint-2.0.1/changepoint/man/cpt.var.Rd | 26 changepoint-2.0.1/changepoint/man/cpts.full--methods.Rd |only changepoint-2.0.1/changepoint/man/cpts.full-.Rd |only changepoint-2.0.1/changepoint/man/cpts.full-methods.Rd |only changepoint-2.0.1/changepoint/man/cpts.full.Rd |only changepoint-2.0.1/changepoint/man/minseglen--methods.Rd |only changepoint-2.0.1/changepoint/man/minseglen-.Rd |only changepoint-2.0.1/changepoint/man/minseglen-methods.Rd |only changepoint-2.0.1/changepoint/man/minseglen.Rd |only changepoint-2.0.1/changepoint/man/nseg-methods.Rd |only changepoint-2.0.1/changepoint/man/nseg.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full--methods.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full-.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full-methods.Rd |only changepoint-2.0.1/changepoint/man/pen.value.full.Rd |only changepoint-2.0.1/changepoint/man/show-methods.Rd |only changepoint-2.0.1/changepoint/man/summary-methods.Rd | 4 changepoint-2.0.1/changepoint/src/BinSeg_one_func_minseglen.c |only changepoint-2.0.1/changepoint/src/PELT_one_func_minseglen.c |only changepoint-2.0.1/changepoint/src/cost_general_functions.c |only changepoint-2.0.1/changepoint/tests |only 99 files changed, 2888 insertions(+), 2166 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre],
Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>
Diff between alineR versions 1.0 dated 2015-07-10 and 1.1 dated 2015-07-27
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 3 +-- R/ALINE.segments.R | 5 ++++- R/map.R | 2 +- R/optimize.features.R | 12 +++--------- man/aline-package.Rd | 3 +++ man/features.plot.Rd | 2 +- man/optimize.features.Rd | 12 ++---------- 9 files changed, 29 insertions(+), 39 deletions(-)
Title: An R Package for Reading and Writing BAM (Binary Alignment)
Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.12.2 dated 2015-07-16 and 2.12.3 dated 2015-07-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/data_frame.h | 20 +++++++++++++++++--- 3 files changed, 22 insertions(+), 8 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.4.1 dated 2015-07-09 and 0.4.2 dated 2015-07-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/SES.R | 1 + R/censIndLR.R | 33 +++++++++++++++++---------------- R/testIndLogistic.R | 6 +++++- man/MXM-package.Rd | 4 ++-- 7 files changed, 36 insertions(+), 30 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.2 dated 2015-06-14 and 0.2.3 dated 2015-07-27
RGA-0.2.2/RGA/R/first-date.R |only RGA-0.2.3/RGA/DESCRIPTION | 15 +- RGA-0.2.3/RGA/MD5 | 117 +++++++++++------------ RGA-0.2.3/RGA/NAMESPACE | 4 RGA-0.2.3/RGA/R/auth.R | 66 +++++++++--- RGA-0.2.3/RGA/R/convert.R | 21 ++-- RGA-0.2.3/RGA/R/custom-sources.R | 2 RGA-0.2.3/RGA/R/firstdate.R |only RGA-0.2.3/RGA/R/get-data.R | 4 RGA-0.2.3/RGA/R/goals.R | 4 RGA-0.2.3/RGA/R/mgmt.R | 2 RGA-0.2.3/RGA/R/package.R | 3 RGA-0.2.3/RGA/R/profiles.R | 6 - RGA-0.2.3/RGA/R/request.R | 7 + RGA-0.2.3/RGA/R/unsampled.R | 6 - RGA-0.2.3/RGA/R/url.R | 29 +++-- RGA-0.2.3/RGA/R/utils.R | 1 RGA-0.2.3/RGA/R/webproperties.R | 2 RGA-0.2.3/RGA/R/zzz.R | 2 RGA-0.2.3/RGA/README.md | 2 RGA-0.2.3/RGA/build/vignette.rds |binary RGA-0.2.3/RGA/data/ga.rda |binary RGA-0.2.3/RGA/inst/NEWS.Rd | 40 +++++-- RGA-0.2.3/RGA/inst/doc/authorize.R | 2 RGA-0.2.3/RGA/inst/doc/authorize.Rmd | 49 ++++++--- RGA-0.2.3/RGA/inst/doc/authorize.html | 22 +++- RGA-0.2.3/RGA/inst/doc/common-queries.R |only RGA-0.2.3/RGA/inst/doc/common-queries.Rmd |only RGA-0.2.3/RGA/inst/doc/common-queries.html |only RGA-0.2.3/RGA/inst/doc/management-api.R | 2 RGA-0.2.3/RGA/inst/doc/management-api.Rmd | 41 ++++---- RGA-0.2.3/RGA/inst/doc/management-api.html | 42 +++++--- RGA-0.2.3/RGA/inst/doc/metadata-api.R | 2 RGA-0.2.3/RGA/inst/doc/metadata-api.Rmd | 15 ++ RGA-0.2.3/RGA/inst/doc/metadata-api.html | 8 - RGA-0.2.3/RGA/inst/doc/reporting-api.R | 2 RGA-0.2.3/RGA/inst/doc/reporting-api.Rmd | 17 +-- RGA-0.2.3/RGA/inst/doc/reporting-api.html | 15 +- RGA-0.2.3/RGA/man/RGA.Rd | 2 RGA-0.2.3/RGA/man/authorize.Rd | 43 ++++++-- RGA-0.2.3/RGA/man/firstdate.Rd | 5 RGA-0.2.3/RGA/man/get_ga.Rd | 5 RGA-0.2.3/RGA/man/get_goal.Rd | 4 RGA-0.2.3/RGA/man/get_mcf.Rd | 5 RGA-0.2.3/RGA/man/get_profile.Rd | 4 RGA-0.2.3/RGA/man/get_rt.Rd | 5 RGA-0.2.3/RGA/man/get_unsampled_report.Rd | 2 RGA-0.2.3/RGA/man/get_webproperty.Rd | 2 RGA-0.2.3/RGA/man/list_custom_sources.Rd | 2 RGA-0.2.3/RGA/man/list_profiles.Rd | 2 RGA-0.2.3/RGA/man/list_unsampled_reports.Rd | 2 RGA-0.2.3/RGA/tests/testthat/test-auth.R |only RGA-0.2.3/RGA/tests/testthat/test-convert-ga.R | 8 - RGA-0.2.3/RGA/tests/testthat/test-convert-mcf.R | 44 ++++---- RGA-0.2.3/RGA/tests/testthat/test-convert-mgmt.R | 14 +- RGA-0.2.3/RGA/tests/testthat/test-metadata.R | 14 +- RGA-0.2.3/RGA/tests/testthat/test-query.R | 18 ++- RGA-0.2.3/RGA/tests/testthat/test-url.R | 8 - RGA-0.2.3/RGA/vignettes/authorize.Rmd | 49 ++++++--- RGA-0.2.3/RGA/vignettes/common-queries.Rmd |only RGA-0.2.3/RGA/vignettes/management-api.Rmd | 41 ++++---- RGA-0.2.3/RGA/vignettes/metadata-api.Rmd | 15 ++ RGA-0.2.3/RGA/vignettes/reporting-api.Rmd | 17 +-- 63 files changed, 525 insertions(+), 336 deletions(-)
Title: Discrete and Global Optimization Routines
Description:
The R package 'adagio' will provide methods and algorithms for
discrete optimization and (evolutionary) global optimization.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between adagio versions 0.5.9 dated 2013-09-28 and 0.6.1 dated 2015-07-27
adagio-0.5.9/adagio/R/linesearch.R |only adagio-0.5.9/adagio/R/qpspecial.R |only adagio-0.5.9/adagio/man/linesearch.Rd |only adagio-0.5.9/adagio/man/qpspecial.Rd |only adagio-0.6.1/adagio/DESCRIPTION | 14 ++++--- adagio-0.6.1/adagio/MD5 | 28 ++++++--------- adagio-0.6.1/adagio/NAMESPACE | 25 +++++++------ adagio-0.6.1/adagio/NEWS | 9 ++++ adagio-0.6.1/adagio/R/testfunctions.R | 36 +++---------------- adagio-0.6.1/adagio/R/trefethen.R | 7 +-- adagio-0.6.1/adagio/man/maxempty.Rd | 8 ++-- adagio-0.6.1/adagio/man/maxquad.Rd | 3 - adagio-0.6.1/adagio/man/nelmin.Rd | 5 +- adagio-0.6.1/adagio/man/simpleDE.Rd | 2 - adagio-0.6.1/adagio/man/simpleEA.Rd | 2 - adagio-0.6.1/adagio/man/testfunctions.Rd | 57 +++++++++++++++++-------------- adagio-0.6.1/adagio/man/trefethen.Rd | 20 ++++++---- 17 files changed, 103 insertions(+), 113 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.1 dated 2015-07-24 and 1.0.2 dated 2015-07-27
warbleR-1.0.1/warbleR/R/autodetec_1.0.R |only warbleR-1.0.1/warbleR/R/checkwavs_1.0.R |only warbleR-1.0.1/warbleR/R/lspec_1.6.R |only warbleR-1.0.1/warbleR/R/manualoc_1.9.R |only warbleR-1.0.1/warbleR/R/mp32wav_1.0.R |only warbleR-1.0.1/warbleR/R/querxc_1.1.R |only warbleR-1.0.1/warbleR/R/snrspecs_1.4.R |only warbleR-1.0.1/warbleR/R/specan_1.2.R |only warbleR-1.0.1/warbleR/R/specreator_2.4.R |only warbleR-1.0.1/warbleR/R/trackfreqs_1.4.R |only warbleR-1.0.1/warbleR/R/xcmaps_1.2.R |only warbleR-1.0.2/warbleR/DESCRIPTION | 10 +- warbleR-1.0.2/warbleR/MD5 | 82 +++++++++++------------ warbleR-1.0.2/warbleR/R/Arre.aura-data.R | 8 -- warbleR-1.0.2/warbleR/R/Phae.cuvi-data.R | 9 -- warbleR-1.0.2/warbleR/R/Phae.long1-data.R | 10 +- warbleR-1.0.2/warbleR/R/Phae.long2-data.R | 10 -- warbleR-1.0.2/warbleR/R/Phae.long3-data.R | 11 +-- warbleR-1.0.2/warbleR/R/Phae.long4-data.R | 9 -- warbleR-1.0.2/warbleR/R/autodetec.R |only warbleR-1.0.2/warbleR/R/checkwavs.R |only warbleR-1.0.2/warbleR/R/lspec.R |only warbleR-1.0.2/warbleR/R/manualoc.R |only warbleR-1.0.2/warbleR/R/manualoc.df-data.R | 2 warbleR-1.0.2/warbleR/R/mp32wav.R |only warbleR-1.0.2/warbleR/R/querxc.R |only warbleR-1.0.2/warbleR/R/sig2noise.R | 48 ++++++++----- warbleR-1.0.2/warbleR/R/snrspecs.R |only warbleR-1.0.2/warbleR/R/specan.R |only warbleR-1.0.2/warbleR/R/specreator.R |only warbleR-1.0.2/warbleR/R/trackfreqs.R |only warbleR-1.0.2/warbleR/R/warbleR-package.R | 36 +++++----- warbleR-1.0.2/warbleR/R/xcmaps.R |only warbleR-1.0.2/warbleR/man/Arre.aura.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.cuvi.Rd | 10 -- warbleR-1.0.2/warbleR/man/Phae.long1.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long2.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long3.Rd | 7 - warbleR-1.0.2/warbleR/man/Phae.long4.Rd | 7 - warbleR-1.0.2/warbleR/man/autodetec.Rd | 103 +++++++++++++++-------------- warbleR-1.0.2/warbleR/man/checkwavs.Rd | 16 +++- warbleR-1.0.2/warbleR/man/lspec.Rd | 57 +++++++++------- warbleR-1.0.2/warbleR/man/manualoc.Rd | 89 +++++++++++++------------ warbleR-1.0.2/warbleR/man/manualoc.df.Rd | 2 warbleR-1.0.2/warbleR/man/mp32wav.Rd | 24 +++++- warbleR-1.0.2/warbleR/man/querxc.Rd | 34 ++++++--- warbleR-1.0.2/warbleR/man/sig2noise.Rd | 48 ++++++++----- warbleR-1.0.2/warbleR/man/snrspecs.Rd | 95 +++++++++++++++----------- warbleR-1.0.2/warbleR/man/specan.Rd | 50 ++++++++------ warbleR-1.0.2/warbleR/man/specreator.Rd | 87 ++++++++++++------------ warbleR-1.0.2/warbleR/man/trackfreqs.Rd | 103 ++++++++++++++++------------- warbleR-1.0.2/warbleR/man/warbleR.Rd | 32 +++++---- warbleR-1.0.2/warbleR/man/xcmaps.Rd | 18 ++--- 53 files changed, 574 insertions(+), 464 deletions(-)
Title: Interpolation of Data with Variable Spatial Support
Description: Geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between rtop versions 0.3-45 dated 2014-02-10 and 0.5-5 dated 2015-07-27
rtop-0.3-45/rtop/R/onLoad.r |only rtop-0.5-5/rtop/DESCRIPTION | 17 rtop-0.5-5/rtop/MD5 | 73 ++- rtop-0.5-5/rtop/NAMESPACE | 191 +++++---- rtop-0.5-5/rtop/R/checkVario.R | 5 rtop-0.5-5/rtop/R/discAreas.R | 84 ++-- rtop-0.5-5/rtop/R/estimateParameters.R | 10 rtop-0.5-5/rtop/R/findOverlap.R | 9 rtop-0.5-5/rtop/R/fitVariogram.R | 38 + rtop-0.5-5/rtop/R/gDist.r | 123 ++---- rtop-0.5-5/rtop/R/krige.R |only rtop-0.5-5/rtop/R/riverNetwork.R | 12 rtop-0.5-5/rtop/R/rtop.R | 495 +++++++++++++------------ rtop-0.5-5/rtop/R/rtopCluster.R |only rtop-0.5-5/rtop/R/rtopKrige.R | 184 +++------ rtop-0.5-5/rtop/R/rtopSim.R |only rtop-0.5-5/rtop/R/rtopVario.R | 352 ++++++++++++----- rtop-0.5-5/rtop/R/sceua.R | 481 ++++++++++++------------ rtop-0.5-5/rtop/R/tskrige.R |only rtop-0.5-5/rtop/R/useRtopWithIntamap.R |only rtop-0.5-5/rtop/R/varMat.R | 177 ++++++-- rtop-0.5-5/rtop/R/zzz.R | 25 - rtop-0.5-5/rtop/man/checkVario.Rd | 196 +++++---- rtop-0.5-5/rtop/man/createRtopObject.Rd | 6 rtop-0.5-5/rtop/man/downloadRtopExampleData.rd | 63 +-- rtop-0.5-5/rtop/man/gDist.Rd | 201 +++++----- rtop-0.5-5/rtop/man/getRtopParams.Rd | 35 + rtop-0.5-5/rtop/man/netProp.rd | 143 +++---- rtop-0.5-5/rtop/man/plot.rtopVariogramCloud.Rd | 2 rtop-0.5-5/rtop/man/readAreaInfo.Rd | 87 ++-- rtop-0.5-5/rtop/man/readAreas.Rd | 89 ++-- rtop-0.5-5/rtop/man/rtop-package.Rd | 12 rtop-0.5-5/rtop/man/rtopCluster.Rd |only rtop-0.5-5/rtop/man/rtopFitVariogram.Rd | 207 +++++----- rtop-0.5-5/rtop/man/rtopKrige.Rd | 283 ++++++++------ rtop-0.5-5/rtop/man/rtopSim.Rd |only rtop-0.5-5/rtop/man/rtopVariogram.Rd | 159 ++++---- rtop-0.5-5/rtop/man/sceua.Rd |only rtop-0.5-5/rtop/man/useRtopWithIntamap.Rd | 51 +- rtop-0.5-5/rtop/man/varMat.Rd | 208 +++++----- rtop-0.5-5/rtop/man/variogramModel.Rd | 132 +++--- rtop-0.5-5/rtop/tests/rtop.R | 33 + 42 files changed, 2279 insertions(+), 1904 deletions(-)
Title: Toolbox for WELL Random Number Generators
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky <savicky@cs.cas.cz>.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rngWELL versions 0.10-3 dated 2014-07-25 and 0.10-4 dated 2015-07-27
DESCRIPTION | 13 ++++++------- LICENSE | 2 +- MD5 | 6 +++--- src/config.h | 52 ++++++++++++++++++++++++++++------------------------ 4 files changed, 38 insertions(+), 35 deletions(-)
Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g.,
density estimation or clustering algorithms research and teaching;
providing the widely used Marron-Wand densities. Now fitting to data
by ML (Maximum Likelihood) or EM estimation.
Author: Martin Mächler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between nor1mix versions 1.2-0 dated 2014-09-02 and 1.2-1 dated 2015-07-27
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 10 ++++++---- R/norMixEM.R | 2 +- man/MarronWand.Rd | 5 +++-- 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.4 dated 2015-06-10 and 0.5 dated 2015-07-27
DESCRIPTION | 6 - MD5 | 44 ++++--- NAMESPACE | 1 NEWS | 6 + R/bson.R | 2 R/hacks.R |only R/iter.R |only R/jeroen.R | 7 - R/mongo.R | 13 +- R/object.R | 27 +++- R/stream.R | 9 - build/vignette.rds |binary inst/doc/intro.html | 4 man/mongo.Rd | 8 - src/bson/bson-stdint.h | 2 src/bson/bson-version.h | 6 - src/client.c | 3 src/cursor.c | 6 + src/mongoc/mongoc-cluster-private.h | 2 src/mongoc/mongoc-cluster.c | 207 +++++++++++++++++++++++------------- src/mongoc/mongoc-init.c | 18 --- src/mongoc/mongoc-read-prefs.c | 6 + src/mongoc/mongoc-version.h | 6 - src/mongoc/mongoc-write-command.c | 4 24 files changed, 249 insertions(+), 138 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.2-28 dated 2015-01-21 and 0.2.44 dated 2015-07-27
DESCRIPTION | 14 - MD5 | 35 ++-- NAMESPACE | 8 NEWS | 421 +++++++++++++++++++++------------------------------ R/adj2HPD.R | 2 R/animateHive.R | 19 +- R/drawHiveSpline.R | 10 - R/manipAxis.R | 7 R/plot3dHive.R | 105 +++++++----- R/plotHive.R | 76 ++++++--- R/ranHiveData.R | 10 - R/rcsr.R | 2 R/sumHPD.R | 10 - build/vignette.rds |binary inst/doc/HiveR.pdf |binary man/HidingAnAxis.Rd |only man/HiveR-package.Rd | 12 - man/ranHiveData.Rd | 2 man/rcsr.Rd | 2 19 files changed, 369 insertions(+), 366 deletions(-)
Title: Analysis of Ontologies and Protein Domain Annotations
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dcGOR versions 1.0.5 dated 2015-07-20 and 1.0.6 dated 2015-07-27
DESCRIPTION | 12 ++-- MD5 | 58 +++++++++---------- R/dcAlgo.r | 4 - R/dcAlgoPredict.r | 4 - R/dcAlgoPredictGenome.r | 4 - R/dcAlgoPredictMain.r | 4 - R/dcAlgoPredictPR.r | 4 - R/dcAlgoPropagate.r | 4 - R/dcEnrichment.r | 2 R/dcList2Matrix.r | 2 R/dcNaivePredict.r | 4 - R/dcRDataLoader.r | 135 ++++++++++++++++++++++++++++++++++++--------- R/dcRWRpredict.r | 4 - R/dcSparseMatrix.r | 2 inst/NEWS | 8 ++ inst/staticdocs/README.md | 2 man/dcAlgo.Rd | 17 +---- man/dcAlgoPredict.Rd | 17 +---- man/dcAlgoPredictGenome.Rd | 17 +---- man/dcAlgoPredictMain.Rd | 17 +---- man/dcAlgoPredictPR.Rd | 17 +---- man/dcAlgoPropagate.Rd | 17 +---- man/dcEnrichment.Rd | 14 ---- man/dcList2Matrix.Rd | 2 man/dcNaivePredict.Rd | 17 +---- man/dcRDataLoader.Rd | 24 ++++---- man/dcRWRpredict.Rd | 17 +---- man/dcSparseMatrix.Rd | 4 - man/onto.DO.Rd | 2 man/onto.MP.Rd | 2 30 files changed, 218 insertions(+), 219 deletions(-)
Title: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'
Description: Create interactive heat maps that are usable from the R console, in the
'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the
mouse pointer over a cell to show details, drag a rectangle to zoom, and click
row/column labels to highlight.
Author: Joe Cheng [aut, cre],
Tal Galili [aut],
RStudio, Inc. [cph],
Michael Bostock [ctb, cph] (D3.js library),
Justin Palmer [ctb, cph] (d3.tip library)
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between d3heatmap versions 0.6.0 dated 2015-06-23 and 0.6.1 dated 2015-07-27
DESCRIPTION | 10 MD5 | 18 NAMESPACE | 10 NEWS | 7 R/d3heatmap.R | 6 README.md | 12 inst/doc/Introduction.html | 35 - inst/htmlwidgets/lib/d3heatmapcore/heatmap.js | 15 tests/smoketest.R | 4 tests/smoketest.Rout.save | 686 +++++++++++++------------- 10 files changed, 415 insertions(+), 388 deletions(-)
Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ajpete@uw.edu>
Diff between flam versions 2.0 dated 2015-06-25 and 3.0 dated 2015-07-26
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/RcppExports.R | 7 +------ R/flam_fcns.R | 4 ++-- man/flam-package.rd | 4 ++-- src/RcppExports.cpp | 8 ++++---- src/fit.cpp | 30 +++++++++++++++--------------- 8 files changed, 39 insertions(+), 41 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.0.8.5 dated 2015-03-11 and 1.0.9.2 dated 2015-07-26
DESCRIPTION | 10 ++++------ MD5 | 10 +++++----- NAMESPACE | 11 ++++++++++- R/lm.R | 13 ++++++------- R/mixlm.R | 19 ------------------- R/statistics.R | 11 ++++++----- 6 files changed, 31 insertions(+), 43 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based on the Clinical Scenario Evaluation (CSE) approach. The package supports a broad class of data models (including clinical trials with continuous, binary, survival-type and count-type endpoints as well as multivariate outcomes that are based on combinations of different endpoints), analysis strategies and commonly used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0 dated 2015-07-26 and 1.0.1 dated 2015-07-26
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/Mediana.R | 10 +++++----- man/Criterion.Rd | 2 +- man/Mediana-package.Rd | 4 ++-- man/SampleSize.Rd | 2 +- 6 files changed, 19 insertions(+), 18 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.18 dated 2015-06-01 and 2.19 dated 2015-07-26
DESCRIPTION | 13 ++- MD5 | 54 ++++++++-------- NAMESPACE | 10 ++- R/MCMC-support.R | 18 +++-- R/aovlist-support.R | 28 +++++--- R/glht-support.R | 3 R/helpers.R | 145 +++++++++++++++++++++++++++++++------------- R/lsmeans.R | 20 +++--- R/lsmip.R | 8 +- R/nonlin-support.R | 4 - R/ordinal-support.R | 8 +- R/ref.grid.R | 12 +-- R/rms-support.R | 8 +- inst/NEWS | 21 ++++++ inst/doc/extending.R | 16 ++-- inst/doc/extending.pdf |binary inst/doc/extending.rnw | 12 ++- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 2 man/extending.Rd | 22 ++++++ man/glht.Rd | 3 man/lsmeans-package.Rd | 2 man/lsmeans.Rd | 45 ++++++++++--- man/models.Rd | 8 +- man/ref.grid.Rd | 15 +++- tests/tests1.Rout.save | 4 - vignettes/extending.rnw | 12 ++- vignettes/using-lsmeans.rnw | 2 28 files changed, 338 insertions(+), 157 deletions(-)
Title: Synergy/Antagonism Analyses of Drug Combinations
Description: A comprehensive synergy/antagonism analyses of drug combinations with
quality graphics and data. The analyses can be performed by Bliss independence and Loewe
additivity models. COMBIA provides improved statistical analysis and makes only very weak assumption of data variability
while calculating bootstrap intervals (BIs). Finally, package saves analyzed data,
2D and 3D plots ready to use in research publications. COMBIA does not require manual
data entry. Data can be directly input from wetlab experimental platforms
for example fluostar, automated robots etc. One needs to call a single function only
to perform all analysis (examples are provided with sample data).
Author: Muhammad Kashif
Maintainer: Muhammad Kashif <Muhammad.Kashif@medsci.uu.se>
Diff between COMBIA versions 1.0-3 dated 2015-07-25 and 1.0-4 dated 2015-07-26
DESCRIPTION | 6 ++-- MD5 | 24 ++++++++-------- R/COMBIA.R | 42 +++++++++++++---------------- inst/raw/FluoOptima_384_2014-03-28test.xls |binary inst/raw/testData.xls |binary man/applyLoewe.Rd | 8 ++--- man/calculateSynergy.Rd | 2 - man/loeweModel.Rd | 4 +- man/readMacSynergyValues.Rd | 2 - man/readOtherValues.Rd | 4 +- man/removeOutliers.Rd | 4 +- man/synAntPlot.Rd | 2 - man/synergySignificant.Rd | 6 ++-- 13 files changed, 51 insertions(+), 53 deletions(-)
Title: 'Rcpp' Integration of Different "Ziggurat" Normal RNG
Implementations
Description: The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (JSS, 2000), has been improved
upon a few times starting with Leong et al (JSS, 2005). This package provides
an aggregation in order to compare different implementations. The goal is to
provide an 'faster but good enough' alternative for use with R and C++ code.
The package is still in an early state. Unless you know what you are doing,
sticking with the generators provided by R may be a good idea as these have
been extremely diligently tested.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppZiggurat versions 0.1.2 dated 2014-01-26 and 0.1.3 dated 2015-07-26
ChangeLog | 49 +++++ DESCRIPTION | 14 - MD5 | 56 +++--- NAMESPACE | 7 R/RcppExports.R | 4 README.md | 18 +- build/vignette.rds |binary demo/benchmark.R | 6 inst/NEWS.Rd | 19 ++ inst/doc/RcppZiggurat.R | 14 + inst/doc/RcppZiggurat.Rnw | 98 +++++++---- inst/doc/RcppZiggurat.bib | 14 - inst/doc/RcppZiggurat.pdf |binary inst/include/Ziggurat.h | 37 ++-- inst/include/ZigguratLZLLV.h | 12 - inst/include/ZigguratMT.h | 12 - inst/include/ZigguratR.h | 30 +-- inst/include/ZigguratV1.h | 33 +-- inst/include/ZigguratV1b.h | 35 ++-- man/ziggurat.Rd | 4 src/Makevars | 2 src/Makevars.win | 3 src/RcppExports.cpp | 334 +++++++++++++++------------------------- src/ziggurat.cpp | 8 tests/zigguratTest.Rout.save | 10 - tests/zigguratTestAll.R |only tests/zigguratTestAll.Rout.save |only vignettes/RcppZiggurat.RData |binary vignettes/RcppZiggurat.Rnw | 98 +++++++---- vignettes/RcppZiggurat.bib | 14 - 30 files changed, 510 insertions(+), 421 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between mvSLOUCH versions 1.1.5 dated 2015-01-21 and 1.2 dated 2015-07-26
DESCRIPTION | 11 +++-- MD5 | 44 ++++++++++++---------- NAMESPACE | 8 ++-- R/PhyloSDEestim.R | 20 +--------- R/estimMAXLIK.R | 45 ++-------------------- R/evolmodelest.R |only R/getESS.R |only R/modelparams.R | 2 - R/modelparamssummary.R | 3 + R/simulVasicekproc.R | 60 +++++++++++++++--------------- R/simulVasicekprocphyl.R | 14 +++---- man/BrownianMotionModel.Rd | 31 ++++++++++----- man/SummarizeBM.Rd | 29 ++++++++++---- man/SummarizeMVSLOUCH.Rd | 29 +++++++++----- man/SummarizeOUCH.Rd | 30 ++++++++++----- man/estimate.evolutionary.model.Rd |only man/fitch.mvsl.Rd | 31 ++++++++++----- man/generate.model.setups.Rd |only man/mvSLOUCH-internal.Rd | 2 + man/mvSLOUCH-package.Rd | 54 +++++++++++++++++++++------ man/mvslouchModel.Rd | 73 ++++++++++++++++++++++--------------- man/ouchModel.Rd | 43 ++++++++++++++------- man/simulBMProcPhylTree.Rd | 10 +++-- man/simulMVSLOUCHProcPhylTree.Rd | 9 +++- man/simulOUCHProcPhylTree.Rd | 23 ++++++++--- 25 files changed, 329 insertions(+), 242 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.1 dated 2015-07-17 and 1.6.2 dated 2015-07-26
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ NAMESPACE | 2 - NEWS | 8 ++++ R/helper.r | 6 ++- R/zzz.r | 2 - build/vignette.rds |binary inst/doc/checkmate.html | 78 ++++++++++++++++++------------------------------ src/any_nan.c | 4 -- src/checks.c | 2 - src/is_integerish.c | 4 +- 11 files changed, 60 insertions(+), 76 deletions(-)
Title: Implementation of Parametric Formulas for Soil Water Retention
or Conductivity Curve
Description: It is a set of R implementations of parametric formulas of soil water
retention or conductivity curve. At the moment, only Van Genuchten (for
soil water retention curve) and Mualem (for hydraulic conductivity) were
implemented. See reference
\url{http://en.wikipedia.org/wiki/Water_retention_curve}.
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between soilwater versions 1.0.1 dated 2012-12-04 and 1.0.2 dated 2015-07-25
soilwater-1.0.1/soilwater/LICENSE |only soilwater-1.0.1/soilwater/R/soilwater-package.R |only soilwater-1.0.1/soilwater/man/soilwater-package.Rd |only soilwater-1.0.2/soilwater/DESCRIPTION | 29 +-- soilwater-1.0.2/soilwater/MD5 | 21 +- soilwater-1.0.2/soilwater/NAMESPACE | 3 soilwater-1.0.2/soilwater/R/additional.water.table.recharge.R |only soilwater-1.0.2/soilwater/R/hydraulic_diffusivity.R | 43 +++- soilwater-1.0.2/soilwater/R/volume.R | 4 soilwater-1.0.2/soilwater/README.md |only soilwater-1.0.2/soilwater/inst/doc/example/SWRC.R | 6 soilwater-1.0.2/soilwater/inst/doc/example/SWRC_1.R |only soilwater-1.0.2/soilwater/man/hydraulic_diffusivity.Rd | 92 +++++----- soilwater-1.0.2/soilwater/man/unitResponse.Rd |only soilwater-1.0.2/soilwater/man/watervolume.Rd | 34 +-- 15 files changed, 129 insertions(+), 103 deletions(-)
Title: Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan <nanx0006@gmail.com>, Yi Yang <yiyang@umn.edu>, Yuhong Yang <yyang@stat.umn.edu>, Chenglong Ye <yexxx323@umn.edu>
Maintainer: Yi Yang <yiyang@umn.edu>
Diff between glmvsd versions 1.2 dated 2015-02-13 and 1.3 dated 2015-07-25
glmvsd-1.2/glmvsd/R/logitBIC.R |only glmvsd-1.2/glmvsd/R/lsBIC.R |only glmvsd-1.3/glmvsd/ChangeLog | 4 ++++ glmvsd-1.3/glmvsd/DESCRIPTION | 10 +++++----- glmvsd-1.3/glmvsd/MD5 | 22 +++++++++++----------- glmvsd-1.3/glmvsd/R/binomialfit.R | 7 +++++-- glmvsd-1.3/glmvsd/R/gaussianfit.R | 6 +++--- glmvsd-1.3/glmvsd/R/glmvsd.R | 28 ++++++++++++++++++---------- glmvsd-1.3/glmvsd/R/logitARM.R | 30 ++++++++++++++++++------------ glmvsd-1.3/glmvsd/R/logitIC.R |only glmvsd-1.3/glmvsd/R/lsARM.R | 18 +++++++++++++----- glmvsd-1.3/glmvsd/R/lsIC.R |only glmvsd-1.3/glmvsd/R/tools.R | 4 +++- glmvsd-1.3/glmvsd/man/glmvsd.Rd | 26 ++++++++++++++++---------- 14 files changed, 96 insertions(+), 59 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.3 dated 2015-07-21 and 0.3.4 dated 2015-07-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mlp_net.R | 14 ++++++++++---- R/mlp_prune.R | 34 ++++++++++++---------------------- R/mlp_teach.R | 7 ++++--- man/mlp_rm_neurons.Rd | 5 +++-- src/fcnn/activation.h | 8 ++++---- src/fcnn/struct.cpp | 4 ++-- 8 files changed, 46 insertions(+), 48 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.9-0 dated 2015-06-30 and 1.10-0 dated 2015-07-25
DESCRIPTION | 13 ++-- MD5 | 49 ++++++++++-------- NAMESPACE | 29 ++++++++++ R/IRT.irfprob.tam.R | 73 +++++++++++++++++---------- R/IRT.itemfit.R |only R/IRT.simulate.R |only R/IRT.threshold.R | 15 ++++- R/IRT.truescore.R |only R/calc_posterior.v2.R | 29 ++++++++-- R/dmvnorm_TAM.R |only R/mstep.regression.R | 17 ++++-- R/stud_prior.R | 37 ++++++++++---- R/tam.calc.counts.R | 18 ++++-- R/tam.mml.2pl.R | 9 ++- R/tam.mml.3pl.R | 23 ++++++-- R/tam.mml.R | 40 +++++++++++---- R/tam.mml.mfr.R | 11 +++- inst/NEWS | 124 ++++++++++++++++++++++++++++------------------- man/IRT.WrightMap.Rd | 4 - man/IRT.itemfit.Rd |only man/IRT.simulate.Rd |only man/IRT.threshold.Rd | 43 +++++++++++++--- man/IRT.truescore.Rd |only man/IRTLikelihood.cfa.Rd | 2 man/TAM-internal.Rd | 6 +- man/TAM-package.Rd | 2 man/plot.tam.Rd | 4 + man/tam.fit.Rd | 2 man/tam.mml.Rd | 8 ++- 29 files changed, 386 insertions(+), 172 deletions(-)
Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits
the computation of the most-used nonlinear statistics/algorithms
including generalized correlation dimension, information dimension,
largest Lyapunov exponent, sample entropy and Recurrence
Quantification Analysis (RQA), among others. Basic routines
for surrogate data testing are also included. Part of this work
was based on the book "Nonlinear time series analysis" by
Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre],
Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantinoantonio.garcia@usc.es>
Diff between nonlinearTseries versions 0.2.2 dated 2015-06-03 and 0.2.3 dated 2015-07-25
nonlinearTseries-0.2.2/nonlinearTseries/src/corrDimFromTakens.c |only nonlinearTseries-0.2.2/nonlinearTseries/src/generalizedCorrDimFromTakens.c |only nonlinearTseries-0.2.2/nonlinearTseries/vignettes/biblio.bib |only nonlinearTseries-0.2.3/nonlinearTseries/DESCRIPTION | 17 +-- nonlinearTseries-0.2.3/nonlinearTseries/MD5 | 43 ++++------ nonlinearTseries-0.2.3/nonlinearTseries/NAMESPACE | 17 +++ nonlinearTseries-0.2.3/nonlinearTseries/R/corrDim.R | 2 nonlinearTseries-0.2.3/nonlinearTseries/R/getMinimumEmbeddingDimension.R | 19 +++- nonlinearTseries-0.2.3/nonlinearTseries/R/informationDimension.R | 22 +++-- nonlinearTseries-0.2.3/nonlinearTseries/R/nonLinearSystems.R | 20 ++-- nonlinearTseries-0.2.3/nonlinearTseries/R/utils.R | 6 + nonlinearTseries-0.2.3/nonlinearTseries/build/vignette.rds |binary nonlinearTseries-0.2.3/nonlinearTseries/inst/doc/nonlinearTseries_quickstart.R |only nonlinearTseries-0.2.3/nonlinearTseries/inst/doc/nonlinearTseries_quickstart.Rmd | 25 ++--- nonlinearTseries-0.2.3/nonlinearTseries/inst/doc/nonlinearTseries_quickstart.html | 36 +++----- nonlinearTseries-0.2.3/nonlinearTseries/man/cliffordMap.Rd | 4 nonlinearTseries-0.2.3/nonlinearTseries/man/ikedaMap.Rd | 4 nonlinearTseries-0.2.3/nonlinearTseries/src/ANN/ANN_CONSTANTS.h |only nonlinearTseries-0.2.3/nonlinearTseries/src/Lyapunov.c | 4 nonlinearTseries-0.2.3/nonlinearTseries/src/LyapunovFromTakens.c | 4 nonlinearTseries-0.2.3/nonlinearTseries/src/corrDim.c | 4 nonlinearTseries-0.2.3/nonlinearTseries/src/informationDimension.c | 17 ++- nonlinearTseries-0.2.3/nonlinearTseries/src/kd_dump.cpp | 11 +- nonlinearTseries-0.2.3/nonlinearTseries/src/kd_split.cpp | 22 +---- nonlinearTseries-0.2.3/nonlinearTseries/vignettes/nonlinearTseries_quickstart.Rmd | 25 ++--- 25 files changed, 163 insertions(+), 139 deletions(-)
More information about nonlinearTseries at CRAN
Permanent link
Title: Video Comparison Tool
Description: It will take the vectors of motion for two videos
(coming from a variant of shotdetect code allowing to store
detailed motion vectors in JSON format, for instance) and it
will look for comparing taking out the common chunk.
Then, provided you have some image's hashes it will compare
their signature in order to make up the decision about
chunk similarity of two video files.
ShotDetect is a free software which detects shots and scenes
from a video (http://johmathe.name/shotdetect.html).
Author: Silvia Espinosa, Joaquin Ordieres, Antonio Bello, Jose Maria Perez
Maintainer: Joaquin Ordieres <j.ordieres@upm.es>
Diff between VideoComparison versions 0.11 dated 2014-07-09 and 0.15 dated 2015-07-25
VideoComparison-0.11/VideoComparison/data/imagehash1.txt.gz |only VideoComparison-0.11/VideoComparison/data/imagehash2.txt.gz |only VideoComparison-0.11/VideoComparison/data/videomotion1.txt.gz |only VideoComparison-0.11/VideoComparison/data/videomotion2.txt.gz |only VideoComparison-0.15/VideoComparison/ChangeLog | 5 + VideoComparison-0.15/VideoComparison/DESCRIPTION | 16 ++--- VideoComparison-0.15/VideoComparison/MD5 | 31 +++++----- VideoComparison-0.15/VideoComparison/NAMESPACE | 6 + VideoComparison-0.15/VideoComparison/R/ExtractMotion.R | 2 VideoComparison-0.15/VideoComparison/R/VideoComparison.R | 6 - VideoComparison-0.15/VideoComparison/R/VideoDistance.R | 4 - VideoComparison-0.15/VideoComparison/data/datalist |only VideoComparison-0.15/VideoComparison/inst/extdata |only VideoComparison-0.15/VideoComparison/man/VideoComparison-package.Rd | 4 - VideoComparison-0.15/VideoComparison/man/VideoComparison.Rd | 7 +- VideoComparison-0.15/VideoComparison/man/VideoDistance.Rd | 4 - VideoComparison-0.15/VideoComparison/man/VideoMatch.Rd | 4 - VideoComparison-0.15/VideoComparison/src/Makevars.win | 2 18 files changed, 52 insertions(+), 39 deletions(-)
More information about VideoComparison at CRAN
Permanent link
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.11.6 dated 2015-05-01 and 0.12.0 dated 2015-07-25
ChangeLog | 127 ++++ DESCRIPTION | 18 MD5 | 269 +++++----- NAMESPACE | 2 R/Attributes.R | 6 R/Rcpp.package.skeleton.R | 2 README.md | 17 build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 44 + inst/doc/Rcpp-FAQ.R | 36 - inst/doc/Rcpp-FAQ.Rnw | 57 +- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.Rnw | 2 inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 42 - inst/include/Rcpp/Benchmark/Timer.h | 2 inst/include/Rcpp/DataFrame.h | 6 inst/include/Rcpp/DottedPairImpl.h | 8 inst/include/Rcpp/Fast.h | 6 inst/include/Rcpp/Function.h | 3 inst/include/Rcpp/Interrupt.h | 2 inst/include/Rcpp/Language.h | 4 inst/include/Rcpp/String.h | 158 ++++- inst/include/Rcpp/Symbol.h | 10 inst/include/Rcpp/api/meat/DottedPairImpl.h | 6 inst/include/Rcpp/api/meat/Rcpp_eval.h | 135 +---- inst/include/Rcpp/api/meat/export.h | 8 inst/include/Rcpp/api/meat/wrap.h | 8 inst/include/Rcpp/config.h | 4 inst/include/Rcpp/internal/Proxy_Iterator.h | 2 inst/include/Rcpp/internal/export.h | 26 inst/include/Rcpp/internal/r_vector.h | 8 inst/include/Rcpp/platform/compiler.h | 5 inst/include/Rcpp/sugar/block/SugarBlock_1.h | 4 inst/include/Rcpp/sugar/block/SugarBlock_2.h | 12 inst/include/Rcpp/sugar/block/SugarBlock_3.h | 4 inst/include/Rcpp/sugar/block/SugarMath.h | 12 inst/include/Rcpp/sugar/block/Vectorized_Math.h | 12 inst/include/Rcpp/sugar/functions/all.h | 8 inst/include/Rcpp/sugar/functions/any.h | 8 inst/include/Rcpp/sugar/functions/clamp.h | 4 inst/include/Rcpp/sugar/functions/complex.h | 4 inst/include/Rcpp/sugar/functions/cumsum.h | 4 inst/include/Rcpp/sugar/functions/diff.h | 20 inst/include/Rcpp/sugar/functions/head.h | 8 inst/include/Rcpp/sugar/functions/ifelse.h | 32 - inst/include/Rcpp/sugar/functions/is_finite.h | 4 inst/include/Rcpp/sugar/functions/is_infinite.h | 4 inst/include/Rcpp/sugar/functions/is_na.h | 12 inst/include/Rcpp/sugar/functions/is_nan.h | 4 inst/include/Rcpp/sugar/functions/lapply.h | 4 inst/include/Rcpp/sugar/functions/mapply/mapply_2.h | 12 inst/include/Rcpp/sugar/functions/mapply/mapply_3.h | 4 inst/include/Rcpp/sugar/functions/max.h | 8 inst/include/Rcpp/sugar/functions/mean.h | 18 inst/include/Rcpp/sugar/functions/min.h | 8 inst/include/Rcpp/sugar/functions/na_omit.h | 14 inst/include/Rcpp/sugar/functions/pmax.h | 8 inst/include/Rcpp/sugar/functions/pmin.h | 8 inst/include/Rcpp/sugar/functions/pow.h | 12 inst/include/Rcpp/sugar/functions/range.h | 8 inst/include/Rcpp/sugar/functions/rep.h | 28 - inst/include/Rcpp/sugar/functions/rep_each.h | 11 inst/include/Rcpp/sugar/functions/rep_len.h | 10 inst/include/Rcpp/sugar/functions/rev.h | 6 inst/include/Rcpp/sugar/functions/sapply.h | 41 + inst/include/Rcpp/sugar/functions/self_match.h | 4 inst/include/Rcpp/sugar/functions/seq_along.h | 10 inst/include/Rcpp/sugar/functions/setdiff.h | 6 inst/include/Rcpp/sugar/functions/sign.h | 6 inst/include/Rcpp/sugar/functions/strings/collapse.h | 4 inst/include/Rcpp/sugar/functions/sum.h | 12 inst/include/Rcpp/sugar/functions/table.h | 6 inst/include/Rcpp/sugar/functions/tail.h | 10 inst/include/Rcpp/sugar/functions/var.h | 23 inst/include/Rcpp/sugar/functions/which_max.h | 18 inst/include/Rcpp/sugar/functions/which_min.h | 18 inst/include/Rcpp/sugar/logical/and.h | 16 inst/include/Rcpp/sugar/logical/or.h | 16 inst/include/Rcpp/sugar/matrix/as_vector.h | 6 inst/include/Rcpp/sugar/matrix/col.h | 2 inst/include/Rcpp/sugar/matrix/diag.h | 6 inst/include/Rcpp/sugar/matrix/lower_tri.h | 2 inst/include/Rcpp/sugar/matrix/outer.h | 2 inst/include/Rcpp/sugar/matrix/row.h | 2 inst/include/Rcpp/sugar/matrix/upper_tri.h | 2 inst/include/Rcpp/sugar/nona/nona.h | 10 inst/include/Rcpp/sugar/operators/Comparator.h | 12 inst/include/Rcpp/sugar/operators/Comparator_With_One_Value.h | 8 inst/include/Rcpp/sugar/operators/divides.h | 64 +- inst/include/Rcpp/sugar/operators/minus.h | 64 +- inst/include/Rcpp/sugar/operators/not.h | 4 inst/include/Rcpp/sugar/operators/plus.h | 64 +- inst/include/Rcpp/sugar/operators/times.h | 64 +- inst/include/Rcpp/sugar/operators/unary_minus.h | 4 inst/include/Rcpp/sugar/tools/iterator.h | 8 inst/include/Rcpp/traits/is_arithmetic.h |only inst/include/Rcpp/traits/traits.h | 1 inst/include/Rcpp/vector/ChildVector.h | 4 inst/include/Rcpp/vector/LazyVector.h | 6 inst/include/Rcpp/vector/ListOf.h | 6 inst/include/Rcpp/vector/Matrix.h | 6 inst/include/Rcpp/vector/MatrixBase.h | 12 inst/include/Rcpp/vector/MatrixColumn.h | 4 inst/include/Rcpp/vector/RangeIndexer.h | 6 inst/include/Rcpp/vector/SubMatrix.h | 2 inst/include/Rcpp/vector/Vector.h | 149 +++-- inst/include/Rcpp/vector/VectorBase.h | 12 inst/include/Rcpp/vector/const_generic_proxy.h | 4 inst/include/Rcpp/vector/const_string_proxy.h | 10 inst/include/Rcpp/vector/generic_proxy.h | 6 inst/include/Rcpp/vector/no_init.h | 6 inst/include/Rcpp/vector/proxy.h | 10 inst/include/Rcpp/vector/string_proxy.h | 10 inst/include/Rcpp/vector/traits.h | 8 inst/unitTests/cpp/Function.cpp | 4 inst/unitTests/cpp/ListOf.cpp | 9 inst/unitTests/cpp/String.cpp | 33 + inst/unitTests/cpp/Vector.cpp | 1 inst/unitTests/runit.Function.R | 6 inst/unitTests/runit.String.R | 18 inst/unitTests/runit.sugar.var.R | 23 man/evalCpp.Rd | 7 src/api.cpp | 2 src/attributes.cpp | 44 + vignettes/Rcpp-FAQ.Rnw | 57 +- vignettes/Rcpp-introduction.Rnw | 2 vignettes/Rcpp.bib | 42 - 136 files changed, 1415 insertions(+), 947 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.0 dated 2015-07-24 and 3.1.1 dated 2015-07-25
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ inst/CITATION | 1 + src/Coordinate_systems.cc | 2 +- src/D.H.cc | 2 +- src/Gneiting.cc | 4 ++-- src/PoissonPolygon.cc | 4 ++-- src/Primitive.cc | 6 +++--- src/circulant.cc | 2 +- src/families.cc | 5 +++-- src/gausslikeli.cc | 3 ++- src/operator.cc | 8 ++++---- src/userinterfaces.cc | 2 +- 13 files changed, 37 insertions(+), 34 deletions(-)
Title: Provides Tests and Graphics for Assessing Tests of Equivalence
Description: Provides statistical tests and graphics for assessing tests
of equivalence. Such tests have similarity as the alternative
hypothesis instead of the null. Sample data sets are included.
Author: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>
Maintainer: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>
Diff between equivalence versions 0.6.0 dated 2014-06-06 and 0.7.0 dated 2015-07-25
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 20 ++++++++++---------- MD5 | 22 +++++++++++----------- NAMESPACE | 9 ++++++++- R/equivalence.xyplot.R | 1 + R/tost.R | 16 ++++++++-------- R/tost.stat.R | 6 +++--- data/pref.4PG.rda |binary data/pref.LAI.rda |binary data/ufc.rda |binary man/equivalence.xyplot.Rd | 3 +-- man/tost.Rd | 2 +- 12 files changed, 58 insertions(+), 36 deletions(-)
Title: Dynamic Simulations of Autoregressive Relationships
Description: Dynamic simulations and graphical depictions of autoregressive relationships.
Author: Christopher Gandrud [aut, cre],
Laron K. Williams [aut],
Guy D. Whitten [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between dynsim versions 1.0 dated 2014-08-13 and 1.2 dated 2015-07-24
dynsim-1.0/dynsim/data/grunfeld.tab.gz |only dynsim-1.2/dynsim/DESCRIPTION | 35 ++++++++----- dynsim-1.2/dynsim/MD5 | 30 +++++++---- dynsim-1.2/dynsim/NAMESPACE | 6 +- dynsim-1.2/dynsim/NEWS | 43 +++++++++++----- dynsim-1.2/dynsim/R/dynsim.R | 87 ++++++++++++++++++++++----------- dynsim-1.2/dynsim/R/dynsimGG.R | 58 +++++++++++++--------- dynsim-1.2/dynsim/R/utils.R | 46 +++++++---------- dynsim-1.2/dynsim/README.md | 8 +-- dynsim-1.2/dynsim/build |only dynsim-1.2/dynsim/data/grunfeld.tab |only dynsim-1.2/dynsim/demo |only dynsim-1.2/dynsim/inst |only dynsim-1.2/dynsim/man/dynsim.Rd | 22 ++++++-- dynsim-1.2/dynsim/man/dynsimGG.Rd | 21 +++++-- dynsim-1.2/dynsim/man/grunfeld.Rd | 3 - dynsim-1.2/dynsim/vignettes |only 17 files changed, 226 insertions(+), 133 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.3 dated 2015-07-23 and 1.1.3.1 dated 2015-07-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/depth.potential.r | 4 ++-- man/ddalpha-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, ctb],
Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4-4 dated 2015-03-08 and 0.4-5 dated 2015-07-24
DESCRIPTION | 13 ++++---- MD5 | 30 +++++++++---------- NAMESPACE | 77 +++++++++++++++++++++++++++++++++++++++++-------- R/Defaults.R | 19 ++++++------ R/addTA.R | 12 +++---- R/getDividends.R | 2 - R/getFinancials.R | 2 + R/getOptionChain.R | 14 +++++++- R/getQuote.R | 2 - R/getSplits.R | 2 - R/getSymbols.R | 64 +++++++++++++++++++++------------------- R/loadSymbols.R | 5 ++- R/tools.R | 34 +++++++++++++++++++++ man/Delt.Rd | 12 +++---- man/getSymbols.FRED.Rd | 12 +++++++ man/getSymbols.csv.Rd | 2 + 16 files changed, 210 insertions(+), 92 deletions(-)
Title: Example Datasets from Archaeological Research
Description: The archdata package provides several types of data that are typically used in archaeological research.
Author: David L. Carlson
Maintainer: David L. Carlson <dcarlson@tamu.edu>
Diff between archdata versions 0.1 dated 2014-07-15 and 1.0 dated 2015-07-24
archdata-0.1/archdata/R |only archdata-1.0/archdata/DESCRIPTION | 10 +-- archdata-1.0/archdata/MD5 | 63 ++++++++++++++++-------- archdata-1.0/archdata/data/Acheulean.rda |binary archdata-1.0/archdata/data/BACups.rda |only archdata-1.0/archdata/data/BarmoseI.grid.rda |binary archdata-1.0/archdata/data/BarmoseI.pp.rda |binary archdata-1.0/archdata/data/Bornholm.rda |only archdata-1.0/archdata/data/DartPoints.rda |binary archdata-1.0/archdata/data/EIAGraves.rda |only archdata-1.0/archdata/data/ESASites.rda |only archdata-1.0/archdata/data/EWBurials.rda |binary archdata-1.0/archdata/data/EndScrapers.rda |binary archdata-1.0/archdata/data/EngrBone.rda |only archdata-1.0/archdata/data/Fibulae.rda |only archdata-1.0/archdata/data/Handaxes.rda |binary archdata-1.0/archdata/data/MaskSite.rda |only archdata-1.0/archdata/data/Mesolithic.rda |only archdata-1.0/archdata/data/Nelson.rda |binary archdata-1.0/archdata/data/Olorgesailie.maj.rda |binary archdata-1.0/archdata/data/Olorgesailie.sub.rda |binary archdata-1.0/archdata/data/PitHouses.rda |only archdata-1.0/archdata/data/RBGlass1.rda |only archdata-1.0/archdata/data/RBGlass2.rda |only archdata-1.0/archdata/data/RBPottery.rda |only archdata-1.0/archdata/data/Snodgrass.rda |binary archdata-1.0/archdata/data/TRBPottery.rda |only archdata-1.0/archdata/man/BACups.Rd |only archdata-1.0/archdata/man/BarmoseI.grid.Rd | 4 - archdata-1.0/archdata/man/Bornholm.Rd |only archdata-1.0/archdata/man/EIAGraves.Rd |only archdata-1.0/archdata/man/ESASites.Rd |only archdata-1.0/archdata/man/EWBurials.Rd | 11 ++-- archdata-1.0/archdata/man/EngrBone.Rd |only archdata-1.0/archdata/man/Fibulae.Rd |only archdata-1.0/archdata/man/MaskSite.Rd |only archdata-1.0/archdata/man/Mesolithic.Rd |only archdata-1.0/archdata/man/Nelson.Rd | 6 +- archdata-1.0/archdata/man/Olorgesailie.sub.Rd | 8 +-- archdata-1.0/archdata/man/PitHouses.Rd |only archdata-1.0/archdata/man/RBGlass1.Rd |only archdata-1.0/archdata/man/RBGlass2.Rd |only archdata-1.0/archdata/man/RBPottery.Rd |only archdata-1.0/archdata/man/Snodgrass.Rd | 4 - archdata-1.0/archdata/man/TRBPottery.Rd |only archdata-1.0/archdata/man/archdata-package.Rd | 22 ++++++-- 46 files changed, 85 insertions(+), 43 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.0.62 dated 2015-02-03 and 3.1.0 dated 2015-07-24
RandomFields-3.0.62/RandomFields/man/Baysian.Rd |only RandomFields-3.0.62/RandomFields/man/Print.Rd |only RandomFields-3.0.62/RandomFields/src/kriging.cc |only RandomFields-3.1.0/RandomFields/DESCRIPTION | 21 RandomFields-3.1.0/RandomFields/MD5 | 492 RandomFields-3.1.0/RandomFields/NAMESPACE | 16 RandomFields-3.1.0/RandomFields/R/Class.R | 61 RandomFields-3.1.0/RandomFields/R/Crossvalidation.R | 118 RandomFields-3.1.0/RandomFields/R/D.H.R | 44 RandomFields-3.1.0/RandomFields/R/Likelihoodratio.R | 53 RandomFields-3.1.0/RandomFields/R/Methods-RFsp.R | 65 RandomFields-3.1.0/RandomFields/R/Methods-aux.R | 124 RandomFields-3.1.0/RandomFields/R/RC_GLOBALS.R | 33 RandomFields-3.1.0/RandomFields/R/RCauto.R | 156 RandomFields-3.1.0/RandomFields/R/RFempvario-Methods-plots.R | 632 - RandomFields-3.1.0/RandomFields/R/RFempvario.R | 396 RandomFields-3.1.0/RandomFields/R/RFfit.R | 584 RandomFields-3.1.0/RandomFields/R/RFgui.R | 54 RandomFields-3.1.0/RandomFields/R/RMmodels-Methods-plots.R | 63 RandomFields-3.1.0/RandomFields/R/RMmodels.R | 6224 ++-------- RandomFields-3.1.0/RandomFields/R/RMmodelsConvenience.R | 126 RandomFields-3.1.0/RandomFields/R/RMmodelsSpecial.R | 60 RandomFields-3.1.0/RandomFields/R/basic.fctns.R | 423 RandomFields-3.1.0/RandomFields/R/bigdata.R |only RandomFields-3.1.0/RandomFields/R/convert.R | 696 - RandomFields-3.1.0/RandomFields/R/convert_new.R | 253 RandomFields-3.1.0/RandomFields/R/fitbernoulli.R | 22 RandomFields-3.1.0/RandomFields/R/fitbr.R | 23 RandomFields-3.1.0/RandomFields/R/fitgauss.R | 4142 ++---- RandomFields-3.1.0/RandomFields/R/fitmaxstable.R | 24 RandomFields-3.1.0/RandomFields/R/fitpoisson.R | 23 RandomFields-3.1.0/RandomFields/R/generatemodels.R | 157 RandomFields-3.1.0/RandomFields/R/getNset.R | 126 RandomFields-3.1.0/RandomFields/R/internal_use.R | 124 RandomFields-3.1.0/RandomFields/R/kriging.R | 1312 -- RandomFields-3.1.0/RandomFields/R/nicht.nachladbar.R | 24 RandomFields-3.1.0/RandomFields/R/obsolete.R | 107 RandomFields-3.1.0/RandomFields/R/rf-plots.R | 298 RandomFields-3.1.0/RandomFields/R/rf.R | 528 RandomFields-3.1.0/RandomFields/R/zzz.R | 33 RandomFields-3.1.0/RandomFields/inst/CITATION | 5 RandomFields-3.1.0/RandomFields/man/BRspecific.Rd | 15 RandomFields-3.1.0/RandomFields/man/Bayesian.Rd |only RandomFields-3.1.0/RandomFields/man/CoordinateSystems.Rd | 36 RandomFields-3.1.0/RandomFields/man/MajorRevisions.Rd | 16 RandomFields-3.1.0/RandomFields/man/QMath.Rd | 58 RandomFields-3.1.0/RandomFields/man/RC.Rd | 27 RandomFields-3.1.0/RandomFields/man/RF.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFboxcox.Rd |only RandomFields-3.1.0/RandomFields/man/RFcrossvalidate.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFempVariog-class.Rd | 65 RandomFields-3.1.0/RandomFields/man/RFempiricalvariogram.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFfit-class.Rd | 82 RandomFields-3.1.0/RandomFields/man/RFfit.Rd | 69 RandomFields-3.1.0/RandomFields/man/RFfitOptimiser.Rd |only 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RandomFields-3.1.0/RandomFields/man/RMS.Rd | 14 RandomFields-3.1.0/RandomFields/man/RMangle.Rd | 17 RandomFields-3.1.0/RandomFields/man/RMaskey.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMball.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbcw.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbernoulli.Rd | 13 RandomFields-3.1.0/RandomFields/man/RMbessel.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbigneiting.Rd | 37 RandomFields-3.1.0/RandomFields/man/RMbiwm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbr2.Rd | 8 RandomFields-3.1.0/RandomFields/man/RMbr2bg.Rd | 7 RandomFields-3.1.0/RandomFields/man/RMbrownresnick.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcauchy.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcauchytbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMchoquet.Rd |only RandomFields-3.1.0/RandomFields/man/RMcircular.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMcovariate.Rd | 58 RandomFields-3.1.0/RandomFields/man/RMcoxisham.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcubic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcurlfree.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcutoff.Rd | 9 RandomFields-3.1.0/RandomFields/man/RMdagum.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdampedcos.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdewijsian.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdivfree.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMepscauchy.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfix.Rd | 78 RandomFields-3.1.0/RandomFields/man/RMfractdiff.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfractgauss.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgauss.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgencauchy.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMgenfbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgengneiting.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgneiting.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMgneitingdiff.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMhyperbolic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMiaco.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMintern.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMintexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMintrinsic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMkolmogorov.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMlgd.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMma.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmastein.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmatern.Rd | 14 RandomFields-3.1.0/RandomFields/man/RMmodel-class.Rd | 59 RandomFields-3.1.0/RandomFields/man/RMmodel.Rd | 21 RandomFields-3.1.0/RandomFields/man/RMmodelsAdvanced.Rd | 175 RandomFields-3.1.0/RandomFields/man/RMmodelsAuxiliary.Rd | 7 RandomFields-3.1.0/RandomFields/man/RMmodelsMultivariate.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsNonstatationary.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsSpaceTime.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsSphere.Rd | 26 RandomFields-3.1.0/RandomFields/man/RMmodelsTailcorrelation.Rd | 13 RandomFields-3.1.0/RandomFields/man/RMmodelsTrend.Rd |only RandomFields-3.1.0/RandomFields/man/RMmppplus.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmqam.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMmult.Rd | 2 RandomFields-3.1.0/RandomFields/man/RMmultiquad.Rd |only RandomFields-3.1.0/RandomFields/man/RMnatsc.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMnonstwm.Rd | 41 RandomFields-3.1.0/RandomFields/man/RMnsst.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMnugget.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMoesting.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMparswm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpenta.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpoissonpoly.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpolynome.Rd |only RandomFields-3.1.0/RandomFields/man/RMpower.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMprod.Rd | 9 RandomFields-3.1.0/RandomFields/man/RMqam.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMqexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMschlather.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMschur.Rd | 6 RandomFields-3.1.0/RandomFields/man/RMsign.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMsinepower.Rd |only RandomFields-3.1.0/RandomFields/man/RMspheric.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstable.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstein.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstrokorb.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMtbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMtrend.Rd | 141 RandomFields-3.1.0/RandomFields/man/RMtruncsupport.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMuser.Rd | 28 RandomFields-3.1.0/RandomFields/man/RMvector.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMwave.Rd | 3 RandomFields-3.1.0/RandomFields/man/RPbernoulli.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPbrownresnick.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPchi2.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPcirculant.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPcoin.Rd | 16 RandomFields-3.1.0/RandomFields/man/RPgauss.Rd | 9 RandomFields-3.1.0/RandomFields/man/RPhyperplane.Rd | 16 RandomFields-3.1.0/RandomFields/man/RPmaxstable.Rd | 24 RandomFields-3.1.0/RandomFields/man/RPmaxstableAdvanced.Rd | 22 RandomFields-3.1.0/RandomFields/man/RPnugget.Rd | 8 RandomFields-3.1.0/RandomFields/man/RPopitz.Rd | 4 RandomFields-3.1.0/RandomFields/man/RPpoisson.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPschlather.Rd | 7 RandomFields-3.1.0/RandomFields/man/RPsequential.Rd | 32 RandomFields-3.1.0/RandomFields/man/RPsmith.Rd | 8 RandomFields-3.1.0/RandomFields/man/RPspecific.Rd | 17 RandomFields-3.1.0/RandomFields/man/RPspectral.Rd | 9 RandomFields-3.1.0/RandomFields/man/RPt.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPtbm.Rd | 10 RandomFields-3.1.0/RandomFields/man/RR.Rd | 6 RandomFields-3.1.0/RandomFields/man/RRdistr.Rd | 15 RandomFields-3.1.0/RandomFields/man/RRmcmc.Rd | 4 RandomFields-3.1.0/RandomFields/man/RRrectangular.Rd | 7 RandomFields-3.1.0/RandomFields/man/RandomFields.Rd | 125 RandomFields-3.1.0/RandomFields/man/fitgauss.Rd | 2 RandomFields-3.1.0/RandomFields/man/internal.Rd | 9 RandomFields-3.1.0/RandomFields/man/obsolete.Rd | 7 RandomFields-3.1.0/RandomFields/man/papers.GSPSJ06.Rd | 21 RandomFields-3.1.0/RandomFields/man/papers.S02.Rd | 7 RandomFields-3.1.0/RandomFields/man/papers.S10.Rd | 97 RandomFields-3.1.0/RandomFields/man/papers.SBS14.Rd | 9 RandomFields-3.1.0/RandomFields/man/papers.SS11.Rd | 11 RandomFields-3.1.0/RandomFields/man/papers.jss14.Rd | 20 RandomFields-3.1.0/RandomFields/man/plot-method.Rd | 181 RandomFields-3.1.0/RandomFields/man/soil.Rd | 55 RandomFields-3.1.0/RandomFields/man/sp2RF.Rd | 2 RandomFields-3.1.0/RandomFields/src/AutoRandomFields.cc | 39 RandomFields-3.1.0/RandomFields/src/AutoRandomFields.h | 102 RandomFields-3.1.0/RandomFields/src/Brown.cc | 95 RandomFields-3.1.0/RandomFields/src/Coordinate_systems.cc | 494 RandomFields-3.1.0/RandomFields/src/Coordinate_systems.h | 42 RandomFields-3.1.0/RandomFields/src/D.H.cc | 2 RandomFields-3.1.0/RandomFields/src/Families.h | 26 RandomFields-3.1.0/RandomFields/src/Gneiting.cc | 206 RandomFields-3.1.0/RandomFields/src/Huetchen.cc | 21 RandomFields-3.1.0/RandomFields/src/InternalCov.cc | 502 RandomFields-3.1.0/RandomFields/src/KeyInfo.cc | 1060 - RandomFields-3.1.0/RandomFields/src/MLE.cc | 1316 +- RandomFields-3.1.0/RandomFields/src/Operator.h | 57 RandomFields-3.1.0/RandomFields/src/PoissonPolygon.h | 25 RandomFields-3.1.0/RandomFields/src/Primitive.cc | 1259 +- RandomFields-3.1.0/RandomFields/src/RF.h | 1286 +- RandomFields-3.1.0/RandomFields/src/RandomFields.h | 117 RandomFields-3.1.0/RandomFields/src/Specific.cc | 38 RandomFields-3.1.0/RandomFields/src/SpherModels.cc | 175 RandomFields-3.1.0/RandomFields/src/SpherModels.h | 14 RandomFields-3.1.0/RandomFields/src/SpherModelsInitNerror.cc |only RandomFields-3.1.0/RandomFields/src/SpherModelsInitNerror.h |only RandomFields-3.1.0/RandomFields/src/Userinterfaces.h |only RandomFields-3.1.0/RandomFields/src/Xempvario.cc | 4 RandomFields-3.1.0/RandomFields/src/auxiliary.cc | 638 - RandomFields-3.1.0/RandomFields/src/auxiliary.h | 35 RandomFields-3.1.0/RandomFields/src/basic.h | 102 RandomFields-3.1.0/RandomFields/src/circulant.cc | 123 RandomFields-3.1.0/RandomFields/src/convhull2D.h | 29 RandomFields-3.1.0/RandomFields/src/cubicsolver.cc |only RandomFields-3.1.0/RandomFields/src/cubicsolver.h |only RandomFields-3.1.0/RandomFields/src/direct.cc | 77 RandomFields-3.1.0/RandomFields/src/empvario.cc | 105 RandomFields-3.1.0/RandomFields/src/error.h | 59 RandomFields-3.1.0/RandomFields/src/extremes.cc | 229 RandomFields-3.1.0/RandomFields/src/families.cc | 103 RandomFields-3.1.0/RandomFields/src/fftVario.cc | 12 RandomFields-3.1.0/RandomFields/src/gauss.cc | 406 RandomFields-3.1.0/RandomFields/src/gausslikeli.cc |only RandomFields-3.1.0/RandomFields/src/getNset.cc | 1413 +- RandomFields-3.1.0/RandomFields/src/hilfsdateien.cc | 4 RandomFields-3.1.0/RandomFields/src/hyperplan.cc | 111 RandomFields-3.1.0/RandomFields/src/initNerror.cc | 942 - RandomFields-3.1.0/RandomFields/src/initNerrorSpherModels.cc |only RandomFields-3.1.0/RandomFields/src/matrix_mult.cc |only RandomFields-3.1.0/RandomFields/src/metropolis.cc | 2 RandomFields-3.1.0/RandomFields/src/nugget.cc | 50 RandomFields-3.1.0/RandomFields/src/operator.cc | 491 RandomFields-3.1.0/RandomFields/src/plusmalS.cc | 940 - RandomFields-3.1.0/RandomFields/src/primitive.h | 64 RandomFields-3.1.0/RandomFields/src/rf_interfaces.cc | 1165 + RandomFields-3.1.0/RandomFields/src/sequential.cc | 45 RandomFields-3.1.0/RandomFields/src/shape_processes.h | 56 RandomFields-3.1.0/RandomFields/src/spectral.cc | 36 RandomFields-3.1.0/RandomFields/src/startGetNset.cc | 190 RandomFields-3.1.0/RandomFields/src/tbm.cc | 307 RandomFields-3.1.0/RandomFields/src/trend.cc | 371 RandomFields-3.1.0/RandomFields/src/userinterfaces.cc | 611 RandomFields-3.1.0/RandomFields/src/variogramAndCo.cc | 404 RandomFields-3.1.0/RandomFields/src/variogramAndCo.h | 163 RandomFields-3.1.0/RandomFields/src/win_linux_aux.cc | 2 RandomFields-3.1.0/RandomFields/src/win_linux_aux.h | 25 RandomFields-3.1.0/RandomFields/src/xport.cc |only RandomFields-3.1.0/RandomFields/src/xport.h |only 261 files changed, 17532 insertions(+), 19196 deletions(-)
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between pipe.design versions 0.2 dated 2015-05-12 and 0.3 dated 2015-07-24
pipe.design-0.2/pipe.design/R/pipe.design_0.2.R |only pipe.design-0.3/pipe.design/DESCRIPTION | 8 ++++---- pipe.design-0.3/pipe.design/MD5 | 10 +++++----- pipe.design-0.3/pipe.design/NAMESPACE | 3 +++ pipe.design-0.3/pipe.design/NEWS | 6 ++++++ pipe.design-0.3/pipe.design/R/pipe.design_0.3.R |only pipe.design-0.3/pipe.design/man/pipe.design.Rd | 6 +++--- 7 files changed, 21 insertions(+), 12 deletions(-)
Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.6.8 dated 2014-03-20 and 0.8.0 dated 2015-07-24
phylobase-0.6.8/phylobase/NEWS |only phylobase-0.6.8/phylobase/R/class-multiphylo4.R |only phylobase-0.6.8/phylobase/R/class-oldclasses.R |only phylobase-0.6.8/phylobase/R/class-phylo4.R |only phylobase-0.6.8/phylobase/R/class-phylo4d.R |only phylobase-0.6.8/phylobase/R/class-phylomats.R |only phylobase-0.6.8/phylobase/R/methods-multiphylo4.R |only phylobase-0.6.8/phylobase/R/methods-oldclasses.R |only phylobase-0.6.8/phylobase/R/methods-phylo4.R |only phylobase-0.6.8/phylobase/R/methods-phylo4d.R |only phylobase-0.6.8/phylobase/R/phylo4.R |only phylobase-0.6.8/phylobase/R/prune.R |only phylobase-0.6.8/phylobase/R/setAs-Methods.R |only phylobase-0.6.8/phylobase/R/subset.R |only phylobase-0.6.8/phylobase/R/treewalk.R |only phylobase-0.6.8/phylobase/inst/doc/developer.Rnw |only phylobase-0.6.8/phylobase/inst/doc/developer.pdf |only phylobase-0.6.8/phylobase/inst/doc/phylobase-plotvcvphylo.pdf |only phylobase-0.6.8/phylobase/inst/nexusfiles/badnex.nex |only phylobase-0.6.8/phylobase/inst/nexusfiles/multiLines.Rdata |only phylobase-0.6.8/phylobase/inst/unitTests |only phylobase-0.6.8/phylobase/man/addData.Rd |only phylobase-0.6.8/phylobase/man/as-methods.Rd |only phylobase-0.6.8/phylobase/man/check.phylo4.Rd |only phylobase-0.6.8/phylobase/man/extract.tree.Rd |only phylobase-0.6.8/phylobase/man/getNode.Rd |only phylobase-0.6.8/phylobase/man/hasSingles.Rd |only phylobase-0.6.8/phylobase/man/phylo4-accessors.Rd |only phylobase-0.6.8/phylobase/man/phylo4-display.Rd |only phylobase-0.6.8/phylobase/man/phylo4-labels.Rd |only phylobase-0.6.8/phylobase/man/phylo4.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-display.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-hasData.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-nData.Rd |only phylobase-0.6.8/phylobase/man/phylo4d.Rd |only phylobase-0.6.8/phylobase/man/phylog.Rd |only phylobase-0.6.8/phylobase/man/printphylo4.Rd |only phylobase-0.6.8/phylobase/man/readNCL.Rd |only phylobase-0.6.8/phylobase/man/tdata.Rd |only phylobase-0.6.8/phylobase/man/treewalk.Rd |only phylobase-0.6.8/phylobase/src/GetNCL.cpp |only phylobase-0.6.8/phylobase/src/ncl |only phylobase-0.6.8/phylobase/src/nxsassumptionsblock.cpp |only phylobase-0.6.8/phylobase/src/nxsblock.cpp |only phylobase-0.6.8/phylobase/src/nxscharactersblock.cpp |only phylobase-0.6.8/phylobase/src/nxscxxdiscretematrix.cpp |only phylobase-0.6.8/phylobase/src/nxsdatablock.cpp |only phylobase-0.6.8/phylobase/src/nxsdistancedatum.cpp |only phylobase-0.6.8/phylobase/src/nxsdistancesblock.cpp |only phylobase-0.6.8/phylobase/src/nxsemptyblock.cpp |only phylobase-0.6.8/phylobase/src/nxsexception.cpp |only phylobase-0.6.8/phylobase/src/nxsmultiformat.cpp |only phylobase-0.6.8/phylobase/src/nxspublicblocks.cpp |only phylobase-0.6.8/phylobase/src/nxsreader.cpp |only phylobase-0.6.8/phylobase/src/nxssetreader.cpp |only phylobase-0.6.8/phylobase/src/nxsstring.cpp |only phylobase-0.6.8/phylobase/src/nxstaxablock.cpp |only phylobase-0.6.8/phylobase/src/nxstoken.cpp |only phylobase-0.6.8/phylobase/src/nxstreesblock.cpp |only phylobase-0.6.8/phylobase/src/nxsunalignedblock.cpp |only phylobase-0.6.8/phylobase/tests/doRUnit.R |only phylobase-0.6.8/phylobase/tests/misctests.Rout.save |only phylobase-0.6.8/phylobase/tests/phylo4dtests.Rout.save |only phylobase-0.6.8/phylobase/tests/phylosubtest.Rout.save |only phylobase-0.6.8/phylobase/tests/phylotorture.Rout.save |only phylobase-0.6.8/phylobase/tests/plottest.Rout.save |only phylobase-0.6.8/phylobase/tests/roundtrip.Rout.save |only phylobase-0.6.8/phylobase/tests/testprune.Rout.save |only phylobase-0.6.8/phylobase/vignettes/developer.Rnw |only phylobase-0.8.0/phylobase/DESCRIPTION | 41 phylobase-0.8.0/phylobase/MD5 | 261 +-- phylobase-0.8.0/phylobase/NAMESPACE | 210 +- phylobase-0.8.0/phylobase/NEWS.md |only phylobase-0.8.0/phylobase/R/MRCA-methods.R |only phylobase-0.8.0/phylobase/R/RcppExports.R | 8 phylobase-0.8.0/phylobase/R/addData-methods.R |only phylobase-0.8.0/phylobase/R/ancestors.R |only phylobase-0.8.0/phylobase/R/checkdata.R | 428 +++-- phylobase-0.8.0/phylobase/R/edgeLength-methods.R |only phylobase-0.8.0/phylobase/R/extractTree.R |only phylobase-0.8.0/phylobase/R/formatData.R | 120 - 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Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.5.9 dated 2014-11-11 and 1.6.0 dated 2015-07-24
mombf-1.5.9/mombf/R/zbfknown.R |only mombf-1.5.9/mombf/R/zbfunknown.R |only mombf-1.5.9/mombf/R/zellnerbf.R |only mombf-1.5.9/mombf/R/zellnerbf.knownsig.R |only mombf-1.5.9/mombf/R/zellnerbf.lm.R |only mombf-1.5.9/mombf/R/zellnerbf.unknownsig.R |only mombf-1.6.0/mombf/ChangeLog | 4 mombf-1.6.0/mombf/DESCRIPTION | 27 mombf-1.6.0/mombf/MD5 | 63 - mombf-1.6.0/mombf/NAMESPACE | 11 mombf-1.6.0/mombf/R/AllGenerics.R | 2 mombf-1.6.0/mombf/R/cox.R | 48 + mombf-1.6.0/mombf/R/derivatives_nlps.R |only mombf-1.6.0/mombf/R/margpimom.R | 4 mombf-1.6.0/mombf/R/margpmom.R | 6 mombf-1.6.0/mombf/R/modelSelection.R | 129 ++- mombf-1.6.0/mombf/R/msPriorSpec.R | 7 mombf-1.6.0/mombf/R/postMode.R | 18 mombf-1.6.0/mombf/R/pplProbit.R | 5 mombf-1.6.0/mombf/R/rmom.R | 85 +- mombf-1.6.0/mombf/R/zellnerLM.R | 224 ++++++ mombf-1.6.0/mombf/build/vignette.rds |binary mombf-1.6.0/mombf/data/hald.rda |binary mombf-1.6.0/mombf/inst/doc/mombf.R | 4 mombf-1.6.0/mombf/inst/doc/mombf.Rnw | 26 mombf-1.6.0/mombf/inst/doc/mombf.pdf |binary mombf-1.6.0/mombf/man/modelSelection.Rd | 27 mombf-1.6.0/mombf/man/msPriorSpec-class.Rd | 7 mombf-1.6.0/mombf/man/nlpMarginals.Rd | 5 mombf-1.6.0/mombf/man/rnlp.Rd | 9 mombf-1.6.0/mombf/src/cstat.cpp | 608 +++++++++++++---- mombf-1.6.0/mombf/src/cstat.h | 51 + mombf-1.6.0/mombf/src/do_mombf.h | 9 mombf-1.6.0/mombf/src/modelSel.cpp | 989 ++++++++++++++++++++++++++--- mombf-1.6.0/mombf/src/modelSel.h | 66 + mombf-1.6.0/mombf/vignettes/mombf.Rnw | 26 36 files changed, 2018 insertions(+), 442 deletions(-)
Title: Community Structure Detection via Modularity Maximization
Description: The algorithms implemented here are used to detect the community structure of a network.
These algorithms follow different approaches, but are all based on the concept of modularity maximization.
Author: Maria Schelling, Cang Hui
Maintainer: Maria Schelling <schelling.rmaintainer@vodafone.de>
Diff between modMax versions 1.0 dated 2015-02-18 and 1.1 dated 2015-07-24
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 4 R/generalFunctions.R | 78 ++++++++++---- R/greedy.R | 235 ++++++++++++++++++++++++++++---------------- R/saMovements.R | 155 +++++++++++++++++++++++------ R/simulatedAnnealing.R | 15 ++ R/spectralOptimization.R | 59 +++++++---- man/geneticAlgorithm.Rd | 10 - man/spectralOptimization.Rd | 4 10 files changed, 404 insertions(+), 182 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson <christina@stat.umn.edu>
Diff between glmm versions 1.0.3 dated 2015-04-28 and 1.0.4 dated 2015-07-24
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>
Diff between MicSim versions 1.0.8 dated 2015-03-05 and 1.0.9 dated 2015-07-24
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 2 R/auxFctMicSim.r | 26 +-- R/convertToLong.r | 100 ++++++------- R/convertToWide.r | 14 - R/micSim.r | 367 ++++++++++++++++++++++++++------------------------ inst/NEWS.Rd | 6 man/MicSim-package.Rd | 4 9 files changed, 284 insertions(+), 259 deletions(-)
Title: Active Set and Generalized PAVA for Isotone Optimization
Description: Contains two main functions: one for
solving general isotone regression problems using the
pool-adjacent-violators algorithm (PAVA); another one provides
a framework for active set methods for isotone optimization
problems with arbitrary order restrictions. Various types of
loss functions are prespecified.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Kurt Hornik [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between isotone versions 1.0-2 dated 2014-09-10 and 1.1-0 dated 2015-07-24
isotone-1.0-2/isotone/COPYING |only isotone-1.0-2/isotone/inst/doc/vignettes |only isotone-1.1-0/isotone/DESCRIPTION | 22 ++++++++++++---------- isotone-1.1-0/isotone/MD5 | 28 +++++++++++++++------------- isotone-1.1-0/isotone/NAMESPACE | 5 ++++- isotone-1.1-0/isotone/R/mregnn.R |only isotone-1.1-0/isotone/build |only isotone-1.1-0/isotone/inst/doc/isotone.R |only isotone-1.1-0/isotone/inst/doc/isotone.Rnw |only isotone-1.1-0/isotone/inst/doc/isotone.pdf |only isotone-1.1-0/isotone/man/mregnn.Rd |only isotone-1.1-0/isotone/man/posturo.Rd | 4 ++-- isotone-1.1-0/isotone/vignettes |only 13 files changed, 33 insertions(+), 26 deletions(-)
Title: A General Framework for Multivariate Analysis with Optimal
Scaling
Description: Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
Author: Patrick Mair [cre, aut],
Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between aspect versions 1.0-3 dated 2014-11-26 and 1.0-4 dated 2015-07-24
DESCRIPTION | 15 ++++++++------- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Tools for Making, Displaying and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games.
This package is an alternative to the earlier sudoku-solver package,
'sudoku'. The present package uses a slightly different algorithm, has a
simpler coding and presents a few more sugar tools, such as plot and print
methods. Solved sudoku games are of some interest in Experimental Design
as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between sudokuAlt versions 0.1-4 dated 2014-11-13 and 0.1-5 dated 2015-07-24
DESCRIPTION | 10 +++---- MD5 | 31 ++++++++++++------------ NAMESPACE | 4 ++- R/sudokuAlt.R | 62 ++++++++++++++++++++++++++++++++++++++++-------- man/as.sudoku.Rd | 3 +- man/as.sudoku.matrix.Rd | 3 +- man/as.sudoku.sudoku.Rd | 3 +- man/daysAgo.Rd | 3 +- man/fetchAUGame.Rd |only man/fetchUKGame.Rd | 5 ++- man/makeGame.Rd | 3 +- man/originalGame.Rd | 3 +- man/plot.sudoku.Rd | 3 +- man/print.sudoku.Rd | 3 +- man/seedGame.Rd | 3 +- man/solve.sudoku.Rd | 3 +- man/solveGame.Rd | 3 +- 17 files changed, 101 insertions(+), 44 deletions(-)
Title: Analytical Tools for Zooarchaeological Data
Description: The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.
Author: Erik Otarola-Castillo, Jesse Wolfhagen, Max D. Price
Maintainer: Erik Otarola-Castillo <eotarolacastillo@fas.harvard.edu>
Diff between zooaRch versions 1.0 dated 2015-04-05 and 1.1 dated 2015-07-24
zooaRch-1.0/zooaRch/data/marjRab_fuse.RData |only zooaRch-1.1/zooaRch/DESCRIPTION | 8 zooaRch-1.1/zooaRch/MD5 | 31 +- zooaRch-1.1/zooaRch/NAMESPACE | 5 zooaRch-1.1/zooaRch/R/zooaRch.r | 223 +++++++++++++++++++-- zooaRch-1.1/zooaRch/data/marjRab.fuse.RData |only zooaRch-1.1/zooaRch/data/winslow.fuse.RData |only zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.R | 55 ++++- zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.html | 55 ++++- zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.rmd | 62 +++++ zooaRch-1.1/zooaRch/man/fuse.func.Rd | 2 zooaRch-1.1/zooaRch/man/marjRab.Rd | 2 zooaRch-1.1/zooaRch/man/marjRab.fuse.Rd | 2 zooaRch-1.1/zooaRch/man/mort.func.Rd |only zooaRch-1.1/zooaRch/man/speth83.Rd | 2 zooaRch-1.1/zooaRch/man/surv.func.Rd | 3 zooaRch-1.1/zooaRch/man/winslow.fuse.Rd |only zooaRch-1.1/zooaRch/man/zooaRch-package.Rd | 6 zooaRch-1.1/zooaRch/vignettes/zooaRch-vignette.rmd | 62 +++++ 19 files changed, 441 insertions(+), 77 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.1.0 dated 2015-05-09 and 0.1.1 dated 2015-07-24
DESCRIPTION | 9 ++-- MD5 | 16 +++---- NAMESPACE | 1 R/GuanTestUnif.R | 102 +++++++++++++++++++++++++++----------------------- R/GuanTestUnif_help.R | 66 ++++++++++++++++++++------------ R/MaityTest.R | 75 ++++++++++++++++++------------------ R/MaityTest_help.R | 13 +----- man/GuanTestUnif.Rd | 30 +++++++------- man/MaityTest.Rd | 34 +++++++++------- 9 files changed, 189 insertions(+), 157 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.0.6 dated 2015-02-03 and 3.0.8 dated 2015-07-24
ChangeLog | 9 ++ DESCRIPTION | 10 +- MD5 | 12 +- NAMESPACE | 3 R/buffesm.R | 258 +++++++++++++++++++++++++++++++++-------------------------- R/carb.R | 2 R/carbb.R |only man/carbb.Rd |only 8 files changed, 170 insertions(+), 124 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.6 dated 2015-07-03 and 0.8.8 dated 2015-07-24
DESCRIPTION | 6 +-- MD5 | 25 ++++++++------ R/gbif_names.R | 23 +++++++----- R/gbif_photos.r | 36 +++++++++++--------- R/occ_search.r | 6 +-- README.md | 2 - man/gbif_names.Rd | 1 man/occ_search.Rd | 6 +-- tests/testthat/test-datasets.r | 22 +++++++----- tests/testthat/test-elevation.R |only tests/testthat/test-gbif_names.R |only tests/testthat/test-gbif_photos.R |only tests/testthat/test-name_lookup.r | 16 +++++--- tests/testthat/test-networks.r | 57 ++++++++++++++++---------------- tests/testthat/test-occ_issues.R |only tests/testthat/test-occ_issues_lookup.R |only 16 files changed, 110 insertions(+), 90 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-10 dated 2015-07-02 and 1.0-11 dated 2015-07-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 11 ++++++----- inst/NEWS | 2 +- inst/doc/rEMM.pdf |binary 5 files changed, 16 insertions(+), 15 deletions(-)
Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop
recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between recommenderlab versions 0.1-6 dated 2015-07-02 and 0.1-7 dated 2015-07-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 6 +++--- build/vignette.rds |binary data/Jester5k.rda |binary data/MSWeb.rda |binary data/MovieLense.rda |binary inst/NEWS | 2 +- inst/doc/recommenderlab.pdf |binary 9 files changed, 16 insertions(+), 16 deletions(-)
More information about recommenderlab at CRAN
Permanent link
Title: Function for Generating Random Names and a Dataset
Description: Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner <dbetebenner@nciea.org>
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between randomNames versions 0.0-8 dated 2015-02-07 and 0.1-0 dated 2015-07-24
DESCRIPTION | 15 +++++++++------ MD5 | 9 +++++---- NAMESPACE | 2 ++ R/zzz.R |only inst/CITATION | 14 +++++++------- man/randomNames-package.Rd | 10 +++++----- 6 files changed, 28 insertions(+), 22 deletions(-)
Title: Power and Sample Size Calculation for Survival Analysis of
Epidemiological Studies
Description: Functions to calculate power and
sample size for testing main effect or interaction effect in
the survival analysis of epidemiological studies
(non-randomized studies), taking into account the
correlation between the covariate of the
interest and other covariates. Some calculations also take
into account the competing risks and stratified analysis.
This package also includes
a set of functions to calculate power and sample size
for testing main effect in the survival analysis of
randomized clinical trials.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>, Jorge Chavarro <JCHAVARR@hsph.harvard.edu>, Ross Lazarus <ross.lazarus@channing.harvard.edu>, Bernard Rosner <stbar@channing.harvard.edu>, Jing Ma <jing.ma@channing.harvard.edu>.
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerSurvEpi versions 0.0.6 dated 2012-03-31 and 0.0.9 dated 2015-07-24
powerSurvEpi-0.0.6/powerSurvEpi/log.txt |only powerSurvEpi-0.0.9/powerSurvEpi/DESCRIPTION | 41 +++++----- powerSurvEpi-0.0.9/powerSurvEpi/MD5 | 48 ++++++------ powerSurvEpi-0.0.9/powerSurvEpi/NAMESPACE | 13 +-- powerSurvEpi-0.0.9/powerSurvEpi/NEWS |only powerSurvEpi-0.0.9/powerSurvEpi/R/power.stratify.R | 2 powerSurvEpi-0.0.9/powerSurvEpi/data/Oph.rda |binary powerSurvEpi-0.0.9/powerSurvEpi/man/numDEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/numDEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/power.stratify.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiCont.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiCont.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt.default0.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt.default1.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt2.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssize.stratify.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiCont.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiCont.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.default0.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.default1.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt2.Rd | 2 26 files changed, 71 insertions(+), 71 deletions(-)
Title: Some Nonparametric Tests for Change-Point Detection in Possibly
Multivariate Observations
Description: Provides nonparametric tests for assessing whether possibly serially dependent univariate or multivariate observations have the same c.d.f. or not. In addition to tests focusing directly on the c.d.f., the package contains tests designed to be particularly sensitive to changes in the underlying copula, Spearman's rho or certain quantities that can be estimated using one-sample U-statistics of order two such as the variance, Gini's mean difference or Kendall's tau. The latest addition is a nonparametric test for detecting changes in the distribution of independent block maxima.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between npcp versions 0.1-1 dated 2014-12-20 and 0.1-6 dated 2015-07-24
DESCRIPTION | 15 +++--- MD5 | 27 ++++++----- NAMESPACE | 2 R/ci.R | 5 +- R/tests.R | 123 ++++++++++++++++++++++++++++++++++++++++++++++++++++- man/bOptEmpProc.Rd | 6 +- man/cpTestBM.Rd |only man/cpTestCn.Rd | 8 +-- man/cpTestFn.Rd | 6 +- man/cpTestRho.Rd | 7 +-- man/cpTestU.Rd | 6 +- src/bmtest.c |only src/ci.c | 75 ++++++++++++++++++++------------ src/utilities.c | 4 - src/utilities.h | 1 src/zeroin.c |only 16 files changed, 217 insertions(+), 68 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut],
Robin Winstanley [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.3.1 dated 2015-07-10 and 0.3.2 dated 2015-07-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/MazamaSpatialUtils.R | 7 ++++++- R/getSpatialData.R | 34 ++++++++++++++++++++++++++-------- man/MazamaSpatialUtils.Rd | 7 ++++++- man/getSpatialData.Rd | 9 ++++++--- 6 files changed, 52 insertions(+), 21 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.1 dated 2015-04-28 and 3.3.3 dated 2015-07-24
lessR-3.3.1/lessR/R/cor_resid.R |only lessR-3.3.1/lessR/R/tAnd.R |only lessR-3.3.1/lessR/R/tNum.R |only lessR-3.3.1/lessR/R/tP.R |only lessR-3.3.1/lessR/R/tRow.R |only lessR-3.3.1/lessR/man/tAnd.Rd |only lessR-3.3.1/lessR/man/tNum.Rd |only lessR-3.3.1/lessR/man/tP.Rd |only lessR-3.3.1/lessR/man/tRow.Rd |only lessR-3.3.3/lessR/DESCRIPTION | 11 lessR-3.3.3/lessR/MD5 | 117 ++--- lessR-3.3.3/lessR/NAMESPACE | 15 lessR-3.3.3/lessR/NEWS | 55 ++ lessR-3.3.3/lessR/R/Correlation.R | 4 lessR-3.3.3/lessR/R/Logit.R | 13 lessR-3.3.3/lessR/R/Read.R | 111 +++-- lessR-3.3.3/lessR/R/Regression.R | 94 +++- lessR-3.3.3/lessR/R/Write.R | 2 lessR-3.3.3/lessR/R/cfa.R | 2 lessR-3.3.3/lessR/R/corCFA.R | 581 +++++++++++++++++----------- lessR-3.3.3/lessR/R/corEFA.R | 95 +--- lessR-3.3.3/lessR/R/corFA.zknitr.R | 243 +++++++++-- lessR-3.3.3/lessR/R/cor_mimm.R | 6 lessR-3.3.3/lessR/R/cr.data.frame.R | 5 lessR-3.3.3/lessR/R/details.R | 47 +- lessR-3.3.3/lessR/R/dist.zknitr.R | 33 + lessR-3.3.3/lessR/R/label.R | 12 lessR-3.3.3/lessR/R/logit.z4Pred.R | 2 lessR-3.3.3/lessR/R/reg.z1anvBasic.R | 6 lessR-3.3.3/lessR/R/reg.z1bckBasic.R | 7 lessR-3.3.3/lessR/R/reg.z1fitBasic.R | 2 lessR-3.3.3/lessR/R/reg.z1modelBasic.R | 4 lessR-3.3.3/lessR/R/reg.z2Relations.R | 10 lessR-3.3.3/lessR/R/reg.z3dnResidual.R | 4 lessR-3.3.3/lessR/R/reg.z3resfitResidual.R | 4 lessR-3.3.3/lessR/R/reg.z3txtResidual.R | 8 lessR-3.3.3/lessR/R/reg.z4Pred.R | 8 lessR-3.3.3/lessR/R/reg.z5Plot.R | 10 lessR-3.3.3/lessR/R/reg.zknitr.R | 595 +++++++++++++++++++---------- lessR-3.3.3/lessR/R/scales.R | 3 lessR-3.3.3/lessR/R/xAnd.R |only lessR-3.3.3/lessR/R/xNum.R |only lessR-3.3.3/lessR/R/xP.R |only lessR-3.3.3/lessR/R/xRow.R |only lessR-3.3.3/lessR/R/xU.R |only lessR-3.3.3/lessR/R/xW.R |only lessR-3.3.3/lessR/R/zzz.R | 238 +++++++++-- lessR-3.3.3/lessR/inst/CITATION | 2 lessR-3.3.3/lessR/man/BarChart.Rd | 9 lessR-3.3.3/lessR/man/BoxPlot.Rd | 2 lessR-3.3.3/lessR/man/Density.Rd | 2 lessR-3.3.3/lessR/man/Histogram.Rd | 2 lessR-3.3.3/lessR/man/LineChart.Rd | 2 lessR-3.3.3/lessR/man/Logit.Rd | 4 lessR-3.3.3/lessR/man/Read.Rd | 30 - lessR-3.3.3/lessR/man/Regression.Rd | 100 ++-- lessR-3.3.3/lessR/man/ScatterPlot.Rd | 10 lessR-3.3.3/lessR/man/Subset.Rd | 2 lessR-3.3.3/lessR/man/SummaryStats.Rd | 2 lessR-3.3.3/lessR/man/Write.Rd | 4 lessR-3.3.3/lessR/man/corCFA.Rd | 153 +++++-- lessR-3.3.3/lessR/man/corRead.Rd | 4 lessR-3.3.3/lessR/man/label.Rd | 4 lessR-3.3.3/lessR/man/ttest.Rd | 28 - lessR-3.3.3/lessR/man/xAnd.Rd |only lessR-3.3.3/lessR/man/xNum.Rd |only lessR-3.3.3/lessR/man/xP.Rd |only lessR-3.3.3/lessR/man/xRow.Rd |only lessR-3.3.3/lessR/man/xU.Rd |only lessR-3.3.3/lessR/man/xW.Rd |only 70 files changed, 1778 insertions(+), 929 deletions(-)
Title: Deconvolution of Tumour Profiles
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using
the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires
mixed tumour profiles and a set of unmatched "basis" normal profiles.
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D
Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros <Paul.Boutros@oicr.on.ca>
Diff between ISOpureR versions 1.0.8 dated 2015-01-08 and 1.0.18 dated 2015-07-24
ISOpureR-1.0.18/ISOpureR/DESCRIPTION | 10 ISOpureR-1.0.18/ISOpureR/MD5 | 64 ISOpureR-1.0.18/ISOpureR/NAMESPACE | 6 ISOpureR-1.0.18/ISOpureR/NEWS | 86 ISOpureR-1.0.18/ISOpureR/R/ISOpure.step1.CPE.R |only ISOpureR-1.0.18/ISOpureR/R/ISOpure.step2.PPE.R |only ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.new_model.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.optmodel.R | 23 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_optimize.opt_kappa.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_core.optmodel.R | 23 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.opt_kappa.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.theta.theta_loglikelihood.R | 2 ISOpureR-1.0.18/ISOpureR/build/vignette.rds |binary ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.Rnw | 871 ++++++++-- ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.pdf |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/alphapurities_full_dataset.txt |only ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.ISOpureS1model.1000.transcripts.30.patients.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.1000.transcripts.30.patients.rounded.RData |only ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.normaldata.1000.transcripts.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.tumordata.1000.transcripts.30.patients.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/probeset_names.txt |only ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step1_beer.R | 3 ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step2_beer.R | 3 ISOpureR-1.0.18/ISOpureR/man/ISOpure.step1.CPE.Rd |only ISOpureR-1.0.18/ISOpureR/man/ISOpure.step2.PPE.Rd |only ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_core.new_model.Rd | 2 ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_optimize.opt_kappa.Rd | 2 ISOpureR-1.0.18/ISOpureR/man/ISOpureS2.model_optimize.opt_kappa.Rd | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.cc_functions.R | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.theta_functions.R | 2 ISOpureR-1.0.18/ISOpureR/vignettes/Figures |only ISOpureR-1.0.18/ISOpureR/vignettes/ISOpureRGuide.Rnw | 871 ++++++++-- ISOpureR-1.0.8/ISOpureR/R/ISOpureS1.model_core.learnmodel.R |only ISOpureR-1.0.8/ISOpureR/R/ISOpureS2.model_core.learnmodel.R |only ISOpureR-1.0.8/ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.1000.transcripts.30.patients.RData |only ISOpureR-1.0.8/ISOpureR/man/ISOpureS1.model_core.learnmodel.Rd |only ISOpureR-1.0.8/ISOpureR/man/ISOpureS2.model_core.learnmodel.Rd |only 38 files changed, 1734 insertions(+), 246 deletions(-)
Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: Provides a collection of tools for
detecting influential cases in generalized mixed effects
models. It analyses models that were estimated using lme4. The
basic rationale behind identifying influential data is that
when iteratively single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice, such as DFBETAS and Cook's Distance.
In addition, we provide a measure of percentage change of the fixed point
estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Diff between influence.ME versions 0.9-5 dated 2014-12-17 and 0.9-6 dated 2015-07-24
DESCRIPTION | 10 MD5 | 26 +- NAMESPACE | 44 ++-- R/cooks.distance.extex.r | 2 R/exclude.influence.R | 21 + R/influence.R | 483 ++++++++++++++++++++++---------------------- man/cooks.distance.estex.Rd | 6 man/dfbetas.estex.Rd | 6 man/exclude.influence.Rd | 6 man/grouping.levels.Rd | 2 man/influence.ME-package.Rd | 2 man/influence.mer.Rd | 17 - man/pchange.Rd | 4 man/plot.estex.Rd | 2 14 files changed, 327 insertions(+), 304 deletions(-)
Title: Into the extRemes Package
Description: Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between in2extRemes versions 1.0-1 dated 2014-01-28 and 1.0-2 dated 2015-07-24
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 13 insertions(+), 8 deletions(-)
Title: Method Functions for Confidence Intervals and to Distill
Information from an Object
Description: Some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between distillery versions 1.0-1 dated 2013-06-26 and 1.0-2 dated 2015-07-24
DESCRIPTION | 13 +++++-------- MD5 | 4 ++-- NAMESPACE | 10 ++++++++++ 3 files changed, 17 insertions(+), 10 deletions(-)
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 1.0.3 dated 2014-12-26 and 2.0.0 dated 2015-07-24
DESCRIPTION | 14 MD5 | 20 NAMESPACE | 8 R/cjoint.R | 2868 +++++++++++++++++++++++++++++++++----------------- demo/cjointdemo.R | 36 man/amce.Rd | 70 - man/cjoint-package.Rd | 8 man/makeDesign.Rd | 313 ++--- man/plot.amce.Rd | 117 +- man/summary.amce.Rd | 91 - tests |only 11 files changed, 2301 insertions(+), 1244 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.0.6 dated 2015-06-19 and 4.1.15 dated 2015-07-24
ChemoSpec-4.0.6/ChemoSpec/R/getMaxCovByFreq.R |only ChemoSpec-4.0.6/ChemoSpec/man/getMaxCovByFreq.Rd |only ChemoSpec-4.1.15/ChemoSpec/DESCRIPTION | 10 +- ChemoSpec-4.1.15/ChemoSpec/MD5 | 73 ++++++++++---------- ChemoSpec-4.1.15/ChemoSpec/NAMESPACE | 20 ++++- ChemoSpec-4.1.15/ChemoSpec/NEWS | 16 ++++ ChemoSpec-4.1.15/ChemoSpec/R/baselineSpectra.R | 6 + ChemoSpec-4.1.15/ChemoSpec/R/check4Gaps.R | 4 - ChemoSpec-4.1.15/ChemoSpec/R/cleanSTOCSYpeaks.R |only ChemoSpec-4.1.15/ChemoSpec/R/collapseRowsOrCols.R |only ChemoSpec-4.1.15/ChemoSpec/R/corSpectra.R | 42 +++++------ ChemoSpec-4.1.15/ChemoSpec/R/covSpectra.R | 14 +-- ChemoSpec-4.1.15/ChemoSpec/R/covSpectraJS.R | 14 +-- ChemoSpec-4.1.15/ChemoSpec/R/hcaScores.R | 5 - ChemoSpec-4.1.15/ChemoSpec/R/hcaSpectra.R | 5 - ChemoSpec-4.1.15/ChemoSpec/R/hmapSpectra.R | 7 + ChemoSpec-4.1.15/ChemoSpec/R/labelExtremes.R | 2 ChemoSpec-4.1.15/ChemoSpec/R/plot2Loadings.R | 5 + ChemoSpec-4.1.15/ChemoSpec/R/plotHCA.R | 8 +- ChemoSpec-4.1.15/ChemoSpec/R/sPlotSpectra.R | 4 - ChemoSpec-4.1.15/ChemoSpec/R/sortCrossPeaks.R |only ChemoSpec-4.1.15/ChemoSpec/R/sumSpectra.R | 14 +++ ChemoSpec-4.1.15/ChemoSpec/R/surveySpectra2.R | 18 +++- ChemoSpec-4.1.15/ChemoSpec/build/vignette.rds |binary ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.R | 14 +++ ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.Rnw | 18 +++- ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-4.1.15/ChemoSpec/man/ChemoSpec-package.Rd | 10 -- ChemoSpec-4.1.15/ChemoSpec/man/check4Gaps.Rd | 3 ChemoSpec-4.1.15/ChemoSpec/man/cleanSTOCSYpeaks.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/corSpectra.Rd | 15 +--- ChemoSpec-4.1.15/ChemoSpec/man/hcaScores.Rd | 6 + ChemoSpec-4.1.15/ChemoSpec/man/hcaSpectra.Rd | 6 + ChemoSpec-4.1.15/ChemoSpec/man/hmapSpectra.Rd | 14 +-- ChemoSpec-4.1.15/ChemoSpec/man/plot2Loadings.Rd | 4 - ChemoSpec-4.1.15/ChemoSpec/man/plotHCA.Rd | 5 + ChemoSpec-4.1.15/ChemoSpec/man/plotSpectraJS.Rd | 2 ChemoSpec-4.1.15/ChemoSpec/man/sPlotSpectra.Rd | 4 - ChemoSpec-4.1.15/ChemoSpec/man/sortCrossPeaks.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/surveySpectra.Rd | 2 ChemoSpec-4.1.15/ChemoSpec/vignettes/ChemoSpec.Rnw | 18 +++- 41 files changed, 239 insertions(+), 149 deletions(-)
Title: Function for Converting Cardinal to Ordinal Numbers by Adding a
Language Specific Ordinal Indicator to the Number
Description: Function for converting cardinal to ordinal numbers by adding a language specific ordinal indicator (http://en.wikipedia.org/wiki/Ordinal_indicator) to the number.
Author: Damian W. Betebenner [aut, cre],
Andrew Martin [ctb],
Jeff Erickson [ctb]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between toOrdinal versions 0.0-1 dated 2015-03-12 and 0.0-4 dated 2015-07-24
DESCRIPTION | 21 +++++-- MD5 | 17 +++--- NAMESPACE | 1 R/toOrdinal.R | 124 +++++++++++++++++++++++++++++++++-------------- inst/CITATION | 4 - inst/NEWS | 13 ++++ man/toOrdinal-package.Rd | 4 - man/toOrdinal.Rd | 12 +++- tests |only 9 files changed, 139 insertions(+), 57 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.2.0 dated 2015-07-07 and 1.2.1 dated 2015-07-24
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++--------------- NEWS | 15 ++++++++++++++ R/EpiModel-package.r | 4 +-- R/control.R | 12 ++++++----- R/icm.R | 3 -- R/net.utils.R | 18 ++++++++-------- R/netest.R | 7 ++---- R/plot.R | 48 +++++++++++++++++++++++++++------------------ R/verbose.R | 2 - inst/doc/Intro.html | 2 - inst/shiny/epiicm/server.R | 10 ++++----- man/EpiModel-package.Rd | 4 +-- man/comp_plot.Rd | 2 - man/control.icm.Rd | 5 ---- man/control.net.Rd | 2 + man/icm.Rd | 3 -- 17 files changed, 98 insertions(+), 79 deletions(-)
Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between mpath versions 0.1-18 dated 2015-06-10 and 0.1-19 dated 2015-07-23
DESCRIPTION | 6 +++--- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 2 ++ NEWS | 7 ++++++- build/vignette.rds |binary inst/doc/german.pdf |binary man/breadReg.Rd | 2 +- man/conv2zipath.Rd | 2 +- man/cv.glmreg.Rd | 2 +- man/cv.glmregNB.Rd | 4 ++-- man/cv.glmreg_fit.Rd | 4 ++-- man/cv.zipath.Rd | 7 +++++-- man/glmreg.Rd | 8 ++++---- man/glmregNB.Rd | 11 +++++++---- man/glmreg_fit.Rd | 12 ++++++------ man/meatReg.Rd | 2 +- man/mpath-internal.Rd | 2 +- man/p_zipath.Rd | 4 ++-- man/se.Rd | 2 +- man/tuning_zipath.Rd | 4 ++-- man/vuong.Rd | 6 +++--- man/zipath.Rd | 14 +++++++------- vignettes/mpath.bib | 2 +- 23 files changed, 80 insertions(+), 67 deletions(-)
Title: Wilcox Robust Estimation and Testing
Description: A user-friendly version of Wilcox' robust statistics functions (WRS package on GitHub). It implements robust tests for various ANOVA and ANCOVA techniques as described in R. Wilcox (2012) 'Introduction to Robust Estimation and Hypothesis Testing'.
Author: Patrick Mair [cre, aut],
Felix Schoenbrodt [aut],
Rand Wilcox [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.3-1 dated 2014-12-03 and 0.3-2 dated 2015-07-23
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 6 ++++-- man/WRS2-package.Rd | 4 ++-- man/spider.Rd | 2 +- 5 files changed, 19 insertions(+), 17 deletions(-)
Title: Bayesian Variable Selection and Model Choice for Generalized
Additive Mixed Models
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression models
via stochastic search variable selection with spike-and-slab priors.
Author: Fabian Scheipl
<fabian.scheipl@stat.uni-muenchen.de>
Maintainer: Fabian Scheipl
<fabian.scheipl@stat.uni-muenchen.de>
Diff between spikeSlabGAM versions 1.1-8 dated 2014-12-04 and 1.1-9 dated 2015-07-23
DESCRIPTION | 21 MD5 | 76 - NAMESPACE | 9 NEWS | 6 R/bugs.R | 84 - R/plot.R | 1307 ++++++++++++----------- R/predict.R | 411 +++---- R/spikeAndSlab.R | 1097 ++++++++++---------- R/spikeSlabGAM.R | 218 ++- R/ssGAMDesign.R | 542 +++++---- R/summary.R | 327 +++-- R/terms.R | 839 ++++++++------- R/utils.R | 1367 ++++++++++++------------- R/zzz.R |only build/vignette.rds |binary inst/CITATION | 16 inst/doc/UsingSpikeSlabGAM.R | 121 +- inst/doc/UsingSpikeSlabGAM.Rnw | 717 ++++++------- inst/doc/UsingSpikeSlabGAM.pdf |binary man/evalTerm.Rd | 30 man/fct.Rd | 6 man/getPosteriorTerm.Rd | 11 man/lin.Rd | 9 man/mrf.Rd | 43 man/plot.spikeSlabGAM.Rd | 97 + man/plotTerm.Rd | 75 - man/predict.spikeSlabGAM.Rd | 50 man/print.summary.spikeSlabGAM.Rd | 17 man/rnd.Rd | 6 man/sm.Rd | 50 man/spikeAndSlab.Rd | 190 +-- man/spikeSlabGAM.Rd | 132 +- man/srf.Rd | 79 - man/ssGAM2Bugs.Rd | 20 man/ssGAMDesign.Rd | 67 - man/summary.spikeSlabGAM.Rd | 30 man/u.Rd | 3 src/Makevars | 2 vignettes/UsingSpikeSlabGAM-plotm1sm2fprep.pdf |only vignettes/UsingSpikeSlabGAM.Rnw | 717 ++++++------- 40 files changed, 4575 insertions(+), 4217 deletions(-)
Title: Rasch Sampler
Description: MCMC based sampling of binary matrices with fixed margins as used in exact Rasch model tests.
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Norman D. Verhelst [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between RaschSampler versions 0.8-7 dated 2014-11-26 and 0.8-8 dated 2015-07-23
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/RaschSampler-package.Rd | 10 ++++------ 3 files changed, 12 insertions(+), 14 deletions(-)
Title: Routines for Constructing and Evaluating Self-Organizing Maps
Description: A set of routines which are useful in constructing
and evaluating self-organizing maps (SOMs).
Author: Lutz Hamel [aut, cre],
Benjamin Ott [aut],
Gregory Breard [aut]
Maintainer: Lutz Hamel <hamel@cs.uri.edu>
Diff between popsom versions 2.3 dated 2013-10-09 and 3.0.1 dated 2015-07-23
DESCRIPTION | 16 +-- MD5 | 12 +- NAMESPACE | 4 R/map-utils.R | 236 +++++++++++++++++++++++++++++++++++++++++++----- man/map.accuracy.Rd |only man/map.quality.Rd |only man/map.significance.Rd | 2 man/popsom-internal.Rd | 14 ++ 8 files changed, 244 insertions(+), 40 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data". The package contains code for designed
experiments, data sets and other convenience functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kevin.dunn@mcmaster.ca>
Diff between pid versions 0.15 dated 2015-07-12 and 0.32 dated 2015-07-23
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++++++++++++------- NAMESPACE | 21 ++++++++++++++++++--- R/contourPlot.R |only R/grocery.R |only R/manufacture.R |only R/paretoPlot.R | 33 ++++++++++++++++++++++----------- R/popcorn.R |only R/tradeOffTable.R |only R/tradeoff.R |only data/boilingpot.rda |only data/golf.rda |only data/solar.rda |binary inst |only man/boilingpot.Rd |only man/contourPlot.Rd |only man/figures |only man/golf.Rd |only man/grocery.Rd |only man/manfacture.Rd |only man/oildoe.Rd | 2 +- man/pid-package.Rd | 13 +++---------- man/popcorn.Rd |only man/solar.Rd | 2 +- man/tradeOffTable.Rd |only man/tradeoff.Rd |only 26 files changed, 77 insertions(+), 38 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <aravindj@nbpgr.ernet.in>
Diff between PGRdup versions 0.2 dated 2015-04-14 and 0.2.1 dated 2015-07-23
DESCRIPTION | 17 MD5 | 70 NAMESPACE | 16 R/AddProbDup.R | 3 R/DisProbDup.R | 5 R/KWCounts.R |only R/KWIC.R | 26 R/MergeKW.R | 12 R/MergeProbDup.R |only R/ParseProbDup.R | 3 R/ProbDup.R | 528 +++--- R/ReconstructProbDup.R | 29 R/ReviewProbDup.R | 11 R/SplitProbDup.R |only R/globals.R | 6 R/print.KWIC.R |only R/print.ProbDup.R |only README.md | 86 build |only inst/CITATION | 6 inst/doc |only inst/extdata/PGRdup.svg | 3969 ++++++++++++++++++++++++++++++++++++++++------ man/AddProbDup.Rd | 5 man/DataClean.Rd | 3 man/DisProbDup.Rd | 5 man/DoubleMetaphone.Rd | 3 man/GN1000.Rd | 3 man/KWCounts.Rd |only man/KWIC.Rd | 9 man/MergeKW.Rd | 3 man/MergeProbDup.Rd |only man/PGRdup-package.Rd | 3 man/ParseProbDup.Rd | 5 man/ProbDup.Rd | 19 man/ReconstructProbDup.Rd | 5 man/ReviewProbDup.Rd | 5 man/SplitProbDup.Rd |only man/ValidatePrimKey.Rd | 3 man/print.KWIC.Rd |only man/print.ProbDup.Rd |only vignettes |only 41 files changed, 4063 insertions(+), 795 deletions(-)
Title: Mixtures of Proportional Hazard Models
Description: Fits multiple variable mixtures of various parametric proportional hazard models using the EM-Algorithm. Proportionality restrictions can be imposed on the latent groups and/or on the variables. Several survival distributions can be specified. Missing values and censored values are allowed. Independence is assumed over the single variables.
Author: Patrick Mair [cre, aut],
Marcus Hudec [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between mixPHM versions 0.7-1 dated 2014-11-26 and 0.7-2 dated 2015-07-23
mixPHM-0.7-1/mixPHM/R/plot.hazard.R |only mixPHM-0.7-1/mixPHM/R/plot.profile.R |only mixPHM-0.7-1/mixPHM/R/plot.survival.R |only mixPHM-0.7-1/mixPHM/man/plot.hazard.Rd |only mixPHM-0.7-2/mixPHM/DESCRIPTION | 16 - mixPHM-0.7-2/mixPHM/MD5 | 16 - mixPHM-0.7-2/mixPHM/NAMESPACE | 6 mixPHM-0.7-2/mixPHM/R/Eclass.R | 298 +++++++++++++++--------------- mixPHM-0.7-2/mixPHM/R/plot_hazard.R |only mixPHM-0.7-2/mixPHM/R/plot_profile.R |only mixPHM-0.7-2/mixPHM/R/plot_survival.R |only mixPHM-0.7-2/mixPHM/man/mixPHM-package.Rd | 4 mixPHM-0.7-2/mixPHM/man/plot_hazard.Rd |only 13 files changed, 170 insertions(+), 170 deletions(-)
Title: Gifi Methods for Optimal Scaling
Description: Performs a homogeneity analysis (multiple correspondence analysis) and various extensions. Rank restrictions on the category quantifications can be imposed (nonlinear PCA). The categories are transformed by means of optimal scaling with options for nominal, ordinal, and numerical scale levels (for rank-1 restrictions). Variables can be grouped into sets, in order to emulate regression analysis and canonical correlation analysis.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between homals versions 1.0-5 dated 2014-03-05 and 1.0-6 dated 2015-07-23
homals-1.0-5/homals/COPYING |only homals-1.0-6/homals/DESCRIPTION | 18 ++++++++---------- homals-1.0-6/homals/MD5 | 9 ++++----- homals-1.0-6/homals/NAMESPACE | 2 ++ homals-1.0-6/homals/man/homals-package.Rd | 2 +- homals-1.0-6/homals/man/plot.homals.Rd | 6 ------ 6 files changed, 15 insertions(+), 22 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.2.3 dated 2015-07-03 and 1.1.3 dated 2015-07-23
ddalpha-1.1.2.3/ddalpha/man/ddalpha.getErrorRateJK.Rd |only ddalpha-1.1.3/ddalpha/DESCRIPTION | 8 ddalpha-1.1.3/ddalpha/MD5 | 90 ++++--- ddalpha-1.1.3/ddalpha/NAMESPACE | 8 ddalpha-1.1.3/ddalpha/R/dataf.geneexp.r | 9 ddalpha-1.1.3/ddalpha/R/dataf.growth.r | 8 ddalpha-1.1.3/ddalpha/R/dataf.medflies.r | 9 ddalpha-1.1.3/ddalpha/R/dataf.sim.r | 8 ddalpha-1.1.3/ddalpha/R/dataf.tecator.r | 9 ddalpha-1.1.3/ddalpha/R/ddalpha-internal.r | 125 +++++----- ddalpha-1.1.3/ddalpha/R/ddalpha.classify.r | 10 ddalpha-1.1.3/ddalpha/R/ddalpha.test.r | 4 ddalpha-1.1.3/ddalpha/R/ddalpha.train.r | 161 ++++++++++---- ddalpha-1.1.3/ddalpha/R/depth.contours.r | 16 - ddalpha-1.1.3/ddalpha/R/depth.potential.r |only ddalpha-1.1.3/ddalpha/R/depth.spatial.r | 44 +++ ddalpha-1.1.3/ddalpha/R/draw.ddplot.r |only ddalpha-1.1.3/ddalpha/R/lda.r | 2 ddalpha-1.1.3/ddalpha/R/mahalanobis.scaling.r | 2 ddalpha-1.1.3/ddalpha/man/ddalpha-package.Rd | 6 ddalpha-1.1.3/ddalpha/man/ddalpha.getErrorRateCV.Rd | 29 -- ddalpha-1.1.3/ddalpha/man/ddalpha.getErrorRatePart.Rd |only ddalpha-1.1.3/ddalpha/man/ddalpha.test.Rd | 2 ddalpha-1.1.3/ddalpha/man/ddalpha.train.Rd | 8 ddalpha-1.1.3/ddalpha/man/depth..Rd | 5 ddalpha-1.1.3/ddalpha/man/depth.Mahalanobis.Rd | 1 ddalpha-1.1.3/ddalpha/man/depth.halfspace.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.potential.Rd |only ddalpha-1.1.3/ddalpha/man/depth.projection.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.simplicial.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.simplicialVolume.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.space..Rd | 3 ddalpha-1.1.3/ddalpha/man/depth.space.Mahalanobis.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.halfspace.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.potential.Rd |only ddalpha-1.1.3/ddalpha/man/depth.space.projection.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.simplicial.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.simplicialVolume.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.spatial.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.zonoid.Rd | 5 ddalpha-1.1.3/ddalpha/man/depth.spatial.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.zonoid.Rd | 2 ddalpha-1.1.3/ddalpha/man/draw.ddplot.Rd |only ddalpha-1.1.3/ddalpha/man/resetPar.Rd |only ddalpha-1.1.3/ddalpha/src/DataStructures.h | 3 ddalpha-1.1.3/ddalpha/src/Knn.cpp | 2 ddalpha-1.1.3/ddalpha/src/PotentialDepth.cpp |only ddalpha-1.1.3/ddalpha/src/PotentialDepth.h |only ddalpha-1.1.3/ddalpha/src/ZonoidDepth.cpp | 3 ddalpha-1.1.3/ddalpha/src/ddalpha.cpp | 50 ++++ ddalpha-1.1.3/ddalpha/src/stdafx.h | 1 51 files changed, 458 insertions(+), 209 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.3.0 dated 2015-06-29 and 0.4.0 dated 2015-07-23
brms-0.3.0/brms/R/bugs.R |only brms-0.3.0/brms/R/extract.old.R |only brms-0.3.0/brms/R/support.internal.R |only brms-0.3.0/brms/man/brm.plot.Rd |only brms-0.3.0/brms/tests/testthat/tests.support.R |only brms-0.4.0/brms/DESCRIPTION | 20 brms-0.4.0/brms/MD5 | 59 +- brms-0.4.0/brms/NAMESPACE | 4 brms-0.4.0/brms/R/data.docu.R | 3 brms-0.4.0/brms/R/internal.postfit.R |only brms-0.4.0/brms/R/internal.prefit.R |only brms-0.4.0/brms/R/main.R | 132 ++-- brms-0.4.0/brms/R/misc.R |only brms-0.4.0/brms/R/parser.R | 54 + brms-0.4.0/brms/R/s3.generics.R | 92 ++- brms-0.4.0/brms/R/s3.methods.R | 312 +++++----- brms-0.4.0/brms/R/stan.R | 488 +++++++++-------- brms-0.4.0/brms/R/support.export.R | 284 +++++---- brms-0.4.0/brms/README.md | 48 + brms-0.4.0/brms/data/epilepsy.rda |binary brms-0.4.0/brms/man/VarCorr.Rd | 5 brms-0.4.0/brms/man/WAIC.Rd |only brms-0.4.0/brms/man/brm.Rd | 45 + brms-0.4.0/brms/man/brm.data.Rd | 21 brms-0.4.0/brms/man/brm.pars.Rd | 17 brms-0.4.0/brms/man/epilepsy.Rd | 1 brms-0.4.0/brms/man/fixef.Rd | 2 brms-0.4.0/brms/man/hypothesis.Rd | 21 brms-0.4.0/brms/man/kidney.Rd | 2 brms-0.4.0/brms/man/plot.brmsfit.Rd | 4 brms-0.4.0/brms/man/posterior.samples.Rd | 3 brms-0.4.0/brms/man/ranef.Rd | 11 brms-0.4.0/brms/tests/testthat/tests.internal.prefit.R |only brms-0.4.0/brms/tests/testthat/tests.parser.R | 44 + brms-0.4.0/brms/tests/testthat/tests.stan.R | 108 ++- brms-0.4.0/brms/tests/testthat/tests.support.export.R |only 36 files changed, 1049 insertions(+), 731 deletions(-)
Title: Simple and Canonical Correspondence Analysis
Description: Performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between anacor versions 1.0-5 dated 2014-09-08 and 1.0-6 dated 2015-07-23
anacor-1.0-5/anacor/COPYING |only anacor-1.0-6/anacor/DESCRIPTION | 15 ++++++++------- anacor-1.0-6/anacor/MD5 | 9 ++++----- anacor-1.0-6/anacor/NAMESPACE | 7 ++++--- anacor-1.0-6/anacor/man/anacor-package.Rd | 6 +++--- anacor-1.0-6/anacor/man/plot.anacor.Rd | 2 +- 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.5 dated 2015-04-14 and 1.6 dated 2015-07-23
openair-1.5/openair/data/mydata.RData |only openair-1.6/openair/DESCRIPTION | 16 openair-1.6/openair/MD5 | 158 - openair-1.6/openair/NAMESPACE | 42 openair-1.6/openair/R/GoogleMapsPlot.R | 5 openair-1.6/openair/R/TheilSen.R | 39 openair-1.6/openair/R/airbaseStats.R | 11 openair-1.6/openair/R/aqStats.R | 33 openair-1.6/openair/R/calendarPlot.R | 14 openair-1.6/openair/R/cutData.R | 2 openair-1.6/openair/R/importAURN.R | 15 openair-1.6/openair/R/importKCL.R | 18 openair-1.6/openair/R/polarPlot.R | 6 openair-1.6/openair/R/scatterPlot.R | 2282 ++++++++++++------------- openair-1.6/openair/R/selectRunning.R | 2 openair-1.6/openair/R/smoothTrend.R | 4 openair-1.6/openair/R/summaryPlot.R | 2 openair-1.6/openair/R/timeAverage.R | 646 +++---- openair-1.6/openair/R/timePlot.R | 187 +- openair-1.6/openair/R/timeProp.R | 36 openair-1.6/openair/R/timeVariation.R | 6 openair-1.6/openair/R/trajCluster.R | 46 openair-1.6/openair/R/trajLevel.R | 93 - openair-1.6/openair/R/trajPlot.R | 222 +- openair-1.6/openair/R/utilities.R | 14 openair-1.6/openair/R/windRose.R | 244 +- openair-1.6/openair/README.md | 20 openair-1.6/openair/data/mydata.rda |only openair-1.6/openair/man/GoogleMapsPlot.Rd | 2 openair-1.6/openair/man/TaylorDiagram.Rd | 2 openair-1.6/openair/man/TheilSen.Rd | 14 openair-1.6/openair/man/airbaseFindCode.Rd | 2 openair-1.6/openair/man/airbaseInfo.Rd | 2 openair-1.6/openair/man/airbaseSplice.Rd | 2 openair-1.6/openair/man/airbaseStats.Rd | 2 openair-1.6/openair/man/aqStats.Rd | 2 openair-1.6/openair/man/calcFno2.Rd | 2 openair-1.6/openair/man/calcPercentile.Rd | 2 openair-1.6/openair/man/calendarPlot.Rd | 2 openair-1.6/openair/man/conditionalEval.Rd | 2 openair-1.6/openair/man/conditionalQuantile.Rd | 2 openair-1.6/openair/man/corPlot.Rd | 2 openair-1.6/openair/man/cutData.Rd | 2 openair-1.6/openair/man/drawOpenKey.Rd | 2 openair-1.6/openair/man/import.Rd | 2 openair-1.6/openair/man/importADMS.Rd | 2 openair-1.6/openair/man/importAURN.Rd | 2 openair-1.6/openair/man/importAURNCsv.Rd | 2 openair-1.6/openair/man/importAirbase.Rd | 2 openair-1.6/openair/man/importKCL.Rd | 2 openair-1.6/openair/man/importMeta.Rd | 2 openair-1.6/openair/man/importSAQN.Rd | 2 openair-1.6/openair/man/importTraj.Rd | 2 openair-1.6/openair/man/kernelExceed.Rd | 2 openair-1.6/openair/man/linearRelation.Rd | 2 openair-1.6/openair/man/modStats.Rd | 2 openair-1.6/openair/man/mydata.Rd | 2 openair-1.6/openair/man/openColours.Rd | 2 openair-1.6/openair/man/openair.Rd | 2 openair-1.6/openair/man/percentileRose.Rd | 2 openair-1.6/openair/man/polarAnnulus.Rd | 2 openair-1.6/openair/man/polarCluster.Rd | 2 openair-1.6/openair/man/polarFreq.Rd | 2 openair-1.6/openair/man/polarPlot.Rd | 2 openair-1.6/openair/man/quickText.Rd | 2 openair-1.6/openair/man/rollingMean.Rd | 2 openair-1.6/openair/man/scatterPlot.Rd | 35 openair-1.6/openair/man/selectByDate.Rd | 2 openair-1.6/openair/man/selectRunning.Rd | 2 openair-1.6/openair/man/smoothTrend.Rd | 2 openair-1.6/openair/man/splitByDate.Rd | 2 openair-1.6/openair/man/summaryPlot.Rd | 2 openair-1.6/openair/man/timeAverage.Rd | 15 openair-1.6/openair/man/timePlot.Rd | 33 openair-1.6/openair/man/timeProp.Rd | 2 openair-1.6/openair/man/timeVariation.Rd | 2 openair-1.6/openair/man/trajCluster.Rd | 4 openair-1.6/openair/man/trajLevel.Rd | 8 openair-1.6/openair/man/trajPlot.Rd | 84 openair-1.6/openair/man/trendLevel.Rd | 2 openair-1.6/openair/man/windRose.Rd | 24 81 files changed, 2505 insertions(+), 1965 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.2.3 dated 2015-01-27 and 0.2.4 dated 2015-07-23
DESCRIPTION | 17 ++- MD5 | 15 ++- NAMESPACE | 15 +-- R/seqemlt.R | 185 ++++++++++++++++++++---------------------- R/seqplot-rf.R |only inst/NEWS | 19 +++- inst/NEWS.Rd | 13 ++ man/TraMineRextras-package.Rd |only man/seqemlt.Rd | 48 +++++----- man/seqplot-rf.Rd |only 10 files changed, 173 insertions(+), 139 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Cluster Distances Through Trees
Description: Create a measure of inter-point dissimilarity useful
for clustering mixed data, and, optionally, perform the clustering.
Author: Sam Buttrey
Maintainer: Sam Buttrey <buttrey@nps.edu>
Diff between treeClust versions 1.0-0 dated 2015-03-19 and 1.1-1 dated 2015-07-23
DESCRIPTION | 9 +- MD5 | 24 +++-- NAMESPACE | 9 +- R/cramer.R | 2 R/d3.dist.R | 10 +- R/plot.treeClust.R | 35 ++++---- R/rpart.predict.leaves.R | 32 +++---- R/treeClust.R | 196 +++++++++++++++++------------------------------ R/treeClust.control.R | 6 - R/treeClust.rpart.R |only man/plot.treeClust.Rd | 8 + man/treeClust.Rd | 14 +-- man/treeClust.control.Rd | 18 +++- man/treeClust.rpart.Rd |only 14 files changed, 178 insertions(+), 185 deletions(-)
More information about SparseFactorAnalysis at CRAN
Permanent link
Title: Spanning Trees Used for Network Inference
Description: Bayesian inference of graphical model structures using spanning trees.
Author: Loïc Schwaller
Maintainer: Loïc Schwaller <loic.schwaller@ens-lyon.org>
Diff between saturnin versions 1.0 dated 2015-04-11 and 1.1.1 dated 2015-07-23
DESCRIPTION | 12 +++++++----- MD5 | 11 +++++++---- NAMESPACE | 6 +++++- R/RcppExports.R |only R/edge.prob.R | 30 ++++++++++++------------------ man/edge.prob.Rd | 6 +----- src |only 7 files changed, 32 insertions(+), 33 deletions(-)
Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between cba versions 0.2-14 dated 2014-01-15 and 0.2-15 dated 2015-07-23
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- NAMESPACE | 10 ++++++++++ 3 files changed, 17 insertions(+), 5 deletions(-)
Title: Probability-Scale Residuals and Residual Correlations
Description: Computes probability-scale residuals and residual correlations
for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont <charles.dupont@vanderbilt.edu>
Diff between PResiduals versions 0.2-1 dated 2015-03-03 and 0.2-2 dated 2015-07-23
DESCRIPTION | 14 ++- MD5 | 44 +++++++---- NAMESPACE | 36 ++++++++- R/cobot.R | 23 +++++- R/cocobot.R | 174 ++++------------------------------------------ R/cocobot_orm.R |only R/condis.R |only R/corTS.R |only R/countbot.R | 173 ++------------------------------------------- R/getCI.R |only R/lm.scores.R |only R/megabot.R |only R/nb.scores.R |only R/newPolr.R | 3 R/orm.scores.R |only R/pgumbel.R | 9 ++ R/poisson.scores.R |only R/presid.R | 14 +++ man/GKGamma.Rd | 3 man/PResiduals-package.Rd | 3 man/cobot.Rd | 3 man/cocobot.Rd | 11 +- man/countbot.Rd | 5 - man/diagn.Rd | 3 man/megabot.Rd |only man/presid.Rd | 3 man/print.cobot.Rd | 3 man/print.cocobot.Rd | 3 28 files changed, 160 insertions(+), 367 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-3 dated 2015-07-12 and 2.2-4 dated 2015-07-23
DESCRIPTION | 12 MD5 | 71 +- NAMESPACE | 11 R/AllClasses.R | 149 ++-- R/genRandDAG.R | 623 +++++++++---------- R/gies.R | 79 -- R/lingamFuns.R | 4 R/pcalg.R | 1407 +++++++++++++++++++++---------------------- TODO | 79 +- inst/NEWS.Rd | 28 inst/doc/pcalgDoc.pdf |binary man/GaussParDAG-class.Rd | 68 +- man/LINGAM.Rd | 76 +- man/ParDAG-class.Rd | 8 man/binCItest.Rd | 5 man/dag2pag.Rd | 18 man/disCItest.Rd | 15 man/fciAlgo-class.Rd | 19 man/fciPlus.Rd | 4 man/gAlgo-class.Rd | 10 man/gies.Rd | 6 man/gmD.Rd | 40 - man/mcor.Rd | 23 man/pcAlgo-class.Rd | 176 ++--- man/pcSelect.Rd | 42 - man/r.gauss.pardag.Rd | 56 - man/randDAG.Rd | 246 ++++--- man/randomDAG.Rd | 7 man/unifDAG.Rd | 178 +++-- man/wgtMatrix.Rd | 50 - tests/test_fciPlus.R | 21 tests/test_gSquareDis.R | 171 +++++ tests/test_gies.R | 32 tests/test_pcSelect.R | 172 ++++- tests/test_randDAG.R | 66 +- tests/test_randDAG.Rout.save |only tests/test_rfci.R | 4 37 files changed, 2252 insertions(+), 1724 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-0 dated 2015-03-05 and 1.4-1 dated 2015-07-23
DESCRIPTION | 12 +- MD5 | 41 ++++---- NAMESPACE | 8 + R/expressions.R | 2 R/glht.R | 2 R/mcp.R | 2 build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 6 + inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary man/cftest.Rd | 4 tests/Examples/multcomp-Ex.Rout.save | 141 +++++++++++++---------------- tests/bugfix.Rout.save | 11 +- tests/regtest-Tukey.Rout.save | 20 ++-- tests/regtest-anova.Rout.save | 8 - tests/regtest-interface-extended.Rout.save | 6 - tests/regtest-interface.Rout.save | 12 +- tests/regtest-lme.Rout.save | 9 - tests/regtest-mmm.Rout.save |only 22 files changed, 146 insertions(+), 138 deletions(-)
More information about munsellinterpol at CRAN
Permanent link
Title: Monotone Multi-Layer Perceptron Neural Network
Description: Train and make predictions from a multi-layer perceptron neural
network with partial monotonicity constraints.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between monmlp versions 1.1.2 dated 2012-09-27 and 1.1.3 dated 2015-07-23
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 8 +++++--- man/monmlp-package.Rd | 2 +- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-6 dated 2015-03-31 and 1.8-7 dated 2015-07-23
mgcv-1.8-6/mgcv/inst/po/po |only mgcv-1.8-6/mgcv/po/R-po.po |only mgcv-1.8-6/mgcv/po/po.po |only mgcv-1.8-7/mgcv/ChangeLog | 49 +++ mgcv-1.8-7/mgcv/DESCRIPTION | 6 mgcv-1.8-7/mgcv/MD5 | 55 +-- mgcv-1.8-7/mgcv/NAMESPACE | 24 + mgcv-1.8-7/mgcv/R/bam.r | 577 +++++++++++++++++++++++++++++++++---- mgcv-1.8-7/mgcv/R/efam.r | 46 +- mgcv-1.8-7/mgcv/R/fast-REML.r | 345 ++++++++++++++++++---- mgcv-1.8-7/mgcv/R/gam.fit3.r | 237 ++++++++++++--- mgcv-1.8-7/mgcv/R/gam.fit4.r | 75 +++- mgcv-1.8-7/mgcv/R/gamm.r | 5 mgcv-1.8-7/mgcv/R/jagam.r | 34 +- mgcv-1.8-7/mgcv/R/mgcv.r | 120 ++++--- mgcv-1.8-7/mgcv/R/misc.r | 88 +++++ mgcv-1.8-7/mgcv/R/smooth.r | 72 +++- mgcv-1.8-7/mgcv/man/bam.Rd | 17 - mgcv-1.8-7/mgcv/man/gam.control.Rd | 4 mgcv-1.8-7/mgcv/man/gam.scale.Rd | 13 mgcv-1.8-7/mgcv/man/initial.sp.Rd | 4 mgcv-1.8-7/mgcv/man/jagam.Rd | 10 mgcv-1.8-7/mgcv/po/R-de.po | 148 ++++----- mgcv-1.8-7/mgcv/po/de.po | 4 mgcv-1.8-7/mgcv/src/discrete.c |only mgcv-1.8-7/mgcv/src/gdi.c | 41 -- mgcv-1.8-7/mgcv/src/init.c | 13 mgcv-1.8-7/mgcv/src/mat.c | 231 +++++++++++++- mgcv-1.8-7/mgcv/src/mgcv.h | 20 + mgcv-1.8-7/mgcv/src/misc.c | 21 - 30 files changed, 1803 insertions(+), 456 deletions(-)
Title: Manipulate, Validate and Resolve IP Addresses
Description: A toolkit for manipulating,
validating and testing IP addresses and ranges, along with
datasets relating to IP addresses. While it primarily has
support for the IPv4 address space, more extensive IPv6 support
is intended.
Author: Bob Rudis <bob@rudis.net> [aut, cre], Oliver Keyes <ironholds@gmail.com> [aut]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between iptools versions 0.2.0 dated 2015-07-01 and 0.2.1 dated 2015-07-23
iptools-0.2.0/iptools/tests/testthat/test_host_resolution.R |only iptools-0.2.1/iptools/DESCRIPTION | 8 +- iptools-0.2.1/iptools/MD5 | 29 ++++--- iptools-0.2.1/iptools/NAMESPACE | 1 iptools-0.2.1/iptools/R/RcppExports.R | 22 +++++ iptools-0.2.1/iptools/build/vignette.rds |binary iptools-0.2.1/iptools/configure | 18 ++-- iptools-0.2.1/iptools/inst/doc/introduction_to_iptools.Rmd | 2 iptools-0.2.1/iptools/inst/doc/introduction_to_iptools.html | 4 - iptools-0.2.1/iptools/inst/doc/iptools_datasets.html | 4 - iptools-0.2.1/iptools/man/xff_extract.Rd |only iptools-0.2.1/iptools/src/RcppExports.cpp | 12 +++ iptools-0.2.1/iptools/src/asio_bindings.cpp | 45 ++++++++++++ iptools-0.2.1/iptools/src/asio_bindings.h | 34 +++++++-- iptools-0.2.1/iptools/src/iptools.cpp | 25 ++++++ iptools-0.2.1/iptools/tests/testthat/text_xff_extraction.R |only iptools-0.2.1/iptools/vignettes/introduction_to_iptools.Rmd | 2 17 files changed, 168 insertions(+), 38 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.0.1 dated 2015-07-01 and 0.1.0.2 dated 2015-07-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/Interplot.R | 2 +- R/Interplot_mi.R | 6 ++---- R/Interplot_mlmmi.R | 7 +++---- 5 files changed, 13 insertions(+), 16 deletions(-)
Title: GEV Conditional Density Estimation Network
Description: Implements a flexible nonlinear modelling framework for nonstationary
generalized extreme value analysis in hydroclimatology.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between GEVcdn versions 1.1.3 dated 2014-04-15 and 1.1.4 dated 2015-07-23
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 8 +++++--- man/GEVcdn-package.Rd | 2 +- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN)
Description: A fast reimplementation of the density-based DBSCAN clustering algorithm for spatial data introduced by Ester et al. 'A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise,' 1996. This implementation uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. The implementation is many times faster than the R-based implementation in package fpc.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-0 dated 2015-07-16 and 0.9-1 dated 2015-07-23
dbscan-0.9-0/dbscan/src/util.cpp |only dbscan-0.9-0/dbscan/src/util.h |only dbscan-0.9-1/dbscan/DESCRIPTION | 14 +- dbscan-0.9-1/dbscan/MD5 | 29 ++-- dbscan-0.9-1/dbscan/NAMESPACE | 3 dbscan-0.9-1/dbscan/R/RcppExports.R | 8 - dbscan-0.9-1/dbscan/R/dbscan.R | 9 + dbscan-0.9-1/dbscan/R/kNNdistplot.R | 24 +++ dbscan-0.9-1/dbscan/inst/NEWS | 6 dbscan-0.9-1/dbscan/man/dbscan.Rd | 97 +++++++++----- dbscan-0.9-1/dbscan/man/kNNdistplot.Rd | 31 +++- dbscan-0.9-1/dbscan/src/ANN/ANN.h | 173 +++++++++++++------------- dbscan-0.9-1/dbscan/src/RcppExports.cpp | 24 +++ dbscan-0.9-1/dbscan/src/brute.cpp | 27 +++- dbscan-0.9-1/dbscan/src/dbscan.cpp | 100 ++++++++------- dbscan-0.9-1/dbscan/src/kNNdist.cpp |only dbscan-0.9-1/dbscan/src/kd_fix_rad_search.cpp | 3 17 files changed, 343 insertions(+), 205 deletions(-)
Title: Conditional Density Estimation Network Construction and
Evaluation
Description: Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, and the like.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between CaDENCE versions 1.2.2 dated 2015-02-20 and 1.2.3 dated 2015-07-23
DESCRIPTION | 4 ++-- MD5 | 8 ++++---- NAMESPACE | 22 ++++++++++++++++++++++ man/cadence.fit.Rd | 13 ++++++------- man/gam.style.Rd | 6 +++--- 5 files changed, 37 insertions(+), 16 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.5-2 dated 2015-04-16 and 2.5-3 dated 2015-07-23
DESCRIPTION | 8 +-- MD5 | 77 +++++++++++++++---------------- NAMESPACE | 2 R/CAPdiscrim.R | 28 +++++++---- R/accumcomp.R | 8 +-- R/accumplot.R | 10 ++-- R/distdisplayed.R | 4 - R/ensemble.analogue.R | 2 R/ensemble.habitat.change.R | 2 R/ensemble.mean.R | 12 ++-- R/ensemble.raster.R | 44 ++++++++--------- R/ensemble.simplified.categories.R | 2 R/ensemble.test.R | 91 +++++++++++++++++++------------------ R/ensemble.test.splits.R | 5 +- R/evaluation.strip.plot.R | 14 ++--- R/import.from.Excel.R | 4 - R/loaded.citations.R | 2 R/multiconstrained.R | 2 R/ordibubble.R | 4 - R/ordicoeno.R | 12 ++-- R/ordiequilibriumcircle.R | 14 ++--- R/ordihull.centroids.R | 10 ++-- R/ordinearest.R | 2 R/ordispider.centroids.R | 4 - R/ordisymbol.R | 10 ++-- R/ordivector.R | 10 ++-- R/radfitresult.R | 4 - R/rankabuncomp.R | 16 +++--- R/rankabunplot.R | 16 +++--- R/renyiplot.R | 26 +++++----- R/replaceNAcomm.R |only R/residualssurface.R | 10 ++-- R/spatialsample.R | 24 ++++----- inst/etc/BiodiversityGUI.R | 9 +++ inst/etc/BiodiversityR-menus.txt | 3 - inst/etc/Rcmdr-menus.txt | 7 ++ man/CAPdiscrim.Rd | 15 +++++- man/add.spec.scores.Rd | 22 +++++--- man/ensemble.raster.Rd | 2 man/removeNAcomm.Rd | 3 + 40 files changed, 297 insertions(+), 243 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package 'CDVine' are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler, Thomas Nagler, Tobias Erhardt
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>
Diff between VineCopula versions 1.5 dated 2015-06-05 and 1.6 dated 2015-07-22
VineCopula-1.5/VineCopula/tests/TRUEadditonalExampleRuns.Rout.save |only VineCopula-1.6/VineCopula/DESCRIPTION | 11 VineCopula-1.6/VineCopula/MD5 | 29 VineCopula-1.6/VineCopula/NAMESPACE | 9 VineCopula-1.6/VineCopula/R/BiCopCDF.r | 6 VineCopula-1.6/VineCopula/R/ClaytonGumbelCopula.R | 870 +++---- VineCopula-1.6/VineCopula/R/RVineMLE.R | 954 +++---- VineCopula-1.6/VineCopula/R/RVineStructureSelect.r | 1226 +++++----- VineCopula-1.6/VineCopula/R/RVineTreePlot.r | 90 VineCopula-1.6/VineCopula/inst/ChangeLog | 13 VineCopula-1.6/VineCopula/man/BiCopGofTest.Rd | 4 VineCopula-1.6/VineCopula/man/RVineTreePlot.Rd | 3 VineCopula-1.6/VineCopula/man/VineCopula-package.Rd | 6 VineCopula-1.6/VineCopula/src/hfunc.c | 2 VineCopula-1.6/VineCopula/tests/Examples/VineCopula-Ex.Rout.save | 45 VineCopula-1.6/VineCopula/tests/additonalExampleRuns.Rout.save | 4 16 files changed, 1684 insertions(+), 1588 deletions(-)
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson
Maintainer: John Lawson <lawson@byu.edu>
Diff between daewr versions 1.1-4 dated 2014-12-17 and 1.1-6 dated 2015-07-22
DESCRIPTION | 17 ++---- MD5 | 130 ++++++++++++++++++++++++++-------------------------- NAMESPACE | 24 ++++----- R/Tukey1df.R | 2 data/Apo.rda |binary data/BPmonitor.rda |binary data/Bdish.rda |binary data/Bff.rda |binary data/BoxM.rda |binary data/COdata.rda |binary data/MPV.rda |binary data/Naph.rda |binary data/SPMPV.rda |binary data/Smotor.rda |binary data/Tet.rda |binary data/Treb.rda |binary data/antifungal.rda |binary data/apple.rda |binary data/arso.rda |binary data/augm.rda |binary data/bha.rda |binary data/bioequiv.rda |binary data/bioeqv.rda |binary data/blood.rda |binary data/bread.rda |binary data/cake.rda |binary data/cement.rda |binary data/chem.rda |binary data/chipman.rda |binary data/cont.rda |binary data/cpipe.rda |binary data/culture.rda |binary data/dairy.rda |binary data/drug.rda |binary data/eptaxr.rda |binary data/eptaxs2.rda |binary data/eptaxyb.rda |binary data/gagerr.rda |binary data/gear.rda |binary data/hardwood.rda |binary data/inject.rda |binary data/pastry.rda |binary data/pest.rda |binary data/pesticide.rda |binary data/plasma.rda |binary data/polvdat.rda |binary data/polymer.rda |binary data/prodstd.rda |binary data/qsar.rda |binary data/rcb.rda |binary data/residue.rda |binary data/rubber.rda |binary data/sausage.rda |binary data/soup.rda |binary data/soupmx.rda |binary data/splitPdes.rda |binary data/strung.rda |binary data/strungtile.rda |binary data/sugarbeet.rda |binary data/taste.rda |binary data/teach.rda |binary data/tile.rda |binary data/virus.rda |binary data/volt.rda |binary data/web.rda |binary man/Tukey1df.Rd | 2 66 files changed, 85 insertions(+), 90 deletions(-)
Title: Semiparametric Bivariate Regression Models
Description: Routine for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.4 dated 2015-06-11 and 3.5 dated 2015-07-22
ChangeLog | 7 DESCRIPTION | 11 MD5 | 55 +++- NAMESPACE | 16 + R/AT.r | 457 +++++++++++++++++++++++++++++++++++----- R/BiCDF.r | 6 R/OR.r |only R/RR.r |only R/SemiParBIVProbit.r | 26 +- R/copgHs2.r |only R/prev.r | 127 ++++++++++- R/print.AT.r | 8 R/print.OR.r |only R/print.RR.r |only R/resp.check.R | 5 R/summary.SemiParBIVProbit.r | 29 +- data |only man/AT.Rd | 47 ++-- man/OR.Rd |only man/RR.Rd |only man/SemiParBIVProbit-package.Rd | 4 man/SemiParBIVProbit.Rd | 110 ++++++--- man/SemiParBIVProbitObject.Rd | 2 man/copgHs2.Rd |only man/hiv.Rd |only man/logLik.SemiParBIVProbit.Rd | 2 man/mb.Rd | 5 man/meps.Rd |only man/plot.SemiParBIVProbit.Rd | 3 man/prev.Rd | 16 - man/print.OR.Rd |only man/print.RR.Rd |only man/resp.check.Rd | 4 man/war.Rd |only 34 files changed, 758 insertions(+), 182 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.7 dated 2015-07-10 and 0.8 dated 2015-07-22
DESCRIPTION | 8 MD5 | 44 NAMESPACE | 3 R/auxilaryfunctions.R | 2348 ++++++++++++++++++++++------------------- R/boral.jags.R | 343 +++-- inst/NEWS.Rd | 84 - man/boral-package.Rd | 12 man/boral.Rd | 214 ++- man/calc.condlogLik.Rd | 31 man/calc.logLik.lv0.Rd | 27 man/calc.marglogLik.Rd | 40 man/create.life.Rd | 73 - man/fitted.boral.Rd | 2 man/get.enviro.cor.Rd | 6 man/get.hpdintervals.Rd | 15 man/get.measures.Rd | 31 man/get.more.measures.Rd | 7 man/get.residual.cor.Rd | 10 man/lvsplot.Rd | 9 man/make.jagsboralmodel.Rd | 56 man/make.jagsboralnullmodel.Rd | 54 man/plot.boral.Rd | 2 man/summary.boral.Rd | 2 23 files changed, 1971 insertions(+), 1450 deletions(-)
Title: Analysis of Habitat Selection by Animals
Description: A collection of tools for the analysis of habitat selection by animals.
Author: Clement Calenge, contributions from Mathieu Basille, Stephane Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitat versions 1.8.17 dated 2015-03-27 and 1.8.18 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 4 ++++ src/tests.c | 2 +- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: PPI and Gaussian Network Construction from Transcriptomic
Analysis Results Integrating a Multilevel Factor
Description: A toolbox for a construction of protein-protein interaction networks through the 'STRING' application programming interface, and an inference of Gaussian networks through 'SIMoNe' and 'WGCNA' approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active 'Cytoscape' session.
Author: Emmanuel Chaplais, Henri-Jean Garchon
Maintainer: Emmanuel Chaplais <emmanuel.chaplais@inserm.fr>
Diff between stringgaussnet versions 1.0 dated 2015-06-16 and 1.1 dated 2015-07-22
stringgaussnet-1.0/stringgaussnet/build/partial.rdb |only stringgaussnet-1.1/stringgaussnet/DESCRIPTION | 15 ++-- stringgaussnet-1.1/stringgaussnet/MD5 | 34 ++++++---- stringgaussnet-1.1/stringgaussnet/NAMESPACE | 4 + stringgaussnet-1.1/stringgaussnet/R/convertAliases.R | 1 stringgaussnet-1.1/stringgaussnet/R/getSTRINGNet.R | 2 stringgaussnet-1.1/stringgaussnet/R/plot.WGCNANet.R | 2 stringgaussnet-1.1/stringgaussnet/R/print.SIMoNeNet.R | 2 stringgaussnet-1.1/stringgaussnet/R/saveCytoscapeSession.R | 2 stringgaussnet-1.1/stringgaussnet/build/vignette.rds |only stringgaussnet-1.1/stringgaussnet/data/SpASamples.rda |binary stringgaussnet-1.1/stringgaussnet/inst |only stringgaussnet-1.1/stringgaussnet/man/SpASamples.Rd | 1 stringgaussnet-1.1/stringgaussnet/man/getSTRINGNet.Rd | 2 stringgaussnet-1.1/stringgaussnet/man/stringgaussnet-package.Rd | 30 ++------ stringgaussnet-1.1/stringgaussnet/vignettes |only 16 files changed, 50 insertions(+), 45 deletions(-)
More information about stringgaussnet at CRAN
Permanent link
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb],
Martin Maechler [ctb],
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-2 dated 2014-12-18 and 1.0-3 dated 2015-07-22
DESCRIPTION | 12 ++-- MD5 | 24 ++++----- NAMESPACE | 5 +- R/mvt.R | 106 ++++++++++++++++--------------------------- build/vignette.rds |binary inst/CITATION | 2 inst/NEWS | 9 +++ inst/doc/MVT_Rnews.pdf |binary man/pmvt.Rd | 1 man/qmvnorm.Rd | 19 +++---- man/qmvt.Rd | 43 ++++++++++------- tests/bugfix-tests.R | 17 ++++++ tests/bugfix-tests.Rout.save | 68 ++++++++++++++++++++------- 13 files changed, 175 insertions(+), 131 deletions(-)
Title: Hybrid Hierarchical Clustering
Description: Hybrid hierarchical clustering via mutual clusters. A mutual cluster is a set of points closer to each other than to all other points. Mutual clusters are used to enrich top-down hierarchical clustering.
Author: Hugh Chipman, Rob Tibshirani, with tsvq code originally from Trevor Hastie
Maintainer: Hugh Chipman <hugh.chipman@acadiau.ca>
Diff between hybridHclust versions 1.0-4 dated 2011-08-12 and 1.0-5 dated 2015-07-22
DESCRIPTION | 19 +++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 5 ++++- data/sorlielabels.RData |binary demo/hybridHclust.R | 2 +- man/hybridHclust.Rd | 1 - man/mutualCluster.Rd | 1 - man/print.mutualCluster.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Data for "GAMs: An Introduction with R"
Description: Data sets and scripts used in the book "Generalized
Additive Models: An Introduction with R", Wood (2006) CRC.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamair versions 0.0-8 dated 2012-03-27 and 0.0-9 dated 2015-07-22
gamair-0.0-8/gamair/changelog |only gamair-0.0-9/gamair/ChangeLog |only gamair-0.0-9/gamair/DESCRIPTION | 7 ++++--- gamair-0.0-9/gamair/MD5 | 12 ++++++------ gamair-0.0-9/gamair/man/cairo.Rd | 2 +- gamair-0.0-9/gamair/man/chl.Rd | 2 +- gamair-0.0-9/gamair/man/co2s.Rd | 2 +- gamair-0.0-9/gamair/man/engine.Rd | 5 +++-- 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Tools to Deal with Raster Maps
Description: A collection of tools to deal with raster maps.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatMA versions 0.3.9 dated 2015-03-27 and 0.3.10 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 4 +++- src/tests.c | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Analysis of Animal Movements
Description: A collection of tools for the analysis of animal movements.
Author: Clement Calenge, contributions from Stephane Dray and Manuela Royer
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatLT versions 0.3.19 dated 2015-03-29 and 0.3.20 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ inst/doc/adehabitatLT.pdf |binary src/tests.c | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Analysis of Habitat Selection by Animals
Description: A collection of tools for the analysis of habitat selection.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatHS versions 0.3.11 dated 2015-03-27 and 0.3.12 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 3 +++ src/tests.c | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Home Range Estimation
Description: A collection of tools for the estimation of animals home range.
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@oncfs.gouv.fr>
Diff between adehabitatHR versions 0.4.13 dated 2015-03-27 and 0.4.14 dated 2015-07-22
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ R/BRB.r | 4 +++- src/tests.c | 12 ++++++++---- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Ancona "Politecnica delle Marche")
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.1 dated 2015-06-07 and 1.2 dated 2015-07-22
DESCRIPTION | 12 ++--- MD5 | 22 ++++----- NAMESPACE | 4 + R/cquad_basic.R | 33 ++++++++----- R/cquad_equ.R | 26 +++++++--- R/cquad_ext.R | 121 ++++++++++++--------------------------------------- R/cquad_pseudo.R | 12 ++--- R/summary.cquad.R | 2 man/cquad-package.Rd | 4 - man/cquad_basic.Rd | 1 man/cquad_equ.Rd | 1 man/cquad_ext.Rd | 1 12 files changed, 102 insertions(+), 137 deletions(-)
More information about PlotPrjNetworks at CRAN
Permanent link
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov <valentin.todorov@chello.at>,
Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Tobias Verbeke <tobias.verbeke@openanalytics.eu>,
Manuel Koller <mkoller@ispm.unibe.ch>,
Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-4 dated 2015-06-10 and 0.92-5 dated 2015-07-22
DESCRIPTION | 10 ++-- MD5 | 58 ++++++++++++++-------------- NAMESPACE | 10 ++-- R/MTestimador2.R | 8 ++- R/glmrob.R | 5 -- R/lmrob.MM.R | 1 R/lmrob.R | 82 ++++++++++++++++++++-------------------- R/nlrob.R | 17 +++++++- TODO | 2 inst/NEWS.Rd | 23 ++++++++++- inst/doc/estimating.functions.R | 2 inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary man/radarImage.Rd | 1 man/summary.lmrob.Rd | 18 +++++--- tests/NAcoef.R | 25 ++++++++---- tests/NAcoef.Rout.save | 50 ++++++++++-------------- tests/binom-ni-small.Rout.save | 14 +++--- tests/glmrob-1.R | 13 ++---- tests/lmrob-psifns.R | 7 --- tests/lmrob-psifns.Rout.save | 19 +++------ tests/poisson-ex.R | 39 +++++++++++++++---- vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 30 files changed, 230 insertions(+), 174 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Author: Francois Michonneau [aut, cre],
Ben Bolker [aut],
Mark Holder [aut],
Paul Lewis [aut],
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.4.0 dated 2015-07-09 and 0.6.0 dated 2015-07-22
rncl-0.4.0/rncl/src/ancestors.c |only rncl-0.4.0/rncl/src/descendants.c |only rncl-0.4.0/rncl/src/phyloXX.c |only rncl-0.4.0/rncl/src/reorderBinary.c |only rncl-0.4.0/rncl/src/reorderRobust.c |only rncl-0.6.0/rncl/DESCRIPTION | 10 +- rncl-0.6.0/rncl/MD5 | 28 +++---- rncl-0.6.0/rncl/NAMESPACE | 1 rncl-0.6.0/rncl/R/collapse_singles.R |only rncl-0.6.0/rncl/R/rncl-package.R | 1 rncl-0.6.0/rncl/R/rncl.R | 60 +++++++--------- rncl-0.6.0/rncl/README.md | 15 ++-- rncl-0.6.0/rncl/inst/nexusfiles/test_empty.nex |only rncl-0.6.0/rncl/inst/nexusfiles/test_subset_alltaxa.nex |only rncl-0.6.0/rncl/inst/nexusfiles/test_subset_taxa.nex | 5 - rncl-0.6.0/rncl/man/read_nexus_phylo.Rd | 2 rncl-0.6.0/rncl/man/rncl.Rd | 14 +-- rncl-0.6.0/rncl/src/GetNCL.cpp | 59 ++++++++++++--- rncl-0.6.0/rncl/tests/testthat/test.rncl.R | 48 ++++++++++++ 19 files changed, 155 insertions(+), 88 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.3 dated 2015-02-23 and 1.4 dated 2015-07-22
RJSDMX-1.3/RJSDMX/man/geCodes.Rd |only RJSDMX-1.4/RJSDMX/DESCRIPTION | 6 RJSDMX-1.4/RJSDMX/MD5 | 31 +- RJSDMX-1.4/RJSDMX/NAMESPACE | 1 RJSDMX-1.4/RJSDMX/R/SdmxClient.R | 256 +++++++++++++++++++++--- RJSDMX-1.4/RJSDMX/R/TSConverter.R | 56 +++-- RJSDMX-1.4/RJSDMX/inst/java/SDMX.jar |binary RJSDMX-1.4/RJSDMX/man/addProvider.Rd | 62 ++--- RJSDMX-1.4/RJSDMX/man/getCodes.Rd |only RJSDMX-1.4/RJSDMX/man/getDSDIdentifier.Rd | 48 +--- RJSDMX-1.4/RJSDMX/man/getDimensions.Rd | 45 +--- RJSDMX-1.4/RJSDMX/man/getFlows.Rd | 77 +++---- RJSDMX-1.4/RJSDMX/man/getProviders.Rd | 55 +---- RJSDMX-1.4/RJSDMX/man/getSDMX.Rd | 80 +++---- RJSDMX-1.4/RJSDMX/man/getTimeSeries.Rd | 59 ++--- RJSDMX-1.4/RJSDMX/man/getTimeSeriesRevisions.Rd |only RJSDMX-1.4/RJSDMX/man/sdmxHelp.Rd | 63 ++--- RJSDMX-1.4/RJSDMX/man/sdmxdf.Rd | 75 +++---- 18 files changed, 518 insertions(+), 396 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram
visualization for the structure of RDML object.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between RDML versions 0.8-4 dated 2015-04-21 and 0.9-1 dated 2015-07-22
RDML-0.8-4/RDML/R/names.RDML.R |only RDML-0.8-4/RDML/man/RDML.class.Rd |only RDML-0.8-4/RDML/man/merge-method.Rd |only RDML-0.8-4/RDML/man/names.RDML.Rd |only RDML-0.9-1/RDML/CHANGELOG | 3 RDML-0.9-1/RDML/DESCRIPTION | 18 RDML-0.9-1/RDML/MD5 | 96 +- RDML-0.9-1/RDML/NAMESPACE | 73 + RDML-0.9-1/RDML/R/RDML.AsDendrogram.R | 32 RDML-0.9-1/RDML/R/RDML.AsTable.R | 39 RDML-0.9-1/RDML/R/RDML.GetFData.R | 118 -- RDML-0.9-1/RDML/R/RDML.Merge.R | 56 - RDML-0.9-1/RDML/R/RDML.R | 562 ++----------- RDML-0.9-1/RDML/R/RDML.SetFData.R | 130 ++- RDML-0.9-1/RDML/R/RDML.asserts.R | 233 +++-- RDML-0.9-1/RDML/R/RDML.init.R | 840 ++++++++++---------- RDML-0.9-1/RDML/R/RDML.types.R |only RDML-0.9-1/RDML/R/functional_wrappers.R |only RDML-0.9-1/RDML/README.md | 4 RDML-0.9-1/RDML/build |only RDML-0.9-1/RDML/inst/doc |only RDML-0.9-1/RDML/man/AsDendrogram-function.Rd |only RDML-0.9-1/RDML/man/GetFData-function.Rd |only RDML-0.9-1/RDML/man/MergeRDMLs.Rd |only RDML-0.9-1/RDML/man/RDML.Rd |only RDML-0.9-1/RDML/man/adpsType.Rd |only RDML-0.9-1/RDML/man/annotationType.Rd |only RDML-0.9-1/RDML/man/asdendrogram-method.Rd | 61 - RDML-0.9-1/RDML/man/astable-function.Rd |only RDML-0.9-1/RDML/man/astable-method.Rd | 155 +-- RDML-0.9-1/RDML/man/baseTemperatureType.Rd |only RDML-0.9-1/RDML/man/cdnaSynthesisMethodType.Rd |only RDML-0.9-1/RDML/man/commercialAssayType.Rd |only RDML-0.9-1/RDML/man/cqDetectionMethodType.Rd |only RDML-0.9-1/RDML/man/dataCollectionSoftwareType.Rd |only RDML-0.9-1/RDML/man/dataType.Rd |only RDML-0.9-1/RDML/man/documentationType.Rd |only RDML-0.9-1/RDML/man/dyeType.Rd |only RDML-0.9-1/RDML/man/enumType.Rd |only RDML-0.9-1/RDML/man/experimentType.Rd |only RDML-0.9-1/RDML/man/experimenterType.Rd |only RDML-0.9-1/RDML/man/getfdata-method.Rd | 109 +- RDML-0.9-1/RDML/man/gradientType.Rd |only RDML-0.9-1/RDML/man/idReferencesType.Rd |only RDML-0.9-1/RDML/man/idType.Rd |only RDML-0.9-1/RDML/man/labelFormatType.Rd |only RDML-0.9-1/RDML/man/lidOpenType.Rd |only RDML-0.9-1/RDML/man/loopType.Rd |only RDML-0.9-1/RDML/man/mdpsType.Rd |only RDML-0.9-1/RDML/man/measureType.Rd |only RDML-0.9-1/RDML/man/new-method.Rd | 80 - RDML-0.9-1/RDML/man/nucleotideType.Rd |only RDML-0.9-1/RDML/man/oligoType.Rd |only RDML-0.9-1/RDML/man/pauseType.Rd |only RDML-0.9-1/RDML/man/pcrFormatType.Rd |only RDML-0.9-1/RDML/man/primingMethodType.Rd |only RDML-0.9-1/RDML/man/quantityType.Rd |only RDML-0.9-1/RDML/man/quantityUnitType.Rd |only RDML-0.9-1/RDML/man/rdmlBaseType.Rd |only RDML-0.9-1/RDML/man/rdmlIdType.Rd |only RDML-0.9-1/RDML/man/reactIdType.Rd |only RDML-0.9-1/RDML/man/reactType.Rd |only RDML-0.9-1/RDML/man/runType.Rd |only RDML-0.9-1/RDML/man/sampleType.Rd |only RDML-0.9-1/RDML/man/sampleTypeType.Rd |only RDML-0.9-1/RDML/man/sequencesType.Rd |only RDML-0.9-1/RDML/man/setfdata-function.Rd |only RDML-0.9-1/RDML/man/setfdata-method.Rd | 105 +- RDML-0.9-1/RDML/man/stepType.Rd |only RDML-0.9-1/RDML/man/targetType.Rd |only RDML-0.9-1/RDML/man/targetTypeType.Rd |only RDML-0.9-1/RDML/man/temperatureType.Rd |only RDML-0.9-1/RDML/man/templateQuantityType.Rd |only RDML-0.9-1/RDML/man/thermalCyclingConditionsType.Rd |only RDML-0.9-1/RDML/man/xRefType.Rd |only RDML-0.9-1/RDML/vignettes |only 76 files changed, 1342 insertions(+), 1372 deletions(-)
Title: Distance Sampling Analyses
Description: Analysis of distance sampling data collected on line transect surveys. Estimates distance-based detection functions and abundances.
Author: Trent McDonald [cre, aut],
Ryan Nielson [aut],
Jason Carlisle [aut],
Ben Augustine [ctb],
James Griswald [ctb],
Joel Reynolds [ctb],
Pham Quang [ctb],
Earl Becker [ctb],
Aaron Christ [ctb],
Brook Russelland [ctb],
Patrick McKann [ctb]
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between Rdistance versions 1.2.2 dated 2015-04-22 and 1.3.2 dated 2015-07-22
DESCRIPTION | 13 +-- MD5 | 64 ++++++++------- NAMESPACE | 5 + R/F.abund.estim.r | 98 ++++++++++++++---------- R/F.automated.CDA.r | 13 +-- R/F.start.limits.r | 2 R/zzz.R | 4 build/vignette.rds |binary data/sparrow.detections.rda |binary data/sparrow.transects.rda |binary inst/doc/Rdistance_BeginnerTutorial.R | 9 +- inst/doc/Rdistance_BeginnerTutorial.Rmd | 21 ++--- inst/doc/Rdistance_BeginnerTutorial.pdf |binary inst/doc/Rdistance_CustomDetectionFunction.R | 6 - inst/doc/Rdistance_CustomDetectionFunction.Rmd | 11 +- inst/doc/Rdistance_CustomDetectionFunction.pdf |binary inst/doc/Rdistance_ModelingAbundance.R |only inst/doc/Rdistance_ModelingAbundance.Rmd |only inst/doc/Rdistance_ModelingAbundance.pdf |only man/AIC.dfunc.Rd | 8 - man/ESW.Rd | 8 - man/F.abund.estim.Rd | 31 +++---- man/F.automated.CDA.Rd | 20 +--- man/F.dfunc.estim.Rd | 10 -- man/Gamma.like.Rd | 14 ++- man/coef.dfunc.Rd | 8 - man/perp.dists.Rd | 2 man/print.abund.Rd | 20 +++- man/print.dfunc.Rd | 15 ++- man/sparrow.detections.Rd | 4 man/sparrow.transects.Rd | 7 - man/uniform.like.Rd | 19 ++-- vignettes/Rdistance_BeginnerTutorial.Rmd | 21 ++--- vignettes/Rdistance_CustomDetectionFunction.Rmd | 11 +- vignettes/Rdistance_ModelingAbundance.Rmd |only 35 files changed, 232 insertions(+), 212 deletions(-)
Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between nadiv versions 2.14.0 dated 2015-07-03 and 2.14.1 dated 2015-07-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/makeAinv.R | 11 ++++++++--- man/makeAinv.Rd | 2 +- man/nadiv-package.Rd | 4 ++-- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multi-variate clustering (MVC), cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 1.2.1 dated 2015-05-24 and 1.2.2 dated 2015-07-22
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 6 +++++- R/HiClimR.R | 17 ++++++++++++----- R/coarseR.R | 3 ++- R/fastCor.R | 3 ++- R/geogMask.R | 3 ++- R/grid2D.R | 3 ++- R/minSigCor.R | 3 ++- R/validClimR.R | 3 ++- README.md | 11 ++++++++++- inst/CITATION | 2 +- src/HiClimR.f90 | 1 + 13 files changed, 58 insertions(+), 31 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
0xdata team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.0.0.22 dated 2015-06-14 and 3.0.0.30 dated 2015-07-22
h2o-3.0.0.22/h2o/man/as.matrix.h2o.Rd |only h2o-3.0.0.22/h2o/man/cut.H2OFrame.Rd |only h2o-3.0.0.22/h2o/man/median-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/quantile.Rd |only h2o-3.0.0.22/h2o/man/transform.H2OFrame.Rd |only h2o-3.0.0.30/h2o/DESCRIPTION | 8 h2o-3.0.0.30/h2o/MD5 | 168 ++++++------ h2o-3.0.0.30/h2o/NAMESPACE | 24 + h2o-3.0.0.30/h2o/R/classes.R | 4 h2o-3.0.0.30/h2o/R/communication.R | 12 h2o-3.0.0.30/h2o/R/connection.R | 2 h2o-3.0.0.30/h2o/R/deeplearning.R | 26 + h2o-3.0.0.30/h2o/R/export.R | 16 - h2o-3.0.0.30/h2o/R/frame.R | 294 ++++++++++++++-------- h2o-3.0.0.30/h2o/R/gbm.R | 28 +- h2o-3.0.0.30/h2o/R/glrm.R | 12 h2o-3.0.0.30/h2o/R/import.R | 28 +- h2o-3.0.0.30/h2o/R/kvstore.R | 44 --- h2o-3.0.0.30/h2o/R/logging.R | 13 h2o-3.0.0.30/h2o/R/models.R | 84 +++++- h2o-3.0.0.30/h2o/R/parse.R | 12 h2o-3.0.0.30/h2o/R/pca.R | 14 - h2o-3.0.0.30/h2o/R/randomforest.R | 26 + h2o-3.0.0.30/h2o/R/shim.R | 8 h2o-3.0.0.30/h2o/R/svd.R | 2 h2o-3.0.0.30/h2o/inst/buildnum.txt | 2 h2o-3.0.0.30/h2o/man/apply-H2OFrame-method.Rd | 2 h2o-3.0.0.30/h2o/man/as.data.frame.H2OFrame.Rd | 2 h2o-3.0.0.30/h2o/man/as.factor-H2OFrame-method.Rd | 2 h2o-3.0.0.30/h2o/man/h2o-package.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.anomaly.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.anyFactor.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.auc.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.biases.Rd |only h2o-3.0.0.30/h2o/man/h2o.cbind.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.centroid_stats.Rd |only h2o-3.0.0.30/h2o/man/h2o.clearLog.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.clusterStatus.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.colnames.Rd | 9 h2o-3.0.0.30/h2o/man/h2o.confusionMatrix.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.cut.Rd |only h2o-3.0.0.30/h2o/man/h2o.ddply.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.deepfeatures.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.deeplearning.Rd | 14 - h2o-3.0.0.30/h2o/man/h2o.dim.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.downloadCSV.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.download_pojo.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.exportHDFS.Rd | 10 h2o-3.0.0.30/h2o/man/h2o.gbm.Rd | 13 h2o-3.0.0.30/h2o/man/h2o.getModel.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.giniCoef.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.glrm.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.head.Rd | 11 h2o-3.0.0.30/h2o/man/h2o.ifelse.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.importFile.Rd | 14 - h2o-3.0.0.30/h2o/man/h2o.impute.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.insertMissingValues.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.interaction.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.length.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.levels.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.loadModel.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.ls.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.match.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.mean.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.median.Rd |only h2o-3.0.0.30/h2o/man/h2o.merge.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.metric.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.mse.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.nrow.Rd | 7 h2o-3.0.0.30/h2o/man/h2o.parseRaw.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.parseSetup.Rd | 6 h2o-3.0.0.30/h2o/man/h2o.performance.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.prcomp.Rd | 13 h2o-3.0.0.30/h2o/man/h2o.quantile.Rd |only h2o-3.0.0.30/h2o/man/h2o.r2.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.randomForest.Rd | 9 h2o-3.0.0.30/h2o/man/h2o.rbind.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.removeAll.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.runif.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.scale.Rd | 5 h2o-3.0.0.30/h2o/man/h2o.sd.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.setLevel.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.splitFrame.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.startLogging.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.stopLogging.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.subset.Rd |only h2o-3.0.0.30/h2o/man/h2o.summary.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.table.Rd | 2 h2o-3.0.0.30/h2o/man/h2o.transform.Rd |only h2o-3.0.0.30/h2o/man/h2o.var.Rd | 4 h2o-3.0.0.30/h2o/man/h2o.weights.Rd |only h2o-3.0.0.30/h2o/man/zzz.Rd |only 92 files changed, 742 insertions(+), 324 deletions(-)
Title: Various R Programming Tools for Model Fitting
Description: Various R programming tools for model fitting.
Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
Johnson. Contributions from Randall C. Johnson are Copyright
(2005) SAIC-Frederick, Inc. Funded by the Intramural Research
Program, of the NIH, National Cancer Institute, Center for
Cancer Research under NCI Contract NO1-CO-12400.
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gmodels versions 2.15.4.1 dated 2013-09-21 and 2.16.2 dated 2015-07-22
ChangeLog | 769 +++++++++++++++++++--------------------------------- DESCRIPTION | 20 - MD5 | 32 +- NAMESPACE | 23 + NEWS | 51 +++ R/ci.R | 83 +++-- R/est.mer.R | 96 +++--- R/estimable.R | 142 +++++---- R/estimable.mlm.R | 24 - R/fit.contrast.R | 163 +++++------ R/to.est.R | 19 - inst/ChangeLog | 769 +++++++++++++++++++--------------------------------- inst/NEWS | 51 +++ man/ci.Rd | 58 ++- man/estimable.Rd | 42 +- man/fit.contrast.Rd | 28 - tests |only 17 files changed, 1052 insertions(+), 1318 deletions(-)
Title: Fitting Mixed Models with Known Covariance Structures
Description: The main functions are 'emmreml', and 'emmremlMultiKernel'. 'emmreml' solves a mixed model with known covariance structure using the 'EMMA' algorithm. 'emmremlMultiKernel' is a wrapper for 'emmreml' to handle multiple random components with known covariance structures. The function 'emmremlMultivariate' solves a multivariate gaussian mixed model with known covariance structure using the 'ECM' algorithm.
Author: Deniz Akdemir, Okeke Uche Godfrey
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between EMMREML versions 3.0 dated 2015-03-31 and 3.1 dated 2015-07-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 7 +++++++ R/emmreml.R | 8 +++++--- R/emmremlMultiKernel.R | 6 +++--- R/emmremlMultivariate.R | 7 ++----- man/EMMREML-package.Rd | 4 ++-- man/emmreml.Rd | 2 +- man/emmremlMultiKernel.Rd | 3 ++- man/emmremlMultivariate.Rd | 5 ++--- 10 files changed, 38 insertions(+), 32 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Various actuarial science functionalities, mostly in the
fields of loss distributions, risk theory (including ruin theory),
simulation of compound hierarchical models and credibility theory.
The package also features 17 probability laws commonly used in
insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 1.1-9 dated 2015-07-07 and 1.1-10 dated 2015-07-22
DESCRIPTION | 10 +++---- MD5 | 20 +++++++------- R/cm.R | 2 - R/hierarc.R | 63 +++++++++++++++++++++++++---------------------- inst/NEWS.Rd | 17 ++++++++++-- inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.pdf |binary inst/doc/lossdist.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary 11 files changed, 64 insertions(+), 48 deletions(-)
Title: Public Subject Attention via Wikipedia Page Access Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied. For the omnipresent Wikipedia those access statistics
are made available via 'http://stats.grok.se' a server
providing the information as file dumps as well as as web API.
This package provides an easy to use, consistent and traffic
minimizing approach to make those data accessible within R.
Author: Peter Meissner [aut, cre], R Core team [ctb] ('wp_date()'
derived from base package's 'as.Date()')
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 1.1.4 dated 2015-06-11 and 1.1.6 dated 2015-07-21
DESCRIPTION | 8 MD5 | 36 ++-- NEWS | 38 +++- R/wp_cache.R | 2 R/wp_df.R | 124 +++++++------- R/wp_download_data.R | 4 R/wp_http_header.R | 6 R/wp_linked_pages.R | 92 +++++----- R/wp_trend.R | 11 - README.md | 2 build/vignette.rds |binary inst/doc/using-wikipediatrend.R | 6 inst/doc/using-wikipediatrend.Rmd | 6 inst/doc/using-wikipediatrend.html | 274 ++++++++++++++++---------------- man/wp_cache.Rd | 2 man/wp_trend.Rd | 6 tests/testthat/test.csv | 59 +++--- tests/testthat/test_caching_gathering.R | 7 vignettes/using-wikipediatrend.Rmd | 6 19 files changed, 362 insertions(+), 327 deletions(-)
More information about wikipediatrend at CRAN
Permanent link
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.18.1 dated 2015-05-13 and 0.19.1 dated 2015-07-21
sdcTable-0.18.1/sdcTable/src/myPaste.cpp |only sdcTable-0.18.1/sdcTable/src/myPasteWithSep.cpp |only sdcTable-0.18.1/sdcTable/src/mySplitFn.cpp |only sdcTable-0.19.1/sdcTable/DESCRIPTION | 11 sdcTable-0.19.1/sdcTable/MD5 | 23 - sdcTable-0.19.1/sdcTable/NAMESPACE | 5 sdcTable-0.19.1/sdcTable/R/RcppExports.R |only sdcTable-0.19.1/sdcTable/R/classes.r | 5 sdcTable-0.19.1/sdcTable/R/helper_functions.r | 13 - sdcTable-0.19.1/sdcTable/R/methods_class_dimVar.r | 14 - sdcTable-0.19.1/sdcTable/R/methods_class_sdcProblem.r | 220 ++++-------------- sdcTable-0.19.1/sdcTable/build/vignette.rds |binary sdcTable-0.19.1/sdcTable/inst/doc/sdcTable.pdf |binary sdcTable-0.19.1/sdcTable/src/RcppExports.cpp |only sdcTable-0.19.1/sdcTable/src/cpp_helpers.cpp |only sdcTable-0.19.1/sdcTable/src/suppMultDimTable.cpp |only 16 files changed, 97 insertions(+), 194 deletions(-)
Title: Distributions to be Used for GAMLSS Modelling
Description: The different distributions used for the response variables in GAMLSS
modelling.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk> with contributions from
Calliope Akantziliotou, Gillian Heller, Raydonal Ospina
<rospina@ime.usp.br>, Nicoletta Motpan, Fiona McElduff, Vlasios
Voudouris, Majid Djennad, Marco Enea and Alexios Ghalanos.
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 4.3-4 dated 2015-02-03 and 4.3-5 dated 2015-07-21
DESCRIPTION | 15 - MD5 | 12 - NAMESPACE | 232 ++++++++++++------------ R/BB.R | 298 +++++++++++++++---------------- R/GT.R | 562 ++++++++++++++++++++++++++++++------------------------------ man/GT.Rd | 2 man/NO.Rd | 162 ++++++++--------- 7 files changed, 642 insertions(+), 641 deletions(-)
Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between cp4p versions 0.2 dated 2015-05-13 and 0.3 dated 2015-07-21
DESCRIPTION | 10 ++-- MD5 | 24 +++++++---- NAMESPACE | 10 ++-- R/adjust_p.R | 21 ++++++---- R/calibration_plot.R | 97 ++++++++++++++++++++++++++++++++++++------------ R/estim_pi0.R | 4 + data |only man/LFQRatio2.Rd |only man/LFQRatio25.Rd |only man/adjust.p.Rd | 9 ++-- man/calibration.plot.Rd | 9 ++-- man/cp4p-package.Rd | 7 +-- man/estim.pi0.Rd | 16 +++++-- 13 files changed, 141 insertions(+), 66 deletions(-)
Title: Multivariate VAM Fitting
Description: The RealVAMs package fits a multivariate value-added model (VAM) (see Broatch and Lohr 2012) with normally distributed test scores and a binary outcome indicator. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew Karl, Jennifer Broatch, and Jennifer Green
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between RealVAMS versions 0.3-1 dated 2014-11-01 and 0.3-2 dated 2015-07-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 5 ++++- NEWS | 5 ++++- R/vp_cp.R | 4 ++-- man/RealVAMS-package.Rd | 11 ++++++----- man/RealVAMS.Rd | 7 ++++--- 7 files changed, 31 insertions(+), 23 deletions(-)
Title: Tools for the 'Parallel' Package
Description: Miscellaneous utilities for the 'parallel' package,
cluster-oriented section; "Snowdoop" alternative to MapReduce;
file splitting and distributed operations such as sort and aggregate.
"Software Alchemy" method for parallelizing most statistical methods,
presented in N. Matloff, Parallel Computation for Data Science,
Chapman and Hall, 2015. Includes a debugging aid.
Author: Norm Matloff <normmatloff@gmail.com> [aut],
Alex Rumbaugh <aprumbaugh@ucdavis.edu> [ctb]
Maintainer: Norm Matloff <normmatloff@gmail.com>
Diff between partools versions 1.0.1 dated 2015-01-03 and 1.1.1 dated 2015-07-21
partools-1.0.1/partools/inst/doc/Snowdoop.R |only partools-1.0.1/partools/inst/doc/Snowdoop.Rnw |only partools-1.0.1/partools/inst/doc/Snowdoop.pdf |only partools-1.0.1/partools/vignettes/Snowdoop.Rnw |only partools-1.1.1/partools/DESCRIPTION | 23 - partools-1.1.1/partools/MD5 | 39 +- partools-1.1.1/partools/NAMESPACE | 11 partools-1.1.1/partools/R/CA.R | 247 +++++++++++++--- partools-1.1.1/partools/R/DebugSnow.R | 6 partools-1.1.1/partools/R/SnowUtils.R | 146 +++++++++ partools-1.1.1/partools/R/Snowdoop.R | 304 +++++++++++++++++--- partools-1.1.1/partools/R/onAttach.R |only partools-1.1.1/partools/README.md |only partools-1.1.1/partools/build/vignette.rds |binary partools-1.1.1/partools/data |only partools-1.1.1/partools/inst/README | 3 partools-1.1.1/partools/inst/doc/partools.Rnw |only partools-1.1.1/partools/inst/doc/partools.pdf |only partools-1.1.1/partools/inst/examples/XformAdjMat.R |only partools-1.1.1/partools/man/ca.Rd | 217 +++++++++++++- partools-1.1.1/partools/man/dbs.Rd | 67 ++-- partools-1.1.1/partools/man/formrowchunks.Rd | 155 ++++++++-- partools-1.1.1/partools/man/newadult.Rd |only partools-1.1.1/partools/man/prgeng.Rd |only partools-1.1.1/partools/man/snowdoop.Rd | 204 +++++++++++-- partools-1.1.1/partools/vignettes/partools.Rnw |only 26 files changed, 1224 insertions(+), 198 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-39 dated 2015-06-26 and 0.9-40 dated 2015-07-21
mkin-0.9-39/mkin/inst/doc/compiled_models.R |only mkin-0.9-39/mkin/inst/doc/compiled_models.Rmd |only mkin-0.9-39/mkin/inst/doc/compiled_models.html |only mkin-0.9-39/mkin/vignettes/compiled_models.Rmd |only mkin-0.9-40/mkin/DESCRIPTION | 13 - mkin-0.9-40/mkin/MD5 | 166 +++++++++++++++------ mkin-0.9-40/mkin/NAMESPACE | 6 mkin-0.9-40/mkin/NEWS.md | 12 + mkin-0.9-40/mkin/R/endpoints.R | 45 +++-- mkin-0.9-40/mkin/R/mkin_wide_to_long.R | 2 mkin-0.9-40/mkin/R/mkinfit.R | 4 mkin-0.9-40/mkin/README.md | 97 ++---------- mkin-0.9-40/mkin/build/vignette.rds |binary mkin-0.9-40/mkin/inst/doc/FOCUS_D.R | 22 -- mkin-0.9-40/mkin/inst/doc/FOCUS_D.html | 20 +- mkin-0.9-40/mkin/inst/doc/FOCUS_L.R | 97 ------------ mkin-0.9-40/mkin/inst/doc/FOCUS_L.html | 88 +++++------ mkin-0.9-40/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-40/mkin/inst/doc/mkin.pdf |binary mkin-0.9-40/mkin/man/DFOP.solution.Rd | 3 mkin-0.9-40/mkin/man/Extract.mmkin.Rd | 5 mkin-0.9-40/mkin/man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 1 mkin-0.9-40/mkin/man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 1 mkin-0.9-40/mkin/man/FOCUS_2006_HS_ref_A_to_F.Rd | 1 mkin-0.9-40/mkin/man/FOCUS_2006_SFO_ref_A_to_F.Rd | 1 mkin-0.9-40/mkin/man/FOCUS_2006_datasets.Rd | 1 mkin-0.9-40/mkin/man/FOMC.solution.Rd | 1 mkin-0.9-40/mkin/man/HS.solution.Rd | 1 mkin-0.9-40/mkin/man/IORE.solution.Rd | 1 mkin-0.9-40/mkin/man/SFO.solution.Rd | 1 mkin-0.9-40/mkin/man/SFORB.solution.Rd | 1 mkin-0.9-40/mkin/man/geometric_mean.Rd | 1 mkin-0.9-40/mkin/man/mccall81_245T.Rd | 2 mkin-0.9-40/mkin/man/mkinerrmin.Rd | 1 mkin-0.9-40/mkin/man/mkinfit.Rd | 7 mkin-0.9-40/mkin/man/mkinresplot.Rd | 2 mkin-0.9-40/mkin/man/mmkin.Rd | 7 mkin-0.9-40/mkin/man/plot.mkinfit.Rd | 4 mkin-0.9-40/mkin/man/plot.mmkin.Rd | 4 mkin-0.9-40/mkin/man/schaefer07_complex_case.Rd | 5 mkin-0.9-40/mkin/man/summary.mkinfit.Rd | 4 mkin-0.9-40/mkin/man/transform_odeparms.Rd | 2 mkin-0.9-40/mkin/vignettes/FOCUS_D_cache |only mkin-0.9-40/mkin/vignettes/FOCUS_D_files |only mkin-0.9-40/mkin/vignettes/FOCUS_L_cache |only mkin-0.9-40/mkin/vignettes/FOCUS_L_files |only mkin-0.9-40/mkin/vignettes/compiled_models.html |only 47 files changed, 279 insertions(+), 350 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.0.2 dated 2015-06-18 and 0.0.3 dated 2015-07-21
DESCRIPTION | 10 +++--- MD5 | 24 +++++++-------- NAMESPACE | 5 +++ R/kdecop.R | 7 ++-- inst/include/hfunc.h | 2 - inst/include/integrate.h | 4 +- inst/include/interp.h | 2 - man/kdecopula-package.Rd | 4 +- src/RcppExports.cpp | 16 +++++----- src/hfunc.cpp | 28 +++++++++++------- src/integrate.cpp | 6 +-- src/interp.cpp | 73 +++++++++++++++++++++++++++-------------------- src/renorm.cpp | 51 ++++++++++++++++++++++---------- 13 files changed, 139 insertions(+), 93 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.2 dated 2015-07-17 and 0.3.3 dated 2015-07-21
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mlp_prune.R | 20 ++++++++++---------- R/mlp_teach.R | 10 +++++----- man/mlp_prune_mag.Rd | 2 +- man/mlp_prune_obs.Rd | 2 +- src/fcnn/struct.cpp | 15 ++++++++------- src/fcnn/utils.cpp | 51 ++++++++++++++++++++++++++------------------------- 8 files changed, 62 insertions(+), 60 deletions(-)
Title: Tools for Ecological Network Analysis
Description: Provides algorithms for the analysis of ecological networks.
Author: M.K. Lau, S.R. Borrett, D.E. Hines, P. Singh
Maintainer: Matthew K. Lau <enaR.maintainer@gmail.com>
Diff between enaR versions 2.8.1 dated 2015-01-14 and 2.9 dated 2015-07-21
DESCRIPTION | 15 ++++++++------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 8 ++++++++ R/pack.R | 31 ++++++++++++++++++++++--------- R/read.wand.R | 2 +- R/write.EcoNet.R |only build/vignette.rds |binary data/bgcModels.rda |binary data/enaModelInfo.rda |binary data/enaModels.rda |binary data/oyster.rda |binary data/troModels.rda |binary inst/doc/enaR-vignette.pdf |binary man/write.EcoNet.Rd |only man/write.nea.Rd | 2 +- 15 files changed, 54 insertions(+), 30 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.0.2 dated 2015-06-19 and 2.0.3 dated 2015-07-21
ChangeLog | 10 +++++----- DESCRIPTION | 12 ++++++------ MD5 | 21 +++++++++++---------- NAMESPACE | 14 +++++++++----- inst/NEWS.Rd |only inst/po/de/LC_MESSAGES/R-cluster.mo |binary inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary inst/po/en@quot/LC_MESSAGES/cluster.mo |binary po/R-cluster.pot | 4 ++-- po/R-de.po | 4 ++-- po/cluster.pot | 4 ++-- po/update-me.sh | 9 ++++++--- 12 files changed, 43 insertions(+), 35 deletions(-)
Title: Modelization for Functional AutoRegressive Processes
Description: Modelizations and previsions functions for
Functional AutoRegressive processes using
nonparametric methods: functional kernel,
estimation of the covariance operator in
a subspace, ...
Author: Damon Julien <julien.damon@gmail.com>
Guillas Serge
Maintainer: Damon Julien <julien.damon@gmail.com>
Diff between far versions 0.6-4 dated 2014-12-08 and 0.6-5 dated 2015-07-20
far-0.6-4/far/INDEX |only far-0.6-5/far/DESCRIPTION | 20 +++++----- far-0.6-5/far/MD5 | 22 +++++------ far-0.6-5/far/NAMESPACE | 69 +++++++++++++++++------------------ far-0.6-5/far/R/far.R | 4 +- far-0.6-5/far/R/fdata.R | 4 +- far-0.6-5/far/R/invgen.R | 4 +- far-0.6-5/far/R/kerfon.R | 4 +- far-0.6-5/far/R/orthonormalization.R | 4 +- far-0.6-5/far/R/simul.R | 4 +- far-0.6-5/far/R/zzz.R | 4 +- far-0.6-5/far/README.md |only far-0.6-5/far/src/far.c | 2 - 13 files changed, 71 insertions(+), 70 deletions(-)
Title: Data Quality Visualization Tools for Partially Accruing Data
Description: Package for visualizing data quality of partially accruing data.
Author: Julie Eaton and Ian Painter
Maintainer: Julie Eaton <jreaton@uw.edu>
Diff between accrued versions 1.3 dated 2015-06-23 and 1.3.5 dated 2015-07-20
DESCRIPTION | 8 ++--- MD5 | 60 +++++++++++++++++++++---------------------- NAMESPACE | 5 ++- R/accruedErrors.R | 2 - R/asOf.R | 2 - R/barcode.R | 2 - R/data.accrued.R | 2 - R/lagHistogram.R | 2 - R/laggedTSarray.R | 2 - R/plot.accrued.R | 2 - R/summary.accrued.R | 2 - R/uploadPattern.R | 2 - man/accrued-package.Rd | 4 +- man/accruedDataExample.Rd | 2 - man/accruedDataILIExample.Rd | 2 - man/accruedErrors.Rd | 2 - man/asOf.Rd | 4 -- man/barcode.Rd | 8 ++--- man/data.accrued.Rd | 8 ++--- man/errorQuantileSummary.Rd | 2 - man/lagHistogram.Rd | 2 - man/laggedTSarray.Rd | 4 +- man/plot.accrued.Rd | 2 - man/plot.accruedErrors.Rd | 2 - man/plot.summary.accrued.Rd | 2 - man/print.accrued.Rd | 2 - man/print.summary.accrued.Rd | 2 - man/stackedUploadData.Rd | 2 - man/summary.accrued.Rd | 2 - man/summary.accruedErrors.Rd | 2 - man/uploadPattern.Rd | 2 - 31 files changed, 74 insertions(+), 73 deletions(-)
Title: Robust Tail Dependence Estimation
Description: Robust tail dependence estimation for bivariate models. This package is based on two papers by the authors:'Robust and bias-corrected estimation of the coefficient of tail dependence' and 'Robust and bias-corrected estimation of probabilities of extreme failure sets'. This work was supported by a research grant (VKR023480) from VILLUM FONDEN and an international project for scientific cooperation (PICS-6416).
Author: Christophe Dutang [aut, cre], Armelle Guillou [ctb], Yuri Goegebeur [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between RTDE versions 0.1-0 dated 2014-07-17 and 0.2-0 dated 2015-07-20
DESCRIPTION | 10 ++++------ MD5 | 14 +++++++------- NAMESPACE | 34 +++++++++++++++++++--------------- R/data-fit-probRTDE.R | 6 ++++-- inst/CITATION | 19 ++++++++----------- inst/NEWS | 5 +++++ man/Frank.Rd | 2 +- tests/test-FGM.R | 32 +++++++++++++++++++++++++------- 8 files changed, 73 insertions(+), 49 deletions(-)
Title: Analysis of Ontologies and Protein Domain Annotations
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dcGOR versions 1.0.4 dated 2014-12-03 and 1.0.5 dated 2015-07-20
DESCRIPTION | 16 - MD5 | 221 ++++++++++--------- NAMESPACE | 7 R/ClassMethod-dcGOR.r | 4 R/dcAlgo.r | 68 ++++-- R/dcAlgoPredict.r | 8 R/dcAlgoPredictGenome.r | 25 +- R/dcAlgoPredictMain.r | 31 ++ R/dcAlgoPredictPR.r |only R/dcAlgoPropagate.r | 376 ++++++++++++++++++++++------------ R/dcBuildAnno.r | 8 R/dcBuildInfoDataFrame.r | 2 R/dcBuildOnto.r | 4 R/dcDAGdomainSim.r | 16 - R/dcFunArgs.r | 17 + R/dcList2Matrix.r |only R/dcNaivePredict.r |only R/dcRDataLoader.r | 2 R/dcRWRpipeline.r | 38 +-- R/dcRWRpredict.r |only R/dcSparseMatrix.r | 21 + R/dcSupraBetter.r |only data/Ancestral_domainome.RData |binary data/InterPro.RData |binary data/InterPro2GOBP.RData |binary data/InterPro2GOCC.RData |binary data/InterPro2GOMF.RData |binary data/Pfam.RData |binary data/Pfam2GOBP.RData |binary data/Pfam2GOCC.RData |binary data/Pfam2GOMF.RData |binary data/Rfam.RData |binary data/Rfam2GOBP.RData |binary data/Rfam2GOCC.RData |binary data/Rfam2GOMF.RData |binary data/SCOP.fa.RData |binary data/SCOP.fa2DO.RData |binary data/SCOP.fa2GOBP.RData |binary data/SCOP.fa2GOCC.RData |binary data/SCOP.fa2GOMF.RData |binary data/SCOP.fa2HPMI.RData |binary data/SCOP.fa2HPON.RData |binary data/SCOP.fa2HPPA.RData |binary data/SCOP.fa2MP.RData |binary data/SCOP.sf.RData |binary data/SCOP.sf2DO.RData |binary data/SCOP.sf2GOBP.RData |binary data/SCOP.sf2GOCC.RData |binary data/SCOP.sf2GOMF.RData |binary data/SCOP.sf2HPMI.RData |binary data/SCOP.sf2HPON.RData |binary data/SCOP.sf2HPPA.RData |binary data/SCOP.sf2MP.RData |binary data/eTOL.RData |binary data/onto.DO.RData |binary data/onto.GOBP.RData |binary data/onto.GOCC.RData |binary data/onto.GOMF.RData |binary data/onto.HPMI.RData |binary data/onto.HPON.RData |binary data/onto.HPPA.RData |binary data/onto.MP.RData |binary inst/NEWS | 10 inst/staticdocs/INSTALLATIONs.md | 20 - inst/staticdocs/README.md | 2 inst/staticdocs/demo/AlgoPred.r |only inst/staticdocs/demo/List_demos.txt | 1 inst/staticdocs/docs.r | 7 inst/staticdocs/templates/footer.html | 2 man/AdjData-class.Rd | 3 man/Anno-class.Rd | 3 man/Anno-method.Rd | 3 man/AnnoData-class.Rd | 3 man/Cnetwork-class.Rd | 3 man/Cnetwork-method.Rd | 3 man/Coutput-class.Rd | 3 man/Coutput-method.Rd | 3 man/Dnetwork-class.Rd | 3 man/Dnetwork-method.Rd | 3 man/Eoutput-class.Rd | 3 man/Eoutput-method.Rd | 3 man/InfoDataFrame-class.Rd | 3 man/InfoDataFrame-method.Rd | 3 man/Onto-class.Rd | 3 man/Onto-method.Rd | 3 man/dcAlgo.Rd | 15 - man/dcAlgoPredict.Rd | 3 man/dcAlgoPredictGenome.Rd | 3 man/dcAlgoPredictMain.Rd | 3 man/dcAlgoPredictPR.Rd |only man/dcAlgoPropagate.Rd | 66 +++-- man/dcAncestralML.Rd | 3 man/dcAncestralMP.Rd | 3 man/dcBuildAnno.Rd | 3 man/dcBuildInfoDataFrame.Rd | 3 man/dcBuildOnto.Rd | 3 man/dcConverter.Rd | 3 man/dcDAGannotate.Rd | 3 man/dcDAGdomainSim.Rd | 3 man/dcDuplicated.Rd | 3 man/dcEnrichment.Rd | 3 man/dcFunArgs.Rd | 9 man/dcList2Matrix.Rd |only man/dcNaivePredict.Rd |only man/dcRDataLoader.Rd | 3 man/dcRWRpipeline.Rd | 3 man/dcRWRpredict.Rd |only man/dcSparseMatrix.Rd | 3 man/dcSplitArch.Rd | 3 man/dcSubtreeClade.Rd | 3 man/dcSubtreeTips.Rd | 3 man/dcSupraBetter.Rd |only man/dcTreeConnectivity.Rd | 3 man/onto.HPMI.Rd | 3 man/onto.HPON.Rd | 3 man/onto.HPPA.Rd | 3 man/visEnrichment.Rd | 3 117 files changed, 702 insertions(+), 414 deletions(-)
Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-24 dated 2015-05-16 and 1.0-26 dated 2015-07-20
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 5 +++++ NEWS | 8 +++++++- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Variance Component Analysis
Description: ANOVA-type estimation (prediction) of random effects in linear mixed models is implemented, following
Searle et al. 1991 (ANOVA for unbalanced data). For better performance the SWEEP-Operator is now implemented
for generating the ANOVA Type-1 error sum of squares. The primary objective of this package is to perform
Variance Component Analyses (VCA). This is a special type of analysis frequently used in verifying the
precision performance of diagnostics.
The Satterthwaite approximation of the total degrees of freedom and for individual variance components is
implemented. These are used in the Chi-Squared tests against a claimed value, and in the respective confidence intervals.
Satterthwaite's approximation of denominator degrees of freedom in t-/F-tests of fixed effects are also
available.
There are several functions for extracting, random effects, fixed effects, variance-covariance
matrices of random and fixed effects. Residuals (marginal, conditional) can be extracted as raw, standardized
and studentized residuals.
Additionally, plotting methods for residuals and random effects and a variability chart are available. The latter
is useful for visualizing the variability in sub-classes emerging from the experimental design.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.1.1 dated 2015-04-27 and 1.2 dated 2015-07-20
VCA-1.1.1/VCA/data/dataEP05A2_example.RData |only VCA-1.1.1/VCA/man/dataEP05A2_example.Rd |only VCA-1.1.1/VCA/man/solveMM.Rd |only VCA-1.2/VCA/DESCRIPTION | 33 VCA-1.2/VCA/MD5 | 113 +- VCA-1.2/VCA/NAMESPACE | 23 VCA-1.2/VCA/R/plot.R | 350 ++++++- VCA-1.2/VCA/R/vca.R | 1135 ++++++++++++++++++------ VCA-1.2/VCA/data/CA19_9.RData |only VCA-1.2/VCA/data/Glucose.RData |only VCA-1.2/VCA/data/sleepstudy.RData |only VCA-1.2/VCA/inst/ChangeLog.txt | 29 VCA-1.2/VCA/inst/UnitTests/runit.VCAinference.R | 84 + VCA-1.2/VCA/inst/UnitTests/runit.anovaMM.R | 11 VCA-1.2/VCA/inst/UnitTests/runit.anovaVCA.R | 74 + VCA-1.2/VCA/inst/UnitTests/runit.misc.R | 88 + VCA-1.2/VCA/man/CA19_9.Rd |only VCA-1.2/VCA/man/Csweep.Rd |only VCA-1.2/VCA/man/DfSattHelper.Rd | 15 VCA-1.2/VCA/man/Glucose.Rd |only VCA-1.2/VCA/man/MPinv.Rd | 15 VCA-1.2/VCA/man/SattDF.Rd | 47 VCA-1.2/VCA/man/Sinv.Rd |only VCA-1.2/VCA/man/Solve.Rd |only VCA-1.2/VCA/man/Trace.Rd | 7 VCA-1.2/VCA/man/VCA-Package.Rd | 4 VCA-1.2/VCA/man/VCAinference.Rd | 246 ++--- VCA-1.2/VCA/man/anovaDF.Rd | 68 - VCA-1.2/VCA/man/anovaMM.Rd | 188 +-- VCA-1.2/VCA/man/anovaVCA.Rd | 247 ++--- VCA-1.2/VCA/man/as.matrix.VCA.Rd | 12 VCA-1.2/VCA/man/buildList.Rd | 101 -- VCA-1.2/VCA/man/coef.VCA.Rd | 14 VCA-1.2/VCA/man/fixef.Rd | 12 VCA-1.2/VCA/man/fixef.VCA.Rd | 52 - VCA-1.2/VCA/man/getAmatrix.Rd | 29 VCA-1.2/VCA/man/getCmatrix.Rd | 94 - VCA-1.2/VCA/man/getDDFM.Rd | 57 - VCA-1.2/VCA/man/getDF.Rd | 33 VCA-1.2/VCA/man/getL.Rd | 36 VCA-1.2/VCA/man/getMM.Rd | 30 VCA-1.2/VCA/man/getMat.Rd | 22 VCA-1.2/VCA/man/getSSQqf.Rd |only VCA-1.2/VCA/man/getSSQsweep.Rd |only VCA-1.2/VCA/man/getV.Rd | 27 VCA-1.2/VCA/man/getVCvar.Rd | 40 VCA-1.2/VCA/man/isBalanced.Rd | 53 - VCA-1.2/VCA/man/lsmMat.Rd | 28 VCA-1.2/VCA/man/lsmeans.Rd | 78 - VCA-1.2/VCA/man/plotRandVar.Rd | 86 - VCA-1.2/VCA/man/print.VCA.Rd | 14 VCA-1.2/VCA/man/print.VCAinference.Rd | 36 VCA-1.2/VCA/man/ranef.Rd | 12 VCA-1.2/VCA/man/ranef.VCA.Rd | 53 - VCA-1.2/VCA/man/residuals.VCA.Rd | 98 -- VCA-1.2/VCA/man/sleepstudy.Rd |only VCA-1.2/VCA/man/solveMME.Rd |only VCA-1.2/VCA/man/stepwiseVCA.Rd | 61 - VCA-1.2/VCA/man/test.fixef.Rd | 109 -- VCA-1.2/VCA/man/test.lsmeans.Rd | 35 VCA-1.2/VCA/man/varPlot.Rd | 311 ++---- VCA-1.2/VCA/man/vcov.VCA.Rd | 28 VCA-1.2/VCA/man/vcovFixed.Rd | 24 VCA-1.2/VCA/man/vcovVC.Rd | 51 - VCA-1.2/VCA/src/vca.c | 381 +++++++- 65 files changed, 2972 insertions(+), 1822 deletions(-)
Title: Tsallis q-Exp Distribution
Description: Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Author: Cosma Shalizi [aut] (original R code), Christophe Dutang [cre] (R code packaging)
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between tsallisqexp versions 0.9-1 dated 2015-03-17 and 0.9-2 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 5 +++-- build/vignette.rds |binary inst/CITATION | 24 ++++++++++++------------ inst/NEWS | 8 +++++++- inst/doc/qexpfamily.pdf |binary 7 files changed, 31 insertions(+), 24 deletions(-)
Title: SBML Integration in Package Sybil
Description: SBML (Systems Biology Markup Language) integration in sybil. Many constraint based metabolic models are published in SBML format (*.xml). Herewith is the ability to read and check SBML files in sybil provided.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
Deya Alzoubi [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybilSBML versions 2.0.8 dated 2014-05-21 and 2.0.10 dated 2015-07-20
DESCRIPTION | 22 ++++++++-------- LICENSE |only MD5 | 52 +++++++++++++++++++------------------- README.md |only build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/sybilSBML.pdf |binary man/closeSBMLfile.Rd | 7 ++++- man/delSBMLmodel.Rd | 7 ++++- man/getSBMLCompartList.Rd | 7 ++++- man/getSBMLReactionsList.Rd | 7 ++++- man/getSBMLSpeciesList.Rd | 7 ++++- man/getSBMLerrors.Rd | 7 ++++- man/getSBMLlevel.Rd | 7 ++++- man/getSBMLmodId.Rd | 7 ++++- man/getSBMLmodName.Rd | 7 ++++- man/getSBMLmodel.Rd | 7 ++++- man/getSBMLnumCompart.Rd | 7 ++++- man/getSBMLnumReactions.Rd | 7 ++++- man/getSBMLnumSpecies.Rd | 7 ++++- man/getSBMLunitDefinitionsList.Rd | 7 ++++- man/getSBMLversion.Rd | 7 ++++- man/openSBMLfile.Rd | 7 ++++- man/readSBMLmod.Rd | 5 ++- man/sbmlError-class.Rd | 7 ++++- man/sbmlPtr-class.Rd | 7 ++++- man/validateSBMLdocument.Rd | 7 ++++- man/versionLibSBML.Rd | 7 ++++- 28 files changed, 170 insertions(+), 56 deletions(-)
Title: Simple GUI for Graph Based Visualization of Cluster of DNA
Sequence Reads
Description: The SeqGrapheR package provide interactive GUI for visualization of DNA sequence clusters. Details and principles of usage are described in user manual and (2010 BMC Bioinformatics 11:378). For full functionality installed NCBI blast is required.
Author: Petr Novak
Maintainer: Petr Novak <petr@umbr.cas.cz>
Diff between SeqGrapheR versions 0.4.8.3 dated 2013-08-19 and 0.4.8.5 dated 2015-07-20
DESCRIPTION | 15 ++++---- MD5 | 10 ++--- NAMESPACE | 61 ++++++++++++++++++++--------------- R/SeqGrapheR.R | 79 ++++++++++++++++++++++++++++++++-------------- man/SeqGrapheR-package.Rd | 15 ++++---- man/SeqGrapheR.Rd | 14 ++++---- 6 files changed, 117 insertions(+), 77 deletions(-)
Title: Side Effect Risks in Hospital : Simulation and Estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between rhosp versions 1.06 dated 2014-12-05 and 1.07 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 14 ++++++++++---- build/vignette.rds |binary inst/CITATION | 6 +++--- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments (psychophysical tasks aimed at visualizing cognitive mental representations of faces).
Author: Ron Dotsch <rdotsch@gmail.com>
Maintainer: Ron Dotsch <rdotsch@gmail.com>
Diff between rcicr versions 0.3.0 dated 2015-01-23 and 0.3.2 dated 2015-07-20
ChangeLog | 32 +++ DESCRIPTION | 18 +- MD5 | 35 ++-- NAMESPACE | 14 + R/rcicr.R | 293 +++++++++++++++++++++++++++++++++- R/rcicr_2IFC.R | 132 +++------------ R/rcicr_simulations.R | 13 + man/autoscale.Rd | 7 man/batchGenerateCI.Rd |only man/batchGenerateCI2IFC.Rd | 13 + man/computeCumulativeCICorrelation.Rd |only man/generateCI.Rd | 52 ++++-- man/generateCI2IFC.Rd | 10 - man/generateCINoise.Rd |only man/generateNoiseImage.Rd | 9 - man/generateNoisePattern.Rd | 3 man/generateSinusoid.Rd | 3 man/generateStimuli2IFC.Rd | 3 man/rcicr-package.Rd | 8 man/simulateNoiseIntensities.Rd | 5 20 files changed, 482 insertions(+), 168 deletions(-)
Title: Principal Tensor Analysis on k Modes
Description: A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.
Author: Didier G. Leibovici <didier.leibovici@nottingham.ac.uk>
Maintainer: Didier G. Leibovici <c3s2i@free.fr>
Diff between PTAk versions 1.2-9 dated 2014-08-17 and 1.2-12 dated 2015-07-20
PTAk-1.2-12/PTAk/DESCRIPTION | 15 ++++++++------- PTAk-1.2-12/PTAk/MD5 | 9 ++++----- PTAk-1.2-12/PTAk/NAMESPACE | 12 +++++++----- PTAk-1.2-12/PTAk/inst/CITATION | 6 +++--- PTAk-1.2-12/PTAk/inst/doc/index.html | 10 +++++----- PTAk-1.2-9/PTAk/inst/doc/citation.html |only 6 files changed, 27 insertions(+), 25 deletions(-)
Title: Vignette Engine Wrapping IPython Notebooks
Description:
Calls the 'Jupyter'/'IPython' script 'nbconvert' to create vignettes from notebooks.
Those notebooks ('.ipynb' files) are files containing rich text, code, and its output.
Code cells can be edited and evaluated interactively.
See <http://ipython.org/notebook.html> for more information.
Author: Philipp Angerer
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
Diff between nbconvertR versions 1.0.1 dated 2015-07-08 and 1.0.2 dated 2015-07-20
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS |only R/nbconvertR.r | 26 ++++++++++++++++++++++---- inst/doc/test-vignette.pdf |binary 5 files changed, 29 insertions(+), 10 deletions(-)
Title: The Gumbel-Hougaard Copula
Description: Provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Anne-Lise Caillat [ctb], Christophe Dutang [aut,cre], Veronique Larrieu [ctb] and Triet Nguyen [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between gumbel versions 1.05 dated 2014-12-05 and 1.10-1 dated 2015-07-20
gumbel-1.05/gumbel/vignettes/img |only gumbel-1.10-1/gumbel/DESCRIPTION | 12 +- gumbel-1.10-1/gumbel/MD5 | 29 ++--- gumbel-1.10-1/gumbel/NAMESPACE | 4 gumbel-1.10-1/gumbel/R/gumbel.R | 2 gumbel-1.10-1/gumbel/build/vignette.rds |binary gumbel-1.10-1/gumbel/data/windEchirolles.rda |binary gumbel-1.10-1/gumbel/data/windStMartin.rda |binary gumbel-1.10-1/gumbel/inst/CITATION | 9 - gumbel-1.10-1/gumbel/inst/doc/gumbel.Rnw | 93 ++++++++---------- gumbel-1.10-1/gumbel/inst/doc/gumbel.pdf |binary gumbel-1.10-1/gumbel/vignettes/gumbel-concordance.tex |only gumbel-1.10-1/gumbel/vignettes/gumbel.Rnw | 93 ++++++++---------- gumbel-1.10-1/gumbel/vignettes/gumbel.tex |only 14 files changed, 115 insertions(+), 127 deletions(-)
Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between GSIF versions 0.4-6 dated 2015-05-11 and 0.4-7 dated 2015-07-20
DESCRIPTION | 10 +++--- MD5 | 40 ++++++++++++++------------ NAMESPACE | 52 ++++++++++++++++++---------------- R/AAAA.R | 69 ++++++++++++++++++++++++---------------------- R/MaxEnt.R | 2 - R/TT2tri.R | 4 +- R/WPSworldgrids.R | 6 ++-- R/as.geosamples.R | 2 - R/fit.gstatModel.R | 41 ++++++++++++++++----------- R/fit.regModel.R | 14 ++++----- R/fit.vgmModel.R | 3 +- R/merge.R | 34 +++++++++++----------- R/predict.gstatModel.R | 27 +++++++++--------- R/sample.grid.R |only R/spc.R | 4 +- man/MaxEnt.Rd | 3 +- man/fit.gstatModel.Rd | 16 +++++----- man/fit.regModel.Rd | 7 ++-- man/fit.vgmModel.Rd | 2 - man/predict.gstatModel.Rd | 4 +- man/sample.grid.Rd |only man/spline.krige.Rd | 2 - 22 files changed, 180 insertions(+), 162 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. Optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between GNE versions 0.99-0 dated 2014-07-31 and 0.99-1 dated 2015-07-20
DESCRIPTION | 11 +++++------ MD5 | 17 +++++++++-------- NAMESPACE | 5 +++++ build/vignette.rds |binary inst/NEWS | 6 ++++++ inst/TODOlist.txt | 2 ++ inst/doc/GNE-howto.Rnw | 11 +---------- inst/doc/GNE-howto.pdf |binary man/eqsolve.depr.Rd |only vignettes/GNE-howto.Rnw | 11 +---------- 10 files changed, 29 insertions(+), 34 deletions(-)
Title: Predicting and Forecasting Time Series via GMDH-Type Neural
Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to predict and forecast a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH versions 1.0 dated 2014-11-25 and 1.1 dated 2015-07-20
DESCRIPTION | 11 ++++--- MD5 | 12 ++++---- NAMESPACE | 13 +++++++- R/fcast.R | 87 ++++++++++++++++++++++++++++++++++++++++++++++------------ man/GMDH.Rd | 7 +--- man/cancer.Rd | 2 - man/fcast.Rd | 10 +++--- 7 files changed, 100 insertions(+), 42 deletions(-)
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (planned inclusion of memory profiling in the next major release)
in a visually appealing way. It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.2.4 dated 2014-11-20 and 0.2.5 dated 2015-07-20
DESCRIPTION | 25 +- MD5 | 23 +- NAMESPACE | 2 R/aprof.R | 461 +++++++++++++++++++++++++------------------------ inst |only man/aprof.Rd | 15 + man/is.aprof.Rd | 3 man/plot.Rd | 11 - man/print.Rd | 3 man/profileplot.Rd | 3 man/readLineDensity.Rd | 3 man/summary.Rd | 3 man/targetedSummary.Rd | 3 13 files changed, 292 insertions(+), 263 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.5 dated 2015-07-16 and 1.5.6 dated 2015-07-20
DESCRIPTION | 6 +-- MD5 | 12 +++--- src/data_frame.h | 18 ---------- src/extptr.h | 33 +++++++++--------- src/grange.h | 5 +- src/gtf.h | 60 ++++++++++++++++----------------- src/tokenize.h | 99 +++++++++++++++++++++++++++---------------------------- 7 files changed, 107 insertions(+), 126 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using MCMC.
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.6.1 dated 2014-12-04 and 0.6.2 dated 2015-07-20
bsts-0.6.1/bsts/R/plot_dynamic_distribution.R |only bsts-0.6.1/bsts/man/PlotDynamicDistribution.Rd |only bsts-0.6.1/bsts/man/plot.seasonal.effect.Rd |only bsts-0.6.2/bsts/DESCRIPTION | 9 - bsts-0.6.2/bsts/MD5 | 36 ++-- bsts-0.6.2/bsts/NAMESPACE | 12 + bsts-0.6.2/bsts/R/add.seasonal.R | 8 - bsts-0.6.2/bsts/R/bsts.R | 178 ++++++++++++++--------- bsts-0.6.2/bsts/R/compare.bsts.models.R | 3 bsts-0.6.2/bsts/R/mixed.frequency.R | 46 ++--- bsts-0.6.2/bsts/R/plot.dynamic.distribution.R |only bsts-0.6.2/bsts/R/plot_seasonal_effect.R | 57 ++++--- bsts-0.6.2/bsts/data/iclaims.RData |only bsts-0.6.2/bsts/man/bsts.Rd | 13 + bsts-0.6.2/bsts/man/iclaims.Rd |only bsts-0.6.2/bsts/man/plot.bsts.Rd | 35 ++++ bsts-0.6.2/bsts/man/plot.bsts.mixed.Rd | 4 bsts-0.6.2/bsts/man/plot.bsts.prediction.Rd | 10 - bsts-0.6.2/bsts/man/plot.bsts.predictors.Rd | 2 bsts-0.6.2/bsts/man/plot.dynamic.distribution.Rd |only bsts-0.6.2/bsts/man/residuals.bsts.Rd |only bsts-0.6.2/bsts/src/btlm.cc | 4 bsts-0.6.2/bsts/src/state_space.cc | 1 23 files changed, 272 insertions(+), 146 deletions(-)
Title: R Version of GENetic Optimization Using Derivatives
Description: A genetic algorithm plus derivative optimizer.
Author: Walter R. Mebane, Jr. <wmebane@umich.edu>,
Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Diff between rgenoud versions 5.7-12 dated 2013-06-28 and 5.7-12.4 dated 2015-07-20
rgenoud-5.7-12.4/rgenoud/ChangeLog | 12 +++++ rgenoud-5.7-12.4/rgenoud/DESCRIPTION | 19 ++++--- rgenoud-5.7-12.4/rgenoud/MD5 | 20 ++++---- rgenoud-5.7-12.4/rgenoud/R/rgenoud.R | 60 +++++++++++++++---------- rgenoud-5.7-12.4/rgenoud/R/zzz.R | 4 - rgenoud-5.7-12.4/rgenoud/build |only rgenoud-5.7-12.4/rgenoud/inst/doc/Figures |only rgenoud-5.7-12.4/rgenoud/inst/doc/rgenoud.bib |only rgenoud-5.7-12.4/rgenoud/inst/doc/rgenoud.pdf |binary rgenoud-5.7-12.4/rgenoud/tests/tests.R | 2 rgenoud-5.7-12.4/rgenoud/tests/tests.Rout.save | 19 ++----- rgenoud-5.7-12/rgenoud/COPYING |only rgenoud-5.7-12/rgenoud/COPYRIGHTS |only 13 files changed, 77 insertions(+), 59 deletions(-)
Title: Person Fit
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <j.n.tendeiro@rug.nl>
Diff between PerFit versions 1.3.1 dated 2015-03-18 and 1.4 dated 2015-07-20
DESCRIPTION | 17 +--- MD5 | 100 +++++++++++------------ NAMESPACE | 2 R/ADE.R | 46 +++++++--- R/Accessory.R | 113 +++++++++++++++----------- R/C.Sato.R | 19 ++-- R/Cstar.R | 24 ++++- R/Cutoff.R | 36 ++++---- R/Flagged.R | 26 +++--- R/G.R | 15 +-- R/Gnormed.R | 18 ++-- R/Gnormedpoly.R | 94 ++++++++++++++++------ R/Gpoly.R | 14 +-- R/Hotdeck.R | 24 ++--- R/Ht.R | 25 +++-- R/MissingValues.R | 8 + R/NCI.R | 20 ++-- R/NPModel.R | 27 +++--- R/NPModelPoly.R | 32 +++---- R/PModel.R | 12 +- R/PModelPoly.R | 10 +- R/PRF.R | 70 +++++++++------- R/PerFitPFS.R | 180 +++++++++++++++++++++--------------------- R/PerFitSE.R | 15 +-- R/PlotPerFit.R | 38 ++++---- R/SanityChecks.R | 40 ++++----- R/SummaryPerFit.R | 2 R/U3.R | 36 ++++++-- R/U3poly.R | 119 +++++++++++++++++++++------- R/ZU3.R | 41 +++++++-- R/lz.R | 14 +-- R/lzpoly.R | 18 +--- R/lzstar.R | 29 +++--- R/rpbis.R | 7 - data/InadequacyData.RData |binary data/IntelligenceData.RData |binary data/PhysFuncData.RData |binary man/ADE.KB.Rd | 10 +- man/C.index.Rd | 184 +++++++++++++++++++++---------------------- man/G.Rd | 186 ++++++++++++++++++++++---------------------- man/Gpoly.Rd | 180 +++++++++++++++++++++--------------------- man/Ht.Rd | 172 ++++++++++++++++++++-------------------- man/NCI.Rd | 160 ++++++++++++++++++------------------- man/PRFplot.Rd | 8 - man/PerFit-package.Rd | 11 ++ man/PerFitPFS.Rd | 4 man/U3.Rd | 186 ++++++++++++++++++++++---------------------- man/U3poly.Rd | 6 - man/lz.Rd | 8 - man/lzpoly.Rd | 164 +++++++++++++++++++------------------- man/r.pbis.Rd | 146 +++++++++++++++++----------------- 51 files changed, 1472 insertions(+), 1244 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.5 dated 2015-06-26 and 1.2.7 dated 2015-07-20
DESCRIPTION | 10 ++-- MD5 | 14 +++--- NAMESPACE | 11 ++++ NEWS | 9 +++ R/Utilities.R | 93 +++++++++++++++++++++++++++++++++++++---- R/user_functions.R | 7 +-- src/icenReg_files/ic_par.cpp | 10 ++-- src/icenReg_files/ic_sp_ch.cpp | 8 +-- 8 files changed, 131 insertions(+), 31 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: Maximum likelihood estimators are obtained via an EM algorithm.
Author: Andrew Karl, Yan Yang, and Sharon Lohr
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.0-2 dated 2014-06-22 and 3.0-3 dated 2015-07-20
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 6 +++++- NEWS | 3 +++ man/GPvam-package.Rd | 4 ++-- man/GPvam.Rd | 7 ++++--- man/plot.Rd | 11 ++++++++--- 7 files changed, 36 insertions(+), 23 deletions(-)
Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between GLSME versions 1.0.2 dated 2014-08-20 and 1.0.3 dated 2015-07-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 11 ++++++----- R/GLSME.R | 6 +++++- 4 files changed, 18 insertions(+), 13 deletions(-)
Title: Temperature Measurement with Thermocouples, RTD and IC Sensors
Description: Temperature measurement data, equations and methods for thermocouples,
wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Diff between thermocouple versions 1.0.0 dated 2014-12-08 and 1.0.2 dated 2015-07-19
thermocouple-1.0.0/thermocouple/data/ErrorLimitsThermocouples.rda |only thermocouple-1.0.0/thermocouple/data/NominalSeebeckCoefficients.rda |only thermocouple-1.0.0/thermocouple/data/PT100.rda |only thermocouple-1.0.0/thermocouple/data/PT1000.rda |only thermocouple-1.0.0/thermocouple/data/TemperatureDataDS18B20.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeB.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeE.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeJ.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeK.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeN.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeR.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeS.rda |only thermocouple-1.0.0/thermocouple/data/coefficientsThermocoupleTypeT.rda |only thermocouple-1.0.0/thermocouple/data/definitionThermocoupleTypes.rda |only thermocouple-1.0.0/thermocouple/data/fixedPointsITS90.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeB.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeE.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeJ.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeK.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeN.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeR.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeS.rda |only thermocouple-1.0.0/thermocouple/data/inverseCoefficientsThermocoupleTypeT.rda |only thermocouple-1.0.0/thermocouple/data/inverseFunctionsThermocoupleRange.rda |only thermocouple-1.0.0/thermocouple/data/recommendedUpperTempLimitsProtectedThermocouples.rda |only thermocouple-1.0.0/thermocouple/data/singleLegThermoelements.rda |only thermocouple-1.0.0/thermocouple/data/standardRTDandThermistorAccuracy.rda |only thermocouple-1.0.0/thermocouple/data/standardRTDandThermistorValues.rda |only thermocouple-1.0.0/thermocouple/man/CalcCRCbitDS1820.Rd |only thermocouple-1.0.0/thermocouple/man/CalculateThermistorBeta.Rd |only thermocouple-1.0.0/thermocouple/man/ConvertThermistorADCreadingToTemperatureC.Rd |only thermocouple-1.0.0/thermocouple/man/ConvertThermistorTemperatureCToADCreading.Rd |only thermocouple-1.0.0/thermocouple/man/EquationThermocouplesTypeB.Rd |only thermocouple-1.0.0/thermocouple/man/ErrorLimitsThermocouples.Rd |only thermocouple-1.0.0/thermocouple/man/InverseEquationThermocouplesTypeB.Rd |only thermocouple-1.0.0/thermocouple/man/NominalSeebeckCoefficients.Rd |only thermocouple-1.0.0/thermocouple/man/PT100.Rd |only thermocouple-1.0.0/thermocouple/man/SteinhartHartThermistorResistance.Rd |only thermocouple-1.0.0/thermocouple/man/SteinhartHartThermistorTemperature.Rd |only thermocouple-1.0.0/thermocouple/man/TemperatureDataDS18B20.Rd |only thermocouple-1.0.0/thermocouple/man/VoltageContributionTwoHomogeneousWires.Rd |only thermocouple-1.0.0/thermocouple/man/VolumeResistivityFromR25.Rd |only thermocouple-1.0.0/thermocouple/man/VolumeResistivityFromRho.Rd |only thermocouple-1.0.0/thermocouple/man/coefficientsThermocoupleTypeB.Rd |only thermocouple-1.0.0/thermocouple/man/definitionThermocoupleTypes.Rd |only thermocouple-1.0.0/thermocouple/man/fixedPointsITS90.Rd |only thermocouple-1.0.0/thermocouple/man/inverseCoefficientsThermocoupleTypeB.Rd |only thermocouple-1.0.0/thermocouple/man/inverseFunctionsThermocoupleRange.Rd |only thermocouple-1.0.0/thermocouple/man/recommendedUpperTempLimitsProtectedThermocouples.Rd |only thermocouple-1.0.0/thermocouple/man/singleLegThermoelements.Rd |only thermocouple-1.0.0/thermocouple/man/standardRTDandThermistorAccuracy.Rd |only thermocouple-1.0.0/thermocouple/man/standardRTDandThermistorValues.Rd |only thermocouple-1.0.2/thermocouple/DESCRIPTION | 16 thermocouple-1.0.2/thermocouple/MD5 | 236 +- thermocouple-1.0.2/thermocouple/R/thermocouple.R | 945 +++++++++- thermocouple-1.0.2/thermocouple/data/adoptedLatentHeatOfVaporizationOfLiquidHe4.rda |only thermocouple-1.0.2/thermocouple/data/dielectricC.Density.ThermExpLiquid4HeSatVapPress.rda |only thermocouple-1.0.2/thermocouple/data/ds18B20TemperatureData.rda |only thermocouple-1.0.2/thermocouple/data/recommendedLatentHeatOfVaporizationOfLiquidHe4.rda |only thermocouple-1.0.2/thermocouple/data/rtdAndThermistorStandardAccuracy.rda |only thermocouple-1.0.2/thermocouple/data/rtdAndThermistorStandardValues.rda |only thermocouple-1.0.2/thermocouple/data/rtdPT100.rda |only thermocouple-1.0.2/thermocouple/data/rtdPT1000.rda |only thermocouple-1.0.2/thermocouple/data/rtdPlatinumToleranceValues.rda |only thermocouple-1.0.2/thermocouple/data/rtdResistanceWireComparison.rda |only thermocouple-1.0.2/thermocouple/data/rtdResistivityAlpha.rda |only thermocouple-1.0.2/thermocouple/data/rtdTypes.rda |only thermocouple-1.0.2/thermocouple/data/tableAWGCuWire.rda |only thermocouple-1.0.2/thermocouple/data/temperatureMeasurementDifficulty.rda |only thermocouple-1.0.2/thermocouple/data/temperatureSensorTypes.rda |binary thermocouple-1.0.2/thermocouple/data/thermistorMaximumMeasuringVoltage.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleAndExtensionWiresInternationalColorCodes.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCables.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeB.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeBrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeE.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeErationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeJ.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeJrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeK.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeKrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeN.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeNrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeR.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeRrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeS.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeSrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeT.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCoefficientsTypeTrationalPolynomial.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleColdJunctionVoltageCoeff.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleCompensatingExtensionWireColorUnitedStatesCanadaMexico.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleDefinitionTypes.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleErrorLimits.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleExtensionCables.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleExtensionWireColorUnitedStatesCanadaMexico.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleFixedPointsITS90.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInsulatingMaterialsCeramicPackedStock.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeB.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeE.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeJ.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeK.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeN.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeR.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeS.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseCoefficientsTypeT.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleInverseFunctionsRange.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleMineralInsulated.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleMounting.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleNominalSeebeckCoefficients.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleRecommendedUpperTempLimitsProtected.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleResponseTime.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleSingleLegThermoelements.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleTypeBthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeEthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeJthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeKthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeNthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeRthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeSthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypeTthermoelectricVoltage.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleTypesASTM.rda |binary thermocouple-1.0.2/thermocouple/data/thermocoupleWireColorUnitedStatesCanadaMexico.rda |only thermocouple-1.0.2/thermocouple/data/thermocoupleWireSizeResistanceImperial.rda |only thermocouple-1.0.2/thermocouple/demo/00Index | 2 thermocouple-1.0.2/thermocouple/demo/ObservedPropertiesLiquidHeliumSaturatedVaporPressure.R |only thermocouple-1.0.2/thermocouple/demo/T-T90computedByDifferentFunctions.R |only thermocouple-1.0.2/thermocouple/man/BimaterialStripCurvatureRadiusFromTemperature.Rd |only thermocouple-1.0.2/thermocouple/man/DS1820CalcCRCbit.Rd |only thermocouple-1.0.2/thermocouple/man/DiameterAWG.Rd |only thermocouple-1.0.2/thermocouple/man/RTDalpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDbeta.Rd |only thermocouple-1.0.2/thermocouple/man/RTDcoefficientA.Rd |only thermocouple-1.0.2/thermocouple/man/RTDdelta.Rd |only thermocouple-1.0.2/thermocouple/man/RTDequation.Rd |only thermocouple-1.0.2/thermocouple/man/RTDmetalResistance.Rd |only thermocouple-1.0.2/thermocouple/man/RTDmetalResistanceFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDmolybdenumResistanceFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDmolybdenumTemperatureFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDnickelIronResistanceFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDnickelIronTemperatureFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDnickelResistance.Rd |only thermocouple-1.0.2/thermocouple/man/RTDnickelResistanceFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDnickelTemperatureFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDplatinumResistance.Rd |only thermocouple-1.0.2/thermocouple/man/RTDplatinumResistanceFromAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/RTDplatinumTemperature.Rd |only thermocouple-1.0.2/thermocouple/man/RTDtemperatureFit.Rd |only thermocouple-1.0.2/thermocouple/man/RTDtemperatureFromResistance.Rd |only thermocouple-1.0.2/thermocouple/man/SelfHeatingError.Rd |only thermocouple-1.0.2/thermocouple/man/SensorSensitivity.Rd |only thermocouple-1.0.2/thermocouple/man/SplineEval.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorAlphaApproximatedFromBeta.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorApproxDriftResistance.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorApproxDriftTime.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalculateBeta.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquation.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquationHoge1.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquationHoge2.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquationHoge3.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquationHoge4.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorCalibrationEquationHoge5.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorConvertADCreadingToTemperatureC.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorConvertTemperatureCtoADCreading.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorHoge1CoeffFromMeasurements.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorResistanceDeviation.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorResistanceSteinhartHart.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorResistanceSteinhartHart2.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorResistanceSteinhartHartUsing3T.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorResistanceTolerance.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorSensitivity.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorSlope.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorSteinhartHartCoeffFromMeasurements.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorTemperature.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorTemperatureAccuracy.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorTemperatureDeviation.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorTemperatureFitPolynomial.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorTemperatureSteinhartHart.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorVolumeResistivityFromR25.Rd |only thermocouple-1.0.2/thermocouple/man/ThermistorVolumeResistivityFromRho.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleEquationTemperatureToVoltage.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleEquationTypeB.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleEquationTypeKrationalPolynomial.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleInverseEquationTypeB.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleLeadWireExternalResistanceUS.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleStemLossErrorEstimate.Rd | 2 thermocouple-1.0.2/thermocouple/man/ThermocoupleTable10colsTo2.Rd |only thermocouple-1.0.2/thermocouple/man/ThermocoupleVoltageContributionTwoHomogeneousWires.Rd |only thermocouple-1.0.2/thermocouple/man/TminusT90CCT2008.Rd |only thermocouple-1.0.2/thermocouple/man/TminusT90Pavese4CubicPolynomials.Rd |only thermocouple-1.0.2/thermocouple/man/TminusT90Pavese6CubicPolynomials.Rd |only thermocouple-1.0.2/thermocouple/man/adoptedLatentHeatOfVaporizationOfLiquidHe4.Rd |only thermocouple-1.0.2/thermocouple/man/dielectricC.Density.ThermExpLiquid4HeSatVapPress.Rd |only thermocouple-1.0.2/thermocouple/man/ds18B20TemperatureData.Rd |only thermocouple-1.0.2/thermocouple/man/recommendedLatentHeatOfVaporizationOfLiquidHe4.Rd |only thermocouple-1.0.2/thermocouple/man/rtdAndThermistorSandardAccuracy.Rd |only thermocouple-1.0.2/thermocouple/man/rtdAndThermistorStandardValues.Rd |only thermocouple-1.0.2/thermocouple/man/rtdPT100.Rd |only thermocouple-1.0.2/thermocouple/man/rtdPlatinumToleranceValues.Rd |only thermocouple-1.0.2/thermocouple/man/rtdResistanceWireComparison.Rd |only thermocouple-1.0.2/thermocouple/man/rtdResistivityAlpha.Rd |only thermocouple-1.0.2/thermocouple/man/rtdTypes.Rd |only thermocouple-1.0.2/thermocouple/man/tableAWGCuWire.Rd |only thermocouple-1.0.2/thermocouple/man/temperatureMeasurementDifficulty.Rd |only thermocouple-1.0.2/thermocouple/man/thermistorMaximumMeasuringVoltage.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleCables.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleCoefficientsTypeB.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleCoefficientsTypeBrationalPolynomial.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleColdJunctionVoltageCoeff.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleDefinitionTypes.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleErrorLimits.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleExtensionCables.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleFixedPointsITS90.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleInsulatingMaterialsCeramicPackedStock.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleInverseCoefficientsTypeB.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleInverseFunctionsRange.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleMineralInsulated.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleMounting.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleNominalSeebeckCoefficients.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleRecommendedUpperTempLimitsProtected.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleResponseTime.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleSingleLegThermoelements.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleWireColorUnitedStatesCanadaMexico.Rd |only thermocouple-1.0.2/thermocouple/man/thermocoupleWireSizeResistanceImperial.Rd |only 223 files changed, 1074 insertions(+), 127 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation.
Author: Andrew T. Karl (Adsurgo LLC), Jennifer Broatch (Arizona State University)
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.0-2 dated 2014-07-10 and 1.1-1 dated 2015-07-19
DESCRIPTION | 10 +- MD5 | 58 +++++++------ NAMESPACE | 9 +- R/NB_cre.R | 172 ++++++++++++++++++++++++++++++++++++---- R/NB_mov.r |only R/PB_cre.R | 184 +++++++++++++++++++++++++++++++++++++++++- R/binary_cre.R | 110 ++++++++++++++++++++++++- R/game.pred.R | 33 ++++++- R/mvglmmRank.R | 27 ++++-- R/normal_cre.R | 197 ++++++++++++++++++++++++++++------------------ R/poisson_cre.R | 132 +++++++++++++++++++++++++++++- data/f2008.rda |binary data/f2009.rda |binary data/f2010.rda |binary data/f2011.rda |binary data/f2012.rda |binary data/nba2013.rda |binary data/ncaab2012.rda |binary data/nfl2012.rda |binary man/NB_mov.Rd |only man/f2008.Rd | 4 man/f2009.Rd | 2 man/f2010.Rd | 4 man/f2011.Rd | 4 man/f2012.Rd | 4 man/game.pred.Rd | 11 +- man/mvglmmRank-package.Rd | 18 ++-- man/mvglmmRank.Rd | 46 ++++++---- man/nba2013.Rd | 4 man/ncaab2012.Rd | 4 man/nfl2012.Rd | 4 31 files changed, 838 insertions(+), 199 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: An implementation of the jDE variant of the Differential Evolution
stochastic algorithm for global optimization of nonlinear programming problems.
Author: Eduardo L. T. Conceicao and Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.0-2 dated 2014-10-19 and 1.0-3 dated 2015-07-19
DESCRIPTION | 19 +++++++++++-------- MD5 | 8 ++++---- NAMESPACE | 1 + R/JDEoptim.R | 9 +++------ man/JDEoptim.Rd | 5 +++++ 5 files changed, 24 insertions(+), 18 deletions(-)
Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@anu.edu.au>
Diff between climwin versions 0.0.1 dated 2015-03-06 and 0.1.0 dated 2015-07-19
climwin-0.0.1/climwin/tests/testthat/testsetprogress.R |only climwin-0.1.0/climwin/DESCRIPTION | 9 climwin-0.1.0/climwin/MD5 | 127 +- climwin-0.1.0/climwin/NAMESPACE | 6 climwin-0.1.0/climwin/R/autowin.R | 262 ++++- climwin-0.1.0/climwin/R/climatewin.R | 457 ++++----- climwin-0.1.0/climwin/R/crosswin.R | 206 ++-- climwin-0.1.0/climwin/R/datasets.R | 48 - climwin-0.1.0/climwin/R/explore.R | 58 - climwin-0.1.0/climwin/R/otherfunctions.R | 686 ++++++++++++--- climwin-0.1.0/climwin/R/plotall.R | 126 +- climwin-0.1.0/climwin/R/plotbest.R | 278 ++++-- climwin-0.1.0/climwin/R/plotbetas.R | 302 +++--- climwin-0.1.0/climwin/R/plotcor.R | 67 - climwin-0.1.0/climwin/R/plotdelta.R | 46 - climwin-0.1.0/climwin/R/plothist.R | 79 - climwin-0.1.0/climwin/R/plotweights.R | 66 - climwin-0.1.0/climwin/R/plotwin.R | 74 - climwin-0.1.0/climwin/R/randwin.R | 136 +- climwin-0.1.0/climwin/R/singlewin.R | 392 +++++--- climwin-0.1.0/climwin/R/weightwin.R | 198 ++-- climwin-0.1.0/climwin/R/zzz.R |only climwin-0.1.0/climwin/README.md | 6 climwin-0.1.0/climwin/build |only climwin-0.1.0/climwin/data/MassOutput.rda |binary climwin-0.1.0/climwin/data/MassRand.rda |binary climwin-0.1.0/climwin/inst |only climwin-0.1.0/climwin/man/Mass.Rd | 2 climwin-0.1.0/climwin/man/MassClimate.Rd | 2 climwin-0.1.0/climwin/man/MassOutput.Rd | 24 climwin-0.1.0/climwin/man/MassRand.Rd | 26 climwin-0.1.0/climwin/man/Offspring.Rd | 4 climwin-0.1.0/climwin/man/OffspringClimate.Rd | 2 climwin-0.1.0/climwin/man/autowin.Rd | 85 + climwin-0.1.0/climwin/man/climatewin.Rd | 237 +++-- climwin-0.1.0/climwin/man/crosswin.Rd | 58 - climwin-0.1.0/climwin/man/explore.Rd | 14 climwin-0.1.0/climwin/man/plotall.Rd | 65 - climwin-0.1.0/climwin/man/plotbest.Rd | 26 climwin-0.1.0/climwin/man/plotbetas.Rd | 14 climwin-0.1.0/climwin/man/plotcor.Rd | 35 climwin-0.1.0/climwin/man/plotdelta.Rd | 12 climwin-0.1.0/climwin/man/plothist.Rd | 20 climwin-0.1.0/climwin/man/plotweights.Rd | 16 climwin-0.1.0/climwin/man/plotwin.Rd | 12 climwin-0.1.0/climwin/man/randwin.Rd | 94 +- climwin-0.1.0/climwin/man/singlewin.Rd | 97 +- climwin-0.1.0/climwin/man/weightwin.Rd | 109 +- climwin-0.1.0/climwin/tests/testthat/testautowin.R | 37 climwin-0.1.0/climwin/tests/testthat/testclimatewin.R | 534 +++++++++-- climwin-0.1.0/climwin/tests/testthat/testcrosswin.R | 29 climwin-0.1.0/climwin/tests/testthat/testdateconverter.R | 100 +- climwin-0.1.0/climwin/tests/testthat/testexplore.R | 9 climwin-0.1.0/climwin/tests/testthat/testplotall.R | 32 climwin-0.1.0/climwin/tests/testthat/testplotbest.R | 11 climwin-0.1.0/climwin/tests/testthat/testplotbetas.R | 18 climwin-0.1.0/climwin/tests/testthat/testplotcor.R | 11 climwin-0.1.0/climwin/tests/testthat/testplotdelta.R | 2 climwin-0.1.0/climwin/tests/testthat/testplothist.R | 4 climwin-0.1.0/climwin/tests/testthat/testplotweights.R | 2 climwin-0.1.0/climwin/tests/testthat/testplotwin.R | 2 climwin-0.1.0/climwin/tests/testthat/testrandwin.R | 34 climwin-0.1.0/climwin/tests/testthat/testsinglewin.R | 163 ++- climwin-0.1.0/climwin/tests/testthat/testweightfuncWG.R | 62 - climwin-0.1.0/climwin/tests/testthat/testweightwin.R | 40 climwin-0.1.0/climwin/vignettes |only 66 files changed, 3474 insertions(+), 2199 deletions(-)
Title: Graph-Constrained Regularization for Sparse Generalized Linear
Models
Description: We propose to use sparse regression model to achieve variable selection while accounting for graph-constraints among coefficients. Different linear combination of a sparsity penalty(L1) and a smoothness(MCP) penalty has been used, which induces both sparsity of the solution and certain smoothness on the linear coefficients.
Author: Li Chen, Jun Chen
Maintainer: Li Chen <li.chen@emory.edu>
Diff between glmgraph versions 1.0.1 dated 2015-03-25 and 1.0.3 dated 2015-07-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 12 ++++++++++++ R/glmgraph.R | 1 + man/glmgraph-package.Rd | 2 +- src/binomial.cpp | 9 +++++---- src/gaussian.cpp | 8 ++++---- 7 files changed, 33 insertions(+), 19 deletions(-)
Title: Fetch Economic and Financial Time Series Data from Public
Sources
Description: Download economic and financial time series from public sources.
Author: Abiel Reinhart <abielr@gmail.com>
Maintainer: Abiel Reinhart <abielr@gmail.com>
Diff between pdfetch versions 0.1.6 dated 2014-09-28 and 0.1.7 dated 2015-07-18
DESCRIPTION | 15 +++++++-------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 ++ NEWS | 5 +++++ R/pdfetch.R | 35 ++++++++++++++++------------------- man/pdfetch.Rd | 5 +++-- man/pdfetch_BLS.Rd | 11 ++++++----- man/pdfetch_BOE.Rd | 12 ++++++------ man/pdfetch_ECB.Rd | 7 ++++--- man/pdfetch_EIA.Rd | 6 ++++-- man/pdfetch_EUROSTAT.Rd | 21 ++++++++------------- man/pdfetch_EUROSTAT_DSD.Rd | 4 +++- man/pdfetch_FRED.Rd | 4 +++- man/pdfetch_INSEE.Rd | 7 ++++--- man/pdfetch_ONS.Rd | 6 ++++-- man/pdfetch_WB.Rd | 9 +++++---- man/pdfetch_YAHOO.Rd | 15 ++++++--------- 17 files changed, 102 insertions(+), 94 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Jonah C. Brooks [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 2.0.1 dated 2015-07-14 and 2.0.2 dated 2015-07-18
DESCRIPTION | 8 +- MD5 | 46 +++++------ NEWS | 5 + R/Index_calculations.r | 132 ++++++++++++++++++--------------- R/internal.r | 83 +++++++++++++++----- R/zzz.r | 2 README.md | 2 inst/doc/algo.Rnw | 53 ++++++------- inst/doc/algo.pdf |binary inst/doc/how_to_migrate.pdf |binary inst/doc/mlg.html | 8 +- inst/doc/poppr_manual.R | 5 - inst/doc/poppr_manual.Rnw | 6 + inst/doc/poppr_manual.pdf |binary inst/msn_explorer/ui.R | 22 ++--- man/locus_table.Rd | 20 ++++- man/poppr.Rd | 35 +++++--- tests/testthat/test-filter.R | 3 tests/testthat/test-locustable.R | 42 ++++++++++ tests/testthat/test-poppr.R | 5 - vignettes/algo-concordance.tex | 2 vignettes/algo.Rnw | 53 ++++++------- vignettes/poppr_manual-concordance.tex | 24 +++--- vignettes/poppr_manual.Rnw | 6 + 24 files changed, 346 insertions(+), 216 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 5.3-4 dated 2015-04-10 and 5.4-0 dated 2015-07-18
ChangeLog | 26 +++ DESCRIPTION | 15 - MD5 | 44 ++--- NAMESPACE | 14 + R/adjustments.R | 37 ++-- R/aggregate.R | 34 +++ R/get_outputs.R | 121 +++++++++++--- R/plot_functions.R | 181 ++++++++++++++++----- R/predict.pop.R | 86 +++++++-- inst/ex-data/Pop/predictions/prediction.rda |binary inst/ex-data/Pop/predictions/totpop_country218.rda |binary inst/ex-data/Pop/predictions/totpop_country528.rda |binary man/bayesPop-package.Rd | 7 man/cohorts.Rd |only man/expressions.Rd | 12 - man/get.pop.Rd | 42 +++- man/pop.aggregate.Rd | 2 man/pop.pyramid.Rd | 16 + man/pop.trajectories.plot.Rd | 6 man/pop.write.projection.summary.Rd | 9 - man/predict.pop.Rd | 8 man/specific_expressions.Rd |only src/projection_functions.c | 4 tests/test_functions.R | 24 ++ 24 files changed, 508 insertions(+), 180 deletions(-)
Title: Software Tools for the Statistical Analysis of Network Data
Description: An integrated set of tools for the representation, visualization, analysis, and simulation of network data. For an introduction, type help(package='statnet').
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut],
Martina Morris [aut, cre]
Maintainer: Martina Morris <morrism@u.washington.edu>
Diff between statnet versions 2014.2.0 dated 2014-02-10 and 2015.6.2 dated 2015-07-18
DESCRIPTION | 37 +++++++++++++++-------------- LICENSE | 2 - MD5 | 16 ++++++------ NAMESPACE | 7 ++++- R/onAttach.R | 1 R/update_statnet.R | 29 ++++++++++++++++++++++ inst/CITATION | 62 ++++++++++++++++++++++++++++++++++++++++++++----- man/statnet-package.Rd | 28 ++++++++-------------- man/update_statnet.Rd | 8 +++--- 9 files changed, 135 insertions(+), 55 deletions(-)
Title: Data Mining Classification and Regression Methods
Description: Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models/algorithms, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vector Machines, Random Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression metrics (improved mmetric function); 1.2 - new input importance methods (improved Importance function); 1.0 - first version.
Author: Paulo Cortez
Maintainer: Paulo Cortez <pcortez@dsi.uminho.pt>
Diff between rminer versions 1.4 dated 2014-11-07 and 1.4.1 dated 2015-07-18
DESCRIPTION | 12 ++-- MD5 | 27 ++++----- NAMESPACE | 7 ++ R/metrics.R | 14 ++++ R/model.R | 147 ++++++++++++++++++++++++++++++++++++++++++------- R/plots.R | 9 +-- man/CasesSeries.Rd | 7 ++ man/fit.Rd | 142 +++++++++++++++++++++++++++++++++-------------- man/imputation.Rd | 14 ++++ man/lforecast.Rd | 7 ++ man/mgraph.Rd | 27 +++++++-- man/mining.Rd | 18 ++++-- man/mmetric.Rd | 17 ++++- man/mparheuristic.Rd |only man/predict-methods.Rd | 7 ++ 15 files changed, 353 insertions(+), 102 deletions(-)
Title: Private Configuration for 'R' Packages
Description: Set configuration options on a per-package basis.
Options set by a given package only apply to that package,
other packages are unaffected.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgconfig versions 1.0.0 dated 2015-07-13 and 2.0.0 dated 2015-07-18
DESCRIPTION | 6 ++-- MD5 | 21 ++++++++------ NAMESPACE | 1 R/getset.R | 58 ++++++++++++++++++++++++++++++++++++---- inst/NEWS.md | 11 +++++++ inst/README.Rmd | 3 +- inst/README.md | 3 +- man/get_config.Rd | 15 +++++++++- man/set_config.Rd | 7 ++++ man/set_config_in.Rd |only tests/testthat/test-api.R |only tests/testthat/test-globalenv.R |only tests/testthat/tests.R | 26 +++++++++++++++++ 13 files changed, 129 insertions(+), 22 deletions(-)
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-rinv', along with various supporting algorithms.
Author: Johann Gagnon-Bartsch <johanngb@umich.edu>
Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>
Diff between ruv versions 0.9.5 dated 2015-05-20 and 0.9.6 dated 2015-07-18
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ man/RUV1.Rd | 2 +- man/RUV2.Rd | 2 +- man/RUV4.Rd | 2 +- man/RUVinv.Rd | 2 +- man/RUVrinv.Rd | 2 +- man/getK.Rd | 2 +- man/invvar.Rd | 2 +- man/randinvvar.Rd | 2 +- man/ruv-package.Rd | 6 +++--- man/sigmashrink.Rd | 2 +- 13 files changed, 33 insertions(+), 30 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with the 'qdap'
package that may be useful outside of the context of discourse analysis. Tools
include removal/extraction/replacement of abbreviations, dates, dollar amounts,
email addresses, hash tags, numbers, percentages, citations, person tags, phone
numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.3.2 dated 2015-04-06 and 0.4.0 dated 2015-07-18
DESCRIPTION | 40 +++--- MD5 | 155 ++++++++++++++------------- NAMESPACE | 8 + NEWS | 51 ++++++++ R/bind_or.R |only R/c.extracted.R |only R/print.extracted.R |only R/qdapRegex-package.R | 23 ++-- R/rm_between.R | 22 +++ R/rm_bracket.R | 2 R/rm_citation.R | 7 - R/rm_citation_tex.R | 2 R/rm_default.R | 10 + R/rm_nchar_words.R | 7 - R/rm_non_ascii.R | 6 - R/rm_non_words.R |only R/rm_number.R | 52 +++++++-- R/utils.R | 14 ++ README.md | 6 - data/regex_supplement.rda |binary data/regex_usa.rda |binary inst/CITATION | 8 - man/S.Rd | 2 man/bind.Rd | 2 man/bind_or.Rd |only man/c.extracted.Rd |only man/case.Rd | 2 man/cheat.Rd | 2 man/escape.Rd | 2 man/explain.Rd | 2 man/grab.Rd | 2 man/group.Rd | 2 man/group_or.Rd | 2 man/is.regex.Rd | 2 man/pastex.Rd | 2 man/print.explain.Rd | 2 man/print.extracted.Rd |only man/print.regexr.Rd | 2 man/qdapRegex.Rd | 6 - man/regex_cheat.Rd | 2 man/regex_supplement.Rd | 16 ++ man/regex_usa.Rd | 7 - man/rm_.Rd | 2 man/rm_abbreviation.Rd | 9 - man/rm_between.Rd | 10 + man/rm_bracket.Rd | 9 - man/rm_caps.Rd | 10 + man/rm_caps_phrase.Rd | 10 + man/rm_citation.Rd | 10 + man/rm_citation_tex.Rd | 10 + man/rm_city_state.Rd | 10 + man/rm_city_state_zip.Rd | 10 + man/rm_date.Rd | 10 + man/rm_default.Rd | 10 + man/rm_dollar.Rd | 10 + man/rm_email.Rd | 10 + man/rm_emoticon.Rd | 10 + man/rm_endmark.Rd | 10 + man/rm_hash.Rd | 10 + man/rm_nchar_words.Rd | 10 + man/rm_non_ascii.Rd | 10 + man/rm_non_words.Rd |only man/rm_number.Rd | 43 +++++-- man/rm_percent.Rd | 10 + man/rm_phone.Rd | 10 + man/rm_postal_code.Rd | 10 + man/rm_repeated_characters.Rd | 10 + man/rm_repeated_phrases.Rd | 10 + man/rm_repeated_words.Rd | 10 + man/rm_tag.Rd | 10 + man/rm_time.Rd | 10 + man/rm_title_name.Rd | 10 + man/rm_url.Rd | 10 + man/rm_white.Rd | 10 + man/rm_zip.Rd | 10 + man/validate.Rd | 2 tests/testthat/test-as_number.R |only tests/testthat/test-bind_or.R |only tests/testthat/test-rm_between.R | 11 + tests/testthat/test-rm_non_words.R |only tests/testthat/test-rm_number.R | 19 +-- tests/testthat/test-rm_repeated_characters.R | 3 tests/testthat/test-rm_repeated_phrases.R | 6 - tests/testthat/test-rm_repeated_words.R | 4 84 files changed, 556 insertions(+), 302 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.25 dated 2015-07-03 and 0.2.33 dated 2015-07-18
DESCRIPTION | 6 MD5 | 10 - README.md | 24 ++- inst/doc/mldr.pdf |binary inst/shiny/server.R | 15 +- inst/shiny/ui.R | 383 +++++++++++++++++++++++++++++++--------------------- 6 files changed, 266 insertions(+), 172 deletions(-)
Title: Causal Mediation Analysis
Description: We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley <dtingley@gov.harvard.edu>,
Teppei Yamamoto <teppei@mit.edu>,
Kentaro Hirose <hirose@princeton.edu>,
Luke Keele <ljk20@psu.edu>,
Kosuke Imai <kimai@princeton.edu>
Maintainer: Teppei Yamamoto <teppei@mit.edu>
Diff between mediation versions 4.4.4 dated 2015-03-02 and 4.4.5 dated 2015-07-18
ChangeLog | 2 + DESCRIPTION | 14 +++---- MD5 | 14 +++---- NAMESPACE | 7 +++ R/mediate.R | 84 ++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/mediation-old.pdf |binary inst/doc/mediation.pdf |binary 8 files changed, 67 insertions(+), 54 deletions(-)
Title: Non-Additive Measure and Integral Manipulation Functions
Description: S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation in a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known Möbius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach based on parametric entropies. The functions contained in Kappalab can for instance be used in the framework of multicriteria decision making or cooperative game theory.
Author: Michel Grabisch, Ivan Kojadinovic, Patrick Meyer.
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between kappalab versions 0.4-6 dated 2012-05-04 and 0.4-7 dated 2015-07-18
kappalab-0.4-6/kappalab/kappalab-Ex.R |only kappalab-0.4-7/kappalab/DESCRIPTION | 34 ++-------- kappalab-0.4-7/kappalab/MD5 | 7 -- kappalab-0.4-7/kappalab/R/card.set.func.R | 66 ++++++++++---------- kappalab-0.4-7/kappalab/man/mini.dist.capa.ident.Rd | 3 5 files changed, 46 insertions(+), 64 deletions(-)
Title: IRT Models for Polytomous and Continuous Item Responses
Description: pcIRT estimates the multidimensional polytomous Rasch model
(Rasch, 1961) and the Continous Rating Scale model (Mueller, 1987).
Author: Christine Hohensinn
Maintainer: Christine Hohensinn <christine.hohensinn@univie.ac.at>
Diff between pcIRT versions 0.1 dated 2014-01-12 and 0.2 dated 2015-07-17
pcIRT-0.1/pcIRT/R/MPRMl.R |only pcIRT-0.1/pcIRT/R/gamfunk.R |only pcIRT-0.1/pcIRT/R/print.LR.R |only pcIRT-0.1/pcIRT/R/summary.MPRMl.R |only pcIRT-0.1/pcIRT/data/example1.rda |only pcIRT-0.1/pcIRT/data/example2.rda |only pcIRT-0.1/pcIRT/man/CRSM.Rd |only pcIRT-0.1/pcIRT/man/LRT.Rd |only pcIRT-0.1/pcIRT/man/MPRM.Rd |only pcIRT-0.1/pcIRT/man/MPRMl.Rd |only pcIRT-0.1/pcIRT/man/dLRT.Rd |only pcIRT-0.1/pcIRT/man/example1.Rd |only pcIRT-0.1/pcIRT/man/example2.Rd |only pcIRT-0.1/pcIRT/man/person_par.Rd |only pcIRT-0.1/pcIRT/man/weight_test.Rd |only pcIRT-0.2/pcIRT/DESCRIPTION | 20 - pcIRT-0.2/pcIRT/MD5 | 99 ++++--- pcIRT-0.2/pcIRT/NAMESPACE | 52 ++- pcIRT-0.2/pcIRT/R/CRSM.R | 121 +++++++-- pcIRT-0.2/pcIRT/R/DRM.R |only pcIRT-0.2/pcIRT/R/LRT.DRM.R |only pcIRT-0.2/pcIRT/R/LRT.MPRM.R |only pcIRT-0.2/pcIRT/R/LRT.R | 75 +++-- pcIRT-0.2/pcIRT/R/MPRM.R | 461 +++++++++++++++++++++++++---------- pcIRT-0.2/pcIRT/R/RcppExports.R |only pcIRT-0.2/pcIRT/R/dLRT.R | 35 ++ pcIRT-0.2/pcIRT/R/gmc.CRSM.R | 26 + pcIRT-0.2/pcIRT/R/gmc.R | 45 +++ pcIRT-0.2/pcIRT/R/gmc.aLR.R | 24 + pcIRT-0.2/pcIRT/R/iccplot.CRSM.R |only pcIRT-0.2/pcIRT/R/iccplot.DRM.R |only pcIRT-0.2/pcIRT/R/iccplot.MPRM.R |only pcIRT-0.2/pcIRT/R/iccplot.R |only pcIRT-0.2/pcIRT/R/pcIRT-package.R |only pcIRT-0.2/pcIRT/R/person_par.CRSM.R | 22 - pcIRT-0.2/pcIRT/R/person_par.MPRM.R | 55 ++-- pcIRT-0.2/pcIRT/R/person_par.R | 40 +++ pcIRT-0.2/pcIRT/R/print.CRSM.R | 22 + pcIRT-0.2/pcIRT/R/print.DRM.R |only pcIRT-0.2/pcIRT/R/print.MPRM.R | 8 pcIRT-0.2/pcIRT/R/print.aLR.R | 10 pcIRT-0.2/pcIRT/R/print.dLR.R | 8 pcIRT-0.2/pcIRT/R/print.wt.R | 9 pcIRT-0.2/pcIRT/R/simCRSM.R | 65 ++++ pcIRT-0.2/pcIRT/R/simMPRM.R | 42 +++ pcIRT-0.2/pcIRT/R/summary.CRSM.R | 28 +- pcIRT-0.2/pcIRT/R/summary.DRM.R |only pcIRT-0.2/pcIRT/R/summary.MPRM.R | 10 pcIRT-0.2/pcIRT/R/summary.aLR.R | 8 pcIRT-0.2/pcIRT/R/summary.dLR.R | 9 pcIRT-0.2/pcIRT/R/summary.wt.R | 9 pcIRT-0.2/pcIRT/R/weight_test.R | 52 +++ pcIRT-0.2/pcIRT/README.md |only pcIRT-0.2/pcIRT/data/analog.rda |only pcIRT-0.2/pcIRT/data/reason.rda |only pcIRT-0.2/pcIRT/man/crsm.Rd |only pcIRT-0.2/pcIRT/man/dLR.Rd |only pcIRT-0.2/pcIRT/man/drm.Rd |only pcIRT-0.2/pcIRT/man/extraversion.Rd |only pcIRT-0.2/pcIRT/man/gmc.Rd | 87 +++--- pcIRT-0.2/pcIRT/man/iccplot.Rd |only pcIRT-0.2/pcIRT/man/lrt.Rd |only pcIRT-0.2/pcIRT/man/mprm.Rd |only pcIRT-0.2/pcIRT/man/pcIRT-package.Rd | 101 ++++--- pcIRT-0.2/pcIRT/man/perspar.Rd |only pcIRT-0.2/pcIRT/man/reason.test.Rd |only pcIRT-0.2/pcIRT/man/simCRSM.Rd | 95 +++---- pcIRT-0.2/pcIRT/man/simMPRM.Rd | 82 +++--- pcIRT-0.2/pcIRT/man/wt.Rd |only pcIRT-0.2/pcIRT/src |only 70 files changed, 1224 insertions(+), 496 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: There lacks an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. To meet this need, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for semantic similarity calculation between ontology terms (and genes), and network affinity calculation using Random Walk with Restart; both can be done via high-performance parallel computing. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.0.6 dated 2014-09-17 and 1.0.7 dated 2015-07-17
dnet-1.0.6/dnet/data/org.Hs.string900.RData |only dnet-1.0.6/dnet/man/org.Hs.string900.Rd |only dnet-1.0.7/dnet/DESCRIPTION | 39 +- dnet-1.0.7/dnet/MD5 | 192 ++++++------- dnet-1.0.7/dnet/NAMESPACE | 6 dnet-1.0.7/dnet/R/dBUMfit.r | 36 +- dnet-1.0.7/dnet/R/dBUMscore.r | 12 dnet-1.0.7/dnet/R/dCheckParallel.r | 29 +- dnet-1.0.7/dnet/R/dCommSignif.r | 4 dnet-1.0.7/dnet/R/dDAGancestor.r | 5 dnet-1.0.7/dnet/R/dDAGannotate.r | 4 dnet-1.0.7/dnet/R/dDAGgeneSim.r | 33 +- dnet-1.0.7/dnet/R/dDAGinduce.r | 4 dnet-1.0.7/dnet/R/dDAGlevel.r | 2 dnet-1.0.7/dnet/R/dDAGreverse.r | 2 dnet-1.0.7/dnet/R/dDAGroot.r | 4 dnet-1.0.7/dnet/R/dDAGtermSim.r | 31 +- dnet-1.0.7/dnet/R/dDAGtip.r | 4 dnet-1.0.7/dnet/R/dEnricher.r | 250 ++++-------------- dnet-1.0.7/dnet/R/dEnricherView.r | 16 - dnet-1.0.7/dnet/R/dFDRscore.r | 8 dnet-1.0.7/dnet/R/dFunArgs.r |only dnet-1.0.7/dnet/R/dGSEA.r | 146 +--------- dnet-1.0.7/dnet/R/dGSEAwrite.r | 2 dnet-1.0.7/dnet/R/dPvalAggregate.r | 4 dnet-1.0.7/dnet/R/dRDataLoader.r | 126 +++++---- dnet-1.0.7/dnet/R/dRWR.r | 137 +++++---- dnet-1.0.7/dnet/R/dRWRcontact.r | 23 - dnet-1.0.7/dnet/R/dRWRpipeline.r | 26 + dnet-1.0.7/dnet/R/dSVDsignif.r | 2 dnet-1.0.7/dnet/R/visBoxplotAdv.r | 74 ++--- dnet-1.0.7/dnet/R/visDAG.r | 28 +- dnet-1.0.7/dnet/R/visGSEA.r | 78 ++--- dnet-1.0.7/dnet/R/visNet.r | 16 - dnet-1.0.7/dnet/R/visNetAnimate.r |only dnet-1.0.7/dnet/R/visNetArc.r | 14 - dnet-1.0.7/dnet/R/visNetCircle.r | 4 dnet-1.0.7/dnet/R/visNetMul.r | 26 - dnet-1.0.7/dnet/R/visNetReorder.r | 28 +- dnet-1.0.7/dnet/data/TCGA_mutations.RData |binary dnet-1.0.7/dnet/data/datalist | 1 dnet-1.0.7/dnet/data/ig.HPPA.RData |binary dnet-1.0.7/dnet/data/org.Hs.egHPPA.RData |binary dnet-1.0.7/dnet/inst/CITATION | 4 dnet-1.0.7/dnet/inst/NEWS | 12 dnet-1.0.7/dnet/inst/staticdocs/CITATIONs.md | 2 dnet-1.0.7/dnet/inst/staticdocs/INSTALLATIONs.md | 35 +- dnet-1.0.7/dnet/inst/staticdocs/RData.md | 6 dnet-1.0.7/dnet/inst/staticdocs/demo/CLL.r | 2 dnet-1.0.7/dnet/inst/staticdocs/demo/Fang.r | 18 - dnet-1.0.7/dnet/inst/staticdocs/demo/Hiratani.r | 4 dnet-1.0.7/dnet/inst/staticdocs/demo/TCGA.r | 6 dnet-1.0.7/dnet/inst/staticdocs/docs.r | 19 - dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ1.r | 5 dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ2.r | 4 dnet-1.0.7/dnet/inst/staticdocs/faq/FAQ6.r | 30 +- dnet-1.0.7/dnet/inst/staticdocs/templates/footer.html | 2 dnet-1.0.7/dnet/man/dBUMfit.Rd | 3 dnet-1.0.7/dnet/man/dBUMscore.Rd | 3 dnet-1.0.7/dnet/man/dCheckParallel.Rd | 3 dnet-1.0.7/dnet/man/dCommSignif.Rd | 5 dnet-1.0.7/dnet/man/dContrast.Rd | 3 dnet-1.0.7/dnet/man/dDAGancestor.Rd | 5 dnet-1.0.7/dnet/man/dDAGannotate.Rd | 7 dnet-1.0.7/dnet/man/dDAGgeneSim.Rd | 11 dnet-1.0.7/dnet/man/dDAGinduce.Rd | 7 dnet-1.0.7/dnet/man/dDAGlevel.Rd | 5 dnet-1.0.7/dnet/man/dDAGreverse.Rd | 5 dnet-1.0.7/dnet/man/dDAGroot.Rd | 7 dnet-1.0.7/dnet/man/dDAGtermSim.Rd | 9 dnet-1.0.7/dnet/man/dDAGtip.Rd | 7 dnet-1.0.7/dnet/man/dEnricher.Rd | 87 +++--- dnet-1.0.7/dnet/man/dEnricherView.Rd | 8 dnet-1.0.7/dnet/man/dFDRscore.Rd | 3 dnet-1.0.7/dnet/man/dFunArgs.Rd |only dnet-1.0.7/dnet/man/dGSEA.Rd | 92 +++--- dnet-1.0.7/dnet/man/dGSEAview.Rd | 3 dnet-1.0.7/dnet/man/dGSEAwrite.Rd | 3 dnet-1.0.7/dnet/man/dNetConfidence.Rd | 3 dnet-1.0.7/dnet/man/dNetFind.Rd | 3 dnet-1.0.7/dnet/man/dNetInduce.Rd | 3 dnet-1.0.7/dnet/man/dNetPipeline.Rd | 3 dnet-1.0.7/dnet/man/dNetReorder.Rd | 3 dnet-1.0.7/dnet/man/dPvalAggregate.Rd | 3 dnet-1.0.7/dnet/man/dRDataLoader.Rd | 181 +++++++------ dnet-1.0.7/dnet/man/dRWR.Rd | 3 dnet-1.0.7/dnet/man/dRWRcontact.Rd | 3 dnet-1.0.7/dnet/man/dRWRpipeline.Rd | 3 dnet-1.0.7/dnet/man/dSVDsignif.Rd | 3 dnet-1.0.7/dnet/man/ig.HPPA.Rd | 3 dnet-1.0.7/dnet/man/org.Hs.egHPPA.Rd | 8 dnet-1.0.7/dnet/man/visBoxplotAdv.Rd | 10 dnet-1.0.7/dnet/man/visDAG.Rd | 5 dnet-1.0.7/dnet/man/visGSEA.Rd | 3 dnet-1.0.7/dnet/man/visNet.Rd | 5 dnet-1.0.7/dnet/man/visNetAnimate.Rd |only dnet-1.0.7/dnet/man/visNetArc.Rd | 3 dnet-1.0.7/dnet/man/visNetCircle.Rd | 3 dnet-1.0.7/dnet/man/visNetMul.Rd | 7 dnet-1.0.7/dnet/man/visNetReorder.Rd | 11 100 files changed, 1026 insertions(+), 1084 deletions(-)
Title: Linear Mixed Effects Models with Non-Stationary Stochastic
Processes
Description: Contains functions to estimate model parameters and filter, smooth and forecast random effects coefficients for mixed models with stationary and non-stationary stochastic processes under multivariate normal and t response distributions, diagnostic checks, bootstrap standard error calculation, etc.
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar <o.asar@lancaster.ac.uk>
Diff between lmenssp versions 1.0 dated 2014-10-22 and 1.1 dated 2015-07-17
lmenssp-1.0/lmenssp/data/data.sim.ibm.short.rda |only lmenssp-1.0/lmenssp/man/data.sim.ibm.short.Rd |only lmenssp-1.1/lmenssp/DESCRIPTION | 14 lmenssp-1.1/lmenssp/MD5 | 40 lmenssp-1.1/lmenssp/NAMESPACE | 21 lmenssp-1.1/lmenssp/R/boot.nm.R |only lmenssp-1.1/lmenssp/R/filtered.R | 125 ++ lmenssp-1.1/lmenssp/R/lmenssp.R | 1451 +++++++++++++++++++++--- lmenssp-1.1/lmenssp/R/lmenssp.heavy.R |only lmenssp-1.1/lmenssp/R/qqplot.t.R |only lmenssp-1.1/lmenssp/R/smoothed.R | 133 ++ lmenssp-1.1/lmenssp/R/smoothed.heavy.R |only lmenssp-1.1/lmenssp/R/var.inspect.R |only lmenssp-1.1/lmenssp/R/variogram.R | 66 - lmenssp-1.1/lmenssp/data/data.sim.ibm.heavy.rda |only lmenssp-1.1/lmenssp/data/data.sim.ibm.rda |binary lmenssp-1.1/lmenssp/man/boot.nm.Rd |only lmenssp-1.1/lmenssp/man/data.sim.ibm.Rd | 10 lmenssp-1.1/lmenssp/man/data.sim.ibm.heavy.Rd |only lmenssp-1.1/lmenssp/man/filtered.Rd | 42 lmenssp-1.1/lmenssp/man/lmenssp-package.Rd | 29 lmenssp-1.1/lmenssp/man/lmenssp.Rd | 91 + lmenssp-1.1/lmenssp/man/lmenssp.heavy.Rd |only lmenssp-1.1/lmenssp/man/qqplot.t.Rd |only lmenssp-1.1/lmenssp/man/smoothed.Rd | 46 lmenssp-1.1/lmenssp/man/smoothed.heavy.Rd |only lmenssp-1.1/lmenssp/man/var.inspect.Rd |only lmenssp-1.1/lmenssp/man/variogram.Rd | 52 28 files changed, 1850 insertions(+), 270 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between aster versions 0.8-30 dated 2014-06-01 and 0.8-31 dated 2015-07-17
CHANGES | 2 ++ DESCRIPTION | 24 +++++++++++++++++------- LICENSE | 2 +- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 12 ++++++++++++ build/vignette.rds |binary inst/doc/design.pdf |binary inst/doc/ktp.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary man/aster.Rd | 2 +- man/chamae.Rd | 2 +- man/chamae2.Rd | 2 +- man/chamae3.Rd | 4 ++-- man/echin2.Rd | 2 +- man/echinacea.Rd | 2 +- man/reaster.Rd | 6 +++--- man/summary.reaster.Rd | 2 +- src/asttrans7.c | 3 +-- src/validtrips.c |only 20 files changed, 63 insertions(+), 39 deletions(-)
Title: Processes Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also includes functions to plot and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Diff between acc versions 1.1.1 dated 2015-06-22 and 1.1.7 dated 2015-07-17
acc-1.1.1/acc/R/accsummary.R |only acc-1.1.1/acc/man/accsummary.Rd |only acc-1.1.7/acc/DESCRIPTION | 12 ++++++------ acc-1.1.7/acc/MD5 | 36 ++++++++++++++++++------------------ acc-1.1.7/acc/NAMESPACE | 32 +++++++++++++++++++++++++++----- acc-1.1.7/acc/R/acc.R | 8 +++++++- acc-1.1.7/acc/R/accBatch.R | 7 ++++++- acc-1.1.7/acc/R/accSummary.R |only acc-1.1.7/acc/R/aggAcc.R | 11 ++++++++++- acc-1.1.7/acc/R/plotAcc.R | 12 +++++++++--- acc-1.1.7/acc/R/readRaw.R | 16 ++++++++++------ acc-1.1.7/acc/R/readRawBatch.R | 20 ++++++++++++++++---- acc-1.1.7/acc/R/simAcc.R | 9 +++++++-- acc-1.1.7/acc/man/acc.Rd | 6 +++--- acc-1.1.7/acc/man/accBatch.Rd | 4 ++-- acc-1.1.7/acc/man/accSummary.Rd |only acc-1.1.7/acc/man/aggAcc.Rd | 2 +- acc-1.1.7/acc/man/plotAcc.Rd | 34 +++++++++++++++++++++------------- acc-1.1.7/acc/man/readRaw.Rd | 11 +++++++---- acc-1.1.7/acc/man/readRawBatch.Rd | 9 +++++---- acc-1.1.7/acc/man/simAcc.Rd | 2 +- 21 files changed, 156 insertions(+), 75 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.1.0 dated 2015-02-26 and 1.2.0 dated 2015-07-17
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 10 +++++++++- NEWS | 15 +++++++++++++++ R/dict.R | 11 +++++++---- R/match.R | 38 ++++++++++++++++++++++++-------------- R/ore.R | 25 ++++++++++++++++--------- README.md | 23 +++++++++++++++++++++++ man/es.Rd | 2 +- man/matches.Rd | 2 +- man/ore.Rd | 21 ++++++++++++++------- man/ore.dict.Rd | 8 ++++++-- man/ore.ismatch.Rd | 3 ++- man/ore.lastmatch.Rd | 10 ++++++++-- man/ore.search.Rd | 4 +++- man/ore.split.Rd | 5 +++-- man/ore.subst.Rd | 3 ++- src/compile.c | 26 +++++++++++++++++++------- src/compile.h | 4 ++-- tests/testthat/test-05-ore.R | 6 ++++++ tests/testthat/test-10-match.R | 3 +++ 21 files changed, 188 insertions(+), 79 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.2.4 dated 2015-05-28 and 2.2.6 dated 2015-07-17
OpenMx-2.2.4/OpenMx/README |only OpenMx-2.2.4/OpenMx/man/imxFilterDefinitionVariables.Rd |only OpenMx-2.2.6/OpenMx/DESCRIPTION | 19 OpenMx-2.2.6/OpenMx/MD5 | 260 +++---- OpenMx-2.2.6/OpenMx/NAMESPACE | 4 OpenMx-2.2.6/OpenMx/R/DefinitionVars.R | 23 OpenMx-2.2.6/OpenMx/R/MxAlgebra.R | 24 OpenMx-2.2.6/OpenMx/R/MxAvailableOptimizers.R |only OpenMx-2.2.6/OpenMx/R/MxCompute.R | 43 + OpenMx-2.2.6/OpenMx/R/MxData.R | 2 OpenMx-2.2.6/OpenMx/R/MxDataWLS.R | 20 OpenMx-2.2.6/OpenMx/R/MxEval.R | 2 OpenMx-2.2.6/OpenMx/R/MxExpectation.R | 6 OpenMx-2.2.6/OpenMx/R/MxExpectationBA81.R | 6 OpenMx-2.2.6/OpenMx/R/MxExpectationGREML.R | 18 OpenMx-2.2.6/OpenMx/R/MxExpectationLISREL.R | 5 OpenMx-2.2.6/OpenMx/R/MxExpectationNormal.R | 12 OpenMx-2.2.6/OpenMx/R/MxExpectationRAM.R | 5 OpenMx-2.2.6/OpenMx/R/MxExpectationStateSpace.R | 104 ++- OpenMx-2.2.6/OpenMx/R/MxFactorScores.R |only OpenMx-2.2.6/OpenMx/R/MxFitFunction.R | 6 OpenMx-2.2.6/OpenMx/R/MxFitFunctionAlgebra.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionGREML.R | 9 OpenMx-2.2.6/OpenMx/R/MxFitFunctionML.R | 12 OpenMx-2.2.6/OpenMx/R/MxFitFunctionMultigroup.R | 4 OpenMx-2.2.6/OpenMx/R/MxFitFunctionR.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionRow.R | 2 OpenMx-2.2.6/OpenMx/R/MxFitFunctionWLS.R | 2 OpenMx-2.2.6/OpenMx/R/MxFlatModel.R | 10 OpenMx-2.2.6/OpenMx/R/MxLISRELModel.R | 6 OpenMx-2.2.6/OpenMx/R/MxMatrix.R | 17 OpenMx-2.2.6/OpenMx/R/MxModelFunctions.R | 41 - OpenMx-2.2.6/OpenMx/R/MxModelParameters.R | 10 OpenMx-2.2.6/OpenMx/R/MxMultiModel.R | 1 OpenMx-2.2.6/OpenMx/R/MxRAMModel.R | 6 OpenMx-2.2.6/OpenMx/R/MxRun.R | 341 ++++++---- OpenMx-2.2.6/OpenMx/R/MxSummary.R | 19 OpenMx-2.2.6/OpenMx/R/MxVersion.R | 6 OpenMx-2.2.6/OpenMx/R/MxVersion.R.in | 4 OpenMx-2.2.6/OpenMx/R/omxGetNPSOL.R | 9 OpenMx-2.2.6/OpenMx/README.md |only OpenMx-2.2.6/OpenMx/inst/CITATION | 4 OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-2pl-se.R | 8 OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-3pl-se.R | 58 + OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-cyh2011-sim1.R | 39 + OpenMx-2.2.6/OpenMx/inst/models/enormous/ifa-grm-se.R | 12 OpenMx-2.2.6/OpenMx/inst/models/enormous/lib/stderrlib.R | 88 +- OpenMx-2.2.6/OpenMx/inst/models/nightly/FactorScores.R |only OpenMx-2.2.6/OpenMx/inst/models/nightly/MultilevelStateSpaceEx5.R | 39 + OpenMx-2.2.6/OpenMx/inst/models/nightly/brooke.R |only OpenMx-2.2.6/OpenMx/inst/models/nightly/fm-example2-1.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-bifactor.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-cai2009.R | 2 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-drm-wide.R | 4 OpenMx-2.2.6/OpenMx/inst/models/nightly/ifa-ms.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/AlgebraComputePassing.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/AlgebraDeriv.R | 55 + OpenMx-2.2.6/OpenMx/inst/models/passing/GREML--minimal_test_model.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/GREML_Error_Detection.R | 52 + OpenMx-2.2.6/OpenMx/inst/models/passing/GREML_intercept_check.R |only OpenMx-2.2.6/OpenMx/inst/models/passing/IntroSEM-OneFactorCov.R | 23 OpenMx-2.2.6/OpenMx/inst/models/passing/IntroSEM-ThreeFactorScale2Test.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/LAD--CheckCode6.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/MultipleGroupML.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/NormalML.R | 5 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleAlgebraCIs.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleConstraint.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/SimpleMLAlgebraCIs.R | 5 OpenMx-2.2.6/OpenMx/inst/models/passing/StateSpaceInputs.R | 12 OpenMx-2.2.6/OpenMx/inst/models/passing/StateSpaceMissingData.R | 4 OpenMx-2.2.6/OpenMx/inst/models/passing/UselessConstraint.R | 6 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-drm-mg2.R | 3 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-drm1.R | 16 OpenMx-2.2.6/OpenMx/inst/models/passing/ifa-grm1.R | 7 OpenMx-2.2.6/OpenMx/inst/models/passing/oneLocusLikelihood.R | 10 OpenMx-2.2.6/OpenMx/inst/models/passing/rfitfunc.R | 6 OpenMx-2.2.6/OpenMx/inst/models/passing/startingValues.R | 2 OpenMx-2.2.6/OpenMx/inst/models/passing/startingValues2.R |only OpenMx-2.2.6/OpenMx/man/MxExpectationGREML-class.Rd | 1 OpenMx-2.2.6/OpenMx/man/MxFitFunctionGREML-class.Rd | 1 OpenMx-2.2.6/OpenMx/man/MxMatrix-class.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxAlgebra.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxAlgebraFromString.Rd |only OpenMx-2.2.6/OpenMx/man/mxAvailableOptimizers.Rd |only OpenMx-2.2.6/OpenMx/man/mxComputeEM.Rd | 8 OpenMx-2.2.6/OpenMx/man/mxComputeHessianQuality.Rd | 14 OpenMx-2.2.6/OpenMx/man/mxComputeStandardError.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxEval.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationBA81.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationGREML.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxExpectationStateSpace.Rd | 3 OpenMx-2.2.6/OpenMx/man/mxExpectationStateSpaceContinuousTime.Rd | 8 OpenMx-2.2.6/OpenMx/man/mxFactorScores.Rd |only OpenMx-2.2.6/OpenMx/man/mxFitFunctionAlgebra.Rd | 9 OpenMx-2.2.6/OpenMx/man/mxFitFunctionGREML.Rd | 4 OpenMx-2.2.6/OpenMx/man/mxFitFunctionML.Rd | 17 OpenMx-2.2.6/OpenMx/man/mxFitFunctionMultigroup.Rd | 122 +++ OpenMx-2.2.6/OpenMx/man/mxMatrix.Rd | 2 OpenMx-2.2.6/OpenMx/man/mxTryHard.Rd | 9 OpenMx-2.2.6/OpenMx/man/omxSaturatedModel.Rd | 2 OpenMx-2.2.6/OpenMx/src/AlgebraFunctions.h | 265 ------- OpenMx-2.2.6/OpenMx/src/Compute.cpp | 268 +++---- OpenMx-2.2.6/OpenMx/src/Compute.h | 1 OpenMx-2.2.6/OpenMx/src/ComputeGD.cpp | 4 OpenMx-2.2.6/OpenMx/src/ComputeNR.cpp | 57 + OpenMx-2.2.6/OpenMx/src/ba81quad.cpp | 22 OpenMx-2.2.6/OpenMx/src/fitMultigroup.cpp | 2 OpenMx-2.2.6/OpenMx/src/glue.cpp | 124 ++- OpenMx-2.2.6/OpenMx/src/glue.h | 9 OpenMx-2.2.6/OpenMx/src/multi_normal_sufficient.hpp | 35 - OpenMx-2.2.6/OpenMx/src/nloptcpp.cpp | 103 ++- OpenMx-2.2.6/OpenMx/src/omxAlgebra.cpp | 1 OpenMx-2.2.6/OpenMx/src/omxData.cpp | 63 + OpenMx-2.2.6/OpenMx/src/omxData.h | 22 OpenMx-2.2.6/OpenMx/src/omxDefines.h | 4 OpenMx-2.2.6/OpenMx/src/omxExpectation.cpp | 155 ---- OpenMx-2.2.6/OpenMx/src/omxExpectation.h | 19 OpenMx-2.2.6/OpenMx/src/omxExpectationBA81.cpp | 2 OpenMx-2.2.6/OpenMx/src/omxExportBackendState.cpp | 2 OpenMx-2.2.6/OpenMx/src/omxFIMLFitFunction.cpp | 10 OpenMx-2.2.6/OpenMx/src/omxFIMLFitFunction.h | 3 OpenMx-2.2.6/OpenMx/src/omxFIMLSingleIteration.cpp | 8 OpenMx-2.2.6/OpenMx/src/omxFitFunction.cpp | 6 OpenMx-2.2.6/OpenMx/src/omxFitFunctionBA81.cpp | 10 OpenMx-2.2.6/OpenMx/src/omxGREMLExpectation.cpp | 85 +- OpenMx-2.2.6/OpenMx/src/omxGREMLExpectation.h | 3 OpenMx-2.2.6/OpenMx/src/omxGREMLfitfunction.cpp | 54 + OpenMx-2.2.6/OpenMx/src/omxHessianCalculation.cpp | 9 OpenMx-2.2.6/OpenMx/src/omxImportFrontendState.cpp | 54 + OpenMx-2.2.6/OpenMx/src/omxImportFrontendState.h | 1 OpenMx-2.2.6/OpenMx/src/omxMLFitFunction.cpp | 22 OpenMx-2.2.6/OpenMx/src/omxRowFitFunction.cpp | 7 OpenMx-2.2.6/OpenMx/src/omxState.cpp | 31 OpenMx-2.2.6/OpenMx/src/omxState.h | 7 OpenMx-2.2.6/OpenMx/src/omxStateSpaceExpectation.cpp | 322 +++++++++ OpenMx-2.2.6/OpenMx/src/omxStateSpaceExpectation.h | 3 OpenMx-2.2.6/OpenMx/src/omxWLSFitFunction.cpp | 1 137 files changed, 2195 insertions(+), 1365 deletions(-)
Title: Mixed Tempered Stable Distribution
Description: We provide detailed functions for univariate Mixed Tempered Stable distribution.
Author: Lorenzo Mercuri, Edit Rroji
Maintainer: Lorenzo Mercuri <lorenzo.mercuri@unimi.it>
Diff between MixedTS versions 1.0.1 dated 2014-08-04 and 1.0.3 dated 2015-07-17
DESCRIPTION | 16 +++---- MD5 | 22 ++++----- NAMESPACE | 7 +-- R/MixedClasses.R | 38 ++++++++++++---- R/MixedTS.R | 101 +++++++++++++++++++++++++++++++++------------ R/dMixedTS.R | 18 ++++---- R/mle.MixedTS.aux.R | 61 ++++++++++++++++----------- R/pMixedTS.R | 21 +++++---- R/qMixedTS.R | 18 ++++---- R/rMixedTS.R | 19 ++++---- man/param.MixedTS-class.Rd | 2 man/setMixedTS.param.Rd | 13 +++++ 12 files changed, 222 insertions(+), 114 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.0.4 dated 2015-07-08 and 0.1.0 dated 2015-07-17
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS | 7 ++- R/visDocumentation.R | 3 - R/visNetwork.R | 3 - README.md | 41 +++++++++--------- build/vignette.rds |binary inst/doc/Introduction-to-visNetwork.Rmd | 2 inst/doc/Introduction-to-visNetwork.html | 68 +++++++++++++++---------------- man/visDocumentation.Rd | 2 man/visNetwork.Rd | 3 - vignettes/Introduction-to-visNetwork.Rmd | 2 12 files changed, 88 insertions(+), 75 deletions(-)
Title: Vertex Enumeration of Polytopes
Description: When given a description of a polyhedral set by a system of linear inequalities Ax <= b, produce the list of the vertices of the set.
Author: Robert Robere
Maintainer: Robert Robere <robere@cs.toronto.edu>
Diff between vertexenum versions 1.0 dated 2015-07-14 and 1.0.1 dated 2015-07-17
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/enumerate.vertices.R | 7 +++---- man/enumerate.vertices.Rd | 2 +- src/Rvertexenum.c | 16 ++++++++++++++-- src/lrslib.c | 13 ++++++++++++- src/lrsmp.c | 32 +++++++++++++++++++++++--------- 8 files changed, 67 insertions(+), 29 deletions(-)
Title: Statistical Analysis of Fuzzy Data
Description: The aim of the package is to provide some basic functions
for doing statistics with one dimensional Fuzzy Data (in the
form of polygonal fuzzy numbers). In particular, the package
contains functions for the basic operations on the class of
fuzzy numbers (sum, scalar product, mean, median, Hukuhara difference)
as well as for calculating (Bertoluzza) distance,
sample variance, sample covariance, and the
Dempster-Shafer (levelwise) histogram. Moreover a function to
simulate fuzzy random variables, bootstrap tests for the
equality of means, and a function to do linear regression given
trapezoidal fuzzy data is included. Version 1.0 fixes some bugs
of previous versions.
Author: Wolfgang Trutschnig <wolfgang@trutschnig.net>, Asun Lubiano
<lubiano@uniovi.es>
Maintainer: Asun Lubiano <lubiano@uniovi.es>
Diff between SAFD versions 0.4 dated 2012-08-10 and 1.0 dated 2015-07-17
SAFD-0.4/SAFD/R/Bcor.R |only SAFD-0.4/SAFD/R/Fquantile.R |only SAFD-0.4/SAFD/man/Bcor.Rd |only SAFD-0.4/SAFD/man/Fquantile.Rd |only SAFD-1.0/SAFD/DESCRIPTION | 25 ++--- SAFD-1.0/SAFD/MD5 | 98 ++++++++++------------ SAFD-1.0/SAFD/NAMESPACE | 3 SAFD-1.0/SAFD/R/Bcov.R | 10 +- SAFD-1.0/SAFD/R/Bvar.R | 4 SAFD-1.0/SAFD/R/DSfrequency.R | 8 - SAFD-1.0/SAFD/R/DShistogram.R | 6 - SAFD-1.0/SAFD/R/Fmedian.R | 51 +++++++---- SAFD-1.0/SAFD/R/Mmean.R | 16 ++- SAFD-1.0/SAFD/R/Msum.R | 37 ++++++-- SAFD-1.0/SAFD/R/bertoluzza.R | 15 +-- SAFD-1.0/SAFD/R/btest.mean.R | 38 ++++---- SAFD-1.0/SAFD/R/btest2.mean.R | 32 +++---- SAFD-1.0/SAFD/R/btestk.mean.R | 30 +++--- SAFD-1.0/SAFD/R/checking.R | 66 +++++++++------ SAFD-1.0/SAFD/R/checking2.R | 48 +++++++--- SAFD-1.0/SAFD/R/defuzzify.R | 4 SAFD-1.0/SAFD/R/generator.R | 12 +- SAFD-1.0/SAFD/R/hukuhara.R | 20 ++-- SAFD-1.0/SAFD/R/lrmodel.R | 12 +- SAFD-1.0/SAFD/R/sc_mult.R | 14 ++- SAFD-1.0/SAFD/R/translator.R | 14 ++- SAFD-1.0/SAFD/data/Trees.rda |binary SAFD-1.0/SAFD/data/XX.rda |binary SAFD-1.0/SAFD/data/quality.rda |only SAFD-1.0/SAFD/man/Bcov.Rd | 81 ++++++++++++++++-- SAFD-1.0/SAFD/man/Bvar.Rd | 53 ++++++++---- SAFD-1.0/SAFD/man/DSfrequency.Rd | 111 +++++++++++++++++++++++-- SAFD-1.0/SAFD/man/DShistogram.Rd | 157 +++++++++++++++++++++++++++++++++-- SAFD-1.0/SAFD/man/Fmedian.Rd | 91 +++++++++++++++++--- SAFD-1.0/SAFD/man/Mmean.Rd | 60 ++++++++++--- SAFD-1.0/SAFD/man/Msum.Rd | 99 +++++++++++++++++++--- SAFD-1.0/SAFD/man/SAFD-package.Rd | 41 ++++----- SAFD-1.0/SAFD/man/Trees.Rd | 15 +-- SAFD-1.0/SAFD/man/XX.Rd | 6 - SAFD-1.0/SAFD/man/bertoluzza.Rd | 62 ++++++++++++-- SAFD-1.0/SAFD/man/btest.mean.Rd | 74 ++++++++++++++-- SAFD-1.0/SAFD/man/btest2.mean.Rd | 96 +++++++++++++++++++-- SAFD-1.0/SAFD/man/btestk.mean.Rd | 166 +++++++++++++++++++++++++++++++++++--- SAFD-1.0/SAFD/man/checking.Rd | 134 ++++++++++++++++++++++++++---- SAFD-1.0/SAFD/man/checking2.Rd | 86 ++++++++++++++++++- SAFD-1.0/SAFD/man/decomposer.Rd | 30 +++++- SAFD-1.0/SAFD/man/defuzzify.Rd | 47 +++++----- SAFD-1.0/SAFD/man/generator.Rd | 114 +++++++++++++++++++++++--- SAFD-1.0/SAFD/man/hukuhara.Rd | 57 ++++++++----- SAFD-1.0/SAFD/man/lrmodel.Rd | 142 +++++++++++++++++++++++++++++--- SAFD-1.0/SAFD/man/quality.Rd |only SAFD-1.0/SAFD/man/sc_mult.Rd | 68 +++++++++++++-- SAFD-1.0/SAFD/man/translator.Rd | 69 +++++++++++---- 53 files changed, 1905 insertions(+), 517 deletions(-)
Title: R Interface to the UNU.RAN Random Variate Generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.21.0 dated 2014-08-27 and 0.22.0 dated 2015-07-17
DESCRIPTION | 13 MD5 | 678 +++++++-------- NAMESPACE | 3 NEWS | 5 build/vignette.rds |binary inst/doc/Runuran.pdf |binary inst/include/unuran.h | 2 man/Runuran-package.Rd | 2 src/Makevars.in | 2 src/unuran-src/distr/cemp.c | 2 src/unuran-src/distr/cemp.h | 2 src/unuran-src/distr/condi.c | 2 src/unuran-src/distr/condi.h | 2 src/unuran-src/distr/cont.c | 2 src/unuran-src/distr/cont.h | 2 src/unuran-src/distr/corder.c | 2 src/unuran-src/distr/corder.h | 2 src/unuran-src/distr/cvec.c | 2 src/unuran-src/distr/cvec.h | 2 src/unuran-src/distr/cvemp.c | 2 src/unuran-src/distr/cvemp.h | 2 src/unuran-src/distr/cxtrans.c | 2 src/unuran-src/distr/cxtrans.h | 2 src/unuran-src/distr/deprecated_distr.h | 2 src/unuran-src/distr/discr.c | 2 src/unuran-src/distr/discr.h | 2 src/unuran-src/distr/distr.c | 2 src/unuran-src/distr/distr.h | 2 src/unuran-src/distr/distr_info.c | 2 src/unuran-src/distr/distr_source.h | 2 src/unuran-src/distr/distr_struct.h | 2 src/unuran-src/distr/matr.c | 2 src/unuran-src/distr/matr.h | 2 src/unuran-src/distributions/c_F.c | 2 src/unuran-src/distributions/c_beta.c | 2 src/unuran-src/distributions/c_beta_gen.c | 2 src/unuran-src/distributions/c_burr.c | 2 src/unuran-src/distributions/c_cauchy.c | 2 src/unuran-src/distributions/c_chi.c | 2 src/unuran-src/distributions/c_chi_gen.c | 2 src/unuran-src/distributions/c_chisquare.c | 2 src/unuran-src/distributions/c_exponential.c | 2 src/unuran-src/distributions/c_exponential_gen.c | 2 src/unuran-src/distributions/c_extremeI.c | 2 src/unuran-src/distributions/c_extremeII.c | 2 src/unuran-src/distributions/c_gamma.c | 2 src/unuran-src/distributions/c_gamma_gen.c | 2 src/unuran-src/distributions/c_ghyp.c | 2 src/unuran-src/distributions/c_gig.c | 2 src/unuran-src/distributions/c_gig2.c | 2 src/unuran-src/distributions/c_gig_gen.c | 2 src/unuran-src/distributions/c_hyperbolic.c | 2 src/unuran-src/distributions/c_ig.c | 2 src/unuran-src/distributions/c_laplace.c | 2 src/unuran-src/distributions/c_logistic.c | 2 src/unuran-src/distributions/c_lognormal.c | 2 src/unuran-src/distributions/c_lomax.c | 2 src/unuran-src/distributions/c_meixner.c | 2 src/unuran-src/distributions/c_normal.c | 2 src/unuran-src/distributions/c_normal_gen.c | 2 src/unuran-src/distributions/c_pareto.c | 2 src/unuran-src/distributions/c_powerexponential.c | 2 src/unuran-src/distributions/c_powerexponential_gen.c | 2 src/unuran-src/distributions/c_rayleigh.c | 2 src/unuran-src/distributions/c_slash.c | 2 src/unuran-src/distributions/c_slash_gen.c | 2 src/unuran-src/distributions/c_student.c | 2 src/unuran-src/distributions/c_student_gen.c | 2 src/unuran-src/distributions/c_triangular.c | 2 src/unuran-src/distributions/c_uniform.c | 2 src/unuran-src/distributions/c_vg.c | 2 src/unuran-src/distributions/c_weibull.c | 2 src/unuran-src/distributions/d_binomial.c | 2 src/unuran-src/distributions/d_binomial_gen.c | 2 src/unuran-src/distributions/d_geometric.c | 2 src/unuran-src/distributions/d_hypergeometric.c | 2 src/unuran-src/distributions/d_hypergeometric_gen.c | 2 src/unuran-src/distributions/d_logarithmic.c | 2 src/unuran-src/distributions/d_logarithmic_gen.c | 2 src/unuran-src/distributions/d_negativebinomial.c | 2 src/unuran-src/distributions/d_poisson.c | 2 src/unuran-src/distributions/d_poisson_gen.c | 2 src/unuran-src/distributions/d_zipf.c | 2 src/unuran-src/distributions/d_zipf_gen.c | 2 src/unuran-src/distributions/m_correlation.c | 2 src/unuran-src/distributions/unur_distributions.h | 2 src/unuran-src/distributions/unur_distributions_source.h | 2 src/unuran-src/distributions/unur_stddistr.h | 2 src/unuran-src/distributions/vc_copula.c | 2 src/unuran-src/distributions/vc_multicauchy.c | 2 src/unuran-src/distributions/vc_multiexponential.c | 2 src/unuran-src/distributions/vc_multinormal.c | 2 src/unuran-src/distributions/vc_multinormal_gen.c | 2 src/unuran-src/distributions/vc_multistudent.c | 2 src/unuran-src/methods/arou.c | 2 src/unuran-src/methods/arou.h | 2 src/unuran-src/methods/arou_struct.h | 2 src/unuran-src/methods/ars.c | 2 src/unuran-src/methods/ars.h | 2 src/unuran-src/methods/ars_struct.h | 2 src/unuran-src/methods/auto.c | 2 src/unuran-src/methods/auto.h | 2 src/unuran-src/methods/auto_struct.h | 2 src/unuran-src/methods/cext.c | 2 src/unuran-src/methods/cext.h | 2 src/unuran-src/methods/cext_struct.h | 2 src/unuran-src/methods/cstd.c | 2 src/unuran-src/methods/cstd.h | 2 src/unuran-src/methods/cstd_struct.h | 2 src/unuran-src/methods/dari.c | 2 src/unuran-src/methods/dari.h | 2 src/unuran-src/methods/dari_struct.h | 2 src/unuran-src/methods/dau.c | 2 src/unuran-src/methods/dau.h | 2 src/unuran-src/methods/dau_struct.h | 2 src/unuran-src/methods/deprecated_methods.h | 2 src/unuran-src/methods/deprecated_tdrgw.h | 2 src/unuran-src/methods/deprecated_vmt.h | 2 src/unuran-src/methods/deprecated_vmt_struct.h | 2 src/unuran-src/methods/dext.c | 2 src/unuran-src/methods/dext.h | 2 src/unuran-src/methods/dext_struct.h | 2 src/unuran-src/methods/dgt.c | 2 src/unuran-src/methods/dgt.h | 2 src/unuran-src/methods/dgt_struct.h | 2 src/unuran-src/methods/dsrou.c | 2 src/unuran-src/methods/dsrou.h | 2 src/unuran-src/methods/dsrou_struct.h | 2 src/unuran-src/methods/dss.c | 2 src/unuran-src/methods/dss.h | 2 src/unuran-src/methods/dss_struct.h | 2 src/unuran-src/methods/dstd.c | 2 src/unuran-src/methods/dstd.h | 2 src/unuran-src/methods/dstd_struct.h | 2 src/unuran-src/methods/empk.c | 2 src/unuran-src/methods/empk.h | 2 src/unuran-src/methods/empk_struct.h | 2 src/unuran-src/methods/empl.c | 2 src/unuran-src/methods/empl.h | 2 src/unuran-src/methods/empl_struct.h | 2 src/unuran-src/methods/gibbs.c | 2 src/unuran-src/methods/gibbs.h | 2 src/unuran-src/methods/gibbs_struct.h | 2 src/unuran-src/methods/hinv.c | 2 src/unuran-src/methods/hinv.h | 2 src/unuran-src/methods/hinv_struct.h | 2 src/unuran-src/methods/hist.c | 2 src/unuran-src/methods/hist.h | 2 src/unuran-src/methods/hist_struct.h | 2 src/unuran-src/methods/hitro.c | 2 src/unuran-src/methods/hitro.h | 2 src/unuran-src/methods/hitro_struct.h | 2 src/unuran-src/methods/hrb.c | 2 src/unuran-src/methods/hrb.h | 2 src/unuran-src/methods/hrb_struct.h | 2 src/unuran-src/methods/hrd.c | 2 src/unuran-src/methods/hrd.h | 2 src/unuran-src/methods/hrd_struct.h | 2 src/unuran-src/methods/hri.c | 2 src/unuran-src/methods/hri.h | 2 src/unuran-src/methods/hri_struct.h | 2 src/unuran-src/methods/itdr.c | 2 src/unuran-src/methods/itdr.h | 2 src/unuran-src/methods/itdr_struct.h | 2 src/unuran-src/methods/mcorr.c | 2 src/unuran-src/methods/mcorr.h | 2 src/unuran-src/methods/mcorr_struct.h | 2 src/unuran-src/methods/mixt.c | 2 src/unuran-src/methods/mixt.h | 2 src/unuran-src/methods/mixt_struct.h | 2 src/unuran-src/methods/mvstd.c | 2 src/unuran-src/methods/mvstd.h | 2 src/unuran-src/methods/mvstd_struct.h | 2 src/unuran-src/methods/mvtdr.c | 2 src/unuran-src/methods/mvtdr.h | 2 src/unuran-src/methods/mvtdr_debug.ch | 2 src/unuran-src/methods/mvtdr_info.ch | 2 src/unuran-src/methods/mvtdr_init.ch | 2 src/unuran-src/methods/mvtdr_newset.ch | 2 src/unuran-src/methods/mvtdr_sample.ch | 2 src/unuran-src/methods/mvtdr_struct.h | 2 src/unuran-src/methods/ninv.c | 2 src/unuran-src/methods/ninv.h | 2 src/unuran-src/methods/ninv_debug.ch | 2 src/unuran-src/methods/ninv_info.ch | 2 src/unuran-src/methods/ninv_init.ch | 2 src/unuran-src/methods/ninv_newset.ch | 2 src/unuran-src/methods/ninv_newton.ch | 2 src/unuran-src/methods/ninv_regula.ch | 2 src/unuran-src/methods/ninv_sample.ch | 2 src/unuran-src/methods/ninv_struct.h | 2 src/unuran-src/methods/norta.c | 2 src/unuran-src/methods/norta.h | 2 src/unuran-src/methods/norta_struct.h | 2 src/unuran-src/methods/nrou.c | 2 src/unuran-src/methods/nrou.h | 2 src/unuran-src/methods/nrou_struct.h | 2 src/unuran-src/methods/pinv.c | 2 src/unuran-src/methods/pinv.h | 2 src/unuran-src/methods/pinv_debug.ch | 2 src/unuran-src/methods/pinv_info.ch | 2 src/unuran-src/methods/pinv_init.ch | 2 src/unuran-src/methods/pinv_newset.ch | 2 src/unuran-src/methods/pinv_newton.ch | 2 src/unuran-src/methods/pinv_prep.ch | 2 src/unuran-src/methods/pinv_sample.ch | 2 src/unuran-src/methods/pinv_struct.h | 2 src/unuran-src/methods/srou.c | 2 src/unuran-src/methods/srou.h | 2 src/unuran-src/methods/srou_struct.h | 2 src/unuran-src/methods/ssr.c | 2 src/unuran-src/methods/ssr.h | 2 src/unuran-src/methods/ssr_struct.h | 2 src/unuran-src/methods/tabl.c | 2 src/unuran-src/methods/tabl.h | 2 src/unuran-src/methods/tabl_debug.ch | 2 src/unuran-src/methods/tabl_info.ch | 2 src/unuran-src/methods/tabl_init.ch | 2 src/unuran-src/methods/tabl_newset.ch | 2 src/unuran-src/methods/tabl_sample.ch | 2 src/unuran-src/methods/tabl_struct.h | 2 src/unuran-src/methods/tdr.c | 2 src/unuran-src/methods/tdr.h | 2 src/unuran-src/methods/tdr_debug.ch | 2 src/unuran-src/methods/tdr_gw_debug.ch | 2 src/unuran-src/methods/tdr_gw_init.ch | 2 src/unuran-src/methods/tdr_gw_sample.ch | 2 src/unuran-src/methods/tdr_ia_sample.ch | 2 src/unuran-src/methods/tdr_info.ch | 2 src/unuran-src/methods/tdr_init.ch | 2 src/unuran-src/methods/tdr_newset.ch | 2 src/unuran-src/methods/tdr_ps_debug.ch | 2 src/unuran-src/methods/tdr_ps_init.ch | 2 src/unuran-src/methods/tdr_ps_sample.ch | 2 src/unuran-src/methods/tdr_sample.ch | 2 src/unuran-src/methods/tdr_struct.h | 2 src/unuran-src/methods/unif.c | 2 src/unuran-src/methods/unif.h | 2 src/unuran-src/methods/unif_struct.h | 2 src/unuran-src/methods/unur_methods.h | 2 src/unuran-src/methods/unur_methods_source.h | 2 src/unuran-src/methods/utdr.c | 2 src/unuran-src/methods/utdr.h | 2 src/unuran-src/methods/utdr_struct.h | 2 src/unuran-src/methods/vempk.c | 2 src/unuran-src/methods/vempk.h | 2 src/unuran-src/methods/vempk_struct.h | 2 src/unuran-src/methods/vnrou.c | 2 src/unuran-src/methods/vnrou.h | 2 src/unuran-src/methods/vnrou_struct.h | 2 src/unuran-src/methods/x_gen.c | 2 src/unuran-src/methods/x_gen.h | 2 src/unuran-src/methods/x_gen_source.h | 2 src/unuran-src/methods/x_gen_struct.h | 2 src/unuran-src/parser/functparser.c | 2 src/unuran-src/parser/functparser_debug.ch | 2 src/unuran-src/parser/functparser_deriv.ch | 2 src/unuran-src/parser/functparser_eval.ch | 2 src/unuran-src/parser/functparser_init.ch | 2 src/unuran-src/parser/functparser_parser.ch | 2 src/unuran-src/parser/functparser_scanner.ch | 2 src/unuran-src/parser/functparser_source.h | 2 src/unuran-src/parser/functparser_stringgen.ch | 2 src/unuran-src/parser/functparser_struct.h | 2 src/unuran-src/parser/functparser_symbols.h | 2 src/unuran-src/parser/parser.c | 2 src/unuran-src/parser/parser.h | 2 src/unuran-src/parser/parser_source.h | 2 src/unuran-src/parser/stringparser.c | 2 src/unuran-src/parser/stringparser_lists.ch | 2 src/unuran-src/specfunct/bessel_asympt.c | 2 src/unuran-src/specfunct/cgamma.c | 2 src/unuran-src/specfunct/hypot.c | 2 src/unuran-src/specfunct/log1p.c | 2 src/unuran-src/specfunct/unur_specfunct_source.h | 2 src/unuran-src/tests/countpdf.c | 2 src/unuran-src/tests/counturn.c | 2 src/unuran-src/tests/inverror.c | 2 src/unuran-src/tests/unuran_tests.h | 2 src/unuran-src/uniform/mrg31k3p.c | 2 src/unuran-src/uniform/urng_builtin.h | 2 src/unuran-src/uniform/urng_fvoid.h | 2 src/unuran-src/uniform/urng_gsl.h | 2 src/unuran-src/uniform/urng_gslqrng.h | 2 src/unuran-src/uniform/urng_prng.h | 2 src/unuran-src/uniform/urng_randomshift.h | 2 src/unuran-src/uniform/urng_rngstreams.h | 2 src/unuran-src/unur_cookies.h | 2 src/unuran-src/unur_source.h | 2 src/unuran-src/unur_struct.h | 2 src/unuran-src/unur_typedefs.h | 2 src/unuran-src/unuran.h | 2 src/unuran-src/urng/urng.c | 2 src/unuran-src/urng/urng.h | 2 src/unuran-src/urng/urng_default.c | 2 src/unuran-src/urng/urng_set.c | 2 src/unuran-src/urng/urng_source.h | 2 src/unuran-src/urng/urng_struct.h | 2 src/unuran-src/urng/urng_unuran.c | 2 src/unuran-src/utils/debug.c | 2 src/unuran-src/utils/debug.h | 2 src/unuran-src/utils/debug_source.h | 2 src/unuran-src/utils/eigensystem.c | 2 src/unuran-src/utils/error.c | 2 src/unuran-src/utils/error.h | 2 src/unuran-src/utils/error_source.h | 2 src/unuran-src/utils/fmax.c | 2 src/unuran-src/utils/fmax_source.h | 2 src/unuran-src/utils/hooke.c | 2 src/unuran-src/utils/hooke_source.h | 2 src/unuran-src/utils/lobatto.c | 2 src/unuran-src/utils/lobatto_source.h | 2 src/unuran-src/utils/lobatto_struct.h | 2 src/unuran-src/utils/matrix.c | 2 src/unuran-src/utils/matrix_source.h | 2 src/unuran-src/utils/mrou_rectangle.c | 2 src/unuran-src/utils/mrou_rectangle_source.h | 2 src/unuran-src/utils/mrou_rectangle_struct.h | 2 src/unuran-src/utils/slist.c | 2 src/unuran-src/utils/slist.h | 2 src/unuran-src/utils/slist_struct.h | 2 src/unuran-src/utils/stream.c | 2 src/unuran-src/utils/stream.h | 2 src/unuran-src/utils/stream_source.h | 2 src/unuran-src/utils/string.c | 2 src/unuran-src/utils/string_source.h | 2 src/unuran-src/utils/string_struct.h | 2 src/unuran-src/utils/umalloc.c | 2 src/unuran-src/utils/umalloc_source.h | 2 src/unuran-src/utils/umath.c | 2 src/unuran-src/utils/umath.h | 2 src/unuran-src/utils/umath_source.h | 2 src/unuran-src/utils/unur_errno.h | 2 src/unuran-src/utils/unur_fp.c | 2 src/unuran-src/utils/unur_fp_const_source.h | 2 src/unuran-src/utils/unur_fp_source.h | 2 src/unuran-src/utils/unur_math_source.h | 2 src/unuran-src/utils/vector.c | 2 src/unuran-src/utils/vector_source.h | 2 vignettes/inputs/version.tex | 2 340 files changed, 687 insertions(+), 680 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.4 dated 2015-07-04 and 0.1.5 dated 2015-07-17
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 8 +++++--- inst/tests/runit.basicRtests.R | 11 +++++++---- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs via simulations
- Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use both point estimate (PE) and mse from stage 1
also for the power monitoring steps.
- The third function power.2stage.fC() calculates power and sample-size
distribution of 2-stage BE studies with a futility criterion
for the PE or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
This function has a sibling power.2stage.pAF(), which performs exactly as
described in A.Fuglsang 2014
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.4-1 dated 2015-06-29 and 0.4-2 dated 2015-07-17
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NAMESPACE | 6 ++ NEWS | 7 +++ R/power.R | 2 R/power_2stage_DL.R | 11 ++-- R/power_2stage_KM.R | 6 +- R/power_2stage_SSR.R | 48 +++++++++++++-------- R/print_pwrtsd_s3.R | 109 ++++++++++++++++++++++++------------------------ R/sampsiz2.R | 6 +- R/sampsiz_n0.R | 77 ++++++++++++++++++--------------- man/power.2stage.GS.Rd | 3 - man/power.2stage.fC.Rd | 4 - man/power.2stage.ssr.Rd | 14 ++++-- 14 files changed, 184 insertions(+), 143 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.6-4 dated 2014-09-01 and 1.6-6 dated 2015-07-17
DESCRIPTION | 14 +++++----- MD5 | 30 ++++++++++----------- NAMESPACE | 10 ++++--- R/hamming.distance.R | 6 ++-- R/matchClasses.R | 63 ++++++++++++++++++++++----------------------- R/svm.R | 40 +++++++++++++++++----------- R/tune.R | 10 +++---- build/vignette.rds |binary inst/NEWS.Rd | 21 +++++++++++++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.Rnw | 19 +++++++++++++ inst/doc/svminternals.pdf |binary man/bclust.Rd | 2 - man/hamming.distance.Rd | 4 ++ man/tune.control.Rd | 2 - vignettes/svminternals.Rnw | 19 +++++++++++++ 16 files changed, 156 insertions(+), 84 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, and Luca Scrucca.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-47 dated 2015-05-06 and 6.0-52 dated 2015-07-17
DESCRIPTION | 16 +-- MD5 | 65 +++++++------ NAMESPACE | 23 ++++ R/aaa.R | 95 +++++++++---------- R/adaptive.R | 3 R/avNNet.R | 2 R/confusionMatrix.R | 2 R/createModel.R | 24 +++- R/findCorrelation.R | 80 ++++++++++++++-- R/lift.R | 19 ++- R/misc.R | 156 +++++++++++++++++++++++++++----- R/preProcess.R | 15 +-- R/print.train.R | 23 +++- R/resamples.R | 19 +++ R/rfe.R | 1 R/train.default.R | 38 ++++++- R/trainControl.R | 2 R/workflows.R | 3 build/vignette.rds |binary inst/NEWS.Rd | 19 +++ inst/doc/caret.R | 1 inst/doc/caret.Rnw | 1 inst/doc/caret.pdf |binary inst/models/models.RData |binary inst/models/sampling.RData |only man/caret-internal.Rd | 20 ++-- man/dummyVars.Rd | 14 ++ man/findCorrelation.Rd | 49 ++++++---- man/getSamplingInfo.Rd |only man/resamples.Rd | 5 + man/safsControl.Rd | 2 man/trainControl.Rd | 30 +++--- tests/testthat/test_BoxCox.R |only tests/testthat/test_bad_class_options.R |only tests/testthat/test_sampling_options.R |only vignettes/caret.Rnw | 1 36 files changed, 536 insertions(+), 192 deletions(-)
Title: Tinflex - Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 1.0 dated 2013-05-14 and 1.1 dated 2015-07-17
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS | 5 +++++ man/Tinflex-package.Rd | 4 ++-- 5 files changed, 24 insertions(+), 15 deletions(-)
Title: Streams of Random Numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.
Author: Josef Leydold <josef.leydold@wu.ac.at>
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between rstream versions 1.3.2 dated 2012-01-31 and 1.3.3 dated 2015-07-17
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- NAMESPACE | 3 ++- NEWS | 4 ++++ inst/doc/rstream.pdf |binary man/rstream-package.Rd | 4 ++-- 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Interface Between R and Qt
Description: Dynamic bindings to the Qt library for calling Qt
methods and extending Qt classes from R. Other packages build upon 'qtbase'
to provide special-purpose high-level interfaces to specific parts of Qt.
Author: Michael Lawrence, Deepayan Sarkar
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between qtbase versions 1.0.9 dated 2015-05-28 and 1.0.11 dated 2015-07-17
qtbase-1.0.11/qtbase/DESCRIPTION | 6 +++--- qtbase-1.0.11/qtbase/MD5 | 16 ++++++++-------- qtbase-1.0.11/qtbase/NAMESPACE | 4 +++- qtbase-1.0.11/qtbase/inst/NOTES |only qtbase-1.0.11/qtbase/inst/doc/qtbase.pdf |binary qtbase-1.0.11/qtbase/kdebindings/CMakeLists.txt | 3 +++ qtbase-1.0.11/qtbase/src/MocProperty.cpp | 2 +- qtbase-1.0.11/qtbase/src/convert.cpp | 2 +- qtbase-1.0.11/qtbase/src/convert.hpp | 2 +- qtbase-1.0.9/qtbase/NOTES |only 10 files changed, 20 insertions(+), 15 deletions(-)
Title: Linear Mixed Effect Model Splines for Modelling and Analysis of
Time Course Data
Description: Linear Mixed effect Model Splines (lmms) implements linear mixed effect model splines for
modelling and differential expression for highly dimensional data sets:
investNoise for quality control and filterNoise for removing
non-informative trajectories; lmmSpline to model time course expression
profiles and lmmsDE performs differential expression analysis to identify
differential expression between groups, time and/or group x time
interaction.
Author: Jasmin Straube [aut, cre],
Kim-Anh Le Cao [aut],
Emma Huang [aut],
Dominique Gorse [ctb]
Maintainer: Jasmin Straube <j.straube@qfab.org>
Diff between lmms versions 1.2 dated 2014-11-20 and 1.3 dated 2015-07-17
lmms-1.2/lmms/INDEX |only lmms-1.3/lmms/DESCRIPTION | 33 - lmms-1.3/lmms/MD5 | 61 +- lmms-1.3/lmms/NAMESPACE | 17 lmms-1.3/lmms/R/AllClasses.R | 23 - lmms-1.3/lmms/R/deriv.lmmspline-method.R | 15 lmms-1.3/lmms/R/filterNoise-method.R | 14 lmms-1.3/lmms/R/investNoise-method.R | 7 lmms-1.3/lmms/R/lmmSpline-method.R | 184 ++++---- lmms-1.3/lmms/R/lmmsDE-method.R | 612 +++++++++++++++++++--------- lmms-1.3/lmms/R/plot.lmmsde-method.R | 204 +++++---- lmms-1.3/lmms/R/plot.lmmspline-method.R | 170 +++++-- lmms-1.3/lmms/R/predict.lmmspline-method.R | 27 + lmms-1.3/lmms/R/summary.lmmsde-methods.R | 25 + lmms-1.3/lmms/data/kidneySimTimeGroup.RData |binary lmms-1.3/lmms/man/deriv.lmmspline.Rd | 5 lmms-1.3/lmms/man/filterNoise-methods.Rd | 7 lmms-1.3/lmms/man/investNoise-methods.Rd | 9 lmms-1.3/lmms/man/lmmSpline-methods.Rd | 27 - lmms-1.3/lmms/man/lmms-class.Rd | 5 lmms-1.3/lmms/man/lmms-package.Rd | 4 lmms-1.3/lmms/man/lmmsDE-methods.Rd | 32 - lmms-1.3/lmms/man/lmmsde-class.Rd | 20 lmms-1.3/lmms/man/lmmspline-class.Rd | 9 lmms-1.3/lmms/man/noise-class.Rd | 3 lmms-1.3/lmms/man/plot.lmmsde.Rd | 15 lmms-1.3/lmms/man/plot.lmmspline.Rd | 30 + lmms-1.3/lmms/man/plot.noise.Rd | 3 lmms-1.3/lmms/man/predict.lmmspline.Rd | 5 lmms-1.3/lmms/man/summary.lmmsde.Rd | 3 lmms-1.3/lmms/man/summary.lmmspline.Rd | 3 lmms-1.3/lmms/man/summary.noise.Rd | 3 32 files changed, 1011 insertions(+), 564 deletions(-)
Title: Random Variate Generator for the GIG Distribution
Description:
Generator and density function for the
Generalized Inverse Gaussian (GIG) distribution.
Author: Josef Leydold and Wolfgang Hormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between GIGrvg versions 0.3 dated 2014-06-04 and 0.4 dated 2015-07-17
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- NEWS | 5 +++++ inst/doc/README | 2 +- man/GIGrvg-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Extra Additive Terms for GAMLSS Models
Description: Interfaces for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.add versions 4.3-3 dated 2015-02-03 and 4.3-4 dated 2015-07-17
DESCRIPTION | 14 ++++---- MD5 | 8 ++-- NAMESPACE | 97 +++++++++++++++++++++++++++++---------------------------- R/gam_gamlss.R | 2 + man/tr.Rd | 2 - 5 files changed, 65 insertions(+), 58 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.1 dated 2015-07-15 and 0.3.2 dated 2015-07-17
FCNN4R-0.3.1/FCNN4R/src/Makevars.include |only FCNN4R-0.3.2/FCNN4R/DESCRIPTION | 8 ++-- FCNN4R-0.3.2/FCNN4R/MD5 | 13 +++---- FCNN4R-0.3.2/FCNN4R/R/mlp_net.R | 4 +- FCNN4R-0.3.2/FCNN4R/man/mlp_net-MSE-gradients.Rd | 4 +- FCNN4R-0.3.2/FCNN4R/src/Makevars | 3 + FCNN4R-0.3.2/FCNN4R/src/Makevars.win | 3 + FCNN4R-0.3.2/FCNN4R/src/interface.cpp | 38 +++++++++++++++-------- 8 files changed, 45 insertions(+), 28 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
This package allows to specify such models, transparently calls a suitable
simulator, parses the results and calculates additional summary statistics.
It supports the simulators 'ms', 'msms' and 'scrm' and can simulate
finite-sites mutation models by combining the simulators with the program
'seq-gen'.
Author: Paul Staab [aut, cre, cph],
Dirk Metzler [ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.1.0 dated 2015-07-14 and 0.1.1 dated 2015-07-17
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 9 +++++++++ build/vignette.rds |binary inst/doc/abc.Rmd | 4 ++-- inst/doc/abc.html | 6 +++--- inst/doc/installation.Rmd | 14 +++++++------- inst/doc/installation.html | 6 +++--- inst/doc/introduction.Rmd | 2 +- inst/doc/introduction.html | 2 +- src/parse_seqgen_output.cpp | 4 ++++ tests/testthat/test-simulator-seqgen.R | 5 ++++- vignettes/abc.Rmd | 4 ++-- vignettes/installation.Rmd | 14 +++++++------- vignettes/introduction.Rmd | 2 +- 15 files changed, 62 insertions(+), 46 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.0 dated 2015-06-19 and 1.6.1 dated 2015-07-17
DESCRIPTION | 9 - MD5 | 271 +++++++++++++++--------------- NAMESPACE | 43 ++++ NEWS | 80 +++++---- R/allMissing.r | 4 R/anyMissing.r | 6 R/anyNaN.r |only R/assert.r | 4 R/checkAccess.r | 8 R/checkArray.r | 9 + R/checkAtomic.r | 9 + R/checkAtomicVector.r | 9 + R/checkCharacter.r | 9 + R/checkChoice.r | 11 + R/checkClass.r | 11 + R/checkComplex.r | 9 + R/checkCount.r | 11 + R/checkDataFrame.r | 21 +- R/checkDirectory.r | 11 + R/checkEnvironment.r | 11 + R/checkFactor.r | 9 + R/checkFile.r | 11 + R/checkFlag.r | 9 + R/checkFunction.r | 32 ++- R/checkInt.r | 11 + R/checkInteger.r | 9 + R/checkIntegerish.r | 9 + R/checkList.r | 13 + R/checkLogical.r | 9 + R/checkMatrix.r | 23 +- R/checkNamed.r | 9 + R/checkNames.r | 9 + R/checkNumber.r | 8 R/checkNumeric.r | 9 + R/checkPathForOutput.r | 11 + R/checkPercentage.r | 11 + R/checkScalar.r | 12 + R/checkScalarNA.r | 11 + R/checkSetEqual.r | 11 + R/checkString.r | 14 + R/checkSubset.r | 11 + R/checkVector.r | 9 + R/coalesce.r |only R/helper.r | 13 + R/qassert.r | 11 + R/qassertr.r | 15 + R/zzz.r | 9 - build/vignette.rds |binary inst/doc/checkmate.R | 26 ++ inst/doc/checkmate.Rmd | 52 +++++ inst/doc/checkmate.html | 91 +++++++--- man/anyMissing.Rd | 10 + man/anyNaN.Rd |only man/assert.Rd | 4 man/checkAccess.Rd | 20 +- man/checkArray.Rd | 50 ++++- man/checkAtomic.Rd | 88 +++++++--- man/checkAtomicVector.Rd | 57 ++++-- man/checkCharacter.Rd | 52 ++++- man/checkChoice.Rd | 21 +- man/checkClass.Rd | 15 + man/checkComplex.Rd | 50 ++++- man/checkCount.Rd | 35 ++- man/checkDataFrame.Rd | 68 +++++-- man/checkDirectory.Rd | 21 +- man/checkEnvironment.Rd | 52 ++++- man/checkFactor.Rd | 52 ++++- man/checkFile.Rd | 21 +- man/checkFlag.Rd | 34 ++- man/checkFunction.Rd | 59 ++++-- man/checkInt.Rd | 35 ++- man/checkInteger.Rd | 52 ++++- man/checkIntegerish.Rd | 54 ++++-- man/checkList.Rd | 51 ++++- man/checkLogical.Rd | 51 ++++- man/checkMatrix.Rd | 76 +++++--- man/checkNamed.Rd | 5 man/checkNames.Rd | 15 + man/checkNull.Rd | 5 man/checkNumber.Rd | 35 ++- man/checkNumeric.Rd | 52 ++++- man/checkPathForOutput.Rd | 23 ++ man/checkPercentage.Rd | 34 ++- man/checkScalar.Rd | 32 ++- man/checkScalarNA.Rd | 31 ++- man/checkSetEqual.Rd | 20 +- man/checkString.Rd | 32 ++- man/checkSubset.Rd | 23 ++ man/checkVector.Rd | 54 ++++-- man/coalesce.Rd |only man/qassert.Rd | 12 + man/qassertr.Rd | 16 + src/all_missing.c | 6 src/all_nchar.c | 7 src/any_infinite.c | 4 src/any_missing.c | 8 src/any_nan.c |only src/any_nan.h |only src/checks.c | 259 +++++++++++++++-------------- src/checks.h | 4 src/cmessages.c | 6 src/cmessages.h | 1 tests/testthat/helper.r | 8 tests/testthat/test_anyMissing.r | 13 + tests/testthat/test_anyNaN.r |only tests/testthat/test_checkArray.r | 4 tests/testthat/test_checkAtomic.r | 4 tests/testthat/test_checkAtomicVector.r | 4 tests/testthat/test_checkCharacter.r | 5 tests/testthat/test_checkChoice.R | 4 tests/testthat/test_checkClass.r | 4 tests/testthat/test_checkComplex.r | 8 tests/testthat/test_checkCount.r | 4 tests/testthat/test_checkDataFrame.r | 36 +++- tests/testthat/test_checkEnvironment.r | 4 tests/testthat/test_checkFactor.r | 4 tests/testthat/test_checkFilesystem.r | 14 - tests/testthat/test_checkFlag.r | 4 tests/testthat/test_checkFunction.r | 10 - tests/testthat/test_checkInt.r | 12 + tests/testthat/test_checkInteger.r | 11 + tests/testthat/test_checkIntegerish.r | 11 + tests/testthat/test_checkList.r | 4 tests/testthat/test_checkLogical.r | 4 tests/testthat/test_checkMatrix.r | 4 tests/testthat/test_checkNamed.r | 4 tests/testthat/test_checkNames.r | 4 tests/testthat/test_checkNull.r | 4 tests/testthat/test_checkNumber.r | 11 + tests/testthat/test_checkNumeric.r | 11 + tests/testthat/test_checkPercentage.r | 4 tests/testthat/test_checkScalar.r | 4 tests/testthat/test_checkScalarNA.r | 1 tests/testthat/test_checkSetEqual.r | 4 tests/testthat/test_checkString.r | 4 tests/testthat/test_checkSubset.r | 4 tests/testthat/test_checkVector.r | 4 tests/testthat/test_qtest.r | 281 ++++++++++++++++---------------- tests/testthat/test_qtestr.r | 32 ++- vignettes/checkmate.Rmd | 52 +++++ 140 files changed, 2376 insertions(+), 959 deletions(-)
Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.1.6 dated 2015-05-08 and 0.1.19 dated 2015-07-16
SpecHelpers-0.1.19/SpecHelpers/DESCRIPTION | 10 ++++----- SpecHelpers-0.1.19/SpecHelpers/MD5 | 23 ++++++++++----------- SpecHelpers-0.1.19/SpecHelpers/NAMESPACE | 16 ++++++++++++++ SpecHelpers-0.1.19/SpecHelpers/NEWS | 3 ++ SpecHelpers-0.1.19/SpecHelpers/R/avgLambda.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/gatherCsv.R | 2 - SpecHelpers-0.1.19/SpecHelpers/R/gatherSpecFiles.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/makeSpec.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/plot2DNMRspec.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/plotNMRspec.R | 1 SpecHelpers-0.1.19/SpecHelpers/R/qMS.R | 2 + SpecHelpers-0.1.19/SpecHelpers/R/txt2csv.R | 1 SpecHelpers-0.1.6/SpecHelpers/README.md |only 13 files changed, 46 insertions(+), 18 deletions(-)
Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three
characteristic wetland plant communities in a semiarid Mediterranean
wetland in response to hydrological pressures from the catchment. The
package includes the data on watershed hydrological pressure and the
initial raster maps of plant communities but also allows for random initial
distribution of plant communities. Ongoing developments of the package
focus on offering easy to use tools for creating other spatio-dynamic
models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi
<naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between spdynmod versions 1.0 dated 2014-06-27 and 1.1 dated 2015-07-16
DESCRIPTION | 13 +++++---- MD5 | 61 ++++++++++++++++++++++++++------------------ NAMESPACE | 7 ++++- NEWS | 6 ++-- R/animate_bs.R | 2 - R/animate_model.R | 2 - R/animate_rb.R | 2 - R/animate_sm.R | 2 - R/animate_ss.R | 2 - R/mc_dynmodv2_7_functions.R | 7 ++--- R/mrgf.R |only R/plot_maps.R | 10 +++---- R/rnd_init_maps.R | 8 ++--- R/run_model.R | 3 +- R/spdynmod.R | 2 + build/vignette.rds |binary inst/doc/isem2013_jml.pdf |binary inst/extdata/y1984_rs.asc |only inst/extdata/y1992_mod.asc |only inst/extdata/y1992_rs.asc |only inst/extdata/y1995_mod.asc |only inst/extdata/y1995_rs.asc |only inst/extdata/y1997_mod.asc |only inst/extdata/y1997_rs.asc |only inst/extdata/y2001_mod.asc |only inst/extdata/y2001_rs.asc |only inst/extdata/y2008_mod.asc |only inst/extdata/y2008_rs.asc |only man/animate_bs.Rd | 3 +- man/animate_model.Rd | 3 +- man/animate_rb.Rd | 3 +- man/animate_sm.Rd | 3 +- man/animate_ss.Rd | 3 +- man/mrgf.Rd |only man/neigh_cell.Rd | 3 +- man/plot_maps.Rd | 3 +- man/run_model.Rd | 3 +- man/spdynmod.Rd | 3 +- 38 files changed, 94 insertions(+), 60 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-2 dated 2015-06-05 and 1.2-3 dated 2015-07-16
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 11 +++++++++++ NEWS | 14 ++++++++++---- R/sn-funct.R | 23 ++++++++++++----------- R/zzz.R | 7 ++++--- man/dmsn.Rd | 33 +++++++++++++++++---------------- man/dmst.Rd | 28 +++++++++++++++------------- man/selm.Rd | 7 ++++--- 9 files changed, 86 insertions(+), 63 deletions(-)
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://eml.berkeley.edu//~train/trainsonnier.pdf.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.1.0 dated 2015-06-08 and 1.1.1 dated 2015-07-16
DESCRIPTION | 9 +++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 4 ++++ NEWS | 3 +++ R/doHB.R | 2 +- R/writeModel.R | 4 +--- build/vignette.rds |binary inst/doc/RSGHB_HowTo.pdf |binary man/doHB.Rd | 3 ++- man/writeModel.Rd | 2 +- tools |only 11 files changed, 27 insertions(+), 19 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.3.2 dated 2015-05-03 and 1.3.3 dated 2015-07-16
DESCRIPTION | 8 MD5 | 30 +-- NAMESPACE | 4 R/RcppExports.R | 66 +++--- R/gibbs.R | 509 +++++++++++++++++++++++++++------------------------- R/manhattan.R | 2 R/report.R |only R/snpQC.R | 10 - man/Internals.Rd | 1 man/NAM-package.Rd | 66 +++--- man/cleanREP.Rd |only man/gibbs.Rd | 165 ++++++++-------- man/report.Rd |only man/snpH2.Rd | 2 man/snpQC.Rd | 5 src/RcppExports.cpp | 23 ++ src/SAMP.cpp | 2 src/SAMP2.cpp |only 18 files changed, 478 insertions(+), 415 deletions(-)
Title: Markov Chain Monte Carlo
Description: Simulates continuous distributions of random vectors using
Markov chain Monte Carlo (MCMC). Users specify the distribution by an
R function that evaluates the log unnormalized density. Algorithms
are random walk Metropolis algorithm (function metrop), simulated
tempering (function temper), and morphometric random walk Metropolis
(Johnson and Geyer, Annals of Statistics, 2012, function morph.metrop),
which achieves geometric ergodicity by change of variable.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif T. Johnson
<ltjohnson@google.com>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between mcmc versions 0.9-3 dated 2014-04-02 and 0.9-4 dated 2015-07-16
mcmc-0.9-3/mcmc/inst/doc/bfst.tex |only mcmc-0.9-3/mcmc/inst/doc/debug.tex |only mcmc-0.9-3/mcmc/inst/doc/demo.tex |only mcmc-0.9-3/mcmc/inst/doc/morph.tex |only mcmc-0.9-4/mcmc/ChangeLog | 3 + mcmc-0.9-4/mcmc/DESCRIPTION | 20 +++++--- mcmc-0.9-4/mcmc/MD5 | 62 ++++++++++++++++--------- mcmc-0.9-4/mcmc/NAMESPACE | 1 mcmc-0.9-4/mcmc/build/vignette.rds |binary mcmc-0.9-4/mcmc/inst/doc/bfst.pdf |binary mcmc-0.9-4/mcmc/inst/doc/debug.Rnw | 6 +- mcmc-0.9-4/mcmc/inst/doc/debug.pdf |binary mcmc-0.9-4/mcmc/inst/doc/demo.pdf |binary mcmc-0.9-4/mcmc/inst/doc/metrop.pdf |binary mcmc-0.9-4/mcmc/inst/doc/morph.pdf |binary mcmc-0.9-4/mcmc/inst/doc/temper.pdf |binary mcmc-0.9-4/mcmc/man/metrop.Rd | 2 mcmc-0.9-4/mcmc/man/morph.metrop.Rd | 4 - mcmc-0.9-4/mcmc/man/temper.Rd | 6 +- mcmc-0.9-4/mcmc/tests/circle.Rout.save |only mcmc-0.9-4/mcmc/tests/initseq.Rout.save |only mcmc-0.9-4/mcmc/tests/isotropic.Rout.save |only mcmc-0.9-4/mcmc/tests/logit.R | 2 mcmc-0.9-4/mcmc/tests/logit.Rout.save |only mcmc-0.9-4/mcmc/tests/logitbat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitfun.Rout.save |only mcmc-0.9-4/mcmc/tests/logitfunarg.Rout.save |only mcmc-0.9-4/mcmc/tests/logitidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitlogidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitmat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitnegidx.Rout.save |only mcmc-0.9-4/mcmc/tests/logitsub.Rout.save |only mcmc-0.9-4/mcmc/tests/logitsubbat.Rout.save |only mcmc-0.9-4/mcmc/tests/logitvec.Rout.save |only mcmc-0.9-4/mcmc/tests/morph.Rout.save |only mcmc-0.9-4/mcmc/tests/morph.metrop.R | 6 +- mcmc-0.9-4/mcmc/tests/morph.metrop.Rout.save |only mcmc-0.9-4/mcmc/tests/morphtoo.Rout.save |only mcmc-0.9-4/mcmc/tests/saveseed.Rout.save |only mcmc-0.9-4/mcmc/tests/saveseedmorph.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-par.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-ser-witch.Rout.save |only mcmc-0.9-4/mcmc/tests/temp-ser.R | 15 +++++- mcmc-0.9-4/mcmc/tests/temp-ser.Rout.save |only mcmc-0.9-4/mcmc/vignettes/debug.Rnw | 6 +- 45 files changed, 90 insertions(+), 43 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: We efficiently approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of our calculations, we also
obtain approximate standard errors for estimated predictive errors, and for
the comparison of predictive errors between two models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.0 dated 2015-06-26 and 0.1.2 dated 2015-07-16
loo-0.1.0/loo/R/loo_and_waic.R |only loo-0.1.0/loo/R/loo_and_waic_diff.R |only loo-0.1.0/loo/R/vgisloo.R |only loo-0.1.0/loo/R/vgislw.R |only loo-0.1.0/loo/man/loo_and_waic_diff.Rd |only loo-0.1.0/loo/man/vgisloo.Rd |only loo-0.1.0/loo/man/vgislw.Rd |only loo-0.1.2/loo/DESCRIPTION | 29 +-- loo-0.1.2/loo/MD5 | 58 +++--- loo-0.1.2/loo/NAMESPACE | 15 + loo-0.1.2/loo/R/compare.R |only loo-0.1.2/loo/R/deprecated.R |only loo-0.1.2/loo/R/extract_log_lik.R | 13 - loo-0.1.2/loo/R/gpdfit.R | 25 +- loo-0.1.2/loo/R/helpers.R | 150 ++++++++++++---- loo-0.1.2/loo/R/loo.R |only loo-0.1.2/loo/R/loo_package.R | 210 +++++++++++------------ loo-0.1.2/loo/R/misc.R |only loo-0.1.2/loo/R/print.R | 36 ++- loo-0.1.2/loo/R/psisloo.R |only loo-0.1.2/loo/R/psislw.R |only loo-0.1.2/loo/R/waic.R |only loo-0.1.2/loo/inst/doc/Example.R | 17 - loo-0.1.2/loo/inst/doc/Example.Rmd | 23 +- loo-0.1.2/loo/inst/doc/Example.html | 21 +- loo-0.1.2/loo/man/compare.Rd |only loo-0.1.2/loo/man/extract_log_lik.Rd | 10 - loo-0.1.2/loo/man/gpdfit.Rd | 6 loo-0.1.2/loo/man/loo-package.Rd | 210 +++++++++++------------ loo-0.1.2/loo/man/loo.Rd |only loo-0.1.2/loo/man/loo_and_waic.Rd | 24 -- loo-0.1.2/loo/man/nlist.Rd |only loo-0.1.2/loo/man/print.loo.Rd | 24 +- loo-0.1.2/loo/man/psisloo.Rd |only loo-0.1.2/loo/man/psislw.Rd |only loo-0.1.2/loo/man/waic.Rd |only loo-0.1.2/loo/tests/testthat/test_gpdfit.R | 6 loo-0.1.2/loo/tests/testthat/test_helpers.R | 28 +-- loo-0.1.2/loo/tests/testthat/test_loo_and_waic.R | 61 +++--- loo-0.1.2/loo/vignettes/Example.Rmd | 23 +- 40 files changed, 572 insertions(+), 417 deletions(-)
Title: GAMLSS Data
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 4.2-7 dated 2014-01-11 and 4.3-0 dated 2015-07-16
DESCRIPTION | 10 +++---- MD5 | 67 ++++++++++++++++++++++++++---------------------- data/CD4.rda |binary data/LGAclaims.rda |binary data/Mums.rda |binary data/VictimsOfCrime.rda |binary data/acidity.rda |binary data/aep.rda |binary data/aids.rda |binary data/alveolar.rda |binary data/computer.rda |binary data/datalist | 4 ++ data/db.rda |binary data/dbbmi.rda |binary data/fabric.rda |binary data/film30.rda |binary data/film90.rda |binary data/glass.rda |binary data/hodges.rda |binary data/hodges1.rda |binary data/lice.rda |binary data/margolin.rda |binary data/mvi.rda |only data/mviBig.rda |only data/parzen.rda |binary data/polio.rda |binary data/rent.rda |binary data/rent99.polys.rda |only data/rent99.rda |only data/species.rda |binary data/stylo.rda |binary data/tensile.rda |binary data/tse.rda |binary data/usair.rda |binary data/vas5.rda |binary man/mvi.Rd |only man/rent99.Rd |only man/rent99.polys.Rd |only 38 files changed, 46 insertions(+), 35 deletions(-)
Title: Demos for GAMLSS
Description: Demos for smoothing and gamlss.family distributions.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby <r.rigby@londonmet.ac.uk>, Paul Eilers <p.eilers@erasmusmc.nl>, Brian Marx \email{bmarx@LSU.EDU}, Konstantinos Pateras <kostas.pateras@gmail.com> with contributions from Larisa Kosidou.
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.demo versions 4.3-1 dated 2015-02-04 and 4.3-3 dated 2015-07-16
DESCRIPTION | 11 ++++--- MD5 | 4 +- NAMESPACE | 87 +++++++++++++++++++++++++++++++----------------------------- 3 files changed, 53 insertions(+), 49 deletions(-)
Title: Interactive Exploration of Contour Data
Description: Interactive tools to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. The functions in this package create
interactive web pages showing the contoured data, possibly with
slices from the original matrix parallel to each dimension. The interactive
behavior is created using the D3.js 'JavaScript' library by Mike Bostock.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between exCon versions 0.1.9 dated 2015-06-23 and 0.1.12 dated 2015-07-16
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 ++ NEWS | 4 ++++ R/exCon-package.R | 2 +- R/exCon.R | 2 ++ man/exCon-package.Rd | 2 +- 7 files changed, 22 insertions(+), 14 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, shared objects, vignettes, or function documentation. It is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The rstan package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.6.0-10 dated 2015-02-10 and 2.7.0 dated 2015-07-16
StanHeaders-2.6.0-10/StanHeaders/README.md |only StanHeaders-2.6.0-10/StanHeaders/inst/CITATION |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/agrad |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/agrad.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/command |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/common |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/common.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/error_handling |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/error_handling.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/gm |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/gm.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/io |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/io.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/functions |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/functions.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/matrix |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/matrix.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/meta |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/meta.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/ode |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/ode.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/math/seq_view.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/mcmc |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/mcmc.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/memory |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/memory.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/meta |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/meta.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/model |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/model.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/optimization |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/prob |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/prob.hpp |only StanHeaders-2.6.0-10/StanHeaders/inst/include/stan/version.hpp |only StanHeaders-2.7.0/StanHeaders/DESCRIPTION | 61 StanHeaders-2.7.0/StanHeaders/LICENSE | 2 StanHeaders-2.7.0/StanHeaders/MD5 | 1890 +++++----- StanHeaders-2.7.0/StanHeaders/NAMESPACE | 6 StanHeaders-2.7.0/StanHeaders/inst/include/src |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math.hpp | 673 +++ StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/fwd |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/memory |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/mix |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/prim |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/rev |only StanHeaders-2.7.0/StanHeaders/inst/include/stan/math/version.hpp |only StanHeaders-2.7.0/StanHeaders/man |only 47 files changed, 1788 insertions(+), 844 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.3 dated 2015-07-12 and 1.5.5 dated 2015-07-16
refGenome-1.5.3/refGenome/src/range_partition.h |only refGenome-1.5.5/refGenome/DESCRIPTION | 8 ++++---- refGenome-1.5.5/refGenome/MD5 | 5 ++--- refGenome-1.5.5/refGenome/src/refGenome.h | 3 --- 4 files changed, 6 insertions(+), 10 deletions(-)
Title: NCA Calculation and Population PK Model Diagnosis
Description: A flexible tool is presented here that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) simulation-based posterior predictive checks for a population
pharmacokinetic (PK) model using NCA metrics.
Author: Chayan Acharya [aut, cre],
Andrew C. Hooker [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut]
Maintainer: Chayan Acharya <chayan.acharya@farmbio.uu.se>
Diff between ncappc versions 0.1 dated 2015-03-04 and 0.2 dated 2015-07-16
ncappc-0.1/ncappc/inst/misc/figTab.Rmd |only ncappc-0.1/ncappc/inst/misc/figTab.Rnw |only ncappc-0.1/ncappc/inst/misc/figTabNoSim.Rmd |only ncappc-0.1/ncappc/inst/misc/figTabNoSim.Rnw |only ncappc-0.1/ncappc/inst/misc/ncappcReport.Rmd |only ncappc-0.1/ncappc/inst/misc/ncappcReport.Rnw |only ncappc-0.1/ncappc/tests/testthat.R |only ncappc-0.1/ncappc/vignettes/conc.png |only ncappc-0.2/ncappc/DESCRIPTION | 16 ncappc-0.2/ncappc/MD5 | 68 ncappc-0.2/ncappc/NAMESPACE | 18 ncappc-0.2/ncappc/R/calc.stat.R | 104 ncappc-0.2/ncappc/R/dv.plot.R | 4 ncappc-0.2/ncappc/R/est.nca.R | 233 + ncappc-0.2/ncappc/R/histobs.plot.R | 70 ncappc-0.2/ncappc/R/histpop.plot.R | 60 ncappc-0.2/ncappc/R/nca.deviation.plot.R | 14 ncappc-0.2/ncappc/R/nca.npde.R | 5 ncappc-0.2/ncappc/R/nca.npde.plot.R | 9 ncappc-0.2/ncappc/R/nca.pde.deviation.outlier.R | 157 - ncappc-0.2/ncappc/R/ncappc.R | 1987 +++++++-------- ncappc-0.2/ncappc/README.md | 13 ncappc-0.2/ncappc/build/vignette.rds |binary ncappc-0.2/ncappc/inst/doc/ncappc-vignette.Rmd | 3 ncappc-0.2/ncappc/inst/doc/ncappc-vignette.html | 329 +- ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA-PPC.Rmd |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA-PPC.Rnw |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA.Rmd |only ncappc-0.2/ncappc/inst/misc/ncappcReport-NCA.Rnw |only ncappc-0.2/ncappc/man/calc.stat.Rd | 2 ncappc-0.2/ncappc/man/est.nca.Rd | 27 ncappc-0.2/ncappc/man/histobs.plot.Rd | 24 ncappc-0.2/ncappc/man/histpop.plot.Rd | 9 ncappc-0.2/ncappc/man/nca.deviation.plot.Rd | 7 ncappc-0.2/ncappc/man/nca.pde.deviation.outlier.Rd | 33 ncappc-0.2/ncappc/man/ncappc.Rd | 51 ncappc-0.2/ncappc/tests/testthat/testthat.R |only ncappc-0.2/ncappc/vignettes/Sub-CommandLineArguments.Rmd | 161 - ncappc-0.2/ncappc/vignettes/Sub-Output.Rmd | 15 ncappc-0.2/ncappc/vignettes/conc.jpeg |only ncappc-0.2/ncappc/vignettes/ncappc-vignette.Rmd | 3 ncappc-0.2/ncappc/vignettes/ncappc-vignette.md | 179 - 42 files changed, 1925 insertions(+), 1676 deletions(-)
Title: Sparse Time Series Chain Graphical Models
Description: Computes sparse vector autoregressive coefficients and precision
matrices for time series chain graphical models.
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz <f.abegaz.yazew@rug.nl>
Diff between SparseTSCGM versions 2.1.1 dated 2014-08-21 and 2.2 dated 2015-07-16
SparseTSCGM-2.1.1/SparseTSCGM/R/sim.data.R |only SparseTSCGM-2.2/SparseTSCGM/DESCRIPTION | 16 ++++++------- SparseTSCGM-2.2/SparseTSCGM/MD5 | 20 ++++++++--------- SparseTSCGM-2.2/SparseTSCGM/NAMESPACE | 2 - SparseTSCGM-2.2/SparseTSCGM/R/compute.sparse.tscgm.R | 4 +-- SparseTSCGM-2.2/SparseTSCGM/R/sim.data.r |only SparseTSCGM-2.2/SparseTSCGM/R/sparse.tscgm.R | 10 ++++---- SparseTSCGM-2.2/SparseTSCGM/man/SparseTSCGM-package.Rd | 10 ++++---- SparseTSCGM-2.2/SparseTSCGM/man/plot.tscgm.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/plot.tscgm.ar2.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/sim.data.Rd | 4 +-- SparseTSCGM-2.2/SparseTSCGM/man/sparse.tscgm.Rd | 4 +-- 12 files changed, 39 insertions(+), 39 deletions(-)
Title: Read and Write TIFF Files
Description: Reads and writes TIFF format images and
returns them as a pixmap object. Because the resulting object
can be very large for even modestly sized TIFF images, images
can be reduced as they are read for improved performance. This
package is a wrapper around libtiff (www.libtiff.org), on which
it depends (i.e. the libtiff shared library must be on your
PATH for the binary to work, and tiffio.h must be on your
system to build the package from source). By using libtiff's
highlevel TIFFReadRGBAImage function, this package inherently
supports a wide range of image formats and compression schemes.
This package also provides an implementation of the Ridler
Autothresholding algorithm for easy generation of binary masks.
Author: Eric Kort <eric.kort@vai.org>
Maintainer: Eric Kort <eric.kort@vai.org>
Diff between rtiff versions 1.4.4 dated 2014-02-14 and 1.4.5 dated 2015-07-16
rtiff-1.4.4/rtiff/LICENSE |only rtiff-1.4.5/rtiff/DESCRIPTION | 25 +++++++++++-------------- rtiff-1.4.5/rtiff/MD5 | 10 +++++----- rtiff-1.4.5/rtiff/R/readTiff.R | 10 +++++++--- rtiff-1.4.5/rtiff/cleanup |only rtiff-1.4.5/rtiff/man/readTiff.Rd | 10 +++++++--- rtiff-1.4.5/rtiff/src/rtiff.c | 1 - 7 files changed, 30 insertions(+), 26 deletions(-)
Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format (described at
<https://github.com/toml-lang/toml>) suitable for both human editing as well
as the common uses of a machine-readable format. This package uses 'Rcpp' to
connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.0.3 dated 2015-04-27 and 0.0.4 dated 2015-07-16
ChangeLog | 21 ++++++++++++++++++++- DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- R/parseToml.R | 2 +- README.md | 28 +++++++++++++++++++++++++--- inst/include/cpptoml.h | 18 ++++++++++++++++-- src/Makevars | 2 +- src/parse.cpp | 1 + 8 files changed, 81 insertions(+), 25 deletions(-)
Title: An R Package for Reading and Writing BAM (Binary Alignment)
Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.12.1 dated 2015-07-15 and 2.12.2 dated 2015-07-16
DESCRIPTION | 6 - MD5 | 10 +-- inst/doc/rbamtools.pdf |binary src/extptr.h | 2 src/range_partition.h | 92 ++++++++++++++-------------- src/rbamtools.cpp | 157 +++++++++++++++++++++++++++---------------------- 6 files changed, 143 insertions(+), 124 deletions(-)
Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras <virmantas.kvedaras@mif.vu.lt>, Vaidotas Zemlys
<vaidotas.zemlys@mif.vu.lt>
Maintainer: Vaidotas Zemlys <zemlys@gmail.com>
Diff between midasr versions 0.4 dated 2015-03-10 and 0.5 dated 2015-07-16
midasr-0.4/midasr/inst/tests |only midasr-0.5/midasr/DESCRIPTION | 9 midasr-0.5/midasr/MD5 | 158 +++---- midasr-0.5/midasr/NAMESPACE | 45 ++ midasr-0.5/midasr/NEWS | 204 +++++---- midasr-0.5/midasr/R/lagspec.R | 48 ++ midasr-0.5/midasr/R/midas_r_methods.R | 53 +- midasr-0.5/midasr/R/midasreg.R | 370 +++++++++------- midasr-0.5/midasr/R/modsel.R | 3 midasr-0.5/midasr/R/nonparametric.R | 1 midasr-0.5/midasr/R/simulate.R | 491 +++++++++++----------- midasr-0.5/midasr/R/tests.R | 548 ++++++++++++------------- midasr-0.5/midasr/README.md | 5 midasr-0.5/midasr/inst/CITATION | 24 - midasr-0.5/midasr/man/USpayems.Rd | 2 midasr-0.5/midasr/man/USqgdp.Rd | 2 midasr-0.5/midasr/man/USrealgdp.Rd | 2 midasr-0.5/midasr/man/USunempr.Rd | 2 midasr-0.5/midasr/man/agk.test.Rd | 2 midasr-0.5/midasr/man/almonp.Rd | 2 midasr-0.5/midasr/man/almonp_gradient.Rd | 2 midasr-0.5/midasr/man/amidas_table.Rd | 2 midasr-0.5/midasr/man/amweights.Rd | 2 midasr-0.5/midasr/man/average_forecast.Rd | 2 midasr-0.5/midasr/man/check_mixfreq.Rd | 2 midasr-0.5/midasr/man/coef.midas_r.Rd | 2 midasr-0.5/midasr/man/deriv_tests.Rd | 2 midasr-0.5/midasr/man/deviance.midas_r.Rd | 2 midasr-0.5/midasr/man/dmls.Rd | 2 midasr-0.5/midasr/man/expand_amidas.Rd | 2 midasr-0.5/midasr/man/expand_weights_lags.Rd | 2 midasr-0.5/midasr/man/fmls.Rd | 2 midasr-0.5/midasr/man/forecast.midas_r.Rd | 4 midasr-0.5/midasr/man/genexp.Rd |only midasr-0.5/midasr/man/genexp_gradient.Rd |only midasr-0.5/midasr/man/get_estimation_sample.Rd | 2 midasr-0.5/midasr/man/gompertzp.Rd | 2 midasr-0.5/midasr/man/gompertzp_gradient.Rd | 2 midasr-0.5/midasr/man/hAh_test.Rd | 2 midasr-0.5/midasr/man/hAhr_test.Rd | 2 midasr-0.5/midasr/man/harstep.Rd | 2 midasr-0.5/midasr/man/harstep_gradient.Rd | 2 midasr-0.5/midasr/man/hf_lags_table.Rd | 2 midasr-0.5/midasr/man/imidas_r.Rd | 2 midasr-0.5/midasr/man/lcauchyp.Rd | 2 midasr-0.5/midasr/man/lcauchyp_gradient.Rd | 2 midasr-0.5/midasr/man/lf_lags_table.Rd | 2 midasr-0.5/midasr/man/lws_table-add.Rd | 2 midasr-0.5/midasr/man/midas_auto_sim.Rd | 2 midasr-0.5/midasr/man/midas_r.Rd | 5 midasr-0.5/midasr/man/midas_r.fit.Rd | 2 midasr-0.5/midasr/man/midas_r_ic_table.Rd | 2 midasr-0.5/midasr/man/midas_r_np.Rd | 2 midasr-0.5/midasr/man/midas_r_simple.Rd | 2 midasr-0.5/midasr/man/midas_sim.Rd | 2 midasr-0.5/midasr/man/midas_u.Rd | 2 midasr-0.5/midasr/man/midasr-package.Rd | 2 midasr-0.5/midasr/man/mls.Rd | 2 midasr-0.5/midasr/man/modsel.Rd | 2 midasr-0.5/midasr/man/nakagamip.Rd | 2 midasr-0.5/midasr/man/nakagamip_gradient.Rd | 2 midasr-0.5/midasr/man/nbeta.Rd | 2 midasr-0.5/midasr/man/nbetaMT.Rd | 2 midasr-0.5/midasr/man/nbetaMT_gradient.Rd | 2 midasr-0.5/midasr/man/nbeta_gradient.Rd | 2 midasr-0.5/midasr/man/nealmon.Rd | 2 midasr-0.5/midasr/man/nealmon_gradient.Rd | 2 midasr-0.5/midasr/man/oos_prec.Rd | 2 midasr-0.5/midasr/man/plot_midas_coef.Rd | 2 midasr-0.5/midasr/man/polystep.Rd | 2 midasr-0.5/midasr/man/polystep_gradient.Rd | 2 midasr-0.5/midasr/man/predict.midas_r.Rd | 2 midasr-0.5/midasr/man/prep_hAh.Rd | 2 midasr-0.5/midasr/man/rvsp500.Rd | 2 midasr-0.5/midasr/man/select_and_forecast.Rd | 2 midasr-0.5/midasr/man/simulate.midas_r.Rd | 2 midasr-0.5/midasr/man/split_data.Rd | 2 midasr-0.5/midasr/man/update_weights.Rd | 2 midasr-0.5/midasr/man/weights_table.Rd | 2 midasr-0.5/midasr/tests |only 80 files changed, 1117 insertions(+), 973 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-42 dated 2015-07-02 and 7.3-43 dated 2015-07-16
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown <patrick.brown@utoronto.ca> [aut, cre]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.3.1 dated 2015-07-07 and 1.3.2 dated 2015-07-16
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- R/colourScale.R | 9 +++++++-- R/getTiles.R | 6 +++++- R/insetMap.R | 8 ++++---- R/map.new.R | 34 ++++++++++++++-------------------- inst/doc/mapLayers.pdf |binary inst/doc/mapmisc.pdf |binary man/map.new.Rd |only man/scaleBar.Rd | 12 +----------- 10 files changed, 46 insertions(+), 52 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-3 dated 2015-07-08 and 1.0-4 dated 2015-07-16
DESCRIPTION | 12 ++-- MD5 | 105 +++++++++++++++++++------------------- NAMESPACE | 2 R/cache.R | 16 +++-- R/codes.R | 66 +++++++++++++++++++---- R/corpus.R | 2 R/dataset.R | 13 +++- R/db_api.R | 22 ++++++- R/manifesto.R | 3 - R/manifestoR-package.r | 1 R/scaling_general.R | 8 +- build/vignette.rds |binary inst/doc/manifestoRworkflow.pdf |binary man/ManifestoAvailability.Rd | 2 man/ManifestoCorpus.Rd | 2 man/ManifestoDocument.Rd | 2 man/ManifestoDocumentMeta.Rd | 2 man/ManifestoSource.Rd | 2 man/cmp_codes.Rd | 2 man/codes.Rd | 2 man/corpusupdate.Rd | 9 ++- man/count_codes.Rd | 9 ++- man/formatids.Rd | 2 man/formatmpds.Rd | 2 man/get_mpdb.Rd | 7 +- man/get_viacache.Rd | 2 man/manifestoR.Rd | 2 man/median_voter.Rd | 2 man/mp_availability.Rd | 2 man/mp_bootstrap.Rd | 2 man/mp_cite.Rd | 2 man/mp_coreversions.Rd | 2 man/mp_corpus.Rd | 2 man/mp_corpusversions.Rd | 2 man/mp_emptycache.Rd | 2 man/mp_interpolate.Rd | 2 man/mp_load_cache.Rd | 2 man/mp_maindataset.Rd | 2 man/mp_metadata.Rd | 2 man/mp_save_cache.Rd | 2 man/mp_scale.Rd | 2 man/mp_setapikey.Rd | 2 man/mp_use_corpus_version.Rd | 2 man/mp_view_originals.Rd | 2 man/mpdb_api_request.Rd | 2 man/null_to_na.Rd | 2 man/readManifesto.Rd | 2 man/rep.data.frame.Rd | 2 man/rescale.Rd | 2 man/rile.Rd | 2 man/scale.Rd | 2 man/vanilla.Rd | 2 vignettes/manifestoRworkflow.Rmd | 9 +-- vignettes/manifestoRworkflow.html |only 54 files changed, 216 insertions(+), 140 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova <alku@dtu.dk>
Diff between lmerTest versions 2.0-28 dated 2015-07-14 and 2.0-29 dated 2015-07-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 3 +-- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: Functions to Explore L-Systems (Lindenmayer Systems)
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can
be used to simulate biological forms and certain kinds of fractals.
Briefly, in an L-system a series of symbols in a string are replaced
iteratively according to rules to give a more complex string. Eventually,
the symbols are translated into turtle graphics for plotting. Wikipedia has
a very good introduction: en.wikipedia.org/wiki/L-system This package
provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between LindenmayeR versions 0.1.4 dated 2015-04-16 and 0.1.6 dated 2015-07-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 3 +++ man/LindenmayeR-package.Rd | 2 +- man/Lsys.Rd | 2 +- man/drawLsys.Rd | 2 +- 7 files changed, 17 insertions(+), 14 deletions(-)
Title: Belief Function Implementation
Description: Some basic functions to implement belief functions including:
transformation between belief functions using the method introduced by
Philippe Smets (arXiv:1304.1122 [cs.AI]), evidence combination, evidence
discounting, decision-making, and constructing masses. Currently, thirteen
combination rules and five decision rules are supported. It can also be
used to generate different types of random masses when working on belief
combination and conflict management.
Author: Kuang Zhou <kzhoumath@163.com>; Arnaud Martin
<arnaud.martin@univ-rennes1.fr>
Maintainer: Kuang Zhou <kzhoumath@163.com>
Diff between ibelief versions 1.1 dated 2015-05-15 and 1.2 dated 2015-07-16
ibelief-1.1/ibelief/R/LCRule.R |only ibelief-1.1/ibelief/man/LCRule.Rd |only ibelief-1.2/ibelief/DESCRIPTION | 17 + ibelief-1.2/ibelief/MD5 | 30 +- ibelief-1.2/ibelief/NAMESPACE | 3 ibelief-1.2/ibelief/NEWS | 18 + ibelief-1.2/ibelief/R/BayesianMass.R | 2 ibelief-1.2/ibelief/R/DST.R | 334 ++++++++++++++++++++++++------ ibelief-1.2/ibelief/R/DST_fmt_functions.R | 3 ibelief-1.2/ibelief/R/LCPrinciple.R |only ibelief-1.2/ibelief/R/RandomMass.R | 224 +++++++++++++++----- ibelief-1.2/ibelief/R/decisionDST.R | 2 ibelief-1.2/ibelief/R/discounting.R | 4 ibelief-1.2/ibelief/README.md | 22 + ibelief-1.2/ibelief/man/DST.Rd | 134 +++++++----- ibelief-1.2/ibelief/man/LCPrincple.Rd |only ibelief-1.2/ibelief/man/RandomMass.Rd | 121 ++++++---- ibelief-1.2/ibelief/man/decisionDST.Rd | 94 ++++---- 18 files changed, 704 insertions(+), 304 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach
to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e.,
data described by univariate histograms. The methods and the basic statistics for
histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification techniques,
least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unina2.it>
Diff between HistDAWass versions 0.1.2 dated 2015-03-17 and 0.1.3 dated 2015-07-16
DESCRIPTION | 11 - MD5 | 194 ++++++++++++++-------------- NAMESPACE | 24 +++ R/Fuzzy_cmeans.R | 2 R/Kohonen_maps.R | 1 R/Met_HTS.R | 6 R/Met_MatH.R | 4 R/Met_distributionH.R | 1 R/Utility.R | 1 R/principal_components.R | 4 R/regression.R | 1 R/unsuperv_classification.R | 2 data/HData.RData |binary man/Age_Pyramids_2014.Rd | 2 man/Agronomique.Rd | 2 man/BLOOD.Rd | 2 man/BloodBRITO.Rd | 2 man/Center.cell.MatH-methods.Rd | 2 man/China_Month.Rd | 2 man/China_Seas.Rd | 2 man/DouglasPeucker.Rd | 2 man/HTS-class.Rd | 2 man/HTS.exponential.smoothing.Rd | 2 man/HTS.moving.averages.Rd | 2 man/HTS.predict.knn.Rd | 2 man/HistDAWass-package.Rd | 2 man/MatH-class.Rd | 2 man/OzoneFull.Rd | 2 man/OzoneH.Rd | 2 man/RetHTS.Rd | 2 man/ShortestDistance.Rd | 2 man/TMatH-class.Rd | 2 man/TdistributionH-class.Rd | 2 man/WH.1d.PCA.Rd | 2 man/WH.MultiplePCA.Rd | 2 man/WH.SSQ-methods.Rd | 2 man/WH.SSQ2-methods.Rd | 2 man/WH.bind-methods.Rd | 2 man/WH.bind.col-methods.Rd | 2 man/WH.bind.row-methods.Rd | 2 man/WH.correlation-methods.Rd | 2 man/WH.correlation2-methods.Rd | 2 man/WH.mat.prod-methods.Rd | 2 man/WH.mat.sum-methods.Rd | 2 man/WH.regression.GOF.Rd | 2 man/WH.regression.two.components.Rd | 2 man/WH.regression.two.components.predict.Rd | 2 man/WH.var.covar-methods.Rd | 2 man/WH.var.covar2-methods.Rd | 2 man/WH.vec.mean-methods.Rd | 2 man/WH.vec.sum-methods.Rd | 2 man/WH_2d_Adaptive_Kohonen_maps.Rd | 2 man/WH_2d_Kohonen_maps.Rd | 2 man/WH_adaptive.kmeans.Rd | 2 man/WH_adaptive_fcmeans.Rd | 2 man/WH_fcmeans.Rd | 4 man/WH_hclust.Rd | 2 man/WH_kmeans.Rd | 2 man/WassSqDistH-methods.Rd | 2 man/checkEmptyBins-methods.Rd | 2 man/compP-methods.Rd | 2 man/compQ-methods.Rd | 2 man/crwtransform-methods.Rd | 2 man/data2hist.Rd | 2 man/distributionH-class.Rd | 2 man/dotpW-methods.Rd | 2 man/extract-methods.Rd | 2 man/get.MatH.main.info-methods.Rd | 2 man/get.MatH.ncols-methods.Rd | 2 man/get.MatH.nrows-methods.Rd | 2 man/get.MatH.rownames-methods.Rd | 2 man/get.MatH.stats-methods.Rd | 2 man/get.MatH.varnames-methods.Rd | 2 man/get.distr-methods.Rd | 2 man/get.histo-methods.Rd | 2 man/get.m-methods.Rd | 2 man/get.s-methods.Rd | 2 man/is.registeredMH-methods.Rd | 2 man/kurtH-methods.Rd | 2 man/meanH-methods.Rd | 2 man/minus.Rd | 2 man/plot-HTS.Rd | 8 - man/plot-MatH.Rd | 4 man/plot-TdistributionH.Rd | 2 man/plot-distributionH.Rd | 2 man/plotPredVsObs.Rd | 2 man/plot_errors.Rd | 2 man/plus-methods.Rd | 2 man/rQQ-methods.Rd | 2 man/register-methods.Rd | 2 man/registerMH-methods.Rd | 2 man/show-MatH-methods.Rd | 2 man/show-distributionH-methods.Rd | 2 man/skewH-methods.Rd | 2 man/stations_coordinates.Rd | 2 man/stdH-methods.Rd | 2 man/subsetHTS-methods.Rd | 2 man/times-methods.Rd | 2 98 files changed, 234 insertions(+), 197 deletions(-)
Title: Visualization of Functional Analysis Data
Description: Implementation of multilayered visualizations for enhanced graphical
representation of functional analysis data. It combines and integrates omics
data derived from expression and functional annotation enrichment analyses.
Its plotting functions have been developed with an hierarchical structure in
mind: starting from a general overview to identify the most enriched
categories (modified bar plot, bubble plot) to a more detailed one displaying
different types of relevant information for the molecules in a given set of
categories (circle plot, chord plot, cluster plot, Venn diagram).
Author: Wencke Walter, Fatima Sanchez-Cabo
Maintainer: Wencke Walter <wencke.walter@arcor.de>
Diff between GOplot versions 1.0 dated 2015-01-30 and 1.0.1 dated 2015-07-16
DESCRIPTION | 17 MD5 | 54 +- NAMESPACE | 6 R/GOCluster.R | 274 ++++++++++++--- R/GOCore.R | 757 ++++++++++++++++-------------------------- R/GOVenn.R | 24 - README.md |only build/vignette.rds |binary inst/doc/GOplot_vignette.Rmd | 4 inst/doc/GOplot_vignette.html | 543 +++++++++--------------------- man/EC.Rd | 2 man/GOBar.Rd | 2 man/GOBubble.Rd | 10 man/GOChord.Rd | 4 man/GOCircle.Rd | 2 man/GOCluster.Rd | 18 man/GOVenn.Rd | 2 man/bezier.Rd | 2 man/chord_dat.Rd | 40 +- man/circleFun.Rd | 2 man/circle_dat.Rd | 2 man/draw_table.Rd | 6 man/get_overlap.Rd | 2 man/get_overlap2.Rd | 2 man/theme_blank.Rd | 2 vignettes/GOBar.png |only vignettes/GOBubble1.png |binary vignettes/GOBubble2.png |binary vignettes/GOCirc.png |binary 29 files changed, 794 insertions(+), 983 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized singular value decomposition of a matrix pair, utilizing Lapack routines.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.5 dated 2015-02-12 and 1.6 dated 2015-07-16
DESCRIPTION | 20 ++++++++++---------- MD5 | 33 +++++++++++++++++++++++++++------ NAMESPACE | 12 +++++++++--- NEWS | 5 +++++ R/gsvd.R |only R/lapackerror.R | 5 +++++ man/geigen-package.Rd | 5 ++++- man/gqz.Rd | 10 +++++----- man/gsvd.Rd |only man/gsvdaux.Rd |only src/xdggsvd.f |only tests/testgsvd.R |only tests/tgsvd1.R |only tests/tgsvd1.Rout.save |only tests/tgsvd2.R |only tests/tgsvd2.Rout.save |only tests/tgsvd3.R |only tests/tgsvd3.Rout.save |only tests/tgsvd4.R |only tests/tgsvd4.Rout.save |only tests/tgsvd5.R |only tests/tgsvd5.Rout.save |only tests/tgsvd6.R |only tests/tgsvd6.Rout.save |only tests/tgsvd7.R |only tests/tgsvd7.Rout.save |only tests/tgsvd8.R |only tests/tgsvd8.Rout.save |only 28 files changed, 65 insertions(+), 25 deletions(-)
Title: Fitting an Interval Response Variable Using gamlss.family
Distributions
Description: This is an add-on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>, Nicoleta Mortan
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.cens versions 4.3.1 dated 2015-02-03 and 4.3-2 dated 2015-07-16
DESCRIPTION | 14 ++-- MD5 | 10 +-- NAMESPACE | 44 +++++++------- data/lip.rda |binary man/cens.d.Rd | 2 man/gamlss.cens-package.Rd | 140 ++++++++++++++++++++++----------------------- 6 files changed, 106 insertions(+), 104 deletions(-)
Title: Scale-Dependent Hyperpriors in Structured Additive
Distributional Regression
Description: Utility functions for scale-dependent and alternative hyperpriors.
Author: Nadja Klein <nklein@uni-goettingen.de>
Maintainer: Nadja Klein <nklein@uni-goettingen.de>
Diff between sdPrior versions 0.2 dated 2015-07-07 and 0.3 dated 2015-07-15
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++++++-- NAMESPACE | 8 ++++++-- R/mdf_aunif.r |only R/mdf_ga.r |only R/mdf_gbp.r |only R/mdf_ig.r |only R/mdf_sd.r |only man/mdf_aunif.Rd |only man/mdf_ga.Rd |only man/mdf_gbp.Rd |only man/mdf_ig.Rd |only man/mdf_sd.Rd |only 13 files changed, 21 insertions(+), 7 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.71 dated 2015-05-14 and 1.0.73 dated 2015-07-15
DESCRIPTION | 9 +- MD5 | 12 +-- NAMESPACE | 123 ++++++++++++++++++++++------------ R/MM.COGARCH.R | 199 ++++++++++++++++++++++++++++++++++++++++++++++++++------ R/setCarma.R | 2 data/LogSPX.rda |only man/LogSPX.Rd |only man/gmm.rd | 2 8 files changed, 273 insertions(+), 74 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.3 dated 2015-06-30 and 1.2.0 dated 2015-07-15
DESCRIPTION | 14 ++--- MD5 | 45 +++++++++-------- NAMESPACE | 3 - NEWS | 13 +++++ R/utilities_svdraws.R | 56 ++++++++++++++++++--- R/wrappers.R | 69 +++++++++++++++++++++------ inst/doc/article.R | 40 +++++++-------- inst/doc/article.Rnw | 5 - inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary man/arpredict.Rd |only man/exrates.Rd | 6 +- man/svsample.Rd | 49 ++++++++++++++++--- man/svsample2.Rd | 1 src/Makevars | 2 src/Makevars.win | 2 src/auxmix.h | 2 src/progutils.cpp | 6 +- src/progutils.h | 5 + src/sampler.cpp | 79 +++++++++++++++++++++++++++---- src/sampler.h | 5 + vignettes/article.Rnw | 5 - vignettes/mybib.bib | 5 - vignettes/vignette_sampling_draws2.RData |binary 24 files changed, 301 insertions(+), 111 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: A data analysis tool for the political science crowd
for ease analyzing random and nonrandom data.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.02.12 dated 2015-02-14 and 1.3.5 dated 2015-07-15
SciencesPo-1.02.12/SciencesPo/R/CONVENIENCE.R |only SciencesPo-1.02.12/SciencesPo/R/STATISTICS.R |only SciencesPo-1.02.12/SciencesPo/R/VISUALIZATION.R |only SciencesPo-1.02.12/SciencesPo/R/center.R |only SciencesPo-1.02.12/SciencesPo/R/followup.R |only SciencesPo-1.02.12/SciencesPo/R/kalmanFilter.R |only SciencesPo-1.02.12/SciencesPo/R/lrtest.R |only SciencesPo-1.02.12/SciencesPo/R/margins.R |only SciencesPo-1.02.12/SciencesPo/R/maxGaussian.R |only SciencesPo-1.02.12/SciencesPo/R/mi.R |only SciencesPo-1.02.12/SciencesPo/R/perc.table.R |only SciencesPo-1.02.12/SciencesPo/R/perspBox.R |only SciencesPo-1.02.12/SciencesPo/R/rprob.R |only SciencesPo-1.02.12/SciencesPo/R/rstack.R |only SciencesPo-1.02.12/SciencesPo/R/scale.R |only SciencesPo-1.02.12/SciencesPo/R/summarize.R |only SciencesPo-1.02.12/SciencesPo/R/tableau.R |only SciencesPo-1.02.12/SciencesPo/R/userPrompt.R |only SciencesPo-1.02.12/SciencesPo/R/zzz.R |only SciencesPo-1.02.12/SciencesPo/inst/doc/fptp2av.pdf |only 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Title: Hive Plots of R Package Function Calls
Description: Analyzes the function calls in an R package and creates a hive plot of the calls, dividing them among functions that only make outgoing calls (sources), functions that have only incoming calls (sinks), and those that have both incoming calls and make outgoing calls (managers). Function calls can be mapped by their absolute numbers, their normalized absolute numbers, or their rank. FuncMap should be useful for comparing packages at a high level for their overall design. Plus, it's just plain fun. The hive plot concept was developed by Martin Krzywinski (www.hiveplot.com) and inspired this package. Note: this package is maintained for historical reasons. HiveR is a full package for creating hive plots.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between FuncMap versions 1.0-3 dated 2015-01-13 and 1.0.8 dated 2015-07-15
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 4 +++- NEWS | 29 +++++++++++++++-------------- man/FuncMap-package.Rd | 23 +++++++++++------------ man/FuncMap.Rd | 1 - 6 files changed, 40 insertions(+), 39 deletions(-)
Title: Wrapper for Nokia's HERE Geocoding API
Description: Wrapper for Nokia's HERE geocoding API. See http://here.com/ for
more information on HERE and https://developer.here.com/geocoder for more
information on the HERE geocoding API.
Author: Cory Nissen <corynissen@gmail.com> [aut, cre]
Maintainer: Cory Nissen <corynissen@gmail.com>
Diff between geocodeHERE versions 0.1.2 dated 2015-03-04 and 0.1.3 dated 2015-07-15
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 +- R/geocodeHERE_batch_get_data.R | 8 ++++---- R/geocodeHERE_batch_status.R | 4 ++-- R/geocodeHERE_batch_upload.R | 4 ++-- R/geocodeHERE_simple.R | 6 +++--- man/chicago_landmarks.Rd | 3 ++- man/df_to_string.Rd | 3 ++- man/geocodeHERE.Rd | 3 ++- man/geocodeHERE_batch_get_data.Rd | 3 ++- man/geocodeHERE_batch_status.Rd | 3 ++- man/geocodeHERE_batch_upload.Rd | 3 ++- man/geocodeHERE_simple.Rd | 3 ++- 14 files changed, 43 insertions(+), 36 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of Rd objects, including function
reprompt() for updating existing Rd documentation for
functions, methods and classes, and function rebib() for
import of references from bibtex files.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 0.4-14 dated 2014-04-16 and 0.4-18 dated 2015-07-15
DESCRIPTION | 18 +++++++++--------- MD5 | 14 +++++++------- NAMESPACE | 8 +++++++- NEWS | 26 ++++++++++++++++++++++++++ R/inspect.R | 25 ++++++++++++++++++++++--- R/slots.R | 23 +++++++++++++++++++++-- TODO | 5 +++++ build/partial.rdb |binary 8 files changed, 97 insertions(+), 22 deletions(-)
Title: An R Package for Reading and Writing BAM (Binary Alignment)
Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.10.0 dated 2014-09-30 and 2.12.1 dated 2015-07-15
rbamtools-2.10.0/rbamtools/man/range2fastq.Rd |only rbamtools-2.10.0/rbamtools/man/reader2fastq.Rd |only rbamtools-2.10.0/rbamtools/src/rbamtools.c |only rbamtools-2.12.1/rbamtools/ChangeLog | 6 rbamtools-2.12.1/rbamtools/DESCRIPTION | 15 rbamtools-2.12.1/rbamtools/MD5 | 67 rbamtools-2.12.1/rbamtools/NAMESPACE | 29 rbamtools-2.12.1/rbamtools/NEWS | 26 rbamtools-2.12.1/rbamtools/R/rbamtools.r | 2216 ++++++++++------ rbamtools-2.12.1/rbamtools/build/vignette.rds |binary rbamtools-2.12.1/rbamtools/inst/doc/rbamtools.R | 247 + rbamtools-2.12.1/rbamtools/inst/doc/rbamtools.Rnw | 860 ++++-- rbamtools-2.12.1/rbamtools/inst/doc/rbamtools.pdf |binary rbamtools-2.12.1/rbamtools/man/GenomePartition-class.Rd |only rbamtools-2.12.1/rbamtools/man/bamRange.Rd | 7 rbamtools-2.12.1/rbamtools/man/bamReader-class.Rd | 12 rbamtools-2.12.1/rbamtools/man/extractBamRegions.Rd |only rbamtools-2.12.1/rbamtools/man/nucStats.Rd | 2 rbamtools-2.12.1/rbamtools/man/rangeSegCount-class.Rd |only rbamtools-2.12.1/rbamtools/man/rangeToFastq.Rd |only rbamtools-2.12.1/rbamtools/man/readerToFastq.Rd |only rbamtools-2.12.1/rbamtools/src/Makevars | 1 rbamtools-2.12.1/rbamtools/src/Makevars.win | 1 rbamtools-2.12.1/rbamtools/src/align_counts.h |only rbamtools-2.12.1/rbamtools/src/align_list.h | 80 rbamtools-2.12.1/rbamtools/src/bitmask.h | 12 rbamtools-2.12.1/rbamtools/src/data_frame.h |only rbamtools-2.12.1/rbamtools/src/extptr.h |only rbamtools-2.12.1/rbamtools/src/gapSiteList.h | 114 rbamtools-2.12.1/rbamtools/src/gapSiteListList.h | 37 rbamtools-2.12.1/rbamtools/src/gap_list.h | 22 rbamtools-2.12.1/rbamtools/src/grange.h |only rbamtools-2.12.1/rbamtools/src/range_partition.h |only rbamtools-2.12.1/rbamtools/src/rbamtools.cpp |only rbamtools-2.12.1/rbamtools/src/rbamtools.h | 61 rbamtools-2.12.1/rbamtools/src/samtools/rdef.h | 2 rbamtools-2.12.1/rbamtools/tests/test-all.R | 30 rbamtools-2.12.1/rbamtools/tests/test_bam_align.r | 12 rbamtools-2.12.1/rbamtools/tests/test_bam_header.r | 36 rbamtools-2.12.1/rbamtools/tests/test_range_seg_count.r |only rbamtools-2.12.1/rbamtools/vignettes/rbamtools.Rnw | 860 ++++-- rbamtools-2.12.1/rbamtools/vignettes/rbamtools.bib | 37 42 files changed, 3265 insertions(+), 1527 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.3.1 dated 2015-07-14 and 1.3.2 dated 2015-07-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++++ R/get_download.R | 5 +++-- README.md | 1 + tests/testthat/test_neotoma.R | 5 +++++ 6 files changed, 22 insertions(+), 11 deletions(-)
Title: Integrated Code Chunk Anchoring and Referencing for R Markdown
Documents
Description: A streamlined cross-referencing system for R Markdown documents
generated with 'knitr'. R Markdown is an authoring format for generating
dynamic content from R. 'kfigr' provides a hook for anchoring code
chunks and a function to cross-reference document elements generated from
said chunks, e.g. figures and tables.
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between kfigr versions 1.1.0 dated 2015-03-16 and 1.2 dated 2015-07-15
kfigr-1.1.0/kfigr/README.md |only kfigr-1.2/kfigr/DESCRIPTION | 14 +++--- kfigr-1.2/kfigr/MD5 | 34 +++++++-------- kfigr-1.2/kfigr/NAMESPACE | 9 ++-- kfigr-1.2/kfigr/R/anchors.R | 45 +++++++++++---------- kfigr-1.2/kfigr/R/figr.R | 44 ++++++++++---------- kfigr-1.2/kfigr/R/hook_anchor.r | 27 ++++++++++++ kfigr-1.2/kfigr/R/index.R | 23 ++++++---- kfigr-1.2/kfigr/R/kfigr-package.R |only kfigr-1.2/kfigr/R/zzz.R | 9 ++-- kfigr-1.2/kfigr/build/vignette.rds |binary kfigr-1.2/kfigr/inst/doc/introduction.Rmd | 2 kfigr-1.2/kfigr/inst/doc/introduction.html | 10 ++-- kfigr-1.2/kfigr/man/anchors.Rd | 60 ++++++++++++++-------------- kfigr-1.2/kfigr/man/figr.Rd | 62 +++++++++++++++-------------- kfigr-1.2/kfigr/man/hook_anchor.Rd | 32 +++++++------- kfigr-1.2/kfigr/man/index.Rd | 41 ++++++++++--------- kfigr-1.2/kfigr/man/kfigr-package.Rd | 44 ++++++-------------- kfigr-1.2/kfigr/vignettes/introduction.Rmd | 2 19 files changed, 248 insertions(+), 210 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>
Diff between GSE versions 3.2 dated 2015-07-05 and 3.2.1 dated 2015-07-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/emve.cpp | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution.
It provides the density function, distribution function, and Quantile-Quantile plots.
It implements a variety of estimation methods for the distribution, including diagnostic plots.
Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation.
These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.3 dated 2015-07-03 and 2.3.1 dated 2015-07-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ R/fxgld.R | 2 +- R/plotgl.R | 2 +- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: The FCNN4R package provides an interface to kernel routines
from the FCNN C++ library. FCNN is based on a completely new
Artificial Neural Network representation that offers unmatched
efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop) and pruning
algorithms (minimum magnitude, Optimal Brain Surgeon), but it is
first and foremost an efficient computational engine. Users
can easily implement their algorithms by taking advantage
of fast gradient computing routines, as well as network
reconstruction functionality (removing weights and redundant
neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.3.0 dated 2015-07-14 and 0.3.1 dated 2015-07-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Makevars.include | 9 +-------- 3 files changed, 7 insertions(+), 14 deletions(-)
Title: Deductive Correction, Deductive Imputation, and Deterministic
Correction
Description: A collection of methods for automated data cleaning where all actions are logged.
Author: Mark van der Loo, Edwin de Jonge, and Sander
Scholtus
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between deducorrect versions 1.3-5 dated 2014-10-01 and 1.3.7 dated 2015-07-15
DESCRIPTION | 20 +++++------ MD5 | 66 +++++++++++++++++++------------------- NAMESPACE | 6 ++- NEWS | 3 + R/pkg.R | 4 ++ build/vignette.rds |binary inst/doc/deducorrect-vignette.pdf |binary inst/doc/index.html | 2 - man/allTotallyUnimodular.Rd | 3 + man/applyFix.Rd | 3 + man/correctRounding.Rd | 3 + man/correctSigns.Rd | 3 + man/correctTypos.Rd | 3 + man/correctWithRules.Rd | 3 + man/correctionRules.Rd | 3 + man/damerauLevenshteinDistance.Rd | 3 + man/deduImpute.Rd | 3 + man/deducorrect-object.Rd | 3 + man/deducorrect-package.Rd | 3 + man/deductiveLevels.Rd | 3 + man/deductiveZeros.Rd | 3 + man/getSignCorrection.Rd | 3 + man/getTypoCorrection.Rd | 3 + man/getUsername.Rd | 3 + man/hellerTompkins.Rd | 3 + man/imputess.Rd | 3 + man/isTotallyUnimodular.Rd | 3 + man/newdeducorrect.Rd | 3 + man/raghavachari.Rd | 3 + man/reduceMatrix.Rd | 3 + man/scapegoat.Rd | 3 + man/solSpace.Rd | 7 ++-- man/status.Rd | 3 + man/tree.Rd | 3 + 34 files changed, 110 insertions(+), 73 deletions(-)
Title: Cross-Recurrence Quantification Analysis for Categorical and
Continuous Time-Series
Description:
Cross-recurrence quantification analysis
of two time-series, of either categorical or
continuous values. It provides different methods
for profiling cross-recurrence, i.e., only looking
at the diagonal recurrent points, as well as more
in-depth measures of the whole cross-recurrence plot,
e.g., recurrence rate.
Author: Moreno I. Coco and Rick Dale with contributions of James D. Dixon and John Nash
Maintainer: Moreno I. Coco <moreno.cocoi@gmail.com>
Diff between crqa versions 1.0.5 dated 2014-12-05 and 1.0.6 dated 2015-07-15
DESCRIPTION | 23 +++-- MD5 | 15 ++- NAMESPACE | 4 + R/ami.R |only R/crqa.R | 19 +++- R/lorenzattractor.R |only R/optimizeParam.R | 193 ++++++++++++++++++++++++++----------------------- R/runcrqa.R | 4 - man/lorenzattractor.Rd |only man/optimizeParam.Rd | 18 ++-- 10 files changed, 152 insertions(+), 124 deletions(-)
Title: Code Analysis Tools for R
Description: Code analysis tools for R.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between codetools versions 0.2-11 dated 2015-03-10 and 0.2-14 dated 2015-07-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/codetools.R | 15 +++++++++++++-- 3 files changed, 18 insertions(+), 7 deletions(-)
Title: Binarization of One-Dimensional Data
Description: Provides methods for the binarization of one-dimensional data and some visualization functions.
Author: Stefan Mundus, Christoph Müssel, Florian Schmid, Ludwig Lausser, Tamara J. Blätte, Martin Hopfensitz, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between Binarize versions 1.0 dated 2015-03-05 and 1.1 dated 2015-07-15
DESCRIPTION | 11 +-- MD5 | 39 +++++++---- NAMESPACE | 15 ++-- R/TASC.R |only R/binarizeBASC.R | 2 R/binarizeMatrix.R | 89 ++++++++++++++++----------- R/result_TASC.R |only build/vignette.rds |binary data/trinarizationExample.rda |only inst/doc/Vignette.R | 87 +++++++++++++++++++------- inst/doc/Vignette.Rnw | 127 ++++++++++++++++++++++++++++++++++++++- inst/doc/Vignette.pdf |binary man/TASC.Rd |only man/TASCResult-class.Rd |only man/TrinarizationResult-class.Rd |only man/binarizeBASC.Rd | 4 - man/plot.TrinarizationResult.Rd |only man/plotStepFunctions.Rd | 15 +++- man/trinarizationExample.Rd |only man/trinarizeMatrix.Rd |only src/TASC.c |only src/TASC_min.c |only src/binarizeBASCB.h | 7 ++ src/common.c | 9 +- src/common.h | 8 ++ vignettes/Vignette.Rnw | 127 ++++++++++++++++++++++++++++++++++++++- 26 files changed, 437 insertions(+), 103 deletions(-)
Title: Bayesian Analysis of Change Point Problems
Description: Provides an implementation of the Barry and Hartigan (1993) product partition model for the normal errors change point problem using Markov Chain Monte Carlo. It also extends the methodology to regression models on a connected graph (Wang and Emerson, 2015); this allows estimation of change point models with multivariate responses. Parallel MCMC, previously available in bcp v.3.0.0, is currently not implemented.
Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
Maintainer: John W. Emerson <john.emerson@yale.edu>
Diff between bcp versions 3.0.1 dated 2012-04-19 and 4.0.0 dated 2015-07-15
bcp-3.0.1/bcp/Makevars |only bcp-3.0.1/bcp/Makevars.win |only bcp-3.0.1/bcp/man/plot.bcp.legacy.Rd |only bcp-4.0.0/bcp/DESCRIPTION | 29 bcp-4.0.0/bcp/MD5 | 60 - bcp-4.0.0/bcp/NAMESPACE | 31 bcp-4.0.0/bcp/R/RcppExports.R |only bcp-4.0.0/bcp/R/bcp-data.R |only bcp-4.0.0/bcp/R/bcp-package.R |only bcp-4.0.0/bcp/R/bcp.R | 726 +++++++++++++---- bcp-4.0.0/bcp/R/output.R | 339 ++++++-- bcp-4.0.0/bcp/README.md |only bcp-4.0.0/bcp/data/NewHavenHousing.rda |only bcp-4.0.0/bcp/data/QuebecRivers.rda |only bcp-4.0.0/bcp/data/lombard.rda |only bcp-4.0.0/bcp/demo |only bcp-4.0.0/bcp/inst/CITATION | 11 bcp-4.0.0/bcp/inst/TODO |only bcp-4.0.0/bcp/man/NewHavenHousing.Rd |only bcp-4.0.0/bcp/man/QuebecRivers.Rd |only bcp-4.0.0/bcp/man/RealInt.Rd | 64 - bcp-4.0.0/bcp/man/bcp-package.Rd |only bcp-4.0.0/bcp/man/bcp.Rd | 406 +++++---- bcp-4.0.0/bcp/man/coriell.Rd | 78 - bcp-4.0.0/bcp/man/fitted.bcp.Rd | 47 - bcp-4.0.0/bcp/man/interval.prob.Rd | 61 - bcp-4.0.0/bcp/man/legacyplot.Rd |only bcp-4.0.0/bcp/man/lombard.Rd |only bcp-4.0.0/bcp/man/makeAdjGrid.Rd |only bcp-4.0.0/bcp/man/plot.bcp.Rd | 97 +- bcp-4.0.0/bcp/man/residuals.bcp.Rd | 47 - bcp-4.0.0/bcp/man/summary.bcp.Rd | 78 - bcp-4.0.0/bcp/src/Cbcp.cpp | 1394 ++++++++++++++++++--------------- bcp-4.0.0/bcp/src/CbcpM.cpp |only bcp-4.0.0/bcp/src/Cbcpgraph.cpp |only bcp-4.0.0/bcp/src/CbcpgraphR.cpp |only bcp-4.0.0/bcp/src/Makevars | 2 bcp-4.0.0/bcp/src/Makevars.win | 8 bcp-4.0.0/bcp/src/RcppExports.cpp |only 39 files changed, 2118 insertions(+), 1360 deletions(-)
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.2-6 dated 2015-06-24 and 0.3-0 dated 2015-07-15
assertive-0.2-6/assertive/R/assert-is-na-nan-null.R |only assertive-0.2-6/assertive/R/assert-is-true-false.R |only assertive-0.2-6/assertive/R/engine.R |only assertive-0.2-6/assertive/R/internal.R |only assertive-0.2-6/assertive/R/is-na-nan-null.R |only assertive-0.2-6/assertive/R/is-true-false.R |only assertive-0.2-6/assertive/R/utils.R |only assertive-0.2-6/assertive/man/is_na.Rd |only assertive-0.2-6/assertive/man/is_true.Rd |only assertive-0.2-6/assertive/man/merge.list.Rd |only assertive-0.2-6/assertive/man/modal_value.Rd |only assertive-0.2-6/assertive/man/print_and_capture.Rd |only assertive-0.2-6/assertive/man/truncate.Rd |only assertive-0.2-6/assertive/man/type_description.Rd |only assertive-0.2-6/assertive/tests/testthat/test-internal.R |only assertive-0.2-6/assertive/tests/testthat/test-is-true-false.R |only assertive-0.2-6/assertive/tests/testthat/test-utils.R |only assertive-0.3-0/assertive/DESCRIPTION | 32 assertive-0.3-0/assertive/MD5 | 236 +- assertive-0.3-0/assertive/NAMESPACE | 33 assertive-0.3-0/assertive/NEWS | 9 assertive-0.3-0/assertive/R/assert-has.R | 206 +- assertive-0.3-0/assertive/R/assert-is-a-type.R | 18 assertive-0.3-0/assertive/R/assert-is-atomic-recursive-vector.R | 40 assertive-0.3-0/assertive/R/assert-is-binding.R | 12 assertive-0.3-0/assertive/R/assert-is-connection.R | 264 +-- assertive-0.3-0/assertive/R/assert-is-empty-scalar.R | 116 - assertive-0.3-0/assertive/R/assert-is-file.R | 304 +-- assertive-0.3-0/assertive/R/assert-is-in-range.R | 663 +++++--- assertive-0.3-0/assertive/R/assert-is-infinity-nan.R |only assertive-0.3-0/assertive/R/assert-is-null.R |only assertive-0.3-0/assertive/R/assert-is-other.R | 223 +- assertive-0.3-0/assertive/R/assert-is-real-imaginary.R | 104 - assertive-0.3-0/assertive/R/assert-is-reflection.R | 399 ++-- assertive-0.3-0/assertive/R/assert-is-set.R | 92 - assertive-0.3-0/assertive/R/assert-is-string-uk.R | 198 +- assertive-0.3-0/assertive/R/assert-is-string-us.R | 86 - assertive-0.3-0/assertive/R/assert-is-string.R | 681 +++++--- assertive-0.3-0/assertive/R/assert-is-time.R | 84 - assertive-0.3-0/assertive/R/assert-is-type.R | 89 - assertive-0.3-0/assertive/R/assert-r-has-capability.R | 292 +-- assertive-0.3-0/assertive/R/assertive-package.R | 74 assertive-0.3-0/assertive/R/has.R | 605 +++---- assertive-0.3-0/assertive/R/imports.R |only assertive-0.3-0/assertive/R/internal-connection.R |only assertive-0.3-0/assertive/R/internal-string.R |only assertive-0.3-0/assertive/R/is-binding.R | 3 assertive-0.3-0/assertive/R/is-empty-scalar.R | 11 assertive-0.3-0/assertive/R/is-in-range.R | 237 +- assertive-0.3-0/assertive/R/is-infinity-nan.R |only assertive-0.3-0/assertive/R/is-null.R |only assertive-0.3-0/assertive/R/is-other.R | 618 ++++--- assertive-0.3-0/assertive/R/is-real-imaginary.R | 121 - assertive-0.3-0/assertive/R/is-reflection.R | 149 + assertive-0.3-0/assertive/R/is-set.R | 173 +- assertive-0.3-0/assertive/R/is-string-uk.R | 814 +++++----- assertive-0.3-0/assertive/R/is-string-us.R | 8 assertive-0.3-0/assertive/R/is-string.R | 53 assertive-0.3-0/assertive/R/is-time.R | 112 - assertive-0.3-0/assertive/R/is-type.R | 71 assertive-0.3-0/assertive/R/locale.R |only assertive-0.3-0/assertive/R/zzz.R | 6 assertive-0.3-0/assertive/README.md | 34 assertive-0.3-0/assertive/build/vignette.rds |binary assertive-0.3-0/assertive/inst/doc/checking_function_inputs.Rmd | 322 +-- assertive-0.3-0/assertive/inst/doc/introduction.Rmd | 257 +-- assertive-0.3-0/assertive/inst/doc/introduction.html | 43 assertive-0.3-0/assertive/man/DIM.Rd | 25 assertive-0.3-0/assertive/man/Truth.Rd |only assertive-0.3-0/assertive/man/as.character.file.Rd | 2 assertive-0.3-0/assertive/man/assert_engine.Rd | 87 - assertive-0.3-0/assertive/man/assert_is_all_of.Rd |only assertive-0.3-0/assertive/man/bapply.Rd | 25 assertive-0.3-0/assertive/man/call_and_name.Rd | 30 assertive-0.3-0/assertive/man/cause.Rd | 24 assertive-0.3-0/assertive/man/changes.Rd |only assertive-0.3-0/assertive/man/character_to_list_of_integer_vectors.Rd | 2 assertive-0.3-0/assertive/man/coerce_to.Rd | 38 assertive-0.3-0/assertive/man/create_regex.Rd | 2 assertive-0.3-0/assertive/man/d.Rd | 2 assertive-0.3-0/assertive/man/dont_stop.Rd | 24 assertive-0.3-0/assertive/man/false.Rd | 17 assertive-0.3-0/assertive/man/get_name_in_parent.Rd | 15 assertive-0.3-0/assertive/man/is2.Rd | 43 assertive-0.3-0/assertive/man/is_binding_locked.Rd | 2 assertive-0.3-0/assertive/man/is_cas_number.Rd | 9 assertive-0.3-0/assertive/man/is_character.Rd | 17 assertive-0.3-0/assertive/man/is_credit_card_number.Rd | 9 assertive-0.3-0/assertive/man/is_current_r.Rd | 4 assertive-0.3-0/assertive/man/is_date_string.Rd | 9 assertive-0.3-0/assertive/man/is_divisible_by.Rd | 23 assertive-0.3-0/assertive/man/is_email_address.Rd | 11 assertive-0.3-0/assertive/man/is_existing.Rd | 23 assertive-0.3-0/assertive/man/is_finite.Rd | 2 assertive-0.3-0/assertive/man/is_hex_color.Rd | 13 assertive-0.3-0/assertive/man/is_honorific.Rd | 15 assertive-0.3-0/assertive/man/is_if_condition.Rd | 7 assertive-0.3-0/assertive/man/is_in_past.Rd | 13 assertive-0.3-0/assertive/man/is_in_range.Rd | 60 assertive-0.3-0/assertive/man/is_ip_address.Rd | 9 assertive-0.3-0/assertive/man/is_isbn_code.Rd | 9 assertive-0.3-0/assertive/man/is_nan.Rd | 2 assertive-0.3-0/assertive/man/is_null.Rd | 13 assertive-0.3-0/assertive/man/is_package_current.Rd |only assertive-0.3-0/assertive/man/is_r.Rd | 9 assertive-0.3-0/assertive/man/is_real.Rd | 20 assertive-0.3-0/assertive/man/is_rstudio_current.Rd |only assertive-0.3-0/assertive/man/is_rstudio_desktop.Rd |only assertive-0.3-0/assertive/man/is_set_equal.Rd | 7 assertive-0.3-0/assertive/man/is_single_character.Rd | 13 assertive-0.3-0/assertive/man/is_uk_car_licence.Rd | 13 assertive-0.3-0/assertive/man/is_uk_national_insurance_number.Rd | 9 assertive-0.3-0/assertive/man/is_uk_postcode.Rd | 9 assertive-0.3-0/assertive/man/is_uk_telephone_number.Rd | 9 assertive-0.3-0/assertive/man/is_us_telephone_number.Rd | 9 assertive-0.3-0/assertive/man/is_us_zip_code.Rd | 9 assertive-0.3-0/assertive/man/is_valid_r_code.Rd | 7 assertive-0.3-0/assertive/man/is_valid_variable_name.Rd | 9 assertive-0.3-0/assertive/man/is_whole_number.Rd | 17 assertive-0.3-0/assertive/man/locale_categories.Rd | 2 assertive-0.3-0/assertive/man/make_range_string.Rd |only assertive-0.3-0/assertive/man/matches_regex.Rd | 2 assertive-0.3-0/assertive/man/merge_dots_with_list.Rd | 30 assertive-0.3-0/assertive/man/n_elements.Rd | 29 assertive-0.3-0/assertive/man/na.Rd | 17 assertive-0.3-0/assertive/man/parenthesize.Rd | 45 assertive-0.3-0/assertive/man/recycle.Rd | 2 assertive-0.3-0/assertive/man/rstudio_version_info.Rd |only assertive-0.3-0/assertive/man/set_cause.Rd | 24 assertive-0.3-0/assertive/man/strip_attributes.Rd | 21 assertive-0.3-0/assertive/man/strip_invalid_chars.Rd | 2 assertive-0.3-0/assertive/man/sys_get_locale.Rd | 2 assertive-0.3-0/assertive/man/use_first.Rd | 20 assertive-0.3-0/assertive/tests/testthat/test-internal-string.R |only assertive-0.3-0/assertive/tests/testthat/test-is-other.R | 185 +- assertive-0.3-0/assertive/tests/testthat/test-is-string.R | 470 ++--- 136 files changed, 5093 insertions(+), 4376 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between abctools versions 1.0.2 dated 2015-05-29 and 1.0.3 dated 2015-07-15
DESCRIPTION | 8 +++--- MD5 | 15 ++++++----- NAMESPACE | 3 ++ R/AS.select.R | 62 ++++++++++++++++++++++++++++++++++++++++++------ data/coal.rda |binary data/coalobs.rda |binary inst |only man/AS.select.Rd | 3 +- man/abctools-package.Rd | 4 +-- 9 files changed, 74 insertions(+), 21 deletions(-)
Title: Weather Forecast Verification Utilities
Description: Utilities for verifying discrete, continuous and probabilistic forecasts, and forecasts expressed as parametric distributions are included.
Author: NCAR - Research Applications Laboratory
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between verification versions 1.41 dated 2014-12-24 and 1.42 dated 2015-07-14
DESCRIPTION | 15 +++++++-------- MD5 | 13 +++++++------ NAMESPACE | 27 +++++++++++++++++++++++++++ R/hgtest.R |only R/predcomptests.R | 41 +++++++++++++++++++++++------------------ R/roc.plot.default.r | 6 +++--- man/predcomp.test.Rd | 45 ++++++++++++++++++--------------------------- man/verify-internal.Rd | 5 ++++- 8 files changed, 89 insertions(+), 63 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph],
Matthew Collins [aut, cre],
Scott Chamberlain [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>
Diff between ridigbio versions 0.2.2 dated 2015-06-11 and 0.3 dated 2015-07-14
ridigbio-0.2.2/ridigbio/man/idig_field_indexes.Rd |only ridigbio-0.3/ridigbio/DESCRIPTION | 12 - ridigbio-0.3/ridigbio/MD5 | 23 +- ridigbio-0.3/ridigbio/R/base.R | 45 ++--- ridigbio-0.3/ridigbio/R/idig_search.R | 87 ++++------ ridigbio-0.3/ridigbio/R/idig_search_records.R | 16 - ridigbio-0.3/ridigbio/R/startup.R | 2 ridigbio-0.3/ridigbio/README.md | 20 +- ridigbio-0.3/ridigbio/man/idig_search_records.Rd | 16 - ridigbio-0.3/ridigbio/man/idig_url.Rd | 2 ridigbio-0.3/ridigbio/tests/testthat/test-base.R | 23 +- ridigbio-0.3/ridigbio/tests/testthat/test-idig_search_media.R | 5 ridigbio-0.3/ridigbio/tests/testthat/test-idig_search_records.R | 32 ++- 13 files changed, 147 insertions(+), 136 deletions(-)
Title: R Interface to the PX-Web/PC-Axis API
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis
API is used by organizations such as Statistics Sweden and Statistics
Finland to disseminate data. The R package can interact with all
PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract
metadata and extract and parse statistics to R data.frame format. PX-Web is
a solution to disseminate PC-Axis data files in dynamic tables on the web.
Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson, Leo Lahti, Love Hansson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between pxweb versions 0.5.54 dated 2015-05-25 and 0.5.57 dated 2015-07-14
DESCRIPTION | 8 ++-- MD5 | 25 +++++++------ NAMESPACE | 2 + R/get_pxweb_data.R | 3 + R/get_pxweb_data_internal.R | 16 ++++++++ R/get_pxweb_metadata.R | 2 - R/interactive_pxweb_internal.R | 36 +++++++++---------- R/pxweb.R | 1 R/utils_internal.R | 13 ++++++- build/vignette.rds |binary inst/extdata/api.json | 13 ++++++- man/reorder_and_check_dims.Rd |only tests/testthat/test-get_pxweb_data.R | 56 +++++++++++++++++++++++++++---- tests/testthat/test-get_pxweb_metadata.R | 2 - 14 files changed, 131 insertions(+), 46 deletions(-)
Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported
count data as well as for Poisson and binomial logit regression models using
spike and slab priors.
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>
Diff between pogit versions 1.0.0 dated 2015-05-02 and 1.0.1 dated 2015-07-14
DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 3 +++ R/logitBvs.R | 9 ++++++--- R/plot.R | 3 +++ R/pogitBvs.R | 9 ++++++--- R/poissonBvs.R | 9 ++++++--- R/simul1.R | 8 +++++--- R/simul2.R | 8 +++++--- inst/CITATION | 11 ++++++----- inst/NEWS.Rd |only man/logitBvs.Rd | 7 ++++--- man/pogit-package.Rd | 7 ++++--- man/pogitBvs.Rd | 7 ++++--- man/poissonBvs.Rd | 7 ++++--- man/simul1.Rd | 7 ++++--- man/simul2.Rd | 7 ++++--- 17 files changed, 85 insertions(+), 58 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future. Web applications are provided
(via 'shiny') for the implemented methods to help in designing and deploying the
computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 0.25.1 dated 2015-06-03 and 0.25.2 dated 2015-07-14
distcomp-0.25.1/distcomp/inst/ex/README.txt |only distcomp-0.25.1/distcomp/man/CoxMaster.Rd |only distcomp-0.25.1/distcomp/man/CoxSlave.Rd |only distcomp-0.25.1/distcomp/man/SVDMaster.Rd |only distcomp-0.25.1/distcomp/man/SVDSlave.Rd |only distcomp-0.25.2/distcomp/DESCRIPTION | 16 - distcomp-0.25.2/distcomp/MD5 | 40 +- distcomp-0.25.2/distcomp/NAMESPACE | 7 distcomp-0.25.2/distcomp/R/distcomp.R | 26 - distcomp-0.25.2/distcomp/R/survivalstuff.R | 6 distcomp-0.25.2/distcomp/README.md | 13 distcomp-0.25.2/distcomp/inst/doc/examples.html | 186 +++++++----- distcomp-0.25.2/distcomp/inst/doc/examples.pdf |binary distcomp-0.25.2/distcomp/inst/doc_src/examples.Rmd | 66 ++-- distcomp-0.25.2/distcomp/inst/doc_src/examples.md | 188 +++++++------ distcomp-0.25.2/distcomp/inst/ex/README.Rmd |only distcomp-0.25.2/distcomp/inst/ex/README.html | 15 + distcomp-0.25.2/distcomp/inst/ex/README.md | 14 distcomp-0.25.2/distcomp/inst/ex/svd-example-full-new.Rout |only distcomp-0.25.2/distcomp/inst/ex/svd-example-full.Rout |only distcomp-0.25.2/distcomp/inst/ex/svd-example.R | 20 + distcomp-0.25.2/distcomp/man/coxMaster.Rd |only distcomp-0.25.2/distcomp/man/coxSlave.Rd |only distcomp-0.25.2/distcomp/man/distcompSetup.Rd | 10 distcomp-0.25.2/distcomp/man/getConfig.Rd | 8 distcomp-0.25.2/distcomp/man/svdMaster.Rd |only distcomp-0.25.2/distcomp/man/svdSlave.Rd |only 27 files changed, 374 insertions(+), 241 deletions(-)
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)). Procedures are included for use with GLM, ivreg, plm (fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>
Diff between clusterSEs versions 2.0 dated 2015-06-23 and 2.0.1 dated 2015-07-14
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 4 ++++ R/clusterBS.glm.R | 4 ++++ R/clusterBS.ivreg.R | 4 ++++ R/clusterBS.mlogit.R | 4 ++++ R/clusterBS.plm.R | 4 ++++ R/clusterIM.glm.R | 12 +++++++----- R/clusterIM.ivreg.R | 10 +++++++--- R/clusterIM.mlogit.R | 17 ++++++++++------- R/clusterwild.glm.R | 4 ++++ R/clusterwild.ivreg.R | 4 ++++ R/clusterwild.plm.R | 4 ++++ man/cluster.im.glm.Rd | 2 +- man/cluster.im.ivreg.Rd | 2 +- man/cluster.im.mlogit.Rd | 2 +- 16 files changed, 79 insertions(+), 38 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Jonah C. Brooks [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 2.0.0 dated 2015-07-08 and 2.0.1 dated 2015-07-14
poppr-2.0.0/poppr/R/zzz.R |only poppr-2.0.1/poppr/DESCRIPTION | 8 poppr-2.0.1/poppr/MD5 | 30 - poppr-2.0.1/poppr/NEWS | 11 poppr-2.0.1/poppr/R/file_handling.r | 1 poppr-2.0.1/poppr/R/imsn.R | 24 + poppr-2.0.1/poppr/R/zzz.r |only poppr-2.0.1/poppr/inst/doc/algo.pdf |binary poppr-2.0.1/poppr/inst/doc/how_to_migrate.pdf |binary poppr-2.0.1/poppr/inst/doc/mlg.html | 8 poppr-2.0.1/poppr/inst/doc/poppr_manual.pdf |binary poppr-2.0.1/poppr/inst/msn_explorer/server.R | 424 +++++++++++++++++++------ poppr-2.0.1/poppr/inst/msn_explorer/ui.R | 16 poppr-2.0.1/poppr/man/imsn.Rd | 22 + poppr-2.0.1/poppr/src/poppr_distance.c | 7 poppr-2.0.1/poppr/tests/testthat/test-import.R | 53 ++- poppr-2.0.1/poppr/tests/testthat/test-poppr.R | 10 17 files changed, 472 insertions(+), 142 deletions(-)
Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between polspline versions 1.1.11 dated 2015-07-02 and 1.1.12 dated 2015-07-14
polspline-1.1.11/polspline/INDEX |only polspline-1.1.12/polspline/DESCRIPTION | 8 ++++---- polspline-1.1.12/polspline/MD5 | 5 ++--- polspline-1.1.12/polspline/R/polspline.R | 1 + 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Heller-Heller-Gorfine Tests of Independence and Equality of
Distributions
Description: Heller-Heller-Gorfine (HHG) tests are a set of powerful statistical tests of multivariate k-sample homogeneity and independence. For the univariate case, the package also offers implementations of the MinP DDP and MinP ADP tests, which are consistent against all continuous alternatives but are distribution-free, and are thus much faster to apply.
Author: Barak Brill & Shachar Kaufman, based in part on an earlier implementation by Ruth Heller and Yair Heller.
Maintainer: Barak Brill <barakbri@mail.tau.ac.il>
Diff between HHG versions 1.5 dated 2015-06-18 and 1.5.1 dated 2015-07-14
HHG-1.5.1/HHG/DESCRIPTION | 9 +- HHG-1.5.1/HHG/MD5 | 33 ++++--- HHG-1.5.1/HHG/NAMESPACE | 1 HHG-1.5.1/HHG/R/HHG_univariate.R | 4 HHG-1.5.1/HHG/R/HHG_utils.R | 4 HHG-1.5.1/HHG/configure.ac |only HHG-1.5.1/HHG/inst/doc/HHG.Rmd | 2 HHG-1.5.1/HHG/inst/doc/HHG.html | 2 HHG-1.5.1/HHG/man/HHG-package.Rd | 4 HHG-1.5.1/HHG/src/HHG.cpp | 135 +++++++++++++++++-------------- HHG-1.5.1/HHG/src/HHG.h | 6 + HHG-1.5.1/HHG/src/Makevars.in |only HHG-1.5.1/HHG/src/Makevars.win | 4 HHG-1.5.1/HHG/src/SequentialTest.cpp | 3 HHG-1.5.1/HHG/src/SequentialTest.h | 3 HHG-1.5.1/HHG/src/StatsComputer.cpp | 148 ++++++++++++++++++++--------------- HHG-1.5.1/HHG/src/StatsComputer.h | 3 HHG-1.5.1/HHG/vignettes/HHG.Rmd | 2 HHG-1.5/HHG/src/Makevars |only 19 files changed, 211 insertions(+), 152 deletions(-)
Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel
(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
'xl[a1] = current.graphics()'. There is an Excel workbook with examples of
calling R from Excel in the 'doc' folder. It tries to keep things as
simple as possible - there are no needs in any additional
installations besides R, only 'VBA' code in the Excel workbook.
Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy includes source code from 'RDCOMClient' (http://www.omegahat.org/RDCOMClient) by Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>
Diff between excel.link versions 0.8.1 dated 2015-05-06 and 0.9.1 dated 2015-07-14
DESCRIPTION | 12 +-- MD5 | 60 ++++++++------- NAMESPACE | 29 +++++++ NEWS | 10 ++ R/0zzzrunTime.R | 10 +- R/address2index.R |only R/current.graphics.R | 29 ++++--- R/dimnames.excel.range.R | 4 - R/excel.link.R | 15 +++ R/xl.R | 142 ++++++++++++++++++++++++------------ R/xl.bind.range.R |only R/xl.connect.table.R | 4 - R/xl.current.region.R |only R/xl.read.file.R | 10 ++ R/xl.workbooks.R | 15 +++ R/xl.write.R | 26 ++++++ build/vignette.rds |binary inst/doc/CallingRFromExcel.html | 4 - inst/doc/R_connection_examples.xlsm |binary man/RDCOMClient.Rd | 12 +-- man/current.graphics.Rd | 11 ++ man/excel.link.Rd | 13 +++ man/xl.Rd | 34 +++----- man/xl.bind.range.Rd |only man/xl.current.region.Rd |only man/xl.index2address.Rd |only src/COMError.cpp | 11 ++ src/RCOMObject.h | 11 ++ src/RUtils.c | 11 ++ src/RUtils.h | 11 ++ src/StdAfx.h | 11 ++ src/connect.cpp | 11 ++ src/converters.cpp | 21 ++++- src/converters.h | 10 ++ 34 files changed, 402 insertions(+), 135 deletions(-)
More information about assertive.base at CRAN
Permanent link
Title: Distance Measures for Time Series Data
Description: A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series.
Author: Usue Mori, Alexander Mendiburu, J.A. Lozano
Maintainer: Usue Mori <usue.mori@ehu.es>
Diff between TSdist versions 2.2 dated 2015-04-14 and 3.1 dated 2015-07-14
TSdist-2.2/TSdist/R/dissimapprox_distance.R |only TSdist-2.2/TSdist/man/acfDistance.Rd |only TSdist-2.2/TSdist/man/ar.lpc.cepsDistance.Rd |only TSdist-2.2/TSdist/man/ar.mahDistance.Rd |only TSdist-2.2/TSdist/man/ar.picDistance.Rd |only TSdist-2.2/TSdist/man/ccorDistance.Rd |only TSdist-2.2/TSdist/man/cdmDistance.Rd |only TSdist-2.2/TSdist/man/cidDistance.Rd |only TSdist-2.2/TSdist/man/corDistance.Rd |only TSdist-2.2/TSdist/man/cortDistance.Rd |only TSdist-2.2/TSdist/man/dissimDistance.Rd |only TSdist-2.2/TSdist/man/dissimapproxDistance.Rd |only TSdist-2.2/TSdist/man/dtwDistance.Rd |only TSdist-2.2/TSdist/man/edrDistance.Rd |only TSdist-2.2/TSdist/man/erpDistance.Rd |only TSdist-2.2/TSdist/man/euclideanDistance.Rd |only TSdist-2.2/TSdist/man/fourierDistance.Rd |only TSdist-2.2/TSdist/man/frechetDistance.Rd |only TSdist-2.2/TSdist/man/infinite.normDistance.Rd |only TSdist-2.2/TSdist/man/int.perDistance.Rd |only TSdist-2.2/TSdist/man/k.medoids.Rd |only TSdist-2.2/TSdist/man/lb.keoghDistance.Rd |only TSdist-2.2/TSdist/man/lcssDistance.Rd |only TSdist-2.2/TSdist/man/lpDistance.Rd |only TSdist-2.2/TSdist/man/manhattanDistance.Rd |only TSdist-2.2/TSdist/man/mindist.saxDistance.Rd |only TSdist-2.2/TSdist/man/minkowskiDistance.Rd |only TSdist-2.2/TSdist/man/ncdDistance.Rd |only TSdist-2.2/TSdist/man/oneNN.Rd |only TSdist-2.2/TSdist/man/pacfDistance.Rd |only TSdist-2.2/TSdist/man/pdcDistance.Rd |only TSdist-2.2/TSdist/man/perDistance.Rd |only TSdist-2.2/TSdist/man/predDistance.Rd |only TSdist-2.2/TSdist/man/spec.glkDistance.Rd |only TSdist-2.2/TSdist/man/spec.isdDistance.Rd |only TSdist-2.2/TSdist/man/spec.llrDistance.Rd |only TSdist-2.2/TSdist/man/stsDistance.Rd |only TSdist-2.2/TSdist/man/tquestDistance.Rd |only TSdist-2.2/TSdist/man/tsDatabaseDistances.Rd |only TSdist-2.2/TSdist/man/tsDistances.Rd |only TSdist-2.2/TSdist/man/wavDistance.Rd |only TSdist-2.2/TSdist/src/DTW.c |only TSdist-2.2/TSdist/src/DTWnw.c |only TSdist-2.2/TSdist/tests/test.R |only TSdist-3.1/TSdist/DESCRIPTION | 13 TSdist-3.1/TSdist/MD5 | 156 ++++--- TSdist-3.1/TSdist/NAMESPACE | 31 - TSdist-3.1/TSdist/R/1NN.R | 46 +- TSdist-3.1/TSdist/R/K-medoids.R | 34 - TSdist-3.1/TSdist/R/TSclust_wrappers.R | 408 +++++++++----------- TSdist-3.1/TSdist/R/cross_correlation_distance.R | 42 -- TSdist-3.1/TSdist/R/database_distances.R | 229 +++++------ TSdist-3.1/TSdist/R/dissim_distance.R | 146 +++---- TSdist-3.1/TSdist/R/dtw_wrapper.R | 14 TSdist-3.1/TSdist/R/edr_distance.R | 76 +-- TSdist-3.1/TSdist/R/erp_distance.R | 154 +++---- TSdist-3.1/TSdist/R/fourier_distance.R | 50 +- TSdist-3.1/TSdist/R/keogh_lb_distance.R | 100 ++-- TSdist-3.1/TSdist/R/lcss_distance.R | 70 +-- TSdist-3.1/TSdist/R/longitudinalData_wrapper.R | 21 - TSdist-3.1/TSdist/R/lp_distances.R | 42 +- TSdist-3.1/TSdist/R/pdc_wrapper.R | 54 -- TSdist-3.1/TSdist/R/proxy_wrappers.R | 100 ++-- TSdist-3.1/TSdist/R/special_pairwise_calculations.R | 382 ++++++++++-------- TSdist-3.1/TSdist/R/sts_distance.R | 49 +- TSdist-3.1/TSdist/R/tquest_distance.R | 105 ++--- TSdist-3.1/TSdist/R/ts_distances.R | 101 ++-- TSdist-3.1/TSdist/R/zzz.R | 28 - TSdist-3.1/TSdist/inst |only TSdist-3.1/TSdist/man/ACFDistance.Rd |only TSdist-3.1/TSdist/man/ARLPCCepsDistance.Rd |only TSdist-3.1/TSdist/man/ARMahDistance.Rd |only TSdist-3.1/TSdist/man/ARPicDistance.Rd |only TSdist-3.1/TSdist/man/CCorDistance.Rd |only TSdist-3.1/TSdist/man/CDMDistance.Rd |only TSdist-3.1/TSdist/man/CIDDistance.Rd |only TSdist-3.1/TSdist/man/CorDistance.Rd |only TSdist-3.1/TSdist/man/CortDistance.Rd |only TSdist-3.1/TSdist/man/DTWDistance.Rd |only TSdist-3.1/TSdist/man/DissimDistance.Rd |only TSdist-3.1/TSdist/man/EDRDistance.Rd |only TSdist-3.1/TSdist/man/ERPDistance.Rd |only TSdist-3.1/TSdist/man/EuclideanDistance.Rd |only TSdist-3.1/TSdist/man/FourierDistance.Rd |only TSdist-3.1/TSdist/man/FrechetDistance.Rd |only TSdist-3.1/TSdist/man/InfNormDistance.Rd |only TSdist-3.1/TSdist/man/IntPerDistance.Rd |only TSdist-3.1/TSdist/man/KMedoids.Rd |only TSdist-3.1/TSdist/man/LBKeoghDistance.Rd |only TSdist-3.1/TSdist/man/LCSSDistance.Rd |only TSdist-3.1/TSdist/man/LPDistance.Rd |only TSdist-3.1/TSdist/man/ManhattanDistance.Rd |only TSdist-3.1/TSdist/man/MindistSaxDistance.Rd |only TSdist-3.1/TSdist/man/MinkowskiDistance.Rd |only TSdist-3.1/TSdist/man/NCDDistance.Rd |only TSdist-3.1/TSdist/man/OneNN.Rd |only TSdist-3.1/TSdist/man/PACFDistance.Rd |only TSdist-3.1/TSdist/man/PDCDistance.Rd |only TSdist-3.1/TSdist/man/PerDistance.Rd |only TSdist-3.1/TSdist/man/PredDistance.Rd |only TSdist-3.1/TSdist/man/STSDistance.Rd |only TSdist-3.1/TSdist/man/SpecGLKDistance.Rd |only TSdist-3.1/TSdist/man/SpecISDDistance.Rd |only TSdist-3.1/TSdist/man/SpecLLRDistance.Rd |only TSdist-3.1/TSdist/man/TSDatabaseDistances.Rd |only TSdist-3.1/TSdist/man/TSDistances.Rd |only TSdist-3.1/TSdist/man/TSdist-package.Rd | 68 +-- TSdist-3.1/TSdist/man/TquestDistance.Rd |only TSdist-3.1/TSdist/man/WavDistance.Rd |only TSdist-3.1/TSdist/src/LCSS.c | 11 TSdist-3.1/TSdist/src/LCSSnw.c | 11 TSdist-3.1/TSdist/tests/testthat.R |only 112 files changed, 1290 insertions(+), 1251 deletions(-)
Title: Sensitivity Analysis for Causal Inference
Description: Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.
Author: Nicole Bohme Carnegie [aut, cre],
Masataka Harada [aut],
Vincent Dorie [aut],
Jennifer Hill [ctb]
Maintainer: Nicole Bohme Carnegie <carnegin@uwm.edu>
Diff between treatSens versions 1.1 dated 2015-04-21 and 2.0 dated 2015-07-14
DESCRIPTION | 35 + MD5 | 94 ++++- NAMESPACE | 28 + R/X_partials.R | 106 ++--- R/calc_range.R | 394 ++++++++++----------- R/cibart.R |only R/cibart_treatmentModel.R |only R/genU_contY.R | 378 ++++++++++---------- R/grid_range.R | 300 ++++++++-------- R/guessNumCores.R |only R/hooks.R |only R/housekeeping.R | 150 ++++---- R/object_def.R | 395 +++++++++++++-------- R/pweight.R | 104 ++--- R/sensPlot.R | 751 ++++++++++++++++++++-------------------- R/treatSens.R | 860 +++++++++++++++++++++++----------------------- R/treatSensBART.R |only R/utility.R |only R/warnings.R | 429 +++++++++++++--------- cleanup |only configure |only configure.ac |only configure.win |only inst/CITATION | 60 +-- man/sensPlot.Rd | 124 +++--- man/summary.Rd | 82 ++-- man/treatSens-package.Rd | 68 +-- man/treatSens.Rd | 296 +++++++-------- man/treatSensBART.Rd |only src |only tests |only tools |only 32 files changed, 2471 insertions(+), 2183 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 1.8-9 dated 2015-01-27 and 1.8-10 dated 2015-07-14
DESCRIPTION | 16 +-- MD5 | 30 +++--- NAMESPACE | 10 +- NEWS | 16 ++- R/TraMineRInternal.R | 4 build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 169 ++--------------------------------- man/TraMineRInternal.Rd | 4 man/disstree2dot.Rd | 2 man/seqdist.Rd | 10 +- man/seqeconstraint.Rd | 11 +- man/seqtree.Rd | 20 ++-- 16 files changed, 88 insertions(+), 204 deletions(-)
Title: Well-Formatted Regression and Summary Statistics Tables
Description: Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted tables that hold
regression analysis results from several models side-by-side, as well as summary
statistics.
Author: Marek Hlavac <hlavac@fas.harvard.edu>
Maintainer: Marek Hlavac <hlavac@fas.harvard.edu>
Diff between stargazer versions 5.1 dated 2014-05-29 and 5.2 dated 2015-07-14
DESCRIPTION | 22 - MD5 | 26 - NAMESPACE | 2 R/stargazer-internal.R | 409 ++++++++++++++++++++----- build/vignette.rds |binary inst/CITATION | 8 inst/ChangeLog | 25 + inst/doc/stargazer.Rtex | 681 +++++++++++++++++++++---------------------- inst/doc/stargazer.pdf |binary man/stargazer.Rd | 2 man/stargazer_acknowledge.Rd | 28 + man/stargazer_models.Rd | 17 + man/stargazer_news.Rd | 25 + vignettes/stargazer.Rtex | 681 +++++++++++++++++++++---------------------- 14 files changed, 1128 insertions(+), 798 deletions(-)
Title: Phonetic-Coding for Portuguese
Description: The SoundexBR package provides an algorithm for decoding names
into phonetic codes, as pronounced in Portuguese. The goal is for
homophones to be encoded to the same representation so that they can be
matched despite minor differences in spelling. The algorithm mainly encodes
consonants; a vowel will not be encoded unless it is the first letter. The
soundex code resultant consists of a four digits long string composed by
one letter followed by three numerical digits: the letter is the first
letter of the name, and the digits encode the remaining consonants.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SoundexBR versions 1.1 dated 2015-01-21 and 1.2 dated 2015-07-14
SoundexBR-1.1/SoundexBR/man/ptSound.Rd |only SoundexBR-1.1/SoundexBR/man/soundexBR-package.Rd |only SoundexBR-1.2/SoundexBR/DESCRIPTION | 12 ++-- SoundexBR-1.2/SoundexBR/MD5 | 26 ++++---- SoundexBR-1.2/SoundexBR/NAMESPACE | 4 - SoundexBR-1.2/SoundexBR/R/accent.R | 11 +-- SoundexBR-1.2/SoundexBR/R/soundexBR.R | 61 +++++++++++++++++--- SoundexBR-1.2/SoundexBR/R/utils.R | 26 ++++++-- SoundexBR-1.2/SoundexBR/README.md | 68 +++++++++++++---------- SoundexBR-1.2/SoundexBR/inst/CITATION | 6 +- SoundexBR-1.2/SoundexBR/man/accent.Rd | 11 +-- SoundexBR-1.2/SoundexBR/man/ascii.table.Rd | 27 ++++----- SoundexBR-1.2/SoundexBR/man/char2int.Rd | 26 ++++---- SoundexBR-1.2/SoundexBR/man/int2char.Rd | 26 ++++---- SoundexBR-1.2/SoundexBR/man/soundexBR.Rd | 16 ++--- 15 files changed, 188 insertions(+), 132 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.4-6 dated 2015-05-01 and 0.4-7 dated 2015-07-14
DESCRIPTION | 35 ++-- MD5 | 34 ++-- NAMESPACE | 48 ++---- R/Class-SDMX.R | 4 R/Class-SDMXComponents.R | 2 R/Class-SDMXStructureSpecificData.R |only R/Class-SDMXTimeDimension.R | 7 R/Class-SDMXType.R | 11 - R/SDMX-methods.R | 16 ++ R/SDMXCompactData-methods.R | 73 +++++---- R/SDMXGenericData-methods.R | 3 R/SDMXStructureSpecificData-methods.R |only R/readSDMX.R | 96 +++++++----- README.md | 143 +++++++++++++++--- inst/extdata/SDMXStructureSpecificDataExample_2.1.xml |only inst/extdata/SDMX_SOAP_Example.xml |only man/SDMXStructureSpecificData-class.Rd |only man/getSoapRequestResult.Rd |only man/isSoapRequestEnvelope.Rd |only man/rsdmx-package.Rd | 4 tests/testthat/test_Soap.R |only tests/testthat/test_StructureSpecificData.R |only vignettes |only 23 files changed, 318 insertions(+), 158 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.5). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.4.0 dated 2015-02-27 and 0.3.2.5.0 dated 2015-07-14
ChangeLog | 28 + DESCRIPTION | 31 - MD5 | 124 ++--- NAMESPACE | 12 R/RcppEigen.package.skeleton.R | 2 README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 8 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/Core | 2 inst/include/Eigen/src/Cholesky/LDLT.h | 7 inst/include/Eigen/src/Cholesky/LLT.h | 8 inst/include/Eigen/src/Cholesky/LLT_MKL.h | 2 inst/include/Eigen/src/Core/Assign.h | 15 inst/include/Eigen/src/Core/Block.h | 5 inst/include/Eigen/src/Core/DenseBase.h | 8 inst/include/Eigen/src/Core/DiagonalProduct.h | 2 inst/include/Eigen/src/Core/Functors.h | 41 + inst/include/Eigen/src/Core/MapBase.h | 2 inst/include/Eigen/src/Core/MatrixBase.h | 2 inst/include/Eigen/src/Core/PermutationMatrix.h | 29 + inst/include/Eigen/src/Core/PlainObjectBase.h | 2 inst/include/Eigen/src/Core/Ref.h | 16 inst/include/Eigen/src/Core/ReturnByValue.h | 11 inst/include/Eigen/src/Core/products/CoeffBasedProduct.h | 73 ++- inst/include/Eigen/src/Core/products/Parallelizer.h | 17 inst/include/Eigen/src/Core/util/Constants.h | 13 inst/include/Eigen/src/Core/util/Macros.h | 12 inst/include/Eigen/src/Core/util/Memory.h | 2 inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h | 8 inst/include/Eigen/src/Eigenvalues/EigenSolver.h | 9 inst/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h | 9 inst/include/Eigen/src/Eigenvalues/RealQZ.h | 12 inst/include/Eigen/src/Eigenvalues/RealSchur.h | 12 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 208 ++++------ inst/include/Eigen/src/Geometry/AlignedBox.h | 83 ++- inst/include/Eigen/src/Geometry/Homogeneous.h | 2 inst/include/Eigen/src/Geometry/Quaternion.h | 22 - inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 15 inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 30 - inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 4 inst/include/Eigen/src/LU/FullPivLU.h | 8 inst/include/Eigen/src/LU/PartialPivLU.h | 8 inst/include/Eigen/src/OrderingMethods/Amd.h | 16 inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 32 - inst/include/Eigen/src/QR/FullPivHouseholderQR.h | 8 inst/include/Eigen/src/QR/HouseholderQR.h | 104 ++--- inst/include/Eigen/src/QR/HouseholderQR_MKL.h | 30 - inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 60 ++ inst/include/Eigen/src/SVD/JacobiSVD.h | 7 inst/include/Eigen/src/SparseCore/SparseBlock.h | 46 ++ inst/include/Eigen/src/SparseCore/SparseDenseProduct.h | 2 inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 6 inst/include/Eigen/src/SparseCore/TriangularSolver.h | 2 inst/include/Eigen/src/SparseLU/SparseLU.h | 81 +++ inst/include/Eigen/src/SparseLU/SparseLU_pivotL.h | 6 inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 54 ++ inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 16 inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 17 inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 15 inst/include/RcppEigenWrap.h | 104 ++--- inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 15 inst/include/unsupported/Eigen/src/IterativeSolvers/MINRES.h | 70 +-- 63 files changed, 999 insertions(+), 598 deletions(-)
Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab. Thus they
are available to the user as a script file or as an aide for the user to
learn R or to copy-and-paste directly into R itself.
Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (Author of original print.summary.nnet)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 3.4.1 dated 2014-12-30 and 3.5.0 dated 2015-07-14
DESCRIPTION | 35 +++----- MD5 | 87 ++++++++++---------- NAMESPACE | 9 ++ R/acquireAuditData.R | 12 +- R/ada.R | 191 +++++++++++----------------------------------- R/associate.R | 10 +- R/biclust.R | 4 R/binning.R | 12 +- R/ctree.R | 4 R/data.R | 123 ++++++++--------------------- R/evaluate.R | 6 - R/ewkm.R | 18 ++-- R/execute.R | 4 R/explore.R | 60 +++++++------- R/export.R | 4 R/hclust.R | 20 ++-- R/help.R | 64 +++++---------- R/kmeans.R | 24 ++--- R/log.R | 22 +++-- R/model.R | 12 +- R/nnet.R | 10 +- R/normVarNames.R | 36 +++++--- R/projects.R | 24 ++--- R/random_forest.R | 69 ++++++---------- R/rattle.R | 77 +++--------------- R/rattleInfo.R | 136 ++++++++++++++++---------------- R/report.R | 4 R/riskchart.R | 23 +++-- R/rpart.R | 9 -- R/survival.R | 4 R/test.R | 4 R/textminer.R | 8 - R/transform.R | 6 - R/zzz.R | 9 -- build/vignette.rds |binary data/locationsAUS.RData |binary data/weather.RData |binary data/weatherAUS.RData |binary inst/NEWS | 26 ++++++ inst/doc/rattle.pdf |binary inst/etc/rattle.ui.150207 |only inst/etc/textviews.xml | 10 +- inst/etc/tooltips.xml | 2 man/modalvalue.Rd | 10 -- man/riskchart.Rd | 12 ++ 45 files changed, 516 insertions(+), 684 deletions(-)
Title: Practical Numerical Math Functions
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 1.8.3 dated 2015-02-08 and 1.8.6 dated 2015-07-14
DESCRIPTION | 14 ++++++-------- MD5 | 34 ++++++++++++++++++---------------- NAMESPACE | 7 +++++++ NEWS | 16 ++++++++++++++++ R/bernoulli.R |only R/fact.R | 16 ++++++++++++++++ R/matlab.R | 8 ++++---- R/strings.R | 2 +- data/brown72.rda |binary data/nile.rda |binary data/titanium.rda |binary man/bernoulli.Rd |only man/entropy.Rd | 2 -- man/fact.Rd | 17 ++++++++++++++--- man/pracma-package.Rd | 12 ++++++------ man/quad.Rd | 2 +- man/quadl.Rd | 2 +- man/strrep.Rd | 8 ++++---- tests/strings.R | 4 ++-- 19 files changed, 96 insertions(+), 48 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.3.0 dated 2015-05-29 and 1.3.1 dated 2015-07-14
neotoma-1.3.0/neotoma/R/compile_list.R |only neotoma-1.3.0/neotoma/inst/doc |only neotoma-1.3.0/neotoma/inst/img/Thumbs.db |only neotoma-1.3.0/neotoma/man/compile_list.Rd |only neotoma-1.3.1/neotoma/DESCRIPTION | 8 neotoma-1.3.1/neotoma/MD5 | 45 ++-- neotoma-1.3.1/neotoma/NAMESPACE | 11 + neotoma-1.3.1/neotoma/NEWS | 7 neotoma-1.3.1/neotoma/R/browse.R |only neotoma-1.3.1/neotoma/R/compile_taxa.R | 5 neotoma-1.3.1/neotoma/R/get_chroncontrol.R | 185 +++++++++++-------- neotoma-1.3.1/neotoma/R/get_download.R | 4 neotoma-1.3.1/neotoma/R/get_geochron.R | 8 neotoma-1.3.1/neotoma/R/get_publication.R | 64 ------ neotoma-1.3.1/neotoma/R/get_table.R | 1 neotoma-1.3.1/neotoma/R/param_check.R | 57 +++++ neotoma-1.3.1/neotoma/R/print.geochronologic.R | 1 neotoma-1.3.1/neotoma/R/write_agefile.R | 54 +++-- neotoma-1.3.1/neotoma/README.md | 7 neotoma-1.3.1/neotoma/man/browse.Rd |only neotoma-1.3.1/neotoma/man/browse.dataset.Rd |only neotoma-1.3.1/neotoma/man/browse.dataset_list.Rd |only neotoma-1.3.1/neotoma/man/browse.default.Rd |only neotoma-1.3.1/neotoma/man/browse.download.Rd |only neotoma-1.3.1/neotoma/man/browse.download_list.Rd |only neotoma-1.3.1/neotoma/man/get_geochron.Rd | 4 neotoma-1.3.1/neotoma/man/write_agefile.Rd | 1 neotoma-1.3.1/neotoma/tests/testthat/test_examples.R | 1 neotoma-1.3.1/neotoma/tests/testthat/test_neotoma.R | 27 +- 29 files changed, 285 insertions(+), 205 deletions(-)
Title: Linear Model with Breakpoint
Description: Exact significance tests for a changepoint in linear or multiple linear regression.
Confidence regions with exact coverage probabilities for the changepoint.
Author: Marc Adams [aut, cre],
authors of R function 'lm' [ctb] (general interface),
authors of 'lm.gls' [ctb] (interface and R code for covariate weights),
U.S. NIST [ctb] (C++ code for TNT::Vector template)
Maintainer: Marc Adams <lm.br.pkg@gmail.com>
Diff between lm.br versions 2.6 dated 2014-11-14 and 2.7 dated 2015-07-14
lm.br-2.6/lm.br/src/Fm_fm.cpp |only lm.br-2.6/lm.br/src/set_acc.cpp |only lm.br-2.7/lm.br/DESCRIPTION | 16 +- lm.br-2.7/lm.br/MD5 | 72 ++++++------- lm.br-2.7/lm.br/NAMESPACE | 4 lm.br-2.7/lm.br/R/cr.R | 7 - lm.br-2.7/lm.br/R/lm.br.R | 2 lm.br-2.7/lm.br/R/sl.R | 16 +- lm.br-2.7/lm.br/build/vignette.rds |binary lm.br-2.7/lm.br/demo/testscript.R | 22 ++-- lm.br-2.7/lm.br/inst/doc/lm.br.R | 11 -- lm.br-2.7/lm.br/inst/doc/lm.br.Rnw | 93 ++++++++--------- lm.br-2.7/lm.br/inst/doc/lm.br.pdf |binary lm.br-2.7/lm.br/inst/po/en@quot/LC_MESSAGES/R-lm.br.mo |binary lm.br-2.7/lm.br/inst/po/en@quot/LC_MESSAGES/lm.br.mo |binary lm.br-2.7/lm.br/inst/po/fr/LC_MESSAGES/lm.br.mo |binary lm.br-2.7/lm.br/man/lm.br.Rd | 47 ++++---- lm.br-2.7/lm.br/man/sety.Rd | 4 lm.br-2.7/lm.br/man/sl.Rd | 10 - lm.br-2.7/lm.br/po/R-lm.br.pot | 4 lm.br-2.7/lm.br/po/fr.po | 40 +++---- lm.br-2.7/lm.br/po/lm.br.pot | 36 ++---- lm.br-2.7/lm.br/src/R_interface.cpp | 48 ++++---- lm.br-2.7/lm.br/src/Rcpp_module.cpp | 8 - lm.br-2.7/lm.br/src/ci.cpp | 58 +++++----- lm.br-2.7/lm.br/src/cr.cpp | 23 ++-- lm.br-2.7/lm.br/src/fm_Fm.cpp |only lm.br-2.7/lm.br/src/geo.cpp | 8 - lm.br-2.7/lm.br/src/initialize.cpp | 6 - lm.br-2.7/lm.br/src/lmbr.h | 50 ++++----- lm.br-2.7/lm.br/src/mle.cpp | 20 +-- lm.br-2.7/lm.br/src/pre_calc.cpp | 5 lm.br-2.7/lm.br/src/rho_etc.cpp | 14 +- lm.br-2.7/lm.br/src/set_sy.cpp | 2 lm.br-2.7/lm.br/src/set_tol.cpp |only lm.br-2.7/lm.br/src/sl_geo.cpp | 2 lm.br-2.7/lm.br/src/sl_mc.cpp | 4 lm.br-2.7/lm.br/vignettes/lm.br.Rnw | 31 ++--- lm.br-2.7/lm.br/vignettes/lm.br.bib | 10 + 39 files changed, 347 insertions(+), 326 deletions(-)
Title: Miscellaneous Functions for "Grid" Graphics
Description: Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.
Author: Baptiste Auguie [aut, cre],
Anton Antonov [ctb]
Maintainer: Baptiste Auguie <baptiste.auguie@gmail.com>
Diff between gridExtra versions 0.9.1 dated 2012-08-09 and 2.0.0 dated 2015-07-14
gridExtra-0.9.1/gridExtra/NEWS |only gridExtra-0.9.1/gridExtra/R/arcText.r |only gridExtra-0.9.1/gridExtra/R/arrange.r |only gridExtra-0.9.1/gridExtra/R/barbedGrob.r |only gridExtra-0.9.1/gridExtra/R/borderGrob.r |only gridExtra-0.9.1/gridExtra/R/colorstripGrob.r |only gridExtra-0.9.1/gridExtra/R/ebimage.r |only gridExtra-0.9.1/gridExtra/R/ellipseGrob.r |only gridExtra-0.9.1/gridExtra/R/patternGrob.r |only gridExtra-0.9.1/gridExtra/R/pixmap.r |only gridExtra-0.9.1/gridExtra/R/polygon.regular.r |only gridExtra-0.9.1/gridExtra/R/rpattern.r |only gridExtra-0.9.1/gridExtra/R/stextGrob.r |only gridExtra-0.9.1/gridExtra/README |only gridExtra-0.9.1/gridExtra/inst/test |only gridExtra-0.9.1/gridExtra/man/arcTextGrob.Rd |only gridExtra-0.9.1/gridExtra/man/barbedGrob.Rd |only gridExtra-0.9.1/gridExtra/man/borderGrob.Rd |only gridExtra-0.9.1/gridExtra/man/colorstripGrob.Rd |only gridExtra-0.9.1/gridExtra/man/ebimageGrob.Rd |only gridExtra-0.9.1/gridExtra/man/ellipseGrob.Rd |only gridExtra-0.9.1/gridExtra/man/expand.arguments.Rd |only gridExtra-0.9.1/gridExtra/man/interleaven.Rd |only gridExtra-0.9.1/gridExtra/man/marrangeGrob.Rd |only gridExtra-0.9.1/gridExtra/man/patternGrob.Rd |only gridExtra-0.9.1/gridExtra/man/pixmapGrob.Rd |only gridExtra-0.9.1/gridExtra/man/polygon.regular.Rd |only gridExtra-0.9.1/gridExtra/man/polygon.star.Rd |only gridExtra-0.9.1/gridExtra/man/polygon1.Rd |only gridExtra-0.9.1/gridExtra/man/read.tiff.Rd |only gridExtra-0.9.1/gridExtra/man/rowMax.units.Rd |only gridExtra-0.9.1/gridExtra/man/rpatternGrob.Rd |only gridExtra-0.9.1/gridExtra/man/stextGrob.Rd |only gridExtra-0.9.1/gridExtra/man/theme.default.Rd |only gridExtra-0.9.1/gridExtra/man/virtualGrob.Rd |only gridExtra-2.0.0/gridExtra/.Rinstignore |only gridExtra-2.0.0/gridExtra/DESCRIPTION | 36 - gridExtra-2.0.0/gridExtra/MD5 | 78 -- gridExtra-2.0.0/gridExtra/NAMESPACE | 63 - gridExtra-2.0.0/gridExtra/R/arrangeGrob.r |only gridExtra-2.0.0/gridExtra/R/gridExtra-package.r | 26 gridExtra-2.0.0/gridExtra/R/grob-utils.r | 202 +++--- gridExtra-2.0.0/gridExtra/R/ngonGrob.r | 193 ++++-- gridExtra-2.0.0/gridExtra/R/tableGrob.r | 667 ++++++--------------- gridExtra-2.0.0/gridExtra/README.md |only gridExtra-2.0.0/gridExtra/TODO | 9 gridExtra-2.0.0/gridExtra/build |only gridExtra-2.0.0/gridExtra/inst/NEWS.md |only gridExtra-2.0.0/gridExtra/inst/doc |only gridExtra-2.0.0/gridExtra/inst/tests |only gridExtra-2.0.0/gridExtra/man/arrangeGrob.Rd | 95 ++ gridExtra-2.0.0/gridExtra/man/gridExtra-package.Rd | 12 gridExtra-2.0.0/gridExtra/man/ngonGrob.Rd | 107 ++- gridExtra-2.0.0/gridExtra/man/tableGrob.Rd | 159 +---- gridExtra-2.0.0/gridExtra/vignettes |only 55 files changed, 743 insertions(+), 904 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.6.0 dated 2015-06-19 and 0.7.0 dated 2015-07-14
future-0.6.0/future/.Rinstignore |only future-0.7.0/future/DESCRIPTION | 6 future-0.7.0/future/MD5 | 38 ++-- future-0.7.0/future/NAMESPACE | 2 future-0.7.0/future/NEWS | 12 + future-0.7.0/future/R/MulticoreFuture.R | 48 +++++ future-0.7.0/future/R/availableCores.R |only future-0.7.0/future/R/multicore.R | 20 +- future-0.7.0/future/R/plan.R | 16 + future-0.7.0/future/demo/fibonacci.R | 5 future-0.7.0/future/demo/mandelbrot.R | 30 ++- future-0.7.0/future/inst/doc/future.html | 8 future-0.7.0/future/inst/doc/future.md.rsp | 5 future-0.7.0/future/man/availableCores.Rd |only future-0.7.0/future/man/multicore.Rd | 146 ++++++++-------- future-0.7.0/future/man/plan.Rd | 178 ++++++++++---------- future-0.7.0/future/man/requestCore.Rd |only future-0.7.0/future/man/usedCores.Rd |only future-0.7.0/future/man/value.Future.Rd | 64 +++---- future-0.7.0/future/tests/MulticoreFutureRegistry.R |only future-0.7.0/future/tests/availableCores.R |only future-0.7.0/future/tests/multicore.R | 8 future-0.7.0/future/tests/plan.R | 13 + future-0.7.0/future/vignettes/future.md.rsp | 5 24 files changed, 367 insertions(+), 237 deletions(-)
Title: Differential Co-Expression and Differential Expression Analysis
Description: Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.
Author: Thomas Lui [aut, cre]
Maintainer: Thomas Lui <tlui27@yahoo.com>
Diff between decode versions 1.1 dated 2015-03-18 and 1.2 dated 2015-07-14
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 4 +++- R/Decode.r | 8 +++++--- R/sumResult_MinGain.r | 4 ++-- build/vignette.rds |binary inst/doc/v.html | 24 ++++++++++++++---------- man/getAssoGeneSetPValue.Rd | 2 +- man/getBestAssociatedGeneSet.Rd | 2 +- man/getBonferroniPValue.Rd | 2 +- man/getDE_DC_OptimalThreshold.Rd | 2 +- man/getFDR.Rd | 2 +- man/getPartitionIndex.Rd | 2 +- man/getPathway.Rd | 2 +- man/openFileToWrite.Rd | 2 +- man/runDecode.Rd | 2 +- man/sumResult_MinGain.Rd | 2 +- vignettes/v.Rmd | 27 ++++++++++++++++----------- 18 files changed, 71 insertions(+), 58 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.0 dated 2015-03-11 and 2.2.1 dated 2015-07-14
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS | 9 +++++++++ R/FillEnvelope.R | 2 +- R/Kdhat.R | 18 +++++++++--------- R/Ktest.r | 6 +++--- R/m_hat.R | 24 ++++++++++++------------ build/vignette.rds |binary man/dbmss-package.Rd | 6 +++--- vignettes/dbmss.bib | 27 ++++----------------------- 11 files changed, 57 insertions(+), 66 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-12 0.9-12
2012-12-10 0.9-11
2010-08-12 0.9-10
2009-12-06 0.9-9
2009-11-03 0.9-8
2007-10-09 0.9-7
2006-10-02 0.9-6
Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between sweidnumbr versions 0.6.0 dated 2015-06-09 and 0.6.1 dated 2015-07-14
sweidnumbr-0.6.0/sweidnumbr/README.md |only sweidnumbr-0.6.1/sweidnumbr/DESCRIPTION | 8 ++++---- sweidnumbr-0.6.1/sweidnumbr/LICENSE | 2 +- sweidnumbr-0.6.1/sweidnumbr/MD5 | 7 +++---- sweidnumbr-0.6.1/sweidnumbr/build/vignette.rds |binary 5 files changed, 8 insertions(+), 9 deletions(-)
More information about speciesgeocodeR at CRAN
Permanent link
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Based on (optionally sparse) quadratic optimization with the main algorithms implemented in C. Includes features for easy processing of many (smaller) records. The algorithm has been tested on fairly large optimization problems with up to a few million variables and several hundred thousand restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.1-7 dated 2015-06-10 and 0.1.8 dated 2015-07-14
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 ++ NEWS | 3 +++ R/rspa.R | 3 ++- inst/doc/getting_started.pdf |binary 6 files changed, 17 insertions(+), 11 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.7-2 dated 2015-06-05 and 1.7-4 dated 2015-07-14
DESCRIPTION | 13 ++--- MD5 | 28 +++++------ NAMESPACE | 38 +++++++++++++++- R/DAS-scale.R | 10 +++- build/vignette.rds |binary inst/doc/rlmer.pdf |binary tests/compare-methods.Rout.save | 19 +++----- tests/getME.Rout.save | 18 +++---- vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary vignettes/figs/fig-ex-penicillin-raw.pdf |binary vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary vignettes/figs/fig-ex-penicillin-ta.pdf |binary vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary vignettes/figs/fig-ex-smoothedHuber.pdf |binary 15 files changed, 85 insertions(+), 41 deletions(-)
Title: Jester Dataset for 'recommenderlab'
Description: Provides the Jester Dataset for package recommenderlab.
Author: Michael Hahsler
Maintainer: Michael Hahsler <mhahsler@smu.edu>
Diff between recommenderlabJester versions 0.1-0 dated 2011-11-10 and 0.1-1 dated 2015-07-14
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NAMESPACE | 11 +---------- data/Jester.rda |binary 4 files changed, 13 insertions(+), 22 deletions(-)
More information about recommenderlabJester at CRAN
Permanent link
Title: Book-Crossing Dataset (BX) for 'recommenderlab'
Description: Provides the Book-Crossing Dataset for the package recommenderlab.
Author: Michael Hahsler
Maintainer: Michael Hahsler <mhahsler@smu.edu>
Diff between recommenderlabBX versions 0.1-0 dated 2011-11-10 and 0.1-1 dated 2015-07-14
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- data/BX.rda |binary data/BXBooks.rda |binary 4 files changed, 12 insertions(+), 12 deletions(-)
More information about recommenderlabBX at CRAN
Permanent link
Title: Number-Theoretic Functions
Description:
Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.5-9 dated 2015-07-10 and 0.6-1 dated 2015-07-14
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 1 + NEWS | 5 +++++ R/fibonacci.R | 19 +++++++++++++++++++ man/bell.Rd |only man/eulersPhi.Rd | 2 +- man/omega.Rd | 2 +- 8 files changed, 38 insertions(+), 12 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova <alku@dtu.dk>
Diff between lmerTest versions 2.0-25 dated 2015-04-20 and 2.0-28 dated 2015-07-14
DESCRIPTION | 6 - MD5 | 32 +++---- NAMESPACE | 17 ++-- R/devfunsLmerTest.R | 27 +----- R/generalFunctions.R | 18 ++-- R/lmerTestFunctions.R | 3 R/utils.R | 8 - man/lmer.Rd | 2 man/lmerTest-package.Rd | 2 man/merModLmerTest-class.Rd | 2 tests/Examples/lmerTest-Ex.Rout.save | 24 ++--- tests/bugRefit.R | 143 ++++++++++++++++++----------------- tests/lmerMod.R | 56 +++++++------ tests/testContrasts.R | 15 +-- tests/testKeep.Rout.save | 9 -- tests/testRand.Rout.save | 7 - tests/testTVbo.Rout.save | 5 - 17 files changed, 199 insertions(+), 177 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.20-31 dated 2015-03-30 and 0.20-33 dated 2015-07-14
DESCRIPTION | 22 +++++++++++----------- MD5 | 20 ++++++++++---------- NAMESPACE | 10 +++++----- R/miscellaneous.R | 37 +++++++++++++++++++++---------------- data/barley.rda |binary data/environmental.rda |binary data/ethanol.rda |binary data/melanoma.rda |binary data/singer.rda |binary man/Lattice.Rd | 15 +++++++-------- po/R-lattice.pot | 4 ++-- 11 files changed, 56 insertions(+), 52 deletions(-)
Title: Higher Order Likelihood Inference
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>
Diff between hoa versions 2.1.1 dated 2015-07-04 and 2.1.2 dated 2015-07-14
hoa-2.1.1/hoa/man/hoa-package.Rd |only hoa-2.1.2/hoa/CHANGES | 10 ++ hoa-2.1.2/hoa/DESCRIPTION | 8 - hoa-2.1.2/hoa/MD5 | 12 +- hoa-2.1.2/hoa/NAMESPACE | 5 - hoa-2.1.2/hoa/man/all.profiles.nlreg.Rd | 130 ++++++++++++++++---------------- hoa-2.1.2/hoa/man/hoa.Rd |only hoa-2.1.2/hoa/vignettes/Rnews-paper.Rnw | 2 8 files changed, 88 insertions(+), 79 deletions(-)
Title: Univariate Outlier Detection
Description: Detect outliers in one-dimensional data.
Author: Mark van der Loo <mark.vanderloo@gmail.com>
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between extremevalues versions 2.3.0 dated 2014-12-03 and 2.3.1 dated 2015-07-14
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 2 +- NEWS | 3 +++ inst/CITATION | 2 +- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.1-7 dated 2015-07-01 and 1.1-9 dated 2015-07-14
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 ++-- R/ruleInduction.R | 2 +- R/support.R | 2 +- build/vignette.rds |binary data/Adult.rda |binary data/AdultUCI.rda |binary data/Epub.rda |binary data/Groceries.rda |binary data/Income.rda |binary data/IncomeESL.rda |binary inst/NEWS | 4 ++++ inst/doc/arules.pdf |binary tests/matrix.Rout.save | 6 +++--- 15 files changed, 29 insertions(+), 25 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.0-3 dated 2015-07-11 and 0.8.0-4 dated 2015-07-13
DESCRIPTION | 10 ++++---- MD5 | 28 +++++++++++------------ NAMESPACE | 1 NEWS | 6 ++++ R/corpus.R | 10 ++++++-- R/dfm-main.R | 2 - R/dfm-methods.R | 13 ++++++---- R/readability.R | 20 +++++++++++----- R/textfile.R | 9 ++++++- README.md | 52 ++++++++++++++++++++++++++++++++++--------- inst/doc/corpus-sources.html | 14 +++++------ inst/doc/quickstart.html | 16 ++++++------- man/corpus.Rd | 1 man/nsentence.Rd | 7 +++++ man/readability.Rd | 4 +++ 15 files changed, 132 insertions(+), 61 deletions(-)
Title: Nonparametric Boundary Regression
Description: A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.
Author: Abdelaati Daouia <Abdelaati.Daouia@tse-fr.eu>, Thibault Laurent <thibault.laurent@univ-tlse1.fr>, Hohsuk Noh <word5810@gmail.com>
Maintainer: Thibault Laurent <thibault.laurent@univ-tlse1.fr>
Diff between npbr versions 1.1 dated 2015-04-01 and 1.2 dated 2015-07-13
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 6 +++++- man/kern_smooth.Rd | 4 +++- man/kern_smooth_bw.Rd | 2 ++ man/quad_spline_est.Rd | 4 +++- 6 files changed, 24 insertions(+), 14 deletions(-)
Title: Download 'Socrata' Data Sets as R Data Frames
Description: Provides easier interaction with
Socrata open data portals http://dev.socrata.com.
Users can provide a 'Socrata' data set resource URL,
or a 'Socrata' Open Data API (SoDA) web query,
or a 'Socrata' "human-friendly" URL,
returns an R data frame.
Converts dates to 'POSIX' format.
Manages throttling by 'Socrata'.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., and John Malc
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Diff between RSocrata versions 1.6.0-12 dated 2015-04-20 and 1.6.2-10 dated 2015-07-13
RSocrata-1.6.0-12/RSocrata/R/tests |only RSocrata-1.6.0-12/RSocrata/man/logMsg.Rd |only RSocrata-1.6.2-10/RSocrata/DESCRIPTION | 25 - RSocrata-1.6.2-10/RSocrata/LICENSE | 2 RSocrata-1.6.2-10/RSocrata/MD5 | 25 - RSocrata-1.6.2-10/RSocrata/NAMESPACE | 24 - RSocrata-1.6.2-10/RSocrata/R/RSocrata.R | 480 ++++++++++++------------- RSocrata-1.6.2-10/RSocrata/README.md |only RSocrata-1.6.2-10/RSocrata/man/fieldName.Rd | 54 +- RSocrata-1.6.2-10/RSocrata/man/isFourByFour.Rd | 48 +- RSocrata-1.6.2-10/RSocrata/man/ls.socrata.Rd | 50 +- RSocrata-1.6.2-10/RSocrata/man/posixify.Rd | 42 +- RSocrata-1.6.2-10/RSocrata/man/read.socrata.Rd | 64 +-- RSocrata-1.6.2-10/RSocrata/man/validateUrl.Rd | 58 +-- RSocrata-1.6.2-10/RSocrata/tests |only 15 files changed, 447 insertions(+), 425 deletions(-)
Title: A Collection of Network Data Sets for the 'igraph' Package
Description: A small collection of various network data sets,
to use with the 'igraph' package: the Enron email network, various food webs,
interactions in the immunoglobulin protein, the karate club network,
Koenigsberg's bridges, visuotactile brain areas of the macaque monkey,
UK faculty friendship network, domestic US flights network, etc.
Author: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraphdata versions 1.0.0 dated 2015-06-26 and 1.0.1 dated 2015-07-13
igraphdata-1.0.0/igraphdata/README.md |only igraphdata-1.0.1/igraphdata/DESCRIPTION | 6 +++--- igraphdata-1.0.1/igraphdata/MD5 | 8 +++++--- igraphdata-1.0.1/igraphdata/data/enron.rda |binary igraphdata-1.0.1/igraphdata/inst/NEWS.md |only igraphdata-1.0.1/igraphdata/inst/README.Rmd |only igraphdata-1.0.1/igraphdata/inst/README.md |only 7 files changed, 8 insertions(+), 6 deletions(-)
Title: Calibrating Parameters for the Samejima's Continuous IRT Model
Description: Estimates item and person parameters for the Samejima's Continuous Response Model (CRM), computes item fit residual statistics, draws empirical 3D item category response curves, draws theoretical 3D item category response curves, and generates data under the CRM for simulation studies.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>
Diff between EstCRM versions 1.3 dated 2012-07-30 and 1.4 dated 2015-07-13
DESCRIPTION | 22 +- MD5 | 26 +-- NAMESPACE | 7 NEWS | 12 + R/EstCRMitem.R | 373 +++++++++++++++++++++++++++++++++++++------------- R/bootCRM.R | 6 R/fitCRM.R | 2 R/plotCRM.R | 8 - R/print.CRM.R | 29 ++- man/EPIA.Rd | 5 man/EstCRM-package.Rd | 6 man/EstCRMitem.Rd | 21 +- man/bootCRM.Rd | 12 + man/simCRM.Rd | 2 14 files changed, 373 insertions(+), 158 deletions(-)
Title: Constrained Inference for Linear Mixed Effects Models
Description: Estimation and inference for linear models where some or all of the fixed-effects coefficients are subject to order restrictions. This package uses the robust residual bootstrap methodology for inference, and can handle some structure in the residual variance matrix.
Author: Casey M. Jelsema, Shyamal D. Peddada
Maintainer: Casey M. Jelsema <jelsema.casey@gmail.com>
Diff between CLME versions 2.0-2 dated 2015-01-27 and 2.0-4 dated 2015-07-13
CLME-2.0-2/CLME/build |only CLME-2.0-2/CLME/inst/doc |only CLME-2.0-2/CLME/man/VarCorr.clme.Rd |only CLME-2.0-2/CLME/man/confint.clme.Rd |only CLME-2.0-2/CLME/man/figures/Thumbs.db |only CLME-2.0-2/CLME/man/shiny.clme.Rd |only CLME-2.0-2/CLME/vignettes |only CLME-2.0-4/CLME/DESCRIPTION | 23 CLME-2.0-4/CLME/MD5 | 114 +-- CLME-2.0-4/CLME/NAMESPACE | 131 ++- CLME-2.0-4/CLME/NEWS | 105 +-- CLME-2.0-4/CLME/R/00Package.r |only CLME-2.0-4/CLME/R/clme.em.fixed.r | 5 CLME-2.0-4/CLME/R/clme.em.mixed.r | 5 CLME-2.0-4/CLME/R/clme.em.r | 130 +++ CLME-2.0-4/CLME/R/clme.r | 208 +++--- CLME-2.0-4/CLME/R/clme_resids.r | 55 + CLME-2.0-4/CLME/R/create.constraints.r | 263 ++++--- CLME-2.0-4/CLME/R/minque.r | 47 + CLME-2.0-4/CLME/R/plot.clme.r | 343 ++++++---- CLME-2.0-4/CLME/R/resid_boot.r | 44 + CLME-2.0-4/CLME/R/shiny_clme.r | 313 +++++---- CLME-2.0-4/CLME/R/summary.clme.r | 251 ++++++- CLME-2.0-4/CLME/R/test.stat.r | 101 ++ CLME-2.0-4/CLME/R/utilities.r | 1013 ++++++++++++++++++++++++++++-- CLME-2.0-4/CLME/inst/CITATION |only CLME-2.0-4/CLME/man/AIC.clme.Rd | 51 - CLME-2.0-4/CLME/man/BIC.clme.Rd |only CLME-2.0-4/CLME/man/CLME-package.Rd | 164 ++-- CLME-2.0-4/CLME/man/VarCorr.Rd |only CLME-2.0-4/CLME/man/as.clme.Rd | 41 - CLME-2.0-4/CLME/man/clme.Rd | 124 ++- CLME-2.0-4/CLME/man/clme_em.Rd | 131 ++- CLME-2.0-4/CLME/man/clme_resids.Rd | 64 - CLME-2.0-4/CLME/man/confint.Rd |only CLME-2.0-4/CLME/man/create.constraints.Rd | 89 +- CLME-2.0-4/CLME/man/fibroid.Rd | 85 +- CLME-2.0-4/CLME/man/fixef.clme.Rd | 70 +- CLME-2.0-4/CLME/man/formula.clme.Rd | 49 - CLME-2.0-4/CLME/man/logLik.clme.Rd | 52 - CLME-2.0-4/CLME/man/lrt.stat.Rd | 52 - CLME-2.0-4/CLME/man/minque.Rd | 69 -- CLME-2.0-4/CLME/man/model.frame.clme.Rd | 39 - CLME-2.0-4/CLME/man/model.matrix.clme.Rd | 43 - CLME-2.0-4/CLME/man/model_terms_clme.Rd | 75 +- CLME-2.0-4/CLME/man/nobs.clme.Rd | 43 - CLME-2.0-4/CLME/man/plot.clme.Rd | 77 -- CLME-2.0-4/CLME/man/plot.summary.clme.Rd |only CLME-2.0-4/CLME/man/print.clme.Rd | 42 - CLME-2.0-4/CLME/man/print.summary.clme.Rd |only CLME-2.0-4/CLME/man/print.varcorr_clme.Rd | 38 - CLME-2.0-4/CLME/man/ranef.Rd |only CLME-2.0-4/CLME/man/ranef.clme.Rd | 46 - CLME-2.0-4/CLME/man/rat.blood.Rd | 84 +- CLME-2.0-4/CLME/man/resid_boot.Rd | 91 +- CLME-2.0-4/CLME/man/residuals.clme.Rd | 54 - CLME-2.0-4/CLME/man/shiny_clme.Rd |only CLME-2.0-4/CLME/man/sigma.Rd |only CLME-2.0-4/CLME/man/sigma.clme.Rd | 41 - CLME-2.0-4/CLME/man/sigma.summary.clme.Rd |only CLME-2.0-4/CLME/man/summary.clme.Rd | 61 - CLME-2.0-4/CLME/man/vcov.clme.Rd | 44 - CLME-2.0-4/CLME/man/w.stat.Rd | 132 +-- 63 files changed, 3391 insertions(+), 1711 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.8.0 dated 2015-06-03 and 0.8.1 dated 2015-07-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/LoadAPSIMouts.R | 3 +-- R/apsim.R | 1 + 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Username, Full Name, Email Address, 'GitHub' Username of the
Current User
Description: Look up the username and full name of the current user,
the current user's email address and 'GitHub' username,
using various sources of system and configuration information.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between whoami versions 1.1.0 dated 2015-06-11 and 1.1.1 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/whoami.R | 1 + 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Sparklines in the 'R' Terminal
Description: A sparkline is a line chart, without axes and labels.
Its goal is to show the general shape of changes over time, or
another quantity. This package is an 'R' implementation
of the original shell project: <http://zachholman.com/spark/>.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between spark versions 1.0.0 dated 2014-10-14 and 1.0.1 dated 2015-07-12
spark-1.0.0/spark/README.md |only spark-1.0.1/spark/DESCRIPTION | 23 ++++++++++++----------- spark-1.0.1/spark/LICENSE | 2 +- spark-1.0.1/spark/MD5 | 22 ++++++++++++---------- spark-1.0.1/spark/NAMESPACE | 4 +++- spark-1.0.1/spark/R/scale.r | 2 ++ spark-1.0.1/spark/R/utils.r | 1 + spark-1.0.1/spark/inst |only spark-1.0.1/spark/man/spark.Rd | 3 ++- spark-1.0.1/spark/man/spark.default.Rd | 3 ++- spark-1.0.1/spark/man/spark.matrix.Rd | 3 ++- spark-1.0.1/spark/man/sparklines.Rd | 3 ++- 12 files changed, 39 insertions(+), 27 deletions(-)
Title: Client Side Load Balancing
Description: Decide which server to connect to,
based on previous response times, and configuration.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between spareserver versions 1.0.0 dated 2014-11-03 and 1.0.1 dated 2015-07-12
spareserver-1.0.0/spareserver/README.md |only spareserver-1.0.1/spareserver/DESCRIPTION | 17 ++++----- spareserver-1.0.1/spareserver/LICENSE | 2 - spareserver-1.0.1/spareserver/MD5 | 26 ++++++++------- spareserver-1.0.1/spareserver/NAMESPACE | 5 +- spareserver-1.0.1/spareserver/R/spare-package.r | 6 ++- spareserver-1.0.1/spareserver/inst |only spareserver-1.0.1/spareserver/man/add_server.Rd | 3 + spareserver-1.0.1/spareserver/man/add_service.Rd | 3 + spareserver-1.0.1/spareserver/man/remove_service.Rd | 3 + spareserver-1.0.1/spareserver/man/server.Rd | 3 + spareserver-1.0.1/spareserver/man/services.Rd | 3 + spareserver-1.0.1/spareserver/man/spare_q.Rd | 3 + spareserver-1.0.1/spareserver/man/spareserver-package.Rd | 3 + 14 files changed, 44 insertions(+), 33 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 1.0.1 dated 2015-06-05 and 1.0.2 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/rversions.R | 2 ++ 4 files changed, 10 insertions(+), 7 deletions(-)
Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data.
It contains all data sets from https://github.com/dariusk/corpora.
Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson,
Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup,
Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,
Ross Barclay, Ross Binden, Justin Alford, Cole Willsea,
Andrew Gorman, Javier Arce, Patrick Rodriguez,
Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody,
Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black,
Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,
Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rcorpora versions 1.1.0 dated 2015-06-08 and 1.1.1 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/corpora.R | 2 ++ build/rcorpora.pdf |binary inst/NEWS.md | 4 ++++ 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance and Weighted Kendall distance.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 0.4.1 dated 2015-05-17 and 1.0.0 dated 2015-07-12
DESCRIPTION | 12 - MD5 | 51 ++++--- NAMESPACE | 12 + R/class.R | 102 ++++++++------- R/method.R | 215 +++++++++++++++++++++++++++----- R/rankdist.R | 139 +++++++++++++++++++- R/utils.R | 24 ++- data/apa_obj.rda |binary data/apa_partial_obj.rda |only man/DistanceBlock.Rd |only man/DistanceMatrix.Rd |only man/DistancePair.Rd |only man/GenerateExample.Rd |only man/GenerateExampleTopQ.Rd |only man/HashtoRank.Rd | 2 man/ModelSummary.Rd |only man/MomentsEst.Rd | 2 man/OrderingToRanking.Rd | 6 man/RankControl-class.Rd | 11 - man/RankControlKendall-class.Rd | 13 + man/RankControlPhiComponent-class.Rd | 17 +- man/RankControlWeightedKendall-class.Rd | 8 - man/RankData-class.Rd | 45 ++++-- man/RankDistanceModel.Rd | 6 man/RankInit-class.Rd | 8 - man/RanktoHash.Rd | 2 man/apa_obj.Rd | 2 man/apa_partial_obj.Rd |only src/RcppExports.cpp | 88 ++++--------- src/utils.cpp | 33 ++++ tests/testthat/test_RankData.R |only 31 files changed, 573 insertions(+), 225 deletions(-)
Title: Pretty, Human Readable Formatting of Quantities
Description: Pretty, human readable formatting of quantities.
Time intervals: 1337000 -> 15d 11h 23m 20s.
Vague time intervals: 2674000 -> about a month ago.
Bytes: 1337 -> 1.34 kB.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between prettyunits versions 1.0.0 dated 2014-10-13 and 1.0.2 dated 2015-07-12
prettyunits-1.0.0/prettyunits/README.md |only prettyunits-1.0.2/prettyunits/DESCRIPTION | 13 +++++------ prettyunits-1.0.2/prettyunits/MD5 | 26 +++++++++++----------- prettyunits-1.0.2/prettyunits/NAMESPACE | 3 +- prettyunits-1.0.2/prettyunits/R/time-ago.r | 3 ++ prettyunits-1.0.2/prettyunits/R/time.r | 1 prettyunits-1.0.2/prettyunits/inst |only prettyunits-1.0.2/prettyunits/man/pretty_bytes.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_dt.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_ms.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_sec.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/prettyunits.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/time_ago.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/vague_dt.Rd | 3 +- 14 files changed, 40 insertions(+), 27 deletions(-)
Title: Create Disposable R Packages for Testing
Description: Create disposable R packages for testing.
You can create, install and load multiple R packages with a single
function call, and then unload, uninstall and destroy them with another
function call. This is handy when testing how some R code or an R package
behaves with respect to other packages.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between disposables versions 1.0.0 dated 2014-11-01 and 1.0.1 dated 2015-07-12
disposables-1.0.0/disposables/README.md |only disposables-1.0.1/disposables/DESCRIPTION | 14 +++--- disposables-1.0.1/disposables/LICENSE | 2 disposables-1.0.1/disposables/MD5 | 16 ++++--- disposables-1.0.1/disposables/NAMESPACE | 4 + disposables-1.0.1/disposables/R/disposable.r | 40 +++++++++++------- disposables-1.0.1/disposables/inst |only disposables-1.0.1/disposables/man/dispose_packages.Rd | 8 ++- disposables-1.0.1/disposables/man/make_packages.Rd | 8 ++- 9 files changed, 56 insertions(+), 36 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'
color support is automatically detected. Colors and highlighting can
be combined and nested. New styles can also be created easily.
This package was inspired by the 'chalk' 'JavaScript' project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between crayon versions 1.3.0 dated 2015-06-05 and 1.3.1 dated 2015-07-12
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 7 +++++++ R/disposable.r | 4 ++++ R/machinery.r | 4 ++++ R/string_operations.r | 2 ++ R/style-var.r | 3 +++ inst/NEWS.md | 4 ++++ tests/testthat.R | 8 +++++--- 9 files changed, 46 insertions(+), 21 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.2 dated 2015-01-06 and 1.0.3 dated 2015-07-12
DESCRIPTION | 9 +++++---- MD5 | 7 ++++--- NAMESPACE | 3 +++ R/Rdsdp.R | 29 ++++++++++++++++++++--------- tests/test3.R |only 5 files changed, 32 insertions(+), 16 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data". The package contains code for designed
experiments, data sets and other convenience functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kevin.dunn@mcmaster.ca>
Diff between pid versions 0.13 dated 2015-07-06 and 0.15 dated 2015-07-12
DESCRIPTION | 8 +-- MD5 | 12 +++-- R/paretoPlot.R | 29 +++++++++--- data/oildoe.rda |only data/solar.rda |only man/oildoe.Rd |only man/paretoPlot.Rd | 31 ++++++++++++- man/pid-package.Rd | 121 ++++++++++++++++++++++++++--------------------------- man/solar.Rd |only 9 files changed, 123 insertions(+), 78 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.0 dated 2015-06-16 and 2.1 dated 2015-07-12
DESCRIPTION | 8 +- MD5 | 22 +++--- NAMESPACE | 20 ++++++ R/ThresholdROC-2states.R | 140 +++++++++++++++++++++----------------------- R/diagnostic.R | 2 man/ThresholdROC-package.Rd | 4 - man/diagnostic.Rd | 4 - man/plot-thres2.Rd | 2 man/thres2.Rd | 8 +- man/thres3.Rd | 8 +- man/thresTH2.Rd | 2 man/thresTH3.Rd | 2 12 files changed, 120 insertions(+), 102 deletions(-)
Title: A Tool for Structural Topic Model Visualizations
Description: Generates an interactive visualization of topic correlations/hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and Tingley. The package performs a hierarchical clustering of topics which are then exported to a JSON object and visualized using D3.
Author: Antonio Coppola, Margaret Roberts, Brandon Stewart, Dustin Tingley
Maintainer: Antonio Coppola <acoppola@college.harvard.edu>
Diff between stmCorrViz versions 1.1 dated 2015-03-02 and 1.2 dated 2015-07-12
DESCRIPTION | 16 ++++++---------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/clusterAnalysis.R | 7 +++---- R/stmCorrViz.R | 24 ++++++++++++------------ R/stmJSON.R | 40 ++++++++++++++++++++-------------------- man/stmJSON.Rd | 4 ++-- 7 files changed, 52 insertions(+), 54 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-2 dated 2015-06-24 and 2.2-3 dated 2015-07-12
pcalg-2.2-2/pcalg/build |only pcalg-2.2-2/pcalg/inst/doc/pcalgDoc.R |only pcalg-2.2-2/pcalg/inst/doc/pcalgDoc.Rnw |only pcalg-2.2-3/pcalg/DESCRIPTION | 14 pcalg-2.2-3/pcalg/MD5 | 47 pcalg-2.2-3/pcalg/NAMESPACE | 9 pcalg-2.2-3/pcalg/R/Aaux.R | 10 pcalg-2.2-3/pcalg/R/AllClasses.R | 8 pcalg-2.2-3/pcalg/R/gacFuns.R | 262 +-- pcalg-2.2-3/pcalg/R/genRandDAG.R | 241 +- pcalg-2.2-3/pcalg/R/jointIda.R |only pcalg-2.2-3/pcalg/R/lingamFuns.R | 928 +++++------ pcalg-2.2-3/pcalg/R/pcalg.R | 2228 ++++++++++++--------------- pcalg-2.2-3/pcalg/inst/doc/pcalgDoc.pdf |binary pcalg-2.2-3/pcalg/inst/external/N_6_1000.rds |only pcalg-2.2-3/pcalg/man/binCItest.Rd | 10 pcalg-2.2-3/pcalg/man/disCItest.Rd | 38 pcalg-2.2-3/pcalg/man/fci.Rd | 41 pcalg-2.2-3/pcalg/man/fciPlus.Rd | 56 pcalg-2.2-3/pcalg/man/jointIda.Rd | 159 + pcalg-2.2-3/pcalg/man/udag2apag.Rd | 66 pcalg-2.2-3/pcalg/man/udag2pag.Rd | 88 - pcalg-2.2-3/pcalg/tests/test_LINGAM.R | 218 ++ pcalg-2.2-3/pcalg/tests/test_fciPlus.R | 196 +- pcalg-2.2-3/pcalg/tests/test_gSquareBin.R | 207 +- pcalg-2.2-3/pcalg/tests/test_gSquareDis.R | 132 + pcalg-2.2-3/pcalg/tests/test_jointIda.R | 63 27 files changed, 2560 insertions(+), 2461 deletions(-)
Title: Orthogonal Array Package
Description: Interface to D-optimal design generation code of the Orthogonal Array package. Can generate D-optimal designs with specified number of runs and factors. The optimality of the designs is defined in terms of a user specified optimization function based on the D-efficiency and Ds-efficiency.
Author: Pieter Thijs Eendebak
Maintainer: Pieter Thijs Eendebak <pieter.eendebak@gmail.com>
Diff between oapackage versions 2.0.22 dated 2015-06-19 and 2.0.23 dated 2015-07-12
DESCRIPTION | 10 - MD5 | 24 +- R/Doptimize.R | 49 +++-- man/Defficiencies.Rd | 11 - man/Doptimize.Rd | 16 + man/oapackage-package.Rd | 26 +-- src/arrayproperties.h | 2 src/arraytools.cpp | 365 +++++++++++++++++++++++++------------------ src/arraytools.h | 3 src/mathtools.h | 16 + src/oaoptions.cpp | 2 tests/example_Doptimize.R | 23 +- tests/example_design_usage.R | 12 - 13 files changed, 325 insertions(+), 234 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.0-15 dated 2015-04-18 and 1.0-16 dated 2015-07-12
DESCRIPTION | 17 MD5 | 142 +-- NAMESPACE | 6 NEWS | 3 build/vignette.rds |binary data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/Oslo.RData |binary data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/doc/HE-examples.R | 1096 +++++++++++++-------------- inst/doc/repeated.R | 1266 ++++++++++++++++---------------- man/MockJury.Rd | 2 man/heplot-package.Rd | 4 vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 72 files changed, 1271 insertions(+), 1265 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.1.5.2 dated 2015-06-10 and 0.2.0 dated 2015-07-12
DESCRIPTION | 12 ++-- MD5 | 22 ++++---- NEWS.md | 13 +++++ R/ggMarginal.R | 96 +++++++++++++++++++++++++------------- R/plotCount.R | 7 +- build/vignette.rds |binary inst/doc/overview.R | 5 + inst/doc/overview.Rmd | 53 +++++++++++--------- inst/doc/overview.html | 35 +++++++------ inst/examples/ggMarginal/server.R | 28 ++++++++++- inst/examples/ggMarginal/ui.R | 12 +++- man/plotCount.Rd | 6 +- 12 files changed, 195 insertions(+), 94 deletions(-)
Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models.
Author: Wayne Zhang
Maintainer: Wayne Zhang <actuary_zhang@hotmail.com>
Diff between cplm versions 0.7-2 dated 2014-03-10 and 0.7-3 dated 2015-07-12
DESCRIPTION | 10 - MD5 | 26 ++-- NAMESPACE | 68 +++++----- NEWS | 9 + R/cpglmm.R | 6 R/gini.R | 298 +++++++++++++++++++++++------------------------ data/AutoClaim.RData |binary data/ClaimTriangle.RData |binary data/FineRoot.RData |binary man/bcplm.Rd | 1 man/cpglmm.Rd | 1 man/cplm-package.Rd | 2 src/cpglmm.c | 5 vignettes/literatur.bib | 5 14 files changed, 226 insertions(+), 205 deletions(-)
Title: Bootstrapped Confidence Intervals for (Negative) Likelihood
Ratio Tests
Description: Computes appropriate confidence intervals for the likelihood ratio tests commonly used in medicine/epidemiology. It is particularly useful when the sensitivity or specificity in the sample is 100%. Note that this does not perform the test on nested models--for that, see 'epicalc::lrtest'.
Author: Keith A. Marill and Ari B. Friedman
Maintainer: Ari B. Friedman <abfriedman@gmail.com>
Diff between bootLR versions 0.9 dated 2014-05-27 and 1.0 dated 2015-07-12
DESCRIPTION | 20 ++--- MD5 | 24 +++---- NAMESPACE | 3 NEWS |only R/bootLR.R | 146 ++++++++++++++++++++++++++++++------------- inst |only man/BayesianLR.test.Rd | 97 ++++++++++++++++------------ man/bca.Rd | 19 ++--- man/confusionStatistics.Rd | 25 ++----- man/drawMaxedOut.Rd | 28 ++++---- man/medianConsistentlyOne.Rd | 28 ++++---- man/print.lrtest.Rd | 22 ++++-- man/run.BayesianLR.test.Rd | 44 +++++------- man/sequentialGridSearch.Rd | 37 ++++------ 14 files changed, 282 insertions(+), 211 deletions(-)
Title: GUI Implementing Bayesian Working Memory Models
Description: A GUI R implementation of hierarchical Bayesian models of working memory, used for analyzing change detection data.
Author: R. D. Morey <richarddmorey@gmail.com>
Maintainer: R. D. Morey <richarddmorey@gmail.com>
Diff between WMCapacity versions 0.9.6.6 dated 2011-11-24 and 0.9.6.7 dated 2015-07-12
DESCRIPTION | 16 MD5 | 23 NAMESPACE | 30 NEWS |only R/analysistab.R | 1512 +++++++++++------------ R/datatab.R | 1414 +++++++++++----------- R/diagnosticstab.R | 1136 ++++++++--------- R/gui_functions.R | 488 +++---- R/modeltab.R | 3312 ++++++++++++++++++++++++++-------------------------- R/savetab.R | 22 R/wommbat.R | 172 +- man/wommbatGUI.Rd | 109 - man/wommbatNoGUI.Rd | 60 13 files changed, 4145 insertions(+), 4149 deletions(-)
Title: Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>
Diff between cpm versions 2.0 dated 2015-06-05 and 2.1 dated 2015-07-12
DESCRIPTION | 12 +++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- man/changeDetected.Rd | 2 +- man/cpmPackage.Rd | 18 +++++++++++------- man/cpmReset.Rd | 2 +- man/detectChangePoint.Rd | 14 ++++++++------ man/detectChangePointBatch.Rd | 12 +++++++----- man/getBatchThreshold.Rd | 12 +++++++----- man/getStatistics.Rd | 2 +- man/makeChangePointModel.Rd | 12 +++++++----- man/processObservation.Rd | 2 +- man/processStream.Rd | 9 +++++---- 13 files changed, 68 insertions(+), 56 deletions(-)
Title: Correct for Verification Bias in Diagnostic Accuracy & Agreement
Description: A standard test is observed on all specimens. We treat the second test (or sampled test) as being conducted on only a stratified sample of specimens. Verification Bias is this situation when the specimens for doing the second (sampled) test is not under investigator control. We treat the total sample as stratified two-phase sampling and use inverse probability weighting. We estimate diagnostic accuracy (category-specific classification probabilities; for binary tests reduces to specificity and sensitivity, and also predictive values) and agreement statistics (percent agreement, percent agreement by category, Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating the agreement and diagnostic accuracy of two diagnostic tests when one test is conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5): 10.1002/sim.4422.
Author: Hormuzd A. Katki and David W. Edelstein
Maintainer: Hormuzd Katki <katkih@mail.nih.gov>
Diff between CompareTests versions 1.0 dated 2011-04-04 and 1.1 dated 2015-07-12
DESCRIPTION | 27 - MD5 |only NAMESPACE |only NEWS |only R/CompareTests.R | 638 +++++++++++++++++++++++++------------------- man/CompareTests-package.Rd | 14 man/CompareTests.Rd | 118 +++++--- man/fulltable.Rd | 10 man/specimens.Rd | 6 9 files changed, 454 insertions(+), 359 deletions(-)
Title: Interface for FAME Time Series Database
Description: Read and write FAME databases.
Author: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Maintainer: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Diff between fame versions 2.18 dated 2011-12-30 and 2.21 dated 2015-07-12
fame-2.18/fame/COPYRIGHTS |only fame-2.21/fame/DESCRIPTION | 16 ++--- fame-2.21/fame/MD5 | 30 ++++----- fame-2.21/fame/NAMESPACE | 8 +- fame-2.21/fame/NEWS | 18 +++++ fame-2.21/fame/R/fame.R | 103 +++++++++++++++++++++++---------- fame-2.21/fame/R/windows/zzz.R | 2 fame-2.21/fame/configure | 4 - fame-2.21/fame/configure.ac | 4 - fame-2.21/fame/inst/COPYRIGHTS |only fame-2.21/fame/man/fameAddAttribute.Rd | 4 - fame-2.21/fame/man/fameIsScalar.Rd | 9 +- fame-2.21/fame/man/lowLevelFame.Rd | 39 ++++++++++-- fame-2.21/fame/man/tifToFameName.Rd | 8 +- fame-2.21/fame/src/chli.c | 1 fame-2.21/fame/src/fame.c | 8 ++ fame-2.21/fame/src/fame.h | 2 17 files changed, 182 insertions(+), 74 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series
from the HIS Central catalog based on geographic bounding box, server, or keyword.
GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The GetValues function can also retrieve WaterML 1 or WaterML 2.0 data
from a custom URL. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.2.3 dated 2015-06-29 and 1.3.2 dated 2015-07-12
DESCRIPTION | 11 ++-- MD5 | 12 ++-- NAMESPACE | 2 R/GetValues.R | 98 ++++++++++++++++++++++++++++++++++++++-- R/HISCentral_GetSeriesCatalog.R | 3 - R/WaterMLVersion.R |only man/GetValues.Rd | 8 ++- man/WaterMLVersion.Rd |only 8 files changed, 118 insertions(+), 16 deletions(-)
Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized
queries.
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>
Diff between RODBCext versions 0.2.3 dated 2014-07-29 and 0.2.5 dated 2015-07-12
DESCRIPTION | 10 ++-- MD5 | 32 +++++++------- NAMESPACE | 2 NEWS | 23 ++++++++-- R/sqlExecute.R | 34 +++++++++++++-- R/sqlPrepare.R | 4 + README.md | 5 +- build/vignette.rds |binary inst/doc/Parameterized_SQL_queries.Rmd | 25 ++++++----- inst/doc/Parameterized_SQL_queries.html | 69 +++++++++++++++++--------------- man/odbcFetchRows.Rd | 3 - man/sqlExecute.Rd | 16 +++++-- man/sqlFetchMore.Rd | 3 - man/sqlPrepare.Rd | 3 - src/RODBC.c | 17 ++++--- src/RODBCext.c | 10 ++-- vignettes/Parameterized_SQL_queries.Rmd | 25 ++++++----- 17 files changed, 172 insertions(+), 109 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: The packge contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.3.0 dated 2014-09-18 and 1.5.3 dated 2015-07-12
refGenome-1.3.0/refGenome/src/ptr_pair_list.h |only refGenome-1.3.0/refGenome/src/refGenome.c |only refGenome-1.5.3/refGenome/ChangeLog | 8 refGenome-1.5.3/refGenome/DESCRIPTION | 10 refGenome-1.5.3/refGenome/MD5 | 58 - refGenome-1.5.3/refGenome/NAMESPACE | 8 refGenome-1.5.3/refGenome/NEWS | 38 refGenome-1.5.3/refGenome/R/refGenome.r | 803 ++++++++----------- refGenome-1.5.3/refGenome/build/vignette.rds |binary refGenome-1.5.3/refGenome/inst/doc/readGTF.R |only refGenome-1.5.3/refGenome/inst/doc/readGTF.Rnw |only refGenome-1.5.3/refGenome/inst/doc/readGTF.pdf |only refGenome-1.5.3/refGenome/inst/doc/refGenome.R | 171 ++-- refGenome-1.5.3/refGenome/inst/doc/refGenome.Rnw | 513 +++++++++--- refGenome-1.5.3/refGenome/inst/doc/refGenome.pdf |binary refGenome-1.5.3/refGenome/man/ensemblGenome-class.Rd | 15 refGenome-1.5.3/refGenome/man/overlapJuncs.Rd | 18 refGenome-1.5.3/refGenome/man/readGtf.Rd |only refGenome-1.5.3/refGenome/man/refExons-class.Rd | 6 refGenome-1.5.3/refGenome/man/refGenome-class.Rd | 51 - refGenome-1.5.3/refGenome/man/refGenome-package.Rd | 2 refGenome-1.5.3/refGenome/man/ucscGenome-class.Rd | 8 refGenome-1.5.3/refGenome/man/unifyJuncs.Rd | 10 refGenome-1.5.3/refGenome/man/unifyRanges.Rd |only refGenome-1.5.3/refGenome/src/Makevars | 1 refGenome-1.5.3/refGenome/src/Makevars.win | 1 refGenome-1.5.3/refGenome/src/data_frame.h |only refGenome-1.5.3/refGenome/src/extptr.h |only refGenome-1.5.3/refGenome/src/grange.h |only refGenome-1.5.3/refGenome/src/gtf.h |only refGenome-1.5.3/refGenome/src/range_partition.h |only refGenome-1.5.3/refGenome/src/refGenome.cpp |only refGenome-1.5.3/refGenome/src/refGenome.h | 88 -- refGenome-1.5.3/refGenome/src/tokenize.h |only refGenome-1.5.3/refGenome/tests/test-all.R | 33 refGenome-1.5.3/refGenome/tests/test_unify_ranges.r |only refGenome-1.5.3/refGenome/vignettes/readGTF.Rnw |only refGenome-1.5.3/refGenome/vignettes/refGenome.Rnw | 513 +++++++++--- 38 files changed, 1519 insertions(+), 836 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.2.1 dated 2015-06-15 and 0.2.2 dated 2015-07-11
DESCRIPTION | 12 +++++------ MD5 | 50 ++++++++++++++++++++++++------------------------ NAMESPACE | 6 +++-- NEWS | 5 ++++ R/fitbs.R | 3 +- R/fitgamma.R | 2 - R/fitgeom.R | 3 +- R/fitgs.R | 3 +- R/fitlnorm.R | 2 - R/fitls.R | 3 +- R/fitmand.R | 2 - R/fitmzsm.R | 2 - R/fitnbinom.R | 2 - R/fitpareto.R | 2 - R/fitpoilog.R | 2 - R/fitpower.R | 3 +- R/fitrbs.R | 3 +- R/fitweibull.R | 16 +++++++-------- R/fitzipf.R | 2 - R/plotprofmle.R | 25 ++++++++++++++++-------- R/sads-methods.R | 2 - build/vignette.rds |binary inst/doc/sads_intro.pdf |binary man/fitsad.Rd | 5 +++- man/plotprofmle.Rd | 23 ++++++++++++++-------- man/sads-package.Rd | 4 +-- 26 files changed, 106 insertions(+), 76 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.6-8 dated 2015-04-16 and 0.6-9 dated 2015-07-11
vcdExtra-0.6-8/vcdExtra/man/summarise-old.Rd |only vcdExtra-0.6-9/vcdExtra/DESCRIPTION | 14 - vcdExtra-0.6-9/vcdExtra/MD5 | 119 ++++++------- vcdExtra-0.6-9/vcdExtra/NAMESPACE | 21 +- vcdExtra-0.6-9/vcdExtra/NEWS | 7 vcdExtra-0.6-9/vcdExtra/R/summarise-old.R | 183 ++++++++++----------- vcdExtra-0.6-9/vcdExtra/build/vignette.rds |binary vcdExtra-0.6-9/vcdExtra/data/Abortion.rda |binary vcdExtra-0.6-9/vcdExtra/data/Accident.RData |binary vcdExtra-0.6-9/vcdExtra/data/AirCrash.RData |binary vcdExtra-0.6-9/vcdExtra/data/Alligator.RData |binary vcdExtra-0.6-9/vcdExtra/data/Bartlett.rda |binary vcdExtra-0.6-9/vcdExtra/data/Caesar.rda |binary vcdExtra-0.6-9/vcdExtra/data/Cancer.rda |binary vcdExtra-0.6-9/vcdExtra/data/Cormorants.RData |binary vcdExtra-0.6-9/vcdExtra/data/CyclingDeaths.RData |binary vcdExtra-0.6-9/vcdExtra/data/DaytonSurvey.RData |binary vcdExtra-0.6-9/vcdExtra/data/Depends.RData |binary vcdExtra-0.6-9/vcdExtra/data/Detergent.rda |binary vcdExtra-0.6-9/vcdExtra/data/Donner.RData |binary vcdExtra-0.6-9/vcdExtra/data/Draft1970.RData |binary vcdExtra-0.6-9/vcdExtra/data/Draft1970table.RData |binary vcdExtra-0.6-9/vcdExtra/data/Dyke.rda |binary vcdExtra-0.6-9/vcdExtra/data/Fungicide.rda |binary vcdExtra-0.6-9/vcdExtra/data/GSS.rda |binary vcdExtra-0.6-9/vcdExtra/data/Geissler.RData |binary vcdExtra-0.6-9/vcdExtra/data/Gilby.rda |binary vcdExtra-0.6-9/vcdExtra/data/HairEyePlace.RData |binary vcdExtra-0.6-9/vcdExtra/data/Hauser79.RData |binary vcdExtra-0.6-9/vcdExtra/data/Heart.rda |binary vcdExtra-0.6-9/vcdExtra/data/Heckman.rda |binary vcdExtra-0.6-9/vcdExtra/data/Hoyt.rda |binary vcdExtra-0.6-9/vcdExtra/data/ICU.RData |binary vcdExtra-0.6-9/vcdExtra/data/JobSat.rda |binary vcdExtra-0.6-9/vcdExtra/data/Mammograms.RData |binary vcdExtra-0.6-9/vcdExtra/data/Mental.rda |binary vcdExtra-0.6-9/vcdExtra/data/Mice.RData |only vcdExtra-0.6-9/vcdExtra/data/Mobility.rda |binary vcdExtra-0.6-9/vcdExtra/data/PhdPubs.RData |binary vcdExtra-0.6-9/vcdExtra/data/ShakeWords.RData |binary vcdExtra-0.6-9/vcdExtra/data/TV.rda |binary vcdExtra-0.6-9/vcdExtra/data/Titanicp.rda |binary vcdExtra-0.6-9/vcdExtra/data/Toxaemia.RData |binary vcdExtra-0.6-9/vcdExtra/data/Vietnam.RData |binary vcdExtra-0.6-9/vcdExtra/data/Vietnam.rda |binary vcdExtra-0.6-9/vcdExtra/data/Vote1980.RData |binary vcdExtra-0.6-9/vcdExtra/data/WorkerSat.RData |binary vcdExtra-0.6-9/vcdExtra/data/Yamaguchi87.RData |binary vcdExtra-0.6-9/vcdExtra/demo/Wong2-3.R | 2 vcdExtra-0.6-9/vcdExtra/demo/vision-quasi.R | 66 +++---- vcdExtra-0.6-9/vcdExtra/demo/yamaguchi-xie.R | 36 ++-- vcdExtra-0.6-9/vcdExtra/man/Accident.Rd | 8 vcdExtra-0.6-9/vcdExtra/man/Crossings.Rd | 4 vcdExtra-0.6-9/vcdExtra/man/Donner.Rd | 2 vcdExtra-0.6-9/vcdExtra/man/Hauser79.Rd | 16 - vcdExtra-0.6-9/vcdExtra/man/Kway.Rd | 11 - vcdExtra-0.6-9/vcdExtra/man/Mice.Rd |only vcdExtra-0.6-9/vcdExtra/man/ShakeWords.Rd | 2 vcdExtra-0.6-9/vcdExtra/man/glmlist.Rd | 4 vcdExtra-0.6-9/vcdExtra/man/modFit.Rd | 3 vcdExtra-0.6-9/vcdExtra/man/vcdExtra-deprecated.Rd | 24 +- vcdExtra-0.6-9/vcdExtra/man/vcdExtra-package.Rd | 8 62 files changed, 276 insertions(+), 254 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.3 dated 2015-01-06 and 1.4.4 dated 2015-07-11
DESCRIPTION | 14 +- LICENSE | 2 MD5 | 172 ++++++++++++++++----------------- NAMESPACE | 2 NEWS | 6 + R/BuildInnerBreakdownsRecursively.R | 106 ++++++++++---------- R/GetDataWarehouseDisplay.R | 2 R/ParseRanked.R | 10 - R/ParseTrended.R | 115 +++++++++++----------- R/RSiteCatalyst.R | 6 - R/SCAuth.R | 2 man/ApiRequest.Rd | 2 man/BuildClassificationValueSegment.Rd | 2 man/BuildHeader.Rd | 2 man/BuildInnerBreakdownsRecursively.Rd | 2 man/BuildLineItemSegment.Rd | 2 man/BuildRealTimeReportStructure.Rd | 2 man/CancelReport.Rd | 2 man/GetActivation.Rd | 2 man/GetAxleStartDate.Rd | 2 man/GetBaseCurrency.Rd | 2 man/GetBaseURL.Rd | 2 man/GetBookmarks.Rd | 2 man/GetCalculatedMetrics.Rd | 2 man/GetClassifications.Rd | 2 man/GetCustomCalendar.Rd | 2 man/GetDashboards.Rd | 2 man/GetDataWarehouseDisplay.Rd | 4 man/GetDefaultPage.Rd | 2 man/GetDiscoverEnabled.Rd | 2 man/GetEcommerce.Rd | 2 man/GetElements.Rd | 2 man/GetEndpoint.Rd | 2 man/GetEvars.Rd | 2 man/GetFeed.Rd | 2 man/GetFeeds.Rd | 2 man/GetGeoSegmentation.Rd | 2 man/GetGroups.Rd | 2 man/GetIPAddressExclusions.Rd | 2 man/GetIPObfuscation.Rd | 2 man/GetInternalURLFilters.Rd | 2 man/GetKeyVisitors.Rd | 2 man/GetListVariables.Rd | 2 man/GetLocalization.Rd | 2 man/GetLogin.Rd | 2 man/GetLogins.Rd | 2 man/GetMarketingChannelExpiration.Rd | 2 man/GetMarketingChannelRules.Rd | 2 man/GetMarketingChannels.Rd | 2 man/GetMetrics.Rd | 2 man/GetMobileAppReporting.Rd | 2 man/GetPaidSearchDetection.Rd | 2 man/GetPermanentTraffic.Rd | 2 man/GetProps.Rd | 2 man/GetQueue.Rd | 2 man/GetRealTimeReport.Rd | 2 man/GetRealTimeSettings.Rd | 2 man/GetReportDescription.Rd | 2 man/GetReportSuites.Rd | 2 man/GetScheduledSpike.Rd | 2 man/GetSegments.Rd | 2 man/GetSiteTitle.Rd | 2 man/GetSuccessEvents.Rd | 2 man/GetTimeZone.Rd | 2 man/GetTrackingServer.Rd | 2 man/GetTransactionEnabled.Rd | 2 man/GetUniqueVisitorVariable.Rd | 2 man/GetUsageLog.Rd | 2 man/GetVersionAccess.Rd | 2 man/GetVideoSettings.Rd | 2 man/JsonQueueRealTimeReport.Rd | 2 man/ParseFallout.Rd | 2 man/ParseOvertime.Rd | 2 man/ParsePathing.Rd | 2 man/ParseRanked.Rd | 2 man/ParseTrended.Rd | 2 man/QueueFallout.Rd | 2 man/QueueOvertime.Rd | 2 man/QueuePathing.Rd | 2 man/QueueRanked.Rd | 2 man/QueueTrended.Rd | 2 man/RSiteCatalyst.Rd | 8 - man/SCAuth.Rd | 2 man/SaveRealTimeSettings.Rd | 2 man/SubmitJsonQueueReport.Rd | 2 man/ValidateReport.Rd | 2 tests/testthat/test-scauth.R | 2 87 files changed, 308 insertions(+), 289 deletions(-)
Title: Additional Binary Operators
Description: A set of binary operators for common tasks such as regex
manipulation.
Author: Romain Francois <romain@r-enthusiasts.com>
Maintainer: Romain Francois <romain@r-enthusiasts.com>
Diff between operators versions 0.1-7 dated 2014-09-08 and 0.1-8 dated 2015-07-11
DESCRIPTION | 12 +++++++----- LICENSE | 2 +- MD5 | 8 ++++---- NAMESPACE | 1 + tests/testthat/test-but.R | 5 +---- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. nplr can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre],
Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>
Diff between nplr versions 0.1-2 dated 2015-07-08 and 0.1-3 dated 2015-07-11
DESCRIPTION | 8 +- MD5 | 34 ++++----- NAMESPACE | 4 - NEWS | 10 ++ R/AllClasses.R | 8 +- R/helpers.R | 186 +++++++++++++++++++++++++++++++++++++++++---------- R/nplr.R | 2 R/overlay.R |only R/plot.nplr.R | 59 ++++------------ build/vignette.rds |binary inst/doc/nplr.R | 29 ++++++- inst/doc/nplr.Rnw | 31 +++++++- inst/doc/nplr.pdf |binary man/convertToProp.Rd | 2 man/getEstimates.Rd | 2 man/nplr.Rd | 4 - man/overlay.Rd |only man/plot.nplr.Rd | 8 +- vignettes/nplr.Rnw | 31 +++++++- 19 files changed, 299 insertions(+), 119 deletions(-)
Title: Spatial Analysis of Phenotypic, Genotypic and Environmental Data
Description: Geostatistical tools for analyzing spatial patterns in
population biology. Easy integration of information from multiple sources
with "ecogen" objects.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <learoser@gmail.com>
Diff between EcoGenetics versions 1.2.0-1 dated 2015-06-18 and 1.2.0-2 dated 2015-07-11
EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2columns.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/eco.append.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/int.ecogen.definition.R |only EcoGenetics-1.2.0-1/EcoGenetics/man/aue.char2num.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/aue.idig.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/auxiliar2.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.2columns.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.append.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.n.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/ecogen-summary.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/ecogen2genind-genind2ecogen.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/DESCRIPTION | 46 EcoGenetics-1.2.0-2/EcoGenetics/MD5 | 266 ++- EcoGenetics-1.2.0-2/EcoGenetics/NAMESPACE | 95 + EcoGenetics-1.2.0-2/EcoGenetics/NEWS | 31 EcoGenetics-1.2.0-2/EcoGenetics/R/ZZZ.R | 37 EcoGenetics-1.2.0-2/EcoGenetics/R/accesors.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/auxiliar.R | 668 ++++++---- EcoGenetics-1.2.0-2/EcoGenetics/R/classes.R | 184 ++ EcoGenetics-1.2.0-2/EcoGenetics/R/control.R | 295 +++- EcoGenetics-1.2.0-2/EcoGenetics/R/deprecated.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/eco.2geneland.R | 67 - EcoGenetics-1.2.0-2/EcoGenetics/R/eco.2genepop.R | 135 -- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.2gstudio.R | 35 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.2hierfstat.R | 31 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.2spagedi.R | 82 - EcoGenetics-1.2.0-2/EcoGenetics/R/eco.NDVI.R | 83 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.NDVI.post.R | 93 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.alfreq.R | 50 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.association.R | 43 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.cbind.R | 224 ++- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.clear.R | 26 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.convert.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/eco.cormantel.R | 125 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.correlog.R | 210 +++ EcoGenetics-1.2.0-2/EcoGenetics/R/eco.detrend.R | 90 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.forestplot.R | 58 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.format.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/eco.genepop2df.R | 26 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.gsa.R | 180 ++ EcoGenetics-1.2.0-2/EcoGenetics/R/eco.kin.loiselle.R | 42 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.lagweight.R | 154 ++ EcoGenetics-1.2.0-2/EcoGenetics/R/eco.lmtree.R | 145 +- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.lsa.R | 230 +++ EcoGenetics-1.2.0-2/EcoGenetics/R/eco.malecot.R | 296 ++++ EcoGenetics-1.2.0-2/EcoGenetics/R/eco.mantel.R | 83 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.merge.R | 193 +- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.order.R | 142 -- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.pairtest.R | 54 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.post.geneland.R | 61 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.rankplot.R | 75 - EcoGenetics-1.2.0-2/EcoGenetics/R/eco.rbind.R | 175 +- EcoGenetics-1.2.0-2/EcoGenetics/R/eco.remove.R | 35 EcoGenetics-1.2.0-2/EcoGenetics/R/eco.subset.R | 74 - EcoGenetics-1.2.0-2/EcoGenetics/R/eco.theilsen.R | 74 - EcoGenetics-1.2.0-2/EcoGenetics/R/eco.variogram.R | 82 + EcoGenetics-1.2.0-2/EcoGenetics/R/eco.weight.R | 145 ++ EcoGenetics-1.2.0-2/EcoGenetics/R/ecogen.1OF5.definition.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/ecogen.2OF5.constructor.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/ecogen.3OF5.basic.methods.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/ecogen.4OF5.brackets.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/ecogen.5OF5.get&set.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/int.break.R | 29 EcoGenetics-1.2.0-2/EcoGenetics/R/int.convert.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/int.crosscor.R | 23 EcoGenetics-1.2.0-2/EcoGenetics/R/int.geary.R | 17 EcoGenetics-1.2.0-2/EcoGenetics/R/int.genind.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/int.jackknife.R | 10 EcoGenetics-1.2.0-2/EcoGenetics/R/int.joincount.R | 54 EcoGenetics-1.2.0-2/EcoGenetics/R/int.kin.loiselle.R | 14 EcoGenetics-1.2.0-2/EcoGenetics/R/int.mantel.R | 19 EcoGenetics-1.2.0-2/EcoGenetics/R/int.moran.R | 20 EcoGenetics-1.2.0-2/EcoGenetics/R/int.multitable.R | 12 EcoGenetics-1.2.0-2/EcoGenetics/R/int.random.test.R | 9 EcoGenetics-1.2.0-2/EcoGenetics/R/miscellaneous.R |only EcoGenetics-1.2.0-2/EcoGenetics/R/plot.methods.R | 94 + EcoGenetics-1.2.0-2/EcoGenetics/R/show_summary.methods.R | 287 ++-- EcoGenetics-1.2.0-2/EcoGenetics/data/eco.test.RData |binary EcoGenetics-1.2.0-2/EcoGenetics/data/eco2.RData |binary EcoGenetics-1.2.0-2/EcoGenetics/data/eco3.RData |binary EcoGenetics-1.2.0-2/EcoGenetics/man/EcoGenetics-accessors.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/EcoGenetics-package.Rd | 423 ++++-- EcoGenetics-1.2.0-2/EcoGenetics/man/aue.access.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.filter.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/aue.fqal.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.genlab.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.image2df.Rd | 6 EcoGenetics-1.2.0-2/EcoGenetics/man/aue.is.poly.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.rescale.Rd | 7 EcoGenetics-1.2.0-2/EcoGenetics/man/aue.rm.nonpoly.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.rmspaces.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.seqlist.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/aue.sort.Rd | 80 + EcoGenetics-1.2.0-2/EcoGenetics/man/eco.2geneland.Rd | 17 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.2genepop.Rd | 17 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.2gstudio.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.2hierfstat.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.2spagedi.Rd | 13 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.IBD-class.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/eco.NDVI.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.NDVI.post.Rd | 5 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.alfreq.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.association.Rd | 1 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.cbind.Rd | 28 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.clear.Rd | 10 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.convert.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/eco.cormantel.Rd | 50 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.correlog.Rd | 91 - EcoGenetics-1.2.0-2/EcoGenetics/man/eco.detrend.Rd | 42 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.format.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/eco.genepop2df.Rd | 6 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.gsa-class.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.gsa.Rd | 113 + EcoGenetics-1.2.0-2/EcoGenetics/man/eco.kin.loiselle.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.lagweight.Rd | 71 - EcoGenetics-1.2.0-2/EcoGenetics/man/eco.lmtree.Rd | 67 - EcoGenetics-1.2.0-2/EcoGenetics/man/eco.lmtree.mctree-summary.Rd | 4 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.lsa.Rd | 159 +- EcoGenetics-1.2.0-2/EcoGenetics/man/eco.malecot.Rd | 73 - EcoGenetics-1.2.0-2/EcoGenetics/man/eco.mantel.Rd | 39 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.mctree-class.Rd | 4 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.merge.Rd | 9 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.mlm-class.Rd | 4 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.order.Rd | 13 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.pairtest.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.post.geneland.Rd | 3 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.rbind.Rd | 32 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.remove.Rd | 23 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.subset.Rd | 15 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.theilsen.Rd | 11 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.variogram.Rd | 33 EcoGenetics-1.2.0-2/EcoGenetics/man/eco.weight.Rd | 55 EcoGenetics-1.2.0-2/EcoGenetics/man/ecogen-class.Rd | 8 EcoGenetics-1.2.0-2/EcoGenetics/man/ecogen-methods.Rd | 45 EcoGenetics-1.2.0-2/EcoGenetics/man/ecogen.Rd | 175 +- EcoGenetics-1.2.0-2/EcoGenetics/man/int.2symmetric.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.colnames.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.con.Rd | 14 EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.group.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.ncod.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.numeric.Rd | 9 EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.rownames.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.check.vnames.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.df2genind.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.dlatlon2distm.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/int.gendata-class.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.gendata2genind.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.genind-class.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.genind.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.genind2df.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.genind2gendata.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.joincount.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/int.loc2al.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.multiplot-class.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/int.undimmattg.Rd | 2 EcoGenetics-1.2.0-2/EcoGenetics/man/is.meta.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/meta2char.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/rankplot-methods.Rd | 18 EcoGenetics-1.2.0-2/EcoGenetics/man/sub-sub-ecogen-numeric-missing-method.Rd |only EcoGenetics-1.2.0-2/EcoGenetics/man/sub-subset-ecogen-numeric-missing-method.Rd |only 160 files changed, 5790 insertions(+), 1861 deletions(-)
Title: CreditRisk+ Portfolio Model
Description: Modelling credit risks based on the concept of "CreditRisk+", First Boston Financial Products, 1997 and "CreditRisk+ in the Banking Industry", Gundlach & Lehrbass, Springer, 2003.
Author: Kevin Jakob, Dr. Matthias Fischer & Stefan Kolb
Maintainer: Kevin Jakob <Kevin.Jakob@Student.uni-augsburg.de>
Diff between crp.CSFP versions 2.0 dated 2013-11-04 and 2.0.1 dated 2015-07-11
crp.CSFP-2.0.1/crp.CSFP/DESCRIPTION | 14 crp.CSFP-2.0.1/crp.CSFP/MD5 | 18 crp.CSFP-2.0.1/crp.CSFP/NAMESPACE | 109 ---- crp.CSFP-2.0.1/crp.CSFP/R/crpCSFPclass.r | 474 +----------------- crp.CSFP-2.0.1/crp.CSFP/R/other_functions.r | 7 crp.CSFP-2.0.1/crp.CSFP/man/crp.CSFP-class.Rd | 6 crp.CSFP-2.0.1/crp.CSFP/man/crp.CSFP-package.Rd | 10 crp.CSFP-2.0.1/crp.CSFP/man/sigma_k-methods.Rd |only crp.CSFP-2.0.1/crp.CSFP/man/sigma_sqr_div-methods.Rd |only crp.CSFP-2.0.1/crp.CSFP/man/sigma_sqr_syst-methods.Rd |only crp.CSFP-2.0/crp.CSFP/man/sigma.k-methods.Rd |only crp.CSFP-2.0/crp.CSFP/man/sigma.sqr.div-methods.Rd |only crp.CSFP-2.0/crp.CSFP/man/sigma.sqr.syst-methods.Rd |only 13 files changed, 78 insertions(+), 560 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.7.2-1 dated 2015-06-02 and 0.8.0-3 dated 2015-07-11
quanteda-0.7.2-1/quanteda/R/corpus-sources-S4.R |only quanteda-0.7.2-1/quanteda/R/dictionaryFunctions.R |only quanteda-0.7.2-1/quanteda/R/gui.R |only quanteda-0.7.2-1/quanteda/R/onLoad.R |only quanteda-0.7.2-1/quanteda/man/language.Rd |only quanteda-0.7.2-1/quanteda/man/tokenizeOnly.Rd |only quanteda-0.7.2-1/quanteda/src/clean.cpp |only quanteda-0.7.2-1/quanteda/src/tokenize.cpp |only quanteda-0.7.2-1/quanteda/src/tokenizeOnly.cpp |only quanteda-0.8.0-3/quanteda/DESCRIPTION | 30 quanteda-0.8.0-3/quanteda/MD5 | 168 +- quanteda-0.8.0-3/quanteda/NAMESPACE | 42 quanteda-0.8.0-3/quanteda/NEWS | 70 quanteda-0.8.0-3/quanteda/R/RcppExports.R | 4 quanteda-0.8.0-3/quanteda/R/clean.R | 170 -- quanteda-0.8.0-3/quanteda/R/collocations.R | 153 +- quanteda-0.8.0-3/quanteda/R/converters.R | 19 quanteda-0.8.0-3/quanteda/R/corpus.R | 621 ++++---- quanteda-0.8.0-3/quanteda/R/dataDocs.R | 64 quanteda-0.8.0-3/quanteda/R/describe-texts.R | 10 quanteda-0.8.0-3/quanteda/R/dfm-main.R | 849 ++---------- quanteda-0.8.0-3/quanteda/R/dfm-methods.R |only quanteda-0.8.0-3/quanteda/R/dictionaries.R |only quanteda-0.8.0-3/quanteda/R/encoding.R |only quanteda-0.8.0-3/quanteda/R/ngrams.R | 59 quanteda-0.8.0-3/quanteda/R/readability.R |only quanteda-0.8.0-3/quanteda/R/stopwords.R | 47 quanteda-0.8.0-3/quanteda/R/syllables.R | 125 + quanteda-0.8.0-3/quanteda/R/textfile.R |only quanteda-0.8.0-3/quanteda/R/textmodel-generics.R | 7 quanteda-0.8.0-3/quanteda/R/textmodel-wordscores.R | 10 quanteda-0.8.0-3/quanteda/R/toLower.R |only quanteda-0.8.0-3/quanteda/R/tokenize.R | 426 +++--- quanteda-0.8.0-3/quanteda/R/wordstem.R |only quanteda-0.8.0-3/quanteda/README.md | 138 - quanteda-0.8.0-3/quanteda/build/vignette.rds |binary quanteda-0.8.0-3/quanteda/data/datalist | 2 quanteda-0.8.0-3/quanteda/data/encodedTexts.RData |only quanteda-0.8.0-3/quanteda/data/ie2010Corpus.RData |binary quanteda-0.8.0-3/quanteda/data/wordlists.RData |only quanteda-0.8.0-3/quanteda/inst/doc/corpus-sources.R | 2 quanteda-0.8.0-3/quanteda/inst/doc/corpus-sources.Rmd | 6 quanteda-0.8.0-3/quanteda/inst/doc/corpus-sources.html | 82 - quanteda-0.8.0-3/quanteda/inst/doc/design-and-workflow.R |only quanteda-0.8.0-3/quanteda/inst/doc/design-and-workflow.Rmd |only quanteda-0.8.0-3/quanteda/inst/doc/design-and-workflow.html |only quanteda-0.8.0-3/quanteda/inst/doc/development-plans.Rmd | 73 - quanteda-0.8.0-3/quanteda/inst/doc/development-plans.html | 91 + quanteda-0.8.0-3/quanteda/inst/doc/quickstart.R | 5 quanteda-0.8.0-3/quanteda/inst/doc/quickstart.Rmd | 5 quanteda-0.8.0-3/quanteda/inst/doc/quickstart.html | 170 +- quanteda-0.8.0-3/quanteda/man/changeunits.Rd | 13 quanteda-0.8.0-3/quanteda/man/clean.Rd | 58 quanteda-0.8.0-3/quanteda/man/collocations.Rd | 79 - quanteda-0.8.0-3/quanteda/man/convert.Rd | 13 quanteda-0.8.0-3/quanteda/man/corpus.Rd | 101 - quanteda-0.8.0-3/quanteda/man/corpusSource-class.Rd | 12 quanteda-0.8.0-3/quanteda/man/dfm.Rd | 109 - quanteda-0.8.0-3/quanteda/man/dictionary.Rd | 33 quanteda-0.8.0-3/quanteda/man/docfreq.Rd | 20 quanteda-0.8.0-3/quanteda/man/docnames.Rd | 2 quanteda-0.8.0-3/quanteda/man/docvars.Rd | 14 quanteda-0.8.0-3/quanteda/man/encodedTexts.Rd |only quanteda-0.8.0-3/quanteda/man/encoding.Rd | 53 quanteda-0.8.0-3/quanteda/man/exampleString.Rd | 1 quanteda-0.8.0-3/quanteda/man/features.Rd | 2 quanteda-0.8.0-3/quanteda/man/inaugCorpus.Rd | 2 quanteda-0.8.0-3/quanteda/man/metadoc.Rd | 2 quanteda-0.8.0-3/quanteda/man/ndoc.Rd | 18 quanteda-0.8.0-3/quanteda/man/ngrams.Rd | 7 quanteda-0.8.0-3/quanteda/man/nsentence.Rd |only quanteda-0.8.0-3/quanteda/man/ntoken.Rd | 61 quanteda-0.8.0-3/quanteda/man/phrasetotoken.Rd | 4 quanteda-0.8.0-3/quanteda/man/readability.Rd |only quanteda-0.8.0-3/quanteda/man/removeFeatures.Rd | 25 quanteda-0.8.0-3/quanteda/man/segment.Rd | 2 quanteda-0.8.0-3/quanteda/man/sort.dfm.Rd | 2 quanteda-0.8.0-3/quanteda/man/summary.corpus.Rd | 3 quanteda-0.8.0-3/quanteda/man/syllables.Rd | 56 quanteda-0.8.0-3/quanteda/man/textfile.Rd | 77 - quanteda-0.8.0-3/quanteda/man/textmodel_wordscores.Rd | 2 quanteda-0.8.0-3/quanteda/man/texts.Rd | 26 quanteda-0.8.0-3/quanteda/man/toLower.Rd |only quanteda-0.8.0-3/quanteda/man/tokenize.Rd | 89 + quanteda-0.8.0-3/quanteda/man/topfeatures.Rd | 2 quanteda-0.8.0-3/quanteda/man/trim.Rd | 2 quanteda-0.8.0-3/quanteda/man/ukimmigTexts.Rd | 8 quanteda-0.8.0-3/quanteda/man/weight.Rd | 6 quanteda-0.8.0-3/quanteda/man/wordlists.Rd |only quanteda-0.8.0-3/quanteda/man/wordstem.Rd | 13 quanteda-0.8.0-3/quanteda/src/RcppExports.cpp | 13 quanteda-0.8.0-3/quanteda/tests |only quanteda-0.8.0-3/quanteda/vignettes/corpus-sources.Rmd | 6 quanteda-0.8.0-3/quanteda/vignettes/corpus-sources.md |only quanteda-0.8.0-3/quanteda/vignettes/design-and-workflow.Rmd |only quanteda-0.8.0-3/quanteda/vignettes/design-and-workflow.md |only quanteda-0.8.0-3/quanteda/vignettes/development-plans.Rmd | 73 - quanteda-0.8.0-3/quanteda/vignettes/development-plans.md |only quanteda-0.8.0-3/quanteda/vignettes/quickstart.Rmd | 5 quanteda-0.8.0-3/quanteda/vignettes/quickstart.md |only 100 files changed, 2322 insertions(+), 2140 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kent Russel [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.1.7 dated 2015-06-14 and 0.1.8 dated 2015-07-11
DESCRIPTION | 14 ++-- MD5 | 40 ++++++------ NAMESPACE | 1 NEWS | 23 ++++++- R/forceNetwork.R | 63 +++++++++++++++---- R/sankeyNetwork.R | 3 R/simpleNetwork.R | 4 + R/treeNetwork.R | 48 +++++++------- R/utils.R | 8 +- README.md | 10 --- inst/examples/examples.R | 80 +++++++++++++++++++++++- inst/htmlwidgets/forceNetwork.js | 124 ++++++++++++++++++++++---------------- inst/htmlwidgets/sankeyNetwork.js | 2 inst/htmlwidgets/simpleNetwork.js | 6 - inst/htmlwidgets/treeNetwork.js | 6 - man/JS.Rd | 10 +-- man/as.treeNetwork.Rd | 11 +-- man/forceNetwork.Rd | 45 ++++++++++++- man/sankeyNetwork.Rd | 4 - man/simpleNetwork.Rd | 5 + man/treeNetwork.Rd | 8 +- 21 files changed, 360 insertions(+), 155 deletions(-)
Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data.
It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm).
Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom.
Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between MVR versions 1.30.1 dated 2015-06-19 and 1.30.2 dated 2015-07-11
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- NAMESPACE | 6 +++++- R/MVRr.r | 16 ++++++++-------- inst/NEWS | 11 +++++++++++ man/cluster.diagnostic.Rd | 4 ++-- man/normalization.diagnostic.Rd | 4 ++-- man/stabilization.diagnostic.Rd | 4 ++-- man/target.diagnostic.Rd | 4 ++-- 9 files changed, 45 insertions(+), 29 deletions(-)
Title: Modern Measures of Population Differentiation
Description: Provides functions for measuring
population divergence from genotypic data.
Author: David Winter [aut, cre],
Peter Green [ctb],
Zhian Kamvar [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between mmod versions 1.2.1 dated 2014-08-02 and 1.3.0 dated 2015-07-11
mmod-1.2.1/mmod/R/pairwise_D.R |only mmod-1.2.1/mmod/R/pairwise_Gst_Hedrick.R |only mmod-1.2.1/mmod/R/pairwise_Gst_Nei.R |only mmod-1.2.1/mmod/README.md |only mmod-1.3.0/mmod/DESCRIPTION | 26 ++++++---- mmod-1.3.0/mmod/MD5 | 69 +++++++++++++--------------- mmod-1.3.0/mmod/NAMESPACE | 9 +++ mmod-1.3.0/mmod/NEWS | 9 +++ mmod-1.3.0/mmod/R/D_Jost.R | 37 ++++++++------- mmod-1.3.0/mmod/R/HsHt.R | 18 ++++--- mmod-1.3.0/mmod/R/chao_bootstrap.R | 3 - mmod-1.3.0/mmod/R/diff_test.R | 4 + mmod-1.3.0/mmod/R/dist.codom.R | 9 +++ mmod-1.3.0/mmod/R/harmonic_mean.R | 16 ++++-- mmod-1.3.0/mmod/R/pairwise.R |only mmod-1.3.0/mmod/R/rgenotypes.R | 6 +- mmod-1.3.0/mmod/R/summarise_bootstrap.R | 2 mmod-1.3.0/mmod/build/vignette.rds |binary mmod-1.3.0/mmod/inst/doc/mmod-demo.R | 2 mmod-1.3.0/mmod/inst/doc/mmod-demo.pdf |binary mmod-1.3.0/mmod/man/D_Jost.Rd | 10 +++- mmod-1.3.0/mmod/man/Gst_Hedrick.Rd | 7 +- mmod-1.3.0/mmod/man/Gst_Nei.Rd | 7 +- mmod-1.3.0/mmod/man/Phi_st_Meirmans.Rd | 3 - mmod-1.3.0/mmod/man/as.genind.DNAbin.Rd | 3 - mmod-1.3.0/mmod/man/chao_bootstrap.Rd | 3 - mmod-1.3.0/mmod/man/diff_stats.Rd | 3 - mmod-1.3.0/mmod/man/diff_test.Rd | 5 +- mmod-1.3.0/mmod/man/dist.codom.Rd | 3 - mmod-1.3.0/mmod/man/harmonic_mean.Rd | 7 ++ mmod-1.3.0/mmod/man/jacknife_populations.Rd | 3 - mmod-1.3.0/mmod/man/mmod.Rd | 3 - mmod-1.3.0/mmod/man/pairwise_D.Rd | 8 ++- mmod-1.3.0/mmod/man/pairwise_Gst_Hedrick.Rd | 3 - mmod-1.3.0/mmod/man/pairwise_Gst_Nei.Rd | 3 - mmod-1.3.0/mmod/man/rgenotypes.Rd | 3 - mmod-1.3.0/mmod/man/summarise_bootstrap.Rd | 3 - mmod-1.3.0/mmod/tests/testthat/test_stats.r | 2 38 files changed, 185 insertions(+), 104 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Wayne Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [aut],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.0 dated 2015-03-04 and 0.2.1 dated 2015-07-11
ChainLadder-0.2.0/ChainLadder/vignettes/ChainLadder-035.pdf |only ChainLadder-0.2.0/ChainLadder/vignettes/ChainLadder-037.pdf |only ChainLadder-0.2.1/ChainLadder/DESCRIPTION | 26 ChainLadder-0.2.1/ChainLadder/MD5 | 50 ChainLadder-0.2.1/ChainLadder/NAMESPACE | 26 ChainLadder-0.2.1/ChainLadder/NEWS | 24 ChainLadder-0.2.1/ChainLadder/R/BootstrapReserve.R | 67 ChainLadder-0.2.1/ChainLadder/R/MackChainLadderFunctions.R | 1019 +-- ChainLadder-0.2.1/ChainLadder/R/MultiChainLadder.R | 6 ChainLadder-0.2.1/ChainLadder/R/PIC.R |only ChainLadder-0.2.1/ChainLadder/R/Triangles.R | 20 ChainLadder-0.2.1/ChainLadder/R/clark.r | 2826 +++++----- ChainLadder-0.2.1/ChainLadder/R/zzz.R | 13 ChainLadder-0.2.1/ChainLadder/README.md | 12 ChainLadder-0.2.1/ChainLadder/build/vignette.rds |binary ChainLadder-0.2.1/ChainLadder/data/USAAincurred.RData |only ChainLadder-0.2.1/ChainLadder/data/USAApaid.RData |only ChainLadder-0.2.1/ChainLadder/inst/doc/ChainLadder.R | 196 ChainLadder-0.2.1/ChainLadder/inst/doc/ChainLadder.Rnw | 166 ChainLadder-0.2.1/ChainLadder/inst/doc/ChainLadder.pdf |binary ChainLadder-0.2.1/ChainLadder/man/ChainLadder-package.Rd | 4 ChainLadder-0.2.1/ChainLadder/man/MultiChainLadder.Rd | 5 ChainLadder-0.2.1/ChainLadder/man/PaidIncurredChain.Rd |only ChainLadder-0.2.1/ChainLadder/man/USAA.Rd |only ChainLadder-0.2.1/ChainLadder/man/plot.BootChainLadder.Rd | 4 ChainLadder-0.2.1/ChainLadder/man/plot.MackChainLadder.Rd | 4 ChainLadder-0.2.1/ChainLadder/vignettes/ChainLadder.Rnw | 166 ChainLadder-0.2.1/ChainLadder/vignettes/ChainLadder.bib | 38 ChainLadder-0.2.1/ChainLadder/vignettes/Log-incremental |only ChainLadder-0.2.1/ChainLadder/vignettes/SpreadsheetTriangle.png |only 30 files changed, 2566 insertions(+), 2106 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between arm versions 1.8-5 dated 2015-05-13 and 1.8-6 dated 2015-07-11
CHANGELOG | 6 +++++- DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 59 ++++++++++++++++++++++++++++++++++++++++++++++++----------- R/display.R | 40 ++++++++++++++++++++-------------------- R/simmer.R | 24 ++++++++++++------------ 6 files changed, 95 insertions(+), 54 deletions(-)
Title: Unconstrained Optimization using the Subplex Algorithm
Description: The subplex algorithm for unconstrained optimization, developed by Tom Rowan.
Author: Aaron A. King
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between subplex versions 1.1-4 dated 2014-06-30 and 1.1-6 dated 2015-07-10
DESCRIPTION | 17 +++++++---------- MD5 | 6 +++--- NAMESPACE | 7 +------ R/subplex.R | 2 +- 4 files changed, 12 insertions(+), 20 deletions(-)
Title: Penalized Classification using Fisher's Linear Discriminant
Description: Implements the penalized LDA proposal of "Witten and Tibshirani (2011), Penalized classification using Fisher's linear discriminant, to appear in Journal of the Royal Statistical Society, Series B".
Author: Daniela Witten
Maintainer: Daniela Witten <dwitten@u.washington.edu>
Diff between penalizedLDA versions 1.0 dated 2011-03-29 and 1.1 dated 2015-07-10
penalizedLDA-1.0/penalizedLDA/man/penalizedLDA-internal.Rd |only penalizedLDA-1.1/penalizedLDA/DESCRIPTION | 19 ++++++------- penalizedLDA-1.1/penalizedLDA/MD5 |only penalizedLDA-1.1/penalizedLDA/NAMESPACE | 9 ++++++ penalizedLDA-1.1/penalizedLDA/man/PenalizedLDA.cv.Rd | 3 +- penalizedLDA-1.1/penalizedLDA/man/penalizedLDA-package.Rd | 4 +- penalizedLDA-1.1/penalizedLDA/man/plot.penlda.Rd |only penalizedLDA-1.1/penalizedLDA/man/plot.penldacv.Rd |only penalizedLDA-1.1/penalizedLDA/man/print.penlda.Rd |only penalizedLDA-1.1/penalizedLDA/man/print.penldacv.Rd |only 10 files changed, 22 insertions(+), 13 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut],
Robin Winstanley [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.2.4 dated 2015-05-21 and 0.3.1 dated 2015-07-10
DESCRIPTION | 14 MD5 | 84 ++-- NAMESPACE | 3 R/MazamaSpatialUtils.R | 34 + R/convertGADM.R | 37 +- R/convertLayer.R | 6 R/convertNaturalEarthAdm1.R | 62 +-- R/convertTMWorldBorders.R | 33 - R/convertTMWorldBordersSimple.R | 40 +- R/convertUSCensusCounties.R | 70 +-- R/convertUSGSHUC8.R | 34 - R/convertWBDHUC.R |only R/convertWorldEEZ.R |only R/convertWorldTimezones.R | 18 - R/getCountry.R | 6 R/getCountryCode.R | 6 R/getCountryName.R | 6 R/getSpatialData.R | 85 ++++ R/getState.R | 6 R/getStateCode.R | 6 R/getStateName.R | 6 R/getTimezone.R | 10 R/getUSCounty.R | 6 R/getVariable.R | 8 R/installSpatialData.R | 5 R/organizePolygons.R | 10 build/vignette.rds |binary data/SimpleCountries.RData |binary data/SimpleTimezones.RData |binary inst/doc/introduction.Rmd | 6 inst/doc/introduction.html | 658 +++++++++++++++++++++++++------------ man/MazamaSpatialUtils.Rd | 11 man/SpatialDataDir.Rd | 4 man/convertLayer.Rd | 2 man/convertTMWorldBorders.Rd | 3 man/convertTMWorldBordersSimple.Rd | 10 man/convertUSCensusCounties.Rd | 10 man/convertWBDHUC.Rd |only man/convertWorldEEZ.Rd |only man/getSpatialData.Rd | 24 + man/installSpatialData.Rd | 4 man/organizePolygons.Rd | 2 tests/testthat.R | 5 tests/testthat/test1.R | 8 vignettes/introduction.Rmd | 6 45 files changed, 847 insertions(+), 501 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit a CMP regression model to count data. The code provides functions for model estimation, dispersion testing, and diagnostics.
Author: Kimberly Sellers <kfs7@georgetown.edu>, Thomas Lotze <thomas.lotze@thomaslotze.com>
Maintainer: Thomas Lotze <thomas.lotze@thomaslotze.com>
Diff between COMPoissonReg versions 0.3.4 dated 2011-05-11 and 0.3.5 dated 2015-07-10
COMPoissonReg-0.3.4/COMPoissonReg/.project |only COMPoissonReg-0.3.5/COMPoissonReg/DESCRIPTION | 17 +--- COMPoissonReg-0.3.5/COMPoissonReg/MD5 |only COMPoissonReg-0.3.5/COMPoissonReg/NAMESPACE | 12 ++ COMPoissonReg-0.3.5/COMPoissonReg/R/CMPDeviance.R | 4 COMPoissonReg-0.3.5/COMPoissonReg/R/ComputeBetasAndNuHat.R | 8 - COMPoissonReg-0.3.5/COMPoissonReg/R/ComputeOptimalLogLi.GivenNuHat.R | 4 COMPoissonReg-0.3.5/COMPoissonReg/R/cmp.R | 16 +-- COMPoissonReg-0.3.5/COMPoissonReg/R/makeCMPdata.R | 4 COMPoissonReg-0.3.5/COMPoissonReg/README.md |only COMPoissonReg-0.3.5/COMPoissonReg/man/CMP.MSE.Rd | 6 - COMPoissonReg-0.3.5/COMPoissonReg/man/CMPDeviance.Rd | 3 COMPoissonReg-0.3.5/COMPoissonReg/man/CMPLeverage.Rd | 10 -- COMPoissonReg-0.3.5/COMPoissonReg/man/CMPParamBoot.Rd | 14 +-- COMPoissonReg-0.3.5/COMPoissonReg/man/CMPStdErrors.Rd | 13 +-- COMPoissonReg-0.3.5/COMPoissonReg/man/COMPoissonReg-package.Rd | 41 +++++----- COMPoissonReg-0.3.5/COMPoissonReg/man/ComputeBetasAndNuHat.Rd | 11 -- COMPoissonReg-0.3.5/COMPoissonReg/man/LRT.Rd | 11 -- COMPoissonReg-0.3.5/COMPoissonReg/man/chisq.Rd | 6 - COMPoissonReg-0.3.5/COMPoissonReg/man/cmp.Rd | 37 ++++----- COMPoissonReg-0.3.5/COMPoissonReg/man/makeCMPdata.Rd | 13 +-- 21 files changed, 107 insertions(+), 123 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.2 dated 2015-06-10 and 0.3.4 dated 2015-07-10
DESCRIPTION | 13 +++--- MD5 | 48 ++++++++++++---------- NAMESPACE | 5 +- R/linarr.R |only R/lingpg.R | 5 -- R/linrmi.R |only R/vardchangespoor.R | 94 ++++++++++++++++++++++++++++++++++++++++--- R/vardcrospoor.R | 97 +++++++++++++++++++++++++++++++++++++++++--- R/vardomh.R | 2 R/varpoord.R | 104 ++++++++++++++++++++++++++++++++++++++++++++++-- inst/CITATION | 4 - inst/NEWS | 4 + man/linarpr.Rd | 2 man/linarpt.Rd | 2 man/linarr.Rd |only man/lingini.Rd | 4 + man/lingini2.Rd | 2 man/lingpg.Rd | 2 man/linpoormed.Rd | 2 man/linqsr.Rd | 2 man/linrmi.Rd |only man/linrmpg.Rd | 2 man/vardchanges.Rd | 2 man/vardchangespoor.Rd | 33 ++++++++++++--- man/vardcrospoor.Rd | 43 ++++++++++++++++--- man/vardpoor-package.Rd | 10 +++- man/varpoord.Rd | 19 +++++++- 27 files changed, 418 insertions(+), 83 deletions(-)
Title: Technical Trading Rules
Description: Functions and data to construct technical trading rules with R.
Author: Joshua Ulrich
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.22-0 dated 2013-03-17 and 0.23-0 dated 2015-07-10
TTR-0.22-0/TTR/WISHLIST |only TTR-0.23-0/TTR/CHANGES | 35 ++ TTR-0.23-0/TTR/DESCRIPTION | 15 - TTR-0.23-0/TTR/MD5 | 135 ++++----- TTR-0.23-0/TTR/NAMESPACE | 65 ++-- TTR-0.23-0/TTR/R/ATR.R | 6 TTR-0.23-0/TTR/R/CCI.R | 4 TTR-0.23-0/TTR/R/CLV.R | 2 TTR-0.23-0/TTR/R/CMF.R | 2 TTR-0.23-0/TTR/R/DVI.R | 16 - TTR-0.23-0/TTR/R/KST.R | 7 TTR-0.23-0/TTR/R/MACD.R | 4 TTR-0.23-0/TTR/R/MFI.R | 6 TTR-0.23-0/TTR/R/MovingAverages.R | 77 ++++- TTR-0.23-0/TTR/R/OBV.R | 7 TTR-0.23-0/TTR/R/SAR.R | 2 TTR-0.23-0/TTR/R/TTR-package.R | 7 TTR-0.23-0/TTR/R/WebData.R | 4 TTR-0.23-0/TTR/R/ZigZag.R | 2 TTR-0.23-0/TTR/R/bollingerBands.R | 4 TTR-0.23-0/TTR/R/changes.R | 2 TTR-0.23-0/TTR/R/percentRank.R | 4 TTR-0.23-0/TTR/R/runFun.R | 20 - TTR-0.23-0/TTR/R/stochastics.R | 2 TTR-0.23-0/TTR/R/ultimateOscillator.R |only TTR-0.23-0/TTR/R/volatility.R | 32 +- TTR-0.23-0/TTR/man/ADX.Rd | 81 ++--- TTR-0.23-0/TTR/man/ATR.Rd | 72 ++--- TTR-0.23-0/TTR/man/CCI.Rd | 75 ++--- TTR-0.23-0/TTR/man/CLV.Rd | 33 +- TTR-0.23-0/TTR/man/CMF.Rd | 53 +-- TTR-0.23-0/TTR/man/CMO.Rd | 46 +-- TTR-0.23-0/TTR/man/DPO.Rd | 65 ++-- TTR-0.23-0/TTR/man/DVI.Rd | 51 +-- TTR-0.23-0/TTR/man/DonchianChannel.Rd | 68 ++-- TTR-0.23-0/TTR/man/EMV.Rd | 69 ++-- TTR-0.23-0/TTR/man/GMMA.Rd | 58 ++-- TTR-0.23-0/TTR/man/KST.Rd | 93 +++--- TTR-0.23-0/TTR/man/MACD.Rd | 111 +++---- TTR-0.23-0/TTR/man/MFI.Rd | 59 ++-- TTR-0.23-0/TTR/man/MovingAverages.Rd | 236 ++++++++--------- TTR-0.23-0/TTR/man/OBV.Rd | 45 +-- TTR-0.23-0/TTR/man/RSI.Rd | 84 +++--- TTR-0.23-0/TTR/man/SAR.Rd | 50 +-- TTR-0.23-0/TTR/man/TDI.Rd | 67 ++-- TTR-0.23-0/TTR/man/TRIX.Rd | 78 ++--- TTR-0.23-0/TTR/man/TTR.Rd | 39 +- TTR-0.23-0/TTR/man/TTRtools.Rd | 46 +-- TTR-0.23-0/TTR/man/VHF.Rd | 48 +-- TTR-0.23-0/TTR/man/WPR.Rd | 49 +-- TTR-0.23-0/TTR/man/WebData.Rd | 101 +++---- TTR-0.23-0/TTR/man/ZigZag.Rd | 65 ++-- TTR-0.23-0/TTR/man/adjRatios.Rd | 39 +- TTR-0.23-0/TTR/man/aroon.Rd | 76 ++--- TTR-0.23-0/TTR/man/bollingerBands.Rd | 87 +++--- TTR-0.23-0/TTR/man/chaikinAD.Rd | 52 +-- TTR-0.23-0/TTR/man/chaikinVolatility.Rd | 49 +-- TTR-0.23-0/TTR/man/changes.Rd | 39 +- TTR-0.23-0/TTR/man/priceBands.Rd | 82 ++--- TTR-0.23-0/TTR/man/rollFun.Rd | 35 +- TTR-0.23-0/TTR/man/runFun.Rd | 105 +++---- TTR-0.23-0/TTR/man/runPercentRank.Rd | 53 +-- TTR-0.23-0/TTR/man/stochastics.Rd | 175 ++++++------ TTR-0.23-0/TTR/man/ttrc.Rd | 14 - TTR-0.23-0/TTR/man/ultimateOscillator.Rd |only TTR-0.23-0/TTR/man/volatility.Rd | 226 +++++++--------- TTR-0.23-0/TTR/man/williamsAD.Rd | 40 +- TTR-0.23-0/TTR/tests/unitTests/output.Oscillators.rda |binary TTR-0.23-0/TTR/tests/unitTests/output.volume.rda |binary TTR-0.23-0/TTR/tests/unitTests/runit.TTR.Oscillators.R | 17 + 70 files changed, 1717 insertions(+), 1674 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-9 dated 2015-06-03 and 0.9-10 dated 2015-07-10
DESCRIPTION | 11 ++- MD5 | 78 +++++++++++++------------- NAMESPACE | 15 ++++- NEWS | 9 ++- R/GMRF.R | 20 +++--- R/covarianceFunctions.R | 12 ++-- R/log_posteriors_and_derivatives.R | 39 +++++-------- R/log_posteriors_and_derivatives_SPDE.R | 70 ++++++++++------------- R/log_posteriors_and_derivatives_gridded.R | 68 +++++++++------------- R/log_posteriors_and_derivatives_polygonal.R | 68 +++++++++------------- R/nonspatial_log_likelihood_and_derivatives.R | 54 +++++++++++------- R/plottingfunctions.R | 40 +++++++++++-- R/postprocessing.R | 34 +++++++++++ R/spatsurv.R | 51 ++++++++++------- R/spatsurvMisc.R | 2 R/survspat.R | 67 ++++++++++++++++++++++ R/survspatNS.R | 26 ++++++++ man/ExponentialCovFct.Rd | 2 man/GammaFromY_SPDE.Rd | 2 man/NonSpatialLogLikelihood_or_gradient.Rd | 2 man/SPDE.Rd | 2 man/SPDEprec.Rd | 2 man/SpikedExponentialCovFct.Rd | 2 man/YFromGamma_SPDE.Rd | 2 man/allocate.Rd | 2 man/covmodel.Rd | 2 man/getBackground.Rd |only man/getGrid.Rd | 19 ++---- man/getgrd.Rd |only man/logPosterior.Rd | 2 man/logPosterior_SPDE.Rd | 2 man/logPosterior_gridded.Rd | 2 man/logPosterior_polygonal.Rd | 2 man/maxlikparamPHsurv.Rd | 2 man/neighLocs.Rd | 2 man/neighOrder.Rd | 2 man/setupPrecMatStruct.Rd | 2 man/spatsurv-package.Rd | 8 +- man/spplot1.Rd | 6 +- man/survspat.Rd | 2 man/survspatNS.Rd | 2 41 files changed, 447 insertions(+), 288 deletions(-)
Title: Stochastic Multi-Criteria Acceptability Analysis
Description: Implementation of the Stochastic Multi-Criteria Acceptability Analysis (SMAA) family of Multiple Criteria Decision Analysis (MCDA) methods.
Author: Gert van Valkenhoef
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between smaa versions 0.2-3 dated 2014-12-03 and 0.2-4 dated 2015-07-10
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NAMESPACE | 2 ++ NEWS | 9 ++++++++- 4 files changed, 20 insertions(+), 10 deletions(-)
Title: Implements the Scout Method for Covariance-Regularized
Regression
Description: Implements the Scout method for regression, described in "Covariance-regularized regression and classification for high-dimensional problems", by Witten and Tibshirani (2008), Journal of the Royal Statistical Society, Series B 71(3): 615-636.
Author: Daniela M. Witten and Robert Tibshirani
Maintainer: Daniela M. Witten <dwitten@uw.edu>
Diff between scout versions 1.0.3 dated 2011-01-11 and 1.0.4 dated 2015-07-10
scout-1.0.3/scout/man/scout-internal.Rd |only scout-1.0.4/scout/DESCRIPTION | 20 +++++++++----------- scout-1.0.4/scout/MD5 |only scout-1.0.4/scout/NAMESPACE | 9 +++++++-- scout-1.0.4/scout/R/scout.R | 4 ++-- scout-1.0.4/scout/man/crossProdLasso.Rd | 8 +++++--- scout-1.0.4/scout/man/cv.scout.Rd | 17 ++++++++++------- scout-1.0.4/scout/man/predict.scoutobject.Rd | 21 +++++++++++---------- scout-1.0.4/scout/man/print.cvobject.Rd |only scout-1.0.4/scout/man/print.scoutobject.Rd |only scout-1.0.4/scout/man/scout-package.Rd | 9 +++++---- scout-1.0.4/scout/man/scout.Rd | 4 +++- 12 files changed, 52 insertions(+), 40 deletions(-)
Title: Select Point Pattern Models Based on Minimum Contrast, AIC and
Goodness of Fit
Description: Fit and selects point pattern models based on minimum contrast, AIC and and goodness of fit.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between selectspm versions 0.1 dated 2014-11-18 and 0.2 dated 2015-07-10
DESCRIPTION | 15 +-- MD5 | 20 +++- NAMESPACE | 11 ++ R/LF.gof.R |only R/envelope.selectedmod.R |only R/envelope.selectedmodgof.R |only R/plot.selectedmodgof.R |only R/print.selectedmodgof.R |only R/select.model.gof.R |only R/select.model2.R | 178 ++++++++++++++++---------------------------- R/simulate.selectedmod.R |only R/simulate.selectedmodgof.R |only data |only man/LF.gof.Rd |only man/select.model.gof.Rd |only man/select.model2.Rd | 75 +++++++++++++++--- man/teucrium.Rd |only 17 files changed, 163 insertions(+), 136 deletions(-)
Title: Reversible Jump MCMC for the Analysis of CGH Arrays
Description: Bayesian analysis of CGH microarrays fitting Hidden Markov
Chain models. The selection of the number of states is made via
their posterior probability computed by Reversible Jump Markov
Chain Monte Carlo Methods. Also returns probabilistic common
regions for gains/losses.
Author: Oscar Rueda <rueda.om@gmail.com> and Ramon Diaz-Uriarte
<rdiaz02@gmail.com>. zlib from Jean-loup Gailly and Mark Adler;
see README. Function "getHostname.System" from package R.utils
by Henrik Bengtsson.
Maintainer: Oscar Rueda <rueda.om@gmail.com>
Diff between RJaCGH versions 2.0.3 dated 2014-12-11 and 2.0.4 dated 2015-07-10
RJaCGH-2.0.3/RJaCGH/man/Q.NH.Rd |only RJaCGH-2.0.3/RJaCGH/man/plot.Q.NH.Rd |only RJaCGH-2.0.4/RJaCGH/Changes | 5 +++-- RJaCGH-2.0.4/RJaCGH/DESCRIPTION | 10 +++++----- RJaCGH-2.0.4/RJaCGH/MD5 | 16 ++++++++-------- RJaCGH-2.0.4/RJaCGH/NAMESPACE | 3 ++- RJaCGH-2.0.4/RJaCGH/R/RJaCGH.R | 22 +++++++++------------- RJaCGH-2.0.4/RJaCGH/man/QNH.Rd |only RJaCGH-2.0.4/RJaCGH/man/genomePlot.Rd | 2 ++ RJaCGH-2.0.4/RJaCGH/man/plot.RJaCGH.Rd | 4 +++- RJaCGH-2.0.4/RJaCGH/man/plotQNH.Rd |only 11 files changed, 32 insertions(+), 30 deletions(-)
Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Carl Boettiger [aut],
Ted Hart [aut],
Scott Chamberlain [aut, cre],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.3.0 dated 2015-03-04 and 0.3.4 dated 2015-07-10
rcrossref-0.3.0/rcrossref/NEWS |only rcrossref-0.3.4/rcrossref/DESCRIPTION | 24 rcrossref-0.3.4/rcrossref/MD5 | 126 +-- rcrossref-0.3.4/rcrossref/NAMESPACE | 21 rcrossref-0.3.4/rcrossref/R/cr_agency.r | 13 rcrossref-0.3.4/rcrossref/R/cr_cn.r | 157 +++- rcrossref-0.3.4/rcrossref/R/cr_ft_links.R | 19 rcrossref-0.3.4/rcrossref/R/cr_ft_text.R | 30 rcrossref-0.3.4/rcrossref/R/cr_journals.r | 2 rcrossref-0.3.4/rcrossref/R/cr_prefixes.r | 4 rcrossref-0.3.4/rcrossref/R/cr_search_free.r | 15 rcrossref-0.3.4/rcrossref/R/cr_works.R | 4 rcrossref-0.3.4/rcrossref/R/crosscite.R |only rcrossref-0.3.4/rcrossref/R/extract_pdf.R | 6 rcrossref-0.3.4/rcrossref/R/rcrossref-package.R | 3 rcrossref-0.3.4/rcrossref/R/zzz.R | 64 - rcrossref-0.3.4/rcrossref/README.md | 132 ++- rcrossref-0.3.4/rcrossref/build/vignette.rds |binary rcrossref-0.3.4/rcrossref/inst/doc/crossref_filters.Rmd | 1 rcrossref-0.3.4/rcrossref/inst/doc/crossref_filters.html | 1 rcrossref-0.3.4/rcrossref/inst/doc/crossref_vignette.Rmd | 358 +++++----- rcrossref-0.3.4/rcrossref/inst/doc/crossref_vignette.html | 358 +++++----- rcrossref-0.3.4/rcrossref/inst/examples |only rcrossref-0.3.4/rcrossref/inst/vign/crossref_filters.Rmd | 3 rcrossref-0.3.4/rcrossref/inst/vign/crossref_filters.md | 1 rcrossref-0.3.4/rcrossref/inst/vign/crossref_vignette.Rmd | 3 rcrossref-0.3.4/rcrossref/inst/vign/crossref_vignette.md | 358 +++++----- rcrossref-0.3.4/rcrossref/man/as.tdmurl.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_agency.Rd | 8 rcrossref-0.3.4/rcrossref/man/cr_citation-defunct.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_citation_count.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_cn.Rd | 61 + rcrossref-0.3.4/rcrossref/man/cr_ft_links.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_ft_text.Rd | 9 rcrossref-0.3.4/rcrossref/man/cr_fundref.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_journals.Rd | 4 rcrossref-0.3.4/rcrossref/man/cr_licenses.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_members.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_prefixes.Rd | 6 rcrossref-0.3.4/rcrossref/man/cr_r.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_search.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_search_free.Rd | 2 rcrossref-0.3.4/rcrossref/man/cr_works.Rd | 2 rcrossref-0.3.4/rcrossref/man/crosscite.Rd |only rcrossref-0.3.4/rcrossref/man/extract_xpdf.Rd | 4 rcrossref-0.3.4/rcrossref/man/get_styles.Rd | 2 rcrossref-0.3.4/rcrossref/man/pmid2doi.Rd | 2 rcrossref-0.3.4/rcrossref/man/rcrossref-defunct.Rd | 2 rcrossref-0.3.4/rcrossref/man/rcrossref-package.Rd | 2 rcrossref-0.3.4/rcrossref/tests/test-all.R |only rcrossref-0.3.4/rcrossref/tests/testthat/test_as.tdmurl.R | 23 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_agency.R | 10 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_citation_count.R | 18 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_cn.R | 28 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_ft_links.R | 26 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_fundref.R | 15 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_journals.R | 10 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_licenses.R | 16 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_members.R | 21 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_prefixes.R | 8 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_r.R | 24 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_search.R | 23 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_search_free.R | 27 rcrossref-0.3.4/rcrossref/tests/testthat/test_cr_works.R | 36 - rcrossref-0.3.4/rcrossref/vignettes/crossref_filters.Rmd | 1 rcrossref-0.3.4/rcrossref/vignettes/crossref_vignette.Rmd | 358 +++++----- 66 files changed, 1369 insertions(+), 1100 deletions(-)
Title: Interface to the 'Biodiversity' 'Heritage' Library
Description: Interface to 'Biodiversity' 'Heritage' Library ('BHL') 'API'
methods. 'BHL' is a repository of 'digitized' literature on 'biodiversity'
studies, including 'floras', research papers, and more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbhl versions 0.1.0 dated 2014-01-17 and 0.2.0 dated 2015-07-10
rbhl-0.1.0/rbhl/NEWS |only rbhl-0.1.0/rbhl/inst/doc/rbhl_vignette.pdf |only rbhl-0.1.0/rbhl/inst/vign |only rbhl-0.1.0/rbhl/man/getkey.Rd |only rbhl-0.1.0/rbhl/man/query2message.Rd |only rbhl-0.1.0/rbhl/man/return_results.Rd |only rbhl-0.1.0/rbhl/vignettes/rbhl_vignette.html |only rbhl-0.1.0/rbhl/vignettes/rbhl_vignette.md |only rbhl-0.2.0/rbhl/DESCRIPTION | 27 rbhl-0.2.0/rbhl/LICENSE | 4 rbhl-0.2.0/rbhl/MD5 | 189 +- rbhl-0.2.0/rbhl/NAMESPACE | 49 rbhl-0.2.0/rbhl/R/bhl_authorsearch.R | 37 rbhl-0.2.0/rbhl/R/bhl_bioherlib.R | 38 rbhl-0.2.0/rbhl/R/bhl_booksearch.R | 54 rbhl-0.2.0/rbhl/R/bhl_getauthorparts.R |only rbhl-0.2.0/rbhl/R/bhl_getauthortitles.R | 38 rbhl-0.2.0/rbhl/R/bhl_getcollections.R | 47 rbhl-0.2.0/rbhl/R/bhl_getitembyidentifier.R | 41 rbhl-0.2.0/rbhl/R/bhl_getitemmetadata.R | 51 rbhl-0.2.0/rbhl/R/bhl_getitempages.R | 37 rbhl-0.2.0/rbhl/R/bhl_getitemparts.R |only rbhl-0.2.0/rbhl/R/bhl_getlanguages.R | 37 rbhl-0.2.0/rbhl/R/bhl_getpagemetadata.R | 39 rbhl-0.2.0/rbhl/R/bhl_getpagenames.R | 27 rbhl-0.2.0/rbhl/R/bhl_getpageocrtext.R | 32 rbhl-0.2.0/rbhl/R/bhl_getpartbibtex.R |only rbhl-0.2.0/rbhl/R/bhl_getpartbyidentifier.R |only rbhl-0.2.0/rbhl/R/bhl_getpartendnote.R |only rbhl-0.2.0/rbhl/R/bhl_getpartmetadata.R |only rbhl-0.2.0/rbhl/R/bhl_getpartnames.R |only rbhl-0.2.0/rbhl/R/bhl_getsubjectparts.R |only rbhl-0.2.0/rbhl/R/bhl_getsubjecttitles.R | 27 rbhl-0.2.0/rbhl/R/bhl_gettitlebibtex.R | 28 rbhl-0.2.0/rbhl/R/bhl_gettitlebyidentifier.R | 30 rbhl-0.2.0/rbhl/R/bhl_gettitleendnote.R | 22 rbhl-0.2.0/rbhl/R/bhl_gettitleitems.R | 28 rbhl-0.2.0/rbhl/R/bhl_gettitlemetadata.R | 38 rbhl-0.2.0/rbhl/R/bhl_getunpublisheditems.R | 28 rbhl-0.2.0/rbhl/R/bhl_getunpublishedparts.R |only rbhl-0.2.0/rbhl/R/bhl_getunpublishedtitles.R | 28 rbhl-0.2.0/rbhl/R/bhl_namecount.R |only rbhl-0.2.0/rbhl/R/bhl_namegetdetail.R |only rbhl-0.2.0/rbhl/R/bhl_namelist.R |only rbhl-0.2.0/rbhl/R/bhl_namesearch.R |only rbhl-0.2.0/rbhl/R/bhl_openurl.R | 71 rbhl-0.2.0/rbhl/R/bhl_partsearch.R |only rbhl-0.2.0/rbhl/R/bhl_subjectsearch.R | 26 rbhl-0.2.0/rbhl/R/bhl_titlesearchsimple.R | 33 rbhl-0.2.0/rbhl/R/getpages.R |only rbhl-0.2.0/rbhl/R/rbhl-package.R | 25 rbhl-0.2.0/rbhl/R/tbldf.R |only rbhl-0.2.0/rbhl/R/zzz.R | 122 - rbhl-0.2.0/rbhl/README.md | 430 ++-- rbhl-0.2.0/rbhl/build/vignette.rds |binary rbhl-0.2.0/rbhl/inst/doc/rbhl_vignette.Rmd | 911 ++-------- rbhl-0.2.0/rbhl/inst/doc/rbhl_vignette.html |only rbhl-0.2.0/rbhl/man/bhl_authorsearch.Rd | 29 rbhl-0.2.0/rbhl/man/bhl_bioherlib.Rd | 35 rbhl-0.2.0/rbhl/man/bhl_booksearch.Rd | 60 rbhl-0.2.0/rbhl/man/bhl_getauthorparts.Rd |only rbhl-0.2.0/rbhl/man/bhl_getauthortitles.Rd | 34 rbhl-0.2.0/rbhl/man/bhl_getcollections.Rd | 31 rbhl-0.2.0/rbhl/man/bhl_getitembyidentifier.Rd | 35 rbhl-0.2.0/rbhl/man/bhl_getitemmetadata.Rd | 39 rbhl-0.2.0/rbhl/man/bhl_getitempages.Rd | 29 rbhl-0.2.0/rbhl/man/bhl_getitemparts.Rd |only rbhl-0.2.0/rbhl/man/bhl_getlanguages.Rd | 29 rbhl-0.2.0/rbhl/man/bhl_getpagemetadata.Rd | 36 rbhl-0.2.0/rbhl/man/bhl_getpagenames.Rd | 26 rbhl-0.2.0/rbhl/man/bhl_getpageocrtext.Rd | 33 rbhl-0.2.0/rbhl/man/bhl_getpartbibtex.Rd |only rbhl-0.2.0/rbhl/man/bhl_getpartbyidentifier.Rd |only rbhl-0.2.0/rbhl/man/bhl_getpartendnote.Rd |only rbhl-0.2.0/rbhl/man/bhl_getpartmetadata.Rd |only rbhl-0.2.0/rbhl/man/bhl_getpartnames.Rd |only rbhl-0.2.0/rbhl/man/bhl_getsubjectparts.Rd |only rbhl-0.2.0/rbhl/man/bhl_getsubjecttitles.Rd | 27 rbhl-0.2.0/rbhl/man/bhl_gettitlebibTex.Rd | 28 rbhl-0.2.0/rbhl/man/bhl_gettitlebyidentifier.Rd | 34 rbhl-0.2.0/rbhl/man/bhl_gettitleendNote.Rd | 12 rbhl-0.2.0/rbhl/man/bhl_gettitleitems.Rd | 28 rbhl-0.2.0/rbhl/man/bhl_gettitlemetadata.Rd | 39 rbhl-0.2.0/rbhl/man/bhl_getunpublisheditems.Rd | 25 rbhl-0.2.0/rbhl/man/bhl_getunpublishedparts.Rd |only rbhl-0.2.0/rbhl/man/bhl_getunpublishedtitles.Rd | 25 rbhl-0.2.0/rbhl/man/bhl_namecount.Rd |only rbhl-0.2.0/rbhl/man/bhl_namegetdetail.Rd |only rbhl-0.2.0/rbhl/man/bhl_namelist.Rd |only rbhl-0.2.0/rbhl/man/bhl_namesearch.Rd |only rbhl-0.2.0/rbhl/man/bhl_openurl.Rd | 43 rbhl-0.2.0/rbhl/man/bhl_partsearch.Rd |only rbhl-0.2.0/rbhl/man/bhl_subjectsearch.Rd | 28 rbhl-0.2.0/rbhl/man/bhl_titlesearchsimple.Rd | 30 rbhl-0.2.0/rbhl/man/getpages.Rd |only rbhl-0.2.0/rbhl/man/rbhl-package.Rd | 14 rbhl-0.2.0/rbhl/man/rbhlmethods.Rd | 6 rbhl-0.2.0/rbhl/man/type_sum.Rd |only rbhl-0.2.0/rbhl/tests/test-all.R |only rbhl-0.2.0/rbhl/tests/testthat/test-bhl_authorsearch.R | 33 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_bioherlib.R | 44 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_booksearch.R | 35 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getauthorities.R | 27 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getcollections.R | 28 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getitembyidentifier.R | 35 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getitemmetadata.R | 34 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getitempages.R | 35 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getlanguages.R | 34 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getpagemetadata.R | 33 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getpagenames.R | 35 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getpageocrtext.R | 33 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_getsubjecttitles.R | 32 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_gettitlebibtex.R | 27 rbhl-0.2.0/rbhl/tests/testthat/test-bhl_gettitlebyidentifier.R | 42 rbhl-0.2.0/rbhl/vignettes/rbhl_vignette.Rmd | 911 ++-------- 115 files changed, 1745 insertions(+), 3022 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.7 dated 2015-06-03 and 0.0.10 dated 2015-07-10
DESCRIPTION | 7 ++++--- MD5 | 18 +++++++++--------- NAMESPACE | 3 +++ R/RFutils.R | 5 +++++ inst/include/Error_utils.h | 18 +++++++++++++++--- inst/include/utils.h | 12 +++--------- src/Basic_utils.h | 4 ++-- src/Error_utils.h | 18 +++++++++++++++--- src/solve.cc | 7 +++---- src/utils.h | 12 +++--------- 10 files changed, 62 insertions(+), 42 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.2-07 dated 2015-06-04 and 1.2-08 dated 2015-07-10
DESCRIPTION | 14 ++--- MD5 | 20 +++---- NAMESPACE | 18 +++++-- NEWS | 9 +++ R/power_RSABE.R | 9 ++- R/power_RSABE_NTID.R | 74 +++++++++++++++++------------ R/power_scABEL.R | 5 + R/samplesize_RSABE_NTID.R | 47 +++++++++++------- inst/doc/Implementation_scaledABE_sims.pdf |binary man/power.NTIDFDA.Rd | 23 +++++++-- man/sampleN.NTIDFDA.Rd | 27 +++++++--- 11 files changed, 161 insertions(+), 85 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, unit conversions.
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 0.6 dated 2015-05-11 and 0.6-3 dated 2015-07-10
plantecophys-0.6-3/plantecophys/DESCRIPTION | 6 plantecophys-0.6-3/plantecophys/MD5 | 24 +-- plantecophys-0.6-3/plantecophys/NAMESPACE | 16 +- plantecophys-0.6-3/plantecophys/R/FARAO.R | 3 plantecophys-0.6-3/plantecophys/R/LeafEnergyBalance.R | 1 plantecophys-0.6-3/plantecophys/R/findCiTransition.R | 8 - plantecophys-0.6-3/plantecophys/R/fitBB.R |only plantecophys-0.6-3/plantecophys/R/fitaci.R | 139 ++++++++++++++---- plantecophys-0.6-3/plantecophys/R/fitacis.R | 2 plantecophys-0.6-3/plantecophys/R/photosyn.R | 12 + plantecophys-0.6-3/plantecophys/man/Photosyn.Rd | 11 - plantecophys-0.6-3/plantecophys/man/fitBB.Rd |only plantecophys-0.6-3/plantecophys/man/fitaci.Rd | 14 + plantecophys-0.6/plantecophys/R/fitBBOpti.R |only plantecophys-0.6/plantecophys/man/fitBBOpti.Rd |only 15 files changed, 175 insertions(+), 61 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.4-56 dated 2015-04-29 and 0.4-60 dated 2015-07-10
DESCRIPTION | 13 ++-- MD5 | 16 ++--- NAMESPACE | 11 +++ R/contMap.R | 13 ++-- R/ltt.R | 144 +++++++++++++++++++++++++++++++++++++++++----------- R/phenogram.R | 1 R/rerootingMethod.R | 37 ++++++++----- R/writeAncestors.R | 4 - man/ltt.Rd | 18 +++--- 9 files changed, 181 insertions(+), 76 deletions(-)
Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative
Hypotheses
Description: Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
Author: Aaron A. King <kingaa@umich.edu> and Marguerite A. Butler <mbutler@hawaii.edu>
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between ouch versions 2.8-4 dated 2014-03-24 and 2.9-2 dated 2015-07-10
ouch-2.8-4/ouch/tests |only ouch-2.9-2/ouch/DESCRIPTION | 23 ++++++++++------------- ouch-2.9-2/ouch/MD5 | 20 +++++++------------- ouch-2.9-2/ouch/NAMESPACE | 6 ++++-- ouch-2.9-2/ouch/R/methods.R | 4 ++-- ouch-2.9-2/ouch/data/bimac.csv.gz |binary ouch-2.9-2/ouch/inst/CITATION | 4 ++-- ouch-2.9-2/ouch/man/hansen.Rd | 5 +++-- ouch-2.9-2/ouch/src/weight-matrix.c | 5 ++--- 9 files changed, 30 insertions(+), 37 deletions(-)
Title: Number-Theoretic Functions
Description:
Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.5-6 dated 2015-03-14 and 0.5-9 dated 2015-07-10
DESCRIPTION | 15 ++++++--------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 6 +++--- NEWS | 23 +++++++++++++++++------ R/functions.R | 7 ++++--- R/mersenne.R | 5 +++++ R/primes.R | 35 +++++++++++++++++++++++++++++++++++ R/primroot.R | 22 ++++++---------------- R/rabin.R | 7 ++++++- man/droplet_e.Rd | 2 +- man/factorize.Rd | 2 +- man/mersenne.Rd | 22 +++++++++++----------- man/primes.Rd | 23 ++++++++++++++++++----- man/rabin.Rd | 28 +++++++++++++++++----------- man/sigma.Rd | 26 +++++++------------------- 15 files changed, 151 insertions(+), 100 deletions(-)
Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological processes to capture evolutionary signals in transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>
Diff between myTAI versions 0.1.0 dated 2015-05-24 and 0.2.0 dated 2015-07-10
myTAI-0.1.0/myTAI/R/FilterRNASeqCT.R |only myTAI-0.1.0/myTAI/man/FilterRNASeqCT.Rd |only myTAI-0.1.0/myTAI/tests/testthat/test-FilterRNASeqCT.R |only myTAI-0.2.0/myTAI/DESCRIPTION | 14 myTAI-0.2.0/myTAI/MD5 | 123 +++-- myTAI-0.2.0/myTAI/NAMESPACE | 13 myTAI-0.2.0/myTAI/R/DiffGenes.R |only myTAI-0.2.0/myTAI/R/EarlyConservationTest.R | 59 +- myTAI-0.2.0/myTAI/R/EnrichmentTest.R |only myTAI-0.2.0/myTAI/R/Expressed.R |only myTAI-0.2.0/myTAI/R/FlatLineTest.R | 62 +- myTAI-0.2.0/myTAI/R/MatchMap.R |only myTAI-0.2.0/myTAI/R/PlotBarRE.R | 78 ++- myTAI-0.2.0/myTAI/R/PlotContribution.R |only myTAI-0.2.0/myTAI/R/PlotCorrelation.R | 9 myTAI-0.2.0/myTAI/R/PlotEnrichment.R |only myTAI-0.2.0/myTAI/R/PlotGeneSet.R |only myTAI-0.2.0/myTAI/R/PlotMeans.R | 26 + myTAI-0.2.0/myTAI/R/PlotPattern.R | 37 - myTAI-0.2.0/myTAI/R/PlotRE.R | 27 + myTAI-0.2.0/myTAI/R/RcppExports.R | 4 myTAI-0.2.0/myTAI/R/ReductiveHourglassTest.R | 94 ++-- myTAI-0.2.0/myTAI/R/SelectGeneSet.R |only myTAI-0.2.0/myTAI/R/TDI.R | 2 myTAI-0.2.0/myTAI/R/base.R | 255 +---------- myTAI-0.2.0/myTAI/R/geom.mean.R |only myTAI-0.2.0/myTAI/R/harm.mean.R |only myTAI-0.2.0/myTAI/R/is.ExpressionSet.R |only myTAI-0.2.0/myTAI/R/omitMatrix.R |only myTAI-0.2.0/myTAI/R/pTAI.R |only myTAI-0.2.0/myTAI/R/pTDI.R |only myTAI-0.2.0/myTAI/R/taxonomy.R |only myTAI-0.2.0/myTAI/README.md | 58 ++ myTAI-0.2.0/myTAI/build/vignette.rds |binary myTAI-0.2.0/myTAI/inst/doc/Advanced.Rmd | 12 myTAI-0.2.0/myTAI/inst/doc/Advanced.html | 14 myTAI-0.2.0/myTAI/inst/doc/Enrichment.R |only myTAI-0.2.0/myTAI/inst/doc/Enrichment.Rmd |only myTAI-0.2.0/myTAI/inst/doc/Enrichment.html |only myTAI-0.2.0/myTAI/inst/doc/Expression.R |only myTAI-0.2.0/myTAI/inst/doc/Expression.Rmd |only myTAI-0.2.0/myTAI/inst/doc/Expression.html |only myTAI-0.2.0/myTAI/inst/doc/Intermediate.Rmd | 26 - myTAI-0.2.0/myTAI/inst/doc/Intermediate.html | 22 myTAI-0.2.0/myTAI/inst/doc/Introduction.R | 91 +++- myTAI-0.2.0/myTAI/inst/doc/Introduction.Rmd | 335 ++++++++++++--- myTAI-0.2.0/myTAI/inst/doc/Introduction.html | 254 +++++++++-- myTAI-0.2.0/myTAI/inst/doc/Taxonomy.R |only myTAI-0.2.0/myTAI/inst/doc/Taxonomy.Rmd |only myTAI-0.2.0/myTAI/inst/doc/Taxonomy.html |only myTAI-0.2.0/myTAI/man/DiffGenes.Rd |only myTAI-0.2.0/myTAI/man/EnrichmentTest.Rd |only myTAI-0.2.0/myTAI/man/Expressed.Rd |only myTAI-0.2.0/myTAI/man/MatchMap.Rd | 2 myTAI-0.2.0/myTAI/man/PlotBarRE.Rd | 29 + myTAI-0.2.0/myTAI/man/PlotContribution.Rd |only myTAI-0.2.0/myTAI/man/PlotEnrichment.Rd |only myTAI-0.2.0/myTAI/man/PlotGeneSet.Rd |only myTAI-0.2.0/myTAI/man/PlotMeans.Rd | 17 myTAI-0.2.0/myTAI/man/PlotPattern.Rd | 2 myTAI-0.2.0/myTAI/man/PlotRE.Rd | 18 myTAI-0.2.0/myTAI/man/SelectGeneSet.Rd |only myTAI-0.2.0/myTAI/man/TDI.Rd | 2 myTAI-0.2.0/myTAI/man/geom.mean.Rd |only myTAI-0.2.0/myTAI/man/harm.mean.Rd |only myTAI-0.2.0/myTAI/man/is.ExpressionSet.Rd | 2 myTAI-0.2.0/myTAI/man/omitMatrix.Rd | 2 myTAI-0.2.0/myTAI/man/pTAI.Rd |only myTAI-0.2.0/myTAI/man/pTDI.Rd |only myTAI-0.2.0/myTAI/man/taxonomy.Rd |only myTAI-0.2.0/myTAI/src/RcppExports.cpp | 11 myTAI-0.2.0/myTAI/src/rcpp_funcs.cpp | 17 myTAI-0.2.0/myTAI/tests/testthat/Rplots.pdf |only myTAI-0.2.0/myTAI/tests/testthat/test-DiffGenes.R |only myTAI-0.2.0/myTAI/tests/testthat/test-Expressed.R |only myTAI-0.2.0/myTAI/tests/testthat/test-PlotContribution.R |only myTAI-0.2.0/myTAI/tests/testthat/test-PlotEnrichment.R |only myTAI-0.2.0/myTAI/tests/testthat/test-PlotGeneSet.R |only myTAI-0.2.0/myTAI/tests/testthat/test-geom.mean.R |only myTAI-0.2.0/myTAI/tests/testthat/test-harm.mean.R |only myTAI-0.2.0/myTAI/tests/testthat/test-pTAI.R |only myTAI-0.2.0/myTAI/tests/testthat/test-pTDI.R |only myTAI-0.2.0/myTAI/tests/testthat/test-taxonomy.R |only myTAI-0.2.0/myTAI/vignettes/Advanced.Rmd | 12 myTAI-0.2.0/myTAI/vignettes/Enrichment.Rmd |only myTAI-0.2.0/myTAI/vignettes/Expression.Rmd |only myTAI-0.2.0/myTAI/vignettes/Intermediate.Rmd | 26 - myTAI-0.2.0/myTAI/vignettes/Introduction.Rmd | 335 ++++++++++++--- myTAI-0.2.0/myTAI/vignettes/Taxonomy.Rmd |only 89 files changed, 1430 insertions(+), 660 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors, nested multiple imputation, and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between miceadds versions 1.2-0 dated 2015-05-20 and 1.3-0 dated 2015-07-10
DESCRIPTION | 17 ++--- MD5 | 93 +++++++++++++++++----------- NAMESPACE | 110 +++++++++++++++++++++++++--------- R/MIwaldtest.R |only R/NMIcombine.R |only R/NMIextract.R |only R/NMIwaldtest.R |only R/create.designMatrices.waldtest.R |only R/draw.pv.ctt.R | 2 R/fast.groupmean.R | 12 +++ R/glm.cluster.R | 7 +- R/jomo2datlist.R |only R/latent.regression.em.R | 4 - R/library_install.R |only R/lm.cluster.R | 8 ++ R/mice.impute.2l.latentgroupmean.R | 9 +- R/mice.impute.2l.plausible.values.R | 8 +- R/mice.impute.grouped.R |only R/norm.draw3.R | 1 R/pool.mids.nmi.R | 13 +++- R/pool.nmi.scalar.helper.R | 37 ++++++++--- R/summary.mipo.nmi.R | 11 +++ data/data.graham.ex3.rda |only data/data.graham.ex6.rda |only data/data.graham.ex8a.rda |only data/data.graham.ex8b.rda |only data/data.graham.ex8c.rda |only data/data.ma06.rda |only inst/NEWS | 74 ++++++++++++++++------ man/NMIwaldtest.Rd |only man/NestedImputationList.Rd | 5 - man/complete.miceadds.Rd | 3 man/data.graham.Rd |only man/data.ma.Rd | 23 +++++++ man/datalist2mids.Rd | 4 - man/draw.pv.ctt.Rd | 5 - man/fast.groupmean.Rd | 10 ++- man/jomo2datlist.Rd |only man/kernelpls.fit2.Rd | 8 +- man/library_install.Rd |only man/lm.cluster.Rd | 37 ++++++++++- man/load.data.Rd | 4 - man/ma.scale2.Rd | 6 - man/mice.1chain.Rd | 32 ++++----- man/mice.impute.2l.contextual.pmm.Rd | 4 - man/mice.impute.2l.latentgroupmean.Rd | 9 +- man/mice.impute.grouped.Rd |only man/mice.nmi.Rd | 10 +-- man/miceadds-package.Rd | 2 man/micombine.chisquare.Rd | 2 man/pca.covridge.Rd | 4 - man/pool.mids.nmi.Rd | 74 ++++++++++++++++++++++ man/save.data.Rd | 4 - man/visitSequence.determine.Rd | 4 - man/with.miceadds.Rd | 20 +++--- man/write.mice.imputation.Rd | 6 - man/write.pspp.Rd | 7 -- 57 files changed, 489 insertions(+), 200 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J. Owens [ctb], Christophe Dutang [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.1.6 dated 2015-04-25 and 1.1.9 dated 2015-07-10
lifecontingencies-1.1.6/lifecontingencies/vignettes/introToLifecontingencies_files |only lifecontingencies-1.1.6/lifecontingencies/vignettes/jsslogo.jpg |only lifecontingencies-1.1.9/lifecontingencies/DESCRIPTION | 12 - lifecontingencies-1.1.9/lifecontingencies/MD5 | 79 +++++----- lifecontingencies-1.1.9/lifecontingencies/NAMESPACE | 14 + lifecontingencies-1.1.9/lifecontingencies/NEWS | 11 - lifecontingencies-1.1.9/lifecontingencies/R/3_demographicFunctions.R | 45 +++++ lifecontingencies-1.1.9/lifecontingencies/R/5_actuarialFunctions.R | 2 lifecontingencies-1.1.9/lifecontingencies/R/6_randomGenerationFunctions.R | 27 +-- lifecontingencies-1.1.9/lifecontingencies/R/8_mdtFunctions.R | 63 +++++++ lifecontingencies-1.1.9/lifecontingencies/R/RcppExports.R | 8 - lifecontingencies-1.1.9/lifecontingencies/R/zzz.R | 21 +- lifecontingencies-1.1.9/lifecontingencies/README.md | 4 lifecontingencies-1.1.9/lifecontingencies/build/vignette.rds |binary lifecontingencies-1.1.9/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.R | 60 ++++--- lifecontingencies-1.1.9/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 29 ++- lifecontingencies-1.1.9/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary lifecontingencies-1.1.9/lifecontingencies/inst/doc/introToLifecontingencies.R | 3 lifecontingencies-1.1.9/lifecontingencies/inst/doc/introToLifecontingencies.Rmd | 16 -- lifecontingencies-1.1.9/lifecontingencies/inst/doc/introToLifecontingencies.pdf |binary lifecontingencies-1.1.9/lifecontingencies/inst/doc/mortality_projection.R | 2 lifecontingencies-1.1.9/lifecontingencies/inst/doc/mortality_projection.Rnw | 5 lifecontingencies-1.1.9/lifecontingencies/inst/doc/mortality_projection.pdf |binary lifecontingencies-1.1.9/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.R | 19 ++ lifecontingencies-1.1.9/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.Rnw | 23 ++ lifecontingencies-1.1.9/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.pdf |binary lifecontingencies-1.1.9/lifecontingencies/man/axyn.Rd | 4 lifecontingencies-1.1.9/lifecontingencies/man/lifecontingencies-package.Rd | 4 lifecontingencies-1.1.9/lifecontingencies/man/multidecrins.Rd |only lifecontingencies-1.1.9/lifecontingencies/man/mx2qx.Rd |only lifecontingencies-1.1.9/lifecontingencies/man/qx2mx.Rd |only lifecontingencies-1.1.9/lifecontingencies/man/rmdt.Rd | 2 lifecontingencies-1.1.9/lifecontingencies/src/RcppExports.cpp | 16 +- lifecontingencies-1.1.9/lifecontingencies/src/lifecontingenciesRcpp.cpp | 12 - lifecontingencies-1.1.9/lifecontingencies/tests/testthat.R | 1 lifecontingencies-1.1.9/lifecontingencies/tests/testthat/testDemography.R |only lifecontingencies-1.1.9/lifecontingencies/tests/testthat/testMultipleLives.R |only lifecontingencies-1.1.9/lifecontingencies/tests/testthat/testSimulationFunctions.R |only lifecontingencies-1.1.9/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.Rnw | 29 ++- lifecontingencies-1.1.9/lifecontingencies/vignettes/introToLifecontingencies.Rmd | 16 -- lifecontingencies-1.1.9/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 19 ++ lifecontingencies-1.1.9/lifecontingencies/vignettes/mortality_projection.Rnw | 5 lifecontingencies-1.1.9/lifecontingencies/vignettes/multiple_decrements_with_lifecontingencies_package.Rnw | 23 ++ 43 files changed, 379 insertions(+), 195 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly from
Convex Shapes
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between hitandrun versions 0.5-1 dated 2015-04-19 and 0.5-2 dated 2015-07-10
hitandrun-0.5-1/hitandrun/tests/degenerate.R |only hitandrun-0.5-1/hitandrun/tests/seedPoint.R |only hitandrun-0.5-1/hitandrun/tests/simplex3d.R |only hitandrun-0.5-1/hitandrun/tests/solution.basis.R |only hitandrun-0.5-1/hitandrun/tests/transform.R |only hitandrun-0.5-1/hitandrun/tests/transformRegular.R |only hitandrun-0.5-1/hitandrun/tests/transformSeedPoint.R |only hitandrun-0.5-2/hitandrun/DESCRIPTION | 11 - hitandrun-0.5-2/hitandrun/MD5 | 38 ++--- hitandrun-0.5-2/hitandrun/NAMESPACE | 2 hitandrun-0.5-2/hitandrun/NEWS | 14 + hitandrun-0.5-2/hitandrun/R/bound.R | 23 ++- hitandrun-0.5-2/hitandrun/R/sample.R | 140 +++++++------------ hitandrun-0.5-2/hitandrun/man/createTransform.Rd | 4 hitandrun-0.5-2/hitandrun/src/bbReject.c | 10 - hitandrun-0.5-2/hitandrun/src/har.c | 18 +- hitandrun-0.5-2/hitandrun/src/har.h | 10 - hitandrun-0.5-2/hitandrun/src/rsabDir.c | 10 - hitandrun-0.5-2/hitandrun/src/sab.c | 18 +- hitandrun-0.5-2/hitandrun/tests/test.R |only hitandrun-0.5-2/hitandrun/tests/testthat |only 21 files changed, 148 insertions(+), 150 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.6 dated 2014-12-13 and 0.7 dated 2015-07-10
DESCRIPTION | 10 +- MD5 | 34 ++++----- NAMESPACE | 12 +++ R/auxilaryfunctions.R | 129 +++++++++++++++++++++--------------- R/boral.jags.R | 144 +++++++++++++++++++++++++++++++---------- inst/NEWS.Rd | 94 ++++++++++---------------- man/boral.Rd | 20 ++--- man/calc.condlogLik.Rd | 2 man/calc.logLik.lv0.Rd | 6 - man/calc.marglogLik.Rd | 6 - man/create.life.Rd | 4 - man/get.hpdintervals.Rd | 2 man/get.measures.Rd | 2 man/get.more.measures.Rd | 2 man/get.residual.cor.Rd | 10 +- man/lvsplot.Rd | 20 +++-- man/make.jagsboralmodel.Rd | 8 +- man/make.jagsboralnullmodel.Rd | 8 +- 18 files changed, 306 insertions(+), 207 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre],
Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.2-6 dated 2015-02-22 and 1.3-0 dated 2015-07-10
DESCRIPTION | 18 ++-- MD5 | 127 +++++++++++++++------------- NAMESPACE | 98 ++++++++++++++++------ R/BIFIE.bifiedata2bifiecdata.R | 3 R/BIFIE.by.R | 51 ++++++----- R/BIFIE.correl.R | 66 ++++++++++++-- R/BIFIE.crosstab.R | 70 ++++++++++++++- R/BIFIE.data.R | 11 ++ R/BIFIE.data.boot.R | 2 R/BIFIE.data.jack.R | 24 ++++- R/BIFIE.data.select.R | 24 ++++- R/BIFIE.data.transform.R | 30 +++++- R/BIFIE.derivedParameters.R | 43 +++++++-- R/BIFIE.ecdf.R | 1 R/BIFIE.freq.R | 27 +++++- R/BIFIE.hist.R | 1 R/BIFIE.linreg.R | 20 +--- R/BIFIE.logistreg.R | 21 +--- R/BIFIE.mva.R | 59 ++++++++++--- R/BIFIE.pathmodel.R | 25 +---- R/BIFIE.summary.R | 19 ++++ R/BIFIE.twolevelreg.R | 22 +++- R/BIFIE.univar.R | 49 +++++++++++ R/BIFIE.univar.test.R | 66 +++++++++++--- R/BIFIE.waldtest.R | 65 ++++++++++---- R/BIFIE_NMI_inference_parameters.R |only R/BIFIE_by_helper_pureR.R |only R/BIFIE_data_nested_MI.R |only R/clean_summary_table.R |only R/create_summary_table.R |only R/extract.replicated.pars.R | 6 + R/rubin_calc_df.R |only R/summary.BIFIE.data.R | 22 ++++ R/vcov.BIFIE.survey.R | 9 +- R/write.BIFIE.data.R | 5 - data/data.bifie01.rda |binary data/data.pisaNLD.rda |binary data/data.test1.rda |binary data/data.timss1.ind.rda |binary data/data.timss1.rda |binary data/data.timss2.rda |binary data/data.timss3.rda |binary data/data.timss4.rda |only data/data.timssrep.rda |binary data/datalist | 1 inst/NEWS | 33 +++++++ man/BIFIE.by.Rd | 12 ++ man/BIFIE.correl.Rd | 10 +- man/BIFIE.crosstab.Rd | 4 man/BIFIE.data.Rd | 24 ++++- man/BIFIE.data.jack.Rd | 4 man/BIFIE.data.transform.Rd | 7 + man/BIFIE.derivedParameters.Rd | 2 man/BIFIE.ecdf.Rd | 4 man/BIFIE.freq.Rd | 6 - man/BIFIE.hist.Rd | 2 man/BIFIE.linreg.Rd | 8 - man/BIFIE.logistreg.Rd | 6 - man/BIFIE.twolevelreg.Rd | 2 man/BIFIE.univar.Rd | 20 ++-- man/BIFIE.univar.test.Rd | 4 man/BIFIE.waldtest.Rd | 6 - man/BIFIEsurvey-package.Rd | 9 +- man/bifietable.Rd | 2 man/data.timss1.Rd | 28 ++++++ man/save.BIFIEdata.Rd | 21 ++-- src/univar.cpp | 163 ++++++++++++++++++++++++++++++++----- src/univar_helpers.h | 12 +- 68 files changed, 1022 insertions(+), 352 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 4.1-2 dated 2015-01-16 and 4.2-0 dated 2015-07-10
ChangeLog | 23 ++++++ DESCRIPTION | 11 +-- MD5 | 40 ++++++------ NAMESPACE | 5 + R/diagnostics.R | 2 R/get_outputs.R | 148 +++++++++++++++++++++++++++++++++------------ R/mcmc_sampling.R | 10 ++- R/mcmc_storage.R | 2 R/mcmc_update.R | 48 ++++++++++---- R/plot_functions.R | 10 +-- R/predict_tfr.R | 13 ++- R/run_mcmc.R | 2 R/wpp_data.R | 5 - man/bayesTFR-package.Rd | 10 +-- man/plot-trajectories.Rd | 2 man/predict-tfr.Rd | 14 +--- man/run-mcmc.Rd | 6 - man/run.tfr3.mcmc.Rd | 6 - man/tfr.parameter.names.Rd | 5 - man/tfr.raftery.diag.Rd | 2 tests/test_functions.R | 5 - 21 files changed, 247 insertions(+), 122 deletions(-)
Title: Improved Communication to Users with Respect to Problems in
Function Arguments
Description: The typical process of checking arguments in functions is
iterative. In this process, an error may be returned and the user may fix
it only to receive another error on a different argument. 'ArgumentCheck'
facilitates a more helpful way to perform argument checks allowing the
programmer to run all of the checks and then return all of the errors and
warnings in a single message.
Author: Benjamin Nutter
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between ArgumentCheck versions 0.9.0 dated 2015-06-09 and 0.10.0 dated 2015-07-10
DESCRIPTION | 10 ++-- MD5 | 40 +++++++++------- NAMESPACE | 2 NEWS | 23 +++++++++ R/ArgumentCheck.R | 38 +++++++-------- R/addError.R | 19 ++++--- R/addMessage.R |only R/addWarning.R | 18 ++++--- R/finishArgCheck.R | 25 ++++++++-- R/match_arg.R |only R/newArgCheck.R | 65 ++++++++++++++------------ R/zzz.R |only README.md | 82 +++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/ArgumentChecking.R | 49 +++++++++++++------- inst/doc/ArgumentChecking.Rmd | 81 ++++++++++++++++++++------------- inst/doc/ArgumentChecking.html | 99 +++++++++++++++++++++-------------------- man/ArgumentCheck.Rd | 38 +++++++-------- man/match_arg.Rd |only man/newArgCheck.Rd | 59 +++++++++++++----------- tests |only vignettes/ArgumentChecking.Rmd | 81 ++++++++++++++++++++------------- 22 files changed, 463 insertions(+), 266 deletions(-)
Title: Command-Line Argument Parser
Description: Cross-platform command-line argument parser written purely in R
with no external dependencies. It is useful with the Rscript
front-end and facilitates turning an R script into an executable script.
Author: David J. H. Shih
Maintainer: David J. H. Shih <djh.shih@gmail.com>
Diff between argparser versions 0.1 dated 2014-05-29 and 0.3 dated 2015-07-10
argparser-0.1/argparser/inst |only argparser-0.3/argparser/COPYING | 8 argparser-0.3/argparser/DESCRIPTION | 19 - argparser-0.3/argparser/MD5 | 29 +- argparser-0.3/argparser/NAMESPACE | 5 argparser-0.3/argparser/R/argparser.R | 284 ++++++++++++++++-------- argparser-0.3/argparser/R/deprecated.R |only argparser-0.3/argparser/R/zzz.R |only argparser-0.3/argparser/README.md |only argparser-0.3/argparser/demo |only argparser-0.3/argparser/man/add.argument.Rd | 36 --- argparser-0.3/argparser/man/add_argument.Rd |only argparser-0.3/argparser/man/arg.parser.Rd | 10 argparser-0.3/argparser/man/arg_parser.Rd |only argparser-0.3/argparser/man/argparser.Rd | 8 argparser-0.3/argparser/man/parse.args.Rd | 33 -- argparser-0.3/argparser/man/parse_args.Rd |only argparser-0.3/argparser/man/print.arg.parser.Rd | 4 18 files changed, 247 insertions(+), 189 deletions(-)
Title: Various Methods for Measuring Agreement
Description: Bland-Altman plot and scatter plot with identity line
for visualization and point and
interval estimates for different metrics related to
reproducibility/repeatability/agreement including
the concordance correlation coefficient,
intraclass correlation coefficient,
within-subject coefficient of variation,
smallest detectable difference,
and mean normalized smallest detectable difference.
Author: Dai Feng
Maintainer: Dai Feng <dai_feng@merck.com>
Diff between agRee versions 0.3-1 dated 2014-06-04 and 0.4-0 dated 2015-07-10
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 21 ++++++++++++++------- MD5 | 18 +++++++++++++----- NAMESPACE | 7 +++++-- R/agree.icc1.R |only R/agree.sdd.R |only R/agree.sddm.R |only data/petVT.rda |only man/agree.ccc.Rd | 28 +++++++++++++++------------- man/agree.icc1.Rd |only man/agree.plot.Rd | 2 +- man/agree.sdd.Rd |only man/agree.sddm.Rd |only man/petVT.Rd |only 14 files changed, 64 insertions(+), 28 deletions(-)
Title: Gene Set Analysis Exploiting Pathway Topology
Description: Using Gaussian graphical models we propose a novel approach to
perform pathway analysis using gene expression. Given the
structure of a graph (a pathway) we introduce two statistical
tests to compare the mean and the concentration matrices between
two groups. Specifically, these tests can be performed on the
graph and on its connected components (cliques).
Author: Sofia Massa, Gabriele Sales
Maintainer: Gabriele Sales <gabriele.sales@unipd.it>
Diff between topologyGSA versions 1.4.4 dated 2014-08-02 and 1.4.5 dated 2015-07-09
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 10 +++++++--- R/render.R | 8 ++++---- man/pathway.var.test.Rd | 18 ++++++++++++++++-- 5 files changed, 36 insertions(+), 18 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'.
Author: Francois Michonneau [aut, cre],
Ben Bolker [aut],
Mark Holder [aut],
Paul Lewis [aut],
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.2.2 dated 2015-02-06 and 0.4.0 dated 2015-07-09
DESCRIPTION | 13 - LICENSE | 2 MD5 | 26 +- NAMESPACE | 2 R/rncl.R | 199 +++++++++++++++++--- README.md | 43 ++-- inst/newick_good/missing_edge_lengths.tre |only inst/nexusfiles/test_subset_taxa.nex |only inst/nexusfiles/test_underscores.nex |only inst/nexusfiles/treeWithDiscreteData.nex |only man/read_nexus_phylo.Rd | 21 +- man/rncl.Rd | 110 ++++++++++- src/GetNCL.cpp | 8 src/RcppExports.cpp | 294 ++++++++++-------------------- src/nxsreader.cpp | 5 tests/testthat/test.rncl.R | 97 +++++++++ 16 files changed, 531 insertions(+), 289 deletions(-)
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between plotKML versions 0.5-2 dated 2015-05-06 and 0.5-3 dated 2015-07-09
DESCRIPTION | 8 ++-- MD5 | 34 +++++++++---------- NAMESPACE | 10 ++++- R/AAAA.R | 58 +++++++++++++++++----------------- R/getWikiMedia.ImageInfo.R | 43 ++++++++++++------------- R/kml_open.R | 2 - R/layer.SoilProfileCollection.R | 5 ++ R/normalizeFilename.R | 2 - R/plotKML.SpatialMaxEntOutput.R | 5 +- R/plotKML.SpatialPredictions.R | 22 +++++------- R/plotKML.SpatialVectorsSimulations.R | 6 +-- R/plotKML.sp.R | 6 +-- R/reproject.R | 2 - R/spPhoto.R | 53 ++++++++++++++----------------- inst/doc/jss1079.pdf |binary man/SAGA_pal.Rd | 4 +- man/getWikimedia.Rd | 2 - man/plotKML.Rd | 3 - 18 files changed, 132 insertions(+), 133 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 1.99-13 dated 2015-04-07 and 1.99.14 dated 2015-07-09
DESCRIPTION | 16 MD5 | 79 ++- NAMESPACE | 28 + NEWS | 46 ++ R/clanistic.R | 2 R/distSeq.R | 19 R/distTree.R |only R/fitch.R | 2 R/modelTest.R |only R/neighborNet.R | 9 R/networx.R | 20 R/parsimony.R | 10 R/phyDat.R | 58 ++ R/phylo.R | 1010 +++++++++++++------------------------------------ R/treeManipulation.R | 1 R/treedist.R | 39 + README.md | 6 TODO |only build/vignette.rds |binary inst/doc/Networx.R | 14 inst/doc/Networx.Rmd | 2 inst/doc/Networx.html | 2 inst/doc/Trees.R | 2 inst/doc/Trees.Rnw | 2 man/bootstrap.pml.Rd | 5 man/densiTree.Rd | 3 man/dist.hamming.Rd | 6 man/modelTest.Rd | 7 man/parsimony.Rd | 4 man/phyDat.Rd | 17 man/plot.networx.Rd | 2 man/pml.fit.Rd | 3 man/splitsNetwork.Rd | 2 man/treedist.Rd | 3 src/fitch.c | 42 -- src/ml.c | 495 ++++++++++++++---------- src/sankoff.c | 2 tests |only vignettes/Networx.Rmd | 2 vignettes/Trees.Rnw | 2 vignettes/phangorn.bib | 203 +++++++++ 41 files changed, 1054 insertions(+), 1111 deletions(-)
Title: Flexible Pair-Copula Estimation in D-Vines using Bivariate
Penalized Splines
Description: Flexible Pair-Copula Estimation in D-vines using Bivariate Penalized Splines.
Author: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Diff between penDvine versions 0.2.2 dated 2013-03-12 and 0.2.4 dated 2015-07-09
penDvine-0.2.2/penDvine/R.css |only penDvine-0.2.4/penDvine/DESCRIPTION | 17 - penDvine-0.2.4/penDvine/MD5 | 72 ++++---- penDvine-0.2.4/penDvine/NAMESPACE | 7 penDvine-0.2.4/penDvine/R/Dvine.r | 216 ++++++++++++------------ penDvine-0.2.4/penDvine/R/cal.Dvine.r | 3 penDvine-0.2.4/penDvine/R/distr.func.help.r | 3 penDvine-0.2.4/penDvine/R/help.func.r | 4 penDvine-0.2.4/penDvine/R/marg.likelihood.r | 2 penDvine-0.2.4/penDvine/R/my.IC.r | 8 penDvine-0.2.4/penDvine/R/my.bspline.r | 8 penDvine-0.2.4/penDvine/R/my.loop.r | 5 penDvine-0.2.4/penDvine/R/new.lambda.r | 8 penDvine-0.2.4/penDvine/R/new.weights.r | 36 +++- penDvine-0.2.4/penDvine/R/order.Dvine.r | 49 ++--- penDvine-0.2.4/penDvine/R/paircopula.R | 19 +- penDvine-0.2.4/penDvine/R/plot.paircopula.r | 98 ++++++---- penDvine-0.2.4/penDvine/R/sim.Dvine.r | 5 penDvine-0.2.4/penDvine/R/spline.apply.r |only penDvine-0.2.4/penDvine/R/start.valgrid.r | 10 - penDvine-0.2.4/penDvine/man/Derv1.Rd | 3 penDvine-0.2.4/penDvine/man/Derv2.Rd | 3 penDvine-0.2.4/penDvine/man/Dvine.Rd | 5 penDvine-0.2.4/penDvine/man/bernstein.Rd | 3 penDvine-0.2.4/penDvine/man/cal.Dvine.Rd | 3 penDvine-0.2.4/penDvine/man/cond.cop.Rd | 6 penDvine-0.2.4/penDvine/man/f.hat.val.Rd | 3 penDvine-0.2.4/penDvine/man/marg.likelihood.Rd | 4 penDvine-0.2.4/penDvine/man/my.IC.Rd | 4 penDvine-0.2.4/penDvine/man/my.loop.Rd | 3 penDvine-0.2.4/penDvine/man/new.weights.Rd | 4 penDvine-0.2.4/penDvine/man/order.Dvine.Rd | 4 penDvine-0.2.4/penDvine/man/paircopula.Rd | 4 penDvine-0.2.4/penDvine/man/pen.log.like.Rd | 3 penDvine-0.2.4/penDvine/man/pen.matrix.Rd | 4 penDvine-0.2.4/penDvine/man/penDvine-package.Rd | 12 - penDvine-0.2.4/penDvine/man/plot.paircopula.Rd | 17 + penDvine-0.2.4/penDvine/man/sim.Dvine.Rd | 3 38 files changed, 378 insertions(+), 280 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.4 dated 2015-07-01 and 0.4.1 dated 2015-07-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 6 ++++++ R/SES.R | 23 ++++++++++++++++++++++- R/cv.ses.R | 1 + man/MXM-package.Rd | 4 ++-- 6 files changed, 41 insertions(+), 13 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the 'pan' package, and
several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.2-2 dated 2015-05-22 and 0.2-3 dated 2015-07-09
DESCRIPTION | 10 - MD5 | 56 +++++------ NAMESPACE | 7 + NEWS |only R/as.mitml.list.R | 5 R/internal-getLR.R | 5 R/panImpute.R | 44 +++++--- R/plot.mitml.R | 244 ++++++++++++++++++++++++++++++++++++------------ R/print.mitml.R | 6 - R/print.mitml.summary.R | 33 ++++-- R/write.mitmlMplus.R | 6 - R/zzz.R |only data/studentratings.rda |binary man/as.mitml.list.Rd | 1 man/clusterMeans.Rd | 10 - man/is.mitml.list.Rd | 2 man/mitmlComplete.Rd | 2 man/panImpute.Rd | 39 +++---- man/plot.mitml.Rd | 11 +- man/read.mitml.Rd | 2 man/studentratings.Rd | 2 man/summary.mitml.Rd | 5 man/testConstraints.Rd | 20 +-- man/testEstimates.Rd | 2 man/testModels.Rd | 16 +-- man/with.mitml.Rd | 8 - man/write.mitml.Rd | 2 man/write.mitmlMplus.Rd | 2 man/write.mitmlSAV.Rd | 2 man/write.mitmlSPSS.Rd | 2 30 files changed, 352 insertions(+), 192 deletions(-)
Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
Author: Klaus Schliep & Klaus Hechenbichler
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between kknn versions 1.2-5 dated 2014-02-11 and 1.3.0 dated 2015-07-09
kknn-1.2-5/kknn/man/simulation.Rd |only kknn-1.3.0/kknn/DESCRIPTION | 14 ++++--- kknn-1.3.0/kknn/MD5 | 19 +++++----- kknn-1.3.0/kknn/NAMESPACE | 4 +- kknn-1.3.0/kknn/NEWS | 10 +++++ kknn-1.3.0/kknn/R/kknn.R | 62 +++++++++++++++++++++++++++++---- kknn-1.3.0/kknn/R/specClust.R | 2 - kknn-1.3.0/kknn/README.md |only kknn-1.3.0/kknn/inst |only kknn-1.3.0/kknn/man/kknn-deprecated.Rd |only kknn-1.3.0/kknn/man/train.kknn.Rd | 2 - kknn-1.3.0/kknn/src/dm.c | 2 - 12 files changed, 90 insertions(+), 25 deletions(-)
Title: Spatial Terms in GAMLSS Models
Description: It allows us to fit Markov Random Field (MRF) within the GAMLSS algorithms.
Author: Fernanda De Bastiani [aut, cre, cph],
Mikis Stasinopoulos [aut],
Bob Rigby [aut]
Maintainer: Fernanda De Bastiani <fernandadebastiani@gmail.com>
Diff between gamlss.spatial versions 0.2 dated 2015-02-05 and 1.3 dated 2015-07-09
DESCRIPTION | 27 ++++++++++++++++++--------- MD5 | 4 ++-- NAMESPACE | 7 +++++-- 3 files changed, 25 insertions(+), 13 deletions(-)
More information about gamlss.spatial at CRAN
Permanent link
Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rlist versions 0.4 dated 2015-01-24 and 0.4.2.3 dated 2015-07-09
rlist-0.4.2.3/rlist/DESCRIPTION | 14 rlist-0.4.2.3/rlist/MD5 | 268 ++++++-------- rlist-0.4.2.3/rlist/NAMESPACE | 7 rlist-0.4.2.3/rlist/NEWS | 16 rlist-0.4.2.3/rlist/R/List.R | 56 +- rlist-0.4.2.3/rlist/R/data.R | 2 rlist-0.4.2.3/rlist/R/functions.R | 103 ++--- rlist-0.4.2.3/rlist/R/internal.R | 120 +++--- rlist-0.4.2.3/rlist/R/lambda.R | 11 rlist-0.4.2.3/rlist/R/list.all.R | 44 +- rlist-0.4.2.3/rlist/R/list.clean.R | 37 + rlist-0.4.2.3/rlist/R/list.common.R | 21 - rlist-0.4.2.3/rlist/R/list.count.R | 20 - rlist-0.4.2.3/rlist/R/list.do.R | 51 ++ rlist-0.4.2.3/rlist/R/list.extract.R | 5 rlist-0.4.2.3/rlist/R/list.filter.R | 22 - rlist-0.4.2.3/rlist/R/list.find.R | 34 + rlist-0.4.2.3/rlist/R/list.first.R | 32 - rlist-0.4.2.3/rlist/R/list.flatten.R | 11 rlist-0.4.2.3/rlist/R/list.group.R | 125 ++++++ rlist-0.4.2.3/rlist/R/list.insert.R | 59 ++- rlist-0.4.2.3/rlist/R/list.is.R | 15 rlist-0.4.2.3/rlist/R/list.join.R | 40 +- rlist-0.4.2.3/rlist/R/list.load.R | 77 ++-- rlist-0.4.2.3/rlist/R/list.map.R | 66 +++ rlist-0.4.2.3/rlist/R/list.match.R | 12 rlist-0.4.2.3/rlist/R/list.merge.R | 25 + rlist-0.4.2.3/rlist/R/list.names.R | 10 rlist-0.4.2.3/rlist/R/list.order.R | 34 + rlist-0.4.2.3/rlist/R/list.parse.R | 75 ++-- rlist-0.4.2.3/rlist/R/list.remove.R | 31 + rlist-0.4.2.3/rlist/R/list.reverse.R | 2 rlist-0.4.2.3/rlist/R/list.sample.R | 14 rlist-0.4.2.3/rlist/R/list.save.R | 30 - rlist-0.4.2.3/rlist/R/list.search.R | 66 +-- rlist-0.4.2.3/rlist/R/list.select.R | 8 rlist-0.4.2.3/rlist/R/list.serialize.R | 48 ++ rlist-0.4.2.3/rlist/R/list.skip.R | 37 + rlist-0.4.2.3/rlist/R/list.stack.R | 6 rlist-0.4.2.3/rlist/R/list.subset.R | 14 rlist-0.4.2.3/rlist/R/list.table.R | 12 rlist-0.4.2.3/rlist/R/list.take.R | 41 +- rlist-0.4.2.3/rlist/R/list.update.R | 28 - rlist-0.4.2.3/rlist/R/list.which.R | 17 rlist-0.4.2.3/rlist/R/list.zip.R | 55 +- rlist-0.4.2.3/rlist/R/rlist.R | 2 rlist-0.4.2.3/rlist/R/subset.list.R | 29 - rlist-0.4.2.3/rlist/R/utils.R | 19 - rlist-0.4.2.3/rlist/README.md | 4 rlist-0.4.2.3/rlist/man/List.Rd | 18 rlist-0.4.2.3/rlist/man/list.all.Rd | 10 rlist-0.4.2.3/rlist/man/list.any.Rd | 12 rlist-0.4.2.3/rlist/man/list.append.Rd | 11 rlist-0.4.2.3/rlist/man/list.apply.Rd | 4 rlist-0.4.2.3/rlist/man/list.cases.Rd | 20 - rlist-0.4.2.3/rlist/man/list.cbind.Rd | 9 rlist-0.4.2.3/rlist/man/list.class.Rd | 27 - rlist-0.4.2.3/rlist/man/list.clean.Rd | 32 + rlist-0.4.2.3/rlist/man/list.common.Rd | 16 rlist-0.4.2.3/rlist/man/list.count.Rd | 23 - rlist-0.4.2.3/rlist/man/list.do.Rd | 9 rlist-0.4.2.3/rlist/man/list.exclude.Rd | 12 rlist-0.4.2.3/rlist/man/list.extract.Rd | 8 rlist-0.4.2.3/rlist/man/list.filter.Rd | 25 - rlist-0.4.2.3/rlist/man/list.find.Rd | 22 - rlist-0.4.2.3/rlist/man/list.findi.Rd | 25 - rlist-0.4.2.3/rlist/man/list.first.Rd | 8 rlist-0.4.2.3/rlist/man/list.flatten.Rd | 8 rlist-0.4.2.3/rlist/man/list.group.Rd | 21 - rlist-0.4.2.3/rlist/man/list.insert.Rd | 13 rlist-0.4.2.3/rlist/man/list.is.Rd | 10 rlist-0.4.2.3/rlist/man/list.iter.Rd | 12 rlist-0.4.2.3/rlist/man/list.join.Rd | 16 rlist-0.4.2.3/rlist/man/list.last.Rd | 8 rlist-0.4.2.3/rlist/man/list.load.Rd | 18 rlist-0.4.2.3/rlist/man/list.map.Rd | 8 rlist-0.4.2.3/rlist/man/list.maps.Rd | 4 rlist-0.4.2.3/rlist/man/list.mapv.Rd | 8 rlist-0.4.2.3/rlist/man/list.match.Rd | 12 rlist-0.4.2.3/rlist/man/list.merge.Rd | 24 + rlist-0.4.2.3/rlist/man/list.names.Rd | 4 rlist-0.4.2.3/rlist/man/list.order.Rd | 14 rlist-0.4.2.3/rlist/man/list.parse.Rd | 34 + rlist-0.4.2.3/rlist/man/list.prepend.Rd | 11 rlist-0.4.2.3/rlist/man/list.rbind.Rd | 9 rlist-0.4.2.3/rlist/man/list.remove.Rd | 10 rlist-0.4.2.3/rlist/man/list.reverse.Rd | 2 rlist-0.4.2.3/rlist/man/list.sample.Rd | 8 rlist-0.4.2.3/rlist/man/list.save.Rd | 10 rlist-0.4.2.3/rlist/man/list.search.Rd | 48 +- rlist-0.4.2.3/rlist/man/list.select.Rd | 8 rlist-0.4.2.3/rlist/man/list.serialize.Rd | 6 rlist-0.4.2.3/rlist/man/list.skip.Rd | 11 rlist-0.4.2.3/rlist/man/list.skipWhile.Rd | 23 - rlist-0.4.2.3/rlist/man/list.sort.Rd | 16 rlist-0.4.2.3/rlist/man/list.stack.Rd | 2 rlist-0.4.2.3/rlist/man/list.subset.Rd | 14 rlist-0.4.2.3/rlist/man/list.table.Rd | 10 rlist-0.4.2.3/rlist/man/list.take.Rd | 17 rlist-0.4.2.3/rlist/man/list.takeWhile.Rd | 25 - rlist-0.4.2.3/rlist/man/list.ungroup.Rd | 37 + rlist-0.4.2.3/rlist/man/list.unserialize.Rd | 8 rlist-0.4.2.3/rlist/man/list.unzip.Rd | 27 - rlist-0.4.2.3/rlist/man/list.update.Rd | 20 - rlist-0.4.2.3/rlist/man/list.which.Rd | 23 - rlist-0.4.2.3/rlist/man/list.zip.Rd | 4 rlist-0.4.2.3/rlist/man/nyweather.Rd | 4 rlist-0.4.2.3/rlist/man/rlist-package.Rd | 2 rlist-0.4.2.3/rlist/man/subset.list.Rd | 25 - rlist-0.4.2.3/rlist/man/tryEval.Rd | 2 rlist-0.4.2.3/rlist/man/tryGet.Rd | 2 rlist-0.4.2.3/rlist/tests/testthat.R | 2 rlist-0.4.2.3/rlist/tests/testthat/test-List.R | 85 ++-- rlist-0.4.2.3/rlist/tests/testthat/test-basic.R | 393 ++++++++++++--------- rlist-0.4.2.3/rlist/tests/testthat/test-class.R |only rlist-0.4.2.3/rlist/tests/testthat/test-filter.R |only rlist-0.4.2.3/rlist/tests/testthat/test-find.R |only rlist-0.4.2.3/rlist/tests/testthat/test-group.R |only rlist-0.4.2.3/rlist/tests/testthat/test-internal.R |only rlist-0.4.2.3/rlist/tests/testthat/test-io.R |only rlist-0.4.2.3/rlist/tests/testthat/test-join.R |only rlist-0.4.2.3/rlist/tests/testthat/test-map.R |only rlist-0.4.2.3/rlist/tests/testthat/test-search.R |only rlist-0.4.2.3/rlist/tests/testthat/test-select.R |only rlist-0.4.2.3/rlist/tests/testthat/test-sort.R |only rlist-0.4.2.3/rlist/tests/testthat/test-subset.R |only rlist-0.4.2.3/rlist/tests/testthat/test-update.R |only rlist-0.4.2.3/rlist/tests/testthat/test-utils.R |only rlist-0.4/rlist/R/list.any.R |only rlist-0.4/rlist/R/list.append.R |only rlist-0.4/rlist/R/list.apply.R |only rlist-0.4/rlist/R/list.cases.R |only rlist-0.4/rlist/R/list.cbind.R |only rlist-0.4/rlist/R/list.class.R |only rlist-0.4/rlist/R/list.exclude.R |only rlist-0.4/rlist/R/list.findi.R |only rlist-0.4/rlist/R/list.iter.R |only rlist-0.4/rlist/R/list.maps.R |only rlist-0.4/rlist/R/list.prepend.R |only rlist-0.4/rlist/R/list.rbind.R |only rlist-0.4/rlist/R/list.skipWhile.R |only rlist-0.4/rlist/R/list.sort.R |only rlist-0.4/rlist/R/list.takeWhile.R |only rlist-0.4/rlist/R/list.ungroup.R |only rlist-0.4/rlist/R/list.unserialize.R |only rlist-0.4/rlist/tests/testthat/test-list.class.R |only rlist-0.4/rlist/tests/testthat/test-list.filter.R |only rlist-0.4/rlist/tests/testthat/test-list.find.R |only rlist-0.4/rlist/tests/testthat/test-list.group.R |only rlist-0.4/rlist/tests/testthat/test-list.join.R |only rlist-0.4/rlist/tests/testthat/test-list.map.R |only rlist-0.4/rlist/tests/testthat/test-list.search.R |only rlist-0.4/rlist/tests/testthat/test-list.select.R |only rlist-0.4/rlist/tests/testthat/test-list.sort.R |only rlist-0.4/rlist/tests/testthat/test-list.update.R |only rlist-0.4/rlist/tests/testthat/test-subset.list.R |only 156 files changed, 2001 insertions(+), 1243 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions
for searching for bird observations by geographic location (latitude,
longitude), eBird hotspots, location identifiers, by notable sightings, by
region, and by taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut],
Andy Teucher [aut],
Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 0.1.1 dated 2014-03-05 and 0.2 dated 2015-07-09
rebird-0.1.1/rebird/NEWS |only rebird-0.1.1/rebird/tests/testthat/test-all.R |only rebird-0.2/rebird/DESCRIPTION | 38 +-- rebird-0.2/rebird/LICENSE | 2 rebird-0.2/rebird/MD5 | 68 +++--- rebird-0.2/rebird/NAMESPACE | 12 - rebird-0.2/rebird/R/ebirdfreq.R |only rebird-0.2/rebird/R/ebirdgeo.R | 108 +++------ rebird-0.2/rebird/R/ebirdhotspot.R | 79 ++----- rebird-0.2/rebird/R/ebirdloc.R | 66 ++--- rebird-0.2/rebird/R/ebirdnotable.R | 106 +++------ rebird-0.2/rebird/R/ebirdregion.R | 87 ++----- rebird-0.2/rebird/R/ebirdregioncheck.R |only rebird-0.2/rebird/R/ebirdtaxonomy.R | 47 +--- rebird-0.2/rebird/R/getlatlng.R | 6 rebird-0.2/rebird/R/nearestobs.R | 83 +++---- rebird-0.2/rebird/R/rebird-package.R | 21 + rebird-0.2/rebird/R/zzz.R |only rebird-0.2/rebird/README.md | 157 +++++++++++++- rebird-0.2/rebird/build |only rebird-0.2/rebird/inst |only rebird-0.2/rebird/man/ebirdfreq.Rd |only rebird-0.2/rebird/man/ebirdgeo.Rd | 138 ++++++------ rebird-0.2/rebird/man/ebirdhotspot.Rd | 111 ++++------ rebird-0.2/rebird/man/ebirdloc.Rd | 142 +++++++----- rebird-0.2/rebird/man/ebirdnotable.Rd | 166 ++++++--------- rebird-0.2/rebird/man/ebirdregion.Rd | 131 +++++------ rebird-0.2/rebird/man/ebirdregioncheck.Rd |only rebird-0.2/rebird/man/ebirdtaxonomy.Rd | 51 ++-- rebird-0.2/rebird/man/getlatlng.Rd | 14 - rebird-0.2/rebird/man/nearestobs.Rd | 101 ++++----- rebird-0.2/rebird/man/rebird-package.Rd | 25 +- rebird-0.2/rebird/tests/test-all.R |only rebird-0.2/rebird/tests/testthat/test-ebirdfreq.R |only rebird-0.2/rebird/tests/testthat/test-ebirdgeo.R |only rebird-0.2/rebird/tests/testthat/test-ebirdhotspot.R |only rebird-0.2/rebird/tests/testthat/test-ebirdloc.R |only rebird-0.2/rebird/tests/testthat/test-ebirdnotable.R |only rebird-0.2/rebird/tests/testthat/test-ebirdregion.R |only rebird-0.2/rebird/tests/testthat/test-ebirdregioncheck.R |only rebird-0.2/rebird/tests/testthat/test-ebirdtaxonomy.R |only rebird-0.2/rebird/tests/testthat/test-nearestobs.R |only rebird-0.2/rebird/vignettes |only 43 files changed, 904 insertions(+), 855 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>
Diff between maps versions 2.3-9 dated 2014-09-22 and 2.3-10 dated 2015-07-09
DESCRIPTION | 15 ++++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 3 +++ R/db.r | 10 +++++----- R/map.r | 5 ++--- R/misc.r | 10 +++++----- R/polygon.r | 2 +- man/map.axes.Rd | 7 +++++-- man/map.cities.Rd | 6 +++--- man/smooth.map.Rd | 4 ++-- man/state.carto.Rd | 2 +- src/world.name | 4 ++-- 12 files changed, 48 insertions(+), 42 deletions(-)
Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P
Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>
Diff between mapproj versions 1.2-2 dated 2014-01-16 and 1.2-3 dated 2015-07-09
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 6 +++--- R/mapproj.r | 41 +++++++++++++++++++++++------------------ man/map.grid.Rd | 37 +++++++++++++++++++------------------ man/mapproject.Rd | 13 +------------ src/lambert.c | 26 ++++++++++++++++++++------ 7 files changed, 77 insertions(+), 67 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or
higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>
Diff between mapdata versions 2.2-3 dated 2014-06-03 and 2.2-4 dated 2015-07-09
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- src/nzHires.name | 8 ++++---- src/worldHires.name | 4 ++-- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.2 dated 2015-07-06 and 1.31.3 dated 2015-07-09
DESCRIPTION | 8 ++-- MD5 | 30 ++++++++--------- R/CA.R | 8 +--- R/CaGalt.R | 2 + R/DMFA.R | 12 +++--- R/FAMD.R | 2 + R/MCA.R | 6 +-- R/MFA.R | 17 ++++++--- R/PCA.R | 13 ++----- R/summary.CA.r | 12 +++--- R/summary.FAMD.r | 12 +++--- R/summary.MCA.r | 12 +++--- R/summary.MFA.r | 8 ++-- R/summary.PCA.r | 12 +++--- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary 16 files changed, 76 insertions(+), 78 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.0.2 dated 2015-05-20 and 2.1.1 dated 2015-07-09
emil-2.0.2/emil/man/emil_list_method.Rd |only emil-2.1.1/emil/DESCRIPTION | 18 - emil-2.1.1/emil/MD5 | 119 ++++--- emil-2.1.1/emil/NAMESPACE | 47 +++ emil-2.1.1/emil/R/caret.r | 18 - emil-2.1.1/emil/R/cforest.r | 2 emil-2.1.1/emil/R/error-functions.r | 84 +++-- emil-2.1.1/emil/R/glmnet.r | 180 ++++++++--- emil-2.1.1/emil/R/helpers.r | 58 +++ emil-2.1.1/emil/R/lda.r | 4 emil-2.1.1/emil/R/learning-curve.r | 38 +- emil-2.1.1/emil/R/modeling.r | 363 +++++++----------------- emil-2.1.1/emil/R/modeling_procedure.r |only emil-2.1.1/emil/R/pamr.r | 57 ++- emil-2.1.1/emil/R/preprocessing.r | 54 ++- emil-2.1.1/emil/R/qda.r | 4 emil-2.1.1/emil/R/randomForest.r | 19 - emil-2.1.1/emil/R/resampling.r | 169 ++++++----- emil-2.1.1/emil/R/reshape-result.r | 78 +++-- emil-2.1.1/emil/R/rpart.r |only emil-2.1.1/emil/R/survival.r | 50 ++- emil-2.1.1/emil/man/as.modeling_procedure.Rd |only emil-2.1.1/emil/man/emil.Rd | 8 emil-2.1.1/emil/man/error_fun.Rd | 21 + emil-2.1.1/emil/man/evaluate.Rd | 33 -- emil-2.1.1/emil/man/extension.Rd | 29 + emil-2.1.1/emil/man/fit.Rd | 5 emil-2.1.1/emil/man/fit_caret.Rd | 4 emil-2.1.1/emil/man/fit_cforest.Rd | 2 emil-2.1.1/emil/man/fit_coxph.Rd |only emil-2.1.1/emil/man/fit_glmnet.Rd | 17 - emil-2.1.1/emil/man/fit_lda.Rd | 2 emil-2.1.1/emil/man/fit_pamr.Rd | 13 emil-2.1.1/emil/man/fit_qda.Rd | 2 emil-2.1.1/emil/man/fit_randomForest.Rd | 8 emil-2.1.1/emil/man/fit_rpart.Rd |only emil-2.1.1/emil/man/get_importance.Rd | 8 emil-2.1.1/emil/man/get_prediction.Rd | 6 emil-2.1.1/emil/man/get_response.Rd |only emil-2.1.1/emil/man/get_tuning.Rd | 4 emil-2.1.1/emil/man/image.resample.Rd | 4 emil-2.1.1/emil/man/importance_glmnet.Rd |only emil-2.1.1/emil/man/learning_curve.Rd | 15 emil-2.1.1/emil/man/list_method.Rd |only emil-2.1.1/emil/man/modeling_procedure.Rd | 4 emil-2.1.1/emil/man/neg_gmpa.Rd | 4 emil-2.1.1/emil/man/pre_process.Rd | 15 emil-2.1.1/emil/man/predict.model.Rd | 6 emil-2.1.1/emil/man/predict_caret.Rd | 14 emil-2.1.1/emil/man/predict_coxph.Rd |only emil-2.1.1/emil/man/predict_glmnet.Rd | 19 - emil-2.1.1/emil/man/predict_lda.Rd | 2 emil-2.1.1/emil/man/predict_qda.Rd | 2 emil-2.1.1/emil/man/predict_rpart.Rd |only emil-2.1.1/emil/man/print.preprocessed_data.Rd |only emil-2.1.1/emil/man/pvalue.Rd | 2 emil-2.1.1/emil/man/resample.Rd | 23 - emil-2.1.1/emil/man/select.Rd | 6 emil-2.1.1/emil/man/subresample.Rd | 12 emil-2.1.1/emil/man/subtree.Rd | 2 emil-2.1.1/emil/man/tune.Rd | 2 emil-2.1.1/emil/tests/testthat/test-helpers.r | 2 emil-2.1.1/emil/tests/testthat/test-methods.r | 2 emil-2.1.1/emil/tests/testthat/test-modeling.r | 5 emil-2.1.1/emil/tests/testthat/test-procedure.r |only emil-2.1.1/emil/tests/testthat/test-resample.r | 46 +-- emil-2.1.1/emil/tests/testthat/test-survival.r | 8 67 files changed, 1002 insertions(+), 717 deletions(-)
Title: Download Files over HTTP and HTTPS
Description: Provides a wrapper for the download.file function,
making it possible to download files over HTTPS on Windows, Mac OS X, and
other Unix-like platforms. The 'RCurl' package provides this functionality
(and much more) but can be difficult to install because it must be compiled
with external dependencies. This package has no external dependencies, so
it is much easier to install.
Author: Winston Chang <winston@stdout.org>
Maintainer: Winston Chang <winston@stdout.org>
Diff between downloader versions 0.3 dated 2013-05-01 and 0.4 dated 2015-07-09
DESCRIPTION | 25 ++++++------- MD5 | 20 +++++----- NAMESPACE | 3 + NEWS | 5 ++ R/download.r | 99 +++++++++++++++++++++++++++++++++--------------------- R/sha_url.r | 11 ++++-- R/source_url.r | 15 ++++++-- man/download.Rd | 48 ++++++++++++-------------- man/downloader.Rd | 15 ++++---- man/sha_url.Rd | 31 +++++++++------- man/source_url.Rd | 81 ++++++++++++++++++++++---------------------- 11 files changed, 203 insertions(+), 150 deletions(-)
Title: Biodemography Functions
Description: The Biodem package provides a number of functions for Biodemographic analysis.
Author: Alessio Boattini and Federico C. F. Calboli; Vincente Canto Cassola together with Martin Maechler authored the function mtx.exp.
Maintainer: Federico Calboli <federico.calboli@helsinki.fi>
Diff between Biodem versions 0.3 dated 2012-10-29 and 0.4 dated 2015-07-09
DESCRIPTION | 22 +++++++++++----------- MD5 | 48 ++++++++++++++++++++++++------------------------ R/sur.freq.R | 4 ++-- data/N.rda |binary data/P.rda |binary data/S.rda |binary data/raw.mig.rda |binary data/surnames.rda |binary data/valley.rda |binary man/Fst.Rd | 4 ++-- man/col.sto.Rd | 2 +- man/hedrick.Rd | 2 +- man/lasker.Rd | 2 +- man/mal.cond.Rd | 2 +- man/mal.eq.Rd | 2 +- man/mal.phi.Rd | 2 +- man/mar.iso.Rd | 2 +- man/r.pairs.Rd | 2 +- man/rel.cond.Rd | 2 +- man/rel.phi.Rd | 2 +- man/rri.Rd | 2 +- man/sur.freq.Rd | 8 ++++---- man/sur.inbr.Rd | 2 +- man/sym.P.Rd | 2 +- man/uri.Rd | 2 +- 25 files changed, 57 insertions(+), 57 deletions(-)
Title: Creation and Evaluation of Acceptance Sampling Plans
Description: Provides functionality for creating and
evaluating acceptance sampling plans. Sampling plans can be single,
double or multiple.
Author: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>
Maintainer: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>
Diff between AcceptanceSampling versions 1.0-3 dated 2014-01-14 and 1.0-4 dated 2015-07-09
DESCRIPTION | 18 +++++++++--------- MD5 | 12 ++++++------ NAMESPACE | 4 +++- R/code_generic.R | 7 +++---- R/code_twoclass.R | 1 - R/code_var.R | 1 - build/vignette.rds |binary 7 files changed, 21 insertions(+), 22 deletions(-)
More information about AcceptanceSampling at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-27 1.2.0
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (http://www.synbiosys.alterra.nl/turboveg/) and other sources (http://www.vegetweb.de). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", http://www.botanik.uni-greifswald.de/GermanSL.html).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.6.9 dated 2015-04-18 and 0.7 dated 2015-07-08
DESCRIPTION | 10 ++++---- MD5 | 58 +++++++++++++++++++++++++------------------------- NAMESPACE | 3 +- R/child.r | 6 ++--- R/internal.r | 18 ++++++++++----- R/monotypic.r | 2 - R/reflist.r | 20 ++++++++--------- R/syntab.r | 38 ++++++++++++++------------------ R/tax.r | 10 ++++---- R/tax_add.r | 2 - R/taxval.r | 4 +-- R/tv.biblio.r | 19 ++++++---------- R/tv.coverperc.r | 14 ++++++------ R/tv.site.r | 28 ++++++++++++++---------- R/tv.traits.r | 19 +++++++++------- R/tv.veg.r | 11 +++++---- R/tv.write.r | 44 ++++++++++++++++++++++--------------- inst/ChangeLog | 8 ++++++ inst/doc/vegdata.R | 6 ++--- inst/doc/vegdata.Rnw | 8 +++--- inst/doc/vegdata.pdf |binary man/syntab.Rd | 17 +++++++++----- man/tax.Rd | 4 +-- man/tv.biblio.Rd | 5 ++-- man/tv.coverperc.Rd | 3 -- man/tv.site.Rd | 4 ++- man/tv.traits.Rd | 3 -- man/tv.write.Rd | 13 ++++++----- tests |only vignettes/vegdata.Rnw | 8 +++--- 30 files changed, 210 insertions(+), 175 deletions(-)
Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Description: Implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate
of the "correlation-adjusted t-score" (CAT score) described in
Zuber and Strimmer (2009). It also offers a convenient interface
to a number of other regularized t-statistics commonly
employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between st versions 1.2.4 dated 2015-03-21 and 1.2.5 dated 2015-07-08
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NAMESPACE | 9 +++------ NEWS | 6 ++++++ 4 files changed, 19 insertions(+), 15 deletions(-)
Title: Structural Estimators and Algorithms for the Analysis of Stable
Matchings
Description: Implements structural estimators to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.co.uk>
Diff between matchingMarkets versions 0.1-4 dated 2015-05-18 and 0.1-5 dated 2015-07-08
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/daa.R | 1 + R/khb.R | 2 ++ R/mfx.R | 2 ++ R/plp.R | 2 +- R/stabit.R | 2 +- R/stabsim.R | 2 ++ data/baac00.RData |binary data/klein15a.RData |binary data/klein15b.RData |binary man/matchingMarkets-package.Rd | 6 +++--- 13 files changed, 31 insertions(+), 23 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Diagnostic Tests for Models with a Binomial Response
Description: Diagnostic tests and plots for GLMs (generalized linear models)
with binomial/ binary outcomes, particularly logistic regression.
Author: Chris Dardis
Maintainer: Chris Dardis <christopherdardis@gmail.com>
Diff between LogisticDx versions 0.1 dated 2014-05-14 and 0.2 dated 2015-07-08
LogisticDx-0.1/LogisticDx/R/LogisticDx-internal.R |only LogisticDx-0.1/LogisticDx/R/genLogi.R |only LogisticDx-0.1/LogisticDx/R/logiDx.R |only LogisticDx-0.1/LogisticDx/R/logiGOF.R |only LogisticDx-0.1/LogisticDx/R/logiProb.R |only LogisticDx-0.1/LogisticDx/R/logiSS.R |only LogisticDx-0.1/LogisticDx/R/multiPlot.R |only LogisticDx-0.1/LogisticDx/R/plotLogiDx.R |only LogisticDx-0.1/LogisticDx/R/stukel.R |only LogisticDx-0.1/LogisticDx/R/summaryLogiGOF.R |only LogisticDx-0.1/LogisticDx/man/LogisticDx-package.Rd |only LogisticDx-0.1/LogisticDx/man/genLogi.Rd |only LogisticDx-0.1/LogisticDx/man/logiDx.Rd |only LogisticDx-0.1/LogisticDx/man/logiGOF.Rd |only LogisticDx-0.1/LogisticDx/man/logiProb.Rd |only LogisticDx-0.1/LogisticDx/man/logiSS.Rd |only LogisticDx-0.1/LogisticDx/man/plotLogiDx.Rd |only LogisticDx-0.1/LogisticDx/man/stukel.Rd |only LogisticDx-0.2/LogisticDx/DESCRIPTION | 32 ++++--- LogisticDx-0.2/LogisticDx/MD5 | 80 ++++++++++++++----- LogisticDx-0.2/LogisticDx/NAMESPACE | 42 +++++++-- LogisticDx-0.2/LogisticDx/NEWS | 4 LogisticDx-0.2/LogisticDx/R/LogisticDx_package.R |only LogisticDx-0.2/LogisticDx/R/OR.R |only LogisticDx-0.2/LogisticDx/R/ageChd.R |only LogisticDx-0.2/LogisticDx/R/bbdm.R |only LogisticDx-0.2/LogisticDx/R/dx.R |only LogisticDx-0.2/LogisticDx/R/genBinom.R |only LogisticDx-0.2/LogisticDx/R/gof.R |only LogisticDx-0.2/LogisticDx/R/icu.R |only LogisticDx-0.2/LogisticDx/R/lbw.R |only LogisticDx-0.2/LogisticDx/R/llbw.R |only LogisticDx-0.2/LogisticDx/R/mes.R |only LogisticDx-0.2/LogisticDx/R/mlbw.R |only LogisticDx-0.2/LogisticDx/R/nhanes3.R |only LogisticDx-0.2/LogisticDx/R/pcs.R |only LogisticDx-0.2/LogisticDx/R/plotGlm.R |only LogisticDx-0.2/LogisticDx/R/printGofGlm.R |only LogisticDx-0.2/LogisticDx/R/printSSglm.R |only LogisticDx-0.2/LogisticDx/R/printSigGlm.R |only LogisticDx-0.2/LogisticDx/R/sig.R |only LogisticDx-0.2/LogisticDx/R/ss.R |only LogisticDx-0.2/LogisticDx/R/uis.R |only LogisticDx-0.2/LogisticDx/README.md |only LogisticDx-0.2/LogisticDx/build |only LogisticDx-0.2/LogisticDx/data |only LogisticDx-0.2/LogisticDx/inst |only LogisticDx-0.2/LogisticDx/man/OR.Rd |only LogisticDx-0.2/LogisticDx/man/ageChd.Rd |only LogisticDx-0.2/LogisticDx/man/bbdm.Rd |only LogisticDx-0.2/LogisticDx/man/dx.Rd |only LogisticDx-0.2/LogisticDx/man/genBinom.Rd |only LogisticDx-0.2/LogisticDx/man/gof.Rd |only LogisticDx-0.2/LogisticDx/man/icu.Rd |only LogisticDx-0.2/LogisticDx/man/lbw.Rd |only LogisticDx-0.2/LogisticDx/man/llbw.Rd |only LogisticDx-0.2/LogisticDx/man/logisticDx2-package.Rd |only LogisticDx-0.2/LogisticDx/man/mes.Rd |only LogisticDx-0.2/LogisticDx/man/mlbw.Rd |only LogisticDx-0.2/LogisticDx/man/nhanes3.Rd |only LogisticDx-0.2/LogisticDx/man/pcs.Rd |only LogisticDx-0.2/LogisticDx/man/plotGlm.Rd |only LogisticDx-0.2/LogisticDx/man/sig.Rd |only LogisticDx-0.2/LogisticDx/man/ss.Rd |only LogisticDx-0.2/LogisticDx/man/uis.Rd |only LogisticDx-0.2/LogisticDx/vignettes |only 66 files changed, 111 insertions(+), 47 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between eHOF versions 1.5.8 dated 2015-04-18 and 1.5.9 dated 2015-07-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 12 +++++++----- R/Para.niche.r | 8 ++++++-- inst/ChangeLog | 4 +++- 5 files changed, 24 insertions(+), 16 deletions(-)
Title: Bayesian Non- and Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 1.0.4 dated 2015-06-23 and 1.0.5 dated 2015-07-08
BNSP-1.0.4/BNSP/R/bnpglmf.R |only BNSP-1.0.5/BNSP/ChangeLog | 4 BNSP-1.0.5/BNSP/DESCRIPTION | 8 - BNSP-1.0.5/BNSP/MD5 | 21 +-- BNSP-1.0.5/BNSP/NAMESPACE | 2 BNSP-1.0.5/BNSP/R/bnpglm.R | 13 + BNSP-1.0.5/BNSP/man/BNSP-package.Rd | 4 BNSP-1.0.5/BNSP/man/bnpglm.Rd | 4 BNSP-1.0.5/BNSP/src/OneResLtnt.c | 17 +- BNSP-1.0.5/BNSP/src/SpecOneRL.h | 236 ++++++++++++++++++++++++++++++++-- BNSP-1.0.5/BNSP/src/mathm.h | 5 BNSP-1.0.5/BNSP/src/other.functions.h | 35 ++++- 12 files changed, 305 insertions(+), 44 deletions(-)
Title: A Simple Framework to Analyse Population Genetic Data
Description: Provides beginner friendly framework to analyse population genetic data. It uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit www.popgenreport.org.
Author: Bernd Gruber [aut, cre],
Aaron Adamack [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between PopGenReport versions 2.1 dated 2014-10-27 and 2.2 dated 2015-07-08
PopGenReport-2.1/PopGenReport/inst/doc/PopGenReportIntroduction.R |only PopGenReport-2.1/PopGenReport/inst/doc/PopGenReportIntroduction.rnw |only PopGenReport-2.1/PopGenReport/vignettes/PopGenReportIntroduction.rnw |only PopGenReport-2.1/PopGenReport/vignettes/figures/PopGenReport_bilby.pdf |only PopGenReport-2.1/PopGenReport/vignettes/figures/PopGenReport_counts.pdf |only PopGenReport-2.1/PopGenReport/vignettes/figures/landgenreport_example.pdf |only PopGenReport-2.1/PopGenReport/vignettes/figures/platy-map.pdf |only PopGenReport-2.1/PopGenReport/vignettes/figures/tiger-map.pdf |only PopGenReport-2.1/PopGenReport/vignettes/lgr.bib |only PopGenReport-2.2/PopGenReport/DESCRIPTION | 30 - PopGenReport-2.2/PopGenReport/MD5 | 93 ++-- PopGenReport-2.2/PopGenReport/NAMESPACE | 16 PopGenReport-2.2/PopGenReport/R/allel.rich.r | 24 - PopGenReport-2.2/PopGenReport/R/allele.dist.r | 18 PopGenReport-2.2/PopGenReport/R/costdistances.r |only PopGenReport-2.2/PopGenReport/R/gd.kosman.r | 76 +-- PopGenReport-2.2/PopGenReport/R/gd.smouse.r | 12 PopGenReport-2.2/PopGenReport/R/genleastcost.r | 117 ++++- PopGenReport-2.2/PopGenReport/R/landgenreport.r | 50 +- PopGenReport-2.2/PopGenReport/R/null.all.r | 20 PopGenReport-2.2/PopGenReport/R/opt.landgen.r |only PopGenReport-2.2/PopGenReport/R/popdynfun.r |only PopGenReport-2.2/PopGenReport/R/popgenreport.r | 26 - PopGenReport-2.2/PopGenReport/R/read.genetable.r | 4 PopGenReport-2.2/PopGenReport/R/wassermann.r | 6 PopGenReport-2.2/PopGenReport/build/vignette.rds |binary PopGenReport-2.2/PopGenReport/data/bilby.rda |binary PopGenReport-2.2/PopGenReport/data/landgen.rda |binary PopGenReport-2.2/PopGenReport/inst/CITATION | 37 + PopGenReport-2.2/PopGenReport/inst/doc/PopGenReportIntroduction.Rnw |only PopGenReport-2.2/PopGenReport/inst/doc/PopGenReportIntroduction.pdf |binary PopGenReport-2.2/PopGenReport/inst/doc/Tutorial_landgenreport.pdf |binary PopGenReport-2.2/PopGenReport/inst/swchunks/allele.dist.snw | 20 PopGenReport-2.2/PopGenReport/inst/swchunks/counts.snw | 14 PopGenReport-2.2/PopGenReport/inst/swchunks/differ.stats.snw | 108 +++- PopGenReport-2.2/PopGenReport/inst/swchunks/fst.snw | 2 PopGenReport-2.2/PopGenReport/inst/swchunks/gd.kosman.snw | 2 PopGenReport-2.2/PopGenReport/inst/swchunks/hwe.snw | 6 PopGenReport-2.2/PopGenReport/inst/swchunks/locihz.snw | 4 PopGenReport-2.2/PopGenReport/inst/swchunks/null.all.snw | 216 ++++----- PopGenReport-2.2/PopGenReport/inst/swchunks/pcoa.snw | 3 PopGenReport-2.2/PopGenReport/inst/swchunks/pmantel.snw | 10 PopGenReport-2.2/PopGenReport/inst/swchunks/required.snw | 44 + PopGenReport-2.2/PopGenReport/man/PopGenReport-package.Rd | 16 PopGenReport-2.2/PopGenReport/man/addline.Rd |only PopGenReport-2.2/PopGenReport/man/addpoly.Rd |only PopGenReport-2.2/PopGenReport/man/allele.dist.Rd | 66 +- PopGenReport-2.2/PopGenReport/man/costdistances.Rd |only PopGenReport-2.2/PopGenReport/man/emigration.Rd |only PopGenReport-2.2/PopGenReport/man/genleastcost.Rd | 12 PopGenReport-2.2/PopGenReport/man/init.popgensim.Rd |only PopGenReport-2.2/PopGenReport/man/mutation.Rd |only PopGenReport-2.2/PopGenReport/man/opt.landgen.Rd |only PopGenReport-2.2/PopGenReport/man/p2p.Rd |only PopGenReport-2.2/PopGenReport/man/pairwise.fstb.Rd |only PopGenReport-2.2/PopGenReport/man/pops2genind.Rd |only PopGenReport-2.2/PopGenReport/man/read.genetable.Rd | 224 +++++----- PopGenReport-2.2/PopGenReport/man/reproduction.Rd |only PopGenReport-2.2/PopGenReport/man/run.popgensim.Rd |only PopGenReport-2.2/PopGenReport/vignettes/PopGenReportIntroduction.Rnw |only PopGenReport-2.2/PopGenReport/vignettes/figures/PopGenReportIntroduction.pdf |only 61 files changed, 731 insertions(+), 545 deletions(-)
Title: Multi-Paradigm Pipeline Implementation
Description: Provides various styles of function chaining methods: Pipe
operator, Pipe object, and pipeline function, each representing a distinct
pipeline model yet sharing almost a common set of features: A value can be
piped to the first unnamed argument of a function and to dot symbol in an
enclosed expression. The syntax is designed to make the pipeline more
readable and friendly to a wide range of operations.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between pipeR versions 0.6 dated 2015-01-23 and 0.6.0.6 dated 2015-07-08
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- R/functions.R | 15 +++++++++------ R/pipe.R | 1 + R/utils.R | 4 ---- README.md | 16 +++++++++------- man/Pipe.Rd | 2 +- man/grapes-greater-than-greater-than-grapes.Rd | 2 +- man/pipeR-package.Rd | 2 +- man/pipeline.Rd | 2 +- tests/testthat/test1-operator.R | 20 +++++++++++++------- tests/testthat/test2-Pipe.R | 12 ++++++++++++ 13 files changed, 67 insertions(+), 46 deletions(-)
Title: Estimation of Meiotic Recombination Rates Using Marey Maps
Description: Local recombination rates are graphically estimated across a genome using marey maps.
Author: Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between MareyMap versions 1.2 dated 2014-10-07 and 1.3.0 dated 2015-07-08
MareyMap-1.2/MareyMap/data/Arabidopsis_thalianan.rda |only MareyMap-1.2/MareyMap/man/Arabidopsis_thalianan.Rd |only MareyMap-1.2/MareyMap/vignettes/vignette.Rnw.backup |only MareyMap-1.3.0/MareyMap/DESCRIPTION | 16 +++++++-------- MareyMap-1.3.0/MareyMap/MD5 | 19 ++++++++---------- MareyMap-1.3.0/MareyMap/NAMESPACE | 14 +++++++++---- MareyMap-1.3.0/MareyMap/build/vignette.rds |binary MareyMap-1.3.0/MareyMap/data/Arabidopsis_thaliana.rda |only MareyMap-1.3.0/MareyMap/inst/doc/vignette.pdf |binary MareyMap-1.3.0/MareyMap/man/Arabidopsis_thaliana.Rd |only MareyMap-1.3.0/MareyMap/man/Interpolation-class.Rd | 4 ++- MareyMap-1.3.0/MareyMap/man/MapCollection-class.Rd | 1 MareyMap-1.3.0/MareyMap/vignettes/test_query.txt | 6 ++--- 13 files changed, 34 insertions(+), 26 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-1 dated 2015-05-22 and 1.0-3 dated 2015-07-08
DESCRIPTION | 12 ++-- MD5 | 29 +++++----- NAMESPACE | 11 ++- R/cache.R | 8 +- R/codes.R | 111 +++++++++++++++++++++++++++++++++------- R/corpus.R | 7 +- R/db_api.R | 5 + R/manifesto.R | 14 ++--- R/manifestoR-package.r | 2 R/scaling_bootstrap.R | 5 + R/scaling_general.R | 61 +++++++++++++++------ inst/doc/manifestoRworkflow.pdf |binary man/cmp_codes.Rd | 6 +- man/count_codes.Rd | 12 ++-- man/mp_scale.Rd | 8 +- man/null_to_na.Rd |only 16 files changed, 207 insertions(+), 84 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package allows for retrieval of five datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; and the International Tree Ring Data Bank. Additional data sources are in the works, including global DEM resources (ETOPO1, ETOPO5, ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 1.1.0 dated 2015-05-06 and 2.0.0 dated 2015-07-08
FedData-1.1.0/FedData/man/SPDFfromPolygon.Rd |only FedData-1.1.0/FedData/man/curlDownload.Rd |only FedData-1.1.0/FedData/man/downloadGHCNDailyStation.Rd |only FedData-1.1.0/FedData/man/downloadHUC4.Rd |only FedData-1.1.0/FedData/man/downloadITRDB.Rd |only FedData-1.1.0/FedData/man/downloadNEDTile.Rd |only FedData-1.1.0/FedData/man/downloadNHDSubregion.Rd |only FedData-1.1.0/FedData/man/downloadSSURGOInventory.Rd |only FedData-1.1.0/FedData/man/downloadSSURGOStudyArea.Rd |only FedData-1.1.0/FedData/man/extractSSURGOData.Rd |only FedData-1.1.0/FedData/man/getGHCNDaily.Rd |only FedData-1.1.0/FedData/man/getGHCNDailyStation.Rd |only FedData-1.1.0/FedData/man/getGHCNInventory.Rd |only FedData-1.1.0/FedData/man/getHUC4.Rd |only FedData-1.1.0/FedData/man/getITRDB.Rd |only FedData-1.1.0/FedData/man/getNED.Rd |only FedData-1.1.0/FedData/man/getNEDTile.Rd |only FedData-1.1.0/FedData/man/getNHD.Rd |only FedData-1.1.0/FedData/man/getNHDSubregion.Rd |only FedData-1.1.0/FedData/man/getSSURGO.Rd |only FedData-1.1.0/FedData/man/getSSURGOInventory.Rd |only FedData-1.1.0/FedData/man/getSSURGOStudyArea.Rd |only FedData-1.1.0/FedData/man/pkgTest.Rd |only FedData-1.1.0/FedData/man/polygonFromExtent.Rd |only FedData-1.1.0/FedData/man/read.crn.Rd |only FedData-1.1.0/FedData/man/read.crn.data.Rd |only FedData-1.1.0/FedData/man/read.crn.metadata.Rd |only FedData-1.1.0/FedData/man/sequential.duplicated.Rd |only FedData-1.1.0/FedData/man/substrRight.Rd |only FedData-1.1.0/FedData/man/wgetDownload.Rd |only FedData-2.0.0/FedData/DESCRIPTION | 12 - FedData-2.0.0/FedData/MD5 | 81 ++++----- FedData-2.0.0/FedData/NAMESPACE | 61 +++--- FedData-2.0.0/FedData/R/GHCN_FUNCTIONS.R | 50 ++--- FedData-2.0.0/FedData/R/ITRDB_FUNCTIONS.R | 95 +++++----- FedData-2.0.0/FedData/R/NED_FUNCTIONS.R | 71 ++------ FedData-2.0.0/FedData/R/NHD_FUNCTIONS.R | 49 ++--- FedData-2.0.0/FedData/R/SSURGO_FUNCTIONS.R | 131 +++++++-------- FedData-2.0.0/FedData/R/UTILITY_FUNCTIONS.R | 59 +----- FedData-2.0.0/FedData/README.md | 12 - FedData-2.0.0/FedData/inst/FedDataTester.R | 99 ++++++----- FedData-2.0.0/FedData/man/FedData-package.Rd | 98 +++++++---- FedData-2.0.0/FedData/man/curl_download.Rd |only FedData-2.0.0/FedData/man/download_ghcn_daily_station.Rd |only FedData-2.0.0/FedData/man/download_huc4.Rd |only FedData-2.0.0/FedData/man/download_itrdb.Rd |only FedData-2.0.0/FedData/man/download_ned_tile.Rd |only FedData-2.0.0/FedData/man/download_nhd_subregion.Rd |only FedData-2.0.0/FedData/man/download_ssurgo_inventory.Rd |only FedData-2.0.0/FedData/man/download_ssurgo_study_area.Rd |only FedData-2.0.0/FedData/man/extract_ssurgo_data.Rd |only FedData-2.0.0/FedData/man/get_ghcn_daily.Rd |only FedData-2.0.0/FedData/man/get_ghcn_daily_station.Rd |only FedData-2.0.0/FedData/man/get_ghcn_inventory.Rd |only FedData-2.0.0/FedData/man/get_huc4.Rd |only FedData-2.0.0/FedData/man/get_itrdb.Rd |only FedData-2.0.0/FedData/man/get_ned.Rd |only FedData-2.0.0/FedData/man/get_ned_tile.Rd |only FedData-2.0.0/FedData/man/get_nhd.Rd |only FedData-2.0.0/FedData/man/get_nhd_subregion.Rd |only FedData-2.0.0/FedData/man/get_ssurgo.Rd |only FedData-2.0.0/FedData/man/get_ssurgo_inventory.Rd |only FedData-2.0.0/FedData/man/get_ssurgo_study_area.Rd |only FedData-2.0.0/FedData/man/pkg_test.Rd |only FedData-2.0.0/FedData/man/polygon_from_extent.Rd |only FedData-2.0.0/FedData/man/read_crn.Rd |only FedData-2.0.0/FedData/man/read_crn_data.Rd |only FedData-2.0.0/FedData/man/read_crn_metadata.Rd |only FedData-2.0.0/FedData/man/sequential_duplicated.Rd |only FedData-2.0.0/FedData/man/spdf_from_polygon.Rd |only FedData-2.0.0/FedData/man/substr_right.Rd |only 71 files changed, 408 insertions(+), 410 deletions(-)
Title: Discrete Weibull Distributions (Type 1 and 3)
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.
Author: Alessandro Barbiero
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteWeibull versions 1.0 dated 2013-08-07 and 1.0.1 dated 2015-07-08
DiscreteWeibull-1.0.1/DiscreteWeibull/DESCRIPTION | 14 +++++----- DiscreteWeibull-1.0.1/DiscreteWeibull/MD5 | 13 ++++----- DiscreteWeibull-1.0.1/DiscreteWeibull/NAMESPACE | 3 +- DiscreteWeibull-1.0.1/DiscreteWeibull/man/DiscreteWeibull-package.Rd | 6 ++-- DiscreteWeibull-1.0.1/DiscreteWeibull/man/Edweibull3.Rd | 2 - DiscreteWeibull-1.0.1/DiscreteWeibull/man/estdweibull.Rd | 2 - DiscreteWeibull-1.0.1/DiscreteWeibull/man/estdweibull3.Rd | 7 ----- DiscreteWeibull-1.0/DiscreteWeibull/doc |only 8 files changed, 21 insertions(+), 26 deletions(-)
More information about DiscreteWeibull at CRAN
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Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier
analysis, Data Envelopment Analysis (DEA), under different
technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+),
and using different efficiency measures (input based, output based,
hyperbolic graph, additive, super, and directional efficiency). Peers
and slacks are available, partial price information can be included,
and optimal cost, revenue and profit can be calculated. Evaluation of
mergers is also supported. Methods for graphing the technology sets
are also included. There is also support comparative methods based
on Stochastic Frontier Analyses (SFA). In general, the methods can be
used to solve not only standard models, but also many other model
variants. It complements the book, Bogetoft and Otto,
Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of
course also be used as a stand-alone package.
Author: Peter Bogetoft and Lars Otto
Maintainer: Lars Otto <larsot23@gmail.com>
Diff between Benchmarking versions 0.24 dated 2014-10-10 and 0.26 dated 2015-07-08
DESCRIPTION | 17 +++--- MD5 | 56 ++++++++++----------- NAMESPACE | 10 +++ NEWS | 18 ++++++ R/dea.R | 45 +++++++++-------- R/dea.boot.R | 116 +++++++++++++++++++------------------------- R/dea.direct.R | 3 - R/dea.dual.R | 3 - R/dea.plot.R | 24 ++++----- R/dea.web.R | 10 +-- R/deaUtil.R | 27 +++++----- R/eff.dens.R | 4 - R/fdh.R | 8 +-- R/fdhPlus.R | 13 +++- R/fdhPlus.plot.R | 12 +--- R/graphEff.R | 26 ++++----- R/make.merge.R | 8 +-- R/malmq.R | 18 +++--- R/malmquist.R | 18 +++--- R/minDirection.R | 6 +- R/outlier.R | 4 - R/profit.R | 8 +-- R/sfa.R | 84 ++++++++++++++++++++++--------- R/slack.R | 4 - man/Benchmarking-package.Rd | 6 +- man/dea.Rd | 18 ++++-- man/dea.boot.Rd | 26 ++++++--- man/mea.Rd | 9 +-- man/sfa.Rd | 12 +++- 29 files changed, 346 insertions(+), 267 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut],
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-0 dated 2015-06-09 and 1.4-1 dated 2015-07-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/shadings.R | 8 +++++--- inst/NEWS.Rd | 8 ++++++++ inst/doc/residual-shadings.pdf |binary man/assoc.Rd | 2 +- man/legends.Rd | 2 +- 8 files changed, 27 insertions(+), 16 deletions(-)
Title: Read and Write StatDataML Files
Description: Support for reading and writing files in StatDataML---an XML-based data exchange format.
Author: David Meyer [aut, cre],
Torsten Hothorn [aut],
Friedrich Leisch [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between StatDataML versions 1.0-25 dated 2014-03-17 and 1.0-26 dated 2015-07-08
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- inst/doc/StatDataML.pdf |binary 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Auxiliary Functions to Estimate Centers of Biodiversity
Description: Provides some easy-to-use functions to interpolate species range based on species occurrences and to estimate centers of biodiversity.
Author: Maximilian Lange, Sven Lautenbach, Claudia Raedig
Maintainer: Maximilian Lange <maximilian-lange@t-online.de>
Diff between sperich versions 1.5-5 dated 2012-12-21 and 1.5-7 dated 2015-07-08
sperich-1.5-5/sperich/index |only sperich-1.5-7/sperich/DESCRIPTION | 19 ++-- sperich-1.5-7/sperich/MD5 | 23 ++--- sperich-1.5-7/sperich/NAMESPACE | 6 + sperich-1.5-7/sperich/R/createImage.R | 20 +--- sperich-1.5-7/sperich/R/exportAsGDAL.R | 75 ++++++++--------- sperich-1.5-7/sperich/R/searchClusters.R | 20 +--- sperich-1.5-7/sperich/R/species.richness.CV.R | 10 +- sperich-1.5-7/sperich/R/species.richness.R | 10 +- sperich-1.5-7/sperich/R/species.richness.nonweighted.R | 10 +- sperich-1.5-7/sperich/man/createImage.Rd | 6 - sperich-1.5-7/sperich/man/evaluate.Rd | 2 sperich-1.5-7/sperich/man/exportAsGDAL.Rd | 3 13 files changed, 98 insertions(+), 106 deletions(-)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and
fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between sets versions 1.0-14 dated 2015-04-30 and 1.0-15 dated 2015-07-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 6 ++++-- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/sets.pdf |binary 6 files changed, 19 insertions(+), 11 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: Provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between sda versions 1.3.6 dated 2015-03-21 and 1.3.7 dated 2015-07-08
DESCRIPTION | 15 ++++++++------- MD5 | 6 +++--- NAMESPACE | 9 ++++----- NEWS | 5 +++++ 4 files changed, 20 insertions(+), 15 deletions(-)
Title: Infrastructure for R Package Registries
Description: Provides a generic infrastructure for creating and using registries.
Author: David Meyer
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between registry versions 0.2 dated 2011-04-26 and 0.3 dated 2015-07-08
registry-0.2/registry/inst/doc/abbrvnat.bst |only registry-0.2/registry/inst/doc/registry.bib |only registry-0.3/registry/DESCRIPTION | 14 +++++++------- registry-0.3/registry/MD5 |only registry-0.3/registry/NAMESPACE | 2 ++ registry-0.3/registry/build |only registry-0.3/registry/inst/doc/registry.R |only registry-0.3/registry/inst/doc/registry.pdf |binary registry-0.3/registry/man/regobj.Rd | 5 +++-- registry-0.3/registry/vignettes |only 10 files changed, 12 insertions(+), 9 deletions(-)
Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre],
Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between proxy versions 0.4-14 dated 2015-02-04 and 0.4-15 dated 2015-07-08
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Jonah C. Brooks [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 1.1.5 dated 2015-05-12 and 2.0.0 dated 2015-07-08
poppr-1.1.5/poppr/R/zzz.r |only poppr-1.1.5/poppr/man/hierarchy-methods.Rd |only poppr-1.1.5/poppr/man/is.genclone.Rd |only poppr-1.1.5/poppr/man/population-methods.Rd |only poppr-1.1.5/poppr/man/splitcombine.Rd |only poppr-1.1.5/poppr/vignettes/poppr_man.bib |only poppr-2.0.0/poppr/DESCRIPTION | 21 poppr-2.0.0/poppr/MD5 | 237 poppr-2.0.0/poppr/NAMESPACE | 90 poppr-2.0.0/poppr/NEWS | 66 poppr-2.0.0/poppr/R/Index_calculations.r | 590 + poppr-2.0.0/poppr/R/aaaMLGclass.R |only poppr-2.0.0/poppr/R/aaaMLGmethods.R |only poppr-2.0.0/poppr/R/amova.r | 121 poppr-2.0.0/poppr/R/bitwise.r |only poppr-2.0.0/poppr/R/bootstraping.R |only poppr-2.0.0/poppr/R/bruvo.r | 460 + poppr-2.0.0/poppr/R/classes.r | 130 poppr-2.0.0/poppr/R/data_subset.r | 978 +-- poppr-2.0.0/poppr/R/deprecated.R |only poppr-2.0.0/poppr/R/distances.r | 200 poppr-2.0.0/poppr/R/file_handling.r | 186 poppr-2.0.0/poppr/R/filter_stats.R |only poppr-2.0.0/poppr/R/global_memory.R |only poppr-2.0.0/poppr/R/imsn.R |only poppr-2.0.0/poppr/R/internal.r | 1554 +++-- poppr-2.0.0/poppr/R/internal_methods.R |only poppr-2.0.0/poppr/R/messages.r | 27 poppr-2.0.0/poppr/R/methods.r | 1632 +++-- poppr-2.0.0/poppr/R/mlg.r | 463 + poppr-2.0.0/poppr/R/poppr.R | 210 poppr-2.0.0/poppr/R/print_methods.r | 42 poppr-2.0.0/poppr/R/sample_schemes.r | 169 poppr-2.0.0/poppr/R/sandbox.r | 495 - poppr-2.0.0/poppr/R/visualizations.r | 694 +- poppr-2.0.0/poppr/R/zzz.R |only poppr-2.0.0/poppr/README.md | 75 poppr-2.0.0/poppr/build/vignette.rds |binary poppr-2.0.0/poppr/data/Aeut.rda |binary poppr-2.0.0/poppr/data/Pinf.rda |binary poppr-2.0.0/poppr/data/Pram.rda |only poppr-2.0.0/poppr/data/monpop.rda |binary poppr-2.0.0/poppr/data/old_Pinf.rda |only poppr-2.0.0/poppr/data/old_partial_clone.rda |only poppr-2.0.0/poppr/data/partial_clone.rda |binary poppr-2.0.0/poppr/inst/CITATION | 26 poppr-2.0.0/poppr/inst/doc/algo.R | 4 poppr-2.0.0/poppr/inst/doc/algo.Rnw | 133 poppr-2.0.0/poppr/inst/doc/algo.pdf |binary poppr-2.0.0/poppr/inst/doc/how_to_migrate.R |only poppr-2.0.0/poppr/inst/doc/how_to_migrate.Rnw |only poppr-2.0.0/poppr/inst/doc/how_to_migrate.pdf |only poppr-2.0.0/poppr/inst/doc/mlg.R |only poppr-2.0.0/poppr/inst/doc/mlg.Rmd |only poppr-2.0.0/poppr/inst/doc/mlg.html |only poppr-2.0.0/poppr/inst/doc/poppr_manual.R | 797 -- poppr-2.0.0/poppr/inst/doc/poppr_manual.Rnw | 3836 ++----------- poppr-2.0.0/poppr/inst/doc/poppr_manual.pdf |binary poppr-2.0.0/poppr/inst/msn_explorer |only poppr-2.0.0/poppr/man/Aeut.Rd | 1 poppr-2.0.0/poppr/man/MLG-class.Rd |only poppr-2.0.0/poppr/man/MLG-method.Rd |only poppr-2.0.0/poppr/man/Pinf.Rd | 6 poppr-2.0.0/poppr/man/Pram.Rd |only poppr-2.0.0/poppr/man/aboot.Rd | 45 poppr-2.0.0/poppr/man/bitwise.IA.Rd |only poppr-2.0.0/poppr/man/bitwise.dist.Rd |only poppr-2.0.0/poppr/man/bootgen-methods.Rd | 9 poppr-2.0.0/poppr/man/bruvo.boot.Rd | 45 poppr-2.0.0/poppr/man/bruvo.dist.Rd | 46 poppr-2.0.0/poppr/man/bruvo.msn.Rd | 44 poppr-2.0.0/poppr/man/bruvomat-class.Rd | 4 poppr-2.0.0/poppr/man/clonecorrect.Rd | 74 poppr-2.0.0/poppr/man/coercion-methods.Rd | 34 poppr-2.0.0/poppr/man/cutoff_predictor.Rd |only poppr-2.0.0/poppr/man/deprecated.Rd |only poppr-2.0.0/poppr/man/diss.dist.Rd | 2 poppr-2.0.0/poppr/man/diversity_boot.Rd |only poppr-2.0.0/poppr/man/diversity_ci.Rd |only poppr-2.0.0/poppr/man/diversity_stats.Rd |only poppr-2.0.0/poppr/man/filter_stats.Rd |only poppr-2.0.0/poppr/man/fix_replen.Rd |only poppr-2.0.0/poppr/man/genclone-class.Rd | 6 poppr-2.0.0/poppr/man/genclone-method.Rd | 48 poppr-2.0.0/poppr/man/genind2genalex.Rd | 17 poppr-2.0.0/poppr/man/genotype_curve.Rd | 4 poppr-2.0.0/poppr/man/ia.Rd | 121 poppr-2.0.0/poppr/man/imsn.Rd |only poppr-2.0.0/poppr/man/informloci.Rd | 74 poppr-2.0.0/poppr/man/is.clone.Rd |only poppr-2.0.0/poppr/man/levels-methods.Rd |only poppr-2.0.0/poppr/man/missingno.Rd | 22 poppr-2.0.0/poppr/man/mlg.Rd | 94 poppr-2.0.0/poppr/man/mlg.filter.Rd |only poppr-2.0.0/poppr/man/mll-method.Rd |only poppr-2.0.0/poppr/man/mll.custom.Rd |only poppr-2.0.0/poppr/man/mll.reset-method.Rd |only poppr-2.0.0/poppr/man/monpop.Rd | 8 poppr-2.0.0/poppr/man/old2new_genclone.Rd |only poppr-2.0.0/poppr/man/partial_clone.Rd | 1 poppr-2.0.0/poppr/man/plot_filter_stats.Rd |only poppr-2.0.0/poppr/man/plot_poppr_msn.Rd | 44 poppr-2.0.0/poppr/man/poppr-package.Rd | 166 poppr-2.0.0/poppr/man/poppr.Rd | 167 poppr-2.0.0/poppr/man/poppr.amova.Rd | 56 poppr-2.0.0/poppr/man/poppr.msn.Rd | 53 poppr-2.0.0/poppr/man/poppr_has_parallel.Rd |only poppr-2.0.0/poppr/man/popsub.Rd | 2 poppr-2.0.0/poppr/man/private_alleles.Rd | 38 poppr-2.0.0/poppr/man/read.genalex.Rd | 19 poppr-2.0.0/poppr/man/recode_polyploids.Rd | 60 poppr-2.0.0/poppr/man/samp.ia.Rd |only poppr-2.0.0/poppr/man/snpclone-class.Rd |only poppr-2.0.0/poppr/man/snpclone-coercion-methods.Rd |only poppr-2.0.0/poppr/man/snpclone-method.Rd |only poppr-2.0.0/poppr/man/test_replen.Rd |only poppr-2.0.0/poppr/man/unique-methods.Rd |only poppr-2.0.0/poppr/man/win.ia.Rd |only poppr-2.0.0/poppr/src/Makevars |only poppr-2.0.0/poppr/src/bitwise_distance.c |only poppr-2.0.0/poppr/src/mlg_clustering.c |only poppr-2.0.0/poppr/src/msn.c |only poppr-2.0.0/poppr/src/omp_test.c |only poppr-2.0.0/poppr/src/permut_shuffler.c | 120 poppr-2.0.0/poppr/src/poppr_distance.c | 33 poppr-2.0.0/poppr/tests/testthat/test-amova.R | 97 poppr-2.0.0/poppr/tests/testthat/test-bitwise.R |only poppr-2.0.0/poppr/tests/testthat/test-colors.R | 9 poppr-2.0.0/poppr/tests/testthat/test-deprecated.R |only poppr-2.0.0/poppr/tests/testthat/test-distpop.R | 30 poppr-2.0.0/poppr/tests/testthat/test-errors.R |only poppr-2.0.0/poppr/tests/testthat/test-filter.R |only poppr-2.0.0/poppr/tests/testthat/test-genclone.R | 87 poppr-2.0.0/poppr/tests/testthat/test-import.R | 98 poppr-2.0.0/poppr/tests/testthat/test-informloci.R |only poppr-2.0.0/poppr/tests/testthat/test-locustable.R |only poppr-2.0.0/poppr/tests/testthat/test-missing.R | 14 poppr-2.0.0/poppr/tests/testthat/test-mlg.R | 345 - poppr-2.0.0/poppr/tests/testthat/test-msn.R |only poppr-2.0.0/poppr/tests/testthat/test-plots.R |only poppr-2.0.0/poppr/tests/testthat/test-polyploids.R | 16 poppr-2.0.0/poppr/tests/testthat/test-poppr.R | 130 poppr-2.0.0/poppr/tests/testthat/test-popsub.R | 32 poppr-2.0.0/poppr/tests/testthat/test-private.R |only poppr-2.0.0/poppr/tests/testthat/test-sampling.R |only poppr-2.0.0/poppr/tests/testthat/test-trees.R |only poppr-2.0.0/poppr/tests/testthat/test-values.R | 189 poppr-2.0.0/poppr/vignettes/algo-concordance.tex | 2 poppr-2.0.0/poppr/vignettes/algo.Rnw | 133 poppr-2.0.0/poppr/vignettes/authordate1.bst |only poppr-2.0.0/poppr/vignettes/how_to_migrate-concordance.tex |only poppr-2.0.0/poppr/vignettes/how_to_migrate.Rnw |only poppr-2.0.0/poppr/vignettes/mlg.Rmd |only poppr-2.0.0/poppr/vignettes/msg.txt |only poppr-2.0.0/poppr/vignettes/nancybruvo.rda |only poppr-2.0.0/poppr/vignettes/poppr_manual-concordance.tex | 30 poppr-2.0.0/poppr/vignettes/poppr_manual.Rnw | 3836 ++----------- poppr-2.0.0/poppr/vignettes/the_bibliography.bib |only 158 files changed, 9109 insertions(+), 10638 deletions(-)
Title: Analysis of Multiple Time Course Data
Description: Contains general data structures and
functions for longitudinal data with multiple variables,
repeated measurements, and irregularly spaced time points.
Also implements a shrinkage estimator of dynamical correlation
and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between longitudinal versions 1.1.11 dated 2015-03-09 and 1.1.12 dated 2015-07-08
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 8 +++++--- NEWS | 4 ++++ 4 files changed, 18 insertions(+), 11 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions of type I, II, III and IV tailored to
distributions with left and right fat tails like those that occur
in financial markets. These distributions can be used to estimate
with a high accuracy market risks and value-at-risk. Also include power
hyperbolas and power hyperbolic functions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.2-0 dated 2015-06-18 and 1.2-3 dated 2015-07-08
DESCRIPTION | 8 +++--- MD5 | 62 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 - NEWS | 12 ++++++--- R/z_data.R | 13 +++++----- man/FatTailsR.Rd | 3 +- man/aw2k.Rd | 7 +++-- man/checkquantiles.Rd | 3 +- man/ckiener.Rd | 3 +- man/dfData.Rd | 3 +- man/elevenprobs.Rd | 3 +- man/estimkappa6.Rd | 3 +- man/estimkiener11.Rd | 11 ++++---- man/estimkienerX.Rd | 3 +- man/exphp.Rd | 3 +- man/fitkienerLX.Rd | 3 +- man/getDSdata.Rd | 3 +- man/kashp.Rd | 3 +- man/kiener1.Rd | 23 +++++++++-------- man/kiener2.Rd | 23 +++++++++-------- man/kiener3.Rd | 23 +++++++++-------- man/kiener4.Rd | 23 +++++++++-------- man/kmoments.Rd | 3 +- man/laplacegaussnorm.Rd | 3 +- man/loghp.Rd | 3 +- man/logishp.Rd | 13 +++++----- man/logit.Rd | 3 +- man/pk2pk.Rd | 3 +- man/regkienerLX.Rd | 3 +- man/tData.Rd | 3 +- man/xData.Rd | 3 +- man/zData.Rd | 3 +- 32 files changed, 156 insertions(+), 124 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Description: Implements the regression approach
of Zuber and Strimmer (2011) "High-dimensional regression and variable
selection using CAR scores" SAGMB 10: 34.
CAR scores measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is a
natural measure of variable importance and provides a canonical
ordering of variables. This package provides functions for estimating
CAR scores, for variable selection using CAR scores, and for estimating
corresponding regression coefficients. Both shrinkage as well as
empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between care versions 1.1.8 dated 2015-03-09 and 1.1.9 dated 2015-07-08
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 5 ++--- NEWS | 5 +++++ man/efron2004.Rd | 2 +- 5 files changed, 19 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-10 0.2
2013-09-24 0.1
Title: Weighted k-Means Clustering
Description: Entropy weighted k-means (ewkm) is a weighted subspace
clustering algorithm that is well suited to very high
dimensional data. Weights are calculated as the importance of
a variable with regard to cluster membership. The two-level
variable weighting clustering algorithm tw-k-means (twkm)
introduces two types of weights, the weights on individual
variables and the weights on variable groups, and they are
calculated during the clustering process. The feature group
weighted k-means (fgkm) extends this concept by grouping
features and weighting the group in addition to weighting
individual features.
Author: Graham Williams [aut],
Joshua Z Huang [aut],
Xiaojun Chen [aut],
Qiang Wang [aut],
Longfei Xiao [aut],
He Zhao [cre]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wskm versions 1.4.19 dated 2014-12-26 and 1.4.28 dated 2015-07-08
DESCRIPTION | 35 +++++++++++++++++++---------------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- inst/CITATION |only inst/ChangeLog | 33 ++++++++++++++++++++++++++++----- man/ewkm.Rd | 8 ++++---- man/fgkm.Rd | 6 +++--- man/twkm.Rd | 8 +++++--- 8 files changed, 69 insertions(+), 38 deletions(-)
Title: Variogram Diagnostics
Description: Interactive variogram diagnostics.
Author: Ernst Glatzer <ernst.glatzer@wu-wien.ac.at>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between vardiag versions 0.2-0 dated 2013-05-02 and 0.2-1 dated 2015-07-08
DESCRIPTION | 15 ++++++++------- MD5 | 6 +++--- NAMESPACE | 4 ++++ R/VARDIAG.R | 4 ++-- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.1-0 dated 2015-02-20 and 1.1-1 dated 2015-07-08
synthpop-1.1-0/synthpop/man/syn.surv.ctree.Rd |only synthpop-1.1-1/synthpop/DESCRIPTION | 12 synthpop-1.1-1/synthpop/MD5 | 65 +-- synthpop-1.1-1/synthpop/NAMESPACE | 44 +- synthpop-1.1-1/synthpop/NEWS | 45 ++ synthpop-1.1-1/synthpop/R/compare.syn.r | 412 +++++++++++++------- synthpop-1.1-1/synthpop/R/functions.syn.r | 134 +++--- synthpop-1.1-1/synthpop/R/methods.syn.r | 328 +++++++++++---- synthpop-1.1-1/synthpop/R/padMis.syn.r | 24 - synthpop-1.1-1/synthpop/R/padModel.syn.r | 3 synthpop-1.1-1/synthpop/R/sampler.syn.r | 93 +++- synthpop-1.1-1/synthpop/R/syn.r | 290 ++++++++------ synthpop-1.1-1/synthpop/build/vignette.rds |binary synthpop-1.1-1/synthpop/inst/doc/synthpop.R | 113 ++--- synthpop-1.1-1/synthpop/inst/doc/synthpop.Rnw | 139 +++--- synthpop-1.1-1/synthpop/inst/doc/synthpop.pdf |binary synthpop-1.1-1/synthpop/man/compare.Rd |only synthpop-1.1-1/synthpop/man/compare.fit.synds.Rd | 25 - synthpop-1.1-1/synthpop/man/compare.synds.Rd | 39 + synthpop-1.1-1/synthpop/man/glm.synds.Rd | 25 - synthpop-1.1-1/synthpop/man/summary.fit.synds.Rd | 17 synthpop-1.1-1/synthpop/man/summary.synds.Rd | 28 - synthpop-1.1-1/synthpop/man/syn.Rd | 117 +++-- synthpop-1.1-1/synthpop/man/syn.cart.Rd | 37 + synthpop-1.1-1/synthpop/man/syn.normrank.Rd | 7 synthpop-1.1-1/synthpop/man/syn.polr.Rd | 17 synthpop-1.1-1/synthpop/man/syn.polyreg.Rd | 14 synthpop-1.1-1/synthpop/man/syn.sample.Rd | 10 synthpop-1.1-1/synthpop/man/syn.survctree.Rd |only synthpop-1.1-1/synthpop/man/synthpop-package.Rd | 6 synthpop-1.1-1/synthpop/vignettes/Figure1ls.pdf |binary synthpop-1.1-1/synthpop/vignettes/Figure2income.pdf |binary synthpop-1.1-1/synthpop/vignettes/Figure3Z.pdf |binary synthpop-1.1-1/synthpop/vignettes/synthpop.Rnw | 139 +++--- synthpop-1.1-1/synthpop/vignettes/synthpop.bib | 17 35 files changed, 1370 insertions(+), 830 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb]
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb]
Amandine Gasc [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 1.7.6 dated 2014-09-12 and 2.0.1 dated 2015-07-08
seewave-1.7.6/seewave/man/pulse.Rd |only seewave-2.0.1/seewave/DESCRIPTION | 30 seewave-2.0.1/seewave/MD5 | 107 seewave-2.0.1/seewave/NAMESPACE | 2 seewave-2.0.1/seewave/NEWS | 1112 +++--- seewave-2.0.1/seewave/R/seewave.r | 3090 ++++++++++--------- seewave-2.0.1/seewave/R/zzz.r | 20 seewave-2.0.1/seewave/build/vignette.rds |binary seewave-2.0.1/seewave/inst/CITATION | 2 seewave-2.0.1/seewave/inst/doc/seewave_IO.pdf |binary seewave-2.0.1/seewave/inst/doc/seewave_analysis.R | 2 seewave-2.0.1/seewave/inst/doc/seewave_analysis.pdf |binary seewave-2.0.1/seewave/inst/doc/seewave_analysis.rnw | 11 seewave-2.0.1/seewave/man/AR.Rd |only seewave-2.0.1/seewave/man/M.Rd |only seewave-2.0.1/seewave/man/Q.Rd | 7 seewave-2.0.1/seewave/man/attenuation.Rd | 2 seewave-2.0.1/seewave/man/ccoh.Rd | 10 seewave-2.0.1/seewave/man/cepstro.Rd | 4 seewave-2.0.1/seewave/man/combfilter.Rd |only seewave-2.0.1/seewave/man/convSPL.Rd | 4 seewave-2.0.1/seewave/man/corenv.Rd | 2 seewave-2.0.1/seewave/man/corspec.Rd | 25 seewave-2.0.1/seewave/man/cutspec.Rd | 21 seewave-2.0.1/seewave/man/diffcumspec.Rd | 22 seewave-2.0.1/seewave/man/diffspec.Rd | 51 seewave-2.0.1/seewave/man/discrets.Rd | 27 seewave-2.0.1/seewave/man/drawfilter.Rd |only seewave-2.0.1/seewave/man/dynoscillo.Rd | 2 seewave-2.0.1/seewave/man/env.Rd | 28 seewave-2.0.1/seewave/man/fbands.Rd | 15 seewave-2.0.1/seewave/man/fpeaks.Rd | 24 seewave-2.0.1/seewave/man/fund.Rd | 2 seewave-2.0.1/seewave/man/hilbert.Rd | 10 seewave-2.0.1/seewave/man/itakura.dist.Rd | 19 seewave-2.0.1/seewave/man/kl.dist.Rd | 6 seewave-2.0.1/seewave/man/ks.dist.Rd | 29 seewave-2.0.1/seewave/man/localpeaks.Rd | 27 seewave-2.0.1/seewave/man/logspec.dist.Rd | 21 seewave-2.0.1/seewave/man/oscillo.Rd | 32 seewave-2.0.1/seewave/man/oscilloST.Rd | 3 seewave-2.0.1/seewave/man/pastew.Rd | 11 seewave-2.0.1/seewave/man/playlist.Rd | 4 seewave-2.0.1/seewave/man/pulsew.Rd |only seewave-2.0.1/seewave/man/seewave.internal.Rd | 12 seewave-2.0.1/seewave/man/seewave.package.Rd | 15 seewave-2.0.1/seewave/man/sh.Rd | 45 seewave-2.0.1/seewave/man/simspec.Rd | 40 seewave-2.0.1/seewave/man/songmeter.Rd | 2 seewave-2.0.1/seewave/man/spec.Rd | 2 seewave-2.0.1/seewave/man/specprop.Rd | 14 seewave-2.0.1/seewave/man/spectro.Rd | 18 seewave-2.0.1/seewave/man/spectro3D.Rd | 10 seewave-2.0.1/seewave/man/squarefilter.Rd |only seewave-2.0.1/seewave/man/synth.Rd | 22 seewave-2.0.1/seewave/man/timer.Rd | 162 seewave-2.0.1/seewave/man/wav2flac.Rd | 2 seewave-2.0.1/seewave/vignettes/seewave_analysis.rnw | 11 58 files changed, 2842 insertions(+), 2297 deletions(-)
Title: Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede <tyler.tiede7@gmail.com>
Diff between PopVar versions 1.2 dated 2015-06-17 and 1.2.1 dated 2015-07-08
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 4 ++-- R/pop.predict_function_4.28.15.R | 26 ++++++++++++++------------ R/x.val_function_4.28.15.R | 26 ++++++++++++++------------ man/pop.predict.Rd | 8 ++++---- man/x.val.Rd | 8 ++++---- 7 files changed, 50 insertions(+), 46 deletions(-)
Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. nplr can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre],
Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>
Diff between nplr versions 0.1-1 dated 2014-05-13 and 0.1-2 dated 2015-07-08
nplr-0.1-1/nplr/README.md |only nplr-0.1-2/nplr/DESCRIPTION | 12 - nplr-0.1-2/nplr/MD5 | 28 +-- nplr-0.1-2/nplr/NAMESPACE | 14 + nplr-0.1-2/nplr/NEWS |only nplr-0.1-2/nplr/R/AllClasses.R | 17 +- nplr-0.1-2/nplr/R/AllGenerics.R | 5 nplr-0.1-2/nplr/R/helpers.R | 261 ++++++++++++++++++----------------- nplr-0.1-2/nplr/R/nplr.R | 215 ++++++++++++++++------------ nplr-0.1-2/nplr/R/plot.nplr.R | 2 nplr-0.1-2/nplr/build/vignette.rds |binary nplr-0.1-2/nplr/inst/doc/nplr.R | 37 +--- nplr-0.1-2/nplr/inst/doc/nplr.Rnw | 28 +++ nplr-0.1-2/nplr/inst/doc/nplr.pdf |binary nplr-0.1-2/nplr/man/convertToProp.Rd | 8 - nplr-0.1-2/nplr/vignettes/nplr.Rnw | 28 +++ 16 files changed, 369 insertions(+), 286 deletions(-)
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2S versions 1.0.1 dated 2015-06-17 and 1.0.2 dated 2015-07-08
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 2 +- NEWS | 9 +++++++++ 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between mclust versions 5.0.1 dated 2015-04-22 and 5.0.2 dated 2015-07-08
DESCRIPTION | 11 MD5 | 70 +- NAMESPACE | 14 R/bootstrap.R | 122 ++- R/densityMclust.R | 6 R/init.R | 92 +- R/mclust.R | 1022 -------------------------------- R/mclustaddson.R | 70 +- R/mclustda.R | 15 R/mclustdr.R | 35 - R/util.R |only R/weights.R | 3 build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/NEWS | 9 inst/doc/mclust.Rmd | 5 inst/doc/mclust.html | 196 +++--- man/MclustBootstrap.Rd | 37 - man/MclustDR.Rd | 27 man/clPairs.Rd | 64 +- man/covw.Rd |only man/errorBars.Rd |only man/mclust.options.Rd | 11 man/mclustBootstrapLRT.Rd | 11 man/plot.MclustBoostrap.Rd |only man/plot.MclustDR.Rd | 4 man/plot.densityMclust.Rd | 2 man/summary.MclustBootstrap.Rd | 4 src/mclust.f | 41 - src/mclustaddson.f | 232 +++---- vignettes/mclust.Rmd | 5 38 files changed, 615 insertions(+), 1493 deletions(-)
Title: A GUI-Based Program to Compute Probabilities Regarding Group
Sequential Designs
Description: A graphical user interface to compute group sequential designs
based on normally distributed test statistics, particularly critical
boundaries, power, drift, and confidence intervals of such designs. All
computations are based on the alpha spending approach by Lan-DeMets with
various alpha spending functions being available to choose among.
Author: Roman Pahl
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between GroupSeq versions 1.3.2 dated 2014-01-10 and 1.3.3 dated 2015-07-08
GroupSeq-1.3.2/GroupSeq/R/asHSdeCani.R |only GroupSeq-1.3.2/GroupSeq/R/asOBF.R |only GroupSeq-1.3.2/GroupSeq/R/asPocock.R |only GroupSeq-1.3.2/GroupSeq/R/asPowerFamily.R |only GroupSeq-1.3.2/GroupSeq/R/outputBounds.R |only GroupSeq-1.3.2/GroupSeq/R/outputDriftWithBounds.R |only GroupSeq-1.3.2/GroupSeq/R/outputForDifferentDrifts.R |only GroupSeq-1.3.3/GroupSeq/DESCRIPTION | 28 - GroupSeq-1.3.3/GroupSeq/MD5 | 71 +-- GroupSeq-1.3.3/GroupSeq/NAMESPACE | 3 GroupSeq-1.3.3/GroupSeq/NEWS | 20 - GroupSeq-1.3.3/GroupSeq/R/alphaByUseFunction.R | 16 GroupSeq-1.3.3/GroupSeq/R/alpha_spending_functions.R |only GroupSeq-1.3.3/GroupSeq/R/calculateEqualBounds.R | 46 +- GroupSeq-1.3.3/GroupSeq/R/calculateTask1.R | 50 +- GroupSeq-1.3.3/GroupSeq/R/calculateTask2.R | 50 +- GroupSeq-1.3.3/GroupSeq/R/calculateTask3.R | 38 - GroupSeq-1.3.3/GroupSeq/R/calculateTask4.R | 42 +- GroupSeq-1.3.3/GroupSeq/R/computeAlphaLevel.R | 60 +-- GroupSeq-1.3.3/GroupSeq/R/computeBounds.R | 102 ++--- GroupSeq-1.3.3/GroupSeq/R/computeConfidenceIntervall.R | 2 GroupSeq-1.3.3/GroupSeq/R/computeCurrentProbability.R | 10 GroupSeq-1.3.3/GroupSeq/R/computeDrift.R | 60 +-- GroupSeq-1.3.3/GroupSeq/R/consoleMode.R | 324 ++++++++--------- GroupSeq-1.3.3/GroupSeq/R/console_output.R |only GroupSeq-1.3.3/GroupSeq/R/findDrift.R | 2 GroupSeq-1.3.3/GroupSeq/R/guiInputTask1.R | 2 GroupSeq-1.3.3/GroupSeq/R/guiInputTask2.R | 2 GroupSeq-1.3.3/GroupSeq/R/guiInputTask3.R | 2 GroupSeq-1.3.3/GroupSeq/R/guiInputTask4.R | 2 GroupSeq-1.3.3/GroupSeq/R/guiMode.R | 12 GroupSeq-1.3.3/GroupSeq/R/guiOutputTask1.R | 82 ++-- GroupSeq-1.3.3/GroupSeq/R/guiOutputTask2.R | 132 +++--- GroupSeq-1.3.3/GroupSeq/R/guiOutputTask3.R | 4 GroupSeq-1.3.3/GroupSeq/R/guiOutputTask4.R | 108 ++--- GroupSeq-1.3.3/GroupSeq/R/jointDensity.R | 22 - GroupSeq-1.3.3/GroupSeq/R/searchForBound.R | 108 ++--- GroupSeq-1.3.3/GroupSeq/R/stdDeviations.R | 12 GroupSeq-1.3.3/GroupSeq/R/tailProbability.R | 8 GroupSeq-1.3.3/GroupSeq/R/useSpendingFunction.R | 180 ++++----- GroupSeq-1.3.3/GroupSeq/man/groupseq.Rd | 2 41 files changed, 804 insertions(+), 798 deletions(-)
Title: Plot Publication-Grade Gene and Genome Maps
Description: Draws gene or genome maps and comparisons between these, in a
publication-grade manner. Starting from simple, common files, it will
draw postscript or pdf files that can be sent as such to journals.
Author: Lionel Guy <lionel.guy@imbim.uu.se>
Maintainer: Lionel Guy <lionel.guy@imbim.uu.se>
Diff between genoPlotR versions 0.8.2 dated 2013-12-23 and 0.8.4 dated 2015-07-08
DESCRIPTION | 27 ++++++++++++++------------- MD5 | 20 ++++++++++---------- NAMESPACE | 9 +++++++++ NEWS | 7 +++++++ R/genoPlotR.R | 2 +- build/vignette.rds |binary data/barto.RData |binary data/chrY_subseg.RData |binary data/mauve_bbone.RData |binary data/three_genes.RData |binary inst/doc/genoPlotR.pdf |binary 11 files changed, 41 insertions(+), 24 deletions(-)
Title: Generic Functions for Cross Validation
Description: Contains generic functions for performing
cross validation and for computing diagnostic errors.
Author: Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between crossval versions 1.0.2 dated 2014-11-14 and 1.0.3 dated 2015-07-08
DESCRIPTION | 15 ++++++++------- MD5 | 8 ++++---- NAMESPACE | 2 +- NEWS | 6 ++++++ man/crossval.package.Rd | 2 +- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Efficient Estimation of Covariance and (Partial) Correlation
Description: Implements a James-Stein-type shrinkage estimator for
the covariance matrix, with separate shrinkage for variances and correlations.
The details of the method are explained in Sch\"afer and Strimmer (2005) and
Opgen-Rhein and Strimmer (2007). The approach is both computationally as well
as statistically very efficient, it is applicable to "small n, large p" data,
and always returns a positive definite and well-conditioned covariance matrix.
In addition to inferring the covariance matrix the package also provides
shrinkage estimators for partial correlations and partial variances.
The inverse of the covariance and correlation matrix
can be efficiently computed, as well as any arbitrary power of the
shrinkage correlation matrix. Furthermore, functions are available for fast
singular value decomposition, for computing the pseudoinverse, and for
checking the rank and positive definiteness of a matrix.
Author: Juliane Sch\"afer, Rainer Opgen-Rhein, Verena Zuber, Miika Ahdesm\"aki,
A. Pedro Duarte Silva, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between corpcor versions 1.6.7 dated 2014-09-29 and 1.6.8 dated 2015-07-08
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 1 + NEWS | 3 +++ man/fast.svd.Rd | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Distributed Gaussian Process Calculations
Description: Distributes Gaussian process calculations across nodes
in a distributed memory setting, using Rmpi. The bigGP class
provides high-level methods for maximum likelihood with normal data,
prediction, calculation of uncertainty (i.e., posterior covariance
calculations), and simulation of realizations. In addition, bigGP
provides an API for basic matrix calculations with distributed
covariance matrices, including Cholesky decomposition, back/forwardsolve,
crossproduct, and matrix multiplication.
Author: Christopher Paciorek [aut, cre],
Benjamin Lipshitz [aut],
Prabhat [ctb],
Cari Kaufman [ctb],
Tina Zhuo [ctb],
Rollin Thomas [ctb]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between bigGP versions 0.1-5 dated 2015-01-21 and 0.1-6 dated 2015-07-08
DESCRIPTION | 14 +++++++------- MD5 | 27 ++++++++++++++------------- NAMESPACE | 5 +++-- NEWS | 6 ++++++ R/bigGP.R | 13 +++++++------ README | 8 ++++++++ README.md |only data/SN2011fe.rda |binary man/SN2011fe.Rd | 8 ++++---- man/bigGP.Rd | 2 +- man/remoteCalcChol.Rd | 6 +++--- man/remoteCrossProdMatSelf.Rd | 5 ++--- man/remoteCrossProdMatVec.Rd | 5 ++--- man/remoteForwardsolve.Rd | 5 ++--- man/remoteMultChol.Rd | 8 ++++---- 15 files changed, 63 insertions(+), 49 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 1.3.0 dated 2015-04-16 and 1.3.1 dated 2015-07-08
DESCRIPTION | 10 ++++---- MD5 | 56 +++++++++++++++++++++++----------------------- NAMESPACE | 4 ++- R/BAT.R | 57 ++++++++++++++++++++++------------------------- man/accuracy.Rd | 2 - man/alpha.Rd | 2 - man/alpha.accum.Rd | 6 ++-- man/alpha.estimate.Rd | 2 - man/arrabida.Rd | 2 - man/beta.Rd | 2 - man/beta.accum.Rd | 2 - man/beta.multi.Rd | 2 - man/contribution.Rd | 2 - man/dispersion.Rd | 2 - man/functree.Rd | 2 - man/geres.Rd | 2 - man/guadiana.Rd | 2 - man/optim.alpha.Rd | 2 - man/optim.alpha.stats.Rd | 2 - man/optim.beta.Rd | 2 - man/optim.beta.stats.Rd | 2 - man/phylotree.Rd | 2 - man/sim.plot.Rd | 2 - man/sim.sad.Rd | 2 - man/sim.sample.Rd | 2 - man/sim.spatial.Rd | 2 - man/sim.tree.Rd | 2 - man/slope.Rd | 2 - man/uniqueness.Rd | 2 - 29 files changed, 90 insertions(+), 91 deletions(-)
Title: Instance Feature Calculation and Evolutionary Instance
Generation for the Traveling Salesman Problem
Description: Instance feature calculation and evolutionary instance generation
for the traveling salesman problem. Also contains code to "morph" two TSP
instances into each other. And the possibility to conveniently run a couple
of solvers on TSP instances.
Author: Bernd Bischl <bernd_bischl@gmx.net>,
Jakob Bossek <jakob.bossek@tu-dortmund.de>,
Olaf Mersmann <olafm@p-value.net>
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between tspmeta versions 1.1 dated 2014-02-25 and 1.2 dated 2015-07-08
tspmeta-1.1/tspmeta/inst/tests |only tspmeta-1.1/tspmeta/tests/run-all.R |only tspmeta-1.2/tspmeta/DESCRIPTION | 12 - tspmeta-1.2/tspmeta/LICENSE | 2 tspmeta-1.2/tspmeta/MD5 | 127 +++++++++---------- tspmeta-1.2/tspmeta/NAMESPACE | 8 + tspmeta-1.2/tspmeta/R/feature_angle.R | 8 - tspmeta-1.2/tspmeta/R/feature_bounding_box.R | 32 ++-- tspmeta-1.2/tspmeta/R/feature_chull.R | 12 + tspmeta-1.2/tspmeta/R/feature_cluster.R | 14 +- tspmeta-1.2/tspmeta/R/feature_distance.R | 2 tspmeta-1.2/tspmeta/R/feature_mst.R | 32 ++-- tspmeta-1.2/tspmeta/R/feature_nnds.R | 6 tspmeta-1.2/tspmeta/R/features.R | 34 ++--- tspmeta-1.2/tspmeta/R/helpers.R | 50 +++---- tspmeta-1.2/tspmeta/R/morph_inst_match.R | 23 +-- tspmeta-1.2/tspmeta/R/numvec_feature_statistics.R | 2 tspmeta-1.2/tspmeta/R/point_matching.R | 80 ++++++----- tspmeta-1.2/tspmeta/R/random_instance.R | 6 tspmeta-1.2/tspmeta/R/read_tsplib_instance.R | 42 +++--- tspmeta-1.2/tspmeta/R/read_tsplib_instances.R | 27 ++-- tspmeta-1.2/tspmeta/R/rescale_instance.R | 18 +- tspmeta-1.2/tspmeta/R/rotation_utilities.R | 123 +++++++++--------- tspmeta-1.2/tspmeta/R/run_solver.R | 24 +-- tspmeta-1.2/tspmeta/R/tour_length.R | 6 tspmeta-1.2/tspmeta/R/tsp_generation_ea.R | 92 +++++++------ tspmeta-1.2/tspmeta/R/tsp_instance.R | 27 +--- tspmeta-1.2/tspmeta/R/zzz.R | 4 tspmeta-1.2/tspmeta/man/as_TSP.Rd | 5 tspmeta-1.2/tspmeta/man/autoplot.tsp_instance.Rd | 15 +- tspmeta-1.2/tspmeta/man/center_of_mass.Rd | 9 - tspmeta-1.2/tspmeta/man/fast_two_opt.Rd | 14 +- tspmeta-1.2/tspmeta/man/feature_angle.Rd | 8 - tspmeta-1.2/tspmeta/man/feature_bounding_box.Rd | 9 - tspmeta-1.2/tspmeta/man/feature_centroid.Rd | 10 - tspmeta-1.2/tspmeta/man/feature_chull.Rd | 10 + tspmeta-1.2/tspmeta/man/feature_cluster.Rd | 12 + tspmeta-1.2/tspmeta/man/feature_distance.Rd | 13 + tspmeta-1.2/tspmeta/man/feature_modes.Rd | 8 - tspmeta-1.2/tspmeta/man/feature_mst.Rd | 12 + tspmeta-1.2/tspmeta/man/feature_nnds.Rd | 9 - tspmeta-1.2/tspmeta/man/features.Rd | 26 ++- tspmeta-1.2/tspmeta/man/get_solvers.Rd | 2 tspmeta-1.2/tspmeta/man/greedy_point_matching.Rd | 18 +- tspmeta-1.2/tspmeta/man/instance_dim.Rd | 5 tspmeta-1.2/tspmeta/man/morph_instances.Rd | 16 +- tspmeta-1.2/tspmeta/man/normalization_angle.Rd | 10 - tspmeta-1.2/tspmeta/man/normalize_rotation.Rd | 8 - tspmeta-1.2/tspmeta/man/number_of_cities.Rd | 5 tspmeta-1.2/tspmeta/man/numvec_feature_statistics.Rd | 22 +-- tspmeta-1.2/tspmeta/man/print.tsp_instance.Rd | 8 - tspmeta-1.2/tspmeta/man/random_instance.Rd | 23 ++- tspmeta-1.2/tspmeta/man/read_tsplib_instance.Rd | 14 +- tspmeta-1.2/tspmeta/man/read_tsplib_instances.Rd | 27 ++-- tspmeta-1.2/tspmeta/man/read_tsplib_tour.Rd | 15 +- tspmeta-1.2/tspmeta/man/remove_zero_distances.Rd | 8 - tspmeta-1.2/tspmeta/man/rescale_instance.Rd | 15 +- tspmeta-1.2/tspmeta/man/rotate_coordinates.Rd | 14 +- tspmeta-1.2/tspmeta/man/rotate_instance.Rd | 16 +- tspmeta-1.2/tspmeta/man/run_solver.Rd | 35 ++--- tspmeta-1.2/tspmeta/man/tsp_generation_ea.Rd | 80 ++++++----- tspmeta-1.2/tspmeta/man/tsp_instance.Rd | 17 +- tspmeta-1.2/tspmeta/tests/testthat |only 63 files changed, 733 insertions(+), 598 deletions(-)
Title: Small Area Estimation
Description: Functions for small area estimation.
Author: Isabel Molina, Yolanda Marhuenda
Maintainer: Yolanda Marhuenda <y.marhuenda@umh.es>
Diff between sae versions 1.0-5 dated 2015-03-30 and 1.1 dated 2015-07-08
DESCRIPTION | 10 ++--- MD5 | 22 ++++++------ NAMESPACE | 1 R/ebBHF.R | 2 - R/eblupFH.R | 77 ++++++++++++++++++++++++++++++++++++++++--- R/mseFH.R | 4 +- inst/CITATION | 43 +++++++----------------- inst/doc/sae_basicdirect.pdf |binary inst/doc/sae_methodology.pdf |binary man/eblupFH.Rd | 10 +++-- man/mseFH.Rd | 8 +++- man/sae-package.Rd | 8 ++-- 12 files changed, 123 insertions(+), 62 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo, ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.28 dated 2015-05-18 and 1.29 dated 2015-07-08
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- NAMESPACE | 4 +++ NEWS | 6 ++++ R/EZR.R | 67 ++++++++++++++++++++++++++++++++++++------------------- inst/CHANGES | 4 +++ inst/doc/EZR.htm | 4 +-- inst/doc/EZR.pdf |binary man/EZR.Rd | 4 +-- 9 files changed, 73 insertions(+), 40 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Group Sequential Bayes Design
Description: Group Sequential Operating Characteristics for Clinical,
Bayesian two-arm Trials with known Sigma and Normal Endpoints.
Author: Florian Gerber, Thomas Gsponer
Maintainer: Florian Gerber <flora.fauna.gerber@gmail.com>
Diff between gsbDesign versions 0.96-2 dated 2013-05-04 and 0.96-3 dated 2015-07-08
gsbDesign-0.96-2/gsbDesign/changeLog |only gsbDesign-0.96-2/gsbDesign/man/gsb-internal.Rd |only gsbDesign-0.96-3/gsbDesign/ChangeLog |only gsbDesign-0.96-3/gsbDesign/DESCRIPTION | 11 ++++++----- gsbDesign-0.96-3/gsbDesign/MD5 | 16 ++++++++-------- gsbDesign-0.96-3/gsbDesign/NAMESPACE | 11 +++++------ gsbDesign-0.96-3/gsbDesign/R/package.r | 2 +- gsbDesign-0.96-3/gsbDesign/inst |only gsbDesign-0.96-3/gsbDesign/man/gsb-package.Rd | 11 +++++------ gsbDesign-0.96-3/gsbDesign/man/gsb.Rd | 11 +++++------ gsbDesign-0.96-3/gsbDesign/man/plot.gsbMainOut.Rd | 3 ++- 11 files changed, 32 insertions(+), 33 deletions(-)
Title: Computation of Spatial Covariance Matrices for Data on
Rectangles
Description: Functions that compute the spatial covariance matrix for the matern and power classes of spatial models, for data that arise on rectangular units. This code can also be used for the change of support problem and for spatial data that arise on irregularly shaped regions like counties or zipcodes by laying a fine grid of rectangles and aggregating the integrals in a form of Riemann integration.
Author: David Clifford <david.clifford+CRAN@gmail.com>
Maintainer: David Clifford <david.clifford+CRAN@gmail.com>
Diff between spatialCovariance versions 0.6-8 dated 2013-04-19 and 0.6-9 dated 2015-07-08
DESCRIPTION | 25 +++++++------------- INDEX |only MD5 | 9 ++++--- NAMESPACE | 3 ++ man/computeV.Rd | 3 +- tests/spatialCovTests.R | 59 +++++++++++++++++++++++++++++++----------------- 6 files changed, 58 insertions(+), 41 deletions(-)
More information about spatialCovariance at CRAN
Permanent link
Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better printing of large matrices via a new generic function
for "pretty" printing, and (iii) a number of convenience functions for users
more familiar with other scientific languages like Julia, Matlab/Octave, or
Python+NumPy.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between ramify versions 0.3.0 dated 2015-06-07 and 0.3.1 dated 2015-07-08
DESCRIPTION | 17 +++-- MD5 | 16 ++--- NAMESPACE | 3 NEWS | 7 ++ R/convenience.R | 6 + R/pprint.R | 25 +++++++ README.md | 5 - man/pprint.Rd | 19 +++++ tests/testthat/test-convenience.R | 121 +++++++++++++++++++------------------- 9 files changed, 135 insertions(+), 84 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometrics and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle <revelle@northwestern.edu>
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 1.5.4 dated 2015-04-27 and 1.5.6 dated 2015-07-08
DESCRIPTION | 12 - MD5 | 156 ++++++++++++------------ NAMESPACE | 16 ++ R/Promax.R | 81 ++++++++++++ R/alpha.R | 21 ++- R/describe.R | 3 R/df2latex.R | 14 +- R/diagram.R | 11 + R/error.crosses.R | 8 - R/fa.R | 18 +- R/fa.ci.R | 5 R/faBy.R | 120 ++++++++++++++----- R/mediate.r | 282 ++++++++++++++++++++++++++++----------------- R/misc.R | 75 +++++++++++ R/pairs.panels.R | 18 +- R/plot.irt.R | 43 +++--- R/principal.R | 2 R/print.psych.R | 89 +++++++++++--- R/scoreOverlap.r | 2 R/set.cor.R | 2 R/statsBy.r | 45 ++++++- R/summary.psych.R | 39 +++--- R/test.psych.r | 14 +- build/vignette.rds |binary data/Bechtoldt.1.rda |binary data/Bechtoldt.2.rda |binary data/Bechtoldt.rda |binary data/Dwyer.rda |binary data/Gleser.rda |binary data/Gorsuch.rda |binary data/Harman.5.rda |binary data/Harman.8.rda |binary data/Harman.political.rda |binary data/Harman.rda |binary data/Holzinger.9.rda |binary data/Holzinger.rda |binary data/Reise.rda |binary data/Schmid.rda |binary data/Thurstone.33.rda |binary data/Thurstone.rda |binary data/Tucker.rda |binary data/ability.rda |binary data/affect.rda |binary data/bfi.dictionary.rda |binary data/bfi.rda |binary data/blot.rda |binary data/bock.rda |binary data/burt.rda |binary data/cities.rda |binary data/cubits.rda |binary data/cushny.rda |binary data/epi.bfi.rda |binary data/epi.dictionary.rda |binary data/epi.rda |binary data/galton.rda |binary data/heights.rda |binary data/income.rda |binary data/iqitems.rda |binary data/msq.rda |binary data/neo.rda |binary data/peas.rda |binary data/sat.act.rda |binary data/vegetables.rda |binary data/withinBetween.rda |binary inst/CITATION | 4 inst/NEWS.Rd | 43 +++++- inst/doc/overview.pdf |binary inst/doc/psych_for_sem.pdf |binary man/alpha.Rd | 2 man/cosinor.Rd | 8 - man/describe.Rd | 4 man/diagram.Rd | 2 man/error.crosses.Rd | 3 man/fa.Rd | 8 - man/mediate.Rd | 22 ++- man/pairs.panels.Rd | 2 man/plot.psych.Rd | 5 man/principal.Rd | 3 man/statsBy.Rd | 10 + 79 files changed, 837 insertions(+), 355 deletions(-)
Title: Simulating from the Polya Posterior
Description: Simulate via Markov chain Monte Carlo (hit-and-run algorithm)
a Dirichlet distribution conditioned to satisfy a finite set of linear
equality and inequality constraints (hence to lie in a convex polytope
that is a subset of the unit simplex).
Author: Glen Meeden <glen@stat.umn.edu> and Radu Lazar
<lazar@stat.umn.edu> and Charles J. Geyer <charlie@stat.umn.edu>
Maintainer: Glen Meeden <glen@stat.umn.edu>
Diff between polyapost versions 1.1-6 dated 2014-04-22 and 1.4-2 dated 2015-07-08
polyapost |only 1 file changed
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-1 dated 2015-06-01 and 1.2-2 dated 2015-07-08
.Rinstignore | 1 + DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 39 +++++++++++++++++++++++---------------- R/colSums.R | 30 +----------------------------- TODO | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 18 +++++++++++++++++- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary man/colSums.Rd | 26 ++++++++++++++++++++++++-- src/dgeMatrix.c | 3 +++ src/t_gCMatrix_colSums.c | 9 +++++++-- 16 files changed, 95 insertions(+), 69 deletions(-)
Title: A Collection of Tools to Conduct Levins' Loop Analysis
Description: Loop analysis makes qualitative predictions of variable change in a system of causally interdependent variables, where "qualitative" means sign only (i.e. increases, decreases, non change, and ambiguous). This implementation includes output support for graphs in .dot file format for use with visualization software such as graphviz (graphviz.org). 'LoopAnalyst' provides tools for the construction and output of community matrices, computation and output of community effect matrices, tables of correlations, adjoint, absolute feedback, weighted feedback and weighted prediction matrices, change in life expectancy matrices, and feedback, path and loop enumeration tools.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between LoopAnalyst versions 1.2-3 dated 2013-07-10 and 1.2-4 dated 2015-07-08
LoopAnalyst-1.2-3/LoopAnalyst/LoopAnalyst-Ex.R |only LoopAnalyst-1.2-3/LoopAnalyst/data/cm.zavaleta.rda |only LoopAnalyst-1.2-3/LoopAnalyst/man/cm.zavaleta.Rd |only LoopAnalyst-1.2-4/LoopAnalyst/DESCRIPTION | 14 +--- LoopAnalyst-1.2-4/LoopAnalyst/MD5 | 43 ++++++-------- LoopAnalyst-1.2-4/LoopAnalyst/R/feedback.R | 15 ++-- LoopAnalyst-1.2-4/LoopAnalyst/R/make.cem.R | 4 - LoopAnalyst-1.2-4/LoopAnalyst/data/cem.levins.rda |binary LoopAnalyst-1.2-4/LoopAnalyst/data/cm.dambacher.rda |only LoopAnalyst-1.2-4/LoopAnalyst/data/cm.levins.rda |binary LoopAnalyst-1.2-4/LoopAnalyst/data/submatrix.rda |binary LoopAnalyst-1.2-4/LoopAnalyst/man/cem.levins.Rd | 2 LoopAnalyst-1.2-4/LoopAnalyst/man/cm.dambacher.Rd |only LoopAnalyst-1.2-4/LoopAnalyst/man/cm.levins.Rd | 2 LoopAnalyst-1.2-4/LoopAnalyst/man/graph.cem.Rd | 6 - LoopAnalyst-1.2-4/LoopAnalyst/man/graph.cm.Rd | 4 - LoopAnalyst-1.2-4/LoopAnalyst/man/make.T.Rd | 8 +- LoopAnalyst-1.2-4/LoopAnalyst/man/make.adjoint.Rd | 6 - LoopAnalyst-1.2-4/LoopAnalyst/man/make.clem.Rd | 2 LoopAnalyst-1.2-4/LoopAnalyst/man/make.cm.Rd | 2 LoopAnalyst-1.2-4/LoopAnalyst/man/make.wfm.Rd | 6 - LoopAnalyst-1.2-4/LoopAnalyst/man/out.cm.Rd | 4 - LoopAnalyst-1.2-4/LoopAnalyst/man/save.cm.Rd | 2 LoopAnalyst-1.2-4/LoopAnalyst/man/submatrix.Rd | 4 - LoopAnalyst-1.2-4/LoopAnalyst/man/weighted.predictions.Rd | 8 +- 25 files changed, 64 insertions(+), 68 deletions(-)
Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Description: Estimates both tail area-based false
discovery rates (Fdr) as well as local false discovery rates (fdr) for a
variety of null models (p-values, z-scores, correlation coefficients,
t-scores). The proportion of null values and the parameters of the null
distribution are adaptively estimated from the data. In addition, the package
contains functions for non-parametric density estimation (Grenander estimator),
for monotone regression (isotonic regression and antitonic regression with weights),
for computing the greatest convex minorant (GCM) and the least concave majorant (LCM),
for the half-normal and correlation distributions, and for computing
empirical higher criticism (HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between fdrtool versions 1.2.14 dated 2015-03-09 and 1.2.15 dated 2015-07-08
fdrtool |only 1 file changed
Title: Client for the 'Enigma' 'API'
Description: The company 'Enigma' (https://enigma.io) holds many public 'datasets' from
governments, companies, universities, and organizations. 'Enigma' provides an
'API' for data, 'metadata', and statistics on each of the 'datasets'. 'enigma' is
a client to interact with the 'Enigma' 'API', including getting the data
and 'metadata' for 'datasets' in 'Enigma', as well as collecting statistics on
'datasets'. In addition, you can download a 'gzipped' 'csv' file of a 'dataset'
if you want the whole 'dataset'. An 'API' key from 'Enigma' is required to use
'enigma'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between enigma versions 0.1.1 dated 2014-12-11 and 0.2.0 dated 2015-07-08
enigma-0.1.1/enigma/NEWS |only enigma-0.1.1/enigma/man/error_handler.Rd |only enigma-0.1.1/enigma/vignettes/figure |only enigma-0.2.0/enigma/DESCRIPTION | 29 - enigma-0.2.0/enigma/LICENSE | 4 enigma-0.2.0/enigma/MD5 | 63 +- enigma-0.2.0/enigma/NAMESPACE | 22 enigma-0.2.0/enigma/R/enigma-package.r | 4 enigma-0.2.0/enigma/R/enigma_data.r | 59 +- enigma-0.2.0/enigma/R/enigma_fetch.r | 62 +- enigma-0.2.0/enigma/R/enigma_metadata.r | 3 enigma-0.2.0/enigma/R/enigma_stats.r | 32 - enigma-0.2.0/enigma/R/rate_limit.R | 18 enigma-0.2.0/enigma/R/tbldf_utils.R |only enigma-0.2.0/enigma/R/zzz.r | 16 enigma-0.2.0/enigma/README.md | 81 +- enigma-0.2.0/enigma/build/vignette.rds |binary enigma-0.2.0/enigma/inst/assets/figure/unnamed-chunk-16-1.png |only enigma-0.2.0/enigma/inst/assets/figure/unnamed-chunk-17-1.png |only enigma-0.2.0/enigma/inst/doc/enigma_vignette.Rmd | 288 ++++------ enigma-0.2.0/enigma/inst/doc/enigma_vignette.html | 274 ++++----- enigma-0.2.0/enigma/inst/vign/enigma_vignette.Rmd | 12 enigma-0.2.0/enigma/inst/vign/enigma_vignette.md | 288 ++++------ enigma-0.2.0/enigma/inst/vign/figure/unnamed-chunk-16-1.png |binary enigma-0.2.0/enigma/inst/vign/figure/unnamed-chunk-17-1.png |only enigma-0.2.0/enigma/man/enigma.Rd | 5 enigma-0.2.0/enigma/man/enigma_data.Rd | 25 enigma-0.2.0/enigma/man/enigma_fetch.Rd | 52 + enigma-0.2.0/enigma/man/enigma_metadata.Rd | 3 enigma-0.2.0/enigma/man/enigma_stats.Rd | 18 enigma-0.2.0/enigma/man/rate_limit.Rd | 3 enigma-0.2.0/enigma/man/type_sum.Rd |only enigma-0.2.0/enigma/tests/testthat.R |only enigma-0.2.0/enigma/tests/testthat/test-enigma_data.R | 12 enigma-0.2.0/enigma/tests/testthat/test-enigma_metadata.R | 6 enigma-0.2.0/enigma/tests/testthat/test-enigma_stats.R | 6 enigma-0.2.0/enigma/vignettes/enigma_vignette.Rmd | 288 ++++------ 37 files changed, 892 insertions(+), 781 deletions(-)
Title: Circular Visualization in R
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.2.4 dated 2015-03-20 and 0.2.5 dated 2015-07-08
circlize |only 1 file changed
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC'
climate 'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with
functions for each of the 'API' 'endpoints': data, data categories, data sets,
data types, locations, location categories, and stations. In addition, we
have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory,
'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data,
'NOAA' storm data via 'IBTrACS', and tornado data via the 'NOAA' storm prediction
center.
Author: Hart Edmund [ctb],
Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Adam Erickson [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.4.0 dated 2015-06-19 and 0.4.2 dated 2015-07-07
rnoaa-0.4.0/rnoaa/NEWS |only rnoaa-0.4.0/rnoaa/R/ncdc_legacy.R |only rnoaa-0.4.0/rnoaa/man/ncdc_legacy.Rd |only rnoaa-0.4.2/rnoaa/DESCRIPTION | 12 rnoaa-0.4.2/rnoaa/MD5 | 169 +++++++------- rnoaa-0.4.2/rnoaa/NAMESPACE | 15 - rnoaa-0.4.2/rnoaa/R/defunct.R | 43 +++ rnoaa-0.4.2/rnoaa/R/ghcnd.R | 2 rnoaa-0.4.2/rnoaa/R/homr.R | 59 ++-- rnoaa-0.4.2/rnoaa/R/homr_definitions.R | 8 rnoaa-0.4.2/rnoaa/R/isd.R | 29 +- rnoaa-0.4.2/rnoaa/R/ncdc.r | 7 rnoaa-0.4.2/rnoaa/R/ncdc_combine.r | 107 -------- rnoaa-0.4.2/rnoaa/R/ncdc_datacats.r | 9 rnoaa-0.4.2/rnoaa/R/ncdc_datasets.r | 6 rnoaa-0.4.2/rnoaa/R/ncdc_datatypes.r | 4 rnoaa-0.4.2/rnoaa/R/ncdc_locs.r | 4 rnoaa-0.4.2/rnoaa/R/ncdc_locs_cats.r | 6 rnoaa-0.4.2/rnoaa/R/ncdc_plot.r | 2 rnoaa-0.4.2/rnoaa/R/ncdc_stations.r | 5 rnoaa-0.4.2/rnoaa/R/rnoaa-package.r | 3 rnoaa-0.4.2/rnoaa/R/seaice.r | 20 - rnoaa-0.4.2/rnoaa/R/storm_shp.R | 40 +-- rnoaa-0.4.2/rnoaa/R/storms.R | 37 +-- rnoaa-0.4.2/rnoaa/R/swdi.r | 8 rnoaa-0.4.2/rnoaa/R/tornadoes.R | 9 rnoaa-0.4.2/rnoaa/README.md | 181 +++++---------- rnoaa-0.4.2/rnoaa/build/vignette.rds |binary rnoaa-0.4.2/rnoaa/inst/doc/buoy_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/doc/buoy_vignette.html | 1 rnoaa-0.4.2/rnoaa/inst/doc/homr_vignette.Rmd | 75 +++--- rnoaa-0.4.2/rnoaa/inst/doc/homr_vignette.html | 75 +++--- rnoaa-0.4.2/rnoaa/inst/doc/ncdc_attributes.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/doc/ncdc_attributes.html | 1 rnoaa-0.4.2/rnoaa/inst/doc/ncdc_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/doc/ncdc_vignette.html | 3 rnoaa-0.4.2/rnoaa/inst/doc/ncdc_workflow.Rmd | 9 rnoaa-0.4.2/rnoaa/inst/doc/ncdc_workflow.html | 9 rnoaa-0.4.2/rnoaa/inst/doc/seaice_vignette.Rmd | 14 - rnoaa-0.4.2/rnoaa/inst/doc/seaice_vignette.html | 12 rnoaa-0.4.2/rnoaa/inst/doc/storms_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/doc/storms_vignette.html | 1 rnoaa-0.4.2/rnoaa/inst/doc/swdi_vignette.Rmd | 9 rnoaa-0.4.2/rnoaa/inst/doc/swdi_vignette.html | 9 rnoaa-0.4.2/rnoaa/inst/vign/buoy_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/buoy_vignette.md | 1 rnoaa-0.4.2/rnoaa/inst/vign/figure/unnamed-chunk-3-1.png |binary rnoaa-0.4.2/rnoaa/inst/vign/homr_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/homr_vignette.md | 75 +++--- rnoaa-0.4.2/rnoaa/inst/vign/myfile.kmz |binary rnoaa-0.4.2/rnoaa/inst/vign/myfile.zip |binary rnoaa-0.4.2/rnoaa/inst/vign/ncdc_attributes.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/ncdc_attributes.md | 1 rnoaa-0.4.2/rnoaa/inst/vign/ncdc_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/ncdc_vignette.md | 1 rnoaa-0.4.2/rnoaa/inst/vign/ncdc_workflow.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/ncdc_workflow.md | 9 rnoaa-0.4.2/rnoaa/inst/vign/seaice_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/seaice_vignette.md | 14 - rnoaa-0.4.2/rnoaa/inst/vign/storms_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/storms_vignette.md | 1 rnoaa-0.4.2/rnoaa/inst/vign/swdi_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/inst/vign/swdi_vignette.md | 9 rnoaa-0.4.2/rnoaa/man/homr.Rd | 8 rnoaa-0.4.2/rnoaa/man/homr_definitions.Rd | 4 rnoaa-0.4.2/rnoaa/man/isd.Rd | 5 rnoaa-0.4.2/rnoaa/man/ncdc.Rd | 4 rnoaa-0.4.2/rnoaa/man/ncdc_datasets.Rd | 4 rnoaa-0.4.2/rnoaa/man/ncdc_datatypes.Rd | 4 rnoaa-0.4.2/rnoaa/man/ncdc_leg_data-defunct.Rd |only rnoaa-0.4.2/rnoaa/man/ncdc_leg_site_info-defunct.Rd |only rnoaa-0.4.2/rnoaa/man/ncdc_leg_sites-defunct.Rd |only rnoaa-0.4.2/rnoaa/man/ncdc_leg_variables-defunct.Rd |only rnoaa-0.4.2/rnoaa/man/ncdc_stations.Rd | 20 - rnoaa-0.4.2/rnoaa/man/rnoaa-defunct.Rd | 11 rnoaa-0.4.2/rnoaa/man/seaice.Rd | 13 - rnoaa-0.4.2/rnoaa/man/storms.Rd | 14 - rnoaa-0.4.2/rnoaa/man/swdi.Rd | 2 rnoaa-0.4.2/rnoaa/man/tornadoes.Rd | 4 rnoaa-0.4.2/rnoaa/tests/testthat/test-ncdc_legacy.R | 10 rnoaa-0.4.2/rnoaa/tests/testthat/test-storms.R | 4 rnoaa-0.4.2/rnoaa/vignettes/buoy_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/vignettes/homr_vignette.Rmd | 75 +++--- rnoaa-0.4.2/rnoaa/vignettes/ncdc_attributes.Rmd | 1 rnoaa-0.4.2/rnoaa/vignettes/ncdc_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/vignettes/ncdc_workflow.Rmd | 9 rnoaa-0.4.2/rnoaa/vignettes/seaice_vignette.Rmd | 14 - rnoaa-0.4.2/rnoaa/vignettes/storms_vignette.Rmd | 1 rnoaa-0.4.2/rnoaa/vignettes/swdi_vignette.Rmd | 9 89 files changed, 652 insertions(+), 692 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e., clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.4 dated 2015-05-17 and 1.1.5 dated 2015-07-07
DESCRIPTION | 14 +++--- MD5 | 34 +++++++-------- NAMESPACE | 10 ++++ NEWS | 7 +++ R/Clickstream.r | 2 R/Fitting.r | 82 +++++++++++++++++++++++++++++++------ R/MarkovChain.r | 5 +- R/clickstream-package.R | 7 ++- man/Pattern-class.Rd | 4 - man/clickstream-package.Rd | 2 man/clusterClickstreams.Rd | 4 - man/fitMarkovChain.Rd | 21 ++++++--- man/predict-methods.Rd | 6 +- man/predict.ClickstreamClusters.Rd | 12 ++--- man/randomClicks-methods.Rd | 11 ++-- man/readClickstreams.Rd | 4 - man/transientStates-methods.Rd | 6 +- man/writeClickstreams.Rd | 14 +++--- 18 files changed, 165 insertions(+), 80 deletions(-)
Title: Parameter Space Exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Also implements the PLUE method.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom <andrechalom@gmail.com>
Diff between pse versions 0.4.0 dated 2014-12-20 and 0.4.2 dated 2015-07-07
pse-0.4.0/pse/Changelog |only pse-0.4.2/pse/DESCRIPTION | 13 +++++++------ pse-0.4.2/pse/MD5 | 25 +++++++++++++------------ pse-0.4.2/pse/NAMESPACE | 3 +-- pse-0.4.2/pse/NEWS |only pse-0.4.2/pse/R/PLUE.R | 7 +++++-- pse-0.4.2/pse/R/cluster.R | 6 +++--- pse-0.4.2/pse/R/external.R | 8 ++++---- pse-0.4.2/pse/R/pic.R | 2 +- pse-0.4.2/pse/README.md |only pse-0.4.2/pse/build/vignette.rds |binary pse-0.4.2/pse/inst/doc/multiple.pdf |binary pse-0.4.2/pse/inst/doc/pse_tutorial.pdf |binary pse-0.4.2/pse/man/LHS.Rd | 3 +-- pse-0.4.2/pse/man/PLUE.Rd | 19 ------------------- 15 files changed, 35 insertions(+), 51 deletions(-)
Title: Bayesian Methods for Identifying the Most Harmful Medication
Errors
Description: Two distinct but related statistical approaches to the problem of identifying the combinations of medication error characteristics that are more likely to result in harm are implemented in this package: 1) a Bayesian hierarchical model with optimal Bayesian ranking on the log odds of harm, and 2) an empirical Bayes model that estimates the ratio of the observed count of harm to the count that would be expected if error characteristics and harm were independent. In addition, for the Bayesian hierarchical model, the package provides functions to assess the sensitivity of results to different specifications of the random effects distributions.
Author: Sergio Venturini, Jessica Myers
Maintainer: Sergio Venturini <sergio.venturini@unibocconi.it>
Diff between mederrRank versions 0.0.7 dated 2012-11-17 and 0.0.8 dated 2015-07-07
DESCRIPTION | 22 +++++++--------------- MD5 | 6 +++--- NAMESPACE | 6 +++--- R/AllClasses.R | 28 ++++++++++++++-------------- 4 files changed, 27 insertions(+), 35 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown <patrick.brown@utoronto.ca> [aut, cre]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.2.4 dated 2015-05-21 and 1.3.1 dated 2015-07-07
mapmisc-1.2.4/mapmisc/inst/doc/mapLayers.R |only mapmisc-1.2.4/mapmisc/inst/doc/mapmisc.R |only mapmisc-1.3.1/mapmisc/DESCRIPTION | 16 - mapmisc-1.3.1/mapmisc/MD5 | 52 +-- mapmisc-1.3.1/mapmisc/NAMESPACE | 15 - mapmisc-1.3.1/mapmisc/R/geonames.R | 33 +- mapmisc-1.3.1/mapmisc/R/getTiles.R | 348 ++++++++++--------------- mapmisc-1.3.1/mapmisc/R/insetMap.R | 56 ++-- mapmisc-1.3.1/mapmisc/R/legendBreaks.R | 2 mapmisc-1.3.1/mapmisc/R/map.new.R | 7 mapmisc-1.3.1/mapmisc/R/omerc.R | 11 mapmisc-1.3.1/mapmisc/R/openmap.R | 55 ++- mapmisc-1.3.1/mapmisc/R/openmapAttribution.R | 106 +++++++ mapmisc-1.3.1/mapmisc/R/scaleBar.R | 21 - mapmisc-1.3.1/mapmisc/R/utils.R | 72 +++-- mapmisc-1.3.1/mapmisc/build/vignette.rds |binary mapmisc-1.3.1/mapmisc/inst/doc/mapLayers.pdf |binary mapmisc-1.3.1/mapmisc/inst/doc/mapLayers.rnw | 7 mapmisc-1.3.1/mapmisc/inst/doc/mapmisc.pdf |binary mapmisc-1.3.1/mapmisc/inst/extdata/tiles.RData |binary mapmisc-1.3.1/mapmisc/man/crsMerc.Rd |only mapmisc-1.3.1/mapmisc/man/geonames.Rd | 6 mapmisc-1.3.1/mapmisc/man/legendBreaks.Rd | 2 mapmisc-1.3.1/mapmisc/man/omerc.Rd | 4 mapmisc-1.3.1/mapmisc/man/openmap.Rd | 4 mapmisc-1.3.1/mapmisc/man/scaleBar.Rd | 7 mapmisc-1.3.1/mapmisc/tests/north.R |only mapmisc-1.3.1/mapmisc/tests/openmap.R | 23 + mapmisc-1.3.1/mapmisc/vignettes/mapLayers.rnw | 7 29 files changed, 500 insertions(+), 354 deletions(-)
Title: Gamma Shape Mixture
Description: Implementation of a Bayesian approach for estimating a mixture of gamma distributions in which the mixing occurs over the shape parameter. This family provides a flexible and novel approach for modeling heavy-tailed distributions, it is computationally efficient, and it only requires to specify a prior distribution for a single parameter.
Author: Sergio Venturini
Maintainer: Sergio Venturini <sergio.venturini@unibocconi.it>
Diff between GSM versions 1.3.1 dated 2014-02-24 and 1.3.2 dated 2015-07-07
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- NAMESPACE | 4 ++++ 3 files changed, 12 insertions(+), 9 deletions(-)
Title: Objective Bayesian Testing for the Hardy-Weinberg Equilibrium
Problem
Description: General (multi-allelic) Hardy-Weinberg equilibrium problem from an objective Bayesian testing standpoint. This aim is achieved through the identification of a class of priors specifically designed for this testing problem. A class of intrinsic priors under the full model is considered. This class is indexed by a tuning quantity, the training sample size, as discussed in Consonni, Moreno and Venturini (2010). These priors are objective, satisfy Savage's continuity condition and have proved to behave extremely well for many statistical testing problems.
Author: Sergio Venturini
Maintainer: Sergio Venturini <sergio.venturini@unibocconi.it>
Diff between HWEintrinsic versions 1.2.1 dated 2012-11-17 and 1.2.2 dated 2015-07-07
DESCRIPTION | 21 +++++++-------------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 7 ++++--- man/GuoThompson8.Rd | 10 ++++++++-- man/GuoThompson9.Rd | 11 ++++++++--- man/Lindley.Rd | 5 ++++- man/LouisDempster.Rd | 10 ++++++++-- man/Wordsworth.Rd | 10 ++++++++-- man/cip.2.Rd | 5 ++++- man/hwe.ibf.Rd | 5 ++++- man/hwe.ibf.mc.Rd | 10 ++++++++-- man/hwe.ibf.plot.Rd | 14 ++++++++------ man/ip.2.Rd | 5 ++++- man/lik.multin.Rd | 9 +++++---- man/simdata.Rd | 9 +++++---- 15 files changed, 99 insertions(+), 60 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.2.1 dated 2015-02-27 and 1.3.4 dated 2015-07-07
DESCRIPTION | 22 - MD5 | 80 ++- NAMESPACE | 23 + R/0gm.R | 7 R/NNmat.R |only R/RFsimulate.R | 11 R/boxcox.R |only R/excProb.R | 9 R/glgm.R | 80 ++- R/krige.R | 17 R/lgm.R | 112 ++++- R/lgm.Raster.R | 220 +++++----- R/loglikGmrf.R | 1021 ++++++++++++++++++++----------------------------- R/loglikLgm.R | 57 +- R/maternGmrfPrec.R | 147 ------- R/profLlgm.R | 72 ++- R/simLgcp.R | 8 R/squareRaster.R | 2 R/utils.R | 2 R/variog.R | 11 data/gambiaUTM.RData |binary data/loaloa.RData |binary data/murder.RData |binary data/nn32.RData |binary data/rongelapUTM.RData |binary data/swissRain.RData |binary data/swissRainR.RData |binary data/torontoPop.RData |binary data/wheat.RData |binary man/RFsimulate.Rd | 3 man/glgm.Rd | 5 man/inla.models.Rd | 3 man/krige.Rd | 2 man/lgm.Rd | 28 - man/swissRain.Rd | 7 src/Makevars | 3 src/gmrfLik.c |only src/maternLogL.c | 14 src/maternLogLopt.c | 4 src/optimize.c |only tests/glgm.R | 37 + tests/lgcp.R | 14 tests/lgmRaster.R | 36 - 43 files changed, 999 insertions(+), 1058 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.1.6 dated 2015-05-16 and 1.2.0 dated 2015-07-07
EpiModel-1.1.6/EpiModel/man/node_active.Rd |only EpiModel-1.2.0/EpiModel/DESCRIPTION | 16 EpiModel-1.2.0/EpiModel/MD5 | 120 - EpiModel-1.2.0/EpiModel/NAMESPACE | 40 EpiModel-1.2.0/EpiModel/NEWS | 41 EpiModel-1.2.0/EpiModel/R/EpiModel-package.r | 18 EpiModel-1.2.0/EpiModel/R/as.data.frame.R | 35 EpiModel-1.2.0/EpiModel/R/control.R | 80 - EpiModel-1.2.0/EpiModel/R/get.R | 47 EpiModel-1.2.0/EpiModel/R/init.R | 26 EpiModel-1.2.0/EpiModel/R/merge.R | 29 EpiModel-1.2.0/EpiModel/R/net.mod.getprev.R |only EpiModel-1.2.0/EpiModel/R/net.mod.simnet.R | 22 EpiModel-1.2.0/EpiModel/R/net.mod.vital.R | 2 EpiModel-1.2.0/EpiModel/R/net.utils.R | 449 ------ EpiModel-1.2.0/EpiModel/R/netdx.R | 34 EpiModel-1.2.0/EpiModel/R/netest.R | 79 - EpiModel-1.2.0/EpiModel/R/netsim.R | 40 EpiModel-1.2.0/EpiModel/R/param.R | 64 EpiModel-1.2.0/EpiModel/R/plot.R | 1043 +++++++++------ EpiModel-1.2.0/EpiModel/R/print.r | 30 EpiModel-1.2.0/EpiModel/R/shiny.R | 9 EpiModel-1.2.0/EpiModel/R/summary.R | 115 - EpiModel-1.2.0/EpiModel/R/test.R | 92 - EpiModel-1.2.0/EpiModel/R/verbose.R | 28 EpiModel-1.2.0/EpiModel/build/vignette.rds |binary EpiModel-1.2.0/EpiModel/inst/doc/Intro.html | 2 EpiModel-1.2.0/EpiModel/man/EpiModel-package.Rd | 4 EpiModel-1.2.0/EpiModel/man/calc_eql.Rd | 5 EpiModel-1.2.0/EpiModel/man/edgelist_censor.Rd | 12 EpiModel-1.2.0/EpiModel/man/edgelist_meanage.Rd | 8 EpiModel-1.2.0/EpiModel/man/epiweb.Rd | 4 EpiModel-1.2.0/EpiModel/man/get_network.Rd | 16 EpiModel-1.2.0/EpiModel/man/get_nwstats.Rd | 15 EpiModel-1.2.0/EpiModel/man/get_prev.net.Rd | 2 EpiModel-1.2.0/EpiModel/man/get_transmat.Rd | 16 EpiModel-1.2.0/EpiModel/man/merge.netsim.Rd | 13 EpiModel-1.2.0/EpiModel/man/netdx.Rd | 12 EpiModel-1.2.0/EpiModel/man/netest.Rd | 47 EpiModel-1.2.0/EpiModel/man/netsim.Rd | 27 EpiModel-1.2.0/EpiModel/man/netsim_parallel.Rd | 5 EpiModel-1.2.0/EpiModel/man/plot.icm.Rd | 47 EpiModel-1.2.0/EpiModel/man/plot.netdx.Rd | 87 - EpiModel-1.2.0/EpiModel/man/plot.netsim.Rd | 137 + EpiModel-1.2.0/EpiModel/man/summary.netest.Rd | 4 EpiModel-1.2.0/EpiModel/man/summary.netsim.Rd | 19 EpiModel-1.2.0/EpiModel/tests/testthat/test-dcm-long.R | 174 ++ EpiModel-1.2.0/EpiModel/tests/testthat/test-get.R | 11 EpiModel-1.2.0/EpiModel/tests/testthat/test-icm-long.R | 455 +----- EpiModel-1.2.0/EpiModel/tests/testthat/test-merge.R | 122 + EpiModel-1.2.0/EpiModel/tests/testthat/test-net-long.R | 420 ++---- EpiModel-1.2.0/EpiModel/tests/testthat/test-netattr.R | 64 EpiModel-1.2.0/EpiModel/tests/testthat/test-netdx.R | 157 -- EpiModel-1.2.0/EpiModel/tests/testthat/test-netest.R | 67 EpiModel-1.2.0/EpiModel/tests/testthat/test-netoffset.R | 23 EpiModel-1.2.0/EpiModel/tests/testthat/test-netpids.R | 20 EpiModel-1.2.0/EpiModel/tests/testthat/test-netrestart.R | 31 EpiModel-1.2.0/EpiModel/tests/testthat/test-netsim.R | 12 EpiModel-1.2.0/EpiModel/tests/testthat/test-netvary.R | 28 EpiModel-1.2.0/EpiModel/tests/testthat/test-newnet.R | 60 EpiModel-1.2.0/EpiModel/tests/testthat/test-print.R |only EpiModel-1.2.0/EpiModel/tests/testthat/test-shiny.R |only EpiModel-1.2.0/EpiModel/tests/testthat/test-utils.R | 84 - 63 files changed, 2013 insertions(+), 2656 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between diseasemapping versions 1.2.0 dated 2015-03-25 and 1.2.3 dated 2015-07-07
diseasemapping-1.2.0/diseasemapping/R/excProb.R |only diseasemapping-1.2.0/diseasemapping/man/excProb.Rd |only diseasemapping-1.2.3/diseasemapping/DESCRIPTION | 14 +++---- diseasemapping-1.2.3/diseasemapping/MD5 | 22 +++++------- diseasemapping-1.2.3/diseasemapping/NAMESPACE | 6 ++- diseasemapping-1.2.3/diseasemapping/R/cancerRates.R | 5 +- diseasemapping-1.2.3/diseasemapping/R/getSMR.R | 2 + diseasemapping-1.2.3/diseasemapping/data/casedata.RData |binary diseasemapping-1.2.3/diseasemapping/data/kentucky.RData |binary diseasemapping-1.2.3/diseasemapping/data/popdata.RData |binary diseasemapping-1.2.3/diseasemapping/data/referencepop.RData |binary diseasemapping-1.2.3/diseasemapping/man/bym.Rd | 2 - diseasemapping-1.2.3/diseasemapping/man/inla.models.Rd | 2 - 13 files changed, 28 insertions(+), 25 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Concordance Correlation Coefficient for Repeated (and
Non-Repeated) Measures
Description: Estimates the Concordance Correlation Coefficient to assess agreement. The scenarios considered are non-repeated measures, non-longitudinal repeated measures (replicates) and longitudinal repeated measures. The estimation approaches implemented are variance components and U-statistics approaches.
Author: Josep Lluis Carrasco <jlcarrasco@ub.edu>, Josep Puig Martinez
<j.puig04@gmail.com>
Maintainer: Josep Lluis Carrasco <jlcarrasco@ub.edu>
Diff between cccrm versions 1.1 dated 2012-04-10 and 1.2.1 dated 2015-07-07
cccrm-1.1/cccrm/R/ccc-internal.R |only cccrm-1.1/cccrm/R/cccUst.default.R |only cccrm-1.1/cccrm/R/ccclon.default.R |only cccrm-1.1/cccrm/R/ccclonw.default.R |only cccrm-1.1/cccrm/R/cccvc1.default.R |only cccrm-1.1/cccrm/R/cccvc2.default.R |only cccrm-1.1/cccrm/R/print.ccclon.R |only cccrm-1.1/cccrm/R/print.ccclonw.R |only cccrm-1.1/cccrm/R/print.cccvc1.R |only cccrm-1.1/cccrm/R/print.cccvc2.R |only cccrm-1.1/cccrm/R/print.summary.cccUst.R |only cccrm-1.1/cccrm/R/print.summary.ccclon.R |only cccrm-1.1/cccrm/R/print.summary.ccclonw.R |only cccrm-1.1/cccrm/R/print.summary.cccvc1.R |only cccrm-1.1/cccrm/R/print.summary.cccvc2.R |only cccrm-1.1/cccrm/R/summary.cccUst.R |only cccrm-1.1/cccrm/R/summary.ccclon.R |only cccrm-1.1/cccrm/R/summary.ccclonw.R |only cccrm-1.1/cccrm/R/summary.cccvc1.R |only cccrm-1.1/cccrm/R/summary.cccvc2.R |only cccrm-1.1/cccrm/data/bdaw.rda |only cccrm-1.1/cccrm/data/bfat.rda |only cccrm-1.1/cccrm/data/bpres.rda |only cccrm-1.1/cccrm/man/ccc-internal.Rd |only cccrm-1.1/cccrm/man/cccrm.Rd |only cccrm-1.2.1/cccrm/DESCRIPTION | 22 +-- cccrm-1.2.1/cccrm/MD5 | 64 +++-------- cccrm-1.2.1/cccrm/NAMESPACE | 43 ++----- cccrm-1.2.1/cccrm/R/cccUst.R | 91 +++++++++++++++ cccrm-1.2.1/cccrm/R/ccclon.R | 153 ++++++++++++++++++++++++++ cccrm-1.2.1/cccrm/R/ccclonw.R | 172 +++++++++++++++++++++++++++++- cccrm-1.2.1/cccrm/R/cccvc.R | 4 cccrm-1.2.1/cccrm/R/cccvc1.R | 111 +++++++++++++++++++ cccrm-1.2.1/cccrm/R/cccvc2.R | 100 +++++++++++++++++ cccrm-1.2.1/cccrm/R/ic.ccc.R | 15 +- cccrm-1.2.1/cccrm/R/print.ccc.R |only cccrm-1.2.1/cccrm/R/print.cccUst.R | 15 +- cccrm-1.2.1/cccrm/R/summary.ccc.R |only cccrm-1.2.1/cccrm/data/bdaw.txt |only cccrm-1.2.1/cccrm/data/bfat.txt |only cccrm-1.2.1/cccrm/data/bpres.txt |only cccrm-1.2.1/cccrm/man/bdaw.Rd | 21 +-- cccrm-1.2.1/cccrm/man/bfat.Rd | 21 +-- cccrm-1.2.1/cccrm/man/bpres.Rd | 27 +--- cccrm-1.2.1/cccrm/man/cccUst.Rd | 103 ++++++++--------- cccrm-1.2.1/cccrm/man/ccclon.Rd | 96 +++++++++------- cccrm-1.2.1/cccrm/man/ccclonw.Rd | 100 ++++++++++------- cccrm-1.2.1/cccrm/man/cccvc.Rd | 123 ++++++++++----------- 48 files changed, 946 insertions(+), 335 deletions(-)
Title: Multi-Class Discriminant Analysis using Binary Predictors
Description: The "binda" package implements functions for multi-class
discriminant analysis using binary predictors, for corresponding
variable selection, and for dichotomizing continuous data.
Author: Sebastian Gibb and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between binda versions 1.0.2 dated 2015-03-05 and 1.0.3 dated 2015-07-07
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NAMESPACE | 9 ++++++--- NEWS | 6 ++++++ man/binda.Rd | 2 +- man/binda.package.Rd | 4 ++-- man/dichotomize.Rd | 2 +- 7 files changed, 28 insertions(+), 18 deletions(-)
Title: Penn World Table (Version 8.x)
Description: The Penn World Table 8.x provides information on relative levels of
income, output, inputs, and productivity for 167 countries
between 1950 and 2011.
Author: Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between pwt8 versions 8.0-0 dated 2013-07-28 and 8.1-0 dated 2015-07-07
DESCRIPTION | 16 ++++++++-------- MD5 | 13 ++++++++----- NEWS | 7 +++++++ data/datalist |only data/pwt8.0.rda |binary data/pwt8.1.rda |only inst/CITATION | 16 ++++++++-------- man/pwt8.0.Rd | 23 +++++++++++++---------- man/pwt8.1.Rd |only 9 files changed, 44 insertions(+), 31 deletions(-)
Title: Densities and Sampling for the Skellam Distribution
Description: Functions for the Skellam distribution, including: density
(pmf), cdf, quantiles and random variates.
Author: Jerry W. Lewis, Patrick E. Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick E. Brown <patrick.brown@utoronto.ca>
Diff between skellam versions 0.1 dated 2015-06-23 and 0.1.3 dated 2015-07-07
DESCRIPTION | 14 ++++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 ++ inst/CITATION | 26 ++++++++++++-------------- inst/doc/skellam.pdf |binary inst/doc/skellam.rnw | 9 +++++---- vignettes/skellam.rnw | 9 +++++---- 7 files changed, 38 insertions(+), 34 deletions(-)
Title: Replication Interval Functions
Description: A common problem faced by journal reviewers and authors is the
question of whether the results of a replication study are consistent with
the original published study. One solution to this problem is to examine
the effect size from the published study and generate the range of effect
sizes that could reasonably be obtained (due to random sampling) in a
replication attempt (i.e., calculate a replication interval). If a
replication effect size falls outside the replication interval then that
value could not have occurred to due the effects of sampling error alone.
Alternatively, if a replication effect size falls within the replication
interval then the replication results could have reasonably occurred due to
the effects of sampling error alone. This package has functions that
calculate the replication interval for two different types of effect sizes,
namely correlation (i.e., r) and the standardized mean difference
(i.e., d-value).
Author: David Stanley
Maintainer: David Stanley <dstanley@uoguelph.ca>
Diff between replicationInterval versions 0.3 dated 2015-02-04 and 1.0.0 dated 2015-07-07
DESCRIPTION | 10 +- MD5 | 12 +-- NAMESPACE | 2 R/replicationInterval.R | 145 +++++++++++++++++++++++++------------ man/replicationInterval-package.Rd | 11 +- man/ri.d.Rd | 23 +++-- man/ri.r.Rd | 15 ++- 7 files changed, 141 insertions(+), 77 deletions(-)
More information about replicationInterval at CRAN
Permanent link
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in movebank.org as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Author: Bart Kranstauber <bart.kranstauber@uni-konstanz.de>, Marco Smolla <marco.smolla@postgrad.manchester.ac.uk>
Maintainer: Bart Kranstauber <bart.kranstauber@uni-konstanz.de>
Diff between move versions 1.4.496 dated 2015-03-19 and 1.5.514 dated 2015-07-07
move-1.4.496/move/inst/unitTests |only move-1.4.496/move/tests/doRUnit.R |only move-1.5.514/move/ChangeLog | 46 +++ move-1.5.514/move/DESCRIPTION | 16 - move-1.5.514/move/MD5 | 108 ++++---- move-1.5.514/move/NAMESPACE | 15 + move-1.5.514/move/R/WebImport.R | 3 move-1.5.514/move/R/brownianbridgedyn.R | 4 move-1.5.514/move/R/burstId.R |only move-1.5.514/move/R/contour.R | 2 move-1.5.514/move/R/corridor.R | 15 - move-1.5.514/move/R/extcalc.R | 4 move-1.5.514/move/R/hrBootstrap.R | 8 move-1.5.514/move/R/lineMidpoint.R | 2 move-1.5.514/move/R/lines.R | 7 move-1.5.514/move/R/move.R | 151 ++++++------ move-1.5.514/move/R/moveStack.R | 9 move-1.5.514/move/R/nindiv.R | 2 move-1.5.514/move/R/plotBursts.R | 2 move-1.5.514/move/R/print.R | 2 move-1.5.514/move/R/spTransform.R | 2 move-1.5.514/move/R/timelag.R | 40 +-- move-1.5.514/move/build/vignette.rds |binary move-1.5.514/move/inst/doc/browseMovebank.pdf |binary move-1.5.514/move/inst/doc/move.R | 2 move-1.5.514/move/inst/doc/move.Rnw | 2 move-1.5.514/move/inst/doc/move.pdf |binary move-1.5.514/move/man/brownian.bridge.dyn.Rd | 2 move-1.5.514/move/man/brownian.motion.variance.dyn.Rd | 2 move-1.5.514/move/man/burstId.Rd |only move-1.5.514/move/man/distance.Rd | 2 move-1.5.514/move/man/dynBGB-methods.Rd | 2 move-1.5.514/move/man/hrBootstrap.Rd | 2 move-1.5.514/move/man/lines.Rd | 4 move-1.5.514/move/man/move-package.Rd | 2 move-1.5.514/move/man/move.Rd | 14 - move-1.5.514/move/man/spTransform.Rd | 4 move-1.5.514/move/man/time.lag.Rd | 8 move-1.5.514/move/tests/test-all.R | 13 + move-1.5.514/move/tests/testthat/test.brownian.bridge.dyn.R | 64 ++--- move-1.5.514/move/tests/testthat/test.burst.R |only move-1.5.514/move/tests/testthat/test.citations.R |only move-1.5.514/move/tests/testthat/test.dBGB.R | 11 move-1.5.514/move/tests/testthat/test.extentCalc.R | 16 - move-1.5.514/move/tests/testthat/test.getMotionVariance.R | 6 move-1.5.514/move/tests/testthat/test.idData.R |only move-1.5.514/move/tests/testthat/test.interpolateTime.R |only move-1.5.514/move/tests/testthat/test.measures.R |only move-1.5.514/move/tests/testthat/test.move.R |only move-1.5.514/move/tests/testthat/test.moveAde.R |only move-1.5.514/move/tests/testthat/test.moveStack.R |only move-1.5.514/move/tests/testthat/test.seglength.R | 2 move-1.5.514/move/tests/testthat/test.smallFunctions.R |only move-1.5.514/move/tests/testthat/test.spTransform.R |only move-1.5.514/move/tests/testthat/test.storedData.R |only move-1.5.514/move/tests/testthat/test.subSet.R |only move-1.5.514/move/tests/testthat/test.turnAngle.R |only move-1.5.514/move/vignettes/move.Rnw | 2 58 files changed, 349 insertions(+), 249 deletions(-)
Title: Tools for Biostatistics, Public Policy, and Law
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness,
measures of relative variability etc, the package contains new robust tests of symmetry,
omnibus and directional tests of normality, and their graphical counterparts such as
Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods
are illustrated by simulations and real-life examples from legal statistics, economics,
and biostatistics.
Author: (in alphabetical order)
Joseph L. Gastwirth <jlgast@gwu.edu>;
Yulia R. Gel <ygl@utdallas.edu>;
W. L. Wallace Hui <wlwhui@uwaterloo.ca>;
Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>;
Weiwen Miao <miao@macalester.edu>;
Kimihiro Noguchi <kinoguchi@ucdavis.edu>
Maintainer: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>
Diff between lawstat versions 2.5 dated 2015-01-27 and 3.0 dated 2015-07-07
DESCRIPTION | 13 ++-- MD5 | 12 ++-- NAMESPACE | 15 ++--- R/symmetry.test.R | 125 +++++++++++++++++++++++++++------------------ man/brunner.munzel.test.Rd | 3 + man/levene.test.Rd | 6 +- man/symmetry.test.Rd | 67 ++++++++++++++++-------- 7 files changed, 148 insertions(+), 93 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 2.2.0 dated 2015-04-14 and 2.3.0 dated 2015-07-07
DESCRIPTION | 16 +- MD5 | 221 +++++++++++++++++---------------- NAMESPACE | 10 + R/EGRET.R | 6 R/modelEstimation.R | 242 ++++++++++++++++++++++++++++++++----- R/populateDaily.r | 3 R/readMetaData.r | 2 R/runSurvReg.R | 10 + build/vignette.rds |binary inst/doc/EGRET.pdf |binary inst/doc/SeasonalFraction.R |only inst/doc/SeasonalFraction.Rmd |only inst/doc/SeasonalFraction.html |only inst/doc/vignetteFlowWeighted.R |only inst/doc/vignetteFlowWeighted.Rmd |only inst/doc/vignetteFlowWeighted.html |only inst/extdata/James.rds |only inst/extdata/Susquehanna.rds |only man/Choptank_eList.Rd | 5 man/Constants.Rd | 2 man/EGRET-package.Rd | 2 man/INFOdataframe.Rd | 2 man/as.egret.Rd | 2 man/blankTime.Rd | 2 man/boxConcMonth.Rd | 2 man/boxConcThree.Rd | 2 man/boxQTwice.Rd | 2 man/boxResidMonth.Rd | 2 man/calculateMonthlyResults.Rd | 2 man/censoredSegments.Rd | 2 man/checkStartEndDate.Rd | 2 man/compressData.Rd | 2 man/dataOverview.Rd | 2 man/dateFormatCheck.Rd | 2 man/estCrossVal.Rd | 2 man/estDailyFromSurfaces.Rd | 2 man/estFNsegs.Rd |only man/estSurfaces.Rd | 2 man/fixSampleFrame.Rd | 2 man/flexFN.Rd |only man/flowDuration.Rd | 2 man/fluxBiasMulti.Rd | 2 man/fluxBiasStat.Rd | 2 man/fluxUnit-class.Rd | 2 man/formatCheckDate.Rd | 2 man/formatCheckParameterCd.Rd | 2 man/generalAxis.Rd | 2 man/genericEGRETDotPlot.Rd | 2 man/getDaily.Rd | 2 man/getInfo.Rd | 2 man/getSample.Rd | 2 man/getSurfaces.Rd | 2 man/is.egret.Rd | 2 man/logPretty1.Rd | 2 man/logPretty3.Rd | 2 man/makeAnnualSeries.Rd | 2 man/mergeReport.Rd | 2 man/modelEstimation.Rd | 7 - man/monthLabel-class.Rd | 2 man/multiPlotDataOverview.Rd | 2 man/plot15.Rd | 2 man/plot1of15.Rd | 2 man/plotConcHist.Rd | 2 man/plotConcPred.Rd | 2 man/plotConcQ.Rd | 2 man/plotConcQSmooth.Rd | 2 man/plotConcTime.Rd | 2 man/plotConcTimeDaily.Rd | 2 man/plotConcTimeSmooth.Rd | 2 man/plotContours.Rd | 2 man/plotDiffContours.Rd | 2 man/plotFlowSingle.Rd | 2 man/plotFluxHist.Rd | 2 man/plotFluxPred.Rd | 2 man/plotFluxQ.Rd | 2 man/plotFluxTimeDaily.Rd | 2 man/plotFour.Rd | 2 man/plotFourStats.Rd | 2 man/plotQTimeDaily.Rd | 2 man/plotResidPred.Rd | 2 man/plotResidQ.Rd | 2 man/plotResidTime.Rd | 2 man/plotSDLogQ.Rd | 2 man/populateConcentrations.Rd | 2 man/populateDaily.Rd | 2 man/populateDateColumns.Rd | 2 man/populateParameterINFO.Rd | 2 man/populateSampleColumns.Rd | 2 man/populateSiteINFO.Rd | 2 man/print.egret.Rd | 2 man/printFluxUnitCheatSheet.Rd | 2 man/printSeries.Rd | 2 man/printqUnitCheatSheet.Rd | 2 man/processQWData.Rd | 2 man/qUnit-class.Rd | 2 man/readDataFromFile.Rd | 2 man/readNWISDaily.Rd | 2 man/readNWISSample.Rd | 2 man/readUserDaily.Rd | 2 man/readUserSample.Rd | 2 man/readWQPSample.Rd | 2 man/removeDuplicates.Rd | 2 man/runSurvReg.Rd | 2 man/saveResults.Rd | 2 man/selectDays.Rd | 2 man/setPA.Rd | 2 man/setSeasonLabel.Rd | 2 man/setSeasonLabelByUser.Rd | 2 man/setUpEstimation.Rd |only man/setupYears.Rd | 2 man/surfaceIndex.Rd | 2 man/tableChange.Rd | 2 man/tableChangeSingle.Rd | 2 man/tableFlowChange.Rd | 2 man/tableResults.Rd | 2 man/triCube.Rd | 2 man/yPretty.Rd | 2 117 files changed, 457 insertions(+), 253 deletions(-)
Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between EffectTreat versions 0.1-11 dated 2015-04-27 and 0.2 dated 2015-07-07
EffectTreat-0.1-11/EffectTreat/R/plot.PAC.ContCont.R |only EffectTreat-0.2/EffectTreat/DESCRIPTION | 9 EffectTreat-0.2/EffectTreat/MD5 | 37 +- EffectTreat-0.2/EffectTreat/NAMESPACE | 11 EffectTreat-0.2/EffectTreat/NEWS | 4 EffectTreat-0.2/EffectTreat/R/CausalPCA.ContCont.R | 10 EffectTreat-0.2/EffectTreat/R/Min.Max.Multivar.PCA.R |only EffectTreat-0.2/EffectTreat/R/MultivarPCAContCont.R |only EffectTreat-0.2/EffectTreat/R/Predict.Treat.Multivar.ContCont.R |only EffectTreat-0.2/EffectTreat/R/plot.PCA.ContCont.R |only EffectTreat-0.2/EffectTreat/R/plot.Predict.Treat.ContCont.R | 151 +++++++++- EffectTreat-0.2/EffectTreat/R/summary.Multivar.PCA.ContCont.R |only EffectTreat-0.2/EffectTreat/R/summary.Predict.Treat.ContCont.R | 97 ++++++ EffectTreat-0.2/EffectTreat/man/CausalPCA.ContCont.Rd | 5 EffectTreat-0.2/EffectTreat/man/GoodPretreatContCont.Rd | 2 EffectTreat-0.2/EffectTreat/man/Min.Max.Multivar.PCA.Rd |only EffectTreat-0.2/EffectTreat/man/Multivar.PCAContCont.Rd |only EffectTreat-0.2/EffectTreat/man/PCAContCont.Rd | 13 EffectTreat-0.2/EffectTreat/man/Predict.Treat.ContCont.Rd | 3 EffectTreat-0.2/EffectTreat/man/Predict.Treat.Multivar.ContCont.Rd |only EffectTreat-0.2/EffectTreat/man/plot.GoodPretreatContCont.Rd | 4 EffectTreat-0.2/EffectTreat/man/plot.PCA.ContCont.Rd | 25 - EffectTreat-0.2/EffectTreat/man/plot.Predict.Treat.ContCont.Rd | 5 EffectTreat-0.2/EffectTreat/man/summary.gen.Rd | 4 24 files changed, 328 insertions(+), 52 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.2.1 dated 2015-04-27 and 2.3.0 dated 2015-07-07
DESCRIPTION | 10 +++--- MD5 | 50 +++++++++++++++---------------- NAMESPACE | 5 ++- NEWS | 6 +++ R/checkWQPdates.r | 1 R/constructNWISURL.r | 3 + R/importRDB1.r | 2 + R/importWQP.R | 18 ++++++----- R/importWaterML1.r | 16 ++++++--- R/readNWISdata.r | 19 ++++------- R/readNWISqw.r | 16 ++++++--- R/readWQPdata.R | 10 +----- R/readWQPqw.r | 2 - R/tabbedDataRetrievals.R | 4 +- R/whatNWISsites.R | 2 - R/whatWQPsites.R | 10 ++---- build/vignette.rds |binary man/checkWQPdates.Rd | 1 man/pCodeToName.Rd | 3 - man/parameterCdFile.Rd | 2 - man/readNWISdata.Rd | 6 --- man/whatNWISsites.Rd | 5 --- tests/testthat/tests_general.R | 21 ++++++------- tests/testthat/tests_imports.R | 28 ++++++++--------- tests/testthat/tests_userFriendly_fxns.R | 14 +++++++- vignettes/dataRetrieval.Rnw | 2 - 26 files changed, 137 insertions(+), 119 deletions(-)
Title: Actuarial Functions
Description: Various actuarial science functionalities, mostly in the
fields of loss distributions, risk theory (including ruin theory),
simulation of compound hierarchical models and credibility theory.
The package also features 17 probability laws commonly used in
insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 1.1-8 dated 2014-12-15 and 1.1-9 dated 2015-07-07
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 1 + build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.pdf |binary inst/doc/lossdist.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary 11 files changed, 26 insertions(+), 16 deletions(-)
Title: Exploratory Analysis of Genetic and Genomic Data
Description: Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Author: Thibaut Jombart, Caitlin Collins, Zhian N. Kamvar, Roman Lustrik, Peter Solymos, Ismail Ahmed, Federico Calboli, Anne Cori, Klaus Schliep
Maintainer: Thibaut Jombart <t.jombart@imperial.ac.uk>
Diff between adegenet versions 1.4-2 dated 2014-05-13 and 2.0.0 dated 2015-07-07
adegenet-1.4-2/adegenet/data/H3N2.RData |only adegenet-1.4-2/adegenet/data/dapcIllus.RData |only adegenet-1.4-2/adegenet/data/eHGDP.RData |only adegenet-1.4-2/adegenet/data/microbov.RData |only adegenet-1.4-2/adegenet/data/nancycats.RData |only adegenet-1.4-2/adegenet/data/rupica.RData |only adegenet-1.4-2/adegenet/data/sim2pop.RData |only adegenet-1.4-2/adegenet/data/spcaIllus.RData |only adegenet-1.4-2/adegenet/man/as.genind.Rd |only adegenet-1.4-2/adegenet/man/as.genpop.Rd |only adegenet-1.4-2/adegenet/man/export.Rd |only adegenet-1.4-2/adegenet/man/fstat.Rd |only adegenet-1.4-2/adegenet/man/gstat.randtest.Rd |only adegenet-1.4-2/adegenet/man/import.Rd |only adegenet-1.4-2/adegenet/man/na.replace.Rd |only adegenet-1.4-2/adegenet/man/scale.Rd |only adegenet-2.0.0/adegenet/ChangeLog | 89 ++ adegenet-2.0.0/adegenet/DESCRIPTION | 43 - adegenet-2.0.0/adegenet/MD5 | 218 +++-- adegenet-2.0.0/adegenet/NAMESPACE | 200 ++++- adegenet-2.0.0/adegenet/R/HWE.R | 89 +- adegenet-2.0.0/adegenet/R/Hs.R | 4 adegenet-2.0.0/adegenet/R/SNPbin.R | 167 +++- adegenet-2.0.0/adegenet/R/accessors.R |only adegenet-2.0.0/adegenet/R/adegenet.package.R |only adegenet-2.0.0/adegenet/R/auxil.R | 31 adegenet-2.0.0/adegenet/R/basicMethods.R | 716 ++++++++++------- adegenet-2.0.0/adegenet/R/chooseCN.R | 77 + adegenet-2.0.0/adegenet/R/classes.R | 362 +-------- adegenet-2.0.0/adegenet/R/constructors.R |only adegenet-2.0.0/adegenet/R/coords.monmonier.R | 1 adegenet-2.0.0/adegenet/R/dapc.R | 50 - adegenet-2.0.0/adegenet/R/datasets.R |only adegenet-2.0.0/adegenet/R/dist.genpop.R | 4 adegenet-2.0.0/adegenet/R/export.R | 231 ++--- adegenet-2.0.0/adegenet/R/find.clust.R | 2 adegenet-2.0.0/adegenet/R/fstat.R | 190 ++-- adegenet-2.0.0/adegenet/R/gengraph.R | 62 - adegenet-2.0.0/adegenet/R/genind2genpop.R | 232 +++-- adegenet-2.0.0/adegenet/R/glFunctions.R | 4 adegenet-2.0.0/adegenet/R/glHandle.R | 132 ++- adegenet-2.0.0/adegenet/R/gstat.randtest.R | 87 +- adegenet-2.0.0/adegenet/R/handling.R | 703 ++++++----------- adegenet-2.0.0/adegenet/R/haploGen.R | 5 adegenet-2.0.0/adegenet/R/hierarchyMethods.R |only adegenet-2.0.0/adegenet/R/hybridize.R | 91 +- adegenet-2.0.0/adegenet/R/import.R | 877 +++++++++++++++------- adegenet-2.0.0/adegenet/R/inbreeding.R | 117 -- adegenet-2.0.0/adegenet/R/makefreq.R | 143 ++- adegenet-2.0.0/adegenet/R/monmonier.R | 1 adegenet-2.0.0/adegenet/R/old2new.R | 204 +++-- adegenet-2.0.0/adegenet/R/orthobasis.R |only adegenet-2.0.0/adegenet/R/pairDist.R |only adegenet-2.0.0/adegenet/R/propShared.R | 129 --- adegenet-2.0.0/adegenet/R/scale.R | 165 ++-- adegenet-2.0.0/adegenet/R/sequences.R | 6 adegenet-2.0.0/adegenet/R/servers.R | 1 adegenet-2.0.0/adegenet/R/setAs.R | 8 adegenet-2.0.0/adegenet/R/snpzip.R | 155 +-- adegenet-2.0.0/adegenet/R/spca.R | 12 adegenet-2.0.0/adegenet/R/spca.rtests.R | 6 adegenet-2.0.0/adegenet/R/strataMethods.R |only adegenet-2.0.0/adegenet/R/xvalDapc.R | 232 ++++- adegenet-2.0.0/adegenet/R/zzz.R | 16 adegenet-2.0.0/adegenet/README.md |only adegenet-2.0.0/adegenet/data/H3N2.rda |only adegenet-2.0.0/adegenet/data/dapcIllus.rda |only adegenet-2.0.0/adegenet/data/datalist | 2 adegenet-2.0.0/adegenet/data/eHGDP.rda |only adegenet-2.0.0/adegenet/data/microbov.rda |only adegenet-2.0.0/adegenet/data/nancycats.rda |only adegenet-2.0.0/adegenet/data/rupica.rda |only adegenet-2.0.0/adegenet/data/sim2pop.rda |only adegenet-2.0.0/adegenet/data/spcaIllus.rda |only adegenet-2.0.0/adegenet/inst/dapcServer/server.R | 7 adegenet-2.0.0/adegenet/man/H3N2.Rd | 67 - adegenet-2.0.0/adegenet/man/SNPbin.Rd | 1 adegenet-2.0.0/adegenet/man/accessors.Rd | 154 ++- adegenet-2.0.0/adegenet/man/adegenet.package.Rd | 447 ++++------- adegenet-2.0.0/adegenet/man/as-methods.Rd | 2 adegenet-2.0.0/adegenet/man/chooseCN.Rd | 135 +-- adegenet-2.0.0/adegenet/man/coords.monmonier.Rd | 2 adegenet-2.0.0/adegenet/man/dapc.Rd | 19 adegenet-2.0.0/adegenet/man/dapcIllus.Rd | 76 - adegenet-2.0.0/adegenet/man/df2genind.Rd | 143 +-- adegenet-2.0.0/adegenet/man/dist.genpop.Rd | 2 adegenet-2.0.0/adegenet/man/eHGDP.Rd | 86 +- adegenet-2.0.0/adegenet/man/gengraph.Rd | 31 adegenet-2.0.0/adegenet/man/genind.Rd | 35 adegenet-2.0.0/adegenet/man/genind2df.Rd |only adegenet-2.0.0/adegenet/man/genind2genpop.Rd | 107 +- adegenet-2.0.0/adegenet/man/genlight.Rd | 27 adegenet-2.0.0/adegenet/man/genpop.Rd | 13 adegenet-2.0.0/adegenet/man/glPlot.Rd | 1 adegenet-2.0.0/adegenet/man/hierarchy-methods.Rd |only adegenet-2.0.0/adegenet/man/hybridize.Rd | 15 adegenet-2.0.0/adegenet/man/import2genind.Rd |only adegenet-2.0.0/adegenet/man/inbreeding.Rd | 27 adegenet-2.0.0/adegenet/man/makefreq.Rd | 92 +- adegenet-2.0.0/adegenet/man/microbov.Rd | 66 - adegenet-2.0.0/adegenet/man/nancycats.Rd | 36 adegenet-2.0.0/adegenet/man/new.genind.Rd |only adegenet-2.0.0/adegenet/man/new.genpop.Rd |only adegenet-2.0.0/adegenet/man/old2new.Rd | 51 - adegenet-2.0.0/adegenet/man/pairDist.Rd |only adegenet-2.0.0/adegenet/man/population-methods.Rd |only adegenet-2.0.0/adegenet/man/propShared.Rd | 4 adegenet-2.0.0/adegenet/man/read.PLINK.Rd | 164 ++-- adegenet-2.0.0/adegenet/man/read.fstat.Rd | 70 - adegenet-2.0.0/adegenet/man/read.genepop.Rd | 73 - adegenet-2.0.0/adegenet/man/read.genetix.Rd | 73 - adegenet-2.0.0/adegenet/man/read.snp.Rd | 126 +-- adegenet-2.0.0/adegenet/man/read.structure.Rd | 139 +-- adegenet-2.0.0/adegenet/man/rupica.Rd | 73 - adegenet-2.0.0/adegenet/man/scaleGen.Rd |only adegenet-2.0.0/adegenet/man/sequences.Rd | 2 adegenet-2.0.0/adegenet/man/sim2pop.Rd | 58 - adegenet-2.0.0/adegenet/man/snpzip.rd | 70 - adegenet-2.0.0/adegenet/man/spcaIllus.Rd | 69 - adegenet-2.0.0/adegenet/man/strata-methods.Rd |only adegenet-2.0.0/adegenet/man/tab.Rd |only adegenet-2.0.0/adegenet/man/truenames.Rd | 16 adegenet-2.0.0/adegenet/man/virClasses.Rd | 2 adegenet-2.0.0/adegenet/man/web.Rd | 12 adegenet-2.0.0/adegenet/man/xvalDapc.Rd | 77 + adegenet-2.0.0/adegenet/src/adesub.c | 17 adegenet-2.0.0/adegenet/tests |only 127 files changed, 4690 insertions(+), 3861 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.5.14 dated 2015-06-09 and 1.5.24 dated 2015-07-07
wsrf-1.5.14/wsrf/inst/doc/wsrfGuide.R |only wsrf-1.5.14/wsrf/inst/doc/wsrfGuide.Rnw |only wsrf-1.5.14/wsrf/inst/doc/wsrfGuide.pdf |only wsrf-1.5.14/wsrf/vignettes/wsrfGuide.Rnw |only wsrf-1.5.14/wsrf/vignettes/wsrfGuide.bib |only wsrf-1.5.24/wsrf/DESCRIPTION | 10 ++++----- wsrf-1.5.24/wsrf/MD5 | 26 +++++++++++------------ wsrf-1.5.24/wsrf/NAMESPACE | 5 ++-- wsrf-1.5.24/wsrf/README.md | 19 ++++++++++------- wsrf-1.5.24/wsrf/build/vignette.rds |binary wsrf-1.5.24/wsrf/inst/NEWS.Rd | 29 ++++++++++++++++++++++++++ wsrf-1.5.24/wsrf/inst/doc/wsrf-guide.R |only wsrf-1.5.24/wsrf/inst/doc/wsrf-guide.Rmd |only wsrf-1.5.24/wsrf/inst/doc/wsrf-guide.html |only wsrf-1.5.24/wsrf/man/combine.wsrf.Rd | 33 ++++++++++++++++++++++++++++++ wsrf-1.5.24/wsrf/man/subset.wsrf.Rd | 27 ++++++++++++++++++++++++ wsrf-1.5.24/wsrf/man/wsrf.Rd | 23 +++++++++----------- wsrf-1.5.24/wsrf/vignettes/wsrf-guide.Rmd |only wsrf-1.5.24/wsrf/vignettes/wsrf-guide.bib |only 19 files changed, 131 insertions(+), 41 deletions(-)
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal shaped
particles based on the same measured quantities of corresponding planar section
profiles. A single trivariate discretized version of the (stereological) integral
equation in the case of prolate and oblate spheroids is solved numerically by the
EM algorithm. The estimation of diameter distribution of spheres from planar sections
(Wicksell's corpuscle problem) is also implemented. Further, the package provides routines
for the simulation of a Poisson germ-grain process with either spheroids or spheres as grains
together with functions for planar sections.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.2 dated 2015-07-03 and 0.3 dated 2015-07-07
DESCRIPTION | 6 ++--- MD5 | 28 +++++++++++++-------------- R/spheroid.R | 4 --- R/unfolding.R | 15 ++++++++++---- src/GeometricPrimitives.cpp | 6 ----- src/GeometricPrimitives.h | 7 ------ src/Intersector.cpp | 7 ------ src/SimEllipsoid.cpp | 7 ------ src/SimEllipsoid.h | 7 ------ src/SimSphere.cpp | 7 ------ src/SimSphere.h | 7 ------ src/Utils.h | 45 ++++++++++++++++++-------------------------- src/Vector.h | 2 - src/unfold.cpp | 30 +++++++++++++++-------------- src/unfold.h | 7 ------ 15 files changed, 65 insertions(+), 120 deletions(-)
Title: Automatically Set the Width Option on Terminal Emulators
Description: Automatically sets the value of options("width") when the
terminal emulator is resized. The functions of this package only work if R
is compiled for Linux systems and it is running interactively in a terminal
emulator.
Author: Jakson Aquino
Maintainer: Jakson Alves de Aquino <jalvesaq@gmail.com>
Diff between setwidth versions 1.0-3 dated 2013-01-16 and 1.0-4 dated 2015-07-07
setwidth-1.0-3/setwidth/LICENSE |only setwidth-1.0-4/setwidth/DESCRIPTION | 17 +++++++++-------- setwidth-1.0-4/setwidth/MD5 | 11 +++++------ setwidth-1.0-4/setwidth/NEWS | 4 ++++ setwidth-1.0-4/setwidth/R/setwidth.R | 12 ++++++------ setwidth-1.0-4/setwidth/man/setwidth-package.Rd | 3 ++- setwidth-1.0-4/setwidth/src/setwidth.c | 2 +- 7 files changed, 27 insertions(+), 22 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.3.0.1 dated 2015-06-19 and 0.3.1 dated 2015-07-07
markovchain-0.3.0.1/markovchain/vignettes/an_introduction_to_markovchain_package-mcPlot.pdf |only markovchain-0.3.1/markovchain/DESCRIPTION | 10 markovchain-0.3.1/markovchain/MD5 | 76 +-- markovchain-0.3.1/markovchain/NAMESPACE | 3 markovchain-0.3.1/markovchain/NEWS | 10 markovchain-0.3.1/markovchain/R/0_classesAndMethods.R | 63 +- markovchain-0.3.1/markovchain/R/0_ctmcClassesAndMethodsSAI.R |only markovchain-0.3.1/markovchain/R/1_ctmcProbabilisticSAI.R |only markovchain-0.3.1/markovchain/R/1_functions4Fitting.R | 1 markovchain-0.3.1/markovchain/R/2_probabilistic.R | 92 ++- markovchain-0.3.1/markovchain/R/RcppExports.R | 36 + markovchain-0.3.1/markovchain/build/vignette.rds |binary markovchain-0.3.1/markovchain/demo/mathematica.R | 6 markovchain-0.3.1/markovchain/inst/CITATION | 8 markovchain-0.3.1/markovchain/inst/doc/BayesianInference.pdf |binary markovchain-0.3.1/markovchain/inst/doc/CTMC.R |only markovchain-0.3.1/markovchain/inst/doc/CTMC.Rmd |only markovchain-0.3.1/markovchain/inst/doc/CTMC.pdf |only markovchain-0.3.1/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 1 markovchain-0.3.1/markovchain/inst/doc/an_introduction_to_markovchain_package.Rnw | 22 markovchain-0.3.1/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary markovchain-0.3.1/markovchain/inst/doc/markovchainCrashIntro.pdf |binary markovchain-0.3.1/markovchain/man/absorbingStates.Rd | 9 markovchain-0.3.1/markovchain/man/ctmc-class.Rd |only markovchain-0.3.1/markovchain/man/generatorToTransitionMatrix.Rd |only markovchain-0.3.1/markovchain/man/markovchain-class.Rd | 7 markovchain-0.3.1/markovchain/man/markovchain-package.Rd | 4 markovchain-0.3.1/markovchain/man/markovchainFit.Rd | 2 markovchain-0.3.1/markovchain/man/priorDistribution.Rd |only markovchain-0.3.1/markovchain/man/rctmc.Rd |only markovchain-0.3.1/markovchain/src/0_classesAndMethods.cpp | 81 --- markovchain-0.3.1/markovchain/src/0_ctmcClassesAndMethodsSAI.cpp |only markovchain-0.3.1/markovchain/src/1_functions4Fitting.cpp | 88 --- markovchain-0.3.1/markovchain/src/2_probabilistic.cpp | 241 ++++++++-- markovchain-0.3.1/markovchain/src/3_multinomCI.cpp |only markovchain-0.3.1/markovchain/src/Makevars | 1 markovchain-0.3.1/markovchain/src/RcppExports.cpp | 99 +++- markovchain-0.3.1/markovchain/src/mapFitFunctionsSAI.h | 5 markovchain-0.3.1/markovchain/tests/testthat/Rplots.pdf |only markovchain-0.3.1/markovchain/tests/testthat/testBasic1.R | 36 + markovchain-0.3.1/markovchain/tests/testthat/testMultinomCI.R |only markovchain-0.3.1/markovchain/tests/testthat/testOptimization.R |only markovchain-0.3.1/markovchain/tests/testthat/testParallelBootstrap.R |only markovchain-0.3.1/markovchain/tests/testthat/testPeriod.R |only markovchain-0.3.1/markovchain/tests/testthat/testPlot.R |only markovchain-0.3.1/markovchain/tests/testthat/testRecurrentClasses.R |only markovchain-0.3.1/markovchain/vignettes/CTMC.Rmd |only markovchain-0.3.1/markovchain/vignettes/an_introduction_to_markovchain_package.Rnw | 22 markovchain-0.3.1/markovchain/vignettes/markovchainBiblio.bib | 21 49 files changed, 623 insertions(+), 321 deletions(-)
Title: Fuzzy Rank Tests and Confidence Intervals
Description: Does fuzzy tests and confidence intervals (following Geyer
and Meeden, Statistical Science, 2005) for sign test and Wilcoxon
signed rank and rank sum tests.
Author: Charles J. Geyer <charlie@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between fuzzyRankTests versions 0.3-5 dated 2013-07-15 and 0.3-7 dated 2015-07-07
ChangeLog | 6 + DESCRIPTION | 15 ++-- LICENSE | 23 ------ MD5 | 34 +++++---- NAMESPACE | 5 + inst/doc/design.pdf |binary inst/doc/design.tex | 2 src/fpvranksum.c | 14 +++- src/fpvsign.c | 5 + src/fpvsignrank.c | 2 tests/sign-ci.Rout.save | 11 ++- tests/sign.R | 40 ++++++----- tests/sign.Rout.save | 167 +++++++++++++++++++++++++----------------------- tests/testc.R | 6 - tests/testc.Rout.save | 15 +--- tests/testd.R | 4 - tests/testd.Rout.save | 17 ++-- tests/teste.R |only tests/teste.Rout.save |only 19 files changed, 194 insertions(+), 172 deletions(-)
More information about fuzzyRankTests at CRAN
Permanent link
Title: A Tiny Utility Providing Polymorphic Operations
Description: This utility package provides polymorphism over common operations and is now subsumed by lambda.tools.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between futile.any versions 1.3.0 dated 2013-02-03 and 1.3.2 dated 2015-07-07
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 1 + man/futile.any-package.Rd | 4 ++-- tests/run_tests.R | 2 +- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Metrics of Difference for Comparing Pairs of Maps
Diff between diffeR versions 0.0-2 dated 2015-02-07 and 0.0-3 dated 2015-07-07
Description: Metrics of difference for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr.
Maintainer: Alí Santacruz
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
NAMESPACE | 4 +++-
R/MAD.R | 2 +-
R/MADscatterplot.R | 2 +-
man/diffeR-package.Rd | 10 +++++-----
6 files changed, 22 insertions(+), 19 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing
and/or imputed values are introduced, which can be used for exploring the data and the
structure of the missing and/or imputed values. Depending on this structure
of the missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.1.0 dated 2014-10-25 and 4.3.0 dated 2015-07-07
DESCRIPTION | 32 +-- MD5 | 92 ++++----- NAMESPACE | 234 ++++++++++++------------- NEWS | 9 R/gower.dist.R | 33 ++- R/hotdeck.R | 13 + R/irmi.R | 16 + R/kNNFaster.R | 36 ++- R/regressionImp.R | 7 man/SBS5242.Rd | 57 +++--- man/VIM-package.Rd | 103 +++++------ man/aggr.Rd | 429 +++++++++++++++++++++++----------------------- man/alphablend.Rd | 61 +++--- man/barMiss.Rd | 267 ++++++++++++++-------------- man/bgmap.Rd | 81 ++++---- man/chorizonDL.Rd | 183 +++++++++---------- man/colSequence.Rd | 149 ++++++++------- man/colormapMiss.Rd | 317 +++++++++++++++++---------------- man/countInf.Rd | 57 +++--- man/growdotMiss.Rd | 271 ++++++++++++++--------------- man/histMiss.Rd | 277 ++++++++++++++--------------- man/hotdeck.Rd | 127 ++++++------- man/initialise.Rd | 83 ++++---- man/irmi.Rd | 237 ++++++++++++------------- man/kNN.Rd | 173 +++++++++--------- man/kola.background.Rd | 45 ++-- man/mapMiss.Rd | 173 +++++++++--------- man/marginmatrix.Rd | 151 ++++++++-------- man/marginplot.Rd | 259 +++++++++++++-------------- man/matrixplot.Rd | 243 +++++++++++++------------- man/mosaicMiss.Rd | 183 +++++++++---------- man/pairsVIM.Rd | 183 +++++++++---------- man/parcoordMiss.Rd | 293 +++++++++++++++---------------- man/pbox.Rd | 249 +++++++++++++------------- man/prepare.Rd | 151 ++++++++-------- man/print.summary.aggr.Rd | 57 +++--- man/regressionImp.Rd | 103 +++++------ man/rugNA.Rd | 129 ++++++------- man/scattJitt.Rd | 205 +++++++++++---------- man/scattMiss.Rd | 233 ++++++++++++------------ man/scattmatrixMiss.Rd | 241 ++++++++++++------------- man/sleep.Rd | 57 +++--- man/spineMiss.Rd | 293 +++++++++++++++---------------- man/tao.Rd | 59 +++--- man/testdata.Rd | 59 +++--- man/vmGUIenvir.Rd | 101 +++++----- src/gowerD.cpp | 5 47 files changed, 3458 insertions(+), 3358 deletions(-)
Title: Social Position Indicators Construction Toolbox
Description: Provides to sociologists (and related scientists) a toolbox to facilitate the construction of social position indicators from survey data. Social position indicators refer to what is commonly known as social class and social status. There exists in the sociological literature many theoretical conceptualisation and empirical operationalization of social class and social status. This first version of the package offers tools to construct the International Socio-Economic Index of Occupational Status (ISEI) and the Oesch social class schema. It also provides tools to convert several occupational classifications (PCS82, PCS03, and ISCO08) into a common one (ISCO88) to facilitate data harmonisation work, and tools to collapse (i.e. group) modalities of social position indicators.
Author: Julie Falcon (University of Lausanne)
Maintainer: Julie Falcon <julie.falcon@unil.ch>
Diff between SocialPosition versions 1.0 dated 2015-01-26 and 1.0.1 dated 2015-07-07
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ R/recode_from_ISCO88_to_ISEI.R | 9 +++++++++ man/SocialPosition-package.Rd | 12 ++++++------ man/collapse_PCS2003_2l.Rd | 4 ++-- man/collapse_PCS2003_3l.Rd | 4 ++-- man/collapse_PCS2003_4l.Rd | 4 ++-- man/convert_from_ISCO08_to_ISCO88_3d.Rd | 4 ++-- man/convert_from_PCS1982_4l_to_PCS2003_4l.Rd | 2 +- man/convert_from_PCS2003_4l_to_ISCO88_3d.Rd | 4 ++-- man/data_MCH2007.Rd | 2 +- man/recode_from_ISCO88_to_ISEI.Rd | 4 ++-- man/recode_from_ISCO88_to_Oesch.Rd | 4 ++-- 13 files changed, 50 insertions(+), 41 deletions(-)
More information about SocialPosition at CRAN
Permanent link
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.4 dated 2015-07-05 and 1.3.5 dated 2015-07-07
DESCRIPTION | 8 MD5 | 8 cleanup | 4 configure | 5760 +++++++++++++++++++++++++++++------------------------------ configure.ac | 54 5 files changed, 2917 insertions(+), 2917 deletions(-)
Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices
The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data
structures and R using concepts from 'Rcpp' which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses 'Rcpp' to connect to another third-party library. The 'autoconf'
script, 'inline' plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGSL versions 0.2.4 dated 2015-01-24 and 0.2.5 dated 2015-07-07
ChangeLog | 40 ++ DESCRIPTION | 24 - MD5 | 48 +- NAMESPACE | 4 R/RcppExports.R | 4 R/fastLm.R | 2 README.md | 8 build/vignette.rds |binary cleanup | 2 inst/NEWS.Rd | 19 + inst/doc/RcppGSL-intro.R | 66 +-- inst/doc/RcppGSL-intro.Rnw | 387 +++++++++++------------ inst/doc/RcppGSL-intro.pdf |binary inst/doc/RcppGSL-unitTests.pdf |binary inst/examples/RcppGSLExample/DESCRIPTION | 9 inst/examples/RcppGSLExample/R/RcppExports.R |only inst/examples/RcppGSLExample/R/colNorm.R | 5 inst/examples/RcppGSLExample/src/RcppExports.cpp |only inst/examples/RcppGSLExample/src/colNorm.cpp | 23 + inst/examples/bSpline/bSpline.cpp | 3 inst/unitTests/runit.client.package.R | 6 inst/unitTests/runit.fastLm.R | 4 src/Makevars.win | 8 src/RcppExports.cpp | 36 +- src/fastLm.cpp | 72 +--- vignettes/RcppGSL-intro.Rnw | 387 +++++++++++------------ 26 files changed, 600 insertions(+), 557 deletions(-)
Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation
and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GlobalOptions versions 0.0.6 dated 2015-01-28 and 0.0.7 dated 2015-07-07
DESCRIPTION | 11 MD5 | 24 - NAMESPACE | 2 NEWS | 80 +++--- R/setGlobalOptions.R | 580 ++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/GlobalOptions.R | 224 ++++++++-------- inst/doc/GlobalOptions.Rnw | 564 +++++++++++++++++++++--------------------- inst/doc/GlobalOptions.pdf |binary inst/tests/test.R | 398 +++++++++++++++--------------- man/setGlobalOptions.rd | 72 ++--- tests/test-all.R | 8 vignettes/GlobalOptions.Rnw | 564 +++++++++++++++++++++--------------------- 13 files changed, 1264 insertions(+), 1263 deletions(-)
Title: Estimating the Proportion of True Null Hypotheses for FDR
Description: Methods for estimating the proportion of true null hypotheses, i.e., the pi0, when a very large number of hypotheses are simultaneously tested, especially for the purpose of (local) false discovery rate control for microarray data. It also contains functions to estimate the distribution of noncentrality parameters from a large number of parametric tests.
Author: Long Qu [aut, cre, ctb],
Kun Liang [ctb],
Yudi Pawitan [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Alexander Ploner [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Egil Ferkingstad [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Mette Langaas [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Marcus Davy [aut] (The author(s) of limma::convest, which was modified
slightly leading to convest in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between pi0 versions 1.3-250 dated 2012-09-06 and 1.4-0 dated 2015-07-06
pi0-1.3-250/pi0/R/loadOrInstall.R |only pi0-1.3-250/pi0/ToDoList.txt |only pi0-1.3-250/pi0/man/loadOrInstall.Rd |only pi0-1.4-0/pi0/DESCRIPTION | 49 +- pi0-1.4-0/pi0/MD5 | 144 +++--- pi0-1.4-0/pi0/NAMESPACE | 362 ++++++++-------- pi0-1.4-0/pi0/R/ToDoList.R |only pi0-1.4-0/pi0/R/cond.cdf.R | 39 + pi0-1.4-0/pi0/R/discTMix.R | 347 +++++++-------- pi0-1.4-0/pi0/R/dncp.R | 20 pi0-1.4-0/pi0/R/dtn.mix.R | 62 -- pi0-1.4-0/pi0/R/extrp.pi0.known.gam2.R | 4 pi0-1.4-0/pi0/R/extrp.pi0.master.R | 2 pi0-1.4-0/pi0/R/extrp.pi0.unknown.gam2.R | 4 pi0-1.4-0/pi0/R/fdr.R | 24 - pi0-1.4-0/pi0/R/histf1.R | 170 +++---- pi0-1.4-0/pi0/R/hypergeometric1F1.R |only pi0-1.4-0/pi0/R/int.nct.R | 10 pi0-1.4-0/pi0/R/lfdr.R | 13 pi0-1.4-0/pi0/R/matrix.t.test.R | 64 +- pi0-1.4-0/pi0/R/ncpest.R | 33 - pi0-1.4-0/pi0/R/ncpest.iter.R | 2 pi0-1.4-0/pi0/R/nparncp.R | 86 ++- pi0-1.4-0/pi0/R/nparncpF.R | 687 ++++++++++++++++--------------- pi0-1.4-0/pi0/R/parncp.R | 14 pi0-1.4-0/pi0/R/parncp2.R |only pi0-1.4-0/pi0/R/parncpF.R | 79 ++- pi0-1.4-0/pi0/R/pavaf1.R | 2 pi0-1.4-0/pi0/R/plot.extrpi0.R | 2 pi0-1.4-0/pi0/R/plot.subex.R | 66 +- pi0-1.4-0/pi0/R/plot.subt.R | 4 pi0-1.4-0/pi0/R/print.extrpi0.R | 36 - pi0-1.4-0/pi0/R/print.subex.R | 22 pi0-1.4-0/pi0/R/print.subt.R | 28 - pi0-1.4-0/pi0/R/sparncp.R | 53 +- pi0-1.4-0/pi0/R/sparncpF.R | 20 pi0-1.4-0/pi0/R/subt.R | 156 +++---- pi0-1.4-0/pi0/R/summary.extrpi0.R | 6 pi0-1.4-0/pi0/R/summary.subex.R | 6 pi0-1.4-0/pi0/R/summary.subt.R | 6 pi0-1.4-0/pi0/R/znormix.R | 3 pi0-1.4-0/pi0/man/CBUM.Rd | 6 pi0-1.4-0/pi0/man/coef.ncpest.Rd | 128 ++--- pi0-1.4-0/pi0/man/combn2R.Rd | 3 pi0-1.4-0/pi0/man/cond.cdf.Rd | 4 pi0-1.4-0/pi0/man/convest.Rd | 3 pi0-1.4-0/pi0/man/discTMix.Rd | 180 ++++---- pi0-1.4-0/pi0/man/dncp.Rd | 6 pi0-1.4-0/pi0/man/dt.int2.Rd | 126 ++--- pi0-1.4-0/pi0/man/dt.lap.Rd | 134 +++--- pi0-1.4-0/pi0/man/dtn.mix.Rd | 143 +++--- pi0-1.4-0/pi0/man/fdr.Rd | 2 pi0-1.4-0/pi0/man/fitted.discTMix.Rd | 106 ++-- pi0-1.4-0/pi0/man/fitted.nparncp.Rd | 132 +++-- pi0-1.4-0/pi0/man/grid.search.Rd | 164 +++---- pi0-1.4-0/pi0/man/histf1.Rd | 8 pi0-1.4-0/pi0/man/lfdr.Rd | 164 +++---- pi0-1.4-0/pi0/man/logLik.ncpest.Rd | 106 ++-- pi0-1.4-0/pi0/man/mTruncNorm.Rd | 162 +++---- pi0-1.4-0/pi0/man/mdt.Rd | 2 pi0-1.4-0/pi0/man/ncpest.Rd | 4 pi0-1.4-0/pi0/man/ncpest.iter.Rd | 4 pi0-1.4-0/pi0/man/nparncp.Rd | 242 +++++----- pi0-1.4-0/pi0/man/parncp.Rd | 213 ++++----- pi0-1.4-0/pi0/man/pi0-package.Rd | 14 pi0-1.4-0/pi0/man/plot.nparncp.Rd | 120 ++--- pi0-1.4-0/pi0/man/plot.parncp.Rd | 120 ++--- pi0-1.4-0/pi0/man/plot.sparncp.Rd | 2 pi0-1.4-0/pi0/man/pt.sad.Rd | 133 +++--- pi0-1.4-0/pi0/man/sparncp.Rd | 3 pi0-1.4-0/pi0/man/subt.Rd | 184 ++++---- pi0-1.4-0/pi0/man/summary.nparncp.Rd | 112 ++--- pi0-1.4-0/pi0/man/summary.parncp.Rd | 114 ++--- pi0-1.4-0/pi0/man/summary.sparncp.Rd | 2 pi0-1.4-0/pi0/man/vcov.ncpest.Rd | 104 ++-- pi0-1.4-0/pi0/man/znormix.Rd | 6 76 files changed, 2876 insertions(+), 2705 deletions(-)
Title: A Package to Test for Pleiotropic Effects
Description: Performs genetic association tests between SNPs
(one-at-a-time) and multiple phenotypes (separately or in joint
model).
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart
and Federico Calboli
Maintainer: Federico Calboli <federico.calboli@helsinki.fi>
Diff between MultiPhen versions 2.0.0 dated 2014-01-08 and 2.0.1 dated 2015-07-06
DESCRIPTION | 15 +++++++-------- MD5 | 10 +++++----- NAMESPACE | 10 +++++++--- build/vignette.rds |binary inst/doc/MultiPhen.pdf |binary man/MultiPhen-internal.Rd | 3 ++- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Relabelling MCMC Outputs of Mixture Models
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between label.switching versions 1.3 dated 2014-11-05 and 1.4 dated 2015-07-06
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/relabelling_algorithms.R | 10 +++++++++- 3 files changed, 16 insertions(+), 8 deletions(-)
More information about label.switching at CRAN
Permanent link
Title: Synthesizing List of Differentially Expressed Features
Description: Performs two tests to evaluate if the
experiments are associated and returns a list of interesting
features common to all the experiments.
Author: Alberto Cassese, Marta Blangiardo
Maintainer: Alberto Cassese <alberto.cassese@maastrichtuniversity.nl>
Diff between sdef versions 1.5 dated 2010-03-11 and 1.6 dated 2015-07-06
DESCRIPTION | 15 ++++++++------- MD5 |only NAMESPACE |only man/Tmc.Rd | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.30 dated 2015-06-15 and 1.31.2 dated 2015-07-06
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++--------- NAMESPACE | 3 ++ R/DMFA.R | 2 - R/MCA.R | 4 +- R/PCA.R | 2 - R/spMCA.R | 5 ++- data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/DMFA.Rd | 2 - 13 files changed, 29 insertions(+), 23 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE)
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations (ODE), of
partial differential equations (PDE), of differential
algebraic equations (DAE), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions lsoda, lsodar, lsode, lsodes of the ODEPACK
collection, to the FORTRAN functions dvode and daspk and a
C-implementation of solvers of the Runge-Kutta family with
fixed or variable time steps. The package contains routines
designed for solving ODEs resulting from 1-D, 2-D and 3-D
partial differential equations (PDE) that have been converted
to ODEs by numerical differencing.
Author: Karline Soetaert [aut],
Thomas Petzoldt [aut, cre],
R. Woodrow Setzer [aut],
odepack authors [cph]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.11 dated 2014-10-29 and 1.12 dated 2015-07-06
DESCRIPTION | 13 +- MD5 | 47 ++++---- NAMESPACE | 4 NEWS | 6 + R/DLLfunc.R | 4 R/Utilities.R | 246 +++++++++------------------------------------- R/checkevents.R | 4 R/forcings.R | 8 - R/lsoda.R | 4 R/lsodar.R | 2 R/lsode.R | 2 R/lsodes.R | 7 - R/matplot.R |only R/vode.R | 4 build/vignette.rds |binary data/ccl4data.rda |binary inst/doc/compiledCode.pdf |binary inst/doc/deSolve.pdf |binary man/deSolve.Rd | 4 man/ode.1D.Rd | 2 man/ode.2D.Rd | 2 man/ode.3D.Rd | 2 man/ode.band.Rd | 2 man/plot.deSolve.Rd | 40 +++++-- src/call_lsoda.c | 3 25 files changed, 149 insertions(+), 257 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) prior distributions. A number of different random effects structures are available, and full details are given in the vignette accompanying this package and the references below. The creation of this package was supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee and Alastair Rushworth
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 1.1 dated 2014-11-14 and 2.0 dated 2015-07-06
CARBayesST-1.1/CARBayesST/R/ST.ARCAR.R |only CARBayesST-1.1/CARBayesST/R/ST.ARCARadaptive.R |only CARBayesST-1.1/CARBayesST/R/ST.ARCARcluster.R |only CARBayesST-1.1/CARBayesST/R/ST.KHinteraction.R |only CARBayesST-1.1/CARBayesST/R/ST.KHmain.R |only CARBayesST-1.1/CARBayesST/R/ST.cluster.R |only CARBayesST-1.1/CARBayesST/R/results.summarise.R |only CARBayesST-1.1/CARBayesST/man/ST.ARCAR.Rd |only CARBayesST-1.1/CARBayesST/man/ST.ARCARadaptive.Rd |only CARBayesST-1.1/CARBayesST/man/ST.ARCARcluster.Rd |only CARBayesST-1.1/CARBayesST/man/ST.KHinteraction.Rd |only CARBayesST-1.1/CARBayesST/man/ST.KHmain.Rd |only CARBayesST-1.1/CARBayesST/man/ST.cluster.Rd |only CARBayesST-1.1/CARBayesST/man/results.summarise.Rd |only CARBayesST-2.0/CARBayesST/DESCRIPTION | 17 CARBayesST-2.0/CARBayesST/MD5 | 60 CARBayesST-2.0/CARBayesST/NAMESPACE | 20 CARBayesST-2.0/CARBayesST/R/RcppExports.R | 95 - CARBayesST-2.0/CARBayesST/R/ST.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/ST.CARanova.R |only CARBayesST-2.0/CARBayesST/R/ST.CARar.R |only CARBayesST-2.0/CARBayesST/R/ST.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/ST.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARanova.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARar.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARanova.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARar.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARanova.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARar.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/print.carbayesST.R | 22 CARBayesST-2.0/CARBayesST/build |only CARBayesST-2.0/CARBayesST/inst |only CARBayesST-2.0/CARBayesST/man/CARBayesST-package.Rd | 80 CARBayesST-2.0/CARBayesST/man/ST.CARadaptive.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARanova.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARar.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARlinear.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARlocalised.Rd |only CARBayesST-2.0/CARBayesST/man/print.carbayesST.Rd | 7 CARBayesST-2.0/CARBayesST/src/CARBayesST.cpp | 1822 +++++++++++++++----- CARBayesST-2.0/CARBayesST/src/RcppExports.cpp | 699 +++++-- CARBayesST-2.0/CARBayesST/vignettes |only 50 files changed, 2074 insertions(+), 748 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-08-26 0.7
Title: Statistical Analysis of Mixed Ploidy Populations
Description: Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation
Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single
ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values
around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to
utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects
allowing integration with other packages such adegenet.
Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton <luke.pembleton@ecodev.vic.gov.au>
Diff between StAMPP versions 1.3 dated 2014-09-01 and 1.4 dated 2015-07-06
ChangeLog | 9 ++++++++- DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ R/stampp2genlight.R | 4 ++-- R/stamppAmova.R | 2 +- R/stamppConvert.R | 9 +++++---- R/stamppFst.R | 2 +- R/stamppGmatrix.R | 2 +- R/stamppNeisD.R | 2 +- R/stamppPhylip.R | 4 ++-- man/StAMPP-package.Rd | 8 ++++---- 12 files changed, 45 insertions(+), 35 deletions(-)
Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte <d.harte@gns.cri.nz>
Diff between HiddenMarkov versions 1.8-3 dated 2015-04-12 and 1.8-4 dated 2015-07-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 6 +++++- NEWS | 2 +- man/Changes.Rd | 4 +++- man/HiddenMarkov.Rd | 8 +++++--- 6 files changed, 23 insertions(+), 15 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>
Diff between schoRsch versions 1.1 dated 2014-08-23 and 1.2 dated 2015-07-05
DESCRIPTION | 17 ++- MD5 | 20 ++-- NAMESPACE | 1 R/anova_out.R | 238 +++++++++++++++++++++++++++---------------------------- R/outlier.R | 10 +- man/anova_out.Rd | 2 man/cd.Rd | 2 man/cor_out.Rd | 2 man/outlier.Rd | 4 man/schoRsch.Rd | 9 +- man/t_out.Rd | 4 11 files changed, 157 insertions(+), 152 deletions(-)
Title: A Framework for Comparing the Performance of MCMC Samplers
Description: A framework for running sets of MCMC samplers on sets of
distributions with a variety of tuning parameters, along with plotting
functions to visualize the results of those simulations. See sc-intro.pdf
for an introduction.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by
G. W. Stewart.
Maintainer: Madeleine Thompson <madeleineth@gmail.com>
Diff between SamplerCompare versions 1.2.6 dated 2015-02-22 and 1.2.7 dated 2015-07-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 4 +++- build/vignette.rds |binary inst/doc/glue.pdf |binary inst/doc/sc-intro.pdf |binary man/SamplerCompare-package.Rd | 6 +++--- 7 files changed, 16 insertions(+), 14 deletions(-)
More information about SamplerCompare at CRAN
Permanent link
Title: "Redis" Key/Value Database Client
Description: R client interface to the "Redis" key-value database.
Author: B. W. Lewis
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between rredis versions 1.6.9 dated 2014-09-15 and 1.7.0 dated 2015-07-05
rredis-1.6.9/rredis/inst/doc/rredis.R |only rredis-1.6.9/rredis/man/redis-package.Rd |only rredis-1.6.9/rredis/man/redisDecr.Rd |only rredis-1.6.9/rredis/man/redisDecrBy.Rd |only rredis-1.6.9/rredis/man/redisIncr.Rd |only rredis-1.6.9/rredis/man/redisIncrBy.Rd |only rredis-1.7.0/rredis/.Rinstignore |only rredis-1.7.0/rredis/DESCRIPTION | 12 ++-- rredis-1.7.0/rredis/MD5 | 51 +++++++++-------- rredis-1.7.0/rredis/NEWS | 14 ++++ rredis-1.7.0/rredis/R/controlCMD.R | 26 ++++---- rredis-1.7.0/rredis/R/redis-internal.R | 21 ++++++- rredis-1.7.0/rredis/R/strValCMD.R | 2 rredis-1.7.0/rredis/README | 70 +++++++++++++++++++++++ rredis-1.7.0/rredis/README.md | 71 +++++++++++++++++++++++- rredis-1.7.0/rredis/build |only rredis-1.7.0/rredis/inst/doc/rredis.Rnw | 53 ++++++++++++----- rredis-1.7.0/rredis/inst/doc/rredis.pdf |binary rredis-1.7.0/rredis/inst/test/basicTest.R |only rredis-1.7.0/rredis/inst/test/bitopTest.R |only rredis-1.7.0/rredis/inst/test/endTest.R |only rredis-1.7.0/rredis/inst/test/runTest.R |only rredis-1.7.0/rredis/inst/test/runit.basicTest.R | 3 - rredis-1.7.0/rredis/inst/test/runit.bitopTest.R | 2 rredis-1.7.0/rredis/inst/test/runit.setTest.R | 1 rredis-1.7.0/rredis/inst/test/runit.zsetTest.R | 2 rredis-1.7.0/rredis/inst/test/setTest.R |only rredis-1.7.0/rredis/inst/test/zsetTest.R |only rredis-1.7.0/rredis/man/incr.Rd |only rredis-1.7.0/rredis/man/redisConnect.Rd | 40 +++++-------- rredis-1.7.0/rredis/man/redisGet.Rd | 20 +++++- rredis-1.7.0/rredis/man/redisHIncrBy.Rd | 3 - rredis-1.7.0/rredis/man/redisTTL.Rd | 4 - rredis-1.7.0/rredis/man/rredis-package.Rd |only rredis-1.7.0/rredis/vignettes/rredis.Rnw | 53 ++++++++++++----- 35 files changed, 334 insertions(+), 114 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.3 dated 2015-06-24 and 1.3.4 dated 2015-07-05
DESCRIPTION | 11 MD5 | 49 NAMESPACE | 5 R/RcppExports.R | 15 R/Rlibeemd-package.R | 1 R/ceemdan.R | 10 R/ecg.R | 32 R/eemd.R | 10 R/emd.R | 17 R/emd_num_imfs.R |only R/extrema.R | 2 configure | 5760 +++++++++++++++++++++++++------------------------- man/ECG.Rd | 2 man/Rlibeemd.Rd | 2 man/ceemdan.Rd | 2 man/eemd.Rd | 2 man/emd.Rd | 2 man/extrema.Rd | 2 man/nIMFs.Rd | 4 src/RcppExports.cpp | 8 src/emd_num_imfsR.cpp | 12 src/extremaR.cpp | 2 src/printError.cpp | 8 tests |only 24 files changed, 2979 insertions(+), 2979 deletions(-)
Title: Computational Geometry
Description: R interface to (some of) cddlib
(http://www.ifor.math.ethz.ch/~fukuda/cdd_home/cdd.html).
Converts back and forth between two representations of a convex polytope:
as solution of a set of linear equalities and inequalities and as
convex hull of set of points and rays.
Also does linear programming and redundant generator elimination
(for example, convex hull in n dimensions). All functions can use exact
infinite-precision rational arithmetic.
Author: Charles J. Geyer <charlie@stat.umn.edu> and
Glen D. Meeden <glen@stat.umn.edu>, incorporates code from
cddlib (ver 0.94f) written by Komei Fukuda <fukuda@ifor.math.ethz.ch>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between rcdd versions 1.1-8 dated 2014-03-30 and 1.1-9 dated 2015-07-05
CHANGES | 5 DESCRIPTION | 13 +- MD5 | 68 +++++----- NAMESPACE | 1 build/vignette.rds |binary configure | 315 +++++++++++++++++++++---------------------------- inst/doc/vinny.pdf |binary man/allfaces.Rd | 2 man/linearity.Rd | 2 man/lpcdd.Rd | 2 man/redundant.Rd | 2 man/scdd.Rd | 2 src/allfaces.c | 3 src/allfaces_f.c | 3 src/cddcore.c | 9 + src/cddcore_f.c | 9 + src/cddio.c | 3 src/cddio_f.c | 3 src/cddlp.c | 25 +++ src/cddlp_f.c | 26 +++- src/linearity.c | 3 src/linearity_f.c | 3 src/lpcdd.c | 3 src/lpcdd_f.c | 3 src/my_unif_rand.c |only src/my_unif_rand.h |only src/qo.c | 1 src/qoq.c | 1 src/redund.c | 3 src/redund_f.c | 3 src/scdd.c | 3 src/scdd_f.c | 3 tests/bar.R | 3 tests/bar.Rout.save | 18 +- tests/chull2.R | 6 tests/chull2.Rout.save | 15 +- 36 files changed, 327 insertions(+), 234 deletions(-)
Title: Markov Chain Monte Carlo for Potts Models
Description: Does Markov chain Monte Carlo (MCMC) simulation of Potts models
and composite likelihood inference for Potts models.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif Johnson
<leif@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between potts versions 0.5-3 dated 2015-06-06 and 0.5-4 dated 2015-07-05
ChangeLog | 3 +++ DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ build/vignette.rds |binary 5 files changed, 15 insertions(+), 8 deletions(-)
Title: Rapid Digital Image Analysis of Leaf Area
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
Author: Masatoshi Katabuchi <mattocci27@gmail.com>
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>
Diff between LeafArea versions 0.1.0 dated 2015-04-20 and 0.1.1 dated 2015-07-05
DESCRIPTION | 13 ++++++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 6 +++++- R/eximg.r | 38 ++++++++++++++++---------------------- R/find.ij.R | 1 - R/readtext.ij.R | 9 ++++++--- R/run.ij.R | 38 +++++++++++++++++++++++++++----------- README.md |only data/leafdata.RData |binary man/LeafArea-package.Rd | 4 ++-- man/readtext.ij.Rd | 6 +++++- man/resmerge.ij.Rd | 16 +++++++++++++++- man/run.ij.Rd | 42 ++++++++++++++++++++---------------------- 13 files changed, 116 insertions(+), 80 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>
Diff between GSE versions 3.1 dated 2014-09-25 and 3.2 dated 2015-07-05
ChangeLog | 12 + DESCRIPTION | 17 +- MD5 | 44 +++--- NAMESPACE | 9 - R/CovEM.R | 16 +- R/GSE-utils.R | 64 +++++++- R/GSE.R | 39 +++-- R/TSGS.R | 37 ++++- R/emve-utils.R | 13 + R/emve.R | 259 +++++++++++++++++------------------- R/generic.R | 18 -- R/plots-utils.R | 4 R/simulation-utils.R | 3 man/CovEM.Rd | 5 man/GSE-class.Rd | 10 - man/GSE.Rd | 218 +++++++++++++++--------------- man/TSGS.Rd | 185 ++++++++++++++----------- man/emve-class.Rd | 10 - man/emve.Rd | 25 --- man/get-methods.Rd | 11 - src/emve.cpp | 363 ++++++++++++++++++++------------------------------- src/gse.cpp | 44 +++--- src/gse.h | 2 23 files changed, 694 insertions(+), 714 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.2-0 dated 2015-03-11 and 1.2-1 dated 2015-07-05
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NAMESPACE | 6 ++++-- man/baseline-package.Rd | 32 ++++++++++++++++++++++++++++++-- man/baseline.Rd | 28 ++++++++++++++++++++++++++++ man/getBaseline.Rd | 8 ++++---- man/optimWizard.Rd | 1 + man/plotBaseline.Rd | 5 +++-- 8 files changed, 84 insertions(+), 24 deletions(-)
Title: Gromov-Hausdorff Type Distances for Labeled Metric Spaces
Description: Computing Gromov-Hausdorff type l^p distances for labeled metric spaces. These distances were introduced in V.Liebscher, Gromov meets Phylogenetics - new Animals for the Zoo of Metrics on Tree Space. preprint arXiv:1504.05795, for phylogenetic trees but may apply to much more situations.
Author: Volkmar Liebscher
Maintainer: Volkmar Liebscher <volkmar.liebscher@uni-greifswald.de>
Diff between gromovlab versions 0.6-16 dated 2015-05-25 and 0.7-6 dated 2015-07-05
CHANGELOG | 9 +++++++++ DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 13 ++++++++----- man/gromovdist.Rd | 2 +- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Gender Prediction Based on First Names
Description: Utilizes the 'genderize.io' API to predict gender from first
names extracted from a text vector. The accuracy of prediction could be
controlled by two parameters: counts of a first name in the database and
probability of prediction.
Author: Kamil Wais [aut, cre]
Maintainer: Kamil Wais <kamil.wais@gmail.com>
Diff between genderizeR versions 1.1.0 dated 2015-04-22 and 1.2.0 dated 2015-07-05
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 11 +++++++++++ R/genderizeAPI.R | 10 ++++++---- R/genderizeR.R | 2 ++ README.md | 37 +++++++++++++++++++++++++------------ 7 files changed, 57 insertions(+), 28 deletions(-)
Title: Local Correlation, Spatial Inequalities and Other Tools
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <skalo@hua.gr>
Diff between lctools versions 0.2-2 dated 2015-04-15 and 0.2-3 dated 2015-07-05
lctools-0.2-2/lctools/inst/doc/SpatialAutocorrelation.R |only lctools-0.2-2/lctools/inst/doc/SpatialAutocorrelation.Rmd |only lctools-0.2-2/lctools/inst/doc/SpatialAutocorrelation.pdf |only lctools-0.2-3/lctools/DESCRIPTION | 12 ++-- lctools-0.2-3/lctools/MD5 | 39 +++++++------ lctools-0.2-3/lctools/NAMESPACE | 1 lctools-0.2-3/lctools/R/moransI.R | 12 ++-- lctools-0.2-3/lctools/R/moransI.w.R |only lctools-0.2-3/lctools/R/spGini.R | 27 ++++++--- lctools-0.2-3/lctools/R/spGini.w.R |only lctools-0.2-3/lctools/R/w.matrix.R |only lctools-0.2-3/lctools/build/vignette.rds |binary lctools-0.2-3/lctools/data/GR.Municipalities.RData |binary lctools-0.2-3/lctools/data/VotesGR.RData |binary lctools-0.2-3/lctools/inst/doc/SpatialInequalities.Rmd | 10 +-- lctools-0.2-3/lctools/inst/doc/SpatialInequalities.pdf |binary lctools-0.2-3/lctools/man/lctools-package.Rd | 10 +-- lctools-0.2-3/lctools/man/mc_spGini.Rd | 2 lctools-0.2-3/lctools/man/moransI.Rd | 18 +++--- lctools-0.2-3/lctools/man/moransI.w.Rd |only lctools-0.2-3/lctools/man/spGini.Rd | 9 +-- lctools-0.2-3/lctools/man/spGini.w.Rd |only lctools-0.2-3/lctools/man/w.matrix.Rd |only lctools-0.2-3/lctools/vignettes/SpatialAutocorrelation.Rmd | 14 ++-- lctools-0.2-3/lctools/vignettes/SpatialInequalities.Rmd | 10 +-- 25 files changed, 91 insertions(+), 73 deletions(-)
Title: R Interface to LTP-Cloud Service
Description: R interface to LTP-Cloud service for Natural Language Processing
in Chinese. For more details please visit http://www.ltp-cloud.com/. Visit
https://github.com/hetong007/rLTP for up-to-date version.
Author: Tong He <hetong007@gmail.com>
Maintainer: Tong He <hetong007@gmail.com>
Diff between rLTP versions 0.1 dated 2015-01-28 and 0.1.2 dated 2015-07-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ltp.R | 2 +- README.md | 12 ++++++++++++ 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative
discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences,
turns of talk, syllables and other assorted analysis tasks. The
package provides parsing tools for preparing transcript data.
Many functions enable the user to aggregate data by any number
of grouping variables, providing analysis and seamless
integration with other R packages that undertake higher level
analysis and visualization of text. This affords the user a
more efficient and targeted analysis. 'qdap' is designed for
transcript analysis, however, many functions are applicable to
other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.1 dated 2015-05-11 and 2.2.2 dated 2015-07-05
qdap-2.2.1/qdap/man/deprecated.Rd |only qdap-2.2.1/qdap/man/type_text_ratio.Rd |only qdap-2.2.2/qdap/DESCRIPTION | 45 - qdap-2.2.2/qdap/MD5 | 172 ++-- qdap-2.2.2/qdap/NAMESPACE | 13 qdap-2.2.2/qdap/NEWS | 26 qdap-2.2.2/qdap/R/Network.R | 8 qdap-2.2.2/qdap/R/adjacency_matrix.R | 6 qdap-2.2.2/qdap/R/as.tdm.R | 29 qdap-2.2.2/qdap/R/automated_readability_index.R | 314 ++++---- qdap-2.2.2/qdap/R/build_qdap_vignette.R | 4 qdap-2.2.2/qdap/R/chaining.R | 3 qdap-2.2.2/qdap/R/check_spelling.R | 18 qdap-2.2.2/qdap/R/chunker.R | 2 qdap-2.2.2/qdap/R/cm_bidist.R | 6 qdap-2.2.2/qdap/R/cm_debug.R | 2 qdap-2.2.2/qdap/R/cm_df.temp.R | 2 qdap-2.2.2/qdap/R/cm_distance.R | 16 qdap-2.2.2/qdap/R/cm_dummy2long.R | 2 qdap-2.2.2/qdap/R/cm_long2dummy.R | 2 qdap-2.2.2/qdap/R/cm_time.temp.R | 2 qdap-2.2.2/qdap/R/cmspans.R | 4 qdap-2.2.2/qdap/R/col.fn.R | 6 qdap-2.2.2/qdap/R/deprecated.R | 686 +++++++++--------- qdap-2.2.2/qdap/R/dir_map.R | 2 qdap-2.2.2/qdap/R/discourse_map.R | 22 qdap-2.2.2/qdap/R/dissimilarity.R | 2 qdap-2.2.2/qdap/R/diversity.R | 2 qdap-2.2.2/qdap/R/end_mark.R | 10 qdap-2.2.2/qdap/R/formality.R | 36 qdap-2.2.2/qdap/R/gantt.R | 28 qdap-2.2.2/qdap/R/gantt_wrap.R | 6 qdap-2.2.2/qdap/R/gradient_cloud.R | 16 qdap-2.2.2/qdap/R/htruncdf.R | 2 qdap-2.2.2/qdap/R/inspect_text.R |only qdap-2.2.2/qdap/R/kullback_leibler.R | 8 qdap-2.2.2/qdap/R/left_just.R | 4 qdap-2.2.2/qdap/R/lexical_classification.R | 54 - qdap-2.2.2/qdap/R/mcsv_r.R | 4 qdap-2.2.2/qdap/R/multiscale.R | 6 qdap-2.2.2/qdap/R/name2sex.R | 2 qdap-2.2.2/qdap/R/new_project.R | 4 qdap-2.2.2/qdap/R/ngrams.R | 38 qdap-2.2.2/qdap/R/object_pronoun_type.R | 13 qdap-2.2.2/qdap/R/partition.R | 2 qdap-2.2.2/qdap/R/phrase_net.R | 2 qdap-2.2.2/qdap/R/polarity.R | 59 - qdap-2.2.2/qdap/R/pos.R | 20 qdap-2.2.2/qdap/R/pronoun_type.R | 13 qdap-2.2.2/qdap/R/qda.handler.R | 4 qdap-2.2.2/qdap/R/qheat.R | 12 qdap-2.2.2/qdap/R/random_sent.R | 2 qdap-2.2.2/qdap/R/read.docx.R | 2 qdap-2.2.2/qdap/R/read.transcript.R | 6 qdap-2.2.2/qdap/R/sentSplit.R | 2 qdap-2.2.2/qdap/R/stemmer.R | 4 qdap-2.2.2/qdap/R/strWrap.R | 2 qdap-2.2.2/qdap/R/subject_pronoun_type.R | 13 qdap-2.2.2/qdap/R/termco.h.R | 6 qdap-2.2.2/qdap/R/tot_plot.R | 2 qdap-2.2.2/qdap/R/trans_cloud.R | 16 qdap-2.2.2/qdap/R/trans_context.R | 2 qdap-2.2.2/qdap/R/trans_venn.R | 6 qdap-2.2.2/qdap/R/type_token_ratio.R | 8 qdap-2.2.2/qdap/R/unique_by.R | 4 qdap-2.2.2/qdap/R/utils.R | 10 qdap-2.2.2/qdap/R/wfm.R | 20 qdap-2.2.2/qdap/R/which.R | 8 qdap-2.2.2/qdap/R/word_associate.R | 4 qdap-2.2.2/qdap/R/word_cor.R | 8 qdap-2.2.2/qdap/R/word_count.R | 3 qdap-2.2.2/qdap/R/word_network_plot.R | 8 qdap-2.2.2/qdap/R/word_position.R | 19 qdap-2.2.2/qdap/R/word_proximity.R | 4 qdap-2.2.2/qdap/R/word_stats.R | 6 qdap-2.2.2/qdap/inst/CITATION | 4 qdap-2.2.2/qdap/inst/doc/cleaning_and_debugging.pdf |binary qdap-2.2.2/qdap/inst/doc/tm_package_compatibility.pdf |binary qdap-2.2.2/qdap/man/as.tdm.Rd | 3 qdap-2.2.2/qdap/man/chain.Rd | 3 qdap-2.2.2/qdap/man/check_spelling.Rd | 2 qdap-2.2.2/qdap/man/discourse_map.Rd | 10 qdap-2.2.2/qdap/man/formality.Rd | 2 qdap-2.2.2/qdap/man/inspect_text.Rd |only qdap-2.2.2/qdap/man/ngrams.Rd | 38 qdap-2.2.2/qdap/man/polarity.Rd | 7 qdap-2.2.2/qdap/man/print.inspect_text.Rd |only qdap-2.2.2/qdap/man/stemmer.Rd | 2 qdap-2.2.2/qdap/man/type_token_ratio.Rd |only qdap-2.2.2/qdap/tests/testthat/test-as.tdm.R | 4 90 files changed, 1061 insertions(+), 918 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.3.0 dated 2015-07-02 and 0.3.1 dated 2015-07-05
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NAMESPACE | 1 R/latex2exp.R | 44 +++++++++++++++--------- inst/doc/latex2exp.html | 86 ++++++++++++++++++------------------------------ vignettes/latex2exp.Rmd | 11 +++--- 6 files changed, 77 insertions(+), 83 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Diff between bit64 versions 0.9-4 dated 2014-04-09 and 0.9-5 dated 2015-07-05
Description:
Package 'bit64' provides serializable S3 atomic 64bit (signed) integers
that can be used in vectors, matrices, arrays and data.frames. Methods are
available for coercion from and to logicals, integers, doubles, characters
and factors as well as many elementwise and summary functions. Many fast
algorithmic operations such as 'match' and 'order' support interactive data
exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel
DESCRIPTION | 10 +++++-----
MD5 | 22 +++++++++++-----------
NAMESPACE | 21 ++++++++++-----------
NEWS | 35 ++++++++++++++++++++++++++++-------
R/integer64.R | 17 +++++++++++++++++
R/sort64.R | 12 +++++-------
R/zzz.R | 1 -
man/as.integer64.character.rd | 2 ++
man/bit64-package.rd | 1 +
src/integer64.c | 10 ++++++++--
src/sort64.c | 8 ++++++--
src/sort64.h | 2 +-
12 files changed, 94 insertions(+), 47 deletions(-)
Title: Standard Processing Tools for Electromyogram Signals
Description: Data processing tools for electromyogram (EMG) signals to compute the rectified, integrated and averaged EMG. Tools to plot the ensemble average of the EMG.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero <jaguerrero@correo.uaa.mx>
Diff between biosignalEMG versions 1.0.2 dated 2015-04-09 and 1.0.3 dated 2015-07-05
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS | 6 ++++++ man/biosignalEMG-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as defined by Kalbfleisch and Prentice. The underlying survival functions of the event of interest in each group can be estimated using either the (weighted) Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition probabilities in Markov multi-state models. Right-censored and left-truncated data is supported. Moreover, the difference in restricted mean survival can be estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.1 dated 2015-07-03 and 1.2 dated 2015-07-05
DESCRIPTION | 8 +- MD5 | 18 +++--- R/ahr.R | 2 R/aj.R | 4 - R/fastkm.R | 2 R/quantiles.R | 3 + R/wkm.R | 13 ++-- inst/tests/test-aj.R | 29 ++-------- inst/tests/test-wkm.R | 6 +- src/prodlim.cpp | 138 ++++++++++++++++++++++++++------------------------ 10 files changed, 112 insertions(+), 111 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', and 'AntWeb'. Includes functionality for retrieving
species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.2.4 dated 2015-01-22 and 0.3.0 dated 2015-07-04
spocc-0.2.4/spocc/NEWS |only spocc-0.2.4/spocc/R/clean_spocc.r |only spocc-0.2.4/spocc/R/mapggplot.R |only spocc-0.2.4/spocc/R/mapgist.r |only spocc-0.2.4/spocc/R/mapleaflet.r |only spocc-0.2.4/spocc/R/occ_to_sp.r |only spocc-0.2.4/spocc/R/util_github.r |only spocc-0.2.4/spocc/R/util_rcharts.r |only spocc-0.2.4/spocc/man/basemaps.Rd |only spocc-0.2.4/spocc/man/clean_spocc.Rd |only spocc-0.2.4/spocc/man/get_colors.Rd |only spocc-0.2.4/spocc/man/get_palette.Rd |only spocc-0.2.4/spocc/man/handle_sp.Rd |only spocc-0.2.4/spocc/man/mapggplot.Rd |only spocc-0.2.4/spocc/man/mapgist.Rd |only spocc-0.2.4/spocc/man/mapleaflet.Rd |only spocc-0.2.4/spocc/man/occ_to_sp.Rd |only spocc-0.2.4/spocc/man/palettes.Rd |only spocc-0.2.4/spocc/man/spocc_blanktheme.Rd |only spocc-0.2.4/spocc/man/spocc_rcharts_togeojson.Rd |only spocc-0.2.4/spocc/man/spocc_stylegeojson.Rd |only spocc-0.2.4/spocc/man/spocc_togeojson.Rd |only spocc-0.2.4/spocc/tests/testthat/test-ggmap.R |only spocc-0.2.4/spocc/tests/testthat/test-mapleaflet.R |only spocc-0.3.0/spocc/DESCRIPTION | 26 spocc-0.3.0/spocc/MD5 | 118 ++-- spocc-0.3.0/spocc/NAMESPACE | 110 ++- spocc-0.3.0/spocc/R/as.antweb.R |only spocc-0.3.0/spocc/R/as.bison.R |only spocc-0.3.0/spocc/R/as.ecoengine.R |only spocc-0.3.0/spocc/R/as.gbif.R |only spocc-0.3.0/spocc/R/as.inat.R |only spocc-0.3.0/spocc/R/handle_sp.R | 88 +-- spocc-0.3.0/spocc/R/inat.R |only spocc-0.3.0/spocc/R/inspect.R |only spocc-0.3.0/spocc/R/methods.r | 115 ++-- spocc-0.3.0/spocc/R/occ.r | 292 ++-------- spocc-0.3.0/spocc/R/occ2df.R |only spocc-0.3.0/spocc/R/occ_names.R | 67 +- spocc-0.3.0/spocc/R/occ_options.r | 13 spocc-0.3.0/spocc/R/on_load.R |only spocc-0.3.0/spocc/R/plugins.r | 258 ++++++--- spocc-0.3.0/spocc/R/read_wkt.R |only spocc-0.3.0/spocc/R/rename.R |only spocc-0.3.0/spocc/R/spocc-package.R | 9 spocc-0.3.0/spocc/R/tbldf.R |only spocc-0.3.0/spocc/R/wkt_bbox.R |only spocc-0.3.0/spocc/R/wkt_vis.r | 52 - spocc-0.3.0/spocc/R/zzz.r | 347 ------------ spocc-0.3.0/spocc/README.md | 208 ++----- spocc-0.3.0/spocc/build/vignette.rds |binary spocc-0.3.0/spocc/inst/doc/spocc_vignette.Rmd | 492 +++++++---------- spocc-0.3.0/spocc/inst/doc/spocc_vignette.html | 504 +++++++----------- spocc-0.3.0/spocc/inst/js |only spocc-0.3.0/spocc/man/as.antweb.Rd |only spocc-0.3.0/spocc/man/as.bison.Rd |only spocc-0.3.0/spocc/man/as.ecoengine.Rd |only spocc-0.3.0/spocc/man/as.gbif.Rd |only spocc-0.3.0/spocc/man/as.inat.Rd |only spocc-0.3.0/spocc/man/bbox2wkt.Rd | 11 spocc-0.3.0/spocc/man/fixnames.Rd | 2 spocc-0.3.0/spocc/man/inspect.Rd |only spocc-0.3.0/spocc/man/occ.Rd | 105 ++- spocc-0.3.0/spocc/man/occ2df.Rd | 43 + spocc-0.3.0/spocc/man/occ_coverage.Rd | 2 spocc-0.3.0/spocc/man/occ_names.Rd | 15 spocc-0.3.0/spocc/man/occ_names_options.Rd | 2 spocc-0.3.0/spocc/man/occ_options.Rd | 6 spocc-0.3.0/spocc/man/spocc-package.Rd | 9 spocc-0.3.0/spocc/man/spocc_capwords.Rd | 2 spocc-0.3.0/spocc/man/spocc_colClasses.Rd | 2 spocc-0.3.0/spocc/man/spocc_duplicates.Rd | 2 spocc-0.3.0/spocc/man/spocc_objects.Rd | 10 spocc-0.3.0/spocc/man/spocc_type_sum.Rd | 4 spocc-0.3.0/spocc/man/wkt.Rd |only spocc-0.3.0/spocc/man/wkt_vis.Rd | 11 spocc-0.3.0/spocc/tests/testthat.R |only spocc-0.3.0/spocc/tests/testthat/test-common_params.R |only spocc-0.3.0/spocc/tests/testthat/test-geometry.R |only spocc-0.3.0/spocc/tests/testthat/test-idbasedsearch.R |only spocc-0.3.0/spocc/tests/testthat/test-occ.R | 82 -- spocc-0.3.0/spocc/tests/testthat/test-options.R |only spocc-0.3.0/spocc/vignettes/spocc_vignette.Rmd | 492 +++++++---------- 83 files changed, 1477 insertions(+), 2022 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. The retrieved data has flat structure, i.e. the relationship between comments is not preserved.This may be addressed in the next update of this package. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 3 functions, one for extracting relevant URLS, one for extracting features out of given URLs and one that does both together.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 1.0.0 dated 2015-06-16 and 1.1.1 dated 2015-07-04
RedditExtractoR-1.0.0/RedditExtractoR/man/ExtractAttributes.Rd |only RedditExtractoR-1.0.0/RedditExtractoR/man/GetReddit.Rd |only RedditExtractoR-1.0.0/RedditExtractoR/man/ObtainRedditURLs.Rd |only RedditExtractoR-1.1.1/RedditExtractoR/DESCRIPTION | 9 RedditExtractoR-1.1.1/RedditExtractoR/MD5 | 14 RedditExtractoR-1.1.1/RedditExtractoR/NAMESPACE | 8 RedditExtractoR-1.1.1/RedditExtractoR/R/RedditExtractoR.R | 215 +++++----- RedditExtractoR-1.1.1/RedditExtractoR/man/RedditExtractoR-package.Rd | 10 RedditExtractoR-1.1.1/RedditExtractoR/man/get_reddit.Rd |only RedditExtractoR-1.1.1/RedditExtractoR/man/reddit_content.Rd |only RedditExtractoR-1.1.1/RedditExtractoR/man/reddit_urls.Rd |only 11 files changed, 133 insertions(+), 123 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9 dated 2015-06-19 and 0.9.1 dated 2015-07-04
DESCRIPTION | 6 +++--- MD5 | 20 +++++++++++--------- NEWS | 5 +++++ R/escape.R | 4 ++-- R/handle.R | 7 ++++++- build/vignette.rds |binary inst/doc/intro.html | 32 ++++++++++++++++---------------- src/curl.c | 10 ++++++++-- src/escape.c | 4 ++-- src/handle.c | 5 +++++ tests/testthat/test-certificates.R |only tests/testthat/test-escape.R |only 12 files changed, 58 insertions(+), 35 deletions(-)
Title: Trust Region Optimization
Description: Does local optimization using two derivatives and trust regions.
Guaranteed to converge to local minimum of objective function.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between trust versions 0.1-6 dated 2014-03-29 and 0.1-7 dated 2015-07-04
ChangeLog | 2 ++ DESCRIPTION | 14 ++++++++------ MD5 | 26 ++++++++++++++++++-------- NAMESPACE | 1 + build/vignette.rds |binary tests/bar.Rout.save |only tests/baz.Rout.save |only tests/foo.Rout.save |only tests/fred.R | 6 ++++-- tests/fred.Rout.save |only tests/goo.R | 2 ++ tests/goo.Rout.save |only tests/gred.R | 2 ++ tests/gred.Rout.save |only tests/hero.Rout.save |only tests/hoo.R | 16 ++++++++++------ tests/hoo.Rout.save |only tests/poo.Rout.save |only tests/qux.Rout.save |only 19 files changed, 47 insertions(+), 22 deletions(-)
Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma in [-1,0], offers several estimates to compute estimates of gamma. The estimates are based on the principle of replacing the order statistics by quantiles of a distribution function based on a log--concave density function. This procedure is justified by the fact that the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Ru{f}{i}bach <kaspar.rufibach@gmail.com> and Samuel Mueller <samuel.mueller@sydney.edu.au>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between smoothtail versions 2.0.3 dated 2014-02-06 and 2.0.4 dated 2015-07-04
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 26 +++++++++++++------------- NEWS | 4 ++++ man/smoothtail-package.Rd | 8 ++++---- 5 files changed, 31 insertions(+), 26 deletions(-)
Title: Generate LaTeX Tables of Descriptive Statistics
Description: These functions are especially helpful when writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between reporttools versions 1.1.1 dated 2013-11-06 and 1.1.2 dated 2015-07-04
DESCRIPTION | 13 +++++++------ MD5 | 19 ++++++++++--------- NAMESPACE | 4 ++-- NEWS | 4 ++++ build |only inst/doc/reporttools.pdf |binary man/displayKbyC.Rd | 2 +- man/formatPercent.Rd | 2 +- man/reporttools-package.Rd | 10 +++++----- man/tableContinuous.Rd | 2 +- man/tableNominal.Rd | 2 +- 11 files changed, 32 insertions(+), 26 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.3 dated 2014-12-10 and 0.1.4 dated 2015-07-04
ChangeLog | 24 +++++++++++++++++++++ DESCRIPTION | 14 ++++++------ MD5 | 14 ++++++------ README.md | 46 ++++++++++++++++++++++++----------------- inst/NEWS.Rd | 8 +++++++ inst/tests/runit.basicRtests.R | 2 - man/rhiredis.Rd | 1 tests/runUnitTests.R | 6 ++--- 8 files changed, 78 insertions(+), 37 deletions(-)
Title: Least Squares, Logistic, and Cox-Regression with Ordered
Predictors
Description: In biomedical studies, researchers are often interested in assessing the association between one or more ordinal explanatory variables and an outcome variable, at the same time adjusting for covariates of any type. The outcome variable may be continuous, binary, or represent censored survival times. In the absence of a precise knowledge of the response function, using monotonicity constraints on the ordinal variables improves efficiency in estimating parameters, especially when sample sizes are small. This package implements an active set algorithm that efficiently computes such estimators.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between OrdFacReg versions 1.0.5 dated 2014-09-06 and 1.0.6 dated 2015-07-04
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NAMESPACE | 15 +++++++++------ NEWS | 4 ++++ R/logRegSubspace.r | 4 ++-- man/ordFacReg-package.Rd | 4 ++-- 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Communication Between Editor and Viewer for Literate Programs
Description: This utility eases the debugging of literate documents
('noweb' files) by patching the synchronization information
(the '.synctex(.gz)' file) produced by 'pdflatex' with
concordance information produced by 'Sweave' or 'knitr' and
'Sweave' or 'knitr' ; this allows for bilateral communication
between a text editor (visualizing the 'noweb' source) and
a viewer (visualizing the resultant 'PDF'), thus bypassing
the intermediate 'TeX' file.
Author: Jan Gleixner [aut],
Daniel Hicks [ctb],
Emmanuel Charpentier [aut, cre]
Maintainer: Emmanuel Charpentier <emm.charpentier@free.fr>
Diff between patchSynctex versions 0.1-2 dated 2015-05-01 and 0.1-3 dated 2015-07-04
patchSynctex-0.1-2/patchSynctex/.Rinstignore |only patchSynctex-0.1-3/patchSynctex/DESCRIPTION | 8 ++++---- patchSynctex-0.1-3/patchSynctex/MD5 | 8 ++++---- patchSynctex-0.1-3/patchSynctex/NAMESPACE | 1 + patchSynctex-0.1-3/patchSynctex/NEWS | 1 + patchSynctex-0.1-3/patchSynctex/man/patchSynctex-package.Rd | 2 +- 6 files changed, 11 insertions(+), 9 deletions(-)
Title: File System Utility Functions for 'NeuroAnatomy Toolbox'
Description: Utility functions that may be of general interest but are
specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes
functions to provide a basic make style system to update files based on
timestamp information, file locking and 'touch' utility. Convenience
functions for working with file paths include 'abs2rel', 'split_path'
and 'common_path'. Finally there are utility functions for working with
'zip' and 'gzip' files including integrity tests.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat.utils versions 0.5 dated 2015-07-02 and 0.5.1 dated 2015-07-04
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS | 5 +++++ R/gziputils.r | 18 +++++++++++------- man/gzip.crc.Rd | 12 +++++++++--- tests/testthat/test-gziputils.r | 10 ++-------- tests/testthat/testdata/hello.gz |only 7 files changed, 37 insertions(+), 27 deletions(-)
Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users
to create interactive charts based on data frames. Charts
are displayed locally via the R HTTP help server. A modern
browser with Internet connection is required and for some
charts a Flash player. The data remains local and is not
uploaded to Google.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between googleVis versions 0.5.8 dated 2015-01-21 and 0.5.9 dated 2015-07-04
googleVis-0.5.8/googleVis/DESCRIPTION |only googleVis-0.5.8/googleVis/MD5 |only googleVis-0.5.8/googleVis/README.md |only googleVis-0.5.8/googleVis/THANKS |only googleVis-0.5.8/googleVis/build |only googleVis-0.5.8/googleVis/man |only googleVis-0.5.8/googleVis/vignettes/Ideas |only googleVis-0.5.8/googleVis/vignettes/Using_Roles_via_googleVis.Rmd |only googleVis-0.5.8/googleVis/vignettes/Using_Trendlines_with_googleVis.Rmd |only googleVis-0.5.8/googleVis/vignettes/Using_googleVis_with_knitr.Rmd |only googleVis-0.5.8/googleVis/vignettes/figures/Apostrophe.pdf |only googleVis-0.5.8/googleVis/vignettes/figures/CambR_googleVis_29_May_2012.pdf |only googleVis-0.5.8/googleVis/vignettes/figures/CreatePost.pdf |only googleVis-0.5.8/googleVis/vignettes/figures/MotionChart.pdf |only googleVis-0.5.8/googleVis/vignettes/figures/Options.pdf |only googleVis-0.5.8/googleVis/vignettes/figures/googleVisDemoPlots.pdf |only googleVis-0.5.8/googleVis/vignettes/googleVis.bib |only googleVis-0.5.8/googleVis/vignettes/googleVis_examples.Rmd |only googleVis-0.5.8/googleVis/vignettes/mystyle.css |only googleVis-0.5.9/googleVis/NAMESPACE | 7 googleVis-0.5.9/googleVis/NEWS | 12 googleVis-0.5.9/googleVis/R/gvisIntensityMap.R | 4 googleVis-0.5.9/googleVis/inst/doc/Using_Roles_via_googleVis.html | 220 +-- googleVis-0.5.9/googleVis/inst/doc/Using_Trendlines_with_googleVis.html | 80 - googleVis-0.5.9/googleVis/inst/doc/Using_googleVis_with_knitr.html | 76 - googleVis-0.5.9/googleVis/inst/doc/googleVis.pdf |binary googleVis-0.5.9/googleVis/inst/doc/googleVis_examples.html | 730 +++++----- googleVis-0.5.9/googleVis/vignettes/figures/MarkdownExample.pdf |binary 28 files changed, 572 insertions(+), 557 deletions(-)
Title: Fit GLD Regression Model and GLD Quantile Regression Model to
Empirical Data
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDreg versions 1.0.2 dated 2015-03-05 and 1.0.3 dated 2015-07-04
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 4 +++- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDEX versions 2.0.0.2 dated 2014-12-22 and 2.0.0.3 dated 2015-07-04
GLDEX-2.0.0.2/GLDEX/README |only GLDEX-2.0.0.3/GLDEX/DESCRIPTION | 10 +++++----- GLDEX-2.0.0.3/GLDEX/MD5 | 5 ++--- GLDEX-2.0.0.3/GLDEX/NAMESPACE | 3 +++ 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Foraminifera and Community Ecology Analyses
Description: SHE, FORAM Index and ABC Method analyses and custom plot
functions for community data.
Author: Rodrigo Aluizio
Maintainer: Rodrigo Aluizio <r.aluizio@gmail.com>
Diff between forams versions 2.0-4 dated 2014-02-18 and 2.0-5 dated 2015-07-04
forams-2.0-4/forams/man/plot.abc.Rd |only forams-2.0-4/forams/man/plot.fi.Rd |only forams-2.0-4/forams/man/plot.she.Rd |only forams-2.0-5/forams/CHANGELOG | 7 ++++++- forams-2.0-5/forams/DESCRIPTION | 12 ++++++------ forams-2.0-5/forams/MD5 | 14 ++++++-------- forams-2.0-5/forams/NAMESPACE | 2 ++ forams-2.0-5/forams/R/Classes.r | 2 +- forams-2.0-5/forams/man/forams-package.Rd | 6 +++--- forams-2.0-5/forams/man/plot-methods.Rd |only 10 files changed, 24 insertions(+), 19 deletions(-)
More information about tseriesEntropy at CRAN
Permanent link
Title: Various R Programming Tools for Data Manipulation
Description: Various R programming tools for data manipulation, including:
- medical unit conversions ('ConvertMedUnits', 'MedUnits'),
- combining objects ('bindData', 'cbindX', 'combine', 'interleave'),
- character vector operations ('centerText', 'startsWith', 'trim'),
- factor manipulation ('levels', 'reorder.factor', 'mapLevels'),
- obtaining information about R objects ('object.size', 'elem', 'env',
'humanReadable', 'is.what', 'll', 'keep', 'ls.funs',
'Args','nPairs', 'nobs'),
- manipulating MS-Excel formatted files ('read.xls',
'installXLSXsupport', 'sheetCount', 'xlsFormats'),
- generating fixed-width format files ('write.fwf'),
- extricating components of date & time objects ('getYear', 'getMonth',
'getDay', 'getHour', 'getMin', 'getSec'),
- operations on columns of data frames ('matchcols', 'rename.vars'),
- matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'),
- operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'),
- operations on data frames ('frameApply', 'wideByFactor'),
- value of last evaluated expression ('ans'), and
- wrapper for 'sample' that ensures consistent behavior for both
scalar and vector arguments ('resample').
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
Magnusson, Jim Rogers, and others
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gdata versions 2.16.1 dated 2015-05-01 and 2.17.0 dated 2015-07-04
gdata-2.16.1/gdata/ChangeLog |only gdata-2.16.1/gdata/NEWS |only gdata-2.17.0/gdata/DESCRIPTION | 10 gdata-2.17.0/gdata/MD5 | 28 gdata-2.17.0/gdata/NAMESPACE | 4 gdata-2.17.0/gdata/R/upperTriangle.R | 34 gdata-2.17.0/gdata/inst/ChangeLog | 1790 ++++++----------- gdata-2.17.0/gdata/inst/NEWS | 18 gdata-2.17.0/gdata/inst/doc/mapLevels.pdf |binary gdata-2.17.0/gdata/inst/doc/unknown.pdf |binary gdata-2.17.0/gdata/man/upperTriangle.Rd | 39 gdata-2.17.0/gdata/tests/test.humanReadable.Rout.save | 2 gdata-2.17.0/gdata/tests/test.read.xls.R | 74 gdata-2.17.0/gdata/tests/test.read.xls.Rout.save | 76 gdata-2.17.0/gdata/tests/test.reorder.factor.Rout.save | 2 gdata-2.17.0/gdata/tests/tests.write.fwf.Rout.save | 2 16 files changed, 849 insertions(+), 1230 deletions(-)
Title: A Collection of Tools for the Analysis of Remote Acoustic
Telemetry Data
Description: Designed to facilitate the assimilation, analysis and synthesis of animal location and movement data collected by the VEMCO suite of acoustic transmitters and receivers. As well as database and geographic information capabilities the principal feature of VTrack is the qualification and identification of ecologically relevant events from the acoustic detection and sensor data. This procedure condenses the acoustic detection database by orders of magnitude, greatly enhancing the synthesis of acoustic detection data.
Author: Ross G. Dwyer, Mathew E. Watts, Hamish A. Campbell & Craig E. Franklin
Maintainer: Ross Dwyer <ross.dwyer@uq.edu.au>
Diff between VTrack versions 1.10 dated 2015-07-02 and 1.11 dated 2015-07-04
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/GenerateAnimationKMLFile_Multitag.R | 13 +++++++------ man/ExtractRecSummary.Rd | 11 +++++++++++ man/ExtractTagSummary.Rd | 12 ++++++++++++ man/GenerateAnimationKMLFile_Multitag.Rd | 13 +++++++++++-- man/GenerateAnimationKMLFile_Track.Rd | 12 +++++++----- man/ReadInputData.Rd | 2 +- man/VTrack-package.Rd | 4 ++-- 9 files changed, 65 insertions(+), 30 deletions(-)
Title: Routines for Fitting Kinetic Models to Chemical Degradation Data
Description:
The FOCUS Kinetics Report first published in 2006 describes mathematical
models and recommends statistical methods for the evaluation of
chemical degradation data. This package implements fitting the kinetic
models suitable for observations of the decline of a single chemical
compound (no metabolite formation/decline or multi-compartment kinetics).
Please note that no warranty is implied for correctness of results or
fitness for a particular purpose. 'kinfit' is maintained, but not
actively developed at the moment. Please check the 'mkin' package for an
actively developed package for kinetic evaluations of degradation data.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between kinfit versions 1.1.13 dated 2014-11-25 and 1.1.14 dated 2015-07-04
DESCRIPTION | 42 +++++++++++++++++++----------------- MD5 | 30 ++++++++++++------------- NAMESPACE | 4 +++ build/vignette.rds |binary data/FOCUS_2006_A.rda |binary data/FOCUS_2006_B.rda |binary data/FOCUS_2006_C.rda |binary data/FOCUS_2006_D.rda |binary data/FOCUS_2006_DFOP_ref_A_to_B.rda |binary data/FOCUS_2006_E.rda |binary data/FOCUS_2006_F.rda |binary data/FOCUS_2006_FOMC_ref_A_to_F.rda |binary data/FOCUS_2006_HS_ref_A_to_F.rda |binary data/FOCUS_2006_SFO_ref_A_to_F.rda |binary inst/doc/examples.pdf |binary inst/doc/kinfit.pdf |binary 16 files changed, 42 insertions(+), 34 deletions(-)
Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on spatstat), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones".
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@upm.es>
Diff between ecespa versions 1.1-7 dated 2013-03-13 and 1.1-8 dated 2015-07-04
DESCRIPTION | 18 +++++-------- MD5 | 42 ++++++++++++++++---------------- NAMESPACE | 1 R/Kinhom.log.R | 2 - R/Kmm.R | 2 - R/LF.gof.R |only R/getis.R | 2 - R/haz.ppp.R | 2 - R/marksum.R | 2 - R/plot.ecespa.getis.R | 2 - R/plot.ecespa.marksum.R | 8 +++--- R/rIPCP.R | 63 ++++++++++++++++++------------------------------ R/syrjala.test.R | 6 ++-- R/syrjala0.R | 2 - man/Helianthemum.Rd | 2 - man/K012.Rd | 1 man/K1K2.rd | 2 - man/LF.gof.Rd |only man/dixon2002.Rd | 4 ++- man/getis.rd | 4 +-- man/gypsophylous.rd | 1 man/marksum.rd | 17 ++++++++---- man/seedlings.Rd | 2 - 23 files changed, 86 insertions(+), 99 deletions(-)
Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference
semantics, similar to R's built-in reference classes. Compared to reference
classes, R6 classes are simpler and lighter-weight, and they are not built
on S4 classes so they do not require the methods package. These classes
allow public and private members, and they support inheritance, even when
the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.0.1 dated 2014-10-29 and 2.1.0 dated 2015-07-03
DESCRIPTION | 14 - LICENSE | 2 MD5 | 54 +++--- NAMESPACE | 2 NEWS | 25 ++- R/clone.R |only R/generator_funs.R | 20 ++ R/new.R | 5 R/print.R | 40 +++- R/r6_class.R | 208 ++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/Debugging.html | 3 inst/doc/Introduction.R | 143 +++++++++++++++++ inst/doc/Introduction.Rmd | 186 +++++++++++++++++++++- inst/doc/Introduction.html | 146 ++++++++++++++++- inst/doc/Performance.R | 112 ++++++++----- inst/doc/Performance.Rmd | 160 +++++++++++-------- inst/doc/Performance.html | 315 ++++++++++++++++++++------------------ inst/doc/Portable.R | 14 + inst/doc/Portable.Rmd | 37 ++++ inst/doc/Portable.html | 29 +++ man/R6Class.Rd | 174 ++++++++++++++++++++ tests/testthat/test-clone.R |only tests/testthat/test-nonportable.R | 6 tests/testthat/test-portable.R | 23 ++ tests/testthat/test-set.R | 28 +++ vignettes/Introduction.Rmd | 186 +++++++++++++++++++++- vignettes/Performance.Rmd | 160 +++++++++++-------- vignettes/Portable.Rmd | 37 ++++ 29 files changed, 1704 insertions(+), 425 deletions(-)
Title: Partial Orders and Relations
Description: Finds equivalence classes corresponding to a symmetric relation
or undirected graph. Finds total order consistent with partial order
or directed graph (so-called topological sort).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between pooh versions 0.3 dated 2015-01-05 and 0.3-1 dated 2015-07-03
DESCRIPTION | 12 +++++++----- LICENSE | 2 +- MD5 | 15 ++++++++------- NEWS |only R/tsort.R | 7 +++++-- man/tsort.Rd | 4 +++- src/tsort.c | 14 ++++++++------ tests/heffalump.R | 11 ++++++++++- tests/heffalump.Rout.save | 24 ++++++++++++++++++++---- 9 files changed, 62 insertions(+), 27 deletions(-)
Title: Compute Chi-Square Measures with Corrections
Description: Chi-square tests are computed with corrections.
Author: Aurélie Siberchicot, Eléonore Hellard, Dominique Pontier, David Fouchet and Franck Sauvage
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between Interatrix versions 1.0 dated 2015-03-19 and 1.1.1 dated 2015-07-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 26 +++++++++++++++----------- build/vignette.rds |binary inst/doc/Interatrix.pdf |binary man/Interatrix-package.Rd | 4 ++-- 6 files changed, 27 insertions(+), 23 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.2.2 dated 2015-07-01 and 1.1.2.3 dated 2015-07-03
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- man/ddalpha-package.Rd | 8 ++++---- man/depth.halfspace.Rd | 2 +- man/depth.space.halfspace.Rd | 10 ++++++++-- man/depth.space.simplicial.Rd | 2 +- src/Common.cpp | 11 +++++++++++ src/DataStructures.h | 1 + src/HD.cpp | 21 +++++++++++++-------- src/ddalpha.cpp | 9 ++++++++- 10 files changed, 61 insertions(+), 31 deletions(-)
Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets. Through
the use of Rcpp, read/write times are comparable to the xlsx and XLConnect
packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker <Alexander.Walker1989@gmail.com>
Diff between openxlsx versions 2.4.0 dated 2015-03-07 and 3.0.0 dated 2015-07-03
DESCRIPTION | 14 MD5 | 151 + NAMESPACE | 13 NEWS | 37 R/CommentClass.R |only R/RcppExports.R | 56 R/StyleClass.R | 23 R/WorkbookClass.R | 946 +++++++++-- R/baseXML.R | 79 R/helperFunctions.R | 103 + R/loadWorkbook.R | 730 +++----- R/openXL.R | 8 R/openxlsx.R | 2 R/readWorkbook.R | 572 +++--- R/wrappers.R | 686 +++++++- R/writeData.R | 128 + README.md | 31 build/vignette.rds |binary inst/doc/Introduction.pdf |binary inst/doc/formatting.Rnw | 25 inst/doc/formatting.pdf |binary man/addFilter.Rd | 2 man/addStyle.Rd | 2 man/addWorksheet.Rd | 2 man/all.equal.Rd |only man/conditionalFormat.Rd | 18 man/conditionalFormatting.Rd | 2 man/convertFromExcelRef.Rd | 2 man/convertToDate.Rd | 2 man/convertToDateTime.Rd | 9 man/createComment.Rd |only man/createStyle.Rd | 6 man/createWorkbook.Rd | 2 man/deleteData.Rd | 2 man/freezePane.Rd | 2 man/getBaseFont.Rd | 2 man/getCellRefs.Rd | 2 man/getDateOrigin.Rd | 2 man/getNamedRegions.Rd |only man/getSheetNames.Rd |only man/getStyles.Rd | 2 man/insertImage.Rd | 2 man/insertPlot.Rd | 2 man/int2col.Rd |only man/loadWorkbook.Rd | 2 man/mergeCells.Rd | 2 man/modifyBaseFont.Rd | 4 man/names.Rd | 2 man/openXL.Rd | 2 man/openxlsx.Rd | 4 man/pageSetup.Rd | 2 man/read.xlsx.Rd | 40 man/readWorkbook.Rd | 21 man/removeCellMerge.Rd | 2 man/removeColWidths.Rd | 2 man/removeComment.Rd |only man/removeFilter.Rd | 2 man/removeRowHeights.Rd | 2 man/removeWorksheet.Rd | 2 man/renameWorksheet.Rd | 2 man/replaceStyle.Rd | 2 man/saveWorkbook.Rd | 2 man/setColWidths.Rd | 2 man/setFooter.Rd | 2 man/setHeader.Rd | 2 man/setHeaderFooter.Rd | 2 man/setRowHeights.Rd | 2 man/sheets.Rd | 2 man/showGridLines.Rd | 2 man/worksheetOrder.Rd | 2 man/write.xlsx.Rd | 2 man/writeComment.Rd |only man/writeData.Rd | 21 man/writeDataTable.Rd | 2 man/writeFormula.Rd |only src/RcppExports.cpp | 924 +++++------ src/cppFunctions.cpp | 1639 +++++++++++++++++--- tests/testthat/test-load_read_file_read_equality.R | 297 --- tests/testthat/test-load_read_file_read_equality2.R |only tests/testthat/test-load_read_file_read_equality3.R |only tests/testthat/test-load_read_file_read_equality4.R |only tests/testthat/test-load_read_file_read_equality5.R |only vignettes/formatting.Rnw | 25 83 files changed, 4541 insertions(+), 2147 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.1-7 dated 2015-05-06 and 0.1-8 dated 2015-07-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/annotators.R | 6 +++++- R/string.R | 9 ++++++++- man/String.Rd | 6 ++++-- 6 files changed, 27 insertions(+), 12 deletions(-)
Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between nadiv versions 2.13.3 dated 2015-06-03 and 2.14.0 dated 2015-07-03
nadiv-2.13.3/nadiv/data/FG90.tab.gz |only nadiv-2.13.3/nadiv/data/Mrode2.tab.gz |only nadiv-2.13.3/nadiv/data/Mrode9.tab.gz |only nadiv-2.13.3/nadiv/data/warcolak.tab.gz |only nadiv-2.13.3/nadiv/man/is.numPed.Rd |only nadiv-2.13.3/nadiv/man/is.proLik.Rd |only nadiv-2.13.3/nadiv/man/plot.proLik.Rd |only nadiv-2.13.3/nadiv/src/ddiag.cc |only nadiv-2.13.3/nadiv/src/ddiag.h |only nadiv-2.14.0/nadiv/DESCRIPTION | 18 ++- nadiv-2.14.0/nadiv/MD5 | 73 +++++++------- nadiv-2.14.0/nadiv/NAMESPACE | 5 + nadiv-2.14.0/nadiv/R/founderLine.R | 6 - nadiv-2.14.0/nadiv/R/ggcontrib.R | 26 ++--- nadiv-2.14.0/nadiv/R/makeA.R | 22 ++-- nadiv-2.14.0/nadiv/R/makeAinv.R | 140 +++++++++++++++++++--------- nadiv-2.14.0/nadiv/R/makeDsim.R | 12 +- nadiv-2.14.0/nadiv/R/makeS.R | 67 ++++++------- nadiv-2.14.0/nadiv/R/numPed.R | 33 +++++- nadiv-2.14.0/nadiv/R/prepPed.R | 8 - nadiv-2.14.0/nadiv/R/prunePed.R | 4 nadiv-2.14.0/nadiv/README.md | 20 ++++ nadiv-2.14.0/nadiv/data/FG90.tab |only nadiv-2.14.0/nadiv/data/Mrode2.tab |only nadiv-2.14.0/nadiv/data/Mrode3.tab |only nadiv-2.14.0/nadiv/data/Mrode9.tab |only nadiv-2.14.0/nadiv/data/Q1988.tab |only nadiv-2.14.0/nadiv/data/datalist |only nadiv-2.14.0/nadiv/data/warcolak.tab |only nadiv-2.14.0/nadiv/man/Mrode3.Rd |only nadiv-2.14.0/nadiv/man/Q1988.Rd |only nadiv-2.14.0/nadiv/man/aiCI.Rd | 2 nadiv-2.14.0/nadiv/man/aiFun.Rd | 2 nadiv-2.14.0/nadiv/man/makeAinv.Rd | 59 +++++++++++- nadiv-2.14.0/nadiv/man/makeS.Rd | 2 nadiv-2.14.0/nadiv/man/nadiv-package.Rd | 6 - nadiv-2.14.0/nadiv/man/numPed.Rd | 37 +++++-- nadiv-2.14.0/nadiv/man/proLik.Rd | 21 +++- nadiv-2.14.0/nadiv/man/varTrans.Rd | 2 nadiv-2.14.0/nadiv/man/warcolak.Rd | 111 ++++++++++++++++++++-- nadiv-2.14.0/nadiv/src/General.h | 1 nadiv-2.14.0/nadiv/src/ainv.cc | 157 +++++++++++++++++++++++++++++++- nadiv-2.14.0/nadiv/src/ainv.h |only nadiv-2.14.0/nadiv/src/dfc.cc | 10 +- nadiv-2.14.0/nadiv/src/dij.cc | 14 +- nadiv-2.14.0/nadiv/src/ga.cc | 2 nadiv-2.14.0/nadiv/src/sinv.cc | 2 47 files changed, 643 insertions(+), 219 deletions(-)
Title: Hadoop InteractiVE
Description: Hadoop InteractiVE facilitates distributed
computing via the MapReduce paradigm through R and Hadoop. An easy to use
interface to Hadoop, the Hadoop Distributed File System (HDFS),
and Hadoop Streaming is provided.
Author: Ingo Feinerer [aut],
Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between hive versions 0.1-16 dated 2014-02-21 and 0.2-0 dated 2015-07-03
ChangeLog | 4 ++ DESCRIPTION | 23 ++++++----- MD5 | 18 ++++----- NAMESPACE | 1 R/configuration.R | 30 +++++++-------- R/handler.R | 101 +++++++++++++++++++++++++++++++++++++++++---------- R/java.R | 42 +++++++++++++-------- man/DFS.Rd | 2 - man/configuration.Rd | 2 - man/hive_stream.Rd | 2 - 10 files changed, 153 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-09 1.0.2
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.1.70 dated 2015-02-13 and 0.2.25 dated 2015-07-03
DESCRIPTION | 16 ++++++----- MD5 | 50 ++++++++++++++++++++++-------------- NAMESPACE | 5 ++- R/evaluate.R |only R/graphics.R | 23 +++++++++++++++- R/mldr.R | 62 ++++++++++++++++++++++++++++++++++----------- README.md | 15 +++++++--- build |only inst/doc |only man/birds.Rd | 2 - man/emotions.Rd | 2 - man/equals-.mldr.Rd | 2 - man/genbase.Rd | 2 - man/mldr.Rd | 18 ++++++++++--- man/mldrGUI.Rd | 2 - man/mldr_evaluate.Rd |only man/mldr_from_dataframe.Rd | 2 - man/mldr_transform.Rd | 2 - man/plot.mldr.Rd | 4 +- man/plus-.mldr.Rd | 2 - man/print.mldr.Rd | 2 - man/sub-.mldr.Rd | 2 - man/summary.mldr.Rd | 2 - man/write_arff.Rd | 2 - vignettes |only 25 files changed, 153 insertions(+), 64 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals from the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath <ken.beath@mq.edu.au>
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-2 dated 2015-06-03 and 0.7-4 dated 2015-07-03
DESCRIPTION | 10 MD5 | 22 - NAMESPACE | 4 R/globals.R | 2 R/makestart.profilemix.metaplus.R | 369 ++++++++++++------------ R/metaplus.R | 33 +- R/outlier.probs.metaplus.R | 22 - R/profilemix.metaplus.R | 321 ++++++++++----------- R/profilemix.profile.R | 578 +++++++++++++++++++------------------- R/profilenorm.metaplus.R | 210 +++++++------ R/profilet.metaplus.R | 383 ++++++++++++------------- inst/NEWS | 16 + 12 files changed, 1009 insertions(+), 961 deletions(-)
Title: Read Data from Files Readable by Gnumeric
Description: Read data files readable by gnumeric into R. Can read
whole sheet or a range, from several file formats, including
the native format of gnumeric. Reading is done by using
ssconvert (a file converter utility included in the gnumeric
distribution http://projects.gnome.org/gnumeric/) to convert
the requested part to CSV. From gnumeric files (but not other
formats) can list sheet names and sheet sizes or read all
sheets.
Author: Karoly Antal <antalk2@gmail.com>.
Maintainer: Karoly Antal <antalk2@gmail.com>
Diff between gnumeric versions 0.7-2 dated 2012-10-30 and 0.7-4 dated 2015-07-03
gnumeric-0.7-2/gnumeric/changelog |only gnumeric-0.7-4/gnumeric/DESCRIPTION | 12 +++++++----- gnumeric-0.7-4/gnumeric/MD5 | 9 ++++----- gnumeric-0.7-4/gnumeric/NAMESPACE | 2 ++ gnumeric-0.7-4/gnumeric/man/read.gnumeric.sheet.Rd | 15 ++++++++------- gnumeric-0.7-4/gnumeric/man/read.gnumeric.sheet.info.Rd | 5 +++-- 6 files changed, 24 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-08 1.2.1
2015-03-05 1.2
2014-09-29 1.1
2014-08-07 1.0
Title: Tag Clouds
Description: Generating Tag and Word Clouds.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tagcloud versions 0.5 dated 2014-11-06 and 0.6 dated 2015-07-03
tagcloud-0.5/tagcloud/R/is.overlap.R |only tagcloud-0.5/tagcloud/inst/doc/tagcloud.Rnw |only tagcloud-0.5/tagcloud/vignettes/tagcloud.Rnw |only tagcloud-0.6/tagcloud/DESCRIPTION | 13 tagcloud-0.6/tagcloud/MD5 | 47 +- tagcloud-0.6/tagcloud/NAMESPACE | 29 + tagcloud-0.6/tagcloud/NEWS | 4 tagcloud-0.6/tagcloud/R/RcppExports.R |only tagcloud-0.6/tagcloud/R/editor.tagcloud.R | 30 + tagcloud-0.6/tagcloud/R/gambia.R |only tagcloud-0.6/tagcloud/R/plot.tagcloud.R | 2 tagcloud-0.6/tagcloud/R/smoothPalette.R | 45 ++ tagcloud-0.6/tagcloud/R/strmultline.R | 20 - tagcloud-0.6/tagcloud/R/summary.tagcloud.R | 2 tagcloud-0.6/tagcloud/R/tagcloud.R | 196 ++++++++++ tagcloud-0.6/tagcloud/build/vignette.rds |binary tagcloud-0.6/tagcloud/inst/doc/tagcloud.R | 60 --- tagcloud-0.6/tagcloud/inst/doc/tagcloud.pdf |binary tagcloud-0.6/tagcloud/inst/doc/tagcloud.rmd |only tagcloud-0.6/tagcloud/man/editor.tagcloud.Rd | 56 +- tagcloud-0.6/tagcloud/man/gambia.Rd | 60 +-- tagcloud-0.6/tagcloud/man/smoothPalette.Rd | 89 ++-- tagcloud-0.6/tagcloud/man/strmultline.Rd | 45 -- tagcloud-0.6/tagcloud/man/tagcloud.Rd | 345 ++++++++---------- tagcloud-0.6/tagcloud/src/Makevars.win | 8 tagcloud-0.6/tagcloud/src/RcppExports.cpp |only tagcloud-0.6/tagcloud/src/overlap.cpp | 30 - tagcloud-0.6/tagcloud/vignettes/tagcloud-fig5plot.png |only tagcloud-0.6/tagcloud/vignettes/tagcloud.rmd |only 29 files changed, 651 insertions(+), 430 deletions(-)
Title: Estimation of Weight Functions in Meta Analysis
Description: Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. In this package we provide implementations of several parametric and nonparametric weight functions. The novelty in Rufibach (2011) is the proposal of a non-increasing variant of the nonparametric weight function of Dear & Begg (1992). The new approach potentially offers more insight in the selection process than other methods, but is more flexible than parametric approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992) under a monotonicity constraint we use a differential evolution algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al (2009). In addition, we offer a method to compute a confidence interval for the overall effect size theta, adjusted for selection bias as well as a function that computes the simulation-based p-value to assess the null hypothesis of no selection as described in Rufibach (2011, Section 6).
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between selectMeta versions 1.0.7 dated 2014-09-06 and 1.0.8 dated 2015-07-03
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 2 ++ NEWS | 4 ++++ R/DearBeggMonotonePvalSelection.r | 2 +- R/pPval.r | 5 ++++- man/selectMeta-package.Rd | 4 ++-- 7 files changed, 24 insertions(+), 14 deletions(-)
Title: Parametric Linkage Analysis in R
Description: Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>
Diff between paramlink versions 0.9-6 dated 2014-04-01 and 0.9-7 dated 2015-07-03
DESCRIPTION | 14 MD5 | 49 - NAMESPACE | 7 NEWS | 13 R/SNPsim.R | 4 R/likelihood.R | 1159 +++++++++++++++++++++---------------------- R/likelihoodSNP.R | 2 R/likelihood_LINKAGE.R | 44 - R/linkage.power.R | 2 R/linkageSim.R | 4 R/linkres.R | 96 ++- R/markerSim.R | 438 ++++++++-------- R/markers.R | 23 R/merlin.R | 16 R/modify.R | 4 R/oneMarkerDistribution.R | 128 ++-- R/setMap.R | 2 R/twoMarkerDistribution.R | 102 +-- R/utils.R | 22 man/allGenotypes.Rd |only man/examineKinships.Rd | 2 man/linkres.Rd | 14 man/markers.Rd | 14 man/merlin.Rd | 17 man/oneMarkerDistribution.Rd | 8 man/simpleSim.Rd | 2 26 files changed, 1131 insertions(+), 1055 deletions(-)
Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.14.0 dated 2015-06-04 and 1.15.1 dated 2015-07-03
MuMIn-1.14.0/MuMIn/man/avgpred.Rd |only MuMIn-1.14.0/MuMIn/man/beetle.Rd |only MuMIn-1.14.0/MuMIn/man/cement.Rd |only MuMIn-1.14.0/MuMIn/man/glm.link.Rd |only MuMIn-1.14.0/MuMIn/man/gpa.Rd |only MuMIn-1.14.0/MuMIn/man/mod.sel.Rd |only MuMIn-1.14.0/MuMIn/man/weights.Rd |only MuMIn-1.15.1/MuMIn/DESCRIPTION | 15 - MuMIn-1.15.1/MuMIn/MD5 | 132 ++++----- MuMIn-1.15.1/MuMIn/NAMESPACE | 80 ++++- MuMIn-1.15.1/MuMIn/NEWS | 33 ++ MuMIn-1.15.1/MuMIn/R/AICc.R | 3 MuMIn-1.15.1/MuMIn/R/ICOMP.R | 14 - MuMIn-1.15.1/MuMIn/R/Weights.R | 25 + MuMIn-1.15.1/MuMIn/R/arm.glm.R |only MuMIn-1.15.1/MuMIn/R/coefTable.R | 4 MuMIn-1.15.1/MuMIn/R/coeffs.R | 2 MuMIn-1.15.1/MuMIn/R/dredge.R | 170 ++++++------ MuMIn-1.15.1/MuMIn/R/ext.R | 1 MuMIn-1.15.1/MuMIn/R/get.models.R | 2 MuMIn-1.15.1/MuMIn/R/init.R | 27 + MuMIn-1.15.1/MuMIn/R/makeArgs.R | 2 MuMIn-1.15.1/MuMIn/R/methods-nobs.R | 2 MuMIn-1.15.1/MuMIn/R/methods-predict.R | 8 MuMIn-1.15.1/MuMIn/R/model.avg.R | 181 +++++++------ MuMIn-1.15.1/MuMIn/R/model.sel.R | 96 +++---- MuMIn-1.15.1/MuMIn/R/model.selection.R | 315 +++++------------------ MuMIn-1.15.1/MuMIn/R/modify.model.selection.R |only MuMIn-1.15.1/MuMIn/R/nested.R | 22 - MuMIn-1.15.1/MuMIn/R/par.avg.R | 2 MuMIn-1.15.1/MuMIn/R/pdredge.R | 126 +++++---- MuMIn-1.15.1/MuMIn/R/plots.R | 16 - MuMIn-1.15.1/MuMIn/R/predict-new.R | 4 MuMIn-1.15.1/MuMIn/R/predict.R | 13 MuMIn-1.15.1/MuMIn/R/quasiLik.R | 4 MuMIn-1.15.1/MuMIn/R/r.squaredGLMM.R | 2 MuMIn-1.15.1/MuMIn/R/rbind.model.selection.R |only MuMIn-1.15.1/MuMIn/R/std.coef.R | 20 - MuMIn-1.15.1/MuMIn/R/stdize.R | 6 MuMIn-1.15.1/MuMIn/R/substitution.R | 61 ++-- MuMIn-1.15.1/MuMIn/R/updateable.R | 37 +- MuMIn-1.15.1/MuMIn/R/utils-misc.R | 23 - MuMIn-1.15.1/MuMIn/R/utils-models.R | 13 MuMIn-1.15.1/MuMIn/R/xtable-methods.R |only MuMIn-1.15.1/MuMIn/data/Beetle.rda |binary MuMIn-1.15.1/MuMIn/data/Cement.rda |binary MuMIn-1.15.1/MuMIn/data/GPA.rda |binary MuMIn-1.15.1/MuMIn/demo/dredge.distsamp.R | 4 MuMIn-1.15.1/MuMIn/demo/dredge.subset.R | 4 MuMIn-1.15.1/MuMIn/demo/pdredge.pcount.R | 9 MuMIn-1.15.1/MuMIn/inst/TODO | 4 MuMIn-1.15.1/MuMIn/man/AICc.Rd | 4 MuMIn-1.15.1/MuMIn/man/QAIC.Rd | 2 MuMIn-1.15.1/MuMIn/man/QIC.Rd | 2 MuMIn-1.15.1/MuMIn/man/Weights.Rd |only MuMIn-1.15.1/MuMIn/man/arm.glm.Rd |only MuMIn-1.15.1/MuMIn/man/data-Beetle.Rd |only MuMIn-1.15.1/MuMIn/man/data-Cement.Rd |only MuMIn-1.15.1/MuMIn/man/data-GPA.Rd |only MuMIn-1.15.1/MuMIn/man/dredge.Rd | 85 ++---- MuMIn-1.15.1/MuMIn/man/exprApply.Rd | 22 + MuMIn-1.15.1/MuMIn/man/merge.model.selection.Rd | 18 - MuMIn-1.15.1/MuMIn/man/model.avg.Rd | 22 - MuMIn-1.15.1/MuMIn/man/model.sel.Rd |only MuMIn-1.15.1/MuMIn/man/model.selection.object.Rd |only MuMIn-1.15.1/MuMIn/man/par.avg.Rd | 6 MuMIn-1.15.1/MuMIn/man/pdredge.Rd | 4 MuMIn-1.15.1/MuMIn/man/predict.averaging.Rd | 2 MuMIn-1.15.1/MuMIn/man/r.squaredGLMM.Rd | 39 +- MuMIn-1.15.1/MuMIn/man/r.squaredLR.Rd | 33 +- MuMIn-1.15.1/MuMIn/man/std.coef.Rd | 16 - MuMIn-1.15.1/MuMIn/man/subset.model.selection.Rd | 53 ++- MuMIn-1.15.1/MuMIn/tests/classes.R | 150 +++++----- MuMIn-1.15.1/MuMIn/tests/parallel.R | 2 MuMIn-1.15.1/MuMIn/tests/singularities.R | 3 MuMIn-1.15.1/MuMIn/tests/unmarked.R | 9 76 files changed, 958 insertions(+), 996 deletions(-)
Title: Estimate a Log-Concave Probability Mass Function from Discrete
i.i.d. Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), allows to compute the maximum likelihood estimator (MLE) of probability mass function (pmf) under the assumption that it is log-concave, see Weyermann (2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main functions of the package are 'logConDiscrMLE' that allows computation of the log-concave MLE, 'logConDiscrCI' that computes pointwise confidence bands for the MLE, and 'kInflatedLogConDiscr' that computes a mixture of a log-concave PMF and a point mass at k.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Fadoua Balabdaoui <fadoua@ceremade.dauphine.fr> and Hanna Jankowski <hkj@mathstat.yorku.ca> and Kathrin Weyermann <kathrin.weyermann@bkw-fmb.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between logcondiscr versions 1.0.5 dated 2014-02-05 and 1.0.6 dated 2015-07-03
DESCRIPTION | 13 +++++----- MD5 | 8 +++--- NAMESPACE | 56 +++++++++++++++++++++------------------------ NEWS | 4 +++ man/logcondiscr-package.Rd | 8 +++--- 5 files changed, 46 insertions(+), 43 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>
Diff between IBDsim versions 0.9-4 dated 2014-05-30 and 0.9-5 dated 2015-07-03
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 5 ++++- R/ibd.runs.R | 13 +++---------- R/map_utils.R | 2 +- R/ped_utils.R | 2 +- R/range_utils.R | 4 ++-- data/DecodeMap.rda |binary data/dominant1.rda |binary 9 files changed, 26 insertions(+), 29 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. kriging models, are
applied to global multiobjective optimization of black-box functions.
Multiobjective Expected Improvement and Stepwise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mickael.binois@mines-stetienne.fr>
Diff between GPareto versions 1.0.0 dated 2014-12-17 and 1.0.1 dated 2015-07-03
GPareto-1.0.0/GPareto/man/GPareto-package.Rd |only GPareto-1.0.1/GPareto/DESCRIPTION | 15 +-- GPareto-1.0.1/GPareto/MD5 | 71 +++++++------- GPareto-1.0.1/GPareto/NAMESPACE | 13 ++ GPareto-1.0.1/GPareto/NEWS |only GPareto-1.0.1/GPareto/R/CPF.R | 35 +++---- GPareto-1.0.1/GPareto/R/EHI_2d.R | 2 GPareto-1.0.1/GPareto/R/GPareto-package.R | 24 ++-- GPareto-1.0.1/GPareto/R/GParetoptim.R | 8 + GPareto-1.0.1/GPareto/R/SAA_MEI.R | 2 GPareto-1.0.1/GPareto/R/TestFunctions.R | 20 +--- GPareto-1.0.1/GPareto/R/crit_EHI.R | 11 +- GPareto-1.0.1/GPareto/R/crit_EMI.R | 4 GPareto-1.0.1/GPareto/R/crit_SMS.R | 4 GPareto-1.0.1/GPareto/R/crit_SUR.R | 7 - GPareto-1.0.1/GPareto/R/crit_optimizer.R | 2 GPareto-1.0.1/GPareto/R/fastfun.R | 5 - GPareto-1.0.1/GPareto/R/plotParetoEmp.R | 90 ++++++++++++------ GPareto-1.0.1/GPareto/R/plotParetoGrid.R | 7 - GPareto-1.0.1/GPareto/R/plotSymDevFun.R | 11 -- GPareto-1.0.1/GPareto/man/CPF.Rd | 14 +- GPareto-1.0.1/GPareto/man/GPareto.Rd |only GPareto-1.0.1/GPareto/man/GParetoptim.Rd | 7 - GPareto-1.0.1/GPareto/man/TestFunctions.Rd | 22 ++-- GPareto-1.0.1/GPareto/man/checkPredict.Rd | 3 GPareto-1.0.1/GPareto/man/crit_EHI.Rd | 7 - GPareto-1.0.1/GPareto/man/crit_EMI.Rd | 7 - GPareto-1.0.1/GPareto/man/crit_SMS.Rd | 7 - GPareto-1.0.1/GPareto/man/crit_SUR.Rd | 8 - GPareto-1.0.1/GPareto/man/crit_optimizer.Rd | 3 GPareto-1.0.1/GPareto/man/fastfun-class.Rd | 3 GPareto-1.0.1/GPareto/man/fastfun.Rd | 7 - GPareto-1.0.1/GPareto/man/integration_design_optim.Rd | 3 GPareto-1.0.1/GPareto/man/plotParetoEmp.Rd | 13 ++ GPareto-1.0.1/GPareto/man/plotParetoGrid.Rd | 9 - GPareto-1.0.1/GPareto/man/plotSymDevFun.Rd | 13 +- GPareto-1.0.1/GPareto/man/plotSymDifRNP.Rd | 3 GPareto-1.0.1/GPareto/src/RcppExports.cpp | 58 ++++------- 38 files changed, 268 insertions(+), 250 deletions(-)
Title: Classical Goodness-of-Fit Tests for Univariate Distributions
Description: Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit
for continuous univariate distributions, using
efficient algorithms.
Author: Julian Faraway [aut],
George Marsaglia [aut],
John Marsaglia [aut],
Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between goftest versions 1.0-2 dated 2014-06-24 and 1.0-3 dated 2015-07-03
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 4.3-4 dated 2015-02-03 and 4.3-5 dated 2015-07-03
gamlss-4.3-4/gamlss/R/VGD03-10-13.R |only gamlss-4.3-4/gamlss/R/pbm.R |only gamlss-4.3-4/gamlss/R/stepGAICAll-B.R |only gamlss-4.3-4/gamlss/R/stepTGD-25-03-10.R |only gamlss-4.3-4/gamlss/R/term-plot.R |only gamlss-4.3-4/gamlss/man/VGD.Rd |only gamlss-4.3-4/gamlss/man/ridge.Rd |only gamlss-4.3-5/gamlss/DESCRIPTION | 36 - gamlss-4.3-5/gamlss/MD5 | 87 +- gamlss-4.3-5/gamlss/NAMESPACE | 24 gamlss-4.3-5/gamlss/R/DropAddStepGAIC-Parallel.R |only gamlss-4.3-5/gamlss/R/confint-gamlss-03-10-13.R | 7 gamlss-4.3-5/gamlss/R/edf.R | 5 gamlss-4.3-5/gamlss/R/extra.R | 44 - gamlss-4.3-5/gamlss/R/gamlss.R | 14 gamlss-4.3-5/gamlss/R/gamlssML-31-10-13.R | 5 gamlss-4.3-5/gamlss/R/gamlssVGD.R |only gamlss-4.3-5/gamlss/R/getSmo-18-6-13.R | 5 gamlss-4.3-5/gamlss/R/lms.R | 4 gamlss-4.3-5/gamlss/R/lpred.R | 4 gamlss-4.3-5/gamlss/R/pb_new.R | 10 gamlss-4.3-5/gamlss/R/pbm_new.R |only gamlss-4.3-5/gamlss/R/plot2way.R | 4 gamlss-4.3-5/gamlss/R/predict.gamlss.R | 4 gamlss-4.3-5/gamlss/R/pvc.R | 673 ++++++++++++++--------- gamlss-4.3-5/gamlss/R/ri.R | 422 +++++++++----- gamlss-4.3-5/gamlss/R/rqres.R | 87 ++ gamlss-4.3-5/gamlss/R/rqresplot03-10-13.R | 4 gamlss-4.3-5/gamlss/R/stepGAIC-03-10-13..R | 374 ++++++------ gamlss-4.3-5/gamlss/R/stepGAICAll-B-Parallel.R |only gamlss-4.3-5/gamlss/R/stepTGD.R |only gamlss-4.3-5/gamlss/R/term.plot-new.R |only gamlss-4.3-5/gamlss/R/update.R | 138 ++-- gamlss-4.3-5/gamlss/inst/doc/NEWS.txt | 69 ++ gamlss-4.3-5/gamlss/man/coef.gamlss.Rd | 82 +- gamlss-4.3-5/gamlss/man/deviance.gamlss.Rd | 88 +-- gamlss-4.3-5/gamlss/man/edf.Rd | 118 ++-- gamlss-4.3-5/gamlss/man/fitted.gamlss.Rd | 96 +-- gamlss-4.3-5/gamlss/man/formula.gamlss.Rd | 84 +- gamlss-4.3-5/gamlss/man/gamlssVGD.Rd |only gamlss-4.3-5/gamlss/man/getSmo.Rd | 5 gamlss-4.3-5/gamlss/man/lpred.Rd | 5 gamlss-4.3-5/gamlss/man/model.frame.gamlss.Rd | 100 +-- gamlss-4.3-5/gamlss/man/plot2way.Rd | 3 gamlss-4.3-5/gamlss/man/predict.gamlss.Rd | 184 +++--- gamlss-4.3-5/gamlss/man/ps.Rd | 9 gamlss-4.3-5/gamlss/man/ri.Rd |only gamlss-4.3-5/gamlss/man/rqres.plot.Rd | 2 gamlss-4.3-5/gamlss/man/stepGAIC.Rd | 175 +++-- gamlss-4.3-5/gamlss/man/summary.gamlss.Rd | 2 gamlss-4.3-5/gamlss/man/term.plot.Rd | 9 gamlss-4.3-5/gamlss/man/update.gamlss.Rd | 109 +-- 52 files changed, 1806 insertions(+), 1285 deletions(-)
Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing
and visualisation of network of contacts.
Author: Maria Noremark [aut],
Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between EpiContactTrace versions 0.9.0 dated 2015-07-02 and 0.9.1 dated 2015-07-03
DESCRIPTION | 10 ++++----- MD5 | 10 ++++----- NAMESPACE | 2 + R/report.r | 6 +++-- man/Report-methods.Rd | 2 - src/trace.cpp | 53 +++++++++++++++++++++++++++----------------------- 6 files changed, 46 insertions(+), 37 deletions(-)
More information about EpiContactTrace at CRAN
Permanent link
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre],
Kurt Hornik [aut],
Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL
Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.6-1 dated 2015-05-07 and 0.6-2 dated 2015-07-03
DESCRIPTION | 14 +++++++------- MD5 | 26 +++++++++++++------------- NAMESPACE | 5 +++-- R/doc.R | 4 ++-- R/matrix.R | 14 +++++++------- build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/NEWS.Rd | 28 ++++++++++++++++++++++------ inst/doc/extensions.pdf |binary inst/doc/tm.R | 21 +++++++++++---------- inst/doc/tm.Rnw | 1 + inst/doc/tm.pdf |binary vignettes/tm.Rnw | 1 + 14 files changed, 67 insertions(+), 47 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.4 dated 2015-06-08 and 0.8.6 dated 2015-07-03
rgbif-0.8.4/rgbif/NEWS |only rgbif-0.8.4/rgbif/R/startup.r |only rgbif-0.8.4/rgbif/inst/js/terraformer-wkt-parser2.js |only rgbif-0.8.4/rgbif/inst/vign/cache |only rgbif-0.8.6/rgbif/DESCRIPTION | 13 rgbif-0.8.6/rgbif/MD5 | 191 - rgbif-0.8.6/rgbif/NAMESPACE | 27 rgbif-0.8.6/rgbif/R/dataset_metrics.r | 4 rgbif-0.8.6/rgbif/R/datasets.r | 38 rgbif-0.8.6/rgbif/R/downloads.R |only rgbif-0.8.6/rgbif/R/enumeration.R | 4 rgbif-0.8.6/rgbif/R/installations.r | 2 rgbif-0.8.6/rgbif/R/name_suggest.r | 2 rgbif-0.8.6/rgbif/R/name_usage.r | 2 rgbif-0.8.6/rgbif/R/networks.r | 2 rgbif-0.8.6/rgbif/R/nodes.r | 2 rgbif-0.8.6/rgbif/R/occ_count.r | 56 rgbif-0.8.6/rgbif/R/occ_download.R |only rgbif-0.8.6/rgbif/R/occ_download_cancel.R |only rgbif-0.8.6/rgbif/R/occ_download_get.r |only rgbif-0.8.6/rgbif/R/occ_download_import.R |only rgbif-0.8.6/rgbif/R/occ_download_list.R |only rgbif-0.8.6/rgbif/R/occ_download_meta.R |only rgbif-0.8.6/rgbif/R/occ_get.r | 4 rgbif-0.8.6/rgbif/R/occ_metadata.r | 2 rgbif-0.8.6/rgbif/R/occ_search.r | 5 rgbif-0.8.6/rgbif/R/on_load.R | 2 rgbif-0.8.6/rgbif/R/organizations.r | 4 rgbif-0.8.6/rgbif/R/parsenames.R | 6 rgbif-0.8.6/rgbif/R/rgbif-package.r | 47 rgbif-0.8.6/rgbif/R/zzz.r | 1 rgbif-0.8.6/rgbif/README.md | 105 rgbif-0.8.6/rgbif/build/vignette.rds |binary rgbif-0.8.6/rgbif/inst/assets/img/unnamed-chunk-8-1.png |binary rgbif-0.8.6/rgbif/inst/doc/issues_vignette.Rmd | 229 + rgbif-0.8.6/rgbif/inst/doc/issues_vignette.html | 229 + rgbif-0.8.6/rgbif/inst/doc/rgbif_vignette.html | 119 rgbif-0.8.6/rgbif/inst/js/LICENSE |only rgbif-0.8.6/rgbif/inst/js/README.md |only rgbif-0.8.6/rgbif/inst/js/terraformer-wkt-parser.js | 2085 +++++++++++++++- rgbif-0.8.6/rgbif/inst/vign/figure/gbifmap1-1.png |binary rgbif-0.8.6/rgbif/inst/vign/issues_vignette.Rmd | 24 rgbif-0.8.6/rgbif/inst/vign/issues_vignette.md | 229 + rgbif-0.8.6/rgbif/inst/vign/rgbif_vignette.Rmd | 8 rgbif-0.8.6/rgbif/inst/vign/rgbif_vignette.md | 117 rgbif-0.8.6/rgbif/man/datasets.Rd | 2 rgbif-0.8.6/rgbif/man/downloads.Rd |only rgbif-0.8.6/rgbif/man/installations.Rd | 2 rgbif-0.8.6/rgbif/man/name_suggest.Rd | 2 rgbif-0.8.6/rgbif/man/name_usage.Rd | 2 rgbif-0.8.6/rgbif/man/networks.Rd | 2 rgbif-0.8.6/rgbif/man/nodes.Rd | 2 rgbif-0.8.6/rgbif/man/occ_count.Rd | 4 rgbif-0.8.6/rgbif/man/occ_download.Rd |only rgbif-0.8.6/rgbif/man/occ_download_cancel.Rd |only rgbif-0.8.6/rgbif/man/occ_download_get.Rd |only rgbif-0.8.6/rgbif/man/occ_download_import.Rd |only rgbif-0.8.6/rgbif/man/occ_download_list.Rd |only rgbif-0.8.6/rgbif/man/occ_download_meta.Rd |only rgbif-0.8.6/rgbif/man/occ_get.Rd | 2 rgbif-0.8.6/rgbif/man/occ_metadata.Rd | 2 rgbif-0.8.6/rgbif/man/occ_search.Rd | 5 rgbif-0.8.6/rgbif/man/organizations.Rd | 2 rgbif-0.8.6/rgbif/man/parsenames.Rd | 6 rgbif-0.8.6/rgbif/tests/testthat/test-enumeration.r | 2 rgbif-0.8.6/rgbif/tests/testthat/test-read_wkt.R |only rgbif-0.8.6/rgbif/vignettes/issues_vignette.Rmd | 229 + rgbif-0.8.6/rgbif/vignettes/rgbif_vignette.Rmd | 117 68 files changed, 3060 insertions(+), 880 deletions(-)
Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations X(1), ..., X(n) from a density f,
provides five methods to perform a multiscale analysis about f as well as the necessary critical
values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements
for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by
any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of
I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive
correction term Gamma in either method offers another two approaches which are more powerful on small scales and
less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a
compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically
equivalent to the first and was introduced in Rufibach and Walther (2010).
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Guenther Walther <gwalther@stanford.edu>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between modehunt versions 1.0.6 dated 2011-11-29 and 1.0.7 dated 2015-07-03
DESCRIPTION | 12 +++++++----- MD5 | 12 ++++++------ NAMESPACE | 31 +++++++++++++++++-------------- data/cvModeAll.rda |binary data/cvModeApprox.rda |binary data/cvModeBlock.rda |binary man/modehunt-package.Rd | 8 ++++---- 7 files changed, 34 insertions(+), 29 deletions(-)
Title: Semi Parametric Distribution
Description: The Semi Parametric Piecewise Distribution blends the Generalized Pareto Distribution for the tails with a kernel based interior.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between spd versions 2.0-0 dated 2014-07-02 and 2.0-1 dated 2015-07-03
ChangeLog | 4 ++++ DESCRIPTION | 16 ++++++++-------- MD5 | 7 ++++--- NAMESPACE | 3 +++ README.md |only 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Estimating the Proportion of Genetically Modified Seeds in
Seedlots via Multinomial Group Testing
Description: Estimate the percentage of seeds in a seedlot that contain stacks
of genetically modified traits. Estimates are calculated using a
multinomial group testing model with maximum likelihood estimation of the
parameters.
Author: Kevin Wright [aut, cre],
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between rseedcalc versions 1.2 dated 2013-10-10 and 1.3 dated 2015-07-03
DESCRIPTION | 20 ++++++++++++-------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- NEWS |only R/stacks.r | 5 +++-- man/rseedcalc-package.Rd | 16 ++++++++-------- man/stack2.Rd | 40 ++++++++++++++++++++-------------------- man/valid.Rd | 12 ++++++------ 8 files changed, 59 insertions(+), 51 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g.,
http://en.wikipedia.org/wiki/GitHub#Gist,
https://help.github.com/articles/about-gists/). A 'gist' is simply one or
more files with code/text/images/etc. This package allows the user to
create new 'gists', update 'gists' with new files, rename files, delete files,
get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in
your default browser, get embed code for a 'gist', list 'gist' 'commits', and
get rate limit information when 'authenticated'. Some requests require
authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.2.0 dated 2015-05-01 and 0.3.0 dated 2015-07-03
gistr-0.2.0/gistr/NEWS |only gistr-0.2.0/gistr/inst/vign/cache |only gistr-0.3.0/gistr/DESCRIPTION | 41 +- gistr-0.3.0/gistr/MD5 | 209 +++--------- gistr-0.3.0/gistr/NAMESPACE | 7 gistr-0.3.0/gistr/R/add_files.R | 6 gistr-0.3.0/gistr/R/commits.R | 3 gistr-0.3.0/gistr/R/delete.R | 3 gistr-0.3.0/gistr/R/embed.R | 3 gistr-0.3.0/gistr/R/forks.R | 8 gistr-0.3.0/gistr/R/gist.R | 49 ++ gistr-0.3.0/gistr/R/gist_create.R | 58 ++- gistr-0.3.0/gistr/R/gist_save.R |only gistr-0.3.0/gistr/R/gistr-package.R | 3 gistr-0.3.0/gistr/R/gists.R | 1 gistr-0.3.0/gistr/R/rate_limit.R | 4 gistr-0.3.0/gistr/R/star.R | 5 gistr-0.3.0/gistr/R/tabl.R | 7 gistr-0.3.0/gistr/R/update.R | 27 + gistr-0.3.0/gistr/R/zzz.R | 4 gistr-0.3.0/gistr/README.md | 119 +++---- gistr-0.3.0/gistr/build/vignette.rds |binary gistr-0.3.0/gistr/inst/doc/gistr_vignette.Rmd | 163 +++++---- gistr-0.3.0/gistr/inst/doc/gistr_vignette.html | 264 ++++++++-------- gistr-0.3.0/gistr/inst/examples/ggplot_imgur.Rmd |only gistr-0.3.0/gistr/inst/examples/rmarkdown_eg.Rmd |only gistr-0.3.0/gistr/inst/examples/rmarkdown_eg.md |only gistr-0.3.0/gistr/inst/examples/stuff.md | 28 - gistr-0.3.0/gistr/inst/ignore/gist_create_git.R | 6 gistr-0.3.0/gistr/inst/vign/gistr_vignette.Rmd | 49 +- gistr-0.3.0/gistr/inst/vign/gistr_vignette.md | 163 +++++---- gistr-0.3.0/gistr/man/commits.Rd | 3 gistr-0.3.0/gistr/man/embed.Rd | 3 gistr-0.3.0/gistr/man/files.Rd | 6 gistr-0.3.0/gistr/man/fork.Rd | 5 gistr-0.3.0/gistr/man/forks.Rd | 3 gistr-0.3.0/gistr/man/gist.Rd | 11 gistr-0.3.0/gistr/man/gist_create.Rd | 13 gistr-0.3.0/gistr/man/gist_save.Rd |only gistr-0.3.0/gistr/man/star.Rd | 5 gistr-0.3.0/gistr/man/tabl.Rd | 7 gistr-0.3.0/gistr/man/update.Rd | 21 - gistr-0.3.0/gistr/tests/localtests/test-gist_create.R | 12 gistr-0.3.0/gistr/tests/test-all.R |only gistr-0.3.0/gistr/tests/testthat/test-commits.R | 4 gistr-0.3.0/gistr/tests/testthat/test-delete.R | 4 gistr-0.3.0/gistr/tests/testthat/test-embed.R | 2 gistr-0.3.0/gistr/tests/testthat/test-fork.R | 4 gistr-0.3.0/gistr/tests/testthat/test-gist.R | 29 + gistr-0.3.0/gistr/tests/testthat/test-gist_create_obj.R | 6 gistr-0.3.0/gistr/tests/testthat/test-gist_save.R |only gistr-0.3.0/gistr/tests/testthat/test-gists.R | 4 gistr-0.3.0/gistr/tests/testthat/test-rate_limit.R | 2 gistr-0.3.0/gistr/tests/testthat/test-star.R | 42 +- gistr-0.3.0/gistr/tests/testthat/test-update.R | 2 gistr-0.3.0/gistr/vignettes/gistr_vignette.Rmd | 163 +++++---- 56 files changed, 877 insertions(+), 704 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution.
It provides the density function, distribution function, and Quantile-Quantile plots.
It implements a variety of estimation methods for the distribution, including diagnostic plots.
Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation.
These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.2.1 dated 2014-02-19 and 2.3 dated 2015-07-03
Changelog | 10 ++- DESCRIPTION | 25 +++++---- MD5 | 41 ++++++++------ NAMESPACE | 14 +++-- NEWS | 5 + R/fxgld.R | 16 ++--- R/methods.R | 15 +---- R/moment.R |only R/plotgl.R | 6 +- R/qfgld.R | 10 ++- R/qqgl.R | 8 +- R/rgld.R | 8 +- R/starship.R | 97 +++++++++++++++-------------------- TODO | 5 - man/GeneralisedLambdaDistribution.Rd | 21 ++----- man/StarshipClassDocs.Rd | 11 +-- man/fit.fkml.moments.val.Rd |only man/gl.check.lambda.Rd | 8 -- man/gld-Deprecated.Rd |only man/gld.moments.Rd |only man/plot.starship.Rd | 15 +---- man/plotgl.Rd | 2 man/qdgl-deprecated.Rd |only man/starship.Rd | 32 +++-------- 24 files changed, 161 insertions(+), 188 deletions(-)
Title: Plot a Correlogram
Description: Calculates correlation of variables and displays the results graphically.
Included panel functions can display points, shading, ellipses, and correlation
values with confidence intervals.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between corrgram versions 1.7 dated 2015-02-13 and 1.8 dated 2015-07-03
DESCRIPTION | 21 ++++++++++++--------- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS | 24 ++++++++++++++---------- build/vignette.rds |binary data/auto.rda |binary data/baseball.rda |binary data/vote.rda |binary inst/doc/corrgram_examples.Rnw | 21 ++++++++++++++++++--- inst/doc/corrgram_examples.pdf |binary man/corrgram.Rd | 3 +++ vignettes/corrgram_examples.Rnw | 21 ++++++++++++++++++--- 12 files changed, 77 insertions(+), 36 deletions(-)
Title: The Analysis of Biological Data
Description: The abd package contains data sets and sample code for The
Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009;
Roberts & Company Publishers).
Author: Kevin M. Middleton <middletonk@missouri.edu>, Randall Pruim
<rpruim@calvin.edu>
Maintainer: Kevin M. Middleton <middletonk@missouri.edu>
Diff between abd versions 0.2-7 dated 2015-02-02 and 0.2-8 dated 2015-07-03
DESCRIPTION | 8 - MD5 | 304 +++++++++++++++++++++---------------------- NAMESPACE | 4 R/datasets.R | 28 --- man/AlgaeCO2.Rd | 5 man/Antilles.Rd | 2 man/Aspirin.Rd | 4 man/BeeGenes.Rd | 2 man/BeeLifespans.Rd | 2 man/Beetles.Rd | 2 man/BirdSexRatio.Rd | 2 man/Blackbirds.Rd | 2 man/BodyFatHeatLoss.Rd | 2 man/BrainExpression.Rd | 2 man/BrookTrout.Rd | 2 man/Cavalry.Rd | 2 man/Chickadees.Rd | 2 man/ChimpBrains.Rd | 2 man/Cichlids.Rd | 2 man/CichlidsGnRH.Rd | 2 man/Clearcuts.Rd | 2 man/CocaineDopamine.Rd | 2 man/Convictions.Rd | 2 man/ConvictionsAndIncome.Rd | 2 man/Crickets.Rd | 2 man/DEET.Rd | 2 man/DaphniaLongevity.Rd | 2 man/DaphniaResistance.Rd | 2 man/DayOfBirth.Rd | 2 man/DesertBirds.Rd | 2 man/Dioecy.Rd | 2 man/Dolphins.Rd | 2 man/DungBeetles.Rd | 2 man/Earthworms.Rd | 2 man/Earwigs.Rd | 2 man/Eelgrass.Rd | 2 man/ElVerde.Rd | 2 man/ElectricFish.Rd | 2 man/EndangeredSpecies.Rd | 2 man/FingerRatio.Rd | 2 man/Fireflies.Rd | 2 man/FireflyFlash.Rd | 2 man/FlyTestes.Rd | 2 man/FlycatcherPatch.Rd | 2 man/GeneRegulation.Rd | 2 man/GlidingSnakes.Rd | 2 man/GodwitArrival.Rd | 2 man/Grassland.Rd | 2 man/GreatTitMalaria.Rd | 2 man/Greenspace.Rd | 2 man/Guppies.Rd | 2 man/Hemoglobin.Rd | 2 man/HippocampusLesions.Rd | 2 man/HornedLizards.Rd | 2 man/HumanBodyTemp.Rd | 2 man/HumanGeneLengths.Rd | 2 man/Hurricanes.Rd | 2 man/Iguanas.Rd | 2 man/IntertidalAlgae.Rd | 2 man/JetLagKnees.Rd | 2 man/KenyaFinches.Rd | 5 man/LanguageBrains.Rd | 2 man/LarvalFish.Rd | 2 man/Lefthanded.Rd | 2 man/LionCubs.Rd | 2 man/LionNoses.Rd | 2 man/LiverPreparation.Rd | 4 man/LizardBite.Rd | 2 man/LizardSprint.Rd | 2 man/Lobsters.Rd | 2 man/LodgepolePines.Rd | 2 man/LupusMice.Rd | 2 man/Lynx.Rd | 2 man/MarineReserve.Rd | 2 man/MassExtinctions.Rd | 2 man/MoleRats.Rd | 2 man/Mosquitoes.Rd | 2 man/MouseEmpathy.Rd | 2 man/NeanderthalBrains.Rd | 2 man/NematodeLifespan.Rd | 2 man/NeotropicalTrees.Rd | 2 man/Newts.Rd | 2 man/NoSmokingDay.Rd | 2 man/NorthSeaCod.Rd | 2 man/OstrichTemp.Rd | 2 man/Penguins.Rd | 2 man/PlantPersistence.Rd | 2 man/Pollen.Rd | 2 man/Powerball.Rd | 2 man/PrimateMetabolism.Rd | 2 man/PrimateWBC.Rd | 2 man/ProgesteroneExercise.Rd | 2 man/Pseudoscorpions.Rd | 2 man/Pufferfish.Rd | 2 man/Rattlesnakes.Rd | 2 man/Rigormortis.Rd | 2 man/RopeTrick.Rd | 2 man/SagebrushCrickets.Rd | 2 man/SalmonColor.Rd | 2 man/Seedlings.Rd | 2 man/Selection.Rd | 2 man/SexualSelection.Rd | 2 man/ShadParasites.Rd | 4 man/ShrinkingSeals.Rd | 2 man/ShuttleDisaster.Rd | 2 man/Silversword.Rd | 2 man/SleepAndPerformance.Rd | 4 man/SockeyeFemales.Rd | 5 man/Sparrows.Rd | 2 man/SpiderColonies.Rd | 2 man/SpiderSpeed.Rd | 2 man/Stalkies1.Rd | 2 man/Stalkies2.Rd | 5 man/SticklebackPlates.Rd | 2 man/SticklebackPreference.Rd | 2 man/Sumo.Rd | 2 man/SyrupSwimming.Rd | 2 man/TeenDeaths.Rd | 2 man/Telomeres.Rd | 2 man/TimeOfDeath.Rd | 2 man/Toads.Rd | 2 man/Tobacco.Rd | 2 man/Tobacco2.Rd | 2 man/ToothAge.Rd | 5 man/TreeSeedlings.Rd | 2 man/Trematodes.Rd | 2 man/Trillium.Rd | 7 man/Truffles.Rd | 2 man/TsetseLearning.Rd | 2 man/TwoKids.Rd | 2 man/VampireBites.Rd | 2 man/VasopressinVoles.Rd | 5 man/Vines.Rd | 2 man/VoleDispersal.Rd | 2 man/WalkingStickFemurs.Rd | 2 man/WalkingStickHeads.Rd | 2 man/WeddellSeals.Rd | 2 man/WillsDebates.Rd | 2 man/WillsPresidents.Rd | 2 man/WolfTeeth.Rd | 2 man/Wolves.Rd | 2 man/WorldCup.Rd | 2 man/WrasseSexes.Rd | 2 man/YeastGenes.Rd | 2 man/ZebraFinchBeaks.Rd | 2 man/ZebraFinches.Rd | 2 man/ZooMortality.Rd | 5 man/Zooplankton.Rd | 2 man/abd-package.Rd | 6 man/abdData.Rd | 2 man/dataInfo.Rd | 2 man/histochart.Rd | 2 man/themes.Rd | 2 153 files changed, 321 insertions(+), 359 deletions(-)
Title: GUI for Entering Test Items and Obtaining Raw and Transformed
Scores
Description: GUI for entering test items and obtaining raw
and transformed scores. The results are shown on the
console and can be saved to a tabular text file for further
statistical analysis. The user can define his own tests and
scoring procedures through a GUI.
Author: Manel Salamero
Maintainer: Manel Salamero <manelsalamero@gmail.com>
Diff between TestScorer versions 1.7 dated 2015-04-20 and 1.7.1 dated 2015-07-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 3 +++ R/TestScorer.R | 6 +++--- inst/doc/TestScorerHelp.pdf |binary inst/some.stuff/TST_DASS.r | 2 +- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.1.5 dated 2014-11-07 and 0.2.0 dated 2015-07-02
rnrfa-0.1.5/rnrfa/R/GetStationSummary.R |only rnrfa-0.1.5/rnrfa/R/SearchNRFA.R |only rnrfa-0.1.5/rnrfa/man/GetStationSummary.Rd |only rnrfa-0.1.5/rnrfa/man/SearchNRFA.Rd |only rnrfa-0.2.0/rnrfa/DESCRIPTION | 28 +++++++++++++--------------- rnrfa-0.2.0/rnrfa/MD5 | 26 +++++++++++++------------- rnrfa-0.2.0/rnrfa/NAMESPACE | 4 ++-- rnrfa-0.2.0/rnrfa/R/NRFA_Catalogue.R |only rnrfa-0.2.0/rnrfa/R/NRFA_TS.R |only rnrfa-0.2.0/rnrfa/R/rnrfa-package.R | 20 ++++++++++---------- rnrfa-0.2.0/rnrfa/R/zzz.R | 2 +- rnrfa-0.2.0/rnrfa/man/FindInfo.Rd | 3 ++- rnrfa-0.2.0/rnrfa/man/FindTS.Rd | 3 ++- rnrfa-0.2.0/rnrfa/man/NRFA_Catalogue.Rd |only rnrfa-0.2.0/rnrfa/man/NRFA_TS.Rd |only rnrfa-0.2.0/rnrfa/man/OSG2LatLon.Rd | 3 ++- rnrfa-0.2.0/rnrfa/man/OSGParse.Rd | 3 ++- rnrfa-0.2.0/rnrfa/man/ToJSONarray.Rd | 3 ++- 18 files changed, 49 insertions(+), 46 deletions(-)
Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rmgarch versions 1.2-8 dated 2014-06-30 and 1.2-9 dated 2015-07-02
ChangeLog | 5 +++++ DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 6 ++++-- R/copula-main.R | 10 +++++----- R/rmgarch-ica.R | 2 +- R/rmgarch-scenario.R | 6 +++--- README.md |only build/vignette.rds |binary inst/doc/The_rmgarch_models.pdf |binary 10 files changed, 35 insertions(+), 27 deletions(-)
Title: Time Dependent Point Process Modelling
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte <d.harte@gns.cri.nz>
Diff between PtProcess versions 3.3-9 dated 2015-04-12 and 3.3-10 dated 2015-07-02
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 5 ++++- data/NthChina.rda |binary data/Ogata.rda |binary data/Phuket.rda |binary data/Tangshan.rda |binary man/Changes.Rd | 6 ++++++ man/PtProcess.Rd | 2 +- 9 files changed, 23 insertions(+), 14 deletions(-)
Title: Power Calculations for GxE and GxG Interactions for GWAS
Description: Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.
Author: Charles Kooperberg <clk@fredhutch.org> and Li Hsu <lih@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between powerGWASinteraction versions 1.1.1 dated 2014-12-21 and 1.1.3 dated 2015-07-02
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NAMESPACE | 1 + man/powerGE.Rd | 4 ++-- man/powerGG.Rd | 2 +- man/powerGWASinteraction.Rd | 2 +- 6 files changed, 15 insertions(+), 13 deletions(-)
More information about powerGWASinteraction at CRAN
Permanent link
Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between polspline versions 1.1.9 dated 2013-11-20 and 1.1.11 dated 2015-07-02
DESCRIPTION | 17 +++++----- INDEX |only MD5 | 63 +++++++++++++++++++-------------------- NAMESPACE | 26 ++++++++++++++++ man/beta.polyclass.Rd | 2 - man/clspec.Rd | 2 - man/cpolyclass.Rd | 2 - man/dhare.Rd | 2 - man/dheft.Rd | 2 - man/dlogspline.Rd | 2 - man/doldlogspline.Rd | 2 - man/hare.Rd | 2 - man/heft.Rd | 2 - man/logspline.Rd | 2 - man/lspec.Rd | 2 - man/oldlogspline.Rd | 2 - man/oldlogspline.to.logspline.Rd | 2 - man/plot.hare.Rd | 2 - man/plot.heft.Rd | 2 - man/plot.logspline.Rd | 2 - man/plot.lspec.Rd | 2 - man/plot.oldlogspline.Rd | 2 - man/plot.polyclass.Rd | 2 - man/polyclass.Rd | 2 - man/summary.hare.Rd | 2 - man/summary.heft.Rd | 2 - man/summary.logspline.Rd | 2 - man/summary.lspec.Rd | 2 - man/summary.oldlogspline.Rd | 2 - man/summary.polyclass.Rd | 2 - man/testhare.Rd | 2 - man/unstrip.Rd | 2 - man/xhare.Rd | 2 - 33 files changed, 96 insertions(+), 68 deletions(-)
Title: Mandallaz' Model-Assisted Small Area Estimators
Description: An S4 implementation of the unbiased extension of the model-assisted synthetic-regression estimator proposed by Mandallaz (2013), Mandallaz et al. (2013) and Mandallaz (2014).
It yields smaller variances than the standard bias correction, the generalised regression estimator.
Author: Andreas Dominik Cullmann [aut, cre],
Daniel Mandallaz [ctb],
Alexander Francis Massey [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_masae@arcor.de>
Diff between maSAE versions 0.1-2 dated 2014-04-28 and 0.1-3 dated 2015-07-02
DESCRIPTION | 14 ++++----- MD5 | 26 +++++++++--------- build/vignette.rds |binary inst/doc/maSAE.pdf |binary man/maSAE-internal.Rd | 15 ++++++---- man/maSAE-package.Rd | 70 ++++++++++++++++++++++++------------------------- man/predict-methods.Rd | 53 ++++++++++++++++++------------------- man/s0.Rd | 21 +++++++------- man/s1.Rd | 21 +++++++------- man/s2.Rd | 21 ++++++++------ man/saObj.Rd | 33 +++++++++++------------ man/sadObj-class.Rd | 21 +++++++------- man/saeObj-class.Rd | 59 +++++++++++++++++++++-------------------- man/savObj-class.Rd | 9 ++++-- 14 files changed, 187 insertions(+), 176 deletions(-)
Title: Logspline Density Estimation Routines
Description: Routines for the logspline density estimation. oldlogspline
uses the same algorithm as the logspline 1.0.x package - the Kooperberg
and Stone (1992) algorithm (with an improved interface). The recommended
routine logspline uses an algorithm from Stone et al (1997).
Author: Charles Kooperberg <clk@fredhutch.org>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between logspline versions 2.1.5 dated 2013-04-24 and 2.1.8 dated 2015-07-02
DESCRIPTION | 24 ++++++++++++------------ MD5 | 24 ++++++++++++------------ NAMESPACE | 8 ++++++++ man/dlogspline.Rd | 2 +- man/doldlogspline.Rd | 2 +- man/logspline.Rd | 2 +- man/oldlogspline.Rd | 2 +- man/oldlogspline.to.logspline.Rd | 2 +- man/plot.logspline.Rd | 2 +- man/plot.oldlogspline.Rd | 2 +- man/summary.logspline.Rd | 2 +- man/summary.oldlogspline.Rd | 2 +- man/unstrip.Rd | 2 +- 13 files changed, 42 insertions(+), 34 deletions(-)
Title: Logic Regression
Description: Routines for fitting Logic Regression models.
Author: Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski <ingo@jhu.edu>
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between LogicReg versions 1.5.6 dated 2015-01-23 and 1.5.8 dated 2015-07-02
DESCRIPTION | 11 +++++----- MD5 | 44 +++++++++++++++++++++---------------------- NAMESPACE | 13 ++++++++++++ R/LogicReg.R | 2 - man/cumhaz.Rd | 2 - man/eval.logreg.Rd | 2 - man/frame.logreg.Rd | 2 - man/logreg.Rd | 2 - man/logreg.anneal.control.Rd | 2 - man/logreg.mc.control.Rd | 2 - man/logreg.myown.Rd | 2 - man/logreg.savefit1.Rd | 2 - man/logreg.tree.control.Rd | 2 - man/logregmodel.Rd | 2 - man/logregtree.Rd | 2 - man/plot.logreg.Rd | 2 - man/plot.logregmodel.Rd | 2 - man/plot.logregtree.Rd | 2 - man/predict.logreg.Rd | 2 - man/print.logreg.Rd | 2 - man/print.logregmodel.Rd | 2 - man/print.logregtree.Rd | 2 - src/slogic.f | 2 - 23 files changed, 61 insertions(+), 47 deletions(-)
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Lutz Duembgen <duembgen@stat.unibe.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between logcondens versions 2.1.3 dated 2015-06-10 and 2.1.4 dated 2015-07-02
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ NEWS | 4 ++++ inst/doc/logcondens.pdf |binary vignettes/plots/-plot1.pdf |binary vignettes/plots/-plot2.pdf |binary vignettes/plots/-plot2sample.pdf |binary vignettes/plots/-plotSimul.pdf |binary vignettes/plots/-sim1.pdf |binary 10 files changed, 20 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-11 0.1.9
2013-12-30 0.1.8
2013-11-28 0.1.7
2013-09-23 0.1.6
2013-05-07 0.1.5
2013-03-11 0.1.4
2010-11-22 0.1.3
2010-11-18 0.1.2
2010-04-29 0.0.8
2010-02-23 0.0.7
2009-11-24 0.0.6
2008-11-04 0.0.5
2008-10-29 0.0.4
2008-09-28 0.0.3
2008-05-20 0.0.2
2008-05-02 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-09 2.6.4
2014-04-22 2.6.3
2014-02-24 2.6.2
2014-01-10 2.6.1
2013-12-04 2.6.0
2013-11-01 2.5.8
2013-09-23 2.5.7
2013-06-27 2.5.6
2013-05-07 2.5.5
2013-04-04 2.5.4
2010-06-29 2.5.3
2010-05-28 2.5.2
2010-05-22 2.5.1
2010-05-10 2.5.0
2010-05-01 2.4.4
2010-04-28 2.4.3
2010-03-23 2.4.2
2009-09-18 2.4.1
2009-07-21 2.4.0
2009-04-14 2.3.1
2009-03-09 2.3.0
2009-02-12 2.2.0
2008-12-18 2.1.0
2008-10-29 2.0.2
2008-10-14 2.0.1
2008-10-02 1.1.5
2008-09-11 1.1.4
2008-08-06 1.1.3
2008-07-28 1.1.2
2008-07-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-15 3.0.3
2014-05-14 3.0.2
2013-10-21 3.0.1
2013-09-23 3.0.0
2013-05-20 2.2.6
2013-03-04 2.2.5
2012-02-24 2.2.4
2012-02-22 2.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-16 1.2.5
2014-10-21 1.2.4
2014-08-21 1.2.3
2014-06-24 1.2.2
2014-04-20 1.2.1
2013-05-07 1.2.0
2013-03-11 1.1.9
2009-04-14 1.1.8
2009-02-01 1.1.7
2008-12-16 1.1.6
2007-05-21 1.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-21 0.2.2
2014-09-23 0.2.1
2014-05-21 0.2.0
2013-10-25 0.1.9
2013-09-23 0.1.8
2013-05-07 0.1.7
2013-03-08 0.1.6
2009-10-12 0.1.5
2008-11-04 0.1.4
2008-10-30 0.1.3
2008-10-16 0.1.2
2008-04-10 0.1.1
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 3.6.0 dated 2015-06-24 and 3.6.1 dated 2015-07-02
DESCRIPTION | 9 MD5 | 135 - NAMESPACE | 2 inst/Perl/Archive/Zip.pm | 781 ++++--- inst/Perl/Archive/Zip/Archive.pm | 538 ++--- inst/Perl/Archive/Zip/BufferedFileHandle.pm | 38 inst/Perl/Archive/Zip/DirectoryMember.pm | 22 inst/Perl/Archive/Zip/FAQ.pod | 811 +++---- inst/Perl/Archive/Zip/FileMember.pm | 14 inst/Perl/Archive/Zip/Member.pm | 676 +++--- inst/Perl/Archive/Zip/MemberRead.pm | 91 inst/Perl/Archive/Zip/MockFileHandle.pm | 6 inst/Perl/Archive/Zip/NewFileMember.pm | 38 inst/Perl/Archive/Zip/StringMember.pm | 20 inst/Perl/Archive/Zip/Tree.pm | 7 inst/Perl/Archive/Zip/ZipFileMember.pm | 152 - inst/Perl/Excel/Writer/XLSX.pm | 312 ++ inst/Perl/Excel/Writer/XLSX/Chart.pm | 2023 ++++++++++++++++--- inst/Perl/Excel/Writer/XLSX/Chart/Area.pm | 12 inst/Perl/Excel/Writer/XLSX/Chart/Bar.pm | 59 inst/Perl/Excel/Writer/XLSX/Chart/Column.pm | 37 inst/Perl/Excel/Writer/XLSX/Chart/Doughnut.pm |only inst/Perl/Excel/Writer/XLSX/Chart/Line.pm | 21 inst/Perl/Excel/Writer/XLSX/Chart/Pie.pm | 125 - inst/Perl/Excel/Writer/XLSX/Chart/Radar.pm | 12 inst/Perl/Excel/Writer/XLSX/Chart/Scatter.pm | 60 inst/Perl/Excel/Writer/XLSX/Chart/Stock.pm | 82 inst/Perl/Excel/Writer/XLSX/Chartsheet.pm | 6 inst/Perl/Excel/Writer/XLSX/Drawing.pm | 6 inst/Perl/Excel/Writer/XLSX/Examples.pm | 984 +++++++-- inst/Perl/Excel/Writer/XLSX/Format.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/App.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Comments.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/ContentTypes.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Core.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Packager.pm | 80 inst/Perl/Excel/Writer/XLSX/Package/Relationships.pm | 10 inst/Perl/Excel/Writer/XLSX/Package/SharedStrings.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Styles.pm | 19 inst/Perl/Excel/Writer/XLSX/Package/Table.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/Theme.pm | 6 inst/Perl/Excel/Writer/XLSX/Package/VML.pm | 257 ++ inst/Perl/Excel/Writer/XLSX/Package/XMLwriter.pm | 6 inst/Perl/Excel/Writer/XLSX/Shape.pm | 6 inst/Perl/Excel/Writer/XLSX/Utility.pm | 34 inst/Perl/Excel/Writer/XLSX/Workbook.pm | 515 +++- inst/Perl/Excel/Writer/XLSX/Worksheet.pm | 664 ++++-- inst/Perl/Spreadsheet/WriteExcel.pm | 40 inst/Perl/Spreadsheet/WriteExcel/BIFFwriter.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Big.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Chart.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Chart/Area.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/Bar.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/Column.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/External.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Chart/Line.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/Pie.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/Scatter.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Chart/Stock.pm | 2 inst/Perl/Spreadsheet/WriteExcel/Examples.pm | 752 +------ inst/Perl/Spreadsheet/WriteExcel/Format.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Formula.pm | 4 inst/Perl/Spreadsheet/WriteExcel/OLEwriter.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Properties.pm | 6 inst/Perl/Spreadsheet/WriteExcel/Utility.pm | 4 inst/Perl/Spreadsheet/WriteExcel/Workbook.pm | 8 inst/Perl/Spreadsheet/WriteExcel/Worksheet.pm | 4 inst/Perl/Text/CSV.pm | 60 inst/Perl/Text/CSV_PP.pm | 101 69 files changed, 6483 insertions(+), 3252 deletions(-)
Title: Uniformly Most Powerful Tests
Description: Does uniformly most powerful (UMP) and uniformly most
powerful unbiased (UMPU) tests. At present only distribution implemented
is binomial distribution. Also does fuzzy tests and confidence intervals
(following Geyer and Meeden, Statistical Science, 2005) for the binomial
distribution (one-tailed procedures based on UMP test and two-tailed
procedures based on UMPU test).
Author: Charles J. Geyer <charlie@stat.umn.edu> and
Glen D. Meeden <glen@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between ump versions 0.5-4 dated 2014-04-02 and 0.5-6 dated 2015-07-02
CHANGES | 3 +++ DESCRIPTION | 18 ++++++++++++------ MD5 | 8 ++++---- NAMESPACE | 2 ++ build/vignette.rds |binary 5 files changed, 21 insertions(+), 10 deletions(-)
Title: Hidden Markov Models for ChIP-on-Chip Analysis
Description: Methods and classes to build HMMs
that are suitable for the analysis of ChIP-chip data. The
provided parameter estimation methods include the Baum-Welch
algorithm and Viterbi training as well as a combination of
both.
Author: Peter Humburg [aut, cre]
Maintainer: Peter Humburg <peter.humburg@gmail.com>
Diff between tileHMM versions 1.0-6 dated 2013-12-12 and 1.0-7 dated 2015-07-02
DESCRIPTION | 22 - MD5 | 84 +-- NAMESPACE | 13 NEWS.md |only R/utils.R | 1 README.md |only build/vignette.rds |binary data/datalist | 2 inst/CITATION | 6 inst/COPYING | 2 inst/doc/tileHMM.R | 476 +++++++++++----------- inst/doc/tileHMM.Rnw | 904 +++++++++++++++++++++--------------------- man/baumWelch.Rd | 162 +++---- man/contDist-class.Rd | 76 +-- man/contHMM-access.Rd | 146 +++--- man/contHMM-class.Rd | 92 ++-- man/discDist-class.Rd | 82 +-- man/dist-class.Rd | 42 - man/forward.Rd | 130 +++--- man/generate.data.Rd | 82 +-- man/getHMM.Rd | 76 +-- man/gff2index.Rd | 130 +++--- man/hmm-class.Rd | 80 +-- man/hmm.setup.Rd | 122 ++--- man/initializeDist-methods.Rd | 110 ++--- man/internals.Rd | 28 - man/logSum.Rd | 90 ++-- man/plot.Rd | 112 ++--- man/posterior.Rd | 98 ++-- man/reg2gff.Rd | 138 +++--- man/region.length.Rd | 72 +-- man/region.position.Rd | 88 ++-- man/remove.short.Rd | 146 +++--- man/sampleObs.Rd | 78 +-- man/sampleSeq.Rd | 88 ++-- man/shrinkt.st.Rd | 102 ++-- man/simChIP.Rd | 110 ++--- man/states.Rd | 94 ++-- man/tDist-class.Rd | 94 ++-- man/tileHMM-package.Rd | 104 ++-- man/viterbi.Rd | 116 ++--- man/viterbiEM.Rd | 116 ++--- man/viterbiTraining.Rd | 140 +++--- vignettes/tileHMM.Rnw | 904 +++++++++++++++++++++--------------------- 44 files changed, 2788 insertions(+), 2770 deletions(-)
Title: Portfolio Allocation and Risk Management Applications
Description: Methods for Portfolio Optimization and Risk Management.
Author: Alexios Ghalanos and Bernhard Pfaff
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between parma versions 1.5-1 dated 2014-02-23 and 1.5-2 dated 2015-07-02
Changelog | 6 + DESCRIPTION | 22 +++--- MD5 | 23 +++---- NAMESPACE | 4 - R/p-LP.R | 6 - R/p-QP.R | 2 R/p-fun.R | 3 README.md |only build/vignette.rds |binary data/etfdata.rda |binary inst/doc/Portfolio_Optimization_in_parma.pdf |binary man/parma-package.Rd | 4 - vignettes/Portfolio_Optimization_in_parma.tex | 82 +++++++++++++------------- 13 files changed, 79 insertions(+), 73 deletions(-)
Title: File System Utility Functions for 'NeuroAnatomy Toolbox'
Description: Utility functions that may be of general interest but are
specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes
functions to provide a basic make style system to update files based on
timestamp information, file locking and 'touch' utility. Convenience
functions for working with file paths include 'abs2rel', 'split_path'
and 'common_path'. Finally there are utility functions for working with
'zip' and 'gzip' files including integrity tests.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat.utils versions 0.4.2 dated 2014-06-16 and 0.5 dated 2015-07-02
nat.utils-0.4.2/nat.utils/inst |only nat.utils-0.4.2/nat.utils/man/file.hardlink.Rd |only nat.utils-0.5/nat.utils/DESCRIPTION | 22 +-- nat.utils-0.5/nat.utils/MD5 | 60 ++++---- nat.utils-0.5/nat.utils/NAMESPACE | 6 nat.utils-0.5/nat.utils/NEWS | 15 ++ nat.utils-0.5/nat.utils/R/filelocks.r | 3 nat.utils-0.5/nat.utils/R/fsutils.r | 144 +++++++++++++++++++-- nat.utils-0.5/nat.utils/R/gziputils.r | 1 nat.utils-0.5/nat.utils/R/sysutils.r | 10 - nat.utils-0.5/nat.utils/R/ziputils.r | 18 ++ nat.utils-0.5/nat.utils/README.md | 43 ++---- nat.utils-0.5/nat.utils/man/RunCmdForNewerInput.Rd | 3 nat.utils-0.5/nat.utils/man/abs2rel.Rd | 10 + nat.utils-0.5/nat.utils/man/common_path.Rd |only nat.utils-0.5/nat.utils/man/file.swap.Rd | 3 nat.utils-0.5/nat.utils/man/gzip.crc.Rd | 3 nat.utils-0.5/nat.utils/man/is.gzip.Rd | 4 nat.utils-0.5/nat.utils/man/makelock.Rd | 6 nat.utils-0.5/nat.utils/man/nat.utils-defunct.Rd |only nat.utils-0.5/nat.utils/man/nat.utils.Rd | 3 nat.utils-0.5/nat.utils/man/ncpus.Rd | 7 - nat.utils-0.5/nat.utils/man/split_path.Rd |only nat.utils-0.5/nat.utils/man/touch.Rd | 3 nat.utils-0.5/nat.utils/man/zipinfo.Rd | 3 nat.utils-0.5/nat.utils/man/zipok.Rd | 3 nat.utils-0.5/nat.utils/tests |only 27 files changed, 268 insertions(+), 102 deletions(-)
Title: Mountain Plots, Folded Empirical Cumulative Distribution Plots
Description: Lattice functions for drawing folded empirical cumulative
distribution plots, or mountain plots. A mountain plot is similar
to an empirical CDF plot, except that the curve increases from
0 to 0.5, then decreases from 0.5 to 1 using an inverted scale at
the right side. See: Monti (1995), Folded empirical distribution
function curves-mountain plots. The American Statistician, 49, 342-345.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between mountainplot versions 1.0 dated 2015-01-26 and 1.1 dated 2015-07-02
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS | 4 ++++ build/vignette.rds |binary inst/doc/mountainplot.R | 11 ++++++----- inst/doc/mountainplot.Rnw | 28 ++++++++++++++++++---------- inst/doc/mountainplot.pdf |binary man/mountainplot.Rd | 7 ++++++- vignettes/mountainplot.Rnw | 28 ++++++++++++++++++---------- 10 files changed, 77 insertions(+), 44 deletions(-)
Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers
using a non-scientific format optimized for human readers. Vectors
of numbers are rounded using significant digits, aligned at the
decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between lucid versions 1.2 dated 2015-04-14 and 1.3 dated 2015-07-02
lucid-1.2/lucid/vignettes/figure |only lucid-1.3/lucid/DESCRIPTION | 20 ++++++---- lucid-1.3/lucid/MD5 | 17 ++++----- lucid-1.3/lucid/NEWS | 4 ++ lucid-1.3/lucid/build/vignette.rds |binary lucid-1.3/lucid/inst/doc/lucid_printing.R | 9 +++- lucid-1.3/lucid/inst/doc/lucid_printing.Rnw | 40 ++++++++++++--------- lucid-1.3/lucid/inst/doc/lucid_printing.pdf |binary lucid-1.3/lucid/vignettes/lucid.bib | 50 ++++++++++++++++----------- lucid-1.3/lucid/vignettes/lucid_printing.Rnw | 40 ++++++++++++--------- 10 files changed, 107 insertions(+), 73 deletions(-)
Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7)
by David J. Hand and Robert J. Till (2001). A Simple Generalisation of
the Area Under the ROC Curve for Multiple Class Classification Problems.
Machine Learning, 45 (2), p. 171--186. DOI:10.1023/A:1010920819831.
Author: Andreas Dominik Cullmann [aut, cre],
Edgar Kublin [ctb]
Maintainer: Andreas Dominik Cullmann <r-package_handtill2001@arcor.de>
Diff between HandTill2001 versions 0.2-9 dated 2013-11-23 and 0.2-10 dated 2015-07-02
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/AllClasses.R | 2 -- build/vignette.rds |binary inst/doc/consensus_auc.pdf |binary tests/constructors.R | 37 +++++++++++++------------------------ 7 files changed, 29 insertions(+), 39 deletions(-)
Title: Exact P-Values and Matching Confidence Intervals for Simple
Discrete Parametric Cases
Description: Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between exactci versions 1.3-0 dated 2014-09-25 and 1.3-1 dated 2015-07-02
ChangeLog | 7 +++++++ DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 5 +++++ build/vignette.rds |binary inst/doc/exactci.pdf |binary man/exactci-internal.Rd | 3 +-- man/exactci-package.Rd | 4 ++-- 8 files changed, 28 insertions(+), 17 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine.
Interacts with the 'Elasticsearch' 'HTTP' 'API' (http://elasticsearch.org), including
functions for setting connection details to 'Elasticsearch' instances, loading bulk
data, searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs' for
'indices', documents, nodes, clusters, an interface to the cat 'API', and more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.4.0 dated 2015-05-01 and 0.5.0 dated 2015-07-02
elastic-0.4.0/elastic/NEWS |only elastic-0.5.0/elastic/DESCRIPTION | 23 +- elastic-0.5.0/elastic/MD5 | 87 +++++----- elastic-0.5.0/elastic/NAMESPACE | 20 ++ elastic-0.5.0/elastic/NEWS.md |only elastic-0.5.0/elastic/R/Search.R | 42 ++--- elastic-0.5.0/elastic/R/docs_bulk.r | 11 + elastic-0.5.0/elastic/R/docs_create.R | 1 elastic-0.5.0/elastic/R/docs_delete.R | 1 elastic-0.5.0/elastic/R/docs_get.r | 2 elastic-0.5.0/elastic/R/docs_mget.r | 23 +- elastic-0.5.0/elastic/R/elastic-package.r | 40 ++-- elastic-0.5.0/elastic/R/httr-verbs.R | 9 - elastic-0.5.0/elastic/R/index.R | 33 +++- elastic-0.5.0/elastic/R/nodes.R | 8 elastic-0.5.0/elastic/R/search_body.R | 1 elastic-0.5.0/elastic/R/zzz.r | 2 elastic-0.5.0/elastic/README.md | 36 ++-- elastic-0.5.0/elastic/build/vignette.rds |binary elastic-0.5.0/elastic/inst/doc/elastic_intro.Rmd | 19 +- elastic-0.5.0/elastic/inst/doc/elastic_intro.html | 119 ++++++++------ elastic-0.5.0/elastic/inst/doc/search.Rmd | 37 ++-- elastic-0.5.0/elastic/inst/doc/search.html | 137 +++++++++-------- elastic-0.5.0/elastic/inst/vign/elastic_intro.Rmd | 13 - elastic-0.5.0/elastic/inst/vign/elastic_intro.md | 19 +- elastic-0.5.0/elastic/inst/vign/search.Rmd | 11 - elastic-0.5.0/elastic/inst/vign/search.md | 37 ++-- elastic-0.5.0/elastic/man/elastic.Rd | 6 elastic-0.5.0/elastic/man/index.Rd | 14 + elastic-0.5.0/elastic/tests/other/test-mlt.R | 23 ++ elastic-0.5.0/elastic/tests/test-all.R |only elastic-0.5.0/elastic/tests/testthat/test-alias.R | 14 + elastic-0.5.0/elastic/tests/testthat/test-cat.R | 16 + elastic-0.5.0/elastic/tests/testthat/test-cluster.R | 24 ++ elastic-0.5.0/elastic/tests/testthat/test-connect.R | 4 elastic-0.5.0/elastic/tests/testthat/test-count.R | 10 - elastic-0.5.0/elastic/tests/testthat/test-docs.R | 55 ++++-- elastic-0.5.0/elastic/tests/testthat/test-explain.R | 14 - elastic-0.5.0/elastic/tests/testthat/test-indices.R | 25 ++- elastic-0.5.0/elastic/tests/testthat/test-mappings.R | 47 +++-- elastic-0.5.0/elastic/tests/testthat/test-nodes.R | 6 elastic-0.5.0/elastic/tests/testthat/test-ping.R | 4 elastic-0.5.0/elastic/tests/testthat/test-search.R | 28 ++- elastic-0.5.0/elastic/tests/testthat/test-search_uri.R | 14 + elastic-0.5.0/elastic/vignettes/elastic_intro.Rmd | 19 +- elastic-0.5.0/elastic/vignettes/search.Rmd | 37 ++-- 46 files changed, 668 insertions(+), 423 deletions(-)
Title: Distributed Storage and List
Description: An abstract DList class helps storing large list-type objects in a distributed manner. Corresponding high-level functions and methods for handling distributed storage (DStorage) and lists allows for processing such DLists on distributed systems efficiently. In doing so it uses a well defined storage backend implemented based on the DStorage class.
Author: Ingo Feinerer [aut],
Stefan Theussl [aut, cre],
Christian Buchta [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between DSL versions 0.1-5 dated 2014-02-21 and 0.1-6 dated 2015-07-02
DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ R/HDFS.R | 18 +++++++++--------- R/list.R | 3 ++- build/vignette.rds |binary inst/doc/DSL.R | 2 +- inst/doc/DSL.Rnw | 2 +- inst/doc/DSL.pdf |binary man/gather.Rd | 2 +- vignettes/DSL.Rnw | 2 +- 11 files changed, 36 insertions(+), 30 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.2.5 dated 2015-06-04 and 1.2.6 dated 2015-07-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 5 ++++- NEWS | 4 +++- R/kmciFunctions.R | 2 +- man/bpcp-package.Rd | 4 ++-- 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Copula Density and 2-D Hazard Estimation using Smoothing Splines
Description: A collection of routines for the estimation of copula density
and 2-D hazard function using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>
Diff between gsscopu versions 0.9-2 dated 2014-12-06 and 0.9-3 dated 2015-07-02
ChangeLog | 12 +++++++++--- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ data/DiaRet.rda |binary 5 files changed, 19 insertions(+), 11 deletions(-)
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>
Diff between gss versions 2.1-4 dated 2014-12-06 and 2.1-5 dated 2015-07-02
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 4 ++++ data/ColoCan.rda |binary data/LakeAcidity.rda |binary data/NO2.rda |binary data/Sachs.rda |binary data/aids.rda |binary data/bacteriuria.rda |binary data/buffalo.rda |binary data/clim.rda |binary data/esc.rda |binary data/eyetrack.rda |binary data/gastric.rda |binary data/nox.rda |binary data/ozone.rda |binary data/penny.rda |binary data/stan.rda |binary data/wesdr.rda |binary 20 files changed, 33 insertions(+), 23 deletions(-)
Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing
and visualisation of network of contacts.
Author: Maria Noremark [aut],
Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between EpiContactTrace versions 0.8.8 dated 2013-11-05 and 0.9.0 dated 2015-07-02
EpiContactTrace-0.8.8/EpiContactTrace/R/animate.r |only EpiContactTrace-0.8.8/EpiContactTrace/R/trace.R |only EpiContactTrace-0.8.8/EpiContactTrace/inst/tests |only EpiContactTrace-0.8.8/EpiContactTrace/man/Animate.Rd |only EpiContactTrace-0.8.8/EpiContactTrace/src/Makevars |only EpiContactTrace-0.8.8/EpiContactTrace/src/Makevars.win |only EpiContactTrace-0.8.8/EpiContactTrace/src/trace.h |only EpiContactTrace-0.8.8/EpiContactTrace/tests/run-all.R |only EpiContactTrace-0.9.0/EpiContactTrace/DESCRIPTION | 38 EpiContactTrace-0.9.0/EpiContactTrace/MD5 | 92 EpiContactTrace-0.9.0/EpiContactTrace/NAMESPACE | 17 EpiContactTrace-0.9.0/EpiContactTrace/NEWS | 27 EpiContactTrace-0.9.0/EpiContactTrace/R/ContactTrace.r | 20 EpiContactTrace-0.9.0/EpiContactTrace/R/EpiContactTrace-package.r | 1 EpiContactTrace-0.9.0/EpiContactTrace/R/in-degree.r | 86 EpiContactTrace-0.9.0/EpiContactTrace/R/ingoing-contact-chain.r | 85 EpiContactTrace-0.9.0/EpiContactTrace/R/network-structure.r | 60 EpiContactTrace-0.9.0/EpiContactTrace/R/network-summary.r | 55 EpiContactTrace-0.9.0/EpiContactTrace/R/out-degree.r | 86 EpiContactTrace-0.9.0/EpiContactTrace/R/outgoing-contact-chain.r | 84 EpiContactTrace-0.9.0/EpiContactTrace/R/plot.r |only EpiContactTrace-0.9.0/EpiContactTrace/R/report.r | 611 ++++-- EpiContactTrace-0.9.0/EpiContactTrace/R/shortest-paths.r | 401 +++- EpiContactTrace-0.9.0/EpiContactTrace/R/show.r | 66 EpiContactTrace-0.9.0/EpiContactTrace/R/trace.r |only EpiContactTrace-0.9.0/EpiContactTrace/R/tree.r |only EpiContactTrace-0.9.0/EpiContactTrace/inst/CITATION |only EpiContactTrace-0.9.0/EpiContactTrace/inst/extdata |only EpiContactTrace-0.9.0/EpiContactTrace/man/ContactTrace-class.Rd | 53 EpiContactTrace-0.9.0/EpiContactTrace/man/Contacts-class.Rd | 114 - EpiContactTrace-0.9.0/EpiContactTrace/man/EpiContactTrace-package.Rd | 107 - EpiContactTrace-0.9.0/EpiContactTrace/man/InDegree-methods.Rd | 212 +- EpiContactTrace-0.9.0/EpiContactTrace/man/IngoingContactChain-methods.Rd | 224 +- EpiContactTrace-0.9.0/EpiContactTrace/man/NetworkStructure-methods.Rd | 133 - EpiContactTrace-0.9.0/EpiContactTrace/man/NetworkSummary-methods.Rd | 241 +- EpiContactTrace-0.9.0/EpiContactTrace/man/OutDegree-methods.Rd | 227 +- EpiContactTrace-0.9.0/EpiContactTrace/man/OutgoingContactChain-methods.Rd | 158 - EpiContactTrace-0.9.0/EpiContactTrace/man/Report-methods.Rd | 148 - EpiContactTrace-0.9.0/EpiContactTrace/man/ReportObject.Rd | 39 EpiContactTrace-0.9.0/EpiContactTrace/man/ShortestPaths-methods.Rd | 161 + EpiContactTrace-0.9.0/EpiContactTrace/man/Trace.Rd | 175 - EpiContactTrace-0.9.0/EpiContactTrace/man/build_tree.Rd |only EpiContactTrace-0.9.0/EpiContactTrace/man/plot-methods.Rd |only EpiContactTrace-0.9.0/EpiContactTrace/man/position_tree.Rd |only EpiContactTrace-0.9.0/EpiContactTrace/man/show-methods.Rd | 81 EpiContactTrace-0.9.0/EpiContactTrace/man/transfers.Rd | 30 EpiContactTrace-0.9.0/EpiContactTrace/src/trace.cpp | 926 ++++++---- EpiContactTrace-0.9.0/EpiContactTrace/tests/arguments.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/contact-chain.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/degree.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/misc.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/network-summary.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/shortest-paths.R |only EpiContactTrace-0.9.0/EpiContactTrace/tests/tree.R |only 54 files changed, 2720 insertions(+), 2038 deletions(-)
More information about EpiContactTrace at CRAN
Permanent link
Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence
intervals based on the stage-wise ordering in group sequential designs and
adaptive group sequential designs. For adaptive group sequential designs
the confidence intervals are based on the conditional rejection probability
principle. Currently the procedures do not support the use of futility
boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AGSDest versions 2.2 dated 2015-01-29 and 2.3 dated 2015-07-02
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 5 ++++- R/AGSDest.R | 2 +- build/vignette.rds |binary inst/doc/vignette.pdf |binary man/AGSDest.Rd | 3 ++- man/AGSTobj.Rd | 3 ++- man/GSTobj.Rd | 3 ++- man/adapt.Rd | 3 ++- man/as.AGST.Rd | 3 ++- man/as.GST.Rd | 3 ++- man/cer.Rd | 3 ++- man/cp.Rd | 3 ++- man/plan.GST.Rd | 3 ++- man/pvalue.Rd | 3 ++- man/seqconfint.Rd | 3 ++- man/typeIerr.Rd | 3 ++- 18 files changed, 51 insertions(+), 36 deletions(-)
Title: Diving Calculations and Decompression Models
Description: Code for describing and manipulating scuba diving profiles
(depth-time curves) and decompression models,
for calculating the predictions of decompression models,
for calculating maximum no-decompression time and decompression tables,
and for performing mixed gas calculations.
Author: Adrian Baddeley [aut, cre],
Vittorio Broglio [ctb, dtc],
Pedro Antonio Neves [ctb, dtc],
Andrew Bassom [ctb],
Peter Buzzacott [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between scuba versions 1.7-0 dated 2013-12-15 and 1.8-0 dated 2015-07-02
DESCRIPTION | 32 +++++++++---- MD5 | 26 +++++------ NAMESPACE | 18 +++++++ NEWS | 11 ++++ R/dive.R | 49 ++++++++++++++++---- build/vignette.rds |binary data/Bookspan.rda |binary data/baron.rda |binary data/deepmine.rda |binary data/pedro.rda |binary inst/doc/intro.R | 122 +++++++++++++++++++++++++++++++--------------------- inst/doc/intro.Rnw | 41 ++++++++++++++++- inst/doc/intro.pdf |binary vignettes/intro.Rnw | 41 ++++++++++++++++- 14 files changed, 254 insertions(+), 86 deletions(-)
Title: GUI for Renext
Description: Graphical User Interface for Renext.
Author: Yves Deville <deville.yves@alpestat.com> and IRSN <renext@irsn.fr>
Maintainer: Lise Bardet <lise.bardet@irsn.fr>
Diff between RenextGUI versions 1.0-2 dated 2013-10-08 and 1.3-0 dated 2015-07-02
ChangeLog | 38 DESCRIPTION | 14 MD5 | 13 NAMESPACE | 5 R/HTMLmisc.R | 8 R/RenextGUI.R | 5870 +++++++++++++++++++++++------------------------ inst/doc/index.html |only man/RenextGUI-package.Rd | 10 8 files changed, 3009 insertions(+), 2949 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-9 dated 2015-05-15 and 1.0-10 dated 2015-07-02
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 6 ++++-- inst/NEWS | 3 +++ inst/doc/rEMM.pdf |binary 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop
recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between recommenderlab versions 0.1-5 dated 2014-08-18 and 0.1-6 dated 2015-07-02
DESCRIPTION | 12 ++-- MD5 | 22 ++++---- NAMESPACE | 4 + R/dissimilarity.R | 3 - R/evaluate.R | 104 +++++++++++++++++++++--------------------- build/vignette.rds |binary data/Jester5k.rda |binary data/MSWeb.rda |binary data/MovieLense.rda |binary inst/NEWS | 3 + inst/doc/recommenderlab.pdf |binary man/evaluationScheme-class.Rd | 5 +- 12 files changed, 80 insertions(+), 73 deletions(-)
More information about recommenderlab at CRAN
Permanent link
Title: Read, Write, and Process Brain Imaging Data
Description: A collection of data structures that represent
volumetric brain imaging data. The focus is on basic data handling for 3D
and 4D neuroimaging data. In addition, there are function to read and write
NIFTI files and limited support for reading AFNI files.
Author: Bradley R. Buchsbaum
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between neuroim versions 0.0.3 dated 2014-04-04 and 0.0.4 dated 2015-07-02
neuroim-0.0.3/neuroim/README.md |only neuroim-0.0.3/neuroim/man/dim-methods.Rd |only neuroim-0.0.3/neuroim/man/length-ROIVolume-method.Rd |only neuroim-0.0.3/neuroim/man/seriesIter-methods.Rd |only neuroim-0.0.3/neuroim/man/show-methods.Rd |only neuroim-0.0.3/neuroim/man/sub-sub-BrainBucket-character-missing-method.Rd |only neuroim-0.0.3/neuroim/man/sub-sub-BrainBucket-numeric-missing-method.Rd |only neuroim-0.0.4/neuroim/DESCRIPTION | 27 neuroim-0.0.4/neuroim/MD5 | 388 +++++----- neuroim-0.0.4/neuroim/NAMESPACE | 64 + neuroim-0.0.4/neuroim/R/AFNI_IO.R | 4 neuroim-0.0.4/neuroim/R/AllClass.R | 174 ++-- neuroim-0.0.4/neuroim/R/AllGeneric.R | 350 +++++++-- neuroim-0.0.4/neuroim/R/Axis.R | 81 +- neuroim-0.0.4/neuroim/R/BinaryIO.R | 8 neuroim-0.0.4/neuroim/R/BrainData.R | 17 neuroim-0.0.4/neuroim/R/BrainMetaInfo.R | 10 neuroim-0.0.4/neuroim/R/BrainRegion3D.R | 234 +++++- neuroim-0.0.4/neuroim/R/BrainSlice.R | 23 neuroim-0.0.4/neuroim/R/BrainSpace.R | 131 ++- neuroim-0.0.4/neuroim/R/BrainVector.R | 333 ++++++-- neuroim-0.0.4/neuroim/R/BrainVolume.R | 251 +++++- neuroim-0.0.4/neuroim/R/Display.R | 135 ++- neuroim-0.0.4/neuroim/R/IndexLookupVolume.R | 3 neuroim-0.0.4/neuroim/R/Ops.R | 19 neuroim-0.0.4/neuroim/R/RcppExports.R |only neuroim-0.0.4/neuroim/R/SparseBrainVector.R | 258 +++--- neuroim-0.0.4/neuroim/R/common.R | 168 +++- neuroim-0.0.4/neuroim/R/conncomp.R | 2 neuroim-0.0.4/neuroim/R/datadoc.R |only neuroim-0.0.4/neuroim/R/neuroim.R |only neuroim-0.0.4/neuroim/build |only neuroim-0.0.4/neuroim/data |only neuroim-0.0.4/neuroim/inst/doc |only neuroim-0.0.4/neuroim/man/AFNIFileDescriptor-class.Rd | 5 neuroim-0.0.4/neuroim/man/AFNIMetaInfo-class.Rd | 3 neuroim-0.0.4/neuroim/man/AxisSet-class.Rd | 5 neuroim-0.0.4/neuroim/man/AxisSet1D-class.Rd | 5 neuroim-0.0.4/neuroim/man/AxisSet2D-class.Rd | 7 neuroim-0.0.4/neuroim/man/AxisSet3D-class.Rd | 5 neuroim-0.0.4/neuroim/man/AxisSet4D-class.Rd | 5 neuroim-0.0.4/neuroim/man/AxisSet5D-class.Rd | 5 neuroim-0.0.4/neuroim/man/Base-class.Rd |only neuroim-0.0.4/neuroim/man/BaseMetaInfo-class.Rd | 5 neuroim-0.0.4/neuroim/man/BaseSource-class.Rd | 5 neuroim-0.0.4/neuroim/man/BinaryReader-class.Rd | 3 neuroim-0.0.4/neuroim/man/BinaryReader.Rd | 3 neuroim-0.0.4/neuroim/man/BinaryWriter-class.Rd | 3 neuroim-0.0.4/neuroim/man/BootstrapSearchlight.Rd |only neuroim-0.0.4/neuroim/man/BrainBucket-class.Rd | 24 neuroim-0.0.4/neuroim/man/BrainBucketSource-class.Rd | 3 neuroim-0.0.4/neuroim/man/BrainData-class.Rd | 3 neuroim-0.0.4/neuroim/man/BrainFileDescriptor-class.Rd | 5 neuroim-0.0.4/neuroim/man/BrainFileSource-class.Rd | 6 neuroim-0.0.4/neuroim/man/BrainMetaInfo-class.Rd | 5 neuroim-0.0.4/neuroim/man/BrainSlice-class.Rd | 3 neuroim-0.0.4/neuroim/man/BrainSlice.Rd | 3 neuroim-0.0.4/neuroim/man/BrainSource-class.Rd | 6 neuroim-0.0.4/neuroim/man/BrainSpace-class.Rd | 3 neuroim-0.0.4/neuroim/man/BrainSpace.Rd | 9 neuroim-0.0.4/neuroim/man/BrainVector-class.Rd | 16 neuroim-0.0.4/neuroim/man/BrainVectorSource-class.Rd | 16 neuroim-0.0.4/neuroim/man/BrainVectorSource.Rd |only neuroim-0.0.4/neuroim/man/BrainVolume-class.Rd | 33 neuroim-0.0.4/neuroim/man/BrainVolume.Rd |only neuroim-0.0.4/neuroim/man/BrainVolumeSource-class.Rd | 5 neuroim-0.0.4/neuroim/man/ClusteredBrainVolume-class.Rd | 18 neuroim-0.0.4/neuroim/man/DenseBrainVector-class.Rd | 5 neuroim-0.0.4/neuroim/man/DenseBrainVolume-class.Rd | 3 neuroim-0.0.4/neuroim/man/FileMetaInfo-class.Rd | 9 neuroim-0.0.4/neuroim/man/IndexLookupVolume-class.Rd | 3 neuroim-0.0.4/neuroim/man/Kernel-class.Rd | 3 neuroim-0.0.4/neuroim/man/Kernel.Rd | 3 neuroim-0.0.4/neuroim/man/Layer-class.Rd | 7 neuroim-0.0.4/neuroim/man/Layer.Rd | 20 neuroim-0.0.4/neuroim/man/LogicalBrainVolume-class.Rd | 5 neuroim-0.0.4/neuroim/man/MNI_SPACE_1MM.Rd |only neuroim-0.0.4/neuroim/man/NIfTIFileDescriptor-class.Rd | 5 neuroim-0.0.4/neuroim/man/NIfTIMetaInfo-class.Rd | 3 neuroim-0.0.4/neuroim/man/NamedAxis-class.Rd | 5 neuroim-0.0.4/neuroim/man/NullMetaInfo-class.Rd | 5 neuroim-0.0.4/neuroim/man/ROIVolume-class.Rd | 9 neuroim-0.0.4/neuroim/man/ROIVolume.Rd | 3 neuroim-0.0.4/neuroim/man/RandomSearchlight.Rd | 3 neuroim-0.0.4/neuroim/man/RegionCube.Rd | 17 neuroim-0.0.4/neuroim/man/RegionSphere.Rd | 12 neuroim-0.0.4/neuroim/man/RegionSquare.Rd |only neuroim-0.0.4/neuroim/man/Searchlight.Rd | 3 neuroim-0.0.4/neuroim/man/SparseBrainVector-class.Rd | 10 neuroim-0.0.4/neuroim/man/SparseBrainVectorSource-class.Rd | 3 neuroim-0.0.4/neuroim/man/SparseBrainVolume-class.Rd | 24 neuroim-0.0.4/neuroim/man/addDim-methods.Rd | 9 neuroim-0.0.4/neuroim/man/as-methods.Rd | 9 neuroim-0.0.4/neuroim/man/as.array-BrainData-method.Rd | 5 neuroim-0.0.4/neuroim/man/as.list-methods.Rd | 16 neuroim-0.0.4/neuroim/man/as.logical-methods.Rd | 13 neuroim-0.0.4/neuroim/man/as.mask-methods.Rd | 3 neuroim-0.0.4/neuroim/man/as.matrix-BrainData-method.Rd | 5 neuroim-0.0.4/neuroim/man/as.matrix-methods.Rd | 9 neuroim-0.0.4/neuroim/man/as.numeric-methods.Rd | 5 neuroim-0.0.4/neuroim/man/as.raster-methods.Rd | 5 neuroim-0.0.4/neuroim/man/as.sparse-methods.Rd | 30 neuroim-0.0.4/neuroim/man/as.vector-BrainData-ANY-method.Rd | 5 neuroim-0.0.4/neuroim/man/axes-methods.Rd | 7 neuroim-0.0.4/neuroim/man/axisToIndex-methods.Rd | 5 neuroim-0.0.4/neuroim/man/bounds-methods.Rd | 14 neuroim-0.0.4/neuroim/man/close-methods.Rd | 7 neuroim-0.0.4/neuroim/man/clusterCenters-methods.Rd | 5 neuroim-0.0.4/neuroim/man/concat-methods.Rd | 32 neuroim-0.0.4/neuroim/man/connComp-methods.Rd | 3 neuroim-0.0.4/neuroim/man/connComp3D.Rd | 3 neuroim-0.0.4/neuroim/man/coordToGrid-methods.Rd | 8 neuroim-0.0.4/neuroim/man/coordToIndex-methods.Rd | 8 neuroim-0.0.4/neuroim/man/coords-methods.Rd | 5 neuroim-0.0.4/neuroim/man/dataFile-methods.Rd | 3 neuroim-0.0.4/neuroim/man/dataFileMatches-methods.Rd | 3 neuroim-0.0.4/neuroim/man/dataReader-methods.Rd | 3 neuroim-0.0.4/neuroim/man/dim-BrainData-method.Rd |only neuroim-0.0.4/neuroim/man/dim-BrainSpace-method.Rd |only neuroim-0.0.4/neuroim/man/dim-FileMetaInfo-method.Rd |only neuroim-0.0.4/neuroim/man/dropDim-methods.Rd | 23 neuroim-0.0.4/neuroim/man/eachSeries-methods.Rd | 11 neuroim-0.0.4/neuroim/man/eachSlice-methods.Rd | 3 neuroim-0.0.4/neuroim/man/eachVolume-methods.Rd | 66 + neuroim-0.0.4/neuroim/man/fileMatches-methods.Rd | 3 neuroim-0.0.4/neuroim/man/fill-methods.Rd | 22 neuroim-0.0.4/neuroim/man/gridToCoord-methods.Rd |only neuroim-0.0.4/neuroim/man/gridToIndex-methods.Rd | 13 neuroim-0.0.4/neuroim/man/headerFile-methods.Rd | 3 neuroim-0.0.4/neuroim/man/headerFileMatches-methods.Rd | 3 neuroim-0.0.4/neuroim/man/image-methods.Rd | 21 neuroim-0.0.4/neuroim/man/imageGrid.Rd |only neuroim-0.0.4/neuroim/man/indexToCoord-methods.Rd | 12 neuroim-0.0.4/neuroim/man/indexToGrid-methods.Rd | 15 neuroim-0.0.4/neuroim/man/indices-methods.Rd | 7 neuroim-0.0.4/neuroim/man/internal-methods.Rd | 8 neuroim-0.0.4/neuroim/man/inverseTrans-methods.Rd | 12 neuroim-0.0.4/neuroim/man/length-methods.Rd | 10 neuroim-0.0.4/neuroim/man/loadBucket.Rd | 3 neuroim-0.0.4/neuroim/man/loadData-methods.Rd | 7 neuroim-0.0.4/neuroim/man/loadVector.Rd | 3 neuroim-0.0.4/neuroim/man/loadVolume.Rd | 5 neuroim-0.0.4/neuroim/man/loadVolumeList.Rd | 3 neuroim-0.0.4/neuroim/man/lookup-methods.Rd | 5 neuroim-0.0.4/neuroim/man/makeVector.Rd | 7 neuroim-0.0.4/neuroim/man/makeVolume.Rd | 22 neuroim-0.0.4/neuroim/man/map-methods.Rd | 5 neuroim-0.0.4/neuroim/man/matchAnatomy2D.Rd | 3 neuroim-0.0.4/neuroim/man/matchAnatomy3D.Rd | 5 neuroim-0.0.4/neuroim/man/matrixToVolumeList.Rd |only neuroim-0.0.4/neuroim/man/mergePartitions-methods.Rd | 3 neuroim-0.0.4/neuroim/man/names-methods.Rd | 11 neuroim-0.0.4/neuroim/man/ndim-methods.Rd | 15 neuroim-0.0.4/neuroim/man/neuroim.Rd |only neuroim-0.0.4/neuroim/man/numClusters-methods.Rd | 3 neuroim-0.0.4/neuroim/man/origin-methods.Rd | 11 neuroim-0.0.4/neuroim/man/overlay-methods.Rd | 13 neuroim-0.0.4/neuroim/man/partition-methods.Rd | 3 neuroim-0.0.4/neuroim/man/permMat-methods.Rd | 14 neuroim-0.0.4/neuroim/man/pick-methods.Rd | 3 neuroim-0.0.4/neuroim/man/print-AxisSet2D-method.Rd |only neuroim-0.0.4/neuroim/man/print-AxisSet3D-method.Rd |only neuroim-0.0.4/neuroim/man/print-NamedAxis-method.Rd |only neuroim-0.0.4/neuroim/man/print-methods.Rd | 28 neuroim-0.0.4/neuroim/man/readAFNIHeader.Rd |only neuroim-0.0.4/neuroim/man/readElements-methods.Rd | 3 neuroim-0.0.4/neuroim/man/readHeader.Rd | 3 neuroim-0.0.4/neuroim/man/readMetaInfo-methods.Rd | 3 neuroim-0.0.4/neuroim/man/scaleSeries-methods.Rd |only neuroim-0.0.4/neuroim/man/series-methods.Rd | 11 neuroim-0.0.4/neuroim/man/seriesIter.Rd |only neuroim-0.0.4/neuroim/man/show-AxisSet1D-method.Rd |only neuroim-0.0.4/neuroim/man/show-AxisSet2D-method.Rd |only neuroim-0.0.4/neuroim/man/show-AxisSet3D-method.Rd |only neuroim-0.0.4/neuroim/man/show-AxisSet4D-method.Rd |only neuroim-0.0.4/neuroim/man/show-BaseMetaInfo-method.Rd |only neuroim-0.0.4/neuroim/man/show-BrainSpace-method.Rd |only neuroim-0.0.4/neuroim/man/show-BrainVector-method.Rd |only neuroim-0.0.4/neuroim/man/show-BrainVectorSource-method.Rd |only neuroim-0.0.4/neuroim/man/show-BrainVolume-method.Rd |only neuroim-0.0.4/neuroim/man/show-FileMetaInfo-method.Rd |only neuroim-0.0.4/neuroim/man/show-NamedAxis-method.Rd |only neuroim-0.0.4/neuroim/man/show-NullMetaInfo-method.Rd |only neuroim-0.0.4/neuroim/man/show-ROIVolume-method.Rd |only neuroim-0.0.4/neuroim/man/show-SparseBrainVector-method.Rd |only neuroim-0.0.4/neuroim/man/slice-methods.Rd | 7 neuroim-0.0.4/neuroim/man/space-methods.Rd | 23 neuroim-0.0.4/neuroim/man/spacing-methods.Rd | 9 neuroim-0.0.4/neuroim/man/splitFill-methods.Rd | 23 neuroim-0.0.4/neuroim/man/splitReduce-methods.Rd | 54 + neuroim-0.0.4/neuroim/man/splitScale-methods.Rd | 30 neuroim-0.0.4/neuroim/man/stripExtension-methods.Rd | 3 neuroim-0.0.4/neuroim/man/sub-BrainBucket-index-missing-ANY-method.Rd |only neuroim-0.0.4/neuroim/man/sub-ROIVolume-numeric-missing-ANY-method.Rd | 38 neuroim-0.0.4/neuroim/man/sub-SparseBrainVector-missing-missing-ANY-method.Rd | 52 - neuroim-0.0.4/neuroim/man/sub-SparseBrainVector-missing-numeric-ANY-method.Rd | 52 - neuroim-0.0.4/neuroim/man/sub-SparseBrainVector-numeric-missing-ANY-method.Rd | 52 - neuroim-0.0.4/neuroim/man/sub-SparseBrainVector-numeric-numeric-ANY-method.Rd | 52 - neuroim-0.0.4/neuroim/man/sub-SparseBrainVolume-matrix-missing-ANY-method.Rd |only neuroim-0.0.4/neuroim/man/sub-SparseBrainVolume-missing-missing-ANY-method.Rd |only neuroim-0.0.4/neuroim/man/sub-SparseBrainVolume-missing-numeric-ANY-method.Rd |only neuroim-0.0.4/neuroim/man/sub-SparseBrainVolume-numeric-missing-missing-method.Rd |only neuroim-0.0.4/neuroim/man/sub-SparseBrainVolume-numeric-numeric-ANY-method.Rd |only neuroim-0.0.4/neuroim/man/sub-sub-BrainBucket-index-missing-method.Rd |only neuroim-0.0.4/neuroim/man/takeSeries-methods.Rd | 3 neuroim-0.0.4/neuroim/man/takeVolume-methods.Rd | 22 neuroim-0.0.4/neuroim/man/tesselate-methods.Rd | 3 neuroim-0.0.4/neuroim/man/trans-methods.Rd | 16 neuroim-0.0.4/neuroim/man/values-methods.Rd |only neuroim-0.0.4/neuroim/man/voxels-methods.Rd | 7 neuroim-0.0.4/neuroim/man/writeElements-methods.Rd | 3 neuroim-0.0.4/neuroim/man/writeVector-methods.Rd | 29 neuroim-0.0.4/neuroim/man/writeVolume-methods.Rd | 30 neuroim-0.0.4/neuroim/src |only neuroim-0.0.4/neuroim/tests/runit-filtertest.R | 6 neuroim-0.0.4/neuroim/tests/test-all.R | 6 neuroim-0.0.4/neuroim/tests/testthat |only neuroim-0.0.4/neuroim/vignettes |only 218 files changed, 2821 insertions(+), 1400 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.2-0 dated 2015-05-08 and 4.3-0 dated 2015-07-02
DESCRIPTION | 8 MD5 | 44 +-- NAMESPACE | 30 +- NEWS | 40 +++ R/asin2p.R | 4 R/chklogical.R | 5 R/forest.meta.R | 632 +++++++++++++++++++++++++++++++++++++++--------------- R/format.p.R | 2 R/meta-internal.R | 8 R/metabin.R | 16 - R/metacont.R | 2 R/metainc.R | 2 R/metaprop.R | 6 R/metareg.R | 32 ++ R/settings.meta.R | 23 + R/subgroup.R | 54 ++-- man/forest.Rd | 108 ++++++++- man/metacr.Rd | 2 man/metainf.Rd | 1 man/metareg.Rd | 49 +++- man/print.meta.Rd | 2 man/print.rm5.Rd | 2 man/read.rm5.Rd | 2 23 files changed, 795 insertions(+), 279 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-64 dated 2015-06-28 and 0.8-65 dated 2015-07-02
ChangeLog | 11 +++++++++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/read.dta.R | 2 +- tests/stata.R | 1 + tests/stata.Rout.save | 7 ++++--- 6 files changed, 25 insertions(+), 12 deletions(-)
Title: Exact Binary Sequential Designs and Analysis
Description: For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.
Author: Jenn Kirk, Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between binseqtest versions 1.0 dated 2014-08-08 and 1.0.1 dated 2015-07-02
CHANGELOG | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 15 +++++++++++---- build/vignette.rds |binary inst/CITATION | 8 ++++---- inst/doc/ExactBinarySequentialDesigns.pdf |binary man/binseqtest-package.Rd | 2 +- 8 files changed, 32 insertions(+), 20 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.1-0 dated 2015-05-22 and 1.1-1 dated 2015-07-02
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 3 +++ R/DSC_DenStream.R | 21 +++++++++++++-------- inst/NEWS | 5 +++++ inst/doc/streamMOA.pdf |binary inst/java/StreamMOA.jar |binary java/Makefile | 2 +- man/DSC_DenStream.Rd | 16 ++++++++++------ 9 files changed, 47 insertions(+), 29 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-4 dated 2015-05-24 and 1.1-5 dated 2015-07-02
DESCRIPTION | 10 +-- MD5 | 28 ++++---- NAMESPACE | 5 + R/DSC_DBSTREAM.R | 82 ++++++++----------------- R/DSD.R | 8 ++ R/DSD_mlbenchGenerator.R | 6 + R/evaluate.R | 150 +++++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/NEWS | 12 ++- inst/doc/stream.pdf |binary man/DSC_DBSTREAM.Rd | 21 +++--- man/evaluate.Rd | 8 +- man/get_assignment.Rd | 2 src/DBSTREAM.cpp | 102 ++++++++++++++++++++----------- src/DStream.cpp | 4 - 15 files changed, 237 insertions(+), 201 deletions(-)
Title: Randomized Response Techniques for Complex Surveys
Description: Point and interval estimation of linear parameters with data
obtained from complex surveys (including stratified and clustered samples)
when randomization techniques are used. The randomized response technique
was developed to obtain estimates that are more valid when studying
sensitive topics. Estimators and variances for 14 randomized response
methods for qualitative variables and 7 randomized response methods for
quantitative variables are also implemented. In addition, some data sets
from surveys with these randomization methods are included in the package.
Author: Beatriz Cobo RodrÃguez, MarÃa del Mar Rueda GarcÃa, Antonio Arcos
Cebrián
Maintainer: Beatriz Cobo RodrÃguez <beacr@ugr.es>
Diff between RRTCS versions 0.0.1 dated 2015-04-24 and 0.0.2 dated 2015-07-02
RRTCS-0.0.1/RRTCS/R/internal.R |only RRTCS-0.0.2/RRTCS/DESCRIPTION | 8 - RRTCS-0.0.2/RRTCS/MD5 | 96 +++++++++--------- RRTCS-0.0.2/RRTCS/NAMESPACE | 4 RRTCS-0.0.2/RRTCS/R/RRTCS-internal.R |only RRTCS-0.0.2/RRTCS/man/BarLev.Rd | 3 RRTCS-0.0.2/RRTCS/man/BarLevData.Rd | 3 RRTCS-0.0.2/RRTCS/man/ChaudhuriChristofides.Rd | 3 RRTCS-0.0.2/RRTCS/man/ChaudhuriChristofidesData.Rd | 3 RRTCS-0.0.2/RRTCS/man/ChaudhuriChristofidesDatapij.Rd | 3 RRTCS-0.0.2/RRTCS/man/Christofides.Rd | 3 RRTCS-0.0.2/RRTCS/man/ChristofidesData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Devore.Rd | 3 RRTCS-0.0.2/RRTCS/man/DevoreData.Rd | 3 RRTCS-0.0.2/RRTCS/man/DianaPerri1.Rd | 3 RRTCS-0.0.2/RRTCS/man/DianaPerri1Data.Rd | 3 RRTCS-0.0.2/RRTCS/man/DianaPerri2.Rd | 3 RRTCS-0.0.2/RRTCS/man/DianaPerri2Data.Rd | 3 RRTCS-0.0.2/RRTCS/man/EichhornHayre.Rd | 3 RRTCS-0.0.2/RRTCS/man/EichhornHayreData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Eriksson.Rd | 3 RRTCS-0.0.2/RRTCS/man/ErikssonData.Rd | 3 RRTCS-0.0.2/RRTCS/man/ForcedResponse.Rd | 3 RRTCS-0.0.2/RRTCS/man/ForcedResponseData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Horvitz.Rd | 3 RRTCS-0.0.2/RRTCS/man/HorvitzData.Rd | 3 RRTCS-0.0.2/RRTCS/man/HorvitzDataStCl.Rd | 3 RRTCS-0.0.2/RRTCS/man/HorvitzUB.Rd | 3 RRTCS-0.0.2/RRTCS/man/HorvitzUBData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Kuk.Rd | 3 RRTCS-0.0.2/RRTCS/man/KukData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Mangat.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSingh.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSinghData.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSinghSingh.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSinghSinghData.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSinghSinghUB.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatSinghSinghUBData.Rd | 3 RRTCS-0.0.2/RRTCS/man/MangatUB.Rd | 3 RRTCS-0.0.2/RRTCS/man/RRTCS-internal.Rd | 1 RRTCS-0.0.2/RRTCS/man/RRTCS-package.Rd | 3 RRTCS-0.0.2/RRTCS/man/ResamplingVariance.Rd | 3 RRTCS-0.0.2/RRTCS/man/Saha.Rd | 3 RRTCS-0.0.2/RRTCS/man/SahaData.Rd | 3 RRTCS-0.0.2/RRTCS/man/SinghJoarder.Rd | 3 RRTCS-0.0.2/RRTCS/man/SinghJoarderData.Rd | 3 RRTCS-0.0.2/RRTCS/man/SoberanisCruz.Rd | 3 RRTCS-0.0.2/RRTCS/man/SoberanisCruzData.Rd | 3 RRTCS-0.0.2/RRTCS/man/Warner.Rd | 3 RRTCS-0.0.2/RRTCS/man/WarnerData.Rd | 3 50 files changed, 143 insertions(+), 98 deletions(-)
Title: Pretty Heatmaps
Description: Implementation of heatmaps that offers more control
over dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde <rkolde@gmail.com>
Diff between pheatmap versions 1.0.2 dated 2015-03-10 and 1.0.7 dated 2015-07-02
DESCRIPTION | 14 +++--- MD5 | 14 +++--- NAMESPACE | 5 +- NEWS | 21 ++++++++++ R/pheatmap-package.r | 7 ++- R/pheatmap.r | 97 ++++++++++++++++++++++++++++++++++-------------- man/pheatmap-package.Rd | 7 +-- man/pheatmap.Rd | 26 +++++++++++- 8 files changed, 141 insertions(+), 50 deletions(-)
Title: Weighted Cox-Regression for Nested Case-Control Data
Description: Fits Cox proportional hazard models with a weighted partial
likelihood. It handles one and multiple endpoints, additional matching
and makes it possible to reuse controls for other endpoints.
Author: Nathalie C. Stoer, Sven Ove Samuelsen
Maintainer: Nathalie C. Stoer <nathalcs@math.uio.no>
Diff between multipleNCC versions 1.0 dated 2014-09-19 and 1.1 dated 2015-07-02
multipleNCC-1.0/multipleNCC/R/wpl4.r |only multipleNCC-1.1/multipleNCC/DESCRIPTION | 16 ++++----- multipleNCC-1.1/multipleNCC/MD5 | 26 +++++++++------- multipleNCC-1.1/multipleNCC/NAMESPACE | 14 ++++++-- multipleNCC-1.1/multipleNCC/R/wpl6.R |only multipleNCC-1.1/multipleNCC/man/CVD_Accidents.Rd | 8 ++-- multipleNCC-1.1/multipleNCC/man/Chenprob.Rd | 8 ++-- multipleNCC-1.1/multipleNCC/man/GAMprob.Rd | 12 ++++--- multipleNCC-1.1/multipleNCC/man/GLMprob.Rd | 11 ++++-- multipleNCC-1.1/multipleNCC/man/KMprob.Rd | 9 +++-- multipleNCC-1.1/multipleNCC/man/ModelbasedVar.Rd |only multipleNCC-1.1/multipleNCC/man/PoststratVar.Rd |only multipleNCC-1.1/multipleNCC/man/multipleNCC-internal.rd | 12 +++---- multipleNCC-1.1/multipleNCC/man/multipleNCC-package.Rd | 19 +++++++---- multipleNCC-1.1/multipleNCC/man/print.wpl.Rd |only multipleNCC-1.1/multipleNCC/man/summary.wpl.Rd |only multipleNCC-1.1/multipleNCC/man/wpl.Rd | 25 ++++++++------- 17 files changed, 94 insertions(+), 66 deletions(-)
Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package mgcv (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author: Jacolien van Rij [aut, cre],
Martijn Wieling [aut],
R. Harald Baayen [aut],
Hedderik van Rijn [aut]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Diff between itsadug versions 0.8 dated 2015-02-27 and 1.0.1 dated 2015-07-02
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More information about ComplexAnalysis at CRAN
Permanent link
Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm
for mining NB-frequent itemsets presented in "Michael Hahsler. A
model-based frequency constraint for mining associations from
transaction data. Data Mining and Knowledge Discovery, 13(2):137-166,
September 2006." In addition an extension for NB-precise rules is
implemented.
Author: Michael Hahsler
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesNBMiner versions 0.1-4 dated 2014-07-30 and 0.1-5 dated 2015-07-02
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ data/Agrawal.rda |binary inst/java/arulesNBMiner.jar |binary 5 files changed, 11 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-10 1.0
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.38-2 dated 2015-06-12 and 2.38-3 dated 2015-07-02
survival-2.38-2/survival/noweb/concord2.Rnw |only survival-2.38-3/survival/DESCRIPTION | 8 +-- survival-2.38-3/survival/MD5 | 23 +++++----- survival-2.38-3/survival/NAMESPACE | 55 ++++++++++++++----------- survival-2.38-3/survival/inst/NEWS.Rd | 5 ++ survival-2.38-3/survival/inst/doc/adjcurve.pdf |binary survival-2.38-3/survival/inst/doc/compete.pdf |binary survival-2.38-3/survival/inst/doc/splines.pdf |binary survival-2.38-3/survival/inst/doc/tests.pdf |binary survival-2.38-3/survival/inst/doc/timedep.pdf |binary survival-2.38-3/survival/noweb/all.pdf |binary survival-2.38-3/survival/noweb/concordance.Rnw | 17 ++++--- survival-2.38-3/survival/noweb/coxph.Rnw | 4 + 13 files changed, 65 insertions(+), 47 deletions(-)
Title: Sparse Autoencoder for Automatic Learning of Representative
Features from Unlabeled Data
Description: Implementation of the sparse autoencoder in R environment, following the notes of Andrew Ng (http://www.stanford.edu/class/archive/cs/cs294a/cs294a.1104/sparseAutoencoder.pdf). The features learned by the hidden layer of the autoencoder (through unsupervised learning of unlabeled data) can be used in constructing deep belief neural networks.
Author: Eugene Dubossarsky (project leader, chief designer), Yuriy Tyshetskiy (design, implementation, testing)
Maintainer: Yuriy Tyshetskiy <yuriy.tyshetskiy@nicta.com.au>
Diff between autoencoder versions 1.0 dated 2014-05-21 and 1.1 dated 2015-07-02
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 2 ++ R/autoencoder.R | 11 ++++++++--- 4 files changed, 21 insertions(+), 14 deletions(-)
Title: R Manuals Literally Translated in Korean
Description: R version 2.1.0 and later support Korean translations of program messages. The continuous efforts have been made by <http://developer.r-project.org/TranslationTeams.html> The R Documentation files are licensed under the General Public License, version 2 or 3. This means that the pilot project to translate them into Korean has permission to reproduce them and translate them. This work is done with GNU 'gettext' utilities. The portable object template is updated a weekly basis or whenever changes are necessary. Comments and corrections via email to the maintainer is of course most welcome. In order to voluntarily participate in or offer your help with this translation, please contact the maintainer. To check the change and progress of Korean translation, please visit <http://www.openstatistics.net>.
Author: Chel Hee Lee [aut, cre],
Edward Kang [ctb],
Sunyoung Kim [ctb],
Heather Kim [ctb]
Maintainer: Chel Hee Lee <chl948@mail.usask.ca>
Diff between translation.ko versions 0.0.1.3 dated 2015-06-25 and 0.0.1.5.2 dated 2015-07-02
ChangeLog | 13 +++- DESCRIPTION | 16 +++- MD5 | 19 +++-- R/translation.R | 19 ++++- TODO |only inst/doc/R-FAQ-ko | 169 +++++++++++++++++++++++++--------------------------- inst/doc/R-admin-ko | 32 ++++----- inst/doc/R-data-ko |only inst/doc/R-exts-ko |only inst/doc/R-intro-ko | 6 - inst/doc/R-ints-ko |only inst/doc/R-lang-ko |only inst/doc/rw-FAQ-ko | 83 ++++++++++++------------- 13 files changed, 193 insertions(+), 164 deletions(-)
More information about translation.ko at CRAN
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Title: Statistical Ranking Color Scheme for Multiple Pairwise
Comparisons
Description: Implementation of the SRCS method for a color-based visualization of the
results of multiple pairwise tests on a large number of problem configurations, proposed in:
I.G. del Amo, D.A. Pelta. SRCS: a technique for comparing multiple algorithms under several
factors in dynamic optimization problems. In: E. Alba, A. Nakib, P. Siarry
(Eds.), Metaheuristics for Dynamic Optimization. Series: Studies in
Computational Intelligence 433, Springer, Berlin/Heidelberg, 2012.
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between SRCS versions 1.0 dated 2015-01-01 and 1.1 dated 2015-07-02
SRCS-1.0/SRCS/data/ML2.rdata |only SRCS-1.0/SRCS/man/ML2.Rd |only SRCS-1.1/SRCS/DESCRIPTION | 14 ++++++++------ SRCS-1.1/SRCS/MD5 | 26 ++++++++++++++------------ SRCS-1.1/SRCS/NAMESPACE | 2 +- SRCS-1.1/SRCS/R/core.R | 21 +++++++++++++++------ SRCS-1.1/SRCS/R/graphics.R | 24 ++++++++++++++++-------- SRCS-1.1/SRCS/build |only SRCS-1.1/SRCS/data/ML1.rdata |binary SRCS-1.1/SRCS/data/datalist | 1 - SRCS-1.1/SRCS/inst |only SRCS-1.1/SRCS/man/SRCS.Rd | 2 +- SRCS-1.1/SRCS/man/SRCScomparison.Rd | 2 +- SRCS-1.1/SRCS/man/SRCSranks.Rd | 11 +++++++---- SRCS-1.1/SRCS/man/plot.SRCS.Rd | 13 +++++++------ SRCS-1.1/SRCS/vignettes |only 16 files changed, 70 insertions(+), 46 deletions(-)
Title: Data from the US National Health and Nutrition Examination Study
Description: Body Shape and related measurements from the US National Health
and Nutrition Examination Survey (NHANES, 1999-2004). See
http://www.cdc.gov/nchs/nhanes.htm for details.
Author: Randall Pruim <rpruim@calvin.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between NHANES versions 2.0 dated 2015-05-12 and 2.1.0 dated 2015-07-02
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/datasets.R | 34 +++++++++++++++++++++++++++++++++- README.md | 2 +- data/NHANES.rda |binary data/NHANESraw.rda |binary man/NHANES.Rd | 33 ++++++++++++++++++++++++++++++++- 7 files changed, 77 insertions(+), 13 deletions(-)
Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix?
How much ram is your current R session using? How much ram do you even have?
Learn the scintillating answer to these and many more such questions with
the 'memuse' package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [ctb],
Wei-Chen Chen [ctb]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between memuse versions 1.1 dated 2013-08-07 and 2.5 dated 2015-07-02
memuse-1.1/memuse/COPYING |only memuse-1.1/memuse/R/02_methods.r |only memuse-1.1/memuse/R/03_accessor.r |only memuse-1.1/memuse/R/howbig_par.r |only memuse-1.1/memuse/R/howmany_par.r |only memuse-1.1/memuse/README |only memuse-1.1/memuse/data |only memuse-1.1/memuse/demo/demo1.r |only memuse-1.1/memuse/demo/demo1_plain.r |only memuse-1.1/memuse/demo/demo2.r |only memuse-1.1/memuse/demo/demo2_plain.r |only memuse-1.1/memuse/demo/demo3.r |only memuse-1.1/memuse/demo/demo3_plain.r |only memuse-1.1/memuse/man/00_fs_package.Rd |only memuse-1.1/memuse/man/01_classes.Rd |only memuse-1.1/memuse/man/02_control.Rd |only memuse-1.1/memuse/man/03_envir.Rd |only memuse-1.1/memuse/man/aa_constructor.Rd |only memuse-1.1/memuse/man/ab_convert.Rd |only memuse-1.1/memuse/man/ba_print.Rd |only memuse-1.1/memuse/man/ca_accessor.Rd |only memuse-1.1/memuse/man/cb_replacer.Rd |only memuse-1.1/memuse/man/da_arithmetic.Rd |only memuse-1.1/memuse/man/ea_swaps.Rd |only memuse-1.1/memuse/man/ha_howbig.Rd |only memuse-1.1/memuse/man/hb_howmany.Rd |only memuse-1.1/memuse/man/zz_internal.Rd |only memuse-1.1/memuse/vignettes/cover/DODO1.png |only memuse-1.1/memuse/vignettes/cover/build_cover.sh |only memuse-1.1/memuse/vignettes/cover/cover.tex |only memuse-1.1/memuse/vignettes/include/gpl.png |only memuse-2.5/memuse/ChangeLog | 71 ++-- memuse-2.5/memuse/DESCRIPTION | 42 +- memuse-2.5/memuse/MD5 | 155 ++++++---- memuse-2.5/memuse/NAMESPACE | 91 ++++-- memuse-2.5/memuse/R/000_globalVariables.r |only memuse-2.5/memuse/R/00_classes.r | 50 ++- memuse-2.5/memuse/R/01_constructor.r | 13 memuse-2.5/memuse/R/accessors.r |only memuse-2.5/memuse/R/approx.r |only memuse-2.5/memuse/R/arith.r | 126 +++++++- memuse-2.5/memuse/R/comparators.r |only memuse-2.5/memuse/R/constructor.r | 131 +++++++- memuse-2.5/memuse/R/converters.r |only memuse-2.5/memuse/R/data.r |only memuse-2.5/memuse/R/howbig.r | 112 +++++++ memuse-2.5/memuse/R/howmany.r | 190 ++++++++++--- memuse-2.5/memuse/R/meminfo.r |only memuse-2.5/memuse/R/memuse-package.R |only memuse-2.5/memuse/R/print.r | 55 ++- memuse-2.5/memuse/R/sum.r |only memuse-2.5/memuse/R/swap.r | 80 +++++ memuse-2.5/memuse/R/util.r | 94 ++---- memuse-2.5/memuse/README.md |only memuse-2.5/memuse/TODO |only memuse-2.5/memuse/build |only memuse-2.5/memuse/cleanup | 18 - memuse-2.5/memuse/demo/00Index | 11 memuse-2.5/memuse/demo/arithmetic.r |only memuse-2.5/memuse/demo/basics.r |only memuse-2.5/memuse/demo/howbig.r |only memuse-2.5/memuse/demo/misc.r |only memuse-2.5/memuse/demo/sys.r |only memuse-2.5/memuse/inst/CITATION | 2 memuse-2.5/memuse/inst/RNACI |only memuse-2.5/memuse/inst/doc/memuse-guide.Rnw | 25 - memuse-2.5/memuse/inst/doc/memuse-guide.pdf |binary memuse-2.5/memuse/inst/meminfo_LICENSE |only memuse-2.5/memuse/man/accessors.Rd |only memuse-2.5/memuse/man/approx.size.Rd |only memuse-2.5/memuse/man/arithmetic.Rd |only memuse-2.5/memuse/man/cachelinesize.Rd |only memuse-2.5/memuse/man/cachesize.Rd |only memuse-2.5/memuse/man/comparators.Rd |only memuse-2.5/memuse/man/constructor.Rd |only memuse-2.5/memuse/man/control.Rd |only memuse-2.5/memuse/man/converters.Rd |only memuse-2.5/memuse/man/filesize.Rd |only memuse-2.5/memuse/man/howbig.Rd |only memuse-2.5/memuse/man/howmany.Rd |only memuse-2.5/memuse/man/meminfo.Rd |only memuse-2.5/memuse/man/memuse-class.Rd |only memuse-2.5/memuse/man/memuse-package.Rd |only memuse-2.5/memuse/man/object.size.Rd |only memuse-2.5/memuse/man/print-approx.Rd |only memuse-2.5/memuse/man/print-sysinfo.Rd |only memuse-2.5/memuse/man/print.Rd |only memuse-2.5/memuse/man/procmem.Rd |only memuse-2.5/memuse/man/replacers.Rd |only memuse-2.5/memuse/man/sum.Rd |only memuse-2.5/memuse/man/swapinfo.Rd |only memuse-2.5/memuse/man/swaps.Rd |only memuse-2.5/memuse/src |only memuse-2.5/memuse/tests |only memuse-2.5/memuse/vignettes/build_pdf.sh | 14 memuse-2.5/memuse/vignettes/cover/cover.pdf |binary memuse-2.5/memuse/vignettes/include/00-acknowledgement.tex |only memuse-2.5/memuse/vignettes/include/00-copyright.tex |only memuse-2.5/memuse/vignettes/include/01-introduction.tex | 8 memuse-2.5/memuse/vignettes/include/02-installation.tex | 8 memuse-2.5/memuse/vignettes/include/03-sizematters.tex | 1 memuse-2.5/memuse/vignettes/include/05-other.tex | 18 - memuse-2.5/memuse/vignettes/include/06-meminfo.tex |only memuse-2.5/memuse/vignettes/include/pics |only memuse-2.5/memuse/vignettes/include/preamble.tex | 120 +++++++- memuse-2.5/memuse/vignettes/include/titlepage.tex |only memuse-2.5/memuse/vignettes/memuse-guide.Rnw | 25 - 107 files changed, 1061 insertions(+), 399 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-41 dated 2015-06-18 and 7.3-42 dated 2015-07-02
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 24 ++++++++++++++++++++---- R/contr.sdif.R | 5 +++-- R/polr.R | 2 +- R/profiles.R | 2 +- 6 files changed, 36 insertions(+), 18 deletions(-)
Title: Discretization-Based Direct Random Sample Generation
Description: Two discretization-based Monte Carlo algorithms, namely the Fu-Wang algorithm and the Wang-Lee algorithm, are provided for random sample generation from a high dimensional distribution of complex structure. The normalizing constant of the target distribution needs not to be known.
Author: Chel Hee Lee [aut, cre],
Liqun Wang [aut]
Maintainer: Chel Hee Lee <gnustats@gmail.com>
Diff between dsample versions 0.91.1 dated 2013-05-14 and 0.91.1.5 dated 2015-07-02
dsample-0.91.1.5/dsample/ChangeLog |only dsample-0.91.1.5/dsample/DESCRIPTION | 28 +++++++++++++----------- dsample-0.91.1.5/dsample/MD5 | 15 +++++------- dsample-0.91.1.5/dsample/NAMESPACE | 5 +++- dsample-0.91.1.5/dsample/R/dsample.R |only dsample-0.91.1.5/dsample/man/dsample.Rd |only dsample-0.91.1.5/dsample/man/summary.dsample.Rd |only dsample-0.91.1/dsample/R/sample.fw.R |only dsample-0.91.1/dsample/R/sample.wl.R |only dsample-0.91.1/dsample/R/summary.samplefwl.R |only dsample-0.91.1/dsample/man/dsample-package.Rd |only dsample-0.91.1/dsample/man/sample.fw.Rd |only dsample-0.91.1/dsample/man/sample.wl.Rd |only dsample-0.91.1/dsample/man/summary.samplefwl.Rd |only 14 files changed, 26 insertions(+), 22 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.6 dated 2015-06-16 and 0.9.10 dated 2015-07-01
DESCRIPTION | 6 +- MD5 | 70 ++++++++++++++------------- NAMESPACE | 21 ++++++++ NEWS | 24 ++++++++- R/AllClasses.R | 23 ++++++-- R/Install.R | 111 ++++++++++++++++++++++++------------------- R/Utilities.R | 23 +++++--- R/accessors.R | 18 +++++- R/allGenerics.R | 7 ++ R/biocManifest.R |only R/biocversion.R | 39 +++++++++++++-- R/conditionalCode.R | 1 R/crandbtmp.R | 13 +++-- R/findCtx.R | 1 R/flushSession.R | 29 ++++++++++- R/head-methods.R |only R/lazyRepo.R | 62 +++++++++++++++--------- R/makePkgSourceDir-methods.R | 4 - R/manifest.R | 10 ++- R/manifestFromLib.R | 5 + R/methods.R | 26 +++++----- R/retrievePkgVersion.R | 29 ++++++----- R/saveManifest.R | 12 +++- build/vignette.rds |binary inst/doc/switchrvign.pdf |binary inst/localcheckoutest.R | 11 +--- inst/talk2015.html |only man/BiocSVNManifest.Rd |only man/ManifestRow.Rd | 12 +++- man/SessionManifest.Rd | 6 +- man/cranPkgVersManifest.Rd | 2 man/headtail.Rd |only man/lazyRepo.Rd | 9 +++ man/libManifest.Rd | 5 + man/makeBiocSVNURL.Rd | 9 ++- man/rVersionManifest.Rd | 2 man/switchTo.Rd | 8 +++ man/switchrNoUnload.Rd |only tests/winpath.R | 37 +++++++++++++- 39 files changed, 449 insertions(+), 186 deletions(-)
Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programming Kit.
GLPK is open source software for solving large-scale linear programming (LP),
mixed integer linear programming (MILP) and other related problems.
Author: Stefan Theussl [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb],
Heinrich Schuchardt [ctb],
Andrew Makhorin [cph],
Timothy A. Davis [cph],
Niklas Sorensson [cph],
Mark Adler [cph],
Jean-loup Gailly [cph]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between Rglpk versions 0.6-0 dated 2014-06-16 and 0.6-1 dated 2015-07-01
DESCRIPTION | 11 +-- MD5 | 11 +-- NAMESPACE | 2 inst/CHANGELOG | 7 ++ src/Rglpk.h | 3 src/Rglpk_error.c |only src/Rglpk_solve.c | 171 ++++++++++++++++++++++++++++-------------------------- 7 files changed, 114 insertions(+), 91 deletions(-)
Title: Interface to the 'USGS' 'BISON' 'API'
Description: Interface to the 'USGS' 'BISON' 'API', a 'database' for
species occurrence data on the web. Data comes from species in the
United States from participating data providers. You can get
data via 'taxonomic' and location based queries. A simple function
is provided to help visualize data.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbison versions 0.4.5 dated 2014-12-10 and 0.4.8 dated 2015-07-01
rbison-0.4.5/rbison/NEWS |only rbison-0.4.5/rbison/R/startup.R |only rbison-0.4.5/rbison/inst/readmecache |only rbison-0.4.5/rbison/inst/readmeimg |only rbison-0.4.5/rbison/man/bison_blanktheme.Rd |only rbison-0.4.5/rbison/man/bison_map_maker.Rd |only rbison-0.4.5/rbison/vignettes/figure |only rbison-0.4.8/rbison/DESCRIPTION | 26 - rbison-0.4.8/rbison/LICENSE | 4 rbison-0.4.8/rbison/MD5 | 99 ++---- rbison-0.4.8/rbison/NAMESPACE | 38 +- rbison-0.4.8/rbison/R/bison.R | 71 ++-- rbison-0.4.8/rbison/R/bison_providers.R | 3 rbison-0.4.8/rbison/R/bison_solr.R | 6 rbison-0.4.8/rbison/R/bison_stats.R | 1 rbison-0.4.8/rbison/R/bison_tax.R | 29 + rbison-0.4.8/rbison/R/bisonmap.R | 85 ++--- rbison-0.4.8/rbison/R/rbison-package.R | 3 rbison-0.4.8/rbison/R/zzz.R | 19 - rbison-0.4.8/rbison/README.md | 310 ++++++++----------- rbison-0.4.8/rbison/build/vignette.rds |binary rbison-0.4.8/rbison/inst/doc/other_functions.Rmd | 261 +++++++-------- rbison-0.4.8/rbison/inst/doc/other_functions.html | 261 +++++++-------- rbison-0.4.8/rbison/inst/doc/rbison_vignette.Rmd | 149 ++++----- rbison-0.4.8/rbison/inst/doc/rbison_vignette.html | 145 ++++---- rbison-0.4.8/rbison/man/all_states.Rd | 3 rbison-0.4.8/rbison/man/bison.Rd | 78 ++++ rbison-0.4.8/rbison/man/bison_datause.Rd | 3 rbison-0.4.8/rbison/man/bison_providers.Rd | 5 rbison-0.4.8/rbison/man/bison_solr.Rd | 5 rbison-0.4.8/rbison/man/bison_stats.Rd | 3 rbison-0.4.8/rbison/man/bison_tax.Rd | 13 rbison-0.4.8/rbison/man/bisonmap.Rd | 3 rbison-0.4.8/rbison/man/fips.Rd | 3 rbison-0.4.8/rbison/man/is.bison.Rd | 3 rbison-0.4.8/rbison/man/is.bison_solr.Rd | 3 rbison-0.4.8/rbison/man/rbison-package.Rd | 3 rbison-0.4.8/rbison/tests/test-all.R |only rbison-0.4.8/rbison/tests/testthat/Rplots.pdf |binary rbison-0.4.8/rbison/tests/testthat/test-bison.R | 18 - rbison-0.4.8/rbison/tests/testthat/test-bison_solr.R | 27 - rbison-0.4.8/rbison/tests/testthat/test-bison_tax.R | 20 - rbison-0.4.8/rbison/tests/testthat/test-bisonmap.R | 16 rbison-0.4.8/rbison/tests/testthat/test-is.bison.R | 10 rbison-0.4.8/rbison/vignettes/other_functions.Rmd | 261 +++++++-------- rbison-0.4.8/rbison/vignettes/rbison_vignette.Rmd | 149 ++++----- 46 files changed, 1108 insertions(+), 1028 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.3-40 dated 2015-04-11 and 2.4-15 dated 2015-07-01
raster-2.3-40/raster/R/aggregate.R |only raster-2.3-40/raster/R/aggregate_old.R |only raster-2.3-40/raster/src/minmax.c |only raster-2.3-40/raster/src/mode.c |only raster-2.3-40/raster/src/rasterize.c |only raster-2.4-15/raster/ChangeLog | 10 raster-2.4-15/raster/DESCRIPTION | 18 - raster-2.4-15/raster/MD5 | 389 +++++++++++++------------- raster-2.4-15/raster/NAMESPACE | 1 raster-2.4-15/raster/R/AAAClasses.R | 2 raster-2.4-15/raster/R/GDALtransient.R | 8 raster-2.4-15/raster/R/Geary.R | 2 raster-2.4-15/raster/R/RGB.R | 6 raster-2.4-15/raster/R/RcppExports.R |only raster-2.4-15/raster/R/VectorLayer.R | 36 +- raster-2.4-15/raster/R/adjacent.R | 10 raster-2.4-15/raster/R/aggregate_sp.R | 207 ++++++++++--- raster-2.4-15/raster/R/approxNA.R | 4 raster-2.4-15/raster/R/area.R | 41 ++ raster-2.4-15/raster/R/artith.R | 56 +-- raster-2.4-15/raster/R/as.data.frame.R | 152 ---------- raster-2.4-15/raster/R/as.raster.R | 2 raster-2.4-15/raster/R/as.spatial.R | 4 raster-2.4-15/raster/R/bilinearValue.R | 52 +-- raster-2.4-15/raster/R/bind.R | 34 +- raster-2.4-15/raster/R/blockSize.R | 2 raster-2.4-15/raster/R/brick.R | 10 raster-2.4-15/raster/R/cellRowCol.R | 11 raster-2.4-15/raster/R/cellStats.R | 14 raster-2.4-15/raster/R/cellValues.R | 2 raster-2.4-15/raster/R/clearValues.R | 2 raster-2.4-15/raster/R/click.R | 30 +- raster-2.4-15/raster/R/clump.R | 4 raster-2.4-15/raster/R/clusterR.R | 4 raster-2.4-15/raster/R/coerce.R | 56 +-- raster-2.4-15/raster/R/colortable.R |only raster-2.4-15/raster/R/commonDataType.R | 2 raster-2.4-15/raster/R/compareCRS.R | 4 raster-2.4-15/raster/R/compare_Logical.R | 40 +- raster-2.4-15/raster/R/contour.R | 4 raster-2.4-15/raster/R/cor.R | 8 raster-2.4-15/raster/R/corLocal.R | 32 +- raster-2.4-15/raster/R/coverPolygons.R | 4 raster-2.4-15/raster/R/crop.R | 2 raster-2.4-15/raster/R/cropSpatial.R | 10 raster-2.4-15/raster/R/crosstab.R | 4 raster-2.4-15/raster/R/cut.R | 13 raster-2.4-15/raster/R/cv.R | 4 raster-2.4-15/raster/R/density.R | 12 raster-2.4-15/raster/R/destair.R | 6 raster-2.4-15/raster/R/distanceRows.R | 2 raster-2.4-15/raster/R/dotdens.R | 11 raster-2.4-15/raster/R/drawExtent.R | 6 raster-2.4-15/raster/R/drawPoly.R | 4 raster-2.4-15/raster/R/erase.R | 4 raster-2.4-15/raster/R/extend.R | 4 raster-2.4-15/raster/R/extent.R | 10 raster-2.4-15/raster/R/extractLines.R | 10 raster-2.4-15/raster/R/extractPoints.R | 9 raster-2.4-15/raster/R/extractPoints_sp.R | 2 raster-2.4-15/raster/R/extractPolygons.R | 14 raster-2.4-15/raster/R/factor.R | 6 raster-2.4-15/raster/R/focalWeight.R | 4 raster-2.4-15/raster/R/fourCellsFromXY.R | 40 -- raster-2.4-15/raster/R/freq.R | 6 raster-2.4-15/raster/R/gainoffset.R | 2 raster-2.4-15/raster/R/geom.R |only raster-2.4-15/raster/R/getData.R | 51 +-- raster-2.4-15/raster/R/getValuesFocal.R | 2 raster-2.4-15/raster/R/hdrRaster.R | 8 raster-2.4-15/raster/R/head.R | 4 raster-2.4-15/raster/R/hist.R | 8 raster-2.4-15/raster/R/image.R | 3 raster-2.4-15/raster/R/imageplot.R | 44 +- raster-2.4-15/raster/R/imageplot2.R | 64 ++-- raster-2.4-15/raster/R/index.R | 6 raster-2.4-15/raster/R/indexReplace.R | 13 raster-2.4-15/raster/R/inifile.R | 2 raster-2.4-15/raster/R/interpolate.R | 8 raster-2.4-15/raster/R/intersect_sp.R | 142 +++++++-- raster-2.4-15/raster/R/kernelDens.R | 6 raster-2.4-15/raster/R/kml.R | 6 raster-2.4-15/raster/R/kml_multiple.R | 4 raster-2.4-15/raster/R/makeProjString.R | 2 raster-2.4-15/raster/R/makeRasterList.R | 6 raster-2.4-15/raster/R/mask.R | 3 raster-2.4-15/raster/R/math.R | 10 raster-2.4-15/raster/R/modal.R | 96 +++--- raster-2.4-15/raster/R/moran.R | 4 raster-2.4-15/raster/R/movingFun.R | 6 raster-2.4-15/raster/R/multiCore.R | 8 raster-2.4-15/raster/R/naValue.R | 2 raster-2.4-15/raster/R/names.R | 4 raster-2.4-15/raster/R/netCDFutil.R | 6 raster-2.4-15/raster/R/netCDFwriteCD.R | 12 raster-2.4-15/raster/R/newPLot.R | 53 +-- raster-2.4-15/raster/R/pairs.R | 12 raster-2.4-15/raster/R/plot.R | 23 + raster-2.4-15/raster/R/plot2rasters.R | 8 raster-2.4-15/raster/R/plotCT.R | 10 raster-2.4-15/raster/R/plotRGB.R | 31 +- raster-2.4-15/raster/R/plotRaster.R | 2 raster-2.4-15/raster/R/plotRaster2.R | 2 raster-2.4-15/raster/R/pointdistance.R | 59 ++- raster-2.4-15/raster/R/predict.R | 5 raster-2.4-15/raster/R/print.R | 7 raster-2.4-15/raster/R/progressBar.R | 8 raster-2.4-15/raster/R/project.R | 4 raster-2.4-15/raster/R/projectRaster.R | 18 - raster-2.4-15/raster/R/projection.R | 4 raster-2.4-15/raster/R/quad.R | 2 raster-2.4-15/raster/R/quantile.R | 6 raster-2.4-15/raster/R/raster.R | 24 - raster-2.4-15/raster/R/rasterFromASCII.R | 4 raster-2.4-15/raster/R/rasterFromFile.R | 9 raster-2.4-15/raster/R/rasterFromGDAL.R | 6 raster-2.4-15/raster/R/rasterFromRasterFile.R | 4 raster-2.4-15/raster/R/rasterOptions.R | 2 raster-2.4-15/raster/R/rasterToPoints.R | 2 raster-2.4-15/raster/R/rasterToPolygons.R | 64 ++-- raster-2.4-15/raster/R/rasterize.R | 2 raster-2.4-15/raster/R/rasterizeLines.R | 4 raster-2.4-15/raster/R/rasterizePoints.R | 6 raster-2.4-15/raster/R/rasterizePolygons.R | 12 raster-2.4-15/raster/R/rasterizePolygons3.R | 2 raster-2.4-15/raster/R/ratify.R | 4 raster-2.4-15/raster/R/readAscii.R | 2 raster-2.4-15/raster/R/readCells.R | 15 - raster-2.4-15/raster/R/resample.R | 30 +- raster-2.4-15/raster/R/resolution.R | 2 raster-2.4-15/raster/R/roundExtent.R | 8 raster-2.4-15/raster/R/rowMinMax.R | 13 raster-2.4-15/raster/R/rowSums.R |only raster-2.4-15/raster/R/sampleInt.R | 4 raster-2.4-15/raster/R/sampleRandom.R | 6 raster-2.4-15/raster/R/scalebar.R | 16 - raster-2.4-15/raster/R/select.R | 18 - raster-2.4-15/raster/R/setCV.R | 4 raster-2.4-15/raster/R/shift.R | 12 raster-2.4-15/raster/R/shp.R | 18 - raster-2.4-15/raster/R/simplifyPols.R |only raster-2.4-15/raster/R/slopeAspect.R | 2 raster-2.4-15/raster/R/spplot.R | 10 raster-2.4-15/raster/R/stack.R | 20 - raster-2.4-15/raster/R/stackFile.R | 8 raster-2.4-15/raster/R/stretch.R | 8 raster-2.4-15/raster/R/subset.R | 4 raster-2.4-15/raster/R/summary-methods.R | 2 raster-2.4-15/raster/R/summary.R | 4 raster-2.4-15/raster/R/text.R | 4 raster-2.4-15/raster/R/tmpFile.R | 12 raster-2.4-15/raster/R/union_sp.R | 8 raster-2.4-15/raster/R/update.R | 14 raster-2.4-15/raster/R/writeAllAscii.R | 2 raster-2.4-15/raster/R/writeAllGDAL.R | 4 raster-2.4-15/raster/R/writeRaster.R | 1 raster-2.4-15/raster/R/writeStartStopGDAL.R | 2 raster-2.4-15/raster/R/writeValues.R | 4 raster-2.4-15/raster/R/xyCell.R | 24 - raster-2.4-15/raster/R/xyMinMax.R | 21 + raster-2.4-15/raster/R/xyValuesBuffer.R | 12 raster-2.4-15/raster/R/zonal.R | 46 +-- raster-2.4-15/raster/R/zoom.R | 6 raster-2.4-15/raster/build/vignette.rds |binary raster-2.4-15/raster/inst/doc/Raster.pdf |binary raster-2.4-15/raster/inst/doc/functions.pdf |binary raster-2.4-15/raster/inst/doc/rasterfile.pdf |binary raster-2.4-15/raster/inst/external/rlogo.grd | 2 raster-2.4-15/raster/man/addLayer.Rd | 6 raster-2.4-15/raster/man/adjacent.Rd | 4 raster-2.4-15/raster/man/aggregate.Rd | 9 raster-2.4-15/raster/man/calc.Rd | 13 raster-2.4-15/raster/man/colortable.Rd |only raster-2.4-15/raster/man/coordinates.Rd | 28 + raster-2.4-15/raster/man/extract.Rd | 2 raster-2.4-15/raster/man/focal.Rd | 2 raster-2.4-15/raster/man/geom.Rd |only raster-2.4-15/raster/man/interpolate.Rd | 38 ++ raster-2.4-15/raster/man/intersect.Rd | 42 +- raster-2.4-15/raster/man/localFun.Rd | 2 raster-2.4-15/raster/man/modal.Rd | 12 raster-2.4-15/raster/man/persp.Rd | 25 - raster-2.4-15/raster/man/plot.Rd | 1 raster-2.4-15/raster/man/pointdistance.Rd | 6 raster-2.4-15/raster/man/predict.Rd | 30 +- raster-2.4-15/raster/man/projectRaster.Rd | 1 raster-2.4-15/raster/man/rasterTmpFile.Rd | 2 raster-2.4-15/raster/man/rasterToPolygons.Rd | 9 raster-2.4-15/raster/man/resample.Rd | 2 raster-2.4-15/raster/man/rowSums.Rd |only raster-2.4-15/raster/man/shapefile.Rd | 12 raster-2.4-15/raster/man/spplot.Rd | 1 raster-2.4-15/raster/man/stackApply.Rd | 18 - raster-2.4-15/raster/man/trim.Rd | 4 raster-2.4-15/raster/man/writeRaster.Rd | 2 raster-2.4-15/raster/src/RcppExports.cpp |only raster-2.4-15/raster/src/bilinear.cpp |only raster-2.4-15/raster/src/cellRowCol.cpp |only raster-2.4-15/raster/src/distance.c | 7 raster-2.4-15/raster/src/geodesic.c |only raster-2.4-15/raster/src/geodesic.h |only raster-2.4-15/raster/src/geolib.c |only raster-2.4-15/raster/src/getPolygons.cpp |only raster-2.4-15/raster/src/intersect.c | 41 +- raster-2.4-15/raster/src/modal.cpp |only raster-2.4-15/raster/src/ppmin.cpp |only raster-2.4-15/raster/src/xyCell.cpp |only 207 files changed, 1651 insertions(+), 1413 deletions(-)
Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geosphere versions 1.3-13 dated 2015-04-11 and 1.4-3 dated 2015-07-01
geosphere-1.3-13/geosphere/man/gcIntermediate.Rd |only geosphere-1.4-3/geosphere/ChangeLog | 2 geosphere-1.4-3/geosphere/DESCRIPTION | 10 +-- geosphere-1.4-3/geosphere/MD5 | 67 ++++++++++++--------- geosphere-1.4-3/geosphere/NAMESPACE | 1 geosphere-1.4-3/geosphere/R/areaPolygon.R | 59 +++++++++++-------- geosphere-1.4-3/geosphere/R/bearing.R | 31 +++++++--- geosphere-1.4-3/geosphere/R/destPoint.R | 57 ++++++------------ geosphere-1.4-3/geosphere/R/dist2Line.R | 2 geosphere-1.4-3/geosphere/R/distGeo.R |only geosphere-1.4-3/geosphere/R/finalBearing.R | 19 +++++- geosphere-1.4-3/geosphere/R/gcIntermediate.R | 68 +++++++++------------- geosphere-1.4-3/geosphere/R/geodesic.R |only geosphere-1.4-3/geosphere/R/geomean.R | 2 geosphere-1.4-3/geosphere/R/geomedian.R | 6 - geosphere-1.4-3/geosphere/R/helper.R | 2 geosphere-1.4-3/geosphere/R/old_destPoint.R |only geosphere-1.4-3/geosphere/R/perimeter.R | 63 ++++++++++++-------- geosphere-1.4-3/geosphere/R/plotPoly.R | 10 +-- geosphere-1.4-3/geosphere/R/pointsToMatrix.R | 4 - geosphere-1.4-3/geosphere/R/randomCoordinates.R | 4 - geosphere-1.4-3/geosphere/build/vignette.rds |binary geosphere-1.4-3/geosphere/inst/doc/geosphere.R | 26 ++++---- geosphere-1.4-3/geosphere/inst/doc/geosphere.Rnw | 10 ++- geosphere-1.4-3/geosphere/inst/doc/geosphere.pdf |binary geosphere-1.4-3/geosphere/man/area.Rd | 20 +++--- geosphere-1.4-3/geosphere/man/bearing.Rd | 7 +- geosphere-1.4-3/geosphere/man/destPoint.Rd | 29 ++++----- geosphere-1.4-3/geosphere/man/distGeo.Rd |only geosphere-1.4-3/geosphere/man/distMeeus.Rd | 7 +- geosphere-1.4-3/geosphere/man/finalDirection.Rd | 33 ++++------ geosphere-1.4-3/geosphere/man/geodesic.Rd |only geosphere-1.4-3/geosphere/man/intermediate.Rd |only geosphere-1.4-3/geosphere/man/perimeter.Rd | 27 +++++--- geosphere-1.4-3/geosphere/src |only geosphere-1.4-3/geosphere/vignettes/geosphere.Rnw | 10 ++- 36 files changed, 323 insertions(+), 253 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.1 dated 2015-05-29 and 1.8.2 dated 2015-07-01
sjPlot-1.8.1/sjPlot/man/view_spss.Rd |only sjPlot-1.8.2/sjPlot/DESCRIPTION | 17 sjPlot-1.8.2/sjPlot/MD5 | 154 sjPlot-1.8.2/sjPlot/NAMESPACE | 199 - sjPlot-1.8.2/sjPlot/NEWS | 28 sjPlot-1.8.2/sjPlot/R/helpfunctions.R | 1427 ++++---- sjPlot-1.8.2/sjPlot/R/sjPlotAncovaLSMeans.R | 2 sjPlot-1.8.2/sjPlot/R/sjPlotAnova.R | 937 ++--- sjPlot-1.8.2/sjPlot/R/sjPlotClusterAnalysis.R | 1741 +++++----- sjPlot-1.8.2/sjPlot/R/sjPlotCorr.R | 97 sjPlot-1.8.2/sjPlot/R/sjPlotDist.R | 59 sjPlot-1.8.2/sjPlot/R/sjPlotFrequencies.R | 1743 +++++----- sjPlot-1.8.2/sjPlot/R/sjPlotGLME.R | 3973 +++++++++++++------------ sjPlot-1.8.2/sjPlot/R/sjPlotGroupFrequencies.R | 2372 +++++++------- sjPlot-1.8.2/sjPlot/R/sjPlotInteractions.R | 2824 +++++++++-------- sjPlot-1.8.2/sjPlot/R/sjPlotLikert.R | 1289 ++++---- sjPlot-1.8.2/sjPlot/R/sjPlotLinreg.R | 2188 +++++++------ sjPlot-1.8.2/sjPlot/R/sjPlotLinregMultiple.R | 764 ++-- sjPlot-1.8.2/sjPlot/R/sjPlotOdds.R | 1768 +++++------ sjPlot-1.8.2/sjPlot/R/sjPlotOddsMultiple.R | 788 ++-- sjPlot-1.8.2/sjPlot/R/sjPlotPCA.R | 933 ++--- sjPlot-1.8.2/sjPlot/R/sjPlotPearsonsChi2Test.R | 291 - sjPlot-1.8.2/sjPlot/R/sjPlotPolynomials.R |only sjPlot-1.8.2/sjPlot/R/sjPlotPropTable.R | 1338 ++++---- sjPlot-1.8.2/sjPlot/R/sjPlotScatter.R | 660 ++-- sjPlot-1.8.2/sjPlot/R/sjPlotSetTheme.R | 1683 +++++----- sjPlot-1.8.2/sjPlot/R/sjPlotStackFrequencies.R | 989 +++--- sjPlot-1.8.2/sjPlot/R/sjTabCorr.R | 1040 +++--- sjPlot-1.8.2/sjPlot/R/sjTabDataFrame.R | 763 ++-- sjPlot-1.8.2/sjPlot/R/sjTabFrequencies.R | 205 - sjPlot-1.8.2/sjPlot/R/sjTabGrpmean.R | 46 sjPlot-1.8.2/sjPlot/R/sjTabItemAnalysis.R | 833 ++--- sjPlot-1.8.2/sjPlot/R/sjTabLinReg.R | 443 +- sjPlot-1.8.2/sjPlot/R/sjTabMannWhitney.R | 38 sjPlot-1.8.2/sjPlot/R/sjTabOdds.R | 448 +- sjPlot-1.8.2/sjPlot/R/sjTabPCA.R | 1209 +++---- sjPlot-1.8.2/sjPlot/R/sjTabPropTable.R | 256 - sjPlot-1.8.2/sjPlot/R/sjTabSPSS.R | 701 ++-- sjPlot-1.8.2/sjPlot/R/sjTabStackFrq.R | 1056 +++--- sjPlot-1.8.2/sjPlot/README.md | 50 sjPlot-1.8.2/sjPlot/man/adjust_plot_range.Rd | 15 sjPlot-1.8.2/sjPlot/man/sjPlot-package.Rd | 6 sjPlot-1.8.2/sjPlot/man/sjc.cluster.Rd | 168 - sjPlot-1.8.2/sjPlot/man/sjc.dend.Rd | 98 sjPlot-1.8.2/sjPlot/man/sjc.elbow.Rd | 8 sjPlot-1.8.2/sjPlot/man/sjc.grpdisc.Rd | 16 sjPlot-1.8.2/sjPlot/man/sjc.kgap.Rd | 134 sjPlot-1.8.2/sjPlot/man/sjc.qclus.Rd | 360 +- sjPlot-1.8.2/sjPlot/man/sjp.aov1.Rd | 303 - sjPlot-1.8.2/sjPlot/man/sjp.chi2.Rd | 122 sjPlot-1.8.2/sjPlot/man/sjp.corr.Rd | 273 - sjPlot-1.8.2/sjPlot/man/sjp.frq.Rd | 273 - sjPlot-1.8.2/sjPlot/man/sjp.glm.Rd | 469 +- sjPlot-1.8.2/sjPlot/man/sjp.glmer.Rd | 431 +- sjPlot-1.8.2/sjPlot/man/sjp.glmm.Rd | 316 - sjPlot-1.8.2/sjPlot/man/sjp.grpfrq.Rd | 575 +-- sjPlot-1.8.2/sjPlot/man/sjp.int.Rd | 131 sjPlot-1.8.2/sjPlot/man/sjp.likert.Rd | 455 +- sjPlot-1.8.2/sjPlot/man/sjp.lm.Rd | 473 +- sjPlot-1.8.2/sjPlot/man/sjp.lmer.Rd | 457 +- sjPlot-1.8.2/sjPlot/man/sjp.lmm.Rd | 306 - sjPlot-1.8.2/sjPlot/man/sjp.poly.Rd |only sjPlot-1.8.2/sjPlot/man/sjp.scatter.Rd | 332 +- sjPlot-1.8.2/sjPlot/man/sjp.setTheme.Rd | 202 - sjPlot-1.8.2/sjPlot/man/sjp.stackfrq.Rd | 87 sjPlot-1.8.2/sjPlot/man/sjp.xtab.Rd | 469 +- sjPlot-1.8.2/sjPlot/man/sjt.corr.Rd | 359 +- sjPlot-1.8.2/sjPlot/man/sjt.df.Rd | 304 - sjPlot-1.8.2/sjPlot/man/sjt.frq.Rd | 498 +-- sjPlot-1.8.2/sjPlot/man/sjt.glm.Rd | 656 ++-- sjPlot-1.8.2/sjPlot/man/sjt.glmer.Rd | 122 sjPlot-1.8.2/sjPlot/man/sjt.grpmean.Rd | 174 - sjPlot-1.8.2/sjPlot/man/sjt.itemanalysis.Rd | 373 +- sjPlot-1.8.2/sjPlot/man/sjt.lm.Rd | 806 ++--- sjPlot-1.8.2/sjPlot/man/sjt.lmer.Rd | 107 sjPlot-1.8.2/sjPlot/man/sjt.mwu.Rd | 141 sjPlot-1.8.2/sjPlot/man/sjt.pca.Rd | 369 +- sjPlot-1.8.2/sjPlot/man/sjt.stackfrq.Rd | 401 +- sjPlot-1.8.2/sjPlot/man/sjt.xtab.Rd | 425 +- sjPlot-1.8.2/sjPlot/man/view_df.Rd |only 80 files changed, 23559 insertions(+), 23007 deletions(-)
Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between pca3d versions 0.3 dated 2014-11-04 and 0.8 dated 2015-07-01
DESCRIPTION | 16 - MD5 | 30 + NAMESPACE | 16 - R/helpers.R | 236 +++++++++++++-- R/metabo.R |only R/misc.R |only R/objects3d.R | 96 +++--- R/pca2d.R | 334 +++++++++++----------- R/pca3d-package.R |only R/pca3d.R | 681 ++++++++++++++++++++------------------------- man/defaultPalettePCA3D.Rd |only man/listShapes.Rd |only man/makeMoviePCA.Rd |only man/metabo.Rd | 470 +------------------------------ man/pca3d-package.Rd | 340 +++++++++------------- man/snapshotPCA3d.Rd |only vignettes |only 17 files changed, 931 insertions(+), 1288 deletions(-)
Title: NeuroAnatomy Toolbox (nat) Extension for Handling Template
Brains
Description: Extends package nat (NeuroAnatomy Toolbox) by providing objects
and functions for handling template brains.
Author: James Manton and Gregory Jefferis
Maintainer: James Manton <ajd.manton@googlemail.com>
Diff between nat.templatebrains versions 0.4.1 dated 2014-09-16 and 0.6 dated 2015-07-01
DESCRIPTION | 14 +- MD5 | 48 ++++-- NAMESPACE | 17 ++ NEWS | 20 ++ R/PACKAGE.R | 30 +++- R/display_slice.R | 2 R/reg_repos.R |only R/templatebrain.R | 40 +++-- R/transformation.R | 244 ++++++++++++++++++++++++++++++----- R/zzz.R |only README.md | 11 + man/FCWB.demo.Rd | 3 man/add_reg_folders.Rd |only man/allreg_dataframe.Rd |only man/as.templatebrain.Rd | 3 man/bridging_sequence.Rd | 29 ++-- man/display_slice.Rd | 5 man/download_reg_repo.Rd |only man/local_reg_dir_for_url.Rd |only man/mirror_brain.Rd | 15 +- man/nat.templatebrains-package.Rd | 33 +++- man/plot3d.templatebrain.Rd | 3 man/shortest_bridging_seq.Rd |only man/templatebrain-meths.Rd | 19 +- man/templatebrain.Rd | 23 +-- man/update_reg_repos.Rd |only man/xform_brain.Rd | 51 ++++++- tests/testthat/test-reg_repos.R |only tests/testthat/test-transformation.r | 101 ++++++++++++-- tests/testthat/testdata |only 30 files changed, 559 insertions(+), 152 deletions(-)
More information about nat.templatebrains at CRAN
Permanent link
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.0.0 dated 2015-06-26 and 0.1.0.1 dated 2015-07-01
DESCRIPTION | 7 ++++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/Interplot_mlm.R | 4 ++-- R/Interplot_mlmmi.R | 4 ++-- README.md | 16 ++++++++++++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/interplot-vignette.R | 8 ++++---- inst/doc/interplot-vignette.Rmd | 7 +++++++ inst/doc/interplot-vignette.html | 12 ++++++++++-- vignettes/interplot-vignette.Rmd | 7 +++++++ 12 files changed, 62 insertions(+), 25 deletions(-)
Title: Creating Continuously Integrated Package Repositories from
Manifests
Description: Repository based tools for department and analysis level
reproducibility. 'GRANBase' allows creation of custom branched,
continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between GRANBase versions 1.0.8 dated 2015-06-19 and 1.0.12 dated 2015-07-01
GRANBase-1.0.12/GRANBase/DESCRIPTION | 6 +-- GRANBase-1.0.12/GRANBase/MD5 | 34 +++++++++---------- GRANBase-1.0.12/GRANBase/NAMESPACE | 5 ++ GRANBase-1.0.12/GRANBase/NEWS |only GRANBase-1.0.12/GRANBase/R/AllClasses.R | 17 +++++---- GRANBase-1.0.12/GRANBase/R/GRANonGRAN.R | 20 ++--------- GRANBase-1.0.12/GRANBase/R/Install.R | 3 + GRANBase-1.0.12/GRANBase/R/accessors.R | 5 ++ GRANBase-1.0.12/GRANBase/R/buildBranchesInRepo.R | 2 + GRANBase-1.0.12/GRANBase/R/locateRisk.R | 1 GRANBase-1.0.12/GRANBase/R/makeGRANRepos.R | 20 +++++------ GRANBase-1.0.12/GRANBase/build/vignette.rds |binary GRANBase-1.0.12/GRANBase/inst/GRAN/R/myGRAN.R | 2 - GRANBase-1.0.12/GRANBase/inst/doc/GRAN-Overview.R | 4 +- GRANBase-1.0.12/GRANBase/inst/doc/GRAN-Overview.Rnw | 7 +++ GRANBase-1.0.12/GRANBase/inst/doc/GRAN-Overview.pdf |binary GRANBase-1.0.12/GRANBase/man/repobuildparam.Rd | 11 +++--- GRANBase-1.0.12/GRANBase/vignettes/GRAN-Overview.Rnw | 7 +++ GRANBase-1.0.8/GRANBase/inst/testonrescomp.R |only 19 files changed, 79 insertions(+), 65 deletions(-)
More information about FractalParameterEstimation at CRAN
Permanent link
Title: Scrapes Data from 'www.fitbit.com'
Description: Scrapes data from www.fitbit.com, the website that contains data
for the popular fitness tracker. This does not use the official API,
but instead uses the API that the web dashboard uses to generate the graphs
displayed on the dashboard after login at www.fitbit.com.
Author: Cory Nissen <corynissen@gmail.com> [aut, cre]
Maintainer: Cory Nissen <corynissen@gmail.com>
Diff between fitbitScraper versions 0.1.3 dated 2015-05-14 and 0.1.4 dated 2015-07-01
DESCRIPTION | 13 +++++++------ MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + R/get_activity_data.R |only R/get_daily_data.R | 27 +++++++++++++++++++-------- R/get_intraday_data.R | 2 +- R/get_premium_export.R | 4 ++-- R/get_sleep_data.R | 2 +- R/get_weight_data.R | 2 +- R/login.R | 16 +++++++++++++--- README.md | 8 +++----- man/get_activity_data.Rd |only man/get_daily_data.Rd | 2 +- man/login.Rd | 4 +++- 14 files changed, 65 insertions(+), 40 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.1 dated 2015-05-19 and 1.1.2.2 dated 2015-07-01
ddalpha-1.1.1/ddalpha/R/depth.randomTukey.r |only ddalpha-1.1.1/ddalpha/R/depth.space.randomTukey.r |only ddalpha-1.1.1/ddalpha/man/depth.randomTukey.Rd |only ddalpha-1.1.1/ddalpha/man/depth.space.randomTukey.Rd |only ddalpha-1.1.2.2/ddalpha/DESCRIPTION | 20 - ddalpha-1.1.2.2/ddalpha/MD5 | 80 ++-- ddalpha-1.1.2.2/ddalpha/NAMESPACE | 10 ddalpha-1.1.2.2/ddalpha/R/ddalpha-internal.r | 229 +++++++++--- ddalpha-1.1.2.2/ddalpha/R/ddalpha.classify.r | 14 ddalpha-1.1.2.2/ddalpha/R/ddalpha.test.r | 7 ddalpha-1.1.2.2/ddalpha/R/ddalpha.train.r | 44 +- ddalpha-1.1.2.2/ddalpha/R/depth.contours.r |only ddalpha-1.1.2.2/ddalpha/R/depth.graph.r | 14 ddalpha-1.1.2.2/ddalpha/R/depth.halfspace.r |only ddalpha-1.1.2.2/ddalpha/R/depth.simplicial.r |only ddalpha-1.1.2.2/ddalpha/R/depth.simplicialVolume.r |only ddalpha-1.1.2.2/ddalpha/man/dataf.medflies.Rd | 2 ddalpha-1.1.2.2/ddalpha/man/ddalpha-package.Rd | 16 ddalpha-1.1.2.2/ddalpha/man/ddalpha.classify.Rd | 5 ddalpha-1.1.2.2/ddalpha/man/ddalpha.getErrorRateCV.Rd | 13 ddalpha-1.1.2.2/ddalpha/man/ddalpha.getErrorRateJK.Rd | 2 ddalpha-1.1.2.2/ddalpha/man/ddalpha.train.Rd | 30 - ddalpha-1.1.2.2/ddalpha/man/depth..Rd | 16 ddalpha-1.1.2.2/ddalpha/man/depth.Mahalanobis.Rd | 10 ddalpha-1.1.2.2/ddalpha/man/depth.contours.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.contours.ddalpha.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.graph.Rd | 5 ddalpha-1.1.2.2/ddalpha/man/depth.halfspace.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.projection.Rd | 19 ddalpha-1.1.2.2/ddalpha/man/depth.simplicial.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.simplicialVolume.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.space..Rd | 6 ddalpha-1.1.2.2/ddalpha/man/depth.space.halfspace.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.space.projection.Rd | 2 ddalpha-1.1.2.2/ddalpha/man/depth.space.simplicial.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.space.simplicialVolume.Rd |only ddalpha-1.1.2.2/ddalpha/man/depth.space.zonoid.Rd | 3 ddalpha-1.1.2.2/ddalpha/man/depth.spatial.Rd | 10 ddalpha-1.1.2.2/ddalpha/man/depth.zonoid.Rd | 15 ddalpha-1.1.2.2/ddalpha/src/AlphaProcedure.cpp | 4 ddalpha-1.1.2.2/ddalpha/src/Common.cpp | 166 ++++++++ ddalpha-1.1.2.2/ddalpha/src/Common.h | 13 ddalpha-1.1.2.2/ddalpha/src/DataStructures.h | 12 ddalpha-1.1.2.2/ddalpha/src/HD.cpp |only ddalpha-1.1.2.2/ddalpha/src/HD.h |only ddalpha-1.1.2.2/ddalpha/src/OjaDepth.cpp |only ddalpha-1.1.2.2/ddalpha/src/OjaDepth.h |only ddalpha-1.1.2.2/ddalpha/src/RcppExports.cpp | 20 - ddalpha-1.1.2.2/ddalpha/src/SimplicialDepth.cpp |only ddalpha-1.1.2.2/ddalpha/src/SimplicialDepth.h |only ddalpha-1.1.2.2/ddalpha/src/ddalpha.cpp | 86 ++++ ddalpha-1.1.2.2/ddalpha/src/stdafx.h | 5 52 files changed, 677 insertions(+), 201 deletions(-)
Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>
Diff between astrochron versions 0.4.2 dated 2015-03-19 and 0.4.3 dated 2015-07-01
astrochron-0.4.2/astrochron/R/FUNCTION-ar1_v6.R |only astrochron-0.4.2/astrochron/R/FUNCTION-autoPlot_v7.R |only astrochron-0.4.2/astrochron/R/FUNCTION-constantSedrate_v2.R |only astrochron-0.4.2/astrochron/R/FUNCTION-delPts_v4.R |only astrochron-0.4.2/astrochron/R/FUNCTION-eAsm_v2.R |only astrochron-0.4.2/astrochron/R/FUNCTION-eha_v15.R |only astrochron-0.4.2/astrochron/R/FUNCTION-idPts_v9.R |only astrochron-0.4.2/astrochron/R/FUNCTION-linage.R |only astrochron-0.4.2/astrochron/R/FUNCTION-logT_v3.R |only astrochron-0.4.2/astrochron/R/FUNCTION-mtm_v12.R |only astrochron-0.4.2/astrochron/R/FUNCTION-strats_v9.R |only astrochron-0.4.3/astrochron/DESCRIPTION | 8 - astrochron-0.4.3/astrochron/MD5 | 52 ++++++------ astrochron-0.4.3/astrochron/NAMESPACE | 4 astrochron-0.4.3/astrochron/R/FUNCTION-ar1_v7.R |only astrochron-0.4.3/astrochron/R/FUNCTION-autoPlot_v8.R |only astrochron-0.4.3/astrochron/R/FUNCTION-constantSedrate_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-delPts_v5.R |only astrochron-0.4.3/astrochron/R/FUNCTION-eAsm_v3.R |only astrochron-0.4.3/astrochron/R/FUNCTION-eha_v17.R |only astrochron-0.4.3/astrochron/R/FUNCTION-idPts_v10.R |only astrochron-0.4.3/astrochron/R/FUNCTION-linage_v2.R |only astrochron-0.4.3/astrochron/R/FUNCTION-logT_v4.R |only astrochron-0.4.3/astrochron/R/FUNCTION-mtm_v13.R |only astrochron-0.4.3/astrochron/R/FUNCTION-strats_v10.R |only astrochron-0.4.3/astrochron/data/modelA.rda |binary astrochron-0.4.3/astrochron/inst/CITATION | 3 astrochron-0.4.3/astrochron/man/ar1.Rd | 8 - astrochron-0.4.3/astrochron/man/astrochron-package.Rd | 4 astrochron-0.4.3/astrochron/man/autoPlot.Rd | 6 - astrochron-0.4.3/astrochron/man/delPts.Rd | 3 astrochron-0.4.3/astrochron/man/eha.Rd | 2 astrochron-0.4.3/astrochron/man/idPts.Rd | 3 astrochron-0.4.3/astrochron/man/linage.Rd | 3 astrochron-0.4.3/astrochron/man/linterp.Rd | 2 astrochron-0.4.3/astrochron/man/logT.Rd | 3 astrochron-0.4.3/astrochron/man/mtmML96.Rd | 2 astrochron-0.4.3/astrochron/man/taner.Rd | 2 38 files changed, 57 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-31 0.2-1
2011-08-27 0.1-5
2011-01-24 0.1-4
Title: Topic Models
Description: Provides an interface to the C code for Latent Dirichlet
Allocation (LDA) models and Correlated Topics Models
(CTM) by David M. Blei and co-authors and the C++ code
for fitting LDA models using Gibbs sampling by Xuan-Hieu
Phan and co-authors.
Author: Bettina Grün [aut, cre],
Kurt Hornik [aut]
Maintainer: Bettina Grün <Bettina.Gruen@jku.at>
Diff between topicmodels versions 0.2-1 dated 2014-06-11 and 0.2-2 dated 2015-07-01
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/topicmodels.R | 1 + inst/doc/topicmodels.Rnw | 2 +- inst/doc/topicmodels.pdf |binary man/associatedpress.Rd | 2 +- src/rctm.c | 6 +++++- vignettes/topicmodels.Rnw | 2 +- vignettes/topicmodels.bib | 30 ++++++++++++++++++++++++++---- 12 files changed, 61 insertions(+), 25 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.3.1 dated 2015-05-25 and 0.4 dated 2015-07-01
DESCRIPTION | 13 +++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 32 +++++++++++++++++++++++++------- R/SES.R | 8 ++++++-- R/cv.ses.R |only R/gSquare.R | 6 ++++++ R/testIndFisher.R | 11 ++++++----- R/testIndLogistic.R | 8 ++++---- man/MXM-package.Rd | 6 +++--- man/SES.Rd | 3 ++- man/cv.ses.Rd |only 11 files changed, 69 insertions(+), 36 deletions(-)
Title: Maximally Selected Rank Statistics
Description: Maximally selected rank statistics with
several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between maxstat versions 0.7-22 dated 2015-02-20 and 0.7-23 dated 2015-07-01
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 3 +++ R/maxstat.R | 4 ++-- build/vignette.rds |binary data/treepipit.rda |binary inst/NEWS | 8 +++++++- inst/doc/maxstat.pdf |binary man/maxstat.test.Rd | 3 ++- man/plot.maxtest.Rd | 4 ++-- tests/Examples/maxstat-Ex.Rout.save | 15 ++++++--------- 11 files changed, 37 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-24 1.1
2011-10-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-07-24 2.2
2009-06-09 2.1
2008-06-23 1.0-1
2008-06-23 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-28 0.9-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-10-21 0.1.2
2009-07-30 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-08-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-03-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-19 2.0.1
2011-08-04 2.0
2006-02-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-09 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-10 2.1.1
2014-01-07 2.1.0
2013-07-22 2.0.3
2013-06-12 2.0.2
2013-03-20 2.0.1
2013-01-15 2.0.0
2012-09-07 0.19
2012-03-01 0.17
2011-06-30 0.16
2011-06-28 0.15
2011-03-04 0.14
2011-02-15 0.13
2010-11-05 0.12
2010-10-27 0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-25 1.0
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.4.9 dated 2015-04-18 and 1.4.10 dated 2015-07-01
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 43 +++++++++++++++++++++++++++++++++++++++++++ R/ABtext.R | 3 ++- R/PANDabove.R | 2 +- R/PANDbelow.R | 2 +- 6 files changed, 58 insertions(+), 13 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>
Diff between nat versions 1.6.6 dated 2015-05-27 and 1.7.0 dated 2015-07-01
nat-1.6.6/nat/man/as.data.frame.neuronlist.Rd |only nat-1.6.6/nat/man/scale.dotprops.Rd |only nat-1.7.0/nat/DESCRIPTION | 18 nat-1.7.0/nat/MD5 | 182 +++-- nat-1.7.0/nat/NAMESPACE | 37 + nat-1.7.0/nat/NEWS | 29 nat-1.7.0/nat/R/amiramesh-io.R | 16 nat-1.7.0/nat/R/cmtk-reformat.R | 135 +++- nat-1.7.0/nat/R/cmtk.R | 2 nat-1.7.0/nat/R/coordinates.R | 11 nat-1.7.0/nat/R/dotprops.R | 45 - nat-1.7.0/nat/R/graph-nodes.R | 15 nat-1.7.0/nat/R/hxsurf.R | 40 - nat-1.7.0/nat/R/im3d.R | 56 + nat-1.7.0/nat/R/nat-package.R | 2 nat-1.7.0/nat/R/neuron-io-amira.R | 1 nat-1.7.0/nat/R/neuron-io-neuroml.R | 1 nat-1.7.0/nat/R/neuron-io.R | 33 - nat-1.7.0/nat/R/neuron-plot.R | 30 nat-1.7.0/nat/R/neuron.R | 18 nat-1.7.0/nat/R/neuronlist.R | 169 ++++- nat-1.7.0/nat/R/neuronlistfh.R | 56 + nat-1.7.0/nat/R/ngraph.R | 24 nat-1.7.0/nat/R/nrrd-io.R | 305 +++++++--- nat-1.7.0/nat/R/seglist.R | 22 nat-1.7.0/nat/R/xform.R | 55 + nat-1.7.0/nat/R/xformimage.R | 84 +- nat-1.7.0/nat/R/xformpoints.R | 65 +- nat-1.7.0/nat/R/zzz.R | 2 nat-1.7.0/nat/man/as.im3d.Rd | 14 nat-1.7.0/nat/man/boundingbox.Rd | 21 nat-1.7.0/nat/man/cmtk.reformatx.Rd | 19 nat-1.7.0/nat/man/cmtk.statistics.Rd | 49 + nat-1.7.0/nat/man/cmtk.targetvolume.Rd | 5 nat-1.7.0/nat/man/coord2ind.Rd | 2 nat-1.7.0/nat/man/dotprops.Rd | 3 nat-1.7.0/nat/man/get-set-neuronlist-data.frame.Rd |only nat-1.7.0/nat/man/im3d-coords.Rd | 12 nat-1.7.0/nat/man/im3d-io.Rd | 10 nat-1.7.0/nat/man/im3d.Rd | 10 nat-1.7.0/nat/man/imexpand.grid.Rd | 10 nat-1.7.0/nat/man/imslice.Rd | 10 nat-1.7.0/nat/man/ind2coord.Rd | 8 nat-1.7.0/nat/man/is.im3d.Rd |only nat-1.7.0/nat/man/is.neuronlist.Rd | 12 nat-1.7.0/nat/man/neuronlist-arithmetic.Rd | 17 nat-1.7.0/nat/man/neuronlist-dataframe-methods.Rd | 70 ++ nat-1.7.0/nat/man/neuronlist.Rd | 15 nat-1.7.0/nat/man/neuronlistfh.Rd | 20 nat-1.7.0/nat/man/ngraph.Rd | 4 nat-1.7.0/nat/man/nlapply.Rd | 12 nat-1.7.0/nat/man/nrrd.voxdims.Rd | 5 nat-1.7.0/nat/man/origin.Rd | 8 nat-1.7.0/nat/man/plot.neuron.Rd | 21 nat-1.7.0/nat/man/plot.neuronlist.Rd | 2 nat-1.7.0/nat/man/plot3d.neuronlist.Rd | 6 nat-1.7.0/nat/man/projection.Rd | 8 nat-1.7.0/nat/man/read.hxsurf.Rd | 35 - nat-1.7.0/nat/man/read.neuronlistfh.Rd | 3 nat-1.7.0/nat/man/read.neurons.Rd | 16 nat-1.7.0/nat/man/read.nrrd.Rd | 30 nat-1.7.0/nat/man/remotesync.Rd | 3 nat-1.7.0/nat/man/scale.neuron.Rd | 24 nat-1.7.0/nat/man/sub-.neuronlistfh.Rd | 58 + nat-1.7.0/nat/man/threshold.Rd | 7 nat-1.7.0/nat/man/unmask.Rd | 8 nat-1.7.0/nat/man/voxdims.Rd | 7 nat-1.7.0/nat/man/write.neuronlistfh.Rd | 3 nat-1.7.0/nat/man/write.neurons.Rd | 12 nat-1.7.0/nat/man/write.nrrd.Rd | 98 +++ nat-1.7.0/nat/man/xform.Rd | 55 + nat-1.7.0/nat/man/xformimage.Rd | 35 - nat-1.7.0/nat/man/xformpoints.Rd | 16 nat-1.7.0/nat/tests/test-all.R | 14 nat-1.7.0/nat/tests/testthat/test-cmtk-reformat.R | 11 nat-1.7.0/nat/tests/testthat/test-cmtk.R | 13 nat-1.7.0/nat/tests/testthat/test-dotprops.R | 19 nat-1.7.0/nat/tests/testthat/test-graph-nodes.R | 5 nat-1.7.0/nat/tests/testthat/test-hxsurf.R | 2 nat-1.7.0/nat/tests/testthat/test-im3d.R | 27 nat-1.7.0/nat/tests/testthat/test-landmarks-io.R | 6 nat-1.7.0/nat/tests/testthat/test-neuroml-io.R | 8 nat-1.7.0/nat/tests/testthat/test-neuron-io.R | 36 + nat-1.7.0/nat/tests/testthat/test-neuronlist.R | 55 + nat-1.7.0/nat/tests/testthat/test-neuronlistfh.R | 14 nat-1.7.0/nat/tests/testthat/test-ngraph.R | 21 nat-1.7.0/nat/tests/testthat/test-nrrd-io.R | 107 +++ nat-1.7.0/nat/tests/testthat/test-pop3d.R | 2 nat-1.7.0/nat/tests/testthat/test-xform.R | 6 nat-1.7.0/nat/tests/testthat/test-xformimage.R | 21 nat-1.7.0/nat/tests/testthat/testdata/nrrd/LHMask.nhdr |only nat-1.7.0/nat/tests/testthat/testdata/nrrd/LHMask.nrrd |binary nat-1.7.0/nat/tests/testthat/testdata/nrrd/badenc.nhdr |only nat-1.7.0/nat/tests/testthat/testdata/nrrd/badtype.nhdr |only nat-1.7.0/nat/tests/testthat/testdata/nrrd/datafile_list.nhdr |only nat-1.7.0/nat/tests/testthat/testdata/nrrd/datafile_listslab.nhdr |only nat-1.7.0/nat/tests/testthat/testdata/v3draw/L1DS1_crop_straight_crop_ch1.nhdr |only 97 files changed, 1958 insertions(+), 645 deletions(-)
More information about OneArmPhaseTwoStudy at CRAN
Permanent link
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between missMDA versions 1.7.3 dated 2014-11-24 and 1.8.2 dated 2015-07-01
DESCRIPTION | 17 ++++++------- MD5 | 34 +++++++++++++-------------- NAMESPACE | 7 ++++- R/MIPCA.R | 16 ++++++------- R/estim_ncpPCA.R | 2 - R/imputeFAMD.R | 2 - R/imputeMCA.R | 28 +++++++++++++--------- R/imputeMFA.R | 64 ++++++++++++++++++++++++++-------------------------- R/imputePCA.R | 47 +++++++++++++++++++------------------- man/MIPCA.Rd | 2 - man/estim_ncpPCA.Rd | 4 +-- man/gene.Rd | 10 ++++---- man/geno.Rd | 4 +-- man/imputeFAMD.Rd | 2 - man/imputeMCA.Rd | 6 ++-- man/imputePCA.Rd | 4 +-- man/ozone.Rd | 2 - man/snorena.Rd | 2 - 18 files changed, 132 insertions(+), 121 deletions(-)
Title: Flexible Mediation Analysis Using Natural Effect Models
Description: Run flexible mediation analyses using natural
effect models as described in Lange, Vansteelandt and Bekaert (2012),
Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet,
Buysse, Steen and Vansteelandt (2013).
Author: Johan Steen [aut, cre],
Tom Loeys [aut],
Beatrijs Moerkerke [aut],
Stijn Vansteelandt [aut],
Joris Meys [ctb] (technical support),
Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen <johan.steen@gmail.com>
Diff between medflex versions 0.5-0 dated 2015-02-07 and 0.5-1 dated 2015-07-01
DESCRIPTION | 15 +- MD5 | 44 ++++---- NAMESPACE | 4 NEWS | 7 + R/neImpute.R | 13 +- R/neLht.R | 13 ++ R/neModel.R | 2 R/neWeight.R | 31 ++---- R/utils.R | 4 data/UPBdata.rda |binary inst/CITATION | 4 inst/doc/medflex.Rnw |only inst/doc/medflex.pdf |binary inst/doc/sandwich.Rnw |only man/neImpute.default.Rd | 2 man/neImpute.formula.Rd | 2 man/neLht.Rd | 2 man/neModel.Rd | 9 - man/neWeight.default.Rd | 2 man/neWeight.formula.Rd | 2 vignettes/bib.bib | 162 ++++++++++++++++--------------- vignettes/medflex-fig2.pdf |binary vignettes/medflex.Rnw | 229 ++++++++++++++++++++------------------------- vignettes/medflex.pdf |binary 24 files changed, 278 insertions(+), 269 deletions(-)
Title: High Dimensional Supervised Classification and Clustering
Description: Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.
Author: Laurent Berge, Charles Bouveyron and Stephane Girard
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between HDclassif versions 1.2.3 dated 2015-02-16 and 1.3 dated 2015-07-01
ChangeLog | 14 +++++- DESCRIPTION | 10 ++-- MD5 | 15 +++--- NAMESPACE | 9 ++- R/hdclassif.R | 119 ++++++++------------------------------------------- R/mdaHD.R |only man/hddc.Rd | 2 man/hdmda.Rd |only man/predict.hdc.Rd | 4 - man/predict.hdmda.Rd |only 10 files changed, 56 insertions(+), 117 deletions(-)
Title: Bayesian Mixture Models with JAGS
Description: The fitting of finite mixture models of univariate
Gaussian distributions using JAGS within a Bayesian
framework is provided.
Author: Bettina Gruen [aut, cre],
Martyn Plummer [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@jku.at>
Diff between bayesmix versions 0.7-3 dated 2014-03-11 and 0.7-4 dated 2015-07-01
DESCRIPTION | 16 +++++++++------- MD5 | 14 +++++++------- R/BMMmodel.R | 2 +- R/BMMpriors.R | 13 +++++-------- R/Inits.R | 10 +++++----- R/JAGSrun.R | 16 ++++++++-------- R/plots.R | 46 +++++++++++++++++++++++----------------------- inst/NEWS.Rd | 6 ++++++ 8 files changed, 64 insertions(+), 59 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-04 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-30 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-05-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-23 2.2.5
2012-09-11 2.2.0
2012-06-07 2.1.4
2012-04-06 2.1.3
2011-11-04 2.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-27 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-05 1.2
2013-05-30 1.1
2013-05-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-24 2.0
2013-05-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-21 1.7-1
2014-05-20 1.7-0
2013-12-12 1.6-4
2013-05-27 1.6-3
2013-05-03 1.6-2
2012-10-04 1.6-1
2012-05-15 1.5-0
2011-08-30 1.4-0
2011-08-28 1.3-0
2011-02-14 1.1-0
2010-03-02 1.0-1
2010-01-19 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-24 1.2
2014-09-13 1.1
2014-09-02 1.0
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.4.7 dated 2015-04-27 and 0.5.0 dated 2015-07-01
rplos-0.4.7/rplos/NEWS |only rplos-0.4.7/rplos/R/startup.R |only rplos-0.5.0/rplos/DESCRIPTION | 23 - rplos-0.5.0/rplos/MD5 | 102 +++--- rplos-0.5.0/rplos/NAMESPACE | 14 rplos-0.5.0/rplos/NEWS.md |only rplos-0.5.0/rplos/R/citations.R | 11 rplos-0.5.0/rplos/R/facetplos.r | 3 rplos-0.5.0/rplos/R/fulltext.R | 8 rplos-0.5.0/rplos/R/highbrow.r | 16 rplos-0.5.0/rplos/R/highplos.r | 4 rplos-0.5.0/rplos/R/journalnamekey.R | 1 rplos-0.5.0/rplos/R/plosabstract.R | 3 rplos-0.5.0/rplos/R/plosviews.R | 2 rplos-0.5.0/rplos/R/rplos-package.R | 7 rplos-0.5.0/rplos/R/searchplos.R | 3 rplos-0.5.0/rplos/R/zzz.R | 1 rplos-0.5.0/rplos/README.md | 174 +++++----- rplos-0.5.0/rplos/build/vignette.rds |binary rplos-0.5.0/rplos/inst/doc/facethighlight.Rmd | 59 +-- rplos-0.5.0/rplos/inst/doc/facethighlight.html | 159 +++++---- rplos-0.5.0/rplos/inst/doc/fulltext.Rmd | 154 ++++----- rplos-0.5.0/rplos/inst/doc/fulltext.html | 254 +++++++-------- rplos-0.5.0/rplos/inst/doc/rplos_vignette.Rmd | 83 ++-- rplos-0.5.0/rplos/inst/doc/rplos_vignette.html | 187 +++++------ rplos-0.5.0/rplos/inst/vign/facethighlight.Rmd | 1 rplos-0.5.0/rplos/inst/vign/facethighlight.md | 59 +-- rplos-0.5.0/rplos/inst/vign/figure/plosword1plot-1.png |binary rplos-0.5.0/rplos/inst/vign/figure/throughtime1-1.png |binary rplos-0.5.0/rplos/inst/vign/fulltext.Rmd | 1 rplos-0.5.0/rplos/inst/vign/fulltext.md | 154 ++++----- rplos-0.5.0/rplos/inst/vign/rplos_vignette.Rmd | 1 rplos-0.5.0/rplos/inst/vign/rplos_vignette.md | 83 ++-- rplos-0.5.0/rplos/man/facetplos.Rd | 11 rplos-0.5.0/rplos/man/plosabstract.Rd | 3 rplos-0.5.0/rplos/man/rplos.Rd | 8 rplos-0.5.0/rplos/tests/test-all.R |only rplos-0.5.0/rplos/tests/testthat/test-check_response.R | 8 rplos-0.5.0/rplos/tests/testthat/test-citations.R | 35 +- rplos-0.5.0/rplos/tests/testthat/test-formatarticleurl.R | 8 rplos-0.5.0/rplos/tests/testthat/test-journalnamekey.R | 6 rplos-0.5.0/rplos/tests/testthat/test-plosabstract.R | 4 rplos-0.5.0/rplos/tests/testthat/test-plosauthor.R | 4 rplos-0.5.0/rplos/tests/testthat/test-plosfields.R | 13 rplos-0.5.0/rplos/tests/testthat/test-plosfigtabcaps.R | 12 rplos-0.5.0/rplos/tests/testthat/test-plossubject.R | 6 rplos-0.5.0/rplos/tests/testthat/test-plostitle.R | 4 rplos-0.5.0/rplos/tests/testthat/test-plosviews.R | 4 rplos-0.5.0/rplos/tests/testthat/test-plosword.R | 4 rplos-0.5.0/rplos/tests/testthat/test-plot_throughtime.R | 10 rplos-0.5.0/rplos/tests/testthat/test-searchplos.R | 19 - rplos-0.5.0/rplos/vignettes/facethighlight.Rmd | 59 +-- rplos-0.5.0/rplos/vignettes/fulltext.Rmd | 154 ++++----- rplos-0.5.0/rplos/vignettes/rplos_vignette.Rmd | 83 ++-- 54 files changed, 1056 insertions(+), 966 deletions(-)
Title: Predict Protein-Protein Interactions Based on Functional and
Topological Similarities
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng <anfdeng@163.com>
Diff between ppiPre versions 1.7 dated 2015-03-02 and 1.8 dated 2015-07-01
DESCRIPTION | 14 +++----- MD5 | 14 ++++---- NAMESPACE | 4 ++ R/TopologicSims.r | 79 ++++++++++++++++++++++++++------------------------ man/AASim.Rd | 2 - man/JaccardSim.Rd | 2 - man/RASim.Rd | 2 - man/ppiPre-package.Rd | 6 +-- 8 files changed, 65 insertions(+), 58 deletions(-)
Title: 'MicroRNA' Set Enrichment Analysis
Description: The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.
Author: Junwei Han, Siyao Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between MiRSEA versions 1.0 dated 2015-05-31 and 1.1 dated 2015-07-01
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 11 ++++++++--- R/PlotCorrelation.R | 2 +- inst/doc/MiRSEA.Rnw | 41 ++++++++++++++++++++++++----------------- inst/doc/MiRSEA.pdf |binary man/MiRSEA-package.Rd | 10 +++++----- man/MirSEA.Rd | 10 ++++++---- man/MsReport.Rd | 2 ++ man/PlotCorrelation.Rd | 2 +- man/PlotHeatMap.Rd | 2 ++ vignettes/MiRSEA.Rnw | 41 ++++++++++++++++++++++++----------------- 12 files changed, 91 insertions(+), 65 deletions(-)
Title: Extra Themes, Scales and Geoms for `ggplot2`
Description: Some extra themes, geoms, and scales for `ggplot2`.
Author: Jeffrey B. Arnold [aut, cre],
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Justin Talbot [ctb] (Some code from the labeling package)
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 2.1.2 dated 2015-03-01 and 2.2.1 dated 2015-07-01
DESCRIPTION | 18 - MD5 | 210 ++++++------ NAMESPACE | 11 NEWS | 10 R/banking.R | 422 ++++++++++++------------ R/calc.R | 104 +++--- R/colorblind.R | 60 +-- R/economist.R | 230 ++++++------- R/excel.R | 171 ++++----- R/few.R | 104 +++--- R/fivethirtyeight.R | 85 ++-- R/gdocs.R | 78 ++-- R/geom-rangeframe.R | 139 +++----- R/geom-tufteboxplot.R | 227 +++++-------- R/ggthemes-data.R | 10 R/ggthemes-package.R | 30 + R/hc.R | 177 ++++------ R/igray.R | 57 +-- R/pander.R | 271 ++++++--------- R/scale-tufte.R | 128 +++---- R/shapes.R | 246 +++++++------- R/solarized.R | 305 ++++++++--------- R/stat-fivenumber.R | 79 ++-- R/stata.R | 589 ++++++++++++++++------------------ R/tableau.R | 291 ++++++++-------- R/theme-foundation.R | 33 - R/theme-map.R |only R/theme-solid.R | 41 +- R/tufte.R | 114 +++--- R/utils.R | 186 +++++----- R/wsj.R | 191 ++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggthemes.R | 11 inst/doc/ggthemes.html | 66 ++- man/bank_slopes.Rd | 48 +- man/calc_pal.Rd | 2 man/calc_shape_pal.Rd | 2 man/circlefill_shape_pal.Rd | 2 man/cleveland_shape_pal.Rd | 2 man/colorblind.Rd | 12 man/economist_pal.Rd | 2 man/excel_pal.Rd | 8 man/few_pal.Rd | 2 man/fivethirtyeight_pal.Rd | 2 man/gdocs_pal.Rd | 2 man/geom_rangeframe.Rd | 6 man/geom_tufteboxplot.Rd | 14 man/ggthemes.Rd | 2 man/ggthemes_data.Rd | 2 man/hc_pal.Rd | 6 man/palette_pander.Rd | 2 man/range_breaks.Rd | 2 man/scale_calc.Rd | 2 man/scale_color_tableau.Rd | 22 - man/scale_colour_gradient2_tableau.Rd | 10 man/scale_colour_gradient_tableau.Rd | 12 man/scale_economist.Rd | 2 man/scale_excel.Rd | 6 man/scale_few.Rd | 2 man/scale_fivethirtyeight.Rd | 2 man/scale_gdocs.Rd | 2 man/scale_hc.Rd | 2 man/scale_linetype_stata.Rd | 2 man/scale_pander.Rd | 2 man/scale_shape_calc.Rd | 2 man/scale_shape_circlefill.Rd | 2 man/scale_shape_cleveland.Rd | 2 man/scale_shape_stata.Rd | 2 man/scale_shape_tableau.Rd | 2 man/scale_shape_tremmel.Rd | 2 man/scale_solarized.Rd | 2 man/scale_stata.Rd | 2 man/scale_tufte.Rd | 2 man/scale_wsj.Rd | 2 man/show_linetypes.Rd | 2 man/show_shapes.Rd | 2 man/smart_digits.Rd | 2 man/solarized_pal.Rd | 4 man/solarized_rebase.Rd | 2 man/stat_fivenumber.Rd | 4 man/stata_linetype_pal.Rd | 2 man/stata_pal.Rd | 2 man/stata_shape_pal.Rd | 2 man/tableau_color_pal.Rd | 30 - man/tableau_div_gradient_pal.Rd | 8 man/tableau_seq_gradient_pal.Rd | 8 man/tableau_shape_pal.Rd | 2 man/theme_calc.Rd | 2 man/theme_economist.Rd | 6 man/theme_excel.Rd | 8 man/theme_few.Rd | 2 man/theme_fivethirtyeight.Rd | 12 man/theme_foundation.Rd | 6 man/theme_gdocs.Rd | 2 man/theme_hc.Rd | 18 - man/theme_igray.Rd | 2 man/theme_map.Rd |only man/theme_pander.Rd | 4 man/theme_solarized.Rd | 8 man/theme_solid.Rd | 2 man/theme_stata.Rd | 2 man/theme_tufte.Rd | 18 - man/theme_wsj.Rd | 24 - man/tremmel_shape_pal.Rd | 2 man/wsj_pal.Rd | 4 vignettes/children/examples.Rmd | 17 107 files changed, 2484 insertions(+), 2623 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between CDM versions 4.3-0 dated 2015-06-05 and 4.4-1 dated 2015-07-01
DESCRIPTION | 13 +++++---- MD5 | 29 +++++++++++---------- NAMESPACE | 62 ++++++++++++++++++++++++++++++++++------------- R/gdina.R | 59 +++++++++++++++++++++++++++++++++++--------- R/gdina.dif.R | 4 +-- R/gdina.dif_aux.R | 2 - R/gdina_hogdina_alg.R | 2 - R/gdm.R | 1 R/rrum.param.R |only R/sequential.items.R | 2 - R/sim.gdina.R | 2 - R/summary.gdina.R | 26 ------------------- inst/NEWS | 11 ++++++++ man/CDM-package.Rd | 39 +++++++++++++++-------------- man/din.Rd | 2 - man/din.deterministic.Rd | 2 - 16 files changed, 155 insertions(+), 101 deletions(-)
Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates
for group means and standard deviations and their differences and
effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between BEST versions 0.2.2 dated 2014-06-06 and 0.3.0 dated 2015-07-01
DESCRIPTION | 12 - MD5 | 37 ++--- NAMESPACE | 12 + NEWS | 46 +++++- R/BESTmcmc.R | 273 +++++++++++++++++++++++++------------- R/converters.R |only R/makeData.R | 63 +++++--- R/plotDataPPC.R | 22 +-- R/plotPostPred.R | 10 - R/postPriorOverlap.R |only R/print.BEST.R | 7 build/vignette.rds |binary inst/doc/BEST.R | 4 inst/doc/BEST.Rnw | 68 +++++---- inst/doc/BEST.pdf |binary inst/tests/test-BESTmcmc.R | 68 ++++----- inst/tests/test-BESTmcmc_errors.R |only inst/tests/test-BESTmcmc_priors.R |only inst/tests/test-BESTpower.R | 46 +++--- man/BESTmcmc.Rd | 55 +++++-- man/postPriorOverlap.Rd |only vignettes/BEST.Rnw | 68 +++++---- 22 files changed, 500 insertions(+), 291 deletions(-)
Title: Obtain Alpha-Outlier Regions for Well-Known Probability
Distributions
Description: Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, doi: 10.1080/01621459.1993.10476339 for details.
Author: Andre Rehage, Sonja Kuhnt
Maintainer: Andre Rehage <rehage@statistik.tu-dortmund.de>
Diff between alphaOutlier versions 1.0.1 dated 2015-05-15 and 1.1.0 dated 2015-07-01
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 21 +++++++++++++++++++-- NEWS | 7 +++++++ R/aout.conttab.R | 50 +++++++++++++++++++++++++------------------------- R/createDesMat.R |only man/createDesMat.Rd |only 7 files changed, 61 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-05 1.1
2014-11-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-17 1.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-22 2.1-10
2012-04-22 2.1-9
2010-10-12 2.1-8
2010-05-20 2.1-6
2009-11-19 2.1-4
2009-11-18 2.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-05 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-17 1.3.9
2009-06-17 1.2.0
2009-04-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-03 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-30 2.0-0.2
2014-08-27 2.0-0.1
2014-04-16 2.0-0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-08 2.0
2013-05-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-24 1.3
2014-04-07 1.2
2014-02-05 1.1
2014-01-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-26 0.3.1
2013-12-11 0.3
2013-10-03 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-15 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-24 1.0
2012-01-24 1.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-13 2.18.1
2013-08-19 2.17.1
2013-06-06 2.16.1
2013-05-02 2.10
2013-04-30 2.7
2013-04-25 2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-08 1.2
2013-04-05 1.1
2010-08-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-21 1.0-2
2009-09-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-23 1.1
2013-07-15 1.0
Title: Approximate Gaussian Processes Using the Fourier Basis
Description: Routines for creating, manipulating, and performing
Bayesian inference about Gaussian processes in
one and two dimensions using the Fourier basis approximation:
simulation and plotting of processes, calculation of
coefficient variances, calculation of process density,
coefficient proposals (for use in MCMC). It uses R environments to
store GP objects as references/pointers.
Author: Chris Paciorek <paciorek@alumni.cmu.edu>
Maintainer: Chris Paciorek <paciorek@alumni.cmu.edu>
Diff between spectralGP versions 1.3.2 dated 2014-12-05 and 1.3.3 dated 2015-07-01
DESCRIPTION | 13 +++++++------ MD5 | 27 ++++++++++++++------------- NAMESPACE | 8 +++++--- NEWS |only R/Gibbs.sample.coeff.gp.R | 2 +- R/Hastings.coeff.gp.R | 2 +- R/image.plot.R | 6 +++--- R/image.plot.info.R | 2 +- R/image.plot.plt.R | 2 +- R/onLoad.R | 2 +- R/plot.gp.R | 4 ++-- R/propose.coeff.gp.R | 6 +++--- man/image.plot.Rd | 12 ++++++------ man/plot.gp.Rd | 2 +- man/spectralGP-generic.Rd | 4 ++-- 15 files changed, 48 insertions(+), 44 deletions(-)
Title: Interface to 'Sunlight' Foundation 'APIs'
Description: Interface to four 'Sunlight' Foundation 'APIs'
(http://sunlightfoundation.com/api/) for government data, including the
Congress 'API' 'v3', the Capitol Words 'API', the Influence Explorer 'API', and the
Open States 'API'. 'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that
collects and provides data on government activities, and those that
influence government. Functions are provided to interact with each of the
four 'APIs'.
Author: Scott Chamberlain [aut, cre],
Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rsunlight versions 0.3.0 dated 2014-08-20 and 0.4.0 dated 2015-07-01
rsunlight-0.3.0/rsunlight/NEWS |only rsunlight-0.3.0/rsunlight/R/sunlight_tocsv.R |only rsunlight-0.3.0/rsunlight/man/suncompact.Rd |only rsunlight-0.3.0/rsunlight/man/sunlight_tocsv.Rd |only rsunlight-0.3.0/rsunlight/vignettes/figure |only rsunlight-0.4.0/rsunlight/DESCRIPTION | 27 rsunlight-0.4.0/rsunlight/LICENSE | 4 rsunlight-0.4.0/rsunlight/MD5 | 175 ++-- rsunlight-0.4.0/rsunlight/NAMESPACE | 20 rsunlight-0.4.0/rsunlight/R/cg_amendments.R | 26 rsunlight-0.4.0/rsunlight/R/cg_bills.R | 41 rsunlight-0.4.0/rsunlight/R/cg_committees.R | 64 - rsunlight-0.4.0/rsunlight/R/cg_districts.R | 22 rsunlight-0.4.0/rsunlight/R/cg_documents.R |only rsunlight-0.4.0/rsunlight/R/cg_floor_updates.R | 26 rsunlight-0.4.0/rsunlight/R/cg_hearings.R | 53 - rsunlight-0.4.0/rsunlight/R/cg_legislators.R | 61 - rsunlight-0.4.0/rsunlight/R/cg_nominations.R | 16 rsunlight-0.4.0/rsunlight/R/cg_upcoming_bills.R | 34 rsunlight-0.4.0/rsunlight/R/cg_votes.R | 23 rsunlight-0.4.0/rsunlight/R/cw_dates.R | 40 rsunlight-0.4.0/rsunlight/R/cw_phrases.R | 42 rsunlight-0.4.0/rsunlight/R/cw_text.R | 38 rsunlight-0.4.0/rsunlight/R/cw_timeseries.R | 60 - rsunlight-0.4.0/rsunlight/R/ie_contr.R | 48 - rsunlight-0.4.0/rsunlight/R/ie_contr_bundled.R | 23 rsunlight-0.4.0/rsunlight/R/ie_earmarks.R | 30 rsunlight-0.4.0/rsunlight/R/ie_entities.R | 49 - rsunlight-0.4.0/rsunlight/R/ie_epa.R | 36 rsunlight-0.4.0/rsunlight/R/ie_faca.R | 27 rsunlight-0.4.0/rsunlight/R/ie_getcontracts.R | 24 rsunlight-0.4.0/rsunlight/R/ie_getgrants.R | 25 rsunlight-0.4.0/rsunlight/R/ie_getlobbying.R | 64 - rsunlight-0.4.0/rsunlight/R/ie_individuals.R | 30 rsunlight-0.4.0/rsunlight/R/ie_industries.R | 22 rsunlight-0.4.0/rsunlight/R/ie_misconduct.R | 29 rsunlight-0.4.0/rsunlight/R/ie_organizations.R | 21 rsunlight-0.4.0/rsunlight/R/ie_politicians.R | 22 rsunlight-0.4.0/rsunlight/R/os_billlookup.R | 30 rsunlight-0.4.0/rsunlight/R/os_billsearch.R | 57 - rsunlight-0.4.0/rsunlight/R/os_legislatorsearch.R | 33 rsunlight-0.4.0/rsunlight/R/os_statemetasearch.R | 31 rsunlight-0.4.0/rsunlight/R/query.R |only rsunlight-0.4.0/rsunlight/R/rsunlight-package.R | 16 rsunlight-0.4.0/rsunlight/R/tbldf.R |only rsunlight-0.4.0/rsunlight/R/zzz.R | 124 ++ rsunlight-0.4.0/rsunlight/README.md | 240 +++-- rsunlight-0.4.0/rsunlight/build/vignette.rds |binary rsunlight-0.4.0/rsunlight/inst/doc/rsunlight_vignette.Rmd | 457 +++++----- rsunlight-0.4.0/rsunlight/inst/doc/rsunlight_vignette.html | 562 ++++++------- rsunlight-0.4.0/rsunlight/inst/ignore/sunlight_tocsv.R |only rsunlight-0.4.0/rsunlight/inst/img/unnamed-chunk-10-1.png |only rsunlight-0.4.0/rsunlight/inst/img/unnamed-chunk-8-1.png |only rsunlight-0.4.0/rsunlight/man/cg_amendments.Rd | 32 rsunlight-0.4.0/rsunlight/man/cg_bills.Rd | 115 +- rsunlight-0.4.0/rsunlight/man/cg_committees.Rd | 56 - rsunlight-0.4.0/rsunlight/man/cg_districts.Rd | 27 rsunlight-0.4.0/rsunlight/man/cg_documents.Rd |only rsunlight-0.4.0/rsunlight/man/cg_floor_updates.Rd | 30 rsunlight-0.4.0/rsunlight/man/cg_hearings.Rd | 57 - rsunlight-0.4.0/rsunlight/man/cg_legislators.Rd | 35 rsunlight-0.4.0/rsunlight/man/cg_nominations.Rd | 30 rsunlight-0.4.0/rsunlight/man/cg_upcoming_bills.Rd | 43 rsunlight-0.4.0/rsunlight/man/cg_votes.Rd | 29 rsunlight-0.4.0/rsunlight/man/cw_dates.Rd | 38 rsunlight-0.4.0/rsunlight/man/cw_phrases.Rd | 26 rsunlight-0.4.0/rsunlight/man/cw_text.Rd | 30 rsunlight-0.4.0/rsunlight/man/cw_timeseries.Rd | 43 rsunlight-0.4.0/rsunlight/man/ie_contr.Rd | 21 rsunlight-0.4.0/rsunlight/man/ie_contr_bundled.Rd | 20 rsunlight-0.4.0/rsunlight/man/ie_contracts.Rd | 38 rsunlight-0.4.0/rsunlight/man/ie_earmarks.Rd | 20 rsunlight-0.4.0/rsunlight/man/ie_entities.Rd | 22 rsunlight-0.4.0/rsunlight/man/ie_epa.Rd | 26 rsunlight-0.4.0/rsunlight/man/ie_faca.Rd | 20 rsunlight-0.4.0/rsunlight/man/ie_grants.Rd | 41 rsunlight-0.4.0/rsunlight/man/ie_individuals.Rd | 26 rsunlight-0.4.0/rsunlight/man/ie_industries.Rd | 19 rsunlight-0.4.0/rsunlight/man/ie_lobbying.Rd | 57 - rsunlight-0.4.0/rsunlight/man/ie_misconduct.Rd | 21 rsunlight-0.4.0/rsunlight/man/ie_organizations.Rd | 19 rsunlight-0.4.0/rsunlight/man/ie_politicians.Rd | 19 rsunlight-0.4.0/rsunlight/man/ie_sectors.Rd | 3 rsunlight-0.4.0/rsunlight/man/os_billlookup.Rd | 12 rsunlight-0.4.0/rsunlight/man/os_billsearch.Rd | 36 rsunlight-0.4.0/rsunlight/man/os_legislatorsearch.Rd | 20 rsunlight-0.4.0/rsunlight/man/os_statemetasearch.Rd | 8 rsunlight-0.4.0/rsunlight/man/rsunlight-package.Rd | 17 rsunlight-0.4.0/rsunlight/man/sessions.Rd | 3 rsunlight-0.4.0/rsunlight/man/type_sum.Rd |only rsunlight-0.4.0/rsunlight/tests |only rsunlight-0.4.0/rsunlight/vignettes/rsunlight_vignette.Rmd | 457 +++++----- 92 files changed, 2236 insertions(+), 2052 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.1.0 dated 2015-05-11 and 0.2.0 dated 2015-07-01
DESCRIPTION | 14 +-- MD5 | 61 +++++++------ NAMESPACE | 12 ++ NEWS | 22 ++++ R/cache.R |only R/fipscounty.R | 7 + R/grid.R | 68 ++++++++++---- R/info.R | 14 ++- R/keywords.R | 7 + R/rerddap-package.r | 3 R/search.R | 2 R/servers.R | 3 R/table.R | 12 +- README.md | 83 ++++++++++-------- build/vignette.rds |binary inst/doc/rerddap_vignette.Rmd | 64 +++++++------- inst/doc/rerddap_vignette.html | 164 +++++++++++++++++++----------------- inst/vign/rerddap_vignette.md | 64 +++++++------- man/cache_list.Rd |only man/griddap.Rd | 28 +++--- man/info.Rd | 2 man/tabledap.Rd | 8 - tests/test-all.R |only tests/testthat/test-convert_time.R | 4 tests/testthat/test-convert_units.R | 4 tests/testthat/test-disk.R | 2 tests/testthat/test-ed_datasets.R | 15 ++- tests/testthat/test-ed_search.R | 16 ++- tests/testthat/test-ed_search_adv.R | 23 +++-- tests/testthat/test-griddap.R | 18 ++- tests/testthat/test-info.R | 24 +++-- tests/testthat/test-tabledap.R | 21 +++- vignettes/rerddap_vignette.Rmd | 64 +++++++------- 33 files changed, 498 insertions(+), 331 deletions(-)
Title: Parametric Time Warping
Description: Parametric Time Warping aligns patterns, i.e. it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation). Both
warping of peak profiles and of peak lists are supported.
Author: Jan Gerretzen <j.gerretzen@science.ru.nl>, Paul Eilers
<p.eilers@erasmusmc.nl>, Hans Wouters, Tom Bloemberg
<t.bloemberg@science.ru.nl>, Ron Wehrens <ron.wehrens@gmail.com>
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ptw versions 1.0-7 dated 2014-03-29 and 1.9-10 dated 2015-07-01
ptw-1.0-7/ptw/R/interpol.R |only ptw-1.0-7/ptw/inst/COPYRIGHT |only ptw-1.0-7/ptw/man/interpol.Rd |only ptw-1.9-10/ptw/DESCRIPTION | 21 ++-- ptw-1.9-10/ptw/MD5 | 71 ++++++++++----- ptw-1.9-10/ptw/NAMESPACE | 23 ++++- ptw-1.9-10/ptw/R/RMS.R | 12 +- ptw-1.9-10/ptw/R/WCC.R | 16 ++- ptw-1.9-10/ptw/R/asysm.R | 32 +++---- ptw-1.9-10/ptw/R/calc.multicoef.R | 119 ++++++++++++-------------- ptw-1.9-10/ptw/R/calc.zerocoef.R | 24 ++--- ptw-1.9-10/ptw/R/plot.ptw.R | 153 +++++++++++++++++----------------- ptw-1.9-10/ptw/R/pmwarp.R | 32 ++++--- ptw-1.9-10/ptw/R/predict.ptw.R | 11 +- ptw-1.9-10/ptw/R/ptw.R | 67 ++++++-------- ptw-1.9-10/ptw/R/summary.ptw.R | 9 +- ptw-1.9-10/ptw/R/warp.sample.R |only ptw-1.9-10/ptw/R/wccStick.R |only ptw-1.9-10/ptw/TODO |only ptw-1.9-10/ptw/build |only ptw-1.9-10/ptw/data/datalist | 4 ptw-1.9-10/ptw/data/gaschrom.RData |binary ptw-1.9-10/ptw/data/lcms.RData |binary ptw-1.9-10/ptw/inst/CITATION | 10 ++ ptw-1.9-10/ptw/inst/NEWS |only ptw-1.9-10/ptw/inst/doc |only ptw-1.9-10/ptw/man/RMS.Rd | 6 - ptw-1.9-10/ptw/man/asysm.Rd | 4 ptw-1.9-10/ptw/man/gaschrom.Rd | 39 ++++++++ ptw-1.9-10/ptw/man/lcms.Rd | 49 +++++++++- ptw-1.9-10/ptw/man/mzchannel2pktab.Rd |only ptw-1.9-10/ptw/man/plot.ptw.Rd | 64 +++++++------- ptw-1.9-10/ptw/man/ptw.Rd | 109 +++++++++++++++++++----- ptw-1.9-10/ptw/man/warp.time.Rd |only ptw-1.9-10/ptw/man/wcc.Rd | 32 +++++-- ptw-1.9-10/ptw/src/wccStick.c |only ptw-1.9-10/ptw/vignettes |only 37 files changed, 563 insertions(+), 344 deletions(-)
Title: Client for the HuffPost Pollster API
Description: Client for the HuffPost Pollster API, which provides
access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre],
Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between pollstR versions 1.2.0 dated 2015-03-09 and 1.2.1 dated 2015-07-01
pollstR-1.2.0/pollstR/inst/vign-src/figures |only pollstR-1.2.0/pollstR/inst/vign-src/introduction.md |only pollstR-1.2.1/pollstR/DESCRIPTION | 10 ++++----- pollstR-1.2.1/pollstR/MD5 | 21 ++++++++------------ pollstR-1.2.1/pollstR/NAMESPACE | 3 +- pollstR-1.2.1/pollstR/NEWS | 4 +++ pollstR-1.2.1/pollstR/R/pollstR-package.R | 1 pollstR-1.2.1/pollstR/build/vignette.rds |binary pollstR-1.2.1/pollstR/man/pollstR.Rd | 2 - pollstR-1.2.1/pollstR/man/pollstr_chart.Rd | 2 - pollstR-1.2.1/pollstR/man/pollstr_charts.Rd | 2 - pollstR-1.2.1/pollstR/man/pollstr_polls.Rd | 2 - 12 files changed, 25 insertions(+), 22 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 0.1-2 dated 2015-06-10 and 0.1-3 dated 2015-07-01
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NAMESPACE | 1 + inst/NEWS.Rd | 10 +++++++++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 2.2-2 dated 2014-12-04 and 2.2-3 dated 2015-07-01
DESCRIPTION | 12 ++--- MD5 | 14 ++--- NAMESPACE | 1 inst/NEWS.Rd | 11 ++++ man/Delaporte-package.Rd | 4 - man/Delaporte.Rd | 2 src/RcppExports.cpp | 104 +++++++++++++++++--------------------------- tests/testthat/test-delap.r | 40 ++++++++-------- 8 files changed, 90 insertions(+), 98 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.4.0 dated 2015-06-14 and 0.5.0 dated 2015-07-01
DESCRIPTION | 15 +++++---- MD5 | 41 ++++++++++++++------------ NAMESPACE | 2 + NEWS | 13 +++++++- R/add_sub.R |only R/draw.R | 69 ++++++++++++++++++++++++++++++++++++++------ R/plot_grid.R | 15 ++++++++- R/save.R | 4 +- inst/doc/axis_position.html | 4 +- inst/doc/introduction.R | 14 +++++--- inst/doc/introduction.Rmd | 14 +++++--- inst/doc/introduction.html | 14 ++++---- inst/doc/plot_grid.R | 10 ++++-- inst/doc/plot_grid.Rmd | 18 ++++++++--- inst/doc/plot_grid.html | 23 ++++++++------ man/add_sub.Rd |only man/draw_label.Rd |only man/draw_plot_label.Rd | 9 +++-- man/draw_text.Rd | 6 +-- man/ggsave.Rd | 4 +- man/plot_grid.Rd | 10 +++++- vignettes/introduction.Rmd | 14 +++++--- vignettes/plot_grid.Rmd | 18 ++++++++--- 23 files changed, 218 insertions(+), 99 deletions(-)
Title: Selection Bias Approach to Sensitivity Analysis for Causal
Effects
Description: The causalsens package provides functions to perform sensitivity analyses and to study how various assumptions about selection bias affects estimates of causal effects.
Author: Matthew Blackwell <mblackwell@gov.harvard.edu.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>
Diff between causalsens versions 0.1 dated 2013-04-21 and 0.1.1 dated 2015-07-01
causalsens-0.1.1/causalsens/DESCRIPTION | 18 ++++---- causalsens-0.1.1/causalsens/MD5 | 13 +++--- causalsens-0.1.1/causalsens/NAMESPACE | 22 +++++++++- causalsens-0.1.1/causalsens/R/causalsens.R | 41 ++++++++++---------- causalsens-0.1.1/causalsens/README.md | 6 +- causalsens-0.1.1/causalsens/build |only causalsens-0.1.1/causalsens/inst/doc/causalsens.R |only causalsens-0.1.1/causalsens/inst/doc/causalsens.pdf |binary causalsens-0.1/causalsens/vignettes/causalsens.R |only 9 files changed, 60 insertions(+), 40 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-1 dated 2015-06-26 and 1.0-2 dated 2015-07-01
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 5 +++++ R/save.R | 2 ++ inst/NEWS | 3 +++ inst/doc/arulesViz.pdf |binary 6 files changed, 21 insertions(+), 10 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.1-6 dated 2014-12-08 and 1.1-7 dated 2015-07-01
DESCRIPTION | 15 +--- MD5 | 148 +++++++++++++++++++++--------------------- NAMESPACE | 9 +- R/AAADefs.R | 2 R/crossTable.R | 41 +++++++++-- R/cut2.R | 4 - R/discretize.R | 4 - R/dissimilarity.R | 16 ++-- R/interestMeasures.R | 10 +- R/itemFrequency.R | 41 +++++------ R/random.transactions.R | 26 +++---- R/setsItemwise.R | 8 +- build/vignette.rds |binary data/Adult.rda |binary data/AdultUCI.rda |binary data/Epub.rda |binary data/Groceries.rda |binary data/Income.rda |binary data/IncomeESL.rda |binary inst/NEWS | 5 + inst/doc/arules.pdf |binary man/APappearance-class.Rd | 1 man/AScontrol-class.Rd | 1 man/ASparameter-class.Rd | 1 man/Adult.Rd | 3 man/Epub.Rd | 1 man/Groceries.Rd | 1 man/Income.Rd | 1 man/LIST.Rd | 1 man/Xtrct-methods.Rd | 1 man/addComplement.Rd | 1 man/affinity.Rd | 1 man/aggregate.Rd | 1 man/apriori.Rd | 4 - man/associations-class.Rd | 1 man/combine.Rd | 1 man/coverage.Rd | 1 man/crossTable.Rd | 20 ++++- man/discretize.Rd | 1 man/dissimilarity.Rd | 1 man/duplicated.Rd | 1 man/eclat.Rd | 3 man/image.Rd | 1 man/inspect.Rd | 1 man/interestMeasure.Rd | 3 man/is.closed.Rd | 1 man/is.maximal.Rd | 1 man/is.superset.Rd | 1 man/itemCoding.Rd | 1 man/itemFrequency.Rd | 1 man/itemFrequencyPlot.Rd | 3 man/itemMatrix-class.Rd | 1 man/itemsets-class.Rd | 1 man/length.Rd | 1 man/match.Rd | 1 man/merge.Rd | 1 man/pmml.Rd | 1 man/predict.Rd | 1 man/proximity-classes.Rd | 1 man/random.transactions.Rd | 1 man/read.transactions.Rd | 1 man/ruleInduction.Rd | 1 man/rules-class.Rd | 1 man/sample.Rd | 1 man/sets.Rd | 1 man/setsItemwise.Rd | 1 man/size.Rd | 1 man/sort.Rd | 1 man/subset.Rd | 1 man/support.Rd | 1 man/supportingTransactions.Rd | 1 man/tidLists-class.Rd | 1 man/transactions-class.Rd | 1 man/unique.Rd | 1 man/write.Rd | 1 75 files changed, 260 insertions(+), 153 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.3 dated 2015-03-01 and 1.5 dated 2015-07-01
archivist-1.3/archivist/vignettes |only archivist-1.5/archivist/DESCRIPTION | 8 archivist-1.5/archivist/MD5 | 83 ++---- archivist-1.5/archivist/NAMESPACE | 15 + archivist-1.5/archivist/R/ahistory.R |only archivist-1.5/archivist/R/archivist-package.R | 8 archivist-1.5/archivist/R/aread.R |only archivist-1.5/archivist/R/asearch.R |only archivist-1.5/archivist/R/loadFromRepo.R | 2 archivist-1.5/archivist/R/magrittr.R |only archivist-1.5/archivist/R/saveSetToRepo.R |only archivist-1.5/archivist/R/saveToRepo.R | 28 +- archivist-1.5/archivist/R/shinySearchInLocalRepo.R | 6 archivist-1.5/archivist/R/showRepo.R | 31 ++ archivist-1.5/archivist/R/zzz.R | 8 archivist-1.5/archivist/man/Repository.Rd | 97 ++++--- archivist-1.5/archivist/man/Tags.Rd | 235 ++++++++++++------ archivist-1.5/archivist/man/addTagsRepo.Rd | 103 +++---- archivist-1.5/archivist/man/ahistory.Rd |only archivist-1.5/archivist/man/archivist-package.Rd | 81 +++--- archivist-1.5/archivist/man/aread.Rd |only archivist-1.5/archivist/man/asearch.Rd |only archivist-1.5/archivist/man/cache.Rd | 91 +++---- archivist-1.5/archivist/man/copyToRepo.Rd | 120 ++++----- archivist-1.5/archivist/man/createEmptyRepo.Rd | 107 +++----- archivist-1.5/archivist/man/deleteRepo.Rd | 59 ++-- archivist-1.5/archivist/man/getTags.Rd | 153 +++++------ archivist-1.5/archivist/man/loadFromRepo.Rd | 165 +++++------- archivist-1.5/archivist/man/magrittr.Rd |only archivist-1.5/archivist/man/md5hash.Rd | 104 ++++---- archivist-1.5/archivist/man/rmFromRepo.Rd | 180 ++++++------- archivist-1.5/archivist/man/saveSetToRepo.Rd |only archivist-1.5/archivist/man/saveToRepo.Rd | 272 +++++++++------------ archivist-1.5/archivist/man/searchInRepo.Rd | 163 +++++------- archivist-1.5/archivist/man/setRepo.Rd | 182 ++++++-------- archivist-1.5/archivist/man/shinySearchInRepo.Rd | 92 +++---- archivist-1.5/archivist/man/showRepo.Rd | 161 ++++++------ archivist-1.5/archivist/man/summaryRepo.Rd | 100 +++---- archivist-1.5/archivist/man/zipRepo.Rd | 176 ++++++------- 39 files changed, 1407 insertions(+), 1423 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-1 dated 2015-05-15 and 1.1-2 dated 2015-06-30
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 6 ++++-- build/vignette.rds |binary data/USCA312.rda |binary data/USCA312_map.rda |binary data/USCA50.rda |binary inst/NEWS | 3 +++ inst/doc/TSP.pdf |binary 9 files changed, 20 insertions(+), 15 deletions(-)
Title: Infrastructure for Seriation
Description: Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.1-0 dated 2015-06-09 and 1.1-1 dated 2015-06-30
DESCRIPTION | 11 +-- MD5 | 48 +++++++-------- NAMESPACE | 7 +- R/dissimilartiy.R | 140 ++++++++++++++++++++++++++++++++++------------ R/permutation_vector.R | 18 +++-- R/permute.R | 2 R/pimage.R | 12 +-- build/vignette.rds |binary data/Chameleon.rda |binary data/Irish.rda |binary data/Munsingen.rda |binary data/Psych24.rda |binary data/Townships.rda |binary data/Wood.rda |binary data/Zoo.rda |binary inst/NEWS | 11 +++ inst/doc/seriation.pdf |binary man/col.Rd | 2 man/criterion.Rd | 1 man/dissimilarity.Rd | 66 +++++++++++++-------- man/get_order.Rd | 40 ++++++++----- man/hmap.Rd | 12 ++- man/permutation.Rd | 2 man/permutation_vector.Rd | 5 - man/pimage.Rd | 16 ++--- 25 files changed, 257 insertions(+), 136 deletions(-)
Title: Survey Sampling
Diff between sampling versions 2.6 dated 2013-11-08 and 2.7 dated 2015-06-30
Description: Functions for drawing and calibrating samples.
Author: Yves Tillé
Maintainer: Alina Matei <alina.matei@unine.ch>
sampling-2.6/sampling/R/gencalib.r |only
sampling-2.6/sampling/inst/doc/vignettes |only
sampling-2.7/sampling/DESCRIPTION | 8 -
sampling-2.7/sampling/MD5 | 53 +++++----
sampling-2.7/sampling/NAMESPACE | 2
sampling-2.7/sampling/R/HTstrata.r | 2
sampling-2.7/sampling/R/Hajekstrata.r | 17 +-
sampling-2.7/sampling/R/gencalib.R |only
sampling-2.7/sampling/R/getdata.r | 1
sampling-2.7/sampling/R/mstage.r | 98 +++++++++--------
sampling-2.7/sampling/R/varHT.r |only
sampling-2.7/sampling/build |only
sampling-2.7/sampling/data/MU284.rda |binary
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.R |only
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.Snw |only
sampling-2.7/sampling/inst/doc/HT_Hajek_estimators.pdf |only
sampling-2.7/sampling/inst/doc/UPexamples.R |only
sampling-2.7/sampling/inst/doc/UPexamples.Snw |only
sampling-2.7/sampling/inst/doc/UPexamples.pdf |only
sampling-2.7/sampling/inst/doc/calibration.R |only
sampling-2.7/sampling/inst/doc/calibration.Snw |only
sampling-2.7/sampling/inst/doc/calibration.pdf |only
sampling-2.7/sampling/man/Hajekstrata.Rd | 2
sampling-2.7/sampling/man/calibev.Rd | 10 -
sampling-2.7/sampling/man/gencalib.Rd | 2
sampling-2.7/sampling/man/mstage.Rd | 57 +++++++--
sampling-2.7/sampling/man/samplecube.Rd | 2
sampling-2.7/sampling/man/varHT.Rd |only
sampling-2.7/sampling/man/varest.Rd | 2
sampling-2.7/sampling/man/vartaylor_ratio.Rd | 8 -
sampling-2.7/sampling/vignettes |only
31 files changed, 156 insertions(+), 108 deletions(-)
Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG
website created by Mads Haahr samples atmospheric noise via radio tuned to
an unused broadcasting frequency together with a skew correction algorithm
due to John von Neumann. More background is available in the included
vignette based on an essay by Mads Haahr. In its current form, the package
offers functions to retrieve random integers, randomized sequences and
random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between random versions 0.2.4 dated 2015-05-17 and 0.2.5 dated 2015-06-30
ChangeLog | 10 ++++++++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + R/random.R | 8 ++++---- README.md | 3 ++- inst/doc/random-essay.pdf |binary inst/doc/random-intro.pdf |binary 8 files changed, 29 insertions(+), 17 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others,
functions for automatic language detection, hyphenation, several indices of
lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability
(e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language
corpora are also provided, to enable frequency analyses (supports Celex and
Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For
full functionality a local installation of TreeTagger is recommended. 'koRpus'
also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs
for its basic features. The respective R package 'rkward' cannot be installed
directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from https://rkward.kde.org (plugins are detected
automatically). Due to some restrictions on CRAN, the full package sources are
only available from the project homepage.
Author: m.eik michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: m.eik michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.05-5 dated 2014-03-19 and 0.05-6 dated 2015-06-30
koRpus-0.05-5/koRpus/inst/rkward/plugins/koRpus.js |only koRpus-0.05-5/koRpus/inst/rkward/plugins/koRpus.xml |only koRpus-0.05-5/koRpus/inst/rkward/rkwarddev_koRpus_plugin_script_NG.R |only koRpus-0.05-5/koRpus/inst/tests |only koRpus-0.05-5/koRpus/tests/test_koRpus_package.R |only koRpus-0.05-6/koRpus/ChangeLog | 25 koRpus-0.05-6/koRpus/DESCRIPTION | 40 koRpus-0.05-6/koRpus/MD5 | 267 +- koRpus-0.05-6/koRpus/NAMESPACE | 6 koRpus-0.05-6/koRpus/R/00_class_10_kRp.readability.R | 3 koRpus-0.05-6/koRpus/R/01_method_plot.kRp.tagged.R | 5 koRpus-0.05-6/koRpus/R/01_method_show.kRp.readability.R | 17 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.TTR.R | 1 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.lang.R | 5 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.readability.R | 13 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.tagged.R | 1 koRpus-0.05-6/koRpus/R/01_method_summary.kRp.txt.freq.R | 1 koRpus-0.05-6/koRpus/R/freq.analysis.R | 4 koRpus-0.05-6/koRpus/R/guess.lang.R | 6 koRpus-0.05-6/koRpus/R/kRp.POS.tags.R | 8 koRpus-0.05-6/koRpus/R/kRp.text.transform.R | 64 koRpus-0.05-6/koRpus/R/koRpus-internal.R | 20 koRpus-0.05-6/koRpus/R/koRpus-internal.lexdiv.formulae.R | 2 koRpus-0.05-6/koRpus/R/koRpus-internal.rdb.formulae.R | 269 +- koRpus-0.05-6/koRpus/R/koRpus-internal.rdb.params.grades.R | 1 koRpus-0.05-6/koRpus/R/koRpus-internal.roxy.all.R | 62 koRpus-0.05-6/koRpus/R/koRpus-package.R | 14 koRpus-0.05-6/koRpus/R/readability.R | 21 koRpus-0.05-6/koRpus/R/readability.num.R | 34 koRpus-0.05-6/koRpus/R/set.kRp.env.R | 3 koRpus-0.05-6/koRpus/R/treetag.R | 13 koRpus-0.05-6/koRpus/R/tuldava.R |only koRpus-0.05-6/koRpus/inst/CITATION | 8 koRpus-0.05-6/koRpus/inst/NEWS.Rd | 31 koRpus-0.05-6/koRpus/inst/doc/koRpus_vignette.pdf |binary koRpus-0.05-6/koRpus/inst/rkward/koRpus.pluginmap | 173 - koRpus-0.05-6/koRpus/inst/rkward/plugins/FrequencyAnalysis.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/FrequencyAnalysis.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Hyphenation.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Hyphenation.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/LexicalDiversity.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/LexicalDiversity.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Readability.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/Readability.xml |only koRpus-0.05-6/koRpus/inst/rkward/plugins/TokenizingPOStagging.js |only koRpus-0.05-6/koRpus/inst/rkward/plugins/TokenizingPOStagging.xml |only koRpus-0.05-6/koRpus/inst/rkward/rkwarddev_koRpus_plugin_script.R | 1319 ++++++---- koRpus-0.05-6/koRpus/inst/shiny/demo/server.R | 98 koRpus-0.05-6/koRpus/inst/shiny/demo/ui.R | 223 - koRpus-0.05-6/koRpus/man/ARI.Rd | 56 koRpus-0.05-6/koRpus/man/C.ld.Rd | 31 koRpus-0.05-6/koRpus/man/CTTR.Rd | 31 koRpus-0.05-6/koRpus/man/DRP.Rd | 39 koRpus-0.05-6/koRpus/man/ELF.Rd | 47 koRpus-0.05-6/koRpus/man/FOG.Rd | 72 koRpus-0.05-6/koRpus/man/FORCAST.Rd | 48 koRpus-0.05-6/koRpus/man/HDD.Rd | 44 koRpus-0.05-6/koRpus/man/K.ld.Rd | 31 koRpus-0.05-6/koRpus/man/LIX.Rd | 48 koRpus-0.05-6/koRpus/man/MATTR.Rd | 42 koRpus-0.05-6/koRpus/man/MSTTR.Rd | 31 koRpus-0.05-6/koRpus/man/MTLD.Rd | 74 koRpus-0.05-6/koRpus/man/R.ld.Rd | 31 koRpus-0.05-6/koRpus/man/RIX.Rd | 51 koRpus-0.05-6/koRpus/man/S.ld.Rd | 31 koRpus-0.05-6/koRpus/man/SMOG.Rd | 68 koRpus-0.05-6/koRpus/man/TRI.Rd | 41 koRpus-0.05-6/koRpus/man/TTR.Rd | 34 koRpus-0.05-6/koRpus/man/U.ld.Rd | 31 koRpus-0.05-6/koRpus/man/bormuth.Rd | 63 koRpus-0.05-6/koRpus/man/cTest-methods.Rd | 63 koRpus-0.05-6/koRpus/man/clozeDelete-methods.Rd | 62 koRpus-0.05-6/koRpus/man/coleman.Rd | 67 koRpus-0.05-6/koRpus/man/coleman.liau.Rd | 46 koRpus-0.05-6/koRpus/man/correct-methods.Rd | 122 koRpus-0.05-6/koRpus/man/dale.chall.Rd | 47 koRpus-0.05-6/koRpus/man/danielson.bryan.Rd | 40 koRpus-0.05-6/koRpus/man/dickes.steiwer.Rd | 40 koRpus-0.05-6/koRpus/man/farr.jenkins.paterson.Rd | 55 koRpus-0.05-6/koRpus/man/flesch.Rd | 62 koRpus-0.05-6/koRpus/man/flesch.kincaid.Rd | 39 koRpus-0.05-6/koRpus/man/freq.analysis.Rd | 114 koRpus-0.05-6/koRpus/man/fucks.Rd | 38 koRpus-0.05-6/koRpus/man/get.kRp.env.Rd | 41 koRpus-0.05-6/koRpus/man/guess.lang.Rd | 75 koRpus-0.05-6/koRpus/man/harris.jacobson.Rd | 84 koRpus-0.05-6/koRpus/man/hyph.XX.Rd | 72 koRpus-0.05-6/koRpus/man/hyphen.Rd | 132 - koRpus-0.05-6/koRpus/man/jumbleWords.Rd | 32 koRpus-0.05-6/koRpus/man/kRp.POS.tags.Rd | 129 koRpus-0.05-6/koRpus/man/kRp.TTR-class.Rd | 28 koRpus-0.05-6/koRpus/man/kRp.analysis-class.Rd | 7 koRpus-0.05-6/koRpus/man/kRp.cluster.Rd | 36 koRpus-0.05-6/koRpus/man/kRp.corp.freq-class.Rd | 69 koRpus-0.05-6/koRpus/man/kRp.filter.wclass.Rd | 31 koRpus-0.05-6/koRpus/man/kRp.hyph.pat-class.Rd | 15 koRpus-0.05-6/koRpus/man/kRp.hyphen-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.lang-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.readability-class.Rd | 74 koRpus-0.05-6/koRpus/man/kRp.tagged-class.Rd | 29 koRpus-0.05-6/koRpus/man/kRp.taggedText-methods.Rd | 23 koRpus-0.05-6/koRpus/man/kRp.text.analysis.Rd | 107 koRpus-0.05-6/koRpus/man/kRp.text.paste.Rd | 20 koRpus-0.05-6/koRpus/man/kRp.text.transform.Rd | 58 koRpus-0.05-6/koRpus/man/kRp.txt.freq-class.Rd | 5 koRpus-0.05-6/koRpus/man/kRp.txt.trans-class.Rd | 19 koRpus-0.05-6/koRpus/man/koRpus-package.Rd | 56 koRpus-0.05-6/koRpus/man/lex.div.Rd | 342 +- koRpus-0.05-6/koRpus/man/lex.div.num.Rd | 55 koRpus-0.05-6/koRpus/man/linsear.write.Rd | 39 koRpus-0.05-6/koRpus/man/maas.Rd | 34 koRpus-0.05-6/koRpus/man/manage.hyph.pat.Rd | 83 koRpus-0.05-6/koRpus/man/nWS.Rd | 72 koRpus-0.05-6/koRpus/man/plot-methods.Rd | 48 koRpus-0.05-6/koRpus/man/query-methods.Rd | 117 koRpus-0.05-6/koRpus/man/read.BAWL.Rd | 41 koRpus-0.05-6/koRpus/man/read.corp.LCC.Rd | 77 koRpus-0.05-6/koRpus/man/read.corp.celex.Rd | 19 koRpus-0.05-6/koRpus/man/read.corp.custom.Rd | 65 koRpus-0.05-6/koRpus/man/read.hyph.pat.Rd | 42 koRpus-0.05-6/koRpus/man/read.tagged.Rd | 115 koRpus-0.05-6/koRpus/man/readability.Rd | 897 +++--- koRpus-0.05-6/koRpus/man/readability.num.Rd | 135 - koRpus-0.05-6/koRpus/man/segment.optimizer.Rd | 64 koRpus-0.05-6/koRpus/man/set.kRp.env.Rd | 42 koRpus-0.05-6/koRpus/man/show-methods.Rd | 33 koRpus-0.05-6/koRpus/man/spache.Rd | 46 koRpus-0.05-6/koRpus/man/strain.Rd | 39 koRpus-0.05-6/koRpus/man/summary-methods.Rd | 47 koRpus-0.05-6/koRpus/man/textFeatures.Rd | 67 koRpus-0.05-6/koRpus/man/tokenize.Rd | 195 - koRpus-0.05-6/koRpus/man/traenkle.bailer.Rd | 41 koRpus-0.05-6/koRpus/man/treetag.Rd | 268 -- koRpus-0.05-6/koRpus/man/tuldava.Rd |only koRpus-0.05-6/koRpus/man/wheeler.smith.Rd | 66 koRpus-0.05-6/koRpus/tests/testthat |only koRpus-0.05-6/koRpus/tests/testthat.R |only 137 files changed, 4388 insertions(+), 4349 deletions(-)
Title: Coercion Routines for Network Data Objects
Description: Functions implemented in this package allow to coerce (i.e.
convert) network data between classes provided by other R packages.
Currently supported classes are those defined in packages: network and
igraph.
Author: Michal Bojanowski
Maintainer: Michal Bojanowski <m.bojanowski@icm.edu.pl>
Diff between intergraph versions 2.0-1 dated 2015-01-17 and 2.0-2 dated 2015-06-30
DESCRIPTION | 10 ++++----- MD5 | 42 ++++++++++++++++++------------------- NAMESPACE | 2 - R/attrmap.R | 4 +-- R/netcompare.R | 4 +-- README.md | 1 build/vignette.rds |binary data/exIgraph.rda |binary data/exIgraph2.rda |binary inst/doc/howto.R | 5 ++-- inst/doc/howto.Rmd | 9 ++++---- inst/doc/howto.html | 50 ++++++++++++--------------------------------- inst/tests/test-asIgraph.R | 4 +-- man/as.matrix.igraph.Rd | 2 - man/asDF.Rd | 2 - man/asIgraph.Rd | 2 - man/asNetwork.Rd | 2 - man/attrmap.Rd | 2 - man/dumpAttr.Rd | 2 - man/exNetwork.Rd | 2 - man/intergraph-package.Rd | 2 - man/netcompare.Rd | 2 - 22 files changed, 65 insertions(+), 84 deletions(-)
Title: Information Retrieval for Genetic Datasets
Description: Information retrieval from National Center for Biotechnology Information (NCBI) databases, with main focus on identifying genes in unannotated organisms via Blast similarity search in annotated organisms.
Author: Daniel Fischer [aut, cre],
Anu Sironen [aut]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between hoardeR versions 0.0-2 dated 2014-06-06 and 0.1 dated 2015-06-30
DESCRIPTION | 26 +++++++---- MD5 | 69 +++++++++++++++++++++++-------- NAMESPACE | 20 +++++++-- R/blastSeq.R | 106 +++++++++++++++++++++++++++++++++++++++++------- R/getAssemblies.R |only R/getBlastResult.R | 6 +- R/getEnsgInfo.R | 5 +- R/helpFunctions.R |only R/importBlastTab.R |only R/importFA.R | 1 R/importGTF.R | 15 +++--- R/importPedMap.R |only R/importVCF.R |only R/importXML.R | 24 +++++----- R/plot.xmlImport.R |only R/print.ensgInfo.R |only R/print.fa.R |only R/print.pedMap.R |only R/print.xmlImport.R |only R/speciesFigure.R |only R/subDose.R |only R/subGProbs.R |only R/subPhased.R |only R/summary.ensgInfo.R |only R/summary.fa.R |only R/summary.pedMap.R |only R/summary.xmlImport.R |only ToDo | 2 data |only inst/ChangeLog | 16 +++++++ inst/extdata |only man/blastSeq.Rd | 23 +++++++--- man/getAssemblies.Rd |only man/getEnsgInfo.Rd | 2 man/getGeneLocation.Rd | 2 man/hoardeR-package.Rd | 16 +++---- man/importBlastTab.Rd |only man/importFA.Rd | 82 +++++++++++++++++++------------------ man/importGTF.Rd | 6 +- man/importPedMap.Rd |only man/importXML.Rd | 7 +-- man/print.ensgInfo.Rd |only man/print.fa.Rd |only man/print.pedMap.Rd |only man/print.xmlImport.Rd |only man/species.Rd |only man/speciesFigure.Rd |only man/subDose.Rd |only man/subGprobs.Rd |only man/subPhased.Rd |only man/summary.ensgInfo.Rd |only man/summary.fa.Rd |only man/summary.pedMap.Rd |only 53 files changed, 297 insertions(+), 131 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, and full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 4.1 dated 2015-04-01 and 4.2 dated 2015-06-30
CARBayes-4.1/CARBayes/R/S.CARcluster.R |only CARBayes-4.1/CARBayes/R/binomial.clusterCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.bymCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.clusterCAR.R |only CARBayes-4.1/CARBayes/R/gaussian.independent.R |only CARBayes-4.1/CARBayes/R/poisson.clusterCAR.R |only CARBayes-4.1/CARBayes/R/poisson.clusterCARagg.R |only CARBayes-4.1/CARBayes/man/S.CARcluster.Rd |only CARBayes-4.2/CARBayes/DESCRIPTION | 16 - CARBayes-4.2/CARBayes/MD5 | 85 +++--- CARBayes-4.2/CARBayes/NAMESPACE | 7 CARBayes-4.2/CARBayes/R/S.CARbym.R | 9 CARBayes-4.2/CARBayes/R/S.CARlocalised.R |only CARBayes-4.2/CARBayes/R/S.independent.R | 9 CARBayes-4.2/CARBayes/R/binomial.bymCAR.R | 26 + CARBayes-4.2/CARBayes/R/binomial.dissimilarityCAR.R | 38 +- CARBayes-4.2/CARBayes/R/binomial.iarCAR.R | 33 +- CARBayes-4.2/CARBayes/R/binomial.independent.R | 15 - CARBayes-4.2/CARBayes/R/binomial.lerouxCAR.R | 29 +- CARBayes-4.2/CARBayes/R/binomial.localisedCAR.R |only CARBayes-4.2/CARBayes/R/combine.data.shapefile.R | 8 CARBayes-4.2/CARBayes/R/gaussian.dissimilarityCAR.R | 67 +++- CARBayes-4.2/CARBayes/R/gaussian.iarCAR.R | 50 ++- CARBayes-4.2/CARBayes/R/gaussian.lerouxCAR.R | 41 +-- CARBayes-4.2/CARBayes/R/poisson.bymCAR.R | 26 + CARBayes-4.2/CARBayes/R/poisson.dissimilarityCAR.R | 38 +- CARBayes-4.2/CARBayes/R/poisson.iarCAR.R | 33 +- CARBayes-4.2/CARBayes/R/poisson.independent.R | 17 - CARBayes-4.2/CARBayes/R/poisson.lerouxCAR.R | 28 +- CARBayes-4.2/CARBayes/R/poisson.localisedCAR.R |only CARBayes-4.2/CARBayes/R/poisson.localisedCARagg.R |only CARBayes-4.2/CARBayes/R/print.carbayes.R | 83 ++++-- CARBayes-4.2/CARBayes/R/summarise.lincomb.R | 3 CARBayes-4.2/CARBayes/build/vignette.rds |binary CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.R | 53 +-- CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.Rnw | 152 +++++------ CARBayes-4.2/CARBayes/inst/doc/CARBayesvignette.pdf |binary CARBayes-4.2/CARBayes/man/CARBayes-package.Rd | 51 --- CARBayes-4.2/CARBayes/man/S.CARbym.Rd | 58 ++-- CARBayes-4.2/CARBayes/man/S.CARdissimilarity.Rd | 31 +- CARBayes-4.2/CARBayes/man/S.CARiar.Rd | 29 +- CARBayes-4.2/CARBayes/man/S.CARleroux.Rd | 29 +- CARBayes-4.2/CARBayes/man/S.CARlocalised.Rd |only CARBayes-4.2/CARBayes/man/S.independent.Rd | 33 +- CARBayes-4.2/CARBayes/man/combine.data.shapefile.Rd | 6 CARBayes-4.2/CARBayes/man/highlight.borders.Rd | 2 CARBayes-4.2/CARBayes/man/print.carbayes.Rd | 10 CARBayes-4.2/CARBayes/src/RcppExports.cpp | 256 ++++++++----------- CARBayes-4.2/CARBayes/vignettes/CARBayesvignette.Rnw | 152 +++++------ CARBayes-4.2/CARBayes/vignettes/jss996.bib | 46 ++- 50 files changed, 831 insertions(+), 738 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.2 dated 2015-05-31 and 3.98-1.3 dated 2015-06-30
DESCRIPTION | 11 ++++------- MD5 | 6 +++--- NAMESPACE | 1 + man/readHTMLTable.Rd | 34 +++++++++++++++++++++------------- 4 files changed, 29 insertions(+), 23 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.8-0 dated 2015-06-26 and 1.9-0 dated 2015-06-30
DESCRIPTION | 14 ++--- MD5 | 41 ++++++++------- NAMESPACE | 71 +++++++++++++++++++-------- R/acceleration_algorithm.R |only R/calc_exp_TK.R | 1 R/calc_posterior.v2.R | 9 +-- R/calc_prob.v5.R | 2 R/stud_prior.R | 28 ++++------ R/tam.fa.R | 4 - R/tam.latreg.R | 2 R/tam.mml.2pl.R | 76 ++++++++++++++++++++++++++-- R/tam.mml.3pl.R | 118 ++++++++++++++++++++++++++++++++++++++++++--- R/tam.mml.3pl.preproc.R | 4 + R/tam.mml.R | 59 ++++++++++++++++++++-- R/tam.mml.mfr.R | 64 +++++++++++++++++++----- R/tam.pv.R | 2 R/tam.se.R | 6 +- inst/NEWS | 24 +++++++++ man/TAM-internal.Rd | 2 man/TAM-package.Rd | 2 man/tam.mml.Rd | 55 ++++++++++++++++++++ man/tamaanify.Rd | 2 22 files changed, 471 insertions(+), 115 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between RCurl versions 1.95-4.6 dated 2015-04-24 and 1.95-4.7 dated 2015-06-30
RCurl-1.95-4.6/RCurl/FAQ.html |only RCurl-1.95-4.6/RCurl/cacert.pem |only RCurl-1.95-4.7/RCurl/DESCRIPTION | 16 ++++++----- RCurl-1.95-4.7/RCurl/MD5 | 36 +++++++++++++------------ RCurl-1.95-4.7/RCurl/R/zzz.R |only RCurl-1.95-4.7/RCurl/inst/doc/FAQ.html |only RCurl-1.95-4.7/RCurl/inst/doc/philosophy.html | 24 +++++++++------- RCurl-1.95-4.7/RCurl/inst/etc |only RCurl-1.95-4.7/RCurl/man/basicTextGatherer.Rd | 9 ++++-- RCurl-1.95-4.7/RCurl/man/curlPerform.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/dynCurlReader.Rd | 6 ++-- RCurl-1.95-4.7/RCurl/man/ftpUpload.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getBinaryURL.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getCurlHandle.Rd | 3 +- RCurl-1.95-4.7/RCurl/man/getURIAsynchronous.Rd | 7 ++-- RCurl-1.95-4.7/RCurl/man/getURL.Rd | 8 +++-- RCurl-1.95-4.7/RCurl/man/guessMIMEType.Rd | 5 +-- RCurl-1.95-4.7/RCurl/man/mimeTypeExtensions.Rd | 4 +- RCurl-1.95-4.7/RCurl/man/postForm.Rd | 11 ++++--- RCurl-1.95-4.7/RCurl/man/scp.Rd | 6 ++-- RCurl-1.95-4.7/RCurl/tests/dynSetReader.R | 4 +- 21 files changed, 85 insertions(+), 63 deletions(-)
Title: Function to Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of
sequences (treatment sequences).
If a blocksize is given, the randomization will be done within blocks.
The randomization may be controlled by a Wald-Wolfowitz runs test.
Functions to obtain the p-value of that test are included.
The package is mainly intended for randomization of bioequivalence studies
but may be used also for other clinical crossover studies.
Contains two helper functions sequences() and williams() to get the sequences
of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>
Diff between randomizeBE versions 0.3-1 dated 2012-12-27 and 0.3-2 dated 2015-06-30
DESCRIPTION | 31 ++++++++++++++++--------------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ NEWS | 4 ++++ man/pruns.exact.Rd | 3 --- man/runs.pvalue.Rd | 6 ++---- man/sequences.Rd | 2 +- 7 files changed, 32 insertions(+), 29 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between phenology versions 4.2 dated 2015-05-09 and 4.2.4 dated 2015-06-30
phenology-4.2.4/phenology/DESCRIPTION | 11 phenology-4.2.4/phenology/MD5 | 49 - phenology-4.2.4/phenology/NAMESPACE | 8 phenology-4.2.4/phenology/NEWS | 12 phenology-4.2.4/phenology/R/LikelihoodRMU.R |only phenology-4.2.4/phenology/R/Likelihood_phenology.R | 28 phenology-4.2.4/phenology/R/Lnegbin.R | 12 phenology-4.2.4/phenology/R/add_phenology.R | 24 phenology-4.2.4/phenology/R/fitRMU.R | 546 +++++++++++++----- phenology-4.2.4/phenology/R/fitRMU_MHmcmc.R |only phenology-4.2.4/phenology/R/fitRMU_MHmcmc_p.R |only phenology-4.2.4/phenology/R/fit_phenology.R | 8 phenology-4.2.4/phenology/R/format_par.R | 2 phenology-4.2.4/phenology/R/logLik.fitRMU.R |only phenology-4.2.4/phenology/R/phenology-package.R | 32 - phenology-4.2.4/phenology/R/phenology_MHmcmc.R |only phenology-4.2.4/phenology/R/phenology_MHmcmc_p.R | 29 phenology-4.2.4/phenology/R/plot.fitRMU.R |only phenology-4.2.4/phenology/R/plot.phenology.R | 51 - phenology-4.2.4/phenology/man/add_phenology.Rd | 7 phenology-4.2.4/phenology/man/fitRMU.Rd | 132 +++- phenology-4.2.4/phenology/man/fitRMU_MHmcmc.Rd |only phenology-4.2.4/phenology/man/fitRMU_MHmcmc_p.Rd |only phenology-4.2.4/phenology/man/likelihood_phenology.Rd | 2 phenology-4.2.4/phenology/man/logLik.fitRMU.Rd |only phenology-4.2.4/phenology/man/phenology-package.Rd | 34 - phenology-4.2.4/phenology/man/phenology_MHmcmc.Rd | 8 phenology-4.2.4/phenology/man/plot.fitRMU.Rd |only phenology-4.2.4/phenology/man/plot.phenology.Rd | 2 phenology-4.2/phenology/R/Script_MCMC.r |only phenology-4.2/phenology/R/fonctionfit.R |only phenology-4.2/phenology/R/phenology_fonctionMCMC.R |only 32 files changed, 717 insertions(+), 280 deletions(-)
Title: Wrapper Functions for MAESTRA/MAESPA
Description: A bundle of functions for modifying MAESTRA/MAESPA input files,reading output files, and visualizing the stand in 3D. Handy for running sensitivity analyses, scenario analyses, etc.
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between Maeswrap versions 1.4.11 dated 2012-05-25 and 1.7 dated 2015-06-30
Maeswrap-1.4.11/Maeswrap/R/Maeswrap-internal.R |only Maeswrap-1.4.11/Maeswrap/R/replacePAR.R |only Maeswrap-1.4.11/Maeswrap/R/trim.R |only Maeswrap-1.4.11/Maeswrap/man/BatchUtilities.Rd |only Maeswrap-1.4.11/Maeswrap/man/addarrow.Rd |only Maeswrap-1.4.11/Maeswrap/man/readPAR.Rd |only Maeswrap-1.4.11/Maeswrap/man/replaceNAMELIST.Rd |only Maeswrap-1.4.11/Maeswrap/man/utilities.Rd |only Maeswrap-1.7/Maeswrap/DESCRIPTION | 16 - Maeswrap-1.7/Maeswrap/MD5 | 100 +++++----- Maeswrap-1.7/Maeswrap/NAMESPACE | 44 ++++ Maeswrap-1.7/Maeswrap/R/Maeswrap-package.R |only Maeswrap-1.7/Maeswrap/R/Openstand.R | 23 +- Maeswrap-1.7/Maeswrap/R/Plotstand.R | 215 ++++++++++++++++++----- Maeswrap-1.7/Maeswrap/R/addarrow.R | 16 - Maeswrap-1.7/Maeswrap/R/checkwatbal.R | 14 + Maeswrap-1.7/Maeswrap/R/coord3dshape.R | 5 Maeswrap-1.7/Maeswrap/R/crownsurface.R |only Maeswrap-1.7/Maeswrap/R/delempty.R | 3 Maeswrap-1.7/Maeswrap/R/maesparunall.R | 104 +++++++++++ Maeswrap-1.7/Maeswrap/R/maestrarunall.R | 2 Maeswrap-1.7/Maeswrap/R/maybeQuote.R | 5 Maeswrap-1.7/Maeswrap/R/parseFile.R |only Maeswrap-1.7/Maeswrap/R/parsePARline.R |only Maeswrap-1.7/Maeswrap/R/plot3dtriangles.R | 7 Maeswrap-1.7/Maeswrap/R/plottree.R | 2 Maeswrap-1.7/Maeswrap/R/plotuspar.R | 119 ++++++++---- Maeswrap-1.7/Maeswrap/R/printme.R | 3 Maeswrap-1.7/Maeswrap/R/randomstand.R |only Maeswrap-1.7/Maeswrap/R/readNameList.R |only Maeswrap-1.7/Maeswrap/R/readPAR.R | 128 ++++++------- Maeswrap-1.7/Maeswrap/R/readdayflux.R | 24 ++ Maeswrap-1.7/Maeswrap/R/readhrflux.R | 28 ++ Maeswrap-1.7/Maeswrap/R/readmet.R | 32 ++- Maeswrap-1.7/Maeswrap/R/readuspar.R | 22 +- Maeswrap-1.7/Maeswrap/R/readwatbal.R | 29 ++- Maeswrap-1.7/Maeswrap/R/replaceNAMELIST.R | 164 ++++++++++++----- Maeswrap-1.7/Maeswrap/R/replacemetdata.R | 72 ++++--- Maeswrap-1.7/Maeswrap/R/replacemetvar.R | 71 ++++++- Maeswrap-1.7/Maeswrap/R/revchar.R | 39 ++++ Maeswrap-1.7/Maeswrap/R/runmaespa.R | 148 ++++++++------- Maeswrap-1.7/Maeswrap/R/runmaestra.R | 2 Maeswrap-1.7/Maeswrap/R/trynumeric.R |only Maeswrap-1.7/Maeswrap/R/writeListToFile.R |only Maeswrap-1.7/Maeswrap/man/Maeswrap-package.Rd | 41 ++-- Maeswrap-1.7/Maeswrap/man/Plotstand.Rd | 169 ++++++++++-------- Maeswrap-1.7/Maeswrap/man/batchutil.Rd |only Maeswrap-1.7/Maeswrap/man/checkwatbal.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/maeswrapdefinitions.Rd | 20 +- Maeswrap-1.7/Maeswrap/man/parseFile.Rd |only Maeswrap-1.7/Maeswrap/man/plotuspar.Rd | 70 ++++--- Maeswrap-1.7/Maeswrap/man/randomstand.Rd |only Maeswrap-1.7/Maeswrap/man/readNameList.Rd |only Maeswrap-1.7/Maeswrap/man/readdayflux.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/readhrflux.Rd | 23 +- Maeswrap-1.7/Maeswrap/man/readmet.Rd | 28 +- Maeswrap-1.7/Maeswrap/man/readwatbal.Rd | 23 +- Maeswrap-1.7/Maeswrap/man/replacePAR.Rd | 68 ++++--- Maeswrap-1.7/Maeswrap/man/replacemetvar.Rd | 59 +++--- Maeswrap-1.7/Maeswrap/man/revchar.Rd | 42 ++-- Maeswrap-1.7/Maeswrap/man/runfiletest.Rd | 21 +- 61 files changed, 1370 insertions(+), 687 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions in
Causal Models
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.1.1 dated 2015-04-28 and 1.1.3 dated 2015-06-30
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 4 +++- NEWS |only R/id.R | 7 +++---- R/idc.R | 5 +++-- R/observed.graph.R | 6 +++--- R/unobserved.graph.R | 2 +- man/causaleffect-package.Rd | 7 +++---- 9 files changed, 28 insertions(+), 26 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.2 dated 2015-06-29 and 1.1.3 dated 2015-06-30
stochvol-1.1.2/stochvol/vignettes/heavytails.R |only stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only stochvol-1.1.2/stochvol/vignettes/heavytails.tex |only stochvol-1.1.3/stochvol/DESCRIPTION | 6 +++--- stochvol-1.1.3/stochvol/MD5 | 17 +++++++++-------- stochvol-1.1.3/stochvol/NEWS | 3 +++ stochvol-1.1.3/stochvol/build/vignette.rds |binary stochvol-1.1.3/stochvol/inst/doc/article.pdf |binary stochvol-1.1.3/stochvol/inst/doc/heavytails.R |only stochvol-1.1.3/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.3/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.3/stochvol/vignettes/Makefile | 2 +- stochvol-1.1.3/stochvol/vignettes/heavytails.Rnw |only 13 files changed, 16 insertions(+), 12 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.4 dated 2015-05-28 and 1.5 dated 2015-06-30
DESCRIPTION | 19 ++--- MD5 | 12 +-- NAMESPACE | 20 ++++- R/forestFloor_source.R | 166 +++++++++++++++++++++------------------------ man/forestFloor-package.Rd | 5 - man/plot.forestFloor.Rd | 39 ++-------- tests/stdUsage.R | 12 ++- 7 files changed, 130 insertions(+), 143 deletions(-)
Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts
Consortium
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between climdex.pcic versions 1.1-5.1 dated 2015-03-13 and 1.1-6 dated 2015-06-30
CHANGELOG | 6 + DESCRIPTION | 8 +- MD5 | 102 ++++++++++++++-------------- R/climdex.r | 80 ++++++++++++++------- man/climdex.cdd.Rd | 2 man/climdex.csdi.Rd | 2 man/climdex.cwd.Rd | 2 man/climdex.dtr.Rd | 2 man/climdex.fd.Rd | 2 man/climdex.get.available.indices.Rd | 2 man/climdex.gsl.Rd | 2 man/climdex.id.Rd | 2 man/climdex.pcic.Rd | 2 man/climdex.prcptot.Rd | 2 man/climdex.quantile.Rd | 2 man/climdex.r10mm.Rd | 2 man/climdex.r20mm.Rd | 2 man/climdex.r95ptot.Rd | 2 man/climdex.r99ptot.Rd | 2 man/climdex.rnnmm.Rd | 2 man/climdex.rx1day.Rd | 2 man/climdex.rx5day.Rd | 2 man/climdex.sdii.Rd | 2 man/climdex.su.Rd | 2 man/climdex.tn10p.Rd | 2 man/climdex.tn90p.Rd | 2 man/climdex.tnn.Rd | 2 man/climdex.tnx.Rd | 2 man/climdex.tr.Rd | 2 man/climdex.tx10p.Rd | 2 man/climdex.tx90p.Rd | 2 man/climdex.txn.Rd | 2 man/climdex.txx.Rd | 2 man/climdex.wsdi.Rd | 2 man/climdexInput.Rd | 7 + man/climdexInput.csv.Rd | 4 - man/climdexInput.raw.Rd | 78 +++++++++++++++++++-- man/ec.1018935.Rd | 2 man/get.last.monthday.of.year.Rd | 2 man/get.outofbase.quantiles.Rd | 4 - man/get.series.lengths.at.ends.Rd | 2 man/growing.season.length.Rd | 2 man/nday.consec.prec.max.Rd | 2 man/number.days.op.threshold.Rd | 2 man/percent.days.op.threshold.Rd | 2 man/select.blocks.gt.length.Rd | 2 man/simple.precipitation.intensity.index.Rd | 2 man/spell.length.max.Rd | 2 man/threshold.exceedance.duration.index.Rd | 2 man/total.precip.op.threshold.Rd | 2 src/zhang_running_quantile.cc | 4 - tests/test_primitives.R | 2 52 files changed, 239 insertions(+), 140 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.1 dated 2015-05-22 and 1.1.2 dated 2015-06-29
stochvol-1.1.1/stochvol/inst/doc/heavytails.R |only stochvol-1.1.1/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.1/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.1/stochvol/vignettes/heavytails.Rnw |only stochvol-1.1.2/stochvol/DESCRIPTION | 10 +++++----- stochvol-1.1.2/stochvol/MD5 | 22 ++++++++++------------ stochvol-1.1.2/stochvol/NAMESPACE | 3 +++ stochvol-1.1.2/stochvol/NEWS | 3 +++ stochvol-1.1.2/stochvol/build/vignette.rds |binary stochvol-1.1.2/stochvol/data/exrates.RData |binary stochvol-1.1.2/stochvol/inst/doc/article.pdf |binary stochvol-1.1.2/stochvol/src/sampler.cpp | 4 ++-- stochvol-1.1.2/stochvol/vignettes/Makefile | 2 +- stochvol-1.1.2/stochvol/vignettes/heavytails.R |only stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only 15 files changed, 24 insertions(+), 20 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 0.98 dated 2015-03-30 and 0.99 dated 2015-06-29
DESCRIPTION | 14 +++++++------- MD5 | 10 ++++++---- NAMESPACE | 11 ++++++++--- NEWS | 25 ++++++++++++++++++------- R/mi.t.test.R |only man/0MKmisc-package.Rd | 14 ++++++++------ man/mi.t.test.Rd |only 7 files changed, 47 insertions(+), 27 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.1 dated 2015-05-17 and 1.2 dated 2015-06-29
HelpersMG-1.1/HelpersMG/R/getTide.R |only HelpersMG-1.1/HelpersMG/R/moon_phase.R |only HelpersMG-1.1/HelpersMG/R/temperature.periodic.R |only HelpersMG-1.1/HelpersMG/man/getTide.Rd |only HelpersMG-1.1/HelpersMG/man/moon_phase.Rd |only HelpersMG-1.1/HelpersMG/man/temperature.periodic.Rd |only HelpersMG-1.2/HelpersMG/DESCRIPTION | 10 - HelpersMG-1.2/HelpersMG/MD5 | 49 +++++---- HelpersMG-1.2/HelpersMG/NAMESPACE | 14 ++ HelpersMG-1.2/HelpersMG/NEWS | 11 +- HelpersMG-1.2/HelpersMG/R/HelpersMG-package.R | 7 - HelpersMG-1.2/HelpersMG/R/LD50.R |only HelpersMG-1.2/HelpersMG/R/LD50_fit.R |only HelpersMG-1.2/HelpersMG/R/MHalgoGen.R | 2 HelpersMG-1.2/HelpersMG/R/compare_AIC.R | 5 HelpersMG-1.2/HelpersMG/R/ind_long_lat.R | 8 - HelpersMG-1.2/HelpersMG/R/index.periodic.R |only HelpersMG-1.2/HelpersMG/R/logLik.LD50.R |only HelpersMG-1.2/HelpersMG/R/minmax.periodic.R | 104 +++++++++++++------- HelpersMG-1.2/HelpersMG/R/moon.info.R |only HelpersMG-1.2/HelpersMG/R/plot.LD50.R |only HelpersMG-1.2/HelpersMG/R/predict.LD50.R |only HelpersMG-1.2/HelpersMG/R/sun.info.R | 7 - HelpersMG-1.2/HelpersMG/R/tide.info.R |only HelpersMG-1.2/HelpersMG/man/HelpersMG-package.Rd | 7 - HelpersMG-1.2/HelpersMG/man/LD50.Rd |only HelpersMG-1.2/HelpersMG/man/compare_AIC.Rd | 5 HelpersMG-1.2/HelpersMG/man/ind_long_lat.Rd | 8 - HelpersMG-1.2/HelpersMG/man/index.periodic.Rd |only HelpersMG-1.2/HelpersMG/man/logLik.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/minmax.periodic.Rd | 46 +++++--- HelpersMG-1.2/HelpersMG/man/moon.info.Rd |only HelpersMG-1.2/HelpersMG/man/plot.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/predict.LD50.Rd |only HelpersMG-1.2/HelpersMG/man/sun.info.Rd | 11 +- HelpersMG-1.2/HelpersMG/man/tide.info.Rd |only 36 files changed, 192 insertions(+), 102 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal causality based on evidence from functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.0.2 dated 2015-03-04 and 2.1.0 dated 2015-06-29
FunChisq-2.0.2/FunChisq/src/AdjustPvalue.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqDirTest.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqTests.cpp |only FunChisq-2.0.2/FunChisq/src/ChisqTests.h |only FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.cpp |only FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.h |only FunChisq-2.0.2/FunChisq/src/StatDistributions.cpp |only FunChisq-2.0.2/FunChisq/src/StatDistributions.h |only FunChisq-2.0.2/FunChisq/src/TransitionTable.cpp |only FunChisq-2.0.2/FunChisq/src/TransitionTable.h |only FunChisq-2.1.0/FunChisq/DESCRIPTION | 15 FunChisq-2.1.0/FunChisq/MD5 | 37 FunChisq-2.1.0/FunChisq/NAMESPACE | 1 FunChisq-2.1.0/FunChisq/NEWS | 12 FunChisq-2.1.0/FunChisq/R/FunChisq.R | 17 FunChisq-2.1.0/FunChisq/inst/CITATION | 4 FunChisq-2.1.0/FunChisq/man/FunChisq-package.Rd | 13 FunChisq-2.1.0/FunChisq/man/cp.fun.chisq.test.Rd | 6 FunChisq-2.1.0/FunChisq/man/fun.chisq.test.Rd | 2 FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.cpp | 918 +++++++++++------ FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.h | 180 ++- FunChisq-2.1.0/FunChisq/src/Makevars |only FunChisq-2.1.0/FunChisq/src/Makevars.win |only FunChisq-2.1.0/FunChisq/src/define.h |only FunChisq-2.1.0/FunChisq/src/main.cpp | 22 FunChisq-2.1.0/FunChisq/tests/testthat/test_FunChisq.R | 9 26 files changed, 820 insertions(+), 416 deletions(-)
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture.
Example analyses are included. Includes functions for plotting field
designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.11 dated 2015-03-03 and 1.12 dated 2015-06-29
DESCRIPTION | 10 +-- MD5 | 98 +++++++++++++++++++++------------------ NAMESPACE | 3 + NEWS | 23 ++++++--- R/desplot.r | 27 ++++++---- R/gge.r | 4 - build/vignette.rds |binary data/cochran.beets.txt.gz |only data/cochran.lattice.txt.gz |only data/datalist | 4 + data/jansen.apple.txt.gz |only data/jansen.carrot.txt.gz |only data/karcher.turfgrass.txt.gz |binary inst/doc/agridat_examples.Rnw | 16 +++--- inst/doc/agridat_examples.pdf |binary man/agridat.Rd | 36 +++++++++++--- man/beall.webworms.Rd | 4 - man/besag.bayesian.Rd | 2 man/besag.beans.Rd | 2 man/besag.triticale.Rd | 2 man/bliss.borers.Rd | 2 man/burgueno.alpha.Rd | 2 man/burgueno.rowcol.Rd | 3 + man/burgueno.unreplicated.Rd | 3 + man/cochran.beets.Rd |only man/cochran.latin.Rd | 2 man/cochran.lattice.Rd |only man/cochran.wireworms.Rd | 11 +++- man/connolly.potato.Rd | 10 ++- man/crowder.seeds.Rd | 27 +++++----- man/cullis.earlygen.Rd | 6 +- man/diggle.cow.Rd | 2 man/hayman.tobacco.Rd | 2 man/ilri.sheep.Rd | 2 man/jansen.apple.Rd |only man/jansen.carrot.Rd |only man/jansen.strawberry.Rd | 21 +++++--- man/jenkyn.mildew.Rd | 4 - man/karcher.turfgrass.Rd | 9 +-- man/keen.potatodamage.Rd | 9 +++ man/kempton.barley.uniformity.Rd | 2 man/lasrosas.corn.Rd | 12 ++-- man/lonnquist.maize.Rd | 2 man/mercer.wheat.uniformity.Rd | 30 ++++++++--- man/snijders.fusarium.Rd | 2 man/stroup.nin.Rd | 21 ++++++-- man/theobald.covariate.Rd | 6 +- man/turner.herbicide.Rd | 45 ++++++++++++++++- man/vold.longterm.Rd | 36 +++++++------- man/wallace.iowaland.Rd | 2 man/wedderburn.barley.Rd | 2 man/welch.bermudagrass.Rd | 14 +++-- man/wiebe.wheat.uniformity.Rd | 29 ++++++----- vignettes/agridat_examples.Rnw | 16 +++--- 54 files changed, 363 insertions(+), 202 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between spatial versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 11 +++-------- R/pp.R | 2 +- 4 files changed, 11 insertions(+), 16 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between rpart versions 4.1-9 dated 2015-02-11 and 4.1-10 dated 2015-06-29
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 7 ++++--- build/vignette.rds |binary inst/doc/longintro.pdf |binary inst/doc/usercode.pdf |binary tests/Examples/rpart-Ex.Rout.save | 13 ++++++------- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between nnet versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 11 +++-------- 3 files changed, 9 insertions(+), 14 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-120 dated 2015-02-20 and 3.1-121 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 7 ++----- tests/missing.Rout.save | 2 +- 4 files changed, 10 insertions(+), 13 deletions(-)
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between KernSmooth versions 2.23-14 dated 2015-02-11 and 2.23-15 dated 2015-06-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 3 ++- PORTING | 5 +++++ 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-12 dated 2015-02-11 and 7.3-13 dated 2015-06-29
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/knn1.Rd | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-16 dated 2015-06-07 and 1.3-17 dated 2015-06-29
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- INDEX | 7 +------ MD5 | 10 +++++----- NAMESPACE | 6 ++++-- man/print.boot.Rd | 3 ++- 6 files changed, 20 insertions(+), 18 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series
from the HIS Central catalog based on geographic bounding box, server, or keyword.
GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.0.0 dated 2015-05-05 and 1.2.3 dated 2015-06-29
DESCRIPTION | 21 - MD5 | 44 +- NAMESPACE | 4 R/AddMethods.R | 2 R/GetServices.R | 1 R/GetSiteInfo.R | 748 ++++++++++++++++++++++++++----------- R/GetSites.R | 365 +++++++++++++----- R/GetValues.R | 425 +++++++++++++++++---- R/GetVariables.R | 174 +++++++- R/HISCentral_GetSeriesCatalog.R |only R/HISCentral_GetSites.R |only R/MakeSOAPEnvelope.R | 6 R/PackageDocumentation.R |only R/WaterOneFlowNamespace.R |only README.md | 12 build |only inst |only man/GetSiteInfo.Rd | 94 ++++ man/GetSites.Rd | 40 + man/GetValues.Rd | 43 ++ man/GetVariables.Rd | 23 + man/HISCentral_GetSeriesCatalog.Rd |only man/HISCentral_GetSites.Rd |only man/MakeSOAPEnvelope.Rd | 3 man/WaterML-package.Rd |only man/WaterOneFlowNamespace.Rd |only vignettes |only 27 files changed, 1569 insertions(+), 436 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.2.0 dated 2015-05-26 and 0.3.0 dated 2015-06-29
DESCRIPTION | 16 + MD5 | 70 ++++---- NAMESPACE | 12 + R/bugs.R | 27 +-- R/data.docu.R | 19 +- R/extract.old.R | 2 R/main.R | 151 +++++++++++------- R/parser.R |only R/s3.correlations.R |only R/s3.generics.R | 108 +++++++++++- R/s3.methods.R | 139 ++++++++++++++-- R/stan.R | 342 +++++++++++++++++++++++------------------ R/support.export.R | 150 +++++++++++++---- R/support.internal.R | 102 ++++-------- data/kidney.rda |binary man/VarCorr.Rd | 3 man/brm.Rd | 118 +++++++++----- man/brm.data.Rd | 16 + man/brm.pars.Rd | 11 + man/brm.plot.Rd | 3 man/brms-package.Rd | 2 man/brmsfit-class.Rd | 6 man/cor.ar.Rd |only man/cor.arma.Rd |only man/cor.brms.Rd |only man/cor.ma.Rd |only man/epilepsy.Rd | 2 man/fixef.Rd | 3 man/hypothesis.Rd |only man/inhaler.Rd | 2 man/kidney.Rd | 15 - man/ngrps.Rd | 5 man/par.names.Rd |only man/plot.brmsfit.Rd | 3 man/posterior.samples.Rd |only man/print.brmsfit.Rd | 3 man/ranef.Rd | 7 man/summary.brmsfit.Rd | 3 tests/testthat/tests.parser.R |only tests/testthat/tests.stan.R | 35 +++- tests/testthat/tests.support.R | 6 41 files changed, 916 insertions(+), 465 deletions(-)
Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Description: Functions to obtain the operational characteristics of
bioequivalence studies with 2-stage designs via simulations
- Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use both point estimate (PE) and mse from stage 1
also for the power monitoring steps.
- The third function power.2stage.fC() calculates power and sample-size
distribution of 2-stage BE studies with a futility criterion
for the PE or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
This function has a sibling power.2stage.pAF(), which performs exactly as
described in A.Fuglsang 2014
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between Power2Stage versions 0.3-1 dated 2015-01-23 and 0.4-1 dated 2015-06-29
Power2Stage-0.3-1/Power2Stage/R/sampsiz.R |only Power2Stage-0.4-1/Power2Stage/DESCRIPTION | 54 ++--- Power2Stage-0.4-1/Power2Stage/MD5 | 41 ++-- Power2Stage-0.4-1/Power2Stage/NAMESPACE | 6 Power2Stage-0.4-1/Power2Stage/NEWS | 25 ++ Power2Stage-0.4-1/Power2Stage/R/power.R | 6 Power2Stage-0.4-1/Power2Stage/R/power_2stage.R | 71 +++---- Power2Stage-0.4-1/Power2Stage/R/power_2stage_DL.R |only Power2Stage-0.4-1/Power2Stage/R/power_2stage_GS.R | 47 +--- Power2Stage-0.4-1/Power2Stage/R/power_2stage_KM.R | 61 ++---- Power2Stage-0.4-1/Power2Stage/R/power_2stage_SSR.R | 70 ++----- Power2Stage-0.4-1/Power2Stage/R/power_2stage_fC.R | 86 +++----- Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel.R | 126 +++++-------- Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel_AF.R | 81 ++------ Power2Stage-0.4-1/Power2Stage/R/print_pwrtsd_s3.R |only Power2Stage-0.4-1/Power2Stage/R/sampsiz2.R | 28 +- Power2Stage-0.4-1/Power2Stage/R/sampsiz_n0.R | 6 Power2Stage-0.4-1/Power2Stage/man/power.2stage.GS.Rd | 58 +++-- Power2Stage-0.4-1/Power2Stage/man/power.2stage.KM.Rd | 23 +- Power2Stage-0.4-1/Power2Stage/man/power.2stage.Rd | 71 +++++-- Power2Stage-0.4-1/Power2Stage/man/power.2stage.fC.Rd | 57 ++++- Power2Stage-0.4-1/Power2Stage/man/power.2stage.p.Rd | 35 ++- Power2Stage-0.4-1/Power2Stage/man/power.2stage.ssr.Rd | 30 +-- 23 files changed, 503 insertions(+), 479 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between tree versions 1.0-35 dated 2014-03-03 and 1.0-36 dated 2015-06-29
ChangeLog | 6 ++++++ DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 5 +++++ tests/Examples/tree-Ex.Rout.save | 12 ++++++------ 5 files changed, 28 insertions(+), 17 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between RODBC versions 1.3-11 dated 2015-02-26 and 1.3-12 dated 2015-06-29
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 46 +++++++++++++++++++++++----------------------- NAMESPACE | 1 + R/RODBC.R | 3 ++- R/sql.R | 3 ++- build/vignette.rds |binary inst/doc/RODBC.pdf |binary man/odbc.Rd | 3 ++- man/odbcClose.Rd | 3 ++- man/odbcConnect.Rd | 3 ++- man/odbcDataSources.Rd | 2 +- man/odbcGetInfo.Rd | 3 ++- man/odbcSetAutoCommit.Rd | 2 +- man/setSqlTypeInfo.Rd | 2 +- man/sqlColumns.Rd | 3 ++- man/sqlCopy.Rd | 3 ++- man/sqlDrop.Rd | 3 ++- man/sqlFetch.Rd | 3 ++- man/sqlQuery.Rd | 3 ++- man/sqlSave.Rd | 3 ++- man/sqlTables.Rd | 3 ++- man/sqlTypeInfo.Rd | 3 ++- src/RODBC.c | 41 +++++++++++++++++++++++------------------ 24 files changed, 87 insertions(+), 63 deletions(-)
Title: Penalized Smoothing Splines
Description: Smoothing splines with penalties on order m derivatives.
Author: S original by Jim Ramsey <ramsay@psych.mcgill.ca>.
R port by Brian Ripley <ripley@stats.ox.ac.uk>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between pspline versions 1.0-16 dated 2013-04-16 and 1.0-17 dated 2015-06-29
ChangeLog | 5 +++++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 +++ 4 files changed, 17 insertions(+), 9 deletions(-)
Title: Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical
and continuous data.
Author: Original by Joseph L. Schafer <jls@stat.psu.edu>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between mix versions 1.0-8 dated 2010-01-03 and 1.0-9 dated 2015-06-29
ChangeLog | 9 +++++++++ DESCRIPTION | 17 +++++++++-------- MD5 |only NAMESPACE | 2 ++ R/mix.R | 2 +- data/stlouis.rda |binary 6 files changed, 21 insertions(+), 9 deletions(-)
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and 4.4)
and Brian Ripley <ripley@stats.ox.ac.uk> (version 4.13).
Note that maintainers are not available to give advice on using a
package they did not author.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between gee versions 4.13-18 dated 2012-03-14 and 4.13-19 dated 2015-06-29
ChangeLog | 10 ++++++++++ DESCRIPTION | 21 +++++++++++---------- MD5 | 14 +++++++------- NAMESPACE | 4 +++- R/ugee.R | 6 ++---- src/ugee.c | 18 ++++++++++++++++++ src/ugee.h | 3 --- tests/Examples/gee-Ex.Rout.save | 13 +++++++------ 8 files changed, 58 insertions(+), 31 deletions(-)
Title: Tools for Inference with Set-Theoretic Comparative Methods
Description: Provides a number of functions for carrying out
inference with set-theoretic comparative methods, including
facilities for examining causal paths, assessing the sensitivity
of results to measurement and model specification error,
and performing Random Forest Comparative Analysis.
Author: Chris Krogslund [aut, cre]
Maintainer: Chris Krogslund <ckrogslund@berkeley.edu>
Diff between stcm versions 0.1.0 dated 2015-04-02 and 0.1.1 dated 2015-06-29
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- R/caret_infer.R | 6 +++--- R/cond_expand.R | 2 +- R/fsqca_sim.R | 2 +- R/fsqca_sim_inclcut.R | 4 ++-- R/get_qca_datasets.R | 6 +++--- R/hicks_20.R | 2 +- R/hicks_29.R | 2 +- R/meas_error.R | 4 ++-- R/mod_error.R | 6 +++--- R/paths_summary.R | 21 ++++++++++----------- R/rfca.R | 10 +++++----- man/fsqca_sim.Rd | 2 +- man/hicks_20.Rd | 2 +- man/hicks_29.Rd | 2 +- man/rfca.Rd | 6 +++--- 17 files changed, 59 insertions(+), 60 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers.
Among available features there are: pattern searching
(e.g. via regular expressions), random string generation,
string collation, transliteration, concatenation,
date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.5-4 dated 2015-06-28 and 0.5-5 dated 2015-06-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 +++--- configure | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
V. Shcherbakov;
G.C. Shen;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-1 dated 2015-06-05 and 1.42-2 dated 2015-06-29
DESCRIPTION | 18 +-- MD5 | 237 ++++++++++++++++++++++----------------------- NAMESPACE | 10 + NEWS | 108 ++++++++++++++++++++ R/First.R | 65 ++++++------ R/affine.R | 13 -- R/clusterinfo.R | 11 ++ R/formulae.R | 26 ++++ R/images.R | 51 +++++++-- R/kppm.R | 149 +++++++++++++++++++++++----- R/lppm.R | 8 + R/mincontrast.R | 4 R/objsurf.R | 2 R/options.R | 6 + R/pcf.R | 31 +++-- R/pcfinhom.R | 47 +++++--- R/plot.fv.R | 8 + R/plot.im.R | 24 ++-- R/ppmclass.R | 7 - R/randomNS.R | 38 ++++++- R/resolve.defaults.R | 2 R/rose.R | 79 +++++++++++++-- R/rotmean.R | 9 + R/summary.im.R | 16 +-- R/tess.R | 52 ++++----- R/triangulate.R |only R/update.ppm.R | 14 -- R/wingeom.R | 63 ++++++++--- README.md | 37 ++++--- build/vignette.rds |binary data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/cells.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/CITATION | 4 inst/doc/BEGINNER.txt | 17 ++- inst/doc/datasets.Rnw | 2 inst/doc/datasets.pdf |binary inst/doc/getstart.R | 42 +++---- inst/doc/getstart.Rnw | 32 +++--- inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.R | 42 +++---- inst/doc/shapefiles.Rnw | 2 inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 4 inst/doc/updates.Rnw | 45 +++++++- inst/doc/updates.pdf |binary man/clusterfit.Rd | 7 + man/density.ppp.Rd | 10 - man/fitted.lppm.Rd |only man/fitted.ppm.Rd | 2 man/kppm.Rd | 9 + man/padimage.Rd | 22 +++- man/quad.ppm.Rd | 5 man/rCauchy.Rd | 15 ++ man/rMatClust.Rd | 16 ++- man/rThomas.Rd | 15 ++ man/rVarGamma.Rd | 15 ++ man/rose.Rd | 51 ++++++++- man/rotmean.Rd | 23 +++- man/spatstat-internal.Rd | 27 +++-- man/spatstat-package.Rd | 81 ++++++++++++--- man/tess.Rd | 7 + man/triangulate.owin.Rd |only man/update.kppm.Rd | 49 +++++---- tests/alltests.R | 10 + vignettes/datasets.Rnw | 2 vignettes/getstart.Rnw | 32 +++--- vignettes/packagesizes.txt | 3 vignettes/shapefiles.Rnw | 2 vignettes/updates.Rnw | 45 +++++++- 121 files changed, 1265 insertions(+), 508 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.2 dated 2015-06-10 and 4.5 dated 2015-06-29
seqminer-4.2/seqminer/demo/workflow.R |only seqminer-4.5/seqminer/ChangeLog | 14 seqminer-4.5/seqminer/DESCRIPTION | 13 seqminer-4.5/seqminer/MD5 | 97 +++--- seqminer-4.5/seqminer/NAMESPACE | 4 seqminer-4.5/seqminer/R/seqminer.R | 149 ++++++++-- seqminer-4.5/seqminer/README.md | 2 seqminer-4.5/seqminer/configure | 42 +- seqminer-4.5/seqminer/configure.ac | 23 - seqminer-4.5/seqminer/configure.win | 2 seqminer-4.5/seqminer/demo/00Index | 4 seqminer-4.5/seqminer/demo/annotate.R |only seqminer-4.5/seqminer/demo/meta.workflow.R |only seqminer-4.5/seqminer/demo/vcf.workflow.R |only seqminer-4.5/seqminer/inst/rvtests/cfh.refFlat.txt |only seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz |only seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz.tbi |only seqminer-4.5/seqminer/man/SeqMiner.Rd | 16 - seqminer-4.5/seqminer/man/annotateGene.Rd | 13 seqminer-4.5/seqminer/man/annotatePlain.Rd | 8 seqminer-4.5/seqminer/man/annotateVcf.Rd | 8 seqminer-4.5/seqminer/man/download.annotation.resource.Rd |only seqminer-4.5/seqminer/man/getCovPair.Rd | 21 - seqminer-4.5/seqminer/man/getRefBase.Rd | 11 seqminer-4.5/seqminer/man/hasIndex.Rd | 8 seqminer-4.5/seqminer/man/isDirWritable.Rd |only seqminer-4.5/seqminer/man/isInRange.Rd | 7 seqminer-4.5/seqminer/man/isURL.Rd |only seqminer-4.5/seqminer/man/makeAnnotationParameter.Rd | 4 seqminer-4.5/seqminer/man/readVCFToListByGene.Rd | 32 -- seqminer-4.5/seqminer/man/readVCFToListByRange.Rd | 29 - seqminer-4.5/seqminer/man/readVCFToMatrixByGene.Rd | 19 - seqminer-4.5/seqminer/man/readVCFToMatrixByRange.Rd | 16 - seqminer-4.5/seqminer/man/rvmeta.readCovByRange.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.readDataByGene.Rd | 22 - seqminer-4.5/seqminer/man/rvmeta.readDataByRange.Rd | 19 - seqminer-4.5/seqminer/man/rvmeta.readNullModel.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.readScoreByRange.Rd | 11 seqminer-4.5/seqminer/man/rvmeta.readSkewByRange.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.writeCovData.Rd | 8 seqminer-4.5/seqminer/man/rvmeta.writeScoreData.Rd | 11 seqminer-4.5/seqminer/man/tabix.createIndex.Rd | 18 - seqminer-4.5/seqminer/man/tabix.createIndex.meta.Rd | 4 seqminer-4.5/seqminer/man/tabix.createIndex.vcf.Rd | 4 seqminer-4.5/seqminer/man/tabix.read.Rd | 7 seqminer-4.5/seqminer/man/tabix.read.header.Rd | 7 seqminer-4.5/seqminer/man/tabix.read.table.Rd | 13 seqminer-4.5/seqminer/man/validateAnnotationParameter.Rd | 9 seqminer-4.5/seqminer/man/verifyFilename.Rd |only seqminer-4.5/seqminer/src/Makevars.in | 2 seqminer-4.5/seqminer/src/Makevars.win | 2 seqminer-4.5/seqminer/src/Profiler.cpp | 27 + seqminer-4.5/seqminer/src/Profiler.h | 6 seqminer-4.5/seqminer/src/SimpleTimer.h | 138 +++++++++ seqminer-4.5/seqminer/src/rvMetaLoader.cpp | 44 ++ 55 files changed, 585 insertions(+), 333 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), latent regression models,
DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between sirt versions 1.7-0 dated 2015-06-05 and 1.8-9 dated 2015-06-28
sirt-1.7-0/sirt/R/plot.noharm.sirt.R |only sirt-1.8-9/sirt/DESCRIPTION | 22 ++--- sirt-1.8-9/sirt/MD5 | 61 ++++++++------- sirt-1.8-9/sirt/NAMESPACE | 74 +++++++++++------- sirt-1.8-9/sirt/R/likelihood_adjustment.R |only sirt-1.8-9/sirt/R/likelihood_adjustment_aux.R |only sirt-1.8-9/sirt/R/likelihood_moments.R |only sirt-1.8-9/sirt/R/mcmc.list.descriptives.R | 5 - sirt-1.8-9/sirt/R/plot.mcmc.sirt.R | 71 ++++++++++++++---- sirt-1.8-9/sirt/R/rasch.mml2.R | 41 +++++----- sirt-1.8-9/sirt/R/rasch.mml2.missing1.R | 36 ++++++--- sirt-1.8-9/sirt/R/sia.sirt.R | 13 --- sirt-1.8-9/sirt/inst/NEWS | 21 +++++ sirt-1.8-9/sirt/man/automatic.recode.Rd | 2 sirt-1.8-9/sirt/man/data.big5.Rd | 12 --- sirt-1.8-9/sirt/man/data.eid.Rd | 14 +-- sirt-1.8-9/sirt/man/data.read.Rd | 12 --- sirt-1.8-9/sirt/man/data.wide2long.Rd | 2 sirt-1.8-9/sirt/man/dif.logistic.regression.Rd | 2 sirt-1.8-9/sirt/man/dirichlet.mle.Rd | 2 sirt-1.8-9/sirt/man/dirichlet.simul.Rd | 2 sirt-1.8-9/sirt/man/greenyang.reliability.Rd | 2 sirt-1.8-9/sirt/man/invariance.alignment.Rd | 2 sirt-1.8-9/sirt/man/isop.scoring.Rd | 2 sirt-1.8-9/sirt/man/likelihood.adjustment.Rd |only sirt-1.8-9/sirt/man/lsem.estimate.Rd | 2 sirt-1.8-9/sirt/man/mcmc.list.descriptives.Rd | 5 - sirt-1.8-9/sirt/man/monoreg.rowwise.Rd | 2 sirt-1.8-9/sirt/man/noharm.sirt.Rd | 38 ++++----- sirt-1.8-9/sirt/man/plot.mcmc.sirt.Rd | 5 - sirt-1.8-9/sirt/man/rasch.evm.pcm.Rd | 4 - sirt-1.8-9/sirt/man/rasch.mirtlc.Rd | 2 sirt-1.8-9/sirt/man/rasch.mml.Rd | 98 ++++++++++++++++++++++--- sirt-1.8-9/sirt/man/sirt-package.Rd | 96 ++++++++++++------------ 34 files changed, 398 insertions(+), 252 deletions(-)
Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut, cre],
Patrick Miller [aut],
Alexander Schoemann [aut],
Corbin Quick [ctb],
Terry Jorgensen [ctb]
Maintainer: Sunthud Pornprasertmanit <sunthud.pornprasertmanit@ttu.edu>
Diff between simsem versions 0.5-8 dated 2014-10-03 and 0.5-11 dated 2015-06-28
DESCRIPTION | 16 - MD5 | 76 ++++----- NAMESPACE | 8 R/AllClass.R | 4 R/analyze.R | 12 - R/bindDist.R | 1 R/clean.R | 7 R/combineSim.R | 11 - R/createData.R | 4 R/drawParam.R | 16 + R/exportData.R | 2 R/generate.R | 10 - R/getCutoff.R | 6 R/getKeywords.R | 2 R/getPowerCoverage.R | 3 R/imposeMissing.R | 7 R/likRatioFit.R | 1 R/miss.R | 2 R/model.R | 385 ++++++++++++++++++++++++++++++++++++++-------- R/openMx.R | 59 +++---- R/pValue.R | 12 - R/plotCutoff.R | 14 - R/plotDist.R | 9 - R/plotPowerCoverage.R | 3 R/sim.R | 316 +++++++++++++++++++++++++++++-------- R/summary-methods.R | 5 R/summarySimResult.R | 144 +++++++++++------ R/validate.R | 3 man/SimResult-class.Rd | 2 man/bindDist.Rd | 9 - man/getPopulation.Rd | 5 man/inspect.Rd | 3 man/miss.Rd | 2 man/plotDist.Rd | 7 man/plotPowerFitNested.Rd | 8 man/sim.Rd | 7 man/summaryConverge.Rd | 5 man/summaryParam.Rd | 7 man/summaryPopulation.Rd | 5 39 files changed, 856 insertions(+), 342 deletions(-)
Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Sunthud Pornprasertmanit [aut, cre],
Patrick Miller [aut],
Alexander Schoemann [aut],
Yves Rosseel [aut],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb],
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher Preacher [ctb],
Donna Coffman [ctb],
Mijke Rhemtulla [ctb],
Alexander Robitzsch [ctb],
Craig Enders [ctb],
Ruber Arslan [ctb],
Bell Clinton [ctb],
Pavel Panko [ctb],
Edgar Merkle [ctb],
Terry Jorgensen [ctb],
Steven Chesnut [ctb],
Jarrett Byrnes [ctb]
Maintainer: Sunthud Pornprasertmanit <sunthud.pornprasertmanit@ttu.edu>
Diff between semTools versions 0.4-6 dated 2014-10-03 and 0.4-9 dated 2015-06-28
DESCRIPTION | 64 +++---- MD5 | 86 +++++----- NAMESPACE | 14 + R/NET.R | 4 R/auxiliary.R | 11 - R/clipboard.R | 14 - R/dataDiagnosis.R | 2 R/efa.R | 11 - R/fitIndices.R | 142 +++++++++-------- R/fitOpenMx.R | 309 +++++++++++++++++++------------------ R/fmi.R | 14 - R/lavSpatialCorrect.R |only R/longInvariance.R | 326 +++++++++++++++++++++++++++++----------- R/measurementInvariance.R | 144 +++++------------ R/measurementInvarianceCat.R | 89 +--------- R/miPowerFit.R | 37 ++++ R/monteCarloMed.R | 1 R/partialInvariance.R | 47 +++-- R/partialInvarianceCat.R | 51 +++--- R/permuteMeasEq.R |only R/powerAnalysisSS.R | 4 R/quark.R | 4 R/reliability.R | 7 R/runMI.R | 22 +- R/singleParamTest.R | 115 ++++++++------ build/vignette.rds |binary data/boreal.rda |only inst/CITATION |only man/BootMiss-class.Rd | 82 +++++----- man/Net-class.Rd | 68 ++++---- man/boreal.Rd |only man/bsBootMiss.Rd | 2 man/longInvariance.Rd | 4 man/measurementInvariance.Rd | 5 man/measurementInvarianceCat.Rd | 5 man/miPowerFit.Rd | 19 +- man/moreFitIndices.Rd | 12 - man/net.Rd | 2 man/partialInvariance.Rd | 7 man/permuteMeasEq-class.Rd |only man/permuteMeasEq.Rd |only man/probe2WayMC.Rd | 2 man/probe3WayMC.Rd | 2 man/reliability.Rd | 4 man/runMI.Rd | 19 ++ man/singleParamTest.Rd | 9 - man/spatialCorrect.Rd |only man/standardizeMx.Rd | 2 48 files changed, 968 insertions(+), 794 deletions(-)
Title: Hierarchical and Grouped Time Series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Shanika Wickramasuriya
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between hts versions 4.4 dated 2014-07-23 and 4.5 dated 2015-06-28
hts-4.4/hts/inst/tests |only hts-4.4/hts/tests |only hts-4.5/hts/ChangeLog | 12 + hts-4.5/hts/DESCRIPTION | 19 +- hts-4.5/hts/MD5 | 56 ++--- hts-4.5/hts/NAMESPACE | 3 hts-4.5/hts/R/RcppExports.R |only hts-4.5/hts/R/accuracy.gts.R | 16 + hts-4.5/hts/R/aggts.R | 2 hts-4.5/hts/R/combinef.R | 380 ++++++++++------------------------------ hts-4.5/hts/R/combineg.R | 14 - hts-4.5/hts/R/forecast.gts.R | 35 ++- hts-4.5/hts/R/gts.R | 31 +-- hts-4.5/hts/R/plot.gts.R | 37 +++ hts-4.5/hts/R/recursive.R |only hts-4.5/hts/R/smatrix.R | 64 +++--- hts-4.5/hts/R/summary.gts.R | 4 hts-4.5/hts/R/topdown.R | 12 - hts-4.5/hts/R/tracemin.R |only hts-4.5/hts/README.md | 2 hts-4.5/hts/build/vignette.rds |binary hts-4.5/hts/data/htseg2.rda |binary hts-4.5/hts/inst/doc/hts.pdf |binary hts-4.5/hts/man/combinef.Rd | 10 - hts-4.5/hts/man/forecast.gts.Rd | 8 hts-4.5/hts/man/gts.Rd | 2 hts-4.5/hts/man/hts.Rd | 3 hts-4.5/hts/src |only 28 files changed, 292 insertions(+), 418 deletions(-)
Title: Generalized Credit Portfolio Model
Description: Analyze the default risk of credit portfolios. Commonly known models,
like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings.
The portfolio loss distribution can be achieved either by simulation or analytically
in case of the classic CreditRisk+ model. Models are only implemented to respect losses
caused by defaults, i.e. migration risk is not included. The package structure is kept
flexible especially with respect to distributional assumptions in order to quantify the
sensitivity of risk figures with respect to several assumptions. Therefore the package
can be used to determine the credit risk of a given portfolio as well as to quantify
model sensitivities.
Author: Kevin Jakob
Maintainer: Kevin Jakob <Kevin.Jakob@Student.uni-augsburg.de>
Diff between GCPM versions 1.1.1 dated 2014-12-01 and 1.2 dated 2015-06-28
DESCRIPTION | 12 +- MD5 | 24 ++--- NAMESPACE | 2 R/GCPM.R | 228 ++++++++++++++++++++++++++++++++----------------- R/cpploss.R | 4 R/other_functions.R | 18 ++- data/portfolios.RData |only man/GCPM-class.Rd | 4 man/GCPM-package.Rd | 8 - man/analyze-methods.Rd | 15 ++- man/init.Rd | 12 +- man/portfolios.Rd |only src/cpploss.cpp | 4 src/cpploss.h | 2 14 files changed, 210 insertions(+), 123 deletions(-)
Title: Wrapper for the Duke Deploy REST API
Description: A wrapper for the Duke Analytics model deployment API. See <http://www.dukeanalytics.com/products/dukedeployR.php> for more details.
Author: person("Niall", "McGearailt", role = c("aut", "cre"),email = "niall@dukeanalytics.com")
Maintainer: Niall McGearailt <niall@dukeanalytics.com>
Diff between ddeploy versions 1.0.2 dated 2015-05-08 and 1.0.4 dated 2015-06-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/duke_deploy.R | 3 ++- R/duke_list.R | 10 +++++----- R/duke_predict.R | 5 +++-- README.md | 10 ++++++++++ man/duke_deploy.Rd | 5 ++++- man/duke_list.Rd | 9 ++++++--- man/duke_predict.Rd | 7 +++++-- 9 files changed, 47 insertions(+), 26 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2015.1-21 dated 2015-01-21 and 2015.6-28 dated 2015-06-28
DESCRIPTION | 12 ++++---- MD5 | 16 +++++----- NAMESPACE | 44 +++++++++++++++++++---------- R/clmm.R | 6 ++-- R/clmm.ssr.R | 5 +++ R/clmm2.R | 65 ++++++++++++++++++++++++++++++++++++++++++++ inst/doc/clm_intro.pdf |binary inst/doc/clm_tutorial.pdf |binary inst/doc/clmm2_tutorial.pdf |binary 9 files changed, 117 insertions(+), 31 deletions(-)
Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a trees graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 0.18.3 dated 2015-01-31 and 1.0.1 dated 2015-06-28
ChangeLog | 1240 ++++++++++++++++ DESCRIPTION | 17 MD5 | 362 ++-- NAMESPACE | 17 NEWS | 131 + R/all.equal.R | 36 R/ape.R | 1 R/attr_access.R | 350 +++- R/bk_method.R | 4 R/branches_attr_by.R | 78 - R/color_branches.R | 176 +- R/colored_bars.R | 2 R/common_subtrees.R |only R/cor.dendlist.R | 128 + R/cor_bakers_gamma.R | 76 - R/cor_cophenetic.R | 48 R/cut_lower_fun.R | 24 R/cutree.dendrogram.R | 96 - R/data.R |only R/dendextend-package.R | 2 R/dendextend_options.R | 46 R/dendlist.R | 20 R/distinct_edges.R | 116 - R/entanglement.R | 88 - R/get_nodes_xy.R | 6 R/ggdend.R | 90 + R/ggdendro.R | 2 R/labels_colors.R | 28 R/magrittr.R | 4 R/nleaves.R | 13 R/prune.R | 154 +- R/pvclust.R | 13 R/rect.dendrogram.R | 51 R/rotate.R | 26 R/set.dendrogram.R | 85 - R/stats_imports.R | 605 ++++---- R/tanglegram.R | 216 ++ R/unbranch.R | 28 R/untangle.R | 662 ++++---- R/zzz.R | 35 README.md | 53 TODO | 18 build/vignette.rds |binary data |only inst/doc/Cluster_Analysis.R |only inst/doc/Cluster_Analysis.Rmd |only inst/doc/Cluster_Analysis.html |only inst/doc/FAQ.R |only inst/doc/FAQ.Rmd |only inst/doc/FAQ.html |only inst/doc/introduction.R | 234 --- inst/doc/introduction.Rmd | 379 +---- inst/doc/introduction.html | 2154 ++++++++--------------------- inst/tests/test-attr_access.R | 19 inst/tests/test-branches_attr_by.R | 33 inst/tests/test-common_subtrees.R |only inst/tests/test-cut_lower_fun.R | 14 inst/tests/test-cutree.dendrogram.R | 30 inst/tests/test-dendlist.R | 158 +- inst/tests/test-distinct_edges.R | 2 inst/tests/test-entanglement.R | 2 inst/tests/test-ggdend.R |only inst/tests/test-rect.dendrogram.R |only inst/tests/test-set.dendrogram.R | 15 man/Bk.Rd | 5 man/Bk_permutations.Rd | 3 man/Bk_plot.Rd | 3 man/DendSer.dendrogram.Rd | 3 man/FM_index.Rd | 3 man/FM_index_R.Rd | 3 man/FM_index_permutation.Rd | 3 man/FM_index_profdpm.Rd | 3 man/all.equal.dendrogram.Rd | 8 man/all_couple_rotations_at_k.Rd | 3 man/all_unique.Rd | 3 man/as.dendlist.Rd | 3 man/as.phylo.dendrogram.Rd | 3 man/as_hclust_fixed.Rd | 3 man/assign_dendextend_options.Rd | 3 man/assign_values_to_branches_edgePar.Rd | 27 man/assign_values_to_leaves_edgePar.Rd | 13 man/assign_values_to_leaves_nodePar.Rd | 9 man/assign_values_to_nodes_nodePar.Rd | 7 man/bakers_gamma_for_2_k_matrix.Rd | 9 man/branches_attr_by_clusters.Rd | 21 man/branches_attr_by_labels.Rd | 3 man/click_rotate.Rd | 3 man/collapse_branch.Rd | 3 man/color_branches.Rd | 33 man/color_labels.Rd | 9 man/colored_bars.Rd | 5 man/common_subtrees_clusters.Rd |only man/cor.dendlist.Rd | 26 man/cor_FM_index.Rd |only man/cor_bakers_gamma.Rd | 15 man/cor_common_nodes.Rd |only man/cor_cophenetic.Rd | 17 man/count_terminal_nodes.Rd | 3 man/cut_lower_fun.Rd | 13 man/cutree-methods.Rd | 3 man/cutree_1h.dendrogram.Rd | 9 man/cutree_1k.dendrogram.Rd | 7 man/d3dendro_options.Rd | 3 man/d3dendrogram.Rd | 3 man/dend_diff.Rd | 15 man/dendextend-package.Rd | 3 man/dendextend_labels.dendrogram.Rd |only man/dendextend_options.Rd | 3 man/dendlist.Rd | 14 man/dist.dendlist.Rd | 7 man/dist_long.Rd | 3 man/distinct_edges.Rd | 12 man/duplicate_leaf.Rd | 3 man/entanglement.Rd | 17 man/fac2num.Rd | 3 man/fix_members_attr.dendrogram.Rd | 3 man/flatten.dendrogram.Rd | 3 man/flip_leaves.Rd | 3 man/get_branches_heights.Rd | 7 man/get_childrens_heights.Rd | 3 man/get_leaves_attr.Rd | 7 man/get_leaves_branches_attr.Rd |only man/get_leaves_branches_col.Rd |only man/get_leaves_edgePar.Rd |only man/get_leaves_nodePar.Rd | 8 man/get_nodes_attr.Rd | 7 man/get_nodes_xy.Rd | 7 man/get_root_branches_attr.Rd | 3 man/ggdend.Rd | 8 man/hang.dendrogram.Rd | 3 man/heights_per_k.dendrogram.Rd | 7 man/highlight_distinct_edges.Rd | 17 man/identify.dendrogram.Rd | 9 man/intersect_trees.Rd | 9 man/is.dendlist.Rd | 3 man/is.dendrogram.Rd | 3 man/is.hclust.Rd | 3 man/is.natural.number.Rd | 3 man/is.phylo.Rd | 3 man/is_null_list.Rd | 3 man/khan.Rd |only man/labels-assign.Rd | 3 man/labels_colors.Rd | 9 man/ladderize.Rd | 9 man/leaf_Colors.Rd | 3 man/lowest_common_branch.Rd | 3 man/match_order_by_labels.Rd | 3 man/match_order_dendrogram_by_old_order.Rd | 3 man/na_locf.Rd | 3 man/nleaves.Rd | 8 man/nnodes.Rd | 3 man/noded_with_condition.Rd | 3 man/order.dendrogram-assign.Rd | 3 man/order.hclust.Rd | 3 man/partition_leaves.Rd | 7 man/pipe.Rd | 3 man/plot_horiz.dendrogram.Rd | 3 man/prune.Rd | 16 man/prune_common_subtrees.dendlist.Rd |only man/prune_leaf.Rd | 7 man/pvclust_show_signif.Rd | 3 man/pvclust_show_signif_gradient.Rd | 3 man/raise.dendrogram.Rd | 3 man/rank_branches.Rd | 3 man/rank_order.dendrogram.Rd | 5 man/rank_values_with_clusters.Rd |only man/rect.dendrogram.Rd | 20 man/remove_branches_edgePar.Rd | 7 man/remove_leaves_nodePar.Rd | 7 man/remove_nodes_nodePar.Rd | 7 man/rllply.Rd | 3 man/rotate.Rd | 6 man/rotate_DendSer.Rd | 3 man/sample.dendrogram.Rd | 3 man/set.Rd | 22 man/shuffle.Rd | 15 man/sort_2_clusters_vectors.Rd | 3 man/sort_dist_mat.Rd | 3 man/sort_levels_values.Rd | 3 man/tanglegram.Rd | 64 man/theme_dendro.Rd | 3 man/unbranch.Rd | 13 man/unclass_dend.Rd | 3 man/untangle.Rd | 10 man/untangle_DendSer.Rd | 3 man/untangle_random_search.Rd | 9 man/untangle_step_rotate_1side.Rd | 3 man/untangle_step_rotate_2side.Rd | 3 man/which_leaf.Rd | 3 man/which_node.Rd | 3 tests/test-all.R | 17 vignettes/Cluster_Analysis.Rmd |only vignettes/FAQ.Rmd |only vignettes/introduction.Rmd | 379 +---- 194 files changed, 5393 insertions(+), 4013 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-63 dated 2015-02-20 and 0.8-64 dated 2015-06-28
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 3 ++- 3 files changed, 10 insertions(+), 9 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers.
Among available features there are: pattern searching
(e.g. via regular expressions), random string generation,
string collation, transliteration, concatenation,
date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.5-2 dated 2015-06-22 and 0.5-4 dated 2015-06-28
stringi-0.5-2/stringi/src/icu55_found.txt.in |only stringi-0.5-2/stringi/src/install.libs.R |only stringi-0.5-2/stringi/src/sys |only stringi-0.5-2/stringi/src/uconfig_local.h |only stringi-0.5-4/stringi/DESCRIPTION | 11 stringi-0.5-4/stringi/INSTALL | 115 + stringi-0.5-4/stringi/MD5 | 45 stringi-0.5-4/stringi/NAMESPACE | 5 stringi-0.5-4/stringi/NEWS | 102 - stringi-0.5-4/stringi/R/ICU_settings.R | 15 stringi-0.5-4/stringi/R/install.R | 16 stringi-0.5-4/stringi/R/stringi-package.R | 13 stringi-0.5-4/stringi/configure | 1199 ++++++++++-------- stringi-0.5-4/stringi/configure.win | 22 stringi-0.5-4/stringi/inst/CITATION | 4 stringi-0.5-4/stringi/man/stri_info.Rd | 4 stringi-0.5-4/stringi/man/stri_install.Rd | 5 stringi-0.5-4/stringi/man/stringi-package.Rd | 7 stringi-0.5-4/stringi/src/install.libs.R.in | 9 stringi-0.5-4/stringi/src/stri_ICU_settings.cpp | 12 stringi-0.5-4/stringi/src/stri_container_listutf8.cpp | 8 stringi-0.5-4/stringi/src/stri_container_listutf8.h | 2 stringi-0.5-4/stringi/src/stri_exception.cpp | 6 stringi-0.5-4/stringi/src/stri_messages.h | 2 stringi-0.5-4/stringi/src/stri_stringi.cpp | 19 stringi-0.5-4/stringi/src/uconfig_local.h.in |only 26 files changed, 965 insertions(+), 656 deletions(-)
Title: Data Sets, Functions and Examples from the Book: "The Elements
of Statistical Learning, Data Mining, Inference, and
Prediction" by Trevor Hastie, Robert Tibshirani and Jerome
Friedman
Description: Useful when reading the book above mentioned, in the
documentation referred to as `the book'.
Author: Material from the book's webpage, R port and packaging by
Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between ElemStatLearn versions 2012.04-0 dated 2012-04-10 and 2015.6.26 dated 2015-06-27
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- NEWS | 6 ++++++ man/marketing.Rd | 4 ++-- man/spam.Rd | 2 ++ 5 files changed, 23 insertions(+), 14 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and
pedigree-based partitioning of individual variation into a range of
environmental and genetic variance components for individual and
maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 1.6-1 dated 2015-05-09 and 1.6-2 dated 2015-06-27
DESCRIPTION | 8 MD5 | 45 ++-- NAMESPACE | 5 R/am.zandrel.R | 4 R/gresponse.dmm.R | 395 ++++++++++++++++++++++++++++++++++++------- R/make.dmmobj.R |only R/part.add.R |only R/pedcheck.R | 37 +++- R/print.gresponse.dmm.R | 26 -- R/summary.gresponse.dmm.R |only data/sheep.df.rda |binary data/tstmo1.df.rda |binary inst/doc/bugs.txt | 6 inst/doc/dmmOverview.pdf |binary inst/doc/mods.txt | 12 + man/dmm-package.Rd | 12 - man/dmm.Rd | 23 +- man/gprint.Rd | 2 man/gprint.dmm.Rd | 2 man/gresponse.dmm.Rd | 75 +++++--- man/make.dmmobj.Rd |only man/pedcheck.Rd | 20 +- man/print.dmm.Rd | 2 man/print.gresponse.dmm.Rd | 11 - man/sheep.df.Rd | 4 man/summary.gresponse.dmm.Rd |only 26 files changed, 527 insertions(+), 162 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre],
Achim Zeileis [aut]
Maintainer: Jakob Messner <Jakob.Messner@uibk.ac.at>
Diff between crch versions 0.1-0 dated 2013-10-22 and 0.9-0 dated 2015-06-27
DESCRIPTION | 27 +-- MD5 | 42 ++++- NAMESPACE | 28 +++ NEWS | 29 +++ R/clogis.R |only R/cnorm.R |only R/crch.R | 383 ++++++++++++++++++++++++++++++++++++---------------- R/ct.R |only R/hxlr.R | 40 ++--- R/tlogis.R |only R/tnorm.R |only R/tt.R |only build |only data/RainIbk.rda |binary inst/CITATION | 13 + inst/doc |only man/clogis.Rd |only man/cnorm.Rd |only man/coef.hxlr.Rd | 3 man/crch.Rd | 48 ++++-- man/crch.control.Rd | 17 +- man/ct.Rd |only man/hxlr.Rd | 16 +- man/tlogis.Rd |only man/tnorm.Rd |only man/tt.Rd |only tests |only vignettes |only 28 files changed, 457 insertions(+), 189 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.1.3 dated 2015-05-01 and 0.2.0 dated 2015-06-27
DESCRIPTION | 8 MD5 | 26 NEWS | 87 + R/paretochart.R | 176 +-- R/qic.R | 2209 ++++++++++++++++++++++++------------------------ R/trc.R | 303 +++--- build/vignette.rds |binary inst/doc/runcharts.R | 109 +- inst/doc/runcharts.Rmd | 17 inst/doc/runcharts.html | 447 ++++----- man/paretochart.Rd | 2 man/qic.Rd | 50 - man/trc.Rd | 28 vignettes/runcharts.Rmd | 17 14 files changed, 1779 insertions(+), 1700 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.7-1 dated 2015-06-05 and 1.8-0 dated 2015-06-26
DESCRIPTION | 10 - MD5 | 55 +++++----- NAMESPACE | 10 + R/IRT.informationCurve.R |only R/calc_exp_TK.R | 31 ++++- R/mml.3pl.calc_prob.v5.R | 4 R/plot.IRT.informationCurves.R |only R/plotDevianceTAM.R | 2 R/tam.latreg.R | 3 R/tam.mml.2pl.R | 8 + R/tam.mml.3pl.R | 18 ++- R/tam.mml.3pl.est.guessing.R | 28 ++++- R/tam.mml.3pl.est.slopes.R | 3 R/tam.mml.3pl.preproc.R | 34 +++++- R/tam.mml.R | 79 ++++++-------- R/tam.mml.mfr.R | 10 + R/tamaan.3pl.trait.R | 3 R/tamaanify.R | 15 +- R/tamaanify.modelconstraint.loadings.R | 2 R/tamaanify.proc.items.R | 12 ++ R/tamaanify.proc.loadings.B.fixed.R | 10 + R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R | 22 +++- inst/NEWS | 69 ++++++++---- man/IRT.informationCurves.Rd |only man/TAM-package.Rd | 2 man/tam.mml.3pl.Rd | 33 +++++- man/tam.mml.Rd | 17 ++- man/tamaanify.Rd | 1 src/tam_calcexp.cpp | 134 ++++++++++++++++++++++++- src/tam_mml_3pl_helper_functions.cpp | 20 ++- 30 files changed, 487 insertions(+), 148 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed
by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL
license, and it is the base of most of the software tools of the Visual
Computing Lab of the Italian National Research Council Institute ISTI
(http://vcg.isti.cnr.it), like 'metro' and 'MeshLab'.
The 'VCGLIB' source is pulled from
trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work
with options determined by the configure script as well as
to work with the header files included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.12.1 dated 2015-06-23 and 0.12.2 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Rvcg-package.R | 4 ++-- man/Rvcg-package.Rd | 4 ++-- src/Rmarch.cpp | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Latent Budget Analysis for Compositional Data
Description: Latent budget analysis is a method for the analysis of a two-way contingency table with an exploratory variable and a response variable. It is specially designed for compositional data.
Author: Enio G. Jelihovschi <eniojelihovs@gmail.com> and
Ivan Bezerra Allaman <ivanalaman@gmail.com>
Maintainer: Enio G. Jelihovschi <eniojelihovs@gmail.com>
Diff between lba versions 1.0 dated 2015-01-22 and 1.2 dated 2015-06-26
ChangeLog |only DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 22 ++++++++++++++++++++++ R/goodnessfit.R | 12 ++++++------ R/lba.ls.fe.R | 9 +++++++++ R/lba.ls.logit.R | 29 ++++++++++++++++++++++++++++- R/lba.mle.R | 2 +- R/lba.mle.fe.R | 18 ++++++++++++++++++ R/lba.mle.logit.R | 27 +++++++++++++++++++++++++++ R/plot.lba.R | 12 ++++++++---- R/summary.lba.ls.fe.R | 14 ++++++++++---- R/summary.lba.ls.logit.R | 22 ++++++++++++++-------- R/summary.lba.mle.fe.R | 14 ++++++++++---- R/summary.lba.mle.logit.R | 22 ++++++++++++++-------- README.md |only man/lba.Rd | 6 ++++-- 17 files changed, 192 insertions(+), 57 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.4 dated 2015-06-04 and 1.2.5 dated 2015-06-26
icenReg-1.2.4/icenReg/data/mice_data.RData |only icenReg-1.2.4/icenReg/man/mice_data.Rd |only icenReg-1.2.5/icenReg/DESCRIPTION | 10 icenReg-1.2.5/icenReg/MD5 | 35 +- icenReg-1.2.5/icenReg/NEWS |only icenReg-1.2.5/icenReg/R/Utilities.R | 144 +++++++++-- icenReg-1.2.5/icenReg/R/user_functions.R | 98 ++++--- icenReg-1.2.5/icenReg/data/essIncData.RData |only icenReg-1.2.5/icenReg/data/essIncData_small.RData |only icenReg-1.2.5/icenReg/data/miceData.RData |only icenReg-1.2.5/icenReg/man/diag_baseline.Rd | 36 +- icenReg-1.2.5/icenReg/man/diag_covar.Rd | 40 +-- icenReg-1.2.5/icenReg/man/essIncData.Rd |only icenReg-1.2.5/icenReg/man/essIncData_small.Rd |only icenReg-1.2.5/icenReg/man/ic_par.Rd | 11 icenReg-1.2.5/icenReg/man/ic_sp.Rd | 8 icenReg-1.2.5/icenReg/man/miceData.Rd |only icenReg-1.2.5/icenReg/man/simIC_weib.Rd | 2 icenReg-1.2.5/icenReg/src/icenReg_files/basicUtilities.cpp | 15 - icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.cpp | 66 +++-- icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.h | 11 icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.cpp | 160 ++++++++++--- icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.h | 49 +++ 23 files changed, 489 insertions(+), 196 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Description: Analysis of dyadic network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor
models (Hoff(2009)). Four different link functions accommodate different
relational data structures, including binary/network data (bin), normal
relational data (nrm), ordinal relational data (ord) and data from
fixed-rank nomination schemes (frn). Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this
software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff <pdhoff@uw.edu>
Diff between amen versions 1.0 dated 2015-02-26 and 1.1 dated 2015-06-26
amen-1.0/amen/R/rs2_rep.R |only amen-1.0/amen/data/YX_bin.rda |only amen-1.0/amen/data/YX_bin_long.rda |only amen-1.0/amen/data/YX_cbin.rda |only amen-1.0/amen/data/YX_frn.rda |only amen-1.0/amen/data/YX_nrm.rda |only amen-1.0/amen/data/YX_ord.rda |only amen-1.0/amen/data/YX_rrl.rda |only amen-1.0/amen/data/conflict90s.RData |only amen-1.0/amen/man/conflict90s.Rd |only amen-1.1/amen/DESCRIPTION | 33 - amen-1.1/amen/MD5 | 215 ++++++----- amen-1.1/amen/NAMESPACE | 13 amen-1.1/amen/R/Xbeta.R | 12 amen-1.1/amen/R/addlines.R |only amen-1.1/amen/R/ame.R | 324 +++++++++++----- amen-1.1/amen/R/ame_rep.R | 674 ++++++++++++++++++++--------------- amen-1.1/amen/R/amen-package.R | 93 +++- amen-1.1/amen/R/circplot.R |only amen-1.1/amen/R/design_array.R | 11 amen-1.1/amen/R/el2sm.R |only amen-1.1/amen/R/gofstats.R | 7 amen-1.1/amen/R/mhalf.R | 9 amen-1.1/amen/R/netplot.R |only amen-1.1/amen/R/plot.ame.R | 43 -- amen-1.1/amen/R/rUV_fc.R | 63 --- amen-1.1/amen/R/rUV_rep_fc.R | 62 --- amen-1.1/amen/R/rUV_sym_fc.R |only amen-1.1/amen/R/rZ_bin_fc.R | 28 - amen-1.1/amen/R/rZ_cbin_fc.R | 51 -- amen-1.1/amen/R/rZ_frn_fc.R | 59 --- amen-1.1/amen/R/rZ_nrm_fc.R | 13 amen-1.1/amen/R/rZ_ord_fc.R | 36 - amen-1.1/amen/R/rZ_rrl.R | 52 -- amen-1.1/amen/R/raSab_bin_fc.R | 27 - amen-1.1/amen/R/raSab_cbin_fc.R | 31 - amen-1.1/amen/R/raSab_frn_fc.R | 24 - amen-1.1/amen/R/rbeta_ab_fc.R | 84 ---- amen-1.1/amen/R/rbeta_ab_rep_fc.R | 94 ---- amen-1.1/amen/R/rmvnorm.R | 9 amen-1.1/amen/R/rrho_mh.R | 22 - amen-1.1/amen/R/rrho_mh_rep.R | 29 - amen-1.1/amen/R/rs2_fc.R | 10 amen-1.1/amen/R/rs2_rep_fc.R |only amen-1.1/amen/R/simY_bin.R | 15 amen-1.1/amen/R/simY_frn.R | 30 - amen-1.1/amen/R/simY_nrm.R | 14 amen-1.1/amen/R/simY_ord.R | 20 - amen-1.1/amen/R/simY_rrl.R | 24 - amen-1.1/amen/R/simZ.R | 12 amen-1.1/amen/R/sm2el.R |only amen-1.1/amen/R/summary.ame.R | 34 - amen-1.1/amen/R/xnet.R |only amen-1.1/amen/R/zscores.R | 9 amen-1.1/amen/build |only amen-1.1/amen/data/IR90s.RData |only amen-1.1/amen/data/YX_bin.RData |only amen-1.1/amen/data/YX_bin_long.RData |only amen-1.1/amen/data/YX_cbin.RData |only amen-1.1/amen/data/YX_frn.RData |only amen-1.1/amen/data/YX_nrm.RData |only amen-1.1/amen/data/YX_ord.RData |only amen-1.1/amen/data/YX_rrl.RData |only amen-1.1/amen/data/coldwar.RData |binary amen-1.1/amen/data/comtrade.RData |binary amen-1.1/amen/data/datalist | 3 amen-1.1/amen/data/sheep.RData |only amen-1.1/amen/inst |only amen-1.1/amen/man/IR90s.Rd |only amen-1.1/amen/man/Xbeta.Rd | 14 amen-1.1/amen/man/YX_bin.Rd | 3 amen-1.1/amen/man/YX_bin_long.Rd | 3 amen-1.1/amen/man/YX_cbin.Rd | 3 amen-1.1/amen/man/YX_frn.Rd | 3 amen-1.1/amen/man/YX_nrm.Rd | 3 amen-1.1/amen/man/YX_ord.Rd | 3 amen-1.1/amen/man/YX_rrl.Rd | 3 amen-1.1/amen/man/addhealthc3.Rd | 5 amen-1.1/amen/man/addhealthc9.Rd | 3 amen-1.1/amen/man/addlines.Rd |only amen-1.1/amen/man/ame.Rd | 28 - amen-1.1/amen/man/ame_rep.Rd | 29 - amen-1.1/amen/man/amen-package.Rd | 5 amen-1.1/amen/man/circplot.Rd |only amen-1.1/amen/man/coldwar.Rd | 7 amen-1.1/amen/man/comtrade.Rd | 22 - amen-1.1/amen/man/design_array.Rd | 7 amen-1.1/amen/man/dutchcollege.Rd | 6 amen-1.1/amen/man/el2sm.Rd |only amen-1.1/amen/man/gofstats.Rd | 3 amen-1.1/amen/man/lazegalaw.Rd | 3 amen-1.1/amen/man/mhalf.Rd | 11 amen-1.1/amen/man/netplot.Rd |only amen-1.1/amen/man/plot.ame.Rd | 38 - amen-1.1/amen/man/rUV_fc.Rd | 55 -- amen-1.1/amen/man/rUV_rep_fc.Rd | 63 --- amen-1.1/amen/man/rUV_sym_fc.Rd |only amen-1.1/amen/man/rZ_bin_fc.Rd | 30 - amen-1.1/amen/man/rZ_cbin_fc.Rd | 51 -- amen-1.1/amen/man/rZ_frn_fc.Rd | 62 --- amen-1.1/amen/man/rZ_nrm_fc.Rd | 13 amen-1.1/amen/man/rZ_ord_fc.Rd | 34 - amen-1.1/amen/man/rZ_rrl_fc.Rd | 48 -- amen-1.1/amen/man/raSab_bin_fc.Rd | 28 - amen-1.1/amen/man/raSab_cbin_fc.Rd | 30 - amen-1.1/amen/man/raSab_frn_fc.Rd | 24 - amen-1.1/amen/man/rbeta_ab_fc.Rd | 86 ---- amen-1.1/amen/man/rbeta_ab_rep_fc.Rd | 95 ---- amen-1.1/amen/man/rmvnorm.Rd | 11 amen-1.1/amen/man/rrho_mh.Rd | 24 - amen-1.1/amen/man/rrho_mh_rep.Rd | 30 - amen-1.1/amen/man/rs2_fc.Rd | 12 amen-1.1/amen/man/rs2_rep_fc.Rd | 17 amen-1.1/amen/man/rwish.Rd | 3 amen-1.1/amen/man/sampsonmonks.Rd | 3 amen-1.1/amen/man/sheep.Rd |only amen-1.1/amen/man/simY_bin.Rd | 17 amen-1.1/amen/man/simY_frn.Rd | 30 - amen-1.1/amen/man/simY_nrm.Rd | 16 amen-1.1/amen/man/simY_ord.Rd | 21 - amen-1.1/amen/man/simY_rrl.Rd | 26 - amen-1.1/amen/man/simZ.Rd | 14 amen-1.1/amen/man/sm2el.Rd |only amen-1.1/amen/man/summary.ame.Rd | 24 - amen-1.1/amen/man/xnet.Rd |only amen-1.1/amen/man/zscores.Rd | 10 amen-1.1/amen/vignettes |only 127 files changed, 1033 insertions(+), 2335 deletions(-)
Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as
CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy <jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between spcadjust versions 0.1-3 dated 2014-08-26 and 0.9 dated 2015-06-26
DESCRIPTION | 14 - MD5 | 35 ++ R/main.R | 17 + build |only inst/doc/CUSUM_LinearRegression.R |only inst/doc/CUSUM_LinearRegression.Rmd |only inst/doc/CUSUM_LinearRegression.html |only inst/doc/CUSUM_LogisticRegression.R |only inst/doc/CUSUM_LogisticRegression.Rmd |only inst/doc/CUSUM_LogisticRegression.html |only inst/doc/CUSUM_NormalNormal.R |only inst/doc/CUSUM_NormalNormal.Rmd |only inst/doc/CUSUM_NormalNormal.html |only inst/doc/Methods.pdf |only inst/doc/Shewhart_NormalNormal.R |only inst/doc/Shewhart_NormalNormal.Rmd |only inst/doc/Shewhart_NormalNormal.html |only inst/doc/papers.bib |only inst/doc/spcadjust-intro.R | 401 +++++++++++++++------------------ inst/doc/spcadjust-intro.pdf |binary man/SPCShew-class.Rd | 5 man/SPCShewNormalCenterScale-class.Rd | 25 +- vignettes/CUSUM_LinearRegression.Rmd |only vignettes/CUSUM_LogisticRegression.Rmd |only vignettes/CUSUM_NormalNormal.Rmd |only vignettes/Shewhart_NormalNormal.Rmd |only vignettes/spcadjust-intro.Rnw | 131 +++++++--- vignettes/spcadjustClasses.pdf |binary 28 files changed, 362 insertions(+), 266 deletions(-)
Title: Entrez in R
Description: Provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 0.4.1 dated 2015-03-03 and 0.4.2 dated 2015-06-26
DESCRIPTION | 12 ++++---- MD5 | 42 ++++++++++++++-------------- NAMESPACE | 2 - NEWS | 4 ++ build/vignette.rds |binary inst/doc/rentrez_tutorial.R | 61 ++++++++++++++++------------------------- inst/doc/rentrez_tutorial.html | 8 ++--- man/entrez_citmatch.Rd | 2 - man/entrez_db_links.Rd | 2 - man/entrez_db_searchable.Rd | 2 - man/entrez_db_summary.Rd | 2 - man/entrez_dbs.Rd | 2 - man/entrez_fetch.Rd | 2 - man/entrez_global_query.Rd | 2 - man/entrez_info.Rd | 2 - man/entrez_link.Rd | 2 - man/entrez_post.Rd | 2 - man/entrez_search.Rd | 2 - man/entrez_summary.Rd | 2 - man/parse_pubmed_xml.Rd | 2 - man/rentrez.Rd | 2 - tests/testthat/test_webenv.r | 4 +- 22 files changed, 76 insertions(+), 85 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013).
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.7-0 dated 2015-02-04 and 0.8-0 dated 2015-06-26
DESCRIPTION | 10 +++++----- MD5 | 17 ++++++++++------- NAMESPACE | 4 +++- NEWS | 26 ++++++++++++++++++++++++-- R/netmeta.R | 2 +- R/netrank.R |only R/print.netmeta.R | 4 ++-- R/print.netrank.R |only man/netgraph.Rd | 46 +++++++++++++++++++++++++++------------------- man/netmeta.Rd | 27 ++++++++++++++++++--------- man/netrank.Rd |only 11 files changed, 90 insertions(+), 46 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-38 dated 2015-06-23 and 0.9-39 dated 2015-06-26
mkin-0.9-38/mkin/NEWS |only mkin-0.9-38/mkin/inst/staticdocs |only mkin-0.9-39/mkin/DESCRIPTION | 10 +-- mkin-0.9-39/mkin/MD5 | 42 +++++++------- mkin-0.9-39/mkin/NAMESPACE | 5 + mkin-0.9-39/mkin/NEWS.md |only mkin-0.9-39/mkin/R/mkinparplot.R | 2 mkin-0.9-39/mkin/R/mmkin.R |only mkin-0.9-39/mkin/R/plot.mmkin.R |only mkin-0.9-39/mkin/README.md | 3 - mkin-0.9-39/mkin/inst/doc/FOCUS_D.html | 17 +++-- mkin-0.9-39/mkin/inst/doc/FOCUS_L.html | 74 ++++++++++++------------- mkin-0.9-39/mkin/inst/doc/FOCUS_Z.R | 2 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.Rnw | 2 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-39/mkin/inst/doc/compiled_models.html | 42 +++++++------- mkin-0.9-39/mkin/inst/doc/mkin.pdf |binary mkin-0.9-39/mkin/man/DFOP.solution.Rd | 2 mkin-0.9-39/mkin/man/Extract.mmkin.Rd |only mkin-0.9-39/mkin/man/FOMC.solution.Rd | 2 mkin-0.9-39/mkin/man/HS.solution.Rd | 2 mkin-0.9-39/mkin/man/mkinresplot.Rd | 13 +--- mkin-0.9-39/mkin/man/mmkin.Rd |only mkin-0.9-39/mkin/man/plot.mkinfit.Rd | 10 +-- mkin-0.9-39/mkin/man/plot.mmkin.Rd |only mkin-0.9-39/mkin/vignettes/FOCUS_Z.Rnw | 2 26 files changed, 115 insertions(+), 115 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.1-0 dated 2015-06-12 and 1.2-0 dated 2015-06-26
DESCRIPTION | 8 +- MD5 | 122 ++++++++++++++++++++--------------------- R/jomo1.MCMCchain.R | 10 +-- R/jomo1.R | 10 +-- R/jomo1cat.MCMCchain.R | 34 ++++++++--- R/jomo1cat.R | 37 +++++++++--- R/jomo1con.MCMCchain.R | 22 ++++--- R/jomo1con.R | 25 +++++--- R/jomo1mix.MCMCchain.R | 34 ++++++++--- R/jomo1mix.R | 37 +++++++++--- R/jomo1ran.MCMCchain.R | 22 +++---- R/jomo1ran.R | 22 +++---- R/jomo1rancat.MCMCchain.R | 45 ++++++++++----- R/jomo1rancat.R | 48 +++++++++++----- R/jomo1rancathr.MCMCchain.R | 47 +++++++++++---- R/jomo1rancathr.R | 52 ++++++++++++----- R/jomo1rancon.MCMCchain.R | 33 ++++++----- R/jomo1rancon.R | 36 +++++++----- R/jomo1ranconhr.MCMCchain.R | 35 +++++++---- R/jomo1ranconhr.R | 40 ++++++++----- R/jomo1ranmix.MCMCchain.R | 45 ++++++++++----- R/jomo1ranmix.R | 48 +++++++++++----- R/jomo1ranmixhr.MCMCchain.R | 47 +++++++++++---- R/jomo1ranmixhr.R | 52 ++++++++++++----- man/jomo1.MCMCchain.Rd | 12 +++- man/jomo1.Rd | 9 ++- man/jomo1cat.MCMCchain.Rd | 11 ++- man/jomo1cat.Rd | 10 +++ man/jomo1con.MCMCchain.Rd | 10 ++- man/jomo1con.Rd | 9 ++- man/jomo1mix.MCMCchain.Rd | 13 ++++ man/jomo1mix.Rd | 9 ++- man/jomo1ran.MCMCchain.Rd | 12 +++- man/jomo1ran.Rd | 11 +++ man/jomo1rancat.MCMCchain.Rd | 13 +++- man/jomo1rancat.Rd | 10 ++- man/jomo1rancathr.MCMCchain.Rd | 11 +++ man/jomo1rancathr.Rd | 10 +++ man/jomo1rancon.MCMCchain.Rd | 11 ++- man/jomo1rancon.Rd | 9 ++- man/jomo1ranconhr.MCMCchain.Rd | 12 ++-- man/jomo1ranconhr.Rd | 10 ++- man/jomo1ranmix.MCMCchain.Rd | 12 +++- man/jomo1ranmix.Rd | 9 ++- man/jomo1ranmixhr.MCMCchain.Rd | 12 +++- man/jomo1ranmixhr.Rd | 9 ++- src/MCMCjomo1con.c | 18 ++---- src/MCMCjomo1mix.c | 22 ++----- src/MCMCjomo1rancon.c | 23 ++----- src/MCMCjomo1ranconhf.c | 23 ++----- src/MCMCjomo1ranconhr.c | 29 +++------ src/MCMCjomo1ranmix.c | 26 +++----- src/MCMCjomo1ranmixhf.c | 27 +++------ src/MCMCjomo1ranmixhr.c | 32 ++++------ src/jomo1con.c | 8 +- src/jomo1mix.c | 12 ++-- src/jomo1rancon.c | 12 ++-- src/jomo1ranconhf.c | 12 ++-- src/jomo1ranconhr.c | 18 +++--- src/jomo1ranmix.c | 16 ++--- src/jomo1ranmixhf.c | 16 ++--- src/jomo1ranmixhr.c | 22 +++---- 62 files changed, 906 insertions(+), 555 deletions(-)
Title: Racing for Unbalanced Methods Selection
Description: A dataset is said to be unbalanced when the class of interest (minority class) is much rarer than normal behaviour (majority class). The cost of missing a minority class is typically much higher that missing a majority class. Most learning systems are not prepared to cope with unbalanced data and several techniques have been proposed. This package implements some of most well-known techniques and propose a racing algorithm to select adaptively the most appropriate strategy for a given unbalanced task.
Author: Andrea Dal Pozzolo, Olivier Caelen and Gianluca Bontempi
Maintainer: Andrea Dal Pozzolo <adalpozz@ulb.ac.be>
Diff between unbalanced versions 1.1 dated 2014-02-05 and 2.0 dated 2015-06-26
DESCRIPTION | 17 +++--- MD5 | 51 ++++++++++--------- NAMESPACE | 4 - R/ubBalance.R | 122 ++++++++++++++++++++++++---------------------- R/ubCNN.R | 2 R/ubENN.R | 19 ++++--- R/ubNCL.R | 102 ++++++++++++++++++-------------------- R/ubOSS.R | 19 ++++--- R/ubOver.R | 60 +++++++++++----------- R/ubRacing.R |only R/ubSMOTE.R | 4 - R/ubSmoteExs.R | 21 +++++-- R/ubTomek.R | 9 +-- R/ubUnder.R | 73 +++++++++++++-------------- R/unbalanced-internal.R |only data/ubIonosphere.rda |binary man/ubBalance.Rd | 30 ++++++----- man/ubCNN.Rd | 2 man/ubENN.Rd | 2 man/ubIonosphere.Rd | 4 - man/ubNCL.Rd | 2 man/ubOSS.Rd | 4 - man/ubOver.Rd | 5 + man/ubRacing.Rd |only man/ubSMOTE.Rd | 2 man/ubTomek.Rd | 2 man/ubUnder.Rd | 19 ++++--- man/unbalanced-package.Rd | 42 +++++++++------ 28 files changed, 334 insertions(+), 283 deletions(-)
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-8 dated 2015-06-03 and 0.1-9 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/parallelSVM-package.Rd | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: A Parallel-Voting Algorithm for many Classifiers
Description: By sampling your data, running the provided classifier on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular machine learning algorithm and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelML versions 1.1 dated 2015-06-23 and 1.2 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++------- NAMESPACE | 1 R/convertAverage.R |only R/parallelML.R | 8 +++--- R/predictML.R | 28 +++++++++++++++++++-- R/trainSample.R | 60 +++++++++++++++++++++++++++++----------------- man/convertAverage.Rd |only man/parallelML-package.Rd | 1 man/parallelML.Rd | 29 +++++++++++++++++++++- man/predictML.Rd | 24 +++++++++++++++++- man/trainSample.Rd | 15 +++++++++-- 12 files changed, 150 insertions(+), 44 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between KFAS versions 1.1.1 dated 2015-04-29 and 1.1.2 dated 2015-06-26
ChangeLog | 6 DESCRIPTION | 8 MD5 | 89 +++--- NAMESPACE | 1 R/KFAS-package.R | 4 R/KFS.R | 695 +++++++++++++++++++++++++-------------------------- R/SSMarima.R | 130 ++++----- R/SSMcustom.R | 151 +++++------ R/SSMcycle.R | 173 ++++++------ R/SSModel.R | 433 ++++++++++++++++--------------- R/SSMregression.R | 344 ++++++++++++------------- R/SSMseasonal.R | 235 ++++++++--------- R/SSMtrend.R | 183 ++++++------- R/approxSSM.R | 32 +- R/checkModel.R | 95 +++--- R/coef.KFS.R | 10 R/deviance.KFS.R | 7 R/extract.SSModel.R | 199 +++++++------- R/fitSSM.R | 6 R/hatvalues.KFS.R | 6 R/importanceSSM.R | 146 +++++----- R/initTheta.R | 51 +-- R/internalResids.R | 71 ++--- R/interval.R | 162 +++++------ R/ldl.R | 15 - R/logLik.SSModel.R | 189 ++++++------- R/mvInnovations.R | 12 R/predict.SSModel.R | 128 ++++----- R/print.objects.R | 59 ++-- R/residuals.KFS.R | 163 ++++++----- R/rstandard.KFS.R | 32 +- R/signals.R | 110 ++++---- R/simHelper.R | 11 R/simulateSSM.R | 138 +++++----- R/subset.SSModel.R | 11 R/transformSSM.R | 250 +++++++++--------- build/vignette.rds |binary inst/CITATION | 2 inst/doc/KFAS.pdf |binary man/KFS.Rd | 3 man/SSModel.Rd | 44 ++- man/alcohol.Rd | 4 man/mvInnovations.Rd |only src/approx.f95 | 6 src/gloglik.f95 | 12 src/ngloglik.f95 | 2 46 files changed, 2239 insertions(+), 2189 deletions(-)
Title: A Collection of Network Data Sets for the 'igraph' Package
Description: A small collection of various network data sets,
to use with the 'igraph' package: the Enron email network, various food webs,
interactions in the immunoglobulin protein, the karate club network,
Koenigsberg's bridges, visuotactile brain areas of the macaque monkey,
UK faculty friendship network, domestic US flights network, etc.
Author: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraphdata versions 0.2.2 dated 2015-04-09 and 1.0.0 dated 2015-06-26
DESCRIPTION | 18 +-- LICENSE | 27 +++++ MD5 | 31 +++--- README.md |only data/Koenigsberg.rda |binary data/UKfaculty.rda |binary data/USairports.rda |binary data/enron.rda |only data/foodwebs.rda |binary data/immuno.rda |binary data/karate.rda |binary data/kite.rda |only data/macaque.rda |binary data/rfid.rda |only data/yeast.rda |binary inst/getdata.R | 256 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/enron.Rd |only man/karate.Rd | 3 man/kite.Rd |only man/rfid.Rd |only 20 files changed, 305 insertions(+), 30 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.20 dated 2015-05-30 and 0.22.0 dated 2015-06-26
BrailleR-0.20/BrailleR/inst/PREFERENCES |only BrailleR-0.22.0/BrailleR/DESCRIPTION | 13 +- BrailleR-0.22.0/BrailleR/MD5 | 36 +++--- BrailleR-0.22.0/BrailleR/NAMESPACE | 3 BrailleR-0.22.0/BrailleR/R/BRLThis.R |only BrailleR-0.22.0/BrailleR/R/MakeBatch.R | 2 BrailleR-0.22.0/BrailleR/R/MakeRprofile.R |only BrailleR-0.22.0/BrailleR/R/Options.R | 79 +++++++++++++ BrailleR-0.22.0/BrailleR/R/Premiere100.R |only BrailleR-0.22.0/BrailleR/R/SVGThis.R |only BrailleR-0.22.0/BrailleR/R/VIMethod1_JG.R | 4 BrailleR-0.22.0/BrailleR/R/zzz.R | 10 + BrailleR-0.22.0/BrailleR/inst/DEFAULTS |only BrailleR-0.22.0/BrailleR/inst/NEWS | 23 +++ BrailleR-0.22.0/BrailleR/inst/doc/BrailleRHistory.html | 29 ++--- BrailleR-0.22.0/BrailleR/inst/doc/Ex1histograms.html | 98 ++++++++--------- BrailleR-0.22.0/BrailleR/inst/fonts |only BrailleR-0.22.0/BrailleR/man/BRLThis.Rd |only BrailleR-0.22.0/BrailleR/man/BrailleR-package.Rd | 10 - BrailleR-0.22.0/BrailleR/man/Embossers.Rd |only BrailleR-0.22.0/BrailleR/man/MakeRprofile.Rd |only BrailleR-0.22.0/BrailleR/man/Options.Rd | 4 BrailleR-0.22.0/BrailleR/man/SVGThis.Rd |only BrailleR-0.22.0/BrailleR/man/SetOptions.Rd | 33 +++++ 24 files changed, 244 insertions(+), 100 deletions(-)
Title: Genetic Association Studies
Description: Some procedures including EIGENSTRAT (a procedure for
detecting and correcting for population stratification through
searching for the eigenvectors in genetic association studies),
PCoC (a procedure for correcting for population stratification
through calculating the principal coordinates and the clustering
of the subjects), Tracy-Wisdom test (a procedure for detecting
the significant eigenvalues of a matrix), distance regression (a
procedure for detecting the association between a distance matrix
and some independent variants of interest), single-marker test (a
procedure for identifying the association between the genotype at
a biallelic marker and a trait using the Wald test or the Fisher
exact test), MAX3 (a procedure for testing for the association
between a single nucleotide polymorphism and a binary phenotype
using the maximum value of the three test statistics derived for
the recessive, additive, and dominant models), nonparametric trend
test (a procedure for testing for the association between a genetic
variant and a non-normal distributed quantitative trait based on the
nonparametric risk), and nonparametric MAX3 (a procedure for testing
for the association between a biallelic single nucleotide polymorphism
and a quantitative trait using the maximum value of the three
nonparametric trend tests derived for the recessive, additive, and
dominant models), which are commonly used in genetic association studies.
Author: Lin Wang [aut],
Wei Zhang [aut],
Qizhai Li [aut],
Weicheng Zhu [ctb]
Maintainer: Lin Wang <wanglin2009@amss.ac.cn>
Diff between AssocTests versions 0.0-1 dated 2015-06-21 and 0.0-2 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-13 1.6
2012-06-28 1.2
2012-04-06 1.1
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.2 dated 2014-03-31 and 2.3 dated 2015-06-26
DESCRIPTION | 12 - MD5 | 54 ++--- NAMESPACE | 2 NEWS | 8 R/comp2col.R | 13 - R/createRec.R | 4 R/dens2col.R | 6 R/itreemap.R | 2 R/pkg.R | 4 R/str2rect.R | 40 ++- R/tmColorsLegend.R | 10 R/tmDrawRect.R | 20 + R/treecolors.R | 2 R/treefunctions.R | 2 R/treegraph.R | 19 + R/treemap.R | 21 +- R/treepalette.R | 4 R/value2col.R | 6 man/GNI2010.Rd | 9 man/business.Rd | 16 - man/itreemap.Rd | 33 --- man/random.hierarchical.data.Rd | 87 ++------ man/tmPlot.Rd | 4 man/treecolors.Rd | 14 - man/treegraph.Rd | 127 ++++-------- man/treemap-package.Rd | 24 +- man/treemap.Rd | 414 +++++++++++----------------------------- man/treepalette.Rd | 85 ++------ 28 files changed, 395 insertions(+), 647 deletions(-)
Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between soilphysics versions 2.3 dated 2015-05-09 and 2.4 dated 2015-06-26
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS | 7 + R/iwc.R | 9 +- R/llwr.R | 193 ++++++++++++++++++++++++++++----------------- man/iwc.Rd | 21 ++-- man/llwr.Rd | 74 +++++++++++------ man/soilphysics-package.Rd | 78 ++++++------------ 8 files changed, 240 insertions(+), 166 deletions(-)
Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>
Diff between libamtrack versions 0.6.1 dated 2015-05-22 and 0.6.2 dated 2015-06-26
libamtrack-0.6.1/libamtrack/man/AT.Bethe.mean.energy.loss.MeV.Rd |only libamtrack-0.6.1/libamtrack/man/AT.Vavilov.energy.loss.distribution.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.FWHM.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.distribution.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.mode.Rd |only libamtrack-0.6.1/libamtrack/man/AT.lambda.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/DESCRIPTION | 13 libamtrack-0.6.2/libamtrack/MD5 | 173 - libamtrack-0.6.2/libamtrack/NAMESPACE | 94 libamtrack-0.6.2/libamtrack/R/initial.R | 2 libamtrack-0.6.2/libamtrack/R/libamtrack.R | 385 ++- libamtrack-0.6.2/libamtrack/configure | 922 ++----- libamtrack-0.6.2/libamtrack/configure.ac | 36 libamtrack-0.6.2/libamtrack/man/AT.A.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.CSDA.energy.after.slab.E.MeV.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.CSDA.range.Bethe.g.cm2.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.D.RDD.Gy.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.E.from.beta.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Gauss.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Gauss.PDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.I.eV.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Landau.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Landau.PDF.Rd | 11 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Rutherford.SDCS.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Vavilov.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Vavilov.PDF.Rd | 11 libamtrack-0.6.2/libamtrack/man/AT.WEPL.Bethe.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Z.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.atomic.weight.from.Z.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.average.A.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.average.Z.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.beam.par.physical.to.technical.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.beam.par.technical.to.physical.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.beta.from.E.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.dose.Gy.from.fluence.cm2.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.effective.Z.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.effective.charge.from.E.MeV.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.material.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.gauss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.landau.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.vavilov.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.MeV2.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.cm2.from.dose.Gy.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.gamma.from.E.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.get.materials.data.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.kappa.Rd | 15 libamtrack-0.6.2/libamtrack/man/AT.lambda.landau.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.max.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.mean.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.vavilov.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.new.Rd |only libamtrack-0.6.2/libamtrack/man/AT.max.electron.ranges.m.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.mean.energy.loss.keV.Rd |only libamtrack-0.6.2/libamtrack/man/AT.mean.number.of.tracks.contrib.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.nuclear.spin.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.particle.no.from.Z.and.A.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.r.RDD.m.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.CPPSC.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.GSM.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.IGK.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.stopping.power.ratio.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.total.D.Gy.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.total.fluence.cm2.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.translate.dose.into.DSB.distribution.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.xi.keV.Rd |only libamtrack-0.6.2/libamtrack/man/libamtrack-package.Rd | 4 libamtrack-0.6.2/libamtrack/src/AT.c | 4 libamtrack-0.6.2/libamtrack/src/AT.h | 4 libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.c |only libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.h |only libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.c | 1240 ++++------ libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.h | 517 ++-- libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.c | 113 libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.h | 73 libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.c | 650 ++++- libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.h | 137 - libamtrack-0.6.2/libamtrack/src/AT_SPC.c | 11 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.c | 176 + libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.h | 75 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataFromFile.c | 2 libamtrack-0.6.2/libamtrack/src/CERNLIBFUNS.f |only libamtrack-0.6.2/libamtrack/src/Makevars.in | 8 libamtrack-0.6.2/libamtrack/src/config.h | 26 99 files changed, 2928 insertions(+), 1908 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraph versions 1.0.0 dated 2015-06-24 and 1.0.1 dated 2015-06-26
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++---------------- R/adjacency.R | 28 ++++++++++----------- R/attributes.R | 22 ++++++++-------- R/centrality.R | 22 ++++++++-------- R/conversion.R | 10 +++---- R/make.R | 25 ++++++++++++++++++- R/structural.properties.R | 14 +++++----- R/topology.R | 20 +++++++-------- man/arpack.Rd | 22 ++++++++-------- man/as.directed.Rd | 10 +++---- man/canonical_permutation.Rd | 20 +++++++-------- man/graph_from_adjacency_matrix.Rd | 28 ++++++++++----------- man/igraph-attribute-combination.Rd | 22 ++++++++-------- man/make_.Rd | 28 ++++++++++++++++++++- man/transitivity.Rd | 14 +++++----- src/Makevars.in | 2 - src/Makevars.win | 4 --- src/gengraph_graph_molloy_hash.cpp | 4 +-- src/gengraph_graph_molloy_optimized.cpp | 12 ++++----- src/prpack/prpack_solver.cpp | 3 +- src/uuid/gen_uuid.c | 25 ++++++++++++++----- 22 files changed, 221 insertions(+), 162 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between wgaim versions 1.4-8 dated 2015-05-06 and 1.4-10 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- R/wgaim9.R | 65 +++++------------------------------------------------ R/zzz.R | 4 +-- inst/NEWS.Rd | 11 +++++++- inst/doc/wgaim.pdf |binary 6 files changed, 27 insertions(+), 71 deletions(-)
Title: Transcriptome Overlap Measure
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette.
Author: Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Maintainer: Jingyi Jessica Li <jli@stat.ucla.edu>
Diff between TROM versions 1.0 dated 2015-04-08 and 1.1 dated 2015-06-26
TROM-1.0/TROM/inst/doc/Vignette.pdf |only TROM-1.1/TROM/DESCRIPTION | 19 + TROM-1.1/TROM/MD5 | 51 ++-- TROM-1.1/TROM/NAMESPACE | 1 TROM-1.1/TROM/R/TROM-internal.R | 250 +++++++++++------------ TROM-1.1/TROM/R/bs.trom.R | 16 + TROM-1.1/TROM/R/choose.z.R |only TROM-1.1/TROM/R/find.top.GO.slim.terms.R | 2 TROM-1.1/TROM/R/find.top.GO.terms.R | 1 TROM-1.1/TROM/R/select.associated.genes.R | 6 TROM-1.1/TROM/R/select.associated.orthologs.R | 9 TROM-1.1/TROM/R/sp.associated.idx.R | 4 TROM-1.1/TROM/R/ws.trom.R | 133 ++++++------ TROM-1.1/TROM/R/ws.trom.forZ.R |only TROM-1.1/TROM/R/ws.trom.orthologs.R | 178 ++++++++-------- TROM-1.1/TROM/R/ws.trom.three.R |only TROM-1.1/TROM/R/ws.trom.two.R |only TROM-1.1/TROM/data/GO_slim_id.rda |binary TROM-1.1/TROM/inst/dm_associated_orthologs.xlsx |binary TROM-1.1/TROM/inst/doc/TROM_Vignette.pdf |only TROM-1.1/TROM/man/TROM-package.Rd | 9 TROM-1.1/TROM/man/bs.trom.Rd | 17 - TROM-1.1/TROM/man/choose.z.Rd |only TROM-1.1/TROM/man/find.top.GO.slim.terms.Rd | 2 TROM-1.1/TROM/man/find.top.GO.terms.Rd | 2 TROM-1.1/TROM/man/heatmap.3.Rd | 4 TROM-1.1/TROM/man/select.associated.genes.Rd | 18 - TROM-1.1/TROM/man/select.associated.orthologs.Rd | 16 - TROM-1.1/TROM/man/ws.trom.Rd | 52 +++- TROM-1.1/TROM/man/ws.trom.orthologs.Rd | 66 +++--- 30 files changed, 465 insertions(+), 391 deletions(-)
Title: Datasets from Sen & Srivastava
Description: Collection of datasets from Sen & Srivastava: "Regression
Analysis, Theory, Methods and Applications", Springer. Sources
for individual data files are more fully documented in the
book.
Author: Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between SenSrivastava versions 2012-04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26
SenSrivastava-2012-04-0/SenSrivastava/SenSrivastava-Ex.R |only SenSrivastava-2015.6.25/SenSrivastava/DESCRIPTION | 17 +++++++-------- SenSrivastava-2015.6.25/SenSrivastava/MD5 | 5 +--- SenSrivastava-2015.6.25/SenSrivastava/NEWS | 3 ++ 4 files changed, 14 insertions(+), 11 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.2.2 dated 2015-01-21 and 0.3.0 dated 2015-06-26
rvertnet-0.2.2/rvertnet/NEWS |only rvertnet-0.3.0/rvertnet/DESCRIPTION | 19 rvertnet-0.3.0/rvertnet/MD5 | 71 +- rvertnet-0.3.0/rvertnet/NAMESPACE | 5 rvertnet-0.3.0/rvertnet/R/bigsearch.R | 11 rvertnet-0.3.0/rvertnet/R/searchbyterm.R | 45 - rvertnet-0.3.0/rvertnet/R/vertmap.R | 25 rvertnet-0.3.0/rvertnet/R/vertsearch.R | 13 rvertnet-0.3.0/rvertnet/R/vertsummary.R | 2 rvertnet-0.3.0/rvertnet/R/yyy.R | 4 rvertnet-0.3.0/rvertnet/R/zzz.R | 163 +++-- rvertnet-0.3.0/rvertnet/README.md | 196 ++++-- rvertnet-0.3.0/rvertnet/build/vignette.rds |binary rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.Rmd | 363 +++++++++--- rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.html | 346 ++++++++--- rvertnet-0.3.0/rvertnet/inst/ignore |only rvertnet-0.3.0/rvertnet/inst/vign/figure |only rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.Rmd | 79 ++ rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.md | 361 +++++++++-- rvertnet-0.3.0/rvertnet/man/bigsearch.Rd | 11 rvertnet-0.3.0/rvertnet/man/rvertnet-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/rvertnet-package.Rd | 2 rvertnet-0.3.0/rvertnet/man/searchbyterm.Rd | 34 - rvertnet-0.3.0/rvertnet/man/spatialsearch.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertavailablemaps-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertlocations-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertmap.Rd | 16 rvertnet-0.3.0/rvertnet/man/vertoccurrence-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertoccurrencecount-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertproviders-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertsearch.Rd | 8 rvertnet-0.3.0/rvertnet/man/vertsummary.Rd | 4 rvertnet-0.3.0/rvertnet/man/verttaxa-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/tests/testthat.R |only rvertnet-0.3.0/rvertnet/tests/testthat/test-bigsearch.R | 10 rvertnet-0.3.0/rvertnet/tests/testthat/test-searchbyterm.R | 65 +- rvertnet-0.3.0/rvertnet/tests/testthat/test-spatialsearch.R | 28 rvertnet-0.3.0/rvertnet/vignettes/rvertnet_vignette.Rmd | 363 +++++++++--- 38 files changed, 1646 insertions(+), 614 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com>
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.5.3 dated 2013-07-26 and 0.6.1 dated 2015-06-26
Nippon-0.5.3/Nippon/Nippon-Ex.R |only Nippon-0.5.3/Nippon/configure.ac.orig |only Nippon-0.5.3/Nippon/man/ja |only Nippon-0.5.3/Nippon/src/Makevars.in.orig |only Nippon-0.5.3/Nippon/src/Makevars.orig |only Nippon-0.6.1/Nippon/ChangeLog | 14 + Nippon-0.6.1/Nippon/DESCRIPTION | 14 - Nippon-0.6.1/Nippon/MD5 | 44 ++--- Nippon-0.6.1/Nippon/NAMESPACE | 1 Nippon-0.6.1/Nippon/R/JapanPrefecturesMap.R | 2 Nippon-0.6.1/Nippon/R/jholiday.R | 7 Nippon-0.6.1/Nippon/R/kakasi.R | 32 --- Nippon-0.6.1/Nippon/R/zen2han.R | 28 ++- Nippon-0.6.1/Nippon/TODO | 3 Nippon-0.6.1/Nippon/configure | 212 ++++++++++++------------- Nippon-0.6.1/Nippon/configure.ac | 4 Nippon-0.6.1/Nippon/man/JapanPrefecturesMap.Rd | 4 Nippon-0.6.1/Nippon/man/Nippon-package.Rd | 12 - Nippon-0.6.1/Nippon/man/jyear.Rd | 1 Nippon-0.6.1/Nippon/man/kakasi.Rd | 23 +- Nippon-0.6.1/Nippon/man/zen2han.Rd | 15 - Nippon-0.6.1/Nippon/src/kakasi/config.h.in | 10 - Nippon-0.6.1/Nippon/src/kakasi/libdict.c | 4 Nippon-0.6.1/Nippon/src/kakasi/libhh2.c | 132 ++++++++++----- Nippon-0.6.1/Nippon/src/kakasi/libhh2.c.new |only Nippon-0.6.1/Nippon/src/kakasi/libkanjiio.c | 10 - 26 files changed, 308 insertions(+), 264 deletions(-)
Title: Two Stage Least Squares with Model Implied Instrumental Variable
Search
Description: Functions for estimating structural equation models
using a model-implied instrumental variable (MIIV) search
and two stage least squares (2SLS) estimator (MIIV-2SLS).
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.2 dated 2015-06-05 and 0.3 dated 2015-06-26
DESCRIPTION | 9 ++-- MD5 | 12 ++--- R/miive.R | 117 +++++++++++++++++++++++++++++++++----------------------- R/miivs.R | 82 +++++++++++++-------------------------- R/print.miivs.R | 10 ++++ man/miive.Rd | 2 man/miivs.Rd | 4 + 7 files changed, 123 insertions(+), 113 deletions(-)
Title: Data from the Book "Multivariate Statistical Modelling Based on
Generalized Linear Models", First Edition, by Ludwig Fahrmeir
and Gerhard Tutz
Description: Data and functions for the book "Multivariate Statistical
Modelling Based on Generalized Linear Models", first edition, by
Ludwig Fahrmeir and Gerhard Tutz. Useful when using the book.
Author: compiled by Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between Fahrmeir versions 2012.04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26
DESCRIPTION | 23 ++++++++++++----------- MD5 | 4 ++-- NEWS | 5 +++++ 3 files changed, 19 insertions(+), 13 deletions(-)
Title: Empirical Bayesian Elastic Net
Description: Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet'
package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBEN versions 1.1.1 dated 2014-06-09 and 4.1 dated 2015-06-26
DESCRIPTION | 13 MD5 | 30 - R/EBelasticNet.Binomial.R |only R/EBelasticNet.BinomialCV.R |only R/EBelasticNet.Gaussian.R | 41 +- R/EBelasticNet.GaussianCV.R | 15 data/BASISbinomial.rda |only data/yBinomial.rda |only man/BASIS.Rd | 3 man/BASISbinomial.Rd |only man/EBEN-package.Rd | 34 + man/EBelasticNet.Binomial.Rd |only man/EBelasticNet.BinomialCV.Rd |only man/EBelasticNet.Gaussian.Rd | 41 -- man/EBelasticNet.GaussianCV.Rd | 33 - man/y.Rd | 3 man/yBinomial.Rd |only src/ElasticNetBinaryNEmainEff.c |only src/ElasticNetBinaryNeFull.c |only src/elasticNetLinearNeFull2.c | 629 +++++++++++++++++++------------ src/elasticNetLinearNeMainEff.c | 809 +++++++++++++++++++++++++++------------- 21 files changed, 1070 insertions(+), 581 deletions(-)
Title: Useful Functions for Box, Hunter and Hunter II
Description: Functions and data sets reproducing some examples in
Box, Hunter and Hunter II. Useful for statistical design
of experiments, especially factorial experiments.
Author: Ernesto Barrios
Maintainer: Kjetil B.Halvorsen <kjetil1001@gmail.com>
Diff between BHH2 versions 2012.04-0 dated 2012-04-04 and 2015.06.25 dated 2015-06-26
DESCRIPTION | 14 ++++++++------ MD5 | 26 ++++++++++++++------------ NEWS | 2 ++ build |only data/corrosion.data.rda |binary data/heads.data.rda |binary data/penicillin.data.rda |binary data/poison.data.rda |binary data/shoes.data.rda |binary data/tab03B1.rda |binary data/tab03B2.rda |binary data/tomato.data.rda |binary data/woolen.data.rda |binary inst/doc/BHH2.R |only inst/doc/BHH2.pdf |binary 15 files changed, 24 insertions(+), 18 deletions(-)
Title: Calculate Power Utilizing Asymptotic Likelihood Ratio Methods
Description: A set of routines written in the S language
that calculate power and related quantities utilizing asymptotic
likelihood ratio methods.
Author: S original by Barry W. Brown, James Lovato and Kathy Russel.
R port by Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between asypow versions 2013.9-1 dated 2013-09-24 and 2015.6.25 dated 2015-06-26
asypow-2013.9-1/asypow/library.README |only asypow-2015.6.25/asypow/DESCRIPTION | 8 ++++---- asypow-2015.6.25/asypow/MD5 | 10 +++++----- asypow-2015.6.25/asypow/NEWS | 5 +++++ asypow-2015.6.25/asypow/README |only asypow-2015.6.25/asypow/inst/doc/asypow.pdf |binary asypow-2015.6.25/asypow/inst/doc/asypow.statlib.pdf |binary 7 files changed, 14 insertions(+), 9 deletions(-)
Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions
that have to be met so that errors in data used in
analysis pipelines can fail quickly. Similar to
'stopifnot()' but more powerful, friendly, and easier
for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>
Diff between assertr versions 0.4.1 dated 2015-03-24 and 1.0.0 dated 2015-06-26
DESCRIPTION | 10 - MD5 | 53 +++-- NAMESPACE | 11 + NEWS | 29 ++ R/assertions.R | 378 ++++++++++++++++++++++++++++++++++----- R/assertr.R | 27 ++ R/predicates.R | 129 ++++++++++--- R/row-redux.R |only R/utils.R | 56 +++++ README.md | 87 +++++++- build/vignette.rds |binary inst/doc/assertr.R | 7 inst/doc/assertr.Rmd | 295 +++++++++++++++++++++++++++--- inst/doc/assertr.html | 171 +++++++++++++++-- man/assert.Rd | 38 +++ man/assert_rows.Rd |only man/assertr.Rd | 29 ++ man/in_set.Rd | 2 man/insist.Rd | 28 ++ man/insist_rows.Rd |only man/maha_dist.Rd |only man/not_na.Rd | 16 - man/num_row_NAs.Rd |only man/verify.Rd | 7 man/within_bounds.Rd | 12 - man/within_n_mads.Rd |only man/within_n_sds.Rd | 7 tests/testthat/test-assertions.R | 367 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-predicates.R | 100 +++++++++- tests/testthat/test-row-redux.R |only vignettes/assertr.Rmd | 295 +++++++++++++++++++++++++++--- 31 files changed, 1908 insertions(+), 246 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 0.4-1 dated 2015-05-04 and 0.4-4 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- R/mstmap10.R | 56 +++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/asmapvignette.Rnw | 2 - vignettes/asmapvignette.Rnw | 2 - 7 files changed, 52 insertions(+), 35 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-0 dated 2014-12-08 and 1.0-1 dated 2015-06-26
DESCRIPTION | 17 MD5 | 29 NAMESPACE | 7 R/graph.R | 1405 ++++++++++++++++++++++++------------------------ R/plot.R | 152 ++--- R/save.R | 2 R/scatterplot.R | 7 build/vignette.rds |binary inst/NEWS | 9 inst/doc/arulesViz.R | 7 inst/doc/arulesViz.Rnw | 22 inst/doc/arulesViz.pdf |binary inst/n.html |only man/plot.Rd | 20 man/save.Rd | 1 vignettes/arulesViz.Rnw | 22 16 files changed, 868 insertions(+), 832 deletions(-)
Title: Finnish Open Government Data Toolkit
Description: Algorithms for Finnish open government data.
Author: Leo Lahti, Juuso Parkkinen, Joona Lehtomaki, Juuso Haapanen, Jussi
Paananen, Einari Happonen
Maintainer: Leo Lahti <louhos@googlegroups.com>
Diff between sorvi versions 0.7.20 dated 2015-02-17 and 0.7.26 dated 2015-06-25
sorvi-0.7.20/sorvi/R/postalcodes.R |only sorvi-0.7.20/sorvi/R/provinceinfo.R |only sorvi-0.7.20/sorvi/R/utilities.R |only sorvi-0.7.20/sorvi/R/visualization.R |only sorvi-0.7.20/sorvi/inst/NEWS |only sorvi-0.7.20/sorvi/man/get_postal_code_info.Rd |only sorvi-0.7.20/sorvi/man/get_province_info_wikipedia.Rd |only sorvi-0.7.20/sorvi/man/korvaa_skandit.Rd |only sorvi-0.7.20/sorvi/man/strip.Rd |only sorvi-0.7.20/sorvi/man/strstrip.Rd |only sorvi-0.7.20/sorvi/man/strstrip_single.Rd |only sorvi-0.7.20/sorvi/vignettes/TODO.Rmd |only sorvi-0.7.20/sorvi/vignettes/figure |only sorvi-0.7.26/sorvi/DESCRIPTION | 12 sorvi-0.7.26/sorvi/LICENSE | 2 sorvi-0.7.26/sorvi/MD5 | 86 ++-- sorvi-0.7.26/sorvi/NAMESPACE | 16 sorvi-0.7.26/sorvi/NEWS.md |only sorvi-0.7.26/sorvi/R/convert_municipality_codes.R |only sorvi-0.7.26/sorvi/R/convert_municipality_names.R |only sorvi-0.7.26/sorvi/R/data.R |only sorvi-0.7.26/sorvi/R/firstlib.R | 4 sorvi-0.7.26/sorvi/R/get_municipality_info_mml.R |only sorvi-0.7.26/sorvi/R/harmonize_names.R |only sorvi-0.7.26/sorvi/R/hetu.R | 115 ++++- sorvi-0.7.26/sorvi/R/is_url.R |only sorvi-0.7.26/sorvi/R/load_sorvi_data.R |only sorvi-0.7.26/sorvi/R/municipality_to_province.R |only sorvi-0.7.26/sorvi/R/regression_plot.R |only sorvi-0.7.26/sorvi/R/ropengov_storage_path.R |only sorvi-0.7.26/sorvi/R/sorvi-package.R | 6 sorvi-0.7.26/sorvi/R/synonymes.R |only sorvi-0.7.26/sorvi/README.md | 19 sorvi-0.7.26/sorvi/build/vignette.rds |binary sorvi-0.7.26/sorvi/inst/CITATION | 6 sorvi-0.7.26/sorvi/inst/doc/sorvi.pdf |binary sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.R | 86 ++-- sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.Rmd | 118 +++-- sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.html | 232 ++++------- sorvi-0.7.26/sorvi/inst/extdata/municipality_synonymes.csv |only sorvi-0.7.26/sorvi/man/check_synonymes.Rd |only sorvi-0.7.26/sorvi/man/convert_municipality_codes.Rd | 4 sorvi-0.7.26/sorvi/man/convert_municipality_names.Rd | 6 sorvi-0.7.26/sorvi/man/fi.en.maakunnat.Rd | 4 sorvi-0.7.26/sorvi/man/get_municipality_info_mml.Rd | 9 sorvi-0.7.26/sorvi/man/harmonize_names.Rd |only sorvi-0.7.26/sorvi/man/hetu.Rd | 41 + sorvi-0.7.26/sorvi/man/is_url.Rd | 4 sorvi-0.7.26/sorvi/man/load_sorvi_data.Rd | 4 sorvi-0.7.26/sorvi/man/municipality_to_province.Rd | 4 sorvi-0.7.26/sorvi/man/regression_plot.Rd | 16 sorvi-0.7.26/sorvi/man/ropengov_storage_path.Rd | 4 sorvi-0.7.26/sorvi/man/sorvi-package.Rd | 8 sorvi-0.7.26/sorvi/man/valid_hetu.Rd | 15 sorvi-0.7.26/sorvi/tests |only sorvi-0.7.26/sorvi/vignettes/TODO.md |only sorvi-0.7.26/sorvi/vignettes/sorvi_tutorial.Rmd | 118 +++-- sorvi-0.7.26/sorvi/vignettes/sorvi_tutorial.md | 272 +++++-------- 58 files changed, 644 insertions(+), 567 deletions(-)
Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based
tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and
performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Brian Davis <Brian.Davis281@gmail.com>
Diff between seqMeta versions 1.5 dated 2014-10-28 and 1.6.0 dated 2015-06-25
seqMeta-1.5/seqMeta/man/prepAdj.Rd |only seqMeta-1.6.0/seqMeta/DESCRIPTION | 20 seqMeta-1.6.0/seqMeta/MD5 | 67 seqMeta-1.6.0/seqMeta/NAMESPACE | 23 seqMeta-1.6.0/seqMeta/R/burdenMeta.R | 313 ++-- seqMeta-1.6.0/seqMeta/R/c.seqMeta.R | 44 seqMeta-1.6.0/seqMeta/R/check_format_skat.R | 37 seqMeta-1.6.0/seqMeta/R/coxlr.fit.R | 170 +- seqMeta-1.6.0/seqMeta/R/pchisqsum2.R | 140 - seqMeta-1.6.0/seqMeta/R/prepAdjust.R | 154 +- seqMeta-1.6.0/seqMeta/R/prepCox.R | 276 +-- seqMeta-1.6.0/seqMeta/R/prepScores.R | 882 ++++++----- seqMeta-1.6.0/seqMeta/R/prepScores2.R |only seqMeta-1.6.0/seqMeta/R/seqMeta.R |only seqMeta-1.6.0/seqMeta/R/singlesnpMeta.R | 321 ++-- seqMeta-1.6.0/seqMeta/R/skatMeta.R | 358 +++- seqMeta-1.6.0/seqMeta/R/skatOMeta.R | 698 +++++---- seqMeta-1.6.0/seqMeta/R/utils.R |only seqMeta-1.6.0/seqMeta/README.md |only seqMeta-1.6.0/seqMeta/build/vignette.rds |binary seqMeta-1.6.0/seqMeta/data/datalist | 4 seqMeta-1.6.0/seqMeta/data/seqMetaExample.rda |binary seqMeta-1.6.0/seqMeta/inst/doc/seqMeta.R | 390 ++--- seqMeta-1.6.0/seqMeta/inst/doc/seqMeta.Rnw | 1994 +++++++++++++------------- seqMeta-1.6.0/seqMeta/man/SNPInfo.Rd | 70 seqMeta-1.6.0/seqMeta/man/burdenMeta.Rd | 226 +- seqMeta-1.6.0/seqMeta/man/prepCondScores.Rd |only seqMeta-1.6.0/seqMeta/man/prepScores.Rd | 326 ++-- seqMeta-1.6.0/seqMeta/man/prepScores2.Rd |only seqMeta-1.6.0/seqMeta/man/seqMeta.Rd |only seqMeta-1.6.0/seqMeta/man/seqMetaExample.Rd | 136 - seqMeta-1.6.0/seqMeta/man/singlesnpMeta.Rd | 208 +- seqMeta-1.6.0/seqMeta/man/skatMeta.Rd | 312 +--- seqMeta-1.6.0/seqMeta/man/skatOMeta.Rd | 375 ++-- seqMeta-1.6.0/seqMeta/tests |only seqMeta-1.6.0/seqMeta/vignettes/seqMeta.Rnw | 1994 +++++++++++++------------- 36 files changed, 5112 insertions(+), 4426 deletions(-)
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using
various projection pursuit indices.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PPtreeViz versions 1.0.3 dated 2015-05-15 and 1.1.0 dated 2015-06-25
DESCRIPTION | 14 - MD5 | 58 ++-- NAMESPACE | 1 R/Huberplot.R | 27 +- R/LDAopt.R | 13 - R/PDAopt.R | 17 - R/PPclassNodeViz.R | 15 - R/PPclassify.R | 23 + R/PPoptViz.R | 4 R/PPtreeClass.R | 31 +- R/RcppExports.R | 27 +- R/plotPPtreeclass.R | 8 R/predictPPtreeclass.R |only R/printPPtreeclass.R | 6 man/ENTROPYindex1D.Rd | 5 man/GINIindex1D.Rd | 5 man/Huber.plot.Rd | 22 + man/LDAindex.Rd | 2 man/LDAopt.Rd | 15 - man/Lrindex.Rd | 5 man/PDAindex.Rd | 5 man/PDAopt.Rd | 19 - man/PP.Tree.class.Rd | 25 +- man/PP.classify.Rd | 27 +- man/PPclassNode.Viz.Rd | 13 - man/PPopt.Rd | 15 - man/PPopt.Viz.Rd | 7 man/plot.PPtreeclass.Rd | 10 man/predict.PPtreeclass.Rd |only man/print.PPtreeclass.Rd | 4 src/PPoptimize.cpp | 528 +++++++++++++++++++++------------------------ 31 files changed, 503 insertions(+), 448 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora <ctortora@math.mcmaster.ca>
Diff between MixGHD versions 1.6 dated 2015-05-26 and 1.7 dated 2015-06-25
DESCRIPTION | 12 +- MD5 | 45 +++++---- NAMESPACE | 4 R/ARI.R |only R/DA.R | 30 +++--- R/GHD.R | 258 ++++++++++++++++++++++++++++++++---------------------- R/MCGHD.R | 50 ++++------ R/MGHD.R | 47 +++++---- R/MGHFA.R | 57 +++++++---- R/MSGHD.R | 44 +++++---- R/Selection.R | 67 +++++++------- R/cMSGHD.R | 50 +++++----- R/usedSelection.R |only data/banknote.rda |only data/datalist | 1 man/ARI.Rd |only man/DA.Rd | 3 man/MCGHD.Rd | 13 +- man/MGHD.Rd | 17 ++- man/MGHFA.Rd | 14 +- man/MSGHD.Rd | 9 + man/Selection.Rd | 11 +- man/banknote.Rd |only man/bankruptcy.Rd | 2 man/cMSGHD.Rd | 30 ++++-- man/sonar.Rd | 4 26 files changed, 440 insertions(+), 328 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch> and Sören Vogel <soeren.vogel@posteo.ch>
Maintainer: Sören Vogel <soeren.vogel@posteo.ch>
Diff between GUTS versions 0.9.3 dated 2015-05-15 and 1.0.0 dated 2015-06-25
GUTS-0.9.3/GUTS/R/RcppExports.R |only GUTS-0.9.3/GUTS/src/guts_calc_loglikelihood.cpp |only GUTS-1.0.0/GUTS/DESCRIPTION | 13 - GUTS-1.0.0/GUTS/MD5 | 17 -- GUTS-1.0.0/GUTS/R/GUTS.R | 198 +++++++----------------- GUTS-1.0.0/GUTS/data/diazinon.rda |binary GUTS-1.0.0/GUTS/man/GUTS-package.Rd | 15 - GUTS-1.0.0/GUTS/man/GUTS.Rd | 114 +++++-------- GUTS-1.0.0/GUTS/man/diazinon.Rd | 6 GUTS-1.0.0/GUTS/src/RcppExports.cpp | 21 +- GUTS-1.0.0/GUTS/src/guts_engine.cpp |only 11 files changed, 141 insertions(+), 243 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like Codecov (http://codecov.io)
or Coveralls (http://coveralls.io). Code coverage is a measure of the
amount of code being exercised by the tests. It is an indirect measure of
test quality. This package is compatible with any testing methodology or
framework and tracks coverage of both R code and compiled C/C++/Fortran code.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 1.0.0 dated 2015-05-20 and 1.2.0 dated 2015-06-25
DESCRIPTION | 11 +- MD5 | 36 +++---- R/codecov.R | 74 +++++++++----- R/covr.R | 18 ++- R/exclusions.R | 48 ++++++++- R/shiny.R | 28 ++--- R/subprocess.R | 2 R/summary_functions.R | 14 +- R/trace_calls.R | 3 README.md | 45 ++++++++ build/vignette.rds |binary man/codecov.Rd | 11 +- man/exclusions.Rd |only man/package_coverage.Rd | 9 + tests/testthat/test-closures.R |only tests/testthat/test-codecov.R | 204 +++++++++++++++++----------------------- tests/testthat/test-coveralls.R | 8 - tests/testthat/test-print.R | 10 - tests/testthat/test-summary.R | 4 vignettes/how_it_works.Rmd | 2 20 files changed, 318 insertions(+), 209 deletions(-)
More information about translation.ko at CRAN
Permanent link
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-147 dated 2015-05-28 and 0.15-176 dated 2015-06-25
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- README | 4 ++-- configure | 22 +++++++++------------- configure.ac | 25 +++++++++++-------------- src/worker/Makefile.in | 2 +- src/worker/Rhpc.cmd.in | 18 +++++++++++------- src/worker/RhpcWin.cmd.in | 44 ++++++++++++++++++++++++++++---------------- 9 files changed, 84 insertions(+), 65 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr versions 0.6.1 dated 2015-01-01 and 1.0.0 dated 2015-06-25
httr-0.6.1/httr/R/http--request.r |only httr-0.6.1/httr/R/perform.R |only httr-0.6.1/httr/man/brew_dr.Rd |only httr-0.6.1/httr/src |only httr-0.6.1/httr/tests/testthat/test-oauth-listener.R |only httr-1.0.0/httr/DESCRIPTION | 21 - httr-1.0.0/httr/MD5 | 258 +++++++++---------- httr-1.0.0/httr/NAMESPACE | 28 -- httr-1.0.0/httr/R/authenticate.r | 8 httr-1.0.0/httr/R/body.R | 98 +++---- httr-1.0.0/httr/R/cache.R | 17 - httr-1.0.0/httr/R/config.r | 106 +------ httr-1.0.0/httr/R/content-parse.r | 48 +-- httr-1.0.0/httr/R/content.r | 12 httr-1.0.0/httr/R/cookies.r | 12 httr-1.0.0/httr/R/doctor.R | 4 httr-1.0.0/httr/R/envvar.R | 2 httr-1.0.0/httr/R/handle.r | 22 - httr-1.0.0/httr/R/headers.r | 54 +++ httr-1.0.0/httr/R/hmac.r | 2 httr-1.0.0/httr/R/http-delete.r | 5 httr-1.0.0/httr/R/http-get.r | 5 httr-1.0.0/httr/R/http-head.r | 7 httr-1.0.0/httr/R/http-patch.r | 5 httr-1.0.0/httr/R/http-post.r | 12 httr-1.0.0/httr/R/http-put.r | 6 httr-1.0.0/httr/R/http-verb.R | 15 - httr-1.0.0/httr/R/httr.r | 4 httr-1.0.0/httr/R/media-parse.r | 2 httr-1.0.0/httr/R/oauth-app.r | 11 httr-1.0.0/httr/R/oauth-endpoint.r | 2 httr-1.0.0/httr/R/oauth-init.R | 1 httr-1.0.0/httr/R/oauth-listener.r | 16 - httr-1.0.0/httr/R/oauth-signature.r | 4 httr-1.0.0/httr/R/oauth-token.r | 14 - httr-1.0.0/httr/R/progress.R | 7 httr-1.0.0/httr/R/proxy.r | 12 httr-1.0.0/httr/R/request.R |only httr-1.0.0/httr/R/safe-callback.R | 29 -- httr-1.0.0/httr/R/timeout.r | 2 httr-1.0.0/httr/R/upload-file.r | 17 - httr-1.0.0/httr/R/url-query.r | 14 - httr-1.0.0/httr/R/url.r | 4 httr-1.0.0/httr/R/utils.r | 52 +++ httr-1.0.0/httr/R/verbose.r | 9 httr-1.0.0/httr/R/write-function.R | 128 +-------- httr-1.0.0/httr/README.md | 6 httr-1.0.0/httr/build/vignette.rds |binary httr-1.0.0/httr/demo/oauth1-twitter.r | 10 httr-1.0.0/httr/demo/oauth1-vimeo.r | 7 httr-1.0.0/httr/demo/oauth1-withings.r | 23 + httr-1.0.0/httr/demo/oauth1-yahoo.r | 7 httr-1.0.0/httr/demo/oauth2-github.r | 13 httr-1.0.0/httr/demo/oauth2-google.r | 7 httr-1.0.0/httr/demo/oauth2-linkedin.r | 10 httr-1.0.0/httr/inst/doc/api-packages.R | 10 httr-1.0.0/httr/inst/doc/api-packages.Rmd | 12 httr-1.0.0/httr/inst/doc/api-packages.html | 42 +-- httr-1.0.0/httr/inst/doc/quickstart.R | 10 httr-1.0.0/httr/inst/doc/quickstart.Rmd | 2 httr-1.0.0/httr/inst/doc/quickstart.html | 151 ++++------- httr-1.0.0/httr/man/BROWSE.Rd | 2 httr-1.0.0/httr/man/DELETE.Rd | 2 httr-1.0.0/httr/man/GET.Rd | 2 httr-1.0.0/httr/man/HEAD.Rd | 4 httr-1.0.0/httr/man/PATCH.Rd | 7 httr-1.0.0/httr/man/POST.Rd | 7 httr-1.0.0/httr/man/PUT.Rd | 7 httr-1.0.0/httr/man/Token-class.Rd | 2 httr-1.0.0/httr/man/VERB.Rd | 33 ++ httr-1.0.0/httr/man/add_headers.Rd | 2 httr-1.0.0/httr/man/authenticate.Rd | 2 httr-1.0.0/httr/man/cache_info.Rd | 2 httr-1.0.0/httr/man/config.Rd | 6 httr-1.0.0/httr/man/content.Rd | 15 - httr-1.0.0/httr/man/content_type.Rd | 2 httr-1.0.0/httr/man/cookies.Rd | 2 httr-1.0.0/httr/man/guess_media.Rd | 2 httr-1.0.0/httr/man/handle.Rd | 5 httr-1.0.0/httr/man/handle_pool.Rd | 2 httr-1.0.0/httr/man/has_content.Rd | 2 httr-1.0.0/httr/man/headers.Rd | 2 httr-1.0.0/httr/man/hmac_sha1.Rd | 2 httr-1.0.0/httr/man/http_condition.Rd | 2 httr-1.0.0/httr/man/http_error.Rd | 2 httr-1.0.0/httr/man/http_status.Rd | 2 httr-1.0.0/httr/man/httr.Rd | 6 httr-1.0.0/httr/man/httr_dr.Rd |only httr-1.0.0/httr/man/httr_options.Rd | 2 httr-1.0.0/httr/man/init_oauth1.0.Rd | 2 httr-1.0.0/httr/man/init_oauth2.0.Rd | 2 httr-1.0.0/httr/man/insensitive.Rd | 2 httr-1.0.0/httr/man/jwt_signature.Rd | 2 httr-1.0.0/httr/man/modify_url.Rd | 2 httr-1.0.0/httr/man/oauth1.0_token.Rd | 2 httr-1.0.0/httr/man/oauth2.0_token.Rd | 2 httr-1.0.0/httr/man/oauth_app.Rd | 13 httr-1.0.0/httr/man/oauth_callback.Rd | 2 httr-1.0.0/httr/man/oauth_endpoint.Rd | 4 httr-1.0.0/httr/man/oauth_endpoints.Rd | 2 httr-1.0.0/httr/man/oauth_exchanger.Rd | 2 httr-1.0.0/httr/man/oauth_listener.Rd | 6 httr-1.0.0/httr/man/oauth_service_token.Rd | 2 httr-1.0.0/httr/man/oauth_signature.Rd | 2 httr-1.0.0/httr/man/parse_http_date.Rd | 2 httr-1.0.0/httr/man/parse_media.Rd | 2 httr-1.0.0/httr/man/parse_url.Rd | 2 httr-1.0.0/httr/man/progress.Rd | 2 httr-1.0.0/httr/man/response.Rd | 2 httr-1.0.0/httr/man/revoke_all.Rd | 2 httr-1.0.0/httr/man/safe_callback.Rd | 15 - httr-1.0.0/httr/man/set_config.Rd | 2 httr-1.0.0/httr/man/set_cookies.Rd | 2 httr-1.0.0/httr/man/sign_oauth.Rd | 2 httr-1.0.0/httr/man/status_code.Rd | 2 httr-1.0.0/httr/man/timeout.Rd | 2 httr-1.0.0/httr/man/upload_file.Rd | 9 httr-1.0.0/httr/man/url_ok.Rd | 2 httr-1.0.0/httr/man/url_success.Rd | 2 httr-1.0.0/httr/man/use_proxy.Rd | 8 httr-1.0.0/httr/man/user_agent.Rd | 2 httr-1.0.0/httr/man/verbose.Rd | 2 httr-1.0.0/httr/man/with_config.Rd | 2 httr-1.0.0/httr/man/write_disk.Rd | 2 httr-1.0.0/httr/man/write_function.Rd | 23 - httr-1.0.0/httr/man/write_stream.Rd | 10 httr-1.0.0/httr/tests/testthat/test-body.r | 18 + httr-1.0.0/httr/tests/testthat/test-config.r | 72 ----- httr-1.0.0/httr/tests/testthat/test-header.r | 27 - httr-1.0.0/httr/tests/testthat/test-oauth.R |only httr-1.0.0/httr/tests/testthat/test-request.r | 36 -- httr-1.0.0/httr/tests/testthat/test-response.r | 38 ++ httr-1.0.0/httr/vignettes/api-packages.Rmd | 12 httr-1.0.0/httr/vignettes/quickstart.Rmd | 2 134 files changed, 876 insertions(+), 986 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.1 dated 2015-06-17 and 4.4.2 dated 2015-06-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ R/as.char.R | 13 +++++++++---- R/lib.R | 3 +++ R/model.matrix.earth.R | 10 ++++++---- R/stop.if.dots.R | 1 + inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/test.full.Rout.save | 4 ++-- 10 files changed, 39 insertions(+), 22 deletions(-)
Title: Fault Tolerant Simple Network of Workstations
Description: Extension of the snow package supporting fault tolerant and reproducible applications, as well as supporting easy-to-use parallel programming - only one function is needed.
Author: Hana Sevcikova, A. J. Rossini
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between snowFT versions 1.3-0 dated 2012-12-13 and 1.4-0 dated 2015-06-25
ChangeLog | 4 ++ DESCRIPTION | 15 +++----- MD5 | 14 +++---- NAMESPACE | 2 - R/snowFT.R | 89 +++++++++++-------------------------------------- man/snowFT-internal.Rd | 10 ++--- man/snowFT-package.Rd | 4 +- man/snowFT-rand.Rd | 27 ++++---------- 8 files changed, 55 insertions(+), 110 deletions(-)
Title: An Interactive Environment for Learning Statistics
Description: Allows students to use R as an interactive educational environment
for statistical concepts, ranging from p-values to confidence intervals
to stability in time series.
Author: Daniel Walter [aut, cre]
Maintainer: Daniel Walter <dswalter@gmail.com>
Diff between learnstats versions 0.1.0 dated 2015-05-02 and 0.1.1 dated 2015-06-25
learnstats-0.1.0/learnstats/inst/uniform_two |only learnstats-0.1.0/learnstats/man/s_uniform.Rd |only learnstats-0.1.1/learnstats/DESCRIPTION | 17 learnstats-0.1.1/learnstats/MD5 | 82 - learnstats-0.1.1/learnstats/NAMESPACE | 33 learnstats-0.1.1/learnstats/R/Rcmdr.R | 15 learnstats-0.1.1/learnstats/R/call_shinies.R | 139 +- learnstats-0.1.1/learnstats/R/learnstats.R | 24 learnstats-0.1.1/learnstats/R/prob.R | 530 +++++------ learnstats-0.1.1/learnstats/R/pval.R | 722 +++++++-------- learnstats-0.1.1/learnstats/R/qqsim.R | 562 +++++------ learnstats-0.1.1/learnstats/R/timeseriessim.R | 490 +++++----- learnstats-0.1.1/learnstats/inst/betabinomial/server.R | 158 +-- learnstats-0.1.1/learnstats/inst/betabinomial/ui.R | 107 +- learnstats-0.1.1/learnstats/inst/fdist/server.R | 44 learnstats-0.1.1/learnstats/inst/fdist/ui.R | 44 learnstats-0.1.1/learnstats/inst/introbinomial/server.R | 114 +- learnstats-0.1.1/learnstats/inst/introbinomial/ui.R | 56 - learnstats-0.1.1/learnstats/inst/normapprox2bin/server.R | 102 +- learnstats-0.1.1/learnstats/inst/normapprox2bin/ui.R | 60 - learnstats-0.1.1/learnstats/inst/propconfint/server.R | 112 +- learnstats-0.1.1/learnstats/inst/propconfint/ui.R | 92 - learnstats-0.1.1/learnstats/inst/tdist/server.R | 88 - learnstats-0.1.1/learnstats/inst/tdist/ui.R | 74 - learnstats-0.1.1/learnstats/inst/timeseries/server.R | 190 +-- learnstats-0.1.1/learnstats/inst/timeseries/ui.R | 72 - learnstats-0.1.1/learnstats/inst/twonorm/server.R | 114 +- learnstats-0.1.1/learnstats/inst/twonorm/ui.R | 62 - learnstats-0.1.1/learnstats/inst/uniform/server.R | 64 - learnstats-0.1.1/learnstats/inst/uniform/ui.R | 42 learnstats-0.1.1/learnstats/man/Rcmdr.Rd | 34 learnstats-0.1.1/learnstats/man/prob.Rd | 30 learnstats-0.1.1/learnstats/man/pval.Rd | 30 learnstats-0.1.1/learnstats/man/qqsim.Rd | 30 learnstats-0.1.1/learnstats/man/s_fdist.Rd | 30 learnstats-0.1.1/learnstats/man/s_introbinom.Rd | 30 learnstats-0.1.1/learnstats/man/s_normbinom.Rd | 30 learnstats-0.1.1/learnstats/man/s_propci.Rd | 30 learnstats-0.1.1/learnstats/man/s_tdist.Rd | 30 learnstats-0.1.1/learnstats/man/s_timeseries.Rd | 30 learnstats-0.1.1/learnstats/man/s_twonorm.Rd | 30 learnstats-0.1.1/learnstats/man/stats250.Rd | 22 learnstats-0.1.1/learnstats/man/timeseressim.Rd | 30 43 files changed, 2288 insertions(+), 2307 deletions(-)
Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ajpete@uw.edu>
Diff between flam versions 1.0 dated 2014-10-13 and 2.0 dated 2015-06-25
flam-1.0/flam/R/R_package_fcns_all_C.R |only flam-1.0/flam/man/flam-package.Rd |only flam-1.0/flam/man/flam.Rd |only flam-1.0/flam/man/flamCV.Rd |only flam-1.0/flam/man/flamDOF.Rd |only flam-1.0/flam/man/plot.flam.Rd |only flam-1.0/flam/man/plot.flamCV.Rd |only flam-1.0/flam/man/sim.data.Rd |only flam-1.0/flam/man/summary.flamCV.Rd |only flam-1.0/flam/src/Fit.cpp |only flam-2.0/flam/DESCRIPTION | 11 ++++++----- flam-2.0/flam/MD5 | 26 ++++++++++++++------------ flam-2.0/flam/NAMESPACE | 1 + flam-2.0/flam/R/RcppExports.R |only flam-2.0/flam/R/flam_fcns.R |only flam-2.0/flam/man/flam-package.rd |only flam-2.0/flam/man/flam.rd |only flam-2.0/flam/man/flamcv.rd |only flam-2.0/flam/man/flamdof.rd |only flam-2.0/flam/man/plot.flam.rd |only flam-2.0/flam/man/plot.flamcv.rd |only flam-2.0/flam/man/sim.data.rd |only flam-2.0/flam/man/summary.flamcv.rd |only flam-2.0/flam/src/RcppExports.cpp |only flam-2.0/flam/src/fit.cpp |only 25 files changed, 21 insertions(+), 17 deletions(-)
Title: Wavelet Analysis of Genomic Data from Admixed Populations
Description: Implements wavelet-based approaches for describing population admixture. Principal Components Analysis (PCA) is used to define the population structure and produce a localized admixture signal for each individual. Wavelet summaries of the PCA output describe variation present in the data and can be related to population-level demographic processes. For more details, see Sanderson et al. (2015).
Author: Jean Sanderson
Maintainer: Murray Cox <m.p.cox@massey.ac.nz>
Diff between adwave versions 1.0 dated 2014-10-10 and 1.1 dated 2015-06-25
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/signal.R | 8 ++++---- data/admix.rda |binary man/admix.Rd | 6 ++++-- man/adwave-package.Rd | 8 ++++---- man/plotsignal.Rd | 2 +- man/signal.Rd | 2 +- man/wavesum.Rd | 2 +- 9 files changed, 29 insertions(+), 27 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
'shinyjs' can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.6.2 dated 2015-05-29 and 0.0.7.0 dated 2015-06-24
DESCRIPTION | 10 - MD5 | 55 +++--- NAMESPACE | 2 NEWS.md |only R/colourInput.R |only R/extendShinyjs.R | 224 ++++++++++++++++---------- R/hidden.R | 33 ++- R/jsFunc-classFuncs.R | 4 R/jsFunc-stateFuncs.R | 8 R/jsFunc-visibilityFuncs.R | 8 R/utils.R | 23 +- README.md | 247 +++++++++++++---------------- inst/doc/overview.Rmd | 176 ++++++-------------- inst/doc/overview.html | 121 ++++++-------- inst/examples/colourInput |only inst/examples/demo/helpers.R | 1 inst/examples/sandbox/helpers.R | 1 inst/srcjs/input_binding_colour.js |only inst/srcjs/shinyjs-default-funcs.js | 302 ++++++++++++++++++++++++------------ inst/www |only man/classFuncs.Rd | 4 man/colourInput.Rd |only man/extendShinyjs.Rd | 206 +++++++++++++++--------- man/hidden.Rd | 10 - man/js.Rd | 2 man/stateFuncs.Rd | 8 man/updateColourInput.Rd |only man/visibilityFuncs.Rd | 8 tests/testthat/test-hidden.R | 33 +++ vignettes/overview.Rmd | 176 ++++++-------------- 30 files changed, 898 insertions(+), 764 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraph versions 0.7.1 dated 2014-04-22 and 1.0.0 dated 2015-06-24
igraph-0.7.1/igraph/AUTHORS |only igraph-0.7.1/igraph/NEWS |only igraph-0.7.1/igraph/R/revolver.R |only igraph-0.7.1/igraph/R/structure.generators.R |only igraph-0.7.1/igraph/configure.in |only igraph-0.7.1/igraph/man/SCGintro.Rd |only igraph-0.7.1/igraph/man/adjacent.triangles.Rd |only igraph-0.7.1/igraph/man/aging.prefatt.game.Rd |only igraph-0.7.1/igraph/man/all.st.cuts.Rd |only igraph-0.7.1/igraph/man/all.st.mincuts.Rd |only igraph-0.7.1/igraph/man/alpha.centrality.Rd |only igraph-0.7.1/igraph/man/articulation.points.Rd |only igraph-0.7.1/igraph/man/attribute.combination.Rd |only igraph-0.7.1/igraph/man/attributes.Rd |only igraph-0.7.1/igraph/man/autocurve.edges.Rd |only igraph-0.7.1/igraph/man/ba.game.Rd |only igraph-0.7.1/igraph/man/biconnected.components.Rd |only igraph-0.7.1/igraph/man/bipartite.projection.Rd |only igraph-0.7.1/igraph/man/bipartite.random.game.Rd |only igraph-0.7.1/igraph/man/bonpow.Rd |only igraph-0.7.1/igraph/man/canonical.permutation.Rd |only igraph-0.7.1/igraph/man/centralization.Rd |only igraph-0.7.1/igraph/man/clusters.Rd |only igraph-0.7.1/igraph/man/cohesive.blocks.Rd |only igraph-0.7.1/igraph/man/community.edge.betweenness.Rd |only igraph-0.7.1/igraph/man/community.structure.Rd |only igraph-0.7.1/igraph/man/compare.communities.Rd |only igraph-0.7.1/igraph/man/contract.vertices.Rd |only igraph-0.7.1/igraph/man/conversion.Rd |only igraph-0.7.1/igraph/man/convex.hull.Rd |only igraph-0.7.1/igraph/man/decompose.graph.Rd |only igraph-0.7.1/igraph/man/degree.sequence.game.Rd |only igraph-0.7.1/igraph/man/dendPlot.Rd |only igraph-0.7.1/igraph/man/dendPlot.communities.Rd |only igraph-0.7.1/igraph/man/dendPlot.igraphHRG.Rd |only igraph-0.7.1/igraph/man/dominator.tree.Rd |only igraph-0.7.1/igraph/man/dyad.census.Rd |only igraph-0.7.1/igraph/man/edge.connectivity.Rd |only igraph-0.7.1/igraph/man/evcent.Rd |only igraph-0.7.1/igraph/man/evolver.Rd |only igraph-0.7.1/igraph/man/fastgreedy.community.Rd |only 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igraph-0.7.1/igraph/man/graph.formula.Rd |only igraph-0.7.1/igraph/man/graph.full.bipartite.Rd |only igraph-0.7.1/igraph/man/graph.graphdb.Rd |only igraph-0.7.1/igraph/man/graph.incidence.Rd |only igraph-0.7.1/igraph/man/graph.intersection.Rd |only igraph-0.7.1/igraph/man/graph.isomorphism.Rd |only igraph-0.7.1/igraph/man/graph.kautz.Rd |only igraph-0.7.1/igraph/man/graph.kcores.Rd |only igraph-0.7.1/igraph/man/graph.knn.Rd |only igraph-0.7.1/igraph/man/graph.laplacian.Rd |only igraph-0.7.1/igraph/man/graph.lcf.Rd |only igraph-0.7.1/igraph/man/graph.maxflow.Rd |only igraph-0.7.1/igraph/man/graph.motifs.Rd |only igraph-0.7.1/igraph/man/graph.strength.Rd |only igraph-0.7.1/igraph/man/graph.structure.Rd |only igraph-0.7.1/igraph/man/graph.union.Rd |only igraph-0.7.1/igraph/man/graphNEL.Rd |only igraph-0.7.1/igraph/man/graphlets.Rd |only igraph-0.7.1/igraph/man/grg.game.Rd |only igraph-0.7.1/igraph/man/growing.random.game.Rd |only igraph-0.7.1/igraph/man/igraph.console.Rd |only igraph-0.7.1/igraph/man/igraph.par.Rd |only igraph-0.7.1/igraph/man/igraph.sample.Rd |only igraph-0.7.1/igraph/man/igraph.version.Rd |only igraph-0.7.1/igraph/man/igraph.vertex.shapes.Rd |only igraph-0.7.1/igraph/man/igraphdemo.Rd |only igraph-0.7.1/igraph/man/igraphtest.Rd |only igraph-0.7.1/igraph/man/independent.sets.Rd |only igraph-0.7.1/igraph/man/infomap.Rd |only igraph-0.7.1/igraph/man/interconnected.islands.Rd |only igraph-0.7.1/igraph/man/is.bipartite.Rd |only igraph-0.7.1/igraph/man/is.chordal.Rd |only igraph-0.7.1/igraph/man/is.dag.Rd |only igraph-0.7.1/igraph/man/is.degree.sequence.Rd |only igraph-0.7.1/igraph/man/is.graph.Rd |only igraph-0.7.1/igraph/man/is.multiple.Rd |only igraph-0.7.1/igraph/man/is.mutual.Rd |only igraph-0.7.1/igraph/man/is.named.Rd |only igraph-0.7.1/igraph/man/is.separator.Rd |only igraph-0.7.1/igraph/man/is.weighted.Rd |only igraph-0.7.1/igraph/man/iterators.Rd |only igraph-0.7.1/igraph/man/k.regular.game.Rd |only igraph-0.7.1/igraph/man/kleinberg.Rd 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igraph-0.7.1/igraph/man/triad.census.Rd |only igraph-0.7.1/igraph/man/undocumented.Rd |only igraph-0.7.1/igraph/man/unfold.tree.Rd |only igraph-0.7.1/igraph/man/vertex.connectivity.Rd |only igraph-0.7.1/igraph/man/walktrap.community.Rd |only igraph-0.7.1/igraph/man/watts.strogatz.game.Rd |only igraph-0.7.1/igraph/man/write.graph.Rd |only igraph-0.7.1/igraph/src/Color.cpp |only igraph-0.7.1/igraph/src/Color.h |only igraph-0.7.1/igraph/src/Light.cpp |only igraph-0.7.1/igraph/src/Light.h |only igraph-0.7.1/igraph/src/Point.cpp |only igraph-0.7.1/igraph/src/Point.h |only igraph-0.7.1/igraph/src/RIgraphRay.cpp |only igraph-0.7.1/igraph/src/Ray.cpp |only igraph-0.7.1/igraph/src/Ray.h |only igraph-0.7.1/igraph/src/RayTracer.cpp |only igraph-0.7.1/igraph/src/RayTracer.h |only igraph-0.7.1/igraph/src/RayVector.cpp |only igraph-0.7.1/igraph/src/RayVector.h |only igraph-0.7.1/igraph/src/Shape.cpp |only igraph-0.7.1/igraph/src/Shape.h |only igraph-0.7.1/igraph/src/Sphere.cpp |only 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igraph-0.7.1/igraph/src/cs_dmperm.c |only igraph-0.7.1/igraph/src/cs_droptol.c |only igraph-0.7.1/igraph/src/cs_dropzeros.c |only igraph-0.7.1/igraph/src/cs_dupl.c |only igraph-0.7.1/igraph/src/cs_entry.c |only igraph-0.7.1/igraph/src/cs_ereach.c |only igraph-0.7.1/igraph/src/cs_etree.c |only igraph-0.7.1/igraph/src/cs_fkeep.c |only igraph-0.7.1/igraph/src/cs_gaxpy.c |only igraph-0.7.1/igraph/src/cs_happly.c |only igraph-0.7.1/igraph/src/cs_house.c |only igraph-0.7.1/igraph/src/cs_ipvec.c |only igraph-0.7.1/igraph/src/cs_leaf.c |only igraph-0.7.1/igraph/src/cs_load.c |only igraph-0.7.1/igraph/src/cs_lsolve.c |only igraph-0.7.1/igraph/src/cs_ltsolve.c |only igraph-0.7.1/igraph/src/cs_lu.c |only igraph-0.7.1/igraph/src/cs_lusol.c |only igraph-0.7.1/igraph/src/cs_malloc.c |only igraph-0.7.1/igraph/src/cs_maxtrans.c |only igraph-0.7.1/igraph/src/cs_multiply.c |only igraph-0.7.1/igraph/src/cs_norm.c |only igraph-0.7.1/igraph/src/cs_permute.c |only igraph-0.7.1/igraph/src/cs_pinv.c |only igraph-0.7.1/igraph/src/cs_post.c |only igraph-0.7.1/igraph/src/cs_print.c |only igraph-0.7.1/igraph/src/cs_pvec.c |only igraph-0.7.1/igraph/src/cs_qr.c |only igraph-0.7.1/igraph/src/cs_qrsol.c |only igraph-0.7.1/igraph/src/cs_randperm.c |only igraph-0.7.1/igraph/src/cs_reach.c |only igraph-0.7.1/igraph/src/cs_scatter.c |only igraph-0.7.1/igraph/src/cs_scc.c |only igraph-0.7.1/igraph/src/cs_schol.c |only igraph-0.7.1/igraph/src/cs_spsolve.c |only igraph-0.7.1/igraph/src/cs_sqr.c |only igraph-0.7.1/igraph/src/cs_symperm.c |only igraph-0.7.1/igraph/src/cs_tdfs.c |only igraph-0.7.1/igraph/src/cs_transpose.c |only igraph-0.7.1/igraph/src/cs_updown.c |only igraph-0.7.1/igraph/src/cs_usolve.c |only igraph-0.7.1/igraph/src/cs_util.c |only igraph-0.7.1/igraph/src/cs_utsolve.c |only igraph-0.7.1/igraph/src/error.c |only igraph-0.7.1/igraph/src/evolver_cit.c |only igraph-0.7.1/igraph/src/f2c.h |only igraph-0.7.1/igraph/src/f2c_dummy.c |only igraph-0.7.1/igraph/src/glpapi01.c |only igraph-0.7.1/igraph/src/glpapi02.c |only igraph-0.7.1/igraph/src/glpapi03.c |only igraph-0.7.1/igraph/src/glpapi04.c |only igraph-0.7.1/igraph/src/glpapi05.c |only igraph-0.7.1/igraph/src/glpapi06.c |only igraph-0.7.1/igraph/src/glpapi07.c |only igraph-0.7.1/igraph/src/glpapi08.c |only igraph-0.7.1/igraph/src/glpapi09.c |only igraph-0.7.1/igraph/src/glpapi10.c |only igraph-0.7.1/igraph/src/glpapi11.c |only igraph-0.7.1/igraph/src/glpapi12.c |only igraph-0.7.1/igraph/src/glpapi13.c |only igraph-0.7.1/igraph/src/glpapi14.c |only igraph-0.7.1/igraph/src/glpapi15.c |only igraph-0.7.1/igraph/src/glpapi16.c |only igraph-0.7.1/igraph/src/glpapi17.c |only igraph-0.7.1/igraph/src/glpapi18.c |only igraph-0.7.1/igraph/src/glpapi19.c |only igraph-0.7.1/igraph/src/glpavl.c |only igraph-0.7.1/igraph/src/glpbfd.c |only igraph-0.7.1/igraph/src/glpbfx.c |only igraph-0.7.1/igraph/src/glpcpx.c |only igraph-0.7.1/igraph/src/glpdmp.c |only igraph-0.7.1/igraph/src/glpdmx.c |only igraph-0.7.1/igraph/src/glpenv01.c |only igraph-0.7.1/igraph/src/glpenv02.c |only igraph-0.7.1/igraph/src/glpenv03.c |only igraph-0.7.1/igraph/src/glpenv04.c |only igraph-0.7.1/igraph/src/glpenv05.c |only igraph-0.7.1/igraph/src/glpenv06.c |only igraph-0.7.1/igraph/src/glpenv07.c |only igraph-0.7.1/igraph/src/glpenv08.c |only igraph-0.7.1/igraph/src/glpfhv.c |only igraph-0.7.1/igraph/src/glpgmp.c |only igraph-0.7.1/igraph/src/glphbm.c |only igraph-0.7.1/igraph/src/glpini01.c |only igraph-0.7.1/igraph/src/glpini02.c |only igraph-0.7.1/igraph/src/glpios01.c |only igraph-0.7.1/igraph/src/glpios02.c |only igraph-0.7.1/igraph/src/glpios03.c |only igraph-0.7.1/igraph/src/glpios04.c |only igraph-0.7.1/igraph/src/glpios05.c |only igraph-0.7.1/igraph/src/glpios06.c |only igraph-0.7.1/igraph/src/glpios07.c |only igraph-0.7.1/igraph/src/glpios08.c |only igraph-0.7.1/igraph/src/glpios09.c |only igraph-0.7.1/igraph/src/glpios10.c |only igraph-0.7.1/igraph/src/glpios11.c |only igraph-0.7.1/igraph/src/glpios12.c |only igraph-0.7.1/igraph/src/glpipm.c |only igraph-0.7.1/igraph/src/glplib01.c |only igraph-0.7.1/igraph/src/glplib02.c |only igraph-0.7.1/igraph/src/glplib03.c |only igraph-0.7.1/igraph/src/glplpf.c |only igraph-0.7.1/igraph/src/glplpx01.c |only igraph-0.7.1/igraph/src/glplpx02.c |only igraph-0.7.1/igraph/src/glplpx03.c |only igraph-0.7.1/igraph/src/glpluf.c |only igraph-0.7.1/igraph/src/glplux.c |only igraph-0.7.1/igraph/src/glpmat.c |only igraph-0.7.1/igraph/src/glpmpl01.c |only igraph-0.7.1/igraph/src/glpmpl02.c |only igraph-0.7.1/igraph/src/glpmpl03.c |only igraph-0.7.1/igraph/src/glpmpl04.c |only igraph-0.7.1/igraph/src/glpmpl05.c |only igraph-0.7.1/igraph/src/glpmpl06.c |only igraph-0.7.1/igraph/src/glpmps.c |only igraph-0.7.1/igraph/src/glpnet01.c |only igraph-0.7.1/igraph/src/glpnet02.c |only igraph-0.7.1/igraph/src/glpnet03.c |only igraph-0.7.1/igraph/src/glpnet04.c |only igraph-0.7.1/igraph/src/glpnet05.c |only igraph-0.7.1/igraph/src/glpnet06.c |only igraph-0.7.1/igraph/src/glpnet07.c |only igraph-0.7.1/igraph/src/glpnet08.c |only igraph-0.7.1/igraph/src/glpnet09.c |only igraph-0.7.1/igraph/src/glpnpp01.c |only igraph-0.7.1/igraph/src/glpnpp02.c |only igraph-0.7.1/igraph/src/glpnpp03.c |only igraph-0.7.1/igraph/src/glpnpp04.c |only igraph-0.7.1/igraph/src/glpnpp05.c |only igraph-0.7.1/igraph/src/glpqmd.c |only igraph-0.7.1/igraph/src/glprgr.c |only igraph-0.7.1/igraph/src/glprng01.c |only igraph-0.7.1/igraph/src/glprng02.c |only igraph-0.7.1/igraph/src/glpscf.c |only igraph-0.7.1/igraph/src/glpscl.c |only igraph-0.7.1/igraph/src/glpsdf.c |only igraph-0.7.1/igraph/src/glpspm.c |only igraph-0.7.1/igraph/src/glpspx01.c |only igraph-0.7.1/igraph/src/glpspx02.c |only igraph-0.7.1/igraph/src/glpsql.c |only igraph-0.7.1/igraph/src/glpssx01.c |only igraph-0.7.1/igraph/src/glpssx02.c |only igraph-0.7.1/igraph/src/glptsp.c |only igraph-0.7.1/igraph/src/gss.c |only igraph-0.7.1/igraph/src/igraph.h 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igraph-0.7.1/igraph/src/igraph_eigen.h |only igraph-0.7.1/igraph/src/igraph_epidemics.h |only igraph-0.7.1/igraph/src/igraph_error.h |only igraph-0.7.1/igraph/src/igraph_flow.h |only igraph-0.7.1/igraph/src/igraph_foreign.h |only igraph-0.7.1/igraph/src/igraph_games.h |only igraph-0.7.1/igraph/src/igraph_graphlets.h |only igraph-0.7.1/igraph/src/igraph_heap.h |only igraph-0.7.1/igraph/src/igraph_heap_pmt.h |only igraph-0.7.1/igraph/src/igraph_hrg.h |only igraph-0.7.1/igraph/src/igraph_interface.h |only igraph-0.7.1/igraph/src/igraph_interrupt.h |only igraph-0.7.1/igraph/src/igraph_iterators.h |only igraph-0.7.1/igraph/src/igraph_lapack.h |only igraph-0.7.1/igraph/src/igraph_layout.h |only igraph-0.7.1/igraph/src/igraph_matching.h |only igraph-0.7.1/igraph/src/igraph_matrix.h |only igraph-0.7.1/igraph/src/igraph_matrix_pmt.h |only igraph-0.7.1/igraph/src/igraph_memory.h |only igraph-0.7.1/igraph/src/igraph_microscopic_update.h |only igraph-0.7.1/igraph/src/igraph_mixing.h |only 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igraph-0.7.1/igraph/src/igraph_topology.h |only igraph-0.7.1/igraph/src/igraph_transitivity.h |only igraph-0.7.1/igraph/src/igraph_types.h |only igraph-0.7.1/igraph/src/igraph_vector.h |only igraph-0.7.1/igraph/src/igraph_vector_pmt.h |only igraph-0.7.1/igraph/src/igraph_vector_ptr.h |only igraph-0.7.1/igraph/src/igraph_vector_type.h |only igraph-0.7.1/igraph/src/igraph_visitor.h |only igraph-0.7.1/igraph/src/kolmogorov.c |only igraph-0.7.1/igraph/src/lbfgs.c |only igraph-0.7.1/igraph/src/options.c |only igraph-0.7.1/igraph/src/plfit.c |only igraph-0.7.1/igraph/src/prpack_base_graph.cpp |only igraph-0.7.1/igraph/src/prpack_igraph_graph.cpp |only igraph-0.7.1/igraph/src/prpack_preprocessed_ge_graph.cpp |only igraph-0.7.1/igraph/src/prpack_preprocessed_gs_graph.cpp |only igraph-0.7.1/igraph/src/prpack_preprocessed_scc_graph.cpp |only igraph-0.7.1/igraph/src/prpack_preprocessed_schur_graph.cpp |only igraph-0.7.1/igraph/src/prpack_result.cpp |only igraph-0.7.1/igraph/src/prpack_solver.cpp |only igraph-0.7.1/igraph/src/prpack_utils.cpp |only igraph-0.7.1/igraph/src/revolver_cit.c |only igraph-0.7.1/igraph/src/revolver_grow.c |only igraph-0.7.1/igraph/src/revolver_ml_cit.c |only igraph-0.7.1/igraph/src/unit_limiter.cpp |only igraph-0.7.1/igraph/src/unit_limiter.h |only igraph-0.7.1/igraph/src/zeta.c |only igraph-1.0.0/igraph/DESCRIPTION | 36 igraph-1.0.0/igraph/MD5 | 1795 + igraph-1.0.0/igraph/NAMESPACE | 1266 - igraph-1.0.0/igraph/R/adjacency.R |only igraph-1.0.0/igraph/R/assortativity.R |only igraph-1.0.0/igraph/R/attributes.R | 802 igraph-1.0.0/igraph/R/auto.R | 1317 - igraph-1.0.0/igraph/R/basic.R | 70 igraph-1.0.0/igraph/R/bipartite.R | 130 igraph-1.0.0/igraph/R/centrality.R | 683 igraph-1.0.0/igraph/R/centralization.R |only igraph-1.0.0/igraph/R/cliques.R | 242 igraph-1.0.0/igraph/R/cocitation.R | 55 igraph-1.0.0/igraph/R/cohesive.blocks.R | 302 igraph-1.0.0/igraph/R/community.R | 1599 + igraph-1.0.0/igraph/R/components.R | 134 igraph-1.0.0/igraph/R/console.R | 154 igraph-1.0.0/igraph/R/conversion.R | 613 igraph-1.0.0/igraph/R/data_frame.R |only igraph-1.0.0/igraph/R/decomposition.R | 62 igraph-1.0.0/igraph/R/degseq.R |only igraph-1.0.0/igraph/R/demo.R | 106 igraph-1.0.0/igraph/R/embedding.R |only igraph-1.0.0/igraph/R/epi.R | 64 igraph-1.0.0/igraph/R/fit.R | 119 igraph-1.0.0/igraph/R/flow.R | 639 igraph-1.0.0/igraph/R/foreign.R | 206 igraph-1.0.0/igraph/R/games.R | 1421 + igraph-1.0.0/igraph/R/glet.R | 99 igraph-1.0.0/igraph/R/hrg.R | 468 igraph-1.0.0/igraph/R/igraph-package.R |only igraph-1.0.0/igraph/R/incidence.R |only igraph-1.0.0/igraph/R/indexing.R | 234 igraph-1.0.0/igraph/R/interface.R | 415 igraph-1.0.0/igraph/R/iterators.R | 1611 + igraph-1.0.0/igraph/R/layout.R | 2530 +- igraph-1.0.0/igraph/R/layout_drl.R |only igraph-1.0.0/igraph/R/lazyeval.R |only igraph-1.0.0/igraph/R/make.R |only igraph-1.0.0/igraph/R/mgclust.R |only igraph-1.0.0/igraph/R/minimum.spanning.tree.R | 47 igraph-1.0.0/igraph/R/motifs.R | 172 igraph-1.0.0/igraph/R/nexus.R | 214 igraph-1.0.0/igraph/R/operators.R | 780 igraph-1.0.0/igraph/R/other.R | 98 igraph-1.0.0/igraph/R/package.R | 9 igraph-1.0.0/igraph/R/palette.R |only igraph-1.0.0/igraph/R/par.R | 122 igraph-1.0.0/igraph/R/paths.R |only igraph-1.0.0/igraph/R/plot.R | 154 igraph-1.0.0/igraph/R/plot.common.R | 83 igraph-1.0.0/igraph/R/plot.shapes.R | 268 igraph-1.0.0/igraph/R/pp.R |only igraph-1.0.0/igraph/R/print.R | 440 igraph-1.0.0/igraph/R/printr.R |only igraph-1.0.0/igraph/R/random_walk.R |only igraph-1.0.0/igraph/R/rewire.R |only igraph-1.0.0/igraph/R/scan.R |only igraph-1.0.0/igraph/R/scg.R | 539 igraph-1.0.0/igraph/R/sgm.R |only igraph-1.0.0/igraph/R/similarity.R |only igraph-1.0.0/igraph/R/simple.R |only igraph-1.0.0/igraph/R/sir.R |only igraph-1.0.0/igraph/R/socnet.R | 1063 - igraph-1.0.0/igraph/R/sparsedf.R | 6 igraph-1.0.0/igraph/R/structural.properties.R | 2067 ++ igraph-1.0.0/igraph/R/structure.info.R | 30 igraph-1.0.0/igraph/R/test.R | 50 igraph-1.0.0/igraph/R/tkplot.R | 683 igraph-1.0.0/igraph/R/topology.R | 895 igraph-1.0.0/igraph/R/triangles.R |only igraph-1.0.0/igraph/R/utils.R |only igraph-1.0.0/igraph/R/uuid.R |only igraph-1.0.0/igraph/R/versions.R |only igraph-1.0.0/igraph/R/weakref.R |only igraph-1.0.0/igraph/R/zzz-deprecate.R |only igraph-1.0.0/igraph/configure | 115 igraph-1.0.0/igraph/configure.ac |only igraph-1.0.0/igraph/demo/centrality.R | 62 igraph-1.0.0/igraph/demo/cohesive.R | 14 igraph-1.0.0/igraph/demo/community.R | 66 igraph-1.0.0/igraph/demo/crashR.R | 52 igraph-1.0.0/igraph/demo/hrg.R | 30 igraph-1.0.0/igraph/demo/smallworld.R | 54 igraph-1.0.0/igraph/inst/AUTHORS | 5 igraph-1.0.0/igraph/inst/NEWS.md |only igraph-1.0.0/igraph/inst/README.md |only igraph-1.0.0/igraph/inst/benchmarks/correlated.R |only igraph-1.0.0/igraph/inst/benchmarks/local.scan.R |only igraph-1.0.0/igraph/inst/benchmarks/time_dirSelect.R |only igraph-1.0.0/igraph/inst/benchmarks/time_fr_layout.R |only igraph-1.0.0/igraph/inst/benchmarks/time_kk_layout.R |only igraph-1.0.0/igraph/inst/benchmarks/time_print.R |only igraph-1.0.0/igraph/inst/benchmarks/time_sgm.R |only igraph-1.0.0/igraph/inst/benchmarks/time_sir.R | 2 igraph-1.0.0/igraph/inst/tests/dyad.census.R | 20 igraph-1.0.0/igraph/inst/tests/test-constructor-modifiers.R |only igraph-1.0.0/igraph/inst/tests/test-index-es.R |only igraph-1.0.0/igraph/inst/tests/test-isomorphism.R |only igraph-1.0.0/igraph/inst/tests/test-make.R |only igraph-1.0.0/igraph/inst/tests/test-make_graph.R |only igraph-1.0.0/igraph/inst/tests/test-new-layout-api.R |only igraph-1.0.0/igraph/inst/tests/test-notable.R |only igraph-1.0.0/igraph/inst/tests/test-old-data-type.R |only igraph-1.0.0/igraph/inst/tests/test-random_walk.R |only igraph-1.0.0/igraph/inst/tests/test-version.R |only igraph-1.0.0/igraph/inst/tests/test-versions.R |only igraph-1.0.0/igraph/inst/tests/test-vs-es-printing.R |only igraph-1.0.0/igraph/inst/tests/test-vs-es-quirks.R |only 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igraph-1.0.0/igraph/inst/tests/test_average.path.length.R | 28 igraph-1.0.0/igraph/inst/tests/test_ba.game.R | 50 igraph-1.0.0/igraph/inst/tests/test_betweenness.R | 6 igraph-1.0.0/igraph/inst/tests/test_biconnected.components.R | 15 igraph-1.0.0/igraph/inst/tests/test_bipartite.projection.R | 78 igraph-1.0.0/igraph/inst/tests/test_bipartite.random.game.R | 40 igraph-1.0.0/igraph/inst/tests/test_bonpow.R | 12 igraph-1.0.0/igraph/inst/tests/test_bug-1019624.R | 4 igraph-1.0.0/igraph/inst/tests/test_bug-1032819.R | 6 igraph-1.0.0/igraph/inst/tests/test_bug-1033045.R | 6 igraph-1.0.0/igraph/inst/tests/test_bug-1073705-indexing.R | 10 igraph-1.0.0/igraph/inst/tests/test_bug-1073800-clique.R | 7 igraph-1.0.0/igraph/inst/tests/test_callbacks.R | 2 igraph-1.0.0/igraph/inst/tests/test_canonical.permutation.R | 20 igraph-1.0.0/igraph/inst/tests/test_cliques.R | 12 igraph-1.0.0/igraph/inst/tests/test_closeness.R | 42 igraph-1.0.0/igraph/inst/tests/test_clusters.R | 40 igraph-1.0.0/igraph/inst/tests/test_communities.R | 52 igraph-1.0.0/igraph/inst/tests/test_constraint.R | 6 igraph-1.0.0/igraph/inst/tests/test_contract.vertices.R | 8 igraph-1.0.0/igraph/inst/tests/test_correlated.R |only igraph-1.0.0/igraph/inst/tests/test_count.multiple.R | 16 igraph-1.0.0/igraph/inst/tests/test_decompose.graph.R | 34 igraph-1.0.0/igraph/inst/tests/test_degree.R | 8 igraph-1.0.0/igraph/inst/tests/test_degree.sequence.game.R | 26 igraph-1.0.0/igraph/inst/tests/test_delete.edges.R | 8 igraph-1.0.0/igraph/inst/tests/test_delete.vertices.R | 10 igraph-1.0.0/igraph/inst/tests/test_diameter.R | 20 igraph-1.0.0/igraph/inst/tests/test_dimSelect.R |only igraph-1.0.0/igraph/inst/tests/test_dominator.tree.R | 16 igraph-1.0.0/igraph/inst/tests/test_dot.product.game.R |only igraph-1.0.0/igraph/inst/tests/test_dyad.census.R | 10 igraph-1.0.0/igraph/inst/tests/test_edge.betweenness.R | 28 igraph-1.0.0/igraph/inst/tests/test_edge.betweenness.community.R | 19 igraph-1.0.0/igraph/inst/tests/test_edge.connectivity.R | 42 igraph-1.0.0/igraph/inst/tests/test_edgenames.R | 26 igraph-1.0.0/igraph/inst/tests/test_evcent.R | 32 igraph-1.0.0/igraph/inst/tests/test_fartherst.nodes.R | 38 igraph-1.0.0/igraph/inst/tests/test_fastgreedy.community.R | 19 igraph-1.0.0/igraph/inst/tests/test_forestfire.R | 6 igraph-1.0.0/igraph/inst/tests/test_get.adjacency.R | 24 igraph-1.0.0/igraph/inst/tests/test_get.adjlist.R | 36 igraph-1.0.0/igraph/inst/tests/test_get.all.shortest.paths.R | 13 igraph-1.0.0/igraph/inst/tests/test_get.diameter.R | 14 igraph-1.0.0/igraph/inst/tests/test_get.edge.R | 8 igraph-1.0.0/igraph/inst/tests/test_get.edgelist.R | 8 igraph-1.0.0/igraph/inst/tests/test_get.incidence.R | 10 igraph-1.0.0/igraph/inst/tests/test_get.shortest.paths.R | 12 igraph-1.0.0/igraph/inst/tests/test_girth.R | 8 igraph-1.0.0/igraph/inst/tests/test_graph.adhesion.R | 68 igraph-1.0.0/igraph/inst/tests/test_graph.adjacency.R | 66 igraph-1.0.0/igraph/inst/tests/test_graph.adjlist.R | 16 igraph-1.0.0/igraph/inst/tests/test_graph.bfs.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.bipartite.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.complementer.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.compose.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.coreness.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.data.frame.R | 18 igraph-1.0.0/igraph/inst/tests/test_graph.de.bruijn.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.density.R | 12 igraph-1.0.0/igraph/inst/tests/test_graph.edgelist.R | 22 igraph-1.0.0/igraph/inst/tests/test_graph.eigen.R | 10 igraph-1.0.0/igraph/inst/tests/test_graph.formula.R | 6 igraph-1.0.0/igraph/inst/tests/test_graph.isoclass.R | 14 igraph-1.0.0/igraph/inst/tests/test_graph.kautz.R | 8 igraph-1.0.0/igraph/inst/tests/test_graph.knn.R | 24 igraph-1.0.0/igraph/inst/tests/test_graph.maxflow.R | 16 igraph-1.0.0/igraph/inst/tests/test_graph.mincut.R | 12 igraph-1.0.0/igraph/inst/tests/test_graph.subisomorphic.lad.R | 69 igraph-1.0.0/igraph/inst/tests/test_graph.subisomorphic.vf2.R | 4 igraph-1.0.0/igraph/inst/tests/test_graphNEL.R | 14 igraph-1.0.0/igraph/inst/tests/test_graphlets.R | 39 igraph-1.0.0/igraph/inst/tests/test_hrg.R | 6 igraph-1.0.0/igraph/inst/tests/test_hsbm.R |only igraph-1.0.0/igraph/inst/tests/test_igraph.options.R | 12 igraph-1.0.0/igraph/inst/tests/test_independent.vertex.sets.R | 10 igraph-1.0.0/igraph/inst/tests/test_indexing.R | 111 igraph-1.0.0/igraph/inst/tests/test_indexing2.R | 14 igraph-1.0.0/igraph/inst/tests/test_indexing3.R |only igraph-1.0.0/igraph/inst/tests/test_is.bipartite.R | 12 igraph-1.0.0/igraph/inst/tests/test_is.chordal.R | 29 igraph-1.0.0/igraph/inst/tests/test_iterators.R | 40 igraph-1.0.0/igraph/inst/tests/test_label.propagation.community.R | 8 igraph-1.0.0/igraph/inst/tests/test_laplacian.spectral.embedding.R |only igraph-1.0.0/igraph/inst/tests/test_largest.cliques.R | 10 igraph-1.0.0/igraph/inst/tests/test_largest.independent.vertex.sets.R | 12 igraph-1.0.0/igraph/inst/tests/test_layout.fr.R |only igraph-1.0.0/igraph/inst/tests/test_layout.gem.R |only igraph-1.0.0/igraph/inst/tests/test_layout.kk.R |only igraph-1.0.0/igraph/inst/tests/test_layout.mds.R | 18 igraph-1.0.0/igraph/inst/tests/test_layout.merge.R | 14 igraph-1.0.0/igraph/inst/tests/test_leading.eigenvector.community.R | 27 igraph-1.0.0/igraph/inst/tests/test_maximal_cliques.R | 30 igraph-1.0.0/igraph/inst/tests/test_minimal.st.separators.R | 10 igraph-1.0.0/igraph/inst/tests/test_minimum.size.separators.R | 32 igraph-1.0.0/igraph/inst/tests/test_modularity_matrix.R | 12 igraph-1.0.0/igraph/inst/tests/test_motifs.R | 32 igraph-1.0.0/igraph/inst/tests/test_multilevel.community.R | 10 igraph-1.0.0/igraph/inst/tests/test_neighborhood.R | 52 igraph-1.0.0/igraph/inst/tests/test_neighbors.R | 6 igraph-1.0.0/igraph/inst/tests/test_operators.R | 45 igraph-1.0.0/igraph/inst/tests/test_operators3.R | 16 igraph-1.0.0/igraph/inst/tests/test_operators4.R | 98 igraph-1.0.0/igraph/inst/tests/test_optimal.community.R | 16 igraph-1.0.0/igraph/inst/tests/test_pajek.R | 4 igraph-1.0.0/igraph/inst/tests/test_print.R | 25 igraph-1.0.0/igraph/inst/tests/test_sample.R |only igraph-1.0.0/igraph/inst/tests/test_sbm.game.R | 16 igraph-1.0.0/igraph/inst/tests/test_scan.R |only igraph-1.0.0/igraph/inst/tests/test_scg.R | 6 igraph-1.0.0/igraph/inst/tests/test_sdf.R | 7 igraph-1.0.0/igraph/inst/tests/test_sgm.R |only igraph-1.0.0/igraph/inst/tests/test_sir.R | 2 igraph-1.0.0/igraph/inst/tests/test_sphere.R |only igraph-1.0.0/igraph/inst/tests/test_transitivity.R | 12 igraph-1.0.0/igraph/inst/tests/test_triangles.R |only igraph-1.0.0/igraph/inst/tests/test_unfold.tree.R | 10 igraph-1.0.0/igraph/inst/tests/test_walktrap.community.R | 19 igraph-1.0.0/igraph/inst/tests/test_watts.strogatz.game.R | 8 igraph-1.0.0/igraph/man/E.Rd |only igraph-1.0.0/igraph/man/V.Rd |only 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igraph-1.0.0/igraph/man/closeness.Rd | 114 igraph-1.0.0/igraph/man/cluster_edge_betweenness.Rd |only igraph-1.0.0/igraph/man/cluster_fast_greedy.Rd |only igraph-1.0.0/igraph/man/cluster_infomap.Rd |only igraph-1.0.0/igraph/man/cluster_label_prop.Rd |only igraph-1.0.0/igraph/man/cluster_leading_eigen.Rd |only igraph-1.0.0/igraph/man/cluster_louvain.Rd |only igraph-1.0.0/igraph/man/cluster_optimal.Rd |only igraph-1.0.0/igraph/man/cluster_spinglass.Rd |only igraph-1.0.0/igraph/man/cluster_walktrap.Rd |only igraph-1.0.0/igraph/man/cocitation.Rd | 61 igraph-1.0.0/igraph/man/cohesive_blocks.Rd |only igraph-1.0.0/igraph/man/communities.Rd | 463 igraph-1.0.0/igraph/man/compare.Rd |only igraph-1.0.0/igraph/man/complementer.Rd |only igraph-1.0.0/igraph/man/component_wise.Rd |only igraph-1.0.0/igraph/man/components.Rd | 102 igraph-1.0.0/igraph/man/compose.Rd |only igraph-1.0.0/igraph/man/consensus_tree.Rd |only igraph-1.0.0/igraph/man/console.Rd |only igraph-1.0.0/igraph/man/constraint.Rd | 81 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igraph-1.0.0/igraph/src/cs/cs_amd.c |only igraph-1.0.0/igraph/src/cs/cs_chol.c |only igraph-1.0.0/igraph/src/cs/cs_cholsol.c |only igraph-1.0.0/igraph/src/cs/cs_compress.c |only igraph-1.0.0/igraph/src/cs/cs_counts.c |only igraph-1.0.0/igraph/src/cs/cs_cumsum.c |only igraph-1.0.0/igraph/src/cs/cs_dfs.c |only igraph-1.0.0/igraph/src/cs/cs_dmperm.c |only igraph-1.0.0/igraph/src/cs/cs_droptol.c |only igraph-1.0.0/igraph/src/cs/cs_dropzeros.c |only igraph-1.0.0/igraph/src/cs/cs_dupl.c |only igraph-1.0.0/igraph/src/cs/cs_entry.c |only igraph-1.0.0/igraph/src/cs/cs_ereach.c |only igraph-1.0.0/igraph/src/cs/cs_etree.c |only igraph-1.0.0/igraph/src/cs/cs_fkeep.c |only igraph-1.0.0/igraph/src/cs/cs_gaxpy.c |only igraph-1.0.0/igraph/src/cs/cs_happly.c |only igraph-1.0.0/igraph/src/cs/cs_house.c |only igraph-1.0.0/igraph/src/cs/cs_ipvec.c |only igraph-1.0.0/igraph/src/cs/cs_leaf.c |only igraph-1.0.0/igraph/src/cs/cs_load.c |only igraph-1.0.0/igraph/src/cs/cs_lsolve.c |only igraph-1.0.0/igraph/src/cs/cs_ltsolve.c |only igraph-1.0.0/igraph/src/cs/cs_lu.c |only igraph-1.0.0/igraph/src/cs/cs_lusol.c |only igraph-1.0.0/igraph/src/cs/cs_malloc.c |only igraph-1.0.0/igraph/src/cs/cs_maxtrans.c |only igraph-1.0.0/igraph/src/cs/cs_multiply.c |only igraph-1.0.0/igraph/src/cs/cs_norm.c |only igraph-1.0.0/igraph/src/cs/cs_permute.c |only igraph-1.0.0/igraph/src/cs/cs_pinv.c |only igraph-1.0.0/igraph/src/cs/cs_post.c |only igraph-1.0.0/igraph/src/cs/cs_print.c |only igraph-1.0.0/igraph/src/cs/cs_pvec.c |only igraph-1.0.0/igraph/src/cs/cs_qr.c |only igraph-1.0.0/igraph/src/cs/cs_qrsol.c |only igraph-1.0.0/igraph/src/cs/cs_randperm.c |only igraph-1.0.0/igraph/src/cs/cs_reach.c |only igraph-1.0.0/igraph/src/cs/cs_scatter.c |only igraph-1.0.0/igraph/src/cs/cs_scc.c |only igraph-1.0.0/igraph/src/cs/cs_schol.c |only igraph-1.0.0/igraph/src/cs/cs_spsolve.c |only igraph-1.0.0/igraph/src/cs/cs_sqr.c |only igraph-1.0.0/igraph/src/cs/cs_symperm.c |only igraph-1.0.0/igraph/src/cs/cs_tdfs.c |only igraph-1.0.0/igraph/src/cs/cs_transpose.c |only igraph-1.0.0/igraph/src/cs/cs_updown.c |only igraph-1.0.0/igraph/src/cs/cs_usolve.c |only igraph-1.0.0/igraph/src/cs/cs_util.c |only igraph-1.0.0/igraph/src/cs/cs_utsolve.c |only igraph-1.0.0/igraph/src/dotproduct.c |only igraph-1.0.0/igraph/src/dqueue.c | 6 igraph-1.0.0/igraph/src/dqueue.pmt | 1 igraph-1.0.0/igraph/src/drl_layout.cpp | 2 igraph-1.0.0/igraph/src/embedding.c |only igraph-1.0.0/igraph/src/flow.c | 16 igraph-1.0.0/igraph/src/foreign-dl-lexer.c | 58 igraph-1.0.0/igraph/src/foreign-dl-parser.c | 116 igraph-1.0.0/igraph/src/foreign-dl-parser.h | 2 igraph-1.0.0/igraph/src/foreign-gml-lexer.c | 28 igraph-1.0.0/igraph/src/foreign-gml-parser.c | 38 igraph-1.0.0/igraph/src/foreign-gml-parser.h | 2 igraph-1.0.0/igraph/src/foreign-graphml.c | 602 igraph-1.0.0/igraph/src/foreign-lgl-lexer.c | 20 igraph-1.0.0/igraph/src/foreign-lgl-parser.c | 16 igraph-1.0.0/igraph/src/foreign-lgl-parser.h | 2 igraph-1.0.0/igraph/src/foreign-ncol-lexer.c | 18 igraph-1.0.0/igraph/src/foreign-ncol-parser.c | 14 igraph-1.0.0/igraph/src/foreign-ncol-parser.h | 2 igraph-1.0.0/igraph/src/foreign-pajek-lexer.c | 104 igraph-1.0.0/igraph/src/foreign-pajek-parser.c | 176 igraph-1.0.0/igraph/src/foreign-pajek-parser.h | 2 igraph-1.0.0/igraph/src/foreign.c | 16 igraph-1.0.0/igraph/src/games.c | 270 igraph-1.0.0/igraph/src/gengraph_box_list.h | 2 igraph-1.0.0/igraph/src/gengraph_definitions.h | 4 igraph-1.0.0/igraph/src/gengraph_graph_molloy_optimized.cpp | 4 igraph-1.0.0/igraph/src/gengraph_qsort.h | 4 igraph-1.0.0/igraph/src/gengraph_vertex_cover.h | 4 igraph-1.0.0/igraph/src/glpk/COPYING |only igraph-1.0.0/igraph/src/glpk/README |only igraph-1.0.0/igraph/src/glpk/amd/COPYING |only igraph-1.0.0/igraph/src/glpk/amd/README |only igraph-1.0.0/igraph/src/glpk/amd/amd_1.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_2.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_aat.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_control.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_defaults.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_dump.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_info.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_order.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_post_tree.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_postorder.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_preprocess.c |only igraph-1.0.0/igraph/src/glpk/amd/amd_valid.c |only igraph-1.0.0/igraph/src/glpk/colamd/COPYING |only igraph-1.0.0/igraph/src/glpk/colamd/README |only igraph-1.0.0/igraph/src/glpk/colamd/colamd.c |only igraph-1.0.0/igraph/src/glpk/glpapi01.c |only igraph-1.0.0/igraph/src/glpk/glpapi02.c |only igraph-1.0.0/igraph/src/glpk/glpapi03.c |only igraph-1.0.0/igraph/src/glpk/glpapi04.c |only igraph-1.0.0/igraph/src/glpk/glpapi05.c |only igraph-1.0.0/igraph/src/glpk/glpapi06.c |only igraph-1.0.0/igraph/src/glpk/glpapi07.c |only igraph-1.0.0/igraph/src/glpk/glpapi08.c |only igraph-1.0.0/igraph/src/glpk/glpapi09.c |only igraph-1.0.0/igraph/src/glpk/glpapi10.c |only igraph-1.0.0/igraph/src/glpk/glpapi11.c |only igraph-1.0.0/igraph/src/glpk/glpapi12.c |only igraph-1.0.0/igraph/src/glpk/glpapi13.c |only igraph-1.0.0/igraph/src/glpk/glpapi14.c |only igraph-1.0.0/igraph/src/glpk/glpapi15.c |only igraph-1.0.0/igraph/src/glpk/glpapi16.c |only igraph-1.0.0/igraph/src/glpk/glpapi17.c |only igraph-1.0.0/igraph/src/glpk/glpapi18.c |only igraph-1.0.0/igraph/src/glpk/glpapi19.c |only igraph-1.0.0/igraph/src/glpk/glpavl.c |only igraph-1.0.0/igraph/src/glpk/glpbfd.c |only igraph-1.0.0/igraph/src/glpk/glpbfx.c |only igraph-1.0.0/igraph/src/glpk/glpcpx.c |only igraph-1.0.0/igraph/src/glpk/glpdmp.c |only igraph-1.0.0/igraph/src/glpk/glpdmx.c |only igraph-1.0.0/igraph/src/glpk/glpenv01.c |only igraph-1.0.0/igraph/src/glpk/glpenv02.c |only igraph-1.0.0/igraph/src/glpk/glpenv03.c |only igraph-1.0.0/igraph/src/glpk/glpenv04.c |only igraph-1.0.0/igraph/src/glpk/glpenv05.c |only igraph-1.0.0/igraph/src/glpk/glpenv06.c |only igraph-1.0.0/igraph/src/glpk/glpenv07.c |only igraph-1.0.0/igraph/src/glpk/glpenv08.c |only igraph-1.0.0/igraph/src/glpk/glpfhv.c |only igraph-1.0.0/igraph/src/glpk/glpgmp.c |only igraph-1.0.0/igraph/src/glpk/glphbm.c |only igraph-1.0.0/igraph/src/glpk/glpini01.c |only igraph-1.0.0/igraph/src/glpk/glpini02.c |only igraph-1.0.0/igraph/src/glpk/glpios01.c |only igraph-1.0.0/igraph/src/glpk/glpios02.c |only igraph-1.0.0/igraph/src/glpk/glpios03.c |only igraph-1.0.0/igraph/src/glpk/glpios04.c |only igraph-1.0.0/igraph/src/glpk/glpios05.c |only igraph-1.0.0/igraph/src/glpk/glpios06.c |only igraph-1.0.0/igraph/src/glpk/glpios07.c |only igraph-1.0.0/igraph/src/glpk/glpios08.c |only igraph-1.0.0/igraph/src/glpk/glpios09.c |only igraph-1.0.0/igraph/src/glpk/glpios10.c |only igraph-1.0.0/igraph/src/glpk/glpios11.c |only igraph-1.0.0/igraph/src/glpk/glpios12.c |only igraph-1.0.0/igraph/src/glpk/glpipm.c |only igraph-1.0.0/igraph/src/glpk/glpk.inc |only igraph-1.0.0/igraph/src/glpk/glplib01.c |only igraph-1.0.0/igraph/src/glpk/glplib02.c |only igraph-1.0.0/igraph/src/glpk/glplib03.c |only igraph-1.0.0/igraph/src/glpk/glplpf.c |only igraph-1.0.0/igraph/src/glpk/glplpx01.c |only igraph-1.0.0/igraph/src/glpk/glplpx02.c |only igraph-1.0.0/igraph/src/glpk/glplpx03.c |only igraph-1.0.0/igraph/src/glpk/glpluf.c |only igraph-1.0.0/igraph/src/glpk/glplux.c |only igraph-1.0.0/igraph/src/glpk/glpmat.c |only igraph-1.0.0/igraph/src/glpk/glpmpl01.c |only igraph-1.0.0/igraph/src/glpk/glpmpl02.c |only igraph-1.0.0/igraph/src/glpk/glpmpl03.c |only igraph-1.0.0/igraph/src/glpk/glpmpl04.c |only igraph-1.0.0/igraph/src/glpk/glpmpl05.c |only igraph-1.0.0/igraph/src/glpk/glpmpl06.c |only igraph-1.0.0/igraph/src/glpk/glpmps.c |only igraph-1.0.0/igraph/src/glpk/glpnet01.c |only igraph-1.0.0/igraph/src/glpk/glpnet02.c |only igraph-1.0.0/igraph/src/glpk/glpnet03.c |only igraph-1.0.0/igraph/src/glpk/glpnet04.c |only igraph-1.0.0/igraph/src/glpk/glpnet05.c |only igraph-1.0.0/igraph/src/glpk/glpnet06.c |only igraph-1.0.0/igraph/src/glpk/glpnet07.c |only igraph-1.0.0/igraph/src/glpk/glpnet08.c |only igraph-1.0.0/igraph/src/glpk/glpnet09.c |only igraph-1.0.0/igraph/src/glpk/glpnpp01.c |only igraph-1.0.0/igraph/src/glpk/glpnpp02.c |only igraph-1.0.0/igraph/src/glpk/glpnpp03.c |only igraph-1.0.0/igraph/src/glpk/glpnpp04.c |only igraph-1.0.0/igraph/src/glpk/glpnpp05.c |only igraph-1.0.0/igraph/src/glpk/glpqmd.c |only igraph-1.0.0/igraph/src/glpk/glprgr.c |only igraph-1.0.0/igraph/src/glpk/glprng01.c |only igraph-1.0.0/igraph/src/glpk/glprng02.c |only igraph-1.0.0/igraph/src/glpk/glpscf.c |only igraph-1.0.0/igraph/src/glpk/glpscl.c |only igraph-1.0.0/igraph/src/glpk/glpsdf.c |only igraph-1.0.0/igraph/src/glpk/glpspm.c |only igraph-1.0.0/igraph/src/glpk/glpspx01.c |only igraph-1.0.0/igraph/src/glpk/glpspx02.c |only igraph-1.0.0/igraph/src/glpk/glpsql.c |only igraph-1.0.0/igraph/src/glpk/glpssx01.c |only igraph-1.0.0/igraph/src/glpk/glpssx02.c |only igraph-1.0.0/igraph/src/glpk/glptsp.c |only igraph-1.0.0/igraph/src/heap.pmt | 1 igraph-1.0.0/igraph/src/igraph_blas_internal.h | 10 igraph-1.0.0/igraph/src/igraph_lapack_internal.h | 6 igraph-1.0.0/igraph/src/igraph_math.h | 4 igraph-1.0.0/igraph/src/igraph_stack.c | 6 igraph-1.0.0/igraph/src/igraph_version.h | 6 igraph-1.0.0/igraph/src/include |only igraph-1.0.0/igraph/src/lad.c | 48 igraph-1.0.0/igraph/src/lapack.c | 17 igraph-1.0.0/igraph/src/layout.c | 993 - igraph-1.0.0/igraph/src/layout_dh.c |only igraph-1.0.0/igraph/src/layout_fr.c |only igraph-1.0.0/igraph/src/layout_gem.c |only igraph-1.0.0/igraph/src/layout_kk.c |only igraph-1.0.0/igraph/src/lazyeval.c |only igraph-1.0.0/igraph/src/lsap.c |only igraph-1.0.0/igraph/src/matching.c | 12 igraph-1.0.0/igraph/src/matrix.c | 30 igraph-1.0.0/igraph/src/matrix.pmt | 11 igraph-1.0.0/igraph/src/operators.c | 8 igraph-1.0.0/igraph/src/other.c | 81 igraph-1.0.0/igraph/src/paths.c |only igraph-1.0.0/igraph/src/plfit/error.c |only igraph-1.0.0/igraph/src/plfit/gss.c |only igraph-1.0.0/igraph/src/plfit/kolmogorov.c |only igraph-1.0.0/igraph/src/plfit/lbfgs.c |only igraph-1.0.0/igraph/src/plfit/options.c |only igraph-1.0.0/igraph/src/plfit/plfit.c |only igraph-1.0.0/igraph/src/plfit/plfit.inc |only igraph-1.0.0/igraph/src/plfit/zeta.c |only igraph-1.0.0/igraph/src/prpack.cpp | 2 igraph-1.0.0/igraph/src/prpack/prpack.inc |only igraph-1.0.0/igraph/src/prpack/prpack_base_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_igraph_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_preprocessed_ge_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_preprocessed_gs_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_preprocessed_scc_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_preprocessed_schur_graph.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_result.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_solver.cpp |only igraph-1.0.0/igraph/src/prpack/prpack_utils.cpp |only igraph-1.0.0/igraph/src/random.c | 339 igraph-1.0.0/igraph/src/random_walk.c |only igraph-1.0.0/igraph/src/rinterface.c | 9414 +++------- igraph-1.0.0/igraph/src/rinterface.h | 6 igraph-1.0.0/igraph/src/rinterface_extra.c | 115 igraph-1.0.0/igraph/src/sbm.c | 387 igraph-1.0.0/igraph/src/scan.c |only igraph-1.0.0/igraph/src/simpleraytracer |only igraph-1.0.0/igraph/src/sparsemat.c | 317 igraph-1.0.0/igraph/src/stack.pmt | 1 igraph-1.0.0/igraph/src/structural_properties.c | 71 igraph-1.0.0/igraph/src/triangles.c | 52 igraph-1.0.0/igraph/src/triangles_template.h | 21 igraph-1.0.0/igraph/src/triangles_template1.h | 12 igraph-1.0.0/igraph/src/type_indexededgelist.c | 33 igraph-1.0.0/igraph/src/uuid |only igraph-1.0.0/igraph/src/vector.c | 100 igraph-1.0.0/igraph/src/visitors.c | 5 1286 files changed, 30960 insertions(+), 16217 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-11 1.0
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 3.5.1 dated 2014-10-02 and 3.6.0 dated 2015-06-24
DESCRIPTION | 14 +++++++------- INSTALL | 9 ++++----- MD5 | 16 ++++++++-------- R/WriteXLS.R | 2 +- R/testPerl.R | 1 - inst/INSTALL | 9 ++++----- inst/Perl/WriteXLS.pl | 47 ++++++++++++++++++++++++----------------------- inst/Perl/WriteXLSX.pl | 44 ++++++++++++++++++++++++-------------------- man/WriteXLS.Rd | 16 ++++++++-------- 9 files changed, 80 insertions(+), 78 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description:
R interface to a W3C Markup Validation service.
See <http://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.1-3 dated 2015-06-23 and 0.1-4 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 3 +++ 3 files changed, 9 insertions(+), 6 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Spherical k-Means Clustering
Description: Algorithms to compute spherical k-means partitions.
Features several methods, including a genetic and a fixed-point
algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre],
Ingo Feinerer [aut],
Martin Kober [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between skmeans versions 0.2-6 dated 2014-04-02 and 0.2-7 dated 2015-06-24
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- man/skmeans.Rd | 4 ++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Apache OpenNLP Jars and Basic English Language Models
Description: Apache OpenNLP jars and basic English language models.
Author: Kurt Hornik [aut, cre],
The Apache Software Foundation [ctb, cph] (Apache OpenNLP Java
libraries),
JWNL development team [ctb, cph] (JWNL Java WordNet Library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between openNLPdata versions 1.5.3-1 dated 2013-08-17 and 1.5.3-2 dated 2015-06-24
openNLPdata-1.5.3-1/openNLPdata/getsp.class |only openNLPdata-1.5.3-1/openNLPdata/getsp.java |only openNLPdata-1.5.3-2/openNLPdata/DESCRIPTION | 23 ++++++++++++++++------- openNLPdata-1.5.3-2/openNLPdata/MD5 | 9 +++++---- openNLPdata-1.5.3-2/openNLPdata/configure | 2 +- openNLPdata-1.5.3-2/openNLPdata/java |only openNLPdata-1.5.3-2/openNLPdata/tools |only 7 files changed, 22 insertions(+), 12 deletions(-)
Title: Natural Language Processing Utilities
Description: Utilities for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLPutils versions 0.0-2 dated 2015-05-06 and 0.0-3 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from local and regional-scale co-occurrence data (species x site matrices).
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between netassoc versions 0.4.3 dated 2015-03-13 and 0.4.7 dated 2015-06-24
DESCRIPTION | 8 +-- MD5 | 8 +-- R/netassoc.R | 97 +++++++++++++++++++++++-------------------- man/makenetwork.Rd | 13 +++-- man/plot_netassoc_network.Rd | 2 5 files changed, 68 insertions(+), 60 deletions(-)
Title: Methods that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.14.1 dated 2015-06-20 and 0.14.2 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ R/logSumExp.R | 2 +- inst/doc/matrixStats-methods.html | 4 ++-- man/logSumExp.Rd | 2 +- man/matrixStats-package.Rd | 2 +- src/x_OP_y_TYPE-template.h | 32 ++++++++++++++++++++++++-------- 8 files changed, 46 insertions(+), 24 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com> and Dominic Magirr <d.magirr@gmail.co.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 0.4 dated 2015-02-27 and 0.5 dated 2015-06-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mams.sim.R | 1 + inst/NEWS | 8 +++++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Exact Test from the Combinations of Mutually Exclusive
Alterations (CoMEt) Algorithm
Description: An algorithm for identifying combinations of mutually exclusive alterations in cancer genomes. CoMEt represents the mutations in a set M of k genes with a 2^k dimensional contingency table, and then computes the tail probability of observing T(M) exclusive alterations using an exact statistical test.
Author: Max Leiserson [aut, cre],
Hsin-Ta Wu [aut],
Fabio Vandin [ctb],
Vivian Hsiao [ctb],
Benjamin Raphael [ctb]
Maintainer: Max Leiserson <mdml@cs.brown.edu>
Diff between cometExactTest versions 0.1 dated 2015-06-22 and 0.1.2 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about cometExactTest at CRAN
Permanent link
Title: Chronological Objects which can Handle Dates and Times
Description: Chronological objects which can handle dates and times.
Author: David James [aut] (S original),
Kurt Hornik [aut, trl, cre],
Gabor Grothendieck [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between chron versions 2.3-46 dated 2015-06-19 and 2.3-47 dated 2015-06-24
ChangeLog | 6 ++++++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 4 ++-- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Color Palettes Generator
Description: Different methods to generate a color palette based on a specified base color and a number of colors that should be created.
Author: Carl Ambroselli [aut, cre]
Maintainer: Carl Ambroselli <colorpalette@carl-ambroselli.de>
Diff between ColorPalette versions 1.0-0 dated 2015-05-27 and 1.0-1 dated 2015-06-24
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Convex Clustering Methods and Clustering Indexes
Description: Convex Clustering methods, including K-means algorithm,
On-line Update algorithm (Hard Competitive Learning) and Neural Gas
algorithm (Soft Competitive Learning), and calculation of several
indexes for finding the number of clusters in a data set.
Author: Evgenia Dimitriadou [aut],
Kurt Hornik [ctb, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between cclust versions 0.6-19 dated 2014-10-08 and 0.6-20 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/Rindexes.Rd | 7 +------ 3 files changed, 7 insertions(+), 12 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-2 dated 2015-04-27 and 1.0-3 dated 2015-06-24
DESCRIPTION | 15 ++-- MD5 | 107 +++++++++++++++++---------------- NAMESPACE | 5 + R/ADEg.C1.R | 2 R/ADEg.R | 2 R/ADEg.S1.R | 8 +- R/ADEg.S2.R | 4 - R/ADEgS.R | 2 R/C1.barchart.R | 2 R/C1.curve.R | 6 - R/C1.density.R | 2 R/C1.dotplot.R | 6 - R/C1.gauss.R | 2 R/C1.hist.R | 7 +- R/C1.interval.R | 6 - R/S1.boxplot.R | 2 R/S1.class.R | 2 R/S1.distri.R | 2 R/S1.label.R | 2 R/S1.match.R | 2 R/S2.arrow.R | 2 R/S2.class.R | 2 R/S2.corcircle.R | 2 R/S2.density.R | 2 R/S2.distri.R | 2 R/S2.image.R | 2 R/S2.label.R | 2 R/S2.logo.R | 2 R/S2.match.R | 2 R/S2.traject.R | 2 R/S2.value.R | 2 R/T.image.R | 2 R/T.value.R | 2 R/Tr.class.R | 2 R/Tr.label.R | 2 R/Tr.match.R | 2 R/Tr.traject.R | 2 R/ade4-kplot.R | 22 +++--- R/ade4-plot.R | 147 +++++++++++++++++++++------------------------- R/ade4-scatter.R | 28 ++++---- R/multiplot.R | 8 +- R/panelfunctions.R | 2 R/s.Spatial.R | 22 ++++-- R/s.hist.R | 2 R/utils.R | 8 +- R/utilsADEgS.R | 14 ++-- R/utilstriangle.R | 2 build/vignette.rds |binary inst/doc/adegraphics.R | 127 ++++++++++++++++++++++++++++++++------- inst/doc/adegraphics.Rnw | 121 +++++++++++++++++++++++++++++++++++++ inst/doc/adegraphics.pdf |binary man/plotEig.Rd |only man/setlimits1D.Rd |only man/sortparamADEg.Rd |only tests/panelSpatial.R | 6 + vignettes/adegraphics.Rnw | 121 +++++++++++++++++++++++++++++++++++++ 56 files changed, 595 insertions(+), 255 deletions(-)
Title: Tools for Sotkanet Open Data Portal
Description: Tools to download data from the Sotkanet open data portal.
Author: Leo Lahti, Einari Happonen, Juuso Parkkinen, Joona Lehtomaki
Maintainer: Leo Lahti <louhos@googlegroups.com>
Diff between sotkanet versions 0.9.10 dated 2015-04-21 and 0.9.14 dated 2015-06-24
sotkanet-0.9.10/sotkanet/README |only sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.R |only sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.Rmd |only sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.html |only sotkanet-0.9.10/sotkanet/vignettes/sotkanet_tutorial.Rmd |only sotkanet-0.9.14/sotkanet/DESCRIPTION | 13 sotkanet-0.9.14/sotkanet/MD5 | 42 +- sotkanet-0.9.14/sotkanet/NAMESPACE | 3 sotkanet-0.9.14/sotkanet/R/GetDataSotkanet.R |only sotkanet-0.9.14/sotkanet/R/SotkanetData.R |only sotkanet-0.9.14/sotkanet/R/SotkanetIndicators.R |only sotkanet-0.9.14/sotkanet/R/base_url.R |only sotkanet-0.9.14/sotkanet/R/csv.R |only sotkanet-0.9.14/sotkanet/R/firstlib.R | 6 sotkanet-0.9.14/sotkanet/R/internal.R | 166 ---------- sotkanet-0.9.14/sotkanet/R/json.R |only sotkanet-0.9.14/sotkanet/R/sotkanet.R | 106 ------ sotkanet-0.9.14/sotkanet/README.md |only sotkanet-0.9.14/sotkanet/build/vignette.rds |binary sotkanet-0.9.14/sotkanet/inst/doc/tutorial.R |only sotkanet-0.9.14/sotkanet/inst/doc/tutorial.Rmd |only sotkanet-0.9.14/sotkanet/inst/doc/tutorial.html |only sotkanet-0.9.14/sotkanet/man/GetDataSotkanet.Rd | 20 - sotkanet-0.9.14/sotkanet/man/GetDataSotkanetSingleIndicator.Rd | 4 sotkanet-0.9.14/sotkanet/man/SotkanetData.Rd | 2 sotkanet-0.9.14/sotkanet/man/SotkanetIndicators.Rd | 4 sotkanet-0.9.14/sotkanet/man/base_url.Rd | 2 sotkanet-0.9.14/sotkanet/man/sotkanet.csv_query.Rd | 2 sotkanet-0.9.14/sotkanet/man/sotkanet.json_query.Rd | 2 sotkanet-0.9.14/sotkanet/vignettes/tutorial.Rmd |only 30 files changed, 49 insertions(+), 323 deletions(-)
More information about runittotestthat at CRAN
Permanent link
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.2 dated 2015-02-16 and 1.3.3 dated 2015-06-24
DESCRIPTION | 8 ++-- MD5 | 34 +++++++++--------- NAMESPACE | 2 - R/Rlibeemd-package.R | 2 - R/ceemdan.R | 22 +++++------ R/eemd.R | 32 +++++++++-------- R/emd.R | 18 ++++----- R/extrema.R | 29 ++++++++------- inst/CITATION | 2 - man/ECG.Rd | 3 + man/Rlibeemd.Rd | 5 +- man/ceemdan.Rd | 9 ++-- man/eemd.Rd | 15 ++++---- man/emd.Rd | 3 + man/extrema.Rd | 23 ++++++------ man/nIMFs.Rd | 3 + src/RcppExports.cpp | 94 ++++++++++++++++++++------------------------------- src/eemd.h | 2 + 18 files changed, 150 insertions(+), 156 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.1.2 dated 2015-06-15 and 3.1.3 dated 2015-06-24
DESCRIPTION | 6 MD5 | 35 NEWS | 10 R/as.char.R | 13 R/glmnet.R | 14 R/lib.R | 43 R/stop.if.dots.R | 1 R/xy.R | 36 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/linmod.R |only inst/slowtests/linmod.leisch.tutorial.R |only inst/slowtests/linmod.milbo.tutorial.R |only inst/slowtests/test.glmnet.R | 7 inst/slowtests/test.glmnet.Rout.save | 152 ++- inst/slowtests/test.ltut.R | 676 +++++++-------- inst/slowtests/test.ltut.Rout.save | 1381 +++++++++++++++++++------------- inst/slowtests/test.non.earth.R | 2 inst/slowtests/test.non.earth.Rout.save | 6 20 files changed, 1321 insertions(+), 1061 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.8 dated 2015-05-19 and 0.8-1 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 9 +++++++++ build/vignette.rds |binary inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 8 ++------ 6 files changed, 20 insertions(+), 15 deletions(-)
Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.2 dated 2015-02-03 and 0.3 dated 2015-06-24
MetaLandSim-0.2/MetaLandSim/R/merge.with.order.R |only MetaLandSim-0.2/MetaLandSim/data/param2.rda |only MetaLandSim-0.2/MetaLandSim/man/merge.with.order.Rd |only MetaLandSim-0.2/MetaLandSim/man/param2.Rd |only MetaLandSim-0.3/MetaLandSim/DESCRIPTION | 10 - MetaLandSim-0.3/MetaLandSim/MD5 | 78 ++++------ MetaLandSim-0.3/MetaLandSim/NAMESPACE | 1 MetaLandSim-0.3/MetaLandSim/R/MetaLandSim.GUI.R | 41 +---- MetaLandSim-0.3/MetaLandSim/R/addpoints.R | 2 MetaLandSim-0.3/MetaLandSim/R/cluster.id.R | 2 MetaLandSim-0.3/MetaLandSim/R/convert.graph.R | 2 MetaLandSim-0.3/MetaLandSim/R/iterate.graph.R | 4 MetaLandSim-0.3/MetaLandSim/R/manage_expansion_sim.R | 22 +- MetaLandSim-0.3/MetaLandSim/R/manage_landscape_sim.R | 55 +++---- MetaLandSim-0.3/MetaLandSim/R/merge_order.R |only MetaLandSim-0.3/MetaLandSim/R/range_expansion.R | 6 MetaLandSim-0.3/MetaLandSim/R/simulate_graph.R | 19 -- MetaLandSim-0.3/MetaLandSim/R/span.graph.R | 6 MetaLandSim-0.3/MetaLandSim/R/species.graph.R | 56 +++---- MetaLandSim-0.3/MetaLandSim/R/spom.R | 19 +- MetaLandSim-0.3/MetaLandSim/build/vignette.rds |binary MetaLandSim-0.3/MetaLandSim/data/cabrera.rda |binary MetaLandSim-0.3/MetaLandSim/data/datalist | 1 MetaLandSim-0.3/MetaLandSim/data/landscape_change.rda |binary MetaLandSim-0.3/MetaLandSim/data/mc_df.rda |binary MetaLandSim-0.3/MetaLandSim/data/occ.landscape.rda |binary MetaLandSim-0.3/MetaLandSim/data/occ.landscape2.rda |binary MetaLandSim-0.3/MetaLandSim/data/param1.rda |binary MetaLandSim-0.3/MetaLandSim/data/rg_exp.rda |binary MetaLandSim-0.3/MetaLandSim/data/rland.rda |binary MetaLandSim-0.3/MetaLandSim/inst/doc/MetaLandSim.pdf |binary MetaLandSim-0.3/MetaLandSim/inst/doc/landscape_simulation.pdf |binary MetaLandSim-0.3/MetaLandSim/inst/doc/range_expansion.pdf |binary MetaLandSim-0.3/MetaLandSim/man/MetaLandSim-package.Rd | 14 - MetaLandSim-0.3/MetaLandSim/man/iterate.graph.Rd | 9 - MetaLandSim-0.3/MetaLandSim/man/list.stats.Rd | 2 MetaLandSim-0.3/MetaLandSim/man/manage_expansion_sim.Rd | 9 - MetaLandSim-0.3/MetaLandSim/man/manage_landscape_sim.Rd | 6 MetaLandSim-0.3/MetaLandSim/man/merge_order.Rd |only MetaLandSim-0.3/MetaLandSim/man/range_raster.Rd | 8 - MetaLandSim-0.3/MetaLandSim/man/simulate_graph.Rd | 6 MetaLandSim-0.3/MetaLandSim/man/species.graph.Rd | 7 MetaLandSim-0.3/MetaLandSim/man/spom.Rd | 6 43 files changed, 170 insertions(+), 221 deletions(-)
Title: Facilitate Generating of Distance Matrices Used in Package
'spacom' and Plotting Data on Maps
Description: Generates distance matrices from shape files and represents spatially weighted multilevel analysis results (see 'spacom')
Author: Davide Morselli [aut, cre],
Mathieu Cossuta [aut],
Till Junge [aut],
Sandra Penic [aut],
Guy Elcheroth [ctb],
Stephanie Glaeser [ctb]
Maintainer: Davide Morselli <davide.morselli@unil.ch>
Diff between geospacom versions 0.5-7 dated 2014-03-19 and 0.5-8 dated 2015-06-24
DESCRIPTION | 15 +++++++-------- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS |only R/ImagePoly.R | 2 +- R/Spatial.R | 14 +++++++------- 6 files changed, 21 insertions(+), 20 deletions(-)
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.2-4 dated 2015-03-24 and 0.2-6 dated 2015-06-24
assertive-0.2-4/assertive/inst/tests |only assertive-0.2-4/assertive/man/r_can_build_translations.Rd |only assertive-0.2-4/assertive/man/r_can_compile_code.Rd |only assertive-0.2-4/assertive/tests/run-all.R |only assertive-0.2-6/assertive/DESCRIPTION | 10 assertive-0.2-6/assertive/MD5 | 326 ++--- assertive-0.2-6/assertive/NAMESPACE | 14 assertive-0.2-6/assertive/NEWS | 2 assertive-0.2-6/assertive/R/are-same.R | 15 assertive-0.2-6/assertive/R/assert-are-same.R | 8 assertive-0.2-6/assertive/R/assert-is-a-type.R | 134 +- assertive-0.2-6/assertive/R/assert-is-binding.R |only assertive-0.2-6/assertive/R/assert-is-reflection.R | 7 assertive-0.2-6/assertive/R/assert-is-set.R | 10 assertive-0.2-6/assertive/R/assert-is-true-false.R | 7 assertive-0.2-6/assertive/R/assert-r-has-capability.R | 285 ++-- assertive-0.2-6/assertive/R/engine.R |only assertive-0.2-6/assertive/R/has.R | 600 +++++----- assertive-0.2-6/assertive/R/internal.R | 108 - assertive-0.2-6/assertive/R/is-binding.R |only assertive-0.2-6/assertive/R/is-empty-scalar.R | 450 +++---- assertive-0.2-6/assertive/R/is-file.R | 6 assertive-0.2-6/assertive/R/is-in-range.R | 2 assertive-0.2-6/assertive/R/is-reflection.R | 159 ++ assertive-0.2-6/assertive/R/is-set.R | 160 +- assertive-0.2-6/assertive/R/is-true-false.R | 228 ++- assertive-0.2-6/assertive/R/is-type.R | 35 assertive-0.2-6/assertive/R/r-has-capability.R | 589 ++++----- assertive-0.2-6/assertive/README.md | 525 ++++---- assertive-0.2-6/assertive/build/vignette.rds |binary assertive-0.2-6/assertive/man/DIM.Rd | 2 assertive-0.2-6/assertive/man/are_identical.Rd | 2 assertive-0.2-6/assertive/man/are_same_length.Rd | 17 assertive-0.2-6/assertive/man/as.character.file.Rd | 2 assertive-0.2-6/assertive/man/assert_engine.Rd | 62 - assertive-0.2-6/assertive/man/assertive.Rd | 2 assertive-0.2-6/assertive/man/bapply.Rd | 9 assertive-0.2-6/assertive/man/call_and_name.Rd | 2 assertive-0.2-6/assertive/man/cause.Rd | 2 assertive-0.2-6/assertive/man/character_to_list_of_integer_vectors.Rd | 2 assertive-0.2-6/assertive/man/coerce_to.Rd | 2 assertive-0.2-6/assertive/man/create_regex.Rd | 2 assertive-0.2-6/assertive/man/d.Rd | 2 assertive-0.2-6/assertive/man/dont_stop.Rd | 2 assertive-0.2-6/assertive/man/false.Rd | 4 assertive-0.2-6/assertive/man/get_name_in_parent.Rd | 2 assertive-0.2-6/assertive/man/has_any_attributes.Rd | 2 assertive-0.2-6/assertive/man/has_arg.Rd | 2 assertive-0.2-6/assertive/man/has_attributes.Rd | 2 assertive-0.2-6/assertive/man/has_cols.Rd | 2 assertive-0.2-6/assertive/man/has_dims.Rd | 2 assertive-0.2-6/assertive/man/has_duplicates.Rd | 2 assertive-0.2-6/assertive/man/has_names.Rd | 2 assertive-0.2-6/assertive/man/has_terms.Rd | 2 assertive-0.2-6/assertive/man/is2.Rd | 5 assertive-0.2-6/assertive/man/is_array.Rd | 2 assertive-0.2-6/assertive/man/is_atomic.Rd | 2 assertive-0.2-6/assertive/man/is_batch_mode.Rd | 2 assertive-0.2-6/assertive/man/is_binding_locked.Rd |only assertive-0.2-6/assertive/man/is_cas_number.Rd | 2 assertive-0.2-6/assertive/man/is_character.Rd | 2 assertive-0.2-6/assertive/man/is_class.Rd | 2 assertive-0.2-6/assertive/man/is_complex.Rd | 2 assertive-0.2-6/assertive/man/is_connection.Rd | 2 assertive-0.2-6/assertive/man/is_credit_card_number.Rd | 2 assertive-0.2-6/assertive/man/is_current_r.Rd |only assertive-0.2-6/assertive/man/is_data.frame.Rd | 2 assertive-0.2-6/assertive/man/is_date_string.Rd | 2 assertive-0.2-6/assertive/man/is_debugged.Rd | 2 assertive-0.2-6/assertive/man/is_dir.Rd | 2 assertive-0.2-6/assertive/man/is_divisible_by.Rd | 2 assertive-0.2-6/assertive/man/is_email_address.Rd | 2 assertive-0.2-6/assertive/man/is_empty.Rd | 4 assertive-0.2-6/assertive/man/is_empty_file.Rd | 2 assertive-0.2-6/assertive/man/is_empty_model.Rd | 2 assertive-0.2-6/assertive/man/is_environment.Rd | 2 assertive-0.2-6/assertive/man/is_error_free.Rd | 2 assertive-0.2-6/assertive/man/is_executable_file.Rd | 2 assertive-0.2-6/assertive/man/is_existing.Rd | 2 assertive-0.2-6/assertive/man/is_existing_file.Rd | 6 assertive-0.2-6/assertive/man/is_factor.Rd | 2 assertive-0.2-6/assertive/man/is_finite.Rd | 2 assertive-0.2-6/assertive/man/is_function.Rd | 2 assertive-0.2-6/assertive/man/is_hex_color.Rd | 2 assertive-0.2-6/assertive/man/is_honorific.Rd | 2 assertive-0.2-6/assertive/man/is_if_condition.Rd |only assertive-0.2-6/assertive/man/is_in_past.Rd | 2 assertive-0.2-6/assertive/man/is_in_range.Rd | 4 assertive-0.2-6/assertive/man/is_inherited_from.Rd | 2 assertive-0.2-6/assertive/man/is_integer.Rd | 2 assertive-0.2-6/assertive/man/is_ip_address.Rd | 2 assertive-0.2-6/assertive/man/is_isbn_code.Rd | 2 assertive-0.2-6/assertive/man/is_language.Rd | 2 assertive-0.2-6/assertive/man/is_leaf.Rd | 2 assertive-0.2-6/assertive/man/is_library.Rd | 2 assertive-0.2-6/assertive/man/is_list.Rd | 2 assertive-0.2-6/assertive/man/is_loaded.Rd | 2 assertive-0.2-6/assertive/man/is_logical.Rd | 2 assertive-0.2-6/assertive/man/is_na.Rd | 2 assertive-0.2-6/assertive/man/is_nan.Rd | 2 assertive-0.2-6/assertive/man/is_null.Rd | 2 assertive-0.2-6/assertive/man/is_numeric.Rd | 2 assertive-0.2-6/assertive/man/is_on_os_path.Rd | 8 assertive-0.2-6/assertive/man/is_qr.Rd | 2 assertive-0.2-6/assertive/man/is_r.Rd | 2 assertive-0.2-6/assertive/man/is_raster.Rd | 2 assertive-0.2-6/assertive/man/is_raw.Rd | 2 assertive-0.2-6/assertive/man/is_real.Rd | 2 assertive-0.2-6/assertive/man/is_relistable.Rd | 2 assertive-0.2-6/assertive/man/is_s4.Rd | 2 assertive-0.2-6/assertive/man/is_set_equal.Rd | 11 assertive-0.2-6/assertive/man/is_single_character.Rd | 2 assertive-0.2-6/assertive/man/is_symmetric_matrix.Rd | 2 assertive-0.2-6/assertive/man/is_table.Rd | 2 assertive-0.2-6/assertive/man/is_true.Rd | 2 assertive-0.2-6/assertive/man/is_ts.Rd | 2 assertive-0.2-6/assertive/man/is_uk_car_licence.Rd | 2 assertive-0.2-6/assertive/man/is_uk_national_insurance_number.Rd | 2 assertive-0.2-6/assertive/man/is_uk_postcode.Rd | 2 assertive-0.2-6/assertive/man/is_uk_telephone_number.Rd | 2 assertive-0.2-6/assertive/man/is_unsorted.Rd | 2 assertive-0.2-6/assertive/man/is_us_telephone_number.Rd | 2 assertive-0.2-6/assertive/man/is_us_zip_code.Rd | 2 assertive-0.2-6/assertive/man/is_valid_r_code.Rd | 2 assertive-0.2-6/assertive/man/is_valid_variable_name.Rd | 2 assertive-0.2-6/assertive/man/is_whole_number.Rd | 2 assertive-0.2-6/assertive/man/is_windows.Rd | 2 assertive-0.2-6/assertive/man/is_xxx_for_decimal_point.Rd | 2 assertive-0.2-6/assertive/man/locale_categories.Rd | 2 assertive-0.2-6/assertive/man/matches_regex.Rd | 2 assertive-0.2-6/assertive/man/merge.list.Rd | 2 assertive-0.2-6/assertive/man/merge_dots_with_list.Rd | 2 assertive-0.2-6/assertive/man/modal_value.Rd | 2 assertive-0.2-6/assertive/man/n_elements.Rd | 2 assertive-0.2-6/assertive/man/na.Rd | 4 assertive-0.2-6/assertive/man/not_this_build.Rd |only assertive-0.2-6/assertive/man/not_this_os.Rd |only assertive-0.2-6/assertive/man/parenthesize.Rd | 2 assertive-0.2-6/assertive/man/print_and_capture.Rd | 2 assertive-0.2-6/assertive/man/r_can_find_tools.Rd |only assertive-0.2-6/assertive/man/r_has_jpeg_capability.Rd | 2 assertive-0.2-6/assertive/man/recycle.Rd | 2 assertive-0.2-6/assertive/man/set_cause.Rd | 2 assertive-0.2-6/assertive/man/strip_attributes.Rd | 2 assertive-0.2-6/assertive/man/strip_invalid_chars.Rd | 2 assertive-0.2-6/assertive/man/sys_get_locale.Rd | 2 assertive-0.2-6/assertive/man/truncate.Rd | 2 assertive-0.2-6/assertive/man/type_description.Rd |only assertive-0.2-6/assertive/man/use_first.Rd | 2 assertive-0.2-6/assertive/man/warn_about_file.access_under_windows.Rd | 2 assertive-0.2-6/assertive/tests/testthat |only assertive-0.2-6/assertive/tests/testthat.R |only 152 files changed, 2135 insertions(+), 1883 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-22 1.0
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams (q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler). An implementation of soundex is provided as well.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.1 dated 2015-06-22 and 0.9.2 dated 2015-06-24
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 4 ++++ R/stringdist.R | 2 ++ R/stringsim.R | 20 ++++++++++++-------- man/stringsim.Rd | 4 +++- src/Rstringdist.c | 24 +++++++++++++++--------- src/dl.c | 13 ++++++++++--- src/soundex.c | 1 + src/utf8ToInt.c | 4 +++- src/utils.c | 15 --------------- tests/testthat/testPhonetic.R | 3 ++- tests/testthat/testQgrams.R | 5 ++++- tests/testthat/testStringdist.R | 4 ++++ tests/testthat/testStringsim.R | 25 +++++++++++++++++++++++++ 15 files changed, 103 insertions(+), 57 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from http://www.ncbi.nlm.nih.gov/pubmed.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramu@igib.in>
Diff between pubmed.mineR versions 1.0.3.1 dated 2015-02-06 and 1.0.4 dated 2015-06-24
pubmed.mineR-1.0.3.1/pubmed.mineR/R/R2S4.R |only pubmed.mineR-1.0.3.1/pubmed.mineR/man/R2S4.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/DESCRIPTION | 39 ++-- pubmed.mineR-1.0.4/pubmed.mineR/MD5 | 87 +++++----- pubmed.mineR-1.0.4/pubmed.mineR/NAMESPACE | 36 ++-- pubmed.mineR-1.0.4/pubmed.mineR/R/BWI.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/altnamesfun.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/currentabs_fn.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/genes_BWI.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/get_original_term2.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/local_uniprotfun.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/previousabs_fn.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/pubtator_function.R | 49 ++++- pubmed.mineR-1.0.4/pubmed.mineR/R/pubtator_result_list_to_table.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/subsetabs.R |only pubmed.mineR-1.0.4/pubmed.mineR/R/uniprotfun.R | 21 +- pubmed.mineR-1.0.4/pubmed.mineR/data/GeneToEntrez.rda |binary pubmed.mineR-1.0.4/pubmed.mineR/data/HGNC2UniprotID.rda |binary pubmed.mineR-1.0.4/pubmed.mineR/data/HGNCdata.rda |binary pubmed.mineR-1.0.4/pubmed.mineR/data/common_words_new.rda |binary pubmed.mineR-1.0.4/pubmed.mineR/inst/CITATION | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/Abstracts-class.Rd | 5 pubmed.mineR-1.0.4/pubmed.mineR/man/BWI.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/Find_conclusion.Rd | 3 pubmed.mineR-1.0.4/pubmed.mineR/man/Genewise.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/HGNC2UniprotID.Rd | 4 pubmed.mineR-1.0.4/pubmed.mineR/man/HGNCdata.Rd | 4 pubmed.mineR-1.0.4/pubmed.mineR/man/altnamesfun.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/cleanabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/combineabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/common_words_new.Rd | 3 pubmed.mineR-1.0.4/pubmed.mineR/man/contextSearch.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/cos_sim_calc.Rd | 3 pubmed.mineR-1.0.4/pubmed.mineR/man/cos_sim_calc_boot.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/currentabs_fn.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/find_intro_conc_html.Rd | 6 pubmed.mineR-1.0.4/pubmed.mineR/man/gene_atomization.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/genes_BWI.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/get_original_term.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/get_original_term2.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/getabsT.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/input_for_find_intro_conc_html.Rd | 4 pubmed.mineR-1.0.4/pubmed.mineR/man/local_uniprotfun.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/previousabs_fn.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/pubtator_function.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/pubtator_result_list_to_table.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/readabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/removeabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/sendabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/subabs.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/subsetabs-methods.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/subsetabs.Rd |only pubmed.mineR-1.0.4/pubmed.mineR/man/tdm_for_lsa.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/uniprotfun.Rd | 2 pubmed.mineR-1.0.4/pubmed.mineR/man/wordsclusterview.Rd | 2 55 files changed, 189 insertions(+), 109 deletions(-)
Title: Paired Response Curve
Description: Estimation, prediction and testing for analyzing serial dilution assay data using paired response curve.
Author: Youyi Fong
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between prc versions 2014.11-4 dated 2014-11-04 and 2015.6-24 dated 2015-06-24
ChangeLog | 15 + DESCRIPTION | 7 MD5 | 19 - NAMESPACE | 19 + R/prc.R | 151 ++++++---- R/prcsp.R | 591 +++++++++++++++++++++++++------------------ R/quadratic.sp.R | 7 inst/unitTests/runit.prc.R | 11 inst/unitTests/runit.prcsp.R |only man/prc.Rd | 46 ++- src/computeA.c | 33 ++ 11 files changed, 552 insertions(+), 347 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-0 dated 2015-05-13 and 2.2-2 dated 2015-06-24
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++++----------- NAMESPACE | 3 ++- R/gacFuns.R |only R/genRandDAG.R | 33 +++++++++++++++++++++++++++++---- R/pcalg.R | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ man/backdoor.Rd | 2 +- man/disCItest.Rd | 11 ++++++----- man/gac.Rd |only man/randomDAG.Rd | 3 ++- tests/gacData.rda |only tests/test_gac.R |only tests/test_randDAG.R | 7 +++++++ tests/test_skeleton.R | 4 ++-- 16 files changed, 81 insertions(+), 32 deletions(-)
Title: Utilities for Formulas, Expressions, Calls and Other Objects
Description: These utilities facilitate the programmatic manipulations of
formulas, expressions, calls, names, symbols and other objects.
Author: Christopher Brown
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between formula.tools versions 1.5.2 dated 2015-05-26 and 1.5.4 dated 2015-06-24
formula.tools-1.5.2/formula.tools/tests/testthat/test-as.character.formula.R |only formula.tools-1.5.2/formula.tools/tests/testthat/test-catcont.R |only formula.tools-1.5.2/formula.tools/tests/testthat/test-is.cat.R |only formula.tools-1.5.4/formula.tools/DESCRIPTION | 10 +-- formula.tools-1.5.4/formula.tools/MD5 | 18 ++++-- formula.tools-1.5.4/formula.tools/NEWS | 9 +++ formula.tools-1.5.4/formula.tools/R/get.vars.R | 27 +++++++--- formula.tools-1.5.4/formula.tools/man/get.vars.Rd | 11 +++- formula.tools-1.5.4/formula.tools/tests/testthat/test-as.character.formula.r |only formula.tools-1.5.4/formula.tools/tests/testthat/test-catcont.r |only formula.tools-1.5.4/formula.tools/tests/testthat/test-get.vars.r |only formula.tools-1.5.4/formula.tools/tests/testthat/test-is.cat.r |only formula.tools-1.5.4/formula.tools/tests/testthat/test-lhs.r |only formula.tools-1.5.4/formula.tools/vignettes |only 14 files changed, 55 insertions(+), 20 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-0 dated 2015-04-29 and 2.7-2 dated 2015-06-24
dae-2.7-0/dae/man/fitted.errors.rd |only dae-2.7-0/dae/man/proj2.decomp.Rd |only dae-2.7-0/dae/man/proj2.ops.Rd |only dae-2.7-2/dae/DESCRIPTION | 24 ++++----- dae-2.7-2/dae/MD5 | 28 +++++----- dae-2.7-2/dae/NAMESPACE | 3 - dae-2.7-2/dae/R/diagnostic.checking.r | 90 +++++++++++++++++----------------- dae-2.7-2/dae/R/fac.layout.r | 74 +++++++++++++++++---------- dae-2.7-2/dae/R/proj.canon.v3.r | 6 ++ dae-2.7-2/dae/R/proj.r | 8 +-- dae-2.7-2/dae/R/projs.canon.v3.r | 43 ++++++++++++---- dae-2.7-2/dae/inst/NEWS.Rd |only dae-2.7-2/dae/inst/doc/dae-manual.pdf |binary dae-2.7-2/dae/man/dae-deprecated.Rd |only dae-2.7-2/dae/man/dae-package.Rd | 76 ++++++++++++++++------------ dae-2.7-2/dae/man/fac.layout.Rd | 37 +++++++++---- dae-2.7-2/dae/man/fitted.errors.Rd |only dae-2.7-2/dae/man/resid.errors.Rd | 5 - 18 files changed, 231 insertions(+), 163 deletions(-)
Title: Augments the Use of 'Asreml' in Fitting Mixed Models
Description: Assists in automating the testing of terms in mixed models when 'asreml' is used
to fit the models. The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the
fitting of a sequence of models is kept in a data frame. Procedures are available for choosing
models that conform to the hierarchy or marginality principle and for displaying predictions
for significant terms in tables and graphs. The package 'asreml' provides a computationally
efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It can be
purchased from 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R', who will supply a zip file for
local installation/updating.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between asremlPlus versions 1.10-16 dated 2015-06-06 and 2.0-0 dated 2015-06-24
asremlPlus-1.10-16/asremlPlus/R/reml.v18.r |only asremlPlus-1.10-16/asremlPlus/man/addrm.terms.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/choose.model.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/recalc.wald.tab.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/rmboundary.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/sig.devn.reparam.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/testranfix.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/testrcov.asreml.Rd |only asremlPlus-1.10-16/asremlPlus/man/testswapran.asreml.Rd |only asremlPlus-2.0-0/asremlPlus/DESCRIPTION | 32 - asremlPlus-2.0-0/asremlPlus/MD5 | 54 +- asremlPlus-2.0-0/asremlPlus/NAMESPACE | 8 asremlPlus-2.0-0/asremlPlus/R/reml.lrt.r | 31 + asremlPlus-2.0-0/asremlPlus/R/reml.v19.r |only asremlPlus-2.0-0/asremlPlus/inst/NEWS.Rd |only asremlPlus-2.0-0/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-2.0-0/asremlPlus/man/addrm.terms.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/asremlPlus-deprecated.Rd |only asremlPlus-2.0-0/asremlPlus/man/asremlPlus-package.Rd | 200 +++++------ asremlPlus-2.0-0/asremlPlus/man/asrtests.Rd | 10 asremlPlus-2.0-0/asremlPlus/man/choose.model.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/info.crit.asreml.Rd | 4 asremlPlus-2.0-0/asremlPlus/man/newfit.asreml.Rd | 2 asremlPlus-2.0-0/asremlPlus/man/plotvariofaces.asreml.Rd | 2 asremlPlus-2.0-0/asremlPlus/man/pred.present.asreml.Rd | 12 asremlPlus-2.0-0/asremlPlus/man/predictionplot.asreml.Rd | 8 asremlPlus-2.0-0/asremlPlus/man/predictparallel.asreml.Rd | 4 asremlPlus-2.0-0/asremlPlus/man/print.asrtests.Rd | 6 asremlPlus-2.0-0/asremlPlus/man/recalc.wald.tab.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/reml.lrt.asreml.Rd | 7 asremlPlus-2.0-0/asremlPlus/man/rmboundary.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/setvarianceterms.asreml.Rd | 6 asremlPlus-2.0-0/asremlPlus/man/sig.devn.reparam.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/simulate.asreml.Rd | 13 asremlPlus-2.0-0/asremlPlus/man/testranfix.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/testrcov.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/testswapran.asrtests.Rd |only asremlPlus-2.0-0/asremlPlus/man/variofaces.Rd | 8 38 files changed, 209 insertions(+), 198 deletions(-)
Title: Bayesian Non- and Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 1.0.3 dated 2015-06-08 and 1.0.4 dated 2015-06-23
ChangeLog | 10 +- DESCRIPTION | 8 - MD5 | 19 ++-- R/bnpglm.R | 18 +-- R/bnpglmf.R |only man/bnpglm.Rd | 11 +- src/OneResLtnt.c | 129 ++++++++++++++++++--------- src/SpecOneRL.h | 233 +++++++++++++++++++++++++++++++++++++++++++++++++- src/other.functions.h | 145 +++++++++++++++++++++++++++++-- src/pdfs.h | 46 +++++++++ src/sampling.h | 4 11 files changed, 535 insertions(+), 88 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 1.1.4 dated 2015-05-05 and 1.2.0 dated 2015-06-23
DESCRIPTION | 10 +++--- MD5 | 22 ++++++------- NEWS | 15 +++++++++ R/CJS.R | 77 ++++++++++++++++++++++++++++-------------------- R/Closed.R | 75 ++++++++++++++++++++++++++++------------------ R/multimark_functions.R | 4 +- man/multimarkCJS.Rd | 12 ++++--- man/multimarkClosed.Rd | 12 ++++--- man/multimodelCJS.Rd | 13 +++++--- man/multimodelClosed.Rd | 10 ++++-- src/Closed.c | 13 ++++---- src/ProbitCJS.c | 18 +++++------ 12 files changed, 172 insertions(+), 109 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)). Procedures are included for use with GLM, ivreg, plm (fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>
Diff between clusterSEs versions 1.2 dated 2015-03-11 and 2.0 dated 2015-06-23
clusterSEs-1.2/clusterSEs/R/clusterBS.R |only clusterSEs-1.2/clusterSEs/R/clusterBSmlogit.R |only clusterSEs-1.2/clusterSEs/R/clusterIM.R |only clusterSEs-1.2/clusterSEs/R/clusterIMmlogit.R |only clusterSEs-1.2/clusterSEs/R/clusterwild.R |only clusterSEs-1.2/clusterSEs/man/cluster.bs.Rd |only clusterSEs-1.2/clusterSEs/man/cluster.im.Rd |only clusterSEs-1.2/clusterSEs/man/cluster.wild.Rd |only clusterSEs-2.0/clusterSEs/DESCRIPTION | 13 ++-- clusterSEs-2.0/clusterSEs/MD5 | 34 +++++++---- clusterSEs-2.0/clusterSEs/NAMESPACE | 33 +++++++++-- clusterSEs-2.0/clusterSEs/R/clusterBS.glm.R |only clusterSEs-2.0/clusterSEs/R/clusterBS.ivreg.R |only clusterSEs-2.0/clusterSEs/R/clusterBS.mlogit.R |only clusterSEs-2.0/clusterSEs/R/clusterBS.plm.R |only clusterSEs-2.0/clusterSEs/R/clusterIM.glm.R |only clusterSEs-2.0/clusterSEs/R/clusterIM.ivreg.R |only clusterSEs-2.0/clusterSEs/R/clusterIM.mlogit.R |only clusterSEs-2.0/clusterSEs/R/clusterwild.glm.R |only clusterSEs-2.0/clusterSEs/R/clusterwild.ivreg.R |only clusterSEs-2.0/clusterSEs/R/clusterwild.plm.R |only clusterSEs-2.0/clusterSEs/man/cluster.bs.glm.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.bs.ivreg.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.bs.mlogit.Rd | 58 ++++++++++++-------- clusterSEs-2.0/clusterSEs/man/cluster.bs.plm.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.im.glm.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.im.ivreg.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.im.mlogit.Rd | 35 ++++-------- clusterSEs-2.0/clusterSEs/man/cluster.wild.glm.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.wild.ivreg.Rd |only clusterSEs-2.0/clusterSEs/man/cluster.wild.plm.Rd |only 31 files changed, 106 insertions(+), 67 deletions(-)
Title: Bayesian Sparse Group Selection
Description: The integration of Bayesian variable and sparse group variable selection approaches for regression models.
Author: Kuo-Jung Lee and Ray-Bin Chen
Maintainer: Kuo-Jung Lee <kuojunglee@mail.ncku.edu.tw>
Diff between BSGS versions 1.0 dated 2015-02-13 and 2.0 dated 2015-06-23
BSGS-1.0/BSGS/R/BSGS.r |only BSGS-1.0/BSGS/man/BSGS.Rd |only BSGS-2.0/BSGS/DESCRIPTION | 10 - BSGS-2.0/BSGS/MD5 | 30 ++- BSGS-2.0/BSGS/NAMESPACE | 6 BSGS-2.0/BSGS/R/BSGS.PE.r |only BSGS-2.0/BSGS/R/BSGS.Sample.r |only BSGS-2.0/BSGS/R/BSGS.Simple.r | 260 ++++++++++++++----------------- BSGS-2.0/BSGS/R/CGS.SMP.PE.r |only BSGS-2.0/BSGS/R/CompWiseGibbs.r | 49 +++-- BSGS-2.0/BSGS/R/CompWiseGibbs_SMP.r | 39 ++-- BSGS-2.0/BSGS/man/BSGS.PE.Rd |only BSGS-2.0/BSGS/man/BSGS.Sample.Rd |only BSGS-2.0/BSGS/man/BSGS.Simple.Rd | 87 +++++----- BSGS-2.0/BSGS/man/CGS.SMP.PE.Rd |only BSGS-2.0/BSGS/man/CompWiseGibbsSMP.Rd | 13 - BSGS-2.0/BSGS/man/CompWiseGibbsSimple.Rd | 18 +- BSGS-2.0/BSGS/man/Crisis2008.Rd | 2 BSGS-2.0/BSGS/man/MSE.BSGS.Rd |only BSGS-2.0/BSGS/man/MSE.CGS.SMP.Rd |only BSGS-2.0/BSGS/man/TCR.TPR.FPR.BSGS.Rd |only BSGS-2.0/BSGS/man/TCR.TPR.FPR.CGS.SMP.Rd |only 22 files changed, 258 insertions(+), 256 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description:
R interface to a W3C Markup Validation service.
See <http://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.1-2 dated 2015-05-02 and 0.1-3 dated 2015-06-23
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- man/w3c_markup_validate.Rd | 10 +++++++--- man/w3c_markup_validate_db.Rd | 37 ++++++++++++++++++++----------------- 4 files changed, 34 insertions(+), 26 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Renewal Method for Extreme Values Extrapolation
Description: Peaks Over Threshold (POT) or 'methode du renouvellement'. The distribution for the exceedances can be chosen, and heterogeneous data (including historical data or block data) can be used in a Maximum-Likelihood framework.
Author: Yves Deville <deville.yves@alpestat.com>, IRSN <renext@irsn.fr>
Maintainer: Lise Bardet <lise.bardet@irsn.fr>
Diff between Renext versions 2.1-10 dated 2015-04-28 and 3.0-0 dated 2015-06-23
Renext-2.1-10/Renext/R/Renouv3.R |only Renext-2.1-10/Renext/R/rRenouv.R |only Renext-2.1-10/Renext/inst/doc/RenextGuide.R |only Renext-2.1-10/Renext/man/rRenouv.Rd |only Renext-3.0-0/Renext/ChangeLog | 353 +++++++ Renext-3.0-0/Renext/DESCRIPTION | 12 Renext-3.0-0/Renext/MD5 | 185 ++-- Renext-3.0-0/Renext/NAMESPACE | 35 Renext-3.0-0/Renext/R/CV2.R |only Renext-3.0-0/Renext/R/GPD.R |only Renext-3.0-0/Renext/R/GreenwoodUtils.R |only Renext-3.0-0/Renext/R/Hpoints.R |only Renext-3.0-0/Renext/R/Jackson.R |only Renext-3.0-0/Renext/R/LR.R |only Renext-3.0-0/Renext/R/LomaxGpd.R |only Renext-3.0-0/Renext/R/NBlevy.R | 1 Renext-3.0-0/Renext/R/OT2MAX.R |only Renext-3.0-0/Renext/R/PPandQQ.R |only Renext-3.0-0/Renext/R/RLplot.R | 404 +++++--- Renext-3.0-0/Renext/R/Ren2gev.R |only Renext-3.0-0/Renext/R/Ren2gumbel.R |only Renext-3.0-0/Renext/R/Rendata.R | 872 ++++++++++-------- Renext-3.0-0/Renext/R/Renouv4.R |only Renext-3.0-0/Renext/R/RenouvMethods.R | 173 +-- Renext-3.0-0/Renext/R/RenouvNoEst.R | 98 +- Renext-3.0-0/Renext/R/SandT.R |only Renext-3.0-0/Renext/R/anova.Renouv.R |only Renext-3.0-0/Renext/R/fGEV.MAX.R |only Renext-3.0-0/Renext/R/fML.R | 492 +++++----- Renext-3.0-0/Renext/R/fgamma.R | 17 Renext-3.0-0/Renext/R/fgpd.R | 88 + Renext-3.0-0/Renext/R/flomax.R | 389 ++++---- Renext-3.0-0/Renext/R/fmaxlo.R | 458 +++++---- Renext-3.0-0/Renext/R/fweibull.R | 33 Renext-3.0-0/Renext/R/gof.date.R | 595 ++++++------ Renext-3.0-0/Renext/R/iniMAXOTS.R |only Renext-3.0-0/Renext/R/interevt.R | 379 ++++---- Renext-3.0-0/Renext/R/makeFuns.R | 8 Renext-3.0-0/Renext/R/miscutils.R | 174 +++ Renext-3.0-0/Renext/R/mixexp2.R | 18 Renext-3.0-0/Renext/R/parDeriv.R |only Renext-3.0-0/Renext/R/plot.Renouv.R | 1062 +++++++++++------------ Renext-3.0-0/Renext/R/predict.Renouv.R | 394 ++++---- Renext-3.0-0/Renext/R/randomRendata.R |only Renext-3.0-0/Renext/R/readXML.R | 717 ++++++++++----- Renext-3.0-0/Renext/R/spacings.R |only Renext-3.0-0/Renext/R/sysdata.rda |only Renext-3.0-0/Renext/R/transexp.R | 1 Renext-3.0-0/Renext/R/weibplot.R | 203 ++-- Renext-3.0-0/Renext/R/zzz.R |only Renext-3.0-0/Renext/data/Brest.rda |binary Renext-3.0-0/Renext/data/Brest.years.missing.rda |binary Renext-3.0-0/Renext/data/Brest.years.rda |binary Renext-3.0-0/Renext/data/Dunkerque.rda |binary Renext-3.0-0/Renext/data/Garonne.rda |binary Renext-3.0-0/Renext/inst/doc/RenextGuide.pdf |binary Renext-3.0-0/Renext/inst/doc/index.html |only Renext-3.0-0/Renext/man/Brest.Rd | 54 - Renext-3.0-0/Renext/man/Brest.years.missing.Rd | 14 Renext-3.0-0/Renext/man/CV2.Rd |only Renext-3.0-0/Renext/man/CV2.test.Rd |only Renext-3.0-0/Renext/man/Dunkerque.Rd | 10 Renext-3.0-0/Renext/man/EM.mixexp.Rd | 81 + Renext-3.0-0/Renext/man/GPD.Rd |only Renext-3.0-0/Renext/man/Garonne.Rd | 6 Renext-3.0-0/Renext/man/Hpoints.Rd |only Renext-3.0-0/Renext/man/Jackson.Rd |only Renext-3.0-0/Renext/man/Jackson.test.Rd |only Renext-3.0-0/Renext/man/LRExp.Rd |only Renext-3.0-0/Renext/man/LRExp.test.Rd |only Renext-3.0-0/Renext/man/LRGumbel.Rd |only Renext-3.0-0/Renext/man/LRGumbel.test.Rd |only Renext-3.0-0/Renext/man/Lomax.Rd | 11 Renext-3.0-0/Renext/man/Maxlo.Rd | 9 Renext-3.0-0/Renext/man/MixExp2.Rd | 90 + Renext-3.0-0/Renext/man/NBlevy.Rd | 26 Renext-3.0-0/Renext/man/OT2MAX.Rd |only Renext-3.0-0/Renext/man/PPplot.Rd |only Renext-3.0-0/Renext/man/RLlegend.Rd | 84 + Renext-3.0-0/Renext/man/RLpar.Rd | 65 - Renext-3.0-0/Renext/man/RLplot.Rd | 128 +- Renext-3.0-0/Renext/man/Ren2gev.Rd |only Renext-3.0-0/Renext/man/Ren2gumbel.Rd |only Renext-3.0-0/Renext/man/Renext-package.Rd | 118 +- Renext-3.0-0/Renext/man/Renouv.Rd | 533 ++++++++--- Renext-3.0-0/Renext/man/RenouvNoEst.Rd | 2 Renext-3.0-0/Renext/man/SLTW.Rd | 98 +- Renext-3.0-0/Renext/man/SandT.Rd |only Renext-3.0-0/Renext/man/anova.Renouv.Rd |only Renext-3.0-0/Renext/man/barplotRenouv.Rd | 145 ++- Renext-3.0-0/Renext/man/expplot.Rd | 86 + Renext-3.0-0/Renext/man/fGEV.MAX.Rd |only Renext-3.0-0/Renext/man/fGPD.Rd |only Renext-3.0-0/Renext/man/fgamma.Rd | 82 + Renext-3.0-0/Renext/man/flomax.Rd | 138 ++ Renext-3.0-0/Renext/man/fmaxlo.Rd | 158 ++- Renext-3.0-0/Renext/man/fweibull.Rd | 104 +- Renext-3.0-0/Renext/man/gev2Ren.Rd |only Renext-3.0-0/Renext/man/gof.date.Rd | 181 ++- Renext-3.0-0/Renext/man/gofExp.test.Rd | 35 Renext-3.0-0/Renext/man/gumbel2Ren.Rd |only Renext-3.0-0/Renext/man/ini.mixexp2.Rd | 92 + Renext-3.0-0/Renext/man/iniMAX.Rd |only Renext-3.0-0/Renext/man/interevt.Rd | 114 +- Renext-3.0-0/Renext/man/logLik.Renouv.Rd | 30 Renext-3.0-0/Renext/man/mom.mixexp2.Rd | 66 + Renext-3.0-0/Renext/man/pGreenwood1.Rd |only Renext-3.0-0/Renext/man/parDeriv.Rd |only Renext-3.0-0/Renext/man/plot.Rendata.Rd | 73 + Renext-3.0-0/Renext/man/plot.Renouv.Rd | 278 +++--- Renext-3.0-0/Renext/man/predict.Renouv.Rd | 91 + Renext-3.0-0/Renext/man/qStat.Rd |only Renext-3.0-0/Renext/man/rRendata.Rd |only Renext-3.0-0/Renext/man/readXML.Rd | 125 ++ Renext-3.0-0/Renext/man/skip2noskip.Rd | 68 + Renext-3.0-0/Renext/man/spacings.Rd |only Renext-3.0-0/Renext/man/summary.Rendata.Rd | 28 Renext-3.0-0/Renext/man/summary.Renouv.Rd | 100 +- Renext-3.0-0/Renext/man/translude.Rd |only Renext-3.0-0/Renext/man/vcov.Renouv.Rd | 94 +- 120 files changed, 6547 insertions(+), 4031 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.2 dated 2015-06-17 and 0.3 dated 2015-06-23
stationaRy-0.2/stationaRy/R/get_ncdc_station_data.R |only stationaRy-0.2/stationaRy/R/get_ncdc_station_info.R |only stationaRy-0.2/stationaRy/R/get_tz_offset.R |only stationaRy-0.2/stationaRy/R/select_ncdc_station.R |only stationaRy-0.2/stationaRy/inst/time_zones.rda |only stationaRy-0.2/stationaRy/man/get_ncdc_station_data.Rd |only stationaRy-0.2/stationaRy/man/get_ncdc_station_info.Rd |only stationaRy-0.2/stationaRy/man/get_tz_offset.Rd |only stationaRy-0.2/stationaRy/man/select_ncdc_station.Rd |only stationaRy-0.3/stationaRy/DESCRIPTION | 12 stationaRy-0.3/stationaRy/MD5 | 22 - stationaRy-0.3/stationaRy/NAMESPACE | 12 stationaRy-0.3/stationaRy/R/get_isd_station_data.R |only stationaRy-0.3/stationaRy/R/get_isd_stations.R |only stationaRy-0.3/stationaRy/R/select_isd_station.R |only stationaRy-0.3/stationaRy/README.md | 243 ++++++++++------- stationaRy-0.3/stationaRy/inst/stations.rda |only stationaRy-0.3/stationaRy/man/get_isd_station_data.Rd |only stationaRy-0.3/stationaRy/man/get_isd_stations.Rd |only stationaRy-0.3/stationaRy/man/select_isd_station.Rd |only 20 files changed, 169 insertions(+), 120 deletions(-)
More information about translateSPSS2R at CRAN
Permanent link
Title: Sample Size Adjusted for Nonadherence or Variability of Input
Parameters
Description: A set of functions to calculate sample size for two-sample difference in means tests. Does adjustments for either nonadherence or variability that comes from using data to estimate parameters.
Author: Michael P. Fay <mfay@niaid.nih.gov>
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between ssanv versions 1.0-2 dated 2010-02-12 and 1.1 dated 2015-06-23
ChangeLog | 5 +++++ DESCRIPTION | 24 +++++++++++------------- MD5 |only NAMESPACE |only R/uniroot.integer.R | 38 +++++++++++++++++++++++++++++++------- data/example.of.Fisher.exact.rda |binary man/ssanv.package.Rd | 8 ++++---- man/uniroot.integer.Rd | 13 ++++++------- tests |only 9 files changed, 57 insertions(+), 31 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed
by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL
license, and it is the base of most of the software tools of the Visual
Computing Lab of the Italian National Research Council Institute ISTI
(http://vcg.isti.cnr.it), like 'metro' and 'MeshLab'.
The 'VCGLIB' source is pulled from
trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work
with options determined by the configure script as well as
to work with the header files included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.11 dated 2015-04-14 and 0.12.1 dated 2015-06-23
Rvcg-0.11/Rvcg/README.md |only Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/poisson_solver.h.rej |only Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature.h.rej |only Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_util.h.rej |only Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/kdtree.h.rej |only Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/priorityqueue.h.rej |only Rvcg-0.12.1/Rvcg/DESCRIPTION | 22 Rvcg-0.12.1/Rvcg/MD5 | 125 Rvcg-0.12.1/Rvcg/NAMESPACE | 2 Rvcg-0.12.1/Rvcg/R/Rvcg-package.R | 4 Rvcg-0.12.1/Rvcg/R/vcgClean.r | 69 Rvcg-0.12.1/Rvcg/R/vcgIsosurface.r | 11 Rvcg-0.12.1/Rvcg/R/vcgKDtree.r | 2 Rvcg-0.12.1/Rvcg/R/vcgOneRingArea.r |only Rvcg-0.12.1/Rvcg/R/vcgQEdecim.r | 2 Rvcg-0.12.1/Rvcg/inst/NEWS.Rd | 17 Rvcg-0.12.1/Rvcg/man/Rvcg-package.Rd | 6 Rvcg-0.12.1/Rvcg/man/dummyhead.Rd | 2 Rvcg-0.12.1/Rvcg/man/humface.Rd | 2 Rvcg-0.12.1/Rvcg/man/meshintegrity.Rd | 2 Rvcg-0.12.1/Rvcg/man/setRays.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgBary.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgBorder.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgClean.Rd | 6 Rvcg-0.12.1/Rvcg/man/vcgClost.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgClostKD.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgCurve.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgGetEdge.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgImport.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgIsolated.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgIsosurface.Rd | 7 Rvcg-0.12.1/Rvcg/man/vcgKDtree.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgMeshres.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgNonBorderEdge.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgPlyRead.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgPlyWrite.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgQEdecim.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgRaySearch.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgSample.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgSmooth.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgStlWrite.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgUniformRemesh.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgUpdateNormals.Rd | 2 Rvcg-0.12.1/Rvcg/man/vcgVFadj.Rd | 2 Rvcg-0.12.1/Rvcg/src/Makevars.in | 2 Rvcg-0.12.1/Rvcg/src/Makevars.win | 2 Rvcg-0.12.1/Rvcg/src/ROneRing.cpp |only Rvcg-0.12.1/Rvcg/src/Rmarch.cpp | 9 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/create/platonic.h | 25 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/geodesic.h | 16 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/implicit_smooth.h | 14 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_collapse.h | 103 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/mesh_to_matrix.h | 19 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/tangent_field_operators.h | 23 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_polychord_collapse.h | 373 +- Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/update/flag.h | 5 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/algorithms/update/quality.h | 6 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/complex/base.h | 9 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/simplex/edge/component.h | 24 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/space/intersection2.h | 51 Rvcg-0.12.1/Rvcg/src/vcglib/vcg/space/polygon3.h | 510 ++ Rvcg-0.12.1/Rvcg/src/vcglib/vcg/space/tetra3.h | 6 Rvcg-0.12.1/Rvcg/src/vcglib/wrap/gl/gl_field.h | 25 Rvcg-0.12.1/Rvcg/src/vcglib/wrap/igl/lscm_parametrization.h |only Rvcg-0.12.1/Rvcg/src/vcglib/wrap/igl/miq_parametrization.h | 22 Rvcg-0.12.1/Rvcg/src/vcglib/wrap/igl/smooth_field.h | 16 Rvcg-0.12.1/Rvcg/src/vcglib/wrap/io_trimesh/import_dae.h | 1764 +++++----- Rvcg-0.12.1/Rvcg/src/vcglib/wrap/io_trimesh/import_stl.h | 100 68 files changed, 2140 insertions(+), 1307 deletions(-)
Title: Analise Multivariada (Brazilian Portuguese)
Description: Pacote para Analise Multivariada, que possui funcoes que executam Analise de Correspondencia Simples (CA) e Multipla (MCA), Analise de Componentes Principais (PCA), Analise de Multiplos Fatores (MFA) para dados Quantitativos, Qualitativos, Frequencia (MFACT) e dados Mistos. Tambem possuim outras funcoes uteis para a Analise Multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.1 dated 2015-06-10 and 1.2 dated 2015-06-23
DESCRIPTION | 8 ++++---- MD5 | 38 ++++++++++++++++++++------------------ R/Biplot.R |only data/DataFreq.rda |binary data/DataQuan.rda |binary man/Biplot.Rd |only man/CA.Rd | 2 +- man/DataFreq.Rd | 11 +++++++---- man/DataMix.Rd | 2 +- man/DataQuan.Rd | 8 +++++--- man/Data_Cafes.Rd | 8 ++++---- man/Data_Individuos.Rd | 8 ++++---- man/GSVD.Rd | 4 ++-- man/IM.Rd | 4 ++-- man/MFA.Rd | 4 ++-- man/MVar.pt-package.Rd | 4 ++-- man/NormData.Rd | 4 ++-- man/PCA.Rd | 2 +- man/Plot.CA.Rd | 10 +++++----- man/Plot.MFA.Rd | 13 +++++++------ man/Plot.PCA.Rd | 6 +++--- 21 files changed, 72 insertions(+), 64 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-36 dated 2015-06-21 and 0.9-38 dated 2015-06-23
mkin-0.9-36/mkin/vignettes/FOCUS_Z.fdb_latexmk |only mkin-0.9-36/mkin/vignettes/FOCUS_Z.fls |only mkin-0.9-36/mkin/vignettes/compiled_models_cache |only mkin-0.9-38/mkin/DESCRIPTION | 8 mkin-0.9-38/mkin/MD5 | 75 -- mkin-0.9-38/mkin/NEWS | 17 mkin-0.9-38/mkin/R/mkinmod.R | 36 - mkin-0.9-38/mkin/build/vignette.rds |binary mkin-0.9-38/mkin/inst/doc/FOCUS_D.R | 3 mkin-0.9-38/mkin/inst/doc/FOCUS_D.Rmd | 26 mkin-0.9-38/mkin/inst/doc/FOCUS_D.html | 338 ++--------- mkin-0.9-38/mkin/inst/doc/FOCUS_L.Rmd | 21 mkin-0.9-38/mkin/inst/doc/FOCUS_L.html | 682 ++++++----------------- mkin-0.9-38/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-38/mkin/inst/doc/compiled_models.R | 44 + mkin-0.9-38/mkin/inst/doc/compiled_models.Rmd | 62 +- mkin-0.9-38/mkin/inst/doc/compiled_models.html | 81 +- mkin-0.9-38/mkin/inst/doc/mkin.pdf |binary mkin-0.9-38/mkin/man/IORE.solution.Rd | 17 mkin-0.9-38/mkin/man/mccall81_245T.Rd | 6 mkin-0.9-38/mkin/man/mkinfit.Rd | 2 mkin-0.9-38/mkin/man/mkinmod.Rd | 13 mkin-0.9-38/mkin/man/mkinparplot.Rd | 4 mkin-0.9-38/mkin/vignettes/FOCUS_D.Rmd | 26 mkin-0.9-38/mkin/vignettes/FOCUS_L.Rmd | 21 mkin-0.9-38/mkin/vignettes/compiled_models.Rmd | 62 +- 26 files changed, 610 insertions(+), 934 deletions(-)
Title: Binary Classifier and Regression Model Interpretation Functions
Description: Compute permutation- based performance measures and create partial
dependence plots for (cross-validated) 'randomForest' and 'ada' models.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@GMail.com>
Diff between interpretR versions 0.2.2 dated 2015-05-10 and 0.2.3 dated 2015-06-23
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/interpretRNews.R | 2 +- R/parDepPlot.R | 4 ++-- inst/NEWS | 3 +++ man/interpretRNews.Rd | 2 +- 6 files changed, 19 insertions(+), 16 deletions(-)
Title: Interactive Exploration of Contour Data
Description: Interactive tools to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. The functions in this package create
interactive web pages showing the contoured data, possibly with
slices from the original matrix parallel to each dimension. The interactive
behavior is created using the D3.js JavaScript library by Mike Bostock.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between exCon versions 0.1.5 dated 2015-05-07 and 0.1.9 dated 2015-06-23
DESCRIPTION | 17 +-- MD5 | 24 +++- NAMESPACE | 1 NEWS | 75 +++++++-------- R/exCon-package.R | 11 +- R/exCon.R | 190 +++++++++++++++++++++++++++++++-------- inst/extdata/eC2_brushNguides.js |only inst/extdata/eC2_contours.js |only inst/extdata/eC2_controls.js |only inst/extdata/eC2_globals.js |only inst/extdata/eC2_main.js |only inst/extdata/eC_globals.js | 16 +-- inst/extdata/exCon.html | 15 +-- inst/extdata/exCon2.html |only man/exCon-package.Rd | 10 +- man/exCon.Rd | 51 +++++----- 16 files changed, 268 insertions(+), 142 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 0.9-3 dated 2015-05-21 and 1.0-4 dated 2015-06-23
ChangeLog | 68 +++++++ DESCRIPTION | 18 +- MD5 | 51 +++-- R/AAA.R | 8 R/gdal.R | 6 R/ogr.R | 100 +++++++---- R/ogr_sp.R | 35 +++- R/ogr_write.R | 10 + build/vignette.rds |binary configure | 52 +++--- configure.ac | 29 ++- inst/ChangeLog | 68 +++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/vectors/test64.csv |only inst/vectors/test64.csvt |only inst/vectors/test64.vrt |only man/GDALMajorObject-class.Rd | 2 man/GDALReadOnlyDataset-class.Rd | 2 man/readOGR.Rd | 16 + man/writeOGR.Rd | 25 +- src/OGR_write.cpp | 209 ++++++++++++++++++++---- src/gdal-bindings.cpp | 18 ++ src/ogr_geom.cpp | 60 ++++++- src/ogr_proj.cpp | 11 + src/ogrdrivers.cpp | 31 +++ src/ogrsource.cpp | 332 ++++++++++++++++++++++++++++++++++++--- src/rgdal.h | 7 28 files changed, 981 insertions(+), 179 deletions(-)
Title: Growth Charts via Regression Quantiles
Description: Fits non-crossing regression quantiles as a function of linear covariates and a smooth terms via B-splines with difference penalties.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 0.3-0 dated 2014-07-25 and 0.3-1 dated 2015-06-23
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/gcrq.R | 18 +++++++++--------- R/ncross.rq.fitX.R | 8 ++++---- R/ncross.rq.fitXB.R | 10 +++++----- R/plot.gcrq.R | 4 ++-- R/predictQR.R | 4 ++-- man/gcrq.Rd | 9 +++++---- man/quantregGrowth-package.Rd | 12 ++++++------ 10 files changed, 57 insertions(+), 48 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <stefan.schlager@uniklinik-freiburg.de>
Diff between Morpho versions 2.2 dated 2014-12-16 and 2.3.0 dated 2015-06-23
Morpho-2.2/Morpho/R/warp.mesh.r |only Morpho-2.2/Morpho/README.md |only Morpho-2.2/Morpho/man/meanMat.Rd |only Morpho-2.2/Morpho/man/warp.mesh.Rd |only Morpho-2.2/Morpho/src/meanMat.cpp |only Morpho-2.3.0/Morpho/DESCRIPTION | 32 - Morpho-2.3.0/Morpho/MD5 | 344 +++++++++-------- Morpho-2.3.0/Morpho/NAMESPACE | 23 + Morpho-2.3.0/Morpho/R/CAC.r | 4 Morpho-2.3.0/Morpho/R/CVA.crova.r | 16 Morpho-2.3.0/Morpho/R/CVA.r | 28 - Morpho-2.3.0/Morpho/R/CVAdists.r | 5 Morpho-2.3.0/Morpho/R/ComputeTransform.r | 24 + Morpho-2.3.0/Morpho/R/CreateL.r | 6 Morpho-2.3.0/Morpho/R/Morpho-package.R | 19 Morpho-2.3.0/Morpho/R/PCmeaning.r |only Morpho-2.3.0/Morpho/R/ProcGPA.r | 4 Morpho-2.3.0/Morpho/R/RegScore.r | 8 Morpho-2.3.0/Morpho/R/applyTransform.r | 48 +- Morpho-2.3.0/Morpho/R/armaGinv.r | 10 Morpho-2.3.0/Morpho/R/asymPermu.r | 33 - Morpho-2.3.0/Morpho/R/bindArr.r | 10 Morpho-2.3.0/Morpho/R/cSize.r | 2 Morpho-2.3.0/Morpho/R/check.lm.r | 2 Morpho-2.3.0/Morpho/R/classify.r | 92 +++- Morpho-2.3.0/Morpho/R/covDist.r | 2 Morpho-2.3.0/Morpho/R/createVarTable.r |only Morpho-2.3.0/Morpho/R/deform.grid.r | 8 Morpho-2.3.0/Morpho/R/deformGrid2d.r | 57 +- Morpho-2.3.0/Morpho/R/eigenPCA.r | 4 Morpho-2.3.0/Morpho/R/fx.r | 32 - Morpho-2.3.0/Morpho/R/groupPCA.r | 46 +- Morpho-2.3.0/Morpho/R/groupPCAcrova.r | 5 Morpho-2.3.0/Morpho/R/kendalldist.r | 4 Morpho-2.3.0/Morpho/R/line2plane.r |only Morpho-2.3.0/Morpho/R/list2array.r |only Morpho-2.3.0/Morpho/R/mergeMeshes.r | 11 Morpho-2.3.0/Morpho/R/meshDist.r | 80 ++-- Morpho-2.3.0/Morpho/R/meshDistMatrix.r | 29 - Morpho-2.3.0/Morpho/R/mirror.r | 55 +- Morpho-2.3.0/Morpho/R/name2.r | 82 +--- Morpho-2.3.0/Morpho/R/orp.r | 2 Morpho-2.3.0/Morpho/R/pcAlign.r | 65 ++- Morpho-2.3.0/Morpho/R/pcaplot3d.r | 31 - Morpho-2.3.0/Morpho/R/permudist.r | 12 Morpho-2.3.0/Morpho/R/permuvec.r | 8 Morpho-2.3.0/Morpho/R/place.patch.r | 6 Morpho-2.3.0/Morpho/R/pls2B.r | 462 +++++++++++++++++++----- Morpho-2.3.0/Morpho/R/procAOVsym.r | 4 Morpho-2.3.0/Morpho/R/procSym.r | 23 + Morpho-2.3.0/Morpho/R/relax.lm.r | 55 ++ Morpho-2.3.0/Morpho/R/relwarps.r | 7 Morpho-2.3.0/Morpho/R/retrodeform.r | 6 Morpho-2.3.0/Morpho/R/rotmesh.onto.r | 2 Morpho-2.3.0/Morpho/R/rotonto.r | 4 Morpho-2.3.0/Morpho/R/scalemesh.r | 4 Morpho-2.3.0/Morpho/R/showPC.r | 25 - Morpho-2.3.0/Morpho/R/slider3d.r | 12 Morpho-2.3.0/Morpho/R/tps3d.r | 61 +-- Morpho-2.3.0/Morpho/R/typprob.r | 64 ++- Morpho-2.3.0/Morpho/R/vecx.r | 43 +- Morpho-2.3.0/Morpho/R/warpmovie.matrix.r | 4 Morpho-2.3.0/Morpho/R/write.pts.r | 12 Morpho-2.3.0/Morpho/inst/NEWS.Rd | 44 ++ Morpho-2.3.0/Morpho/inst/extdata |only Morpho-2.3.0/Morpho/man/CAC.Rd | 3 Morpho-2.3.0/Morpho/man/CVA.Rd | 7 Morpho-2.3.0/Morpho/man/CreateL.Rd | 7 Morpho-2.3.0/Morpho/man/Morpho-deprecated.Rd | 7 Morpho-2.3.0/Morpho/man/Morpho-package.Rd | 13 Morpho-2.3.0/Morpho/man/NNshapeReg.Rd | 3 Morpho-2.3.0/Morpho/man/PCdist.Rd | 3 Morpho-2.3.0/Morpho/man/ProcGPA.Rd | 3 Morpho-2.3.0/Morpho/man/RegScore.Rd | 3 Morpho-2.3.0/Morpho/man/angle.calc.Rd | 3 Morpho-2.3.0/Morpho/man/anonymize.Rd | 3 Morpho-2.3.0/Morpho/man/applyTransform.Rd | 7 Morpho-2.3.0/Morpho/man/armaGinv.Rd |only Morpho-2.3.0/Morpho/man/arrMean3.Rd | 3 Morpho-2.3.0/Morpho/man/asymPermute.Rd | 3 Morpho-2.3.0/Morpho/man/barycenter.Rd | 3 Morpho-2.3.0/Morpho/man/bindArr.Rd | 3 Morpho-2.3.0/Morpho/man/boneData.Rd | 3 Morpho-2.3.0/Morpho/man/cExtract.Rd | 3 Morpho-2.3.0/Morpho/man/cSize.Rd | 3 Morpho-2.3.0/Morpho/man/checkLM.Rd | 5 Morpho-2.3.0/Morpho/man/classify.Rd | 17 Morpho-2.3.0/Morpho/man/closemeshKD.Rd | 3 Morpho-2.3.0/Morpho/man/colors.Rd | 3 Morpho-2.3.0/Morpho/man/computeTransform.Rd | 14 Morpho-2.3.0/Morpho/man/covDist.Rd | 3 Morpho-2.3.0/Morpho/man/covW.Rd | 3 Morpho-2.3.0/Morpho/man/createAtlas.Rd | 3 Morpho-2.3.0/Morpho/man/createMissingList.Rd | 3 Morpho-2.3.0/Morpho/man/cutMeshPlane.Rd | 3 Morpho-2.3.0/Morpho/man/cutSpace.Rd | 3 Morpho-2.3.0/Morpho/man/deformGrid2d.Rd | 10 Morpho-2.3.0/Morpho/man/deformGrid3d.Rd | 3 Morpho-2.3.0/Morpho/man/exVar.Rd | 3 Morpho-2.3.0/Morpho/man/find.outliers.Rd | 3 Morpho-2.3.0/Morpho/man/fixLMmirror.Rd | 3 Morpho-2.3.0/Morpho/man/fixLMtps.Rd | 3 Morpho-2.3.0/Morpho/man/getFaces.Rd | 3 Morpho-2.3.0/Morpho/man/getMeaningfulPCs.Rd |only Morpho-2.3.0/Morpho/man/getPCtol.Rd |only Morpho-2.3.0/Morpho/man/getPLSfromScores.Rd |only Morpho-2.3.0/Morpho/man/getPLSscores.Rd |only Morpho-2.3.0/Morpho/man/getTrafo4x4.Rd | 3 Morpho-2.3.0/Morpho/man/getTrafoRotaxis.Rd | 3 Morpho-2.3.0/Morpho/man/groupPCA.Rd | 16 Morpho-2.3.0/Morpho/man/histGroup.Rd | 3 Morpho-2.3.0/Morpho/man/icpmat.Rd | 8 Morpho-2.3.0/Morpho/man/invertFaces.Rd | 3 Morpho-2.3.0/Morpho/man/kendalldist.Rd | 3 Morpho-2.3.0/Morpho/man/line2plane.Rd |only Morpho-2.3.0/Morpho/man/lineplot.Rd | 3 Morpho-2.3.0/Morpho/man/list2array.Rd |only Morpho-2.3.0/Morpho/man/mcNNindex.Rd | 3 Morpho-2.3.0/Morpho/man/mergeMeshes.Rd | 3 Morpho-2.3.0/Morpho/man/mesh2grey.Rd | 3 Morpho-2.3.0/Morpho/man/mesh2ply.Rd | 3 Morpho-2.3.0/Morpho/man/meshDist.Rd | 84 ++-- Morpho-2.3.0/Morpho/man/meshPlaneIntersect.Rd | 3 Morpho-2.3.0/Morpho/man/meshcube.Rd | 3 Morpho-2.3.0/Morpho/man/meshres.Rd | 3 Morpho-2.3.0/Morpho/man/mirror.Rd | 15 Morpho-2.3.0/Morpho/man/name2factor.Rd | 7 Morpho-2.3.0/Morpho/man/nose.Rd | 3 Morpho-2.3.0/Morpho/man/pcAlign.Rd | 20 - Morpho-2.3.0/Morpho/man/pcaplot3d.Rd | 20 - Morpho-2.3.0/Morpho/man/permudist.Rd | 12 Morpho-2.3.0/Morpho/man/permuvec.Rd | 3 Morpho-2.3.0/Morpho/man/placePatch.Rd | 7 Morpho-2.3.0/Morpho/man/plotAtlas.Rd | 3 Morpho-2.3.0/Morpho/man/plotNormals.Rd | 3 Morpho-2.3.0/Morpho/man/pls2B.Rd | 32 + Morpho-2.3.0/Morpho/man/plsCoVar.Rd |only Morpho-2.3.0/Morpho/man/ply2mesh.Rd | 3 Morpho-2.3.0/Morpho/man/points2plane.Rd | 3 Morpho-2.3.0/Morpho/man/predictPLSfromData.Rd |only Morpho-2.3.0/Morpho/man/predictPLSfromScores.Rd |only Morpho-2.3.0/Morpho/man/predictShape.lm.Rd | 3 Morpho-2.3.0/Morpho/man/proc.weight.Rd | 3 Morpho-2.3.0/Morpho/man/procAOVsym.Rd | 3 Morpho-2.3.0/Morpho/man/procSym.Rd | 5 Morpho-2.3.0/Morpho/man/projRead.Rd | 3 Morpho-2.3.0/Morpho/man/qqmat.Rd | 3 Morpho-2.3.0/Morpho/man/quad2trimesh.Rd | 3 Morpho-2.3.0/Morpho/man/r2morphoj.Rd | 3 Morpho-2.3.0/Morpho/man/ray2mesh.Rd | 3 Morpho-2.3.0/Morpho/man/read.csv.folder.Rd | 3 Morpho-2.3.0/Morpho/man/read.lmdta.Rd | 3 Morpho-2.3.0/Morpho/man/read.mpp.Rd | 3 Morpho-2.3.0/Morpho/man/read.pts.Rd | 3 Morpho-2.3.0/Morpho/man/readLandmarks.csv.Rd | 3 Morpho-2.3.0/Morpho/man/readallTPS.Rd | 3 Morpho-2.3.0/Morpho/man/regdist.Rd | 3 Morpho-2.3.0/Morpho/man/relWarps.Rd | 7 Morpho-2.3.0/Morpho/man/relaxLM.Rd | 39 +- Morpho-2.3.0/Morpho/man/render.Rd | 35 + Morpho-2.3.0/Morpho/man/retroDeform3d.Rd | 3 Morpho-2.3.0/Morpho/man/retroDeformMesh.Rd | 7 Morpho-2.3.0/Morpho/man/rotaxis3d.Rd | 3 Morpho-2.3.0/Morpho/man/rotaxisMat.Rd | 3 Morpho-2.3.0/Morpho/man/rotmesh.onto.Rd | 5 Morpho-2.3.0/Morpho/man/rotonmat.Rd | 3 Morpho-2.3.0/Morpho/man/rotonto.Rd | 3 Morpho-2.3.0/Morpho/man/scalemesh.Rd | 3 Morpho-2.3.0/Morpho/man/showPC.Rd | 7 Morpho-2.3.0/Morpho/man/slider3d.Rd | 10 Morpho-2.3.0/Morpho/man/solutionSpace.Rd | 3 Morpho-2.3.0/Morpho/man/symmetrize.Rd | 3 Morpho-2.3.0/Morpho/man/tangentPlane.Rd | 3 Morpho-2.3.0/Morpho/man/tps3d.Rd | 47 +- Morpho-2.3.0/Morpho/man/typprob.Rd | 32 - Morpho-2.3.0/Morpho/man/updateNormals.Rd | 3 Morpho-2.3.0/Morpho/man/vecx.Rd | 3 Morpho-2.3.0/Morpho/man/vertex.Rd | 3 Morpho-2.3.0/Morpho/man/warpmovie3d.Rd | 7 Morpho-2.3.0/Morpho/man/write.pts.Rd | 7 Morpho-2.3.0/Morpho/src/tpsfx.cpp | 13 Morpho-2.3.0/Morpho/tests |only 182 files changed, 1841 insertions(+), 991 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JM versions 1.3-0 dated 2014-05-01 and 1.4-0 dated 2015-06-23
DESCRIPTION | 11 +++++------ MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 6 +++++- R/fitted.jointModel.R | 16 ++++++++++++---- R/globals.R | 2 +- R/predict.jointModel.R | 18 +++++++++--------- R/summary.jointModel.R | 4 ++-- R/survfitJM.jointModel.R | 20 ++++++++++---------- R/xtable.jointModel.R | 2 +- data/aids.id.rda |binary data/aids.rda |binary data/pbc2.id.rda |binary data/pbc2.rda |binary data/prothro.rda |binary data/prothros.rda |binary man/JM.Rd | 4 ++-- man/jointModel.Rd | 2 +- man/plot-rocJM.Rd | 2 -- 18 files changed, 65 insertions(+), 56 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.5 dated 2015-05-22 and 2.1.6 dated 2015-06-23
geomorph-2.1.5/geomorph/R/define.sliders.2d.r |only geomorph-2.1.5/geomorph/R/define.sliders.3d.r |only geomorph-2.1.5/geomorph/R/pairwise.slope.test.r |only geomorph-2.1.5/geomorph/R/pairwiseD.test.r |only geomorph-2.1.6/geomorph/DESCRIPTION | 8 +-- geomorph-2.1.6/geomorph/MD5 | 46 ++++++++++----------- geomorph-2.1.6/geomorph/NAMESPACE | 1 geomorph-2.1.6/geomorph/NEWS | 18 +++++++- geomorph-2.1.6/geomorph/R/compare.evol.rates.r | 22 +++++++--- geomorph-2.1.6/geomorph/R/digit.curves.r | 14 ++++-- geomorph-2.1.6/geomorph/R/digitize2d.r | 11 ++--- geomorph-2.1.6/geomorph/R/geomorph.support.code.r | 39 +++++++++++++++++ geomorph-2.1.6/geomorph/R/globalIntegration.r |only geomorph-2.1.6/geomorph/R/physignal.r | 7 +-- geomorph-2.1.6/geomorph/R/plotTangentSpace.r | 6 ++ geomorph-2.1.6/geomorph/R/read.morphologika.r | 3 - geomorph-2.1.6/geomorph/R/writeland.tps.r | 10 ++++ geomorph-2.1.6/geomorph/man/compare.evol.rates.Rd | 11 +++-- geomorph-2.1.6/geomorph/man/define.sliders.2d.Rd | 10 +--- geomorph-2.1.6/geomorph/man/define.sliders.3d.Rd | 10 +--- geomorph-2.1.6/geomorph/man/digitize2d.Rd | 2 geomorph-2.1.6/geomorph/man/globalIntegration.Rd |only geomorph-2.1.6/geomorph/man/pairwise.slope.test.Rd | 10 +--- geomorph-2.1.6/geomorph/man/pairwiseD.test.Rd | 10 +--- geomorph-2.1.6/geomorph/man/physignal.Rd | 4 + geomorph-2.1.6/geomorph/man/plotTangentSpace.Rd | 4 + geomorph-2.1.6/geomorph/man/writeland.tps.Rd | 4 + 27 files changed, 170 insertions(+), 80 deletions(-)
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 17 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo <danlu.guo@adelaide.edu.au>, Seth Westra <swestra@civeng.adelaide.edu.au>
Maintainer: Danlu Guo <danlu.guo@adelaide.edu.au>
Diff between Evapotranspiration versions 1.5 dated 2015-01-15 and 1.6 dated 2015-06-23
DESCRIPTION | 16 ++++---- MD5 | 16 ++++---- NAMESPACE | 19 +++++++++ NEWS | 25 +++--------- R/Evapotranspiration.R | 8 ---- R/Plotting.R | 54 ++++++++++++++++----------- R/Reading.R | 96 +++++++++++++++++++++++++++++++++++-------------- man/ETComparison.Rd | 14 +++---- man/ReadInputs.Rd | 9 +++- 9 files changed, 157 insertions(+), 100 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: Data Quality Visualization Tools for Partially Accruing Data
Description: Package for visualizing data quality of partially accruing data.
Author: Julie Eaton and Ian Painter
Maintainer: Julie Eaton <jreaton@uw.edu>
Diff between accrued versions 1.2 dated 2014-09-08 and 1.3 dated 2015-06-23
DESCRIPTION | 14 +++++++------- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 9 ++++++++- data/accruedDataExample.rda |binary data/accruedDataILIExample.rda |binary inst/doc/accrued_vignette.pdf |binary man/accrued-package.Rd | 25 +++++++++++++------------ man/accruedDataILIExample.Rd | 6 +++--- man/accruedErrors.Rd | 13 ++++++------- man/asOf.Rd | 28 +++++++++++++++++++--------- man/barcode.Rd | 7 ++++--- man/laggedTSarray.Rd | 14 +++++++++++--- man/plot.accrued.Rd | 5 +++-- man/plot.summary.accrued.Rd | 9 ++++++--- man/print.accrued.Rd | 4 ++-- man/print.summary.accrued.Rd | 4 ++-- man/summary.accrued.Rd | 4 ++-- man/summary.accruedErrors.Rd | 4 ++-- man/uploadPattern.Rd | 6 +++--- 19 files changed, 109 insertions(+), 79 deletions(-)
Title: Select Features Reliably with Cohen's Effect Sizes
Description: Functions using Cohen's effect sizes (Cohen, Jacob. Statistical power analysis for the behavioral sciences. Academic press, 2013) are provided for reliable feature selection in biology data analysis. In addition to Cohen's effect sizes, p-values are calculated and adjusted from quasi-Poisson GLM, negative binomial GLM and Normal distribution ANOVA. Significant features (genes, RNAs or proteins) are selected by adjusted p-value and minimum Cohen's effect sizes, calculated to keep certain level of statistical power of biology data analysis given p-value threshold and sample size.
Author: Lang Ho Lee, Arnold Saxton, Nathan Verberkmoes
Maintainer: Lang Ho Lee <langholee@gmail.com>
Diff between selfea versions 1.0 dated 2015-05-31 and 1.0.1 dated 2015-06-22
DESCRIPTION | 12 MD5 | 27 - NAMESPACE | 2 R/selfea.R | 721 +++++++++++++++++++++++++---------- data/example_data1.rda |binary man/calculate_cohen_f2.Rd |only man/draw_scatter_plots.Rd |only man/example_data.Rd | 4 man/example_data1.Rd | 4 man/example_data2.Rd | 6 man/example_group.Rd | 2 man/get_statistics_from_dataFrame.Rd | 70 ++- man/get_statistics_from_file.Rd | 33 + man/selfea-package.Rd | 42 +- man/top_table.Rd | 73 ++- man/ttest_cohens_d.Rd |only 16 files changed, 690 insertions(+), 306 deletions(-)
Title: Create 2D Principal Component Plots with Bootstrapping
Description: Draws a 2D principal component plot using the first 2 principal
components from the original and bootstrapped data to give some sense of
variability.
Author: Joshua Starmer
Maintainer: Joshua Starmer <starmer@unc.edu>
Diff between pcaBootPlot versions 0.1.0 dated 2015-05-21 and 0.2.0 dated 2015-06-22
DESCRIPTION | 9 MD5 | 9 R/pcaBootPlot.R | 510 ++++++++++++++++++++++++++++++++-------------- README.md |only inst/doc/pcaBootPlot.html | 4 man/pcaBootPlot.Rd | 35 ++- 6 files changed, 404 insertions(+), 163 deletions(-)
Title: Diagnostic Tools for Hierarchical (Multilevel) Linear Models
Description: A suite of diagnostic tools for hierarchical
(multilevel) linear models. The tools include
not only leverage and traditional deletion diagnostics (Cook's
distance, covratio, covtrace, and MDFFITS) but also
convenience functions and graphics for residual analysis. Models
can be fit using either lmer in the 'lme4' package or lme in the 'nlme' package,
but only two-level models fit using lme are currently supported.
Author: Adam Loy <loyad01@gmail.com>
Maintainer: Adam Loy <loyad01@gmail.com>
Diff between HLMdiag versions 0.2.5 dated 2014-01-30 and 0.3.0 dated 2015-06-22
HLMdiag-0.2.5/HLMdiag/man/adjust_lmList-class.Rd |only HLMdiag-0.2.5/HLMdiag/man/adjust_lmList.Rd |only HLMdiag-0.3.0/HLMdiag/DESCRIPTION | 27 HLMdiag-0.3.0/HLMdiag/MD5 | 67 +- HLMdiag-0.3.0/HLMdiag/NAMESPACE | 122 ++-- HLMdiag-0.3.0/HLMdiag/NEWS | 28 + HLMdiag-0.3.0/HLMdiag/R/HLMresid.R | 34 - HLMdiag-0.3.0/HLMdiag/R/LSresids.R | 39 - HLMdiag-0.3.0/HLMdiag/R/adjust_formula_lmList.R | 251 ++++----- HLMdiag-0.3.0/HLMdiag/R/case_delete.R | 92 +-- HLMdiag-0.3.0/HLMdiag/R/influence_functions.R | 572 ++++++++++----------- HLMdiag-0.3.0/HLMdiag/R/quantile_functions.R | 19 HLMdiag-0.3.0/HLMdiag/R/rotate_ranefs.R | 155 +++-- HLMdiag-0.3.0/HLMdiag/R/utility_functions.R | 190 +++--- HLMdiag-0.3.0/HLMdiag/README.md | 4 HLMdiag-0.3.0/HLMdiag/man/HLMdiag.Rd | 101 +-- HLMdiag-0.3.0/HLMdiag/man/HLMresid.mer.Rd | 164 ++---- HLMdiag-0.3.0/HLMdiag/man/LSresids.mer.Rd | 55 -- HLMdiag-0.3.0/HLMdiag/man/adjust_lmList.formula.Rd |only HLMdiag-0.3.0/HLMdiag/man/ahd.Rd | 29 - HLMdiag-0.3.0/HLMdiag/man/autism.Rd | 30 - HLMdiag-0.3.0/HLMdiag/man/case_delete.mer.Rd | 110 +--- HLMdiag-0.3.0/HLMdiag/man/compare_eb_ls.Rd | 35 - HLMdiag-0.3.0/HLMdiag/man/cooks.distance.Rd | 100 +-- HLMdiag-0.3.0/HLMdiag/man/covratio.Rd | 98 +-- HLMdiag-0.3.0/HLMdiag/man/diagnostics.Rd | 99 +-- HLMdiag-0.3.0/HLMdiag/man/dotplot_diag.Rd | 59 -- HLMdiag-0.3.0/HLMdiag/man/ggplot_qqnorm.Rd | 31 - HLMdiag-0.3.0/HLMdiag/man/group_qqnorm.Rd | 44 - HLMdiag-0.3.0/HLMdiag/man/leverage.mer.Rd | 104 +-- HLMdiag-0.3.0/HLMdiag/man/radon.Rd | 22 HLMdiag-0.3.0/HLMdiag/man/rotate_ranef.mer.Rd | 58 +- HLMdiag-0.3.0/HLMdiag/man/rvc.mer.Rd | 72 +- HLMdiag-0.3.0/HLMdiag/man/varcomp.mer.Rd | 24 HLMdiag-0.3.0/HLMdiag/man/wages.Rd | 4 HLMdiag-0.3.0/HLMdiag/src/covratio.cpp | 2 36 files changed, 1460 insertions(+), 1381 deletions(-)
Title: Simulation-Based Regularized Logistic Regression
Description: Regularized (polychotomous) logistic regression
by Gibbs sampling. The package implements subtly different
MCMC schemes with varying efficiency depending on the data type
(binary v. binomial, say) and the desired estimator (regularized maximum
likelihood, or Bayesian maximum a posteriori/posterior mean, etc.) through a
unified interface.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Diff between reglogit versions 1.2-2 dated 2014-01-15 and 1.2-4 dated 2015-06-22
ChangeLog | 14 + DESCRIPTION | 10 - MD5 | 18 +- R/reglogit.R | 71 ++------- man/reglogit-internal.Rd | 2 man/reglogit.Rd | 12 - src/Makevars | 3 src/gibbs.c | 338 ++++++++++++++--------------------------------- src/rand_draws.c |only src/rand_draws.h |only src/randomkit.c |only src/randomkit.h |only 12 files changed, 156 insertions(+), 312 deletions(-)
Title: Generation of Regular Factorial Designs
Description: Automatic generation of regular factorial designs, including fractional designs, orthogonal block designs, row-column designs and split-plots.
Author: Hervé Monod, Annie Bouvier, André Kobilinsky
Maintainer: Annie Bouvier <Annie.Bouvier@jouy.inra.fr>
Diff between planor versions 0.2-3 dated 2015-03-04 and 0.2-4 dated 2015-06-22
planor-0.2-3/planor/ChangeLog |only planor-0.2-4/planor/DESCRIPTION | 8 - planor-0.2-4/planor/MD5 | 102 +++++++++--------- planor-0.2-4/planor/NAMESPACE | 9 - planor-0.2-4/planor/NEWS |only planor-0.2-4/planor/R/basep.R | 24 ---- planor-0.2-4/planor/R/designkey.R | 17 +-- planor-0.2-4/planor/R/keymatrix.R | 23 ++-- planor-0.2-4/planor/R/keyring.R | 6 + planor-0.2-4/planor/R/listofdesignkeys.R | 11 + planor-0.2-4/planor/R/listofkeyrings.R | 10 + planor-0.2-4/planor/R/planor.R | 62 +++------- planor-0.2-4/planor/R/planordesign.R | 44 +++++++ planor-0.2-4/planor/R/zzz.R | 2 planor-0.2-4/planor/inst/doc/index.html | 2 planor-0.2-4/planor/inst/doc/planor-manual.pdf |binary planor-0.2-4/planor/inst/doc/planorVignette.pdf |binary planor-0.2-4/planor/man/alias-methods.Rd | 40 +++---- planor-0.2-4/planor/man/as.data.frame.planordesign.Rd | 22 ++- planor-0.2-4/planor/man/bind-methods.Rd | 13 +- planor-0.2-4/planor/man/designfactors-class.Rd | 25 +--- planor-0.2-4/planor/man/designkey-class.Rd | 43 +++---- planor-0.2-4/planor/man/getDesign-methods.Rd | 26 ++-- planor-0.2-4/planor/man/keymatrix-class.Rd | 41 +++---- planor-0.2-4/planor/man/keyring-class.Rd | 35 +++--- planor-0.2-4/planor/man/listofdesignkeys-class.Rd | 40 +++---- planor-0.2-4/planor/man/listofkeyrings-class.Rd | 32 ++--- planor-0.2-4/planor/man/makedesignkey.Rd | 22 +-- planor-0.2-4/planor/man/pick-methods.Rd | 30 ++--- planor-0.2-4/planor/man/planor-package.Rd | 25 ++-- planor-0.2-4/planor/man/planor.design-methods.Rd | 21 +-- planor-0.2-4/planor/man/planor.designkey.Rd | 26 ++-- planor-0.2-4/planor/man/planor.factors.Rd | 32 ++--- planor-0.2-4/planor/man/planor.harmonize.Rd | 22 +-- planor-0.2-4/planor/man/planor.model.Rd | 14 +- planor-0.2-4/planor/man/planor.randomize.Rd | 33 +++-- planor-0.2-4/planor/man/planordesign-class.Rd | 50 +++----- planor-0.2-4/planor/man/regular.design.Rd | 40 +++---- planor-0.2-4/planor/man/show-methods.Rd | 34 +++--- planor-0.2-4/planor/man/summary-methods.Rd | 64 ++++++----- planor-0.2-4/planor/src/planor.cpp | 37 ++---- planor-0.2-4/planor/tests/Kobi0.Rout.save | 4 planor-0.2-4/planor/tests/Kobi1.Rout.save | 4 planor-0.2-4/planor/tests/Kobi2.Rout.save | 4 planor-0.2-4/planor/tests/Kobi3.Rout.save | 4 planor-0.2-4/planor/tests/KobiRecursive.Rout.save | 4 planor-0.2-4/planor/tests/NewKobi1.Rout.save | 4 planor-0.2-4/planor/tests/Touzeau2.Rout.save | 4 planor-0.2-4/planor/tests/exsimple.Rout.save | 4 planor-0.2-4/planor/tests/generate.Rout.save | 12 +- planor-0.2-4/planor/tests/haies.Rout.save | 6 - planor-0.2-4/planor/tests/mixkey.Rout.save | 4 planor-0.2-4/planor/tests/noineligible.Rout.save | 4 53 files changed, 580 insertions(+), 565 deletions(-)
Title: Working with Frequency Tables
Description: The frequency of a particular data value is the number of times it
occurs. A frequency table is a table of values with their corresponding
frequencies. Frequency weights are integer numbers that indicate how many
cases each case represents. This package provides some functions to work
with such type of collected data.
Author: Emilio Torres-Manzanera
Maintainer: Emilio Torres-Manzanera <torres@uniovi.es>
Diff between freqweights versions 1.0.1 dated 2014-10-09 and 1.0.2 dated 2015-06-22
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 2 +- NEWS | 11 +++++++++++ R/lmfreq.R | 4 ++-- R/preprocesshflights.R | 8 ++++---- R/tablefreq.R | 4 ++-- man/biglmfreq.Rd | 3 ++- man/clarachunk.Rd | 3 ++- man/evaldp.Rd | 3 ++- man/freqweights-package.Rd | 3 ++- man/hclustvfreq.Rd | 3 ++- man/lmfreq.Rd | 3 ++- man/make.readchunk.Rd | 3 ++- man/pcafreq.Rd | 3 ++- man/preprocesshflights.Rd | 3 ++- man/quickround.Rd | 3 ++- man/statsfreq.Rd | 3 ++- man/tablefreq.Rd | 5 +++-- 19 files changed, 68 insertions(+), 45 deletions(-)
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest.
Some of the functions in this package are optionally enhanced by the 'gurobi'
software and its accompanying R package. For their installation, please follow the
instructions at www.gurobi.com and http://www.gurobi.com/documentation, respectively.
Author: Jelle Goeman, Aldo Solari, Rosa Meijer
Maintainer: Jelle Goeman <jelle.goeman@radboudumc.nl>
Diff between cherry versions 0.5-10 dated 2014-07-18 and 0.6-11 dated 2015-06-22
ChangeLog | 6 DESCRIPTION | 33 +--- MD5 | 42 ++--- NAMESPACE | 6 R/DAGmethod.R | 29 ++- R/Meinshausen.R | 10 - R/closed.R | 7 R/regionmethod.R | 9 - R/shortcuts.R | 359 ++++++++++++++++++++++++++++++++++++++++++-- R/structuredHolm.R |only build/vignette.rds |binary inst/CITATION | 18 -- inst/doc/cherry.R | 66 +++++++- inst/doc/cherry.Rnw | 230 ++++++++++++++++++++++++---- inst/doc/cherry.pdf |binary man/DAG-class.Rd | 4 man/DAGmethod.Rd | 2 man/hommel-class.Rd |only man/hommelFast.Rd |only man/regionmethod.Rd | 2 man/shortcuts.Rd | 15 - man/structuredHolm.Rd |only vignettes/cherry.Rnw | 132 ++++++++++++---- vignettes/cherrypackage.bib | 44 +++++ 24 files changed, 860 insertions(+), 154 deletions(-)
More information about cometExactTest at CRAN
Permanent link
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging for linear models,
generalizable linear models and survival models (cox
regression).
Author: Adrian Raftery <raftery@stat.washington.edu>, Jennifer Hoeting,
Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Chris Fraley <fraley@u.washington.edu>
Diff between BMA versions 3.18.1 dated 2014-10-04 and 3.18.4 dated 2015-06-22
ChangeLog | 8 +++ DESCRIPTION | 12 ++--- MD5 | 12 ++--- NAMESPACE | 138 ++++++++++++++++++++++++++++++++++++++-------------------- R/mc3.R | 2 man/bicreg.Rd | 3 - man/glib.Rd | 7 -- 7 files changed, 113 insertions(+), 69 deletions(-)
Title: A Package to Processes Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also includes functions to plot and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>
Diff between acc versions 1.0.2 dated 2015-05-13 and 1.1.1 dated 2015-06-22
acc-1.0.2/acc/R/rtb.R |only acc-1.0.2/acc/man/acc-package.Rd |only acc-1.0.2/acc/man/rtb.Rd |only acc-1.1.1/acc/DESCRIPTION | 15 -- acc-1.1.1/acc/MD5 | 29 ++- acc-1.1.1/acc/R/acc.R | 285 ++------------------------------------ acc-1.1.1/acc/R/accBatch.R |only acc-1.1.1/acc/R/accsummary.R |only acc-1.1.1/acc/R/aggAcc.R |only acc-1.1.1/acc/R/plotAcc.R | 214 +++------------------------- acc-1.1.1/acc/R/readRaw.R | 40 +++-- acc-1.1.1/acc/R/readRawBatch.R |only acc-1.1.1/acc/R/simAcc.R | 2 acc-1.1.1/acc/man/acc.Rd | 95 +++++------- acc-1.1.1/acc/man/accBatch.Rd |only acc-1.1.1/acc/man/accsummary.Rd |only acc-1.1.1/acc/man/aggAcc.Rd |only acc-1.1.1/acc/man/plotAcc.Rd | 78 ++++++++-- acc-1.1.1/acc/man/readRaw.Rd | 2 acc-1.1.1/acc/man/readRawBatch.Rd |only acc-1.1.1/acc/man/simAcc.Rd | 36 ++-- 21 files changed, 219 insertions(+), 577 deletions(-)
Title: SYMPHONY in R
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut],
Kurt Hornik [aut, cre],
Stefan Theussl [aut],
Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between Rsymphony versions 0.1-20 dated 2015-05-30 and 0.1-21 dated 2015-06-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/symphony.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-30 0.1.0
Title: N-Gram Analysis of Biological Sequences
Description: Tools for extraction and analysis of various
n-grams (k-mers) derived from biological sequences (proteins
or nucleic acids). Uses QuiPT (quick permutation test) for fast
feature-filtering to deal with the dimensionality of the n-gram data.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut],
Chris Lauber [aut]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between biogram versions 1.1 dated 2015-02-03 and 1.2 dated 2015-06-22
biogram-1.1/biogram/R/check_criterion.R |only biogram-1.1/biogram/R/check_ngrams.R |only biogram-1.1/biogram/R/decode_ngrams.R |only biogram-1.1/biogram/man/calc_ig_single.Rd |only biogram-1.1/biogram/man/criterions.Rd |only biogram-1.2/biogram/CHANGELOG | 15 - biogram-1.2/biogram/DESCRIPTION | 20 - biogram-1.2/biogram/MD5 | 107 ++++--- biogram-1.2/biogram/NAMESPACE | 17 + biogram-1.2/biogram/R/add_ngrams.R |only biogram-1.2/biogram/R/biogram.R | 35 +- biogram-1.2/biogram/R/construct_ngrams.R |only biogram-1.2/biogram/R/count_ngrams.R | 32 +- biogram-1.2/biogram/R/count_specified.R |only biogram-1.2/biogram/R/criterion_distribution.R | 195 ++++++-------- biogram-1.2/biogram/R/criterions.R | 77 ++++- biogram-1.2/biogram/R/degenerate.R | 22 + biogram-1.2/biogram/R/distr_crit.R |only biogram-1.2/biogram/R/feature_test_class.R | 3 biogram-1.2/biogram/R/indices_and_positions.R |only biogram-1.2/biogram/R/information_gain.R | 50 --- biogram-1.2/biogram/R/is_ngram.R |only biogram-1.2/biogram/R/kl_divergence.R |only biogram-1.2/biogram/R/ngram_coding.R |only biogram-1.2/biogram/R/ngrams.R | 122 ++++---- biogram-1.2/biogram/R/position_ngrams.R | 72 +++-- biogram-1.2/biogram/R/table_ngrams.R |only biogram-1.2/biogram/R/test_features.R | 55 ++- biogram-1.2/biogram/R/utilities.R | 2 biogram-1.2/biogram/README.md | 2 biogram-1.2/biogram/inst/CITATION | 19 - biogram-1.2/biogram/man/add_1grams.Rd |only biogram-1.2/biogram/man/biogram-package.Rd | 35 +- biogram-1.2/biogram/man/calc_criterion.Rd |only biogram-1.2/biogram/man/calc_ig.Rd | 52 ++- biogram-1.2/biogram/man/calc_kl.Rd |only biogram-1.2/biogram/man/code_ngrams.Rd |only biogram-1.2/biogram/man/construct_ngrams.Rd |only biogram-1.2/biogram/man/count_multigrams.Rd | 4 biogram-1.2/biogram/man/count_ngrams.Rd | 6 biogram-1.2/biogram/man/count_specified.Rd |only biogram-1.2/biogram/man/count_total.Rd |only biogram-1.2/biogram/man/create_feature_target.Rd | 2 biogram-1.2/biogram/man/create_ngrams.Rd | 8 biogram-1.2/biogram/man/criterion_distribution.Rd | 51 +-- biogram-1.2/biogram/man/cut.feature_test.Rd | 2 biogram-1.2/biogram/man/decode_ngrams.Rd | 15 - biogram-1.2/biogram/man/degenerate.Rd | 5 biogram-1.2/biogram/man/distr_crit.Rd |only biogram-1.2/biogram/man/fast_crosstable.Rd | 2 biogram-1.2/biogram/man/feature_test.Rd | 5 biogram-1.2/biogram/man/gap_ngrams.Rd |only biogram-1.2/biogram/man/get_ngrams_ind.Rd | 11 biogram-1.2/biogram/man/human_cleave.Rd | 2 biogram-1.2/biogram/man/is_ngram.Rd | 4 biogram-1.2/biogram/man/l2n.Rd | 7 biogram-1.2/biogram/man/n2l.Rd | 7 biogram-1.2/biogram/man/ngrams2df.Rd |only biogram-1.2/biogram/man/plot.criterion_distribution.Rd |only biogram-1.2/biogram/man/position_ngrams.Rd | 24 + biogram-1.2/biogram/man/print.feature_test.Rd | 2 biogram-1.2/biogram/man/seq2ngrams.Rd | 10 biogram-1.2/biogram/man/summary.feature_test.Rd | 2 biogram-1.2/biogram/man/table_ngrams.Rd |only biogram-1.2/biogram/man/test_features.Rd | 31 +- biogram-1.2/biogram/tests/testthat/test_is_ngram.R |only biogram-1.2/biogram/tests/testthat/test_position_ngrams.R | 23 + biogram-1.2/biogram/tests/testthat/test_seq2grams.R | 18 - 68 files changed, 668 insertions(+), 505 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers.
Among available features there are: pattern searching
(e.g. via regular expressions), random string generation,
string collation, transliteration, concatenation,
date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.4-1 dated 2014-12-14 and 0.5-2 dated 2015-06-22
stringi-0.4-1/stringi/R/todo_other.R |only stringi-0.4-1/stringi/configure.ac |only stringi-0.4-1/stringi/man/search_match.Rd |only stringi-0.4-1/stringi/man/stri_extract_words.Rd |only stringi-0.4-1/stringi/src/icu52 |only stringi-0.4-1/stringi/src/icu52_common_c.txt |only stringi-0.4-1/stringi/src/icu52_common_cpp.txt |only stringi-0.4-1/stringi/src/icu52_found.txt.in |only stringi-0.4-1/stringi/src/icu52_i18n_c.txt |only stringi-0.4-1/stringi/src/icu52_i18n_cpp.txt |only stringi-0.4-1/stringi/src/icu52_stubdata_c.txt |only stringi-0.4-1/stringi/src/icu52_stubdata_cpp.txt |only stringi-0.5-2/stringi/DESCRIPTION | 22 stringi-0.5-2/stringi/INSTALL | 64 stringi-0.5-2/stringi/LICENSE | 10 stringi-0.5-2/stringi/MD5 | 1983 +++++----- stringi-0.5-2/stringi/NAMESPACE | 20 stringi-0.5-2/stringi/NEWS | 552 +- stringi-0.5-2/stringi/R/ICU_settings.R | 2 stringi-0.5-2/stringi/R/compare.R | 36 stringi-0.5-2/stringi/R/draft_encdetect.R | 4 stringi-0.5-2/stringi/R/draft_files.R | 2 stringi-0.5-2/stringi/R/encoding.R | 2 stringi-0.5-2/stringi/R/encoding_conversion.R | 20 stringi-0.5-2/stringi/R/encoding_detection.R | 2 stringi-0.5-2/stringi/R/encoding_management.R | 2 stringi-0.5-2/stringi/R/escape.R | 2 stringi-0.5-2/stringi/R/install.R | 30 stringi-0.5-2/stringi/R/internal_prepare_arg.R | 15 stringi-0.5-2/stringi/R/internal_test.R | 2 stringi-0.5-2/stringi/R/join.R | 20 stringi-0.5-2/stringi/R/length.R | 56 stringi-0.5-2/stringi/R/locale.R | 24 stringi-0.5-2/stringi/R/locale_management.R | 5 stringi-0.5-2/stringi/R/opts.R | 2 stringi-0.5-2/stringi/R/pad.R | 48 stringi-0.5-2/stringi/R/random.R | 2 stringi-0.5-2/stringi/R/reverse.R | 2 stringi-0.5-2/stringi/R/search.R | 430 +- stringi-0.5-2/stringi/R/search_count_4.R | 7 stringi-0.5-2/stringi/R/search_count_bound.R | 8 stringi-0.5-2/stringi/R/search_detect_4.R | 6 stringi-0.5-2/stringi/R/search_extract_4.R | 8 stringi-0.5-2/stringi/R/search_extract_bound.R | 76 stringi-0.5-2/stringi/R/search_locate_4.R | 5 stringi-0.5-2/stringi/R/search_locate_bound.R | 11 stringi-0.5-2/stringi/R/search_match_4.R | 16 stringi-0.5-2/stringi/R/search_replace_4.R | 10 stringi-0.5-2/stringi/R/search_replace_na.R | 2 stringi-0.5-2/stringi/R/search_split_4.R | 7 stringi-0.5-2/stringi/R/search_split_bound.R | 2 stringi-0.5-2/stringi/R/search_startsendswith_4.R | 6 stringi-0.5-2/stringi/R/search_subset_4.R | 7 stringi-0.5-2/stringi/R/stats.R | 2 stringi-0.5-2/stringi/R/stringi-package.R | 59 stringi-0.5-2/stringi/R/sub.R | 2 stringi-0.5-2/stringi/R/time_calendar.R |only stringi-0.5-2/stringi/R/time_format.R |only stringi-0.5-2/stringi/R/time_symbols.R |only stringi-0.5-2/stringi/R/time_zone.R |only stringi-0.5-2/stringi/R/todo_charclass.R | 2 stringi-0.5-2/stringi/R/todo_justify.R | 2 stringi-0.5-2/stringi/R/todo_rbnf.R | 2 stringi-0.5-2/stringi/R/todo_search_in.R | 2 stringi-0.5-2/stringi/R/todo_split.R | 2 stringi-0.5-2/stringi/R/trans_casemap.R | 2 stringi-0.5-2/stringi/R/trans_normalization.R | 2 stringi-0.5-2/stringi/R/trans_other.R |only stringi-0.5-2/stringi/R/trans_transliterate.R | 2 stringi-0.5-2/stringi/R/trim.R | 16 stringi-0.5-2/stringi/R/utils.R | 2 stringi-0.5-2/stringi/R/wrap.R | 34 stringi-0.5-2/stringi/cleanup | 2 stringi-0.5-2/stringi/configure | 1779 +++++--- stringi-0.5-2/stringi/inst/AUTHORS | 2 stringi-0.5-2/stringi/inst/CITATION | 4 stringi-0.5-2/stringi/man/oper_comparison.Rd | 6 stringi-0.5-2/stringi/man/oper_plus.Rd | 7 stringi-0.5-2/stringi/man/stri_compare.Rd | 14 stringi-0.5-2/stringi/man/stri_count.Rd | 8 stringi-0.5-2/stringi/man/stri_count_boundaries.Rd | 17 stringi-0.5-2/stringi/man/stri_datetime_add.Rd |only stringi-0.5-2/stringi/man/stri_datetime_create.Rd |only stringi-0.5-2/stringi/man/stri_datetime_fields.Rd |only stringi-0.5-2/stringi/man/stri_datetime_format.Rd |only stringi-0.5-2/stringi/man/stri_datetime_fstr.Rd |only stringi-0.5-2/stringi/man/stri_datetime_now.Rd |only stringi-0.5-2/stringi/man/stri_datetime_symbols.Rd |only stringi-0.5-2/stringi/man/stri_detect.Rd | 7 stringi-0.5-2/stringi/man/stri_dup.Rd | 7 stringi-0.5-2/stringi/man/stri_duplicated.Rd | 17 stringi-0.5-2/stringi/man/stri_enc_detect.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_detect2.Rd | 6 stringi-0.5-2/stringi/man/stri_enc_fromutf32.Rd | 5 stringi-0.5-2/stringi/man/stri_enc_info.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_isascii.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_isutf16.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_isutf8.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_list.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_mark.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_set.Rd | 3 stringi-0.5-2/stringi/man/stri_enc_toascii.Rd | 5 stringi-0.5-2/stringi/man/stri_enc_tonative.Rd | 5 stringi-0.5-2/stringi/man/stri_enc_toutf32.Rd | 5 stringi-0.5-2/stringi/man/stri_enc_toutf8.Rd | 9 stringi-0.5-2/stringi/man/stri_encode.Rd | 7 stringi-0.5-2/stringi/man/stri_escape_unicode.Rd | 3 stringi-0.5-2/stringi/man/stri_extract.Rd | 14 stringi-0.5-2/stringi/man/stri_extract_boundaries.Rd |only stringi-0.5-2/stringi/man/stri_flatten.Rd | 7 stringi-0.5-2/stringi/man/stri_info.Rd | 3 stringi-0.5-2/stringi/man/stri_install.Rd | 11 stringi-0.5-2/stringi/man/stri_isempty.Rd | 5 stringi-0.5-2/stringi/man/stri_join.Rd | 9 stringi-0.5-2/stringi/man/stri_length.Rd | 7 stringi-0.5-2/stringi/man/stri_list2matrix.Rd | 3 stringi-0.5-2/stringi/man/stri_locale_info.Rd | 6 stringi-0.5-2/stringi/man/stri_locale_list.Rd | 3 stringi-0.5-2/stringi/man/stri_locale_set.Rd | 3 stringi-0.5-2/stringi/man/stri_locate.Rd | 6 stringi-0.5-2/stringi/man/stri_locate_boundaries.Rd | 18 stringi-0.5-2/stringi/man/stri_match.Rd |only stringi-0.5-2/stringi/man/stri_numbytes.Rd | 5 stringi-0.5-2/stringi/man/stri_opts_brkiter.Rd | 6 stringi-0.5-2/stringi/man/stri_opts_collator.Rd | 6 stringi-0.5-2/stringi/man/stri_opts_fixed.Rd | 3 stringi-0.5-2/stringi/man/stri_opts_regex.Rd | 3 stringi-0.5-2/stringi/man/stri_order.Rd | 16 stringi-0.5-2/stringi/man/stri_pad.Rd | 41 stringi-0.5-2/stringi/man/stri_rand_lipsum.Rd | 3 stringi-0.5-2/stringi/man/stri_rand_shuffle.Rd | 3 stringi-0.5-2/stringi/man/stri_rand_strings.Rd | 3 stringi-0.5-2/stringi/man/stri_read_lines.Rd | 3 stringi-0.5-2/stringi/man/stri_read_raw.Rd | 3 stringi-0.5-2/stringi/man/stri_replace.Rd | 11 stringi-0.5-2/stringi/man/stri_replace_na.Rd | 3 stringi-0.5-2/stringi/man/stri_reverse.Rd | 3 stringi-0.5-2/stringi/man/stri_split.Rd | 8 stringi-0.5-2/stringi/man/stri_split_boundaries.Rd | 9 stringi-0.5-2/stringi/man/stri_split_lines.Rd | 6 stringi-0.5-2/stringi/man/stri_startsendswith.Rd | 7 stringi-0.5-2/stringi/man/stri_stats_general.Rd | 3 stringi-0.5-2/stringi/man/stri_stats_latex.Rd | 3 stringi-0.5-2/stringi/man/stri_sub.Rd | 3 stringi-0.5-2/stringi/man/stri_subset.Rd | 8 stringi-0.5-2/stringi/man/stri_timezone_info.Rd |only stringi-0.5-2/stringi/man/stri_timezone_list.Rd |only stringi-0.5-2/stringi/man/stri_timezone_set.Rd |only stringi-0.5-2/stringi/man/stri_trans_casemap.Rd | 12 stringi-0.5-2/stringi/man/stri_trans_char.Rd |only stringi-0.5-2/stringi/man/stri_trans_general.Rd | 6 stringi-0.5-2/stringi/man/stri_trans_list.Rd | 6 stringi-0.5-2/stringi/man/stri_trans_nf.Rd | 6 stringi-0.5-2/stringi/man/stri_trim.Rd | 17 stringi-0.5-2/stringi/man/stri_unescape_unicode.Rd | 3 stringi-0.5-2/stringi/man/stri_unique.Rd | 12 stringi-0.5-2/stringi/man/stri_width.Rd |only stringi-0.5-2/stringi/man/stri_wrap.Rd | 39 stringi-0.5-2/stringi/man/stri_write_lines.Rd | 3 stringi-0.5-2/stringi/man/stringi-arguments.Rd | 7 stringi-0.5-2/stringi/man/stringi-encoding.Rd | 7 stringi-0.5-2/stringi/man/stringi-locale.Rd | 31 stringi-0.5-2/stringi/man/stringi-package.Rd | 59 stringi-0.5-2/stringi/man/stringi-search-boundaries.Rd | 13 stringi-0.5-2/stringi/man/stringi-search-charclass.Rd | 231 - stringi-0.5-2/stringi/man/stringi-search-coll.Rd | 10 stringi-0.5-2/stringi/man/stringi-search-fixed.Rd | 7 stringi-0.5-2/stringi/man/stringi-search-regex.Rd | 211 - stringi-0.5-2/stringi/man/stringi-search.Rd | 15 stringi-0.5-2/stringi/src/Makevars.in | 6 stringi-0.5-2/stringi/src/Makevars.win | 18 stringi-0.5-2/stringi/src/icu55 |only stringi-0.5-2/stringi/src/icu55_common_c.txt |only stringi-0.5-2/stringi/src/icu55_common_cpp.txt |only stringi-0.5-2/stringi/src/icu55_found.txt.in |only stringi-0.5-2/stringi/src/icu55_i18n_c.txt |only stringi-0.5-2/stringi/src/icu55_i18n_cpp.txt |only stringi-0.5-2/stringi/src/icu55_stubdata_c.txt |only stringi-0.5-2/stringi/src/icu55_stubdata_cpp.txt |only stringi-0.5-2/stringi/src/install.libs.R | 11 stringi-0.5-2/stringi/src/install.libs.R.in |only stringi-0.5-2/stringi/src/stri_ICU_settings.cpp | 4 stringi-0.5-2/stringi/src/stri_TODO_justify.cpp | 2 stringi-0.5-2/stringi/src/stri_TODO_splitpos.cpp | 2 stringi-0.5-2/stringi/src/stri_TODO_uchar.cpp | 2 stringi-0.5-2/stringi/src/stri_brkiter.cpp | 2 stringi-0.5-2/stringi/src/stri_brkiter.h | 7 stringi-0.5-2/stringi/src/stri_bytesearch_matcher.h |only stringi-0.5-2/stringi/src/stri_collator.cpp | 2 stringi-0.5-2/stringi/src/stri_common.cpp | 43 stringi-0.5-2/stringi/src/stri_compare.cpp | 2 stringi-0.5-2/stringi/src/stri_container_base.cpp | 2 stringi-0.5-2/stringi/src/stri_container_base.h | 2 stringi-0.5-2/stringi/src/stri_container_bytesearch.cpp | 943 +--- stringi-0.5-2/stringi/src/stri_container_bytesearch.h | 196 stringi-0.5-2/stringi/src/stri_container_charclass.h | 2 stringi-0.5-2/stringi/src/stri_container_double.h |only stringi-0.5-2/stringi/src/stri_container_integer.h | 2 stringi-0.5-2/stringi/src/stri_container_listint.cpp | 2 stringi-0.5-2/stringi/src/stri_container_listint.h | 2 stringi-0.5-2/stringi/src/stri_container_listraw.cpp | 11 stringi-0.5-2/stringi/src/stri_container_listraw.h | 2 stringi-0.5-2/stringi/src/stri_container_listutf8.cpp | 2 stringi-0.5-2/stringi/src/stri_container_listutf8.h | 2 stringi-0.5-2/stringi/src/stri_container_logical.h | 2 stringi-0.5-2/stringi/src/stri_container_regex.cpp | 2 stringi-0.5-2/stringi/src/stri_container_regex.h | 2 stringi-0.5-2/stringi/src/stri_container_usearch.cpp | 2 stringi-0.5-2/stringi/src/stri_container_usearch.h | 2 stringi-0.5-2/stringi/src/stri_container_utf16.cpp | 38 stringi-0.5-2/stringi/src/stri_container_utf16.h | 10 stringi-0.5-2/stringi/src/stri_container_utf8.cpp | 17 stringi-0.5-2/stringi/src/stri_container_utf8.h | 30 stringi-0.5-2/stringi/src/stri_container_utf8_indexable.cpp | 24 stringi-0.5-2/stringi/src/stri_container_utf8_indexable.h | 5 stringi-0.5-2/stringi/src/stri_cpp.txt | 6 stringi-0.5-2/stringi/src/stri_encoding_conversion.cpp | 4 stringi-0.5-2/stringi/src/stri_encoding_detection.cpp | 50 stringi-0.5-2/stringi/src/stri_encoding_management.cpp | 8 stringi-0.5-2/stringi/src/stri_escape.cpp | 2 stringi-0.5-2/stringi/src/stri_exception.cpp | 6 stringi-0.5-2/stringi/src/stri_exception.h | 2 stringi-0.5-2/stringi/src/stri_external.h | 3 stringi-0.5-2/stringi/src/stri_interval.h | 2 stringi-0.5-2/stringi/src/stri_intvec.h | 2 stringi-0.5-2/stringi/src/stri_join.cpp | 2 stringi-0.5-2/stringi/src/stri_length.cpp | 127 stringi-0.5-2/stringi/src/stri_macros.h | 2 stringi-0.5-2/stringi/src/stri_messages.h | 11 stringi-0.5-2/stringi/src/stri_pad.cpp | 59 stringi-0.5-2/stringi/src/stri_prepare_arg.cpp | 260 + stringi-0.5-2/stringi/src/stri_random.cpp | 2 stringi-0.5-2/stringi/src/stri_reverse.cpp | 2 stringi-0.5-2/stringi/src/stri_search_boundaries_count.cpp | 2 stringi-0.5-2/stringi/src/stri_search_boundaries_extract.cpp |only stringi-0.5-2/stringi/src/stri_search_boundaries_locate.cpp | 2 stringi-0.5-2/stringi/src/stri_search_boundaries_split.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_count.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_detect.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_extract.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_locate.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_replace.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_split.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_startsendswith.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_subset.cpp | 2 stringi-0.5-2/stringi/src/stri_search_class_trim.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_count.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_detect.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_extract.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_locate.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_replace.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_split.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_startsendswith.cpp | 2 stringi-0.5-2/stringi/src/stri_search_coll_subset.cpp | 2 stringi-0.5-2/stringi/src/stri_search_common.cpp | 2 stringi-0.5-2/stringi/src/stri_search_fixed_count.cpp | 10 stringi-0.5-2/stringi/src/stri_search_fixed_detect.cpp | 10 stringi-0.5-2/stringi/src/stri_search_fixed_extract.cpp | 27 stringi-0.5-2/stringi/src/stri_search_fixed_locate.cpp | 27 stringi-0.5-2/stringi/src/stri_search_fixed_replace.cpp | 36 stringi-0.5-2/stringi/src/stri_search_fixed_split.cpp | 14 stringi-0.5-2/stringi/src/stri_search_fixed_startsendswith.cpp | 18 stringi-0.5-2/stringi/src/stri_search_fixed_subset.cpp | 10 stringi-0.5-2/stringi/src/stri_search_in.cpp | 2 stringi-0.5-2/stringi/src/stri_search_other_replace.cpp | 2 stringi-0.5-2/stringi/src/stri_search_other_split.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_count.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_detect.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_extract.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_locate.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_match.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_replace.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_split.cpp | 2 stringi-0.5-2/stringi/src/stri_search_regex_subset.cpp | 2 stringi-0.5-2/stringi/src/stri_stats.cpp | 2 stringi-0.5-2/stringi/src/stri_string8.h | 113 stringi-0.5-2/stringi/src/stri_string8buf.h | 40 stringi-0.5-2/stringi/src/stri_stringi.cpp | 85 stringi-0.5-2/stringi/src/stri_stringi.h | 51 stringi-0.5-2/stringi/src/stri_sub.cpp | 2 stringi-0.5-2/stringi/src/stri_test.cpp | 2 stringi-0.5-2/stringi/src/stri_time_calendar.cpp |only stringi-0.5-2/stringi/src/stri_time_format.cpp |only stringi-0.5-2/stringi/src/stri_time_symbols.cpp |only stringi-0.5-2/stringi/src/stri_time_zone.cpp |only stringi-0.5-2/stringi/src/stri_trans_casemap.cpp | 2 stringi-0.5-2/stringi/src/stri_trans_normalization.cpp | 2 stringi-0.5-2/stringi/src/stri_trans_other.cpp |only stringi-0.5-2/stringi/src/stri_trans_transliterate.cpp | 2 stringi-0.5-2/stringi/src/stri_ucnv.cpp | 2 stringi-0.5-2/stringi/src/stri_ucnv.h | 2 stringi-0.5-2/stringi/src/stri_uloc.cpp | 10 stringi-0.5-2/stringi/src/stri_utils.cpp | 2 stringi-0.5-2/stringi/src/stri_wrap.cpp | 117 stringi-0.5-2/stringi/src/uconfig_local.h | 2 295 files changed, 5043 insertions(+), 4111 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut], Martin Maechler [aut],
Ben Bolker [aut, cre], Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb], Bin Dai [ctb],
Gabor Grothendieck [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-7 dated 2014-07-03 and 1.1-8 dated 2015-06-22
lme4-1.1-7/lme4/data/GQN.rda |only lme4-1.1-7/lme4/inst/testdata/rankMatrix.rda |only lme4-1.1-7/lme4/man/GQN.Rd |only lme4-1.1-7/lme4/man/lmList-class.Rd |only lme4-1.1-7/lme4/tests/lmList.R |only lme4-1.1-8/lme4/DESCRIPTION | 29 lme4-1.1-8/lme4/MD5 | 237 +++--- lme4-1.1-8/lme4/NAMESPACE | 65 + lme4-1.1-8/lme4/R/AllClass.R | 190 ++--- lme4-1.1-8/lme4/R/AllGeneric.R | 70 - lme4-1.1-8/lme4/R/GHrule.R | 158 ---- lme4-1.1-8/lme4/R/bootMer.R | 166 ---- lme4-1.1-8/lme4/R/checkConv.R | 83 +- lme4-1.1-8/lme4/R/deriv.R | 4 lme4-1.1-8/lme4/R/lmList.R | 295 +++++-- lme4-1.1-8/lme4/R/lmer.R | 924 +++++++++++++------------ lme4-1.1-8/lme4/R/lmerControl.R | 10 lme4-1.1-8/lme4/R/modular.R | 336 +++++---- lme4-1.1-8/lme4/R/nbinom.R | 4 lme4-1.1-8/lme4/R/optimizer.R | 2 lme4-1.1-8/lme4/R/plot.R | 598 ++++++++-------- lme4-1.1-8/lme4/R/predict.R | 397 +++++----- lme4-1.1-8/lme4/R/profile.R | 820 ++++++++++++---------- lme4-1.1-8/lme4/R/sparsegrid.R | 33 lme4-1.1-8/lme4/R/sysdata.rda |only lme4-1.1-8/lme4/R/utilities.R | 481 ++++++++----- lme4-1.1-8/lme4/R/vcconv.R | 55 - lme4-1.1-8/lme4/README.md | 40 - lme4-1.1-8/lme4/build/vignette.rds |binary lme4-1.1-8/lme4/data/Arabidopsis.rda |only lme4-1.1-8/lme4/inst/CITATION | 8 lme4-1.1-8/lme4/inst/NEWS.Rd | 78 ++ lme4-1.1-8/lme4/inst/doc/PLSvGLS.R |only lme4-1.1-8/lme4/inst/doc/PLSvGLS.Rnw |only lme4-1.1-8/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-8/lme4/inst/doc/Theory.R |only lme4-1.1-8/lme4/inst/doc/Theory.Rnw |only lme4-1.1-8/lme4/inst/doc/Theory.pdf |binary lme4-1.1-8/lme4/inst/doc/lme4-extras.pdf |only lme4-1.1-8/lme4/inst/doc/lmer.R |only lme4-1.1-8/lme4/inst/doc/lmer.Rnw |only lme4-1.1-8/lme4/inst/doc/lmer.pdf |binary lme4-1.1-8/lme4/inst/doc/lmerperf.R |only lme4-1.1-8/lme4/inst/doc/lmerperf.Rmd |only lme4-1.1-8/lme4/inst/doc/lmerperf.html |only lme4-1.1-8/lme4/inst/testdata/badhess.RData |only lme4-1.1-8/lme4/inst/testdata/dataEx_Glmer.txt |only lme4-1.1-8/lme4/inst/testdata/lme-tst-fits.R | 76 +- lme4-1.1-8/lme4/inst/testdata/lme-tst-fits.rda |binary lme4-1.1-8/lme4/inst/testdata/lme-tst-funs.R | 8 lme4-1.1-8/lme4/inst/testdata/rankMatrix.rds |only lme4-1.1-8/lme4/inst/testdata/sbTobb.Rdata |only lme4-1.1-8/lme4/inst/tests/napredict2.R | 15 lme4-1.1-8/lme4/inst/tests/test-NAhandling.R | 170 ++-- lme4-1.1-8/lme4/inst/tests/test-formulaEval.R | 17 lme4-1.1-8/lme4/inst/tests/test-glmer.R | 50 + lme4-1.1-8/lme4/inst/tests/test-glmmFail.R | 5 lme4-1.1-8/lme4/inst/tests/test-lmer.R | 44 - lme4-1.1-8/lme4/inst/tests/test-methods.R | 399 ++++++++-- lme4-1.1-8/lme4/inst/tests/test-rank.R | 6 lme4-1.1-8/lme4/inst/tests/test-start.R | 3 lme4-1.1-8/lme4/inst/tests/test-utils.R | 41 + lme4-1.1-8/lme4/inst/utils |only lme4-1.1-8/lme4/man/Arabidopsis.Rd |only lme4-1.1-8/lme4/man/GHrule.Rd | 34 lme4-1.1-8/lme4/man/GQdk.Rd | 47 - lme4-1.1-8/lme4/man/VarCorr.Rd | 7 lme4-1.1-8/lme4/man/bootMer.Rd | 23 lme4-1.1-8/lme4/man/confint.merMod.Rd | 36 lme4-1.1-8/lme4/man/convergence.Rd |only lme4-1.1-8/lme4/man/expandDoubleVerts.Rd | 12 lme4-1.1-8/lme4/man/factorize.Rd |only lme4-1.1-8/lme4/man/fixef.Rd | 12 lme4-1.1-8/lme4/man/getME.Rd | 21 lme4-1.1-8/lme4/man/glmer.Rd | 289 +++---- lme4-1.1-8/lme4/man/glmerLaplaceHandle.Rd |only lme4-1.1-8/lme4/man/hatvalues.merMod.Rd |only lme4-1.1-8/lme4/man/lmList.Rd | 105 +- lme4-1.1-8/lme4/man/lmList4-class.Rd |only lme4-1.1-8/lme4/man/lmer.Rd | 215 ++--- lme4-1.1-8/lme4/man/lmerControl.Rd | 25 lme4-1.1-8/lme4/man/merMod-class.Rd | 89 ++ lme4-1.1-8/lme4/man/merPredD-class.Rd | 45 - lme4-1.1-8/lme4/man/merPredD.Rd | 40 - lme4-1.1-8/lme4/man/mkMerMod.Rd | 16 lme4-1.1-8/lme4/man/mkReTrms.Rd | 45 - lme4-1.1-8/lme4/man/mkSimulationTemplate.Rd |only lme4-1.1-8/lme4/man/mkdevfun.Rd | 47 - lme4-1.1-8/lme4/man/modular.Rd | 11 lme4-1.1-8/lme4/man/ngrps.Rd | 27 lme4-1.1-8/lme4/man/nlmer.Rd | 190 ++--- lme4-1.1-8/lme4/man/nloptwrap.Rd | 45 + lme4-1.1-8/lme4/man/plot.lmList4.Rd |only lme4-1.1-8/lme4/man/plot.merMod.Rd | 13 lme4-1.1-8/lme4/man/plots.thpr.Rd | 15 lme4-1.1-8/lme4/man/predict.merMod.Rd | 82 +- lme4-1.1-8/lme4/man/profile-methods.Rd | 100 +- lme4-1.1-8/lme4/man/pvalues.Rd | 6 lme4-1.1-8/lme4/man/refit.Rd | 107 +- lme4-1.1-8/lme4/man/refitML.Rd | 35 lme4-1.1-8/lme4/man/sigma.Rd | 30 lme4-1.1-8/lme4/man/simulate.merMod.Rd | 130 +-- lme4-1.1-8/lme4/man/troubleshooting.Rd |only lme4-1.1-8/lme4/man/vcconv.Rd |only lme4-1.1-8/lme4/src/external.cpp | 64 + lme4-1.1-8/lme4/src/glmFamily.cpp | 10 lme4-1.1-8/lme4/src/lme4CholmodDecomposition.h | 2 lme4-1.1-8/lme4/src/predModule.cpp | 6 lme4-1.1-8/lme4/src/predModule.h | 1 lme4-1.1-8/lme4/tests/AAAtest-all.Rout | 191 ++++- lme4-1.1-8/lme4/tests/REMLdev.R | 6 lme4-1.1-8/lme4/tests/Rplots.pdf |binary lme4-1.1-8/lme4/tests/agridat_gotway.R | 3 lme4-1.1-8/lme4/tests/bootMer.R | 29 lme4-1.1-8/lme4/tests/bootMer.Rout |only lme4-1.1-8/lme4/tests/boundary.R | 96 +- lme4-1.1-8/lme4/tests/condVar.R | 8 lme4-1.1-8/lme4/tests/confint.R | 22 lme4-1.1-8/lme4/tests/fewlevels.R | 3 lme4-1.1-8/lme4/tests/glmer-1.R | 3 lme4-1.1-8/lme4/tests/hatvalues.R | 29 lme4-1.1-8/lme4/tests/lmList-tst.R |only lme4-1.1-8/lme4/tests/lme-tst-fits.rda |only lme4-1.1-8/lme4/tests/lmer-1.Rout.save | 21 lme4-1.1-8/lme4/tests/nbinom.R | 27 lme4-1.1-8/lme4/tests/predict.R | 255 +++--- lme4-1.1-8/lme4/tests/predict.Rout | 551 +++----------- lme4-1.1-8/lme4/tests/predict_basis.R | 15 lme4-1.1-8/lme4/tests/predict_basis.Rout | 34 lme4-1.1-8/lme4/tests/profile-tst.R | 40 + lme4-1.1-8/lme4/tests/refit.R | 203 +++-- lme4-1.1-8/lme4/tests/refit.Rout | 18 lme4-1.1-8/lme4/tests/refit_allequal.RData |only lme4-1.1-8/lme4/tests/simulate.R | 5 lme4-1.1-8/lme4/vignettes/Theory.Rnw | 8 lme4-1.1-8/lme4/vignettes/blkarray.sty |only lme4-1.1-8/lme4/vignettes/lmer.Rnw | 492 ++++++------- lme4-1.1-8/lme4/vignettes/lmerperf.Rmd |only lme4-1.1-8/lme4/vignettes/lmerperf.md |only 139 files changed, 5502 insertions(+), 4456 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams (q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler). An implementation of soundex is provided as well.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.0 dated 2015-01-09 and 0.9.1 dated 2015-06-22
DESCRIPTION | 9 - MD5 | 67 ++++++----- NAMESPACE | 3 NEWS | 10 + R/amatch.R | 23 +-- R/doc_encoding.R | 2 R/doc_metrics.R | 2 R/doc_parallel.R | 2 R/stringdist.R | 219 +++++++++++++++++++++++++------------- R/stringsim.R |only R/utils.R | 7 + man/amatch.Rd | 2 man/phonetic.Rd | 2 man/printable_ascii.Rd | 2 man/qgrams.Rd | 2 man/stringdist-encoding.Rd | 4 man/stringdist-metrics.Rd | 4 man/stringdist-package.Rd | 28 ++++ man/stringdist-parallelization.Rd | 4 man/stringdist.Rd | 43 +++---- man/stringsim.Rd |only src/Rstringdist.c |only src/dictionary.h |only src/dist.h |only src/dl.c | 202 +---------------------------------- src/hamming.c | 146 ------------------------- src/jaro.c | 178 +----------------------------- src/lcs.c | 156 --------------------------- src/lv.c | 166 ---------------------------- src/osa.c | 168 ----------------------------- src/qgram.c | 205 ++--------------------------------- src/qtree.h |only src/soundex.c | 169 ----------------------------- src/stringdist.c |only src/stringdist.h |only src/utf8ToInt.c | 37 ------ src/utils.h | 5 tests/testthat/testStringdist.R | 87 ++++++++------- tests/testthat/testStringsim.R |only 39 files changed, 380 insertions(+), 1574 deletions(-)
Title: Arps Decline Curve Analysis in R
Description: Functions for Arps decline-curve analysis on oil and gas data. Includes exponential, hyperbolic, harmonic, and hyperbolic-to-exponential models as well as the preceding with initial curtailment. Functions included for computing rate, cumulative production, instantaneous decline, EUR, time to economic limit, and performing least-squares best fits.
Author: Derrick Turk [aut, cre, cph]
Maintainer: Derrick Turk <dwt@terminusdatascience.com>
Diff between aRpsDCA versions 1.0.0 dated 2014-04-03 and 1.0.1 dated 2015-06-22
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/arps.R | 19 +++++++++++++++---- R/bestfit.R | 2 +- R/curtail.R | 2 +- R/eur.R | 2 +- R/s3.R | 6 +++--- README.md | 8 +++++++- tests/fit_and_plot.R | 2 +- tests/fit_and_plot_from_Np.R | 2 +- 10 files changed, 43 insertions(+), 26 deletions(-)
More information about STMedianPolish at CRAN
Permanent link
Title: Regression Analysis of Proportional Data Using Simplex
Distribution
Description: Simplex density, distribution, quantile functions as well as random variable
generation of the simplex distribution are given. Regression analysis of proportional data
using various kinds of simplex models is available. In addition, GEE method can be applied
to longitudinal data to model the correlation. Residual analysis is also involved. Some
subroutines are written in C with GNU Scientific Library (GSL) so as to facilitate the
computation.
Author: Peng Zhang, Zhengguo Qiu and Chengchun Shi
Maintainer: Peng Zhang <pengz@zju.edu.cn>
Diff between simplexreg versions 1.0 dated 2014-01-31 and 1.1 dated 2015-06-21
DESCRIPTION | 9 +++-- MD5 | 12 +++---- NAMESPACE | 3 + R/simplexgee.R | 18 +++++++---- R/simplexreg.R | 6 +++ src/Makevars | 4 +- src/sim.gee.cpp | 87 ++++++++++++++++++++++++++++---------------------------- 7 files changed, 76 insertions(+), 63 deletions(-)
Title: Interface to the Bird-Watching Dataset Proyecto AVIS
Description: Interface to <http://proyectoavis.com> database.
It provides means to download data filtered by species, order,
family, and several other criteria. Provides also basic functionality to
plot exploratory maps of the datasets.
Author: Javier González Hernández <javigzz@yahoo.es>, Sara Varela <svarela@paleobiogeography.org>
Maintainer: Sara Varela <svarela@paleobiogeography.org>
Diff between rAvis versions 0.1.3 dated 2015-06-18 and 0.1.4 dated 2015-06-21
rAvis-0.1.3/rAvis/tests/testthat |only rAvis-0.1.4/rAvis/DESCRIPTION | 8 +- rAvis-0.1.4/rAvis/MD5 | 40 +++++++------ rAvis-0.1.4/rAvis/R/apiClient.R |only rAvis-0.1.4/rAvis/R/loginFunctions.R | 2 rAvis-0.1.4/rAvis/R/remoteSpeciesDataFunctions.R | 20 +----- rAvis-0.1.4/rAvis/R/remoteUsersDataFunctions.R | 70 +---------------------- rAvis-0.1.4/rAvis/R/searchInterfaceFunctions.R | 41 +++++-------- rAvis-0.1.4/rAvis/tests/apitest |only rAvis-0.1.4/rAvis/tests/test-all.R | 11 ++- rAvis-0.1.4/rAvis/tests/testthat_disabled |only 11 files changed, 62 insertions(+), 130 deletions(-)
Title: Likelihood Inference in Meta-Analysis and Meta-Regression Models
Description: First- and higher-order likelihood inference in
meta-analysis and meta-regression models.
Author: Annamaria Guolo and Cristiano Varin
Maintainer: Cristiano Varin <sammy@unive.it>
Diff between metaLik versions 0.41.0 dated 2014-04-09 and 0.42.0 dated 2015-06-21
metaLik-0.41.0/metaLik/man/profile.metaLik.Rd |only metaLik-0.42.0/metaLik/DESCRIPTION | 11 - metaLik-0.42.0/metaLik/MD5 | 15 +- metaLik-0.42.0/metaLik/NAMESPACE | 2 metaLik-0.42.0/metaLik/NEWS | 6 + metaLik-0.42.0/metaLik/R/metaLik.R | 144 ++++---------------------- metaLik-0.42.0/metaLik/man/metaLik.Rd | 17 --- metaLik-0.42.0/metaLik/man/summary.metaLik.Rd | 4 metaLik-0.42.0/metaLik/man/test.metaLik.Rd | 6 - 9 files changed, 47 insertions(+), 158 deletions(-)
Title: Latent Variable Models
Description: Estimation and simulation of latent variable models.
Author: Klaus K. Holst
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.4.0 dated 2015-02-17 and 1.4.1 dated 2015-06-21
DESCRIPTION | 8 MD5 | 115 ++-- NAMESPACE | 4 NEWS | 3 R/Objective.R | 4 R/addhook.R | 2 R/bootstrap.R | 6 R/coef.R | 280 +++++----- R/confint.R | 5 R/constrain.R | 5 R/covariance.R | 17 R/diagtest.R | 26 R/distribution.R | 8 R/dsort.R | 23 R/estimate.default.R | 61 +- R/estimate.lvm.R | 1287 +++++++++++++++++++++++------------------------ R/estimate.multigroup.R | 4 R/eventTime.R | 17 R/fix.R | 16 R/fplot.R |only R/glmest.R | 2 R/iid.R | 25 R/labels.R | 12 R/measurement.error.R |only R/normal.R | 9 R/onload.R | 14 R/plot.R | 6 R/plot.estimate.R |only R/regression.R | 41 - R/spaghetti.R | 6 R/stack.R | 64 -- R/transform.R | 2 R/utils.R | 3 R/zclick.R | 20 R/zconfband.R | 5 R/zksmooth.R | 32 - R/zplotConf.R | 14 inst/doc/reference.pdf |binary inst/gof1.png |binary inst/lava1.png |binary inst/me1.png |only man/bootstrap.lvm.Rd | 2 man/click.Rd | 16 man/confint.lvmfit.Rd | 4 man/constrain-set.Rd | 5 man/diagtest.Rd | 2 man/dsort.Rd | 4 man/estimate.default.Rd | 11 man/estimate.lvm.Rd | 6 man/eventTime.Rd | 2 man/fplot.Rd |only man/iid.Rd | 8 man/ksmooth2.Rd | 26 man/labels-set.Rd | 8 man/measurement.error.Rd | 14 man/plot.lvm.Rd | 4 man/plotConf.Rd | 5 man/regression-set.Rd | 2 man/spaghetti.Rd | 3 man/stack.estimate.Rd | 3 man/timedep.Rd | 7 61 files changed, 1184 insertions(+), 1094 deletions(-)
Title: An Import Mechanism for R
Description: This is an alternative mechanism for importing
objects from packages. The syntax allows for importing multiple objects
from a package with a single command in an expressive way. The import
package bridges some of the gap between using library (or require) and
direct (single-object) imports. Furthermore the imported objects are not
placed in the current environment. It is also possible to import
objects from stand-alone .R files. For more information, refer to
the package vignette.
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache <stefan@stefanbache.dk>
Diff between import versions 1.0.2 dated 2015-04-09 and 1.1.0 dated 2015-06-21
DESCRIPTION | 12 ++- MD5 | 38 +++++++---- NAMESPACE | 2 NEWS | 9 ++ R/from.R |only R/here.R |only R/import.R | 147 --------------------------------------------- R/into.R |only R/is_script.R |only R/modified.R |only R/scripts.R |only R/suppress_output.R |only R/symbol_as_character.R | 6 - R/zzz.R | 2 README | 84 ++++++------------------- build |only inst |only man/import.Rd | 2 man/importfunctions.Rd | 22 ++++-- man/make_import_call.Rd | 2 man/symbol_as_character.Rd | 2 man/symbol_list.Rd | 2 vignettes |only 23 files changed, 89 insertions(+), 241 deletions(-)
Title: Bootstrap on Classical Biplots and Clustering Disjoint Biplot
Description: A GUI with which the user can construct and interact with Bootstrap methods on Classical Biplots and with Clustering and/or Disjoint Biplot.
Author: Ana Belen Nieto Librero<ananieto@usal.es>, Purificacion Galindo Villardon<pgalindo@usal.es>
Maintainer: Ana Belen Nieto Librero <ananieto@usal.es>
Diff between biplotbootGUI versions 1.0 dated 2013-12-31 and 1.1 dated 2015-06-21
biplotbootGUI-1.0/biplotbootGUI/R/biplotbootGUI-internal.R |only biplotbootGUI-1.1/biplotbootGUI/DESCRIPTION | 22 biplotbootGUI-1.1/biplotbootGUI/MD5 | 13 biplotbootGUI-1.1/biplotbootGUI/NAMESPACE | 19 biplotbootGUI-1.1/biplotbootGUI/R/CDBiplot.R |only biplotbootGUI-1.1/biplotbootGUI/R/biplotboot.R | 6548 +++++------ biplotbootGUI-1.1/biplotbootGUI/man/CDBiplot.Rd |only biplotbootGUI-1.1/biplotbootGUI/man/biplotboot.Rd | 149 biplotbootGUI-1.1/biplotbootGUI/man/biplotbootGUI-package.Rd | 90 9 files changed, 3535 insertions(+), 3306 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-35 dated 2015-05-15 and 0.9-36 dated 2015-06-21
DESCRIPTION | 14 MD5 | 93 +- NAMESPACE | 5 NEWS | 22 R/IORE.solution.R | 4 R/endpoints.R | 2 R/mkinerrmin.R | 6 R/mkinfit.R | 125 ++- R/mkinmod.R | 83 ++ R/mkinpredict.R | 62 + R/transform_odeparms.R | 12 README.md | 96 ++ build/vignette.rds |binary inst/doc/FOCUS_D.R |only inst/doc/FOCUS_D.Rmd |only inst/doc/FOCUS_D.html |only inst/doc/FOCUS_L.html | 330 +++++----- inst/doc/FOCUS_Z.Rnw | 2 inst/doc/FOCUS_Z.pdf |binary inst/doc/compiled_models.R |only inst/doc/compiled_models.Rmd |only inst/doc/compiled_models.html |only inst/doc/mkin.pdf |binary inst/staticdocs/README | 2 man/IORE.solution.Rd | 4 man/mkinfit.Rd | 46 - man/mkinmod.Rd | 25 man/mkinpredict.Rd | 24 man/synthetic_data_for_UBA.Rd | 2 man/transform_odeparms.Rd | 8 tests/testthat.R | 4 tests/testthat/test_FOCUS_D_UBA_expertise.R | 32 tests/testthat/test_FOCUS_chi2_error_level.R | 2 tests/testthat/test_mkinpredict_SFO_SFO.R | 4 tests/testthat/test_schaefer07_complex_case.R | 2 tests/testthat/test_synthetic_data_for_UBA_2014.R | 15 vignettes/FOCUS_D.Rmd |only vignettes/FOCUS_Z.Rnw | 2 vignettes/FOCUS_Z.fdb_latexmk |only vignettes/FOCUS_Z.fls |only vignettes/compiled_models.Rmd |only vignettes/compiled_models_cache/html/benchmark_FOMC_SFO_101fecfdff46216fe1f33d51e3a46470.RData |binary vignettes/compiled_models_cache/html/benchmark_FOMC_SFO_101fecfdff46216fe1f33d51e3a46470.rdb |binary vignettes/compiled_models_cache/html/benchmark_FOMC_SFO_101fecfdff46216fe1f33d51e3a46470.rdx |binary vignettes/compiled_models_cache/html/benchmark_SFO_SFO_c67508532843e0f19735d63034f79cc2.RData |binary vignettes/compiled_models_cache/html/benchmark_SFO_SFO_c67508532843e0f19735d63034f79cc2.rdb |binary vignettes/compiled_models_cache/html/benchmark_SFO_SFO_c67508532843e0f19735d63034f79cc2.rdx |binary vignettes/compiled_models_cache/html/create_SFO_SFO_e1bc636fa6683157ac064f4e09a81368.RData |binary vignettes/compiled_models_cache/html/create_SFO_SFO_e1bc636fa6683157ac064f4e09a81368.rdb |binary vignettes/compiled_models_cache/html/create_SFO_SFO_e1bc636fa6683157ac064f4e09a81368.rdx |binary vignettes/compiled_models_cache/html/unnamed-chunk-2_3dae0ff3076a934b8fe5a08561e07f97.RData |binary vignettes/compiled_models_cache/html/unnamed-chunk-2_3dae0ff3076a934b8fe5a08561e07f97.rdx |binary vignettes/mkin_vignettes.css |only 53 files changed, 684 insertions(+), 344 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut, cre],
Joe Cheng [aut],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between htmlwidgets versions 0.4 dated 2015-05-18 and 0.5 dated 2015-06-21
htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.R |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.Rmd |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.html |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-intro.Rmd |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-intro.html |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-sizing.Rmd |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-sizing.html |only htmlwidgets-0.4/htmlwidgets/vignettes/htmlwidgets-advanced.Rmd |only htmlwidgets-0.4/htmlwidgets/vignettes/htmlwidgets-intro.Rmd |only htmlwidgets-0.4/htmlwidgets/vignettes/htmlwidgets-sizing.Rmd |only htmlwidgets-0.5/htmlwidgets/DESCRIPTION | 12 ++- htmlwidgets-0.5/htmlwidgets/MD5 | 35 +++++----- htmlwidgets-0.5/htmlwidgets/NEWS | 15 ++++ htmlwidgets-0.5/htmlwidgets/R/htmlwidgets.R | 13 ++- htmlwidgets-0.5/htmlwidgets/R/savewidget.R | 5 - htmlwidgets-0.5/htmlwidgets/build/vignette.rds |binary htmlwidgets-0.5/htmlwidgets/inst/doc/develop_advanced.R |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_advanced.Rmd |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_advanced.html |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_intro.R |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_intro.Rmd |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_intro.html |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_sizing.Rmd |only htmlwidgets-0.5/htmlwidgets/inst/doc/develop_sizing.html |only htmlwidgets-0.5/htmlwidgets/inst/www/htmlwidgets.js | 23 ++++-- htmlwidgets-0.5/htmlwidgets/man/saveWidget.Rd | 7 +- htmlwidgets-0.5/htmlwidgets/vignettes/develop_advanced.Rmd |only htmlwidgets-0.5/htmlwidgets/vignettes/develop_intro.Rmd |only htmlwidgets-0.5/htmlwidgets/vignettes/develop_sizing.Rmd |only 29 files changed, 74 insertions(+), 36 deletions(-)
Title: A Convex Formulation for Modeling Interactions with Strong
Heredity
Description: Fits penalized linear and logistic regression models with pairwise interaction terms.
Author: Asad Haris
Maintainer: Asad Haris <aharis@uw.edu>
Diff between FAMILY versions 0.1.18 dated 2014-11-04 and 0.1.19 dated 2015-06-21
FAMILY-0.1.18/FAMILY/R/ADMM_0.1.17.R |only FAMILY-0.1.19/FAMILY/DESCRIPTION | 8 ++++---- FAMILY-0.1.19/FAMILY/MD5 | 12 ++++++------ FAMILY-0.1.19/FAMILY/NAMESPACE | 2 +- FAMILY-0.1.19/FAMILY/R/ADMM_0.1.19.R |only FAMILY-0.1.19/FAMILY/R/ef_1.R | 13 +++++++++++++ FAMILY-0.1.19/FAMILY/man/FAMILY-package.Rd | 6 +++--- FAMILY-0.1.19/FAMILY/man/FAMILY.Rd | 18 ++++++++++-------- 8 files changed, 37 insertions(+), 22 deletions(-)
Title: Canonical Non-Symmetrical Correspondence Analysis in R
Description: A GUI with which users can construct and interact
with Canonical Correspondence Analysis and Canonical Non-Symmetrical Correspondence Analysis and provides inferential results by using Bootstrap Methods.
Author: Ana Belen Nieto Librero <ananieto@usal.es>, Priscila Willems
<pwillems@bariloche.inta.gov.ar>, Purificacion Galindo
Villardon <pgalindo@usal.es>
Maintainer: Ana Belen Nieto Librero <ananieto@usal.es>
Diff between cncaGUI versions 0.0-2 dated 2012-07-18 and 1.0 dated 2015-06-21
cncaGUI-0.0-2/cncaGUI/ChangeLog |only cncaGUI-0.0-2/cncaGUI/cncaGUI-Ex.R |only cncaGUI-1.0/cncaGUI/DESCRIPTION | 22 cncaGUI-1.0/cncaGUI/MD5 | 16 cncaGUI-1.0/cncaGUI/NAMESPACE | 34 cncaGUI-1.0/cncaGUI/R/cnca.R | 6462 +++++++++++++++++++---------- cncaGUI-1.0/cncaGUI/man/cnca.Rd | 183 cncaGUI-1.0/cncaGUI/man/cncaGUI-package.Rd | 59 cncaGUI-1.0/cncaGUI/man/especies.Rd | 43 cncaGUI-1.0/cncaGUI/man/variables.Rd | 40 10 files changed, 4626 insertions(+), 2233 deletions(-)
Title: Miscellaneous Data Management Tools
Description: Collection of several utility functions (especially intended for
people coming from other statistical software packages like 'SPSS',
and/or who are new to R), supporting following common tasks:
1) Reading and writing data between R and other statistical software packages
like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy
ways to get and set label attributes, to convert labelled vectors into
factors (and vice versa) etc.
2) Data transformation tasks like recoding, dichotomizing or
grouping variables, setting and replacing missing values.
3) Convenient functions to perform frequently used statistical tests,
or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.0.2 dated 2015-05-17 and 1.0.3 dated 2015-06-20
sjmisc-1.0.2/sjmisc/data/efc2.RData |only sjmisc-1.0.2/sjmisc/data/efc3.RData |only sjmisc-1.0.2/sjmisc/man/efc2.Rd |only sjmisc-1.0.2/sjmisc/man/efc3.Rd |only sjmisc-1.0.3/sjmisc/DESCRIPTION | 20 sjmisc-1.0.3/sjmisc/MD5 | 107 - sjmisc-1.0.3/sjmisc/NAMESPACE | 7 sjmisc-1.0.3/sjmisc/NEWS | 133 - sjmisc-1.0.3/sjmisc/R/efc.R | 117 - sjmisc-1.0.3/sjmisc/R/helpfunctions.R | 234 +- sjmisc-1.0.3/sjmisc/R/sjImportSPSS.R | 2635 ++++++++++++++++------------- sjmisc-1.0.3/sjmisc/R/sjRecode.R | 541 ++++- sjmisc-1.0.3/sjmisc/R/sjStatistics.R | 2711 +++++++++++++++--------------- sjmisc-1.0.3/sjmisc/README.md | 45 sjmisc-1.0.3/sjmisc/inst/CITATION | 18 sjmisc-1.0.3/sjmisc/man/add_labels.Rd |only sjmisc-1.0.3/sjmisc/man/chisq_gof.Rd | 2 sjmisc-1.0.3/sjmisc/man/cod.Rd | 12 sjmisc-1.0.3/sjmisc/man/cramer.Rd | 2 sjmisc-1.0.3/sjmisc/man/cronb.Rd | 6 sjmisc-1.0.3/sjmisc/man/cv.Rd | 2 sjmisc-1.0.3/sjmisc/man/dicho.Rd | 49 sjmisc-1.0.3/sjmisc/man/efc.Rd | 11 sjmisc-1.0.3/sjmisc/man/eta_sq.Rd | 4 sjmisc-1.0.3/sjmisc/man/get_val_labels.Rd | 63 sjmisc-1.0.3/sjmisc/man/get_values.Rd |only sjmisc-1.0.3/sjmisc/man/get_var_labels.Rd | 30 sjmisc-1.0.3/sjmisc/man/group_labels.Rd | 48 sjmisc-1.0.3/sjmisc/man/group_str.Rd | 11 sjmisc-1.0.3/sjmisc/man/group_var.Rd | 59 sjmisc-1.0.3/sjmisc/man/hoslem_gof.Rd | 11 sjmisc-1.0.3/sjmisc/man/icc.Rd | 2 sjmisc-1.0.3/sjmisc/man/is_empty.Rd |only sjmisc-1.0.3/sjmisc/man/is_even.Rd |only sjmisc-1.0.3/sjmisc/man/is_odd.Rd |only sjmisc-1.0.3/sjmisc/man/mean_n.Rd | 144 - sjmisc-1.0.3/sjmisc/man/mic.Rd | 9 sjmisc-1.0.3/sjmisc/man/mwu.Rd | 2 sjmisc-1.0.3/sjmisc/man/phi.Rd | 4 sjmisc-1.0.3/sjmisc/man/pseudo_r2.Rd | 10 sjmisc-1.0.3/sjmisc/man/read_spss.Rd | 3 sjmisc-1.0.3/sjmisc/man/rec.Rd | 63 sjmisc-1.0.3/sjmisc/man/recode_to.Rd | 21 sjmisc-1.0.3/sjmisc/man/reliab_test.Rd | 2 sjmisc-1.0.3/sjmisc/man/remove_labels.Rd |only sjmisc-1.0.3/sjmisc/man/replace_na.Rd |only sjmisc-1.0.3/sjmisc/man/rmse.Rd | 2 sjmisc-1.0.3/sjmisc/man/set_na.Rd | 26 sjmisc-1.0.3/sjmisc/man/set_val_labels.Rd | 53 sjmisc-1.0.3/sjmisc/man/set_var_labels.Rd | 55 sjmisc-1.0.3/sjmisc/man/sjmisc-package.Rd | 17 sjmisc-1.0.3/sjmisc/man/std_beta.Rd | 2 sjmisc-1.0.3/sjmisc/man/std_e.Rd | 2 sjmisc-1.0.3/sjmisc/man/str_pos.Rd | 2 sjmisc-1.0.3/sjmisc/man/table_values.Rd | 2 sjmisc-1.0.3/sjmisc/man/to_fac.Rd | 2 sjmisc-1.0.3/sjmisc/man/to_label.Rd | 2 sjmisc-1.0.3/sjmisc/man/to_value.Rd | 7 sjmisc-1.0.3/sjmisc/man/trim.Rd | 4 sjmisc-1.0.3/sjmisc/man/word_wrap.Rd | 7 60 files changed, 4039 insertions(+), 3282 deletions(-)
Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre],
Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>
Diff between rDEA versions 1.1-1 dated 2015-03-27 and 1.2-1 dated 2015-06-20
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/dea.env.robust.R | 16 ++++++++++++++-- R/dea.robust.R | 32 ++++++++++++++++++++++++++------ R/rts.test.R | 27 +++++++++++++-------------- README.md | 6 +++++- inst/CHANGELOG | 5 +++++ man/dea.Rd | 2 ++ man/dea_env_robust.Rd | 2 +- man/rts_test.Rd | 25 ++++++++++++++++++++----- src/tags |only 11 files changed, 99 insertions(+), 41 deletions(-)
Title: Methods that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.14.0 dated 2015-02-13 and 0.14.1 dated 2015-06-20
DESCRIPTION | 16 +- MD5 | 162 ++++++++++++------------- NEWS | 35 +++++ R/anyMissing.R | 7 - R/binCounts.R | 2 R/binMeans.R | 2 R/rowAvgsPerColSet.R | 4 R/rowCounts.R | 36 ++++- R/rowIQRs.R | 16 +- R/rowMads.R | 7 - R/rowQuantiles.R | 30 ++-- R/rowRanks.R | 2 R/rowWeightedMeans.R | 13 +- R/rowWeightedMedians.R | 10 - R/weightedMean.R | 15 ++ build/vignette.rds |binary inst/benchmarking/anyMissing.md.rsp | 2 inst/benchmarking/colRowAlls.md.rsp | 1 inst/benchmarking/colRowAnyMissings.md.rsp | 1 inst/benchmarking/colRowAnys.md.rsp | 1 inst/benchmarking/colRowCounts.md.rsp | 1 inst/benchmarking/colRowCummins.md.rsp | 1 inst/benchmarking/colRowCumprods.md.rsp | 1 inst/benchmarking/colRowCumsums.md.rsp | 1 inst/benchmarking/colRowDiffs.md.rsp | 1 inst/benchmarking/colRowLogSumExps.md.rsp | 1 inst/benchmarking/colRowMads.md.rsp | 1 inst/benchmarking/colRowMeans.md.rsp | 1 inst/benchmarking/colRowMedians.md.rsp | 1 inst/benchmarking/colRowMins.md.rsp | 1 inst/benchmarking/colRowOrderStats.md.rsp | 1 inst/benchmarking/colRowProds.md.rsp | 1 inst/benchmarking/colRowQuantiles.md.rsp | 1 inst/benchmarking/colRowRanges.md.rsp | 1 inst/benchmarking/colRowRanks.md.rsp | 1 inst/benchmarking/colRowSums.md.rsp | 1 inst/benchmarking/colRowTabulates.md.rsp | 1 inst/benchmarking/colRowVars.md.rsp | 1 inst/benchmarking/colRowWeightedMeans.md.rsp | 1 inst/benchmarking/colRowWeightedMedians.md.rsp | 1 inst/benchmarking/includes/results.md.rsp | 22 ++- inst/doc/matrixStats-methods.html | 4 man/binCounts.Rd | 2 man/binMeans.Rd | 2 man/matrixStats-package.Rd | 5 man/weightedMean.Rd | 15 ++ man/weightedMedian.Rd | 2 src/binCounts.c | 9 + src/binMeans.c | 5 src/logSumExp_internal.c | 18 +- src/productExpSumLog_TYPE-template.h | 7 - src/rowCounts_TYPE-template.h | 7 - src/rowCumMinMaxs_TYPE-template.h | 2 src/rowCumprods_TYPE-template.h | 50 ++++--- src/rowCumsums_TYPE-template.h | 2 src/weightedMean_TYPE-template.h | 9 - src/x_OP_y_TYPE-template.h | 35 ++++- tests/anyMissing.R | 30 ++-- tests/benchmark.R | 16 +- tests/binCounts.R | 42 ++++++ tests/binMeans,binCounts.R | 18 ++ tests/logSumExp.R | 43 ++++++ tests/meanOver.R | 4 tests/product.R | 9 + tests/psortKM.R | 6 tests/rowAllAnys.R | 95 ++++++++++---- tests/rowCounts.R | 7 + tests/rowCumMinMaxs.R | 93 ++++++++++---- tests/rowCumprods.R | 75 ++++++++++- tests/rowCumsums.R | 68 ++++++++-- tests/rowIQRs.R | 12 + tests/rowLogSumExps.R | 4 tests/rowMedians.R | 7 - tests/rowOrderStats.R | 18 +- tests/rowProds.R | 6 tests/rowQuantiles.R | 30 +++- tests/rowRanks.R | 13 +- tests/rowWeightedMedians.R | 9 + tests/sumOver.R | 4 tests/varDiff_etal.R | 12 - tests/weightedMean.R | 27 ++++ tests/x_OP_y.R | 32 ++++ 82 files changed, 909 insertions(+), 349 deletions(-)
Title: Bayesian Output Analysis Program (BOA) for MCMC
Description: A menu-driven program and library of functions for carrying out
convergence diagnostics and statistical and graphical analysis of Markov
chain Monte Carlo sampling output.
Author: Brian J. Smith
Maintainer: Brian J. Smith <brian-j-smith@uiowa.edu>
Diff between boa versions 1.1.7-2 dated 2008-05-02 and 1.1.8-1 dated 2015-06-20
boa-1.1.7-2/boa/data/line.R |only boa-1.1.7-2/boa/doc |only boa-1.1.7-2/boa/man/boa |only boa-1.1.8-1/boa/DESCRIPTION | 29 ++++++++++++++++------------- boa-1.1.8-1/boa/MD5 |only boa-1.1.8-1/boa/R/boa.chain.add.R | 3 ++- boa-1.1.8-1/boa/R/boa.core.R | 2 +- boa-1.1.8-1/boa/R/boa.handw.R | 4 +--- boa-1.1.8-1/boa/R/boa.menu.parms.R | 2 +- boa-1.1.8-1/boa/R/boa.randl.R | 4 ++-- boa-1.1.8-1/boa/data/line.rda |only boa-1.1.8-1/boa/man/boa.menu.Rd | 7 +++++++ boa-1.1.8-1/boa/man/boa.plot.geweke.Rd | 4 +++- boa-1.1.8-1/boa/man/boa.print.randl.Rd | 3 ++- 14 files changed, 35 insertions(+), 23 deletions(-)
Title: Translate Spreadsheet Cell Ranges to Rows and Columns
Description: Helper functions to work with spreadsheets and the "A1:D10" style
of cell range specification.
Author: Jennifer Bryan [cre, aut],
Hadley Wickham [ctb]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>
Diff between cellranger versions 0.1.0 dated 2015-04-22 and 1.0.0 dated 2015-06-20
DESCRIPTION | 10 +-- MD5 | 26 +++---- NAMESPACE | 1 R/anchor.R | 47 +++++++++----- R/cell-limits.R | 89 ++++++++++++++++----------- R/cell-rows-cell-cols.R | 28 ++++---- R/utils.R | 3 README.md | 56 ++++++++++------- man/anchored.Rd | 26 ++++--- man/as.range.Rd | 2 man/cell_cols.Rd | 10 +-- man/cell_limits.Rd | 50 ++++++++------- man/cell_rows.Rd | 14 ++-- tests/testthat/test-cell-specification.R | 101 ++++++++++++++++++++----------- 14 files changed, 275 insertions(+), 188 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-04 0.3
2014-05-12 0.2
2013-11-22 0.1
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)),
Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see
Jiang, Manchanda, Rossi 2009)
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric
Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.0-1 dated 2015-06-15 and 3.0-2 dated 2015-06-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/lndIWishart_rcpp.cpp | 2 +- src/lndMvst_rcpp.cpp | 2 +- src/rscaleUsage_rcpp_loop.cpp | 4 ++-- src/utilityFunctions.cpp | 6 +++--- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.1.0 dated 2015-04-28 and 1.2.0 dated 2015-06-19
urltools-1.1.0/urltools/man/query.Rd |only urltools-1.2.0/urltools/DESCRIPTION | 11 +-- urltools-1.2.0/urltools/MD5 | 57 +++++++++-------- urltools-1.2.0/urltools/NAMESPACE | 6 + urltools-1.2.0/urltools/NEWS | 29 ++++++++ urltools-1.2.0/urltools/R/RcppExports.R | 35 ++++++++-- urltools-1.2.0/urltools/R/accessors.R | 52 +++++++++++---- urltools-1.2.0/urltools/R/suffix.R |only urltools-1.2.0/urltools/README.md | 22 +++--- urltools-1.2.0/urltools/data |only urltools-1.2.0/urltools/inst/doc/urltools.R | 19 +++++ urltools-1.2.0/urltools/inst/doc/urltools.Rmd | 41 +++++++++--- urltools-1.2.0/urltools/inst/doc/urltools.html | 40 +++++++++-- urltools-1.2.0/urltools/man/domain.Rd | 4 + urltools-1.2.0/urltools/man/fragment.Rd | 8 +- urltools-1.2.0/urltools/man/parameters.Rd |only urltools-1.2.0/urltools/man/path.Rd | 6 + urltools-1.2.0/urltools/man/port.Rd | 6 + urltools-1.2.0/urltools/man/scheme.Rd | 4 + urltools-1.2.0/urltools/man/suffix_dataset.Rd |only urltools-1.2.0/urltools/man/suffix_extract.Rd |only urltools-1.2.0/urltools/man/suffix_refresh.Rd |only urltools-1.2.0/urltools/man/url_compose.Rd |only urltools-1.2.0/urltools/man/url_parse.Rd | 11 +-- urltools-1.2.0/urltools/src/RcppExports.cpp | 11 +++ urltools-1.2.0/urltools/src/compose.cpp |only urltools-1.2.0/urltools/src/compose.h |only urltools-1.2.0/urltools/src/parsing.cpp | 24 +++---- urltools-1.2.0/urltools/src/parsing.h | 13 --- urltools-1.2.0/urltools/src/urltools.cpp | 52 ++++++++++++--- urltools-1.2.0/urltools/tests/testthat/test_encoding.R | 4 - urltools-1.2.0/urltools/tests/testthat/test_get_set.R | 6 - urltools-1.2.0/urltools/tests/testthat/test_parsing.R | 20 +++++ urltools-1.2.0/urltools/tests/testthat/test_suffixes.R |only urltools-1.2.0/urltools/vignettes/urltools.Rmd | 41 +++++++++--- 35 files changed, 386 insertions(+), 136 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes for performing exact sequential analysis. These calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. For group sequential analyses, the group sizes do not have to be specified in advance and, for binomial data, the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 2.0 dated 2015-06-06 and 2.0.1 dated 2015-06-19
DESCRIPTION | 10 ++++----- MD5 | 10 ++++----- R/CV.Poisson.R | 9 ++------ man/SampleSize.Binomial.Rd | 24 ++++++++++++---------- man/SampleSize.Poisson.Rd | 48 +++++++++++++++++++++++++++++---------------- man/Sequential-package.Rd | 35 ++++++++++++++++++-------------- 6 files changed, 77 insertions(+), 59 deletions(-)
Title: R MTC Jags Rcmdr Plugin
Description: Mixed Treatment Comparison is a methodology to compare directly and/or indirectly health strategies (drugs, treatments, devices). This package provides an Rcmdr "plug-in" to perform Mixed Treatment Comparison for binary outcome using BUGS code from Bristol University (Lu and Ades).
Author: Marcelo Goulart Correia <mgoulart.inc@gmail.com>
Maintainer: Marcelo Goulart Correia <mgoulart.inc@gmail.com>
Diff between RcmdrPlugin.RMTCJags versions 1.0 dated 2014-12-17 and 1.0-1 dated 2015-06-19
DESCRIPTION | 14 ++++---- MD5 | 17 +++++----- NAMESPACE | 2 - R/RcmdrPlugin.RMTCJags.R | 59 +++++++++++++---------------------- R/globals.R | 2 - inst/CHANGES | 6 +++ man/RcmdrPlugin.RMTCJags-internal.Rd | 7 ---- man/RcmdrPlugin.RMTCJags-package.Rd | 35 +++++++++----------- man/database.Rd | 38 +++++++++++----------- tests |only 10 files changed, 83 insertions(+), 97 deletions(-)
More information about RcmdrPlugin.RMTCJags at CRAN
Permanent link
Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the
language at a deeper level.
Author: Hadley Wickham [aut, cre],
R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pryr versions 0.1.1 dated 2015-05-26 and 0.1.2 dated 2015-06-19
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++++------- NAMESPACE | 1 + R/active.r |only R/assign-active.r | 2 +- R/inspect.r | 9 +++++++-- R/s3.r | 2 +- README.md | 1 + man/is_active_binding.Rd |only man/track_copy.Rd | 2 ++ tests/testthat/test-active-binding.r |only tests/testthat/test-track-copy.R |only 12 files changed, 27 insertions(+), 14 deletions(-)
Title: Orthogonal Array Package
Description: Interface to D-optimal design generation code of the Orthogonal Array package. Can generate D-optimal designs with specified number of runs and factors. The optimality of the designs is defined in terms of a user specified optimization function based on the D-efficiency and Ds-efficiency.
Author: Pieter Thijs Eendebak
Maintainer: Pieter Thijs Eendebak <pieter.eendebak@gmail.com>
Diff between oapackage versions 2.0.20 dated 2015-06-18 and 2.0.22 dated 2015-06-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/Deff.cpp | 2 +- src/mathtools.h | 41 ++++++++++++++++++----------------------- 4 files changed, 27 insertions(+), 32 deletions(-)
Title: Latent Position and Cluster Models for Statistical Networks
Description: Fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between latentnet versions 2.7.0 dated 2015-03-22 and 2.7.1 dated 2015-06-19
latentnet-2.7.0/latentnet/tests/examples.R |only latentnet-2.7.1/latentnet/ChangeLog | 8 ++++++++ latentnet-2.7.1/latentnet/DESCRIPTION | 8 ++++---- latentnet-2.7.1/latentnet/LICENSE | 8 -------- latentnet-2.7.1/latentnet/MD5 | 19 +++++++++---------- latentnet-2.7.1/latentnet/R/simulate.ergmm.R | 2 +- latentnet-2.7.1/latentnet/R/summary.ergmm.R | 4 ++-- latentnet-2.7.1/latentnet/R/zzz.R | 2 +- latentnet-2.7.1/latentnet/man/summary.ergmm.Rd | 10 +++++----- latentnet-2.7.1/latentnet/tests/normal.R | 3 +++ latentnet-2.7.1/latentnet/tests/onlymcmc.R | 5 +++++ 11 files changed, 38 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-30 0.9.9.20121030
2011-04-25 0.9.9.20110424
2010-05-23 0.9.9.20100522
Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data.
It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm).
Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom.
Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between MVR versions 1.20.0 dated 2013-11-13 and 1.30.1 dated 2015-06-19
MVR-1.20.0/MVR/R/MVR.news.r |only MVR-1.20.0/MVR/R/zzz.r |only MVR-1.20.0/MVR/man/MeanVarReg.Rd |only MVR-1.20.0/MVR/man/is.empty.Rd |only MVR-1.20.0/MVR/man/is.valid.Rd |only MVR-1.20.0/MVR/man/km.clustering.Rd |only MVR-1.20.0/MVR/man/merging.cluster.Rd |only MVR-1.20.0/MVR/man/mvrt.Rd |only MVR-1.20.0/MVR/man/pooled.mean.Rd |only MVR-1.20.0/MVR/man/pooled.sd.Rd |only MVR-1.20.0/MVR/man/sim.dis.Rd |only MVR-1.20.0/MVR/man/withinsumsq.Rd |only MVR-1.20.0/MVR/src/MVRc.c |only MVR-1.30.1/MVR/DESCRIPTION | 34 MVR-1.30.1/MVR/MD5 | 49 MVR-1.30.1/MVR/NAMESPACE | 6 MVR-1.30.1/MVR/R/MVRr.internal.r |only MVR-1.30.1/MVR/R/MVRr.r | 2204 ++++++++----------------- MVR-1.30.1/MVR/data/Real.rda |binary MVR-1.30.1/MVR/data/Synthetic.rda |binary MVR-1.30.1/MVR/inst/CITATION | 32 MVR-1.30.1/MVR/inst/NEWS | 13 MVR-1.30.1/MVR/man/MVR-package.Rd | 59 MVR-1.30.1/MVR/man/MVR.news.Rd | 3 MVR-1.30.1/MVR/man/Synthetic-data.Rd | 6 MVR-1.30.1/MVR/man/cluster.diagnostic.Rd | 210 +- MVR-1.30.1/MVR/man/mvr.Rd | 296 +-- MVR-1.30.1/MVR/man/mvrt.test.Rd | 219 +- MVR-1.30.1/MVR/man/normalization.diagnostic.Rd | 196 +- MVR-1.30.1/MVR/man/stabilization.diagnostic.Rd | 208 +- MVR-1.30.1/MVR/man/target.diagnostic.Rd | 195 +- MVR-1.30.1/MVR/src/MVRc.cpp |only MVR-1.30.1/MVR/src/MVRc.h | 10 33 files changed, 1635 insertions(+), 2105 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.2 dated 2015-06-18 and 0.2.1 dated 2015-06-19
DESCRIPTION | 8 ++-- MD5 | 14 +++---- inst/doc/References.pdf |binary inst/doc/hsdar-intro.Rnw | 46 +++++++++++-------------- inst/doc/hsdar-intro.pdf |binary src/unmix.c | 3 + vignettes/hsdar-intro.Rnw | 46 +++++++++++-------------- vignettes/hsdar-intro.tex | 82 +++++++++++++++++++++++----------------------- 8 files changed, 96 insertions(+), 103 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-24 dated 2015-06-19 and 1.0-25 dated 2015-06-19
gstat-1.0-24/gstat/src/xxx |only gstat-1.0-25/gstat/DESCRIPTION | 8 ++++---- gstat-1.0-25/gstat/MD5 | 13 ++++++------- gstat-1.0-25/gstat/inst/doc/gstat.pdf |binary gstat-1.0-25/gstat/inst/doc/prs.pdf |binary gstat-1.0-25/gstat/inst/doc/spatio-temporal-kriging.pdf |binary gstat-1.0-25/gstat/inst/doc/st.pdf |binary gstat-1.0-25/gstat/src/matrix.h | 4 +++- 8 files changed, 13 insertions(+), 12 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.0.1 dated 2015-03-16 and 4.0.6 dated 2015-06-19
ChemoSpec-4.0.1/ChemoSpec/R/loopThruSpectra.R |only ChemoSpec-4.0.1/ChemoSpec/man/loopThruSpectra.Rd |only ChemoSpec-4.0.6/ChemoSpec/DESCRIPTION | 10 - ChemoSpec-4.0.6/ChemoSpec/MD5 | 47 +++--- ChemoSpec-4.0.6/ChemoSpec/NAMESPACE | 2 ChemoSpec-4.0.6/ChemoSpec/NEWS | 26 +++ ChemoSpec-4.0.6/ChemoSpec/R/LoopThruSpectra.R |only ChemoSpec-4.0.6/ChemoSpec/R/corSpectra.R | 23 +-- ChemoSpec-4.0.6/ChemoSpec/R/covSpectra.R | 51 ++++--- ChemoSpec-4.0.6/ChemoSpec/R/covSpectraJS.R |only ChemoSpec-4.0.6/ChemoSpec/R/getMaxCovByFreq.R | 22 ++- ChemoSpec-4.0.6/ChemoSpec/R/hmapSpectra.R | 18 -- ChemoSpec-4.0.6/ChemoSpec/R/plotSpectraJS.R | 4 ChemoSpec-4.0.6/ChemoSpec/R/surveySpectra2.R |only ChemoSpec-4.0.6/ChemoSpec/build/vignette.rds |binary ChemoSpec-4.0.6/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS.css |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS_brushNguides.js |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS_controls.js |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS_globals.js |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS_main.js |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/cS_spectra.js |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/covSpectraJS.html |only ChemoSpec-4.0.6/ChemoSpec/inst/extdata/pS_brushNguides.js | 101 +++++++------- ChemoSpec-4.0.6/ChemoSpec/inst/extdata/pS_globals.js | 4 ChemoSpec-4.0.6/ChemoSpec/man/ChemoSpec-package.Rd | 7 ChemoSpec-4.0.6/ChemoSpec/man/LoopThruSpectra.Rd |only ChemoSpec-4.0.6/ChemoSpec/man/corSpectra.Rd | 50 +++++- ChemoSpec-4.0.6/ChemoSpec/man/getMaxCovByFreq.Rd | 8 - ChemoSpec-4.0.6/ChemoSpec/man/hmapSpectra.Rd | 19 -- ChemoSpec-4.0.6/ChemoSpec/man/surveySpectra.Rd | 17 ++ 31 files changed, 260 insertions(+), 149 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-03 1.1
2013-02-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-07 1.0.01
2011-01-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-01-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-10-22 1.5
2006-07-24 1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-06 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-09-03 0.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-10 1.2
2007-10-22 1.1
2005-08-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-20 0.0-3
2011-01-06 0.0-2
2010-11-13 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-18 0.1-0
Title: Multibiplot Analysis in R
Description: A GUI with which users can construct and interact
with Multibiplot Analysis and provides inferential results by using Bootstrap Methods.
Author: Ana Belen Nieto Librero <ananieto@usal.es>, Nora Baccala
<norabaccala@gmail.com>, Purificacion Vicente Galindo
<purivg@usal.es>, Purificacion Galindo Villardon
<pgalindo@usal.es>
Maintainer: Ana Belen Nieto Librero <ananieto@usal.es>
Diff between multibiplotGUI versions 0.0-1 dated 2011-01-25 and 1.0 dated 2015-06-19
multibiplotGUI-0.0-1/multibiplotGUI/inst |only multibiplotGUI-0.0-1/multibiplotGUI/po |only multibiplotGUI-1.0/multibiplotGUI/DESCRIPTION | 19 multibiplotGUI-1.0/multibiplotGUI/MD5 | 12 multibiplotGUI-1.0/multibiplotGUI/NAMESPACE | 30 multibiplotGUI-1.0/multibiplotGUI/R/multibiplot.R | 5093 +++++++--- multibiplotGUI-1.0/multibiplotGUI/man/multibiplot.Rd | 141 multibiplotGUI-1.0/multibiplotGUI/man/multibiplotGUI-package.Rd | 68 8 files changed, 3857 insertions(+), 1506 deletions(-)
More information about multibiplotGUI at CRAN
Permanent link
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.8 dated 2015-06-06 and 0.9 dated 2015-06-19
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/handle.R | 7 +++++-- configure | 2 +- src/callbacks.c | 2 +- src/curl.c | 2 +- src/download.c | 4 ++-- src/fetch.c | 4 ++-- src/form.c | 4 ++-- src/handle.c | 2 +- tests/testthat/test-handle.R | 12 ++++++++++++ 12 files changed, 47 insertions(+), 27 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-15 3.1
2010-03-13 3.0
2009-03-01 2.1
2009-02-03 1.1
2009-01-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-05-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-15 1.15
2011-10-17 1.0-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-19 1.2
2009-07-30 1.1
2009-07-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-06-16 1.4.1
2009-05-06 1.4
2009-04-16 1.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-10 1.0.1
2011-08-29 0.20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-09 1.0
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical VAR model in combination with LASSO and EBIC.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.1.2 dated 2015-03-12 and 0.1.3 dated 2015-06-19
DESCRIPTION | 7 +--- MD5 | 7 ++-- NEWS |only R/graphicalVAR.R | 2 - src/RcppExports.cpp | 82 ++++++++++++++++++++-------------------------------- 5 files changed, 41 insertions(+), 57 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.count versions 3.1.1 dated 2013-11-28 and 3.2.0 dated 2015-06-19
ergm.count-3.1.1/ergm.count/tests/examples.R |only ergm.count-3.2.0/ergm.count/DESCRIPTION | 14 ++-- ergm.count-3.2.0/ergm.count/LICENSE | 2 ergm.count-3.2.0/ergm.count/MD5 | 38 +++++------ ergm.count-3.2.0/ergm.count/R/InitReference.R | 9 -- ergm.count-3.2.0/ergm.count/R/InitWtErgmTerm.R | 11 --- ergm.count-3.2.0/ergm.count/R/InitWtMHP.R | 19 +++-- ergm.count-3.2.0/ergm.count/R/zzz.R | 22 ++---- ergm.count-3.2.0/ergm.count/inst/CITATION | 43 ++++++++++++ ergm.count-3.2.0/ergm.count/inst/NEWS.Rd | 44 ++++++++----- ergm.count-3.2.0/ergm.count/man/ergm-references.Rd | 53 +++++++++------ ergm.count-3.2.0/ergm.count/man/ergm-terms.Rd | 21 ++---- ergm.count-3.2.0/ergm.count/man/ergm.count-package.Rd | 9 -- ergm.count-3.2.0/ergm.count/man/zach.Rd | 22 ++---- ergm.count-3.2.0/ergm.count/src/include_stubs.c | 9 -- ergm.count-3.2.0/ergm.count/src/wtMHproposals.c | 60 +++++++++++++++--- ergm.count-3.2.0/ergm.count/src/wtMHproposals.h | 9 -- ergm.count-3.2.0/ergm.count/src/wtchangestats.c | 15 ---- ergm.count-3.2.0/ergm.count/src/wtchangestats.h | 55 ---------------- ergm.count-3.2.0/ergm.count/tests/valued_fit.R |only ergm.count-3.2.0/ergm.count/tests/valued_sim.R | 19 ++--- 21 files changed, 227 insertions(+), 247 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.5.3 dated 2015-05-13 and 1.6.0 dated 2015-06-19
DESCRIPTION | 11 ++-- MD5 | 97 ++++++++++++++++++++++--------------------- NEWS | 10 +++- R/assert.r | 48 ++++++++++++++------- R/checkDataFrame.r | 4 - R/checkMatrix.r | 2 R/checkNamed.r | 1 R/checkNames.r | 1 R/checkSubset.r | 1 R/checkVector.r | 1 R/qassert.r | 3 - build |only inst |only man/assert.Rd | 14 +++--- man/checkAtomic.Rd | 3 - man/checkCharacter.Rd | 3 - man/checkComplex.Rd | 3 - man/checkDataFrame.Rd | 10 ++-- man/checkFactor.Rd | 3 - man/checkInteger.Rd | 3 - man/checkIntegerish.Rd | 3 - man/checkList.Rd | 3 - man/checkLogical.Rd | 3 - man/checkMatrix.Rd | 6 +- man/checkNamed.Rd | 3 - man/checkNames.Rd | 3 - man/checkNumeric.Rd | 3 - man/checkSubset.Rd | 1 man/checkVector.Rd | 3 - man/qassert.Rd | 3 - src/all_missing.c | 20 ++++---- src/all_missing.h | 1 src/all_nchar.c | 8 +-- src/all_nchar.h | 3 - src/any_infinite.c | 8 +-- src/any_infinite.h | 1 src/any_missing.c | 20 ++++---- src/any_missing.h | 1 src/checks.c | 62 +++++++++++++-------------- src/checks.h | 1 src/cmessages.h | 1 src/helper.c | 10 ++-- src/helper.h | 3 - src/is_integerish.h | 1 src/qassert.c | 30 ++++++------- src/qassert.h | 1 src/which_first.c | 8 +-- src/which_first.h | 1 tests/testthat/test_assert.r | 13 +++++ vignettes |only 50 files changed, 262 insertions(+), 180 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-23 dated 2015-06-05 and 1.0-24 dated 2015-06-19
DESCRIPTION | 8 ++-- MD5 | 61 ++++++++++++++++----------------- demo/stkrige.R | 4 +- inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.R | 64 ++++++++++++++++++----------------- inst/doc/st.Rnw | 4 +- inst/doc/st.pdf |binary man/krigeST.Rd | 3 + man/vv.Rd | 2 + src/chfactor.c | 6 +-- src/copy.c | 10 ++--- src/hsehldr.c | 10 ++--- src/init.c | 2 - src/ivecop.c | 10 ++--- src/lm.c | 4 +- src/lufactor.c | 2 - src/matop.c | 12 +++--- src/matrix.h | 30 ++++++++-------- src/matrix2.h | 14 +++---- src/memory.c | 14 +++---- src/pxop.c | 10 ++--- src/qrfactor.c | 10 ++--- src/solve.c | 10 ++--- src/submat.c | 20 +++++----- src/vario.c | 2 - src/vecop.c | 12 +++--- src/version.c | 2 - src/xxx |only src/zmatrix.h | 12 +++--- vignettes/st.Rnw | 4 +- 32 files changed, 178 insertions(+), 164 deletions(-)
Title: Chronological Objects which can Handle Dates and Times
Description: Chronological objects which can handle dates and times.
Author: David James [aut] (S original),
Kurt Hornik [aut, trl, cre],
Gabor Grothendieck [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between chron versions 2.3-45 dated 2014-02-11 and 2.3-46 dated 2015-06-19
ChangeLog | 11 +++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 + R/times.R | 24 ++++++++++++++++++++++++ man/trunc.times.Rd | 4 ++++ 6 files changed, 51 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-07 1.0-8
2013-11-01 1.0-7
2013-10-28 1.0-6
2011-02-27 1.0-5
2011-01-31 1.0-4
2011-01-05 1.0-3
2010-12-21 1.0-2
2010-12-10 1.0-0
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.0.1 dated 2015-01-31 and 2.0.2 dated 2015-06-19
DESCRIPTION | 17 +++++----- MD5 | 50 +++++++++++++++++-------------- R/0aaa.R | 10 ++++++ R/agnes.q | 4 +- R/clara.q | 26 +++++++++------- R/clusGap.R | 6 +-- R/daisy.q | 4 +- R/diana.q | 4 +- R/ellipsoidhull.R | 2 - R/fanny.q | 4 +- R/pam.q | 4 +- R/plotpart.q | 43 +++++++++++++------------- inst/po/de/LC_MESSAGES/R-cluster.mo |binary inst/po/de/LC_MESSAGES/cluster.mo |only inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary inst/po/en@quot/LC_MESSAGES/cluster.mo |binary inst/po/ko |only man/clusplot.default.Rd | 12 +++++-- po/R-cluster.pot | 4 +- po/R-de.po | 34 ++++++++++----------- po/R-ko.po |only po/cluster.pot | 8 ++-- po/de.po |only po/ko.po |only src/clara.c | 8 +++- src/pam.c | 1 tests/ellipsoid-ex.R | 2 - tests/ellipsoid-ex.Rout.save | 2 - 28 files changed, 138 insertions(+), 107 deletions(-)
Title: R Binder for the Yhat API
Description: Deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp <greg@yhathq.com>, Eric Chiang <eric@yhathq.com>
Maintainer: Greg Lamp <greg@yhathq.com>
Diff between yhatr versions 0.13.4 dated 2015-03-06 and 0.13.6 dated 2015-06-19
DESCRIPTION | 6 +- MD5 | 45 ++++++++------- NAMESPACE | 2 NEWS | 5 + R/yhatR.R | 105 +++++++++++++++++++++++++++++-------- man/capture.src.Rd | 3 - man/check.dependencies.Rd | 3 - man/check.image.size.Rd | 3 - man/is.https.Rd |only man/yhat.deploy.Rd | 9 +-- man/yhat.deploy.to.file.Rd | 9 +-- man/yhat.deploy.with.scp.Rd | 7 +- man/yhat.get.Rd | 3 - man/yhat.ls.Rd | 3 - man/yhat.post.Rd | 3 - man/yhat.predict.Rd | 5 - man/yhat.predict_raw.Rd | 3 - man/yhat.scaffolding.Rd | 3 - man/yhat.show_models.Rd | 5 - man/yhat.spider.block.Rd | 3 - man/yhat.spider.func.Rd | 3 - man/yhat.test_predict.Rd | 3 - man/yhat.transform_from_example.Rd | 3 - man/yhat.verify.Rd | 3 - 24 files changed, 148 insertions(+), 89 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.1-8 dated 2014-09-24 and 1.1-9 dated 2015-06-19
ChangeLog | 14 DESCRIPTION | 17 MD5 | 82 +- NAMESPACE | 8 R/bfgs.R | 73 - R/bivar.smooth.const.R | 40 R/check.analytical.R | 14 R/derivative.smooth.R | 6 R/estimate.scam.R | 31 R/plot.scam.R | 1184 ++++++++++++++--------------- R/predict.scam.R | 32 R/residuals.scam.R | 9 R/scam.check.R | 2 R/scam.r | 111 +- R/uni.smooth.const.R | 60 - man/Predict.matrix.mpi.smooth.Rd | 2 man/bfgs_gcv.ubre.Rd | 12 man/derivative.scam.Rd | 2 man/gcv.ubre_grad.Rd | 11 man/marginal.matrices.tesmi1.ps.Rd | 2 man/marginal.matrices.tesmi2.ps.Rd | 2 man/plot.scam.Rd | 53 - man/predict.scam.Rd | 4 man/scam-package.Rd | 18 man/scam.Rd | 36 man/scam.fit.Rd | 15 man/shape.constrained.smooth.terms.Rd | 2 man/smooth.construct.cv.smooth.spec.rd | 2 man/smooth.construct.cx.smooth.spec.Rd | 2 man/smooth.construct.mdcv.smooth.spec.Rd | 2 man/smooth.construct.mdcx.smooth.spec.Rd | 2 man/smooth.construct.micv.smooth.spec.Rd | 2 man/smooth.construct.micx.smooth.spec.Rd | 2 man/smooth.construct.mpd.smooth.spec.Rd | 2 man/smooth.construct.mpi.smooth.spec.Rd | 2 man/smooth.construct.tedmd.smooth.spec.Rd | 2 man/smooth.construct.tedmi.smooth.spec.Rd | 2 man/smooth.construct.tesmd1.smooth.spec.Rd | 2 man/smooth.construct.tesmd2.smooth.spec.Rd | 2 man/smooth.construct.tesmi1.smooth.spec.Rd | 2 man/smooth.construct.tesmi2.smooth.spec.Rd | 2 man/summary.scam.Rd | 2 42 files changed, 949 insertions(+), 923 deletions(-)
Title: 'NOAA' Climate Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC'
climate 'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with
functions for each of the 'API' 'endpoints': data, data categories, data sets,
data types, locations, location categories, and stations. In addition, we
have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory,
'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data,
'NOAA' storm data via 'IBTrACS', and tornado data via the 'NOAA' storm prediction
center.
Author: Hart Edmund [ctb],
Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Adam Erickson [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.3.3 dated 2014-12-20 and 0.4.0 dated 2015-06-19
rnoaa-0.3.3/rnoaa/R/erddap.R |only rnoaa-0.3.3/rnoaa/R/erddap_grid.R |only rnoaa-0.3.3/rnoaa/R/erddap_info.R |only rnoaa-0.3.3/rnoaa/R/erddap_search.R |only rnoaa-0.3.3/rnoaa/R/erddap_table.R |only rnoaa-0.3.3/rnoaa/R/erddap_utils.R |only rnoaa-0.3.3/rnoaa/R/startup.r |only rnoaa-0.3.3/rnoaa/inst/doc/erddap_vignette.Rmd |only rnoaa-0.3.3/rnoaa/inst/doc/erddap_vignette.html |only rnoaa-0.3.3/rnoaa/inst/vign/erddap_vignette.Rmd |only rnoaa-0.3.3/rnoaa/inst/vign/erddap_vignette.md |only rnoaa-0.3.3/rnoaa/man/check_response_erddap.Rd |only rnoaa-0.3.3/rnoaa/man/disk.Rd |only rnoaa-0.3.3/rnoaa/man/erddap.Rd |only rnoaa-0.3.3/rnoaa/man/erddap_clear_cache.Rd |only rnoaa-0.3.3/rnoaa/man/erddap_grid.Rd |only rnoaa-0.3.3/rnoaa/man/erddap_info.Rd |only rnoaa-0.3.3/rnoaa/man/erddap_search.Rd |only rnoaa-0.3.3/rnoaa/man/erddap_table.Rd |only rnoaa-0.3.3/rnoaa/man/latlong2bbox.Rd |only rnoaa-0.3.3/rnoaa/man/type_sum.Rd |only rnoaa-0.3.3/rnoaa/tests/testthat/test-erddap_info.R |only rnoaa-0.3.3/rnoaa/tests/testthat/test-erddap_table.R |only rnoaa-0.3.3/rnoaa/vignettes/erddap_vignette.Rmd |only rnoaa-0.4.0/rnoaa/DESCRIPTION | 49 - rnoaa-0.4.0/rnoaa/LICENSE | 2 rnoaa-0.4.0/rnoaa/MD5 | 283 ++++--- rnoaa-0.4.0/rnoaa/NAMESPACE | 85 +- rnoaa-0.4.0/rnoaa/NEWS | 31 rnoaa-0.4.0/rnoaa/R/buoy.R |only rnoaa-0.4.0/rnoaa/R/caching.R | 45 - rnoaa-0.4.0/rnoaa/R/defunct.R | 65 + rnoaa-0.4.0/rnoaa/R/ghcnd.R |only rnoaa-0.4.0/rnoaa/R/globals.R | 2 rnoaa-0.4.0/rnoaa/R/homr_definitions.R | 1 rnoaa-0.4.0/rnoaa/R/isd.R | 120 ++- rnoaa-0.4.0/rnoaa/R/ncdc.r | 42 - rnoaa-0.4.0/rnoaa/R/ncdc_datatypes.r | 4 rnoaa-0.4.0/rnoaa/R/ncdc_legacy.R | 51 - rnoaa-0.4.0/rnoaa/R/ncdc_locs.r | 6 rnoaa-0.4.0/rnoaa/R/ncdc_plot.r | 15 rnoaa-0.4.0/rnoaa/R/ncdc_stations.r | 55 - rnoaa-0.4.0/rnoaa/R/rnoaa-package.r | 55 - rnoaa-0.4.0/rnoaa/R/seaice.r | 97 +- rnoaa-0.4.0/rnoaa/R/storms.R | 2 rnoaa-0.4.0/rnoaa/R/swdi.r | 63 - rnoaa-0.4.0/rnoaa/R/utils.r | 83 +- rnoaa-0.4.0/rnoaa/R/zzz.r | 105 -- rnoaa-0.4.0/rnoaa/README.md | 438 +++--------- rnoaa-0.4.0/rnoaa/build/vignette.rds |binary rnoaa-0.4.0/rnoaa/inst/doc/buoy_vignette.Rmd |only rnoaa-0.4.0/rnoaa/inst/doc/buoy_vignette.html |only rnoaa-0.4.0/rnoaa/inst/doc/homr_vignette.Rmd | 90 +- rnoaa-0.4.0/rnoaa/inst/doc/homr_vignette.html | 88 +- rnoaa-0.4.0/rnoaa/inst/doc/ncdc_attributes.Rmd | 3 rnoaa-0.4.0/rnoaa/inst/doc/ncdc_attributes.html | 3 rnoaa-0.4.0/rnoaa/inst/doc/ncdc_vignette.Rmd | 112 +-- rnoaa-0.4.0/rnoaa/inst/doc/ncdc_vignette.html | 110 +-- rnoaa-0.4.0/rnoaa/inst/doc/ncdc_workflow.Rmd | 93 +- rnoaa-0.4.0/rnoaa/inst/doc/ncdc_workflow.html | 92 +- rnoaa-0.4.0/rnoaa/inst/doc/seaice_vignette.Rmd | 20 rnoaa-0.4.0/rnoaa/inst/doc/seaice_vignette.html | 16 rnoaa-0.4.0/rnoaa/inst/doc/storms_vignette.Rmd | 10 rnoaa-0.4.0/rnoaa/inst/doc/storms_vignette.html | 10 rnoaa-0.4.0/rnoaa/inst/doc/swdi_vignette.Rmd | 36 rnoaa-0.4.0/rnoaa/inst/doc/swdi_vignette.html | 36 rnoaa-0.4.0/rnoaa/inst/js |only rnoaa-0.4.0/rnoaa/inst/vign/buoy_vignette.Rmd |only rnoaa-0.4.0/rnoaa/inst/vign/buoy_vignette.md |only rnoaa-0.4.0/rnoaa/inst/vign/figure |only rnoaa-0.4.0/rnoaa/inst/vign/homr_vignette.md | 90 +- rnoaa-0.4.0/rnoaa/inst/vign/myfile.kmz |binary rnoaa-0.4.0/rnoaa/inst/vign/myfile.zip |binary rnoaa-0.4.0/rnoaa/inst/vign/ncdc_attributes.Rmd | 3 rnoaa-0.4.0/rnoaa/inst/vign/ncdc_attributes.md | 3 rnoaa-0.4.0/rnoaa/inst/vign/ncdc_vignette.md | 112 +-- rnoaa-0.4.0/rnoaa/inst/vign/ncdc_workflow.md | 93 +- rnoaa-0.4.0/rnoaa/inst/vign/seaice_vignette.md | 20 rnoaa-0.4.0/rnoaa/inst/vign/storms_vignette.Rmd | 2 rnoaa-0.4.0/rnoaa/inst/vign/storms_vignette.md | 10 rnoaa-0.4.0/rnoaa/inst/vign/swdi_vignette.Rmd | 6 rnoaa-0.4.0/rnoaa/inst/vign/swdi_vignette.md | 36 rnoaa-0.4.0/rnoaa/man/buoy.Rd |only rnoaa-0.4.0/rnoaa/man/caching.Rd |only rnoaa-0.4.0/rnoaa/man/check_response.Rd | 2 rnoaa-0.4.0/rnoaa/man/check_response_swdi.Rd | 2 rnoaa-0.4.0/rnoaa/man/erddap_clear_cache-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/erddap_data-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/erddap_datasets-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/erddap_grid-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/erddap_info-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/erddap_search-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/erddap_table-defunct.Rd |only rnoaa-0.4.0/rnoaa/man/fipscodes.Rd | 2 rnoaa-0.4.0/rnoaa/man/ghcnd.Rd |only rnoaa-0.4.0/rnoaa/man/homr.Rd | 2 rnoaa-0.4.0/rnoaa/man/homr_definitions.Rd | 2 rnoaa-0.4.0/rnoaa/man/is.ncdc_data.Rd | 2 rnoaa-0.4.0/rnoaa/man/isd.Rd | 41 - rnoaa-0.4.0/rnoaa/man/ncdc.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_combine.Rd | 2 rnoaa-0.4.0/rnoaa/man/ncdc_datacats.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_datasets.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_datatypes.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_legacy.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_locs.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_locs_cats.Rd | 4 rnoaa-0.4.0/rnoaa/man/ncdc_plot.Rd | 6 rnoaa-0.4.0/rnoaa/man/ncdc_stations.Rd | 29 rnoaa-0.4.0/rnoaa/man/ncdc_theme.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_combine-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_datacats-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_datasets-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_datatypes-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_locs-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_locs_cats-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_plot-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_seaice-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/noaa_stations-defunct.Rd | 2 rnoaa-0.4.0/rnoaa/man/readshpfile.Rd | 2 rnoaa-0.4.0/rnoaa/man/rnoaa-defunct.Rd | 16 rnoaa-0.4.0/rnoaa/man/rnoaa-package.Rd | 28 rnoaa-0.4.0/rnoaa/man/seaice.Rd | 6 rnoaa-0.4.0/rnoaa/man/seaiceeurls.Rd | 2 rnoaa-0.4.0/rnoaa/man/storm_columns.Rd | 2 rnoaa-0.4.0/rnoaa/man/storm_names.Rd | 2 rnoaa-0.4.0/rnoaa/man/storms.Rd | 2 rnoaa-0.4.0/rnoaa/man/swdi.Rd | 6 rnoaa-0.4.0/rnoaa/man/theme_ice.Rd | 2 rnoaa-0.4.0/rnoaa/man/tornadoes.Rd | 2 rnoaa-0.4.0/rnoaa/man/type_summ.Rd |only rnoaa-0.4.0/rnoaa/tests/testthat.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-buoy.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-check_response.r | 26 rnoaa-0.4.0/rnoaa/tests/testthat/test-check_response_swdi.R | 11 rnoaa-0.4.0/rnoaa/tests/testthat/test-ghcnd.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-homr.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-isd.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc.r | 34 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_datacats.r | 22 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_datasets.r | 18 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_datatypes.r | 14 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_legacy.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_locs.r | 18 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_locs_cats.r | 25 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_plot.r | 14 rnoaa-0.4.0/rnoaa/tests/testthat/test-ncdc_stations.r | 24 rnoaa-0.4.0/rnoaa/tests/testthat/test-seaice.R |only rnoaa-0.4.0/rnoaa/tests/testthat/test-storms.R |only rnoaa-0.4.0/rnoaa/vignettes/buoy_vignette.Rmd |only rnoaa-0.4.0/rnoaa/vignettes/homr_vignette.Rmd | 90 +- rnoaa-0.4.0/rnoaa/vignettes/ncdc_attributes.Rmd | 3 rnoaa-0.4.0/rnoaa/vignettes/ncdc_vignette.Rmd | 112 +-- rnoaa-0.4.0/rnoaa/vignettes/ncdc_workflow.Rmd | 93 +- rnoaa-0.4.0/rnoaa/vignettes/seaice_vignette.Rmd | 20 rnoaa-0.4.0/rnoaa/vignettes/storms_vignette.Rmd | 10 rnoaa-0.4.0/rnoaa/vignettes/swdi_vignette.Rmd | 36 158 files changed, 1757 insertions(+), 1818 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.3 dated 2015-06-14 and 0.3.0.1 dated 2015-06-19
ChangeLog | 7 DESCRIPTION | 9 MD5 | 43 +-- NEWS | 11 R/RcppExports.R | 4 README.md | 4 inst/CITATION | 2 inst/doc/an_introduction_to_markovchain_package.R | 96 ++++--- inst/doc/an_introduction_to_markovchain_package.Rnw | 40 ++- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.R | 3 inst/doc/markovchainCrashIntro.Rmd | 15 - inst/doc/markovchainCrashIntro.pdf |binary man/markovchain-package.Rd | 4 man/markovchainFit.Rd | 2 src/0_classesAndMethods.cpp | 14 - src/1_functions4Fitting.cpp | 149 +++++++----- src/2_probabilistic.cpp | 4 src/RcppExports.cpp | 7 src/mapFitFunctionsSAI.h | 2 tests/testthat/testBasic1.R | 61 ++++ vignettes/an_introduction_to_markovchain_package-mcPlot.pdf |only vignettes/an_introduction_to_markovchain_package.Rnw | 27 +- 23 files changed, 345 insertions(+), 159 deletions(-)
Title: 3D Lever and Linkage Mechanism Modeling
Description: Creates kinematic and static force models of 3D levers and linkage mechanisms, with particular application to the fields of engineering and biomechanics.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aolsen@uchicago.edu>
Diff between linkR versions 1.0.0 dated 2015-01-02 and 1.0.1 dated 2015-06-19
linkR-1.0.0/linkR/R/analyzeLinkage.R |only linkR-1.0.1/linkR/DESCRIPTION | 11 linkR-1.0.1/linkR/MD5 | 62 - linkR-1.0.1/linkR/R/CSToEA.R |only linkR-1.0.1/linkR/R/angleOnCircleFromPoint.R | 48 linkR-1.0.1/linkR/R/animateLinkage.R | 549 ++++------ linkR-1.0.1/linkR/R/applySolveChain.R |only linkR-1.0.1/linkR/R/applyTransformationsChain.R |only linkR-1.0.1/linkR/R/avectors.R | 64 + linkR-1.0.1/linkR/R/connJointSeq.R |only linkR-1.0.1/linkR/R/copyTransformation.R | 74 + linkR-1.0.1/linkR/R/defineLinkage.R | 306 ++--- linkR-1.0.1/linkR/R/distPointToPlane.R | 17 linkR-1.0.1/linkR/R/drawLinkage.R | 273 +++- linkR-1.0.1/linkR/R/intersectCirclePlane.R |only linkR-1.0.1/linkR/R/intersectCircles.R | 26 linkR-1.0.1/linkR/R/intersectSphereLine.R | 5 linkR-1.0.1/linkR/R/linkR_examples.R | 104 + linkR-1.0.1/linkR/R/linkageKinematics.R |only linkR-1.0.1/linkR/R/pointNormalOnLine.R | 3 linkR-1.0.1/linkR/R/pointOnPlaneFromPoints.R | 6 linkR-1.0.1/linkR/R/pointPlaneProj.R | 6 linkR-1.0.1/linkR/R/pointsInPlaneFromPoints.R |only linkR-1.0.1/linkR/R/proj3DTo2D.R | 12 linkR-1.0.1/linkR/R/reverseLinkage.R | 7 linkR-1.0.1/linkR/R/solveKinematicChain.R |only linkR-1.0.1/linkR/R/uvector.R | 2 linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH488595.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH490463.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH492487.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH493661.txt |only linkR-1.0.1/linkR/inst/extdata/owl_link_associations.txt | 44 linkR-1.0.1/linkR/inst/extdata/salmo_salar_1.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_2.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_3.txt |only linkR-1.0.1/linkR/inst/extdata/salmon_landmarks.txt | 1 linkR-1.0.1/linkR/inst/extdata/salmon_link_associations.txt | 169 ++- linkR-1.0.1/linkR/man/animateLinkage.Rd | 78 + linkR-1.0.1/linkR/man/defineLinkage.Rd | 147 +- linkR-1.0.1/linkR/man/linkR-package.Rd | 17 40 files changed, 1195 insertions(+), 836 deletions(-)
Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of trading
strategies, based on the Sharpe ratio and overfit of the same.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between SharpeR versions 0.1501 dated 2014-12-23 and 1.0.0 dated 2015-06-18
DESCRIPTION | 23 +- MD5 | 98 +++++----- NAMESPACE | 4 R/SharpeR.r | 10 + R/distributions.r | 14 - R/estimation.r | 137 +++++++++++++- R/sr.r | 12 - R/tests.r | 323 ++++++++++++++++++++++++---------- README.md | 255 +++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/SharpeR.pdf |binary inst/doc/SharpeRatio.pdf |binary inst/extdata/autocorr_study.rda |binary inst/extdata/haircut_study.rda |binary inst/extdata/hotelling_power_rule.rda |binary inst/extdata/ret_data.rda |binary inst/extdata/skew_study.rda |binary inst/tests/test-distributions.r | 118 ++++++++++++ inst/tests/test-estimation.r | 143 ++++++++++++++- inst/tests/test-tests.r | 280 +++++++++++++++++++++++++++++ inst/tests/test-unified.r | 6 man/NEWS.Rd | 14 + man/SharpeR.Rd | 2 man/as.del_sropt.Rd | 4 man/as.sr.Rd | 14 - man/as.sropt.Rd | 4 man/confint.Rd | 12 - man/del_sropt.Rd | 4 man/dsr.Rd | 10 - man/dsropt.Rd | 4 man/inference.Rd | 2 man/is.del_sropt.Rd | 2 man/is.sr.Rd | 8 man/is.sropt.Rd | 2 man/ism_vcov.Rd | 2 man/pco_sropt.Rd | 4 man/plambdap.Rd | 8 man/power.sr_test.Rd | 15 - man/power.sropt_test.Rd | 4 man/predint.Rd |only man/print.Rd | 9 man/reannualize.Rd | 11 - man/se.Rd | 11 - man/sm_vcov.Rd | 2 man/sr.Rd | 13 - man/sr_equality_test.Rd | 13 - man/sr_test.Rd | 35 +-- man/sr_unpaired_test.Rd |only man/sr_vcov.Rd | 13 - man/sropt.Rd | 4 man/sropt_test.Rd | 4 51 files changed, 1363 insertions(+), 290 deletions(-)
Title: Sankey or Ribbon Plots
Description: Sankey plots are a type of diagram that is convenient to
illustrate how flow of information, resources etc. separates and joins,
much like observing how rivers split and merge. For example, they can be
used to compare different clusterings.
Author: January Weiner <january.weiner@gmail.com>
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between riverplot versions 0.3 dated 2014-08-29 and 0.5 dated 2015-06-18
riverplot-0.3/riverplot/man/default.style.Rd |only riverplot-0.5/riverplot/DESCRIPTION | 10 riverplot-0.5/riverplot/MD5 | 29 +- riverplot-0.5/riverplot/NAMESPACE | 2 riverplot-0.5/riverplot/R/curveseg.R | 5 riverplot-0.5/riverplot/R/importexport.R | 3 riverplot-0.5/riverplot/R/riverplot-styles.R |only riverplot-0.5/riverplot/R/riverplot.R | 19 + riverplot-0.5/riverplot/R/styles.R | 80 ------- riverplot-0.5/riverplot/man/colorRampPaletteAlpha.Rd | 39 +-- riverplot-0.5/riverplot/man/curveseg.Rd | 38 +-- riverplot-0.5/riverplot/man/makeRiver.Rd | 200 +++++++++---------- riverplot-0.5/riverplot/man/minard.Rd | 29 +- riverplot-0.5/riverplot/man/riverplot-package.Rd | 53 ++--- riverplot-0.5/riverplot/man/riverplot-styles.Rd |only riverplot-0.5/riverplot/man/riverplot.Rd | 111 ++++------ riverplot-0.5/riverplot/man/riverplot.example.Rd | 10 17 files changed, 277 insertions(+), 351 deletions(-)
Title: Interface to the Bird-Watching Dataset Proyecto AVIS
Description: Interface to <http://proyectoavis.com> database.
It provides means to download data filtered by species, order,
family, and several other criteria. Provides also basic functionality to
plot exploratory maps of the datasets.
Author: Javier González Hernández <javigzz@yahoo.es>, Sara Varela <svarela@paleobiogeography.org>
Maintainer: Sara Varela <svarela@paleobiogeography.org>
Diff between rAvis versions 0.1.2 dated 2014-08-28 and 0.1.3 dated 2015-06-18
DESCRIPTION | 14 ++-- MD5 | 44 ++++++------- R/rAvis_package.R | 4 - R/remoteUsersDataFunctions.R | 2 man/avisAllSpecies.Rd | 5 - man/avisContributorAggregatedObservations.Rd | 7 +- man/avisContributorsSummary.Rd | 6 + man/avisHasSpecies.Rd | 9 +- man/avisMap.Rd | 29 +++----- man/avisMapSpecies.Rd | 31 ++++----- man/avisQuery.Rd | 89 ++++++++++----------------- man/avisQueryContributor.Rd | 17 ++--- man/avisQuerySpecies.Rd | 23 +++--- man/avisSetup.Rd | 8 +- man/avisSpeciesId.Rd | 5 - man/avisSpeciesSummary.Rd | 14 ++-- man/canarias.Rd | 5 - man/peninsula.Rd | 5 - man/rAvis.Rd | 34 ++++++---- man/ravisUTMLatLong.Rd | 5 - man/ravis_credentials.Rd | 2 man/ravis_shape_spain.Rd | 4 - tests/test-all.R | 2 23 files changed, 180 insertions(+), 184 deletions(-)
Title: Orthogonal Array Package
Description: Interface to D-optimal design generation code of the Orthogonal Array package. Can generate D-optimal designs with specified number of runs and factors. The optimality of the designs is defined in terms of a user specified optimization function based on the D-efficiency and Ds-efficiency.
Author: P. T. Eendebak
Maintainer: P. T. Eendebak <pieter.eendebak@gmail.com>
Diff between oapackage versions 2.0.17 dated 2015-06-17 and 2.0.20 dated 2015-06-18
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/Doptimize.R | 23 ++++++++++++++++++++++- man/Defficiencies.Rd |only man/Doptimize.Rd | 2 +- man/oapackage-package.Rd | 22 ++++++++++++---------- src/Deff.cpp | 25 +++++++++++++++++++------ src/arrayproperties.cpp | 22 ++++++++++------------ src/mathtools.h | 8 ++++---- src/oaoptions.cpp | 2 +- tests/example_Doptimize.R | 4 ++++ 11 files changed, 87 insertions(+), 48 deletions(-)
Title: Penalized Likelihood Estimation under the Joint Cox Models
Between Tumour Progression and Death for Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 1.1 dated 2015-05-24 and 2.0 dated 2015-06-18
joint.Cox-1.1/joint.Cox/R/joint.Cox-internal.R |only joint.Cox-2.0/joint.Cox/DESCRIPTION | 14 joint.Cox-2.0/joint.Cox/MD5 | 15 joint.Cox-2.0/joint.Cox/R/jointCox.indep.reg.R | 449 +++++++++++----------- joint.Cox-2.0/joint.Cox/R/jointCox.reg.R | 97 ++-- joint.Cox-2.0/joint.Cox/man/dataOvarian.Rd | 8 joint.Cox-2.0/joint.Cox/man/joint.Cox-package.Rd | 12 joint.Cox-2.0/joint.Cox/man/jointCox.indep.reg.Rd | 18 joint.Cox-2.0/joint.Cox/man/jointCox.reg.Rd | 18 9 files changed, 321 insertions(+), 310 deletions(-)
Title: Analysis Tools for the 'JAMES' Framework
Description: Analyze and visualize results of studies performed with the
analysis tools in 'JAMES', a modern object-oriented Java
framework for discrete optimization using local search
metaheuristics (see http://www.jamesframework.org).
Author: Herman De Beukelaer
Maintainer: Herman De Beukelaer <Herman.DeBeukelaer@UGent.be>
Diff between james.analysis versions 1.0.0 dated 2015-03-19 and 1.0.1 dated 2015-06-18
DESCRIPTION | 8 - MD5 | 42 ++++----- NAMESPACE | 2 R/data.R | 19 ++-- R/package.R | 10 -- R/utils.R | 26 +++++ R/visualizations.R | 191 +++++++++++++++++++++++-------------------- README.md | 12 ++ man/boxplot.james.Rd | 30 ++++-- man/getBestSolutionValues.Rd | 2 man/getBestSolutions.Rd | 4 man/getConvergenceTimes.Rd | 9 +- man/getNumSearchRuns.Rd | 2 man/getProblems.Rd | 2 man/getSearchRuns.Rd | 4 man/getSearches.Rd | 2 man/james.Rd | 4 man/james.analysis.Rd | 12 +- man/mergeJAMES.Rd | 2 man/plotConvergence.Rd | 56 ++++++------ man/readJAMES.Rd | 6 - man/reduceJAMES.Rd | 2 22 files changed, 253 insertions(+), 194 deletions(-)
More information about james.analysis at CRAN
Permanent link
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.1.5 dated 2015-05-22 and 0.2 dated 2015-06-18
ChangeLog | 10 +++++++ DESCRIPTION | 10 +++---- MD5 | 24 +++++++++++-------- R/nri.R | 15 +++++++++++ R/nri_plot.R | 58 +++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/References.pdf |binary inst/doc/hsdar-intro.Rnw |only inst/doc/hsdar-intro.pdf |only man/hsdar-package.Rd | 2 - man/integrateToSensor.Rd | 2 - vignettes/Makefile | 7 ++++- vignettes/hsdar-intro.Rnw |only vignettes/hsdar-intro.tex |only vignettes/hsdar.bib | 11 ++++++++ 15 files changed, 94 insertions(+), 45 deletions(-)
Title: Generalized Partially Linear Tree-Based Regression Model
Description: Combining a generalized linear model with an additional tree part
on the same scale. A four-step procedure is proposed to fit the model and test
the joint effect of the selected tree part while adjusting on confounding factors.
We also proposed an ensemble procedure based on the bagging to improve prediction
accuracy and computed several scores of importance for variable selection.
Author: Cyprien Mbogning <cyprien.mbogning@inserm.fr> and Wilson Toussile
Maintainer: Cyprien Mbogning <cyprien.mbogning@gmail.com>
Diff between GPLTR versions 1.1 dated 2014-12-19 and 1.2 dated 2015-06-18
DESCRIPTION | 10 +++--- MD5 | 46 ++++++++++++++++---------------- R/Imp_Score.R | 10 +++--- R/Logistic_Split_Rpart.R | 19 ++++--------- R/bagging.pltr.R | 24 ++-------------- R/best.tree.BIC.AIC.R | 66 +++++++++++++++++++++++----------------------- R/best.tree.CV.R | 23 ++++++++-------- R/best.tree.bootstrap.R | 59 ++++++++++++++++------------------------- R/nested.trees.R | 58 ++++++++++++++++++++-------------------- R/p.val.tree.R | 36 ++++++++++++------------- R/pltr.glm.R | 34 +++++++++++------------ R/predict_bagg.pltr.R | 5 ++- R/tree2glm.R | 10 +++--- R/tree2indicators.R | 24 ++++++++-------- inst/doc/GPLTR-manual.pdf |binary inst/doc/intro.R | 8 +++-- inst/doc/intro.Rnw | 4 ++ inst/doc/intro.pdf |binary man/GPLTR-package.Rd | 6 ++-- man/VIMPBAG.Rd | 4 +- man/bagging.pltr.Rd | 2 - man/predict_bagg.pltr.Rd | 2 - vignettes/Bibliopltr.bib | 4 +- vignettes/intro.Rnw | 4 ++ 24 files changed, 215 insertions(+), 243 deletions(-)
Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to integrate multiple experimental treatments for analyzing pathways and kinases from microarray, RNA-seq, proteomics, or phosphoproteomics data.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between directPA versions 1.1 dated 2015-03-19 and 1.2 dated 2015-06-18
DESCRIPTION | 8 ++++---- MD5 | 5 ++++- data/PhosphoELM.rda |only man/PhosphoELM.human.Rd |only man/PhosphoELM.mouse.Rd |only 5 files changed, 8 insertions(+), 5 deletions(-)
Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut],
Thomas Hotz [aut],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between stepR versions 1.0-2 dated 2015-04-29 and 1.0-3 dated 2015-06-18
ChangeLog | 26 ++++++++++++++++++++++++-- DESCRIPTION | 22 +++++++++++----------- MD5 | 22 +++++++++++----------- R/jumpint.R | 11 +++++++---- man/MRC.Rd | 8 +++++--- man/bounds.Rd | 2 +- man/compare.Rd | 6 +++--- man/jumpint.Rd | 3 ++- man/smuceR.Rd | 3 ++- man/stepR-package.Rd | 9 ++++++++- man/stepbound.Rd | 5 +++-- man/stepsel.Rd | 1 + 12 files changed, 78 insertions(+), 40 deletions(-)
Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data. Methods might be relevant to other categorical data situations on non-migration data, where for example, marginal totals are known and only auxiliary bilateral data is available.
Author: Guy J. Abel
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 1.6 dated 2014-07-27 and 1.7 dated 2015-06-18
migest-1.6/migest/R/cm2.R |only migest-1.6/migest/R/cm3.R |only migest-1.6/migest/R/ffs.R |only migest-1.6/migest/R/fm.R |only migest-1.6/migest/R/ipf2.R |only migest-1.6/migest/R/ipf3.R |only migest-1.6/migest/R/ipf3.qi.R |only migest-1.6/migest/R/migest-internal.R |only migest-1.6/migest/R/rc9.R |only migest-1.7/migest/DESCRIPTION | 11 - migest-1.7/migest/MD5 | 27 +-- migest-1.7/migest/R/fn_migest.R |only migest-1.7/migest/README.md |only migest-1.7/migest/data/rc9.fund.rda |binary migest-1.7/migest/demo/cfplot_nat.R | 262 +++++++++++++++++++------------- migest-1.7/migest/demo/cfplot_reg.R | 243 ++++++++++++++++++----------- migest-1.7/migest/man/ffs.Rd | 5 migest-1.7/migest/man/ipf2.Rd | 4 migest-1.7/migest/man/ipf3.qi.Rd | 2 migest-1.7/migest/man/migest-package.Rd | 14 + 20 files changed, 341 insertions(+), 227 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy
rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 1.1 dated 2015-06-03 and 1.2 dated 2015-06-18
lfl-1.1/lfl/src/Makevars |only lfl-1.2/lfl/DESCRIPTION | 10 ++-- lfl-1.2/lfl/MD5 | 22 +++++----- lfl-1.2/lfl/configure |only lfl-1.2/lfl/configure.ac |only lfl-1.2/lfl/src/Makevars.in |only lfl-1.2/lfl/src/Makevars.win | 1 lfl-1.2/lfl/src/common/ChainCombiner.h | 1 lfl-1.2/lfl/src/pbld/Rule.h | 8 ++- lfl-1.2/lfl/src/perceiveGlobal.cpp | 60 ++++++++++++++++++----------- lfl-1.2/lfl/src/reduce.cpp | 8 +-- lfl-1.2/lfl/src/reduce/Reduce.h | 15 ++----- lfl-1.2/lfl/src/search/Search.h | 18 ++------ lfl-1.2/lfl/tests/testthat/test-perceive.R | 3 - 14 files changed, 76 insertions(+), 70 deletions(-)
Title: Heller-Heller-Gorfine Tests of Independence and Equality of
Distributions
Description: Heller-Heller-Gorfine (HHG) tests are a set of powerful statistical tests of multivariate k-sample homogeneity and independence. For the univariate case, the package also offers implementations of the MinP DDP and MinP ADP tests, which are consistent against all continuous alternatives but are distribution-free, and are thus much faster to apply.
Author: Barak Brill & Shachar Kaufman, based in part on an earlier implementation by Ruth Heller and Yair Heller.
Maintainer: Barak Brill <barakbri@mail.tau.ac.il>
Diff between HHG versions 1.4 dated 2014-05-06 and 1.5 dated 2015-06-18
HHG-1.4/HHG/data/hughes.RData |only HHG-1.4/HHG/man/hughes.Rd |only HHG-1.4/HHG/man/xdp.test.Rd |only HHG-1.5/HHG/DESCRIPTION | 20 HHG-1.5/HHG/MD5 | 55 HHG-1.5/HHG/NAMESPACE | 9 HHG-1.5/HHG/R/HHG.R | 256 HHG-1.5/HHG/R/HHG_extras.R | 36 HHG-1.5/HHG/R/HHG_univariate.R |only HHG-1.5/HHG/R/HHG_utils.R | 171 HHG-1.5/HHG/build |only HHG-1.5/HHG/data/Yeast_hughes.RData |only HHG-1.5/HHG/inst |only HHG-1.5/HHG/man/HHG-package.Rd | 145 HHG-1.5/HHG/man/Yeast_hughes.Rd |only HHG-1.5/HHG/man/hhg.example.datagen.Rd | 8 HHG-1.5/HHG/man/hhg.test.Rd | 98 HHG-1.5/HHG/man/hhg.univariate.ind.combined.test.Rd |only HHG-1.5/HHG/man/hhg.univariate.ind.nulltable.Rd |only HHG-1.5/HHG/man/hhg.univariate.ind.pvalue.Rd |only HHG-1.5/HHG/man/hhg.univariate.ind.stat.Rd |only HHG-1.5/HHG/man/hhg.univariate.ks.combined.test.Rd |only HHG-1.5/HHG/man/hhg.univariate.ks.nulltable.Rd |only HHG-1.5/HHG/man/hhg.univariate.ks.pvalue.Rd |only HHG-1.5/HHG/man/hhg.univariate.ks.stat.Rd |only HHG-1.5/HHG/man/hhg.univariate.nulltable.from.mstats.Rd |only HHG-1.5/HHG/man/print.HHG.Test.Result.Rd |only HHG-1.5/HHG/man/print.UnivariateObject.Rd |only HHG-1.5/HHG/man/print.UnivariateStatistic.Rd |only HHG-1.5/HHG/src/HHG.cpp | 1181 +--- HHG-1.5/HHG/src/HHG.h | 265 HHG-1.5/HHG/src/SequentialTest.cpp | 468 - HHG-1.5/HHG/src/SequentialTest.h | 60 HHG-1.5/HHG/src/StatsComputer.cpp | 4709 ++++++++++------ HHG-1.5/HHG/src/StatsComputer.h | 240 HHG-1.5/HHG/vignettes |only 36 files changed, 4631 insertions(+), 3090 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions of type I, II, III and IV tailored to
distributions with left and right fat tails like those that occur
in financial markets. These distributions can be used to estimate
with a high accuracy market risks and value-at-risk. Also include power
hyperbolas and power hyperbolic functions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.0-3 dated 2014-07-14 and 1.2-0 dated 2015-06-18
FatTailsR-1.0-3/FatTailsR/R/FatTailsR-package.r |only FatTailsR-1.0-3/FatTailsR/R/conversion.R |only FatTailsR-1.0-3/FatTailsR/R/kiener1.R |only FatTailsR-1.0-3/FatTailsR/R/kiener2.R |only FatTailsR-1.0-3/FatTailsR/R/kiener3.R |only FatTailsR-1.0-3/FatTailsR/R/kiener4.R |only FatTailsR-1.0-3/FatTailsR/R/logishp.R |only FatTailsR-1.0-3/FatTailsR/R/regression.R |only FatTailsR-1.0-3/FatTailsR/R/trigohp.R |only FatTailsR-1.0-3/FatTailsR/man/FatTailsR-package.Rd |only FatTailsR-1.2-0/FatTailsR/DESCRIPTION | 30 +++++---- FatTailsR-1.2-0/FatTailsR/MD5 | 64 ++++++++++++++------ FatTailsR-1.2-0/FatTailsR/NAMESPACE | 29 +++++++++ FatTailsR-1.2-0/FatTailsR/NEWS |only FatTailsR-1.2-0/FatTailsR/R/a_FatTailsR-package.R |only FatTailsR-1.2-0/FatTailsR/R/b_trigohp.R |only FatTailsR-1.2-0/FatTailsR/R/c_logishp.R |only FatTailsR-1.2-0/FatTailsR/R/d_conversion.R |only FatTailsR-1.2-0/FatTailsR/R/e_kiener1.R |only FatTailsR-1.2-0/FatTailsR/R/f_kiener2.R |only FatTailsR-1.2-0/FatTailsR/R/g_kiener3.R |only FatTailsR-1.2-0/FatTailsR/R/h_kiener4.R |only FatTailsR-1.2-0/FatTailsR/R/i_moments.R |only FatTailsR-1.2-0/FatTailsR/R/j_tailskiener.R |only FatTailsR-1.2-0/FatTailsR/R/k_estimation.R |only FatTailsR-1.2-0/FatTailsR/R/l_regression.R |only FatTailsR-1.2-0/FatTailsR/R/m_regression2.R |only FatTailsR-1.2-0/FatTailsR/R/n_regression3.R |only FatTailsR-1.2-0/FatTailsR/R/z_data.R |only FatTailsR-1.2-0/FatTailsR/data |only FatTailsR-1.2-0/FatTailsR/inst |only FatTailsR-1.2-0/FatTailsR/man/FatTailsR.Rd |only FatTailsR-1.2-0/FatTailsR/man/aw2k.Rd | 4 - FatTailsR-1.2-0/FatTailsR/man/checkquantiles.Rd |only FatTailsR-1.2-0/FatTailsR/man/ckiener.Rd |only FatTailsR-1.2-0/FatTailsR/man/dfData.Rd |only FatTailsR-1.2-0/FatTailsR/man/elevenprobs.Rd |only FatTailsR-1.2-0/FatTailsR/man/estimkappa6.Rd |only FatTailsR-1.2-0/FatTailsR/man/estimkiener11.Rd |only FatTailsR-1.2-0/FatTailsR/man/estimkienerX.Rd |only FatTailsR-1.2-0/FatTailsR/man/fitkienerLX.Rd |only FatTailsR-1.2-0/FatTailsR/man/getDSdata.Rd |only FatTailsR-1.2-0/FatTailsR/man/kiener1.Rd | 26 +++++++- FatTailsR-1.2-0/FatTailsR/man/kiener2.Rd | 22 ++++++- FatTailsR-1.2-0/FatTailsR/man/kiener3.Rd | 25 +++++++ FatTailsR-1.2-0/FatTailsR/man/kiener4.Rd | 25 +++++++ FatTailsR-1.2-0/FatTailsR/man/kmoments.Rd |only FatTailsR-1.2-0/FatTailsR/man/logishp.Rd | 14 +++- FatTailsR-1.2-0/FatTailsR/man/pk2pk.Rd |only FatTailsR-1.2-0/FatTailsR/man/regkienerLX.Rd | 66 ++++++++++++--------- FatTailsR-1.2-0/FatTailsR/man/tData.Rd |only FatTailsR-1.2-0/FatTailsR/man/xData.Rd |only FatTailsR-1.2-0/FatTailsR/man/zData.Rd |only 53 files changed, 228 insertions(+), 77 deletions(-)
More information about CopyNumber450kCancer at CRAN
Permanent link
Title: 'Blowfish' Password Hashing Algorithm
Description: An R interface to the OpenBSD 'blowfish' password hashing algorithm,
as described in "A Future-Adaptable Password Scheme" by Niels Provos. The
implementation is derived from the 'py-bcrypt' module for Python which is a
wrapper for the OpenBSD implementation.
Author: Jeroen Ooms [cre, aut],
Damien Miller [cph],
Niels Provos [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between bcrypt versions 0.1 dated 2015-06-16 and 0.2 dated 2015-06-18
bcrypt-0.1/bcrypt/src/bcrypt_pbkdf.c |only bcrypt-0.1/bcrypt/src/pybc_sha2.h |only bcrypt-0.1/bcrypt/src/sha2.c |only bcrypt-0.2/bcrypt/DESCRIPTION | 15 +++++++++------ bcrypt-0.2/bcrypt/MD5 | 11 ++++------- bcrypt-0.2/bcrypt/R/bcrypt.R | 3 +-- bcrypt-0.2/bcrypt/man/bcrypt.Rd | 3 +-- bcrypt-0.2/bcrypt/src/bcrypt.c | 5 +++++ 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-40 dated 2015-03-21 and 7.3-41 dated 2015-06-18
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- tests/Examples/MASS-Ex.Rout.save | 31 +++++++++++++++++-------------- 3 files changed, 25 insertions(+), 22 deletions(-)
Title: Diversification Rate Estimation and Fast Simulation of
Reconstructed Phylogenetic Trees under Tree-Wide
Time-Heterogeneous Birth-Death Processes Including
Mass-Extinction Events
Description: Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna and Michael R. May
Maintainer: Sebastian Hoehna <Sebastian.Hoehna@gmail.com>
Diff between TESS versions 1.2.1 dated 2013-04-22 and 2.0.0 dated 2015-06-18
TESS-1.2.1/TESS/R/globalBiDe.equations.R |only TESS-1.2.1/TESS/R/globalBiDe.likelihood.R |only TESS-1.2.1/TESS/R/globalBiDe.nTaxa.expected.R |only TESS-1.2.1/TESS/R/sim.globalBiDe.age.R |only TESS-1.2.1/TESS/R/sim.globalBiDe.taxa.R |only TESS-1.2.1/TESS/R/sim.globalBiDe.taxa.age.R |only TESS-1.2.1/TESS/man/globalBiDe.likelihood.Rd |only TESS-1.2.1/TESS/man/globalBiDe.nTaxa.expected.Rd |only TESS-1.2.1/TESS/man/sim.globalBiDe.age.Rd |only TESS-1.2.1/TESS/man/sim.globalBiDe.taxa.Rd |only TESS-1.2.1/TESS/man/sim.globalBiDe.taxa.age.Rd |only TESS-2.0.0/TESS/DESCRIPTION | 33 ++---- TESS-2.0.0/TESS/MD5 | 70 +++++++++----- TESS-2.0.0/TESS/NAMESPACE | 6 - TESS-2.0.0/TESS/NEWS | 65 ++++++++++++- TESS-2.0.0/TESS/R/RcppExports.R |only TESS-2.0.0/TESS/R/tess.PathSampling.R | 21 ++-- TESS-2.0.0/TESS/R/tess.PosteriorPrediction.R | 12 +- TESS-2.0.0/TESS/R/tess.SteppingStoneSampling.R | 4 TESS-2.0.0/TESS/R/tess.analysis.R |only TESS-2.0.0/TESS/R/tess.equations.R |only TESS-2.0.0/TESS/R/tess.likelihood.R |only TESS-2.0.0/TESS/R/tess.likelihood.rateshift.R |only TESS-2.0.0/TESS/R/tess.mcmc.R | 72 ++++++++------- TESS-2.0.0/TESS/R/tess.nTaxa.expected.R |only TESS-2.0.0/TESS/R/tess.plot.multichain.diagnostics.R |only TESS-2.0.0/TESS/R/tess.plot.output.R |only TESS-2.0.0/TESS/R/tess.plot.singlechain.diagnostics.R |only TESS-2.0.0/TESS/R/tess.process.output.R |only TESS-2.0.0/TESS/R/tess.sim.age.R |only TESS-2.0.0/TESS/R/tess.sim.taxa.R |only TESS-2.0.0/TESS/R/tess.sim.taxa.age.R |only TESS-2.0.0/TESS/R/tess.utilities.R | 15 ++- TESS-2.0.0/TESS/data/conifers.rda |only TESS-2.0.0/TESS/inst |only TESS-2.0.0/TESS/man/TESS-package.Rd | 14 +- TESS-2.0.0/TESS/man/cettiidae.Rd | 2 TESS-2.0.0/TESS/man/conifers.Rd |only TESS-2.0.0/TESS/man/tess.PosteriorPrediction.Rd | 16 ++- TESS-2.0.0/TESS/man/tess.PosteriorPredictiveTest.Rd | 13 +- TESS-2.0.0/TESS/man/tess.analysis.Rd |only TESS-2.0.0/TESS/man/tess.likelihood.Rd |only TESS-2.0.0/TESS/man/tess.likelihood.rateshift.Rd |only TESS-2.0.0/TESS/man/tess.mcmc.Rd | 33 ++++-- TESS-2.0.0/TESS/man/tess.nTaxa.expected.Rd |only TESS-2.0.0/TESS/man/tess.pathSampling.Rd |only TESS-2.0.0/TESS/man/tess.plot.multichain.diagnostics.Rd |only TESS-2.0.0/TESS/man/tess.plot.output.Rd |only TESS-2.0.0/TESS/man/tess.plot.singlechain.diagnostics.Rd |only TESS-2.0.0/TESS/man/tess.process.output.Rd |only TESS-2.0.0/TESS/man/tess.sim.age.Rd |only TESS-2.0.0/TESS/man/tess.sim.taxa.Rd |only TESS-2.0.0/TESS/man/tess.sim.taxa.age.Rd |only TESS-2.0.0/TESS/man/tess.steppingStoneSampling.Rd | 15 ++- TESS-2.0.0/TESS/src |only TESS-2.0.0/TESS/vignettes |only 56 files changed, 252 insertions(+), 139 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.0.1 dated 2015-06-17 and 0.0.2 dated 2015-06-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/kdecopula-package.Rd | 2 +- src/hfunc.cpp | 4 ++-- src/kernels.cpp | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Description: Easy integration of information from multiple sources with
"ecogen" objects. Geostatistical tools for analyzing spatial patterns in
population biology and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <learoser@gmail.com>
Diff between EcoGenetics versions 1.2.0 dated 2015-05-11 and 1.2.0-1 dated 2015-06-18
EcoGenetics-1.2.0-1/EcoGenetics/DESCRIPTION | 44 EcoGenetics-1.2.0-1/EcoGenetics/MD5 | 156 +-- EcoGenetics-1.2.0-1/EcoGenetics/NAMESPACE | 7 EcoGenetics-1.2.0-1/EcoGenetics/NEWS | 12 EcoGenetics-1.2.0-1/EcoGenetics/R/auxiliar.R | 391 ++++---- EcoGenetics-1.2.0-1/EcoGenetics/R/classes.R | 23 EcoGenetics-1.2.0-1/EcoGenetics/R/control.R | 10 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2columns.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2geneland.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2genepop.R | 38 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2gstudio.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2hierfstat.R | 15 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.2spagedi.R | 205 ++-- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.NDVI.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.NDVI.post.R | 11 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.alfreq.R | 96 +- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.append.R | 11 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.association.R | 17 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.cbind.R | 6 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.clear.R | 6 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.cormantel.R | 177 +-- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.correlog.R | 39 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.detrend.R | 62 - EcoGenetics-1.2.0-1/EcoGenetics/R/eco.forestplot.R | 261 ++--- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.genepop2df.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/eco.gsa.R | 56 - EcoGenetics-1.2.0-1/EcoGenetics/R/eco.kin.loiselle.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/eco.lagweight.R | 493 +++++----- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.lmtree.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.lsa.R | 468 ++++----- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.malecot.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/eco.mantel.R | 103 +- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.merge.R | 8 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.order.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.pairtest.R | 215 ++-- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.post.geneland.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.rankplot.R | 513 +++++----- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.rbind.R | 15 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.remove.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.subset.R | 15 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.theilsen.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/eco.variogram.R | 158 +-- EcoGenetics-1.2.0-1/EcoGenetics/R/eco.weight.R | 259 ++--- EcoGenetics-1.2.0-1/EcoGenetics/R/int.break.R | 408 ++++---- EcoGenetics-1.2.0-1/EcoGenetics/R/int.crosscor.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/int.ecogen.definition.R | 568 ++++++------ EcoGenetics-1.2.0-1/EcoGenetics/R/int.geary.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/int.jackknife.R | 60 - EcoGenetics-1.2.0-1/EcoGenetics/R/int.joincount.R | 9 EcoGenetics-1.2.0-1/EcoGenetics/R/int.kin.loiselle.R |only EcoGenetics-1.2.0-1/EcoGenetics/R/int.mantel.R | 8 EcoGenetics-1.2.0-1/EcoGenetics/R/int.moran.R | 7 EcoGenetics-1.2.0-1/EcoGenetics/R/int.multitable.R | 83 - EcoGenetics-1.2.0-1/EcoGenetics/R/int.random.test.R | 363 +++---- EcoGenetics-1.2.0-1/EcoGenetics/R/plot.methods.R | 519 +++++++--- EcoGenetics-1.2.0-1/EcoGenetics/R/show_summary.methods.R | 127 +- EcoGenetics-1.2.0-1/EcoGenetics/data/eco.test.RData |binary EcoGenetics-1.2.0-1/EcoGenetics/inst |only EcoGenetics-1.2.0-1/EcoGenetics/man/EcoGenetics-package.Rd | 37 EcoGenetics-1.2.0-1/EcoGenetics/man/aue.char2num.Rd | 2 EcoGenetics-1.2.0-1/EcoGenetics/man/aue.idig.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/auxiliar2.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.2gstudio.Rd | 2 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.2spagedi.Rd | 1 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.IBD-methods.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.IBD.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.NDVI.Rd | 1 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.NDVI.post.Rd | 2 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.correlog-methods.Rd | 3 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.correlog.Rd | 63 + EcoGenetics-1.2.0-1/EcoGenetics/man/eco.genepop2df.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.kin.loiselle.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.lsa.Rd | 47 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.malecot.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.n.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/eco.pairtest.Rd | 14 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.rbind.Rd | 18 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.subset.Rd | 6 EcoGenetics-1.2.0-1/EcoGenetics/man/eco.theilsen.Rd | 2 EcoGenetics-1.2.0-1/EcoGenetics/man/ecogen-methods.Rd | 3 EcoGenetics-1.2.0-1/EcoGenetics/man/ecogen-summary.Rd | 10 EcoGenetics-1.2.0-1/EcoGenetics/man/ecogen.Rd | 70 - EcoGenetics-1.2.0-1/EcoGenetics/man/int.jackknife.Rd | 10 EcoGenetics-1.2.0-1/EcoGenetics/man/int.kin.loiselle.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/int.multiplot.Rd |only EcoGenetics-1.2.0-1/EcoGenetics/man/rankplot-methods.Rd | 3 EcoGenetics-1.2.0/EcoGenetics/R/deprecated.R |only 87 files changed, 3517 insertions(+), 2906 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.2.1 dated 2015-05-26 and 1.3.2 dated 2015-06-18
DESCRIPTION | 8 MD5 | 98 +++--- NAMESPACE | 7 R/AllClasses.R | 5 R/AllGenerics.R | 3 R/api.R | 17 - R/append-dataset.R | 16 - R/batches.R | 72 +++- R/dataset-catalog.R | 7 R/dataset.R | 4 R/new-dataset.R | 8 R/share.R | 6 R/shoji-catalog.R | 14 R/teams.R |only R/user.R | 36 ++ R/variable-catalog.R | 27 - R/variable-update.R | 6 man/appendDataset.Rd | 4 man/catalog-extract.Rd | 25 + man/createWithMetadataAndFile.Rd | 8 man/delete.Rd | 9 man/describe-catalog.Rd | 22 + man/describe.Rd | 5 man/getAccountUserCatalog.Rd |only man/getTeams.Rd |only man/teams.Rd |only tests/testthat/api/accounts |only tests/testthat/api/datasets/dataset1/permissions.json | 56 +-- tests/testthat/api/root.json | 1 tests/testthat/api/teams |only tests/testthat/api/teams.json |only tests/testthat/api/users/user1.json | 3 tests/testthat/conflicts.R | 269 ++++++++++++------ tests/testthat/helper.R | 36 ++ tests/testthat/test-add-array.R | 1 tests/testthat/test-api.R | 11 tests/testthat/test-append-arrays.R | 16 - tests/testthat/test-append-conflicts.R | 68 ++++ tests/testthat/test-appending.R | 42 +- tests/testthat/test-appending.R.orig |only tests/testthat/test-auth.R | 4 tests/testthat/test-hide-variables.R | 27 + tests/testthat/test-new-dataset.R | 5 tests/testthat/test-teams.R |only tests/testthat/test-update.R | 2 tests/testthat/test-user.R | 60 +++- tests/testthat/test-variable-catalog.R | 5 vignettes/analyze.RData |binary vignettes/array-variables.RData |binary vignettes/derive.RData |binary vignettes/getting-started.RData |binary vignettes/variable-order.RData |binary vignettes/variables.RData |binary 53 files changed, 734 insertions(+), 279 deletions(-)
Title: R Interface to WinEdt
Description: A plug in for using WinEdt as an editor for R.
Author: Uwe Ligges <Uwe.Ligges@R-project.org>
with contributions (the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller
Maintainer: Uwe Ligges <Uwe.Ligges@R-project.org>
Diff between RWinEdt versions 2.0-3 dated 2015-05-31 and 2.0-4 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/zzz.R | 2 +- inst/doc/RWinEdt.pdf |binary src/Makevars.win | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede <tyler.tiede7@gmail.com>
Diff between PopVar versions 1.1 dated 2015-04-28 and 1.2 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Internal_PopVar_functions_4.28.15.R | 7 ++----- R/pop.predict_function_4.28.15.R | 34 ++++++++++++++++++++++++---------- R/x.val_function_4.28.15.R | 32 ++++++++++++++++++++++---------- man/pop.predict.Rd | 11 +++++++++-- man/x.val.Rd | 11 +++++++++-- 7 files changed, 76 insertions(+), 39 deletions(-)
Title: Efficient Constrained Based Modelling in R
Description: This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybil versions 1.2.6 dated 2014-06-04 and 1.3.0 dated 2015-06-17
DESCRIPTION | 25 +- LICENSE |only MD5 | 294 +++++++++++++++++----------------- R/addReact.R | 39 +++- R/doubleFluxDel.R | 50 +++-- R/findExchReact.R | 18 +- R/geneDel.R | 15 + R/generics.R | 2 R/getsybilenv.R | 4 R/modelorgClass.R | 52 +++++- R/multiDel.R | 9 - R/optimizer.R | 12 + R/parseBoolean.R | 19 -- R/rmReact.R | 12 + R/sysBiolAlgClass.R | 35 ++-- R/sysBiolAlg_roomClass.R | 32 ++- README.md |only build/vignette.rds |binary inst/NEWS.Rd | 49 +++++ inst/doc/sybil.R | 168 +++++++++---------- inst/doc/sybil.Rnw | 4 inst/doc/sybil.pdf |binary man/SYBIL_SETTINGS.Rd | 5 man/addAlgorithm.Rd | 5 man/addCols-methods.Rd | 5 man/addColsToProb-methods.Rd | 5 man/addExchReact.Rd | 7 man/addReact.Rd | 19 ++ man/addRows-methods.Rd | 5 man/addRowsCols-methods.Rd | 5 man/addRowsToProb-methods.Rd | 5 man/addSolver.Rd | 7 man/applyChanges-methods.Rd | 17 + man/backupProb-methods.Rd | 5 man/blockedReact.Rd | 5 man/changeBounds.Rd | 7 man/changeColsBnds-methods.Rd | 5 man/changeColsBndsObjCoefs-methods.Rd | 5 man/changeGPR.Rd | 7 man/changeMatrixRow-methods.Rd | 5 man/changeObjCoefs-methods.Rd | 5 man/changeObjFunc.Rd | 7 man/changeRowsBnds-methods.Rd | 5 man/changeUptake-methods.Rd | 5 man/checkAkgorithm.Rd | 5 man/checkDefaultMethod.Rd | 5 man/checkOptSol-methods.Rd | 7 man/checkReactId.Rd | 7 man/checksol-class.Rd | 7 man/deadEndMetabolites-methods.Rd | 5 man/delProb-methods.Rd | 5 man/deprecated.Rd | 5 man/doubleFluxDel.Rd | 7 man/doubleGeneDel.Rd | 7 man/doubleReact.Rd | 7 man/editEnvir.Rd | 7 man/findExchReact.Rd | 7 man/fluxDistribution-class.Rd | 7 man/fluxVar.Rd | 7 man/geneDel.Rd | 5 man/geneDeletion.Rd | 7 man/getColPrim-methods.Rd | 5 man/getColsLowBnds-methods.Rd | 5 man/getColsNames-methods.Rd | 5 man/getColsUppBnds-methods.Rd | 5 man/getFluxDist-methods.Rd | 5 man/getNumCols-methods.Rd | 5 man/getNumNnz-methods.Rd | 5 man/getNumRows-methods.Rd | 5 man/getObjCoefs-methods.Rd | 5 man/getObjDir-methods.Rd | 5 man/getObjVal-methods.Rd | 5 man/getRedCosts-methods.Rd | 5 man/getRowsLowBnds-methods.Rd | 5 man/getRowsNames-methods.Rd | 5 man/getRowsUppBnds-methods.Rd | 5 man/getSolStat-methods.Rd | 5 man/getSolverParm-methods.Rd | 5 man/getsybilenv.Rd | 7 man/initProb-methods.Rd | 5 man/loadLPprob-methods.Rd | 5 man/loadQobj-methods.Rd | 5 man/makeOptsolMO.Rd | 7 man/mod2irrev.Rd | 7 man/modelorg-class.Rd | 18 +- man/modelorg2ExPA.Rd | 5 man/modelorg2tsv.Rd | 5 man/modelorg_irrev-class.Rd | 7 man/multiDel.Rd | 5 man/netFlux-class.Rd | 7 man/oneFluxDel.Rd | 7 man/oneGeneDel.Rd | 7 man/onlyChangeGPR.Rd | 7 man/onlyCheckGPR.Rd | 7 man/optObj-class.Rd | 7 man/optObj.Rd | 5 man/optObj_clpAPI-class.Rd | 7 man/optObj_cplexAPI-class.Rd | 7 man/optObj_glpkAPI-class.Rd | 7 man/optObj_lpSolveAPI-class.Rd | 7 man/optimizeProb-methods.Rd | 23 ++ man/optimizer.Rd | 7 man/optsol-class.Rd | 7 man/optsol_blockedReact-class.Rd | 7 man/optsol_fluxVar-class.Rd | 7 man/optsol_fluxdel-class.Rd | 7 man/optsol_genedel-class.Rd | 10 - man/optsol_optimizeProb-class.Rd | 7 man/optsol_phpp-class.Rd | 7 man/optsol_robAna-class.Rd | 7 man/phpp.Rd | 7 man/ppProc-class.Rd | 7 man/printMetabolite-methods.Rd | 5 man/printReaction-methods.Rd | 5 man/promptSysBiolAlg.Rd | 5 man/reactId-class.Rd | 7 man/reactId_Exch-class.Rd | 21 +- man/readProb-methods.Rd | 32 +++ man/readTSVmod.Rd | 5 man/resetChanges-methods.Rd | 5 man/rmReact.Rd | 7 man/robAna.Rd | 7 man/scaleProb-methods.Rd | 5 man/sensitivityAnalysis-methods.Rd | 5 man/setColsNames-methods.Rd | 5 man/setObjDir-methods.Rd | 5 man/setRhsZero-methods.Rd | 5 man/setRowsNames-methods.Rd | 5 man/setSolverParm-methods.Rd | 5 man/shrinkMatrix-methods.Rd | 5 man/singletonMetabolites-methods.Rd | 5 man/solveLp-methods.Rd | 5 man/summaryOptsol-class.Rd | 5 man/summaryOptsol.Rd | 5 man/sybil-package.Rd | 9 - man/sybilError-class.Rd | 7 man/sybilLog-class.Rd | 7 man/sybilStack.Rd | 5 man/sysBiolAlg-class.Rd | 5 man/sysBiolAlg.Rd | 5 man/sysBiolAlg_fba-class.Rd | 5 man/sysBiolAlg_fv-class.Rd | 5 man/sysBiolAlg_lmoma-class.Rd | 5 man/sysBiolAlg_moma-class.Rd | 5 man/sysBiolAlg_mtf-class.Rd | 5 man/sysBiolAlg_room-class.Rd | 5 man/writeProb-methods.Rd | 31 +++ man/ypd.Rd | 5 vignettes/sybil.Rnw | 4 149 files changed, 1221 insertions(+), 477 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.2.0 dated 2015-06-13 and 1.3.0 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/phylocurve.R | 38 ++++++++++++++++++++++++++++++-------- man/phylocurve-package.Rd | 4 ++-- 4 files changed, 39 insertions(+), 17 deletions(-)
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2S versions 1.0.0 dated 2015-06-11 and 1.0.1 dated 2015-06-17
DESCRIPTION | 10 +++---- MD5 | 18 +++++++------ NEWS |only R/MM2S.human.R | 11 ++++++++ R/MM2S.mouse.R | 12 ++++++++ R/PCARender.R | 12 ++++++++ R/PredictionsHeatmap.R | 12 ++++++++ inst |only man/MM2S.human.Rd | 2 - man/MM2S.mouse.Rd | 2 - vignettes/MM2S.Rnw | 67 ++++++++++++++++++++++++++++++++++--------------- 11 files changed, 111 insertions(+), 35 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.0 dated 2015-05-29 and 4.4.1 dated 2015-06-17
DESCRIPTION | 6 - MD5 | 30 ++++---- NEWS | 25 ++++++- R/earth.R | 20 +++-- R/earth.cv.R | 2 R/expand.arg.R | 132 +++++++++++++++++++------------------ R/lib.R | 42 ----------- R/model.matrix.earth.R | 16 ++-- R/plotd.R | 5 - inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/test.full.R | 44 ++++++++++++ inst/slowtests/test.full.Rout.save | 89 ++++++++++++++++++++++++ inst/slowtests/test.glm.R | 6 + inst/slowtests/test.glm.Rout.save | 19 ++++- man/earth.Rd | 2 16 files changed, 287 insertions(+), 151 deletions(-)
Title: Seasonal/Sequential (Instants/'Durations', Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time 'durations' are handled. Both can be regularly or unevenly spaced (overlapping 'durations' are allowed). Only 'POSIX*' format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.6.5 dated 2014-12-08 and 1.7.0 dated 2015-06-17
DESCRIPTION | 12 +++++----- MD5 | 18 ++++++++-------- NAMESPACE | 3 ++ R/TimeInstantDataFrame.R | 40 ++++++++++++++++++++++++++++++++++-- R/TimeIntervalDataFrame.R | 41 +++++++++++++++++++++++++++++++++++-- README | 12 ++++++++++ man/TimeInstantDataFrame-class.Rd | 15 +++++++++++++ man/TimeIntervalDataFrame-class.Rd | 15 +++++++++++++ man/timetools-package.Rd | 4 +-- src/Makevars | 2 - 10 files changed, 140 insertions(+), 22 deletions(-)
Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations in Scalable Vector Graphics (SVG) format that can be viewed in a web browser.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aolsen@uchicago.edu>
Diff between svgViewR versions 1.0.0 dated 2014-12-28 and 1.0.1 dated 2015-06-17
svgViewR-1.0.0/svgViewR/inst/extdata/svg_viewer_3d_n.js |only svgViewR-1.0.0/svgViewR/inst/extdata/svg_viewer_n.js |only svgViewR-1.0.1/svgViewR/DESCRIPTION | 10 svgViewR-1.0.1/svgViewR/MD5 | 32 - svgViewR-1.0.1/svgViewR/R/svgviewr.circles.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.lines.R | 59 +-- svgViewR-1.0.1/svgViewR/R/svgviewr.new.R | 25 - svgViewR-1.0.1/svgViewR/R/svgviewr.paths.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.pathsC.R | 2 svgViewR-1.0.1/svgViewR/R/svgviewr.points.R | 71 ++- svgViewR-1.0.1/svgViewR/R/svgviewr.pointsC.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.text.R |only svgViewR-1.0.1/svgViewR/inst/extdata/control_panel.js |only svgViewR-1.0.1/svgViewR/inst/extdata/math.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shape_operations.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shapes.js |only svgViewR-1.0.1/svgViewR/inst/extdata/ui_functions.js | 286 +++++++++++++++ svgViewR-1.0.1/svgViewR/man/svgViewR-package.Rd | 11 svgViewR-1.0.1/svgViewR/man/svgviewr.lines.Rd | 36 - svgViewR-1.0.1/svgViewR/man/svgviewr.new.Rd | 5 svgViewR-1.0.1/svgViewR/man/svgviewr.pathsC.Rd | 2 svgViewR-1.0.1/svgViewR/man/svgviewr.points.Rd | 34 + 22 files changed, 439 insertions(+), 134 deletions(-)
Title: Facilitating Estimation of the Intraclass Correlation
Coefficient
Description: Assist in the estimation of the Intraclass Correlation Coefficient (ICC) from variance components of a one-way analysis of variance and also estimate the number of individuals or groups necessary to obtain an ICC estimate with a desired confidence interval width.
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between ICC versions 2.2.1 dated 2013-10-04 and 2.3.0 dated 2015-06-17
ICC-2.2.1/ICC/R/ICCbare.r |only ICC-2.2.1/ICC/R/ICCbareF.r |only ICC-2.2.1/ICC/R/ICCest.r |only ICC-2.2.1/ICC/R/Nest.r |only ICC-2.2.1/ICC/R/effort.r |only ICC-2.3.0/ICC/DESCRIPTION | 23 +++++++++++++---------- ICC-2.3.0/ICC/MD5 | 27 ++++++++++++++------------- ICC-2.3.0/ICC/NAMESPACE | 6 +++++- ICC-2.3.0/ICC/R/ICCbare.R |only ICC-2.3.0/ICC/R/ICCbareF.R |only ICC-2.3.0/ICC/R/ICCest.R |only ICC-2.3.0/ICC/R/Nest.R |only ICC-2.3.0/ICC/R/effort.R |only ICC-2.3.0/ICC/README.md |only ICC-2.3.0/ICC/man/ICC-package.Rd | 10 +++++----- ICC-2.3.0/ICC/man/ICCbare.Rd | 14 +++++++------- ICC-2.3.0/ICC/man/ICCbareF.Rd | 15 ++++++++------- ICC-2.3.0/ICC/man/ICCest.Rd | 33 ++++++++++++++++----------------- ICC-2.3.0/ICC/man/Nest.Rd | 38 +++++++++++++++++++------------------- ICC-2.3.0/ICC/man/effort.Rd | 26 ++++++++++++-------------- 20 files changed, 99 insertions(+), 93 deletions(-)
Title: An R Plug-in for the Distributed Hydrological Model GEOtop
Description: It analyzes raster maps and other information as input/output
files from the Hydrological Distributed Model GEOtop. It contains functions
and methods to import maps and other keywords from geotop.inpts file. Some
examples with simulation cases of GEOtop 2.0 are presented in the package.
Any information about the GEOtop Distributed Hydrological Model source code
is available on http://code.google.com/p/geotop/ or
https://github.com/se27xx/GEOtop. Technical details about the model are
available in Endrizzi et al, 2014
(http://www.geosci-model-dev.net/7/2831/2014/gmd-7-2831-2014.html).
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between geotopbricks versions 1.3.6 dated 2015-02-23 and 1.3.7.2 dated 2015-06-17
DESCRIPTION | 8 MD5 | 89 ++++---- NAMESPACE | 2 R/brickFromOutput3DTensor.R | 2 R/create.geotop.inpts.keywords.R | 2 R/get.keyword.value.R | 91 +++++++- R/getProjection.R | 2 R/listFromOutput3DTensor.R | 4 R/writeRasterxgeotop.R | 8 data/bondone.rda |binary inst/doc/examples/example.brickFromOutput3DTensor.R | 2 inst/doc/examples/example.geotopmeteostation.R | 2 inst/doc/examples/example.time.aggragation.R | 2 inst/png___kml.R |only man/GeotopRasterBrick-class.Rd | 28 +- man/KML-methods.Rd | 16 - man/Ops-methods.Rd | 11 - man/brick-methods.Rd | 54 +---- man/brick.decimal.formatter.Rd | 52 +---- man/brickFromOutputSoil3DTensor.Rd | 99 +++------ man/color.bar.Rd | 39 +-- man/color.bar.raster.Rd | 15 - man/create.geotop.inpts.keyword.Rd | 31 +- man/create.geotop.meteo.files.Rd | 47 +--- man/declared.geotop.inpts.keywords.Rd | 29 -- man/geotopbrick.Rd | 44 ++-- man/get.geotop.inpts.keyword.value.Rd | 208 +++++++------------- man/get.geotop.recovery.state.Rd | 25 -- man/getProjection.Rd | 14 - man/getvalues.brick.at.depth.Rd | 38 +-- man/listFromOutputSoil3DTensor.Rd | 99 ++------- man/max_value.Rd | 11 - man/min_value.Rd | 11 - man/plot-methods.Rd | 8 man/pointer.to.maps.xyz.time.Rd | 24 -- man/read.ascii.vectorized.brick.Rd | 25 -- man/read.raster.from.url.Rd | 16 - man/read.vectorized.geotop.recovery.Rd | 31 -- man/replace.keyword.Rd | 35 --- man/set.geotop.recovery.state.Rd | 12 - man/vertical.aggregate.brick.within.depth.Rd | 40 +-- man/write.ascii.vectorized.brick.Rd | 28 -- man/write.vectorized.geotop.recovery.Rd | 29 -- man/write.vectorized.variable.in.string.Rd | 21 -- man/writeRasterxGEOtop.Rd | 70 ++---- man/zoo-class.Rd | 4 46 files changed, 579 insertions(+), 849 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-22 1.0.3
2013-04-12 1.0.2
2013-04-09 1.0.1
Title: An Infra-Structure for Performance Estimation of Predictive
Models
Description: An infra-structure for estimating the predictive performance
of predictive models. In this context, it can also be used to compare and/or select among
different alternative ways of solving one or more predictive tasks. The main goal of the
package is to provide a generic infra-structure to estimate the values of different metrics
of predictive performance using different estimation procedures. These estimation tasks can be
applied to any solutions (workflows) to the predictive tasks. The package provides easy to use
standard workflows that allow the usage of any available R modeling algorithm together with
some pre-defined data pre-processing steps and also prediction post-processing methods. It also provides means for addressing issues related with the statistical significance of the observed differences.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between performanceEstimation versions 1.0.0 dated 2014-12-05 and 1.0.1 dated 2015-06-16
CHANGES | 9 +++++++++ DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/classDefs.R | 9 ++++++--- R/experiments.R | 18 +++++++++--------- R/workflows.R | 10 +++++----- inst/doc/performanceEstimation.pdf |binary man/EstimationTask-class.Rd | 31 +++++++++++++++++++++++++++++-- man/standardPOST.Rd | 36 +++++++++++++++++++----------------- man/subset-methods.Rd | 17 ++++++++++++++--- 10 files changed, 105 insertions(+), 53 deletions(-)
More information about performanceEstimation at CRAN
Permanent link
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 1.0 dated 2013-08-29 and 2.0 dated 2015-06-16
ThresholdROC-1.0/ThresholdROC/R/DensRatio2.R |only ThresholdROC-1.0/ThresholdROC/R/Der1.R |only ThresholdROC-1.0/ThresholdROC/R/Der2.R |only ThresholdROC-1.0/ThresholdROC/R/SS.R |only ThresholdROC-1.0/ThresholdROC/R/SSRatio.R |only ThresholdROC-1.0/ThresholdROC/R/SecondDer2st.R |only ThresholdROC-1.0/ThresholdROC/R/SecondDer3st.R |only ThresholdROC-1.0/ThresholdROC/R/VDel3st.R |only ThresholdROC-1.0/ThresholdROC/R/VarThr3.R |only ThresholdROC-1.0/ThresholdROC/R/ablines3.R |only ThresholdROC-1.0/ThresholdROC/R/ablinesEmp2.R |only ThresholdROC-1.0/ThresholdROC/R/ablinesEq2.R |only ThresholdROC-1.0/ThresholdROC/R/ablinesUn2.R |only ThresholdROC-1.0/ThresholdROC/R/control.R |only ThresholdROC-1.0/ThresholdROC/R/cost3fun.R |only ThresholdROC-1.0/ThresholdROC/R/dens.R |only ThresholdROC-1.0/ThresholdROC/R/derMeanDisEq.R |only ThresholdROC-1.0/ThresholdROC/R/derMeanDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/derMeanNDisEq.R |only ThresholdROC-1.0/ThresholdROC/R/derMeanNDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/derVarDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/derVarEq.R |only ThresholdROC-1.0/ThresholdROC/R/derVarNDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/icBoot3.R |only ThresholdROC-1.0/ThresholdROC/R/icBootEq2.R |only ThresholdROC-1.0/ThresholdROC/R/icBootUn2.R |only ThresholdROC-1.0/ThresholdROC/R/icDeltaEq2.R |only ThresholdROC-1.0/ThresholdROC/R/icDeltaUn2.R |only ThresholdROC-1.0/ThresholdROC/R/icEmp2.R |only ThresholdROC-1.0/ThresholdROC/R/icParam3.R |only ThresholdROC-1.0/ThresholdROC/R/parDerMeanDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/parDerMeanNonDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/parDerVarDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/parDerVarNonDisUn.R |only ThresholdROC-1.0/ThresholdROC/R/parMeanUn.R |only ThresholdROC-1.0/ThresholdROC/R/parVarUn.R |only ThresholdROC-1.0/ThresholdROC/R/plotCostROC.R |only ThresholdROC-1.0/ThresholdROC/R/plotDens2.R |only ThresholdROC-1.0/ThresholdROC/R/plotDens3.R |only ThresholdROC-1.0/ThresholdROC/R/print.DELTAEQ.R |only ThresholdROC-1.0/ThresholdROC/R/print.DELTAUN.R |only ThresholdROC-1.0/ThresholdROC/R/print.ICBOOT3.R |only ThresholdROC-1.0/ThresholdROC/R/print.ICEMP2.R |only ThresholdROC-1.0/ThresholdROC/R/print.ICEQ2.R |only ThresholdROC-1.0/ThresholdROC/R/print.ICPARAM3.R |only ThresholdROC-1.0/ThresholdROC/R/print.ICUN2.R |only ThresholdROC-1.0/ThresholdROC/R/print.SS.R |only ThresholdROC-1.0/ThresholdROC/R/print.THRESNLM3.R |only ThresholdROC-1.0/ThresholdROC/R/print.THRESTH3.R |only ThresholdROC-1.0/ThresholdROC/R/print.thresEmp2.R |only ThresholdROC-1.0/ThresholdROC/R/print.thresEq2.R |only ThresholdROC-1.0/ThresholdROC/R/print.thresTH2.R |only ThresholdROC-1.0/ThresholdROC/R/print.thresUn2.R |only ThresholdROC-1.0/ThresholdROC/R/quant.R |only ThresholdROC-1.0/ThresholdROC/R/rand.R |only ThresholdROC-1.0/ThresholdROC/R/resample2.R |only ThresholdROC-1.0/ThresholdROC/R/resample3.R |only ThresholdROC-1.0/ThresholdROC/R/slope.R |only ThresholdROC-1.0/ThresholdROC/R/sqroot.R |only ThresholdROC-1.0/ThresholdROC/R/th1st3.R |only ThresholdROC-1.0/ThresholdROC/R/th2st3.R |only ThresholdROC-1.0/ThresholdROC/R/thresEmp2.R |only ThresholdROC-1.0/ThresholdROC/R/thresEq2.R |only ThresholdROC-1.0/ThresholdROC/R/thresNLM3.R |only ThresholdROC-1.0/ThresholdROC/R/thresTH2.R |only ThresholdROC-1.0/ThresholdROC/R/thresTH3.R |only ThresholdROC-1.0/ThresholdROC/R/thresUn2.R |only ThresholdROC-1.0/ThresholdROC/R/varDeltaEq2.R |only ThresholdROC-1.0/ThresholdROC/R/varDeltaUn2.R |only ThresholdROC-1.0/ThresholdROC/R/varMeanEq.R |only ThresholdROC-1.0/ThresholdROC/R/varMeanUn.R |only ThresholdROC-1.0/ThresholdROC/R/varPooled.R |only ThresholdROC-1.0/ThresholdROC/R/varVarEq.R |only ThresholdROC-1.0/ThresholdROC/R/varVarUn.R |only ThresholdROC-1.0/ThresholdROC/man/DensRatio2.Rd |only ThresholdROC-1.0/ThresholdROC/man/Der1.Rd |only ThresholdROC-1.0/ThresholdROC/man/Der2.Rd |only ThresholdROC-1.0/ThresholdROC/man/SSRatio.Rd |only ThresholdROC-1.0/ThresholdROC/man/SecondDer2st.Rd |only ThresholdROC-1.0/ThresholdROC/man/SecondDer3st.Rd |only ThresholdROC-1.0/ThresholdROC/man/VDel3st.Rd |only ThresholdROC-1.0/ThresholdROC/man/VarThr3.Rd |only ThresholdROC-1.0/ThresholdROC/man/ablines3.Rd |only ThresholdROC-1.0/ThresholdROC/man/ablinesEmp2.Rd |only ThresholdROC-1.0/ThresholdROC/man/ablinesEq2.Rd |only ThresholdROC-1.0/ThresholdROC/man/ablinesUn2.Rd |only ThresholdROC-1.0/ThresholdROC/man/control.Rd |only ThresholdROC-1.0/ThresholdROC/man/cost3fun.Rd |only ThresholdROC-1.0/ThresholdROC/man/dens.Rd |only ThresholdROC-1.0/ThresholdROC/man/derMeanDisEq.Rd |only ThresholdROC-1.0/ThresholdROC/man/derMeanDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/derMeanNDisEq.Rd |only ThresholdROC-1.0/ThresholdROC/man/derMeanNDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/derVarDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/derVarEq.Rd |only ThresholdROC-1.0/ThresholdROC/man/derVarNDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/icBoot3.Rd |only ThresholdROC-1.0/ThresholdROC/man/icBootEq2.Rd |only ThresholdROC-1.0/ThresholdROC/man/icBootUn2.Rd |only ThresholdROC-1.0/ThresholdROC/man/icDeltaEq2.Rd |only ThresholdROC-1.0/ThresholdROC/man/icDeltaUn2.Rd |only ThresholdROC-1.0/ThresholdROC/man/icEmp2.Rd |only ThresholdROC-1.0/ThresholdROC/man/icParam3.Rd |only ThresholdROC-1.0/ThresholdROC/man/parDerMeanDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/parDerMeanNonDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/parDerVarDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/parDerVarNonDisUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/parMeanUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/parVarUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/plotDens2.Rd |only ThresholdROC-1.0/ThresholdROC/man/plotDens3.Rd |only ThresholdROC-1.0/ThresholdROC/man/quant.Rd |only ThresholdROC-1.0/ThresholdROC/man/rand.Rd |only ThresholdROC-1.0/ThresholdROC/man/resample2.Rd |only ThresholdROC-1.0/ThresholdROC/man/resample3.Rd |only ThresholdROC-1.0/ThresholdROC/man/slope.Rd |only ThresholdROC-1.0/ThresholdROC/man/sqroot.Rd |only ThresholdROC-1.0/ThresholdROC/man/th1st3.Rd |only ThresholdROC-1.0/ThresholdROC/man/th2st3.Rd |only ThresholdROC-1.0/ThresholdROC/man/thresEmp2.Rd |only ThresholdROC-1.0/ThresholdROC/man/thresEq2.Rd |only ThresholdROC-1.0/ThresholdROC/man/thresNLM3.Rd |only ThresholdROC-1.0/ThresholdROC/man/thresUn2.Rd |only ThresholdROC-1.0/ThresholdROC/man/varDeltaEq2.Rd |only ThresholdROC-1.0/ThresholdROC/man/varDeltaUn2.Rd |only ThresholdROC-1.0/ThresholdROC/man/varMeanEq.Rd |only ThresholdROC-1.0/ThresholdROC/man/varMeanUn.Rd |only ThresholdROC-1.0/ThresholdROC/man/varPooled.Rd |only ThresholdROC-1.0/ThresholdROC/man/varVarEq.Rd |only ThresholdROC-1.0/ThresholdROC/man/varVarUn.Rd |only ThresholdROC-2.0/ThresholdROC/DESCRIPTION | 20 - ThresholdROC-2.0/ThresholdROC/MD5 | 156 +------------- ThresholdROC-2.0/ThresholdROC/NAMESPACE | 69 +----- ThresholdROC-2.0/ThresholdROC/R/ThresholdROC-2states.R |only ThresholdROC-2.0/ThresholdROC/R/ThresholdROC-3states.R |only ThresholdROC-2.0/ThresholdROC/R/diagnostic.R |only ThresholdROC-2.0/ThresholdROC/man/SS.Rd | 94 ++++---- ThresholdROC-2.0/ThresholdROC/man/ThresholdROC-package.Rd | 41 ++- ThresholdROC-2.0/ThresholdROC/man/diagnostic.Rd |only ThresholdROC-2.0/ThresholdROC/man/lines-thres2.Rd |only ThresholdROC-2.0/ThresholdROC/man/lines-thres3.Rd |only ThresholdROC-2.0/ThresholdROC/man/plot-thres2.Rd |only ThresholdROC-2.0/ThresholdROC/man/plot-thres3.Rd |only ThresholdROC-2.0/ThresholdROC/man/plotCostROC.Rd | 93 ++++---- ThresholdROC-2.0/ThresholdROC/man/secondDer2.Rd |only ThresholdROC-2.0/ThresholdROC/man/secondDer3.Rd |only ThresholdROC-2.0/ThresholdROC/man/thres2.Rd |only ThresholdROC-2.0/ThresholdROC/man/thres3.Rd |only ThresholdROC-2.0/ThresholdROC/man/thresTH2.Rd | 115 ++++++---- ThresholdROC-2.0/ThresholdROC/man/thresTH3.Rd | 152 ++++++++----- 150 files changed, 339 insertions(+), 401 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.4 dated 2015-06-05 and 0.9.6 dated 2015-06-16
DESCRIPTION | 6 ++--- MD5 | 21 +++++++++++-------- NAMESPACE | 2 + NEWS | 21 ++++++++++++++----- R/Utilities.R | 50 +++++++++++++++++++++++++++++++++++++---------- R/biocversion.R | 5 +++- R/conditionalCode.R | 8 +++++-- inst/doc/switchrvign.pdf |binary inst/ropensciman.R | 3 +- man/fileFromFileURL.Rd |only man/makeFileURL.Rd |only man/normalizePath2.Rd | 5 +++- tests |only 13 files changed, 88 insertions(+), 33 deletions(-)
Title: Create Dashboards with 'Shiny'
Description: Create dashboards with 'Shiny'. This package provides
a theme on top of 'Shiny', making it easy to create attractive dashboards.
Author: Winston Chang [aut, cre],
RStudio [cph],
Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinydashboard versions 0.4.0 dated 2015-04-22 and 0.5.0 dated 2015-06-16
DESCRIPTION | 10 MD5 | 35 - NEWS |only R/dashboardBody.R | 6 R/dashboardHeader.R | 28 R/dashboardPage.R | 16 R/dashboardSidebar.R | 72 +- R/deps.R | 12 README.md | 6 inst/AdminLTE/AdminLTE.css | 861 +++++++++++++------------- inst/AdminLTE/AdminLTE.min.css | 4 inst/AdminLTE/README-shiny-mods.md | 4 inst/AdminLTE/_all-skins.css | 1217 ++++++++++++++++++++++++++++++++----- inst/AdminLTE/_all-skins.min.css | 2 inst/AdminLTE/app.js | 329 ++++++++-- inst/AdminLTE/app.min.js | 2 inst/AdminLTE/app.min.js.map | 2 man/dashboardHeader.Rd | 7 man/dashboardSidebar.Rd | 6 19 files changed, 1942 insertions(+), 677 deletions(-)
More information about shinydashboard at CRAN
Permanent link
Title: Gene Expression Datasets for the 'MM2S' Package
Description: Gene Expression datasets for the 'MM2S' package. Contains normalized expression data for Human Medulloblastoma ('GSE37418') as well as Mouse Medulloblastoma models ('GSE36594').
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2Sdata versions 1.0.0 dated 2015-06-13 and 1.0.1 dated 2015-06-16
DESCRIPTION | 8 ++--- MD5 | 10 ++++--- NEWS |only inst |only man/GSE36594Expr.Rd | 9 +++--- man/GSE37418Expr.Rd | 7 ++--- vignettes/MM2Sdata.Rnw | 67 ++++++++++++++++++++++++++++++++++++------------- 7 files changed, 69 insertions(+), 32 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.0 dated 2015-02-20 and 1.1 dated 2015-06-16
DESCRIPTION | 13 - MD5 | 23 ++- NAMESPACE | 8 - R/hisse.R | 105 +++++--------- R/hisseNull4.R |only R/marginRecon.R | 325 ++++++++++++++++++++++++++++++++++----------- R/plotHisse.R |only R/supportRegion.R | 49 ++++-- man/hisse.Rd | 3 man/hisseNull4.Rd |only man/marginRecon.Rd | 11 - man/plotHisse.Rd |only man/supportRegion.Rd | 2 src/hissenull-ext-derivs.c |only tests |only 15 files changed, 355 insertions(+), 184 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.2.4 dated 2014-12-15 and 3.3.0 dated 2015-06-16
BUGS |only DESCRIPTION | 18 - LICENSE | 2 MD5 | 60 +++-- NAMESPACE | 66 ++++++ R/InitConstraint.R | 2 R/InitErgmTerm.duration.R | 99 ++++----- R/InitMHP.DynMLE.R | 35 ++- R/InitMHP.DynMLE.blockdiag.R | 44 ++++ R/combine.networks.R | 15 + R/control.stergm.R | 5 R/stergm.CMLE.R | 19 + R/stergm.EGMME.GD.R | 40 ++- R/stergm.EGMME.SA.R | 16 + R/stergm.utils.R | 2 R/zzz.R | 4 build/vignette.rds |binary inst/CITATION | 40 +++ inst/NEWS.Rd | 82 ++++++-- inst/doc/STERGM.pdf |binary man/control.stergm.Rd | 19 + man/mcmc.diagnostics.stergm.Rd | 2 man/stergm.getMCMCsample.Rd |only man/tergm-internal.Rd | 55 +---- man/tergm-package.Rd | 1 man/tergm.godfather.Rd | 12 + man/tergm_MH_proposals.Rd |only src/changestats_duration.c | 414 ++++++++++++++++++++++++++++++----------- src/changestats_duration.h | 4 tests/combine.networks.R |only tests/dynamic_MLE.R | 21 +- tests/dynamic_MLE_2.R | 21 +- tests/dynamic_MLE_blockdiag.R | 21 +- 33 files changed, 804 insertions(+), 315 deletions(-)
Title: Global-Value-Chain Decomposition
Description: Two global-value-chain decompositions are implemented.
Firstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu, 2013) algorithm splits bilateral gross
exports into 16 value-added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu
(Wang, Z., S.-J. Wei, and K. Zhu. 2013. "Quantifying International Production Sharing at the Bilateral and Sector Levels.").
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between decompr versions 4.0.0 dated 2015-06-01 and 4.1.0 dated 2015-06-16
DESCRIPTION | 7 ++--- MD5 | 22 ++++++++-------- NEWS | 6 ++++ R/decomp.R | 34 ++++++++++++------------- R/leontief.R | 61 ++++++++++++++++++++++++++++----------------- R/load_tables_vectors.R | 21 ++++++++------- R/wwz.R | 2 - README.md | 2 - inst/doc/decompr.html | 11 ++------ man/leontief.Rd | 4 +- man/load_tables_vectors.Rd | 2 - man/wwz.Rd | 2 - 12 files changed, 96 insertions(+), 78 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik <thomas.mendlik@uni-graz.at>
Diff between wux versions 2.0-0 dated 2015-04-08 and 2.0-2 dated 2015-06-16
wux-2.0-0/wux/data/CMIP5_example_timeseries.csv.gz |only wux-2.0-0/wux/data/alpinesummer.csv.gz |only wux-2.0-0/wux/data/cmip3_2050.csv.gz |only wux-2.0-0/wux/data/cmip3_2100.csv.gz |only wux-2.0-0/wux/data/cmip5_2050.csv.gz |only wux-2.0-0/wux/data/cmip5_2100.csv.gz |only wux-2.0-0/wux/data/ensembles.csv.gz |only wux-2.0-0/wux/data/ensembles_gcms.csv.gz |only wux-2.0-2/wux/DESCRIPTION | 10 wux-2.0-2/wux/MD5 | 55 ++- wux-2.0-2/wux/R/InitModelDictionary.R | 280 +++++++++++++++++++- wux-2.0-2/wux/data/CMIP5_example_changesignal.rda |binary wux-2.0-2/wux/data/CMIP5_example_timeseries.csv.xz |only wux-2.0-2/wux/data/alpinesummer.csv.xz |only wux-2.0-2/wux/data/alpinesummer.rda |only wux-2.0-2/wux/data/cmip3_2050.csv.bz2 |only wux-2.0-2/wux/data/cmip3_2050.rda |binary wux-2.0-2/wux/data/cmip3_2100.csv.bz2 |only wux-2.0-2/wux/data/cmip3_2100.rda |binary wux-2.0-2/wux/data/cmip5_2050.csv.bz2 |only wux-2.0-2/wux/data/cmip5_2050.rda |binary wux-2.0-2/wux/data/cmip5_2100.csv.bz2 |only wux-2.0-2/wux/data/cmip5_2100.rda |only wux-2.0-2/wux/data/datalist | 4 wux-2.0-2/wux/data/ensembles.csv.bz2 |only wux-2.0-2/wux/data/ensembles.rda |binary wux-2.0-2/wux/data/ensembles_gcms.csv.bz2 |only wux-2.0-2/wux/data/ensembles_gcms.rda |binary wux-2.0-2/wux/data/modelinput_test.rda |binary wux-2.0-2/wux/data/userinput_CMIP5_changesignal.rda |binary wux-2.0-2/wux/data/userinput_CMIP5_timeseries.rda |binary wux-2.0-2/wux/exec/CMIP5_downloader.py | 4 wux-2.0-2/wux/exec/WuxModelDir.R |only wux-2.0-2/wux/exec/WuxModelDir_.R |only wux-2.0-2/wux/exec/WuxModelDir_rcp26.R |only wux-2.0-2/wux/exec/WuxModelDir_rcp45.R |only wux-2.0-2/wux/exec/WuxModelDir_rcp60.R |only wux-2.0-2/wux/exec/WuxModelDir_rcp85.R |only wux-2.0-2/wux/exec/modelinput.R |only wux-2.0-2/wux/man/userinput_CMIP5_changesignal.Rd | 2 wux-2.0-2/wux/man/wux-package.Rd | 3 41 files changed, 319 insertions(+), 39 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.1.0 dated 2015-06-15 and 0.1.1 dated 2015-06-16
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS | 5 +++++ tests/testthat/test_basic.R |only tests/testthat/test_metadata.R | 1 + 5 files changed, 13 insertions(+), 6 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.11-8 dated 2015-06-08 and 0.11-10 dated 2015-06-16
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/codeGeno.r | 2 ++ R/kinship.r | 36 ++++++++++++++++-------------------- 4 files changed, 27 insertions(+), 29 deletions(-)
More information about stringgaussnet at CRAN
Permanent link
More information about RedditExtractoR at CRAN
Permanent link
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.8 dated 2015-01-08 and 0.0.10 dated 2015-06-16
MCDA-0.0.10/MCDA/DESCRIPTION | 14 +-- MCDA-0.0.10/MCDA/MD5 | 44 ++++++---- MCDA-0.0.10/MCDA/NAMESPACE | 12 +- MCDA-0.0.10/MCDA/R/AHP.R |only MCDA-0.0.10/MCDA/R/MARE.R |only MCDA-0.0.10/MCDA/R/MRSort.R |only MCDA-0.0.10/MCDA/R/MRSortIdentifyIncompatibleAssignments.R |only MCDA-0.0.10/MCDA/R/MRSortInference.R |only MCDA-0.0.10/MCDA/R/TOPSIS.R |only MCDA-0.0.10/MCDA/R/plotMRSortSortingProblem.R |only MCDA-0.0.10/MCDA/README | 6 - MCDA-0.0.10/MCDA/inst/extdata/MRSortIdentifyIncompatibleAssignmentsModel.gmpl |only MCDA-0.0.10/MCDA/inst/extdata/MRSortInferenceModel.gmpl |only MCDA-0.0.10/MCDA/man/AHP.Rd |only MCDA-0.0.10/MCDA/man/MARE.Rd |only MCDA-0.0.10/MCDA/man/MRSort.Rd |only MCDA-0.0.10/MCDA/man/MRSortIdentifyIncompatibleAssignments.Rd |only MCDA-0.0.10/MCDA/man/MRSortInference.Rd |only MCDA-0.0.10/MCDA/man/TOPSIS.Rd |only MCDA-0.0.10/MCDA/man/plotMARE.Rd |only MCDA-0.0.10/MCDA/man/plotMRSortSortingProblem.Rd |only MCDA-0.0.10/MCDA/tests/AHP.R |only MCDA-0.0.10/MCDA/tests/MARE.R |only MCDA-0.0.10/MCDA/tests/MRSort.R |only MCDA-0.0.10/MCDA/tests/MRSortIdentifyIncompatibleAssignments.R |only MCDA-0.0.10/MCDA/tests/MRSortInference.R |only MCDA-0.0.10/MCDA/tests/TOPSIS.R |only MCDA-0.0.10/MCDA/tests/plotMRSortSortingProblem.R |only MCDA-0.0.8/MCDA/R/ElectreTRIBM.R |only MCDA-0.0.8/MCDA/R/ElectreTRIBMIdentifyIncompatibleAssignments.R |only MCDA-0.0.8/MCDA/R/ElectreTRIBMInference.R |only MCDA-0.0.8/MCDA/R/plotElectreTRISortingProblem.R |only MCDA-0.0.8/MCDA/inst/extdata/ElectreTRIBMIdentifyIncompatibleAssignmentsModel.gmpl |only MCDA-0.0.8/MCDA/inst/extdata/ElectreTRIBMInferenceModel.gmpl |only MCDA-0.0.8/MCDA/man/ElectreTRIBM.Rd |only MCDA-0.0.8/MCDA/man/ElectreTRIBMIdentifyIncompatibleAssignments.Rd |only MCDA-0.0.8/MCDA/man/ElectreTRIBMInference.Rd |only MCDA-0.0.8/MCDA/man/plotElectreTRISortingProblem.Rd |only MCDA-0.0.8/MCDA/tests/ElectreTRIBM.R |only MCDA-0.0.8/MCDA/tests/ElectreTRIBMIdentifyIncompatibleAssignments.R |only MCDA-0.0.8/MCDA/tests/ElectreTRIBMInference.R |only MCDA-0.0.8/MCDA/tests/plotElectreTRISortingProblem.R |only 42 files changed, 45 insertions(+), 31 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.2.4 dated 2014-12-14 and 3.4.0 dated 2015-06-16
ergm-3.2.4/ergm/tests/examples.R |only ergm-3.4.0/ergm/DESCRIPTION | 12 ergm-3.4.0/ergm/LICENSE | 11 ergm-3.4.0/ergm/MD5 | 520 ++++++++-------- ergm-3.4.0/ergm/NAMESPACE | 357 ++++++++++ ergm-3.4.0/ergm/R/InitConstraint.R | 4 ergm-3.4.0/ergm/R/InitErgmTerm.R | 8 ergm-3.4.0/ergm/R/InitErgmTerm.coincidence.R | 2 ergm-3.4.0/ergm/R/InitErgmTerm.transitiveties.R | 2 ergm-3.4.0/ergm/R/InitErgmTermcondegmple.R | 2 ergm-3.4.0/ergm/R/InitMHP.R | 27 ergm-3.4.0/ergm/R/InitMHP.blockdiag.R | 17 ergm-3.4.0/ergm/R/InitReferences.R | 2 ergm-3.4.0/ergm/R/InitWtErgmTerm.R | 2 ergm-3.4.0/ergm/R/InitWtMHP.R | 2 ergm-3.4.0/ergm/R/MHproposal.R | 2 ergm-3.4.0/ergm/R/WtReferences.R | 4 ergm-3.4.0/ergm/R/anova.ergm.R | 2 ergm-3.4.0/ergm/R/anova.ergmlist.R | 2 ergm-3.4.0/ergm/R/approx.hotelling.diff.test.R | 30 ergm-3.4.0/ergm/R/as.network.numeric.R | 2 ergm-3.4.0/ergm/R/build_term_index.R | 4 ergm-3.4.0/ergm/R/check.ErgmTerm.R | 2 ergm-3.4.0/ergm/R/coef.ergm.R | 2 ergm-3.4.0/ergm/R/control.ergm.R | 88 +- ergm-3.4.0/ergm/R/control.ergm.bridge.R | 8 ergm-3.4.0/ergm/R/control.gof.R | 2 ergm-3.4.0/ergm/R/control.logLik.ergm.R | 8 ergm-3.4.0/ergm/R/control.san.R | 4 ergm-3.4.0/ergm/R/control.simulate.R | 2 ergm-3.4.0/ergm/R/delete.isolates.R | 67 +- ergm-3.4.0/ergm/R/edgelist.R | 2 ergm-3.4.0/ergm/R/ergm.CD.fixed.R |only ergm-3.4.0/ergm/R/ergm.Cprepare.R | 17 ergm-3.4.0/ergm/R/ergm.MCMCse.R | 2 ergm-3.4.0/ergm/R/ergm.MCMCse.lognormal.R | 2 ergm-3.4.0/ergm/R/ergm.MCMLE.R | 90 +- ergm-3.4.0/ergm/R/ergm.R | 82 ++ ergm-3.4.0/ergm/R/ergm.allstats.R | 2 ergm-3.4.0/ergm/R/ergm.bounddeg.R | 2 ergm-3.4.0/ergm/R/ergm.bridge.R | 57 - ergm-3.4.0/ergm/R/ergm.check.R | 6 ergm-3.4.0/ergm/R/ergm.coefficient.degeneracy.R | 2 ergm-3.4.0/ergm/R/ergm.curved.statsmatrix.R | 4 ergm-3.4.0/ergm/R/ergm.degeneracy.R | 2 ergm-3.4.0/ergm/R/ergm.design.R | 2 ergm-3.4.0/ergm/R/ergm.estimate.R | 2 ergm-3.4.0/ergm/R/ergm.eta.R | 2 ergm-3.4.0/ergm/R/ergm.etagrad.R | 2 ergm-3.4.0/ergm/R/ergm.etagradmult.R | 2 ergm-3.4.0/ergm/R/ergm.etamap.R | 2 ergm-3.4.0/ergm/R/ergm.geodistn.R | 2 ergm-3.4.0/ergm/R/ergm.getCDsample.R |only ergm-3.4.0/ergm/R/ergm.getMCMCsample.R | 28 ergm-3.4.0/ergm/R/ergm.getglobalstats.R | 2 ergm-3.4.0/ergm/R/ergm.getmodel.R | 2 ergm-3.4.0/ergm/R/ergm.getnetwork.R | 2 ergm-3.4.0/ergm/R/ergm.getterms.R | 2 ergm-3.4.0/ergm/R/ergm.initialfit.R | 4 ergm-3.4.0/ergm/R/ergm.llik.R | 123 +-- ergm-3.4.0/ergm/R/ergm.llik.obs.R | 2 ergm-3.4.0/ergm/R/ergm.logitreg.R | 2 ergm-3.4.0/ergm/R/ergm.mahalanobis.R | 3 ergm-3.4.0/ergm/R/ergm.mapl.R | 2 ergm-3.4.0/ergm/R/ergm.maple.R | 2 ergm-3.4.0/ergm/R/ergm.model.utils.R | 6 ergm-3.4.0/ergm/R/ergm.phase12.R | 2 ergm-3.4.0/ergm/R/ergm.pl.R | 2 ergm-3.4.0/ergm/R/ergm.reviseinit.R | 2 ergm-3.4.0/ergm/R/ergm.robmon.R | 18 ergm-3.4.0/ergm/R/ergm.sample.eta2theta.R | 2 ergm-3.4.0/ergm/R/ergm.san.R | 2 ergm-3.4.0/ergm/R/ergm.sociality.R | 7 ergm-3.4.0/ergm/R/ergm.stepping.R | 7 ergm-3.4.0/ergm/R/ergm.stocapprox.R | 2 ergm-3.4.0/ergm/R/ergm.sufftoprob.R | 2 ergm-3.4.0/ergm/R/ergm.utility.R | 158 ++-- ergm-3.4.0/ergm/R/formula.utils.R | 8 ergm-3.4.0/ergm/R/get.node.attr.R | 17 ergm-3.4.0/ergm/R/gof.ergm.R | 2 ergm-3.4.0/ergm/R/is.durational.R | 2 ergm-3.4.0/ergm/R/is.dyad.independent.R | 2 ergm-3.4.0/ergm/R/is.inCH.R | 75 +- ergm-3.4.0/ergm/R/logLik.ergm.R | 7 ergm-3.4.0/ergm/R/mcmc.diagnostics.ergm.R | 81 -- ergm-3.4.0/ergm/R/midarrow.R | 54 - ergm-3.4.0/ergm/R/mvmodel.R | 8 ergm-3.4.0/ergm/R/network.update.R | 2 ergm-3.4.0/ergm/R/parallel.utils.R | 5 ergm-3.4.0/ergm/R/plot.ergm.R | 2 ergm-3.4.0/ergm/R/plot.network.ergm.R | 6 ergm-3.4.0/ergm/R/print.ergm.R | 2 ergm-3.4.0/ergm/R/print.network.list.R | 2 ergm-3.4.0/ergm/R/print.summary.ergm.R | 2 ergm-3.4.0/ergm/R/robust.inverse.R | 2 ergm-3.4.0/ergm/R/simulate.ergm.R | 20 ergm-3.4.0/ergm/R/summary.ergm.R | 6 ergm-3.4.0/ergm/R/summary.network.list.R | 2 ergm-3.4.0/ergm/R/summary.statistics.network.R | 2 ergm-3.4.0/ergm/R/wtd.median.R | 2 ergm-3.4.0/ergm/R/zzz.R | 16 ergm-3.4.0/ergm/build/vignette.rds |binary ergm-3.4.0/ergm/data/datalist | 2 ergm-3.4.0/ergm/data/faux.desert.high.RData |only ergm-3.4.0/ergm/data/faux.dixon.high.RData |only ergm-3.4.0/ergm/data/sampson.RData |binary ergm-3.4.0/ergm/inst/CITATION | 42 + ergm-3.4.0/ergm/inst/NEWS.Rd | 116 ++- ergm-3.4.0/ergm/inst/doc/ergm-term-crossRef.R | 10 ergm-3.4.0/ergm/inst/doc/ergm-term-crossRef.html | 16 ergm-3.4.0/ergm/inst/doc/ergm.R | 110 +-- ergm-3.4.0/ergm/inst/doc/ergm.Rnw | 187 +++-- ergm-3.4.0/ergm/inst/doc/ergm.pdf |binary ergm-3.4.0/ergm/man/Getting.Started.Rd | 2 ergm-3.4.0/ergm/man/MHproposal.Rd |only ergm-3.4.0/ergm/man/anova.ergm.Rd | 6 ergm-3.4.0/ergm/man/approx.hotelling.diff.test.Rd |only ergm-3.4.0/ergm/man/as.edgelist.Rd |only ergm-3.4.0/ergm/man/as.network.numeric.Rd | 2 ergm-3.4.0/ergm/man/check.ErgmTerm.Rd |only ergm-3.4.0/ergm/man/coef.ergm.Rd | 6 ergm-3.4.0/ergm/man/coef.length.model.Rd |only ergm-3.4.0/ergm/man/control.ergm.Rd | 118 +++ ergm-3.4.0/ergm/man/control.ergm.bridge.Rd | 21 ergm-3.4.0/ergm/man/control.gof.Rd | 2 ergm-3.4.0/ergm/man/control.logLik.ergm.Rd | 21 ergm-3.4.0/ergm/man/control.san.Rd | 2 ergm-3.4.0/ergm/man/control.simulate.ergm.Rd | 2 ergm-3.4.0/ergm/man/degreedist.Rd |only ergm-3.4.0/ergm/man/ecoli.Rd | 2 ergm-3.4.0/ergm/man/enformulate.curved.Rd | 2 ergm-3.4.0/ergm/man/ergm-MetropolisHastingsProposals.Rd | 41 + ergm-3.4.0/ergm/man/ergm-constraints.Rd | 6 ergm-3.4.0/ergm/man/ergm-internal.Rd | 247 ++----- ergm-3.4.0/ergm/man/ergm-package.Rd | 2 ergm-3.4.0/ergm/man/ergm-parallel.Rd | 38 - ergm-3.4.0/ergm/man/ergm-references.Rd | 2 ergm-3.4.0/ergm/man/ergm-terms.Rd | 5 ergm-3.4.0/ergm/man/ergm.ConstraintImplication.Rd |only ergm-3.4.0/ergm/man/ergm.Cprepare.Rd |only ergm-3.4.0/ergm/man/ergm.MHP.table.Rd |only ergm-3.4.0/ergm/man/ergm.Rd | 24 ergm-3.4.0/ergm/man/ergm.allstats.Rd | 2 ergm-3.4.0/ergm/man/ergm.bounddeg.Rd |only ergm-3.4.0/ergm/man/ergm.bridge.dindstart.llk.Rd | 2 ergm-3.4.0/ergm/man/ergm.bridge.llr.Rd | 27 ergm-3.4.0/ergm/man/ergm.degeneracy.Rd |only ergm-3.4.0/ergm/man/ergm.eta.Rd |only ergm-3.4.0/ergm/man/ergm.exact.Rd | 2 ergm-3.4.0/ergm/man/ergm.geodistdist.Rd |only ergm-3.4.0/ergm/man/ergm.getMCMCsample.Rd |only ergm-3.4.0/ergm/man/ergm.getglobalstats.Rd |only ergm-3.4.0/ergm/man/ergm.init.methods.Rd |only ergm-3.4.0/ergm/man/ergm.mple.Rd |only ergm-3.4.0/ergm/man/ergm_deprecated.Rd |only ergm-3.4.0/ergm/man/ergm_formula_utils.Rd |only ergm-3.4.0/ergm/man/eut-upgrade.Rd | 2 ergm-3.4.0/ergm/man/faux.desert.high.Rd |only ergm-3.4.0/ergm/man/faux.dixon.high.Rd |only ergm-3.4.0/ergm/man/faux.magnolia.high.Rd | 2 ergm-3.4.0/ergm/man/faux.mesa.high.Rd | 2 ergm-3.4.0/ergm/man/fix.curved.Rd | 2 ergm-3.4.0/ergm/man/flobusiness.Rd | 2 ergm-3.4.0/ergm/man/flomarriage.Rd | 2 ergm-3.4.0/ergm/man/florentine.Rd | 2 ergm-3.4.0/ergm/man/g4.Rd | 2 ergm-3.4.0/ergm/man/get.free.dyads.Rd |only ergm-3.4.0/ergm/man/get.node.attr.Rd |only ergm-3.4.0/ergm/man/gof.ergm.Rd | 2 ergm-3.4.0/ergm/man/is.dyad.independent.Rd | 24 ergm-3.4.0/ergm/man/is.inCH.Rd | 52 + ergm-3.4.0/ergm/man/kapferer.Rd | 2 ergm-3.4.0/ergm/man/lasttoggle.Rd | 2 ergm-3.4.0/ergm/man/logLik.ergm.Rd | 2 ergm-3.4.0/ergm/man/mcmc.diagnostics.ergm.Rd | 39 - ergm-3.4.0/ergm/man/mcmc.list_utils.Rd |only ergm-3.4.0/ergm/man/molecule.Rd | 2 ergm-3.4.0/ergm/man/network.update.Rd | 2 ergm-3.4.0/ergm/man/newnw.extract.Rd |only ergm-3.4.0/ergm/man/nvattr.copy.network.Rd |only ergm-3.4.0/ergm/man/plot.ergm.Rd | 2 ergm-3.4.0/ergm/man/plot.gofobject.Rd | 2 ergm-3.4.0/ergm/man/plot.network.ergm.Rd | 2 ergm-3.4.0/ergm/man/print.ergm.Rd | 2 ergm-3.4.0/ergm/man/robust.inverse.Rd |only ergm-3.4.0/ergm/man/samplk.Rd | 2 ergm-3.4.0/ergm/man/sampson.Rd | 42 - ergm-3.4.0/ergm/man/san.Rd | 2 ergm-3.4.0/ergm/man/simulate.ergm.Rd | 7 ergm-3.4.0/ergm/man/standardize.network.Rd |only ergm-3.4.0/ergm/man/summary.ergm.Rd | 2 ergm-3.4.0/ergm/man/summary.gofobject.Rd | 2 ergm-3.4.0/ergm/man/summary.network.list.Rd | 2 ergm-3.4.0/ergm/man/summary.statistics.Rd | 2 ergm-3.4.0/ergm/man/vcov.ergm.Rd | 2 ergm-3.4.0/ergm/man/vector.namesmatch.Rd |only ergm-3.4.0/ergm/man/wtd.median.Rd | 2 ergm-3.4.0/ergm/src/CD.c |only ergm-3.4.0/ergm/src/CD.h |only ergm-3.4.0/ergm/src/MCMC.c | 12 ergm-3.4.0/ergm/src/MCMC.h | 2 ergm-3.4.0/ergm/src/MHproposal.c | 2 ergm-3.4.0/ergm/src/MHproposal.h | 2 ergm-3.4.0/ergm/src/MHproposals.c | 72 ++ ergm-3.4.0/ergm/src/MHproposals.h | 2 ergm-3.4.0/ergm/src/MHproposals_bipartite.c | 2 ergm-3.4.0/ergm/src/MHproposals_bipartite.h | 2 ergm-3.4.0/ergm/src/MHproposals_block.c | 2 ergm-3.4.0/ergm/src/MHproposals_block.h | 2 ergm-3.4.0/ergm/src/MHproposals_degree.c | 18 ergm-3.4.0/ergm/src/MHproposals_degree.h | 2 ergm-3.4.0/ergm/src/MPLE.c | 2 ergm-3.4.0/ergm/src/MPLE.h | 2 ergm-3.4.0/ergm/src/MPLEconddeg.c | 2 ergm-3.4.0/ergm/src/MPLEconddeg.h | 2 ergm-3.4.0/ergm/src/SAN.c | 10 ergm-3.4.0/ergm/src/SAN.h | 2 ergm-3.4.0/ergm/src/allstatistics.c | 2 ergm-3.4.0/ergm/src/changestat.c | 2 ergm-3.4.0/ergm/src/changestat.h | 2 ergm-3.4.0/ergm/src/changestats.c | 2 ergm-3.4.0/ergm/src/changestats.h | 2 ergm-3.4.0/ergm/src/conddegmple.c | 2 ergm-3.4.0/ergm/src/conddegmple.h | 2 ergm-3.4.0/ergm/src/edgelist.c | 2 ergm-3.4.0/ergm/src/edgelist.h | 2 ergm-3.4.0/ergm/src/edgetree.c | 2 ergm-3.4.0/ergm/src/edgetree.h | 2 ergm-3.4.0/ergm/src/geodist.c | 2 ergm-3.4.0/ergm/src/geodist.h | 2 ergm-3.4.0/ergm/src/model.c | 2 ergm-3.4.0/ergm/src/model.h | 2 ergm-3.4.0/ergm/src/netstats.c | 2 ergm-3.4.0/ergm/src/netstats.h | 2 ergm-3.4.0/ergm/src/wtCD.c |only ergm-3.4.0/ergm/src/wtCD.h |only ergm-3.4.0/ergm/src/wtMCMC.c | 12 ergm-3.4.0/ergm/src/wtMCMC.h | 2 ergm-3.4.0/ergm/src/wtMHproposal.c | 2 ergm-3.4.0/ergm/src/wtMHproposal.h | 2 ergm-3.4.0/ergm/src/wtMHproposals.c | 2 ergm-3.4.0/ergm/src/wtMHproposals.h | 2 ergm-3.4.0/ergm/src/wtSAN.c | 10 ergm-3.4.0/ergm/src/wtSAN.h | 2 ergm-3.4.0/ergm/src/wtchangestat.h | 2 ergm-3.4.0/ergm/src/wtchangestats.c | 2 ergm-3.4.0/ergm/src/wtchangestats.h | 2 ergm-3.4.0/ergm/src/wtedgetree.c | 5 ergm-3.4.0/ergm/src/wtedgetree.h | 2 ergm-3.4.0/ergm/src/wtmodel.c | 2 ergm-3.4.0/ergm/src/wtmodel.h | 2 ergm-3.4.0/ergm/src/wtnetstats.c | 2 ergm-3.4.0/ergm/src/wtnetstats.h | 2 ergm-3.4.0/ergm/tests/constrain_blockdiag.R | 2 ergm-3.4.0/ergm/tests/constrain_degrees.R | 2 ergm-3.4.0/ergm/tests/constrain_observed.R | 2 ergm-3.4.0/ergm/tests/constraint_conflict.R | 2 ergm-3.4.0/ergm/tests/constraint_generalized.R | 2 ergm-3.4.0/ergm/tests/drop_tests.R | 2 ergm-3.4.0/ergm/tests/ergm.mixed.R | 2 ergm-3.4.0/ergm/tests/ergm.update.formula.R | 2 ergm-3.4.0/ergm/tests/ergmMPLEtest.R | 2 ergm-3.4.0/ergm/tests/ergm_term_doc_test.R | 11 ergm-3.4.0/ergm/tests/estflo.R | 2 ergm-3.4.0/ergm/tests/fix.curved.R | 2 ergm-3.4.0/ergm/tests/flomarkov.R | 2 ergm-3.4.0/ergm/tests/hamming_termtests.R | 2 ergm-3.4.0/ergm/tests/misc_tests.R |only ergm-3.4.0/ergm/tests/miss_tests.CD.R |only ergm-3.4.0/ergm/tests/miss_tests.R | 19 ergm-3.4.0/ergm/tests/mle_offset.R | 2 ergm-3.4.0/ergm/tests/mple_largenetwork.R | 2 ergm-3.4.0/ergm/tests/mple_offset.R | 2 ergm-3.4.0/ergm/tests/mple_target.stats.R | 2 ergm-3.4.0/ergm/tests/nodemix.R | 2 ergm-3.4.0/ergm/tests/nodrop.R | 2 ergm-3.4.0/ergm/tests/parallel.R | 7 ergm-3.4.0/ergm/tests/scoping.R | 10 ergm-3.4.0/ergm/tests/steppingtest.R | 1 ergm-3.4.0/ergm/tests/testgmonkmiss.R | 10 ergm-3.4.0/ergm/vignettes/ergm.Rnw | 187 +++-- 281 files changed, 2433 insertions(+), 1554 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.4.1 dated 2015-01-14 and 0.4.2 dated 2015-06-16
dplyr-0.4.1/dplyr/inst/include/tools/stop.h |only dplyr-0.4.1/dplyr/inst/include/tools/tinyformat.h |only dplyr-0.4.1/dplyr/vignettes/databases.md |only dplyr-0.4.1/dplyr/vignettes/figure |only dplyr-0.4.1/dplyr/vignettes/hybrid-evaluation.md |only dplyr-0.4.1/dplyr/vignettes/introduction.md |only dplyr-0.4.1/dplyr/vignettes/memory.html |only dplyr-0.4.2/dplyr/DESCRIPTION | 12 dplyr-0.4.2/dplyr/LICENSE | 2 dplyr-0.4.2/dplyr/MD5 | 367 ++-- dplyr-0.4.2/dplyr/NAMESPACE | 9 dplyr-0.4.2/dplyr/R/RcppExports.R | 1 dplyr-0.4.2/dplyr/R/chain.r | 15 dplyr-0.4.2/dplyr/R/compute-collect.r | 2 dplyr-0.4.2/dplyr/R/dataframe.R | 3 dplyr-0.4.2/dplyr/R/funs.R | 2 dplyr-0.4.2/dplyr/R/lead-lag.R | 2 dplyr-0.4.2/dplyr/R/manip.r | 1 dplyr-0.4.2/dplyr/R/progress.R | 1 dplyr-0.4.2/dplyr/R/rbind.r | 6 dplyr-0.4.2/dplyr/R/tbl-df.r | 8 dplyr-0.4.2/dplyr/R/tbl-sql.r | 2 dplyr-0.4.2/dplyr/R/utils-format.r | 19 dplyr-0.4.2/dplyr/README.md | 109 - dplyr-0.4.2/dplyr/build/vignette.rds |binary dplyr-0.4.2/dplyr/demo/bench-merge.R | 4 dplyr-0.4.2/dplyr/inst/doc/data_frames.R | 2 dplyr-0.4.2/dplyr/inst/doc/data_frames.html | 61 dplyr-0.4.2/dplyr/inst/doc/databases.R | 12 dplyr-0.4.2/dplyr/inst/doc/databases.Rmd | 10 dplyr-0.4.2/dplyr/inst/doc/databases.html | 51 dplyr-0.4.2/dplyr/inst/doc/hybrid-evaluation.R | 6 dplyr-0.4.2/dplyr/inst/doc/hybrid-evaluation.Rmd | 20 dplyr-0.4.2/dplyr/inst/doc/hybrid-evaluation.html | 210 +- dplyr-0.4.2/dplyr/inst/doc/introduction.R | 16 dplyr-0.4.2/dplyr/inst/doc/introduction.Rmd | 4 dplyr-0.4.2/dplyr/inst/doc/introduction.html | 26 dplyr-0.4.2/dplyr/inst/doc/new-sql-backend.R | 8 dplyr-0.4.2/dplyr/inst/doc/new-sql-backend.html | 4 dplyr-0.4.2/dplyr/inst/doc/nse.R | 2 dplyr-0.4.2/dplyr/inst/doc/nse.html | 4 dplyr-0.4.2/dplyr/inst/doc/two-table.R | 4 dplyr-0.4.2/dplyr/inst/doc/two-table.html | 16 dplyr-0.4.2/dplyr/inst/doc/window-functions.R | 24 dplyr-0.4.2/dplyr/inst/doc/window-functions.Rmd | 2 dplyr-0.4.2/dplyr/inst/doc/window-functions.html | 30 dplyr-0.4.2/dplyr/inst/include/dplyr.h | 29 dplyr-0.4.2/dplyr/inst/include/dplyr/BoolResult.h | 4 dplyr-0.4.2/dplyr/inst/include/dplyr/Collecter.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/DataFrameJoinVisitors.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/DataFrameVisitors.h | 40 dplyr-0.4.2/dplyr/inst/include/dplyr/Gatherer.h | 8 dplyr-0.4.2/dplyr/inst/include/dplyr/GroupedDataFrame.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/JoinVisitorImpl.h | 45 dplyr-0.4.2/dplyr/inst/include/dplyr/Order.h | 5 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/CallProxy.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/CallbackProcessor.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/DelayedProcessor.h | 76 - dplyr-0.4.2/dplyr/inst/include/dplyr/Result/DelayedReducer.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/First.h | 3 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/GroupedCallProxy.h | 4 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/GroupedHybridCall.h | 8 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/GroupedSubset.h | 1 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Lag.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/LazyGroupedSubsets.h | 56 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/LazyRowwiseSubsets.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/LazySubsets.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Lead.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Reducer.h | 82 - dplyr-0.4.2/dplyr/inst/include/dplyr/Result/Result.h | 1 dplyr-0.4.2/dplyr/inst/include/dplyr/Result/ResultSet.h | 6 dplyr-0.4.2/dplyr/inst/include/dplyr/VectorVisitorImpl.h | 77 - dplyr-0.4.2/dplyr/inst/include/dplyr/registration.h | 2 dplyr-0.4.2/dplyr/inst/include/dplyr/visitor.h | 15 dplyr-0.4.2/dplyr/inst/include/dplyr/white_list.h | 52 dplyr-0.4.2/dplyr/inst/include/dplyr/workarounds.h |only dplyr-0.4.2/dplyr/inst/include/tools/Call.h | 13 dplyr-0.4.2/dplyr/inst/include/tools/delete_all.h | 7 dplyr-0.4.2/dplyr/inst/include/tools/get_single_class.h | 3 dplyr-0.4.2/dplyr/inst/include/tools/pointer_vector.h |only dplyr-0.4.2/dplyr/inst/include/tools/tools.h | 1 dplyr-0.4.2/dplyr/man/add_rownames.Rd | 2 dplyr-0.4.2/dplyr/man/all.equal.tbl_df.Rd | 2 dplyr-0.4.2/dplyr/man/arrange.Rd | 2 dplyr-0.4.2/dplyr/man/as.tbl_cube.Rd | 2 dplyr-0.4.2/dplyr/man/as_data_frame.Rd | 2 dplyr-0.4.2/dplyr/man/backend_db.Rd | 2 dplyr-0.4.2/dplyr/man/backend_sql.Rd | 2 dplyr-0.4.2/dplyr/man/backend_src.Rd | 2 dplyr-0.4.2/dplyr/man/bench_compare.Rd | 2 dplyr-0.4.2/dplyr/man/between.Rd | 2 dplyr-0.4.2/dplyr/man/bind.Rd | 14 dplyr-0.4.2/dplyr/man/build_sql.Rd | 2 dplyr-0.4.2/dplyr/man/chain.Rd | 15 dplyr-0.4.2/dplyr/man/compute.Rd | 4 dplyr-0.4.2/dplyr/man/copy_to.Rd | 2 dplyr-0.4.2/dplyr/man/copy_to.src_sql.Rd | 2 dplyr-0.4.2/dplyr/man/cumall.Rd | 2 dplyr-0.4.2/dplyr/man/data_frame.Rd | 5 dplyr-0.4.2/dplyr/man/desc.Rd | 2 dplyr-0.4.2/dplyr/man/distinct.Rd | 2 dplyr-0.4.2/dplyr/man/do.Rd | 2 dplyr-0.4.2/dplyr/man/dplyr-cluster.Rd | 2 dplyr-0.4.2/dplyr/man/dplyr-formatting.Rd | 2 dplyr-0.4.2/dplyr/man/dplyr.Rd | 2 dplyr-0.4.2/dplyr/man/explain.Rd | 2 dplyr-0.4.2/dplyr/man/failwith.Rd | 2 dplyr-0.4.2/dplyr/man/filter.Rd | 2 dplyr-0.4.2/dplyr/man/funs.Rd | 4 dplyr-0.4.2/dplyr/man/glimpse.Rd | 2 dplyr-0.4.2/dplyr/man/group_by.Rd | 2 dplyr-0.4.2/dplyr/man/group_indices.Rd | 2 dplyr-0.4.2/dplyr/man/group_size.Rd | 2 dplyr-0.4.2/dplyr/man/grouped_df.Rd | 2 dplyr-0.4.2/dplyr/man/grouped_dt.Rd | 2 dplyr-0.4.2/dplyr/man/groups.Rd | 2 dplyr-0.4.2/dplyr/man/id.Rd | 2 dplyr-0.4.2/dplyr/man/join.Rd | 2 dplyr-0.4.2/dplyr/man/join.tbl_df.Rd | 2 dplyr-0.4.2/dplyr/man/join.tbl_dt.Rd | 2 dplyr-0.4.2/dplyr/man/join.tbl_sql.Rd | 2 dplyr-0.4.2/dplyr/man/knit_print.trunc_mat.Rd | 2 dplyr-0.4.2/dplyr/man/lahman.Rd | 2 dplyr-0.4.2/dplyr/man/lead-lag.Rd | 6 dplyr-0.4.2/dplyr/man/location.Rd | 2 dplyr-0.4.2/dplyr/man/make_tbl.Rd | 2 dplyr-0.4.2/dplyr/man/mutate.Rd | 2 dplyr-0.4.2/dplyr/man/n.Rd | 2 dplyr-0.4.2/dplyr/man/n_distinct.Rd | 2 dplyr-0.4.2/dplyr/man/nasa.Rd | 2 dplyr-0.4.2/dplyr/man/nth.Rd | 2 dplyr-0.4.2/dplyr/man/nycflights13.Rd | 2 dplyr-0.4.2/dplyr/man/order_by.Rd | 2 dplyr-0.4.2/dplyr/man/partial_eval.Rd | 2 dplyr-0.4.2/dplyr/man/progress_estimated.Rd | 2 dplyr-0.4.2/dplyr/man/query.Rd | 2 dplyr-0.4.2/dplyr/man/ranking.Rd | 2 dplyr-0.4.2/dplyr/man/rowwise.Rd | 2 dplyr-0.4.2/dplyr/man/same_src.Rd | 2 dplyr-0.4.2/dplyr/man/sample.Rd | 2 dplyr-0.4.2/dplyr/man/select.Rd | 2 dplyr-0.4.2/dplyr/man/select_vars.Rd | 2 dplyr-0.4.2/dplyr/man/setops.Rd | 2 dplyr-0.4.2/dplyr/man/slice.Rd | 2 dplyr-0.4.2/dplyr/man/sql.Rd | 2 dplyr-0.4.2/dplyr/man/sql_quote.Rd | 2 dplyr-0.4.2/dplyr/man/sql_variant.Rd | 2 dplyr-0.4.2/dplyr/man/src.Rd | 2 dplyr-0.4.2/dplyr/man/src_local.Rd | 2 dplyr-0.4.2/dplyr/man/src_mysql.Rd | 2 dplyr-0.4.2/dplyr/man/src_postgres.Rd | 2 dplyr-0.4.2/dplyr/man/src_sql.Rd | 2 dplyr-0.4.2/dplyr/man/src_sqlite.Rd | 2 dplyr-0.4.2/dplyr/man/src_tbls.Rd | 2 dplyr-0.4.2/dplyr/man/summarise.Rd | 3 dplyr-0.4.2/dplyr/man/summarise_each.Rd | 2 dplyr-0.4.2/dplyr/man/tally.Rd | 2 dplyr-0.4.2/dplyr/man/tbl.Rd | 2 dplyr-0.4.2/dplyr/man/tbl_cube.Rd | 2 dplyr-0.4.2/dplyr/man/tbl_df.Rd | 10 dplyr-0.4.2/dplyr/man/tbl_dt.Rd | 2 dplyr-0.4.2/dplyr/man/tbl_sql.Rd | 4 dplyr-0.4.2/dplyr/man/tbl_vars.Rd | 2 dplyr-0.4.2/dplyr/man/temp_srcs.Rd | 2 dplyr-0.4.2/dplyr/man/top_n.Rd | 2 dplyr-0.4.2/dplyr/man/translate_sql.Rd | 2 dplyr-0.4.2/dplyr/man/type_sum.Rd | 2 dplyr-0.4.2/dplyr/man/with_order.Rd | 2 dplyr-0.4.2/dplyr/src/RcppExports.cpp | 755 +++------- dplyr-0.4.2/dplyr/src/arrange.cpp | 6 dplyr-0.4.2/dplyr/src/bind.cpp | 19 dplyr-0.4.2/dplyr/src/dplyr.cpp | 162 -- dplyr-0.4.2/dplyr/src/filter.cpp | 31 dplyr-0.4.2/dplyr/src/join.cpp | 25 dplyr-0.4.2/dplyr/src/select.cpp | 5 dplyr-0.4.2/dplyr/src/summarise.cpp | 24 dplyr-0.4.2/dplyr/tests/testthat/test-arrange.r | 20 dplyr-0.4.2/dplyr/tests/testthat/test-cbind.R | 11 dplyr-0.4.2/dplyr/tests/testthat/test-do.R | 4 dplyr-0.4.2/dplyr/tests/testthat/test-equality.r | 26 dplyr-0.4.2/dplyr/tests/testthat/test-group-by.r | 16 dplyr-0.4.2/dplyr/tests/testthat/test-lead-lag.R | 22 dplyr-0.4.2/dplyr/tests/testthat/test-mutate.r | 15 dplyr-0.4.2/dplyr/tests/testthat/test-rbind.r | 7 dplyr-0.4.2/dplyr/tests/testthat/test-sets.R | 11 dplyr-0.4.2/dplyr/vignettes/databases.Rmd | 10 dplyr-0.4.2/dplyr/vignettes/hybrid-evaluation.Rmd | 20 dplyr-0.4.2/dplyr/vignettes/introduction.Rmd | 4 dplyr-0.4.2/dplyr/vignettes/window-functions.Rmd | 2 189 files changed, 1458 insertions(+), 1613 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-2 dated 2015-06-14 and 0.1-3 dated 2015-06-16
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ man/DESP-package.Rd | 4 ++-- src/Makevars | 50 ++++++++++++++++---------------------------------- src/scs/Makefile | 12 ++++++------ src/scs/scs.mk | 13 +++++++++---- 7 files changed, 49 insertions(+), 57 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 1.0.1 dated 2015-05-26 and 2.0.1 dated 2015-06-16
DESCRIPTION | 15 ++- MD5 | 8 - R/CMplot.r | 249 ++++++++++++++++++++++++++++++++++++++++++++++---- man/CMplot-package.Rd | 47 ++++++--- man/pig60K.Rd | 2 5 files changed, 280 insertions(+), 41 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.18 dated 2015-04-19 and 2.19 dated 2015-06-16
DESCRIPTION |only MD5 |only NAMESPACE |only NEWS |only R |only build |only data |only inst/doc/vignette.pdf |binary man |only src |only vignettes |only 11 files changed
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Functions for Bayesian mete-analysis of diagnostic test data which are based on a scale mixtures bivariate random-effects model.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 1.1-1 dated 2011-12-08 and 2.0 dated 2015-06-16
bamdit-1.1-1/bamdit/R/bamdit.plot.R |only bamdit-1.1-1/bamdit/R/helpers.R |only bamdit-1.1-1/bamdit/R/model.handler.R |only bamdit-1.1-1/bamdit/R/read.RevMgr.R |only bamdit-1.1-1/bamdit/man/bamdit.plot.Rd |only bamdit-1.1-1/bamdit/man/read.RevMan.Rd |only bamdit-2.0/bamdit/ChangeLog | 68 ++- bamdit-2.0/bamdit/DESCRIPTION | 36 -- bamdit-2.0/bamdit/MD5 | 47 +- bamdit-2.0/bamdit/NAMESPACE | 16 bamdit-2.0/bamdit/R/bamdit-package.R |only bamdit-2.0/bamdit/R/bsroc.R |only bamdit-2.0/bamdit/R/metadiag.R | 574 +++++++++++++++++++++++++++----- bamdit-2.0/bamdit/R/plotcompare.R |only bamdit-2.0/bamdit/R/plotcont.R |only bamdit-2.0/bamdit/R/plotdata.R |only bamdit-2.0/bamdit/R/plotsesp.R |only bamdit-2.0/bamdit/R/plotw.R |only bamdit-2.0/bamdit/data/ct.rda |binary bamdit-2.0/bamdit/data/ep.rda |only bamdit-2.0/bamdit/data/glas.rda |only bamdit-2.0/bamdit/data/gould.rda |only bamdit-2.0/bamdit/data/safdar05.rda |only bamdit-2.0/bamdit/data/scheidler.rda |only bamdit-2.0/bamdit/man/bamdit-package.Rd | 66 +-- bamdit-2.0/bamdit/man/bsroc.Rd |only bamdit-2.0/bamdit/man/ct.Rd | 56 +-- bamdit-2.0/bamdit/man/ep.Rd |only bamdit-2.0/bamdit/man/glas.Rd |only bamdit-2.0/bamdit/man/gould.Rd |only bamdit-2.0/bamdit/man/metadiag.Rd | 99 +++-- bamdit-2.0/bamdit/man/mri.Rd | 48 +- bamdit-2.0/bamdit/man/plotcompare.Rd |only bamdit-2.0/bamdit/man/plotcont.Rd |only bamdit-2.0/bamdit/man/plotdata.Rd |only bamdit-2.0/bamdit/man/plotsesp.Rd |only bamdit-2.0/bamdit/man/plotw.Rd |only bamdit-2.0/bamdit/man/safdar05.Rd |only bamdit-2.0/bamdit/man/scheidler.Rd |only 39 files changed, 754 insertions(+), 256 deletions(-)
Title: Adaptive Semiparametric Regression with Simultaneous Confidence
Bands
Description: Fits semiparametric regression models with spatially adaptive penalized splines and computes simultaneous confidence bands.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>
Diff between AdaptFitOS versions 0.54 dated 2014-07-22 and 0.62 dated 2015-06-16
DESCRIPTION | 14 - MD5 | 25 +- NAMESPACE | 22 ++ R/asp-internal.r | 8 R/aspmFormReadOS.r | 4 R/default.knots.r |only R/firstlib.r | 9 inst |only man/AdaptFitOS-package.Rd | 12 - man/asp2.Rd | 456 ++++++++++++++++++++++------------------------ man/aspFormula.Rd | 2 man/aspHetero.Rd | 4 man/default.knots.Rd |only man/fitted.asp.Rd | 88 ++++---- man/summary.asp.Rd | 116 +++++------ 15 files changed, 383 insertions(+), 377 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.9.4 dated 2015-03-24 and 2.9.5 dated 2015-06-15
DESCRIPTION | 8 +-- MD5 | 114 ++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS | 33 ++++++++++++ R/DENSITY.R | 4 - R/esa.R | 1 R/ip.secr.R | 20 +++++-- R/join.R | 98 ++++++++++++++++++++++--------------- R/joinold.R |only R/make.capthist.R | 19 +++++-- R/methods.R | 20 +++---- R/pdot.R | 22 +++++++- R/raster.R | 18 +++--- R/read.traps.R | 11 ++++ R/reduce.R | 2 R/regionN.R | 1 R/score.test.R | 35 +------------ R/secr.fit.R | 90 ++++++++++++++++++++++++---------- R/secr.test.R | 2 R/secrloglik.R | 48 ++++++++++++++---- R/sim.capthist.R | 66 +++++++++++++++++-------- R/sim.popn.R | 79 +++++++++++++++++------------- R/sim.secr.R | 6 +- R/usagePlot.R | 4 - R/utility.R | 43 ++++++++++++++++ build/vignette.rds |binary data/OVpossum.RData |binary data/deermouse.RData |binary data/hornedlizard.RData |binary data/housemouse.RData |binary data/ovenbird.RData |binary data/ovensong.RData |binary data/possum.RData |binary data/secrdemo.RData |binary data/skink.RData |binary data/stoatDNA.RData |binary inst/doc/secr-datainput.R | 10 +-- inst/doc/secr-datainput.pdf |binary inst/doc/secr-manual.pdf |binary inst/doc/secr-overview.R | 26 +++++----- inst/doc/secr-overview.Rmd | 4 + inst/doc/secr-overview.pdf |binary man/DENSITY.Rd | 5 + man/RMarkInput.Rd | 2 man/addTelemetry.Rd | 3 - man/clone.Rd | 2 man/contour.Rd | 5 + man/details.Rd | 3 + man/join.Rd | 8 +++ man/make.capthist.Rd | 6 +- man/raster2.Rd |only man/secr-package.Rd | 9 ++- man/secr.fit.Rd | 1 man/secrtest.Rd | 14 ++--- man/sim.popn.Rd | 8 +-- man/simpopndetails.Rd | 8 +-- src/trapping.c | 3 - src/utils.c | 5 + vignettes/secr-overview.Rmd | 4 + 59 files changed, 556 insertions(+), 315 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.46 dated 2015-03-28 and 1.47 dated 2015-06-15
Changelog | 26 +++++++++ DESCRIPTION | 8 +- MD5 | 28 +++++----- R/Functions.R | 70 +++++++++++++++++++++++-- R/blockwiseModulesC.R | 73 ++++++++++++++++++++------ R/corFunctions.R | 2 R/empiricalBayesLM.R | 106 +++++++++++++++++++++++++-------------- R/smaFunctions.R |only man/WGCNA-package.Rd | 4 - man/blockwiseConsensusModules.Rd | 4 + man/blockwiseIndividualTOMs.Rd | 5 + man/blockwiseModules.Rd | 17 ++++++ man/empiricalBayesLM.Rd | 16 +++++ man/labeledHeatmap.multiPage.Rd | 32 +++++++++++ man/plotCor.Rd |only man/plotMat.Rd |only man/rgcolors.func.Rd |only 17 files changed, 312 insertions(+), 79 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.1.10 dated 2014-07-02 and 0.2.1 dated 2015-06-15
sads-0.1.10/sads/R/is.wholenumber.R |only sads-0.1.10/sads/R/pth.R |only sads-0.1.10/sads/R/qth.R |only sads-0.1.10/sads/R/trueLL.R |only sads-0.1.10/sads/man/trueLL.Rd |only sads-0.2.1/sads/DESCRIPTION | 18 - sads-0.2.1/sads/MD5 | 199 ++++++------ sads-0.2.1/sads/NAMESPACE | 18 - sads-0.2.1/sads/NEWS |only sads-0.2.1/sads/R/dbs.R | 15 sads-0.2.1/sads/R/dgs.R | 18 - sads-0.2.1/sads/R/dls.R | 23 - sads-0.2.1/sads/R/dmand.R | 23 - sads-0.2.1/sads/R/dmzsm.R | 24 - sads-0.2.1/sads/R/dpareto.R | 11 sads-0.2.1/sads/R/dpoig.R | 23 - sads-0.2.1/sads/R/dpoilog.R | 26 + sads-0.2.1/sads/R/dpoix.R | 31 - sads-0.2.1/sads/R/dpower.R | 25 - sads-0.2.1/sads/R/drbs.R | 16 sads-0.2.1/sads/R/dvolkov.R | 22 - sads-0.2.1/sads/R/dzipf.R | 19 - sads-0.2.1/sads/R/fitbs.R | 7 sads-0.2.1/sads/R/fitgamma.R | 57 ++- sads-0.2.1/sads/R/fitgeom.R | 2 sads-0.2.1/sads/R/fitgs.R | 6 sads-0.2.1/sads/R/fitlnorm.R | 8 sads-0.2.1/sads/R/fitls.R | 10 sads-0.2.1/sads/R/fitmand.R | 10 sads-0.2.1/sads/R/fitmzsm.R | 6 sads-0.2.1/sads/R/fitnbinom.R | 2 sads-0.2.1/sads/R/fitpareto.R | 10 sads-0.2.1/sads/R/fitpoilog.R | 3 sads-0.2.1/sads/R/fitpower.R | 2 sads-0.2.1/sads/R/fitrad.R | 1 sads-0.2.1/sads/R/fitrbs.R | 4 sads-0.2.1/sads/R/fitsad.R | 12 sads-0.2.1/sads/R/fitvolkov.R | 19 - sads-0.2.1/sads/R/fitweibull.R | 8 sads-0.2.1/sads/R/fitzipf.R | 6 sads-0.2.1/sads/R/octav.R | 15 sads-0.2.1/sads/R/pbs.R | 18 - sads-0.2.1/sads/R/pgs.R | 17 - sads-0.2.1/sads/R/plotprofmle.R | 11 sads-0.2.1/sads/R/pls.R | 17 - sads-0.2.1/sads/R/pmand.R | 29 - sads-0.2.1/sads/R/pmzsm.R | 18 - sads-0.2.1/sads/R/ppareto.R | 17 - sads-0.2.1/sads/R/ppoig.R |only sads-0.2.1/sads/R/ppoilog.R | 14 sads-0.2.1/sads/R/ppoix.R |only sads-0.2.1/sads/R/ppower.R | 25 - sads-0.2.1/sads/R/prbs.R | 15 sads-0.2.1/sads/R/pvolkov.R | 18 - sads-0.2.1/sads/R/pzipf.R | 24 - sads-0.2.1/sads/R/qbs.R | 41 -- sads-0.2.1/sads/R/qgs.R | 7 sads-0.2.1/sads/R/qls.R | 38 -- sads-0.2.1/sads/R/qmand.R | 13 sads-0.2.1/sads/R/qmzsm.R |only sads-0.2.1/sads/R/qpareto.R | 17 - sads-0.2.1/sads/R/qpoig.R |only sads-0.2.1/sads/R/qpoilog.R | 40 -- sads-0.2.1/sads/R/qpoix.R |only sads-0.2.1/sads/R/qpower.R | 36 -- sads-0.2.1/sads/R/qrbs.R | 11 sads-0.2.1/sads/R/qvolkov.R | 23 - sads-0.2.1/sads/R/qzipf.R | 11 sads-0.2.1/sads/R/rsad.R | 4 sads-0.2.1/sads/R/sads-classes.R | 23 + sads-0.2.1/sads/R/sads-methods.R | 513 +++++++++++-------------------- sads-0.2.1/sads/R/updatesad.R |only sads-0.2.1/sads/R/utils.R |only sads-0.2.1/sads/README.md |only sads-0.2.1/sads/build/vignette.rds |binary sads-0.2.1/sads/inst/doc/sads_intro.R | 82 ++-- sads-0.2.1/sads/inst/doc/sads_intro.Rnw | 164 ++++++--- sads-0.2.1/sads/inst/doc/sads_intro.pdf |binary sads-0.2.1/sads/man/ICtab.Rd |only sads-0.2.1/sads/man/birds.Rd | 6 sads-0.2.1/sads/man/dbs.Rd | 16 sads-0.2.1/sads/man/dgs.Rd | 4 sads-0.2.1/sads/man/dls.Rd | 12 sads-0.2.1/sads/man/dman.Rd | 6 sads-0.2.1/sads/man/dmzsm.Rd | 22 - sads-0.2.1/sads/man/dpareto.Rd | 10 sads-0.2.1/sads/man/dpoig.Rd | 45 ++ sads-0.2.1/sads/man/dpoilog.Rd | 26 - sads-0.2.1/sads/man/dpoix.Rd | 50 ++- sads-0.2.1/sads/man/dpower.Rd | 4 sads-0.2.1/sads/man/dtrunc.Rd | 2 sads-0.2.1/sads/man/dvolkov.Rd | 35 +- sads-0.2.1/sads/man/dzipf.Rd | 11 sads-0.2.1/sads/man/fitrad-class.Rd | 9 sads-0.2.1/sads/man/fitrad.Rd | 2 sads-0.2.1/sads/man/fitsad-class.Rd | 9 sads-0.2.1/sads/man/fitsad.Rd | 125 ++++--- sads-0.2.1/sads/man/octav-class.Rd | 8 sads-0.2.1/sads/man/octav.Rd | 4 sads-0.2.1/sads/man/octavpred.Rd | 2 sads-0.2.1/sads/man/plotprofmle.Rd | 2 sads-0.2.1/sads/man/pred.logser.Rd | 2 sads-0.2.1/sads/man/radpred.Rd | 11 sads-0.2.1/sads/man/rsad.Rd | 10 sads-0.2.1/sads/man/sads-package.Rd | 11 sads-0.2.1/sads/man/updatesad.Rd |only sads-0.2.1/sads/src |only sads-0.2.1/sads/vignettes/sads_intro.Rnw | 164 ++++++--- 108 files changed, 1222 insertions(+), 1331 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between PDQutils versions 0.1.1 dated 2015-02-26 and 0.1.2 dated 2015-06-15
DESCRIPTION | 10 MD5 | 48 +- NAMESPACE | 2 R/PDQutils.r | 33 + R/edgeworth.r | 5 R/gram_charlier.r | 316 ++++++++++++++--- R/moments.r | 9 README.md | 89 ++++- build/vignette.rds |binary inst/doc/PDQutils.R | 26 + inst/doc/PDQutils.Rnw | 868 ++++++++++++++++++++++++------------------------- inst/doc/PDQutils.pdf |binary inst/tests |only man/AS269.Rd | 2 man/NEWS.Rd | 10 man/PDQutils.Rd | 33 + man/cumulant2moment.Rd | 2 man/dapx_edgeworth.Rd | 2 man/dapx_gca.Rd | 132 +++++-- man/moment2cumulant.Rd | 2 man/qapx_cf.Rd | 8 man/rapx_cf.Rd | 8 tests |only vignettes/PDQutils.Rnw | 868 ++++++++++++++++++++++++------------------------- vignettes/PDQutils.bib | 61 +++ 25 files changed, 1514 insertions(+), 1020 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.3 dated 2015-01-28 and 0.4.4 dated 2015-06-15
DESCRIPTION | 11 ++-- MD5 | 80 ++++++++++++++++++----------------- NAMESPACE | 9 +++ R/bundle.R | 14 ++++++ R/cache.R | 90 +++++++++++++++++++++++++-------------- R/cranlike-repositories.R |only R/dependencies.R | 93 +++++++++++++++++++++++++++++++++-------- R/install.R | 16 ++++--- R/library-support.R | 23 +++++++--- R/options.R | 13 ++++- R/packrat-mode.R | 26 ++++++++--- R/packrat.R | 22 ++++++--- R/paths.R | 2 R/pkg.R | 13 ++++- R/restore.R | 62 ++++++++++++++++++++------- R/snapshot.R | 24 ++++++---- R/utils.R | 38 ++++++++++++++-- inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 man/appDependencies.Rd | 2 man/bundle.Rd | 2 man/clean.Rd | 2 man/disable.Rd | 2 man/init.Rd | 2 man/install.Rd | 2 man/install_github.Rd | 2 man/install_local.Rd | 2 man/migrate.Rd | 2 man/packify.Rd | 2 man/packrat-external.Rd | 2 man/packrat-mode.Rd | 2 man/packrat-options.Rd | 5 +- man/packrat.Rd | 2 man/repos_create.Rd |only man/repos_upload.Rd |only man/repository-management.Rd |only man/restore.Rd | 2 man/search_path.Rd | 2 man/snapshot.Rd | 2 man/snapshotImpl.Rd | 2 man/status.Rd | 2 man/unbundle.Rd | 2 man/unused_packages.Rd | 2 43 files changed, 407 insertions(+), 178 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.9 dated 2015-03-29 and 1.10 dated 2015-06-15
mirt-1.10/mirt/DESCRIPTION | 18 mirt-1.10/mirt/MD5 | 245 +- mirt-1.10/mirt/NAMESPACE | 8 mirt-1.10/mirt/NEWS | 113 + mirt-1.10/mirt/R/00-classes.R | 8 mirt-1.10/mirt/R/01-itemclass.R |only mirt-1.10/mirt/R/02-item_methods.R | 2337 +++++++++++++++++---- mirt-1.10/mirt/R/03-estimation.R | 213 + mirt-1.10/mirt/R/DIF.R | 31 mirt-1.10/mirt/R/DTF.R | 309 +- mirt-1.10/mirt/R/EMstep.group.R | 35 mirt-1.10/mirt/R/EMstep.utils.R | 16 mirt-1.10/mirt/R/LoadPars.R | 135 - mirt-1.10/mirt/R/M2.R | 89 mirt-1.10/mirt/R/MDIFF.R |only mirt-1.10/mirt/R/MDISC.R |only mirt-1.10/mirt/R/MHRM.group.R | 10 mirt-1.10/mirt/R/Mixed-methods.R | 2 mirt-1.10/mirt/R/MultipleGroup-methods.R | 15 mirt-1.10/mirt/R/PLCI.mirt.R | 32 mirt-1.10/mirt/R/PrepData.R | 43 mirt-1.10/mirt/R/SE.methods.R | 22 mirt-1.10/mirt/R/SingleGroup-methods.R | 157 - mirt-1.10/mirt/R/averageMI.R | 6 mirt-1.10/mirt/R/bfactor.R | 35 mirt-1.10/mirt/R/boot.mirt.R | 16 mirt-1.10/mirt/R/calcLogLik.R | 12 mirt-1.10/mirt/R/createItem.R | 2 mirt-1.10/mirt/R/expand.table.R | 4 mirt-1.10/mirt/R/expected.item.R | 4 mirt-1.10/mirt/R/expected.test.R | 4 mirt-1.10/mirt/R/extract.group.R | 6 mirt-1.10/mirt/R/extract.item.R | 5 mirt-1.10/mirt/R/fixef.R | 12 mirt-1.10/mirt/R/fscores.R | 44 mirt-1.10/mirt/R/fscores.internal.R | 167 - mirt-1.10/mirt/R/imputeMissing.R | 4 mirt-1.10/mirt/R/itemGAM.R |only mirt-1.10/mirt/R/itemfit.R | 55 mirt-1.10/mirt/R/iteminfo.R | 7 mirt-1.10/mirt/R/itemplot.R | 7 mirt-1.10/mirt/R/itemplot.internal.R | 43 mirt-1.10/mirt/R/key2binary.R | 5 mirt-1.10/mirt/R/marginal_rxx.R |only mirt-1.10/mirt/R/mdirt.R | 2 mirt-1.10/mirt/R/mirt-package.R | 6 mirt-1.10/mirt/R/mirt.R | 123 - mirt-1.10/mirt/R/mirt.model.R | 41 mirt-1.10/mirt/R/mirtCluster.R | 2 mirt-1.10/mirt/R/mixedmirt.R | 29 mirt-1.10/mirt/R/mod2values.R | 4 mirt-1.10/mirt/R/model.elements.R | 130 + mirt-1.10/mirt/R/multipleGroup.R | 42 mirt-1.10/mirt/R/personfit.R | 12 mirt-1.10/mirt/R/probtrace.R | 4 mirt-1.10/mirt/R/randef.R | 6 mirt-1.10/mirt/R/read.mirt.R | 42 mirt-1.10/mirt/R/shinyItemplot.R | 10 mirt-1.10/mirt/R/simdata.R | 18 mirt-1.10/mirt/R/utils.R | 223 +- mirt-1.10/mirt/R/wald.R | 19 mirt-1.10/mirt/build/vignette.rds |binary mirt-1.10/mirt/man/Bock1997.Rd | 2 mirt-1.10/mirt/man/DIF.Rd | 10 mirt-1.10/mirt/man/DTF.Rd | 59 mirt-1.10/mirt/man/DiscreteClass-class.Rd | 2 mirt-1.10/mirt/man/LSAT6.Rd | 6 mirt-1.10/mirt/man/LSAT7.Rd | 2 mirt-1.10/mirt/man/M2.Rd | 25 mirt-1.10/mirt/man/MDIFF.Rd |only mirt-1.10/mirt/man/MDISC.Rd |only mirt-1.10/mirt/man/MixedClass-class.Rd | 2 mirt-1.10/mirt/man/MultipleGroupClass-class.Rd | 2 mirt-1.10/mirt/man/PLCI.mirt.Rd | 8 mirt-1.10/mirt/man/SAT12.Rd | 2 mirt-1.10/mirt/man/Science.Rd | 2 mirt-1.10/mirt/man/SingleGroupClass-class.Rd | 5 mirt-1.10/mirt/man/anova-method.Rd | 4 mirt-1.10/mirt/man/averageMI.Rd | 4 mirt-1.10/mirt/man/bfactor.Rd | 24 mirt-1.10/mirt/man/boot.mirt.Rd | 2 mirt-1.10/mirt/man/coef-method.Rd | 5 mirt-1.10/mirt/man/createItem.Rd | 2 mirt-1.10/mirt/man/deAyala.Rd | 2 mirt-1.10/mirt/man/expand.table.Rd | 4 mirt-1.10/mirt/man/expected.item.Rd | 2 mirt-1.10/mirt/man/expected.test.Rd | 6 mirt-1.10/mirt/man/extract.group.Rd | 4 mirt-1.10/mirt/man/extract.item.Rd | 2 mirt-1.10/mirt/man/fixef.Rd | 10 mirt-1.10/mirt/man/fscores.Rd | 47 mirt-1.10/mirt/man/imputeMissing.Rd | 2 mirt-1.10/mirt/man/itemGAM.Rd |only mirt-1.10/mirt/man/itemfit.Rd | 20 mirt-1.10/mirt/man/iteminfo.Rd | 2 mirt-1.10/mirt/man/itemplot.Rd | 2 mirt-1.10/mirt/man/key2binary.Rd | 5 mirt-1.10/mirt/man/marginal_rxx.Rd |only mirt-1.10/mirt/man/mdirt.Rd | 2 mirt-1.10/mirt/man/mirt-package.Rd | 6 mirt-1.10/mirt/man/mirt.Rd | 121 - mirt-1.10/mirt/man/mirt.model.Rd | 47 mirt-1.10/mirt/man/mirtCluster.Rd | 2 mirt-1.10/mirt/man/mixedmirt.Rd | 14 mirt-1.10/mirt/man/mod2values.Rd | 4 mirt-1.10/mirt/man/multipleGroup.Rd | 36 mirt-1.10/mirt/man/personfit.Rd | 5 mirt-1.10/mirt/man/plot-method.Rd | 9 mirt-1.10/mirt/man/print-method.Rd | 2 mirt-1.10/mirt/man/probtrace.Rd | 2 mirt-1.10/mirt/man/randef.Rd | 4 mirt-1.10/mirt/man/residuals-method.Rd | 14 mirt-1.10/mirt/man/show-method.Rd | 2 mirt-1.10/mirt/man/simdata.Rd | 6 mirt-1.10/mirt/man/summary-method.Rd | 14 mirt-1.10/mirt/man/testinfo.Rd | 2 mirt-1.10/mirt/man/wald.Rd | 8 mirt-1.10/mirt/src/Misc.cpp | 20 mirt-1.10/mirt/src/traceLinePts.cpp | 3 mirt-1.10/mirt/tests/extratests/test-02-wideData.R | 6 mirt-1.10/mirt/tests/tests/test-01-mirtOne.R | 12 mirt-1.10/mirt/tests/tests/test-02-mirtTwo.R | 23 mirt-1.10/mirt/tests/tests/test-03-bfactor.R | 10 mirt-1.10/mirt/tests/tests/test-04-multipleGroup.R | 6 mirt-1.10/mirt/tests/tests/test-07-mixedmirt.R | 6 mirt-1.10/mirt/tests/tests/test-09-mirt.model.R | 45 mirt-1.10/mirt/tests/tests/test-10-extras.R | 14 mirt-1.9/mirt/R/01-itemtypes.R |only mirt-1.9/mirt/R/04-derivatives.R |only 129 files changed, 3998 insertions(+), 1712 deletions(-)
Title: Drawing Graphs with 'grid'
Description: Functions for drawing node-and-edge graphs that have been
laid out by graphviz. This provides an alternative
rendering to that provided by the 'Rgraphviz' package, with
two main advantages: the rendering provided by 'gridGraphviz'
should be more similar to what 'graphviz' itself would draw;
and rendering with 'grid' allows for post-hoc customisations
using the named viewports and grobs that 'gridGraphviz'
produces.
Author: Paul Murrell [cre, aut],
Ashley Noel Hinton [aut]
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between gridGraphviz versions 0.1 dated 2012-03-31 and 0.3 dated 2015-06-15
DESCRIPTION | 29 ++++++-- MD5 | 13 ++- NAMESPACE | 10 ++ R/graph.R | 181 +++++++++++++++++++++++++++++++++++++----------------- R/grobs.R |only R/methods.R |only inst |only man/agopenTrue.Rd |only man/graphWidth.Rd |only man/grid.graph.Rd | 6 + 10 files changed, 169 insertions(+), 70 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)),
Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see
Jiang, Manchanda, Rossi 2009)
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric
Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.0-0 dated 2015-06-12 and 3.0-1 dated 2015-06-15
DESCRIPTION | 8 +++--- MD5 | 44 +++++++++++++++++------------------ man/rbayesBLP.Rd | 2 - src/bayesBLP_rcpp_loop.cpp | 14 +++++------ src/rDPGibbs_rcpp_loop.cpp | 14 +++++------ src/rbprobitGibbs_rcpp_loop.cpp | 2 - src/rhierLinearMixture_rcpp_loop.cpp | 10 +++---- src/rhierLinearModel_rcpp_loop.cpp | 8 +++--- src/rhierMnlDP_rcpp_loop.cpp | 20 +++++++-------- src/rhierMnlRwMixture_rcpp_loop.cpp | 10 +++---- src/rhierNegbinRw_rcpp_loop.cpp | 10 +++---- src/rivDP_rcpp_loop.cpp | 18 +++++++------- src/rivgibbs_rcpp_loop.cpp | 8 +++--- src/rmnlIndepMetrop_rcpp_loop.cpp | 4 +-- src/rmnpGibbs_rcpp_loop.cpp | 4 +-- src/rmvpGibbs_rcpp_loop.cpp | 4 +-- src/rnegbinRw_rcpp_loop.cpp | 4 +-- src/rnmixGibbs_rcpp_loop.cpp | 6 ++-- src/rordprobitGibbs_rcpp_loop.cpp | 8 +++--- src/rscaleUsage_rcpp_loop.cpp | 2 - src/rsurGibbs_rcpp_loop.cpp | 4 +-- src/runiregGibbs_rcpp_loop.cpp | 4 +-- src/runireg_rcpp_loop.cpp | 4 +-- 23 files changed, 106 insertions(+), 106 deletions(-)
Title: Rewrite of gWidgets API for Simplified GUI Construction
Description: Re-implementation of gWidgets API. The API is defined in this
package. A second, toolkit-specific package is required to use it. There
are three in development: 'gWidgets2RGtk2', 'gWidgets2Qt', and 'gWidgets2tcltk'.
Author: John Verzani
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgets2 versions 1.0-5 dated 2014-03-05 and 1.0-6 dated 2015-06-15
gWidgets2-1.0-5/gWidgets2/README.md |only gWidgets2-1.0-6/gWidgets2/DESCRIPTION | 37 gWidgets2-1.0-6/gWidgets2/MD5 | 203 ++-- gWidgets2-1.0-6/gWidgets2/NAMESPACE | 12 gWidgets2-1.0-6/gWidgets2/R/BasicInterface.R | 14 gWidgets2-1.0-6/gWidgets2/R/dialogs.R | 14 gWidgets2-1.0-6/gWidgets2/R/gdf.R | 6 gWidgets2-1.0-6/gWidgets2/R/gedit.R | 12 gWidgets2-1.0-6/gWidgets2/R/gexpandgroup.R | 4 gWidgets2-1.0-6/gWidgets2/R/gfilter.R | 460 ++++++++- gWidgets2-1.0-6/gWidgets2/R/gframe.R | 5 gWidgets2-1.0-6/gWidgets2/R/gnotebook.R | 45 gWidgets2-1.0-6/gWidgets2/R/gpanedgroup.R | 5 gWidgets2-1.0-6/gWidgets2/R/gprogressbar.R | 4 gWidgets2-1.0-6/gWidgets2/R/gtable.R | 4 gWidgets2-1.0-6/gWidgets2/R/guiToolkit.R | 9 gWidgets2-1.0-6/gWidgets2/R/handler-methods.R | 61 + gWidgets2-1.0-6/gWidgets2/R/methods.R | 15 gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gbutton.R | 12 gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gdf.R |only gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gexpandgroup.R |only gWidgets2-1.0-6/gWidgets2/man/S4-classes.Rd | 115 +- gWidgets2-1.0-6/gWidgets2/man/XXX.Rd | 9 gWidgets2-1.0-6/gWidgets2/man/add.Rd | 66 - gWidgets2-1.0-6/gWidgets2/man/call_meth.Rd | 15 gWidgets2-1.0-6/gWidgets2/man/check_deprecated.Rd | 11 gWidgets2-1.0-6/gWidgets2/man/check_return_class.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/dispose.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/editable.Rd | 27 gWidgets2-1.0-6/gWidgets2/man/enabled.Rd | 28 gWidgets2-1.0-6/gWidgets2/man/flatten.Rd | 11 gWidgets2-1.0-6/gWidgets2/man/focus.Rd | 26 gWidgets2-1.0-6/gWidgets2/man/font.Rd | 63 - gWidgets2-1.0-6/gWidgets2/man/gWidgets-handlers.Rd | 471 ++++----- gWidgets2-1.0-6/gWidgets2/man/gWidgets2-S3methods.Rd | 102 +- gWidgets2-1.0-6/gWidgets2/man/gWidgets2-package.Rd | 475 ++++------ gWidgets2-1.0-6/gWidgets2/man/gWidgets2-undocumented.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/gaction.Rd | 55 - gWidgets2-1.0-6/gWidgets2/man/galert.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/gbasicdialog.Rd | 74 - gWidgets2-1.0-6/gWidgets2/man/gbutton.Rd | 143 +-- gWidgets2-1.0-6/gWidgets2/man/gcalendar.Rd | 62 - gWidgets2-1.0-6/gWidgets2/man/gcheckbox.Rd | 92 - gWidgets2-1.0-6/gWidgets2/man/gcheckboxgroup.Rd | 169 +-- gWidgets2-1.0-6/gWidgets2/man/gcombobox.Rd | 140 +- gWidgets2-1.0-6/gWidgets2/man/gconfirm.Rd | 36 gWidgets2-1.0-6/gWidgets2/man/gcontainer.Rd | 29 gWidgets2-1.0-6/gWidgets2/man/gdf.Rd | 74 - gWidgets2-1.0-6/gWidgets2/man/gdfnotebook.Rd | 21 gWidgets2-1.0-6/gWidgets2/man/gedit.Rd | 110 +- gWidgets2-1.0-6/gWidgets2/man/getToolkitWidget.Rd | 51 - gWidgets2-1.0-6/gWidgets2/man/getWithDefault.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/get_index_in_list.Rd | 12 gWidgets2-1.0-6/gWidgets2/man/get_object_from_string.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/gexpandgroup.Rd | 78 - gWidgets2-1.0-6/gWidgets2/man/gfile.Rd | 176 +-- gWidgets2-1.0-6/gWidgets2/man/gfilter.Rd | 164 +-- gWidgets2-1.0-6/gWidgets2/man/gformlayout.Rd | 98 -- gWidgets2-1.0-6/gWidgets2/man/gframe.Rd | 51 - gWidgets2-1.0-6/gWidgets2/man/ggraphics.Rd | 98 +- gWidgets2-1.0-6/gWidgets2/man/ggraphicsnotebook.Rd | 63 - gWidgets2-1.0-6/gWidgets2/man/ggroup.Rd | 127 +- gWidgets2-1.0-6/gWidgets2/man/ghtml.Rd | 75 - gWidgets2-1.0-6/gWidgets2/man/gimage.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/ginput.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/glabel.Rd | 73 - gWidgets2-1.0-6/gWidgets2/man/glayout.Rd | 100 +- gWidgets2-1.0-6/gWidgets2/man/gmenu.Rd | 173 +-- gWidgets2-1.0-6/gWidgets2/man/gmessage.Rd | 35 gWidgets2-1.0-6/gWidgets2/man/gnotebook.Rd | 238 ++--- gWidgets2-1.0-6/gWidgets2/man/gpanedgroup.Rd | 75 - gWidgets2-1.0-6/gWidgets2/man/gprogressbar.Rd | 68 - gWidgets2-1.0-6/gWidgets2/man/gradio.Rd | 169 +-- gWidgets2-1.0-6/gWidgets2/man/gseparator.Rd | 46 gWidgets2-1.0-6/gWidgets2/man/gslider.Rd | 132 +- gWidgets2-1.0-6/gWidgets2/man/gspinbutton.Rd | 119 +- gWidgets2-1.0-6/gWidgets2/man/gstackwidget.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/gstatusbar.Rd | 36 gWidgets2-1.0-6/gWidgets2/man/gtable.Rd | 221 ++-- gWidgets2-1.0-6/gWidgets2/man/gtext.Rd | 220 ++-- gWidgets2-1.0-6/gWidgets2/man/gtimer.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/gtoolbar.Rd | 100 -- gWidgets2-1.0-6/gWidgets2/man/gtoolkit.Rd | 8 gWidgets2-1.0-6/gWidgets2/man/gtree.Rd | 221 ++-- gWidgets2-1.0-6/gWidgets2/man/guiToolkit.Rd | 28 gWidgets2-1.0-6/gWidgets2/man/gvarbrowser.Rd | 165 +-- gWidgets2-1.0-6/gWidgets2/man/gwidget.Rd | 78 - gWidgets2-1.0-6/gWidgets2/man/gwindow.Rd | 146 +-- gWidgets2-1.0-6/gWidgets2/man/icons.Rd | 91 - gWidgets2-1.0-6/gWidgets2/man/installing_gWidgets_toolkits.Rd | 6 gWidgets2-1.0-6/gWidgets2/man/isExtant.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/is_MacOSX.Rd | 9 gWidgets2-1.0-6/gWidgets2/man/is_Windows.Rd | 8 gWidgets2-1.0-6/gWidgets2/man/is_empty.Rd | 10 gWidgets2-1.0-6/gWidgets2/man/methods.Rd | 34 gWidgets2-1.0-6/gWidgets2/man/observer.Rd | 14 gWidgets2-1.0-6/gWidgets2/man/redo.Rd | 14 gWidgets2-1.0-6/gWidgets2/man/short_summary.Rd | 44 gWidgets2-1.0-6/gWidgets2/man/size.Rd | 23 gWidgets2-1.0-6/gWidgets2/man/svalue.Rd | 91 - gWidgets2-1.0-6/gWidgets2/man/tag.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/tooltip.Rd | 22 gWidgets2-1.0-6/gWidgets2/man/undo.Rd | 15 gWidgets2-1.0-6/gWidgets2/man/visible.Rd | 30 104 files changed, 3922 insertions(+), 3573 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.29 dated 2015-02-06 and 1.30 dated 2015-06-15
DESCRIPTION | 10 MD5 | 50 ++-- R/CA.R | 120 ++++++----- R/FAMD.R | 179 ++++++++++++++--- R/HCPC.R | 7 R/MCA.R | 89 +++++--- R/MFA.R | 86 ++++---- R/PCA.R | 174 ++++++++-------- R/condes.r | 3 R/dimdesc.r | 22 +- R/plot.FAMD.R | 43 ++-- R/plot.MCA.R | 5 R/plot.MFA.R | 72 ++++++ R/plot.PCA.R | 2 R/plotellipses.r | 20 + R/summary.MFA.r | 1 R/svd.triplet.R | 88 ++++---- R/tab.disjonctif.R | 31 +- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/FAMD.Rd | 2 man/children.Rd | 2 man/geomorphology.Rd | 3 man/plot.FAMD.Rd | 1 man/plotellipses.Rd | 2 man/poulet.Rd | 18 - 26 files changed, 661 insertions(+), 369 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 1.6.2 dated 2015-02-23 and 1.7 dated 2015-06-15
DESCRIPTION | 12 ++++++------ MD5 | 41 +++++++++++++++++++++-------------------- NAMESPACE | 7 +++++-- R/calc.imp.pval.R | 2 -- R/clean.rf.data.R | 7 +++---- R/plot.rfPermute.R | 7 +++---- R/plot.rp.importance.r | 6 +++--- R/proximity.plot.r | 5 ++--- R/rfPermute.R | 12 +++++------- R/rfPermute.default.R | 10 +++++----- R/rfPermute.formula.R | 7 +++---- R/rp.combine.R | 4 ++-- R/rp.importance.R | 5 ++--- inst |only man/calc.imp.pval.Rd | 2 +- man/clean.rf.data.Rd | 2 +- man/plot.rfPermute.Rd | 4 ++-- man/plot.rp.importance.Rd | 5 +++-- man/proximity.plot.Rd | 2 +- man/rfPermute.Rd | 17 +++++++---------- man/rp.combine.Rd | 2 +- man/rp.importance.Rd | 2 +- 22 files changed, 77 insertions(+), 84 deletions(-)
Title: An Improved Evaluation of Kolmogorov's Distribution
Description: Provides an alternative, more efficient evaluation of extreme
probabilities of Kolmogorov's goodness-of-fit measure, Dn, when compared to
the original implementation of Wang, Marsaglia, and Tsang. These
probabilities are used in Kolmogorov-Smirnov tests when comparing two
samples.
Author: Luis Carvalho
Maintainer: Luis Carvalho <lexcarvalho@gmail.com>
Diff between kolmim versions 0.2 dated 2014-04-20 and 1.0 dated 2015-06-15
DESCRIPTION | 20 ++++++++++---------- MD5 | 9 +++++---- inst |only man/ks.test.imp.Rd | 8 +++++--- man/pkolmim.Rd | 8 +++++--- src/kolmim.c | 13 +++++++------ 6 files changed, 32 insertions(+), 26 deletions(-)
Title: Perform Factorial Analysis from FactoMineR with a Shiny
Application
Description: Perform factorial analysis with a menu and draw graphs interactively thanks to FactoMineR and a Shiny application.
Author: Pauline Vaissie, Astrid Monge, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between Factoshiny versions 1.0 dated 2015-02-20 and 1.0.2 dated 2015-06-15
DESCRIPTION | 8 +- MD5 | 53 ++++++++------ NAMESPACE | 3 R/FAMDshiny.R |only R/HCPCshiny.R | 2 R/print.FAMDshiny.R |only inst/FactoCAapp2/global.R | 3 inst/FactoCAapp2/server.R | 68 +++++++++++++++--- inst/FactoCAapp2/ui.R | 24 +++--- inst/FactoFAMDapp2 |only inst/FactoHCPCapp2/global.R | 29 +++++++ inst/FactoHCPCapp2/server.R | 15 ++-- inst/FactoHCPCapp2/ui.R | 14 ++- inst/FactoHCPCappdf2/global.R | 10 ++ inst/FactoHCPCappdf2/server.R | 17 ++-- inst/FactoHCPCappdf2/ui.R | 14 ++- inst/FactoMCAapp2/global.R | 13 +++ inst/FactoMCAapp2/server.R | 157 ++++++++++++++++++++++++++++++++---------- inst/FactoMCAapp2/ui.R | 46 +++++++----- inst/FactoMFAapp/server.R | 41 +++++++--- inst/FactoMFAapp/ui.R | 15 +++- inst/FactoMFAapp2/global.R | 10 ++ inst/FactoMFAapp2/server.R | 45 ++++++++---- inst/FactoMFAapp2/ui.R | 15 +++- inst/FactoPCAapp2/global.R | 6 + inst/FactoPCAapp2/server.R | 47 +++++++++--- inst/FactoPCAapp2/ui.R | 13 ++- man/FAMDshiny.Rd |only man/print.FAMDshiny.Rd |only 29 files changed, 496 insertions(+), 172 deletions(-)
Title: Construction and Evaluation of Metamodels
Description: Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceEval versions 1.3 dated 2014-05-27 and 1.4 dated 2015-06-15
DESCRIPTION | 13 ++--- MD5 | 9 ++- R/modelFit.R | 116 ++++++++++++++++++++++++------------------------ R/modelPredict.R | 34 +++++++------- inst |only man/DiceEval-package.Rd | 6 +- 6 files changed, 90 insertions(+), 88 deletions(-)
Title: Designs of Computer Experiments
Description: Space-Filling Designs and Uniformity Criteria.
Author: Jessica Franco, Delphine Dupuy, Olivier Roustant, Guillaume
Damblin and Bertrand Iooss.
Maintainer: Celine Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceDesign versions 1.6 dated 2014-05-09 and 1.7 dated 2015-06-15
DiceDesign-1.6/DiceDesign/inst/po |only DiceDesign-1.6/DiceDesign/po |only DiceDesign-1.7/DiceDesign/DESCRIPTION | 8 DiceDesign-1.7/DiceDesign/MD5 | 18 - DiceDesign-1.7/DiceDesign/R/rss3d.R | 99 +++++---- DiceDesign-1.7/DiceDesign/inst/CITATION |only DiceDesign-1.7/DiceDesign/man/DiceDesign-package.Rd | 200 ++++++++++---------- DiceDesign-1.7/DiceDesign/man/coverage.Rd | 76 +++---- DiceDesign-1.7/DiceDesign/man/meshRatio.Rd | 80 ++++---- DiceDesign-1.7/DiceDesign/man/mindist.Rd | 86 ++++---- DiceDesign-1.7/DiceDesign/src/C_StraussDesign.c | 19 + 11 files changed, 298 insertions(+), 288 deletions(-)
Title: Bayesian Bootstrap Predictive Mean Matching - Multiple and
Single Imputation for Discrete Data
Description: Included are two variants of Bayesian Bootstrap
Predictive Mean Matching to multiply impute missing data. The
first variant is a variable-by-variable imputation combining
sequential regression and Predictive Mean Matching (PMM) that
has been extended for unordered categorical data. The Bayesian
Bootstrap allows for generating approximately proper multiple
imputations. The second variant is also based on PMM, but the
focus is on imputing several variables at the same time. The
suggestion is to use this variant, if the missing-data pattern
resembles a data fusion situation, or any other
missing-by-design pattern, where several variables have
identical missing-data patterns. Both variants can be run as
'single imputation' versions, in case the analysis objective is
of a purely descriptive nature.
Author: Florian Meinfelder [aut, cre],
Thorsten Schnapp [aut]
Maintainer: Florian Meinfelder <florian.meinfelder@uni-bamberg.de>
Diff between BaBooN versions 0.1-6 dated 2011-03-26 and 0.2-0 dated 2015-06-15
BaBooN-0.1-6/BaBooN/R/BBPMMcol.R |only BaBooN-0.2-0/BaBooN/DESCRIPTION | 22 BaBooN-0.2-0/BaBooN/MD5 |only BaBooN-0.2-0/BaBooN/NAMESPACE | 11 BaBooN-0.2-0/BaBooN/NEWS |only BaBooN-0.2-0/BaBooN/R/BB.R | 5 BaBooN-0.2-0/BaBooN/R/BBPMM.R |only BaBooN-0.2-0/BaBooN/R/BBPMMrow.R | 640 +++++++++++++-------- BaBooN-0.2-0/BaBooN/R/BBmodstab_glm.R | 72 +- BaBooN-0.2-0/BaBooN/R/BBmodstab_mlog.R | 92 +-- BaBooN-0.2-0/BaBooN/R/MIinference.R | 4 BaBooN-0.2-0/BaBooN/R/PMMC.R |only BaBooN-0.2-0/BaBooN/R/PMMsearch.R | 7 BaBooN-0.2-0/BaBooN/R/classes.R | 7 BaBooN-0.2-0/BaBooN/R/dmi.R |only BaBooN-0.2-0/BaBooN/R/impdiagnosticconversion.R |only BaBooN-0.2-0/BaBooN/R/inbind.R |only BaBooN-0.2-0/BaBooN/R/rowimpprep.R | 163 +++-- BaBooN-0.2-0/BaBooN/man/BBPMMcol.Rd | 104 ++- BaBooN-0.2-0/BaBooN/man/BBPMMrow.Rd | 76 +- BaBooN-0.2-0/BaBooN/man/BaBooN-package.Rd |only BaBooN-0.2-0/BaBooN/man/MIinference.Rd | 40 - BaBooN-0.2-0/BaBooN/man/SummaryImp.Rd | 2 BaBooN-0.2-0/BaBooN/man/SummaryImpprep.Rd | 2 BaBooN-0.2-0/BaBooN/man/dmi.Rd |only BaBooN-0.2-0/BaBooN/man/impdiagnosticconversion.Rd |only BaBooN-0.2-0/BaBooN/man/rowimpprep.Rd | 7 BaBooN-0.2-0/BaBooN/src |only 28 files changed, 790 insertions(+), 464 deletions(-)
Title: Assess Tumor Microsatellite Instability with a Decision Tree
Classifier from Exome Somatic Mutations
Description: A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.
Author: Mini Huang
Maintainer: Mini Huang <mini.huang@nus.edu.sg>
Diff between MSIseq versions 0.99.1 dated 2014-09-03 and 1.0.0 dated 2015-06-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/MSIseq.classify.R | 16 +++++++++++++--- inst/doc/MSIseq.pdf |binary man/MSIseq-package.Rd | 6 +++--- man/MSIseq.classify.Rd | 4 ++-- vignettes/MSIseq.Rnw | 2 +- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Description: An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley
in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package FuzzyNumbers is used to represent the output probabilities.
Author: Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between FuzzyStatProb versions 2.0 dated 2015-03-18 and 2.0.1 dated 2015-06-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/main.R | 35 ++++++++++++++++++----------------- build/vignette.rds |binary 4 files changed, 25 insertions(+), 24 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.2.0 dated 2015-05-29 and 0.3.0 dated 2015-06-15
diagonals-0.2.0/diagonals/R/block_matrix.R |only diagonals-0.2.0/diagonals/R/minus_block_matrix.R |only diagonals-0.2.0/diagonals/R/minus_rectangle_matrix.R |only diagonals-0.2.0/diagonals/R/rectangle_matrix.R |only diagonals-0.2.0/diagonals/inst/doc/diagonals.R |only diagonals-0.2.0/diagonals/inst/doc/diagonals.Rmd |only diagonals-0.2.0/diagonals/inst/doc/diagonals.html |only diagonals-0.2.0/diagonals/inst/doc/network.R |only diagonals-0.2.0/diagonals/inst/doc/network.Rmd |only diagonals-0.2.0/diagonals/inst/doc/network.html |only diagonals-0.2.0/diagonals/man/block_matrix.Rd |only diagonals-0.2.0/diagonals/man/minus_block_matrix.Rd |only diagonals-0.2.0/diagonals/man/minus_rectangle_matrix.Rd |only diagonals-0.2.0/diagonals/man/rectangle_matrix.Rd |only diagonals-0.2.0/diagonals/tests |only diagonals-0.2.0/diagonals/vignettes/diagonals.Rmd |only diagonals-0.2.0/diagonals/vignettes/network.Rmd |only diagonals-0.3.0/diagonals/DESCRIPTION | 6 - diagonals-0.3.0/diagonals/MD5 | 41 +++----- diagonals-0.3.0/diagonals/NAMESPACE | 7 - diagonals-0.3.0/diagonals/NEWS | 8 + diagonals-0.3.0/diagonals/R/diag.R |only diagonals-0.3.0/diagonals/R/diagonals.R | 7 + diagonals-0.3.0/diagonals/R/fatdiag.R |only diagonals-0.3.0/diagonals/R/split_vector.R |only diagonals-0.3.0/diagonals/README.md | 75 ++++++++++------ diagonals-0.3.0/diagonals/build/vignette.rds |binary diagonals-0.3.0/diagonals/inst/doc/fatdiag.R |only diagonals-0.3.0/diagonals/inst/doc/fatdiag.Rmd |only diagonals-0.3.0/diagonals/inst/doc/fatdiag.html |only diagonals-0.3.0/diagonals/man/diag-set.Rd |only diagonals-0.3.0/diagonals/man/fatdiag.Rd |only diagonals-0.3.0/diagonals/man/split_vector.Rd |only diagonals-0.3.0/diagonals/vignettes/fatdiag.Rmd |only 34 files changed, 84 insertions(+), 60 deletions(-)
Title: Mixed Effects Cox Models
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau@mayo.edu>
Diff between coxme versions 2.2-4 dated 2015-03-03 and 2.2-5 dated 2015-06-15
coxme-2.2-4/coxme/noweb/noweb.Rnw |only coxme-2.2-5/coxme/DESCRIPTION | 7 ++---- coxme-2.2-5/coxme/MD5 | 33 +++++++++++++++++++------------- coxme-2.2-5/coxme/NAMESPACE | 1 coxme-2.2-5/coxme/R/anova.coxme.R | 8 ------- coxme-2.2-5/coxme/R/anova.coxmelist.R |only coxme-2.2-5/coxme/build/vignette.rds |binary coxme-2.2-5/coxme/inst/NEWS.Rd | 6 +++++ coxme-2.2-5/coxme/inst/doc/coxme.R | 22 ++++++++++----------- coxme-2.2-5/coxme/inst/doc/coxme.Rnw | 11 ++++------ coxme-2.2-5/coxme/inst/doc/coxme.pdf |binary coxme-2.2-5/coxme/inst/doc/laplace.pdf |binary coxme-2.2-5/coxme/inst/doc/lmekin.pdf |binary coxme-2.2-5/coxme/inst/doc/variance.pdf |binary coxme-2.2-5/coxme/noweb/all.aux |only coxme-2.2-5/coxme/noweb/all.log |only coxme-2.2-5/coxme/noweb/all.out |only coxme-2.2-5/coxme/noweb/all.pdf |only coxme-2.2-5/coxme/noweb/all.tex |only coxme-2.2-5/coxme/noweb/all.toc |only coxme-2.2-5/coxme/noweb/noweb.sty |only coxme-2.2-5/coxme/vignettes/coxme.Rnw | 11 ++++------ 22 files changed, 52 insertions(+), 47 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.0 dated 2015-04-16 and 1.0.1 dated 2015-06-15
DESCRIPTION | 8 MD5 | 6 inst/doc/compendiumdb.pdf |binary inst/scripts/Perl/parsingSoftFile_forESET.pl | 581 +++++++++++++-------------- 4 files changed, 298 insertions(+), 297 deletions(-)
Title: Computed ABC Analysis
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many"). Package is based on Ultsch. A ., Lotsch J.: Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data, PLoS One, 2015.
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between ABCanalysis versions 1.0.1 dated 2015-04-20 and 1.0.2 dated 2015-06-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/ABCanalysis-package.Rd | 3 +++ man/ABCanalysis.Rd | 4 +++- man/ABCcurve.Rd | 3 +++ 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.0-7.1 dated 2014-02-21 and 0.1.0 dated 2015-06-15
treebase-0.0-7.1/treebase/tests/testthat/metadata.R |only treebase-0.0-7.1/treebase/tests/testthat/treebase.R |only treebase-0.1.0/treebase/DESCRIPTION | 21 +-- treebase-0.1.0/treebase/MD5 | 46 +++---- treebase-0.1.0/treebase/NAMESPACE | 2 treebase-0.1.0/treebase/NEWS | 6 treebase-0.1.0/treebase/README.md | 7 - treebase-0.1.0/treebase/man/cache_treebase.Rd | 23 +-- treebase-0.1.0/treebase/man/clean_data.Rd | 4 treebase-0.1.0/treebase/man/download_metadata.Rd | 21 +-- treebase-0.1.0/treebase/man/drop_nonascii.Rd | 4 treebase-0.1.0/treebase/man/drop_nontrees.Rd | 8 - treebase-0.1.0/treebase/man/dryad_metadata.Rd | 9 - treebase-0.1.0/treebase/man/get_nex.Rd | 29 ++-- treebase-0.1.0/treebase/man/get_study.Rd | 22 +-- treebase-0.1.0/treebase/man/get_study_id.Rd | 12 - treebase-0.1.0/treebase/man/have_branchlength.Rd | 5 treebase-0.1.0/treebase/man/metadata.Rd | 24 ++- treebase-0.1.0/treebase/man/metadata_from_oai.Rd | 12 - treebase-0.1.0/treebase/man/oai_metadata.Rd | 18 +- treebase-0.1.0/treebase/man/phylo_metadata.Rd | 16 +- treebase-0.1.0/treebase/man/search_treebase.Rd | 107 +++++++---------- treebase-0.1.0/treebase/man/show_metadata.Rd | 19 +-- treebase-0.1.0/treebase/man/treebase.Rd | 10 + treebase-0.1.0/treebase/tests/testthat/test_metadata.R |only treebase-0.1.0/treebase/tests/testthat/test_treebase.R |only 26 files changed, 212 insertions(+), 213 deletions(-)
Title: An R Interface to 'figshare'
Description: An interface to 'figshare' (http://figshare.com), a scientific repository to archive and assign 'DOIs' to data, software, figures, and more.
Author: Carl Boettiger [aut, cre],
Scott Chamberlain [aut],
Karthik Ram [aut],
Edmund Hart [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfigshare versions 0.3.6 dated 2014-08-04 and 0.3.7 dated 2015-06-15
rfigshare-0.3.6/rfigshare/build |only rfigshare-0.3.6/rfigshare/inst/doc/README.R |only rfigshare-0.3.6/rfigshare/inst/doc/README.Rmd |only rfigshare-0.3.6/rfigshare/inst/doc/README.html |only rfigshare-0.3.6/rfigshare/inst/doc/vignettes/README.Rmd |only rfigshare-0.3.6/rfigshare/vignettes |only rfigshare-0.3.7/rfigshare/DESCRIPTION | 16 +-- rfigshare-0.3.7/rfigshare/MD5 | 78 ++++++--------- rfigshare-0.3.7/rfigshare/NAMESPACE | 2 rfigshare-0.3.7/rfigshare/NEWS | 3 rfigshare-0.3.7/rfigshare/R/fs_browse.R | 9 - rfigshare-0.3.7/rfigshare/R/fs_object_methods.R | 8 - rfigshare-0.3.7/rfigshare/R/fs_search.R | 8 - rfigshare-0.3.7/rfigshare/README.md | 2 rfigshare-0.3.7/rfigshare/man/fs_add_author.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_authors.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_categories.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_links.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_add_tags.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_auth.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_author_ids.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_author_search.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_browse.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_cat_to_id.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_category_list.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_create.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_create_author.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_delete.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_details.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_download.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_embed.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_ids.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_image_url.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_make_private.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_make_public.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_new_article.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_search.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_update.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_upload.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_upload_one.Rd | 3 rfigshare-0.3.7/rfigshare/man/plot_to_filename.Rd | 3 rfigshare-0.3.7/rfigshare/man/summary_fs_details.Rd | 3 rfigshare-0.3.7/rfigshare/tests/testthat/test_figshare.R | 8 - 43 files changed, 127 insertions(+), 103 deletions(-)
Title: Application in R for Queueing Analysis and Simulation
Description: Provides functions to compute the main characteristics of the
following queueing models: M/M/1, M/M/s, M/M/1/k, M/M/s/k, M/M/1/Inf/H, M/
M/s/Inf/H, M/M/s/Inf/H with Y replacements, M/M/Inf, Open Jackson Networks
and Closed Jackson Networks. Moreover, it is also possible to simulate
similar queueing models with any type of arrival or service distribution: G/
G/1, G/G/s, G/G/1/k, G/G/s/k, G/G/1/Inf/H, G/G/s/Inf/H, G/G/s/Inf/H with Y
replacements, Open Networks and Closed Networks. Finally, contains functions
for fit data to a statistic distribution.
Author: Borja Varela
Maintainer: Borja Varela <borja.varela.brea@gmail.com>
Diff between arqas versions 1.0 dated 2015-06-01 and 1.1 dated 2015-06-15
DESCRIPTION | 10 ++++---- MD5 | 34 ++++++++++++++-------------- R/1_ModelsHeader.R | 34 +++++++++++++++++----------- R/2_SimpleModels.R | 11 ++++----- R/3_ComplexModels.R | 20 ++++++++-------- R/4_NetworkModels.R | 51 +++++++++++++++++++++++------------------- R/5_SimulateModels.R | 26 +++++++++++++++++++++ R/6_DistributionAnalysis.R | 2 - man/ClosedJacksonNetwork.Rd | 20 +++++++++------- man/M_M_1.Rd | 2 - man/M_M_1_INF_H.Rd | 6 ++-- man/M_M_1_K.Rd | 2 - man/M_M_S.Rd | 2 - man/M_M_S_INF_H_Y.Rd | 14 +++++------ man/M_M_S_K.Rd | 2 - man/OpenJacksonNetwork.Rd | 11 ++++----- man/fitData.Rd | 3 +- man/summary.MarkovianModel.Rd | 7 ++++- 18 files changed, 153 insertions(+), 104 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.2.1 dated 2015-05-12 and 0.3 dated 2015-06-14
ChangeLog | 10 DESCRIPTION | 17 MD5 | 65 NAMESPACE | 1 NEWS | 16 R/0_classesAndMethods.R | 61 R/2_probabilistic.R | 263 - R/RcppExports.R | 44 R/zzz.R | 8 build/vignette.rds |binary demo/00Index | 1 demo/mathematica.R |only demo/quickStart.R | 11 inst/CITATION | 4 inst/doc/BayesianInference.R |only inst/doc/BayesianInference.Rmd |only inst/doc/BayesianInference.pdf |only inst/doc/an_introduction_to_markovchain_package.R | 77 inst/doc/an_introduction_to_markovchain_package.Rnw | 49 inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.R |only inst/doc/markovchainCrashIntro.Rmd |only inst/doc/markovchainCrashIntro.pdf |only man/inferHyperparam.Rd |only man/markovchain-package.Rd | 4 man/markovchainFit.Rd | 26 man/predictiveDistribution.Rd |only src/0_classesAndMethods.cpp |only src/1_functions4Fitting.cpp | 350 +- src/2_probabilistic.cpp |only src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 125 src/mapFitFunctionsSAI.h |only src/mathHelperFunctions.h |only tests/testthat.R | 1 tests/testthat/testBasic1.R | 17 vignettes/BayesianInference.Rmd |only vignettes/an_introduction_to_markovchain_package.Rnw | 62 vignettes/jss.dtx | 2824 +++++++++---------- vignettes/markovchainBiblio.bib | 23 vignettes/markovchainCrashIntro.Rmd |only 42 files changed, 2278 insertions(+), 1781 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.3.1 dated 2015-06-04 and 0.4.0 dated 2015-06-14
DESCRIPTION | 12 MD5 | 65 +++-- NAMESPACE | 8 NEWS | 12 R/cowplot.R | 541 -------------------------------------------- R/draw.R |only R/gtable.R |only R/plot_grid.R |only R/save.R |only R/setup.R |only R/switch_axis.R |only R/themes.R |only build/vignette.rds |binary inst/doc/axis_position.R |only inst/doc/axis_position.Rmd |only inst/doc/axis_position.html |only inst/doc/introduction.R | 42 ++- inst/doc/introduction.Rmd | 40 ++- inst/doc/introduction.html | 62 ++--- inst/doc/plot_grid.R |only inst/doc/plot_grid.Rmd |only inst/doc/plot_grid.html |only man/background_grid.Rd | 3 man/cowplot.Rd | 3 man/draw_grob.Rd |only man/draw_line.Rd | 3 man/draw_plot.Rd | 5 man/draw_plot_label.Rd | 3 man/draw_text.Rd | 3 man/ggdraw.Rd | 5 man/ggsave.Rd | 3 man/gtable_remove_grobs.Rd |only man/gtable_squash_cols.Rd |only man/gtable_squash_rows.Rd |only man/panel_border.Rd | 3 man/plot_grid.Rd | 37 ++- man/plot_theme.Rd |only man/save_plot.Rd | 3 man/switch_axis_position.Rd |only man/theme_cowplot.Rd | 3 man/theme_nothing.Rd | 3 vignettes/axis_position.Rmd |only vignettes/introduction.Rmd | 38 ++- vignettes/plot_grid.Rmd |only 44 files changed, 228 insertions(+), 669 deletions(-)
Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between clue versions 0.3-49 dated 2015-02-02 and 0.3-50 dated 2015-06-14
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/predict.R | 18 ++++++++++++++++-- build/vignette.rds |binary data/CKME.rda |binary data/Cassini.rda |binary data/GVME.rda |binary data/GVME_Consensus.rda |binary data/Kinship82.rda |binary data/Kinship82_Consensus.rda |binary data/Phonemes.rda |binary inst/doc/clue.pdf |binary 13 files changed, 35 insertions(+), 20 deletions(-)
Title: Extensions of Exponential Random Graph Models
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), and Temporal Network Autocorrelation Models (TNAM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld <philip.leifeld@uni-konstanz.de>
Diff between xergm versions 1.4.1 dated 2015-02-10 and 1.5 dated 2015-06-14
xergm-1.4.1/xergm/R/mtergm.R |only xergm-1.4.1/xergm/build |only xergm-1.4.1/xergm/inst/doc |only xergm-1.4.1/xergm/vignettes |only xergm-1.5/xergm/DESCRIPTION | 17 xergm-1.5/xergm/MD5 | 50 -- xergm-1.5/xergm/NAMESPACE | 5 xergm-1.5/xergm/R/btergm.R | 806 ++++++++++++++++++++++++++------- xergm-1.5/xergm/R/gof.R | 509 ++++++++------------ xergm-1.5/xergm/R/interpretation.R | 93 +++ xergm-1.5/xergm/R/preprocess.R | 283 ++++++++--- xergm-1.5/xergm/R/tnam.R | 78 +-- xergm-1.5/xergm/data/chemnet.rda |only xergm-1.5/xergm/data/knecht.rda |binary xergm-1.5/xergm/man/adjust.Rd | 7 xergm-1.5/xergm/man/btergm-class.Rd | 4 xergm-1.5/xergm/man/btergm.Rd | 16 xergm-1.5/xergm/man/chemnet.Rd |only xergm-1.5/xergm/man/gof.Rd | 60 -- xergm-1.5/xergm/man/simulate.btergm.Rd | 4 xergm-1.5/xergm/man/timecov.Rd | 2 xergm-1.5/xergm/man/tnam-terms.Rd | 37 + xergm-1.5/xergm/man/xergm-package.Rd | 2 xergm-1.5/xergm/src/RcppExports.cpp | 4 xergm-1.5/xergm/src/tnam.cpp | 94 ++- 25 files changed, 1363 insertions(+), 708 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.0.7 dated 2015-04-19 and 1.0.9 dated 2015-06-14
SKAT-1.0.7/SKAT/R/Main.R |only SKAT-1.0.9/SKAT/DESCRIPTION | 10 +++++----- SKAT-1.0.9/SKAT/MD5 | 12 ++++++------ SKAT-1.0.9/SKAT/R/Binary_Function.R | 10 ++++++++-- SKAT-1.0.9/SKAT/R/Binary_MAIN_ExactBin.R | 1 + SKAT-1.0.9/SKAT/R/MAIN.R |only SKAT-1.0.9/SKAT/R/Main_SSD.R | 4 +++- SKAT-1.0.9/SKAT/inst/doc/SKAT.pdf |binary 8 files changed, 23 insertions(+), 14 deletions(-)
Title: Probabilistic Knowledge Structures
Description: Fitting and testing probabilistic knowledge structures,
especially the basic local independence model (BLIM, Doignon & Flamagne,
1999), using the minimum discrepancy maximum likelihood (MDML) method.
Author: Florian Wickelmaier [cre, aut], Juergen Heller [aut],
Pasquale Anselmi [ctb]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between pks versions 0.3-0 dated 2014-03-28 and 0.3-1 dated 2015-06-14
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 3 ++- R/blim.R | 37 ++++++++++++++++++++++++------------- R/cblim.R | 12 ++++++------ R/jacobian.R |only data/DoignonFalmagne7.rda |binary data/Taagepera.rda |binary data/endm.rda |binary man/blim.Rd | 4 +++- man/delineate.Rd | 4 ++-- man/jacobian.Rd |only man/simulate.blim.Rd | 2 +- 14 files changed, 65 insertions(+), 39 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.0.4 dated 2015-06-13 and 1.1.0 dated 2015-06-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Methods_for_result_objects.R | 4 ++-- man/nodiv-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
More information about metricsgraphics at CRAN
Permanent link
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kent Russel [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.1.2.1 dated 2015-03-04 and 0.1.7 dated 2015-06-14
DESCRIPTION | 29 +++--- MD5 | 63 ++++++------- NAMESPACE | 3 NEWS | 43 ++++++++- R/data-definitions.R | 19 +--- R/forceNetwork.R | 174 +++++++++++++++++++++++++------------- R/sankeyNetwork.R | 43 ++++++--- R/simpleNetwork.R | 8 + R/treeNetwork.R | 6 + R/utils.R | 60 ++++++++----- README.md | 6 - data/MisNodes.tab | 156 +++++++++++++++++----------------- inst/examples/examples.R | 12 ++ inst/examples/examples.Rmd | 2 inst/examples/shiny/server.R | 9 + inst/examples/shiny/ui.R | 1 inst/htmlwidgets/forceNetwork.js | 91 +++++++++++++++---- inst/htmlwidgets/sankeyNetwork.js | 2 inst/htmlwidgets/simpleNetwork.js | 37 +++++++- man/JS.Rd |only man/JSONtoDF.Rd | 2 man/MisLinks.Rd | 2 man/MisNodes.Rd | 5 - man/as.treeNetwork.Rd | 2 man/energy.Rd | 2 man/flare.Rd | 2 man/forceNetwork.Rd | 56 +++++++++--- man/networkD3-package.Rd | 2 man/networkD3-shiny.Rd | 2 man/sankeyNetwork.Rd | 15 ++- man/saveNetwork.Rd | 2 man/simpleNetwork.Rd | 10 +- man/treeNetwork.Rd | 8 + 33 files changed, 590 insertions(+), 284 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.1 dated 2015-03-17 and 0.2.2 dated 2015-06-14
RGA-0.2.1/RGA/R/custom.R |only RGA-0.2.2/RGA/DESCRIPTION | 20 ++-- RGA-0.2.2/RGA/MD5 | 112 ++++++++++++----------- RGA-0.2.2/RGA/NAMESPACE | 9 + RGA-0.2.2/RGA/R/custom-dims.R |only RGA-0.2.2/RGA/R/custom-mets.R |only RGA-0.2.2/RGA/R/custom-sources.R |only RGA-0.2.2/RGA/R/experiments.R | 4 RGA-0.2.2/RGA/R/filters.R | 4 RGA-0.2.2/RGA/R/metadata.R | 6 - RGA-0.2.2/RGA/R/profiles.R | 2 RGA-0.2.2/RGA/R/request.R | 7 - RGA-0.2.2/RGA/R/url.R | 4 RGA-0.2.2/RGA/R/zzz.R | 2 RGA-0.2.2/RGA/README.md | 136 ++++++++++++++-------------- RGA-0.2.2/RGA/data/ga.rda |binary RGA-0.2.2/RGA/inst/NEWS.Rd | 47 +++++---- RGA-0.2.2/RGA/inst/doc/authorize.R | 9 + RGA-0.2.2/RGA/inst/doc/authorize.Rmd | 24 ++-- RGA-0.2.2/RGA/inst/doc/authorize.html | 24 ++-- RGA-0.2.2/RGA/inst/doc/management-api.R | 9 + RGA-0.2.2/RGA/inst/doc/management-api.Rmd | 9 + RGA-0.2.2/RGA/inst/doc/management-api.html | 4 RGA-0.2.2/RGA/inst/doc/metadata-api.R | 9 + RGA-0.2.2/RGA/inst/doc/metadata-api.Rmd | 9 + RGA-0.2.2/RGA/inst/doc/metadata-api.html | 4 RGA-0.2.2/RGA/inst/doc/reporting-api.R | 9 + RGA-0.2.2/RGA/inst/doc/reporting-api.Rmd | 13 +- RGA-0.2.2/RGA/inst/doc/reporting-api.html | 8 - RGA-0.2.2/RGA/man/RGA.Rd | 2 RGA-0.2.2/RGA/man/authorize.Rd | 2 RGA-0.2.2/RGA/man/dimsmets.Rd | 2 RGA-0.2.2/RGA/man/firstdate.Rd | 2 RGA-0.2.2/RGA/man/ga.Rd | 4 RGA-0.2.2/RGA/man/get_custom_dimension.Rd |only RGA-0.2.2/RGA/man/get_custom_metric.Rd |only RGA-0.2.2/RGA/man/get_experiment.Rd | 10 +- RGA-0.2.2/RGA/man/get_filter.Rd | 10 +- RGA-0.2.2/RGA/man/get_ga.Rd | 2 RGA-0.2.2/RGA/man/get_goal.Rd | 10 +- RGA-0.2.2/RGA/man/get_mcf.Rd | 2 RGA-0.2.2/RGA/man/get_profile.Rd | 12 +- RGA-0.2.2/RGA/man/get_rt.Rd | 2 RGA-0.2.2/RGA/man/get_unsampled_report.Rd | 12 +- RGA-0.2.2/RGA/man/get_webproperty.Rd | 11 +- RGA-0.2.2/RGA/man/list_accounts.Rd | 11 +- RGA-0.2.2/RGA/man/list_custom_dimensions.Rd |only RGA-0.2.2/RGA/man/list_custom_metrics.Rd |only RGA-0.2.2/RGA/man/list_custom_sources.Rd | 13 +- RGA-0.2.2/RGA/man/list_experiments.Rd | 15 +-- RGA-0.2.2/RGA/man/list_filters.Rd | 15 +-- RGA-0.2.2/RGA/man/list_goals.Rd | 11 +- RGA-0.2.2/RGA/man/list_metadata.Rd | 2 RGA-0.2.2/RGA/man/list_profiles.Rd | 11 +- RGA-0.2.2/RGA/man/list_segments.Rd | 11 +- RGA-0.2.2/RGA/man/list_unsampled_reports.Rd | 11 +- RGA-0.2.2/RGA/man/list_webproperties.Rd | 11 +- RGA-0.2.2/RGA/vignettes/authorize.Rmd | 24 ++-- RGA-0.2.2/RGA/vignettes/management-api.Rmd | 9 + RGA-0.2.2/RGA/vignettes/metadata-api.Rmd | 9 + RGA-0.2.2/RGA/vignettes/reporting-api.Rmd | 13 +- 61 files changed, 429 insertions(+), 304 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
0xdata team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 2.8.4.4 dated 2015-02-07 and 3.0.0.22 dated 2015-06-14
h2o-2.8.4.4/h2o/R/Algorithms.R |only h2o-2.8.4.4/h2o/R/Classes.R |only h2o-2.8.4.4/h2o/R/Internal.R |only h2o-2.8.4.4/h2o/R/ParseImport.R |only h2o-2.8.4.4/h2o/R/Wrapper.R |only h2o-2.8.4.4/h2o/man/AAA_DownloadAndStartBeforeExamples.Rd |only h2o-2.8.4.4/h2o/man/Extremes.Rd |only h2o-2.8.4.4/h2o/man/H2OClient-class.Rd |only h2o-2.8.4.4/h2o/man/H2ODRFGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2ODRFModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2ODeepLearningGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2ODeepLearningModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGBMGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGBMModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGLMGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGLMModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGLMModelList-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGapStatModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2OKMeansGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2OKMeansModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2ONBModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OPCAModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OParsedData-class.Rd |only h2o-2.8.4.4/h2o/man/H2OPerfModel-class.Rd |only h2o-2.8.4.4/h2o/man/H2OSpeeDRFGrid-class.Rd |only h2o-2.8.4.4/h2o/man/H2OSpeeDRFModel-class.Rd |only h2o-2.8.4.4/h2o/man/apply.Rd |only h2o-2.8.4.4/h2o/man/as.Date.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/as.data.frame.Rd |only h2o-2.8.4.4/h2o/man/as.factor.Rd |only h2o-2.8.4.4/h2o/man/as.matrix.Rd |only h2o-2.8.4.4/h2o/man/as.table.Rd |only h2o-2.8.4.4/h2o/man/cbind.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/colnames.Rd |only h2o-2.8.4.4/h2o/man/data.frameORnull-class.Rd |only h2o-2.8.4.4/h2o/man/diff.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/doNotCallThisMethod...Unsupported.Rd |only h2o-2.8.4.4/h2o/man/h2o.SpeeDRF.Rd |only h2o-2.8.4.4/h2o/man/h2o.addFunction.Rd |only h2o-2.8.4.4/h2o/man/h2o.clearLogs.Rd |only h2o-2.8.4.4/h2o/man/h2o.coxph.Rd |only h2o-2.8.4.4/h2o/man/h2o.cut.Rd |only h2o-2.8.4.4/h2o/man/h2o.exec.Rd |only h2o-2.8.4.4/h2o/man/h2o.gains.Rd |only h2o-2.8.4.4/h2o/man/h2o.gapStatistic.Rd |only h2o-2.8.4.4/h2o/man/h2o.getGLMLambdaModel.Rd |only h2o-2.8.4.4/h2o/man/h2o.getLogPath.Rd |only h2o-2.8.4.4/h2o/man/h2o.hitRatio.Rd |only h2o-2.8.4.4/h2o/man/h2o.ignoreColumns.Rd |only h2o-2.8.4.4/h2o/man/h2o.importFolder.Rd |only h2o-2.8.4.4/h2o/man/h2o.importHDFS.Rd |only h2o-2.8.4.4/h2o/man/h2o.importURL.Rd |only h2o-2.8.4.4/h2o/man/h2o.loadAll.Rd |only h2o-2.8.4.4/h2o/man/h2o.nFoldExtractor.Rd |only h2o-2.8.4.4/h2o/man/h2o.order.Rd |only h2o-2.8.4.4/h2o/man/h2o.pcr.Rd |only h2o-2.8.4.4/h2o/man/h2o.predict.Rd |only h2o-2.8.4.4/h2o/man/h2o.rebalance.Rd |only h2o-2.8.4.4/h2o/man/h2o.sample.Rd |only h2o-2.8.4.4/h2o/man/h2o.saveAll.Rd |only h2o-2.8.4.4/h2o/man/h2o.setLogPath.Rd |only h2o-2.8.4.4/h2o/man/h2o.uploadFile.Rd |only h2o-2.8.4.4/h2o/man/head.Rd |only h2o-2.8.4.4/h2o/man/hist.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/ifelse.Rd |only h2o-2.8.4.4/h2o/man/is.factor.Rd |only h2o-2.8.4.4/h2o/man/levels.Rd |only h2o-2.8.4.4/h2o/man/mean.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/nrow.Rd |only h2o-2.8.4.4/h2o/man/plot.H2OGapStatModel.Rd |only h2o-2.8.4.4/h2o/man/plot.H2OPerfModel.Rd |only h2o-2.8.4.4/h2o/man/quantile.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/rbind.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/revalue.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/revalue.Rd |only h2o-2.8.4.4/h2o/man/round.Rd |only h2o-2.8.4.4/h2o/man/screeplot.H2OPCAModel.Rd |only h2o-2.8.4.4/h2o/man/sd.Rd |only h2o-2.8.4.4/h2o/man/str.Rd |only h2o-2.8.4.4/h2o/man/strsplit.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/strsplit.Rd |only h2o-2.8.4.4/h2o/man/sum.Rd |only h2o-2.8.4.4/h2o/man/summary.H2OGapStatModel.Rd |only h2o-2.8.4.4/h2o/man/summary.H2OPCAModel.Rd |only h2o-2.8.4.4/h2o/man/summary.Rd |only h2o-2.8.4.4/h2o/man/tolower.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/tolower.Rd |only h2o-2.8.4.4/h2o/man/toupper.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/toupper.Rd |only h2o-2.8.4.4/h2o/man/unique.H2OParsedData.Rd |only h2o-2.8.4.4/h2o/man/which.Rd |only h2o-2.8.4.4/h2o/man/zzz_ShutdownAfterExamples.Rd |only h2o-3.0.0.22/h2o/DESCRIPTION | 36 h2o-3.0.0.22/h2o/MD5 | 380 +- h2o-3.0.0.22/h2o/NAMESPACE | 342 +- h2o-3.0.0.22/h2o/R/ast.R |only h2o-3.0.0.22/h2o/R/astfun.R |only h2o-3.0.0.22/h2o/R/classes.R |only h2o-3.0.0.22/h2o/R/communication.R |only h2o-3.0.0.22/h2o/R/connection.R |only h2o-3.0.0.22/h2o/R/constants.R |only h2o-3.0.0.22/h2o/R/deeplearning.R |only h2o-3.0.0.22/h2o/R/edicts.R |only h2o-3.0.0.22/h2o/R/exec.R |only h2o-3.0.0.22/h2o/R/export.R |only h2o-3.0.0.22/h2o/R/frame.R |only h2o-3.0.0.22/h2o/R/gbm.R |only h2o-3.0.0.22/h2o/R/glm.R |only h2o-3.0.0.22/h2o/R/glrm.R |only h2o-3.0.0.22/h2o/R/import.R |only h2o-3.0.0.22/h2o/R/kmeans.R |only h2o-3.0.0.22/h2o/R/kvstore.R |only h2o-3.0.0.22/h2o/R/locate.R |only h2o-3.0.0.22/h2o/R/logging.R |only h2o-3.0.0.22/h2o/R/models.R | 1383 ++++++++-- h2o-3.0.0.22/h2o/R/naivebayes.R |only h2o-3.0.0.22/h2o/R/ops.R |only h2o-3.0.0.22/h2o/R/parse.R |only h2o-3.0.0.22/h2o/R/pca.R |only h2o-3.0.0.22/h2o/R/randomforest.R |only h2o-3.0.0.22/h2o/R/shim.R |only h2o-3.0.0.22/h2o/R/svd.R |only h2o-3.0.0.22/h2o/R/word2vec.R |only h2o-3.0.0.22/h2o/demo/00Index | 3 h2o-3.0.0.22/h2o/demo/h2o.deeplearning.R | 58 h2o-3.0.0.22/h2o/demo/h2o.deeplearning.remote.R |only h2o-3.0.0.22/h2o/demo/h2o.gbm.R | 10 h2o-3.0.0.22/h2o/demo/h2o.gbm.remote.R | 6 h2o-3.0.0.22/h2o/demo/h2o.glm.R | 4 h2o-3.0.0.22/h2o/demo/h2o.glm.remote.R | 4 h2o-3.0.0.22/h2o/demo/h2o.kmeans.R | 29 h2o-3.0.0.22/h2o/demo/h2o.kmeans.remote.R | 28 h2o-3.0.0.22/h2o/demo/h2o.naiveBayes.R | 10 h2o-3.0.0.22/h2o/demo/h2o.naiveBayes.remote.R | 8 h2o-3.0.0.22/h2o/demo/h2o.prcomp.R | 11 h2o-3.0.0.22/h2o/demo/h2o.prcomp.remote.R | 11 h2o-3.0.0.22/h2o/demo/h2o.randomForest.R | 6 h2o-3.0.0.22/h2o/demo/h2o.randomForest.remote.R | 4 h2o-3.0.0.22/h2o/inst/branch.txt | 2 h2o-3.0.0.22/h2o/inst/buildnum.txt | 2 h2o-3.0.0.22/h2o/inst/extdata/housevotes.csv | 466 +-- h2o-3.0.0.22/h2o/inst/extdata/iris_header.csv | 2 h2o-3.0.0.22/h2o/inst/extdata/prostate_folder/prostate.p1.csv | 202 - h2o-3.0.0.22/h2o/inst/extdata/prostate_folder/prostate.p2.csv | 202 - h2o-3.0.0.22/h2o/inst/extdata/prostate_folder/prostate.p3.csv | 362 +- h2o-3.0.0.22/h2o/inst/source_code_repository_info.txt | 2 h2o-3.0.0.22/h2o/man/ASTNode-class.Rd |only h2o-3.0.0.22/h2o/man/H2OClusteringModel-class.Rd |only h2o-3.0.0.22/h2o/man/H2OConnection-class.Rd |only h2o-3.0.0.22/h2o/man/H2OFrame-Extract.Rd |only h2o-3.0.0.22/h2o/man/H2OFrame-class.Rd |only h2o-3.0.0.22/h2o/man/H2OModel-class.Rd | 64 h2o-3.0.0.22/h2o/man/H2OModelFuture-class.Rd |only h2o-3.0.0.22/h2o/man/H2OModelMetrics-class.Rd |only h2o-3.0.0.22/h2o/man/H2OObject-class.Rd |only h2o-3.0.0.22/h2o/man/H2ORawData-class.Rd | 58 h2o-3.0.0.22/h2o/man/H2OS4groupGeneric.Rd |only h2o-3.0.0.22/h2o/man/H2OW2V-class.Rd |only h2o-3.0.0.22/h2o/man/ModelAccessors.Rd |only h2o-3.0.0.22/h2o/man/Node-class.Rd |only h2o-3.0.0.22/h2o/man/aaa.Rd |only h2o-3.0.0.22/h2o/man/apply-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/as.character-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/as.data.frame.H2OFrame.Rd |only h2o-3.0.0.22/h2o/man/as.environment-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/as.factor-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/as.h2o.Rd | 49 h2o-3.0.0.22/h2o/man/as.matrix.h2o.Rd |only h2o-3.0.0.22/h2o/man/as.numeric-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/cut.H2OFrame.Rd |only h2o-3.0.0.22/h2o/man/h2o-package.Rd | 35 h2o-3.0.0.22/h2o/man/h2o.aic.Rd |only h2o-3.0.0.22/h2o/man/h2o.anomaly.Rd | 36 h2o-3.0.0.22/h2o/man/h2o.anyFactor.Rd | 26 h2o-3.0.0.22/h2o/man/h2o.assign.Rd | 32 h2o-3.0.0.22/h2o/man/h2o.auc.Rd |only h2o-3.0.0.22/h2o/man/h2o.betweenss.Rd |only h2o-3.0.0.22/h2o/man/h2o.cbind.Rd |only h2o-3.0.0.22/h2o/man/h2o.centers.Rd |only h2o-3.0.0.22/h2o/man/h2o.centersSTD.Rd |only h2o-3.0.0.22/h2o/man/h2o.clearLog.Rd |only h2o-3.0.0.22/h2o/man/h2o.clusterInfo.Rd | 27 h2o-3.0.0.22/h2o/man/h2o.clusterIsUp.Rd |only h2o-3.0.0.22/h2o/man/h2o.clusterStatus.Rd | 54 h2o-3.0.0.22/h2o/man/h2o.cluster_sizes.Rd |only h2o-3.0.0.22/h2o/man/h2o.coef.Rd |only h2o-3.0.0.22/h2o/man/h2o.coef_norm.Rd |only h2o-3.0.0.22/h2o/man/h2o.colnames.Rd |only h2o-3.0.0.22/h2o/man/h2o.confusionMatrix.Rd | 74 h2o-3.0.0.22/h2o/man/h2o.createFrame.Rd | 119 h2o-3.0.0.22/h2o/man/h2o.day.Rd |only h2o-3.0.0.22/h2o/man/h2o.dayOfWeek.Rd |only h2o-3.0.0.22/h2o/man/h2o.ddply.Rd | 67 h2o-3.0.0.22/h2o/man/h2o.deepfeatures.Rd | 44 h2o-3.0.0.22/h2o/man/h2o.deeplearning.Rd | 304 +- h2o-3.0.0.22/h2o/man/h2o.dim.Rd |only h2o-3.0.0.22/h2o/man/h2o.downloadAllLogs.Rd | 35 h2o-3.0.0.22/h2o/man/h2o.downloadCSV.Rd | 67 h2o-3.0.0.22/h2o/man/h2o.download_pojo.Rd |only h2o-3.0.0.22/h2o/man/h2o.exportFile.Rd | 79 h2o-3.0.0.22/h2o/man/h2o.exportHDFS.Rd |only h2o-3.0.0.22/h2o/man/h2o.filterNACols.Rd |only h2o-3.0.0.22/h2o/man/h2o.gbm.Rd | 178 - h2o-3.0.0.22/h2o/man/h2o.getConnection.Rd |only h2o-3.0.0.22/h2o/man/h2o.getFrame.Rd | 37 h2o-3.0.0.22/h2o/man/h2o.getGLMModel.Rd |only h2o-3.0.0.22/h2o/man/h2o.getModel.Rd | 40 h2o-3.0.0.22/h2o/man/h2o.getTimezone.Rd | 47 h2o-3.0.0.22/h2o/man/h2o.giniCoef.Rd |only h2o-3.0.0.22/h2o/man/h2o.glm.Rd | 305 -- h2o-3.0.0.22/h2o/man/h2o.glrm.Rd |only h2o-3.0.0.22/h2o/man/h2o.group_by.Rd |only h2o-3.0.0.22/h2o/man/h2o.gsub.Rd | 38 h2o-3.0.0.22/h2o/man/h2o.head.Rd |only h2o-3.0.0.22/h2o/man/h2o.hist.Rd |only h2o-3.0.0.22/h2o/man/h2o.hit_ratio_table.Rd |only h2o-3.0.0.22/h2o/man/h2o.hour.Rd |only h2o-3.0.0.22/h2o/man/h2o.ifelse.Rd |only h2o-3.0.0.22/h2o/man/h2o.importFile.Rd | 126 h2o-3.0.0.22/h2o/man/h2o.impute.Rd | 72 h2o-3.0.0.22/h2o/man/h2o.init.Rd | 94 h2o-3.0.0.22/h2o/man/h2o.insertMissingValues.Rd | 48 h2o-3.0.0.22/h2o/man/h2o.interaction.Rd | 137 h2o-3.0.0.22/h2o/man/h2o.killMinus3.Rd |only h2o-3.0.0.22/h2o/man/h2o.kmeans.Rd | 97 h2o-3.0.0.22/h2o/man/h2o.length.Rd |only h2o-3.0.0.22/h2o/man/h2o.levels.Rd |only h2o-3.0.0.22/h2o/man/h2o.listTimezones.Rd | 32 h2o-3.0.0.22/h2o/man/h2o.loadModel.Rd | 45 h2o-3.0.0.22/h2o/man/h2o.logAndEcho.Rd | 34 h2o-3.0.0.22/h2o/man/h2o.logloss.Rd |only h2o-3.0.0.22/h2o/man/h2o.ls.Rd | 29 h2o-3.0.0.22/h2o/man/h2o.makeGLMModel.Rd | 45 h2o-3.0.0.22/h2o/man/h2o.match.Rd |only h2o-3.0.0.22/h2o/man/h2o.mean.Rd |only h2o-3.0.0.22/h2o/man/h2o.merge.Rd |only h2o-3.0.0.22/h2o/man/h2o.metric.Rd |only h2o-3.0.0.22/h2o/man/h2o.month.Rd | 31 h2o-3.0.0.22/h2o/man/h2o.mse.Rd | 51 h2o-3.0.0.22/h2o/man/h2o.naiveBayes.Rd | 98 h2o-3.0.0.22/h2o/man/h2o.networkTest.Rd |only h2o-3.0.0.22/h2o/man/h2o.nlevels.Rd |only h2o-3.0.0.22/h2o/man/h2o.nrow.Rd |only h2o-3.0.0.22/h2o/man/h2o.null_deviance.Rd |only h2o-3.0.0.22/h2o/man/h2o.null_dof.Rd |only h2o-3.0.0.22/h2o/man/h2o.num_iterations.Rd |only h2o-3.0.0.22/h2o/man/h2o.openLog.Rd | 29 h2o-3.0.0.22/h2o/man/h2o.parseRaw.Rd | 96 h2o-3.0.0.22/h2o/man/h2o.parseSetup.Rd |only h2o-3.0.0.22/h2o/man/h2o.performance.Rd | 79 h2o-3.0.0.22/h2o/man/h2o.prcomp.Rd | 93 h2o-3.0.0.22/h2o/man/h2o.r2.Rd |only h2o-3.0.0.22/h2o/man/h2o.randomForest.Rd | 172 - h2o-3.0.0.22/h2o/man/h2o.rbind.Rd |only h2o-3.0.0.22/h2o/man/h2o.removeAll.Rd |only h2o-3.0.0.22/h2o/man/h2o.removeVecs.Rd | 25 h2o-3.0.0.22/h2o/man/h2o.rep_len.Rd |only h2o-3.0.0.22/h2o/man/h2o.residual_deviance.Rd |only h2o-3.0.0.22/h2o/man/h2o.residual_dof.Rd |only h2o-3.0.0.22/h2o/man/h2o.rm.Rd | 35 h2o-3.0.0.22/h2o/man/h2o.runif.Rd | 31 h2o-3.0.0.22/h2o/man/h2o.saveModel.Rd | 55 h2o-3.0.0.22/h2o/man/h2o.scale.Rd |only h2o-3.0.0.22/h2o/man/h2o.scoreHistory.Rd |only h2o-3.0.0.22/h2o/man/h2o.sd.Rd |only h2o-3.0.0.22/h2o/man/h2o.setLevel.Rd |only h2o-3.0.0.22/h2o/man/h2o.setLevels.Rd |only h2o-3.0.0.22/h2o/man/h2o.setTimezone.Rd | 50 h2o-3.0.0.22/h2o/man/h2o.shim.Rd |only h2o-3.0.0.22/h2o/man/h2o.shutdown.Rd | 40 h2o-3.0.0.22/h2o/man/h2o.splitFrame.Rd | 29 h2o-3.0.0.22/h2o/man/h2o.startGLMJob.Rd |only h2o-3.0.0.22/h2o/man/h2o.startLogging.Rd | 24 h2o-3.0.0.22/h2o/man/h2o.stopLogging.Rd | 19 h2o-3.0.0.22/h2o/man/h2o.strsplit.Rd |only h2o-3.0.0.22/h2o/man/h2o.sub.Rd | 40 h2o-3.0.0.22/h2o/man/h2o.summary.Rd |only h2o-3.0.0.22/h2o/man/h2o.svd.Rd |only h2o-3.0.0.22/h2o/man/h2o.table.Rd | 35 h2o-3.0.0.22/h2o/man/h2o.tolower.Rd |only h2o-3.0.0.22/h2o/man/h2o.tot_withinss.Rd |only h2o-3.0.0.22/h2o/man/h2o.totss.Rd |only h2o-3.0.0.22/h2o/man/h2o.toupper.Rd |only h2o-3.0.0.22/h2o/man/h2o.trim.Rd | 32 h2o-3.0.0.22/h2o/man/h2o.var.Rd |only h2o-3.0.0.22/h2o/man/h2o.varimp.Rd |only h2o-3.0.0.22/h2o/man/h2o.week.Rd |only h2o-3.0.0.22/h2o/man/h2o.withinss.Rd |only h2o-3.0.0.22/h2o/man/h2o.year.Rd | 32 h2o-3.0.0.22/h2o/man/is.factor-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/median-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/predict.H2OModel.Rd |only h2o-3.0.0.22/h2o/man/print.H2OTable.Rd |only h2o-3.0.0.22/h2o/man/quantile.Rd |only h2o-3.0.0.22/h2o/man/sapply-H2OFrame-method.Rd |only h2o-3.0.0.22/h2o/man/str.H2OFrame.Rd |only h2o-3.0.0.22/h2o/man/summary-H2OModel-method.Rd |only h2o-3.0.0.22/h2o/man/transform.H2OFrame.Rd |only h2o-3.0.0.22/h2o/tests |only 300 files changed, 4006 insertions(+), 3237 deletions(-)
Title: Optimal Binning for Scoring Modeling
Description: It categorizes a numeric variable into bins mapped to a binary target variable for its ulterior usage in scoring modeling. Its purpose is to automate the time consuming process of selecting the right cut points, quickly calculate metrics such as Weight of Evidence and Information Value; and also document SQL codes, tables, and plots used throughout the development stage. The package also allows users to establish their own cut points for numeric characteristics and run the analysis for categorical variables.
Author: Herman Jopia
Maintainer: Herman Jopia <hjopia@gmail.com>
Diff between smbinning versions 0.1 dated 2015-02-15 and 0.2 dated 2015-06-13
DESCRIPTION | 10 MD5 | 12 - R/smbinning.R | 503 +++++++++++++++++++++++++++++++++++++++++++++--- man/smbinning.Rd | 13 - man/smbinning.custom.Rd |only man/smbinning.factor.Rd |only man/smbinning.gen.Rd | 2 man/smbinning.plot.Rd | 2 8 files changed, 500 insertions(+), 42 deletions(-)
Title: Periodogram Peaks in Correlated Time Series
Description: Calculates the periodogram of a time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null model and evaluates the statistical significance of periodogram peaks against the OUSS null hypothesis. The OUSS is a parsimonious model for stochastically fluctuating variables with linear stabilizing forces, subject to uncorrelated measurement errors. Contrary to the classical white noise null model for detecting cyclicity, the OUSS model can account for temporal correlations typically occurring in ecological and geological time series.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@math.ubc.ca>
Diff between peacots versions 1.1 dated 2014-10-29 and 1.2 dated 2015-06-13
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/runExample.R | 6 +++--- inst/CITATION | 5 ++++- man/evaluate.pm.Rd | 2 +- man/evaluate.pm.wn.Rd | 2 +- man/generate_ouss.Rd | 2 +- man/peacots-package.Rd | 6 +++--- man/plotReport.Rd | 2 +- man/ps_ouss.Rd | 2 +- man/ps_ouss_asymptotic.Rd | 2 +- man/runExample.Rd | 2 +- man/significanceOfLocalPeak.Rd | 2 +- 13 files changed, 34 insertions(+), 31 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>
Diff between MPTinR versions 1.8.0 dated 2015-04-30 and 1.9.2 dated 2015-06-13
DESCRIPTION | 12 ++++++------ MD5 | 17 ++++++++++++----- NEWS | 21 +++++++++++++++++++++ R/fit.mptinr.R | 2 +- R/select.mpt.R | 2 +- build |only inst/CITATION | 9 ++++++--- inst/doc |only vignettes |only 9 files changed, 47 insertions(+), 16 deletions(-)
Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized
linear mixed-effects models in a Bayesian setting. Extends
'lme4' by Douglas Bates, Martin Maechler, Ben Bolker, and Steve Walker.
Author: Vincent Dorie <vjd4@nyu.edu>
Maintainer: Vincent Dorie <vjd4@nyu.edu>
Diff between blme versions 1.0-3 dated 2015-05-30 and 1.0-4 dated 2015-06-13
DESCRIPTION | 14 - MD5 | 14 - NAMESPACE | 4 R/blmer.R | 457 +++++++++++++++++++++-------------------- R/devFun.R | 43 ++- README.md | 4 man/blmer.Rd | 3 tests/testthat/test-10-refit.R | 79 +++---- 8 files changed, 333 insertions(+), 285 deletions(-)
Title: Easily Play Notification Sounds on any Platform
Description: The sole function of this package is beep(), with the purpose to
make it easy to play notification sounds on whatever platform you are on.
It is intended to be useful, for example, if you are running a long analysis
in the background and want to know when it is ready.
Author: Rasmus Bååth <rasmus.baath@gmail.com>
Maintainer: Rasmus Bååth <rasmus.baath@gmail.com>
Diff between beepr versions 1.1 dated 2014-06-26 and 1.2 dated 2015-06-13
DESCRIPTION | 12 ++++---- MD5 | 17 ++++++------ NAMESPACE | 2 - NEWS | 12 ++++++++ R/beepr.R | 49 +++++++++++++++++++++++++----------- README.md | 13 ++++++++- inst/sounds/microwave_ping_mono.wav |binary inst/sounds/sword.wav |only man/beep.Rd | 19 ++++++++----- man/beepr.Rd | 3 +- 10 files changed, 86 insertions(+), 41 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.5.2 dated 2014-12-19 and 0.6.0 dated 2015-06-13
taxize-0.5.2/taxize/data/apg_genera.RData |only taxize-0.5.2/taxize/data/datalist |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.RData |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdb |only taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdx |only taxize-0.5.2/taxize/man/apg_genera.Rd |only taxize-0.5.2/taxize/man/eol_invasive-deprecated.Rd |only taxize-0.5.2/taxize/man/gisd_invasive-deprecated.Rd |only taxize-0.5.2/taxize/man/nbn_classifcation.Rd |only taxize-0.5.2/taxize/man/ncbi_getbyid-deprecated.Rd |only taxize-0.5.2/taxize/man/ncbi_getbyname-deprecated.Rd |only taxize-0.5.2/taxize/man/ncbi_search-deprecated.Rd |only taxize-0.5.2/taxize/tests/testthat/test-eol_invasive.R |only taxize-0.5.2/taxize/tests/testthat/test-gisd_isinvasive.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyid.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyname.R |only taxize-0.5.2/taxize/tests/testthat/test-ncbi_search.R |only taxize-0.6.0/taxize/DESCRIPTION | 41 taxize-0.6.0/taxize/LICENSE | 4 taxize-0.6.0/taxize/MD5 | 553 +++++----- taxize-0.6.0/taxize/NAMESPACE | 12 taxize-0.6.0/taxize/NEWS | 58 + taxize-0.6.0/taxize/R/apg.R |only taxize-0.6.0/taxize/R/apg_lookup.R | 33 taxize-0.6.0/taxize/R/children.R | 23 taxize-0.6.0/taxize/R/class2tree.R | 77 + taxize-0.6.0/taxize/R/classification.R | 94 - taxize-0.6.0/taxize/R/col_children.R | 14 taxize-0.6.0/taxize/R/col_classification.R | 21 taxize-0.6.0/taxize/R/col_downstream.R | 26 taxize-0.6.0/taxize/R/col_search.R | 114 +- taxize-0.6.0/taxize/R/comm2sci.R | 33 taxize-0.6.0/taxize/R/downstream.R | 18 taxize-0.6.0/taxize/R/eol_dataobjects.R | 38 taxize-0.6.0/taxize/R/eol_hierarchy.R | 4 taxize-0.6.0/taxize/R/eol_invasive.R | 160 +- taxize-0.6.0/taxize/R/eol_pages.R | 31 taxize-0.6.0/taxize/R/eol_search.R | 24 taxize-0.6.0/taxize/R/eol_utiils.R |only taxize-0.6.0/taxize/R/genbank2uid.R | 39 taxize-0.6.0/taxize/R/get_boldid.R | 143 +- taxize-0.6.0/taxize/R/get_colid.R | 133 +- taxize-0.6.0/taxize/R/get_eolid.R | 97 - taxize-0.6.0/taxize/R/get_gbifid.R | 170 ++- taxize-0.6.0/taxize/R/get_ids.R | 13 taxize-0.6.0/taxize/R/get_nbnid.R | 5 taxize-0.6.0/taxize/R/get_tpsid.R | 116 +- taxize-0.6.0/taxize/R/get_tsn.R | 24 taxize-0.6.0/taxize/R/get_ubioid.R | 165 ++ taxize-0.6.0/taxize/R/get_uid.R | 162 ++ taxize-0.6.0/taxize/R/gisd_isinvasive.R | 68 - taxize-0.6.0/taxize/R/gnr_datasources.R | 7 taxize-0.6.0/taxize/R/gnr_resolve.R | 66 - taxize-0.6.0/taxize/R/itis.R | 366 ++---- taxize-0.6.0/taxize/R/itis_acceptname.R | 12 taxize-0.6.0/taxize/R/itis_native.R | 8 taxize-0.6.0/taxize/R/itis_terms.R | 16 taxize-0.6.0/taxize/R/names_list.r | 2 taxize-0.6.0/taxize/R/nbn_classification.R | 8 taxize-0.6.0/taxize/R/nbn_search.R | 2 taxize-0.6.0/taxize/R/ncbi_children.R | 38 taxize-0.6.0/taxize/R/ncbi_get_taxon_summary.R | 11 taxize-0.6.0/taxize/R/ncbi_getbyid.R | 63 - taxize-0.6.0/taxize/R/ncbi_getbyname.R | 232 ++-- taxize-0.6.0/taxize/R/ncbi_search.R | 316 ++--- taxize-0.6.0/taxize/R/phylomatic_format.R | 24 taxize-0.6.0/taxize/R/phylomatic_tree.R | 4 taxize-0.6.0/taxize/R/ping.R | 7 taxize-0.6.0/taxize/R/rankagg.R | 4 taxize-0.6.0/taxize/R/rename.R |only taxize-0.6.0/taxize/R/resolve.R | 12 taxize-0.6.0/taxize/R/sci2comm.R | 6 taxize-0.6.0/taxize/R/synonyms.R | 155 ++ taxize-0.6.0/taxize/R/tax_agg.R | 16 taxize-0.6.0/taxize/R/taxize-package.R | 95 + taxize-0.6.0/taxize/R/taxize_cite.R | 263 ++++ taxize-0.6.0/taxize/R/tnrs.R | 22 taxize-0.6.0/taxize/R/tp_accnames.R | 19 taxize-0.6.0/taxize/R/tp_classification.R | 6 taxize-0.6.0/taxize/R/tp_dist.R | 17 taxize-0.6.0/taxize/R/tp_refs.R | 9 taxize-0.6.0/taxize/R/tp_search.R | 20 taxize-0.6.0/taxize/R/tp_summary.R | 10 taxize-0.6.0/taxize/R/tp_synonyms.R | 23 taxize-0.6.0/taxize/R/tpl_families.r | 21 taxize-0.6.0/taxize/R/tpl_get.r | 54 taxize-0.6.0/taxize/R/tpl_search.r | 29 taxize-0.6.0/taxize/R/ubio_search.R | 26 taxize-0.6.0/taxize/R/upstream.R | 16 taxize-0.6.0/taxize/R/vascan_search.r | 5 taxize-0.6.0/taxize/R/zzz.R | 37 taxize-0.6.0/taxize/README.md | 107 - taxize-0.6.0/taxize/build/vignette.rds |binary taxize-0.6.0/taxize/data/theplantlist.RData |binary taxize-0.6.0/taxize/inst/doc/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/inst/doc/taxize_infotable.html | 1 taxize-0.6.0/taxize/inst/doc/taxize_vignette.Rmd | 252 +--- taxize-0.6.0/taxize/inst/doc/taxize_vignette.html | 239 +--- taxize-0.6.0/taxize/inst/vign/cache/__packages | 14 taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.RData |only taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdb |only taxize-0.6.0/taxize/inst/vign/cache/taxname_0f3fcc7119f159af267de7a029f64f5e.rdx |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.RData |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdb |only taxize-0.6.0/taxize/inst/vign/cache/tnrs_c39c1e0c556437f6b37ba3c369e8be54.rdx |only taxize-0.6.0/taxize/inst/vign/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/inst/vign/taxize_infotable.md | 1 taxize-0.6.0/taxize/inst/vign/taxize_vignette.Rmd | 24 taxize-0.6.0/taxize/inst/vign/taxize_vignette.md | 252 +--- taxize-0.6.0/taxize/man/apg.Rd |only taxize-0.6.0/taxize/man/apg_families.Rd | 20 taxize-0.6.0/taxize/man/apg_lookup.Rd | 25 taxize-0.6.0/taxize/man/apg_orders.Rd | 19 taxize-0.6.0/taxize/man/bold_search.Rd | 2 taxize-0.6.0/taxize/man/children.Rd | 22 taxize-0.6.0/taxize/man/class2tree.Rd | 4 taxize-0.6.0/taxize/man/classification.Rd | 20 taxize-0.6.0/taxize/man/col_children.Rd | 6 taxize-0.6.0/taxize/man/col_classification-defunct.Rd | 24 taxize-0.6.0/taxize/man/col_downstream.Rd | 7 taxize-0.6.0/taxize/man/col_search.Rd | 9 taxize-0.6.0/taxize/man/comm2sci.Rd | 9 taxize-0.6.0/taxize/man/downstream.Rd | 17 taxize-0.6.0/taxize/man/eol_dataobjects.Rd | 27 taxize-0.6.0/taxize/man/eol_hierarchy-defunct.Rd | 8 taxize-0.6.0/taxize/man/eol_invasive-defunct.Rd |only taxize-0.6.0/taxize/man/eol_pages.Rd | 8 taxize-0.6.0/taxize/man/eol_search.Rd | 6 taxize-0.6.0/taxize/man/gbif_name_usage.Rd | 2 taxize-0.6.0/taxize/man/gbif_parse.Rd | 2 taxize-0.6.0/taxize/man/genbank2uid.Rd | 2 taxize-0.6.0/taxize/man/get_boldid.Rd | 52 taxize-0.6.0/taxize/man/get_colid.Rd | 57 - taxize-0.6.0/taxize/man/get_eolid.Rd | 2 taxize-0.6.0/taxize/man/get_gbifid.Rd | 57 - taxize-0.6.0/taxize/man/get_genes-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_genes_avail-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_ids.Rd | 7 taxize-0.6.0/taxize/man/get_nbnid.Rd | 7 taxize-0.6.0/taxize/man/get_seqs-deprecated.Rd | 2 taxize-0.6.0/taxize/man/get_tpsid.Rd | 41 taxize-0.6.0/taxize/man/get_tsn.Rd | 26 taxize-0.6.0/taxize/man/get_ubioid.Rd | 47 taxize-0.6.0/taxize/man/get_uid.Rd | 55 taxize-0.6.0/taxize/man/getacceptednamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getanymatchcount.Rd | 2 taxize-0.6.0/taxize/man/getcommentdetailfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcommonnamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcoremetadatafromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcoveragefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcredibilityratingfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getcredibilityratings.Rd | 2 taxize-0.6.0/taxize/man/getcurrencyfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getdatedatafromtsn.Rd | 2 taxize-0.6.0/taxize/man/getdescription.Rd | 2 taxize-0.6.0/taxize/man/getexpertsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getfullhierarchyfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getfullrecordfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getfullrecordfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getgeographicdivisionsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getgeographicvalues.Rd | 2 taxize-0.6.0/taxize/man/getglobalspeciescompletenessfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gethierarchydownfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gethierarchyupfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getitisterms.Rd | 2 taxize-0.6.0/taxize/man/getitistermsfromcommonname.Rd | 2 taxize-0.6.0/taxize/man/getitistermsfromscientificname.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionoriginvalues.Rd | 2 taxize-0.6.0/taxize/man/getjurisdictionvalues.Rd | 2 taxize-0.6.0/taxize/man/getkey.Rd | 2 taxize-0.6.0/taxize/man/getkingdomnamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getkingdomnames.Rd | 2 taxize-0.6.0/taxize/man/getlastchangedate.Rd | 2 taxize-0.6.0/taxize/man/getlsidfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getothersourcesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getparenttsnfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getpublicationsfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getranknames.Rd | 2 taxize-0.6.0/taxize/man/getrecordfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getreviewyearfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getscientificnamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/getsynonymnamesfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonauthorshipfromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonomicranknamefromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettaxonomicusagefromtsn.Rd | 2 taxize-0.6.0/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.6.0/taxize/man/gettsnfromlsid.Rd | 2 taxize-0.6.0/taxize/man/getunacceptabilityreasonfromtsn.Rd | 2 taxize-0.6.0/taxize/man/getvernacularlanguages.Rd | 2 taxize-0.6.0/taxize/man/gisd_invasive-defunct.Rd |only taxize-0.6.0/taxize/man/gni_details.Rd | 2 taxize-0.6.0/taxize/man/gni_parse.Rd | 2 taxize-0.6.0/taxize/man/gni_search.Rd | 2 taxize-0.6.0/taxize/man/gnr_datasources.Rd | 4 taxize-0.6.0/taxize/man/gnr_resolve.Rd | 6 taxize-0.6.0/taxize/man/ifelsedata.Rd | 2 taxize-0.6.0/taxize/man/iplant_resolve.Rd | 2 taxize-0.6.0/taxize/man/ipni_search.Rd | 2 taxize-0.6.0/taxize/man/itis-api.Rd | 2 taxize-0.6.0/taxize/man/itis_acceptname.Rd | 2 taxize-0.6.0/taxize/man/itis_downstream.Rd | 2 taxize-0.6.0/taxize/man/itis_getrecord.Rd | 2 taxize-0.6.0/taxize/man/itis_hierarchy.Rd | 2 taxize-0.6.0/taxize/man/itis_kingdomnames.Rd | 2 taxize-0.6.0/taxize/man/itis_lsid.Rd | 2 taxize-0.6.0/taxize/man/itis_name-deprecated.Rd | 2 taxize-0.6.0/taxize/man/itis_native.Rd | 2 taxize-0.6.0/taxize/man/itis_refs.Rd | 2 taxize-0.6.0/taxize/man/itis_searchcommon.Rd | 2 taxize-0.6.0/taxize/man/itis_taxrank.Rd | 2 taxize-0.6.0/taxize/man/itis_terms.Rd | 2 taxize-0.6.0/taxize/man/iucn_getname.Rd | 2 taxize-0.6.0/taxize/man/iucn_status.Rd | 2 taxize-0.6.0/taxize/man/iucn_summary.Rd | 2 taxize-0.6.0/taxize/man/names_list.Rd | 2 taxize-0.6.0/taxize/man/nbn_classification.Rd |only taxize-0.6.0/taxize/man/nbn_search.Rd | 4 taxize-0.6.0/taxize/man/nbn_synonyms.Rd | 2 taxize-0.6.0/taxize/man/ncbi_children.Rd | 16 taxize-0.6.0/taxize/man/ncbi_get_taxon_summary.Rd | 10 taxize-0.6.0/taxize/man/ncbi_getbyid-defunct.Rd |only taxize-0.6.0/taxize/man/ncbi_getbyname-defunct.Rd |only taxize-0.6.0/taxize/man/ncbi_search-defunct.Rd |only taxize-0.6.0/taxize/man/phylomatic_format.Rd | 2 taxize-0.6.0/taxize/man/phylomatic_tree-deprecated.Rd | 6 taxize-0.6.0/taxize/man/ping.Rd | 7 taxize-0.6.0/taxize/man/plantGenusNames.Rd | 12 taxize-0.6.0/taxize/man/plantNames.Rd | 13 taxize-0.6.0/taxize/man/plantminer.Rd | 2 taxize-0.6.0/taxize/man/rank_ref.Rd | 2 taxize-0.6.0/taxize/man/rankagg.Rd | 3 taxize-0.6.0/taxize/man/resolve.Rd | 6 taxize-0.6.0/taxize/man/sci2comm.Rd | 8 taxize-0.6.0/taxize/man/scrapenames.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonname.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonnamebeginswith.Rd | 2 taxize-0.6.0/taxize/man/searchbycommonnameendswith.Rd | 2 taxize-0.6.0/taxize/man/searchbyscientificname.Rd | 2 taxize-0.6.0/taxize/man/searchforanymatch.Rd | 2 taxize-0.6.0/taxize/man/searchforanymatchpaged.Rd | 2 taxize-0.6.0/taxize/man/status_codes.Rd | 2 taxize-0.6.0/taxize/man/synonyms.Rd | 49 taxize-0.6.0/taxize/man/tax_agg.Rd | 3 taxize-0.6.0/taxize/man/tax_name.Rd | 2 taxize-0.6.0/taxize/man/tax_rank.Rd | 2 taxize-0.6.0/taxize/man/taxize-defunct.Rd | 7 taxize-0.6.0/taxize/man/taxize-deprecated.Rd | 21 taxize-0.6.0/taxize/man/taxize-package.Rd | 2 taxize-0.6.0/taxize/man/taxize_capwords.Rd | 2 taxize-0.6.0/taxize/man/taxize_cite.Rd | 12 taxize-0.6.0/taxize/man/taxize_ldfast.Rd | 2 taxize-0.6.0/taxize/man/theplantlist.Rd | 17 taxize-0.6.0/taxize/man/tnrs.Rd | 9 taxize-0.6.0/taxize/man/tnrs_sources.Rd | 2 taxize-0.6.0/taxize/man/tp_acceptednames-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_accnames.Rd | 6 taxize-0.6.0/taxize/man/tp_classification-defunct.Rd | 9 taxize-0.6.0/taxize/man/tp_dist.Rd | 6 taxize-0.6.0/taxize/man/tp_namedistributions-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_namereferences-deprecated.Rd | 2 taxize-0.6.0/taxize/man/tp_refs.Rd | 6 taxize-0.6.0/taxize/man/tp_search.Rd | 6 taxize-0.6.0/taxize/man/tp_summary.Rd | 6 taxize-0.6.0/taxize/man/tp_synonyms.Rd | 6 taxize-0.6.0/taxize/man/tpl_families.Rd | 4 taxize-0.6.0/taxize/man/tpl_get.Rd | 27 taxize-0.6.0/taxize/man/tpl_search-defunct.Rd | 15 taxize-0.6.0/taxize/man/ubio_classification.Rd | 2 taxize-0.6.0/taxize/man/ubio_classification_search.Rd | 2 taxize-0.6.0/taxize/man/ubio_id.Rd | 2 taxize-0.6.0/taxize/man/ubio_search.Rd | 6 taxize-0.6.0/taxize/man/ubio_synonyms.Rd | 2 taxize-0.6.0/taxize/man/upstream.Rd | 15 taxize-0.6.0/taxize/man/vascan_search.Rd | 7 taxize-0.6.0/taxize/tests/testthat/test-apgscraping.R |only taxize-0.6.0/taxize/tests/testthat/test-class2tree.R | 19 taxize-0.6.0/taxize/tests/testthat/test-classification.R | 6 taxize-0.6.0/taxize/tests/testthat/test-col_children.R | 16 taxize-0.6.0/taxize/tests/testthat/test-col_downstream.R | 11 taxize-0.6.0/taxize/tests/testthat/test-eol_dataobjects.R | 5 taxize-0.6.0/taxize/tests/testthat/test-get_ids.R | 14 taxize-0.6.0/taxize/tests/testthat/test-gnr_datasources.R | 20 taxize-0.6.0/taxize/tests/testthat/test-itis_downstream.R | 4 taxize-0.6.0/taxize/tests/testthat/test-names_list.R | 8 taxize-0.6.0/taxize/tests/testthat/test-phylomatic_tree.R | 12 taxize-0.6.0/taxize/tests/testthat/test-rankagg.R |only taxize-0.6.0/taxize/tests/testthat/test-sci2comm.R | 4 taxize-0.6.0/taxize/tests/testthat/test-synonyms.R | 6 taxize-0.6.0/taxize/tests/testthat/test-tax_agg.R | 4 taxize-0.6.0/taxize/tests/testthat/test-tnrs.R | 8 taxize-0.6.0/taxize/tests/testthat/test-tp_dist.R | 2 taxize-0.6.0/taxize/tests/testthat/test-vascan_search.r | 6 taxize-0.6.0/taxize/vignettes/taxize_infotable.Rmd | 1 taxize-0.6.0/taxize/vignettes/taxize_vignette.Rmd | 252 +--- 295 files changed, 3985 insertions(+), 2981 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.1.0 dated 2015-05-11 and 1.2.0 dated 2015-06-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/phylocurve.R | 14 +++++++------- man/phylocurve-package.Rd | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.0.3 dated 2015-03-26 and 1.0.4 dated 2015-06-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/Add_to_data_object.R | 13 ++++++++----- R/General_figure_functions.R | 10 ++++++++-- R/Methods_for_data_objects.R | 33 +++++++++++++++++++++++++-------- R/Methods_for_result_objects.R | 4 +++- R/Prepare_data.R | 4 ++-- man/Nspecies.Rd | 10 ++++++++-- man/nodiv-package.Rd | 6 +++--- 9 files changed, 70 insertions(+), 36 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.6.1 dated 2015-05-07 and 0.7 dated 2015-06-13
rmarkdown-0.6.1/rmarkdown/inst/rmd/beamer |only rmarkdown-0.7/rmarkdown/DESCRIPTION | 8 - rmarkdown-0.7/rmarkdown/MD5 | 38 +++--- rmarkdown-0.7/rmarkdown/NEWS | 22 +++ rmarkdown-0.7/rmarkdown/R/beamer_presentation.R | 10 + rmarkdown-0.7/rmarkdown/R/html_dependencies.R | 19 +++ rmarkdown-0.7/rmarkdown/R/html_document_base.R | 9 + rmarkdown-0.7/rmarkdown/R/html_fragment.R | 27 +++- rmarkdown-0.7/rmarkdown/R/html_resources.R | 57 ++++++++++ rmarkdown-0.7/rmarkdown/R/output_format.R | 15 ++ rmarkdown-0.7/rmarkdown/R/pandoc.R | 5 rmarkdown-0.7/rmarkdown/R/pdf_document.R | 57 ++++++++-- rmarkdown-0.7/rmarkdown/R/render.R | 46 ++++++-- rmarkdown-0.7/rmarkdown/inst/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd | 2 rmarkdown-0.7/rmarkdown/inst/rmd/latex/default-1.14.tex |only rmarkdown-0.7/rmarkdown/man/beamer_presentation.Rd | 7 - rmarkdown-0.7/rmarkdown/man/html_fragment.Rd | 17 +- rmarkdown-0.7/rmarkdown/man/output_format.Rd | 12 +- rmarkdown-0.7/rmarkdown/tests/testthat/resources/empty.bib |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/empty.csl |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/pdf.Rmd |only rmarkdown-0.7/rmarkdown/tests/testthat/resources/period.Rmd |only rmarkdown-0.7/rmarkdown/tests/testthat/test-resources.R | 33 +++++ 23 files changed, 320 insertions(+), 64 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi,
POPDIST, STRand, and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics are also available. polysat can assist the user in estimating the
ploidy of samples, and it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to SPAGeDi and adegenet. Functions are also
included for assigning alleles to isoloci in cases where one pair of
microsatellite primers amplifies alleles from two or more independently
segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.3-3 dated 2014-09-22 and 1.4-0 dated 2015-06-13
DESCRIPTION | 24 +++-- MD5 | 49 ++++++---- NAMESPACE | 3 NEWS | 22 ++++ R/allopolyploidy.R |only R/dataimport.R | 6 + R/individual_distance.R | 36 ++----- build/vignette.rds |binary data/AllopolyTutorialData.RData |only data/FCRinfo.txt.gz |binary inst/CITATION | 19 ++-- inst/doc/allopolyVignette.R |only inst/doc/allopolyVignette.Rnw |only inst/doc/allopolyVignette.pdf |only inst/doc/polysattutorial.Rnw | 96 ++++++++++++--------- inst/doc/polysattutorial.pdf |binary man/AllopolyTutorialData.Rd |only man/FCRinfo.Rd | 6 + man/alleleCorrelations.Rd |only man/catalanAlleles.Rd |only man/mergeAlleleAssignments.Rd |only man/read.GeneMapper.Rd | 2 man/read.SPAGeDi.Rd | 2 man/recodeAllopoly.Rd |only man/simAllopoly.Rd |only man/testgenotypes.Rd | 6 + man/write.GeneMapper.Rd | 2 man/write.SPAGeDi.Rd | 2 man/write.freq.SPAGeDi.Rd | 2 vignettes/allopolyVignette.Rnw |only vignettes/polysattutorial.Rnw | 96 ++++++++++++--------- vignettes/vignettebuild/AllopolyTutorialDist.RData |only 32 files changed, 233 insertions(+), 140 deletions(-)
Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little
packages which pass R package checks. This sets it apart from
package.skeleton() which it calls, and which leaves imperfect files
behind. As this is not exactly helpful for beginners, kitten() offers
an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pkgKitten versions 0.1.2 dated 2014-09-11 and 0.1.3 dated 2015-06-13
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/pkgKitten.R | 37 ++++++++++++++++++++++++++----------- README.md | 4 ++-- inst/NEWS.Rd | 15 +++++++++++++-- man/kitten.Rd | 18 ++++++++++-------- man/playWithPerPackageHelpPage.Rd | 3 ++- 9 files changed, 99 insertions(+), 38 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.15.17 dated 2015-06-03 and 0.16.0 dated 2015-06-13
ChangeLog | 53 +++++++ DESCRIPTION | 11 - MD5 | 186 +++++++++++++-------------- NAMESPACE | 2 NEWS | 12 + R/install.R | 12 + R/updateR.R | 22 ++- R/zzz.R | 3 README.md | 4 man/R_version_in_a_folder.Rd | 20 +- man/add.installr.GUI.Rd | 8 - man/add_load_installr_on_startup_menu.Rd | 5 man/add_remove_installr_from_startup_menu.Rd | 5 man/add_to_.First_in_Rprofile.site.Rd | 16 +- man/ask.user.for.a.row.Rd | 34 +--- man/ask.user.yn.question.Rd | 18 -- man/barplot_package_users_per_day.Rd | 30 +--- man/browse.latest.R.NEWS.Rd | 11 - man/check.for.updates.R.Rd | 25 +-- man/check.integer.Rd | 10 - man/checkMD5sums2.Rd | 23 +-- man/copy.packages.between.libraries.Rd | 47 ++---- man/cranometer.Rd | 50 +++---- man/create.global.library.Rd | 10 - man/download_RStudio_CRAN_data.Rd | 50 ++----- man/fetch_tag_from_Rd.Rd | 18 +- man/file.name.from.url.Rd | 15 -- man/format_RStudio_CRAN_data.Rd | 18 +- man/freegeoip.Rd | 21 +-- man/get.installed.R.folders.Rd | 27 +-- man/get_Rscript_PID.Rd | 15 -- man/get_pid.Rd | 25 +-- man/get_tasklist.Rd | 15 -- man/install.7zip.Rd | 47 +++--- man/install.CMake.Rd | 26 +-- man/install.Cygwin.Rd | 18 +- man/install.FFmpeg.Rd | 29 +--- man/install.GitHub.Rd | 20 +- man/install.GraphicsMagick.Rd | 26 +-- man/install.ImageMagick.Rd | 26 +-- man/install.LaTeX2RTF.Rd | 24 +-- man/install.LyX.Rd | 37 +---- man/install.MikTeX.Rd | 29 +--- man/install.R.Rd | 39 +---- man/install.RStudio.Rd | 20 +- man/install.Rdevel.Rd | 17 +- man/install.Rtools.Rd | 46 +----- man/install.SWFTools.Rd | 27 +-- man/install.Texmaker.Rd | 22 +-- man/install.URL.Rd | 38 +---- man/install.git.Rd | 18 +- man/install.notepadpp.Rd | 32 +--- man/install.npptor.Rd | 31 +--- man/install.packages.zip.Rd | 27 +-- man/install.pandoc.Rd | 30 +--- man/installr.Rd | 26 +-- man/is.RStudio.Rd | 13 - man/is.Rgui.Rd | 13 - man/is.empty.Rd | 15 +- man/is.exe.installed.Rd | 10 - man/is.windows.Rd | 17 -- man/is_in_.First_in_Rprofile.site.Rd | 10 - man/kill_all_Rscript_s.Rd | 31 +--- man/kill_pid.Rd | 31 +--- man/kill_process.Rd | 34 ++-- man/lineplot_package_downloads.Rd | 25 +-- man/load_installr_on_startup.Rd | 5 man/most_downloaded_packages.Rd | 19 +- man/myip.Rd | 8 - man/os.hibernate.Rd | 29 +--- man/os.lock.Rd | 25 +-- man/os.manage.Rd | 29 +--- man/os.restart.Rd | 25 +-- man/os.shutdown.Rd | 36 +---- man/os.sleep.Rd | 32 +--- man/package_authors.Rd | 33 ++-- man/pkgDNLs_worldmapcolor.Rd | 24 +-- man/read_RStudio_CRAN_data.Rd | 38 ++--- man/remove.installr.GUI.Rd | 5 man/remove_from_.First_in_Rprofile.site.Rd | 16 +- man/rename_r_to_R.Rd | 32 ++-- man/require2.Rd | 20 -- man/restart_RGui.Rd | 4 man/rm_installr_from_startup.Rd | 5 man/source.https.Rd | 28 +--- man/system.PATH.Rd | 8 - man/turn.number.version.Rd | 9 - man/turn.version.to.number.Rd | 9 - man/turn.version.to.number1.Rd | 8 - man/uninstall.R.Rd | 20 +- man/uninstall.packages.Rd | 23 +-- man/up_folder.Rd | 12 - man/updateR.Rd | 132 +++++-------------- man/xlsx2csv.Rd | 15 -- 94 files changed, 921 insertions(+), 1403 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different
degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large
for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional
parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>
Diff between Kernelheaping versions 0.5 dated 2015-04-27 and 0.9 dated 2015-06-13
Kernelheaping-0.5/Kernelheaping/data/students.R |only Kernelheaping-0.5/Kernelheaping/man/Rprx.Rd |only Kernelheaping-0.9/Kernelheaping/DESCRIPTION | 19 Kernelheaping-0.9/Kernelheaping/MD5 | 31 - Kernelheaping-0.9/Kernelheaping/NAMESPACE | 8 Kernelheaping-0.9/Kernelheaping/R/Kernelheaping.R | 17 Kernelheaping-0.9/Kernelheaping/R/functions.R | 303 ++++++++-- Kernelheaping-0.9/Kernelheaping/data/students.rda |only Kernelheaping-0.9/Kernelheaping/man/Kernelheaping.Rd | 17 Kernelheaping-0.9/Kernelheaping/man/createSim.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/dbivr.Rd |only Kernelheaping-0.9/Kernelheaping/man/dheaping.Rd | 9 Kernelheaping-0.9/Kernelheaping/man/plot.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/plot.bivrounding.Rd |only Kernelheaping-0.9/Kernelheaping/man/sim.Kernelheaping.Rd | 4 Kernelheaping-0.9/Kernelheaping/man/simSummary.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/students.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/summary.Kernelheaping.Rd | 2 Kernelheaping-0.9/Kernelheaping/man/tracePlots.Rd | 2 19 files changed, 320 insertions(+), 100 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 0.2-0 dated 2015-03-24 and 1.1-0 dated 2015-06-12
jomo-0.2-0/jomo/src/jomo1mix2.c |only jomo-0.2-0/jomo/src/jomo1ranmix2.c |only jomo-1.1-0/jomo/DESCRIPTION | 12 - jomo-1.1-0/jomo/MD5 | 91 +++++++++---- jomo-1.1-0/jomo/NAMESPACE | 4 jomo-1.1-0/jomo/R/jomo1.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1.R |only jomo-1.1-0/jomo/R/jomo1cat.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1cat.R | 27 +--- jomo-1.1-0/jomo/R/jomo1con.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1con.R | 13 + jomo-1.1-0/jomo/R/jomo1mix.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1mix.R | 27 +--- jomo-1.1-0/jomo/R/jomo1ran.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1ran.R |only jomo-1.1-0/jomo/R/jomo1rancat.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1rancat.R | 34 +++-- jomo-1.1-0/jomo/R/jomo1rancathr.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1rancathr.R | 38 +++++ jomo-1.1-0/jomo/R/jomo1rancon.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1rancon.R | 20 ++- jomo-1.1-0/jomo/R/jomo1ranconhr.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1ranconhr.R | 26 +++ jomo-1.1-0/jomo/R/jomo1ranmix.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1ranmix.R | 34 +++-- jomo-1.1-0/jomo/R/jomo1ranmixhr.MCMCchain.R |only jomo-1.1-0/jomo/R/jomo1ranmixhr.R | 40 +++++- jomo-1.1-0/jomo/inst/CITATION | 12 - jomo-1.1-0/jomo/man/jomo-package.Rd | 8 - jomo-1.1-0/jomo/man/jomo1.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1.Rd |only jomo-1.1-0/jomo/man/jomo1cat.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1cat.Rd | 17 -- jomo-1.1-0/jomo/man/jomo1con.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1con.Rd | 4 jomo-1.1-0/jomo/man/jomo1mix.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1mix.Rd | 21 +-- jomo-1.1-0/jomo/man/jomo1ran.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1ran.Rd |only jomo-1.1-0/jomo/man/jomo1rancat.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1rancat.Rd | 20 +-- jomo-1.1-0/jomo/man/jomo1rancathr.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1rancathr.Rd | 18 +- jomo-1.1-0/jomo/man/jomo1rancon.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1rancon.Rd | 2 jomo-1.1-0/jomo/man/jomo1ranconhr.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1ranconhr.Rd | 10 - jomo-1.1-0/jomo/man/jomo1ranmix.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1ranmix.Rd | 20 --- jomo-1.1-0/jomo/man/jomo1ranmixhr.MCMCchain.Rd |only jomo-1.1-0/jomo/man/jomo1ranmixhr.Rd | 19 +- jomo-1.1-0/jomo/src/MCMCjomo1con.c |only jomo-1.1-0/jomo/src/MCMCjomo1mix.c |only jomo-1.1-0/jomo/src/MCMCjomo1rancon.c |only jomo-1.1-0/jomo/src/MCMCjomo1ranconhf.c |only jomo-1.1-0/jomo/src/MCMCjomo1ranconhr.c |only jomo-1.1-0/jomo/src/MCMCjomo1ranmix.c |only jomo-1.1-0/jomo/src/MCMCjomo1ranmixhf.c |only jomo-1.1-0/jomo/src/MCMCjomo1ranmixhr.c |only jomo-1.1-0/jomo/src/jomo1ranconhr.c | 14 +- jomo-1.1-0/jomo/src/jomo1ranmix.c | 24 --- jomo-1.1-0/jomo/src/jomo1ranmixhf.c |only jomo-1.1-0/jomo/src/jomo1ranmixhr.c | 164 +++++++++++++------------ jomo-1.1-0/jomo/src/pdflib.c | 22 +-- jomo-1.1-0/jomo/src/pdflib.h | 10 - 65 files changed, 437 insertions(+), 314 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.9-0 dated 2015-06-11 and 1.9-1 dated 2015-06-12
Description: Implementation of statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g., discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models,
or continuous-space point process data such as the
occurrence of infectious diseases. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of communicable diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently, the package contains implementations of many typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Höhle and Paul (2008). A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Furthermore, inference methods for the retrospective infectious
disease models in Held et al (2005), Held et al (2006),
Paul et al (2008), Paul and Held (2011), Held and Paul (2012),
and Meyer and Held (2014) are provided.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ('twinSIR', discrete
space) and Meyer et al (2012) ('twinstim', continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: Using the 'boda' algorithm requires the 'INLA'
package, which should be installed automatically through the
specified Additional_repositories, if uninstalled dependencies
are also requested. As this might not work under OS X it
might be necessary to manually install the 'INLA' package as
specified at
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
DESCRIPTION | 10 +-
MD5 | 32 ++++----
R/bodaDelay.R | 122 ++++++++++++++++++++-------------
R/hhh4.R | 7 -
R/hhh4_W.R | 16 ++--
R/hhh4_methods.R | 29 ++++---
R/zzz.R | 16 ++--
build/partial.rdb |binary
inst/NEWS.Rd | 15 ++++
inst/doc/glrnb.pdf |binary
inst/doc/hhh4.pdf |binary
inst/doc/surveillance.pdf |binary
man/bodaDelay.Rd | 71 -------------------
man/formatPval.Rd | 6 -
man/surveillance.options.Rd | 12 +--
tests/testthat/test-bodaDelay.R | 32 ++++----
tests/testthat/test-hhh4+derivatives.R | 4 -
17 files changed, 184 insertions(+), 188 deletions(-)
Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using
structural equations, with emphasis on problems in causal inference.
Specify interventions and simulate from intervened data generating
distributions. Define and evaluate treatment-specific means, the average
treatment effects and coefficients from working marginal structural models.
User interface designed to facilitate the conduct of transparent and
reproducible simulation studies, and allows concise expression of complex
functional dependencies for a large number of time-varying nodes. See the
package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between simcausal versions 0.1 dated 2015-05-16 and 0.2.0 dated 2015-06-12
simcausal-0.1/simcausal/man/node.depr.Rd |only simcausal-0.2.0/simcausal/DESCRIPTION | 20 simcausal-0.2.0/simcausal/MD5 | 118 +- simcausal-0.2.0/simcausal/NAMESPACE | 3 simcausal-0.2.0/simcausal/NEWS | 14 simcausal-0.2.0/simcausal/R/action_node_indexing.R | 10 simcausal-0.2.0/simcausal/R/distributions.R | 32 simcausal-0.2.0/simcausal/R/estimatetarget.r | 10 simcausal-0.2.0/simcausal/R/interface.r | 229 +--- simcausal-0.2.0/simcausal/R/node.R | 339 ++---- simcausal-0.2.0/simcausal/R/simcausal-package.r | 107 +- simcausal-0.2.0/simcausal/R/simcausal.r | 171 --- simcausal-0.2.0/simcausal/R/simulation.r | 80 - simcausal-0.2.0/simcausal/R/targetparam.r | 16 simcausal-0.2.0/simcausal/R/zzz.R |only simcausal-0.2.0/simcausal/README.md | 110 ++ simcausal-0.2.0/simcausal/build |only simcausal-0.2.0/simcausal/inst |only simcausal-0.2.0/simcausal/man/A.Rd | 8 simcausal-0.2.0/simcausal/man/DAG.empty.Rd | 2 simcausal-0.2.0/simcausal/man/DF.to.long.Rd | 12 simcausal-0.2.0/simcausal/man/DF.to.longDT.Rd | 8 simcausal-0.2.0/simcausal/man/N.Rd | 10 simcausal-0.2.0/simcausal/man/add.action.Rd | 18 simcausal-0.2.0/simcausal/man/add.nodes.Rd | 16 simcausal-0.2.0/simcausal/man/distr.list.Rd | 6 simcausal-0.2.0/simcausal/man/doLTCF.Rd | 62 + simcausal-0.2.0/simcausal/man/eval.target.Rd | 4 simcausal-0.2.0/simcausal/man/node.Rd | 122 +- simcausal-0.2.0/simcausal/man/parents.Rd | 2 simcausal-0.2.0/simcausal/man/plotDAG.Rd | 6 simcausal-0.2.0/simcausal/man/plotSurvEst.Rd | 22 simcausal-0.2.0/simcausal/man/print.DAG.Rd | 6 simcausal-0.2.0/simcausal/man/print.DAG.action.Rd | 6 simcausal-0.2.0/simcausal/man/print.DAG.node.Rd | 6 simcausal-0.2.0/simcausal/man/rbern.Rd | 10 simcausal-0.2.0/simcausal/man/rcategor.Rd | 8 simcausal-0.2.0/simcausal/man/rcategor.int.Rd | 8 simcausal-0.2.0/simcausal/man/rconst.Rd | 10 simcausal-0.2.0/simcausal/man/rdistr.template.Rd | 4 simcausal-0.2.0/simcausal/man/set.DAG.Rd | 165 ++- simcausal-0.2.0/simcausal/man/set.targetE.Rd | 6 simcausal-0.2.0/simcausal/man/set.targetMSM.Rd | 4 simcausal-0.2.0/simcausal/man/sim.Rd | 54 + simcausal-0.2.0/simcausal/man/simcausal.Rd | 74 + simcausal-0.2.0/simcausal/man/simfull.Rd | 14 simcausal-0.2.0/simcausal/man/simobs.Rd | 12 simcausal-0.2.0/simcausal/man/vecfun.add.Rd | 4 simcausal-0.2.0/simcausal/man/vecfun.all.print.Rd | 6 simcausal-0.2.0/simcausal/man/vecfun.print.Rd | 6 simcausal-0.2.0/simcausal/man/vecfun.remove.Rd | 4 simcausal-0.2.0/simcausal/man/vecfun.reset.Rd | 4 simcausal-0.2.0/simcausal/tests/RUnit/add.action.R |only simcausal-0.2.0/simcausal/tests/RUnit/runittests.R | 491 ++-------- simcausal-0.2.0/simcausal/tests/RUnit/set.DAG.R |only simcausal-0.2.0/simcausal/tests/RUnit/sim.impute.examples12.R |only simcausal-0.2.0/simcausal/vignettes |only 57 files changed, 1214 insertions(+), 1245 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.12.0 dated 2015-05-18 and 0.12.1 dated 2015-06-12
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 11 +++++++++++ R/bootstrap.R | 3 --- R/shinywrappers.R | 10 +++------- inst/www/shared/shiny.js | 8 +++++--- inst/www/shared/shiny.js.map | 2 +- inst/www/shared/shiny.min.js | 6 +++--- inst/www/shared/shiny.min.js.map | 2 +- man/renderDataTable.Rd | 7 +++---- 10 files changed, 40 insertions(+), 35 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide
methods for automatically determining breaks and labels
for axes and legends.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 0.2.4 dated 2014-04-22 and 0.2.5 dated 2015-06-12
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Title: Node Harvest for Regression and Classification
Description: Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between nodeHarvest versions 0.7-2 dated 2015-06-09 and 0.7-3 dated 2015-06-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/getI.R | 17 +++++++++++++---- R/nodeHarvest.R | 12 ++++++------ R/predict.nodeHarvest.R | 7 ++++--- 5 files changed, 31 insertions(+), 21 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut],
Zachary Jones [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.3 dated 2015-02-04 and 2.4 dated 2015-06-12
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mlr-2.4/mlr/man/oversample.Rd | 2 mlr-2.4/mlr/man/performance.Rd | 21 mlr-2.4/mlr/man/pid.task.Rd | 2 mlr-2.4/mlr/man/plotFilterValues.Rd | 35 mlr-2.4/mlr/man/plotFilterValuesGGVIS.Rd |only mlr-2.4/mlr/man/plotLearnerPrediction.Rd | 2 mlr-2.4/mlr/man/plotLearningCurve.Rd |only mlr-2.4/mlr/man/plotLearningCurveGGVIS.Rd |only mlr-2.4/mlr/man/plotROCRCurves.Rd | 104 - mlr-2.4/mlr/man/plotROCRCurvesGGVIS.Rd |only mlr-2.4/mlr/man/plotThreshVsPerf.Rd | 49 mlr-2.4/mlr/man/plotThreshVsPerfGGVIS.Rd |only mlr-2.4/mlr/man/plotTuneMultiCritResult.Rd | 5 mlr-2.4/mlr/man/plotTuneMultiCritResultGGVIS.Rd |only mlr-2.4/mlr/man/plotViperCharts.Rd | 6 mlr-2.4/mlr/man/predict.WrappedModel.Rd | 4 mlr-2.4/mlr/man/predictLearner.Rd | 2 mlr-2.4/mlr/man/reimpute.Rd | 2 mlr-2.4/mlr/man/removeConstantFeatures.Rd | 2 mlr-2.4/mlr/man/removeHyperPars.Rd | 4 mlr-2.4/mlr/man/resample.Rd | 36 mlr-2.4/mlr/man/selectFeatures.Rd | 2 mlr-2.4/mlr/man/setAggregation.Rd | 2 mlr-2.4/mlr/man/setHyperPars.Rd | 4 mlr-2.4/mlr/man/setHyperPars2.Rd | 2 mlr-2.4/mlr/man/setId.Rd | 4 mlr-2.4/mlr/man/setPredictThreshold.Rd | 6 mlr-2.4/mlr/man/setPredictType.Rd | 7 mlr-2.4/mlr/man/setThreshold.Rd | 2 mlr-2.4/mlr/man/smote.Rd | 2 mlr-2.4/mlr/man/sonar.task.Rd | 2 mlr-2.4/mlr/man/subsetTask.Rd | 5 mlr-2.4/mlr/man/summarizeColumns.Rd | 2 mlr-2.4/mlr/man/summarizeLevels.Rd | 2 mlr-2.4/mlr/man/train.Rd | 2 mlr-2.4/mlr/man/trainLearner.Rd | 2 mlr-2.4/mlr/man/tuneParams.Rd | 5 mlr-2.4/mlr/man/tuneParamsMultiCrit.Rd | 3 mlr-2.4/mlr/man/tuneThreshold.Rd | 5 mlr-2.4/mlr/man/wpbc.task.Rd | 2 mlr-2.4/mlr/tests/testthat/Rplots.pdf |binary mlr-2.4/mlr/tests/testthat/helper_objects.R | 2 mlr-2.4/mlr/tests/testthat/test_base_BaseWrapper.R | 2 mlr-2.4/mlr/tests/testthat/test_base_Learner.R | 2 mlr-2.4/mlr/tests/testthat/test_base_PreprocWrapperCaret.R | 6 mlr-2.4/mlr/tests/testthat/test_base_SupervisedTask.R | 9 mlr-2.4/mlr/tests/testthat/test_base_TuneWrapper.R | 29 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Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters and a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.1.9225 dated 2015-04-30 and 0.0.1.9425 dated 2015-06-12
DESCRIPTION | 10 - MD5 | 72 +++++------ NAMESPACE | 52 ++++---- R/AQSearch.CAS.R | 80 ++++++------ R/AQSearch.R | 162 ++++++++++++------------- R/AQSearchUtils.R | 38 ++--- R/AQSys.R | 260 ++++++++++++++++++++-------------------- R/AQSys.err.R | 90 ++++++------- R/AQSys.gsnchk.R | 140 ++++++++++----------- R/AQSys.mathDesc.R | 88 ++++++------- R/AQSys.mrchk.R | 192 ++++++++++++++--------------- R/AQSys.mrgsn.R | 154 +++++++++++------------ R/AQSysCurve.R | 116 +++++++++--------- R/AQSysDB.R | 277 +++++++++++++++++++++---------------------- R/AQSysFormulas.R | 128 +++++++++---------- R/AQSysUtils.R | 101 ++++++++++----- R/LLSRUtils.R | 21 +-- R/LLSRxy.R | 42 +++--- R/datasets.R | 38 ++--- README.md | 8 - man/AQSearch.CAS.Rd | 48 +++---- man/AQSearch.Rd | 94 +++++++------- man/AQSys.Rd | 98 +++++++-------- man/AQSys.crpt.Rd | 70 +++++----- man/AQSys.gsnchk.Rd | 112 ++++++++--------- man/AQSys.plot.Rd | 130 ++++++++++---------- man/AQSys.tielines.Rd | 86 ++++++------- man/AQSysBancroft.Rd | 80 ++++++------ man/AQSysCurve.Rd | 122 +++++++++--------- man/AQSysDB.Rd | 48 +++---- man/AQSysList.Rd | 24 +-- man/AQSysOthmer.Rd | 80 ++++++------ man/LLSR.info.Rd | 24 +-- man/LLSRxy.Rd | 62 ++++----- man/peg4kslt.Rd | 52 ++++---- tests/testthat.R | 8 - tests/testthat/testMainFns.R | 26 ++-- 37 files changed, 1635 insertions(+), 1598 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.2 dated 2015-05-19 and 1.1.3 dated 2015-06-12
DESCRIPTION | 8 +-- MD5 | 9 ++-- R/drgeeData.R | 128 +++++++++++++++++++++++++++++++++++++++++++++------------- R/eFit.R | 6 -- R/geeFit.R | 2 inst |only 6 files changed, 111 insertions(+), 42 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)),
Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see
Jiang, Manchanda, Rossi 2009)
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric
Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 2.2-5 dated 2012-05-16 and 3.0-0 dated 2015-06-12
bayesm-2.2-5/bayesm/R/breg.R |only bayesm-2.2-5/bayesm/R/cgetC.R |only bayesm-2.2-5/bayesm/R/clusterMix.R |only bayesm-2.2-5/bayesm/R/ghkvec.R |only bayesm-2.2-5/bayesm/R/llmnl.R |only bayesm-2.2-5/bayesm/R/lndIChisq.R |only bayesm-2.2-5/bayesm/R/lndIWishart.R |only bayesm-2.2-5/bayesm/R/lndMvn.R |only bayesm-2.2-5/bayesm/R/lndMvst.R |only bayesm-2.2-5/bayesm/R/rDPGibbs.R |only bayesm-2.2-5/bayesm/R/rbprobitGibbs.R |only bayesm-2.2-5/bayesm/R/rdirichlet.R |only bayesm-2.2-5/bayesm/R/rhierLinearMixture.R |only bayesm-2.2-5/bayesm/R/rhierLinearModel.R |only bayesm-2.2-5/bayesm/R/rhierMnlDP.R |only bayesm-2.2-5/bayesm/R/rhierMnlRwMixture.R |only bayesm-2.2-5/bayesm/R/rhierNegbinRw.R |only bayesm-2.2-5/bayesm/R/rivDP.R |only bayesm-2.2-5/bayesm/R/rivGibbs.R |only bayesm-2.2-5/bayesm/R/rmixGibbs.R |only bayesm-2.2-5/bayesm/R/rmixture.R |only bayesm-2.2-5/bayesm/R/rmnlIndepMetrop.R |only bayesm-2.2-5/bayesm/R/rmnpGibbs.R |only bayesm-2.2-5/bayesm/R/rmultireg.R |only bayesm-2.2-5/bayesm/R/rmvpGibbs.R |only bayesm-2.2-5/bayesm/R/rmvst.R |only bayesm-2.2-5/bayesm/R/rnegbinRw.R |only bayesm-2.2-5/bayesm/R/rnmixGibbs.R |only bayesm-2.2-5/bayesm/R/rordprobitGibbs.R |only bayesm-2.2-5/bayesm/R/rscaleUsage.R |only bayesm-2.2-5/bayesm/R/rsurGibbs.R |only bayesm-2.2-5/bayesm/R/rtrun.R |only bayesm-2.2-5/bayesm/R/runireg.R |only bayesm-2.2-5/bayesm/R/runiregGibbs.R |only bayesm-2.2-5/bayesm/R/rwishart.R |only bayesm-2.2-5/bayesm/data/datalist |only bayesm-2.2-5/bayesm/inst/doc |only bayesm-2.2-5/bayesm/src/bayesmc.c |only bayesm-2.2-5/bayesm/src/bayesmcpp.cpp |only bayesm-2.2-5/bayesm/src/thetadraw.c |only bayesm-3.0-0/bayesm/DESCRIPTION | 64 +- bayesm-3.0-0/bayesm/MD5 | 257 ++++---- bayesm-3.0-0/bayesm/NAMESPACE | 23 bayesm-3.0-0/bayesm/R/BayesmConstants.R |only bayesm-3.0-0/bayesm/R/BayesmFunctions.R |only bayesm-3.0-0/bayesm/R/clusterMix_rcpp.R |only bayesm-3.0-0/bayesm/R/createX.R | 143 ++-- bayesm-3.0-0/bayesm/R/llnhlogit.R | 9 bayesm-3.0-0/bayesm/R/mnpProb.R | 9 bayesm-3.0-0/bayesm/R/plot.bayesm.hcoef.R | 89 +- bayesm-3.0-0/bayesm/R/plot.bayesm.mat.R | 117 +-- bayesm-3.0-0/bayesm/R/rbayesBLP_rcpp.R |only bayesm-3.0-0/bayesm/R/rbiNormGibbs.R | 235 +++---- bayesm-3.0-0/bayesm/R/rbprobitgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rcppexports.r |only bayesm-3.0-0/bayesm/R/rdpgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rhierBinLogit.R | 455 +++++++-------- bayesm-3.0-0/bayesm/R/rhierLinearMixture_rcpp.r |only bayesm-3.0-0/bayesm/R/rhierLinearModel_rcpp.R |only bayesm-3.0-0/bayesm/R/rhierMnlDP_rcpp.r |only bayesm-3.0-0/bayesm/R/rhierMnlRwMixture_rcpp.r |only bayesm-3.0-0/bayesm/R/rhiernegbinrw_rcpp.r |only bayesm-3.0-0/bayesm/R/rivDP_rcpp.R |only bayesm-3.0-0/bayesm/R/rivGibbs_rcpp.R |only bayesm-3.0-0/bayesm/R/rmnlIndepMetrop_rcpp.R |only bayesm-3.0-0/bayesm/R/rmnpgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rmvpgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rnegbinrw_rcpp.r |only bayesm-3.0-0/bayesm/R/rnmixgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rordprobitgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/rscaleusage_rcpp.r |only bayesm-3.0-0/bayesm/R/rsurgibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/runireg_rcpp.r |only bayesm-3.0-0/bayesm/R/runireggibbs_rcpp.r |only bayesm-3.0-0/bayesm/R/simnhlogit.R | 14 bayesm-3.0-0/bayesm/R/summary.bayesm.var.R | 2 bayesm-3.0-0/bayesm/data/Scotch.rda |binary bayesm-3.0-0/bayesm/data/bank.rda |binary bayesm-3.0-0/bayesm/data/cheese.rda |binary bayesm-3.0-0/bayesm/data/customerSat.rda |binary bayesm-3.0-0/bayesm/data/detailing.rda |binary bayesm-3.0-0/bayesm/data/margarine.rda |binary bayesm-3.0-0/bayesm/data/orangeJuice.rda |binary bayesm-3.0-0/bayesm/data/tuna.rda |binary bayesm-3.0-0/bayesm/inst/include |only bayesm-3.0-0/bayesm/man/bank.Rd | 254 ++++---- bayesm-3.0-0/bayesm/man/breg.Rd | 2 bayesm-3.0-0/bayesm/man/cgetC.Rd | 2 bayesm-3.0-0/bayesm/man/cheese.Rd | 166 ++--- bayesm-3.0-0/bayesm/man/clusterMix.Rd | 176 ++--- bayesm-3.0-0/bayesm/man/condMom.Rd | 2 bayesm-3.0-0/bayesm/man/customerSat.Rd | 76 +- bayesm-3.0-0/bayesm/man/detailing.Rd | 24 bayesm-3.0-0/bayesm/man/eMixMargDen.Rd | 4 bayesm-3.0-0/bayesm/man/ghkvec.Rd | 115 ++- bayesm-3.0-0/bayesm/man/llmnl.Rd | 2 bayesm-3.0-0/bayesm/man/llnhlogit.Rd | 27 bayesm-3.0-0/bayesm/man/lndIChisq.Rd | 8 bayesm-3.0-0/bayesm/man/lndMvn.Rd | 2 bayesm-3.0-0/bayesm/man/lndMvst.Rd | 4 bayesm-3.0-0/bayesm/man/logMargDenNR.Rd | 70 +- bayesm-3.0-0/bayesm/man/margarine.Rd | 52 - bayesm-3.0-0/bayesm/man/mixDen.Rd | 4 bayesm-3.0-0/bayesm/man/mixDenBi.Rd | 4 bayesm-3.0-0/bayesm/man/mnlHess.Rd | 88 +- bayesm-3.0-0/bayesm/man/momMix.Rd | 2 bayesm-3.0-0/bayesm/man/orangeJuice.Rd | 68 +- bayesm-3.0-0/bayesm/man/plot.bayesm.hcoef.Rd | 2 bayesm-3.0-0/bayesm/man/plot.bayesm.mat.Rd | 10 bayesm-3.0-0/bayesm/man/plot.bayesm.nmix.Rd | 12 bayesm-3.0-0/bayesm/man/rDPGibbs.Rd | 79 +- bayesm-3.0-0/bayesm/man/rbayesBLP.Rd |only bayesm-3.0-0/bayesm/man/rbiNormGibbs.Rd | 2 bayesm-3.0-0/bayesm/man/rbprobitGibbs.Rd | 3 bayesm-3.0-0/bayesm/man/rhierBinLogit.Rd | 6 bayesm-3.0-0/bayesm/man/rhierLinearMixture.Rd | 308 +++++----- bayesm-3.0-0/bayesm/man/rhierLinearModel.Rd | 201 +++--- bayesm-3.0-0/bayesm/man/rhierMnlDP.Rd | 454 +++++++------- bayesm-3.0-0/bayesm/man/rhierMnlRwMixture.Rd | 366 ++++++------ bayesm-3.0-0/bayesm/man/rhierNegbinRw.Rd | 284 ++++----- bayesm-3.0-0/bayesm/man/rivDP.Rd | 64 +- bayesm-3.0-0/bayesm/man/rivGibbs.Rd | 197 +++--- bayesm-3.0-0/bayesm/man/rmixGibbs.Rd | 3 bayesm-3.0-0/bayesm/man/rmixture.Rd | 2 bayesm-3.0-0/bayesm/man/rmnlIndepMetrop.Rd | 187 +++--- bayesm-3.0-0/bayesm/man/rmnpGibbs.Rd | 239 +++---- bayesm-3.0-0/bayesm/man/rmultireg.Rd | 8 bayesm-3.0-0/bayesm/man/rmvpGibbs.Rd | 9 bayesm-3.0-0/bayesm/man/rnegbinRw.Rd | 13 bayesm-3.0-0/bayesm/man/rnmixGibbs.Rd | 13 bayesm-3.0-0/bayesm/man/rordprobitGibbs.Rd | 231 +++---- bayesm-3.0-0/bayesm/man/rscaleUsage.Rd | 4 bayesm-3.0-0/bayesm/man/rsurGibbs.Rd | 9 bayesm-3.0-0/bayesm/man/runireg.Rd | 11 bayesm-3.0-0/bayesm/man/runiregGibbs.Rd | 7 bayesm-3.0-0/bayesm/man/rwishart.Rd | 2 bayesm-3.0-0/bayesm/man/simnhlogit.Rd | 101 +-- bayesm-3.0-0/bayesm/man/summary.bayesm.mat.Rd | 9 bayesm-3.0-0/bayesm/man/summary.bayesm.nmix.Rd | 2 bayesm-3.0-0/bayesm/man/summary.bayesm.var.Rd | 4 bayesm-3.0-0/bayesm/man/tuna.Rd | 222 +++---- bayesm-3.0-0/bayesm/src/Makevars |only bayesm-3.0-0/bayesm/src/Makevars.win |only bayesm-3.0-0/bayesm/src/bayesBLP_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/breg_rcpp.cpp |only bayesm-3.0-0/bayesm/src/cgetC_rcpp.cpp |only bayesm-3.0-0/bayesm/src/clusterMix_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/functionTiming.cpp |only bayesm-3.0-0/bayesm/src/ghkvec_rcpp.cpp |only bayesm-3.0-0/bayesm/src/llmnl_rcpp.cpp |only bayesm-3.0-0/bayesm/src/lndIChisq_rcpp.cpp |only bayesm-3.0-0/bayesm/src/lndIWishart_rcpp.cpp |only bayesm-3.0-0/bayesm/src/lndMvn_rcpp.cpp |only bayesm-3.0-0/bayesm/src/lndMvst_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rDPGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rbprobitGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rcppexports.cpp |only bayesm-3.0-0/bayesm/src/rdirichlet_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rhierLinearMixture_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rhierLinearModel_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rhierMnlDP_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rhierMnlRwMixture_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rhierNegbinRw_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rivDP_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rivgibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rmixGibbs_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rmixture_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rmnlIndepMetrop_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rmnpGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rmultireg_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rmvpGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rmvst_rcpp.cpp |only bayesm-3.0-0/bayesm/src/rnegbinRw_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rnmixGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rordprobitGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rscaleUsage_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rsurGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rtrun_rcpp.cpp |only bayesm-3.0-0/bayesm/src/runiregGibbs_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/runireg_rcpp_loop.cpp |only bayesm-3.0-0/bayesm/src/rwishart_rcpp.cpp |only bayesm-3.0-0/bayesm/src/utilityFunctions.cpp |only 182 files changed, 2871 insertions(+), 2762 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
Author: David I. Hastie <david.hastie@rsimony.com>, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson <sylvia.richardson@mrc-bsu.cam.ac.uk> with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.1.0 dated 2015-03-13 and 3.1.1 dated 2015-06-12
PReMiuM-3.1.0/PReMiuM/inst/citation |only PReMiuM-3.1.1/PReMiuM/ChangeLog | 8 + PReMiuM-3.1.1/PReMiuM/DESCRIPTION | 8 - PReMiuM-3.1.1/PReMiuM/MD5 | 26 +-- PReMiuM-3.1.1/PReMiuM/R/postProcess.R | 23 ++- PReMiuM-3.1.1/PReMiuM/inst/CITATION |only PReMiuM-3.1.1/PReMiuM/man/PReMiuM-package.Rd | 4 PReMiuM-3.1.1/PReMiuM/man/profRegr.Rd | 41 ++++- PReMiuM-3.1.1/PReMiuM/man/setHyperparams.Rd | 5 PReMiuM-3.1.1/PReMiuM/src/PReMiuM.cpp | 28 +++ PReMiuM-3.1.1/PReMiuM/src/include/PReMiuMIO.h | 12 + PReMiuM-3.1.1/PReMiuM/src/include/PReMiuMModel.h | 29 +++ PReMiuM-3.1.1/PReMiuM/src/include/PReMiuMOptions.h | 14 + PReMiuM-3.1.1/PReMiuM/src/include/PReMiuMProposals.h | 145 ++++++++++++++++++- PReMiuM-3.1.1/PReMiuM/src/postProcess.cpp | 4 15 files changed, 301 insertions(+), 46 deletions(-)
Title: Data Sets, Functions and Examples from the Book: "Modern
Industrial Statistics" by Kenett, Zacks and Amberti
Description: This R package is providing all the data sets and statistical analysis applications used in "Modern Industrial Statistics: with applications in R, MINITAB and JMP" by R.S. Kenett and S. Zacks with contributions by D. Amberti, John Wiley and Sons, 2013, which is a second revised and expanded revision of "Modern Industrial Statistics: Design and Control of Quality and Reliability", R. Kenett and S. Zacks, Duxbury/Wadsworth Publishing, 1998.
Author: Daniele Amberti
Maintainer: Daniele Amberti <daniele.amberti@gmail.com>
Diff between mistat versions 1.0-2 dated 2014-01-20 and 1.0-3 dated 2015-06-12
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- R/availDis.R | 5 ++--- R/randomizationTest.R | 3 +-- 4 files changed, 13 insertions(+), 15 deletions(-)
Title: Sensitivity Analysis
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis of model output.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Sebastien Da Veiga, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Bernardo Ramos, Taieb Touati
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.11 dated 2015-03-06 and 1.11.1 dated 2015-06-12
DESCRIPTION | 8 - MD5 | 26 +-- R/sobol.R | 352 +++++++++++++++++++++++++-------------------------- R/sobol2002.R | 238 +++++++++++++++++----------------- R/sobolMultOut.R | 9 - R/sobolmartinez.R | 23 +-- man/sobol.Rd | 4 man/sobol2002.Rd | 2 man/sobol2007.Rd | 2 man/sobolGP.Rd | 2 man/sobolMultOut.Rd | 11 - man/soboljansen.Rd | 2 man/sobolmara.Rd | 2 man/sobolmartinez.Rd | 11 + 14 files changed, 349 insertions(+), 343 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.38-1 dated 2015-02-24 and 2.38-2 dated 2015-06-12
survival-2.38-1/survival/R/anova.coxmelist.R |only survival-2.38-1/survival/R/anova.coxph.S |only survival-2.38-1/survival/vignettes/figures |only survival-2.38-2/survival/DESCRIPTION | 6 survival-2.38-2/survival/MD5 | 154 ++++++++++---------- survival-2.38-2/survival/NAMESPACE | 1 survival-2.38-2/survival/R/agreg.fit.R | 3 survival-2.38-2/survival/R/anova.coxph.R |only survival-2.38-2/survival/R/anova.coxph.penal.R |only survival-2.38-2/survival/R/coxexact.fit.R | 38 ++++ survival-2.38-2/survival/R/coxph.R | 6 survival-2.38-2/survival/R/logLik.coxph.R | 9 - survival-2.38-2/survival/R/print.coxph.S | 18 +- survival-2.38-2/survival/R/print.coxph.penal.S | 22 +- survival-2.38-2/survival/R/print.survfit.S | 17 ++ survival-2.38-2/survival/R/pyears.R | 4 survival-2.38-2/survival/R/summary.pyears.S | 3 survival-2.38-2/survival/R/survexp.R | 3 survival-2.38-2/survival/R/survfit.coxph.R | 4 survival-2.38-2/survival/R/tmerge.R | 2 survival-2.38-2/survival/build/vignette.rds |binary survival-2.38-2/survival/data/kidney.rda |binary survival-2.38-2/survival/data/ovarian.rda |binary survival-2.38-2/survival/inst/NEWS.Rd | 53 ++++++ survival-2.38-2/survival/inst/NEWS.Rd.orig | 72 ++++++++- survival-2.38-2/survival/inst/doc/adjcurve.Rnw | 4 survival-2.38-2/survival/inst/doc/adjcurve.pdf |binary survival-2.38-2/survival/inst/doc/compete.R | 76 ++++++--- survival-2.38-2/survival/inst/doc/compete.Rnw | 106 ++++++++----- survival-2.38-2/survival/inst/doc/compete.pdf |binary survival-2.38-2/survival/inst/doc/splines.R | 33 +++- survival-2.38-2/survival/inst/doc/splines.Rnw | 65 +++++++- survival-2.38-2/survival/inst/doc/splines.pdf |binary survival-2.38-2/survival/inst/doc/tests.R | 13 - survival-2.38-2/survival/inst/doc/tests.Rnw | 9 - survival-2.38-2/survival/inst/doc/tests.pdf |binary survival-2.38-2/survival/inst/doc/timedep.R | 38 +++- survival-2.38-2/survival/inst/doc/timedep.Rnw | 61 ++++++- survival-2.38-2/survival/inst/doc/timedep.pdf |binary survival-2.38-2/survival/man/clogit.Rd | 17 +- survival-2.38-2/survival/man/coxph.Rd | 30 +++ survival-2.38-2/survival/man/logLik.coxph.Rd |only survival-2.38-2/survival/man/pyears.Rd | 3 survival-2.38-2/survival/man/survfit.coxph.Rd | 2 survival-2.38-2/survival/man/transplant.Rd | 2 survival-2.38-2/survival/noweb/Makefile | 3 survival-2.38-2/survival/noweb/Readme | 3 survival-2.38-2/survival/noweb/agreg.Rnw | 85 ++++++++--- survival-2.38-2/survival/noweb/all.pdf |only survival-2.38-2/survival/noweb/coxph.Rnw | 8 + survival-2.38-2/survival/noweb/coxsurv.Rnw | 4 survival-2.38-2/survival/noweb/exact.nw | 19 +- survival-2.38-2/survival/noweb/plot.Rnw | 2 survival-2.38-2/survival/noweb/pyears.Rnw | 1 survival-2.38-2/survival/noweb/survexp.Rnw | 7 survival-2.38-2/survival/noweb/survfitCI.Rnw | 13 - survival-2.38-2/survival/noweb/tmerge.Rnw | 2 survival-2.38-2/survival/src/agfit4.c | 104 ++++++++++--- survival-2.38-2/survival/src/coxexact.c | 14 + survival-2.38-2/survival/src/coxfit6.c | 2 survival-2.38-2/survival/src/init.c | 2 survival-2.38-2/survival/src/survproto.h | 3 survival-2.38-2/survival/tests/bladder.Rout.save | 86 +++++------ survival-2.38-2/survival/tests/book5.Rout.save | 18 +- survival-2.38-2/survival/tests/book6.Rout.save | 18 +- survival-2.38-2/survival/tests/book7.Rout.save | 8 - survival-2.38-2/survival/tests/cancer.Rout.save | 37 ++-- survival-2.38-2/survival/tests/doaml.Rout.save | 27 +-- survival-2.38-2/survival/tests/doweight.Rout.save | 32 ++-- survival-2.38-2/survival/tests/fr_cancer.Rout.save | 55 +++---- survival-2.38-2/survival/tests/fr_kidney.Rout.save | 118 +++++++-------- survival-2.38-2/survival/tests/fr_ovarian.Rout.save | 19 +- survival-2.38-2/survival/tests/fr_rat1.Rout.save | 22 +- survival-2.38-2/survival/tests/fr_rat2.Rout.save | 44 ++--- survival-2.38-2/survival/tests/fr_resid.Rout.save | 25 +-- survival-2.38-2/survival/tests/jasa.Rout.save | 65 ++++---- survival-2.38-2/survival/tests/ovarian.Rout.save | 85 +++++------ survival-2.38-2/survival/vignettes/adjcurve.Rnw | 4 survival-2.38-2/survival/vignettes/compete.Rnw | 106 ++++++++----- survival-2.38-2/survival/vignettes/splines.Rnw | 65 +++++++- survival-2.38-2/survival/vignettes/tests.Rnw | 9 - survival-2.38-2/survival/vignettes/timedep.Rnw | 61 ++++++- 82 files changed, 1361 insertions(+), 689 deletions(-)
Title: Neural Networks in R using the Stuttgart Neural Network
Simulator (SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks. This
package wraps the SNNS functionality to make it available from
within R. Using the RSNNS low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be accessed.
Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and
learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir and José M. BenÃtez
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RSNNS versions 0.4-6 dated 2014-12-22 and 0.4-7 dated 2015-06-12
ChangeLog | 5 DESCRIPTION | 10 - MD5 | 162 ++++++++--------- NAMESPACE | 2 R/RSNNS-package.R | 3 R/SnnsR_patterns.R | 13 - man/RSNNS-package.Rd | 6 man/SnnsR-class.Rd | 3 man/SnnsRObject-createNet.Rd | 3 man/SnnsRObject-createPatSet.Rd | 3 man/SnnsRObject-extractNetInfo.Rd | 3 man/SnnsRObject-extractPatterns.Rd | 3 man/SnnsRObject-genericPredictCurrPatSet.Rd | 3 man/SnnsRObject-getAllHiddenUnits.Rd | 3 man/SnnsRObject-getAllInputUnits.Rd | 3 man/SnnsRObject-getAllOutputUnits.Rd | 3 man/SnnsRObject-getAllUnits.Rd | 3 man/SnnsRObject-getAllUnitsTType.Rd | 3 man/SnnsRObject-getCompleteWeightMatrix.Rd | 3 man/SnnsRObject-getInfoHeader.Rd | 3 man/SnnsRObject-getSiteDefinitions.Rd | 3 man/SnnsRObject-getTypeDefinitions.Rd | 3 man/SnnsRObject-getUnitDefinitions.Rd | 3 man/SnnsRObject-getUnitsByName.Rd | 3 man/SnnsRObject-getWeightMatrix.Rd | 3 man/SnnsRObject-initializeNet.Rd | 3 man/SnnsRObject-predictCurrPatSet.Rd | 3 man/SnnsRObject-resetRSNNS.Rd | 3 man/SnnsRObject-setTTypeUnitsActFunc.Rd | 3 man/SnnsRObject-setUnitDefaults.Rd | 3 man/SnnsRObject-somPredictComponentMaps.Rd | 3 man/SnnsRObject-somPredictCurrPatSetWinners.Rd | 3 man/SnnsRObject-somPredictCurrPatSetWinnersSpanTree.Rd | 3 man/SnnsRObject-train.Rd | 3 man/SnnsRObject-whereAreResults.Rd | 3 man/SnnsRObjectFactory.Rd | 3 man/SnnsRObjectMethodCaller.Rd | 3 man/analyzeClassification.Rd | 3 man/art1.Rd | 3 man/art2.Rd | 3 man/artmap.Rd | 3 man/assoz.Rd | 3 man/confusionMatrix.Rd | 3 man/decodeClassLabels.Rd | 3 man/denormalizeData.Rd | 3 man/dlvq.Rd | 3 man/elman.Rd | 3 man/encodeClassLabels.Rd | 3 man/exportToSnnsNetFile.Rd | 3 man/extractNetInfo.Rd | 3 man/getNormParameters.Rd | 3 man/getSnnsRDefine.Rd | 3 man/getSnnsRFunctionTable.Rd | 3 man/inputColumns.Rd | 3 man/jordan.Rd | 3 man/matrixToActMapList.Rd | 3 man/mlp.Rd | 3 man/normTrainingAndTestSet.Rd | 3 man/normalizeData.Rd | 3 man/outputColumns.Rd | 3 man/plotActMap.Rd | 3 man/plotIterativeError.Rd | 3 man/plotROC.Rd | 3 man/plotRegressionError.Rd | 3 man/predict.rsnns.Rd | 3 man/print.rsnns.Rd | 3 man/rbf.Rd | 3 man/rbfDDA.Rd | 3 man/readPatFile.Rd | 3 man/readResFile.Rd | 3 man/resolveSnnsRDefine.Rd | 3 man/rsnnsObjectFactory.Rd | 3 man/savePatFile.Rd | 3 man/setSnnsRSeedValue.Rd | 3 man/snnsData.Rd | 3 man/som.Rd | 3 man/splitForTrainingAndTest.Rd | 3 man/summary.rsnns.Rd | 3 man/toNumericClassLabels.Rd | 3 man/train.Rd | 3 man/vectorToActMap.Rd | 3 man/weightMatrix.Rd | 3 82 files changed, 258 insertions(+), 168 deletions(-)
Title: Empirical Orthogonal Teleconnections in R
Description:
Empirical orthogonal teleconnections in R.
'remote' is short for "R(-based) EMpirical Orthogonal TEleconnections".
It implements a collection of functions to facilitate empirical
orthogonal teleconnection analysis. Empirical Orthogonal Teleconnections
(EOTs) denote a regression based approach to decompose spatio-temporal
fields into a set of independent orthogonal patterns. They are quite
similar to Empirical Orthogonal Functions (EOFs) with EOTs producing
less abstract results. In contrast to EOFs, which are orthogonal in both
space and time, EOT analysis produces patterns that are orthogonal in
either space or time.
Author: Tim Appelhans, Florian Detsch, Thomas Nauss
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between remote versions 0.3.0 dated 2014-08-25 and 1.0.0 dated 2015-06-12
DESCRIPTION | 9 +-- MD5 | 89 +++++++++++++++--------------- NAMESPACE | 28 +++++---- R/EotCycle.R | 5 - R/RcppExports.R | 8 ++ R/denoise.R | 52 +++++++++++------ R/deseason.R | 27 ++++++--- R/eot.R | 6 -- R/getWeights.R | 2 R/nXplain.R | 6 +- R/names.R | 1 R/plot.R | 3 + R/subset.R | 1 README.md | 4 - data/australiaGPCP.RData |binary data/pacificSST.RData |binary data/vdendool.RData |binary inst |only man/EotCycle.Rd | 9 +-- man/EotMode-class.Rd | 3 - man/EotStack-class.Rd | 3 - man/anomalize.Rd | 3 - man/australiaGPCP.Rd | 3 - man/calcVar.Rd | 3 - man/covWeight.Rd | 3 - man/cutStack.Rd | 3 - man/deg2rad.Rd | 3 - man/denoise.Rd | 12 +++- man/deseason.Rd | 8 ++ man/eot.Rd | 3 - man/geoWeight.Rd | 3 - man/getWeights.Rd | 3 - man/lagalize.Rd | 3 - man/nXplain.Rd | 9 +-- man/names.Rd | 6 +- man/nmodes.Rd | 3 - man/pacificSST.Rd | 3 - man/plot.Rd | 6 +- man/predict.Rd | 3 - man/remote-package.Rd | 3 - man/subset.Rd | 26 +------- man/vdendool.Rd | 3 - man/writeEot.Rd | 3 - src/EotCppFun.cpp | 67 ++++++++++++++++++++++ src/RcppExports.cpp | 138 ++++++++++++++++++++++------------------------- vignettes |only 46 files changed, 347 insertions(+), 229 deletions(-)
Title: Tools for Splitting, Applying and Combining Data
Description: A set of tools that solves a common set of problems: you
need to break a big problem down into manageable pieces, operate on each
piece and then put all the pieces back together. For example, you might
want to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of 'plyr' has been generously supported
by 'Becton Dickinson'.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between plyr versions 1.8.2 dated 2015-04-21 and 1.8.3 dated 2015-06-12
plyr-1.8.2/plyr/src/loop-apply.cpp |only plyr-1.8.3/plyr/DESCRIPTION | 8 - plyr-1.8.3/plyr/MD5 | 199 +++++++++++++------------- plyr-1.8.3/plyr/NAMESPACE | 2 plyr-1.8.3/plyr/R/RcppExports.R | 14 - plyr-1.8.3/plyr/R/loop_apply.R |only plyr-1.8.3/plyr/man/a_ply.Rd | 2 plyr-1.8.3/plyr/man/aaply.Rd | 2 plyr-1.8.3/plyr/man/adply.Rd | 2 plyr-1.8.3/plyr/man/alply.Rd | 2 plyr-1.8.3/plyr/man/amv_dim.Rd | 2 plyr-1.8.3/plyr/man/amv_dimnames.Rd | 2 plyr-1.8.3/plyr/man/arrange.Rd | 2 plyr-1.8.3/plyr/man/as.data.frame.function.Rd | 2 plyr-1.8.3/plyr/man/as.list.split.Rd | 2 plyr-1.8.3/plyr/man/as.quoted.Rd | 2 plyr-1.8.3/plyr/man/baseball.Rd | 2 plyr-1.8.3/plyr/man/colwise.Rd | 2 plyr-1.8.3/plyr/man/compact.Rd | 2 plyr-1.8.3/plyr/man/count.Rd | 2 plyr-1.8.3/plyr/man/create_progress_bar.Rd | 2 plyr-1.8.3/plyr/man/d_ply.Rd | 2 plyr-1.8.3/plyr/man/daply.Rd | 2 plyr-1.8.3/plyr/man/ddply.Rd | 2 plyr-1.8.3/plyr/man/defaults.Rd | 2 plyr-1.8.3/plyr/man/desc.Rd | 2 plyr-1.8.3/plyr/man/dims.Rd | 2 plyr-1.8.3/plyr/man/dlply.Rd | 2 plyr-1.8.3/plyr/man/each.Rd | 2 plyr-1.8.3/plyr/man/empty.Rd | 2 plyr-1.8.3/plyr/man/eval.quoted.Rd | 2 plyr-1.8.3/plyr/man/failwith.Rd | 2 plyr-1.8.3/plyr/man/get-split.Rd | 2 plyr-1.8.3/plyr/man/here.Rd | 2 plyr-1.8.3/plyr/man/id.Rd | 2 plyr-1.8.3/plyr/man/id_var.Rd | 2 plyr-1.8.3/plyr/man/idata.frame.Rd | 2 plyr-1.8.3/plyr/man/indexed_array.Rd | 2 plyr-1.8.3/plyr/man/indexed_df.Rd | 2 plyr-1.8.3/plyr/man/is.discrete.Rd | 2 plyr-1.8.3/plyr/man/is.formula.Rd | 2 plyr-1.8.3/plyr/man/isplit2.Rd | 2 plyr-1.8.3/plyr/man/join.Rd | 2 plyr-1.8.3/plyr/man/join.keys.Rd | 2 plyr-1.8.3/plyr/man/join_all.Rd | 2 plyr-1.8.3/plyr/man/l_ply.Rd | 2 plyr-1.8.3/plyr/man/laply.Rd | 2 plyr-1.8.3/plyr/man/ldply.Rd | 2 plyr-1.8.3/plyr/man/liply.Rd | 2 plyr-1.8.3/plyr/man/list_to_array.Rd | 2 plyr-1.8.3/plyr/man/list_to_dataframe.Rd | 2 plyr-1.8.3/plyr/man/list_to_vector.Rd | 2 plyr-1.8.3/plyr/man/llply.Rd | 2 plyr-1.8.3/plyr/man/loop_apply.Rd | 6 plyr-1.8.3/plyr/man/m_ply.Rd | 2 plyr-1.8.3/plyr/man/maply.Rd | 2 plyr-1.8.3/plyr/man/mapvalues.Rd | 2 plyr-1.8.3/plyr/man/match_df.Rd | 2 plyr-1.8.3/plyr/man/mdply.Rd | 2 plyr-1.8.3/plyr/man/mlply.Rd | 2 plyr-1.8.3/plyr/man/mutate.Rd | 2 plyr-1.8.3/plyr/man/name_rows.Rd | 2 plyr-1.8.3/plyr/man/names.quoted.Rd | 2 plyr-1.8.3/plyr/man/nunique.Rd | 2 plyr-1.8.3/plyr/man/ozone.Rd | 2 plyr-1.8.3/plyr/man/plyr-deprecated.Rd | 2 plyr-1.8.3/plyr/man/plyr.Rd | 2 plyr-1.8.3/plyr/man/print.quoted.Rd | 2 plyr-1.8.3/plyr/man/print.split.Rd | 2 plyr-1.8.3/plyr/man/progress_none.Rd | 2 plyr-1.8.3/plyr/man/progress_text.Rd | 2 plyr-1.8.3/plyr/man/progress_time.Rd | 2 plyr-1.8.3/plyr/man/progress_tk.Rd | 2 plyr-1.8.3/plyr/man/progress_win.Rd | 2 plyr-1.8.3/plyr/man/quickdf.Rd | 2 plyr-1.8.3/plyr/man/quoted.Rd | 2 plyr-1.8.3/plyr/man/r_ply.Rd | 2 plyr-1.8.3/plyr/man/raply.Rd | 2 plyr-1.8.3/plyr/man/rbind.fill.Rd | 2 plyr-1.8.3/plyr/man/rbind.fill.matrix.Rd | 2 plyr-1.8.3/plyr/man/rdply.Rd | 2 plyr-1.8.3/plyr/man/reduce_dim.Rd | 2 plyr-1.8.3/plyr/man/rename.Rd | 2 plyr-1.8.3/plyr/man/revalue.Rd | 2 plyr-1.8.3/plyr/man/rlply.Rd | 2 plyr-1.8.3/plyr/man/round_any.Rd | 2 plyr-1.8.3/plyr/man/splat.Rd | 2 plyr-1.8.3/plyr/man/split_indices.Rd | 2 plyr-1.8.3/plyr/man/split_labels.Rd | 2 plyr-1.8.3/plyr/man/splitter_a.Rd | 2 plyr-1.8.3/plyr/man/splitter_d.Rd | 2 plyr-1.8.3/plyr/man/strip_splits.Rd | 2 plyr-1.8.3/plyr/man/summarise.Rd | 2 plyr-1.8.3/plyr/man/take.Rd | 2 plyr-1.8.3/plyr/man/true.Rd | 2 plyr-1.8.3/plyr/man/try_default.Rd | 2 plyr-1.8.3/plyr/man/tryapply.Rd | 2 plyr-1.8.3/plyr/man/unrowname.Rd | 2 plyr-1.8.3/plyr/man/vaggregate.Rd | 2 plyr-1.8.3/plyr/src/RcppExports.cpp | 12 - plyr-1.8.3/plyr/src/loop_apply.c |only plyr-1.8.3/plyr/tests/testthat/test-rbind.r | 4 102 files changed, 202 insertions(+), 227 deletions(-)
Title: Discrete Laplace Mixture Inference using the EM Algorithm
Description: Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between disclapmix versions 1.6 dated 2015-01-16 and 1.6.1 dated 2015-06-12
DESCRIPTION | 12 +-- MD5 | 18 ++--- NAMESPACE | 5 + NEWS | 6 + R/RcppExports.R | 16 ++++ R/disclapmix.R | 2 R/helper.R | 177 +++++++++++++++++++++++++++++++++++++++++++--------- man/happrobsum.Rd |only src/RcppExports.cpp | 72 +++++++++++++++++++++ src/happrobsum.cpp |only src/helper.cpp | 65 +++++++++++++++++++ 11 files changed, 330 insertions(+), 43 deletions(-)
Title: Copula Mixed Effect Models for Bivariate and Trivariate
Meta-Analysis of Diagnostic Test Accuracy Studies
Description: It has functions to implement the copula mixed models for bivariate and trivariate meta-analysis of diagnostic test accuracy studies in Nikoloulopoulos, A.K. (2015a,b).
Author: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Diff between CopulaREMADA versions 0.5-1 dated 2015-02-22 and 0.9 dated 2015-06-12
CopulaREMADA-0.5-1/CopulaREMADA/man/meshgrid.Rd |only CopulaREMADA-0.9/CopulaREMADA/DESCRIPTION | 16 +++--- CopulaREMADA-0.9/CopulaREMADA/INDEX | 17 ++++++- CopulaREMADA-0.9/CopulaREMADA/MD5 | 31 ++++++++----- CopulaREMADA-0.9/CopulaREMADA/NAMESPACE | 14 ++++- CopulaREMADA-0.9/CopulaREMADA/R/CopulaREMADA.R | 30 +++--------- CopulaREMADA-0.9/CopulaREMADA/R/MLest.R |only CopulaREMADA-0.9/CopulaREMADA/R/Vuong.R | 40 ++++++++--------- CopulaREMADA-0.9/CopulaREMADA/R/simFUN.R |only CopulaREMADA-0.9/CopulaREMADA/R/tMLest.R |only CopulaREMADA-0.9/CopulaREMADA/R/vine-vuong.R |only CopulaREMADA-0.9/CopulaREMADA/data/OGT.rda |only CopulaREMADA-0.9/CopulaREMADA/data/betaDG.rda |only CopulaREMADA-0.9/CopulaREMADA/man/CopulaREMADA.Rd | 7 +- CopulaREMADA-0.9/CopulaREMADA/man/OGT.Rd |only CopulaREMADA-0.9/CopulaREMADA/man/SROC.Rd | 3 - CopulaREMADA-0.9/CopulaREMADA/man/VineCopulaREMADA.Rd |only CopulaREMADA-0.9/CopulaREMADA/man/Vuong.Rd | 5 -- CopulaREMADA-0.9/CopulaREMADA/man/betaDG.Rd |only CopulaREMADA-0.9/CopulaREMADA/man/cvinesim.Rd |only CopulaREMADA-0.9/CopulaREMADA/man/rCopulaREMADA.Rd | 2 CopulaREMADA-0.9/CopulaREMADA/man/rVineCopulaREMADA.Rd |only CopulaREMADA-0.9/CopulaREMADA/man/vineVuong.Rd |only 23 files changed, 90 insertions(+), 75 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris <nathan.morris@cwru.edu>
Diff between strum versions 0.6.1 dated 2015-05-11 and 0.6.2 dated 2015-06-12
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/strum.R | 4 ++-- build/vignette.rds |binary inst/doc/strum-example.pdf |binary inst/doc/strum-intro.pdf |binary man/strum-package.Rd | 6 +++--- 8 files changed, 25 insertions(+), 17 deletions(-)
Title: Rcmdr Support for the HH package
Description: Rcmdr menu support for many of the functions in the HH package.
The focus is on menu items for functions we use in our introductory
courses.
Author: Richard M. Heiberger, with contributions from Burt Holland
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between RcmdrPlugin.HH versions 1.1-42 dated 2015-01-09 and 1.1-43 dated 2015-06-12
DESCRIPTION | 17 +++---- MD5 | 6 +- NAMESPACE | 86 +++++++++++++++++++++++++++++++++++--- R/bestSubsetsRegressionModel.HH.R | 14 +++--- 4 files changed, 97 insertions(+), 26 deletions(-)
More information about RcmdrPlugin.HH at CRAN
Permanent link
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between HH versions 3.1-15 dated 2015-02-16 and 3.1-19 dated 2015-06-12
HH-3.1-15/HH/data/nottem.rda |only HH-3.1-15/HH/demo/book.plots.r |only HH-3.1-19/HH/DESCRIPTION | 13 HH-3.1-19/HH/MD5 | 156 ++- HH-3.1-19/HH/NAMESPACE | 33 HH-3.1-19/HH/NEWS | 71 + HH-3.1-19/HH/R/F.curve.R | 4 HH-3.1-19/HH/R/HHscriptnames.R | 36 HH-3.1-19/HH/R/ae.dotplot.R | 46 - HH-3.1-19/HH/R/ancova.R | 11 HH-3.1-19/HH/R/ancovaplot.R | 5 HH-3.1-19/HH/R/as.matrix.listOfMatrices.R | 18 HH-3.1-19/HH/R/chisq.curve.R | 4 HH-3.1-19/HH/R/dstrplot.r |only HH-3.1-19/HH/R/hhpdf.R | 7 HH-3.1-19/HH/R/hovBF.R | 8 HH-3.1-19/HH/R/interaction2wt.R | 4 HH-3.1-19/HH/R/lmatPairwise.R |only HH-3.1-19/HH/R/lmplot.R | 20 HH-3.1-19/HH/R/mmcplot.R | 45 - HH-3.1-19/HH/R/normal.and.t.R | 26 HH-3.1-19/HH/R/normal.and.t.htest.R | 3 HH-3.1-19/HH/R/normal.and.t.shiny.R | 144 ++- HH-3.1-19/HH/R/panel.bwplot.intermediate.hh.R | 3 HH-3.1-19/HH/R/plotOddsRatio.R | 13 HH-3.1-19/HH/R/regrDiagn.R | 4 HH-3.1-19/HH/R/residual.plots.lattice.R | 5 HH-3.1-19/HH/R/showHex.R |only HH-3.1-19/HH/data/Discrete4.rda |only HH-3.1-19/HH/data/col3x2.rda |only HH-3.1-19/HH/data/wheat.rda |binary HH-3.1-19/HH/demo/00Index | 1 HH-3.1-19/HH/inst/scripts/hh2/HHApx.R | 6 HH-3.1-19/HH/inst/scripts/hh2/MSword.R |only HH-3.1-19/HH/inst/scripts/hh2/PrcnApx.R |only HH-3.1-19/HH/inst/scripts/hh2/RApx.R | 73 + HH-3.1-19/HH/inst/scripts/hh2/RExcelApx.R | 42 - HH-3.1-19/HH/inst/scripts/hh2/RcmdrApx.R | 6 HH-3.1-19/HH/inst/scripts/hh2/Rpack.R |only HH-3.1-19/HH/inst/scripts/hh2/ShinyApx.R |only HH-3.1-19/HH/inst/scripts/hh2/conc.R | 270 ++++-- HH-3.1-19/HH/inst/scripts/hh2/data.R |only HH-3.1-19/HH/inst/scripts/hh2/dsgn.R | 309 ++++--- HH-3.1-19/HH/inst/scripts/hh2/dsgntwo.R | 483 ++++++------ HH-3.1-19/HH/inst/scripts/hh2/dstr.R |only HH-3.1-19/HH/inst/scripts/hh2/edit.R |only HH-3.1-19/HH/inst/scripts/hh2/emcs.R |only HH-3.1-19/HH/inst/scripts/hh2/grap.R | 419 +++++++--- HH-3.1-19/HH/inst/scripts/hh2/iinf.R | 299 +++++-- HH-3.1-19/HH/inst/scripts/hh2/intr.R |only HH-3.1-19/HH/inst/scripts/hh2/latexApx.R |only HH-3.1-19/HH/inst/scripts/hh2/logi.R | 337 ++++---- HH-3.1-19/HH/inst/scripts/hh2/mcomp.R | 228 +++-- HH-3.1-19/HH/inst/scripts/hh2/mthp.R |only HH-3.1-19/HH/inst/scripts/hh2/npar.R | 126 +-- HH-3.1-19/HH/inst/scripts/hh2/otherApx.R |only HH-3.1-19/HH/inst/scripts/hh2/oway.R | 174 +++- HH-3.1-19/HH/inst/scripts/hh2/rega.R | 121 +-- HH-3.1-19/HH/inst/scripts/hh2/regb.R | 202 ++--- HH-3.1-19/HH/inst/scripts/hh2/regbb.R | 219 ++--- HH-3.1-19/HH/inst/scripts/hh2/regc.R | 183 ++-- HH-3.1-19/HH/inst/scripts/hh2/tser.R | 290 +++---- HH-3.1-19/HH/inst/scripts/hh2/tway.R | 296 ++++--- HH-3.1-19/HH/inst/scripts/hh2/twtb.R | 473 +++++++---- HH-3.1-19/HH/inst/scripts/hh2/typg.R |only HH-3.1-19/HH/inst/shiny/NormalAndTplot/ui.R | 16 HH-3.1-19/HH/inst/shiny/PopulationPyramid/ui.R | 2 HH-3.1-19/HH/inst/shiny/bivariateNormalScatterplot/server.R | 3 HH-3.1-19/HH/man/Discrete4.color.Rd |only HH-3.1-19/HH/man/F.curve.Rd | 6 HH-3.1-19/HH/man/HH.package.Rd | 57 - HH-3.1-19/HH/man/HHscriptnames.Rd | 6 HH-3.1-19/HH/man/NormalAndT.Rd | 5 HH-3.1-19/HH/man/ancova.Rd | 6 HH-3.1-19/HH/man/ancovaplot.Rd | 8 HH-3.1-19/HH/man/bivariateNormal.Rd | 11 HH-3.1-19/HH/man/col3x2.Rd |only HH-3.1-19/HH/man/datasets.Rd | 1 HH-3.1-19/HH/man/hhpdf.Rd | 18 HH-3.1-19/HH/man/hovBF.Rd | 7 HH-3.1-19/HH/man/interaction2wt.Rd | 69 - HH-3.1-19/HH/man/lmatPairwise.Rd |only HH-3.1-19/HH/man/lmplot.Rd | 15 HH-3.1-19/HH/man/mmc.Rd | 12 HH-3.1-19/HH/man/mmcisomeans.Rd | 13 HH-3.1-19/HH/man/mmcplot.Rd | 16 HH-3.1-19/HH/man/odds.ratio.Rd | 7 HH-3.1-19/HH/man/panel.confintMMC.Rd | 4 HH-3.1-19/HH/man/panel.isomeans.Rd | 4 HH-3.1-19/HH/man/residual.plots.lattice.Rd | 2 HH-3.1-19/HH/man/showHex.Rd |only 91 files changed, 3391 insertions(+), 2133 deletions(-)
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@univ-montp2.fr>
Diff between SpatialExtremes versions 2.0-0 dated 2013-03-04 and 2.0-2 dated 2015-06-11
SpatialExtremes-2.0-0/SpatialExtremes/Copyright |only SpatialExtremes-2.0-0/SpatialExtremes/man/logLik.maxstab.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/predict.copula.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/predict.maxstab.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/predict.pspline.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/predict.spatgev.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/print.copula.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/print.latent.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/print.maxstab.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/print.pspline.Rd |only SpatialExtremes-2.0-0/SpatialExtremes/man/print.spatgev.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/DESCRIPTION | 29 SpatialExtremes-2.0-2/SpatialExtremes/MD5 | 111 - SpatialExtremes-2.0-2/SpatialExtremes/NAMESPACE | 35 SpatialExtremes-2.0-2/SpatialExtremes/R/brownresnick.R | 35 SpatialExtremes-2.0-2/SpatialExtremes/R/concurrence.R |only SpatialExtremes-2.0-2/SpatialExtremes/R/condSimMaxStab.R | 40 SpatialExtremes-2.0-2/SpatialExtremes/R/exploratoryAnalysis.R |only SpatialExtremes-2.0-2/SpatialExtremes/R/extremalt.R | 47 SpatialExtremes-2.0-2/SpatialExtremes/R/fitcovmat.R | 8 SpatialExtremes-2.0-2/SpatialExtremes/R/geomgauss.R | 4 SpatialExtremes-2.0-2/SpatialExtremes/R/madogram.R | 196 +- SpatialExtremes-2.0-2/SpatialExtremes/R/methods.R | 2 SpatialExtremes-2.0-2/SpatialExtremes/R/modelChecking.R | 49 SpatialExtremes-2.0-2/SpatialExtremes/R/plots.R | 1 SpatialExtremes-2.0-2/SpatialExtremes/R/predict.R | 8 SpatialExtremes-2.0-2/SpatialExtremes/R/schlather.R | 43 SpatialExtremes-2.0-2/SpatialExtremes/R/schlatherind.R | 4 SpatialExtremes-2.0-2/SpatialExtremes/R/selection.R | 74 - SpatialExtremes-2.0-2/SpatialExtremes/R/smith.R | 4 SpatialExtremes-2.0-2/SpatialExtremes/R/spatgev.R | 2 SpatialExtremes-2.0-2/SpatialExtremes/R/standardErrors.R | 69 SpatialExtremes-2.0-2/SpatialExtremes/R/swiss.R | 6 SpatialExtremes-2.0-2/SpatialExtremes/R/utils.R | 31 SpatialExtremes-2.0-2/SpatialExtremes/build |only SpatialExtremes-2.0-2/SpatialExtremes/data/USHCNTemp.RData |only SpatialExtremes-2.0-2/SpatialExtremes/data/rainfall.RData |binary SpatialExtremes-2.0-2/SpatialExtremes/data/swissalt.RData |binary SpatialExtremes-2.0-2/SpatialExtremes/data/wind.RData |only SpatialExtremes-2.0-2/SpatialExtremes/inst/Copyright |only SpatialExtremes-2.0-2/SpatialExtremes/inst/doc/SpatialExtremesGuide.R |only SpatialExtremes-2.0-2/SpatialExtremes/inst/doc/SpatialExtremesGuide.Rnw | 4 SpatialExtremes-2.0-2/SpatialExtremes/inst/doc/SpatialExtremesGuide.pdf |binary SpatialExtremes-2.0-2/SpatialExtremes/man/USHCNTemp.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/anova.Rd | 9 SpatialExtremes-2.0-2/SpatialExtremes/man/concprob.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/concurrencemap.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/condrmaxstab.Rd | 2 SpatialExtremes-2.0-2/SpatialExtremes/man/internals.Rd | 9 SpatialExtremes-2.0-2/SpatialExtremes/man/logLik.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/predict.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/print.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/rainfall.Rd | 2 SpatialExtremes-2.0-2/SpatialExtremes/man/swissalt.Rd | 3 SpatialExtremes-2.0-2/SpatialExtremes/man/symbolplot.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/man/windgust.Rd |only SpatialExtremes-2.0-2/SpatialExtremes/src/completedLogLik.c |only SpatialExtremes-2.0-2/SpatialExtremes/src/concurrence.c |only SpatialExtremes-2.0-2/SpatialExtremes/src/condsimMaxStab.c | 716 ++++++++++ SpatialExtremes-2.0-2/SpatialExtremes/src/direct.c | 7 SpatialExtremes-2.0-2/SpatialExtremes/src/gpdproc.c |only SpatialExtremes-2.0-2/SpatialExtremes/src/header.h | 43 SpatialExtremes-2.0-2/SpatialExtremes/src/latentVariable.c | 44 SpatialExtremes-2.0-2/SpatialExtremes/src/madogram.c | 41 SpatialExtremes-2.0-2/SpatialExtremes/src/pairwiselik.c | 14 SpatialExtremes-2.0-2/SpatialExtremes/src/simBrownResnick.c | 4 SpatialExtremes-2.0-2/SpatialExtremes/src/simextremalt.c | 2 SpatialExtremes-2.0-2/SpatialExtremes/src/simgeometric.c | 2 SpatialExtremes-2.0-2/SpatialExtremes/src/simschlather.c | 2 SpatialExtremes-2.0-2/SpatialExtremes/src/standardErrors.c | 4 SpatialExtremes-2.0-2/SpatialExtremes/vignettes/SpatialExtremesGuide.Rnw | 4 71 files changed, 1336 insertions(+), 374 deletions(-)
More information about SpatialExtremes at CRAN
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Title: Semiparametric Bivariate Regression Models
Description: Routine for fitting bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.3 dated 2015-02-09 and 3.4 dated 2015-06-11
SemiParBIVProbit-3.3/SemiParBIVProbit/R/S.mPL.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/SemiParBIVProbit.fit1.R |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/VuongClarke.bcm.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/bprobgHsPL.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/est.prev.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/penPL.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/print.est.prev.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/sem.checks.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/startSS.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/working.comp1.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/R/working.comp3.r |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/S.mPL.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/SemiParBIVProbit.fit1.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/VuongClarke.bcm.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/bprobgHsPL.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/est.prev.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/penPL.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/print.est.prev.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/sem.checks.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/startSS.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/working.comp1.Rd |only SemiParBIVProbit-3.3/SemiParBIVProbit/man/working.comp3.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/ChangeLog | 7 SemiParBIVProbit-3.4/SemiParBIVProbit/DESCRIPTION | 14 SemiParBIVProbit-3.4/SemiParBIVProbit/MD5 | 144 SemiParBIVProbit-3.4/SemiParBIVProbit/NAMESPACE | 25 SemiParBIVProbit-3.4/SemiParBIVProbit/R/AT.r | 590 + SemiParBIVProbit-3.4/SemiParBIVProbit/R/BCDF.r | 3 SemiParBIVProbit-3.4/SemiParBIVProbit/R/BiCDF.r | 6 SemiParBIVProbit-3.4/SemiParBIVProbit/R/LM.bpm.r | 47 SemiParBIVProbit-3.4/SemiParBIVProbit/R/S.m.r | 40 SemiParBIVProbit-3.4/SemiParBIVProbit/R/SemiParBIVProbit.fit.R | 178 SemiParBIVProbit-3.4/SemiParBIVProbit/R/SemiParBIVProbit.fit.post.r | 272 SemiParBIVProbit-3.4/SemiParBIVProbit/R/SemiParBIVProbit.r | 606 + SemiParBIVProbit-3.4/SemiParBIVProbit/R/VuongClarke.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/adjCov.r | 46 SemiParBIVProbit-3.4/SemiParBIVProbit/R/adjCovSD.r | 47 SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHs.r | 100 SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHsCont.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHsContUniv.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHsPO.r | 98 SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHsPO0.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/bprobgHsSS.r | 105 SemiParBIVProbit-3.4/SemiParBIVProbit/R/conv.check.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/copgHs.r | 3099 +--------- SemiParBIVProbit-3.4/SemiParBIVProbit/R/copgHsAT.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/copgHsCont.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/distrHs.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/distrHsAT.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/gt.bpm.R | 34 SemiParBIVProbit-3.4/SemiParBIVProbit/R/logLik.SemiParBIVProbit.r | 2 SemiParBIVProbit-3.4/SemiParBIVProbit/R/mb.r | 2 SemiParBIVProbit-3.4/SemiParBIVProbit/R/pen.r | 87 SemiParBIVProbit-3.4/SemiParBIVProbit/R/plot.SemiParBIVProbit.r | 27 SemiParBIVProbit-3.4/SemiParBIVProbit/R/polys.map.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/predict.SemiParBIVProbit.r | 18 SemiParBIVProbit-3.4/SemiParBIVProbit/R/prev.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/print.AT.r | 8 SemiParBIVProbit-3.4/SemiParBIVProbit/R/print.SemiParBIVProbit.r | 104 SemiParBIVProbit-3.4/SemiParBIVProbit/R/print.prev.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/print.summary.SemiParBIVProbit.r | 191 SemiParBIVProbit-3.4/SemiParBIVProbit/R/rMVN.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/regH.r |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/resp.check.R |only SemiParBIVProbit-3.4/SemiParBIVProbit/R/summary.SemiParBIVProbit.r | 507 - SemiParBIVProbit-3.4/SemiParBIVProbit/R/working.comp.r | 105 SemiParBIVProbit-3.4/SemiParBIVProbit/inst/CITATION | 21 SemiParBIVProbit-3.4/SemiParBIVProbit/man/AT.Rd | 63 SemiParBIVProbit-3.4/SemiParBIVProbit/man/LM.bpm.Rd | 16 SemiParBIVProbit-3.4/SemiParBIVProbit/man/S.m.Rd | 2 SemiParBIVProbit-3.4/SemiParBIVProbit/man/SemiParBIVProbit-package.Rd | 46 SemiParBIVProbit-3.4/SemiParBIVProbit/man/SemiParBIVProbit.Rd | 297 SemiParBIVProbit-3.4/SemiParBIVProbit/man/SemiParBIVProbitObject.Rd | 40 SemiParBIVProbit-3.4/SemiParBIVProbit/man/VuongClarke.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/adjCov.Rd | 6 SemiParBIVProbit-3.4/SemiParBIVProbit/man/adjCovSD.Rd | 4 SemiParBIVProbit-3.4/SemiParBIVProbit/man/bprobgHs.Rd | 4 SemiParBIVProbit-3.4/SemiParBIVProbit/man/bprobgHsCont.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/bprobgHsContUniv.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/bprobgHsPO.Rd | 7 SemiParBIVProbit-3.4/SemiParBIVProbit/man/bprobgHsPO0.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/conv.check.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/copgHs.Rd | 4 SemiParBIVProbit-3.4/SemiParBIVProbit/man/copgHsAT.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/copgHsCont.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/distrHs.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/distrHsAT.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/gt.bpm.Rd | 16 SemiParBIVProbit-3.4/SemiParBIVProbit/man/mb.Rd | 7 SemiParBIVProbit-3.4/SemiParBIVProbit/man/plot.SemiParBIVProbit.Rd | 22 SemiParBIVProbit-3.4/SemiParBIVProbit/man/polys.map.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/predict.SemiParBIVProbit.Rd | 12 SemiParBIVProbit-3.4/SemiParBIVProbit/man/prev.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/print.prev.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/rMVN.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/regH.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/resp.check.Rd |only SemiParBIVProbit-3.4/SemiParBIVProbit/man/summary.SemiParBIVProbit.Rd | 81 SemiParBIVProbit-3.4/SemiParBIVProbit/man/working.comp.Rd | 21 99 files changed, 2607 insertions(+), 4574 deletions(-)
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Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner <ken@kenkellner.com>
Maintainer: Ken Kellner <ken@kenkellner.com>
Diff between jagsUI versions 1.3.1 dated 2015-01-16 and 1.3.7 dated 2015-06-11
DESCRIPTION | 12 - MD5 | 71 ++++----- NAMESPACE | 48 +++--- NEWS | 108 ++++++++----- R/autojags.R | 296 ++++++++++++++++++++----------------- R/bindmcmc.R |only R/datacheck.R | 70 ++++---- R/densityplot.R | 6 R/geninits.R | 58 +++---- R/getdim.R | 46 ++--- R/jags.R | 177 +++++++++++----------- R/jagsbasic.R | 121 +++++++-------- R/orderparams.R | 36 ++-- R/plot.R | 10 - R/ppcheck.R | 28 +-- R/print.R | 132 ++++++++-------- R/processinput.R | 153 ++++++++++--------- R/processoutput.R | 314 ++++++++++++++++++++------------------- R/runmodel.R | 129 +++++++++------- R/runparallel.R | 154 +++++++++---------- R/setmodules.R | 46 ++--- R/summary.R | 8 - R/summarymatrix.R | 36 ++-- R/testrhat.R | 65 ++++---- R/traceplot.R | 94 +++++------ R/translateparams.R | 118 +++++++-------- R/update.R | 168 ++++++++++----------- R/updatebasic.R | 106 ++++++------- R/whiskerplot.R | 78 ++++----- R/xyplot.R | 8 - man/autojags.Rd | 96 ++++++------ man/jags.Rd | 409 ++++++++++++++++++++++++++-------------------------- man/jagsbasic.Rd | 107 ++++++------- man/ppcheck.Rd | 186 +++++++++++------------ man/traceplot.Rd | 48 +++--- man/update.Rd | 60 +++---- man/whiskerplot.Rd | 198 ++++++++++++------------- 37 files changed, 1951 insertions(+), 1849 deletions(-)
Title: Tools for Exploring Differential Shannon Entropy, Differential
Coefficient of Variation and Differential Expression
Description: Rows of two matrices are compared for Shannon entropy,
coefficient of variation, and expression. P-values can be requested for all metrics.
Author: Kai Wang, Charles A. Phillips, Arnold M. Saxton and Michael A. Langston
Maintainer: Kai Wang <kwang11@eecs.utk.edu>
Diff between EntropyExplorer versions 1.0 dated 2015-03-17 and 1.1 dated 2015-06-11
DESCRIPTION | 7 MD5 | 6 R/EntropyExplorer.r | 520 +++++++++++++++++++++++++++++++++++-------------- man/EntropyExplorer.Rd | 124 ++++++----- 4 files changed, 463 insertions(+), 194 deletions(-)
More information about EntropyExplorer at CRAN
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Title: Create Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.6 dated 2015-04-30 and 0.7 dated 2015-06-11
DiagrammeR-0.6/DiagrammeR/R/graphviz_graph.R |only DiagrammeR-0.6/DiagrammeR/R/graphviz_render.R |only DiagrammeR-0.6/DiagrammeR/inst/examples |only DiagrammeR-0.6/DiagrammeR/man/graphviz_graph.Rd |only DiagrammeR-0.6/DiagrammeR/man/graphviz_render.Rd |only DiagrammeR-0.7/DiagrammeR/DESCRIPTION | 15 DiagrammeR-0.7/DiagrammeR/MD5 | 140 + DiagrammeR-0.7/DiagrammeR/NAMESPACE | 33 DiagrammeR-0.7/DiagrammeR/R/DiagrammeR.R | 26 DiagrammeR-0.7/DiagrammeR/R/add_edges.R |only DiagrammeR-0.7/DiagrammeR/R/add_node.R |only DiagrammeR-0.7/DiagrammeR/R/add_to_series.R |only DiagrammeR-0.7/DiagrammeR/R/combine_edges.R | 29 DiagrammeR-0.7/DiagrammeR/R/combine_nodes.R | 34 DiagrammeR-0.7/DiagrammeR/R/create_edges.R | 40 DiagrammeR-0.7/DiagrammeR/R/create_graph.R |only DiagrammeR-0.7/DiagrammeR/R/create_nodes.R | 23 DiagrammeR-0.7/DiagrammeR/R/create_series.R |only DiagrammeR-0.7/DiagrammeR/R/create_subgraph.R |only DiagrammeR-0.7/DiagrammeR/R/delete_edge.R |only DiagrammeR-0.7/DiagrammeR/R/delete_node.R |only DiagrammeR-0.7/DiagrammeR/R/display_graph_object.R |only DiagrammeR-0.7/DiagrammeR/R/edge_count.R |only DiagrammeR-0.7/DiagrammeR/R/edge_info.R |only DiagrammeR-0.7/DiagrammeR/R/edge_present.R |only DiagrammeR-0.7/DiagrammeR/R/edge_relationship.R |only DiagrammeR-0.7/DiagrammeR/R/get_edges.R |only DiagrammeR-0.7/DiagrammeR/R/get_nodes.R | 101 + DiagrammeR-0.7/DiagrammeR/R/get_predecessors.R |only DiagrammeR-0.7/DiagrammeR/R/get_successors.R |only DiagrammeR-0.7/DiagrammeR/R/grViz.R | 9 DiagrammeR-0.7/DiagrammeR/R/graph_count.R |only DiagrammeR-0.7/DiagrammeR/R/graphviz_export.R | 7 DiagrammeR-0.7/DiagrammeR/R/image_icon.R |only DiagrammeR-0.7/DiagrammeR/R/is_graph_directed.R |only DiagrammeR-0.7/DiagrammeR/R/is_graph_empty.R |only DiagrammeR-0.7/DiagrammeR/R/mermaid.R | 60 DiagrammeR-0.7/DiagrammeR/R/node_count.R |only DiagrammeR-0.7/DiagrammeR/R/node_info.R | 191 +- DiagrammeR-0.7/DiagrammeR/R/node_present.R |only DiagrammeR-0.7/DiagrammeR/R/node_type.R |only DiagrammeR-0.7/DiagrammeR/R/remove_from_series.R |only DiagrammeR-0.7/DiagrammeR/R/render_graph.R |only DiagrammeR-0.7/DiagrammeR/R/render_graph_from_series.R |only DiagrammeR-0.7/DiagrammeR/R/roll_palette.R |only DiagrammeR-0.7/DiagrammeR/R/scale_edges.R | 26 DiagrammeR-0.7/DiagrammeR/R/scale_nodes.R | 28 DiagrammeR-0.7/DiagrammeR/R/series_info.R |only DiagrammeR-0.7/DiagrammeR/R/spectools.R | 12 DiagrammeR-0.7/DiagrammeR/R/subset_series.R |only DiagrammeR-0.7/DiagrammeR/R/trigger_script.R |only DiagrammeR-0.7/DiagrammeR/R/x11_hex.R | 2 DiagrammeR-0.7/DiagrammeR/README.md | 989 ----------- DiagrammeR-0.7/DiagrammeR/build/vignette.rds |binary DiagrammeR-0.7/DiagrammeR/inst/doc/DiagrammeR.html | 44 DiagrammeR-0.7/DiagrammeR/inst/htmlwidgets/graph_object.html |only DiagrammeR-0.7/DiagrammeR/inst/img |only DiagrammeR-0.7/DiagrammeR/man/add_edges.Rd |only DiagrammeR-0.7/DiagrammeR/man/add_node.Rd |only DiagrammeR-0.7/DiagrammeR/man/add_to_series.Rd |only DiagrammeR-0.7/DiagrammeR/man/combine_edges.Rd | 28 DiagrammeR-0.7/DiagrammeR/man/combine_nodes.Rd | 33 DiagrammeR-0.7/DiagrammeR/man/create_edges.Rd | 17 DiagrammeR-0.7/DiagrammeR/man/create_graph.Rd |only DiagrammeR-0.7/DiagrammeR/man/create_nodes.Rd | 22 DiagrammeR-0.7/DiagrammeR/man/create_series.Rd |only DiagrammeR-0.7/DiagrammeR/man/create_subgraph.Rd |only DiagrammeR-0.7/DiagrammeR/man/delete_edge.Rd |only DiagrammeR-0.7/DiagrammeR/man/delete_node.Rd |only DiagrammeR-0.7/DiagrammeR/man/display_graph_object.Rd |only DiagrammeR-0.7/DiagrammeR/man/edge_count.Rd |only DiagrammeR-0.7/DiagrammeR/man/edge_info.Rd |only DiagrammeR-0.7/DiagrammeR/man/edge_present.Rd |only DiagrammeR-0.7/DiagrammeR/man/edge_relationship.Rd |only DiagrammeR-0.7/DiagrammeR/man/exportSVG.Rd | 3 DiagrammeR-0.7/DiagrammeR/man/get_edges.Rd |only DiagrammeR-0.7/DiagrammeR/man/get_nodes.Rd | 48 DiagrammeR-0.7/DiagrammeR/man/get_predecessors.Rd |only DiagrammeR-0.7/DiagrammeR/man/get_successors.Rd |only DiagrammeR-0.7/DiagrammeR/man/grViz.Rd | 7 DiagrammeR-0.7/DiagrammeR/man/graph_count.Rd |only DiagrammeR-0.7/DiagrammeR/man/image_icon.Rd |only DiagrammeR-0.7/DiagrammeR/man/is_graph_directed.Rd |only DiagrammeR-0.7/DiagrammeR/man/is_graph_empty.Rd |only DiagrammeR-0.7/DiagrammeR/man/mermaid.Rd | 31 DiagrammeR-0.7/DiagrammeR/man/node_count.Rd |only DiagrammeR-0.7/DiagrammeR/man/node_info.Rd | 41 DiagrammeR-0.7/DiagrammeR/man/node_present.Rd |only DiagrammeR-0.7/DiagrammeR/man/node_type.Rd |only DiagrammeR-0.7/DiagrammeR/man/remove_from_series.Rd |only DiagrammeR-0.7/DiagrammeR/man/render_graph.Rd |only DiagrammeR-0.7/DiagrammeR/man/render_graph_from_series.Rd |only DiagrammeR-0.7/DiagrammeR/man/replace_in_spec.Rd | 7 DiagrammeR-0.7/DiagrammeR/man/roll_palette.Rd |only DiagrammeR-0.7/DiagrammeR/man/scale_edges.Rd | 25 DiagrammeR-0.7/DiagrammeR/man/scale_nodes.Rd | 24 DiagrammeR-0.7/DiagrammeR/man/series_info.Rd |only DiagrammeR-0.7/DiagrammeR/man/subset_series.Rd |only DiagrammeR-0.7/DiagrammeR/man/trigger_script.Rd |only DiagrammeR-0.7/DiagrammeR/man/x11_hex.Rd | 6 100 files changed, 856 insertions(+), 1245 deletions(-)
Title: Username, Full Name, Email Address, 'GitHub' Username of the
Current User
Description: Look up the username and full name of the current user,
the current user's email address and 'GitHub' username,
using various sources of system and configuration information.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between whoami versions 1.0.0 dated 2015-06-09 and 1.1.0 dated 2015-06-11
DESCRIPTION | 6 +-- MD5 | 21 +++++++------ NAMESPACE | 2 - R/whoami.R | 59 ++++++++++++++++++++++++++++---------- inst/NEWS.md | 5 +++ man/email_address.Rd | 6 +++ man/fullname.Rd | 7 +++- man/gh_username.Rd | 6 +++ man/username.Rd | 6 +++ man/whoami.Rd | 4 +- tests/testthat/test-fallbacks.R |only tests/testthat/test-gh-username.R | 20 +++++++++--- 12 files changed, 101 insertions(+), 41 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-6 dated 2015-05-14 and 0.1-61 dated 2015-06-11
Surrogate-0.1-6/Surrogate/data/Schizo_Bin_ST.rda |only Surrogate-0.1-6/Surrogate/data/Schizo_Bin_ST2.rda |only Surrogate-0.1-6/Surrogate/man/Schizo_Bin_ST.Rd |only Surrogate-0.1-6/Surrogate/man/Schizo_Bin_ST2.Rd |only Surrogate-0.1-61/Surrogate/DESCRIPTION | 8 ++-- Surrogate-0.1-61/Surrogate/MD5 | 32 +++++++----------- Surrogate-0.1-61/Surrogate/R/CausalDiagramContCont.R | 4 +- Surrogate-0.1-61/Surrogate/R/ICA.BinBin.Grid.Full.R | 7 +++ Surrogate-0.1-61/Surrogate/R/ICA.BinBin.Grid.Sample.R | 11 +++++- Surrogate-0.1-61/Surrogate/R/ICABinBin.R | 7 +++ Surrogate-0.1-61/Surrogate/R/ICAContCont.R | 22 +++++++++++- Surrogate-0.1-61/Surrogate/R/MICAContCont.R | 17 +++++++++ Surrogate-0.1-61/Surrogate/R/plot_ICABinBin.R | 9 ++++- Surrogate-0.1-61/Surrogate/data/Schizo_Bin.rda |binary Surrogate-0.1-61/Surrogate/man/ICAContCont.Rd | 15 +++++++- Surrogate-0.1-61/Surrogate/man/MICAContCont.Rd | 10 +++++ Surrogate-0.1-61/Surrogate/man/MarginalProbs.Rd | 4 +- Surrogate-0.1-61/Surrogate/man/Schizo_Bin.Rd | 12 +++--- Surrogate-0.1-61/Surrogate/man/plot.ICABinBin.Rd | 3 + 19 files changed, 121 insertions(+), 40 deletions(-)
Title: Some Additional Distributions
Description: Provides the density, distribution, quantile and generation functions of some obscure probability
distributions, including the doubly non-central t, F, Beta, and Eta distributions;
Lecoutre's lambda-prime and K-prime; the upsilon distribution; the (weighted) sum of
non-central chi-squares to a power; the (weighted) sum of log non-central chi-squares;
the product of non-central chi-squares to powers; the product of doubly non-central
F variates.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between sadists versions 0.2.0 dated 2015-03-30 and 0.2.1 dated 2015-06-11
.Rinstignore |only DESCRIPTION |only MD5 |only NAMESPACE |only R |only README.md |only build |only inst/doc/sadists.R |only inst/doc/sadists.pdf |binary inst/shiny-examples |only man |only vignettes |only 12 files changed
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for MALDI-TOF and other mass
spectrometry data. Distinctive features include baseline
subtraction methods such as TopHat or SNIP, peak alignment
using warping functions, handling of replicated measurements as
well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.11 dated 2014-08-11 and 1.12 dated 2015-06-11
MALDIquant-1.11/MALDIquant/R/plotImsSlice-functions.R |only MALDIquant-1.11/MALDIquant/man/plotImsSlice-functions.Rd |only MALDIquant-1.12/MALDIquant/DESCRIPTION | 22 MALDIquant-1.12/MALDIquant/MD5 | 280 +++++----- MALDIquant-1.12/MALDIquant/NAMESPACE | 8 MALDIquant-1.12/MALDIquant/NEWS | 67 ++ MALDIquant-1.12/MALDIquant/R/AllClasses.R | 1 MALDIquant-1.12/MALDIquant/R/AllGenerics.R | 30 - MALDIquant-1.12/MALDIquant/R/Deprecated.R | 76 ++ MALDIquant-1.12/MALDIquant/R/alignSpectra-functions.R | 7 MALDIquant-1.12/MALDIquant/R/approxfun-methods.R | 7 MALDIquant-1.12/MALDIquant/R/as-methods.R |only MALDIquant-1.12/MALDIquant/R/as.matrix-functions.R | 27 MALDIquant-1.12/MALDIquant/R/as.matrix-methods.R | 5 MALDIquant-1.12/MALDIquant/R/averageMassSpectra-functions.R | 13 MALDIquant-1.12/MALDIquant/R/binPeaks-functions.R | 52 - MALDIquant-1.12/MALDIquant/R/calculateLabelPositions-methods.R | 35 - MALDIquant-1.12/MALDIquant/R/calibrateIntensity-functions.R | 21 MALDIquant-1.12/MALDIquant/R/calibrateIntensity-methods.R | 27 MALDIquant-1.12/MALDIquant/R/colMedians-functions.R | 3 MALDIquant-1.12/MALDIquant/R/constructor-functions.R | 10 MALDIquant-1.12/MALDIquant/R/coordinates-methods.R |only MALDIquant-1.12/MALDIquant/R/deprecated-functions.R | 7 MALDIquant-1.12/MALDIquant/R/detectPeaks-methods.R | 15 MALDIquant-1.12/MALDIquant/R/determineWarpingFunctions-functions.R | 35 - MALDIquant-1.12/MALDIquant/R/doByLabels-functions.R | 9 MALDIquant-1.12/MALDIquant/R/estimateBaseline-functions.R | 61 +- MALDIquant-1.12/MALDIquant/R/estimateBaseline-methods.R | 28 - MALDIquant-1.12/MALDIquant/R/estimateNoise-functions.R | 35 - MALDIquant-1.12/MALDIquant/R/estimateNoise-methods.R | 8 MALDIquant-1.12/MALDIquant/R/filterPeaks-functions.R | 13 MALDIquant-1.12/MALDIquant/R/findEmptyMassObjects-functions.R | 3 MALDIquant-1.12/MALDIquant/R/findLocalMaxima-methods.R | 11 MALDIquant-1.12/MALDIquant/R/grouper-functions.R | 25 MALDIquant-1.12/MALDIquant/R/intensity-methods.R | 7 MALDIquant-1.12/MALDIquant/R/intensityMatrix-functions.R | 13 MALDIquant-1.12/MALDIquant/R/irregular-functions.R | 3 MALDIquant-1.12/MALDIquant/R/isEmpty-methods.R | 8 MALDIquant-1.12/MALDIquant/R/isFunctionList-functions.R | 8 MALDIquant-1.12/MALDIquant/R/isMassObject-functions.R | 6 MALDIquant-1.12/MALDIquant/R/isMassObjectList-functions.R | 22 MALDIquant-1.12/MALDIquant/R/isRegular-methods.R | 3 MALDIquant-1.12/MALDIquant/R/isValidHalfWindowSize-functions.R | 5 MALDIquant-1.12/MALDIquant/R/labelPeaks-methods.R | 5 MALDIquant-1.12/MALDIquant/R/lapply-functions.R |only MALDIquant-1.12/MALDIquant/R/length-methods.R | 3 MALDIquant-1.12/MALDIquant/R/lines-methods.R | 5 MALDIquant-1.12/MALDIquant/R/localMaxima-functions.R | 8 MALDIquant-1.12/MALDIquant/R/mapply-functions.R | 8 MALDIquant-1.12/MALDIquant/R/mass-methods.R | 7 MALDIquant-1.12/MALDIquant/R/memoryUsage-functions.R | 7 MALDIquant-1.12/MALDIquant/R/merge-functions.R | 26 MALDIquant-1.12/MALDIquant/R/metaData-methods.R | 5 MALDIquant-1.12/MALDIquant/R/morphologicalFilter-functions.R | 5 MALDIquant-1.12/MALDIquant/R/msiSlices-functions.R |only MALDIquant-1.12/MALDIquant/R/plot-methods.R | 4 MALDIquant-1.12/MALDIquant/R/plotMsiSlice-functions.R |only MALDIquant-1.12/MALDIquant/R/plotMsiSlice-methods.R |only MALDIquant-1.12/MALDIquant/R/points-methods.R | 1 MALDIquant-1.12/MALDIquant/R/range-functions.R | 6 MALDIquant-1.12/MALDIquant/R/referencePeaks-functions.R | 3 MALDIquant-1.12/MALDIquant/R/removeBaseline-methods.R | 11 MALDIquant-1.12/MALDIquant/R/removeEmptyMassObjects-functions.R | 4 MALDIquant-1.12/MALDIquant/R/replaceNegativeIntensityValues-functions.R | 4 MALDIquant-1.12/MALDIquant/R/show-functions.R | 5 MALDIquant-1.12/MALDIquant/R/show-methods.R | 5 MALDIquant-1.12/MALDIquant/R/smoothIntensity-methods.R | 35 - MALDIquant-1.12/MALDIquant/R/smoothingFilters-functions.R | 34 - MALDIquant-1.12/MALDIquant/R/snr-methods.R | 3 MALDIquant-1.12/MALDIquant/R/subset-methods.R | 9 MALDIquant-1.12/MALDIquant/R/textLabelRects-functions.R | 15 MALDIquant-1.12/MALDIquant/R/totalIonCurrent-methods.R | 3 MALDIquant-1.12/MALDIquant/R/transformIntensity-methods.R | 21 MALDIquant-1.12/MALDIquant/R/trim-methods.R | 15 MALDIquant-1.12/MALDIquant/R/unlist-functions.R | 1 MALDIquant-1.12/MALDIquant/R/valid-methods.R | 7 MALDIquant-1.12/MALDIquant/R/warp-functions.R | 17 MALDIquant-1.12/MALDIquant/R/warpingFunction-functions.R | 9 MALDIquant-1.12/MALDIquant/R/which.closest-functions.R | 9 MALDIquant-1.12/MALDIquant/build/vignette.rds |binary MALDIquant-1.12/MALDIquant/demo/baseline.R | 1 MALDIquant-1.12/MALDIquant/inst/doc/MALDIquant-intro.pdf |binary MALDIquant-1.12/MALDIquant/man/AbstractMassObject-class.Rd | 14 MALDIquant-1.12/MALDIquant/man/MALDIquant-defunct.Rd | 2 MALDIquant-1.12/MALDIquant/man/MALDIquant-deprecated.Rd | 13 MALDIquant-1.12/MALDIquant/man/MALDIquant-package.Rd | 9 MALDIquant-1.12/MALDIquant/man/MALDIquant-parallel.Rd |only MALDIquant-1.12/MALDIquant/man/alignSpectra-functions.Rd | 4 MALDIquant-1.12/MALDIquant/man/averageMassSpectra-functions.Rd | 4 MALDIquant-1.12/MALDIquant/man/calibrateIntensity-methods.Rd | 13 MALDIquant-1.12/MALDIquant/man/createMassPeaks-functions.Rd | 2 MALDIquant-1.12/MALDIquant/man/detectPeaks-methods.Rd | 5 MALDIquant-1.12/MALDIquant/man/intensityMatrix-functions.Rd | 2 MALDIquant-1.12/MALDIquant/man/mergeMassPeaks-functions.Rd | 5 MALDIquant-1.12/MALDIquant/man/msiSlices-functions.Rd |only MALDIquant-1.12/MALDIquant/man/plotMsiSlice-methods.Rd |only MALDIquant-1.12/MALDIquant/man/removeBaseline-methods.Rd | 4 MALDIquant-1.12/MALDIquant/man/transformIntensity-methods.Rd | 3 MALDIquant-1.12/MALDIquant/man/trim-methods.Rd | 6 MALDIquant-1.12/MALDIquant/src/init.c | 1 MALDIquant-1.12/MALDIquant/src/localMaxima.c | 1 MALDIquant-1.12/MALDIquant/src/lowerConvexHull.c | 1 MALDIquant-1.12/MALDIquant/src/morphologicalFilters.c | 1 MALDIquant-1.12/MALDIquant/src/snip.c | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_approxfun-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_as-methods.R |only MALDIquant-1.12/MALDIquant/tests/testthat/test_as.matrix-functions.R | 7 MALDIquant-1.12/MALDIquant/tests/testthat/test_averageMassSpectra-functions.R | 8 MALDIquant-1.12/MALDIquant/tests/testthat/test_calibrateIntensity-methods.R | 3 MALDIquant-1.12/MALDIquant/tests/testthat/test_colMedians-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_coordinates-methods.R |only MALDIquant-1.12/MALDIquant/tests/testthat/test_deprecated-functons.R | 20 MALDIquant-1.12/MALDIquant/tests/testthat/test_detectPeaks-methods.R | 8 MALDIquant-1.12/MALDIquant/tests/testthat/test_determineWarpingFunctions-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_doByLabel-functions.R | 10 MALDIquant-1.12/MALDIquant/tests/testthat/test_estimateBaseline-methods.R | 86 +-- MALDIquant-1.12/MALDIquant/tests/testthat/test_estimateNoise-methods.R | 23 MALDIquant-1.12/MALDIquant/tests/testthat/test_findEmptyMassObjects-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_intensityMatrix-functions.R | 5 MALDIquant-1.12/MALDIquant/tests/testthat/test_irregular-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_isEmpty-methods.R | 9 MALDIquant-1.12/MALDIquant/tests/testthat/test_isRegular-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_length-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_localMaxima-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_mapply-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_mass-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_merge-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_metaData-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_morphologicalFilter-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_msiSlices-functions.R |only MALDIquant-1.12/MALDIquant/tests/testthat/test_plotMsiSlice-functions.R |only MALDIquant-1.12/MALDIquant/tests/testthat/test_range-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_referencePeaks-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_removeBaseline-methods.R | 10 MALDIquant-1.12/MALDIquant/tests/testthat/test_removeEmptyMassObjects-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_show-methods.R | 101 ++- MALDIquant-1.12/MALDIquant/tests/testthat/test_smoothIntensity-methods.R | 17 MALDIquant-1.12/MALDIquant/tests/testthat/test_smoothingFilters-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_snr-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_subset-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_totalIonCurrent-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_transformIntensity-methods.R | 6 MALDIquant-1.12/MALDIquant/tests/testthat/test_trim-methods.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_unlist-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_valid-functions.R |only MALDIquant-1.12/MALDIquant/tests/testthat/test_warp-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_warpingFunctions-functions.R | 1 MALDIquant-1.12/MALDIquant/tests/testthat/test_which.closest-functions.R | 1 MALDIquant-1.12/MALDIquant/vignettes/bibliography.bib | 1 149 files changed, 925 insertions(+), 822 deletions(-)
Title: Identifying Functional Polymorphisms
Description: A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
Author: Leeyoung Park
Maintainer: Leeyoung Park <lypark@yonsei.ac.kr>
Diff between IFP versions 0.1.2 dated 2015-02-08 and 0.2.0 dated 2015-06-11
DESCRIPTION | 8 ++++---- MD5 | 17 ++++++++++++++--- NAMESPACE | 2 +- R/allele.freq.G.R |only R/geno.freq.G.R |only R/genotype.G.R |only R/lrt.G.R |only data/apoeG.RData |only man/allele.freq.G.Rd |only man/apoe.G.Rd |only man/geno.freq.G.Rd |only man/genotype.G.Rd |only man/iter.mcmc.Rd | 7 +++---- man/lrt.G.Rd |only src/lrtG.cpp |only 15 files changed, 22 insertions(+), 12 deletions(-)
Title: ERG Modeling Based on Graphlet Properties
Description: Integrates graphlet statistics based model terms for use in exponential-family random graph models ('ergm') as part of the 'statnet' suite of packages.
Author: Omer Nebil Yaveroglu [aut, cre],
Sean M. Fitzhugh [aut],
Maciej Kurant [aut],
Athina Markopoulou [aut],
Natasa Przulj [aut],
Carter T. Butts [aut]
Maintainer: Omer Nebil Yaveroglu <o.yaveroglu10@imperial.ac.uk>
Diff between ergm.graphlets versions 1.0.2 dated 2014-08-12 and 1.0.3 dated 2015-06-11
DESCRIPTION | 16 +++++------- MD5 | 23 +++++++++-------- NAMESPACE | 5 ++- data/datalist |only inst/CITATION | 22 ++++++++--------- man/emon3.Rd | 50 ++++++++++++++++++++++++++++++-------- man/ergm.graphlets-package.Rd | 8 +++--- man/graphletCount.Rd | 8 +++--- man/grorbitCov.Rd | 8 +++--- man/grorbitDist.Rd | 8 +++--- man/grorbitFactor.Rd | 8 +++--- man/spi.Rd | 54 ++++++++++++++++++++++++++++++------------ tests/example.R | 1 13 files changed, 131 insertions(+), 80 deletions(-)
More information about ergm.graphlets at CRAN
Permanent link
Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.4.3 dated 2015-04-07 and 0.4.5 dated 2015-06-11
DESCRIPTION | 12 ++-- MD5 | 57 ++++++++++++----------- NAMESPACE | 3 - NEWS | 20 ++++++++ R/dygraph.R | 1 R/event.R | 74 ++++++++++++++++++++++++++---- R/options.R | 9 +++ R/range-selector.R | 7 ++ R/shading.R | 14 ++++- R/utils.R | 4 + inst/examples/examples.html | 8 +-- inst/htmlwidgets/dygraphs.js | 101 ++++++++++++++++++++++++++++-------------- man/dyAnnotation.Rd | 2 man/dyAxis.Rd | 2 man/dyCSS.Rd | 2 man/dyCallbacks.Rd | 2 man/dyEvent.Rd | 20 ++++---- man/dyHighlight.Rd | 2 man/dyLegend.Rd | 2 man/dyLimit.Rd |only man/dyOptions.Rd | 9 ++- man/dyRangeSelector.Rd | 9 ++- man/dyRoller.Rd | 2 man/dySeries.Rd | 2 man/dySeriesData.Rd | 2 man/dyShading.Rd | 12 +++- man/dygraph-shiny.Rd | 2 man/dygraph.Rd | 2 man/dygraphs-exports.Rd | 2 tests/testthat/test-shading.R | 4 - 30 files changed, 268 insertions(+), 120 deletions(-)
More information about EditImputeCont at CRAN
Permanent link
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.5 dated 2015-05-27 and 1.0.6 dated 2015-06-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/CCAGFA.R | 4 ++-- R/CCAGFAtools.R | 12 ++++++++++++ 5 files changed, 26 insertions(+), 10 deletions(-)
Title: Public Subject Attention via Wikipedia Page Access Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied. For the omnipresent Wikipedia those access statistics
are made available via 'http://stats.grok.se' a server
providing the information as file dumps as well as as web API.
This package provides an easy to use, consistent and traffic
minimizing approach to make those data accessible within R.
Author: Peter Meissner [aut, cre], R Core team [ctb] ('wp_date()'
derived from base package's 'as.Date()')
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 1.1.3 dated 2015-06-06 and 1.1.4 dated 2015-06-11
DESCRIPTION | 8 - MD5 | 18 +- NEWS | 12 + R/aa_pversion_inc.r | 74 +++++----- README.md | 55 ++++++- inst/doc/using-wikipediatrend.R | 243 +++++++++++++++++----------------- inst/doc/using-wikipediatrend.Rmd | 108 ++++----------- inst/doc/using-wikipediatrend.html | 263 ++++++++++++------------------------- man/wp_cache.Rd | 32 ++-- vignettes/using-wikipediatrend.Rmd | 108 ++++----------- 10 files changed, 398 insertions(+), 523 deletions(-)
More information about wikipediatrend at CRAN
Permanent link
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.8-3 dated 2015-01-06 and 1.9-0 dated 2015-06-11
Description: Implementation of statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g., discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models,
or continuous-space point process data such as the
occurrence of infectious diseases. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of communicable diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently, the package contains implementations of many typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Höhle and Paul (2008). A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Furthermore, inference methods for the retrospective infectious
disease models in Held et al (2005), Held et al (2006),
Paul et al (2008), Paul and Held (2011), Held and Paul (2012),
and Meyer and Held (2014) are provided.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ('twinSIR', discrete
space) and Meyer et al (2012) ('twinstim', continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: Using the 'boda' algorithm requires the 'INLA'
package, which should be installed automatically through the
specified Additional_repositories, if uninstalled dependencies
are also requested. As this might not work under OS X it
might be necessary to manually install the 'INLA' package as
specified at http://www.r-inla.org/download.
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
surveillance-1.8-3/surveillance/R/bdist.R |only
surveillance-1.8-3/surveillance/po |only
surveillance-1.8-3/surveillance/tests/test-all.R |only
surveillance-1.9-0/surveillance/DESCRIPTION | 49 -
surveillance-1.9-0/surveillance/MD5 | 172 ++---
surveillance-1.9-0/surveillance/NAMESPACE | 38 +
surveillance-1.9-0/surveillance/R/AllGeneric.R | 29
surveillance-1.9-0/surveillance/R/addSeason2formula.R |only
surveillance-1.9-0/surveillance/R/boda.R | 95 +-
surveillance-1.9-0/surveillance/R/bodaDelay.R |only
surveillance-1.9-0/surveillance/R/checkDerivatives.R | 10
surveillance-1.9-0/surveillance/R/epidataCS.R | 38 -
surveillance-1.9-0/surveillance/R/epidataCS_methods.R | 103 ++-
surveillance-1.9-0/surveillance/R/epidataCS_plot.R | 257 +++++--
surveillance-1.9-0/surveillance/R/hhh4.R | 131 +--
surveillance-1.9-0/surveillance/R/hhh4_W.R | 151 +++-
surveillance-1.9-0/surveillance/R/hhh4_W_powerlaw.R | 35 -
surveillance-1.9-0/surveillance/R/hhh4_methods.R | 55 +
surveillance-1.9-0/surveillance/R/hhh4_plot.R | 80 +-
surveillance-1.9-0/surveillance/R/intersectPolyCircle.R | 12
surveillance-1.9-0/surveillance/R/isoWeekYear.R | 42 -
surveillance-1.9-0/surveillance/R/knox.R |only
surveillance-1.9-0/surveillance/R/linelist2sts.R | 2
surveillance-1.9-0/surveillance/R/nowcast.R | 228 +++---
surveillance-1.9-0/surveillance/R/permutationTest.R | 17
surveillance-1.9-0/surveillance/R/plapply.R |only
surveillance-1.9-0/surveillance/R/spatial_tools.R | 108 +++
surveillance-1.9-0/surveillance/R/stK.R |only
surveillance-1.9-0/surveillance/R/sts.R | 21
surveillance-1.9-0/surveillance/R/sts_animate.R | 23
surveillance-1.9-0/surveillance/R/sts_coerce.R | 22
surveillance-1.9-0/surveillance/R/sts_creation.R |only
surveillance-1.9-0/surveillance/R/sts_observation.R |only
surveillance-1.9-0/surveillance/R/twinstim.R | 171 ++---
surveillance-1.9-0/surveillance/R/twinstim_epitest.R |only
surveillance-1.9-0/surveillance/R/twinstim_helper.R | 42 -
surveillance-1.9-0/surveillance/R/twinstim_iafplot.R | 71 +-
surveillance-1.9-0/surveillance/R/twinstim_intensity.R | 18
surveillance-1.9-0/surveillance/R/twinstim_methods.R | 128 ++-
surveillance-1.9-0/surveillance/R/twinstim_siaf.R | 18
surveillance-1.9-0/surveillance/R/twinstim_simulation.R | 227 ++++--
surveillance-1.9-0/surveillance/R/zzz.R | 7
surveillance-1.9-0/surveillance/build/partial.rdb |binary
surveillance-1.9-0/surveillance/build/vignette.rds |binary
surveillance-1.9-0/surveillance/data/salmAllOnset.RData |only
surveillance-1.9-0/surveillance/data/salmNewportTruncated.RData |only
surveillance-1.9-0/surveillance/inst/CITATION | 6
surveillance-1.9-0/surveillance/inst/NEWS.Rd | 168 ++++
surveillance-1.9-0/surveillance/inst/THANKS | 1
surveillance-1.9-0/surveillance/inst/doc/glrnb.R | 1
surveillance-1.9-0/surveillance/inst/doc/glrnb.pdf |binary
surveillance-1.9-0/surveillance/inst/doc/hhh4.pdf |binary
surveillance-1.9-0/surveillance/inst/doc/surveillance.R | 1
surveillance-1.9-0/surveillance/inst/doc/surveillance.pdf |binary
surveillance-1.9-0/surveillance/inst/jags/bhpm.bugs | 50 -
surveillance-1.9-0/surveillance/man/R0.Rd | 68 +-
surveillance-1.9-0/surveillance/man/addSeason2formula.Rd | 3
surveillance-1.9-0/surveillance/man/algo.outbreakP.Rd | 4
surveillance-1.9-0/surveillance/man/boda.Rd | 18
surveillance-1.9-0/surveillance/man/bodaDelay.Rd |only
surveillance-1.9-0/surveillance/man/coeflist.Rd |only
surveillance-1.9-0/surveillance/man/epidataCS.Rd | 41 -
surveillance-1.9-0/surveillance/man/epidataCS_permute.Rd |only
surveillance-1.9-0/surveillance/man/epidataCS_plot.Rd | 85 ++
surveillance-1.9-0/surveillance/man/formatPval.Rd | 11
surveillance-1.9-0/surveillance/man/hhh4.Rd | 68 --
surveillance-1.9-0/surveillance/man/hhh4_W.Rd | 4
surveillance-1.9-0/surveillance/man/hhh4_formula.Rd | 50 -
surveillance-1.9-0/surveillance/man/imdepi.Rd | 3
surveillance-1.9-0/surveillance/man/isoWeekYear.Rd | 2
surveillance-1.9-0/surveillance/man/knox.Rd |only
surveillance-1.9-0/surveillance/man/layout.labels.Rd | 79 +-
surveillance-1.9-0/surveillance/man/linelist2sts.Rd | 19
surveillance-1.9-0/surveillance/man/measles.weser.Rd | 6
surveillance-1.9-0/surveillance/man/momo.Rd | 11
surveillance-1.9-0/surveillance/man/nowcast.Rd | 49 +
surveillance-1.9-0/surveillance/man/permutationTest.Rd | 10
surveillance-1.9-0/surveillance/man/plapply.Rd |only
surveillance-1.9-0/surveillance/man/residualsCT.Rd | 9
surveillance-1.9-0/surveillance/man/salmAllOnset.Rd |only
surveillance-1.9-0/surveillance/man/salmNewportTruncated.Rd |only
surveillance-1.9-0/surveillance/man/stK.Rd |only
surveillance-1.9-0/surveillance/man/sts-class.Rd | 340 +++++-----
surveillance-1.9-0/surveillance/man/sts_animate.Rd | 11
surveillance-1.9-0/surveillance/man/sts_creation.Rd |only
surveillance-1.9-0/surveillance/man/sts_observation.Rd |only
surveillance-1.9-0/surveillance/man/stsplot_spacetime.Rd | 2
surveillance-1.9-0/surveillance/man/surveillance-package.Rd | 28
surveillance-1.9-0/surveillance/man/twinstim.Rd | 143 +---
surveillance-1.9-0/surveillance/man/twinstim_epitest.Rd |only
surveillance-1.9-0/surveillance/man/twinstim_iafplot.Rd | 28
surveillance-1.9-0/surveillance/man/twinstim_methods.Rd | 7
surveillance-1.9-0/surveillance/man/twinstim_simulation.Rd | 39 -
surveillance-1.9-0/surveillance/man/untie.Rd | 4
surveillance-1.9-0/surveillance/tests/testthat.R |only
surveillance-1.9-0/surveillance/tests/testthat/test-bodaDelay.R |only
surveillance-1.9-0/surveillance/tests/testthat/test-hhh4+derivatives.R |only
surveillance-1.9-0/surveillance/tests/testthat/test-nbOrder.R | 33
surveillance-1.9-0/surveillance/tests/testthat/test-plapply.R |only
surveillance-1.9-0/surveillance/tests/testthat/test-tiafs.R | 2
surveillance-1.9-0/surveillance/tests/testthat/test-twinstim_score.R |only
101 files changed, 2439 insertions(+), 1365 deletions(-)
Title: Parsing, Applying, and Manipulating Data Cleaning Rules
Description: Facilitates reading and manipulating (multivariate) data restrictions
(edit rules) on numerical and categorical data. Rules can be defined with common R syntax
and parsed to an internal (matrix-like format). Rules can be manipulated with
variable elimination and value substitution methods, allowing for feasibility checks
and more. Data can be tested against the rules and erroneous fields can be found based
on Fellegi and Holt's generalized principle. Rules dependencies can be visualized with
using the igraph package.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between editrules versions 2.7.2 dated 2013-07-03 and 2.9.0 dated 2015-06-11
editrules-2.7.2/editrules/inst/doc/editrules-vignette.R |only editrules-2.7.2/editrules/inst/script/bench/benchordered.txt |only editrules-2.7.2/editrules/inst/tests |only editrules-2.7.2/editrules/man/errorLocalizer.mip.Rd |only editrules-2.9.0/editrules/DESCRIPTION | 48 - editrules-2.9.0/editrules/MD5 | 304 +++++----- editrules-2.9.0/editrules/NAMESPACE | 98 +-- editrules-2.9.0/editrules/NEWS | 15 editrules-2.9.0/editrules/R/adjacency.R | 1 editrules-2.9.0/editrules/R/as.igraph.R | 31 - editrules-2.9.0/editrules/R/as.matrix.R | 5 editrules-2.9.0/editrules/R/c.R | 10 editrules-2.9.0/editrules/R/cateditmatrix.R | 4 editrules-2.9.0/editrules/R/contains.R | 31 - editrules-2.9.0/editrules/R/editarray.R | 12 editrules-2.9.0/editrules/R/editfile.R | 8 editrules-2.9.0/editrules/R/errorLocalizer.R | 2 editrules-2.9.0/editrules/R/errorLocalizer_mip.R | 95 +-- editrules-2.9.0/editrules/R/getVars.R | 6 editrules-2.9.0/editrules/R/localizeErrors.R | 26 editrules-2.9.0/editrules/R/mip.R | 95 ++- editrules-2.9.0/editrules/R/parseCat.R | 2 editrules-2.9.0/editrules/R/parseMix.R | 7 editrules-2.9.0/editrules/R/pkg.R | 9 editrules-2.9.0/editrules/R/plot.R | 24 editrules-2.9.0/editrules/R/reduce.R | 75 ++ editrules-2.9.0/editrules/R/removeRedundant.R | 8 editrules-2.9.0/editrules/R/softEdits.R | 37 + editrules-2.9.0/editrules/R/str.R | 1 editrules-2.9.0/editrules/R/subsetting.R | 6 editrules-2.9.0/editrules/R/substValue.R | 21 editrules-2.9.0/editrules/R/summary.R | 12 editrules-2.9.0/editrules/R/violatedEdits.R | 3 editrules-2.9.0/editrules/R/writeELAsMip.R | 4 editrules-2.9.0/editrules/R/zzz.R | 12 editrules-2.9.0/editrules/build |only editrules-2.9.0/editrules/inst/doc/editrules-vignette.pdf |binary editrules-2.9.0/editrules/inst/doc/index.html | 2 editrules-2.9.0/editrules/inst/script/bench/benchmip_balance.R |only editrules-2.9.0/editrules/inst/script/bench/benchmip_categorical.R |only editrules-2.9.0/editrules/inst/script/bench/benchmip_mixed.R |only editrules-2.9.0/editrules/inst/script/bench/benchmip_mixed2.R |only editrules-2.9.0/editrules/man/adddummies.Rd | 13 editrules-2.9.0/editrules/man/adjacency.Rd | 94 +-- editrules-2.9.0/editrules/man/as.character.cateditmatrix.Rd | 15 editrules-2.9.0/editrules/man/as.editmatrix.Rd | 34 - editrules-2.9.0/editrules/man/as.editset.Rd | 12 editrules-2.9.0/editrules/man/as.lp.mip.Rd |only editrules-2.9.0/editrules/man/as.mip.Rd |only editrules-2.9.0/editrules/man/asLevels.Rd | 6 editrules-2.9.0/editrules/man/backtracker.Rd | 71 -- editrules-2.9.0/editrules/man/blocks.Rd | 28 editrules-2.9.0/editrules/man/cateditmatrix.Rd | 24 editrules-2.9.0/editrules/man/checkDatamodel.Rd | 30 editrules-2.9.0/editrules/man/condition.Rd | 14 editrules-2.9.0/editrules/man/contains.Rd | 48 - editrules-2.9.0/editrules/man/contains.boolmat.Rd | 12 editrules-2.9.0/editrules/man/datamodel.Rd | 13 editrules-2.9.0/editrules/man/disjunct.Rd | 35 - editrules-2.9.0/editrules/man/duplicated.editarray.Rd | 11 editrules-2.9.0/editrules/man/duplicated.editmatrix.Rd | 12 editrules-2.9.0/editrules/man/echelon.Rd | 30 editrules-2.9.0/editrules/man/editType.Rd | 14 editrules-2.9.0/editrules/man/editarray.Rd | 122 +--- editrules-2.9.0/editrules/man/editfile.Rd | 35 - editrules-2.9.0/editrules/man/editmatrix.Rd | 112 +-- editrules-2.9.0/editrules/man/editnames.Rd | 9 editrules-2.9.0/editrules/man/editrules-package.Rd | 132 ++-- editrules-2.9.0/editrules/man/editrules.plotting.Rd | 170 ++--- editrules-2.9.0/editrules/man/edits.Rd | 8 editrules-2.9.0/editrules/man/editset.Rd | 70 +- editrules-2.9.0/editrules/man/eliminate.Rd | 106 +-- editrules-2.9.0/editrules/man/errorLocalizer.Rd | 224 +++---- editrules-2.9.0/editrules/man/errorLocalizer_mip.Rd |only editrules-2.9.0/editrules/man/errorLocation.Rd | 89 +- editrules-2.9.0/editrules/man/expandEdits.Rd | 32 - editrules-2.9.0/editrules/man/fcf.env.Rd | 23 editrules-2.9.0/editrules/man/generateEdits.Rd | 43 - editrules-2.9.0/editrules/man/getA.Rd | 13 editrules-2.9.0/editrules/man/getAb.Rd | 16 editrules-2.9.0/editrules/man/getArr.Rd | 10 editrules-2.9.0/editrules/man/getInd.Rd | 17 editrules-2.9.0/editrules/man/getOps.Rd | 13 editrules-2.9.0/editrules/man/getSep.Rd | 11 editrules-2.9.0/editrules/man/getUpperBounds.Rd | 14 editrules-2.9.0/editrules/man/getVars.Rd | 47 - editrules-2.9.0/editrules/man/getVars.cateditmatrix.Rd | 12 editrules-2.9.0/editrules/man/getVars.editarray.Rd | 6 editrules-2.9.0/editrules/man/getVars.editlist.Rd |only editrules-2.9.0/editrules/man/getVars.editmatrix.Rd | 7 editrules-2.9.0/editrules/man/getb.Rd | 13 editrules-2.9.0/editrules/man/geth.Rd | 32 - editrules-2.9.0/editrules/man/getlevels.Rd | 10 editrules-2.9.0/editrules/man/getnames.Rd | 10 editrules-2.9.0/editrules/man/impliedValues.Rd |only editrules-2.9.0/editrules/man/ind2char.Rd | 21 editrules-2.9.0/editrules/man/indFromArray.Rd | 10 editrules-2.9.0/editrules/man/is.editrules.Rd | 14 editrules-2.9.0/editrules/man/isFeasible.Rd | 34 - editrules-2.9.0/editrules/man/isNormalized.Rd | 13 editrules-2.9.0/editrules/man/isObviouslyInfeasible.Rd | 60 + editrules-2.9.0/editrules/man/isObviouslyRedundant.Rd | 53 - editrules-2.9.0/editrules/man/isSubset.Rd | 21 editrules-2.9.0/editrules/man/localize.Rd | 31 - editrules-2.9.0/editrules/man/localizeErrors.Rd | 125 +--- editrules-2.9.0/editrules/man/nedits.Rd | 11 editrules-2.9.0/editrules/man/neweditarray.Rd | 11 editrules-2.9.0/editrules/man/neweditmatrix.Rd | 20 editrules-2.9.0/editrules/man/newerrorlocation.Rd | 20 editrules-2.9.0/editrules/man/normalize.Rd | 17 editrules-2.9.0/editrules/man/parseCat.Rd | 19 editrules-2.9.0/editrules/man/parseCatEdit.Rd | 10 editrules-2.9.0/editrules/man/parseEdits.Rd | 19 editrules-2.9.0/editrules/man/parseMix.Rd | 21 editrules-2.9.0/editrules/man/parseNum.Rd | 11 editrules-2.9.0/editrules/man/print.backtracker.Rd | 12 editrules-2.9.0/editrules/man/print.cateditmatrix.Rd | 11 editrules-2.9.0/editrules/man/print.editarray.Rd | 14 editrules-2.9.0/editrules/man/print.editlist.Rd | 11 editrules-2.9.0/editrules/man/print.editmatrix.Rd | 14 editrules-2.9.0/editrules/man/print.editset.Rd | 11 editrules-2.9.0/editrules/man/print.editsummary.Rd |only editrules-2.9.0/editrules/man/print.errorLocation.Rd | 10 editrules-2.9.0/editrules/man/print.locationsummary.Rd |only editrules-2.9.0/editrules/man/print.violatedEdits.Rd | 8 editrules-2.9.0/editrules/man/reduce.Rd | 33 - editrules-2.9.0/editrules/man/removeRedundantDummies.Rd | 10 editrules-2.9.0/editrules/man/separate.Rd | 32 - editrules-2.9.0/editrules/man/simplify.Rd | 14 editrules-2.9.0/editrules/man/softEdits.Rd | 14 editrules-2.9.0/editrules/man/softEdits.cateditmatrix.Rd | 16 editrules-2.9.0/editrules/man/softEdits.editarray.Rd |only editrules-2.9.0/editrules/man/softEdits.editmatrix.Rd |only editrules-2.9.0/editrules/man/subsetting.Rd | 36 - editrules-2.9.0/editrules/man/substValue.Rd | 83 +- editrules-2.9.0/editrules/man/violatedEdits.Rd | 102 +-- editrules-2.9.0/editrules/man/writeELAsMip.Rd | 26 editrules-2.9.0/editrules/tests/testthat |only 138 files changed, 1984 insertions(+), 1950 deletions(-)
Title: Read and Analyze 'PLEXOS' Solutions
Description: Efficiently read and analyze 'PLEXOS' solutions by converting them
into 'SQLite' databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios. 'PLEXOS' is a power systems
production cost model, created and distributed by Energy Exemplar
(see URL below for more information).
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez <eduardo.ibanez@nrel.gov>
Diff between rplexos versions 1.0 dated 2015-04-22 and 1.1.1 dated 2015-06-11
DESCRIPTION | 25 +++--- MD5 | 46 +++++------ NAMESPACE | 1 R/auxiliary.R | 83 +++++---------------- R/globalVariables.R | 2 R/help.R | 2 R/parallel.R | 3 R/plexos_open.R | 5 - R/process_folder.R | 31 ++++--- R/process_input.R | 8 +- R/process_solution.R | 2 R/query.R | 171 +++++++++++++++++++++++++++++++------------- R/query_summary.R | 26 ++++-- inst/doc/rplexos.R | 10 +- inst/doc/rplexos.Rmd | 6 - inst/doc/rplexos.html | 17 +--- man/process_folder.Rd | 10 ++ man/query_config.Rd | 9 ++ man/query_log.Rd | 10 ++ man/query_master.Rd | 13 +++ man/query_master_each.Rd | 2 man/query_property.Rd | 9 ++ man/query_sql.Rd | 10 ++ tests/testthat/test_query.R | 26 +++++- 24 files changed, 318 insertions(+), 209 deletions(-)
Title: LTPD and AOQL Plans for Acceptance Sampling Inspection by
Variables
Description: Calculation of rectifying LTPD and AOQL plans for sampling inspection by variables which minimize mean inspection cost per lot of process average quality.
Author: Nikola Kasprikova
Maintainer: Nikola Kasprikova <data@tulipany.cz>
Diff between LTPDvar versions 1.1 dated 2012-11-20 and 1.2 dated 2015-06-11
LTPDvar-1.1/LTPDvar/R/kL.R |only LTPDvar-1.1/LTPDvar/man/kL.Rd |only LTPDvar-1.2/LTPDvar/DESCRIPTION | 17 -- LTPDvar-1.2/LTPDvar/MD5 | 34 +--- LTPDvar-1.2/LTPDvar/NAMESPACE | 4 LTPDvar-1.2/LTPDvar/R/AOQ.R | 4 LTPDvar-1.2/LTPDvar/R/Ims.R | 6 LTPDvar-1.2/LTPDvar/R/OC.R | 29 ++- LTPDvar-1.2/LTPDvar/R/classes.R | 2 LTPDvar-1.2/LTPDvar/R/cmBE.R | 9 - LTPDvar-1.2/LTPDvar/R/planAOQL.R | 243 ++++++++++++++--------------- LTPDvar-1.2/LTPDvar/R/planLTPD.R | 104 ++++++------ LTPDvar-1.2/LTPDvar/man/AOQ.Rd | 7 LTPDvar-1.2/LTPDvar/man/Ims.Rd | 17 +- LTPDvar-1.2/LTPDvar/man/LTPDvar-package.Rd | 56 +++--- LTPDvar-1.2/LTPDvar/man/OC.Rd | 9 - LTPDvar-1.2/LTPDvar/man/cmBE.Rd | 15 + LTPDvar-1.2/LTPDvar/man/planAOQL.Rd | 14 + LTPDvar-1.2/LTPDvar/man/planLTPD.Rd | 13 + 19 files changed, 315 insertions(+), 268 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.0-3 dated 2014-12-10 and 3.0-4 dated 2015-06-11
DESCRIPTION | 18 - MD5 | 41 +- NAMESPACE | 14 NEWS | 24 + R/Effect.R | 6 R/effects.R | 9 R/effectsclmm.R |only R/effectsmer.R | 106 ++++-- R/plot-methods.R | 789 +++++++++++++++++++++++++++++++++++++++++------ R/plot.effpoly.R | 5 R/utilities.R | 31 + data/Arrests.rda |binary data/BEPS.rda |binary data/Cowles.rda |binary data/Hartnagel.rda |binary data/Prestige.rda |binary data/TitanicSurvival.rda |binary data/WVS.rda |binary data/Wells.rda |binary man/effect.Rd | 105 +++--- man/effects-package.Rd | 10 man/summary.effect.Rd | 81 +++- 22 files changed, 1000 insertions(+), 239 deletions(-)
Title: Geophysical Inverse Theory and Optimization
Description: Several functions introduced in Aster et al.'s book on inverse theory. The functions are often translations of MATLAB code developed by the authors to illustrate concepts of inverse theory as applied to geophysics. Generalized inversion, tomographic inversion algorithms (conjugate gradients, 'ART' and 'SIRT'), non-linear least squares, first and second order Tikhonov regularization, roughness constraints, and procedures for estimating smoothing parameters are included. Includes a wrapper for the FORTRAN based 'LSQR' (Paige and Saunders) routine.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between PEIP versions 2.0 dated 2015-06-09 and 2.0-1 dated 2015-06-10
DESCRIPTION | 6 +++--- MD5 | 5 +++-- src/Makevars | 3 +-- src/Makevars.win |only 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-1 dated 2013-09-04 and 0.5-2 dated 2015-06-10
DESCRIPTION | 19 +- MD5 | 82 +++++----- NAMESPACE | 2 R/merge.rspec.R | 3 R/plot.rspec.r | 3 R/subset.rspec.R | 9 - R/summary.rspec.R | 3 R/summary.tcs.R | 3 R/summary.vismodel.R | 3 R/sysdata.rda |binary R/tcs.R | 2 R/vismodel.R | 8 - man/aggplot.Rd | 69 ++++----- man/aggspec.Rd | 48 ++---- man/as.rspec.Rd | 36 +--- man/bgandilum.Rd | 10 - man/coldist.Rd | 149 ++++++++----------- man/explorespec.Rd | 44 ++--- man/getspec.Rd | 54 +++---- man/irrad2flux.Rd | 25 +-- man/merge.rspec.Rd | 22 +- man/pavo-package.Rd | 20 +- man/peakshape.Rd | 55 +++---- man/plot.rspec.Rd | 54 +++---- man/plotsmooth.Rd | 38 ++--- man/procspec.Rd | 94 +++++------- man/projplot.Rd | 40 ++--- man/segclass.Rd | 31 +--- man/sensmodel.Rd | 102 +++++-------- man/sicalis.Rd | 10 - man/spec2rgb.Rd | 31 +--- man/subset.rspec.Rd | 25 +-- man/summary.rspec.Rd | 358 ++++++++++++++++++++---------------------------- man/summary.tcs.Rd | 69 +++------ man/summary.vismodel.Rd | 36 +--- man/tcs.Rd | 63 +++----- man/tcsplot.Rd | 122 ++++++---------- man/teal.Rd | 10 - man/ttvertex.Rd | 12 - man/vismodel.Rd | 174 ++++++++++------------- man/vissyst.Rd | 11 - man/voloverlap.Rd | 169 +++++++++------------- 42 files changed, 920 insertions(+), 1198 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.3 dated 2015-05-13 and 0.4 dated 2015-06-10
DESCRIPTION | 13 MD5 | 80 +- NAMESPACE | 4 NEWS | 5 R/jeroen.R | 5 R/mongo.R | 30 - R/object.R | 96 ++- R/stream.R | 66 ++ configure | 6 inst/doc/intro.Rmd | 32 + inst/doc/intro.html | 40 + man/mongo.Rd | 29 src/Makevars | 56 + src/Makevars.win | 5 src/bson.c | 11 src/bson/bson-config.h | 30 - src/bson/bson-stdint.h | 2 src/bson/bson-utf8.c | 17 src/bson/bson-version.h | 6 src/bson/bson.c | 11 src/cursor.c | 66 ++ src/mongoc/mongoc-bulk-operation.c | 73 ++ src/mongoc/mongoc-client.c | 2 src/mongoc/mongoc-cluster-private.h | 1 src/mongoc/mongoc-cluster.c | 87 ++ src/mongoc/mongoc-collection.c | 8 src/mongoc/mongoc-config.h | 11 src/mongoc/mongoc-error.h | 2 src/mongoc/mongoc-init.c | 74 ++ src/mongoc/mongoc-matcher-op.c | 104 +++ src/mongoc/mongoc-sasl.c | 18 src/mongoc/mongoc-stream.c | 9 src/mongoc/mongoc-uri.c | 18 src/mongoc/mongoc-util-private.h | 9 src/mongoc/mongoc-version.h | 6 src/mongoc/mongoc-write-command-private.h | 40 - src/mongoc/mongoc-write-command.c | 874 ++++++++++++++++++++---------- src/reader.c |only src/tests |only src/utils.c | 6 tests |only vignettes/intro.Rmd | 32 + 42 files changed, 1484 insertions(+), 500 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov <valentin.todorov@chello.at>,
Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Tobias Verbeke <tobias.verbeke@openanalytics.eu>,
Manuel Koller <mkoller@ispm.unibe.ch>,
Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-3 dated 2015-01-14 and 0.92-4 dated 2015-06-10
DESCRIPTION | 25 ++++---- MD5 | 82 +++++++++++++------------- NAMESPACE | 9 ++ R/AAA.R | 13 ++-- R/BYlogreg.R | 2 R/MTestimador2.R | 19 +++--- R/OGK.R | 3 R/glmrobMqle.R | 32 ++++------ R/huber.R | 4 - R/lmrob.MM.R | 59 +++++++++---------- R/lmrob.R | 2 R/ltsPlot.R | 130 +++++++++++++++--------------------------- R/plot.lmrob.R | 74 +++++++++++++++++++---- TODO | 4 - build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary inst/po |only man/adjbox.Rd | 17 ++--- man/colMedians.Rd | 4 - man/condroz.Rd | 8 -- man/lmrob..M..fit.Rd | 4 - man/lmrob.Rd | 6 - man/lmrob.control.Rd | 2 man/los.Rd | 7 -- man/mc.Rd | 5 - man/plot.lmrob.Rd | 28 +++++++-- man/predict.lmrob.Rd | 74 ++++++++++++++++++++++- man/pulpfiber.Rd | 2 man/salinity.Rd | 49 +++++++++++++-- man/sigma.Rd | 26 +++++--- po |only src/mc.c | 4 - tests/glmrob-1.R | 34 ++++++++++ vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 43 files changed, 451 insertions(+), 277 deletions(-)
Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between mpath versions 0.1-17 dated 2014-11-10 and 0.1-18 dated 2015-06-10
DESCRIPTION | 9 ++-- MD5 | 79 ++++++++++++++++++++------------------- NAMESPACE | 2 NEWS | 9 ++++ R/cv.glmregNegbin.R | 5 +- R/glmreg.R | 29 +++++++++++--- R/glmregNB.R | 4 - R/zipath.R | 8 --- build/vignette.rds |binary inst/doc/german.R | 65 ++++++++++++++++++++++++++------ inst/doc/german.Rnw | 45 +++++++++++++++++----- inst/doc/german.pdf |binary inst/doc/static_german.pdf |only inst/doc/static_german.pdf.asis |only man/be_zeroinfl.Rd | 4 - man/breadReg.Rd | 3 - man/cv.glmreg.Rd | 21 +++++----- man/cv.glmregNB.Rd | 20 ++++----- man/cv.glmreg_fit.Rd | 21 +++++----- man/cv.zipath.Rd | 13 ++---- man/estfunReg.Rd | 3 - man/glmreg.Rd | 3 - man/glmregNB.Rd | 2 man/glmreg_fit.Rd | 6 +- man/hessianReg.Rd | 2 man/meatReg.Rd | 2 man/methods.Rd | 6 +- man/mpath-internal.Rd | 2 man/p_zipath.Rd | 4 - man/predict.glmreg.Rd | 2 man/predict.zipath.Rd | 6 +- man/rzi.Rd | 4 - man/sandwichReg.Rd | 2 man/se.Rd | 2 man/summary.glmregNB.Rd | 2 man/tuning_zipath.Rd | 6 +- man/zipath.Rd | 6 +- src/lmnetGaussian.f | 27 ++++++------- src/midloop.f | 11 ++--- vignettes/german.Rnw | 45 +++++++++++++++++----- vignettes/mpath.bib | 5 +- vignettes/static_german.pdf.asis |only 42 files changed, 309 insertions(+), 176 deletions(-)
Title: Variable Selection for Model-Based Clustering using the
Integrated Complete-Data Likelihood of a Latent Class Model
Description: Uses a finite mixture model for performing the cluster analysis with variable selection of continuous data by assuming independence between classes. The package deals dataset with missing values by assuming that values are missing at random. The one-dimensional marginals of the components follow Gaussian distributions for facilitating both model interpretation and model selection. The variable selection is led by the Maximum Integrated Complete-Data Likelihood criterion. The maximum likelihood inference is done by an EM algorithm for the selected model. This package also performs the imputation of missing values.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 1.1 dated 2015-05-22 and 1.2 dated 2015-06-10
VarSelLCM-1.1/VarSelLCM/R/VSLCM_Classes.R |only VarSelLCM-1.1/VarSelLCM/R/VSLCM_initialization.R |only VarSelLCM-1.1/VarSelLCM/R/onAttach.R |only VarSelLCM-1.1/VarSelLCM/inst/CITATION |only VarSelLCM-1.1/VarSelLCM/inst/include/Algo.h |only VarSelLCM-1.1/VarSelLCM/man/VSLCMparameters-class.Rd |only VarSelLCM-1.1/VarSelLCM/man/VSLCMresults-class.Rd |only VarSelLCM-1.1/VarSelLCM/src/Algo.cpp |only VarSelLCM-1.1/VarSelLCM/src/Algo.h |only VarSelLCM-1.1/VarSelLCM/src/VarSelLCM.cpp |only VarSelLCM-1.2/VarSelLCM/DESCRIPTION | 22 VarSelLCM-1.2/VarSelLCM/MD5 | 68 +- VarSelLCM-1.2/VarSelLCM/NAMESPACE | 9 VarSelLCM-1.2/VarSelLCM/R/CheckInputs.R |only VarSelLCM-1.2/VarSelLCM/R/DataCstr.R |only VarSelLCM-1.2/VarSelLCM/R/DesignOutput.R |only VarSelLCM-1.2/VarSelLCM/R/ICLexact.R | 30 - VarSelLCM-1.2/VarSelLCM/R/Imputation.R |only VarSelLCM-1.2/VarSelLCM/R/Print.R | 35 - VarSelLCM-1.2/VarSelLCM/R/RcppExports.R | 4 VarSelLCM-1.2/VarSelLCM/R/Summary.R | 43 + VarSelLCM-1.2/VarSelLCM/R/VSLCMGrlClasses.R |only VarSelLCM-1.2/VarSelLCM/R/VarSelLCM.R | 238 ++++------ VarSelLCM-1.2/VarSelLCM/R/withoutmixture.R |only VarSelLCM-1.2/VarSelLCM/data |only VarSelLCM-1.2/VarSelLCM/inst/include/Algorithm.h |only VarSelLCM-1.2/VarSelLCM/inst/include/AlgorithmContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/Data.h |only VarSelLCM-1.2/VarSelLCM/inst/include/DataContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/Param.h |only VarSelLCM-1.2/VarSelLCM/inst/include/ParamContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/XEM.h |only VarSelLCM-1.2/VarSelLCM/inst/include/XEMContinuous.h |only VarSelLCM-1.2/VarSelLCM/man/VSLCMcriteria-class.Rd | 3 VarSelLCM-1.2/VarSelLCM/man/VSLCMdataContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMmodel-class.Rd | 2 VarSelLCM-1.2/VarSelLCM/man/VSLCMparametersContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMpartitions-class.Rd | 2 VarSelLCM-1.2/VarSelLCM/man/VSLCMresultsContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMstrategy-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VarSeLCluster.Rd | 102 ++-- VarSelLCM-1.2/VarSelLCM/man/VarSelImputation.Rd |only VarSelLCM-1.2/VarSelLCM/man/VarSelLCM-package.Rd | 45 - VarSelLCM-1.2/VarSelLCM/man/banknote.Rd |only VarSelLCM-1.2/VarSelLCM/man/print-methods.Rd | 11 VarSelLCM-1.2/VarSelLCM/man/summary-methods.Rd | 13 VarSelLCM-1.2/VarSelLCM/src/Algorithm.cpp |only VarSelLCM-1.2/VarSelLCM/src/AlgorithmContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/DataContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/ParamContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/RcppExports.cpp | 20 VarSelLCM-1.2/VarSelLCM/src/VarSelLCMmixte.cpp |only VarSelLCM-1.2/VarSelLCM/src/XEM.cpp |only VarSelLCM-1.2/VarSelLCM/src/XEMContinuous.cpp |only 54 files changed, 342 insertions(+), 305 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-2 dated 2015-05-04 and 0.3-3 dated 2015-06-10
InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/computeDelta.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/edgeRetention.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/edgeSelection.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/hiddenICE.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/man/hiddenICE.Rd |only InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/DESCRIPTION | 10 +++--- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/MD5 | 15 +++------- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/NAMESPACE | 4 +- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/ICP.Rd | 5 +-- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/InvariantCausalPrediction-package.Rd | 2 - InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/hiddenICP.Rd | 5 ++- 11 files changed, 18 insertions(+), 23 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Automated C Code Generation for Use with the 'deSolve' and
'bvpSolve' Packages
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
Diff between cOde versions 0.1 dated 2015-03-09 and 0.2 dated 2015-06-10
DESCRIPTION | 14 - MD5 | 36 ++-- NAMESPACE | 3 R/cOde.R | 351 ++++++++++++++++++++++++++++++++++++--------- R/derivedEquations.R | 71 +++++---- R/symbolics.R | 63 +++++--- R/tools.R |only inst/code |only inst/examples/example1.R | 15 + inst/examples/example2_2.R |only inst/examples/example3.R | 2 inst/examples/example4.R | 2 inst/examples/example5.R | 2 man/adjointSymb.Rd | 2 man/bvptwpC.Rd | 2 man/cOde-package.Rd | 2 man/funC.Rd | 42 ++++- man/loadDLL.Rd | 2 man/odeC.Rd | 15 + man/reduceSensitivities.Rd |only man/sensitivitiesSymb.Rd | 8 - 21 files changed, 472 insertions(+), 160 deletions(-)
Title: Posterior Predictive Checks of Coalescent Models
Description: Conducts posterior predictive checks of coalescent models using gene and species trees generated by 'BEAST' or '*BEAST'. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites: 'genealogicalSorting' and 'phybase'. To use these optional packages, the installation of the Python libraries 'NumPy' (>= 1.9.0) and 'DendroPy' (= 3.12.0) is required.
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl <mi.gruenstaeudl@gmail.com>
Diff between P2C2M versions 0.6 dated 2015-01-30 and 0.7.6 dated 2015-06-10
P2C2M-0.6/P2C2M/R/calc.coal_liu.R |only P2C2M-0.6/P2C2M/R/calc.coal_reid.R |only P2C2M-0.6/P2C2M/R/corehelpers.repl.R |only P2C2M-0.6/P2C2M/R/loghelpers.dbg.R |only P2C2M-0.6/P2C2M/R/loghelpers.prnt1.R |only P2C2M-0.6/P2C2M/R/loghelpers.prnt2.R |only P2C2M-0.6/P2C2M/R/loghelpers.wrt1.R |only P2C2M-0.6/P2C2M/R/loghelpers.wrt2.R |only P2C2M-0.6/P2C2M/R/p2c2M.statcalc.R |only P2C2M-0.6/P2C2M/R/p2c2m.init.R |only P2C2M-0.6/P2C2M/R/readhelpers.constit.R |only P2C2M-0.6/P2C2M/R/readhelpers.extract.R |only P2C2M-0.6/P2C2M/R/readhelpers.meta.R |only P2C2M-0.6/P2C2M/R/readhelpers.parse.R |only P2C2M-0.6/P2C2M/R/stats.acrossGenes.R |only P2C2M-0.7.6/P2C2M/DESCRIPTION | 17 - P2C2M-0.7.6/P2C2M/MD5 | 84 ++--- P2C2M-0.7.6/P2C2M/R/P2C2M-internal.R | 2 P2C2M-0.7.6/P2C2M/R/calc.coal.R |only P2C2M-0.7.6/P2C2M/R/calc.gsi.R | 16 - P2C2M-0.7.6/P2C2M/R/calc.lcwt.R |only P2C2M-0.7.6/P2C2M/R/calc.ndc.R | 8 P2C2M-0.7.6/P2C2M/R/calc.parse.R | 39 +- P2C2M-0.7.6/P2C2M/R/calchelpers.brprob.R | 10 P2C2M-0.7.6/P2C2M/R/calchelpers.descend.R | 14 P2C2M-0.7.6/P2C2M/R/calchelpers.dmvparse.R | 43 +- P2C2M-0.7.6/P2C2M/R/calchelpers.gtreeparse.R | 10 P2C2M-0.7.6/P2C2M/R/calchelpers.nodetips.R | 34 +- P2C2M-0.7.6/P2C2M/R/calchelpers.probcalc.R | 12 P2C2M-0.7.6/P2C2M/R/corehelpers.metrics.R | 34 +- P2C2M-0.7.6/P2C2M/R/loghelpers.prntmngr.R |only P2C2M-0.7.6/P2C2M/R/ms.exec.R | 86 ++--- P2C2M-0.7.6/P2C2M/R/p2c2m.analyze.R | 285 ++++++++++-------- P2C2M-0.7.6/P2C2M/R/p2c2m.complete.R | 115 +++---- P2C2M-0.7.6/P2C2M/R/p2c2m.readstarb.R | 187 +++++------ P2C2M-0.7.6/P2C2M/R/readhelpers.extract_br_and_meta.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.formatmeta.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.makeCFtable.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.parsetrees.R |only P2C2M-0.7.6/P2C2M/R/readtree.gtree.R | 80 +++-- P2C2M-0.7.6/P2C2M/R/readtree.phybase.R | 18 - P2C2M-0.7.6/P2C2M/R/readtree.stree.R | 113 ++++--- P2C2M-0.7.6/P2C2M/R/sourceDir.R | 2 P2C2M-0.7.6/P2C2M/R/stats.acrGenes.R |only P2C2M-0.7.6/P2C2M/R/stats.coord.R |only P2C2M-0.7.6/P2C2M/R/stats.main.R | 97 ++---- P2C2M-0.7.6/P2C2M/R/stats.perGene.R | 15 P2C2M-0.7.6/P2C2M/R/statshelpers.cv.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.diffrnce.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.qntls.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.sigsgn.R | 6 P2C2M-0.7.6/P2C2M/build/vignette.rds |binary P2C2M-0.7.6/P2C2M/exec/parseBEAUTiXML_1.8.py | 110 ++---- P2C2M-0.7.6/P2C2M/inst/doc/P2C2M_CmdList.pdf |binary P2C2M-0.7.6/P2C2M/man/p2c2m.complete.Rd | 30 + 55 files changed, 758 insertions(+), 727 deletions(-)
Title: Structural Equation Models
Description: Functions for fitting general linear structural
equation models (with observed and latent variables) using the RAM approach,
and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre],
Zhenghua Nie [aut],
Jarrett Byrnes [aut],
Michael Culbertson [ctb],
Saikat DebRoy [ctb],
Michael Friendly [ctb],
Goodrich Benjamin [ctb],
Richard H. Jones [ctb],
Adam Kramer [ctb],
Georges Monette [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between sem versions 3.1-5 dated 2014-08-03 and 3.1-6 dated 2015-06-10
sem-3.1-5/sem/data/Klein.txt.bz2 |only sem-3.1-6/sem/DESCRIPTION | 29 -- sem-3.1-6/sem/MD5 | 46 +-- sem-3.1-6/sem/NAMESPACE | 9 sem-3.1-6/sem/NEWS | 10 sem-3.1-6/sem/R/bootSem.R | 37 +- sem-3.1-6/sem/R/cfa.R |only sem-3.1-6/sem/R/miSem.R | 94 +++--- sem-3.1-6/sem/R/modIndices.R | 95 ------ sem-3.1-6/sem/R/pathDiagram.R | 457 ++++++++++++++++++++++++-------- sem-3.1-6/sem/R/readMoments.R | 6 sem-3.1-6/sem/R/robust.R | 2 sem-3.1-6/sem/R/specifyModel.R | 79 ----- sem-3.1-6/sem/R/update.R | 9 sem-3.1-6/sem/data/Bollen.rda |binary sem-3.1-6/sem/data/CNES.rda |binary sem-3.1-6/sem/data/Klein.txt.gz |only sem-3.1-6/sem/data/Kmenta.txt.gz |binary sem-3.1-6/sem/data/Tests.rda |binary sem-3.1-6/sem/inst/etc/GreekLetters.txt |only sem-3.1-6/sem/man/bootSem.Rd | 21 - sem-3.1-6/sem/man/miSem.Rd | 42 +- sem-3.1-6/sem/man/pathDiagram.Rd | 243 +++++++++++++---- sem-3.1-6/sem/man/readMoments.Rd | 28 + sem-3.1-6/sem/man/sem.Rd | 40 ++ sem-3.1-6/sem/man/specifyModel.Rd | 116 +++++++- 26 files changed, 912 insertions(+), 451 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Based on (optionally sparse) quadratic optimization with the main algorithms implemented in C. Includes features for easy processing of many (smaller) records. The algorithm has been tested on fairly large optimization problems with up to a few million variables and several hundred thousand restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.1-6 dated 2014-11-26 and 0.1-7 dated 2015-06-10
DESCRIPTION | 21 ++++++++++----------- MD5 | 24 ++++++++++++++---------- NAMESPACE | 2 +- NEWS | 7 +++++-- build |only inst/doc |only man/adjust.Rd | 5 +++-- man/adjustRecords.Rd | 3 ++- man/adjusted.Rd | 3 ++- man/adjustedRecords.Rd | 3 ++- man/rspa-package.Rd | 3 ++- man/sparseConstraints.Rd | 9 +++++---- vignettes/getting_started.Rnw | 20 +++++++------------- 13 files changed, 53 insertions(+), 47 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extension to Rcmdr (R Commander) made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 2.0-3 dated 2015-06-09 and 2.0-4 dated 2015-06-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 15 ++++++++------- R/RcmdrPlugin.UCA.R | 6 ++++-- man/RcmdrPlugin.UCA-internal.Rd | 2 ++ man/RcmdrPlugin.UCA-package.Rd | 2 +- man/RcmdrPlugin.UCA.es-package.Rd | 2 +- 7 files changed, 25 insertions(+), 20 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Analise Multivariada (Brazilian Portuguese)
Description: Pacote para Analise Multivariada, que possui funcoes que executam Analise de Correspondencia Simples (CA) e Multipla (MCA), Analise de Componentes Principais (PCA), Analise de Multiplos Fatores (MFA) para dados Quantitativos, Qualitativos, Frequencia (MFACT) e dados Mistos. Tambem possuim outras funcoes uteis para a Analise Multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.0 dated 2014-12-30 and 1.1 dated 2015-06-10
DESCRIPTION | 8 +++---- MD5 | 38 +++++++++++++++++----------------- R/MFA.R | 20 +++++++++--------- R/Plot.MFA.R | 4 +-- man/CA.Rd | 5 +--- man/DataFreq.Rd | 4 +-- man/DataMix.Rd | 1 man/DataQuali.Rd | 1 man/DataQuan.Rd | 3 -- man/Data_Cafes.Rd | 7 ++++-- man/Data_Individuos.Rd | 6 +++-- man/GSVD.Rd | 3 -- man/IM.Rd | 1 man/MFA.Rd | 37 +++++++++++++++++++-------------- man/MVar.pt-package.Rd | 54 +++++++++++++++++++++++++++++-------------------- man/NormData.Rd | 1 man/PCA.Rd | 5 +--- man/Plot.CA.Rd | 1 man/Plot.MFA.Rd | 1 man/Plot.PCA.Rd | 1 20 files changed, 105 insertions(+), 96 deletions(-)
Title: Pretty Scientific Plotting with Minor-Tick and log Minor-Tick
Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between magicaxis versions 1.9.3 dated 2014-09-29 and 1.9.4 dated 2015-06-10
DESCRIPTION | 14 +++++----- MD5 | 28 ++++++++++----------- NEWS | 30 +++++++++++++++++----- R/magaxis.R | 19 +++++++++----- R/magbar.R | 3 +- R/magcon.R | 3 +- R/magerr.R | 57 +++++++++++++++++++++++++++++++------------ R/magmap.R | 32 ++++++++++++++++++++---- R/magplot.R | 17 +++--------- R/magrun.R | 3 +- man/magaxis.Rd | 26 +++++++++++-------- man/magicaxis-package.Rd | 12 ++++----- man/maglab.Rd | 8 +++--- man/magmap.Rd | 33 ++++++++++++++++++++++--- man/magplot.Rd | 62 +++++++++++++++++++++++++++++------------------ 15 files changed, 228 insertions(+), 119 deletions(-)
Title: Generalized Mann-Whitney Type Tests
Description: Generalized Mann-Whitney type tests based on probabilistic
indices and new diagnostic plots.
Author: Daniel Fischer , Hannu Oja
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between gMWT versions 0.9 dated 2014-08-06 and 1.0 dated 2015-06-10
DESCRIPTION | 13 ++++++------- MD5 | 13 +++++++------ NAMESPACE | 2 +- inst/CITATION |only inst/ChangeLog | 8 ++++++++ man/gMWT-package.Rd | 10 +++++----- man/gmw.Rd | 2 +- src/helpFunctions.cpp | 28 ++++++++++++++++++++++------ 8 files changed, 50 insertions(+), 26 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.1.0 dated 2015-03-26 and 0.1.5.2 dated 2015-06-10
ggExtra-0.1.0/ggExtra/vignettes/overview.md |only ggExtra-0.1.5.2/ggExtra/DESCRIPTION | 16 +- ggExtra-0.1.5.2/ggExtra/MD5 | 32 +++-- ggExtra-0.1.5.2/ggExtra/NAMESPACE | 3 ggExtra-0.1.5.2/ggExtra/NEWS.md |only ggExtra-0.1.5.2/ggExtra/R/ggExtra.R | 7 + ggExtra-0.1.5.2/ggExtra/R/ggMarginal.R | 138 ++++++++++++++++++----- ggExtra-0.1.5.2/ggExtra/R/runExample.R |only ggExtra-0.1.5.2/ggExtra/README.md | 98 +++++++++------- ggExtra-0.1.5.2/ggExtra/inst/examples |only ggExtra-0.1.5.2/ggExtra/man/ggExtra.Rd | 10 + ggExtra-0.1.5.2/ggExtra/man/ggMarginal.Rd | 36 ++++-- ggExtra-0.1.5.2/ggExtra/man/plotCount.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/print.ggExtraPlot.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/removeGrid.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/rotateTextX.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/runExample.Rd |only ggExtra-0.1.5.2/ggExtra/vignettes/overview.Rmd | 53 ++++---- 18 files changed, 275 insertions(+), 126 deletions(-)
Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite. 'Domino' is a service that makes it easy to run your code on scalable hardware, with integrated version control and collaboration features designed for analytical workflows (see <http://www.dominoup.com> for more information).
Author: Jacek Glodek <jacek@theiterators.com>
Maintainer: Nick Elprin <nick@dominoup.com>
Diff between domino versions 0.2-6 dated 2015-04-15 and 0.2-7 dated 2015-06-10
DESCRIPTION | 10 ++++---- MD5 | 8 +++---- R/domino.R | 56 ++++++++++++++++++++++++++++++++------------------ man/domino-package.Rd | 4 +-- man/domino.run.Rd | 6 ++++- 5 files changed, 52 insertions(+), 32 deletions(-)
Title: Get Energy Data from the UK Dept of Energy and Climate Change
Description: Provides functions for retrieving energy statistics from
the United Kingdom Department of Energy and Climate Change and
related data sources. The current version focuses on total final
energy consumption statistics at the local authority, MSOA, and
LSOA geographies. Methods for calculating the generation mix of
grid electricity and its associated carbon intensity are also
provided.
Author: James Keirstead <j.keirstead@imperial.ac.uk>
Maintainer: James Keirstead <j.keirstead@imperial.ac.uk>
Diff between decctools versions 0.2.0 dated 2014-08-04 and 0.2.1 dated 2015-06-10
DESCRIPTION | 28 +++++---- MD5 | 22 +++---- NEWS | 11 +++ R/carbon-intensity.r | 138 +++++++++++++++++++++++++++---------------------- R/lad.r | 5 + R/utils.r | 10 +-- README.md | 8 +- inst/CITATION | 20 +++---- man/get_geo_lookup.Rd | 4 - man/get_grid_carbon.Rd | 2 man/get_grid_mix.Rd | 2 man/get_last_date.Rd | 4 + 12 files changed, 145 insertions(+), 109 deletions(-)
Title: Collection of Common Astronomical Conversion Routines and
Functions
Description: Contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between celestial versions 1.2 dated 2015-01-10 and 1.3 dated 2015-06-10
DESCRIPTION | 17 +- MD5 | 54 ++++-- NAMESPACE | 1 NEWS | 10 + R/IAUID.R | 2 R/coordmatch.R |only R/cosdist.R | 377 +++++++++++++++++++++++++++++++++++++++++++---- R/cosgrow.R |only R/coshalo.R |only R/cosmap.R |only R/cosorb.R |only R/cosvar.R |only R/cosvol.R | 16 + R/deg2dms.R | 9 - R/deg2hms.R | 9 - R/dms2deg.R | 12 - R/hms2deg.R | 13 + R/skyarea.R | 5 R/sph2car.R |only data |only man/IAUID.Rd | 6 man/celestial-package.Rd | 13 - man/coordmatch.Rd |only man/cosdist.Rd | 140 +++++++++++++---- man/cosgrow.Rd |only man/coshalo.Rd |only man/cosmap.Rd |only man/cosorb.Rd |only man/cosref.Rd |only man/cosvar.Rd |only man/cosvol.Rd | 30 ++- man/deg2dms.Rd | 5 man/deg2hms.Rd | 13 - man/hms2deg.Rd | 8 man/skyarea.Rd | 21 +- man/sph2car.Rd |only 36 files changed, 611 insertions(+), 150 deletions(-)
Title: Process the Apache Web Server Log Combined Files
Description: Provides a function to process Apache Log Combined files. The main functionality is to extract data from log files to data frames.
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>
Diff between ApacheLogProcessor versions 0.1.3 dated 2015-05-28 and 0.1.5 dated 2015-06-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ApacheLogProcessor.R | 17 +++++++++++++++++ 3 files changed, 23 insertions(+), 6 deletions(-)
More information about ApacheLogProcessor at CRAN
Permanent link
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.0 dated 2015-05-05 and 0.3.2 dated 2015-06-10
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++++--------------- NAMESPACE | 3 +++ R/domain.R | 6 +++--- R/linpoormed.R | 5 +---- R/linqsr.R | 1 + R/linrmpg.R | 5 +---- R/vardchanges.R | 2 +- R/vardchangespoor.R |only R/vardcros.R | 15 +++++++-------- R/vardcrospoor.R |only R/varpoord.R | 9 +++++---- inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/vardchanges.Rd | 3 ++- man/vardchangespoor.Rd |only man/vardcros.Rd | 2 +- man/vardcrospoor.Rd |only man/vardpoor-package.Rd | 11 +++++++++-- man/varpoord.Rd | 4 ++-- 20 files changed, 65 insertions(+), 51 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 3.9 dated 2015-05-21 and 4.2 dated 2015-06-10
ChangeLog | 12 + DESCRIPTION | 8 - MD5 | 8 - R/seqminer.R | 6 src/rvMetaLoader.cpp | 382 +++++++++++++++++++++++++++++++++++++++------------ 5 files changed, 323 insertions(+), 93 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 0.1-1 dated 2015-06-09 and 0.1-2 dated 2015-06-10
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- README.md | 12 ++++++------ inst/NEWS.Rd | 10 ++++++++++ man/Pade-package.Rd | 4 ++-- man/Pade.Rd | 22 +++++++++++----------- 6 files changed, 40 insertions(+), 30 deletions(-)
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Lutz Duembgen <duembgen@stat.unibe.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between logcondens versions 2.1.2 dated 2014-09-06 and 2.1.3 dated 2015-06-10
DESCRIPTION | 10 ++--- MD5 | 74 +++++++++++++++++++-------------------- NAMESPACE | 5 ++ NEWS | 4 ++ inst/doc/logcondens.pdf |binary man/Jfunctions.Rd | 2 - man/Lhat_eta.Rd | 2 - man/Local_LL.Rd | 2 - man/Local_LL_all.Rd | 2 - man/MLE.Rd | 2 - man/Q00.Rd | 2 - man/activeSetLogCon.Rd | 2 - man/activeSetRoutines.Rd | 2 - man/brightstar.Rd | 5 +- man/confIntBootLogConROC_t0.Rd | 2 - man/evaluateLogConDens.Rd | 2 - man/icmaLogCon.Rd | 4 +- man/intECDF.Rd | 4 +- man/intF.Rd | 4 +- man/isoMean.Rd | 2 - man/logConDens.Rd | 2 - man/logconTwoSample.Rd | 2 - man/logcondens-package.Rd | 10 ++--- man/maxDiffCDF.Rd | 2 - man/plot.dlc.Rd | 2 - man/preProcess.Rd | 2 - man/qloglin.Rd | 2 - man/quadDeriv.Rd | 2 - man/quantilesLogConDens.Rd | 2 - man/reparametrizations.Rd | 2 - man/rlogcon.Rd | 2 - man/robust.Rd | 4 +- man/summary.dlc.Rd | 2 - vignettes/plots/-plot1.pdf |binary vignettes/plots/-plot2.pdf |binary vignettes/plots/-plot2sample.pdf |binary vignettes/plots/-plotSimul.pdf |binary vignettes/plots/-sim1.pdf |binary 38 files changed, 87 insertions(+), 81 deletions(-)
Title: Bayesian Accrual Prediction
Description: Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. We developed a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. In this R package, we present functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.
Author: Yu Jiang, Cen Wu, Steve Simon, Matthew S. Mayo , Rama Raghavan, Byron J. Gajewski
Maintainer: Yu Jiang <yu.jiang@yale.edu>
Diff between accrual versions 1.0 dated 2014-02-24 and 1.1 dated 2015-06-10
DESCRIPTION | 16 +- MD5 | 18 +-- NAMESPACE | 1 R/accrual.R | 268 ++++++++++++++++++------------------------------- man/accrual-package.Rd | 12 +- man/accrual.T.Rd | 10 - man/accrual.T.plot.Rd |only man/accrual.gui.Rd | 2 man/accrual.n.Rd | 10 - man/accrual.n.plot.Rd |only man/accrual.plots.Rd | 2 11 files changed, 139 insertions(+), 200 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extension to Rcmdr (R Commander) made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 1.0-2 dated 2013-10-18 and 2.0-3 dated 2015-06-09
RcmdrPlugin.UCA-1.0-2/RcmdrPlugin.UCA/po/R-RcmdrPlugin.UCA-es.mo |only RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/ChangeLog | 6 RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/DESCRIPTION | 12 - RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/MD5 | 24 +- RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/NAMESPACE | 11 RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/R/RcmdrPlugin.UCA.R | 118 ++++------ RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/R/globals.R |only RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/inst/etc/menus.txt | 9 RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/inst/po/es/LC_MESSAGES/R-RcmdrPlugin.UCA.mo |binary RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/man/RcmdrPlugin.UCA-internal.Rd | 5 RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/man/RcmdrPlugin.UCA-package.Rd | 31 ++ RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/man/RcmdrPlugin.UCA.es-package.Rd | 30 ++ RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/po/R-RcmdrPlugin.UCA-es.po | 28 +- RcmdrPlugin.UCA-2.0-3/RcmdrPlugin.UCA/po/R-RcmdrPlugin.UCA.pot | 19 + 14 files changed, 185 insertions(+), 108 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Node Harvest for Regression and Classification
Description: Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between nodeHarvest versions 0.7-1 dated 2015-05-15 and 0.7-2 dated 2015-06-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/getI.R | 2 +- R/getw.R | 27 +++++++++++++++++++++++++++ R/nodeHarvest.R | 8 +++++++- 5 files changed, 43 insertions(+), 10 deletions(-)
Title: Maximum Entropy Bootstrap for Time Series
Description: This package performs maximum entropy density based
dependent data bootstrap. An algorithm is provided to create a
population of time series (ensemble) without assuming
stationarity. The reference paper (Vinod, H.D., 2004) explains
how the algorithm satisfies the ergodic theorem and the central
limit theorem.
Author: Hrishikesh D. Vinod <Vinod@fordham.edu> and Javier
López-de-Lacalle
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>
Diff between meboot versions 1.4-5 dated 2014-09-28 and 1.4-6 dated 2015-06-09
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- inst/doc/index.html |only inst/doc/meboot.pdf |binary 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Spatial Stochastic Frontier Analysis
Description: Spatial Stochastic Frontier Analysis (SSFA) is an original method for controlling the spatial heterogeneity in Stochastic Frontier Analysis (SFA) models, for cross-sectional data, by splitting the inefficiency term into three terms: the first one related to spatial peculiarities of the territory in which each single unit operates, the second one related to the specific production features and the third one representing the error term.
Author: Elisa Fusco, Francesco Vidoli
Maintainer: Elisa Fusco <fusco_elisa@libero.it>
Diff between ssfa versions 1.0 dated 2015-05-17 and 1.1 dated 2015-06-09
DESCRIPTION | 12 +++++++----- MD5 | 13 +++++++++++-- NEWS |only build |only inst |only man/ssfa-package.Rd | 6 +++--- vignettes |only 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Infrastructure for Seriation
Description: Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.0-14 dated 2014-12-03 and 1.1-0 dated 2015-06-09
seriation-1.0-14/seriation/R/AAAdefs.R |only seriation-1.0-14/seriation/R/grid.R |only seriation-1.0-14/seriation/R/map.R |only seriation-1.0-14/seriation/R/seriate.hclust.R |only seriation-1.0-14/seriation/inst/tests/criterion.R |only seriation-1.0-14/seriation/inst/tests/permuation_vector.R |only seriation-1.1-0/seriation/DESCRIPTION | 22 seriation-1.1-0/seriation/MD5 | 131 - seriation-1.1-0/seriation/NAMESPACE | 30 seriation-1.1-0/seriation/R/AAAcolors.R |only seriation-1.1-0/seriation/R/AAAgrid.R |only seriation-1.1-0/seriation/R/AAAmap.R |only seriation-1.1-0/seriation/R/AAAparameter.R |only seriation-1.1-0/seriation/R/AAAregistry.R |only seriation-1.1-0/seriation/R/VAT.R |only seriation-1.1-0/seriation/R/bertinplot.R | 293 +- seriation-1.1-0/seriation/R/criterion.R | 91 seriation-1.1-0/seriation/R/criterion.array.R | 4 seriation-1.1-0/seriation/R/criterion.dist.R | 144 - seriation-1.1-0/seriation/R/criterion.matrix.R | 2 seriation-1.1-0/seriation/R/data.R |only seriation-1.1-0/seriation/R/dissimilartiy.R |only seriation-1.1-0/seriation/R/dissplot.R | 1070 ++++------ seriation-1.1-0/seriation/R/hmap.R | 349 +-- seriation-1.1-0/seriation/R/permutation.R | 64 seriation-1.1-0/seriation/R/permutation_vector.R | 133 - seriation-1.1-0/seriation/R/permute.R | 129 - seriation-1.1-0/seriation/R/pimage.R | 165 - seriation-1.1-0/seriation/R/reorder.hclust.R |only seriation-1.1-0/seriation/R/seriate.R | 64 seriation-1.1-0/seriation/R/seriate.array.R | 38 seriation-1.1-0/seriation/R/seriate.dist.R | 686 ++++-- seriation-1.1-0/seriation/R/seriate.matrix.R | 210 + seriation-1.1-0/seriation/build/vignette.rds |binary seriation-1.1-0/seriation/data/Chameleon.rda |only seriation-1.1-0/seriation/data/Irish.rda |binary seriation-1.1-0/seriation/data/Munsingen.rda |binary seriation-1.1-0/seriation/data/Psych24.rda |binary seriation-1.1-0/seriation/data/Townships.rda |binary seriation-1.1-0/seriation/data/Wood.rda |only seriation-1.1-0/seriation/data/Zoo.rda |binary seriation-1.1-0/seriation/inst/NEWS | 48 seriation-1.1-0/seriation/inst/doc/seriation.R | 120 - seriation-1.1-0/seriation/inst/doc/seriation.Rnw | 129 - seriation-1.1-0/seriation/inst/doc/seriation.pdf |binary seriation-1.1-0/seriation/inst/tests/test-criterion.R |only seriation-1.1-0/seriation/inst/tests/test-permuation_vector.R |only seriation-1.1-0/seriation/inst/tests/test-seriate.R |only seriation-1.1-0/seriation/man/Chameleon.Rd |only seriation-1.1-0/seriation/man/Irish.Rd | 6 seriation-1.1-0/seriation/man/Psych24.Rd | 2 seriation-1.1-0/seriation/man/Townships.Rd | 9 seriation-1.1-0/seriation/man/VAT.Rd |only seriation-1.1-0/seriation/man/Wood.Rd |only seriation-1.1-0/seriation/man/Zoo.Rd | 8 seriation-1.1-0/seriation/man/bertinplot.Rd | 4 seriation-1.1-0/seriation/man/col.Rd |only seriation-1.1-0/seriation/man/criterion.Rd | 93 seriation-1.1-0/seriation/man/criterion_methods.Rd | 17 seriation-1.1-0/seriation/man/data.Rd |only seriation-1.1-0/seriation/man/dissimilarity.Rd |only seriation-1.1-0/seriation/man/dissplot.Rd | 91 seriation-1.1-0/seriation/man/get_order.Rd | 25 seriation-1.1-0/seriation/man/hmap.Rd | 107 - seriation-1.1-0/seriation/man/permutation.Rd | 22 seriation-1.1-0/seriation/man/permutation_matrix.Rd |only seriation-1.1-0/seriation/man/permutation_vector.Rd | 27 seriation-1.1-0/seriation/man/permute.Rd | 24 seriation-1.1-0/seriation/man/pimage.Rd | 117 - seriation-1.1-0/seriation/man/reorder_hclust.Rd |only seriation-1.1-0/seriation/man/seriate.Rd | 204 + seriation-1.1-0/seriation/man/seriation_methods.Rd | 11 seriation-1.1-0/seriation/src/RNG_wrapper.c | 8 seriation-1.1-0/seriation/src/bburcg.f | 9 seriation-1.1-0/seriation/src/bbwrcg.f | 13 seriation-1.1-0/seriation/src/criterion.c | 89 seriation-1.1-0/seriation/src/dist.c | 9 seriation-1.1-0/seriation/src/lt.h | 16 seriation-1.1-0/seriation/src/pathdist.c |only seriation-1.1-0/seriation/vignettes/seriation.Rnw | 129 - seriation-1.1-0/seriation/vignettes/seriation.bib | 8 81 files changed, 2889 insertions(+), 2081 deletions(-)
Title: Unified Interface to Parallelization Back-Ends
Description: Unified parallelization framework for multiple back-end,
designed for internal package and interactive usage.
The main operation is a parallel "map" over lists.
Supports local, multicore, mpi and BatchJobs mode.
Allows "tagging" of the parallel operation
with a level name that can be later selected by the user to
switch on parallel execution for exactly this operation.
Author: Bernd Bischl <bernd_bischl@gmx.net>, Michel Lang
<michellang@gmail.com>
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between parallelMap versions 1.2 dated 2015-02-03 and 1.3 dated 2015-06-09
parallelMap-1.2/parallelMap/man/parallelShowOptions.Rd |only parallelMap-1.2/parallelMap/tests/testthat/test_parallelShowOptions.R |only parallelMap-1.3/parallelMap/DESCRIPTION | 18 ++-- parallelMap-1.3/parallelMap/LICENSE | 3 parallelMap-1.3/parallelMap/MD5 | 43 +++++----- parallelMap-1.3/parallelMap/NAMESPACE | 5 - parallelMap-1.3/parallelMap/NEWS | 4 parallelMap-1.3/parallelMap/R/parallelRegisterLevels.R | 25 ++++- parallelMap-1.3/parallelMap/R/parallelShowOptions.R | 26 ++++-- parallelMap-1.3/parallelMap/R/parallelStart.R | 16 ++- parallelMap-1.3/parallelMap/man/parallelExport.Rd | 2 parallelMap-1.3/parallelMap/man/parallelGetOptions.Rd |only parallelMap-1.3/parallelMap/man/parallelGetRegisteredLevels.Rd | 14 ++- parallelMap-1.3/parallelMap/man/parallelLapply.Rd | 2 parallelMap-1.3/parallelMap/man/parallelLibrary.Rd | 2 parallelMap-1.3/parallelMap/man/parallelMap.Rd | 2 parallelMap-1.3/parallelMap/man/parallelRegisterLevels.Rd | 10 +- parallelMap-1.3/parallelMap/man/parallelSource.Rd | 2 parallelMap-1.3/parallelMap/man/parallelStart.Rd | 7 - parallelMap-1.3/parallelMap/man/parallelStop.Rd | 2 parallelMap-1.3/parallelMap/tests/testthat/helpers.R | 10 +- parallelMap-1.3/parallelMap/tests/testthat/test_multicore.R | 5 - parallelMap-1.3/parallelMap/tests/testthat/test_parallelGetOptions.R |only parallelMap-1.3/parallelMap/tests/testthat/test_parallelStart.R |only parallelMap-1.3/parallelMap/tests/testthat/test_registerLevels.R | 3 25 files changed, 126 insertions(+), 75 deletions(-)
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
Author: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Maintainer: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Diff between tis versions 1.27 dated 2014-10-18 and 1.30 dated 2015-06-09
DESCRIPTION | 7 +- MD5 | 28 +++++------ NAMESPACE | 4 + NEWS | 20 ++++++++ R/barplot.tis.R | 2 R/constantGrowthSeries.R | 2 R/screenPage.R | 2 R/ti.R | 12 ++--- R/tier.R | 2 R/tis.R | 110 ++++++++++++++++++++++------------------------- R/tisFromCsv.R | 12 ++++- R/tisPlot.R | 34 +++++++------- man/aggregate.tis.Rd | 57 +++++++----------------- man/mergeSeries.Rd | 13 +++-- man/tisFromCsv.Rd | 11 ++++ 15 files changed, 167 insertions(+), 149 deletions(-)
Title: Tools for Modeling Data with Functional Programming
Description: Provides tools that manipulate and transform data using methods
and techniques consistent with functional programming. The idea is that
through the use of these tools, a program can be reasoned about insomuch
that the implementation can be proven to be equivalent to the mathematical
model.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between lambda.tools versions 1.0.6 dated 2015-03-21 and 1.0.7 dated 2015-06-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fold.R | 10 ++++++++-- R/lambda.tools-package.R | 4 ++-- man/lambda.tools-package.Rd | 4 ++-- tests/run_tests.R | 2 +- 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Discriminant Non-Negative Matrix Factorization
Description: Discriminant Non-Negative Matrix Factorization aims to extend the Non-negative Matrix Factorization algorithm in order to extract features that enforce not only the spatial locality, but also the separability between classes in a discriminant manner. It refers to three article, Zafeiriou, Stefanos, et al. "Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification." Neural Networks, IEEE Transactions on 17.3 (2006): 683-695. Kim, Bo-Kyeong, and Soo-Young Lee. "Spectral Feature Extraction Using dNMF for Emotion Recognition in Vowel Sounds." Neural Information Processing. Springer Berlin Heidelberg, 2013. and Lee, Soo-Young, Hyun-Ah Song, and Shun-ichi Amari. "A new discriminant NMF algorithm and its application to the extraction of subtle emotional differences in speech." Cognitive neurodynamics 6.6 (2012): 525-535.
Author: Zhilong Jia [aut, cre],
Xiang Zhang [aut]
Maintainer: Zhilong Jia <zhilongjia@gmail.com>
Diff between DNMF versions 1.0 dated 2015-02-16 and 1.3 dated 2015-06-09
DESCRIPTION | 20 +++++++++++++------- MD5 | 17 +++++++++++------ NAMESPACE | 9 ++++++++- NEWS.md |only R/DNMF.R | 53 +++++++++++++++++++++++++++++++++++++++++------------ R/NMFpval.R |only R/ndNMF.R |only R/rnk.R | 34 ++++++++++++++++++++++++++-------- man/DNMF.Rd | 43 +++++++++++++++++++++++++++++++++---------- man/NMFpval.Rd |only man/ndNMF.Rd |only man/rnk.Rd | 15 +++++++++------ 12 files changed, 141 insertions(+), 50 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.4 dated 2015-05-05 and 3.5.4 dated 2015-06-09
Deriv-3.4/Deriv/tests/testthat/test_Deriv.R.bck |only Deriv-3.4/Deriv/tests/testthat/test_Simplify.R.bck |only Deriv-3.5.4/Deriv/DESCRIPTION | 10 Deriv-3.5.4/Deriv/MD5 | 28 - Deriv-3.5.4/Deriv/NAMESPACE | 2 Deriv-3.5.4/Deriv/NEWS | 43 ++ Deriv-3.5.4/Deriv/R/Deriv.R | 237 ++++++++----- Deriv-3.5.4/Deriv/R/Simplify.R | 356 ++++++++++++++------- Deriv-3.5.4/Deriv/README.md | 2 Deriv-3.5.4/Deriv/inst/CITATION | 4 Deriv-3.5.4/Deriv/man/Deriv-package.Rd | 23 - Deriv-3.5.4/Deriv/man/Deriv.Rd | 15 Deriv-3.5.4/Deriv/man/Simplify.Rd | 11 Deriv-3.5.4/Deriv/man/format1.Rd | 3 Deriv-3.5.4/Deriv/tests/testthat/test_Deriv.R | 87 ++++- Deriv-3.5.4/Deriv/tests/testthat/test_Simplify.R | 26 + 16 files changed, 588 insertions(+), 259 deletions(-)
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.4.0 dated 2015-01-06 and 1.5.0 dated 2015-06-09
strvalidator-1.4.0/strvalidator/R/loadPackage.r |only strvalidator-1.4.0/strvalidator/man/loadPackage.Rd |only strvalidator-1.5.0/strvalidator/DESCRIPTION | 26 strvalidator-1.5.0/strvalidator/MD5 | 410 +++++----- strvalidator-1.5.0/strvalidator/NAMESPACE | 9 strvalidator-1.5.0/strvalidator/NEWS | 48 + strvalidator-1.5.0/strvalidator/R/addColor.r | 6 strvalidator-1.5.0/strvalidator/R/addData.r | 13 strvalidator-1.5.0/strvalidator/R/addData_gui.r | 9 strvalidator-1.5.0/strvalidator/R/addDye_gui.r | 4 strvalidator-1.5.0/strvalidator/R/addMarker.r | 4 strvalidator-1.5.0/strvalidator/R/addMarker_gui.r | 4 strvalidator-1.5.0/strvalidator/R/addSize.r | 4 strvalidator-1.5.0/strvalidator/R/addSize_gui.r | 4 strvalidator-1.5.0/strvalidator/R/blockAT.r |only strvalidator-1.5.0/strvalidator/R/calculateAT.r |only strvalidator-1.5.0/strvalidator/R/calculateAT6.r |only strvalidator-1.5.0/strvalidator/R/calculateAT6_gui.r |only strvalidator-1.5.0/strvalidator/R/calculateAT_gui.r |only strvalidator-1.5.0/strvalidator/R/calculateBalance.r | 9 strvalidator-1.5.0/strvalidator/R/calculateBalance_gui.r | 42 - strvalidator-1.5.0/strvalidator/R/calculateCapillary.r | 4 strvalidator-1.5.0/strvalidator/R/calculateCapillary_gui.r | 5 strvalidator-1.5.0/strvalidator/R/calculateConcordance.r | 4 strvalidator-1.5.0/strvalidator/R/calculateConcordance_gui.r | 3 strvalidator-1.5.0/strvalidator/R/calculateDropout.r | 5 strvalidator-1.5.0/strvalidator/R/calculateDropout_gui.r | 8 strvalidator-1.5.0/strvalidator/R/calculateHeight.r | 4 strvalidator-1.5.0/strvalidator/R/calculateHeight_gui.r | 5 strvalidator-1.5.0/strvalidator/R/calculateHeterozygous.r | 4 strvalidator-1.5.0/strvalidator/R/calculateHeterozygous_gui.r | 6 strvalidator-1.5.0/strvalidator/R/calculateMixture.r | 4 strvalidator-1.5.0/strvalidator/R/calculateMixture_gui.r | 8 strvalidator-1.5.0/strvalidator/R/calculateOL.r | 4 strvalidator-1.5.0/strvalidator/R/calculateOL_gui.r | 5 strvalidator-1.5.0/strvalidator/R/calculateOverlap.r | 4 strvalidator-1.5.0/strvalidator/R/calculateOverlap_gui.r | 5 strvalidator-1.5.0/strvalidator/R/calculatePeaks.r | 7 strvalidator-1.5.0/strvalidator/R/calculatePeaks_gui.r | 5 strvalidator-1.5.0/strvalidator/R/calculatePullup.r | 15 strvalidator-1.5.0/strvalidator/R/calculatePullup_gui.r | 11 strvalidator-1.5.0/strvalidator/R/calculateResultType.r | 4 strvalidator-1.5.0/strvalidator/R/calculateResultType_gui.r | 6 strvalidator-1.5.0/strvalidator/R/calculateStutter.r | 4 strvalidator-1.5.0/strvalidator/R/calculateStutter_gui.r | 8 strvalidator-1.5.0/strvalidator/R/checkDataset.r | 59 - strvalidator-1.5.0/strvalidator/R/checkSubset.r | 51 - strvalidator-1.5.0/strvalidator/R/checkSubset_gui.r | 8 strvalidator-1.5.0/strvalidator/R/colNames.r | 80 + strvalidator-1.5.0/strvalidator/R/columns.r |only strvalidator-1.5.0/strvalidator/R/columns_gui.r |only strvalidator-1.5.0/strvalidator/R/combineBinsAndPanels.r | 9 strvalidator-1.5.0/strvalidator/R/combine_gui.r | 4 strvalidator-1.5.0/strvalidator/R/compact.r | 4 strvalidator-1.5.0/strvalidator/R/cropData_gui.r | 5 strvalidator-1.5.0/strvalidator/R/detectKit.r | 4 strvalidator-1.5.0/strvalidator/R/editData_gui.r | 40 strvalidator-1.5.0/strvalidator/R/export.r | 2 strvalidator-1.5.0/strvalidator/R/export_gui.r | 4 strvalidator-1.5.0/strvalidator/R/filterProfile.r | 35 strvalidator-1.5.0/strvalidator/R/filterProfile_gui.r | 28 strvalidator-1.5.0/strvalidator/R/generateEPG.r | 12 strvalidator-1.5.0/strvalidator/R/generateEPG_gui.r | 8 strvalidator-1.5.0/strvalidator/R/getDb.r | 4 strvalidator-1.5.0/strvalidator/R/getKit.r | 4 strvalidator-1.5.0/strvalidator/R/ggsave_gui.r | 4 strvalidator-1.5.0/strvalidator/R/globals.R | 6 strvalidator-1.5.0/strvalidator/R/guessProfile.r | 2 strvalidator-1.5.0/strvalidator/R/guessProfile_gui.r | 4 strvalidator-1.5.0/strvalidator/R/heightToPeak.r | 6 strvalidator-1.5.0/strvalidator/R/import.r | 195 +++- strvalidator-1.5.0/strvalidator/R/import_gui.r | 330 ++++++-- strvalidator-1.5.0/strvalidator/R/listObjects.r | 4 strvalidator-1.5.0/strvalidator/R/makeKit_gui.r | 4 strvalidator-1.5.0/strvalidator/R/modelDropout_gui.r | 9 strvalidator-1.5.0/strvalidator/R/plotAT_gui.r |only strvalidator-1.5.0/strvalidator/R/plotBalance_gui.r | 74 + strvalidator-1.5.0/strvalidator/R/plotCapillary_gui.r | 3 strvalidator-1.5.0/strvalidator/R/plotDistribution_gui.r | 130 ++- strvalidator-1.5.0/strvalidator/R/plotDropout_gui.r | 13 strvalidator-1.5.0/strvalidator/R/plotKit_gui.r | 4 strvalidator-1.5.0/strvalidator/R/plotPeaks_gui.r | 3 strvalidator-1.5.0/strvalidator/R/plotPrecision_gui.r | 2 strvalidator-1.5.0/strvalidator/R/plotPullup_gui.r | 8 strvalidator-1.5.0/strvalidator/R/plotResultType_gui.r | 3 strvalidator-1.5.0/strvalidator/R/plotStutter_gui.r | 2 strvalidator-1.5.0/strvalidator/R/readBinsFile.r | 2 strvalidator-1.5.0/strvalidator/R/readPanelsFile.r | 4 strvalidator-1.5.0/strvalidator/R/saveObject.r | 6 strvalidator-1.5.0/strvalidator/R/slim.r | 36 strvalidator-1.5.0/strvalidator/R/slim_gui.r | 34 strvalidator-1.5.0/strvalidator/R/sortMarker.r | 4 strvalidator-1.5.0/strvalidator/R/strvalidator-package.r | 4 strvalidator-1.5.0/strvalidator/R/strvalidator.r | 134 ++- strvalidator-1.5.0/strvalidator/R/tableBalance.r | 4 strvalidator-1.5.0/strvalidator/R/tableBalance_gui.r | 4 strvalidator-1.5.0/strvalidator/R/tableCapillary.r | 4 strvalidator-1.5.0/strvalidator/R/tableCapillary_gui.r | 2 strvalidator-1.5.0/strvalidator/R/tablePrecision.r | 4 strvalidator-1.5.0/strvalidator/R/tablePrecision_gui.r | 8 strvalidator-1.5.0/strvalidator/R/tableStutter.r | 4 strvalidator-1.5.0/strvalidator/R/tableStutter_gui.r | 2 strvalidator-1.5.0/strvalidator/R/trim.r | 95 ++ strvalidator-1.5.0/strvalidator/R/trim_gui.r | 122 +- strvalidator-1.5.0/strvalidator/man/addColor.Rd | 9 strvalidator-1.5.0/strvalidator/man/addData.Rd | 16 strvalidator-1.5.0/strvalidator/man/addData_gui.Rd | 11 strvalidator-1.5.0/strvalidator/man/addDye_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/addMarker.Rd | 7 strvalidator-1.5.0/strvalidator/man/addMarker_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/addSize.Rd | 7 strvalidator-1.5.0/strvalidator/man/addSize_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/blockAT.Rd |only strvalidator-1.5.0/strvalidator/man/calculateAT.Rd |only strvalidator-1.5.0/strvalidator/man/calculateAT6.Rd |only strvalidator-1.5.0/strvalidator/man/calculateAT6_gui.Rd |only strvalidator-1.5.0/strvalidator/man/calculateAT_gui.Rd |only strvalidator-1.5.0/strvalidator/man/calculateBalance.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateBalance_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/calculateCapillary.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateCapillary_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateConcordance.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateConcordance_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/calculateDropout.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateDropout_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateHeight.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateHeight_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateHeterozygous.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateHeterozygous_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateMixture.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateMixture_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateOL.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateOL_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculateOverlap.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateOverlap_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculatePeaks.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculatePeaks_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/calculatePullup.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculatePullup_gui.Rd | 10 strvalidator-1.5.0/strvalidator/man/calculateResultType.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateResultType_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/calculateStutter.Rd | 7 strvalidator-1.5.0/strvalidator/man/calculateStutter_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/checkDataset.Rd | 11 strvalidator-1.5.0/strvalidator/man/checkSubset.Rd | 11 strvalidator-1.5.0/strvalidator/man/checkSubset_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/colNames.Rd | 17 strvalidator-1.5.0/strvalidator/man/columns.Rd |only strvalidator-1.5.0/strvalidator/man/columns_gui.Rd |only strvalidator-1.5.0/strvalidator/man/combineBinsAndPanels.Rd | 7 strvalidator-1.5.0/strvalidator/man/combine_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/compact.Rd | 7 strvalidator-1.5.0/strvalidator/man/cropData_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/detectKit.Rd | 7 strvalidator-1.5.0/strvalidator/man/editData_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/export.Rd | 5 strvalidator-1.5.0/strvalidator/man/export_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/filterProfile.Rd | 23 strvalidator-1.5.0/strvalidator/man/filterProfile_gui.Rd | 11 strvalidator-1.5.0/strvalidator/man/generateEPG.Rd | 5 strvalidator-1.5.0/strvalidator/man/generateEPG_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/getDb.Rd | 7 strvalidator-1.5.0/strvalidator/man/getKit.Rd | 7 strvalidator-1.5.0/strvalidator/man/ggsave_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/guessProfile.Rd | 5 strvalidator-1.5.0/strvalidator/man/guessProfile_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/heightToPeak.Rd | 9 strvalidator-1.5.0/strvalidator/man/import.Rd | 48 + strvalidator-1.5.0/strvalidator/man/import_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/listObjects.Rd | 7 strvalidator-1.5.0/strvalidator/man/makeKit_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/modelDropout_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/plotAT_gui.Rd |only strvalidator-1.5.0/strvalidator/man/plotBalance_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/plotCapillary_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/plotDistribution_gui.Rd | 11 strvalidator-1.5.0/strvalidator/man/plotDropout_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/plotKit_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/plotPeaks_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/plotPrecision_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/plotPullup_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/plotResultType_gui.Rd | 6 strvalidator-1.5.0/strvalidator/man/plotStutter_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/readBinsFile.Rd | 5 strvalidator-1.5.0/strvalidator/man/readPanelsFile.Rd | 7 strvalidator-1.5.0/strvalidator/man/ref1.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref11.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref2.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref3.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref4.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref51.Rd | 3 strvalidator-1.5.0/strvalidator/man/ref52.Rd | 3 strvalidator-1.5.0/strvalidator/man/saveObject.Rd | 7 strvalidator-1.5.0/strvalidator/man/set1.Rd | 3 strvalidator-1.5.0/strvalidator/man/set2.Rd | 3 strvalidator-1.5.0/strvalidator/man/set3.Rd | 3 strvalidator-1.5.0/strvalidator/man/set4.Rd | 3 strvalidator-1.5.0/strvalidator/man/set5.Rd | 3 strvalidator-1.5.0/strvalidator/man/slim.Rd | 19 strvalidator-1.5.0/strvalidator/man/slim_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/sortMarker.Rd | 7 strvalidator-1.5.0/strvalidator/man/strValidator-package.Rd | 3 strvalidator-1.5.0/strvalidator/man/strvalidator.Rd | 12 strvalidator-1.5.0/strvalidator/man/tableBalance.Rd | 7 strvalidator-1.5.0/strvalidator/man/tableBalance_gui.Rd | 7 strvalidator-1.5.0/strvalidator/man/tableCapillary.Rd | 7 strvalidator-1.5.0/strvalidator/man/tableCapillary_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/tablePrecision.Rd | 7 strvalidator-1.5.0/strvalidator/man/tablePrecision_gui.Rd | 8 strvalidator-1.5.0/strvalidator/man/tableStutter.Rd | 7 strvalidator-1.5.0/strvalidator/man/tableStutter_gui.Rd | 5 strvalidator-1.5.0/strvalidator/man/trim.Rd | 23 strvalidator-1.5.0/strvalidator/man/trim_gui.Rd | 7 strvalidator-1.5.0/strvalidator/tests/testthat.R | 1 strvalidator-1.5.0/strvalidator/tests/testthat/test-filterProfile.r | 117 ++ 215 files changed, 2124 insertions(+), 1141 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with
bibliographic references. It greatly enhances the 'bibentry' class by
providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references,
supports 'UTF-8' encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files
can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez',
'CrossRef', and 'Zotero' are provided for importing references and
references can be created from locally stored 'PDF' files using 'Poppler'. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.8.45 dated 2015-01-09 and 0.8.63 dated 2015-06-09
RefManageR-0.8.45/RefManageR/inst/doc/TestAuthorYear.html |only RefManageR-0.8.45/RefManageR/inst/doc/TestNumeric.html |only RefManageR-0.8.45/RefManageR/inst/doc/figure |only RefManageR-0.8.45/RefManageR/man/format.Bibentry.Rd |only RefManageR-0.8.63/RefManageR/DESCRIPTION | 31 RefManageR-0.8.63/RefManageR/LICENSE | 4 RefManageR-0.8.63/RefManageR/MD5 | 178 RefManageR-0.8.63/RefManageR/R/02BibOptions.R | 314 RefManageR-0.8.63/RefManageR/R/03BibLaTeX_entry_field_db.R | 276 RefManageR-0.8.63/RefManageR/R/04InternalFunctions.R | 1769 +- RefManageR-0.8.63/RefManageR/R/05makeBibLatex.R | 2613 +-- RefManageR-0.8.63/RefManageR/R/06BibEntry.R | 358 RefManageR-0.8.63/RefManageR/R/07makeBibLatexAuthoryear.R | 2290 +- RefManageR-0.8.63/RefManageR/R/08asBibEntry.R | 224 RefManageR-0.8.63/RefManageR/R/09sort.R | 260 RefManageR-0.8.63/RefManageR/R/BibEntryAddOp.R | 256 RefManageR-0.8.63/RefManageR/R/BibEntryAssignOp.R | 142 RefManageR-0.8.63/RefManageR/R/BibEntryCombineOp.R | 58 RefManageR-0.8.63/RefManageR/R/BibEntryDollarExtract.R | 60 RefManageR-0.8.63/RefManageR/R/BibEntryExtractOp.R | 615 RefManageR-0.8.63/RefManageR/R/BibEntryListExtract.R | 88 RefManageR-0.8.63/RefManageR/R/BibEntryReplaceBibEntry.R | 66 RefManageR-0.8.63/RefManageR/R/BibEntryReplaceOp.R | 258 RefManageR-0.8.63/RefManageR/R/GetBibEntryWithDOI.R | 85 RefManageR-0.8.63/RefManageR/R/GetDOIs.R | 204 RefManageR-0.8.63/RefManageR/R/NamesAssign.R | 20 RefManageR-0.8.63/RefManageR/R/ReadBib.R | 90 RefManageR-0.8.63/RefManageR/R/ReadCrossRef.R | 209 RefManageR-0.8.63/RefManageR/R/ReadGS.R | 190 RefManageR-0.8.63/RefManageR/R/ReadPDFs.R | 350 RefManageR-0.8.63/RefManageR/R/ReadPDFsSupport.R | 1048 - RefManageR-0.8.63/RefManageR/R/ReadPubMed.R | 866 - RefManageR-0.8.63/RefManageR/R/ReadZotero.R | 226 RefManageR-0.8.63/RefManageR/R/RefManageR-package.R | 130 RefManageR-0.8.63/RefManageR/R/SearchBib.R | 48 RefManageR-0.8.63/RefManageR/R/UpdateFieldName.R | 48 RefManageR-0.8.63/RefManageR/R/WriteBib.R | 118 RefManageR-0.8.63/RefManageR/R/asdataframe.R | 86 RefManageR-0.8.63/RefManageR/R/format.R | 188 RefManageR-0.8.63/RefManageR/R/head.BibEntry.R | 122 RefManageR-0.8.63/RefManageR/R/levels.R | 58 RefManageR-0.8.63/RefManageR/R/names.R | 38 RefManageR-0.8.63/RefManageR/R/open.BibEntry.R | 155 RefManageR-0.8.63/RefManageR/R/print.R | 171 RefManageR-0.8.63/RefManageR/R/relist.R | 72 RefManageR-0.8.63/RefManageR/R/rmdCite.R | 785 RefManageR-0.8.63/RefManageR/R/toBiblatex.R | 162 RefManageR-0.8.63/RefManageR/R/toBibtex.R | 226 RefManageR-0.8.63/RefManageR/R/unlist.R | 62 RefManageR-0.8.63/RefManageR/README.md |only RefManageR-0.8.63/RefManageR/build/vignette.rds |binary RefManageR-0.8.63/RefManageR/inst/Bib/RJC.bib | 9500 +++++------ RefManageR-0.8.63/RefManageR/inst/Bib/badFormat.bib |only RefManageR-0.8.63/RefManageR/inst/Bib/biblatexExamples.bib | 3346 +-- RefManageR-0.8.63/RefManageR/inst/Bib/test.bib | 2104 +- RefManageR-0.8.63/RefManageR/inst/CITATION | 2 RefManageR-0.8.63/RefManageR/inst/NEWS | 277 RefManageR-0.8.63/RefManageR/inst/Rhtml/TestAuthorYear.Rhtml | 96 RefManageR-0.8.63/RefManageR/inst/Rhtml/TestHtml.Rhtml | 96 RefManageR-0.8.63/RefManageR/inst/Rmd/TestAlphabetic.Rmd | 62 RefManageR-0.8.63/RefManageR/inst/Rmd/TestNumeric.Rmd | 64 RefManageR-0.8.63/RefManageR/inst/Rmd/TestPandoc.Rmd |only RefManageR-0.8.63/RefManageR/inst/Rmd/TestRmd.Rmd | 72 RefManageR-0.8.63/RefManageR/inst/doc/TestAlphabetic.R | 30 RefManageR-0.8.63/RefManageR/inst/doc/TestAlphabetic.Rmd | 68 RefManageR-0.8.63/RefManageR/inst/doc/TestAlphabetic.html | 173 RefManageR-0.8.63/RefManageR/inst/doc/TestHtml.R | 38 RefManageR-0.8.63/RefManageR/inst/doc/TestHtml.Rhtml | 106 RefManageR-0.8.63/RefManageR/inst/doc/TestHtml.html | 422 RefManageR-0.8.63/RefManageR/inst/doc/TestRmd.R | 40 RefManageR-0.8.63/RefManageR/inst/doc/TestRmd.Rmd | 80 RefManageR-0.8.63/RefManageR/inst/doc/TestRmd.html | 177 RefManageR-0.8.63/RefManageR/inst/doc/manual.Rnw | 32 RefManageR-0.8.63/RefManageR/inst/doc/manual.pdf |binary RefManageR-0.8.63/RefManageR/inst/pdf |only RefManageR-0.8.63/RefManageR/man/BibEntry.Rd | 4 RefManageR-0.8.63/RefManageR/man/Cite.Rd | 3 RefManageR-0.8.63/RefManageR/man/GetPubMedByID.Rd | 6 RefManageR-0.8.63/RefManageR/man/ReadBib.Rd | 8 RefManageR-0.8.63/RefManageR/man/ReadZotero.Rd | 4 RefManageR-0.8.63/RefManageR/man/print.BibEntry.Rd | 40 RefManageR-0.8.63/RefManageR/man/toBiblatex.Rd | 2 RefManageR-0.8.63/RefManageR/tests |only RefManageR-0.8.63/RefManageR/vignettes/TestAlphabetic.Rmd | 68 RefManageR-0.8.63/RefManageR/vignettes/TestHtml.Rhtml | 106 RefManageR-0.8.63/RefManageR/vignettes/TestRmd.Rmd | 80 RefManageR-0.8.63/RefManageR/vignettes/manual.Rnw | 32 87 files changed, 16598 insertions(+), 16157 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data, and is
also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
Diff between PrevMap versions 1.1.4 dated 2015-01-14 and 1.1.5 dated 2015-06-09
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- R/foo.R | 15 +++++++++------ man/Laplace.sampling.Rd | 4 ++-- man/Laplace.sampling.lr.Rd | 4 ++-- man/adjust.sigma2.Rd | 2 +- man/binomial.logistic.Bayes.Rd | 2 +- man/binomial.logistic.MCML.Rd | 2 +- man/linear.model.Bayes.Rd | 2 +- 9 files changed, 31 insertions(+), 29 deletions(-)
Title: Geophysical Inverse Theory and Optimization
Description: Several functions introduced in Aster et al.'s book on inverse theory. The functions are often translations of MATLAB code developed by the authors to illustrate concepts of inverse theory as applied to geophysics. Generalized inversion, tomographic inversion algorithms (conjugate gradients, 'ART' and 'SIRT'), non-linear least squares, first and second order Tikhonov regularization, roughness constraints, and procedures for estimating smoothing parameters are included. Includes a wrapper for the FORTRAN based 'LSQR' (Paige and Saunders) routine.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between PEIP versions 1.7 dated 2014-01-07 and 2.0 dated 2015-06-09
PEIP-1.7/PEIP/R/astercode.R |only PEIP-1.7/PEIP/R/wGSVD.R |only PEIP-1.7/PEIP/man/astercode.Rd |only PEIP-1.7/PEIP/man/wGSVD.Rd |only PEIP-2.0/PEIP/DESCRIPTION | 12 +-- PEIP-2.0/PEIP/MD5 | 100 ++++++++++++++++--------------- PEIP-2.0/PEIP/R/GSVD.R | 105 ++++++++++++++++----------------- PEIP-2.0/PEIP/R/blf2.R | 8 +- PEIP-2.0/PEIP/R/ginv.R | 5 + PEIP-2.0/PEIP/R/imagesc.R | 13 ++++ PEIP-2.0/PEIP/R/occam.R | 4 - PEIP-2.0/PEIP/R/rlsqr.R | 4 - PEIP-2.0/PEIP/R/setDesignG.R |only PEIP-2.0/PEIP/R/shawG.R |only PEIP-2.0/PEIP/R/vspprofile.R |only PEIP-2.0/PEIP/man/Ainv.Rd | 14 ++++ PEIP-2.0/PEIP/man/GSVD.Rd | 51 ++++++++++++---- PEIP-2.0/PEIP/man/Mnorm.Rd | 7 ++ PEIP-2.0/PEIP/man/art.Rd | 34 ++++++++++ PEIP-2.0/PEIP/man/bayes.Rd | 33 ++++++++++ PEIP-2.0/PEIP/man/blf2.Rd | 30 ++++++++- PEIP-2.0/PEIP/man/cgls.Rd | 19 +++++ PEIP-2.0/PEIP/man/chi.Rd | 10 +++ PEIP-2.0/PEIP/man/chi2cdf.Rd | 6 + PEIP-2.0/PEIP/man/chi2inv.Rd | 8 ++ PEIP-2.0/PEIP/man/dcost.Rd | 14 ++++ PEIP-2.0/PEIP/man/flipGSVD.Rd | 32 ++++++---- PEIP-2.0/PEIP/man/gcval.Rd | 39 ++++++++++++ PEIP-2.0/PEIP/man/get_l_rough.Rd | 20 +++++- PEIP-2.0/PEIP/man/ginv.Rd | 15 ++++ PEIP-2.0/PEIP/man/idcost.Rd | 15 ++++ PEIP-2.0/PEIP/man/imagesc.Rd | 19 +++++ PEIP-2.0/PEIP/man/interp2grid.Rd | 6 - PEIP-2.0/PEIP/man/irls.Rd | 30 +++++++++ PEIP-2.0/PEIP/man/irlsl1reg.Rd | 29 +++++++++ PEIP-2.0/PEIP/man/kac.Rd | 30 +++++++++ PEIP-2.0/PEIP/man/l_curve_corner.Rd | 43 +++++++++++++ PEIP-2.0/PEIP/man/l_curve_tgsvd.Rd | 50 +++++++++++++++ PEIP-2.0/PEIP/man/l_curve_tikh_gsvd.Rd | 48 +++++++++++++++ PEIP-2.0/PEIP/man/l_curve_tikh_svd.Rd | 38 +++++++++++ PEIP-2.0/PEIP/man/linesconst.Rd | 8 ++ PEIP-2.0/PEIP/man/lmarq.Rd | 35 +++++++++++ PEIP-2.0/PEIP/man/mcmc.Rd | 89 +++++++++++++++++++++++++++ PEIP-2.0/PEIP/man/nnz.Rd | 8 ++ PEIP-2.0/PEIP/man/phi.Rd | 10 +++ PEIP-2.0/PEIP/man/phiinv.Rd | 10 +++ PEIP-2.0/PEIP/man/picard_vals.Rd | 44 ++++++++++++- PEIP-2.0/PEIP/man/plotconst.Rd | 10 +++ PEIP-2.0/PEIP/man/quadlin.Rd | 18 +++++ PEIP-2.0/PEIP/man/rlsqr.Rd | 19 ++++- PEIP-2.0/PEIP/man/setDesignG.Rd |only PEIP-2.0/PEIP/man/shawG.Rd |only PEIP-2.0/PEIP/man/sirt.Rd | 36 ++++++++++- PEIP-2.0/PEIP/man/vspprofile.Rd |only PEIP-2.0/PEIP/src/Makevars |only PEIP-2.0/PEIP/src/zdggsvd.f |only PEIP-2.0/PEIP/tests |only 57 files changed, 1022 insertions(+), 156 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut],
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.3-2 dated 2014-08-03 and 1.4-0 dated 2015-06-09
vcd-1.3-2/vcd/man/oddsratio.Rd |only vcd-1.4-0/vcd/DESCRIPTION | 20 - vcd-1.4-0/vcd/MD5 | 154 ++++----- vcd-1.4-0/vcd/NAMESPACE | 44 ++ vcd-1.4-0/vcd/R/Kappa.R | 21 - vcd-1.4-0/vcd/R/Ord_plot.R | 12 vcd-1.4-0/vcd/R/agreementplot.R | 28 + vcd-1.4-0/vcd/R/assocstats.R | 20 - vcd-1.4-0/vcd/R/binregplot.R |only vcd-1.4-0/vcd/R/cd_plot.R | 22 - vcd-1.4-0/vcd/R/cotabplot.R | 52 ++- vcd-1.4-0/vcd/R/distplot.R | 262 ++++++++------- vcd-1.4-0/vcd/R/fourfold.R | 18 - vcd-1.4-0/vcd/R/goodfit.R | 387 ++++++++++++---------- vcd-1.4-0/vcd/R/grid_legend.R | 169 +++++---- vcd-1.4-0/vcd/R/loddsratio.R |only vcd-1.4-0/vcd/R/mosaic.R | 441 +++++++++++++------------- vcd-1.4-0/vcd/R/mplot.R |only vcd-1.4-0/vcd/R/oddsratioplot.R | 333 +++++++++---------- vcd-1.4-0/vcd/R/pairsplot.R | 59 ++- vcd-1.4-0/vcd/R/rootogram.R | 246 +++++++++----- vcd-1.4-0/vcd/R/shadings.R | 37 ++ vcd-1.4-0/vcd/R/sieve.R | 8 vcd-1.4-0/vcd/R/strucplot.R | 21 - vcd-1.4-0/vcd/R/tabletools.R | 4 vcd-1.4-0/vcd/R/ternaryplot.R | 8 vcd-1.4-0/vcd/R/tile.R | 2 vcd-1.4-0/vcd/build/vignette.rds |binary vcd-1.4-0/vcd/data/Butterfly.rda |binary vcd-1.4-0/vcd/data/Employment.rda |binary vcd-1.4-0/vcd/data/Federalist.rda |binary vcd-1.4-0/vcd/data/HorseKicks.rda |binary vcd-1.4-0/vcd/data/Hospital.rda |binary vcd-1.4-0/vcd/data/Lifeboats.rda |binary vcd-1.4-0/vcd/data/MSPatients.rda |binary vcd-1.4-0/vcd/data/PreSex.rda |binary vcd-1.4-0/vcd/data/RepVict.rda |binary vcd-1.4-0/vcd/data/Rochdale.rda |binary vcd-1.4-0/vcd/data/Saxony.rda |binary vcd-1.4-0/vcd/data/Suicide.rda |binary vcd-1.4-0/vcd/data/UKSoccer.rda |binary vcd-1.4-0/vcd/data/WeldonDice.rda |binary vcd-1.4-0/vcd/data/WomenQueue.rda |binary vcd-1.4-0/vcd/demo/twoway.R | 46 +- vcd-1.4-0/vcd/inst/NEWS.Rd | 37 ++ vcd-1.4-0/vcd/inst/doc/residual-shadings.R | 1 vcd-1.4-0/vcd/inst/doc/residual-shadings.pdf |binary vcd-1.4-0/vcd/inst/doc/strucplot.R | 9 vcd-1.4-0/vcd/man/Bundestag2005.Rd | 2 vcd-1.4-0/vcd/man/CoalMiners.Rd | 18 - vcd-1.4-0/vcd/man/Kappa.Rd | 22 + vcd-1.4-0/vcd/man/MSPatients.Rd | 17 - vcd-1.4-0/vcd/man/Ord_plot.Rd | 15 vcd-1.4-0/vcd/man/VisualAcuity.Rd | 3 vcd-1.4-0/vcd/man/agreementplot.Rd | 16 vcd-1.4-0/vcd/man/assocstats.Rd | 16 vcd-1.4-0/vcd/man/binregplot.Rd |only vcd-1.4-0/vcd/man/cd_plot.Rd | 8 vcd-1.4-0/vcd/man/cotab_panel.Rd | 4 vcd-1.4-0/vcd/man/cotabplot.Rd | 4 vcd-1.4-0/vcd/man/distplot.Rd | 7 vcd-1.4-0/vcd/man/fourfold.Rd | 10 vcd-1.4-0/vcd/man/goodfit.Rd | 17 - vcd-1.4-0/vcd/man/grid_barplot.Rd | 3 vcd-1.4-0/vcd/man/grid_legend.Rd | 43 +- vcd-1.4-0/vcd/man/loddsratio.Rd |only vcd-1.4-0/vcd/man/mplot.Rd |only vcd-1.4-0/vcd/man/pairs.table.Rd | 7 vcd-1.4-0/vcd/man/panel_pairs_off-diagonal.Rd | 2 vcd-1.4-0/vcd/man/plot.loddsratio.Rd |only vcd-1.4-0/vcd/man/rootogram.Rd | 81 ++++ vcd-1.4-0/vcd/man/shadings.Rd | 48 ++ vcd-1.4-0/vcd/man/sieve.Rd | 3 vcd-1.4-0/vcd/man/struc_assoc.Rd | 2 vcd-1.4-0/vcd/man/struc_mosaic.Rd | 2 vcd-1.4-0/vcd/man/struc_sieve.Rd | 4 vcd-1.4-0/vcd/man/strucplot.Rd | 8 vcd-1.4-0/vcd/man/table2d_summary.Rd | 4 vcd-1.4-0/vcd/man/ternaryplot.Rd | 5 vcd-1.4-0/vcd/man/tile.Rd | 6 vcd-1.4-0/vcd/vignettes/residual-shadings.Rnw | 3 vcd-1.4-0/vcd/vignettes/strucplot.Rnw | 3 82 files changed, 1722 insertions(+), 1122 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-08 1.0.2
2013-06-10 1.0.1
2013-05-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-21 1.5.0
2013-10-09 1.3.6
2013-06-15 1.3.5
2013-06-01 1.3.4
2013-05-12 1.3.2
2013-04-15 1.2.4.1
2010-11-12 1.2.4
2008-02-29 1.2.3
2007-11-11 1.2.2
2007-11-05 1.2.1
2007-11-03 1.2.0
2007-10-03 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-02 1.3
2014-04-29 1.2
2014-01-04 1.1
2013-06-07 1.0
2012-01-31 0.8
2012-01-12 0.6
2011-12-31 0.5
2011-11-25 0.3
2011-08-24 0.2
2011-08-12 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-10 1.0
Title: Linear Regression Based on Linear Structure Between Covariates
Description: Linear regression based on a recursive structural equation model
(explicit correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elastic net, etc.). It also provides some graphical tools for basic
statistics and regression trees.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY <monsieur.thery@therysolutions.com>
Diff between CorReg versions 1.0 dated 2015-01-13 and 1.0.5 dated 2015-06-09
CorReg-1.0.5/CorReg/DESCRIPTION | 27 +-- CorReg-1.0.5/CorReg/MD5 | 182 +++++++++++--------------- CorReg-1.0.5/CorReg/NAMESPACE | 23 --- CorReg-1.0.5/CorReg/R/BICZmiss.R | 14 +- CorReg-1.0.5/CorReg/R/BicZ.R | 35 +++-- CorReg-1.0.5/CorReg/R/BicZcurve.R | 16 +- CorReg-1.0.5/CorReg/R/CVMSE.R | 16 +- CorReg-1.0.5/CorReg/R/Conan.R |only CorReg-1.0.5/CorReg/R/CorReg-package.R | 45 +++--- CorReg-1.0.5/CorReg/R/Estep.R | 34 ++-- CorReg-1.0.5/CorReg/R/GM_Loglikelihood.R | 23 --- CorReg-1.0.5/CorReg/R/Gibbs.R | 10 - CorReg-1.0.5/CorReg/R/Gibbs_X_ij_IF.R | 2 CorReg-1.0.5/CorReg/R/Gibbs_miss.R | 4 CorReg-1.0.5/CorReg/R/MSEZ.R | 14 +- CorReg-1.0.5/CorReg/R/MSE_loc.R | 18 ++ CorReg-1.0.5/CorReg/R/MakeF.R | 2 CorReg-1.0.5/CorReg/R/MakeH.R | 2 CorReg-1.0.5/CorReg/R/MakeJ.R | 2 CorReg-1.0.5/CorReg/R/OLS.R | 30 ++-- CorReg-1.0.5/CorReg/R/ProbaZ.R | 18 +- CorReg-1.0.5/CorReg/R/R2Z.R | 14 +- CorReg-1.0.5/CorReg/R/SEM.R | 10 - CorReg-1.0.5/CorReg/R/Terminator.R | 42 ++++-- CorReg-1.0.5/CorReg/R/WhoIs.R | 8 - CorReg-1.0.5/CorReg/R/Winitial.R | 28 ++-- CorReg-1.0.5/CorReg/R/Y_generator.R | 22 +-- CorReg-1.0.5/CorReg/R/cleanYtest.R | 36 +++-- CorReg-1.0.5/CorReg/R/cleanZ.R | 20 +- CorReg-1.0.5/CorReg/R/cleanZR2.R | 14 +- CorReg-1.0.5/CorReg/R/cleanZlars.R | 2 CorReg-1.0.5/CorReg/R/cleanZtest.R | 14 +- CorReg-1.0.5/CorReg/R/cleancolZ.R | 18 +- CorReg-1.0.5/CorReg/R/compare_beta.R | 13 - CorReg-1.0.5/CorReg/R/compare_sign.R | 6 CorReg-1.0.5/CorReg/R/compare_struct.R | 24 ++- CorReg-1.0.5/CorReg/R/compare_zero.R | 8 - CorReg-1.0.5/CorReg/R/confint_coef.R | 37 +++-- CorReg-1.0.5/CorReg/R/correg.R | 101 +++++++++++--- CorReg-1.0.5/CorReg/R/density_estimation.R | 81 +++++++---- CorReg-1.0.5/CorReg/R/fillmiss.R | 28 ++-- CorReg-1.0.5/CorReg/R/generateurA_ou.R | 16 +- CorReg-1.0.5/CorReg/R/hatB.R | 12 - CorReg-1.0.5/CorReg/R/inkei.R | 5 CorReg-1.0.5/CorReg/R/loglikcond.R | 2 CorReg-1.0.5/CorReg/R/matplot_zone.R | 40 ++++- CorReg-1.0.5/CorReg/R/missing_penalty.R | 14 +- CorReg-1.0.5/CorReg/R/mixture_generator.R | 90 +++++++----- CorReg-1.0.5/CorReg/R/mon_AIC.R | 2 CorReg-1.0.5/CorReg/R/muiZ.R | 18 +- CorReg-1.0.5/CorReg/R/newhatB.R | 2 CorReg-1.0.5/CorReg/R/newtheta.R | 2 CorReg-1.0.5/CorReg/R/readY.R | 18 +- CorReg-1.0.5/CorReg/R/readZ.R | 28 +++- CorReg-1.0.5/CorReg/R/recursive_tree.R | 21 ++- CorReg-1.0.5/CorReg/R/rforge.R | 8 - CorReg-1.0.5/CorReg/R/searchZ_sparse.R | 38 ++--- CorReg-1.0.5/CorReg/R/searchZmiss.R | 4 CorReg-1.0.5/CorReg/R/showdata.R | 32 +++- CorReg-1.0.5/CorReg/R/structureFinder.R | 108 ++++++++++++--- CorReg-1.0.5/CorReg/R/tik.R | 2 CorReg-1.0.5/CorReg/R/victory_int.R | 2 CorReg-1.0.5/CorReg/man/BicZ.Rd | 21 ++- CorReg-1.0.5/CorReg/man/Conan.Rd |only CorReg-1.0.5/CorReg/man/CorReg-package.Rd | 49 ++++--- CorReg-1.0.5/CorReg/man/MSE_loc.Rd | 23 ++- CorReg-1.0.5/CorReg/man/Terminator.Rd | 17 ++ CorReg-1.0.5/CorReg/man/compare_struct.Rd | 25 ++- CorReg-1.0.5/CorReg/man/correg.Rd | 77 ++++++++--- CorReg-1.0.5/CorReg/man/density_estimation.Rd | 28 +++- CorReg-1.0.5/CorReg/man/matplot_zone.Rd | 40 +++-- CorReg-1.0.5/CorReg/man/mixture_generator.Rd | 67 ++++++--- CorReg-1.0.5/CorReg/man/readZ.Rd | 33 +++- CorReg-1.0.5/CorReg/man/recursive_tree.Rd | 22 ++- CorReg-1.0.5/CorReg/man/showdata.Rd | 31 +++- CorReg-1.0.5/CorReg/man/structureFinder.Rd | 106 +++++++++++---- CorReg-1.0.5/CorReg/src/CVMSE.cpp | 2 CorReg-1.0.5/CorReg/src/GM_likelihood.cpp | 12 - CorReg-1.0.5/CorReg/src/ProbaZ_cpp.cpp | 6 CorReg-1.0.5/CorReg/src/rechercheZ_rejet.cpp | 6 CorReg-1.0.5/CorReg/src/rechercheZ_relax.cpp | 6 CorReg-1.0/CorReg/R/compass.R |only CorReg-1.0/CorReg/man/BicZcurve.Rd |only CorReg-1.0/CorReg/man/CVMSE.Rd |only CorReg-1.0/CorReg/man/Estep.Rd |only CorReg-1.0/CorReg/man/MSEZ.Rd |only CorReg-1.0/CorReg/man/OLS.Rd |only CorReg-1.0/CorReg/man/ProbaZ.Rd |only CorReg-1.0/CorReg/man/R2Z.Rd |only CorReg-1.0/CorReg/man/WhoIs.Rd |only CorReg-1.0/CorReg/man/Winitial.Rd |only CorReg-1.0/CorReg/man/Y_generator.Rd |only CorReg-1.0/CorReg/man/cleanYtest.Rd |only CorReg-1.0/CorReg/man/cleanZ.Rd |only CorReg-1.0/CorReg/man/cleanZR2.Rd |only CorReg-1.0/CorReg/man/cleancolZ.Rd |only CorReg-1.0/CorReg/man/compare_beta.Rd |only CorReg-1.0/CorReg/man/compare_sign.Rd |only CorReg-1.0/CorReg/man/compare_zero.Rd |only CorReg-1.0/CorReg/man/confint_coef.Rd |only CorReg-1.0/CorReg/man/fillmiss.Rd |only CorReg-1.0/CorReg/man/hatB.Rd |only CorReg-1.0/CorReg/man/readY.Rd |only CorReg-1.0/CorReg/man/rforge.Rd |only CorReg-1.0/CorReg/man/searchZ_sparse.Rd |only 105 files changed, 1302 insertions(+), 776 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.5.0 dated 2015-05-24 and 1.5.14 dated 2015-06-09
DESCRIPTION | 8 ++-- MD5 | 56 ++++++++++++++--------------- R/predict.wsrf.R | 55 ++++++++++++++++------------- README.md | 7 --- build/vignette.rds |binary inst/NEWS.Rd | 41 ++++++++++++++++++++- inst/doc/wsrfGuide.Rnw | 2 - inst/doc/wsrfGuide.pdf |binary man/wsrf.Rd | 25 ++++++++++--- src/IGR.cpp | 17 +++++++-- src/IGR.h | 13 +++--- src/c4_5_var_selector.cpp | 41 +++++++++++++-------- src/c4_5_var_selector.h | 14 ------- src/dataset.cpp | 12 +++--- src/dataset.h | 18 ++------- src/meta_data.cpp | 16 ++++---- src/meta_data.h | 2 - src/node.h | 19 +++++----- src/rforest.cpp | 86 ++++++++++++++++++++++++++++------------------ src/rforest.h | 26 ++++++------- src/tree.cpp | 51 ++++++++++++++------------- src/tree.h | 6 --- src/utility.h | 2 - src/var_selector.h | 16 +++----- src/wsrf.cpp | 9 +++- src/wsrf.h | 11 ----- tests/wsrftest.R | 10 +---- tests/wsrftest.Rout.save | 12 +----- vignettes/wsrfGuide.Rnw | 2 - 29 files changed, 311 insertions(+), 266 deletions(-)
Title: Estimating Systems of Simultaneous Equations
Description: Fitting simultaneous
systems of linear and nonlinear equations using Ordinary Least
Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated
Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted
Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS).
Author: Arne Henningsen and Jeff D. Hamann
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between systemfit versions 1.1-14 dated 2012-11-18 and 1.1-16 dated 2015-06-09
DESCRIPTION | 24 MD5 | 56 NAMESPACE | 2 NEWS | 10 R/createSystemfitModel.R | 2 R/linear.hypothesis.R | 8 R/nlsystemfit.r | 53 R/systemfit.R | 8 build |only inst/doc/systemfit.R |only tests/KleinI.R | 8 tests/KleinI.Rout.save |36419 +++++++++++++++++++++---------------------- tests/KleinI_noMat.R | 1 tests/KleinI_noMat.Rout.save | 9293 +++++----- tests/test_2sls.R | 9 tests/test_2sls.Rout.save | 6357 +++---- tests/test_3sls.R | 139 tests/test_3sls.Rout.save |23267 +++++++++++++-------------- tests/test_hausman.R | 3 tests/test_hausman.Rout.save | 35 tests/test_ols.R | 9 tests/test_ols.Rout.save | 4855 ++--- tests/test_panel.R | 9 tests/test_panel.Rout.save |12599 +++++++------- tests/test_sur.R | 41 tests/test_sur.Rout.save |11205 ++++++------- tests/test_w2sls.R | 9 tests/test_w2sls.Rout.save | 5693 +++--- tests/test_wls.R | 7 tests/test_wls.Rout.save | 6081 +++---- 30 files changed, 57805 insertions(+), 58397 deletions(-)
Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish
administration such as personal identity numbers ('personnummer') and
organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between sweidnumbr versions 0.2 dated 2014-09-28 and 0.6.0 dated 2015-06-09
sweidnumbr-0.2/sweidnumbr/inst/tests |only sweidnumbr-0.2/sweidnumbr/man/pin_add_zero.Rd |only sweidnumbr-0.6.0/sweidnumbr/DESCRIPTION | 18 - sweidnumbr-0.6.0/sweidnumbr/LICENSE | 2 sweidnumbr-0.6.0/sweidnumbr/MD5 | 114 ++++---- sweidnumbr-0.6.0/sweidnumbr/NAMESPACE | 18 + sweidnumbr-0.6.0/sweidnumbr/R/create_s3_methods.R |only sweidnumbr-0.6.0/sweidnumbr/R/data_documentation.R |only sweidnumbr-0.6.0/sweidnumbr/R/firstlib.R | 2 sweidnumbr-0.6.0/sweidnumbr/R/oin.R | 67 ++++- sweidnumbr-0.6.0/sweidnumbr/R/oin_methods.R |only sweidnumbr-0.6.0/sweidnumbr/R/pin.R | 108 ++++++-- sweidnumbr-0.6.0/sweidnumbr/R/pin_internal.R | 114 ++++++-- sweidnumbr-0.6.0/sweidnumbr/R/pin_methods.R | 14 + sweidnumbr-0.6.0/sweidnumbr/R/sweidnumbr.R | 2 sweidnumbr-0.6.0/sweidnumbr/README.md | 18 + sweidnumbr-0.6.0/sweidnumbr/build/vignette.rds |binary sweidnumbr-0.6.0/sweidnumbr/data |only sweidnumbr-0.6.0/sweidnumbr/inst/CITATION | 2 sweidnumbr-0.6.0/sweidnumbr/inst/doc/sweidnumbr.R | 17 - sweidnumbr-0.6.0/sweidnumbr/inst/doc/sweidnumbr.Rmd | 78 +++++- sweidnumbr-0.6.0/sweidnumbr/inst/doc/sweidnumbr.html | 97 +++++-- sweidnumbr-0.6.0/sweidnumbr/inst/doc/sweidnumbr.md | 165 +++++++++++-- sweidnumbr-0.6.0/sweidnumbr/man/as.oin.Rd |only sweidnumbr-0.6.0/sweidnumbr/man/as.pin.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/fake_pins.Rd |only sweidnumbr-0.6.0/sweidnumbr/man/is.oin.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/is.pin.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/luhn_algo.Rd | 27 +- sweidnumbr-0.6.0/sweidnumbr/man/oin_ctrl.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/oin_group.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/oin_group_element.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_age.Rd | 7 sweidnumbr-0.6.0/sweidnumbr/man/pin_birthplace.Rd | 7 sweidnumbr-0.6.0/sweidnumbr/man/pin_birthplace_internal.Rd | 7 sweidnumbr-0.6.0/sweidnumbr/man/pin_century.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_convert.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_coordn.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_coordn_correct.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_ctrl.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_sex.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/pin_to_date.Rd | 3 sweidnumbr-0.6.0/sweidnumbr/man/sweidnumbr.Rd | 5 sweidnumbr-0.6.0/sweidnumbr/tests |only sweidnumbr-0.6.0/sweidnumbr/vignettes/sweidnumbr.Rmd | 46 ++- 45 files changed, 719 insertions(+), 255 deletions(-)
Title: Integrates R and Essentia
Description: Contains two functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.udb' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>
Diff between RESS versions 1.0 dated 2015-03-06 and 1.1 dated 2015-06-09
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/RESS-package.Rd | 6 +++--- man/essQuery.Rd | 15 ++++++++------- man/read.udb.Rd | 14 +++++++------- 5 files changed, 27 insertions(+), 26 deletions(-)
Title: Package to Patch .dvi or .synctex Files
Description: Functions to patch specials in .dvi files,
or entries in .synctex files. Works with "concordance=TRUE"
in Sweave or knitr to link sources to previews.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between patchDVI versions 1.9.1601 dated 2013-12-15 and 1.9.1616 dated 2015-06-09
patchDVI-1.9.1601/patchDVI/vignettes/Japanese-concordance.tex |only patchDVI-1.9.1601/patchDVI/vignettes/Japanese.synctex.gz |only patchDVI-1.9.1601/patchDVI/vignettes/Japanese.tex |only patchDVI-1.9.1601/patchDVI/vignettes/patchDVI-concordance.tex |only patchDVI-1.9.1601/patchDVI/vignettes/patchDVI.log.new |only patchDVI-1.9.1601/patchDVI/vignettes/patchDVI.tex |only patchDVI-1.9.1616/patchDVI/DESCRIPTION | 19 patchDVI-1.9.1616/patchDVI/MD5 | 45 patchDVI-1.9.1616/patchDVI/NAMESPACE | 7 patchDVI-1.9.1616/patchDVI/R/SweaveAll.R | 4 patchDVI-1.9.1616/patchDVI/R/knitr.R |only patchDVI-1.9.1616/patchDVI/R/patchLog.R | 1 patchDVI-1.9.1616/patchDVI/R/patchPDF.R | 850 +++++----- patchDVI-1.9.1616/patchDVI/R/zzz.R |only patchDVI-1.9.1616/patchDVI/build/vignette.rds |binary patchDVI-1.9.1616/patchDVI/inst/NEWS | 7 patchDVI-1.9.1616/patchDVI/inst/doc/Japanese.Rnw | 61 patchDVI-1.9.1616/patchDVI/inst/doc/Japanese.pdf |binary patchDVI-1.9.1616/patchDVI/inst/doc/patchDVI.R | 7 patchDVI-1.9.1616/patchDVI/inst/doc/patchDVI.Rnw | 121 - patchDVI-1.9.1616/patchDVI/inst/doc/patchDVI.pdf |binary patchDVI-1.9.1616/patchDVI/man/SweaveAll.Rd | 176 +- patchDVI-1.9.1616/patchDVI/man/SweaveMiktex.Rd | 229 +- patchDVI-1.9.1616/patchDVI/man/defSconcordance.Rd |only patchDVI-1.9.1616/patchDVI/po |only patchDVI-1.9.1616/patchDVI/vignettes/Japanese.Rnw | 61 patchDVI-1.9.1616/patchDVI/vignettes/patchDVI.Rnw | 121 - patchDVI-1.9.1616/patchDVI/vignettes/patchDVI.bib | 10 28 files changed, 930 insertions(+), 789 deletions(-)
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://eml.berkeley.edu//~train/trainsonnier.pdf.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.0.2 dated 2014-05-30 and 1.1.0 dated 2015-06-08
RSGHB-1.0.2/RSGHB/R/plotA.R |only RSGHB-1.0.2/RSGHB/R/plotF.R |only RSGHB-1.0.2/RSGHB/R/plotLog.R |only RSGHB-1.0.2/RSGHB/R/writeLog.R |only RSGHB-1.0.2/RSGHB/data/Example1_F.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_A.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_B.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_Bsd.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_C.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_Csd.txt.gz |only RSGHB-1.0.2/RSGHB/data/Example2_D.txt.gz |only RSGHB-1.0.2/RSGHB/data/datalist |only RSGHB-1.0.2/RSGHB/man/Example1_F.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_A.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_B.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_Bsd.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_C.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_Csd.Rd |only RSGHB-1.0.2/RSGHB/man/Example2_D.Rd |only RSGHB-1.0.2/RSGHB/man/RSGHB-internal.Rd |only RSGHB-1.0.2/RSGHB/man/plotA.Rd |only RSGHB-1.0.2/RSGHB/man/plotC.Rd |only RSGHB-1.0.2/RSGHB/man/plotF.Rd |only RSGHB-1.0.2/RSGHB/man/plotLog.Rd |only RSGHB-1.0.2/RSGHB/man/vech.Rd |only RSGHB-1.0.2/RSGHB/man/xpnd.Rd |only RSGHB-1.0.2/RSGHB/tools |only RSGHB-1.0.2/RSGHB/vignettes/MNL_logPlot1.png |only RSGHB-1.0.2/RSGHB/vignettes/MNL_logPlot2.png |only RSGHB-1.0.2/RSGHB/vignettes/MNL_markovChains2.png |only RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.synctex.gz |only RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.tex |only RSGHB-1.0.2/RSGHB/vignettes/figure |only RSGHB-1.0.2/RSGHB/vignettes/framed.sty |only RSGHB-1.1.0/RSGHB/DESCRIPTION | 28 RSGHB-1.1.0/RSGHB/MD5 | 78 -- RSGHB-1.1.0/RSGHB/NAMESPACE | 19 RSGHB-1.1.0/RSGHB/NEWS |only RSGHB-1.1.0/RSGHB/R/checkModel.R | 160 ++-- RSGHB-1.1.0/RSGHB/R/doHB.R | 240 +++--- RSGHB-1.1.0/RSGHB/R/hb.R | 162 +--- RSGHB-1.1.0/RSGHB/R/methods.R |only RSGHB-1.1.0/RSGHB/R/nextD.R | 15 RSGHB-1.1.0/RSGHB/R/nextDind.R | 8 RSGHB-1.1.0/RSGHB/R/onLoad.R |only RSGHB-1.1.0/RSGHB/R/plotC.R | 15 RSGHB-1.1.0/RSGHB/R/progreport.R |only RSGHB-1.1.0/RSGHB/R/writeModel.R |only RSGHB-1.1.0/RSGHB/build/vignette.rds |binary RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.R | 350 ++++----- RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.pdf |binary RSGHB-1.1.0/RSGHB/inst/doc/RSGHB_HowTo.rnw | 573 ++++++---------- RSGHB-1.1.0/RSGHB/man/doHB.Rd | 182 ++--- RSGHB-1.1.0/RSGHB/man/plot.Rd |only RSGHB-1.1.0/RSGHB/man/writeModel.Rd |only RSGHB-1.1.0/RSGHB/vignettes/MMNL_MarkovChains.png |only RSGHB-1.1.0/RSGHB/vignettes/MNL_markovChains.png |binary RSGHB-1.1.0/RSGHB/vignettes/RSGHB_HowTo-concordance.tex | 5 RSGHB-1.1.0/RSGHB/vignettes/RSGHB_HowTo.rnw | 573 ++++++---------- 59 files changed, 1020 insertions(+), 1388 deletions(-)
Title: Bayesian Non- and Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 1.0.2 dated 2015-01-02 and 1.0.3 dated 2015-06-08
ChangeLog | 14 ++- DESCRIPTION | 12 +-- MD5 | 18 ++-- R/bnpglm.R | 64 ++++++++++------ man/BNSP-package.Rd | 4 - man/bnpglm.Rd | 138 +++++++++++++++++++++++++----------- src/OneResLtnt.c | 191 ++++++++++++++++++++++++++++++++++++++------------ src/other.functions.h | 39 +++++++++- src/pdfs.h | 77 +++++++++++++++++++- src/sampling.h | 24 ++++++ 10 files changed, 449 insertions(+), 132 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, 326, 261--273), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language, Plant Physiology, 167, 617--627).
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@ulg.ac.be>
Diff between archiDART versions 1.0 dated 2014-12-05 and 1.1 dated 2015-06-08
DESCRIPTION | 15 +- MD5 | 31 ++--- NAMESPACE | 3 R/archidraw.R | 95 ++++++++++++--- R/archigrow.R | 10 - R/architect.R | 235 ++++++++++++++++++++++++++++----------- R/latdist.R | 157 ++++++++++++++++++++++---- R/rsmlToDART.R |only R/trajectory.R | 322 +++++++++++++++++++++++++++++++++++------------------- man/archidraw.Rd | 49 ++++---- man/archigrow.Rd | 30 ++--- man/architect.Rd | 52 +++++--- man/ch7lie.Rd | 3 man/ch7rac.Rd | 7 - man/ch7tps.Rd | 12 +- man/latdist.Rd | 39 +++--- man/trajectory.Rd | 51 ++++---- 17 files changed, 757 insertions(+), 354 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.11-4 dated 2015-05-27 and 0.11-8 dated 2015-06-08
DESCRIPTION | 12 +- MD5 | 8 - R/codeGeno.r | 273 +++++++++++++++++++++++++++-------------------------- R/create.gpData.r | 4 R/read.write.vcf.r | 2 5 files changed, 156 insertions(+), 143 deletions(-)
Title: Smoothing for Stream Network Data
Description: Fits flexible additive models to data on stream networks, taking account of flow-connectivity of the network. Models are fitted using penalised least squares.
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastair.rushworth@strath.ac.uk>
Diff between smnet versions 1.0 dated 2014-12-09 and 2.0 dated 2015-06-08
smnet-1.0/smnet/R/plot_continuous.R |only smnet-1.0/smnet/R/simulateNetwork.R |only smnet-1.0/smnet/man/simulateNetwork.Rd |only smnet-2.0/smnet/DESCRIPTION | 16 +- smnet-2.0/smnet/MD5 | 62 +++++----- smnet-2.0/smnet/NAMESPACE | 11 - smnet-2.0/smnet/R/adjacency_to_shreve.R |only smnet-2.0/smnet/R/check_additive_weight.R |only smnet-2.0/smnet/R/check_weight.R |only smnet-2.0/smnet/R/get_adjacency.R | 40 +++--- smnet-2.0/smnet/R/get_crit.R | 53 ++------ smnet-2.0/smnet/R/get_crit_exact.R | 36 ++---- smnet-2.0/smnet/R/get_lm_fit.R | 32 +++-- smnet-2.0/smnet/R/get_max_df.R |only smnet-2.0/smnet/R/get_model_objects.R | 51 ++++++-- smnet-2.0/smnet/R/get_optimal_smooth.R | 179 +++++++++++++++--------------- smnet-2.0/smnet/R/get_penalty.R | 4 smnet-2.0/smnet/R/is.wholenumber.R |only smnet-2.0/smnet/R/network.R | 4 smnet-2.0/smnet/R/plot.smnet.R | 84 ++++++-------- smnet-2.0/smnet/R/plot_cov.R | 143 +++++++++++------------ smnet-2.0/smnet/R/plot_full.R |only smnet-2.0/smnet/R/plot_node.R | 123 +++++++++++++++----- smnet-2.0/smnet/R/plot_segments.R |only smnet-2.0/smnet/R/predict.smnet.R | 13 -- smnet-2.0/smnet/R/predictSSNobject.R | 73 +++++------- smnet-2.0/smnet/R/re_map_rid.R |only smnet-2.0/smnet/R/show_weights.R |only smnet-2.0/smnet/R/smnet.R | 155 +++++++++++++++++-------- smnet-2.0/smnet/R/summary.smnet.R | 82 +++++-------- smnet-2.0/smnet/inst |only smnet-2.0/smnet/man/get_adjacency.Rd | 129 +++++++++++++-------- smnet-2.0/smnet/man/m.Rd | 129 +++++++++++++-------- smnet-2.0/smnet/man/network.Rd | 133 +++++++++++++--------- smnet-2.0/smnet/man/plot.smnet.Rd | 139 ++++++++++++++--------- smnet-2.0/smnet/man/predict.smnet.Rd | 140 +++++++++++++---------- smnet-2.0/smnet/man/show_weights.Rd |only smnet-2.0/smnet/man/smnet.Rd | 155 ++++++++++++++++--------- smnet-2.0/smnet/man/summary.smnet.Rd | 129 +++++++++++++-------- 39 files changed, 1208 insertions(+), 907 deletions(-)
Title: Interface to the Global Biodiversity Information Facility 'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.0 dated 2015-03-09 and 0.8.4 dated 2015-06-08
rgbif-0.8.0/rgbif/inst/vign/figure/densitylist2.png |only rgbif-0.8.0/rgbif/inst/vign/figure/gbifmap1.png |only rgbif-0.8.0/rgbif/inst/vign/figure/occurrencelist_many.png |only rgbif-0.8.0/rgbif/man/ldfast.Rd |only rgbif-0.8.0/rgbif/vignettes/figure |only rgbif-0.8.4/rgbif/DESCRIPTION | 23 rgbif-0.8.4/rgbif/MD5 | 258 ++++---- rgbif-0.8.4/rgbif/NAMESPACE | 23 rgbif-0.8.4/rgbif/NEWS | 42 + rgbif-0.8.4/rgbif/R/check_wkt.r | 26 rgbif-0.8.4/rgbif/R/count_facet.r | 43 - rgbif-0.8.4/rgbif/R/dataset_metrics.r | 13 rgbif-0.8.4/rgbif/R/dataset_search.r | 2 rgbif-0.8.4/rgbif/R/dataset_suggest.r | 2 rgbif-0.8.4/rgbif/R/elevation.r | 45 - rgbif-0.8.4/rgbif/R/enumeration.R |only rgbif-0.8.4/rgbif/R/gbif_names.R | 4 rgbif-0.8.4/rgbif/R/gbif_photos.r | 14 rgbif-0.8.4/rgbif/R/gbifmap.r | 54 - rgbif-0.8.4/rgbif/R/name_backbone.r | 2 rgbif-0.8.4/rgbif/R/name_lookup.r | 54 + rgbif-0.8.4/rgbif/R/name_suggest.r | 4 rgbif-0.8.4/rgbif/R/name_usage.r | 2 rgbif-0.8.4/rgbif/R/nodes.r | 25 rgbif-0.8.4/rgbif/R/occ_count.r | 11 rgbif-0.8.4/rgbif/R/occ_get.r | 63 +- rgbif-0.8.4/rgbif/R/occ_issues.r | 56 - rgbif-0.8.4/rgbif/R/occ_metadata.r | 1 rgbif-0.8.4/rgbif/R/occ_search.r | 119 +-- rgbif-0.8.4/rgbif/R/on_load.R |only rgbif-0.8.4/rgbif/R/parsenames.R | 2 rgbif-0.8.4/rgbif/R/plyr_fxns.R |only rgbif-0.8.4/rgbif/R/read_wkt.R |only rgbif-0.8.4/rgbif/R/zzz.r | 207 +++--- rgbif-0.8.4/rgbif/README.md | 2 rgbif-0.8.4/rgbif/build/vignette.rds |binary rgbif-0.8.4/rgbif/inst/doc/issues_vignette.Rmd | 166 ++--- rgbif-0.8.4/rgbif/inst/doc/issues_vignette.html | 166 ++--- rgbif-0.8.4/rgbif/inst/doc/rgbif_vignette.html | 398 ++++++------- rgbif-0.8.4/rgbif/inst/js |only rgbif-0.8.4/rgbif/inst/vign/figure/gbifmap1-1.png |binary rgbif-0.8.4/rgbif/inst/vign/issues_vignette.md | 166 ++--- rgbif-0.8.4/rgbif/inst/vign/rgbif_vignette.Rmd | 8 rgbif-0.8.4/rgbif/inst/vign/rgbif_vignette.md | 396 ++++++------ rgbif-0.8.4/rgbif/man/blanktheme.Rd | 2 rgbif-0.8.4/rgbif/man/check_wkt.Rd | 2 rgbif-0.8.4/rgbif/man/commas_to_periods.Rd | 2 rgbif-0.8.4/rgbif/man/count_facet.Rd | 2 rgbif-0.8.4/rgbif/man/create_gist.Rd | 2 rgbif-0.8.4/rgbif/man/dataset_metrics.Rd | 6 rgbif-0.8.4/rgbif/man/dataset_search.Rd | 2 rgbif-0.8.4/rgbif/man/dataset_suggest.Rd | 2 rgbif-0.8.4/rgbif/man/datasetparser.Rd | 2 rgbif-0.8.4/rgbif/man/datasets.Rd | 2 rgbif-0.8.4/rgbif/man/density_spplist.Rd | 2 rgbif-0.8.4/rgbif/man/densitylist.Rd | 2 rgbif-0.8.4/rgbif/man/elevation.Rd | 22 rgbif-0.8.4/rgbif/man/enumeration.Rd |only rgbif-0.8.4/rgbif/man/gbif_bbox2wkt.Rd | 8 rgbif-0.8.4/rgbif/man/gbif_capwords.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_issues.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_names.Rd | 2 rgbif-0.8.4/rgbif/man/gbif_photos.Rd | 2 rgbif-0.8.4/rgbif/man/gbifdata.Rd | 2 rgbif-0.8.4/rgbif/man/gbifmap.Rd | 10 rgbif-0.8.4/rgbif/man/gbifmap_dens.Rd | 2 rgbif-0.8.4/rgbif/man/gbifmap_list.Rd | 2 rgbif-0.8.4/rgbif/man/gbifparser.Rd | 2 rgbif-0.8.4/rgbif/man/gbifparser_verbatim.Rd | 2 rgbif-0.8.4/rgbif/man/get_credentials.Rd | 2 rgbif-0.8.4/rgbif/man/gist.Rd | 2 rgbif-0.8.4/rgbif/man/installations.Rd | 2 rgbif-0.8.4/rgbif/man/isocodes.Rd | 2 rgbif-0.8.4/rgbif/man/name_backbone.Rd | 2 rgbif-0.8.4/rgbif/man/name_lookup.Rd | 11 rgbif-0.8.4/rgbif/man/name_suggest.Rd | 2 rgbif-0.8.4/rgbif/man/name_usage.Rd | 2 rgbif-0.8.4/rgbif/man/namelkupparser.Rd | 2 rgbif-0.8.4/rgbif/man/networks.Rd | 2 rgbif-0.8.4/rgbif/man/nodes.Rd | 23 rgbif-0.8.4/rgbif/man/occ_count.Rd | 9 rgbif-0.8.4/rgbif/man/occ_fields.Rd | 2 rgbif-0.8.4/rgbif/man/occ_get.Rd | 14 rgbif-0.8.4/rgbif/man/occ_issues.Rd | 12 rgbif-0.8.4/rgbif/man/occ_issues_lookup.Rd | 2 rgbif-0.8.4/rgbif/man/occ_metadata.Rd | 2 rgbif-0.8.4/rgbif/man/occ_search.Rd | 29 rgbif-0.8.4/rgbif/man/occurrencecount.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencedensity.Rd | 2 rgbif-0.8.4/rgbif/man/occurrenceget.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist_all.Rd | 2 rgbif-0.8.4/rgbif/man/occurrencelist_many.Rd | 2 rgbif-0.8.4/rgbif/man/organizations.Rd | 2 rgbif-0.8.4/rgbif/man/parsenames.Rd | 2 rgbif-0.8.4/rgbif/man/parseresults.Rd | 2 rgbif-0.8.4/rgbif/man/pipe.Rd | 2 rgbif-0.8.4/rgbif/man/providers.Rd | 2 rgbif-0.8.4/rgbif/man/read_wkt.Rd |only rgbif-0.8.4/rgbif/man/resources.Rd | 2 rgbif-0.8.4/rgbif/man/rgb_country_codes.Rd | 2 rgbif-0.8.4/rgbif/man/rgbif-defunct.Rd | 2 rgbif-0.8.4/rgbif/man/rgbif-package.Rd | 2 rgbif-0.8.4/rgbif/man/stylegeojson.Rd | 2 rgbif-0.8.4/rgbif/man/suggestfields.Rd | 2 rgbif-0.8.4/rgbif/man/taxoncount.Rd | 2 rgbif-0.8.4/rgbif/man/taxonget.Rd | 2 rgbif-0.8.4/rgbif/man/taxonsearch.Rd | 2 rgbif-0.8.4/rgbif/man/taxrank.Rd | 2 rgbif-0.8.4/rgbif/man/togeojson.Rd | 2 rgbif-0.8.4/rgbif/man/type_sum.Rd | 2 rgbif-0.8.4/rgbif/man/typestatus.Rd | 2 rgbif-0.8.4/rgbif/tests/test-all.R |only rgbif-0.8.4/rgbif/tests/testthat/test-count_facet.r | 29 rgbif-0.8.4/rgbif/tests/testthat/test-country_codes.r | 6 rgbif-0.8.4/rgbif/tests/testthat/test-dataset_metrics.r | 20 rgbif-0.8.4/rgbif/tests/testthat/test-dataset_search.r | 36 - rgbif-0.8.4/rgbif/tests/testthat/test-dataset_suggest.r | 14 rgbif-0.8.4/rgbif/tests/testthat/test-datasets.r | 36 - rgbif-0.8.4/rgbif/tests/testthat/test-enumeration.r |only rgbif-0.8.4/rgbif/tests/testthat/test-gbifmap.r | 25 rgbif-0.8.4/rgbif/tests/testthat/test-installations.r | 37 - rgbif-0.8.4/rgbif/tests/testthat/test-name_backbone.r | 9 rgbif-0.8.4/rgbif/tests/testthat/test-name_lookup.r | 35 - rgbif-0.8.4/rgbif/tests/testthat/test-name_suggest.r | 19 rgbif-0.8.4/rgbif/tests/testthat/test-name_usage.r | 18 rgbif-0.8.4/rgbif/tests/testthat/test-nodes.r | 19 rgbif-0.8.4/rgbif/tests/testthat/test-occ_count.r | 25 rgbif-0.8.4/rgbif/tests/testthat/test-occ_get.r | 24 rgbif-0.8.4/rgbif/tests/testthat/test-occ_metadata.r | 32 - rgbif-0.8.4/rgbif/tests/testthat/test-occ_search.r | 91 +- rgbif-0.8.4/rgbif/tests/testthat/test-organizations.r | 13 rgbif-0.8.4/rgbif/tests/testthat/test-parsenames.r | 20 rgbif-0.8.4/rgbif/vignettes/issues_vignette.Rmd | 166 ++--- rgbif-0.8.4/rgbif/vignettes/rgbif_vignette.Rmd | 396 ++++++------ 135 files changed, 1921 insertions(+), 1802 deletions(-)
Title: Reverse Ecology Analysis on Microbiome
Description: An implementation of the reverse ecology framework. Reverse ecology
refers to the use of genomics to study ecology with no a priori assumptions
about the organism(s) under consideration, linking organisms to their
environment. It allows researchers to reconstruct the metabolic networks and
study the ecology of poorly characterized microbial species from their
genomic information, and has substantial potentials for microbial community
ecological analysis.
Author: Yang Cao, Fei Li
Maintainer: Yang Cao <yiluheihei@gmail.com>
Diff between RevEcoR versions 0.99.1 dated 2015-06-04 and 0.99.2 dated 2015-06-08
DESCRIPTION | 15 ++--- MD5 | 28 +++++---- NAMESPACE | 5 - R/AllClasses.R | 3 - R/RevEcoR.R | 5 - R/getOrgMetabolicData.R | 21 +++++-- R/getSeedSets.R | 3 - R/reconsructGsMN.R | 5 - README.md | 37 ++++++------ data/RefDbcache.rda |only inst/doc/RevEcoR.R | 14 ++-- inst/doc/RevEcoR.Rmd | 120 +++++++++++++++++++----------------------- inst/doc/RevEcoR.html | 137 ++++++++++++++++++++---------------------------- man/RefDbcache.Rd |only man/reconstructGsMN.Rd | 4 - vignettes/RevEcoR.Rmd | 120 +++++++++++++++++++----------------------- 16 files changed, 244 insertions(+), 273 deletions(-)
Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data.
It contains all data sets from https://github.com/dariusk/corpora.
Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson,
Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup,
Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,
Ross Barclay, Ross Binden, Justin Alford, Cole Willsea,
Andrew Gorman, Javier Arce, Patrick Rodriguez,
Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody,
Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black,
Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,
Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rcorpora versions 1.0.1 dated 2015-04-07 and 1.1.0 dated 2015-06-08
DESCRIPTION | 6 MD5 | 44 NAMESPACE | 2 build/rcorpora.pdf |binary inst/NEWS.md |only inst/README.markdown |only inst/corpora/README.md | 1 inst/corpora/data/animals/dinosaurs.json | 3189 ++++++---------- inst/corpora/data/architecture |only inst/corpora/data/art |only inst/corpora/data/corporations/fortune500.json |only inst/corpora/data/foods/breads_and_pastries.json |only inst/corpora/data/foods/condiments.json |only inst/corpora/data/foods/curds.json |only inst/corpora/data/games/street_fighter_ii.json |only inst/corpora/data/governments/uk_political_parties.json |only inst/corpora/data/humans/moods.json |only inst/corpora/data/materials |only inst/corpora/data/music |only inst/corpora/data/mythology |only inst/corpora/data/objects/objects.json | 453 ++ inst/corpora/data/technology/appliances.json |only man/categories.Rd | 2 man/corpora.Rd | 2 24 files changed, 1877 insertions(+), 1822 deletions(-)
Title: Methods for Causal Inference with Interference
Description: Provides methods for estimating causal effects in the presence of interference. Currently it implements the IPW estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele in "On causal inference in the presence of interference" (Statistical Methods in Medical Research, 21(1) 55-75).
Author: Bradley Saul
Maintainer: Bradley Saul <saulb@live.unc.edu>
Diff between inferference versions 0.4.61 dated 2015-03-09 and 0.4.62 dated 2015-06-08
DESCRIPTION | 10 MD5 | 43 NAMESPACE | 2 R/effect_calc.R | 2 R/interference.R | 6 R/ipw_interference.R | 2 README.md |only build/vignette.rds |binary inst/doc/inferference_intro.R | 4 inst/doc/inferference_intro.Rmd | 8 inst/doc/inferference_intro.html |23054 --------------------------------------- inst/doc/inferference_plots.html | 4 man/direct_effect.Rd | 2 man/indirect_effect.Rd | 2 man/inferference.Rd | 2 man/interference.Rd | 8 man/logit_integrand.Rd | 2 man/overall_effect.Rd | 2 man/print.interference.Rd | 2 man/total_effect.Rd | 2 man/vaccinesim.Rd | 2 man/voters.Rd | 2 vignettes/inferference_intro.Rmd | 8 23 files changed, 215 insertions(+), 22954 deletions(-)
Title: Hartigan's Dip Test Statistic for Unimodality - Corrected
Description: Compute Hartigan's dip test statistic for unimodality /
multimodality and provide a test with simulation based p-values, where
the original public code has been corrected.
Author: Martin Maechler (originally from Fortran and S-plus by Dario Ringach, NYU.edu)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between diptest versions 0.75-6 dated 2014-11-25 and 0.75-7 dated 2015-06-08
DESCRIPTION | 13 +++++++------ MD5 | 21 +++++++++++---------- R/dip.R | 3 +-- build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/diptest-issues.R | 2 +- man/dip.Rd | 9 +++++++-- man/dip.test.Rd | 4 ++-- man/qDiptab.Rd | 3 ++- tests/ex1.Rout.save | 12 ++++++------ tests/sim1.Rout.save | 16 ++++++++-------- vignettes/diptest-issues.Rnw | 16 ++++++++-------- 12 files changed, 53 insertions(+), 46 deletions(-)
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Modeling mixtures with normalized random measures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Ernesto Barrios, Antonio Lijoi, Luis E. Nieto-Barajas and Igor Prünster. R implementation by Ernesto Barrios and Luis E. Nieto-Barajas.
Maintainer: Ernesto Barrios <ebarrios@itam.mx>
Diff between BNPdensity versions 2013.8 dated 2013-07-31 and 2015.5 dated 2015-06-08
DESCRIPTION | 18 - MD5 | 74 +++---- R/MixNRMI1.R | 164 ++++++++--------- R/MixNRMI2.R | 170 ++++++++--------- R/Mv.R | 24 +- R/MvInv.R | 35 ++- R/comp1.R | 48 ++--- R/comp2.R | 60 +++--- R/cpo.R | 14 - R/dk.R | 84 ++++---- R/fcondXA.R | 22 +- R/fcondXA2.R | 22 +- R/fcondYXA.R | 24 +- R/fcondYZXA.R | 32 +-- R/gs3.R | 40 ++-- R/gs4.R | 40 ++-- R/gs5.R | 40 ++-- R/gsHP.R | 78 ++++---- R/gsYZstar.R | 86 ++++---- R/p0.R | 62 +++--- R/rfystar.R | 28 +- R/rfyzstar.R | 34 +-- R/rk.R | 86 ++++---- data/Enzyme1.out.rda |binary data/Enzyme2.out.rda |binary data/Galaxy1.out.rda |binary data/Galaxy2.out.rda |binary data/acidity.rda |binary data/enzyme.rda |binary data/galaxy.rda |binary man/BNPdensity-package.Rd | 109 +++++------ man/Enzyme1.out.Rd | 39 +--- man/Enzyme2.out.Rd | 41 ++-- man/Galaxy1.out.Rd | 39 +--- man/Galaxy2.out.Rd | 41 ++-- man/MixNRMI1.Rd | 441 +++++++++++++++++++++++----------------------- man/MixNRMI2.Rd | 423 +++++++++++++++++++++----------------------- man/MvInv.Rd | 66 +++--- 38 files changed, 1245 insertions(+), 1239 deletions(-)
Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better default printing of large matrices, and (iii) a number
of convenience functions for users more familiar with other scientific
languages like Julia, Matlab/Octave, or Python+NumPy.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between ramify versions 0.2.0 dated 2015-04-13 and 0.3.0 dated 2015-06-07
ramify-0.2.0/ramify/man/as.mat.Rd |only ramify-0.2.0/ramify/man/print.mat.Rd |only ramify-0.3.0/ramify/DESCRIPTION | 12 ramify-0.3.0/ramify/MD5 | 75 ++- ramify-0.3.0/ramify/NAMESPACE | 68 +-- ramify-0.3.0/ramify/NEWS | 12 ramify-0.3.0/ramify/R/bmat.R | 16 ramify-0.3.0/ramify/R/convenience.R | 370 ++++++++++++------ ramify-0.3.0/ramify/R/dmat.R | 8 ramify-0.3.0/ramify/R/mat.R | 190 +-------- ramify-0.3.0/ramify/R/pprint.R |only ramify-0.3.0/ramify/R/ramify.R | 2 ramify-0.3.0/ramify/R/utils.R | 21 - ramify-0.3.0/ramify/R/zzz.R | 7 ramify-0.3.0/ramify/README.md | 18 ramify-0.3.0/ramify/man/add_dots.Rd | 2 ramify-0.3.0/ramify/man/argmax.Rd | 2 ramify-0.3.0/ramify/man/atleast_2d.Rd |only ramify-0.3.0/ramify/man/bmat.Rd | 12 ramify-0.3.0/ramify/man/desc_mat.Rd | 2 ramify-0.3.0/ramify/man/dmat.Rd | 4 ramify-0.3.0/ramify/man/eye.Rd | 5 ramify-0.3.0/ramify/man/fill.Rd | 22 - ramify-0.3.0/ramify/man/flatten.Rd | 6 ramify-0.3.0/ramify/man/hcat.Rd | 7 ramify-0.3.0/ramify/man/inv.Rd | 6 ramify-0.3.0/ramify/man/is.tril.Rd |only ramify-0.3.0/ramify/man/is.triu.Rd |only ramify-0.3.0/ramify/man/linspace.Rd | 4 ramify-0.3.0/ramify/man/logspace.Rd | 2 ramify-0.3.0/ramify/man/mat.Rd | 13 ramify-0.3.0/ramify/man/meshgrid.Rd |only ramify-0.3.0/ramify/man/pprint.Rd |only ramify-0.3.0/ramify/man/ramify.Rd | 4 ramify-0.3.0/ramify/man/rand.Rd | 14 ramify-0.3.0/ramify/man/randi.Rd | 12 ramify-0.3.0/ramify/man/randn.Rd | 14 ramify-0.3.0/ramify/man/resize.Rd | 5 ramify-0.3.0/ramify/man/size.Rd | 9 ramify-0.3.0/ramify/man/tr.Rd |only ramify-0.3.0/ramify/man/tri.Rd |only ramify-0.3.0/ramify/man/tril.Rd |only ramify-0.3.0/ramify/man/triu.Rd |only ramify-0.3.0/ramify/tests/testthat/test-convenience.R |only ramify-0.3.0/ramify/tests/testthat/test-mat.R | 46 -- 45 files changed, 501 insertions(+), 489 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.1 dated 2015-06-06 and 1.6.2 dated 2015-06-07
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/QGIS2sp.R | 1 - man/PermTest.rd | 9 +++++---- man/QGIS2sp.Rd | 13 +++++-------- man/gps2gpx.rd | 1 + man/readVista.rd | 5 ++++- man/rmls.rd | 4 +--- man/uploadGPS.rd | 1 + 9 files changed, 30 insertions(+), 30 deletions(-)
Title: Introductory Statistics with R
Description: Data sets and scripts for text examples and exercises in
P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Author: Peter Dalgaard
Maintainer: Peter Dalgaard <pd.mes@cbs.dk>
Diff between ISwR versions 2.0-6 dated 2012-03-22 and 2.0-7 dated 2015-06-07
DESCRIPTION | 14 - MD5 | 6 tests/allexercises.Rout.save | 410 ++++++++++++++++----------------- tests/allscripts.Rout.save | 534 +++++++++++++++++++++---------------------- 4 files changed, 487 insertions(+), 477 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-15 dated 2015-02-11 and 1.3-16 dated 2015-06-07
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/Examples/boot-Ex.Rout.save | 19 +++++++++---------- 4 files changed, 21 insertions(+), 18 deletions(-)
Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently
scatter plots, histograms, parallel coordinate plots and choropleth maps are
supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.1.0 dated 2014-09-20 and 0.1.1 dated 2015-06-07
vdmR-0.1.0/vdmR/inst/tests/vdmR-test.R |only vdmR-0.1.1/vdmR/DESCRIPTION | 14 ++++---- vdmR-0.1.1/vdmR/MD5 | 38 +++++++++++----------- vdmR-0.1.1/vdmR/NAMESPACE | 2 - vdmR-0.1.1/vdmR/R/misc.R | 6 +-- vdmR-0.1.1/vdmR/R/vcmap.R | 5 ++ vdmR-0.1.1/vdmR/R/vhist.R | 15 ++++---- vdmR-0.1.1/vdmR/R/vlaunch.R | 50 ++++++++++++++++------------- vdmR-0.1.1/vdmR/R/vpcp.R | 7 +++- vdmR-0.1.1/vdmR/R/vscat.R | 10 ++++- vdmR-0.1.1/vdmR/build/vignette.rds |binary vdmR-0.1.1/vdmR/inst/doc/vdmR-vignette.pdf |binary vdmR-0.1.1/vdmR/inst/tests/test-vdmR.R |only vdmR-0.1.1/vdmR/man/kw2011.Rd | 3 + vdmR-0.1.1/vdmR/man/vcmap.Rd | 3 + vdmR-0.1.1/vdmR/man/vdmR-package.Rd | 3 + vdmR-0.1.1/vdmR/man/vhist.Rd | 3 + vdmR-0.1.1/vdmR/man/vlaunch.Rd | 3 + vdmR-0.1.1/vdmR/man/vpcp.Rd | 3 + vdmR-0.1.1/vdmR/man/vscat.Rd | 3 + vdmR-0.1.1/vdmR/man/vsfuk2012.Rd | 3 + 21 files changed, 99 insertions(+), 72 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter) and work with panel data (elapsed
quarters/month, lead/lag, fill in rows of values, rolling functions).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.2 dated 2015-06-03 and 0.3.0 dated 2015-06-07
statar-0.2/statar/R/demean.R |only statar-0.2/statar/R/floor_date.R |only statar-0.2/statar/R/vars.R |only statar-0.2/statar/man/demean.Rd |only statar-0.2/statar/man/floor_date.Rd |only statar-0.2/statar/man/graph.Rd |only statar-0.2/statar/man/vars.Rd |only statar-0.3.0/statar/DESCRIPTION | 23 statar-0.3.0/statar/MD5 | 82 +-- statar-0.3.0/statar/NAMESPACE | 48 +- statar-0.3.0/statar/R/count_combinations.R | 72 +-- statar-0.3.0/statar/R/elapsed_dates.R | 4 statar-0.3.0/statar/R/find_duplicates.R | 20 statar-0.3.0/statar/R/fuzzy_join.R | 172 +++---- statar-0.3.0/statar/R/graph.R | 251 ---------- statar-0.3.0/statar/R/group.R |only statar-0.3.0/statar/R/join.R | 16 statar-0.3.0/statar/R/pctile.R |only statar-0.3.0/statar/R/stat_binmean.R |only statar-0.3.0/statar/R/statar.R | 39 + statar-0.3.0/statar/R/sum_up.R | 41 - statar-0.3.0/statar/R/tab.R | 58 +- statar-0.3.0/statar/R/utils.R | 508 +++++++++++++++------- statar-0.3.0/statar/R/xtile.R | 53 -- statar-0.3.0/statar/README.md | 26 + statar-0.3.0/statar/build/vignette.rds |binary statar-0.3.0/statar/inst/doc/macros.html | 242 +--------- statar-0.3.0/statar/inst/doc/merge-records.html | 296 +++--------- statar-0.3.0/statar/inst/doc/panel-data.html | 364 +++++---------- statar-0.3.0/statar/inst/doc/summary.Rmd | 73 --- statar-0.3.0/statar/inst/doc/summary.html | 398 +++-------------- statar-0.3.0/statar/inst/doc/vector.Rmd | 12 statar-0.3.0/statar/inst/doc/vector.html | 254 +++-------- statar-0.3.0/statar/man/compute_distance.Rd | 13 statar-0.3.0/statar/man/count_combinations.Rd | 11 statar-0.3.0/statar/man/find_duplicates.Rd | 6 statar-0.3.0/statar/man/fuzzy_join.Rd | 34 - statar-0.3.0/statar/man/group.Rd |only statar-0.3.0/statar/man/join.Rd | 10 statar-0.3.0/statar/man/pctile.Rd |only statar-0.3.0/statar/man/stat_binmean.Rd |only statar-0.3.0/statar/man/tab.Rd | 10 statar-0.3.0/statar/man/xtile.Rd | 4 statar-0.3.0/statar/tests/testthat/test_elapsed.R | 3 statar-0.3.0/statar/vignettes/output_2_0.png |binary statar-0.3.0/statar/vignettes/output_3_0.png |binary statar-0.3.0/statar/vignettes/output_4_0.png |only statar-0.3.0/statar/vignettes/summary.Rmd | 73 --- statar-0.3.0/statar/vignettes/vector.Rmd | 12 49 files changed, 1161 insertions(+), 2067 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution. Different to
other coalescent based simulations, it has an optional approximation
parameter that allows for high accuracy while maintaining a linear run time
cost for long sequences. It is optimized for simulating massive data sets as
produced by Next-Generation Sequencing technologies for up to several thousand
sequences.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between scrm versions 1.5.0-1 dated 2015-04-11 and 1.6.0-2 dated 2015-06-07
DESCRIPTION | 22 MD5 | 60 +- NAMESPACE | 2 NEWS | 25 - README.md | 25 - build/vignette.rds |binary inst/CITATION | 11 inst/doc/scrm-Arguments.Rmd | 9 inst/doc/scrm-Arguments.html | 12 inst/doc/scrm-TreesForApe.R | 2 inst/doc/scrm-TreesForApe.html | 4 man/scrm-package.Rd | 2 man/scrm.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/scrm/forest.cc | 110 ++-- src/scrm/forest.h | 56 +- src/scrm/model.cc | 539 ++++++++++------------- src/scrm/model.h | 181 +++---- src/scrm/node.cc | 10 src/scrm/node.h | 22 src/scrm/param.cc | 187 +++---- src/scrm/param.h | 86 +-- src/scrm/summary_statistics/frequency_spectrum.h | 4 src/scrm/summary_statistics/newick_tree.cc | 41 - src/scrm/summary_statistics/newick_tree.h | 88 +-- src/scrm/summary_statistics/oriented_forest.cc | 2 src/scrm/summary_statistics/oriented_forest.h | 59 +- src/scrmr.cpp | 5 src/summary_statistics.cpp | 36 - vignettes/scrm-Arguments.Rmd | 9 31 files changed, 798 insertions(+), 817 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions allow to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>;
Yulia R. Gel <ygl@utdallas.edu>;
Xingyu Wang <x263wang@uwaterloo.ca>
Maintainer: Vyacheslav Lyubchich <lyubchic@cbl.umces.edu>
Diff between funtimes versions 1.0 dated 2015-01-27 and 1.1 dated 2015-06-07
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/sync.test.R | 86 ++++++++++++++++++++++++++++++------------------------- R/wavk.test.R | 2 - man/sync.test.Rd | 7 ++-- 5 files changed, 61 insertions(+), 50 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.2.0 dated 2015-06-05 and 0.2.1 dated 2015-06-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fbroc.methods.R | 2 +- src/roc.cpp | 12 ++++++------ 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Perugia)
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.0 dated 2015-01-05 and 1.1 dated 2015-06-07
cquad-1.0/cquad/data/PSID.RData |only cquad-1.0/cquad/man/PSID.Rd |only cquad-1.1/cquad/DESCRIPTION | 14 +++++++------- cquad-1.1/cquad/MD5 | 26 +++++++++++++------------- cquad-1.1/cquad/NAMESPACE | 5 +++++ cquad-1.1/cquad/R/cquad_pseudo.R | 5 +++-- cquad-1.1/cquad/data/data_sim.RData |only cquad-1.1/cquad/man/cquad-package.Rd | 18 +++++++++--------- cquad-1.1/cquad/man/cquad_basic.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_equ.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_ext.Rd | 10 +++++----- cquad-1.1/cquad/man/cquad_pseudo.Rd | 13 +++++-------- cquad-1.1/cquad/man/data_sim.Rd |only cquad-1.1/cquad/man/print.cquad.Rd | 2 +- cquad-1.1/cquad/man/sim_panel_logit.Rd | 4 ++-- cquad-1.1/cquad/man/summary.cquad.Rd | 2 +- 16 files changed, 61 insertions(+), 58 deletions(-)
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Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: The R Sequential package is designed for performing exact sequential analysis. There are functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes. These calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. For group sequential analyses, the group sizes do not have to be specified in advance and, for binomial data, the alpha spending can be arbitrarely settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 1.1 dated 2014-01-17 and 2.0 dated 2015-06-06
Sequential-1.1/Sequential/R/Sequential-internal.R |only Sequential-2.0/Sequential/DESCRIPTION | 12 Sequential-2.0/Sequential/MD5 | 37 + Sequential-2.0/Sequential/R/Analyze.Binomial.R |only Sequential-2.0/Sequential/R/AnalyzeSetUp.Binomial.R |only Sequential-2.0/Sequential/R/CV.Binomial.R |only Sequential-2.0/Sequential/R/CV.G.Binomial.R |only Sequential-2.0/Sequential/R/CV.G.Poisson.R | 4 Sequential-2.0/Sequential/R/CV.Poisson.R | 9 Sequential-2.0/Sequential/R/Performance.Binomial.R |only Sequential-2.0/Sequential/R/Performance.G.Binomial.R |only Sequential-2.0/Sequential/R/Performance.G.Poisson.R | 4 Sequential-2.0/Sequential/R/Performance.Poisson.R | 2 Sequential-2.0/Sequential/R/SampleSize.Binomial.R |only Sequential-2.0/Sequential/man/Analyze.Binomial.Rd |only Sequential-2.0/Sequential/man/AnalyzeSetUp.Binomial.Rd |only Sequential-2.0/Sequential/man/CV.Binomial.Rd |only Sequential-2.0/Sequential/man/CV.G.Binomial.Rd |only Sequential-2.0/Sequential/man/CV.G.Poisson.Rd | 38 - Sequential-2.0/Sequential/man/CV.Poisson.Rd | 30 - Sequential-2.0/Sequential/man/Performance.Binomial.Rd |only Sequential-2.0/Sequential/man/Performance.G.Binomial.Rd |only Sequential-2.0/Sequential/man/Performance.G.Poisson.Rd | 39 - Sequential-2.0/Sequential/man/Performance.Poisson.Rd | 43 -- Sequential-2.0/Sequential/man/SampleSize.Binomial.Rd |only Sequential-2.0/Sequential/man/SampleSize.Poisson.Rd | 45 +- Sequential-2.0/Sequential/man/Sequential-package.Rd | 324 +++++++++++----- 27 files changed, 364 insertions(+), 223 deletions(-)
Title: Markov Chain Monte Carlo for Potts Models
Description: Does Markov chain Monte Carlo (MCMC) simulation of Potts models
and composite likelihood inference for Potts models.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif Johnson
<leif@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between potts versions 0.5-2 dated 2014-04-02 and 0.5-3 dated 2015-06-06
ChangeLog | 6 ++++++ DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- build/vignette.rds |binary inst/doc/cll.pdf |binary man/cachet.Rd | 4 ++-- man/calct.Rd | 2 +- man/cll.Rd | 2 +- tests/debug-cond.Rout.save | 15 +++++++++------ tests/debug-free.Rout.save | 16 +++++++++------- tests/debug.Rout.save | 15 +++++++++------ 11 files changed, 54 insertions(+), 39 deletions(-)
Title: Testing, Monitoring, and Dating Structural Changes
Description: Testing, monitoring and dating structural changes in (linear)
regression models. strucchange features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM,
recursive/moving estimates) and F statistics, respectively.
It is possible to monitor incoming data online using
fluctuation processes.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals.
Emphasis is always given to methods for visualizing the data.
Author: Achim Zeileis [aut, cre],
Friedrich Leisch [aut],
Kurt Hornik [aut],
Christian Kleiber [aut],
Bruce Hansen [ctb],
Edgar C. Merkle [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between strucchange versions 1.5-0 dated 2013-10-28 and 1.5-1 dated 2015-06-06
DESCRIPTION | 18 ++- MD5 | 55 +++++------ NAMESPACE | 1 NEWS | 12 ++ R/breakpoints.R | 8 - R/gefp.R | 6 - R/simul-monitoring.R | 3 R/zzz.R | 97 ++++++++++++++------ build |only data/BostonHomicide.rda |binary data/DJIA.rda |binary data/GermanM1.rda |binary data/Grossarl.rda |binary data/PhillipsCurve.rda |binary data/RealInt.rda |binary data/SP2001.rda |binary data/USIncExp.rda |binary data/durab.rda |binary data/scPublications.rda |binary inst/doc/strucchange-intro.pdf |binary man/breakpoints.Rd | 2 man/catL2BB.Rd | 31 +++--- man/efpFunctional.Rd | 7 - man/gefp.Rd | 2 man/mefp.Rd | 2 man/sctest.default.Rd | 9 + tests/Examples/strucchange-Ex.Rout.save | 155 +++++++++++++------------------- tests/strucchange-tests.Rout.save | 40 ++++---- vignettes/strucchange-intro.Rout.save | 8 - 29 files changed, 246 insertions(+), 210 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.0-20 dated 2015-02-18 and 1.0-21 dated 2015-06-06
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- build/vignette.rds |binary data/readingSkills.rda |binary inst/NEWS | 6 ++++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary tests/Examples/party-Ex.Rout.save | 20 +++++++++----------- tests/IndependenceTest-regtest.Rout.save | 21 +++++++++++---------- 9 files changed, 39 insertions(+), 34 deletions(-)
Title: Mann-Whitney-Wilcoxon Test for Nested Ranks
Description: Calculate a Mann-Whitney-Wilcoxon test for a difference between treatment levels using nested ranks. This test can be used when observations are structured into several groups and each group has received both treatment levels. The p-value is determined via bootstrapping. The nested ranks test is intended to be one possible mixed-model extension of the Mann-Whitney-Wilcoxon test, for which treatment is a fixed effect and group membership is a random effect.
Author: Douglas G. Scofield [aut, cre]
Maintainer: Douglas G. Scofield <douglasgscofield@gmail.com>
Diff between nestedRanksTest versions 0.1 dated 2015-02-08 and 0.2 dated 2015-06-06
DESCRIPTION | 9 - MD5 | 45 +++--- NAMESPACE | 2 NEWS | 14 + R/htest_boot-class.R |only R/nestedRanksTest-data.R |only R/nestedRanksTest-package.R |only R/nestedRanksTest.R | 197 ---------------------------- README.md | 23 ++- build/vignette.rds |binary inst/doc/nestedRanksTest.R | 21 +- inst/doc/nestedRanksTest.Rmd | 35 ++-- inst/doc/nestedRanksTest.html | 43 +++--- man/nestedRanksTest-package.Rd | 8 - man/nestedRanksTest.Rd | 2 man/nestedRanksTest_Z.Rd | 2 man/nestedRanksTest_weights.Rd | 2 man/plot.htest_boot.Rd | 61 ++++---- man/print.htest_boot.Rd | 32 ++-- man/woodpecker_multiyear.Rd | 5 tests/Examples/nestedRanksTest-Ex.Rout.save | 24 +-- tests/test_interface.Rout.save | 26 +-- tests/testthat/test_iface_err.R | 2 tests/testthat/test_iface_ident.R | 2 vignettes/nestedRanksTest.Rmd | 35 ++-- 25 files changed, 218 insertions(+), 372 deletions(-)
More information about nestedRanksTest at CRAN
Permanent link
Title: Testing Linear Regression Models
Description: A collection of tests, data sets, and examples
for diagnostic checking in linear regression models. Furthermore,
some generic tools for inference in parametric models are provided.
Author: Torsten Hothorn [aut],
Achim Zeileis [aut, cre],
Richard W. Farebrother [aut] (pan.f),
Clint Cummins [aut] (pan.f),
Giovanni Millo [ctb],
David Mitchell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between lmtest versions 0.9-33 dated 2014-01-23 and 0.9-34 dated 2015-06-06
DESCRIPTION | 10 +-- MD5 | 56 ++++++++++---------- NAMESPACE | 8 ++ NEWS | 8 ++ R/coeftest.R | 3 - build/vignette.rds |binary data/ChickEgg.rda |binary data/Mandible.rda |binary data/USDistLag.rda |binary data/bondyield.rda |binary data/currencysubstitution.rda |binary data/ftemp.rda |binary data/fyff.rda |binary data/gmdc.rda |binary data/growthofmoney.rda |binary data/ip.rda |binary data/jocci.rda |binary data/lhur.rda |binary data/moneydemand.rda |binary data/pw561.rda |binary data/unemployment.rda |binary data/valueofstocks.rda |binary data/wages.rda |binary inst/doc/lmtest-intro.Rnw | 9 ++- inst/doc/lmtest-intro.pdf |binary man/jocci.Rd | 2 tests/Examples/lmtest-Ex.Rout.save | 100 ++++++++++++++++++------------------- vignettes/lmtest-intro.Rnw | 9 ++- vignettes/lmtest-intro.Rout.save | 27 +++++---- 29 files changed, 130 insertions(+), 102 deletions(-)
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between AER versions 1.2-3 dated 2015-02-24 and 1.2-4 dated 2015-06-06
DESCRIPTION | 10 - MD5 | 230 +++++++++++++++++------------------ NEWS | 5 build/vignette.rds |binary data/Affairs.rda |binary data/ArgentinaCPI.rda |binary data/BankWages.rda |binary data/BenderlyZwick.rda |binary data/BondYield.rda |binary data/CASchools.rda |binary data/CPS1985.rda |binary data/CPS1988.rda |binary data/CPSSW04.rda |binary data/CPSSW3.rda |binary data/CPSSW8.rda |binary data/CPSSW9204.rda |binary data/CPSSW9298.rda |binary data/CPSSWEducation.rda |binary data/CartelStability.rda |binary data/ChinaIncome.rda |binary data/CigarettesB.rda |binary data/CigarettesSW.rda |binary data/CollegeDistance.rda |binary data/ConsumerGood.rda |binary data/CreditCard.rda |binary data/DJFranses.rda |binary data/DoctorVisits.rda |binary data/DutchAdvert.rda |binary data/DutchSales.rda |binary data/Electricity1955.rda |binary data/Electricity1970.rda |binary data/EquationCitations.rda |binary data/Equipment.rda |binary data/EuroEnergy.rda |binary data/Fatalities.rda |binary data/Fertility.rda |binary data/Fertility2.rda |binary data/FrozenJuice.rda |binary data/GSOEP9402.rda |binary data/GSS7402.rda |binary data/GermanUnemployment.rda |binary data/GrowthDJ.rda |binary data/GrowthSW.rda |binary data/Grunfeld.rda |binary data/Guns.rda |binary data/HMDA.rda |binary data/HealthInsurance.rda |binary data/HousePrices.rda |binary data/Journals.rda |binary data/KleinI.rda |binary data/Longley.rda |binary data/MASchools.rda |binary data/ManufactCosts.rda |binary data/MarkDollar.rda |binary data/MarkPound.rda |binary data/Medicaid1986.rda |binary data/Mortgage.rda |binary data/MotorCycles.rda |binary data/Municipalities.rda |binary data/MurderRates.rda |binary data/NMES1988.rda |binary data/NYSESW.rda |binary data/NaturalGas.rda |binary data/OECDGas.rda |binary data/OECDGrowth.rda |binary data/OlympicTV.rda |binary data/OrangeCounty.rda |binary data/PSID1976.rda |binary data/PSID1982.rda |binary data/PSID7682.rda |binary data/Parade2005.rda |binary data/PepperPrice.rda |binary data/PhDPublications.rda |binary data/ProgramEffectiveness.rda |binary data/RecreationDemand.rda |binary data/ResumeNames.rda |binary data/SIC33.rda |binary data/STAR.rda |binary data/ShipAccidents.rda |binary data/SmokeBan.rda |binary data/SportsCards.rda |binary data/StrikeDuration.rda |binary data/SwissLabor.rda |binary data/TeachingRatings.rda |binary data/TechChange.rda |binary data/TradeCredit.rda |binary data/TravelMode.rda |binary data/UKInflation.rda |binary data/UKNonDurables.rda |binary data/USAirlines.rda |binary data/USConsump1950.rda |binary data/USConsump1979.rda |binary data/USConsump1993.rda |binary data/USCrudes.rda |binary data/USGasB.rda |binary data/USGasG.rda |binary data/USInvest.rda |binary data/USMacroB.rda |binary data/USMacroG.rda |binary data/USMacroSW.rda |binary data/USMacroSWM.rda |binary data/USMacroSWQ.rda |binary data/USMoney.rda |binary data/USProdIndex.rda |binary data/USSeatBelts.rda |binary data/USStocksSW.rda |binary data/WeakInstrument.rda |binary inst/doc/AER.pdf |binary inst/doc/Sweave-journals.pdf |binary tests/Ch-Basics.Rout.save | 9 - tests/Ch-Intro.Rout.save | 6 tests/Ch-LinearRegression.Rout.save | 13 - tests/Ch-Microeconometrics.Rout.save | 22 --- tests/Ch-Programming.Rout.save | 7 - tests/Ch-TimeSeries.Rout.save | 23 +-- tests/Ch-Validation.Rout.save | 25 +-- 116 files changed, 170 insertions(+), 180 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.0 dated 2015-04-30 and 1.6.1 dated 2015-06-06
pgirmess-1.6.0/pgirmess/R/clipQGIS2df.R |only pgirmess-1.6.0/pgirmess/man/clipQGIS2df.Rd |only pgirmess-1.6.1/pgirmess/DESCRIPTION | 13 +- pgirmess-1.6.1/pgirmess/MD5 | 12 +- pgirmess-1.6.1/pgirmess/NAMESPACE | 10 +- pgirmess-1.6.1/pgirmess/R/QGIS2sp.R |only pgirmess-1.6.1/pgirmess/R/readVista.r | 132 ++++------------------------- pgirmess-1.6.1/pgirmess/man/QGIS2sp.Rd |only pgirmess-1.6.1/pgirmess/man/readVista.rd | 15 +-- 9 files changed, 52 insertions(+), 130 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.0.0.1 dated 2015-02-06 and 1.0.0.2 dated 2015-06-06
DESCRIPTION | 13 MD5 | 16 R/SpatPCA.R | 1032 ++++++++++++++++++++++++------------------------- man/SpatPCA-package.Rd | 35 - man/cv.covfn.Rd | 93 ++-- man/cv.spatpca.Rd | 164 +++---- man/spatpca.Rd | 6 src/RcppExports.cpp | 118 ++--- src/rcpp_SpatPCA.cpp | 157 +++---- 9 files changed, 806 insertions(+), 828 deletions(-)
Title: Genetic Analysis Package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
Diff between gap versions 1.1-14 dated 2015-06-04 and 1.1-16 dated 2015-06-06
gap-1.1-14/gap/inst/doc/h2.R |only gap-1.1-14/gap/vignettes/figures/MCMCglmm1.pdf |only gap-1.1-14/gap/vignettes/figures/MCMCglmm2.pdf |only gap-1.1-14/gap/vignettes/figures/bugs.pdf |only gap-1.1-14/gap/vignettes/figures/h2.pdf |only gap-1.1-14/gap/vignettes/figures/h2l.pdf |only gap-1.1-14/gap/vignettes/figures/jags.pdf |only gap-1.1-14/gap/vignettes/figures/l51.pdf |only gap-1.1-14/gap/vignettes/h2.bib |only gap-1.1-14/gap/vignettes/model.txt |only gap-1.1-16/gap/ChangeLog | 7 gap-1.1-16/gap/DESCRIPTION | 12 gap-1.1-16/gap/MD5 | 41 - gap-1.1-16/gap/build/vignette.rds |binary gap-1.1-16/gap/inst/doc/gap.pdf |binary gap-1.1-16/gap/inst/doc/h2.Rnw | 562 ------------------------- gap-1.1-16/gap/inst/doc/h2.pdf |binary gap-1.1-16/gap/inst/doc/jss.pdf |binary gap-1.1-16/gap/inst/doc/pedtodot.pdf |binary gap-1.1-16/gap/inst/doc/rnews.pdf |binary gap-1.1-16/gap/vignettes/1-1-13.pdf |only gap-1.1-16/gap/vignettes/figures/4w.pdf |binary gap-1.1-16/gap/vignettes/figures/ESplot.pdf |binary gap-1.1-16/gap/vignettes/figures/asplot.pdf |binary gap-1.1-16/gap/vignettes/figures/lukas.pdf |binary gap-1.1-16/gap/vignettes/figures/qqunif.pdf |binary gap-1.1-16/gap/vignettes/h2.Rnw | 562 ------------------------- 27 files changed, 41 insertions(+), 1143 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.7 dated 2015-05-22 and 0.8 dated 2015-06-06
curl-0.7/curl/src/Makevars |only curl-0.8/curl/DESCRIPTION | 18 +++++++++--------- curl-0.8/curl/MD5 | 15 +++++++-------- curl-0.8/curl/NEWS | 3 +++ curl-0.8/curl/R/onload.R | 8 ++++++-- curl-0.8/curl/configure | 16 +++++++++------- curl-0.8/curl/inst/doc/intro.html | 14 +++++++------- curl-0.8/curl/src/curl.c | 9 +++++++++ curl-0.8/curl/src/fetch.c | 8 ++++++-- 9 files changed, 56 insertions(+), 35 deletions(-)
Title: Bayesian Analysis of Generalized Elliptical Semi-Parametric
Models and Flexible Measurement Error Models
Description: Set of tools to perform the statistical inference based on the Bayesian approach for regression models under the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distributions, i.e., additive errors follow a scale mixtures of normal distributions. The regression models considered in this package are: (i) Generalized elliptical semi-parametric models, where both location and dispersion parameters of the response variable distribution include non-parametric additive components described by using B-splines; and (ii) Flexible measurement error models under the presence of homoscedastic and heteroscedastic random errors, which admit explanatory variables with and without measurement additive errors as well as the presence of a non-parametric components approximated by using B-splines.
Author: Luz Marina Rondon <lumarp@gmail.com> and Heleno Bolfarine
Maintainer: Luz Marina Rondon <lumarp@gmail.com>
Diff between BayesGESM versions 1.3 dated 2015-03-24 and 1.4 dated 2015-06-06
BayesGESM-1.3/BayesGESM/R/bsp.graph.R |only BayesGESM-1.3/BayesGESM/man/bsp.graph.Rd |only BayesGESM-1.4/BayesGESM/DESCRIPTION | 12 BayesGESM-1.4/BayesGESM/MD5 | 41 - BayesGESM-1.4/BayesGESM/NAMESPACE | 4 BayesGESM-1.4/BayesGESM/R/BayesGESM-internal.R |only BayesGESM-1.4/BayesGESM/R/bsp.graph.fmem.R | 4 BayesGESM-1.4/BayesGESM/R/bsp.graph.gesm.R |only BayesGESM-1.4/BayesGESM/R/fmem.R | 65 +- BayesGESM-1.4/BayesGESM/R/gesm.R | 679 ++++++++++++----------- BayesGESM-1.4/BayesGESM/R/mcmc.fmem.R | 168 ++++- BayesGESM-1.4/BayesGESM/R/mcmc.gesm.R | 406 ++++++++----- BayesGESM-1.4/BayesGESM/R/summary.fmem.R | 28 BayesGESM-1.4/BayesGESM/R/summary.gesm.R | 104 ++- BayesGESM-1.4/BayesGESM/data |only BayesGESM-1.4/BayesGESM/man/BayesGESM-package.Rd | 31 - BayesGESM-1.4/BayesGESM/man/TexasData.Rd |only BayesGESM-1.4/BayesGESM/man/bsp.Rd | 2 BayesGESM-1.4/BayesGESM/man/bsp.graph.gesm.Rd |only BayesGESM-1.4/BayesGESM/man/fmem.Rd | 23 BayesGESM-1.4/BayesGESM/man/gesm.Rd | 16 BayesGESM-1.4/BayesGESM/man/mcmc.fmem.Rd | 3 BayesGESM-1.4/BayesGESM/man/mcmc.gesm.Rd | 4 BayesGESM-1.4/BayesGESM/man/summary.fmem.Rd | 2 BayesGESM-1.4/BayesGESM/man/summary.gesm.Rd | 2 25 files changed, 949 insertions(+), 645 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.3 dated 2015-06-03 and 0.9.4 dated 2015-06-05
DESCRIPTION | 6 ++--- MD5 | 21 ++++++++++--------- NEWS |only R/Utilities.R | 2 - R/accessors.R | 4 --- R/findCtx.R | 3 +- R/lazyRepo.R | 31 ++++++++++++++++++++++++++++ R/loadManifest.R | 2 - R/makePkgSourceDir-methods.R | 5 ++-- R/methods.R | 47 ++++++++++++++++++++++++++++++++++--------- inst/doc/switchrvign.pdf |binary man/lazyRepo.Rd | 7 ++++++ 12 files changed, 97 insertions(+), 31 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 1.0.0 dated 2015-04-22 and 1.0.1 dated 2015-06-05
DESCRIPTION | 23 +++++++++++--------- MD5 | 14 +++++++----- NAMESPACE | 16 +++++++------- R/rversions.R | 61 ++++++++++++++++++++++++------------------------------ inst |only man/r_oldrel.Rd | 2 - man/r_release.Rd | 2 - man/r_versions.Rd | 2 - 8 files changed, 61 insertions(+), 59 deletions(-)
Title: Two Stage Least Squares with Model Implied Instrumental Search
Description: Functions for estimating structural equation models
using a model-implied instrumental variable (MIIV) search
and two stage least squares (2SLS) estimator (MIIV-2SLS).
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.1 dated 2015-04-10 and 0.2 dated 2015-06-05
DESCRIPTION | 10 - MD5 | 24 +-- NAMESPACE | 3 R/MIIVsem-data.R | 8 - R/MIIVsem.R | 2 R/miive.R | 356 +++++++++++++++++++++++++++++++++++++++++------------ R/miivs.R | 214 +++++++++++++++++++------------ R/print.miive.R | 72 +++++++++- R/print.miivs.R | 1 man/MIIVsem.Rd | 2 man/bollen1989a.Rd | 8 - man/miive.Rd | 12 + man/miivs.Rd | 5 13 files changed, 516 insertions(+), 201 deletions(-)
Title: Interactive Grammar of Graphics
Description: An implementation of an interactive grammar of graphics, taking the
best parts of 'ggplot2', combining them with the reactive framework from
'shiny' and web graphics from 'vega'.
Author: Winston Chang [aut, cre],
Hadley Wickham [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/lib/jquery/AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/lib/jquery-ui/AUTHORS.txt),
Mike Bostock [ctb, cph] (D3 library),
D3 contributors [ctb] (D3 library; authors listed at
https://github.com/mbostock/d3/graphs/contributors),
Trifacta Inc. [cph] (Vega library),
Vega contributors [ctb] (Vega library; authors listed at
https://github.com/trifacta/vega/graphs/contributors),
Sebasti<c3><a1>n D<c3><a9>cima [ctb, cph]
(javascript-detect-element-resize library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between ggvis versions 0.4.1 dated 2015-03-12 and 0.4.2 dated 2015-06-05
ggvis-0.4.1/ggvis/inst/www/lib/jquery-ui/css |only ggvis-0.4.1/ggvis/inst/www/lib/jquery-ui/js |only ggvis-0.4.2/ggvis/DESCRIPTION | 22 ggvis-0.4.2/ggvis/LICENSE | 29 ggvis-0.4.2/ggvis/MD5 | 335 ggvis-0.4.2/ggvis/NAMESPACE | 2 ggvis-0.4.2/ggvis/R/compute_stack.R | 18 ggvis-0.4.2/ggvis/R/ggvis_html.R | 12 ggvis-0.4.2/ggvis/R/options.R | 27 ggvis-0.4.2/ggvis/R/shiny_layout.R | 4 ggvis-0.4.2/ggvis/R/vega.R | 2 ggvis-0.4.2/ggvis/build/vignette.rds |binary ggvis-0.4.2/ggvis/demo/apps/basic/server.r | 4 ggvis-0.4.2/ggvis/demo/apps/basic/ui.r | 4 ggvis-0.4.2/ggvis/inst/doc/axes-legends.R | 20 ggvis-0.4.2/ggvis/inst/doc/axes-legends.html | 3025 +-- ggvis-0.4.2/ggvis/inst/doc/cookbook.R | 32 ggvis-0.4.2/ggvis/inst/doc/cookbook.html | 5526 +++--- ggvis-0.4.2/ggvis/inst/doc/data-hierarchy.R | 6 ggvis-0.4.2/ggvis/inst/doc/ggplot2.R | 2 ggvis-0.4.2/ggvis/inst/doc/ggvis-basics.R | 4 ggvis-0.4.2/ggvis/inst/doc/ggvis-basics.html | 8902 ++++------ ggvis-0.4.2/ggvis/inst/doc/interactivity.R | 10 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Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.1.0 dated 2015-05-05 and 0.2.0 dated 2015-06-05
fbroc-0.1.0/fbroc/man/calculate.thresholds.Rd |only fbroc-0.1.0/fbroc/src/rocboot.cpp |only fbroc-0.2.0/fbroc/DESCRIPTION | 19 +-- fbroc-0.2.0/fbroc/MD5 | 52 +++++--- fbroc-0.2.0/fbroc/NAMESPACE | 1 fbroc-0.2.0/fbroc/R/RcppExports.R | 36 +++-- fbroc-0.2.0/fbroc/R/fbroc.R | 26 ++-- fbroc-0.2.0/fbroc/R/fbroc.data.doc.R |only fbroc-0.2.0/fbroc/R/fbroc.methods.R | 69 +++++++---- fbroc-0.2.0/fbroc/R/fbroc.perf.R | 61 ++++++++- fbroc-0.2.0/fbroc/R/fbroc.roc.R | 162 +++++++++++++------------- fbroc-0.2.0/fbroc/README.md | 5 fbroc-0.2.0/fbroc/data |only fbroc-0.2.0/fbroc/man/boot.roc.Rd | 42 ++++-- fbroc-0.2.0/fbroc/man/boot.tpr.at.fpr.Rd | 13 -- fbroc-0.2.0/fbroc/man/conf.roc.Rd | 4 fbroc-0.2.0/fbroc/man/fbroc.Rd | 25 ++-- fbroc-0.2.0/fbroc/man/perf.roc.Rd | 10 + fbroc-0.2.0/fbroc/man/plot.fbroc.perf.Rd | 4 fbroc-0.2.0/fbroc/man/plot.fbroc.roc.Rd | 2 fbroc-0.2.0/fbroc/man/roc.examples.Rd |only fbroc-0.2.0/fbroc/src/RcppExports.cpp | 106 ++++++++++++----- fbroc-0.2.0/fbroc/src/bootstrapper.cpp |only fbroc-0.2.0/fbroc/src/bootstrapper.h |only fbroc-0.2.0/fbroc/src/disc_roc.cpp |only fbroc-0.2.0/fbroc/src/interface.common.cpp |only fbroc-0.2.0/fbroc/src/interface.common.h |only fbroc-0.2.0/fbroc/src/interface.paired.cpp |only fbroc-0.2.0/fbroc/src/interface.single.cpp |only fbroc-0.2.0/fbroc/src/paired.roc.cpp |only fbroc-0.2.0/fbroc/src/paired.roc.h |only fbroc-0.2.0/fbroc/src/performance.cpp |only fbroc-0.2.0/fbroc/src/performance.h |only fbroc-0.2.0/fbroc/src/roc.cpp |only fbroc-0.2.0/fbroc/src/roc.h |only fbroc-0.2.0/fbroc/src/sampler.cpp |only fbroc-0.2.0/fbroc/src/sampler.h |only 37 files changed, 412 insertions(+), 225 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.6-0 dated 2015-04-03 and 1.7-1 dated 2015-06-05
TAM-1.6-0/TAM/data/sim.facets.rda |only TAM-1.6-0/TAM/data/sim.mfr.rda |only TAM-1.6-0/TAM/data/sim.rasch.missing.rda |only TAM-1.6-0/TAM/data/sim.rasch.pweights.rda |only TAM-1.6-0/TAM/data/sim.rasch.rda |only TAM-1.6-0/TAM/inst/sim.facets.R |only TAM-1.6-0/TAM/inst/sim.mfr.R |only TAM-1.6-0/TAM/inst/sim.rasch.R |only TAM-1.6-0/TAM/inst/sim.rasch.missing.R |only TAM-1.6-0/TAM/inst/sim.rasch.pweights.R |only TAM-1.6-0/TAM/man/sim.mfr.Rd |only TAM-1.6-0/TAM/man/sim.rasch.Rd |only TAM-1.7-1/TAM/DESCRIPTION | 14 TAM-1.7-1/TAM/MD5 | 127 ++++---- TAM-1.7-1/TAM/NAMESPACE | 20 + TAM-1.7-1/TAM/R/IRT.residuals.R |only TAM-1.7-1/TAM/R/TAM_utils.R |only TAM-1.7-1/TAM/R/calc_prob.v5.R | 2 TAM-1.7-1/TAM/R/mfr.dataprep.R | 40 +- TAM-1.7-1/TAM/R/msq.itemfit.R | 18 - TAM-1.7-1/TAM/R/msq.itemfitWLE.R |only TAM-1.7-1/TAM/R/plot.tam.R | 5 TAM-1.7-1/TAM/R/plotDevianceTAM.R | 18 - TAM-1.7-1/TAM/R/summary.msq.itemfit.R | 24 + TAM-1.7-1/TAM/R/summary.msq.itemfitWLE.R |only TAM-1.7-1/TAM/R/summary.tam.Q3.R |only TAM-1.7-1/TAM/R/summary.tam.R | 17 - TAM-1.7-1/TAM/R/summary.tam.modelfit.R |only TAM-1.7-1/TAM/R/tam.Q3.R |only TAM-1.7-1/TAM/R/tam.calc.counts.R | 1 TAM-1.7-1/TAM/R/tam.mml.2pl.R | 3 TAM-1.7-1/TAM/R/tam.mml.3pl.R | 44 +- TAM-1.7-1/TAM/R/tam.mml.3pl.algorithm.R | 10 TAM-1.7-1/TAM/R/tam.mml.3pl.est.slopes.R | 13 TAM-1.7-1/TAM/R/tam.mml.R | 11 TAM-1.7-1/TAM/R/tam.mml.mfr.R | 15 TAM-1.7-1/TAM/R/tam.modelfit.R | 56 ++- TAM-1.7-1/TAM/R/tam.wle.R | 40 +- TAM-1.7-1/TAM/R/tamaan.3pl.lca.R | 6 TAM-1.7-1/TAM/data/data.sim.facets.rda |only TAM-1.7-1/TAM/data/data.sim.mfr.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.missing.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.pweights.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.rda |only TAM-1.7-1/TAM/inst/NEWS | 320 +++++++++++---------- TAM-1.7-1/TAM/man/IRT.WrightMap.Rd | 9 TAM-1.7-1/TAM/man/IRT.data.tam.Rd | 10 TAM-1.7-1/TAM/man/IRT.drawPV.Rd | 4 TAM-1.7-1/TAM/man/IRT.expectedCounts.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.factor.scores.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.irfprob.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.likelihood.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.residuals.Rd |only TAM-1.7-1/TAM/man/IRT.threshold.Rd | 9 TAM-1.7-1/TAM/man/IRTLikelihood.cfa.Rd | 2 TAM-1.7-1/TAM/man/TAM-package.Rd | 8 TAM-1.7-1/TAM/man/anova.tam.Rd | 6 TAM-1.7-1/TAM/man/cfa.extract.itempars.Rd | 6 TAM-1.7-1/TAM/man/data.cqc.Rd | 13 TAM-1.7-1/TAM/man/data.sim.mfr.Rd |only TAM-1.7-1/TAM/man/data.sim.rasch.Rd |only TAM-1.7-1/TAM/man/designMatrices.Rd | 2 TAM-1.7-1/TAM/man/lavaanify.IRT.Rd | 10 TAM-1.7-1/TAM/man/msq.itemfit.Rd | 148 ++++++++- TAM-1.7-1/TAM/man/plot.tam.Rd | 18 - TAM-1.7-1/TAM/man/plotDevianceTAM.Rd | 12 TAM-1.7-1/TAM/man/predict.Rd | 10 TAM-1.7-1/TAM/man/tam.fit.Rd | 14 TAM-1.7-1/TAM/man/tam.jml.Rd | 4 TAM-1.7-1/TAM/man/tam.mml.3pl.Rd | 14 TAM-1.7-1/TAM/man/tam.mml.Rd | 44 +- TAM-1.7-1/TAM/man/tam.modelfit.Rd | 66 +++- TAM-1.7-1/TAM/man/tam.pv.Rd | 4 TAM-1.7-1/TAM/man/tam.se.Rd | 6 TAM-1.7-1/TAM/man/tam.threshold.Rd | 4 TAM-1.7-1/TAM/man/tam.wle.Rd | 21 - TAM-1.7-1/TAM/man/tamaanify.Rd | 21 - TAM-1.7-1/TAM/src/tam_mml_3pl_helper_functions.cpp | 117 +++++++ 78 files changed, 963 insertions(+), 471 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.100.1.0 dated 2015-05-01 and 0.5.200.1.0 dated 2015-06-05
ChangeLog | 26 ++ DESCRIPTION | 10 MD5 | 48 ++-- README.md | 2 inst/NEWS.Rd | 19 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/examples/fastLm.r | 46 ++++ inst/include/RcppArmadilloAs.h | 38 +-- inst/include/armadillo_bits/Col_bones.hpp | 7 inst/include/armadillo_bits/Col_meat.hpp | 114 +++++----- inst/include/armadillo_bits/Mat_bones.hpp | 16 + inst/include/armadillo_bits/Mat_meat.hpp | 270 ++++++++++++++++++------- inst/include/armadillo_bits/Row_bones.hpp | 7 inst/include/armadillo_bits/Row_meat.hpp | 114 +++++----- inst/include/armadillo_bits/arma_rng.hpp | 45 ++-- inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/cond_rel_bones.hpp | 2 inst/include/armadillo_bits/cond_rel_meat.hpp | 22 ++ inst/include/armadillo_bits/diskio_meat.hpp | 60 +++-- inst/include/armadillo_bits/fn_misc.hpp | 30 ++ inst/include/armadillo_bits/fn_rank.hpp | 44 +--- inst/include/armadillo_bits/op_misc_bones.hpp | 14 + inst/include/armadillo_bits/op_misc_meat.hpp | 57 +++++ inst/include/armadillo_bits/span.hpp | 3 25 files changed, 690 insertions(+), 308 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
G.C. Shen;
V. Shcherbakov;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-0 dated 2015-06-01 and 1.42-1 dated 2015-06-05
DESCRIPTION | 10 ++++---- MD5 | 44 ++++++++++++++++++------------------- NAMESPACE | 4 +++ NEWS | 45 ++++++++++++++++++++++++++++++++++++++ R/boundingbox.R | 7 +++++ R/hyperframe.R | 31 ++++++++++++++++++-------- R/hypersub.R | 2 - R/measures.R | 4 ++- R/mppm.R | 25 +++++++++++---------- R/randomNS.R | 17 +++++++++++--- R/solist.R | 53 ++++++++++++++++++++++++--------------------- R/util.R | 18 ++++++++++++--- R/window.R | 5 ++++ inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.pdf |binary man/boundingbox.Rd | 5 ++++ man/rNeymanScott.Rd | 10 +++++++- man/rpoispp.Rd | 3 +- man/spatstat-internal.Rd | 4 +++ vignettes/packagesizes.txt | 1 23 files changed, 207 insertions(+), 81 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.1 dated 2015-05-13 and 1.2.2 dated 2015-06-05
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mnlogit.R | 4 +++- man/hyptests.Rd | 2 +- man/mnlogit.Rd | 2 +- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic, local structural
equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between sirt versions 1.6-0 dated 2015-05-20 and 1.7-0 dated 2015-06-05
DESCRIPTION | 8 - MD5 | 57 ++++---- NAMESPACE | 5 R/btm.R |only R/btm_fit.R |only R/categorize.R | 6 R/lsem.estimate.R | 12 - R/lsem.parameter.summary.R | 2 R/lsem.permutationTest.R | 5 R/osink.R |only R/plot.lsem.permutationTest.R | 21 ++- R/summary.btm.R |only R/summary.lsem.R | 15 +- R/summary.lsem.permutationTest.R | 15 +- data/data.pw01.rda |only inst/NEWS | 18 ++ man/brm.sim.Rd | 2 man/btm.Rd |only man/categorize.Rd | 2 man/data.pw01.Rd |only man/lavaan2mirt.Rd | 16 +- man/lsem.estimate.Rd | 6 man/lsem.permutationTest.Rd | 16 +- man/mirt.wrapper.Rd | 18 +- man/modelfit.sirt.Rd | 20 +- man/noharm.sirt.Rd | 2 man/pcm.conversion.Rd | 2 man/personfit.stat.Rd | 6 man/rasch.mirtlc.Rd | 3 man/rasch.mml.Rd | 2 man/sirt-package.Rd | 266 +++++++++++++++++++-------------------- man/tam2mirt.Rd | 2 man/testlet.marginalized.Rd | 4 33 files changed, 299 insertions(+), 232 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2 dated 2015-05-13 and 2.2.1 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- man/absolute.plot.Rd | 3 ++- man/contrast.plot.Rd | 3 ++- man/nma.ab.Rd | 3 ++- man/nma.ab.cont.Rd | 3 ++- man/nma.ab.followup.Rd | 3 ++- man/nma.ab.py.Rd | 3 ++- man/rank.prob.Rd | 5 +++-- 9 files changed, 27 insertions(+), 20 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-22 dated 2015-03-14 and 1.0-23 dated 2015-06-05
DESCRIPTION | 12 MD5 | 110 NAMESPACE | 1 R/krige0.R | 207 R/krigeTg.R | 2 R/stVariogramModels.R | 84 R/variogramST.R | 6 build/vignette.rds |binary configure | 7146 ++++++++++++++++++++++++---------- configure.in | 2 data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary demo/00Index | 1 demo/localKrigeST.R | 27 demo/stkrige.R | 75 demo/zonal.R |only inst/doc/gstat.pdf |binary inst/doc/prs.Rnw | 380 - inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.Rnw |only inst/doc/spatio-temporal-kriging.pdf |only inst/doc/st.pdf |binary man/get.contr.Rd | 4 man/gstat.Rd | 34 man/krige.Rd | 14 man/krige.cv.Rd | 4 man/krigeST.Rd | 7 man/krigeTg.Rd | 6 man/map.to.lev.Rd | 4 man/predict.gstat.Rd | 12 man/vgmST.Rd | 9 man/vv.Rd | 3 src/meschach/dmacheps.c | 2 src/meschach/fmacheps.c | 2 src/meschach/maxint.c | 2 src/nsearch.c | 15 tests/merge.R | 4 tests/merge.Rout.save | 12 tests/unproj.R | 1 tests/unproj.Rout.save | 70 tests/windst.Rout.save | 19 vignettes/figures |only vignettes/prs.Rnw | 380 - vignettes/spatio-temporal-kriging.Rnw |only vignettes/spatio-temporal-kriging.bib |only 57 files changed, 6014 insertions(+), 2643 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.12.0 dated 2015-05-25 and 0.12.1 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 41 +++++++++++++++++++++-------------------- NAMESPACE | 12 ++++++++++++ NEWS | 3 +++ R/Summary_ff.R | 6 ++++++ R/compact.R | 2 +- R/cumsum.R | 9 +++++---- R/droplevels.R | 4 ++-- R/ffappend.R | 6 +++--- R/ffrep.R | 2 +- R/merge.R | 4 ++-- R/quantile_ff.R | 1 + R/rbind_ffdf.R | 4 ++-- R/save_ffdf.R | 12 ++++++------ R/subset.R | 2 +- R/table_ff.R | 2 ++ R/tabulate_ff.R | 1 + R/transform.R | 1 + R/unique.R | 1 + R/with.R | 1 + tests/testthat/testlaf.R | 7 ++++--- tests/testthat/testsave_ffdf.R |only 22 files changed, 80 insertions(+), 49 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between CDM versions 4.2-12 dated 2015-02-23 and 4.3-0 dated 2015-06-05
CDM-4.2-12/CDM/R/gdm_temp.R |only CDM-4.3-0/CDM/DESCRIPTION | 10 +++--- CDM-4.3-0/CDM/MD5 | 25 ++++++++-------- CDM-4.3-0/CDM/NAMESPACE | 2 - CDM-4.3-0/CDM/R/IRT.jackknife.gdina.R | 2 + CDM-4.3-0/CDM/R/gdina.R | 25 ++++++++++------ CDM-4.3-0/CDM/R/summary.gdina.R | 9 ++++-- CDM-4.3-0/CDM/inst/NEWS | 12 +++++++- CDM-4.3-0/CDM/man/CDM-package.Rd | 51 ++++++++++++++++------------------ CDM-4.3-0/CDM/man/data.Students.Rd | 8 ++--- CDM-4.3-0/CDM/man/data.fraction1.Rd | 2 - CDM-4.3-0/CDM/man/data.mg.Rd | 2 - CDM-4.3-0/CDM/man/entropy.lca.Rd | 6 ++-- CDM-4.3-0/CDM/man/mcdina.Rd | 4 +- 14 files changed, 88 insertions(+), 70 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-1 dated 2015-04-29 and 1.2-2 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 15 ++++++++++----- R/sn-funct.R | 43 ++++++++++++++++++++++++++++--------------- man/Qpenalty.Rd | 4 ++-- man/barolo.Rd | 10 ++++------ man/extractSECdistr.Rd | 2 +- man/selm.Rd | 18 ++++++++++-------- man/selm.fit.Rd | 15 ++++++++++----- 9 files changed, 77 insertions(+), 54 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.1-0 dated 2015-04-24 and 1.1-1 dated 2015-06-05
ChangeLog | 80 +++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++-- MD5 | 54 ++++++++++++------------ NAMESPACE | 8 +++ R/Spatial-methods.R | 22 ++++++---- R/SpatialGridDataFrame-methods.R | 6 -- R/SpatialPointsDataFrame-methods.R | 4 - R/bubble.R | 5 +- R/merge.R | 12 +++++ R/spdists.R | 58 ++++++++++++++++++++------ R/spplot.R | 67 +++++++++++++++--------------- inst/ChangeLog | 80 +++++++++++++++++++++++++++++++++++++ inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 4 + man/Spatial-class.Rd | 2 man/SpatialLines.Rd | 7 +-- man/bubble.Rd | 6 ++ man/merge.Rd | 5 +- man/spDistsN1.Rd | 54 +++++++++++++++++++++++- src/gcdist.c | 31 ++++++++++---- src/init.c | 1 src/sp.h | 4 + src/zerodist.c | 2 tests/base.Rout.save | 27 +++++++++--- tests/grid.Rout.save | 16 +++++-- tests/pass1.Rout.save | 14 +++--- 28 files changed, 445 insertions(+), 134 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package 'CDVine' are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler, Thomas Nagler, Tobias Erhardt
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>
Diff between VineCopula versions 1.4 dated 2015-01-28 and 1.5 dated 2015-06-05
DESCRIPTION | 14 MD5 | 201 +-- NAMESPACE | 11 R/0_prep_object.R | 359 +++--- R/AD.R | 37 R/BetaMatrix.r | 65 - R/BiCop.R |only R/BiCopCDF.r | 325 +++-- R/BiCopChiPlot.r | 361 +++--- R/BiCopDeriv.r | 289 ++--- R/BiCopDeriv2.r | 364 +++--- R/BiCopEst.r | 1842 +++++++++++++++++---------------- R/BiCopGofTest.r | 1172 +++++++++++--------- R/BiCopHfunc.r | 226 ++-- R/BiCopHfuncDeriv.r | 192 +-- R/BiCopHfuncDeriv2.r | 251 ++-- R/BiCopIndTest.r | 34 R/BiCopLambda.r | 600 +++++----- R/BiCopMetaContour.r | 1389 ++++++++++++------------ R/BiCopName.r | 442 +++++-- R/BiCopPDF.r | 176 ++- R/BiCopPar2Beta.r | 106 + R/BiCopPar2TailDep.r | 310 +++-- R/BiCopPar2Tau.r | 605 ++++++---- R/BiCopSelect.r | 837 ++++++++------ R/BiCopSim.R | 187 ++- R/BiCopTau2Par.r | 101 - R/BiCopVuongClarke.r | 438 ++++--- R/C2RVine.r | 175 +-- R/ChatZj.R | 87 - R/CvM.R | 34 R/D2RVine.r | 173 +-- R/Fhat.R | 50 R/KS.R | 41 R/RVineAIC.r | 370 +++--- R/RVineClarkeTest.R | 80 - R/RVineCopSelect.r | 226 ++-- R/RVineGofTest3.r | 95 - R/RVineGrad.r | 211 +-- R/RVineHessian.r | 169 +-- R/RVineLogLik.r | 224 +--- R/RVineMLE.R | 876 ++++++++------- R/RVineMatrix.R | 940 +++++++++------- R/RVinePIT.r | 198 +-- R/RVinePar2Beta.r | 33 R/RVinePar2Tau.r | 33 R/RVinePartialcorr.R | 337 +++--- R/RVineSeqEst.R | 309 +++-- R/RVineSim.R | 134 +- R/RVineStdError.r | 128 +- R/RVineStructureSelect.r | 1136 ++++++++++---------- R/RVineTreePlot.r | 744 +++++++------ R/RVineVuongTest.R | 96 - R/TauMatrix.r | 93 - R/as.copuladata.R |only R/gof_ECP.r | 310 ++--- R/gof_PIT.r | 322 ++--- R/gof_White.r | 416 +++---- R/pairs.R |only R/plot.BiCop.R |only inst/ChangeLog | 27 man/BB8Copula.Rd | 8 man/BiCop.Rd |only man/BiCopCDF.Rd | 19 man/BiCopDeriv.Rd | 20 man/BiCopDeriv2.Rd | 21 man/BiCopEst.Rd | 6 man/BiCopGofTest.Rd | 12 man/BiCopHfunc.Rd | 12 man/BiCopHfuncDeriv.Rd | 22 man/BiCopHfuncDeriv2.Rd | 22 man/BiCopLambda.Rd | 31 man/BiCopMetaContour.Rd | 3 man/BiCopPDF.Rd | 19 man/BiCopPar2Beta.Rd | 10 man/BiCopPar2TailDep.Rd | 10 man/BiCopPar2Tau.Rd | 11 man/BiCopSelect.Rd | 8 man/BiCopSim.Rd | 9 man/BiCopVuongClarke.Rd | 7 man/RVineClarkeTest.Rd | 6 man/RVineCopSelect.Rd | 8 man/RVineCor2pcor.Rd | 94 - man/RVineGofTest.Rd | 11 man/RVineMLE.Rd | 8 man/RVineMatrix.Rd | 11 man/RVinePDF.Rd |only man/RVinePIT.Rd | 13 man/RVineStructureSelect.Rd | 12 man/RVineVuongTest.Rd | 4 man/VineCopula-package.Rd | 22 man/as.copuladata.Rd |only man/pairs.copuladata.Rd |only man/plot.BiCop.Rd |only man/vineCopula.Rd | 3 src/cdvine.c | 59 - src/deriv.c | 88 + src/deriv2.c | 51 src/evCopula.c | 70 + src/gof.c | 129 +- src/incompleteBeta.c | 9 src/logderiv.c | 22 src/pit.c | 29 src/rvinederiv.c | 73 - tests/Examples/VineCopula-Ex.Rout.save | 966 ++++++++++++++--- tests/additonalExampleRuns.Rout.save | 4 106 files changed, 11910 insertions(+), 9033 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Robust mixed effects modeling by robustification
of scoring equations using the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.6 dated 2014-07-11 and 1.7-2 dated 2015-06-05
robustlmm-1.6/robustlmm/R/zero.theta.R |only robustlmm-1.6/robustlmm/vignettes/cache |only robustlmm-1.7-2/robustlmm/DESCRIPTION | 10 robustlmm-1.7-2/robustlmm/MD5 | 70 +- robustlmm-1.7-2/robustlmm/NAMESPACE | 7 robustlmm-1.7-2/robustlmm/R/AllClass.R | 4 robustlmm-1.7-2/robustlmm/R/DAS-scale.R | 59 -- robustlmm-1.7-2/robustlmm/R/accessors.R | 16 robustlmm-1.7-2/robustlmm/R/fit.effects.R | 2 robustlmm-1.7-2/robustlmm/R/fromLme4.R | 10 robustlmm-1.7-2/robustlmm/R/helpers.R | 4 robustlmm-1.7-2/robustlmm/R/mutators.R | 11 robustlmm-1.7-2/robustlmm/R/rlmer.R | 2 robustlmm-1.7-2/robustlmm/inst/doc/rlmer.R | 237 -------- robustlmm-1.7-2/robustlmm/inst/doc/rlmer.Rnw | 291 ---------- robustlmm-1.7-2/robustlmm/inst/doc/rlmer.pdf |binary robustlmm-1.7-2/robustlmm/tests/compare-methods.Rout.save | 22 robustlmm-1.7-2/robustlmm/tests/getME.R | 3 robustlmm-1.7-2/robustlmm/tests/getME.Rout.save | 122 ++-- robustlmm-1.7-2/robustlmm/tests/tau.R | 9 robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-raw.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-ta.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ex-comparsion-subsample.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ex-comparsion.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-qq-ranef.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-qq-resid.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ranef-scatterplot.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ta.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-smoothedHuber.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/rlmer.Rnw | 291 ---------- 34 files changed, 197 insertions(+), 973 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.1 dated 2015-05-26 and 0.2 dated 2015-06-05
DESCRIPTION | 6 ++--- MD5 | 13 ++++++----- NAMESPACE | 1 R/provenance.R | 62 ++++++++++++++++++++++++++++----------------------------- man/dist.Rd | 3 ++ man/get.n.Rd |only man/get.p.Rd | 2 - man/getKDE.Rd | 3 -- 8 files changed, 47 insertions(+), 43 deletions(-)
Title: Support for Linear Models
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course graduate series in
General, Generalized, and Multi-level Linear Models (PSY 610/710).
Author: John Curtin <jjcurtin@wisc.edu>
Maintainer: John Curtin <jjcurtin@wisc.edu>
Diff between lmSupport versions 2.9.1 dated 2014-09-26 and 2.9.2 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 3 ++- R/dfMerge.R | 39 +++++++++++++++++++++++++++++++++++---- R/dfReadDat.R | 6 +++--- R/dfRownames.R | 7 +++++-- R/modelCompare.R | 12 +++++++++--- R/modelPredictions.R | 2 +- R/varOdd.R |only man/dfMerge.Rd | 19 ++++++++++++------- man/dfReadDat.Rd | 5 +++-- man/dfRownames.Rd | 3 ++- man/modelCompare.Rd | 4 +--- man/varOdd.Rd |only 14 files changed, 90 insertions(+), 42 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos <martin.loos@alumni.ethz.ch>
Diff between enviPat versions 1.9 dated 2014-07-14 and 2.0 dated 2015-06-05
enviPat-1.9/enviPat/src/n-tuple.c |only enviPat-1.9/enviPat/src/n-tuple.h |only enviPat-2.0/enviPat/DESCRIPTION | 17 enviPat-2.0/enviPat/MD5 | 62 enviPat-2.0/enviPat/NEWS | 7 enviPat-2.0/enviPat/R/envelope.R | 1 enviPat-2.0/enviPat/R/enviPat.R | 7 enviPat-2.0/enviPat/R/getR.R | 2 enviPat-2.0/enviPat/R/isopattern.R | 102 enviPat-2.0/enviPat/data/adducts.rda |binary enviPat-2.0/enviPat/data/isotopes.rda |binary enviPat-2.0/enviPat/data/resolution_list.rda |binary enviPat-2.0/enviPat/inst |only enviPat-2.0/enviPat/man/adducts.Rd | 16 enviPat-2.0/enviPat/man/envelope.Rd | 1 enviPat-2.0/enviPat/man/enviPat-package.Rd | 14 enviPat-2.0/enviPat/man/isopattern.Rd | 80 enviPat-2.0/enviPat/man/isotopes.Rd | 2 enviPat-2.0/enviPat/man/mergeform.Rd | 4 enviPat-2.0/enviPat/man/resolution_list.Rd | 12 enviPat-2.0/enviPat/man/vdetect.Rd | 1 enviPat-2.0/enviPat/src/combination.c | 3634 ++++++++++++++++++++------- enviPat-2.0/enviPat/src/combination.h | 317 +- enviPat-2.0/enviPat/src/data.h |only enviPat-2.0/enviPat/src/element.c | 13 enviPat-2.0/enviPat/src/element.h | 9 enviPat-2.0/enviPat/src/isotope.c | 20 enviPat-2.0/enviPat/src/isotope.h | 11 enviPat-2.0/enviPat/src/main.c | 3218 ++++++++++++++++++----- enviPat-2.0/enviPat/src/parse.c | 372 ++ enviPat-2.0/enviPat/src/parse.h | 52 enviPat-2.0/enviPat/src/preferences.h | 126 enviPat-2.0/enviPat/src/profile.c | 72 enviPat-2.0/enviPat/src/profile.h | 19 34 files changed, 6136 insertions(+), 2055 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on
terminals that support ANSI color and highlight codes.
ANSI color support is automatically detected.
Colors and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by the chalk
JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between crayon versions 1.2.1 dated 2015-05-17 and 1.3.0 dated 2015-06-05
DESCRIPTION | 10 ++++---- MD5 | 48 ++++++++++++++++++++-------------------- NAMESPACE | 6 ++++- R/has_color.r | 8 +++++- R/parts.r |only R/utils.r | 13 ++++++++++ inst/NEWS.md | 8 ++++++ man/chr.Rd | 2 - man/col_nchar.Rd | 2 - man/col_strsplit.Rd | 2 - man/col_substr.Rd | 2 - man/col_substring.Rd | 2 - man/combine_styles.Rd | 2 - man/concat.Rd | 2 - man/crayon.Rd | 2 - man/drop_style.Rd | 2 - man/has_color.Rd | 2 - man/has_style.Rd | 2 - man/make_style.Rd | 2 - man/num_colors.Rd | 2 - man/show_ansi_colors.Rd | 2 - man/start.crayon.Rd |only man/strip_style.Rd | 2 - man/style.Rd | 2 - man/styles.Rd | 2 - tests/testthat/test-has-color.r | 31 +++++++++++++++++++++++++ 26 files changed, 110 insertions(+), 48 deletions(-)
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at (http://www.phidot.org/software/mark/downloads/)
but is not open source.
Author: Jeff Laake <jeff.laake@noaa.gov> with code contributions from Eldar
Rakhimberdiev, Ben Augustine and Daniel Turek, and example data and
analysis from Bret Collier, Jay Rotella, David Pavlacky, and Andrew Paul.
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between RMark versions 2.1.12 dated 2015-03-15 and 2.1.13 dated 2015-06-04
DESCRIPTION | 8 +-- MD5 | 49 +++++++++++---------- NAMESPACE | 3 + NEWS | 22 +++++++++ R/RMark-package.R | 32 +++++++------ R/convert.link.to.real.r | 2 R/covariate.predictions.r | 100 +++++++++++++++++++++++++------------------ R/extract.mark.output.R | 11 ++-- R/make.mark.model.R | 42 +++++++++++++----- R/mark.R | 6 +- R/model.table.R | 4 + R/process.ch.R |only R/process.data.R | 2 R/read.mark.binary.R | 32 +++++++------ R/read.mark.binary.linux.R | 32 +++++++------ R/store.r | 2 R/utility.r | 92 +++++++++++++++++++++++++++++++++++++++ inst/MarkModels.pdf |binary man/MStruncate.Rd |only man/covariate.predictions.Rd | 12 ++++- man/deer.Rd | 2 man/larksparrow.Rd | 24 +++++----- man/make.mark.model.Rd | 5 +- man/mallard.Rd | 1 man/mark.Rd | 5 +- man/process.ch.Rd |only man/wwdo.popan.Rd | 2 27 files changed, 338 insertions(+), 152 deletions(-)
Title: Terminal Progress Bars
Description: Terminal progress bars. They are
configurable, may include percentage, elapsed time, and/or
the estimated completion time. They work in the command line,
in Emacs, R Studio, Windows Rgui and Mac OSX R.app. The package
also provides a C++ API, that works with or without Rcpp.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between progress versions 1.0.1 dated 2015-05-30 and 1.0.2 dated 2015-06-04
DESCRIPTION | 6 ++--- MD5 | 11 ++++++--- inst/NEWS.md |only inst/README.md |only inst/include/RProgress.h | 50 ++++++++++++++++++++++---------------------- inst/progresstest/NAMESPACE | 1 inst/progresstest/R/test.R | 6 ++++- tests/testthat/test-cpp.R |only 8 files changed, 41 insertions(+), 33 deletions(-)
Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.13.4 dated 2015-02-25 and 1.14.0 dated 2015-06-04
MuMIn-1.13.4/MuMIn/R/beta.weights.R |only MuMIn-1.13.4/MuMIn/tests/_gam.R |only MuMIn-1.14.0/MuMIn/DESCRIPTION | 19 - MuMIn-1.14.0/MuMIn/MD5 | 81 ++++---- MuMIn-1.14.0/MuMIn/NAMESPACE | 30 +-- MuMIn-1.14.0/MuMIn/NEWS | 39 +++- MuMIn-1.14.0/MuMIn/R/DIC.R | 8 MuMIn-1.14.0/MuMIn/R/coefTable.R | 18 - MuMIn-1.14.0/MuMIn/R/coeffs.R | 18 - MuMIn-1.14.0/MuMIn/R/dredge.R | 62 ++++-- MuMIn-1.14.0/MuMIn/R/ext.R | 272 ++++++++-------------------- MuMIn-1.14.0/MuMIn/R/getAllTerms.R | 51 ++++- MuMIn-1.14.0/MuMIn/R/glm-link-new.R |only MuMIn-1.14.0/MuMIn/R/is.R | 9 MuMIn-1.14.0/MuMIn/R/methods-nobs.R | 13 - MuMIn-1.14.0/MuMIn/R/methods-predict.R |only MuMIn-1.14.0/MuMIn/R/model.avg.R | 51 +++-- MuMIn-1.14.0/MuMIn/R/model.sel.R | 31 ++- MuMIn-1.14.0/MuMIn/R/pdredge.R | 37 ++- MuMIn-1.14.0/MuMIn/R/predict-new.R |only MuMIn-1.14.0/MuMIn/R/predict.R | 8 MuMIn-1.14.0/MuMIn/R/quasiLik.R | 34 ++- MuMIn-1.14.0/MuMIn/R/r.squaredGLMM.R | 11 - MuMIn-1.14.0/MuMIn/R/r.squaredLR.R | 32 ++- MuMIn-1.14.0/MuMIn/R/std.coef.R |only MuMIn-1.14.0/MuMIn/R/stdize.R | 27 ++ MuMIn-1.14.0/MuMIn/R/updateable.R | 10 - MuMIn-1.14.0/MuMIn/R/utils-models.R | 11 - MuMIn-1.14.0/MuMIn/data/Beetle.rda |binary MuMIn-1.14.0/MuMIn/data/Cement.rda |binary MuMIn-1.14.0/MuMIn/data/GPA.rda |only MuMIn-1.14.0/MuMIn/man/ICs.Rd | 2 MuMIn-1.14.0/MuMIn/man/QIC.Rd | 8 MuMIn-1.14.0/MuMIn/man/avgpred.Rd |only MuMIn-1.14.0/MuMIn/man/dredge.Rd | 14 + MuMIn-1.14.0/MuMIn/man/glm.link.Rd |only MuMIn-1.14.0/MuMIn/man/gpa.Rd |only MuMIn-1.14.0/MuMIn/man/importance.Rd | 4 MuMIn-1.14.0/MuMIn/man/mod.sel.Rd | 9 MuMIn-1.14.0/MuMIn/man/model-utils.Rd | 34 +-- MuMIn-1.14.0/MuMIn/man/model.avg.Rd | 11 - MuMIn-1.14.0/MuMIn/man/pdredge.Rd | 3 MuMIn-1.14.0/MuMIn/man/std.coef.Rd |only MuMIn-1.14.0/MuMIn/man/stdize.Rd | 43 ++-- MuMIn-1.14.0/MuMIn/man/supported-classes.Rd | 5 MuMIn-1.14.0/MuMIn/tests/coxme.R | 14 - MuMIn-1.14.0/MuMIn/tests/misc-tests.R | 4 47 files changed, 575 insertions(+), 448 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.2.4 dated 2014-11-21 and 1.2.5 dated 2015-06-04
bpcp-1.2.4/bpcp/demo/Figure3.R |only bpcp-1.2.4/bpcp/demo/Figure4.R |only bpcp-1.2.4/bpcp/demo/Simulation.R |only bpcp-1.2.4/bpcp/demo/SimulationBootOnly.R |only bpcp-1.2.5/bpcp/DESCRIPTION | 8 ++--- bpcp-1.2.5/bpcp/MD5 | 36 +++++++++++++---------- bpcp-1.2.5/bpcp/NAMESPACE | 2 - bpcp-1.2.5/bpcp/NEWS | 8 +++++ bpcp-1.2.5/bpcp/R/bpcp2sample.R | 5 +-- bpcp-1.2.5/bpcp/R/kmciFunctions.R | 40 ++++++++++++++++++++------ bpcp-1.2.5/bpcp/demo/00Index | 14 +++------ bpcp-1.2.5/bpcp/demo/FigureSclerosis.R |only bpcp-1.2.5/bpcp/demo/FigureWilms.R |only bpcp-1.2.5/bpcp/demo/NotesMMandMC.R |only bpcp-1.2.5/bpcp/demo/Simulation2013.R |only bpcp-1.2.5/bpcp/demo/Simulation2015.R |only bpcp-1.2.5/bpcp/demo/SimulationBootOnly2013.R |only bpcp-1.2.5/bpcp/inst/CITATION | 27 +++++++++++++---- bpcp-1.2.5/bpcp/inst/doc |only bpcp-1.2.5/bpcp/man/bpcp-internal.Rd | 5 +-- bpcp-1.2.5/bpcp/man/bpcp-package.Rd | 14 +++++---- bpcp-1.2.5/bpcp/man/bpcp2samp.Rd | 4 +- bpcp-1.2.5/bpcp/man/bpcpControl.Rd |only bpcp-1.2.5/bpcp/man/fixtdiff.Rd | 4 +- bpcp-1.2.5/bpcp/man/kmciALL.Rd | 15 +++++---- 25 files changed, 118 insertions(+), 64 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.2 dated 2015-01-08 and 1.5.3 dated 2015-06-04
ssym-1.5.2/ssym/R/itpM.R |only ssym-1.5.2/ssym/R/itpM2.R |only ssym-1.5.2/ssym/R/itpM3.R |only ssym-1.5.2/ssym/R/lambda.hat.R |only ssym-1.5.2/ssym/R/print.ssym.R |only ssym-1.5.2/ssym/man/itpM.Rd |only ssym-1.5.2/ssym/man/itpM2.Rd |only ssym-1.5.2/ssym/man/itpM3.Rd |only ssym-1.5.2/ssym/man/lambda.hat.Rd |only ssym-1.5.3/ssym/DESCRIPTION | 16 ssym-1.5.3/ssym/MD5 | 115 +-- ssym-1.5.3/ssym/NAMESPACE | 16 ssym-1.5.3/ssym/R/AIC.ssym.R | 9 ssym-1.5.3/ssym/R/BIC.ssym.R | 9 ssym-1.5.3/ssym/R/coef.ssym.R | 2 ssym-1.5.3/ssym/R/envelope.R |only ssym-1.5.3/ssym/R/estfun.ssym.R | 2 ssym-1.5.3/ssym/R/extra.parameter.R |only ssym-1.5.3/ssym/R/influence.ssym.R | 35 ssym-1.5.3/ssym/R/itpE.R | 55 + ssym-1.5.3/ssym/R/itpE2.R | 68 + ssym-1.5.3/ssym/R/itpE3.R | 42 + ssym-1.5.3/ssym/R/itpEC.R |only ssym-1.5.3/ssym/R/itpEC2.R |only ssym-1.5.3/ssym/R/logLik.ssym.R | 7 ssym-1.5.3/ssym/R/ncs.R | 82 +- ssym-1.5.3/ssym/R/np.graph.R | 153 ++-- ssym-1.5.3/ssym/R/plot.ssym.R | 26 ssym-1.5.3/ssym/R/psp.R | 56 + ssym-1.5.3/ssym/R/residuals.ssym.R | 5 ssym-1.5.3/ssym/R/ssym.l.R | 1240 +++++++++------------------------ ssym-1.5.3/ssym/R/ssym.l2.R |only ssym-1.5.3/ssym/R/ssym.nl.R | 818 ++++++++------------- ssym-1.5.3/ssym/R/summary.ssym.R | 131 +-- ssym-1.5.3/ssym/R/vcov.ssym.R | 3 ssym-1.5.3/ssym/data/Baboons.rda |only ssym-1.5.3/ssym/data/Steel.rda |only ssym-1.5.3/ssym/man/AIC.ssym.Rd | 2 ssym-1.5.3/ssym/man/BIC.ssym.Rd | 2 ssym-1.5.3/ssym/man/Baboons.Rd |only ssym-1.5.3/ssym/man/Biaxial.Rd | 2 ssym-1.5.3/ssym/man/Claims.Rd | 4 ssym-1.5.3/ssym/man/Erabbits.Rd | 15 ssym-1.5.3/ssym/man/Ovocytes.Rd | 6 ssym-1.5.3/ssym/man/Steel.Rd |only ssym-1.5.3/ssym/man/coef.ssym.Rd | 2 ssym-1.5.3/ssym/man/envelope.Rd |only ssym-1.5.3/ssym/man/estfun.ssym.Rd | 2 ssym-1.5.3/ssym/man/extra.parameter.Rd |only ssym-1.5.3/ssym/man/fitted.ssym.Rd | 2 ssym-1.5.3/ssym/man/influence.ssym.Rd | 2 ssym-1.5.3/ssym/man/itpE.Rd | 2 ssym-1.5.3/ssym/man/itpE2.Rd | 2 ssym-1.5.3/ssym/man/itpE3.Rd | 2 ssym-1.5.3/ssym/man/itpEC.Rd |only ssym-1.5.3/ssym/man/itpEC2.Rd |only ssym-1.5.3/ssym/man/logLik.ssym.Rd | 2 ssym-1.5.3/ssym/man/ncs.Rd | 23 ssym-1.5.3/ssym/man/np.graph.Rd | 39 - ssym-1.5.3/ssym/man/plot.ssym.Rd | 6 ssym-1.5.3/ssym/man/print.ssym.Rd | 4 ssym-1.5.3/ssym/man/psp.Rd | 17 ssym-1.5.3/ssym/man/residuals.ssym.Rd | 2 ssym-1.5.3/ssym/man/rvgs.Rd | 8 ssym-1.5.3/ssym/man/ssym-package.Rd | 14 ssym-1.5.3/ssym/man/ssym.l.Rd | 262 ++++-- ssym-1.5.3/ssym/man/ssym.l2.Rd |only ssym-1.5.3/ssym/man/ssym.nl.Rd | 222 +++-- ssym-1.5.3/ssym/man/summary.ssym.Rd | 4 ssym-1.5.3/ssym/man/vcov.ssym.Rd | 2 70 files changed, 1604 insertions(+), 1936 deletions(-)
Title: Predicting Species Accumulation Curves
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>
Diff between preseqR versions 1.1.1 dated 2015-04-01 and 1.2.1 dated 2015-06-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/continued_fraction.R | 16 ++++++++++------ README.md | 4 ++-- man/preseqR.rfa.curve.Rd | 6 +++++- man/preseqR.rfa.species.accum.curve.Rd | 6 +++++- 6 files changed, 31 insertions(+), 19 deletions(-)
Title: Genetic Analysis Package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
Diff between gap versions 1.1-13 dated 2015-06-03 and 1.1-14 dated 2015-06-04
ChangeLog | 4 +++ DESCRIPTION | 15 ++++++------- MD5 | 46 ++++++++++++++++++++-------------------- inst/doc/gap.Rnw | 2 - inst/doc/gap.pdf |binary inst/doc/h2.R | 35 +----------------------------- inst/doc/h2.Rnw | 15 ++++++------- inst/doc/h2.pdf |binary inst/doc/jss.pdf |binary inst/doc/pedtodot.pdf |binary inst/doc/rnews.pdf |binary vignettes/figures/4w.pdf |binary vignettes/figures/ESplot.pdf |binary vignettes/figures/MCMCglmm1.pdf |binary vignettes/figures/asplot.pdf |binary vignettes/figures/bugs.pdf |binary vignettes/figures/h2.pdf |binary vignettes/figures/h2l.pdf |binary vignettes/figures/jags.pdf |binary vignettes/figures/l51.pdf |binary vignettes/figures/lukas.pdf |binary vignettes/figures/qqunif.pdf |binary vignettes/gap.Rnw | 2 - vignettes/h2.Rnw | 15 ++++++------- 24 files changed, 52 insertions(+), 82 deletions(-)
More information about odds.converter at CRAN
Permanent link
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml versions 2.3 dated 2015-05-20 and 2.3.1 dated 2015-06-04
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/kml.R | 8 ++++++++ 3 files changed, 15 insertions(+), 7 deletions(-)
Title: Model Based Clustering for Mixed Data
Description: Model-based clustering of mixed data (i.e. data which consist of continuous, binary, ordinal or nominal variables) using a parsimonious mixture of latent Gaussian variable models.
Author: Damien McParland
Maintainer: Damien McParland <damien.mcparland@ucd.ie>
Diff between clustMD versions 1.0 dated 2014-06-12 and 1.1 dated 2015-06-04
DESCRIPTION | 10 - MD5 | 22 +- R/E.step.R | 82 +++++----- R/M.step.R | 397 ++++++++++++++++++++++++++------------------------- R/ObsLogLikelihood.R | 88 +++++------ R/clustMD-internal.R | 260 ++++++++++++++++----------------- R/clustMD.R | 331 ++++++++++++++++++++++-------------------- R/npars_clustMD.R | 74 ++++----- R/perc.cutoffs.R | 10 - R/z.moments.R | 84 +++++----- R/z.nom.diag.R | 34 ++-- man/clustMD.Rd | 16 +- 12 files changed, 718 insertions(+), 690 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.2-06 dated 2015-01-23 and 1.2-07 dated 2015-06-04
PowerTOST-1.2-06/PowerTOST/R/power2.R |only PowerTOST-1.2-07/PowerTOST/DESCRIPTION | 14 ++-- PowerTOST-1.2-07/PowerTOST/MD5 | 31 ++++----- PowerTOST-1.2-07/PowerTOST/NAMESPACE | 2 PowerTOST-1.2-07/PowerTOST/NEWS | 10 ++ PowerTOST-1.2-07/PowerTOST/R/Fieller.R | 14 ++-- PowerTOST-1.2-07/PowerTOST/R/expSampleSize.R | 1 PowerTOST-1.2-07/PowerTOST/R/pa.scABE.R | 78 ++++++++++++----------- PowerTOST-1.2-07/PowerTOST/R/power_scABEL.R | 23 ++---- PowerTOST-1.2-07/PowerTOST/R/pwrA_S3methods.R | 3 PowerTOST-1.2-07/PowerTOST/R/samplesize_scABEL.R | 33 +++++---- PowerTOST-1.2-07/PowerTOST/R/scABEL.R |only PowerTOST-1.2-07/PowerTOST/man/pa.ABE.Rd | 11 +-- PowerTOST-1.2-07/PowerTOST/man/pa.scABE.Rd | 6 + PowerTOST-1.2-07/PowerTOST/man/power.TOST.Rd | 16 +--- PowerTOST-1.2-07/PowerTOST/man/power.scABEL.Rd | 10 ++ PowerTOST-1.2-07/PowerTOST/man/sampleN.scABEL.Rd | 12 ++- PowerTOST-1.2-07/PowerTOST/man/scABEL.Rd |only 18 files changed, 144 insertions(+), 120 deletions(-)
Title: Clustering Indices
Description: Compute clustering validation indices.
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes <bernard.desgraupes@u-paris10.fr>
Diff between clusterCrit versions 1.2.4 dated 2014-12-11 and 1.2.5 dated 2015-06-04
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ build/clusterCrit.pdf |binary build/partial.rdb |binary build/vignette.rds |binary inst/benchmark/Makefile | 17 +++-------------- inst/unitTests/Makefile | 14 +------------- src/logFile.f95 |only src/timer.f95 |only 9 files changed, 17 insertions(+), 38 deletions(-)
Title: Coarsened Exact Matching
Description: Implementation of the Coarsened Exact Matching algorithm.
Author: Iacus, Stefano M., King, Gary, Porro, Giuseppe
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between cem versions 1.1.10 dated 2014-03-25 and 1.1.16 dated 2015-06-04
.Rinstignore | 7 +- DESCRIPTION | 17 +++---- MD5 | 85 +++++++++++++++++++++++++---------- NAMESPACE | 12 +++- R/att.R | 8 ++- R/cem.R | 2 R/cem.main.R | 16 ++---- R/imbspace.plot.R | 2 R/k2k.R | 92 ++++++++++++++++++++++++++++++++++++-- R/relax.cem.R | 35 +++++++++++--- R/relax.plot.R | 9 ++- R/search.match.R | 4 - R/spacegraph.R | 4 - build/vignette.rds |binary inst/doc/Columbus_egg.jpg |only inst/doc/DW.tex |only inst/doc/JSS-paper.tex |only inst/doc/JSSstyle |only inst/doc/JSSstyle.zip |only inst/doc/att.tex |only inst/doc/balance-scale-redone.jpg |only inst/doc/cem.R | 90 ++++++++++++++++++------------------- inst/doc/cem.Rnw | 67 +++++++++++++-------------- inst/doc/cem.bib |only inst/doc/cem.pdf |binary inst/doc/coarsen1.pdf |only inst/doc/coarsen2.pdf |only inst/doc/d.tex |only inst/doc/imbalance.tex |only inst/doc/index.shtml |only inst/doc/outdata1.csv |only inst/doc/outdata2.csv |only inst/doc/outdata3.csv |only inst/doc/outdata4.csv |only inst/doc/outdata5.csv |only inst/doc/pair.tex |only inst/doc/resprev.tex |only inst/doc/teff.pdf |only inst/doc/upquote.sty |only man/L1.profile.Rd | 16 +++--- man/att.Rd | 2 man/cem.Rd | 1 man/combine.spacegraphs.Rd | 3 - man/imbspace.plot.Rd | 8 ++- man/k2k.Rd | 5 +- man/relax.cem.Rd | 6 +- man/spacegraph.Rd | 9 ++- vignettes/cem.Rnw | 4 + 48 files changed, 333 insertions(+), 171 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.2 dated 2015-05-04 and 1.2.1 dated 2015-06-04
ChangeLog | 3 +++ DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/mask2Te.R | 2 +- man/sglasso-package.Rd | 4 ++-- src/sglasso_ccd_path.f90 | 4 ++-- src/sglasso_ccd_single.f90 | 4 ++-- src/sglasso_ccm_path.f90 | 4 ++-- src/sglasso_ccm_single.f90 | 4 ++-- 9 files changed, 28 insertions(+), 25 deletions(-)
Title: A Stacked Autoencoder Implementation with Interface to
'neuralnet'
Description: An implementation of a stacked sparse autoencoder for dimension reduction of features and pre-training of feed-forward neural networks
with the 'neuralnet' package is contained within this package. The package also includes a predict function for the stacked autoencoder object to generate the compressed
representation of new data if required. For the purposes of this package, 'stacked' is defined in line with http://ufldl.stanford.edu/wiki/index.php/Stacked_Autoencoders .
The underlying sparse autoencoder is defined in the documentation of 'autoencoder'.
Author: Stephen Hogg [aut, cre],
Eugene Dubossarsky [aut]
Maintainer: Stephen Hogg <saenet.r@gmail.com>
Diff between SAENET versions 1.0 dated 2015-02-03 and 1.1 dated 2015-06-04
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/SAENET.R | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and proportional odds models and fully parametric Cox-PH and proportional odds models. Also includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.3 dated 2015-06-03 and 1.2.4 dated 2015-06-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/icenReg_files/ic_par.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.3.0 dated 2015-06-03 and 0.3.1 dated 2015-06-04
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NEWS | 4 ++++ README.md | 6 +++++- build/vignette.rds |binary vignettes/introduction.Rmd | 2 +- 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.33 dated 2015-05-27 and 1.35 dated 2015-06-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/aSPUpath.r | 8 ++++---- README.md | 17 +++++++---------- 4 files changed, 18 insertions(+), 21 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: Tools inspired by Stata for tabular datasets. It
includes a set of functions to summarize and tabulate datasets, to join
datasets using an SQL-syntax, to manipulate datasets with a panel structure
(elapsed dates, lead/lag, rolling functions, fill in missing values based
on previous dates, add rows for missing dates).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.1.3 dated 2015-01-08 and 0.2 dated 2015-06-03
statar-0.1.3/statar/R/bin.R |only statar-0.1.3/statar/R/lead-lag.R |only statar-0.1.3/statar/R/setkeep.R |only statar-0.1.3/statar/R/setmutate.R |only statar-0.1.3/statar/man/bin.Rd |only statar-0.1.3/statar/man/lead-lag.Rd |only statar-0.1.3/statar/man/sample_mode.Rd |only statar-0.1.3/statar/man/setdrop.Rd |only statar-0.1.3/statar/man/setmutate.Rd |only statar-0.1.3/statar/man/setmutate_each.Rd |only statar-0.2/statar/DESCRIPTION | 23 - statar-0.2/statar/MD5 | 123 +++--- statar-0.2/statar/NAMESPACE | 79 +++- statar-0.2/statar/R/count_combinations.R |only statar-0.2/statar/R/demean.R | 54 +- statar-0.2/statar/R/elapsed_dates.R | 3 statar-0.2/statar/R/fill_gap.R | 10 statar-0.2/statar/R/find_duplicates.R | 44 -- statar-0.2/statar/R/fuzzy_join.R |only statar-0.2/statar/R/graph.R | 185 ++++----- statar-0.2/statar/R/join.R | 203 ++++------ statar-0.2/statar/R/pastem.R | 44 +- statar-0.2/statar/R/print_all.R |only statar-0.2/statar/R/roll.R | 52 +- statar-0.2/statar/R/sample_mode.R | 56 ++- statar-0.2/statar/R/set.R |only statar-0.2/statar/R/setna.R | 2 statar-0.2/statar/R/setpanel.R |only statar-0.2/statar/R/spread_.R | 2 statar-0.2/statar/R/statar.R | 38 +- statar-0.2/statar/R/sum_up.R | 120 +++--- statar-0.2/statar/R/tab.R |only statar-0.2/statar/R/tlead-tlag.R |only statar-0.2/statar/R/utils.R | 250 +++++++++++++ statar-0.2/statar/R/vars.R |only statar-0.2/statar/R/winsorize.R | 28 - statar-0.2/statar/R/xtile.R |only statar-0.2/statar/README.md | 2 statar-0.2/statar/build/vignette.rds |binary statar-0.2/statar/inst/doc/macros.html | 242 ++++++++++--- statar-0.2/statar/inst/doc/merge-records.html | 296 +++++++++++---- statar-0.2/statar/inst/doc/panel-data.Rmd | 11 statar-0.2/statar/inst/doc/panel-data.html | 367 ++++++++++++------- statar-0.2/statar/inst/doc/summary.Rmd | 158 ++------ statar-0.2/statar/inst/doc/summary.html | 482 +++++++++++++++----------- statar-0.2/statar/inst/doc/vector.Rmd |only statar-0.2/statar/inst/doc/vector.html |only statar-0.2/statar/man/compute_distance.Rd |only statar-0.2/statar/man/count_combinations.Rd |only statar-0.2/statar/man/demean.Rd | 13 statar-0.2/statar/man/discard.Rd |only statar-0.2/statar/man/discard_if.Rd |only statar-0.2/statar/man/elapsed.Rd | 5 statar-0.2/statar/man/fill_gap.Rd | 5 statar-0.2/statar/man/find_duplicates.Rd | 17 statar-0.2/statar/man/floor_date.Rd | 2 statar-0.2/statar/man/fuzzy_join.Rd |only statar-0.2/statar/man/graph.Rd | 23 - statar-0.2/statar/man/is.panel.Rd |only statar-0.2/statar/man/join.Rd | 38 +- statar-0.2/statar/man/keep.Rd |only statar-0.2/statar/man/keep_if.Rd |only statar-0.2/statar/man/pastem.Rd | 22 - statar-0.2/statar/man/roll.Rd | 31 - statar-0.2/statar/man/setdiscard.Rd |only statar-0.2/statar/man/setkeep.Rd | 4 statar-0.2/statar/man/setna.Rd | 2 statar-0.2/statar/man/statar.Rd | 2 statar-0.2/statar/man/sum_up.Rd | 25 - statar-0.2/statar/man/tab.Rd |only statar-0.2/statar/man/tag.Rd | 2 statar-0.2/statar/man/tempname.Rd | 2 statar-0.2/statar/man/tlead-tlag.Rd |only statar-0.2/statar/man/vars.Rd |only statar-0.2/statar/man/winsorize.Rd | 2 statar-0.2/statar/man/xtile.Rd |only statar-0.2/statar/tests/testthat/test_lag.R | 10 statar-0.2/statar/vignettes/panel-data.Rmd | 11 statar-0.2/statar/vignettes/summary.Rmd | 158 ++------ statar-0.2/statar/vignettes/vector.Rmd |only 80 files changed, 1974 insertions(+), 1274 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.15.3 dated 2014-06-14 and 0.15.17 dated 2015-06-03
installr-0.15.17/installr/ChangeLog |only installr-0.15.17/installr/DESCRIPTION | 21 - installr-0.15.17/installr/MD5 | 198 +++++----- installr-0.15.17/installr/NAMESPACE | 9 installr-0.15.17/installr/NEWS | 103 +++++ installr-0.15.17/installr/R/RStudio_CRAN_data.R |only installr-0.15.17/installr/R/create.global.library.R |only installr-0.15.17/installr/R/geo_functions.R |only installr-0.15.17/installr/R/install.R |only installr-0.15.17/installr/R/is.x.R |only installr-0.15.17/installr/R/kill_pid.R |only installr-0.15.17/installr/R/os.manage.R |only installr-0.15.17/installr/R/rename_r_to_R.R |only installr-0.15.17/installr/R/startup.R |only installr-0.15.17/installr/R/updateR.R |only installr-0.15.17/installr/R/xlsx2csv.R |only installr-0.15.17/installr/R/zzz.R |only installr-0.15.17/installr/README.md | 33 + installr-0.15.17/installr/TODO |only installr-0.15.17/installr/man/R_version_in_a_folder.Rd | 3 installr-0.15.17/installr/man/add.installr.GUI.Rd | 3 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|only installr-0.15.3/installr/R/zzz.r |only 114 files changed, 465 insertions(+), 237 deletions(-)
Title: Statistical Analysis of Environmental Space-Time Processes
Description: Functions and datasets to support the book by Nhu D Le and James V Zidek, Springer (2006).
Author: Nhu Le, Jim Zidek, Rick White, and Davor Cubranic, with
Fortran code for Sampson-Guttorp estimation authored by Paul D.
Sampson, Peter Guttorp, Wendy Meiring, and Catherine Hurley, and
Runge-Kutta-Fehlberg method implementation by H.A. Watts and L.F. Shampine.
Maintainer: Davor Cubranic <cubranic@stat.ubc.ca>
Diff between EnviroStat versions 0.4-0 dated 2014-03-07 and 0.4-2 dated 2015-06-03
DESCRIPTION | 12 ++--- MD5 | 10 ++-- NEWS |only R/LZ-EM.est.R | 100 +++++++++++++++++++++++++----------------------- build |only inst/doc/EnviroStat.pdf |binary src/LZ-design.c | 2 7 files changed, 67 insertions(+), 57 deletions(-)
Title: The Bayesian Dynamic Conditional Correlation GARCH Model
Description: Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635).
Author: Jose A Fioruci <jafioruci@gmail.com>, Ricardo S Ehlers <ehlers@icmc.usp.br>, Francisco Louzada <louzada@icmc.usp.br>
Maintainer: Jose A Fioruci <jafioruci@gmail.com>
Diff between bayesDccGarch versions 1.0 dated 2015-01-13 and 1.1 dated 2015-06-03
ChangeLog |only DESCRIPTION | 17 +++++------ MD5 | 17 +++++------ NAMESPACE | 1 R/mainFunctions.R | 65 +++++++++++++------------------------------ man/bayesDccGarch-package.Rd | 17 ++++++----- man/bayesDccGarch.Rd | 11 ++++--- man/logLikDccGarch.Rd | 5 ++- man/plotVol.Rd | 6 +++ src/bayesDccGarch.c | 4 +- 10 files changed, 68 insertions(+), 75 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-8 dated 2014-11-13 and 0.9-9 dated 2015-06-03
DESCRIPTION | 18 - MD5 | 290 ++++++++++++++------------ NAMESPACE | 107 +++++++++ NEWS | 8 R/BsplineHaz.R | 143 ------------ R/GMRF.R |only R/calibratemcmc.R | 186 ++++++++++++++++ R/covarianceFunctions.R | 89 +++++++ R/log_posteriors_and_derivatives.R | 29 ++ R/log_posteriors_and_derivatives_SPDE.R |only R/log_posteriors_and_derivatives_gridded.R | 27 ++ R/log_posteriors_and_derivatives_polygonal.R |only R/maplayers.R |only R/mcmcPriors.R | 48 +++- R/nonspatial_log_likelihood_and_derivatives.R | 29 ++ R/plottingfunctions.R |only R/postprocessing.R | 255 ++++++++++++++++++++-- R/spatgrid.R | 24 +- R/spatsurv.R | 30 +- R/spatsurvMisc.R | 42 +++ R/splineFunctions.R |only R/survspat.R | 163 +++++++++++++- R/survspatNS.R | 10 man/B.Rd |only man/Bspline.construct.Rd |only man/BsplineHaz.Rd | 3 man/CSplot.Rd |only man/Et_PP.Rd | 3 man/EvalCov.Rd | 3 man/ExponentialCovFct.Rd | 3 man/FFTgrid.Rd | 3 man/GammaFromY_SPDE.Rd |only man/GammafromY.Rd | 3 man/MCE.Rd | 3 man/NonSpatialLogLikelihood_or_gradient.Rd | 8 man/QuadApprox.Rd | 3 man/SPDE.Rd |only man/SPDEprec.Rd |only man/SpikedExponentialCovFct.Rd | 3 man/YFromGamma_SPDE.Rd |only man/YfromGamma.Rd | 3 man/allocate.Rd |only man/alpha.Rd |only man/basehazard.Rd | 3 man/basehazard.basehazardspec.Rd | 3 man/baselinehazard.Rd | 7 man/betapriorGauss.Rd | 3 man/checkSurvivalData.Rd | 3 man/circulant.Rd | 3 man/circulant.matrix.Rd | 3 man/circulant.numeric.Rd | 3 man/circulantij.Rd | 3 man/covmodel.Rd | 3 man/cumbasehazard.Rd | 3 man/cumbasehazard.basehazardspec.Rd | 3 man/cumulativeBspline.construct.Rd |only man/density_PP.Rd | 3 man/densityquantile.Rd | 3 man/densityquantile.basehazardspec.Rd | 3 man/densityquantile_PP.Rd | 3 man/derivindepGaussianprior.Rd | 3 man/distinfo.Rd | 3 man/distinfo.basehazardspec.Rd | 3 man/estimateY.Rd | 3 man/etapriorGauss.Rd | 3 man/exponentialHaz.Rd | 3 man/fixedpars.Rd | 3 man/fixmatrix.Rd | 3 man/frailtylag1.Rd | 9 man/gencens.Rd | 3 man/getBbasis.Rd |only man/getGrid.Rd |only man/getcov.Rd | 3 man/getleneta.Rd | 3 man/getparranges.Rd | 3 man/getsurvdata.Rd | 3 man/gompertzHaz.Rd | 3 man/gradbasehazard.Rd | 3 man/gradbasehazard.basehazardspec.Rd | 3 man/gradcumbasehazard.Rd | 3 man/gradcumbasehazard.basehazardspec.Rd | 3 man/grid2spdf.Rd | 3 man/grid2spix.Rd | 3 man/grid2spts.Rd | 3 man/gridY.Rd | 3 man/gridY_polygonal.Rd |only man/guess_t.Rd | 3 man/hasNext.Rd | 3 man/hasNext.iter.Rd | 3 man/hazard_PP.Rd | 3 man/hazardexceedance.Rd | 3 man/hazardpars.Rd | 3 man/hessbasehazard.Rd | 3 man/hessbasehazard.basehazardspec.Rd | 3 man/hesscumbasehazard.Rd | 3 man/hesscumbasehazard.basehazardspec.Rd | 3 man/indepGaussianprior.Rd | 3 man/inference.control.Rd | 3 man/invtransformweibull.Rd | 3 man/is.burnin.Rd | 3 man/is.retain.Rd | 3 man/iteration.Rd | 3 man/logPosterior.Rd | 8 man/logPosterior_SPDE.Rd |only man/logPosterior_gridded.Rd | 8 man/logPosterior_polygonal.Rd |only man/loop.mcmc.Rd | 3 man/makehamHaz.Rd | 3 man/maxlikparamPHsurv.Rd | 8 man/mcmcLoop.Rd | 3 man/mcmcPriors.Rd | 3 man/mcmcProgressNone.Rd | 3 man/mcmcProgressPrint.Rd | 3 man/mcmcProgressTextBar.Rd | 3 man/mcmcpars.Rd | 3 man/midpts.Rd |only man/neighLocs.Rd |only man/neighOrder.Rd |only man/nextStep.Rd | 3 man/omegapriorGauss.Rd | 3 man/plotsurv.Rd | 3 man/polyadd.Rd |only man/polymult.Rd |only man/posteriorcov.Rd | 7 man/predict.mcmcspatsurv.Rd | 7 man/print.mcmc.Rd | 3 man/print.mcmcspatsurv.Rd | 3 man/print.mlspatsurv.Rd | 3 man/priorposterior.Rd | 7 man/proposalVariance.Rd | 3 man/proposalVariance_SPDE.Rd |only man/proposalVariance_gridded.Rd | 3 man/proposalVariance_polygonal.Rd |only man/quantile.mcmcspatsurv.Rd | 3 man/quantile.mlspatsurv.Rd | 3 man/randompars.Rd | 3 man/reconstruct.bs.Rd |only man/resetLoop.Rd | 3 man/residuals.mcmcspatsurv.Rd |only man/setTxtProgressBar2.Rd | 3 man/setupHazard.Rd | 3 man/setupPrecMatStruct.Rd |only man/simsurv.Rd | 3 man/spatialpars.Rd | 3 man/spatsurv-package.Rd | 5 man/spatsurvVignette.Rd | 3 man/spplot1.Rd |only man/spplot_compare.Rd |only man/summary.mcmc.Rd | 3 man/summary.mcmcspatsurv.Rd | 3 man/surv3d.Rd | 3 man/survival_PP.Rd | 3 man/survspat.Rd | 15 + man/survspatNS.Rd | 8 man/tpowHaz.Rd | 3 man/transformweibull.Rd | 3 man/txtProgressBar2.Rd | 7 man/urlTemplate.Rd |only man/vcov.mcmcspatsurv.Rd | 3 man/vcov.mlspatsurv.Rd | 3 man/weibullHaz.Rd | 3 tests/test_sim_ana.R | 1 tests/test_survspat.R | 3 163 files changed, 1412 insertions(+), 485 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.3 dated 2015-03-04 and 2.1.4 dated 2015-06-03
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 3 +++ R/GetDODS.R | 7 ++----- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package randomForests, written by Andy Liaw.
Author: Nicolai Meinshausen, Lukas Schiesser
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between quantregForest versions 0.2-3 dated 2012-06-01 and 1.0 dated 2015-06-03
DESCRIPTION | 15 +-- MD5 | 37 ++++++- NAMESPACE | 11 +- R/getnodes.R | 15 +-- R/importance.quantregForest.R |only R/loss.R |only R/myorder.R |only R/plot.all.R |only R/plot.fast.R |only R/plot.quantregForest.R | 44 ++------- R/predict.all.R |only R/predict.fast.R |only R/predict.imp.R |only R/predict.quantregForest.R | 184 ++++----------------------------------- R/quantregForest.R | 127 ++++++++++++++------------ R/varImpPlot.qrf.R |only build |only inst |only man/importance.quantregForest.rd |only man/plot.quantregForest.rd |only man/predict.quantregForest.Rd | 106 +++++++++++++++------- man/quantregForest.Rd | 181 ++++++++++++++++++++------------------ man/varImpPlot.qrf.rd |only src/findweightsfast.c |only src/findweightsinbagfast.c |only src/findweightsinbagfastimp.c |only vignettes |only 27 files changed, 319 insertions(+), 401 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-7 dated 2015-06-01 and 0.1-8 dated 2015-06-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/parallelSVM.R | 3 +++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder <bblonder@gmail.com>
Diff between hypervolume versions 1.2.2 dated 2015-03-12 and 1.3.0 dated 2015-06-03
hypervolume-1.2.2/hypervolume/R/ZZZ.R |only hypervolume-1.2.2/hypervolume/R/negativefeatures.R |only hypervolume-1.2.2/hypervolume/demo/negative_finch.R |only hypervolume-1.2.2/hypervolume/demo/negative_quercus.R |only hypervolume-1.2.2/hypervolume/man/negative_features.Rd |only hypervolume-1.3.0/hypervolume/DESCRIPTION | 14 - hypervolume-1.3.0/hypervolume/MD5 | 62 ++++--- hypervolume-1.3.0/hypervolume/NAMESPACE | 9 - hypervolume-1.3.0/hypervolume/R/AllClassDefinitions.R | 11 - hypervolume-1.3.0/hypervolume/R/RcppExports.R | 4 hypervolume-1.3.0/hypervolume/R/estimate_bandwidth.R | 59 ++++++ hypervolume-1.3.0/hypervolume/R/expectation.R |only hypervolume-1.3.0/hypervolume/R/hypervolume.R | 2 hypervolume-1.3.0/hypervolume/R/hypervolume_distance.R | 2 hypervolume-1.3.0/hypervolume/R/hypervolume_holes.R |only hypervolume-1.3.0/hypervolume/R/hypervolume_plot.R | 85 +++++----- hypervolume-1.3.0/hypervolume/R/hypervolume_prune.R |only hypervolume-1.3.0/hypervolume/R/hypervolume_segment.R |only hypervolume-1.3.0/hypervolume/R/hypervolume_sorensen_overlap.R | 2 hypervolume-1.3.0/hypervolume/R/hypervolume_thin.R |only hypervolume-1.3.0/hypervolume/R/inhull.R | 15 + hypervolume-1.3.0/hypervolume/demo/00Index | 3 hypervolume-1.3.0/hypervolume/demo/holes_finch.R |only hypervolume-1.3.0/hypervolume/man/estimate_bandwidth.Rd | 26 ++- hypervolume-1.3.0/hypervolume/man/expectation_box.Rd | 10 - hypervolume-1.3.0/hypervolume/man/expectation_convex.Rd | 16 - hypervolume-1.3.0/hypervolume/man/finch.Rd | 2 hypervolume-1.3.0/hypervolume/man/hypervolume-package.Rd | 3 hypervolume-1.3.0/hypervolume/man/hypervolume.Rd | 2 hypervolume-1.3.0/hypervolume/man/hypervolume_holes.Rd |only hypervolume-1.3.0/hypervolume/man/hypervolume_prune.Rd |only hypervolume-1.3.0/hypervolume/man/hypervolume_segment.Rd |only hypervolume-1.3.0/hypervolume/man/hypervolume_set.Rd | 12 - hypervolume-1.3.0/hypervolume/man/hypervolume_thin.Rd |only hypervolume-1.3.0/hypervolume/man/plot.Hypervolume.Rd | 6 hypervolume-1.3.0/hypervolume/man/quercus.Rd | 2 hypervolume-1.3.0/hypervolume/src/Makevars | 27 --- hypervolume-1.3.0/hypervolume/src/Makevars.win | 3 hypervolume-1.3.0/hypervolume/src/RcppExports.cpp | 17 ++ hypervolume-1.3.0/hypervolume/src/fastPdist2.cpp |only 40 files changed, 230 insertions(+), 164 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R interface.
It contains several machine learning model learning techniques in classification and regression,
for example classification and regression trees with optional constructive induction and models in the leaves,
random forests, kNN, naive Bayes, and locally weighted regression.
It is especially strong in feature evaluation where it contains several variants of Relief
algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM.
These methods can be used for example to discretize numeric attributes.
Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with
ordinal features and class enabling analysis according to the Kano model.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 0.9.45 dated 2015-01-27 and 0.9.46 dated 2015-06-03
CORElearn-0.9.45/CORElearn/src/Makevars |only CORElearn-0.9.46/CORElearn/ChangeLog | 2 CORElearn-0.9.46/CORElearn/DESCRIPTION | 16 CORElearn-0.9.46/CORElearn/MD5 | 90 - CORElearn-0.9.46/CORElearn/NAMESPACE | 4 CORElearn-0.9.46/CORElearn/R/Rinterface.R | 393 +++++-- CORElearn-0.9.46/CORElearn/R/rfVisualize.R | 26 CORElearn-0.9.46/CORElearn/R/util.R | 1117 ++++++++++---------- CORElearn-0.9.46/CORElearn/configure | 8 CORElearn-0.9.46/CORElearn/man/CORElearn-package.Rd | 10 CORElearn-0.9.46/CORElearn/man/CoreModel.Rd | 22 CORElearn-0.9.46/CORElearn/man/attrEval.Rd | 39 CORElearn-0.9.46/CORElearn/man/calibrate.Rd | 26 CORElearn-0.9.46/CORElearn/man/discretize.Rd |only CORElearn-0.9.46/CORElearn/man/getRFsizes.Rd | 2 CORElearn-0.9.46/CORElearn/man/helpCore.Rd | 42 CORElearn-0.9.46/CORElearn/man/modelEval.Rd | 2 CORElearn-0.9.46/CORElearn/man/noEqualRows.Rd |only CORElearn-0.9.46/CORElearn/man/ordEval.Rd | 18 CORElearn-0.9.46/CORElearn/man/paramCoreIO.Rd | 2 CORElearn-0.9.46/CORElearn/man/saveRF.Rd | 7 CORElearn-0.9.46/CORElearn/src/Makevars.in |only CORElearn-0.9.46/CORElearn/src/Makevars.win | 2 CORElearn-0.9.46/CORElearn/src/Rfront.cpp | 227 +++- CORElearn-0.9.46/CORElearn/src/Rfront.h | 5 CORElearn-0.9.46/CORElearn/src/binarize.cpp | 243 ---- CORElearn-0.9.46/CORElearn/src/binarizeReg.cpp | 98 - CORElearn-0.9.46/CORElearn/src/calibrate.cpp | 582 +++++----- CORElearn-0.9.46/CORElearn/src/calibrate.h | 2 CORElearn-0.9.46/CORElearn/src/dataStore.h | 2 CORElearn-0.9.46/CORElearn/src/estimator.cpp | 2 CORElearn-0.9.46/CORElearn/src/estimator.h | 4 CORElearn-0.9.46/CORElearn/src/estimatorReg.cpp | 55 CORElearn-0.9.46/CORElearn/src/estimatorReg.h | 3 CORElearn-0.9.46/CORElearn/src/expr.cpp | 2 CORElearn-0.9.46/CORElearn/src/frontend.cpp | 2 CORElearn-0.9.46/CORElearn/src/ftree.cpp | 2 CORElearn-0.9.46/CORElearn/src/general.h | 2 CORElearn-0.9.46/CORElearn/src/options.cpp | 31 CORElearn-0.9.46/CORElearn/src/options.h | 3 CORElearn-0.9.46/CORElearn/src/regtree.h | 2 CORElearn-0.9.46/CORElearn/src/relieff.cpp | 9 CORElearn-0.9.46/CORElearn/src/rfUtil.cpp | 15 CORElearn-0.9.46/CORElearn/src/rndforest.cpp | 9 CORElearn-0.9.46/CORElearn/src/rrelieff.cpp | 1 CORElearn-0.9.46/CORElearn/src/treenode.cpp | 2 CORElearn-0.9.46/CORElearn/src/treenodeReg.cpp | 2 CORElearn-0.9.46/CORElearn/src/trutilReg.cpp | 40 48 files changed, 1805 insertions(+), 1368 deletions(-)
Title: Convert Text into Speech
Description: Convert text into speech (voice file in 'mp3' or 'wav' format) with APIs offered by Google Translate and ITRI TTS (Text-To-Speech service, Industrial Technology Research Institute, Taiwan. http://tts.itri.org.tw/). Two main functions are given corresponding these two APIs, tts_google() and tts_ITRI(). For tts_google(), only English is supported. For tts_ITRI(), English and Chinese (both traditional and simplified) are supported, and user can specify the speaker accent, speed and volume. Both functions require internet connection.
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between Rtts versions 0.2.5 dated 2015-05-26 and 0.3.1 dated 2015-06-03
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++++++--- R/tts_ITRI.R |only R/tts_ITRI_getID.R |only R/tts_ITRI_getStatus.R |only R/tts_ITRI_getURL.R |only R/tts_google.R | 5 ++--- man/tts_ITRI.Rd |only man/tts_ITRI_getID.Rd |only man/tts_ITRI_getStatus.Rd |only man/tts_ITRI_getURL.Rd |only man/tts_google.Rd | 8 ++++++-- 12 files changed, 25 insertions(+), 14 deletions(-)
Title: Point Density for Geospatial Data
Description: For every spatial point in a list, calculates the density
and temporal tendency (average age) of points within a user defined
neighborhood; also supports point density and temporal tendency
visualization using 'ggmap'.
Author: Paul Evangelista <paul.evangelista@usma.edu> and Dave Beskow
<david.beskow@usma.edu>
Maintainer: Paul Evangelista <paul.evangelista@usma.edu>
Diff between pointdensityP versions 0.1 dated 2014-11-26 and 0.2.1 dated 2015-06-03
pointdensityP-0.1/pointdensityP/R/point_density_R_script_1.6_temporal.R |only pointdensityP-0.2.1/pointdensityP/DESCRIPTION | 23 +++----- pointdensityP-0.2.1/pointdensityP/MD5 | 6 +- pointdensityP-0.2.1/pointdensityP/R/pointdensity2.R |only pointdensityP-0.2.1/pointdensityP/man/pointdensity.Rd | 26 +++++----- 5 files changed, 28 insertions(+), 27 deletions(-)
Title: Opasnet Modelling Environment Utility Functions
Description: Contains tools for open assessment and modelling in Opasnet,
a wiki-based web site and workspace for societal decision making
(see <http://en.opasnet.org/w/Main_Page> for more information).
The core principle of the workspace is maximal openness and modularity.
Variables are defined on public wiki pages using wiki inputs/tables,
databases and R code. This package provides the functionality to download and use these
variables. It also contains health impact assessment tools such as
spatial methods for exposure modelling.
Author: Teemu Rintala, Einari Happonen, Jouni Tuomisto
Maintainer: Teemu Rintala <teemu.rintala.a@gmail.com>
Diff between OpasnetUtils versions 1.1.0 dated 2014-09-01 and 1.2.0 dated 2015-06-03
CHANGELOG | 10 ++- DESCRIPTION | 28 +++++--- MD5 | 42 ++++++------- NAMESPACE | 3 R/CheckDecisions.r | 6 - R/DropAll.r | 2 R/EvalOutput.r | 20 +++++- R/Interpret.r | 42 +++++++++++-- R/OVariable.r | 76 +++++++++++++++++++---- R/Oapply.r | 162 +++++++++++++++++++++++++++++++++++++++++---------- R/odebug.R | 4 - R/odist.R | 2 man/Fetch.Rd | 8 +- man/GIS.Rd | 3 man/Ovariable.Rd | 4 - man/convert.units.Rd | 4 - man/oapply.Rd | 18 ++++- man/objects.Rd | 12 ++- man/opasnet.Rd | 2 man/opbase.Rd | 5 - man/oprint.Rd | 1 man/tidy.Rd | 2 22 files changed, 345 insertions(+), 111 deletions(-)
Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package for ASReml software, which can be obtained upon purchase from VSN international (<www.vsni.co.uk/software/asreml>).
Author: Matthew Wolak
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between nadiv versions 2.13.2 dated 2014-06-20 and 2.13.3 dated 2015-06-03
nadiv-2.13.2/nadiv/CHANGELOG |only nadiv-2.13.2/nadiv/R/makeA2.R |only nadiv-2.13.2/nadiv/R/makeSself.R |only nadiv-2.13.2/nadiv/R/slSimS.R |only nadiv-2.13.2/nadiv/src/slsims.cc |only nadiv-2.13.2/nadiv/src/slsims.h |only nadiv-2.13.3/nadiv/DESCRIPTION | 18 ++-- nadiv-2.13.3/nadiv/MD5 | 84 ++++++++++---------- nadiv-2.13.3/nadiv/NAMESPACE | 5 + nadiv-2.13.3/nadiv/R/LDtL.R |only nadiv-2.13.3/nadiv/R/LRTest.R | 12 ++ nadiv-2.13.3/nadiv/R/aiCI.R | 2 nadiv-2.13.3/nadiv/R/constrainFun.R | 8 - nadiv-2.13.3/nadiv/R/drfx.R | 22 ++--- nadiv-2.13.3/nadiv/R/findDFC.R | 3 nadiv-2.13.3/nadiv/R/founderLine.R |only nadiv-2.13.3/nadiv/R/ggcontrib.R | 16 +-- nadiv-2.13.3/nadiv/R/grfx.R | 16 ++- nadiv-2.13.3/nadiv/R/makeA.R | 3 nadiv-2.13.3/nadiv/R/makeAinv.R | 15 +-- nadiv-2.13.3/nadiv/R/makeD.R | 16 +-- nadiv-2.13.3/nadiv/R/makeDsim.R | 17 ++-- nadiv-2.13.3/nadiv/R/makeDufam.R | 7 - nadiv-2.13.3/nadiv/R/makeS.R | 12 +- nadiv-2.13.3/nadiv/R/numPed.R | 36 +++++--- nadiv-2.13.3/nadiv/R/plot.proLik.R | 9 +- nadiv-2.13.3/nadiv/R/proLik.R | 28 ++++-- nadiv-2.13.3/nadiv/R/remlSupport.R | 7 - nadiv-2.13.3/nadiv/R/simPedDFC.R | 13 ++- nadiv-2.13.3/nadiv/R/simPedHS.R | 31 ++++--- nadiv-2.13.3/nadiv/R/varTrans.R | 7 - nadiv-2.13.3/nadiv/README.md |only nadiv-2.13.3/nadiv/man/drfx.Rd | 11 +- nadiv-2.13.3/nadiv/man/founderLine.Rd |only nadiv-2.13.3/nadiv/man/ggcontrib.Rd | 18 ++-- nadiv-2.13.3/nadiv/man/grfx.Rd | 18 +++- nadiv-2.13.3/nadiv/man/is.numPed.Rd |only nadiv-2.13.3/nadiv/man/is.proLik.Rd |only nadiv-2.13.3/nadiv/man/nadiv-package.Rd | 10 +- nadiv-2.13.3/nadiv/man/numPed.Rd | 6 - nadiv-2.13.3/nadiv/man/pcc.Rd | 5 - nadiv-2.13.3/nadiv/man/proLik.Rd | 7 - nadiv-2.13.3/nadiv/man/simPedDFC.Rd | 6 + nadiv-2.13.3/nadiv/man/simPedHS.Rd | 12 +- nadiv-2.13.3/nadiv/man/varTrans.Rd | 2 nadiv-2.13.3/nadiv/man/warcolak.Rd | 2 nadiv-2.13.3/nadiv/src/ainv.cc | 134 -------------------------------- nadiv-2.13.3/nadiv/src/dsim.cc | 13 +-- nadiv-2.13.3/nadiv/src/ga.cc | 1 49 files changed, 285 insertions(+), 347 deletions(-)
Title: Genetic Analysis Package
Description: It is designed as an integrated package for genetic data
analysis of both population and family data. Currently, it
contains functions for sample size calculations of both
population-based and family-based designs, probability of
familial disease aggregation, kinship calculation, statistics
in linkage analysis, and association analysis involving genetic
markers including haplotype analysis with or without environmental
covariates.
Author: Jing Hua Zhao and colleagues with inputs from Kurt Hornik and
Brian Ripley
Maintainer: Jing Hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>
Diff between gap versions 1.1-12 dated 2014-08-18 and 1.1-13 dated 2015-06-03
ChangeLog | 11 + DESCRIPTION | 17 - INDEX | 2 MD5 | 99 +++++---- NAMESPACE | 7 R/AE3.R | 84 ++++---- R/MCMCgrm.R |only R/gc.em.R | 13 - R/hap.em.R | 9 R/hap.score.R | 7 R/hwe.cc.R | 7 R/masize.R | 7 R/mhtplot.R | 7 R/mhtplot2.R | 7 R/mtdt2.R | 7 R/mvmeta.R | 10 R/qqfun.R | 7 R/utils.R | 9 data/datalist | 1 data/meyer.rda |only inst/CITATION | 4 inst/doc/gap.R | 111 +++++------ inst/doc/gap.Rnw | 194 +++++++++++-------- inst/doc/gap.pdf |binary inst/doc/h2.R | 251 ++++++++++++++++++++++-- inst/doc/h2.Rnw | 402 ++++++++++++++++++++++++++++++++++++---- inst/doc/h2.pdf |binary inst/doc/jss.pdf |binary inst/doc/pedtodot.pdf |binary inst/doc/rnews.pdf |binary inst/tests/kinship/bdsmatrix.R |only inst/tests/no | 2 inst/tests/references.txt | 39 +++ man/MCMCgrm.Rd |only man/crohn.Rd | 5 man/gap-package.Rd | 8 man/meyer.Rd |only src/hap.c | 8 src/hap.h | 5 src/hwe.hardy.c | 22 +- vignettes/figures/4w.pdf |binary vignettes/figures/ESplot.pdf |binary vignettes/figures/MCMCglmm1.pdf |only vignettes/figures/MCMCglmm2.pdf |only vignettes/figures/asplot.pdf |binary vignettes/figures/bugs.pdf |only vignettes/figures/h2.pdf |only vignettes/figures/h2l.pdf |binary vignettes/figures/jags.pdf |only vignettes/figures/l51.pdf |binary vignettes/figures/lukas.pdf |binary vignettes/figures/qqunif.pdf |binary vignettes/gap.Rnw | 194 +++++++++++-------- vignettes/h2.Rnw | 402 ++++++++++++++++++++++++++++++++++++---- vignettes/h2.bib | 54 +++++ vignettes/model.txt |only 56 files changed, 1590 insertions(+), 422 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present, together with some diagnostic tools. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class 'etasclass').
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi <marcello.chiodi@unipa.it>
Diff between etasFLP versions 1.2.1 dated 2015-04-16 and 1.3.0 dated 2015-06-03
etasFLP-1.2.1/etasFLP/R/etasflp.integral.R |only etasFLP-1.3.0/etasFLP/ChangeLog | 6 ++ etasFLP-1.3.0/etasFLP/DESCRIPTION | 10 ++-- etasFLP-1.3.0/etasFLP/MD5 | 27 +++++------ etasFLP-1.3.0/etasFLP/R/etasclass.R | 9 --- etasFLP-1.3.0/etasFLP/R/flp1.etas.nlm.R | 5 -- etasFLP-1.3.0/etasFLP/R/flpkspace.R | 7 -- etasFLP-1.3.0/etasFLP/R/plot.etasclass.R | 16 ------ etasFLP-1.3.0/etasFLP/data/californiacatalog.RData |binary etasFLP-1.3.0/etasFLP/data/italycatalog.RData |binary etasFLP-1.3.0/etasFLP/man/etasFLP-internal.Rd | 2 etasFLP-1.3.0/etasFLP/man/etasFLP-package.Rd | 4 - etasFLP-1.3.0/etasFLP/man/etasclass.Rd | 46 +++++-------------- etasFLP-1.3.0/etasFLP/man/profile.etasclass.Rd | 15 +++--- etasFLP-1.3.0/etasFLP/man/summary.etasclass.Rd | 50 +++++++++++---------- 15 files changed, 81 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-03 1.3.0-2
2010-08-27 0.2.2-1
2010-08-20 0.2.1-3
2010-08-13 0.2.1-2
2010-08-09 0.2.1-1
Title: Miscellaneous Tools for Reproducible Research
Description: Tools to load 'R' packages
and automatically generate BibTeX files citing them as well as load
plain-text and 'Excel' formatted data stored on 'Dropbox', 'GitHub', and
from other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between repmis versions 0.4.2 dated 2015-03-26 and 0.4.4 dated 2015-06-03
DESCRIPTION | 18 +++++++++--------- MD5 | 25 +++++++++++++------------ NAMESPACE | 3 ++- NEWS | 8 ++++++++ R/utils.R | 22 ++++++++++++++++++++++ README.md | 5 ++++- man/InstallOldPackages.Rd | 2 +- man/LoadandCite.Rd | 2 +- man/git_stamp.Rd | 2 +- man/scan_https.Rd | 2 +- man/set_valid_wd.Rd |only man/source_DropboxData.Rd | 2 +- man/source_XlsxData.Rd | 2 +- man/source_data.Rd | 2 +- 14 files changed, 65 insertions(+), 30 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scatterpoints by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.7.1 dated 2014-12-21 and 1.8.1 dated 2015-06-03
berryFunctions-1.7.1/berryFunctions/R/deprecatedFunctions.r |only berryFunctions-1.7.1/berryFunctions/inst/extdata/solitaire2.txt |only berryFunctions-1.7.1/berryFunctions/man/deprecatedFunctions.Rd |only berryFunctions-1.8.1/berryFunctions/ChangeLog | 44 - berryFunctions-1.8.1/berryFunctions/DESCRIPTION | 13 berryFunctions-1.8.1/berryFunctions/MD5 | 116 +- berryFunctions-1.8.1/berryFunctions/R/betaPlot.R | 3 berryFunctions-1.8.1/berryFunctions/R/colPointsHist.R | 8 berryFunctions-1.8.1/berryFunctions/R/colPointsLegend.R | 6 berryFunctions-1.8.1/berryFunctions/R/combineFiles.r | 2 berryFunctions-1.8.1/berryFunctions/R/groupHist.R |only berryFunctions-1.8.1/berryFunctions/R/linLogHist.R |only berryFunctions-1.8.1/berryFunctions/R/linLogTrans.R | 105 +- berryFunctions-1.8.1/berryFunctions/R/linReg.R | 4 berryFunctions-1.8.1/berryFunctions/R/logAxis.R | 15 berryFunctions-1.8.1/berryFunctions/R/logVals.R | 119 +- berryFunctions-1.8.1/berryFunctions/R/monthAxis.R |only berryFunctions-1.8.1/berryFunctions/R/monthLabs.R | 2 berryFunctions-1.8.1/berryFunctions/R/movAv.R | 21 berryFunctions-1.8.1/berryFunctions/R/movAvLines.R |only berryFunctions-1.8.1/berryFunctions/R/normPlot.R | 3 berryFunctions-1.8.1/berryFunctions/R/owa.r | 2 berryFunctions-1.8.1/berryFunctions/R/panelDim.R |only berryFunctions-1.8.1/berryFunctions/R/pastec.R |only berryFunctions-1.8.1/berryFunctions/R/pretty2.R | 12 berryFunctions-1.8.1/berryFunctions/R/quantileBands.R | 6 berryFunctions-1.8.1/berryFunctions/R/quantileMean.R | 30 berryFunctions-1.8.1/berryFunctions/R/smallPlot.R | 36 berryFunctions-1.8.1/berryFunctions/R/smoothLines.R | 4 berryFunctions-1.8.1/berryFunctions/inst/extdata/pmedians.txt |only berryFunctions-1.8.1/berryFunctions/inst/extdata/solitaire.txt | 439 +++++++--- berryFunctions-1.8.1/berryFunctions/man/berryFunctions-package.Rd | 93 +- berryFunctions-1.8.1/berryFunctions/man/betaPlot.Rd | 7 berryFunctions-1.8.1/berryFunctions/man/climateGraph.Rd | 4 berryFunctions-1.8.1/berryFunctions/man/colPointsHist.Rd | 10 berryFunctions-1.8.1/berryFunctions/man/colPointsLegend.Rd | 7 berryFunctions-1.8.1/berryFunctions/man/combineFiles.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/dupes.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/funTinn.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/groupHist.Rd |only berryFunctions-1.8.1/berryFunctions/man/linLogHist.Rd |only berryFunctions-1.8.1/berryFunctions/man/linLogTrans.Rd | 156 ++- berryFunctions-1.8.1/berryFunctions/man/logAxis.Rd | 11 berryFunctions-1.8.1/berryFunctions/man/logVals.Rd | 19 berryFunctions-1.8.1/berryFunctions/man/lsMem.Rd | 1 berryFunctions-1.8.1/berryFunctions/man/lsc.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/mReg.Rd | 11 berryFunctions-1.8.1/berryFunctions/man/monthAxis.Rd |only berryFunctions-1.8.1/berryFunctions/man/monthLabs.Rd | 16 berryFunctions-1.8.1/berryFunctions/man/movAv.Rd | 15 berryFunctions-1.8.1/berryFunctions/man/movAvLines.Rd |only berryFunctions-1.8.1/berryFunctions/man/nameSample.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/normPlot.Rd | 6 berryFunctions-1.8.1/berryFunctions/man/owa.Rd | 4 berryFunctions-1.8.1/berryFunctions/man/panelDim.Rd |only berryFunctions-1.8.1/berryFunctions/man/pastec.Rd |only berryFunctions-1.8.1/berryFunctions/man/pointZoom.Rd | 4 berryFunctions-1.8.1/berryFunctions/man/pretty2.Rd | 15 berryFunctions-1.8.1/berryFunctions/man/quantileBands.Rd | 14 berryFunctions-1.8.1/berryFunctions/man/quantileMean.Rd | 64 + berryFunctions-1.8.1/berryFunctions/man/randomPoints.Rd | 4 berryFunctions-1.8.1/berryFunctions/man/require2.Rd | 1 berryFunctions-1.8.1/berryFunctions/man/smallPlot.Rd | 20 berryFunctions-1.8.1/berryFunctions/man/superPos.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/tableColVal.Rd | 2 berryFunctions-1.8.1/berryFunctions/man/textField.Rd | 4 berryFunctions-1.8.1/berryFunctions/man/unitHydrograph.Rd | 2 67 files changed, 1029 insertions(+), 463 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <brenning@uwaterloo.ca>
Diff between RSAGA versions 0.93-6 dated 2013-07-24 and 0.94-1 dated 2015-06-03
DESCRIPTION | 25 - LICENSE |only MD5 | 107 +++--- NAMESPACE | 5 R/RSAGA-core.R | 64 ++- R/RSAGA-modules.R | 537 ++++++++++++++++++++++++++------- R/RSAGA-package.R | 4 R/gridtools.R | 412 +++++++++++++------------ man/RSAGA-package.Rd | 84 ++--- man/centervalue.Rd | 14 man/create.variable.name.Rd | 14 man/focal.function.Rd | 263 ++++------------ man/grid.predict.Rd | 113 +----- man/grid.to.xyz.Rd | 31 - man/match.arg.ext.Rd | 75 +--- man/multi.focal.function.Rd | 320 +++++-------------- man/pick.from.points.Rd | 373 ++++++---------------- man/read.ascii.grid.Rd | 207 ++++-------- man/relative.position.Rd | 27 - man/resid.median.Rd | 50 --- man/rsaga.add.grid.values.to.points.Rd | 46 -- man/rsaga.close.gaps.Rd | 56 +-- man/rsaga.contour.Rd | 38 +- man/rsaga.copy.sgrd.Rd | 31 - man/rsaga.default.path.Rd | 39 -- man/rsaga.env.Rd | 176 ++-------- man/rsaga.esri.to.sgrd.Rd | 51 --- man/rsaga.esri.wrapper.Rd | 134 ++------ man/rsaga.fill.sinks.Rd | 116 ++----- man/rsaga.filter.gauss.Rd | 32 - man/rsaga.filter.simple.Rd | 38 -- man/rsaga.geoprocessor.Rd | 209 +++--------- man/rsaga.get.modules.Rd | 107 ++---- man/rsaga.get.usage.Rd | 38 -- man/rsaga.get.version.Rd | 27 - man/rsaga.grid.calculus.Rd | 125 ++----- man/rsaga.grid.to.points.Rd | 62 +-- man/rsaga.hillshade.Rd | 69 +--- man/rsaga.html.help.Rd | 39 -- man/rsaga.import.gdal.Rd | 206 ++++++------ man/rsaga.insolation.Rd | 184 +++-------- man/rsaga.inverse.distance.Rd | 111 ++---- man/rsaga.lib.prefix.Rd | 22 - man/rsaga.local.morphometry.Rd | 156 ++------- man/rsaga.parallel.processing.Rd | 145 ++------ man/rsaga.pisr.Rd | 211 +++--------- man/rsaga.sgrd.to.esri.Rd | 73 +--- man/rsaga.sink.removal.Rd | 42 -- man/rsaga.sink.route.Rd | 39 -- man/rsaga.slope.asp.curv.Rd |only man/rsaga.solar.radiation.Rd | 123 ++----- man/rsaga.target.Rd | 68 +--- man/rsaga.topdown.processing.Rd |only man/rsaga.wetness.index.Rd | 102 +----- man/set.file.extension.Rd | 34 -- man/wind.shelter.Rd | 117 ++----- 56 files changed, 2243 insertions(+), 3548 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.0.2 dated 2015-04-20 and 0.0.7 dated 2015-06-03
RandomFieldsUtils-0.0.2/RandomFieldsUtils/src/RF.h |only RandomFieldsUtils-0.0.7/RandomFieldsUtils/DESCRIPTION | 6 RandomFieldsUtils-0.0.7/RandomFieldsUtils/MD5 | 41 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/R/RFutils.R | 34 RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/Basic_utils.h | 27 RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/Error_utils.h | 39 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/Matrix_mult.h | 27 RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/Solve.h | 41 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/Struve.h | 26 RandomFieldsUtils-0.0.7/RandomFieldsUtils/inst/include/utils.h | 42 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/man/solvePosDef.Rd | 10 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/Basic_utils.h | 31 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/Error_utils.h | 39 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/Matrix_mult.h | 27 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/RFutils.cc | 15 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/R_init.h | 25 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/RandomFieldsUtils.h | 26 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/Solve.h | 41 - RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/Struve.h | 26 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/solve.cc | 354 +++++++--- RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/spamown.f | 1 RandomFieldsUtils-0.0.7/RandomFieldsUtils/src/utils.h | 42 - 22 files changed, 745 insertions(+), 175 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Calculate Indices and Theoretical Properties of Protein
Sequences
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio <daniel.osorio@correo.uis.edu.co>
Diff between Peptides versions 1.0.4 dated 2015-04-30 and 1.1.0 dated 2015-06-03
Peptides-1.0.4/Peptides/R/AAcomp.R |only Peptides-1.0.4/Peptides/R/Boman.R |only Peptides-1.0.4/Peptides/R/MW.R |only Peptides-1.0.4/Peptides/man/AAcomp.Rd |only Peptides-1.0.4/Peptides/man/Boman.Rd |only Peptides-1.0.4/Peptides/man/MW.Rd |only Peptides-1.0.4/Peptides/man/Pepdata.Rd |only Peptides-1.1.0/Peptides/DESCRIPTION | 8 ++-- Peptides-1.1.0/Peptides/MD5 | 48 +++++++++++++----------- Peptides-1.1.0/Peptides/NAMESPACE | 1 Peptides-1.1.0/Peptides/NEWS | 3 + Peptides-1.1.0/Peptides/R/aacomp.R |only Peptides-1.1.0/Peptides/R/aindex.R | 22 +++++------ Peptides-1.1.0/Peptides/R/boman.R |only Peptides-1.1.0/Peptides/R/charge.R | 6 +-- Peptides-1.1.0/Peptides/R/hmoment.R | 6 +-- Peptides-1.1.0/Peptides/R/hydrophobicity.R | 6 +-- Peptides-1.1.0/Peptides/R/instaindex.R | 6 +-- Peptides-1.1.0/Peptides/R/kidera.R |only Peptides-1.1.0/Peptides/R/lengthpep.R | 2 - Peptides-1.1.0/Peptides/R/membpos.R | 8 ++-- Peptides-1.1.0/Peptides/R/mw.R |only Peptides-1.1.0/Peptides/R/pI.R | 5 +- Peptides-1.1.0/Peptides/R/plot.xvg.R | 2 - Peptides-1.1.0/Peptides/R/read.xvg.R | 2 - Peptides-1.1.0/Peptides/data/Kfactors.RData |only Peptides-1.1.0/Peptides/data/datalist | 1 Peptides-1.1.0/Peptides/man/Kfactors.Rd |only Peptides-1.1.0/Peptides/man/Peptides-package.Rd | 7 +-- Peptides-1.1.0/Peptides/man/aacomp.Rd |only Peptides-1.1.0/Peptides/man/boman.Rd |only Peptides-1.1.0/Peptides/man/kidera.Rd |only Peptides-1.1.0/Peptides/man/mw.Rd |only Peptides-1.1.0/Peptides/man/pepdata.Rd |only 34 files changed, 69 insertions(+), 64 deletions(-)
Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits
the estimation of the most-used nonlinear statistics/algorithms
including generalized correlation dimension, information dimension,
largest Lyapunov exponent, sample entropy and Recurrence
Quantification Analysis (RQA), among others. Basic routines
for surrogate data testing are also included. Part of this work
was based on the book "Nonlinear time series analysis" by
Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre],
Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantinoantonio.garcia@usc.es>
Diff between nonlinearTseries versions 0.2.1 dated 2014-01-30 and 0.2.2 dated 2015-06-03
nonlinearTseries-0.2.1/nonlinearTseries/man/timeReversibility.Rd |only nonlinearTseries-0.2.2/nonlinearTseries/DESCRIPTION | 37 - nonlinearTseries-0.2.2/nonlinearTseries/MD5 | 146 ++-- nonlinearTseries-0.2.2/nonlinearTseries/NAMESPACE | 17 nonlinearTseries-0.2.2/nonlinearTseries/R/DFA.R | 130 ++- nonlinearTseries-0.2.2/nonlinearTseries/R/Lyapunov.R | 148 +++- nonlinearTseries-0.2.2/nonlinearTseries/R/RQA.R | 165 ++-- nonlinearTseries-0.2.2/nonlinearTseries/R/RcppExports.R |only nonlinearTseries-0.2.2/nonlinearTseries/R/basicNonLinearFunctions.R | 217 +++--- nonlinearTseries-0.2.2/nonlinearTseries/R/corrDim.R | 271 +++++-- nonlinearTseries-0.2.2/nonlinearTseries/R/generics.R | 13 nonlinearTseries-0.2.2/nonlinearTseries/R/getMinimumEmbeddingDimension.R | 33 nonlinearTseries-0.2.2/nonlinearTseries/R/informationDimension.R | 267 +++++-- nonlinearTseries-0.2.2/nonlinearTseries/R/mutualInformation.R |only nonlinearTseries-0.2.2/nonlinearTseries/R/neighbourSearch.R | 11 nonlinearTseries-0.2.2/nonlinearTseries/R/nonlinearStatistics.R | 27 nonlinearTseries-0.2.2/nonlinearTseries/R/poincareMap.R | 25 nonlinearTseries-0.2.2/nonlinearTseries/R/sampleEntropy.R | 173 +++-- nonlinearTseries-0.2.2/nonlinearTseries/R/spaceTimePlot.R | 71 +- nonlinearTseries-0.2.2/nonlinearTseries/R/surrogate.data.R | 184 ++++- nonlinearTseries-0.2.2/nonlinearTseries/R/utils.R |only nonlinearTseries-0.2.2/nonlinearTseries/build |only nonlinearTseries-0.2.2/nonlinearTseries/inst/doc |only nonlinearTseries-0.2.2/nonlinearTseries/man/FFTsurrogate.Rd | 39 - nonlinearTseries-0.2.2/nonlinearTseries/man/buildTakens.Rd | 39 - nonlinearTseries-0.2.2/nonlinearTseries/man/cliffordMap.Rd | 59 - nonlinearTseries-0.2.2/nonlinearTseries/man/contourLines.Rd | 14 nonlinearTseries-0.2.2/nonlinearTseries/man/corrDim.Rd | 344 +++++----- nonlinearTseries-0.2.2/nonlinearTseries/man/corrMatrix.Rd | 17 nonlinearTseries-0.2.2/nonlinearTseries/man/dfa.Rd | 164 ++-- nonlinearTseries-0.2.2/nonlinearTseries/man/divTime.Rd | 17 nonlinearTseries-0.2.2/nonlinearTseries/man/divergence.Rd | 19 nonlinearTseries-0.2.2/nonlinearTseries/man/embeddingDims.Rd | 19 nonlinearTseries-0.2.2/nonlinearTseries/man/estimate.Rd | 30 nonlinearTseries-0.2.2/nonlinearTseries/man/estimateEmbeddingDim.Rd | 123 +-- nonlinearTseries-0.2.2/nonlinearTseries/man/findAllNeighbours.Rd | 41 - nonlinearTseries-0.2.2/nonlinearTseries/man/fixedMass.Rd | 16 nonlinearTseries-0.2.2/nonlinearTseries/man/fluctuationFunction.Rd | 16 nonlinearTseries-0.2.2/nonlinearTseries/man/gaussMap.Rd | 51 - nonlinearTseries-0.2.2/nonlinearTseries/man/henon.Rd | 58 - nonlinearTseries-0.2.2/nonlinearTseries/man/ikedaMap.Rd | 59 - nonlinearTseries-0.2.2/nonlinearTseries/man/infDim.Rd | 328 +++++---- nonlinearTseries-0.2.2/nonlinearTseries/man/logRadius.Rd | 17 nonlinearTseries-0.2.2/nonlinearTseries/man/logisticMap.Rd | 50 - nonlinearTseries-0.2.2/nonlinearTseries/man/lorenz.Rd | 62 - nonlinearTseries-0.2.2/nonlinearTseries/man/maxLyapunov.Rd | 319 ++++----- nonlinearTseries-0.2.2/nonlinearTseries/man/mutualInformation.Rd |only nonlinearTseries-0.2.2/nonlinearTseries/man/neighbourSearch.Rd | 46 - nonlinearTseries-0.2.2/nonlinearTseries/man/nlOrder.Rd | 21 nonlinearTseries-0.2.2/nonlinearTseries/man/nonLinearNoiseReduction.Rd | 32 nonlinearTseries-0.2.2/nonlinearTseries/man/nonLinearPrediction.Rd | 54 - nonlinearTseries-0.2.2/nonlinearTseries/man/nonlinearityTest.Rd | 37 - nonlinearTseries-0.2.2/nonlinearTseries/man/plotLocalScalingExp.Rd |only nonlinearTseries-0.2.2/nonlinearTseries/man/poincareMap.Rd | 78 -- nonlinearTseries-0.2.2/nonlinearTseries/man/radius.Rd | 21 nonlinearTseries-0.2.2/nonlinearTseries/man/recurrencePlot.Rd | 38 - nonlinearTseries-0.2.2/nonlinearTseries/man/rossler.Rd | 59 - nonlinearTseries-0.2.2/nonlinearTseries/man/rqa.Rd | 105 +-- nonlinearTseries-0.2.2/nonlinearTseries/man/sampleEntropy.Rd | 182 ++--- nonlinearTseries-0.2.2/nonlinearTseries/man/sampleEntropyFunction.Rd | 19 nonlinearTseries-0.2.2/nonlinearTseries/man/sinaiMap.Rd | 56 - nonlinearTseries-0.2.2/nonlinearTseries/man/spaceTimePlot.Rd | 120 +-- nonlinearTseries-0.2.2/nonlinearTseries/man/surrogateTest.Rd | 95 +- nonlinearTseries-0.2.2/nonlinearTseries/man/timeAsymmetry.Rd |only nonlinearTseries-0.2.2/nonlinearTseries/man/timeAsymmetry2.Rd |only nonlinearTseries-0.2.2/nonlinearTseries/man/timeLag.Rd | 121 ++- nonlinearTseries-0.2.2/nonlinearTseries/man/windowSizes.Rd | 15 nonlinearTseries-0.2.2/nonlinearTseries/src/Lyapunov.c | 5 nonlinearTseries-0.2.2/nonlinearTseries/src/LyapunovFromTakens.c | 2 nonlinearTseries-0.2.2/nonlinearTseries/src/RcppExports.cpp |only nonlinearTseries-0.2.2/nonlinearTseries/src/corrDim.c | 4 nonlinearTseries-0.2.2/nonlinearTseries/src/corrDimFromTakens.c | 3 nonlinearTseries-0.2.2/nonlinearTseries/src/generalizedCorrDimFromTakens.c | 4 nonlinearTseries-0.2.2/nonlinearTseries/src/informationDimension.c | 16 nonlinearTseries-0.2.2/nonlinearTseries/src/kd_dump.cpp | 9 nonlinearTseries-0.2.2/nonlinearTseries/src/mutualInformation.cpp |only nonlinearTseries-0.2.2/nonlinearTseries/src/neighbourSearch.c | 2 nonlinearTseries-0.2.2/nonlinearTseries/src/neighbourSearch.h | 8 nonlinearTseries-0.2.2/nonlinearTseries/src/utils.cpp |only nonlinearTseries-0.2.2/nonlinearTseries/vignettes |only 80 files changed, 2859 insertions(+), 2129 deletions(-)
More information about nonlinearTseries at CRAN
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Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals from the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath <ken.beath@mq.edu.au>
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-1 dated 2015-01-13 and 0.7-2 dated 2015-06-03
DESCRIPTION | 12 - MD5 | 8 - R/profilet.metaplus.R | 375 +++++++++++++++++++++++++------------------------- inst/NEWS | 56 ++++--- man/metaplus.Rd | 154 ++++++++++---------- 5 files changed, 308 insertions(+), 297 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy
rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 1.0 dated 2015-01-15 and 1.1 dated 2015-06-03
lfl-1.0/lfl/src/farules.cpp |only lfl-1.0/lfl/src/farules.h |only lfl-1.0/lfl/src/search/AbstractFloatFuzzyChain.h |only lfl-1.0/lfl/src/search/AbstractFuzzyChain.h |only lfl-1.0/lfl/src/search/LukasFloatFuzzyChain.h |only lfl-1.0/lfl/src/search/MinFloatFuzzyChain.h |only lfl-1.0/lfl/src/search/ProductFloatFuzzyChain.h |only lfl-1.0/lfl/src/search/typedefs.h |only lfl-1.1/lfl/DESCRIPTION | 9 lfl-1.1/lfl/MD5 | 109 ++- lfl-1.1/lfl/NAMESPACE | 6 lfl-1.1/lfl/R/as.data.frame.farules.R |only lfl-1.1/lfl/R/frbe.R | 14 lfl-1.1/lfl/R/frbemodel.R | 685 +++++++++++++++-------- lfl-1.1/lfl/R/is.specific.R | 23 lfl-1.1/lfl/R/pbld.R | 8 lfl-1.1/lfl/R/perceive.R | 31 - lfl-1.1/lfl/R/plot.fsets.R |only lfl-1.1/lfl/R/reduce.R | 66 +- lfl-1.1/lfl/R/searchrules.R | 2 lfl-1.1/lfl/R/slices.R | 3 lfl-1.1/lfl/inst |only lfl-1.1/lfl/man/as.data.frame.farules.Rd |only lfl-1.1/lfl/man/evalfrbe.Rd | 9 lfl-1.1/lfl/man/frbe.Rd | 9 lfl-1.1/lfl/man/is.frbe.Rd | 7 lfl-1.1/lfl/man/lfl-package.Rd | 2 lfl-1.1/lfl/man/pbld.Rd | 7 lfl-1.1/lfl/man/plot.fsets.Rd |only lfl-1.1/lfl/man/print.frbe.Rd | 9 lfl-1.1/lfl/man/rbcoverage.Rd | 9 lfl-1.1/lfl/man/reduce.Rd | 28 lfl-1.1/lfl/src/Makevars.win | 4 lfl-1.1/lfl/src/common |only lfl-1.1/lfl/src/common.h | 54 + lfl-1.1/lfl/src/isSpecific.cpp |only lfl-1.1/lfl/src/isSpecific.h |only lfl-1.1/lfl/src/pbld |only lfl-1.1/lfl/src/perceiveGlobal.cpp |only lfl-1.1/lfl/src/perceiveGlobal.h |only lfl-1.1/lfl/src/reduce |only lfl-1.1/lfl/src/reduce.cpp |only lfl-1.1/lfl/src/reduce.h |only lfl-1.1/lfl/src/search.cpp |only lfl-1.1/lfl/src/search.h |only lfl-1.1/lfl/src/search/AbstractExtension.h | 9 lfl-1.1/lfl/src/search/AbstractStorage.h | 8 lfl-1.1/lfl/src/search/Attribute.h | 33 - lfl-1.1/lfl/src/search/BasicExtension.h | 9 lfl-1.1/lfl/src/search/BoundedStorage.h | 9 lfl-1.1/lfl/src/search/CombinationTrie.h | 8 lfl-1.1/lfl/src/search/Data.h | 13 lfl-1.1/lfl/src/search/DummyExtension.h | 9 lfl-1.1/lfl/src/search/IntervalStorage.h | 12 lfl-1.1/lfl/src/search/LiftExtension.h | 12 lfl-1.1/lfl/src/search/Rule.h | 15 lfl-1.1/lfl/src/search/RuleQueue.h | 8 lfl-1.1/lfl/src/search/Search.h | 24 lfl-1.1/lfl/src/search/SearchConfig.h | 30 - lfl-1.1/lfl/src/search/Statistics.h | 8 lfl-1.1/lfl/src/search/Task.h | 33 - lfl-1.1/lfl/src/search/TaskQueue.h | 9 lfl-1.1/lfl/src/search/TrieExtension.h | 9 lfl-1.1/lfl/src/search/UnlimitedStorage.h | 8 lfl-1.1/lfl/tests/testthat/test-searchrules.R | 3 65 files changed, 870 insertions(+), 493 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters. In press.
Author: Rampal S. Etienne, Luis M. Valente & Albert B. Phillimore
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 1.0 dated 2015-05-21 and 1.0.1 dated 2015-06-03
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/DAISIE-package.Rd | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcuk.korkmaz@hacettepe.edu.tr>
Diff between MVN versions 3.9 dated 2015-03-18 and 4.0 dated 2015-06-03
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- R/mvOutlier.R | 40 ++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/MVN.pdf |binary man/mvOutlier.Rd | 23 +++++++++++++++++++++-- 6 files changed, 59 insertions(+), 25 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and proportional odds models and fully parametric Cox-PH and proportional odds models. Also includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.0 dated 2015-05-31 and 1.2.3 dated 2015-06-03
icenReg-1.2.0/icenReg/data/mdata.RData |only icenReg-1.2.0/icenReg/man/mdata.Rd |only icenReg-1.2.0/icenReg/man/oldFiles |only icenReg-1.2.0/icenReg/src/Eigen_local/SPQRSupport |only icenReg-1.2.0/icenReg/src/Eigen_local/Sparse |only icenReg-1.2.0/icenReg/src/Eigen_local/SparseCholesky |only icenReg-1.2.0/icenReg/src/Eigen_local/SparseCore |only icenReg-1.2.0/icenReg/src/Eigen_local/SparseLU |only icenReg-1.2.0/icenReg/src/Eigen_local/SparseQR |only icenReg-1.2.0/icenReg/src/Eigen_local/src/SPQRSupport |only icenReg-1.2.0/icenReg/src/Eigen_local/src/SparseCholesky |only icenReg-1.2.0/icenReg/src/Eigen_local/src/SparseCore |only icenReg-1.2.0/icenReg/src/Eigen_local/src/SparseLU |only icenReg-1.2.0/icenReg/src/Eigen_local/src/SparseQR |only icenReg-1.2.0/icenReg/src/icenReg_files/ic_ph.cpp |only icenReg-1.2.0/icenReg/src/icenReg_files/ic_ph.h |only icenReg-1.2.0/icenReg/src/icenReg_files/ic_po.cpp |only icenReg-1.2.0/icenReg/src/icenReg_files/ic_po.h |only icenReg-1.2.3/icenReg/DESCRIPTION | 10 - icenReg-1.2.3/icenReg/MD5 | 98 ++---------- icenReg-1.2.3/icenReg/R/Utilities.R | 24 +- icenReg-1.2.3/icenReg/R/user_functions.R | 7 icenReg-1.2.3/icenReg/data/mice_data.RData |only icenReg-1.2.3/icenReg/man/diag_baseline.Rd | 15 - icenReg-1.2.3/icenReg/man/diag_covar.Rd | 5 icenReg-1.2.3/icenReg/man/getFitEsts.Rd | 17 +- icenReg-1.2.3/icenReg/man/getSCurves.Rd | 15 + icenReg-1.2.3/icenReg/man/ic_par.Rd | 6 icenReg-1.2.3/icenReg/man/ic_sp.Rd | 10 - icenReg-1.2.3/icenReg/man/mice_data.Rd |only icenReg-1.2.3/icenReg/man/simIC_weib.Rd | 10 - icenReg-1.2.3/icenReg/src/icenReg.cpp | 23 -- icenReg-1.2.3/icenReg/src/icenReg_files/basicUtilities.cpp | 3 icenReg-1.2.3/icenReg/src/icenReg_files/ic_par.cpp | 46 +++++ icenReg-1.2.3/icenReg/src/icenReg_files/ic_par.h | 34 ++-- icenReg-1.2.3/icenReg/src/icenReg_files/ic_sp_ch.cpp | 106 +++++++++++-- icenReg-1.2.3/icenReg/src/icenReg_files/ic_sp_ch.h | 7 37 files changed, 242 insertions(+), 194 deletions(-)
Title: N-Gram Based Text Categorization
Description: Text categorization based on n-grams.
Author: Kurt Hornik [aut, cre],
Johannes Rauch [aut],
Christian Buchta [aut],
Ingo Feinerer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between textcat versions 1.0-2 dated 2014-06-11 and 1.0-3 dated 2015-06-02
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/textcat.R | 22 ++++++++++++++++++---- data/ECIMCI_profiles.rda |binary data/TC_byte_profiles.rda |binary data/TC_char_profiles.rda |binary 6 files changed, 28 insertions(+), 14 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.7.2 dated 2015-04-07 and 0.7.2-1 dated 2015-06-02
DESCRIPTION | 14 ++-- MD5 | 132 ++++++++++++++++++++-------------------- NAMESPACE | 2 R/clean.R | 4 - R/dfm-main.R | 12 ++- README.md | 6 - build/vignette.rds |binary inst/doc/corpus-sources.R | 4 - inst/doc/corpus-sources.Rmd | 4 - inst/doc/corpus-sources.html | 18 ++--- inst/doc/development-plans.html | 4 - inst/doc/quickstart.html | 18 ++--- man/LBGexample.Rd | 2 man/bigrams.Rd | 2 man/changeunits.Rd | 2 man/clean.Rd | 6 - man/collocations.Rd | 2 man/convert.Rd | 2 man/corpus.Rd | 2 man/corpusSource-class.Rd | 2 man/dfm-class.Rd | 2 man/dfm.Rd | 2 man/dictionary.Rd | 2 man/docfreq.Rd | 2 man/docnames.Rd | 2 man/docvars.Rd | 2 man/encoding.Rd | 2 man/exampleString.Rd | 2 man/features.Rd | 2 man/ie2010Corpus.Rd | 2 man/inaugCorpus.Rd | 2 man/kwic.Rd | 2 man/language.Rd | 2 man/lexdiv.Rd | 2 man/metacorpus.Rd | 2 man/metadoc.Rd | 2 man/ndoc.Rd | 2 man/ngrams.Rd | 2 man/ntoken.Rd | 2 man/phrasetotoken.Rd | 2 man/plot.dfm.Rd | 2 man/print.dfm.Rd | 2 man/quanteda-package.Rd | 2 man/removeFeatures.Rd | 2 man/segment.Rd | 2 man/settings.Rd | 2 man/similarity.Rd | 2 man/sort.dfm.Rd | 2 man/stopwords.Rd | 2 man/subset.corpus.Rd | 2 man/summary.corpus.Rd | 2 man/syllables.Rd | 2 man/textfile.Rd | 2 man/textmodel.Rd | 2 man/textmodel_ca.Rd | 2 man/textmodel_fitted-class.Rd | 2 man/textmodel_wordfish.Rd | 2 man/textmodel_wordscores.Rd | 2 man/texts.Rd | 2 man/tokenize.Rd | 2 man/tokenizeOnly.Rd | 2 man/topfeatures.Rd | 2 man/trim.Rd | 2 man/ukimmigTexts.Rd | 2 man/weight.Rd | 2 man/wordstem.Rd | 2 vignettes/corpus-sources.Rmd | 4 - 67 files changed, 168 insertions(+), 166 deletions(-)
Title: Multi-Locus Stepwise Regression
Description: The multi-locus stepwise regression (MSR) combines the advantages of stepwise regression and haplotype-based analysis. The MSR can be used to identify informative combinations of single nucleotide polymorphisms (SNPs) from unlinked SNPs (allele combinations) or SNPs within a chromosomal region (haplotypes).
Author: Sven Knueppel and Klaus Rohde
Maintainer: Sven Knueppel <sven.knueppel@dife.de>
Diff between HapEstXXR versions 0.1-7 dated 2014-11-12 and 0.1-8 dated 2015-06-02
DESCRIPTION | 15 +++++++-------- MD5 | 16 ++++++++-------- src/HapRshort.c | 4 ++-- src/haptdpnZR.c | 4 ++-- src/itegeppXXR.c | 8 +++++--- src/matalloc.c | 4 ++-- src/matrix.c | 5 +++-- src/powerset.c | 8 ++++---- src/readin.c | 2 +- 9 files changed, 34 insertions(+), 32 deletions(-)
Title: Gaussian Copula Marginal Regression
Description: Likelihood inference in Gaussian copula marginal
regression models.
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin <sammy@unive.it>
Diff between gcmr versions 0.7.0 dated 2015-04-20 and 0.7.5 dated 2015-06-02
gcmr-0.7.0/gcmr/man/estfun.gcmr.Rd |only gcmr-0.7.0/gcmr/man/se.Rd |only gcmr-0.7.0/gcmr/man/vcov.gcmr.Rd |only gcmr-0.7.5/gcmr/DESCRIPTION | 8 gcmr-0.7.5/gcmr/MD5 | 35 +-- gcmr-0.7.5/gcmr/NAMESPACE | 31 +- gcmr-0.7.5/gcmr/NEWS | 11 gcmr-0.7.5/gcmr/R/cormat.R | 8 gcmr-0.7.5/gcmr/R/gcmr.R | 375 ++++++++++++++-------------------- gcmr-0.7.5/gcmr/man/epilepsy.Rd | 12 - gcmr-0.7.5/gcmr/man/gcmr-package.Rd | 10 gcmr-0.7.5/gcmr/man/gcmr.Rd | 45 ++-- gcmr-0.7.5/gcmr/man/gcmr.options.Rd | 7 gcmr-0.7.5/gcmr/man/gs.marg.Rd | 14 - gcmr-0.7.5/gcmr/man/malaria.Rd | 4 gcmr-0.7.5/gcmr/man/matern.cormat.Rd | 4 gcmr-0.7.5/gcmr/man/plot.gcmr.Rd | 24 +- gcmr-0.7.5/gcmr/man/profile.gcmr.Rd | 8 gcmr-0.7.5/gcmr/man/residuals.gcmr.Rd | 6 gcmr-0.7.5/gcmr/man/summary.gcmr.Rd | 51 +++- 20 files changed, 326 insertions(+), 327 deletions(-)
Title: Calculation of Evolvability Parameters
Description: An implementation of the evolvability parameters defined in Hansen and Houle (2008).
Author: Geir H. Bolstad [aut, cre]
Maintainer: Geir H. Bolstad <geir.bolstad@nina.no>
Diff between evolvability versions 1.0 dated 2014-06-10 and 1.1.0 dated 2015-06-02
DESCRIPTION | 19 +++-- MD5 | 25 ++++--- NAMESPACE | 20 +++++- R/evolvabilityBeta.R | 85 ++++++++++++-------------- R/evolvabilityBetaMCMC.R | 140 +++++++++++++++++++++----------------------- R/evolvabilityBetaMCMC2.R | 64 ++++++++++---------- R/evolvabilityMeans.R | 39 ++++++------ R/evolvabilityMeansMCMC.R | 70 +++++++++++----------- R/meanStdG.R | 5 - R/meanStdGMCMC.R | 13 ++-- R/randomBeta.R | 35 ++++++++--- inst |only man/evolvability-package.Rd | 38 +++++++---- man/randomBeta.Rd | 76 ++++++++++------------- 14 files changed, 333 insertions(+), 296 deletions(-)
Title: Clustering of Variables Around Latent Variables
Description: Functions for the clustering of variables around Latent Variables. Each cluster of variables, which may be defined as a local or directional cluster, is associated with a latent variable.
External variables measured on the same observations or/and additional information on the variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau <evelyne.vigneau@oniris-nantes.fr>
Diff between ClustVarLV versions 1.3.2 dated 2015-03-17 and 1.4.0 dated 2015-06-02
ClustVarLV-1.3.2/ClustVarLV/R/critcpp.r |only ClustVarLV-1.3.2/ClustVarLV/R/gpmb_on_pc.R |only ClustVarLV-1.3.2/ClustVarLV/R/mincpp.r |only ClustVarLV-1.3.2/ClustVarLV/R/print.clvkmeans.r |only ClustVarLV-1.3.2/ClustVarLV/man/descrip_gp.Rd |only ClustVarLV-1.3.2/ClustVarLV/man/gpmb_on_pc.Rd |only ClustVarLV-1.3.2/ClustVarLV/man/print.clvkmeans.Rd |only ClustVarLV-1.3.2/ClustVarLV/vignettes/ClustVarLV_RR_2014.pdf |only ClustVarLV-1.4.0/ClustVarLV/DESCRIPTION | 11 - ClustVarLV-1.4.0/ClustVarLV/MD5 | 72 +++++--- ClustVarLV-1.4.0/ClustVarLV/NAMESPACE | 22 +- ClustVarLV-1.4.0/ClustVarLV/R/CLV.R | 59 ++---- ClustVarLV-1.4.0/ClustVarLV/R/CLV_kmeans.R | 43 ++-- ClustVarLV-1.4.0/ClustVarLV/R/LCLV.R | 27 --- ClustVarLV-1.4.0/ClustVarLV/R/RcppExports.R |only ClustVarLV-1.4.0/ClustVarLV/R/clvk_kp1.R | 2 ClustVarLV-1.4.0/ClustVarLV/R/clvk_sparse.R | 5 ClustVarLV-1.4.0/ClustVarLV/R/consol_calcul_s.R | 48 +---- ClustVarLV-1.4.0/ClustVarLV/R/data_biplot.R |only ClustVarLV-1.4.0/ClustVarLV/R/descrip_gp.R | 42 ++-- ClustVarLV-1.4.0/ClustVarLV/R/get_comp.R |only ClustVarLV-1.4.0/ClustVarLV/R/get_load.R |only ClustVarLV-1.4.0/ClustVarLV/R/get_partition.R |only ClustVarLV-1.4.0/ClustVarLV/R/plot.clv.R |only ClustVarLV-1.4.0/ClustVarLV/R/plot.lclv.R |only ClustVarLV-1.4.0/ClustVarLV/R/plot_var.R |only ClustVarLV-1.4.0/ClustVarLV/R/print.clv.r | 88 +++++++--- ClustVarLV-1.4.0/ClustVarLV/R/print.lclv.r | 12 - ClustVarLV-1.4.0/ClustVarLV/R/stand_quali.R |only ClustVarLV-1.4.0/ClustVarLV/R/summary_clv.R |only ClustVarLV-1.4.0/ClustVarLV/R/tabdisj.R |only ClustVarLV-1.4.0/ClustVarLV/build |only ClustVarLV-1.4.0/ClustVarLV/inst |only ClustVarLV-1.4.0/ClustVarLV/man/CLV.Rd | 26 +- ClustVarLV-1.4.0/ClustVarLV/man/CLV_kmeans.Rd | 14 - ClustVarLV-1.4.0/ClustVarLV/man/LCLV.Rd | 7 ClustVarLV-1.4.0/ClustVarLV/man/data_biplot.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/get_comp.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/get_load.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/get_partition.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/plot.clv.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/plot.lclv.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/plot_var.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/print.clv.Rd | 4 ClustVarLV-1.4.0/ClustVarLV/man/print.lclv.Rd | 4 ClustVarLV-1.4.0/ClustVarLV/man/stand_quali.Rd |only ClustVarLV-1.4.0/ClustVarLV/man/summary_clv.Rd |only ClustVarLV-1.4.0/ClustVarLV/src/RcppExports.cpp |only ClustVarLV-1.4.0/ClustVarLV/src/critcpp.cpp | 40 ++-- ClustVarLV-1.4.0/ClustVarLV/src/mincpp.cpp | 45 ++--- ClustVarLV-1.4.0/ClustVarLV/vignettes/ClustVarLV_RR2014_ve.pdf |only ClustVarLV-1.4.0/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.Rmd |only ClustVarLV-1.4.0/ClustVarLV/vignettes/Getting_started_with_ClustVarLV.html |only 53 files changed, 292 insertions(+), 279 deletions(-)
More information about spectral.methods at CRAN
Permanent link
Title: Phylogenetic Comparative Tools for Missing Data and
Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Available functions allow ancestral state reconstruction, missing data imputation, phylogenetic regression (phylogenetic generalized least squares), and phylogenetic principal components analysis (pPCA).
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between Rphylopars versions 0.1.0 dated 2015-06-01 and 0.1.1 dated 2015-06-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/Rphylopars-package.Rd | 4 ++-- src/RcppExports.cpp | 42 +++++++++++++++++++++--------------------- src/phylopars_rcpp.cpp | 14 +++++++------- 5 files changed, 38 insertions(+), 38 deletions(-)
Title: Parallel Programming Tools for Rcpp
Description: High level functions for doing parallel programming with 'Rcpp'.
For example, the parallelFor() function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce()
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between RcppParallel versions 4.3.8 dated 2015-04-14 and 4.3.14 dated 2015-06-02
RcppParallel-4.3.14/RcppParallel/DESCRIPTION | 17 +-- RcppParallel-4.3.14/RcppParallel/MD5 | 47 ++++------ RcppParallel-4.3.14/RcppParallel/NEWS | 9 + RcppParallel-4.3.14/RcppParallel/R/build.R | 12 +- RcppParallel-4.3.14/RcppParallel/inst/include/RcppParallel.h | 2 RcppParallel-4.3.14/RcppParallel/inst/include/RcppParallel/RMatrix.h | 10 +- RcppParallel-4.3.14/RcppParallel/inst/tests |only RcppParallel-4.3.14/RcppParallel/src/Makevars | 17 ++- RcppParallel-4.3.14/RcppParallel/src/tbb/build/SunOS.gcc.inc | 1 RcppParallel-4.3.14/RcppParallel/src/tbb/build/linux.clang.inc | 2 RcppParallel-4.3.14/RcppParallel/tests/doRUnit.R |only RcppParallel-4.3.8/RcppParallel/tests/testthat |only RcppParallel-4.3.8/RcppParallel/tests/testthat.R |only 13 files changed, 62 insertions(+), 55 deletions(-)
Title: Pedometric Tools and Techniques
Description: Functions to employ many tools and
techniques used in the field of pedometrics (see
http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics).
These functions were developed to fulfil the demands created by the PhD
research project (2012-2016) entitled Contribution to the Construction of
Models for Predicting Soil Properties, developed by Alessandro Samuel-Rosa
under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do
Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and
Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands).
The project is supported by the CAPES, Ministério da Educação, BrasÃlia -
DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions are
simple wrapper functions that extend the functionalities of other functions
commonly used for the analysis of pedometric data. It should be noted that
changes are likely to occur quite often and using this package as a
dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths], Gerard B. M. Heuvelink [ths], Tony Olsen
[ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo
Garcia [ctb], Pablo Garcia Rodriguez [ctb], Joshua French [ctb],
Ken Kleinman [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.4-1 dated 2014-12-01 and 0.6-2 dated 2015-06-02
pedometrics-0.4-1/pedometrics/R/spJitter.R |only pedometrics-0.4-1/pedometrics/R/spSANN.R |only pedometrics-0.4-1/pedometrics/R/spsannMSSD.R |only pedometrics-0.4-1/pedometrics/R/spsannPPL.R |only pedometrics-0.4-1/pedometrics/inst |only pedometrics-0.4-1/pedometrics/man/spJitterFinite.Rd |only pedometrics-0.4-1/pedometrics/man/spsannMSSD.Rd |only pedometrics-0.4-1/pedometrics/man/spsannPPL.Rd |only pedometrics-0.4-1/pedometrics/src/calcMSSDCpp.cpp |only pedometrics-0.4-1/pedometrics/src/spJitterCpp.cpp |only pedometrics-0.4-1/pedometrics/src/updateMSSDCpp.cpp |only pedometrics-0.4-1/pedometrics/src/updatePPLCpp.cpp |only pedometrics-0.6-2/pedometrics/DESCRIPTION | 31 ++---- pedometrics-0.6-2/pedometrics/MD5 | 72 ++++++--------- pedometrics-0.6-2/pedometrics/NAMESPACE | 23 ++-- pedometrics-0.6-2/pedometrics/R/RcppExports.R | 16 --- pedometrics-0.6-2/pedometrics/R/buildMS.R | 15 +-- pedometrics-0.6-2/pedometrics/R/cdfTable.R | 8 - pedometrics-0.6-2/pedometrics/R/cont2cat.R |only pedometrics-0.6-2/pedometrics/R/cramer.R |only pedometrics-0.6-2/pedometrics/R/numint.R |only pedometrics-0.6-2/pedometrics/R/pedometrics.R | 14 ++ pedometrics-0.6-2/pedometrics/R/plotHD.R | 22 ++-- pedometrics-0.6-2/pedometrics/R/plotMS.R | 9 + pedometrics-0.6-2/pedometrics/R/statsMS.R | 6 - pedometrics-0.6-2/pedometrics/R/stepVIF.R | 4 pedometrics-0.6-2/pedometrics/man/adjR2.Rd | 3 pedometrics-0.6-2/pedometrics/man/bbox2sp.Rd | 3 pedometrics-0.6-2/pedometrics/man/buildMS.Rd | 3 pedometrics-0.6-2/pedometrics/man/cdfPlot.Rd | 3 pedometrics-0.6-2/pedometrics/man/cdfStats.Rd | 3 pedometrics-0.6-2/pedometrics/man/cdfTable.Rd | 3 pedometrics-0.6-2/pedometrics/man/cont2cat.Rd |only pedometrics-0.6-2/pedometrics/man/coordenadas.Rd | 3 pedometrics-0.6-2/pedometrics/man/cramer.Rd |only pedometrics-0.6-2/pedometrics/man/gcpDiff.Rd | 3 pedometrics-0.6-2/pedometrics/man/gcpVector.Rd | 3 pedometrics-0.6-2/pedometrics/man/is.numint.Rd |only pedometrics-0.6-2/pedometrics/man/pedometrics-package.Rd | 15 ++- pedometrics-0.6-2/pedometrics/man/plotESDA.Rd | 3 pedometrics-0.6-2/pedometrics/man/plotHD.Rd | 5 - pedometrics-0.6-2/pedometrics/man/plotMS.Rd | 3 pedometrics-0.6-2/pedometrics/man/rowMinCpp.Rd | 3 pedometrics-0.6-2/pedometrics/man/statsMS.Rd | 3 pedometrics-0.6-2/pedometrics/man/stepVIF.Rd | 3 pedometrics-0.6-2/pedometrics/src/RcppExports.cpp | 71 -------------- 46 files changed, 148 insertions(+), 205 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification arose from verifying high-resolution forecasts, where coarser-resolution models generally are favored even when a human forecaster finds the higher-resolution model to be considerably better. Most newly proposed methods, which largely come from image analysis, computer vision, and similar, are available, with more on the way.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.2-3 dated 2015-05-19 and 0.2-4 dated 2015-06-01
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/deltamm.R | 31 ++----------------------------- 3 files changed, 11 insertions(+), 38 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names and default values.
Settings can then be retrieved, altered and reset to defaults with ease.
For R programmers and package developers it offers cloning and merging
functionality which allows for conveniently defining global and local
options, possibly in a multilevel options hierarchy. See the package
vignette for some examples concerning functions, S4 classes, and reference
classes. There are convenience functions to reset par() and options() to
their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.1 dated 2015-04-13 and 0.2.2 dated 2015-06-01
settings-0.2.1/settings/README.md |only settings-0.2.2/settings/DESCRIPTION | 8 ++--- settings-0.2.2/settings/MD5 | 33 +++++++++++------------- settings-0.2.2/settings/NAMESPACE | 2 - settings-0.2.2/settings/NEWS | 11 +++++--- settings-0.2.2/settings/R/utils.R | 1 settings-0.2.2/settings/build/vignette.rds |binary settings-0.2.2/settings/inst/doc/settings.R | 4 +- settings-0.2.2/settings/inst/doc/settings.html | 2 - settings-0.2.2/settings/man/clone_and_merge.Rd | 3 +- settings-0.2.2/settings/man/defaults.Rd | 3 +- settings-0.2.2/settings/man/is_setting.Rd | 3 +- settings-0.2.2/settings/man/options_manager.Rd | 3 +- settings-0.2.2/settings/man/reset.Rd | 3 +- settings-0.2.2/settings/man/reset_options.Rd | 3 +- settings-0.2.2/settings/man/reset_par.Rd | 3 +- settings-0.2.2/settings/man/settings.Rd | 3 +- settings-0.2.2/settings/man/stop_if_reserved.Rd | 3 +- 18 files changed, 50 insertions(+), 38 deletions(-)
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-6 dated 2015-05-29 and 0.1-7 dated 2015-06-01
DESCRIPTION | 13 ++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- R/parallelSVM.R | 6 ++++-- R/predict.parallelSVM.R | 4 ++-- R/registerCores.R | 11 ++--------- 6 files changed, 20 insertions(+), 26 deletions(-)
Title: Misc Small Tools and Helper Functions for Other Code of J.
Buttlar
Description: Collection of several tools and helper functions used across the other packages of J. Buttlar ('ncdf.tools' and 'spectral.methods').
Author: Jannis v. Buttlar
Maintainer: Jannis v. Buttlar <jbuttlar@bgc-jena.mpg.de>
Diff between JBTools versions 0.7.2.6 dated 2014-04-03 and 0.7.2.9 dated 2015-06-01
DESCRIPTION | 18 +++++++++------ MD5 | 54 ++++++++++++++++++++++++--------------------- R/plotColorScale.R | 12 +++++----- R/registerParallel.R | 42 +++++++++++++++++++---------------- R/seqLength.R |only R/seqLongest.R |only man/JBTools-package.Rd | 10 ++++---- man/MEF.Rd | 3 +- man/RMSE.Rd | 3 +- man/checkInstalled.Rd | 3 +- man/colorChangeDarkness.Rd | 3 +- man/convertArgs2String.Rd | 1 man/getSysinfo.Rd | 3 +- man/getVecInfo.Rd | 3 +- man/indexDimVecs2Matrix.Rd | 3 +- man/indexVec2Matrix.Rd | 3 +- man/isSeriesConstant.Rd | 3 +- man/isSeriesContinuous.Rd | 3 +- man/labelMargins.Rd | 3 +- man/plotBG.Rd | 3 +- man/plotColorScale.Rd | 3 +- man/plotImageRotated.Rd | 3 +- man/plotNLines.Rd | 3 +- man/printStatus.Rd | 3 +- man/rangeZeroEqui.Rd | 3 +- man/registerParallel.Rd | 3 +- man/seqLength.Rd |only man/seqLongest.Rd |only man/userCoords.Rd | 3 +- man/whichClosest.Rd | 3 +- 30 files changed, 115 insertions(+), 82 deletions(-)
Title: Download Data from the FAOSTAT Database of the Food and
Agricultural Organization (FAO) of the United Nations
Description: A list of functions to download statistics from FAOSTAT (database
of the Food and Agricultural Organization of the United Nations) and WDI
(database of the World Bank), and to perform some harmonization operations.
Author: Michael C. J. Kao <michael.kao@fao.org>, Markus Gesmann, Filippo Gheri
Maintainer: Filippo Gheri <filippo.gheri@fao.org>
Diff between FAOSTAT versions 1.9 dated 2014-10-28 and 2.0 dated 2015-06-01
DESCRIPTION | 20 ++++------ MD5 | 20 +++++----- R/FAOsearch.R | 95 ++++++++++++++++++++++++++++++------------------ R/getFAO.R | 51 +++++++------------------ R/getFAOtoSYB.R | 4 -- R/translateUnit.R | 2 - data/FAOmetaTable.RData |binary inst/doc/FAOSTAT.pdf |binary man/getFAO.Rd | 8 +--- man/getFAOtoSYB.Rd | 8 +--- man/translateUnit.Rd | 2 - 11 files changed, 103 insertions(+), 107 deletions(-)
Title: Global-Value-Chain Decomposition
Description: Two global-value-chain decompositions are implemented.
Firstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu, 2013) algorithm splits bilateral gross
exports into 16 value-added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu
(Wang, Z., S.-J. Wei, and K. Zhu. 2013. "Quantifying International Production Sharing at the Bilateral and Sector Levels.").
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between decompr versions 3.0.0 dated 2015-04-01 and 4.0.0 dated 2015-06-01
decompr-3.0.0/decompr/R/leontief_output.R |only decompr-3.0.0/decompr/man/leontief_output.Rd |only decompr-3.0.0/decompr/tests/testthat/test_leontief_output.R |only decompr-4.0.0/decompr/DESCRIPTION | 21 +-- decompr-4.0.0/decompr/MD5 | 45 +++---- decompr-4.0.0/decompr/NAMESPACE | 3 decompr-4.0.0/decompr/NEWS | 10 + decompr-4.0.0/decompr/R/decomp.R | 10 - decompr-4.0.0/decompr/R/leontief.R | 26 +++- decompr-4.0.0/decompr/R/load_tables_vectors.R | 19 ++- decompr-4.0.0/decompr/README.md | 71 ++++++++++-- decompr-4.0.0/decompr/build/vignette.rds |binary decompr-4.0.0/decompr/inst/doc/decompr.html | 4 decompr-4.0.0/decompr/man/countries.Rd | 2 decompr-4.0.0/decompr/man/decomp.Rd | 9 - decompr-4.0.0/decompr/man/decompr.Rd | 2 decompr-4.0.0/decompr/man/final.Rd | 2 decompr-4.0.0/decompr/man/industries.Rd | 2 decompr-4.0.0/decompr/man/inter.Rd | 2 decompr-4.0.0/decompr/man/leontief.Rd | 11 + decompr-4.0.0/decompr/man/load_tables.Rd | 2 decompr-4.0.0/decompr/man/load_tables_vectors.Rd | 6 - decompr-4.0.0/decompr/man/out.Rd | 2 decompr-4.0.0/decompr/man/wwz.Rd | 2 decompr-4.0.0/decompr/tests/testthat/test_leontief.R | 48 ++++++-- 25 files changed, 205 insertions(+), 94 deletions(-)
Title: Class Cover Catch Digraphs
Description: Class Cover Catch Digraphs, neighborhood graphs, and
relatives.
Author: David J. Marchette <dmarchette@gmail.com>
Maintainer: David J. Marchette <dmarchette@gmail.com>
Diff between cccd versions 1.04 dated 2013-10-29 and 1.5 dated 2015-06-01
DESCRIPTION | 17 +++---- MD5 | 31 +++++++------ NAMESPACE | 6 ++ R/cccd.R | 127 ++++++++++++++++++++++++++++++++++++++++---------------- R/ccd.R | 8 +-- R/circle.R |only R/class.R | 2 R/dominate.R | 20 ++++---- R/gg.R | 116 +++++++++++++++++++++++++++++++++------------------ R/juggling.R | 8 +-- R/nng.R | 69 ++++++++++++++++++++---------- R/rng.R | 117 ++++++++++++++++++++++++++++++++++++--------------- man/cccd.Rd | 48 ++++++++++++++++++--- man/dominate.Rd | 11 +++- man/gg.Rd | 12 ++++- man/nng.Rd | 10 +++- man/rng.Rd | 25 ++++++++++- 17 files changed, 435 insertions(+), 192 deletions(-)
Title: Fast, Exact Bootstrap Principal Component Analysis for High
Dimensional Data
Description: Implements fast, exact bootstrap Principal Component Analysis and
Singular Value Decompositions for high dimensional data, as described in
<http://arxiv.org/abs/1405.0922>. For data matrices that are too large to operate
on in memory, users can input objects with class 'ff' (see the 'ff'
package), where the actual data is stored on disk. In response, this
package will implement a block matrix algebra procedure for calculating the
principal components (PCs) and bootstrap PCs. Depending on options set by
the user, the 'parallel' package can be used to parallelize the calculation of
the bootstrap PCs.
Author: Aaron Fisher <fisher@jhu.edu>
Maintainer: Aaron Fisher <fisher@jhu.edu>
Diff between bootSVD versions 0.2 dated 2015-04-22 and 0.5 dated 2015-06-01
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- R/bootstrap_functions.R | 33 ++++++++++++++++++++------------- man/As2Vs.Rd | 2 +- man/bootSVD.Rd | 4 ++-- man/bootSVD_LD.Rd | 2 +- man/getMomentsAndMomentCI.Rd | 4 ++-- man/reindexMatricesByK.Rd | 2 +- man/reindexVectorsByK.Rd | 2 +- 9 files changed, 41 insertions(+), 33 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-0 dated 2015-04-04 and 1.2-1 dated 2015-06-01
ChangeLog | 2 DESCRIPTION | 12 - MD5 | 175 +++++++++-------- NAMESPACE | 5 R/AllClass.R | 102 +++++++--- R/AllGeneric.R | 6 R/Auxiliaries.R | 11 - R/CHMfactor.R | 5 R/Csparse.R | 5 R/Matrix.R | 47 +++- R/Ops.R | 20 +- R/Rsparse.R | 6 R/Summary.R | 25 +- R/Tsparse.R | 37 ++- R/abIndex.R | 2 R/dgCMatrix.R | 19 - R/diagMatrix.R | 17 - R/lsparseMatrix.R | 2 R/nsparseMatrix.R | 2 R/products.R | 9 R/sparseMatrix.R | 13 - R/sparseQR.R | 45 ++-- R/sparseVector.R | 21 +- R/zzz.R | 1 TODO | 70 +++---- inst/NEWS.Rd | 176 +++++++++++++++--- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/po/de/LC_MESSAGES/Matrix.mo |binary inst/po/de/LC_MESSAGES/R-Matrix.mo |binary inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary inst/po/fr/LC_MESSAGES/Matrix.mo |binary inst/po/fr/LC_MESSAGES/R-Matrix.mo |binary inst/po/ko/LC_MESSAGES/R-Matrix.mo |binary inst/po/pl/LC_MESSAGES/Matrix.mo |binary inst/po/pl/LC_MESSAGES/R-Matrix.mo |binary inst/test-tools-1.R | 37 +++ man/Cholesky.Rd | 8 man/compMatrix-class.Rd | 44 ++-- man/diagU2N.Rd | 13 - man/drop0.Rd | 3 man/image-methods.Rd | 23 ++ man/lu.Rd | 24 ++ man/matrix-products.Rd | 1 man/nnzero.Rd | 2 man/qr-methods.Rd | 67 ++++++ man/sparseLU-class.Rd | 14 - man/sparseMatrix.Rd | 2 man/sparseVector-class.Rd | 1 man/symmetricMatrix-class.Rd | 15 + po/Matrix.pot | 241 ++++++++++++++---------- po/R-Matrix.pot | 10 - po/R-de.po | 64 +++--- po/R-fr.po | 22 +- po/R-ko.po | 20 +- po/R-pl.po | 30 +-- po/de.po | 312 ++++++++++++++++++-------------- po/fr.po | 240 ++++++++++++++---------- po/ko.po |only po/pl.po | 260 +++++++++++++++----------- src/Mutils.c | 64 ++++++ src/Mutils.h | 14 + src/Syms.h | 2 src/chm_common.c | 16 - src/cs_utils.c | 25 +- src/cs_utils.h | 2 src/dense.c | 3 src/dgCMatrix.c | 112 +++++++++-- src/dgCMatrix.h | 4 src/dgTMatrix.c | 57 ----- src/dgTMatrix.h | 3 src/dgeMatrix.c | 50 ++--- src/dspMatrix.c | 14 - src/dsyMatrix.c | 18 + src/dtrMatrix.c | 85 ++++++-- src/factorizations.c | 28 ++ src/factorizations.h | 3 src/init.c | 16 + src/sparseQR.c | 107 ++++++---- src/sparseQR.h | 2 tests/Simple.R | 8 tests/factorizing.R | 69 ++++--- tests/indexing.R | 54 ++++- tests/indexing.Rout.save | 89 +++++++-- tests/matprod.R | 123 +++++++++--- 89 files changed, 2075 insertions(+), 1181 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.17 dated 2015-04-16 and 2.18 dated 2015-06-01
DESCRIPTION | 20 ++++---- MD5 | 34 +++++++------- R/MCMC-support.R | 24 ++++++++++ R/cld.lsm.R | 2 R/helpers.R | 104 ++++++++++++++++----------------------------- R/lsm-contr.R | 42 ++++++++++++++++++ R/lsmeans.R | 2 R/summary.R | 33 ++++++++++---- build/vignette.rds |binary inst/NEWS | 14 ++++++ inst/doc/extending.R | 1 inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 1 inst/doc/using-lsmeans.pdf |binary man/lsmeans.Rd | 2 man/models.Rd | 11 +++- man/pairwise.lsmc.Rd | 9 +++ tests/tests1.Rout.save | 9 +-- 18 files changed, 197 insertions(+), 111 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
G.C. Shen;
V. Shcherbakov;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.41-1 dated 2015-02-27 and 1.42-0 dated 2015-06-01
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spatstat-1.42-0/spatstat/inst/rawdata/finpines |only spatstat-1.42-0/spatstat/inst/rawdata/vesicles/vesicles.csv |only spatstat-1.42-0/spatstat/inst/rawdata/vesicles/vesicleswindow.csv |only spatstat-1.42-0/spatstat/inst/rawdata/vesicles/vesicleswindow.txt |only spatstat-1.42-0/spatstat/man/Extract.tess.Rd | 23 spatstat-1.42-0/spatstat/man/HierHard.Rd |only spatstat-1.42-0/spatstat/man/HierStrauss.Rd | 11 spatstat-1.42-0/spatstat/man/HierStraussHard.Rd |only spatstat-1.42-0/spatstat/man/Kcross.Rd | 6 spatstat-1.42-0/spatstat/man/Kdot.Rd | 3 spatstat-1.42-0/spatstat/man/Kest.Rd | 7 spatstat-1.42-0/spatstat/man/Lcross.Rd | 5 spatstat-1.42-0/spatstat/man/Ldot.Rd | 3 spatstat-1.42-0/spatstat/man/Lest.Rd | 2 spatstat-1.42-0/spatstat/man/Smooth.msr.Rd | 2 spatstat-1.42-0/spatstat/man/Smooth.ppp.Rd | 2 spatstat-1.42-0/spatstat/man/adaptive.density.Rd | 22 spatstat-1.42-0/spatstat/man/allstats.Rd | 4 spatstat-1.42-0/spatstat/man/alltypes.Rd | 10 spatstat-1.42-0/spatstat/man/anova.ppm.Rd | 17 spatstat-1.42-0/spatstat/man/as.data.frame.owin.Rd |only spatstat-1.42-0/spatstat/man/as.im.Rd | 5 spatstat-1.42-0/spatstat/man/as.owin.Rd | 4 spatstat-1.42-0/spatstat/man/auc.Rd |only spatstat-1.42-0/spatstat/man/begins.Rd |only spatstat-1.42-0/spatstat/man/branchlabelfun.Rd |only spatstat-1.42-0/spatstat/man/bw.diggle.Rd | 20 spatstat-1.42-0/spatstat/man/by.ppp.Rd | 3 spatstat-1.42-0/spatstat/man/chicago.Rd | 14 spatstat-1.42-0/spatstat/man/clickbox.Rd | 6 spatstat-1.42-0/spatstat/man/clickpoly.Rd | 3 spatstat-1.42-0/spatstat/man/colourtools.Rd | 7 spatstat-1.42-0/spatstat/man/copyExampleFiles.Rd |only spatstat-1.42-0/spatstat/man/dclf.progress.Rd | 24 spatstat-1.42-0/spatstat/man/delaunay.Rd | 17 spatstat-1.42-0/spatstat/man/delaunayDistance.Rd |only spatstat-1.42-0/spatstat/man/delaunayNetwork.Rd |only spatstat-1.42-0/spatstat/man/deletebranch.Rd |only spatstat-1.42-0/spatstat/man/density.lpp.Rd |only spatstat-1.42-0/spatstat/man/density.ppp.Rd | 20 spatstat-1.42-0/spatstat/man/density.splitppp.Rd | 36 spatstat-1.42-0/spatstat/man/dirichlet.Rd | 2 spatstat-1.42-0/spatstat/man/dirichletAreas.Rd |only spatstat-1.42-0/spatstat/man/dirichletVertices.Rd |only spatstat-1.42-0/spatstat/man/dirichletWeights.Rd |only spatstat-1.42-0/spatstat/man/distcdf.Rd | 11 spatstat-1.42-0/spatstat/man/edit.hyperframe.Rd |only spatstat-1.42-0/spatstat/man/edit.ppp.Rd |only spatstat-1.42-0/spatstat/man/effectfun.Rd | 7 spatstat-1.42-0/spatstat/man/envelope.Rd | 11 spatstat-1.42-0/spatstat/man/envelope.lpp.Rd | 9 spatstat-1.42-0/spatstat/man/envelope.pp3.Rd | 7 spatstat-1.42-0/spatstat/man/eval.fv.Rd | 18 spatstat-1.42-0/spatstat/man/foo.Rd | 15 spatstat-1.42-0/spatstat/man/gridweights.Rd | 2 spatstat-1.42-0/spatstat/man/harmonise.fv.Rd | 22 spatstat-1.42-0/spatstat/man/harmonise.owin.Rd |only spatstat-1.42-0/spatstat/man/identify.ppp.Rd | 8 spatstat-1.42-0/spatstat/man/idw.Rd | 2 spatstat-1.42-0/spatstat/man/incircle.Rd | 14 spatstat-1.42-0/spatstat/man/integral.im.Rd | 9 spatstat-1.42-0/spatstat/man/integral.msr.Rd | 13 spatstat-1.42-0/spatstat/man/intersect.owin.Rd | 63 - spatstat-1.42-0/spatstat/man/iplot.Rd | 5 spatstat-1.42-0/spatstat/man/istat.Rd | 6 spatstat-1.42-0/spatstat/man/kppm.Rd | 5 spatstat-1.42-0/spatstat/man/lineardisc.Rd | 15 spatstat-1.42-0/spatstat/man/linnet.Rd | 2 spatstat-1.42-0/spatstat/man/logLik.kppm.Rd |only spatstat-1.42-0/spatstat/man/lurking.Rd | 7 spatstat-1.42-0/spatstat/man/markstat.Rd | 2 spatstat-1.42-0/spatstat/man/marktable.Rd | 34 spatstat-1.42-0/spatstat/man/mergeLevels.Rd |only spatstat-1.42-0/spatstat/man/methods.linim.Rd |only spatstat-1.42-0/spatstat/man/methods.rho2hat.Rd | 32 spatstat-1.42-0/spatstat/man/model.images.Rd | 6 spatstat-1.42-0/spatstat/man/nncorr.Rd | 8 spatstat-1.42-0/spatstat/man/nnmark.Rd | 2 spatstat-1.42-0/spatstat/man/owin.Rd | 36 spatstat-1.42-0/spatstat/man/parameters.Rd |only spatstat-1.42-0/spatstat/man/plot.fv.Rd | 2 spatstat-1.42-0/spatstat/man/plot.hyperframe.Rd | 4 spatstat-1.42-0/spatstat/man/plot.imlist.Rd | 8 spatstat-1.42-0/spatstat/man/plot.owin.Rd | 8 spatstat-1.42-0/spatstat/man/plot.tess.Rd | 20 spatstat-1.42-0/spatstat/man/plot.texturemap.Rd | 7 spatstat-1.42-0/spatstat/man/ppm.ppp.Rd | 33 spatstat-1.42-0/spatstat/man/quadrat.test.Rd | 19 spatstat-1.42-0/spatstat/man/quadratcount.Rd | 6 spatstat-1.42-0/spatstat/man/quadscheme.Rd | 2 spatstat-1.42-0/spatstat/man/quadscheme.logi.Rd | 8 spatstat-1.42-0/spatstat/man/quantess.Rd | 11 spatstat-1.42-0/spatstat/man/quantile.ewcdf.Rd | 10 spatstat-1.42-0/spatstat/man/rLGCP.Rd | 20 spatstat-1.42-0/spatstat/man/rSSI.Rd | 24 spatstat-1.42-0/spatstat/man/relevel.im.Rd |only spatstat-1.42-0/spatstat/man/relrisk.ppm.Rd | 2 spatstat-1.42-0/spatstat/man/relrisk.ppp.Rd | 2 spatstat-1.42-0/spatstat/man/residuals.kppm.Rd |only spatstat-1.42-0/spatstat/man/rnoise.Rd |only spatstat-1.42-0/spatstat/man/roc.Rd |only spatstat-1.42-0/spatstat/man/rose.Rd | 17 spatstat-1.42-0/spatstat/man/rpoislinetess.Rd | 3 spatstat-1.42-0/spatstat/man/rpoispp.Rd | 9 spatstat-1.42-0/spatstat/man/rpoispp3.Rd | 9 spatstat-1.42-0/spatstat/man/runifpoint.Rd | 12 spatstat-1.42-0/spatstat/man/runifpoint3.Rd | 9 spatstat-1.42-0/spatstat/man/spatstat-deprecated.Rd | 27 spatstat-1.42-0/spatstat/man/spatstat-internal.Rd | 83 + spatstat-1.42-0/spatstat/man/spatstat-package.Rd | 33 spatstat-1.42-0/spatstat/man/split.im.Rd | 2 spatstat-1.42-0/spatstat/man/split.ppp.Rd | 13 spatstat-1.42-0/spatstat/man/split.ppx.Rd | 7 spatstat-1.42-0/spatstat/man/square.Rd | 11 spatstat-1.42-0/spatstat/man/stienen.Rd | 1 spatstat-1.42-0/spatstat/man/studpermu.test.Rd |only spatstat-1.42-0/spatstat/man/summary.kppm.Rd |only spatstat-1.42-0/spatstat/man/superimpose.Rd | 16 spatstat-1.42-0/spatstat/man/tess.Rd | 12 spatstat-1.42-0/spatstat/man/textureplot.Rd | 29 spatstat-1.42-0/spatstat/man/transmat.Rd |only spatstat-1.42-0/spatstat/man/treebranchlabels.Rd |only spatstat-1.42-0/spatstat/man/treeprune.Rd |only spatstat-1.42-0/spatstat/man/unitname.Rd | 5 spatstat-1.42-0/spatstat/man/vcov.ppm.Rd | 17 spatstat-1.42-0/spatstat/man/with.msr.Rd |only spatstat-1.42-0/spatstat/tests/alltests.R | 63 - spatstat-1.42-0/spatstat/vignettes/datasets.Rnw | 15 spatstat-1.42-0/spatstat/vignettes/packagesizes.txt | 1 spatstat-1.42-0/spatstat/vignettes/updates.Rnw | 397 +++++- 343 files changed, 5478 insertions(+), 2328 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Inference methods for partially observed Markov processes (AKA stochastic dynamical systems, state-space models).
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 0.53-5 dated 2014-08-04 and 0.65-1 dated 2015-06-01
pomp-0.53-5/pomp/inst/examples/ou2.c |only pomp-0.53-5/pomp/inst/examples/verhulst.R |only pomp-0.53-5/pomp/man/abc-methods.Rd |only pomp-0.53-5/pomp/man/dmeasure-pomp.Rd |only pomp-0.53-5/pomp/man/dprocess-pomp.Rd |only pomp-0.53-5/pomp/man/init.state-pomp.Rd |only pomp-0.53-5/pomp/man/mif-methods.Rd |only pomp-0.53-5/pomp/man/pfilter-methods.Rd |only pomp-0.53-5/pomp/man/pmcmc-methods.Rd |only pomp-0.53-5/pomp/man/prior-pomp.Rd |only pomp-0.53-5/pomp/man/probed-pomp-methods.Rd |only pomp-0.53-5/pomp/man/profile-design.Rd |only pomp-0.53-5/pomp/man/rmeasure-pomp.Rd |only pomp-0.53-5/pomp/man/rprocess-pomp.Rd |only pomp-0.53-5/pomp/man/skeleton-pomp.Rd |only pomp-0.53-5/pomp/man/slice-design.Rd |only pomp-0.53-5/pomp/man/sobol.Rd |only pomp-0.53-5/pomp/man/trajectory-pomp.Rd |only pomp-0.53-5/pomp/man/verhulst.Rd |only pomp-0.65-1/pomp/DESCRIPTION | 37 +- pomp-0.65-1/pomp/MD5 | 213 +++++------ pomp-0.65-1/pomp/NAMESPACE | 13 pomp-0.65-1/pomp/R/aaa.R | 18 pomp-0.65-1/pomp/R/abc.R | 129 ++---- pomp-0.65-1/pomp/R/bsmc.R | 24 - pomp-0.65-1/pomp/R/bsmc2.R |only pomp-0.65-1/pomp/R/builder.R | 462 +++++++++++++------------ pomp-0.65-1/pomp/R/dmeasure-pomp.R | 8 pomp-0.65-1/pomp/R/dprior-pomp.R | 8 pomp-0.65-1/pomp/R/dprocess-pomp.R | 14 pomp-0.65-1/pomp/R/example.R | 52 +- pomp-0.65-1/pomp/R/generics.R | 7 pomp-0.65-1/pomp/R/init-state-pomp.R | 12 pomp-0.65-1/pomp/R/load.R |only pomp-0.65-1/pomp/R/mif-methods.R | 5 pomp-0.65-1/pomp/R/mif.R | 145 +------ pomp-0.65-1/pomp/R/minim.R | 8 pomp-0.65-1/pomp/R/nlf.R | 68 +-- pomp-0.65-1/pomp/R/pfilter.R | 36 + pomp-0.65-1/pomp/R/pmcmc-methods.R | 10 pomp-0.65-1/pomp/R/pmcmc.R | 144 +++---- pomp-0.65-1/pomp/R/pomp-class.R | 10 pomp-0.65-1/pomp/R/pomp-fun.R | 23 - pomp-0.65-1/pomp/R/pomp-methods.R | 67 ++- pomp-0.65-1/pomp/R/pomp.R | 232 +++++++----- pomp-0.65-1/pomp/R/probe-match.R | 7 pomp-0.65-1/pomp/R/probe.R | 16 pomp-0.65-1/pomp/R/proposals.R |only pomp-0.65-1/pomp/R/rmeasure-pomp.R | 10 pomp-0.65-1/pomp/R/rprior-pomp.R | 10 pomp-0.65-1/pomp/R/rprocess-pomp.R | 9 pomp-0.65-1/pomp/R/simulate-pomp.R | 29 + pomp-0.65-1/pomp/R/skeleton-pomp.R | 10 pomp-0.65-1/pomp/R/spect-match.R | 44 +- pomp-0.65-1/pomp/R/spect.R | 4 pomp-0.65-1/pomp/R/traj-match.R | 2 pomp-0.65-1/pomp/R/trajectory-pomp.R | 6 pomp-0.65-1/pomp/build/pomp.pdf |binary pomp-0.65-1/pomp/data/LondonYorke.rda |binary pomp-0.65-1/pomp/inst/CITATION | 51 ++ pomp-0.65-1/pomp/inst/NEWS | 144 +++++++ pomp-0.65-1/pomp/inst/NEWS.Rd | 118 ++++++ pomp-0.65-1/pomp/inst/examples/bbs.R | 4 pomp-0.65-1/pomp/inst/examples/blowflies.R | 4 pomp-0.65-1/pomp/inst/examples/dacca.R | 4 pomp-0.65-1/pomp/inst/examples/euler.sir.R | 4 pomp-0.65-1/pomp/inst/examples/gillespie.sir.R | 4 pomp-0.65-1/pomp/inst/examples/gompertz.R | 4 pomp-0.65-1/pomp/inst/examples/ricker.R | 4 pomp-0.65-1/pomp/inst/include/pomp.h | 430 ++++++++++++----------- pomp-0.65-1/pomp/man/abc.Rd | 105 +++-- pomp-0.65-1/pomp/man/basic-probes.Rd | 11 pomp-0.65-1/pomp/man/blowflies.Rd | 1 pomp-0.65-1/pomp/man/bsmc.Rd | 26 - pomp-0.65-1/pomp/man/bsplines.Rd | 7 pomp-0.65-1/pomp/man/builder.Rd | 32 - pomp-0.65-1/pomp/man/csnippet.Rd | 92 ++++ pomp-0.65-1/pomp/man/dacca.Rd | 7 pomp-0.65-1/pomp/man/design.Rd |only pomp-0.65-1/pomp/man/eulermultinom.Rd | 47 -- pomp-0.65-1/pomp/man/example.Rd | 32 + pomp-0.65-1/pomp/man/gompertz.Rd | 3 pomp-0.65-1/pomp/man/logmeanexp.Rd | 3 pomp-0.65-1/pomp/man/lowlevel.Rd |only pomp-0.65-1/pomp/man/mif.Rd | 113 ++++-- pomp-0.65-1/pomp/man/nlf.Rd | 28 - pomp-0.65-1/pomp/man/ou2.Rd | 4 pomp-0.65-1/pomp/man/particles-mif.Rd | 1 pomp-0.65-1/pomp/man/pfilter.Rd | 88 +++- pomp-0.65-1/pomp/man/plugins.Rd | 54 +- pomp-0.65-1/pomp/man/pmcmc.Rd | 65 ++- pomp-0.65-1/pomp/man/pomp-fun.Rd | 5 pomp-0.65-1/pomp/man/pomp-methods.Rd | 77 ---- pomp-0.65-1/pomp/man/pomp-package.Rd | 60 ++- pomp-0.65-1/pomp/man/pomp.Rd | 316 +++++++++-------- pomp-0.65-1/pomp/man/probe.Rd | 77 +++- pomp-0.65-1/pomp/man/proposals.Rd |only pomp-0.65-1/pomp/man/ricker.Rd | 3 pomp-0.65-1/pomp/man/rw2.Rd | 3 pomp-0.65-1/pomp/man/sannbox.Rd | 5 pomp-0.65-1/pomp/man/simulate-pomp.Rd | 18 pomp-0.65-1/pomp/man/sir.Rd | 12 pomp-0.65-1/pomp/man/spect.Rd | 41 +- pomp-0.65-1/pomp/man/traj-match.Rd | 10 pomp-0.65-1/pomp/src/Makevars | 2 pomp-0.65-1/pomp/src/dmeasure.c | 12 pomp-0.65-1/pomp/src/dprior.c | 6 pomp-0.65-1/pomp/src/dprocess.c | 5 pomp-0.65-1/pomp/src/euler.c | 26 - pomp-0.65-1/pomp/src/initstate.c | 2 pomp-0.65-1/pomp/src/partrans.c | 10 pomp-0.65-1/pomp/src/pfilter.c | 4 pomp-0.65-1/pomp/src/pomp.h | 430 ++++++++++++----------- pomp-0.65-1/pomp/src/pomp_fun.c | 77 +++- pomp-0.65-1/pomp/src/pomp_internal.h | 60 +-- pomp-0.65-1/pomp/src/rmeasure.c | 12 pomp-0.65-1/pomp/src/rprior.c | 8 pomp-0.65-1/pomp/src/rprocess.c | 3 pomp-0.65-1/pomp/src/skeleton.c | 8 pomp-0.65-1/pomp/src/trajectory.c | 22 - 120 files changed, 2762 insertions(+), 1934 deletions(-)
Title: Functions to Perform Isotonic Regression
Description: Linear order and unimodal order (univariate)
isotonic regression; bivariate isotonic regression
with linear order on both variables.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between Iso versions 0.0-15 dated 2013-04-18 and 0.0-17 dated 2015-06-01
ChangeLog | 35 +++++++++++++++++++++- DESCRIPTION | 18 +++++------ MD5 | 22 +++++++------ NAMESPACE | 2 - R/unimode.sa.R |only inst/makefor | 2 - inst/ufit.r | 26 +++++++++++----- inst/unimode.r | 55 ++++++++++++++++++++++++---------- man/Iso-internal.Rd |only man/biviso.Rd | 2 - man/pava.Rd | 2 - man/ufit.Rd | 2 - src/unimode.f | 82 +++++++++++++++++++++++++++++++--------------------- 13 files changed, 166 insertions(+), 82 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by Wobbrock et al.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.9.4 dated 2015-05-27 and 0.9.5 dated 2015-06-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test.artlm.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: R Interface to FOAAS
Description: R access to the FOAAS (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rfoaas versions 0.1.3 dated 2015-02-07 and 0.1.6 dated 2015-05-31
ChangeLog | 12 +++++ DESCRIPTION | 8 +-- MD5 | 12 ++--- R/foaas.R | 96 +++++++++++++++++++++++++------------------ README.md | 33 ++++++++++++-- man/rfoaas-package.Rd | 70 +++++++++++++++++-------------- tests/runTestsAgainstFOAAS.R | 11 ++++ 7 files changed, 156 insertions(+), 86 deletions(-)
More information about ShapeSelectForest at CRAN
Permanent link
Title: Tools for Designing and Weighting Survey Samples
Description: Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example datasets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <rvallian@umd.edu>
Diff between PracTools versions 0.1 dated 2015-01-21 and 0.2 dated 2015-05-31
DESCRIPTION | 10 ++--- MD5 | 28 +++++++-------- R/dub.R | 44 ++++++++--------------- R/strAlloc.R | 92 +++++++++++++++++++++++--------------------------- data/Domainy1y2.RData |binary data/MDarea.pop.RData |binary data/hospital.RData |binary data/labor.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary man/smho.N874.Rd | 2 - man/smho98.Rd | 9 +--- 15 files changed, 81 insertions(+), 104 deletions(-)
Title: Diffusion Kernels on a Set of Genotypes
Description: Compute diffusion kernels on DNA polymorphisms, including SNP and bi-allelic genotypes.
Author: Gota Morota and Masanori Koyama
Maintainer: Gota Morota <morota@unl.edu>
Diff between dkDNA versions 0.1.0 dated 2012-04-20 and 0.1.1 dated 2015-05-31
CHANGELOG | 4 ++++ DESCRIPTION | 18 +++++++++--------- MD5 | 12 ++++++------ man/dkDNA-package.Rd | 6 +++--- man/hypercube.Rd | 4 ++-- man/snpgrid.Rd | 4 ++-- man/snphamming.Rd | 4 ++-- 7 files changed, 28 insertions(+), 24 deletions(-)
Title: Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
Description: Invoke a 'BUGS' model in 'OpenBUGS' or 'WinBUGS', a class "bugs" for 'BUGS'
results and functions to work with that class.
Function write.model() allows a 'BUGS' model file to be written.
The class and auxiliary functions could be used with other MCMC programs, including 'JAGS'.
Author: originally written by Andrew Gelman <gelman@stat.columbia.edu>;
changes and packaged by Sibylle Sturtz <sturtz@statistik.tu-dortmund.de>
and Uwe Ligges <ligges@statistik.tu-dortmund.de>.
With considerable contributions by Gregor Gorjanc <gregor.gorjanc@bfro.uni-lj.si>
and Jouni Kerman <kerman@stat.columbia.edu>.
Ported to S-PLUS by Insightful Corp.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between R2WinBUGS versions 2.1-19 dated 2013-04-07 and 2.1-20 dated 2015-05-31
DESCRIPTION | 34 ++++++++++++++++------------------ MD5 | 16 +++++++++------- R/openbugs.R | 2 +- R/read.bugs.R | 2 +- build |only inst/doc/R2WinBUGS.Rnw |only man/bugs.Rd | 3 +-- man/openbugs.Rd | 3 +-- vignettes/R2WinBUGS.Rnw | 2 +- vignettes/bugs.tex | 2 +- 10 files changed, 31 insertions(+), 33 deletions(-)
Title: Signal processing
Description: A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions,
resampling routines, and visualization of filter models. It also
includes interpolation functions.
Author: Uwe Ligges [aut, cre] (new maintainer),
Tom Short [aut] (port to R),
Paul Kienzle [aut] (majority of the original sources),
Sarah Schnackenberg [ctb] (various test cases and bug fixes),
David Billinghurst [ctb],
Hans-Werner Borchers [ctb],
Andre Carezia [ctb],
Pascal Dupuis [ctb],
John W. Eaton [ctb],
E. Farhi [ctb],
Kai Habel [ctb],
Kurt Hornik [ctb],
Sebastian Krey [ctb],
Bill Lash [ctb],
Friedrich Leisch [ctb],
Olaf Mersmann [ctb],
Paulo Neis [ctb],
Jaakko Ruohio [ctb],
Julius O. Smith III [ctb],
Doug Stewart [ctb],
Andreas Weingessel [ctb]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between signal versions 0.7-4 dated 2014-04-04 and 0.7-5 dated 2015-05-31
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/filter.R | 4 ++-- inst/CITATION | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: R Interface to WinEdt
Description: A plug in for using WinEdt as an editor for R.
Author: Uwe Ligges <Uwe.Ligges@R-project.org>
with contributions (the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller
Maintainer: Uwe Ligges <Uwe.Ligges@R-project.org>
Diff between RWinEdt versions 2.0-2 dated 2013-11-17 and 2.0-3 dated 2015-05-31
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/RWinEdt.pdf |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Simulation of Longitudinal Data
Description: Simulation and visualization of complex
models for longitudinal data. The models are encoded using the model coding
language 'Mlxtran', automatically converted into C++ codes, compiled on the
fly and linked to R using the 'Rcpp' package. That allows one to implement
very easily complex ODE-based models and complex statistical models,
including mixed effects models, for continuous, count, categorical, and
time-to-event data.
Author: Marc Lavielle [aut, cre],
Raphael Kuate [ctb],
Romain Francois [ctb],
Fazia Bellal [ctb]
Maintainer: Marc Lavielle <Marc.Lavielle@inria.fr>
Diff between mlxR versions 2.1.1 dated 2015-02-05 and 2.2.0 dated 2015-05-31
DESCRIPTION | 22 MD5 | 59 + NAMESPACE | 10 R/convertmlx.R | 36 - R/exposure.R |only R/ggplotmlx.R | 1 R/hformat.R | 115 ++- R/hgdata.R | 2 R/initMlxLibrary.R | 175 +++- R/mlxComputeRLibraryBuilder.R | 11 R/mlxDataReaderRLibraryBuilder.R |only R/mlxtoolboxReadData.R |only R/monolix2simulx.R |only R/pkmodel.R | 43 + R/prctilemlx.R | 29 R/processing_monolix.R | 1384 ++++++++++++++++++++------------------- R/processing_setting.R | 24 R/read.vector.R |only R/shinymlx.R |only R/simulx.R | 477 ++++++++----- R/stoolsmlx.R |only man/catplotmlx.Rd | 2 man/exposure.Rd |only man/ggplotmlx.Rd | 2 man/inlineDataFrame.Rd | 2 man/inlineModel.Rd | 2 man/kmplotmlx.Rd | 2 man/mlxplore.Rd | 2 man/mlxtoolboxReadData.Rd |only man/monolix2simulx.Rd |only man/pharmml2mlxtran.Rd | 2 man/pkmodel.Rd | 2 man/prctilemlx.Rd | 4 man/read.vector.Rd |only man/setMlxLibraryPath.Rd |only man/shinymlx.Rd |only man/simulx.Rd | 6 37 files changed, 1417 insertions(+), 997 deletions(-)
Title: R interface to the OpenBUGS MCMC software
Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between BRugs versions 0.8-3 dated 2013-08-19 and 0.8-4 dated 2015-05-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ R/windows/findOpenBUGS.R | 2 +- data/ratsdata.RData |binary data/ratsinits.RData |binary 6 files changed, 17 insertions(+), 10 deletions(-)
Title: Session Reconstruction and Analysis
Description: Functions to aid in reconstructing sessions
and efficiently calculating an array of metrics from the resulting data,
including bounce rate, time-on-page, and session length. Although primarily
designed for web data and analytics, its approach is plausibly applicable
to other domains.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between reconstructr versions 0.5 dated 2014-12-23 and 1.1.0 dated 2015-05-31
reconstructr-0.5/reconstructr/man/sessionise.Rd |only reconstructr-1.1.0/reconstructr/DESCRIPTION | 10 reconstructr-1.1.0/reconstructr/MD5 | 60 +-- reconstructr-1.1.0/reconstructr/NAMESPACE | 4 reconstructr-1.1.0/reconstructr/NEWS |only reconstructr-1.1.0/reconstructr/R/RcppExports.R | 24 - reconstructr-1.1.0/reconstructr/R/metrics.R | 8 reconstructr-1.1.0/reconstructr/R/parameter_fillers.R | 4 reconstructr-1.1.0/reconstructr/R/to_seconds.R | 4 reconstructr-1.1.0/reconstructr/README.md | 13 reconstructr-1.1.0/reconstructr/build/vignette.rds |binary reconstructr-1.1.0/reconstructr/data/session_dataset.RData |binary reconstructr-1.1.0/reconstructr/inst/doc/Introduction.R | 14 reconstructr-1.1.0/reconstructr/inst/doc/Introduction.Rmd | 4 reconstructr-1.1.0/reconstructr/inst/doc/Introduction.html | 4 reconstructr-1.1.0/reconstructr/man/bounce_rate.Rd | 7 reconstructr-1.1.0/reconstructr/man/event_time.Rd | 7 reconstructr-1.1.0/reconstructr/man/padding_value.Rd | 7 reconstructr-1.1.0/reconstructr/man/reconstruct_sessions.Rd |only reconstructr-1.1.0/reconstructr/man/reconstructr.Rd | 3 reconstructr-1.1.0/reconstructr/man/session_dataset.Rd | 3 reconstructr-1.1.0/reconstructr/man/session_events.Rd | 11 reconstructr-1.1.0/reconstructr/man/session_length.Rd | 11 reconstructr-1.1.0/reconstructr/man/to_seconds.Rd | 7 reconstructr-1.1.0/reconstructr/src/Makevars |only reconstructr-1.1.0/reconstructr/src/RcppExports.cpp | 72 +--- reconstructr-1.1.0/reconstructr/src/reconstructr.cpp | 36 +- reconstructr-1.1.0/reconstructr/src/session_metrics.cpp |only reconstructr-1.1.0/reconstructr/src/session_metrics.h | 180 +++------- reconstructr-1.1.0/reconstructr/src/sessionise.cpp |only reconstructr-1.1.0/reconstructr/src/sessionise.h | 103 ++--- reconstructr-1.1.0/reconstructr/tests/testthat/test_padding_value.R | 2 reconstructr-1.1.0/reconstructr/tests/testthat/test_sessionisation.R | 8 reconstructr-1.1.0/reconstructr/vignettes/Introduction.Rmd | 4 34 files changed, 274 insertions(+), 336 deletions(-)
Title: Robust Coefficient Alpha and Omega with Missing and Non-Normal
Data
Description: Cronbach's alpha and McDonald's omega are widely used reliability or internal consistency measures in social, behavioral and education sciences. Alpha is reported in nearly every study that involves measuring a construct through multiple test items. The package 'coefficientalpha' calculates coefficient alpha and coefficient omega with missing data and non-normal data. Robust standard errors and confidence intervals are also provided. A test is also available to test the tau-equivalent and homogeneous assumptions. Version 0.5 added the bootstrap confidence intervals.
Author: Zhiyong Zhang and Ke-Hai Yuan
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>
Diff between coefficientalpha versions 0.3.3 dated 2014-12-10 and 0.5 dated 2015-05-31
DESCRIPTION | 14 +- MD5 | 11 + NAMESPACE | 8 + R/Cronbach.R | 284 ++++++++++++++++++++++++++++++++++++++++++--------- man/alpha.Rd | 16 ++ man/bootstrap.Rd |only man/summary.alpha.Rd | 7 - 7 files changed, 275 insertions(+), 65 deletions(-)
More information about coefficientalpha at CRAN
Permanent link
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and proportional odds models (both fit via ic_sp) and fully parametric Cox-PH and proportional odds models (via ic_par). Easy diagnostics of fit can be evaluated via diag_covar and diag_baseline.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.1.1 dated 2015-05-10 and 1.2.0 dated 2015-05-31
icenReg-1.1.1/icenReg/R/coxph.R |only icenReg-1.1.1/icenReg/man/ic_ph.Rd |only icenReg-1.1.1/icenReg/man/impute_ic_ph.Rd |only icenReg-1.1.1/icenReg/man/simICPH_beta.Rd |only icenReg-1.1.1/icenReg/src/intCoxFast.h |only icenReg-1.2.0/icenReg/DESCRIPTION | 8 icenReg-1.2.0/icenReg/MD5 | 34 icenReg-1.2.0/icenReg/NAMESPACE | 19 icenReg-1.2.0/icenReg/R/Utilities.R |only icenReg-1.2.0/icenReg/R/user_functions.R |only icenReg-1.2.0/icenReg/man/diag_baseline.Rd |only icenReg-1.2.0/icenReg/man/diag_covar.Rd |only icenReg-1.2.0/icenReg/man/getFitEsts.Rd |only icenReg-1.2.0/icenReg/man/getSCurves.Rd | 12 icenReg-1.2.0/icenReg/man/ic_par.Rd |only icenReg-1.2.0/icenReg/man/ic_sp.Rd |only icenReg-1.2.0/icenReg/man/mdata.Rd | 2 icenReg-1.2.0/icenReg/man/oldFiles |only icenReg-1.2.0/icenReg/man/simIC_weib.Rd |only icenReg-1.2.0/icenReg/src/icenReg.cpp | 1090 ----------------------------- icenReg-1.2.0/icenReg/src/icenReg_files |only 21 files changed, 81 insertions(+), 1084 deletions(-)
Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the estimation of multinomial logit models with random coefficients. Specifically, it allows estimating models with continuous heterogeneity such as the mixed multinomial logit and the generalized multinomial logit. It also allows estimating models with discrete heterogeneity such as the latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre],
Ricardo Daziano [aut],
Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between gmnl versions 1.0 dated 2015-02-22 and 1.1 dated 2015-05-31
DESCRIPTION | 22 +++---- MD5 | 34 ++++++------ NAMESPACE | 2 R/gmnl.R | 26 ++++----- R/gmnl.draws.R | 21 ++++++- R/gmnl.logliks.R | 20 ++++--- R/gmnl.methods.R | 138 +++++++++++++++++++++++++++++++++++-------------- inst |only man/AIC.gmnl.Rd | 2 man/bread.gmnl.Rd | 2 man/cov.gmnl.Rd | 2 man/effect.gmnl.Rd | 2 man/estfun.gmnl.Rd | 2 man/gFormula.Rd | 2 man/getSummary.gmnl.Rd | 2 man/gmnl.Rd | 5 - man/plot.gmnl.Rd | 2 man/vcov.gmnl.Rd |only man/wtp.gmnl.Rd | 2 19 files changed, 183 insertions(+), 103 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.1 dated 2013-06-20 and 3.98-1.2 dated 2015-05-31
XML-3.98-1.1/XML/Copyright |only XML-3.98-1.1/XML/a.out.dSYM |only XML-3.98-1.1/XML/symbols.rds |only XML-3.98-1.2/XML/DESCRIPTION | 21 +++++++-------- XML-3.98-1.2/XML/LICENSE |only XML-3.98-1.2/XML/MD5 | 40 ++++++++++++++---------------- XML-3.98-1.2/XML/NAMESPACE | 2 + XML-3.98-1.2/XML/R/SAXMethods.S | 2 - XML-3.98-1.2/XML/R/bitList.R | 2 - XML-3.98-1.2/XML/R/flatTree.R | 4 +++ XML-3.98-1.2/XML/R/schema.S | 2 - XML-3.98-1.2/XML/R/tree.R | 4 +++ XML-3.98-1.2/XML/R/xmlInternalSource.R | 2 - XML-3.98-1.2/XML/R/xmlNodes.R | 1 XML-3.98-1.2/XML/R/zzz.R | 2 - XML-3.98-1.2/XML/inst/COPYRIGHTS |only XML-3.98-1.2/XML/inst/exampleData/dtd.zip |binary XML-3.98-1.2/XML/man/parseDTD.Rd | 2 - XML-3.98-1.2/XML/src/DocParse.c | 3 +- XML-3.98-1.2/XML/src/EventParse.c | 2 - XML-3.98-1.2/XML/src/NodeGC.c | 2 - XML-3.98-1.2/XML/src/NodeGC.h | 6 ++-- XML-3.98-1.2/XML/src/XMLTree.c | 2 - 23 files changed, 54 insertions(+), 45 deletions(-)
Title: SYMPHONY in R
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut],
Kurt Hornik [aut, cre],
Stefan Theussl [aut],
Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between Rsymphony versions 0.1-19 dated 2015-02-23 and 0.1-20 dated 2015-05-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- configure | 19 ++++++++++++------- 3 files changed, 18 insertions(+), 13 deletions(-)
Title: Build, Deploy and Evaluate Hybrid Ensembles
Description: Functions to build and deploy a hybrid ensemble consisting of eight different sub-ensembles: bagged logistic regressions, random forest, stochastic boosting, kernel factory, bagged neural networks, bagged support vector machines, rotation forest, and bagged k-nearest neighbors. Functions to cross-validate the hybrid ensemble and plot and summarize the results are also provided. There is also a function to assess the importance of the predictors.
Author: Michel Ballings, Dauwe Vercamer, and Dirk Van den Poel
Maintainer: Michel Ballings <Michel.Ballings@GMail.com>
Diff between hybridEnsemble versions 0.1.1 dated 2014-03-23 and 1.0.0 dated 2015-05-30
DESCRIPTION | 23 MD5 | 38 NAMESPACE | 2 R/CVhybridEnsemble.R | 1146 +++++++++--------- R/hybridEnsemble.R | 2397 ++++++++++++++++++++------------------- R/hybridEnsembleNews.R | 30 R/importance.hybridEnsemble.R | 154 +- R/plot.CVhybridEnsemble.R | 187 +-- R/predict.hybridEnsemble.R | 347 +++-- R/summary.CVhybridEnsemble.R | 299 ++-- R/zzz.R | 2 inst/NEWS | 33 man/CVhybridEnsemble.Rd | 498 +++----- man/hybridEnsemble.Rd | 529 +++----- man/hybridEnsembleNews.Rd | 60 man/importance.hybridEnsemble.Rd | 139 -- man/plot.CVhybridEnsemble.Rd | 136 -- man/predict.hybridEnsemble.Rd | 123 -- man/summary.CVhybridEnsemble.Rd | 174 +- tests |only 20 files changed, 3149 insertions(+), 3168 deletions(-)
More information about hybridEnsemble at CRAN
Permanent link
More information about signmedian.test at CRAN
Permanent link
Title: Interactive Web-Maps Based on the Leaflet JavaScript Library
Description: Display your spatial data on interactive web-maps using the open-source JavaScript library Leaflet. 'leafletR' provides basic web-mapping functionality to combine vector data and online map tiles from different sources. See <http://leafletjs.com> for more information on Leaflet.
Author: Christian Graul, with contributions from Francois Guillem
Maintainer: Christian Graul <christian.graul@gmail.com>
Diff between leafletR versions 0.3-2 dated 2015-04-09 and 0.3-3 dated 2015-05-30
DESCRIPTION | 10 ++++----- MD5 | 38 ++++++++++++++++++------------------- R/dfToGeoJSON.R | 20 ++++++++++++++++--- R/leaflet.R | 10 ++++----- R/print.categorized.style.R | 4 +-- R/print.graduated.style.R | 4 +-- R/print.single.style.R | 28 +++++++++++++++++---------- R/styleGrad.R | 37 ++++++++++++++++++++++++++++-------- R/styleSingle.R | 6 +++-- R/zzz.R | 4 +-- inst/CITATION | 4 +-- inst/NEWS | 27 ++++++++++++++++++++++++-- inst/templates/css.brew | 33 +++++++++++++++++++++++--------- inst/templates/data.brew | 14 +++++++++---- inst/templates/legend.brew | 45 ++++++++++++++++++++++++++++---------------- inst/templates/main.brew | 19 +++++++++++++++--- inst/templates/style.brew | 8 +++---- man/leaflet.Rd | 4 +++ man/styleGrad.Rd | 25 +++++++++++++++--------- man/styleSingle.Rd | 12 +++++++---- 20 files changed, 241 insertions(+), 111 deletions(-)
Title: Bindings to the 'CommonMark' Reference Implementation
Description: The 'CommonMark' spec is a rationalized version of Markdown syntax.
This package converts markdown text to various formats including a parse
tree in XML format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.2 dated 2015-05-27 and 0.4 dated 2015-05-30
commonmark-0.2/commonmark/configure |only commonmark-0.2/commonmark/src/cmark/config.h |only commonmark-0.4/commonmark/DESCRIPTION | 8 ++++---- commonmark-0.4/commonmark/MD5 | 17 ++++++++--------- commonmark-0.4/commonmark/R/markdown.R | 15 +++++++++------ commonmark-0.4/commonmark/man/commonmark.Rd | 3 +-- commonmark-0.4/commonmark/src/Makevars | 16 ++++++++++------ commonmark-0.4/commonmark/src/cmark/buffer.c | 6 ++++++ commonmark-0.4/commonmark/src/cmark/chunk.h | 4 +++- commonmark-0.4/commonmark/src/config.h |only commonmark-0.4/commonmark/src/wrapper.c | 4 ++-- 11 files changed, 43 insertions(+), 30 deletions(-)
Title: Case Influence in Structural Equation Models
Description: Influence measures in Structural Equation Models: a set of tools for evaluating several measures of case influence for Structural Equation Models following the approach of Pek and MacCallum (2011).
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between influence.SEM versions 1.4 dated 2014-07-26 and 1.5 dated 2015-05-30
DESCRIPTION | 10 ++++---- MD5 | 18 ++++++++------ NAMESPACE | 2 - NEWS |only R/Deltachi.R | 4 +-- R/Likedist.R | 4 +-- R/fitinfluence.R | 63 +++++++++++++++++++++++++++++++--------------------- R/genCookDist.R | 4 +-- R/influence.SEM.R |only R/parinfluence.R | 4 +-- man/fitinfluence.Rd | 2 - 11 files changed, 63 insertions(+), 48 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.18-1 dated 2015-03-31 and 0.20 dated 2015-05-30
BrailleR-0.18-1/BrailleR/R/Setup.R |only BrailleR-0.18-1/BrailleR/inst/Settings |only BrailleR-0.18-1/BrailleR/inst/doc/BrailleRManual.R |only BrailleR-0.18-1/BrailleR/inst/doc/BrailleRManual.html |only BrailleR-0.18-1/BrailleR/inst/doc/BrailleRManual.rmd |only BrailleR-0.18-1/BrailleR/vignettes/BrailleRManual.rmd |only BrailleR-0.20/BrailleR/DESCRIPTION | 12 BrailleR-0.20/BrailleR/MD5 | 90 ++-- BrailleR-0.20/BrailleR/NAMESPACE | 11 BrailleR-0.20/BrailleR/R/GettingStarted.R |only BrailleR-0.20/BrailleR/R/Internal.R |only BrailleR-0.20/BrailleR/R/MakeBatch.R |only BrailleR-0.20/BrailleR/R/MaskedFunctions.R | 4 BrailleR-0.20/BrailleR/R/OneFactor.R | 13 BrailleR-0.20/BrailleR/R/OnePredictor.R |only BrailleR-0.20/BrailleR/R/Options.R | 54 ++ BrailleR-0.20/BrailleR/R/TwoFactors.R | 7 BrailleR-0.20/BrailleR/R/UniDesc.R | 87 ++-- BrailleR-0.20/BrailleR/R/VIMethod1_JG.R | 51 ++ BrailleR-0.20/BrailleR/R/VIMethod2_TB.R | 43 ++ BrailleR-0.20/BrailleR/R/WhereXY.R | 14 BrailleR-0.20/BrailleR/R/dotplots.R |only BrailleR-0.20/BrailleR/R/zzz.R | 14 BrailleR-0.20/BrailleR/build/vignette.rds |binary BrailleR-0.20/BrailleR/inst/CITATION | 2 BrailleR-0.20/BrailleR/inst/NEWS |only BrailleR-0.20/BrailleR/inst/PREFERENCES |only BrailleR-0.20/BrailleR/inst/css |only BrailleR-0.20/BrailleR/inst/doc/BrailleRHistory.R |only BrailleR-0.20/BrailleR/inst/doc/BrailleRHistory.html |only BrailleR-0.20/BrailleR/inst/doc/BrailleRHistory.rmd |only BrailleR-0.20/BrailleR/inst/doc/Ex1histograms.html | 204 +++++----- BrailleR-0.20/BrailleR/inst/doc/Ex1histograms.rmd | 14 BrailleR-0.20/BrailleR/inst/doc/Ex2BasicNumerical.html | 102 ++--- BrailleR-0.20/BrailleR/inst/doc/Ex2BasicNumerical.rmd | 13 BrailleR-0.20/BrailleR/inst/doc/Ex3UnivariateDescription.html | 100 ++-- BrailleR-0.20/BrailleR/inst/doc/Ex3UnivariateDescription.rmd | 14 BrailleR-0.20/BrailleR/inst/doc/Ex4SingleResponseOneGroupingFactor.html | 103 ++--- BrailleR-0.20/BrailleR/inst/doc/Ex4SingleResponseOneGroupingFactor.rmd | 16 BrailleR-0.20/BrailleR/inst/doc/GettingStarted.R |only BrailleR-0.20/BrailleR/inst/doc/GettingStarted.Rmd |only BrailleR-0.20/BrailleR/inst/doc/GettingStarted.html |only BrailleR-0.20/BrailleR/man/BrailleR-package.Rd | 4 BrailleR-0.20/BrailleR/man/GetGoing.Rd |only BrailleR-0.20/BrailleR/man/Internal.Rd |only BrailleR-0.20/BrailleR/man/MakeBatch.Rd | 8 BrailleR-0.20/BrailleR/man/OneFactor.Rd | 7 BrailleR-0.20/BrailleR/man/OnePredictor.Rd |only BrailleR-0.20/BrailleR/man/SetOptions.Rd | 18 BrailleR-0.20/BrailleR/man/UniDesc.Rd | 7 BrailleR-0.20/BrailleR/man/VI.Rd | 2 BrailleR-0.20/BrailleR/man/dotplot.Rd |only BrailleR-0.20/BrailleR/vignettes/BrailleRHistory.rmd |only BrailleR-0.20/BrailleR/vignettes/BrailleRPublications.bib |only BrailleR-0.20/BrailleR/vignettes/Ex1histograms.rmd | 14 BrailleR-0.20/BrailleR/vignettes/Ex2BasicNumerical.rmd | 13 BrailleR-0.20/BrailleR/vignettes/Ex3UnivariateDescription.rmd | 14 BrailleR-0.20/BrailleR/vignettes/Ex4SingleResponseOneGroupingFactor.rmd | 16 BrailleR-0.20/BrailleR/vignettes/GettingStarted.Rmd |only 59 files changed, 662 insertions(+), 409 deletions(-)
Title: Recommender System using Matrix Factorization
Description: R wrapper of the 'libmf' library
(http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender
system using matrix factorization. It is typically used to
approximate an incomplete matrix using the product of two
matrices in a latent space. Other common names for this task
include "collaborative filtering", "matrix completion",
"matrix recovery", etc.
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang,
Wei-Sheng Chin and other contributors. See file AUTHORS for
details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between recosystem versions 0.2.5 dated 2015-02-07 and 0.3 dated 2015-05-30
recosystem-0.2.5/recosystem/R/RecoDat.R |only recosystem-0.2.5/recosystem/man/convert.Rd |only recosystem-0.2.5/recosystem/src/convert.cpp |only recosystem-0.2.5/recosystem/src/memalign.cpp |only recosystem-0.2.5/recosystem/src/output.cpp |only recosystem-0.2.5/recosystem/src/predict.cpp |only recosystem-0.2.5/recosystem/src/rand.h |only recosystem-0.2.5/recosystem/src/train.cpp |only recosystem-0.2.5/recosystem/src/view.cpp |only recosystem-0.3/recosystem/DESCRIPTION | 10 recosystem-0.3/recosystem/LICENSE | 2 recosystem-0.3/recosystem/MD5 | 57 recosystem-0.3/recosystem/R/RecoModel.R | 39 recosystem-0.3/recosystem/R/RecoSys.R | 738 +++++---- recosystem-0.3/recosystem/README.md | 242 +-- recosystem-0.3/recosystem/build/vignette.rds |binary recosystem-0.3/recosystem/inst/AUTHORS | 4 recosystem-0.3/recosystem/inst/COPYRIGHTS | 4 recosystem-0.3/recosystem/inst/NEWS.Rd | 10 recosystem-0.3/recosystem/inst/doc/introduction.R | 13 recosystem-0.3/recosystem/inst/doc/introduction.Rmd | 147 - recosystem-0.3/recosystem/inst/doc/introduction.html | 284 +-- recosystem-0.3/recosystem/man/Reco.Rd | 25 recosystem-0.3/recosystem/man/output.Rd | 57 recosystem-0.3/recosystem/man/predict.Rd | 60 recosystem-0.3/recosystem/man/train.Rd | 105 - recosystem-0.3/recosystem/man/tune.Rd |only recosystem-0.3/recosystem/src/Makevars | 23 recosystem-0.3/recosystem/src/Makevars.win | 23 recosystem-0.3/recosystem/src/mf.cpp | 1502 ++++++++++++++++--- recosystem-0.3/recosystem/src/mf.h | 166 -- recosystem-0.3/recosystem/src/reco-output.cpp |only recosystem-0.3/recosystem/src/reco-predict.cpp |only recosystem-0.3/recosystem/src/reco-train.cpp |only recosystem-0.3/recosystem/src/reco-tune.cpp |only recosystem-0.3/recosystem/src/reco-utils.h |only recosystem-0.3/recosystem/vignettes/introduction.Rmd | 147 - 37 files changed, 2410 insertions(+), 1248 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 2.8-0 dated 2014-11-15 and 2.8-1 dated 2015-05-30
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NEWS | 8 ++++++++ R/cv.grpreg.R | 18 +++++++++++------- R/grpreg.R | 1 + R/predict.R | 14 ++++++++++++-- README.md |only man/grpreg-package.Rd | 16 ++++++++++------ man/grpreg.Rd | 10 +++++----- 9 files changed, 61 insertions(+), 33 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.2 dated 2015-01-05 and 1.6.3 dated 2015-05-30
dplR-1.6.2/dplR/inst/unitTests |only dplR-1.6.2/dplR/tests/doRUnit.R |only dplR-1.6.3/dplR/ChangeLog | 148 ++++++++++++++++ dplR-1.6.3/dplR/DESCRIPTION | 30 +-- dplR-1.6.3/dplR/MD5 | 235 +++++++++++++------------- dplR-1.6.3/dplR/NAMESPACE | 16 + dplR-1.6.3/dplR/R/ccf.series.rwl.R | 2 dplR-1.6.3/dplR/R/chron.R | 12 - dplR-1.6.3/dplR/R/common.interval.R | 6 dplR-1.6.3/dplR/R/corr.rwl.seg.R | 5 dplR-1.6.3/dplR/R/corr.series.seg.R | 5 dplR-1.6.3/dplR/R/crn.plot.R | 3 dplR-1.6.3/dplR/R/detrend.series.R | 15 - dplR-1.6.3/dplR/R/ffcsaps.R | 12 - dplR-1.6.3/dplR/R/helpers.R | 53 +++++ dplR-1.6.3/dplR/R/i.detrend.series.R | 2 dplR-1.6.3/dplR/R/latexify.R | 11 - dplR-1.6.3/dplR/R/morlet.R | 36 +-- dplR-1.6.3/dplR/R/net.R |only dplR-1.6.3/dplR/R/pointer.R | 2 dplR-1.6.3/dplR/R/read.crn.R | 2 dplR-1.6.3/dplR/R/read.fh.R | 3 dplR-1.6.3/dplR/R/read.ids.R | 10 - dplR-1.6.3/dplR/R/read.tucson.R | 19 +- dplR-1.6.3/dplR/R/redfit.R | 39 ++-- dplR-1.6.3/dplR/R/rwi.stats.running.R | 7 dplR-1.6.3/dplR/R/rwl.stats.R | 19 +- dplR-1.6.3/dplR/R/series.rwl.plot.R | 9 dplR-1.6.3/dplR/R/skel.plot.R | 16 + dplR-1.6.3/dplR/R/spag.plot.R | 2 dplR-1.6.3/dplR/R/wc.to.po.R | 6 dplR-1.6.3/dplR/R/write.compact.R | 5 dplR-1.6.3/dplR/R/write.crn.R | 56 +++--- dplR-1.6.3/dplR/R/write.tridas.R | 15 - dplR-1.6.3/dplR/R/write.tucson.R | 2 dplR-1.6.3/dplR/build/vignette.rds |binary dplR-1.6.3/dplR/inst/CITATION | 4 dplR-1.6.3/dplR/inst/doc/intro-dplR.pdf |binary dplR-1.6.3/dplR/inst/doc/math-dplR.R | 29 --- dplR-1.6.3/dplR/inst/doc/math-dplR.Rnw.txt | 22 +- dplR-1.6.3/dplR/inst/doc/math-dplR.bib | 10 - dplR-1.6.3/dplR/inst/doc/math-dplR.pdf |binary dplR-1.6.3/dplR/inst/doc/timeseries-dplR.pdf |binary dplR-1.6.3/dplR/inst/doc/xdate-dplR.pdf |binary dplR-1.6.3/dplR/man/anos1.Rd | 9 dplR-1.6.3/dplR/man/bai.in.Rd | 40 +++- dplR-1.6.3/dplR/man/bai.out.Rd | 44 +++- dplR-1.6.3/dplR/man/ca533.Rd | 10 - dplR-1.6.3/dplR/man/cana157.Rd | 11 - dplR-1.6.3/dplR/man/ccf.series.rwl.Rd | 48 ++--- dplR-1.6.3/dplR/man/chron.Rd | 23 +- dplR-1.6.3/dplR/man/cms.Rd | 52 ++++- dplR-1.6.3/dplR/man/co021.Rd | 1 dplR-1.6.3/dplR/man/combine.rwl.Rd | 6 dplR-1.6.3/dplR/man/common.interval.Rd | 6 dplR-1.6.3/dplR/man/corr.rwl.seg.Rd | 10 - dplR-1.6.3/dplR/man/corr.series.seg.Rd | 20 +- dplR-1.6.3/dplR/man/crn.plot.Rd | 32 ++- dplR-1.6.3/dplR/man/detrend.Rd | 32 +-- dplR-1.6.3/dplR/man/detrend.series.Rd | 70 +++---- dplR-1.6.3/dplR/man/dplR-package.Rd | 12 - dplR-1.6.3/dplR/man/ffcsaps.Rd | 12 - dplR-1.6.3/dplR/man/fill.internal.NA.Rd | 24 +- dplR-1.6.3/dplR/man/gini.coef.Rd | 12 - dplR-1.6.3/dplR/man/glk.Rd | 18 + dplR-1.6.3/dplR/man/gp.d2pith.Rd | 11 - dplR-1.6.3/dplR/man/gp.dbh.Rd | 11 - dplR-1.6.3/dplR/man/gp.po.Rd | 11 - dplR-1.6.3/dplR/man/gp.rwl.Rd | 9 dplR-1.6.3/dplR/man/hanning.Rd | 6 dplR-1.6.3/dplR/man/i.detrend.Rd | 17 - dplR-1.6.3/dplR/man/i.detrend.series.Rd | 19 +- dplR-1.6.3/dplR/man/insert.ring.Rd | 8 dplR-1.6.3/dplR/man/interseries.cor.Rd | 10 - dplR-1.6.3/dplR/man/latexDate.Rd | 1 dplR-1.6.3/dplR/man/latexify.Rd | 21 +- dplR-1.6.3/dplR/man/morlet.Rd | 45 ++-- dplR-1.6.3/dplR/man/net.Rd |only dplR-1.6.3/dplR/man/plot.rwl.Rd | 9 dplR-1.6.3/dplR/man/po.to.wc.Rd | 10 - dplR-1.6.3/dplR/man/pointer.Rd | 25 +- dplR-1.6.3/dplR/man/powt.Rd | 8 dplR-1.6.3/dplR/man/print.redfit.Rd | 8 dplR-1.6.3/dplR/man/rasterPlot.Rd | 5 dplR-1.6.3/dplR/man/rcs.Rd | 46 ++--- dplR-1.6.3/dplR/man/read.compact.Rd | 3 dplR-1.6.3/dplR/man/read.crn.Rd | 11 - dplR-1.6.3/dplR/man/read.fh.Rd | 20 +- dplR-1.6.3/dplR/man/read.ids.Rd | 16 - dplR-1.6.3/dplR/man/read.rwl.Rd | 1 dplR-1.6.3/dplR/man/read.tridas.Rd | 223 +++++++++++++----------- dplR-1.6.3/dplR/man/read.tucson.Rd | 13 - dplR-1.6.3/dplR/man/redfit.Rd | 18 + dplR-1.6.3/dplR/man/rwi.stats.running.Rd | 61 +++--- dplR-1.6.3/dplR/man/rwl.stats.Rd | 18 + dplR-1.6.3/dplR/man/sea.Rd | 10 - dplR-1.6.3/dplR/man/seg.plot.Rd | 8 dplR-1.6.3/dplR/man/sens1.Rd | 8 dplR-1.6.3/dplR/man/sens2.Rd | 8 dplR-1.6.3/dplR/man/series.rwl.plot.Rd | 9 dplR-1.6.3/dplR/man/skel.plot.Rd | 38 ++-- dplR-1.6.3/dplR/man/spag.plot.Rd | 12 - dplR-1.6.3/dplR/man/strip.rwl.Rd | 6 dplR-1.6.3/dplR/man/tbrm.Rd | 26 +- dplR-1.6.3/dplR/man/tridas.vocabulary.Rd | 27 +- dplR-1.6.3/dplR/man/uuid.gen.Rd | 9 dplR-1.6.3/dplR/man/wavelet.plot.Rd | 45 ++-- dplR-1.6.3/dplR/man/wc.to.po.Rd | 12 - dplR-1.6.3/dplR/man/write.compact.Rd | 22 +- dplR-1.6.3/dplR/man/write.crn.Rd | 40 ++-- dplR-1.6.3/dplR/man/write.rwl.Rd | 12 - dplR-1.6.3/dplR/man/write.tridas.Rd | 112 ++++++------ dplR-1.6.3/dplR/man/write.tucson.Rd | 52 ++--- dplR-1.6.3/dplR/man/xskel.ccf.plot.Rd | 54 +++-- dplR-1.6.3/dplR/man/xskel.plot.Rd | 54 +++-- dplR-1.6.3/dplR/tests/testthat |only dplR-1.6.3/dplR/tests/testthat.R |only dplR-1.6.3/dplR/vignettes/timeseries-dplR.Rnw | 2 118 files changed, 1522 insertions(+), 1068 deletions(-)
Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized
linear mixed-effects models in a Bayesian setting. Extends
lme4 by Douglas Bates, Martin Maechler, Ben Bolker, and Steve Walker.
Author: Vincent Dorie <vjd4@nyu.edu>
Maintainer: Vincent Dorie <vjd4@nyu.edu>
Diff between blme versions 1.0-2 dated 2014-03-12 and 1.0-3 dated 2015-05-30
blme-1.0-2/blme/.Rinstignore |only blme-1.0-2/blme/README |only blme-1.0-2/blme/inst/tests |only blme-1.0-2/blme/tests/doRUnit.R |only blme-1.0-3/blme/ChangeLog | 34 +- blme-1.0-3/blme/DESCRIPTION | 16 - blme-1.0-3/blme/MD5 | 64 ++-- blme-1.0-3/blme/NAMESPACE | 13 blme-1.0-3/blme/R/blmer.R | 563 ++++++++++++++++++++++++++++----------- blme-1.0-3/blme/R/control.R | 108 +++---- blme-1.0-3/blme/R/devFun.R | 334 +++++++++++++---------- blme-1.0-3/blme/R/dist.R | 328 +++++++++++----------- blme-1.0-3/blme/R/dist_custom.R | 20 - blme-1.0-3/blme/R/dist_gamma.R | 82 ++--- blme-1.0-3/blme/R/dist_normal.R | 46 +-- blme-1.0-3/blme/R/dist_point.R | 5 blme-1.0-3/blme/R/dist_t.R | 43 +- blme-1.0-3/blme/R/dist_wishart.R | 150 +++++----- blme-1.0-3/blme/R/generics.R | 9 blme-1.0-3/blme/R/optimize.R | 211 -------------- blme-1.0-3/blme/R/parameters.R | 105 ++++--- blme-1.0-3/blme/R/priorEval.R | 151 +++++----- blme-1.0-3/blme/R/string.R | 28 - blme-1.0-3/blme/R/util.R | 30 +- blme-1.0-3/blme/README.md |only blme-1.0-3/blme/inst/CITATION |only blme-1.0-3/blme/man/blmer.Rd | 1 blme-1.0-3/blme/tests/test-all.R |only blme-1.0-3/blme/tests/testthat |only 29 files changed, 1267 insertions(+), 1074 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-8 dated 2014-09-21 and 0.3-11 dated 2015-05-29
rgeos-0.3-11/rgeos/ChangeLog | 2165 +++++------- rgeos-0.3-11/rgeos/DESCRIPTION | 14 rgeos-0.3-11/rgeos/MD5 | 62 rgeos-0.3-11/rgeos/NAMESPACE | 1 rgeos-0.3-11/rgeos/R/AAA.R | 5 rgeos-0.3-11/rgeos/R/labelpt.R | 42 rgeos-0.3-11/rgeos/R/over.R | 10 rgeos-0.3-11/rgeos/configure | 94 rgeos-0.3-11/rgeos/configure.ac | 29 rgeos-0.3-11/rgeos/inst/ChangeLog | 2165 +++++------- rgeos-0.3-11/rgeos/inst/README |only rgeos-0.3-11/rgeos/inst/SVN_VERSION | 2 rgeos-0.3-11/rgeos/man/class-SpatialCollections.Rd | 4 rgeos-0.3-11/rgeos/man/comment-functions.Rd | 3 rgeos-0.3-11/rgeos/man/experimental-functions.Rd | 3 rgeos-0.3-11/rgeos/man/labelpt.Rd | 5 rgeos-0.3-11/rgeos/man/pred-binary-gIntersects.Rd | 2 rgeos-0.3-11/rgeos/man/pred-unary-gIsSimple.Rd | 2 rgeos-0.3-11/rgeos/man/pred-unary-gIsValid.Rd | 2 rgeos-0.3-11/rgeos/man/topo-bin-gIntersection.Rd | 5 rgeos-0.3-11/rgeos/man/topo-bin-gUnion.Rd | 4 rgeos-0.3-11/rgeos/man/topo-unary-gDelaunayTriangulation.Rd | 3 rgeos-0.3-11/rgeos/src/init.c | 2 rgeos-0.3-11/rgeos/src/rgeos.c | 4 rgeos-0.3-11/rgeos/src/rgeos.h | 1 rgeos-0.3-11/rgeos/src/rgeos_coord.c | 2 rgeos-0.3-11/rgeos/src/rgeos_geos2R.c | 4 rgeos-0.3-11/rgeos/src/rgeos_poly2nb.c | 2 rgeos-0.3-11/rgeos/src/rgeos_predicate_binary.c | 8 rgeos-0.3-11/rgeos/src/rgeos_topology.c | 6 rgeos-0.3-11/rgeos/src/rgeos_topology_binary.c | 3 rgeos-0.3-11/rgeos/src/rgeos_validate.c | 6 rgeos-0.3-8/rgeos/inst/README.windows |only 33 files changed, 2177 insertions(+), 2483 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.4 dated 2015-01-23 and 1.1.5 dated 2015-05-29
ExomeDepth-1.1.4/ExomeDepth/inst/doc/ExomeDepth-vignette.R |only ExomeDepth-1.1.4/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.4/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw |only ExomeDepth-1.1.5/ExomeDepth/DESCRIPTION | 8 +-- ExomeDepth-1.1.5/ExomeDepth/MD5 | 23 ++++------ ExomeDepth-1.1.5/ExomeDepth/R/class_definition.R | 22 +++------ ExomeDepth-1.1.5/ExomeDepth/build/vignette.rds |binary ExomeDepth-1.1.5/ExomeDepth/data/Conrad.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/ExomeCount.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/exons.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/exons.hg19.X.RData |binary ExomeDepth-1.1.5/ExomeDepth/data/genes.hg19.RData |binary ExomeDepth-1.1.5/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary ExomeDepth-1.1.5/ExomeDepth/vignettes/.install_extras |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.R |only ExomeDepth-1.1.5/ExomeDepth/vignettes/ExomeDepth-vignette.pdf |only 16 files changed, 23 insertions(+), 30 deletions(-)
Title: Goodness-of-Fit Tests for the Exponential and Two-Parameter
Weibull Distributions
Description: An implementation of a large number of the goodness-of-fit tests for the exponential and Weibull distributions classified into families: the tests based on the empirical distribution function, the tests based on the probability plot, the tests based on the normalized spacings, the tests based on the Laplace transform and the likelihood-based tests.
Author: Meryam Krit
Maintainer: Meryam Krit <meryam.krit@imag.fr>
Diff between EWGoF versions 2.0 dated 2014-04-08 and 2.1 dated 2015-05-29
EWGoF-2.0/EWGoF/src/Makevars |only EWGoF-2.0/EWGoF/src/Makevars.win |only EWGoF-2.1/EWGoF/DESCRIPTION | 20 ++++++------- EWGoF-2.1/EWGoF/MD5 | 20 ++++++------- EWGoF-2.1/EWGoF/NAMESPACE | 2 - EWGoF-2.1/EWGoF/R/LK.test.R | 30 +++++--------------- EWGoF-2.1/EWGoF/R/MLEst.R | 25 ++++++++++++++++ EWGoF-2.1/EWGoF/R/WLK.test.R | 52 ++++++++++++++++++++++++++--------- EWGoF-2.1/EWGoF/R/WNS.test.R | 2 - EWGoF-2.1/EWGoF/man/EWGoF-package.Rd | 12 ++++---- EWGoF-2.1/EWGoF/man/WLK.test.Rd | 9 +++++- EWGoF-2.1/EWGoF/man/WNS.test.Rd | 2 - 12 files changed, 108 insertions(+), 66 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-20 0.1.0
Title: Read Tabular Data
Description: Read flat/tabular text files from disk.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: ORPHANED
Diff between readr versions 0.1.0 dated 2015-04-08 and 0.1.1 dated 2015-05-29
DESCRIPTION | 12 ++++++++---- MD5 | 4 ++-- src/Iconv.h | 16 ++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-)
Title: Easier 'NetCDF' File Handling
Description: Set of tools to simplify the handling of 'NetCDF' files with the 'RNetCDF' package.
Most functions are wrappers of basic functions from the 'RNetCDF' package to easily run combinations of these
functions for frequently encountered tasks.
Author: Jannis v. Buttlar
Maintainer: Jannis v. Buttlar <jbuttlar@bgc-jena.mpg.de>
Diff between ncdf.tools versions 0.7.1.291 dated 2014-04-07 and 0.7.1.295 dated 2015-05-29
DESCRIPTION | 19 +++++---- MD5 | 80 +++++++++++++++++++++-------------------- R/createLatLongTime.R | 2 - R/infoNcdfVars.R | 2 - R/modifyNcdfCopyAtts.R | 4 ++ R/modifyNcdfSetMissing.R | 2 - R/modifyNcdfStdFile.R |only R/transNcdfRotate.R | 47 +++++++++++++++++------- R/transNcdfSubset.R | 73 +++++++++++++++++++------------------ man/aggregateNcdf.Rd | 3 + man/checkNcdfFile.Rd | 3 + man/classR2Ncdf.Rd | 3 + man/closeAllNcfiles.Rd | 1 man/convertBinary2Ncdf.Rd | 3 + man/convertDateNcdf2R.Rd | 3 + man/convertDateR2Ncdf.Rd | 3 + man/convertFilename2Date.Rd | 3 + man/createLatLongTime.Rd | 3 + man/createStdNcdfFile.Rd | 3 + man/indexDatacube.Rd | 4 +- man/infoNcdfAtts.Rd | 3 + man/infoNcdfDims.Rd | 3 + man/infoNcdfVars.Rd | 3 + man/modifyNcdfAddDim.Rd | 3 + man/modifyNcdfAppendHistory.Rd | 3 + man/modifyNcdfCopyAtts.Rd | 4 +- man/modifyNcdfCopyMetadata.Rd | 3 + man/modifyNcdfCopyVar.Rd | 3 + man/modifyNcdfDefAtts.Rd | 3 + man/modifyNcdfSetMissing.Rd | 5 +- man/modifyNcdfStdFile.Rd |only man/modifyNcdfStdNames.Rd | 3 + man/ncdf.tools-package.Rd | 12 +++--- man/plotDatacube.Rd | 3 + man/readFLUXNETNcdf.Rd | 3 + man/readNcdf.Rd | 3 + man/readNcdfCoordinates.Rd | 3 + man/readNcdfVarName.Rd | 3 + man/transNcdfCutFiles.Rd | 3 + man/transNcdfMerge.Rd | 3 + man/transNcdfRotate.Rd | 9 +++- man/transNcdfSubset.Rd | 15 ++++--- 42 files changed, 212 insertions(+), 142 deletions(-)
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-5 dated 2015-05-29 and 0.1-6 dated 2015-05-29
DESCRIPTION | 11 ++++++----- MD5 | 8 +++++--- data |only man/parallelSVM-package.Rd | 8 ++++---- man/parallelSVM.Rd | 6 +++--- 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.3.0 dated 2015-04-30 and 4.4.0 dated 2015-05-29
DESCRIPTION | 8 MD5 | 94 NAMESPACE | 1 NEWS | 45 R/check.index.R | 12 R/earth.R | 879 +++-- R/earth.cv.R | 195 - R/earth.methods.R | 3 R/elegend.R | 4 R/evimp.R | 7 R/lib.R | 8 R/mars.to.earth.R | 5 R/model.matrix.earth.R | 18 R/plot.earth.R | 232 + R/plotd.R | 3 R/print.earth.R | 151 inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/make.bat | 4 inst/slowtests/test.big.R | 130 inst/slowtests/test.big.Rout.save | 413 +- inst/slowtests/test.cv.R | 8 inst/slowtests/test.cv.Rout.save | 2358 ++++++-------- inst/slowtests/test.earthc.bat | 32 inst/slowtests/test.earthc.c | 9 inst/slowtests/test.earthc.mak | 8 inst/slowtests/test.earthc.out.save | 2852 +++++++++-------- inst/slowtests/test.earthmain.out.save | 12 inst/slowtests/test.full.R | 22 inst/slowtests/test.full.Rout.save | 3485 ++++++++++----------- inst/slowtests/test.glm.Rout.save | 4958 +++++++++++++++--------------- inst/slowtests/test.incorrect.R |only inst/slowtests/test.incorrect.Rout.save |only inst/slowtests/test.incorrect.bat |only inst/slowtests/test.mods.R | 683 +++- inst/slowtests/test.mods.Rout.save | 945 +++-- inst/slowtests/test.mods.bat | 8 inst/slowtests/test.pmethod.cv.R |only inst/slowtests/test.pmethod.cv.Rout.save |only inst/slowtests/test.pmethod.cv.bat |only inst/slowtests/test.varmod.Rout.save | 1665 +++++----- inst/slowtests/test.varmod.mgcv.Rout.save | 160 inst/slowtests/test.weights.R | 174 + inst/slowtests/test.weights.Rout.save | 300 + man/earth.Rd | 232 - man/plot.earth.Rd | 16 man/plot.earth.models.Rd | 2 man/update.earth.Rd | 3 src/earth.c | 1440 ++++---- src/earth.h | 105 src/leaps.f | 8 51 files changed, 11758 insertions(+), 9939 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-16 2.0.7
2012-03-29 2.0.5
2012-03-22 2.0.1
2009-07-18 1.9.4
2009-03-22 1.9.3
2009-02-28 1.9.2
2008-09-05 1.8.1
2008-04-24 1.7.7
2008-04-14 1.7.6
2006-12-12 1.6.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-29 0.1
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 3.2 dated 2014-12-05 and 3.3 dated 2015-05-29
DESCRIPTION | 14 ++- MD5 | 98 ++++++++++++------------ NAMESPACE | 5 + R/CDF.birth.death.R | 174 ++++++++++++++++++++++++++++++++++++++++++-- R/DNA.R | 29 ++++--- R/PGLS.R | 7 - R/ace.R | 14 ++- R/as.bitsplits.R | 10 ++ R/as.phylo.R | 7 - R/binaryPGLMM.R |only R/compar.gee.R | 7 + R/corphylo.R |only R/dbd.R | 9 +- R/dist.topo.R | 72 +++++++++++------- R/parafit.R | 6 - R/plot.phylo.R | 38 ++++----- R/read.tree.R | 8 +- R/root.R | 8 +- R/write.nexus.R | 15 +-- R/write.nexus.data.R | 6 - build/vignette.rds |binary data/hivtree.newick.rda |binary data/landplants.newick.rda |binary data/opsin.newick.rda |binary inst/doc/MoranI.pdf |binary man/DNAbin.Rd | 2 man/LTT.Rd | 6 + man/MoranI.Rd | 4 - man/ace.Rd | 14 ++- man/as.bitsplits.Rd | 8 +- man/binaryPGLMM.Rd |only man/boot.phylo.Rd | 3 man/coalescent.intervals.Rd | 7 - man/collapsed.intervals.Rd | 13 --- man/corphylo.Rd |only man/def.Rd | 2 man/del.gaps.Rd | 32 ++++---- man/dist.topo.Rd | 18 ++-- man/is.binary.tree.Rd | 2 man/landplants.Rd | 3 man/node.depth.Rd | 10 -- man/read.dna.Rd | 6 - man/read.tree.Rd | 2 man/rlineage.Rd | 53 ++++++++++--- man/root.Rd | 11 ++ man/seg.sites.Rd | 5 - man/skyline.Rd | 42 ++-------- man/skylineplot.Rd | 34 ++------ man/where.Rd | 3 man/woodmouse.Rd | 3 man/write.dna.Rd | 6 - src/dist_dna.c | 24 ++---- 52 files changed, 513 insertions(+), 327 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between abctools versions 1.0 dated 2014-12-16 and 1.0.2 dated 2015-05-29
DESCRIPTION | 18 ++++++++++-------- MD5 | 14 +++++++------- R/semiauto.abc.R | 4 ++-- data/coal.rda |binary data/coalobs.rda |binary man/abctools-package.Rd | 11 ++++++----- man/cov.pi.Rd | 5 +++-- man/mc.ci.Rd | 5 +++-- 8 files changed, 31 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-22 1.1.1
2014-11-07 0.2.0
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes.
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gtools versions 3.4.2 dated 2015-04-10 and 3.5.0 dated 2015-05-29
ChangeLog | 796 ++++++++++++++++++++----------------------- DESCRIPTION | 35 + MD5 | 42 +- NAMESPACE | 10 NEWS | 47 ++ R/asc.R |only R/checkReverseDependencies.R |only R/dirichlet.R | 6 R/keywords.R | 11 R/mixedsort.R | 98 +++-- R/quantcut.R | 7 R/roman2int.R |only R/smartbind.R | 1 R/strmacro.R | 23 - R/trimws.R |only R/unByteCode.R |only data/ELISA.rda |binary inst/ChangeLog | 796 ++++++++++++++++++++----------------------- inst/NEWS | 47 ++ man/ASCIIfy.Rd | 3 man/asc.Rd |only man/mixedsort.Rd | 91 +++- man/quantcut.Rd | 26 - man/roman2int.Rd |only man/unByteCode.Rd |only src/roman2int.c |only tests/test_ddirichlet.R |only 27 files changed, 1082 insertions(+), 957 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.0 dated 2014-11-04 and 1.1 dated 2015-05-29
DESCRIPTION | 6 - MD5 | 22 ++-- R/GEE.var.fg.R | 288 ++++++++++++++++++++++++++++---------------------------- R/GEE.var.gst.R | 22 ++-- R/GEE.var.kc.R | 18 +-- R/GEE.var.lz.R | 14 +- R/GEE.var.mbn.R | 39 ++++--- R/GEE.var.md.R | 18 +-- R/GEE.var.mk.R | 14 +- R/GEE.var.pan.R | 21 ++-- R/GEE.var.wl.R | 39 ++++--- man/geesmv.Rd | 2 12 files changed, 268 insertions(+), 235 deletions(-)
Title: Functional Data Analysis: K-Mean Alignment
Description: It performs simultaneously clustering and alignment of a multidimensional or unidimensional functional dataset by means of k-mean alignment.
Author: Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi, Simone Vantini, Valeria Vitelli
Maintainer: Alice Parodi <alicecarla.parodi@polimi.it>
Diff between fdakma versions 1.2 dated 2015-03-12 and 1.2.1 dated 2015-05-29
DESCRIPTION | 10 MD5 | 6 R/kma.R | 1202 ++++++++++++++++++++++++----------------------------- R/kma.similarity.R | 57 +- 4 files changed, 591 insertions(+), 684 deletions(-)
Title: Explorer of World Population Prospects
Description: A shiny interface for exploring data in the 'wpp2012' (or 2010, 2008) package.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 1.6-1 dated 2015-04-11 and 1.6-2 dated 2015-05-29
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/explore/server.R | 13 ++++++------- man/wppExplorer-package.Rd | 4 ++-- 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of several plotting and table output functions for visualizing data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8 dated 2015-04-22 and 1.8.1 dated 2015-05-29
sjPlot-1.8.1/sjPlot/DESCRIPTION | 13 sjPlot-1.8.1/sjPlot/MD5 | 159 - sjPlot-1.8.1/sjPlot/NAMESPACE | 3 sjPlot-1.8.1/sjPlot/NEWS | 29 sjPlot-1.8.1/sjPlot/R/helpfunctions.R | 113 sjPlot-1.8.1/sjPlot/R/sjPlotAncovaLSMeans.R | 1255 ++++---- sjPlot-1.8.1/sjPlot/R/sjPlotAnova.R | 201 - sjPlot-1.8.1/sjPlot/R/sjPlotClusterAnalysis.R | 200 - sjPlot-1.8.1/sjPlot/R/sjPlotCorr.R | 725 ++-- sjPlot-1.8.1/sjPlot/R/sjPlotDist.R | 8 sjPlot-1.8.1/sjPlot/R/sjPlotFrequencies.R | 1794 ++++++------ sjPlot-1.8.1/sjPlot/R/sjPlotGLME.R | 3683 ++++++++++++------------- sjPlot-1.8.1/sjPlot/R/sjPlotGroupFrequencies.R | 13 sjPlot-1.8.1/sjPlot/R/sjPlotInteractions.R | 2718 +++++++++--------- sjPlot-1.8.1/sjPlot/R/sjPlotLikert.R | 65 sjPlot-1.8.1/sjPlot/R/sjPlotLinreg.R | 454 +-- sjPlot-1.8.1/sjPlot/R/sjPlotLinregMultiple.R | 26 sjPlot-1.8.1/sjPlot/R/sjPlotOdds.R | 1655 +++++------ sjPlot-1.8.1/sjPlot/R/sjPlotOddsMultiple.R | 848 ++--- sjPlot-1.8.1/sjPlot/R/sjPlotPCA.R | 934 +++--- sjPlot-1.8.1/sjPlot/R/sjPlotPropTable.R | 1388 ++++----- sjPlot-1.8.1/sjPlot/R/sjPlotScatter.R | 38 sjPlot-1.8.1/sjPlot/R/sjPlotSetTheme.R | 1675 +++++------ sjPlot-1.8.1/sjPlot/R/sjPlotStackFrequencies.R | 37 sjPlot-1.8.1/sjPlot/R/sjTabCorr.R | 1058 +++---- sjPlot-1.8.1/sjPlot/R/sjTabDataFrame.R | 786 ++--- sjPlot-1.8.1/sjPlot/R/sjTabFrequencies.R | 341 +- sjPlot-1.8.1/sjPlot/R/sjTabGrpmean.R | 408 +- sjPlot-1.8.1/sjPlot/R/sjTabItemAnalysis.R | 867 ++--- sjPlot-1.8.1/sjPlot/R/sjTabLinReg.R | 669 +++- sjPlot-1.8.1/sjPlot/R/sjTabMannWhitney.R | 214 - sjPlot-1.8.1/sjPlot/R/sjTabOdds.R | 957 ++++-- sjPlot-1.8.1/sjPlot/R/sjTabPCA.R | 1224 ++++---- sjPlot-1.8.1/sjPlot/R/sjTabPropTable.R | 35 sjPlot-1.8.1/sjPlot/R/sjTabSPSS.R | 655 ++-- sjPlot-1.8.1/sjPlot/R/sjTabStackFrq.R | 1097 +++---- sjPlot-1.8.1/sjPlot/R/zzz.R | 4 sjPlot-1.8.1/sjPlot/README.md | 65 sjPlot-1.8.1/sjPlot/man/adjust_plot_range.Rd | 2 sjPlot-1.8.1/sjPlot/man/dist_chisq.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_f.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_norm.Rd | 4 sjPlot-1.8.1/sjPlot/man/dist_t.Rd | 4 sjPlot-1.8.1/sjPlot/man/sjPlot-package.Rd | 103 sjPlot-1.8.1/sjPlot/man/sjc.qclus.Rd | 21 sjPlot-1.8.1/sjPlot/man/sjp.aov1.Rd | 6 sjPlot-1.8.1/sjPlot/man/sjp.chi2.Rd | 122 sjPlot-1.8.1/sjPlot/man/sjp.corr.Rd | 57 sjPlot-1.8.1/sjPlot/man/sjp.frq.Rd | 607 ++-- sjPlot-1.8.1/sjPlot/man/sjp.glm.Rd | 122 sjPlot-1.8.1/sjPlot/man/sjp.glmer.Rd | 437 +- sjPlot-1.8.1/sjPlot/man/sjp.glmm.Rd | 24 sjPlot-1.8.1/sjPlot/man/sjp.grpfrq.Rd | 15 sjPlot-1.8.1/sjPlot/man/sjp.int.Rd | 766 ++--- sjPlot-1.8.1/sjPlot/man/sjp.likert.Rd | 48 sjPlot-1.8.1/sjPlot/man/sjp.lm.Rd | 63 sjPlot-1.8.1/sjPlot/man/sjp.lmer.Rd | 410 +- sjPlot-1.8.1/sjPlot/man/sjp.lmm.Rd | 20 sjPlot-1.8.1/sjPlot/man/sjp.pca.Rd | 5 sjPlot-1.8.1/sjPlot/man/sjp.scatter.Rd | 38 sjPlot-1.8.1/sjPlot/man/sjp.setTheme.Rd | 22 sjPlot-1.8.1/sjPlot/man/sjp.stackfrq.Rd | 19 sjPlot-1.8.1/sjPlot/man/sjp.xtab.Rd | 21 sjPlot-1.8.1/sjPlot/man/sjt.corr.Rd | 368 +- sjPlot-1.8.1/sjPlot/man/sjt.df.Rd | 310 +- sjPlot-1.8.1/sjPlot/man/sjt.frq.Rd | 476 +-- sjPlot-1.8.1/sjPlot/man/sjt.glm.Rd | 658 ++-- sjPlot-1.8.1/sjPlot/man/sjt.glmer.Rd |only sjPlot-1.8.1/sjPlot/man/sjt.grpmean.Rd | 30 sjPlot-1.8.1/sjPlot/man/sjt.itemanalysis.Rd | 380 +- sjPlot-1.8.1/sjPlot/man/sjt.lm.Rd | 812 ++--- sjPlot-1.8.1/sjPlot/man/sjt.lmer.Rd |only sjPlot-1.8.1/sjPlot/man/sjt.mwu.Rd | 22 sjPlot-1.8.1/sjPlot/man/sjt.pca.Rd | 381 +- sjPlot-1.8.1/sjPlot/man/sjt.stackfrq.Rd | 425 +- sjPlot-1.8.1/sjPlot/man/sjt.xtab.Rd | 444 +-- sjPlot-1.8.1/sjPlot/man/view_spss.Rd | 247 - sjPlot-1.8/sjPlot/man/sj.setGeomColors.Rd |only sjPlot-1.8/sjPlot/man/sjp.emm.int.Rd |only sjPlot-1.8/sjPlot/tests |only 80 files changed, 17485 insertions(+), 16426 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
shinyjs can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. shinyjs can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.6.0 dated 2015-05-26 and 0.0.6.2 dated 2015-05-29
DESCRIPTION | 6 +- MD5 | 23 +++++----- R/extendShinyjs.R | 80 ++++++++++++++++++++++++++++++------ R/useShinyjs.R | 2 R/utils.R | 28 ++++++++++-- README.md | 65 ++++++++++++++++++++--------- inst/doc/overview.Rmd | 64 +++++++++++++++++++++------- inst/doc/overview.html | 47 ++++++++++++++------- man/extendShinyjs.Rd | 41 +++++++++++++++++- man/js.Rd | 2 tests/test-empty.js |only tests/testthat/test-extendShinyjs.R | 37 ++++++++++++++-- vignettes/overview.Rmd | 64 +++++++++++++++++++++------- 13 files changed, 352 insertions(+), 107 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.2-0 dated 2015-05-03 and 1.3.0 dated 2015-05-29
DESCRIPTION | 6 - MD5 | 21 +++--- NAMESPACE | 3 NEWS | 4 + R/get_chroncontrol.R | 116 ++++++++++++++++++++++++++-------- R/write_agefile.R | 2 README.md | 22 ++++-- inst/img/histogramplot.png |binary man/get_chroncontrol.Rd | 10 ++ man/get_chroncontrol.default.Rd |only man/get_chroncontrol.download.Rd |only man/get_chroncontrol.download_list.Rd |only tests/testthat/test_neotoma.R | 15 ++++ 13 files changed, 152 insertions(+), 47 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.1.0 dated 2015-02-16 and 1.1.1 dated 2015-05-29
mets-1.1.0/mets/man/survpois.Rd |only mets-1.1.1/mets/DESCRIPTION | 10 mets-1.1.1/mets/MD5 | 88 +++--- mets-1.1.1/mets/NAMESPACE | 8 mets-1.1.1/mets/NEWS | 14 - mets-1.1.1/mets/R/bicomprisk.R | 80 ++++- mets-1.1.1/mets/R/bicomprisksim.R | 153 +++++------ mets-1.1.1/mets/R/binomial.twostage.R | 2 mets-1.1.1/mets/R/biprobit.R | 8 mets-1.1.1/mets/R/biprobit.time.R | 140 +++++++++- mets-1.1.1/mets/R/casewise.R | 4 mets-1.1.1/mets/R/clusterindex-reshape.R | 4 mets-1.1.1/mets/R/cor.R | 361 +++++++++++++++----------- mets-1.1.1/mets/R/divide.conquer.R | 10 mets-1.1.1/mets/R/exmarg.R |only mets-1.1.1/mets/R/ipw.R | 297 +++++++++++++++++++-- mets-1.1.1/mets/R/lifetable.R | 254 ++++++++++++++---- mets-1.1.1/mets/R/methodstwinlm.R | 2 mets-1.1.1/mets/R/mets-package.R | 4 mets-1.1.1/mets/R/plot.bptwin.R | 19 + mets-1.1.1/mets/R/procformula.R | 1 mets-1.1.1/mets/R/sim-nordic-twin.R | 305 +++++++++++++++++++-- mets-1.1.1/mets/R/twinlm.R | 10 mets-1.1.1/mets/R/twostage.R | 2 mets-1.1.1/mets/R/utils.R | 136 --------- mets-1.1.1/mets/man/Grandom.cif.Rd | 98 +++---- mets-1.1.1/mets/man/bicomprisk.Rd | 54 +++ mets-1.1.1/mets/man/biprobit.Rd | 6 mets-1.1.1/mets/man/casewise.Rd | 2 mets-1.1.1/mets/man/casewise.test.Rd | 2 mets-1.1.1/mets/man/concordance.Rd | 2 mets-1.1.1/mets/man/cor.cif.Rd | 10 mets-1.1.1/mets/man/divide.conquer.Rd | 2 mets-1.1.1/mets/man/divide.conquer.timereg.Rd | 7 mets-1.1.1/mets/man/easy.binomial.twostage.Rd | 2 mets-1.1.1/mets/man/eventpois.Rd |only mets-1.1.1/mets/man/internal.Rd | 2 mets-1.1.1/mets/man/ipw.Rd | 5 mets-1.1.1/mets/man/ipw2.Rd |only mets-1.1.1/mets/man/random.cif.Rd | 55 +-- mets-1.1.1/mets/man/summary.cor.Rd | 12 mets-1.1.1/mets/man/twinlm.Rd | 2 mets-1.1.1/mets/man/twostage.Rd | 2 mets-1.1.1/mets/src/cor.cpp | 49 ++- mets-1.1.1/mets/src/mvn.cpp | 49 +++ mets-1.1.1/mets/src/plackettMLE.cpp | 2 mets-1.1.1/mets/src/tools.cpp | 66 +++- 47 files changed, 1623 insertions(+), 718 deletions(-)
Title: Longitudinal Targeted Maximum Likelihood Estimation
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data.
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab <joshuaschwab@yahoo.com>
Diff between ltmle versions 0.9-5 dated 2015-05-07 and 0.9-6 dated 2015-05-29
DESCRIPTION | 10 ++-- MD5 | 34 +++++++------ NAMESPACE | 2 NEWS | 9 +++ R/GeneralUtilities.R | 14 +++++ R/ltmle.R | 87 ++++++++++++++++++++--------------- R/zzz.R | 6 -- data/PreviousReleaseTests.RData |binary data/datalist |only man/ltmle.rd | 4 - tests/testthat/test-(init).R |only tests/testthat/test-BaselineCovMSM.R | 14 ++--- tests/testthat/test-CheckInputs.R | 37 ++++++-------- tests/testthat/test-CleanData.R | 2 tests/testthat/test-GetDefaultForm.R | 2 tests/testthat/test-Weights.R | 5 -- tests/testthat/test-prevRelease.R | 6 ++ tests/testthat/test-random.R | 2 tests/testthat/test-summary.ltmle.R | 24 ++++++++- 19 files changed, 157 insertions(+), 101 deletions(-)
Title: Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Author: Art B. Owen [aut],
Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang <wangjingshususan@gmail.com>
Diff between esaBcv versions 1.1.1 dated 2015-04-11 and 1.2.1 dated 2015-05-29
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/ESA_BCV.R | 4 ++-- man/ESA.Rd | 2 +- man/EsaBcv.Rd | 2 +- man/esaBcv_package.Rd | 2 +- man/plot.esabcv.Rd | 2 +- man/simdat.Rd | 2 +- 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Compute Statistics Helper Functions
Description: A small package containing helper utilities for creating function
for computing statistics.
Author: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Diff between dostats versions 1.3.1 dated 2014-05-28 and 1.3.2 dated 2015-05-29
dostats-1.3.1/dostats/R/formula.R |only dostats-1.3.1/dostats/R/hdf.R |only dostats-1.3.1/dostats/inst/tests |only dostats-1.3.1/dostats/man/Table1.Rd |only dostats-1.3.1/dostats/man/hdf.Rd |only dostats-1.3.1/dostats/man/internal.Rd |only dostats-1.3.2/dostats/DESCRIPTION | 13 - dostats-1.3.2/dostats/MD5 | 79 ++++---- dostats-1.3.2/dostats/NAMESPACE | 82 +++----- dostats-1.3.2/dostats/NEWS | 68 +++---- dostats-1.3.2/dostats/R/T.R | 8 dostats-1.3.2/dostats/R/capply.R | 28 +-- dostats-1.3.2/dostats/R/collect.R | 108 +++++------ dostats-1.3.2/dostats/R/onarg.R | 128 ++++++------- dostats-1.3.2/dostats/R/pval.R | 166 ++++++++--------- dostats-1.3.2/dostats/R/utils.R | 222 +++++++++++++----------- dostats-1.3.2/dostats/R/wargs.R | 164 ++++++++--------- dostats-1.3.2/dostats/README.md | 34 +-- dostats-1.3.2/dostats/inst/ex_dostats.R | 8 dostats-1.3.2/dostats/man/T.Rd | 35 +-- dostats-1.3.2/dostats/man/capply.Rd | 41 ++-- dostats-1.3.2/dostats/man/class.stats.Rd | 69 +++---- dostats-1.3.2/dostats/man/collect.Rd | 59 +++--- dostats-1.3.2/dostats/man/compose.Rd | 105 +++++------ dostats-1.3.2/dostats/man/contains.Rd | 55 +++-- dostats-1.3.2/dostats/man/dostats.Rd | 71 +++---- dostats-1.3.2/dostats/man/fill_v.Rd | 41 ++-- dostats-1.3.2/dostats/man/head-tail-utils.Rd.Rd |only dostats-1.3.2/dostats/man/listrows.Rd | 29 +-- dostats-1.3.2/dostats/man/make_call.Rd | 51 ++--- dostats-1.3.2/dostats/man/make_new_id.Rd | 29 +-- dostats-1.3.2/dostats/man/me.Rd | 29 +-- dostats-1.3.2/dostats/man/onarg.Rd | 59 +++--- dostats-1.3.2/dostats/man/pval.Rd | 57 +++--- dostats-1.3.2/dostats/man/redirf.Rd | 35 +-- dostats-1.3.2/dostats/man/seq_consecutive.Rd | 41 ++-- dostats-1.3.2/dostats/man/wargs.Rd | 59 +++--- dostats-1.3.2/dostats/tests/test_package.R | 6 dostats-1.3.2/dostats/tests/testthat |only 39 files changed, 997 insertions(+), 982 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models.
Author: Adrien Taudiere, Cyrille Violle with contribution by Francois Munoz
Maintainer: Adrien Taudiere <adrien.taudiere@cefe.cnrs.fr>
Diff between cati versions 0.96 dated 2015-02-13 and 0.99 dated 2015-05-29
DESCRIPTION | 14 - MD5 | 66 ++--- NAMESPACE | 66 ++--- R/allfunctions_cati.r | 3 inst/CITATION | 24 + man/AbToInd.Rd | 88 +++---- man/Auxiliary.functions.rd | 68 ++--- man/CVNND.Rd | 196 ++++++++-------- man/ComIndex.Rd | 474 +++++++++++++++++++-------------------- man/ComIndexMulti.Rd | 432 +++++++++++++++++------------------ man/Fred.Rd | 114 ++++----- man/IndexByGroups.Rd | 74 +++--- man/MinMaxMST.Rd | 136 +++++------ man/Pval.Rd | 96 +++---- man/RandCom.Rd | 172 +++++++------- man/RaoRel.Rd | 360 ++++++++++++++--------------- man/SumBL.Rd | 132 +++++----- man/Tstats.Rd | 546 +++++++++++++++++++++++---------------------- man/as.listofindex.Rd | 154 ++++++------ man/cati-package.Rd | 65 ++--- man/decompCTRE.Rd | 176 +++++++------- man/finch.ind.Rd | 74 +++--- man/partvar.Rd | 186 +++++++-------- man/plot.listofindex.Rd | 292 ++++++++++++------------ man/plotCorTstats.Rd | 158 ++++++------- man/plotDistri.Rd | 274 +++++++++++----------- man/plotRandtest.Rd | 126 +++++----- man/plotSESvar.Rd | 162 ++++++------- man/plotSpPop.Rd | 256 ++++++++++----------- man/plotSpVar.Rd | 268 +++++++++++----------- man/samplingSubsetData.Rd | 118 ++++----- man/ses.Rd | 126 +++++----- man/ses.listofindex.Rd | 80 +++--- man/traitflex.anova.Rd | 186 +++++++-------- 34 files changed, 2890 insertions(+), 2872 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.16-0 dated 2014-11-18 and 0.16-3 dated 2015-05-29
analogue-0.16-0/analogue/inst/tests |only analogue-0.16-3/analogue/DESCRIPTION | 10 - analogue-0.16-3/analogue/MD5 | 31 ++-- analogue-0.16-3/analogue/NAMESPACE | 1 analogue-0.16-3/analogue/R/Stratiplot.matrix.R |only analogue-0.16-3/analogue/R/join.R | 71 +--------- analogue-0.16-3/analogue/R/predict.logitreg.R | 4 analogue-0.16-3/analogue/R/tran.R | 7 analogue-0.16-3/analogue/README.md | 10 - analogue-0.16-3/analogue/build/vignette.rds |binary analogue-0.16-3/analogue/inst/ChangeLog | 12 + analogue-0.16-3/analogue/inst/NEWS.Rd | 26 +++ analogue-0.16-3/analogue/inst/doc/analogue_methods.pdf |binary analogue-0.16-3/analogue/man/Stratiplot.Rd | 5 analogue-0.16-3/analogue/man/tran.Rd | 1 analogue-0.16-3/analogue/tests/Examples/analogue-Ex.Rout.save | 19 +- analogue-0.16-3/analogue/tests/test-all.R | 7 analogue-0.16-3/analogue/tests/testthat |only 18 files changed, 105 insertions(+), 99 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-146 dated 2015-05-26 and 0.15-147 dated 2015-05-28
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/Makevars.win | 2 +- 4 files changed, 10 insertions(+), 8 deletions(-)
Title: 'DRNG' on Intel CPUs with the 'RdRand' Instruction for R
Description: Make use of the hardware random number accessed by the 'RdRand'
instruction in recent Intel CPUs (Ivy Bridge and later).
'DRNG' is "Digital Random Number Generator".
Author: Ei-ji Nakama <nakama@com-one.com>, Junji NAKANO <nakanoj@ism.ac.jp>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rrdrand versions 0.1-10 dated 2014-10-16 and 0.1-14 dated 2015-05-28
Changelog | 2 ++ DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- man/Rrdrand-package.Rd | 8 ++++---- src/Rrdrand.c | 6 +++--- 5 files changed, 22 insertions(+), 20 deletions(-)
Title: Package for the Analysis of Lake Physics
Description: Standardized methods for calculating common important derived
physical features of lakes including water density based based on
temperature, thermal layers, thermocline depth, lake number, Wedderburn
number, Schmidt stability and others.
Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor
Leach, Jake Zwart
Maintainer: Luke Winslow <lawinslow@gmail.com>
Diff between rLakeAnalyzer versions 1.7.3 dated 2015-04-05 and 1.7.6 dated 2015-05-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/meta.depths.R | 18 +++++++----------- README.md | 2 ++ build/vignette.rds |binary man/internal.energy.Rd | 2 +- man/meta.depths.Rd | 2 +- man/thermo.depth.Rd | 2 +- man/wtr.plot.temp.Rd | 2 +- 9 files changed, 24 insertions(+), 26 deletions(-)
Title: Control the Number of Threads on 'BLAS'
Description: Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'ACML' and 'MKL').
and possible to control the number of threads in 'OpenMP'.
get a number of logical cores and physical cores if feasible.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between RhpcBLASctl versions 0.14-256 dated 2014-09-12 and 0.15-148 dated 2015-05-28
ChangeLog | 4 ++++ DESCRIPTION | 20 +++++++++----------- MD5 | 7 ++++--- README |only man/RhpcBLASctl-package.Rd | 10 +++++----- 5 files changed, 22 insertions(+), 19 deletions(-)
Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.0-4 dated 2013-04-04 and 2.0-5 dated 2015-05-28
DESCRIPTION | 19 +-- MD5 | 30 +++-- NAMESPACE | 1 R/Rcode.r | 284 +++++++++++++++++++--------------------------------- R/cmprel.r | 10 - R/mystrata.r |only R/rformulate.r |only R/rsdiff.r |only data/rdata.rda |binary data/slopop.rda |binary man/cmprel.Rd | 4 man/joinrate.Rd | 3 man/rsadd.Rd | 4 man/rsmul.Rd | 7 - man/rssurv.Rd | 7 - man/rstrans.Rd | 2 src/netfastpinter.c |only src/survprotomoj.h | 2 18 files changed, 153 insertions(+), 220 deletions(-)
Title: Tools for the Analysis of Ecosystem Metabolism
Description: A collection of tools for the calculation of freewater metabolism.
Author: Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul
Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Maintainer: Luke Winslow <lawinslow@gmail.com>
Diff between LakeMetabolizer versions 1.3.1 dated 2015-04-05 and 1.3.3 dated 2015-05-28
DESCRIPTION | 6 +-- MD5 | 76 +++++++++++++++++++++-------------------- NAMESPACE | 2 - R/metab.R | 14 +++---- R/metab.bayesian.R | 6 +-- R/metab.kalman.R | 6 +-- R/metab.ols.R | 6 +-- README.md | 23 +++--------- demo |only inst/jags/bayes.mod.allk.JAGS | 3 - inst/jags/bayes.mod.bothk.JAGS | 11 +---- man/calc.lw.net.Rd | 2 - man/calc.zeng.Rd | 2 - man/get.Ts.Rd | 2 - man/get.vars.Rd | 2 - man/getSchmidt.Rd | 2 - man/has.vars.Rd | 2 - man/is.day.Rd | 2 - man/is.night.Rd | 2 - man/k.read.Rd | 2 - man/k.read.base.Rd | 2 - man/k600.2.kGAS.Rd | 2 - man/load.all.data.Rd | 2 - man/load.meta.Rd | 2 - man/metab.Rd | 3 + man/metab.bayesian.Rd | 4 +- man/metab.bookkeep.Rd | 2 - man/metab.kalman.Rd | 10 +++-- man/metab.mle.Rd | 2 - man/metab.ols.Rd | 2 - man/o2.at.sat.Rd | 2 - man/par.to.sw.Rd | 2 - man/rmv.vars.Rd | 2 - man/sun.rise.set.Rd | 2 - man/sw.to.par.Rd | 2 - man/temp.kalman.Rd | 2 - man/var.indx.Rd | 2 - man/wind.scale.Rd | 2 - 38 files changed, 103 insertions(+), 115 deletions(-)
More information about LakeMetabolizer at CRAN
Permanent link
Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain.
Author: Andreas Borg <borga@uni-mainz.de>, Murat Sariyar <murat.sariyar@charite.de>
Maintainer: Andreas Borg <borga@uni-mainz.de>
Diff between RecordLinkage versions 0.4-7 dated 2015-01-15 and 0.4-8 dated 2015-05-28
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 12 +++++++++++- NEWS | 7 ++++++- R/classify.r | 6 +++--- R/compare.r | 45 +++++++++++++++++++++------------------------ R/em-methods.r | 14 +++++++------- R/evt.r | 10 +++++----- R/getPairs.r | 14 ++++---------- R/internals.r | 2 +- R/stochastic.r | 2 +- R/summary.r | 2 +- build/vignette.rds |binary inst/doc/BigData.pdf |binary inst/doc/EVT.pdf |binary inst/doc/Supervised.pdf |binary inst/doc/WeightBased.pdf |binary man/RLdata.rd | 2 +- 18 files changed, 81 insertions(+), 75 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which statistical data are visualized. This package offers a flexible, layer-based, way to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 0.7 dated 2015-03-27 and 1.0 dated 2015-05-28
tmap-0.7/tmap/R/convert_shape_data.R |only tmap-0.7/tmap/R/crop_shape.R |only tmap-0.7/tmap/R/double_line.R |only tmap-0.7/tmap/R/fit_polylines.R |only tmap-0.7/tmap/R/get_polygon_directions.R |only tmap-0.7/tmap/R/get_polygon_ranges.R |only tmap-0.7/tmap/R/map_points_to_line.R |only tmap-0.7/tmap/R/split_lines_equal.R |only tmap-0.7/tmap/R/split_lines_poly.R |only tmap-0.7/tmap/data/cities.rda |only tmap-0.7/tmap/inst/shiny_leaflet |only tmap-0.7/tmap/man/Shapes2.Rd |only tmap-0.7/tmap/man/convert_shape_data.Rd |only tmap-0.7/tmap/man/crop_shape.Rd |only tmap-0.7/tmap/man/double_line.Rd |only tmap-0.7/tmap/man/fit_polylines.Rd |only tmap-0.7/tmap/man/get_polygon_directions.Rd |only tmap-0.7/tmap/man/get_polygon_ranges.Rd |only tmap-0.7/tmap/man/intersection_shapes.Rd |only tmap-0.7/tmap/man/map_points_to_line.Rd |only tmap-0.7/tmap/man/split_lines_equal.Rd |only tmap-0.7/tmap/man/split_lines_poly.Rd |only tmap-0.7/tmap/man/tm_borders.Rd |only tmap-0.7/tmap/man/tm_fill.Rd |only tmap-1.0/tmap/DESCRIPTION | 12 tmap-1.0/tmap/MD5 | 184 +++++------- tmap-1.0/tmap/NAMESPACE | 24 - tmap-1.0/tmap/NEWS | 16 + tmap-1.0/tmap/R/animation_tmap.R | 21 + tmap-1.0/tmap/R/append_data.R | 8 tmap-1.0/tmap/R/approx_areas.R | 33 -- tmap-1.0/tmap/R/calc_densities.R | 18 - tmap-1.0/tmap/R/cat2pal.R | 31 +- tmap-1.0/tmap/R/cellplot.R | 14 tmap-1.0/tmap/R/get_IDs.R | 2 tmap-1.0/tmap/R/get_asp_ratio.R |only tmap-1.0/tmap/R/get_raster_data.R |only tmap-1.0/tmap/R/grid_shp.R | 1 tmap-1.0/tmap/R/gridplot.R | 13 tmap-1.0/tmap/R/is_projected.R |only tmap-1.0/tmap/R/legend_hist.R | 159 ++++++---- tmap-1.0/tmap/R/legend_plot.R | 417 ++++++++++++++------------- tmap-1.0/tmap/R/legend_prepare.R | 149 ++++++--- tmap-1.0/tmap/R/map2scale.R | 16 - tmap-1.0/tmap/R/num2pal.R | 63 ++-- tmap-1.0/tmap/R/pkg.R | 56 ++- tmap-1.0/tmap/R/plot_map.R | 264 +++++++++++++---- tmap-1.0/tmap/R/print_tmap.R | 146 +++++++-- tmap-1.0/tmap/R/process_bubbles.R | 102 ++++-- tmap-1.0/tmap/R/process_data.R | 28 + tmap-1.0/tmap/R/process_fill.R | 50 ++- tmap-1.0/tmap/R/process_layers.R | 44 +- tmap-1.0/tmap/R/process_lines.R | 73 ++++ tmap-1.0/tmap/R/process_meta.R | 86 ++--- tmap-1.0/tmap/R/process_raster.R |only tmap-1.0/tmap/R/process_shapes.R | 214 +++++++++----- tmap-1.0/tmap/R/process_text.R | 22 - tmap-1.0/tmap/R/process_tm.R | 82 ++--- tmap-1.0/tmap/R/process_varnames.R | 15 - tmap-1.0/tmap/R/qtm.R | 58 ++- tmap-1.0/tmap/R/read_shape.R | 16 - tmap-1.0/tmap/R/set_projection.R | 21 - tmap-1.0/tmap/R/split_shps.R | 2 tmap-1.0/tmap/R/split_tm.R | 6 tmap-1.0/tmap/R/tm_layers.R | 419 ++++++++++++++-------------- tmap-1.0/tmap/R/tm_layout.R | 123 +++++--- tmap-1.0/tmap/R/tm_misc_elements.R |only tmap-1.0/tmap/R/tm_shape.R |only tmap-1.0/tmap/build/vignette.rds |binary tmap-1.0/tmap/data/Europe.rda |binary tmap-1.0/tmap/data/NLD_muni.rda |binary tmap-1.0/tmap/data/NLD_prov.rda |binary tmap-1.0/tmap/data/World.rda |binary tmap-1.0/tmap/data/datalist | 3 tmap-1.0/tmap/data/land.rda |only tmap-1.0/tmap/data/metro.rda |only tmap-1.0/tmap/data/rivers.rda |binary tmap-1.0/tmap/inst/doc/tmap-nutshell.R | 112 ++++--- tmap-1.0/tmap/inst/doc/tmap-nutshell.Rmd | 161 ++++++---- tmap-1.0/tmap/inst/doc/tmap-nutshell.html | 217 +++++++++----- tmap-1.0/tmap/man/Shapes.Rd | 17 - tmap-1.0/tmap/man/animation_tmap.Rd | 23 + tmap-1.0/tmap/man/append_data.Rd | 4 tmap-1.0/tmap/man/approx_areas.Rd | 33 +- tmap-1.0/tmap/man/calc_densities.Rd | 16 - tmap-1.0/tmap/man/get_IDs.Rd | 2 tmap-1.0/tmap/man/get_asp_ratio.Rd |only tmap-1.0/tmap/man/land.Rd |only tmap-1.0/tmap/man/metro.Rd |only tmap-1.0/tmap/man/plus-.tmap.Rd | 8 tmap-1.0/tmap/man/polygons.Rd |only tmap-1.0/tmap/man/print.tmap.Rd | 8 tmap-1.0/tmap/man/qtm.Rd | 61 ++-- tmap-1.0/tmap/man/read_shape.Rd | 13 tmap-1.0/tmap/man/rivers.Rd |only tmap-1.0/tmap/man/sbind.Rd | 2 tmap-1.0/tmap/man/set_projection.Rd | 21 - tmap-1.0/tmap/man/split_shapes.Rd | 4 tmap-1.0/tmap/man/tm_bubbles.Rd | 71 +++- tmap-1.0/tmap/man/tm_credits.Rd |only tmap-1.0/tmap/man/tm_facets.Rd | 55 ++- tmap-1.0/tmap/man/tm_grid.Rd | 8 tmap-1.0/tmap/man/tm_layout.Rd | 122 ++++---- tmap-1.0/tmap/man/tm_lines.Rd | 49 ++- tmap-1.0/tmap/man/tm_raster.Rd |only tmap-1.0/tmap/man/tm_scale_bar.Rd |only tmap-1.0/tmap/man/tm_shape.Rd | 66 ++-- tmap-1.0/tmap/man/tm_text.Rd | 29 - tmap-1.0/tmap/man/tmap-element.Rd | 94 ++++-- tmap-1.0/tmap/man/tmap-package.Rd | 6 tmap-1.0/tmap/man/write_shape.Rd | 6 tmap-1.0/tmap/vignettes/tmap-nutshell.Rmd | 161 ++++++---- 112 files changed, 2682 insertions(+), 1698 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.2.2 dated 2015-05-19 and 2.2.4 dated 2015-05-28
DESCRIPTION | 15 - MD5 | 135 ++++++------- R/MxCompute.R | 30 ++ R/MxMI.R | 7 R/MxModelFunctions.R | 1 R/MxOptions.R | 5 R/MxRun.R | 3 R/MxSummary.R | 17 + R/MxVersion.R | 2 R/omxConstrainThresholds.R | 67 ------ demo/00Index | 2 demo/mxThreshold.R |only demo/omxConstrainMLThresholds.R |only inst/CITATION | 13 - inst/models/passing/AlgebraDeriv.R | 3 inst/models/passing/IntroSEM-BivariateRaw.R | 2 inst/models/passing/IntroSEM-BivariateStd.R | 2 inst/models/passing/IntroSEM-MultiRegRaw.R | 2 inst/models/passing/IntroSEM-MultiRegStd.R | 2 inst/models/passing/IntroSEM-MultivariateRegRaw.R | 2 inst/models/passing/IntroSEM-OneFactorCov.R | 4 inst/models/passing/IntroSEM-OneFactorRaw.R | 4 inst/models/passing/IntroSEM-ThreeFactorScale1Test.R | 8 inst/models/passing/IntroSEM-ThreeFactorScale2Test.R | 12 - inst/models/passing/IntroSEM-ThreeLatentMediationTest1.R | 10 inst/models/passing/IntroSEM-ThreeLatentMediationTest2.R | 10 inst/models/passing/IntroSEM-ThreeLatentMultipleRegTest1.R | 10 inst/models/passing/IntroSEM-ThreeLatentMultipleRegTest2.R | 10 inst/models/passing/IntroSEM-UnivariateRaw.R | 2 inst/models/passing/IntroSEM-UnivariateStd.R | 2 inst/models/passing/LAD--CheckCode6.R | 9 inst/models/passing/Simple--CheckCode6.R | 12 - inst/models/passing/SimpleMLAlgebraCIs.R | 2 inst/models/passing/bivLognormDemo.R |only inst/models/passing/checkStandardizedLoadingsEtcetera.R | 14 - inst/models/passing/derivFilter.R | 2 inst/models/passing/rowAlgTest140708.R | 2 man/mxComputeGradientDescent.Rd | 3 man/mxComputeNumericDeriv.Rd | 19 + man/mxOption.Rd | 1 man/mxThreshold.Rd | 69 ------ man/omxConstrainMLThresholds.Rd | 66 ------ src/AlgebraFunctions.h | 11 - src/Compute.cpp | 9 src/Compute.h | 1 src/ComputeGD.cpp | 29 -- src/ComputeSD.h | 2 src/ba81quad.cpp | 11 - src/ba81quad.h | 2 src/fitMultigroup.cpp | 10 src/glue.cpp | 14 + src/glue.h | 2 src/nloptcpp.cpp | 8 src/omxAlgebra.cpp | 58 ++--- src/omxAlgebra.h | 3 src/omxAlgebraFitFunction.cpp | 18 - src/omxExpectation.cpp | 2 src/omxExpectationBA81.cpp | 4 src/omxFitFunction.cpp | 14 - src/omxFitFunction.h | 1 src/omxFitFunctionBA81.cpp | 34 +-- src/omxHessianCalculation.cpp | 134 +++++++++--- src/omxImportFrontendState.cpp | 24 +- src/omxMLFitFunction.cpp | 6 src/omxMatrix.cpp | 33 +-- src/omxMatrix.h | 3 src/omxRAMExpectation.cpp | 2 src/omxState.cpp | 9 src/omxState.h | 3 src/subnp.cpp | 42 ++-- 70 files changed, 514 insertions(+), 556 deletions(-)
Title: Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic'
Data)
Description: Provides function to read data from the 'Igor Pro' data analysis
program by Wavemetrics. The data formats supported are 'Igor' packed
experiment format (pxp) and 'Igor' binary wave (ibw). See:
http://www.wavemetrics.com/ for details. Also includes functions to load
special pxp files produced by the 'Igor Pro' 'Neuromatic' and 'Nclamp'
packages for recording and analysing neuronal data. See
http://www.neuromatic.thinkrandom.com/ for details.
Author: Greg Jefferis with contributions from Thomas Braun
Maintainer: Greg Jefferis <jefferis@gmail.com>
Diff between IgorR versions 0.7.1 dated 2014-02-11 and 0.8 dated 2015-05-28
IgorR-0.7.1/IgorR/inst/igor/ExperimentWithHigherChars.pxp |only IgorR-0.7.1/IgorR/inst/igor/ExperimentWithProcHistoryAndNBs.pxp |only IgorR-0.7.1/IgorR/inst/tests |only IgorR-0.7.1/IgorR/tests/test-all.R |only IgorR-0.8/IgorR/DESCRIPTION | 24 +- IgorR-0.8/IgorR/MD5 | 47 ++--- IgorR-0.8/IgorR/NAMESPACE | 2 IgorR-0.8/IgorR/NEWS | 17 + IgorR-0.8/IgorR/R/ReadIgorBinary.R | 86 +++++----- IgorR-0.8/IgorR/R/ReadNclamp.R | 53 +++--- IgorR-0.8/IgorR/README.md | 58 ++++-- IgorR-0.8/IgorR/man/IgorR-package.Rd | 17 - IgorR-0.8/IgorR/man/IgorR-private.Rd | 13 - IgorR-0.8/IgorR/man/ReadAllNclampLogTables.Rd | 15 - IgorR-0.8/IgorR/man/ReadNclampLogTable.Rd | 17 - IgorR-0.8/IgorR/man/SummariseSweepFile.Rd | 18 +- IgorR-0.8/IgorR/man/SweepFilesToDataFrame.Rd | 11 - IgorR-0.8/IgorR/man/UpdateSweepDataFrame.Rd | 21 +- IgorR-0.8/IgorR/man/WaveToTimeSeries.Rd | 13 - IgorR-0.8/IgorR/man/read.ibw.Rd | 27 +-- IgorR-0.8/IgorR/man/read.pxp.Rd | 59 +++--- IgorR-0.8/IgorR/man/tsp.igorwave.Rd | 4 IgorR-0.8/IgorR/tests/testthat |only IgorR-0.8/IgorR/tests/testthat.R |only 24 files changed, 273 insertions(+), 229 deletions(-)
Title: Analyze Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner, Charlotte Rennuit, Jin Mi Triolo, and Ali Heidarzadeh Vazifehkhoran.
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.0 dated 2015-03-05 and 1.0.1 dated 2015-05-28
biogas-1.0.1/biogas/ChangeLog |only biogas-1.0.1/biogas/DESCRIPTION | 8 - biogas-1.0.1/biogas/MD5 | 44 ++++----- biogas-1.0.1/biogas/R/stdVol.R | 8 - biogas-1.0.1/biogas/R/summBg.R | 137 +++++++++++++++++++++--------- biogas-1.0.1/biogas/data/comp.rda |binary biogas-1.0.1/biogas/data/comp2.rda |binary biogas-1.0.1/biogas/data/mass.rda |binary biogas-1.0.1/biogas/data/massw.rda |binary biogas-1.0.1/biogas/data/setup.rda |binary biogas-1.0.1/biogas/data/setup2.rda |binary biogas-1.0.1/biogas/data/vol.rda |binary biogas-1.0.1/biogas/data/vol2.rda |binary biogas-1.0.1/biogas/man/biogas-package.Rd | 44 +++++---- biogas-1.0.1/biogas/man/comp2.Rd | 2 biogas-1.0.1/biogas/man/interp.Rd | 10 +- biogas-1.0.1/biogas/man/mass2vol.Rd | 9 + biogas-1.0.1/biogas/man/massw.Rd | 2 biogas-1.0.1/biogas/man/setup2.Rd | 2 biogas-1.0.1/biogas/man/stdVol.Rd | 25 ++++- biogas-1.0.1/biogas/man/summBg.Rd | 22 +++- biogas-1.0.1/biogas/man/vol2.Rd | 2 biogas-1.0.1/biogas/man/vol2mass.Rd | 6 - biogas-1.0/biogas/R/biogas-internal.R |only 24 files changed, 209 insertions(+), 112 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.8.8 dated 2015-05-27 and 1.8.9 dated 2015-05-28
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/two.stage.reg.Rd | 4 ++-- src/ipcw-residualmean.c | 2 +- src/two-stage-reg.c | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low
Dimensions
Description: An R wrapper for 'libnabo', an exact or approximate k nearest
neighbour library which is optimised for low dimensional spaces (e.g. 3D).
'libnabo' has speed and space advantages over the 'ANN' library wrapped by
package 'RANN'. 'nabor' includes a knn function that is designed as a
drop-in replacement for 'RANN' function nn2. In addition, objects which
include the k-d tree search structure can be returned to speed up repeated
queries of the same set of target points.
Author: Stephane Mangenat (for 'libnabo'), Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nabor versions 0.4.4 dated 2015-01-12 and 0.4.6 dated 2015-05-28
DESCRIPTION | 25 ++++++++++++------------- LICENSE | 2 +- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS | 11 +++++++++++ R/knn.R | 12 ++++++++++-- README.md | 3 +++ man/WKNN-class.Rd | 3 ++- man/kcpoints.Rd | 3 ++- man/knn.Rd | 13 +++++++++++-- man/nabor-package.Rd | 3 ++- src/RcppExports.cpp | 22 +++++++++------------- tests/testthat/test-knn.R | 8 +++++--- 13 files changed, 81 insertions(+), 50 deletions(-)
Title: Statistical Inference for Parametric and Semiparametric Models
Based on Dependently Truncated Data
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj), subject to Xj<=Yj, for all j=1,...,n, are called truncated data. Parametric approach (Emura & Konno 2012 Stat Papers), semiparametric approach (Chaieb et al. 2006 Biometrika; Emura et al. 2011 Sinica; Emura & Murotani 2015 TEST), nonparametric maximum likelihood approach (Emura & Wang 2012 JMVA), and regression approach (Emura & Wang 2015 AISM) are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians (Emura & Murotani 2015 TEST).
Author: Takeshi Emura
Maintainer: Takeshi Emura <emura@stat.ncu.edu.tw>
Diff between depend.truncation versions 2.3 dated 2015-05-10 and 2.4 dated 2015-05-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- man/depend.truncation-package.Rd | 8 ++++---- man/dependAFT.reg.Rd | 11 ++++++----- 4 files changed, 18 insertions(+), 17 deletions(-)
More information about depend.truncation at CRAN
Permanent link
Title: Search and Download Papers from the bioRxiv Preprint Server
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
Diff between biorxivr versions 0.1.0 dated 2015-05-05 and 0.1.1 dated 2015-05-28
CHANGELOG |only DESCRIPTION | 6 MD5 | 7 - R/bx_extract.R | 8 + inst/doc/vignette.html | 332 ++++++++++++------------------------------------- 5 files changed, 102 insertions(+), 251 deletions(-)
Title: Analysis of Growth Data
Description: Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23
2012, Rotterdam.
Author: Stef van Buuren <stef.vanbuuren@tno.nl>
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between AGD versions 0.32 dated 2015-01-11 and 0.35 dated 2015-05-28
DESCRIPTION | 8 MD5 | 44 ++--- R/AGD-package.R | 71 +++++--- R/agd.r | 412 ++++++++++++++++++++++++++------------------------ R/wp.twin.r | 6 data/boys7482.rda |binary data/nl4.hgt.rda |binary data/nl4.wgt.rda |binary data/who.bmi.rda |only data/who.hgt.rda |only data/who.wfh.rda |only data/who.wfl.rda |only data/who.wgt.rda |binary inst/CITATION | 4 inst/NEWS | 9 + man/References-CDC.Rd | 3 man/References-NL3.Rd | 6 man/References-NL4.Rd | 6 man/References-WHO.Rd | 47 ++++- man/ageGrid.Rd | 3 man/boys7482.Rd | 9 - man/extractLMS.Rd | 3 man/wp.twin.Rd | 8 man/y2z.Rd | 8 man/z2y.Rd | 3 25 files changed, 359 insertions(+), 291 deletions(-)
Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.utils versions 2.0.2 dated 2015-04-27 and 2.1.0 dated 2015-05-28
DESCRIPTION | 12 +++--- MD5 | 73 +++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS | 16 ++++++++ R/OperatorDelayedAssign.R | 16 +++++++- R/captureOutput.R | 30 +++++++++++----- R/compressPDF.R |only R/copyFile.R | 15 +++++++- R/createLink.R | 2 - R/renameFile.R | 8 +++- R/withCapture.R | 1 R/withRepos.R | 6 +++ man/PERCENTLT_-PERCENT.Rd | 18 +++++++--- man/captureOutput.Rd | 31 ++++++++++++++++- man/compressPDF.Rd |only man/copyFile.Rd | 4 +- man/getCharacters.Arguments.Rd | 5 ++ man/renameFile.Rd | 4 +- man/withRepos.Rd | 6 +++ tests/GString.R | 4 ++ tests/OperatorDelayedAssign.R | 10 +++++ tests/Verbose.R | 2 + tests/callHooks.R | 10 +++++ tests/captureOutput.R | 46 +++++++++++++++---------- tests/cmdArgs.R | 10 +++++ tests/compressFile.R | 21 +++++++++++ tests/compressPDF.R |only tests/copyRenameFile.R | 28 +++++++++++++++ tests/dimNA.R | 6 +++ tests/displayCode.R | 20 +++++++++++ tests/doCall.R |only tests/gcat.R | 27 ++++++++++++++- tests/insert.R | 7 +++ tests/listDirectory.R | 5 ++ tests/loadObject.R | 8 ++++ tests/readBinFragments.R | 9 ++++- tests/resetWarnings.R |only tests/seqToHumanReadable.R | 6 ++- tests/systemR.R | 7 +++ tests/writeDataFrame.R | 4 ++ 40 files changed, 391 insertions(+), 87 deletions(-)
Title: Interface Between R and Qt
Description: Dynamic bindings to the Qt library for calling Qt
methods and extending Qt classes from R. Other packages build upon 'qtbase'
to provide special-purpose high-level interfaces to specific parts of Qt.
Author: Michael Lawrence, Deepayan Sarkar
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between qtbase versions 1.0.4 dated 2012-03-03 and 1.0.9 dated 2015-05-28
qtbase-1.0.4/qtbase/.gitignore |only qtbase-1.0.4/qtbase/inst/doc/.Rhistory |only qtbase-1.0.4/qtbase/inst/qdoc/qtbase.qhc |only qtbase-1.0.4/qtbase/questions.txt |only qtbase-1.0.4/qtbase/vignettes/.gitignore |only qtbase-1.0.9/qtbase/DESCRIPTION | 16 qtbase-1.0.9/qtbase/INSTALL | 73 ++- qtbase-1.0.9/qtbase/MD5 | 77 ++-- qtbase-1.0.9/qtbase/NAMESPACE | 1 qtbase-1.0.9/qtbase/R/class.R | 10 qtbase-1.0.9/qtbase/R/metaobject.R | 7 qtbase-1.0.9/qtbase/R/object.R | 4 qtbase-1.0.9/qtbase/R/zzz.R | 27 + qtbase-1.0.9/qtbase/build |only qtbase-1.0.9/qtbase/inst/doc/qtbase.R |only qtbase-1.0.9/qtbase/inst/doc/qtbase.pdf |binary qtbase-1.0.9/qtbase/kdebindings/CMakeLists.txt | 24 - qtbase-1.0.9/qtbase/kdebindings/generator/CMakeLists.txt | 3 qtbase-1.0.9/qtbase/kdebindings/generator/generators/smoke/CMakeLists.txt | 3 qtbase-1.0.9/qtbase/kdebindings/generator/generators/smoke/generator_smoke.cpp | 3 qtbase-1.0.9/qtbase/kdebindings/generator/name_compiler.cpp | 2 qtbase-1.0.9/qtbase/kdebindings/generator/parser/CMakeLists.txt | 3 qtbase-1.0.9/qtbase/kdebindings/generator/parser/name_compiler.cpp | 2 qtbase-1.0.9/qtbase/kdebindings/generator/parser/parser.cpp | 7 qtbase-1.0.9/qtbase/kdebindings/smoke/qt/CMakeLists.txt | 9 qtbase-1.0.9/qtbase/kdebindings/smoke/qt/smokeconfig.xml | 2 qtbase-1.0.9/qtbase/man/RQtObject.Rd | 1 qtbase-1.0.9/qtbase/src/CMakeLists.txt | 31 + qtbase-1.0.9/qtbase/src/DataFrameModel.cpp | 24 - qtbase-1.0.9/qtbase/src/DataFrameModel.hpp | 4 qtbase-1.0.9/qtbase/src/EventLoop.cpp | 184 +++++++++- qtbase-1.0.9/qtbase/src/InstanceObjectTable.cpp | 2 qtbase-1.0.9/qtbase/src/Makefile | 19 - qtbase-1.0.9/qtbase/src/Makefile.common |only qtbase-1.0.9/qtbase/src/Makefile.win | 29 - qtbase-1.0.9/qtbase/src/MocMethod.cpp | 8 qtbase-1.0.9/qtbase/src/RTextFormattingDelegate.cpp | 110 +++++ qtbase-1.0.9/qtbase/src/RTextFormattingDelegate.hpp | 6 qtbase-1.0.9/qtbase/src/SmokeObject.cpp | 49 +- qtbase-1.0.9/qtbase/src/SmokeObject.hpp | 6 qtbase-1.0.9/qtbase/src/SmokeType.hpp | 3 qtbase-1.0.9/qtbase/src/convert.cpp | 67 ++- qtbase-1.0.9/qtbase/src/mkdef.sh | 2 qtbase-1.0.9/qtbase/src/module.cpp | 10 qtbase-1.0.9/qtbase/src/type-handlers.cpp | 4 45 files changed, 622 insertions(+), 210 deletions(-)
Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>
Diff between fishmethods versions 1.7-0 dated 2014-11-18 and 1.8-0 dated 2015-05-28
DESCRIPTION | 12 - MD5 | 26 ++- R/bt.log.R |only R/catchmsy.R | 391 +++++++++++++++++++++++++------------------------------ R/dbsra.R |only R/dlproj.R |only R/gap.R |only R/grotag.R | 2 R/mort.al.R |only data/cowcod.rda |only data/tanaka.rda |only man/bt.log.Rd |only man/catchmsy.Rd | 159 ++++++++++++---------- man/clus.mean.Rd | 3 man/cowcod.Rd |only man/dbsra.Rd |only man/dlproj.Rd |only man/gap.Rd |only man/mort.al.Rd |only man/tanaka.Rd |only man/vblrt.Rd | 14 - 21 files changed, 306 insertions(+), 301 deletions(-)
Title: Process the Apache Web Server Log Combined Files
Description: Provides a function to process Apache Log Combined files. The main functionality is to extract data from log files to data frames.
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>
Diff between ApacheLogProcessor versions 0.1 dated 2015-05-08 and 0.1.3 dated 2015-05-28
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- R/ApacheLogProcessor.R | 23 +++++++++++++++++++---- man/read.apache.log.combined.Rd | 7 +++++-- 4 files changed, 31 insertions(+), 12 deletions(-)
More information about ApacheLogProcessor at CRAN
Permanent link
Title: Toy Example of S4 Package
Description: Illustration of the book "Petit Manuel de Programmation Orientee Objet sous R". The english version "A (Not so) Short Introduction to S4" is on CRAN, 'Contributed documentation'.
Author: Christophe Genolini
Maintainer: Christophe Genolini <genolini@u-paris10.fr>
Diff between packS4 versions 0.9.1 dated 2012-06-29 and 0.9.3 dated 2015-05-27
packS4-0.9.1/packS4/main.R |only packS4-0.9.3/packS4/DESCRIPTION | 18 +++++++++--------- packS4-0.9.3/packS4/MD5 | 14 ++++++++------ packS4-0.9.3/packS4/NAMESPACE | 6 ++++-- packS4-0.9.3/packS4/R/codeVerif.R |only packS4-0.9.3/packS4/R/global.R | 4 ++++ packS4-0.9.3/packS4/man/classCreator.Rd | 4 ++-- packS4-0.9.3/packS4/man/detectGlobal.Rd |only packS4-0.9.3/packS4/man/plot-methods.Rd | 2 +- packS4-0.9.3/packS4/man/tryBug.Rd |only 10 files changed, 28 insertions(+), 20 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>
Diff between nat versions 1.6.4 dated 2015-02-09 and 1.6.6 dated 2015-05-27
DESCRIPTION | 31 MD5 | 334 ++++----- NAMESPACE | 10 NEWS | 42 + R/cmtk-reformat.R | 40 - R/cmtk.R | 2 R/cmtk_geometry.R | 27 R/dotprops.R | 31 R/hxsurf.R | 75 +- R/im3d.R | 7 R/nat-data.R | 47 + R/neuron-io-neuroml.R | 2 R/neuron-io.R | 48 + R/neuron-plot.R | 103 ++ R/neuron.R | 6 R/neuronlist.R | 350 +++------- R/neuronlist_interactive_3d.R |only R/neuronlistfh.R | 2 R/xform.R | 97 ++ R/xformimage.R | 2 R/xformpoints.R | 13 README.md | 15 data/MBL.surf.rda |only man/Cell07PNs.Rd | 29 man/MBL.surf.Rd |only man/affmat2cmtkparams.Rd | 19 man/all.equal.dotprops.Rd | 24 man/all.equal.im3d.Rd | 27 man/all.equal.neuron.Rd | 39 - man/amiramesh-io.Rd | 42 - man/amiratype.Rd | 27 man/as.data.frame.neuronlist.Rd |only man/as.im3d.Rd | 51 - man/as.mesh3d.Rd | 26 man/as.neuronlist.Rd | 26 man/as.neuronlist.neuronlistfh.Rd | 7 man/boundingbox.Rd | 115 +-- man/c.neuronlist.Rd | 10 man/clampmax.Rd | 23 man/cmtk.bindir.Rd | 70 -- man/cmtk.call.Rd | 53 - man/cmtk.dof2mat.Rd | 23 man/cmtk.extract_affine.Rd | 17 man/cmtk.mat2dof.Rd | 28 man/cmtk.reformatx.Rd | 76 -- man/cmtk.statistics.Rd | 41 - man/cmtk.targetvolume.Rd | 25 man/cmtk.version.Rd | 17 man/cmtkparams2affmat.Rd | 33 man/cmtkreg.Rd | 42 - man/cmtkreglist.Rd | 29 man/coord2ind.Rd | 20 man/dotprops-arithmetic.Rd | 7 man/dotprops.Rd | 75 -- man/fileformats.Rd | 115 +-- man/find.neuron.Rd | 30 man/find.soma.Rd | 33 man/flip.Rd | 21 man/graph.nodes.Rd | 19 man/im3d-coords.Rd | 46 - man/im3d-io.Rd | 75 +- man/im3d.Rd | 83 +- man/image.im3d.Rd | 115 +-- man/imexpand.grid.Rd | 32 man/imscalebar.Rd | 32 man/imslice.Rd | 50 - man/ind2coord.Rd | 15 man/intersect.Rd | 14 man/is.amiramesh.Rd | 22 man/is.fijitraces.Rd | 18 man/is.neuroml.Rd | 14 man/is.neuronlist.Rd | 20 man/is.nrrd.Rd | 25 man/is.swc.Rd | 17 man/is.vaa3draw.Rd | 19 man/kcs20.Rd | 39 - man/materials.Rd | 32 man/mirror.Rd | 64 - man/nat-internal.Rd | 7 man/nat-package.Rd | 84 +- man/ndigest.Rd | 67 - man/neuron-arithmetic.Rd | 13 man/neuron.Rd | 116 +-- man/neuronlist-arithmetic.Rd | 13 man/neuronlist-dataframe-methods.Rd | 46 - man/neuronlist.Rd | 42 - man/neuronlistfh.Rd | 256 +++---- man/ngraph.Rd | 114 +-- man/nlapply.Rd | 107 +-- man/nlscan.Rd | 66 - man/nopen3d.Rd | 17 man/normalise_swc.Rd | 29 man/npop3d.Rd | 14 man/nrrd.voxdims.Rd | 18 man/origin.Rd | 43 - man/pan3d.Rd | 14 man/plot.neuron.Rd | 82 +- man/plot.neuronlist.Rd | 88 +- man/plot3d.Rd |only man/plot3d.boundingbox.Rd | 11 man/plot3d.dotprops.Rd | 57 - man/plot3d.hxsurf.Rd | 47 - man/plot3d.neuron.Rd | 53 - man/plot3d.neuronlist.Rd | 171 ++-- man/pointsinside.Rd | 26 man/potential_synapses.Rd | 25 man/projection.Rd | 69 - man/prune.Rd | 26 man/read.cmtk.Rd | 28 man/read.cmtkreg.Rd | 15 man/read.hxsurf.Rd | 80 +- man/read.landmarks.Rd | 74 -- man/read.morphml.Rd | 60 - man/read.neuron.Rd | 80 +- man/read.neuron.fiji.Rd | 21 man/read.neuron.neuroml.Rd | 16 man/read.neuron.swc.Rd | 18 man/read.neuronlistfh.Rd | 118 +-- man/read.neurons.Rd | 121 +-- man/read.nrrd.Rd | 33 man/read.vaa3draw.Rd | 14 man/remotesync.Rd | 35 - man/resample.Rd | 17 man/rootpoints.Rd | 19 man/scale.dotprops.Rd | 16 man/scale.neuron.Rd | 13 man/seglengths.Rd | 29 man/seglist.Rd | 62 - man/seglist2swc.Rd | 40 - man/segmentgraph.Rd | 32 man/setdiff.Rd | 23 man/spine.Rd | 34 man/sub-.neuronlistfh.Rd | 16 man/sub2ind.Rd | 7 man/subset.Rd |only man/subset.dotprops.Rd | 28 man/subset.hxsurf.Rd | 43 - man/subset.neuronlist.Rd | 42 - man/threshold.Rd | 56 - man/union.Rd | 16 man/unmask.Rd | 67 - man/voxdims.Rd | 48 - man/write.amiramesh.Rd | 27 man/write.cmtk.Rd | 28 man/write.cmtkreg.Rd | 28 man/write.hxsurf.Rd | 30 man/write.neuron.Rd | 50 - man/write.neuronlistfh.Rd | 59 - man/write.neurons.Rd | 57 - man/write.nrrd.Rd | 19 man/xform.Rd | 113 +-- man/xformimage.Rd | 81 +- man/xformpoints.Rd | 84 +- man/xyzmatrix.Rd | 64 + tests/testthat/test-cmtk-reformat.R | 11 tests/testthat/test-cmtk.R | 17 tests/testthat/test-cmtkreg.R | 6 tests/testthat/test-hxsurf.R | 19 tests/testthat/test-im3d.R | 5 tests/testthat/test-landmarks-io.R | 14 tests/testthat/test-neuroml-io.R | 10 tests/testthat/test-neuron-io.R | 23 tests/testthat/test-neuron.R | 29 tests/testthat/test-neuronlist.R | 59 + tests/testthat/test-neuronlistfh.R | 2 tests/testthat/test-potential_synapses.R | 1 tests/testthat/test-seglist.R | 7 tests/testthat/test-xform.R | 52 + tests/testthat/test-xformimage.R | 40 + tests/testthat/testdata/amira/tetrahedron_badtrianglenum.surf |only tests/testthat/testdata/amira/tetrahedron_nocol.surf |only tests/testthat/testdata/amira/tetrahedron_notriangles.surf |only tests/testthat/testdata/selfun_cell07.rds |only 173 files changed, 3680 insertions(+), 3552 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.8.7 dated 2015-03-05 and 1.8.8 dated 2015-05-27
DESCRIPTION | 18 MD5 | 53 +- NAMESPACE | 38 + R/Cpred.r | 3 R/base.r | 20 R/comprisk.ipw.r | 34 + R/comprisk.r | 332 ++++++++++--- R/cox.ipw.r | 23 R/glm-comprisk.r |only R/ipcw-residualmean.r |only R/predict-timereg.r | 88 ++- R/prop-odds-subdist.r | 80 ++- R/restricted.residual.mean.r | 38 + R/two-stage-reg.r | 10 man/Gprop.odds.Rd | 3 man/comp.risk.Rd | 51 +- man/dynreg.Rd | 2 man/internal-addreg.Rd | 15 man/plot.dynreg.Rd | 3 man/prep.comp.risk.Rd |only man/prop.odds.subdist.Rd | 4 man/res.mean.Rd |only man/restricted.residual.mean.Rd | 9 man/wald.test.Rd | 7 src/comprisk.c | 1020 +++++++++++++++++++++------------------- src/cox-aalen-lwy-resamp.c |only src/cox-aalen-stratum.c |only src/ipcw-residualmean.c |only src/matrix.h | 16 src/pred.c | 71 +- src/prop-odds-subdist2.c | 3 31 files changed, 1281 insertions(+), 660 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.11-2 dated 2015-05-26 and 0.11-4 dated 2015-05-27
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/codeGeno.r | 13 +++++++++++-- R/create.gpData.r | 2 +- man/read.vcf2list.Rd | 2 +- 5 files changed, 23 insertions(+), 14 deletions(-)
Title: Uses an Archive to Amend Previous Stages of a Pipe using Current
Output
Description: Remedies a common problem in piping: not having access to
intermediate outputs of the pipe. Within a "loop", a piping intermediate
is stored in a stack archive, data is processed, and then both the
stored intermediate and the current output are reintegrated using an
"ending" function. Two special ending functions are provided: amend and
insert. However, any ending function can be specified, including merge
functions, join functions, setNames(), etc. This framework allows the
following work-flow: focus on a particular aspect or section of a
data set, conduct specific operations, and then reintegrate changes into
the whole.
Author: Brandon Taylor
Maintainer: Brandon Taylor <Brandon.Taylor221@gmail.com>
Diff between loopr versions 1.0.0 dated 2015-05-07 and 1.0.1 dated 2015-05-27
loopr-1.0.0/loopr/man/loop.Rd |only loopr-1.0.0/loopr/man/loopr-package.Rd |only loopr-1.0.0/loopr/man/stack.Rd |only loopr-1.0.1/loopr/DESCRIPTION | 12 loopr-1.0.1/loopr/MD5 | 29 - loopr-1.0.1/loopr/NAMESPACE | 6 loopr-1.0.1/loopr/R/loopr.R | 36 +- loopr-1.0.1/loopr/build/vignette.rds |binary loopr-1.0.1/loopr/inst/doc/Looping.R | 88 ++++- loopr-1.0.1/loopr/inst/doc/Looping.Rmd | 118 ++++++- loopr-1.0.1/loopr/inst/doc/Looping.html | 482 +++++++++++++++++++++++++++----- loopr-1.0.1/loopr/man/amend.Rd | 2 loopr-1.0.1/loopr/man/amendColumns.Rd | 2 loopr-1.0.1/loopr/man/fillColumns.Rd | 2 loopr-1.0.1/loopr/man/insert.Rd | 2 loopr-1.0.1/loopr/man/loopClass.Rd |only loopr-1.0.1/loopr/man/stackClass.Rd |only loopr-1.0.1/loopr/vignettes/Looping.Rmd | 118 ++++++- 18 files changed, 705 insertions(+), 192 deletions(-)
Title: Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Description: Functions to compare two or more survival curves with:
a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>
Diff between FHtest versions 1.1 dated 2013-12-02 and 1.2 dated 2015-05-27
DESCRIPTION | 19 +++--- MD5 | 18 +++--- NAMESPACE | 8 ++ R/FHtesticp.default.R | 148 +++++++++++++++++++++++++------------------------- R/FHtestics.default.R | 6 +- man/FHtest-package.Rd | 10 +-- man/FHtesticp.Rd | 24 ++++---- man/FHtestics.Rd | 16 ++--- man/FHtestrcc.Rd | 10 +-- man/FHtestrcp.Rd | 16 ++--- 10 files changed, 144 insertions(+), 131 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.0.0 dated 2015-04-22 and 1.1.0 dated 2015-05-27
DESCRIPTION | 8 ++--- MD5 | 9 +++-- R/DiscSurvEvaluation.R | 59 ++++++++++++++++++++++++++++++++++++- man/adjDevResidShort.Rd |only man/devResidShort.Rd |only man/gumbel.Rd | 6 --- tests/UnitTestsDiscSurvEvalShort.R |only 7 files changed, 69 insertions(+), 13 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by Wobbrock et al.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.9.3 dated 2014-12-02 and 0.9.4 dated 2015-05-27
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ tests/testthat.R | 2 -- tests/testthat/test.art.R | 1 + tests/testthat/test.artlm.R | 17 ++++++++--------- tests/testthat/test.parse.art.formula.R | 1 + tests/testthat/test.summary.art.R | 1 + 7 files changed, 25 insertions(+), 25 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.1.0 dated 2015-05-07 and 3.1.1 dated 2015-05-27
DESCRIPTION | 6 MD5 | 47 - NEWS | 13 R/check.index.R | 12 R/elegend.R |only R/gbm.R | 2 R/lib.R | 8 R/meta.R | 2 R/plot.gbmx.R | 13 R/plot.glmnetx.R | 2 R/plotmo.R | 4 R/plotres.R | 2 R/plotresids.R | 4 R/residuals.R | 2 R/xy.R | 4 inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/test.emma.Rout.save | 164 +++--- inst/slowtests/test.non.earth.R | 3 inst/slowtests/test.non.earth.Rout.save | 71 +- inst/slowtests/test.plotmo.Rout.save | 761 ++++++++++++++---------------- inst/slowtests/test.plotmo.args.Rout.save | 2 inst/slowtests/test.plotmo3.Rout.save | 36 - inst/slowtests/test.plotres.Rout.save | 5 man/plotmo.misc.Rd | 25 25 files changed, 598 insertions(+), 590 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the 'evd' package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott <carl.scarrott@canterbury.ac.nz>
Diff between evmix versions 2.5 dated 2015-04-29 and 2.6 dated 2015-05-27
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/evmix-package.r | 4 ++-- R/pickandsplot.r | 10 +++++----- inst/CITATION | 2 +- inst/doc/Rd2.pdf |binary man/evmix-package.Rd | 4 ++-- man/pickandsplot.Rd | 12 ++++++------ 8 files changed, 28 insertions(+), 28 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.4 dated 2014-11-18 and 1.0.5 dated 2015-05-27
DESCRIPTION | 24 ++++++++++++++++-------- MD5 | 10 +++++----- NEWS | 4 ++++ R/CCAGFA.R | 20 +++++++++++--------- R/CCAGFAtools.R | 14 +++++++------- man/CCAGFA-package.Rd | 4 ++-- 6 files changed, 45 insertions(+), 31 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 0.65-0 dated 2014-10-07 and 0.65-1 dated 2015-05-27
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 4 ++-- R/ordiplot3d.R | 2 +- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Model-Based Clustering and Classification with the Multivariate
t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews <jeffrey.andrews@macewan.ca>
Diff between teigen versions 2.0.8 dated 2015-01-29 and 2.0.81 dated 2015-05-27
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/teigen.R | 3 ++- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Polygon Clipping
Description: R port of the Clipper library. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Also computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines.
Author: Angus Johnson. Ported to R by Adrian Baddeley and Brian Ripley.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between polyclip versions 1.3-0 dated 2014-05-05 and 1.3-2 dated 2015-05-27
DESCRIPTION | 8 +-- MD5 | 12 ++--- configure | 114 +++++++++++++++++++++++++++--------------------------- configure.ac | 87 +++++++++++++++++++++++++---------------- src/Makevars.in | 1 src/clipper.cpp | 25 +++++++---- src/interface.cpp | 1 7 files changed, 137 insertions(+), 111 deletions(-)
Title: Simulation-Based False Discovery Rate in RNA-Seq
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between empiricalFDR.DESeq2 versions 1.0.1 dated 2015-03-29 and 1.0.3 dated 2015-05-27
empiricalFDR.DESeq2-1.0.1/empiricalFDR.DESeq2/R/fdrBiCurve_work.R |only empiricalFDR.DESeq2-1.0.1/empiricalFDR.DESeq2/R/fdrTable_work.R |only empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/DESCRIPTION | 8 +++--- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/MD5 | 12 ++++------ empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/empiricalFDR.R | 4 +-- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/fdrBiCurve.R | 2 - empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/fdrTable.R | 5 ++-- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/man/empiricalFDR.DESeq2-package.Rd | 4 +-- 8 files changed, 17 insertions(+), 18 deletions(-)
More information about empiricalFDR.DESeq2 at CRAN
Permanent link
Title: Coenocline Simulation
Description: Simulate species occurrence and abundances (counts) along
gradients.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [ctb],
Francisco Rodriguez-Sanchez [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between coenocliner versions 0.1-0 dated 2014-07-31 and 0.2-0 dated 2015-05-27
coenocliner-0.1-0/coenocliner/inst/tests |only coenocliner-0.2-0/coenocliner/DESCRIPTION | 16 coenocliner-0.2-0/coenocliner/MD5 | 60 +- coenocliner-0.2-0/coenocliner/NAMESPACE | 17 coenocliner-0.2-0/coenocliner/R/coenocline.R | 85 ++- coenocliner-0.2-0/coenocliner/R/coenocliner.R | 2 coenocliner-0.2-0/coenocliner/R/distributions.R | 55 +- coenocliner-0.2-0/coenocliner/R/extractor-functions.R |only coenocliner-0.2-0/coenocliner/R/persp.coenocline.R |only coenocliner-0.2-0/coenocliner/R/plot.coenocline.R |only coenocliner-0.2-0/coenocliner/R/response-functions.R | 2 coenocliner-0.2-0/coenocliner/R/utils.R | 139 ++++++ coenocliner-0.2-0/coenocliner/README.md | 11 coenocliner-0.2-0/coenocliner/build/vignette.rds |binary coenocliner-0.2-0/coenocliner/inst/ChangeLog | 13 coenocliner-0.2-0/coenocliner/inst/NEWS | 41 + coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.R | 32 - coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.Rnw | 60 +- coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.pdf |binary coenocliner-0.2-0/coenocliner/man/coenocline.Rd | 61 +- coenocliner-0.2-0/coenocliner/man/coenocliner-internal.Rd |only coenocliner-0.2-0/coenocliner/man/coenocliner.Rd | 5 coenocliner-0.2-0/coenocliner/man/distributions.Rd | 21 coenocliner-0.2-0/coenocliner/man/expand.Rd | 3 coenocliner-0.2-0/coenocliner/man/locations.Rd |only coenocliner-0.2-0/coenocliner/man/persp.coenocline.Rd |only coenocliner-0.2-0/coenocliner/man/plot.coenocline.Rd |only coenocliner-0.2-0/coenocliner/man/showParams.Rd | 3 coenocliner-0.2-0/coenocliner/man/simJamil.Rd | 3 coenocliner-0.2-0/coenocliner/man/species-response.Rd | 3 coenocliner-0.2-0/coenocliner/man/stack.coenocline.Rd |only coenocliner-0.2-0/coenocliner/tests/Examples/coenocliner-Ex.Rout.save | 229 +++++++++- coenocliner-0.2-0/coenocliner/tests/test-all.R | 3 coenocliner-0.2-0/coenocliner/tests/testthat |only coenocliner-0.2-0/coenocliner/vignettes/coenocliner.Rnw | 60 +- 35 files changed, 702 insertions(+), 222 deletions(-)
Title: Bubble Chart to Compare Biological Annotations by using DAVID
Description: R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service. It provides R functions to perform enrichment analysis (via DAVID - http://david.abcc.ncifcrf.gov) on several gene lists at once, and then visualizing all the results in one generated figure that allows R users to compare the annotations found for each list.
Author: Vittorio Fortino and Dario Greco
Maintainer: Vittorio Fortino <vittorio.fortino@ttl.fi>
Diff between BACA versions 0.99.0 dated 2015-01-10 and 1.3 dated 2015-05-27
BACA-0.99.0/BACA/inst/doc/BACA.R |only BACA-0.99.0/BACA/inst/doc/BACA.Rmd |only BACA-0.99.0/BACA/vignettes |only BACA-1.3/BACA/DESCRIPTION | 12 ++++++------ BACA-1.3/BACA/MD5 | 19 ++++++++++--------- BACA-1.3/BACA/R/bbplots.R | 10 ++++++++-- BACA-1.3/BACA/build/vignette.rds |binary BACA-1.3/BACA/inst/CITATION |only BACA-1.3/BACA/inst/doc/BACA.html | 32 +++++++++++++------------------- BACA-1.3/BACA/inst/doc/BACA.md | 33 ++++++++++++--------------------- BACA-1.3/BACA/inst/doc/BACA.pdf |only BACA-1.3/BACA/inst/doc/figure |only BACA-1.3/BACA/man/BBplot.Rd | 14 ++++++++++---- 13 files changed, 59 insertions(+), 61 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.13.0 dated 2015-01-20 and 2.13.2 dated 2015-05-27
DESCRIPTION | 38 MD5 | 185 - NAMESPACE | 1176 ++++++++++ NEWS | 18 R/021.dynamic_imports.R | 569 ++-- R/999.package.R | 16 R/AffinePlm.R | 5 R/AffymetrixCdfFile.MONOCELL.R | 22 R/AffymetrixCelSet.R | 2 R/AffymetrixCelSet.convertToUnique.R | 4 R/ChipEffectSet.calculateBaseline.R | 4 R/CnagCfhSet.R | 2 R/CopyNumberChromosomalModel.applyCCF.R | 4 R/GcContentNormalization2.plotCovariateEffects.R | 2 R/SnpChipEffectSet.exportTotalAndFracB.R | 2 R/doCRMAv1.R | 2 R/doCRMAv2.R | 6 R/doGCRMA.R | 4 R/doRMA.R | 4 R/setupExampleData.R | 83 inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R | 3 inst/vignettes/replication-CRLMM/R/01a.downloadAnnotData.R | 38 inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R | 74 inst/vignettes/replication-GCRMA/R/01a.downloadAnnotData.R | 38 inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R | 74 inst/vignettes/replication-MAT/R/01a.downloadAnnotationData.R | 66 inst/vignettes/replication-MAT/R/01b.downloadRawData.R | 148 - inst/vignettes/replication-RMA/R/01a.downloadAnnotationData.R | 32 inst/vignettes/replication-RMA/R/01b.downloadRawData.R | 82 man/AbstractProbeSequenceNormalization.Rd | 2 man/AdditiveCovariatesNormalization.Rd | 2 man/AffinePlm.Rd | 5 man/AffymetrixCdfFile.Rd | 16 man/AffymetrixCelFile.Rd | 20 man/AffymetrixCelSet.Rd | 26 man/AffymetrixCelSetReporter.Rd | 2 man/AffymetrixCnChpSet.Rd | 4 man/AffymetrixFileSet.Rd | 6 man/AffymetrixPgfFile.Rd | 2 man/AlleleSummation.Rd | 2 man/AllelicCrosstalkCalibration.Rd | 2 man/AromaChipTypeAnnotationFile.Rd | 4 man/ArrayExplorer.Rd | 6 man/BackgroundCorrection.Rd | 2 man/ChipEffectFile.Rd | 2 man/ChipEffectGroupMerge.Rd | 2 man/ChipEffectSet.Rd | 6 man/CnChipEffectSet.Rd | 2 man/CnagCfhFile.Rd | 4 man/CnagCfhSet.Rd | 10 man/CrlmmParametersSet.Rd | 2 man/DChipDcpSet.Rd | 4 man/DChipGenomeInformation.Rd | 2 man/DChipQuantileNormalization.Rd | 2 man/DChipSnpInformation.Rd | 2 man/ExonChipEffectSet.Rd | 2 man/FirmaModel.Rd | 4 man/FirmaSet.Rd | 2 man/FragmentEquivalentClassNormalization.Rd | 2 man/FragmentLengthNormalization.Rd | 2 man/GcContentNormalization.Rd | 2 man/GcRmaBackgroundCorrection.Rd | 2 man/GenericReporter.Rd | 6 man/GenomeInformation.Rd | 10 man/LimmaBackgroundCorrection.Rd | 2 man/MatNormalization.Rd | 2 man/MatSmoothing.Rd | 2 man/Model.Rd | 14 man/OpticalBackgroundCorrection.Rd | 2 man/ParameterCelSet.Rd | 6 man/ProbeLevelModel.Rd | 6 man/QualityAssessmentModel.Rd | 4 man/QualityAssessmentSet.Rd | 2 man/QuantileNormalization.Rd | 2 man/ReseqCrosstalkCalibration.Rd | 2 man/ResidualSet.Rd | 2 man/RmaBackgroundCorrection.Rd | 2 man/ScaleNormalization.Rd | 2 man/ScaleNormalization3.Rd | 2 man/SingleArrayUnitModel.Rd | 2 man/SnpChipEffectSet.Rd | 2 man/SnpInformation.Rd | 6 man/SpatialReporter.Rd | 2 man/TransformReport.Rd | 12 man/UgpGenomeInformation.Rd | 2 man/UnitModel.Rd | 2 man/UnitTypeScaleNormalization.Rd | 2 man/WeightsSet.Rd | 2 man/aroma.affymetrix-package.Rd | 15 man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd | 178 - man/createMonocellCdf.AffymetrixCdfFile.Rd | 2 man/setupExampleData.AromaAffymetrix.Rd | 10 man/writeCdf.AffyGenePDInfo.Rd | 96 tests/AffymetrixCdfFile.R |only 94 files changed, 2251 insertions(+), 1008 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-26 1.1
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in NeXML format. The
package should add new functionality to R such as the possibility to
manipulate NeXML objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.2 dated 2015-05-01 and 2.0.3 dated 2015-05-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ tests/testthat/test_simmap.R | 25 ++++++++++--------------- 4 files changed, 21 insertions(+), 22 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.15-145 dated 2015-05-25 and 0.15-146 dated 2015-05-26
Rhpc-0.15-145/Rhpc/src/windows |only Rhpc-0.15-146/Rhpc/ChangeLog | 2 + Rhpc-0.15-146/Rhpc/DESCRIPTION | 18 +++++----- Rhpc-0.15-146/Rhpc/MD5 | 31 ++++++++---------- Rhpc-0.15-146/Rhpc/README | 17 +++++++++ Rhpc-0.15-146/Rhpc/cleanup | 6 +++ Rhpc-0.15-146/Rhpc/man/Rhpc-package.Rd | 2 - Rhpc-0.15-146/Rhpc/src/Makevars.win | 20 +++++------ Rhpc-0.15-146/Rhpc/src/RhpcMPI.c | 2 - Rhpc-0.15-146/Rhpc/src/RhpcMPIWorkerCall.h | 2 - Rhpc-0.15-146/Rhpc/src/RhpcMPIlapplyLB.h | 2 - Rhpc-0.15-146/Rhpc/src/RhpcMPIlapplyseq.h | 2 - Rhpc-0.15-146/Rhpc/src/worker/Makefile.win | 10 ++--- Rhpc-0.15-146/Rhpc/src/worker/RhpcWorker.c | 2 - Rhpc-0.15-146/Rhpc/src/worker/RhpcWorker_LapplyLB.h | 2 - Rhpc-0.15-146/Rhpc/src/worker/RhpcWorker_Lapplyseq.h | 2 - Rhpc-0.15-146/Rhpc/src/worker/RhpcWorker_WorkerCall.h | 2 - 17 files changed, 73 insertions(+), 49 deletions(-)
Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the
language at a deeper level.
Author: Hadley Wickham [aut, cre],
R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pryr versions 0.1 dated 2014-07-25 and 0.1.1 dated 2015-05-26
DESCRIPTION | 20 +- MD5 | 106 +++++++-------- NAMESPACE | 2 R/RcppExports.R | 6 R/explicit-promise.R | 32 ---- R/inspect.r | 7 + R/s3.r | 10 + README.md | 8 - man/as.envlist.Rd | 3 man/assign-active.Rd | 3 man/assign-constant.Rd | 3 man/assign-delayed.Rd | 3 man/bytes.Rd | 3 man/call_tree.Rd | 3 man/compose.Rd | 3 man/dots.Rd | 3 man/enclosing_env.Rd | 3 man/explicit.Rd | 33 ---- man/f.Rd | 3 man/fget.Rd | 3 man/find_funs.Rd | 3 man/find_uses.Rd | 3 man/ftype.Rd | 3 man/inspect.Rd | 11 - man/is_promise.Rd | 3 man/is_s3_generic.Rd | 7 - man/make_call.Rd | 3 man/make_function.Rd | 3 man/mem_change.Rd | 3 man/mem_used.Rd | 3 man/method_from_call.Rd | 3 man/modify_call.Rd | 3 man/modify_lang.Rd | 3 man/names_c.Rd | 3 man/object_size.Rd | 7 - man/otype.Rd | 3 man/parent_promise.Rd | 3 man/parenv.Rd | 3 man/parenvs.Rd | 3 man/partial.Rd | 3 man/print.envlist.Rd | 3 man/rebind.Rd | 3 man/rls.Rd | 3 man/show_c_source.Rd | 3 man/standardise_call.Rd | 3 man/subs.Rd | 3 man/substitute_q.Rd | 3 man/track_copy.Rd | 3 man/unenclose.Rd | 3 man/uneval.Rd | 3 man/where.Rd | 3 src/RcppExports.cpp | 327 +++++++++++++++++------------------------------- src/bytes.cpp | 6 src/inspect.cpp | 4 54 files changed, 299 insertions(+), 404 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Diff between laGP versions 1.1-3 dated 2014-10-31 and 1.1-5 dated 2015-05-26
ChangeLog | 34 + DESCRIPTION | 12 INSTALL | 8 MD5 | 87 +-- NAMESPACE | 4 R/auglag.R | 94 ++- R/gp.R | 49 - R/gp_sep.R | 137 ++++ R/laGP.R | 2 R/parallel.R | 2 R/prior.R | 10 R/util.R | 18 build/vignette.rds |binary demo/00Index | 1 demo/ALfhat.R |only inst/doc/laGP.R | 565 +++++++++----------- inst/doc/laGP.Rnw | 1430 ++++++++++++++++++++++++++-------------------------- inst/doc/laGP.pdf |binary man/aGP.Rd | 5 man/alcGP.Rd | 5 man/darg.Rd | 11 man/deleteGP.Rd | 4 man/discrep.est.Rd | 4 man/fcalib.Rd | 1 man/laGP.Rd | 5 man/llikGP.Rd | 4 man/mleGP.Rd | 12 man/newGP.Rd | 13 man/optim.auglag.Rd | 54 + man/predGP.Rd | 13 src/covar.c | 39 + src/covar.h | 5 src/covar_sep.c | 92 +++ src/covar_sep.h | 11 src/gp.c | 133 +--- src/gp.h | 5 src/gp_sep.c | 426 +++++++++++++++ src/gp_sep.h | 10 src/ieci.c | 82 +- src/ieci.h | 8 src/laGP.c | 8 src/matrix.c | 34 + src/matrix.h | 1 vignettes/laGP.Rnw | 1430 ++++++++++++++++++++++++++-------------------------- vignettes/laGP.bib | 167 +++++- 45 files changed, 2998 insertions(+), 2037 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.1 dated 2015-05-17 and 0.2 dated 2015-05-26
DESCRIPTION | 6 +- MD5 | 22 +++++----- NAMESPACE | 3 - R/core.R | 29 ++++++++++++-- R/helpers.R | 9 ++++ man/infuse.Rd | 18 ++++++-- man/print.infuse.Rd |only man/print_requested_params.Rd | 2 man/read_template.Rd | 2 man/trim.Rd | 2 man/variables_requested.Rd | 2 tests/testthat/test_core_functionality.R | 58 +++++++++++++++++++++++++--- tests/testthat/test_helpers_functionality.R |only 13 files changed, 120 insertions(+), 33 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear and ordinal mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.1.0 dated 2015-05-08 and 0.2.0 dated 2015-05-26
DESCRIPTION | 14 +-- MD5 | 47 ++++++----- NAMESPACE | 17 ++++ R/bugs.R | 19 +--- R/data.docu.R | 46 +++++----- R/extract.old.R |only R/main.R | 173 +++++++++++++++++++++-------------------- R/s3.generics.R |only R/s3.methods.R |only R/stan.R | 80 +++++++++--------- R/support.export.R | 76 ++++-------------- R/support.internal.R | 73 +++++++++++++---- README.md | 63 ++++++++------ man/VarCorr.Rd |only man/brm.Rd | 104 ++++++++++++------------ man/brm.data.Rd | 6 - man/brm.pars.Rd | 12 +- man/brm.plot.Rd | 18 +--- man/brms-package.Rd | 10 +- man/brmsfit-class.Rd |only man/epilepsy.Rd | 16 +-- man/fixef.Rd |only man/inhaler.Rd | 14 +-- man/kidney.Rd | 16 +-- man/ngrps.Rd |only man/plot.brmsfit.Rd |only man/print.brmsfit.Rd |only man/ranef.Rd |only man/summary.brmsfit.Rd |only tests/testthat/tests.support.R | 2 30 files changed, 429 insertions(+), 377 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for arXiv, a repository of
electronic preprints for computer science, mathematics, physics,
quantitative biology, quantitative finance, and statistics.
Author: Karthik Ram [aut],
Karl Broman [aut, cre]
Maintainer: Karl Broman <kbroman@biostat.wisc.edu>
Diff between aRxiv versions 0.5.8 dated 2014-12-28 and 0.5.10 dated 2015-05-26
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- R/arxiv_count.R | 6 ++++-- R/arxiv_search.R | 8 +++++--- R/query_util.R | 7 +++++++ build/vignette.rds |binary data/arxiv_cats.RData |binary data/query_terms.RData |binary man/arxiv_cats.Rd | 2 +- man/arxiv_count.Rd | 2 +- man/arxiv_open.Rd | 2 +- man/arxiv_search.Rd | 2 +- man/can_arxiv_connect.Rd | 2 +- man/query_terms.Rd | 2 +- tests/testthat/test-clean.R | 14 ++++++++++++++ 17 files changed, 59 insertions(+), 34 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.10-5 dated 2014-11-25 and 0.11-2 dated 2015-05-26
DESCRIPTION | 21 +-- MD5 | 168 ++++++++++++++++++++++++-- NAMESPACE | 42 ++++-- R/codeGeno.r | 257 +++++++++++++++++++++++++++++------------ R/create.gpData.r | 30 ++-- R/crossVal.r | 5 R/discard.markers.r | 19 +-- R/kinship.r | 215 ++++++++++++++++++---------------- R/plot.relationshipMatrix.r | 57 ++++----- R/read.write.vcf.r |only R/simul.pedigree.r | 24 ++- R/summary.relationshipMatrix.r | 8 - inst/java |only java |only man/codeGeno.Rd | 35 ++--- man/kinship.Rd | 40 ++++-- man/plot.relationshipMatrix.Rd | 11 - man/read.vcf2list.Rd |only man/read.vcf2matrix.Rd |only man/write.vcf.Rd |only vignettes/Makefile | 2 21 files changed, 628 insertions(+), 306 deletions(-)
Title: Utilities for Formulas, Expressions, Calls and Other Objects
Description: These utilities facilitate the programmatic manipulations of
formulas, expressions,calls, names, symbols and other objects.
Author: Christopher Brown
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between formula.tools versions 1.3.4 dated 2014-03-20 and 1.5.2 dated 2015-05-26
formula.tools-1.3.4/formula.tools/ChangeLog |only formula.tools-1.3.4/formula.tools/R/lhs.R |only formula.tools-1.3.4/formula.tools/R/op.R |only formula.tools-1.3.4/formula.tools/R/rhs.R |only formula.tools-1.3.4/formula.tools/R/which.class.R |only formula.tools-1.3.4/formula.tools/inst |only formula.tools-1.3.4/formula.tools/man/formula.parts-methods.Rd |only formula.tools-1.3.4/formula.tools/man/formula.tools-package.Rd |only formula.tools-1.3.4/formula.tools/man/get.vars-methods.Rd |only formula.tools-1.3.4/formula.tools/man/which.class.Rd |only formula.tools-1.3.4/formula.tools/tests/run-all.R |only formula.tools-1.5.2/formula.tools/DESCRIPTION | 32 +- formula.tools-1.5.2/formula.tools/MD5 | 62 ++-- formula.tools-1.5.2/formula.tools/NAMESPACE | 26 + formula.tools-1.5.2/formula.tools/NEWS |only formula.tools-1.5.2/formula.tools/R/as.character.formula.R | 32 ++ formula.tools-1.5.2/formula.tools/R/catcont.R |only formula.tools-1.5.2/formula.tools/R/get.vars.R | 66 +++- formula.tools-1.5.2/formula.tools/R/invert.R | 77 +++-- formula.tools-1.5.2/formula.tools/R/is.one.sided.R | 76 +++-- formula.tools-1.5.2/formula.tools/R/is.two.sided.R |only formula.tools-1.5.2/formula.tools/R/lhs.vars.R | 15 + formula.tools-1.5.2/formula.tools/R/op.type.R | 34 ++ formula.tools-1.5.2/formula.tools/R/parts.R |only formula.tools-1.5.2/formula.tools/R/parts.lhs.get.R |only formula.tools-1.5.2/formula.tools/R/parts.lhs.set.R |only formula.tools-1.5.2/formula.tools/R/parts.op.get.R |only formula.tools-1.5.2/formula.tools/R/parts.op.set.R |only formula.tools-1.5.2/formula.tools/R/parts.rhs.get.R |only formula.tools-1.5.2/formula.tools/R/parts.rhs.set.R |only formula.tools-1.5.2/formula.tools/R/rhs.vars.R | 14 - formula.tools-1.5.2/formula.tools/R/terms.R | 43 ++- formula.tools-1.5.2/formula.tools/R/zzz.R | 19 - formula.tools-1.5.2/formula.tools/README.md |only formula.tools-1.5.2/formula.tools/man/as.character.formula.Rd | 52 +-- formula.tools-1.5.2/formula.tools/man/catcont.Rd |only formula.tools-1.5.2/formula.tools/man/formula.parts.Rd |only formula.tools-1.5.2/formula.tools/man/get.vars.Rd |only formula.tools-1.5.2/formula.tools/man/invert-methods.Rd | 67 ++-- formula.tools-1.5.2/formula.tools/man/invert.Rd |only formula.tools-1.5.2/formula.tools/man/is.one.sided.Rd | 139 +++------- formula.tools-1.5.2/formula.tools/man/op.type.Rd |only formula.tools-1.5.2/formula.tools/man/terms.Rd | 73 ++--- formula.tools-1.5.2/formula.tools/tests/testthat |only formula.tools-1.5.2/formula.tools/tests/testthat.R |only 45 files changed, 487 insertions(+), 340 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.2-1 dated 2015-01-12 and 2.3-0 dated 2015-05-26
vegan-2.2-1/vegan/R/goodness.rda.R |only vegan-2.3-0/vegan/DESCRIPTION | 8 - vegan-2.3-0/vegan/MD5 | 172 ++++++++++++------------ vegan-2.3-0/vegan/NAMESPACE | 18 +- vegan-2.3-0/vegan/R/CCorA.R | 16 +- vegan-2.3-0/vegan/R/MDSrotate.R | 2 vegan-2.3-0/vegan/R/adipart.default.R | 18 +- vegan-2.3-0/vegan/R/adonis.R | 2 vegan-2.3-0/vegan/R/anosim.R | 2 vegan-2.3-0/vegan/R/anova.ccabyterm.R | 2 vegan-2.3-0/vegan/R/betadiver.R | 2 vegan-2.3-0/vegan/R/bioenv.default.R | 9 + vegan-2.3-0/vegan/R/capscale.R | 26 +-- vegan-2.3-0/vegan/R/cascadeKM.R | 3 vegan-2.3-0/vegan/R/cca.default.R | 43 +++--- vegan-2.3-0/vegan/R/centroids.cca.R | 11 - vegan-2.3-0/vegan/R/estimateR.default.R | 2 vegan-2.3-0/vegan/R/factorfit.R | 24 +-- vegan-2.3-0/vegan/R/fitspecaccum.R | 13 + vegan-2.3-0/vegan/R/goodness.cca.R | 72 ++++++---- vegan-2.3-0/vegan/R/make.commsim.R | 56 +++---- vegan-2.3-0/vegan/R/multipart.default.R | 38 ++--- vegan-2.3-0/vegan/R/nesteddisc.R | 4 vegan-2.3-0/vegan/R/nestedtemp.R | 6 vegan-2.3-0/vegan/R/ordiArrowMul.R | 26 ++- vegan-2.3-0/vegan/R/ordiArrowTextXY.R | 54 ++++++- vegan-2.3-0/vegan/R/ordiGetData.R | 2 vegan-2.3-0/vegan/R/ordiParseFormula.R | 23 ++- vegan-2.3-0/vegan/R/ordiR2step.R | 3 vegan-2.3-0/vegan/R/orditkplot.R | 20 ++ vegan-2.3-0/vegan/R/pcnm.R | 13 + vegan-2.3-0/vegan/R/permustats.R | 2 vegan-2.3-0/vegan/R/plot.cca.R | 2 vegan-2.3-0/vegan/R/plot.meandist.R | 14 + vegan-2.3-0/vegan/R/plot.radfit.frame.R | 6 vegan-2.3-0/vegan/R/plot.specaccum.R | 4 vegan-2.3-0/vegan/R/predict.fitspecaccum.R | 16 ++ vegan-2.3-0/vegan/R/predict.specaccum.R | 43 +++++- vegan-2.3-0/vegan/R/print.oecosimu.R | 2 vegan-2.3-0/vegan/R/print.specaccum.R | 2 vegan-2.3-0/vegan/R/print.varpart.R | 4 vegan-2.3-0/vegan/R/print.varpart234.R | 2 vegan-2.3-0/vegan/R/rankindex.R | 2 vegan-2.3-0/vegan/R/rarecurve.R | 2 vegan-2.3-0/vegan/R/rarefy.R | 5 vegan-2.3-0/vegan/R/rareslope.R |only vegan-2.3-0/vegan/R/rda.default.R | 7 vegan-2.3-0/vegan/R/read.cep.R | 10 - vegan-2.3-0/vegan/R/scores.cca.R | 4 vegan-2.3-0/vegan/R/scores.ordihull.R | 2 vegan-2.3-0/vegan/R/scores.rda.R | 4 vegan-2.3-0/vegan/R/showvarparts.R | 89 +++++++++--- vegan-2.3-0/vegan/R/specaccum.R | 9 - vegan-2.3-0/vegan/R/specslope.R |only vegan-2.3-0/vegan/R/summary.anosim.R | 6 vegan-2.3-0/vegan/R/summary.bioenv.R | 2 vegan-2.3-0/vegan/R/summary.cca.R | 4 vegan-2.3-0/vegan/R/summary.radfit.frame.R | 4 vegan-2.3-0/vegan/R/varpart.R | 18 +- vegan-2.3-0/vegan/R/vegemite.R | 50 +++--- vegan-2.3-0/vegan/build/vignette.rds |binary vegan-2.3-0/vegan/inst/NEWS.Rd | 109 +++++++++++++++ vegan-2.3-0/vegan/inst/doc/FAQ-vegan.pdf |binary vegan-2.3-0/vegan/inst/doc/NEWS.html | 127 +++++++++++++++++ vegan-2.3-0/vegan/inst/doc/decision-vegan.pdf |binary vegan-2.3-0/vegan/inst/doc/diversity-vegan.pdf |binary vegan-2.3-0/vegan/inst/doc/intro-vegan.pdf |binary vegan-2.3-0/vegan/man/cascadeKM.Rd | 12 - vegan-2.3-0/vegan/man/cca.Rd | 2 vegan-2.3-0/vegan/man/diversity.Rd | 12 + vegan-2.3-0/vegan/man/envfit.Rd | 19 ++ vegan-2.3-0/vegan/man/goodness.cca.Rd | 46 +++--- vegan-2.3-0/vegan/man/oecosimu.Rd | 4 vegan-2.3-0/vegan/man/ordiArrowTextXY.Rd |only vegan-2.3-0/vegan/man/ordiarrows.Rd | 8 - vegan-2.3-0/vegan/man/orditkplot.Rd | 41 ++--- vegan-2.3-0/vegan/man/permustats.Rd | 20 +- vegan-2.3-0/vegan/man/procrustes.Rd | 2 vegan-2.3-0/vegan/man/sipoo.Rd | 4 vegan-2.3-0/vegan/man/specaccum.Rd | 49 ++++-- vegan-2.3-0/vegan/man/varpart.Rd | 49 ++++-- vegan-2.3-0/vegan/man/vegan-internal.Rd | 22 --- vegan-2.3-0/vegan/man/vegan-package.Rd | 11 - vegan-2.3-0/vegan/vignettes/FAQ-vegan.pdf |binary vegan-2.3-0/vegan/vignettes/FAQ-vegan.texi | 35 +++- vegan-2.3-0/vegan/vignettes/NEWS.html | 127 +++++++++++++++++ vegan-2.3-0/vegan/vignettes/decision-vegan.tex | 18 +- vegan-2.3-0/vegan/vignettes/diversity-vegan.tex | 80 +++++------ vegan-2.3-0/vegan/vignettes/intro-vegan.tex | 48 +++--- 89 files changed, 1259 insertions(+), 591 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.2-1699 dated 2015-04-13 and 2.3-1709 dated 2015-05-26
DESCRIPTION | 12 +++++------ MD5 | 40 +++++++++++++++++++-------------------- R/felm.R | 34 ++++++++++++++++++++++++++++----- R/startup.R | 22 +++++++++++---------- exec/lfescript | 45 +++++++++++++++++++++++++++++++++++++------- inst/NEWS.Rd | 13 +++++++++++- inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/bccorr.Rd | 10 ++++----- man/condfstat.Rd | 8 ++++--- man/felm.Rd | 20 +++++++++++++++++-- man/fevcov.Rd | 8 ++----- man/lfe-package.Rd | 33 +++++++++++++++++++++++--------- man/makeDmatrix.Rd | 2 - man/waldtest.Rd | 2 - src/demean.c | 11 ++++++---- tests/anomalies.R | 8 +++++++ tests/anomalies.Rout.save | 15 ++++++++++++-- tests/ivtest.R | 1 tests/ivtest.Rout.save | 27 ++++++++++++++++++++++++-- 21 files changed, 228 insertions(+), 83 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.44 dated 2014-12-11 and 0.45 dated 2015-05-26
DESCRIPTION | 14 ++++++++------ MD5 | 34 ++++++++++++++++++---------------- R/util.R | 28 ++++++++++++++++++++++++++-- inst/doc/diagnostics.html | 42 +++++++++++++++++++++--------------------- inst/include/libifa-rpf.h | 4 +++- inst/tests/test-dTheta.R | 8 ++++---- inst/tests/test-gamma.R | 2 +- inst/tests/test-ld.R | 8 ++++---- inst/tests/test-multinomial.R | 24 ++++++++++++------------ inst/tests/test-raschfit.R | 18 +++++++++--------- inst/tests/test-score.R | 4 ++-- man/EAPscores.Rd | 4 +--- man/fromFactorThreshold.Rd |only man/toFactorThreshold.Rd |only src/ba81quad.cpp | 4 ++-- src/ba81quad.h | 2 +- src/diagnose.cpp | 2 +- src/eap.cpp | 2 +- src/glue.cpp | 4 ++-- 19 files changed, 116 insertions(+), 88 deletions(-)
Title: Utilities for Working with R's Operators
Description: These utilities allow for programatically working with
R's operators: translating between an operator and its underlying
function, inverting an operator, determining an operator's type, etc.
Author: Decision Patterns
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between operator.tools versions 1.3.0 dated 2012-11-30 and 1.4.4 dated 2015-05-26
operator.tools-1.3.0/operator.tools/R/setOperators.R |only operator.tools-1.3.0/operator.tools/TODO |only operator.tools-1.3.0/operator.tools/operator.Rproj |only operator.tools-1.3.0/operator.tools/tests/1_init.R |only operator.tools-1.3.0/operator.tools/tests/2_operators.R |only operator.tools-1.3.0/operator.tools/tests/3_inverse.R |only operator.tools-1.4.4/operator.tools/DESCRIPTION | 24 + operator.tools-1.4.4/operator.tools/MD5 | 63 ++-- operator.tools-1.4.4/operator.tools/NAMESPACE | 30 ++ operator.tools-1.4.4/operator.tools/R/can.operator.R | 47 +-- operator.tools-1.4.4/operator.tools/R/fun2name.R | 27 + operator.tools-1.4.4/operator.tools/R/init.R | 4 operator.tools-1.4.4/operator.tools/R/inverse.R | 114 ++------ operator.tools-1.4.4/operator.tools/R/is.operator.R | 81 ++++- operator.tools-1.4.4/operator.tools/R/not-in.R | 12 operator.tools-1.4.4/operator.tools/R/operator-tools-package.R |only operator.tools-1.4.4/operator.tools/R/operator.type.R | 61 +++- operator.tools-1.4.4/operator.tools/R/operators.R | 88 ++++-- operator.tools-1.4.4/operator.tools/R/rel.type.R | 57 +++- operator.tools-1.4.4/operator.tools/R/removeOperator.R | 25 + operator.tools-1.4.4/operator.tools/R/setOperator.R | 69 ++++- operator.tools-1.4.4/operator.tools/R/zzz.R | 17 - operator.tools-1.4.4/operator.tools/README.md |only operator.tools-1.4.4/operator.tools/man/can.operator.Rd |only operator.tools-1.4.4/operator.tools/man/fun2name.Rd | 65 +--- operator.tools-1.4.4/operator.tools/man/initOps.Rd |only operator.tools-1.4.4/operator.tools/man/inverse.Rd | 76 ++--- operator.tools-1.4.4/operator.tools/man/is.operator.Rd | 118 +++----- operator.tools-1.4.4/operator.tools/man/not-in.Rd | 40 -- operator.tools-1.4.4/operator.tools/man/operator.tools-package.Rd | 35 +- operator.tools-1.4.4/operator.tools/man/operator.type.Rd | 82 ++---- operator.tools-1.4.4/operator.tools/man/operators.Rd | 136 +++------- operator.tools-1.4.4/operator.tools/man/rel.type.Rd | 71 ++--- operator.tools-1.4.4/operator.tools/man/removeOperator.Rd | 53 +-- operator.tools-1.4.4/operator.tools/man/setOperator.Rd | 123 +++------ operator.tools-1.4.4/operator.tools/tests/testthat |only operator.tools-1.4.4/operator.tools/tests/testthat.R |only 37 files changed, 795 insertions(+), 723 deletions(-)
More information about operator.tools at CRAN
Permanent link
Title: Functions for Soil Texture Plot, Classification and
Transformation
Description: "The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().
Author: Julien Moeys [aut, cre], Wei Shangguan [ctb], Rainer Petzold [ctb], Budiman Minasny [ctb], Bogdan Rosca [ctb], Nic Jelinski [ctb], Wiktor Zelazny [ctb], Rodolfo Marcondes Silva Souza [ctb], Jose Lucas Safanelli [ctb], Alexandre ten Caten [ctb]
Maintainer: Julien Moeys <jules_m78-soiltexture@yahoo.fr>
Diff between soiltexture versions 1.2.19 dated 2014-09-29 and 1.3.3 dated 2015-05-26
DESCRIPTION | 34 +- MD5 | 139 ++++++----- NAMESPACE | 10 NEWS | 55 ++++ R/soiltexture.R | 278 +++++++++-------------- R/soiltextureInfo.R | 4 R/soiltexture_text_gui.R |only build/vignette.rds |binary inst/SVN_VERSION | 2 inst/doc/soiltexture_vignette.R | 313 +++++++++++++------------- inst/doc/soiltexture_vignette.Rnw | 101 +++++--- inst/doc/soiltexture_vignette.pdf |binary man/TT.DJ.col.Rd | 4 man/TT.add.Rd | 2 man/TT.auto.set.Rd | 2 man/TT.axis.arrows.Rd | 2 man/TT.baseplot.Rd | 2 man/TT.blr.ps.lim.Rd | 2 man/TT.blr.tx.check.Rd | 2 man/TT.check.ps.lim.Rd | 2 man/TT.chemometrics.alr.Rd | 2 man/TT.classes.Rd | 2 man/TT.classes.tbl.Rd | 2 man/TT.col2hsv.Rd | 4 man/TT.contour.Rd | 2 man/TT.css2xy.Rd | 4 man/TT.data.test.Rd | 2 man/TT.data.test.X.Rd | 2 man/TT.dataset.Rd | 2 man/TT.deg2rad.Rd | 4 man/TT.dia2phi.Rd | 4 man/TT.edges.Rd | 2 man/TT.gen.op.set.Rd | 2 man/TT.geo.get.Rd | 2 man/TT.geo.set.Rd | 2 man/TT.get.Rd | 2 man/TT.grid.Rd | 2 man/TT.ifelse.Rd | 2 man/TT.image.Rd | 2 man/TT.iwd.Rd | 2 man/TT.kde2d.Rd | 2 man/TT.lines.Rd | 2 man/TT.locator.Rd | 2 man/TT.mahalanobis.Rd | 2 man/TT.normalise.sum.Rd | 2 man/TT.normalise.sum.X.Rd | 2 man/TT.par.op.set.Rd | 2 man/TT.phi2dia.Rd | 4 man/TT.plot.Rd | 7 man/TT.points.Rd | 2 man/TT.points.in.classes.Rd | 2 man/TT.polygon.area.Rd | 4 man/TT.polygon.centroids.Rd | 4 man/TT.set.Rd | 2 man/TT.str.Rd | 2 man/TT.switch.Rd | 2 man/TT.text.Rd | 2 man/TT.text.transf.Rd | 2 man/TT.text.transf.X.Rd | 2 man/TT.ticks.Rd | 2 man/TT.ticks.lab.Rd | 2 man/TT.vertices.plot.Rd | 4 man/TT.vertices.tbl.Rd | 2 man/TT.xy.grid.Rd | 2 man/TT.xy2css.Rd | 2 man/soiltexture-package.Rd | 34 +- man/soiltextureInfo.Rd | 2 man/soiltexture_gui.Rd |only tests/TT.plot.R | 5 tests/soiltexture_gui.R |only vignettes/soiltexture_vignette.Rnw | 101 +++++--- vignettes/soiltexture_vignette.bib | 433 ++++++++++++++++++------------------- 72 files changed, 854 insertions(+), 786 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-22 0.9
Title: T-Distributed Stochastic Neighbor Embedding using Barnes-Hut
Implementation
Description: An R wrapper around the fast T-distributed Stochastic
Neighbor Embedding implementation by Van der Maaten.
Author: Jesse Krijthe <jkrijthe@gmail.com>
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between Rtsne versions 0.9 dated 2014-09-18 and 0.10 dated 2015-05-26
DESCRIPTION | 15 +- MD5 | 25 ++- NAMESPACE | 5 R/RcppExports.R | 4 R/Rtsne.R | 69 ++++++++-- R/bhtsne.R |only man/Rtsne.Rd | 53 ++++++- src/Makevars.win | 2 src/RcppExports.cpp | 27 +-- src/Rtsne.cpp | 14 +- src/tsne.cpp | 353 ++++++++++++++++++++++++++++++++++++++-------------- src/tsne.h | 8 - src/vptree.h | 5 tests |only 14 files changed, 429 insertions(+), 151 deletions(-)
Title: Drat R Archive Template
Description: Creation and Use of R Repositories via two helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.0.3 dated 2015-04-10 and 0.0.4 dated 2015-05-26
ChangeLog | 60 +++++ DESCRIPTION | 8 MD5 | 62 +++-- NAMESPACE | 4 R/addRepo.R | 11 R/initRepo.R |only R/insertPackage.R | 108 +++++++-- R/pruneRepo.R | 76 +++++- README.md | 54 ++-- build/vignette.rds |binary inst/TODO.md | 3 inst/doc/CombiningDratAndTravis.Rmd | 154 ++++++++----- inst/doc/CombiningDratAndTravis.html | 289 +++++++------------------ inst/doc/DratFAQ.Rmd |only inst/doc/DratFAQ.html |only inst/doc/DratForPackageAuthors.R | 8 inst/doc/DratForPackageAuthors.Rmd | 7 inst/doc/DratForPackageAuthors.html | 402 ++++++++--------------------------- inst/doc/DratForPackageUsers.R | 4 inst/doc/DratForPackageUsers.Rmd | 9 inst/doc/DratForPackageUsers.html | 310 ++++++-------------------- inst/doc/WhyDrat.R | 6 inst/doc/WhyDrat.Rmd | 4 inst/doc/WhyDrat.html | 340 +++++++---------------------- man/addRepo.Rd | 8 man/drat-package.Rd | 7 man/getPathForPackageType.Rd |only man/identifyPackageType.Rd |only man/initRepo.Rd |only man/insertPackage.Rd | 21 - man/pruneRepo.Rd |only vignettes/CombiningDratAndTravis.Rmd | 154 ++++++++----- vignettes/DratFAQ.Rmd |only vignettes/DratForPackageAuthors.Rmd | 7 vignettes/DratForPackageUsers.Rmd | 9 vignettes/WhyDrat.Rmd | 4 36 files changed, 867 insertions(+), 1262 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny
applications without having to know any JavaScript. Examples include hiding an
element, disabling an input, resetting an input back to its original value,
and many more useful functions. Even if you do know JavaScript,
shinyjs can be used as convenience functions to avoid dealing with message
passing and writing JavaScript code. shinyjs can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.0.3.3 dated 2015-04-22 and 0.0.6.0 dated 2015-05-26
shinyjs-0.0.3.3/shinyjs/inst/srcjs/shinyjs-message-handler.js |only shinyjs-0.0.6.0/shinyjs/DESCRIPTION | 19 shinyjs-0.0.6.0/shinyjs/MD5 | 84 +- shinyjs-0.0.6.0/shinyjs/NAMESPACE | 5 shinyjs-0.0.6.0/shinyjs/R/extendShinyjs.R |only shinyjs-0.0.6.0/shinyjs/R/hidden.R | 7 shinyjs-0.0.6.0/shinyjs/R/inlineCSS.R | 3 shinyjs-0.0.6.0/shinyjs/R/jsFunc-aaa.R | 9 shinyjs-0.0.6.0/shinyjs/R/jsFunc-classFuncs.R | 41 - shinyjs-0.0.6.0/shinyjs/R/jsFunc-messageFuncs.R | 7 shinyjs-0.0.6.0/shinyjs/R/jsFunc-runjs.R |only shinyjs-0.0.6.0/shinyjs/R/jsFunc-stateFuncs.R | 40 - shinyjs-0.0.6.0/shinyjs/R/jsFunc-text.R | 5 shinyjs-0.0.6.0/shinyjs/R/jsFunc-visibilityFuncs.R | 35 shinyjs-0.0.6.0/shinyjs/R/onclick.R | 7 shinyjs-0.0.6.0/shinyjs/R/reset.R |only shinyjs-0.0.6.0/shinyjs/R/runExample.R | 9 shinyjs-0.0.6.0/shinyjs/R/shinyjs.R | 13 shinyjs-0.0.6.0/shinyjs/R/useShinyjs.R | 36 shinyjs-0.0.6.0/shinyjs/R/utils.R | 39 + shinyjs-0.0.6.0/shinyjs/README.md | 368 ++++++---- shinyjs-0.0.6.0/shinyjs/inst/doc/overview.Rmd | 357 ++++++--- shinyjs-0.0.6.0/shinyjs/inst/doc/overview.html | 184 +++-- shinyjs-0.0.6.0/shinyjs/inst/examples/basic/DESCRIPTION |only shinyjs-0.0.6.0/shinyjs/inst/examples/basic/app.R | 92 -- shinyjs-0.0.6.0/shinyjs/inst/examples/basic/helper-text.R |only shinyjs-0.0.6.0/shinyjs/inst/examples/demo/helpers.R | 3 shinyjs-0.0.6.0/shinyjs/inst/examples/demo/ui.R | 7 shinyjs-0.0.6.0/shinyjs/inst/examples/sandbox/helpers.R | 2 shinyjs-0.0.6.0/shinyjs/inst/srcjs/shinyjs-default-funcs.js |only shinyjs-0.0.6.0/shinyjs/man/classFuncs.Rd | 42 - shinyjs-0.0.6.0/shinyjs/man/extendShinyjs.Rd |only shinyjs-0.0.6.0/shinyjs/man/hidden.Rd | 5 shinyjs-0.0.6.0/shinyjs/man/inlineCSS.Rd | 4 shinyjs-0.0.6.0/shinyjs/man/js.Rd |only shinyjs-0.0.6.0/shinyjs/man/messageFuncs.Rd | 7 shinyjs-0.0.6.0/shinyjs/man/reset.Rd |only shinyjs-0.0.6.0/shinyjs/man/resettable.Rd |only shinyjs-0.0.6.0/shinyjs/man/runExample.Rd | 6 shinyjs-0.0.6.0/shinyjs/man/runjs.Rd |only shinyjs-0.0.6.0/shinyjs/man/shinyjs.Rd | 13 shinyjs-0.0.6.0/shinyjs/man/stateFuncs.Rd | 41 - shinyjs-0.0.6.0/shinyjs/man/text.Rd | 5 shinyjs-0.0.6.0/shinyjs/man/useShinyjs.Rd | 1 shinyjs-0.0.6.0/shinyjs/man/visibilityFuncs.Rd | 35 shinyjs-0.0.6.0/shinyjs/tests/test-error.js |only shinyjs-0.0.6.0/shinyjs/tests/test-nofunc.js |only shinyjs-0.0.6.0/shinyjs/tests/test-success.js |only shinyjs-0.0.6.0/shinyjs/tests/testthat/test-extendShinyjs.R |only shinyjs-0.0.6.0/shinyjs/tests/testthat/test-hidden.R | 10 shinyjs-0.0.6.0/shinyjs/vignettes/overview.Rmd | 357 ++++++--- 51 files changed, 1242 insertions(+), 656 deletions(-)
Title: Repeated Function Evaluation for Sensitivity Analysis
Description: Simplified scenario testing and sensitivity analysis with R via a
generalized function for one-factor-at-a-time (OFAT) sensitivity analysis,
evaluation of parameter sets and (sampled) parameter permutations. Options
for formatting output and parallel processing are also provided.
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between reval versions 1.0 dated 2015-03-26 and 2.0.0 dated 2015-05-26
DESCRIPTION | 8 ++-- MD5 | 19 +++++---- NAMESPACE | 2 - R/reval.r | 92 +++++++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/quickstart.R | 4 +- inst/doc/quickstart.Rmd | 4 +- inst/doc/quickstart.html | 4 +- man/evalmany.Rd | 42 +++++++++++++-------- man/reval-package.Rd |only vignettes/quickstart.Rmd | 4 +- 11 files changed, 103 insertions(+), 76 deletions(-)
Title: Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Description: Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>
Diff between NMF versions 0.20.5 dated 2014-03-18 and 0.20.6 dated 2015-05-26
DESCRIPTION | 20 ++++++++++---------- MD5 | 30 +++++++++++++++--------------- NEWS | 7 +++++++ R/Bioc-layer.R | 3 ++- R/aheatmap.R | 4 +++- R/algorithms-lsnmf.R | 7 ++++--- R/algorithms-pe-nmf.R | 2 +- R/atracks.R | 2 ++ R/nmf-package.R | 3 ++- R/parallel.R | 26 +++++++++++++++++--------- R/run.R | 5 +++-- R/seed-ica.R | 5 +++-- R/utils.R | 16 ++++++++++++++++ build/vignette.rds |binary inst/doc/consensus.pdf |binary man/esGolub.Rd | 2 +- 16 files changed, 86 insertions(+), 46 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora <ctortora@math.mcmaster.ca>
Diff between MixGHD versions 1.5 dated 2015-04-30 and 1.6 dated 2015-05-26
MixGHD-1.5/MixGHD/man/MixGHD-package.Rd |only MixGHD-1.6/MixGHD/DESCRIPTION | 6 MixGHD-1.6/MixGHD/MD5 | 5 MixGHD-1.6/MixGHD/R/GHD.R | 1418 ++++++++++++++++---------------- 4 files changed, 719 insertions(+), 710 deletions(-)
Title: Kernel Factory: An Ensemble of Kernel Machines
Description: Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
Author: Michel Ballings, Dirk Van den Poel
Maintainer: Michel Ballings <Michel.Ballings@GMail.com>
Diff between kernelFactory versions 0.2.1 dated 2015-05-22 and 0.2.2 dated 2015-05-26
DESCRIPTION | 8 - MD5 | 10 - R/kernelFactory.R | 35 +++- R/predict.kernelFactory.R | 328 +++++++++++++++++++++++----------------------- inst/NEWS | 5 man/kernelFactory.Rd | 9 - 6 files changed, 209 insertions(+), 186 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.1.1 dated 2015-04-20 and 1.2.1 dated 2015-05-26
crunch-1.1.1/crunch/tests/testthat/api/datasets/dataset1/variables/old-hierarchical.json |only crunch-1.1.1/crunch/tests/testthat/api/datasets/dataset1/variables/old-nested-hierarchical.json |only crunch-1.1.1/crunch/tests/testthat/api/datasets/dataset1/variables/old-relative-and-nested-hierarchical.json |only crunch-1.1.1/crunch/tests/testthat/api/datasets/dataset1/variables/old-relative-hierarchical.json |only crunch-1.1.1/crunch/vignettes/economist.RData |only crunch-1.1.1/crunch/vignettes/hidden.png |only crunch-1.2.1/crunch/.Rinstignore |only crunch-1.2.1/crunch/DESCRIPTION | 10 crunch-1.2.1/crunch/MD5 | 282 ++--- crunch-1.2.1/crunch/NAMESPACE | 6 crunch-1.2.1/crunch/R/AllClasses.R | 27 crunch-1.2.1/crunch/R/AllGenerics.R | 7 crunch-1.2.1/crunch/R/append-dataset.R | 28 crunch-1.2.1/crunch/R/crest.R | 2 crunch-1.2.1/crunch/R/crunch.R | 2 crunch-1.2.1/crunch/R/cube-result.R | 7 crunch-1.2.1/crunch/R/dataset.R | 4 crunch-1.2.1/crunch/R/new-dataset.R | 17 crunch-1.2.1/crunch/R/ordering.R | 2 crunch-1.2.1/crunch/R/share.R | 75 + crunch-1.2.1/crunch/R/tuple.R | 2 crunch-1.2.1/crunch/R/variable-order-slots.R | 51 - crunch-1.2.1/crunch/R/variable-order.R | 175 +++ crunch-1.2.1/crunch/build/vignette.rds |binary crunch-1.2.1/crunch/inst/doc/analyze.R |only crunch-1.2.1/crunch/inst/doc/analyze.Rmd | 227 ++++ crunch-1.2.1/crunch/inst/doc/analyze.html | 493 +++++++++- crunch-1.2.1/crunch/inst/doc/array-card.png |only crunch-1.2.1/crunch/inst/doc/array-variables.R | 54 - crunch-1.2.1/crunch/inst/doc/array-variables.html | 26 crunch-1.2.1/crunch/inst/doc/datasets.R | 21 crunch-1.2.1/crunch/inst/doc/datasets.Rmd | 5 crunch-1.2.1/crunch/inst/doc/datasets.html | 7 crunch-1.2.1/crunch/inst/doc/derive.R |only crunch-1.2.1/crunch/inst/doc/derive.Rmd | 71 + crunch-1.2.1/crunch/inst/doc/derive.html | 106 ++ crunch-1.2.1/crunch/inst/doc/getting-started.R | 4 crunch-1.2.1/crunch/inst/doc/variable-order.R | 52 - crunch-1.2.1/crunch/inst/doc/variable-order.Rmd | 78 + crunch-1.2.1/crunch/inst/doc/variable-order.html | 429 ++++++++ crunch-1.2.1/crunch/inst/doc/variables.R | 45 crunch-1.2.1/crunch/inst/doc/variables.Rmd | 7 crunch-1.2.1/crunch/inst/doc/variables.html | 8 crunch-1.2.1/crunch/man/Categories.Rd | 2 crunch-1.2.1/crunch/man/CrunchDataset.Rd | 2 crunch-1.2.1/crunch/man/CrunchVariable.Rd | 2 crunch-1.2.1/crunch/man/ShojiObject-class.Rd | 2 crunch-1.2.1/crunch/man/Subvariables.Rd | 2 crunch-1.2.1/crunch/man/VariableCatalog.Rd | 2 crunch-1.2.1/crunch/man/VariableOrder-extract.Rd | 34 crunch-1.2.1/crunch/man/VariableOrder-length.Rd | 2 crunch-1.2.1/crunch/man/VariableOrder-slots.Rd | 32 crunch-1.2.1/crunch/man/VariableOrder.Rd | 8 crunch-1.2.1/crunch/man/appendDataset.Rd | 2 crunch-1.2.1/crunch/man/catalog-extract.Rd | 2 crunch-1.2.1/crunch/man/catalog-length.Rd | 2 crunch-1.2.1/crunch/man/category-extract.Rd | 2 crunch-1.2.1/crunch/man/cloneDataset.Rd | 2 crunch-1.2.1/crunch/man/createDataset.Rd | 2 crunch-1.2.1/crunch/man/createWithMetadataAndFile.Rd | 2 crunch-1.2.1/crunch/man/crtabs.Rd | 2 crunch-1.2.1/crunch/man/crunch-is.Rd | 2 crunch-1.2.1/crunch/man/crunch-summary.Rd | 2 crunch-1.2.1/crunch/man/crunch-uni.Rd | 2 crunch-1.2.1/crunch/man/crunch.Rd | 2 crunch-1.2.1/crunch/man/crunchAPI.Rd | 2 crunch-1.2.1/crunch/man/cube-computing.Rd | 7 crunch-1.2.1/crunch/man/cube-methods.Rd | 2 crunch-1.2.1/crunch/man/dataset-extract.Rd | 2 crunch-1.2.1/crunch/man/dataset-to-R.Rd | 2 crunch-1.2.1/crunch/man/dataset-update.Rd | 2 crunch-1.2.1/crunch/man/dataset-variables.Rd | 2 crunch-1.2.1/crunch/man/delete.Rd | 2 crunch-1.2.1/crunch/man/deleteDataset.Rd | 2 crunch-1.2.1/crunch/man/describe-catalog.Rd | 2 crunch-1.2.1/crunch/man/describe-category.Rd | 2 crunch-1.2.1/crunch/man/describe.Rd | 2 crunch-1.2.1/crunch/man/dichotomize.Rd | 2 crunch-1.2.1/crunch/man/dim-dataset.Rd | 2 crunch-1.2.1/crunch/man/expressions.Rd | 2 crunch-1.2.1/crunch/man/findVariables.Rd | 2 crunch-1.2.1/crunch/man/graftDataset.Rd | 2 crunch-1.2.1/crunch/man/grouped.Rd | 2 crunch-1.2.1/crunch/man/hiddenVariables.Rd | 2 crunch-1.2.1/crunch/man/hide.Rd | 2 crunch-1.2.1/crunch/man/hideVariables.Rd | 2 crunch-1.2.1/crunch/man/http-methods.Rd | 2 crunch-1.2.1/crunch/man/index.Rd | 2 crunch-1.2.1/crunch/man/is-na-categories.Rd | 2 crunch-1.2.1/crunch/man/listDatasets.Rd | 2 crunch-1.2.1/crunch/man/loadDataset.Rd | 2 crunch-1.2.1/crunch/man/login.Rd | 2 crunch-1.2.1/crunch/man/logout.Rd | 2 crunch-1.2.1/crunch/man/makeArray.Rd | 2 crunch-1.2.1/crunch/man/na-omit-categories.Rd | 2 crunch-1.2.1/crunch/man/newDataset.Rd | 5 crunch-1.2.1/crunch/man/newDatasetByCSV.Rd | 5 crunch-1.2.1/crunch/man/newDatasetByColumn.Rd | 6 crunch-1.2.1/crunch/man/newDatasetFromFile.Rd | 2 crunch-1.2.1/crunch/man/ordering.Rd | 2 crunch-1.2.1/crunch/man/prepareBindInputs.Rd | 2 crunch-1.2.1/crunch/man/refresh.Rd | 2 crunch-1.2.1/crunch/man/self.Rd | 2 crunch-1.2.1/crunch/man/session_store.Rd | 2 crunch-1.2.1/crunch/man/share.Rd |only crunch-1.2.1/crunch/man/shojifyMetadata.Rd | 2 crunch-1.2.1/crunch/man/show-crunch.Rd | 2 crunch-1.2.1/crunch/man/subvars-extract.Rd | 2 crunch-1.2.1/crunch/man/table.Rd | 2 crunch-1.2.1/crunch/man/toVariable.Rd | 2 crunch-1.2.1/crunch/man/tojson-crunch.Rd | 4 crunch-1.2.1/crunch/man/tuple-methods.Rd | 8 crunch-1.2.1/crunch/man/type.Rd | 2 crunch-1.2.1/crunch/man/unbind.Rd | 2 crunch-1.2.1/crunch/man/updateDatasetList.Rd | 2 crunch-1.2.1/crunch/man/urls.Rd | 2 crunch-1.2.1/crunch/man/var-categories.Rd | 2 crunch-1.2.1/crunch/man/variable-extract.Rd | 2 crunch-1.2.1/crunch/man/variable-to-R.Rd | 2 crunch-1.2.1/crunch/man/variable-update.Rd | 2 crunch-1.2.1/crunch/man/weight.Rd | 2 crunch-1.2.1/crunch/tests/testthat/api/datasets/dataset1.json | 3 crunch-1.2.1/crunch/tests/testthat/api/datasets/dataset1/permissions.json |only crunch-1.2.1/crunch/tests/testthat/helper.R | 9 crunch-1.2.1/crunch/tests/testthat/test-add-variable.R | 5 crunch-1.2.1/crunch/tests/testthat/test-appending.R | 76 - crunch-1.2.1/crunch/tests/testthat/test-cube-errors.R | 6 crunch-1.2.1/crunch/tests/testthat/test-cubes.R | 16 crunch-1.2.1/crunch/tests/testthat/test-dataset.R | 5 crunch-1.2.1/crunch/tests/testthat/test-expression.R | 4 crunch-1.2.1/crunch/tests/testthat/test-graft.R | 42 crunch-1.2.1/crunch/tests/testthat/test-join.R | 11 crunch-1.2.1/crunch/tests/testthat/test-make-array.R | 14 crunch-1.2.1/crunch/tests/testthat/test-new-dataset.R | 24 crunch-1.2.1/crunch/tests/testthat/test-share.R |only crunch-1.2.1/crunch/tests/testthat/test-timing.R | 24 crunch-1.2.1/crunch/tests/testthat/test-update.R | 41 crunch-1.2.1/crunch/tests/testthat/test-variable-catalog.R | 7 crunch-1.2.1/crunch/tests/testthat/test-variable-order.R | 203 +++- crunch-1.2.1/crunch/vignettes/analyze.RData |only crunch-1.2.1/crunch/vignettes/analyze.Rmd | 227 ++++ crunch-1.2.1/crunch/vignettes/array-variables.RData |binary crunch-1.2.1/crunch/vignettes/datasets.Rmd | 5 crunch-1.2.1/crunch/vignettes/derive.RData |only crunch-1.2.1/crunch/vignettes/derive.Rmd | 71 + crunch-1.2.1/crunch/vignettes/getting-started.RData |binary crunch-1.2.1/crunch/vignettes/variable-order.RData |binary crunch-1.2.1/crunch/vignettes/variable-order.Rmd | 78 + crunch-1.2.1/crunch/vignettes/variables.RData |binary crunch-1.2.1/crunch/vignettes/variables.Rmd | 7 150 files changed, 2894 insertions(+), 559 deletions(-)
Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box'
(https://www.box.com/). In addition to uploading and downloading files, this
package includes functions which mirror base R operations for local files,
(e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git'
style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <rocks.brendan@gmail.com>
Diff between boxr versions 0.2.5 dated 2015-04-15 and 0.2.6 dated 2015-05-26
DESCRIPTION | 12 MD5 | 58 +-- NAMESPACE | 62 +-- R/boxr__internal_misc.R | 386 ++++++++++++------------ R/boxr__internal_package_homepage.R |only R/boxr_auth.R | 575 ++++++++++++++++++------------------ R/zzz.R | 37 +- build/vignette.rds |binary inst/doc/boxr.R | 14 inst/doc/boxr.Rmd | 203 ++++++------ inst/doc/boxr.html | 473 +++++++++++++++++++---------- man/box_auth.Rd | 199 ++++++------ man/box_auth_on_attach.Rd | 80 ++--- man/box_delete_file.Rd | 98 +++--- man/box_dir_create.Rd | 56 +-- man/box_dir_diff.Rd | 306 +++++++++---------- man/box_dl.Rd | 170 +++++----- man/box_fetch.Rd | 190 +++++------ man/box_ls.Rd | 54 +-- man/box_previous_versions.Rd | 68 ++-- man/box_read.Rd | 134 ++++---- man/box_save.Rd | 110 +++--- man/box_setwd.Rd | 64 ++-- man/box_source.Rd | 48 +-- man/box_upload_new.Rd | 70 ++-- man/boxr-package.Rd |only man/boxr_options.Rd | 78 ++-- man/create_loc_dir_df.Rd | 42 +- man/dirTreeRecursive.Rd | 50 +-- man/downloadDirFiles.Rd | 64 ++-- vignettes/boxr.Rmd | 203 ++++++------ 31 files changed, 2043 insertions(+), 1861 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 2.13.0 dated 2015-01-16 and 2.13.1 dated 2015-05-26
DESCRIPTION | 41 MD5 | 50 NAMESPACE | 842 ++++++------- NEWS | 23 R/AromaTabularBinaryFile.R | 7 R/AromaTransform.R | 33 R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 6 R/RawMirroredAlleleBFractions.R | 5 man/AromaMicroarrayDataSet.Rd | 2 man/AromaTabularBinarySet.Rd | 2 man/AromaUnitCallSet.Rd | 2 man/AromaUnitFracBCnBinarySet.Rd | 2 man/AromaUnitGenotypeCallSet.Rd | 2 man/AromaUnitPscnBinarySet.Rd | 2 man/AromaUnitSignalBinarySet.Rd | 2 man/AromaUnitTotalCnBinarySet.Rd | 2 man/CbsModel.Rd | 62 man/HaarSegModel.Rd | 54 man/PairedPSCNData.Rd | 2 man/ParametersInterface.Rd | 4 man/RawGenomicSignals.Rd | 10 man/RawMirroredAlleleBFractions.Rd | 26 man/UnitNamesFile.Rd | 2 man/aroma.core-package.Rd | 2 man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd | 7 tests/SegmentedCopyNumbers.R | 74 - 26 files changed, 705 insertions(+), 561 deletions(-)
Title: Citations for Knitr Markdown Files
Description: A tool which provides the ability to create dynamic citations
in which the bibliographic information is pulled from the web rather
than having to be entered into a local database such as bibtex ahead of
time. Knitcitations is primarily aimed at authoring in the R markdown
format, and can provide outputs for web-based authoring such as linked
text and tooltips over inline citations. Cite using a DOI, URL, or
bibtex file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between knitcitations versions 1.0.5 dated 2014-11-26 and 1.0.6 dated 2015-05-25
knitcitations-1.0.5/knitcitations/tests/testthat/cite.R |only knitcitations-1.0.5/knitcitations/tests/testthat/ref.R |only knitcitations-1.0.6/knitcitations/DESCRIPTION | 13 +-- knitcitations-1.0.6/knitcitations/MD5 | 38 +++++----- knitcitations-1.0.6/knitcitations/NAMESPACE | 2 knitcitations-1.0.6/knitcitations/NEWS | 6 + knitcitations-1.0.6/knitcitations/R/write.bibtex.R | 4 - knitcitations-1.0.6/knitcitations/build/vignette.rds |binary knitcitations-1.0.6/knitcitations/inst/doc/tutorial.R | 2 knitcitations-1.0.6/knitcitations/inst/doc/tutorial.pdf |binary knitcitations-1.0.6/knitcitations/man/bib_metadata.Rd | 3 knitcitations-1.0.6/knitcitations/man/bibliography.Rd | 3 knitcitations-1.0.6/knitcitations/man/cite_options.Rd | 3 knitcitations-1.0.6/knitcitations/man/citep.Rd | 3 knitcitations-1.0.6/knitcitations/man/citet.Rd | 3 knitcitations-1.0.6/knitcitations/man/cleanbib.Rd | 3 knitcitations-1.0.6/knitcitations/man/greycite.Rd | 3 knitcitations-1.0.6/knitcitations/man/read.bibtex.Rd | 3 knitcitations-1.0.6/knitcitations/man/record_as_cited.Rd | 3 knitcitations-1.0.6/knitcitations/man/write.bibtex.Rd | 7 + knitcitations-1.0.6/knitcitations/tests/testthat/test_bib_metadata.R |only knitcitations-1.0.6/knitcitations/tests/testthat/test_cite.R |only 22 files changed, 58 insertions(+), 41 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.11.3 dated 2014-03-08 and 0.12.0 dated 2015-05-25
ffbase-0.11.3/ffbase/inst |only ffbase-0.11.3/ffbase/tests/test_all.R |only ffbase-0.12.0/ffbase/DESCRIPTION | 17 - ffbase-0.12.0/ffbase/MD5 | 311 ++++++++++++------------ ffbase-0.12.0/ffbase/NAMESPACE | 91 +++++-- ffbase-0.12.0/ffbase/NEWS | 4 ffbase-0.12.0/ffbase/R/Summary_ff.R | 6 ffbase-0.12.0/ffbase/R/as.R | 202 ++++++++------- ffbase-0.12.0/ffbase/R/auxilary.R | 318 ++++++++++++------------- ffbase-0.12.0/ffbase/R/bigglm.R | 8 ffbase-0.12.0/ffbase/R/binned_sum.R | 162 ++++++------ ffbase-0.12.0/ffbase/R/binned_sumsq.R | 155 ++++++------ ffbase-0.12.0/ffbase/R/binned_tabulate.R | 189 +++++++------- ffbase-0.12.0/ffbase/R/byMean.R | 160 ++++++------ ffbase-0.12.0/ffbase/R/bySum.R | 6 ffbase-0.12.0/ffbase/R/chunkify.R | 2 ffbase-0.12.0/ffbase/R/compact.R | 108 ++++---- ffbase-0.12.0/ffbase/R/cumsum.R | 137 +++++----- ffbase-0.12.0/ffbase/R/cut_ff.R | 98 ++++--- ffbase-0.12.0/ffbase/R/date_formatting.R | 54 ++-- ffbase-0.12.0/ffbase/R/diff_ff.R | 65 ++--- ffbase-0.12.0/ffbase/R/droplevels.R | 2 ffbase-0.12.0/ffbase/R/duplicated.R | 155 ++++++------ ffbase-0.12.0/ffbase/R/expand_ffgrid.R | 140 +++++------ ffbase-0.12.0/ffbase/R/extract.R | 6 ffbase-0.12.0/ffbase/R/ffappend.R | 267 ++++++++++---------- ffbase-0.12.0/ffbase/R/ffdfdply.R | 226 ++++++++--------- ffbase-0.12.0/ffbase/R/ffdfwith.R | 144 +++++------ ffbase-0.12.0/ffbase/R/ffifelse.R | 68 ++--- ffbase-0.12.0/ffbase/R/ffmatch.R | 226 ++++++++--------- ffbase-0.12.0/ffbase/R/ffordered.R | 104 ++++---- ffbase-0.12.0/ffbase/R/ffrandom.R | 74 ++--- ffbase-0.12.0/ffbase/R/ffseq.R | 298 +++++++++++------------ ffbase-0.12.0/ffbase/R/ffwhich.R | 166 ++++++------- ffbase-0.12.0/ffbase/R/hist_ff.R | 105 ++++---- ffbase-0.12.0/ffbase/R/ikey.R | 44 +-- ffbase-0.12.0/ffbase/R/isNA.R | 78 +++--- ffbase-0.12.0/ffbase/R/laf_to_ffdf.R | 118 ++++----- ffbase-0.12.0/ffbase/R/logging.R | 66 ++--- ffbase-0.12.0/ffbase/R/mean.R | 69 ++--- ffbase-0.12.0/ffbase/R/merge.R | 231 +++++++++--------- ffbase-0.12.0/ffbase/R/pkg.R | 145 +++++------ ffbase-0.12.0/ffbase/R/quantile_ff.R | 68 ++--- ffbase-0.12.0/ffbase/R/rbind_ffdf.R | 97 +++---- ffbase-0.12.0/ffbase/R/rev_ff.R | 26 +- ffbase-0.12.0/ffbase/R/rle_ff.R | 94 +++---- ffbase-0.12.0/ffbase/R/save_ffdf.R | 4 ffbase-0.12.0/ffbase/R/subset.R | 97 +++---- ffbase-0.12.0/ffbase/R/table_ff.R | 227 ++++++++--------- ffbase-0.12.0/ffbase/R/tabulate_ff.R | 126 ++++----- ffbase-0.12.0/ffbase/R/transform.R | 2 ffbase-0.12.0/ffbase/R/tsum.R | 164 ++++++------ ffbase-0.12.0/ffbase/R/unique.R | 189 +++++++------- ffbase-0.12.0/ffbase/R/with.R | 282 +++++++++++----------- ffbase-0.12.0/ffbase/R/zzz.R | 6 ffbase-0.12.0/ffbase/man/all.ff.Rd | 12 ffbase-0.12.0/ffbase/man/any.ff.Rd | 12 ffbase-0.12.0/ffbase/man/as.Date.ff_vector.Rd | 12 ffbase-0.12.0/ffbase/man/as.character.ff.Rd | 9 ffbase-0.12.0/ffbase/man/as.ffdf.ffdf.Rd | 6 ffbase-0.12.0/ffbase/man/as.ram.ffdf.Rd | 6 ffbase-0.12.0/ffbase/man/bigglm.ffdf.Rd | 27 +- ffbase-0.12.0/ffbase/man/binned_sum.Rd | 17 - ffbase-0.12.0/ffbase/man/binned_sumsq.Rd | 26 -- ffbase-0.12.0/ffbase/man/binned_tabulate.Rd | 29 +- ffbase-0.12.0/ffbase/man/byMean.Rd | 18 - ffbase-0.12.0/ffbase/man/bySum.Rd | 22 - ffbase-0.12.0/ffbase/man/c.ff.Rd | 4 ffbase-0.12.0/ffbase/man/chunkexpr.Rd | 18 - ffbase-0.12.0/ffbase/man/chunkify.Rd | 15 - ffbase-0.12.0/ffbase/man/compact.Rd | 49 +-- ffbase-0.12.0/ffbase/man/condMean.Rd | 15 - ffbase-0.12.0/ffbase/man/condSum.Rd | 15 - ffbase-0.12.0/ffbase/man/cumsum.ff.Rd | 25 - ffbase-0.12.0/ffbase/man/cut.ff.Rd | 21 - ffbase-0.12.0/ffbase/man/diff.ff.Rd | 12 ffbase-0.12.0/ffbase/man/droplevels.ff.Rd | 16 - ffbase-0.12.0/ffbase/man/droplevels.ffdf.Rd | 19 - ffbase-0.12.0/ffbase/man/duplicated.ff.Rd | 44 +-- ffbase-0.12.0/ffbase/man/expand.ffgrid.Rd | 24 - ffbase-0.12.0/ffbase/man/ff_arithmetic.Rd | 29 +- ffbase-0.12.0/ffbase/man/ff_math.Rd | 29 +- ffbase-0.12.0/ffbase/man/ff_ops.Rd | 31 +- ffbase-0.12.0/ffbase/man/ffappend.Rd | 24 - ffbase-0.12.0/ffbase/man/ffbase-package.Rd | 131 ++++------ ffbase-0.12.0/ffbase/man/ffdfappend.Rd | 31 -- ffbase-0.12.0/ffbase/man/ffdfdply.Rd | 38 +- ffbase-0.12.0/ffbase/man/ffdfrbind.fill.Rd | 19 - ffbase-0.12.0/ffbase/man/ffdfwith.Rd | 29 +- ffbase-0.12.0/ffbase/man/ffextract.Rd | 55 +--- ffbase-0.12.0/ffbase/man/ffifelse.Rd | 15 - ffbase-0.12.0/ffbase/man/ffmatch.Rd | 42 +-- ffbase-0.12.0/ffbase/man/ffordered.Rd | 17 - ffbase-0.12.0/ffbase/man/ffrandom.Rd | 34 +- ffbase-0.12.0/ffbase/man/ffrep.int.Rd | 14 - ffbase-0.12.0/ffbase/man/ffseq.Rd | 25 - ffbase-0.12.0/ffbase/man/ffseq_len.Rd | 8 ffbase-0.12.0/ffbase/man/ffwhich.Rd | 14 - ffbase-0.12.0/ffbase/man/format.ff_vector.Rd | 12 ffbase-0.12.0/ffbase/man/grouprunningcumsum.Rd | 15 - ffbase-0.12.0/ffbase/man/hist.ff.Rd | 17 - ffbase-0.12.0/ffbase/man/hist2d.ff.Rd | 2 ffbase-0.12.0/ffbase/man/ikey.Rd | 16 - ffbase-0.12.0/ffbase/man/is.na.ff.Rd | 16 - ffbase-0.12.0/ffbase/man/laf_to_ffdf.Rd | 21 - ffbase-0.12.0/ffbase/man/load.ffdf.Rd | 17 - ffbase-0.12.0/ffbase/man/mean.ff.Rd | 12 ffbase-0.12.0/ffbase/man/merge.ffdf.Rd | 64 +---- ffbase-0.12.0/ffbase/man/min.ff.Rd | 15 - ffbase-0.12.0/ffbase/man/move.ffdf.Rd | 20 - ffbase-0.12.0/ffbase/man/pack.ffdf.Rd | 12 ffbase-0.12.0/ffbase/man/pkg-deprecated.Rd | 19 - ffbase-0.12.0/ffbase/man/quantile.ff.Rd | 27 -- ffbase-0.12.0/ffbase/man/rle_ff.Rd | 28 +- ffbase-0.12.0/ffbase/man/save.ffdf.Rd | 59 +--- ffbase-0.12.0/ffbase/man/set_ffbase_logging.Rd | 7 ffbase-0.12.0/ffbase/man/subset.ff.Rd | 13 - ffbase-0.12.0/ffbase/man/sum.ff.Rd | 15 - ffbase-0.12.0/ffbase/man/table.Rd | 28 +- ffbase-0.12.0/ffbase/man/tabulate.ff.Rd | 12 ffbase-0.12.0/ffbase/man/transform.ffdf.Rd | 16 - ffbase-0.12.0/ffbase/man/unique.ff.Rd | 26 -- ffbase-0.12.0/ffbase/man/unpack.ffdf.Rd | 18 - ffbase-0.12.0/ffbase/man/with.ffdf.Rd | 32 +- ffbase-0.12.0/ffbase/man/within.ffdf.Rd | 17 - ffbase-0.12.0/ffbase/tests/testthat |only ffbase-0.12.0/ffbase/tests/testthat.R |only 127 files changed, 3881 insertions(+), 3940 deletions(-)
Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The "M" in the name "geeM" is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel <lmcda4@lsuhsc.edu>
Diff between geeM versions 0.7.3 dated 2015-04-13 and 0.7.4 dated 2015-05-25
DESCRIPTION | 12 MD5 | 8 NAMESPACE | 4 R/geem.R | 931 ++++++++++++++++++++++++++++++------------------------------ R/utility.R | 202 ++++++------- 5 files changed, 586 insertions(+), 571 deletions(-)
Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency
tables. Unconditional exact tests are often more powerful than conditional exact tests and asymptotic tests.
Author: Peter Calhoun
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between Exact versions 1.5 dated 2015-03-28 and 1.6 dated 2015-05-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/binomialCode.R | 5 +++-- man/Exact-package.Rd | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Fitting Linear and Generalized Linear Models to Large Data Sets
Description: Fitting linear models and generalized linear models to large data sets by updating algorithms.
Author: Marco Enea, with contributions by Ronen Meiri and Tomer Kalimi on behalf of DMWay Analytics LTD.
Maintainer: Marco Enea <emarco76@libero.it>
Diff between speedglm versions 0.2-1.0 dated 2014-10-22 and 0.3 dated 2015-05-25
DESCRIPTION | 18 - MD5 | 34 +- NAMESPACE | 23 + NEWS | 54 ++- R/miscellanea.r | 198 +++++++------- R/predict.r |only R/speedglm.r | 494 ++++++++++++++++++------------------ R/speedlm.r | 603 ++++++++++++++++++++++++++------------------ R/summary.speedglm.r | 259 +++++++++--------- R/summary.speedlm.r | 526 +++++++++++++++++++++++++++----------- R/uncommented.r | 115 ++++---- man/add1&drop1.Rd |only man/miscellanea-Internal.Rd | 2 man/predict.speedglm.Rd |only man/predict.speedlm.Rd |only man/speedglm-package.rd | 14 - man/speedglm.Rd | 422 ++++++++++++++++-------------- man/speedlm.Rd | 333 ++++++++++++++---------- man/summary.speedglm.Rd | 138 +++++----- man/summary.speedlm.Rd | 131 ++++----- 20 files changed, 1930 insertions(+), 1434 deletions(-)
Title: Read and Write 'JSON-stat' Data Sets
Description: Read and write the 'JSON-stat' format (http://json-stat.org) to and
from (lists of) R data frames. Not all features are supported, especially
the extensive metadata features of 'JSON-stat'.
Author: Aaron Schumacher <ajschumacher@gmail.com>, HÃ¥kon Malmedal
Maintainer: Aaron Schumacher <ajschumacher@gmail.com>
Diff between rjstat versions 0.2 dated 2014-09-29 and 0.2.1 dated 2015-05-25
DESCRIPTION | 14 ++-- LICENSE | 2 MD5 | 27 +++++--- NAMESPACE | 2 R/rjstat.R | 111 ++++++++++++++--------------------- README.md | 17 ++++- man/fromJSONstat.Rd | 3 man/rjstat.Rd | 3 man/toJSONstat.Rd | 3 tests/testthat/dataset.json | 65 +++++++++++++++++--- tests/testthat/test-attributes.R |only tests/testthat/test-columns.R |only tests/testthat/test-datasets.R |only tests/testthat/test-factors.R |only tests/testthat/test-input.R | 21 ++++++ tests/testthat/test-output.R | 122 ++++++++------------------------------- tests/testthat/test-values.R |only 17 files changed, 190 insertions(+), 200 deletions(-)
Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via a non-Monte Carlo method. Different routines
are used for the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-2 dated 2015-04-03 and 1.5-3 dated 2015-05-25
mnormt-1.5-2/mnormt/INDEX |only mnormt-1.5-3/mnormt/DESCRIPTION | 8 ++++---- mnormt-1.5-3/mnormt/MD5 | 11 +++++------ mnormt-1.5-3/mnormt/NEWS | 4 +++- mnormt-1.5-3/mnormt/R/mnormt.R | 8 +++++--- mnormt-1.5-3/mnormt/man/dmnorm.Rd | 4 ++-- mnormt-1.5-3/mnormt/man/dmt.Rd | 6 ++---- 7 files changed, 21 insertions(+), 20 deletions(-)
Title: R Interface to the PX-Web/PC-Axis API
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis
API is used by organizations such as Statistics Sweden and Statistics
Finland to disseminate data. The R package can interact with all
PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract
metadata and extract and parse statistics to R data.frame format. PX-Web is
a solution to disseminate PC-Axis data files in dynamic tables on the web.
Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson, Leo Lahti, Love Hansson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between pxweb versions 0.5.5 dated 2015-03-04 and 0.5.54 dated 2015-05-25
DESCRIPTION | 8 +- MD5 | 88 ++++++++++++++++---------------- NAMESPACE | 2 inst/doc/pxweb.R | 4 - inst/extras/build.cran.sh | 10 +-- man/api_catalogue.Rd | 3 - man/api_parameters.Rd | 3 - man/api_timer.Rd | 3 - man/base_url.Rd | 3 - man/buildPath.Rd | 3 - man/calc_dim_type.Rd | 3 - man/calculate_data_dim.Rd | 3 - man/checkForLevels.Rd | 3 - man/check_new_pxweb_apis.Rd | 3 - man/choose_pxweb_api.Rd | 3 - man/choose_pxweb_database_url.Rd | 3 - man/clean_pxweb.Rd | 3 - man/create_batch_list.Rd | 3 - man/deparseLevels.Rd | 3 - man/download_pxweb.Rd | 3 - man/findData.input.Rd | 3 - man/getContent.Rd | 3 - man/get_api_index.Rd | 3 - man/get_api_list.Rd | 3 - man/get_api_list_remote.Rd | 3 - man/get_dim_size.Rd | 3 - man/get_github_api_urls.Rd | 3 - man/get_pxweb_data.Rd | 3 - man/get_pxweb_dims.Rd | 3 - man/get_pxweb_levels.Rd | 3 - man/get_pxweb_metadata.Rd | 3 - man/interactive_pxweb.Rd | 3 - man/print.api_parameters.Rd | 3 - man/pxweb.Rd | 3 - man/pxweb_api-class.Rd | 3 - man/test_pxweb_api.Rd | 3 - man/test_pxweb_api_get_data.Rd | 3 - man/test_pxweb_api_get_node_metadata.Rd | 3 - man/test_pxweb_api_get_nodes.Rd | 3 - man/text_to_url.Rd | 3 - man/update_pxweb_apis.Rd | 3 - man/write_api_list.Rd | 3 - tests/testthat/test-apis_in_catalogue.R | 9 +-- tests/testthat_api_in_catalogue.R | 2 vignettes/pxweb.Rmd | 4 - 45 files changed, 137 insertions(+), 101 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>
Diff between MXM versions 0.3 dated 2015-02-12 and 0.3.1 dated 2015-05-25
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 26 +++++++++++--------------- R/SES.R | 6 +++--- R/censIndLR.R | 10 +++++----- R/gSquare.R | 4 ++-- R/testIndLogistic.R | 16 ++++++++-------- man/SES.Rd | 2 +- man/censIndLR.Rd | 2 ++ man/gSquare.Rd | 2 ++ man/testIndLogistic.Rd | 6 +++--- 11 files changed, 52 insertions(+), 52 deletions(-)
Title: Permits *apply() Style Dispatch for HPC
Description: Function of apply style using MPI provides better HPC environment on R(works fast on HPC).
and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Eiji NAKAMA<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>
Diff between Rhpc versions 0.14-261 dated 2014-09-19 and 0.15-145 dated 2015-05-25
ChangeLog | 10 ++++ DESCRIPTION | 16 ++---- MD5 | 35 ++++++++------ R/Rhpc.R | 2 README |only configure | 48 ++++++++++++++------ configure.ac | 32 ++++++++++--- configure.win |only man/Rhpc-package.Rd | 2 src/Makevars.in | 7 -- src/Makevars.win |only src/RhpcMPI.c | 76 +++++++++++++++++--------------- src/common/Rhpc.h | 4 + src/common/config.h.in | 2 src/windows |only src/worker/Makefile.in | 5 -- src/worker/Makefile.win |only src/worker/Rhpc.cmd.in |only src/worker/Rhpc.in | 2 src/worker/RhpcSpawn.in | 2 src/worker/RhpcWin.cmd.in |only src/worker/RhpcWorker.c | 108 +++++++++++++++++++++++----------------------- 22 files changed, 205 insertions(+), 146 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-23 1.0-1
Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM)
analysis for both metric and
non-metric data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: Gaston Sanchez <gaston.stat@gmail.com>
Diff between plspm versions 0.4.2 dated 2015-02-20 and 0.4.7 dated 2015-05-25
DESCRIPTION | 28 +++---- MD5 | 51 +++++++------- NAMESPACE | 6 + NEWS | 49 +++++++++++++ R/get_boots.r | 13 ++- R/get_dummies.r | 6 + R/get_weights_nonmetric.r | 80 +++++++++++++++------- R/innerplot.r | 6 - R/it.reb.r | 2 R/outerplot.r | 3 R/plspm-package.r |only R/plspm.r | 11 +-- R/rebus.pls.r | 6 - R/res.clus.r | 2 inst/doc/plspm_introduction.R | 138 ++++++++++++++++----------------------- inst/doc/plspm_introduction.Rnw | 29 ++++---- inst/doc/plspm_introduction.pdf |binary man/cereals.Rd | 2 man/college.Rd | 3 man/futbol.Rd | 3 man/get_dummy.Rd | 4 - man/it.reb.Rd | 2 man/offense.Rd | 3 man/plspm.Rd | 33 +++++++-- man/rebus.pls.Rd | 6 - man/spainfoot.Rd | 3 vignettes/plspm_introduction.Rnw | 29 ++++---- 27 files changed, 300 insertions(+), 218 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.7.1 dated 2015-04-28 and 2.7.2 dated 2015-05-25
DESCRIPTION | 10 +-- MD5 | 38 ++++++------ NAMESPACE | 1 NEWS | 15 +++++ R/GenericDataFile.R | 14 +++- R/GenericDataFileSet.PARALLEL.R | 13 ++-- R/GenericDataFileSet.R | 110 +++++++++++++++++++++++++++++++++---- R/TabularTextFile.R | 18 +++++- man/ChecksumFileSet.Rd | 2 man/GenericDataFileSet.Rd | 3 - man/GenericTabularFileSet.Rd | 2 man/RDataFileSet.Rd | 2 man/RdsFileSet.Rd | 2 man/TabularTextFileSet.Rd | 2 man/dsApply.GenericDataFileSet.Rd | 7 +- man/getNames.GenericDataFileSet.Rd | 8 ++ man/linkTo.GenericDataFile.Rd | 7 ++ tests/GenericDataFileSet,dsApply.R | 5 + tests/GenericDataFileSet.R | 19 ++++++ tests/TabularTextFile,extend.R |only tests/readDataFrame.R |only 21 files changed, 220 insertions(+), 58 deletions(-)
Title: Mixture and Flexible Discriminant Analysis
Description: Mixture and flexible discriminant analysis, multivariate
adaptive regression splines (MARS), BRUTO, ...
Author: S original by Trevor Hastie & Robert Tibshirani. Original R port by Friedrich Leisch, Kurt Hornik and Brian D. Ripley.
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between mda versions 0.4-6 dated 2015-05-10 and 0.4-7 dated 2015-05-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/dmarss.f | 1 + src/rat/dmarss.r | 3 ++- 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer).
Author: Steven P. Millard <EnvStats@ProbStatInfo.com>
Maintainer: Steven P. Millard <EnvStats@ProbStatInfo.com>
Diff between EnvStats versions 2.0.0 dated 2015-03-09 and 2.0.1 dated 2015-05-25
DESCRIPTION | 8 MD5 | 212 ++++++++++++------------ NEWS | 16 + R/errorBar.R | 62 ++++--- R/stripChart.default.R | 18 +- R/summaryStats.formula.R | 7 data/Air.df.rda |binary data/Benthic.df.rda |binary data/Distribution.df.rda |binary data/EPA.02d.Ex.2.ug.per.L.vec.rda |binary data/EPA.02d.Ex.4.mg.per.kg.vec.rda |binary data/EPA.02d.Ex.6.mg.per.kg.vec.rda |binary data/EPA.02d.Ex.9.mg.per.L.vec.rda |binary data/EPA.09.Ex.10.1.nickel.df.rda |binary data/EPA.09.Ex.11.1.arsenic.df.rda |binary data/EPA.09.Ex.12.1.ccl4.df.rda |binary data/EPA.09.Ex.12.4.naphthalene.df.rda |binary data/EPA.09.Ex.13.1.iron.df.rda |binary data/EPA.09.Ex.14.1.manganese.df.rda |binary data/EPA.09.Ex.14.3.alkalinity.df.rda |binary data/EPA.09.Ex.14.4.arsenic.df.rda |binary data/EPA.09.Ex.14.8.df.rda |binary data/EPA.09.Ex.15.1.manganese.df.rda |binary data/EPA.09.Ex.16.1.sulfate.df.rda |binary data/EPA.09.Ex.16.2.benzene.df.rda |binary data/EPA.09.Ex.16.4.copper.df.rda |binary data/EPA.09.Ex.16.5.PCE.df.rda |binary data/EPA.09.Ex.17.1.loglead.df.rda |binary data/EPA.09.Ex.17.2.toluene.df.rda |binary data/EPA.09.Ex.17.3.chrysene.df.rda |binary data/EPA.09.Ex.17.3.log.chrysene.df.rda |binary data/EPA.09.Ex.17.4.copper.df.rda |binary data/EPA.09.Ex.17.5.chloride.df.rda |binary data/EPA.09.Ex.17.6.sulfate.df.rda |binary data/EPA.09.Ex.17.7.sodium.df.rda |binary data/EPA.09.Ex.18.1.arsenic.df.rda |binary data/EPA.09.Ex.18.2.chrysene.df.rda |binary data/EPA.09.Ex.18.3.TCE.df.rda |binary data/EPA.09.Ex.18.4.xylene.df.rda |binary data/EPA.09.Ex.19.1.sulfate.df.rda |binary data/EPA.09.Ex.19.2.chloride.df.rda |binary data/EPA.09.Ex.19.5.mercury.df.rda |binary data/EPA.09.Ex.20.1.nickel.df.rda |binary data/EPA.09.Ex.21.1.aldicarb.df.rda |binary data/EPA.09.Ex.21.2.benzene.df.rda |binary data/EPA.09.Ex.21.5.beryllium.df.rda |binary data/EPA.09.Ex.21.6.nitrate.df.rda |binary data/EPA.09.Ex.21.7.TCE.df.rda |binary data/EPA.09.Ex.22.1.VC.df.rda |binary data/EPA.09.Ex.22.2.Specific.Conductance.df.rda |binary data/EPA.09.Ex.6.3.sulfate.df.rda |binary data/EPA.09.Ex.7.1.arsenic.df.rda |binary data/EPA.09.Table.9.1.TCE.df.rda |binary data/EPA.09.Table.9.3.df.rda |binary data/EPA.09.Table.9.4.nickel.vec.rda |binary data/EPA.89b.aldicarb1.df.rda |binary data/EPA.89b.aldicarb2.df.rda |binary data/EPA.89b.benzene.df.rda |binary data/EPA.89b.cadmium.df.rda |binary data/EPA.89b.chlordane1.df.rda |binary data/EPA.89b.chlordane2.df.rda |binary data/EPA.89b.edb.df.rda |binary data/EPA.89b.lead.df.rda |binary data/EPA.89b.loglead.df.rda |binary data/EPA.89b.manganese.df.rda |binary data/EPA.89b.sulfate.df.rda |binary data/EPA.89b.t29.df.rda |binary data/EPA.89b.toc.vec.rda |binary data/EPA.92c.arsenic1.df.rda |binary data/EPA.92c.arsenic2.df.rda |binary data/EPA.92c.arsenic3.df.rda |binary data/EPA.92c.benzene1.df.rda |binary data/EPA.92c.benzene2.df.rda |binary data/EPA.92c.ccl4.df.rda |binary data/EPA.92c.chrysene.df.rda |binary data/EPA.92c.copper1.df.rda |binary data/EPA.92c.copper2.df.rda |binary data/EPA.92c.lognickel1.df.rda |binary data/EPA.92c.nickel1.df.rda |binary data/EPA.92c.nickel2.df.rda |binary data/EPA.92c.toluene.df.rda |binary data/EPA.92c.zinc.df.rda |binary data/EPA.92d.chromium.df.rda |binary data/EPA.92d.chromium.vec.rda |binary data/EPA.94b.lead.df.rda |binary data/EPA.94b.tccb.df.rda |binary data/EPA.97.cadmium.111.df.rda |binary data/Environmental.df.rda |binary data/Gibbons.et.al.09.Alkilinity.vec.rda |binary data/Gibbons.et.al.09.Vinyl.Chloride.vec.rda |binary data/Graham.et.al.75.etu.df.rda |binary data/Helsel.Cohn.88.app.b.df.rda |binary data/Helsel.Cohn.88.silver.df.rda |binary data/Lin.Evans.80.df.rda |binary data/Millard.Deverel.88.df.rda |binary data/Modified.TcCB.df.rda |binary data/NIOSH.89.air.lead.vec.rda |binary data/Olympic.NH4.df.rda |binary data/Ozone.NE.df.rda |binary data/Refinery.CO.df.rda |binary data/Skagit.NH3_N.df.rda |binary data/Total.P.df.rda |binary inst/CITATION | 2 inst/doc/EnvStats-manual.pdf |binary man/EnvStats-package.Rd | 4 man/stripChart.Rd | 17 + man/summaryStats.Rd | 11 + 107 files changed, 213 insertions(+), 144 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-3 dated 2015-05-23 and 1.1-4 dated 2015-05-24
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NAMESPACE | 1 R/DSC_DStream.R | 2 R/DSC_R.R | 3 - build/vignette.rds |binary inst/NEWS | 2 inst/doc/stream.pdf |binary src/DBSTREAM.cpp | 105 +++++++++++++++++++++++++--------------------------- src/DStream.cpp | 67 ++++++++++++++++++--------------- 10 files changed, 108 insertions(+), 100 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.4.0 dated 2014-05-30 and 1.5.0 dated 2015-05-24
wsrf-1.4.0/wsrf/R/merge.wsrf.R |only wsrf-1.4.0/wsrf/R/oobErrorRate.wsrf.R |only wsrf-1.4.0/wsrf/R/summary.wsrf.R |only wsrf-1.4.0/wsrf/man/oobErrorRate.wsrf.Rd |only wsrf-1.4.0/wsrf/man/summary.wsrf.Rd |only wsrf-1.4.0/wsrf/src/RF_deployment.cpp |only wsrf-1.4.0/wsrf/src/RF_deployment.h |only wsrf-1.4.0/wsrf/src/attribute_selection_method.cpp |only wsrf-1.4.0/wsrf/src/attribute_selection_method.h |only wsrf-1.4.0/wsrf/src/attribute_value_mapper.cpp |only wsrf-1.4.0/wsrf/src/attribute_value_mapper.h |only wsrf-1.4.0/wsrf/src/c4_5_attribute_selection_method.cpp |only wsrf-1.4.0/wsrf/src/c4_5_attribute_selection_method.h |only wsrf-1.4.0/wsrf/src/decision_tree.cpp |only wsrf-1.4.0/wsrf/src/decision_tree.h |only wsrf-1.4.0/wsrf/src/node.cpp |only wsrf-1.4.0/wsrf/src/random_forests.cpp |only wsrf-1.4.0/wsrf/src/random_forests.h |only wsrf-1.4.0/wsrf/src/training_set.cpp |only wsrf-1.4.0/wsrf/src/training_set.h |only wsrf-1.4.0/wsrf/src/weighted_random_forest.cpp |only wsrf-1.4.0/wsrf/src/weighted_random_forest.h |only wsrf-1.5.0/wsrf/DESCRIPTION | 42 +- wsrf-1.5.0/wsrf/MD5 | 93 ++--- wsrf-1.5.0/wsrf/NAMESPACE | 10 wsrf-1.5.0/wsrf/R/combine.wsrf.R |only wsrf-1.5.0/wsrf/R/correlation.wsrf.R | 2 wsrf-1.5.0/wsrf/R/importance.wsrf.R |only wsrf-1.5.0/wsrf/R/oob.error.rate.wsrf.R |only wsrf-1.5.0/wsrf/R/predict.wsrf.R | 66 +-- wsrf-1.5.0/wsrf/R/print.wsrf.R | 92 ----- wsrf-1.5.0/wsrf/R/strength.wsrf.R | 4 wsrf-1.5.0/wsrf/R/subset.wsrf.R |only wsrf-1.5.0/wsrf/R/varCounts.wsrf.R | 57 +-- wsrf-1.5.0/wsrf/R/wsrf.R | 259 +++++++------- wsrf-1.5.0/wsrf/R/wsrf.R.in | 259 +++++++------- wsrf-1.5.0/wsrf/README.md | 17 wsrf-1.5.0/wsrf/build/vignette.rds |binary wsrf-1.5.0/wsrf/configure | 18 wsrf-1.5.0/wsrf/inst/NEWS.Rd | 102 ++++- wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.R | 50 -- wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.Rnw | 3 wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.pdf |binary wsrf-1.5.0/wsrf/man/combine.wsrf.Rd |only wsrf-1.5.0/wsrf/man/importance.wsrf.Rd |only wsrf-1.5.0/wsrf/man/oob.error.rate.wsrf.Rd |only wsrf-1.5.0/wsrf/man/print.wsrf.Rd | 13 wsrf-1.5.0/wsrf/man/subset.wsrf.Rd |only wsrf-1.5.0/wsrf/man/wsrf.Rd | 76 ++-- wsrf-1.5.0/wsrf/src/IGR.cpp | 209 ++++++----- wsrf-1.5.0/wsrf/src/IGR.h | 43 +- wsrf-1.5.0/wsrf/src/c4_5_var_selector.cpp |only wsrf-1.5.0/wsrf/src/c4_5_var_selector.h |only wsrf-1.5.0/wsrf/src/dataset.cpp |only wsrf-1.5.0/wsrf/src/dataset.h |only wsrf-1.5.0/wsrf/src/meta_data.cpp |only wsrf-1.5.0/wsrf/src/meta_data.h |only wsrf-1.5.0/wsrf/src/node.h | 289 +++++++++++----- wsrf-1.5.0/wsrf/src/rforest.cpp |only wsrf-1.5.0/wsrf/src/rforest.h |only wsrf-1.5.0/wsrf/src/tree.cpp |only wsrf-1.5.0/wsrf/src/tree.h |only wsrf-1.5.0/wsrf/src/utility.h | 142 ++++--- wsrf-1.5.0/wsrf/src/var_selector.h |only wsrf-1.5.0/wsrf/src/wsrf.cpp |only wsrf-1.5.0/wsrf/src/wsrf.h |only wsrf-1.5.0/wsrf/tests/wsrftest.R | 48 +- wsrf-1.5.0/wsrf/tests/wsrftest.Rout.save | 127 +++---- wsrf-1.5.0/wsrf/vignettes/wsrfGuide.Rnw | 3 69 files changed, 1116 insertions(+), 908 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multi-variate clustering (MVC), cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 1.2.0 dated 2015-03-27 and 1.2.1 dated 2015-05-24
DESCRIPTION | 12 +++--- MD5 | 40 +++++++++++----------- R/HiClimR.R | 93 ++++++++++++++++++++++++++++++---------------------- R/coarseR.R | 3 + R/fastCor.R | 3 + R/geogMask.R | 49 ++++++++++++++------------- R/grid2D.R | 3 + R/minSigCor.R | 3 + R/validClimR.R | 25 +++++++------- README.md | 95 +++++++++++++++++++++++++++++++++++++++++++----------- inst/CITATION | 15 +++++--- man/HiClimR.Rd | 29 +++++++++++----- man/TestCase.Rd | 2 - man/WorldMask.Rd | 2 - man/coarseR.Rd | 2 - man/fastCor.Rd | 4 +- man/geogMask.Rd | 18 +++++++--- man/grid2D.Rd | 13 +++---- man/minSigCor.Rd | 2 - man/validClimR.Rd | 13 +++++-- src/HiClimR.f90 | 17 +++++---- 21 files changed, 278 insertions(+), 165 deletions(-)
Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological (developmental) processes to capture evolutionary signals in developmental transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>
Diff between myTAI versions 0.0.2 dated 2014-12-27 and 0.1.0 dated 2015-05-24
myTAI-0.0.2/myTAI/man/combinatorialSignificance.Rd |only myTAI-0.1.0/myTAI/DESCRIPTION | 19 myTAI-0.1.0/myTAI/MD5 | 160 ++-- myTAI-0.1.0/myTAI/NAMESPACE | 7 myTAI-0.1.0/myTAI/R/CollapseReplicates.R |only myTAI-0.1.0/myTAI/R/EarlyConservationTest.R | 60 + myTAI-0.1.0/myTAI/R/FilterRNASeqCT.R |only myTAI-0.1.0/myTAI/R/FlatLineTest.R | 52 + myTAI-0.1.0/myTAI/R/PlotBarRE.R | 12 myTAI-0.1.0/myTAI/R/PlotCorrelation.R | 18 myTAI-0.1.0/myTAI/R/PlotDistribution.R | 6 myTAI-0.1.0/myTAI/R/PlotMeans.R | 4 myTAI-0.1.0/myTAI/R/PlotPattern.R | 186 ++++- myTAI-0.1.0/myTAI/R/PlotRE.R | 2 myTAI-0.1.0/myTAI/R/ReductiveHourglassTest.R | 48 - myTAI-0.1.0/myTAI/R/TAI.R | 7 myTAI-0.1.0/myTAI/R/TDI.R | 4 myTAI-0.1.0/myTAI/R/age.apply.R | 11 myTAI-0.1.0/myTAI/R/base.R | 23 myTAI-0.1.0/myTAI/R/bootMatrix.R | 16 myTAI-0.1.0/myTAI/R/combinatorialSignificance.R | 35 - myTAI-0.1.0/myTAI/R/datasets.R | 16 myTAI-0.1.0/myTAI/R/ecScore.R | 3 myTAI-0.1.0/myTAI/R/pMatrix.R | 5 myTAI-0.1.0/myTAI/R/pStrata.R |only myTAI-0.1.0/myTAI/R/rel_exp.R | 16 myTAI-0.1.0/myTAI/R/tf.R | 10 myTAI-0.1.0/myTAI/README.md | 125 +-- myTAI-0.1.0/myTAI/build/vignette.rds |binary myTAI-0.1.0/myTAI/inst/doc/Advanced.R | 78 -- myTAI-0.1.0/myTAI/inst/doc/Advanced.Rmd | 141 ---- myTAI-0.1.0/myTAI/inst/doc/Advanced.html | 113 --- myTAI-0.1.0/myTAI/inst/doc/Intermediate.R | 66 - myTAI-0.1.0/myTAI/inst/doc/Intermediate.Rmd | 78 +- myTAI-0.1.0/myTAI/inst/doc/Intermediate.html | 79 +- myTAI-0.1.0/myTAI/inst/doc/Introduction.R | 160 ++-- myTAI-0.1.0/myTAI/inst/doc/Introduction.Rmd | 551 ++++++++++------ myTAI-0.1.0/myTAI/inst/doc/Introduction.html | 406 +++++++---- myTAI-0.1.0/myTAI/man/CollapseReplicates.Rd |only myTAI-0.1.0/myTAI/man/CombinatorialSignificance.Rd |only myTAI-0.1.0/myTAI/man/DivergenceExpressionSetExample.Rd | 10 myTAI-0.1.0/myTAI/man/EarlyConservationTest.Rd | 27 myTAI-0.1.0/myTAI/man/FilterRNASeqCT.Rd |only myTAI-0.1.0/myTAI/man/FlatLineTest.Rd | 29 myTAI-0.1.0/myTAI/man/MatchMap.Rd | 9 myTAI-0.1.0/myTAI/man/PhyloExpressionSetExample.Rd | 10 myTAI-0.1.0/myTAI/man/PlotBarRE.Rd | 6 myTAI-0.1.0/myTAI/man/PlotCorrelation.Rd | 13 myTAI-0.1.0/myTAI/man/PlotDistribution.Rd | 6 myTAI-0.1.0/myTAI/man/PlotMeans.Rd | 4 myTAI-0.1.0/myTAI/man/PlotPattern.Rd | 73 +- myTAI-0.1.0/myTAI/man/PlotRE.Rd | 4 myTAI-0.1.0/myTAI/man/RE.Rd | 8 myTAI-0.1.0/myTAI/man/REMatrix.Rd | 9 myTAI-0.1.0/myTAI/man/ReductiveHourglassTest.Rd | 27 myTAI-0.1.0/myTAI/man/TAI.Rd | 8 myTAI-0.1.0/myTAI/man/TDI.Rd | 6 myTAI-0.1.0/myTAI/man/age.apply.Rd | 7 myTAI-0.1.0/myTAI/man/bar.colors.Rd | 8 myTAI-0.1.0/myTAI/man/bootMatrix.Rd | 12 myTAI-0.1.0/myTAI/man/ecScore.Rd | 5 myTAI-0.1.0/myTAI/man/is.ExpressionSet.Rd | 4 myTAI-0.1.0/myTAI/man/omitMatrix.Rd | 6 myTAI-0.1.0/myTAI/man/pMatrix.Rd | 7 myTAI-0.1.0/myTAI/man/pStrata.Rd |only myTAI-0.1.0/myTAI/man/rhScore.Rd | 2 myTAI-0.1.0/myTAI/man/tf.Rd | 12 myTAI-0.1.0/myTAI/src/RcppExports.cpp | 94 +- myTAI-0.1.0/myTAI/src/rcpp_funcs.cpp | 2 myTAI-0.1.0/myTAI/tests |only myTAI-0.1.0/myTAI/vignettes/Advanced.Rmd | 141 ---- myTAI-0.1.0/myTAI/vignettes/Intermediate.Rmd | 78 +- myTAI-0.1.0/myTAI/vignettes/Introduction.Rmd | 551 ++++++++++------ 73 files changed, 2033 insertions(+), 1662 deletions(-)
Title: Penalized Likelihood Estimation under the Joint Cox Models
Between TTP and OS for Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between TTP and OS for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <emura@stat.ncu.edu.tw>
Diff between joint.Cox versions 1.0 dated 2015-02-28 and 1.1 dated 2015-05-24
DESCRIPTION | 10 - MD5 | 14 +- R/joint.Cox-internal.R | 250 +++++++++++++++++++++++----------------------- R/jointCox.indep.reg.R |only R/jointCox.reg.R | 229 +++++++++++++++++++++--------------------- data |only man/dataOvarian.Rd |only man/joint.Cox-package.Rd | 11 +- man/jointCox.indep.reg.Rd |only man/jointCox.reg.Rd | 85 +++++++++------ 10 files changed, 315 insertions(+), 284 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts
('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and
supporting most output formats of R graphics including PNG, PDF and
SVG. Text glyphs will be converted into polygons or raster images,
hence after the plot has been created, it no longer relies on the font files.
No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-1 dated 2015-04-27 and 0.4-2 dated 2015-05-24
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- inst/NEWS.Rd | 8 ++++++++ man/showtext.auto.Rd | 2 +- man/showtext.begin.Rd | 2 +- man/showtext.end.Rd | 2 +- man/showtext.opts.Rd | 2 +- src/fonts.c | 44 ++++++++++++++++++++++++++------------------ 8 files changed, 50 insertions(+), 34 deletions(-)
Title: Simulating Data to Study Performance of Clustering Algorithms
Description: The utility of this package is in simulating mixtures of Gaussian
distributions with different levels of overlap between mixture
components. Pairwise overlap, defined as a sum of two
misclassification probabilities, measures the degree of
interaction between components and can be readily employed to
control the clustering complexity of datasets simulated from
mixtures. These datasets can then be used for systematic
performance investigation of clustering and finite mixture
modeling algorithms. Among other capabilities of 'MixSim', there
are computing the exact overlap for Gaussian mixtures,
simulating Gaussian and non-Gaussian data, simulating outliers
and noise variables, calculating various measures of agreement
between two partitionings, and constructing parallel
distribution plots for the graphical display of finite mixture
models.
Author: Volodymyr Melnykov [aut, cre],
Wei-Chen Chen [aut],
Ranjan Maitra [aut]
Maintainer: Volodymyr Melnykov <vmelnykov@cba.ua.edu>
Diff between MixSim versions 1.0-9 dated 2013-12-10 and 1.1-1 dated 2015-05-24
DESCRIPTION | 15 ++-- MD5 | 20 +++-- NAMESPACE | 10 ++ NEWS |only R/main.R | 102 +++++++++++++++++++++++++++--- cleanup |only man/MixGOM.Rd |only man/overlapGOM.Rd |only man/print.summary.Rd | 10 +- src/libEVD.c | 24 +------ src/libMixSim.c | 16 ++-- src/libOverlap.c | 173 +++++++++++++++++++++++++++++++++++++++++++++------ src/overlap.h | 4 - 13 files changed, 296 insertions(+), 78 deletions(-)
Title: R Functions for Elementary Statistics
Description: A collection of data sets and functions that are useful in the
teaching of statistics at an elementary level to students who may have
little or no previous experience with the command line. The functions for
elementary inferential procedures follow a uniform interface for user
input. Some of the functions are instructional applets that can only be
run on the R Studio integrated development environment with package
'manipulate' attached. R Studio is freely available (www.rstudio.org), and
includes package 'manipulate'. Other instructional applets are Shiny apps
that may be run locally. In teaching the package is used alongside of
package 'mosaic', 'mosaicData' and 'abd', which are therefore listed as
dependencies.
Author: Rebekah Robinson <rrobinson20@humana.com> and Homer
White <hwhite0@georgetowncollege.edu>
Maintainer: Homer White <hwhite0@georgetowncollege.edu>
Diff between tigerstats versions 0.2 dated 2014-12-03 and 0.2-6 dated 2015-05-23
DESCRIPTION | 38 +++++++++--------- MD5 | 70 +++++++++++++++++----------------- R/data.R | 3 - R/tigerstats-package.R | 2 R/ttestGC.R | 2 R/utilities.R | 24 +++++++++++ README.md | 4 + build/vignette.rds |binary inst/SlowGoodness/server.R | 86 +++++++++++++++++++++++++++++++++--------- inst/SlowGoodness/ui.R | 55 ++++++++++---------------- inst/doc/R_Descriptive.Rmd | 2 inst/doc/R_Descriptive.html | 8 +-- inst/doc/R_Inferential.R | 2 inst/doc/R_Inferential.Rmd | 6 +- inst/doc/R_Inferential.html | 6 +- inst/doc/binomtestGC.html | 2 inst/doc/chisqtestGC.html | 8 +-- inst/doc/favstats.R | 15 ++----- inst/doc/favstats.Rmd | 23 +++++------ inst/doc/favstats.html | 24 ++++++----- inst/doc/instructorNotes.R | 2 inst/doc/instructorNotes.Rmd | 2 inst/doc/instructorNotes.html | 6 +- inst/doc/pbinomGC.html | 14 +++--- inst/doc/pnormGC.html | 10 ++-- inst/doc/proptestGC.html | 16 +++---- inst/doc/qnorm.html | 6 +- inst/doc/qnormGC.html | 10 ++-- inst/doc/ttestGC.html | 20 ++++----- man/deathpen.Rd | 2 man/music.Rd | 1 man/tigerstats-package.Rd | 2 vignettes/R_Descriptive.Rmd | 2 vignettes/R_Inferential.Rmd | 6 +- vignettes/favstats.Rmd | 23 +++++------ vignettes/instructorNotes.Rmd | 2 36 files changed, 284 insertions(+), 220 deletions(-)
Title: R Client for the MTurk Requester API
Description: Provides programmatic access to the Amazon Mechanical Turk (MTurk) Requester API.
Author: Thomas J. Leeper [aut, cre],
Solomon Messing [ctb],
Sean Murphy [ctb],
Jonathan Chang [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between MTurkR versions 0.6 dated 2015-01-07 and 0.6.5.1 dated 2015-05-23
MTurkR-0.6.5.1/MTurkR/DESCRIPTION | 18 MTurkR-0.6.5.1/MTurkR/MD5 | 87 +- MTurkR-0.6.5.1/MTurkR/NAMESPACE | 6 MTurkR-0.6.5.1/MTurkR/NEWS | 28 MTurkR-0.6.5.1/MTurkR/R/BulkCreate.R |only MTurkR-0.6.5.1/MTurkR/R/CreateHIT.R | 18 MTurkR-0.6.5.1/MTurkR/R/DisableHIT.R | 16 MTurkR-0.6.5.1/MTurkR/R/ExtendHIT.R | 4 MTurkR-0.6.5.1/MTurkR/R/GenerateAnswerKey.R | 13 MTurkR-0.6.5.1/MTurkR/R/GenerateHITLayoutParameter.R | 9 MTurkR-0.6.5.1/MTurkR/R/GenerateHITsFromTemplate.R | 16 MTurkR-0.6.5.1/MTurkR/R/GenerateHTMLQuestion.R | 9 MTurkR-0.6.5.1/MTurkR/R/GenerateNotification.R | 32 MTurkR-0.6.5.1/MTurkR/R/GetStatistic.R | 54 - MTurkR-0.6.5.1/MTurkR/R/GrantBonus.R | 15 MTurkR-0.6.5.1/MTurkR/R/RejectQualification.R | 22 MTurkR-0.6.5.1/MTurkR/R/asdataframe.R | 4 MTurkR-0.6.5.1/MTurkR/R/onLoad.r | 20 MTurkR-0.6.5.1/MTurkR/R/wizard.R | 366 ++++++++-- MTurkR-0.6.5.1/MTurkR/README.md | 6 MTurkR-0.6.5.1/MTurkR/inst/templates/htmlquestion2.xml |only MTurkR-0.6.5.1/MTurkR/inst/templates/surveylink.xml |only MTurkR-0.6.5.1/MTurkR/man/AssignQualification.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/BulkCreate.Rd |only MTurkR-0.6.5.1/MTurkR/man/CreateHIT.Rd | 14 MTurkR-0.6.5.1/MTurkR/man/DisableHIT.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/DisposeHIT.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/ExtendHIT.Rd | 14 MTurkR-0.6.5.1/MTurkR/man/GenerateAnswerKey.Rd | 8 MTurkR-0.6.5.1/MTurkR/man/GenerateExternalQuestion.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GenerateHITLayoutParameter.Rd | 11 MTurkR-0.6.5.1/MTurkR/man/GenerateHITsFromTemplate.Rd | 45 - MTurkR-0.6.5.1/MTurkR/man/GenerateNotification.Rd | 5 MTurkR-0.6.5.1/MTurkR/man/GenerateQualificationRequirement.Rd | 5 MTurkR-0.6.5.1/MTurkR/man/GenerateReviewPolicy.Rd | 4 MTurkR-0.6.5.1/MTurkR/man/GetAssignment.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GetHIT.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GetHITsForQualificationType.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GetReviewableHITs.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GetStatistic.Rd | 4 MTurkR-0.6.5.1/MTurkR/man/GrantBonus.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/GrantQualification.Rd | 45 - MTurkR-0.6.5.1/MTurkR/man/MTurkR-package.Rd | 4 MTurkR-0.6.5.1/MTurkR/man/SearchHITs.Rd | 2 MTurkR-0.6.5.1/MTurkR/man/credentials.Rd | 5 MTurkR-0.6/MTurkR/R/hitsfromtemplate.R |only MTurkR-0.6/MTurkR/man/RejectQualification.Rd |only MTurkR-0.6/MTurkR/man/authenticate-internal.Rd |only 48 files changed, 642 insertions(+), 285 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-2 dated 2015-05-22 and 1.1-3 dated 2015-05-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS | 6 +++--- inst/doc/stream.pdf |binary src/DStream.cpp | 6 +++--- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.5 dated 2015-05-03 and 1.6 dated 2015-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/build.dist.struct.R | 4 ++-- man/rcbalance-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: R for Amplicon-Sequencing-Based Microbial-Ecology
Description: Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.
Author: Wen Chen, Joshua Simpson, C. Andre Levesque
Maintainer: Wen Chen <Wen.Chen@agr.gc.ca>
Diff between RAM versions 1.2.0 dated 2014-12-10 and 1.2.1 dated 2015-05-23
ChangeLog | 42 +++++ DESCRIPTION | 21 +- LICENSE | 4 MD5 | 51 ++++--- NAMESPACE | 10 - NEWS | 156 +++++++++++++--------- R/assist_NB.R | 23 +-- R/core.R | 17 +- R/group.Taxa.R | 11 - R/internal_functions.R | 46 ++++++ R/metadata.R | 50 ++++--- R/network.R |only R/phylo_taxonomy.R |only R/plot_heatmaps.R | 21 +- R/plot_misc.R | 311 ++++++++++++++++++++++++++++++++++++++++++-- R/process_data.R | 22 +-- R/seq_var.R |only R/summary.R | 20 +- R/taxonomy_functions.R | 58 +++++--- build/RAM.pdf |binary data/alignment.RData |only man/RAM-package.Rd | 4 man/alignment.Rd |only man/factor.abundance.Rd |only man/group.OTU.Rd | 6 man/group.abundance.meta.Rd |only man/group.heatmap.Rd | 3 man/network_data.Rd |only man/phylo_taxonomy.Rd |only man/phylog_taxonomy.Rd |only man/sample.map.Rd | 7 man/seq_var.Rd |only 32 files changed, 676 insertions(+), 207 deletions(-)
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.qpcr versions 1.1.7 dated 2015-04-30 and 1.2 dated 2015-05-23
DESCRIPTION | 8 +-- MD5 | 18 +++---- R/HPDsummary.R | 14 ++++- R/mcmc.qpcr.R | 28 +++++++---- R/mcmc.qpcr.classic.R | 20 ++++++-- R/mcmc.qpcr.lognormal.R | 109 +++++++++++++++++++-------------------------- man/MCMC.qpcr-package.Rd | 6 +- man/mcmc.qpcr.Rd | 16 +++--- man/mcmc.qpcr.classic.Rd | 14 ++++- man/mcmc.qpcr.lognormal.Rd | 39 ++++++++++------ 10 files changed, 156 insertions(+), 116 deletions(-)
Title: Foundations and Applications of Statistics Using R
Description: Data sets and utilities to accompany
"Foundations and Applications of Statistics: an Introduction
using R" (R Pruim, published by AMS, 2011), a text covering
topics from probability and mathematical statistics at an advanced
undergraduate level. R is integrated throughout, and access to all
the R code in the book is provided via the snippet function.
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between fastR versions 0.8-1 dated 2014-08-28 and 0.10 dated 2015-05-23
DESCRIPTION | 21 ++-- MD5 | 160 +++++++++++++++++++------------------- NAMESPACE | 2 R/datasets.R | 39 +-------- R/fastR-package.R | 5 - README.md |only inst/NEWS.Rd | 6 + inst/doc/Errata.Rnw | 4 inst/doc/Errata.pdf |binary inst/doc/Updates.Rnw | 11 +- inst/doc/Updates.pdf |binary inst/snippet/concrete-lm1.R | 4 inst/snippet/concrete-load.R | 4 man/Jordan8687.Rd | 3 man/actgpa.Rd | 3 man/airlineArrival.Rd | 3 man/airpollution.Rd | 3 man/balldrop.Rd | 3 man/batting.Rd | 3 man/births78.Rd | 3 man/buckthorn.Rd | 3 man/bugs.Rd | 3 man/col.fastR.Rd | 3 man/col.perc.Rd | 3 man/concrete.Rd | 3 man/corn.Rd | 9 +- man/cuckoo.Rd | 3 man/deathPenalty.Rd | 3 man/drag.Rd | 3 man/endurance.Rd | 9 +- man/familySmoking.Rd | 3 man/fastR-package.Rd | 27 ------ man/fumbles.Rd | 3 man/fusion.Rd | 3 man/geolm.Rd | 3 man/givenOrder.Rd | 3 man/golfballs.Rd | 3 man/gpa.Rd | 3 man/heliumFootballs.Rd | 3 man/ice.Rd | 3 man/inflation.Rd | 3 man/kids.Rd | 3 man/littleSurvey.Rd | 3 man/mathnoise.Rd | 3 man/miaa05.Rd | 3 man/mlb2004.Rd | 3 man/ncaa2010.Rd | 3 man/nfl2007.Rd | 3 man/nlmax.Rd | 3 man/noise.Rd | 3 man/palettes.Rd | 3 man/paperplanes.Rd | 3 man/pendulum.Rd | 3 man/petstress.Rd | 3 man/pigs.Rd | 3 man/pitching2005.Rd | 3 man/poison.Rd | 3 man/punting.Rd | 3 man/ratpoison.Rd | 3 man/rgolfballs.Rd | 3 man/rubberband.Rd | 3 man/scent.Rd | 3 man/snippet.Rd | 29 +++--- man/soap.Rd | 3 man/spheres.Rd | 3 man/step.Rd | 3 man/stereogram.Rd | 3 man/students.Rd | 3 man/tastetest.Rd | 3 man/tdf.Rd | 3 man/tirewear.Rd | 3 man/traffic.Rd | 3 man/trebuchet.Rd | 3 man/undocumented.Rd | 3 man/utilities.Rd | 3 man/vaov.Rd | 3 man/wilson.ci.Rd | 3 man/workingWomen.Rd | 3 man/xplot.Rd | 27 +++--- vignettes/Errata.Rnw | 4 vignettes/Updates-concordance.tex |only vignettes/Updates.Rnw | 11 +- 82 files changed, 302 insertions(+), 253 deletions(-)
Title: Public Subject Attention via Wikipedia Page Access Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied. For the omnipresent Wikipedia those access statistics
are made available via 'http://stats.grok.se' a server providing
the information as file dumps as well as as web API. This package
provides an easy to use, consistent and traffic minimizing
approach to make those data accessible within R.
Author: Peter Meissner [aut, cre], R Core team [ctb] ('wp_date()'
derived from base package's 'as.Date()')
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 0.2.0 dated 2014-11-07 and 1.1.1 dated 2015-05-22
wikipediatrend-0.2.0/wikipediatrend/R/chunk.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_date.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_day.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_extract_data.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_friendly_load.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_friendly_save.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_month.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_wday.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_year.R |only wikipediatrend-0.2.0/wikipediatrend/R/wp_yearmonth.R |only wikipediatrend-0.2.0/wikipediatrend/man/chunk.Rd |only wikipediatrend-0.2.0/wikipediatrend/man/wp_extract_data.Rd |only wikipediatrend-0.2.0/wikipediatrend/man/wp_friendly_load.Rd |only wikipediatrend-0.2.0/wikipediatrend/man/wp_friendly_save.Rd |only wikipediatrend-1.1.1/wikipediatrend/DESCRIPTION | 45 +- wikipediatrend-1.1.1/wikipediatrend/MD5 | 92 +++- wikipediatrend-1.1.1/wikipediatrend/NAMESPACE | 37 + wikipediatrend-1.1.1/wikipediatrend/NEWS |only wikipediatrend-1.1.1/wikipediatrend/R/aa_pversion_inc.r |only wikipediatrend-1.1.1/wikipediatrend/R/wp_cache.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_check_date_inputs.R | 24 + wikipediatrend-1.1.1/wikipediatrend/R/wp_date_functions.r |only wikipediatrend-1.1.1/wikipediatrend/R/wp_df.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_download_data.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_expand_ts.R | 1 wikipediatrend-1.1.1/wikipediatrend/R/wp_get_data.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_http_header.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_jsons_to_df.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_last_month.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_linked_pages.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_load_and_save.r |only wikipediatrend-1.1.1/wikipediatrend/R/wp_prepare_urls.R |only wikipediatrend-1.1.1/wikipediatrend/R/wp_trend.R | 189 +++++----- wikipediatrend-1.1.1/wikipediatrend/R/zzz.R |only wikipediatrend-1.1.1/wikipediatrend/README.md |only wikipediatrend-1.1.1/wikipediatrend/build |only wikipediatrend-1.1.1/wikipediatrend/inst |only wikipediatrend-1.1.1/wikipediatrend/man/prev_month_end.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/prev_month_start.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/print.wp_df.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/pversion_inc.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/read_utf8_csv.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/toUTF8.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_add_to_cache.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_cache.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_cache_default.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_cache_file.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_cache_load.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_cache_reset.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_check_date_inputs.Rd | 5 wikipediatrend-1.1.1/wikipediatrend/man/wp_date.Rd | 18 wikipediatrend-1.1.1/wikipediatrend/man/wp_day.Rd | 61 +-- wikipediatrend-1.1.1/wikipediatrend/man/wp_download_data.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_expand_ts.Rd | 3 wikipediatrend-1.1.1/wikipediatrend/man/wp_get_cache.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_get_data.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_http_header.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_jsons_to_df.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_linked_pages.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_load.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_month.Rd | 61 +-- wikipediatrend-1.1.1/wikipediatrend/man/wp_prepare_urls.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_save.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_save_cache.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_set_cache_file.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_set_print_options.Rd |only wikipediatrend-1.1.1/wikipediatrend/man/wp_trend.Rd | 129 +++--- wikipediatrend-1.1.1/wikipediatrend/man/wp_wday.Rd | 67 +-- wikipediatrend-1.1.1/wikipediatrend/man/wp_year.Rd | 57 +-- wikipediatrend-1.1.1/wikipediatrend/man/wp_yearmonth.Rd | 33 - wikipediatrend-1.1.1/wikipediatrend/man/write_utf8_csv.Rd |only wikipediatrend-1.1.1/wikipediatrend/tests |only wikipediatrend-1.1.1/wikipediatrend/vignettes |only 73 files changed, 459 insertions(+), 363 deletions(-)
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Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.1.0 dated 2015-05-15 and 1.1.1 dated 2015-05-22
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ inst/doc/article.R | 8 ++++---- inst/doc/article.Rnw | 8 ++++---- inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary src/progutils.cpp | 2 +- vignettes/article.Rnw | 8 ++++---- vignettes/mybib.bib | 2 +- 10 files changed, 34 insertions(+), 27 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.1.4 dated 2015-05-21 and 0.1.5 dated 2015-05-22
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 8 +- inst/doc/References.pdf |binary src/smgm.f90 | 147 ++++++++++++++++++++++++++++++------------------ 5 files changed, 106 insertions(+), 62 deletions(-)
Title: Variable Selection in Clustering by Mixture Models for Discrete
Data
Description: An implementation of a variable selection procedure in clustering by mixture of multinomial models for discrete data. Genotype data are examples of such data with two unordered observations (alleles) at each locus for diploid individual. The two-fold problem of variable selection and clustering is seen as a model selection problem where competing models are characterized by the number of clusters K, and the subset S of clustering variables. Competing models are compared by penalized maximum likelihood criteria. We considered asymptotic criteria such as Akaike and Bayesian Information criteria, and a family of penalized criteria with penalty function to be data driven calibrated.
Author: Wilson Toussile
Maintainer: Wilson Toussile <wilson.toussile@gmail.com>
Diff between ClustMMDD versions 1.0.0 dated 2015-05-20 and 1.0.1 dated 2015-05-22
DESCRIPTION | 8 - MD5 | 13 +- NAMESPACE | 1 R/modelKS.R | 19 +++ man/ClustMMDD-package.Rd | 2 man/model-methods.Rd |only man/modelKS-class.Rd | 2 src/ClustMMDD.cpp | 235 +++++++++++++++++++++++------------------------ 8 files changed, 152 insertions(+), 128 deletions(-)
Title: 'TSdbi' Illustration
Description: Illustrates the various 'TSdbi' packages with a vignette using time series
data from several sources. The vignette also illustrates some simple time series
manipulation and plotting using packages 'tframe' and 'tfplot'.
Author: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between TSdata versions 2015.4-1 dated 2015-05-01 and 2015.4-2 dated 2015-05-22
TSdata-2015.4-1/TSdata/tests |only TSdata-2015.4-2/TSdata/DESCRIPTION | 6 +++--- TSdata-2015.4-2/TSdata/MD5 | 6 +++--- TSdata-2015.4-2/TSdata/NEWS | 6 ++++++ TSdata-2015.4-2/TSdata/inst/testWithAllServers |only 5 files changed, 12 insertions(+), 6 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 0.9.1 dated 2014-10-01 and 0.10.0 dated 2015-05-22
testthat-0.10.0/testthat/DESCRIPTION | 39 testthat-0.10.0/testthat/MD5 | 184 ++-- testthat-0.10.0/testthat/NAMESPACE | 23 testthat-0.10.0/testthat/R/auto-test.r | 4 testthat-0.10.0/testthat/R/colour-text.r | 86 - testthat-0.10.0/testthat/R/compare.r | 168 +++ testthat-0.10.0/testthat/R/evaluate-promise.r | 2 testthat-0.10.0/testthat/R/expect-that.r | 58 - testthat-0.10.0/testthat/R/expectations-equality.R |only testthat-0.10.0/testthat/R/expectations-matches.R |only testthat-0.10.0/testthat/R/expectations-old.R |only testthat-0.10.0/testthat/R/expectations.r | 524 +----------- testthat-0.10.0/testthat/R/mock.r | 6 testthat-0.10.0/testthat/R/reporter-check.R |only testthat-0.10.0/testthat/R/reporter-list.r | 47 - testthat-0.10.0/testthat/R/reporter-minimal.r | 10 testthat-0.10.0/testthat/R/reporter-rstudio.R |only testthat-0.10.0/testthat/R/reporter-silent.r | 1 testthat-0.10.0/testthat/R/reporter-stop.r | 1 testthat-0.10.0/testthat/R/reporter-summary.r | 43 testthat-0.10.0/testthat/R/reporter-tap.r | 4 testthat-0.10.0/testthat/R/reporter-teamcity.r | 1 testthat-0.10.0/testthat/R/reporter-zzz.r | 6 testthat-0.10.0/testthat/R/reporter.r | 7 testthat-0.10.0/testthat/R/test-example.R |only testthat-0.10.0/testthat/R/test-files.r | 106 +- testthat-0.10.0/testthat/R/test-package.r | 38 testthat-0.10.0/testthat/R/test-results.r |only testthat-0.10.0/testthat/R/test-that.r | 11 testthat-0.10.0/testthat/R/traceback.r | 2 testthat-0.10.0/testthat/R/utils.r | 33 testthat-0.10.0/testthat/README.md | 11 testthat-0.10.0/testthat/man/CheckReporter-class.Rd |only testthat-0.10.0/testthat/man/ListReporter-class.Rd | 3 testthat-0.10.0/testthat/man/MinimalReporter-class.Rd | 3 testthat-0.10.0/testthat/man/MultiReporter-class.Rd | 3 testthat-0.10.0/testthat/man/Reporter-class.Rd | 3 testthat-0.10.0/testthat/man/RstudioReporter-class.Rd |only testthat-0.10.0/testthat/man/SilentReporter-class.Rd | 3 testthat-0.10.0/testthat/man/StopReporter-class.Rd | 3 testthat-0.10.0/testthat/man/SummaryReporter-class.Rd | 3 testthat-0.10.0/testthat/man/TapReporter-class.Rd | 3 testthat-0.10.0/testthat/man/TeamcityReporter-class.Rd | 3 testthat-0.10.0/testthat/man/auto_test.Rd | 3 testthat-0.10.0/testthat/man/auto_test_package.Rd | 3 testthat-0.10.0/testthat/man/compare.Rd |only testthat-0.10.0/testthat/man/compare_state.Rd | 3 testthat-0.10.0/testthat/man/context.Rd | 3 testthat-0.10.0/testthat/man/describe.Rd | 3 testthat-0.10.0/testthat/man/dir_state.Rd | 3 testthat-0.10.0/testthat/man/equivalence.Rd |only testthat-0.10.0/testthat/man/evaluate_promise.Rd | 3 testthat-0.10.0/testthat/man/expect-compare.Rd | 52 - testthat-0.10.0/testthat/man/expect_equal_to_reference.Rd |only testthat-0.10.0/testthat/man/expect_is.Rd |only testthat-0.10.0/testthat/man/expect_named.Rd |only testthat-0.10.0/testthat/man/expect_null.Rd |only testthat-0.10.0/testthat/man/expect_that.Rd | 28 testthat-0.10.0/testthat/man/expect_true.Rd |only testthat-0.10.0/testthat/man/expectation.Rd | 3 testthat-0.10.0/testthat/man/fail.Rd | 5 testthat-0.10.0/testthat/man/find_reporter.Rd | 8 testthat-0.10.0/testthat/man/find_test_scripts.Rd |only testthat-0.10.0/testthat/man/make_expectation.Rd | 3 testthat-0.10.0/testthat/man/matching-expectations.Rd |only testthat-0.10.0/testthat/man/not.Rd | 3 testthat-0.10.0/testthat/man/oldskool.Rd |only testthat-0.10.0/testthat/man/reporter-accessors.Rd | 3 testthat-0.10.0/testthat/man/safe_digest.Rd | 3 testthat-0.10.0/testthat/man/setup_test_dir.Rd |only testthat-0.10.0/testthat/man/skip.Rd | 28 testthat-0.10.0/testthat/man/source_dir.Rd | 3 testthat-0.10.0/testthat/man/source_test_helpers.Rd |only testthat-0.10.0/testthat/man/succeed.Rd |only testthat-0.10.0/testthat/man/takes_less_than.Rd | 37 testthat-0.10.0/testthat/man/test_dir.Rd | 9 testthat-0.10.0/testthat/man/test_env.Rd | 3 testthat-0.10.0/testthat/man/test_examples.Rd |only testthat-0.10.0/testthat/man/test_file.Rd | 10 testthat-0.10.0/testthat/man/test_package.Rd | 13 testthat-0.10.0/testthat/man/test_that.Rd | 3 testthat-0.10.0/testthat/man/testthat.Rd | 3 testthat-0.10.0/testthat/man/testthat_results.Rd |only testthat-0.10.0/testthat/man/watch.Rd | 3 testthat-0.10.0/testthat/man/with_mock.Rd | 3 testthat-0.10.0/testthat/src/reassign.c | 6 testthat-0.10.0/testthat/tests/testthat.R | 1 testthat-0.10.0/testthat/tests/testthat/helper-assign.R |only testthat-0.10.0/testthat/tests/testthat/test-bare.r | 11 testthat-0.10.0/testthat/tests/testthat/test-colour.r |only testthat-0.10.0/testthat/tests/testthat/test-compare.r | 4 testthat-0.10.0/testthat/tests/testthat/test-context.r | 6 testthat-0.10.0/testthat/tests/testthat/test-environment.R | 8 testthat-0.10.0/testthat/tests/testthat/test-expectations.r | 38 testthat-0.10.0/testthat/tests/testthat/test-helpers.R |only testthat-0.10.0/testthat/tests/testthat/test-mock.r | 18 testthat-0.10.0/testthat/tests/testthat/test-silence.R |only testthat-0.10.0/testthat/tests/testthat/test-test_dir.r | 49 - testthat-0.10.0/testthat/tests/testthat/test-xxx.r | 4 testthat-0.9.1/testthat/R/library.r |only testthat-0.9.1/testthat/man/colourise.Rd |only testthat-0.9.1/testthat/man/equals.Rd |only testthat-0.9.1/testthat/man/equals_reference.Rd |only testthat-0.9.1/testthat/man/gives_warning.Rd |only testthat-0.9.1/testthat/man/has_names.Rd |only testthat-0.9.1/testthat/man/is_a.Rd |only testthat-0.9.1/testthat/man/is_equivalent_to.Rd |only testthat-0.9.1/testthat/man/is_identical_to.Rd |only testthat-0.9.1/testthat/man/is_null.Rd |only testthat-0.9.1/testthat/man/is_true.Rd |only testthat-0.9.1/testthat/man/library_if_available.Rd |only testthat-0.9.1/testthat/man/matches.Rd |only testthat-0.9.1/testthat/man/prints_text.Rd |only testthat-0.9.1/testthat/man/shows_message.Rd |only testthat-0.9.1/testthat/man/throws_error.Rd |only 115 files changed, 805 insertions(+), 1026 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: The reproducer R package includes data analysis functions and data sets (e.g., related to software defect prediction) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut],
Marian Jureczko [ctb] (Data contributor),
Barbara Kitchenham [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.1.2 dated 2015-01-25 and 0.1.3 dated 2015-05-22
DESCRIPTION | 18 + MD5 | 44 ++-- NAMESPACE | 11 - R/MadeyskiKitchenhamMetaAnalysis.R |only R/data.R | 62 +++++ R/reproducer.R | 107 +++++++++- data/Ciolkowski09ESEM.MetaAnalysis.PBRvsCBRorAR.rda |only data/Madeyski15EISEJ.StudProjects.rda |binary data/MadeyskiKitchenham.MetaAnalysis.PBRvsCBRorAR.rda |only inst/CITATION | 45 ++++ inst/extdata/DataSet.xlsx |binary man/Ciolkowski09ESEM.MetaAnalysis.PBRvsCBRorAR.Rd |only man/Madeyski15EISEJ.OpenProjects.Rd | 2 man/Madeyski15EISEJ.PropProjects.Rd | 2 man/Madeyski15EISEJ.StudProjects.Rd | 4 man/Madeyski15SQJ.NDC.Rd | 2 man/MadeyskiKitchenham.MetaAnalysis.PBRvsCBRorAR.Rd |only man/boxplotAndDensityCurveOnHistogram.Rd | 4 man/boxplotHV.Rd | 2 man/cloudOfWords.Rd |only man/densityCurveOnHistogram.Rd | 2 man/printXTable.Rd |only man/readExcelSheet.Rd | 4 man/reproduceForestPlotRandomEffects.Rd |only man/reproduceMixedEffectsAnalysisWithEstimatedVarianceAndExperimentalDesignModerator.Rd |only man/reproduceMixedEffectsAnalysisWithExperimentalDesignModerator.Rd |only man/reproduceMixedEffectsForestPlotWithExperimentalDesignModerator.Rd |only man/reproduceTableWithEffectSizesBasedOnMeanDifferences.Rd |only man/reproduceTableWithPossibleModeratingFactors.Rd |only man/reproduceTableWithSourceDataByCiolkowski.Rd |only 30 files changed, 271 insertions(+), 38 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 0.9-12 dated 2015-05-05 and 1.0-1 dated 2015-05-22
manifestoR-0.9-12/manifestoR/R/renaming.R |only manifestoR-0.9-12/manifestoR/man/renamev9.Rd |only manifestoR-1.0-1/manifestoR/DESCRIPTION | 12 manifestoR-1.0-1/manifestoR/MD5 | 44 +-- manifestoR-1.0-1/manifestoR/NAMESPACE | 16 - manifestoR-1.0-1/manifestoR/R/codes.R | 68 ++++ manifestoR-1.0-1/manifestoR/R/corpus.R | 8 manifestoR-1.0-1/manifestoR/R/dataset.R |only manifestoR-1.0-1/manifestoR/R/manifesto.R | 12 manifestoR-1.0-1/manifestoR/R/manifestoR-package.r | 9 manifestoR-1.0-1/manifestoR/R/scaling_bootstrap.R | 9 manifestoR-1.0-1/manifestoR/R/scaling_functions.R | 21 + manifestoR-1.0-1/manifestoR/R/scaling_general.R | 24 + manifestoR-1.0-1/manifestoR/R/scaling_rile.R | 6 manifestoR-1.0-1/manifestoR/README.md | 30 +- manifestoR-1.0-1/manifestoR/inst/doc/manifestoRworkflow.pdf |binary manifestoR-1.0-1/manifestoR/man/ManifestoDocument.Rd | 8 manifestoR-1.0-1/manifestoR/man/cmp_codes.Rd | 17 - manifestoR-1.0-1/manifestoR/man/median_voter.Rd |only manifestoR-1.0-1/manifestoR/man/mp_bootstrap.Rd | 5 manifestoR-1.0-1/manifestoR/man/mp_interpolate.Rd |only manifestoR-1.0-1/manifestoR/man/mp_scale.Rd | 8 manifestoR-1.0-1/manifestoR/man/rile.Rd | 18 - manifestoR-1.0-1/manifestoR/man/scale.Rd | 4 manifestoR-1.0-1/manifestoR/man/vanilla.Rd |only manifestoR-1.0-1/manifestoR/vignettes/manifestoRworkflow.Rmd | 152 ++++++++++- 26 files changed, 348 insertions(+), 123 deletions(-)
Title: Kernel Factory: An Ensemble of Kernel Machines
Description: Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
Author: Michel Ballings, Dirk Van den Poel
Maintainer: Michel Ballings <Michel.Ballings@GMail.com>
Diff between kernelFactory versions 0.2.0 dated 2014-03-23 and 0.2.1 dated 2015-05-22
DESCRIPTION | 12 MD5 | 12 R/kernelFactory.R | 960 ++++++++++++++++++++++--------------------- inst/NEWS | 10 man/kFNews.Rd | 57 +- man/kernelFactory.Rd | 162 +++---- man/predict.kernelFactory.Rd | 95 ++-- 7 files changed, 666 insertions(+), 642 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for HTTP 2.0, SSL (https://, ftps://), gzip, and other 'libcurl' goodies.
The core of the package implements a framework for performing fully customizable
requests where data can be processed either in memory, on disk, or streaming via
the callback or connection interfaces. Some knowledge of 'libcurl' is recommended;
for a more-user-friendly web client see the 'httr' package which builds on this
package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.6 dated 2015-05-19 and 0.7 dated 2015-05-22
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + NEWS | 5 +++++ R/onload.R | 12 ++++++++++-- build/vignette.rds |binary inst/doc/intro.Rmd | 2 +- inst/doc/intro.html | 32 ++++++++++++++++---------------- src/curl.c | 7 ++++--- src/handle.c | 4 ++++ tests/testthat/helper-version.R |only vignettes/intro.Rmd | 2 +- 12 files changed, 56 insertions(+), 36 deletions(-)
Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms for design and
analysis of probability surveys. The functions are tailored for Generalized
Random Tessellation Stratified survey designs.
Author: Tom Kincaid [aut, cre],
Tony Olsen [aut],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Tom Kincaid <Kincaid.Tom@epa.gov>
Diff between spsurvey versions 2.6 dated 2013-09-26 and 3.0 dated 2015-05-22
spsurvey-2.6/spsurvey/R/adjwgt.s |only spsurvey-2.6/spsurvey/R/albersgeod.r |only spsurvey-2.6/spsurvey/R/ash1.wgt.r |only spsurvey-2.6/spsurvey/R/attisk.est.r |only spsurvey-2.6/spsurvey/R/attrisk.analysis.r |only spsurvey-2.6/spsurvey/R/attrisk.var.r |only spsurvey-2.6/spsurvey/R/cat.analysis.s |only spsurvey-2.6/spsurvey/R/category.est.s |only spsurvey-2.6/spsurvey/R/catvar.prop.s |only spsurvey-2.6/spsurvey/R/catvar.size.s |only spsurvey-2.6/spsurvey/R/cdf.decon.s |only spsurvey-2.6/spsurvey/R/cdf.est.s |only spsurvey-2.6/spsurvey/R/cdf.nresp.s |only spsurvey-2.6/spsurvey/R/cdf.plot.s |only spsurvey-2.6/spsurvey/R/cdf.prop.s |only spsurvey-2.6/spsurvey/R/cdf.size.prop.s |only spsurvey-2.6/spsurvey/R/cdf.size.total.s |only spsurvey-2.6/spsurvey/R/cdf.test.prop.s |only spsurvey-2.6/spsurvey/R/cdf.test.s |only spsurvey-2.6/spsurvey/R/cdf.test.size.prop.s |only spsurvey-2.6/spsurvey/R/cdf.total.s |only spsurvey-2.6/spsurvey/R/cdfvar.prop.s |only spsurvey-2.6/spsurvey/R/cdfvar.size.prop.s |only spsurvey-2.6/spsurvey/R/cdfvar.size.total.s |only spsurvey-2.6/spsurvey/R/cdfvar.test.s |only spsurvey-2.6/spsurvey/R/cdfvar.total.s |only spsurvey-2.6/spsurvey/R/cell.wt.r |only spsurvey-2.6/spsurvey/R/change.analysis.r |only spsurvey-2.6/spsurvey/R/change.est.r |only spsurvey-2.6/spsurvey/R/changevar.mean.r |only spsurvey-2.6/spsurvey/R/changevar.prop.r |only spsurvey-2.6/spsurvey/R/changevar.size.r |only spsurvey-2.6/spsurvey/R/cont.analysis.s |only spsurvey-2.6/spsurvey/R/cont.cdfplot.s |only spsurvey-2.6/spsurvey/R/cont.cdftest.s |only spsurvey-2.6/spsurvey/R/dcdf.prop.s |only spsurvey-2.6/spsurvey/R/dcdf.size.prop.s |only spsurvey-2.6/spsurvey/R/dcdf.size.total.s |only spsurvey-2.6/spsurvey/R/dcdf.total.s |only spsurvey-2.6/spsurvey/R/dcdfvar.prop.s |only spsurvey-2.6/spsurvey/R/dcdfvar.size.prop.s |only spsurvey-2.6/spsurvey/R/dcdfvar.size.total.s |only spsurvey-2.6/spsurvey/R/dcdfvar.total.s |only spsurvey-2.6/spsurvey/R/dframe.check.s |only spsurvey-2.6/spsurvey/R/dsgnsum.r |only spsurvey-2.6/spsurvey/R/framesum.r |only spsurvey-2.6/spsurvey/R/geodalbers.r |only spsurvey-2.6/spsurvey/R/grts.r |only spsurvey-2.6/spsurvey/R/grtsarea.r |only spsurvey-2.6/spsurvey/R/grtslin.r |only spsurvey-2.6/spsurvey/R/grtspts.r |only spsurvey-2.6/spsurvey/R/input.check.s |only spsurvey-2.6/spsurvey/R/input.format.s |only spsurvey-2.6/spsurvey/R/interp.axis.s |only spsurvey-2.6/spsurvey/R/interp.cdf.s |only spsurvey-2.6/spsurvey/R/irs.r |only spsurvey-2.6/spsurvey/R/irsarea.r |only spsurvey-2.6/spsurvey/R/irslin.r |only spsurvey-2.6/spsurvey/R/irspts.r |only spsurvey-2.6/spsurvey/R/isotonic.s |only spsurvey-2.6/spsurvey/R/localmean.cov.s |only spsurvey-2.6/spsurvey/R/localmean.df.s |only spsurvey-2.6/spsurvey/R/localmean.var.s |only spsurvey-2.6/spsurvey/R/localmean.weight.s |only spsurvey-2.6/spsurvey/R/localmean.weight2.s |only spsurvey-2.6/spsurvey/R/marinus.s |only spsurvey-2.6/spsurvey/R/mdmarea.r |only spsurvey-2.6/spsurvey/R/mdmlin.r |only spsurvey-2.6/spsurvey/R/mdmpts.r |only spsurvey-2.6/spsurvey/R/onAttach.r |only spsurvey-2.6/spsurvey/R/read.dbf.r |only spsurvey-2.6/spsurvey/R/read.sas.s |only spsurvey-2.6/spsurvey/R/read.shape.r |only spsurvey-2.6/spsurvey/R/relrisk.analysis.s |only spsurvey-2.6/spsurvey/R/relrisk.est.s |only spsurvey-2.6/spsurvey/R/relrisk.var.s |only spsurvey-2.6/spsurvey/R/sbcframe.r |only spsurvey-2.6/spsurvey/R/sbcsamp.r |only spsurvey-2.6/spsurvey/R/selectframe.r |only spsurvey-2.6/spsurvey/R/selectpts.r |only spsurvey-2.6/spsurvey/R/selectrecordID.r |only spsurvey-2.6/spsurvey/R/shape2spList.r |only spsurvey-2.6/spsurvey/R/simex.s |only spsurvey-2.6/spsurvey/R/sorted.s |only spsurvey-2.6/spsurvey/R/sp2shape.r |only spsurvey-2.6/spsurvey/R/spbalance.r |only spsurvey-2.6/spsurvey/R/spsurvey.analysis.s |only spsurvey-2.6/spsurvey/R/total.est.s |only spsurvey-2.6/spsurvey/R/total.var.s |only spsurvey-2.6/spsurvey/R/uniqueID.s |only spsurvey-2.6/spsurvey/R/vecprint.r |only spsurvey-2.6/spsurvey/R/vecprint.s |only spsurvey-2.6/spsurvey/R/warnprnt.s |only spsurvey-2.6/spsurvey/R/wnas.s |only spsurvey-2.6/spsurvey/R/write.dbf.r |only spsurvey-2.6/spsurvey/R/write.object.s |only spsurvey-2.6/spsurvey/inst/NEWS |only spsurvey-2.6/spsurvey/inst/NEWS.pdf |only spsurvey-2.6/spsurvey/inst/doc/FL_lakes.tab |only spsurvey-2.6/spsurvey/inst/doc/IN_streams.tab |only spsurvey-2.6/spsurvey/inst/doc/Luck_Ash_streams.dbf |only spsurvey-2.6/spsurvey/inst/doc/Luck_Ash_streams.shp |only spsurvey-2.6/spsurvey/inst/doc/Luck_Ash_streams.shx |only spsurvey-2.6/spsurvey/inst/doc/NE_lakes.dbf |only spsurvey-2.6/spsurvey/inst/doc/NE_lakes.prj |only spsurvey-2.6/spsurvey/inst/doc/NE_lakes.shp |only spsurvey-2.6/spsurvey/inst/doc/NE_lakes.shx |only spsurvey-2.6/spsurvey/inst/doc/NLA_2007.tab |only spsurvey-2.6/spsurvey/inst/doc/SC_estuaries.tab |only spsurvey-2.6/spsurvey/inst/doc/UT_ecoregions.dbf |only spsurvey-2.6/spsurvey/inst/doc/UT_ecoregions.prj |only spsurvey-2.6/spsurvey/inst/doc/UT_ecoregions.shp |only spsurvey-2.6/spsurvey/inst/doc/UT_ecoregions.shx |only spsurvey-2.6/spsurvey/inst/doc/decon_data.tab |only spsurvey-2.6/spsurvey/inst/doc/lLuck_Ash_streams.prj |only spsurvey-2.6/spsurvey/inst/doc/luck-ash.prj |only spsurvey-2.6/spsurvey/inst/doc/luck_ash.dbf |only spsurvey-2.6/spsurvey/inst/doc/luck_ash.shp |only spsurvey-2.6/spsurvey/inst/doc/luck_ash.shx |only spsurvey-3.0/spsurvey/DESCRIPTION | 35 - spsurvey-3.0/spsurvey/MD5 | 353 +++++++-------- spsurvey-3.0/spsurvey/NAMESPACE | 11 spsurvey-3.0/spsurvey/R/AAA.R |only spsurvey-3.0/spsurvey/R/SpatialDesign-class.R |only spsurvey-3.0/spsurvey/R/SpatialDesign-methods.R |only spsurvey-3.0/spsurvey/R/adjwgt.R |only spsurvey-3.0/spsurvey/R/albersgeod.R |only spsurvey-3.0/spsurvey/R/ash1.wgt.R |only spsurvey-3.0/spsurvey/R/attisk.est.R |only spsurvey-3.0/spsurvey/R/attrisk.analysis.R |only 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spsurvey-3.0/spsurvey/src/spsurvey.h | 6 spsurvey-3.0/spsurvey/vignettes/Area_Analysis.Rnw | 2 spsurvey-3.0/spsurvey/vignettes/Area_Design.Rnw | 37 - spsurvey-3.0/spsurvey/vignettes/Area_Design_plot.pdf |only spsurvey-3.0/spsurvey/vignettes/CDF_Analysis.Rnw | 34 - spsurvey-3.0/spsurvey/vignettes/CDF_Analysis_plot.pdf |only spsurvey-3.0/spsurvey/vignettes/Finite_Analysis.Rnw | 37 - spsurvey-3.0/spsurvey/vignettes/Finite_Analysis_plot.pdf |only spsurvey-3.0/spsurvey/vignettes/Finite_Design.Rnw | 44 - spsurvey-3.0/spsurvey/vignettes/Finite_Design_plot.pdf |only spsurvey-3.0/spsurvey/vignettes/Linear_Analysis.Rnw | 36 - spsurvey-3.0/spsurvey/vignettes/Linear_Analysis_plot.pdf |only spsurvey-3.0/spsurvey/vignettes/Linear_Design.Rnw | 63 -- spsurvey-3.0/spsurvey/vignettes/Linear_Design_plot1.pdf |only spsurvey-3.0/spsurvey/vignettes/Linear_Design_plot2.pdf |only 292 files changed, 696 insertions(+), 969 deletions(-)
Title: Visualization of Multivariate Functions, Sets, and Data
Description:
We provide tools to
(1) visualize multivariate density functions and density estimates
with level set trees,
(2) visualize level sets with shape trees,
(3) visualize multivariate data with tail trees,
(4) visualize scales of multivariate density estimates with
mode graphs and branching maps, and
(5) visualize anisotropic spread with 2D volume functions and
2D probability content functions.
Level set trees visualize mode structure,
shape trees visualize shapes of level sets of unimodal densities,
and tail trees visualize connected data sets.
The kernel estimator is implemented
but the package may also be applied for visualizing other density estimates.
Author: Jussi Klemela <jussi.klemela@gmail.com>
Maintainer: Jussi Klemela <jussi.klemela@gmail.com>
Diff between denpro versions 0.9.1 dated 2013-08-13 and 0.9.2 dated 2015-05-22
DESCRIPTION | 20 ++++----- MD5 | 93 ++++++++++++++++++++++++++++++------------- NAMESPACE | 18 ++++++-- R/alpha.complex.R |only R/colobary.merge.R |only R/colobary.nodes.R |only R/colors2data.R |only R/colorsofdata.R |only R/colorsofdata.adagrid.R |only R/colorsofdata.adagrid.new.R |only R/colorsofdata.adagrid2.R |only R/colorsofdata.new.R |only R/colorsofdata.tail.R |only R/colorsofdata2.R |only R/colorsofdata3.R |only R/dendat2lst.R |only R/denpro.R |only R/dist.func.R | 5 +- R/eva.t.R |only R/findbnodes.R |only R/fs.calc.R |only R/fs.calc.parti.R |only R/kernesti.dens.R | 7 ++- R/lambda2emass.R |only R/leafsfirst.R | 20 ++++++--- R/leafsfirst.adagrid.R |only R/leafsfirst.boundary.R |only R/leafsfirst.complex.R | 8 ++- R/leafsfirst.delaunay.R |only R/leafsfirst.tail.R | 1 R/paracoor.R | 4 - R/paracoor.dens.R |only R/pcf.boundary.R |only R/pcf.kern.R | 9 ++-- R/pcf.kern.vech.R |only R/pcf.matrix.R |only R/plot.histdata.R | 2 R/plotbary.R | 7 ++- R/plotvolu.R | 12 ++++- R/preprocess.R | 8 +++ R/qq.plot.R | 7 --- R/rotation2d.R |only R/sphere.map.R |only R/sphere.para.R |only R/tail.plot.R | 6 +- R/tail.plot.dens.R |only R/touchi.boundary.R |only R/touchi.dela.R |only R/touchstep.boundary.R |only R/touchstep.delaunay.R |only R/travel.tree.R |only R/treedisc.ada.R |only R/vols.complex.R | 12 ++++- R/volsimplex.R |only man/branchmap.Rd | 2 man/colors2data.Rd |only man/denpro-package.Rd | 44 ++++++++++---------- man/draw.pcf.Rd | 2 man/excmas.Rd | 2 man/exmap.Rd | 2 man/findbnodes.Rd |only man/leafsfirst.Rd | 12 +++-- man/leafsfirst.adagrid.Rd |only man/paracoor.Rd | 3 - man/pcf.kern.Rd | 18 ++++++-- man/plotbary.Rd | 3 - man/plotvolu.Rd | 11 ++++- man/undocumented.Rd |only 68 files changed, 227 insertions(+), 111 deletions(-)
Title: Faster Dendrogram Manipulation using 'Rcpp'
Description: Offers faster manipulation of dendrogram objects in
R. A dendrogram object in R is a list structure with attributes in its
nodes and leaves. Working with dendrogram objects often require a function
to recursively go through all (or most) element in the list object.
Naturally, such function are rather slow in R, but can become much faster
thanks to 'Rcpp'.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Romain Francois [ctb],
Dirk Eddelbuettel [ctb],
Kevin Ushey [ctb],
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextendRcpp versions 0.5.1 dated 2014-03-16 and 0.6.1 dated 2015-05-22
dendextendRcpp-0.5.1/dendextendRcpp/man/labels.dendrogram.Rd |only dendextendRcpp-0.6.1/dendextendRcpp/ChangeLog |only dendextendRcpp-0.6.1/dendextendRcpp/DESCRIPTION | 18 ++-- dendextendRcpp-0.6.1/dendextendRcpp/MD5 | 29 +++---- dendextendRcpp-0.6.1/dendextendRcpp/NAMESPACE | 7 - dendextendRcpp-0.6.1/dendextendRcpp/NEWS | 35 +++++++++ dendextendRcpp-0.6.1/dendextendRcpp/R/cut_lower_fun.r | 2 dendextendRcpp-0.6.1/dendextendRcpp/R/heights_per_k.r | 2 dendextendRcpp-0.6.1/dendextendRcpp/R/imports_dendextend.r | 6 - dendextendRcpp-0.6.1/dendextendRcpp/R/labels_dendrogram.r | 12 +-- dendextendRcpp-0.6.1/dendextendRcpp/R/zzz.r | 23 ++++-- dendextendRcpp-0.6.1/dendextendRcpp/README.md | 25 +++++- dendextendRcpp-0.6.1/dendextendRcpp/man/dendextendRcpp-package.Rd | 2 dendextendRcpp-0.6.1/dendextendRcpp/man/dendextendRcpp_cut_lower_fun.Rd | 38 ++++------ dendextendRcpp-0.6.1/dendextendRcpp/man/dendextendRcpp_get_branches_heights.Rd | 25 ++---- dendextendRcpp-0.6.1/dendextendRcpp/man/dendextendRcpp_heights_per_k.dendrogram.Rd | 20 ++--- dendextendRcpp-0.6.1/dendextendRcpp/man/dendextendRcpp_labels.dendrogram.Rd |only 17 files changed, 149 insertions(+), 95 deletions(-)
More information about dendextendRcpp at CRAN
Permanent link
Title: Targeted Learning of a NP Importance of a Continuous Exposure
Description: Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.
Author: Antoine Chambaz, Pierre Neuvial
Maintainer: Pierre Neuvial <pierre.neuvial@genopole.cnrs.fr>
Diff between tmle.npvi versions 0.9.3 dated 2015-02-05 and 0.10.0 dated 2015-05-22
DESCRIPTION | 10 +- MD5 | 31 ++++----- NAMESPACE | 1 R/NPVI.R | 4 - R/NPVI.update.R | 3 R/NPVI.updatePsi.R | 3 R/mu.R | 88 +++++++++++++++++++------- R/simulateData.R | 25 +++++-- R/simulateParsimoniouslyXgivenW.R | 98 +++++++++++++++++++---------- R/tmle.npvi.R | 35 +++++++--- data/learningLib.rda |binary inst/CITATION |only inst/NEWS | 9 ++ inst/doc/tmle-npvi.pdf |binary inst/system/installSuggestedPackages.R | 6 + inst/testScripts/tcga2012brca/03.pValues.R | 19 ++++- man/tmle.npvi..Rd | 24 ++++--- 17 files changed, 243 insertions(+), 113 deletions(-)
Title: Variable Selection for Model-Based Clustering using the
Integrated Complete-Data Likelihood of a Latent Class Model
Description: Variable Selection for model-based clustering by using a mixture model of Gaussian distributions
assuming conditional independence between variables. The algorithm carries out the model
selection by optimizing the MICL criterion which has a closed form for such a distribution.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 1.0 dated 2015-03-19 and 1.1 dated 2015-05-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/VSLCM_initialization.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in a (cross-sectional)
population sample into an estimate of the frequency with which
seroconversions (infections) occur in the sampled population.
Author: Peter Teunis [aut] (Author of the method and original code),
Daniel Lewandowski [com, ctb] (Creator of the R package),
Chantal Quinten [ctb, cre] (Project manager and the package maintainer)
Maintainer: Chantal Quinten <seroincidence@ecdc.europa.eu>
Diff between seroincidence versions 1.0.3 dated 2015-04-10 and 1.0.4 dated 2015-05-22
DESCRIPTION | 10 +++--- MD5 | 48 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 6 ++++ inst/doc/cover.R | 2 - inst/doc/cover.Rmd | 2 - inst/doc/cover.html | 14 ++++----- inst/doc/installation.R | 22 +++++++------- inst/doc/installation.Rmd | 2 - inst/doc/installation.pdf |binary inst/doc/methodology.pdf |binary inst/doc/tutorial.R | 20 ++++++------- inst/doc/tutorial.pdf |binary man/campylobacterResponseParams.Rd | 2 - man/campylobacterSerologyData.Rd | 2 - man/estimateSeroincidence.Rd | 2 - man/print.seroincidence.Rd | 2 - man/print.summary.seroincidence.Rd | 2 - man/salmonellaSerologyData.Rd | 2 - man/seroincidence.Rd | 2 - man/simulateSalmonellaResponseParams.Rd | 2 - man/simulateSerologyData.Rd | 2 - man/summary.seroincidence.Rd | 2 - vignettes/cover.Rmd | 2 - vignettes/installation.Rmd | 2 - 25 files changed, 79 insertions(+), 73 deletions(-)
Title: Multivariate and Univariate Meta-Analysis and Meta-Regression
Description: Collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mvmeta versions 0.4.5 dated 2014-08-09 and 0.4.7 dated 2015-05-22
DESCRIPTION | 10 MD5 | 34 +- R/initpar.R | 140 +++++----- R/mvmeta.control.R | 52 ++- R/mvmeta.fit.R | 2 R/mvmeta.ml.R | 9 R/mvmeta.reml.R | 9 inst/ChangeLog | 646 +++++++++++++++++++++++++------------------------ man/berkey98.Rd | 112 ++++---- man/inputna.Rd | 162 ++++++------ man/mlprof.fn.Rd | 4 man/mvmeta-package.Rd | 234 ++++++++--------- man/mvmeta.control.Rd | 138 +++++----- man/mvmeta.ml.Rd | 4 man/mvmeta.mm.Rd | 2 man/mvmeta.vc.Rd | 2 man/mvmetaCovStruct.Rd | 8 man/mvmetaObject.Rd | 2 18 files changed, 796 insertions(+), 774 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
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Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.5 dated 2014-11-16 and 1.6 dated 2015-05-22
DESCRIPTION | 10 - MD5 | 28 +-- NAMESPACE | 8 R/coneproj.R | 512 +++++++++++++++++++++++++++++++++++++++++++++---------- man/conc.Rd |only man/coneA.Rd | 7 man/coneB.Rd | 7 man/constreg.Rd | 5 man/conv.Rd |only man/decr.Rd |only man/decr.conc.Rd |only man/decr.conv.Rd |only man/feet.Rd | 2 man/incr.Rd |only man/incr.conc.Rd |only man/incr.conv.Rd |only man/qprog.Rd | 7 man/shapereg.Rd | 312 ++++++++++++++++++--------------- src/coneproj.cpp | 6 19 files changed, 638 insertions(+), 266 deletions(-)
Title: Fuzzy Rule-Based Systems for Classification and Regression Tasks
Description: An implementation of various learning algorithms based on fuzzy rule-based systems (FRBSs) for dealing with classification and regression tasks. Moreover, it allows to construct an FRBS model defined by human experts.
FRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims at
representing the reasoning of human experts in a set of IF-THEN rules, to
handle real-life problems in, e.g., control, prediction and inference, data
mining, bioinformatics data processing, and robotics. FRBSs are also known
as fuzzy inference systems and fuzzy models. During the modeling of an
FRBS, there are two important steps that need to be conducted: structure
identification and parameter estimation. Nowadays, there exists a wide
variety of algorithms to generate fuzzy IF-THEN rules automatically from
numerical data, covering both steps. Approaches that have been used in the
past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering
methods, genetic algorithms, squares methods, etc. Furthermore, in this
version we provide a universal framework named 'frbsPMML', which is adopted
from the Predictive Model Markup Language (PMML), for representing FRBS
models. PMML is an XML-based language to provide a standard for describing
models produced by data mining and machine learning algorithms. Therefore,
we are allowed to export and import an FRBS model to/from 'frbsPMML'.
Finally, this package aims to implement the most widely used standard
procedures, thus offering a standard package for FRBS modeling to the R
community.
Author: Lala Septem Riza, Christoph Bergmeir, Francisco Herrera, and
Jose Manuel Benitez
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between frbs versions 3.0-0 dated 2015-01-16 and 3.1-0 dated 2015-05-22
DESCRIPTION | 17 ++++++++--------- MD5 | 43 ++++++++++++++++++++++--------------------- R/FCluster.Methods.R | 2 +- R/FGradDescent.Methods.R | 2 +- R/FNN.FunctionCollection.R | 13 +++++++++---- R/FNN.Methods.R | 4 ++-- R/FRBS.pmml.R | 4 ++-- R/FSpacePartition.Method.R | 2 +- R/GFS.FunctionCollection.R | 29 ++++++++++++++++------------- R/GFS.Methods.R | 14 +++++++++++--- R/frbs-package.R | 18 +++++++++++------- R/pmml.frbs.R | 22 ++++++++++++++++++---- inst |only man/ANFIS.Rd | 4 ++-- man/DENFIS.Rd | 2 +- man/FS.HGD.Rd | 2 +- man/GFS.FR.MOGUL.Rd | 4 ++-- man/SLAVE.Rd | 2 +- man/WM.Rd | 2 +- man/frbs-package.Rd | 18 +++++++++++------- man/frbsPMML.Rd | 22 ++++++++++++++++++---- man/read.frbsPMML.Rd | 2 +- man/write.frbsPMML.Rd | 2 +- 23 files changed, 141 insertions(+), 89 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Provides an interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.0-0 dated 2014-12-19 and 1.1-0 dated 2015-05-22
DESCRIPTION | 16 ++--- MD5 | 46 +++++++------- NAMESPACE | 15 +--- R/AAA.R | 12 ++- R/DSC_CluStream.R | 35 ++--------- R/DSC_ClusTree.R | 3 R/DSC_DenStream.R | 30 ++------- R/DSC_MOA.R | 77 ++++++++++++++---------- R/DSD_MOA.R | 11 ++- R/DSD_RandomRBFGeneratorEvents.R | 114 ++++++++++++++++++------------------ R/ellipse.R | 2 R/onLoad.R | 2 build/vignette.rds |binary inst/NEWS | 10 ++- inst/doc/streamMOA.R | 14 ++-- inst/doc/streamMOA.Rnw | 30 ++++----- inst/doc/streamMOA.pdf |binary inst/java/StreamMOA.jar |only inst/java/moa.jar |binary java/Makefile |only java/StreamMOA.java |only man/DSC_CluStream.Rd | 3 man/DSC_DenStream.Rd | 7 +- man/DSD_RandomRBFGeneratorEvents.Rd | 13 +--- man/saveMOA.Rd |only vignettes/streamMOA.Rnw | 30 ++++----- 26 files changed, 231 insertions(+), 239 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-1 dated 2015-01-16 and 1.1-2 dated 2015-05-22
stream-1.1-1/stream/R/DSC_tNN.R |only stream-1.1-1/stream/inst/tests/DSD.R |only stream-1.1-1/stream/man/DSC_tNN.Rd |only stream-1.1-2/stream/DESCRIPTION | 13 stream-1.1-2/stream/MD5 | 102 +++-- stream-1.1-2/stream/NAMESPACE | 19 - stream-1.1-2/stream/R/AAA.R | 9 stream-1.1-2/stream/R/DSC.R | 3 stream-1.1-2/stream/R/DSC_DBSTREAM.R |only stream-1.1-2/stream/R/DSC_DStream.R | 474 +++++++++------------------ stream-1.1-2/stream/R/DSC_Hierarchical.R | 14 stream-1.1-2/stream/R/DSC_R.R | 18 - stream-1.1-2/stream/R/DSC_Static.R | 3 stream-1.1-2/stream/R/DSC_TwoStage.R | 6 stream-1.1-2/stream/R/DSD.R | 1 stream-1.1-2/stream/R/DSD_BarsAndGaussians.R | 3 stream-1.1-2/stream/R/DSD_Cubes.R | 3 stream-1.1-2/stream/R/DSD_Gaussians.R | 3 stream-1.1-2/stream/R/DSD_MG.R | 2 stream-1.1-2/stream/R/DSD_Memory.R | 3 stream-1.1-2/stream/R/DSD_ReadCSV.R | 67 ++- stream-1.1-2/stream/R/DSD_ReadDB.R | 5 stream-1.1-2/stream/R/DSD_ScaleStream.R | 17 stream-1.1-2/stream/R/DSD_Target.R | 4 stream-1.1-2/stream/R/DSD_UniformNoise.R | 3 stream-1.1-2/stream/R/DSD_mlbenchGenerator.R | 25 - stream-1.1-2/stream/R/DSO_Sample.R | 7 stream-1.1-2/stream/R/DSO_Window.R | 28 + stream-1.1-2/stream/R/ellipse.R | 21 - stream-1.1-2/stream/R/evaluate.R | 108 ++++-- stream-1.1-2/stream/R/kmeansW.R | 16 stream-1.1-2/stream/R/zzz.R |only stream-1.1-2/stream/build/vignette.rds |binary stream-1.1-2/stream/inst/NEWS | 10 stream-1.1-2/stream/inst/doc/stream.R | 4 stream-1.1-2/stream/inst/doc/stream.Rnw | 65 ++- stream-1.1-2/stream/inst/doc/stream.pdf |binary stream-1.1-2/stream/inst/tests/test-DSD.R |only stream-1.1-2/stream/man/DSC_DBSTREAM.Rd |only stream-1.1-2/stream/man/DSC_DStream.Rd | 61 ++- stream-1.1-2/stream/man/DSC_Hierarchical.Rd | 8 stream-1.1-2/stream/man/DSC_Reachability.Rd | 14 stream-1.1-2/stream/man/DSD.Rd | 4 stream-1.1-2/stream/man/DSD_MG.Rd | 8 stream-1.1-2/stream/man/DSD_Memory.Rd | 4 stream-1.1-2/stream/man/DSD_ReadCSV.Rd | 19 - stream-1.1-2/stream/man/animation.Rd | 8 stream-1.1-2/stream/man/get_assignment.Rd | 16 stream-1.1-2/stream/man/prune_clusters.Rd | 12 stream-1.1-2/stream/src/DBSTREAM.cpp |only stream-1.1-2/stream/src/DStream.cpp |only stream-1.1-2/stream/src/NumericVector.cpp |only stream-1.1-2/stream/src/NumericVector.h |only stream-1.1-2/stream/src/dist.h |only stream-1.1-2/stream/vignettes/classes.pdf |binary stream-1.1-2/stream/vignettes/mcs.pdf |binary stream-1.1-2/stream/vignettes/stream.Rnw | 65 ++- stream-1.1-2/stream/vignettes/time.pdf |binary 58 files changed, 650 insertions(+), 625 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including ADCP
measurements, CTD measurements, sectional data, sea-level time series,
coastline files, etc. Handles dozens of specialized functions for calculating
seawater properties such as potential temperature and density, as well as
derived properties such as buoyancy frequency and dynamic height. Map projections
are calculated using PROJ.4 functions included within the oce.
Author: Dan Kelley [aut, cre],
Clark Richards [aut],
Chantelle Layton [ctb, cph] (curl() coauthor),
Gerald Evenden [ctb, cph] (PROJ.4 author),
Frank Warmerdam [ctb, cph] (PROJ.4 author),
Howard Butler [ctb, cph] (PROJ.4 author),
Brent Fraser [ctb, cph] (PROJ.4 contributor),
Chris Stuber [ctb, cph] (PROJ.4 contributor),
Craig Bruce [ctb, cph] (PROJ.4 contributor),
Victor Osipkov [ctb, cph] (PROJ.4 contributor),
Andrea Antonello [ctb, cph] (PROJ.4 contributor),
Charles Karney [ctb, cph] (PROJ.4 contributor),
Karsten Engsager [ctb, cph] (PROJ.4 contributor),
Knud Poder [ctb, cph] (PROJ.4 contributor),
Robert Gentleman [ctb, cph] (author of approx() code, used in
binmapAdp()),
Ross Ihaka [ctb, cph] (author of approx() code, used in binmapAdp())
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 0.9-16 dated 2015-05-20 and 0.9-17 dated 2015-05-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ inst/doc/oce.pdf |binary man/landsat-class.Rd | 2 +- src/pj_param.c | 2 +- 6 files changed, 14 insertions(+), 11 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 1.9-6 dated 2015-05-07 and 1.9-7 dated 2015-05-22
DESCRIPTION | 8 MD5 | 64 +-- NEWS | 18 + R/rma.glmm.r | 6 R/rma.mv.r | 3 R/rma.uni.r | 4 R/zzz.R | 2 tests/testthat/test_analysis_example_berkey1995.r | 22 - tests/testthat/test_analysis_example_berkey1998.r | 28 - tests/testthat/test_analysis_example_dersimonian2007.r | 8 tests/testthat/test_analysis_example_gleser2009.r | 46 +- tests/testthat/test_analysis_example_konstantopoulos2011.r | 66 +-- tests/testthat/test_analysis_example_lipsey2001.r | 50 +- tests/testthat/test_analysis_example_miller1978.r | 24 - tests/testthat/test_analysis_example_morris2008.r | 24 - tests/testthat/test_analysis_example_normand1999.r | 60 +-- tests/testthat/test_analysis_example_raudenbush1985.r | 38 +- tests/testthat/test_analysis_example_raudenbush2009.r | 34 - tests/testthat/test_analysis_example_rothman2008.r | 222 ++++++------- tests/testthat/test_analysis_example_stijnen2010.r | 174 +++++----- tests/testthat/test_analysis_example_vanhouwelingen1993.r | 24 - tests/testthat/test_analysis_example_vanhouwelingen2002.r | 77 ++-- tests/testthat/test_confint.r | 32 - tests/testthat/test_escalc.r | 4 tests/testthat/test_handling_of_edge_cases_due_to_zeros.r | 22 - tests/testthat/test_metan_vs_rma.mh_with_dat.bcg.r | 42 +- tests/testthat/test_metan_vs_rma.peto_with_dat.bcg.r | 16 tests/testthat/test_metan_vs_rma.uni_with_dat.bcg.r | 90 ++--- tests/testthat/test_regression_with_rma.r | 26 - tests/testthat/test_rma_error_handling.r | 10 tests/testthat/test_rma_vs_direct_computation.r | 12 tests/testthat/test_rma_vs_lm_and_lme.r | 28 - tests/testthat/test_rma_weights.r | 16 33 files changed, 660 insertions(+), 640 deletions(-)
Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>
Diff between libamtrack versions 0.6.0 dated 2015-05-21 and 0.6.1 dated 2015-05-22
DESCRIPTION | 10 - MD5 | 136 ++++++++++++------------- R/initial.R | 2 man/AT.A.from.particle.no.Rd | 2 man/AT.Bethe.mean.energy.loss.MeV.Rd | 2 man/AT.CSDA.energy.after.slab.E.MeV.u.Rd | 2 man/AT.CSDA.range.Bethe.g.cm2.Rd | 2 man/AT.D.RDD.Gy.Rd | 2 man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 2 man/AT.E.from.beta.Rd | 2 man/AT.I.eV.from.composition.Rd | 2 man/AT.Landau.PDF.Rd | 2 man/AT.Mass.Stopping.Power.Rd | 2 man/AT.Mass.Stopping.Power.with.no.Rd | 2 man/AT.Rutherford.SDCS.Rd | 2 man/AT.Stopping.Power.Rd | 2 man/AT.Stopping.Power.with.no.Rd | 2 man/AT.Vavilov.PDF.Rd | 2 man/AT.Vavilov.energy.loss.distribution.Rd | 2 man/AT.WEPL.Bethe.Rd | 2 man/AT.Z.from.particle.no.Rd | 2 man/AT.atomic.weight.from.Z.Rd | 2 man/AT.average.A.from.composition.Rd | 2 man/AT.average.Z.from.composition.Rd | 2 man/AT.beam.par.physical.to.technical.Rd | 2 man/AT.beam.par.technical.to.physical.Rd | 2 man/AT.beta.from.E.Rd | 2 man/AT.dose.Gy.from.fluence.cm2.Rd | 2 man/AT.dose.weighted.E.MeV.u.Rd | 2 man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 2 man/AT.effective.Z.from.composition.Rd | 2 man/AT.effective.charge.from.E.MeV.u.Rd | 2 man/AT.electron.density.m3.Rd | 2 man/AT.electron.density.m3.from.composition.Rd | 2 man/AT.electron.density.m3.from.material.no.Rd | 2 man/AT.energy.loss.FWHM.Rd | 2 man/AT.energy.loss.distribution.Rd | 2 man/AT.energy.loss.mode.Rd | 2 man/AT.energy.straggling.MeV2.cm2.g.Rd | 2 man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 2 man/AT.fluence.cm2.from.dose.Gy.Rd | 2 man/AT.fluence.weighted.E.MeV.u.Rd | 2 man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 2 man/AT.gamma.from.E.Rd | 2 man/AT.get.materials.data.Rd | 2 man/AT.kappa.Rd | 2 man/AT.lambda.from.energy.loss.Rd | 2 man/AT.max.E.transfer.MeV.Rd | 2 man/AT.max.electron.ranges.m.Rd | 2 man/AT.mean.number.of.tracks.contrib.Rd | 2 man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 2 man/AT.nuclear.spin.from.particle.no.Rd | 2 man/AT.particle.no.from.Z.and.A.Rd | 2 man/AT.r.RDD.m.Rd | 2 man/AT.run.CPPSC.method.Rd | 2 man/AT.run.GSM.method.Rd | 2 man/AT.run.IGK.method.Rd | 2 man/AT.set.user.material.Rd | 2 man/AT.set.user.material.from.composition.Rd | 2 man/AT.stopping.power.ratio.Rd | 2 man/AT.total.D.Gy.Rd | 2 man/AT.total.fluence.cm2.Rd | 2 man/AT.translate.dose.into.DSB.distribution.Rd | 2 man/libamtrack-package.Rd | 2 src/AT_StoppingPowerDataBethe.c | 2 src/AT_StoppingPowerDataBethe.h | 2 src/AT_StoppingPowerDataPSTAR.c | 24 ---- src/AT_StoppingPowerDataPSTAR.h | 11 +- src/config.h | 10 - 69 files changed, 150 insertions(+), 169 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.4 dated 2015-04-02 and 2.1.5 dated 2015-05-22
DESCRIPTION | 10 +- MD5 | 164 +++++++++++++++++++------------------- NAMESPACE | 5 - NEWS | 151 ++++------------------------------ R/advanced.procD.lm.r | 79 ++++++++++++------ R/build.template.r | 30 +++++- R/define.sliders.2d.r | 76 ++--------------- R/define.sliders.3d.r | 102 ++--------------------- R/define.sliders.r |only R/digit.curves.r |only R/digitize2d.r | 31 +++---- R/digitsurface.r | 45 +++++++--- R/geomorph.support.code.r | 21 ++-- R/gridPar.R |only R/pairwise.slope.test.r | 143 +-------------------------------- R/pairwiseD.test.r | 124 +--------------------------- R/plotAllometry.r | 12 +- R/plotGMPhyloMorphoSpace.r | 21 +++- R/plotOutliers.r | 15 ++- R/plotRefToTarget.r | 153 +++++++++++++++++++++++++---------- R/procD.lm.r | 2 R/read.morphologika.r | 12 +- R/readland.nts.r | 10 +- R/readland.tps.r | 4 R/readmulti.nts.r | 5 - R/trajectory.analysis.r | 61 +++++++++++--- R/two.b.pls.r | 11 +- man/advanced.procD.lm.Rd | 77 ++++++++++++----- man/arrayspecs.Rd | 2 man/bilat.symmetry.Rd | 2 man/buildtemplate.Rd | 11 ++ man/compare.evol.rates.Rd | 2 man/compare.modular.partitions.Rd | 2 man/define.links.Rd | 2 man/define.modules.Rd | 2 man/define.sliders.2d.Rd | 53 +----------- man/define.sliders.3d.Rd | 69 +-------------- man/define.sliders.Rd |only man/digit.curves.Rd |only man/digit.fixed.Rd | 2 man/digitize2d.Rd | 25 ++--- man/digitsurface.Rd | 15 ++- man/editTemplate.Rd | 2 man/estimate.missing.Rd | 2 man/findMeanSpec.Rd | 2 man/fixed.angle.Rd | 2 man/geomorph-package.Rd | 2 man/gpagen.Rd | 2 man/gridPar.Rd |only man/hummingbirds.Rd | 2 man/morphol.disparity.Rd | 2 man/morphol.integr.Rd | 2 man/mosquito.Rd | 2 man/motionpaths.Rd | 2 man/mshape.Rd | 2 man/pairwise.slope.test.Rd | 91 +-------------------- man/pairwiseD.test.Rd | 83 +------------------ man/phylo.pls.Rd | 2 man/physignal.Rd | 2 man/plethShapeFood.Rd | 2 man/plethodon.Rd | 2 man/plethspecies.Rd | 2 man/plotAllSpecimens.Rd | 2 man/plotAllometry.Rd | 8 - man/plotGMPhyloMorphoSpace.Rd | 9 +- man/plotOutliers.Rd | 2 man/plotRefToTarget.Rd | 25 ++++- man/plotTangentSpace.Rd | 2 man/plotspec.Rd | 2 man/procD.lm.Rd | 4 man/procD.pgls.Rd | 2 man/pupfish.Rd | 2 man/ratland.Rd | 2 man/read.morphologika.Rd | 2 man/read.ply.Rd | 2 man/readland.nts.Rd | 2 man/readland.tps.Rd | 2 man/readmulti.nts.Rd | 2 man/scallopPLY.Rd | 2 man/scallops.Rd | 2 man/trajectory.analysis.Rd | 24 ++++- man/two.b.pls.Rd | 4 man/two.d.array.Rd | 2 man/warpRefMesh.Rd | 2 man/warpRefOutline.Rd | 2 man/writeland.tps.Rd | 2 86 files changed, 697 insertions(+), 1172 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-4 dated 2015-05-21 and 0.1-5 dated 2015-05-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/l_modularity.R | 2 +- src/l-modularity.cpp | 3 ++- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Data and Workspace Browser for Terminals
Description: Tools for deciphering the contents of
unknown objects or environments from within the terminal,
a problem often encountered when working with unfamiliar packages or debugging complex functions.
If working in xterm256 or ANSI terminals the output is coloured by default
to improve readability (e.g. the standard Ubuntu terminal).
Author: Christofer Backlin [aut, cre]
Maintainer: Christofer Backlin <christofer.backlin@medsci.uu.se>
Diff between dataview versions 2.0-9 dated 2014-04-10 and 2.1.1 dated 2015-05-22
dataview-2.0-9/dataview/R/helpers.R |only dataview-2.0-9/dataview/R/views.R |only dataview-2.0-9/dataview/man/tree.view.Rd |only dataview-2.0-9/dataview/man/whos.set.mask.Rd |only dataview-2.0-9/dataview/man/wrap.view.Rd |only dataview-2.1.1/dataview/DESCRIPTION | 31 ++++++++---------- dataview-2.1.1/dataview/MD5 | 24 ++++++++------ dataview-2.1.1/dataview/NAMESPACE | 19 +++++++++-- dataview-2.1.1/dataview/R/browse.R |only dataview-2.1.1/dataview/R/entry_view.R |only dataview-2.1.1/dataview/R/heat_view.R |only dataview-2.1.1/dataview/R/options.R |only dataview-2.1.1/dataview/R/whos.R |only dataview-2.1.1/dataview/man/as.whos.Rd |only dataview-2.1.1/dataview/man/browse.Rd |only dataview-2.1.1/dataview/man/entry.view.Rd | 16 ++------- dataview-2.1.1/dataview/man/getOpt.Rd |only dataview-2.1.1/dataview/man/heat.view.Rd | 27 +++++++-------- dataview-2.1.1/dataview/man/whos.Rd | 46 ++++++++++++++------------- dataview-2.1.1/dataview/man/whos.options.Rd |only 20 files changed, 87 insertions(+), 76 deletions(-)
Title: Cross-Validation for the SVD (Bi-Cross-Validation)
Description:
Methods for choosing the rank of an SVD approximation via cross
validation. The package provides both Gabriel-style "block"
holdouts and Wold-style "speckled" holdouts. It also includes an
implementation of the SVDImpute algorithm. For more information about
Bi-cross-validation, see Owen & Perry's 2009 AoAS article
(at http://arxiv.org/abs/0908.2062) and Perry's 2009 PhD thesis
(at http://arxiv.org/abs/0909.3052).
Author: Patrick O. Perry
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between bcv versions 1.0 dated 2009-10-15 and 1.0.1 dated 2015-05-22
DESCRIPTION | 29 +++++++++++++++-------------- LICENSE | 33 +++------------------------------ MD5 |only NAMESPACE | 4 ++++ R/impute.svd.R | 2 +- src/bcv-align-private.h | 11 ++++++----- src/bcv-matrix-private.c | 6 +++--- src/bcv-partition.c | 7 +++---- src/bcv-svd-gabriel-rep.c | 18 +++++++++--------- src/bcv-svd-gabriel.c | 8 ++++---- src/bcv-svd-impute.c | 18 +++++++++--------- src/bcv-svd-wold-rep.c | 10 +++++----- src/bcv-svd-wold.c | 8 ++++---- 13 files changed, 66 insertions(+), 88 deletions(-)
Title: Autoregressive Conditional Poisson
Description: Analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios <Siakoulis.Vasilios@atticabank.gr>
Diff between acp versions 1.1 dated 2015-01-08 and 2.0 dated 2015-05-22
acp-1.1/acp/man/forecast.Rd |only acp-2.0/acp/DESCRIPTION | 12 - acp-2.0/acp/MD5 | 13 - acp-2.0/acp/NAMESPACE | 9 - acp-2.0/acp/R/acp.R | 376 +++++++++++++++++++++--------------------- acp-2.0/acp/man/Berkowitz.Rd | 2 acp-2.0/acp/man/acp.Rd | 48 +++-- acp-2.0/acp/man/evaluation.Rd | 2 8 files changed, 241 insertions(+), 221 deletions(-)
Title: Estimation of R0 and Real-Time Reproduction Number from
Epidemics
Description: Estimation of reproduction numbers for disease outbreak, based on
incidence data. The R0 package implements several documented methods. It is
therefore possible to compare estimations according to the methods used.
Depending on the methods requested by user, basic reproduction number
(commonly denoted as R0) or real-time reproduction number (referred to as
R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs
will give different graphs depending on the methods requested : basic
reproductive number estimations will only show the epidemic curve
(collected data) and an adjusted model, whereas real-time methods will also
show the R(t) variations throughout the outbreak time period. Sensitivity
analysis tools are also provided, and allow for investigating effects of
varying Generation Time distribution or time window on estimates.
Author: Pierre-Yves Boelle, Thomas Obadia
Maintainer: Thomas Obadia <thomas.obadia@iplesp.upmc.fr>
Diff between R0 versions 1.2-5 dated 2014-11-25 and 1.2-6 dated 2015-05-21
DESCRIPTION | 28 ++++++++++++++++--------- MD5 | 12 +++++----- R/sim.epid.indiv.R | 12 +++++----- data/GT.chld.hsld.rda |binary data/Germany.1918.rda |binary data/H1N1.serial.interval.rda |binary man/R0-package.Rd | 47 ++++++++++++++++++++---------------------- 7 files changed, 54 insertions(+), 45 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.43 dated 2014-10-19 and 0.45 dated 2015-05-21
meteoForecast-0.43/meteoForecast/R/pointOpenMeteo.R |only meteoForecast-0.43/meteoForecast/R/rasterOpenMeteo.R |only meteoForecast-0.43/meteoForecast/data/varsOM.RData |only meteoForecast-0.45/meteoForecast/DESCRIPTION | 15 + meteoForecast-0.45/meteoForecast/MD5 | 45 ++--- meteoForecast-0.45/meteoForecast/NAMESPACE | 3 meteoForecast-0.45/meteoForecast/R/checkDays.R | 4 meteoForecast-0.45/meteoForecast/R/composeURL.R | 35 +--- meteoForecast-0.45/meteoForecast/R/getPoint.R | 8 - meteoForecast-0.45/meteoForecast/R/getPointDays.R | 9 - meteoForecast-0.45/meteoForecast/R/getPointRuns.R | 9 - meteoForecast-0.45/meteoForecast/R/getRaster.R | 1 meteoForecast-0.45/meteoForecast/R/getRasterDays.R | 1 meteoForecast-0.45/meteoForecast/R/grepVar.R | 11 - meteoForecast-0.45/meteoForecast/R/misc.R | 2 meteoForecast-0.45/meteoForecast/R/pointMeteoGalicia.R | 2 meteoForecast-0.45/meteoForecast/R/pointNCDC.R | 14 + meteoForecast-0.45/meteoForecast/R/rasterMeteoGalicia.R | 2 meteoForecast-0.45/meteoForecast/R/zzz.R | 6 meteoForecast-0.45/meteoForecast/inst/CITATION | 10 - meteoForecast-0.45/meteoForecast/man/getPoint.Rd | 95 ++++------- meteoForecast-0.45/meteoForecast/man/getRaster.Rd | 127 ++++------------ meteoForecast-0.45/meteoForecast/man/meteo-package.Rd | 39 +--- meteoForecast-0.45/meteoForecast/man/options.Rd | 38 ++-- meteoForecast-0.45/meteoForecast/man/vars.Rd | 34 +--- 25 files changed, 193 insertions(+), 317 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown <patrick.brown@utoronto.ca> [aut, cre], Barry Rowlingson [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.2.1 dated 2015-03-25 and 1.2.4 dated 2015-05-21
DESCRIPTION | 13 +--- MD5 | 24 +++---- R/getTiles.R | 1 R/insetMap.R | 6 + R/legendTable.R | 17 ++++- R/scaleBar.R | 153 +++++++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/mapLayers.pdf |binary inst/doc/mapmisc.pdf |binary man/scaleBar.Rd | 19 ++++-- man/tpeqd.Rd | 4 - tests/omerc.R | 29 ++++----- tests/openmap.R | 16 ++--- 13 files changed, 161 insertions(+), 121 deletions(-)
Title: Wrapper Functions for FSL (FMRIB Software Library) from
Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL
(http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used
neuroimaging software, using system commands. The goal is to be able to
interface with FSL completely in R, where you pass R nifti objects and the
function executes an FSL command and returns an R nifti object if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 1.3 dated 2014-11-03 and 1.4.4 dated 2015-05-21
fslr-1.3/fslr/man/cal_img.Rd |only fslr-1.3/fslr/man/check_nifti.Rd |only fslr-1.3/fslr/man/checkimg.Rd |only fslr-1.3/fslr/man/drop_img_dim.Rd |only fslr-1.3/fslr/man/onefile.Rd |only fslr-1.3/fslr/man/voxdim.Rd |only fslr-1.3/fslr/man/zero_trans.Rd |only fslr-1.4.4/fslr/DESCRIPTION | 15 fslr-1.4.4/fslr/MD5 | 381 ++++++++++++++++++------ fslr-1.4.4/fslr/NAMESPACE | 119 +++++++ fslr-1.4.4/fslr/NEWS |only fslr-1.4.4/fslr/R/applywarp.R | 5 fslr-1.4.4/fslr/R/aux_file.R |only fslr-1.4.4/fslr/R/bitpix.R |only fslr-1.4.4/fslr/R/cal_max.R |only fslr-1.4.4/fslr/R/cal_min.R |only fslr-1.4.4/fslr/R/check_nifti.R |only fslr-1.4.4/fslr/R/check_outfile.R |only fslr-1.4.4/fslr/R/checkimg.R |only fslr-1.4.4/fslr/R/checknii.R |only fslr-1.4.4/fslr/R/copyNIfTIHeader.R |only fslr-1.4.4/fslr/R/data_type.R |only fslr-1.4.4/fslr/R/datatype.R |only fslr-1.4.4/fslr/R/descrip.R |only fslr-1.4.4/fslr/R/dim_.R |only fslr-1.4.4/fslr/R/double_ortho.R |only fslr-1.4.4/fslr/R/dropEmptyImageDimensions.R |only fslr-1.4.4/fslr/R/fast.R | 84 +++-- fslr-1.4.4/fslr/R/file_imgext.R |only fslr-1.4.4/fslr/R/flirt_apply.R | 6 fslr-1.4.4/fslr/R/fnirt.R | 96 ++---- fslr-1.4.4/fslr/R/fsl_anat.R | 6 fslr-1.4.4/fslr/R/fslabs.R |only fslr-1.4.4/fslr/R/fslabs.help.R |only fslr-1.4.4/fslr/R/fslacos.R |only fslr-1.4.4/fslr/R/fslacos.help.R |only fslr-1.4.4/fslr/R/fsladd.R |only fslr-1.4.4/fslr/R/fsladd.help.R |only fslr-1.4.4/fslr/R/fslasin.R |only fslr-1.4.4/fslr/R/fslasin.help.R |only fslr-1.4.4/fslr/R/fslatan.R |only fslr-1.4.4/fslr/R/fslatan.help.R |only fslr-1.4.4/fslr/R/fslbin.help.R |only fslr-1.4.4/fslr/R/fslbinv.R |only fslr-1.4.4/fslr/R/fslbinv.help.R |only fslr-1.4.4/fslr/R/fslchfiletype.R |only fslr-1.4.4/fslr/R/fslcos.R |only fslr-1.4.4/fslr/R/fslcos.help.R |only fslr-1.4.4/fslr/R/fslcpgeom.R |only fslr-1.4.4/fslr/R/fsldilate.R |only fslr-1.4.4/fslr/R/fsldiv.R |only fslr-1.4.4/fslr/R/fsldiv.help.R |only fslr-1.4.4/fslr/R/fsledge.R |only fslr-1.4.4/fslr/R/fsledge.help.R |only fslr-1.4.4/fslr/R/fslerode.help.R |only fslr-1.4.4/fslr/R/fslexp.R |only fslr-1.4.4/fslr/R/fslexp.help.R |only fslr-1.4.4/fslr/R/fslfill.help.R |only fslr-1.4.4/fslr/R/fslfill2.R |only fslr-1.4.4/fslr/R/fslhd.R | 244 +++++---------- fslr-1.4.4/fslr/R/fslindex.R |only fslr-1.4.4/fslr/R/fslindex.help.R |only fslr-1.4.4/fslr/R/fsllog.R |only fslr-1.4.4/fslr/R/fsllog.help.R |only fslr-1.4.4/fslr/R/fslmask.help.R |only fslr-1.4.4/fslr/R/fslmul.R |only fslr-1.4.4/fslr/R/fslmul.help.R |only fslr-1.4.4/fslr/R/fslnan.R |only fslr-1.4.4/fslr/R/fslnan.help.R |only fslr-1.4.4/fslr/R/fslnanm.R |only fslr-1.4.4/fslr/R/fslnanm.help.R |only fslr-1.4.4/fslr/R/fslrand.R |only fslr-1.4.4/fslr/R/fslrand.help.R |only fslr-1.4.4/fslr/R/fslrandn.R |only fslr-1.4.4/fslr/R/fslrandn.help.R |only fslr-1.4.4/fslr/R/fslrecip.R |only fslr-1.4.4/fslr/R/fslrecip.help.R |only fslr-1.4.4/fslr/R/fslrem.R |only fslr-1.4.4/fslr/R/fslrem.help.R |only fslr-1.4.4/fslr/R/fslsin.R |only fslr-1.4.4/fslr/R/fslsin.help.R |only fslr-1.4.4/fslr/R/fslsmooth.help.R |only fslr-1.4.4/fslr/R/fslsqr.R |only fslr-1.4.4/fslr/R/fslsqr.help.R |only fslr-1.4.4/fslr/R/fslsqrt.R |only fslr-1.4.4/fslr/R/fslsqrt.help.R |only fslr-1.4.4/fslr/R/fslsub.R |only fslr-1.4.4/fslr/R/fslsub.help.R |only fslr-1.4.4/fslr/R/fslsub2.help.R |only fslr-1.4.4/fslr/R/fslsum.R |only fslr-1.4.4/fslr/R/fsltan.R |only fslr-1.4.4/fslr/R/fsltan.help.R |only fslr-1.4.4/fslr/R/fslthresh.help.R |only fslr-1.4.4/fslr/R/fslvol.R |only fslr-1.4.4/fslr/R/import_methods.R |only fslr-1.4.4/fslr/R/intent_code.R |only fslr-1.4.4/fslr/R/intent_name.R |only fslr-1.4.4/fslr/R/intent_p1.R |only fslr-1.4.4/fslr/R/intent_p2.R |only fslr-1.4.4/fslr/R/intent_p3.R |only fslr-1.4.4/fslr/R/magic.R |only fslr-1.4.4/fslr/R/mask_img.R | 8 fslr-1.4.4/fslr/R/niftiarr.R | 6 fslr-1.4.4/fslr/R/nii.stub.R | 88 ----- fslr-1.4.4/fslr/R/ortho2.R | 200 ++++++++++-- fslr-1.4.4/fslr/R/pixdim.R |only fslr-1.4.4/fslr/R/qform.R |only fslr-1.4.4/fslr/R/qform_code.R |only fslr-1.4.4/fslr/R/rescale_img.R | 136 ++++---- fslr-1.4.4/fslr/R/robust_window.R | 2 fslr-1.4.4/fslr/R/scl_inter.R |only fslr-1.4.4/fslr/R/scl_slope.R |only fslr-1.4.4/fslr/R/sform.R |only fslr-1.4.4/fslr/R/sform_code.R |only fslr-1.4.4/fslr/R/sizeof_hdr.R |only fslr-1.4.4/fslr/R/slice_code.R |only fslr-1.4.4/fslr/R/slice_duration.R |only fslr-1.4.4/fslr/R/slice_end.R |only fslr-1.4.4/fslr/R/slice_start.R |only fslr-1.4.4/fslr/R/susan.R | 4 fslr-1.4.4/fslr/R/tempimg.R |only fslr-1.4.4/fslr/R/toffset.R |only fslr-1.4.4/fslr/R/vox_offset.R |only fslr-1.4.4/fslr/R/window_img.R | 4 fslr-1.4.4/fslr/build/vignette.rds |binary fslr-1.4.4/fslr/man/aux_file-methods.Rd |only fslr-1.4.4/fslr/man/bitpix-methods.Rd |only fslr-1.4.4/fslr/man/cal_max-methods.Rd |only fslr-1.4.4/fslr/man/cal_min-methods.Rd |only fslr-1.4.4/fslr/man/check_file.Rd | 3 fslr-1.4.4/fslr/man/check_nifti-methods.Rd |only fslr-1.4.4/fslr/man/check_outfile.Rd |only fslr-1.4.4/fslr/man/checkimg-methods.Rd |only fslr-1.4.4/fslr/man/checknii-methods.Rd |only fslr-1.4.4/fslr/man/checkout.Rd | 3 fslr-1.4.4/fslr/man/cog.Rd | 3 fslr-1.4.4/fslr/man/colorbar.Rd |only fslr-1.4.4/fslr/man/copyNIfTIHeader.Rd |only fslr-1.4.4/fslr/man/data_type-methods.Rd |only fslr-1.4.4/fslr/man/datatype-methods.Rd |only fslr-1.4.4/fslr/man/datatype.Rd | 6 fslr-1.4.4/fslr/man/descrip-methods.Rd |only fslr-1.4.4/fslr/man/dim_-methods.Rd |only fslr-1.4.4/fslr/man/double_ortho.Rd |only fslr-1.4.4/fslr/man/dropEmptyImageDimensions.Rd |only fslr-1.4.4/fslr/man/fast.Rd | 11 fslr-1.4.4/fslr/man/fast.help.Rd | 3 fslr-1.4.4/fslr/man/file_imgext.Rd |only fslr-1.4.4/fslr/man/flirt.Rd | 10 fslr-1.4.4/fslr/man/flirt.help.Rd | 3 fslr-1.4.4/fslr/man/flirt_apply.Rd | 7 fslr-1.4.4/fslr/man/fnirt.Rd | 7 fslr-1.4.4/fslr/man/fnirt.help.Rd | 3 fslr-1.4.4/fslr/man/fnirt_with_affine.Rd | 5 fslr-1.4.4/fslr/man/fnirt_with_affine_apply.Rd | 9 fslr-1.4.4/fslr/man/fsl_anat.Rd | 9 fslr-1.4.4/fslr/man/fsl_anat.help.Rd | 3 fslr-1.4.4/fslr/man/fsl_applywarp.Rd | 7 fslr-1.4.4/fslr/man/fsl_applywarp.help.Rd | 3 fslr-1.4.4/fslr/man/fsl_biascorrect.Rd | 16 - fslr-1.4.4/fslr/man/fslabs.Rd |only fslr-1.4.4/fslr/man/fslabs.help.Rd |only fslr-1.4.4/fslr/man/fslacos.Rd |only fslr-1.4.4/fslr/man/fslacos.help.Rd |only fslr-1.4.4/fslr/man/fsladd.Rd |only fslr-1.4.4/fslr/man/fsladd.help.Rd |only fslr-1.4.4/fslr/man/fslasin.Rd |only fslr-1.4.4/fslr/man/fslasin.help.Rd |only fslr-1.4.4/fslr/man/fslatan.Rd |only fslr-1.4.4/fslr/man/fslatan.help.Rd |only fslr-1.4.4/fslr/man/fslbet.Rd | 9 fslr-1.4.4/fslr/man/fslbet.help.Rd | 3 fslr-1.4.4/fslr/man/fslbin.Rd | 7 fslr-1.4.4/fslr/man/fslbin.help.Rd |only fslr-1.4.4/fslr/man/fslbinv.Rd |only fslr-1.4.4/fslr/man/fslbinv.help.Rd |only fslr-1.4.4/fslr/man/fslchfiletype.Rd |only fslr-1.4.4/fslr/man/fslchfiletype.help.Rd |only fslr-1.4.4/fslr/man/fslcmd.Rd | 7 fslr-1.4.4/fslr/man/fslcog.Rd | 3 fslr-1.4.4/fslr/man/fslcos.Rd |only fslr-1.4.4/fslr/man/fslcos.help.Rd |only fslr-1.4.4/fslr/man/fslcpgeom.Rd |only fslr-1.4.4/fslr/man/fslcpgeom.help.Rd |only fslr-1.4.4/fslr/man/fsldilate.Rd |only fslr-1.4.4/fslr/man/fsldir.Rd | 3 fslr-1.4.4/fslr/man/fsldiv.Rd |only fslr-1.4.4/fslr/man/fsldiv.help.Rd |only fslr-1.4.4/fslr/man/fsledge.Rd |only fslr-1.4.4/fslr/man/fsledge.help.Rd |only fslr-1.4.4/fslr/man/fslerode.Rd | 7 fslr-1.4.4/fslr/man/fslerode.help.Rd |only fslr-1.4.4/fslr/man/fslexp.Rd |only fslr-1.4.4/fslr/man/fslexp.help.Rd |only fslr-1.4.4/fslr/man/fslfill.Rd | 7 fslr-1.4.4/fslr/man/fslfill.help.Rd |only fslr-1.4.4/fslr/man/fslfill2.Rd |only fslr-1.4.4/fslr/man/fslhd.Rd | 3 fslr-1.4.4/fslr/man/fslhd.help.Rd | 3 fslr-1.4.4/fslr/man/fslhd.parse.Rd | 3 fslr-1.4.4/fslr/man/fslhelp.Rd | 3 fslr-1.4.4/fslr/man/fslindex.Rd |only fslr-1.4.4/fslr/man/fslindex.help.Rd |only fslr-1.4.4/fslr/man/fsllog.Rd |only fslr-1.4.4/fslr/man/fsllog.help.Rd |only fslr-1.4.4/fslr/man/fslmask.Rd | 7 fslr-1.4.4/fslr/man/fslmask.help.Rd |only fslr-1.4.4/fslr/man/fslmaths.Rd | 7 fslr-1.4.4/fslr/man/fslmaths.help.Rd | 10 fslr-1.4.4/fslr/man/fslmerge.Rd | 5 fslr-1.4.4/fslr/man/fslmerge.help.Rd | 3 fslr-1.4.4/fslr/man/fslmul.Rd |only fslr-1.4.4/fslr/man/fslmul.help.Rd |only fslr-1.4.4/fslr/man/fslnan.Rd |only fslr-1.4.4/fslr/man/fslnan.help.Rd |only fslr-1.4.4/fslr/man/fslnanm.Rd |only fslr-1.4.4/fslr/man/fslnanm.help.Rd |only fslr-1.4.4/fslr/man/fslorient.Rd | 5 fslr-1.4.4/fslr/man/fslorient.help.Rd | 3 fslr-1.4.4/fslr/man/fslrand.Rd |only fslr-1.4.4/fslr/man/fslrand.help.Rd |only fslr-1.4.4/fslr/man/fslrandn.Rd |only fslr-1.4.4/fslr/man/fslrandn.help.Rd |only fslr-1.4.4/fslr/man/fslrange.Rd | 3 fslr-1.4.4/fslr/man/fslrecip.Rd |only fslr-1.4.4/fslr/man/fslrecip.help.Rd |only fslr-1.4.4/fslr/man/fslrem.Rd |only fslr-1.4.4/fslr/man/fslrem.help.Rd |only fslr-1.4.4/fslr/man/fslreorient2std.Rd | 5 fslr-1.4.4/fslr/man/fslreorient2std.help.Rd | 3 fslr-1.4.4/fslr/man/fslsin.Rd |only fslr-1.4.4/fslr/man/fslsin.help.Rd |only fslr-1.4.4/fslr/man/fslsmooth.Rd | 11 fslr-1.4.4/fslr/man/fslsmooth.help.Rd |only fslr-1.4.4/fslr/man/fslsqr.Rd |only fslr-1.4.4/fslr/man/fslsqr.help.Rd |only fslr-1.4.4/fslr/man/fslsqrt.Rd |only fslr-1.4.4/fslr/man/fslsqrt.help.Rd |only fslr-1.4.4/fslr/man/fslstats.Rd | 3 fslr-1.4.4/fslr/man/fslstats.help.Rd | 3 fslr-1.4.4/fslr/man/fslsub.Rd |only fslr-1.4.4/fslr/man/fslsub.help.Rd |only fslr-1.4.4/fslr/man/fslsub2.Rd | 7 fslr-1.4.4/fslr/man/fslsub2.help.Rd |only fslr-1.4.4/fslr/man/fslsum.Rd |only fslr-1.4.4/fslr/man/fslswapdim.Rd | 7 fslr-1.4.4/fslr/man/fslswapdim.help.Rd | 3 fslr-1.4.4/fslr/man/fsltan.Rd |only fslr-1.4.4/fslr/man/fsltan.help.Rd |only fslr-1.4.4/fslr/man/fslthresh.Rd | 5 fslr-1.4.4/fslr/man/fslthresh.help.Rd |only fslr-1.4.4/fslr/man/fslval.Rd | 3 fslr-1.4.4/fslr/man/fslval.help.Rd | 3 fslr-1.4.4/fslr/man/fslview.Rd | 3 fslr-1.4.4/fslr/man/fslview.help.Rd | 3 fslr-1.4.4/fslr/man/fslvol.Rd |only fslr-1.4.4/fslr/man/get.fsl.Rd | 3 fslr-1.4.4/fslr/man/get.fsloutput.Rd | 3 fslr-1.4.4/fslr/man/get.imgext.Rd | 3 fslr-1.4.4/fslr/man/getForms.Rd | 3 fslr-1.4.4/fslr/man/have.fsl.Rd | 3 fslr-1.4.4/fslr/man/intent_code-methods.Rd |only fslr-1.4.4/fslr/man/intent_name-methods.Rd |only fslr-1.4.4/fslr/man/intent_p1-methods.Rd |only fslr-1.4.4/fslr/man/intent_p2-methods.Rd |only fslr-1.4.4/fslr/man/intent_p3-methods.Rd |only fslr-1.4.4/fslr/man/magic-methods.Rd |only fslr-1.4.4/fslr/man/mask_img.Rd | 3 fslr-1.4.4/fslr/man/melodic.Rd | 5 fslr-1.4.4/fslr/man/melodic.help.Rd | 3 fslr-1.4.4/fslr/man/newnii.Rd | 3 fslr-1.4.4/fslr/man/niftiarr.Rd | 3 fslr-1.4.4/fslr/man/nii.stub.Rd | 6 fslr-1.4.4/fslr/man/orientation-methods.Rd |only fslr-1.4.4/fslr/man/ortho2.Rd | 49 ++- fslr-1.4.4/fslr/man/pixdim-methods.Rd |only fslr-1.4.4/fslr/man/qform_code-methods.Rd |only fslr-1.4.4/fslr/man/rescale_img.Rd | 3 fslr-1.4.4/fslr/man/robust_window.Rd | 3 fslr-1.4.4/fslr/man/scl_inter-methods.Rd |only fslr-1.4.4/fslr/man/scl_slope-methods.Rd |only fslr-1.4.4/fslr/man/sform_code-methods.Rd |only fslr-1.4.4/fslr/man/sizeof_hdr-methods.Rd |only fslr-1.4.4/fslr/man/slice_code-methods.Rd |only fslr-1.4.4/fslr/man/slice_duration-methods.Rd |only fslr-1.4.4/fslr/man/slice_end-methods.Rd |only fslr-1.4.4/fslr/man/slice_start-methods.Rd |only fslr-1.4.4/fslr/man/susan.Rd | 7 fslr-1.4.4/fslr/man/susan.help.Rd | 3 fslr-1.4.4/fslr/man/tempimg.Rd | 13 fslr-1.4.4/fslr/man/toffset-methods.Rd |only fslr-1.4.4/fslr/man/vox_offset-methods.Rd |only fslr-1.4.4/fslr/man/window_img.Rd | 8 fslr-1.4.4/fslr/man/xyz.Rd |only fslr-1.4.4/fslr/man/zscore_img.Rd | 6 295 files changed, 1124 insertions(+), 681 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.1-3 dated 2015-05-20 and 0.1-4 dated 2015-05-21
evolqg-0.1-3/evolqg/src/Makevars |only evolqg-0.1-3/evolqg/src/Makevars.win |only evolqg-0.1-4/evolqg/DESCRIPTION | 10 +++++----- evolqg-0.1-4/evolqg/MD5 | 4 +--- 4 files changed, 6 insertions(+), 8 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.55.0-3 dated 2015-01-05 and 1.58.0-1 dated 2015-05-21
ChangeLog | 17 DESCRIPTION | 8 MD5 | 8087 +++++----- README.md | 6 inst/NEWS.Rd | 8 inst/include/boost/algorithm/algorithm.hpp |only inst/include/boost/algorithm/clamp.hpp | 40 inst/include/boost/algorithm/cxx11/all_of.hpp | 5 inst/include/boost/algorithm/cxx11/any_of.hpp | 5 inst/include/boost/algorithm/cxx11/copy_if.hpp | 5 inst/include/boost/algorithm/cxx11/copy_n.hpp | 5 inst/include/boost/algorithm/cxx11/find_if_not.hpp | 5 inst/include/boost/algorithm/cxx11/iota.hpp | 9 inst/include/boost/algorithm/cxx11/is_partitioned.hpp | 5 inst/include/boost/algorithm/cxx11/is_permutation.hpp | 65 inst/include/boost/algorithm/cxx11/is_sorted.hpp | 6 inst/include/boost/algorithm/cxx11/none_of.hpp | 5 inst/include/boost/algorithm/cxx11/partition_copy.hpp | 5 inst/include/boost/algorithm/cxx11/partition_point.hpp | 7 inst/include/boost/algorithm/cxx14/is_permutation.hpp | 176 inst/include/boost/algorithm/hex.hpp | 1 inst/include/boost/algorithm/searching/detail/bm_traits.hpp | 12 inst/include/boost/algorithm/string/detail/finder.hpp | 2 inst/include/boost/algorithm/string/find_iterator.hpp | 7 inst/include/boost/algorithm/string/sequence_traits.hpp | 73 inst/include/boost/algorithm/string/std/list_traits.hpp | 17 inst/include/boost/algorithm/string/std/rope_traits.hpp | 20 inst/include/boost/algorithm/string/std/slist_traits.hpp | 16 inst/include/boost/algorithm/string/std/string_traits.hpp | 8 inst/include/boost/align |only inst/include/boost/aligned_storage.hpp | 50 inst/include/boost/any.hpp | 78 inst/include/boost/archive/add_facet.hpp | 2 inst/include/boost/archive/archive_exception.hpp | 10 inst/include/boost/archive/basic_archive.hpp | 7 inst/include/boost/archive/basic_binary_iarchive.hpp | 22 inst/include/boost/archive/basic_binary_iprimitive.hpp | 15 inst/include/boost/archive/basic_binary_oarchive.hpp | 22 inst/include/boost/archive/basic_binary_oprimitive.hpp | 13 inst/include/boost/archive/basic_streambuf_locale_saver.hpp | 12 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inst/include/boost/xpressive/regex_error.hpp | 2 inst/include/boost/xpressive/regex_iterator.hpp | 2 inst/include/boost/xpressive/regex_token_iterator.hpp | 2 inst/include/boost/xpressive/regex_traits.hpp | 2 inst/include/boost/xpressive/sub_match.hpp | 14 inst/include/boost/xpressive/traits/c_regex_traits.hpp | 2 inst/include/boost/xpressive/traits/cpp_regex_traits.hpp | 2 inst/include/boost/xpressive/traits/detail/c_ctype.hpp | 2 inst/include/boost/xpressive/xpressive_fwd.hpp | 5 inst/include/boost/xpressive/xpressive_static.hpp | 2 man/BH-package.Rd | 4 4091 files changed, 101108 insertions(+), 70474 deletions(-)
Title: White Matter Normalization for Magnetic Resonance Images using
Whitestripe
Description: Shinohara et. al introduced Whitestripe, an
intensity-based normalization of T1 and T2 images, where normal
appearing white matter performs well, but requires segmentation.
This method performs white matter mean and standard deviation
estimates on data that has been rigidly-registered to the MNI
template and uses histogram-based methods.
Author: Taki Shinohara, John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between WhiteStripe versions 1.0 dated 2014-11-04 and 1.1.1 dated 2015-05-21
DESCRIPTION | 31 ++++++++++--------- MD5 | 39 ++++++++++++------------ NAMESPACE | 9 +++-- R/get.largest.mode.R | 65 ++++++++++++++++++++++++++++++++++++++++- R/smooth_hist.R | 4 +- R/whitestripe_ind.R | 15 ++++++--- man/download_img_data.Rd | 3 + man/get.deriv.smooth.hist.Rd | 3 + man/get.first.mode.Rd |only man/get.largest.mode.Rd | 3 + man/get.last.mode.Rd | 3 + man/make_img_voi.Rd | 3 + man/s.hist.Rd | 3 + man/smooth_hist.Rd | 5 +-- man/t1.voi.hist.Rd | 3 + man/t2.voi.hist.Rd | 3 + man/whitestripe.Rd | 3 + man/whitestripe_hybrid.Rd | 3 + man/whitestripe_ind_to_mask.Rd | 3 + man/whitestripe_norm.Rd | 6 ++- man/xvals.Rd | 3 + 21 files changed, 150 insertions(+), 60 deletions(-)
Title: Selection and/or Smoothing of Ordinal Predictors
Description: Selection and/or smoothing of ordinally scaled independent variables using a group lasso or generalized ridge penalty.
Author: Jan Gertheiss
Maintainer: Jan Gertheiss <jgerthe@uni-goettingen.de>
Diff between ordPens versions 0.2-1 dated 2013-06-14 and 0.3-1 dated 2015-05-21
DESCRIPTION | 14 ++++---- MD5 | 26 ++++++++-------- NAMESPACE | 8 +++- R/ordAOV.R | 12 +++---- R/ordGene.r |only R/ordPens-internal.R | 78 ++++++++++++++++++++++++++++++++++++++++-------- R/ordSelect.R | 5 --- R/ordSmooth.R | 5 --- man/ICFCoreSetCWP.Rd | 2 - man/ordAOV.Rd | 19 ++++++----- man/ordGene.Rd |only man/ordPens-internal.Rd | 4 +- man/ordPens-package.Rd | 16 ++++++--- man/ordSelect.Rd | 5 --- man/ordSmooth.Rd | 5 --- 15 files changed, 125 insertions(+), 74 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.2.3 dated 2015-03-26 and 0.2.4 dated 2015-05-21
DESCRIPTION | 8 - MD5 | 62 ++++++------- NAMESPACE | 5 - R/MazamaSpatialUtils.R | 18 ++- R/convertGADM.R | 3 R/convertLayer.R | 8 - R/convertNaturalEarthAdm1.R | 4 R/convertUSCensusCounties.R | 1 R/convertUSGSHUC8.R | 5 - R/convertWikipediaTimezoneTable.R | 34 +++---- R/convertWorldTimezones.R | 14 +- R/getCountryCode.R | 2 R/getSpatialData.R | 1 R/organizePolygons.R | 1 build/vignette.rds |binary data/SimpleCountries.RData |binary data/SimpleTimezones.RData |binary demo/findCountries.R | 3 demo/findStates.R | 5 - demo/findTimezones.R | 3 inst/doc/introduction.R | 5 - inst/doc/introduction.Rmd | 9 - inst/doc/introduction.html | 11 +- man/MazamaSpatialUtils.Rd | 8 + man/SimpleTimezones.Rd | 2 man/SpatialDataDir.Rd | 2 man/convertLayer.Rd | 2 man/convertWorldTimezones.Rd | 12 +- man/getCountryCode.Rd | 6 - tests/testthat.R | 5 - tests/testthat/test1.R | 178 ++++++++------------------------------ vignettes/introduction.Rmd | 9 - 32 files changed, 158 insertions(+), 268 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>
Diff between libamtrack versions 0.5.5 dated 2014-07-08 and 0.6.0 dated 2015-05-21
libamtrack-0.5.5/libamtrack/man/AT.Highland.angle.Rd |only libamtrack-0.5.5/libamtrack/man/AT.I.eV.from.element.acronym.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Moliere.function.f0.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Moliere.function.f1.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Moliere.function.f2.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Stopping.Power.MeV.cm2.g.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Stopping.Power.keV.um.Rd |only libamtrack-0.5.5/libamtrack/man/AT.Z.from.element.acronym.Rd |only libamtrack-0.5.5/libamtrack/man/AT.atomic.weight.from.element.acronym.Rd |only libamtrack-0.5.5/libamtrack/man/AT.characteristic.single.scattering.angle.Rd |only libamtrack-0.5.5/libamtrack/man/AT.characteristicple.scattering.angle.Rd |only libamtrack-0.5.5/libamtrack/man/AT.density.g.cm3.from.element.acronym.Rd |only libamtrack-0.5.5/libamtrack/man/AT.effective.collision.number.Rd |only libamtrack-0.5.5/libamtrack/man/AT.element.acronym.from.Z.Rd |only libamtrack-0.5.5/libamtrack/man/AT.reduced.target.thickness.Rd |only libamtrack-0.5.5/libamtrack/man/AT.scattering.angle.distribution.Rd |only libamtrack-0.5.5/libamtrack/man/AT.screening.angle.Rd |only libamtrack-0.5.5/libamtrack/src/AT_DataStoppingPower.c |only libamtrack-0.5.5/libamtrack/src/AT_DataStoppingPower.h |only libamtrack-0.6.0/libamtrack/DESCRIPTION | 18 libamtrack-0.6.0/libamtrack/INSTALL |only libamtrack-0.6.0/libamtrack/MD5 | 209 +- libamtrack-0.6.0/libamtrack/NAMESPACE | 91 libamtrack-0.6.0/libamtrack/R/AT.SPC.convert.to.DDD.R | 3 libamtrack-0.6.0/libamtrack/R/AT.SPC.export.DEDX.R | 15 libamtrack-0.6.0/libamtrack/R/AT.SPC.spectrum.at.depth.g.cm2.R | 28 libamtrack-0.6.0/libamtrack/R/initial.R | 2 libamtrack-0.6.0/libamtrack/R/libamtrack.R | 542 +---- libamtrack-0.6.0/libamtrack/README |only libamtrack-0.6.0/libamtrack/configure | 191 - libamtrack-0.6.0/libamtrack/inst/extdata/FLUKA_DEDX_ALOX.txt |only libamtrack-0.6.0/libamtrack/inst/extdata/FLUKA_DEDX_WATER_76.8eV.txt |only libamtrack-0.6.0/libamtrack/man/AT.A.from.particle.no.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.Bethe.mean.energy.loss.MeV.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.CSDA.energy.after.slab.E.MeV.u.Rd |only libamtrack-0.6.0/libamtrack/man/AT.CSDA.range.Bethe.g.cm2.Rd |only libamtrack-0.6.0/libamtrack/man/AT.D.RDD.Gy.Rd | 15 libamtrack-0.6.0/libamtrack/man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.E.from.beta.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.I.eV.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.Landau.PDF.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.Mass.Stopping.Power.Rd |only libamtrack-0.6.0/libamtrack/man/AT.Mass.Stopping.Power.with.no.Rd |only libamtrack-0.6.0/libamtrack/man/AT.Rutherford.SDCS.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.SPC.spectrum.at.depth.g.cm2.Rd | 5 libamtrack-0.6.0/libamtrack/man/AT.Stopping.Power.Rd |only libamtrack-0.6.0/libamtrack/man/AT.Stopping.Power.with.no.Rd |only libamtrack-0.6.0/libamtrack/man/AT.Vavilov.PDF.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.Vavilov.energy.loss.distribution.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.WEPL.Bethe.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.Z.from.particle.no.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.atomic.weight.from.Z.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.average.A.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.average.Z.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.beam.par.physical.to.technical.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.beam.par.technical.to.physical.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.beta.from.E.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.dose.Gy.from.fluence.cm2.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.dose.weighted.E.MeV.u.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 8 libamtrack-0.6.0/libamtrack/man/AT.effective.Z.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.effective.charge.from.E.MeV.u.Rd | 17 libamtrack-0.6.0/libamtrack/man/AT.electron.density.m3.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.electron.density.m3.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.electron.density.m3.from.material.no.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.energy.loss.FWHM.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.energy.loss.distribution.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.energy.loss.mode.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.energy.straggling.MeV2.cm2.g.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.fluence.cm2.from.dose.Gy.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.fluence.weighted.E.MeV.u.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 8 libamtrack-0.6.0/libamtrack/man/AT.gamma.from.E.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.get.materials.data.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.kappa.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.lambda.from.energy.loss.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.max.E.transfer.MeV.Rd | 32 libamtrack-0.6.0/libamtrack/man/AT.max.electron.ranges.m.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.mean.number.of.tracks.contrib.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 13 libamtrack-0.6.0/libamtrack/man/AT.nuclear.spin.from.particle.no.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.particle.no.from.Z.and.A.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.r.RDD.m.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.run.CPPSC.method.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.run.GSM.method.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.run.IGK.method.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.set.user.material.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.set.user.material.from.composition.Rd | 4 libamtrack-0.6.0/libamtrack/man/AT.stopping.power.ratio.Rd | 32 libamtrack-0.6.0/libamtrack/man/AT.total.D.Gy.Rd | 8 libamtrack-0.6.0/libamtrack/man/AT.total.fluence.cm2.Rd | 6 libamtrack-0.6.0/libamtrack/man/AT.translate.dose.into.DSB.distribution.Rd | 4 libamtrack-0.6.0/libamtrack/man/libamtrack-package.Rd | 60 libamtrack-0.6.0/libamtrack/man/stopping.power.source.no.Rd | 58 libamtrack-0.6.0/libamtrack/src/AT.h | 6 libamtrack-0.6.0/libamtrack/src/AT_Algorithms_IGK.c | 8 libamtrack-0.6.0/libamtrack/src/AT_Algorithms_IGK.h | 3 libamtrack-0.6.0/libamtrack/src/AT_DataRange.h | 2 libamtrack-0.6.0/libamtrack/src/AT_Error.h | 8 libamtrack-0.6.0/libamtrack/src/AT_KatzModel.c | 20 libamtrack-0.6.0/libamtrack/src/AT_NumericalRoutines.c | 6 libamtrack-0.6.0/libamtrack/src/AT_NumericalRoutines.h | 2 libamtrack-0.6.0/libamtrack/src/AT_PhysicsRoutines.c | 47 libamtrack-0.6.0/libamtrack/src/AT_PhysicsRoutines.h | 2 libamtrack-0.6.0/libamtrack/src/AT_RDD.c | 31 libamtrack-0.6.0/libamtrack/src/AT_RDD.h | 2 libamtrack-0.6.0/libamtrack/src/AT_RDD_Tabulated.c | 44 libamtrack-0.6.0/libamtrack/src/AT_R_Wrapper.c | 1003 ++-------- libamtrack-0.6.0/libamtrack/src/AT_R_Wrapper.h | 178 - libamtrack-0.6.0/libamtrack/src/AT_SPC.c | 10 libamtrack-0.6.0/libamtrack/src/AT_SPC.h | 14 libamtrack-0.6.0/libamtrack/src/AT_StoppingPower.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPower.h |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerData.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerData.h |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataBethe.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataBethe.h |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataFromFile.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataFromFile.h |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataICRU.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataICRU.h |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataPSTAR.c |only libamtrack-0.6.0/libamtrack/src/AT_StoppingPowerDataPSTAR.h |only libamtrack-0.6.0/libamtrack/src/AT_SuccessiveConvolutions.c | 75 libamtrack-0.6.0/libamtrack/src/config.h | 12 126 files changed, 1156 insertions(+), 1874 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.1.3 dated 2015-05-01 and 0.1.4 dated 2015-05-21
ChangeLog | 15 +++++++ DESCRIPTION | 9 ++-- MD5 | 20 +++++---- R/HyperSpecRaster_methods.R | 94 +++++++++++++++++++++++++++++++++++++++++++- R/nri_lm.R | 4 + R/nri_plot.R | 49 ++++++++++++++++++++++ R/plot_HyperSpec_cube.R |only R/speclib.R | 1 inst/doc/References.pdf |binary man/HyperSpecRaster.Rd | 3 + man/cubePlot.Rd |only man/wavelength.Rd | 15 +++++-- 12 files changed, 190 insertions(+), 20 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated from Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between simPH versions 1.3.1 dated 2015-05-04 and 1.3.2 dated 2015-05-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/SurvExpand.R | 3 ++- README.md | 4 +--- 5 files changed, 15 insertions(+), 12 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3, < 2) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 0.9-2 dated 2015-03-15 and 0.9-3 dated 2015-05-21
ChangeLog | 996 +++++++++++++++------------------------- DESCRIPTION | 12 MD5 | 30 - R/AAA.R | 16 R/Class-CRSx.R | 14 R/gdal.R | 4 build/vignette.rds |binary inst/ChangeLog | 996 +++++++++++++++------------------------- inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary man/CRS-class.Rd | 6 src/init.c | 2 src/ogr_polygons.c | 5 src/ogrsource.cpp | 6 src/projectit.cpp | 34 + src/rgdal.h | 2 16 files changed, 896 insertions(+), 1229 deletions(-)
Title: K-Means for Joint Longitudinal Data
Description: An implementation of k-means specifically design
to cluster joint trajectories (longitudinal data on
several variable-trajectories).
Like 'kml', it provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical
interface for choosing the 'best' number of clusters. In addition, the 3D graph
representing the mean joint-trajectories of each cluster can be exported through
LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml3d versions 2.2 dated 2014-03-25 and 2.3 dated 2015-05-21
DESCRIPTION | 18 +++++++++--------- MD5 | 7 ++++--- inst |only man/choice.Rd | 5 +++-- man/kml3d-package.Rd | 4 ++-- 5 files changed, 18 insertions(+), 16 deletions(-)
Title: Classes and Methods for Trajectory Data
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut],
Benedikt Klus [aut],
Benedikt Graeler [ctb],
Nikolai Gorte [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between trajectories versions 0.1-2 dated 2015-04-25 and 0.1-3 dated 2015-05-21
ChangeLog |only DESCRIPTION | 27 +++++---- MD5 | 47 +++++++++------ NAMESPACE | 10 ++- R/Class-Tracks.R | 59 +++++++++++-------- R/Tracks-methods.R | 145 ++++++++++++++++++++++++++----------------------- R/compare-methods.R |only R/difftrack.R |only build/vignette.rds |binary demo/00Index | 3 + demo/Tracks.R | 2 demo/citibikenyc.R |only demo/enviroCaR.R |only demo/geolife.R | 2 demo/stcube.R | 5 + demo/storms.R |only inst/doc/tracks.R | 2 inst/doc/tracks.Rnw | 2 inst/doc/tracks.pdf |binary man/A3.Rd | 2 man/Track-class.Rd | 2 man/compare.Rd |only man/difftrack-class.Rd |only man/dists.Rd |only man/downsample.Rd |only man/frechetDist.Rd |only man/stcube.Rd | 9 ++- tests/tracks.R | 2 tests/tracks.Rout.save | 21 +++---- vignettes/tracks.Rnw | 2 30 files changed, 193 insertions(+), 149 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Description: Contains primarily a function to fit
a regression model with possibly right, left or interval
censored observations and with the error distribution
expressed as a mixture of G-splines. Core part
of the computation is done in compiled C++ written
using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between smoothSurv versions 1.5 dated 2015-02-05 and 1.5-2 dated 2015-05-21
DESCRIPTION | 20 ++++++++++---------- MD5 | 6 +++--- src/Scythe_Matrix.cpp | 8 ++++++-- src/Scythe_Matrix.h | 2 ++ 4 files changed, 21 insertions(+), 15 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 3.7 dated 2015-05-16 and 3.9 dated 2015-05-21
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- README.md | 6 ++++++ configure | 48 ++++++++++++++++++++++++++++-------------------- configure.ac | 36 +++++++++++++++++++++++------------- src/Makevars.in | 6 +++++- src/Makevars.win | 5 ++++- src/knetfile.c | 16 +++++++++++++--- 8 files changed, 92 insertions(+), 51 deletions(-)
Title: A Diceware Passphrase Implementation
Description: The Diceware method can be used to generate strong passphrases.
In short, you roll a 6-faced dice 5 times in a row, the number obtained is
matched against a dictionary of easily remembered words. By combining together 7
words thus generated, you obtain a password that is relatively easy to remember,
but would take several millions years (on average) for a powerful computer to guess.
Author: Francois Michonneau [aut, cre],
Arnold G. Reinhold [cph]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between riceware versions 0.2 dated 2015-05-06 and 0.4 dated 2015-05-21
DESCRIPTION | 14 ++++++++------ MD5 | 6 +++--- R/rice.R | 1 + tests/testthat/test-rice.R | 2 ++ 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Probability of Default Calibration
Description: Implementation of most popular approaches to PD (probability of default) calibration: Quasi Moment Matching algorithm (D. Tasche), algorithm proposed by M. van der Burgt, K. Pluto and D. Tasche's most prudent estimation methodology.
Author: Denis Surzhko
Maintainer: Denis Surzhko <densur@gmail.com>
Diff between LDPD versions 1.0.2 dated 2015-01-03 and 1.1.2 dated 2015-05-21
DESCRIPTION | 10 MD5 | 12 - R/PT.R | 182 +++++++++-------- R/QMM.R | 515 ++++++++++++++++++++++++++------------------------ R/VDB.R | 154 +++++++------- man/QMMRecalibrate.Rd | 12 - man/VDBCalibratePD.Rd | 1 7 files changed, 462 insertions(+), 424 deletions(-)
Title: Tools for the Analysis of Animal Track Data
Description: Functions for accessing and manipulating spatial data for animal
tracking, with straightforward coercion from and to other formats. Filter
for speed and create time spent maps from animal track data.
Author: Michael D. Sumner [aut, cre],
Sebastian Luque [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between trip versions 1.1-19 dated 2014-11-05 and 1.1-21 dated 2015-05-21
trip-1.1-19/trip/inst/doc/trip.Rnw |only trip-1.1-19/trip/inst/doc/trip.pdf |only trip-1.1-19/trip/vignettes/trip.Rnw |only trip-1.1-21/trip/ChangeLog | 1772 +++++++++++---------- trip-1.1-21/trip/DESCRIPTION | 19 trip-1.1-21/trip/MD5 | 93 - trip-1.1-21/trip/NAMESPACE | 125 - trip-1.1-21/trip/NEWS | 491 +++-- trip-1.1-21/trip/R/AllClass.R | 314 +-- trip-1.1-21/trip/R/AllMethod.R | 1100 ++++++------- trip-1.1-21/trip/R/as.trip.R | 122 - trip-1.1-21/trip/R/coerce.R | 307 +-- trip-1.1-21/trip/R/colours.R | 198 +- trip-1.1-21/trip/R/distance.R |only trip-1.1-21/trip/R/filter.R | 574 +++--- trip-1.1-21/trip/R/grid.R | 758 ++++----- trip-1.1-21/trip/R/interpequal.R | 72 trip-1.1-21/trip/R/speedDistanceAngle.R | 150 - trip-1.1-21/trip/R/trip-deprecated.R | 120 - trip-1.1-21/trip/R/trip.R | 1927 +++++++++++------------ trip-1.1-21/trip/README.md | 118 - trip-1.1-21/trip/build/vignette.rds |binary trip-1.1-21/trip/inst/doc/trip.R | 154 - trip-1.1-21/trip/inst/doc/trip.Rmd |only trip-1.1-21/trip/inst/doc/trip.html |only trip-1.1-21/trip/man/TimeOrderedRecords-class.Rd | 59 trip-1.1-21/trip/man/TimeOrderedRecords.Rd | 43 trip-1.1-21/trip/man/adjust.duplicateTimes.Rd | 93 - trip-1.1-21/trip/man/argos.sigma.Rd | 79 trip-1.1-21/trip/man/as.Other.Rd | 127 - trip-1.1-21/trip/man/as.trip-methods.Rd | 89 - trip-1.1-21/trip/man/cut.trip.Rd | 203 +- trip-1.1-21/trip/man/filter.penSS.Rd | 199 +- trip-1.1-21/trip/man/forceCompliance.Rd | 61 trip-1.1-21/trip/man/homedist.Rd |only trip-1.1-21/trip/man/makeGridTopology.Rd | 71 trip-1.1-21/trip/man/oc.theme.Rd | 85 - trip-1.1-21/trip/man/rasterize.Rd |only trip-1.1-21/trip/man/readArgos.Rd | 193 +- trip-1.1-21/trip/man/sda.Rd | 73 trip-1.1-21/trip/man/sepIdGaps.Rd | 91 - trip-1.1-21/trip/man/speedfilter.Rd | 131 - trip-1.1-21/trip/man/trackAngle.Rd | 63 trip-1.1-21/trip/man/trackDistance.Rd | 145 - trip-1.1-21/trip/man/trip-accessors.Rd | 87 - trip-1.1-21/trip/man/trip-class.Rd | 119 - trip-1.1-21/trip/man/trip-internal.Rd | 91 - trip-1.1-21/trip/man/trip-methods.Rd | 275 +-- trip-1.1-21/trip/man/trip.split.exact.Rd | 81 trip-1.1-21/trip/man/tripGrid.Rd | 81 trip-1.1-21/trip/man/tripGrid.interp.Rd | 131 - trip-1.1-21/trip/vignettes/trip.Rmd |only 52 files changed, 5683 insertions(+), 5401 deletions(-)
Title: Dictionaries and Word Lists for the 'qdap' Package
Description: A collection of dictionaries and word lists for use with
the 'qdap' package.
Author: Tyler Rinker
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapDictionaries versions 1.0.5 dated 2015-04-06 and 1.0.6 dated 2015-05-20
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/left.just.R | 7 ++++--- R/view_data.R | 16 +++++++--------- man/view_data.Rd | 11 +++++++---- 6 files changed, 37 insertions(+), 26 deletions(-)
More information about qdapDictionaries at CRAN
Permanent link
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points through the use of U-statistics.
The procedures do not make any distributional assumptions
other than the existence of certain absolute moments. Hierarchical
and exact search methods are included. All methods return the
set of estimated change-points as well as other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James <nj89@cornell.edu>
Diff between ecp versions 1.6.2 dated 2015-01-04 and 2.0.0 dated 2015-05-20
DESCRIPTION | 24 ++++++++++++------------ MD5 | 21 ++++++++++++--------- NAMESPACE | 1 + NEWS | 11 +++++++++-- R/cp3o.R |only R/energyChangePoint.R | 3 +++ build/vignette.rds |binary man/e.cp3o.Rd |only man/e.divisive.Rd | 8 ++++---- man/getBetween.Rd | 2 +- src/Makevars | 1 + src/Makevars.win | 1 + src/efast.cpp |only 13 files changed, 44 insertions(+), 28 deletions(-)
Title: Terminal Text Formatting Using Escape Sequences
Description: Can be used for coloring output in terminals.
It was developed for the standard Ubuntu terminal but should be compatible
with any terminal using xterm or ANSI escape sequences. If run in windows,
RStudio, or any other platform not supporting such escape sequences it
gracefully passes on any output without modifying it.
Author: Christofer Backlin [aut, cre]
Maintainer: Christofer Backlin <christofer.backlin@medsci.uu.se>
Diff between xtermStyle versions 2.2-4 dated 2012-07-19 and 3.0.5 dated 2015-05-20
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Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic, local structural
equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
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Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including ADCP
measurements, CTD measurements, sectional data, sea-level time series,
coastline files, etc. Handles dozens of specialized functions for calculating
seawater properties such as potential temperature and density, as well as
derived properties such as buoyancy frequency and dynamic height. Map projections
are calculated using PROJ.4 functions included within the oce.
Author: Dan Kelley [aut, cre],
Clark Richards [aut],
Chantelle Layton [ctb, cph] (curl() coauthor),
Gerald Evenden [ctb, cph] (PROJ.4 author),
Frank Warmerdam [ctb, cph] (PROJ.4 author),
Howard Butler [ctb, cph] (PROJ.4 author),
Brent Fraser [ctb, cph] (PROJ.4 contributor),
Chris Stuber [ctb, cph] (PROJ.4 contributor),
Craig Bruce [ctb, cph] (PROJ.4 contributor),
Victor Osipkov [ctb, cph] (PROJ.4 contributor),
Andrea Antonello [ctb, cph] (PROJ.4 contributor),
Charles Karney [ctb, cph] (PROJ.4 contributor),
Karsten Engsager [ctb, cph] (PROJ.4 contributor),
Knud Poder [ctb, cph] (PROJ.4 contributor),
Robert Gentleman [ctb, cph] (author of approx() code, used in
binmapAdp()),
Ross Ihaka [ctb, cph] (author of approx() code, used in binmapAdp())
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 0.9-14 dated 2014-05-19 and 0.9-16 dated 2015-05-20
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oce-0.9-16/oce/man/mapLines.Rd | 14 oce-0.9-16/oce/man/mapLocator.Rd | 3 oce-0.9-16/oce/man/mapLongitudeLatitudeXY.Rd | 7 oce-0.9-16/oce/man/mapMeridians.Rd | 9 oce-0.9-16/oce/man/mapPlot.Rd | 492 +++++ oce-0.9-16/oce/man/mapPoints.Rd | 23 oce-0.9-16/oce/man/mapPolygon.Rd | 5 oce-0.9-16/oce/man/mapScalebar.Rd | 12 oce-0.9-16/oce/man/mapText.Rd | 9 oce-0.9-16/oce/man/mapTissot.Rd |only oce-0.9-16/oce/man/mapZones.Rd | 10 oce-0.9-16/oce/man/met-class.Rd | 10 oce-0.9-16/oce/man/met.Rd | 24 oce-0.9-16/oce/man/oce-class.Rd | 18 oce-0.9-16/oce/man/oce.approx.Rd |only oce-0.9-16/oce/man/oce.axis.POSIXct.Rd | 5 oce-0.9-16/oce/man/oce.colors.Rd |only oce-0.9-16/oce/man/oce.contour.Rd |only oce-0.9-16/oce/man/oce.convolve.Rd |only oce-0.9-16/oce/man/oce.debug.Rd |only oce-0.9-16/oce/man/oce.edit.Rd |only oce-0.9-16/oce/man/oce.filter.Rd |only oce-0.9-16/oce/man/oce.grid.Rd |only oce-0.9-16/oce/man/oce.plot.ts.Rd | 43 oce-0.9-16/oce/man/oce.pmatch.Rd |only oce-0.9-16/oce/man/oce.smooth.Rd |only oce-0.9-16/oce/man/oce.spectrum.Rd |only oce-0.9-16/oce/man/oceMagic.Rd | 1 oce-0.9-16/oce/man/odf-class.Rd |only oce-0.9-16/oce/man/plot.adp.Rd | 10 oce-0.9-16/oce/man/plot.adv.Rd | 2 oce-0.9-16/oce/man/plot.coastline.Rd | 38 oce-0.9-16/oce/man/plot.ctd.Rd | 45 oce-0.9-16/oce/man/plot.drifter.Rd | 139 - 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oce-0.9-16/oce/man/tidedata.Rd | 23 oce-0.9-16/oce/man/topoWorld.Rd | 2 oce-0.9-16/oce/man/ungrid.Rd | 2 oce-0.9-16/oce/man/utm2lonlat.Rd |only oce-0.9-16/oce/man/wind.Rd | 3 oce-0.9-16/oce/man/xyzToEnuAdv.Rd | 4 oce-0.9-16/oce/po/R-de.po | 640 ++++++- oce-0.9-16/oce/po/R-es.po | 768 +++++++-- oce-0.9-16/oce/po/R-fr.po | 647 ++++++- oce-0.9-16/oce/po/R-oce.pot | 601 +++++-- oce-0.9-16/oce/po/R-zh.po | 638 ++++++- oce-0.9-16/oce/src/PJ_aea.c |only oce-0.9-16/oce/src/PJ_aeqd.c |only oce-0.9-16/oce/src/PJ_airy.c |only oce-0.9-16/oce/src/PJ_aitoff.c |only oce-0.9-16/oce/src/PJ_august.c |only oce-0.9-16/oce/src/PJ_bacon.c |only oce-0.9-16/oce/src/PJ_bipc.c |only oce-0.9-16/oce/src/PJ_boggs.c |only oce-0.9-16/oce/src/PJ_bonne.c |only oce-0.9-16/oce/src/PJ_calcofi.c |only oce-0.9-16/oce/src/PJ_cass.c |only oce-0.9-16/oce/src/PJ_cc.c |only oce-0.9-16/oce/src/PJ_cea.c |only oce-0.9-16/oce/src/PJ_chamb.c |only oce-0.9-16/oce/src/PJ_collg.c |only oce-0.9-16/oce/src/PJ_crast.c |only oce-0.9-16/oce/src/PJ_denoy.c |only oce-0.9-16/oce/src/PJ_eck1.c |only oce-0.9-16/oce/src/PJ_eck2.c |only oce-0.9-16/oce/src/PJ_eck3.c |only oce-0.9-16/oce/src/PJ_eck4.c |only oce-0.9-16/oce/src/PJ_eck5.c |only oce-0.9-16/oce/src/PJ_eqc.c |only oce-0.9-16/oce/src/PJ_eqdc.c |only oce-0.9-16/oce/src/PJ_fahey.c |only oce-0.9-16/oce/src/PJ_fouc_s.c |only oce-0.9-16/oce/src/PJ_gall.c |only oce-0.9-16/oce/src/PJ_geos.c |only oce-0.9-16/oce/src/PJ_gins8.c |only oce-0.9-16/oce/src/PJ_gn_sinu.c |only oce-0.9-16/oce/src/PJ_gnom.c |only oce-0.9-16/oce/src/PJ_goode.c |only oce-0.9-16/oce/src/PJ_gstmerc.c |only oce-0.9-16/oce/src/PJ_hammer.c |only oce-0.9-16/oce/src/PJ_hatano.c |only oce-0.9-16/oce/src/PJ_healpix.c |only oce-0.9-16/oce/src/PJ_igh.c |only oce-0.9-16/oce/src/PJ_imw_p.c |only oce-0.9-16/oce/src/PJ_isea.c |only oce-0.9-16/oce/src/PJ_krovak.c |only oce-0.9-16/oce/src/PJ_labrd.c |only oce-0.9-16/oce/src/PJ_laea.c |only oce-0.9-16/oce/src/PJ_lagrng.c |only oce-0.9-16/oce/src/PJ_larr.c |only oce-0.9-16/oce/src/PJ_lask.c |only oce-0.9-16/oce/src/PJ_lcc.c |only oce-0.9-16/oce/src/PJ_lcca.c |only oce-0.9-16/oce/src/PJ_loxim.c |only oce-0.9-16/oce/src/PJ_lsat.c |only oce-0.9-16/oce/src/PJ_mbt_fps.c |only oce-0.9-16/oce/src/PJ_mbtfpp.c |only oce-0.9-16/oce/src/PJ_mbtfpq.c |only oce-0.9-16/oce/src/PJ_merc.c |only oce-0.9-16/oce/src/PJ_mill.c |only oce-0.9-16/oce/src/PJ_mod_ster.c |only oce-0.9-16/oce/src/PJ_moll.c |only oce-0.9-16/oce/src/PJ_natearth.c |only oce-0.9-16/oce/src/PJ_nell.c |only oce-0.9-16/oce/src/PJ_nell_h.c |only oce-0.9-16/oce/src/PJ_nocol.c |only oce-0.9-16/oce/src/PJ_nsper.c |only oce-0.9-16/oce/src/PJ_nzmg.c |only oce-0.9-16/oce/src/PJ_ob_tran.c |only oce-0.9-16/oce/src/PJ_ocea.c |only oce-0.9-16/oce/src/PJ_oea.c |only oce-0.9-16/oce/src/PJ_omerc.c |only oce-0.9-16/oce/src/PJ_ortho.c |only oce-0.9-16/oce/src/PJ_poly.c |only oce-0.9-16/oce/src/PJ_putp2.c |only oce-0.9-16/oce/src/PJ_putp3.c |only oce-0.9-16/oce/src/PJ_putp4p.c |only oce-0.9-16/oce/src/PJ_putp5.c |only oce-0.9-16/oce/src/PJ_putp6.c |only oce-0.9-16/oce/src/PJ_qsc.c |only oce-0.9-16/oce/src/PJ_robin.c |only oce-0.9-16/oce/src/PJ_rpoly.c |only oce-0.9-16/oce/src/PJ_sconics.c |only oce-0.9-16/oce/src/PJ_somerc.c |only oce-0.9-16/oce/src/PJ_stere.c |only oce-0.9-16/oce/src/PJ_sterea.c |only oce-0.9-16/oce/src/PJ_sts.c |only oce-0.9-16/oce/src/PJ_tcc.c |only oce-0.9-16/oce/src/PJ_tcea.c |only oce-0.9-16/oce/src/PJ_tmerc.c |only oce-0.9-16/oce/src/PJ_tpeqd.c |only oce-0.9-16/oce/src/PJ_urm5.c |only oce-0.9-16/oce/src/PJ_urmfps.c |only oce-0.9-16/oce/src/PJ_vandg.c |only oce-0.9-16/oce/src/PJ_vandg2.c |only oce-0.9-16/oce/src/PJ_vandg4.c |only oce-0.9-16/oce/src/PJ_wag2.c |only oce-0.9-16/oce/src/PJ_wag3.c |only oce-0.9-16/oce/src/PJ_wag7.c |only oce-0.9-16/oce/src/PJ_wink1.c |only oce-0.9-16/oce/src/PJ_wink2.c |only oce-0.9-16/oce/src/aasincos.c |only oce-0.9-16/oce/src/adjlon.c |only oce-0.9-16/oce/src/bin.cpp | 29 oce-0.9-16/oce/src/curl.c |only oce-0.9-16/oce/src/dmstor.c |only oce-0.9-16/oce/src/emess.h |only oce-0.9-16/oce/src/geocent.c |only oce-0.9-16/oce/src/geocent.h |only oce-0.9-16/oce/src/geod.c | 17 oce-0.9-16/oce/src/geodesic.h |only oce-0.9-16/oce/src/gradient.c | 14 oce-0.9-16/oce/src/landsat.c |only oce-0.9-16/oce/src/ldc_rdi.c | 84 - oce-0.9-16/oce/src/map.c | 4 oce-0.9-16/oce/src/nad_cvt.c |only oce-0.9-16/oce/src/nad_init.c |only oce-0.9-16/oce/src/nad_intr.c |only oce-0.9-16/oce/src/oce_convolve.c | 2 oce-0.9-16/oce/src/ocecp.f | 9 oce-0.9-16/oce/src/org_proj4_Projections.h |only oce-0.9-16/oce/src/pj_apply_gridshift.c |only oce-0.9-16/oce/src/pj_apply_vgridshift.c |only oce-0.9-16/oce/src/pj_auth.c |only oce-0.9-16/oce/src/pj_ctx.c |only oce-0.9-16/oce/src/pj_datum_set.c |only oce-0.9-16/oce/src/pj_datums.c |only oce-0.9-16/oce/src/pj_deriv.c |only oce-0.9-16/oce/src/pj_ell_set.c |only oce-0.9-16/oce/src/pj_ellps.c |only oce-0.9-16/oce/src/pj_errno.c |only oce-0.9-16/oce/src/pj_factors.c |only oce-0.9-16/oce/src/pj_fwd.c |only oce-0.9-16/oce/src/pj_gauss.c |only oce-0.9-16/oce/src/pj_geocent.c |only oce-0.9-16/oce/src/pj_gridinfo.c |only oce-0.9-16/oce/src/pj_gridlist.c |only oce-0.9-16/oce/src/pj_init.c |only oce-0.9-16/oce/src/pj_initcache.c |only oce-0.9-16/oce/src/pj_inv.c |only oce-0.9-16/oce/src/pj_latlong.c |only oce-0.9-16/oce/src/pj_list.c |only oce-0.9-16/oce/src/pj_list.h |only oce-0.9-16/oce/src/pj_log.c |only oce-0.9-16/oce/src/pj_malloc.c |only oce-0.9-16/oce/src/pj_mlfn.c |only oce-0.9-16/oce/src/pj_msfn.c |only oce-0.9-16/oce/src/pj_mutex.c |only oce-0.9-16/oce/src/pj_open_lib.c |only oce-0.9-16/oce/src/pj_param.c |only oce-0.9-16/oce/src/pj_phi2.c |only oce-0.9-16/oce/src/pj_pr_list.c |only oce-0.9-16/oce/src/pj_qsfn.c |only oce-0.9-16/oce/src/pj_release.c |only oce-0.9-16/oce/src/pj_strerrno.c |only oce-0.9-16/oce/src/pj_transform.c |only oce-0.9-16/oce/src/pj_tsfn.c |only oce-0.9-16/oce/src/pj_units.c |only oce-0.9-16/oce/src/pj_utils.c |only oce-0.9-16/oce/src/pj_zpoly1.c |only oce-0.9-16/oce/src/proj4_interface.c |only oce-0.9-16/oce/src/proj_api.h |only oce-0.9-16/oce/src/proj_config.h |only oce-0.9-16/oce/src/proj_etmerc.c |only oce-0.9-16/oce/src/proj_mdist.c |only oce-0.9-16/oce/src/proj_rouss.c |only oce-0.9-16/oce/src/projects.h |only oce-0.9-16/oce/src/sw.c | 191 +- oce-0.9-16/oce/src/trap.c | 6 oce-0.9-16/oce/src/trim.c |only oce-0.9-16/oce/tests/colormap.R | 58 oce-0.9-16/oce/tests/ctd.R |only oce-0.9-16/oce/tests/curl.R |only oce-0.9-16/oce/tests/datasets.R |only oce-0.9-16/oce/tests/geod.R | 3 oce-0.9-16/oce/tests/map.R |only oce-0.9-16/oce/tests/misc.R | 2 oce-0.9-16/oce/tests/readCtd.R | 18 oce-0.9-16/oce/tests/subset.R |only oce-0.9-16/oce/tests/sw.R |only oce-0.9-16/oce/tests/tide.R | 20 oce-0.9-16/oce/vignettes/oce.Rnw | 106 - 435 files changed, 11236 insertions(+), 5188 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors, nested multiple imputation, and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between miceadds versions 1.1-1 dated 2015-02-23 and 1.2-0 dated 2015-05-20
DESCRIPTION | 14 ++--- MD5 | 55 +++++++++++++++------ NAMESPACE | 70 +++++++++++++++++++++++--- R/MIcombine.NestedImputationResultList.R |only R/NestedImputationList.R |only R/complete.miceadds.R |only R/glm.cluster.R |only R/lm.cluster.R |only R/load.data.R | 5 + R/mice.nmi.R |only R/mids2datlist.R | 33 +++++++++--- R/mids2mlwin.R |only R/pool.mids.nmi.R |only R/pool.nmi.scalar.helper.R |only R/save.data.R | 10 ++- R/summary.mipo.nmi.R |only R/summary.mira.nmi.R |only R/systime.R | 6 ++ R/visitSequence.determine.R |only R/with.NestedImputationList.R |only R/with.mids.1chain.R |only R/with.mids.nmi.R |only R/within.NestedImputationList.R |only R/within.imputationList.R |only inst/NEWS | 81 ++++++++++++++++++++++++------- man/NestedImputationList.Rd |only man/complete.miceadds.Rd |only man/data.allison.Rd | 5 + man/datalist2mids.Rd | 12 ++++ man/lm.cluster.Rd |only man/mice.nmi.Rd |only man/miceadds-package.Rd | 7 +- man/mids2datlist.Rd | 38 +++++++++++++- man/mids2mlwin.Rd |only man/pool.mids.nmi.Rd |only man/save.data.Rd | 17 ++---- man/systime.Rd | 7 +- man/visitSequence.determine.Rd |only man/with.miceadds.Rd |only man/write.mice.imputation.Rd | 2 man/write.pspp.Rd | 14 +++++ 41 files changed, 296 insertions(+), 80 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 0.0-1 dated 2015-05-19 and 0.1-1 dated 2015-05-20
lamW-0.0-1/lamW/inst/News.Rd |only lamW-0.1-1/lamW/DESCRIPTION | 10 ++++---- lamW-0.1-1/lamW/MD5 | 14 +++++------ lamW-0.1-1/lamW/build/partial.rdb |binary lamW-0.1-1/lamW/inst/NEWS.Rd |only lamW-0.1-1/lamW/man/lamW-package.Rd | 4 +-- lamW-0.1-1/lamW/man/lamW.Rd | 4 +-- lamW-0.1-1/lamW/src/lambertW.cpp | 36 ++++++++++++++++++++--------- lamW-0.1-1/lamW/tests/testthat/test-lamW.R | 4 +-- 9 files changed, 44 insertions(+), 28 deletions(-)
Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between kyotil versions 2015.2-27 dated 2015-03-04 and 2015.5-20 dated 2015-05-20
kyotil-2015.2-27/kyotil/vignettes/figure |only kyotil-2015.5-20/kyotil/DESCRIPTION | 8 +-- kyotil-2015.5-20/kyotil/MD5 | 30 ++++++++------ kyotil-2015.5-20/kyotil/NAMESPACE | 7 ++- kyotil-2015.5-20/kyotil/R/age_calc.R |only kyotil-2015.5-20/kyotil/R/cox.zph.2.R |only kyotil-2015.5-20/kyotil/R/make.timedep.dataset.R |only kyotil-2015.5-20/kyotil/R/matrix.R | 2 kyotil-2015.5-20/kyotil/R/print.R | 16 +++++-- kyotil-2015.5-20/kyotil/R/regression.model.functions.R | 14 +++++- kyotil-2015.5-20/kyotil/R/sim.dat.tvarying.three.R |only kyotil-2015.5-20/kyotil/R/sim.dat.tvarying.two.R |only kyotil-2015.5-20/kyotil/R/string.R | 4 - kyotil-2015.5-20/kyotil/inst/unitTests/runit.survival.R |only kyotil-2015.5-20/kyotil/man/age_calc.Rd |only kyotil-2015.5-20/kyotil/man/cox.zph.2.Rd |only kyotil-2015.5-20/kyotil/man/make.timedep.dataset.Rd |only kyotil-2015.5-20/kyotil/man/regression.model.functions.Rd | 6 ++ kyotil-2015.5-20/kyotil/man/sim.dat.tvarying.Rd |only kyotil-2015.5-20/kyotil/src/sresids.c |only kyotil-2015.5-20/kyotil/vignettes/kyotil-vignette.Rnw | 3 - 21 files changed, 62 insertions(+), 28 deletions(-)
Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications
The 'RInside' packages makes it easier to have "R inside" your C++ application
by providing a C++ wrapper class providing the R interpreter.
As R itself is embedded into your application, a shared library build of R
is required. This works on Linux, OS X and even on Windows provided you use
the same tools used to build R itself.
Numerous examples are provided in the eight subdirectories of the examples/
directory of the installed package: standard, mpi (for parallel computing)
qt (showing how to embed 'RInside' inside a Qt GUI application), wt (showing
how to build a "web-application" using the Wt toolkit), armadillo (for
'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with 'RcppEigen').
The example use GNUmakefile(s) with GNU extensions, so a GNU make is required
(and will use the GNUmakefile automatically).
Doxygen-generated documentation of the C++ classes is available at the
'RInside' website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RInside versions 0.2.12 dated 2015-01-28 and 0.2.13 dated 2015-05-20
ChangeLog | 17 ++++++++++++++++- DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- README.md | 29 ++++++++++++++++++++++++----- inst/include/RInsideCommon.h | 4 ---- src/RInside.cpp | 4 ++++ 6 files changed, 58 insertions(+), 24 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 3.10 dated 2015-02-06 and 4.0-5 dated 2015-05-20
DESCRIPTION | 10 MD5 | 162 +++++++------- NAMESPACE | 5 NEWS | 4 R/GLMM_MCMC.R | 2 R/GLMM_MCMCwrapper.R | 3 R/GLMM_longitDA.R | 285 ++++++------------------- R/GLMM_longitDA2.R |only R/NMixChainComp.NMixMCMC.R | 20 + R/NMixChainsDerived.R | 4 R/NMixMCMC.R | 99 +++++--- R/NMixMCMCinitr.R | 3 R/NMixMCMCwrapper.R | 107 ++++++--- R/NMixPlugCondDensJoint2.NMixMCMC.R | 2 R/NMixPlugCondDensMarg.NMixMCMC.R | 2 R/NMixPlugDA.R | 2 R/NMixPlugDensJoint2.NMixMCMC.R | 112 +++++++--- R/NMixPlugDensMarg.GLMM_MCMC.R | 2 R/NMixPlugDensMarg.NMixMCMC.R | 117 +++++++--- R/NMixPredCDFMarg.GLMM_MCMC.R | 2 R/NMixPredCDFMarg.NMixMCMC.R | 126 ++++++++--- R/NMixPredCondCDFMarg.NMixMCMC.R | 2 R/NMixPredCondDensJoint2.NMixMCMC.R | 2 R/NMixPredCondDensMarg.NMixMCMC.R | 2 R/NMixPredDA.R | 2 R/NMixPredDensJoint2.NMixMCMC.R | 119 +++++++--- R/NMixPredDensMarg.GLMM_MCMC.R | 2 R/NMixPredDensMarg.NMixMCMC.R | 127 ++++++++--- R/NMixPseudoGOF.NMixMCMC.R | 2 R/NMixRelabel.GLMM_MCMClist.R | 2 R/NMixRelabel.NMixMCMC.R | 15 - R/NMixRelabel.NMixMCMClist.R |only R/NMixSummComp.NMixMCMC.R | 29 ++ R/getProfiles.R | 5 R/plot.NMixPredCDFMarg.R | 131 +++++++---- R/plot.NMixPredDensJoint2.R | 223 ++++++++++++++------ R/plot.NMixPredDensMarg.R | 129 +++++++---- R/plotProfiles.R | 12 - R/print.NMixMCMC.R | 16 + R/print.NMixMCMClist.R | 30 +- R/tracePlots.GLMM_MCMC.R | 6 R/tracePlots.NMixMCMC.R | 77 ++++-- R/tracePlots.NMixMCMClist.R |only man/GLMMlongitDA.Rd | 5 man/GLMMlongitDA2.Rd |only man/NMixMCMC.Rd | 19 + man/NMixMCMCwrapper.Rd | 9 man/NMixPlugDensMarg.Rd | 4 man/NMixPredCDFMarg.Rd | 4 man/NMixPredDensMarg.Rd | 4 man/NMixRelabel.Rd | 5 man/tracePlots.Rd | 7 src/AK_Basic.h | 38 +++ src/GLMM_Deviance.cpp | 22 - src/GLMM_Deviance2.cpp |only src/GLMM_Deviance2.h |only src/GLMM_MCMC.cpp | 66 ++++- src/GLMM_NMixRelabel.cpp | 43 ++- src/GLMM_PED.cpp | 10 src/GLMM_longitDA.cpp | 320 ++++++++++++++--------------- src/GLMM_longitDA.h | 1 src/GLMM_longitDA2.cpp |only src/GLMM_longitDA2.h |only src/MCMC_loglik_Zwork1_stres.cpp | 97 ++++++++ src/MCMC_loglik_Zwork1_stres.h | 29 ++ src/NMix_Deviance.cpp | 32 ++ src/NMix_Deviance.h | 22 + src/NMix_MCMC.cpp | 112 +++++++--- src/NMix_MCMC.h | 10 src/NMix_NMixRelabel.cpp | 42 ++- src/NMix_NMixRelabel.h | 6 src/NMix_PED.cpp | 146 ++++++++----- src/NMix_PED.h | 40 ++- src/NMix_PosterMeanMixParam.cpp | 185 ++++++++++++---- src/NMix_PosterMeanMixParam.h | 11 src/NMix_Pr_y_and_cum_Pr_y.cpp | 171 +++++++++++---- src/NMix_Pr_y_and_cum_Pr_y.h | 12 - src/NMix_PredDA.cpp | 25 +- src/NMix_Utils.cpp | 278 +++++++++++++------------ src/NMix_Utils.h | 57 ++--- src/NMix_fullCondMean_WeightsMeansVars.cpp | 271 +++++++++++++++++------- src/NMix_fullCondMean_WeightsMeansVars.h | 17 + src/NMix_updateAlloc.cpp | 276 +++++++++++++++++-------- src/NMix_updateAlloc.h | 16 + src/NMix_updateWeights.cpp | 80 +++++-- src/NMix_updateWeights.h | 21 + 86 files changed, 2971 insertions(+), 1544 deletions(-)
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml versions 2.2 dated 2014-03-24 and 2.3 dated 2015-05-20
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 2 +- R/clusterLongData.R | 39 +++++++++++++++++++++++++++++++++++++++ R/kml.R | 7 +++++-- inst |only man/choice.Rd | 5 +++-- man/kml-package.Rd | 6 +++--- 8 files changed, 65 insertions(+), 21 deletions(-)
More information about SubpathwayGMir at CRAN
Permanent link
Title: Collection and Analysis of Otolith Shape Data
Description: Studies otolith shape variation among fish populations.
Otoliths are calcified structures found in the inner ear of teleost fish and their shape has
been known to vary among several fish populations and stocks, making them very useful in taxonomy,
species identification and to study geographic variations. The package extends previously described
software used for otolith shape analysis by allowing the user to automatically extract closed
contour outlines from a large number of images, perform smoothing to eliminate pixel noise,
choose from conducting either a Fourier or wavelet transform to the outlines and visualize
the mean shape. The output of the package are independent Fourier or wavelet coefficients
which can be directly imported into a wide range of statistical packages in R. The package
might prove useful in studies of any two dimensional objects.
Author: Lisa Anne Libungan [aut, cre],
Snaebjorn Palsson [aut, ths]
Maintainer: Lisa Anne Libungan <lisa.libungan@gmail.com>
Diff between shapeR versions 0.1-3 dated 2015-04-03 and 0.1-5 dated 2015-05-20
shapeR-0.1-3/shapeR/data/otoliths.RData |only shapeR-0.1-5/shapeR/DESCRIPTION | 8 shapeR-0.1-5/shapeR/MD5 | 50 +++--- shapeR-0.1-5/shapeR/R/shapeR.R | 105 ++++++++----- shapeR-0.1-5/shapeR/data/datalist | 2 shapeR-0.1-5/shapeR/data/shape.RData |only shapeR-0.1-5/shapeR/man/FISH.Rd | 5 shapeR-0.1-5/shapeR/man/cluster.plot.Rd | 2 shapeR-0.1-5/shapeR/man/detect.outline.Rd | 2 shapeR-0.1-5/shapeR/man/enrich.master.list.Rd | 2 shapeR-0.1-5/shapeR/man/estimate.outline.reconstruction.Rd | 2 shapeR-0.1-5/shapeR/man/generateShapeCoefficients.Rd | 5 shapeR-0.1-5/shapeR/man/getMeasurements.Rd | 2 shapeR-0.1-5/shapeR/man/getStdMeasurements.Rd | 2 shapeR-0.1-5/shapeR/man/outline.reconstruction.plot.Rd | 2 shapeR-0.1-5/shapeR/man/plotFourier.Rd | 2 shapeR-0.1-5/shapeR/man/plotFourierShape.Rd | 4 shapeR-0.1-5/shapeR/man/plotWavelet.Rd | 2 shapeR-0.1-5/shapeR/man/plotWaveletShape.Rd | 2 shapeR-0.1-5/shapeR/man/remove.outline.Rd | 2 shapeR-0.1-5/shapeR/man/setFilter.Rd | 2 shapeR-0.1-5/shapeR/man/shape.Rd | 17 +- shapeR-0.1-5/shapeR/man/shapeR.Rd | 57 ++++++- shapeR-0.1-5/shapeR/man/show.original.with.outline.Rd | 2 shapeR-0.1-5/shapeR/man/smoothout.Rd | 2 shapeR-0.1-5/shapeR/man/stdCoefs.Rd | 6 shapeR-0.1-5/shapeR/man/write.image.with.outline.Rd | 2 27 files changed, 191 insertions(+), 98 deletions(-)
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-rinv', along with various supporting algorithms.
Author: Johann Gagnon-Bartsch <johann@stat.berkeley.edu>
Maintainer: Johann Gagnon-Bartsch <johann@stat.berkeley.edu>
Diff between ruv versions 0.9.4 dated 2014-10-24 and 0.9.5 dated 2015-05-20
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/RUV2.R | 36 +++++++++++++++++++++++++----------- R/invvar.R | 8 +++++++- man/RUV2.Rd | 7 ++++++- man/ruv-package.Rd | 6 +++--- 6 files changed, 51 insertions(+), 26 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <christofer.backlin@medsci.uu.se>
Diff between emil versions 1.1-6 dated 2014-08-01 and 2.0.2 dated 2015-05-20
emil-1.1-6/emil/R/caret.R |only emil-1.1-6/emil/R/cforest.R |only emil-1.1-6/emil/R/error_functions.R |only emil-1.1-6/emil/R/glmnet.R |only emil-1.1-6/emil/R/helpers.R |only emil-1.1-6/emil/R/lda.R |only emil-1.1-6/emil/R/lm.R |only emil-1.1-6/emil/R/modeling.R |only emil-1.1-6/emil/R/outcome.R |only emil-1.1-6/emil/R/pamr.R |only emil-1.1-6/emil/R/preprocessing.R |only emil-1.1-6/emil/R/qda.R |only emil-1.1-6/emil/R/randomForest.R |only emil-1.1-6/emil/R/resampling.R |only emil-1.1-6/emil/R/survival.R |only emil-1.1-6/emil/R/variable_importance.R |only emil-1.1-6/emil/inst/tests |only emil-1.1-6/emil/man/as.Surv.Rd |only emil-1.1-6/emil/man/as.Surv.Surv.Rd |only emil-1.1-6/emil/man/as.Surv.outcome.Rd |only emil-1.1-6/emil/man/as.character.outcome.Rd |only emil-1.1-6/emil/man/as.data.frame.outcome.Rd |only emil-1.1-6/emil/man/as.matrix.outcome.Rd |only emil-1.1-6/emil/man/as.outcome.Rd |only emil-1.1-6/emil/man/as.outcome.Surv.Rd |only emil-1.1-6/emil/man/batch.model.Rd |only emil-1.1-6/emil/man/dim.outcome.Rd |only emil-1.1-6/emil/man/emil.extensions.Rd |only emil-1.1-6/emil/man/emil.fit.caret.Rd |only emil-1.1-6/emil/man/emil.fit.cforest.Rd |only emil-1.1-6/emil/man/emil.fit.glmnet.Rd |only emil-1.1-6/emil/man/emil.fit.lda.Rd |only emil-1.1-6/emil/man/emil.fit.lm.Rd |only emil-1.1-6/emil/man/emil.fit.pamr.Rd |only emil-1.1-6/emil/man/emil.fit.qda.Rd |only emil-1.1-6/emil/man/emil.fit.randomForest.Rd |only emil-1.1-6/emil/man/emil.predict.caret.Rd |only emil-1.1-6/emil/man/emil.predict.cforest.Rd |only emil-1.1-6/emil/man/emil.predict.glmnet.Rd |only emil-1.1-6/emil/man/emil.predict.lda.Rd |only emil-1.1-6/emil/man/emil.predict.lm.Rd |only emil-1.1-6/emil/man/emil.predict.pamr.Rd |only emil-1.1-6/emil/man/emil.predict.qda.Rd |only emil-1.1-6/emil/man/emil.predict.randomForest.Rd |only emil-1.1-6/emil/man/emil.vimp.pamr.Rd |only emil-1.1-6/emil/man/emil.vimp.randomForest.Rd |only emil-1.1-6/emil/man/error.fun.Rd |only emil-1.1-6/emil/man/evaluate.modeling.Rd |only emil-1.1-6/emil/man/extract.outcome.Rd |only emil-1.1-6/emil/man/factor.events.Rd |only emil-1.1-6/emil/man/index.fit.Rd |only emil-1.1-6/emil/man/integer.events.Rd |only emil-1.1-6/emil/man/is.blank.Rd |only emil-1.1-6/emil/man/is.na.outcome.Rd |only emil-1.1-6/emil/man/is.outcome.Rd |only emil-1.1-6/emil/man/length.outcome.Rd |only emil-1.1-6/emil/man/modeling.procedure.Rd |only emil-1.1-6/emil/man/neg.gmpa.Rd |only emil-1.1-6/emil/man/nice.require.Rd |only emil-1.1-6/emil/man/outcome.Rd |only emil-1.1-6/emil/man/p.value.Rd |only emil-1.1-6/emil/man/p.value.coxph.Rd |only emil-1.1-6/emil/man/p.value.crr.Rd |only emil-1.1-6/emil/man/p.value.cuminc.Rd |only emil-1.1-6/emil/man/p.value.survdiff.Rd |only emil-1.1-6/emil/man/plot.outcome.Rd |only emil-1.1-6/emil/man/pre.impute.knn.Rd |only emil-1.1-6/emil/man/pre.pamr.Rd |only emil-1.1-6/emil/man/pre.process.Rd |only emil-1.1-6/emil/man/predict.modeling.procedure.Rd |only emil-1.1-6/emil/man/print.outcome.Rd |only emil-1.1-6/emil/man/resample.mapply.Rd |only emil-1.1-6/emil/man/subframe.Rd |only emil-1.1-6/emil/man/trace.msg.Rd |only emil-1.1-6/emil/man/vimp.Rd |only emil-1.1-6/emil/man/warn.once.Rd |only emil-1.1-6/emil/man/weighted.error.rate.Rd |only emil-1.1-6/emil/tests/run-all.R |only emil-2.0.2/emil/DESCRIPTION | 23 +- emil-2.0.2/emil/MD5 | 192 +++++++++++----------- emil-2.0.2/emil/NAMESPACE | 176 +++++++++++--------- emil-2.0.2/emil/R/caret.r |only emil-2.0.2/emil/R/cforest.r |only emil-2.0.2/emil/R/error-functions.r |only emil-2.0.2/emil/R/glmnet.r |only emil-2.0.2/emil/R/helpers.r |only emil-2.0.2/emil/R/lda.r |only emil-2.0.2/emil/R/learning-curve.r |only emil-2.0.2/emil/R/lm.r |only emil-2.0.2/emil/R/message.r |only emil-2.0.2/emil/R/modeling.r |only emil-2.0.2/emil/R/pamr.r |only emil-2.0.2/emil/R/plotting.r |only emil-2.0.2/emil/R/preprocessing.r |only emil-2.0.2/emil/R/qda.r |only emil-2.0.2/emil/R/randomForest.r |only emil-2.0.2/emil/R/resampling.r |only emil-2.0.2/emil/R/reshape-result.r |only emil-2.0.2/emil/R/roc-curve.r |only emil-2.0.2/emil/R/survival.r |only emil-2.0.2/emil/man/dichotomize.Rd |only emil-2.0.2/emil/man/emil.Rd | 108 +++++++----- emil-2.0.2/emil/man/emil_list_method.Rd |only emil-2.0.2/emil/man/error_fun.Rd |only emil-2.0.2/emil/man/evaluate.Rd |only emil-2.0.2/emil/man/extension.Rd |only emil-2.0.2/emil/man/fill.Rd | 9 - emil-2.0.2/emil/man/fit.Rd | 27 +-- emil-2.0.2/emil/man/fit_caret.Rd |only emil-2.0.2/emil/man/fit_cforest.Rd |only emil-2.0.2/emil/man/fit_glmnet.Rd |only emil-2.0.2/emil/man/fit_lda.Rd |only emil-2.0.2/emil/man/fit_lm.Rd |only emil-2.0.2/emil/man/fit_pamr.Rd |only emil-2.0.2/emil/man/fit_qda.Rd |only emil-2.0.2/emil/man/fit_randomForest.Rd |only emil-2.0.2/emil/man/get_color.Rd |only emil-2.0.2/emil/man/get_importance.Rd |only emil-2.0.2/emil/man/get_performance.Rd |only emil-2.0.2/emil/man/get_prediction.Rd |only emil-2.0.2/emil/man/get_tuning.Rd |only emil-2.0.2/emil/man/image.resample.Rd | 11 - emil-2.0.2/emil/man/importance_pamr.Rd |only emil-2.0.2/emil/man/importance_randomForest.Rd |only emil-2.0.2/emil/man/impute.Rd | 29 ++- emil-2.0.2/emil/man/indent.Rd |only emil-2.0.2/emil/man/index_fit.Rd |only emil-2.0.2/emil/man/is_blank.Rd |only emil-2.0.2/emil/man/is_multi_procedure.Rd |only emil-2.0.2/emil/man/learning_curve.Rd |only emil-2.0.2/emil/man/log_message.Rd |only emil-2.0.2/emil/man/modeling_procedure.Rd |only emil-2.0.2/emil/man/na_index.Rd |only emil-2.0.2/emil/man/name_procedure.Rd |only emil-2.0.2/emil/man/neg_gmpa.Rd |only emil-2.0.2/emil/man/nice_axis.Rd |only emil-2.0.2/emil/man/nice_box.Rd |only emil-2.0.2/emil/man/nice_require.Rd |only emil-2.0.2/emil/man/notify_once.Rd |only emil-2.0.2/emil/man/plot.Surv.Rd |only emil-2.0.2/emil/man/plot.learning_curve.Rd |only emil-2.0.2/emil/man/pre_impute.Rd |only emil-2.0.2/emil/man/pre_impute_knn.Rd |only emil-2.0.2/emil/man/pre_pamr.Rd |only emil-2.0.2/emil/man/pre_process.Rd |only emil-2.0.2/emil/man/predict.model.Rd |only emil-2.0.2/emil/man/predict_caret.Rd |only emil-2.0.2/emil/man/predict_cforest.Rd |only emil-2.0.2/emil/man/predict_glmnet.Rd |only emil-2.0.2/emil/man/predict_lda.Rd |only emil-2.0.2/emil/man/predict_lm.Rd |only emil-2.0.2/emil/man/predict_pamr.Rd |only emil-2.0.2/emil/man/predict_qda.Rd |only emil-2.0.2/emil/man/predict_randomForest.Rd |only emil-2.0.2/emil/man/pvalue.Rd |only emil-2.0.2/emil/man/pvalue.coxph.Rd |only emil-2.0.2/emil/man/pvalue.crr.Rd |only emil-2.0.2/emil/man/pvalue.cuminc.Rd |only emil-2.0.2/emil/man/pvalue.survdiff.Rd |only emil-2.0.2/emil/man/resample.Rd | 44 ++--- emil-2.0.2/emil/man/roc_curve.Rd |only emil-2.0.2/emil/man/select.Rd |only emil-2.0.2/emil/man/subresample.Rd | 7 emil-2.0.2/emil/man/subtree.Rd | 91 +++++++++- emil-2.0.2/emil/man/tune.Rd | 40 ++-- emil-2.0.2/emil/man/vlines.Rd |only emil-2.0.2/emil/man/weighted_error_rate.Rd |only emil-2.0.2/emil/tests/test-all.r |only emil-2.0.2/emil/tests/testthat |only 169 files changed, 443 insertions(+), 314 deletions(-)
Title: Execution Functions for Tick Data Back Test
Description: Functions to execute orders in backtesting using tick data. A testing platform was established by the four major execution functions, namely 'LimitBuy', 'LimitSell', 'MarketBuy' and 'MarketSell', which enclosed all tedious aspects (such as queueing for order executions and calculate actual executed volumes) for order execution using tick data. Such that one can focus on the logic of strategies, rather than its execution.
Author: HKUST
Maintainer: SONG Yang <ysongad@connect.ust.hk>
Diff between TickExec versions 1.0 dated 2015-04-22 and 1.1 dated 2015-05-20
DESCRIPTION | 8 - MD5 | 47 +++++--- R/GetLastPrice.R | 42 +++---- R/GetQueueLength.R | 70 ++++++------ R/InitLogEntry.R | 2 R/LimitBuy.R | 206 ++++++++++++++++++------------------ R/LimitSell.R | 220 +++++++++++++++++++-------------------- R/LoadTickData.R | 54 +-------- R/LoadTickDataHK.R |only R/LoadTickDataSHSZ.R |only R/MarketBuy.R | 142 ++++++++++++------------- R/MarketSell.R | 177 +++++++++++++++---------------- R/PerformanceReport.R |only R/PortfolioWorth.R |only R/TotalPnL.R |only inst/extdata/000001/20141015.csv |only inst/extdata/000001/20141016.csv |only inst/extdata/000001/20141017.csv |only man/GetLastPrice.Rd | 37 +++--- man/GetQueueLength.Rd | 46 ++++---- man/LimitBuy.Rd | 92 ++++++++-------- man/LimitSell.Rd | 84 +++++++------- man/LoadTickData.Rd | 39 +++--- man/LoadTickDataHK.Rd |only man/LoadTickDataSHSZ.Rd |only man/MarketBuy.Rd | 68 ++++++------ man/MarketSell.Rd | 77 ++++++------- man/PerformanceReport.Rd |only man/PortfolioWorth.Rd |only man/TotalPnL.Rd |only man/tickexec-package.rd | 4 31 files changed, 703 insertions(+), 712 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 1.34 dated 2014-09-14 and 1.35 dated 2015-05-20
DLMtool-1.34/DLMtool/man/MMHCR.Rd |only DLMtool-1.35/DLMtool/DESCRIPTION | 10 DLMtool-1.35/DLMtool/MD5 | 76 ++++--- DLMtool-1.35/DLMtool/NAMESPACE | 14 + DLMtool-1.35/DLMtool/R/DLM_quota.R | 245 +++++++++++++++++++++-- DLMtool-1.35/DLMtool/R/MSE_source.R | 30 +- DLMtool-1.35/DLMtool/R/Source.r | 9 DLMtool-1.35/DLMtool/data/DLMdat.RData |binary DLMtool-1.35/DLMtool/inst/Atlantic_mackerel.csv | 1 DLMtool-1.35/DLMtool/inst/Canary_Rockfish.csv | 1 DLMtool-1.35/DLMtool/inst/China_rockfish.csv | 1 DLMtool-1.35/DLMtool/inst/Cobia.csv | 1 DLMtool-1.35/DLMtool/inst/Example_datafile.csv | 1 DLMtool-1.35/DLMtool/inst/Gulf_blue_tilefish.csv | 1 DLMtool-1.35/DLMtool/inst/Red_snapper.csv | 1 DLMtool-1.35/DLMtool/inst/Simulation_1.csv | 1 DLMtool-1.35/DLMtool/inst/Simulation_2.csv | 1 DLMtool-1.35/DLMtool/inst/doc/DLMtool.R | 2 DLMtool-1.35/DLMtool/inst/doc/DLMtool.Rnw | 51 ++-- DLMtool-1.35/DLMtool/inst/doc/DLMtool.pdf |binary DLMtool-1.35/DLMtool/inst/ourReefFish.csv | 1 DLMtool-1.35/DLMtool/man/CC1.Rd |only DLMtool-1.35/DLMtool/man/CC4.Rd |only DLMtool-1.35/DLMtool/man/Can.Rd | 6 DLMtool-1.35/DLMtool/man/DBSRA.Rd | 6 DLMtool-1.35/DLMtool/man/DLM-class.Rd | 1 DLMtool-1.35/DLMtool/man/DLMtool-package.Rd | 22 -- DLMtool-1.35/DLMtool/man/Fadapt.Rd |only DLMtool-1.35/DLMtool/man/Islope1.Rd |only DLMtool-1.35/DLMtool/man/Islope4.Rd |only DLMtool-1.35/DLMtool/man/Itarget1.Rd |only DLMtool-1.35/DLMtool/man/Itarget4.Rd |only DLMtool-1.35/DLMtool/man/Kplot.Rd | 6 DLMtool-1.35/DLMtool/man/LstepCC1.Rd |only DLMtool-1.35/DLMtool/man/LstepCC4.Rd |only DLMtool-1.35/DLMtool/man/Ltarget1.Rd |only DLMtool-1.35/DLMtool/man/Ltarget4.Rd |only DLMtool-1.35/DLMtool/man/MSE-class.Rd | 3 DLMtool-1.35/DLMtool/man/Needed.Rd | 6 DLMtool-1.35/DLMtool/man/OM-class.Rd | 2 DLMtool-1.35/DLMtool/man/Observation-class.Rd | 2 DLMtool-1.35/DLMtool/man/Pplot.Rd | 4 DLMtool-1.35/DLMtool/man/SPmod.Rd |only DLMtool-1.35/DLMtool/man/SPslope.Rd |only DLMtool-1.35/DLMtool/man/Tplot.Rd | 5 DLMtool-1.35/DLMtool/vignettes/DLMtool.Rnw | 51 ++-- 46 files changed, 400 insertions(+), 161 deletions(-)
Title: Spatial Forecast Verification
Description: Contains functions to perform spatial forecast verification.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.2-2 dated 2014-12-23 and 0.2-3 dated 2015-05-19
DESCRIPTION | 10 ++-- MD5 | 37 +++++++++------ NAMESPACE | 112 ++++++++++++++++++++++++++++++++++++++++++++++ R/DataObjects.R | 62 ++++++++++++++++++++----- R/Features.R | 64 +++++++++++++++++++++----- R/Fint2d.R |only R/Geom.R | 49 +++++++++++++++----- R/LocMeasures.R | 31 ++++++------ R/QlossRigid.R |only R/craer.R |only R/minboundmatch.R |only R/rigider.R |only man/Fint2d.Rd |only man/SpatialVx-internal.Rd | 2 man/SpatialVx-package.Rd | 16 ++++-- man/craer.Rd |only man/datasets.Rd | 2 man/deltamm.Rd | 14 ++++- man/fss2dfun.Rd | 2 man/hoods2d.Rd | 2 man/minboundmatch.Rd |only man/pphindcast2d.Rd | 4 - man/rigider.Rd |only man/upscale2d.Rd | 2 24 files changed, 326 insertions(+), 83 deletions(-)
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Title: Functions for Generating Restricted Permutations of Data
Description: A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
Author: Gavin L. Simpson [aut, cph, cre],
R Core Team [cph],
Douglas M. Bates [ctb],
Jari Oksanen [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between permute versions 0.8-3 dated 2014-01-29 and 0.8-4 dated 2015-05-19
permute-0.8-3/permute/R/Blocks.R |only permute-0.8-3/permute/inst/tests |only permute-0.8-3/permute/vignettes/Z.cls |only permute-0.8-4/permute/DESCRIPTION | 20 +- permute-0.8-4/permute/MD5 | 34 ++-- permute-0.8-4/permute/R/blocks.R |only permute-0.8-4/permute/README.md |only permute-0.8-4/permute/build/vignette.rds |binary permute-0.8-4/permute/data/jackal.rda |binary permute-0.8-4/permute/inst/ChangeLog | 17 +- permute-0.8-4/permute/inst/doc/permutations.R | 10 - permute-0.8-4/permute/inst/doc/permutations.Rnw | 12 - permute-0.8-4/permute/inst/doc/permutations.pdf |binary permute-0.8-4/permute/man/check.Rd | 102 ++++++------ permute-0.8-4/permute/tests/Examples/permute-Ex.Rout.save | 118 ++++++-------- permute-0.8-4/permute/tests/test-all.R | 6 permute-0.8-4/permute/tests/testthat |only permute-0.8-4/permute/vignettes/permutations.Rnw | 12 - 18 files changed, 165 insertions(+), 166 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.7 dated 2015-03-05 and 0.8 dated 2015-05-19
DESCRIPTION | 12 +- MD5 | 67 +++++++------ NAMESPACE | 23 +++- NEWS | 45 +++++++++ R/IO.R | 117 ++++++++++++++++------- R/VCFloci.R |only R/amova.R | 27 ++--- R/conversion.R | 40 +++++++- R/haplotype.R | 31 +++++- R/hw.test.R | 46 ++++++++- R/summary.loci.R | 17 ++- R/zzz.R | 4 build/vignette.rds |binary data |only inst/doc/ReadingFiles.R | 58 ++--------- inst/doc/ReadingFiles.Rnw | 220 ++++++++++++++++++++++++++++++++++++--------- inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 6 - man/LD.Rd | 9 - man/VCFloci.Rd |only man/alleles2loci.Rd |only man/conversion.Rd | 6 - man/haplotype.Rd | 3 man/heterozygosity.Rd | 5 - man/hw.test.Rd | 31 +++++- man/jaguar.Rd |only man/read.vcf.Rd | 83 ++++++++++------ man/subset.haplotype.Rd |only man/summary.loci.Rd | 12 +- man/theta.h.Rd | 5 - man/theta.k.Rd | 5 - man/theta.msat.Rd | 6 - man/utilities.Rd | 11 +- man/write.loci.Rd | 5 - src/pegas.c | 16 ++- src/readVCFbin.c |only vignettes/ReadingFiles.Rnw | 220 ++++++++++++++++++++++++++++++++++++--------- vignettes/pegas.bib | 7 + 38 files changed, 816 insertions(+), 321 deletions(-)
Title: Statistical Methods for the Item Count Technique and List
Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011), Blair and Imai (2012), Blair, Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock, Crawford, and Green (2015). This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, and a method for combining list experiments with direct questions. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Kosuke Imai [aut, cre], Bethany Park [ctb],
Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@columbia.edu>
Diff between list versions 7.1 dated 2014-11-29 and 8.0 dated 2015-05-19
list-7.1/list/R/onAttach.R |only list-8.0/list/ChangeLog | 16 - list-8.0/list/DESCRIPTION | 43 +--- list-8.0/list/MD5 | 44 +++- list-8.0/list/NAMESPACE | 10 - list-8.0/list/R/bayesglm.R |only list-8.0/list/R/combinedListDirect.R |only list-8.0/list/R/ictreg.R | 262 ++++++++++++++++----------- list-8.0/list/R/ictregBayes.R | 32 +-- list-8.0/list/R/ictregBayesHier.R | 13 - list-8.0/list/README.md |only list-8.0/list/build |only list-8.0/list/data/combinedListExps.rdata |only list-8.0/list/inst/doc |only list-8.0/list/man/combinedListDirect.Rd |only list-8.0/list/man/combinedListExps.Rd |only list-8.0/list/man/comp.listEndorse.Rd | 4 list-8.0/list/man/ictreg.Rd | 5 list-8.0/list/man/ictreg.joint.Rd | 5 list-8.0/list/man/ictregBayes.Rd | 16 - list-8.0/list/man/mexico.Rd | 2 list-8.0/list/man/predict.ictregBayesHier.Rd | 1 list-8.0/list/tests |only list-8.0/list/vignettes |only 24 files changed, 254 insertions(+), 199 deletions(-)
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley <fraley@u.washington.edu>
Diff between ensembleBMA versions 5.1.1 dated 2015-03-19 and 5.1.2 dated 2015-05-19
CHANGELOG | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/fitBMAgamma.R | 9 ++++----- R/fitBMAgamma0.R | 19 +++++++++---------- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.3.1 dated 2014-02-12 and 1.0.5 dated 2015-05-19
CHNOSZ-1.0.3.1/CHNOSZ/demo/TPX.R |only CHNOSZ-1.0.5/CHNOSZ/DESCRIPTION | 29 CHNOSZ-1.0.5/CHNOSZ/MD5 | 229 - CHNOSZ-1.0.5/CHNOSZ/R/affinity.R | 9 CHNOSZ-1.0.5/CHNOSZ/R/diagram.R | 58 CHNOSZ-1.0.5/CHNOSZ/R/equilibrate.R | 16 CHNOSZ-1.0.5/CHNOSZ/R/examples.R | 7 CHNOSZ-1.0.5/CHNOSZ/R/findit.R | 2 CHNOSZ-1.0.5/CHNOSZ/R/iprotein.R | 3 CHNOSZ-1.0.5/CHNOSZ/R/mosaic.R |only CHNOSZ-1.0.5/CHNOSZ/R/species.R | 3 CHNOSZ-1.0.5/CHNOSZ/R/subcrt.R | 6 CHNOSZ-1.0.5/CHNOSZ/R/transfer.R | 5 CHNOSZ-1.0.5/CHNOSZ/R/util.affinity.R | 16 CHNOSZ-1.0.5/CHNOSZ/R/util.data.R | 8 CHNOSZ-1.0.5/CHNOSZ/R/util.expression.R | 2 CHNOSZ-1.0.5/CHNOSZ/R/util.misc.R | 6 CHNOSZ-1.0.5/CHNOSZ/R/util.plot.R | 29 CHNOSZ-1.0.5/CHNOSZ/R/util.program.R | 8 CHNOSZ-1.0.5/CHNOSZ/R/wjd.R | 3 CHNOSZ-1.0.5/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.5/CHNOSZ/data/OBIGT.csv | 2 CHNOSZ-1.0.5/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.5/CHNOSZ/data/protein.csv | 105 CHNOSZ-1.0.5/CHNOSZ/data/refs.csv | 1 CHNOSZ-1.0.5/CHNOSZ/demo/00Index | 11 CHNOSZ-1.0.5/CHNOSZ/demo/buffer.R |only CHNOSZ-1.0.5/CHNOSZ/demo/diagram.R |only CHNOSZ-1.0.5/CHNOSZ/demo/findit.R | 68 CHNOSZ-1.0.5/CHNOSZ/demo/ionize.R |only CHNOSZ-1.0.5/CHNOSZ/demo/mosaic.R |only CHNOSZ-1.0.5/CHNOSZ/demo/revisit.R |only CHNOSZ-1.0.5/CHNOSZ/demo/solubility.R |only CHNOSZ-1.0.5/CHNOSZ/demo/wjd.R |only CHNOSZ-1.0.5/CHNOSZ/demo/yeastgfp.R |only CHNOSZ-1.0.5/CHNOSZ/inst/CHECKLIST | 45 CHNOSZ-1.0.5/CHNOSZ/inst/NEWS | 81 CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.R | 45 CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.Rnw | 193 - CHNOSZ-1.0.5/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.R | 14 CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.Rnw | 18 CHNOSZ-1.0.5/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.R | 469 +- CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.Rnw | 923 +++-- CHNOSZ-1.0.5/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.R | 88 CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.Rnw | 52 CHNOSZ-1.0.5/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.5/CHNOSZ/inst/extdata/protein/DS11.csv |only CHNOSZ-1.0.5/CHNOSZ/inst/extdata/protein/DS13.csv |only CHNOSZ-1.0.5/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv | 2 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-IAPWS95.R | 18 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-affinity.R | 29 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-diagram.R | 32 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-equilibrate.R | 2 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-findit.R | 6 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-ionize.aa.R | 16 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-ionize.aa_pK.R | 18 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-revisit.R | 8 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-subcrt.R | 10 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-water.R | 4 CHNOSZ-1.0.5/CHNOSZ/inst/tests/test-wjd.R | 4 CHNOSZ-1.0.5/CHNOSZ/man/CHNOSZ-package.Rd | 55 CHNOSZ-1.0.5/CHNOSZ/man/EOSregress.Rd | 5 CHNOSZ-1.0.5/CHNOSZ/man/IAPWS95.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/affinity.Rd | 116 CHNOSZ-1.0.5/CHNOSZ/man/anim.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/basis.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/buffer.Rd | 7 CHNOSZ-1.0.5/CHNOSZ/man/data.Rd | 13 CHNOSZ-1.0.5/CHNOSZ/man/diagram.Rd | 65 CHNOSZ-1.0.5/CHNOSZ/man/eos.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/eqdata.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/equilibrate.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/examples.Rd | 29 CHNOSZ-1.0.5/CHNOSZ/man/extdata.Rd | 12 CHNOSZ-1.0.5/CHNOSZ/man/findit.Rd | 40 CHNOSZ-1.0.5/CHNOSZ/man/info.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/ionize.aa.Rd | 24 CHNOSZ-1.0.5/CHNOSZ/man/iprotein.Rd | 5 CHNOSZ-1.0.5/CHNOSZ/man/makeup.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/more.aa.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/mosaic.Rd |only CHNOSZ-1.0.5/CHNOSZ/man/objective.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/protein.Rd | 88 CHNOSZ-1.0.5/CHNOSZ/man/protein.info.Rd | 19 CHNOSZ-1.0.5/CHNOSZ/man/read.expr.Rd | 62 CHNOSZ-1.0.5/CHNOSZ/man/revisit.Rd | 50 CHNOSZ-1.0.5/CHNOSZ/man/sideeffects.Rd | 4 CHNOSZ-1.0.5/CHNOSZ/man/species.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/subcrt.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/swap.basis.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/taxonomy.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/transfer.Rd | 17 CHNOSZ-1.0.5/CHNOSZ/man/util.affinity.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.args.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.array.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.blast.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.character.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.data.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.expression.Rd | 9 CHNOSZ-1.0.5/CHNOSZ/man/util.fasta.Rd | 3 CHNOSZ-1.0.5/CHNOSZ/man/util.formula.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.list.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.matrix.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.misc.Rd | 9 CHNOSZ-1.0.5/CHNOSZ/man/util.plot.Rd | 14 CHNOSZ-1.0.5/CHNOSZ/man/util.program.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.seq.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/util.units.Rd | 2 CHNOSZ-1.0.5/CHNOSZ/man/water.Rd | 6 CHNOSZ-1.0.5/CHNOSZ/man/wjd.Rd | 44 CHNOSZ-1.0.5/CHNOSZ/vignettes/anintro.Rnw | 193 - CHNOSZ-1.0.5/CHNOSZ/vignettes/anintro.lyx | 1607 +++++++-- CHNOSZ-1.0.5/CHNOSZ/vignettes/equilibrium.Rnw | 18 CHNOSZ-1.0.5/CHNOSZ/vignettes/equilibrium.lyx | 33 CHNOSZ-1.0.5/CHNOSZ/vignettes/hotspring.Rnw | 923 +++-- CHNOSZ-1.0.5/CHNOSZ/vignettes/hotspring.lyx | 3218 ++++++++++++-------- CHNOSZ-1.0.5/CHNOSZ/vignettes/vig.bib | 2443 +++------------ CHNOSZ-1.0.5/CHNOSZ/vignettes/wjd.Rnw | 52 CHNOSZ-1.0.5/CHNOSZ/vignettes/wjd.lyx | 986 ++++-- 122 files changed, 6911 insertions(+), 6041 deletions(-)
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Title: Estimating Regional Trends of a Prevalence from a DHS
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey.
Author: Joseph Larmarange - IRD CEPED
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 2.9 dated 2013-12-28 and 3.1 dated 2015-05-19
prevR-2.9/prevR/R/idw.prevR.r |only prevR-2.9/prevR/build |only prevR-2.9/prevR/inst/doc |only prevR-2.9/prevR/man/as.SpatialGrid-prevR-method.Rd |only prevR-2.9/prevR/man/fdhs.prevR.rd |only prevR-2.9/prevR/man/krige-prevR-method.Rd |only prevR-2.9/prevR/man/plot-prevR-method.Rd |only prevR-2.9/prevR/vignettes |only prevR-3.1/prevR/DESCRIPTION | 30 +- prevR-3.1/prevR/MD5 | 118 ++++----- prevR-3.1/prevR/NAMESPACE | 77 ++++-- prevR-3.1/prevR/R/NA.outside.SpatialPolygons.prevR.r | 17 + prevR-3.1/prevR/R/Noptim.r |only prevR-3.1/prevR/R/as.SpatialGrid.prevR.r | 31 ++ prevR-3.1/prevR/R/as.data.frame.prevR.r | 37 ++ prevR-3.1/prevR/R/as.prevR.r | 66 +++++ prevR-3.1/prevR/R/changeproj.prevR.r | 34 ++ prevR-3.1/prevR/R/colors.prevR.r | 87 ++++++- prevR-3.1/prevR/R/create.boundary.prevR.r | 44 +++ prevR-3.1/prevR/R/direct.label_prevR.r |only prevR-3.1/prevR/R/export.prevR.r | 76 +++++- prevR-3.1/prevR/R/eyefit.prevR.r | 208 ++++++++-------- prevR-3.1/prevR/R/import.dhs.prevR.r | 35 ++ prevR-3.1/prevR/R/is.prevR.r | 42 +++ prevR-3.1/prevR/R/kde.prevR.r | 156 +++++++++++- prevR-3.1/prevR/R/krige.prevR.r | 235 ++++++++++++++++++- prevR-3.1/prevR/R/plot.prevR.r | 44 +++ prevR-3.1/prevR/R/point.in.SpatialPolygons.prevR.r | 16 + prevR-3.1/prevR/R/prevR-package.r |only prevR-3.1/prevR/R/print.prevR.r | 18 + prevR-3.1/prevR/R/quick.prevR.r |only prevR-3.1/prevR/R/rings.prevR.r | 77 +++++- prevR-3.1/prevR/R/setClass.prevR.r | 90 +++++++ prevR-3.1/prevR/R/show.prevR.r | 18 + prevR-3.1/prevR/R/summary.prevR.r | 84 ++++-- prevR-3.1/prevR/R/theme_prevR.r |only prevR-3.1/prevR/R/xyz2dataframe.prevR.r | 34 ++ prevR-3.1/prevR/data/TMWorldBorders.rda |binary prevR-3.1/prevR/data/fdhs.rda |binary prevR-3.1/prevR/demo/prevR.r | 4 prevR-3.1/prevR/inst/po/fr/LC_MESSAGES/R-prevR.mo |binary prevR-3.1/prevR/man/NA.outside.SpatialPolygons.Rd | 35 +- prevR-3.1/prevR/man/Noptim.Rd |only prevR-3.1/prevR/man/TMWorldBorders.Rd | 57 ++-- prevR-3.1/prevR/man/as.SpatialGrid.Rd |only prevR-3.1/prevR/man/as.data.frame.prevR.Rd | 46 ++- prevR-3.1/prevR/man/as.prevR.Rd | 100 ++++---- prevR-3.1/prevR/man/changeproj-prevR-method.Rd | 44 ++- prevR-3.1/prevR/man/create.boundary.Rd | 59 ++-- prevR-3.1/prevR/man/direct.label_prevR.Rd |only prevR-3.1/prevR/man/export-prevR-method.Rd | 118 +++++---- prevR-3.1/prevR/man/fdhs.Rd |only prevR-3.1/prevR/man/import.dhs.Rd | 43 ++- prevR-3.1/prevR/man/is.prevR.Rd | 67 +++-- prevR-3.1/prevR/man/kde-prevR-method.Rd | 168 ++++++++----- prevR-3.1/prevR/man/krige-ANY-prevR-method.Rd |only prevR-3.1/prevR/man/plot-prevR-missing-method.Rd |only prevR-3.1/prevR/man/point.in.SpatialPolygons.Rd | 26 +- prevR-3.1/prevR/man/prevR-class.Rd | 116 +++++---- prevR-3.1/prevR/man/prevR-package.Rd | 203 ++++++++++------ prevR-3.1/prevR/man/prevR.colors.Rd | 87 ++++--- prevR-3.1/prevR/man/print-prevR-method.Rd | 42 +-- prevR-3.1/prevR/man/quick.prevR.Rd |only prevR-3.1/prevR/man/rings-prevR-method.Rd | 115 +++++---- prevR-3.1/prevR/man/show-prevR-method.Rd | 33 +- prevR-3.1/prevR/man/summary-prevR-method.Rd | 46 +-- prevR-3.1/prevR/man/theme_prevR.Rd |only prevR-3.1/prevR/man/xyz2dataframe.Rd | 55 ++-- prevR-3.1/prevR/po/R-fr.po | 58 ++-- prevR-3.1/prevR/po/R-prevR.pot | 40 ++- 70 files changed, 2337 insertions(+), 899 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Description: Algebraic procedures for the analysis of multiple social networks
are delivered with this package. Among other things, it is possible to
create and manipulate multivariate network data with different formats,
and there are effective ways available to treat multiple networks with
routines that combine algebraic systems like the partially ordered
semigroup or the semiring structure together with the relational bundles
occurring in different types of multivariate network data sets. As well an
algebraic approach for two-mode networks is made through Galois
derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.5 dated 2015-05-01 and 1.6 dated 2015-05-19
DESCRIPTION | 8 MD5 | 32 +- R/dhc.R | 18 - R/diagram.levels.R | 95 +++--- R/fltr.R |only R/galois.R | 686 ++++++++++++++++++++++++++++------------------- R/print.reduced.R | 7 R/redl.R | 9 inst/CHANGELOG | 12 inst/doc/TwoMode.R | 22 - inst/doc/TwoMode.Rnw | 53 +-- inst/doc/TwoMode.pdf |binary man/diagram.Rd | 4 man/diagram.levels.Rd | 2 man/fltr.Rd |only man/galois.Rd | 3 man/multiplex-package.Rd | 4 vignettes/TwoMode.Rnw | 53 +-- 18 files changed, 581 insertions(+), 427 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.4.3 dated 2015-04-18 and 0.4.4 dated 2015-05-19
DESCRIPTION | 23 MD5 | 275 - NAMESPACE | 39 NEWS | 194 R/Analyse_SAR.OSLdata.R | 993 ++-- R/CW2pHMi.R | 458 +- R/CW2pLM.R | 169 R/CW2pLMi.R | 357 - R/CW2pPMi.R | 322 - R/Luminescence-package.R |only R/RLum.Results-class.R | 25 R/Risoe.BINfileData2RLum.Analysis.R | 274 - R/Risoe.BINfileData2RLum.Data.Curve.R | 242 - R/RisoeBINfileData-class.R | 24 R/Second2Gray.R | 268 - R/analyse_IRSAR.RF.R | 1717 ++++---- R/analyse_SAR.CWOSL.R | 330 - R/analyse_SAR.TL.R | 898 ++-- R/analyse_pIRIRSequence.R | 1458 +++---- R/apply_CosmicRayRemoval.R | 232 - R/apply_EfficiencyCorrection.R | 159 R/calc_AliquotSize.R | 838 ++-- R/calc_CentralDose.R | 498 +- R/calc_CommonDose.R | 346 - R/calc_CosmicDoseRate.R | 1148 ++--- R/calc_FadingCorr.R | 367 + R/calc_FiniteMixture.R | 1155 ++--- R/calc_FuchsLang2001.R | 470 +- R/calc_HomogeneityTest.R | 261 - R/calc_IEU.R | 872 ++-- R/calc_MaxDose.R | 225 - R/calc_MinDose.R | 1598 +++---- R/calc_OSLLxTxRatio.R | 360 - R/calc_SourceDoseRate.R | 313 - R/calc_Statistics.R | 100 R/calc_TLLxTxRatio.R | 292 - R/extract_IrradiationTimes.R | 285 - R/fit_CWCurve.R | 1089 ++--- R/fit_LMCurve.R | 1460 +++---- R/get_Layout.R | 142 R/get_RLum.R | 176 R/merge_RLum.Analysis.R | 256 - R/merge_RLum.Data.Curve.R | 435 +- R/merge_RLum.R | 205 R/merge_Risoe.BINfileData.R | 507 +- R/plot_AbanicoPlot.R | 6357 +++++++++++++++---------------- R/plot_DRTResults.R | 1458 +++---- R/plot_GrowthCurve.R | 1828 ++++---- R/plot_Histogram.R | 362 - R/plot_KDE.R | 1775 ++++---- R/plot_RLum.Analysis.R | 403 - R/plot_RLum.Data.Curve.R | 253 - R/plot_RLum.Data.Image.R | 334 - R/plot_RLum.Data.Spectrum.R | 674 +-- R/plot_RLum.R | 171 R/plot_RLum.Results.R | 1948 ++++----- R/plot_RadialPlot.R | 3062 +++++++------- R/plot_Risoe.BINfileData.R | 413 -- R/readBIN2R.R | 1392 +++--- R/readSPE2R.R | 862 ++-- R/readXSYG2R.R | 263 - R/writeR2BIN.R | 1727 ++++---- R/zzz.R | 24 inst/NEWS.Rd | 157 man/Analyse_SAR.OSLdata.Rd | 271 - man/BaseDataSet.CosmicDoseRate.Rd | 93 man/CW2pHMi.Rd | 340 - man/CW2pLM.Rd | 155 man/CW2pLMi.Rd | 252 - man/CW2pPMi.Rd | 267 - man/ExampleData.BINfileData.Rd | 81 man/ExampleData.CW_OSL_Curve.Rd | 69 man/ExampleData.DeValues.Rd | 156 man/ExampleData.FittingLM.Rd | 50 man/ExampleData.LxTxData.Rd | 40 man/ExampleData.LxTxOSLData.Rd | 31 man/ExampleData.RLum.Analysis.Rd | 58 man/ExampleData.RLum.Data.Image.Rd | 46 man/ExampleData.XSYG.Rd | 124 man/Luminescence-package.Rd | 76 man/RLum-class.Rd | 39 man/RLum.Analysis-class.Rd | 114 man/RLum.Data-class.Rd | 44 man/RLum.Data.Curve-class.Rd | 99 man/RLum.Data.Image-class.Rd | 101 man/RLum.Data.Spectrum-class.Rd | 105 man/RLum.Results-class.Rd | 86 man/Risoe.BINfileData-class.Rd | 316 - man/Risoe.BINfileData2RLum.Analysis.Rd | 121 man/Risoe.BINfileData2RLum.Data.Curve.Rd | 119 man/Second2Gray.Rd | 140 man/analyse_IRSAR.RF.Rd | 450 +- man/analyse_SAR.CWOSL.Rd | 301 - man/analyse_SAR.TL.Rd | 194 man/analyse_pIRIRSequence.Rd | 298 - man/apply_CosmicRayRemoval.Rd | 172 man/apply_EfficiencyCorrection.Rd | 98 man/calc_AliquotSize.Rd | 252 - man/calc_CentralDose.Rd | 166 man/calc_CommonDose.Rd | 168 man/calc_CosmicDoseRate.Rd | 443 +- man/calc_FadingCorr.Rd | 164 man/calc_FiniteMixture.Rd | 321 - man/calc_FuchsLang2001.Rd | 159 man/calc_HomogeneityTest.Rd | 98 man/calc_IEU.Rd | 131 man/calc_MaxDose.Rd | 207 - man/calc_MinDose.Rd | 514 +- man/calc_OSLLxTxRatio.Rd | 202 man/calc_SourceDoseRate.Rd | 185 man/calc_Statistics.Rd | 97 man/calc_TLLxTxRatio.Rd | 146 man/extract_IrradiationTimes.Rd | 224 - man/fit_CWCurve.Rd | 305 - man/fit_LMCurve.Rd | 433 +- man/get_Layout.Rd | 108 man/get_RLum.Rd | 124 man/merge_RLum.Analysis.Rd | 112 man/merge_RLum.Data.Curve.Rd | 168 man/merge_RLum.Rd | 112 man/merge_Risoe.BINfileData.Rd | 160 man/plot_AbanicoPlot.Rd | 703 +-- man/plot_DRTResults.Rd | 309 - man/plot_GrowthCurve.Rd | 271 - man/plot_Histogram.Rd | 207 - man/plot_KDE.Rd | 331 - man/plot_RLum.Analysis.Rd | 179 man/plot_RLum.Data.Curve.Rd | 108 man/plot_RLum.Data.Image.Rd | 177 man/plot_RLum.Data.Spectrum.Rd | 359 - man/plot_RLum.Rd | 121 man/plot_RLum.Results.Rd | 109 man/plot_RadialPlot.Rd | 480 +- man/plot_Risoe.BINfileData.Rd | 199 man/readBIN2R.Rd | 136 man/readSPE2R.Rd | 207 - man/readXSYG2R.Rd | 269 - man/sTeve.Rd | 59 man/writeR2BIN.Rd | 143 139 files changed, 30124 insertions(+), 29466 deletions(-)
Title: Longitudinal Data
Description: Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Dai Fang [ctb],
Luke Tierney [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between longitudinalData versions 2.2 dated 2014-03-20 and 2.3 dated 2015-05-19
longitudinalData-2.2/longitudinalData/data/constants.rda |only longitudinalData-2.3/longitudinalData/DESCRIPTION | 29 longitudinalData-2.3/longitudinalData/MD5 | 33 longitudinalData-2.3/longitudinalData/NAMESPACE | 10 longitudinalData-2.3/longitudinalData/R/constants.r |only longitudinalData-2.3/longitudinalData/R/function.r | 46 longitudinalData-2.3/longitudinalData/R/imputCopyMean.R | 602 +++++----- longitudinalData-2.3/longitudinalData/R/imputLinearInterpol.R | 420 +++--- longitudinalData-2.3/longitudinalData/R/imputation.r | 2 longitudinalData-2.3/longitudinalData/R/longDataPlot.r | 15 longitudinalData-2.3/longitudinalData/R/myMisc3d.r |only longitudinalData-2.3/longitudinalData/man/ListPartition-class.Rd | 5 longitudinalData-2.3/longitudinalData/man/LongData-class.Rd | 2 longitudinalData-2.3/longitudinalData/man/LongData3d-class.Rd | 3 longitudinalData-2.3/longitudinalData/man/longData-internal.Rd | 10 longitudinalData-2.3/longitudinalData/man/longData.Rd | 2 longitudinalData-2.3/longitudinalData/man/longitudinalData-package.Rd | 4 longitudinalData-2.3/longitudinalData/man/reshapeLong.Rd | 13 longitudinalData-2.3/longitudinalData/man/reshapeWide.Rd | 12 19 files changed, 659 insertions(+), 549 deletions(-)
More information about longitudinalData at CRAN
Permanent link
Title: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction
Data
Description: To facilitate retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway, the package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyeok Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min <mbnmbn00@gmail.com>
Diff between RbioRXN versions 1.5 dated 2015-01-14 and 1.5.1 dated 2015-05-19
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/RbioRXN-internal.R | 34 ++++++++++++++++++++++------------ R/get.chebi.all.R | 18 +++++++++--------- R/get.metacyc.all.R | 2 +- R/get.rhea.all.R | 2 +- data/example.rda |binary man/RbioRXN-package.Rd | 10 +++++----- 9 files changed, 56 insertions(+), 45 deletions(-)
Title: Network Generator for Combinatorial Graph Problems
Description: Methods for the generation of a wide range of network geographies, e.g., grid networks or clustered networks. Useful for the generation of benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems or Travelling Salesperson Problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between netgen versions 1.0 dated 2015-02-03 and 1.1 dated 2015-05-19
netgen-1.0/netgen/R/getOptimalPointMatching.R |only netgen-1.0/netgen/man/makeClusteredNetwork.Rd |only netgen-1.1/netgen/DESCRIPTION | 17 netgen-1.1/netgen/MD5 | 140 +++-- netgen-1.1/netgen/NAMESPACE | 10 netgen-1.1/netgen/NEWS |only netgen-1.1/netgen/R/asCharacterNetwork.R | 20 netgen-1.1/netgen/R/asDataFrameNetwork.R | 63 +- netgen-1.1/netgen/R/asMatrixNetwork.R | 13 netgen-1.1/netgen/R/autoplotNetwork.R | 104 ++-- netgen-1.1/netgen/R/buildDepots.R | 18 netgen-1.1/netgen/R/computeDistancesToNearestClusterCenter.R | 48 - netgen-1.1/netgen/R/decorateGGPlot.R | 20 netgen-1.1/netgen/R/determineNumberOfPointsPerCluster.r | 66 +- netgen-1.1/netgen/R/dynamise.R | 78 +-- netgen-1.1/netgen/R/exportToFile.R |only netgen-1.1/netgen/R/exportToTSPlibFormat.R |only netgen-1.1/netgen/R/forceToBounds.R | 22 netgen-1.1/netgen/R/generateClusterCenters.R | 16 netgen-1.1/netgen/R/generateClusteredNetwork.R | 247 +++++----- netgen-1.1/netgen/R/generateGridNetwork.R | 55 +- netgen-1.1/netgen/R/generateRandomNetwork.R | 67 +- netgen-1.1/netgen/R/getDepotCoordinates.R | 11 netgen-1.1/netgen/R/getNumberOfClusters.R | 21 netgen-1.1/netgen/R/getNumberOfDepots.R | 13 netgen-1.1/netgen/R/getNumberOfNodes.R | 9 netgen-1.1/netgen/R/hasDepots.R | 6 netgen-1.1/netgen/R/helpers.R | 30 + netgen-1.1/netgen/R/importFromFile.R |only netgen-1.1/netgen/R/importFromTSPlibFormat.R |only netgen-1.1/netgen/R/makeNetwork.R | 82 +-- netgen-1.1/netgen/R/morphInstances.R | 122 ++-- netgen-1.1/netgen/R/pointMatching.R |only netgen-1.1/netgen/R/printNetwork.R | 32 - netgen-1.1/netgen/R/rescaleNetwork.R |only netgen-1.1/netgen/R/visualizeMorphing.R | 138 ++--- netgen-1.1/netgen/R/visualizePointMatching.R | 105 ++-- netgen-1.1/netgen/R/zzz.R | 2 netgen-1.1/netgen/inst |only netgen-1.1/netgen/man/as.character.Network.Rd | 2 netgen-1.1/netgen/man/as.data.frame.Network.Rd | 6 netgen-1.1/netgen/man/as.matrix.Network.Rd | 8 netgen-1.1/netgen/man/autoplot.Network.Rd | 18 netgen-1.1/netgen/man/dynamise.Rd | 13 netgen-1.1/netgen/man/exportToFile.Rd |only netgen-1.1/netgen/man/exportToTSPlibFormat.Rd |only netgen-1.1/netgen/man/generateClusteredNetwork.Rd | 26 - netgen-1.1/netgen/man/generateGridNetwork.Rd | 12 netgen-1.1/netgen/man/generateRandomNetwork.Rd | 8 netgen-1.1/netgen/man/getDepotCoordinates.Rd | 2 netgen-1.1/netgen/man/getNumberOfClusters.Rd | 2 netgen-1.1/netgen/man/getNumberOfDepots.Rd | 2 netgen-1.1/netgen/man/getNumberOfNodes.Rd | 6 netgen-1.1/netgen/man/getOptimalPointMatching.Rd | 18 netgen-1.1/netgen/man/getPointDistributionStrategies.Rd | 2 netgen-1.1/netgen/man/hasDepots.Rd | 2 netgen-1.1/netgen/man/importFromFile.Rd |only netgen-1.1/netgen/man/importFromTSPlibFormat.Rd |only netgen-1.1/netgen/man/makeNetwork.Rd | 20 netgen-1.1/netgen/man/morphInstances.Rd | 34 - netgen-1.1/netgen/man/rescaleNetwork.Rd |only netgen-1.1/netgen/man/visualizeMorphing.Rd | 6 netgen-1.1/netgen/man/visualizePointMatching.Rd | 16 netgen-1.1/netgen/tests/testthat/test_export_and_import.R |only netgen-1.1/netgen/tests/testthat/test_generateGridNetwork.R | 2 netgen-1.1/netgen/tests/testthat/test_getOptimalPointMatching.R |only netgen-1.1/netgen/tests/testthat/test_import.R |only netgen-1.1/netgen/tests/testthat/test_morphInstances.R | 25 + netgen-1.1/netgen/tests/testthat/test_rescaleNetwork.R |only 69 files changed, 997 insertions(+), 808 deletions(-)
Title: Hierarchical Generalized Linear Models
Description: Implemented here are procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Moudud Alam, Lars Ronnegard, Xia Shen
Maintainer: Xia Shen <xia.shen@ki.se>
Diff between hglm versions 2.0-11 dated 2014-10-30 and 2.1-0 dated 2015-05-19
ChangeLog | 28 DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 21 R/GLM.MME.R | 237 ++--- R/hglm.default.R | 1271 +++++++++++++++--------------- R/hglm.formula.R | 10 R/hglm2.R | 2 R/hglm2.formula.R | 31 R/likelihood.R | 128 ++- R/logLik.hglm.R |only R/lrt.R | 7 R/print.hglm.R | 4 R/print.summary.hglm.R | 4 R/summary.hglm.R | 2 build/vignette.rds |binary inst/doc/hglm.Rnw | 2 inst/doc/hglm.pdf |binary man/hglm-package.Rd | 88 +- man/hglm.Rd | 438 +++++----- man/hglm2.Rd | 4 man/logLik.hglm.Rd |only vignettes/hglm-knitr-knitr-compressed.pdf |binary vignettes/hglm.Rnw | 2 24 files changed, 1248 insertions(+), 1087 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.1 dated 2015-05-09 and 1.1.2 dated 2015-05-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 ++++++- R/drgeeData.R | 16 ++++++++-------- R/gee.R | 1 + 5 files changed, 23 insertions(+), 17 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely nonparametric, in particular the DDalpha-procedure. The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.0 dated 2014-12-20 and 1.1.1 dated 2015-05-19
ddalpha-1.1.0/ddalpha/src/Makevars.win |only ddalpha-1.1.1/ddalpha/DESCRIPTION | 10 +- ddalpha-1.1.1/ddalpha/MD5 | 75 +++++++++---------- ddalpha-1.1.1/ddalpha/NAMESPACE | 1 ddalpha-1.1.1/ddalpha/R/ddalpha-internal.r | 41 +++++----- ddalpha-1.1.1/ddalpha/R/ddalpha.classify.r | 35 ++++++-- ddalpha-1.1.1/ddalpha/R/ddalpha.test.r |only ddalpha-1.1.1/ddalpha/R/ddalpha.train.r | 44 +++++++---- ddalpha-1.1.1/ddalpha/R/ddalphaf.r | 11 +- ddalpha-1.1.1/ddalpha/R/depth.graph.r | 12 ++- ddalpha-1.1.1/ddalpha/R/depth.projection.r | 8 +- ddalpha-1.1.1/ddalpha/R/depth.randomTukey.r | 3 ddalpha-1.1.1/ddalpha/R/depth.space.randomTukey.r | 4 - ddalpha-1.1.1/ddalpha/R/depth.space.zonoid.r | 4 - ddalpha-1.1.1/ddalpha/R/depth.zonoid.r | 4 - ddalpha-1.1.1/ddalpha/R/is.in.convex.r | 4 - ddalpha-1.1.1/ddalpha/R/separator.polynomial.r | 8 +- ddalpha-1.1.1/ddalpha/man/ddalpha-package.Rd | 6 - ddalpha-1.1.1/ddalpha/man/ddalpha.getErrorRateCV.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.getErrorRateJK.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.test.Rd |only ddalpha-1.1.1/ddalpha/man/ddalpha.train.Rd | 7 + ddalpha-1.1.1/ddalpha/man/ddalphaf.train.Rd | 4 + ddalpha-1.1.1/ddalpha/man/depth.graph.Rd | 8 ++ ddalpha-1.1.1/ddalpha/man/depth.projection.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.randomTukey.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.space.projection.Rd | 6 + ddalpha-1.1.1/ddalpha/man/depth.space.randomTukey.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.space.zonoid.Rd | 5 + ddalpha-1.1.1/ddalpha/man/depth.zonoid.Rd | 5 + ddalpha-1.1.1/ddalpha/man/is.in.convex.Rd | 5 + ddalpha-1.1.1/ddalpha/src/Common.cpp | 3 ddalpha-1.1.1/ddalpha/src/Common.h | 2 ddalpha-1.1.1/ddalpha/src/DataStructures.h | 1 ddalpha-1.1.1/ddalpha/src/Knn.cpp | 21 +++-- ddalpha-1.1.1/ddalpha/src/Polynomial.cpp | 25 +++--- ddalpha-1.1.1/ddalpha/src/ProjectionDepth.cpp | 12 ++- ddalpha-1.1.1/ddalpha/src/ZonoidDepth.cpp | 10 +- ddalpha-1.1.1/ddalpha/src/ZonoidDepth.h | 2 ddalpha-1.1.1/ddalpha/src/ddalpha.cpp | 33 ++++++-- ddalpha-1.1.1/ddalpha/src/stdafx.h | 40 +++++++--- 41 files changed, 310 insertions(+), 164 deletions(-)
Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using a Markov Chain Monte Carlo algorithm. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. The algorithm also can be used in combination with efficient simulation methods such as simulated and parallel tempering algorithms. Tools for analysis such as inverse probability reweighting and plotting functionality are included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2015) ``A New Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper available at <http://http://imai.princeton.edu/research/files/redist.pdf>.
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins <mjh5@princeton.edu>, and Kosuke Imai <kimai@princeton.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>
Diff between redist versions 1.0 dated 2015-05-18 and 1.1 dated 2015-05-19
ChangeLog |only DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/redist.R | 29 +++++++++++++++++++++++------ man/redist.mcmc.Rd | 3 ++- src/check_contiguity.h | 2 -- src/constraint_calc_helper.cpp | 20 ++++++++++++++++---- src/constraint_calc_helper.h | 4 ++-- src/make_swaps_helper.h | 4 ++-- src/redist_analysis.h | 4 ++-- src/sw_mh_helper.h | 4 ++-- 11 files changed, 63 insertions(+), 34 deletions(-)
Title: Robust Algorithm for Principal Component Analysis
Description: The FastHCS algorithm of Schmitt and Vakili (2014) for high-dimensional, robust PCA modelling and associated outlier detection and diagnostic tools.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>
Diff between FastHCS versions 0.0.4 dated 2015-01-08 and 0.0.5 dated 2015-05-19
FastHCS-0.0.4/FastHCS/data/Ionosphere.txt.gz |only FastHCS-0.0.4/FastHCS/man/Ionosphere.Rd |only FastHCS-0.0.5/FastHCS/DESCRIPTION | 10 - FastHCS-0.0.5/FastHCS/MD5 | 26 +-- FastHCS-0.0.5/FastHCS/NAMESPACE | 7 FastHCS-0.0.5/FastHCS/R/FastHCS.R | 187 ++++++++++++++++++------ FastHCS-0.0.5/FastHCS/data/datalist | 1 FastHCS-0.0.5/FastHCS/man/DnaAlteration.Rd | 2 FastHCS-0.0.5/FastHCS/man/FHCSkernelEVD.Rd |only FastHCS-0.0.5/FastHCS/man/FHCSpsdo.Rd |only FastHCS-0.0.5/FastHCS/man/FastHCS-package.Rd | 25 +-- FastHCS-0.0.5/FastHCS/man/FastHCS.Rd | 10 - FastHCS-0.0.5/FastHCS/man/compPcaParams.Rd | 17 -- FastHCS-0.0.5/FastHCS/man/plot.FastHCS.Rd | 17 +- FastHCS-0.0.5/FastHCS/src/FastHCS.cpp | 205 +++------------------------ FastHCS-0.0.5/FastHCS/src/mystruc.h |only FastHCS-0.0.5/FastHCS/src/psdo.cpp |only 17 files changed, 224 insertions(+), 283 deletions(-)
Title: Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Description: Implements tests for Type I error in Qualitative Comparative Analysis (QCA) that take into account the multiple hypothesis tests inherent in the procedure. Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation test that provides 95% confidence intervals for the number of counterexamples and degree of consistency, respectively. The distributions of permuted values can be plotted against the observed values. For csQCA and mvQCA, simple binomial tests are implemented in csQCAbinTest() and mvQCAbinTest(), respectively.
Author: Bear Braumoeller <braumoeller.1@osu.edu>
Maintainer: Bear Braumoeller <braumoeller.1@osu.edu>
Diff between QCAfalsePositive versions 1.0 dated 2015-05-06 and 1.1.1 dated 2015-05-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/fsQCApermTest.R | 29 +++++++++++++++++++---------- R/summary.fsQCApt.R | 6 +++--- 4 files changed, 28 insertions(+), 19 deletions(-)
More information about QCAfalsePositive at CRAN
Permanent link
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for HTTP 2.0, SSL (https://, ftps://), gzip, and other 'libcurl' goodies.
The core of the package implements a framework for performing fully customizable
requests where data can be processed either in memory, on disk, or streaming via
the callback or connection interfaces. Some knowledge of 'libcurl' is recommended;
for a more-user-friendly web client see the 'httr' package which builds on this
package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.5 dated 2015-02-01 and 0.6 dated 2015-05-19
curl-0.5/curl/R/curl_download.R |only curl-0.5/curl/R/curl_escape.R |only curl-0.5/curl/R/curl_version.R |only curl-0.5/curl/man/utilities.Rd |only curl-0.5/curl/src/utils.h |only curl-0.6/curl/DESCRIPTION | 38 +++++---- curl-0.6/curl/LICENSE | 2 curl-0.6/curl/MD5 | 80 ++++++++++++++----- curl-0.6/curl/NAMESPACE | 30 ++++++- curl-0.6/curl/NEWS | 6 + curl-0.6/curl/R/curl.R | 12 +- curl-0.6/curl/R/download.R |only curl-0.6/curl/R/escape.R |only curl-0.6/curl/R/fetch.R |only curl-0.6/curl/R/form.R |only curl-0.6/curl/R/handle.R |only curl-0.6/curl/R/onload.R |only curl-0.6/curl/R/parse_headers.R |only curl-0.6/curl/R/proxy.R |only curl-0.6/curl/R/utilities.R |only curl-0.6/curl/build |only curl-0.6/curl/configure | 17 ++-- curl-0.6/curl/data |only curl-0.6/curl/inst |only curl-0.6/curl/man/curl.Rd | 13 +-- curl-0.6/curl/man/curl_download.Rd | 39 ++++++--- curl-0.6/curl/man/curl_escape.Rd |only curl-0.6/curl/man/curl_fetch.Rd |only curl-0.6/curl/man/curl_options.Rd |only curl-0.6/curl/man/form_file.Rd |only curl-0.6/curl/man/handle.Rd |only curl-0.6/curl/man/handle_cookies.Rd |only curl-0.6/curl/man/ie_proxy_info.Rd |only curl-0.6/curl/man/parse_date.Rd |only curl-0.6/curl/man/parse_headers.Rd |only curl-0.6/curl/src/Makevars | 5 + curl-0.6/curl/src/Makevars.win | 25 +++-- curl-0.6/curl/src/apple.h |only curl-0.6/curl/src/callbacks.c |only curl-0.6/curl/src/callbacks.h |only curl-0.6/curl/src/curl-common.h |only curl-0.6/curl/src/curl-symbols.h | 21 +++++ curl-0.6/curl/src/curl.c | 56 +++++++------ curl-0.6/curl/src/download.c | 62 +++++--------- curl-0.6/curl/src/escape.c | 36 +++++--- curl-0.6/curl/src/fetch.c |only curl-0.6/curl/src/form.c |only curl-0.6/curl/src/getdate.c |only curl-0.6/curl/src/handle.c |only curl-0.6/curl/src/ieproxy.c |only curl-0.6/curl/src/init.c |only curl-0.6/curl/src/utils.c | 134 ++++++++++++++++++++++---------- curl-0.6/curl/src/winhttp32.def |only curl-0.6/curl/src/winhttp64.def |only curl-0.6/curl/tests |only curl-0.6/curl/tools/symbols-in-versions |only curl-0.6/curl/tools/symbols.R |only curl-0.6/curl/tools/winlibs.R | 4 curl-0.6/curl/vignettes |only 59 files changed, 385 insertions(+), 195 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.11.1 dated 2015-02-10 and 0.12.0 dated 2015-05-18
shiny-0.11.1/shiny/man/plotOutput.Rd |only shiny-0.12.0/shiny/DESCRIPTION | 25 shiny-0.12.0/shiny/MD5 | 284 shiny-0.12.0/shiny/NAMESPACE | 9 shiny-0.12.0/shiny/NEWS | 62 shiny-0.12.0/shiny/R/bootstrap-layout.R | 4 shiny-0.12.0/shiny/R/bootstrap.R | 405 shiny-0.12.0/shiny/R/globals.R | 14 shiny-0.12.0/shiny/R/graph.R | 2 shiny-0.12.0/shiny/R/image-interact-opts.R |only shiny-0.12.0/shiny/R/image-interact.R |only shiny-0.12.0/shiny/R/middleware-shiny.R | 2 shiny-0.12.0/shiny/R/middleware.R | 3 shiny-0.12.0/shiny/R/progress.R | 16 shiny-0.12.0/shiny/R/reactives.R | 44 shiny-0.12.0/shiny/R/render-plot.R |only shiny-0.12.0/shiny/R/run-url.R | 28 shiny-0.12.0/shiny/R/server.R | 40 shiny-0.12.0/shiny/R/shiny.R | 428 shiny-0.12.0/shiny/R/shinywrappers.R | 152 shiny-0.12.0/shiny/R/update-input.R | 11 shiny-0.12.0/shiny/R/utils.R | 54 shiny-0.12.0/shiny/inst/examples/04_mpg/server.R | 8 shiny-0.12.0/shiny/inst/examples/05_sliders/ui.R | 24 shiny-0.12.0/shiny/inst/tests/test-input-handler.R | 10 shiny-0.12.0/shiny/inst/tests/test-plot-coordmap.R |only shiny-0.12.0/shiny/inst/www/shared/datatables/js/jquery.dataTables.min.js | 313 shiny-0.12.0/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.min.js | 4 shiny-0.12.0/shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.js | 82 shiny-0.12.0/shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 68 shiny-0.12.0/shiny/inst/www/shared/shiny.css | 29 shiny-0.12.0/shiny/inst/www/shared/shiny.js | 7237 +++++----- shiny-0.12.0/shiny/inst/www/shared/shiny.js.map |only shiny-0.12.0/shiny/inst/www/shared/shiny.min.js | 6 shiny-0.12.0/shiny/inst/www/shared/shiny.min.js.map | 2 shiny-0.12.0/shiny/man/Progress.Rd | 2 shiny-0.12.0/shiny/man/absolutePanel.Rd | 2 shiny-0.12.0/shiny/man/actionButton.Rd | 2 shiny-0.12.0/shiny/man/addResourcePath.Rd | 2 shiny-0.12.0/shiny/man/bootstrapPage.Rd | 2 shiny-0.12.0/shiny/man/brushOpts.Rd |only shiny-0.12.0/shiny/man/brushedPoints.Rd |only shiny-0.12.0/shiny/man/checkboxGroupInput.Rd | 2 shiny-0.12.0/shiny/man/checkboxInput.Rd | 2 shiny-0.12.0/shiny/man/clickOpts.Rd |only shiny-0.12.0/shiny/man/column.Rd | 2 shiny-0.12.0/shiny/man/conditionalPanel.Rd | 2 shiny-0.12.0/shiny/man/createWebDependency.Rd | 2 shiny-0.12.0/shiny/man/dateInput.Rd | 2 shiny-0.12.0/shiny/man/dateRangeInput.Rd | 2 shiny-0.12.0/shiny/man/dblclickOpts.Rd |only shiny-0.12.0/shiny/man/domains.Rd | 2 shiny-0.12.0/shiny/man/downloadButton.Rd | 2 shiny-0.12.0/shiny/man/downloadHandler.Rd | 2 shiny-0.12.0/shiny/man/exprToFunction.Rd | 2 shiny-0.12.0/shiny/man/fileInput.Rd | 2 shiny-0.12.0/shiny/man/fixedPage.Rd | 2 shiny-0.12.0/shiny/man/flowLayout.Rd | 6 shiny-0.12.0/shiny/man/fluidPage.Rd | 2 shiny-0.12.0/shiny/man/headerPanel.Rd | 2 shiny-0.12.0/shiny/man/helpText.Rd | 2 shiny-0.12.0/shiny/man/hoverOpts.Rd |only shiny-0.12.0/shiny/man/htmlOutput.Rd | 2 shiny-0.12.0/shiny/man/icon.Rd | 2 shiny-0.12.0/shiny/man/imageOutput.Rd | 261 shiny-0.12.0/shiny/man/inputPanel.Rd | 2 shiny-0.12.0/shiny/man/installExprFunction.Rd | 2 shiny-0.12.0/shiny/man/invalidateLater.Rd | 2 shiny-0.12.0/shiny/man/is.reactivevalues.Rd | 2 shiny-0.12.0/shiny/man/isolate.Rd | 2 shiny-0.12.0/shiny/man/knitr_methods.Rd | 2 shiny-0.12.0/shiny/man/mainPanel.Rd | 2 shiny-0.12.0/shiny/man/makeReactiveBinding.Rd | 2 shiny-0.12.0/shiny/man/markRenderFunction.Rd | 2 shiny-0.12.0/shiny/man/maskReactiveContext.Rd | 2 shiny-0.12.0/shiny/man/navbarPage.Rd | 2 shiny-0.12.0/shiny/man/navlistPanel.Rd | 2 shiny-0.12.0/shiny/man/nearPoints.Rd |only shiny-0.12.0/shiny/man/numericInput.Rd | 2 shiny-0.12.0/shiny/man/observe.Rd | 4 shiny-0.12.0/shiny/man/observeEvent.Rd | 24 shiny-0.12.0/shiny/man/outputOptions.Rd | 2 shiny-0.12.0/shiny/man/pageWithSidebar.Rd | 2 shiny-0.12.0/shiny/man/parseQueryString.Rd | 2 shiny-0.12.0/shiny/man/passwordInput.Rd | 2 shiny-0.12.0/shiny/man/plotPNG.Rd | 2 shiny-0.12.0/shiny/man/radioButtons.Rd | 2 shiny-0.12.0/shiny/man/reactive.Rd | 22 shiny-0.12.0/shiny/man/reactiveFileReader.Rd | 2 shiny-0.12.0/shiny/man/reactivePlot.Rd | 2 shiny-0.12.0/shiny/man/reactivePoll.Rd | 2 shiny-0.12.0/shiny/man/reactivePrint.Rd | 2 shiny-0.12.0/shiny/man/reactiveTable.Rd | 2 shiny-0.12.0/shiny/man/reactiveText.Rd | 2 shiny-0.12.0/shiny/man/reactiveTimer.Rd | 2 shiny-0.12.0/shiny/man/reactiveUI.Rd | 2 shiny-0.12.0/shiny/man/reactiveValues.Rd | 2 shiny-0.12.0/shiny/man/reactiveValuesToList.Rd | 2 shiny-0.12.0/shiny/man/registerInputHandler.Rd | 6 shiny-0.12.0/shiny/man/removeInputHandler.Rd | 4 shiny-0.12.0/shiny/man/renderDataTable.Rd | 10 shiny-0.12.0/shiny/man/renderImage.Rd | 2 shiny-0.12.0/shiny/man/renderPlot.Rd | 9 shiny-0.12.0/shiny/man/renderPrint.Rd | 2 shiny-0.12.0/shiny/man/renderTable.Rd | 2 shiny-0.12.0/shiny/man/renderText.Rd | 2 shiny-0.12.0/shiny/man/renderUI.Rd | 2 shiny-0.12.0/shiny/man/repeatable.Rd | 2 shiny-0.12.0/shiny/man/runApp.Rd | 19 shiny-0.12.0/shiny/man/runExample.Rd | 2 shiny-0.12.0/shiny/man/runUrl.Rd | 12 shiny-0.12.0/shiny/man/selectInput.Rd | 2 shiny-0.12.0/shiny/man/serverInfo.Rd | 2 shiny-0.12.0/shiny/man/session.Rd | 4 shiny-0.12.0/shiny/man/shiny-options.Rd | 4 shiny-0.12.0/shiny/man/shiny-package.Rd | 2 shiny-0.12.0/shiny/man/shinyApp.Rd | 2 shiny-0.12.0/shiny/man/shinyDeprecated.Rd | 2 shiny-0.12.0/shiny/man/shinyServer.Rd | 2 shiny-0.12.0/shiny/man/shinyUI.Rd | 2 shiny-0.12.0/shiny/man/showReactLog.Rd | 2 shiny-0.12.0/shiny/man/sidebarLayout.Rd | 2 shiny-0.12.0/shiny/man/sidebarPanel.Rd | 2 shiny-0.12.0/shiny/man/sliderInput.Rd | 2 shiny-0.12.0/shiny/man/splitLayout.Rd | 2 shiny-0.12.0/shiny/man/stopApp.Rd | 2 shiny-0.12.0/shiny/man/submitButton.Rd | 2 shiny-0.12.0/shiny/man/tabPanel.Rd | 2 shiny-0.12.0/shiny/man/tableOutput.Rd | 2 shiny-0.12.0/shiny/man/tabsetPanel.Rd | 2 shiny-0.12.0/shiny/man/textInput.Rd | 2 shiny-0.12.0/shiny/man/textOutput.Rd | 2 shiny-0.12.0/shiny/man/titlePanel.Rd | 2 shiny-0.12.0/shiny/man/updateCheckboxGroupInput.Rd | 2 shiny-0.12.0/shiny/man/updateCheckboxInput.Rd | 2 shiny-0.12.0/shiny/man/updateDateInput.Rd | 2 shiny-0.12.0/shiny/man/updateDateRangeInput.Rd | 2 shiny-0.12.0/shiny/man/updateNumericInput.Rd | 2 shiny-0.12.0/shiny/man/updateRadioButtons.Rd | 2 shiny-0.12.0/shiny/man/updateSelectInput.Rd | 2 shiny-0.12.0/shiny/man/updateSliderInput.Rd | 2 shiny-0.12.0/shiny/man/updateTabsetPanel.Rd | 2 shiny-0.12.0/shiny/man/updateTextInput.Rd | 2 shiny-0.12.0/shiny/man/validate.Rd | 2 shiny-0.12.0/shiny/man/verbatimTextOutput.Rd | 2 shiny-0.12.0/shiny/man/verticalLayout.Rd | 2 shiny-0.12.0/shiny/man/wellPanel.Rd | 2 shiny-0.12.0/shiny/man/withMathJax.Rd | 2 shiny-0.12.0/shiny/man/withProgress.Rd | 2 149 files changed, 5792 insertions(+), 4149 deletions(-)
Title: River Visualisation Tool
Description: This R package is a flexible and efficient tool to
visualise both quantitative and qualitative data from river surveys.
It can be used to produce diagrams with the topological structure of
the river network.
Author: Feng Mao <rivervis@outlook.com>, Yichuan Shi <yichuan@live.com>,
and Keith Richards <ksr10@cam.ac.uk>
Maintainer: Feng Mao <rivervis@outlook.com>
Diff between rivervis versions 0.45.0 dated 2015-04-10 and 0.46.0 dated 2015-05-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/RiverLayout.R | 16 +++++++++++++++- data/Ballinderry.RData |binary man/RiverLayout.Rd | 11 +++++++++-- 5 files changed, 32 insertions(+), 11 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut, cre],
Joe Cheng [aut],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between htmlwidgets versions 0.3.2 dated 2014-12-09 and 0.4 dated 2015-05-18
htmlwidgets-0.3.2/htmlwidgets/R/to_json.R |only htmlwidgets-0.4/htmlwidgets/DESCRIPTION | 32 +- htmlwidgets-0.4/htmlwidgets/MD5 | 43 +- htmlwidgets-0.4/htmlwidgets/NAMESPACE | 3 htmlwidgets-0.4/htmlwidgets/NEWS |only htmlwidgets-0.4/htmlwidgets/R/htmlwidgets.R | 130 ++++---- htmlwidgets-0.4/htmlwidgets/R/imports.R | 4 htmlwidgets-0.4/htmlwidgets/R/knitr-methods.R | 5 htmlwidgets-0.4/htmlwidgets/R/scaffold.R | 24 + htmlwidgets-0.4/htmlwidgets/R/utils.R | 37 ++ htmlwidgets-0.4/htmlwidgets/build/vignette.rds |binary htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.R |only htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.Rmd | 115 ++++++- htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-advanced.html | 158 ++++++++-- htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-intro.html | 12 htmlwidgets-0.4/htmlwidgets/inst/doc/htmlwidgets-sizing.html | 12 htmlwidgets-0.4/htmlwidgets/inst/www/htmlwidgets.js | 46 ++ htmlwidgets-0.4/htmlwidgets/man/JS.Rd | 3 htmlwidgets-0.4/htmlwidgets/man/createWidget.Rd | 34 +- htmlwidgets-0.4/htmlwidgets/man/htmlwidgets-shiny.Rd | 8 htmlwidgets-0.4/htmlwidgets/man/saveWidget.Rd | 3 htmlwidgets-0.4/htmlwidgets/man/scaffoldWidget.Rd | 3 htmlwidgets-0.4/htmlwidgets/man/sizingPolicy.Rd | 3 htmlwidgets-0.4/htmlwidgets/vignettes/htmlwidgets-advanced.Rmd | 115 ++++++- 24 files changed, 605 insertions(+), 185 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.0.9 dated 2015-02-24 and 1.0.10 dated 2015-05-18
CHANGES | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/pselect.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Statistical Process Control -- Collection of Some Useful
Functions
Description: Evaluation of control charts by means of
the zero-state, steady-state ARL (Average Run Length) and RL quantiles.
Setting up control charts for given in-control ARL. The control charts
under consideration are one- and two-sided EWMA, CUSUM, and
Shiryaev-Roberts schemes for monitoring the mean of normally
distributed independent data. ARL calculation
of the same set of schemes under drift are added.
Other charts and parameters are in preparation.
Further SPC areas will be covered as well
(sampling plans, capability indices ...).
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>
Diff between spc versions 0.5.0 dated 2014-02-03 and 0.5.1 dated 2015-05-18
DESCRIPTION | 8 MD5 | 64 - NAMESPACE | 3 R/dphat.R |only R/mewma.arl.R | 2 R/phat.ewma.arl.R | 24 R/phat.ewma.crit.R | 15 R/phat.ewma.lambda.R | 11 R/pphat.R |only R/qphat.R |only R/xewma.q.crit.prerun.R | 14 R/xewma.q.prerun.R | 5 R/xewma.sf.prerun.R | 5 R/xtewma.ad.R |only R/xtewma.arl.R |only R/xtewma.q.R |only R/xtewma.q.crit.R |only R/xtewma.sf.R |only man/dphat.Rd |only man/mewma.arl.Rd | 7 man/phat.ewma.arl.Rd | 13 man/xewma.q.prerun.Rd | 7 man/xewma.sf.prerun.Rd | 3 man/xtewma.ad.Rd |only man/xtewma.arl.Rd |only man/xtewma.q.Rd |only man/xtewma.sf.Rd |only src/allspc.c | 2801 ++++++++++++++++++++++++++++++++++++++------ src/ewma_phat_arl_coll.c | 18 src/ewma_phat_crit_coll.c | 10 src/ewma_phat_lambda_coll.c | 8 src/mewma_arl.c | 3 src/phat_cdf.c |only src/phat_pdf.c |only src/phat_qf.c |only src/xewma_arl_prerun.c | 11 src/xewma_q.c | 7 src/xewma_q_prerun.c | 39 src/xewma_sf_prerun.c | 57 src/xtewma_ad.c |only src/xtewma_arl.c |only src/xtewma_q.c |only src/xtewma_sf.c |only 43 files changed, 2652 insertions(+), 483 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo, ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.27 dated 2014-11-26 and 1.28 dated 2015-05-18
DESCRIPTION | 10 MD5 | 24 +- NAMESPACE | 8 NEWS | 8 R/EZR.R | 97 ++++++-- inst/CHANGES | 8 inst/doc/EZR.htm | 10 inst/doc/EZR.pdf |binary inst/etc/menus.txt | 3 inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary man/EZR.Rd | 10 man/EZR.dialogs.Rd | 2 po/R-RcmdrPlugin.EZR.po | 313 +++++++--------------------- 13 files changed, 213 insertions(+), 280 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 2.7 dated 2015-04-02 and 2.8 dated 2015-05-18
DESCRIPTION | 8 ++-- MD5 | 60 ++++++++++++++++++--------------- NEWS | 13 +++++++ R/testnslv.R | 30 +++++++++------- inst/iterationreport/00readme.txt | 7 ++- inst/iterationreport/dsdbldog.R | 2 + inst/iterationreport/dsdbldog.Rout | 8 +++- inst/iterationreport/dsdbldog.Rout.txt |only inst/iterationreport/dshook.R | 2 + inst/iterationreport/dshook.Rout | 8 +++- inst/iterationreport/dshook.Rout.txt |only inst/iterationreport/dslnsrch.R | 5 ++ inst/iterationreport/dslnsrch.Rout | 19 +++++++++- inst/iterationreport/dslnsrch.Rout.txt |only inst/iterationreport/dspure.R | 2 + inst/iterationreport/dspure.Rout | 8 +++- inst/iterationreport/dspure.Rout.txt |only inst/iterationreport/dspwldog.R | 2 + inst/iterationreport/dspwldog.Rout | 8 +++- inst/iterationreport/dspwldog.Rout.txt |only man/nleqslv.Rd | 22 +++++++----- man/print.testnslv.Rd | 3 + man/testnslv.Rd | 18 ++++++--- src/liqrev.f | 10 +++-- src/nleqslv.c | 1 src/nwbjac.f | 28 +++++++-------- src/nwbrdn.f | 31 +++++++---------- src/nwnjac.f | 28 +++++++-------- src/nwnleq.f | 4 +- src/nwnwtn.f | 1 src/nwout.c | 17 +++++++++ src/nwutil.f | 21 ++++++----- tests/xtestnslv.R |only tests/xtestnslv.Rout |only tests/xtestnslv.Rout.save |only 35 files changed, 237 insertions(+), 129 deletions(-)
Title: Structural Estimators and Algorithms for the Analysis of Stable
Matchings
Description: Implements structural estimators to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.co.uk>
Diff between matchingMarkets versions 0.1-3 dated 2015-04-02 and 0.1-4 dated 2015-05-18
matchingMarkets-0.1-3/matchingMarkets/data/klein14.RData |only matchingMarkets-0.1-3/matchingMarkets/man/klein14.Rd |only matchingMarkets-0.1-4/matchingMarkets/DESCRIPTION | 18 matchingMarkets-0.1-4/matchingMarkets/MD5 | 48 - matchingMarkets-0.1-4/matchingMarkets/NAMESPACE | 2 matchingMarkets-0.1-4/matchingMarkets/R/daa.R | 94 +- matchingMarkets-0.1-4/matchingMarkets/R/khb.R | 10 matchingMarkets-0.1-4/matchingMarkets/R/mce.R | 53 - matchingMarkets-0.1-4/matchingMarkets/R/mfx.R | 6 matchingMarkets-0.1-4/matchingMarkets/R/stabit.R | 397 +++++----- matchingMarkets-0.1-4/matchingMarkets/R/stabsim.R | 22 matchingMarkets-0.1-4/matchingMarkets/data/baac00.RData |binary matchingMarkets-0.1-4/matchingMarkets/data/datalist | 3 matchingMarkets-0.1-4/matchingMarkets/data/klein15a.RData |only matchingMarkets-0.1-4/matchingMarkets/data/klein15b.RData |only matchingMarkets-0.1-4/matchingMarkets/man/baac00.Rd | 4 matchingMarkets-0.1-4/matchingMarkets/man/daa.Rd | 11 matchingMarkets-0.1-4/matchingMarkets/man/khb.Rd | 13 matchingMarkets-0.1-4/matchingMarkets/man/klein15a.Rd |only matchingMarkets-0.1-4/matchingMarkets/man/klein15b.Rd |only matchingMarkets-0.1-4/matchingMarkets/man/matchingMarkets-package.Rd | 10 matchingMarkets-0.1-4/matchingMarkets/man/mce.Rd | 23 matchingMarkets-0.1-4/matchingMarkets/man/mfx.Rd | 9 matchingMarkets-0.1-4/matchingMarkets/man/plp.Rd | 3 matchingMarkets-0.1-4/matchingMarkets/man/stabit.Rd | 35 matchingMarkets-0.1-4/matchingMarkets/man/stabsim.Rd | 3 matchingMarkets-0.1-4/matchingMarkets/man/ttc.Rd | 3 matchingMarkets-0.1-4/matchingMarkets/src/RcppExports.cpp | 56 - 28 files changed, 462 insertions(+), 361 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Utility Functions to Execute Standard Extract/Transform/Load
Operations (using Package 'ff') on Large Data
Description: Provides functions to facilitate the use of the 'ff' package in
interaction with big data in 'SQL' databases (e.g. in
'Oracle', 'MySQL', 'PostgreSQL', 'Hive') by allowing easy importing directly into 'ffdf'
objects using 'DBI', 'RODBC' and 'RJDBC'. Also contains some basic utility
functions to do fast left outer join merging based on 'match', factorisation of data and a basic
function for re-coding vectors.
Author: Jan Wijffels
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between ETLUtils versions 1.2 dated 2013-01-05 and 1.3 dated 2015-05-18
DESCRIPTION | 31 MD5 | 36 NAMESPACE | 28 NEWS | 29 R/All_Imports.R |only R/ffsql.R | 2124 ++++++++++++++++++++++++++---------------------- R/matchmerge.R | 368 ++++---- R/pkg.R | 24 R/utils.R | 224 +++-- README.md |only man/ETLUtils-package.Rd | 35 man/factorise.Rd |only man/matchmerge.Rd | 249 ++--- man/naLOCFPlusone.Rd | 55 - man/read.dbi.ffdf.Rd | 290 ++---- man/read.jdbc.ffdf.Rd | 201 +--- man/read.odbc.ffdf.Rd | 201 +--- man/recoder.Rd | 57 - man/renameColumns.Rd | 63 - man/write.dbi.ffdf.Rd |only man/write.jdbc.ffdf.Rd |only man/write.odbc.ffdf.Rd |only 22 files changed, 2111 insertions(+), 1904 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-28 0.9.6.5
Title: An R Pandoc Writer
Description: Contains some functions catching all messages, stdout and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in pandoc's markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex pandoc documents to e.g. HTML, PDF, docx or odt. This
latter reporting feature is supported in brew syntax or with a custom
reference class with a smarty caching backend.
Author: Gergely Daróczi <daroczig@rapporter.net>, Roman Tsegelskyi
<roman.tsegelskyi@gmail.com>
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between pander versions 0.5.1 dated 2014-10-29 and 0.5.2 dated 2015-05-18
pander-0.5.1/pander/inst/CITATION |only pander-0.5.2/pander/DESCRIPTION | 16 pander-0.5.2/pander/MD5 | 237 ++-- pander-0.5.2/pander/NAMESPACE | 4 pander-0.5.2/pander/NEWS | 24 pander-0.5.2/pander/R/RcppExports.R |only pander-0.5.2/pander/R/S3.R | 803 ++++++++++----- pander-0.5.2/pander/R/convert.R | 9 pander-0.5.2/pander/R/evals.R | 24 pander-0.5.2/pander/R/helpers.R | 34 pander-0.5.2/pander/R/options.R | 15 pander-0.5.2/pander/R/pandoc.R | 197 ++- pander-0.5.2/pander/README.md | 35 pander-0.5.2/pander/inst/README.brew | 13 pander-0.5.2/pander/inst/tests/test-S3.R | 29 pander-0.5.2/pander/inst/tests/test-brew.R | 2 pander-0.5.2/pander/inst/tests/test-evals.R | 2 pander-0.5.2/pander/inst/tests/test-helpers.R | 2 pander-0.5.2/pander/inst/tests/test-missing.R |only pander-0.5.2/pander/man/Pandoc-class.Rd | 3 pander-0.5.2/pander/man/Pandoc.brew.Rd | 3 pander-0.5.2/pander/man/Pandoc.convert.Rd | 8 pander-0.5.2/pander/man/add.blank.lines.Rd | 3 pander-0.5.2/pander/man/add.lattice.grid.Rd | 3 pander-0.5.2/pander/man/add.lattice.xsubticks.Rd | 3 pander-0.5.2/pander/man/add.minor.ticks.Rd | 3 pander-0.5.2/pander/man/add.significance.stars.Rd | 3 pander-0.5.2/pander/man/brew.Rd | 3 pander-0.5.2/pander/man/cache.off.Rd | 3 pander-0.5.2/pander/man/check_caption.Rd |only pander-0.5.2/pander/man/emphasize.rows.Rd | 3 pander-0.5.2/pander/man/eval.msgs.Rd | 3 pander-0.5.2/pander/man/evals.Rd | 3 pander-0.5.2/pander/man/evalsOptions.Rd | 3 pander-0.5.2/pander/man/get.alignment.Rd | 3 pander-0.5.2/pander/man/get.caption.Rd | 3 pander-0.5.2/pander/man/get.emphasize.Rd | 3 pander-0.5.2/pander/man/get.storage.Rd | 3 pander-0.5.2/pander/man/has.rownames.Rd | 3 pander-0.5.2/pander/man/openFileInOS.Rd | 3 pander-0.5.2/pander/man/p.Rd | 10 pander-0.5.2/pander/man/pander.CrossTable.Rd | 8 pander-0.5.2/pander/man/pander.Date.Rd | 3 pander-0.5.2/pander/man/pander.NULL.Rd | 3 pander-0.5.2/pander/man/pander.POSIXct.Rd | 3 pander-0.5.2/pander/man/pander.POSIXlt.Rd | 3 pander-0.5.2/pander/man/pander.Rd | 4 pander-0.5.2/pander/man/pander.anova.Rd | 3 pander-0.5.2/pander/man/pander.aov.Rd | 3 pander-0.5.2/pander/man/pander.aovlist.Rd | 3 pander-0.5.2/pander/man/pander.call.Rd | 3 pander-0.5.2/pander/man/pander.cast_df.Rd | 3 pander-0.5.2/pander/man/pander.character.Rd | 3 pander-0.5.2/pander/man/pander.clogit.Rd | 3 pander-0.5.2/pander/man/pander.coxph.Rd | 3 pander-0.5.2/pander/man/pander.data.frame.Rd | 3 pander-0.5.2/pander/man/pander.default.Rd | 3 pander-0.5.2/pander/man/pander.density.Rd | 3 pander-0.5.2/pander/man/pander.describe.Rd | 3 pander-0.5.2/pander/man/pander.evals.Rd | 3 pander-0.5.2/pander/man/pander.factor.Rd | 3 pander-0.5.2/pander/man/pander.formula.Rd | 3 pander-0.5.2/pander/man/pander.ftable.Rd | 3 pander-0.5.2/pander/man/pander.function.Rd | 3 pander-0.5.2/pander/man/pander.glm.Rd | 3 pander-0.5.2/pander/man/pander.htest.Rd | 3 pander-0.5.2/pander/man/pander.image.Rd | 3 pander-0.5.2/pander/man/pander.list.Rd | 3 pander-0.5.2/pander/man/pander.lm.Rd | 3 pander-0.5.2/pander/man/pander.lme.Rd | 3 pander-0.5.2/pander/man/pander.logical.Rd | 3 pander-0.5.2/pander/man/pander.matrix.Rd | 3 pander-0.5.2/pander/man/pander.microbenchmark.Rd | 3 pander-0.5.2/pander/man/pander.mtable.Rd | 3 pander-0.5.2/pander/man/pander.numeric.Rd | 3 pander-0.5.2/pander/man/pander.option.Rd |only pander-0.5.2/pander/man/pander.prcomp.Rd | 3 pander-0.5.2/pander/man/pander.rapport.Rd | 3 pander-0.5.2/pander/man/pander.return.Rd |only pander-0.5.2/pander/man/pander.rlm.Rd | 3 pander-0.5.2/pander/man/pander.sessionInfo.Rd | 3 pander-0.5.2/pander/man/pander.smooth.spline.Rd | 3 pander-0.5.2/pander/man/pander.stat.table.Rd | 3 pander-0.5.2/pander/man/pander.summary.aov.Rd | 3 pander-0.5.2/pander/man/pander.summary.aovlist.Rd | 3 pander-0.5.2/pander/man/pander.summary.glm.Rd | 3 pander-0.5.2/pander/man/pander.summary.lm.Rd | 7 pander-0.5.2/pander/man/pander.summary.prcomp.Rd | 3 pander-0.5.2/pander/man/pander.survdiff.Rd | 3 pander-0.5.2/pander/man/pander.survfit.Rd | 5 pander-0.5.2/pander/man/pander.table.Rd | 3 pander-0.5.2/pander/man/pander.tabular.Rd |only pander-0.5.2/pander/man/pander.ts.Rd | 3 pander-0.5.2/pander/man/pander.vector.Rd |only pander-0.5.2/pander/man/pander.zoo.Rd | 3 pander-0.5.2/pander/man/panderOptions.Rd | 6 pander-0.5.2/pander/man/pander_return.Rd |only pander-0.5.2/pander/man/pandoc.date.return.Rd | 3 pander-0.5.2/pander/man/pandoc.emphasis.return.Rd | 3 pander-0.5.2/pander/man/pandoc.footnote.return.Rd | 3 pander-0.5.2/pander/man/pandoc.formula.return.Rd | 3 pander-0.5.2/pander/man/pandoc.header.return.Rd | 3 pander-0.5.2/pander/man/pandoc.horizontal.rule.return.Rd | 3 pander-0.5.2/pander/man/pandoc.image.return.Rd | 3 pander-0.5.2/pander/man/pandoc.indent.Rd | 3 pander-0.5.2/pander/man/pandoc.link.return.Rd | 3 pander-0.5.2/pander/man/pandoc.list.return.Rd | 7 pander-0.5.2/pander/man/pandoc.p.return.Rd | 3 pander-0.5.2/pander/man/pandoc.strikeout.return.Rd | 3 pander-0.5.2/pander/man/pandoc.strong.return.Rd | 3 pander-0.5.2/pander/man/pandoc.table.return.Rd | 11 pander-0.5.2/pander/man/pandoc.title.return.Rd | 3 pander-0.5.2/pander/man/pandoc.verbatim.return.Rd | 3 pander-0.5.2/pander/man/redraw.recordedplot.Rd | 3 pander-0.5.2/pander/man/redrawPlot.Rd | 3 pander-0.5.2/pander/man/remove.extra.newlines.Rd | 3 pander-0.5.2/pander/man/repChar.Rd | 3 pander-0.5.2/pander/man/set.alignment.Rd | 10 pander-0.5.2/pander/man/set.caption.Rd | 3 pander-0.5.2/pander/man/splitLine.Rd | 3 pander-0.5.2/pander/man/trim.spaces.Rd | 3 pander-0.5.2/pander/man/wrap.Rd | 5 pander-0.5.2/pander/src/RcppExports.cpp | 42 pander-0.5.2/pander/src/pandoc.cpp | 23 124 files changed, 1222 insertions(+), 628 deletions(-)
More information about rotationForest at CRAN
Permanent link
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported models include Mallow's Phi-model (Kendall distance), Weighted Kendall distance model and Phi-Component model.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 0.3.1 dated 2015-05-05 and 0.4.1 dated 2015-05-17
DESCRIPTION | 12 - MD5 | 34 +++-- NAMESPACE | 6 R/RcppExports.R | 8 + R/class.R |only R/method.R |only R/rankdist.R | 210 +++++++------------------------- R/utils.R | 78 +++-------- README.md |only man/MomentsEst.Rd | 6 man/RankControl-class.Rd | 20 +-- man/RankControlKendall-class.Rd |only man/RankControlPhiComponent-class.Rd |only man/RankControlWeightedKendall-class.Rd |only man/RankData-class.Rd | 2 man/RankDistanceModel.Rd | 6 man/RankInit-class.Rd | 8 - src/RcppExports.cpp | 31 ++++ src/utils.cpp | 45 ++++++ tests/testthat/test_FindV.R |only tests/testthat/test_LogC_Component.R |only tests/testthat/test_faiw.R | 8 - 22 files changed, 206 insertions(+), 268 deletions(-)
Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG
website created by Mads Haahr samples atmospheric noise via radio tuned to
an unused broadcasting frequency together with a skew correction algorithm
due to John von Neumann. More background is available in the included
vignette based on an essay by Mads Haahr. In its current form, the package
offers functions to retrieve random integers, randomized sequences and
random strings.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between random versions 0.2.3 dated 2015-01-08 and 0.2.4 dated 2015-05-17
ChangeLog | 23 +++++++++++++++++++++-- DESCRIPTION | 24 ++++++++++++------------ MD5 | 16 +++++++++------- R/random.R | 33 ++++++++++++++++++++++++++++----- README.md | 4 +++- build/vignette.rds |binary inst/doc/random-essay.pdf |binary inst/doc/random-intro.pdf |binary tests |only 9 files changed, 73 insertions(+), 27 deletions(-)
Title: Oceanographic Datasets for Oce
Description: Several important and Oceanographic datasets are provided. These are particularly useful to the Oce package, but can be helpful in a general context, as well.
Author: Dan Kelley <Dan.Kelley@Dal.Ca>
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between ocedata versions 0.1.2 dated 2014-05-07 and 0.1.3 dated 2015-05-17
ocedata-0.1.2/ocedata/data/landsat.rda |only ocedata-0.1.2/ocedata/man/landsat.Rd |only ocedata-0.1.3/ocedata/DESCRIPTION | 12 ++-- ocedata-0.1.3/ocedata/MD5 | 61 +++++++++++---------- ocedata-0.1.3/ocedata/NEWS | 7 ++ ocedata-0.1.3/ocedata/data/conveyor.rda |only ocedata-0.1.3/ocedata/data/datalist | 5 + ocedata-0.1.3/ocedata/data/endeavour.rda |binary ocedata-0.1.3/ocedata/data/giss.rda |binary ocedata-0.1.3/ocedata/data/gs.rda |only ocedata-0.1.3/ocedata/data/levitus.rda |binary ocedata-0.1.3/ocedata/data/nao.rda |only ocedata-0.1.3/ocedata/data/soi.rda |only ocedata-0.1.3/ocedata/man/RRprofile.Rd | 2 ocedata-0.1.3/ocedata/man/beaufort.Rd | 7 +- ocedata-0.1.3/ocedata/man/buoy.Rd | 5 + ocedata-0.1.3/ocedata/man/conveyor.Rd |only ocedata-0.1.3/ocedata/man/drag.Rd | 2 ocedata-0.1.3/ocedata/man/endeavour.Rd | 9 +-- ocedata-0.1.3/ocedata/man/geosecs235.Rd | 2 ocedata-0.1.3/ocedata/man/giss.Rd | 40 +++++++------ ocedata-0.1.3/ocedata/man/gs.Rd |only ocedata-0.1.3/ocedata/man/levitus.Rd | 75 ++++++++++++++++++-------- ocedata-0.1.3/ocedata/man/munk.Rd | 8 +- ocedata-0.1.3/ocedata/man/nao.Rd |only ocedata-0.1.3/ocedata/man/oceans.Rd | 2 ocedata-0.1.3/ocedata/man/ocedata.Rd |only ocedata-0.1.3/ocedata/man/papa.Rd | 2 ocedata-0.1.3/ocedata/man/redfieldNC.Rd | 6 -- ocedata-0.1.3/ocedata/man/redfieldNP.Rd | 7 -- ocedata-0.1.3/ocedata/man/redfieldPlankton.Rd | 8 +- ocedata-0.1.3/ocedata/man/riley.Rd | 3 - ocedata-0.1.3/ocedata/man/schmitt.Rd | 2 ocedata-0.1.3/ocedata/man/secchi.Rd | 2 ocedata-0.1.3/ocedata/man/soi.Rd |only ocedata-0.1.3/ocedata/man/turbulence.Rd | 3 - ocedata-0.1.3/ocedata/man/wilson.Rd | 7 +- 37 files changed, 160 insertions(+), 117 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on
terminals that support ANSI color and highlight codes.
ANSI color support is automatically detected.
Colors and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by the chalk
JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between crayon versions 1.2.0 dated 2015-04-08 and 1.2.1 dated 2015-05-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++++-- R/has_color.r | 7 +++---- inst |only 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e. clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.3 dated 2015-01-09 and 1.1.4 dated 2015-05-17
DESCRIPTION | 12 MD5 | 59 ++-- NAMESPACE | 50 ++- NEWS | 10 R/Clickstream.r | 452 +++++++++++++++++++++------------- R/Fitting.r | 178 ++++++------- R/MarkovChain.r | 482 +++++++++++++++++++------------------ R/Pattern.r | 83 +++--- R/clickstream-package.R | 15 - man/MarkovChain-class.Rd | 12 man/Pattern-class.Rd | 21 - man/absorbingStates-methods.Rd | 16 - man/as.transactions.Rd |only man/clickstream-package.Rd | 25 - man/clusterClickstreams.Rd | 42 +-- man/fitMarkovChain.Rd | 50 +-- man/frequencies.Rd |only man/predict-methods.Rd | 67 ++--- man/predict.ClickstreamClusters.Rd | 27 -- man/print.ClickstreamClusters.Rd | 24 - man/print.Clickstreams.Rd | 18 - man/print.MarkovChainSummary.Rd | 18 - man/randomClicks-methods.Rd | 42 +-- man/randomClickstreams.Rd | 30 -- man/readClickstreams.Rd | 27 -- man/show-methods.Rd |only man/states-methods.Rd | 18 - man/summary-methods.Rd | 25 - man/summary.ClickstreamClusters.Rd | 26 - man/summary.Clickstreams.Rd | 19 - man/transientStates-methods.Rd | 20 - man/writeClickstreams.Rd | 32 -- 32 files changed, 1010 insertions(+), 890 deletions(-)
Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the
Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
page text, information about users or the history of pages, and elements of
the category tree.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between WikipediR versions 1.1.0 dated 2014-12-06 and 1.2.0 dated 2015-05-17
WikipediR-1.1.0/WikipediR/R/RDataRebuild.R |only WikipediR-1.1.0/WikipediR/R/handle_API_errors.R |only WikipediR-1.1.0/WikipediR/R/handle_connection_errors.R |only WikipediR-1.1.0/WikipediR/R/handle_invalid_revIDs.R |only WikipediR-1.1.0/WikipediR/R/handle_limits.R |only WikipediR-1.1.0/WikipediR/R/handle_missing_pages.R |only WikipediR-1.1.0/WikipediR/R/handle_missing_users.R |only WikipediR-1.1.0/WikipediR/R/handle_uncached_diffs.R |only WikipediR-1.1.0/WikipediR/R/wiki_call.R |only WikipediR-1.1.0/WikipediR/R/wiki_catpages.R |only WikipediR-1.1.0/WikipediR/R/wiki_con.R |only WikipediR-1.1.0/WikipediR/R/wiki_diff.R |only WikipediR-1.1.0/WikipediR/R/wiki_page.R |only WikipediR-1.1.0/WikipediR/R/wiki_pagecats.R |only WikipediR-1.1.0/WikipediR/R/wiki_parse.R |only WikipediR-1.1.0/WikipediR/R/wiki_recentchanges.R |only WikipediR-1.1.0/WikipediR/R/wiki_revision.R |only WikipediR-1.1.0/WikipediR/R/wiki_timestamp.R |only WikipediR-1.1.0/WikipediR/R/wiki_usercontribs.R |only WikipediR-1.1.0/WikipediR/R/wiki_userinfo.R |only WikipediR-1.1.0/WikipediR/R/wikis.R |only WikipediR-1.1.0/WikipediR/data |only WikipediR-1.1.0/WikipediR/man/RDataRebuild.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_call.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_catpages.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_con.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_diff.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_page.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_pagecats.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_parse.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_recentchanges.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_revision.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_timestamp.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_usercontribs.Rd |only WikipediR-1.1.0/WikipediR/man/wiki_userinfo.Rd |only WikipediR-1.1.0/WikipediR/man/wikis.Rd |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_API_errors.R |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_connection_errors.R |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_invalid_revIDs.R |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_limits.R |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_missing_pages.R |only WikipediR-1.1.0/WikipediR/tests/testthat/test_handle_missing_users.R |only WikipediR-1.2.0/WikipediR/DESCRIPTION | 16 - WikipediR-1.2.0/WikipediR/MD5 | 82 ++++------ WikipediR-1.2.0/WikipediR/NAMESPACE | 28 +-- WikipediR-1.2.0/WikipediR/NEWS | 13 + WikipediR-1.2.0/WikipediR/R/categories.R |only WikipediR-1.2.0/WikipediR/R/content.R |only WikipediR-1.2.0/WikipediR/R/generic_handlers.R |only WikipediR-1.2.0/WikipediR/R/metadata.R |only WikipediR-1.2.0/WikipediR/R/parse.R |only WikipediR-1.2.0/WikipediR/R/query.R |only WikipediR-1.2.0/WikipediR/R/recent_changes.R |only WikipediR-1.2.0/WikipediR/R/user_info.R |only WikipediR-1.2.0/WikipediR/README.md | 36 +--- WikipediR-1.2.0/WikipediR/build |only WikipediR-1.2.0/WikipediR/inst |only WikipediR-1.2.0/WikipediR/man/categories_in_page.Rd |only WikipediR-1.2.0/WikipediR/man/page_backlinks.Rd |only WikipediR-1.2.0/WikipediR/man/page_content.Rd |only WikipediR-1.2.0/WikipediR/man/page_external_links.Rd |only WikipediR-1.2.0/WikipediR/man/page_info.Rd |only WikipediR-1.2.0/WikipediR/man/page_links.Rd |only WikipediR-1.2.0/WikipediR/man/pages_in_category.Rd |only WikipediR-1.2.0/WikipediR/man/query.Rd |only WikipediR-1.2.0/WikipediR/man/random_page.Rd |only WikipediR-1.2.0/WikipediR/man/recent_changes.Rd |only WikipediR-1.2.0/WikipediR/man/revision_content.Rd |only WikipediR-1.2.0/WikipediR/man/revision_diff.Rd |only WikipediR-1.2.0/WikipediR/man/user_contributions.Rd |only WikipediR-1.2.0/WikipediR/man/user_information.Rd |only WikipediR-1.2.0/WikipediR/tests/testthat.R | 3 WikipediR-1.2.0/WikipediR/tests/testthat/test_category_retrieval.R |only WikipediR-1.2.0/WikipediR/tests/testthat/test_content_retrieval.R |only WikipediR-1.2.0/WikipediR/tests/testthat/test_metadata_retrieval.R |only WikipediR-1.2.0/WikipediR/tests/testthat/test_recent_changes.R |only WikipediR-1.2.0/WikipediR/vignettes |only 77 files changed, 89 insertions(+), 89 deletions(-)
Title: Miscellaneous Data Management Tools
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.0.1 dated 2015-04-18 and 1.0.2 dated 2015-05-17
sjmisc-1.0.1/sjmisc/tests |only sjmisc-1.0.2/sjmisc/DESCRIPTION | 10 sjmisc-1.0.2/sjmisc/MD5 | 117 - sjmisc-1.0.2/sjmisc/NAMESPACE | 95 - sjmisc-1.0.2/sjmisc/NEWS | 20 sjmisc-1.0.2/sjmisc/R/efc.R | 161 + sjmisc-1.0.2/sjmisc/R/sjImportSPSS.R | 341 ++-- sjmisc-1.0.2/sjmisc/R/sjRecode.R | 2516 +++++++++++++++--------------- sjmisc-1.0.2/sjmisc/R/sjStatistics.R | 603 ++++++- sjmisc-1.0.2/sjmisc/README.md | 30 sjmisc-1.0.2/sjmisc/data/efc.RData |binary sjmisc-1.0.2/sjmisc/man/chisq_gof.Rd | 94 - sjmisc-1.0.2/sjmisc/man/cod.Rd |only sjmisc-1.0.2/sjmisc/man/cramer.Rd | 52 sjmisc-1.0.2/sjmisc/man/cronb.Rd | 50 sjmisc-1.0.2/sjmisc/man/cv.Rd | 84 - sjmisc-1.0.2/sjmisc/man/dicho.Rd | 94 - sjmisc-1.0.2/sjmisc/man/efc.Rd | 89 - sjmisc-1.0.2/sjmisc/man/efc2.Rd | 50 sjmisc-1.0.2/sjmisc/man/efc3.Rd | 50 sjmisc-1.0.2/sjmisc/man/eta_sq.Rd | 94 - sjmisc-1.0.2/sjmisc/man/get_val_labels.Rd | 171 +- sjmisc-1.0.2/sjmisc/man/get_var_labels.Rd | 143 - sjmisc-1.0.2/sjmisc/man/group_labels.Rd | 163 - sjmisc-1.0.2/sjmisc/man/group_str.Rd | 106 - sjmisc-1.0.2/sjmisc/man/group_var.Rd | 152 - sjmisc-1.0.2/sjmisc/man/hoslem_gof.Rd |only sjmisc-1.0.2/sjmisc/man/icc.Rd |only sjmisc-1.0.2/sjmisc/man/is_crossed.Rd | 92 - sjmisc-1.0.2/sjmisc/man/is_nested.Rd | 104 - sjmisc-1.0.2/sjmisc/man/is_num_fac.Rd | 66 sjmisc-1.0.2/sjmisc/man/levene_test.Rd | 46 sjmisc-1.0.2/sjmisc/man/mean_n.Rd | 38 sjmisc-1.0.2/sjmisc/man/mic.Rd | 81 sjmisc-1.0.2/sjmisc/man/mwu.Rd | 104 - sjmisc-1.0.2/sjmisc/man/phi.Rd | 52 sjmisc-1.0.2/sjmisc/man/pseudo_r2.Rd |only sjmisc-1.0.2/sjmisc/man/read_sas.Rd | 68 sjmisc-1.0.2/sjmisc/man/read_spss.Rd | 159 + sjmisc-1.0.2/sjmisc/man/read_stata.Rd | 64 sjmisc-1.0.2/sjmisc/man/rec.Rd | 131 - sjmisc-1.0.2/sjmisc/man/recode_to.Rd | 112 - sjmisc-1.0.2/sjmisc/man/reliab_test.Rd | 166 + sjmisc-1.0.2/sjmisc/man/rmse.Rd | 87 - sjmisc-1.0.2/sjmisc/man/set_na.Rd | 108 - sjmisc-1.0.2/sjmisc/man/set_val_labels.Rd | 123 - sjmisc-1.0.2/sjmisc/man/set_var_labels.Rd | 179 +- sjmisc-1.0.2/sjmisc/man/sjmisc-package.Rd | 4 sjmisc-1.0.2/sjmisc/man/std_beta.Rd | 92 - sjmisc-1.0.2/sjmisc/man/std_e.Rd | 47 sjmisc-1.0.2/sjmisc/man/str_pos.Rd | 147 - sjmisc-1.0.2/sjmisc/man/table_values.Rd | 72 sjmisc-1.0.2/sjmisc/man/to_fac.Rd | 98 - sjmisc-1.0.2/sjmisc/man/to_label.Rd | 105 - sjmisc-1.0.2/sjmisc/man/to_sjPlot.Rd | 73 sjmisc-1.0.2/sjmisc/man/to_value.Rd | 116 - sjmisc-1.0.2/sjmisc/man/trim.Rd |only sjmisc-1.0.2/sjmisc/man/weight.Rd | 78 sjmisc-1.0.2/sjmisc/man/weight2.Rd | 86 - sjmisc-1.0.2/sjmisc/man/word_wrap.Rd | 60 sjmisc-1.0.2/sjmisc/man/write_spss.Rd | 62 sjmisc-1.0.2/sjmisc/man/write_stata.Rd | 54 62 files changed, 4499 insertions(+), 3660 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct daily time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.0 dated 2015-04-07 and 1.1 dated 2015-05-17
DESCRIPTION | 8 +-- MD5 | 78 ++++++++++++++++++------------------ NAMESPACE | 2 NEWS | 11 ++++- R/HelpersMG-package.R | 11 +++-- R/MHalgoGen.R | 92 +++++++++++++++++++++---------------------- R/ScalePreviousPlot.R | 1 R/barplot_errbar.R | 5 +- R/plot_add.R | 1 R/plot_errbar.R | 1 man/ChangeCoordinate.Rd | 2 man/HelpersMG-package.Rd | 13 +++--- man/MHalgoGen.Rd | 30 +++++++------- man/ScalePreviousPlot.Rd | 6 ++ man/as.mcmc.mcmcComposite.Rd | 2 man/as.parameters.Rd | 2 man/asc.Rd | 2 man/barplot_errbar.Rd | 8 ++- man/chr.Rd | 2 man/clean.knitr.Rd | 2 man/compare_AIC.Rd | 2 man/compassRose2.Rd | 2 man/convert.tz.Rd | 2 man/getTide.Rd | 2 man/growlnotify.Rd | 2 man/ind_long_lat.Rd | 2 man/inside.search.Rd | 2 man/local.search.Rd | 2 man/map.scale2.Rd | 2 man/merge.mcmcComposite.Rd | 2 man/minmax.periodic.Rd | 2 man/moon_phase.Rd | 2 man/plot.mcmcComposite.Rd | 2 man/plot_add.Rd | 6 ++ man/plot_errbar.Rd | 5 +- man/read_folder.Rd | 2 man/similar.Rd | 2 man/summary.mcmcComposite.Rd | 2 man/sun.info.Rd | 2 man/temperature.periodic.Rd | 2 40 files changed, 182 insertions(+), 144 deletions(-)
Title: C++ ODE Solvers Compiled on-Demand
Description: Wraps the Boost 'odeint' library for integration of differential equations.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt <tkeitt@gmail.com>
Diff between odeintr versions 1.0 dated 2015-05-12 and 1.3 dated 2015-05-17
DESCRIPTION | 16 ++++++++----- MD5 | 30 +++++++++++++------------- NAMESPACE | 2 - R/RcppExports.R | 8 +++--- R/odeintr.R | 9 +++++-- inst/include/odeintr.h | 3 +- inst/templates/compile_implicit_template.cpp | 15 ++++++++----- inst/templates/compile_sys_r_obs_template.cpp | 12 ++++++---- inst/templates/compile_sys_template.cpp | 9 +++++-- man/compile_sys.Rd | 2 - man/implicit.Rd | 2 - man/integrate_sys.Rd | 9 ++++++- man/odeintr_package.Rd | 2 - man/set-opt.Rd | 2 - src/RcppExports.cpp | 16 ++++++++----- src/odeintr.cpp | 14 ++++++------ 16 files changed, 91 insertions(+), 60 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 3.8 dated 2015-05-03 and 3.8.1 dated 2015-05-17
Changelog | 6 ++ DESCRIPTION | 8 +-- MD5 | 16 +++---- R/custom.fit.R | 4 - R/fitted.assignment.R | 2 man/bnlearn-package.Rd | 4 - src/allocations.c | 96 ++++++++-------------------------------------- src/data.frame.c | 17 ++++++-- src/include/allocations.h | 13 +++--- 9 files changed, 61 insertions(+), 105 deletions(-)
More information about PoisBinOrdNonNor at CRAN
Permanent link
Title: Hierarchical Exponential-Family Random Graph Models
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger <michael.schweinberger@rice.edu> [aut, cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna <pamela.luna@rice.edu> [ctb]
Maintainer: Michael Schweinberger <michael.schweinberger@rice.edu>
Diff between hergm versions 2.2-1 dated 2015-03-08 and 2.2-2 dated 2015-05-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/hergm.preprocess.R | 13 +++++++------ 3 files changed, 13 insertions(+), 12 deletions(-)
Title: Selecting Variables in Regression Models
Description: A simple method
to select the best model or best subset of variables using
different types of data (binary, Gaussian or Poisson) and
applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between FWDselect versions 1.1 dated 2013-04-16 and 2.0 dated 2015-05-17
FWDselect-1.1/FWDselect/R/qselection2.R |only FWDselect-1.1/FWDselect/inst |only FWDselect-1.1/FWDselect/man/FWDselect-package.Rd |only FWDselect-2.0/FWDselect/DESCRIPTION | 36 - FWDselect-2.0/FWDselect/LICENSE |only FWDselect-2.0/FWDselect/MD5 | 45 - FWDselect-2.0/FWDselect/NAMESPACE | 22 FWDselect-2.0/FWDselect/NEWS |only FWDselect-2.0/FWDselect/R/FWDselect.R |only FWDselect-2.0/FWDselect/R/diabetes.R |only FWDselect-2.0/FWDselect/R/episode.R |only FWDselect-2.0/FWDselect/R/plot.qselection.R | 48 + FWDselect-2.0/FWDselect/R/pollution.R |only FWDselect-2.0/FWDselect/R/print.qselection.R | 41 - FWDselect-2.0/FWDselect/R/print.selection.R | 131 ++- FWDselect-2.0/FWDselect/R/qselection.R | 99 ++ FWDselect-2.0/FWDselect/R/selection.R | 804 ++++++++++++++--------- FWDselect-2.0/FWDselect/R/test.R | 335 +++++++-- FWDselect-2.0/FWDselect/data/diabetes.RData |only FWDselect-2.0/FWDselect/man/FWDselect.Rd |only FWDselect-2.0/FWDselect/man/diabetes.Rd |only FWDselect-2.0/FWDselect/man/episode.Rd | 38 - FWDselect-2.0/FWDselect/man/plot.qselection.Rd | 60 - FWDselect-2.0/FWDselect/man/pollution.Rd | 44 - FWDselect-2.0/FWDselect/man/print.qselection.Rd | 61 - FWDselect-2.0/FWDselect/man/print.selection.Rd | 67 - FWDselect-2.0/FWDselect/man/qselection.Rd | 98 +- FWDselect-2.0/FWDselect/man/selection.Rd | 125 +-- FWDselect-2.0/FWDselect/man/test.Rd | 135 +-- 29 files changed, 1373 insertions(+), 816 deletions(-)
Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-23 dated 2014-12-01 and 1.0-24 dated 2015-05-16
DESCRIPTION | 16 ++++++------ MD5 | 40 +++++++++++++++---------------- NEWS | 24 +++++++++++++++++- R/asciigridimpute.R | 35 +++++++++++++++++++++------ R/ensembleImpute.R | 3 +- R/errorstats.R | 2 - R/impute.R | 45 +++++++++++++++++++++-------------- R/newtargets.R | 12 +++++---- R/print.yai.R | 5 ++- R/varSelection.R | 14 +++++----- R/yai.R | 46 +++++++++++++++++++++-------------- R/yaiRFsummary.R | 2 - R/yaiVarImp.R | 5 ++- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary man/asciigridimpute.Rd | 30 ++++++++++++----------- man/errorStats.Rd | 4 +-- man/newtargets.Rd | 13 ++++++---- man/plot.notablydifferent.Rd | 7 +++-- man/yai.Rd | 55 +++++++++++++++++++++---------------------- man/yaiVarImp.Rd | 44 ++++++++++++++++++---------------- 21 files changed, 241 insertions(+), 161 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions of Heng Li
<lh3@live.co.uk> (this author wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 3.4 dated 2014-12-08 and 3.7 dated 2015-05-16
ChangeLog | 16 DESCRIPTION | 18 - MD5 | 38 +- R/seqminer.R | 75 ++-- README.md |only configure | 199 +++++------ configure.ac | 4 configure.win | 1 src/IO.cpp | 172 +++++---- src/IO.h | 456 ++++++++++++++------------ src/Makevars.in | 3 src/Makevars.win | 7 src/Profiler.cpp |only src/Profiler.h |only src/RangeList.cpp | 2 src/RangeList.h | 1 src/SimpleTimer.h |only src/TabixReader.h | 60 +-- src/VCFInputFile.cpp | 6 src/bgzf.c | 890 +++++++++++++++++++++++++-------------------------- src/knetfile.c |only src/knetfile.h |only src/rvMetaLoader.cpp | 762 ++++++++++++++++++++++--------------------- 23 files changed, 1428 insertions(+), 1282 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.5-11 dated 2015-01-20 and 3.5-12 dated 2015-05-16
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 1 + NEWS | 6 ++++++ R/color.scale.R | 3 ++- R/color2D.matplot.R | 1 + R/dispersion.R | 19 ++++++++++++------- R/gantt.R | 24 +++++++++++++++--------- R/gap.barplot.R | 8 ++++---- R/makeIntersectList.R | 1 + R/taylor.diagram.R | 2 +- data/soils.rda |binary man/box.heresy.Rd | 1 - man/dispersion.Rd | 8 +++++--- man/gantt.chart.Rd | 4 +++- man/gap.barplot.Rd | 4 +++- man/ladderplot.Rd | 4 +--- man/plotrix-package.Rd | 18 +++++++++--------- man/raw.means.plot.Rd | 3 --- man/soil.texture.Rd | 10 +++------- 20 files changed, 91 insertions(+), 74 deletions(-)
Title: Panel Data Regression: Threshold Model and Unit Root Tests
Description: Threshold model, panel version of Hylleberg et al. (1990) seasonal unit root tests, and panel unit root test of Chang (2002).
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@cc.shu.edu.tw>
Diff between pdR versions 1.2 dated 2014-12-03 and 1.3 dated 2015-05-16
DESCRIPTION | 12 ++++++------ MD5 | 29 ++++++++++++++++++++++------- R/hegy.R |only data/inf_M.rda |only data/inf_Q.rda |only man/HEGY.test.Rd |only man/IGF.Rd | 21 +++++++++++++-------- man/SeasComponent.Rd |only man/contts.Rd |only man/hegy.reg.Rd |only man/inf_M.Rd |only man/inf_Q.Rd |only man/interpolpval.Rd |only man/ipsHEGY.Rd |only man/lagSelect.Rd | 2 +- man/lookupCVtable.Rd |only man/pIGF.Rd | 14 ++++++++------ man/pdR-package.Rd | 30 +++++++++++++++--------------- man/ptm.Rd | 2 +- man/ret.Rd |only man/selPabic.Rd |only man/selPsignf.Rd |only man/tbar.Rd | 2 +- 23 files changed, 67 insertions(+), 45 deletions(-)
Title: Reliable Comparison of Floating Point Numbers
Description: Comparisons of floating point numbers are problematic due to errors
associated with the binary representation of decimal numbers.
Despite being aware of these problems, people still use numerical methods
that fail to account for these and other rounding errors (this pitfall is
the first to be highlighted in Circle 1 of Burns (2012)
[The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
This package provides new relational operators useful for performing
floating point number comparisons with a set tolerance.
Author: Alex M Chubaty [aut, cre],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@NRCan.gc.ca>
Diff between fpCompare versions 0.1.0 dated 2015-04-03 and 0.2.0 dated 2015-05-16
DESCRIPTION | 25 - MD5 | 30 - NAMESPACE | 14 NEWS | 29 + R/fpCompare.R | 128 ++++--- R/zzz.R | 14 README.md | 115 +++--- build/vignette.rds |binary inst/doc/fpCompare.Rmd | 141 ++++--- inst/doc/fpCompare.html | 501 ++++++++++++++++------------ inst/examples/examples.R | 32 - man/relational-operators.Rd | 143 ++++--- tests/test-all.R | 4 tests/testthat/test-numerical-comparisons.R | 61 +-- vignettes/bibliography.bib | 34 - vignettes/fpCompare.Rmd | 141 ++++--- 16 files changed, 805 insertions(+), 607 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.1.4 dated 2015-04-12 and 1.1.6 dated 2015-05-16
EpiModel-1.1.4/EpiModel/tests/testthat/test-parallel.R |only EpiModel-1.1.6/EpiModel/DESCRIPTION | 15 EpiModel-1.1.6/EpiModel/MD5 | 260 ++++----- EpiModel-1.1.6/EpiModel/NAMESPACE | 3 EpiModel-1.1.6/EpiModel/NEWS | 37 + EpiModel-1.1.6/EpiModel/R/EpiModel-package.r | 8 EpiModel-1.1.6/EpiModel/R/as.data.frame.R | 16 EpiModel-1.1.6/EpiModel/R/dcm.R | 37 + EpiModel-1.1.6/EpiModel/R/dcm.mods.R | 350 +++++++------ EpiModel-1.1.6/EpiModel/R/get.R | 12 EpiModel-1.1.6/EpiModel/R/icm.mod.init.R | 17 EpiModel-1.1.6/EpiModel/R/icm.mod.status.R | 17 EpiModel-1.1.6/EpiModel/R/icm.mod.vital.R | 4 EpiModel-1.1.6/EpiModel/R/icm.utils.R | 4 EpiModel-1.1.6/EpiModel/R/merge.R | 21 EpiModel-1.1.6/EpiModel/R/net.mod.init.R | 18 EpiModel-1.1.6/EpiModel/R/net.mod.status.R | 2 EpiModel-1.1.6/EpiModel/R/net.mod.vital.R | 293 ++++------- EpiModel-1.1.6/EpiModel/R/net.utils.R | 150 ++++- EpiModel-1.1.6/EpiModel/R/netdx.R | 20 EpiModel-1.1.6/EpiModel/R/netest.R | 86 +++ EpiModel-1.1.6/EpiModel/R/netsim.R | 110 ---- EpiModel-1.1.6/EpiModel/R/plot.R | 78 +- EpiModel-1.1.6/EpiModel/R/saveout.R | 11 EpiModel-1.1.6/EpiModel/R/shiny.R | 4 EpiModel-1.1.6/EpiModel/R/summary.R | 114 ++-- EpiModel-1.1.6/EpiModel/R/test.R | 290 ++++++---- EpiModel-1.1.6/EpiModel/R/utils.R | 10 EpiModel-1.1.6/EpiModel/R/verbose.R | 23 EpiModel-1.1.6/EpiModel/build/vignette.rds |binary EpiModel-1.1.6/EpiModel/inst/doc/Intro.R | 6 EpiModel-1.1.6/EpiModel/inst/doc/Intro.html | 2 EpiModel-1.1.6/EpiModel/inst/shiny/epidcm/server.R | 7 EpiModel-1.1.6/EpiModel/inst/shiny/epidcm/ui.R | 385 ++++++-------- EpiModel-1.1.6/EpiModel/inst/shiny/epiicm/server.R | 4 EpiModel-1.1.6/EpiModel/inst/shiny/epiicm/ui.R | 450 +++++++---------- EpiModel-1.1.6/EpiModel/man/EpiModel-package.Rd | 6 EpiModel-1.1.6/EpiModel/man/as.data.frame.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/as.data.frame.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/bipvals.Rd | 2 EpiModel-1.1.6/EpiModel/man/births.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/births.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/brewer_ramp.Rd | 2 EpiModel-1.1.6/EpiModel/man/calc_eql.Rd |only EpiModel-1.1.6/EpiModel/man/check_bip_degdist.Rd | 2 EpiModel-1.1.6/EpiModel/man/color_tea.Rd | 2 EpiModel-1.1.6/EpiModel/man/comp_plot.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/copy_toall_attr.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/dcm.mods.Rd | 2 EpiModel-1.1.6/EpiModel/man/deaths.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/deaths.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/deleteAttr.Rd | 2 EpiModel-1.1.6/EpiModel/man/discord_edgelist.Rd | 2 EpiModel-1.1.6/EpiModel/man/dissolution_coefs.Rd | 2 EpiModel-1.1.6/EpiModel/man/edgelist_censor.Rd | 2 EpiModel-1.1.6/EpiModel/man/edgelist_meanage.Rd | 2 EpiModel-1.1.6/EpiModel/man/edges_correct.Rd | 2 EpiModel-1.1.6/EpiModel/man/epiweb.Rd | 6 EpiModel-1.1.6/EpiModel/man/get_attr_prop.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_formula_terms.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_network.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_nwparam.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_nwstats.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_prev.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_prev.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_sims.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_transmat.Rd | 2 EpiModel-1.1.6/EpiModel/man/icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/idmode.Rd | 2 EpiModel-1.1.6/EpiModel/man/infection.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/infection.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_pids.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_status.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_status.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/initialize.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/initialize.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/mcat.Rd | 2 EpiModel-1.1.6/EpiModel/man/merge.icm.Rd | 12 EpiModel-1.1.6/EpiModel/man/merge.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/modeids.Rd | 2 EpiModel-1.1.6/EpiModel/man/modules.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/modules.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/netdx.Rd | 2 EpiModel-1.1.6/EpiModel/man/netest.Rd | 9 EpiModel-1.1.6/EpiModel/man/netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/netsim_parallel.Rd | 64 -- EpiModel-1.1.6/EpiModel/man/node_active.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.netdx.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/recovery.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/recovery.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/resim_nets.Rd | 2 EpiModel-1.1.6/EpiModel/man/saveout.dcm.Rd | 4 EpiModel-1.1.6/EpiModel/man/saveout.icm.Rd | 4 EpiModel-1.1.6/EpiModel/man/saveout.net.Rd | 4 EpiModel-1.1.6/EpiModel/man/sim_nets.Rd | 2 EpiModel-1.1.6/EpiModel/man/split_bip.Rd | 2 EpiModel-1.1.6/EpiModel/man/ssample.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.netest.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/test_icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/test_net.Rd | 2 EpiModel-1.1.6/EpiModel/man/transco.Rd | 2 EpiModel-1.1.6/EpiModel/man/update_nwattr.Rd | 2 EpiModel-1.1.6/EpiModel/man/verbose.dcm.Rd | 4 EpiModel-1.1.6/EpiModel/man/verbose.icm.Rd | 4 EpiModel-1.1.6/EpiModel/man/verbose.net.Rd | 4 EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm-dede.R | 2 EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm-long.R | 224 ++++---- EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm.R | 125 ++++ EpiModel-1.1.6/EpiModel/tests/testthat/test-net-long.R | 102 +++ EpiModel-1.1.6/EpiModel/tests/testthat/test-netest.R | 42 + EpiModel-1.1.6/EpiModel/tests/testthat/test-netsim.R | 4 EpiModel-1.1.6/EpiModel/tests/testthat/test-newdcm.R | 44 - EpiModel-1.1.6/EpiModel/tests/testthat/test-utils.R | 97 +++ 132 files changed, 2109 insertions(+), 1668 deletions(-)
Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions,
a procedure increasingly used in ecology to improve species distribution models.
This package integrates the existing methodological approaches with the
objective of generating virtual species distributions with increased
ecological realism.
Author: Boris Leroy, Christine N. Meynard, Celine Bellard and Franck Courchamp
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between virtualspecies versions 1.0 dated 2014-09-25 and 1.1 dated 2015-05-15
DESCRIPTION | 10 +-- MD5 | 53 +++++++++-------- NAMESPACE | 4 - R/formatFunctions.R | 5 + R/generateRandomSp.R | 20 +++++- R/generateSpFromFun.R | 129 ++++++++++++++++-------------------------- R/generateSpFromPCA.R | 53 ++++++----------- R/genericfunctions.R | 14 +--- R/limitDistribution.R | 7 -- R/sp.env.functions.R | 121 +++++++++++++++++++++++++++++++++++++++ R/thermalFunctionDraft.R |only R/virtualspecies-package.R | 7 +- README.md |only inst |only man/betaFun.Rd |only man/convertToPA.Rd | 3 man/custnorm.Rd |only man/formatFunctions.Rd | 5 - man/generateRandomSp.Rd | 23 ++++++- man/generateSpFromFun.Rd | 34 +++++------ man/generateSpFromPCA.Rd | 37 +++++------- man/limitDistribution.Rd | 10 --- man/linearFun.Rd | 3 man/logisticFun.Rd | 3 man/plotResponse.Rd | 3 man/quadraticFun.Rd | 3 man/removeCollinearity.Rd | 3 man/sampleOccurrences.Rd | 3 man/synchroniseNA.Rd | 3 man/virtualspecies-package.Rd | 10 +-- 30 files changed, 341 insertions(+), 225 deletions(-)
More information about virtualspecies at CRAN
Permanent link
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-0 dated 2015-03-15 and 1.1-1 dated 2015-05-15
TSP-1.1-0/TSP/inst/tests/TSPLIB.R |only TSP-1.1-0/TSP/inst/tests/solve_TSP.R |only TSP-1.1-1/TSP/DESCRIPTION | 9 +++--- TSP-1.1-1/TSP/MD5 | 24 +++++++++--------- TSP-1.1-1/TSP/build/vignette.rds |binary TSP-1.1-1/TSP/data/USCA312.rda |binary TSP-1.1-1/TSP/data/USCA312_map.rda |binary TSP-1.1-1/TSP/data/USCA50.rda |binary TSP-1.1-1/TSP/inst/NEWS | 4 +++ TSP-1.1-1/TSP/inst/doc/TSP.pdf |binary TSP-1.1-1/TSP/inst/tests/test-TSPLIB.R |only TSP-1.1-1/TSP/inst/tests/test-solve_TSP.R |only TSP-1.1-1/TSP/src/insertion_cost.c | 28 +++++++++++---------- TSP-1.1-1/TSP/src/tour_length.c | 31 +++++++++++++---------- TSP-1.1-1/TSP/src/two_opt.c | 39 +++++++++++++----------------- 15 files changed, 71 insertions(+), 64 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.0.0 dated 2015-01-28 and 1.1.0 dated 2015-05-15
stochvol-1.0.0/stochvol/R/wrapper.R |only stochvol-1.1.0/stochvol/DESCRIPTION | 8 stochvol-1.1.0/stochvol/MD5 | 73 +- stochvol-1.1.0/stochvol/NEWS | 34 + stochvol-1.1.0/stochvol/R/plotting.R |only stochvol-1.1.0/stochvol/R/simulation.R | 37 - stochvol-1.1.0/stochvol/R/utilities_svdraws.R | 324 +----------- stochvol-1.1.0/stochvol/R/wrappers.R |only stochvol-1.1.0/stochvol/build/vignette.rds |binary stochvol-1.1.0/stochvol/data/exrates.RData |binary stochvol-1.1.0/stochvol/inst/CITATION | 15 stochvol-1.1.0/stochvol/inst/doc/article.R | 39 - stochvol-1.1.0/stochvol/inst/doc/article.Rnw | 19 stochvol-1.1.0/stochvol/inst/doc/article.pdf |binary stochvol-1.1.0/stochvol/inst/doc/heavytails.R |only stochvol-1.1.0/stochvol/inst/doc/heavytails.Rnw |only stochvol-1.1.0/stochvol/inst/doc/heavytails.pdf |only stochvol-1.1.0/stochvol/inst/include/update.h | 6 stochvol-1.1.0/stochvol/man/extractors.Rd | 2 stochvol-1.1.0/stochvol/man/logret.Rd | 2 stochvol-1.1.0/stochvol/man/paradensplot.Rd | 7 stochvol-1.1.0/stochvol/man/paratraceplot.Rd | 6 stochvol-1.1.0/stochvol/man/plot.svdraws.Rd | 4 stochvol-1.1.0/stochvol/man/stochvol-package.Rd | 2 stochvol-1.1.0/stochvol/man/svsample.Rd | 15 stochvol-1.1.0/stochvol/man/svsample2.Rd | 10 stochvol-1.1.0/stochvol/man/svsim.Rd | 13 stochvol-1.1.0/stochvol/man/updatesummary.Rd | 2 stochvol-1.1.0/stochvol/man/volplot.Rd | 6 stochvol-1.1.0/stochvol/src/Makevars.win | 10 stochvol-1.1.0/stochvol/src/densities.h | 18 stochvol-1.1.0/stochvol/src/progutils.cpp | 43 + stochvol-1.1.0/stochvol/src/progutils.h | 23 stochvol-1.1.0/stochvol/src/sampler.cpp | 133 ++-- stochvol-1.1.0/stochvol/src/sampler.h | 2 stochvol-1.1.0/stochvol/vignettes/Makefile | 10 stochvol-1.1.0/stochvol/vignettes/article.Rnw | 19 stochvol-1.1.0/stochvol/vignettes/extrafig/predlik_terr.pdf |only stochvol-1.1.0/stochvol/vignettes/heavytails.Rnw |only stochvol-1.1.0/stochvol/vignettes/heavytails.tex |only stochvol-1.1.0/stochvol/vignettes/macros.tex | 6 stochvol-1.1.0/stochvol/vignettes/mybib.bib | 123 ++++ 42 files changed, 519 insertions(+), 492 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.4 dated 2015-03-24 and 1.0.6 dated 2015-05-15
rscala-1.0.4/rscala/inst/java/rscala_2.10-1.0.4.jar |only rscala-1.0.4/rscala/inst/java/rscala_2.11-1.0.4.jar |only rscala-1.0.4/rscala/java/rscala_2.10-1.0.4-sources.jar |only rscala-1.0.4/rscala/java/rscala_2.11-1.0.4-sources.jar |only rscala-1.0.6/rscala/DESCRIPTION | 11 rscala-1.0.6/rscala/MD5 | 38 + rscala-1.0.6/rscala/NAMESPACE | 7 rscala-1.0.6/rscala/NEWS | 30 + rscala-1.0.6/rscala/R/common.R | 5 rscala-1.0.6/rscala/R/globals.R |only rscala-1.0.6/rscala/R/rServer.R | 64 ++- rscala-1.0.6/rscala/R/scalaInterpreter.R | 327 +++++++++++------ rscala-1.0.6/rscala/R/zzz.R | 7 rscala-1.0.6/rscala/README |only rscala-1.0.6/rscala/inst/bin |only rscala-1.0.6/rscala/inst/doc |only rscala-1.0.6/rscala/inst/java/rscala_2.10-1.0.6.jar |only rscala-1.0.6/rscala/inst/java/rscala_2.11-1.0.6.jar |only rscala-1.0.6/rscala/java/rscala_2.10-1.0.6-sources.jar |only rscala-1.0.6/rscala/java/rscala_2.11-1.0.6-sources.jar |only rscala-1.0.6/rscala/man/close.Rd | 2 rscala-1.0.6/rscala/man/constructor.Rd | 59 +-- rscala-1.0.6/rscala/man/eval.Rd | 33 - rscala-1.0.6/rscala/man/print.Rd | 2 rscala-1.0.6/rscala/man/settings.Rd | 2 rscala-1.0.6/rscala/man/strintrpl.Rd | 4 26 files changed, 403 insertions(+), 188 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-8 dated 2014-01-14 and 1.0-9 dated 2015-05-15
rEMM-1.0-8/rEMM/inst/tests/EMM.R |only rEMM-1.0-8/rEMM/inst/tests/remove.R |only rEMM-1.0-8/rEMM/tests/EMM.R |only rEMM-1.0-8/rEMM/tests/EMM.Rout.save |only rEMM-1.0-8/rEMM/tests/remove.R |only rEMM-1.0-9/rEMM/DESCRIPTION | 29 +++++++++++-------------- rEMM-1.0-9/rEMM/MD5 | 35 ++++++++++++++----------------- rEMM-1.0-9/rEMM/NAMESPACE | 19 ++++++++-------- rEMM-1.0-9/rEMM/R/AAA.R | 3 ++ rEMM-1.0-9/rEMM/R/SimpleMC.R | 4 +-- rEMM-1.0-9/rEMM/R/ellipse.R | 2 - rEMM-1.0-9/rEMM/R/graph.R | 2 - rEMM-1.0-9/rEMM/R/plot.R | 9 ++++--- rEMM-1.0-9/rEMM/build/vignette.rds |binary rEMM-1.0-9/rEMM/data/16S.rda |binary rEMM-1.0-9/rEMM/data/Derwent.rda |binary rEMM-1.0-9/rEMM/data/EMMTraffic.rda |binary rEMM-1.0-9/rEMM/data/EMMsim.rda |binary rEMM-1.0-9/rEMM/inst/NEWS | 6 ++++- rEMM-1.0-9/rEMM/inst/doc/rEMM.pdf |binary rEMM-1.0-9/rEMM/inst/tests/test-EMM.R |only rEMM-1.0-9/rEMM/inst/tests/test-remove.R |only 22 files changed, 56 insertions(+), 53 deletions(-)
Title: Analysis of Queueing Networks and Models
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models
and Single and Multiclass Product-Form Queueing Networks.
It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K,
Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,
Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks
and Single Channel Multiple Class Mixed Networks.
Also it provides a B-Erlang, C-Erlang and Engset calculators.
This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla <pedro.canadilla@gmail.com>
Diff between queueing versions 0.2.4 dated 2015-04-12 and 0.2.5 dated 2015-05-15
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/queueing.R | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Calculating Effective Sizes Based on Known Demographic
Parameters of a Population
Description: Effective population sizes (often abbreviated as "Neff") are essential in biodiversity monitoring and conservation. For the first time, calculating effective sizes with data obtained within less than a generation but considering demographic parameters is possible. This individual based model uses demographic parameters of a population to calculate annual effective sizes and effective population sizes (per generation). A defined number of alleles and loci will be used to simulate the genotypes of the individuals. Stepwise mutation rates can be included. Variations in life history parameters (sex ratio, sex-specific survival, recruitment rate, reproductive skew) are possible. These results will help managers to define existing populations as viable or not.
Author: Annegret Grimm, Bernd Gruber & Klaus Henle
Maintainer: Annegret Grimm <annegret.grimm@ufz.de>
Diff between NEff versions 1.0 dated 2013-09-10 and 1.1 dated 2015-05-15
DESCRIPTION | 14 - MD5 | 8 R/population.R | 466 ++++++++++++++++++++++++++++++++++++++++++++-------- man/NEff-package.Rd | 18 +- man/population.Rd | 65 ++++--- 5 files changed, 469 insertions(+), 102 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-34 dated 2014-11-21 and 0.9-35 dated 2015-05-15
mkin-0.9-34/mkin/inst/unitTests |only mkin-0.9-34/mkin/tests/doRUnit.R |only mkin-0.9-35/mkin/DESCRIPTION | 17 - mkin-0.9-35/mkin/MD5 | 84 +++++--- mkin-0.9-35/mkin/NAMESPACE | 3 mkin-0.9-35/mkin/NEWS |only mkin-0.9-35/mkin/R/ilr.R | 2 mkin-0.9-35/mkin/R/mkin_long_to_wide.R | 2 mkin-0.9-35/mkin/R/mkin_wide_to_long.R | 2 mkin-0.9-35/mkin/R/mkinfit.R | 13 + mkin-0.9-35/mkin/R/mkinparplot.R | 15 - mkin-0.9-35/mkin/README.md | 11 - mkin-0.9-35/mkin/build/vignette.rds |binary mkin-0.9-35/mkin/data/FOCUS_2006_DFOP_ref_A_to_B.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_FOMC_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_HS_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_SFO_ref_A_to_F.rda |binary mkin-0.9-35/mkin/data/FOCUS_2006_datasets.RData |binary mkin-0.9-35/mkin/data/mccall81_245T.RData |binary mkin-0.9-35/mkin/data/schaefer07_complex_case.RData |binary mkin-0.9-35/mkin/data/synthetic_data_for_UBA_2014.RData |only mkin-0.9-35/mkin/inst/doc/FOCUS_L.html | 165 ++++++++-------- mkin-0.9-35/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-35/mkin/inst/doc/mkin.pdf |binary mkin-0.9-35/mkin/man/schaefer07_complex_case.Rd | 2 mkin-0.9-35/mkin/man/synthetic_data_for_UBA.Rd |only mkin-0.9-35/mkin/tests/testthat |only mkin-0.9-35/mkin/tests/testthat.R |only mkin-0.9-35/mkin/vignettes/compiled_models_cache |only 29 files changed, 186 insertions(+), 130 deletions(-)
Title: Belief Function Implementation
Description: Some basic functions to implement belief functions including: transformation between belief functions using the method introduced by Philippe Smets (arXiv:1304.1122 [cs.AI]), evidence combination, evidence discounting, decision-making, and constructing masses. Currently, thirteen combination rules and five decision rules are supported. It can also be used to generate different types of random masses when working on belief combination and conflict management.
Author: Kuang Zhou <kzhoumath@163.com>; Arnaud Martin
<arnaud.martin@univ-rennes1.fr>
Maintainer: Kuang Zhou <kzhoumath@163.com>
Diff between ibelief versions 1.0 dated 2014-10-07 and 1.1 dated 2015-05-15
ibelief-1.0/ibelief/R/BayesianMass.r |only ibelief-1.0/ibelief/R/ConflictPCR6.r |only ibelief-1.0/ibelief/R/ConflictTable.r |only ibelief-1.0/ibelief/R/DST.r |only ibelief-1.0/ibelief/R/DST_fmt_functions.r |only ibelief-1.0/ibelief/R/PCR6.r |only ibelief-1.0/ibelief/R/RandomMass.r |only ibelief-1.0/ibelief/R/dec2bin.r |only ibelief-1.0/ibelief/R/decisionDST.r |only ibelief-1.0/ibelief/R/discounting.r |only ibelief-1.1/ibelief/DESCRIPTION | 11 ++-- ibelief-1.1/ibelief/MD5 | 30 +++++++----- ibelief-1.1/ibelief/NAMESPACE | 71 +++++++++++++++--------------- ibelief-1.1/ibelief/NEWS |only ibelief-1.1/ibelief/R/BayesianMass.R |only ibelief-1.1/ibelief/R/ConflictPCR6.R |only ibelief-1.1/ibelief/R/ConflictTable.R |only ibelief-1.1/ibelief/R/DST.R |only ibelief-1.1/ibelief/R/DST_fmt_functions.R |only ibelief-1.1/ibelief/R/LCRule.R |only ibelief-1.1/ibelief/R/PCR6.R |only ibelief-1.1/ibelief/R/RandomMass.R |only ibelief-1.1/ibelief/R/dec2bin.R |only ibelief-1.1/ibelief/R/decisionDST.R |only ibelief-1.1/ibelief/R/discounting.R |only ibelief-1.1/ibelief/README.md |only ibelief-1.1/ibelief/man/LCRule.Rd |only ibelief-1.1/ibelief/man/discounting.Rd | 58 ++++++++++++------------ 28 files changed, 87 insertions(+), 83 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>
Diff between Haplin versions 5.3 dated 2013-05-23 and 5.5 dated 2015-05-15
Haplin-5.3/Haplin/R/f.batch.R |only Haplin-5.3/Haplin/R/f.load.R |only Haplin-5.3/Haplin/R/f.save.R |only Haplin-5.3/Haplin/R/loadData.R |only Haplin-5.3/Haplin/R/saveData.R |only Haplin-5.5/Haplin/DESCRIPTION | 31 +-- Haplin-5.5/Haplin/MD5 | 86 +++++---- Haplin-5.5/Haplin/NAMESPACE | 47 ++--- Haplin-5.5/Haplin/R/cbindFiles.R |only Haplin-5.5/Haplin/R/coef.haptable.R | 1 Haplin-5.5/Haplin/R/convertPed.R | 64 ++++--- Haplin-5.5/Haplin/R/f.EM.missing.R | 10 - Haplin-5.5/Haplin/R/f.HWE.R | 2 Haplin-5.5/Haplin/R/f.check.pars.R | 23 -- Haplin-5.5/Haplin/R/f.coefnames.R |only Haplin-5.5/Haplin/R/f.data.R | 2 Haplin-5.5/Haplin/R/f.debug.pvalues.R |only Haplin-5.5/Haplin/R/f.get.data.R | 24 -- Haplin-5.5/Haplin/R/f.plot.effects.R | 17 + Haplin-5.5/Haplin/R/f.pos.match.R | 2 Haplin-5.5/Haplin/R/f.post.chisq.R | 2 Haplin-5.5/Haplin/R/f.post.diff.R | 34 ++- Haplin-5.5/Haplin/R/f.post.poo.diff.R |only Haplin-5.5/Haplin/R/f.posttest.R | 29 +-- Haplin-5.5/Haplin/R/f.posttest.score.R | 4 Haplin-5.5/Haplin/R/f.prep.reference.R | 12 + Haplin-5.5/Haplin/R/f.prob.R |only Haplin-5.5/Haplin/R/f.rand.geno.R |only Haplin-5.5/Haplin/R/f.sim.R |only Haplin-5.5/Haplin/R/f.suest.R | 9 - Haplin-5.5/Haplin/R/haplin.R | 2 Haplin-5.5/Haplin/R/haplinSlide.R | 22 +- Haplin-5.5/Haplin/R/lineByLine.R | 79 ++++---- Haplin-5.5/Haplin/R/plot.haplin.R | 17 + Haplin-5.5/Haplin/R/plot.haptable.R | 3 Haplin-5.5/Haplin/R/postTest.R | 110 +++++------- Haplin-5.5/Haplin/R/prepPed.R | 22 +- Haplin-5.5/Haplin/R/print.suest.R | 15 - Haplin-5.5/Haplin/R/print.summary.tri.glm.R | 2 Haplin-5.5/Haplin/R/rbindFiles.R |only Haplin-5.5/Haplin/R/snpPos.R | 18 -- Haplin-5.5/Haplin/R/snpPower.R |only Haplin-5.5/Haplin/R/snpSampleSize.R |only Haplin-5.5/Haplin/R/summary.tri.glm.R | 69 +++++-- Haplin-5.5/Haplin/R/toDataFrame.R | 2 Haplin-5.5/Haplin/R/uniqueID.R |only Haplin-5.5/Haplin/inst/doc/Haplin_data_format.pdf |binary Haplin-5.5/Haplin/man/cbindFiles.Rd |only Haplin-5.5/Haplin/man/convertPed.Rd | 197 +++++++++++----------- Haplin-5.5/Haplin/man/haplin.Rd | 6 Haplin-5.5/Haplin/man/lineByLine.Rd | 157 +++++++++-------- Haplin-5.5/Haplin/man/rbindFiles.Rd |only Haplin-5.5/Haplin/man/snpPower.Rd |only Haplin-5.5/Haplin/man/snpSampleSize.Rd |only 54 files changed, 589 insertions(+), 531 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch> and Sören Vogel <soeren.vogel@posteo.ch>
Maintainer: Sören Vogel <soeren.vogel@posteo.ch>
Diff between GUTS versions 0.9.1 dated 2015-05-06 and 0.9.3 dated 2015-05-15
DESCRIPTION | 15 ++++++---- MD5 | 12 ++++---- R/GUTS.R | 17 ++++++++++-- data/diazinon.rda |binary man/GUTS-package.Rd | 2 - man/GUTS.Rd | 55 ++++++++++++++++++++-------------------- src/guts_calc_loglikelihood.cpp | 21 +-------------- 7 files changed, 61 insertions(+), 61 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at> and Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.1 dated 2015-05-06 and 0.2 dated 2015-05-15
dynRB-0.1/dynRB/R/dynRB_Qn.R |only dynRB-0.1/dynRB/R/dynRB_Qnc.R |only dynRB-0.1/dynRB/R/dynRB_SQa.R |only dynRB-0.1/dynRB/R/dynRB_SQac.R |only dynRB-0.1/dynRB/R/dynRB_Sn.R |only dynRB-0.1/dynRB/R/dynRB_Snc.R |only dynRB-0.1/dynRB/man/dynRB_Qn.Rd |only dynRB-0.1/dynRB/man/dynRB_Qnc.Rd |only dynRB-0.1/dynRB/man/dynRB_SQa.Rd |only dynRB-0.1/dynRB/man/dynRB_SQac.Rd |only dynRB-0.1/dynRB/man/dynRB_Sn.Rd |only dynRB-0.1/dynRB/man/dynRB_Snc.Rd |only dynRB-0.2/dynRB/DESCRIPTION | 6 +++--- dynRB-0.2/dynRB/MD5 | 28 ++++++++++++++-------------- dynRB-0.2/dynRB/R/dynRB_Pn.R |only dynRB-0.2/dynRB/R/dynRB_Pnc.R |only dynRB-0.2/dynRB/R/dynRB_VPa.R |only dynRB-0.2/dynRB/R/dynRB_VPac.R |only dynRB-0.2/dynRB/R/dynRB_Vn.R |only dynRB-0.2/dynRB/R/dynRB_Vnc.R |only dynRB-0.2/dynRB/man/dynRB-package.Rd | 7 ++++--- dynRB-0.2/dynRB/man/dynRB_Pn.Rd |only dynRB-0.2/dynRB/man/dynRB_Pnc.Rd |only dynRB-0.2/dynRB/man/dynRB_VPa.Rd |only dynRB-0.2/dynRB/man/dynRB_VPac.Rd |only dynRB-0.2/dynRB/man/dynRB_Vn.Rd |only dynRB-0.2/dynRB/man/dynRB_Vnc.Rd |only 27 files changed, 21 insertions(+), 20 deletions(-)
Title: Node Harvest for Regression and Classification
Description: Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between nodeHarvest versions 0.6 dated 2013-11-28 and 0.7-1 dated 2015-05-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/nodeHarvest.R | 24 ++++++++++++++---------- 3 files changed, 21 insertions(+), 17 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 0.8.2 dated 2014-05-12 and 1.0.0 dated 2015-05-15
VSURF-0.8.2/VSURF/R/VSURF.interp.R |only VSURF-0.8.2/VSURF/R/VSURF.pred.R |only VSURF-0.8.2/VSURF/R/VSURF.thres.R |only VSURF-0.8.2/VSURF/man/VSURF.interp.Rd |only VSURF-0.8.2/VSURF/man/VSURF.pred.Rd |only VSURF-0.8.2/VSURF/man/VSURF.thres.Rd |only VSURF-1.0.0/VSURF/DESCRIPTION | 22 +- VSURF-1.0.0/VSURF/MD5 | 44 ++-- VSURF-1.0.0/VSURF/NAMESPACE | 64 +++--- VSURF-1.0.0/VSURF/NEWS | 31 ++- VSURF-1.0.0/VSURF/R/VSURF.R | 265 +++++++++----------------- VSURF-1.0.0/VSURF/R/VSURF_interp.R |only VSURF-1.0.0/VSURF/R/VSURF_pred.R |only VSURF-1.0.0/VSURF/R/VSURF_thres.R |only VSURF-1.0.0/VSURF/R/plot.VSURF.R | 332 ++++++++++++++++----------------- VSURF-1.0.0/VSURF/R/predict.VSURF.R |only VSURF-1.0.0/VSURF/R/print.VSURF.R | 7 VSURF-1.0.0/VSURF/R/summary.VSURF.R | 11 - VSURF-1.0.0/VSURF/R/toys.R | 4 VSURF-1.0.0/VSURF/R/tune.R | 113 +++++------ VSURF-1.0.0/VSURF/man/VSURF.Rd | 108 ++++++---- VSURF-1.0.0/VSURF/man/VSURF_interp.Rd |only VSURF-1.0.0/VSURF/man/VSURF_pred.Rd |only VSURF-1.0.0/VSURF/man/VSURF_thres.Rd |only VSURF-1.0.0/VSURF/man/plot.VSURF.Rd | 89 +++++--- VSURF-1.0.0/VSURF/man/predict.VSURF.Rd |only VSURF-1.0.0/VSURF/man/print.VSURF.Rd | 7 VSURF-1.0.0/VSURF/man/summary.VSURF.Rd | 11 - VSURF-1.0.0/VSURF/man/toys.Rd | 7 VSURF-1.0.0/VSURF/man/tune.Rd | 43 ++-- 30 files changed, 568 insertions(+), 590 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.10 dated 2015-03-21 and 0.99.11 dated 2015-05-15
DescTools-0.99.10/DescTools/R/PlotFct.R |only DescTools-0.99.10/DescTools/R/Rev.data.frame.R |only DescTools-0.99.10/DescTools/R/SaveAs.R |only DescTools-0.99.10/DescTools/R/fastPOSIXct.R |only DescTools-0.99.10/DescTools/man/PlotFct.Rd |only DescTools-0.99.10/DescTools/man/SaveAs.Rd |only DescTools-0.99.10/DescTools/man/fastPOSIXct.Rd |only DescTools-0.99.10/DescTools/src/tparse.c |only DescTools-0.99.11/DescTools/DESCRIPTION | 16 DescTools-0.99.11/DescTools/MD5 | 257 +++--- DescTools-0.99.11/DescTools/NAMESPACE | 25 DescTools-0.99.11/DescTools/NEWS | 49 + DescTools-0.99.11/DescTools/R/AddMonths.R | 2 DescTools-0.99.11/DescTools/R/Agree.R | 18 DescTools-0.99.11/DescTools/R/Atkinson.R | 2 DescTools-0.99.11/DescTools/R/BoxCoxLambda.R | 2 DescTools-0.99.11/DescTools/R/ChooseColorDlg.R | 5 DescTools-0.99.11/DescTools/R/CohenD.R | 12 DescTools-0.99.11/DescTools/R/CohenKappa.R | 2 DescTools-0.99.11/DescTools/R/ColorLegend.R | 6 DescTools-0.99.11/DescTools/R/Conf.R |only DescTools-0.99.11/DescTools/R/Conf.default.R |only DescTools-0.99.11/DescTools/R/Conf.glm.R |only DescTools-0.99.11/DescTools/R/Conf.matrix.R |only DescTools-0.99.11/DescTools/R/Conf.multinom.R |only DescTools-0.99.11/DescTools/R/Conf.randomForest.R |only DescTools-0.99.11/DescTools/R/Conf.regr.R |only DescTools-0.99.11/DescTools/R/Conf.rpart.R |only DescTools-0.99.11/DescTools/R/Conf.svm.R |only DescTools-0.99.11/DescTools/R/Conf.table.R |only DescTools-0.99.11/DescTools/R/CorPolychor.R |only DescTools-0.99.11/DescTools/R/Desc.table.R | 21 DescTools-0.99.11/DescTools/R/DescTools-internal.R | 489 ++++++++---- DescTools-0.99.11/DescTools/R/DescWrd.default.R | 4 DescTools-0.99.11/DescTools/R/DunnTest.default.R | 1 DescTools-0.99.11/DescTools/R/Format.default.R | 54 + DescTools-0.99.11/DescTools/R/Freq.R | 74 - DescTools-0.99.11/DescTools/R/GTest.R |only DescTools-0.99.11/DescTools/R/Gini.R | 2 DescTools-0.99.11/DescTools/R/Herfindahl.R | 2 DescTools-0.99.11/DescTools/R/HodgesLehmann.R | 3 DescTools-0.99.11/DescTools/R/HuberM.R | 190 ++-- DescTools-0.99.11/DescTools/R/ImportDlg.R | 4 DescTools-0.99.11/DescTools/R/ImportFileDlg.R |only DescTools-0.99.11/DescTools/R/KendallTauB.R | 53 + DescTools-0.99.11/DescTools/R/Kurt.R | 4 DescTools-0.99.11/DescTools/R/Lc.default.R | 2 DescTools-0.99.11/DescTools/R/MarginTable.R | 2 DescTools-0.99.11/DescTools/R/MoveAvg.R | 31 DescTools-0.99.11/DescTools/R/NemenyiTest.R |only DescTools-0.99.11/DescTools/R/NemenyiTest.default.R |only DescTools-0.99.11/DescTools/R/NemenyiTest.formula.R |only DescTools-0.99.11/DescTools/R/OrderMixed.R | 1 DescTools-0.99.11/DescTools/R/ParseSASDatalines.R | 21 DescTools-0.99.11/DescTools/R/PasswordDlg.R | 70 - DescTools-0.99.11/DescTools/R/PercTable.table.R | 7 DescTools-0.99.11/DescTools/R/PlotCirc.R | 6 DescTools-0.99.11/DescTools/R/PlotDesc.Date.R | 6 DescTools-0.99.11/DescTools/R/PlotDesc.matrix.R |only DescTools-0.99.11/DescTools/R/PlotDot.R |only DescTools-0.99.11/DescTools/R/PlotFaces.R | 45 - DescTools-0.99.11/DescTools/R/PlotFun.R |only DescTools-0.99.11/DescTools/R/PlotLinesA.R |only DescTools-0.99.11/DescTools/R/PlotPar.R | 11 DescTools-0.99.11/DescTools/R/PlotRCol.R | 5 DescTools-0.99.11/DescTools/R/PostHocTest.matrix.R | 16 DescTools-0.99.11/DescTools/R/Rev.matrix.R | 9 DescTools-0.99.11/DescTools/R/Rev.table.R | 14 DescTools-0.99.11/DescTools/R/Rosenbluth.R | 2 DescTools-0.99.11/DescTools/R/SampleTwins.R | 8 DescTools-0.99.11/DescTools/R/SaveAsDlg.R |only DescTools-0.99.11/DescTools/R/Sens.R |only DescTools-0.99.11/DescTools/R/Skew.R | 4 DescTools-0.99.11/DescTools/R/Spec.R |only DescTools-0.99.11/DescTools/R/SplitPath.R |only DescTools-0.99.11/DescTools/R/Stamp.R | 4 DescTools-0.99.11/DescTools/R/StrChop.R | 1 DescTools-0.99.11/DescTools/R/Strata.R | 289 +------ DescTools-0.99.11/DescTools/R/ToLong.R | 3 DescTools-0.99.11/DescTools/R/TukeyBiweight.R | 2 DescTools-0.99.11/DescTools/R/WrdTable.ftable.R |only DescTools-0.99.11/DescTools/R/as.matrix.xtabs.R |only DescTools-0.99.11/DescTools/R/plot.Conf.R |only DescTools-0.99.11/DescTools/R/power.chisq.test.R |only DescTools-0.99.11/DescTools/R/print.Conf.R |only DescTools-0.99.11/DescTools/R/print.CorPolychor.R |only DescTools-0.99.11/DescTools/R/print.DunnTest.R | 2 DescTools-0.99.11/DescTools/R/print.Freq.R | 5 DescTools-0.99.11/DescTools/build/vignette.rds |binary DescTools-0.99.11/DescTools/data/day.abb.rda |binary DescTools-0.99.11/DescTools/data/day.name.rda |binary DescTools-0.99.11/DescTools/data/hblue.rda |binary DescTools-0.99.11/DescTools/data/hecru.rda |binary DescTools-0.99.11/DescTools/data/hgreen.rda |binary DescTools-0.99.11/DescTools/data/horange.rda |binary DescTools-0.99.11/DescTools/data/hred.rda |binary DescTools-0.99.11/DescTools/data/hyellow.rda |binary DescTools-0.99.11/DescTools/data/wdConst.rda |binary DescTools-0.99.11/DescTools/inst/CITATION | 1 DescTools-0.99.11/DescTools/inst/doc/DescTools.pdf |binary DescTools-0.99.11/DescTools/inst/doc/DescToolsCompanion.pdf |binary DescTools-0.99.11/DescTools/inst/extdata/R.ico |only DescTools-0.99.11/DescTools/man/AddMonths.Rd | 4 DescTools-0.99.11/DescTools/man/Agree.Rd | 7 DescTools-0.99.11/DescTools/man/AllDuplicated.Rd | 9 DescTools-0.99.11/DescTools/man/Between.Rd | 4 DescTools-0.99.11/DescTools/man/BreslowDayTest.Rd | 22 DescTools-0.99.11/DescTools/man/CoefVar.Rd | 3 DescTools-0.99.11/DescTools/man/CohenD.Rd | 4 DescTools-0.99.11/DescTools/man/CohenKappa.Rd | 7 DescTools-0.99.11/DescTools/man/ColorLegend.Rd | 4 DescTools-0.99.11/DescTools/man/Conf.Rd |only DescTools-0.99.11/DescTools/man/CorPolychor.Rd |only DescTools-0.99.11/DescTools/man/Desc.table.Rd | 8 DescTools-0.99.11/DescTools/man/DescTools-package.Rd | 46 - DescTools-0.99.11/DescTools/man/ErrBars.Rd | 13 DescTools-0.99.11/DescTools/man/Explore.Rd | 4 DescTools-0.99.11/DescTools/man/FindColor.Rd | 45 - DescTools-0.99.11/DescTools/man/FisherZ.Rd | 2 DescTools-0.99.11/DescTools/man/Format.Rd | 9 DescTools-0.99.11/DescTools/man/Freq.Rd | 26 DescTools-0.99.11/DescTools/man/GTest.Rd |only DescTools-0.99.11/DescTools/man/GetNewWrd.Rd | 5 DescTools-0.99.11/DescTools/man/Gini.Rd | 45 - DescTools-0.99.11/DescTools/man/HuberM.Rd | 88 -- DescTools-0.99.11/DescTools/man/ImportFileDlg.Rd |only DescTools-0.99.11/DescTools/man/Lambda.Rd | 5 DescTools-0.99.11/DescTools/man/Logit.Rd | 112 +- DescTools-0.99.11/DescTools/man/MeanAD.Rd | 4 DescTools-0.99.11/DescTools/man/MoveAvg.Rd | 44 - DescTools-0.99.11/DescTools/man/NemenyiTest.Rd |only DescTools-0.99.11/DescTools/man/OddsRatio.Rd | 41 - DescTools-0.99.11/DescTools/man/ParseSASDatalines.Rd | 36 DescTools-0.99.11/DescTools/man/PlotACF.Rd | 4 DescTools-0.99.11/DescTools/man/PlotDesc.Rd | 4 DescTools-0.99.11/DescTools/man/PlotDot.Rd |only DescTools-0.99.11/DescTools/man/PlotFaces.Rd | 4 DescTools-0.99.11/DescTools/man/PlotFun.Rd |only DescTools-0.99.11/DescTools/man/PlotLinesA.Rd |only DescTools-0.99.11/DescTools/man/Rev.Rd | 26 DescTools-0.99.11/DescTools/man/SampleTwins.Rd | 6 DescTools-0.99.11/DescTools/man/SaveAsDlg.Rd |only DescTools-0.99.11/DescTools/man/Skew.Rd | 43 - DescTools-0.99.11/DescTools/man/SplitPath.Rd |only DescTools-0.99.11/DescTools/man/Stamp.Rd | 3 DescTools-0.99.11/DescTools/man/StrRight.Rd | 2 DescTools-0.99.11/DescTools/man/StrTrunc.Rd | 4 DescTools-0.99.11/DescTools/man/Strata.Rd | 31 DescTools-0.99.11/DescTools/man/StuartMaxwellTest.Rd | 6 DescTools-0.99.11/DescTools/man/StuartTauC.Rd | 14 DescTools-0.99.11/DescTools/man/ToWide.Rd | 2 DescTools-0.99.11/DescTools/man/VarCI.Rd | 3 DescTools-0.99.11/DescTools/man/WrdTable.Rd | 3 DescTools-0.99.11/DescTools/man/as.matrix.Rd |only DescTools-0.99.11/DescTools/man/power.chisq.test.Rd |only 155 files changed, 1486 insertions(+), 1130 deletions(-)
Title: Fishery Stock Assessment by Generalized Depletion Models
Description: Based on fishery Catch Dynamics instead of fish Population Dynamics (hence CatDyn) and using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean fish body weight by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 77 types of models of increasing complexity, and 56 likelihood models for the data.
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta <ruben.roa.ureta@mail.com>
Diff between CatDyn versions 1.0-6 dated 2015-01-18 and 1.1-0 dated 2015-05-15
CatDyn-1.0-6/CatDyn/inst |only CatDyn-1.1-0/CatDyn/DESCRIPTION | 10 CatDyn-1.1-0/CatDyn/MD5 | 47 CatDyn-1.1-0/CatDyn/R/CatDyn-internal.R |74133 +----------------------------- CatDyn-1.1-0/CatDyn/R/CatDynFit.R |24905 ++-------- CatDyn-1.1-0/CatDyn/R/CatDynPred.R | 640 CatDyn-1.1-0/CatDyn/R/CatDynSum.R | 187 CatDyn-1.1-0/CatDyn/R/catdynexp_1.R | 3776 - CatDyn-1.1-0/CatDyn/R/plot.CatDynExp.R | 6 CatDyn-1.1-0/CatDyn/R/plot.CatDynMod.R | 6 CatDyn-1.1-0/CatDyn/data/gayhake.rda |binary CatDyn-1.1-0/CatDyn/data/lolgahi.rda |binary CatDyn-1.1-0/CatDyn/data/twelver.rda |binary CatDyn-1.1-0/CatDyn/man/CatDyn-package.Rd | 47 CatDyn-1.1-0/CatDyn/man/CatDynCor.Rd | 13 CatDyn-1.1-0/CatDyn/man/CatDynExp.Rd | 3 CatDyn-1.1-0/CatDyn/man/CatDynFit.Rd | 347 CatDyn-1.1-0/CatDyn/man/CatDynPred.Rd | 16 CatDyn-1.1-0/CatDyn/man/CatDynSum.Rd | 15 CatDyn-1.1-0/CatDyn/man/as.CatDynData.Rd | 88 CatDyn-1.1-0/CatDyn/man/catdyn.Rd | 2 CatDyn-1.1-0/CatDyn/man/catdynexp_1.Rd | 61 CatDyn-1.1-0/CatDyn/man/deltamethod.Rd | 20 CatDyn-1.1-0/CatDyn/man/plot.CatDynExp.Rd | 15 CatDyn-1.1-0/CatDyn/man/plot.CatDynMod.Rd | 24 25 files changed, 11897 insertions(+), 92464 deletions(-)
Title: Robust Structural Equation Modeling with Missing Data and
Auxiliary Variables
Description: A robust procedure is implemented to estimate means and covariance matrix of multiple variables with missing data using Huber weight and then to estimate a structural equation model.
Author: Ke-Hai Yuan and Zhiyong Zhang
Maintainer: Zhiyong Zhang <zhiyongzhang@nd.edu>
Diff between rsem versions 0.4.5 dated 2013-07-17 and 0.4.6 dated 2015-05-15
DESCRIPTION | 10 ++++---- MD5 | 8 ++++-- NAMESPACE | 4 ++- R/lav_fun.R |only R/rsem.R | 62 +++++++++++++++++++++++++++++++++++++++++------------ man/rsem.lavaan.Rd |only 6 files changed, 61 insertions(+), 23 deletions(-)
Title: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund [aut],
Long Qu [aut, cre, ctb],
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between QuasiSeq versions 1.0-7 dated 2015-05-13 and 1.0-8 dated 2015-05-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/Makevars | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from PSID
delivered raw data. Deals with data downloaded and pre-processed by Stata or SAS,
or can optionally download directly from the PSID server using the SAScii package.
`psidR` takes care of merging data from each wave onto a cross-period index file,
so that individuals can be followed over time. The user must specify which years
they are interested in, and the PSID variable names (e.g. ER21003) for each year
(they differ in each year). There are different panel data designs and
sample subsetting criteria implemented ("SRC", "SEO", "immigrant" and "latino"
samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>
Diff between psidR versions 1.2 dated 2013-09-10 and 1.3 dated 2015-05-15
DESCRIPTION | 19 +-- MD5 | 25 ++-- NAMESPACE | 5 NEWS | 14 ++ R/build.panel.r | 275 ++++++++++++++++++++++++++++------------------------- R/makeids.r | 93 +++++++++++++++++ R/psidR-package.r | 4 man/build.panel.Rd | 188 +++++++++++------------------------- man/get.psid.Rd | 17 +-- man/make.char.Rd | 11 +- man/makeids.Rd | 14 -- man/psidR.Rd | 17 +-- man/testPSID.Rd |only tests |only 14 files changed, 375 insertions(+), 307 deletions(-)
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using LDA,
Lr or PDA projection pursuit index.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PPtreeViz versions 1.0.1 dated 2015-05-08 and 1.0.3 dated 2015-05-15
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- R/LDAopt.R | 15 ++++------ R/PDAopt.R | 20 +++++-------- R/PPclassNodeViz.R | 72 +++++++++++++++++++++++++++++++------------------ R/PPclassify.R | 8 ++--- R/PPoptViz.R | 57 ++++++++++++++++++++++++-------------- R/PPtreeClass.R | 2 - R/plotPPtreeclass.R | 7 +--- R/printPPtreeclass.R | 18 ++++-------- man/PP.classify.Rd | 5 +-- man/PPclassNode.Viz.Rd | 8 +++-- man/PPopt.Viz.Rd | 2 - src/PPoptimize.cpp | 16 ++++------ 14 files changed, 141 insertions(+), 123 deletions(-)
Title: Obtain Alpha-Outlier Regions for Well-Known Probability
Distributions
Description: Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, doi: 10.1080/01621459.1993.10476339 for details.
Author: Andre Rehage, Sonja Kuhnt
Maintainer: Andre Rehage <rehage@statistik.tu-dortmund.de>
Diff between alphaOutlier versions 1.0.0 dated 2015-05-07 and 1.0.1 dated 2015-05-15
DESCRIPTION | 8 +++--- MD5 | 60 ++++++++++++++++++++++++++-------------------------- NEWS | 11 +++++++-- R/aout.binom.R | 6 ++--- R/aout.cg.R | 21 ++++++------------ R/aout.chisq.R | 6 ++--- R/aout.conttab.R | 30 ++++++++++++++------------ R/aout.exp.R | 8 +++--- R/aout.gandh.R | 6 ++--- R/aout.hyper.R | 6 ++--- R/aout.laplace.R | 6 ++--- R/aout.logis.R | 6 ++--- R/aout.mvnorm.R | 6 ++--- R/aout.nbinom.R | 6 ++--- R/aout.norm.R | 6 ++--- R/aout.pareto.R | 6 ++--- R/aout.pois.R | 6 ++--- R/aout.weibull.R | 8 +++--- man/aout.cg.Rd | 2 - man/aout.chisq.Rd | 2 - man/aout.conttab.Rd | 2 - man/aout.exp.Rd | 4 +-- man/aout.gandh.Rd | 2 - man/aout.hyper.Rd | 2 - man/aout.laplace.Rd | 2 - man/aout.mvnorm.Rd | 2 - man/aout.nbinom.Rd | 2 - man/aout.norm.Rd | 2 - man/aout.pareto.Rd | 2 - man/aout.pois.Rd | 2 - man/aout.weibull.Rd | 2 - 31 files changed, 123 insertions(+), 117 deletions(-)
Title: Advanced Data Analysis of T Cell Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 1.3 dated 2015-03-21 and 2.0 dated 2015-05-14
tcR-1.3/tcR/inst/doc/tcrvignette.Rnw |only tcR-1.3/tcR/inst/doc/tcrvignette.pdf |only tcR-1.3/tcR/man/freq.segments.Rd |only tcR-1.3/tcR/man/intersect.Rd |only tcR-1.3/tcR/man/mitcr.stats.Rd |only tcR-1.3/tcR/man/vis.V.usage.Rd |only tcR-1.3/tcR/vignettes/tcrvignette.Rnw |only tcR-2.0/tcR/DESCRIPTION | 16 - tcR-2.0/tcR/MD5 | 208 +++++++------ tcR-2.0/tcR/NAMESPACE | 4 tcR-2.0/tcR/R/crosses.R | 57 +-- tcR-2.0/tcR/R/dataproc.R | 38 +- tcR-2.0/tcR/R/datatools.R | 71 ++++ tcR-2.0/tcR/R/diversity.R | 20 - tcR-2.0/tcR/R/docdata.R | 50 +-- tcR-2.0/tcR/R/filters.R | 2 tcR-2.0/tcR/R/graph.R | 63 +++- tcR-2.0/tcR/R/infoanalysis.R | 71 ++-- tcR-2.0/tcR/R/input.R | 26 - tcR-2.0/tcR/R/kmers.R | 14 tcR-2.0/tcR/R/measures.R | 47 +-- tcR-2.0/tcR/R/plots.R | 230 ++++++--------- tcR-2.0/tcR/R/repdiversity.R |only tcR-2.0/tcR/R/repoverlap.R |only tcR-2.0/tcR/R/segments.R | 249 ++++++++-------- tcR-2.0/tcR/R/shared.R | 81 +++-- tcR-2.0/tcR/R/spectrum.R | 26 - tcR-2.0/tcR/R/stats.R | 84 ++--- tcR-2.0/tcR/R/strtools.R | 18 - tcR-2.0/tcR/build/vignette.rds |binary tcR-2.0/tcR/data/twa.rda |binary tcR-2.0/tcR/data/twb.rda |binary tcR-2.0/tcR/inst/crossanalysis.report.Rmd | 39 +- tcR-2.0/tcR/inst/doc/tcrvignette.R | 417 ++++++++++++---------------- tcR-2.0/tcR/inst/doc/tcrvignette.Rmd |only tcR-2.0/tcR/inst/doc/tcrvignette.html |only tcR-2.0/tcR/inst/library.report.Rmd | 21 - tcR-2.0/tcR/man/AA_TABLE.Rd | 2 tcR-2.0/tcR/man/apply.symm.Rd | 7 tcR-2.0/tcR/man/assymetry.Rd | 2 tcR-2.0/tcR/man/barcodes.to.reads.Rd | 6 tcR-2.0/tcR/man/beta.prob.Rd | 2 tcR-2.0/tcR/man/bootstrap.tcr.Rd | 6 tcR-2.0/tcR/man/check.distribution.Rd | 13 tcR-2.0/tcR/man/clonal.space.homeostasis.Rd | 2 tcR-2.0/tcR/man/cloneset.stats.Rd |only tcR-2.0/tcR/man/codon.variants.Rd | 2 tcR-2.0/tcR/man/column.summary.Rd | 8 tcR-2.0/tcR/man/contamination.stats.Rd | 4 tcR-2.0/tcR/man/convergence.index.Rd | 2 tcR-2.0/tcR/man/cosine.sharing.Rd | 4 tcR-2.0/tcR/man/cosine.similarity.Rd | 22 + tcR-2.0/tcR/man/entropy.Rd | 12 tcR-2.0/tcR/man/entropy.seg.Rd | 36 +- tcR-2.0/tcR/man/find.clonotypes.Rd | 8 tcR-2.0/tcR/man/find.similar.sequences.Rd | 4 tcR-2.0/tcR/man/gc.content.Rd | 2 tcR-2.0/tcR/man/geneUsage.Rd |only tcR-2.0/tcR/man/generate.kmers.Rd | 2 tcR-2.0/tcR/man/generate.tcr.Rd | 2 tcR-2.0/tcR/man/get.all.substrings.Rd | 4 tcR-2.0/tcR/man/get.deletions.alpha.Rd | 2 tcR-2.0/tcR/man/get.inframes.Rd | 4 tcR-2.0/tcR/man/get.kmers.Rd | 6 tcR-2.0/tcR/man/get.n.barcodes.Rd | 6 tcR-2.0/tcR/man/gibbs.sampler.Rd | 6 tcR-2.0/tcR/man/group.clonotypes.Rd | 4 tcR-2.0/tcR/man/has.class.Rd | 2 tcR-2.0/tcR/man/intersectClonesets.Rd |only tcR-2.0/tcR/man/inverse.simpson.Rd | 10 tcR-2.0/tcR/man/kmer.profile.Rd | 4 tcR-2.0/tcR/man/kmer.table.Rd | 2 tcR-2.0/tcR/man/loglikelihood.Rd | 2 tcR-2.0/tcR/man/matrixdiagcopy.Rd | 2 tcR-2.0/tcR/man/mutated.neighbours.Rd | 2 tcR-2.0/tcR/man/mutation.network.Rd | 4 tcR-2.0/tcR/man/parse.cloneset.Rd | 4 tcR-2.0/tcR/man/parse.folder.Rd | 12 tcR-2.0/tcR/man/pca.segments.Rd | 12 tcR-2.0/tcR/man/permutedf.Rd | 2 tcR-2.0/tcR/man/rarefaction.Rd | 8 tcR-2.0/tcR/man/repDiversity.Rd |only tcR-2.0/tcR/man/repOverlap.Rd |only tcR-2.0/tcR/man/revcomp.Rd | 4 tcR-2.0/tcR/man/reverse.string.Rd | 2 tcR-2.0/tcR/man/sample.clones.Rd | 4 tcR-2.0/tcR/man/sample2D.Rd | 2 tcR-2.0/tcR/man/segments.alphabets.Rd | 50 +-- tcR-2.0/tcR/man/segments.list.Rd | 2 tcR-2.0/tcR/man/set.group.vector.Rd | 4 tcR-2.0/tcR/man/set.pb.Rd | 2 tcR-2.0/tcR/man/set.people.vector.Rd | 2 tcR-2.0/tcR/man/set.rank.Rd | 2 tcR-2.0/tcR/man/shared.repertoire.Rd | 29 + tcR-2.0/tcR/man/spectratyping.Rd | 12 tcR-2.0/tcR/man/startmitcr.Rd | 2 tcR-2.0/tcR/man/tailbound.proportion.Rd | 2 tcR-2.0/tcR/man/top.cross.Rd | 18 - tcR-2.0/tcR/man/top.fun.Rd | 4 tcR-2.0/tcR/man/twinsdata.Rd | 2 tcR-2.0/tcR/man/vis.clonal.dynamics.Rd | 4 tcR-2.0/tcR/man/vis.clonal.space.Rd | 6 tcR-2.0/tcR/man/vis.count.len.Rd | 6 tcR-2.0/tcR/man/vis.gene.usage.Rd |only tcR-2.0/tcR/man/vis.group.boxplot.Rd | 6 tcR-2.0/tcR/man/vis.heatmap.Rd | 14 tcR-2.0/tcR/man/vis.kmer.histogram.Rd | 2 tcR-2.0/tcR/man/vis.logo.Rd | 4 tcR-2.0/tcR/man/vis.number.count.Rd | 8 tcR-2.0/tcR/man/vis.pca.Rd | 2 tcR-2.0/tcR/man/vis.radarlike.Rd | 4 tcR-2.0/tcR/man/vis.rarefaction.Rd | 4 tcR-2.0/tcR/man/vis.top.proportions.Rd | 2 tcR-2.0/tcR/vignettes/tcrvignette.Rmd |only 114 files changed, 1193 insertions(+), 1110 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-5 dated 2015-03-26 and 0.1-6 dated 2015-05-14
Surrogate-0.1-5/Surrogate/R/summ.ICA.By.Mon.R |only Surrogate-0.1-5/Surrogate/man/summ.ICA.By.Mon.Rd |only Surrogate-0.1-6/Surrogate/DESCRIPTION | 8 Surrogate-0.1-6/Surrogate/MD5 | 72 Surrogate-0.1-6/Surrogate/NEWS | 6 Surrogate-0.1-6/Surrogate/R/CausalDiagramBinBin.R | 4 Surrogate-0.1-6/Surrogate/R/ICA.BinBin.Grid.Sample.R | 2 Surrogate-0.1-6/Surrogate/R/ICABinBinCounterAssum.R | 14 Surrogate-0.1-6/Surrogate/R/MarginalProbs.R | 7 Surrogate-0.1-6/Surrogate/R/SimDataSTSBinBin.R | 6 Surrogate-0.1-6/Surrogate/R/Test.Mono.R |only Surrogate-0.1-6/Surrogate/R/plot_ICABinBin.R | 1327 +++++++++++-- Surrogate-0.1-6/Surrogate/R/plot_SPPBinBin.R | 2 Surrogate-0.1-6/Surrogate/R/summary_ICABinBin.R | 111 + Surrogate-0.1-6/Surrogate/man/BifixedContCont.Rd | 2 Surrogate-0.1-6/Surrogate/man/BimixedContCont.Rd | 20 Surrogate-0.1-6/Surrogate/man/CausalDiagramBinBin.Rd | 30 Surrogate-0.1-6/Surrogate/man/CausalDiagramContCont.Rd | 5 Surrogate-0.1-6/Surrogate/man/FixedContContIT.Rd | 3 Surrogate-0.1-6/Surrogate/man/ICA.BinBin.Grid.Full.Rd | 6 Surrogate-0.1-6/Surrogate/man/ICA.BinBin.Grid.Sample.Rd | 6 Surrogate-0.1-6/Surrogate/man/ICA.Sample.ContCont.Rd | 5 Surrogate-0.1-6/Surrogate/man/ICABinBin.Rd | 8 Surrogate-0.1-6/Surrogate/man/ICABinBinCounterAssum.Rd | 45 Surrogate-0.1-6/Surrogate/man/ICAContCont.Rd | 14 Surrogate-0.1-6/Surrogate/man/MICA.Sample.ContCont.Rd | 11 Surrogate-0.1-6/Surrogate/man/MICAContCont.Rd | 13 Surrogate-0.1-6/Surrogate/man/MixedContContIT.Rd | 6 Surrogate-0.1-6/Surrogate/man/SPP.BinBin.Rd | 10 Surrogate-0.1-6/Surrogate/man/Single.Trial.RE.AA.Rd | 3 Surrogate-0.1-6/Surrogate/man/Test.Mono.Rd |only Surrogate-0.1-6/Surrogate/man/UnifixedContCont.Rd | 2 Surrogate-0.1-6/Surrogate/man/UnimixedContCont.Rd | 2 Surrogate-0.1-6/Surrogate/man/plot.CausalInference.Rd | 15 Surrogate-0.1-6/Surrogate/man/plot.ICABinBin.Rd | 29 Surrogate-0.1-6/Surrogate/man/plot.InformationTheoretic.Rd | 18 Surrogate-0.1-6/Surrogate/man/plot.MetaAnalytic.Rd | 22 Surrogate-0.1-6/Surrogate/man/plot.MinSurrContCont.Rd | 9 Surrogate-0.1-6/Surrogate/man/plot.SPPBinBin.Rd | 7 39 files changed, 1511 insertions(+), 339 deletions(-)
Title: Measures of Risk for the Compound Poisson Risk Process with
Diffusion
Description: The main purpose of this package is to provide saddlepoint
approximations to some measures of risk, based on the compound Poisson risk
process that is perturbed by a Brownian motion. Various approximation
methods for the probability of ruin are also included. Furthermore, exact
values of both the risk measures as well as the probability of ruin are
available if the individual claims follow a hypo-exponential distribution
(i. e., if it can be represented as a sum of independent exponentially
distributed random variables with different rate parameters).
Author: Benjamin Baumgartner [aut, cre],
Riccardo Gatto [ctb, ths],
Sebastian Szugat [ctb]
Maintainer: Benjamin Baumgartner <benjamin@baumgrt.com>
Diff between sdprisk versions 1.1-0 dated 2015-04-29 and 1.1-3 dated 2015-05-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + man/hypoexp.Rd | 13 ++++++++----- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Probability Models for Ranking Data
Description: Descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce models, distance-based models, and rank-ordered logit models) and visualization with multidimensional preference analysis for ranking data are provided. Current, only complete rankings are supported by this package.
Author: Paul H. Lee and Philip L. H. Yu
Maintainer: Paul H. Lee <honglee@graduate.hku.hk>
Diff between pmr versions 1.2.4 dated 2014-05-17 and 1.2.5 dated 2015-05-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/rankplot.R | 40 ++++++++++++++++++++-------------------- R/rol.R | 2 +- man/pmr-package.Rd | 8 ++++---- 5 files changed, 33 insertions(+), 33 deletions(-)
Title: Functions for Optimal Non-Bipartite Matching
Description: Perform non-bipartite matching and matched randomization. A
"bipartite" matching utilizes two separate groups, e.g. smokers being
matched to nonsmokers or cases being matched to controls. A "non-bipartite"
matching creates mates from one big group, e.g. 100 hospitals being
randomized for a two-arm cluster randomized trial or 5000 children who
have been exposed to various levels of secondhand smoke and are being
paired to form a greater exposure vs. lesser exposure comparison. At the
core of a non-bipartite matching is a N x N distance matrix for N potential
mates. The distance between two units expresses a measure of similarity or
quality as mates (the lower the better). The 'gendistance()' and
'distancematrix()' functions assist in creating this. The 'nonbimatch()'
function creates the matching that minimizes the total sum of distances
between mates; hence, it is referred to as an "optimal" matching. The
'assign.grp()' function aids in performing a matched randomization. Note
bipartite matching can be performed using the prevent option in
'gendistance()'.
Author: Cole Beck [aut, cre], Bo Lu [aut], Robert Greevy [aut]
Maintainer: Cole Beck <cole.beck@vanderbilt.edu>
Diff between nbpMatching versions 1.4.4 dated 2015-01-20 and 1.4.5 dated 2015-05-14
DESCRIPTION | 47 ++++++++++++++++------------------- MD5 | 36 +++++++++++++------------- NAMESPACE | 2 - R/nonbimatch.R | 2 + man/assign.grp.Rd | 3 +- man/distancematrix.Rd | 3 +- man/fill.missing.Rd | 3 +- man/gendistance.Rd | 3 +- man/get.sets.Rd | 3 +- man/make.phantoms.Rd | 3 +- man/nbpMatching-internal.Rd | 3 +- man/nbpMatching-package.Rd | 3 +- man/nonbimatch.Rd | 3 +- man/qom.Rd | 3 +- man/quantile.Rd | 3 +- man/scalar.dist.Rd | 3 +- tests/testthat/test-distancematrix.R | 1 tests/testthat/test-gendistance.R | 10 +++++++ tests/testthat/test-nonbimatch.R | 1 19 files changed, 79 insertions(+), 56 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.1 dated 2014-10-13 and 1.2 dated 2015-05-14
Anthropometry-1.1/Anthropometry/R/Anthropometry-internalDepth.R |only Anthropometry-1.1/Anthropometry/R/Anthropometry-internalHIPAM.R |only Anthropometry-1.1/Anthropometry/R/GetDistMatrix.R |only Anthropometry-1.1/Anthropometry/R/WeightsMixtureUB.R |only Anthropometry-1.1/Anthropometry/R/accommodation.R |only Anthropometry-1.1/Anthropometry/R/cdfDiss.R |only Anthropometry-1.1/Anthropometry/R/compPerc.R |only Anthropometry-1.1/Anthropometry/R/hipamBigGroups.R |only Anthropometry-1.1/Anthropometry/R/indivNearest.R |only Anthropometry-1.1/Anthropometry/R/optraProcrustes.R |only Anthropometry-1.1/Anthropometry/R/outlierHipam.R |only Anthropometry-1.1/Anthropometry/R/overlappingRows.R |only Anthropometry-1.1/Anthropometry/R/plotMedoids.R |only Anthropometry-1.1/Anthropometry/R/plotTreeHipam.R |only Anthropometry-1.1/Anthropometry/R/qtranProcrustes.R |only Anthropometry-1.1/Anthropometry/R/screeArchetyp.R |only Anthropometry-1.1/Anthropometry/R/shapes3dMod.R |only Anthropometry-1.1/Anthropometry/R/skeletonsArchet.R |only Anthropometry-1.1/Anthropometry/R/xyplotPCA.R |only Anthropometry-1.1/Anthropometry/data/cMDSwomen.RData |only Anthropometry-1.1/Anthropometry/data/cube34.RData |only Anthropometry-1.1/Anthropometry/data/cube8.RData |only Anthropometry-1.1/Anthropometry/data/dataDemo.RData |only Anthropometry-1.1/Anthropometry/data/dataUSAF.RData |only Anthropometry-1.1/Anthropometry/data/landmarks.RData |only Anthropometry-1.1/Anthropometry/data/parallelepiped34.RData |only Anthropometry-1.1/Anthropometry/data/parallelepiped8.RData |only Anthropometry-1.1/Anthropometry/man/Anthropometry-internalDepth.Rd |only Anthropometry-1.1/Anthropometry/man/Anthropometry-internalHIPAM.Rd |only Anthropometry-1.1/Anthropometry/man/GetDistMatrix.Rd |only Anthropometry-1.1/Anthropometry/man/WeightsMixtureUB.Rd |only Anthropometry-1.1/Anthropometry/man/accommodation.Rd |only Anthropometry-1.1/Anthropometry/man/cMDSwomen.Rd |only Anthropometry-1.1/Anthropometry/man/cdfDiss.Rd |only Anthropometry-1.1/Anthropometry/man/compPerc.Rd |only Anthropometry-1.1/Anthropometry/man/cube34.Rd |only Anthropometry-1.1/Anthropometry/man/cube8.Rd |only Anthropometry-1.1/Anthropometry/man/dataDemo.Rd |only Anthropometry-1.1/Anthropometry/man/dataUSAF.Rd |only Anthropometry-1.1/Anthropometry/man/hipamBigGroups.Rd |only Anthropometry-1.1/Anthropometry/man/indivNearest.Rd |only Anthropometry-1.1/Anthropometry/man/landmarks.Rd |only Anthropometry-1.1/Anthropometry/man/optraProcrustes.Rd |only Anthropometry-1.1/Anthropometry/man/outlierHipam.Rd |only Anthropometry-1.1/Anthropometry/man/overlappingRows.Rd |only Anthropometry-1.1/Anthropometry/man/parallelepiped34.Rd |only Anthropometry-1.1/Anthropometry/man/parallelepiped8.Rd |only Anthropometry-1.1/Anthropometry/man/plotMedoids.Rd |only Anthropometry-1.1/Anthropometry/man/plotTreeHipam.Rd |only Anthropometry-1.1/Anthropometry/man/qtranProcrustes.Rd |only Anthropometry-1.1/Anthropometry/man/screeArchetyp.Rd |only Anthropometry-1.1/Anthropometry/man/shapes3dMod.Rd |only Anthropometry-1.1/Anthropometry/man/skeletonsArchet.Rd |only Anthropometry-1.1/Anthropometry/man/xyplotPCA.Rd |only Anthropometry-1.1/Anthropometry/vignettes/decisionTree_Rpackage.pdf |only Anthropometry-1.1/Anthropometry/vignettes/decisionTree_Rpackage_1.pdf |only Anthropometry-1.2/Anthropometry/DESCRIPTION | 10 Anthropometry-1.2/Anthropometry/MD5 | 225 +- Anthropometry-1.2/Anthropometry/NAMESPACE | 38 Anthropometry-1.2/Anthropometry/NEWS | 8 Anthropometry-1.2/Anthropometry/R/Anthropometry-internalArchetypoids.R | 24 Anthropometry-1.2/Anthropometry/R/Anthropometry-internalHipamAnthropom.R |only Anthropometry-1.2/Anthropometry/R/Anthropometry-internalTDDclust.R |only Anthropometry-1.2/Anthropometry/R/CCbiclustAnthropo.R | 35 Anthropometry-1.2/Anthropometry/R/HartiganShapes.R | 90 Anthropometry-1.2/Anthropometry/R/LloydShapes.R | 62 Anthropometry-1.2/Anthropometry/R/TDDclust.R | 148 - Anthropometry-1.2/Anthropometry/R/anthrCases.R |only Anthropometry-1.2/Anthropometry/R/archetypesBoundary.R | 9 Anthropometry-1.2/Anthropometry/R/archetypoids.R | 26 Anthropometry-1.2/Anthropometry/R/array3Dlandm.R |only Anthropometry-1.2/Anthropometry/R/bustSizesStandard.R |only Anthropometry-1.2/Anthropometry/R/cdfDissWomenPrototypes.R |only Anthropometry-1.2/Anthropometry/R/checkBranchLocalIMO.R | 19 Anthropometry-1.2/Anthropometry/R/checkBranchLocalMO.R | 13 Anthropometry-1.2/Anthropometry/R/figures8landm.R | 53 Anthropometry-1.2/Anthropometry/R/getBestPamsamIMO.R | 27 Anthropometry-1.2/Anthropometry/R/getBestPamsamMO.R | 25 Anthropometry-1.2/Anthropometry/R/getDistMatrix.R |only Anthropometry-1.2/Anthropometry/R/hipamAnthropom.R | 9 Anthropometry-1.2/Anthropometry/R/matPercs.R |only Anthropometry-1.2/Anthropometry/R/nearestToArchetypes.R |only Anthropometry-1.2/Anthropometry/R/optraShapes.R |only Anthropometry-1.2/Anthropometry/R/overlapBiclustersByRows.R |only Anthropometry-1.2/Anthropometry/R/percentilsArchetypoid.R |only Anthropometry-1.2/Anthropometry/R/plotPrototypes.R |only Anthropometry-1.2/Anthropometry/R/plotTreeHipamAnthropom.R |only Anthropometry-1.2/Anthropometry/R/plotTrimmOutl.R | 36 Anthropometry-1.2/Anthropometry/R/preprocessing.R |only Anthropometry-1.2/Anthropometry/R/projShapes.R |only Anthropometry-1.2/Anthropometry/R/qtranShapes.R |only Anthropometry-1.2/Anthropometry/R/screeArchetypal.R |only Anthropometry-1.2/Anthropometry/R/shapes3dShapes.R |only Anthropometry-1.2/Anthropometry/R/skeletonsArchetypal.R |only Anthropometry-1.2/Anthropometry/R/stepArchetypesMod.R | 11 Anthropometry-1.2/Anthropometry/R/stepArchetypoids.R | 23 Anthropometry-1.2/Anthropometry/R/trimmOutl.R |only Anthropometry-1.2/Anthropometry/R/trimmedLloydShapes.R | 61 Anthropometry-1.2/Anthropometry/R/trimmedoid.R | 52 Anthropometry-1.2/Anthropometry/R/trimowa.R | 22 Anthropometry-1.2/Anthropometry/R/weightsMixtureUB.R |only Anthropometry-1.2/Anthropometry/R/xyplotPCArchetypes.R |only Anthropometry-1.2/Anthropometry/build/vignette.rds |binary Anthropometry-1.2/Anthropometry/data/USAFSurvey.RData |only Anthropometry-1.2/Anthropometry/data/cube34landm.RData |only Anthropometry-1.2/Anthropometry/data/cube8landm.RData |only Anthropometry-1.2/Anthropometry/data/descrDissTrunks.RData |only Anthropometry-1.2/Anthropometry/data/landmarksSampleSpaSurv.RData |only Anthropometry-1.2/Anthropometry/data/parallelep34landm.RData |only Anthropometry-1.2/Anthropometry/data/parallelep8landm.RData |only Anthropometry-1.2/Anthropometry/data/sampleSpanishSurvey.RData |only Anthropometry-1.2/Anthropometry/inst/doc/Anthropometry.R | 409 +-- Anthropometry-1.2/Anthropometry/inst/doc/Anthropometry.Rnw | 1044 +++++----- Anthropometry-1.2/Anthropometry/inst/doc/Anthropometry.pdf |binary Anthropometry-1.2/Anthropometry/man/Anthropometry-internalArchetypoids.Rd | 2 Anthropometry-1.2/Anthropometry/man/Anthropometry-internalHipamAnthropom.Rd |only Anthropometry-1.2/Anthropometry/man/Anthropometry-internalPlotTree.Rd | 7 Anthropometry-1.2/Anthropometry/man/Anthropometry-internalTDDclust.Rd |only Anthropometry-1.2/Anthropometry/man/Anthropometry-package.Rd | 64 Anthropometry-1.2/Anthropometry/man/CCbiclustAnthropo.Rd | 15 Anthropometry-1.2/Anthropometry/man/HartiganShapes.Rd | 98 Anthropometry-1.2/Anthropometry/man/LloydShapes.Rd | 92 Anthropometry-1.2/Anthropometry/man/TDDclust.Rd | 47 Anthropometry-1.2/Anthropometry/man/USAFSurvey.Rd |only Anthropometry-1.2/Anthropometry/man/anthrCases.Rd |only Anthropometry-1.2/Anthropometry/man/archetypesBoundary.Rd | 52 Anthropometry-1.2/Anthropometry/man/archetypoids.Rd | 89 Anthropometry-1.2/Anthropometry/man/array3Dlandm.Rd |only Anthropometry-1.2/Anthropometry/man/bustSizesStandard.Rd |only Anthropometry-1.2/Anthropometry/man/cdfDissWomenPrototypes.Rd |only Anthropometry-1.2/Anthropometry/man/checkBranchLocalIMO.Rd | 12 Anthropometry-1.2/Anthropometry/man/checkBranchLocalMO.Rd | 15 Anthropometry-1.2/Anthropometry/man/cube34landm.Rd |only Anthropometry-1.2/Anthropometry/man/cube8landm.Rd |only Anthropometry-1.2/Anthropometry/man/descrDissTrunks.Rd |only Anthropometry-1.2/Anthropometry/man/figures8landm.Rd | 12 Anthropometry-1.2/Anthropometry/man/getBestPamsamIMO.Rd | 15 Anthropometry-1.2/Anthropometry/man/getBestPamsamMO.Rd | 15 Anthropometry-1.2/Anthropometry/man/getDistMatrix.Rd |only Anthropometry-1.2/Anthropometry/man/hipamAnthropom.Rd | 83 Anthropometry-1.2/Anthropometry/man/landmarksSampleSpaSurv.Rd |only Anthropometry-1.2/Anthropometry/man/matPercs.Rd |only Anthropometry-1.2/Anthropometry/man/nearestToArchetypes.Rd |only Anthropometry-1.2/Anthropometry/man/optraShapes.Rd |only Anthropometry-1.2/Anthropometry/man/overlapBiclustersByRows.Rd |only Anthropometry-1.2/Anthropometry/man/parallelep34landm.Rd |only Anthropometry-1.2/Anthropometry/man/parallelep8landm.Rd |only Anthropometry-1.2/Anthropometry/man/percentilsArchetypoid.Rd |only Anthropometry-1.2/Anthropometry/man/plotPrototypes.Rd |only Anthropometry-1.2/Anthropometry/man/plotTreeHipamAnthropom.Rd |only Anthropometry-1.2/Anthropometry/man/plotTrimmOutl.Rd | 124 - Anthropometry-1.2/Anthropometry/man/preprocessing.Rd |only Anthropometry-1.2/Anthropometry/man/projShapes.Rd |only Anthropometry-1.2/Anthropometry/man/qtranShapes.Rd |only Anthropometry-1.2/Anthropometry/man/sampleSpanishSurvey.Rd |only Anthropometry-1.2/Anthropometry/man/screeArchetypal.Rd |only Anthropometry-1.2/Anthropometry/man/shapes3dShapes.Rd |only Anthropometry-1.2/Anthropometry/man/skeletonsArchetypal.Rd |only Anthropometry-1.2/Anthropometry/man/stepArchetypesMod.Rd | 28 Anthropometry-1.2/Anthropometry/man/stepArchetypoids.Rd | 52 Anthropometry-1.2/Anthropometry/man/trimmOutl.Rd |only Anthropometry-1.2/Anthropometry/man/trimmedLloydShapes.Rd | 58 Anthropometry-1.2/Anthropometry/man/trimmedoid.Rd | 49 Anthropometry-1.2/Anthropometry/man/trimowa.Rd | 52 Anthropometry-1.2/Anthropometry/man/weightsMixtureUB.Rd |only Anthropometry-1.2/Anthropometry/man/xyplotPCArchetypes.Rd |only Anthropometry-1.2/Anthropometry/src/cast.c | 6 Anthropometry-1.2/Anthropometry/vignettes/Anthropometry.Rnw | 1044 +++++----- Anthropometry-1.2/Anthropometry/vignettes/Anthropometry.bib | 121 - Anthropometry-1.2/Anthropometry/vignettes/algorithm2e.sty |only Anthropometry-1.2/Anthropometry/vignettes/algorithmic.sty |only Anthropometry-1.2/Anthropometry/vignettes/decisionTree.png |only Anthropometry-1.2/Anthropometry/vignettes/decisionTree_1.png |only Anthropometry-1.2/Anthropometry/vignettes/prendas_1.png |only Anthropometry-1.2/Anthropometry/vignettes/prendas_2.png |only Anthropometry-1.2/Anthropometry/vignettes/prendas_3.png |only 176 files changed, 2388 insertions(+), 2243 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.69 dated 2015-05-11 and 1.0.71 dated 2015-05-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 9 +++++---- man/MWK151.Rd | 2 +- src/cce_functions.c | 10 +++++++--- 5 files changed, 20 insertions(+), 15 deletions(-)
Title: Generalized Elastic Nets
Description: Implements several extensions of the elastic net regularization scheme. These extensions include individual feature penalties for the L1 term, feature-feature penalties for the L2 term, as well as translation coefficients for the latter.
Author: Artem Sokolov
Maintainer: Artem Sokolov <artem.sokolov@gmail.com>
Diff between gelnet versions 1.0 dated 2015-02-03 and 1.1 dated 2015-05-14
CHANGES |only DESCRIPTION | 11 +-- MD5 | 25 ++++--- NAMESPACE | 1 R/gelnet.R | 157 +++++++++++++++++++++++++++++++++++++++++------ man/adj2lapl.Rd | 2 man/adj2nlapl.Rd | 2 man/gelnet.L1bin.Rd | 2 man/gelnet.klr.Rd |only man/gelnet.krr.Rd |only man/gelnet.lin.Rd | 6 + man/gelnet.lin.obj.Rd | 6 + man/gelnet.logreg.Rd | 9 +- man/gelnet.logreg.obj.Rd | 6 + src/gelnet.c | 71 +++++++++------------ 15 files changed, 214 insertions(+), 84 deletions(-)
Title: Scrapes Data from www.fitbit.com
Description: Scrapes data from www.fitbit.com. This does not use the official API,
but instead uses the API that the web dashboard uses to generate the graphs
displayed on the dashboard after login at www.fitbit.com.
Author: Cory Nissen <corynissen@gmail.com> [aut, cre]
Maintainer: Cory Nissen <corynissen@gmail.com>
Diff between fitbitScraper versions 0.1.2 dated 2015-03-25 and 0.1.3 dated 2015-05-14
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/get_daily_data.R | 2 +- R/get_intraday_data.R | 2 +- R/get_premium_export.R | 4 ++++ R/get_sleep_data.R | 2 +- README.md | 4 ++-- 7 files changed, 20 insertions(+), 16 deletions(-)
Title: ANALYZING RNA SEQUENCE COUNT TABLES USING QUASI-LIKELIHOOD
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund [aut],
Long Qu [aut, cre, ctb],
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between QuasiSeq versions 1.0-6 dated 2015-02-03 and 1.0-7 dated 2015-05-13
QuasiSeq-1.0-6/QuasiSeq/R/fbrglm.R |only QuasiSeq-1.0-6/QuasiSeq/R/glm.fit0.R |only QuasiSeq-1.0-6/QuasiSeq/R/negbin.br.R |only QuasiSeq-1.0-7/QuasiSeq/DESCRIPTION | 33 ++++++++++++++------- QuasiSeq-1.0-7/QuasiSeq/MD5 | 28 +++++++++++------- QuasiSeq-1.0-7/QuasiSeq/NAMESPACE | 17 ++++++++--- QuasiSeq-1.0-7/QuasiSeq/R/NBDev.R | 40 ++++++++++++++++++-------- QuasiSeq-1.0-7/QuasiSeq/R/PoisDev.R | 5 ++- QuasiSeq-1.0-7/QuasiSeq/R/QL.fit.R | 4 +- QuasiSeq-1.0-7/QuasiSeq/R/coefglm.R |only QuasiSeq-1.0-7/QuasiSeq/R/duplicated.matrix.R |only QuasiSeq-1.0-7/QuasiSeq/R/fbrNBglm.R |only QuasiSeq-1.0-7/QuasiSeq/R/glm.fit3.R |only QuasiSeq-1.0-7/QuasiSeq/R/glmsolve.R |only QuasiSeq-1.0-7/QuasiSeq/R/negbin.R |only QuasiSeq-1.0-7/QuasiSeq/R/nlsolve.R |only QuasiSeq-1.0-7/QuasiSeq/man/NBDev.Rd | 17 +++++++++-- QuasiSeq-1.0-7/QuasiSeq/man/QL.fit.Rd | 7 +++- QuasiSeq-1.0-7/QuasiSeq/src |only 19 files changed, 106 insertions(+), 45 deletions(-)
Title: Geological Time Scale Plotting
Description: Function for adding the geological timescale to bivariate plots.
Author: Mark A. Bell <mark.bell521@gmail.com>.
Maintainer: Mark A. Bell <mark.bell521@gmail.com>
Diff between geoscale versions 1.1 dated 2014-03-31 and 2.0 dated 2015-05-13
geoscale-1.1/geoscale/R/geoscale.plot.R |only geoscale-1.1/geoscale/data/timescales.RData |only geoscale-1.1/geoscale/man/geoscale.plot.Rd |only geoscale-2.0/geoscale/DESCRIPTION | 14 ++++++++------ geoscale-2.0/geoscale/MD5 | 14 +++++++++----- geoscale-2.0/geoscale/R/geoscaleBox.R |only geoscale-2.0/geoscale/R/geoscalePlot.R |only geoscale-2.0/geoscale/data/size.rda |only geoscale-2.0/geoscale/data/timescales.rda |only geoscale-2.0/geoscale/man/geoscale-package.Rd | 12 ++++++------ geoscale-2.0/geoscale/man/geoscaleBox.Rd |only geoscale-2.0/geoscale/man/geoscalePlot.Rd |only geoscale-2.0/geoscale/man/size.Rd |only 13 files changed, 23 insertions(+), 17 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.6 dated 2015-03-17 and 0.2.8 dated 2015-05-13
DESCRIPTION | 10 ++-- MD5 | 33 ++++++------- NAMESPACE | 3 - R/rglobi.R | 98 ++++++++++++++++++++++++++-------------- build/vignette.rds |binary man/get_child_taxa.Rd | 4 - man/get_data_fields.Rd |only man/get_interaction_areas.Rd | 6 +- man/get_interaction_matrix.Rd | 4 - man/get_interaction_table.Rd | 4 - man/get_interaction_types.Rd | 7 ++ man/get_interactions.Rd | 7 +- man/get_interactions_by_taxa.Rd | 20 +++++++- man/get_interactions_in_area.Rd | 6 +- man/get_predators_of.Rd | 6 +- man/get_prey_of.Rd | 6 +- man/query.Rd | 4 - tests/testthat/test-globi.R | 21 +++++++- 18 files changed, 155 insertions(+), 84 deletions(-)
Title: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Description: Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.
Author: Mathieu Gautier and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@supagro.inra.fr>
Diff between rehh versions 1.12 dated 2015-04-07 and 1.13 dated 2015-05-13
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/calc_ehh.R | 2 +- R/distribplot.R | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm and the generalized
backdoor criterion is implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.0-10 dated 2015-03-19 and 2.2-0 dated 2015-05-13
DESCRIPTION | 26 ++++++++------ MD5 | 47 +++++++++++++++---------- NAMESPACE | 23 ++++++++---- R/AllClasses.R | 90 +++++++++++++++++++++++++------------------------ R/genRandDAG.R |only R/gies.R | 88 +++++++++++++++++++++++------------------------ R/lingamFuns.R |only R/pcalg.R | 58 +++++++++++++++++++++++++++---- R/sysdata.rda |only build/vignette.rds |binary data/gmB.rda |binary data/gmD.rda |binary data/gmG.rda |binary data/gmI.rda |binary data/gmInt.rda |binary data/gmL.rda |binary inst/NEWS.Rd | 28 +++++++++++++++ man/EssGraph-class.Rd | 32 ++++++++--------- man/LINGAM.Rd |only man/ParDAG-class.Rd | 28 +++++++-------- man/ges.Rd | 4 +- man/randDAG.Rd |only man/simy.Rd | 43 +++++++++++++---------- man/unifDAG.Rd |only tests/test_LINGAM.R |only tests/test_pdag2dag.R | 10 ++++- tests/test_randDAG.R |only tests/test_randomDAG.R | 4 ++ tests/test_unifDAG.R |only 29 files changed, 298 insertions(+), 183 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.5.2 dated 2015-03-19 and 1.5.3 dated 2015-05-13
DESCRIPTION | 6 - MD5 | 149 ++++++++++++++++---------------- NAMESPACE | 2 NEWS | 9 + R/anyInfinite.r | 1 R/anyMissing.r | 1 R/asInteger.r | 1 R/assert.r | 7 + R/backports.r |only R/checkArray.r | 25 +++-- R/checkAtomic.r | 5 + R/checkAtomicVector.r | 2 R/checkCount.r | 3 R/checkDirectory.r | 11 +- R/checkFile.r | 14 +-- R/checkFlag.r | 3 R/checkMatrix.r | 5 - R/checkNames.r | 3 R/checkPathForOutput.r | 3 R/checkPercentage.r | 3 R/checkString.r | 3 R/checkVector.r | 1 man/anyInfinite.Rd | 2 man/anyMissing.Rd | 2 man/asInteger.Rd | 2 man/assert.Rd | 8 + man/checkAccess.Rd | 2 man/checkArray.Rd | 29 ++++-- man/checkAtomic.Rd | 41 ++++++++ man/checkAtomicVector.Rd | 7 + man/checkCharacter.Rd | 2 man/checkChoice.Rd | 2 man/checkClass.Rd | 2 man/checkComplex.Rd | 2 man/checkCount.Rd | 4 man/checkDataFrame.Rd | 2 man/checkDirectory.Rd | 2 man/checkEnvironment.Rd | 2 man/checkFactor.Rd | 2 man/checkFile.Rd | 2 man/checkFlag.Rd | 4 man/checkFunction.Rd | 2 man/checkInt.Rd | 2 man/checkInteger.Rd | 2 man/checkIntegerish.Rd | 2 man/checkList.Rd | 2 man/checkLogical.Rd | 2 man/checkMatrix.Rd | 10 +- man/checkNamed.Rd | 2 man/checkNames.Rd | 4 man/checkNull.Rd | 2 man/checkNumber.Rd | 2 man/checkNumeric.Rd | 2 man/checkPathForOutput.Rd | 5 - man/checkPercentage.Rd | 4 man/checkScalar.Rd | 2 man/checkScalarNA.Rd | 2 man/checkSetEqual.Rd | 2 man/checkString.Rd | 4 man/checkSubset.Rd | 2 man/checkVector.Rd | 8 + man/checkmate.Rd | 2 man/qassert.Rd | 2 man/qassertr.Rd | 2 src/checks.c | 64 ++++++++----- src/checks.h | 2 src/cmessages.c | 2 src/helper.c | 51 ++++++++-- src/helper.h | 1 src/qassert.c | 4 tests/testthat/test_anyMissing.r | 12 ++ tests/testthat/test_checkArray.r | 25 +++++ tests/testthat/test_checkAtomicVector.r | 5 + tests/testthat/test_checkDataFrame.r | 14 +++ tests/testthat/test_checkInteger.r | 1 tests/testthat/test_checkMatrix.r | 25 +++-- 76 files changed, 429 insertions(+), 222 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-08 0.1
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.18.0 dated 2015-04-10 and 0.18.1 dated 2015-05-13
sdcTable-0.18.0/sdcTable/inst/tests |only sdcTable-0.18.0/sdcTable/tests/test-all.R |only sdcTable-0.18.1/sdcTable/DESCRIPTION | 12 - sdcTable-0.18.1/sdcTable/MD5 | 119 ++++++------ sdcTable-0.18.1/sdcTable/NAMESPACE | 2 sdcTable-0.18.1/sdcTable/R/methods_class_dataObj.r | 21 +- sdcTable-0.18.1/sdcTable/inst/doc/sdcTable.pdf |binary sdcTable-0.18.1/sdcTable/man/attack.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.multiple-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/cellInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/changeCellStatus.Rd | 2 sdcTable-0.18.1/sdcTable/man/cutList-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dataObj-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dimInfo-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dimVar-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dimInfo-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.safeObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/getInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/linProb-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/makeProblem.Rd | 2 sdcTable-0.18.1/sdcTable/man/microData1.Rd | 2 sdcTable-0.18.1/sdcTable/man/microData2.Rd | 2 sdcTable-0.18.1/sdcTable/man/primarySuppression.Rd | 2 sdcTable-0.18.1/sdcTable/man/print-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/problem.Rd | 2 sdcTable-0.18.1/sdcTable/man/problemInstance-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/problemWithSupps.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectLinkedTables.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectTable.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectedData.Rd | 2 sdcTable-0.18.1/sdcTable/man/safeObj-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/sdcProblem-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.dimInfo-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/setInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/simpleTriplet-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/summary-method.Rd | 2 sdcTable-0.18.1/sdcTable/tests/testthat |only sdcTable-0.18.1/sdcTable/tests/testthat.R |only 60 files changed, 129 insertions(+), 127 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.1 dated 2015-04-27 and 2.2 dated 2015-05-13
pcnetmeta-2.1/pcnetmeta/R/ci.plot.R |only pcnetmeta-2.1/pcnetmeta/R/forest.plot.R |only pcnetmeta-2.1/pcnetmeta/man/ci.plot.Rd |only pcnetmeta-2.1/pcnetmeta/man/forest.plot.Rd |only pcnetmeta-2.2/pcnetmeta/DESCRIPTION | 10 +- pcnetmeta-2.2/pcnetmeta/MD5 | 70 +++++++++---------- pcnetmeta-2.2/pcnetmeta/NAMESPACE | 2 pcnetmeta-2.2/pcnetmeta/R/absolute.plot.R |only pcnetmeta-2.2/pcnetmeta/R/contrast.plot.R |only pcnetmeta-2.2/pcnetmeta/R/model.binary.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.binary.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.py.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/nma.ab.R | 21 +++-- pcnetmeta-2.2/pcnetmeta/R/nma.ab.cont.R | 21 +++-- pcnetmeta-2.2/pcnetmeta/R/nma.ab.followup.R | 43 ++++++----- pcnetmeta-2.2/pcnetmeta/R/nma.ab.py.R | 43 ++++++----- pcnetmeta-2.2/pcnetmeta/man/absolute.plot.Rd |only pcnetmeta-2.2/pcnetmeta/man/contrast.plot.Rd |only pcnetmeta-2.2/pcnetmeta/man/nma.ab.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.cont.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.followup.Rd | 5 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.py.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/pcnetmeta-package.Rd | 2 40 files changed, 479 insertions(+), 340 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and mongo-c-driver.
Includes support for aggregation, indexing, map-reduce, streaming, TLS and
LDAP (SASL) authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.2 dated 2015-04-12 and 0.3 dated 2015-05-13
mongolite-0.2/mongolite/R/onLoad.R |only mongolite-0.2/mongolite/src/utils.h |only mongolite-0.3/mongolite/DESCRIPTION | 17 mongolite-0.3/mongolite/MD5 | 85 +- mongolite-0.3/mongolite/NAMESPACE | 6 mongolite-0.3/mongolite/NEWS |only mongolite-0.3/mongolite/R/jeroen.R | 3 mongolite-0.3/mongolite/R/mongo.R | 44 + mongolite-0.3/mongolite/R/object.R | 46 + mongolite-0.3/mongolite/build/vignette.rds |binary mongolite-0.3/mongolite/configure | 1 mongolite-0.3/mongolite/inst/doc/intro.Rmd | 37 - mongolite-0.3/mongolite/inst/doc/intro.html | 327 +++------- mongolite-0.3/mongolite/man/mongo.Rd | 25 mongolite-0.3/mongolite/src/Makevars | 72 +- mongolite-0.3/mongolite/src/apple.h | 1 mongolite-0.3/mongolite/src/bson.c | 11 mongolite-0.3/mongolite/src/bson/bson-atomic.c | 1 mongolite-0.3/mongolite/src/bson/bson-atomic.h | 58 - mongolite-0.3/mongolite/src/bson/bson-config.h | 10 mongolite-0.3/mongolite/src/bson/bson-iter.c | 2 mongolite-0.3/mongolite/src/bson/bson-macros.h | 12 mongolite-0.3/mongolite/src/bson/bson-stdint.h | 2 mongolite-0.3/mongolite/src/bson/bson-string.c | 6 mongolite-0.3/mongolite/src/bson/bson-version.h | 6 mongolite-0.3/mongolite/src/bson/bson.c | 8 mongolite-0.3/mongolite/src/client.c | 25 mongolite-0.3/mongolite/src/collection.c | 68 -- mongolite-0.3/mongolite/src/cursor.c | 21 mongolite-0.3/mongolite/src/mongoc/mongoc-bulk-operation.c | 9 mongolite-0.3/mongolite/src/mongoc/mongoc-client-pool.c | 2 mongolite-0.3/mongolite/src/mongoc/mongoc-client.c | 20 mongolite-0.3/mongolite/src/mongoc/mongoc-counters.c | 6 mongolite-0.3/mongolite/src/mongoc/mongoc-database.c | 13 mongolite-0.3/mongolite/src/mongoc/mongoc-gridfs-file-page.c | 2 mongolite-0.3/mongolite/src/mongoc/mongoc-scram.c | 29 mongolite-0.3/mongolite/src/mongoc/mongoc-stream-tls.c | 14 mongolite-0.3/mongolite/src/mongoc/mongoc-uri.c | 24 mongolite-0.3/mongolite/src/mongoc/mongoc-version.h | 6 mongolite-0.3/mongolite/src/mongoc/mongoc-write-command.c | 9 mongolite-0.3/mongolite/src/mongoc/mongoc-write-concern-private.h | 11 mongolite-0.3/mongolite/src/mongoc/mongoc-write-concern.c | 55 + mongolite-0.3/mongolite/src/mongolite.h |only mongolite-0.3/mongolite/src/onload.c |only mongolite-0.3/mongolite/src/utils.c | 35 - mongolite-0.3/mongolite/vignettes/intro.Rmd | 37 - 46 files changed, 615 insertions(+), 551 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.0 dated 2014-09-09 and 1.2.1 dated 2015-05-13
mnlogit-1.2.0/mnlogit/inst/doc/mnlogit_tests.R |only mnlogit-1.2.0/mnlogit/vignettes/tests_sample_output |only mnlogit-1.2.1/mnlogit/ChangeLog | 18 mnlogit-1.2.1/mnlogit/DESCRIPTION | 8 mnlogit-1.2.1/mnlogit/MD5 | 31 mnlogit-1.2.1/mnlogit/NAMESPACE | 1 mnlogit-1.2.1/mnlogit/R/mnlogit.R | 7 mnlogit-1.2.1/mnlogit/R/mnlogit.methods.R | 36 mnlogit-1.2.1/mnlogit/R/predict.R | 20 mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.R | 84 +- mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.Rnw | 601 ++++++++-------- mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.pdf |binary mnlogit-1.2.1/mnlogit/man/hyptests.Rd | 1 mnlogit-1.2.1/mnlogit/man/mnlogit.Rd | 9 mnlogit-1.2.1/mnlogit/src/hessian.h | 2 mnlogit-1.2.1/mnlogit/vignettes/mnlogit.Rnw | 347 +++++---- mnlogit-1.2.1/mnlogit/vignettes/mnlogit.bib | 721 ++++++++++---------- mnlogit-1.2.1/mnlogit/vignettes/table2_Code.R |only 18 files changed, 1014 insertions(+), 872 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in
S" (Chambers and Hastie (eds), 1991), and "Generalized Additive
Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.09.1 dated 2013-09-12 and 1.12 dated 2015-05-13
gam-1.09.1/gam/R/all.wam.R |only gam-1.09.1/gam/R/deviance.default.R |only gam-1.09.1/gam/R/deviance.glm.R |only gam-1.09.1/gam/R/deviance.lm.R |only gam-1.12/gam/DESCRIPTION | 12 +++++------ gam-1.12/gam/MD5 | 39 ++++++++++++++++-------------------- gam-1.12/gam/NAMESPACE | 12 +++++++++-- gam-1.12/gam/R/anova.gam.R | 7 ++---- gam-1.12/gam/R/anova.gamlist.R | 4 +-- gam-1.12/gam/R/gam.R | 2 - gam-1.12/gam/R/gam.fit.R | 4 +-- gam-1.12/gam/R/general.wam.R |only gam-1.12/gam/R/gplot.matrix.R | 14 ++++++++++-- gam-1.12/gam/R/s.wam.R | 3 ++ gam-1.12/gam/R/step.gam.R | 13 ++++++++---- gam-1.12/gam/R/summary.gam.R | 5 ++-- gam-1.12/gam/man/gam-internal.Rd | 5 ---- gam-1.12/gam/man/gam.Rd | 6 +++-- gam-1.12/gam/man/gam.exact.Rd | 7 +++--- gam-1.12/gam/man/lo.Rd | 4 +-- gam-1.12/gam/man/s.Rd | 4 +-- gam-1.12/gam/man/step.gam.Rd | 2 - gam-1.12/gam/src/Makevars.win | 2 - 23 files changed, 83 insertions(+), 62 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between arm versions 1.8-4 dated 2015-04-07 and 1.8-5 dated 2015-05-13
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bayesglm.R | 1 + 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth <russell-lenth@uiowa.edu>
Diff between rsm versions 2.07 dated 2014-10-02 and 2.7-2 dated 2015-05-12
DESCRIPTION | 10 +-- MD5 | 32 ++++++------ R/contour-lm.R | 12 ++-- build/vignette.rds |binary inst/NEWS | 6 ++ inst/doc/rs-illus.Rtex | 82 +++++++++++++++++++++++++------ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary vignettes/rs-illus-SA-anal2-fig.pdf |binary vignettes/rs-illus-SA-anal6-fig.pdf |binary vignettes/rs-illus-boot-anal7-fig.pdf |binary vignettes/rs-illus-contour-anal7-fig.pdf |binary vignettes/rs-illus-varfcn-FO-fig.pdf |binary vignettes/rs-illus-varfcn-SO-fig.pdf |binary vignettes/rs-illus-varfcn-SO2-fig.pdf |binary vignettes/rs-illus.Rtex | 82 +++++++++++++++++++++++++------ 17 files changed, 167 insertions(+), 57 deletions(-)
Title: Descriptive Analysis by Groups
Description: Read, interpret, summarise, display and
analyse epidemiological data. Can be used to create data summaries for
quality control, extensive reports for exploring data, including
publication-ready univariate or bivariate tables in plain text HTML and
LaTeX, and a figures to quickly visualise the distribution of your data.
Depending on the nature of the variable, various statistics are
calculated (mean, median, frequencies, incidences) and appropriate
tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher,
log-rank, ...). The latest version includes functionality for summarising
genetic data, and for performing low-level quality control of your database
(see radiograph()) to help identify data-entry errors. This version has
also been implemented in a web-interface to make this package accessible
to non-R-users.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel
and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.0 dated 2015-01-23 and 3.0.1 dated 2015-05-12
compareGroups-3.0.1/compareGroups/DESCRIPTION | 12 compareGroups-3.0.1/compareGroups/MD5 | 26 compareGroups-3.0.1/compareGroups/build/vignette.rds |binary compareGroups-3.0.1/compareGroups/inst/app/server.R | 395 +++++----- compareGroups-3.0.1/compareGroups/inst/app/ui.R | 81 +- compareGroups-3.0.1/compareGroups/inst/app/www/tablePDF3046.pdf |only compareGroups-3.0.1/compareGroups/inst/doc/changelog | 3 compareGroups-3.0.1/compareGroups/man/compareGroups-package.Rd | 6 compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/age.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/sex.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/tmain.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/age.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/sex.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/tmain.pdf |binary compareGroups-3.0/compareGroups/inst/app/www/tablePDF774.pdf |only 15 files changed, 305 insertions(+), 218 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 1.1.4 dated 2015-02-06 and 1.1.5 dated 2015-05-12
poppr-1.1.4/poppr/vignettes/figure |only poppr-1.1.5/poppr/DESCRIPTION | 16 - poppr-1.1.5/poppr/MD5 | 160 +++++---------- poppr-1.1.5/poppr/NAMESPACE | 2 poppr-1.1.5/poppr/NEWS | 8 poppr-1.1.5/poppr/R/distances.r | 10 poppr-1.1.5/poppr/R/internal.r | 19 + poppr-1.1.5/poppr/build/vignette.rds |binary poppr-1.1.5/poppr/data/Aeut.rda |binary poppr-1.1.5/poppr/data/Pinf.rda |binary poppr-1.1.5/poppr/data/monpop.rda |binary poppr-1.1.5/poppr/data/partial_clone.rda |binary poppr-1.1.5/poppr/inst/doc/algo.Rnw | 2 poppr-1.1.5/poppr/inst/doc/algo.pdf |binary poppr-1.1.5/poppr/inst/doc/poppr_manual.Rnw | 2 poppr-1.1.5/poppr/inst/doc/poppr_manual.pdf |binary poppr-1.1.5/poppr/man/Aeut.Rd | 2 poppr-1.1.5/poppr/man/Pinf.Rd | 2 poppr-1.1.5/poppr/man/aboot.Rd | 2 poppr-1.1.5/poppr/man/bootgen-class.Rd | 2 poppr-1.1.5/poppr/man/bootgen-methods.Rd | 2 poppr-1.1.5/poppr/man/bruvo.boot.Rd | 2 poppr-1.1.5/poppr/man/bruvo.dist.Rd | 2 poppr-1.1.5/poppr/man/bruvo.msn.Rd | 2 poppr-1.1.5/poppr/man/bruvomat-class.Rd | 2 poppr-1.1.5/poppr/man/bruvomat-methods.Rd | 2 poppr-1.1.5/poppr/man/clonecorrect.Rd | 2 poppr-1.1.5/poppr/man/coercion-methods.Rd | 2 poppr-1.1.5/poppr/man/diss.dist.Rd | 2 poppr-1.1.5/poppr/man/genclone-class.Rd | 2 poppr-1.1.5/poppr/man/genclone-method.Rd | 2 poppr-1.1.5/poppr/man/genetic_distance.Rd | 2 poppr-1.1.5/poppr/man/genind2genalex.Rd | 2 poppr-1.1.5/poppr/man/genotype_curve.Rd | 2 poppr-1.1.5/poppr/man/getfile.Rd | 2 poppr-1.1.5/poppr/man/greycurve.Rd | 2 poppr-1.1.5/poppr/man/hierarchy-methods.Rd | 2 poppr-1.1.5/poppr/man/ia.Rd | 2 poppr-1.1.5/poppr/man/info_table.Rd | 2 poppr-1.1.5/poppr/man/informloci.Rd | 2 poppr-1.1.5/poppr/man/is.genclone.Rd | 2 poppr-1.1.5/poppr/man/locus_table.Rd | 2 poppr-1.1.5/poppr/man/missingno.Rd | 2 poppr-1.1.5/poppr/man/mlg.Rd | 2 poppr-1.1.5/poppr/man/monpop.Rd | 4 poppr-1.1.5/poppr/man/partial_clone.Rd | 2 poppr-1.1.5/poppr/man/plot_poppr_msn.Rd | 2 poppr-1.1.5/poppr/man/poppr-package.Rd | 2 poppr-1.1.5/poppr/man/poppr.Rd | 2 poppr-1.1.5/poppr/man/poppr.all.Rd | 2 poppr-1.1.5/poppr/man/poppr.amova.Rd | 2 poppr-1.1.5/poppr/man/poppr.msn.Rd | 2 poppr-1.1.5/poppr/man/popsub.Rd | 2 poppr-1.1.5/poppr/man/population-methods.Rd | 2 poppr-1.1.5/poppr/man/private_alleles.Rd | 2 poppr-1.1.5/poppr/man/read.genalex.Rd | 2 poppr-1.1.5/poppr/man/recode_polyploids.Rd | 2 poppr-1.1.5/poppr/man/shufflepop.Rd | 2 poppr-1.1.5/poppr/man/splitcombine.Rd | 2 poppr-1.1.5/poppr/tests/testthat/test-values.R | 11 + poppr-1.1.5/poppr/vignettes/algo.Rnw | 2 poppr-1.1.5/poppr/vignettes/poppr_manual-concordance.tex | 2 poppr-1.1.5/poppr/vignettes/poppr_manual.Rnw | 2 63 files changed, 156 insertions(+), 168 deletions(-)
Title: Scores Features for Feature Selection
Description: For each feature, a score is computed that can be useful
for feature selection. Several random subsets are sampled from
the input data and for each random subset, various linear
models are fitted using lars method. A score is assigned to
each feature based on the tendency of LASSO in including that
feature in the models.Finally, the average score and the models
are returned as the output. The features with relatively low
scores are recommended to be ignored because they can lead to
overfitting of the model to the training data. Moreover, for
each random subset, the best set of features in terms of global
error is returned. They are useful for applying Bolasso, the
alternative feature selection method that recommends the
intersection of features subsets.
Author: Habil Zare
Maintainer: Habil Zare <zare@txstate.edu>
Diff between FeaLect versions 1.8 dated 2015-03-08 and 1.10 dated 2015-05-12
DESCRIPTION | 6 MD5 | 10 - R/FeaLect.R | 359 ++++++++++++++++++++++----------------------- R/compute.logistic.score.R | 41 ++--- R/input.check.FeaLect.R | 90 +++++------ R/train.doctor.R | 348 +++++++++++++++++++++---------------------- 6 files changed, 425 insertions(+), 429 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-19 2.15.1.0
2012-02-18 2.14.1.6
2012-02-12 2.14.1.5
2012-02-08 2.14.1.3
2012-01-29 2.14.1.0
2012-01-16 2.14.0.3
2012-01-10 2.14.0.2
2011-11-16 2.14.0.0
2011-10-26 2.13.2.2
2011-10-04 2.13.2.1
2011-09-29 2.13.1.6
2011-09-07 2.13.1.4
2011-07-25 2.13.1.3
2011-07-23 2.13.1.0
2011-04-11 2.12.2.3
2011-04-10 2.12.2.2
2011-03-06 2.12.2.0
2011-02-22 2.12.1.1
2011-02-20 2.12.1.0
2010-11-07 2.12.0.0
2010-06-26 2.11.1.0
2010-05-22 2.11.0.0
2010-01-29 2.10.1.1
2010-01-18 2.10.1.0
2009-11-03 2.10.0.0
2009-10-16 2.9.2.8
2009-10-11 2.9.2.7
2009-10-01 2.9.2.5
2009-09-28 2.9.2.3
2009-09-23 2.9.2.2
2009-09-21 2.9.2.1
2009-09-03 2.9.2.0
2009-08-25 2.9.1.7
2009-08-21 2.9.1.6
2009-07-31 2.9.1.5
2009-07-30 2.9.1.4
2009-07-26 2.9.1.3
2009-07-18 2.9.1.2
2009-06-25 2.9.0.1
2009-06-25 2.9.0.2
2009-06-24 2.9.0.0
2009-02-15 2.8.1.1
2009-02-04 2.8.1.0
2008-12-14 2.8.0.1
2008-12-01 2.8.0.0
2008-10-07 2.7.2.3
2008-09-07 2.7.2.1
2008-07-11 2.7.1.2
2008-07-08 2.7.1.1
2008-06-20 2.7.1.0
2008-06-15 2.7.0.4
2008-05-06 2.7.0.3
2008-05-02 2.7.0.2
2008-04-27 2.7.0.1
2008-04-25 2.7.0.0
2008-04-20 2.6.2.11
2008-04-06 2.6.2.10
2008-03-29 2.6.2.8
2008-03-24 2.6.2.7
2008-03-12 2.6.2.6
2008-03-09 2.6.2.5
2008-03-02 2.6.2.3
2008-03-02 2.6.2.4
2008-02-26 2.6.2.2
2008-02-12 2.6.2.0
2008-02-05 2.6.1.7
2008-01-13 2.6.1.6
2007-12-30 2.6.1.5
2007-12-24 2.6.1.3
2007-12-10 2.6.1.1
2007-12-05 2.6.1.0
2007-11-24 2.6.0.5
2007-11-18 2.6.0.4
2007-11-17 2.6.0.3
2007-11-03 2.6.0.2
2007-10-07 2.6.0.1
2007-09-28 2.5.1.5
2007-09-21 2.5.1.4
2007-09-07 2.5.1.3
2007-08-27 2.5.1.2
2007-08-12 2.5.1.1
2007-07-31 2.5.1
2007-07-08 2.5.0.4
2007-06-20 2.5.0.3
Title: Modelling the Population Dynamics of a Stage-Structured Species
in Continuous Time
Description: Provides facilities to implement and run population models of
stage-structured species...
Author: Helen Kettle
Maintainer: David Nutter <david.nutter@bioss.ac.uk>
Diff between stagePop versions 1.0-1 dated 2015-02-03 and 1.1-1 dated 2015-05-12
stagePop-1.0-1/stagePop/inst/doc/Appendix1.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix1.pdf.asis |only stagePop-1.0-1/stagePop/inst/doc/Appendix2.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix2.pdf.asis |only stagePop-1.0-1/stagePop/inst/doc/Appendix3.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix3.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix1.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix2.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix3.pdf.asis |only stagePop-1.1-1/stagePop/DESCRIPTION | 9 +++-- stagePop-1.1-1/stagePop/MD5 | 26 +++++------------ stagePop-1.1-1/stagePop/R/genericPlot.R | 8 +++-- stagePop-1.1-1/stagePop/R/popModel.R | 2 - stagePop-1.1-1/stagePop/build/vignette.rds |binary stagePop-1.1-1/stagePop/inst/DemoFiles/BlowFlies.R | 4 +- stagePop-1.1-1/stagePop/inst/DemoFiles/Briggs.R | 2 + stagePop-1.1-1/stagePop/inst/DemoFiles/ClimateChange.R |only stagePop-1.1-1/stagePop/inst/doc/stagePop.pdf |binary stagePop-1.1-1/stagePop/man/popModel.Rd | 2 - 19 files changed, 27 insertions(+), 26 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin <ostap.okhrin@wiwi.hu-berlin.de> and Alexander Ristig <ristigal@hu-berlin.de>
Maintainer: Alexander Ristig <ristigal@hu-berlin.de>
Diff between HAC versions 1.0-2 dated 2015-02-05 and 1.0-3 dated 2015-05-12
DESCRIPTION | 12 +- MD5 | 32 +++--- NAMESPACE | 2 R/cdf.r | 3 R/constructor.r | 19 ++-- R/estimate.r | 232 +++++++++++++++++++++++++++++++++++++++---------- R/functions.r | 8 - R/pdf.r | 170 ++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/ChangeLog | 10 ++ inst/doc/HAC.R | 26 ++--- inst/doc/HAC.Rnw | 18 ++- inst/doc/HAC.pdf |binary man/dHAC.Rd | 195 ++++++++++++++++++++--------------------- man/estimate.copula.Rd | 161 +++++++++++++++++----------------- vignettes/HAC.Rnw | 18 ++- vignettes/ref.bib | 23 +++- 17 files changed, 613 insertions(+), 316 deletions(-)
Title: Functions for Processing Minute-to-Minute Accelerometer Data
Description: A collection of functions that perform operations on time-series accelerometer data, such as identify non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented. Most of the functions are written in C++ for efficiency.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between accelerometry versions 2.2.4 dated 2014-12-09 and 2.2.5 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/RcppExports.R | 13 +++++++------ man/accelerometry-package.Rd | 4 ++-- src/RcppExports.cpp | 4 ++-- src/intensities.cpp | 2 +- 6 files changed, 23 insertions(+), 22 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.9.3 dated 2014-11-02 and 3.10.4 dated 2015-05-12
DESCRIPTION | 17 - MD5 | 74 +++-- NAMESPACE | 41 ++- R/AllClass.R | 2 R/anova.manyany.R | 116 +++++--- R/anova.manyglm.R | 43 ++- R/anova.manylm.R | 546 ++++++++++++++++++++-------------------- R/anova.traitglm.R |only R/cv.glm1path.R |only R/default.plot.manyglm.R | 108 +++---- R/default.plot.manylm.R | 20 - R/default.plot.mvformula.R | 24 - R/default.print.anova.manyglm.R | 24 + R/glm1.R |only R/glm1path.R |only R/manyany.R | 275 ++++++++++++++------ R/manyglm.R | 5 R/plot.manylm.R | 8 R/plot.mvformula.R | 6 R/plotFormulafeature.R | 4 R/predict.manyglm.R | 44 ++- R/predict.manylm.R | 1 R/predict.traitglm.R |only R/qordinal.R |only R/residuals.glm1path.R |only R/residuals.manyglm.R | 3 R/traitglm.R |only data/antTraits.RData |only man/anova.manyany.Rd | 21 - man/anova.manyglm.Rd | 13 man/anova.manylm.Rd | 2 man/anova.traitglm.Rd |only man/antTraits.Rd |only man/cv.glm1path.Rd |only man/glm1.Rd |only man/glm1path.Rd |only man/manyany.Rd | 49 +++ man/manyglm.Rd | 79 ++--- man/mvabund-package.Rd | 59 ++-- man/plot.manyany.Rd | 11 man/predict.traitglm.Rd |only man/residuals.manyglm.Rd | 13 man/traitglm.Rd |only src/Makevars.in | 11 src/Makevars.win | 4 src/RtoAnovaCpp.cpp | 4 46 files changed, 966 insertions(+), 661 deletions(-)
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between pipe.design versions 0.1 dated 2015-03-19 and 0.2 dated 2015-05-12
pipe.design-0.1/pipe.design/R/pipe.design_0.1.R |only pipe.design-0.2/pipe.design/DESCRIPTION | 8 - pipe.design-0.2/pipe.design/MD5 | 12 - pipe.design-0.2/pipe.design/NAMESPACE | 4 pipe.design-0.2/pipe.design/NEWS | 7 + pipe.design-0.2/pipe.design/R/pipe.design_0.2.R |only pipe.design-0.2/pipe.design/man/pipe.design.Rd | 148 ++++++++++++------------ pipe.design-0.2/pipe.design/man/print.pipe.Rd | 26 ++-- 8 files changed, 106 insertions(+), 99 deletions(-)
Title: Data from the US National Health and Nutrition Examination Study
Description: Body Shape and related measurements from the US National Health
and Nutrition Examination Survey (NHANES, 1999-2004). See
http://www.cdc.gov/nchs/nhanes.htm for details.
Author: Randall Pruim <rpruim@calvin.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between NHANES versions 1.0 dated 2014-08-22 and 2.0 dated 2015-05-12
DESCRIPTION | 15 +- MD5 | 15 +- NAMESPACE | 1 R/datasets.R | 340 +++++++++++++++++++++++++++++++++++++++++++-------- README.md | 14 +- data/NHANES.rda |binary data/NHANESraw.rda |only data/datalist | 1 man/NHANES.Rd | 349 +++++++++++++++++++++++++++++++++++++++++++++-------- 9 files changed, 611 insertions(+), 124 deletions(-)
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1 dated 2015-04-22 and 1.1.2 dated 2015-05-12
MRIaggr-1.1.2/MRIaggr/DESCRIPTION | 13 MRIaggr-1.1.2/MRIaggr/MD5 | 157 +- MRIaggr-1.1.2/MRIaggr/NAMESPACE | 18 MRIaggr-1.1.2/MRIaggr/R/Associated_functions.R | 92 + MRIaggr-1.1.2/MRIaggr/R/Class_Carto3D.R | 56 MRIaggr-1.1.2/MRIaggr/R/Class_MRIaggr.R | 893 +++++++-------- MRIaggr-1.1.2/MRIaggr/R/Generic_functions.R | 114 - MRIaggr-1.1.2/MRIaggr/R/RcppExports.R | 4 MRIaggr-1.1.2/MRIaggr/data/MRIaggr.Pat1_red.RData |binary MRIaggr-1.1.2/MRIaggr/demo/00Index | 2 MRIaggr-1.1.2/MRIaggr/demo/Analysis.R | 8 MRIaggr-1.1.2/MRIaggr/demo/ExtractNifti.R |only MRIaggr-1.1.2/MRIaggr/demo/preProcessing.R | 24 MRIaggr-1.1.2/MRIaggr/inst/List_of_arguments.R | 614 +++++----- MRIaggr-1.1.2/MRIaggr/inst/NEWS | 18 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-1_Carto3D.R | 12 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-1_IRMaggr.R | 114 - MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-3_fctsAssociees.R | 30 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-4_fctsGR.R | 4 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-5_Sweave.R | 4 MRIaggr-1.1.2/MRIaggr/inst/calcSigmaGR.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/Carto3D-class.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/Carto3D2MRIaggr.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/MRIaggr-class.Rd | 34 MRIaggr-1.1.2/MRIaggr/man/MRIaggr.Pat1_red.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/allocClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocTable.Rd |only MRIaggr-1.1.2/MRIaggr/man/array2df.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcBrainMask.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/calcContro_cpp.Rd | 16 MRIaggr-1.1.2/MRIaggr/man/calcControlateral.Rd | 32 MRIaggr-1.1.2/MRIaggr/man/calcDistTissues.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/calcFilter.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcGR.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcGroupsMask.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcGroupsW.Rd | 3 MRIaggr-1.1.2/MRIaggr/man/calcHemi_cpp.Rd | 11 MRIaggr-1.1.2/MRIaggr/man/calcHemisphere.Rd | 30 MRIaggr-1.1.2/MRIaggr/man/calcNormalization.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcRegionaContrast.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcSmoothMask.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcTableHypoReperf.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcThresholdMRIaggr.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/calcTissueType.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcW.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/constCarto3D.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/constCompressMRIaggr.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/constMRIaggr.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/constReduceMRIaggr.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/df2array.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/initIndex.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/multiplot.Rd | 10 MRIaggr-1.1.2/MRIaggr/man/outline.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/outlineMRIaggr.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/plotDistClass.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/pointsHemisphere.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/readMRI.Rd | 10 MRIaggr-1.1.2/MRIaggr/man/selectClinic.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/selectContrast.Rd | 28 MRIaggr-1.1.2/MRIaggr/man/selectCoords.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/selectDescStats.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/selectHemispheres.Rd | 7 MRIaggr-1.1.2/MRIaggr/man/selectMidplane.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/selectNormalization.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectParameter.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectTable.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectVoxelDim.Rd | 20 MRIaggr-1.1.2/MRIaggr/man/selectVoxelSize.Rd | 12 MRIaggr-1.1.2/MRIaggr/man/summary.MRIaggr.Rd | 18 MRIaggr-1.1.2/MRIaggr/man/supprContrast.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/supprDescStats.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/writeMRI.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/writeMRIaggr.Rd | 4 MRIaggr-1.1.2/MRIaggr/src/Associated_functions.cpp | 213 ++- MRIaggr-1.1.2/MRIaggr/src/RcppExports.cpp | 7 MRIaggr-1.1.2/MRIaggr/tests/additionalTest |only MRIaggr-1.1/MRIaggr/demo/ExtractNifty.R |only MRIaggr-1.1/MRIaggr/man/affectClinic.Rd |only MRIaggr-1.1/MRIaggr/man/affectContrast.Rd |only MRIaggr-1.1/MRIaggr/man/affectDescStats.Rd |only MRIaggr-1.1/MRIaggr/man/affectHemisphere.Rd |only MRIaggr-1.1/MRIaggr/man/affectNormalization.Rd |only MRIaggr-1.1/MRIaggr/man/affectTable.Rd |only 87 files changed, 1508 insertions(+), 1291 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.2 dated 2015-04-29 and 0.2.1 dated 2015-05-12
ChangeLog | 6 +++++ DESCRIPTION | 6 ++--- MD5 | 20 +++++++++---------- NEWS | 5 ++++ R/0_classesAndMethods.R | 3 +- build/vignette.rds |binary inst/CITATION | 4 +-- inst/doc/an_introduction_to_markovchain_package.Rnw | 2 - inst/doc/an_introduction_to_markovchain_package.pdf |binary tests/testthat/testBasic1.R | 10 +++++++++ vignettes/an_introduction_to_markovchain_package.Rnw | 2 - 11 files changed, 40 insertions(+), 18 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman <Rob.Hyndman@monash.edu> with contributions from
George Athanasopoulos, Slava Razbash, Drew Schmidt, Zhenyu Zhou, Yousaf Khan,
Christoph Bergmeir, Earo Wang
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 6.0 dated 2015-05-09 and 6.1 dated 2015-05-12
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/bootstrap.R | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- R/newarima2.R | 42 +++++++++++++++++++++++++++-- 5 files changed, 132 insertions(+), 12 deletions(-)
Title: Hierarchical Independent Component Analysis: a Multi-Scale
Sparse Non-Orthogonal Data-Driven Basis
Description: It implements HICA (Hierarchical Independent Component Analysis) algorithm. This approach, obtained through the integration between treelets and Independent Component Analysis, is able to provide a multi-scale non-orthogonal data-driven basis, whose elements have a phenomenological interpretation according to the problem under study.
Author: Piercesare Secchi, Simone Vantini, and Paolo Zanini
Maintainer: Paolo Zanini <paolo.zanini@polimi.it>
Diff between fastHICA versions 1.0 dated 2014-01-16 and 1.0.2 dated 2015-05-12
DESCRIPTION | 14 ++--- MD5 | 6 +- R/energy_hica.R | 138 ++++++++++++++++++++++++++--------------------------- man/energy_hica.Rd | 2 4 files changed, 80 insertions(+), 80 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 1.1 dated 2015-01-31 and 1.1.1 dated 2015-05-12
fclust-1.1.1/fclust/DESCRIPTION | 10 +++++----- fclust-1.1.1/fclust/MD5 | 5 +++-- fclust-1.1.1/fclust/R/fclust.R |only fclust-1.1.1/fclust/inst |only fclust-1.1/fclust/R/Fclust.R |only 5 files changed, 8 insertions(+), 7 deletions(-)
Title: BiCluster Algorithms
Description: The main function biclust provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church,
Spectral, Plaid Model, Xmotifs and Bimax. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova,
Martin Sill, Roberto Theron, Luis Quintales, Friedrich
Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser <Sebastian.Kaiser@stat.uni-muenchen.de>
Diff between biclust versions 1.1.0 dated 2015-03-19 and 1.2.0 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/plaid.r | 2 +- data/BicatYeast.rda |binary data/EisenYeast.rda |binary data/SyntrenEcoli.rda |binary src/rbimax.c | 12 ++++++++---- 7 files changed, 21 insertions(+), 17 deletions(-)
Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data,
using EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Maintainer: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Diff between logbin versions 1.0 dated 2014-10-16 and 1.2 dated 2015-05-12
ChangeLog | 10 ++++- DESCRIPTION | 18 ++++----- MD5 | 44 +++++++++++------------ man/B.Iso.Rd | 6 +-- man/anova.logbin.Rd | 10 ++--- man/confint.logbin.Rd | 4 +- man/contr.isotonic.rev.Rd | 19 +++++----- man/conv.test.Rd | 8 ++-- man/interpret.logbin.smooth.Rd | 4 +- man/logbin-package.Rd | 32 ++++++++--------- man/logbin.Rd | 77 ++++++++++++++++++++--------------------- man/logbin.allref.Rd | 38 ++++++++++---------- man/logbin.control.Rd | 10 ++--- man/logbin.design.Rd | 12 +++--- man/logbin.smooth.Rd | 45 +++++++++++------------ man/logbin.smooth.allref.Rd | 30 +++++++-------- man/logbin.smooth.design.Rd | 30 +++++++-------- man/nplbin.Rd | 32 ++++++++--------- man/plot.logbin.smooth.Rd | 8 ++-- man/predict.logbin.Rd | 10 ++--- man/predict.logbin.smooth.Rd | 8 ++-- man/summary.logbin.Rd | 14 +++---- man/vcov.logbin.Rd | 2 - 23 files changed, 240 insertions(+), 231 deletions(-)
Title: Additive Regression for Discrete Data
Description: Methods for fitting identity-link GLMs and GAMs to discrete data,
using EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Maintainer: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Diff between addreg versions 1.2 dated 2014-10-29 and 2.0 dated 2015-05-12
addreg-1.2/addreg/R/bin.identity.r |only addreg-2.0/addreg/ChangeLog | 8 + addreg-2.0/addreg/DESCRIPTION | 15 +- addreg-2.0/addreg/MD5 | 72 +++++++------ addreg-2.0/addreg/NAMESPACE | 5 addreg-2.0/addreg/R/addbin.r | 2 addreg-2.0/addreg/R/addreg.allref.r | 15 ++ addreg-2.0/addreg/R/addreg.r | 33 ++++-- addreg-2.0/addreg/R/addreg.smooth.allref.r | 2 addreg-2.0/addreg/R/addreg.smooth.r | 20 ++- addreg-2.0/addreg/R/negbin1.r |only addreg-2.0/addreg/R/nnnegbin.r |only addreg-2.0/addreg/R/nnpois.r | 2 addreg-2.0/addreg/R/predict.addreg.r | 1 addreg-2.0/addreg/R/print.addreg.r |only addreg-2.0/addreg/R/print.summary.addreg.r | 11 +- addreg-2.0/addreg/R/summary.addreg.r | 45 +++++++- addreg-2.0/addreg/man/B.Iso.Rd | 6 - addreg-2.0/addreg/man/addbin.Rd | 22 ++-- addreg-2.0/addreg/man/addreg-package.Rd | 58 +++++------ addreg-2.0/addreg/man/addreg.Rd | 120 +++++++++++++---------- addreg-2.0/addreg/man/addreg.allref.Rd | 46 ++++---- addreg-2.0/addreg/man/addreg.control.Rd | 20 +-- addreg-2.0/addreg/man/addreg.design.Rd | 12 +- addreg-2.0/addreg/man/addreg.smooth.Rd | 59 +++++------ addreg-2.0/addreg/man/addreg.smooth.allref.Rd | 32 +++--- addreg-2.0/addreg/man/addreg.smooth.design.Rd | 30 ++--- addreg-2.0/addreg/man/anova.addreg.Rd | 12 +- addreg-2.0/addreg/man/confint.addreg.Rd | 4 addreg-2.0/addreg/man/contr.isotonic.Rd | 12 +- addreg-2.0/addreg/man/conv.test.Rd | 6 - addreg-2.0/addreg/man/interpret.addreg.smooth.Rd | 4 addreg-2.0/addreg/man/negbin1.Rd |only addreg-2.0/addreg/man/nnnegbin.Rd |only addreg-2.0/addreg/man/nnpois.Rd | 52 ++++----- addreg-2.0/addreg/man/plot.addreg.smooth.Rd | 10 - addreg-2.0/addreg/man/predict.addreg.Rd | 10 - addreg-2.0/addreg/man/predict.addreg.smooth.Rd | 8 - addreg-2.0/addreg/man/summary.addreg.Rd | 23 ++-- addreg-2.0/addreg/man/vcov.addreg.Rd | 2 40 files changed, 444 insertions(+), 335 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007). We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use "source('http://bioconductor.org/biocLite.R'); biocLite('ssizeRNA', type = 'source')".
Author: Ran Bi <biran@iastate.edu>, Peng Liu <pliu@iastate.edu>
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.1.1 dated 2015-04-29 and 1.1.2 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 2 +- man/check.power.Rd | 2 +- man/sim.counts.Rd | 2 +- man/ssize.twoSampVaryDelta.Rd | 2 +- man/ssizeRNA_single.Rd | 2 +- man/ssizeRNA_vary.Rd | 2 +- 8 files changed, 19 insertions(+), 19 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris <nathan.morris@cwru.edu>
Diff between strum versions 0.6 dated 2015-03-02 and 0.6.1 dated 2015-05-11
ChangeLog | 11 ++++++++++- DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/strum.R | 22 ++++++++++++++++++---- inst/doc/strum-example.Rnw | 6 +++++- inst/doc/strum-example.pdf |binary inst/doc/strum-intro.Rnw | 6 +++++- inst/doc/strum-intro.pdf |binary man/strum-package.Rd | 8 +++++--- vignettes/strum-example.Rnw | 6 +++++- vignettes/strum-intro.Rnw | 6 +++++- 11 files changed, 67 insertions(+), 26 deletions(-)
Title: Sampling Surface Simulation for Areal Sampling Methods
Description: Sampling surface simulation is useful in the comparison of different areal sampling methods
in forestry, ecology and natural resources. The sampSurf package allows the simulation
of numerous sampling methods for standing trees and downed woody debris in a spatial context.
It also provides an S4 class and method structure that facilitates the addition of new sampling
methods.
Author: Jeffrey H. Gove
Maintainer: Jeffrey H. Gove <jgove@fs.fed.us>
Diff between sampSurf versions 0.7-2 dated 2014-02-03 and 0.7-3 dated 2015-05-11
DESCRIPTION | 21 +++++++++++---------- MD5 | 30 +++++++++++++++--------------- R/TractClass.R | 3 ++- R/chainsawSliver.R | 9 ++++++--- build/vignette.rds |binary inst/doc/ArealSamplingClass.pdf |binary inst/doc/GettingStarted.Rnw | 4 ++-- inst/doc/GettingStarted.pdf |binary inst/doc/InclusionZoneClass.pdf |binary inst/doc/InclusionZoneGridClass.pdf |binary inst/doc/Overview.pdf |binary inst/doc/StemClass.pdf |binary inst/doc/TractClass.pdf |binary inst/doc/sampSurfClass.pdf |binary man/chainSawIZ.Rd | 2 ++ vignettes/GettingStarted.Rnw | 4 ++-- 16 files changed, 40 insertions(+), 33 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-1 dated 2015-03-24 and 0.7-2 dated 2015-05-11
DESCRIPTION | 15 +- MD5 | 149 ++++++++++++++-------------- R/LRT.trend.R | 4 R/RDS.compare.proportions.R | 6 - R/bgk_kde.R | 1 R/errorbar.R |only R/gf.R |only R/llmeC.R | 6 - R/me.impute.R | 29 +++-- R/rds-doc.R | 1 R/robust.inverse.R | 13 +- R/utils.R | 15 ++ data/faux.RData |binary inst/CITATION | 2 man/LRT.trend.test.Rd | 2 man/LRT.value.trend.Rd | 2 man/RDS.I.estimates.Rd | 2 man/RDS.II.estimates.Rd | 2 man/RDS.Rd | 2 man/RDS.SS.estimates.Rd | 2 man/RDS.bootstrap.intervals.Rd | 2 man/RDS.compare.proportions.Rd | 2 man/RDS.compare.two.proportions.Rd | 2 man/as.char.Rd | 2 man/as.rds.data.frame.Rd | 2 man/assert.valid.rds.data.frame.Rd | 2 man/bottleneck.plot.Rd | 2 man/compute.weights.Rd | 2 man/control.rds.estimates.Rd | 2 man/convergence.plot.Rd | 2 man/count.transitions.Rd | 2 man/cumulative.estimate.Rd | 2 man/differential.activity.estimates.Rd | 2 man/extract-methods.Rd | 2 man/faux.Rd | 3 man/fauxmadrona.Rd | 2 man/fauxsycamore.Rd | 2 man/get.h.hat.Rd | 2 man/get.id.Rd | 2 man/get.net.size.Rd | 2 man/get.number.of.recruits.Rd | 2 man/get.population.size.Rd | 2 man/get.rid.Rd | 2 man/get.seed.id.Rd | 2 man/get.seed.rid.Rd | 2 man/get.stationary.distribution.Rd | 2 man/get.wave.Rd | 2 man/gf.weights.Rd |only man/gile.ss.weights.Rd | 2 man/homophily.estimates.Rd | 2 man/impute.degree.Rd | 17 +-- man/indexing-methods.Rd | 2 man/is.rds.data.frame.Rd | 2 man/is.rds.interval.estimate.Rd | 2 man/is.rds.interval.estimate.list.Rd | 2 man/plot.rds.data.frame.Rd | 2 man/print.differential.activity.estimate.Rd | 2 man/print.pvalue.table.Rd | 2 man/print.rds.data.frame.Rd | 2 man/print.rds.interval.estimate.Rd | 2 man/print.summary.svyglm.RDS.Rd | 2 man/rds.I.weights.Rd | 2 man/rds.interval.estimate.Rd | 2 man/read.rdsat.Rd | 2 man/read.rdsobj.Rd | 2 man/reingold.tilford.plot.Rd | 2 man/rid.from.coupons.Rd | 2 man/set.control.class.Rd | 2 man/show.rds.data.frame.Rd | 2 man/summary.svyglm.Rd | 2 man/transition.counts.to.Markov.mle.Rd | 2 man/vh.weights.Rd | 2 man/write.graphviz.Rd | 2 man/write.netdraw.Rd | 2 man/write.rdsat.Rd | 2 man/write.rdsobj.Rd | 2 src/llmeC.c | 6 - 77 files changed, 209 insertions(+), 176 deletions(-)
Title: Probabilistic Fisher Discriminant Analysis
Description: Probabilistic Fisher discriminant analysis (pFDA) is a probabilistic version of the popular and powerful Fisher linear discriminant analysis for dimensionality reduction and classification.
Author: Charles Bouveyron & Camille Brunet
Maintainer: Charles Bouveyron <charles.bouveyron@parisdescartes.fr>
Diff between probFDA versions 1.0 dated 2015-01-27 and 1.0.1 dated 2015-05-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pFDA-internal.R | 3 ++- man/pfda.Rd | 5 +++-- man/predict.pfda.Rd | 5 +++-- man/probFDA-package.Rd | 7 ++++--- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Generalized Beta Distribution of the Second Kind: Properties,
Likelihood, Estimation
Description: Package GB2 explores the Generalized Beta distribution of the second kind. Density, cumulative distribution function, quantiles and moments of the distributions are given. Functions for the full log-likelihood, the profile log-likelihood and the scores are provided. Formulas for various indicators of inequality and poverty under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-likelihood estimation using the full and profile log-likelihood, and non-linear least squares estimation of the model parameters. Various plots for the visualization and analysis of the results are provided. Variance estimation of the parameters is provided for the method of maximum pseudo-likelihood estimation. A mixture distribution based on the compounding property of the GB2 is presented (denoted as "compound" in the documentation). This mixture distribution is based on the discretization of the distribution of the underlying random scale parameter. The discretization can be left or right tail. Density, cumulative distribution function, moments and quantiles for the mixture distribution are provided. The compound mixture distribution is fitted using the method of maximum pseudo-likelihood estimation. The fit can also incorporate the use of auxiliary information. In this new version of the package, the mixture case is complemented with new functions for variance estimation by linearization and comparative density plots.
Author: Monique Graf <monique.p.n.graf@bluewin.ch>, Desislava Nedyalkova <desislava.nedyalkova@gmail.com>.
Maintainer: Desislava Nedyalkova <desislava.nedyalkova@gmail.com>
Diff between GB2 versions 1.2 dated 2014-06-25 and 2.1 dated 2015-05-11
GB2-1.2/GB2/R/CompoundFitAux.R |only GB2-1.2/GB2/man/CompoundFitAux.Rd |only GB2-2.1/GB2/DESCRIPTION | 18 ++--- GB2-2.1/GB2/MD5 | 74 ++++++++++++---------- GB2-2.1/GB2/NAMESPACE | 22 ++++++ GB2-2.1/GB2/R/Compound.R | 16 ++-- GB2-2.1/GB2/R/CompoundAuxDensPlot.r |only GB2-2.1/GB2/R/CompoundAuxFit.R |only GB2-2.1/GB2/R/CompoundAuxVarest.r |only GB2-2.1/GB2/R/CompoundDensPlot.r |only GB2-2.1/GB2/R/CompoundFit.R | 58 ++++++++--------- GB2-2.1/GB2/R/CompoundIndicators.R | 36 +++++++---- GB2-2.1/GB2/R/CompoundMoments.R | 10 +-- GB2-2.1/GB2/R/CompoundQuantiles.R | 26 +++---- GB2-2.1/GB2/R/CompoundVarest.R |only GB2-2.1/GB2/R/Contindic.R | 14 ++-- GB2-2.1/GB2/man/Compound.Rd | 11 +-- GB2-2.1/GB2/man/CompoundAuxDensPlot.Rd |only GB2-2.1/GB2/man/CompoundAuxFit.Rd |only GB2-2.1/GB2/man/CompoundAuxVarest.Rd |only GB2-2.1/GB2/man/CompoundDensPlot.Rd |only GB2-2.1/GB2/man/CompoundFit.Rd | 41 +++++++----- GB2-2.1/GB2/man/CompoundIndicators.Rd | 33 +++++----- GB2-2.1/GB2/man/CompoundMoments.Rd | 8 +- GB2-2.1/GB2/man/CompoundQuantiles.Rd | 8 +- GB2-2.1/GB2/man/CompoundVarest.Rd |only GB2-2.1/GB2/man/Contindic.Rd | 38 +++++------ GB2-2.1/GB2/man/Contprof.Rd | 2 GB2-2.1/GB2/man/Fisk.Rd | 2 GB2-2.1/GB2/man/Gini.Rd | 2 GB2-2.1/GB2/man/Indicators.Rd | 2 GB2-2.1/GB2/man/LogDensity.Rd | 2 GB2-2.1/GB2/man/LogLikelihood.Rd | 2 GB2-2.1/GB2/man/MLfitGB2.Rd | 2 GB2-2.1/GB2/man/MLfullGB2.Rd | 8 +- GB2-2.1/GB2/man/MLprofGB2.Rd | 2 GB2-2.1/GB2/man/Moments.Rd | 2 GB2-2.1/GB2/man/NonlinearFit.Rd | 2 GB2-2.1/GB2/man/PlotsML.Rd | 4 - GB2-2.1/GB2/man/ProfLogLikelihood.Rd | 2 GB2-2.1/GB2/man/RobustWeights.Rd | 2 GB2-2.1/GB2/man/Thomae.Rd | 2 GB2-2.1/GB2/man/Varest.Rd | 108 +++++++++++++-------------------- GB2-2.1/GB2/man/gb2.Rd | 2 44 files changed, 293 insertions(+), 268 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Description: Easy integration of phenotypic, genotypic and environmental information with "ecogen" objects. Geostatistical tools for analyzing spatial patterns in population biology and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <leandroroser@ege.fcen.uba.ar>
Diff between EcoGenetics versions 1.1.0 dated 2015-02-19 and 1.2.0 dated 2015-05-11
EcoGenetics-1.1.0/EcoGenetics/R/eco.autocor.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.boothet.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.char2num.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.geary.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.getisord.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.joincount.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.laglistw.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.localmoran.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.moran.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.rarefact.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.rescale.R |only EcoGenetics-1.1.0/EcoGenetics/R/eco.sort.R |only EcoGenetics-1.1.0/EcoGenetics/R/ecogen.definition.R |only EcoGenetics-1.1.0/EcoGenetics/R/latlon2distm.R |only EcoGenetics-1.1.0/EcoGenetics/R/other.classes.R |only EcoGenetics-1.1.0/EcoGenetics/data/eco.test.rda |only EcoGenetics-1.1.0/EcoGenetics/man/RelDist-class.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/RelDist-methods.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.autocor.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.boothet.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.char2num.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.geary.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.getisord.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.joincount.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.laglistw.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.localmoran.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.moran.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.rarefact.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.rescale.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/eco.sort.Rd |only EcoGenetics-1.1.0/EcoGenetics/man/latlon2distm.Rd |only EcoGenetics-1.2.0/EcoGenetics/DESCRIPTION | 47 EcoGenetics-1.2.0/EcoGenetics/MD5 | 251 +- EcoGenetics-1.2.0/EcoGenetics/NAMESPACE | 145 - EcoGenetics-1.2.0/EcoGenetics/NEWS | 51 EcoGenetics-1.2.0/EcoGenetics/R/ZZZ.R | 2 EcoGenetics-1.2.0/EcoGenetics/R/auxiliar.R |only EcoGenetics-1.2.0/EcoGenetics/R/classes.R |only EcoGenetics-1.2.0/EcoGenetics/R/control.R |only EcoGenetics-1.2.0/EcoGenetics/R/deprecated.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.2columns.R | 102 EcoGenetics-1.2.0/EcoGenetics/R/eco.2geneland.R | 88 EcoGenetics-1.2.0/EcoGenetics/R/eco.2genepop.R | 183 - EcoGenetics-1.2.0/EcoGenetics/R/eco.2gstudio.R | 47 EcoGenetics-1.2.0/EcoGenetics/R/eco.2hierfstat.R | 95 EcoGenetics-1.2.0/EcoGenetics/R/eco.2spagedi.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.NDVI.R | 324 +-- EcoGenetics-1.2.0/EcoGenetics/R/eco.NDVI.post.R | 242 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.alfreq.R | 103 EcoGenetics-1.2.0/EcoGenetics/R/eco.append.R | 45 EcoGenetics-1.2.0/EcoGenetics/R/eco.association.R | 301 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.cbind.R | 226 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.clear.R | 29 EcoGenetics-1.2.0/EcoGenetics/R/eco.cormantel.R | 339 +-- EcoGenetics-1.2.0/EcoGenetics/R/eco.correlog.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.detrend.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.forestplot.R | 264 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.gsa.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.lagweight.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.lmtree.R | 192 - EcoGenetics-1.2.0/EcoGenetics/R/eco.lsa.R |only EcoGenetics-1.2.0/EcoGenetics/R/eco.mantel.R | 118 - EcoGenetics-1.2.0/EcoGenetics/R/eco.merge.R | 239 +- EcoGenetics-1.2.0/EcoGenetics/R/eco.order.R | 172 - EcoGenetics-1.2.0/EcoGenetics/R/eco.pairtest.R | 205 + EcoGenetics-1.2.0/EcoGenetics/R/eco.post.geneland.R | 69 EcoGenetics-1.2.0/EcoGenetics/R/eco.rankplot.R | 382 ++- EcoGenetics-1.2.0/EcoGenetics/R/eco.rbind.R | 94 EcoGenetics-1.2.0/EcoGenetics/R/eco.remove.R | 30 EcoGenetics-1.2.0/EcoGenetics/R/eco.subset.R | 85 EcoGenetics-1.2.0/EcoGenetics/R/eco.theilsen.R | 156 - EcoGenetics-1.2.0/EcoGenetics/R/eco.variogram.R | 151 - EcoGenetics-1.2.0/EcoGenetics/R/eco.weight.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.break.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.crosscor.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.ecogen.definition.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.geary.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.jackknife.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.joincount.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.mantel.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.moran.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.multitable.R |only EcoGenetics-1.2.0/EcoGenetics/R/int.random.test.R |only EcoGenetics-1.2.0/EcoGenetics/R/plot.methods.R |only EcoGenetics-1.2.0/EcoGenetics/R/show_summary.methods.R |only EcoGenetics-1.2.0/EcoGenetics/data/eco.test.RData |only EcoGenetics-1.2.0/EcoGenetics/data/eco2.RData |only EcoGenetics-1.2.0/EcoGenetics/data/eco3.RData |only EcoGenetics-1.2.0/EcoGenetics/data/tab.RData |only EcoGenetics-1.2.0/EcoGenetics/man/EcoGenetics-package.Rd | 1057 +++++----- EcoGenetics-1.2.0/EcoGenetics/man/aue.char2num.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.circle.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.circle.w.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.diamond.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.filter.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.image2df.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.point.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.rescale.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.sort.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/aue.square.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/coordinates.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/eco.2columns.Rd | 64 EcoGenetics-1.2.0/EcoGenetics/man/eco.2geneland.Rd | 76 EcoGenetics-1.2.0/EcoGenetics/man/eco.2genepop.Rd | 74 EcoGenetics-1.2.0/EcoGenetics/man/eco.2gstudio.Rd | 66 EcoGenetics-1.2.0/EcoGenetics/man/eco.2hierfstat.Rd | 64 EcoGenetics-1.2.0/EcoGenetics/man/eco.2spagedi.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.NDVI.Rd | 161 - EcoGenetics-1.2.0/EcoGenetics/man/eco.NDVI.post.Rd | 194 + EcoGenetics-1.2.0/EcoGenetics/man/eco.Rd | 36 EcoGenetics-1.2.0/EcoGenetics/man/eco.alfreq.Rd | 68 EcoGenetics-1.2.0/EcoGenetics/man/eco.append.Rd | 66 EcoGenetics-1.2.0/EcoGenetics/man/eco.association.Rd | 113 - EcoGenetics-1.2.0/EcoGenetics/man/eco.autol-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.cbind.Rd | 81 EcoGenetics-1.2.0/EcoGenetics/man/eco.clear.Rd | 60 EcoGenetics-1.2.0/EcoGenetics/man/eco.cormantel.Rd | 201 + EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.correlog.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.detrend.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.gsa.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lagweight.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lmtree-methods.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/eco.lmtree.Rd | 185 - EcoGenetics-1.2.0/EcoGenetics/man/eco.lmtree.mctree-summary.Rd | 88 EcoGenetics-1.2.0/EcoGenetics/man/eco.lsa-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lsa-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.lsa.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.mantel.Rd | 113 - EcoGenetics-1.2.0/EcoGenetics/man/eco.mctree-class.Rd | 54 EcoGenetics-1.2.0/EcoGenetics/man/eco.merge.Rd | 100 EcoGenetics-1.2.0/EcoGenetics/man/eco.mlm-class.Rd | 54 EcoGenetics-1.2.0/EcoGenetics/man/eco.order.Rd | 79 EcoGenetics-1.2.0/EcoGenetics/man/eco.pairtest.Rd | 108 - EcoGenetics-1.2.0/EcoGenetics/man/eco.post.geneland.Rd | 141 - EcoGenetics-1.2.0/EcoGenetics/man/eco.rbind.Rd | 55 EcoGenetics-1.2.0/EcoGenetics/man/eco.remove.Rd | 73 EcoGenetics-1.2.0/EcoGenetics/man/eco.subset.Rd | 71 EcoGenetics-1.2.0/EcoGenetics/man/eco.theilsen.Rd | 145 - EcoGenetics-1.2.0/EcoGenetics/man/eco.variogram-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.variogram.Rd | 124 - EcoGenetics-1.2.0/EcoGenetics/man/eco.weight-class.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.weight-methods.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco.weight.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco2.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/eco3.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/ecogen-class.Rd | 66 EcoGenetics-1.2.0/EcoGenetics/man/ecogen-methods.Rd | 86 EcoGenetics-1.2.0/EcoGenetics/man/ecogen-summary.Rd | 88 EcoGenetics-1.2.0/EcoGenetics/man/ecogen.Rd | 190 - EcoGenetics-1.2.0/EcoGenetics/man/ecogen2genind-genind2ecogen.Rd | 50 EcoGenetics-1.2.0/EcoGenetics/man/environment.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/forestplot-methods.Rd | 116 - EcoGenetics-1.2.0/EcoGenetics/man/genotype.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/int.2symmetric.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.break.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.check.con.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.check.numeric.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.crosscor.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.dlatlon2distm.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.geary.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.jackknife.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.joincount.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.mantel.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.moran.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.multitable.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.random.test.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/int.undimmattg.Rd |only EcoGenetics-1.2.0/EcoGenetics/man/phenotype.Rd | 38 EcoGenetics-1.2.0/EcoGenetics/man/rankplot-methods.Rd | 139 - EcoGenetics-1.2.0/EcoGenetics/man/structure.Rd | 36 EcoGenetics-1.2.0/EcoGenetics/man/tab.Rd | 48 179 files changed, 5168 insertions(+), 4389 deletions(-)
Title: Import Stata 13 and 14 Data Files
Description: Function to read and write the Stata 13 (and newer) file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.6.1 dated 2015-03-24 and 0.7 dated 2015-05-11
DESCRIPTION | 14 +- MD5 | 43 ++++--- NAMESPACE | 2 NEWS |only R/read.R | 28 +++-- R/readstata13.R | 2 R/save.R | 82 +++++++++++---- R/tools.R | 9 - README.md | 10 - man/as.caldays.Rd | 2 man/get.label.Rd | 2 man/get.label.name.Rd | 2 man/get.lang.Rd | 2 man/get.origin.codes.Rd | 2 man/get.varlabel.Rd | 2 man/read.dta13.Rd | 11 +- man/readstata13.Rd | 4 man/save.dta13.Rd | 8 - man/set.label.Rd | 2 man/set.lang.Rd | 2 man/stbcal.Rd | 2 src/rcpp_readstata.cpp | 262 +++++++++++++++++++++++++++--------------------- src/rcpp_savestata.cpp | 61 ++++++++--- 23 files changed, 342 insertions(+), 212 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with
quantitative discourse analysis of transcripts containing
discourse including frequency counts of sentence types, words,
sentences, turns of talk, syllables and other assorted analysis
tasks. The package provides parsing tools for preparing
transcript data. Many functions enable the user to aggregate
data by any number of grouping variables, providing analysis
and seamless integration with other R packages that undertake
higher level analysis and visualization of text. This affords
the user a more efficient and targeted analysis. 'qdap' is
designed for transcript analysis, however, many functions are
applicable to other areas of Text Mining/Natural Language
Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.0 dated 2014-10-04 and 2.2.1 dated 2015-05-11
DESCRIPTION | 48 MD5 | 947 +++++------ NAMESPACE | 48 NEWS | 127 + R/Animate.character.R |only R/add_incomplete.R |only R/as.tdm.R | 16 R/automated_readability_index.R | 2 R/build_qdap_vignette.R | 25 R/check_text.R | 2 R/dispersion_plot.R | 25 R/end_mark.R | 2 R/formality.R | 165 + R/incomplete_replace.R | 4 R/lexical_classification.R |only R/multigsub.R | 45 R/name2sex.R | 41 R/phrase_net.R | 6 R/polarity.R | 156 + R/pos.R | 21 R/qdap-package.R | 2 R/qdap_df.R | 2 R/scrubber.R | 3 R/sentSplit.R | 28 R/strip.R | 84 R/termco.R | 34 R/termco.h.R | 5 R/trans_context.R | 5 R/type_token_ratio.R |only R/word_length.R |only R/word_position.R |only R/word_stats.R | 2 README.md | 21 build/vignette.rds |binary data/DATA.SPLIT.rda |binary data/DATA.rda |binary data/DATA2.rda |binary data/env.syl.rda |binary data/hamlet.rda |binary data/mraja1.rda |binary data/mraja1spl.rda |binary data/pres_debate_raw2012.rda |binary data/pres_debates2012.rda |binary data/raj.act.1.rda |binary data/raj.act.1POS.rda |binary data/raj.act.2.rda |binary data/raj.act.3.rda |binary data/raj.act.4.rda |binary data/raj.act.5.rda |binary data/raj.demographics.rda |binary data/raj.rda |binary data/rajPOS.rda |binary data/rajSPLIT.rda |binary data/raw.time.span.rda |binary data/sample.time.span.rda |binary inst/CITATION | 4 inst/Rmd_vignette/funs/extra_functions.txt | 20 inst/Rmd_vignette/qdap_vignette.Rmd | 1356 +++++++++++++++- inst/doc/cleaning_and_debugging.pdf |binary inst/doc/tm_package_compatibility.pdf |binary man/Animate.Rd | 3 man/Animate.character.Rd |only man/Animate.discourse_map.Rd | 3 man/Animate.formality.Rd | 21 man/Animate.gantt.Rd | 3 man/Animate.gantt_plot.Rd | 3 man/Animate.lexical_classification.Rd |only man/Animate.polarity.Rd | 25 man/DATA.Rd | 3 man/DATA.SPLIT.Rd | 3 man/DATA2.Rd | 3 man/Dissimilarity.Rd | 3 man/Filter.Rd | 3 man/NAer.Rd | 3 man/Network.Rd | 3 man/Network.formality.Rd | 3 man/Network.lexical_classification.Rd |only man/Network.polarity.Rd | 3 man/Readability.Rd | 5 man/Search.Rd | 3 man/Title.Rd | 3 man/Trim.Rd | 3 man/Word_Frequency_Matrix.Rd | 3 man/addNetwork.Rd | 3 man/add_incomplete.Rd |only man/adjacency_matrix.Rd | 3 man/all_words.Rd | 3 man/as.tdm.Rd | 17 man/bag_o_words.Rd | 3 man/beg2char.Rd | 3 man/blank2NA.Rd | 3 man/bracketX.Rd | 3 man/build_qdap_vignette.Rd | 3 man/capitalizer.Rd | 3 man/chain.Rd | 3 man/check_spelling.Rd | 3 man/check_spelling_interactive.character.Rd | 3 man/check_spelling_interactive.check_spelling.Rd | 3 man/check_spelling_interactive.factor.Rd | 3 man/check_text.Rd | 3 man/chunker.Rd | 3 man/clean.Rd | 3 man/cm_2long.Rd | 3 man/cm_code.blank.Rd | 3 man/cm_code.combine.Rd | 3 man/cm_code.exclude.Rd | 3 man/cm_code.overlap.Rd | 3 man/cm_code.transform.Rd | 3 man/cm_combine.dummy.Rd | 3 man/cm_df.fill.Rd | 3 man/cm_df.temp.Rd | 3 man/cm_df.transcript.Rd | 3 man/cm_df2long.Rd | 3 man/cm_distance.Rd | 3 man/cm_dummy2long.Rd | 3 man/cm_long2dummy.Rd | 3 man/cm_range.temp.Rd | 3 man/cm_range2long.Rd | 3 man/cm_time.temp.Rd | 3 man/cm_time2long.Rd | 3 man/colSplit.Rd | 3 man/colcomb2class.Rd | 3 man/colsplit2df.Rd | 3 man/comma_spacer.Rd | 3 man/common.Rd | 3 man/common.list.Rd | 3 man/condense.Rd | 3 man/counts.Rd | 3 man/counts.SMOG.Rd | 3 man/counts.automated_readability_index.Rd | 3 man/counts.character_table.Rd | 3 man/counts.coleman_liau.Rd | 3 man/counts.end_mark_by.Rd | 3 man/counts.flesch_kincaid.Rd | 3 man/counts.formality.Rd | 3 man/counts.fry.Rd | 3 man/counts.linsear_write.Rd | 3 man/counts.object_pronoun_type.Rd | 3 man/counts.polarity.Rd | 3 man/counts.pos.Rd | 3 man/counts.pos_by.Rd | 3 man/counts.pronoun_type.Rd | 3 man/counts.question_type.Rd | 3 man/counts.subject_pronoun_type.Rd | 3 man/counts.termco.Rd | 3 man/counts.word_length.Rd |only man/counts.word_position.Rd |only man/counts.word_stats.Rd | 3 man/cumulative.Rd | 15 man/data_viewing.Rd | 3 man/deprecated.Rd | 3 man/dir_map.Rd | 3 man/discourse_map.Rd | 3 man/dispersion_plot.Rd | 28 man/dist_tab.Rd | 3 man/diversity.Rd | 3 man/duplicates.Rd | 3 man/end_inc.Rd | 3 man/end_mark.Rd | 3 man/env.syl.Rd | 3 man/exclude.Rd | 3 man/formality.Rd | 3 man/freq_terms.Rd | 3 man/gantt.Rd | 3 man/gantt_plot.Rd | 3 man/gantt_rep.Rd | 3 man/gantt_wrap.Rd | 3 man/gradient_cloud.Rd | 3 man/hamlet.Rd | 5 man/igraph_params.Rd | 3 man/imperative.Rd | 3 man/incomplete_replace.Rd | 3 man/is.global.Rd | 3 man/justification.Rd | 3 man/key_merge.Rd | 3 man/kullback_leibler.Rd | 3 man/lexical_classification.Rd |only man/mraja1.Rd | 3 man/mraja1spl.Rd | 3 man/multicsv.Rd | 3 man/multigsub.Rd | 12 man/multiscale.Rd | 3 man/name2sex.Rd | 3 man/new_project.Rd | 3 man/ngrams.Rd | 3 man/object_pronoun_type.Rd | 3 man/outlier_detect.Rd | 3 man/outlier_labeler.Rd | 3 man/paste2.Rd | 3 man/phrase_net.Rd | 9 man/plot.Network.Rd | 3 man/plot.SMOG.Rd | 3 man/plot.animated_character.Rd |only man/plot.animated_discourse_map.Rd | 3 man/plot.animated_formality.Rd | 3 man/plot.animated_lexical_classification.Rd |only man/plot.animated_polarity.Rd | 7 man/plot.automated_readability_index.Rd | 3 man/plot.character_table.Rd | 3 man/plot.cm_distance.Rd | 3 man/plot.cmspans.Rd | 3 man/plot.coleman_liau.Rd | 3 man/plot.combo_syllable_sum.Rd | 3 man/plot.cumulative_animated_formality.Rd | 3 man/plot.cumulative_animated_lexical_classification.Rd |only man/plot.cumulative_animated_polarity.Rd | 3 man/plot.cumulative_combo_syllable_sum.Rd | 3 man/plot.cumulative_end_mark.Rd | 3 man/plot.cumulative_formality.Rd | 3 man/plot.cumulative_lexical_classification.Rd |only man/plot.cumulative_polarity.Rd | 3 man/plot.cumulative_syllable_freq.Rd | 3 man/plot.discourse_map.Rd | 3 man/plot.diversity.Rd | 3 man/plot.end_mark.Rd | 3 man/plot.end_mark_by.Rd | 3 man/plot.end_mark_by_count.Rd | 3 man/plot.end_mark_by_preprocessed.Rd | 3 man/plot.end_mark_by_proportion.Rd | 3 man/plot.end_mark_by_score.Rd | 3 man/plot.flesch_kincaid.Rd | 3 man/plot.formality.Rd | 3 man/plot.formality_scores.Rd | 3 man/plot.freq_terms.Rd | 3 man/plot.gantt.Rd | 3 man/plot.kullback_leibler.Rd | 3 man/plot.lexical.Rd |only man/plot.lexical_classification.Rd |only man/plot.lexical_classification_preprocessed.Rd |only man/plot.lexical_classification_score.Rd |only man/plot.linsear_write.Rd | 3 man/plot.linsear_write_count.Rd | 3 man/plot.linsear_write_scores.Rd | 3 man/plot.object_pronoun_type.Rd | 3 man/plot.polarity.Rd | 3 man/plot.polarity_count.Rd | 3 man/plot.polarity_score.Rd | 3 man/plot.pos.Rd | 3 man/plot.pos_by.Rd | 3 man/plot.pos_preprocessed.Rd | 3 man/plot.pronoun_type.Rd | 3 man/plot.question_type.Rd | 3 man/plot.question_type_preprocessed.Rd | 3 man/plot.readability_count.Rd | 3 man/plot.readability_score.Rd | 3 man/plot.rmgantt.Rd | 3 man/plot.sent_split.Rd | 3 man/plot.subject_pronoun_type.Rd | 3 man/plot.sum_cmspans.Rd | 3 man/plot.sums_gantt.Rd | 3 man/plot.syllable_freq.Rd | 3 man/plot.table_count.Rd | 3 man/plot.table_proportion.Rd | 3 man/plot.table_score.Rd | 3 man/plot.termco.Rd | 3 man/plot.type_token_ratio.Rd |only man/plot.weighted_wfm.Rd | 3 man/plot.wfdf.Rd | 3 man/plot.wfm.Rd | 3 man/plot.word_cor.Rd | 3 man/plot.word_length.Rd |only man/plot.word_position.Rd |only man/plot.word_proximity.Rd | 3 man/plot.word_stats.Rd | 3 man/plot.word_stats_counts.Rd | 3 man/polarity.Rd | 7 man/pos.Rd | 10 man/potential_NA.Rd | 3 man/power.Rd | 3 man/preprocessed.Rd | 3 man/preprocessed.check_spelling_interactive.Rd | 3 man/preprocessed.end_mark_by.Rd | 3 man/preprocessed.formality.Rd | 3 man/preprocessed.lexical_classification.Rd |only man/preprocessed.object_pronoun_type.Rd | 3 man/preprocessed.pos.Rd | 3 man/preprocessed.pos_by.Rd | 3 man/preprocessed.pronoun_type.Rd | 3 man/preprocessed.question_type.Rd | 3 man/preprocessed.subject_pronoun_type.Rd | 3 man/preprocessed.word_position.Rd |only man/pres_debate_raw2012.Rd | 3 man/pres_debates2012.Rd | 3 man/print.Dissimilarity.Rd | 3 man/print.Network.Rd | 3 man/print.SMOG.Rd | 3 man/print.adjacency_matrix.Rd | 3 man/print.all_words.Rd | 3 man/print.animated_character.Rd |only man/print.animated_discourse_map.Rd | 3 man/print.animated_formality.Rd | 3 man/print.animated_lexical_classification.Rd |only man/print.animated_polarity.Rd | 7 man/print.automated_readability_index.Rd | 3 man/print.boolean_qdap.Rd | 3 man/print.character_table.Rd | 3 man/print.check_spelling.Rd | 3 man/print.check_spelling_interactive.Rd | 3 man/print.check_text.Rd | 3 man/print.cm_distance.Rd | 3 man/print.coleman_liau.Rd | 3 man/print.colsplit2df.Rd | 3 man/print.combo_syllable_sum.Rd | 3 man/print.cumulative_animated_formality.Rd | 3 man/print.cumulative_animated_lexical_classification.Rd |only man/print.cumulative_animated_polarity.Rd | 3 man/print.cumulative_combo_syllable_sum.Rd | 3 man/print.cumulative_end_mark.Rd | 3 man/print.cumulative_formality.Rd | 3 man/print.cumulative_lexical_classification.Rd |only man/print.cumulative_polarity.Rd | 3 man/print.cumulative_syllable_freq.Rd | 3 man/print.discourse_map.Rd | 3 man/print.diversity.Rd | 3 man/print.end_mark.Rd | 3 man/print.end_mark_by.Rd | 3 man/print.end_mark_by_preprocessed.Rd | 3 man/print.flesch_kincaid.Rd | 3 man/print.formality.Rd | 3 man/print.formality_scores.Rd | 3 man/print.fry.Rd | 3 man/print.kullback_leibler.Rd | 3 man/print.lexical_classification.Rd |only man/print.lexical_classification_by.Rd |only man/print.lexical_classification_preprocessed.Rd |only man/print.lexical_classification_score.Rd |only man/print.linsear_write.Rd | 3 man/print.linsear_write_count.Rd | 3 man/print.linsear_write_scores.Rd | 3 man/print.ngrams.Rd | 3 man/print.object_pronoun_type.Rd | 3 man/print.phrase_net.Rd | 3 man/print.polarity.Rd | 3 man/print.polarity_count.Rd | 3 man/print.polarity_score.Rd | 3 man/print.polysyllable_sum.Rd | 3 man/print.pos.Rd | 3 man/print.pos_by.Rd | 3 man/print.pos_preprocessed.Rd | 3 man/print.pronoun_type.Rd | 3 man/print.qdapProj.Rd | 3 man/print.qdap_context.Rd | 3 man/print.question_type.Rd | 3 man/print.question_type_preprocessed.Rd | 3 man/print.readability_count.Rd | 3 man/print.readability_score.Rd | 3 man/print.sent_split.Rd | 3 man/print.sub_holder.Rd | 3 man/print.subject_pronoun_type.Rd | 3 man/print.sum_cmspans.Rd | 3 man/print.sums_gantt.Rd | 3 man/print.syllable_sum.Rd | 3 man/print.table_count.Rd | 3 man/print.table_proportion.Rd | 3 man/print.table_score.Rd | 3 man/print.termco.Rd | 3 man/print.trunc.Rd | 3 man/print.type_token_ratio.Rd |only man/print.wfm.Rd | 3 man/print.wfm_summary.Rd | 3 man/print.which_misspelled.Rd | 3 man/print.word_associate.Rd | 3 man/print.word_cor.Rd | 3 man/print.word_length.Rd |only man/print.word_list.Rd | 3 man/print.word_position.Rd |only man/print.word_proximity.Rd | 3 man/print.word_stats.Rd | 3 man/print.word_stats_counts.Rd | 3 man/pronoun_type.Rd | 3 man/prop.Rd | 3 man/proportions.Rd | 3 man/proportions.character_table.Rd | 3 man/proportions.end_mark_by.Rd | 3 man/proportions.formality.Rd | 3 man/proportions.object_pronoun_type.Rd | 3 man/proportions.pos.Rd | 3 man/proportions.pos_by.Rd | 3 man/proportions.pronoun_type.Rd | 3 man/proportions.question_type.Rd | 3 man/proportions.subject_pronoun_type.Rd | 3 man/proportions.termco.Rd | 3 man/proportions.word_length.Rd |only man/proportions.word_position.Rd |only man/qcombine.Rd | 3 man/qcv.Rd | 3 man/qdap.Rd | 3 man/qdap_df.Rd | 3 man/qheat.Rd | 3 man/qprep.Rd | 3 man/qtheme.Rd | 3 man/question_type.Rd | 3 man/raj.Rd | 3 man/raj.act.1.Rd | 3 man/raj.act.1POS.Rd | 3 man/raj.act.2.Rd | 3 man/raj.act.3.Rd | 3 man/raj.act.4.Rd | 3 man/raj.act.5.Rd | 3 man/raj.demographics.Rd | 3 man/rajPOS.Rd | 3 man/rajSPLIT.Rd | 3 man/random_data.Rd | 3 man/rank_freq_plot.Rd | 3 man/raw.time.span.Rd | 3 man/read.transcript.Rd | 3 man/replace_abbreviation.Rd | 3 man/replace_contraction.Rd | 3 man/replace_number.Rd | 3 man/replace_ordinal.Rd | 3 man/replace_symbol.Rd | 3 man/replacer.Rd | 3 man/rm_row.Rd | 3 man/rm_stopwords.Rd | 3 man/sample.time.span.Rd | 3 man/scores.Rd | 3 man/scores.SMOG.Rd | 3 man/scores.automated_readability_index.Rd | 3 man/scores.character_table.Rd | 3 man/scores.coleman_liau.Rd | 3 man/scores.end_mark_by.Rd | 3 man/scores.flesch_kincaid.Rd | 3 man/scores.formality.Rd | 3 man/scores.fry.Rd | 3 man/scores.lexical_classification.Rd |only man/scores.linsear_write.Rd | 3 man/scores.object_pronoun_type.Rd | 3 man/scores.polarity.Rd | 3 man/scores.pos_by.Rd | 3 man/scores.pronoun_type.Rd | 3 man/scores.question_type.Rd | 3 man/scores.subject_pronoun_type.Rd | 3 man/scores.termco.Rd | 3 man/scores.word_length.Rd |only man/scores.word_position.Rd |only man/scores.word_stats.Rd | 3 man/scrubber.Rd | 3 man/sentSplit.Rd | 16 man/space_fill.Rd | 3 man/spaste.Rd | 3 man/speakerSplit.Rd | 3 man/stemmer.Rd | 3 man/strWrap.Rd | 3 man/strip.Rd | 27 man/subject_pronoun_type.Rd | 3 man/summary.cmspans.Rd | 3 man/summary.wfdf.Rd | 3 man/summary.wfm.Rd | 3 man/syllabication.Rd | 3 man/synonyms.Rd | 3 man/t.DocumentTermMatrix.Rd | 3 man/t.TermDocumentMatrix.Rd | 3 man/termco.Rd | 28 man/termco_c.Rd | 3 man/tot_plot.Rd | 3 man/trans_cloud.Rd | 3 man/trans_context.Rd | 6 man/trans_venn.Rd | 3 man/type_text_ratio.Rd |only man/unique_by.Rd | 3 man/visual.Rd | 3 man/visual.discourse_map.Rd | 3 man/weight.Rd | 3 man/word_associate.Rd | 3 man/word_cor.Rd | 3 man/word_count.Rd | 3 man/word_diff_list.Rd | 3 man/word_length.Rd |only man/word_list.Rd | 3 man/word_network_plot.Rd | 3 man/word_position.Rd |only man/word_proximity.Rd | 3 man/word_stats.Rd | 3 tests/testthat/test-add_incomplete.R |only tests/testthat/test-adjacency_matrix.R | 5 tests/testthat/test-all_words.R | 1 tests/testthat/test-as.tdm.R | 6 tests/testthat/test-bag_o_words.R | 4 tests/testthat/test-beg2char.R | 1 tests/testthat/test-blank2NA.R | 1 tests/testthat/test-bracketX.R | 30 tests/testthat/test-capitalizer.R | 8 tests/testthat/test-chunker.R | 3 tests/testthat/test-cm_2long.R | 8 tests/testthat/test-cm_code.blank.R | 10 tests/testthat/test-cmspans.R | 5 tests/testthat/test-colSplit.R | 5 tests/testthat/test-colcomb2class.R | 3 tests/testthat/test-common.R | 2 tests/testthat/test-dispersion_plot.R | 1 tests/testthat/test-end_mark.R | 3 tests/testthat/test-formality.R |only tests/testthat/test-phrase_net.R | 1 tests/testthat/test-polarity.R |only tests/testthat/test-pos.R |only tests/testthat/test-replace_number.R | 8 tests/testthat/test-strip.R |only tests/testthat/test-syllable_sum.R | 8 tests/testthat/test-wfm.R | 30 tests/testthat/test-word_length.R |only 500 files changed, 3477 insertions(+), 1228 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.0.0 dated 2015-03-19 and 1.1.0 dated 2015-05-11
DESCRIPTION | 11 - MD5 | 15 + NAMESPACE | 8 R/phylocurve.R | 366 +++++++++++++++++++++++++++++++++++++++++- man/GP.fit.Rd |only man/nonlinear.fit.Rd |only man/phylocurve-package.Rd | 4 man/phylocurve.Rd | 4 man/phylocurve.generalized.Rd |only man/phylocurve.trim.Rd |only man/polynomial.fit.Rd |only 11 files changed, 390 insertions(+), 18 deletions(-)
Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between GSIF versions 0.4-5 dated 2015-04-22 and 0.4-6 dated 2015-05-11
DESCRIPTION | 14 +++++++------- MD5 | 18 ++++++++++-------- NAMESPACE | 2 +- R/AAAA.R | 12 ++++++++---- R/autopredict.R |only R/fkmeans.R | 4 ++-- R/spmultinom.R | 4 ++-- demo/cookfarm_3DT_RF.R | 9 +++++---- man/FAO.SoilProfileCollection.Rd | 2 +- man/autopredict.Rd |only man/cookfarm.Rd | 2 +- 11 files changed, 37 insertions(+), 30 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Unlike the aster package, this package does dependence groups (nodes of
the graph need not be conditionally independent given their predecessor
node), including multinomial and two-parameter normal as families. Thus
this package also generalizes mark-capture-recapture analysis.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between aster2 versions 0.1 dated 2010-11-03 and 0.2-1 dated 2015-05-11
DESCRIPTION | 31 +++++++++++++++++++++++-------- MD5 |only NEWS |only R/asterdata.R | 3 +++ R/onAttach.R | 11 ++++++----- data/hornworm.rda |only inst/makedata/sim.Rout |only inst/makedata/toy.Rout |only man/aster2-package.Rd | 2 ++ man/echinacea.Rd | 2 +- man/hornworm.Rd |only src/families.c | 4 ++-- 12 files changed, 37 insertions(+), 16 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.1-4 dated 2014-11-06 and 1.1-5 dated 2015-05-11
GGIR-1.1-4/GGIR/R/g.convert.day.names.R |only GGIR-1.1-5/GGIR/DESCRIPTION | 20 GGIR-1.1-5/GGIR/MD5 | 71 +- GGIR-1.1-5/GGIR/R/g.abr.day.names.R |only GGIR-1.1-5/GGIR/R/g.analyse.R | 290 ++-------- GGIR-1.1-5/GGIR/R/g.binread.R | 865 ++++++++++++++------------------ GGIR-1.1-5/GGIR/R/g.calibrate.R | 223 ++++---- GGIR-1.1-5/GGIR/R/g.createcoordinates.R | 43 - GGIR-1.1-5/GGIR/R/g.detecmidnight.R | 13 GGIR-1.1-5/GGIR/R/g.dotorcomma.R | 6 GGIR-1.1-5/GGIR/R/g.downsample.R | 3 GGIR-1.1-5/GGIR/R/g.extractheadervars.R | 5 GGIR-1.1-5/GGIR/R/g.getM5L5.R | 12 GGIR-1.1-5/GGIR/R/g.getmeta.R | 211 +++---- GGIR-1.1-5/GGIR/R/g.impute.R | 40 - GGIR-1.1-5/GGIR/R/g.inspectfile.R | 328 +++++------- GGIR-1.1-5/GGIR/R/g.metric.R | 37 - GGIR-1.1-5/GGIR/R/g.part1.R | 142 +++-- GGIR-1.1-5/GGIR/R/g.part2.R | 232 +++----- GGIR-1.1-5/GGIR/R/g.plot.R | 28 - GGIR-1.1-5/GGIR/R/g.report.part2.R |only GGIR-1.1-5/GGIR/R/g.shell.GGIR.R | 113 +++- GGIR-1.1-5/GGIR/R/g.weardec.R | 9 GGIR-1.1-5/GGIR/inst/NEWS.Rd | 16 GGIR-1.1-5/GGIR/man/GGIR-package.Rd | 45 - GGIR-1.1-5/GGIR/man/data.calibrate.Rd | 3 GGIR-1.1-5/GGIR/man/data.getmeta.Rd | 3 GGIR-1.1-5/GGIR/man/data.inspectfile.Rd | 3 GGIR-1.1-5/GGIR/man/g.analyse.Rd | 40 - GGIR-1.1-5/GGIR/man/g.binread.Rd | 2 GGIR-1.1-5/GGIR/man/g.calibrate.Rd | 14 GGIR-1.1-5/GGIR/man/g.getmeta.Rd | 20 GGIR-1.1-5/GGIR/man/g.impute.Rd | 6 GGIR-1.1-5/GGIR/man/g.inspectfile.Rd | 6 GGIR-1.1-5/GGIR/man/g.part1.Rd | 36 - GGIR-1.1-5/GGIR/man/g.part2.Rd | 38 + GGIR-1.1-5/GGIR/man/g.plot.Rd | 2 GGIR-1.1-5/GGIR/man/g.shell.GGIR.Rd | 208 ------- 38 files changed, 1384 insertions(+), 1749 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.36 dated 2014-09-29 and 1.0.69 dated 2015-05-11
DESCRIPTION | 11 MD5 | 70 NAMESPACE | 32 NEWS | 9 R/CarmaNoise.R | 10 R/ClassCogarch.R |only R/DiagnosticCogarch.R |only R/MM.COGARCH.R |only R/WoodChanfGn.R | 2 R/adaBayes.R | 2 R/asymptotic_term_second.R | 2 R/asymptotic_term_third.R | 2 R/asymptotic_term_third_function.R | 2 R/cce.R | 5372 ++++++++++++++++++------------------- R/cogarchNoise.R |only R/hyavar.R |only R/llag.R | 31 R/lse.R | 2 R/qgv.R | 2 R/qmle.R | 450 ++- R/rng.R | 6 R/setCarma.R | 37 R/setCogarch.R |only R/sim.euler.R | 20 R/simFunctional.R | 2 R/simulate.R | 978 +++++- R/toLatex.R | 248 + R/yuima.R | 44 R/yuima.model.R | 2 man/Diagnostic.Cogarch.Rd |only man/cce.Rd | 828 +++-- man/cogarch.gmm.incr.rd |only man/cogarch.gmm.rd |only man/cogarch.info-class.Rd |only man/cogarchNoise.Rd |only man/gmm.rd |only man/hyavar.Rd |only man/setCarma.Rd | 3 man/setCogarch.Rd |only man/simulate.Rd | 5 man/toLatex.Rd | 13 man/yuima.cogarch-class.Rd |only src/carmafilter.c |only src/cce_functions.c | 228 + 44 files changed, 4854 insertions(+), 3559 deletions(-)
Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between RVsharing versions 1.1.0 dated 2013-10-30 and 1.3.4 dated 2015-05-11
DESCRIPTION | 14 - MD5 | 42 +-- NAMESPACE | 7 R/AllClasses.R | 12 - R/AllGenerics.R | 4 R/PFU.R | 84 +++---- R/functions.R | 316 +++++++++++++-------------- R/methods-RVsharingProb.R | 138 ++++++------ R/methods-pedigree.R | 63 +++-- R/methods-trio.R | 50 ++-- R/ped2trio.R | 358 +++++++++++++++---------------- R/rare_variant_sharing_v3.R | 424 +++++++++++++++++++++++++++++-------- R/zzz.R | 20 - man/GeneDrop.Rd | 50 ++-- man/GeneDropSim.fn.Rd | 86 +++---- man/GeneDropSimExcessSharing.fn.Rd | 97 ++++---- man/RVsharing.Rd | 96 ++++---- man/RVsharingProb.rd | 48 ++-- man/Trio.Rd | 26 +- man/compute.kinship.prop.coef.Rd | 70 +++--- man/ped.list.Rd | 12 - man/ped2trio.Rd | 60 ++--- 22 files changed, 1175 insertions(+), 902 deletions(-)
Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses,
implementing PLS methods for classification with
microarray data and prediction of transcription factor
activities from combined ChIP-chip analysis. The >=1.2-1
versions include two new classification methods for microarray
data: GSIM and Ridge PLS. The >=1.3 versions includes a
new classification method combining variable selection and
compression in logistic regression context: RIRLS-SPLS; and
an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,
Ghislain Durif <ghislain.durif@univ-lyon1.fr>,
Sophie Lambert-Lacroix <Sophie.Lambert@imag.fr>, Julie Peyre
<Julie.Peyre@imag.fr>, and Korbinian Strimmer
<strimmer@uni-leipzig.de>.
Maintainer: Ghislain Durif <ghislain.durif@univ-lyon1.fr>
Diff between plsgenomics versions 1.3 dated 2015-05-07 and 1.3-1 dated 2015-05-11
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.1 dated 2015-03-06 and 1.2 dated 2015-05-11
httk-1.1/httk/R/Calc_elimination_rate.r |only httk-1.1/httk/R/Parameterize_SteadyState.r |only httk-1.2/httk/DESCRIPTION | 10 httk-1.2/httk/MD5 | 126 ++++++------ httk-1.2/httk/NAMESPACE | 2 httk-1.2/httk/R/3compPBPKmodel_inits.R | 14 - httk-1.2/httk/R/Calc_Hepatic_Clearance.r | 46 ++-- httk-1.2/httk/R/Calc_elimination_rate.R |only httk-1.2/httk/R/Calc_ratioblood2plasma.R | 40 --- httk-1.2/httk/R/Calc_total_clearance.R | 11 - httk-1.2/httk/R/Calc_volume_of_distribution.R | 72 +++---- httk-1.2/httk/R/Export_PBTK_Jarnac.R | 18 - httk-1.2/httk/R/Export_PBTK_SBML.R | 18 - httk-1.2/httk/R/Get_invitroPK_param.r | 2 httk-1.2/httk/R/Parameterize_3comp.r | 7 httk-1.2/httk/R/Parameterize_PBTK.r | 51 ++--- httk-1.2/httk/R/Parameterize_SteadyState.R |only httk-1.2/httk/R/Predict_partitioning_Schmitt.R | 55 ++--- httk-1.2/httk/R/add_chemtable.R | 31 ++- httk-1.2/httk/R/calc_analytic_css.R | 60 ++--- httk-1.2/httk/R/calc_chem_stats.R | 18 - httk-1.2/httk/R/calc_css.R | 30 +- httk-1.2/httk/R/calc_mc_css.R | 9 httk-1.2/httk/R/calc_stats.R | 6 httk-1.2/httk/R/get_cheminfo.R | 26 +- httk-1.2/httk/R/parameterize_1comp.R | 33 ++- httk-1.2/httk/R/parameterize_schmitt.R |only httk-1.2/httk/R/pbtk1comp_inits.R |only httk-1.2/httk/R/solve_1comp.R | 201 ++++++++++++-------- httk-1.2/httk/R/solve_3comp.R | 142 +++++++++----- httk-1.2/httk/R/solve_pbtk.R | 124 ++++++++---- httk-1.2/httk/data/Tables.RData |binary httk-1.2/httk/man/Calc_elimination_rate.Rd | 11 - httk-1.2/httk/man/Calc_ratioblood2plasma.Rd | 13 - httk-1.2/httk/man/Calc_volume_of_distriution.Rd | 20 - httk-1.2/httk/man/PK_physiology_data.Rd | 2 httk-1.2/httk/man/Parameterize_PBTK.Rd | 15 - httk-1.2/httk/man/Parameterize_SteadyState.Rd | 19 - httk-1.2/httk/man/Wetmore_Css.Rd | 4 httk-1.2/httk/man/Wetmore_Oral_Equiv.Rd | 4 httk-1.2/httk/man/add_chemtable.Rd | 6 httk-1.2/httk/man/calc_analytic_css.Rd | 14 - httk-1.2/httk/man/calc_css.Rd | 150 -------------- httk-1.2/httk/man/calc_hepatic_clearance.Rd | 9 httk-1.2/httk/man/calc_mc_css.Rd | 13 - httk-1.2/httk/man/calc_mc_oral_equiv.Rd | 4 httk-1.2/httk/man/calc_stats.Rd | 13 - httk-1.2/httk/man/calc_total_clearance.Rd | 11 - httk-1.2/httk/man/chem_invivo_PK_data.Rd | 2 httk-1.2/httk/man/chem_invivo_PK_summary_data.Rd | 2 httk-1.2/httk/man/chem_physical_and_invitro_data.Rd | 2 httk-1.2/httk/man/export_pbtk_jarnac.Rd | 2 httk-1.2/httk/man/export_pbtk_sbml.Rd | 2 httk-1.2/httk/man/get_cheminfo.Rd | 7 httk-1.2/httk/man/get_wetmore_cheminfo.Rd | 4 httk-1.2/httk/man/monte_carlo.Rd | 18 - httk-1.2/httk/man/parameterize_1comp.Rd | 15 - httk-1.2/httk/man/parameterize_3comp.Rd | 16 - httk-1.2/httk/man/parameterize_schmitt.Rd |only httk-1.2/httk/man/predict_partitioning_schmitt.Rd | 54 ++--- httk-1.2/httk/man/solve_1comp_pk.Rd | 25 +- httk-1.2/httk/man/solve_3comp_pbpk.Rd | 25 +- httk-1.2/httk/man/solve_pbtk.Rd | 25 +- httk-1.2/httk/man/tissue_data.Rd | 2 httk-1.2/httk/src/3compPBPKmodel.c | 50 ++-- httk-1.2/httk/src/pbtk1comp.c |only httk-1.2/httk/tests |only 67 files changed, 880 insertions(+), 831 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes. Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change,
especially before version 1.0.0 is released; see the NEWS
file for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 0.9-7 dated 2015-03-06 and 0.9-8 dated 2015-05-11
VGAM-0.9-7/VGAM/R/family.quantal.R |only VGAM-0.9-8/VGAM/DESCRIPTION | 34 VGAM-0.9-8/VGAM/MD5 | 249 - VGAM-0.9-8/VGAM/NAMESPACE | 13 VGAM-0.9-8/VGAM/NEWS | 38 VGAM-0.9-8/VGAM/R/family.actuary.R | 4323 ++++++++++++++++++---------- VGAM-0.9-8/VGAM/R/family.basics.R | 16 VGAM-0.9-8/VGAM/R/family.binomial.R | 178 - VGAM-0.9-8/VGAM/R/family.categorical.R | 470 --- VGAM-0.9-8/VGAM/R/family.censored.R | 6 VGAM-0.9-8/VGAM/R/family.extremes.R | 266 - VGAM-0.9-8/VGAM/R/family.genetic.R | 326 -- VGAM-0.9-8/VGAM/R/family.glmgam.R | 325 -- VGAM-0.9-8/VGAM/R/family.nonlinear.R | 4 VGAM-0.9-8/VGAM/R/family.normal.R | 543 --- VGAM-0.9-8/VGAM/R/family.positive.R | 12 VGAM-0.9-8/VGAM/R/family.rcim.R | 2 VGAM-0.9-8/VGAM/R/family.rcqo.R | 46 VGAM-0.9-8/VGAM/R/family.ts.R | 497 +++ VGAM-0.9-8/VGAM/R/family.univariate.R | 326 +- VGAM-0.9-8/VGAM/R/family.zeroinf.R | 38 VGAM-0.9-8/VGAM/R/vgam.R | 51 VGAM-0.9-8/VGAM/build |only VGAM-0.9-8/VGAM/data/Huggins89.t1.rda |binary VGAM-0.9-8/VGAM/data/Huggins89table1.rda |binary VGAM-0.9-8/VGAM/data/alclevels.rda |binary VGAM-0.9-8/VGAM/data/alcoff.rda |binary VGAM-0.9-8/VGAM/data/auuc.rda |binary VGAM-0.9-8/VGAM/data/backPain.rda |binary VGAM-0.9-8/VGAM/data/beggs.rda |binary VGAM-0.9-8/VGAM/data/car.all.rda |binary VGAM-0.9-8/VGAM/data/cfibrosis.rda |binary VGAM-0.9-8/VGAM/data/corbet.rda |binary VGAM-0.9-8/VGAM/data/crashbc.rda |binary VGAM-0.9-8/VGAM/data/crashf.rda |binary VGAM-0.9-8/VGAM/data/crashi.rda |binary VGAM-0.9-8/VGAM/data/crashmc.rda |binary VGAM-0.9-8/VGAM/data/crashp.rda |binary VGAM-0.9-8/VGAM/data/crashtr.rda |binary VGAM-0.9-8/VGAM/data/deermice.rda |binary VGAM-0.9-8/VGAM/data/ducklings.rda |binary VGAM-0.9-8/VGAM/data/finney44.rda |binary VGAM-0.9-8/VGAM/data/flourbeetle.rda |binary VGAM-0.9-8/VGAM/data/hspider.rda |binary VGAM-0.9-8/VGAM/data/lakeO.rda |binary VGAM-0.9-8/VGAM/data/leukemia.rda |binary VGAM-0.9-8/VGAM/data/marital.nz.rda |binary VGAM-0.9-8/VGAM/data/melbmaxtemp.rda |binary VGAM-0.9-8/VGAM/data/pneumo.rda |binary VGAM-0.9-8/VGAM/data/prinia.rda |binary VGAM-0.9-8/VGAM/data/ruge.rda |binary VGAM-0.9-8/VGAM/data/toxop.rda |binary VGAM-0.9-8/VGAM/data/venice.rda |binary VGAM-0.9-8/VGAM/data/venice90.rda |binary VGAM-0.9-8/VGAM/data/wine.rda |binary VGAM-0.9-8/VGAM/inst/CITATION | 23 VGAM-0.9-8/VGAM/inst/doc |only VGAM-0.9-8/VGAM/man/AR1.Rd |only VGAM-0.9-8/VGAM/man/AR1UC.Rd |only VGAM-0.9-8/VGAM/man/VGAM-package.Rd | 21 VGAM-0.9-8/VGAM/man/acat.Rd | 9 VGAM-0.9-8/VGAM/man/betaII.Rd | 28 VGAM-0.9-8/VGAM/man/betaR.Rd | 8 VGAM-0.9-8/VGAM/man/betaff.Rd | 6 VGAM-0.9-8/VGAM/man/betaprime.Rd | 6 VGAM-0.9-8/VGAM/man/binom2.or.Rd | 6 VGAM-0.9-8/VGAM/man/brat.Rd | 4 VGAM-0.9-8/VGAM/man/bratt.Rd | 4 VGAM-0.9-8/VGAM/man/cao.Rd | 10 VGAM-0.9-8/VGAM/man/cdf.lmscreg.Rd | 8 VGAM-0.9-8/VGAM/man/constraints.Rd | 4 VGAM-0.9-8/VGAM/man/cqo.Rd | 7 VGAM-0.9-8/VGAM/man/cumulative.Rd | 6 VGAM-0.9-8/VGAM/man/dagum.Rd | 36 VGAM-0.9-8/VGAM/man/deermice.Rd | 3 VGAM-0.9-8/VGAM/man/dirmul.old.Rd | 11 VGAM-0.9-8/VGAM/man/exponential.Rd | 2 VGAM-0.9-8/VGAM/man/fill.Rd | 31 VGAM-0.9-8/VGAM/man/fisk.Rd | 40 VGAM-0.9-8/VGAM/man/genbetaII.Rd | 73 VGAM-0.9-8/VGAM/man/genbetaIIUC.Rd |only VGAM-0.9-8/VGAM/man/genpoisUC.Rd |only VGAM-0.9-8/VGAM/man/genpoisson.Rd | 76 VGAM-0.9-8/VGAM/man/iam.Rd | 12 VGAM-0.9-8/VGAM/man/inv.lomax.Rd | 45 VGAM-0.9-8/VGAM/man/inv.paralogistic.Rd | 41 VGAM-0.9-8/VGAM/man/is.buggy.Rd |only VGAM-0.9-8/VGAM/man/lms.bcg.Rd | 8 VGAM-0.9-8/VGAM/man/lms.bcn.Rd | 19 VGAM-0.9-8/VGAM/man/lms.yjn.Rd | 8 VGAM-0.9-8/VGAM/man/loglinb3.Rd | 6 VGAM-0.9-8/VGAM/man/lomax.Rd | 19 VGAM-0.9-8/VGAM/man/micmen.Rd | 6 VGAM-0.9-8/VGAM/man/multinomial.Rd | 6 VGAM-0.9-8/VGAM/man/negbinomial.Rd | 4 VGAM-0.9-8/VGAM/man/notdocumentedyet.Rd | 10 VGAM-0.9-8/VGAM/man/paralogistic.Rd | 42 VGAM-0.9-8/VGAM/man/plotdeplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/plotqtplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/posbernoulli.t.Rd | 11 VGAM-0.9-8/VGAM/man/posbernoulli.tb.Rd | 1 VGAM-0.9-8/VGAM/man/posnormal.Rd | 16 VGAM-0.9-8/VGAM/man/pospoisson.Rd | 6 VGAM-0.9-8/VGAM/man/propodds.Rd | 6 VGAM-0.9-8/VGAM/man/qtplot.lmscreg.Rd | 6 VGAM-0.9-8/VGAM/man/rhobit.Rd | 14 VGAM-0.9-8/VGAM/man/rrvglm-class.Rd | 2 VGAM-0.9-8/VGAM/man/rrvglm.Rd | 9 VGAM-0.9-8/VGAM/man/s.Rd | 1 VGAM-0.9-8/VGAM/man/sinmad.Rd | 35 VGAM-0.9-8/VGAM/man/sinmadUC.Rd | 5 VGAM-0.9-8/VGAM/man/smartpred.Rd | 6 VGAM-0.9-8/VGAM/man/sratio.Rd | 9 VGAM-0.9-8/VGAM/man/tobit.Rd | 23 VGAM-0.9-8/VGAM/man/undocumented-methods.Rd | 13 VGAM-0.9-8/VGAM/man/uninormal.Rd | 1 VGAM-0.9-8/VGAM/man/vgam-class.Rd | 2 VGAM-0.9-8/VGAM/man/vgam.Rd | 10 VGAM-0.9-8/VGAM/man/vglm-class.Rd | 2 VGAM-0.9-8/VGAM/man/vglm.Rd | 6 VGAM-0.9-8/VGAM/man/vglm.control.Rd | 2 VGAM-0.9-8/VGAM/man/vglmff-class.Rd | 6 VGAM-0.9-8/VGAM/man/wrapup.smart.Rd | 14 VGAM-0.9-8/VGAM/man/zapoisson.Rd | 6 VGAM-0.9-8/VGAM/man/zero.Rd | 2 VGAM-0.9-8/VGAM/vignettes |only 126 files changed, 4654 insertions(+), 3983 deletions(-)
Title: Implementation of the Panel Data Approach Method for Program
Evaluation
Description: Implements the Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an intervention by comparing the evolution of the outcome for a unit affected by an intervention or treatment to the evolution of the unit had it not been affected by the intervention.
Author: Ainhoa Vega-Bayo
Maintainer: Ainhoa Vega-Bayo <ainhoa.vega@gmail.com>
Diff between pampe versions 1.0 dated 2015-02-13 and 1.1.1 dated 2015-05-11
DESCRIPTION | 9 +- MD5 | 18 +++-- R/pampe.R | 152 ++++++++++++++++++++++++++++++++++++-------------- R/pampeData.R |only R/plot.robustness.R | 12 ++- R/robustness.R | 23 +++++-- R/summary.pampe.R | 44 ++++++++++++++ R/xtable.pampe.R |only R/xtable.robustness.R |only man/pampe.Rd | 15 +++- man/pampeData.Rd |only man/robustness.Rd | 18 +---- 12 files changed, 210 insertions(+), 81 deletions(-)
Title: Bindings to OpenSSL
Description: Interfaces to the OpenSSL libraries libssl and libcrypto.
Currently implements bindings to the OpenSSL secure random number
generator, base64 encoder and hashing functions.
Author: Jeroen Ooms, Oliver Keyes
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.3 dated 2015-01-07 and 0.4 dated 2015-05-11
DESCRIPTION | 10 +- MD5 | 43 +++++----- NAMESPACE | 6 + NEWS |only R/base64.R |only R/hash.R | 2 build/vignette.rds |binary configure | 7 - inst/doc/crypto_hashing.R | 2 inst/doc/crypto_hashing.Rmd | 9 -- inst/doc/crypto_hashing.html | 131 ++++++++++++++---------------- inst/doc/secure_rng.R | 2 inst/doc/secure_rng.Rmd | 9 -- inst/doc/secure_rng.html | 136 ++++++++++++++------------------ man/base64.Rd |only man/hash.Rd | 2 man/openssl.Rd | 2 man/rand_bytes.Rd | 2 src/Makevars.win | 6 - src/base64.c |only src/digest.c | 2 tests/testthat/test_hash_output_value.R | 2 tests/testthat/test_salting.R |only vignettes/crypto_hashing.Rmd | 9 -- vignettes/secure_rng.Rmd | 9 -- 25 files changed, 177 insertions(+), 214 deletions(-)
Title: Interface to NetCDF Datasets
Description: An interface to the NetCDF file format designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
The R interface is closely based on the C API of the NetCDF library,
and it includes calendar conversions from the Unidata UDUNITS library.
The current implementation supports all operations on NetCDF datasets
in classic and 64-bit offset file formats, and NetCDF4-classic format
is supported for reading and modification of existing files.
Author: Pavel Michna, with contributions from Milton Woods
Maintainer: Milton Woods <mwoods@users.r-forge.r-project.org>
Diff between RNetCDF versions 1.6.3-1 dated 2014-08-31 and 1.7-3 dated 2015-05-11
RNetCDF-1.6.3-1/RNetCDF/LICENSE.note |only RNetCDF-1.6.3-1/RNetCDF/inst/HDF5_COPYING |only RNetCDF-1.7-3/RNetCDF/DESCRIPTION | 39 - RNetCDF-1.7-3/RNetCDF/INSTALL | 16 RNetCDF-1.7-3/RNetCDF/LICENSE |only RNetCDF-1.7-3/RNetCDF/MD5 | 38 - RNetCDF-1.7-3/RNetCDF/R/RNetCDF.R | 412 +++++++--------- RNetCDF-1.7-3/RNetCDF/R/load.R.in | 24 RNetCDF-1.7-3/RNetCDF/R/windows/load.R | 24 RNetCDF-1.7-3/RNetCDF/configure | 731 ++++++++++++++++++----------- RNetCDF-1.7-3/RNetCDF/configure.ac | 143 ++--- RNetCDF-1.7-3/RNetCDF/configure.win | 2 RNetCDF-1.7-3/RNetCDF/inst/udunits |only RNetCDF-1.7-3/RNetCDF/man/var.get.nc.Rd | 18 RNetCDF-1.7-3/RNetCDF/man/var.put.nc.Rd | 8 RNetCDF-1.7-3/RNetCDF/src/Makevars.in | 4 RNetCDF-1.7-3/RNetCDF/src/Makevars.win | 16 RNetCDF-1.7-3/RNetCDF/src/RNetCDF.c | 352 ++++++------- RNetCDF-1.7-3/RNetCDF/tests/RNetCDF-test.R | 256 +++++----- 19 files changed, 1139 insertions(+), 944 deletions(-)
Title: Retrieve Structured, Textual Data from Various Web Sources
Description: Facilitate text retrieval from feed
formats like XML (RSS, ATOM) and JSON. Also direct retrieval from
HTML is supported. As most (news) feeds only incorporate small
fractions of the original text tm.plugin.webmining even retrieves
and extracts the text of the original text source.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between tm.plugin.webmining versions 1.2.2 dated 2014-11-03 and 1.3 dated 2015-05-10
tm.plugin.webmining-1.2.2/tm.plugin.webmining/inst/googleSearch.R |only tm.plugin.webmining-1.2.2/tm.plugin.webmining/inst/test_internal.R |only tm.plugin.webmining-1.3/tm.plugin.webmining/DESCRIPTION | 14 - tm.plugin.webmining-1.3/tm.plugin.webmining/MD5 | 86 ++++---- tm.plugin.webmining-1.3/tm.plugin.webmining/NAMESPACE | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/R/reader.R | 23 ++ tm.plugin.webmining-1.3/tm.plugin.webmining/R/source.R | 97 ++++++---- tm.plugin.webmining-1.3/tm.plugin.webmining/R/tm.plugin.webmining-package.R | 9 tm.plugin.webmining-1.3/tm.plugin.webmining/build/vignette.rds |binary tm.plugin.webmining-1.3/tm.plugin.webmining/data/nytimes_appid.rda |only tm.plugin.webmining-1.3/tm.plugin.webmining/data/yahoonews.rda |binary tm.plugin.webmining-1.3/tm.plugin.webmining/inst/NEWS.Rd |only tm.plugin.webmining-1.3/tm.plugin.webmining/inst/doc/ShortIntro.pdf |binary tm.plugin.webmining-1.3/tm.plugin.webmining/man/GoogleFinanceSource.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/GoogleNewsSource.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/NYTimesSource.Rd | 20 +- tm.plugin.webmining-1.3/tm.plugin.webmining/man/ReutersNewsSource.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/WebCorpus.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/WebSource.Rd | 7 tm.plugin.webmining-1.3/tm.plugin.webmining/man/YahooFinanceSource.Rd | 6 tm.plugin.webmining-1.3/tm.plugin.webmining/man/YahooInplaySource.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/YahooNewsSource.Rd | 11 - tm.plugin.webmining-1.3/tm.plugin.webmining/man/corpus.update.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/encloseHTML.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/extract.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/extractContentDOM.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/extractHTMLStrip.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/feedquery.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/getEmpty.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/getLinkContent.Rd | 11 - tm.plugin.webmining-1.3/tm.plugin.webmining/man/nytimes_appid.Rd |only tm.plugin.webmining-1.3/tm.plugin.webmining/man/parse.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/readWeb.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/removeNonASCII.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/source.update.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/tm.plugin.webmining-package.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/trimWhiteSpaces.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/man/yahoonews.Rd | 3 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat.R | 4 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat.R.temp |only tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-googlefinance.R | 5 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-googlenews.R | 12 - tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-nytimes.R | 10 - tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-reutersnews.R | 7 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-yahoofinance.R | 5 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-yahooinplay.R | 5 tm.plugin.webmining-1.3/tm.plugin.webmining/tests/testthat/test-source-yahoonews.R | 7 47 files changed, 233 insertions(+), 166 deletions(-)
More information about tm.plugin.webmining at CRAN
Permanent link
Title: Path Manipulation Utilities
Description: Utilities for paths, files and directories.
Author: Richard Cotton [aut, cre], Janko Thyson [ctb]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between pathological versions 0.0-3 dated 2015-01-19 and 0.0-6 dated 2015-05-10
DESCRIPTION | 12 MD5 | 41 +- NAMESPACE | 85 ++-- NEWS | 2 R/paths.R | 220 ++++++++++++ README.md | 48 ++ inst/tests/test_decompose_path.R | 671 +++++++++++++++++++-------------------- man/copy_dir.Rd | 2 man/create_dirs.Rd |only man/cygwinify_path.Rd | 2 man/decompose_path.Rd | 2 man/get_drive.Rd | 5 man/get_libraries.Rd |only man/is_windows_drive.Rd |only man/os_path.Rd | 2 man/parent_dir.Rd |only man/pathological.Rd | 2 man/r_home.Rd | 2 man/r_profile.Rd |only man/split_path.Rd | 2 man/standardize_path.Rd | 2 man/sys_which.Rd | 3 man/system_file.Rd | 2 man/temp_dir.Rd | 2 24 files changed, 695 insertions(+), 412 deletions(-)
Title: Mixture and Flexible Discriminant Analysis
Description: Mixture and flexible discriminant analysis, multivariate
adaptive regression splines (MARS), BRUTO, ...
Author: S original by Trevor Hastie & Robert Tibshirani. Original R port by Friedrich Leisch, Kurt Hornik and Brian D. Ripley.
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between mda versions 0.4-4 dated 2013-08-17 and 0.4-6 dated 2015-05-10
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/confusion.default.R | 2 +- R/kmeans.start.R | 5 +++-- R/mda.fit.R | 2 +- data/glass.rda |binary man/glass.Rd | 2 +- 8 files changed, 19 insertions(+), 18 deletions(-)
Title: Binary Classifier Interpretation Functions
Description: Compute permutation- based performance measures and create
partial dependence plots for (cross-validated) randomForest and ada models.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@GMail.com>
Diff between interpretR versions 0.2.1 dated 2015-03-26 and 0.2.2 dated 2015-05-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/parDepPlot.R | 17 +++++++++++------ inst/NEWS | 3 +++ man/interpretRNews.Rd | 3 ++- man/parDepPlot.Rd | 10 ++++++---- man/variableImportance.Rd | 3 ++- 7 files changed, 34 insertions(+), 22 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and an imputation Cox-PH model which imputes the interval censored times based on Cox-PH model with an parametric baseline and then analyzes each imputed data set with the semi-parametric model.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.1 dated 2015-04-28 and 1.1.1 dated 2015-05-10
DESCRIPTION | 6 MD5 | 18 - NAMESPACE | 2 R/coxph.R | 85 ++++-- data |only man/ic_ph.Rd | 11 man/impute_ic_ph.Rd | 16 - man/mdata.Rd |only man/simICPH_beta.Rd | 11 src/icenReg.cpp | 711 ++++++++++++++++++++++++++++------------------------ src/intCoxFast.h | 34 +- 11 files changed, 498 insertions(+), 396 deletions(-)
Title: Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
Description: The following R functions are used for inference of trait
associations with haplotypes and other covariates in
generalized linear models. The functions are developed
primarily for data collected in cohort or cross-sectional
studies. They can accommodate uncertain haplotype phase and
handle missing genotypes at some SNPs.
Author: K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J.
Graham <jgraham@stat.sfu.ca>, with code for case-control data
contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Maintainer: K. Burkett <kburkett@uottawa.ca>
Diff between hapassoc versions 1.2-7 dated 2014-08-25 and 1.2-8 dated 2015-05-10
DESCRIPTION | 14 +++++++------- MD5 | 15 ++++++++------- NAMESPACE | 5 ++++- R/RecodeHaplos.R | 4 ++-- build |only inst/CITATION | 4 ++-- inst/ChangeLog | 4 ++++ man/hapassoc.Rd | 2 +- man/summaryHap.Rd | 2 +- 9 files changed, 29 insertions(+), 21 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9 dated 2015-04-26 and 0.9.1 dated 2015-05-10
DESCRIPTION | 10 +++++----- MD5 | 12 +++++++----- NAMESPACE | 2 -- R/Dataset-Extend.R | 15 --------------- configure.win |only inst/NEWS.Rd |only man/DataSet-Extend.Rd | 8 -------- tests/testthat/test-H5File.R | 2 +- 8 files changed, 13 insertions(+), 36 deletions(-)
Title: Statistical Inference for Parametric and Semiparametric Models
Based on Dependently Truncated Data
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj), subject to Xj<=Yj, for all j=1,...,n, are called truncated data. Parametric approach (Emura & Konno 2012 Stat Papers), semiparametric approach (Chaieb et al. 2006 Biometrika; Emura et al. 2011 Sinica; Emura and Murotani 2015 TEST), nonparametric maximum likelihood approach (Emura & Wang 2012 JMVA), and regression approach (Emura and Wang 2015 AISM) are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians (Emura and Murotani 2015 TEST).
Author: Takeshi Emura
Maintainer: Takeshi Emura <emura@stat.ncu.edu.tw>
Diff between depend.truncation versions 2.2 dated 2015-03-06 and 2.3 dated 2015-05-10
DESCRIPTION | 14 +++++++------- MD5 | 8 +++++--- R/dependAFT.reg.R |only man/EMURA.Clayton.Rd | 2 +- man/depend.truncation-package.Rd | 11 +++++++---- man/dependAFT.reg.Rd |only 6 files changed, 20 insertions(+), 15 deletions(-)
More information about depend.truncation at CRAN
Permanent link
Title: Interface to the Boilerpipe Java Library
Description: Generic Extraction of main text content from HTML files; removal
of ads, sidebars and headers using the boilerpipe
(http://code.google.com/p/boilerpipe/) Java library. The
extraction heuristics from boilerpipe show a robust performance for a wide
range of web site templates.
Author: See AUTHORS file.
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between boilerpipeR versions 1.2.2 dated 2014-08-21 and 1.3 dated 2015-05-10
boilerpipeR-1.2.2/boilerpipeR/NEWS |only boilerpipeR-1.3/boilerpipeR/DESCRIPTION | 14 ++-- boilerpipeR-1.3/boilerpipeR/MD5 | 34 +++++------ boilerpipeR-1.3/boilerpipeR/NAMESPACE | 2 boilerpipeR-1.3/boilerpipeR/R/Extractor.R | 4 - boilerpipeR-1.3/boilerpipeR/build/vignette.rds |binary boilerpipeR-1.3/boilerpipeR/data/content.rda |binary boilerpipeR-1.3/boilerpipeR/inst/NEWS.Rd |only boilerpipeR-1.3/boilerpipeR/inst/doc/ShortIntro.pdf |binary boilerpipeR-1.3/boilerpipeR/man/ArticleExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/ArticleSentencesExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/CanolaExtractor.Rd | 7 +- boilerpipeR-1.3/boilerpipeR/man/DefaultExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/Extractor.Rd | 5 - boilerpipeR-1.3/boilerpipeR/man/KeepEverythingExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/LargestContentExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/NumWordsRulesExtractor.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/boilerpipeR-package.Rd | 3 boilerpipeR-1.3/boilerpipeR/man/content.Rd | 3 19 files changed, 50 insertions(+), 40 deletions(-)
Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between soilphysics versions 2.2 dated 2015-04-10 and 2.3 dated 2015-05-09
DESCRIPTION | 8 - MD5 | 18 ++-- NEWS | 8 + R/iwc.R | 192 ++++++++++++++++++++++++++++++++++++--------- R/maxcurv.R | 149 ++++++++++++++++++++++++++++++---- man/iwc.Rd | 27 ++++-- man/maxcurv.Rd | 43 ++++++++-- man/sigmaP.Rd | 2 man/soilphysics-package.Rd | 4 man/voidratio.Rd | 15 +-- 10 files changed, 374 insertions(+), 92 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between phenology versions 4.1 dated 2015-04-08 and 4.2 dated 2015-05-09
DESCRIPTION | 8 +-- MD5 | 103 ++++++++++++++++++++++---------------------- NAMESPACE | 3 - NEWS | 6 ++ R/Lnegbin.R | 9 +-- R/add_phenology.R | 23 +++------ R/fitRMU.R |only R/fit_phenology.R | 50 ++++++--------------- R/fonctionfit.R |only R/format_par.R | 10 ++-- R/logLik.phenology.R | 2 R/onAttach.R | 2 R/phenology-package.R | 4 - R/phenology_MHmcmc_p.R | 2 R/phenology_fonctionMCMC.R | 2 man/BE_to_LBLE.Rd | 2 man/Gratiot.Rd | 2 man/LBLE_to_BE.Rd | 2 man/LBLE_to_L.Rd | 2 man/L_to_LBLE.Rd | 2 man/MinBMinE_to_Min.Rd | 2 man/adapt_parameters.Rd | 2 man/add_SD.Rd | 2 man/add_phenology.Rd | 10 ++-- man/extract_result.Rd | 2 man/fitRMU.Rd |only man/fit_phenology.Rd | 8 --- man/likelihood_phenology.Rd | 2 man/logLik.phenology.Rd | 2 man/map_Gratiot.Rd | 2 man/map_phenology.Rd | 2 man/par_init.Rd | 2 man/phenology-package.Rd | 6 +- man/phenology.Rd | 2 man/phenology_MHmcmc.Rd | 2 man/phenology_MHmcmc_p.Rd | 2 man/plot.phenology.Rd | 2 man/plot.phenologymap.Rd | 2 man/plot_delta.Rd | 2 man/plot_phi.Rd | 2 man/print.phenology.Rd | 2 man/print.phenologymap.Rd | 2 man/print.phenologyout.Rd | 2 man/remove_site.Rd | 2 man/result_Gratiot.Rd | 2 man/result_Gratiot1.Rd | 2 man/result_Gratiot2.Rd | 2 man/result_Gratiot_Flat.Rd | 2 man/result_Gratiot_mcmc.Rd | 2 man/shift_sinusoid.Rd | 2 man/summary.phenology.Rd | 2 man/summary.phenologymap.Rd | 2 man/summary.phenologyout.Rd | 2 man/toggle_Min_PMin.Rd | 2 54 files changed, 150 insertions(+), 168 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.4.2 dated 2015-01-25 and 0.5 dated 2015-05-09
mirtCAT-0.4.2/mirtCAT/R/FI.R |only mirtCAT-0.5/mirtCAT/DESCRIPTION | 12 mirtCAT-0.5/mirtCAT/MD5 | 66 +++-- mirtCAT-0.5/mirtCAT/NAMESPACE | 4 mirtCAT-0.5/mirtCAT/NEWS | 30 ++ mirtCAT-0.5/mirtCAT/R/DesignClass.R | 78 ++++-- mirtCAT-0.5/mirtCAT/R/PersonClass.R | 16 - mirtCAT-0.5/mirtCAT/R/ShinyGUIClass.R | 33 +- mirtCAT-0.5/mirtCAT/R/TestClass.R | 2 mirtCAT-0.5/mirtCAT/R/createShinyGUI.R |only mirtCAT-0.5/mirtCAT/R/findNextCATItem.R | 44 +++ mirtCAT-0.5/mirtCAT/R/generate.mirt_object.R | 18 - mirtCAT-0.5/mirtCAT/R/generate_pattern.R | 8 mirtCAT-0.5/mirtCAT/R/mirtCAT.R | 196 ++++------------ mirtCAT-0.5/mirtCAT/R/mirtCAT_preamble.R |only mirtCAT-0.5/mirtCAT/R/selection_criteria.R | 8 mirtCAT-0.5/mirtCAT/R/server.R | 49 ++-- mirtCAT-0.5/mirtCAT/R/ui.R | 2 mirtCAT-0.5/mirtCAT/R/updateDesign.R | 13 - mirtCAT-0.5/mirtCAT/R/util.R | 91 +++---- mirtCAT-0.5/mirtCAT/R/zzz-methods.R | 2 mirtCAT-0.5/mirtCAT/build/vignette.rds |binary mirtCAT-0.5/mirtCAT/man/createShinyGUI.Rd |only mirtCAT-0.5/mirtCAT/man/findNextItem.Rd | 10 mirtCAT-0.5/mirtCAT/man/generate.mirt_object.Rd | 9 mirtCAT-0.5/mirtCAT/man/generate_pattern.Rd | 2 mirtCAT-0.5/mirtCAT/man/mirtCAT-package.Rd | 2 mirtCAT-0.5/mirtCAT/man/mirtCAT.Rd | 62 +++-- mirtCAT-0.5/mirtCAT/man/mirtCAT_preamble.Rd |only mirtCAT-0.5/mirtCAT/man/updateDesign.Rd | 9 mirtCAT-0.5/mirtCAT/src/item_functions.cpp | 7 mirtCAT-0.5/mirtCAT/tests/GUI-tests |only mirtCAT-0.5/mirtCAT/tests/tests/test-mirtCAT_classify.R | 5 mirtCAT-0.5/mirtCAT/tests/tests/test-mirtCAT_extra.R |only mirtCAT-0.5/mirtCAT/tests/tests/test-mirtCAT_ordered.R | 5 mirtCAT-0.5/mirtCAT/tests/tests/test-mirtCAT_uni.R | 6 36 files changed, 440 insertions(+), 349 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman <Rob.Hyndman@monash.edu> with contributions from
George Athanasopoulos, Slava Razbash, Drew Schmidt, Zhenyu Zhou, Yousaf Khan,
Christoph Bergmeir, Earo Wang
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 5.9 dated 2015-02-26 and 6.0 dated 2015-05-09
forecast-5.9/forecast/R/fpp.R |only forecast-6.0/forecast/ChangeLog | 20 ++ forecast-6.0/forecast/DESCRIPTION | 8 - forecast-6.0/forecast/MD5 | 69 ++++---- forecast-6.0/forecast/NAMESPACE | 33 ++-- forecast-6.0/forecast/R/DM2.R | 8 - forecast-6.0/forecast/R/acf.R |only forecast-6.0/forecast/R/arima.R | 211 ++++++++++++++------------- forecast-6.0/forecast/R/armaroots.R |only forecast-6.0/forecast/R/bats.R | 12 + forecast-6.0/forecast/R/bootstrap.R |only forecast-6.0/forecast/R/checkAdmissibility.R | 11 - forecast-6.0/forecast/R/errors.R | 16 +- forecast-6.0/forecast/R/ets.R | 10 + forecast-6.0/forecast/R/forecast.R | 13 + forecast-6.0/forecast/R/forecastBATS.R | 3 forecast-6.0/forecast/R/getResponse.R | 37 ++-- forecast-6.0/forecast/R/graph.R | 4 forecast-6.0/forecast/R/lm.R | 21 ++ forecast-6.0/forecast/R/newarima2.R | 16 +- forecast-6.0/forecast/R/season.R | 51 ++++-- forecast-6.0/forecast/R/tbats.R | 7 forecast-6.0/forecast/man/Acf.Rd | 43 ++++- forecast-6.0/forecast/man/accuracy.Rd | 2 forecast-6.0/forecast/man/arima.Rd | 2 forecast-6.0/forecast/man/auto.arima.Rd | 5 forecast-6.0/forecast/man/bats.Rd | 5 forecast-6.0/forecast/man/ets.Rd | 8 - forecast-6.0/forecast/man/forecast.Rd | 4 forecast-6.0/forecast/man/forecast.ets.Rd | 2 forecast-6.0/forecast/man/forecast.stl.Rd | 18 +- forecast-6.0/forecast/man/forecastplot.Rd | 10 - forecast-6.0/forecast/man/plot.Arima.Rd |only forecast-6.0/forecast/man/rw.f.Rd | 2 forecast-6.0/forecast/man/seasonplot.Rd | 8 - forecast-6.0/forecast/man/spline.f.Rd | 7 forecast-6.0/forecast/man/tbats.Rd | 2 forecast-6.0/forecast/man/ts.display.Rd | 10 - 38 files changed, 418 insertions(+), 260 deletions(-)
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between biotools versions 2.0 dated 2015-01-29 and 2.1 dated 2015-05-09
DESCRIPTION | 8 ++--- MD5 | 23 ++++++++------ NAMESPACE | 9 +++-- NEWS | 14 +++++++- R/mantelPower.R |only R/mantelTest.R |only R/onload.R | 2 - R/samplesize.R | 75 +++++++++++++++++++++++++++++------------------- R/simpval.R |only R/tocher.R | 36 +++++++++++++++++------ man/biotools-package.Rd | 4 +- man/mantelPower.Rd |only man/mantelTest.Rd |only man/samplesize.Rd | 2 - man/tocher.Rd | 24 ++++++++++++--- 15 files changed, 133 insertions(+), 64 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.0 dated 2015-04-23 and 1.1.1 dated 2015-05-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 17 +++++++++++++---- R/drgee.R | 16 +++++++--------- R/drgeeData.R | 29 ++++++++++++++++++++++------- man/drgee.Rd | 12 ++++++------ man/drgeeData.Rd | 22 +++++++++++++++------- 7 files changed, 73 insertions(+), 43 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and
pedigree-based partitioning of individual variation into a range of
environmental and genetic variance components for individual and
maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 1.5-1 dated 2015-03-14 and 1.6-1 dated 2015-05-09
DESCRIPTION | 8 - MD5 | 24 ++-- NAMESPACE | 1 R/dmesolve.R | 2 R/dmm-internal.R | 250 +++++++++++++++++++++++------------------------ R/mdf.R | 38 ++++++- R/plot.dmm.R |only inst/doc/bugs.txt |only inst/doc/dmmOverview.pdf |binary inst/doc/mods.txt |only man/dmm.Rd | 36 ------ man/harv101.df.Rd | 3 man/mdf.Rd | 6 - man/plot.dmm.Rd |only man/quercus.df.Rd | 3 15 files changed, 192 insertions(+), 179 deletions(-)
Title: Datasets from Draper and Smith "Applied Regression Analysis"
(3rd Ed., 1998)
Description: An unofficial companion to the textbook "Applied Regression
Analysis" by N.R. Draper and H. Smith (3rd Ed., 1998) including all the
accompanying datasets.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between aprean3 versions 1.0 dated 2015-01-04 and 1.0.1 dated 2015-05-09
DESCRIPTION | 21 - MD5 | 618 ++++++++++++++++++++++++++--------------------------- NEWS | 5 data/dsa01a.rda |binary data/dsa06b.rda |binary data/dsa15a.rda |binary data/dse03a.rda |binary data/dse03aa.rda |binary data/dse03bb.rda |binary data/dse03c.rda |binary data/dse03cc.rda |binary data/dse03dd.rda |binary data/dse03e.rda |binary data/dse03ee.rda |binary data/dse03f.rda |binary data/dse03g.rda |binary data/dse03gg.rda |binary data/dse03h.rda |binary data/dse03hh.rda |binary data/dse03i.rda |binary data/dse03ii.rda |binary data/dse03j.rda |binary data/dse03jj.rda |binary data/dse03jj2.rda |binary data/dse03jj3.rda |binary data/dse03k.rda |binary data/dse03kk.rda |binary data/dse03ll.rda |binary data/dse03n.rda |binary data/dse03o.rda |binary data/dse03r.rda |binary data/dse03v.rda |binary data/dse03w.rda |binary data/dse03x.rda |binary data/dse03z.rda |binary data/dse04d.rda |binary data/dse04e.rda |binary data/dse04f.rda |binary data/dse06a.rda |binary data/dse06b.rda |binary 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| 2 man/dse03ee.Rd | 2 man/dse03f.Rd | 2 man/dse03g.Rd | 2 man/dse03gg.Rd | 2 man/dse03h.Rd | 2 man/dse03hh.Rd | 2 man/dse03i.Rd | 2 man/dse03ii.Rd | 2 man/dse03j.Rd | 2 man/dse03jj.Rd | 2 man/dse03jj2.Rd | 2 man/dse03jj3.Rd | 2 man/dse03k.Rd | 2 man/dse03kk.Rd | 2 man/dse03ll.Rd | 2 man/dse03n.Rd | 2 man/dse03o.Rd | 2 man/dse03r.Rd | 2 man/dse03v.Rd | 2 man/dse03w.Rd | 2 man/dse03x.Rd | 2 man/dse03z.Rd | 2 man/dse04d.Rd | 2 man/dse04e.Rd | 2 man/dse04f.Rd | 2 man/dse06a.Rd | 2 man/dse06b.Rd | 2 man/dse06c.Rd | 2 man/dse06d.Rd | 2 man/dse06e.Rd | 2 man/dse06f.Rd | 2 man/dse06g.Rd | 2 man/dse06h.Rd | 2 man/dse06i.Rd | 2 man/dse06j.Rd | 2 man/dse06k.Rd | 2 man/dse06l.Rd | 2 man/dse06z.Rd | 2 man/dse07b.Rd | 2 man/dse07c.Rd | 2 man/dse08b.Rd | 2 man/dse09b.Rd | 2 man/dse12a.Rd | 2 man/dse12b.Rd | 2 man/dse12c.Rd | 2 man/dse12d.Rd | 2 man/dse12e.Rd | 2 man/dse12h.Rd | 2 man/dse13a.Rd | 2 man/dse13b.Rd | 2 man/dse13c.Rd | 2 man/dse13d.Rd | 2 man/dse13e.Rd | 2 man/dse13f.Rd | 2 man/dse13g.Rd | 2 man/dse13h.Rd | 2 man/dse14b.Rd | 2 man/dse14c.Rd | 2 man/dse14d.Rd | 2 man/dse14e.Rd | 2 man/dse14f.Rd | 2 man/dse14g.Rd | 2 man/dse14j.Rd | 2 man/dse14l.Rd | 2 man/dse14q.Rd | 2 man/dse14r.Rd | 2 man/dse14s.Rd | 2 man/dse14t.Rd | 2 man/dse14u.Rd | 2 man/dse15a.Rd | 2 man/dse15b.Rd | 2 man/dse15c.Rd | 2 man/dse15e.Rd | 2 man/dse15f.Rd | 2 man/dse15h.Rd | 2 man/dse15i.Rd | 2 man/dse15j.Rd | 2 man/dse15k.Rd | 2 man/dse15l.Rd | 2 man/dse15n.Rd | 2 man/dse15p.Rd | 2 man/dse16a.Rd | 2 man/dse16b.Rd | 2 man/dse16c.Rd | 2 man/dse16d.Rd | 2 man/dse17b.Rd | 2 man/dse19d.Rd | 2 man/dse22a.Rd | 2 man/dse22b.Rd | 2 man/dse22c.Rd | 2 man/dse22d.Rd | 2 man/dse22e.Rd | 2 man/dse22f.Rd | 2 man/dse22g.Rd | 2 man/dse23a_a.Rd | 2 man/dse23a_b.Rd | 2 man/dse23d.Rd | 2 man/dse23e.Rd | 2 man/dse23f.Rd | 2 man/dse23g_1.Rd | 2 man/dse23g_2.Rd | 2 man/dse23h.Rd | 2 man/dse24a.Rd | 2 man/dse24b.Rd | 2 man/dse24c.Rd | 2 man/dse24d.Rd | 2 man/dse24e.Rd | 2 man/dse24g.Rd | 2 man/dse24h.Rd | 2 man/dse24i.Rd | 2 man/dse24j.Rd | 2 man/dse24k.Rd | 2 man/dse24l.Rd | 2 man/dse24m.Rd | 2 man/dse24n.Rd | 2 man/dse24o.Rd | 2 man/dse24p.Rd | 2 man/dsq23_3_3.Rd | 2 man/dsq23_3_7.Rd | 2 man/dsq23_7_5.Rd | 2 man/dss217.Rd | 2 man/dss222.Rd | 2 man/dss2310.Rd | 2 man/dst021.Rd | 2 man/dst032.Rd | 2 man/dst033.Rd | 2 man/dst081.Rd | 2 man/dst121.Rd | 2 man/dst132.Rd | 2 man/dst134.Rd | 2 man/dst141.Rd | 2 man/dst144.Rd | 2 man/dst145.Rd | 2 man/dst146.Rd | 2 man/dst181.Rd | 2 man/dst191.Rd | 2 man/dst192.Rd | 2 man/dst232.Rd | 2 man/dst242.Rd | 2 man/dst252.Rd | 2 man/dst253.Rd | 2 man/dst261.Rd | 2 man/dsx161.Rd | 2 310 files changed, 479 insertions(+), 473 deletions(-)
Title: Calculate Single Station Metabolism from Diurnal Oxygen Curves
Description: I provide functions to calculate Gross Primary Productivity, Net Ecocsystem Production, and Ecosystem Respiration from single station diurnal Oxygen curves.
Author: Stephen A Sefick Jr.
Maintainer: Stephen A Sefick Jr. <ssefick@gmail.com>
Diff between StreamMetabolism versions 1.1 dated 2015-05-01 and 1.1.1 dated 2015-05-09
StreamMetabolism-1.1.1/StreamMetabolism/DESCRIPTION | 6 +++--- StreamMetabolism-1.1.1/StreamMetabolism/MD5 | 5 ++--- StreamMetabolism-1.1.1/StreamMetabolism/R/SM.R | 10 +++++----- StreamMetabolism-1.1/StreamMetabolism/README.md |only 4 files changed, 10 insertions(+), 11 deletions(-)
More information about StreamMetabolism at CRAN
Permanent link
Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working
with Latent Semantic Analysis. For actually building an LSA space, use the
package 'lsa' or other specialized software.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>
Diff between LSAfun versions 0.3.2 dated 2014-09-29 and 0.4 dated 2015-05-09
ChangeLog | 18 +++++++++++++++++ DESCRIPTION | 14 ++++++------- MD5 | 40 +++++++++++++++++++++++---------------- NAMESPACE | 4 +++ R/asym.R |only R/choose.target.r | 2 - R/compose.r | 51 ++++++++++++++++++++++++++++++++++++++++++++++---- R/conSIM.r |only R/distance.r |only R/genericSummary.R | 8 ++++++- R/multicostring.r | 2 - R/neighbors.r | 2 - R/plausibility.r |only R/plot_neighbors.r | 2 - R/plot_wordlist.r | 2 - man/Cosine.Rd | 15 ++++++-------- man/LSAfun-package.Rd | 38 ++++++++++++++++++++++++++++++------- man/asym.Rd |only man/compose.Rd | 34 ++++++++++++++++++++++++++------- man/conSIM.Rd |only man/costring.Rd | 2 - man/distance.Rd |only man/neighbors.Rd | 2 - man/oldbooks.Rd | 10 ++++----- man/plausibility.Rd |only 25 files changed, 184 insertions(+), 62 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.7.0 dated 2015-01-17 and 1.8.0 dated 2015-05-09
DESCRIPTION | 12 - MD5 | 268 +++++++++++++------------ NAMESPACE | 21 + R/R.r | 53 ++++ R/build-github-devtools.r | 2 R/check-cran.r | 57 +---- R/check-devtools.r | 12 - R/check.r | 21 + R/deps.R | 242 ++++++++++++++++++---- R/dev-help.r | 1 R/doctor.R |only R/git.R | 111 +++++----- R/github.R | 37 ++- R/infrastructure-git.R |only R/infrastructure.R | 149 +++++++++---- R/install-git.r | 46 +--- R/install-github.r | 24 +- R/install-svn.r | 26 +- R/install-version.r | 26 +- R/install.r | 53 +--- R/lint.r | 10 R/load-code.r | 2 R/load.r | 6 R/release.r | 46 +++- R/revdep.R | 7 R/rtools.r | 10 R/session-info.r | 18 + R/system.r | 15 + R/test.r | 11 - R/topic-index.r | 2 R/unload.r | 4 R/utils.r | 13 + R/vignettes.r | 4 R/zzz.r | 2 README.md | 13 - inst/templates/CONDUCT.md |only inst/templates/test-example.R |only inst/templates/travis.yml | 22 -- man/RCMD.Rd |only man/as.package.Rd | 2 man/bash.Rd | 2 man/build.Rd | 2 man/build_github_devtools.Rd | 2 man/build_vignettes.Rd | 2 man/build_win.Rd | 2 man/check.Rd | 8 man/check_cran.Rd | 4 man/check_dep_version.Rd | 2 man/check_doc.Rd | 2 man/clean_dll.Rd | 2 man/clean_source.Rd | 2 man/clean_vignettes.Rd | 2 man/compile_dll.Rd | 2 man/compiler_flags.Rd | 2 man/cran_env_vars.Rd | 2 man/create.Rd | 2 man/create_description.Rd | 2 man/dev_example.Rd | 2 man/dev_help.Rd | 2 man/dev_meta.Rd | 2 man/dev_mode.Rd | 2 man/dev_packages.Rd | 2 man/devtest.Rd | 2 man/devtools.Rd | 2 man/document.Rd | 2 man/dr_devtools.Rd |only man/dr_github.Rd |only man/eval_clean.Rd | 2 man/find_rtools.Rd | 2 man/find_topic.Rd | 2 man/github_pat.Rd | 5 man/github_refs.Rd | 2 man/has_devel.Rd | 2 man/has_tests.Rd | 2 man/help.Rd | 2 man/imports_env.Rd | 2 man/infrastructure.Rd | 41 +++ man/inst.Rd | 2 man/install.Rd | 8 man/install_bitbucket.Rd | 2 man/install_deps.Rd | 10 man/install_git.Rd | 7 man/install_github.Rd | 10 man/install_gitorious.Rd | 2 man/install_local.Rd | 2 man/install_svn.Rd | 7 man/install_url.Rd | 2 man/install_version.Rd | 19 - man/is.package.Rd | 2 man/lint.Rd | 12 - man/load_all.Rd | 2 man/load_code.Rd | 2 man/load_data.Rd | 2 man/load_dll.Rd | 2 man/load_imports.Rd | 2 man/loaded_packages.Rd | 2 man/missing_s3.Rd | 2 man/ns_env.Rd | 2 man/on_path.Rd | 2 man/package_deps.Rd |only man/parse_deps.Rd | 2 man/parse_ns_file.Rd | 2 man/path.Rd | 2 man/pkg_env.Rd | 2 man/r_env_vars.Rd | 7 man/release.Rd | 2 man/release_checks.Rd | 2 man/reload.Rd | 2 man/revdep.Rd | 2 man/revdep_check.Rd | 2 man/run_examples.Rd | 2 man/run_pkg_hook.Rd | 2 man/session_info.Rd | 12 - man/show_news.Rd | 2 man/source_gist.Rd | 2 man/source_url.Rd | 2 man/submit_cran.Rd | 2 man/system.file.Rd | 2 man/system_check.Rd |only man/test.Rd | 6 man/unload.Rd | 2 man/update_packages.Rd |only man/use_build_ignore.Rd | 16 - man/use_data.Rd | 16 - man/use_data_raw.Rd | 16 - man/use_git.Rd |only man/use_git_hook.Rd | 24 -- man/use_github.Rd |only man/use_package.Rd | 16 - man/use_readme_rmd.Rd | 16 - man/wd.Rd | 2 man/with_debug.Rd | 2 man/with_something.Rd | 2 tests/testthat/test-check.r |only tests/testthat/test-github.r | 8 tests/testthat/test-load-collate.r | 19 + tests/testthat/test-load-dir.r |only tests/testthat/test-load-hooks.r | 2 tests/testthat/testCollateOrder |only tests/testthat/testDllRcpp/src/RcppExports.cpp | 12 - tests/testthat/testLoadDir |only 141 files changed, 1148 insertions(+), 633 deletions(-)
Title: Latent Semantic Analysis
Description: The basic idea of latent semantic analysis (LSA) is,
that text do have a higher order (=latent semantic) structure which,
however, is obscured by word usage (e.g. through the use of synonyms
or polysemy). By using conceptual indices that are derived statistically
via a truncated singular value decomposition (a two-mode factor analysis)
over a given document-term matrix, this variability problem can be overcome.
Author: Fridolin Wild
Maintainer: Fridolin Wild <f.wild@open.ac.uk>
Diff between lsa versions 0.73 dated 2014-04-02 and 0.73.1 dated 2015-05-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 3 +++ R/textmatrix.R | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Random Projection Ensemble Classification
Description: Implements the methodology of "Cannings, T. I. and Samworth, R. J. (2015) Random projection ensemble classification. http://arxiv.org/abs/1504.04595". The random projection ensemble classifier is a very general method for classification of high-dimensional data, based on careful combination of the results of applying an arbitrary base classifier to random projections of the feature vectors into a lower-dimensional space. The random projections are divided into non-overlapping blocks, and within each block the projection yielding the smallest estimate of the test error is selected. The random projection ensemble classifier then aggregates the results of applying the base classifier on the selected projections, with a data-driven voting threshold to determine the final assignment.
Author: Timothy I. Cannings and Richard J. Samworth
Maintainer: Timothy I. Cannings <t.cannings@statslab.cam.ac.uk>
Diff between RPEnsemble versions 0.1 dated 2015-05-05 and 0.2 dated 2015-05-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/RPEnsemble-package.Rd | 4 ++-- man/RPEnsembleClass.Rd | 2 +- man/RPParallel.Rd | 4 ++-- man/RPalpha.Rd | 2 +- 6 files changed, 15 insertions(+), 15 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.1-0 dated 2015-02-04 and 4.2-0 dated 2015-05-08
DESCRIPTION | 10 ++--- MD5 | 40 ++++++++++----------- NEWS | 35 ++++++++++++++++++ R/catmeth.R | 13 +++++- R/ci.R | 6 +-- R/forest.meta.R | 92 +++++++++++++++++++++++++++++++++---------------- R/kentau.R | 2 - R/meta-internal.R | 3 + R/metacont.R | 41 +++++++++++++++------ R/print.meta.R | 5 +- R/print.summary.meta.R | 10 +++-- R/settings.meta.R | 8 ++++ R/summary.meta.R | 1 R/update.meta.R | 3 + inst/COPYRIGHTS | 7 +-- man/forest.Rd | 5 ++ man/metabin.Rd | 4 +- man/metacont.Rd | 38 ++++++++++++++++++++ man/metacr.Rd | 6 +-- man/read.rm5.Rd | 6 +-- man/update.meta.Rd | 5 ++ 21 files changed, 246 insertions(+), 94 deletions(-)
Title: Estimate Correlations Between Repeatedly Measured Endpoints
(E.g., Reliability) Based on Linear Mixed-Effects Models
Description: In clinical practice and research settings in medicine and the behavioral sciences, it is often of interest to quantify the correlation of a continuous endpoint that was repeatedly measured (e.g., test-retest correlations, ICC, etc.). This package allows for estimating these correlations based on mixed-effects models. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Geert Molenberghs, Dieter Hilgers, & Nicole Heussen
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between CorrMixed versions 0.1-1 dated 2015-04-29 and 0.1-11 dated 2015-05-08
DESCRIPTION | 8 +++--- MD5 | 32 +++++++++++++-------------- R/Explore.WS.Corr.R | 14 ++--------- R/Fract.Poly.R | 2 + R/Spaghetti.Plot.R | 28 ++++++++++++----------- R/WS.Corr.Mixed.R | 52 ++++++++++++++++++++++---------------------- R/WS.Corr.Mixed.SAS.R | 14 +++++------ R/plot.WS.Corr.Mixed.R | 36 ++++++++++++++++-------------- man/Explore.WS.Corr.Rd | 7 ++--- man/Fract.Poly.Rd | 2 - man/Heatmap.Rd | 2 - man/Model.Fit.Rd | 2 - man/Spaghetti.Plot.Rd | 6 +++-- man/WS.Corr.Mixed.Rd | 7 +++-- man/WS.Corr.Mixed.SAS.Rd | 10 ++++---- man/plot.Explore.WS.Corr.Rd | 4 +-- man/plot.WS.Corr.Mixed.Rd | 2 - 17 files changed, 114 insertions(+), 114 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 0.80.0 dated 2015-02-06 and 0.90.0 dated 2015-05-08
seasonal-0.80.0/seasonal/data/cntrade.RData |only seasonal-0.90.0/seasonal/DESCRIPTION | 22 seasonal-0.90.0/seasonal/MD5 | 93 +-- seasonal-0.90.0/seasonal/NAMESPACE | 2 seasonal-0.90.0/seasonal/NEWS | 30 + seasonal-0.90.0/seasonal/R/deparse.R | 6 seasonal-0.90.0/seasonal/R/detect.R | 10 seasonal-0.90.0/seasonal/R/diagnostics.R | 7 seasonal-0.90.0/seasonal/R/extractors.R | 3 seasonal-0.90.0/seasonal/R/inspect-sub.R |only seasonal-0.90.0/seasonal/R/inspect.R | 586 ++++++++++++++++------- seasonal-0.90.0/seasonal/R/out.R | 3 seasonal-0.90.0/seasonal/R/plot.R | 50 + seasonal-0.90.0/seasonal/R/read_est.R | 3 seasonal-0.90.0/seasonal/R/seas.R | 43 + seasonal-0.90.0/seasonal/R/seasonal-package.R | 2 seasonal-0.90.0/seasonal/R/series.R | 17 seasonal-0.90.0/seasonal/R/spclist.R | 2 seasonal-0.90.0/seasonal/R/static.R | 3 seasonal-0.90.0/seasonal/R/summary.R | 5 seasonal-0.90.0/seasonal/README.md | 45 + seasonal-0.90.0/seasonal/data/inspectdata.rdata |only seasonal-0.90.0/seasonal/inst/doc/seas.Rnw | 2 seasonal-0.90.0/seasonal/inst/doc/seas.pdf |binary seasonal-0.90.0/seasonal/inst/inspect |only seasonal-0.90.0/seasonal/man/SPECS.Rd | 3 seasonal-0.90.0/seasonal/man/checkX13.Rd | 2 seasonal-0.90.0/seasonal/man/cpi.Rd | 2 seasonal-0.90.0/seasonal/man/easter.Rd | 2 seasonal-0.90.0/seasonal/man/exp.Rd | 2 seasonal-0.90.0/seasonal/man/final.Rd | 5 seasonal-0.90.0/seasonal/man/genhol.Rd | 2 seasonal-0.90.0/seasonal/man/identify.seas.Rd | 2 seasonal-0.90.0/seasonal/man/iip.Rd | 2 seasonal-0.90.0/seasonal/man/inspect.Rd | 55 +- seasonal-0.90.0/seasonal/man/na.x13.Rd | 2 seasonal-0.90.0/seasonal/man/out.Rd | 5 seasonal-0.90.0/seasonal/man/outlier.Rd | 2 seasonal-0.90.0/seasonal/man/plot.seas.Rd | 19 seasonal-0.90.0/seasonal/man/qs.Rd | 6 seasonal-0.90.0/seasonal/man/seas.Rd | 12 seasonal-0.90.0/seasonal/man/seasonal-defunct.Rd | 2 seasonal-0.90.0/seasonal/man/seasonal-package.Rd | 2 seasonal-0.90.0/seasonal/man/series.Rd | 18 seasonal-0.90.0/seasonal/man/static.Rd | 5 seasonal-0.90.0/seasonal/man/summary.seas.Rd | 4 seasonal-0.90.0/seasonal/vignettes/README.tex | 57 +- seasonal-0.90.0/seasonal/vignettes/images |only seasonal-0.90.0/seasonal/vignettes/seas.Rnw | 2 seasonal-0.90.0/seasonal/vignettes/seas.tex |only 50 files changed, 756 insertions(+), 391 deletions(-)
Title: Power/Sample Size Calculation for Mediation Analysis
Description: Functions to
calculate power and sample size for testing
(1) mediation effects;
(2) the slope in a simple linear regression;
(3) odds ratio in a simple logistic regression;
(4) mean change for longitudinal study with 2 time points;
(5) interaction effect in 2-way ANOVA; and
(6) the slope in a simple Poisson regression.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerMediation versions 0.2.3 dated 2015-02-23 and 0.2.4 dated 2015-05-08
DESCRIPTION | 11 +++++----- INDEX | 2 + MD5 | 15 ++++++++------ NAMESPACE | 2 + NEWS | 5 ++++ R/functions_poisson.R |only man/powerMediation.Sobel.Rd | 46 +++++++++++++++++++++---------------------- man/powerPoisson.Rd |only man/sizePoisson.Rd |only man/ssMediation.Sobel.Rd | 47 +++++++++++++++++++++++--------------------- 10 files changed, 72 insertions(+), 56 deletions(-)
More information about powerMediation at CRAN
Permanent link
More information about ApacheLogProcessor at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-07 1.0
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.5.1 dated 2015-01-26 and 0.6.1 dated 2015-05-07
rmarkdown-0.5.1/rmarkdown/tests/test-all.R |only rmarkdown-0.6.1/rmarkdown/DESCRIPTION | 13 rmarkdown-0.6.1/rmarkdown/MD5 | 139 +++++----- rmarkdown-0.6.1/rmarkdown/NAMESPACE | 4 rmarkdown-0.6.1/rmarkdown/NEWS | 25 + rmarkdown-0.6.1/rmarkdown/R/base64.R | 7 rmarkdown-0.6.1/rmarkdown/R/beamer_presentation.R | 13 rmarkdown-0.6.1/rmarkdown/R/draft.R | 2 rmarkdown-0.6.1/rmarkdown/R/html_document.R | 16 - rmarkdown-0.6.1/rmarkdown/R/html_document_base.R | 98 ++++++- rmarkdown-0.6.1/rmarkdown/R/html_fragment.R | 12 rmarkdown-0.6.1/rmarkdown/R/html_parser.R |only rmarkdown-0.6.1/rmarkdown/R/html_resources.R |only rmarkdown-0.6.1/rmarkdown/R/html_vignette.R | 5 rmarkdown-0.6.1/rmarkdown/R/ioslides_presentation.R | 28 +- rmarkdown-0.6.1/rmarkdown/R/md_document.R | 15 - rmarkdown-0.6.1/rmarkdown/R/output_format.R | 53 ++- rmarkdown-0.6.1/rmarkdown/R/pandoc.R | 35 +- rmarkdown-0.6.1/rmarkdown/R/pdf_document.R | 17 - rmarkdown-0.6.1/rmarkdown/R/render.R | 48 +++ rmarkdown-0.6.1/rmarkdown/R/shiny.R | 15 - rmarkdown-0.6.1/rmarkdown/R/slidy_presentation.R | 10 rmarkdown-0.6.1/rmarkdown/R/tufte_handout.R | 4 rmarkdown-0.6.1/rmarkdown/R/util.R | 47 +++ rmarkdown-0.6.1/rmarkdown/R/word_document.R | 13 rmarkdown-0.6.1/rmarkdown/inst/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd | 2 rmarkdown-0.6.1/rmarkdown/inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 8 rmarkdown-0.6.1/rmarkdown/inst/rmarkdown/templates/tufte_handout/skeleton/skeleton.Rmd | 2 rmarkdown-0.6.1/rmarkdown/inst/rmd/h/default.html | 2 rmarkdown-0.6.1/rmarkdown/inst/rmd/h/jquery-AUTHORS.txt | 15 - rmarkdown-0.6.1/rmarkdown/inst/rmd/latex/default.tex | 15 - rmarkdown-0.6.1/rmarkdown/man/beamer_presentation.Rd | 19 - rmarkdown-0.6.1/rmarkdown/man/default_output_format.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/draft.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/find_external_resources.Rd |only rmarkdown-0.6.1/rmarkdown/man/html_document.Rd | 18 - rmarkdown-0.6.1/rmarkdown/man/html_document_base.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/html_fragment.Rd | 13 rmarkdown-0.6.1/rmarkdown/man/html_vignette.Rd | 5 rmarkdown-0.6.1/rmarkdown/man/includes.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/ioslides_presentation.Rd | 15 - rmarkdown-0.6.1/rmarkdown/man/knitr_options.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/knitr_options_html.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/knitr_options_pdf.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/md_document.Rd | 21 + rmarkdown-0.6.1/rmarkdown/man/metadata.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/output_format.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_args.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_available.Rd | 19 - rmarkdown-0.6.1/rmarkdown/man/pandoc_convert.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_options.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_path_arg.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_self_contained_html.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pandoc_template.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/pdf_document.Rd | 18 - rmarkdown-0.6.1/rmarkdown/man/relative_to.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/render.Rd | 8 rmarkdown-0.6.1/rmarkdown/man/render_delayed.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/render_supporting_files.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/rmarkdown_format.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/run.Rd | 2 rmarkdown-0.6.1/rmarkdown/man/slidy_presentation.Rd | 11 rmarkdown-0.6.1/rmarkdown/man/tufte_handout.Rd | 8 rmarkdown-0.6.1/rmarkdown/man/word_document.Rd | 19 - rmarkdown-0.6.1/rmarkdown/tests/testthat.R |only rmarkdown-0.6.1/rmarkdown/tests/testthat/resources |only rmarkdown-0.6.1/rmarkdown/tests/testthat/test-formats.R |only rmarkdown-0.6.1/rmarkdown/tests/testthat/test-formats.Rmd |only rmarkdown-0.6.1/rmarkdown/tests/testthat/test-htmlparse.R |only rmarkdown-0.6.1/rmarkdown/tests/testthat/test-resources.R |only 70 files changed, 619 insertions(+), 258 deletions(-)
Title: Rigorous - NIfTI + ANALYZE + AFNI : Input / Output
Description: Functions for the input/output and visualization of
medical imaging data that follow either the ANALYZE, NIfTI or AFNI
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [aut],
Karsten Tabelow [ctb],
Jon Clayden [ctb],
John Muschelli [ctb]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.nifti versions 0.4.3 dated 2015-01-18 and 0.5.2 dated 2015-05-07
oro.nifti-0.4.3/oro.nifti/man/afni.Rd |only oro.nifti-0.4.3/oro.nifti/man/as_nifti.Rd |only oro.nifti-0.4.3/oro.nifti/man/calmin-methods.Rd |only oro.nifti-0.4.3/oro.nifti/man/q2R.Rd |only oro.nifti-0.4.3/oro.nifti/man/qformsform.Rd |only oro.nifti-0.4.3/oro.nifti/man/write_afni.Rd |only oro.nifti-0.5.2/oro.nifti/DESCRIPTION | 65 - oro.nifti-0.5.2/oro.nifti/MD5 | 292 +++- oro.nifti-0.5.2/oro.nifti/NAMESPACE | 555 ++++++++- oro.nifti-0.5.2/oro.nifti/R/Operators.R |only oro.nifti-0.5.2/oro.nifti/R/afniS4.R | 484 +++++--- oro.nifti-0.5.2/oro.nifti/R/analyzeS4.R | 175 +- oro.nifti-0.5.2/oro.nifti/R/anlz_Operators.R |only oro.nifti-0.5.2/oro.nifti/R/auditTrail.R | 201 ++- oro.nifti-0.5.2/oro.nifti/R/aux_file.R |only oro.nifti-0.5.2/oro.nifti/R/bitpix.R |only oro.nifti-0.5.2/oro.nifti/R/blend.R |only oro.nifti-0.5.2/oro.nifti/R/cal_img.R |only oro.nifti-0.5.2/oro.nifti/R/cal_max.R |only oro.nifti-0.5.2/oro.nifti/R/cal_min.R |only oro.nifti-0.5.2/oro.nifti/R/cal_units.R |only oro.nifti-0.5.2/oro.nifti/R/coerce.R |only oro.nifti-0.5.2/oro.nifti/R/compressed.R |only oro.nifti-0.5.2/oro.nifti/R/convert_anlz.R | 62 - oro.nifti-0.5.2/oro.nifti/R/convert_nifti.R | 124 +- oro.nifti-0.5.2/oro.nifti/R/data_type.R |only oro.nifti-0.5.2/oro.nifti/R/datatype.R |only oro.nifti-0.5.2/oro.nifti/R/db_name.R |only oro.nifti-0.5.2/oro.nifti/R/descrip.R |only oro.nifti-0.5.2/oro.nifti/R/dim_.R |only oro.nifti-0.5.2/oro.nifti/R/dim_info.R |only oro.nifti-0.5.2/oro.nifti/R/dim_un0.R |only oro.nifti-0.5.2/oro.nifti/R/drop_img_dim.R |only oro.nifti-0.5.2/oro.nifti/R/exp_date.R |only oro.nifti-0.5.2/oro.nifti/R/exp_time.R |only oro.nifti-0.5.2/oro.nifti/R/extender.R |only oro.nifti-0.5.2/oro.nifti/R/extents.R |only oro.nifti-0.5.2/oro.nifti/R/field_skip.R |only oro.nifti-0.5.2/oro.nifti/R/funused1.R |only oro.nifti-0.5.2/oro.nifti/R/funused2.R |only oro.nifti-0.5.2/oro.nifti/R/funused3.R |only oro.nifti-0.5.2/oro.nifti/R/generated.R |only oro.nifti-0.5.2/oro.nifti/R/glmax.R |only oro.nifti-0.5.2/oro.nifti/R/glmin.R |only oro.nifti-0.5.2/oro.nifti/R/hist_un0.R |only oro.nifti-0.5.2/oro.nifti/R/hkey_un0.R |only oro.nifti-0.5.2/oro.nifti/R/hotmetal.R | 29 oro.nifti-0.5.2/oro.nifti/R/intent_code.R |only oro.nifti-0.5.2/oro.nifti/R/intent_name.R |only oro.nifti-0.5.2/oro.nifti/R/intent_p1.R |only oro.nifti-0.5.2/oro.nifti/R/intent_p2.R |only oro.nifti-0.5.2/oro.nifti/R/intent_p3.R |only oro.nifti-0.5.2/oro.nifti/R/is.R |only oro.nifti-0.5.2/oro.nifti/R/magic.R |only oro.nifti-0.5.2/oro.nifti/R/miscellaneous.R | 39 oro.nifti-0.5.2/oro.nifti/R/niftiS4.R | 585 +++++----- oro.nifti-0.5.2/oro.nifti/R/nifti_assign.R |only oro.nifti-0.5.2/oro.nifti/R/omax.R |only oro.nifti-0.5.2/oro.nifti/R/omin.R |only oro.nifti-0.5.2/oro.nifti/R/onefile.R |only oro.nifti-0.5.2/oro.nifti/R/orient.R |only oro.nifti-0.5.2/oro.nifti/R/origin.R |only oro.nifti-0.5.2/oro.nifti/R/patient_id.R |only oro.nifti-0.5.2/oro.nifti/R/pixdim.R |only oro.nifti-0.5.2/oro.nifti/R/plot.R | 178 ++- oro.nifti-0.5.2/oro.nifti/R/qform_code.R |only oro.nifti-0.5.2/oro.nifti/R/qoffset_x.R |only oro.nifti-0.5.2/oro.nifti/R/qoffset_y.R |only oro.nifti-0.5.2/oro.nifti/R/qoffset_z.R |only oro.nifti-0.5.2/oro.nifti/R/quatern_b.R |only oro.nifti-0.5.2/oro.nifti/R/quatern_c.R |only oro.nifti-0.5.2/oro.nifti/R/quatern_d.R |only oro.nifti-0.5.2/oro.nifti/R/quaternion.R |only oro.nifti-0.5.2/oro.nifti/R/readS4.R | 105 + oro.nifti-0.5.2/oro.nifti/R/regular.R |only oro.nifti-0.5.2/oro.nifti/R/remove.R | 32 oro.nifti-0.5.2/oro.nifti/R/scannum.R |only oro.nifti-0.5.2/oro.nifti/R/scl_inter.R |only oro.nifti-0.5.2/oro.nifti/R/scl_slope.R |only oro.nifti-0.5.2/oro.nifti/R/session_error.R |only oro.nifti-0.5.2/oro.nifti/R/sform_code.R |only oro.nifti-0.5.2/oro.nifti/R/sizeof_hdr.R |only oro.nifti-0.5.2/oro.nifti/R/slice_code.R |only oro.nifti-0.5.2/oro.nifti/R/slice_duration.R |only oro.nifti-0.5.2/oro.nifti/R/slice_end.R |only oro.nifti-0.5.2/oro.nifti/R/slice_start.R |only oro.nifti-0.5.2/oro.nifti/R/smax.R |only oro.nifti-0.5.2/oro.nifti/R/smin.R |only oro.nifti-0.5.2/oro.nifti/R/srow_x.R |only oro.nifti-0.5.2/oro.nifti/R/srow_y.R |only oro.nifti-0.5.2/oro.nifti/R/srow_z.R |only oro.nifti-0.5.2/oro.nifti/R/start_field.R |only oro.nifti-0.5.2/oro.nifti/R/tim_colors.R | 31 oro.nifti-0.5.2/oro.nifti/R/toffset.R |only oro.nifti-0.5.2/oro.nifti/R/transform.R | 210 ++- oro.nifti-0.5.2/oro.nifti/R/unused1.R |only oro.nifti-0.5.2/oro.nifti/R/verified.R |only oro.nifti-0.5.2/oro.nifti/R/views.R |only oro.nifti-0.5.2/oro.nifti/R/vols_added.R |only oro.nifti-0.5.2/oro.nifti/R/vox_offset.R |only oro.nifti-0.5.2/oro.nifti/R/vox_units.R |only oro.nifti-0.5.2/oro.nifti/R/voxdim.R |only oro.nifti-0.5.2/oro.nifti/R/wrappers.R | 1 oro.nifti-0.5.2/oro.nifti/R/writeS4.R | 204 ++- oro.nifti-0.5.2/oro.nifti/R/xyzt_units.R |only oro.nifti-0.5.2/oro.nifti/R/zero_trans.R |only oro.nifti-0.5.2/oro.nifti/R/zzz.R | 7 oro.nifti-0.5.2/oro.nifti/build/vignette.rds |binary oro.nifti-0.5.2/oro.nifti/inst/doc/nifti.R | 2 oro.nifti-0.5.2/oro.nifti/inst/doc/nifti.Rnw | 2 oro.nifti-0.5.2/oro.nifti/inst/doc/nifti.pdf |binary oro.nifti-0.5.2/oro.nifti/man/afni-class.Rd | 69 - 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Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 1.9-5 dated 2014-11-24 and 1.9-6 dated 2015-05-07
metafor-1.9-5/metafor/R/metafor.R |only metafor-1.9-5/metafor/tests/testthat/test_example_stijnen2010.r |only metafor-1.9-6/metafor/DESCRIPTION | 22 metafor-1.9-6/metafor/MD5 | 251 +++++++--- metafor-1.9-6/metafor/NAMESPACE | 8 metafor-1.9-6/metafor/NEWS | 116 ++++ metafor-1.9-6/metafor/R/AIC.rma.r |only metafor-1.9-6/metafor/R/BIC.rma.r |only metafor-1.9-6/metafor/R/addpoly.default.r |only metafor-1.9-6/metafor/R/addpoly.r |only metafor-1.9-6/metafor/R/addpoly.rma.r |only metafor-1.9-6/metafor/R/anova.rma.r |only metafor-1.9-6/metafor/R/baujat.r |only metafor-1.9-6/metafor/R/baujat.rma.mh.r |only metafor-1.9-6/metafor/R/baujat.rma.peto.r |only metafor-1.9-6/metafor/R/baujat.rma.uni.r |only metafor-1.9-6/metafor/R/bldiag.r |only metafor-1.9-6/metafor/R/blup.r |only metafor-1.9-6/metafor/R/blup.rma.uni.r |only metafor-1.9-6/metafor/R/coef.permutest.rma.uni.r |only metafor-1.9-6/metafor/R/coef.rma.r |only metafor-1.9-6/metafor/R/coef.summary.rma.r |only 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metafor-1.9-6/metafor/R/weights.rma.peto.r |only metafor-1.9-6/metafor/R/weights.rma.uni.r |only metafor-1.9-6/metafor/R/zzz.R |only metafor-1.9-6/metafor/build/vignette.rds |binary metafor-1.9-6/metafor/data/dat.bourassa1996.rda |binary metafor-1.9-6/metafor/data/dat.curtis1998.rda |binary metafor-1.9-6/metafor/data/dat.senn2013.rda |only metafor-1.9-6/metafor/inst/CITATION | 1 metafor-1.9-6/metafor/inst/doc/metafor.pdf.asis | 2 metafor-1.9-6/metafor/inst/doc/metafor_diagram.pdf.asis | 2 metafor-1.9-6/metafor/man/anova.rma.Rd | 33 - metafor-1.9-6/metafor/man/confint.rma.Rd | 16 metafor-1.9-6/metafor/man/dat.bourassa1996.Rd | 10 metafor-1.9-6/metafor/man/dat.curtis1998.Rd | 1 metafor-1.9-6/metafor/man/dat.hart1999.Rd | 16 metafor-1.9-6/metafor/man/dat.hasselblad1998.Rd | 8 metafor-1.9-6/metafor/man/dat.molloy2014.Rd | 6 metafor-1.9-6/metafor/man/dat.normand1999.Rd | 6 metafor-1.9-6/metafor/man/dat.raudenbush1985.Rd | 7 metafor-1.9-6/metafor/man/dat.senn2013.Rd |only metafor-1.9-6/metafor/man/escalc.Rd | 14 metafor-1.9-6/metafor/man/fitstats.Rd | 2 metafor-1.9-6/metafor/man/forest.cumul.rma.Rd | 15 metafor-1.9-6/metafor/man/forest.default.Rd | 15 metafor-1.9-6/metafor/man/forest.rma.Rd | 26 - metafor-1.9-6/metafor/man/funnel.Rd | 2 metafor-1.9-6/metafor/man/hc.Rd | 2 metafor-1.9-6/metafor/man/influence.rma.mv.Rd | 2 metafor-1.9-6/metafor/man/influence.rma.uni.Rd | 2 metafor-1.9-6/metafor/man/predict.rma.Rd | 14 metafor-1.9-6/metafor/man/print.anova.rma.Rd | 4 metafor-1.9-6/metafor/man/print.list.rma.Rd | 2 metafor-1.9-6/metafor/man/print.rma.uni.Rd | 10 metafor-1.9-6/metafor/man/profile.rma.Rd | 19 metafor-1.9-6/metafor/man/regtest.Rd | 10 metafor-1.9-6/metafor/man/rma.glmm.Rd | 4 metafor-1.9-6/metafor/man/rma.mv.Rd | 32 - metafor-1.9-6/metafor/man/rma.uni.Rd | 19 metafor-1.9-6/metafor/man/trimfill.Rd | 2 metafor-1.9-6/metafor/man/vcov.rma.Rd | 6 metafor-1.9-6/metafor/man/weights.rma.Rd | 2 metafor-1.9-6/metafor/tests/test-all.R | 2 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metafor-1.9-6/metafor/tests/testthat/test_analysis_example_stijnen2010.r |only metafor-1.9-6/metafor/tests/testthat/test_analysis_example_vanhouwelingen1993.r |only metafor-1.9-6/metafor/tests/testthat/test_analysis_example_vanhouwelingen2002.r |only metafor-1.9-6/metafor/tests/testthat/test_confint.r | 4 metafor-1.9-6/metafor/tests/testthat/test_escalc.r | 4 metafor-1.9-6/metafor/tests/testthat/test_handling_of_edge_cases_due_to_zeros.r | 4 metafor-1.9-6/metafor/tests/testthat/test_metan_vs_rma.mh_with_dat.bcg.r | 4 metafor-1.9-6/metafor/tests/testthat/test_metan_vs_rma.peto_with_dat.bcg.r | 4 metafor-1.9-6/metafor/tests/testthat/test_metan_vs_rma.uni_with_dat.bcg.r | 4 metafor-1.9-6/metafor/tests/testthat/test_regression_with_rma.r | 4 metafor-1.9-6/metafor/tests/testthat/test_rma_error_handling.r |only metafor-1.9-6/metafor/tests/testthat/test_rma_vs_direct_computation.r | 5 metafor-1.9-6/metafor/tests/testthat/test_rma_vs_lm_and_lme.r | 14 metafor-1.9-6/metafor/tests/testthat/test_rma_weights.r | 4 metafor-1.9-6/metafor/vignettes/metafor.pdf.asis | 2 metafor-1.9-6/metafor/vignettes/metafor_diagram.pdf.asis | 2 200 files changed, 542 insertions(+), 224 deletions(-)
Title: Longitudinal Targeted Maximum Likelihood Estimation
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data.
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab <joshuaschwab@yahoo.com>
Diff between ltmle versions 0.9.3-1 dated 2014-04-22 and 0.9-5 dated 2015-05-07
ltmle-0.9-5/ltmle/DESCRIPTION | 15 ltmle-0.9-5/ltmle/MD5 | 39 ltmle-0.9-5/ltmle/NAMESPACE | 5 ltmle-0.9-5/ltmle/NEWS | 38 ltmle-0.9-5/ltmle/R/GeneralUtilities.R | 67 ltmle-0.9-5/ltmle/R/ltmle.R | 1801 ++++++---- ltmle-0.9-5/ltmle/R/ltmle_sg.R | 17 ltmle-0.9-5/ltmle/R/zzz.R | 13 ltmle-0.9-5/ltmle/data/PreviousReleaseTests.RData |binary ltmle-0.9-5/ltmle/data/sampleDataForLtmleMSM.RData |binary ltmle-0.9-5/ltmle/man/DeterministicFunctions.Rd | 67 ltmle-0.9-5/ltmle/man/ltmle-package.rd | 13 ltmle-0.9-5/ltmle/man/ltmle.rd | 134 ltmle-0.9-5/ltmle/man/summary.ltmle.Rd | 76 ltmle-0.9-5/ltmle/tests/testthat/test-BaselineCovMSM.R |only ltmle-0.9-5/ltmle/tests/testthat/test-CheckInputs.R | 12 ltmle-0.9-5/ltmle/tests/testthat/test-EstimateVariance.R |only ltmle-0.9-5/ltmle/tests/testthat/test-Weights.R |only ltmle-0.9-5/ltmle/tests/testthat/test-prevRelease.R |only ltmle-0.9-5/ltmle/tests/testthat/test-print.summary.ltmleMSM.R | 3 ltmle-0.9-5/ltmle/tests/testthat/test-random.R | 73 ltmle-0.9-5/ltmle/tests/testthat/test-summary.ltmle.R | 15 ltmle-0.9.3-1/ltmle/tests/testthat/tests-prevRelease.R |only 23 files changed, 1535 insertions(+), 853 deletions(-)
Title: Generalized Regression on Orthogonal Components
Description: Robust multiple or multivariate linear regression, nonparametric regression on orthogonal components, classical or robust partial least squares models.
Author: M. Bilodeau and P. Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux <lafaye@dms.umontreal.ca>
Diff between groc versions 1.0.4 dated 2014-06-30 and 1.0.5 dated 2015-05-07
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 7 ++++++- R/dependencemeasures.R | 2 +- inst/CITATION | 33 ++++++++++++++++++--------------- inst/HISTORY | 8 +++++++- man/groc.Rd | 7 +++++-- man/groc.crossval.Rd | 8 +++++--- man/groc.fit.Rd | 8 +++++--- man/plot.groc.Rd | 8 ++++++++ man/predict.groc.Rd | 8 +++++--- man/summary.groc.Rd | 5 +++++ 12 files changed, 81 insertions(+), 45 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.7 dated 2015-02-23 and 0.10.1 dated 2015-05-07
git2r-0.10.1/git2r/DESCRIPTION | 37 git2r-0.10.1/git2r/MD5 | 587 +++++----- git2r-0.10.1/git2r/NAMESPACE | 10 git2r-0.10.1/git2r/NEWS | 94 + git2r-0.10.1/git2r/R/branch.r | 46 git2r-0.10.1/git2r/R/bundle_r_package.r |only git2r-0.10.1/git2r/R/checkout.r | 69 - git2r-0.10.1/git2r/R/commit.r | 93 + git2r-0.10.1/git2r/R/config.r | 28 git2r-0.10.1/git2r/R/fetch.r | 12 git2r-0.10.1/git2r/R/index.r | 87 + git2r-0.10.1/git2r/R/libgit2.r | 21 git2r-0.10.1/git2r/R/plot.r |only git2r-0.10.1/git2r/R/push.r | 17 git2r-0.10.1/git2r/R/repository.r | 135 ++ git2r-0.10.1/git2r/R/reset.r | 21 git2r-0.10.1/git2r/R/revparse.r |only git2r-0.10.1/git2r/R/status.r | 109 + git2r-0.10.1/git2r/R/tag.r | 13 git2r-0.10.1/git2r/R/time.r | 16 git2r-0.10.1/git2r/configure | 38 git2r-0.10.1/git2r/man/add-methods.Rd | 2 git2r-0.10.1/git2r/man/ahead_behind-methods.Rd | 2 git2r-0.10.1/git2r/man/blame-methods.Rd | 2 git2r-0.10.1/git2r/man/blob_create-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_create-methods.Rd | 13 git2r-0.10.1/git2r/man/branch_delete-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_get_upstream-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_remote_name-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_remote_url-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_rename-methods.Rd | 13 git2r-0.10.1/git2r/man/branch_set_upstream-methods.Rd | 2 git2r-0.10.1/git2r/man/branch_target-methods.Rd | 2 git2r-0.10.1/git2r/man/branches-methods.Rd | 2 git2r-0.10.1/git2r/man/bundle_r_package-methods.Rd |only git2r-0.10.1/git2r/man/checkout-methods.Rd | 2 git2r-0.10.1/git2r/man/clone-methods.Rd | 10 git2r-0.10.1/git2r/man/coerce-git_repository-method.Rd | 2 git2r-0.10.1/git2r/man/coerce-git_tree-data.frame-method.Rd | 2 git2r-0.10.1/git2r/man/coerce-git_tree-list-method.Rd | 2 git2r-0.10.1/git2r/man/commit-methods.Rd | 18 git2r-0.10.1/git2r/man/commits-methods.Rd | 17 git2r-0.10.1/git2r/man/config-methods.Rd | 4 git2r-0.10.1/git2r/man/content-methods.Rd | 2 git2r-0.10.1/git2r/man/contributions-methods.Rd | 2 git2r-0.10.1/git2r/man/cred_ssh_key-class.Rd | 2 git2r-0.10.1/git2r/man/cred_ssh_key-methods.Rd | 2 git2r-0.10.1/git2r/man/cred_user_pass-class.Rd | 2 git2r-0.10.1/git2r/man/cred_user_pass-methods.Rd | 2 git2r-0.10.1/git2r/man/default_signature-methods.Rd | 2 git2r-0.10.1/git2r/man/descendant_of-methods.Rd | 2 git2r-0.10.1/git2r/man/diff-methods.Rd | 2 git2r-0.10.1/git2r/man/discover_repository-methods.Rd | 2 git2r-0.10.1/git2r/man/fetch-methods.Rd | 2 git2r-0.10.1/git2r/man/fetch_heads-methods.Rd | 2 git2r-0.10.1/git2r/man/git2r.Rd | 2 git2r-0.10.1/git2r/man/git_blame-class.Rd | 2 git2r-0.10.1/git2r/man/git_blame_hunk-class.Rd | 2 git2r-0.10.1/git2r/man/git_blob-class.Rd | 2 git2r-0.10.1/git2r/man/git_branch-class.Rd | 2 git2r-0.10.1/git2r/man/git_commit-class.Rd | 2 git2r-0.10.1/git2r/man/git_diff-class.Rd | 2 git2r-0.10.1/git2r/man/git_diff_file-class.Rd | 2 git2r-0.10.1/git2r/man/git_diff_hunk-class.Rd | 2 git2r-0.10.1/git2r/man/git_diff_line-class.Rd | 2 git2r-0.10.1/git2r/man/git_fetch_head.Rd | 2 git2r-0.10.1/git2r/man/git_merge_result.Rd | 2 git2r-0.10.1/git2r/man/git_note-class.Rd | 2 git2r-0.10.1/git2r/man/git_reference-class.Rd | 2 git2r-0.10.1/git2r/man/git_reflog_entry-class.Rd | 2 git2r-0.10.1/git2r/man/git_repository-class.Rd | 2 git2r-0.10.1/git2r/man/git_signature-class.Rd | 2 git2r-0.10.1/git2r/man/git_stash-class.Rd | 2 git2r-0.10.1/git2r/man/git_tag-class.Rd | 2 git2r-0.10.1/git2r/man/git_time-class.Rd | 2 git2r-0.10.1/git2r/man/git_transfer_progress-class.Rd | 2 git2r-0.10.1/git2r/man/git_tree-class.Rd | 2 git2r-0.10.1/git2r/man/hash-methods.Rd | 2 git2r-0.10.1/git2r/man/hashfile-methods.Rd | 2 git2r-0.10.1/git2r/man/head-methods.Rd | 2 git2r-0.10.1/git2r/man/in_repository-methods.Rd |only git2r-0.10.1/git2r/man/init-methods.Rd | 2 git2r-0.10.1/git2r/man/is_bare-methods.Rd | 5 git2r-0.10.1/git2r/man/is_binary-methods.Rd | 2 git2r-0.10.1/git2r/man/is_blob.Rd | 2 git2r-0.10.1/git2r/man/is_commit.Rd | 2 git2r-0.10.1/git2r/man/is_detached-methods.Rd | 5 git2r-0.10.1/git2r/man/is_empty-methods.Rd | 5 git2r-0.10.1/git2r/man/is_head-methods.Rd | 2 git2r-0.10.1/git2r/man/is_local-methods.Rd | 2 git2r-0.10.1/git2r/man/is_merge-methods.Rd | 2 git2r-0.10.1/git2r/man/is_shallow-methods.Rd | 5 git2r-0.10.1/git2r/man/length-git_blob-method.Rd | 2 git2r-0.10.1/git2r/man/length-git_diff-method.Rd | 2 git2r-0.10.1/git2r/man/length-git_tree-method.Rd | 2 git2r-0.10.1/git2r/man/libgit2_features.Rd | 4 git2r-0.10.1/git2r/man/libgit2_sha.Rd |only git2r-0.10.1/git2r/man/libgit2_version.Rd | 9 git2r-0.10.1/git2r/man/lookup-methods.Rd | 2 git2r-0.10.1/git2r/man/merge-methods.Rd | 2 git2r-0.10.1/git2r/man/merge_base-methods.Rd | 2 git2r-0.10.1/git2r/man/merge_branch.Rd | 2 git2r-0.10.1/git2r/man/merge_named_branch.Rd | 2 git2r-0.10.1/git2r/man/note_create-methods.Rd | 2 git2r-0.10.1/git2r/man/note_default_ref-methods.Rd | 2 git2r-0.10.1/git2r/man/note_remove-methods.Rd | 2 git2r-0.10.1/git2r/man/notes-methods.Rd | 2 git2r-0.10.1/git2r/man/odb_blobs-methods.Rd | 2 git2r-0.10.1/git2r/man/odb_objects-methods.Rd | 2 git2r-0.10.1/git2r/man/parents-methods.Rd | 2 git2r-0.10.1/git2r/man/plot-methods.Rd |only git2r-0.10.1/git2r/man/pull-methods.Rd | 2 git2r-0.10.1/git2r/man/push-methods.Rd | 9 git2r-0.10.1/git2r/man/references-methods.Rd | 2 git2r-0.10.1/git2r/man/reflog-methods.Rd | 2 git2r-0.10.1/git2r/man/remote_add-methods.Rd | 2 git2r-0.10.1/git2r/man/remote_remove-methods.Rd | 2 git2r-0.10.1/git2r/man/remote_rename-methods.Rd | 2 git2r-0.10.1/git2r/man/remote_url-methods.Rd | 2 git2r-0.10.1/git2r/man/remotes-methods.Rd | 2 git2r-0.10.1/git2r/man/repository-methods.Rd | 11 git2r-0.10.1/git2r/man/reset-methods.Rd | 14 git2r-0.10.1/git2r/man/revparse_single-methods.Rd |only git2r-0.10.1/git2r/man/rm_file-methods.Rd |only git2r-0.10.1/git2r/man/show-git_blob-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_branch-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_commit-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_diff-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_merge_result-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_note-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_reference-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_reflog_entry-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_repository-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_signature-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_stash-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_tag-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_time-method.Rd | 2 git2r-0.10.1/git2r/man/show-git_tree-method.Rd | 2 git2r-0.10.1/git2r/man/stash-methods.Rd | 2 git2r-0.10.1/git2r/man/stash_drop-methods.Rd | 2 git2r-0.10.1/git2r/man/stash_list-methods.Rd | 2 git2r-0.10.1/git2r/man/status-methods.Rd | 14 git2r-0.10.1/git2r/man/summary-git_blob-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_commit-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_diff-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_repository-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_stash-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_tag-method.Rd | 2 git2r-0.10.1/git2r/man/summary-git_tree-method.Rd | 2 git2r-0.10.1/git2r/man/tag-methods.Rd | 9 git2r-0.10.1/git2r/man/tags-methods.Rd | 2 git2r-0.10.1/git2r/man/tree-index-methods.Rd | 2 git2r-0.10.1/git2r/man/tree-methods.Rd | 2 git2r-0.10.1/git2r/man/when-methods.Rd | 2 git2r-0.10.1/git2r/man/workdir-methods.Rd | 2 git2r-0.10.1/git2r/src/Makevars.in | 7 git2r-0.10.1/git2r/src/Makevars.win | 7 git2r-0.10.1/git2r/src/git2r.c | 23 git2r-0.10.1/git2r/src/git2r_arg.c | 228 +-- git2r-0.10.1/git2r/src/git2r_blame.c | 2 git2r-0.10.1/git2r/src/git2r_blob.c | 10 git2r-0.10.1/git2r/src/git2r_branch.c | 90 - git2r-0.10.1/git2r/src/git2r_branch.h | 14 git2r-0.10.1/git2r/src/git2r_checkout.c | 232 --- git2r-0.10.1/git2r/src/git2r_checkout.h | 4 git2r-0.10.1/git2r/src/git2r_clone.c | 23 git2r-0.10.1/git2r/src/git2r_clone.h | 7 git2r-0.10.1/git2r/src/git2r_commit.c | 16 git2r-0.10.1/git2r/src/git2r_config.c | 2 git2r-0.10.1/git2r/src/git2r_diff.c | 20 git2r-0.10.1/git2r/src/git2r_error.c | 2 git2r-0.10.1/git2r/src/git2r_error.h | 2 git2r-0.10.1/git2r/src/git2r_graph.c | 8 git2r-0.10.1/git2r/src/git2r_index.c | 52 git2r-0.10.1/git2r/src/git2r_index.h | 1 git2r-0.10.1/git2r/src/git2r_merge.c | 28 git2r-0.10.1/git2r/src/git2r_note.c | 20 git2r-0.10.1/git2r/src/git2r_object.c | 2 git2r-0.10.1/git2r/src/git2r_odb.c | 4 git2r-0.10.1/git2r/src/git2r_push.c | 79 - git2r-0.10.1/git2r/src/git2r_push.h | 8 git2r-0.10.1/git2r/src/git2r_reflog.c | 2 git2r-0.10.1/git2r/src/git2r_remote.c | 34 git2r-0.10.1/git2r/src/git2r_remote.h | 3 git2r-0.10.1/git2r/src/git2r_repository.c | 88 + git2r-0.10.1/git2r/src/git2r_repository.h | 2 git2r-0.10.1/git2r/src/git2r_reset.c | 33 git2r-0.10.1/git2r/src/git2r_reset.h | 2 git2r-0.10.1/git2r/src/git2r_revparse.c |only git2r-0.10.1/git2r/src/git2r_revparse.h |only git2r-0.10.1/git2r/src/git2r_revwalk.c | 40 git2r-0.10.1/git2r/src/git2r_revwalk.h | 2 git2r-0.10.1/git2r/src/git2r_stash.c | 10 git2r-0.10.1/git2r/src/git2r_status.c | 8 git2r-0.10.1/git2r/src/git2r_tag.c | 6 git2r-0.10.1/git2r/src/libgit2/annotated_commit.c | 28 git2r-0.10.1/git2r/src/libgit2/attrcache.c | 3 git2r-0.10.1/git2r/src/libgit2/branch.c | 105 + git2r-0.10.1/git2r/src/libgit2/checkout.c | 28 git2r-0.10.1/git2r/src/libgit2/cherrypick.c | 2 git2r-0.10.1/git2r/src/libgit2/clone.c | 48 git2r-0.10.1/git2r/src/libgit2/commit.c | 4 git2r-0.10.1/git2r/src/libgit2/common.h | 1 git2r-0.10.1/git2r/src/libgit2/config.c | 119 +- git2r-0.10.1/git2r/src/libgit2/config.h | 4 git2r-0.10.1/git2r/src/libgit2/config_cache.c | 3 git2r-0.10.1/git2r/src/libgit2/config_file.c | 24 git2r-0.10.1/git2r/src/libgit2/config_file.h | 2 git2r-0.10.1/git2r/src/libgit2/describe.c | 2 git2r-0.10.1/git2r/src/libgit2/diff.c | 6 git2r-0.10.1/git2r/src/libgit2/diff_driver.c | 3 git2r-0.10.1/git2r/src/libgit2/diff_tform.c | 4 git2r-0.10.1/git2r/src/libgit2/fileops.c | 19 git2r-0.10.1/git2r/src/libgit2/filter.c | 3 git2r-0.10.1/git2r/src/libgit2/global.c | 47 git2r-0.10.1/git2r/src/libgit2/hashsig.c | 17 git2r-0.10.1/git2r/src/libgit2/include/git2/annotated_commit.h | 17 git2r-0.10.1/git2r/src/libgit2/include/git2/branch.h | 36 git2r-0.10.1/git2r/src/libgit2/include/git2/checkout.h | 27 git2r-0.10.1/git2r/src/libgit2/include/git2/clone.h | 14 git2r-0.10.1/git2r/src/libgit2/include/git2/config.h | 40 git2r-0.10.1/git2r/src/libgit2/include/git2/index.h | 32 git2r-0.10.1/git2r/src/libgit2/include/git2/merge.h | 23 git2r-0.10.1/git2r/src/libgit2/include/git2/pack.h | 13 git2r-0.10.1/git2r/src/libgit2/include/git2/rebase.h | 7 git2r-0.10.1/git2r/src/libgit2/include/git2/refs.h | 48 git2r-0.10.1/git2r/src/libgit2/include/git2/remote.h | 16 git2r-0.10.1/git2r/src/libgit2/include/git2/repository.h | 59 - git2r-0.10.1/git2r/src/libgit2/include/git2/reset.h | 29 git2r-0.10.1/git2r/src/libgit2/include/git2/submodule.h | 12 git2r-0.10.1/git2r/src/libgit2/include/git2/sys/config.h | 4 git2r-0.10.1/git2r/src/libgit2/include/git2/version.h | 1 git2r-0.10.1/git2r/src/libgit2/index.c | 60 - git2r-0.10.1/git2r/src/libgit2/indexer.c | 12 git2r-0.10.1/git2r/src/libgit2/merge.c | 43 git2r-0.10.1/git2r/src/libgit2/merge.h | 1 git2r-0.10.1/git2r/src/libgit2/merge_file.c | 13 git2r-0.10.1/git2r/src/libgit2/openssl_stream.c | 17 git2r-0.10.1/git2r/src/libgit2/pack-objects.c | 245 ++++ git2r-0.10.1/git2r/src/libgit2/pack-objects.h | 10 git2r-0.10.1/git2r/src/libgit2/pack.c | 3 git2r-0.10.1/git2r/src/libgit2/pack.h | 4 git2r-0.10.1/git2r/src/libgit2/path.c | 37 git2r-0.10.1/git2r/src/libgit2/push.c | 34 git2r-0.10.1/git2r/src/libgit2/push.h | 7 git2r-0.10.1/git2r/src/libgit2/rebase.c | 28 git2r-0.10.1/git2r/src/libgit2/refdb_fs.c | 2 git2r-0.10.1/git2r/src/libgit2/refs.c | 164 +- git2r-0.10.1/git2r/src/libgit2/refs.h | 4 git2r-0.10.1/git2r/src/libgit2/refspec.c | 3 git2r-0.10.1/git2r/src/libgit2/remote.c | 43 git2r-0.10.1/git2r/src/libgit2/repository.c | 316 ++++- git2r-0.10.1/git2r/src/libgit2/repository.h | 45 git2r-0.10.1/git2r/src/libgit2/reset.c | 40 git2r-0.10.1/git2r/src/libgit2/revert.c | 2 git2r-0.10.1/git2r/src/libgit2/revwalk.c | 2 git2r-0.10.1/git2r/src/libgit2/revwalk.h | 2 git2r-0.10.1/git2r/src/libgit2/stash.c | 8 git2r-0.10.1/git2r/src/libgit2/stream.h | 5 git2r-0.10.1/git2r/src/libgit2/submodule.c | 9 git2r-0.10.1/git2r/src/libgit2/tag.c | 4 git2r-0.10.1/git2r/src/libgit2/transports/git.c | 1 git2r-0.10.1/git2r/src/libgit2/transports/http.c | 8 git2r-0.10.1/git2r/src/libgit2/transports/local.c | 47 git2r-0.10.1/git2r/src/libgit2/win32/posix.h | 4 git2r-0.10.1/git2r/src/libgit2/win32/posix_w32.c | 24 git2r-0.10.1/git2r/src/regex/regex.h | 11 git2r-0.10.1/git2r/tests/bare_repository.R | 14 git2r-0.10.1/git2r/tests/blame.R | 20 git2r-0.10.1/git2r/tests/blob.R | 2 git2r-0.10.1/git2r/tests/branch.R | 2 git2r-0.10.1/git2r/tests/checkout-named-branch.R | 8 git2r-0.10.1/git2r/tests/checkout.R | 26 git2r-0.10.1/git2r/tests/checkout_branch.R |only git2r-0.10.1/git2r/tests/checkout_commit.R |only git2r-0.10.1/git2r/tests/checkout_tag.R |only git2r-0.10.1/git2r/tests/clone_bare.R |only git2r-0.10.1/git2r/tests/commit.R | 50 git2r-0.10.1/git2r/tests/config.R | 6 git2r-0.10.1/git2r/tests/diff.R | 2 git2r-0.10.1/git2r/tests/fast_forward_merge.R | 2 git2r-0.10.1/git2r/tests/fetch.R | 4 git2r-0.10.1/git2r/tests/graph.R | 2 git2r-0.10.1/git2r/tests/index.R | 50 git2r-0.10.1/git2r/tests/libgit2.R | 3 git2r-0.10.1/git2r/tests/merge.R | 7 git2r-0.10.1/git2r/tests/merge_named_branch.R | 7 git2r-0.10.1/git2r/tests/note.R | 2 git2r-0.10.1/git2r/tests/odb_blobs.R | 4 git2r-0.10.1/git2r/tests/pull.R | 4 git2r-0.10.1/git2r/tests/push-force.R |only git2r-0.10.1/git2r/tests/push.R | 14 git2r-0.10.1/git2r/tests/reflog.R | 4 git2r-0.10.1/git2r/tests/remotes.R | 2 git2r-0.10.1/git2r/tests/repository.R | 38 git2r-0.10.1/git2r/tests/reset.R | 17 git2r-0.10.1/git2r/tests/revparse.R |only git2r-0.10.1/git2r/tests/stash.R | 2 git2r-0.10.1/git2r/tests/status.R | 20 git2r-0.10.1/git2r/tests/tag.R | 14 git2r-0.10.1/git2r/tests/tree.R | 2 git2r-0.10.1/git2r/tests/when.R | 16 git2r-0.7/git2r/man/checkout_reflog_msg.Rd |only git2r-0.7/git2r/man/display_status.Rd |only 304 files changed, 3272 insertions(+), 2121 deletions(-)
Title: Interactive Exploration of Contour Data
Description: An interactive tool to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. exCon creates an interactive web page
showing the contoured data set along with slices from the original matrix
parallel to each dimension. The page is written in d3/javascript.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between exCon versions 0.1-3 dated 2015-01-14 and 0.1.5 dated 2015-05-07
exCon-0.1-3/exCon/inst/extdata/exCon.js |only exCon-0.1.5/exCon/DESCRIPTION | 11 exCon-0.1.5/exCon/MD5 | 27 exCon-0.1.5/exCon/NAMESPACE | 2 exCon-0.1.5/exCon/NEWS | 10 exCon-0.1.5/exCon/R/exCon.R | 51 + exCon-0.1.5/exCon/inst/extdata/eC_brushNguides.js | 271 +++++---- exCon-0.1.5/exCon/inst/extdata/eC_contours.js | 167 +++-- exCon-0.1.5/exCon/inst/extdata/eC_controls.js | 613 ++++++++++++++-------- exCon-0.1.5/exCon/inst/extdata/eC_globals.js | 55 - exCon-0.1.5/exCon/inst/extdata/eC_main.js | 3 exCon-0.1.5/exCon/inst/extdata/eC_slices.js | 388 +++++++------ exCon-0.1.5/exCon/inst/extdata/exCon.html | 27 exCon-0.1.5/exCon/man/exCon-package.Rd | 2 exCon-0.1.5/exCon/man/exCon.Rd | 29 - 15 files changed, 975 insertions(+), 681 deletions(-)
Title: Using Cloudera 'Impala' Through 'R'
Description: Cloudera 'Impala', which is a massively parallel processing (MPP) SQL query engine runs natively in Apache Hadoop. 'RImpala' facilitates the connection and execution of distributed queries through 'R'. 'Impala' supports JDBC integration which 'RImpala' utilizes to establish the connection between 'R' and 'Impala'. Thanks to Mu Sigma for their continued support throughout the development of the package.
Author: Vijay Raajaa, Austin Chungath Vincent, Sachin Sudarshana, Vikas Raguttahalli
Maintainer: Vijay Raajaa <vijay.raajaa@mu-sigma.com>
Diff between RImpala versions 0.1.5 dated 2014-10-13 and 0.1.6 dated 2015-05-07
RImpala-0.1.5/RImpala/inst/java/RImpala-1.0.jar |only RImpala-0.1.6/RImpala/DESCRIPTION | 12 RImpala-0.1.6/RImpala/MD5 | 14 RImpala-0.1.6/RImpala/R/RImpala.R | 79 - RImpala-0.1.6/RImpala/inst/java/RImpala-2.0.jar |only RImpala-0.1.6/RImpala/java/build.sh | 2 RImpala-0.1.6/RImpala/java/pom.xml | 24 RImpala-0.1.6/RImpala/java/src/main/java/com/musigma/ird/bigdata/RImpala.java | 690 +++++----- RImpala-0.1.6/RImpala/man/RImpala_query.Rd | 13 9 files changed, 437 insertions(+), 397 deletions(-)
Title: Read 'ImageJ' Region of Interest (ROI) Files
Description: Provides functions to read 'ImageJ' (http://imagej.nih.gov/ij/)
Region of Interest (ROI) files, to plot the ROIs and to convert them to
'spatstat' (http://spatstat.org/) spatial patterns.
Author: David C Sterratt [aut, cph, cre],
Mikko Vihtakari [aut, cph]
Maintainer: David C Sterratt <david.c.sterratt@ed.ac.uk>
Diff between RImageJROI versions 0.1 dated 2014-03-31 and 0.1.1 dated 2015-05-07
RImageJROI-0.1.1/RImageJROI/DESCRIPTION | 18 +- RImageJROI-0.1.1/RImageJROI/MD5 | 29 ++-- RImageJROI-0.1.1/RImageJROI/NAMESPACE | 2 RImageJROI-0.1.1/RImageJROI/NEWS |only RImageJROI-0.1.1/RImageJROI/R/read.ijroi.R | 15 +- RImageJROI-0.1.1/RImageJROI/demo/ijroi.R | 1 RImageJROI-0.1.1/RImageJROI/inst/extdata/ijroi/arrow-outline-doubleheaded.roi |only RImageJROI-0.1.1/RImageJROI/man/RImageJROI.Rd | 14 -- RImageJROI-0.1.1/RImageJROI/man/ij2spatstat.Rd | 67 ++-------- RImageJROI-0.1.1/RImageJROI/man/plot.ijroi.Rd | 60 +++----- RImageJROI-0.1.1/RImageJROI/man/plot.ijzip.Rd | 28 +--- RImageJROI-0.1.1/RImageJROI/man/print.ijroi.Rd | 13 + RImageJROI-0.1.1/RImageJROI/man/read.ijroi.Rd | 16 +- RImageJROI-0.1.1/RImageJROI/man/read.ijzip.Rd | 25 +-- RImageJROI-0.1.1/RImageJROI/tests/testthat.R |only RImageJROI-0.1.1/RImageJROI/tests/testthat/test-readroi.R |only RImageJROI-0.1/RImageJROI/inst/extdata/ijroi/test.roi |only RImageJROI-0.1/RImageJROI/tests/test-all.R |only RImageJROI-0.1/RImageJROI/tests/testthat/readroi.R |only 19 files changed, 114 insertions(+), 174 deletions(-)
Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses.
They implements PLS methods for classification with
microarray data and prediction of transcription factor
activities from combined ChIP-chip analysis. The >=1.2-1
versions include two new classification methods for microarray
data: GSIM and Ridge PLS. The >=1.3 versions includes an other
new classification method combining variable selection and
compression in logistic regression context: RIRLS-SPLS; and
an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,
Ghislain Durif <ghislain.durif@univ-lyon1.fr>,
Sophie Lambert-Lacroix <Sophie.Lambert@imag.fr>, Julie Peyre
<Julie.Peyre@imag.fr>, and Korbinian Strimmer
<strimmer@uni-leipzig.de>.
Maintainer: Ghislain Durif <ghislain.durif@univ-lyon1.fr>
Diff between plsgenomics versions 1.2-6 dated 2011-04-08 and 1.3 dated 2015-05-07
plsgenomics-1.2-6/plsgenomics/copying |only plsgenomics-1.2-6/plsgenomics/plsgenomics-Ex.R |only plsgenomics-1.3/plsgenomics/DESCRIPTION | 27 ++++++----- plsgenomics-1.3/plsgenomics/LICENCE.note |only plsgenomics-1.3/plsgenomics/MD5 |only plsgenomics-1.3/plsgenomics/NAMESPACE |only plsgenomics-1.3/plsgenomics/R/rirls.spls.R |only plsgenomics-1.3/plsgenomics/R/rirls.spls.aux.R |only plsgenomics-1.3/plsgenomics/R/rirls.spls.tune.R |only plsgenomics-1.3/plsgenomics/R/sample.bin.R |only plsgenomics-1.3/plsgenomics/R/sample.cont.R |only plsgenomics-1.3/plsgenomics/R/spls.adapt.R |only plsgenomics-1.3/plsgenomics/R/spls.adapt.aux.R |only plsgenomics-1.3/plsgenomics/R/spls.adapt.tune.R |only plsgenomics-1.3/plsgenomics/R/ust.R |only plsgenomics-1.3/plsgenomics/R/ust.adapt.R |only plsgenomics-1.3/plsgenomics/R/wpls.R |only plsgenomics-1.3/plsgenomics/README |only plsgenomics-1.3/plsgenomics/data/datalist |only plsgenomics-1.3/plsgenomics/man/Colon.Rd | 7 +- plsgenomics-1.3/plsgenomics/man/Ecoli.Rd | 10 ++-- plsgenomics-1.3/plsgenomics/man/SRBCT.Rd | 2 plsgenomics-1.3/plsgenomics/man/TFA.estimate.Rd | 17 ++++--- plsgenomics-1.3/plsgenomics/man/gsim.Rd | 13 +++-- plsgenomics-1.3/plsgenomics/man/gsim.cv.Rd | 18 ++++--- plsgenomics-1.3/plsgenomics/man/leukemia.Rd | 3 - plsgenomics-1.3/plsgenomics/man/mgsim.Rd | 16 ++++-- plsgenomics-1.3/plsgenomics/man/mgsim.cv.Rd | 35 ++++++++------ plsgenomics-1.3/plsgenomics/man/mrpls.Rd | 16 ++++-- plsgenomics-1.3/plsgenomics/man/mrpls.cv.Rd | 36 ++++++++------- plsgenomics-1.3/plsgenomics/man/pls.lda.Rd | 31 ++++++++----- plsgenomics-1.3/plsgenomics/man/pls.lda.cv.Rd | 20 +++++--- plsgenomics-1.3/plsgenomics/man/pls.regression.Rd | 38 ++++++++-------- plsgenomics-1.3/plsgenomics/man/pls.regression.cv.Rd | 20 ++++---- plsgenomics-1.3/plsgenomics/man/plsgenomics-internal.Rd | 6 ++ plsgenomics-1.3/plsgenomics/man/preprocess.Rd | 30 +++++++----- plsgenomics-1.3/plsgenomics/man/rirls.spls.Rd |only plsgenomics-1.3/plsgenomics/man/rirls.spls.tune.Rd |only plsgenomics-1.3/plsgenomics/man/rpls.Rd | 13 +++-- plsgenomics-1.3/plsgenomics/man/rpls.cv.Rd | 31 +++++++------ plsgenomics-1.3/plsgenomics/man/sample.bin.Rd |only plsgenomics-1.3/plsgenomics/man/sample.cont.Rd |only plsgenomics-1.3/plsgenomics/man/spls.adapt.Rd |only plsgenomics-1.3/plsgenomics/man/spls.adapt.tune.Rd |only plsgenomics-1.3/plsgenomics/man/variable.selection.Rd | 14 +++-- plsgenomics-1.3/plsgenomics/tests |only 46 files changed, 242 insertions(+), 161 deletions(-)
Title: Prediction of Fish Movement Parameters
Description: Functions to predict fish movement parameters plotting leptokurtic fish dispersal kernels (see Radinger and Wolter, 2014: Patterns and predictors of fish dispersal in rivers. Fish and Fisheries. 15:456-473.)
Author: Johannes Radinger
Maintainer: Johannes Radinger <jradinger@igb-berlin.de>
Diff between fishmove versions 0.3-2 dated 2015-05-04 and 0.3-3 dated 2015-05-07
DESCRIPTION | 6 - MD5 | 6 - R/fishmove.R | 230 +++++++++++++++++++++++++----------------------- man/fishmove-package.Rd | 2 4 files changed, 130 insertions(+), 114 deletions(-)
Title: Automatic Creation of Dummies with Support for Predictive
Modeling
Description: Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set).
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@GMail.com>
Diff between dummy versions 0.1.2 dated 2015-04-14 and 0.1.3 dated 2015-05-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/categories.R | 1 + R/dummy.R | 11 ++++++++--- inst/NEWS | 8 +++----- man/categories.Rd | 3 ++- man/dummy.Rd | 7 +++++-- man/dummyNews.Rd | 3 ++- 8 files changed, 32 insertions(+), 23 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Chung-hong Chan [aut],
Geoffrey CH Chan [aut],
Thomas J. Leeper [aut, cre],
Christopher Gandrud [aut]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.1.2 dated 2013-09-04 and 0.2 dated 2015-05-07
rio-0.1.2/rio/R/rio-package.r |only rio-0.1.2/rio/inst/tests |only rio-0.1.2/rio/tests/run-all.R |only rio-0.2/rio/DESCRIPTION | 35 ++++--- rio-0.2/rio/MD5 | 40 +++++--- rio-0.2/rio/NAMESPACE | 25 +++-- rio-0.2/rio/NEWS | 37 +++++-- rio-0.2/rio/R/convert.R |only rio-0.2/rio/R/export.R | 201 +++++++++++++++++++++++------------------- rio-0.2/rio/R/fwf2.R |only rio-0.2/rio/R/import.R |only rio-0.2/rio/R/set_class.R |only rio-0.2/rio/R/unsupported.R |only rio-0.2/rio/R/utils.R |only rio-0.2/rio/README.md | 175 +++++++++++++++++++++++++++--------- rio-0.2/rio/build |only rio-0.2/rio/inst/CITATION |only rio-0.2/rio/inst/doc |only rio-0.2/rio/man/convert.Rd |only rio-0.2/rio/man/export.Rd | 99 +++++++++++++------- rio-0.2/rio/man/import.Rd | 110 ++++++++++++++-------- rio-0.2/rio/man/rio.Rd | 30 +----- rio-0.2/rio/tests/test-all.R |only rio-0.2/rio/tests/testthat |only rio-0.2/rio/vignettes |only 25 files changed, 481 insertions(+), 271 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.0.0 dated 2015-04-29 and 3.1.0 dated 2015-05-07
DESCRIPTION | 8 - MD5 | 64 ++++++------- NEWS | 18 +++ R/fitted.R | 2 R/gbm.R | 13 +- R/glmnet.R | 7 - R/meta.R | 28 +++-- R/methods.R | 35 ++++++- R/plot.gbmx.R | 10 +- R/plotcum.R | 1 R/plotmo.R | 150 ++++++++++---------------------- R/plotres.R | 2 R/plotresids.R | 6 + R/predict.R | 2 R/prolog.R | 4 R/quantreg.R | 6 - R/residuals.R | 5 - R/response.R | 2 R/singles.R | 2 R/w1.R | 5 - R/xy.R | 70 ++++++++------ inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/test.glmnet.Rout.save | 2 inst/slowtests/test.non.earth.R | 37 ++++++- inst/slowtests/test.non.earth.Rout.save | 73 ++++++++++----- inst/slowtests/test.plotmo.R | 13 +- inst/slowtests/test.plotmo.Rout.save | 41 ++++---- inst/slowtests/test.plotmo3.R | 2 inst/slowtests/test.plotmo3.Rout.save | 16 +++ man/plotmo.Rd | 7 - man/plotmo.misc.Rd | 6 - man/plotres.Rd | 8 + 33 files changed, 363 insertions(+), 282 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre],
Kurt Hornik [aut],
Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL
Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.6 dated 2014-06-11 and 0.6-1 dated 2015-05-07
DESCRIPTION | 14 +++--- MD5 | 72 +++++++++++++++++----------------- NAMESPACE | 31 +++++++++++--- R/corpus.R | 55 +++++++++++++++----------- R/doc.R | 67 ++++++++++++++++++++------------ R/matrix.R | 8 ++- R/meta.R | 26 ++++-------- R/pdftools.R | 4 - R/plot.R | 11 ++--- R/reader.R | 52 +++++++++++++++++------- R/source.R | 98 ++++++++++++++++++++++++++++++++++++++++++++--- R/tokenizer.R | 8 +-- R/transform.R | 5 +- R/utils.R | 7 +++ build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/NEWS.Rd | 20 +++++++++ inst/doc/extensions.R | 16 +++---- inst/doc/extensions.Rnw | 13 +++--- inst/doc/extensions.pdf |binary inst/doc/tm.R | 30 ++++++++------ inst/doc/tm.Rnw | 9 +++- inst/doc/tm.pdf |binary man/Source.Rd | 20 +++++++-- man/ZipSource.Rd |only man/acq.Rd | 2 man/crude.Rd | 2 man/meta.Rd | 12 +++-- man/readReut21578XML.Rd | 2 man/readTagged.Rd |only man/stopwords.Rd | 2 man/termFreq.Rd | 11 ++--- man/tm_reduce.Rd | 5 +- man/weightSMART.Rd | 8 +-- man/weightTfIdf.Rd | 2 vignettes/extensions.Rnw | 13 +++--- vignettes/tm.Rnw | 9 +++- 38 files changed, 426 insertions(+), 208 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 0.34-1 dated 2015-02-03 and 0.34-2 dated 2015-05-06
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NEWS | 6 ++++++ R/DEopt.R | 8 ++++---- R/PSopt.R | 2 +- build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/unitTests/report.txt | 24 ++++++++++++------------ inst/unitTests/unitTestsDEopt.R | 19 +++++++++++++++++++ 16 files changed, 62 insertions(+), 37 deletions(-)
Title: R Tools for Helsinki Open Data
Description: Tools for accessing various open data sources in the Helsinki
region in Finland. Current data sources include
the Real Estate Department (district maps),
the Environmental Services Authority,
Service Map API,
Linked Events API and
Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen <louhos@googlegroups.com>
Diff between helsinki versions 0.9.24 dated 2014-12-22 and 0.9.27 dated 2015-05-06
helsinki-0.9.24/helsinki/inst/extras |only helsinki-0.9.24/helsinki/vignettes/figure |only helsinki-0.9.27/helsinki/DESCRIPTION | 10 - helsinki-0.9.27/helsinki/MD5 | 45 +--- helsinki-0.9.27/helsinki/NAMESPACE | 2 helsinki-0.9.27/helsinki/R/HKK.R | 2 helsinki-0.9.27/helsinki/R/HSY.R | 5 helsinki-0.9.27/helsinki/R/regional_stats.R | 8 helsinki-0.9.27/helsinki/R/services.R | 2 helsinki-0.9.27/helsinki/man/aluejakokartat.Rd | 3 helsinki-0.9.27/helsinki/man/get_hri_stats.Rd | 3 helsinki-0.9.27/helsinki/man/get_hsy.Rd | 3 helsinki-0.9.27/helsinki/man/get_linkedevents.Rd | 3 helsinki-0.9.27/helsinki/man/get_servicemap.Rd | 3 helsinki-0.9.27/helsinki/man/helsinki-package.Rd | 3 helsinki-0.9.27/helsinki/vignettes/helsinki_tutorial.Rmd | 12 - helsinki-0.9.27/helsinki/vignettes/helsinki_tutorial.html | 123 ++++--------- helsinki-0.9.27/helsinki/vignettes/helsinki_tutorial.md | 130 +++++--------- helsinki-0.9.27/helsinki/vignettes/todo-datasets.md | 4 19 files changed, 142 insertions(+), 219 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package allows for retrieval of five datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; and the International Tree Ring Data Bank. Additional data sources are in the works, including global DEM resources (ETOPO1, ETOPO5, ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 1.0 dated 2015-02-13 and 1.1.0 dated 2015-05-06
DESCRIPTION | 18 ++-- MD5 | 75 +++++++++++--------- NAMESPACE | 36 ++++++++- R/GHCN_FUNCTIONS.R | 27 ++++--- R/ITRDB_FUNCTIONS.R |only R/NED_FUNCTIONS.R | 20 +++-- R/NHD_FUNCTIONS.R | 32 +++++--- R/SSURGO_FUNCTIONS.R | 150 ++++++++++++++++++++++++---------------- R/UTILITY_FUNCTIONS.R | 81 ++++++++++++++++++++- R/sysdata.rda |only README.md |only inst/FedDataTester.R | 44 ++++++++--- man/FedData-package.Rd | 17 +++- man/SPDFfromPolygon.Rd | 2 man/curlDownload.Rd |only man/downloadGHCNDailyStation.Rd | 2 man/downloadHUC4.Rd | 2 man/downloadITRDB.Rd |only man/downloadNEDTile.Rd | 2 man/downloadNHDSubregion.Rd | 7 + man/downloadSSURGOInventory.Rd | 2 man/downloadSSURGOStudyArea.Rd | 2 man/extractSSURGOData.Rd | 2 man/getGHCNDaily.Rd | 2 man/getGHCNDailyStation.Rd | 2 man/getGHCNInventory.Rd | 2 man/getHUC4.Rd | 2 man/getITRDB.Rd |only man/getNED.Rd | 2 man/getNEDTile.Rd | 2 man/getNHD.Rd | 7 + man/getNHDSubregion.Rd | 7 + man/getSSURGO.Rd | 7 + man/getSSURGOInventory.Rd | 2 man/getSSURGOStudyArea.Rd | 2 man/pkgTest.Rd | 2 man/polygonFromExtent.Rd | 2 man/read.crn.Rd |only man/read.crn.data.Rd |only man/read.crn.metadata.Rd |only man/sequential.duplicated.Rd | 2 man/substrRight.Rd | 2 man/wgetDownload.Rd | 2 43 files changed, 392 insertions(+), 176 deletions(-)
Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel
(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
'xl[a1] = current.graphics()'. There is an Excel workbook with examples of
calling R from Excel in the 'doc' folder. It tries to keep things as
simple as possible - there are no needs in any additional
installations besides R, only 'VBA' code in the Excel workbook.
Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy includes R source code from 'RDCOMClient' (http://www.omegahat.org/RDCOMClient) by Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>
Diff between excel.link versions 0.6 dated 2013-09-05 and 0.8.1 dated 2015-05-06
excel.link-0.6/excel.link/man/dimnames.excel.range.Rd |only excel.link-0.6/excel.link/man/xl.sheets.Rd |only excel.link-0.6/excel.link/man/xl.workbooks.Rd |only excel.link-0.8.1/excel.link/DESCRIPTION | 32 excel.link-0.8.1/excel.link/MD5 | 59 excel.link-0.8.1/excel.link/NAMESPACE | 142 +- excel.link-0.8.1/excel.link/NEWS | 42 excel.link-0.8.1/excel.link/R/0COMError.R |only excel.link-0.8.1/excel.link/R/0classes.R |only excel.link-0.8.1/excel.link/R/0com.R |only excel.link-0.8.1/excel.link/R/0zzz.R |only excel.link-0.8.1/excel.link/R/0zzzCOMLists.R |only excel.link-0.8.1/excel.link/R/0zzzdebug.R |only excel.link-0.8.1/excel.link/R/0zzzrunTime.R |only excel.link-0.8.1/excel.link/R/RDCOMClient.R |only excel.link-0.8.1/excel.link/R/current.graphics.R |only excel.link-0.8.1/excel.link/R/dimnames.excel.range.R |only excel.link-0.8.1/excel.link/R/excel.link.R | 1267 ------------------ excel.link-0.8.1/excel.link/R/utils.R |only excel.link-0.8.1/excel.link/R/xl.R |only excel.link-0.8.1/excel.link/R/xl.connect.table.R |only excel.link-0.8.1/excel.link/R/xl.get.excel.R |only excel.link-0.8.1/excel.link/R/xl.read.file.R |only excel.link-0.8.1/excel.link/R/xl.sheet.add.R |only excel.link-0.8.1/excel.link/R/xl.workbooks.R |only excel.link-0.8.1/excel.link/R/xl.write.R |only excel.link-0.8.1/excel.link/build |only excel.link-0.8.1/excel.link/inst |only excel.link-0.8.1/excel.link/man/RDCOMClient.Rd |only excel.link-0.8.1/excel.link/man/current.graphics.Rd | 58 excel.link-0.8.1/excel.link/man/excel.link.Rd |only excel.link-0.8.1/excel.link/man/xl.Rd | 127 + excel.link-0.8.1/excel.link/man/xl.connect.table.Rd | 231 +-- excel.link-0.8.1/excel.link/man/xl.get.excel.Rd | 37 excel.link-0.8.1/excel.link/man/xl.read.file.Rd | 112 - excel.link-0.8.1/excel.link/man/xl.sheet.add.Rd |only excel.link-0.8.1/excel.link/man/xl.workbook.add.Rd |only excel.link-0.8.1/excel.link/man/xl.write.Rd | 134 - excel.link-0.8.1/excel.link/src |only excel.link-0.8.1/excel.link/vignettes |only 40 files changed, 580 insertions(+), 1661 deletions(-)
Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data
including robust methods, imputation, methods to replace rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data,
(robust) discriminant analysis for compositional data (Fisher rule), robust
regression with compositional predictors and (robust) Anderson-Darling
normality tests for compositional data as well as popular log-ratio
transformations (addLR, cenLR, isomLR, and their inverse transformations).
In addition, visualisation and diagnostic tools are implemented as well as
high and low-level plot functions for the ternary diagram.
Author: Matthias Templ, Karel Hron, Peter Filzmoser
Maintainer: Matthias Templ <templ@tuwien.ac.at>
Diff between robCompositions versions 1.9.0 dated 2014-08-18 and 1.9.1 dated 2015-05-06
DESCRIPTION | 19 +- MD5 | 106 ++++++------ NAMESPACE | 4 NEWS | 9 - R/aDist.R | 53 +++++- R/addLR.R | 42 ++++ R/addLRinv.R | 46 +++++ R/adjust.R | 63 +++++-- R/adtest.R | 52 +++++ R/adtestWrapper.R | 45 +++++ R/cenLR.R | 30 +++ R/cenLRinv.R | 29 +++ R/constSum.R | 20 ++ R/daFisher.R | 56 ++++++ R/gm.R | 16 + R/impAll.R | 32 +++ R/impCoda.R | 61 +++++++ R/impKNNa.R | 58 ++++++ R/impRZalr.R | 295 ++++++++++++++++++++-------------- R/impRZilr.R | 141 +++++++++++++++- R/isomLR.R | 52 +++++ R/isomLRinv.R | 29 +++ R/lmCoDaX.R | 35 ++++ R/missPatterns.R | 31 +++ R/orthbasis.R | 23 ++ R/outCoDa.R | 47 +++++ R/pcaCoDa.R | 45 +++++ R/pfa.R | 56 ++++++ R/plot.imp.R | 93 ++++++++++ R/plot.outCoDa.R | 26 ++ R/plot.pcaCoDa.R | 38 ++++ R/print.adtestWrapper.R | 21 ++ R/print.daFisher.R | 48 ++++- R/print.imp.R | 27 ++- R/print.outCoDa.R | 19 ++ R/print.pcaCoDa.R | 21 ++ R/rcrox-package.R |only R/robVariation.R | 54 ++++-- R/summary.adtestWrapper.R | 28 +++ R/summary.imp.R | 67 +++++-- R/ternaryDiag.R | 44 +++++ R/ternaryDiagAbline.R | 22 ++ R/ternaryDiagEllipse.R | 27 ++- R/ternaryDiagPoints.R | 23 ++ build/vignette.rds |binary inst/CITATION | 10 - inst/doc/imputation.pdf |binary inst/doc/robCompositions-overview.pdf |binary man/bootnComp.Rd |only man/impRZalr.Rd | 9 - man/impRZilr.Rd | 5 man/isomLR.Rd | 10 - man/print.imp.Rd | 2 tests/rz.R | 3 vignettes/natbib.sty |only vignettes/plainnat.bst |only 56 files changed, 1807 insertions(+), 285 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between plotKML versions 0.5-1 dated 2015-04-23 and 0.5-2 dated 2015-05-06
DESCRIPTION | 26 +++++++++++++------------- MD5 | 12 ++++++------ NAMESPACE | 9 +++++---- R/kml.tiles.R | 8 -------- R/kml_compress.R | 4 ++-- inst/doc/jss1079.pdf |binary man/spMetadata.Rd | 4 ++-- 7 files changed, 28 insertions(+), 35 deletions(-)
Title: Apache OpenNLP Tools Interface
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See <http://opennlp.apache.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between openNLP versions 0.2-4 dated 2015-02-27 and 0.2-5 dated 2015-05-06
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/chunk.R | 2 +- R/ner.R | 2 +- R/parse.R | 6 ++++-- R/pos.R | 21 ++++++++++++++++++++- R/sentdetect.R | 2 +- R/tokenize.R | 2 +- 8 files changed, 40 insertions(+), 19 deletions(-)
Title: Natural Language Processing Utilities
Description: Utilities for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLPutils versions 0.0-1 dated 2014-06-15 and 0.0-2 dated 2015-05-06
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/diversity.R | 6 ++++-- R/formality.R | 6 ++++-- R/polarity.R | 6 ++++-- R/stem.R | 2 +- 6 files changed, 23 insertions(+), 17 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.1-6 dated 2015-01-24 and 0.1-7 dated 2015-05-06
NLP-0.1-6/NLP/R/tagged.R |only NLP-0.1-7/NLP/DESCRIPTION | 10 - NLP-0.1-7/NLP/MD5 | 62 ++++--- NLP-0.1-7/NLP/NAMESPACE | 92 +++++++++-- NLP-0.1-7/NLP/R/annotate.R | 17 -- NLP-0.1-7/NLP/R/annotation.R | 100 +++++++----- NLP-0.1-7/NLP/R/annotators.R | 149 ++++++++++++++---- NLP-0.1-7/NLP/R/aptd.R | 78 +++++++-- NLP-0.1-7/NLP/R/conll.R | 55 +++++- NLP-0.1-7/NLP/R/ngram.R |only NLP-0.1-7/NLP/R/span.R | 4 NLP-0.1-7/NLP/R/string.R | 8 NLP-0.1-7/NLP/R/sysdata.rda |binary NLP-0.1-7/NLP/R/tnt.R |only NLP-0.1-7/NLP/R/tokenize.R | 196 +++++++++++++++++++++--- NLP-0.1-7/NLP/R/tree.R | 12 - NLP-0.1-7/NLP/R/ttd.R |only NLP-0.1-7/NLP/R/utils.R |only NLP-0.1-7/NLP/R/viewers.R | 13 + NLP-0.1-7/NLP/R/wordlist.R | 35 +++- NLP-0.1-7/NLP/inst/texts/stanford.rds |binary NLP-0.1-7/NLP/man/AnnotatedPlainTextDocument.Rd | 30 ++- NLP-0.1-7/NLP/man/Annotation.Rd | 23 +- NLP-0.1-7/NLP/man/Annotator.Rd | 41 +++-- NLP-0.1-7/NLP/man/CoNLLTextDocument.Rd | 9 + NLP-0.1-7/NLP/man/Span.Rd | 5 NLP-0.1-7/NLP/man/TaggedTextDocument.Rd | 16 + NLP-0.1-7/NLP/man/Tagged_Token.Rd |only NLP-0.1-7/NLP/man/Tokenizer.Rd |only NLP-0.1-7/NLP/man/Tree.Rd | 2 NLP-0.1-7/NLP/man/annotate.Rd | 9 - NLP-0.1-7/NLP/man/annotators.Rd | 21 +- NLP-0.1-7/NLP/man/ngrams.Rd |only NLP-0.1-7/NLP/man/tagsets.Rd | 46 +++++ NLP-0.1-7/NLP/man/tokenizers.Rd | 17 +- NLP-0.1-7/NLP/man/viewers.Rd | 14 + 36 files changed, 817 insertions(+), 247 deletions(-)
Title: Estimation and Comparison of Dynamic Treatment Regimes
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials.
Author: Xinyu Tang [aut, cre],
Maria Melguizo [aut]
Maintainer: Xinyu Tang <xtang@uams.edu>
Diff between DTR versions 1.5 dated 2014-07-09 and 1.6 dated 2015-05-06
DESCRIPTION | 15 ++++++++------- MD5 | 13 +++++++------ NAMESPACE | 11 +++++++++++ R/plot.CHR.R | 1 + R/plot.DTR.R | 1 + inst/CITATION |only inst/NEWS.Rd | 6 ++++++ man/DTR-package.Rd | 5 +++-- 8 files changed, 37 insertions(+), 15 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, and Luca Scrucca.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-41 dated 2015-01-03 and 6.0-47 dated 2015-05-06
DESCRIPTION | 14 - MD5 | 112 +++++++------ NAMESPACE | 18 ++ R/aaa.R | 90 ++++++---- R/adaptive.R | 21 -- R/avNNet.R | 5 R/bag.R | 28 +-- R/bagFDA.R | 10 - R/calibration.R | 175 ++++++++++---------- R/confusionMatrix.R | 24 ++ R/createDataPartition.R | 69 ++++---- R/createFolds.R | 86 ++++------ R/createTimeSlices.R | 12 + R/extractPrediction.R | 11 - R/extractProb.R | 50 ++--- R/filterVarImp.R | 6 R/format.bagEarth.R | 2 R/gafs.R | 8 R/icr.R | 5 R/knn3.R | 7 R/knnreg.R | 5 R/lift.R | 287 ++++++++++++++++------------------ R/maxDissim.R | 2 R/misc.R | 28 +++ R/pcaNNet.R | 16 - R/plsda.R | 3 R/preProcess.R | 10 - R/print.varImp.train.R | 2 R/reg_sims.R | 2 R/resamples.R | 13 - R/rfe.R | 32 ++- R/safs.R | 8 R/selectByFilter.R | 16 - R/train.default.R | 153 +++++++++--------- R/trainControl.R | 2 R/trim.R |only R/twoClassSim.R | 2 R/varImp.R | 2 R/workflows.R | 44 ++--- build/vignette.rds |binary inst/NEWS.Rd | 38 ++++ inst/doc/caret.pdf |binary inst/models/models.RData |binary man/calibration.Rd | 2 man/confusionMatrix.Rd | 4 man/createDataPartition.Rd | 8 man/dummyVars.Rd | 7 man/lift.Rd | 6 man/models.Rd | 40 ++++ man/postResample.Rd | 24 ++ man/rf_seq.Rd |only man/selection.Rd | 10 - man/trainControl.Rd | 5 tests/testthat/test_confusionMatrix.R |only tests/testthat/test_mnLogLoss.R |only tests/testthat/trim.R |only tests/testthat/trim_C5.R |only tests/testthat/trim_bayesglm.R |only tests/testthat/trim_glm.R |only tests/testthat/trim_glmnet.R |only tests/testthat/trim_rpart.R |only tests/testthat/trim_train.R |only tests/testthat/trim_treebag.R |only 63 files changed, 851 insertions(+), 673 deletions(-)
Title: Graphical User Interface for Package 'sdcMicro'
Description: A point and click graphical user interface based on top of the
'sdcMicro' package to create anonymized data set. The graphical user
interface provides full reproducibility of any result via the script menu
in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois Fonteneau
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between sdcMicroGUI versions 1.1.1 dated 2013-11-08 and 1.2.0 dated 2015-05-06
DESCRIPTION | 25 MD5 | 41 NAMESPACE | 4 NEWS | 5 R/aux_functions.R | 2 R/plot.indivRisk.r | 284 R/sdcGUI.r | 8288 ++++++++++++++--------------- README.md | 2 build/vignette.rds |binary inst/doc/gui_tutorial.R |only inst/doc/gui_tutorial.pdf |binary inst/doc/gui_tutorial.rnw | 1151 ++-- vignettes/gui_tutorial.rnw | 1151 ++-- vignettes/imgs/gui_age_original.png |binary vignettes/imgs/gui_age_recoded.png |binary vignettes/imgs/gui_frequencies.png |binary vignettes/imgs/gui_localsupp_threshold.png |binary vignettes/imgs/gui_tab1.png |binary vignettes/imgs/gui_tab2.png |binary vignettes/imgs/gui_tab3.png |binary vignettes/imgs/gui_variable_selection.png |binary vignettes/references.bib | 68 22 files changed, 5600 insertions(+), 5421 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.10 dated 2015-04-23 and 1.10.5 dated 2015-05-06
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/block.R | 4 ++++ R/highlight.R | 7 ++++--- R/hooks-latex.R | 8 ++++---- R/output.R | 2 +- R/params.R | 30 +++++++++++++++++++++++++++++- R/spin.R | 4 ++-- R/table.R | 2 ++ R/utils-base64.R | 6 +++--- R/utils-vignettes.R | 12 +++++++++--- R/utils.R | 5 +++-- README.md | 5 +++-- build/knitr.pdf |binary inst/doc/knit_expand.html | 4 ++-- inst/doc/knit_print.html | 4 ++-- inst/doc/knitr-intro.html | 10 +++++----- inst/doc/knitr-markdown.html | 2 +- inst/doc/knitr-refcard.pdf |binary man/image_uri.Rd | 6 +++--- man/spin.Rd | 4 ++-- tests/testit/test-params.R | 22 +++++++++++++++++++++- 22 files changed, 125 insertions(+), 62 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including
constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer
functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: Steve Juggins <Stephen.Juggins@ncl.ac.uk>
Diff between rioja versions 0.9-3 dated 2014-12-17 and 0.9-5 dated 2015-05-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 9 +++++---- R/WA.r | 26 ++++++++++++++++---------- data/aber.rda |binary inst/CITATION | 6 +++--- inst/ChangeLog | 5 +++++ man/IK.Rd | 2 +- man/aber.Rd | 4 ++-- man/rioja.package.Rd | 4 ++-- 10 files changed, 47 insertions(+), 35 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch> and Sören Vogel <soeren.vogel@posteo.ch>
Maintainer: Sören Vogel <soeren.vogel@posteo.ch>
Diff between GUTS versions 0.5.2 dated 2015-04-12 and 0.9.1 dated 2015-05-06
GUTS-0.5.2/GUTS/R/zzz.R |only GUTS-0.5.2/GUTS/data/diazinon.RData |only GUTS-0.5.2/GUTS/man/Rcpp_GUTS-class.Rd |only GUTS-0.5.2/GUTS/src/GUTS_Rcpp.cpp |only GUTS-0.5.2/GUTS/src/GUTS_Rcpp.h |only GUTS-0.9.1/GUTS/DESCRIPTION | 18 - GUTS-0.9.1/GUTS/MD5 | 19 - GUTS-0.9.1/GUTS/NAMESPACE | 14 GUTS-0.9.1/GUTS/R/GUTS.R | 429 +++++++++++++++++++----- GUTS-0.9.1/GUTS/R/RcppExports.R |only GUTS-0.9.1/GUTS/data/diazinon.rda |only GUTS-0.9.1/GUTS/man/GUTS-package.Rd |only GUTS-0.9.1/GUTS/man/GUTS.Rd |only GUTS-0.9.1/GUTS/man/diazinon.Rd | 8 GUTS-0.9.1/GUTS/src/RcppExports.cpp |only GUTS-0.9.1/GUTS/src/guts_calc_loglikelihood.cpp |only 16 files changed, 372 insertions(+), 116 deletions(-)
Title: Descriptive Statistics
Description: Weighted frequency and contingency tables of categorical
variables and of the comparison of the mean value of a numerical
variable by the levels of a factor, and methods to produce xtable
objects of the tables and to plot them. There are also functions to
facilitate the character encoding conversion of objects, to quickly
convert fixed width files into csv ones, and to export a data.frame to
a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation
written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan
Kraft
Maintainer: Jakson Aquino <jalvesaq@gmail.com>
Diff between descr versions 1.1 dated 2015-04-14 and 1.1.1 dated 2015-05-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 6 ++++++ R/forODFTable.R | 4 ++-- R/xtable.R | 3 +-- man/compmeans.Rd | 2 -- man/crosstab.Rd | 3 +-- man/freq.Rd | 4 ++-- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between broom versions 0.3.6 dated 2015-02-18 and 0.3.7 dated 2015-05-06
DESCRIPTION | 19 +++-- LICENSE | 2 MD5 | 153 ++++++++++++++++++++++++------------------ NAMESPACE | 21 +++++ R/anova_tidiers.R | 15 ++-- R/biglm_tidiers.R |only R/broom.R |only R/globals.R | 2 R/list_tidiers.R |only R/lm_tidiers.R | 101 +++++++++++++++++++++------ R/lmtest_tidiers.R |only R/loess_tidiers.R |only R/multinom_tidiers.R |only R/nlme_tidiers.R |only R/optim_tidiers.R |only R/plm_tidiers.R |only R/stats_tidiers.R | 26 +++++++ R/summary_tidiers.R |only R/survival_tidiers.R | 6 - R/utilities.R | 14 ++- build/vignette.rds |binary inst/doc/bootstrapping.html | 10 +- inst/doc/broom_and_dplyr.html | 4 - inst/doc/kmeans.R | 2 inst/doc/kmeans.html | 8 +- man/Arima_tidiers.Rd | 2 man/aareg_tidiers.Rd | 4 - man/anova_tidiers.Rd | 2 man/augment.Rd | 2 man/augment_columns.Rd | 2 man/biglm_tidiers.Rd |only man/bootstrap.Rd | 2 man/broom.Rd |only man/cch_tidiers.Rd | 2 man/compact.Rd | 2 man/confint_tidy.Rd | 2 man/coxph_tidiers.Rd | 2 man/cv.glmnet_tidiers.Rd | 2 man/data.frame_tidiers.Rd | 2 man/felm_tidiers.Rd | 2 man/finish_glance.Rd | 4 - man/fix_data_frame.Rd | 2 man/gam_tidiers.Rd | 2 man/glance.Rd | 2 man/glm_tidiers.Rd | 2 man/glmnet_tidiers.Rd | 2 man/htest_tidiers.Rd | 2 man/inflate.Rd | 2 man/insert_NAs.Rd | 2 man/kmeans_tidiers.Rd | 2 man/list_tidiers.Rd |only man/lm_tidiers.Rd | 18 ++++ man/lme4_tidiers.Rd | 2 man/loess_tidiers.Rd |only man/matrix_tidiers.Rd | 2 man/multcomp_tidiers.Rd | 2 man/multinom_tidiers.Rd |only man/nlme_tidiers.Rd |only man/nls_tidiers.Rd | 2 man/optim_tidiers.Rd |only man/plm_tidiers.Rd |only man/process_lm.Rd |only man/pyears_tidiers.Rd | 2 man/ridgelm_tidiers.Rd | 2 man/rlm_tidiers.Rd | 2 man/rowwise_df_tidiers.Rd | 2 man/sexpfit_tidiers.Rd | 2 man/smooth.spline_tidiers.Rd | 2 man/sp_tidiers.Rd | 2 man/summary_tidiers.Rd |only man/survfit_tidiers.Rd | 2 man/survreg_tidiers.Rd | 2 man/tidy.NULL.Rd | 2 man/tidy.Rd | 2 man/tidy.TukeyHSD.Rd | 2 man/tidy.coeftest.Rd |only man/tidy.default.Rd | 2 man/tidy.density.Rd | 2 man/tidy.ftable.Rd | 2 man/tidy.manova.Rd | 2 man/tidy.map.Rd | 2 man/tidy.pairwise.htest.Rd | 2 man/tidy.power.htest.Rd |only man/tidy.spec.Rd | 2 man/tidy.table.Rd | 2 man/tidy.ts.Rd | 2 man/unrowname.Rd | 2 man/zoo_tidiers.Rd | 2 tests/testthat/test-nlme.R |only 89 files changed, 326 insertions(+), 179 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each set of
nested blocks optimized within the levels of any existing higher-level blocks.
Block sizes are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.5 dated 2015-03-08 and 1.6 dated 2015-05-06
DESCRIPTION | 12 +- MD5 | 18 +-- NAMESPACE | 2 R/blocks.r | 212 ++++++++++++++++++++++++-------------------- R/upper_bounds.r | 4 build/vignette.rds |binary man/blocks.Rd | 94 +++++++------------ man/blocksdesign-package.Rd | 2 man/efficiencies.Rd | 2 man/upper_bounds.Rd | 2 10 files changed, 173 insertions(+), 175 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis.
Author: Gianluca Baio, Andrea Berardi, Anna Heath
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between BCEA versions 2.1-0 dated 2015-01-13 and 2.1-1 dated 2015-05-06
BCEA-2.1-0/BCEA/man/multi.evppi.Rd |only BCEA-2.1-1/BCEA/DESCRIPTION | 15 BCEA-2.1-1/BCEA/MD5 | 67 +- BCEA-2.1-1/BCEA/NAMESPACE | 11 BCEA-2.1-1/BCEA/R/bcea.R | 749 +++++++++++++-------------------- BCEA-2.1-1/BCEA/data/Smoking.RData |binary BCEA-2.1-1/BCEA/data/Vaccine.RData |binary BCEA-2.1-1/BCEA/man/BCEA-package.Rd | 21 BCEA-2.1-1/BCEA/man/CEriskav.Rd | 47 +- BCEA-2.1-1/BCEA/man/CreateInputs.Rd | 9 BCEA-2.1-1/BCEA/man/Smoking.Rd | 52 +- BCEA-2.1-1/BCEA/man/Vaccine.Rd | 60 +- BCEA-2.1-1/BCEA/man/bcea.Rd | 45 + BCEA-2.1-1/BCEA/man/ceac.plot.Rd | 35 + BCEA-2.1-1/BCEA/man/ceaf.plot.Rd | 10 BCEA-2.1-1/BCEA/man/ceef.plot.Rd | 81 ++- BCEA-2.1-1/BCEA/man/ceplane.plot.Rd | 50 +- BCEA-2.1-1/BCEA/man/contour.bcea.Rd | 43 + BCEA-2.1-1/BCEA/man/contour2.Rd | 35 + BCEA-2.1-1/BCEA/man/diag.evppi.Rd | 66 ++ BCEA-2.1-1/BCEA/man/eib.plot.Rd | 52 +- BCEA-2.1-1/BCEA/man/evi.plot.Rd | 15 BCEA-2.1-1/BCEA/man/evppi.Rd | 101 ++-- BCEA-2.1-1/BCEA/man/ib.plot.Rd | 23 - BCEA-2.1-1/BCEA/man/mce.plot.Rd | 19 BCEA-2.1-1/BCEA/man/mixedAn.Rd | 55 +- BCEA-2.1-1/BCEA/man/multi.ce.Rd | 9 BCEA-2.1-1/BCEA/man/plot.CEriskav.Rd | 30 + BCEA-2.1-1/BCEA/man/plot.bcea.Rd | 41 + BCEA-2.1-1/BCEA/man/plot.evppi.Rd | 21 BCEA-2.1-1/BCEA/man/plot.mixedAn.Rd | 28 - BCEA-2.1-1/BCEA/man/sim.table.Rd | 13 BCEA-2.1-1/BCEA/man/struct.psa.Rd | 33 - BCEA-2.1-1/BCEA/man/summary.bcea.Rd | 12 BCEA-2.1-1/BCEA/man/summary.mixedAn.Rd | 17 35 files changed, 1082 insertions(+), 783 deletions(-)
Title: Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Description: Implements tests for Type I error in Qualitative Comparative Analysis (QCA) that take into account the multiple hypothesis tests inherent in the procedure. Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation test that provides 95% confidence intervals for the number of counterexamples and degree of consistency, respectively. The distributions of permuted values can be plotted against the observed values. For csQCA and mvQCA, simple binomial tests are implemented in csQCAbinTest() and mvQCAbinTest(), respectively.
Author: Bear Braumoeller <braumoeller.1@osu.edu>
Maintainer: Bear Braumoeller <braumoeller.1@osu.edu>
Diff between QCAfalsePositive versions 0.11 dated 2015-05-03 and 1.0 dated 2015-05-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/fsQCApermTest.R | 21 ++++++++++++++++++++- R/plot.fsQCApt.R | 19 ++++++++++++++----- 4 files changed, 40 insertions(+), 12 deletions(-)
More information about QCAfalsePositive at CRAN
Permanent link
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between wgaim versions 1.4-7 dated 2015-05-04 and 1.4-8 dated 2015-05-06
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/wgaim9.R | 70 +++++++++++++++++++++++++++-------------------------- inst/doc/wgaim.pdf |binary 4 files changed, 43 insertions(+), 41 deletions(-)
Title: Some Invalid Some Valid Instrumental Variables Estimator
Description: Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome.
Author: Hyunseung Kang <khyuns@wharton.upenn.edu>
Maintainer: Hyunseung Kang <khyuns@wharton.upenn.edu>
Diff between sisVIVE versions 1.0 dated 2014-10-17 and 1.1 dated 2015-05-05
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/sisVIVE.R | 2 +- man/sisVIVE.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.3.0 dated 2015-03-30 and 1.3.1 dated 2015-05-05
DESCRIPTION | 12 ++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 1 + R/import.htmlq.R |only R/import.pqmethod.R | 2 +- R/qmethod.R | 1 + man/import.htmlq.Rd |only man/import.q.sorts.Rd | 6 ++++-- man/make.cards.Rd | 4 +++- man/qmethod-package.Rd | 2 +- man/qzscores.Rd | 3 ++- 11 files changed, 29 insertions(+), 20 deletions(-)
Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in
the Lexis diagram, bootstrapping. Parametric proportional
hazards fitting with left truncation and right censoring for
common families of distributions, piecewise constant hazards,
and discrete models. AFT regression for left truncated and
right censored data. Binary and Poisson regression for
clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström [aut, cre]
Maintainer: Göran Broström <goran.brostrom@umu.se>
Diff between eha versions 2.4-2 dated 2014-12-17 and 2.4-3 dated 2015-05-05
ChangeLog | 19 +++++++++++++++++++ DESCRIPTION | 14 +++++++------- MD5 | 44 +++++++++++++++++++++++--------------------- NAMESPACE | 2 ++ R/check.dist.R | 8 +++++--- R/coxreg.R | 42 +++++++++++++++++++++++++++++++----------- R/getHaz.R | 2 ++ R/glmmMLBoot.R | 2 ++ R/glmmboot.R | 4 ++-- R/phreg.R | 8 ++++++-- R/plot.coxreg.R | 24 +++++++++++++++++++----- R/print.aftreg.R | 4 +++- R/print.phreg.R | 4 ++-- R/print.risksets.R |only R/risksets.R | 29 +++++++++++++++++++++-------- build/vignette.rds |binary man/check.dist.Rd | 3 ++- man/coxreg.Rd | 4 ++-- man/plot.aftreg.Rd | 2 +- man/plot.coxreg.Rd | 13 +++++-------- man/plot.hazdata.Rd | 4 ++-- man/print.risksets.Rd |only man/risksets.Rd | 8 +++++--- man/scania.Rd | 2 +- 24 files changed, 162 insertions(+), 80 deletions(-)
Title: Conduct Univariate and Bivariate Wavelet Analyses
Description: This is a port of the WTC MATLAB package written by Aslak Grinsted
and the wavelet program written by Christopher Torrence and Gibert P.
Compo. This package can be used to perform univariate and bivariate
(cross-wavelet, wavelet coherence, wavelet clustering) analyses.
Author: Tarik C. Gouhier, Aslak Grinsted
Maintainer: Tarik C. Gouhier <tarik.gouhier@gmail.com>
Diff between biwavelet versions 0.17.5 dated 2014-11-07 and 0.17.10 dated 2015-05-05
DESCRIPTION | 8 - MD5 | 16 +- R/check.data.R | 13 + R/plot.biwavelet.R | 323 +++++++++++++++++++++++++---------------------- R/wt.R | 21 +-- R/wt.sig.R | 23 --- inst/NEWS.Rd | 40 +++++ man/biwavelet-package.Rd | 10 - man/plot.biwavelet.Rd | 45 ++++-- 9 files changed, 281 insertions(+), 218 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver.
To see list of available hydroservers, see http://hiscentral.cuahsi.org.
The package has five data download functions: GetServices(): show all public
HydroServers from the HIS Central Catalog. GetVariables(): Show a data.frame with
all variables on the server. GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code, start time
and endtime, fetch a data.frame of all the observation time series data values.
The data.frame has two columns: time and DataValue. This function has an optional "daily"
parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily
values. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a HydroServer Lite ODM database
via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 0.9.6 dated 2015-05-01 and 1.0.0 dated 2015-05-05
DESCRIPTION | 6 - MD5 | 24 +++--- NAMESPACE | 2 R/GetSiteInfo.R | 163 ++++++++++++++++++++++++++++++--------------- R/GetSites.R | 74 +++++++++++++++----- R/GetValues.R | 60 ++++++++++++++-- R/GetVariables.R | 113 ++++++++++++++++++++++++------- R/MakeSOAPEnvelope.R |only R/WaterOneFlowVersion.R |only man/GetSiteInfo.Rd | 6 - man/GetSites.Rd | 7 + man/GetValues.Rd | 4 - man/GetVariables.Rd | 6 - man/MakeSOAPEnvelope.Rd |only man/WaterOneFlowVersion.Rd |only 15 files changed, 337 insertions(+), 128 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-1 dated 2015-04-10 and 0.0-2 dated 2015-05-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 2 +- TODO | 10 +--------- demo/test_functions.R | 10 ++++++++-- src/ghalton.c | 6 +++--- 6 files changed, 21 insertions(+), 23 deletions(-)
Title: Principal Covariates Regression
Description: Analyzing regression data with many and/or highly collinear predictor variables, by simultaneously reducing the predictor variables to a limited number of components and regressing the criterion variables on these components. Several rotation options are provided in this package, as well as model selection options.
Author: Marlies Vervloet [aut, cre],
Henk Kiers [aut],
Eva Ceulemans [ctb]
Maintainer: Marlies Vervloet <marlies.vervloet@ppw.kuleuven.be>
Diff between PCovR versions 2.5 dated 2014-07-16 and 2.6 dated 2015-05-05
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NAMESPACE | 3 ++- R/pcovr.default.R | 3 +++ R/plot.pcovr.R | 2 +- inst |only man/ErrorRatio.Rd | 2 ++ man/PCovR-package.Rd | 8 +++++--- man/SortLoadings.Rd | 2 ++ man/alexithymia.Rd | 2 ++ man/pcovr.Rd | 2 ++ man/pcovr_est.Rd | 4 +++- man/promin.Rd | 2 ++ man/psychiatrists.Rd | 2 ++ man/wvarim.Rd | 2 ++ 15 files changed, 46 insertions(+), 23 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation, annual dose rate determination, growth curve fitting, decay curve decomposition, fast-component equivalent dose estimation, statistical age models optimization, and statistical plots visualization.
Author: Peng Jun
Maintainer: Peng Jun <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 1.7 dated 2014-10-04 and 1.8 dated 2015-05-05
DESCRIPTION | 12 +++---- MD5 | 50 ++++++++++++++++++------------- NAMESPACE | 15 +++++++++ NEWS | 2 + R/analyst.R | 60 +++++++++++++++++++------------------ R/calDA.R |only R/calED.R | 24 ++++++--------- R/fastED.R | 48 +++++++++++++++--------------- R/psRadialPlot.R |only R/select.R |only R/viewer.R |only THANKS | 14 ++++---- inst/CITATION | 27 ++++++++++------- man/EDdata.Rd | 4 +- man/RadialPlotter.Rd | 73 ++++++++++++++++++++++------------------------ man/Signaldata.Rd | 4 +- man/analyst.Rd | 74 +++++++++++++++++++++------------------------- man/calDA.Rd |only man/calED.Rd | 79 +++++++++++++++++++++++++------------------------- man/dbED.Rd | 34 ++++++++++----------- man/decomp.Rd | 74 ++++++++++++++++++++++++---------------------- man/fastED.Rd | 65 ++++++++++++++++++++--------------------- man/fitGrowth.Rd | 55 ++++++++++++++++------------------ man/mcFMM.Rd | 39 ++++++++++++------------ man/mcMAM.Rd | 24 +++++++-------- man/numOSL-package.Rd | 18 +++-------- man/psRadialPlot.Rd |only man/reportSAM.Rd | 26 ++++++++-------- man/select.Rd |only man/viewer.Rd |only 30 files changed, 419 insertions(+), 402 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.2 dated 2015-04-07 and 3.4 dated 2015-05-05
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS | 14 +++++++++++++- R/Deriv.R | 25 +++++++++++++++++-------- R/Simplify.R | 12 ++++++++++-- man/Deriv-package.Rd | 2 +- man/Deriv.Rd | 4 ++-- tests/testthat/test_Deriv.R | 26 +++++++++++++++++++++----- tests/testthat/test_Deriv.R.bck | 34 +++++++++++++++++++++++++--------- tests/testthat/test_Simplify.R | 7 +++++++ tests/testthat/test_Simplify.R.bck | 8 ++++++++ 12 files changed, 120 insertions(+), 44 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.2.8 dated 2015-03-06 and 0.3.0 dated 2015-05-05
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- NAMESPACE | 59 ++++++++++++++++++++++++------------------------ inst/CITATION | 4 +-- inst/NEWS | 4 +++ man/linarpr.Rd | 2 - man/linarpt.Rd | 2 - man/lingini.Rd | 2 - man/lingpg.Rd | 2 - man/linpoormed.Rd | 2 - man/linqsr.Rd | 2 - man/linrmpg.Rd | 2 - man/vardpoor-package.Rd | 4 +-- man/varpoord.Rd | 2 - 14 files changed, 63 insertions(+), 58 deletions(-)
Title: Psychometric Mixture Models
Description: Psychometric mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture models
with different parameterizations of the score distribution (saturated vs. mean/variance specification)
and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without
concomitant variables. See vignette('raschmix', package = 'psychomix') for details on the Rasch mixture
models.
Author: Hannah Frick [aut, cre],
Carolin Strobl [aut],
Friedrich Leisch [aut],
Achim Zeileis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between psychomix versions 1.1-1 dated 2014-07-29 and 1.1-2 dated 2015-05-05
DESCRIPTION | 24 +++++++-------- MD5 | 44 ++++++++++++++-------------- NAMESPACE | 5 +-- NEWS | 29 ++++++++++++++++++ R/allGenerics.R | 2 + R/btmix.R | 2 - R/effects.R | 12 ++----- R/raschmix.R | 36 ++++++++++++++--------- R/raschmixMethods.R | 72 ++++++++++++++++++++++++++++++++++++++++++++++ R/raschmixPlot.R | 21 ++++++++++--- build/vignette.rds |binary inst/CITATION | 10 +++--- inst/doc/raschmix.Rnw | 14 +++++--- inst/doc/raschmix.pdf |binary inst/doc/scores.Rnw | 6 +-- inst/doc/scores.pdf |binary man/raschmix.Rd | 8 ++--- man/raschmixMethods.Rd | 15 +++++++++ man/raschmixPlotMethod.Rd | 18 ++++++----- tests/test.R | 1 tests/test.Rout.save | 47 +++++++++++++++--------------- vignettes/raschmix.Rnw | 14 +++++--- vignettes/scores.Rnw | 6 +-- 23 files changed, 265 insertions(+), 121 deletions(-)
Title: Tools for Approximate Bayesian Computation (ABC)
Description: Implements several ABC algorithms for
performing parameter estimation, model selection, and goodness-of-fit.
Cross-validation tools are also available for measuring the
accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.
Author: Csillery Katalin [aut],
Lemaire Louisiane [aut],
Francois Olivier [aut],
Blum Michael [aut, cre]
Maintainer: Blum Michael <michael.blum@imag.fr>
Diff between abc versions 2.0 dated 2014-07-11 and 2.1 dated 2015-05-05
abc-2.0/abc/data |only abc-2.0/abc/man/human.Rd |only abc-2.0/abc/man/musigma2.Rd |only abc-2.0/abc/man/ppc.Rd |only abc-2.1/abc/CHANGES | 22 ++++++ abc-2.1/abc/DESCRIPTION | 26 +++++--- abc-2.1/abc/MD5 | 43 +++++-------- abc-2.1/abc/NAMESPACE | 1 abc-2.1/abc/R/cv4abc.R | 4 - abc-2.1/abc/R/gfit.R | 2 abc-2.1/abc/inst/CITATION | 5 - abc-2.1/abc/inst/doc/abcvignette.R | 96 ++++++++++++++++++++++-------- abc-2.1/abc/inst/doc/abcvignette.Rnw | 34 ++++++---- abc-2.1/abc/inst/doc/abcvignette.pdf |binary abc-2.1/abc/man/abc.Rd | 4 - abc-2.1/abc/man/cv4abc.Rd | 1 abc-2.1/abc/man/cv4postpr.Rd | 1 abc-2.1/abc/man/gfit.Rd | 107 +++++++++++++++++----------------- abc-2.1/abc/man/gfitpca.Rd | 1 abc-2.1/abc/man/plot.gfit.Rd | 53 ++++++++-------- abc-2.1/abc/man/postpr.Rd | 4 - abc-2.1/abc/man/summary.gfit.Rd | 64 ++++++++++---------- abc-2.1/abc/vignettes/abcvignette.Rnw | 34 ++++++---- 23 files changed, 294 insertions(+), 208 deletions(-)
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez and Markus Müller.
Maintainer: Xavier Robin <robin@lindinglab.org>
Diff between pROC versions 1.7.3 dated 2014-06-13 and 1.8 dated 2015-05-05
pROC-1.7.3/pROC/man/smooth.roc.Rd |only pROC-1.8/pROC/DESCRIPTION | 14 +-- pROC-1.8/pROC/MD5 | 60 ++++++------- pROC-1.8/pROC/NAMESPACE | 165 +++++++++++++++++++++++++++++++------ pROC-1.8/pROC/NEWS | 9 ++ pROC-1.8/pROC/R/auc.R | 8 + pROC-1.8/pROC/R/bootstrap.R | 8 + pROC-1.8/pROC/R/ci.auc.R | 5 - pROC-1.8/pROC/R/ci.coords.R | 2 pROC-1.8/pROC/R/ci.se.R | 2 pROC-1.8/pROC/R/ci.sp.R | 2 pROC-1.8/pROC/R/ci.thresholds.R | 2 pROC-1.8/pROC/R/roc.R | 80 ++++++++++++----- pROC-1.8/pROC/R/roc.utils.R | 2 pROC-1.8/pROC/R/smooth.R | 6 - pROC-1.8/pROC/R/var.R | 5 - pROC-1.8/pROC/README.md | 5 - pROC-1.8/pROC/inst/CITATION | 2 pROC-1.8/pROC/man/are.paired.Rd | 2 pROC-1.8/pROC/man/auc.Rd | 14 ++- pROC-1.8/pROC/man/ci.Rd | 2 pROC-1.8/pROC/man/ci.auc.Rd | 2 pROC-1.8/pROC/man/ci.coords.Rd | 2 pROC-1.8/pROC/man/ci.se.Rd | 2 pROC-1.8/pROC/man/ci.sp.Rd | 2 pROC-1.8/pROC/man/ci.thresholds.Rd | 9 +- pROC-1.8/pROC/man/coords.Rd | 7 + pROC-1.8/pROC/man/pROC-package.Rd | 29 +----- pROC-1.8/pROC/man/roc.Rd | 14 +-- pROC-1.8/pROC/man/roc.test.Rd | 2 pROC-1.8/pROC/man/smooth.Rd |only pROC-1.8/pROC/man/var.Rd | 2 32 files changed, 319 insertions(+), 147 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 1.1.3 dated 2015-04-16 and 1.1.4 dated 2015-05-05
DESCRIPTION | 14 +- MD5 | 37 ++--- NEWS |only R/CJS.R | 239 +++++++++++++++++++---------------- R/Closed.R | 269 ++++++++++++++++++++++------------------ R/multimark_functions.R | 25 +-- inst/CITATION | 70 +++++----- man/bobcat.Rd | 51 +++---- man/getprobsCJS.Rd | 91 ++++++------- man/getprobsClosed.Rd | 83 ++++++------ man/multimarkCJS.Rd | 295 ++++++++++++++++++++++---------------------- man/multimarkClosed.Rd | 247 ++++++++++++++++++------------------ man/multimarksetup-class.Rd | 108 ++++++++-------- man/multimodelCJS.Rd | 193 ++++++++++++++-------------- man/multimodelClosed.Rd | 165 ++++++++++++------------ man/processdata.Rd | 115 ++++++++--------- man/simdataCJS.Rd | 126 +++++++++--------- man/simdataClosed.Rd | 122 +++++++++--------- src/Closed.c | 12 - src/ProbitCJS.c | 12 - 20 files changed, 1170 insertions(+), 1104 deletions(-)
Title: Multiple Testing for Hypotheses with Hierarchical or Group
Structure
Description: Performs multiple testing corrections that take specific structure of hypotheses into account.
Author: Kris Sankaran
Maintainer: Kris Sankaran <kriss1@stanford.edu>
Diff between structSSI versions 1.1 dated 2014-09-05 and 1.1.1 dated 2015-05-05
structSSI-1.1.1/structSSI/DESCRIPTION | 8 +- structSSI-1.1.1/structSSI/MD5 | 12 ++-- structSSI-1.1.1/structSSI/R/pi0.lsl.R | 4 - structSSI-1.1.1/structSSI/R/treePValues.R | 79 +++++++++++++-------------- structSSI-1.1.1/structSSI/data/gtemp.txt |only structSSI-1.1.1/structSSI/man/chlamydiae.Rd | 6 +- structSSI-1.1.1/structSSI/man/treePValues.Rd | 30 +++++++--- structSSI-1.1/structSSI/data/gtemp.txt.gz |only 8 files changed, 77 insertions(+), 62 deletions(-)
Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries
from ASCII sources and provides tools for estimating SEER second cancer risks.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>
Diff between SEERaBomb versions 2014.4.1 dated 2014-04-17 and 2015.1 dated 2015-05-05
SEERaBomb-2014.4.1/SEERaBomb/R/mkHema87.R |only SEERaBomb-2014.4.1/SEERaBomb/inst/doc/courses |only SEERaBomb-2014.4.1/SEERaBomb/man/figures/SEERaBombFig.png |only SEERaBomb-2014.4.1/SEERaBomb/man/mkHema87.Rd |only SEERaBomb-2015.1/SEERaBomb/DESCRIPTION | 27 SEERaBomb-2015.1/SEERaBomb/MD5 | 108 + SEERaBomb-2015.1/SEERaBomb/NAMESPACE | 9 SEERaBomb-2015.1/SEERaBomb/NEWS | 61 + SEERaBomb-2015.1/SEERaBomb/R/RcppExports.R |only SEERaBomb-2015.1/SEERaBomb/R/getBinInfo.R |only SEERaBomb-2015.1/SEERaBomb/R/getE.R |only SEERaBomb-2015.1/SEERaBomb/R/getPY.R |only SEERaBomb-2015.1/SEERaBomb/R/mapCancs.R |only SEERaBomb-2015.1/SEERaBomb/R/mapRegs.R |only SEERaBomb-2015.1/SEERaBomb/R/mapTrts.R |only SEERaBomb-2015.1/SEERaBomb/R/mk2D.R |only SEERaBomb-2015.1/SEERaBomb/R/mkAbomb.R | 112 + SEERaBomb-2015.1/SEERaBomb/R/mkExcel.R |only SEERaBomb-2015.1/SEERaBomb/R/mkSEER.R | 246 +++- SEERaBomb-2015.1/SEERaBomb/R/mkSEERold.R |only SEERaBomb-2015.1/SEERaBomb/R/pickFields.R | 60 - SEERaBomb-2015.1/SEERaBomb/R/plot2D.R |only SEERaBomb-2015.1/SEERaBomb/R/post1PYO.R |only SEERaBomb-2015.1/SEERaBomb/R/seerSet.R |only SEERaBomb-2015.1/SEERaBomb/R/simSeerSet.R |only SEERaBomb-2015.1/SEERaBomb/R/tsd.R |only SEERaBomb-2015.1/SEERaBomb/data/stdUS.rda |only SEERaBomb-2015.1/SEERaBomb/inst/doc/examples |only SEERaBomb-2015.1/SEERaBomb/inst/doc/extraFuncs |only SEERaBomb-2015.1/SEERaBomb/inst/doc/fieldNames.html | 599 ++++------ SEERaBomb-2015.1/SEERaBomb/inst/doc/gettingData.pdf |binary SEERaBomb-2015.1/SEERaBomb/inst/doc/index.html |only SEERaBomb-2015.1/SEERaBomb/inst/doc/overview.pdf |binary SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/JCO2013/MDSAMLsurvMF.R | 4 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/blood2012/blood2012fig5a.R | 12 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/blood2012/blood2012fig5bc.R | 43 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/blood2012/blood2012fig6.R | 2 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/blood2012/vIncidAPLCML.r | 14 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/radiatEnvironBiophys2013/SupplementSEER.R | 37 SEERaBomb-2015.1/SEERaBomb/inst/doc/papers/radiatEnvironBiophys2013/supplementAbomb.R | 65 - SEERaBomb-2015.1/SEERaBomb/man/SEERaBomb-package.Rd | 43 SEERaBomb-2015.1/SEERaBomb/man/figures/mkSEERfig.png |only SEERaBomb-2015.1/SEERaBomb/man/fillPYM.Rd |only SEERaBomb-2015.1/SEERaBomb/man/getBinInfo.Rd |only SEERaBomb-2015.1/SEERaBomb/man/getE.Rd |only SEERaBomb-2015.1/SEERaBomb/man/getFields.Rd | 12 SEERaBomb-2015.1/SEERaBomb/man/getPY.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mapCancs.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mapRegs.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mapTrts.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mk2D.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mkAbomb.Rd | 16 SEERaBomb-2015.1/SEERaBomb/man/mkExcel.Rd |only SEERaBomb-2015.1/SEERaBomb/man/mkSEER.Rd | 38 SEERaBomb-2015.1/SEERaBomb/man/mkSEERold.Rd |only SEERaBomb-2015.1/SEERaBomb/man/pickFields.Rd | 22 SEERaBomb-2015.1/SEERaBomb/man/plot2D.Rd |only SEERaBomb-2015.1/SEERaBomb/man/post1PYO.Rd |only SEERaBomb-2015.1/SEERaBomb/man/seerSet.Rd |only SEERaBomb-2015.1/SEERaBomb/man/simSeerSet.Rd |only SEERaBomb-2015.1/SEERaBomb/man/stdUS.Rd |only SEERaBomb-2015.1/SEERaBomb/man/tsd.Rd |only SEERaBomb-2015.1/SEERaBomb/src |only 63 files changed, 935 insertions(+), 595 deletions(-)
Title: Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and
Destruction Rate Modelling
Description: Distributions that are typically used for exposure rating in
general insurance, in particular to price reinsurance contracts.
The vignettes show code snippets to fit the distribution to
empirical data.
Author: Giorgio Spedicato [aut, cre],
Christophe Dutang [aut],
Markus Gesmann [ctb]
Maintainer: Giorgio Spedicato <spedicato_giorgio@yahoo.it>
Diff between mbbefd versions 0.6.1 dated 2015-03-08 and 0.7 dated 2015-05-05
mbbefd-0.6.1/mbbefd/inst/CITATION |only mbbefd-0.6.1/mbbefd/vignettes/jss.dtx |only mbbefd-0.6.1/mbbefd/vignettes/mbbefd-distrPlot.pdf |only mbbefd-0.6.1/mbbefd/vignettes/mbbefd-drateplot.pdf |only mbbefd-0.6.1/mbbefd/vignettes/mbbefd-survivalPlot.pdf |only mbbefd-0.7/mbbefd/ChangeLog | 11 mbbefd-0.7/mbbefd/DESCRIPTION | 38 mbbefd-0.7/mbbefd/MD5 | 83 mbbefd-0.7/mbbefd/NAMESPACE | 43 mbbefd-0.7/mbbefd/NEWS | 7 mbbefd-0.7/mbbefd/R/1infl-beta.R |only mbbefd-0.7/mbbefd/R/1infl-distr.R |only mbbefd-0.7/mbbefd/R/1infl-shftrncPareto.R |only mbbefd-0.7/mbbefd/R/1infl-unif.R |only mbbefd-0.7/mbbefd/R/RcppExports.R | 73 mbbefd-0.7/mbbefd/R/distributionDefinition.R | 250 +- mbbefd-0.7/mbbefd/R/empiricalfunctions.R |only mbbefd-0.7/mbbefd/R/gendilogintegral.R |only mbbefd-0.7/mbbefd/R/internal-test-mean.R |only mbbefd-0.7/mbbefd/R/mbbefdR-1stparam.R |only mbbefd-0.7/mbbefd/R/mbbefdR-2ndparam.R |only mbbefd-0.7/mbbefd/R/shftrncPareto.R |only mbbefd-0.7/mbbefd/R/theo-ecf.R |only mbbefd-0.7/mbbefd/R/zzz.R | 40 mbbefd-0.7/mbbefd/README.md | 16 mbbefd-0.7/mbbefd/build/vignette.rds |binary mbbefd-0.7/mbbefd/inst/doc/Introduction_to_Exposure_Rating.R |only mbbefd-0.7/mbbefd/inst/doc/Introduction_to_Exposure_Rating.Rmd |only mbbefd-0.7/mbbefd/inst/doc/Introduction_to_Exposure_Rating.pdf |only mbbefd-0.7/mbbefd/inst/doc/mbbefd.R | 291 +- mbbefd-0.7/mbbefd/inst/doc/mbbefd.Rnw | 980 ++++++---- mbbefd-0.7/mbbefd/inst/doc/mbbefd.pdf |binary mbbefd-0.7/mbbefd/man/eecf.Rd |only mbbefd-0.7/mbbefd/man/etl.Rd |only mbbefd-0.7/mbbefd/man/exposureCurve.Rd | 111 - mbbefd-0.7/mbbefd/man/g2a.Rd | 46 mbbefd-0.7/mbbefd/man/mbbefd-package.Rd | 64 mbbefd-0.7/mbbefd/man/mbbefdDistribution.Rd | 184 + mbbefd-0.7/mbbefd/man/oneinfl-Distribution.Rd |only mbbefd-0.7/mbbefd/man/oneinfl-beta-Distribution.Rd |only mbbefd-0.7/mbbefd/man/oneinfl-stpareto-Distribution.Rd |only mbbefd-0.7/mbbefd/man/oneinfl-unif-Distribution.Rd |only mbbefd-0.7/mbbefd/man/sfttrncParetoDistribution.Rd |only mbbefd-0.7/mbbefd/man/swissRe.Rd | 74 mbbefd-0.7/mbbefd/src/RcppExports.cpp | 52 mbbefd-0.7/mbbefd/src/mbbefdRcppCode.cpp | 19 mbbefd-0.7/mbbefd/tests/check-formula-variance.R |only mbbefd-0.7/mbbefd/tests/checkformula.R |only mbbefd-0.7/mbbefd/tests/test-1inf-beta.R |only mbbefd-0.7/mbbefd/tests/test-1inf-mean.R |only mbbefd-0.7/mbbefd/tests/test-1inf-shftrncPareto.R |only mbbefd-0.7/mbbefd/tests/test-1inf-unif.R |only mbbefd-0.7/mbbefd/tests/test-eecf.R |only mbbefd-0.7/mbbefd/tests/test-mbbefd-1stparam.R |only mbbefd-0.7/mbbefd/tests/test-mbbefd-2ndparam.R |only mbbefd-0.7/mbbefd/tests/test-shftrncPareto.R |only mbbefd-0.7/mbbefd/tests/testthat.R | 8 mbbefd-0.7/mbbefd/tests/testthat/testsDistr.R | 38 mbbefd-0.7/mbbefd/vignettes/Introduction_to_Exposure_Rating.Rmd |only mbbefd-0.7/mbbefd/vignettes/mbbefd.Rnw | 980 ++++++---- mbbefd-0.7/mbbefd/vignettes/mbbefd.bib | 147 + 61 files changed, 2161 insertions(+), 1394 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.0.0 dated 2015-03-16 and 3.1.0 dated 2015-05-05
DESCRIPTION | 14 +++-- MD5 | 82 ++++++++++++++++++--------------- NAMESPACE | 4 + NEWS | 9 +++ R/acs.R | 1 R/data.R | 49 +++++++++++++++++++ R/get_county_demographics.R |only R/get_state_demograhpics.R |only README.md | 13 ++--- build/vignette.rds |binary data/df_county_demographics.rdata |only data/df_state_demographics.rdata |only inst/doc/f-world-bank-data.R | 6 +- inst/doc/f-world-bank-data.html | 2 inst/doc/h-creating-your-own-maps.html | 2 man/Admin1Choropleth.Rd | 4 - man/Choropleth.Rd | 4 - man/CountryChoropleth.Rd | 4 - man/CountyChoropleth.Rd | 4 - man/CountyZoomChoropleth.Rd | 4 - man/StateChoropleth.Rd | 4 - man/USAChoropleth.Rd | 4 - man/admin1_choropleth.Rd | 2 man/choroplethr.Rd | 2 man/choroplethr_acs.Rd | 2 man/choroplethr_animate.Rd | 2 man/choroplethr_wdi.Rd | 2 man/country_choropleth.Rd | 2 man/county_choropleth.Rd | 2 man/county_choropleth_acs.Rd | 2 man/county_zoom_choropleth.Rd | 2 man/df_county_demographics.Rd |only man/df_japan_census.Rd | 2 man/df_pop_country.Rd | 2 man/df_pop_county.Rd | 2 man/df_pop_state.Rd | 2 man/df_president.Rd | 2 man/df_president_ts.Rd | 2 man/df_state_demographics.Rd |only man/get_acs_data.Rd | 2 man/get_acs_df.Rd | 2 man/get_county_demographics.Rd |only man/get_state_demographics.Rd |only man/state_choropleth.Rd | 2 man/state_choropleth_acs.Rd | 2 man/zip_map.Rd | 2 46 files changed, 159 insertions(+), 91 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between sglasso versions 1.1-1 dated 2015-04-02 and 1.2 dated 2015-05-04
sglasso-1.1-1/sglasso/man/dglars-internal.Rd |only sglasso-1.2/sglasso/ChangeLog | 19 ++- sglasso-1.2/sglasso/DESCRIPTION | 14 +- sglasso-1.2/sglasso/MD5 | 64 ++++++---- sglasso-1.2/sglasso/NAMESPACE | 5 sglasso-1.2/sglasso/R/fglasso.R | 6 sglasso-1.2/sglasso/R/fglasso_model2mask.R | 2 sglasso-1.2/sglasso/R/gplot.R |only sglasso-1.2/sglasso/R/gplot.fglasso.R |only sglasso-1.2/sglasso/R/gplot.sglasso.R |only sglasso-1.2/sglasso/R/klcv.R | 5 sglasso-1.2/sglasso/R/loglik.R | 8 - sglasso-1.2/sglasso/R/make_sglasso.R | 17 +- sglasso-1.2/sglasso/R/plot.klcv.R |only sglasso-1.2/sglasso/R/print.klcv.R | 4 sglasso-1.2/sglasso/R/print.sglasso.R | 7 - sglasso-1.2/sglasso/R/sglasso.R | 10 - sglasso-1.2/sglasso/R/sglasso.fit.R | 24 +-- sglasso-1.2/sglasso/R/summary.sglasso.R | 15 +- sglasso-1.2/sglasso/R/zero.R |only sglasso-1.2/sglasso/data |only sglasso-1.2/sglasso/inst |only sglasso-1.2/sglasso/man/Kh.Rd | 7 - sglasso-1.2/sglasso/man/fglasso.Rd | 67 +++++----- sglasso-1.2/sglasso/man/gplot.Rd |only sglasso-1.2/sglasso/man/gplot.fglasso.Rd |only sglasso-1.2/sglasso/man/gplot.sglasso.Rd |only sglasso-1.2/sglasso/man/klcv.Rd | 23 ++- sglasso-1.2/sglasso/man/loglik.Rd | 13 +- sglasso-1.2/sglasso/man/neisseria.Rd |only sglasso-1.2/sglasso/man/plot.klcv.Rd |only sglasso-1.2/sglasso/man/plot.sglasso.Rd | 6 sglasso-1.2/sglasso/man/sglasso-internal.Rd |only sglasso-1.2/sglasso/man/sglasso-package.Rd | 16 +- sglasso-1.2/sglasso/man/sglasso.Rd | 26 ++-- sglasso-1.2/sglasso/man/summary.sglasso.Rd | 16 +- sglasso-1.2/sglasso/src/sglasso_ccd_path.f90 | 149 ++++++++++++----------- sglasso-1.2/sglasso/src/sglasso_ccd_single.f90 | 158 ++++++++++++------------- sglasso-1.2/sglasso/src/sglasso_ccm_path.f90 | 76 ++++++------ sglasso-1.2/sglasso/src/sglasso_ccm_single.f90 | 86 +++++++------ 40 files changed, 457 insertions(+), 386 deletions(-)
Title: Sample Size Calculations for Complex Surveys
Description: Computes the required sample size for estimation of totals, means
and proportions under complex sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas <hugogutierrez@usantotomas.edu.co>
Diff between samplesize4surveys versions 2.2.0 dated 2015-04-29 and 2.4.0.900 dated 2015-05-04
samplesize4surveys-2.2.0/samplesize4surveys/data/BigLucyT0T1.txt.gz |only samplesize4surveys-2.4.0.900/samplesize4surveys/DESCRIPTION | 12 samplesize4surveys-2.4.0.900/samplesize4surveys/MD5 | 61 ++- samplesize4surveys-2.4.0.900/samplesize4surveys/NAMESPACE | 14 samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4ddm.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4ddp.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4dm.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4dp.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4m.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/b4p.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4ddm.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4ddp.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4dm.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4dp.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4m.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/e4p.R | 141 ++++---- samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4ddm.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4ddmH.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4ddp.R | 5 samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4ddpH.R |only samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4dm.R | 4 samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4dmH.R | 12 samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4mH.R | 170 +++++----- samplesize4surveys-2.4.0.900/samplesize4surveys/R/ss4p.R | 28 - samplesize4surveys-2.4.0.900/samplesize4surveys/build |only samplesize4surveys-2.4.0.900/samplesize4surveys/data/BigLucyT0T1.rda |only samplesize4surveys-2.4.0.900/samplesize4surveys/inst |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4ddm.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4ddp.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4dm.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4dp.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4m.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/b4p.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4ddm.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4ddp.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4dm.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4dp.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4m.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/e4p.Rd | 12 samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4ddm.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4ddmH.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4ddp.Rd | 4 samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4ddpH.Rd |only samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4dm.Rd | 2 samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4dmH.Rd | 2 samplesize4surveys-2.4.0.900/samplesize4surveys/man/ss4p.Rd | 20 - samplesize4surveys-2.4.0.900/samplesize4surveys/vignettes |only 47 files changed, 266 insertions(+), 221 deletions(-)
More information about samplesize4surveys at CRAN
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Title: Applied Geochemistry EDA
Description: Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot() for concentration-area plots employs package 'akima', however, 'akima' is only licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will have to independently make package 'akima' available through library(....); and use of function caplot() by for-profit users will fail.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett <garrett@NRCan.gc.ca>
Diff between rgr versions 1.1.10 dated 2015-01-03 and 1.1.11 dated 2015-05-04
rgr-1.1.10/rgr/inst/doc/What_is_in_rgr_1-1-10.pdf |only rgr-1.1.10/rgr/inst/doc/rgr_Overview_1-1-10.pdf |only rgr-1.1.10/rgr/inst/doc/rgr_func_list_1-1-10.pdf |only rgr-1.1.10/rgr/man/rgr_1.1.10-package.Rd |only rgr-1.1.11/rgr/DESCRIPTION | 10 - rgr-1.1.11/rgr/MD5 | 152 +++++++++++----------- rgr-1.1.11/rgr/NAMESPACE | 2 rgr-1.1.11/rgr/R/fences.summary.R | 41 ++++- rgr-1.1.11/rgr/R/framework.summary.R | 39 +++-- rgr-1.1.11/rgr/R/gx.hist.R | 28 ++-- rgr-1.1.11/rgr/R/gx.md.display.R | 39 ++--- rgr-1.1.11/rgr/R/gx.md.print.R | 39 +++-- rgr-1.1.11/rgr/R/gx.mvalloc.print.R | 31 ++-- rgr-1.1.11/rgr/R/gx.ngr.ltdl.R |only rgr-1.1.11/rgr/R/gx.ngr.skew.R |only rgr-1.1.11/rgr/R/gx.ngr.stats.R |only rgr-1.1.11/rgr/R/gx.ngr.summary.R |only rgr-1.1.11/rgr/R/gx.rma.R | 126 ++++++++++-------- rgr-1.1.11/rgr/R/gx.rqpca.plot.R | 50 +++++-- rgr-1.1.11/rgr/R/gx.rqpca.print.R | 46 +----- rgr-1.1.11/rgr/R/gx.rqpca.save.R |only rgr-1.1.11/rgr/R/gx.triples.aov.R | 9 - rgr-1.1.11/rgr/R/inset.exporter.R | 23 ++- rgr-1.1.11/rgr/R/map.eda7.R | 6 rgr-1.1.11/rgr/R/map.eda8.R | 6 rgr-1.1.11/rgr/R/map.z.R | 12 - rgr-1.1.11/rgr/R/xyplot.eda7.R | 8 - rgr-1.1.11/rgr/R/xyplot.eda8.R | 6 rgr-1.1.11/rgr/R/xyplot.z.R | 12 - rgr-1.1.11/rgr/data/ad.test.rda |binary rgr-1.1.11/rgr/data/crm.test.new.rda |binary rgr-1.1.11/rgr/data/crm.test.rda |binary rgr-1.1.11/rgr/data/fix.test.asis.rda |binary rgr-1.1.11/rgr/data/fix.test.rda |binary rgr-1.1.11/rgr/data/kola.c.rda |binary rgr-1.1.11/rgr/data/kola.o.rda |binary rgr-1.1.11/rgr/data/ms.data1.rda |binary rgr-1.1.11/rgr/data/ms.data2.rda |binary rgr-1.1.11/rgr/data/ms.data3.rda |binary rgr-1.1.11/rgr/data/ogrady.mat2open.rda |binary rgr-1.1.11/rgr/data/ogrady.rda |binary rgr-1.1.11/rgr/data/sind.mat2open.rda |binary rgr-1.1.11/rgr/data/sind.rda |binary rgr-1.1.11/rgr/data/triples.test1.rda |binary rgr-1.1.11/rgr/data/triples.test2.rda |binary rgr-1.1.11/rgr/inst/doc/What_is_in_rgr_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_Overview_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_func_list_1-1-11.pdf |only rgr-1.1.11/rgr/man/bwplots.Rd | 2 rgr-1.1.11/rgr/man/bwplots.by.var.Rd | 2 rgr-1.1.11/rgr/man/bxplot.Rd | 2 rgr-1.1.11/rgr/man/cnpplt.Rd | 2 rgr-1.1.11/rgr/man/crm.plot.Rd | 8 - rgr-1.1.11/rgr/man/crm.plot.new.Rd | 4 rgr-1.1.11/rgr/man/fences.summary.Rd | 12 + rgr-1.1.11/rgr/man/framework.summary.Rd | 14 +- rgr-1.1.11/rgr/man/gx.cnpplts.Rd | 2 rgr-1.1.11/rgr/man/gx.ecdf.Rd | 2 rgr-1.1.11/rgr/man/gx.hist.Rd | 8 - rgr-1.1.11/rgr/man/gx.md.display.Rd | 29 ++-- rgr-1.1.11/rgr/man/gx.md.print.Rd | 19 +- rgr-1.1.11/rgr/man/gx.mvalloc.Rd | 4 rgr-1.1.11/rgr/man/gx.mvalloc.closed.Rd | 3 rgr-1.1.11/rgr/man/gx.mvalloc.print.Rd | 13 + rgr-1.1.11/rgr/man/gx.ngr.ltdl.Rd |only rgr-1.1.11/rgr/man/gx.ngr.skew.Rd |only rgr-1.1.11/rgr/man/gx.ngr.stats.Rd |only rgr-1.1.11/rgr/man/gx.ngr.summary.Rd |only rgr-1.1.11/rgr/man/gx.rma.Rd | 55 ++++--- rgr-1.1.11/rgr/man/gx.rqpca.plot.Rd | 25 ++- rgr-1.1.11/rgr/man/gx.rqpca.print.Rd | 19 +- rgr-1.1.11/rgr/man/gx.rqpca.save.Rd |only rgr-1.1.11/rgr/man/gx.scores.Rd | 14 +- rgr-1.1.11/rgr/man/gx.summary.Rd | 6 rgr-1.1.11/rgr/man/inset.Rd | 17 +- rgr-1.1.11/rgr/man/inset.exporter.Rd | 41 +++-- rgr-1.1.11/rgr/man/map.eda7.Rd | 5 rgr-1.1.11/rgr/man/map.eda8.Rd | 5 rgr-1.1.11/rgr/man/map.z.Rd | 24 +-- rgr-1.1.11/rgr/man/rgr_1.1.11-package.Rd |only rgr-1.1.11/rgr/man/shape.Rd | 10 - rgr-1.1.11/rgr/man/tbplots.Rd | 2 rgr-1.1.11/rgr/man/tbplots.by.var.Rd | 2 rgr-1.1.11/rgr/man/xyplot.eda7.Rd | 5 rgr-1.1.11/rgr/man/xyplot.eda8.Rd | 5 rgr-1.1.11/rgr/man/xyplot.z.Rd | 20 +- 86 files changed, 584 insertions(+), 482 deletions(-)
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>
Diff between PopGenome versions 2.1.5 dated 2015-05-01 and 2.1.6 dated 2015-05-04
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 2 +- R/get.feature.names.R | 2 +- R/split_data_into_GFF_attributes.R | 6 ++++-- inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary inst/doc/Integration_of_new_Methods.pdf |binary inst/doc/Whole_genome_analyses_using_VCF_files.pdf | 10 +++++----- 8 files changed, 21 insertions(+), 19 deletions(-)
Title: Accurate Numerical Derivatives
Description: Methods for calculating (usually) accurate
numerical first and second order derivatives. Accurate calculations
are done using Richardson's extrapolation or, when applicable, a complex
step derivative is available. A simple difference
method is also provided. Simple difference is (usually) less accurate
but is much quicker than Richardson's extrapolation and provides a
useful cross-check.
Methods are provided for real scalar and vector valued functions.
Author: Paul Gilbert and Ravi Varadhan
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between numDeriv versions 2012.9-1 dated 2012-10-14 and 2014.2-1 dated 2015-05-04
DESCRIPTION | 33 +++--- MD5 | 21 ++-- NEWS | 16 +++ R/num2Deriv.R |only R/numDeriv.R | 263 +++++++++++++++++------------------------------------ build |only inst/doc/Guide.pdf |binary man/genD.Rd | 15 ++- man/grad.Rd | 56 +++++++++-- man/hessian.Rd | 17 ++- man/jacobian.Rd | 19 +-- po |only tests/oneSided.R |only 13 files changed, 213 insertions(+), 227 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.3-0 dated 2015-03-18 and 3.4-0 dated 2015-05-04
ncvreg-3.3-0/ncvreg/inst/tests/par.R |only ncvreg-3.3-0/ncvreg/tests |only ncvreg-3.4-0/ncvreg/DESCRIPTION | 8 +- ncvreg-3.4-0/ncvreg/MD5 | 48 +++++++++-------- ncvreg-3.4-0/ncvreg/NAMESPACE | 7 +- ncvreg-3.4-0/ncvreg/NEWS | 14 ++++ ncvreg-3.4-0/ncvreg/R/cv.ncvreg.R | 2 ncvreg-3.4-0/ncvreg/R/ncvreg.R | 4 + ncvreg-3.4-0/ncvreg/R/ncvsurv.R | 11 +++ ncvreg-3.4-0/ncvreg/R/perm.ncvreg.R | 76 +++++++++++++++++---------- ncvreg-3.4-0/ncvreg/R/permres.ncvreg.R |only ncvreg-3.4-0/ncvreg/R/plot.ncvsurv.func.R |only ncvreg-3.4-0/ncvreg/R/predict.R | 10 +-- ncvreg-3.4-0/ncvreg/R/predict.surv.R | 59 ++++++++++++++++++-- ncvreg-3.4-0/ncvreg/README.md |only ncvreg-3.4-0/ncvreg/inst/tests/fir.R |only ncvreg-3.4-0/ncvreg/inst/tests/parallel.R |only ncvreg-3.4-0/ncvreg/inst/tests/surv.R | 60 +++++++++++++++++++++ ncvreg-3.4-0/ncvreg/inst/tests/test.R | 67 ++++++++++------------- ncvreg-3.4-0/ncvreg/man/cv.ncvreg.Rd | 3 - ncvreg-3.4-0/ncvreg/man/fir.Rd | 2 ncvreg-3.4-0/ncvreg/man/ncvreg.Rd | 6 +- ncvreg-3.4-0/ncvreg/man/ncvsurv.Rd | 37 +++++++++---- ncvreg-3.4-0/ncvreg/man/perm.ncvreg.Rd | 33 +++++++---- ncvreg-3.4-0/ncvreg/man/permres.Rd |only ncvreg-3.4-0/ncvreg/man/plot.fir.Rd | 2 ncvreg-3.4-0/ncvreg/man/plot.ncvsurv.func.Rd |only ncvreg-3.4-0/ncvreg/man/predict.Rd | 6 +- ncvreg-3.4-0/ncvreg/man/predict.ncvsurv.Rd |only ncvreg-3.4-0/ncvreg/src/cox-dh.c | 9 +-- 30 files changed, 321 insertions(+), 143 deletions(-)
Title: Ordination and Multivariate Analysis for Ecology
Description: A variety of ordination and community analyses
useful in analysis of data sets in community ecology.
Includes many of the common ordination methods, with
graphical routines to facilitate their interpretation,
as well as several novel analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between labdsv versions 1.6-1 dated 2013-09-13 and 1.7-0 dated 2015-05-04
labdsv-1.6-1/labdsv/R/indspc.R |only labdsv-1.6-1/labdsv/R/rgl.nmds.R |only labdsv-1.6-1/labdsv/R/rgl.pco.R |only labdsv-1.6-1/labdsv/man/indspc.Rd |only labdsv-1.7-0/labdsv/DESCRIPTION | 11 labdsv-1.7-0/labdsv/INDEX | 24 - labdsv-1.7-0/labdsv/MD5 | 151 +++---- labdsv-1.7-0/labdsv/NAMESPACE | 61 ++ labdsv-1.7-0/labdsv/R/abuocc.R | 76 ++- labdsv-1.7-0/labdsv/R/clustify.R |only labdsv-1.7-0/labdsv/R/compspec.R |only labdsv-1.7-0/labdsv/R/concov.R | 36 - labdsv-1.7-0/labdsv/R/const.R | 65 +-- labdsv-1.7-0/labdsv/R/dematrify.R | 25 - labdsv-1.7-0/labdsv/R/dga.R | 5 labdsv-1.7-0/labdsv/R/disana.R | 50 +- labdsv-1.7-0/labdsv/R/drop.R | 24 - labdsv-1.7-0/labdsv/R/dsvdis.R | 2 labdsv-1.7-0/labdsv/R/envrtest.R | 5 labdsv-1.7-0/labdsv/R/euclidify.R | 3 labdsv-1.7-0/labdsv/R/homoteneity.R | 14 labdsv-1.7-0/labdsv/R/importance.R | 75 +-- labdsv-1.7-0/labdsv/R/indval.R | 41 -- labdsv-1.7-0/labdsv/R/isamic.R | 10 labdsv-1.7-0/labdsv/R/metrify.R | 3 labdsv-1.7-0/labdsv/R/nmds.R | 71 ++- labdsv-1.7-0/labdsv/R/ordcomp.R | 14 labdsv-1.7-0/labdsv/R/orddist.R | 6 labdsv-1.7-0/labdsv/R/ordpart.R | 18 labdsv-1.7-0/labdsv/R/ordtaxa.R | 33 - labdsv-1.7-0/labdsv/R/ordtest.R | 24 - labdsv-1.7-0/labdsv/R/pca.R | 27 - labdsv-1.7-0/labdsv/R/pco.R | 79 ++- labdsv-1.7-0/labdsv/R/raretaxa.R | 38 + labdsv-1.7-0/labdsv/R/reconcile.R | 11 labdsv-1.7-0/labdsv/R/rnddist.R | 8 labdsv-1.7-0/labdsv/R/rndtaxa.R | 4 labdsv-1.7-0/labdsv/R/subset_dist.R |only labdsv-1.7-0/labdsv/R/thull.R | 9 labdsv-1.7-0/labdsv/R/vegtrans.R | 24 - labdsv-1.7-0/labdsv/data/brycesite.rda |binary labdsv-1.7-0/labdsv/data/bryceveg.rda |binary labdsv-1.7-0/labdsv/inst/ChangeLog | 674 +++++++++++++++++---------------- labdsv-1.7-0/labdsv/man/abuocc.Rd | 16 labdsv-1.7-0/labdsv/man/brycesite.Rd | 8 labdsv-1.7-0/labdsv/man/clustify.Rd |only labdsv-1.7-0/labdsv/man/compspec.Rd |only labdsv-1.7-0/labdsv/man/concov.Rd | 7 labdsv-1.7-0/labdsv/man/const.Rd | 8 labdsv-1.7-0/labdsv/man/dematrify.Rd | 2 labdsv-1.7-0/labdsv/man/dga.Rd | 2 labdsv-1.7-0/labdsv/man/disana.Rd | 7 labdsv-1.7-0/labdsv/man/dropplt.Rd | 9 labdsv-1.7-0/labdsv/man/dropspc.Rd | 5 labdsv-1.7-0/labdsv/man/dsvdis.Rd | 12 labdsv-1.7-0/labdsv/man/envrtest.Rd | 2 labdsv-1.7-0/labdsv/man/euclidify.Rd | 2 labdsv-1.7-0/labdsv/man/homoteneity.Rd | 2 labdsv-1.7-0/labdsv/man/importance.Rd | 8 labdsv-1.7-0/labdsv/man/indval.Rd | 2 labdsv-1.7-0/labdsv/man/isamic.Rd | 2 labdsv-1.7-0/labdsv/man/matrify.Rd | 2 labdsv-1.7-0/labdsv/man/metrify.Rd | 4 labdsv-1.7-0/labdsv/man/nmds.Rd | 5 labdsv-1.7-0/labdsv/man/ordcomp.Rd | 2 labdsv-1.7-0/labdsv/man/orddist.Rd | 4 labdsv-1.7-0/labdsv/man/ordpart.Rd | 2 labdsv-1.7-0/labdsv/man/ordtest.Rd | 6 labdsv-1.7-0/labdsv/man/pca.Rd | 11 labdsv-1.7-0/labdsv/man/pco.Rd | 2 labdsv-1.7-0/labdsv/man/plot.nmds.Rd | 13 labdsv-1.7-0/labdsv/man/plot.pca.Rd | 2 labdsv-1.7-0/labdsv/man/plot.pco.Rd | 13 labdsv-1.7-0/labdsv/man/raretaxa.Rd | 5 labdsv-1.7-0/labdsv/man/reconcile.Rd | 1 labdsv-1.7-0/labdsv/man/rnddist.Rd | 2 labdsv-1.7-0/labdsv/man/rndtaxa.Rd | 2 labdsv-1.7-0/labdsv/man/spcdisc.Rd | 2 labdsv-1.7-0/labdsv/man/thull.Rd | 7 labdsv-1.7-0/labdsv/man/vegtab.Rd | 2 labdsv-1.7-0/labdsv/man/vegtrans.Rd | 2 81 files changed, 1042 insertions(+), 862 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-1 dated 2015-04-14 and 0.3-2 dated 2015-05-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/ICP.R | 6 ++++-- R/hiddenICE.R | 30 +++++++++++++++++++----------- R/hiddenICP.R | 2 ++ man/ICP.Rd | 4 +++- man/hiddenICE.Rd | 18 +++++++++++++----- man/hiddenICP.Rd | 4 +++- 8 files changed, 55 insertions(+), 31 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files,
calculate DVH metrics, gEUD, BED, EQD2, NTCP, TCP, show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.2 dated 2015-04-08 and 0.3 dated 2015-05-04
DESCRIPTION | 12 +- MD5 | 73 ++++++------- NAMESPACE | 12 ++ R/getBED.R | 176 ++++++------------------------- R/getDMEAN.R | 4 R/getEQD2.R |only R/getEUD.R | 35 +++--- R/getIsoEffD.R |only R/getMetric.R | 25 ++-- R/getNTCP.R | 33 +++-- R/parseCadplan.R | 2 R/parseConstraint.R |only R/parseEclipse.R | 4 R/parseMasterplan.R | 2 R/parseMetric.R | 8 - R/parsePinnacleDVH.R | 2 R/print.R | 4 R/readConstraint.R | 255 ---------------------------------------------- R/runGUI.R | 7 + R/showDVH.R | 4 R/unix/parseDVH.R | 3 data/dataMZ.rda |binary inst/ChangeLog | 12 +- inst/DVHshiny/server.R | 22 +-- inst/DVHshiny/ui.R | 4 inst/doc/DVHmetrics.R | 11 + inst/doc/DVHmetrics.Rnw | 43 +++++-- inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 8 - man/getBED.Rd | 28 +++-- man/getEQD2.Rd | 30 ++++- man/getEUD.Rd | 14 +- man/getIsoEffD.Rd | 48 +++++--- man/getMetric.Rd | 2 man/getNTCP.Rd | 4 man/getTCP.Rd | 4 vignettes/DVHmetrics.Rnw | 43 +++++-- vignettes/lit.bib | 2 39 files changed, 357 insertions(+), 579 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between wgaim versions 1.4-6 dated 2015-02-03 and 1.4-7 dated 2015-05-04
wgaim-1.4-6/wgaim/R/wgaim8.R |only wgaim-1.4-7/wgaim/DESCRIPTION | 10 +++++----- wgaim-1.4-7/wgaim/MD5 | 12 ++++++------ wgaim-1.4-7/wgaim/R/wgaim9.R |only wgaim-1.4-7/wgaim/inst/NEWS.Rd | 7 +++++++ wgaim-1.4-7/wgaim/inst/doc/wgaim.pdf |binary wgaim-1.4-7/wgaim/man/cross2int.Rd | 9 +++++---- wgaim-1.4-7/wgaim/man/wgaim.asreml.Rd | 5 ++--- 8 files changed, 25 insertions(+), 18 deletions(-)
Title: Stable Distribution Functions
Description: Density, Probability and Quantile functions, and random number
generation for (skew) stable distributions, using the parametrizations of
Nolan.
Author: Diethelm Wuertz, Martin Maechler and Rmetrics core team members.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between stabledist versions 0.6-6 dated 2013-06-12 and 0.7-0 dated 2015-05-04
stabledist-0.6-6/stabledist/Done |only stabledist-0.7-0/stabledist/ChangeLog | 7 ++++++ stabledist-0.7-0/stabledist/DESCRIPTION | 19 ++++++++-------- stabledist-0.7-0/stabledist/MD5 | 15 ++++++------- stabledist-0.7-0/stabledist/R/dpqr-stable.R | 16 ++++++++++---- stabledist-0.7-0/stabledist/R/utils.R | 8 +++++-- stabledist-0.7-0/stabledist/TODO | 28 +++++++++++++++++++++++++ stabledist-0.7-0/stabledist/man/dist-stable.Rd | 5 ++-- stabledist-0.7-0/stabledist/tests/pstab-ex.R | 6 +++++ 9 files changed, 78 insertions(+), 26 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
In addition, various risk estimation methods are included.
Note that the package 'sdcMicroGUI' includes a graphical user interface for various methods
in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 4.4.0 dated 2014-07-18 and 4.5.0 dated 2015-05-04
DESCRIPTION | 14 +++++++------- MD5 | 40 ++++++++++++++++++++-------------------- R/GUIfunctions.R | 15 ++++++++++++--- R/LocalRecProg.R | 2 +- R/aux_functions.r | 2 +- R/methods.r | 4 ++-- R/microaggregation.R | 2 +- R/plot.localSuppression.R | 4 ++-- R/pram.R | 2 +- R/printFunctions.R | 10 +++++----- R/swappNum.R | 2 +- R/valTable.R | 2 +- build/vignette.rds |binary inst/doc/sdc_guidelines.pdf |binary man/dRisk.Rd | 2 +- man/dUtility.Rd | 2 +- man/dataGen.Rd | 2 +- man/groupVars-methods.Rd | 17 +++++++++++------ man/swappNum-deprecated.Rd | 1 - man/swappNum.Rd | 1 - tests/reporting_test.R | 2 +- 21 files changed, 69 insertions(+), 57 deletions(-)
Title: Prediction of Fish Movement Parameters
Description: Functions to predict fish movement parameters plotting leptokurtic fish dispersal kernels (see Radinger and Wolter, 2014: Patterns and predictors of fish dispersal in rivers. Fish and Fisheries. 15:456-473.)
Author: Johannes Radinger
Maintainer: Johannes Radinger <jradinger@igb-berlin.de>
Diff between fishmove versions 0.3-1 dated 2015-03-24 and 0.3-2 dated 2015-05-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/fishmove.R | 2 +- man/fishmove-package.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: The Bee Swarm Plot, an Alternative to Stripchart
Description: The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.
Author: Aron Eklund
Maintainer: Aron Eklund <eklund+beeswarm@cbs.dtu.dk>
Diff between beeswarm versions 0.1.6 dated 2013-09-20 and 0.2.0 dated 2015-05-04
DESCRIPTION | 11 ++-- MD5 | 12 ++-- NEWS | 17 ++++++ R/beeswarm.R | 143 +++++++++++++++++++++++++++++++++++--------------------- R/bxplot.R | 3 - man/beeswarm.Rd | 25 +++++++++ man/swarmx.Rd | 18 ++++++- 7 files changed, 159 insertions(+), 70 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Diff between vdg versions 1.0.1 dated 2015-02-13 and 1.1 dated 2015-05-04
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph]
Maintainer: Pieter Schoonees
DESCRIPTION | 15 ++---
MD5 | 52 ++++++++++--------
NAMESPACE | 4 +
R/plot.spv.R | 119 +++++++++++++++++++++++++-----------------
R/plot.spvforlist.R | 104 +++++++++++++++++++++----------------
R/plot.spvlist.R | 133 +++++++++++++++++++++++++++---------------------
R/plot.spvlistforlist.R | 107 +++++++++++++++++++++-----------------
R/sampler.R | 31 +++++++++--
R/spv.R | 3 -
R/spv.data.frame.R | 37 +++++++------
R/spv.list.R | 48 ++++++++++-------
R/spv.matrix.R | 37 +++++++------
R/stdrange.R | 3 -
R/vdg-package.R | 27 +++++++++
build |only
inst/doc |only
man/GJ54.Rd | 2
man/LHS.Rd | 2
man/meanspv.Rd | 2
man/plot.spv.Rd | 70 ++++++++++++++-----------
man/print.spv.Rd | 2
man/runif_sphere.Rd | 2
man/sampler.Rd | 26 +++++++--
man/spv.Rd | 20 ++++---
man/stdrange.Rd | 4 -
man/vdg-package.Rd | 31 ++++++++++-
vignettes |only
27 files changed, 539 insertions(+), 342 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated from Cox Proportional Hazards Models
Diff between simPH versions 1.3 dated 2015-02-11 and 1.3.1 dated 2015-05-04
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 12 +++---
MD5 | 81 +++++++++++++++++++++----------------------
NAMESPACE | 2 -
NEWS | 10 ++++-
R/SurvExpand.R | 4 ++
R/coxsimInteract.R | 7 +++
R/coxsimLinear.R | 6 ++-
R/coxsimPoly.R | 6 ++-
R/coxsimSpline.R | 6 ++-
R/coxsimtvc.R | 6 ++-
R/simGG.R | 4 ++
R/simGG.siminteract.R | 7 +++
R/simGG.simlinear.R | 7 +++
R/simGG.simpoly.R | 4 ++
R/simGG.simspline.R | 4 ++
R/simGG.simtvc.R | 6 ++-
R/simPH.R | 79 ++++++++++++++++++++++-------------------
README.md | 9 +++-
build/vignette.rds |binary
inst/CITATION |only
man/CarpenterFdaData.Rd | 2 -
man/GolubEUPData.Rd | 2 -
man/MinMaxLines.Rd | 2 -
man/SurvExpand.Rd | 7 +++
man/as.data.frame.coxsim.Rd | 2 -
man/coxsimInteract.Rd | 9 +++-
man/coxsimLinear.Rd | 6 ++-
man/coxsimPoly.Rd | 6 ++-
man/coxsimSpline.Rd | 6 ++-
man/coxsimtvc.Rd | 6 ++-
man/ggfitStrata.Rd | 2 -
man/setXl.Rd | 2 -
man/simGG.Rd | 7 +++
man/simGG.siminteract.Rd | 6 ++-
man/simGG.simlinear.Rd | 6 ++-
man/simGG.simpoly.Rd | 7 +++
man/simGG.simspline.Rd | 7 +++
man/simGG.simtvc.Rd | 6 ++-
man/simPH.Rd | 7 +++
man/tvc.Rd | 2 -
vignettes/HRBibliography.bib | 29 ++++++++++-----
vignettes/simPH-overview.Rnw | 22 ++++++-----
42 files changed, 276 insertions(+), 135 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-15 dated 2015-03-27 and 3.1-16 dated 2015-05-04
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
s20x-3.1-15/s20x/data/airpass.df.txt |only
s20x-3.1-15/s20x/data/apples.df.txt |only
s20x-3.1-15/s20x/data/arousal.df.txt |only
s20x-3.1-15/s20x/data/beer.df.txt |only
s20x-3.1-15/s20x/data/body.df.txt |only
s20x-3.1-15/s20x/data/books.df.txt |only
s20x-3.1-15/s20x/data/bursary.df.txt |only
s20x-3.1-15/s20x/data/butterfat.df.txt |only
s20x-3.1-15/s20x/data/camplake.df.txt |only
s20x-3.1-15/s20x/data/chalk.df.txt |only
s20x-3.1-15/s20x/data/computer.df.txt |only
s20x-3.1-15/s20x/data/course.df.txt |only
s20x-3.1-15/s20x/data/course2way.df.txt |only
s20x-3.1-15/s20x/data/diamonds.df.txt |only
s20x-3.1-15/s20x/data/fire.df.txt |only
s20x-3.1-15/s20x/data/fruitfly.df.txt |only
s20x-3.1-15/s20x/data/house.df.txt |only
s20x-3.1-15/s20x/data/incomes.df.txt |only
s20x-3.1-15/s20x/data/lakemary.df.txt |only
s20x-3.1-15/s20x/data/larain.df.txt |only
s20x-3.1-15/s20x/data/mazda.df.txt |only
s20x-3.1-15/s20x/data/mening.df.txt |only
s20x-3.1-15/s20x/data/mergers.df.txt |only
s20x-3.1-15/s20x/data/mozart.df.txt |only
s20x-3.1-15/s20x/data/nail.df.txt |only
s20x-3.1-15/s20x/data/oysters.df.txt |only
s20x-3.1-15/s20x/data/peru.df.txt |only
s20x-3.1-15/s20x/data/rain.df.txt |only
s20x-3.1-15/s20x/data/seeds.df.txt |only
s20x-3.1-15/s20x/data/sheep.df.txt |only
s20x-3.1-15/s20x/data/skulls.df.txt |only
s20x-3.1-15/s20x/data/soyabean.df.txt |only
s20x-3.1-15/s20x/data/teach.df.txt |only
s20x-3.1-15/s20x/data/technitron.df.txt |only
s20x-3.1-15/s20x/data/thyroid.df.txt |only
s20x-3.1-15/s20x/data/toothpaste.df.txt |only
s20x-3.1-15/s20x/data/zoo.df.txt |only
s20x-3.1-16/s20x/DESCRIPTION | 8
s20x-3.1-16/s20x/LICENSE | 678 +++++-----
s20x-3.1-16/s20x/MD5 | 366 ++---
s20x-3.1-16/s20x/NAMESPACE | 96 -
s20x-3.1-16/s20x/R/autocor.plot.R | 20
s20x-3.1-16/s20x/R/boxqq.r | 106 -
s20x-3.1-16/s20x/R/ciReg.R | 48
s20x-3.1-16/s20x/R/cooks20x.R | 22
s20x-3.1-16/s20x/R/crossFactors.R | 56
s20x-3.1-16/s20x/R/crosstabs.R | 98 -
s20x-3.1-16/s20x/R/eovcheck.R | 290 ++--
s20x-3.1-16/s20x/R/estimateContrasts.R | 18
s20x-3.1-16/s20x/R/estimateContrasts1.R | 90 -
s20x-3.1-16/s20x/R/estimateContrasts2.R | 104 -
s20x-3.1-16/s20x/R/freq1way.r | 230 +--
s20x-3.1-16/s20x/R/getVersion.R | 6
s20x-3.1-16/s20x/R/interactionPlots.R | 306 ++--
s20x-3.1-16/s20x/R/layout20x.R | 8
s20x-3.1-16/s20x/R/levene.test.R | 96 -
s20x-3.1-16/s20x/R/multipleComp.R | 58
s20x-3.1-16/s20x/R/normcheck.R | 134 -
s20x-3.1-16/s20x/R/onewayPlot.R | 466 +++---
s20x-3.1-16/s20x/R/pairs20x.R | 54
s20x-3.1-16/s20x/R/predict20x.R | 101 -
s20x-3.1-16/s20x/R/predictCount.R |only
s20x-3.1-16/s20x/R/propslsd.new.R | 112 -
s20x-3.1-16/s20x/R/residPlot.R | 84 -
s20x-3.1-16/s20x/R/rowdistr.r | 462 +++---
s20x-3.1-16/s20x/R/rr.r | 12
s20x-3.1-16/s20x/R/skewness.r | 6
s20x-3.1-16/s20x/R/stripqq.r | 106 -
s20x-3.1-16/s20x/R/summary1way.R | 140 --
s20x-3.1-16/s20x/R/summary2way.R | 558 ++++----
s20x-3.1-16/s20x/R/summaryStats.R | 174 +-
s20x-3.1-16/s20x/R/trendscatter.R | 122 -
s20x-3.1-16/s20x/README.md | 8
s20x-3.1-16/s20x/data/airpass.df.txt.gz |only
s20x-3.1-16/s20x/data/apples.df.txt.gz |only
s20x-3.1-16/s20x/data/arousal.df.txt.gz |only
s20x-3.1-16/s20x/data/beer.df.txt.gz |only
s20x-3.1-16/s20x/data/body.df.txt.gz |only
s20x-3.1-16/s20x/data/books.df.txt.gz |only
s20x-3.1-16/s20x/data/bursary.df.txt.gz |only
s20x-3.1-16/s20x/data/butterfat.df.txt.gz |only
s20x-3.1-16/s20x/data/camplake.df.txt.gz |only
s20x-3.1-16/s20x/data/chalk.df.txt.gz |only
s20x-3.1-16/s20x/data/computer.df.txt.gz |only
s20x-3.1-16/s20x/data/course.df.txt.gz |only
s20x-3.1-16/s20x/data/course2way.df.txt.gz |only
s20x-3.1-16/s20x/data/diamonds.df.txt.gz |only
s20x-3.1-16/s20x/data/fire.df.txt.gz |only
s20x-3.1-16/s20x/data/fruitfly.df.txt.gz |only
s20x-3.1-16/s20x/data/house.df.txt.gz |only
s20x-3.1-16/s20x/data/incomes.df.txt.gz |only
s20x-3.1-16/s20x/data/lakemary.df.txt.gz |only
s20x-3.1-16/s20x/data/larain.df.txt.gz |only
s20x-3.1-16/s20x/data/mazda.df.txt.gz |only
s20x-3.1-16/s20x/data/mening.df.txt.gz |only
s20x-3.1-16/s20x/data/mergers.df.txt.gz |only
s20x-3.1-16/s20x/data/mozart.df.txt.gz |only
s20x-3.1-16/s20x/data/nail.df.txt.gz |only
s20x-3.1-16/s20x/data/oysters.df.txt.gz |only
s20x-3.1-16/s20x/data/peru.df.txt.gz |only
s20x-3.1-16/s20x/data/rain.df.txt.gz |only
s20x-3.1-16/s20x/data/seeds.df.txt.gz |only
s20x-3.1-16/s20x/data/sheep.df.txt.gz |only
s20x-3.1-16/s20x/data/skulls.df.txt.gz |only
s20x-3.1-16/s20x/data/soyabean.df.txt.gz |only
s20x-3.1-16/s20x/data/teach.df.txt.gz |only
s20x-3.1-16/s20x/data/technitron.df.txt.gz |only
s20x-3.1-16/s20x/data/thyroid.df.txt.gz |only
s20x-3.1-16/s20x/data/toothpaste.df.txt.gz |only
s20x-3.1-16/s20x/data/zoo.df.txt.gz |only
s20x-3.1-16/s20x/demo/00Index | 88 -
s20x-3.1-16/s20x/demo/cs1.r | 16
s20x-3.1-16/s20x/demo/cs10.r | 14
s20x-3.1-16/s20x/demo/cs11.r | 16
s20x-3.1-16/s20x/demo/cs12.r | 26
s20x-3.1-16/s20x/demo/cs13.r | 40
s20x-3.1-16/s20x/demo/cs14.r | 24
s20x-3.1-16/s20x/demo/cs15.r | 30
s20x-3.1-16/s20x/demo/cs16.r | 44
s20x-3.1-16/s20x/demo/cs17.r | 32
s20x-3.1-16/s20x/demo/cs18.r | 24
s20x-3.1-16/s20x/demo/cs19.r | 30
s20x-3.1-16/s20x/demo/cs2.r | 14
s20x-3.1-16/s20x/demo/cs20.r | 36
s20x-3.1-16/s20x/demo/cs21.r | 42
s20x-3.1-16/s20x/demo/cs22.r | 22
s20x-3.1-16/s20x/demo/cs23.r | 66
s20x-3.1-16/s20x/demo/cs24.r | 36
s20x-3.1-16/s20x/demo/cs25.r | 90 -
s20x-3.1-16/s20x/demo/cs26.r | 38
s20x-3.1-16/s20x/demo/cs27.r | 36
s20x-3.1-16/s20x/demo/cs28.r | 18
s20x-3.1-16/s20x/demo/cs29.r | 22
s20x-3.1-16/s20x/demo/cs3.r | 10
s20x-3.1-16/s20x/demo/cs30.r | 20
s20x-3.1-16/s20x/demo/cs31.r | 18
s20x-3.1-16/s20x/demo/cs32.r | 22
s20x-3.1-16/s20x/demo/cs33.r | 20
s20x-3.1-16/s20x/demo/cs34.r | 28
s20x-3.1-16/s20x/demo/cs35.r | 16
s20x-3.1-16/s20x/demo/cs36.r | 26
s20x-3.1-16/s20x/demo/cs37.r | 24
s20x-3.1-16/s20x/demo/cs38.r | 30
s20x-3.1-16/s20x/demo/cs39.r | 30
s20x-3.1-16/s20x/demo/cs4.r | 10
s20x-3.1-16/s20x/demo/cs40.r | 20
s20x-3.1-16/s20x/demo/cs41.r | 24
s20x-3.1-16/s20x/demo/cs42.r | 22
s20x-3.1-16/s20x/demo/cs43.r | 20
s20x-3.1-16/s20x/demo/cs5.r | 12
s20x-3.1-16/s20x/demo/cs6.r | 18
s20x-3.1-16/s20x/demo/cs7.r | 24
s20x-3.1-16/s20x/demo/cs8.r | 34
s20x-3.1-16/s20x/demo/cs9.r | 14
s20x-3.1-16/s20x/inst/rmarkdown/templates/STATS20x_Assignment/skeleton/skeleton.Rmd | 46
s20x-3.1-16/s20x/inst/rmarkdown/templates/STATS20x_Assignment/template.yaml | 6
s20x-3.1-16/s20x/man/airpass.df.Rd | 26
s20x-3.1-16/s20x/man/apples.df.Rd | 72 -
s20x-3.1-16/s20x/man/arousal.df.Rd | 36
s20x-3.1-16/s20x/man/autocor.plot.Rd | 42
s20x-3.1-16/s20x/man/beer.df.Rd | 26
s20x-3.1-16/s20x/man/body.df.Rd | 46
s20x-3.1-16/s20x/man/books.df.Rd | 54
s20x-3.1-16/s20x/man/boxqq.Rd | 60
s20x-3.1-16/s20x/man/bursary.df.Rd | 34
s20x-3.1-16/s20x/man/butterfat.df.Rd | 54
s20x-3.1-16/s20x/man/camplake.df.Rd | 36
s20x-3.1-16/s20x/man/chalk.df.Rd | 40
s20x-3.1-16/s20x/man/ciReg.Rd | 52
s20x-3.1-16/s20x/man/computer.df.Rd | 34
s20x-3.1-16/s20x/man/cooks20x.Rd | 42
s20x-3.1-16/s20x/man/course.df.Rd | 60
s20x-3.1-16/s20x/man/course2way.df.Rd | 36
s20x-3.1-16/s20x/man/crossFactors.Rd | 86 -
s20x-3.1-16/s20x/man/crosstabs.Rd | 54
s20x-3.1-16/s20x/man/diamonds.df.Rd | 34
s20x-3.1-16/s20x/man/eovcheck.Rd | 154 +-
s20x-3.1-16/s20x/man/estimateContrasts.Rd | 74 -
s20x-3.1-16/s20x/man/fire.df.Rd | 34
s20x-3.1-16/s20x/man/freq1way.Rd | 86 -
s20x-3.1-16/s20x/man/fruitfly.df.Rd | 50
s20x-3.1-16/s20x/man/getVersion.Rd | 34
s20x-3.1-16/s20x/man/house.df.Rd | 34
s20x-3.1-16/s20x/man/incomes.df.Rd | 20
s20x-3.1-16/s20x/man/interactionPlots.Rd | 156 +-
s20x-3.1-16/s20x/man/lakemary.df.Rd | 34
s20x-3.1-16/s20x/man/larain.df.Rd | 26
s20x-3.1-16/s20x/man/layout20x.Rd | 46
s20x-3.1-16/s20x/man/levene.test.Rd | 66
s20x-3.1-16/s20x/man/mazda.df.Rd | 34
s20x-3.1-16/s20x/man/mening.df.Rd | 26
s20x-3.1-16/s20x/man/mergers.df.Rd | 20
s20x-3.1-16/s20x/man/mozart.df.Rd | 36
s20x-3.1-16/s20x/man/multipleComp.Rd | 46
s20x-3.1-16/s20x/man/nail.df.Rd | 38
s20x-3.1-16/s20x/man/normcheck.Rd | 104 -
s20x-3.1-16/s20x/man/onewayPlot.Rd | 156 +-
s20x-3.1-16/s20x/man/oysters.df.Rd | 34
s20x-3.1-16/s20x/man/pairs20x.Rd | 56
s20x-3.1-16/s20x/man/peru.df.Rd | 40
s20x-3.1-16/s20x/man/predict20x.Rd | 106 -
s20x-3.1-16/s20x/man/predictCount.Rd |only
s20x-3.1-16/s20x/man/propslsd.new.Rd | 32
s20x-3.1-16/s20x/man/rain.df.Rd | 40
s20x-3.1-16/s20x/man/residPlot.Rd | 60
s20x-3.1-16/s20x/man/rowdistr.Rd | 86 -
s20x-3.1-16/s20x/man/rr.Rd | 14
s20x-3.1-16/s20x/man/seeds.df.Rd | 42
s20x-3.1-16/s20x/man/sheep.df.Rd | 32
s20x-3.1-16/s20x/man/skewness.Rd | 40
s20x-3.1-16/s20x/man/skulls.df.Rd | 48
s20x-3.1-16/s20x/man/soyabean.df.Rd | 38
s20x-3.1-16/s20x/man/stripqq.Rd | 58
s20x-3.1-16/s20x/man/summary1way.Rd | 106 -
s20x-3.1-16/s20x/man/summary2way.Rd | 96 -
s20x-3.1-16/s20x/man/summaryStats.Rd | 146 +-
s20x-3.1-16/s20x/man/teach.df.Rd | 36
s20x-3.1-16/s20x/man/technitron.df.Rd | 46
s20x-3.1-16/s20x/man/thyroid.df.Rd | 36
s20x-3.1-16/s20x/man/toothpaste.df.Rd | 34
s20x-3.1-16/s20x/man/trendscatter.Rd | 110 -
s20x-3.1-16/s20x/man/zoo.df.Rd | 42
222 files changed, 5055 insertions(+), 5062 deletions(-)
Title: Command-Line Interface Specification Language
Diff between docopt versions 0.4.2 dated 2015-01-05 and 0.4.3.3 dated 2015-05-04
Description: Define a command-line interface by just giving it
a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge
DESCRIPTION | 12 ++++++------
MD5 | 25 +++++++++++++------------
NAMESPACE | 2 +-
NEWS | 3 +++
R/Tokens.R | 26 ++++++++++++++++++--------
R/docopt.R | 4 ++--
R/parse.R | 2 +-
man/as.character-Pattern-method.Rd | 2 +-
man/as.character-Tokens-method.Rd | 2 +-
man/docopt-package.Rd | 2 +-
man/docopt.Rd | 2 +-
man/sub-Tokens-method.Rd | 2 +-
man/subset-Tokens-method.Rd | 2 +-
tests/testthat/test_issues.R |only
14 files changed, 50 insertions(+), 36 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Diff between ASMap versions 0.4 dated 2015-04-13 and 0.4-1 dated 2015-05-04
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor
Maintainer: Julian Taylor
ASMap-0.4-1/ASMap/DESCRIPTION | 10 +++++-----
ASMap-0.4-1/ASMap/MD5 | 7 ++++---
ASMap-0.4-1/ASMap/R/mstmap10.R |only
ASMap-0.4-1/ASMap/inst/NEWS.Rd |only
ASMap-0.4-1/ASMap/inst/doc/asmapvignette.pdf |binary
ASMap-0.4/ASMap/R/mstmap9.R |only
6 files changed, 9 insertions(+), 8 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Diff between JMbayes versions 0.7-0 dated 2015-03-13 and 0.7-2 dated 2015-05-04
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 8 +-
MD5 | 31 +++++----
R/ModelMats.R | 11 ++-
R/crLong.R |only
R/fitted.JMbayes.R | 12 +++
R/jointModelBayes.R | 24 ++++---
R/predict.JMbayes.R | 14 +++-
R/print.summary.JMbayes.R | 9 +-
R/summary.JMbayes.R | 6 +
R/survfitJM.JMbayes.R | 17 ++++-
demo/server.R | 144 ++++++++++++++++++++++++++++++++++++++++------
demo/ui.R | 35 ++++-------
inst/NEWS | 6 +
man/JMbayes.Rd | 4 -
man/jointModelBayes.Rd | 25 +++++++
man/predict.Rd | 8 +-
man/survfitJM.Rd | 5 +
17 files changed, 274 insertions(+), 85 deletions(-)
Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Diff between apsimr versions 0.1 dated 2014-06-12 and 1.0 dated 2015-05-04
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely
used simulator of agricultural systems. This package includes
functions to create, edit and run APSIM simulations from R. It
also includes functions to visualize the results of an APSIM simulation
and perform sensitivity/uncertainty analysis of APSIM either via functions
in the sensitivity package or by novel emulator-based functions.
For more on APSIM including download instructions go to
\url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill
DESCRIPTION | 25 ++++++++----
MD5 | 41 ++++++++++++++------
NAMESPACE | 13 ++++--
NEWS |only
R/editAPSIM.R | 102 +++++++++++++++++++++++++++++++++-----------------
R/emulateAPSIM.R |only
R/runAPSIM.R | 56 ++++++++++++++++-----------
R/sensitivityAPSIM.R |only
R/visualize.R | 16 ++++---
build |only
inst |only
man/apsim.Rd | 33 ++++++++++------
man/apsim_emul_sa.Rd |only
man/apsim_vector.Rd |only
man/apsimr-package.Rd | 17 ++++----
man/edit_apsim.Rd | 32 ++++++++++-----
man/edit_sim_file.Rd | 33 ++++++++++------
man/example_apsim.Rd | 23 +++++------
man/plot.apsim.Rd | 20 +++++----
man/plot.gamSA.Rd |only
man/print.gamSA.Rd |only
vignettes |only
22 files changed, 266 insertions(+), 145 deletions(-)
More information about clustering.sc.dp at CRAN
Permanent link
Title: Global Disaster Losses from the EMDAT Database Using R
Diff between emdatr versions 0.2 dated 2014-05-12 and 0.3 dated 2015-05-04
Description: The 'EMDAT' database provides information on human
and financial losses from more than 21,000 major natural global
disasters from 1900 to the present. This package provides the
entire data available from 'EMDAT' and also additional relevant
information such as historical national GDP and population.
Moreover, this package also provides functionality to extract
desired subsets of the 'EMDAT' data. The examples provided in
the vignette demonstrate the functionality provided by 'emdatr'.
The goal of 'emdatr' is to promote the use of 'EMDAT' data, bring
transparency to the data, shed light on the limitations of
the data, and make the analysis of the data easier using R.
Author: Gopi Goteti
Maintainer: Gopi Goteti
emdatr-0.2/emdatr/inst/doc/emdatr.R |only
emdatr-0.2/emdatr/inst/doc/emdatr.Rnw |only
emdatr-0.2/emdatr/inst/doc/emdatr.pdf |only
emdatr-0.2/emdatr/vignettes/emdatr.Rnw |only
emdatr-0.3/emdatr/DESCRIPTION | 40 +++++------
emdatr-0.3/emdatr/LICENSE |only
emdatr-0.3/emdatr/MD5 | 33 ++++-----
emdatr-0.3/emdatr/NAMESPACE | 2
emdatr-0.3/emdatr/NEWS | 16 ++++
emdatr-0.3/emdatr/R/data.r | 74 ++++++++++----------
emdatr-0.3/emdatr/R/extract_emdat.r | 13 +--
emdatr-0.3/emdatr/build/vignette.rds |binary
emdatr-0.3/emdatr/data/emdat_sample.rda |binary
emdatr-0.3/emdatr/data/usa_cpi.rda |binary
emdatr-0.3/emdatr/inst/doc/emdatr_demo.R |only
emdatr-0.3/emdatr/inst/doc/emdatr_demo.Rmd |only
emdatr-0.3/emdatr/inst/doc/emdatr_demo.html |only
emdatr-0.3/emdatr/man/emdat_sample.Rd | 100 +++++++++++++---------------
emdatr-0.3/emdatr/man/emdatr.Rd | 23 ++----
emdatr-0.3/emdatr/man/extract_emdat.Rd | 29 +++-----
emdatr-0.3/emdatr/man/usa_cpi.Rd | 22 +++---
emdatr-0.3/emdatr/vignettes/emdatr_demo.Rmd |only
22 files changed, 182 insertions(+), 170 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Diff between RcppAnnoy versions 0.0.5 dated 2015-01-24 and 0.0.6 dated 2015-05-03
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 26 +++++++++++-
DESCRIPTION | 24 +++++------
MD5 | 12 ++---
README.md | 13 +++---
cleanup | 2
inst/include/annoylib.h | 104 +++++++++++++++++++++++++++++++-----------------
src/annoy.cpp | 8 ++-
7 files changed, 124 insertions(+), 65 deletions(-)
Title: Distributed Model-Based Boosting
Diff between parboost versions 0.1.3 dated 2014-03-02 and 0.1.4 dated 2015-05-03
Description: Distributed gradient boosting based on the mboost package. The
parboost package is designed to scale up component-wise functional
gradient boosting in a distributed memory environment by splitting the
observations into disjoint subsets, or alternatively using bootstrap
samples (bagging). Each cluster node then fits a boosting model to its
subset of the data. These boosting models are combined in an ensemble,
either with equal weights, or by fitting a (penalized) regression
model on the predictions of the individual models on the complete
data.
Author: Ronert Obst
Maintainer: Ronert Obst
DESCRIPTION | 10 -
MD5 | 31 ++--
NAMESPACE | 7 +
NEWS | 5
R/methods.R | 34 ++++-
R/parboost-package.R | 3
inst/CITATION | 26 ++-
man/coef.parboost.Rd | 45 +++---
man/cv_subsample.Rd | 29 ++--
man/friedman2.Rd | 27 ++--
man/parboost.Rd | 280 ++++++++++++++++++++----------------------
man/parboost_fit.Rd | 47 +++----
man/postprocess.Rd | 17 +-
man/predict.parboost.Rd | 32 ++--
man/print.parboost.Rd |only
man/print.summary.parboost.Rd |only
man/selected.parboost.Rd | 13 +
man/summary.parboost.Rd |only
18 files changed, 319 insertions(+), 287 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Diff between mvMORPH versions 1.0.4 dated 2015-03-22 and 1.0.5 dated 2015-05-03
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel
DESCRIPTION | 8 -
MD5 | 41 +++++----
NAMESPACE | 7 +
R/fun.r | 70 ++++++++++++++++
R/mvBM.r | 191 ++++++++++++++++++++++++++++++++++++++--------
R/mvEB.r | 41 ++++-----
R/mvLLIK.r | 87 ++++++++++++--------
R/mvOU.r | 16 ++-
R/mvSHIFT.r | 4
R/mvSIM.r | 9 +-
R/testLRT.r | 20 ++++
man/LRT.Rd | 5 -
man/halflife.Rd |only
man/mvBM.Rd | 4
man/mvEB.Rd | 29 ++----
man/mvLL.Rd | 4
man/mvMORPH-package.Rd | 6 -
man/mvOU.Rd | 2
man/stationary.Rd |only
src/covar-matrix-simmap.c | 1
src/mvmorph-covar-mat.c | 2
src/pic_loglik_mvmorph.c | 37 ++++++--
src/spherical.c |only
23 files changed, 418 insertions(+), 166 deletions(-)
Title: Model and Analyse Interval Data
Diff between MAINT.Data versions 0.3 dated 2014-10-24 and 0.4 dated 2015-05-03
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva
Maintainer: Pedro Duarte Silva
CHANGELOG | 5 +++++
DESCRIPTION | 13 +++++++------
MD5 | 9 +++++----
NAMESPACE | 3 ---
R/ClasGenMetDef.R | 12 +++++++++---
man/stdEr.Rd |only
6 files changed, 26 insertions(+), 16 deletions(-)
Title: Create and Manipulate Discrete Random Variables
Diff between discreteRV versions 1.2 dated 2015-04-10 and 1.2.1 dated 2015-05-03
Description: Create, manipulate, transform, and simulate from discrete random
variables. The syntax is modeled after that which is used in mathematical
statistics and probability courses, but with powerful support for more
advanced probability calculations. This includes the creation of joint
random variables, and the derivation and manipulation of their conditional
and marginal distributions.
Author: Andreas Buja [aut],
Eric Hare [aut, cre],
Heike Hofmann [aut]
Maintainer: Eric Hare
DESCRIPTION | 19 +++++++------
MD5 | 67 +++++++++++++++++++++++++----------------------
NAMESPACE | 2 -
build |only
inst |only
man/E.Rd | 2 -
man/KURT.Rd | 2 -
man/P.Rd | 2 -
man/Prop.Rd | 2 -
man/RV.Rd | 2 -
man/SD.Rd | 2 -
man/SKEW.Rd | 2 -
man/SofI.Rd | 2 -
man/SofIID.Rd | 2 -
man/V.Rd | 2 -
man/as.RV.Rd | 2 -
man/grapes-AND-grapes.Rd | 2 -
man/grapes-OR-grapes.Rd | 2 -
man/grapes-in-grapes.Rd | 2 -
man/iid.Rd | 2 -
man/independent.Rd | 2 -
man/joint.Rd | 2 -
man/jointRV.Rd | 2 -
man/marginal.Rd | 2 -
man/margins.Rd | 2 -
man/outcomes.Rd | 2 -
man/plot.RV.Rd | 2 -
man/plot.RVsim.Rd | 2 -
man/print.RV.Rd | 2 -
man/probs.Rd | 2 -
man/props.Rd | 2 -
man/qqnorm.RV.Rd | 2 -
man/rsim.Rd | 2 -
man/skewSim.Rd | 2 -
vignettes |only
35 files changed, 76 insertions(+), 70 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Diff between rcbalance versions 1.4 dated 2015-03-24 and 1.5 dated 2015-05-03
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel
DESCRIPTION | 8 +--
MD5 | 12 ++---
R/rcbalance-internal.R | 27 ++++++++++++-
R/rcbalance.R | 96 ++++++++++++++++++++++++++---------------------
man/dist2net.Rd | 6 ++
man/rcbalance-package.Rd | 4 -
man/rcbalance.Rd | 8 ++-
7 files changed, 103 insertions(+), 58 deletions(-)
More information about QCAfalsePositive at CRAN
Permanent link
Title: Nested Association Mapping Analysis
Diff between NAM versions 1.3 dated 2015-04-22 and 1.3.2 dated 2015-05-03
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 10 +-
MD5 | 38 ++++-----
NAMESPACE | 2
R/Fst.R | 5 -
R/MCreml.R | 15 ---
R/RcppExports.R | 62 +++++++--------
R/gibbs.R | 66 ++++++++++++----
R/gwas.R | 8 +
R/gwas2.R | 10 ++
R/manhattan.R | 27 ++++--
R/reference.R | 1
R/reml.R | 213 ++++++++++++++++++++++++++++++-----------------------
R/snpH2.R | 5 -
R/snpQC.R | 86 ++++++++++++++++++++-
man/Internals.Rd | 2
man/NAM-package.Rd | 4
man/gibbs.Rd | 6 +
man/reml.Rd | 4
man/snpH2.Rd | 2
man/snpQC.Rd | 83 ++++++++++----------
20 files changed, 408 insertions(+), 241 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Diff between MapGAM versions 0.7-4 dated 2014-12-10 and 0.7-5 dated 2015-05-03
Description: Contains functions for mapping odds ratios or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting for confounding variables, using methods described by Kelsall and Diggle (1998) and Webster at al. (2006). Includes convenient functions for mapping, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Veronica Vieira, Scott Bartell, and Robin Bliss
Maintainer: Scott Bartell
ChangeLog | 10 ++++++++++
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
R/colormap.R | 19 +++++++++++++++----
R/trimdata.R | 2 +-
man/MAdata.Rd | 2 +-
man/MapGAM-package.Rd | 6 +++---
man/colormap.Rd | 5 ++++-
man/modgam.Rd | 5 +----
9 files changed, 47 insertions(+), 26 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Diff between bnlearn versions 3.7.1 dated 2015-01-23 and 3.8 dated 2015-05-03
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari
bnlearn-3.7.1/bnlearn/src/common.h |only
bnlearn-3.8/bnlearn/Changelog | 29 +
bnlearn-3.8/bnlearn/DESCRIPTION | 11
bnlearn-3.8/bnlearn/MD5 | 216 ++++++-------
bnlearn-3.8/bnlearn/NAMESPACE | 13
bnlearn-3.8/bnlearn/R/arc.operations.R | 2
bnlearn-3.8/bnlearn/R/custom.fit.R | 23 -
bnlearn-3.8/bnlearn/R/fit.R | 15
bnlearn-3.8/bnlearn/R/fitted.assignment.R | 29 -
bnlearn-3.8/bnlearn/R/foreign-read.R | 22 -
bnlearn-3.8/bnlearn/R/frontend-data.R | 11
bnlearn-3.8/bnlearn/R/frontend-fit.R | 81 +++-
bnlearn-3.8/bnlearn/R/frontend-graph.R | 2
bnlearn-3.8/bnlearn/R/frontend-packages.R | 19 -
bnlearn-3.8/bnlearn/R/frontend-predict.R | 74 ----
bnlearn-3.8/bnlearn/R/lattice.R | 2
bnlearn-3.8/bnlearn/R/learning-algorithms.R | 25 -
bnlearn-3.8/bnlearn/R/utils-cluster.R | 6
bnlearn-3.8/bnlearn/R/utils-graph.R | 3
bnlearn-3.8/bnlearn/R/utils-misc.R | 42 ++
bnlearn-3.8/bnlearn/R/utils-sanitization.R | 128 +++++--
bnlearn-3.8/bnlearn/inst/CITATION | 4
bnlearn-3.8/bnlearn/inst/network.scripts/clgaussian.test.R | 2
bnlearn-3.8/bnlearn/man/bn.fit.methods.Rd | 64 ++-
bnlearn-3.8/bnlearn/man/bnlearn-package.Rd | 4
bnlearn-3.8/bnlearn/man/compare.Rd | 7
bnlearn-3.8/bnlearn/man/configs.Rd |only
bnlearn-3.8/bnlearn/man/cpquery.Rd | 2
bnlearn-3.8/bnlearn/src/acyclic.c | 7
bnlearn-3.8/bnlearn/src/all.monte.carlo.c | 3
bnlearn-3.8/bnlearn/src/allocations.c | 2
bnlearn-3.8/bnlearn/src/allsubs.test.c | 12
bnlearn-3.8/bnlearn/src/arcs2amat.c | 4
bnlearn-3.8/bnlearn/src/arcs2elist.c | 3
bnlearn-3.8/bnlearn/src/averaging.c | 5
bnlearn-3.8/bnlearn/src/bayesian.network.c | 3
bnlearn-3.8/bnlearn/src/bind.c | 4
bnlearn-3.8/bnlearn/src/bn.recovery.c | 4
bnlearn-3.8/bnlearn/src/bootstrap.c | 6
bnlearn-3.8/bnlearn/src/cache.structure.c | 4
bnlearn-3.8/bnlearn/src/cg.assumptions.c | 6
bnlearn-3.8/bnlearn/src/cg.loglikelihood.c | 9
bnlearn-3.8/bnlearn/src/cg.mutual.information.c | 5
bnlearn-3.8/bnlearn/src/common.c | 5
bnlearn-3.8/bnlearn/src/configurations.c | 4
bnlearn-3.8/bnlearn/src/covariance.c | 3
bnlearn-3.8/bnlearn/src/cpdag.c | 5
bnlearn-3.8/bnlearn/src/cpdist.c | 6
bnlearn-3.8/bnlearn/src/ctest.c | 12
bnlearn-3.8/bnlearn/src/data.frame.c | 3
bnlearn-3.8/bnlearn/src/dedup.c | 5
bnlearn-3.8/bnlearn/src/df.adjust.c | 2
bnlearn-3.8/bnlearn/src/dirichlet.posterior.c | 6
bnlearn-3.8/bnlearn/src/discrete.loglikelihood.c | 5
bnlearn-3.8/bnlearn/src/discrete.monte.carlo.c | 7
bnlearn-3.8/bnlearn/src/discrete.mutual.information.c | 4
bnlearn-3.8/bnlearn/src/filter.arcs.c | 5
bnlearn-3.8/bnlearn/src/fitted.c | 4
bnlearn-3.8/bnlearn/src/gaussian.loglikelihood.c | 7
bnlearn-3.8/bnlearn/src/gaussian.monte.carlo.c | 10
bnlearn-3.8/bnlearn/src/gaussian.mutual.information.c | 3
bnlearn-3.8/bnlearn/src/globals.c | 2
bnlearn-3.8/bnlearn/src/graph.generation.c | 8
bnlearn-3.8/bnlearn/src/graph.priors.c | 7
bnlearn-3.8/bnlearn/src/hash.c | 3
bnlearn-3.8/bnlearn/src/hc.cache.lookup.c | 8
bnlearn-3.8/bnlearn/src/htest.c | 5
bnlearn-3.8/bnlearn/src/include |only
bnlearn-3.8/bnlearn/src/indep.test.c | 3
bnlearn-3.8/bnlearn/src/is.dag.c | 4
bnlearn-3.8/bnlearn/src/is.row.equal.c | 2
bnlearn-3.8/bnlearn/src/jonckheere.c | 5
bnlearn-3.8/bnlearn/src/likelihood.weighting.c | 3
bnlearn-3.8/bnlearn/src/linear.algebra.c | 7
bnlearn-3.8/bnlearn/src/linear.correlation.c | 5
bnlearn-3.8/bnlearn/src/loss.c | 7
bnlearn-3.8/bnlearn/src/map.lw.c | 5
bnlearn-3.8/bnlearn/src/mi.matrix.c | 7
bnlearn-3.8/bnlearn/src/mvber.c | 6
bnlearn-3.8/bnlearn/src/nparams.c | 3
bnlearn-3.8/bnlearn/src/parse.c | 2
bnlearn-3.8/bnlearn/src/path.c | 5
bnlearn-3.8/bnlearn/src/pdag2dag.c | 10
bnlearn-3.8/bnlearn/src/pearson.x2.c | 4
bnlearn-3.8/bnlearn/src/per.node.score.c | 6
bnlearn-3.8/bnlearn/src/predict.c | 7
bnlearn-3.8/bnlearn/src/rbn.c | 8
bnlearn-3.8/bnlearn/src/rcont2.c | 3
bnlearn-3.8/bnlearn/src/sampling.c | 3
bnlearn-3.8/bnlearn/src/sanitization.c | 2
bnlearn-3.8/bnlearn/src/score.delta.c | 4
bnlearn-3.8/bnlearn/src/shd.c | 4
bnlearn-3.8/bnlearn/src/shrinkage.c | 7
bnlearn-3.8/bnlearn/src/simulation.c | 2
bnlearn-3.8/bnlearn/src/strings.c | 2
bnlearn-3.8/bnlearn/src/subsets.c | 5
bnlearn-3.8/bnlearn/src/symmetric.c | 3
bnlearn-3.8/bnlearn/src/tabu.c | 6
bnlearn-3.8/bnlearn/src/test.counter.c | 2
bnlearn-3.8/bnlearn/src/tiers.c | 4
bnlearn-3.8/bnlearn/src/utest.c | 7
bnlearn-3.8/bnlearn/src/which.max.c | 3
bnlearn-3.8/bnlearn/src/wishart.posterior.c | 8
103 files changed, 751 insertions(+), 455 deletions(-)
Title: 'TSdbi' Extensions to Wrap Miscellaneous Data Sources
Diff between TSmisc versions 2015.1-2 dated 2015-04-30 and 2015.1-3 dated 2015-05-02
Description: Methods to
retrieve data from several different sources. This include historical
quote data from Yahoo and Oanda, economic data from FRED, and xls and
csv data from different sources.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NAMESPACE | 5 +++--
NEWS | 6 ++++++
inst/testWithInternet/0serviceCheck-TSxls.R | 2 +-
5 files changed, 17 insertions(+), 10 deletions(-)
Title: Soundscape Ecology
Diff between soundecology versions 1.2 dated 2015-01-12 and 1.3 dated 2015-05-02
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NEWS | 6 ++++++
R/ndsi.R | 21 +++++++++++++++------
build/vignette.rds |binary
man/ndsi.Rd | 8 ++++++--
man/soundecology.package.Rd | 2 +-
7 files changed, 39 insertions(+), 20 deletions(-)
More information about survJamda.data at CRAN
Permanent link
Title: Dynamic Systems Estimation - Extensions
Diff between EvalEst versions 2012.4-1 dated 2012-05-03 and 2015.4-2 dated 2015-05-02
Description: Provides functions for evaluating (time series) model
estimation methods. These facilitate Monte Carlo experiments of repeated
simulations and estimations. Also provides methods for
looking at the distribution of the results from these experiments,
including model roots (which are an equivalence class invariant).
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 29 ++++++++++++++---------------
MD5 | 13 +++++++------
NAMESPACE | 2 +-
NEWS | 16 ++++++++++++++++
build |only
inst/doc/Guide.Stex | 8 +++-----
inst/doc/Guide.pdf |binary
vignettes/Guide.Stex | 8 +++-----
8 files changed, 44 insertions(+), 32 deletions(-)
Title: R Interface to W3C Markup Validation Services
Diff between W3CMarkupValidator versions 0.1-1 dated 2014-08-17 and 0.1-2 dated 2015-05-02
More information about W3CMarkupValidator at CRAN
Description:
R interface to a W3C Markup Validation service.
See
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/w3c.R | 4 ++++
3 files changed, 10 insertions(+), 6 deletions(-)
Permanent link
Title: Various R Programming Tools for Plotting Data
Diff between gplots versions 2.16.0 dated 2015-01-07 and 2.17.0 dated 2015-05-02
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary functionals
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to stats::lowess function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting Venn diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data sets on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes
gplots-2.16.0/gplots/man/smartlegend.Rd |only
gplots-2.17.0/gplots/ChangeLog | 83 ++++++++++++++++++++++
gplots-2.17.0/gplots/DESCRIPTION | 29 ++++++--
gplots-2.17.0/gplots/MD5 | 44 ++++++------
gplots-2.17.0/gplots/NAMESPACE | 4 -
gplots-2.17.0/gplots/NEWS | 46 ++++++++++++
gplots-2.17.0/gplots/R/boxplot2.R | 8 --
gplots-2.17.0/gplots/R/heatmap.2.R | 69 ++++++++++++-------
gplots-2.17.0/gplots/R/lmplot2.R | 5 -
gplots-2.17.0/gplots/R/overplot.R | 4 -
gplots-2.17.0/gplots/R/plotCI.R | 4 -
gplots-2.17.0/gplots/R/smartlegend.R | 5 +
gplots-2.17.0/gplots/R/venn.R | 23 ++++--
gplots-2.17.0/gplots/build/vignette.rds |binary
gplots-2.17.0/gplots/inst/ChangeLog | 83 ++++++++++++++++++++++
gplots-2.17.0/gplots/inst/NEWS | 46 ++++++++++++
gplots-2.17.0/gplots/inst/doc/venn.pdf |binary
gplots-2.17.0/gplots/man/balloonplot.Rd | 3
gplots-2.17.0/gplots/man/gplots-defunct.Rd |only
gplots-2.17.0/gplots/man/gplots-deprecated.Rd | 39 ++--------
gplots-2.17.0/gplots/man/heatmap.2.Rd | 94 ++++++++++++++++----------
gplots-2.17.0/gplots/man/lmplot2.Rd | 8 +-
gplots-2.17.0/gplots/man/sinkplot.Rd | 3
gplots-2.17.0/gplots/man/venn.Rd | 35 ++++++---
24 files changed, 477 insertions(+), 158 deletions(-)
Title: Cox-Type Models for Interval-Censored Data
Diff between coxinterval versions 1.1 dated 2015-04-27 and 1.2 dated 2015-05-02
Description: Fits Cox-type models based on interval-censored data from a survival
or illness-death process.
Author: Audrey Boruvka and Richard J. Cook
Maintainer: Audrey Boruvka
DESCRIPTION | 8 ++--
MD5 | 50 ++++++++++++-------------
NEWS | 16 +++++---
R/coxaalen.R | 10 ++---
R/coxaalen.control.R | 4 +-
R/coxdual.R | 7 ++-
R/print.coxinterval.R | 4 +-
R/print.summary.coxinterval.R | 16 +++++---
R/summary.coxinterval.R | 20 +++++-----
man/const2lin.Rd | 8 ++--
man/cosmesis.Rd | 2 -
man/coxaalen.Rd | 59 +++++++++++++++--------------
man/coxaalen.control.Rd | 41 ++++++++++++--------
man/coxdual.Rd | 83 +++++++++++++++++++++---------------------
man/coxdual.control.Rd | 12 +++---
man/dualic.Rd | 4 +-
man/dualrc.Rd | 4 +-
man/jump2step.Rd | 8 ++--
man/lin2const.Rd | 8 ++--
man/linapprox.Rd | 4 +-
man/step2jump.Rd | 6 +--
man/step2stepfun.Rd | 2 -
man/trans.Rd | 4 +-
src/coxdual.c | 10 ++---
src/rcplex.c | 37 ++++--------------
src/rcplex.h | 3 -
26 files changed, 216 insertions(+), 214 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Diff between paleotree versions 2.3 dated 2015-01-16 and 2.4 dated 2015-05-02
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst
CHANGELOG | 20 ++++
DESCRIPTION | 14 +--
MD5 | 175 +++++++++++++++++++++++-------------------
NAMESPACE | 17 +++-
R/DiversityCurves.R | 6 -
R/SamplingConv.R | 4
R/binTimeData.R | 2
R/cal3TimePaleoPhy.R | 56 +++++++++----
R/degradeTree.R | 58 ++++++++-----
R/expandTaxonTree.R | 5 -
R/fourDateFunctions.R |only
R/freqRat.R | 8 -
R/getSampProbDisc.R | 6 -
R/graptDisparity.R | 9 +-
R/graptPBDB.R |only
R/inverseSurv.R | 10 +-
R/makePBDBtaxonTree.R |only
R/minBranchLength.R | 6 -
R/minCharChange.R |only
R/modelMethods.R | 2
R/modifyTerminalBranches.R | 6 +
R/multiDiv.R | 32 ++++---
R/occData2timeList.R |only
R/paleotree-package.R | 7 +
R/parentChild2taxonTree.R |only
R/plotOccData.R |only
R/resolveTreeChar.R |only
R/retiolitinae.R | 46 ++++++++---
R/reverseList.R | 2
R/sampleRanges.R | 2
R/simFossilTaxa.R | 4
R/simPaleoTrees.R | 5 +
R/taxa2cladogram.R | 9 +-
R/taxa2phylo.R | 2
R/taxonSortPBDBocc.R |only
R/taxonTable2taxonTree.R |only
R/testEdgeMat.R |only
R/timeLadderTree.R | 1
R/timePaleoPhy.R | 35 ++++----
README | 14 +--
data/graptPBDB.rdata |only
data/retiolitinae.rdata |binary
man/DiversityCurves.Rd | 2
man/SamplingConv.Rd | 6 -
man/binTimeData.Rd | 5 -
man/branchClasses.Rd | 2
man/cal3TimePaleoPhy.Rd | 34 +++++---
man/cladogeneticTraitCont.Rd | 2
man/compareTimescaling.Rd | 2
man/constrainParPaleo.Rd | 2
man/dateNodes.Rd | 2
man/degradeTree.Rd | 25 +++---
man/depthRainbow.Rd | 2
man/durationFreq.Rd | 2
man/expandTaxonTree.Rd | 2
man/footeValues.Rd | 2
man/freqRat.Rd | 10 +-
man/getSampProbDisc.Rd | 8 -
man/getSampRateCont.Rd | 2
man/graptDisparity.Rd | 11 +-
man/graptPBDB.Rd |only
man/horizonSampRate.Rd | 2
man/inverseSurv.Rd | 12 +-
man/makePBDBtaxonTree.Rd |only
man/minBranchLength.Rd | 8 +
man/minCharChange.Rd |only
man/modelMethods.Rd | 2
man/modifyTerminalBranches.Rd | 8 +
man/multiDiv.Rd | 34 ++++----
man/nearestNeighborDist.Rd | 2
man/occData2timeList.Rd |only
man/optimPaleo.Rd | 2
man/paleotree-package.Rd | 7 +
man/parentChild2taxonTree.Rd |only
man/perCapitaRates.Rd | 2
man/perfectParsCharTree.Rd | 2
man/plotOccData.Rd |only
man/plotTraitgram.Rd | 2
man/pqr2Ps.Rd | 2
man/probAnc.Rd | 2
man/resolveTreeChar.Rd |only
man/retiolitinae.Rd | 39 ++++++---
man/reverseList.Rd | 2
man/rootSplit.Rd | 2
man/sampleRanges.Rd | 4
man/seqTimeList.Rd | 2
man/simFossilTaxa.Rd | 6 -
man/simFossilTaxa_SRCond.Rd | 2
man/simPaleoTrees.Rd | 2
man/taxa2cladogram.Rd | 11 +-
man/taxa2phylo.Rd | 2
man/taxonSortPBDBocc.Rd |only
man/taxonTable2taxonTree.Rd |only
man/termTaxa.Rd | 2
man/testEdgeMat.Rd |only
man/timeLadderTree.Rd | 3
man/timeList2fourDate.Rd |only
man/timePaleoPhy.Rd | 26 ++++--
man/timeSliceTree.Rd | 2
man/unitLengthTree.Rd | 2
100 files changed, 564 insertions(+), 314 deletions(-)
Title: Nonparametric Methods for Cognitive Diagnosis
Diff between NPCD versions 1.0-7 dated 2014-12-03 and 1.0-8 dated 2015-05-02
Description: An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre],
Chia-Yi Chiu [aut],
Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/AlphaNP.R | 4 ++--
inst/COPYRIGHTS | 2 +-
man/NPCD.Rd | 4 ++--
5 files changed, 14 insertions(+), 14 deletions(-)
More information about ig.vancouver.2014.topcolour at CRAN
Permanent link
Title: Time Series Factor Analysis
Diff between tsfa versions 2014.2-2 dated 2014-02-24 and 2014.10-1 dated 2015-05-01
Description: Extraction of Factors from Multivariate Time Series. See ?00tsfa-Intro for more details.
Author: Paul Gilbert and Erik Meijer
Maintainer: Paul Gilbert
DESCRIPTION | 13 +++++--------
MD5 | 10 +++++-----
NEWS | 4 ++++
R/tsfa.R | 2 +-
build/vignette.rds |binary
inst/doc/Guide.pdf |binary
6 files changed, 15 insertions(+), 14 deletions(-)
Title: Calculate Single Station Metabolism from Diurnal Oxygen Curves
Diff between StreamMetabolism versions 1.0 dated 2013-11-13 and 1.1 dated 2015-05-01
More information about StreamMetabolism at CRAN
Description: I provide functions to calculate Gross Primary Productivity, Net Ecocsystem Production, and Ecosystem Respiration from single station diurnal Oxygen curves.
Author: Stephen A Sefick Jr.
Maintainer: Stephen A Sefick Jr.
StreamMetabolism-1.0/StreamMetabolism/R/EcosystemProduction.20.R |only
StreamMetabolism-1.0/StreamMetabolism/R/EcosystemProduction.K.R |only
StreamMetabolism-1.0/StreamMetabolism/R/EcosystemProduction.R |only
StreamMetabolism-1.0/StreamMetabolism/R/rear.flux.R |only
StreamMetabolism-1.0/StreamMetabolism/R/window.chron.R |only
StreamMetabolism-1.0/StreamMetabolism/man/EcosystemProduction.20.Rd |only
StreamMetabolism-1.0/StreamMetabolism/man/EcosystemProduction.K.Rd |only
StreamMetabolism-1.0/StreamMetabolism/man/EcosystemProduction.Rd |only
StreamMetabolism-1.0/StreamMetabolism/man/StreamMetabolism-package.Rd |only
StreamMetabolism-1.0/StreamMetabolism/man/rear.flux.Rd |only
StreamMetabolism-1.0/StreamMetabolism/man/window.chron.Rd |only
StreamMetabolism-1.1/StreamMetabolism/DESCRIPTION | 15 ++----
StreamMetabolism-1.1/StreamMetabolism/MD5 | 24 +++-------
StreamMetabolism-1.1/StreamMetabolism/R/SM.R |only
StreamMetabolism-1.1/StreamMetabolism/R/window_chron.R |only
StreamMetabolism-1.1/StreamMetabolism/README.md |only
StreamMetabolism-1.1/StreamMetabolism/man/Kt.Rd | 6 +-
StreamMetabolism-1.1/StreamMetabolism/man/ODobbins.Rd | 2
StreamMetabolism-1.1/StreamMetabolism/man/SM.Rd |only
StreamMetabolism-1.1/StreamMetabolism/man/sunrise.set.Rd | 12 ++++-
StreamMetabolism-1.1/StreamMetabolism/man/window_chron.Rd |only
21 files changed, 30 insertions(+), 29 deletions(-)
Permanent link
Title: Components of Canadian Monetary and Credit Aggregates
Diff between CDNmoney versions 2012.4-1 dated 2012-05-03 and 2012.4-2 dated 2015-05-01
Description: Components of Canadian Credit Aggregates and Monetary Aggregates with continuity adjustments.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 10 ++++----
MD5 | 33 ++++++++++++++---------------
NEWS | 4 +++
build |only
data/CanadianCreditData.asof.28Jan2005.rda |binary
data/CanadianCreditData.asof.3Mar2006.rda |binary
data/CanadianCreditData.asof.5Jun2007.rda |binary
data/CanadianCreditData.asof.6Mar2009.rda |binary
data/CanadianCreditData.rda |binary
data/CanadianMoneyData.asof.26Aug2002.rda |binary
data/CanadianMoneyData.asof.28Jan2005.rda |binary
data/CanadianMoneyData.asof.3Mar2006.rda |binary
data/CanadianMoneyData.asof.5Jun2007.rda |binary
data/CanadianMoneyData.asof.6Feb2004.rda |binary
data/CanadianMoneyData.asof.6Mar2009.rda |binary
data/CanadianMoneyData.rda |binary
inst/doc/CDNmoney.pdf |binary
man/CanadianMoneyData.Rd | 9 +++++--
18 files changed, 32 insertions(+), 24 deletions(-)
Title: Work with GitHub Gists
Diff between gistr versions 0.1.0 dated 2015-01-04 and 0.2.0 dated 2015-05-01
Description: Work with GitHub gists from R (e.g.,
http://en.wikipedia.org/wiki/GitHub#Gist,
https://help.github.com/articles/about-gists/). A gist is simply one or
more files with code/text/images/etc. This package allows the user to
create new gists, update gists with new files, rename files, delete files,
get and delete gists, star and un-star gists, fork gists, open a gist in
your default browser, get embed code for a gist, list gist commits, and
get rate limit information when authenticated. Some requests require
authentication and some do not. Gists website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
gistr-0.1.0/gistr/inst/examples/alm_othersources.md |only
gistr-0.1.0/gistr/tests/testthat/test-gist_create.R |only
gistr-0.1.0/gistr/vignettes/img |only
gistr-0.2.0/gistr/DESCRIPTION | 14
gistr-0.2.0/gistr/MD5 | 105 ++++--
gistr-0.2.0/gistr/NAMESPACE | 32 +-
gistr-0.2.0/gistr/NEWS | 37 ++
gistr-0.2.0/gistr/R/commits.R | 7
gistr-0.2.0/gistr/R/forks.R | 9
gistr-0.2.0/gistr/R/gist.R | 26 +
gistr-0.2.0/gistr/R/gist_create.R | 179 +++++++++--
gistr-0.2.0/gistr/R/gist_create_obj.R |only
gistr-0.2.0/gistr/R/gist_map.R |only
gistr-0.2.0/gistr/R/gistr-package.R | 4
gistr-0.2.0/gistr/R/gists.R | 5
gistr-0.2.0/gistr/R/tabl.R |only
gistr-0.2.0/gistr/R/zzz.R | 67 +++-
gistr-0.2.0/gistr/README.md | 226 +++++++++-----
gistr-0.2.0/gistr/build/vignette.rds |binary
gistr-0.2.0/gistr/inst/doc/gistr_vignette.Rmd | 145 ++++-----
gistr-0.2.0/gistr/inst/doc/gistr_vignette.html | 244 +++++++---------
gistr-0.2.0/gistr/inst/examples/alm.md |only
gistr-0.2.0/gistr/inst/examples/artifacts_eg1.Rmd |only
gistr-0.2.0/gistr/inst/examples/ecoengine_eg.geojson |only
gistr-0.2.0/gistr/inst/examples/example1.R |only
gistr-0.2.0/gistr/inst/examples/example1.md |only
gistr-0.2.0/gistr/inst/examples/example2.R |only
gistr-0.2.0/gistr/inst/examples/file.png |only
gistr-0.2.0/gistr/inst/examples/plots.Rmd |only
gistr-0.2.0/gistr/inst/examples/plots.md |only
gistr-0.2.0/gistr/inst/examples/plots_imgur.Rmd |only
gistr-0.2.0/gistr/inst/examples/plots_imgur.Rnw |only
gistr-0.2.0/gistr/inst/examples/plots_imgur.md |only
gistr-0.2.0/gistr/inst/examples/rnw_example.Rnw |only
gistr-0.2.0/gistr/inst/examples/stuff.md | 34 +-
gistr-0.2.0/gistr/inst/ignore |only
gistr-0.2.0/gistr/inst/vign/gistr_vignette.Rmd | 10
gistr-0.2.0/gistr/inst/vign/gistr_vignette.md | 145 ++++-----
gistr-0.2.0/gistr/man/browse.Rd | 2
gistr-0.2.0/gistr/man/commits.Rd | 4
gistr-0.2.0/gistr/man/delete.Rd | 4
gistr-0.2.0/gistr/man/embed.Rd | 2
gistr-0.2.0/gistr/man/files.Rd | 4
gistr-0.2.0/gistr/man/fork.Rd | 2
gistr-0.2.0/gistr/man/forks.Rd | 3
gistr-0.2.0/gistr/man/gist.Rd | 20 +
gistr-0.2.0/gistr/man/gist_auth.Rd | 2
gistr-0.2.0/gistr/man/gist_create.Rd | 73 ++++
gistr-0.2.0/gistr/man/gist_create_obj.Rd |only
gistr-0.2.0/gistr/man/gist_map.Rd |only
gistr-0.2.0/gistr/man/gistr-package.Rd | 6
gistr-0.2.0/gistr/man/gists.Rd | 4
gistr-0.2.0/gistr/man/pipe.Rd | 2
gistr-0.2.0/gistr/man/rate_limit.Rd | 2
gistr-0.2.0/gistr/man/run.Rd | 2
gistr-0.2.0/gistr/man/star.Rd | 4
gistr-0.2.0/gistr/man/tabl.Rd |only
gistr-0.2.0/gistr/man/update.Rd | 4
gistr-0.2.0/gistr/tests/localtests |only
gistr-0.2.0/gistr/tests/testthat/figure |only
gistr-0.2.0/gistr/tests/testthat/test-commits.R | 2
gistr-0.2.0/gistr/tests/testthat/test-gist_create_obj.R |only
gistr-0.2.0/gistr/tests/testthat/test-rate_limit.R | 5
gistr-0.2.0/gistr/vignettes/gistr_vignette.Rmd | 145 ++++-----
64 files changed, 1008 insertions(+), 573 deletions(-)
Title: Companion Animal Population Management
Diff between capm versions 0.7.0 dated 2015-03-04 and 0.8.0 dated 2015-05-01
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero
DESCRIPTION | 10 ++--
MD5 | 68 +++++++++++++--------------
NAMESPACE | 2
NEWS | 27 +++++++++-
R/CalculatePopChange.R | 30 ++++++++----
R/PlotGlobalSens.R | 16 +++---
R/PlotLocalSens.R | 73 ++++++++++++++---------------
R/PlotModels.R | 86 +++++++++++++++++------------------
R/PlotPopPyramid.R | 12 ++--
R/SolveIASA.R | 2
R/SolveTC.R | 17 +++---
R/capm-package.R | 4 -
README.md | 7 --
inst/CITATION | 8 +--
man/Calculate2StageSampleSize.Rd | 2
man/CalculateGlobalSens.Rd | 2
man/CalculateLocalSens.Rd | 2
man/CalculatePopChange.Rd | 2
man/CalculateSimpleSampleSize.Rd | 2
man/CalculateStratifiedSampleSize.Rd | 2
man/DesignSurvey.Rd | 2
man/GraphicInterface.Rd | 2
man/MapkmlPSU.Rd | 2
man/PlotGlobalSens.Rd | 12 ++--
man/PlotLocalSens.Rd | 6 +-
man/PlotModels.Rd | 16 +++---
man/PlotPopPyramid.Rd | 12 ++--
man/SamplePPS.Rd | 2
man/SampleSystematic.Rd | 2
man/SetRanges.Rd | 2
man/SolveIASA.Rd | 2
man/SolveSI.Rd | 2
man/SolveTC.Rd | 6 +-
man/SummarySurvey.Rd | 2
man/capm-package.Rd | 6 +-
35 files changed, 240 insertions(+), 210 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.5.000.0 dated 2015-04-21 and 0.5.100.1.0 dated 2015-05-01
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 15 +
DESCRIPTION | 23 +-
MD5 | 39 ++--
inst/NEWS.Rd | 11 +
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/armadillo | 1
inst/include/armadillo_bits/Mat_bones.hpp | 3
inst/include/armadillo_bits/Mat_meat.hpp | 166 +++++++++++++++++++--
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/compiler_setup.hpp | 110 ++++++-------
inst/include/armadillo_bits/constants.hpp | 48 +++---
inst/include/armadillo_bits/constants_compat.hpp | 48 +++---
inst/include/armadillo_bits/fn_interp1.hpp |only
inst/include/armadillo_bits/glue_hist_meat.hpp | 34 +++-
inst/include/armadillo_bits/glue_histc_meat.hpp | 34 +++-
inst/include/armadillo_bits/mul_gemm.hpp | 6
inst/include/armadillo_bits/mul_gemv.hpp | 6
inst/include/armadillo_bits/op_sort_bones.hpp | 36 ++++
inst/include/armadillo_bits/op_sort_meat.hpp | 64 --------
inst/include/armadillo_bits/typedef_elem_check.hpp | 2
21 files changed, 428 insertions(+), 224 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-29 2013.8-2
2012-10-01 2012.8-1
2012-05-03 2012.4-1
2011-11-02 2011.11-1
2011-08-05 2011.7-1
2011-07-27 2011.6-1
2011-03-23 2011.3-1
2011-01-03 2010.12-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-29 2013.9-1
2012-10-01 2012.8-1
2012-05-03 2012.4-1
2011-11-28 2011.11-2
2011-11-03 2011.11-1
2011-07-27 2011.6-1
2011-03-23 2011.3-1
2010-12-22 2010.12-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-29 2013.9-1
2012-10-01 2012.8-1
2012-05-03 2012.4-1
2011-11-02 2011.11-1
2011-07-27 2011.6-1
2011-03-23 2011.3-1
2010-12-22 2010.12-1
2010-05-31 2010.5-1
2009-12-28 2009.12-1
2009-07-27 2009.7-1
2009-02-24 2009.1-1
2008-11-03 2008.11-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-29 2013.9-1
2012-10-01 2012.8-1
2012-05-03 2012.4-1
2011-11-28 2011.11-2
2011-11-02 2011.11-1
2011-08-05 2011.7-1
2011-07-27 2011.6-1
2011-03-23 2011.3-1
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.11.5 dated 2015-03-06 and 0.11.6 dated 2015-05-01
Description: The Rcpp package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about Rcpp is provided by several vignettes included in this package, via the
Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Douglas Bates, and John Chambers
Maintainer: Dirk Eddelbuettel
ChangeLog | 80 ++++++++
DESCRIPTION | 8
MD5 | 102 +++++-----
R/Attributes.R | 56 +++--
README.md | 11 -
build/Rcpp.pdf |binary
build/vignette.rds |binary
inst/NEWS.Rd | 21 ++
inst/doc/Rcpp-FAQ.R | 37 +--
inst/doc/Rcpp-FAQ.Rnw | 1
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-attributes.pdf |binary
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/include/Rcpp.h | 4
inst/include/Rcpp/Date.h | 98 +++++-----
inst/include/Rcpp/DateVector.h | 8
inst/include/Rcpp/Datetime.h | 110 +++++------
inst/include/Rcpp/DatetimeVector.h | 10 -
inst/include/Rcpp/InternalFunction.h | 16 -
inst/include/Rcpp/InternalFunctionWithStdFunction.h | 139 +++++++-------
inst/include/Rcpp/api/meat/Date.h | 7
inst/include/Rcpp/api/meat/Datetime.h | 27 +-
inst/include/Rcpp/api/meat/is.h | 169 ++++++++---------
inst/include/Rcpp/as.h | 122 ++++++------
inst/include/Rcpp/config.h | 6
inst/include/Rcpp/macros/macros.h | 38 ++-
inst/include/Rcpp/macros/xp.h | 6
inst/include/Rcpp/r/headers.h | 4
inst/include/Rcpp/utils/tinyformat.h | 6
inst/include/Rcpp/vector/00_forward_proxy.h | 4
inst/include/Rcpp/vector/Matrix.h | 4
inst/include/Rcpp/vector/Vector.h | 2
inst/include/Rcpp/vector/const_string_proxy.h | 1
inst/include/Rcpp/vector/string_proxy.h | 1
inst/include/Rcpp/vector/traits.h | 31 ++-
inst/include/RcppCommon.h | 57 ++---
inst/unitTests/cpp/Vector.cpp | 12 +
inst/unitTests/runit.Vector.R | 12 +
src/Makevars.win | 4
src/Module.cpp | 194 ++++++++++----------
src/Rcpp_init.cpp | 35 +--
src/api.cpp | 178 ++++++++----------
src/attributes.cpp | 133 +++++++------
src/barrier.cpp | 160 ++++++++--------
src/internal.h | 124 ++++++------
vignettes/Rcpp-FAQ.Rnw | 1
52 files changed, 1107 insertions(+), 932 deletions(-)
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Diff between PopGenome versions 2.1.0 dated 2014-11-03 and 2.1.5 dated 2015-05-01
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer
PopGenome-2.1.0/PopGenome/src/zlib |only
PopGenome-2.1.5/PopGenome/DESCRIPTION | 28 +
PopGenome-2.1.5/PopGenome/MD5 | 145 ++++------
PopGenome-2.1.5/PopGenome/NAMESPACE | 6
PopGenome-2.1.5/PopGenome/NEWS | 28 +
PopGenome-2.1.5/PopGenome/R/GEN.R | 9
PopGenome-2.1.5/PopGenome/R/GENOME.R | 8
PopGenome-2.1.5/PopGenome/R/GFF_split_into_scaffolds.R |only
PopGenome-2.1.5/PopGenome/R/MS.R | 8
PopGenome-2.1.5/PopGenome/R/PsPn.R | 4
PopGenome-2.1.5/PopGenome/R/VCF_split_into_scaffolds.R |only
PopGenome-2.1.5/PopGenome/R/Whop_readVCF.R | 10
PopGenome-2.1.5/PopGenome/R/calcR2.R | 2
PopGenome-2.1.5/PopGenome/R/calc_diversities.R | 2
PopGenome-2.1.5/PopGenome/R/calc_freqstats.R | 2
PopGenome-2.1.5/PopGenome/R/calc_freqstats_FAST.R | 2
PopGenome-2.1.5/PopGenome/R/calc_hwhafsth.R | 8
PopGenome-2.1.5/PopGenome/R/calc_miss.R |only
PopGenome-2.1.5/PopGenome/R/calc_phi_st.R | 2
PopGenome-2.1.5/PopGenome/R/coalsim.R | 4
PopGenome-2.1.5/PopGenome/R/concatenate.R | 12
PopGenome-2.1.5/PopGenome/R/count.unknowns.R |only
PopGenome-2.1.5/PopGenome/R/fisherextest.R | 8
PopGenome-2.1.5/PopGenome/R/fstcalc.R | 2
PopGenome-2.1.5/PopGenome/R/get.feature.names.R |only
PopGenome-2.1.5/PopGenome/R/get_data.R | 2
PopGenome-2.1.5/PopGenome/R/getsynnonsyndiff.R | 26 -
PopGenome-2.1.5/PopGenome/R/parse_gff.R | 2
PopGenome-2.1.5/PopGenome/R/popgen.R | 4
PopGenome-2.1.5/PopGenome/R/probabilities.R | 2
PopGenome-2.1.5/PopGenome/R/read.big.fasta.R | 2
PopGenome-2.1.5/PopGenome/R/readData.R | 6
PopGenome-2.1.5/PopGenome/R/readHapMap.R | 6
PopGenome-2.1.5/PopGenome/R/readSNP.R | 2
PopGenome-2.1.5/PopGenome/R/readVCF.R | 17 -
PopGenome-2.1.5/PopGenome/R/region.as.fasta.R | 35 ++
PopGenome-2.1.5/PopGenome/R/set.synnonsyn.R | 12
PopGenome-2.1.5/PopGenome/R/sliding.window.transform.new.R | 2
PopGenome-2.1.5/PopGenome/R/slim.R | 4
PopGenome-2.1.5/PopGenome/R/split.GFF.R | 24 +
PopGenome-2.1.5/PopGenome/R/split_data_into_GFF_attributes.R |only
PopGenome-2.1.5/PopGenome/R/splitting.data.R | 18 -
PopGenome-2.1.5/PopGenome/R/update_slim.R | 2
PopGenome-2.1.5/PopGenome/build/vignette.rds |binary
PopGenome-2.1.5/PopGenome/inst/COPYRIGHTS |only
PopGenome-2.1.5/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary
PopGenome-2.1.5/PopGenome/inst/doc/Integration_of_new_Methods.Rnw | 8
PopGenome-2.1.5/PopGenome/inst/doc/Integration_of_new_Methods.pdf |binary
PopGenome-2.1.5/PopGenome/inst/doc/Whole_genome_analyses_using_VCF_files.Rnw |only
PopGenome-2.1.5/PopGenome/inst/doc/Whole_genome_analyses_using_VCF_files.pdf |only
PopGenome-2.1.5/PopGenome/man/F_ST.stats-methods.Rd | 3
PopGenome-2.1.5/PopGenome/man/GENOME-class.Rd | 5
PopGenome-2.1.5/PopGenome/man/GFF_split_into_scaffolds.Rd |only
PopGenome-2.1.5/PopGenome/man/VCF_split_into_scaffolds.Rd |only
PopGenome-2.1.5/PopGenome/man/count.unknowns-methods.Rd |only
PopGenome-2.1.5/PopGenome/man/get.feature.names.Rd |only
PopGenome-2.1.5/PopGenome/man/readData.Rd | 4
PopGenome-2.1.5/PopGenome/man/readVCF.Rd | 2
PopGenome-2.1.5/PopGenome/man/region.as.fasta.Rd | 14
PopGenome-2.1.5/PopGenome/man/set.synnonsyn-methods.Rd | 6
PopGenome-2.1.5/PopGenome/man/split_data_into_GFF_attributes.Rd |only
PopGenome-2.1.5/PopGenome/src/Makevars | 11
PopGenome-2.1.5/PopGenome/src/Makevars.win | 60 ++--
PopGenome-2.1.5/PopGenome/src/VCF_split.cpp |only
PopGenome-2.1.5/PopGenome/src/myReadVCFC.c | 24 +
PopGenome-2.1.5/PopGenome/vignettes/2Lslide.pdf |only
PopGenome-2.1.5/PopGenome/vignettes/GenesTaj.pdf |only
PopGenome-2.1.5/PopGenome/vignettes/Integration_of_new_Methods.Rnw | 8
PopGenome-2.1.5/PopGenome/vignettes/SFS.pdf |only
PopGenome-2.1.5/PopGenome/vignettes/Whole_genome_analyses_using_VCF_files.Rnw |only
PopGenome-2.1.5/PopGenome/vignettes/nucFST.pdf |only
PopGenome-2.1.5/PopGenome/vignettes/nucFSTvsAll.pdf |only
72 files changed, 374 insertions(+), 227 deletions(-)
Title: Communication Between Editor and Viewer for Literate Programs
Diff between patchSynctex versions 0.1-1 dated 2015-05-01 and 0.1-2 dated 2015-05-01
Description: This utility eases the debugging of literate documents
('noweb' files) by patching the synchronization information
(the '.synctex(.gz)' file) produced by 'pdflatex' with
concordance information produced by 'Sweave' or 'knitr' and
'Sweave' or 'knitr' ; this allows for bilateral communication
between a text editor (visualizing the 'noweb' source) and
a viewer (visualizing the resultant 'PDF'), thus bypassing
the intermediate 'TeX' file.
Author: Jan Gleixner [aut],
Daniel Hicks [ctb],
Emmanuel Charpentier [aut, cre]
Maintainer: Emmanuel Charpentier
DESCRIPTION | 9 +++++----
MD5 | 5 +++--
NEWS | 4 +++-
README.md |only
4 files changed, 11 insertions(+), 7 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Diff between hsdar versions 0.1.2 dated 2015-04-08 and 0.1.3 dated 2015-05-01
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert
ChangeLog |only
DESCRIPTION | 10 +-
MD5 | 30 +++---
R/continuum_transform.R | 18 ++-
R/rededge.R | 37 +++-----
R/smgm.R |only
R/soilindex.R |only
R/vegindex.R | 157 +++++++++++++++++++++++++++-------
inst/doc/References.Rnw | 4
inst/doc/References.pdf |binary
man/hsdar-package.Rd | 2
man/rededge.Rd | 2
man/smgm.Rd |only
man/soilindex.Rd |only
man/vegindex.Rd | 56 ++++++++++--
src/smgm.f90 |only
vignettes/References.Rnw | 4
vignettes/References.tex | 4
vignettes/hsdar.bib | 214 +++++++++++++++++++++++++++++++++++++++++------
19 files changed, 426 insertions(+), 112 deletions(-)
Title: Graphical Reporting for Clinical Trials
Diff between greport versions 0.5-2 dated 2014-11-21 and 0.5-3 dated 2015-05-01
Description: Contains many functions useful for
monitoring and reporting the results of clinical trials and other
experiments in which treatments are compared. LaTeX is
used to typeset the resulting reports, recommended to be in the
context of 'knitr'. The 'Hmisc', 'ggplot2', and 'lattice' packages are used
by 'greport' for high-level graphics.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
greport-0.5-2/greport/tests/report.tex |only
greport-0.5-3/greport/DESCRIPTION | 19 +--
greport-0.5-3/greport/INDEX | 2
greport-0.5-3/greport/MD5 | 64 ++++++------
greport-0.5-3/greport/NAMESPACE | 6 -
greport-0.5-3/greport/NEWS | 22 ++++
greport-0.5-3/greport/R/Misc.r | 136 +++++++++++++++++++-------
greport-0.5-3/greport/R/accrualReport.r | 8 -
greport-0.5-3/greport/R/dReport.r | 79 ++++++++++++---
greport-0.5-3/greport/R/eReport.r | 4
greport-0.5-3/greport/R/exReport.r | 10 +
greport-0.5-3/greport/R/greport-package.r | 5
greport-0.5-3/greport/R/nriskReport.r | 6 -
greport-0.5-3/greport/R/survReport.r | 31 +++--
greport-0.5-3/greport/man/Merge.Rd | 3
greport-0.5-3/greport/man/accrualReport.Rd | 3
greport-0.5-3/greport/man/appsection.Rd |only
greport-0.5-3/greport/man/dNeedle.Rd | 3
greport-0.5-3/greport/man/dReport.Rd | 15 +-
greport-0.5-3/greport/man/eReport.Rd | 3
greport-0.5-3/greport/man/exReport.Rd | 3
greport-0.5-3/greport/man/getgreportOption.Rd | 3
greport-0.5-3/greport/man/greport.Rd | 3
greport-0.5-3/greport/man/latticeInit.Rd | 3
greport-0.5-3/greport/man/mfrowSuggest.Rd | 3
greport-0.5-3/greport/man/nriskReport.Rd | 3
greport-0.5-3/greport/man/putFig.Rd | 7 -
greport-0.5-3/greport/man/sampleFrac.Rd | 3
greport-0.5-3/greport/man/setgreportOption.Rd | 5
greport-0.5-3/greport/man/startPlot.Rd | 3
greport-0.5-3/greport/man/survReport.Rd | 10 +
greport-0.5-3/greport/man/upFirst.Rd | 11 +-
greport-0.5-3/greport/tests/report.Rnw | 18 ++-
greport-0.5-3/greport/tests/test.Rnw | 61 ++++++++---
34 files changed, 389 insertions(+), 166 deletions(-)
Title: Various R Programming Tools for Data Manipulation
Diff between gdata versions 2.13.3 dated 2014-04-06 and 2.16.1 dated 2015-05-01
Description: Various R programming tools for data manipulation, including:
- medical unit conversions ('ConvertMedUnits', 'MedUnits'),
- combining objects ('bindData', 'cbindX', 'combine', 'interleave'),
- character vector operations ('centerText', 'startsWith', 'trim'),
- factor manipulation ('levels', 'reorder.factor', 'mapLevels'),
- obtaining information about R objects ('object.size', 'elem', 'env',
'humanReadable', 'is.what', 'll', 'keep', 'ls.funs',
'Args','nPairs', 'nobs'),
- manipulating MS-Excel formatted files ('read.xls',
'installXLSXsupport', 'sheetCount', 'xlsFormats'),
- generating fixed-width format files ('write.fwf'),
- extricating components of date & time objects ('getYear', 'getMonth',
'getDay', 'getHour', 'getMin', 'getSec'),
- operations on columns of data frames ('matchcols', 'rename.vars'),
- matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'),
- operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'),
- operations on data frames ('frameApply', 'wideByFactor'),
- value of last evaluated expression ('ans'), and
- wrapper for 'sample' that ensures consistent behavior for both
scalar and vector arguments ('resample').
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
Magnusson, Jim Rogers, and others
Maintainer: Gregory R. Warnes
gdata-2.13.3/gdata/R/aggregate.table.R |only
gdata-2.13.3/gdata/inst/perl/Spreadsheet/XLSX |only
gdata-2.13.3/gdata/inst/perl/Spreadsheet/XLSX.pm |only
gdata-2.16.1/gdata/ChangeLog | 218 ++
gdata-2.16.1/gdata/DESCRIPTION | 35
gdata-2.16.1/gdata/MD5 | 121 -
gdata-2.16.1/gdata/NAMESPACE | 18
gdata-2.16.1/gdata/NEWS | 97
gdata-2.16.1/gdata/R/first.R |only
gdata-2.16.1/gdata/R/humanReadable.R |only
gdata-2.16.1/gdata/R/installXLSXsupport.R | 9
gdata-2.16.1/gdata/R/left.R |only
gdata-2.16.1/gdata/R/mapLevels.R | 6
gdata-2.16.1/gdata/R/object.size.R | 143 -
gdata-2.16.1/gdata/R/reorder.R | 26
gdata-2.16.1/gdata/R/trim.R | 4
gdata-2.16.1/gdata/R/write.fwf.R | 55
gdata-2.16.1/gdata/build/vignette.rds |binary
gdata-2.16.1/gdata/inst/ChangeLog | 218 ++
gdata-2.16.1/gdata/inst/NEWS | 97
gdata-2.16.1/gdata/inst/doc/mapLevels.pdf |binary
gdata-2.16.1/gdata/inst/doc/unknown.pdf |binary
gdata-2.16.1/gdata/inst/perl/Crypt |only
gdata-2.16.1/gdata/inst/perl/Digest |only
gdata-2.16.1/gdata/inst/perl/Graphics |only
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel.pm | 1039 +++++++---
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Cell.pm | 57
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Dump.pm | 13
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm | 44
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/FmtJapan.pm | 23
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/FmtJapan2.pm | 13
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/FmtUnicode.pm | 13
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Font.pm | 13
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Format.pm | 13
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/SaveParser.pm | 15
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/SaveParser/Workbook.pm | 54
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/SaveParser/Worksheet.pm | 16
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Utility.pm | 85
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Workbook.pm | 38
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseExcel/Worksheet.pm | 114 -
gdata-2.16.1/gdata/inst/perl/Spreadsheet/ParseXLSX.pm |only
gdata-2.16.1/gdata/inst/perl/XML |only
gdata-2.16.1/gdata/inst/perl/install_modules.pl | 4
gdata-2.16.1/gdata/inst/perl/module_tools.pl | 30
gdata-2.16.1/gdata/inst/perl/sheetCount.pl | 13
gdata-2.16.1/gdata/inst/perl/sheetNames.pl | 13
gdata-2.16.1/gdata/inst/perl/supportedFormats.pl | 4
gdata-2.16.1/gdata/inst/perl/xls2csv.pl | 93
gdata-2.16.1/gdata/inst/perl/xls2tab.pl | 93
gdata-2.16.1/gdata/inst/perl/xls2tsv.pl | 93
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile.xls |binary
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile.xlsx |binary
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile_1900.xls |only
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile_1900.xlsx |only
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile_1904.xls |only
gdata-2.16.1/gdata/inst/xls/ExampleExcelFile_1904.xlsx |only
gdata-2.16.1/gdata/inst/xls/wide.xls |only
gdata-2.16.1/gdata/inst/xls/wide.xlsx |only
gdata-2.16.1/gdata/man/first.Rd |only
gdata-2.16.1/gdata/man/humanReadable.Rd | 104 -
gdata-2.16.1/gdata/man/left.Rd |only
gdata-2.16.1/gdata/man/object.size.Rd | 122 -
gdata-2.16.1/gdata/man/reorder.Rd | 67
gdata-2.16.1/gdata/man/write.fwf.Rd | 21
gdata-2.16.1/gdata/tests/test.humanReadable.R |only
gdata-2.16.1/gdata/tests/test.humanReadable.Rout.save |only
gdata-2.16.1/gdata/tests/test.read.xls.R | 146 +
gdata-2.16.1/gdata/tests/test.read.xls.Rout.save | 358 ++-
gdata-2.16.1/gdata/tests/test.reorder.factor.R |only
gdata-2.16.1/gdata/tests/test.reorder.factor.Rout.save |only
gdata-2.16.1/gdata/tests/tests.write.fwf.Rout.save | 8
gdata-2.16.1/gdata/tests/unitTests/runit.write.fwf.R | 57
72 files changed, 2986 insertions(+), 837 deletions(-)
Title: 'TSdbi' Illustration
Diff between TSdata versions 2013.9-1 dated 2013-09-29 and 2015.4-1 dated 2015-05-01
Description: Illustrates the various 'TSdbi' packages with a vignette using time series
data from several sources. The vignette also illustrates some simple time series
manipulation and plotting using packages 'tframe' and 'tfplot'.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 28
MD5 | 21
NAMESPACE | 5
NEWS | 16
build |only
inst/doc/Guide.Stex | 985 +++++++++++++++++-----------
inst/doc/Guide.bib | 32
inst/doc/Guide.pdf |binary
inst/doc/GuideAppendix.Stex |only
inst/doc/GuideAppendix.pdf |only
tests |only
vignettes/Guide.Stex | 1486 +++++++++++++++----------------------------
vignettes/Guide.bib | 32
vignettes/GuideAppendix.Stex |only
14 files changed, 1227 insertions(+), 1378 deletions(-)
Title: Tests for Uniformity
Diff between uniftest versions 1.0 dated 2014-12-24 and 1.1 dated 2015-05-01
Description: Goodness-of-fit tests for the uniform distribution.
Author: Maxim Melnik, Ruslan Pusev
Maintainer: Ruslan Pusev
uniftest-1.0/uniftest/R/sherman.unif.test.R |only
uniftest-1.1/uniftest/DESCRIPTION | 11 ++++++-----
uniftest-1.1/uniftest/MD5 | 20 ++++++++++++++++----
uniftest-1.1/uniftest/NAMESPACE | 3 +--
uniftest-1.1/uniftest/R/dudewicz.unif.test.r |only
uniftest-1.1/uniftest/R/hegazy.unif.test.r |only
uniftest-1.1/uniftest/R/kolmogorov.unif.test.r |only
uniftest-1.1/uniftest/R/kuiper.unif.test.r |only
uniftest-1.1/uniftest/R/neyman.unif.test.r |only
uniftest-1.1/uniftest/R/quesenberry.unif.test.r | 8 ++++----
uniftest-1.1/uniftest/R/sarkadi.unif.test.r |only
uniftest-1.1/uniftest/R/sherman.unif.test.r |only
uniftest-1.1/uniftest/man/dudewicz.unif.test.Rd |only
uniftest-1.1/uniftest/man/hegazy.unif.test.Rd |only
uniftest-1.1/uniftest/man/kolmogorov.unif.test.Rd |only
uniftest-1.1/uniftest/man/kuiper.unif.test.Rd |only
uniftest-1.1/uniftest/man/neyman.unif.test.Rd |only
uniftest-1.1/uniftest/man/sarkadi.unif.test.Rd |only
18 files changed, 27 insertions(+), 15 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Diff between rsdmx versions 0.4-5 dated 2015-02-14 and 0.4-6 dated 2015-05-01
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel
DESCRIPTION | 49 +++--
MD5 | 56 +++---
NAMESPACE | 5
R/Class-SDMX.R | 6
R/Class-SDMXDimension.R | 2
R/Class-SDMXFooter.R |only
R/Class-SDMXFooterMessage.R |only
R/Class-SDMXHeader.R | 4
R/SDMX-methods.R | 12 +
R/SDMXCode-methods.R | 1
R/SDMXCompactData-methods.R | 2
R/SDMXComponents-methods.R | 51 ++++--
R/SDMXDimension-methods.R | 125 +++++++++++----
R/SDMXFooter-methods.R |only
R/SDMXFooterMessage-methods.R |only
R/SDMXGenericData-methods.R | 14 +
R/SDMXHeader-methods.R | 14 -
R/SDMXPrimaryMeasure-methods.R | 73 +++++++-
R/SDMXSchema-methods.R | 2
R/SDMXStructureType-methods.R | 3
R/SDMXTimeDimension-methods.R | 97 +++++++++--
R/readSDMX.R | 27 ++-
README.md | 2
inst/extdata/SDMXDataStructureDefinition_Example_2.1.xml |only
inst/extdata/SDMXDataStructures_Example_2.1.xml |only
inst/extdata/SDMXMessageExample_2.1.xml | 11 +
man/SDMX-class.Rd | 4
man/SDMXFooter-class.Rd |only
man/SDMXFooterMessage-class.Rd |only
man/getSDMXFooter-methods.Rd |only
man/rsdmx-package.Rd | 4
tests/testthat/test_DataStructureDefinition.R | 12 +
tests/testthat/test_DataStructures.R | 10 +
tests/testthat/test_Footer.R |only
34 files changed, 438 insertions(+), 148 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Diff between RNeXML versions 2.0.1 dated 2014-12-26 and 2.0.2 dated 2015-05-01
Description: Provides access to phyloinformatic data in NeXML format. The
package should add new functionality to R such as the possibility to
manipulate NeXML objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger
RNeXML-2.0.1/RNeXML/inst/doc/tutorial.R |only
RNeXML-2.0.1/RNeXML/inst/doc/tutorial.Rmd |only
RNeXML-2.0.1/RNeXML/inst/doc/tutorial.html |only
RNeXML-2.0.1/RNeXML/vignettes/Makefile |only
RNeXML-2.0.1/RNeXML/vignettes/figure |only
RNeXML-2.0.1/RNeXML/vignettes/tutorial.Rmd |only
RNeXML-2.0.1/RNeXML/vignettes/tutorial.md |only
RNeXML-2.0.2/RNeXML/DESCRIPTION | 18 -
RNeXML-2.0.2/RNeXML/MD5 | 156 +++++++------
RNeXML-2.0.2/RNeXML/NAMESPACE | 2
RNeXML-2.0.2/RNeXML/NEWS | 13 +
RNeXML-2.0.2/RNeXML/R/add_basic_meta.R | 4
RNeXML-2.0.2/RNeXML/R/get_rdf.R | 9
RNeXML-2.0.2/RNeXML/R/internal_nexml_id.R | 10
RNeXML-2.0.2/RNeXML/R/nexml_publish.R | 16 -
RNeXML-2.0.2/RNeXML/README.md | 174 +++++++--------
RNeXML-2.0.2/RNeXML/build/vignette.rds |binary
RNeXML-2.0.2/RNeXML/inst/doc/S4.R |only
RNeXML-2.0.2/RNeXML/inst/doc/S4.Rmd |only
RNeXML-2.0.2/RNeXML/inst/doc/S4.html |only
RNeXML-2.0.2/RNeXML/inst/doc/metadata.R |only
RNeXML-2.0.2/RNeXML/inst/doc/metadata.Rmd |only
RNeXML-2.0.2/RNeXML/inst/doc/metadata.html |only
RNeXML-2.0.2/RNeXML/inst/doc/simmap.R |only
RNeXML-2.0.2/RNeXML/inst/doc/simmap.Rmd |only
RNeXML-2.0.2/RNeXML/inst/doc/simmap.html |only
RNeXML-2.0.2/RNeXML/inst/doc/sparql.R |only
RNeXML-2.0.2/RNeXML/inst/doc/sparql.Rmd |only
RNeXML-2.0.2/RNeXML/inst/doc/sparql.html |only
RNeXML-2.0.2/RNeXML/inst/simmap.md | 22 -
RNeXML-2.0.2/RNeXML/man/add_basic_meta.Rd | 8
RNeXML-2.0.2/RNeXML/man/add_characters.Rd | 2
RNeXML-2.0.2/RNeXML/man/add_meta.Rd | 2
RNeXML-2.0.2/RNeXML/man/add_namespaces.Rd | 2
RNeXML-2.0.2/RNeXML/man/add_trees.Rd | 2
RNeXML-2.0.2/RNeXML/man/c-ListOfmeta-method.Rd | 2
RNeXML-2.0.2/RNeXML/man/c-meta-method.Rd | 2
RNeXML-2.0.2/RNeXML/man/c-nexml-method.Rd | 2
RNeXML-2.0.2/RNeXML/man/flatten_multiphylo.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_characters.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_characters_list.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_citation.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_flat_trees.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_license.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_metadata.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_namespaces.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_rdf.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_taxa.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_taxa_list.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_taxa_meta.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_taxa_meta_list.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_trees.Rd | 2
RNeXML-2.0.2/RNeXML/man/get_trees_list.Rd | 2
RNeXML-2.0.2/RNeXML/man/meta.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_add.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_figshare.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_get.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_publish.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_read.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_to_simmap.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_validate.Rd | 2
RNeXML-2.0.2/RNeXML/man/nexml_write.Rd | 2
RNeXML-2.0.2/RNeXML/man/reset_id_counter.Rd | 2
RNeXML-2.0.2/RNeXML/man/simmap_ex.Rd | 2
RNeXML-2.0.2/RNeXML/man/simmap_to_nexml.Rd | 2
RNeXML-2.0.2/RNeXML/man/taxize_nexml.Rd | 2
RNeXML-2.0.2/RNeXML/man/toPhylo.Rd | 2
RNeXML-2.0.2/RNeXML/tests/test-all.R | 10
RNeXML-2.0.2/RNeXML/tests/testthat/conversions.R | 3
RNeXML-2.0.2/RNeXML/tests/testthat/geiger_test.R | 2
RNeXML-2.0.2/RNeXML/tests/testthat/helper-RNeXML.R |only
RNeXML-2.0.2/RNeXML/tests/testthat/test_ape.R | 9
RNeXML-2.0.2/RNeXML/tests/testthat/test_characters.R | 2
RNeXML-2.0.2/RNeXML/tests/testthat/test_comp_analysis.R | 1
RNeXML-2.0.2/RNeXML/tests/testthat/test_get_characters.R | 4
RNeXML-2.0.2/RNeXML/tests/testthat/test_inheritance.R | 2
RNeXML-2.0.2/RNeXML/tests/testthat/test_meta.R | 2
RNeXML-2.0.2/RNeXML/tests/testthat/test_meta_extract.R | 1
RNeXML-2.0.2/RNeXML/tests/testthat/test_parsing.R | 2
RNeXML-2.0.2/RNeXML/tests/testthat/test_publish.R | 1
RNeXML-2.0.2/RNeXML/tests/testthat/test_serializing.R | 3
RNeXML-2.0.2/RNeXML/tests/testthat/test_simmap.R | 1
RNeXML-2.0.2/RNeXML/tests/testthat/test_taxonomy.R | 3
RNeXML-2.0.2/RNeXML/tests/testthat/test_toplevel_api.R | 7
RNeXML-2.0.2/RNeXML/tests/testthat/test_validate.R | 1
RNeXML-2.0.2/RNeXML/tests/testthat/treebase_test.R | 4
RNeXML-2.0.2/RNeXML/vignettes/S4.Rmd |only
RNeXML-2.0.2/RNeXML/vignettes/metadata.Rmd |only
RNeXML-2.0.2/RNeXML/vignettes/references.bib |only
RNeXML-2.0.2/RNeXML/vignettes/simmap.Rmd |only
RNeXML-2.0.2/RNeXML/vignettes/sparql.Rmd |only
91 files changed, 256 insertions(+), 306 deletions(-)
Title: 3D Visualization Using OpenGL
Diff between rgl versions 0.95.1201 dated 2014-12-21 and 0.95.1247 dated 2015-05-01
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler
Maintainer: Duncan Murdoch
DESCRIPTION | 8
MD5 | 60
NAMESPACE | 22
R/Sweave_knitr.R |only
R/animate.R | 3
R/callbacks.R | 6
R/device.R | 104
R/interpSetter.R |only
R/webGL.R | 1134 ++++---
R/webGLcontrols.R |only
build/vignette.rds |binary
inst/NEWS | 27
inst/WebGL/template.html | 34
inst/doc/WebGL.R |only
inst/doc/WebGL.Rmd |only
inst/doc/WebGL.html |only
inst/doc/rgl.Rmd | 29
inst/doc/rgl.html | 7329 ++++++++++++++++++++++++++---------------------
man/3dobjects.Rd | 6
man/ageSetter.Rd |only
man/callbacks.Rd | 15
man/hook_rgl.Rd |only
man/par3d.Rd | 2
man/propertySetter.Rd |only
man/rgl-package.Rd | 3
man/rgl.Sweave.Rd | 6
man/rgl.useNULL.Rd | 8
man/webGLcontrols.Rd |only
man/writeWebGL.Rd | 31
src/ABCLineSet.cpp | 35
src/api.h | 2
src/callbacks.cpp | 50
src/init.cpp | 2
vignettes/WebGL.Rmd |only
vignettes/WebGL.md |only
vignettes/rgl.Rmd | 29
vignettes/setup.R | 66
37 files changed, 5177 insertions(+), 3834 deletions(-)
Title: Quality Improvement Charts
Diff between qicharts versions 0.1.1 dated 2014-11-11 and 0.1.3 dated 2015-05-01
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej
qicharts-0.1.1/qicharts/vignettes/figure |only
qicharts-0.1.3/qicharts/DESCRIPTION | 14
qicharts-0.1.3/qicharts/MD5 | 31 -
qicharts-0.1.3/qicharts/NAMESPACE | 2
qicharts-0.1.3/qicharts/NEWS | 54 ++
qicharts-0.1.3/qicharts/R/paretochart.R | 160 ++++----
qicharts-0.1.3/qicharts/R/qic.R | 311 +++++++++++-----
qicharts-0.1.3/qicharts/R/trc.R | 266 ++++++++------
qicharts-0.1.3/qicharts/build/vignette.rds |binary
qicharts-0.1.3/qicharts/inst/doc/runcharts.R | 110 ++---
qicharts-0.1.3/qicharts/inst/doc/runcharts.html | 444 ++++++++++++------------
qicharts-0.1.3/qicharts/man/paretochart.Rd | 3
qicharts-0.1.3/qicharts/man/qic.Rd | 47 +-
qicharts-0.1.3/qicharts/man/trc.Rd | 27 -
14 files changed, 828 insertions(+), 641 deletions(-)
Title: Communication Between Editor and Viewer for Literate Programs
Diff between patchSynctex versions 0.1-0 dated 2015-01-11 and 0.1-1 dated 2015-05-01
Description: This utility eases the debugging of literate documents
('noweb' files) by patching the synchronization information
(the '.synctex(.gz)' file) produced by 'pdflatex' with
concordance information produced by 'Sweave' or 'knitr' and
'Sweave' or 'knitr' ; this allows for bilateral communication
between a text editor (visualizing the 'noweb' source) and
a viewer (visualizing the resultant 'PDF'), thus bypassing
the intermediate 'TeX' file.
Author: Jan Gleixner [aut],
Daniel Hicks [ctb],
Emmanuel Charpentier [aut, cre]
Maintainer: Emmanuel Charpentier
.Rinstignore |only
DESCRIPTION | 26 ++++++++++++++------------
MD5 | 5 +++--
NEWS |only
R/patchSynctex.R | 11 +++++++++--
5 files changed, 26 insertions(+), 16 deletions(-)
Title: Analysis of Multiple Social Networks with Algebra
Diff between multiplex versions 1.2 dated 2014-02-06 and 1.5 dated 2015-05-01
Description: Algebraic procedures for the analysis of multiple social networks
are delivered with this package. Among other things, it is possible to
create and manipulate multivariate network data with different formats,
and there are effective ways available to treat multiple networks with
routines that combine algebraic systems like the partially ordered
semigroup or the semiring structure together with the relational bundles
occurring in different types of multivariate network data sets. As well an
algebraic approach for two-mode networks is made through Galois
derivations between families of the pair of subsets.
Author: J. Antonio Rivero Ostoic
Maintainer: Antonio Rivero Ostoic
multiplex-1.2/multiplex/R/orden.R |only
multiplex-1.2/multiplex/R/po.levels.R |only
multiplex-1.2/multiplex/man/orden.Rd |only
multiplex-1.2/multiplex/man/po.levels.Rd |only
multiplex-1.5/multiplex/DESCRIPTION | 30
multiplex-1.5/multiplex/MD5 | 177 +--
multiplex-1.5/multiplex/NAMESPACE | 1
multiplex-1.5/multiplex/R/as.semigroup.R | 41
multiplex-1.5/multiplex/R/as.strings.R | 16
multiplex-1.5/multiplex/R/bundle.census.R | 609 ++++++-----
multiplex-1.5/multiplex/R/bundles.R | 1218 ++++++++++++-----------
multiplex-1.5/multiplex/R/cngr.R | 98 -
multiplex-1.5/multiplex/R/convert.R | 75 -
multiplex-1.5/multiplex/R/cph.R | 24
multiplex-1.5/multiplex/R/decomp.R | 239 ++--
multiplex-1.5/multiplex/R/dhc.R | 24
multiplex-1.5/multiplex/R/diagram.R | 21
multiplex-1.5/multiplex/R/diagram.levels.R |only
multiplex-1.5/multiplex/R/dichot.R | 2
multiplex-1.5/multiplex/R/edgeT.R | 17
multiplex-1.5/multiplex/R/expos.R | 405 +++----
multiplex-1.5/multiplex/R/galois.R |only
multiplex-1.5/multiplex/R/hierar.R | 157 +-
multiplex-1.5/multiplex/R/iinc.R | 2
multiplex-1.5/multiplex/R/is.mc.R | 4
multiplex-1.5/multiplex/R/isom.R | 18
multiplex-1.5/multiplex/R/jnt.R | 31
multiplex-1.5/multiplex/R/ltlw.R | 290 ++---
multiplex-1.5/multiplex/R/men.R | 13
multiplex-1.5/multiplex/R/ngbs.R | 28
multiplex-1.5/multiplex/R/pacnet.R | 501 ++++-----
multiplex-1.5/multiplex/R/partial.order.R | 124 +-
multiplex-1.5/multiplex/R/perm.R | 67 -
multiplex-1.5/multiplex/R/pi.rels.R | 100 -
multiplex-1.5/multiplex/R/prev.R | 211 +--
multiplex-1.5/multiplex/R/print.reduced.R |only
multiplex-1.5/multiplex/R/rbox.R | 590 +++++------
multiplex-1.5/multiplex/R/read.gml.R | 267 +++--
multiplex-1.5/multiplex/R/read.srt.R | 371 +++----
multiplex-1.5/multiplex/R/redl.R |only
multiplex-1.5/multiplex/R/reduc.R | 154 --
multiplex-1.5/multiplex/R/reducs.R | 195 +--
multiplex-1.5/multiplex/R/rel.sys.R | 112 +-
multiplex-1.5/multiplex/R/relabel.R | 38
multiplex-1.5/multiplex/R/rm.isol.R | 245 ++--
multiplex-1.5/multiplex/R/semigroup.R | 378 +++----
multiplex-1.5/multiplex/R/semiring.R | 408 +++----
multiplex-1.5/multiplex/R/signed.R | 220 +---
multiplex-1.5/multiplex/R/slc.R | 53 -
multiplex-1.5/multiplex/R/sprt.R | 266 ++---
multiplex-1.5/multiplex/R/strings.R | 561 +++++-----
multiplex-1.5/multiplex/R/summaryBundles.R | 736 +++++++------
multiplex-1.5/multiplex/R/swp.R | 12
multiplex-1.5/multiplex/R/symclos.R | 67 -
multiplex-1.5/multiplex/R/tclos.R | 54 -
multiplex-1.5/multiplex/R/transf.R | 171 +--
multiplex-1.5/multiplex/R/transl.R | 128 +-
multiplex-1.5/multiplex/R/wordT.R | 19
multiplex-1.5/multiplex/R/write.dat.R | 48
multiplex-1.5/multiplex/R/write.dl.R | 154 +-
multiplex-1.5/multiplex/R/write.gml.R | 159 +--
multiplex-1.5/multiplex/R/write.srt.R | 109 +-
multiplex-1.5/multiplex/R/zbind.R | 114 +-
multiplex-1.5/multiplex/R/zbnd.R | 45
multiplex-1.5/multiplex/build |only
multiplex-1.5/multiplex/inst/CHANGELOG | 49
multiplex-1.5/multiplex/inst/doc |only
multiplex-1.5/multiplex/man/bundle.census.Rd | 12
multiplex-1.5/multiplex/man/bundles.Rd | 24
multiplex-1.5/multiplex/man/convert.Rd | 2
multiplex-1.5/multiplex/man/dhc.Rd | 47
multiplex-1.5/multiplex/man/diagram.Rd | 20
multiplex-1.5/multiplex/man/diagram.levels.Rd |only
multiplex-1.5/multiplex/man/galois.Rd |only
multiplex-1.5/multiplex/man/jnt.Rd | 39
multiplex-1.5/multiplex/man/men.Rd | 50
multiplex-1.5/multiplex/man/multiplex-package.Rd | 6
multiplex-1.5/multiplex/man/ngbs.Rd | 36
multiplex-1.5/multiplex/man/partial.order.Rd | 24
multiplex-1.5/multiplex/man/print.reduced.Rd |only
multiplex-1.5/multiplex/man/read.gml.Rd | 21
multiplex-1.5/multiplex/man/redl.Rd |only
multiplex-1.5/multiplex/man/reduc.Rd | 1
multiplex-1.5/multiplex/man/reducs.Rd | 42
multiplex-1.5/multiplex/man/rel.sys.Rd | 6
multiplex-1.5/multiplex/man/slc.Rd | 36
multiplex-1.5/multiplex/man/sprt.Rd | 39
multiplex-1.5/multiplex/man/strings.Rd | 6
multiplex-1.5/multiplex/man/summaryBundles.Rd | 10
multiplex-1.5/multiplex/man/swp.Rd | 49
multiplex-1.5/multiplex/man/symclos.Rd | 36
multiplex-1.5/multiplex/man/tclos.Rd | 38
multiplex-1.5/multiplex/man/transf.Rd | 8
multiplex-1.5/multiplex/man/transl.Rd | 38
multiplex-1.5/multiplex/man/zbnd.Rd | 39
multiplex-1.5/multiplex/vignettes |only
96 files changed, 5409 insertions(+), 5486 deletions(-)
Title: Symbolic Computation and More with Multivariate Polynomials
Diff between mpoly versions 0.0.5 dated 2014-04-29 and 0.1.0 dated 2015-05-01
Description: Data structures, operations, and functions for the symbolic
manipulation of multivariate polynomials.
Author: David Kahle [aut, cre]
Maintainer: David Kahle
mpoly-0.0.5/mpoly/R/mpolyAdd.R |only
mpoly-0.0.5/mpoly/R/mpolyExp.R |only
mpoly-0.0.5/mpoly/R/mpolyListAdd.R |only
mpoly-0.0.5/mpoly/R/mpolyListProd.R |only
mpoly-0.0.5/mpoly/R/mpolyProd.R |only
mpoly-0.0.5/mpoly/man/mpolyAdd.Rd |only
mpoly-0.0.5/mpoly/man/mpolyExp.Rd |only
mpoly-0.0.5/mpoly/man/mpolyListAdd.Rd |only
mpoly-0.0.5/mpoly/man/mpolyListProd.Rd |only
mpoly-0.0.5/mpoly/man/mpolyListSub.Rd |only
mpoly-0.0.5/mpoly/man/mpolyProd.Rd |only
mpoly-0.0.5/mpoly/man/mpolySub.Rd |only
mpoly-0.1.0/mpoly/DESCRIPTION | 29
mpoly-0.1.0/mpoly/MD5 | 111 +--
mpoly-0.1.0/mpoly/NAMESPACE | 14
mpoly-0.1.0/mpoly/NEWS | 17
mpoly-0.1.0/mpoly/R/as.function.mpoly.R | 14
mpoly-0.1.0/mpoly/R/as.function.mpolyList.R | 18
mpoly-0.1.0/mpoly/R/as.mpoly.R | 66 +
mpoly-0.1.0/mpoly/R/burst.R | 143 +---
mpoly-0.1.0/mpoly/R/deriv.mpoly.R | 4
mpoly-0.1.0/mpoly/R/grobner.R | 15
mpoly-0.1.0/mpoly/R/is.linear.R |only
mpoly-0.1.0/mpoly/R/is.mpoly.R | 8
mpoly-0.1.0/mpoly/R/mp.R | 863 ++++++++++++++++---------
mpoly-0.1.0/mpoly/R/mpoly.R | 219 +++---
mpoly-0.1.0/mpoly/R/mpolyArithmetic.R |only
mpoly-0.1.0/mpoly/R/mpolyEqual.R | 31
mpoly-0.1.0/mpoly/R/mpolyList.R | 6
mpoly-0.1.0/mpoly/R/mpolyListArithmetic.R |only
mpoly-0.1.0/mpoly/R/partitions.R | 5
mpoly-0.1.0/mpoly/R/permutations.R | 28
mpoly-0.1.0/mpoly/R/print.mpoly.R | 7
mpoly-0.1.0/mpoly/R/reorder.mpoly.R | 21
mpoly-0.1.0/mpoly/R/round.mpoly.R |only
mpoly-0.1.0/mpoly/R/tuples.R | 8
mpoly-0.1.0/mpoly/R/zzz.r | 3
mpoly-0.1.0/mpoly/README.md |only
mpoly-0.1.0/mpoly/man/LCM.Rd | 9
mpoly-0.1.0/mpoly/man/as.function.mpoly.Rd | 17
mpoly-0.1.0/mpoly/man/as.function.mpolyList.Rd | 20
mpoly-0.1.0/mpoly/man/as.mpoly.Rd | 42 -
mpoly-0.1.0/mpoly/man/burst.Rd | 20
mpoly-0.1.0/mpoly/man/deriv.mpoly.Rd | 11
mpoly-0.1.0/mpoly/man/gradient.Rd | 4
mpoly-0.1.0/mpoly/man/grobner.Rd | 20
mpoly-0.1.0/mpoly/man/insert.Rd | 8
mpoly-0.1.0/mpoly/man/is.linear.Rd |only
mpoly-0.1.0/mpoly/man/is.mpoly.Rd | 4
mpoly-0.1.0/mpoly/man/is.mpolyList.Rd | 4
mpoly-0.1.0/mpoly/man/is.wholenumber.Rd | 7
mpoly-0.1.0/mpoly/man/mp.Rd | 109 ---
mpoly-0.1.0/mpoly/man/mpoly.Rd | 33
mpoly-0.1.0/mpoly/man/mpolyArithmetic.Rd |only
mpoly-0.1.0/mpoly/man/mpolyEqual.Rd | 25
mpoly-0.1.0/mpoly/man/mpolyList.Rd | 4
mpoly-0.1.0/mpoly/man/mpolyListArithmetic.Rd |only
mpoly-0.1.0/mpoly/man/partitions.Rd | 9
mpoly-0.1.0/mpoly/man/permutations.Rd | 7
mpoly-0.1.0/mpoly/man/print.mpoly.Rd | 18
mpoly-0.1.0/mpoly/man/print.mpolyList.Rd | 14
mpoly-0.1.0/mpoly/man/reorder.mpoly.Rd | 15
mpoly-0.1.0/mpoly/man/round.mpoly.Rd |only
mpoly-0.1.0/mpoly/man/terms.mpoly.Rd | 6
mpoly-0.1.0/mpoly/man/tuples.Rd | 9
mpoly-0.1.0/mpoly/man/vars.Rd | 4
mpoly-0.1.0/mpoly/tests |only
67 files changed, 1154 insertions(+), 895 deletions(-)
Title: Support Functions and Data for "Ecological Models and Data"
Diff between emdbook versions 1.3.7 dated 2015-01-12 and 1.3.8 dated 2015-05-01
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker
Maintainer: Ben Bolker
DESCRIPTION | 12 ++++++------
MD5 | 7 ++++---
inst/NEWS.Rd | 7 +++++++
man/Damsel.Rd | 10 +++++-----
man/GobySurvival.Rd |only
5 files changed, 22 insertions(+), 14 deletions(-)
Title: General Purpose Interface to Elasticsearch
Diff between elastic versions 0.3.0 dated 2015-01-29 and 0.4.0 dated 2015-05-01
Description: Connect to Elasticsearch, a NoSQL database built on the Java Virtual Machine.
Interacts with the Elasticsearch HTTP API (http://elasticsearch.org), including
functions for setting connection details to Elasticsearch instances, loading bulk
data, searching for documents with both HTTP query variables and JSON based body
requests. In addition, elastic provides functions for interacting with APIs for
indices, documents, nodes, clusters, an interface to the cat API, and more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
elastic-0.3.0/elastic/R/benchmark.R |only
elastic-0.3.0/elastic/R/search.r |only
elastic-0.3.0/elastic/man/benchmark.Rd |only
elastic-0.3.0/elastic/tests/testthat/test-search.r |only
elastic-0.4.0/elastic/DESCRIPTION | 26 +-
elastic-0.4.0/elastic/MD5 | 163 ++++++++-------
elastic-0.4.0/elastic/NAMESPACE | 8
elastic-0.4.0/elastic/NEWS | 42 ++++
elastic-0.4.0/elastic/R/Search.R |only
elastic-0.4.0/elastic/R/Search_uri.R |only
elastic-0.4.0/elastic/R/alias.R | 52 ++--
elastic-0.4.0/elastic/R/cat.r | 168 +++++++++++++---
elastic-0.4.0/elastic/R/connect.R | 137 +++++--------
elastic-0.4.0/elastic/R/count.r | 1
elastic-0.4.0/elastic/R/docs_bulk.r | 117 ++++++++++-
elastic-0.4.0/elastic/R/docs_create.R | 18 -
elastic-0.4.0/elastic/R/docs_delete.R | 15 -
elastic-0.4.0/elastic/R/docs_get.r | 48 ++--
elastic-0.4.0/elastic/R/docs_mget.r | 75 ++++---
elastic-0.4.0/elastic/R/elastic-package.r | 53 +++--
elastic-0.4.0/elastic/R/explain.R | 15 -
elastic-0.4.0/elastic/R/httr-verbs.R | 81 ++++---
elastic-0.4.0/elastic/R/index.R | 126 +++++-------
elastic-0.4.0/elastic/R/mapping.R | 33 +--
elastic-0.4.0/elastic/R/mlt.R | 88 ++++----
elastic-0.4.0/elastic/R/nodes.R | 65 ++++--
elastic-0.4.0/elastic/R/onstart.R | 1
elastic-0.4.0/elastic/R/ping.r | 14 -
elastic-0.4.0/elastic/R/scroll.R | 2
elastic-0.4.0/elastic/R/search_shards.R | 9
elastic-0.4.0/elastic/R/searchapis.R | 6
elastic-0.4.0/elastic/R/tokenizer_set.R | 14 -
elastic-0.4.0/elastic/R/zzz.r | 40 +++
elastic-0.4.0/elastic/README.md | 103 ++++++---
elastic-0.4.0/elastic/build/vignette.rds |binary
elastic-0.4.0/elastic/inst/doc/elastic_intro.Rmd | 29 +-
elastic-0.4.0/elastic/inst/doc/elastic_intro.html | 129 +++++-------
elastic-0.4.0/elastic/inst/doc/search.Rmd | 36 +--
elastic-0.4.0/elastic/inst/doc/search.html | 136 +++++-------
elastic-0.4.0/elastic/inst/examples/plos_data.json |only
elastic-0.4.0/elastic/inst/ignore/appveyor.yml |only
elastic-0.4.0/elastic/inst/ignore/benchmark.R |only
elastic-0.4.0/elastic/inst/ignore/es_stats.r | 7
elastic-0.4.0/elastic/inst/ignore/notes1.r |only
elastic-0.4.0/elastic/inst/ignore/notes2.r |only
elastic-0.4.0/elastic/inst/ignore/notes3.r |only
elastic-0.4.0/elastic/inst/ignore/notes4.r |only
elastic-0.4.0/elastic/inst/ignore/notes5.r |only
elastic-0.4.0/elastic/inst/vign/elastic_intro.Rmd | 16 -
elastic-0.4.0/elastic/inst/vign/elastic_intro.md | 29 +-
elastic-0.4.0/elastic/inst/vign/search.md | 36 +--
elastic-0.4.0/elastic/man/Search.Rd | 178 +++++++++++++----
elastic-0.4.0/elastic/man/Search_uri.Rd |only
elastic-0.4.0/elastic/man/alias.Rd | 2
elastic-0.4.0/elastic/man/cat.Rd | 86 ++++++--
elastic-0.4.0/elastic/man/cluster.Rd | 2
elastic-0.4.0/elastic/man/connect.Rd | 13 -
elastic-0.4.0/elastic/man/count.Rd | 2
elastic-0.4.0/elastic/man/docs_bulk.Rd | 51 ++++
elastic-0.4.0/elastic/man/docs_create.Rd | 2
elastic-0.4.0/elastic/man/docs_delete.Rd | 6
elastic-0.4.0/elastic/man/docs_get.Rd | 13 -
elastic-0.4.0/elastic/man/docs_mget.Rd | 16 +
elastic-0.4.0/elastic/man/documents.Rd | 2
elastic-0.4.0/elastic/man/elastic.Rd | 56 +++--
elastic-0.4.0/elastic/man/es_auth.Rd | 22 --
elastic-0.4.0/elastic/man/es_parse.Rd | 2
elastic-0.4.0/elastic/man/explain.Rd | 2
elastic-0.4.0/elastic/man/index.Rd | 7
elastic-0.4.0/elastic/man/mapping.Rd | 2
elastic-0.4.0/elastic/man/mlt.Rd | 72 +++---
elastic-0.4.0/elastic/man/nodes.Rd | 15 +
elastic-0.4.0/elastic/man/ping.Rd | 2
elastic-0.4.0/elastic/man/preference.Rd | 2
elastic-0.4.0/elastic/man/scroll.Rd | 2
elastic-0.4.0/elastic/man/search_body.Rd | 2
elastic-0.4.0/elastic/man/search_shards.Rd | 2
elastic-0.4.0/elastic/man/searchapis.Rd | 8
elastic-0.4.0/elastic/man/tokenizer_set.Rd | 2
elastic-0.4.0/elastic/man/units-distance.Rd | 2
elastic-0.4.0/elastic/man/units-time.Rd | 2
elastic-0.4.0/elastic/tests/other |only
elastic-0.4.0/elastic/tests/testthat/test-alias.R |only
elastic-0.4.0/elastic/tests/testthat/test-cat.R |only
elastic-0.4.0/elastic/tests/testthat/test-cluster.R |only
elastic-0.4.0/elastic/tests/testthat/test-connect.R |only
elastic-0.4.0/elastic/tests/testthat/test-count.R |only
elastic-0.4.0/elastic/tests/testthat/test-docs.R |only
elastic-0.4.0/elastic/tests/testthat/test-explain.R |only
elastic-0.4.0/elastic/tests/testthat/test-indices.R |only
elastic-0.4.0/elastic/tests/testthat/test-mappings.R |only
elastic-0.4.0/elastic/tests/testthat/test-nodes.R |only
elastic-0.4.0/elastic/tests/testthat/test-ping.R |only
elastic-0.4.0/elastic/tests/testthat/test-search.R |only
elastic-0.4.0/elastic/tests/testthat/test-search_uri.R |only
elastic-0.4.0/elastic/vignettes/elastic_intro.Rmd | 29 +-
elastic-0.4.0/elastic/vignettes/search.Rmd | 36 +--
97 files changed, 1595 insertions(+), 983 deletions(-)
Title: Configural Frequencies Analysis Using Log-Linear Modeling
Diff between confreq versions 1.3 dated 2014-11-06 and 1.3-1 dated 2015-05-01
Description: Offers several functions for Configural Frequencies
Analysis (CFA), which is a useful statistical tool for the analysis of
multiway contingency tables. CFA was introduced by G. A. Lienert as
'Konfigurations Frequenz Analyse - KFA'.
Author: Joerg-Henrik Heine, R.W. Alexandrowicz (function stirling_cfa() )
and some package testing by Mark Stemmler
Maintainer: Joerg-Henrik Heine
DESCRIPTION | 16 +++++++-------
MD5 | 52 +++++++++++++++++++++++-----------------------
NAMESPACE | 3 +-
NEWS | 10 ++++++++
R/CFA.R | 15 ++++++++-----
R/binomial_test_cfa.R | 38 ++++++++++++++++++++++++++-------
R/confreq-package.R | 3 --
R/expected_cfa.R | 2 -
R/summary.CFA.R | 40 +++++++++++++++++++++++++++--------
R/summary.S2CFA.R | 3 +-
man/CFA.Rd | 3 +-
man/S2CFA.Rd | 3 +-
man/binomial_test_cfa.Rd | 3 +-
man/chi_local_test_cfa.Rd | 3 +-
man/confreq-package.Rd | 3 +-
man/dat2fre.Rd | 3 +-
man/design_cfg_cfa.Rd | 3 +-
man/df_des_cfa.Rd | 3 +-
man/expected_cfa.Rd | 3 +-
man/fre2dat.Rd | 3 +-
man/ftab.Rd | 3 +-
man/lr.Rd | 3 +-
man/pos_cfg_cfa.Rd | 3 +-
man/stirling_cfa.Rd | 3 +-
man/summary.CFA.Rd | 12 +++++++---
man/summary.S2CFA.Rd | 3 +-
man/z_tests_cfa.Rd | 3 +-
27 files changed, 163 insertions(+), 79 deletions(-)
Title: 'TSdbi' Database Comparison
Diff between TScompare versions 2013.9-1 dated 2013-09-29 and 2015.4-1 dated 2015-04-30
Description: Utilities for comparing the equality of series on two databases.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 22 +++++++++++-----------
MD5 | 14 +++++++++-----
NAMESPACE | 1 +
NEWS | 10 ++++++++++
R/TScompare.R | 10 +++++-----
build/vignette.rds |binary
inst/testWithDatabases |only
inst/testWithInternet |only
8 files changed, 36 insertions(+), 21 deletions(-)
Title: Regression Modeling Strategies
Diff between rms versions 4.3-0 dated 2015-02-16 and 4.3-1 dated 2015-04-30
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. rms works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 12 -
MD5 | 42 ++---
NAMESPACE | 6
NEWS | 12 +
R/Rq.s | 18 +-
R/bplot.s | 11 -
R/contrast.s | 2
R/ggplot.Predict.s | 413 +++++++++++++++++++++++++++-----------------------
R/lrm.fit.s | 11 -
R/orm.fit.s | 7
R/plot.Predict.s | 16 -
R/predictrms.s | 2
R/summary.rms.s | 4
R/survplot.npsurv.s | 46 +++++
R/val.surv.s | 6
R/validate.rpart.s | 4
man/Rq.Rd | 5
man/bplot.Rd | 2
man/ggplot.Predict.Rd | 43 +++--
man/survplot.Rd | 8
tests/Rq.s | 2
tests/ggplot2.r | 34 +++-
22 files changed, 419 insertions(+), 287 deletions(-)
Title: Network Dynamic Temporal Visualizations
Diff between ndtv versions 0.5.1 dated 2014-01-31 and 0.6.1 dated 2015-04-30
Description: Renders dynamic network data from "networkDynamic" objects as animated movies or other representations of relational structure and node attributes that change over time.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll
ndtv-0.5.1/ndtv/exec |only
ndtv-0.5.1/ndtv/vignettes/ndtv.pdf |only
ndtv-0.6.1/ndtv/ChangeLog | 11
ndtv-0.6.1/ndtv/DESCRIPTION | 21 -
ndtv-0.6.1/ndtv/MD5 | 70 +++--
ndtv-0.6.1/ndtv/NAMESPACE | 3
ndtv-0.6.1/ndtv/R/animate.layouts.R | 62 ++++-
ndtv-0.6.1/ndtv/R/export.dot.R | 46 ++-
ndtv-0.6.1/ndtv/R/export.movie.R | 36 +--
ndtv-0.6.1/ndtv/R/installers.R | 14 -
ndtv-0.6.1/ndtv/R/proximity.timeline.R | 283 +++++++++++++++++-------
ndtv-0.6.1/ndtv/R/render.d3_animation.R |only
ndtv-0.6.1/ndtv/R/tea_utils.R | 105 +++++++-
ndtv-0.6.1/ndtv/build |only
ndtv-0.6.1/ndtv/data/toy_epi_sim.rda |only
ndtv-0.6.1/ndtv/inst/doc/ndtv.R |only
ndtv-0.6.1/ndtv/inst/doc/ndtv.Rnw |only
ndtv-0.6.1/ndtv/inst/doc/ndtv.pdf |binary
ndtv-0.6.1/ndtv/inst/java |only
ndtv-0.6.1/ndtv/inst/javascript |only
ndtv-0.6.1/ndtv/java |only
ndtv-0.6.1/ndtv/man/export.dot.Rd | 4
ndtv-0.6.1/ndtv/man/export.pajek.net.Rd | 1
ndtv-0.6.1/ndtv/man/msm.sim.Rd | 6
ndtv-0.6.1/ndtv/man/ndtv-package.Rd | 39 ++-
ndtv-0.6.1/ndtv/man/network.layout.animate.Rd | 12 -
ndtv-0.6.1/ndtv/man/proximity.timeline.Rd | 77 +++++-
ndtv-0.6.1/ndtv/man/render.animation.Rd | 8
ndtv-0.6.1/ndtv/man/render.d3movie.Rd |only
ndtv-0.6.1/ndtv/man/timeline.Rd | 65 ++++-
ndtv-0.6.1/ndtv/man/toy_epi_sim.Rd |only
ndtv-0.6.1/ndtv/tests/d3_animation_tests.R |only
ndtv-0.6.1/ndtv/tests/layout_tests.R | 52 ++++
ndtv-0.6.1/ndtv/tests/proximity.timeline_test.R | 91 +++++++
ndtv-0.6.1/ndtv/tests/timeline_test.R | 31 ++
ndtv-0.6.1/ndtv/vignettes/ndtv.Rnw | 145 ++++++++++--
36 files changed, 935 insertions(+), 247 deletions(-)
Title: Row-Based Functions for R Objects
Diff between rowr versions 1.1.1 dated 2014-11-26 and 1.1.2 dated 2015-04-30
Description: Allows the manipulation of R objects as if they were
organized rows in a way that is familiar to people used to working with
databases. It allows more consistent and predictable output to common
functions, and generalizes a number of utility functions to to be failsafe
with any number and type of input objects.
Author: Craig Varrichio
Maintainer: Craig Varrichio
DESCRIPTION | 14 +++++++-------
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/rowr.R | 8 +++++---
man/as2.Rd | 3 ++-
man/buffer.Rd | 3 ++-
man/cbind.fill.Rd | 4 +++-
man/coalesce.Rd | 3 ++-
man/count.Rd | 3 ++-
man/insertRows.Rd | 3 ++-
man/len.Rd | 3 ++-
man/rollApply.Rd | 3 ++-
man/rowApply.Rd | 3 ++-
man/rowr.Rd | 5 +++--
man/rows.Rd | 3 ++-
man/vectorize.Rd | 3 ++-
16 files changed, 54 insertions(+), 39 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Diff between MPTinR versions 1.7.5 dated 2015-03-22 and 1.8.0 dated 2015-04-30
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann
DESCRIPTION | 15 ++++++---------
MD5 | 18 +++++++++---------
NEWS | 20 ++++++++++++++++++++
R/prepare.mpt.fia.R | 11 ++++++++---
data/d.broeder.rda |binary
data/rb.fig1.data.rda |binary
data/rb.fig2.data.rda |binary
man/MPTinR-package.Rd | 6 +++---
src/determinant.cpp | 5 ++++-
src/determinant_c.cpp | 2 +-
10 files changed, 51 insertions(+), 26 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Diff between MixGHD versions 1.4 dated 2015-03-04 and 1.5 dated 2015-04-30
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
DESCRIPTION | 12 -
MD5 | 34 +--
NAMESPACE | 1
R/GHD.R | 427 ++++++++++++++++++++++++++++++++------------------
R/MCGHD.R | 7
R/MGHD.R | 12 -
R/MGHFA.R | 2
R/MSGHD.R | 8
R/Selection.R | 129 +++++++++++++--
R/cMSGHD.R | 9 -
man/DA.Rd | 4
man/MCGHD.Rd | 12 -
man/MGHD.Rd | 3
man/MGHFA.Rd | 2
man/MSGHD.Rd | 15 -
man/MixGHD-package.Rd | 14 -
man/Selection.Rd | 4
man/cMSGHD.Rd | 3
18 files changed, 469 insertions(+), 229 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Diff between LLSR versions 0.0.1.9015 dated 2015-03-12 and 0.0.1.9225 dated 2015-04-30
Description: The methods implemented here were based in the protocol proposed by Merchuk et al. (1998) and Murugesan & Perumalsamy (2005) to analyse Aqueous Two-Phases Systems. Each function brings in its description the reference for the original article which described it. These methods defines nonlinear equations that can be used to fit experimental data through regression methods and also allow us calculate other important system parameters (such as its critical composition, equivolume concentration and phase's composition). The package will include (every other update) new functions in order to comprise useful functions in liquid-liquid analysis.
Author: Diego F Coelho
Maintainer: Diego F Coelho
LLSR-0.0.1.9015/LLSR/R/gsnchk.R |only
LLSR-0.0.1.9015/LLSR/R/mrchk.R |only
LLSR-0.0.1.9015/LLSR/R/mrgsn.R |only
LLSR-0.0.1.9015/LLSR/R/plotll.R |only
LLSR-0.0.1.9015/LLSR/R/xyJn.R |only
LLSR-0.0.1.9015/LLSR/man/gsnchk.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrchk.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrchk.crpt.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrchk.plot.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrchk.tielines.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrgsn.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrgsn.bancroft.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrgsn.othmer.Rd |only
LLSR-0.0.1.9015/LLSR/man/mrgsn.plot.Rd |only
LLSR-0.0.1.9015/LLSR/man/plotll.Rd |only
LLSR-0.0.1.9015/LLSR/man/xyJn.Rd |only
LLSR-0.0.1.9225/LLSR/DESCRIPTION | 11 +---
LLSR-0.0.1.9225/LLSR/MD5 | 58 +++++++++++++---------
LLSR-0.0.1.9225/LLSR/NAMESPACE | 48 +++++++++---------
LLSR-0.0.1.9225/LLSR/R/AQSearch.CAS.R |only
LLSR-0.0.1.9225/LLSR/R/AQSearch.R |only
LLSR-0.0.1.9225/LLSR/R/AQSearchUtils.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.err.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.gsnchk.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.mathDesc.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.mrchk.R |only
LLSR-0.0.1.9225/LLSR/R/AQSys.mrgsn.R |only
LLSR-0.0.1.9225/LLSR/R/AQSysCurve.R |only
LLSR-0.0.1.9225/LLSR/R/AQSysDB.R |only
LLSR-0.0.1.9225/LLSR/R/AQSysFormulas.R |only
LLSR-0.0.1.9225/LLSR/R/AQSysUtils.R |only
LLSR-0.0.1.9225/LLSR/R/LLSRUtils.R |only
LLSR-0.0.1.9225/LLSR/R/LLSRxy.R |only
LLSR-0.0.1.9225/LLSR/R/datasets.R | 38 +++++++-------
LLSR-0.0.1.9225/LLSR/README.md |only
LLSR-0.0.1.9225/LLSR/man/AQSearch.CAS.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSearch.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSys.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSys.crpt.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSys.gsnchk.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSys.plot.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSys.tielines.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSysBancroft.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSysCurve.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSysDB.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSysList.Rd |only
LLSR-0.0.1.9225/LLSR/man/AQSysOthmer.Rd |only
LLSR-0.0.1.9225/LLSR/man/LLSR.info.Rd |only
LLSR-0.0.1.9225/LLSR/man/LLSRxy.Rd |only
LLSR-0.0.1.9225/LLSR/man/peg4kslt.Rd | 52 +++++++++----------
LLSR-0.0.1.9225/LLSR/tests/testthat.R | 8 +--
LLSR-0.0.1.9225/LLSR/tests/testthat/testMainFns.R | 26 ++++-----
53 files changed, 129 insertions(+), 112 deletions(-)
Title: Multivariate Adaptive Regression Splines
Diff between earth versions 4.2.0 dated 2015-01-12 and 4.3.0 dated 2015-04-30
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow
earth-4.2.0/earth/.Rinstignore |only
earth-4.2.0/earth/R/plot.model.selection.R |only
earth-4.2.0/earth/R/plotmor.R |only
earth-4.3.0/earth/DESCRIPTION | 8
earth-4.3.0/earth/MD5 | 171
earth-4.3.0/earth/NAMESPACE | 21
earth-4.3.0/earth/NEWS | 12
earth-4.3.0/earth/R/as.char.R |only
earth-4.3.0/earth/R/call.dots.R |only
earth-4.3.0/earth/R/check.index.R |only
earth-4.3.0/earth/R/do.par.R |only
earth-4.3.0/earth/R/dot.R |only
earth-4.3.0/earth/R/dotlib.R |only
earth-4.3.0/earth/R/earth.R | 396
earth-4.3.0/earth/R/earth.cv.R | 84
earth-4.3.0/earth/R/earth.cv.lib.R | 4
earth-4.3.0/earth/R/earth.glm.R | 91
earth-4.3.0/earth/R/earth.methods.R | 22
earth-4.3.0/earth/R/earth.regress.R | 28
earth-4.3.0/earth/R/earthlib.R | 651 -
earth-4.3.0/earth/R/elegend.R | 58
earth-4.3.0/earth/R/evimp.R | 76
earth-4.3.0/earth/R/expand.arg.R | 41
earth-4.3.0/earth/R/format.earth.R | 86
earth-4.3.0/earth/R/lib.R |only
earth-4.3.0/earth/R/mars.to.earth.R | 43
earth-4.3.0/earth/R/model.matrix.earth.R | 176
earth-4.3.0/earth/R/plot.earth.R | 1002 +
earth-4.3.0/earth/R/plotd.R | 581 -
earth-4.3.0/earth/R/plotmo.methods.earth.R | 54
earth-4.3.0/earth/R/predict.earth.R | 47
earth-4.3.0/earth/R/print.earth.R | 74
earth-4.3.0/earth/R/printcall.R |only
earth-4.3.0/earth/R/residuals.earth.R | 99
earth-4.3.0/earth/R/stop.if.dots.R |only
earth-4.3.0/earth/R/varmod.R | 437
earth-4.3.0/earth/inst/doc/earth-notes.pdf |binary
earth-4.3.0/earth/inst/doc/earth-varmod.pdf |binary
earth-4.3.0/earth/inst/slowtests/earth.times.bat | 2
earth-4.3.0/earth/inst/slowtests/make.bat | 18
earth-4.3.0/earth/inst/slowtests/test.big.R | 41
earth-4.3.0/earth/inst/slowtests/test.big.Rout.save | 273
earth-4.3.0/earth/inst/slowtests/test.big.bat | 7
earth-4.3.0/earth/inst/slowtests/test.cv.R | 13
earth-4.3.0/earth/inst/slowtests/test.cv.Rout.save | 130
earth-4.3.0/earth/inst/slowtests/test.cv.bat | 7
earth-4.3.0/earth/inst/slowtests/test.earthc.bat | 11
earth-4.3.0/earth/inst/slowtests/test.earthc.mak | 2
earth-4.3.0/earth/inst/slowtests/test.earthc.out.save | 186
earth-4.3.0/earth/inst/slowtests/test.earthmain.clang.bat | 13
earth-4.3.0/earth/inst/slowtests/test.earthmain.gcc.bat | 11
earth-4.3.0/earth/inst/slowtests/test.earthmain.gcc64.bat |only
earth-4.3.0/earth/inst/slowtests/test.earthmain.out.save | 6
earth-4.3.0/earth/inst/slowtests/test.earthmain.vc.bat | 12
earth-4.3.0/earth/inst/slowtests/test.full.R | 174
earth-4.3.0/earth/inst/slowtests/test.full.Rout.save | 6825 +++---------
earth-4.3.0/earth/inst/slowtests/test.full.bat | 7
earth-4.3.0/earth/inst/slowtests/test.glm.R | 69
earth-4.3.0/earth/inst/slowtests/test.glm.Rout.save | 5249 ++-------
earth-4.3.0/earth/inst/slowtests/test.glm.bat | 7
earth-4.3.0/earth/inst/slowtests/test.mods.R | 4
earth-4.3.0/earth/inst/slowtests/test.mods.Rout.save | 11
earth-4.3.0/earth/inst/slowtests/test.mods.bat | 7
earth-4.3.0/earth/inst/slowtests/test.plotd.R | 70
earth-4.3.0/earth/inst/slowtests/test.plotd.Rout.save | 269
earth-4.3.0/earth/inst/slowtests/test.plotd.bat | 7
earth-4.3.0/earth/inst/slowtests/test.varmod.R | 92
earth-4.3.0/earth/inst/slowtests/test.varmod.Rout.save | 486
earth-4.3.0/earth/inst/slowtests/test.varmod.bat | 7
earth-4.3.0/earth/inst/slowtests/test.varmod.mgcv.R |only
earth-4.3.0/earth/inst/slowtests/test.varmod.mgcv.Rout.save |only
earth-4.3.0/earth/inst/slowtests/test.varmod.mgcv.bat |only
earth-4.3.0/earth/inst/slowtests/test.weights.R | 47
earth-4.3.0/earth/inst/slowtests/test.weights.Rout.save | 120
earth-4.3.0/earth/inst/slowtests/test.weights.bat | 7
earth-4.3.0/earth/man/contr.earth.response.Rd | 2
earth-4.3.0/earth/man/earth.Rd | 82
earth-4.3.0/earth/man/evimp.Rd | 6
earth-4.3.0/earth/man/format.earth.Rd | 2
earth-4.3.0/earth/man/model.matrix.earth.Rd | 2
earth-4.3.0/earth/man/ozone1.Rd | 4
earth-4.3.0/earth/man/plot.earth.Rd | 529
earth-4.3.0/earth/man/plot.earth.models.Rd | 78
earth-4.3.0/earth/man/plot.evimp.Rd | 9
earth-4.3.0/earth/man/plot.varmod.Rd | 30
earth-4.3.0/earth/man/plotd.Rd | 41
earth-4.3.0/earth/man/predict.earth.Rd | 10
earth-4.3.0/earth/man/predict.varmod.Rd | 2
earth-4.3.0/earth/man/residuals.earth.Rd | 6
earth-4.3.0/earth/man/summary.earth.Rd | 17
earth-4.3.0/earth/man/update.earth.Rd | 2
earth-4.3.0/earth/man/varmod.Rd | 11
earth-4.3.0/earth/src/earth.c | 362
earth-4.3.0/earth/src/earth.h | 12
earth-4.3.0/earth/src/leaps.f | 1810 +--
95 files changed, 7514 insertions(+), 13955 deletions(-)
Title: Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Diff between constrainedKriging versions 0.2.3 dated 2014-05-26 and 0.2.4 dated 2015-04-30
More information about constrainedKriging at CRAN
Description: Provides functions for
efficient computations of nonlinear spatial predictions with
local change of support. This package supplies functions for
tow-dimensional spatial interpolation by constrained,
covariance-matching constrained and universal (external drift)
kriging for points or block of any shape for data with a
nonstationary mean function and an isotropic weakly stationary
variogram. The linear spatial interpolation methods,
constrained and covariance-matching constrained kriging,
provide approximately unbiased prediction for nonlinear target
values under change of support. This package
extends the range of geostatistical tools available in R and
provides a veritable alternative to conditional simulation for
nonlinear spatial prediction problems with local change of
support.
Author: Christoph Hofer
Maintainer: Christoph Hofer
DESCRIPTION | 18 +++---
MD5 | 28 ++++-----
NAMESPACE | 13 ++++
R/f.bb.cov.one.configuration.R | 18 +++---
R/f.build.pixel.R | 8 +-
R/f.calc.Q.R | 2
R/f.covmat.support.R | 43 ++++++++++++++-
R/f.kriging.functions.R | 116 ++++++++++++++++++++++++++++++++++++++++-
R/f.kriging.method.R | 31 ++++++++++
R/f.pixconfig.R | 8 +-
R/f.point.block.cov.R | 26 ++++-----
R/f.points.CKrige.R | 4 -
R/f.polygoncovmat.R | 10 +--
R/f.polygons.CKrige.R | 4 -
inst/ChangeLog.txt | 2
15 files changed, 265 insertions(+), 66 deletions(-)
Permanent link
Title: Compare Two ROC Curves that Intersect
Diff between Comp2ROC versions 1.0 dated 2013-05-20 and 1.1 dated 2015-04-30
Description: Comparison of two ROC curves throughout the methodology propose by Ana C. Braga.
Author: Ana C. Braga with contributions from Hugo Frade and Sara Carvalho
Maintainer: Ana C. Braga
DESCRIPTION | 16 -
MD5 | 70 ++---
NAMESPACE | 4
R/areatriangles.R | 48 +--
R/comp.roc.curves.R | 112 ++++-----
R/comp.roc.delong.R | 214 ++++++++++-------
R/curvesegslope.R | 24 -
R/curvesegsloperef.R | 24 -
R/diffareatriangles.R | 22 -
R/linedistance.R | 50 ++--
R/lineslope.R | 18 -
R/read.file.R | 105 +++++---
R/read.manually.introduced.R | 62 ++---
R/roc.curves.boot.R | 496 ++++++++++++++++++++--------------------
R/roc.curves.plot.R | 20 -
R/rocboot.summary.R | 70 ++---
R/rocsampling.R | 118 ++++-----
R/rocsampling.summary.R | 16 -
R/save.file.summary.R | 72 ++---
man/Comp2ROC-package.Rd | 89 +++----
man/areatriangles.Rd | 69 ++---
man/comp.roc.curves.Rd | 86 +++---
man/comp.roc.delong.Rd | 120 ++++-----
man/curvesegslope.Rd | 57 ++--
man/curvesegsloperef.Rd | 63 ++---
man/diffareatriangles.Rd | 67 ++---
man/linedistance.Rd | 100 ++++----
man/lineslope.Rd | 58 ++--
man/read.file.Rd | 139 +++++------
man/read.manually.introduced.Rd | 126 +++++-----
man/roc.curves.boot.Rd | 136 +++++-----
man/roc.curves.plot.Rd | 101 +++-----
man/rocboot.summary.Rd | 79 +++---
man/rocsampling.Rd | 125 ++++------
man/rocsampling.summary.Rd | 62 ++---
man/save.file.summary.Rd | 118 ++++-----
36 files changed, 1608 insertions(+), 1548 deletions(-)
Title: 'TSdbi' Extensions for 'SQLite'
Diff between TSSQLite versions 2013.9-1 dated 2013-09-29 and 2015.4-1 dated 2015-04-30
Description: An 'SQLite' interface for 'TSdbi'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
TSSQLite-2013.9-1/TSSQLite/tests |only
TSSQLite-2015.4-1/TSSQLite/DESCRIPTION | 21 +--
TSSQLite-2015.4-1/TSSQLite/MD5 | 16 +-
TSSQLite-2015.4-1/TSSQLite/NAMESPACE | 7 -
TSSQLite-2015.4-1/TSSQLite/NEWS | 17 +++
TSSQLite-2015.4-1/TSSQLite/R/TSdbiMethods.R | 33 +++--
TSSQLite-2015.4-1/TSSQLite/build/vignette.rds |binary
TSSQLite-2015.4-1/TSSQLite/inst/testWithInternet |only
TSSQLite-2015.4-1/TSSQLite/inst/testWithSQLiteServer |only
TSSQLite-2015.4-1/TSSQLite/man/TSdbiMethods.Rd | 105 ++++++++-----------
10 files changed, 103 insertions(+), 96 deletions(-)
Title: 'TSdbi' Extensions for 'PostgreSQL'
Diff between TSPostgreSQL versions 2013.9-1 dated 2013-09-29 and 2015.4-1 dated 2015-04-30
Description: A 'PostgreSQL' interface for 'TSdbi'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 21 ++++++++--------
MD5 | 14 ++++++----
NAMESPACE | 7 +++--
NEWS | 16 ++++++++++++
R/TSdbiMethods.R | 28 +++++++++------------
build/vignette.rds |binary
inst/testWithInternet |only
inst/testWithPostgreSQLserver |only
man/TSdbiMethods.Rd | 55 +++++++++++++-----------------------------
9 files changed, 70 insertions(+), 71 deletions(-)
Title: 'TSdbi' Extensions for ODBC
Diff between TSodbc versions 2013.9-1 dated 2013-09-29 and 2015.4-1 dated 2015-04-30
Description: An ODBC interface for 'TSdbi'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 21 ++++-----
MD5 | 15 ++++--
NAMESPACE | 10 +---
NEWS | 26 +++++++++++
R/TSdbiMethods.R | 108 ++++++++++++++++++++----------------------------
build/vignette.rds |binary
inst/testWithInternet |only
inst/testWithODBCserver |only
man/Internal.Rd |only
man/TSdbiMethods.Rd | 74 +++++++-------------------------
10 files changed, 111 insertions(+), 143 deletions(-)
Title: 'TSdbi' Extensions for Fame
Diff between TSfame versions 2013.8-2 dated 2013-09-29 and 2015.4-1 dated 2015-04-30
Description: A 'fame' interface for 'TSdbi'.
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
TSfame-2013.8-2/TSfame/tests |only
TSfame-2015.4-1/TSfame/DESCRIPTION | 20 +++---
TSfame-2015.4-1/TSfame/MD5 | 27 ++++----
TSfame-2015.4-1/TSfame/NAMESPACE | 8 --
TSfame-2015.4-1/TSfame/NEWS | 18 +++++
TSfame-2015.4-1/TSfame/R/TSdbiMethods.R | 71 +++++++++++++---------
TSfame-2015.4-1/TSfame/R/TSdbiMethodsFS.R | 27 +++-----
TSfame-2015.4-1/TSfame/build/vignette.rds |binary
TSfame-2015.4-1/TSfame/inst/testWithFame |only
TSfame-2015.4-1/TSfame/man/Internal.Rd |only
TSfame-2015.4-1/TSfame/man/TSdbiMethods.Rd | 91 ++++++++++++-----------------
11 files changed, 134 insertions(+), 128 deletions(-)
Title: Social Relation Model (SRM) Analyses for Single or Multiple
Groups
Diff between TripleR versions 1.4 dated 2014-09-09 and 1.4.1 dated 2015-04-30
Description: Social Relation Model (SRM) analyses for single or multiple
round-robin groups are performed. These analyses are either based on one
manifest variable, one latent construct measured by two manifest variables,
two manifest variables and their bivariate relations, or two latent
constructs each measured by two manifest variables. Within-group t-tests
for variance components and covariances are provided for single groups,
between-groups t-tests for multiple groups. Handling for missing values is
provided.
Author: F. D. Schönbrodt, M. D. Back, S. C. Schmukle
Maintainer: Felix Schönbrodt
DESCRIPTION | 12 ++++++------
MD5 | 12 ++++++------
NAMESPACE | 2 +-
NEWS | 6 ++++++
R/RR.r | 5 ++++-
R/long2matrix.R | 2 +-
inst/CITATION | 16 +++++++++++++++-
7 files changed, 39 insertions(+), 16 deletions(-)
Title: R-to-Java Interface for 'CMA-ES'
Diff between rCMA versions 1.0.0 dated 2013-03-01 and 1.1 dated 2015-04-30
Description: Tool for providing access to the Java version 'CMAEvolutionStrategy' of
Nikolaus Hansen. 'CMA-ES' is the Covariance Matrix Adaptation Evolution Strategy,
see https://www.lri.fr/~hansen/cmaes_inmatlab.html#java.
Author: Wolfgang Konen
Maintainer: Wolfgang Konen
rCMA-1.0.0/rCMA/demo/demoRJavaTR2.r |only
rCMA-1.1/rCMA/DESCRIPTION | 22 ++--
rCMA-1.1/rCMA/MD5 | 56 +++++++----
rCMA-1.1/rCMA/NAMESPACE | 2
rCMA-1.1/rCMA/R/cmaEvalMeanX.R | 53 ++++++----
rCMA-1.1/rCMA/R/cmaGetters.R | 22 ++--
rCMA-1.1/rCMA/R/rCMA.R | 116 +++++++++++++----------
rCMA-1.1/rCMA/demo/demoCMA2.R | 30 ++++--
rCMA-1.1/rCMA/demo/demoEvalMeanX.R | 17 ++-
rCMA-1.1/rCMA/demo/demoRJavaTR2.R |only
rCMA-1.1/rCMA/inst/doc/aareadme.txt |only
rCMA-1.1/rCMA/inst/doc/changes.html |only
rCMA-1.1/rCMA/inst/doc/index.html | 104 ++++++---------------
rCMA-1.1/rCMA/inst/doc/rCMA-tutorial.pdf |only
rCMA-1.1/rCMA/java |only
rCMA-1.1/rCMA/man/cmaCalcFitness.Rd | 25 ++---
rCMA-1.1/rCMA/man/cmaEvalMeanX.Rd | 141 +++++++++++++++--------------
rCMA-1.1/rCMA/man/cmaInit.Rd | 47 ++++-----
rCMA-1.1/rCMA/man/cmaNew.Rd | 33 ++----
rCMA-1.1/rCMA/man/cmaOptimDP.Rd | 132 +++++++++++++--------------
rCMA-1.1/rCMA/man/cmaSamplePopulation.Rd | 31 ++----
rCMA-1.1/rCMA/man/cmaSetDimension.Rd | 58 +++++------
rCMA-1.1/rCMA/man/cmaSetStopFitness.Rd | 56 +++++------
rCMA-1.1/rCMA/man/cmaUpdateDistribution.Rd | 23 ++--
rCMA-1.1/rCMA/man/rCMA-package.Rd | 79 +++++++---------
25 files changed, 524 insertions(+), 523 deletions(-)
Title: Calculate Indices and Theoretical Properties of Protein
Sequences
Diff between Peptides versions 1.0.3 dated 2014-12-15 and 1.0.4 dated 2015-04-30
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 ++
NEWS | 3 +++
R/AAcomp.R | 1 +
R/Boman.R | 3 ++-
R/MW.R | 1 +
R/aindex.R | 1 +
R/charge.R | 5 +++--
R/hmoment.R | 3 ++-
R/hydrophobicity.R | 3 ++-
R/instaindex.R | 12 +++++-------
R/lengthpep.R | 1 +
R/membpos.R | 3 ++-
R/pI.R | 1 +
man/Peptides-package.Rd | 8 ++++----
16 files changed, 50 insertions(+), 37 deletions(-)
Title: Bayesian Analysis of qRT-PCR Data
Diff between MCMC.qpcr versions 1.1.5 dated 2015-01-27 and 1.1.7 dated 2015-04-30
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/mcmc.qpcr.R | 17 ++++++++++++-----
man/MCMC.qpcr-package.Rd | 4 ++--
man/mcmc.qpcr.Rd | 22 ++++++++++++++++------
5 files changed, 40 insertions(+), 23 deletions(-)
Title: Meta Analysis via Shiny
Diff between MAVIS versions 1.0 dated 2014-11-28 and 1.1 dated 2015-04-30
Description: Interactive shiny application for running a meta-analysis,
provides support for both random effects and fixed effects models with the 'metafor' package.
Additional support is included for calculating effect sizes plus
support for single case designs, graphical output, and detecting publication bias.
Author: Authors@R: c(person("William Kyle", "Hamilton", role = c("aut", "cre"),
email = "kyle.hamilton@gmail.com"),
person("Atsushi", "Mizumoto", role = "aut"),
person("Burak", "Aydin", role = c("ctb", "trl"),
person("Kathleen", "Coburn", role = "ctb"))
Maintainer: William Kyle Hamilton
DESCRIPTION | 23 -
MD5 | 14
NAMESPACE | 3
NEWS |only
R/MAVIS.R | 7
README.md | 34 ++
inst/CITATION |only
inst/shiny/server.R | 782 ++++++++++++++++++++++++++++++++++++----------------
inst/shiny/ui.R | 601 ++++++++++++++++++++++++++++++---------
9 files changed, 1067 insertions(+), 397 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Diff between glmmLasso versions 1.3.3 dated 2014-09-11 and 1.3.4 dated 2015-04-30
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 14 ++++----
MD5 | 8 ++--
R/glmmLasso.r | 77 ++++++++++++++++++++++++++++++------------------
demo/glmmLasso-soccer.r | 14 ++++----
man/glmmLasso.rd | 25 ++++++---------
5 files changed, 78 insertions(+), 60 deletions(-)
Title: Create Diagrams and Flowcharts Using R
Diff between DiagrammeR versions 0.5 dated 2015-03-19 and 0.6 dated 2015-04-30
Description: Allows to create diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone
DiagrammeR-0.5/DiagrammeR/R/graphviz_nodes_edges_df.R |only
DiagrammeR-0.5/DiagrammeR/R/graphviz_single_df.R |only
DiagrammeR-0.5/DiagrammeR/man/graphviz_nodes_edges_df.Rd |only
DiagrammeR-0.5/DiagrammeR/man/graphviz_single_df.Rd |only
DiagrammeR-0.6/DiagrammeR/DESCRIPTION | 21
DiagrammeR-0.6/DiagrammeR/MD5 | 60
DiagrammeR-0.6/DiagrammeR/NAMESPACE | 15
DiagrammeR-0.6/DiagrammeR/R/combine_edges.R |only
DiagrammeR-0.6/DiagrammeR/R/combine_nodes.R |only
DiagrammeR-0.6/DiagrammeR/R/create_edges.R |only
DiagrammeR-0.6/DiagrammeR/R/create_nodes.R |only
DiagrammeR-0.6/DiagrammeR/R/get_nodes.R |only
DiagrammeR-0.6/DiagrammeR/R/graphviz_export.R | 2
DiagrammeR-0.6/DiagrammeR/R/graphviz_graph.R |only
DiagrammeR-0.6/DiagrammeR/R/graphviz_render.R |only
DiagrammeR-0.6/DiagrammeR/R/node_info.R |only
DiagrammeR-0.6/DiagrammeR/R/scale_edges.R |only
DiagrammeR-0.6/DiagrammeR/R/scale_nodes.R |only
DiagrammeR-0.6/DiagrammeR/README.md | 901 ++++++----
DiagrammeR-0.6/DiagrammeR/inst/doc/DiagrammeR.html | 34
DiagrammeR-0.6/DiagrammeR/inst/htmlwidgets/DiagrammeR.js | 9
DiagrammeR-0.6/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.css | 5
DiagrammeR-0.6/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 26
DiagrammeR-0.6/DiagrammeR/man/DiagrammeR.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/DiagrammeROutput.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/combine_edges.Rd |only
DiagrammeR-0.6/DiagrammeR/man/combine_nodes.Rd |only
DiagrammeR-0.6/DiagrammeR/man/create_edges.Rd |only
DiagrammeR-0.6/DiagrammeR/man/create_nodes.Rd |only
DiagrammeR-0.6/DiagrammeR/man/exportSVG.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/get_nodes.Rd |only
DiagrammeR-0.6/DiagrammeR/man/grViz.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/grVizOutput.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/graphviz_graph.Rd |only
DiagrammeR-0.6/DiagrammeR/man/graphviz_render.Rd |only
DiagrammeR-0.6/DiagrammeR/man/mermaid.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/node_info.Rd |only
DiagrammeR-0.6/DiagrammeR/man/renderDiagrammeR.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/renderGrViz.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/replace_in_spec.Rd | 2
DiagrammeR-0.6/DiagrammeR/man/scale_edges.Rd |only
DiagrammeR-0.6/DiagrammeR/man/scale_nodes.Rd |only
DiagrammeR-0.6/DiagrammeR/man/x11_hex.Rd | 2
43 files changed, 682 insertions(+), 411 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Diff between stringr versions 0.6.2 dated 2012-12-06 and 1.0.0 dated 2015-04-30
Description: A consistent, simple and easy to use set of wrappers around the
fantastic 'stringi' package. All function and argument names (and positions)
are consistent, all functions deal with "NA"'s and zero length vectors
in the same way, and the output from one function is easy to feed into
the input of another.
Author: Hadley Wickham [aut, cre, cph],
RStudio [cph]
Maintainer: Hadley Wickham
stringr-0.6.2/stringr/NEWS |only
stringr-0.6.2/stringr/R/checks.r |only
stringr-0.6.2/stringr/R/utils.r |only
stringr-0.6.2/stringr/R/vectorise.r |only
stringr-0.6.2/stringr/inst/tests |only
stringr-0.6.2/stringr/man/fixed.Rd |only
stringr-0.6.2/stringr/man/ignore.case.Rd |only
stringr-0.6.2/stringr/man/perl.Rd |only
stringr-0.6.2/stringr/man/str_extract_all.Rd |only
stringr-0.6.2/stringr/man/str_locate_all.Rd |only
stringr-0.6.2/stringr/man/str_match_all.Rd |only
stringr-0.6.2/stringr/man/str_replace_all.Rd |only
stringr-0.6.2/stringr/man/str_split_fixed.Rd |only
stringr-0.6.2/stringr/man/str_sub_replace.Rd |only
stringr-0.6.2/stringr/tests/test-all.R |only
stringr-1.0.0/stringr/DESCRIPTION | 39 ++--
stringr-1.0.0/stringr/MD5 | 128 ++++++++--------
stringr-1.0.0/stringr/NAMESPACE | 16 ++
stringr-1.0.0/stringr/R/c.r | 45 +++--
stringr-1.0.0/stringr/R/case.R |only
stringr-1.0.0/stringr/R/conv.R |only
stringr-1.0.0/stringr/R/count.r | 42 ++---
stringr-1.0.0/stringr/R/detect.r | 50 +++---
stringr-1.0.0/stringr/R/dup.r | 22 --
stringr-1.0.0/stringr/R/extract.r | 73 ++++-----
stringr-1.0.0/stringr/R/length.r | 35 +++-
stringr-1.0.0/stringr/R/locate.r | 116 +++++---------
stringr-1.0.0/stringr/R/match.r | 88 ++++-------
stringr-1.0.0/stringr/R/modifiers.r | 184 ++++++++++++++++-------
stringr-1.0.0/stringr/R/pad-trim.r | 69 +++-----
stringr-1.0.0/stringr/R/replace.r | 103 ++++++++----
stringr-1.0.0/stringr/R/sort.R |only
stringr-1.0.0/stringr/R/split.r | 128 +++++-----------
stringr-1.0.0/stringr/R/stringr.R |only
stringr-1.0.0/stringr/R/sub.r | 95 ++++-------
stringr-1.0.0/stringr/R/subset.R |only
stringr-1.0.0/stringr/R/utils.R |only
stringr-1.0.0/stringr/R/word.r | 6
stringr-1.0.0/stringr/R/wrap.r | 18 +-
stringr-1.0.0/stringr/README.md | 49 ++++--
stringr-1.0.0/stringr/build |only
stringr-1.0.0/stringr/inst/doc |only
stringr-1.0.0/stringr/man/case.Rd |only
stringr-1.0.0/stringr/man/invert_match.Rd | 13 -
stringr-1.0.0/stringr/man/modifier-deprecated.Rd |only
stringr-1.0.0/stringr/man/modifiers.Rd |only
stringr-1.0.0/stringr/man/pipe.Rd |only
stringr-1.0.0/stringr/man/str_c.Rd | 48 +++---
stringr-1.0.0/stringr/man/str_conv.Rd |only
stringr-1.0.0/stringr/man/str_count.Rd | 43 +++--
stringr-1.0.0/stringr/man/str_detect.Rd | 35 ++--
stringr-1.0.0/stringr/man/str_dup.Rd | 13 -
stringr-1.0.0/stringr/man/str_extract.Rd | 57 +++++--
stringr-1.0.0/stringr/man/str_length.Rd | 38 +++-
stringr-1.0.0/stringr/man/str_locate.Rd | 61 +++++--
stringr-1.0.0/stringr/man/str_match.Rd | 39 +++-
stringr-1.0.0/stringr/man/str_order.Rd |only
stringr-1.0.0/stringr/man/str_pad.Rd | 27 ++-
stringr-1.0.0/stringr/man/str_replace.Rd | 59 ++++---
stringr-1.0.0/stringr/man/str_replace_na.Rd |only
stringr-1.0.0/stringr/man/str_split.Rd | 52 ++++--
stringr-1.0.0/stringr/man/str_sub.Rd | 64 +++++---
stringr-1.0.0/stringr/man/str_subset.Rd |only
stringr-1.0.0/stringr/man/str_trim.Rd | 17 +-
stringr-1.0.0/stringr/man/str_wrap.Rd | 27 +--
stringr-1.0.0/stringr/man/stringr.Rd |only
stringr-1.0.0/stringr/man/word.Rd | 25 +--
stringr-1.0.0/stringr/tests/testthat |only
stringr-1.0.0/stringr/tests/testthat.R |only
stringr-1.0.0/stringr/vignettes |only
70 files changed, 1067 insertions(+), 857 deletions(-)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Diff between sets versions 1.0-13 dated 2013-03-19 and 1.0-14 dated 2015-04-30
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and
fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb]
Maintainer: David Meyer
DESCRIPTION | 26 +++++++++++++-------------
MD5 | 25 ++++++++++++++-----------
R/cset.R | 6 ++++--
R/fuzzyinference.R | 7 +++++--
R/gset.R | 6 ++++--
R/interval.R | 6 ++++--
R/labels.R | 2 +-
R/set.R | 9 ++++++---
R/utilities.R | 13 +++++++++----
build |only
data/fuzzy_docs.rda |binary
inst/NEWS.Rd | 6 ++++++
inst/doc/sets.R |only
inst/doc/sets.bib |only
inst/doc/sets.pdf |binary
15 files changed, 66 insertions(+), 40 deletions(-)
Title: Data Structures and Algorithms for Relations
Diff between relations versions 0.6-4 dated 2015-02-02 and 0.6-5 dated 2015-04-30
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/plot.R | 15 +++++++++++----
build/vignette.rds |binary
data/Cetacea.rda |binary
data/Felines.rda |binary
data/SVM_Benchmarking_Classification.rda |binary
data/SVM_Benchmarking_Classification_Consensus.rda |binary
data/SVM_Benchmarking_Regression.rda |binary
data/SVM_Benchmarking_Regression_Consensus.rda |binary
inst/doc/relations.pdf |binary
11 files changed, 27 insertions(+), 20 deletions(-)
Title: Harrell Miscellaneous
Diff between Hmisc versions 3.15-0 dated 2015-02-16 and 3.16-0 dated 2015-04-30
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 12 +-
INDEX | 3
MD5 | 72 ++++++++--------
NAMESPACE | 3
NEWS | 22 +++++
R/Misc.s | 206 +++++++++++++++++++++++++++++++++++++++++++++++-
R/describe.s | 10 +-
R/ggMisc.s |only
R/hoeffd.s | 30 +++---
R/impute.s | 2
R/label.s | 22 ++---
R/latex.s | 56 +++++++------
R/nobsY.s | 12 ++
R/panel.bpplot.s | 2
R/rcorr.s | 17 +--
R/rcspline.restate.s | 50 +++++++----
R/sas.get.s | 2
R/scat1d.s | 2
R/sedit.s | 9 --
R/summary.formula.s | 8 -
R/summaryM.s | 26 ++++--
R/summaryP.s | 143 +++++++++++++++++++++++++--------
R/summaryS.s | 2
R/wtd.stats.s | 19 +++-
README.md | 2
man/addMarginal.Rd | 5 -
man/getHdata.Rd | 2
man/getRs.Rd |only
man/ggMisc.Rd |only
man/html.Rd | 32 ++++++-
man/knitrSet.Rd |only
man/label.Rd | 8 +
man/rcspline.restate.Rd | 2
man/summaryP.Rd | 59 ++++++++++---
man/wtd.stats.Rd | 20 +++-
src/hoeffd.f | 12 +-
src/ratfor/hoeffd.r | 6 -
src/ratfor/rcorr.r | 26 +++---
src/rcorr.f | 28 +++---
39 files changed, 676 insertions(+), 256 deletions(-)
Title: Generic SQL Helper Functions for 'TSdbi' SQL Plugins
Diff between TSsql versions 2014.4-1 dated 2014-04-08 and 2015.1-2 dated 2015-04-30
Description: Standard SQL query functions used by
SQL plugins packages for the 'TSdbi' interface to time series databases.
It will mainly be used by other packages rather than directly by end
users. The one exception is the function 'TSquery' which can be used to
construct a time series from a database containing observations over
time (e.g. balance statements for multiple years), but where the database
is not specifically designed to store time series (as with other
'TSdbi' SQL plugin packages).
Comprehensive examples of all the 'TS*' packages is provided in the
vignette Guide.pdf with the 'TSdata' package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 34 ++++++++---------
MD5 | 18 ++++-----
NAMESPACE | 15 ++-----
NEWS | 25 ++++++++++++
R/TSquery.R | 5 +-
R/TSsql.R | 88 ++++++++++++++++++++------------------------
inst/TSsql/Populate.TSsql | 4 +-
inst/TSsql/TSdbi.TSsql | 4 +-
inst/TSsql/dbGetQuery.TSsql | 18 ++++-----
man/createTSdbTables.Rd | 27 ++++++-------
10 files changed, 122 insertions(+), 116 deletions(-)
Title: Sparse Group Partial Least Square Methods
Diff between sgPLS versions 1.1 dated 2015-03-14 and 1.2 dated 2015-04-30
Description: The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.
Author: Benoit Liquet and Pierre Lafaye de Micheaux
Maintainer: Benoit Liquet
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/perf.R | 24 ++++++++++++------------
3 files changed, 18 insertions(+), 18 deletions(-)
Title: Data Analysis in Ecology
Diff between pgirmess versions 1.5.9 dated 2014-06-09 and 1.6.0 dated 2015-04-30
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux
Maintainer: Patrick Giraudoux
DESCRIPTION | 12 +++++-----
MD5 | 34 +++++++++++++++--------------
NAMESPACE | 2 -
R/clipQGIS2df.R |only
R/cormat.R | 15 -------------
R/correlog.R | 9 ++++---
R/difshannonbio.R | 6 -----
R/expandpoly.r | 1
R/mergeTrackObs.r | 30 ++++++++++++++------------
R/piankabio.R | 8 ++-----
R/piankabioboot.R | 3 --
R/rwhatbufCat.r | 4 +--
R/shannonbio.R | 5 ----
R/shannonbioboot.R | 5 ----
data/preybiom.rda |binary
data/siegelp179.rda |binary
man/clipQGIS2df.Rd |only
man/correlog.Rd | 2 -
man/mergeTrackObs.rd | 58 +++++++++++++++++++++++++++++++++++----------------
19 files changed, 93 insertions(+), 101 deletions(-)
Title: Bayesian Spectral Inference
Diff between bspec versions 1.4 dated 2013-02-21 and 1.5 dated 2015-04-30
Description: Bayesian inference on the (discrete) power spectrum of time series.
Author: Christian Roever
Maintainer: Christian Roever
DESCRIPTION | 15 +++++++--------
MD5 | 35 ++++++++++++++++++-----------------
inst/CITATION | 15 ++++++++-------
man/acf.Rd | 6 +++---
man/bspec-package.Rd |only
man/bspec.Rd | 19 +++++++++++++++----
man/empiricalspectrum.Rd | 6 +++---
man/expectation.Rd | 6 +++---
man/likelihood.Rd | 6 +++---
man/matchedfilter.Rd | 10 +++++-----
man/onesided.Rd | 2 +-
man/ppsample.Rd | 2 +-
man/quantile.Rd | 2 +-
man/sample.Rd | 2 +-
man/snr.Rd | 6 +++---
man/temper.Rd | 6 +++---
man/temperature.Rd | 6 +++---
man/welchPSD.Rd | 10 +++++-----
man/windowing.Rd | 10 +++++-----
19 files changed, 88 insertions(+), 76 deletions(-)
Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Diff between Rchoice versions 0.2 dated 2014-12-17 and 0.3 dated 2015-04-29
Description: An implementation of simulated maximum likelihood method for the estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters for cross-sectional and longitudinal data.
Author: Mauricio Sarrias
Maintainer: Mauricio Sarrias
Rchoice-0.2/Rchoice/build |only
Rchoice-0.2/Rchoice/inst/doc |only
Rchoice-0.2/Rchoice/vignettes |only
Rchoice-0.3/Rchoice/DESCRIPTION | 18 ++---
Rchoice-0.3/Rchoice/MD5 | 41 +++++--------
Rchoice-0.3/Rchoice/NAMESPACE | 8 +-
Rchoice-0.3/Rchoice/R/Rchoice.R | 2
Rchoice-0.3/Rchoice/R/Rchoice.logLiks.R | 3
Rchoice-0.3/Rchoice/R/Rchoice.methods.R | 79 ++++++++++++++++++--------
Rchoice-0.3/Rchoice/R/Rchoice.modelform.R | 3
Rchoice-0.3/Rchoice/inst/NEWS.Rd |only
Rchoice-0.3/Rchoice/man/AIC.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/Rchoice.Rd | 9 --
Rchoice-0.3/Rchoice/man/bread.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/cov.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/effect.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/estfun.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/getSummary.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/plot.Rchoice.Rd | 2
Rchoice-0.3/Rchoice/man/rFormula.Rd | 2
Rchoice-0.3/Rchoice/man/vcov.Rchoice.Rd |only
21 files changed, 101 insertions(+), 78 deletions(-)
Title: Plot a Model's Response and Residuals
Diff between plotmo versions 2.2.1 dated 2015-01-07 and 3.0.0 dated 2015-04-29
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
plotmo-2.2.1/plotmo/R/plotmo.methods.R |only
plotmo-2.2.1/plotmo/R/plotmo.methods.gbm.R |only
plotmo-2.2.1/plotmo/R/plotmo.methods.misc.R |only
plotmo-2.2.1/plotmo/R/plotmo.methods.quantreg.R |only
plotmo-2.2.1/plotmo/R/plotmo.methods.rpart.R |only
plotmo-2.2.1/plotmo/R/plotmo.pint.R |only
plotmo-2.2.1/plotmo/inst/slowtests/test.plotmo.center.R |only
plotmo-2.2.1/plotmo/inst/slowtests/test.plotmo.center.Rout.save |only
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plotmo-3.0.0/plotmo/DESCRIPTION | 14
plotmo-3.0.0/plotmo/MD5 | 125
plotmo-3.0.0/plotmo/NAMESPACE | 50
plotmo-3.0.0/plotmo/NEWS | 17
plotmo-3.0.0/plotmo/R/as.char.R |only
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plotmo-3.0.0/plotmo/R/bx.R |only
plotmo-3.0.0/plotmo/R/call.dots.R |only
plotmo-3.0.0/plotmo/R/check.index.R | 74
plotmo-3.0.0/plotmo/R/do.par.R |only
plotmo-3.0.0/plotmo/R/dot.R |only
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plotmo-3.0.0/plotmo/R/glmnet.R |only
plotmo-3.0.0/plotmo/R/grid.R | 223
plotmo-3.0.0/plotmo/R/lib.R | 1078 +
plotmo-3.0.0/plotmo/R/meta.R |only
plotmo-3.0.0/plotmo/R/methods.R |only
plotmo-3.0.0/plotmo/R/pint.R |only
plotmo-3.0.0/plotmo/R/plot.gbmx.R |only
plotmo-3.0.0/plotmo/R/plot.glmnetx.R |only
plotmo-3.0.0/plotmo/R/plotcum.R |only
plotmo-3.0.0/plotmo/R/plotmo.R | 2828 ++--
plotmo-3.0.0/plotmo/R/plotqq.R |only
plotmo-3.0.0/plotmo/R/plotres.R |only
plotmo-3.0.0/plotmo/R/plotresids.R |only
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plotmo-3.0.0/plotmo/R/predict.nn.R |only
plotmo-3.0.0/plotmo/R/printcall.R |only
plotmo-3.0.0/plotmo/R/prolog.R |only
plotmo-3.0.0/plotmo/R/quantreg.R |only
plotmo-3.0.0/plotmo/R/residuals.R |only
plotmo-3.0.0/plotmo/R/response.R |only
plotmo-3.0.0/plotmo/R/rpart.R |only
plotmo-3.0.0/plotmo/R/singles.R |only
plotmo-3.0.0/plotmo/R/stop.if.dots.R |only
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plotmo-3.0.0/plotmo/R/xy.R |only
plotmo-3.0.0/plotmo/inst/doc/index.html | 7
plotmo-3.0.0/plotmo/inst/doc/plotmo-notes.pdf |binary
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plotmo-3.0.0/plotmo/inst/slowtests/make.bat | 32
plotmo-3.0.0/plotmo/inst/slowtests/test.center.R |only
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plotmo-3.0.0/plotmo/inst/slowtests/test.plotmo.R | 426
plotmo-3.0.0/plotmo/inst/slowtests/test.plotmo.Rout.save | 6238 ++--------
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plotmo-3.0.0/plotmo/inst/slowtests/test.printcall.R |only
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plotmo-3.0.0/plotmo/tests/test.plotmo.R | 2
plotmo-3.0.0/plotmo/tests/test.plotmo.Rout.save | 99
110 files changed, 4836 insertions(+), 7169 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Diff between markovchain versions 0.1.1 dated 2015-02-21 and 0.2 dated 2015-04-29
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato
ChangeLog | 15 ++++
DESCRIPTION | 19 +++---
MD5 | 35 ++++++-----
NAMESPACE | 3
NEWS | 8 +-
R/1_functions4Fitting.R | 58 +------------------
R/2_probabilistic.R | 30 ++++++---
R/RcppExports.R |only
R/zzz.R |only
README.md |only
build/vignette.rds |binary
inst/CITATION | 8 +-
inst/doc/an_introduction_to_markovchain_package.Rnw | 20 ++----
inst/doc/an_introduction_to_markovchain_package.pdf |binary
man/absorbingStates.Rd | 10 +++
man/blanden.Rd | 2
man/markovchain-package.Rd | 6 -
man/markovchainFit.Rd | 6 +
src |only
vignettes/an_introduction_to_markovchain_package.Rnw | 20 ++----
20 files changed, 120 insertions(+), 120 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Diff between dfmta versions 1.3-1 dated 2015-04-26 and 1.3-2 dated 2015-04-29
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
configure | 18 +++++++++---------
src/dfmta.cpp | 2 +-
4 files changed, 17 insertions(+), 17 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Diff between dfcomb versions 2.1-1 dated 2015-04-26 and 2.1-3 dated 2015-04-29
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/dfcomb.R | 13 +++++++------
configure | 18 +++++++++---------
man/CombIncrease_next.Rd | 16 +++++++++++-----
src/logistic.cpp | 4 +++-
6 files changed, 39 insertions(+), 30 deletions(-)
Title: Selection of Samples and Parameter Estimation in Finite
Population
Diff between TeachingSampling versions 3.2.1 dated 2014-03-27 and 3.2.2 dated 2015-04-29
More information about TeachingSampling at CRAN
Description: Allows the user to draw probabilistic samples and make inferences from a finite population based on several sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas
DESCRIPTION | 19 +++++++++----------
MD5 | 6 +++---
R/PikHol.r | 30 ++++++++++++++++--------------
man/PikHol.rd | 41 ++++++++++++++++++++++++++++++++++++++++-
4 files changed, 68 insertions(+), 28 deletions(-)
Permanent link
Title: Sample Size Calculations for Complex Surveys
Diff between samplesize4surveys versions 2.1.0 dated 2014-09-21 and 2.2.0 dated 2015-04-29
More information about samplesize4surveys at CRAN
Description: Computes the required sample size for estimation of totals, means
and proportions under complex sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas
DESCRIPTION | 10 +-
MD5 | 39 ++++++----
NAMESPACE | 3
R/ss4ddp.R |only
R/ss4dp.R | 190 ++++++++++++++++++++++++++---------------------------
data |only
man/BigLucyT0T1.rd |only
man/DEFF.Rd | 3
man/ICC.Rd | 3
man/e4p.Rd | 3
man/ss2s4m.Rd | 3
man/ss2s4p.Rd | 3
man/ss4ddp.Rd |only
man/ss4dm.Rd | 3
man/ss4dmH.Rd | 3
man/ss4dp.Rd | 3
man/ss4dpH.Rd | 3
man/ss4m.Rd | 3
man/ss4mH.Rd | 3
man/ss4p.Rd | 3
man/ss4pH.Rd | 3
man/ss4stm.Rd | 3
22 files changed, 152 insertions(+), 132 deletions(-)
Permanent link
Title: Extraction of Business Financial Information from 'XBRL'
Documents
Diff between XBRL versions 0.99.15 dated 2015-02-13 and 0.99.16 dated 2015-04-29
Description:
Functions to extract business financial information from
an Extensible Business Reporting Language ('XBRL') instance file and the
associated collection of files that defines its 'Discoverable' Taxonomy
Set ('DTS').
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
ChangeLog | 6 ++++++
DESCRIPTION | 36 +++++++++---------------------------
MD5 | 8 ++++----
configure.in | 2 +-
src/xbrlProcessFacts.cpp | 16 ++++++++++++++++
5 files changed, 36 insertions(+), 32 deletions(-)
Title: Time Series Database Interface
Diff between TSdbi versions 2013.9-1 dated 2013-09-29 and 2015.1-1 dated 2015-04-29
Description: Provides a common interface to time series databases. The
objective is to define a standard interface so users can retrieve time
series data from various sources with a simple, common, set of
commands, and so programs can be written to be portable with respect
to the data source. The SQL implementations also provide a database
table design, so users needing to set up a time series database
have a reasonably complete way to do this easily. The interface
provides for a variety of options with respect to the representation
of time series in R. The interface, and the SQL implementations, also
handle vintages of time series data (sometime called editions or
realtime data). There is also a (not yet well tested) mechanism to
handle multilingual data documentation.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
MD5 | 14 +++++++-------
NAMESPACE | 1 +
NEWS | 17 +++++++++++++++--
R/TSdbi.R | 41 ++++++++++++++++++++++++++---------------
build/vignette.rds |binary
man/TSconnect.Rd | 18 ++++++++++--------
man/TSget.Rd | 27 ++++++++++++++-------------
8 files changed, 80 insertions(+), 52 deletions(-)
More information about replicatedpp2w at CRAN
Permanent link
Title: Phenotypic Integration Index
Diff between PHENIX versions 1.1 dated 2015-01-27 and 1.2 dated 2015-04-29
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++++--------------
NAMESPACE | 2 +-
NEWS | 8 ++++++++
R/pint.jack.R |only
R/pintsc.boot.R | 7 +++++--
R/pintsc.jack.R |only
man/PHENIX-package.Rd | 2 +-
man/cor.par.Rd | 2 +-
man/paeonia.Rd | 2 +-
man/pint.Rd | 8 ++++----
man/pint.boot.Rd | 4 ++--
man/pint.jack.Rd |only
man/pint.p.Rd | 4 ++--
man/pintsc.Rd | 4 ++--
man/pintsc.boot.Rd | 6 +++---
man/pintsc.jack.Rd |only
man/pintsc.p.Rd | 4 ++--
man/tussilago.Rd | 4 ++--
19 files changed, 57 insertions(+), 42 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Diff between KFAS versions 1.1.0 dated 2015-04-18 and 1.1.1 dated 2015-04-29
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-1.1.0/KFAS/README.md |only
KFAS-1.1.0/KFAS/tests/testthat/testSSMarima.R |only
KFAS-1.1.1/KFAS/ChangeLog | 6
KFAS-1.1.1/KFAS/DESCRIPTION | 8
KFAS-1.1.1/KFAS/MD5 | 51 -
KFAS-1.1.1/KFAS/R/KFAS-package.R | 37 +
KFAS-1.1.1/KFAS/R/KFS.R | 4
KFAS-1.1.1/KFAS/R/SSMarima.R | 5
KFAS-1.1.1/KFAS/R/SSMcycle.R | 6
KFAS-1.1.1/KFAS/R/SSMseasonal.R | 184 ++----
KFAS-1.1.1/KFAS/R/SSMtrend.R | 9
KFAS-1.1.1/KFAS/R/artransform.R | 4
KFAS-1.1.1/KFAS/R/ldl.R | 11
KFAS-1.1.1/KFAS/build/vignette.rds |binary
KFAS-1.1.1/KFAS/inst/CITATION |only
KFAS-1.1.1/KFAS/inst/doc/KFAS.pdf |binary
KFAS-1.1.1/KFAS/man/KFAS.Rd | 37 +
KFAS-1.1.1/KFAS/man/ldl.Rd | 10
KFAS-1.1.1/KFAS/src/artransform.f95 | 44 -
KFAS-1.1.1/KFAS/src/declarations.h | 2
KFAS-1.1.1/KFAS/src/filter1step.f95 | 8
KFAS-1.1.1/KFAS/src/filter1stepnovar.f95 | 158 ++---
KFAS-1.1.1/KFAS/src/init.c | 2
KFAS-1.1.1/KFAS/src/kfilter.f95 | 5
KFAS-1.1.1/KFAS/tests/testthat/misc.R |only
KFAS-1.1.1/KFAS/tests/testthat/testArima.R |only
KFAS-1.1.1/KFAS/tests/testthat/testGLM.R | 642 ++++++++++-----------
KFAS-1.1.1/KFAS/tests/testthat/testImportanceSSM.R | 60 -
KFAS-1.1.1/KFAS/tests/testthat/testNumerical.R | 116 +--
29 files changed, 740 insertions(+), 669 deletions(-)
Title: Forecastable Component Analysis
Diff between ForeCA versions 0.2.0 dated 2015-02-20 and 0.2.2 dated 2015-04-29
Description: Implementation of Forecastable Component Analysis ('ForeCA'),
including main algorithms and auxiliary function (summary, plotting, etc.)
to apply 'ForeCA' to multivariate time series data.
'ForeCA' is a novel dimension reduction (DR) technique for temporally
dependent signals. Contrary to other popular DR methods, such as 'PCA' or 'ICA',
'ForeCA' takes time dependency explicitly into account and searches for the
most ''forecastable'' signal. The measure of forecastability is based on
the Shannon entropy of the spectral density of the transformed signal.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
DESCRIPTION | 24 +--
MD5 | 88 +++++++------
NAMESPACE | 5
NEWS | 35 +++++
R/Omega.R | 5
R/SDF2mvspectrum.R | 13 --
R/complete_controls.R | 12 -
R/discrete_entropy.R | 1
R/foreca-utils.R | 25 ++-
R/foreca.EM-aux.R | 51 ++++++--
R/foreca.EM.one_weightvector.R | 41 ++----
R/foreca.R | 52 ++++----
R/initialize_weightvector.R | 36 +++++
R/mvspec2mvspectrum.R | 1
R/mvspectrum-utils.R |only
R/mvspectrum.R | 164 +++++++++++++-------------
R/quadratic_form.R | 46 ++++++-
R/spectral_entropy.R | 19 ++-
R/univariate_spectrum-functions.R | 7 -
R/whiten.R | 10 +
man/ForeCA-package.Rd | 2
man/Omega.Rd | 2
man/common-arguments.Rd | 2
man/complete-controls.Rd | 10 -
man/continuous_entropy.Rd | 2
man/discrete_entropy.Rd | 2
man/foreca-utils.Rd | 2
man/foreca.EM-aux.Rd | 18 ++
man/foreca.EM.one_weightvector.Rd | 2
man/foreca.Rd | 12 -
man/foreca.one_weightvector-utils.Rd | 2
man/initialize_weightvector.Rd | 10 +
man/mvspectrum-utils.Rd |only
man/mvspectrum.Rd | 22 ++-
man/mvspectrum2wcov.Rd | 2
man/quadratic_form.Rd | 27 +++-
man/sfa.Rd | 2
man/spectral_entropy.Rd | 4
man/whiten.Rd | 2
tests/testthat/helper_mvspectrum_methods.R | 3
tests/testthat/test_foreca.EM-aux.R | 19 ++-
tests/testthat/test_initialize_weightvector.R | 1
tests/testthat/test_mvspectrum.R | 99 +++++++++++----
tests/testthat/test_mvspectrum2wcov.R | 4
tests/testthat/test_quadratic_form.R | 52 ++++++++
tests/testthat/test_whiten.R | 10 +
46 files changed, 627 insertions(+), 321 deletions(-)
Title: Fitting Step-Functions
Diff between stepR versions 1.0-1 dated 2015-03-04 and 1.0-2 dated 2015-04-29
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Thomas Hotz [aut, cre],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Thomas Hotz
ChangeLog | 20 ++++++++++++++++++++
DESCRIPTION | 14 ++++++++------
MD5 | 18 +++++++++---------
R/jumpint.R | 4 ++--
R/smuceR.R | 10 +++++++---
R/stepbound.R | 2 +-
R/steppath.R | 2 +-
man/family.Rd | 4 ++--
man/sdrobnorm.Rd | 2 ++
tests/tests.R | 3 +++
10 files changed, 55 insertions(+), 24 deletions(-)
Title: Measures of Risk for the Compound Poisson Risk Process with
Diffusion
Diff between sdprisk versions 1.0-3 dated 2013-12-30 and 1.1-0 dated 2015-04-29
Description: The main purpose of this package is to provide saddlepoint
approximations to some measures of risk, based on the compound Poisson risk
process that is perturbed by a Brownian motion. Various approximation
methods for the probability of ruin are also included. Furthermore, exact
values of both the risk measures as well as the probability of ruin are
available if the individual claims follow a hypo-exponential distribution
(i. e., if it can be represented as a sum of independent exponentially
distributed random variables with different rate parameters).
Author: Benjamin Baumgartner [aut, cre],
Riccardo Gatto [ctb, ths],
Sebastian Szugat [ctb]
Maintainer: Benjamin Baumgartner
DESCRIPTION | 33 +++++++++++++++++++++++++++------
MD5 | 11 ++++++-----
R/boundsRuinprob.R | 3 +--
R/qhypoexp.R |only
R/rhypoexp.R | 23 +++++++++++++++++------
inst/CITATION | 11 ++++++-----
man/hypoexp.Rd | 12 ++++++++++--
7 files changed, 67 insertions(+), 26 deletions(-)
Title: Type-Specific Failure Rate and Hazard Rate on Competing Risks
Data
Diff between NPMLEcmprsk versions 2.0 dated 2014-12-09 and 2.1 dated 2015-04-29
Description: Given a failure type, the function computes covariate-specific probability of failure over time and covariate-specific conditional hazard rate based on possibly right-censored competing risk data. Specifically, it computes the non-parametric maximum-likelihood estimates of these quantities and their asymptotic variances in a semi-parametric mixture model for competing-risks data, as described in Chang et al. (2007a).
Author: Chung-Hsing Chen, I-Shou Chang and Chao A. Hsiung
Maintainer: Chung-Hsing Chen
DESCRIPTION | 10 +++++-----
MD5 | 6 ++++--
R/improved_CompetingRisk_Code_v10.2.r |only
R/improved_CompetingRisk_Code_v10.3.r |only
man/NPMLEcmprsk.Rd | 4 ++--
5 files changed, 11 insertions(+), 9 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Diff between evmix versions 2.4 dated 2015-01-23 and 2.5 dated 2015-04-29
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the evd package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott
DESCRIPTION | 8 -
MD5 | 225 +++++++++++++++++++--------------------
NAMESPACE | 2
R/checking.r | 7 +
R/evmix-package.r | 4
R/evmixdiag.r | 126 ++++++++++++---------
R/fbckdengpd.r | 4
R/fbckdengpdcon.r | 4
R/fbetagpd.r | 4
R/fbetagpdcon.r | 4
R/fgammagpd.r | 4
R/fgammagpdcon.r | 4
R/fgkg.r | 6 -
R/fgkgcon.r | 3
R/fgng.r | 5
R/fgngcon.r | 6 -
R/fhpdcon.r | 2
R/fitmgng.r | 2
R/fitmnormgpd.r | 2
R/fitmweibullgpd.r | 2
R/fkdengpd.r | 4
R/fkdengpdcon.r | 5
R/flognormgpd.r | 4
R/flognormgpdcon.r | 4
R/fmgamma.r | 7 +
R/fmgammagpd.r | 18 ++-
R/fmgammagpdcon.r | 18 ++-
R/fnormgpd.r | 16 +-
R/fnormgpdcon.r | 4
R/fpsden.r | 14 ++
R/fpsdengpd.r | 4
R/fweibullgpd.r | 26 ++--
R/fweibullgpdcon.r | 4
R/hillplot.r | 40 +++++-
R/mrlplot.r | 3
R/pickandsplot.r | 25 +++-
R/tcplot.r | 9 +
inst/CITATION | 4
inst/doc/Rd2.pdf |binary
inst/doc/evmix_supplementary.pdf |only
man/bckden.Rd | 2
man/bckdengpd.Rd | 2
man/bckdengpdcon.Rd | 2
man/betagpd.Rd | 2
man/betagpdcon.Rd | 2
man/checking.Rd | 2
man/dwm.Rd | 2
man/evmix-package.Rd | 6 -
man/evmix.diag.Rd | 2
man/fbckden.Rd | 2
man/fbckdengpd.Rd | 4
man/fbckdengpdcon.Rd | 4
man/fbetagpd.Rd | 4
man/fbetagpdcon.Rd | 4
man/fdwm.Rd | 2
man/fgammagpd.Rd | 4
man/fgammagpdcon.Rd | 4
man/fgkg.Rd | 4
man/fgkgcon.Rd | 4
man/fgng.Rd | 4
man/fgngcon.Rd | 4
man/fgpd.Rd | 2
man/fhpd.Rd | 2
man/fhpdcon.Rd | 4
man/fitmgng.Rd | 4
man/fitmnormgpd.Rd | 4
man/fitmweibullgpd.Rd | 4
man/fkden.Rd | 2
man/fkdengpd.Rd | 4
man/fkdengpdcon.Rd | 4
man/flognormgpd.Rd | 4
man/flognormgpdcon.Rd | 4
man/fmgamma.Rd | 2
man/fmgammagpd.Rd | 4
man/fmgammagpdcon.Rd | 4
man/fnormgpd.Rd | 6 -
man/fnormgpdcon.Rd | 4
man/fpsden.Rd | 2
man/fpsdengpd.Rd | 4
man/fweibullgpd.Rd | 6 -
man/fweibullgpdcon.Rd | 4
man/gammagpd.Rd | 2
man/gammagpdcon.Rd | 2
man/gkg.Rd | 2
man/gkgcon.Rd | 2
man/gng.Rd | 2
man/gngcon.Rd | 2
man/gpd.Rd | 2
man/hillplot.Rd | 5
man/hpd.Rd | 2
man/hpdcon.Rd | 2
man/internal.Rd | 2
man/itmgng.Rd | 2
man/itmnormgpd.Rd | 2
man/itmweibullgpd.Rd | 2
man/kden.Rd | 2
man/kdengpd.Rd | 2
man/kdengpdcon.Rd | 2
man/kernels.Rd | 2
man/kfun.Rd | 2
man/lognormgpd.Rd | 2
man/lognormgpdcon.Rd | 2
man/mgamma.Rd | 2
man/mgammagpd.Rd | 2
man/mgammagpdcon.Rd | 2
man/mrlplot.Rd | 2
man/normgpd.Rd | 2
man/normgpdcon.Rd | 2
man/pickandsplot.Rd | 5
man/psden.Rd | 2
man/psdengpd.Rd | 2
man/tcplot.Rd | 2
man/weibullgpd.Rd | 2
man/weibullgpdcon.Rd | 2
114 files changed, 480 insertions(+), 365 deletions(-)
Title: Data for the Synbreed Package
Diff between synbreedData versions 1.4 dated 2013-12-12 and 1.5 dated 2015-04-29
Description: Data sets for the 'synbreed' package with three data sets from cattle, maize and mice to illustrate the functions in the 'synbreed' R package. All data sets are stored in the gpData format introduced in the 'synbreed'
package. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Theresa Albrecht, Hans-Juergen Auinger, Chris-Carolin Schoen with contributions by Malena Erbe, Ulrike Ober and Christian Reimer
Maintainer: Valentin Wimmer
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
data/cattle.RData |binary
data/maize.RData |binary
data/mice.RData |binary
man/mice.Rd | 2 +-
6 files changed, 13 insertions(+), 12 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Diff between sn versions 1.2-0 dated 2015-03-25 and 1.2-1 dated 2015-04-29
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini
DESCRIPTION | 10 +--
MD5 | 20 +++---
NEWS | 14 +++-
R/sn-funct.R | 151 ++++++++++++++++++++++++++++++++-----------------
R/sn_S4.R | 9 +-
man/dp2cp.Rd | 8 +-
man/extractSECdistr.Rd | 2
man/selm-class.Rd | 5 +
man/selm.Rd | 23 ++++++-
man/selm.fit.Rd | 20 +++---
man/sn-st.info.Rd | 6 -
11 files changed, 176 insertions(+), 92 deletions(-)
Title: Chinese Text Segmentation
Diff between jiebaR versions 0.4 dated 2015-01-04 and 0.5 dated 2015-04-29
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng
DESCRIPTION | 8
MD5 | 57 ++--
NAMESPACE | 2
NEWS | 12 +
R/RcppExports.R | 4
R/filter.R |only
R/jiebar.R | 22 +
R/keywords.R | 21 +
R/overload.R | 30 +-
R/print.R | 15 -
R/quick.R | 63 +++--
R/segment.R | 103 ++++++--
R/simhash.R | 4
R/tagger.R | 108 ++++++---
R/tools.R | 6
README.md | 408 +---------------------------------
build/vignette.rds |binary
inst/include/lib/HMMSegment.hpp | 12 -
inst/include/lib/KeywordExtractor.hpp | 42 +++
inst/include/segtype.hpp | 16 +
inst/model |only
man/edit_dict.Rd | 2
man/filter_segment.Rd |only
man/keywords.Rd | 3
man/tagging.Rd | 2
man/worker.Rd | 4
src/Makevars.win | 6
src/RcppExports.cpp | 318 ++++++++++----------------
src/segtype.cpp | 5
tests/testthat/bylines.utf8 |only
tests/testthat/test-cut.R | 1
31 files changed, 545 insertions(+), 729 deletions(-)
Title: Geographically Weighted Logistic Elastic Net Regression
Diff between GWLelast versions 1.0 dated 2015-04-20 and 1.1 dated 2015-04-29
Description: Fit a geographically weighted logistic elastic net regression.
Author: Daisuke Yoneoka, Eiko Saito
Maintainer: Daisuke Yoneoka
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 1 -
R/GWLelastic.R | 2 +-
4 files changed, 8 insertions(+), 9 deletions(-)
Title: Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF)
Diff between difR versions 4.5 dated 2013-04-07 and 4.6 dated 2015-04-29
Description: Collection of traditional methods to detect differential item functioning among dichotomously scored items.
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles Raiche (UQAM)
Maintainer: David Magis
difR-4.5/difR/R/Logistik.r |only
difR-4.6/difR/DESCRIPTION | 21 -
difR-4.6/difR/LICENSE | 4
difR-4.6/difR/MD5 | 116 +++++----
difR-4.6/difR/NAMESPACE | 26 ++
difR-4.6/difR/NEWS | 60 +++++
difR-4.6/difR/R/Logistik.R |only
difR-4.6/difR/R/dichoDif.r | 61 +++--
difR-4.6/difR/R/difBD.r | 92 +++++--
difR-4.6/difR/R/difGMH.r | 90 +++++--
difR-4.6/difR/R/difGenLogistic.R | 387 +++++++++++++++++++--------------
difR-4.6/difR/R/difGenLord.r | 134 +++++++----
difR-4.6/difR/R/difLRT.r | 24 +-
difR-4.6/difR/R/difLogReg.R |only
difR-4.6/difR/R/difLogistic.r | 184 +++++++++------
difR-4.6/difR/R/difLord.r | 142 ++++++++----
difR-4.6/difR/R/difMH.r | 119 ++++++----
difR-4.6/difR/R/difRaju.r | 132 +++++++----
difR-4.6/difR/R/difStd.r | 105 ++++++--
difR-4.6/difR/R/difTID.r | 102 +++++---
difR-4.6/difR/R/genDichoDif.R | 55 +++-
difR-4.6/difR/R/genLogistik.R | 109 ++++-----
difR-4.6/difR/R/selectDif.r | 18 -
difR-4.6/difR/R/selectGenDif.R | 8
difR-4.6/difR/inst/CITATION | 12 -
difR-4.6/difR/man/LRT.Rd | 8
difR-4.6/difR/man/Logistik.rd | 66 +++--
difR-4.6/difR/man/LordChi2.rd | 30 +-
difR-4.6/difR/man/RajuZ.rd | 36 +--
difR-4.6/difR/man/breslowDay.rd | 6
difR-4.6/difR/man/contrastMatrix.rd | 6
difR-4.6/difR/man/dichoDif.rd | 131 ++++-------
difR-4.6/difR/man/difBD.rd | 36 +--
difR-4.6/difR/man/difGMH.rd | 43 ++-
difR-4.6/difR/man/difGenLogistic.rd | 75 +++---
difR-4.6/difR/man/difGenLord.rd | 81 +++---
difR-4.6/difR/man/difLRT.rd | 30 +-
difR-4.6/difR/man/difLogReg.rd |only
difR-4.6/difR/man/difLogistic.rd | 90 ++++---
difR-4.6/difR/man/difLord.rd | 76 +++---
difR-4.6/difR/man/difMH.rd | 40 ++-
difR-4.6/difR/man/difR-package.Rd | 10
difR-4.6/difR/man/difRaju.rd | 88 ++++---
difR-4.6/difR/man/difStd.rd | 41 ++-
difR-4.6/difR/man/difTID.Rd | 37 +--
difR-4.6/difR/man/genDichoDif.rd | 94 +++-----
difR-4.6/difR/man/genLogistik.rd | 43 ++-
difR-4.6/difR/man/genLordChi2.rd | 34 +-
difR-4.6/difR/man/genMantelHaenszel.rd | 14 -
difR-4.6/difR/man/itemPar1PL.rd | 10
difR-4.6/difR/man/itemPar2PL.rd | 2
difR-4.6/difR/man/itemPar3PL.rd | 4
difR-4.6/difR/man/itemPar3PLconst.rd | 6
difR-4.6/difR/man/itemParEst.rd | 16 -
difR-4.6/difR/man/itemRescale.rd | 25 +-
difR-4.6/difR/man/mantelHaenszel.rd | 12 -
difR-4.6/difR/man/selectDif.rd | 98 +++-----
difR-4.6/difR/man/selectGenDif.rd | 90 +++----
difR-4.6/difR/man/stdPDIF.rd | 10
difR-4.6/difR/man/subtestLogistic.rd | 38 +--
difR-4.6/difR/man/trItemDiff.Rd | 4
61 files changed, 2033 insertions(+), 1398 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Diff between dae versions 2.4-0 dated 2014-12-10 and 2.7-0 dated 2015-04-29
Description: The content falls into the following groupings: (i) Data,
(ii) Factor manipulation functions, (iii) Design functions,
(iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical
efficiency functions, and (vii) Miscellaneous functions. A document
'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for
generating randomized layouts for experiments. The ANOVA functions
facilitate the extraction of information when the 'Error' function has
been used in the call to 'aov'.
Author: Chris Brien
Maintainer: Chris Brien
DESCRIPTION | 22 ++++---
MD5 | 90 +++++++++++++++++++-----------
NAMESPACE | 31 +++++++++-
R/Interaction.ABC.Plot.r | 45 ++++++++-------
R/dae.utilties.r |only
R/fac.functions.r | 13 ++--
R/fac.layout.r | 16 ++++-
R/fac.match.r | 54 +++++++++++++-----
R/harmonic.mean.r |only
R/mat.functions.r | 52 ++++++++++++++++-
R/proj.canon.v3.r |only
R/proj.r | 107 +++++++++++++-----------------------
R/projs.canon.v3.r |only
data/Sensory3Phase.dat.rda |only
inst/doc/dae-manual.pdf |binary
inst/doc/daeDesignRandomization.pdf |binary
man/Sensory3Phase.dat.Rd |only
man/as.numfac.Rd | 3 -
man/correct.degfree.Rd | 4 -
man/dae-package.Rd |only
man/decomp.relate.Rd | 33 +++++------
man/degfree.Rd | 4 -
man/efficiencies.p2canon.Rd |only
man/efficiencies.pcanon.Rd |only
man/efficiency.criteria.Rd |only
man/fac.layout.Rd | 34 ++++++-----
man/fac.match.Rd | 37 +++++++++---
man/fac.vcmat.Rd | 2
man/fitted.aovlist.Rd | 2
man/fitted.errors.rd | 2
man/get.daeTolerance.Rd | 9 ++-
man/harmonic.mean.Rd |only
man/interaction.ABC.plot.Rd | 13 +---
man/is.allzero.Rd | 4 -
man/is.projector.Rd | 3 -
man/mat.ar1.Rd | 2
man/mat.banded.Rd |only
man/mat.dirprod.Rd | 2
man/mat.dirsum.Rd |only
man/mat.exp.Rd |only
man/print.summary.p2canon.Rd |only
man/print.summary.pcanon.Rd |only
man/proj2.combine.Rd |only
man/proj2.decomp.Rd | 58 +------------------
man/proj2.efficiency.Rd | 32 ++++------
man/proj2.eigen.Rd |only
man/proj2.ops.Rd | 72 +-----------------------
man/projector.Rd | 17 +++--
man/projs.2canon.Rd |only
man/projs.canon.Rd |only
man/projs.combine.p2canon.Rd |only
man/projs.structure.Rd |only
man/resid.errors.Rd | 2
man/residuals.aovlist.Rd | 2
man/set.daeTolerance.Rd | 26 ++++++--
man/summary.p2canon.Rd |only
man/summary.pcanon.Rd |only
man/tukey.1df.Rd | 2
58 files changed, 408 insertions(+), 387 deletions(-)
Title: Pretty Descriptive Stats
Diff between prettyR versions 2.1 dated 2015-01-20 and 2.1-1 dated 2015-04-29
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NEWS | 4 ++++
R/R2html.R | 2 +-
R/brkdn.R | 2 +-
R/decimal.align.R | 4 ++--
R/delim.table.R | 4 ++--
R/describe.R | 6 +++---
R/htmlize.R | 4 ++--
R/print.freq.R | 2 +-
R/print.xtab.R | 6 +++---
R/truncString.R | 3 +--
12 files changed, 35 insertions(+), 32 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Diff between phytools versions 0.4-45 dated 2015-02-05 and 0.4-56 dated 2015-04-29
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 53 ++++++++++++++++++--
MD5 | 84 ++++++++++++++++-----------------
NAMESPACE | 4 -
R/bmPlot.R | 5 +
R/branching.diffusion.R | 34 +++++++++----
R/collapseTree.R |only
R/contMap.R | 20 +++++--
R/densityMap.R | 46 ++++++++++++------
R/fancyTree.R | 20 +++++++
R/fastAnc.R | 4 -
R/map.to.singleton.R | 7 +-
R/phenogram.R | 18 +++++--
R/phyl.pca.R | 56 ++++++++++++++++++++--
R/plotBranchbyTrait.R | 3 -
R/plotSimmap.R | 31 +++++++-----
R/plotTree.wBars.R | 49 ++++++++++++++-----
R/utilities.R | 114 ++++++++++++++++++++++++---------------------
man/add.color.bar.Rd | 2
man/add.random.Rd | 2
man/bind.tip.Rd | 2
man/bmPlot.Rd | 2
man/branching.diffusion.Rd | 6 +-
man/collapseTree.Rd |only
man/contMap.Rd | 2
man/densityMap.Rd | 2
man/fancyTree.Rd | 2
man/fastBM.Rd | 2
man/lambda.transform.Rd | 4 -
man/ltt.Rd | 2
man/nodeHeights.Rd | 2
man/orderMappedEdge.Rd | 2
man/pbtree.Rd | 2
man/phenogram.Rd | 4 -
man/phyl.RMA.Rd | 2
man/phyl.pairedttest.Rd | 4 -
man/phyl.pca.Rd | 4 -
man/phyl.vcv.Rd | 4 -
man/phyloDesign.Rd | 2
man/plot.backbonePhylo.Rd | 24 +++++++++
man/plotBranchbyTrait.Rd | 2
man/plotSimmap.Rd | 6 +-
man/plotTree.wBars.Rd | 3 -
man/reroot.Rd | 2
man/setMap.Rd | 2
44 files changed, 435 insertions(+), 206 deletions(-)
Title: Topographic and Geologic Mapping
Diff between GEOmap versions 2.2-2 dated 2014-01-05 and 2.3-5 dated 2015-04-29
Description: Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
GEOmap-2.2-2/GEOmap/inst/doc/GEOmap.R |only
GEOmap-2.2-2/GEOmap/inst/doc/GEOmap.Rnw |only
GEOmap-2.2-2/GEOmap/vignettes |only
GEOmap-2.3-5/GEOmap/DESCRIPTION | 14 ++---
GEOmap-2.3-5/GEOmap/MD5 | 73 +++++++++++++--------------
GEOmap-2.3-5/GEOmap/NAMESPACE | 2
GEOmap-2.3-5/GEOmap/NEWS | 2
GEOmap-2.3-5/GEOmap/R/DATUMinfo.R |only
GEOmap-2.3-5/GEOmap/R/Ellipsoidal.Distance.R | 2
GEOmap-2.3-5/GEOmap/R/GLOBE.ORTH.R | 3 -
GEOmap-2.3-5/GEOmap/R/MAPconstants.R | 2
GEOmap-2.3-5/GEOmap/R/UTM.ll.R |only
GEOmap-2.3-5/GEOmap/R/UTM.xy.R |only
GEOmap-2.3-5/GEOmap/R/UTMzone.R |only
GEOmap-2.3-5/GEOmap/R/geoLEGEND.R | 32 +++++++++--
GEOmap-2.3-5/GEOmap/R/maps2GEOmap.R | 40 +++++++-------
GEOmap-2.3-5/GEOmap/R/plotGEOmap.R | 2
GEOmap-2.3-5/GEOmap/R/setPROJ.R | 45 ++++++++++++++--
GEOmap-2.3-5/GEOmap/R/subsetTOPO.R | 3 -
GEOmap-2.3-5/GEOmap/build/vignette.rds |binary
GEOmap-2.3-5/GEOmap/demo/weathermap.R | 2
GEOmap-2.3-5/GEOmap/inst/doc/GEOmap.pdf |binary
GEOmap-2.3-5/GEOmap/man/BASICTOPOMAP.Rd | 6 +-
GEOmap-2.3-5/GEOmap/man/DATUMinfo.Rd |only
GEOmap-2.3-5/GEOmap/man/GETXprofile.Rd | 4 +
GEOmap-2.3-5/GEOmap/man/NSWath.Rd | 4 +
GEOmap-2.3-5/GEOmap/man/UTM.ll.Rd |only
GEOmap-2.3-5/GEOmap/man/UTM.xy.Rd |only
GEOmap-2.3-5/GEOmap/man/UTMzone.Rd |only
GEOmap-2.3-5/GEOmap/man/XSECEQ.Rd | 6 +-
GEOmap-2.3-5/GEOmap/man/XSECwin.Rd | 10 ++-
GEOmap-2.3-5/GEOmap/man/addLLXY.Rd | 8 +-
GEOmap-2.3-5/GEOmap/man/geoLEGEND.Rd | 64 ++++++++++++++++++++---
GEOmap-2.3-5/GEOmap/man/insideGEOmapXY.Rd | 7 +-
GEOmap-2.3-5/GEOmap/man/plotGEOmapXY.Rd | 12 +---
GEOmap-2.3-5/GEOmap/man/plotUTM.Rd | 7 ++
GEOmap-2.3-5/GEOmap/man/plothypos.Rd | 10 ++-
GEOmap-2.3-5/GEOmap/man/setPROJ.Rd | 11 +++-
GEOmap-2.3-5/GEOmap/man/utm.sphr.ll.Rd | 1
GEOmap-2.3-5/GEOmap/man/utm.sphr.xy.Rd | 2
40 files changed, 253 insertions(+), 121 deletions(-)
Title: A Package for Image Analysis of DCE-MRI (S4 Implementation)
Diff between dcemriS4 versions 0.51 dated 2013-12-30 and 0.55 dated 2015-04-29
Description: A collection of routines and documentation that allows one to
perform voxel-wise quantitative analysis of dynamic contrast-enhanced MRI
(DEC-MRI) and diffusion-weighted imaging (DWI) data, with emphasis on
oncology applications.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [ctb]
Maintainer: Brandon Whitcher
dcemriS4-0.51/dcemriS4/man/aif.Rd |only
dcemriS4-0.51/dcemriS4/man/conv_fft.Rd |only
dcemriS4-0.51/dcemriS4/man/cpmg.Rd |only
dcemriS4-0.51/dcemriS4/man/dam.Rd |only
dcemriS4-0.51/dcemriS4/man/dce_bayes.Rd |only
dcemriS4-0.51/dcemriS4/man/dce_map.Rd |only
dcemriS4-0.51/dcemriS4/man/dce_spline.Rd |only
dcemriS4-0.51/dcemriS4/man/dcemri.Rd |only
dcemriS4-0.51/dcemriS4/man/dwi.Rd |only
dcemriS4-0.51/dcemriS4/man/extract.Rd |only
dcemriS4-0.51/dcemriS4/man/find_center.Rd |only
dcemriS4-0.51/dcemriS4/man/flipangle.Rd |only
dcemriS4-0.51/dcemriS4/man/ftm.Rd |only
dcemriS4-0.51/dcemriS4/man/kineticmodel.Rd |only
dcemriS4-0.51/dcemriS4/man/rcbv.Rd |only
dcemriS4-0.55/dcemriS4/DESCRIPTION | 39
dcemriS4-0.55/dcemriS4/LICENSE | 2
dcemriS4-0.55/dcemriS4/MD5 | 95 +-
dcemriS4-0.55/dcemriS4/NAMESPACE | 61 -
dcemriS4-0.55/dcemriS4/R/aif.R | 116 ++
dcemriS4-0.55/dcemriS4/R/cpmg.R | 102 +-
dcemriS4-0.55/dcemriS4/R/dcemriS4-package.R |only
dcemriS4-0.55/dcemriS4/R/dcemri_bayes.R | 202 +++-
dcemriS4-0.55/dcemriS4/R/dcemri_lm.R | 220 ++++-
dcemriS4-0.55/dcemriS4/R/dcemri_map.R | 174 +++-
dcemriS4-0.55/dcemriS4/R/dcemri_spline.R | 173 +++
dcemriS4-0.55/dcemriS4/R/dwi.R | 132 ++-
dcemriS4-0.55/dcemriS4/R/flipangle.R | 249 ++++-
dcemriS4-0.55/dcemriS4/R/kineticmodel.R | 78 +
dcemriS4-0.55/dcemriS4/R/model.R | 73 +
dcemriS4-0.55/dcemriS4/R/rcbv.R | 76 +
dcemriS4-0.55/dcemriS4/R/template_matching.R | 162 +++
dcemriS4-0.55/dcemriS4/R/wrappers.R | 7
dcemriS4-0.55/dcemriS4/R/zzz.R | 7
dcemriS4-0.55/dcemriS4/build/vignette.rds |binary
dcemriS4-0.55/dcemriS4/data/buckley.rda |binary
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.R | 6
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.Rnw | 25
dcemriS4-0.55/dcemriS4/inst/doc/dcemriS4.pdf |binary
dcemriS4-0.55/dcemriS4/man/ADC-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/CPMG-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/aif-models.Rd |only
dcemriS4-0.55/dcemriS4/man/aifParameters.Rd | 55 -
dcemriS4-0.55/dcemriS4/man/buckley.Rd | 72 -
dcemriS4-0.55/dcemriS4/man/compartmentalModel.Rd | 81 -
dcemriS4-0.55/dcemriS4/man/convFFT.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.bayes-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.lm-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.map-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemri.spline-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/dcemriS4-package.Rd | 133 ---
dcemriS4-0.55/dcemriS4/man/doubleAngleMethod.Rd |only
dcemriS4-0.55/dcemriS4/man/expConv.Rd | 34
dcemriS4-0.55/dcemriS4/man/extractAIF.Rd |only
dcemriS4-0.55/dcemriS4/man/fastTemplateMatching.Rd |only
dcemriS4-0.55/dcemriS4/man/findCenter.Rd |only
dcemriS4-0.55/dcemriS4/man/kineticModel.Rd |only
dcemriS4-0.55/dcemriS4/man/rcbv-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/relaxation-methods.Rd |only
dcemriS4-0.55/dcemriS4/man/shift3D.Rd | 56 -
dcemriS4-0.55/dcemriS4/src/Makevars | 2
dcemriS4-0.55/dcemriS4/tests/Examples/dcemriS4-Ex.Rout.save | 522 +++++-------
dcemriS4-0.55/dcemriS4/tests/testthat |only
dcemriS4-0.55/dcemriS4/tests/testthat.R |only
dcemriS4-0.55/dcemriS4/vignettes/dcemriS4.Rnw | 25
65 files changed, 2052 insertions(+), 927 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Diff between urltools versions 0.6 dated 2014-12-22 and 1.1.0 dated 2015-04-28
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Mark Greenaway [ctb]
Maintainer: Oliver Keyes
urltools-0.6/urltools/man/extract_host.Rd |only
urltools-0.6/urltools/man/extract_parameter.Rd |only
urltools-0.6/urltools/man/replace_parameter.Rd |only
urltools-1.1.0/urltools/DESCRIPTION | 14
urltools-1.1.0/urltools/MD5 | 58 ++--
urltools-1.1.0/urltools/NAMESPACE | 19 +
urltools-1.1.0/urltools/NEWS | 25 +
urltools-1.1.0/urltools/R/RcppExports.R | 117 ++------
urltools-1.1.0/urltools/R/accessors.R |only
urltools-1.1.0/urltools/R/urltools.R | 3
urltools-1.1.0/urltools/README.md | 9
urltools-1.1.0/urltools/build/vignette.rds |binary
urltools-1.1.0/urltools/inst/doc/urltools.R | 48 ++-
urltools-1.1.0/urltools/inst/doc/urltools.Rmd | 66 +++-
urltools-1.1.0/urltools/inst/doc/urltools.html | 68 +++-
urltools-1.1.0/urltools/man/domain.Rd |only
urltools-1.1.0/urltools/man/encoder.Rd | 3
urltools-1.1.0/urltools/man/fragment.Rd |only
urltools-1.1.0/urltools/man/path.Rd |only
urltools-1.1.0/urltools/man/port.Rd |only
urltools-1.1.0/urltools/man/query.Rd |only
urltools-1.1.0/urltools/man/scheme.Rd |only
urltools-1.1.0/urltools/man/url_parameters.Rd |only
urltools-1.1.0/urltools/man/url_parse.Rd | 12
urltools-1.1.0/urltools/man/urltools.Rd | 6
urltools-1.1.0/urltools/src/Makevars |only
urltools-1.1.0/urltools/src/RcppExports.cpp | 132 +++------
urltools-1.1.0/urltools/src/accessors.cpp |only
urltools-1.1.0/urltools/src/encoding.cpp | 58 +++-
urltools-1.1.0/urltools/src/encoding.h | 90 +++---
urltools-1.1.0/urltools/src/parsing.cpp | 241 +++++++++--------
urltools-1.1.0/urltools/src/parsing.h | 158 +++++++++--
urltools-1.1.0/urltools/src/urltools.cpp | 196 ++++---------
urltools-1.1.0/urltools/tests/testthat/test_encoding.R | 4
urltools-1.1.0/urltools/tests/testthat/test_get_set.R |only
urltools-1.1.0/urltools/tests/testthat/test_parsing.R | 54 +--
urltools-1.1.0/urltools/vignettes/urltools.Rmd | 66 +++-
37 files changed, 820 insertions(+), 627 deletions(-)
Title: Seismic Time Series Analysis Tools
Diff between RSEIS versions 3.3-3 dated 2014-01-05 and 3.4-5 dated 2015-04-28
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
RSEIS-3.3-3/RSEIS/man/JGET.seis.Rd |only
RSEIS-3.3-3/RSEIS/man/rseis2sac.Rd |only
RSEIS-3.3-3/RSEIS/man/write1sac.Rd |only
RSEIS-3.4-5/RSEIS/DESCRIPTION | 10 -
RSEIS-3.4-5/RSEIS/MD5 | 85 ++++++----
RSEIS-3.4-5/RSEIS/NEWS | 10 +
RSEIS-3.4-5/RSEIS/R/CHOP.SEISN.R | 11 +
RSEIS-3.4-5/RSEIS/R/FmakeDB.R | 9 -
RSEIS-3.4-5/RSEIS/R/GET.seis.R |only
RSEIS-3.4-5/RSEIS/R/GLUE.GET.seis.R | 30 ++-
RSEIS-3.4-5/RSEIS/R/INSTresponse.R | 13 +
RSEIS-3.4-5/RSEIS/R/JSAC.seis.R | 4
RSEIS-3.4-5/RSEIS/R/JSEGY.seis.R | 4
RSEIS-3.4-5/RSEIS/R/Mine.seis.R | 2
RSEIS-3.4-5/RSEIS/R/PickWIN.R |only
RSEIS-3.4-5/RSEIS/R/WINGH.R | 2
RSEIS-3.4-5/RSEIS/R/X2SAC.R | 2
RSEIS-3.4-5/RSEIS/R/convert2Rseis.R | 2
RSEIS-3.4-5/RSEIS/R/fixcomps.R | 4
RSEIS-3.4-5/RSEIS/R/getphaselag2.R | 7
RSEIS-3.4-5/RSEIS/R/makeDB.R | 2
RSEIS-3.4-5/RSEIS/R/pADDPIX.R |only
RSEIS-3.4-5/RSEIS/R/pickFUNCS.R | 273 ++---------------------------------
RSEIS-3.4-5/RSEIS/R/prepSEIS.R | 25 ++-
RSEIS-3.4-5/RSEIS/R/read1sac.R |only
RSEIS-3.4-5/RSEIS/R/read1segy.R |only
RSEIS-3.4-5/RSEIS/R/rseis2sac.R | 58 +++++--
RSEIS-3.4-5/RSEIS/R/rseis2segy.R |only
RSEIS-3.4-5/RSEIS/R/sac2rseis.R |only
RSEIS-3.4-5/RSEIS/R/segy2rseis.R |only
RSEIS-3.4-5/RSEIS/R/swig.ALLPX.R | 5
RSEIS-3.4-5/RSEIS/R/swig.R | 8 -
RSEIS-3.4-5/RSEIS/R/write1sac.R | 42 ++---
RSEIS-3.4-5/RSEIS/R/write1segy.R |only
RSEIS-3.4-5/RSEIS/man/GET.seis.Rd |only
RSEIS-3.4-5/RSEIS/man/JSAC.seis.Rd | 4
RSEIS-3.4-5/RSEIS/man/PICK.DOC.Rd | 2
RSEIS-3.4-5/RSEIS/man/SPECT.drive.Rd | 2
RSEIS-3.4-5/RSEIS/man/YPIX.Rd | 1
RSEIS-3.4-5/RSEIS/man/ZOOM.SEISN.Rd | 3
RSEIS-3.4-5/RSEIS/man/choosfilt.Rd | 2
RSEIS-3.4-5/RSEIS/man/grotseis.Rd | 15 +
RSEIS-3.4-5/RSEIS/man/plocator.Rd | 2
RSEIS-3.4-5/RSEIS/man/read1segy.Rd |only
RSEIS-3.4-5/RSEIS/man/rseis2segy.Rd |only
RSEIS-3.4-5/RSEIS/man/screens.Rd | 2
RSEIS-3.4-5/RSEIS/man/segy2rseis.Rd |only
RSEIS-3.4-5/RSEIS/man/swig.Rd | 60 ++++---
RSEIS-3.4-5/RSEIS/man/wlet.drive.Rd | 2
RSEIS-3.4-5/RSEIS/man/write1segy.Rd |only
RSEIS-3.4-5/RSEIS/man/zlocator.Rd | 4
RSEIS-3.4-5/RSEIS/src/TTray.c | 4
52 files changed, 311 insertions(+), 400 deletions(-)
Title: API Wrapper for Quandl.com
Diff between Quandl versions 2.4.0 dated 2014-11-04 and 2.6.0 dated 2015-04-28
Description: Functions for interacting directly with the Quandl API to offer data
in a number of formats usable in R, as well as the ability to search.
Author: Raymond McTaggart [aut, cre],
Gergely Daroczi [aut],
Quandl Inc. [cph]
Maintainer: Raymond McTaggart
Quandl-2.4.0/Quandl/R/Quandlpush.R |only
Quandl-2.4.0/Quandl/inst |only
Quandl-2.4.0/Quandl/man/Quandl.curlopts.Rd |only
Quandl-2.4.0/Quandl/man/Quandl.push.Rd |only
Quandl-2.4.0/Quandl/tests/test-all.R |only
Quandl-2.6.0/Quandl/ChangeLog | 27 +
Quandl-2.6.0/Quandl/DESCRIPTION | 29 -
Quandl-2.6.0/Quandl/LICENSE | 2
Quandl-2.6.0/Quandl/MD5 | 34 -
Quandl-2.6.0/Quandl/NAMESPACE | 13
Quandl-2.6.0/Quandl/R/Quandl.R | 499 +++++++++++++++-----------
Quandl-2.6.0/Quandl/R/Quandlapi.R | 87 +---
Quandl-2.6.0/Quandl/R/Quandlsearch.R | 94 ++--
Quandl-2.6.0/Quandl/README.md | 53 --
Quandl-2.6.0/Quandl/man/Quandl.Rd | 20 -
Quandl-2.6.0/Quandl/man/Quandl.auth.Rd | 3
Quandl-2.6.0/Quandl/man/Quandl.dataset.get.Rd |only
Quandl-2.6.0/Quandl/man/Quandl.search.Rd | 7
Quandl-2.6.0/Quandl/man/metaData.Rd | 3
Quandl-2.6.0/Quandl/man/quandl.api.Rd | 11
Quandl-2.6.0/Quandl/tests/testthat |only
Quandl-2.6.0/Quandl/tests/testthat.R |only
22 files changed, 496 insertions(+), 386 deletions(-)
Title: Omics Data Integration Project
Diff between mixOmics versions 5.0-3 dated 2014-09-01 and 5.0-4 dated 2015-04-28
Description: We provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')
to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and
q variables are measured on the same samples or individuals n. These data may come from high throughput
technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other
large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with
the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting
the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent
Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration
of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found
on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao
mixOmics-5.0-3/mixOmics/R/jet.colors.R |only
mixOmics-5.0-3/mixOmics/R/select.var.R |only
mixOmics-5.0-3/mixOmics/data/data.simu.rda |only
mixOmics-5.0-3/mixOmics/man/data.simu.Rd |only
mixOmics-5.0-3/mixOmics/man/jet.colors.Rd |only
mixOmics-5.0-3/mixOmics/man/select.var.Rd |only
mixOmics-5.0-4/mixOmics/DESCRIPTION | 45
mixOmics-5.0-4/mixOmics/MD5 | 244
mixOmics-5.0-4/mixOmics/NAMESPACE | 24
mixOmics-5.0-4/mixOmics/NEWS | 21
mixOmics-5.0-4/mixOmics/R/Mfold.R | 6
mixOmics-5.0-4/mixOmics/R/bin.color.R | 198
mixOmics-5.0-4/mixOmics/R/cim.R | 10
mixOmics-5.0-4/mixOmics/R/cim.pls.R | 6
mixOmics-5.0-4/mixOmics/R/cim.rcc.R | 6
mixOmics-5.0-4/mixOmics/R/cim.spls.R | 6
mixOmics-5.0-4/mixOmics/R/color.GreenRed.R |only
mixOmics-5.0-4/mixOmics/R/color.jet.R |only
mixOmics-5.0-4/mixOmics/R/color.mixo.R |only
mixOmics-5.0-4/mixOmics/R/color.spectral.R |only
mixOmics-5.0-4/mixOmics/R/image.tune.rcc.R | 6
mixOmics-5.0-4/mixOmics/R/imgCor.R | 348 -
mixOmics-5.0-4/mixOmics/R/ipca.R | 240
mixOmics-5.0-4/mixOmics/R/loo.R | 6
mixOmics-5.0-4/mixOmics/R/map.R | 70
mixOmics-5.0-4/mixOmics/R/mat.rank.R | 48
mixOmics-5.0-4/mixOmics/R/multilevel.R | 513 -
mixOmics-5.0-4/mixOmics/R/nearZeroVar.R | 101
mixOmics-5.0-4/mixOmics/R/network.R | 1122 +--
mixOmics-5.0-4/mixOmics/R/network.rcc.R | 6
mixOmics-5.0-4/mixOmics/R/network.spls.R | 6
mixOmics-5.0-4/mixOmics/R/nipals.R | 6
mixOmics-5.0-4/mixOmics/R/pca.R | 222
mixOmics-5.0-4/mixOmics/R/pcasvd.R | 134
mixOmics-5.0-4/mixOmics/R/perf.R | 783 +-
mixOmics-5.0-4/mixOmics/R/pheatmap.multilevel.R | 159
mixOmics-5.0-4/mixOmics/R/pheatmap.multilevel.splsda1fact.R |only
mixOmics-5.0-4/mixOmics/R/pheatmap.multilevel.splsda2fact.R |only
mixOmics-5.0-4/mixOmics/R/plot.pca.R | 48
mixOmics-5.0-4/mixOmics/R/plot.perf.R | 21
mixOmics-5.0-4/mixOmics/R/plot.rcc.R | 32
mixOmics-5.0-4/mixOmics/R/plot3dIndiv.R | 820 +-
mixOmics-5.0-4/mixOmics/R/plot3dVar.R | 3482 ++++++------
mixOmics-5.0-4/mixOmics/R/plotIndiv.R | 411 -
mixOmics-5.0-4/mixOmics/R/plotVar.R | 238
mixOmics-5.0-4/mixOmics/R/pls.R | 197
mixOmics-5.0-4/mixOmics/R/plsda.R | 43
mixOmics-5.0-4/mixOmics/R/predict.R | 4
mixOmics-5.0-4/mixOmics/R/print.methods.R | 784 +-
mixOmics-5.0-4/mixOmics/R/rcc.R | 228
mixOmics-5.0-4/mixOmics/R/s.match.R | 207
mixOmics-5.0-4/mixOmics/R/scatterutil.R | 3
mixOmics-5.0-4/mixOmics/R/selectVar.R |only
mixOmics-5.0-4/mixOmics/R/sipca.R | 258
mixOmics-5.0-4/mixOmics/R/spca.R | 360 -
mixOmics-5.0-4/mixOmics/R/spls.R | 240
mixOmics-5.0-4/mixOmics/R/splsda.R | 41
mixOmics-5.0-4/mixOmics/R/summary.R | 24
mixOmics-5.0-4/mixOmics/R/tau.estim.R |only
mixOmics-5.0-4/mixOmics/R/tune.multilevel.R | 365 -
mixOmics-5.0-4/mixOmics/R/tune.pca.R | 268
mixOmics-5.0-4/mixOmics/R/tune.rcc.R | 6
mixOmics-5.0-4/mixOmics/R/tune.splsdalevel1.R |only
mixOmics-5.0-4/mixOmics/R/tune.splsdalevel2.R |only
mixOmics-5.0-4/mixOmics/R/tune.splslevel.R |only
mixOmics-5.0-4/mixOmics/R/unmap.R | 118
mixOmics-5.0-4/mixOmics/R/valid.R | 6
mixOmics-5.0-4/mixOmics/R/vip.R | 6
mixOmics-5.0-4/mixOmics/R/withinVariation.R |only
mixOmics-5.0-4/mixOmics/R/wrapper.rgcca.R | 23
mixOmics-5.0-4/mixOmics/R/wrapper.sgcca.R | 23
mixOmics-5.0-4/mixOmics/data/breast.tumors.rda |binary
mixOmics-5.0-4/mixOmics/data/datalist | 4
mixOmics-5.0-4/mixOmics/data/linnerud.rda |binary
mixOmics-5.0-4/mixOmics/data/liver.toxicity.rda |binary
mixOmics-5.0-4/mixOmics/data/multidrug.rda |binary
mixOmics-5.0-4/mixOmics/data/nutrimouse.rda |binary
mixOmics-5.0-4/mixOmics/data/prostate.rda |binary
mixOmics-5.0-4/mixOmics/data/srbct.rda |binary
mixOmics-5.0-4/mixOmics/data/vac18.rda |binary
mixOmics-5.0-4/mixOmics/data/vac18.simulated.rda |only
mixOmics-5.0-4/mixOmics/data/yeast.rda |binary
mixOmics-5.0-4/mixOmics/man/breast.tumors.Rd | 114
mixOmics-5.0-4/mixOmics/man/cim.Rd | 364 -
mixOmics-5.0-4/mixOmics/man/color.jet.Rd |only
mixOmics-5.0-4/mixOmics/man/estim.regul.Rd | 20
mixOmics-5.0-4/mixOmics/man/image.estim.regul.Rd | 20
mixOmics-5.0-4/mixOmics/man/image.tune.rcc.Rd | 88
mixOmics-5.0-4/mixOmics/man/imgCor.Rd | 188
mixOmics-5.0-4/mixOmics/man/internal-functions.Rd | 7
mixOmics-5.0-4/mixOmics/man/ipca.Rd | 192
mixOmics-5.0-4/mixOmics/man/linnerud.Rd | 2
mixOmics-5.0-4/mixOmics/man/liver.toxicity.Rd | 2
mixOmics-5.0-4/mixOmics/man/mat.rank.Rd | 113
mixOmics-5.0-4/mixOmics/man/multidrug.Rd | 168
mixOmics-5.0-4/mixOmics/man/multilevel.Rd | 287
mixOmics-5.0-4/mixOmics/man/nearZeroVar.Rd | 8
mixOmics-5.0-4/mixOmics/man/network.Rd | 35
mixOmics-5.0-4/mixOmics/man/nipals.Rd | 148
mixOmics-5.0-4/mixOmics/man/nutrimouse.Rd | 2
mixOmics-5.0-4/mixOmics/man/pca.Rd | 4
mixOmics-5.0-4/mixOmics/man/pcatune.Rd | 20
mixOmics-5.0-4/mixOmics/man/perf.Rd | 202
mixOmics-5.0-4/mixOmics/man/pheatmap.multilevel.Rd | 238
mixOmics-5.0-4/mixOmics/man/plot.perf.Rd | 2
mixOmics-5.0-4/mixOmics/man/plot.rcc.Rd | 90
mixOmics-5.0-4/mixOmics/man/plot3dIndiv.Rd | 6
mixOmics-5.0-4/mixOmics/man/plot3dVar.Rd | 392 -
mixOmics-5.0-4/mixOmics/man/plotIndiv.Rd | 7
mixOmics-5.0-4/mixOmics/man/plotVar.Rd | 70
mixOmics-5.0-4/mixOmics/man/pls.Rd | 176
mixOmics-5.0-4/mixOmics/man/plsda.Rd | 15
mixOmics-5.0-4/mixOmics/man/predict.Rd | 6
mixOmics-5.0-4/mixOmics/man/print.methods.Rd | 178
mixOmics-5.0-4/mixOmics/man/prostate.Rd | 70
mixOmics-5.0-4/mixOmics/man/rcc.Rd | 198
mixOmics-5.0-4/mixOmics/man/s.match.Rd | 4
mixOmics-5.0-4/mixOmics/man/scatterutil.Rd | 2
mixOmics-5.0-4/mixOmics/man/selectVar.Rd |only
mixOmics-5.0-4/mixOmics/man/sipca.Rd | 170
mixOmics-5.0-4/mixOmics/man/spca.Rd | 4
mixOmics-5.0-4/mixOmics/man/spls.Rd | 207
mixOmics-5.0-4/mixOmics/man/splsda.Rd | 189
mixOmics-5.0-4/mixOmics/man/summary.Rd | 210
mixOmics-5.0-4/mixOmics/man/tau.estimate.Rd |only
mixOmics-5.0-4/mixOmics/man/tune.multilevel.Rd | 143
mixOmics-5.0-4/mixOmics/man/tune.pca.Rd | 138
mixOmics-5.0-4/mixOmics/man/tune.rcc.Rd | 160
mixOmics-5.0-4/mixOmics/man/vac18.simulated.Rd |only
mixOmics-5.0-4/mixOmics/man/valid.Rd | 8
mixOmics-5.0-4/mixOmics/man/vip.Rd | 121
mixOmics-5.0-4/mixOmics/man/withinVariation.Rd |only
mixOmics-5.0-4/mixOmics/man/wrapper.rgcca.Rd | 120
mixOmics-5.0-4/mixOmics/man/wrapper.sgcca.Rd | 118
mixOmics-5.0-4/mixOmics/man/yeast.Rd | 78
135 files changed, 8725 insertions(+), 8975 deletions(-)
Title: Regression Models for Interval Censored Data
Diff between icenReg versions 1.0 dated 2015-04-28 and 1.1 dated 2015-04-28
Description: Regression models for interval censored data. Currently supports a semi-parametric Cox-PH and an imputation Cox-PH model which imputes the interval censored times based on Cox-PH model with an parametric baseline and then analyzes each imputed data set with the semi-parametric model.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/coxph.R | 21 +++++++++++++++++----
3 files changed, 22 insertions(+), 9 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Diff between glmm versions 1.0.2 dated 2015-03-19 and 1.0.3 dated 2015-04-28
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NAMESPACE | 1 +
R/summary.mcla.R | 16 ++++++++++++++++
inst/doc/intro.R | 13 ++++++++++++-
inst/doc/intro.Rnw | 50 ++++++++++++++++++++++++++++++++++++++++++++++++--
inst/doc/intro.pdf |binary
man/vcov.glmm.Rd |only
vignettes/intro.Rnw | 50 ++++++++++++++++++++++++++++++++++++++++++++++++--
9 files changed, 137 insertions(+), 16 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Diff between dunn.test versions 1.2.3 dated 2015-02-25 and 1.2.4 dated 2015-04-28
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/dunn.test.R | 24 ++++++++++++------------
3 files changed, 19 insertions(+), 19 deletions(-)
Title: A Fast Solver for Parameterized Linear Programming Problems and
Constrained L1 Minimization Approach to Sparse Precision Matrix
Estimation
Diff between fastclime versions 1.2.4 dated 2014-04-29 and 1.2.5 dated 2015-04-28
Description: An efficient method of recovering precision matrices
by applying the parametric simplex method is provided in this package.
The computation is based on a linear optimization solver.
It also contains a generic Linear Programming solver and a
parameterized Linear Programming solver based on the parametric simplex method.
Author: Haotian Pang, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang
fastclime-1.2.4/fastclime/src/SFGen.c |only
fastclime-1.2.5/fastclime/DESCRIPTION | 22 ++++++++++---------
fastclime-1.2.5/fastclime/MD5 | 9 +++----
fastclime-1.2.5/fastclime/R/fastclime.generator.R | 6 -----
fastclime-1.2.5/fastclime/man/fastclime.generator.Rd | 8 +-----
fastclime-1.2.5/fastclime/src/parametric.c | 11 ++++++---
6 files changed, 26 insertions(+), 30 deletions(-)
Title: Renewal Method for Extreme Values Extrapolation
Diff between Renext versions 2.1-0 dated 2013-10-04 and 2.1-10 dated 2015-04-28
Description: Extreme value analysis using the Peaks Over Threshold (POT) method also called 'methode du renouvellement' by some French-speaking hydrologists.
Author: Yves Deville
Maintainer: Lise Bardet
ChangeLog | 15
DESCRIPTION | 13
MD5 | 32 -
NAMESPACE | 1
R/Maxlo.R | 14
R/NBlevy.R | 306 +++++------
R/rRenouv.R | 4
R/readXML.R | 1287 +++++++++++++++++++++++++-------------------------
R/transexp.R | 19
R/weibplot.R | 2
man/Brest.Rd | 48 +
man/Lomax.Rd | 100 ++-
man/Maxlo.Rd | 94 ++-
man/NBlevy.Rd | 137 +++--
man/Renext-package.Rd | 31 -
man/plot.Rendata.Rd | 18
man/readXML.Rd | 6
17 files changed, 1141 insertions(+), 986 deletions(-)
Title: Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Diff between PopVar versions 1.0 dated 2015-04-01 and 1.1 dated 2015-04-28
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede
PopVar-1.0/PopVar/R/Internal_PopVar_functions_2.20.15.R |only
PopVar-1.0/PopVar/R/PopVar.R |only
PopVar-1.0/PopVar/R/XValidate.nonInd_function_Tiede_3.10.15.R |only
PopVar-1.0/PopVar/R/XValidate_Ind_function_Tiede_3.10.15.R |only
PopVar-1.0/PopVar/R/pop.predict_function_V2_3.10.15.R |only
PopVar-1.0/PopVar/R/x.val_function_3.13.15.R |only
PopVar-1.0/PopVar/man/PopVar.Rd |only
PopVar-1.1/PopVar/DESCRIPTION | 8 +--
PopVar-1.1/PopVar/MD5 | 24 +++++-----
PopVar-1.1/PopVar/NAMESPACE | 2
PopVar-1.1/PopVar/R/Internal_PopVar_functions_4.28.15.R |only
PopVar-1.1/PopVar/R/PopVar-package.R |only
PopVar-1.1/PopVar/R/XValidate.nonInd_function_4.28.15.R |only
PopVar-1.1/PopVar/R/XValidate_Ind_function_4.28.15.R |only
PopVar-1.1/PopVar/R/pop.predict_function_4.28.15.R |only
PopVar-1.1/PopVar/R/x.val_function_4.28.15.R |only
PopVar-1.1/PopVar/man/PopVar-package.Rd |only
PopVar-1.1/PopVar/man/pop.predict.Rd | 24 +++++-----
PopVar-1.1/PopVar/man/think_barley.rda.Rd | 2
PopVar-1.1/PopVar/man/x.val.Rd | 18 ++++---
20 files changed, 41 insertions(+), 37 deletions(-)
Title: Analyze and Gaussianize Heavy-Tailed, Skewed Data
Diff between LambertW versions 0.5 dated 2014-11-21 and 0.5.1 dated 2015-04-28
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. They are based on an input/output system, where
the input random variable (RV) X ~ F, and the output Y is a non-linearly
transformed version of X with similar properties, but slightly skewed and/or
heavy-tailed. This transformed RV Y has a Lambert W x F distribution.
This package contains functions to model and analyze skewed, heavy-tailed
data the Lambert Way: simulate random samples, estimate parameters, compute
quantiles, and plot/print results nicely. Probably the most important
function is 'Gaussianize', which works similarly to 'scale', but actually
makes the data Gaussian. A do-it-yourself toolkit allows users to define
their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis
right away.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
LambertW-0.5.1/LambertW/DESCRIPTION | 10 -
LambertW-0.5.1/LambertW/MD5 | 105 +++++------
LambertW-0.5.1/LambertW/NAMESPACE | 4
LambertW-0.5.1/LambertW/NEWS | 23 ++
LambertW-0.5.1/LambertW/R/0_LambertW-toolkit.R | 4
LambertW-0.5.1/LambertW/R/0_LambertW-utils.R | 4
LambertW-0.5.1/LambertW/R/0_loglik-LambertW-utils.R | 4
LambertW-0.5.1/LambertW/R/Gaussianize.R | 10 -
LambertW-0.5.1/LambertW/R/LambertW-package.R | 8
LambertW-0.5.1/LambertW/R/MLE_LambertW.R | 4
LambertW-0.5.1/LambertW/R/deprecated_functions.R | 11 +
LambertW-0.5.1/LambertW/R/get_input.R | 4
LambertW-0.5.1/LambertW/R/mLambertW.R | 8
LambertW-0.5.1/LambertW/R/test_normality.R |only
LambertW-0.5.1/LambertW/R/zzz.R |only
LambertW-0.5.1/LambertW/man/G_delta_alpha.Rd | 3
LambertW-0.5.1/LambertW/man/Gaussianize.Rd | 9
LambertW-0.5.1/LambertW/man/H.Rd | 3
LambertW-0.5.1/LambertW/man/H_gamma.Rd | 3
LambertW-0.5.1/LambertW/man/IGMM.Rd | 3
LambertW-0.5.1/LambertW/man/LambertW-package.Rd | 11 -
LambertW-0.5.1/LambertW/man/LambertW-toolkit.Rd | 7
LambertW-0.5.1/LambertW/man/LambertW-utils.Rd | 7
LambertW-0.5.1/LambertW/man/LambertW_fit-methods.Rd | 3
LambertW-0.5.1/LambertW/man/LambertW_input_output-methods.Rd | 3
LambertW-0.5.1/LambertW/man/MLE_LambertW.Rd | 3
LambertW-0.5.1/LambertW/man/U-utils.Rd | 3
LambertW-0.5.1/LambertW/man/W.Rd | 3
LambertW-0.5.1/LambertW/man/W_delta.Rd | 3
LambertW-0.5.1/LambertW/man/W_gamma.Rd | 3
LambertW-0.5.1/LambertW/man/beta-utils.Rd | 3
LambertW-0.5.1/LambertW/man/common-arguments.Rd | 3
LambertW-0.5.1/LambertW/man/datasets.Rd | 3
LambertW-0.5.1/LambertW/man/delta_01.Rd | 3
LambertW-0.5.1/LambertW/man/delta_GMM.Rd | 3
LambertW-0.5.1/LambertW/man/delta_Taylor.Rd | 3
LambertW-0.5.1/LambertW/man/deprecated-functions.Rd | 6
LambertW-0.5.1/LambertW/man/distname-utils.Rd | 3
LambertW-0.5.1/LambertW/man/gamma_01.Rd | 3
LambertW-0.5.1/LambertW/man/gamma_GMM.Rd | 3
LambertW-0.5.1/LambertW/man/gamma_Taylor.Rd | 3
LambertW-0.5.1/LambertW/man/get_gamma_bounds.Rd | 3
LambertW-0.5.1/LambertW/man/get_input.Rd | 7
LambertW-0.5.1/LambertW/man/get_output.Rd | 3
LambertW-0.5.1/LambertW/man/get_support.Rd | 3
LambertW-0.5.1/LambertW/man/ks.test.t.Rd | 3
LambertW-0.5.1/LambertW/man/loglik-LambertW-utils.Rd | 49 ++---
LambertW-0.5.1/LambertW/man/lp_norm.Rd | 3
LambertW-0.5.1/LambertW/man/mc.Rd | 3
LambertW-0.5.1/LambertW/man/p_m1.Rd | 3
LambertW-0.5.1/LambertW/man/tau-utils.Rd | 3
LambertW-0.5.1/LambertW/man/test_normality.Rd |only
LambertW-0.5.1/LambertW/man/test_symmetry.Rd | 3
LambertW-0.5.1/LambertW/man/theta-utils.Rd | 3
LambertW-0.5/LambertW/R/normfit.R |only
LambertW-0.5/LambertW/man/normfit.Rd |only
56 files changed, 242 insertions(+), 146 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions in
Causal Models
Diff between causaleffect versions 1.1 dated 2015-04-21 and 1.1.1 dated 2015-04-28
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka
causaleffect-1.1.1/causaleffect/DESCRIPTION | 10 +++---
causaleffect-1.1.1/causaleffect/MD5 | 19 ++++++-----
causaleffect-1.1.1/causaleffect/NAMESPACE | 4 +-
causaleffect-1.1.1/causaleffect/R/causal.effect.R | 20 ++++++------
causaleffect-1.1.1/causaleffect/R/get.expression.R |only
causaleffect-1.1.1/causaleffect/R/idc.R | 13 ++++---
causaleffect-1.1.1/causaleffect/R/unobserved.graph.R |only
causaleffect-1.1.1/causaleffect/man/causal.effect.Rd | 7 ++--
causaleffect-1.1.1/causaleffect/man/causaleffect-package.Rd | 14 ++++----
causaleffect-1.1.1/causaleffect/man/get.expression.Rd |only
causaleffect-1.1.1/causaleffect/man/parse.graphml.Rd | 2 -
causaleffect-1.1/causaleffect/R/getExpression.R |only
causaleffect-1.1/causaleffect/R/getExpression.probability.R |only
13 files changed, 46 insertions(+), 43 deletions(-)
Title: Time Frame User Utilities
Diff between tfplot versions 2014.2-2 dated 2014-02-10 and 2015.4-1 dated 2015-04-28
Description: Utilities for simple manipulation and quick
plotting of time series data. These utilities use the tframe package
which provides a programming kernel for time series. Extensions to
tframe provided in tframePlus can also be used. See the Guide vignette
for examples.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 13 +++++--------
MD5 | 16 ++++++++--------
NEWS | 4 ++++
R/tfplot.R | 4 ++--
build/vignette.rds |binary
tests/autoAxis.R | 2 ++
tests/tfOnePlot.R | 1 +
tests/tfplot.R | 1 +
tests/utils.R | 10 ++++++----
9 files changed, 29 insertions(+), 22 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Diff between R.filesets versions 2.7.0 dated 2015-02-23 and 2.7.1 dated 2015-04-28
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 24 ++-
MD5 | 18 +-
NEWS | 14 +-
R/Arguments.EXTRAS.R | 6
R/FullNameInterface.R | 4
R/GenericDataFile.R | 6
R/GenericDataFileSetList.R | 6
R/GenericTabularFile.writeColumnsToFiles.R | 20 +--
R/RDataFile.R | 188 ++++++++++++++---------------
R/fullname.R | 6
10 files changed, 152 insertions(+), 140 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Diff between multicool versions 0.1-5 dated 2015-02-26 and 0.1-6 dated 2015-04-28
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran
DESCRIPTION | 8 ++--
MD5 | 10 ++---
R/genComp.R | 21 +++++++++-
man/genComp.Rd | 6 ++-
src/RcppExports.cpp | 100 ++++++++++++++++++----------------------------------
src/multicool.cpp | 2 -
6 files changed, 69 insertions(+), 78 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 3.3 dated 2015-03-19 and 3.3.1 dated 2015-04-28
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing
lessR-3.3.1/lessR/DESCRIPTION | 10
lessR-3.3.1/lessR/MD5 | 178 +--
lessR-3.3.1/lessR/NAMESPACE | 5
lessR-3.3.1/lessR/NEWS | 67 +
lessR-3.3.1/lessR/R/ANOVAz1.R | 21
lessR-3.3.1/lessR/R/ANOVAz2.R | 14
lessR-3.3.1/lessR/R/BoxPlot.R | 60 +
lessR-3.3.1/lessR/R/Correlation.R | 32
lessR-3.3.1/lessR/R/Density.R | 93 +
lessR-3.3.1/lessR/R/DotPlot.R | 2
lessR-3.3.1/lessR/R/Help.R | 7
lessR-3.3.1/lessR/R/Histogram.R | 51 -
lessR-3.3.1/lessR/R/Logit.R | 7
lessR-3.3.1/lessR/R/Nest.R | 217 +++-
lessR-3.3.1/lessR/R/Read.R | 16
lessR-3.3.1/lessR/R/Read2.R | 2
lessR-3.3.1/lessR/R/Regression.R | 141 +-
lessR-3.3.1/lessR/R/ScatterPlot.R | 38
lessR-3.3.1/lessR/R/SummaryStats.R | 1
lessR-3.3.1/lessR/R/Write.R | 10
lessR-3.3.1/lessR/R/bc.zmain.R | 22
lessR-3.3.1/lessR/R/bx.R | 2
lessR-3.3.1/lessR/R/bx.zmain.R | 60 -
lessR-3.3.1/lessR/R/corCFA.R | 137 --
lessR-3.3.1/lessR/R/corEFA.R | 209 ++--
lessR-3.3.1/lessR/R/corFA.zknitr.R |only
lessR-3.3.1/lessR/R/corProp.R | 90 +
lessR-3.3.1/lessR/R/corReflect.R | 56 -
lessR-3.3.1/lessR/R/corReorder.R | 113 +-
lessR-3.3.1/lessR/R/corScree.R | 26
lessR-3.3.1/lessR/R/cor_mimm.R |only
lessR-3.3.1/lessR/R/cor_resid.R |only
lessR-3.3.1/lessR/R/cr.data.frame.R | 79 -
lessR-3.3.1/lessR/R/cr.zmain.R | 94 +
lessR-3.3.1/lessR/R/details.R | 5
lessR-3.3.1/lessR/R/dist.zknitr.R |only
lessR-3.3.1/lessR/R/dn.R | 2
lessR-3.3.1/lessR/R/dn.zmain.R | 34
lessR-3.3.1/lessR/R/dp.R | 2
lessR-3.3.1/lessR/R/dp.zmain.R | 3
lessR-3.3.1/lessR/R/hs.R | 2
lessR-3.3.1/lessR/R/hst.zmain.R | 68 -
lessR-3.3.1/lessR/R/lc.zmain.R | 23
lessR-3.3.1/lessR/R/print.outall.r | 5
lessR-3.3.1/lessR/R/rd.R | 2
lessR-3.3.1/lessR/R/rd.brief.R | 2
lessR-3.3.1/lessR/R/reg.R | 3
lessR-3.3.1/lessR/R/reg.brief.R | 3
lessR-3.3.1/lessR/R/reg.z1anvBasic.R | 100 +
lessR-3.3.1/lessR/R/reg.z1bckBasic.R | 6
lessR-3.3.1/lessR/R/reg.z1fitBasic.R | 49
lessR-3.3.1/lessR/R/reg.z1modelBasic.R | 16
lessR-3.3.1/lessR/R/reg.z2Relations.R | 31
lessR-3.3.1/lessR/R/reg.z3dnResidual.R | 2
lessR-3.3.1/lessR/R/reg.z3resfitResidual.R | 7
lessR-3.3.1/lessR/R/reg.z3txtResidual.R | 40
lessR-3.3.1/lessR/R/reg.z4Pred.R | 123 +-
lessR-3.3.1/lessR/R/reg.z5Plot.R | 49
lessR-3.3.1/lessR/R/reg.zknitr.R | 1453 ++++++++++++++++++++++-------
lessR-3.3.1/lessR/R/regPlot.R | 118 +-
lessR-3.3.1/lessR/R/sp.R | 2
lessR-3.3.1/lessR/R/ss.zdata.frame.R | 37
lessR-3.3.1/lessR/R/ss.zfactor.R | 23
lessR-3.3.1/lessR/R/ss.znumeric.R | 20
lessR-3.3.1/lessR/R/tAnd.R |only
lessR-3.3.1/lessR/R/tNum.R |only
lessR-3.3.1/lessR/R/tP.R |only
lessR-3.3.1/lessR/R/tRow.R |only
lessR-3.3.1/lessR/R/tt.z1group.R | 7
lessR-3.3.1/lessR/R/tt.z2group.R | 18
lessR-3.3.1/lessR/R/ttest.R | 6
lessR-3.3.1/lessR/R/zzz.R | 254 +++--
lessR-3.3.1/lessR/man/ANOVA.Rd | 16
lessR-3.3.1/lessR/man/BoxPlot.Rd | 52 -
lessR-3.3.1/lessR/man/Correlation.Rd | 34
lessR-3.3.1/lessR/man/Density.Rd | 33
lessR-3.3.1/lessR/man/Histogram.Rd | 14
lessR-3.3.1/lessR/man/Nest.Rd | 41
lessR-3.3.1/lessR/man/Read.Rd | 6
lessR-3.3.1/lessR/man/Regression.Rd | 135 +-
lessR-3.3.1/lessR/man/ScatterPlot.Rd | 12
lessR-3.3.1/lessR/man/SummaryStats.Rd | 6
lessR-3.3.1/lessR/man/corCFA.Rd | 12
lessR-3.3.1/lessR/man/corEFA.Rd | 38
lessR-3.3.1/lessR/man/corProp.Rd | 4
lessR-3.3.1/lessR/man/corReflect.Rd | 9
lessR-3.3.1/lessR/man/corReorder.Rd | 17
lessR-3.3.1/lessR/man/print_outall.Rd | 16
lessR-3.3.1/lessR/man/regPlot.Rd | 6
lessR-3.3.1/lessR/man/tAnd.Rd |only
lessR-3.3.1/lessR/man/tNum.Rd |only
lessR-3.3.1/lessR/man/tP.Rd |only
lessR-3.3.1/lessR/man/tRow.Rd |only
lessR-3.3/lessR/src |only
94 files changed, 3319 insertions(+), 1507 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Diff between texreg versions 1.34 dated 2014-10-31 and 1.35 dated 2015-04-28
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld
DESCRIPTION | 26 +-
MD5 | 24 +-
NAMESPACE | 7
R/extract.R | 447 +++++++++++++++++++++++++++++++++++++++++++++++----
R/internal.R | 49 ++++-
R/texreg.R | 15 -
build/vignette.rds |binary
inst/doc/v55i08.R | 46 ++---
inst/doc/v55i08.Rnw | 26 +-
inst/doc/v55i08.pdf |binary
man/extract.Rd | 70 +++++++
man/texreg.Rd | 5
vignettes/v55i08.Rnw | 26 +-
13 files changed, 622 insertions(+), 119 deletions(-)
Title: Parsimonious Gaussian Mixture Models
Diff between pgmm versions 1.1 dated 2014-07-13 and 1.2 dated 2015-04-28
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models.
Author: Paul D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F. McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]
Maintainer: Paul D. McNicholas
pgmm-1.1/pgmm/inst |only
pgmm-1.1/pgmm/src/myalloc.c |only
pgmm-1.2/pgmm/ChangeLog | 5
pgmm-1.2/pgmm/DESCRIPTION | 17
pgmm-1.2/pgmm/MD5 | 23
pgmm-1.2/pgmm/R/pgmmEM.R | 35
pgmm-1.2/pgmm/man/pgmm.Rd | 8
pgmm-1.2/pgmm/man/pgmmEM.Rd | 6
pgmm-1.2/pgmm/src/Makevars |only
pgmm-1.2/pgmm/src/aecm.c | 1496 +++++++++++++++++++++++++-----------------
pgmm-1.2/pgmm/src/functions.h | 163 ++--
pgmm-1.2/pgmm/src/gaussj.c | 236 +-----
pgmm-1.2/pgmm/src/pgmm.c | 41 -
pgmm-1.2/pgmm/src/updates.c | 865 ++++++++++++++----------
14 files changed, 1651 insertions(+), 1244 deletions(-)
Title: D3 Scatterplot Matrices
Diff between pairsD3 versions 0.0.6 dated 2015-04-08 and 0.1.0 dated 2015-04-28
Description: Creates an interactive scatterplot matrix using the D3 JavaScript library. See
Author: Garth Tarr [aut, cre]
Maintainer: Garth Tarr
pairsD3-0.0.6/pairsD3/inst/htmlwidgets/lib/pairsD3/d3.v3.min.js |only
pairsD3-0.1.0/pairsD3/DESCRIPTION | 10 +-
pairsD3-0.1.0/pairsD3/MD5 | 27 +++--
pairsD3-0.1.0/pairsD3/NAMESPACE | 2
pairsD3-0.1.0/pairsD3/NEWS |only
pairsD3-0.1.0/pairsD3/R/pairsD3.R | 26 ++++-
pairsD3-0.1.0/pairsD3/README.md | 33 ++++++-
pairsD3-0.1.0/pairsD3/inst/htmlwidgets/lib/d3 |only
pairsD3-0.1.0/pairsD3/inst/htmlwidgets/lib/pairsD3/style.css | 46 +++++-----
pairsD3-0.1.0/pairsD3/inst/htmlwidgets/pairsD3.js | 42 ++++++---
pairsD3-0.1.0/pairsD3/inst/htmlwidgets/pairsD3.yaml | 5 -
pairsD3-0.1.0/pairsD3/man/pairsD3.Rd | 13 ++
pairsD3-0.1.0/pairsD3/man/pairsD3Output.Rd | 4
pairsD3-0.1.0/pairsD3/man/renderPairsD3.Rd | 2
pairsD3-0.1.0/pairsD3/man/savePairs.Rd | 2
pairsD3-0.1.0/pairsD3/man/shinypairs.Rd | 2
16 files changed, 143 insertions(+), 71 deletions(-)
Title: Empirical Likelihood Ratio for Censored/Truncated Data
Diff between emplik versions 0.9-9-6 dated 2014-08-26 and 1.0-1 dated 2015-04-28
Description: Empirical likelihood ratio tests for means/quantiles/hazards
from possibly censored and/or truncated data. Now does regression too.
This version contains some C code.
Author: Mai Zhou. (Art Owen for el.test(). Yifan Yang for C code.)
Maintainer: Mai Zhou
DESCRIPTION | 15 ++++----
MD5 | 45 ++++++++++++++------------
NAMESPACE | 8 ++--
R/DnR.R | 5 +-
R/RankRegTest.R | 2 -
R/RankRegTestH.R |only
R/WCY.R | 4 +-
R/WKM.R | 2 -
R/WRegTest.R | 6 +--
R/Wdataclean3.R | 6 +--
R/Wdataclean5.R | 6 +--
R/bjtestII.R |only
R/cumsumsurv.R | 4 +-
R/el.cen.EM.R | 56 +++++----------------------------
R/el.cen.EM2.R | 22 ++++++------
R/el.ltrc.EM.R | 6 +--
R/el.test.wt.R | 8 ++--
R/el.test.wt2.R | 14 --------
R/emplikHs.test22.R |only
R/iter.R | 26 +++++++--------
README | 18 +++++-----
man/RankRegTestH.Rd |only
man/WRegTest.Rd | 4 +-
man/bjtestII.Rd |only
man/emplik-internal.Rd | 15 +++++++-
src/cumsumsurv.c | 83 +++++++++++++------------------------------------
26 files changed, 143 insertions(+), 212 deletions(-)
Title: Time Frame Coding Kernel Extensions
Diff between tframePlus versions 2013.9-1 dated 2013-09-24 and 2015.1-2 dated 2015-04-27
Description: Extensions and additional tframe utilities.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 18 ++++++-------
MD5 | 17 ++++++------
NAMESPACE | 10 ++++++-
NEWS | 29 +++++++++++++++++++++
R/timeSeries.R | 13 +++++++++
R/utils.R | 70 +++++++++++++++++++++++++++++++++++------------------
R/xts.R | 8 +++---
R/zoo.R | 4 +--
build/vignette.rds |binary
tests/zoo2.R |only
10 files changed, 120 insertions(+), 49 deletions(-)
Title: Various Programming Utilities
Diff between R.utils versions 2.0.1 dated 2015-04-26 and 2.0.2 dated 2015-04-27
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 +++---
MD5 | 49 +++++++++++++++++++--------------------
NEWS | 9 +++++++
R/Arguments.R | 29 ++++++++++++++++++-----
R/Options.R | 54 +++++++++++++++++++++----------------------
R/Sys.readlink2.R | 2 -
R/System.R | 4 +--
R/fileAccess.R | 2 -
R/findFiles.R | 4 +--
R/isEof.connection.R | 4 +--
R/readWindowsShortcut.R | 8 +++---
R/removeDirectory.R | 2 -
R/toUrl.R | 2 -
man/Options.Rd | 54 +++++++++++++++++++++----------------------
man/as.character.Options.Rd | 38 +++++++++++++++---------------
man/as.list.Options.Rd | 28 +++++++++++-----------
man/equals.Options.Rd | 36 ++++++++++++++--------------
man/getFilename.Arguments.Rd | 4 +++
man/getLeaves.Options.Rd | 28 +++++++++++-----------
man/getOption.Options.Rd | 54 +++++++++++++++++++++----------------------
man/hasOption.Options.Rd | 42 ++++++++++++++++-----------------
man/names.Options.Rd | 28 +++++++++++-----------
man/nbrOfOptions.Options.Rd | 28 +++++++++++-----------
man/setOption.Options.Rd | 48 +++++++++++++++++++-------------------
man/str.Options.Rd | 40 +++++++++++++++----------------
tests/Arguments-FILES.R |only
26 files changed, 318 insertions(+), 287 deletions(-)
Title: Interface to the Search API for the 'PLoS' Journals
Diff between rplos versions 0.4.6 dated 2015-01-23 and 0.4.7 dated 2015-04-27
Description: A programmatic interface to the 'SOLR' based
search API (http://api.plos.org/) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing faceted searches, doing
highlight searches, and viewing results of highlighted
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain
rplos-0.4.6/rplos/vignettes/figure |only
rplos-0.4.7/rplos/DESCRIPTION | 23 +-
rplos-0.4.7/rplos/MD5 | 75 ++++-----
rplos-0.4.7/rplos/NAMESPACE | 3
rplos-0.4.7/rplos/NEWS | 11 +
rplos-0.4.7/rplos/R/citations.R |only
rplos-0.4.7/rplos/README.md | 175 +++++++++++-----------
rplos-0.4.7/rplos/build/vignette.rds |binary
rplos-0.4.7/rplos/inst/doc/facethighlight.html | 100 +++++-------
rplos-0.4.7/rplos/inst/doc/fulltext.html | 100 +++++-------
rplos-0.4.7/rplos/inst/doc/rplos_vignette.html | 100 +++++-------
rplos-0.4.7/rplos/man/addmissing.Rd | 2
rplos-0.4.7/rplos/man/check_response.Rd | 2
rplos-0.4.7/rplos/man/citations.Rd |only
rplos-0.4.7/rplos/man/concat_todf.Rd | 2
rplos-0.4.7/rplos/man/crossref-defunct.Rd | 2
rplos-0.4.7/rplos/man/facetplos.Rd | 2
rplos-0.4.7/rplos/man/formatarticleurl.Rd | 2
rplos-0.4.7/rplos/man/full_text_urls.Rd | 2
rplos-0.4.7/rplos/man/highbrow.Rd | 2
rplos-0.4.7/rplos/man/highplos.Rd | 2
rplos-0.4.7/rplos/man/insertnones.Rd | 2
rplos-0.4.7/rplos/man/isocodes.Rd | 2
rplos-0.4.7/rplos/man/journalnamekey.Rd | 2
rplos-0.4.7/rplos/man/plos_fulltext.Rd | 2
rplos-0.4.7/rplos/man/plosabstract.Rd | 2
rplos-0.4.7/rplos/man/plosauthor.Rd | 2
rplos-0.4.7/rplos/man/plosfields.Rd | 2
rplos-0.4.7/rplos/man/plosfigtabcaps.Rd | 2
rplos-0.4.7/rplos/man/plossubject.Rd | 2
rplos-0.4.7/rplos/man/plostitle.Rd | 2
rplos-0.4.7/rplos/man/plosviews.Rd | 2
rplos-0.4.7/rplos/man/plosword.Rd | 2
rplos-0.4.7/rplos/man/plot_throughtime.Rd | 2
rplos-0.4.7/rplos/man/rplos-defunct.Rd | 2
rplos-0.4.7/rplos/man/rplos.Rd | 2
rplos-0.4.7/rplos/man/searchplos.Rd | 2
rplos-0.4.7/rplos/tests/testthat/test-citations.R |only
38 files changed, 305 insertions(+), 332 deletions(-)
Title: Friendly Regular Expressions
Diff between rex versions 0.2.0 dated 2014-11-26 and 1.0.1 dated 2015-04-27
Description: A friendly interface for the construction of regular expressions.
Author: Kevin Ushey [aut],
Jim Hester [aut, cre],
Robert Krzyzanowski [aut]
Maintainer: Jim Hester
DESCRIPTION | 28 ++++++------
MD5 | 90 ++++++++++++++++++++++------------------
NAMESPACE | 2
R/aaa.R | 12 +----
R/character_class.R | 10 ++++
R/escape.R | 26 +++--------
R/lookarounds.R | 7 +++
R/match.R | 60 ++++++++++++--------------
R/rex-mode.R | 2
R/rex.R | 9 ----
R/shortcuts.R | 4 +
R/utils.R | 2
R/zzz.R | 5 +-
README.md | 2
build/vignette.rds |binary
inst/doc/log_parsing.html | 6 +-
inst/doc/stackoverflow.R |only
inst/doc/stackoverflow.Rmd |only
inst/doc/stackoverflow.html |only
inst/doc/url_parsing.html | 4 -
man/as.regex.Rd | 2
man/capture.Rd | 16 +++----
man/character_class.Rd | 7 ++-
man/character_class_escape.Rd | 2
man/counts.Rd | 19 ++++----
man/escape.Rd | 2
man/group.Rd | 19 ++++----
man/lookarounds.Rd | 20 ++++++--
man/not.Rd | 19 ++++----
man/or.Rd | 19 ++++----
man/pipe.Rd | 2
man/re_matches.Rd | 4 -
man/re_substitutes.Rd | 9 ++--
man/regex.Rd | 7 ---
man/register_shortcuts.Rd | 2
man/rex.Rd | 19 ++++----
man/rex_mode.Rd | 2
man/shortcuts.Rd | 25 +++++------
man/single_shortcuts.Rd | 2
man/wildcards.Rd | 19 ++++----
tests/testthat/test-aaa.R |only
tests/testthat/test-common.R | 2
tests/testthat/test-escape.R |only
tests/testthat/test-match.R | 48 +++++++++++++++------
tests/testthat/test-print.R |only
tests/testthat/test-rex_mode.R |only
tests/testthat/test-shortcuts.R |only
tests/testthat/test-zzz.R |only
vignettes/log_parsing.Rmd | 11 +---
vignettes/stackoverflow.Rmd |only
vignettes/url_parsing.Rmd | 16 +++----
51 files changed, 292 insertions(+), 270 deletions(-)
Title: Estimation of Conditional Quantiles using Optimal Quantization
Diff between QuantifQuantile versions 2.0 dated 2015-04-22 and 2.1 dated 2015-04-27
More information about QuantifQuantile at CRAN
Description: Estimation of conditional quantiles using optimal quantization.
Construction of an optimal grid of N quantizers, estimation of conditional
quantiles and data driven selection of the size N of the grid. Graphical
illustrations for the selection of N and of resulting estimated curves or
surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/QuantifQuantile.R | 18 +++++++++++-------
R/QuantifQuantile.d.R | 12 ++++++++----
R/QuantifQuantile.d2.R | 12 ++++++++----
R/plot.QuantifQuantile.R | 6 +++---
R/print.QuantifQuantile.R | 4 ++--
R/summary.QuantifQuantile.R | 4 ++--
man/QuantifQuantile.Rd | 22 +++++++++++++---------
man/QuantifQuantile.d.Rd | 15 ++++++++++-----
man/QuantifQuantile.d2.Rd | 15 ++++++++++-----
man/choice.grid.Rd | 3 ++-
man/plot.QuantifQuantile.Rd | 9 +++++----
man/print.QuantifQuantile.Rd | 7 ++++---
man/summary.QuantifQuantile.Rd | 7 ++++---
16 files changed, 102 insertions(+), 72 deletions(-)
Permanent link
Title: Patient-Centered Network Meta-Analysis
Diff between pcnetmeta versions 2.0 dated 2015-03-20 and 2.1 dated 2015-04-27
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary and continuous outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin
pcnetmeta-2.0/pcnetmeta/R/model.binary.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.hom.R |only
pcnetmeta-2.1/pcnetmeta/DESCRIPTION | 18 +-
pcnetmeta-2.1/pcnetmeta/MD5 | 82 +++++-----
pcnetmeta-2.1/pcnetmeta/NAMESPACE | 4
pcnetmeta-2.1/pcnetmeta/R/ci.plot.R | 17 +-
pcnetmeta-2.1/pcnetmeta/R/forest.plot.R |only
pcnetmeta-2.1/pcnetmeta/R/model.binary.het.cor.R | 37 ++++
pcnetmeta-2.1/pcnetmeta/R/model.binary.het.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.binary.het.ind.R | 69 +++++++-
pcnetmeta-2.1/pcnetmeta/R/model.binary.hom.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.binary.hom.ind.R |only
pcnetmeta-2.1/pcnetmeta/R/model.cont.het.cor.R | 32 +++
pcnetmeta-2.1/pcnetmeta/R/model.cont.het.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.cont.het.ind.R | 59 ++++++-
pcnetmeta-2.1/pcnetmeta/R/model.cont.hom.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.cont.hom.ind.R |only
pcnetmeta-2.1/pcnetmeta/R/model.followup.het.cor.R | 36 ++++
pcnetmeta-2.1/pcnetmeta/R/model.followup.het.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.followup.het.ind.R | 67 +++++++-
pcnetmeta-2.1/pcnetmeta/R/model.followup.hom.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.followup.hom.ind.R |only
pcnetmeta-2.1/pcnetmeta/R/model.py.het.cor.R | 35 +++-
pcnetmeta-2.1/pcnetmeta/R/model.py.het.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.py.het.ind.R | 65 +++++++-
pcnetmeta-2.1/pcnetmeta/R/model.py.hom.eqcor.R |only
pcnetmeta-2.1/pcnetmeta/R/model.py.hom.ind.R |only
pcnetmeta-2.1/pcnetmeta/R/nma.ab.R | 130 +++++++++++-----
pcnetmeta-2.1/pcnetmeta/R/nma.ab.cont.R | 107 +++++++++----
pcnetmeta-2.1/pcnetmeta/R/nma.ab.followup.R | 153 ++++++++++++------
pcnetmeta-2.1/pcnetmeta/R/nma.ab.py.R | 154 ++++++++++++-------
pcnetmeta-2.1/pcnetmeta/R/nma.networkplot.R | 46 ++++-
pcnetmeta-2.1/pcnetmeta/R/rank.prob.R |only
pcnetmeta-2.1/pcnetmeta/data/diabetes.rda |binary
pcnetmeta-2.1/pcnetmeta/data/dietaryfat.rda |binary
pcnetmeta-2.1/pcnetmeta/data/parkinson.rda |binary
pcnetmeta-2.1/pcnetmeta/data/smoke.rda |binary
pcnetmeta-2.1/pcnetmeta/man/ci.plot.Rd | 18 --
pcnetmeta-2.1/pcnetmeta/man/diabetes.Rd | 14 -
pcnetmeta-2.1/pcnetmeta/man/dietaryfat.Rd | 14 -
pcnetmeta-2.1/pcnetmeta/man/forest.plot.Rd |only
pcnetmeta-2.1/pcnetmeta/man/nma.ab.Rd | 103 ++++++------
pcnetmeta-2.1/pcnetmeta/man/nma.ab.cont.Rd | 76 ++++-----
pcnetmeta-2.1/pcnetmeta/man/nma.ab.followup.Rd | 80 ++++-----
pcnetmeta-2.1/pcnetmeta/man/nma.ab.py.Rd | 75 ++++-----
pcnetmeta-2.1/pcnetmeta/man/nma.networkplot.Rd | 48 +++--
pcnetmeta-2.1/pcnetmeta/man/parkinson.Rd | 12 -
pcnetmeta-2.1/pcnetmeta/man/pcnetmeta-package.Rd | 25 ---
pcnetmeta-2.1/pcnetmeta/man/rank.prob.Rd |only
pcnetmeta-2.1/pcnetmeta/man/smoke.Rd | 12 -
52 files changed, 1090 insertions(+), 498 deletions(-)
Title: Empirical Likelihood Analysis for the Cox Model and
Yang-Prentice (2005) Model
Diff between ELYP versions 0.7-1 dated 2015-03-27 and 0.7-2 dated 2015-04-27
Description: Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) models.
Empirical likelihood tests within a Cox model, for parameters defined via
both baseline hazard function and regression parameters.
Author: Mai Zhou
Maintainer: Mai Zhou
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
R/fitYP4.R | 2 +-
R/fitYP41.R | 2 +-
R/myLLfun.R | 2 +-
R/myLLfun2.R | 2 +-
R/myffitYP3.R | 2 +-
R/simuDataYP.R | 2 +-
man/CoxEL.Rd | 16 ++++++++++------
man/CoxFindL2.Rd | 31 +++++++++++++++++++------------
man/CoxFindL3.Rd | 5 +++--
man/CoxFindU2.Rd | 10 ++--------
man/CoxFindU3.Rd | 4 ++--
man/findL3.Rd | 2 +-
man/findU3.Rd | 2 +-
man/simuDataYP.Rd | 10 +++++-----
16 files changed, 68 insertions(+), 62 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Diff between dataRetrieval versions 2.2.0 dated 2015-04-09 and 2.2.1 dated 2015-04-27
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco
dataRetrieval-2.2.0/dataRetrieval/vignettes/dataRetrieval-concordance.tex |only
dataRetrieval-2.2.0/dataRetrieval/vignettes/figure |only
dataRetrieval-2.2.1/dataRetrieval/DESCRIPTION | 10 -
dataRetrieval-2.2.1/dataRetrieval/MD5 | 83 ++++------
dataRetrieval-2.2.1/dataRetrieval/NAMESPACE | 2
dataRetrieval-2.2.1/dataRetrieval/R/importWaterML1.r | 30 ++-
dataRetrieval-2.2.1/dataRetrieval/R/readWQPdata.R | 1
dataRetrieval-2.2.1/dataRetrieval/R/whatWQPsites.R | 16 +
dataRetrieval-2.2.1/dataRetrieval/build/vignette.rds |binary
dataRetrieval-2.2.1/dataRetrieval/inst/doc/dataRetrieval.pdf |binary
dataRetrieval-2.2.1/dataRetrieval/man/checkWQPdates.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/constructNWISURL.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/constructWQPURL.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/countyCd.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/dataRetrieval-package.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/getWebServiceData.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/importRDB1.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/importWQP.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/importWaterML1.Rd | 6
dataRetrieval-2.2.1/dataRetrieval/man/importWaterML2.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/pCodeToName.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/parameterCdFile.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISdata.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISdv.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISgwl.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISmeas.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISpCode.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISpeak.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISqw.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISrating.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISsite.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readNWISuv.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readWQPdata.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/readWQPqw.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/renameNWISColumns.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/stateCd.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/stateCdLookup.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/whatNWISdata.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/whatNWISsites.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/whatWQPsites.Rd | 2
dataRetrieval-2.2.1/dataRetrieval/man/zeroPad.Rd | 2
41 files changed, 116 insertions(+), 92 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Diff between checkpoint versions 0.3.9 dated 2015-03-17 and 0.3.10 dated 2015-04-27
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install
packages as they existed on CRAN on a specific snapshot date as if you had
a CRAN time machine. To achieve reproducibility, the checkpoint() function
installs the packages required or called by your project and scripts to a
local library exactly as they existed at the specified point in time. Only
those packages are available to your project, thereby avoiding any package
updates that came later and may have altered your results. In this way,
anyone using checkpoint's checkpoint() can ensure the reproducibility of
your scripts or projects at any time. To create the snapshot archives, once
a day (at midnight UTC) Revolution Analytics refreshes the Austria CRAN mirror, on the "Managed
R Archived Network" server (http://mran.revolutionanalytics.com/).
Immediately after completion of the rsync mirror process, the process takes a
snapshot, thus creating the archive. Snapshot archives exist starting from
2014-09-17.
Author: Revolution Analytics
Maintainer: Andrie de Vries
DESCRIPTION | 12 ++---
MD5 | 23 +++++-----
NAMESPACE | 1
R/checkpoint.R | 56 +++++++++++++++----------
R/checkpoint_paths.R | 35 +++++++++++++--
R/installMissingBasePackages.R | 11 ++---
R/setSnapshot.R |only
R/test-common-functions.R | 4 -
build/vignette.rds |binary
inst/examples/example_setSnapshot.R |only
man/setSnapshot.Rd |only
tests/testthat/test-0-snapshots.R | 2
tests/testthat/test-2-checkpoint.R | 79 ++++++++++++++++++++++++------------
vignettes/checkpoint.Rmd | 11 ++---
14 files changed, 153 insertions(+), 81 deletions(-)
Title: Simulation and Group Sequential Monitoring of Randomized
Two-Stage Treatment Efficacy Trials with Time-to-Event
Endpoints
Diff between seqDesign versions 1.0.2 dated 2014-10-08 and 1.1 dated 2015-04-27
Description: A modification of the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases) is implemented, with application generally to individual-randomized clinical trials with multiple active treatment groups and a shared control group, and a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment group for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial monitoring outcomes (e.g., stopping early for non-efficacy); unconditional power for comparing treatment efficacies; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with a clinical outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Maintainer: Michal Juraska
seqDesign-1.0.2/seqDesign/inst/extdata/seqDesignReport.Rnw |only
seqDesign-1.1/seqDesign/DESCRIPTION | 16
seqDesign-1.1/seqDesign/MD5 | 31
seqDesign-1.1/seqDesign/NAMESPACE | 6
seqDesign-1.1/seqDesign/R/seqDesign.R | 6526 +++++-----
seqDesign-1.1/seqDesign/build/vignette.rds |binary
seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.R | 101
seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.Rnw | 211
seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.pdf |binary
seqDesign-1.1/seqDesign/inst/extdata/seqDesignReportSample.Rnw |only
seqDesign-1.1/seqDesign/inst/extdata/seqDesignReportSample.pdf |binary
seqDesign-1.1/seqDesign/man/VEpowerPP.Rd | 169
seqDesign-1.1/seqDesign/man/censTrial.Rd | 153
seqDesign-1.1/seqDesign/man/getBlockSize.Rd |only
seqDesign-1.1/seqDesign/man/monitorTrial.Rd | 233
seqDesign-1.1/seqDesign/man/rankTrial.Rd | 186
seqDesign-1.1/seqDesign/man/simTrial.Rd | 181
seqDesign-1.1/seqDesign/vignettes/seqDesignInstructions.Rnw | 211
18 files changed, 4115 insertions(+), 3909 deletions(-)
Title: Utility Sparse Matrix Functions for Quantitative Language
Comparison
Diff between qlcMatrix versions 0.9.2 dated 2014-05-19 and 0.9.4 dated 2015-04-27
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw
qlcMatrix-0.9.2/qlcMatrix/R/qlcMatrix.R |only
qlcMatrix-0.9.4/qlcMatrix/DESCRIPTION | 17 +++---
qlcMatrix-0.9.4/qlcMatrix/MD5 | 55 ++++++++++++---------
qlcMatrix-0.9.4/qlcMatrix/NAMESPACE | 3 -
qlcMatrix-0.9.4/qlcMatrix/R/assoc.R |only
qlcMatrix-0.9.4/qlcMatrix/R/base.R |only
qlcMatrix-0.9.4/qlcMatrix/R/sim.R |only
qlcMatrix-0.9.4/qlcMatrix/R/split.R |only
qlcMatrix-0.9.4/qlcMatrix/R/utils.R |only
qlcMatrix-0.9.4/qlcMatrix/README.md | 10 +++
qlcMatrix-0.9.4/qlcMatrix/build |only
qlcMatrix-0.9.4/qlcMatrix/inst |only
qlcMatrix-0.9.4/qlcMatrix/man/assocSparse.Rd | 6 +-
qlcMatrix-0.9.4/qlcMatrix/man/bibles.Rd | 8 +--
qlcMatrix-0.9.4/qlcMatrix/man/corSparse.Rd | 22 ++++----
qlcMatrix-0.9.4/qlcMatrix/man/cosNominal.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/cosSparse.Rd | 14 ++---
qlcMatrix-0.9.4/qlcMatrix/man/huber.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/pwMatrix.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/qlcMatrix-package.Rd | 8 +--
qlcMatrix-0.9.4/qlcMatrix/man/rowMax.Rd | 10 +--
qlcMatrix-0.9.4/qlcMatrix/man/sim.nominal.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/sim.strings.Rd | 8 +--
qlcMatrix-0.9.4/qlcMatrix/man/sim.wordlist.Rd | 4 -
qlcMatrix-0.9.4/qlcMatrix/man/sim.words.Rd | 4 -
qlcMatrix-0.9.4/qlcMatrix/man/splitStrings.Rd | 6 +-
qlcMatrix-0.9.4/qlcMatrix/man/splitTable.Rd | 10 ++-
qlcMatrix-0.9.4/qlcMatrix/man/splitText.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/splitWordlist.Rd | 4 -
qlcMatrix-0.9.4/qlcMatrix/man/unfold.Rd | 2
qlcMatrix-0.9.4/qlcMatrix/man/wals.Rd | 8 +--
qlcMatrix-0.9.4/qlcMatrix/vignettes |only
32 files changed, 116 insertions(+), 93 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.5.1 dated 2015-01-21 and 1.5.4 dated 2015-04-27
Description: A general purpose toolbox for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
psych-1.5.1/psych/R/CTA_lrn.R |only
psych-1.5.1/psych/R/cosiner.R |only
psych-1.5.1/psych/R/cta.new.R |only
psych-1.5.1/psych/R/nearcor.r |only
psych-1.5.4/psych/DESCRIPTION | 10
psych-1.5.4/psych/MD5 | 177 +++++-----
psych-1.5.4/psych/NAMESPACE | 25 +
psych-1.5.4/psych/R/ICLUST.R | 17
psych-1.5.4/psych/R/biplot.psych.R | 14
psych-1.5.4/psych/R/cluster.plot.R | 14
psych-1.5.4/psych/R/cor.plot.R | 6
psych-1.5.4/psych/R/corr.test.R | 7
psych-1.5.4/psych/R/cosinor.R | 2
psych-1.5.4/psych/R/cta.15.R |only
psych-1.5.4/psych/R/cta.R | 2
psych-1.5.4/psych/R/describe.R | 12
psych-1.5.4/psych/R/df2latex.R | 108 ++++--
psych-1.5.4/psych/R/diagram.R | 10
psych-1.5.4/psych/R/error.bars.by.R | 8
psych-1.5.4/psych/R/fa.R | 27 +
psych-1.5.4/psych/R/fa.diagram.R | 17
psych-1.5.4/psych/R/fa.parallel.R | 314 ++++++++++++------
psych-1.5.4/psych/R/fa.parallel.poly.R | 2
psych-1.5.4/psych/R/faBy.R | 52 ++
psych-1.5.4/psych/R/factor.stats.R | 83 +++-
psych-1.5.4/psych/R/kappa.R | 29 +
psych-1.5.4/psych/R/mat.regress.R | 150 ++++----
psych-1.5.4/psych/R/mediate.r | 143 +++++---
psych-1.5.4/psych/R/misc.R | 73 ++--
psych-1.5.4/psych/R/mixed.cor.R | 11
psych-1.5.4/psych/R/pairs.panels.R | 469 ++++++++++++---------------
psych-1.5.4/psych/R/phi.R | 3
psych-1.5.4/psych/R/principal.R | 2
psych-1.5.4/psych/R/print.psych.R | 71 +++-
psych-1.5.4/psych/R/print.psych.fa.R | 9
psych-1.5.4/psych/R/schmid.R | 2
psych-1.5.4/psych/R/score.items.R | 12
psych-1.5.4/psych/R/scoreOverlap.r | 61 ++-
psych-1.5.4/psych/R/set.cor.R | 37 +-
psych-1.5.4/psych/R/sim.parallel.r | 12
psych-1.5.4/psych/R/sim.structural.R | 11
psych-1.5.4/psych/R/smc.R | 57 +++
psych-1.5.4/psych/R/splitHalf.R | 33 +
psych-1.5.4/psych/R/statsBy.r | 15
psych-1.5.4/psych/R/summary.psych.R | 11
psych-1.5.4/psych/R/target.rot.R | 1
psych-1.5.4/psych/R/test.all.R | 21 +
psych-1.5.4/psych/R/test.psych.r | 40 ++
psych-1.5.4/psych/inst/CITATION | 4
psych-1.5.4/psych/inst/NEWS.Rd | 63 +++
psych-1.5.4/psych/inst/doc/overview.R | 2
psych-1.5.4/psych/inst/doc/overview.Rnw | 4
psych-1.5.4/psych/inst/doc/overview.pdf |binary
psych-1.5.4/psych/inst/doc/psych_for_sem.pdf |binary
psych-1.5.4/psych/man/ICLUST.Rd | 8
psych-1.5.4/psych/man/ICLUST.graph.Rd | 6
psych-1.5.4/psych/man/ICLUST.rgraph.Rd | 6
psych-1.5.4/psych/man/VSS.Rd | 6
psych-1.5.4/psych/man/alpha.Rd | 2
psych-1.5.4/psych/man/best.scales.Rd | 36 --
psych-1.5.4/psych/man/blot.Rd | 2
psych-1.5.4/psych/man/cluster.loadings.Rd | 2
psych-1.5.4/psych/man/cluster.plot.Rd | 2
psych-1.5.4/psych/man/cor.plot.Rd | 6
psych-1.5.4/psych/man/corr.test.Rd | 7
psych-1.5.4/psych/man/cosinor.Rd | 162 +++++++--
psych-1.5.4/psych/man/cta.Rd | 37 +-
psych-1.5.4/psych/man/describe.Rd | 8
psych-1.5.4/psych/man/df2latex.Rd | 39 +-
psych-1.5.4/psych/man/diagram.Rd | 2
psych-1.5.4/psych/man/epi.Rd | 5
psych-1.5.4/psych/man/error.bars.by.Rd | 15
psych-1.5.4/psych/man/fa.Rd | 44 +-
psych-1.5.4/psych/man/fa.diagram.Rd | 6
psych-1.5.4/psych/man/fa.parallel.Rd | 38 +-
psych-1.5.4/psych/man/guttman.Rd | 10
psych-1.5.4/psych/man/kappa.Rd | 4
psych-1.5.4/psych/man/mediate.Rd | 27 +
psych-1.5.4/psych/man/misc.Rd | 17
psych-1.5.4/psych/man/mixed.cor.Rd | 4
psych-1.5.4/psych/man/msq.Rd | 61 ++-
psych-1.5.4/psych/man/omega.Rd | 51 +-
psych-1.5.4/psych/man/pairs.panels.Rd | 10
psych-1.5.4/psych/man/score.items.Rd | 13
psych-1.5.4/psych/man/set.cor.Rd | 5
psych-1.5.4/psych/man/sim.item.Rd | 2
psych-1.5.4/psych/man/sim.structural.Rd | 9
psych-1.5.4/psych/man/simulation.circ.Rd | 2
psych-1.5.4/psych/man/smc.Rd | 4
psych-1.5.4/psych/man/statsBy.Rd | 17
psych-1.5.4/psych/man/test.psych.Rd | 8
psych-1.5.4/psych/vignettes/overview.Rnw | 4
92 files changed, 1916 insertions(+), 1024 deletions(-)
Title: Visualization and Analysis Tools for Neural Networks
Diff between NeuralNetTools versions 1.0.1 dated 2015-01-28 and 1.3.1 dated 2015-04-27
More information about NeuralNetTools at CRAN
Description: Visualization and analysis tools to aid in the interpretation of
neural network models. Functions are available for plotting,
quantifying variable importance, conducting a sensitivity analysis, and
obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
DESCRIPTION | 10 -
MD5 | 30 +++--
NAMESPACE | 10 +
R/NeuralNetTools_gar.R | 266 +++++++++++++++++++++++------------------------
R/NeuralNetTools_lek.R | 2
R/NeuralNetTools_old.R |only
R/NeuralNetTools_plot.R | 12 +-
R/NeuralNetTools_utils.R | 75 ++++++++++++-
README.md | 93 +++++++++++++++-
inst |only
man/garson.Rd | 51 +++++----
man/lekprofile.Rd | 4
man/neuraldat.Rd | 2
man/neuralskips.Rd |only
man/neuralweights.Rd | 6 -
man/olden.Rd |only
man/plotnet.Rd | 4
man/pred_sens.Rd | 2
18 files changed, 379 insertions(+), 188 deletions(-)
Permanent link
Title: Loading System Fonts into R
Diff between sysfonts versions 0.4 dated 2015-01-12 and 0.5 dated 2015-04-27
Description: Using FreeType to load system fonts
and Google Fonts (https://www.google.com/fonts) into R.
It is supposed to support other packages such as 'R2SWF'
and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 14 +++++++-------
MD5 | 7 ++++---
NEWS | 10 ++++++++++
R/google.R | 29 ++++++++++++++++++++++++-----
inst/fonts/webfonts.bz2 |only
5 files changed, 45 insertions(+), 15 deletions(-)
Title: Sequential Parameter Optimization Toolbox
Diff between SPOT versions 1.0.4184 dated 2013-06-26 and 1.0.5543 dated 2015-04-27
Description: The Sequential Parameter Optimization Toolbox provides a set of tools for Parameter-tuning, based on modelling techniques, DoE and statistical methods.
Author: Thomas Bartz-Beielstein [aut],
Martin Zaefferer [cre, ctb],
Joerg Ziegenhirt [ctb],
Wolfgang Konen [ctb],
Oliver Flasch [ctb],
Patrick Koch [ctb],
Martina Friese [ctb]
Maintainer: Martin Zaefferer
SPOT-1.0.4184/SPOT/R/spotComparison.R |only
SPOT-1.0.4184/SPOT/R/spotExplainInterfaces.R |only
SPOT-1.0.4184/SPOT/man/spotAlgStart....Rd |only
SPOT-1.0.4184/SPOT/man/spotCompare.Rd |only
SPOT-1.0.4184/SPOT/man/spotCreateDesign....Rd |only
SPOT-1.0.4184/SPOT/man/spotHelpInterfaces....Rd |only
SPOT-1.0.4184/SPOT/man/spotOcbaTest.Rd |only
SPOT-1.0.4184/SPOT/man/spotPlotPower.Rd |only
SPOT-1.0.4184/SPOT/man/spotPlotSeverity.Rd |only
SPOT-1.0.4184/SPOT/man/spotPower.Rd |only
SPOT-1.0.4184/SPOT/man/spotPredict....Rd |only
SPOT-1.0.4184/SPOT/man/spotPrepareSystem.Rd |only
SPOT-1.0.4184/SPOT/man/spotSeverity.Rd |only
SPOT-1.0.5543/SPOT/DESCRIPTION | 86 -
SPOT-1.0.5543/SPOT/MD5 | 630 ++++++-------
SPOT-1.0.5543/SPOT/NAMESPACE | 41
SPOT-1.0.5543/SPOT/NEWS | 41
SPOT-1.0.5543/SPOT/R/sms_emoa.r | 142 +-
SPOT-1.0.5543/SPOT/R/spot.R | 101 +-
SPOT-1.0.5543/SPOT/R/spotAlgStartEs.R | 74 -
SPOT-1.0.5543/SPOT/R/spotAlgStartEsGlg.R | 12
SPOT-1.0.5543/SPOT/R/spotAlgStartRgp.R | 8
SPOT-1.0.5543/SPOT/R/spotAlgStartSmsEmoaGlg.R | 4
SPOT-1.0.5543/SPOT/R/spotCreateDesignBasicDoe.R | 4
SPOT-1.0.5543/SPOT/R/spotCreateDesignFactors.R | 9
SPOT-1.0.5543/SPOT/R/spotCreateDesignFrF2.R | 14
SPOT-1.0.5543/SPOT/R/spotCreateDesignLhd.R | 94 +
SPOT-1.0.5543/SPOT/R/spotCreateDesignLhs.R | 2
SPOT-1.0.5543/SPOT/R/spotCreateDesignLhsOpt.R | 2
SPOT-1.0.5543/SPOT/R/spotEnsembleFunctions.R | 28
SPOT-1.0.5543/SPOT/R/spotEnsembleSingleBLAbern.R | 2
SPOT-1.0.5543/SPOT/R/spotExpectedImprovement.R | 28
SPOT-1.0.5543/SPOT/R/spotFuncStartBranin.R | 3
SPOT-1.0.5543/SPOT/R/spotFuncStartMexicanHat.R | 3
SPOT-1.0.5543/SPOT/R/spotFuncStartRastrigin.R | 3
SPOT-1.0.5543/SPOT/R/spotFuncStartRosenbrock.R | 4
SPOT-1.0.5543/SPOT/R/spotFuncStartSixHump.R | 51 -
SPOT-1.0.5543/SPOT/R/spotFuncStartSphere.R | 5
SPOT-1.0.5543/SPOT/R/spotFuncTools.R | 202 ++--
SPOT-1.0.5543/SPOT/R/spotGenerateSequentialDesign.R | 45
SPOT-1.0.5543/SPOT/R/spotGetOptions.R | 35
SPOT-1.0.5543/SPOT/R/spotHelpFunctions.R | 4
SPOT-1.0.5543/SPOT/R/spotMcoSort.R | 20
SPOT-1.0.5543/SPOT/R/spotModelOptim.R | 51 -
SPOT-1.0.5543/SPOT/R/spotModelParetoOptim.R | 54 -
SPOT-1.0.5543/SPOT/R/spotModelSelection.R | 12
SPOT-1.0.5543/SPOT/R/spotOcba.R | 178 +--
SPOT-1.0.5543/SPOT/R/spotOptimEs.R | 26
SPOT-1.0.5543/SPOT/R/spotOptimizationFunctions.R | 52 -
SPOT-1.0.5543/SPOT/R/spotPlot.R | 9
SPOT-1.0.5543/SPOT/R/spotPredictCoForrester.R | 364 +++----
SPOT-1.0.5543/SPOT/R/spotPredictDace.R | 234 +---
SPOT-1.0.5543/SPOT/R/spotPredictDice.R | 10
SPOT-1.0.5543/SPOT/R/spotPredictEarth.R | 13
SPOT-1.0.5543/SPOT/R/spotPredictEnsembleMultiAlternate.R | 3
SPOT-1.0.5543/SPOT/R/spotPredictEnsembleMultiRank.R | 5
SPOT-1.0.5543/SPOT/R/spotPredictEsvm.R | 14
SPOT-1.0.5543/SPOT/R/spotPredictForrester.R | 439 ++++-----
SPOT-1.0.5543/SPOT/R/spotPredictGausspr.R | 6
SPOT-1.0.5543/SPOT/R/spotPredictHelpFunctions.R | 22
SPOT-1.0.5543/SPOT/R/spotPredictKrig.R | 5
SPOT-1.0.5543/SPOT/R/spotPredictKsvm.R | 19
SPOT-1.0.5543/SPOT/R/spotPredictLm.R | 17
SPOT-1.0.5543/SPOT/R/spotPredictLmFactor.R | 24
SPOT-1.0.5543/SPOT/R/spotPredictMCO.R | 11
SPOT-1.0.5543/SPOT/R/spotPredictMLP.R | 26
SPOT-1.0.5543/SPOT/R/spotPredictMlegp.R | 24
SPOT-1.0.5543/SPOT/R/spotPredictNeuralnet.R |only
SPOT-1.0.5543/SPOT/R/spotPredictQrnn.R | 10
SPOT-1.0.5543/SPOT/R/spotPredictRandomForest.R | 2
SPOT-1.0.5543/SPOT/R/spotPredictTgp.R | 7
SPOT-1.0.5543/SPOT/R/spotPredictTree.R | 7
SPOT-1.0.5543/SPOT/R/spotPrepareData.R | 14
SPOT-1.0.5543/SPOT/R/spotRepairMissingValues.R |only
SPOT-1.0.5543/SPOT/R/spotRepeats.R | 66 -
SPOT-1.0.5543/SPOT/R/spotReport3d.R | 17
SPOT-1.0.5543/SPOT/R/spotReportContour.R | 7
SPOT-1.0.5543/SPOT/R/spotReportDefault.R | 4
SPOT-1.0.5543/SPOT/R/spotReportEarth.R | 4
SPOT-1.0.5543/SPOT/R/spotReportMAMP.R | 86 -
SPOT-1.0.5543/SPOT/R/spotReportSAMP.R | 30
SPOT-1.0.5543/SPOT/R/spotReportSens.R | 7
SPOT-1.0.5543/SPOT/R/spotStatistics.R | 4
SPOT-1.0.5543/SPOT/R/spotSurf.R | 40
SPOT-1.0.5543/SPOT/R/spotTargetFunctions.R | 16
SPOT-1.0.5543/SPOT/demo/00Index | 1
SPOT-1.0.5543/SPOT/demo/spotDemo23RgpKtfg.R |only
SPOT-1.0.5543/SPOT/inst/demo23RgpKtfg |only
SPOT-1.0.5543/SPOT/inst/doc/SPOT.pdf |binary
SPOT-1.0.5543/SPOT/inst/doc/index.html | 2
SPOT-1.0.5543/SPOT/java |only
SPOT-1.0.5543/SPOT/man/SPOT-package.Rd | 55 -
SPOT-1.0.5543/SPOT/man/Testfunctions.Rd | 76 -
SPOT-1.0.5543/SPOT/man/corrcubic.Rd | 40
SPOT-1.0.5543/SPOT/man/correxp.Rd | 40
SPOT-1.0.5543/SPOT/man/correxpg.Rd | 41
SPOT-1.0.5543/SPOT/man/corrgauss.Rd | 40
SPOT-1.0.5543/SPOT/man/corrkriging.Rd | 38
SPOT-1.0.5543/SPOT/man/corrlin.Rd | 40
SPOT-1.0.5543/SPOT/man/corrnoisygauss.Rd | 38
SPOT-1.0.5543/SPOT/man/corrnoisykriging.Rd | 38
SPOT-1.0.5543/SPOT/man/corrspherical.Rd | 40
SPOT-1.0.5543/SPOT/man/corrspline.Rd | 40
SPOT-1.0.5543/SPOT/man/daceBuilder.Rd | 110 --
SPOT-1.0.5543/SPOT/man/daceEvalFit.Rd | 18
SPOT-1.0.5543/SPOT/man/daceFixTheta.Rd | 44
SPOT-1.0.5543/SPOT/man/daceGetFit.Rd | 52 -
SPOT-1.0.5543/SPOT/man/daceLikelihood.Rd | 20
SPOT-1.0.5543/SPOT/man/daceObjfunc.Rd | 49 -
SPOT-1.0.5543/SPOT/man/dacePredictor.Rd | 67 -
SPOT-1.0.5543/SPOT/man/dacePrepareFit.Rd | 44
SPOT-1.0.5543/SPOT/man/daceStartParameters.Rd | 42
SPOT-1.0.5543/SPOT/man/forrBuilder.Rd | 119 --
SPOT-1.0.5543/SPOT/man/forrCoBuilder.Rd | 137 +-
SPOT-1.0.5543/SPOT/man/forrCoLikelihood.Rd | 40
SPOT-1.0.5543/SPOT/man/forrCoModel.Rd | 21
SPOT-1.0.5543/SPOT/man/forrCoRegPredictor.Rd | 31
SPOT-1.0.5543/SPOT/man/forrIF.Rd | 10
SPOT-1.0.5543/SPOT/man/forrRegLikelihood.Rd | 28
SPOT-1.0.5543/SPOT/man/forrRegPredictor.Rd | 41
SPOT-1.0.5543/SPOT/man/forrReintPredictor.Rd | 41
SPOT-1.0.5543/SPOT/man/predict.forr.Rd |only
SPOT-1.0.5543/SPOT/man/print.Rd | 28
SPOT-1.0.5543/SPOT/man/regpoly0.Rd | 28
SPOT-1.0.5543/SPOT/man/regpoly1.Rd | 31
SPOT-1.0.5543/SPOT/man/regpoly2.Rd | 30
SPOT-1.0.5543/SPOT/man/repmat.Rd | 15
SPOT-1.0.5543/SPOT/man/spot.Rd | 82 -
SPOT-1.0.5543/SPOT/man/spotAlgEs.Rd | 105 --
SPOT-1.0.5543/SPOT/man/spotAlgEsDominantReco.Rd | 22
SPOT-1.0.5543/SPOT/man/spotAlgEsGetSuccessRate.Rd | 16
SPOT-1.0.5543/SPOT/man/spotAlgEsHps.Rd | 17
SPOT-1.0.5543/SPOT/man/spotAlgEsIndividualInitial.Rd | 37
SPOT-1.0.5543/SPOT/man/spotAlgEsInitParentPop.Rd | 37
SPOT-1.0.5543/SPOT/man/spotAlgEsInterReco.Rd | 22
SPOT-1.0.5543/SPOT/man/spotAlgEsInterRecoBeSw02.Rd | 18
SPOT-1.0.5543/SPOT/man/spotAlgEsMarriage.Rd | 16
SPOT-1.0.5543/SPOT/man/spotAlgEsMarriageWithReplace.Rd | 17
SPOT-1.0.5543/SPOT/man/spotAlgEsObjMutation.Rd | 10
SPOT-1.0.5543/SPOT/man/spotAlgEsQuickTest.Rd | 31
SPOT-1.0.5543/SPOT/man/spotAlgEsSelection.Rd | 19
SPOT-1.0.5543/SPOT/man/spotAlgEsStratMutation.Rd | 25
SPOT-1.0.5543/SPOT/man/spotAlgEsTermination.Rd | 34
SPOT-1.0.5543/SPOT/man/spotAlgStartEs.Rd | 42
SPOT-1.0.5543/SPOT/man/spotAlgStartEsGlg.Rd | 43
SPOT-1.0.5543/SPOT/man/spotAlgStartEsVar.Rd | 48
SPOT-1.0.5543/SPOT/man/spotAlgStartRgp.Rd | 40
SPOT-1.0.5543/SPOT/man/spotAlgStartSann.Rd | 46
SPOT-1.0.5543/SPOT/man/spotAlgStartSannVar.Rd | 52 -
SPOT-1.0.5543/SPOT/man/spotAlgStartSmsEmoaGlg.Rd | 43
SPOT-1.0.5543/SPOT/man/spotCalcNoise.Rd | 24
SPOT-1.0.5543/SPOT/man/spotCallCoFunction.Rd | 26
SPOT-1.0.5543/SPOT/man/spotCodeFormulas.Rd | 20
SPOT-1.0.5543/SPOT/man/spotCreateDesignBasicDoe.Rd | 39
SPOT-1.0.5543/SPOT/man/spotCreateDesignFactors.Rd | 29
SPOT-1.0.5543/SPOT/man/spotCreateDesignFrF2.Rd | 33
SPOT-1.0.5543/SPOT/man/spotCreateDesignLhd.Rd | 37
SPOT-1.0.5543/SPOT/man/spotCreateDesignLhs.Rd | 29
SPOT-1.0.5543/SPOT/man/spotCreateDesignLhsOpt.Rd | 29
SPOT-1.0.5543/SPOT/man/spotEnsembleMinimum.Rd | 11
SPOT-1.0.5543/SPOT/man/spotEnsembleModelBuilding.Rd | 25
SPOT-1.0.5543/SPOT/man/spotEnsembleModelEvaluate.Rd | 21
SPOT-1.0.5543/SPOT/man/spotEnsembleMultiAlternate.Rd | 84 -
SPOT-1.0.5543/SPOT/man/spotEnsembleMultiAverage.Rd | 90 -
SPOT-1.0.5543/SPOT/man/spotEnsembleMultiChoose.Rd | 89 -
SPOT-1.0.5543/SPOT/man/spotEnsembleMultiRank.Rd | 74 -
SPOT-1.0.5543/SPOT/man/spotEnsembleMultiRankWeighted.Rd | 72 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleBLAbern.Rd | 78 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleBLAnorm.Rd | 78 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleEpsGreedy.Rd | 84 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSinglePOKER.Rd | 91 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleRoundSearch.Rd | 79 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleSoftMax.Rd | 94 -
SPOT-1.0.5543/SPOT/man/spotEnsembleSingleUCB1.Rd | 83 -
SPOT-1.0.5543/SPOT/man/spotEnsembleStatsMin.Rd | 12
SPOT-1.0.5543/SPOT/man/spotEnsembleStatsSd.Rd | 12
SPOT-1.0.5543/SPOT/man/spotEnsembleSubdesigns.Rd | 26
SPOT-1.0.5543/SPOT/man/spotEnsembleSummedRank.Rd | 14
SPOT-1.0.5543/SPOT/man/spotEnsembleSummedRankWeighted.Rd | 16
SPOT-1.0.5543/SPOT/man/spotExiPsi.Rd | 14
SPOT-1.0.5543/SPOT/man/spotFeedback.Rd | 84 -
SPOT-1.0.5543/SPOT/man/spotForceFactorDesign.Rd | 20
SPOT-1.0.5543/SPOT/man/spotForceFactorX.Rd | 18
SPOT-1.0.5543/SPOT/man/spotFuncStartBranin.Rd | 36
SPOT-1.0.5543/SPOT/man/spotFuncStartDisBranin.Rd | 36
SPOT-1.0.5543/SPOT/man/spotFuncStartMexicanHat.Rd | 36
SPOT-1.0.5543/SPOT/man/spotFuncStartRastrigin.Rd | 38
SPOT-1.0.5543/SPOT/man/spotFuncStartRosenbrock.Rd | 36
SPOT-1.0.5543/SPOT/man/spotFuncStartSixHump.Rd | 38
SPOT-1.0.5543/SPOT/man/spotFuncStartSphere.Rd | 36
SPOT-1.0.5543/SPOT/man/spotGenerateSequentialDesign.Rd | 31
SPOT-1.0.5543/SPOT/man/spotGetAllRepeats.Rd | 12
SPOT-1.0.5543/SPOT/man/spotGetMergedDataMatrixB.Rd | 31
SPOT-1.0.5543/SPOT/man/spotGetOptions.Rd | 263 +----
SPOT-1.0.5543/SPOT/man/spotGetRawDataMatrixB.Rd | 32
SPOT-1.0.5543/SPOT/man/spotGetRawResData.Rd | 26
SPOT-1.0.5543/SPOT/man/spotGetRepeats.Rd | 16
SPOT-1.0.5543/SPOT/man/spotGlgCore.Rd | 34
SPOT-1.0.5543/SPOT/man/spotGlgCreate.Rd | 65 -
SPOT-1.0.5543/SPOT/man/spotGlgCreateN.Rd | 68 -
SPOT-1.0.5543/SPOT/man/spotGlgCreateRot.Rd | 63 -
SPOT-1.0.5543/SPOT/man/spotGlgCreateRotSearched.Rd | 64 -
SPOT-1.0.5543/SPOT/man/spotGlgEval.Rd | 35
SPOT-1.0.5543/SPOT/man/spotGlgEvalN.Rd | 33
SPOT-1.0.5543/SPOT/man/spotGlgEvalRot.Rd | 34
SPOT-1.0.5543/SPOT/man/spotGlgInit.Rd | 72 -
SPOT-1.0.5543/SPOT/man/spotGlgInitN.Rd | 74 -
SPOT-1.0.5543/SPOT/man/spotGui.Rd | 14
SPOT-1.0.5543/SPOT/man/spotHelpBslash.Rd | 13
SPOT-1.0.5543/SPOT/man/spotHlpF.norm.Rd | 13
SPOT-1.0.5543/SPOT/man/spotHlpF.norminv.Rd | 14
SPOT-1.0.5543/SPOT/man/spotInfillExpImp.Rd | 19
SPOT-1.0.5543/SPOT/man/spotInfillHyperVolume.Rd | 22
SPOT-1.0.5543/SPOT/man/spotInfillLcbHyperVolume.Rd | 41
SPOT-1.0.5543/SPOT/man/spotInfillLcbMulti.Rd | 19
SPOT-1.0.5543/SPOT/man/spotInfillLcbSingle.Rd | 14
SPOT-1.0.5543/SPOT/man/spotInfillProbImp.Rd | 20
SPOT-1.0.5543/SPOT/man/spotInfillSD.Rd | 17
SPOT-1.0.5543/SPOT/man/spotInfillSExI2d.Rd | 36
SPOT-1.0.5543/SPOT/man/spotInitializePredictor.Rd | 38
SPOT-1.0.5543/SPOT/man/spotInstAndLoadPackages.Rd | 32
SPOT-1.0.5543/SPOT/man/spotInvChisq.Rd | 14
SPOT-1.0.5543/SPOT/man/spotMcoCrowdTournament.Rd | 23
SPOT-1.0.5543/SPOT/man/spotMcoSelectionHypervol.Rd | 50 -
SPOT-1.0.5543/SPOT/man/spotMcoSort.Rd | 29
SPOT-1.0.5543/SPOT/man/spotMcoTournament.Rd | 22
SPOT-1.0.5543/SPOT/man/spotMetaFlattenFbsRow.Rd | 17
SPOT-1.0.5543/SPOT/man/spotModel.func.Rd | 35
SPOT-1.0.5543/SPOT/man/spotModel.predict.Rd | 26
SPOT-1.0.5543/SPOT/man/spotModel.train.Rd | 36
SPOT-1.0.5543/SPOT/man/spotModelDescentLm.Rd | 24
SPOT-1.0.5543/SPOT/man/spotModelOptim.Rd | 101 --
SPOT-1.0.5543/SPOT/man/spotModelParetoOptim.Rd | 43
SPOT-1.0.5543/SPOT/man/spotNormDesign.Rd | 34
SPOT-1.0.5543/SPOT/man/spotNormalizeMatrix.Rd | 23
SPOT-1.0.5543/SPOT/man/spotNormalizeMatrix2.Rd | 27
SPOT-1.0.5543/SPOT/man/spotOcba.Rd | 26
SPOT-1.0.5543/SPOT/man/spotOptim.Rd | 85 -
SPOT-1.0.5543/SPOT/man/spotOptimEs.Rd | 119 +-
SPOT-1.0.5543/SPOT/man/spotOptimInterface.Rd | 54 -
SPOT-1.0.5543/SPOT/man/spotOptimLHS.Rd | 55 -
SPOT-1.0.5543/SPOT/man/spotOptimizationInterface.Rd | 137 +-
SPOT-1.0.5543/SPOT/man/spotOptimizationInterfaceMco.Rd | 81 -
SPOT-1.0.5543/SPOT/man/spotParetoOptMulti.Rd | 10
SPOT-1.0.5543/SPOT/man/spotPenalizeMissingValues.Rd |only
SPOT-1.0.5543/SPOT/man/spotPlotBst.Rd | 19
SPOT-1.0.5543/SPOT/man/spotPredictCoForrester.Rd | 97 --
SPOT-1.0.5543/SPOT/man/spotPredictDace.Rd | 91 -
SPOT-1.0.5543/SPOT/man/spotPredictDice.Rd | 39
SPOT-1.0.5543/SPOT/man/spotPredictEarth.Rd | 60 -
SPOT-1.0.5543/SPOT/man/spotPredictEsvm.Rd | 36
SPOT-1.0.5543/SPOT/man/spotPredictForrester.Rd | 85 -
SPOT-1.0.5543/SPOT/man/spotPredictGausspr.Rd | 35
SPOT-1.0.5543/SPOT/man/spotPredictKrig.Rd | 34
SPOT-1.0.5543/SPOT/man/spotPredictKsvm.Rd | 36
SPOT-1.0.5543/SPOT/man/spotPredictLm.Rd | 46
SPOT-1.0.5543/SPOT/man/spotPredictLmFactor.Rd | 55 -
SPOT-1.0.5543/SPOT/man/spotPredictMCO.Rd | 65 -
SPOT-1.0.5543/SPOT/man/spotPredictMLP.Rd | 35
SPOT-1.0.5543/SPOT/man/spotPredictMlegp.Rd | 59 -
SPOT-1.0.5543/SPOT/man/spotPredictNeuralnet.Rd |only
SPOT-1.0.5543/SPOT/man/spotPredictOptMulti.Rd | 10
SPOT-1.0.5543/SPOT/man/spotPredictQrnn.Rd | 35
SPOT-1.0.5543/SPOT/man/spotPredictRandomForest.Rd | 58 -
SPOT-1.0.5543/SPOT/man/spotPredictRandomForestMlegp.Rd | 38
SPOT-1.0.5543/SPOT/man/spotPredictTest.Rd | 37
SPOT-1.0.5543/SPOT/man/spotPredictTgp.Rd | 37
SPOT-1.0.5543/SPOT/man/spotPredictTree.Rd | 37
SPOT-1.0.5543/SPOT/man/spotPrepare.Rd | 39
SPOT-1.0.5543/SPOT/man/spotPrepareData.Rd | 46
SPOT-1.0.5543/SPOT/man/spotPrepareDataAsMatrixC.Rd | 28
SPOT-1.0.5543/SPOT/man/spotPrepareResult.Rd |only
SPOT-1.0.5543/SPOT/man/spotPrint.Rd | 19
SPOT-1.0.5543/SPOT/man/spotROI.Rd | 31
SPOT-1.0.5543/SPOT/man/spotReadBstFile.Rd | 26
SPOT-1.0.5543/SPOT/man/spotReadRoi.Rd | 18
SPOT-1.0.5543/SPOT/man/spotRepairMissingValues.Rd |only
SPOT-1.0.5543/SPOT/man/spotRepairMissingValuesCoKriging.Rd |only
SPOT-1.0.5543/SPOT/man/spotRepeats.Rd | 17
SPOT-1.0.5543/SPOT/man/spotRepeatsOcba.Rd | 18
SPOT-1.0.5543/SPOT/man/spotReport3d.Rd | 50 -
SPOT-1.0.5543/SPOT/man/spotReport3dMulti.Rd | 42
SPOT-1.0.5543/SPOT/man/spotReportContour.Rd | 50 -
SPOT-1.0.5543/SPOT/man/spotReportContourMulti.Rd | 29
SPOT-1.0.5543/SPOT/man/spotReportDefault.Rd | 40
SPOT-1.0.5543/SPOT/man/spotReportEarth.Rd | 16
SPOT-1.0.5543/SPOT/man/spotReportMAMP.Rd | 20
SPOT-1.0.5543/SPOT/man/spotReportMetaDefault.Rd | 28
SPOT-1.0.5543/SPOT/man/spotReportSAMP.Rd | 20
SPOT-1.0.5543/SPOT/man/spotReportSens.Rd | 20
SPOT-1.0.5543/SPOT/man/spotReportSensY.Rd | 19
SPOT-1.0.5543/SPOT/man/spotReverseNormalizeMatrix.Rd | 24
SPOT-1.0.5543/SPOT/man/spotRgpTargetFunction.Rd | 27
SPOT-1.0.5543/SPOT/man/spotSExI2d.Rd | 47
SPOT-1.0.5543/SPOT/man/spotSelectionCriteria.Rd | 53 -
SPOT-1.0.5543/SPOT/man/spotSeqDesignIncreaseMultTwo.Rd | 20
SPOT-1.0.5543/SPOT/man/spotSeqDesignIncreasePlusOne.Rd | 20
SPOT-1.0.5543/SPOT/man/spotSmsEmoa.Rd | 43
SPOT-1.0.5543/SPOT/man/spotSmsEmoaKriging.Rd | 38
SPOT-1.0.5543/SPOT/man/spotStepAutoOpt.Rd | 36
SPOT-1.0.5543/SPOT/man/spotStepInitial.Rd | 42
SPOT-1.0.5543/SPOT/man/spotStepMetaOpt.Rd | 26
SPOT-1.0.5543/SPOT/man/spotStepReport.Rd | 26
SPOT-1.0.5543/SPOT/man/spotStepRunAlg.Rd | 47
SPOT-1.0.5543/SPOT/man/spotStepSequential.Rd | 30
SPOT-1.0.5543/SPOT/man/spotSurf3d.Rd | 36
SPOT-1.0.5543/SPOT/man/spotSurfContour.Rd | 64 -
SPOT-1.0.5543/SPOT/man/spotVersion.Rd | 11
SPOT-1.0.5543/SPOT/man/spotWriteAroi.Rd | 22
SPOT-1.0.5543/SPOT/man/spotWriteBest.Rd | 33
SPOT-1.0.5543/SPOT/man/spotWriteDes.Rd | 24
SPOT-1.0.5543/SPOT/man/spotWriteLines.Rd | 23
SPOT-1.0.5543/SPOT/man/spotWriteRes.Rd |only
SPOT-1.0.5543/SPOT/man/spotWriteRoiFileForRepeats.Rd | 15
SPOT-1.0.5543/SPOT/vignettes/SPOT.Rnw | 2
315 files changed, 5270 insertions(+), 7219 deletions(-)
Title: Using Fonts More Easily in R Graphs
Diff between showtext versions 0.3 dated 2015-03-11 and 0.4-1 dated 2015-04-27
Description: Making it easy to use various types of fonts
(TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and
supporting most output formats of R graphics including PNG, PDF and
SVG. Text glyphs will be converted into polygons or raster images,
hence after the plot has been created, it no longer relies on the font files.
No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 12 +-
MD5 | 36 +++---
NAMESPACE | 2
R/showtext.R | 261 ++++++++++++++++++++++++++++++++++++++---------
R/zzz.R | 15 ++
README.md | 272 +++++++++++++++++++++++++++++++++++---------------
inst/NEWS.Rd | 21 +++
man/showtext.auto.Rd |only
man/showtext.begin.Rd | 83 ++++++---------
man/showtext.end.Rd | 6 -
man/showtext.opts.Rd |only
src/devfuns.c | 79 ++++++++++----
src/devfuns.h |only
src/fonts.c |only
src/fonts.h | 21 +++
src/outline.c | 35 ------
src/outline.h | 66 ++++--------
src/raster.c |only
src/raster.h |only
src/showtext.c | 17 +--
src/util.c | 140 +++++--------------------
src/util.h | 27 ++++
22 files changed, 674 insertions(+), 419 deletions(-)
Title: Prediction of Therapeutic Success
Diff between EffectTreat versions 0.1-1 dated 2014-12-11 and 0.1-11 dated 2015-04-27
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NAMESPACE | 9 +++++++++
NEWS | 3 +++
man/Example.Data.Rd | 2 +-
5 files changed, 22 insertions(+), 10 deletions(-)
Title: Full Interactive GUI for Dynamic Biplot in R
Diff between dynBiplotGUI versions 1.1.2 dated 2014-12-10 and 1.1.3 dated 2015-04-27
Description: A GUI to solve dynamic biplots and classical biplot. Try matrices of 2-way and 3-way. The GUI can be run in multiple languages.
Author: Jaime Egido [aut, cre]
Maintainer: Jaime Egido
ChangeLog | 15 +
DESCRIPTION | 10
MD5 | 16 -
R/dynBiplot.R | 529 ++++++++++++++++++++------------------------
inst/lang/Language.csv | 4
man/dynBiplot.Rd | 8
man/dynBiplotGUI-package.Rd | 6
man/panelFormat_en.Rd | 1
man/panelFormat_es.Rd | 1
9 files changed, 293 insertions(+), 297 deletions(-)
Title: Cox-Type Models for Interval-Censored Data
Diff between coxinterval versions 1.0 dated 2014-07-20 and 1.1 dated 2015-04-27
Description: Fits Cox-type models based on interval-censored data from a survival
or illness-death process.
Author: Audrey Boruvka and Richard J. Cook
Maintainer: Audrey Boruvka
coxinterval-1.0/coxinterval/R/coxaalenic.R |only
coxinterval-1.0/coxinterval/R/coxaalenic.control.R |only
coxinterval-1.0/coxinterval/R/coxaalenic.ineq.R |only
coxinterval-1.0/coxinterval/R/coxic.R |only
coxinterval-1.0/coxinterval/R/coxic.control.R |only
coxinterval-1.0/coxinterval/R/coxic.data.R |only
coxinterval-1.0/coxinterval/R/na.coxic.R |only
coxinterval-1.0/coxinterval/man/coxaalenic.Rd |only
coxinterval-1.0/coxinterval/man/coxaalenic.control.Rd |only
coxinterval-1.0/coxinterval/man/coxic.Rd |only
coxinterval-1.0/coxinterval/man/coxic.control.Rd |only
coxinterval-1.0/coxinterval/src/coxaalenic.c |only
coxinterval-1.0/coxinterval/src/coxic.c |only
coxinterval-1.1/coxinterval/DESCRIPTION | 21 ++-
coxinterval-1.1/coxinterval/INSTALL | 38 ++++--
coxinterval-1.1/coxinterval/MD5 | 77 +++++++-------
coxinterval-1.1/coxinterval/NAMESPACE | 23 ++--
coxinterval-1.1/coxinterval/NEWS |only
coxinterval-1.1/coxinterval/R/const2lin.R | 3
coxinterval-1.1/coxinterval/R/coxaalen.R |only
coxinterval-1.1/coxinterval/R/coxaalen.control.R |only
coxinterval-1.1/coxinterval/R/coxaalen.ineq.R |only
coxinterval-1.1/coxinterval/R/coxdual.R |only
coxinterval-1.1/coxinterval/R/coxdual.control.R |only
coxinterval-1.1/coxinterval/R/coxdual.data.R |only
coxinterval-1.1/coxinterval/R/jump2step.R | 3
coxinterval-1.1/coxinterval/R/lin2const.R | 3
coxinterval-1.1/coxinterval/R/maximalint.R | 15 --
coxinterval-1.1/coxinterval/R/na.coxdual.R |only
coxinterval-1.1/coxinterval/R/print.coxinterval.R | 9 +
coxinterval-1.1/coxinterval/R/print.summary.coxinterval.R | 6 -
coxinterval-1.1/coxinterval/R/step2jump.R | 3
coxinterval-1.1/coxinterval/R/step2stepfun.R |only
coxinterval-1.1/coxinterval/R/summary.coxinterval.R | 8 -
coxinterval-1.1/coxinterval/man/const2lin.Rd |only
coxinterval-1.1/coxinterval/man/cosmesis.Rd | 1
coxinterval-1.1/coxinterval/man/coxaalen.Rd |only
coxinterval-1.1/coxinterval/man/coxaalen.control.Rd |only
coxinterval-1.1/coxinterval/man/coxdual.Rd |only
coxinterval-1.1/coxinterval/man/coxdual.control.Rd |only
coxinterval-1.1/coxinterval/man/dualic.Rd | 10 -
coxinterval-1.1/coxinterval/man/dualrc.Rd | 6 -
coxinterval-1.1/coxinterval/man/jump2step.Rd |only
coxinterval-1.1/coxinterval/man/lin2const.Rd |only
coxinterval-1.1/coxinterval/man/linapprox.Rd |only
coxinterval-1.1/coxinterval/man/maximalint.Rd |only
coxinterval-1.1/coxinterval/man/print.coxinterval.Rd | 2
coxinterval-1.1/coxinterval/man/step2jump.Rd |only
coxinterval-1.1/coxinterval/man/step2stepfun.Rd |only
coxinterval-1.1/coxinterval/man/summary.coxinterval.Rd | 10 -
coxinterval-1.1/coxinterval/man/trans.Rd | 6 -
coxinterval-1.1/coxinterval/src/Makevars | 8 -
coxinterval-1.1/coxinterval/src/Makevars.win | 16 +-
coxinterval-1.1/coxinterval/src/coxaalen.c |only
coxinterval-1.1/coxinterval/src/coxdual.c |only
coxinterval-1.1/coxinterval/src/coxinterval.h | 3
coxinterval-1.1/coxinterval/src/rcplex.c | 1
57 files changed, 142 insertions(+), 130 deletions(-)
Title: Seismic Reflection and Scattering Coefficients
Diff between zoeppritz versions 1.0-4 dated 2013-03-13 and 1.0-5 dated 2015-04-27
Description: Calculate and plot scattering matrix coefficients for plane waves at interface.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 19 +++++++++----------
MD5 | 4 ++--
man/pzoeppritz.Rd | 16 +++++++++++-----
3 files changed, 22 insertions(+), 17 deletions(-)
Title: Statistical Analysis for Environmental Data
Diff between StatDA versions 1.6.7 dated 2013-08-22 and 1.6.9 dated 2015-04-27
Description: This package offers different possibilities to make statistical analysis for Environmental Data.
Author: Peter Filzmoser
Maintainer: Peter Filzmoser
DESCRIPTION | 8 +++---
MD5 | 54 +++++++++++++++++++++++----------------------
R/SymbLegend.R | 6 +++--
build |only
data/AuNEW.rda |binary
data/AuOLD.rda |binary
data/CHorANADUP.rda |binary
data/CHorFieldDUP.rda |binary
data/CHorSTANDARD.rda |binary
data/bhorizon.rda |binary
data/bordersKola.rda |binary
data/chorizon.rda |binary
data/kola.background.rda |binary
data/monch.rda |binary
data/moss.rda |binary
data/nizap.rda |binary
data/ohorizon.rda |binary
data/res.eyefit.As_C.rda |binary
data/res.eyefit.As_C_m.rda |binary
data/res.eyefit.AuNEW.rda |binary
data/res.eyefit.Ca_C.rda |binary
data/res.eyefit.Ca_O.rda |binary
data/res.eyefit.Hg_O.rda |binary
data/res.eyefit.Pb_O1.rda |binary
data/res.eyefit.Pb_O2.rda |binary
data/timetrend.rda |binary
data/topsoil.rda |binary
inst/doc/StatDA.R |only
man/plotelement.Rd | 2 -
29 files changed, 37 insertions(+), 33 deletions(-)
Title: Visualization for Seismic Tomography
Diff between RTOMO versions 1.1-2 dated 2014-01-06 and 1.1-3 dated 2015-04-27
Description: Aimed at seismic tomography, the package
plots tomographic images, and allows one to interact and query
three-dimensional tomographic models.
Vertical cross-sectional cuts can be extracted by mouse click.
Geographic information can be added easily.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
RTOMO-1.1-2/RTOMO/R/TOMO.colors.R |only
RTOMO-1.1-2/RTOMO/man/TOMO.colors.Rd |only
RTOMO-1.1-3/RTOMO/DESCRIPTION | 12 ++++-----
RTOMO-1.1-3/RTOMO/MD5 | 40 ++++++++++++++++++---------------
RTOMO-1.1-3/RTOMO/R/FANCY.TOMO.R | 2 -
RTOMO-1.1-3/RTOMO/R/HOZscale.R |only
RTOMO-1.1-3/RTOMO/R/PLOT.TOMOXSEC.R | 6 ++--
RTOMO-1.1-3/RTOMO/R/SHOWTOMO.R | 4 +--
RTOMO-1.1-3/RTOMO/R/TOMO3D.drive.R | 8 +++---
RTOMO-1.1-3/RTOMO/R/TOMOXSEC.R | 2 -
RTOMO-1.1-3/RTOMO/R/XSEC.drive.R | 4 +--
RTOMO-1.1-3/RTOMO/R/get2Drayblox.R | 4 +--
RTOMO-1.1-3/RTOMO/R/jstats.R |only
RTOMO-1.1-3/RTOMO/R/makeMOD.R | 2 -
RTOMO-1.1-3/RTOMO/R/meshgrid.R |only
RTOMO-1.1-3/RTOMO/R/pltomo.R | 2 -
RTOMO-1.1-3/RTOMO/R/tomo.colors.R |only
RTOMO-1.1-3/RTOMO/man/HOZscale.Rd |only
RTOMO-1.1-3/RTOMO/man/PLOT.TOMOXSEC.Rd | 2 -
RTOMO-1.1-3/RTOMO/man/RTOMO-package.Rd | 2 -
RTOMO-1.1-3/RTOMO/man/TOMOXSEC.Rd | 2 -
RTOMO-1.1-3/RTOMO/man/XSEC.drive.Rd | 2 -
RTOMO-1.1-3/RTOMO/man/jstats.Rd |only
RTOMO-1.1-3/RTOMO/man/meshgrid.Rd |only
RTOMO-1.1-3/RTOMO/man/pltomo.Rd | 2 -
RTOMO-1.1-3/RTOMO/man/tomo.colors.Rd |only
26 files changed, 51 insertions(+), 45 deletions(-)
Title: Seismic Hypocenter Determination
Diff between Rquake versions 2.2 dated 2014-01-06 and 2.3-1 dated 2015-04-27
Description: Hypocenter estimation and analysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from RSEIS and GEOmap to help researchers pick, locate, and store hypocenters for detailed seismic investigation.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 12 +++----
MD5 | 14 ++++----
NAMESPACE | 3 +
R/RElocateEQ.R | 37 +++++++++++-----------
R/ROTcovQUAKE.R |only
R/plotJACKLLZ.R | 89 +++++++++++++++++++++++++++++++++++++++--------------
man/RElocateEQ.Rd | 4 +-
man/ROTcovQUAKE.Rd |only
man/plotJACKLLZ.Rd | 15 +++++++-
9 files changed, 117 insertions(+), 57 deletions(-)
Title: Kernel Density Estimation for Heaped Data
Diff between Kernelheaping versions 0.2 dated 2015-01-27 and 0.5 dated 2015-04-27
Description: In self-reported data the user often encounters heaped data, i.e. data which are rounded to a different
degree of coarseness. While this is mostly a minor problem in parametric density estimation the bias can be very large
for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional
parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods.
Additionally varying rounding probabilities (with the true value) and asymmetric rounding is estimable as well.
Author: Marcus Gross
Maintainer: Marcus Gross
Kernelheaping-0.2/Kernelheaping/man/Rprx2.Rd |only
Kernelheaping-0.5/Kernelheaping/DESCRIPTION | 12
Kernelheaping-0.5/Kernelheaping/MD5 | 17
Kernelheaping-0.5/Kernelheaping/NAMESPACE | 4
Kernelheaping-0.5/Kernelheaping/R/Kernelheaping.R | 2
Kernelheaping-0.5/Kernelheaping/R/functions.R | 274 ++++++----
Kernelheaping-0.5/Kernelheaping/man/Rprx.Rd |only
Kernelheaping-0.5/Kernelheaping/man/createSim.Kernelheaping.Rd | 4
Kernelheaping-0.5/Kernelheaping/man/dheaping.Rd | 27
Kernelheaping-0.5/Kernelheaping/man/sim.Kernelheaping.Rd | 32 +
Kernelheaping-0.5/Kernelheaping/man/simSummary.Kernelheaping.Rd |only
11 files changed, 239 insertions(+), 133 deletions(-)
Title: Generalized Hermite Distribution
Diff between hermite versions 1.0.2 dated 2015-03-20 and 1.1.0 dated 2015-04-27
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and MarÃa Oliveira
Maintainer: David Moriña Soler
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++-----------
NAMESPACE | 3 +++
R/glm.hermite.R | 13 +++++++++++++
R/print.summary.glm.hermite.R |only
R/qhermite.R | 30 +++++++++++++++++++-----------
R/summary.glm.hermite.R |only
man/dhermite.Rd | 4 ++--
man/glm.hermite.Rd | 7 +++++--
man/hermite-internal.Rd | 4 ++++
man/hermite-package.Rd | 12 +++++++-----
man/phermite.Rd | 4 ++--
man/qhermite.Rd | 10 +++-------
man/rhermite.Rd | 4 +++-
14 files changed, 78 insertions(+), 45 deletions(-)
Title: Geophysics, Continuum Mechanics, Mogi Models, Gravity
Diff between geophys versions 1.3-6 dated 2014-01-13 and 1.3-8 dated 2015-04-27
Description: Codes for analyzing various problems of Geophysics, Continuum Mechanics and Mogi Models.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
R/mogi1.R | 14 +++++++-------
R/mogiM.R | 18 +++++++++---------
R/okada85.R | 10 +++++-----
demo/Fry.R | 2 +-
demo/Sdemo.R | 12 ++++++------
man/Maxstress.Rd | 2 ++
8 files changed, 43 insertions(+), 41 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Diff between adegraphics versions 1.0-1 dated 2015-04-14 and 1.0-2 dated 2015-04-27
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray
Maintainer: Aurélie Siberchicot
DESCRIPTION | 15 ++++++---------
MD5 | 14 +++++++-------
NAMESPACE | 2 +-
R/ADEg.S2.R | 2 +-
R/ade4-plot.R | 2 +-
R/panelfunctions.R | 2 +-
inst/doc/adegraphics.pdf |binary
man/adegraphics-package.Rd | 4 ++--
8 files changed, 19 insertions(+), 22 deletions(-)
Title: Basic Functions for Supporting an Implementation of Choice
Experiments
Diff between support.CEs versions 0.3-2 dated 2014-06-22 and 0.3-3 dated 2015-04-27
Description: Provides seven basic functions that support an implementation of choice experiments.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
DESCRIPTION | 20 +++++++++-----------
MD5 | 6 +++---
NEWS | 3 +++
man/support.CEs-package.Rd | 2 --
4 files changed, 15 insertions(+), 16 deletions(-)
Title: Basic Functions for Supporting an Implementation of Best-Worst
Scaling
Diff between support.BWS versions 0.1-2 dated 2014-06-22 and 0.1-3 dated 2015-04-27
Description: Provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
NEWS | 3 +++
man/support.BWS-package.Rd | 2 --
4 files changed, 14 insertions(+), 13 deletions(-)
Title: Measuring the Difference Between Two Empirical Distributions
Diff between mded versions 0.1-1 dated 2014-06-22 and 0.1-2 dated 2015-04-27
Description: Provides a function for measuring the difference between two independent or non-independent empirical distributions and returning a significance level of the difference.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
NEWS | 3 +++
man/mded-package.Rd | 2 --
4 files changed, 13 insertions(+), 12 deletions(-)
Title: Graphical User Interface to the 'mi' Package
Diff between migui versions 0.00-09 dated 2011-11-21 and 1.1 dated 2015-04-27
Description: This GUI for the mi package walks the user through the steps of multiple imputation and the analysis of completed data.
Author: Bob Carpenter [ctb],
Ben Goodrich [cre, aut],
Yu-Sung Su [ctb]
Maintainer: Ben Goodrich
migui-0.00-09/migui/LICENSE |only
migui-0.00-09/migui/R/analysis.poolRegressionEstimates.R |only
migui-0.00-09/migui/R/analysis.saveImputedData.R |only
migui-0.00-09/migui/R/file.saveWorkspace.R |only
migui-0.00-09/migui/R/help.menu.R |only
migui-0.00-09/migui/R/imputation.checkModelFit.R |only
migui-0.00-09/migui/R/imputation.runImputation.R |only
migui-0.00-09/migui/R/load.first.R |only
migui-0.00-09/migui/R/setup.displayMissingDataPattern.R |only
migui-0.00-09/migui/R/setup.importDataFrom.R |only
migui-0.00-09/migui/R/setup.loadSession.R |only
migui-0.00-09/migui/R/setup.preprocessData.R |only
migui-0.00-09/migui/R/setup.specifyImputationInformation.R |only
migui-0.00-09/migui/R/utils.R |only
migui-1.1/migui/DESCRIPTION | 29
migui-1.1/migui/MD5 | 23
migui-1.1/migui/NAMESPACE | 8
migui-1.1/migui/R/migui.R | 1268 +++++++++++--
migui-1.1/migui/R/zzz.R |only
migui-1.1/migui/man/migui.Rd | 73
20 files changed, 1197 insertions(+), 204 deletions(-)
Title: A Package for Generalised Linear Spatial Models
Diff between geoRglm versions 0.9-4 dated 2013-12-13 and 0.9-8 dated 2015-04-27
Description: Functions for inference in generalised linear spatial models. The posterior and predictive inference is based on Markov chain Monte Carlo methods. Package geoRglm is an extension to the package geoR, which must be installed first.
Author: Ole F. Christensen [aut, cre],
Paulo J. Ribeiro Jr [aut]
Maintainer: Ole F. Christensen
geoRglm-0.9-4/geoRglm/INDEX |only
geoRglm-0.9-8/geoRglm/DESCRIPTION | 24 +++--
geoRglm-0.9-8/geoRglm/MD5 | 47 +++++-----
geoRglm-0.9-8/geoRglm/NAMESPACE | 5 -
geoRglm-0.9-8/geoRglm/R/bayes.R | 14 +--
geoRglm-0.9-8/geoRglm/R/binom.bayes.R | 6 -
geoRglm-0.9-8/geoRglm/R/binom.pred.R | 4
geoRglm-0.9-8/geoRglm/R/extensions.R | 8 -
geoRglm-0.9-8/geoRglm/R/glsm.krige.R | 2
geoRglm-0.9-8/geoRglm/R/mcmc.R | 9 --
geoRglm-0.9-8/geoRglm/R/nonpar.R | 2
geoRglm-0.9-8/geoRglm/R/pois.bayes.R | 12 +-
geoRglm-0.9-8/geoRglm/R/pois.pred.R | 6 -
geoRglm-0.9-8/geoRglm/R/zzz.R | 18 ++--
geoRglm-0.9-8/geoRglm/build/vignette.rds |binary
geoRglm-0.9-8/geoRglm/data/b50.rda |binary
geoRglm-0.9-8/geoRglm/data/b64.rda |binary
geoRglm-0.9-8/geoRglm/data/p50.rda |binary
geoRglm-0.9-8/geoRglm/data/rongelap.rda |binary
geoRglm-0.9-8/geoRglm/inst/doc/geoRglmintro.pdf |binary
geoRglm-0.9-8/geoRglm/man/binom.krige.bayes.Rd | 108 +++++++++++++-----------
geoRglm-0.9-8/geoRglm/man/glsm.mcmc.Rd | 1
geoRglm-0.9-8/geoRglm/man/output.glm.control.Rd | 14 +--
geoRglm-0.9-8/geoRglm/man/pois.krige.bayes.Rd | 44 ++++-----
geoRglm-0.9-8/geoRglm/src/geoRglm.c | 50 +++++------
25 files changed, 197 insertions(+), 177 deletions(-)
Title: Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Diff between faoutlier versions 0.4 dated 2014-05-24 and 0.5 dated 2015-04-27
Description: Tools for detecting and summarize influential cases that
can affect exploratory and confirmatory factor analysis models as well as
structural equation models more generally.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers
DESCRIPTION | 18 +-
MD5 | 54 ++++----
NAMESPACE | 9 +
NEWS | 8 +
R/GOF.R |only
R/LD.R | 123 +++++++++++--------
R/faoutlier.R | 5
R/forward.search.R | 223 +++++++++++++++++------------------
R/gCD.R | 106 ++++++++--------
R/obs.resid.R | 108 ++++++++--------
R/robustMD.R | 47 +++----
R/setClusters.R | 6
inst |only
man/GOF.Rd |only
man/LD.Rd | 32 +++--
man/faoutlier.Rd | 3
man/forward.search.Rd | 26 ++--
man/gCD.Rd | 15 +-
man/holzinger.Rd | 3
man/holzinger.outlier.Rd | 3
man/obs.resid.Rd | 9 -
man/robustMD.Rd | 11 -
man/setCluster.Rd | 3
tests/testthat/test-GOF.R |only
tests/testthat/test-LD.R | 46 ++-----
tests/testthat/test-forward.search.R | 8 -
tests/testthat/test-gCD.R | 26 ++--
tests/testthat/test-obs.resid.R | 21 ---
28 files changed, 482 insertions(+), 431 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Diff between dfmta versions 1.2 dated 2015-04-21 and 1.3-1 dated 2015-04-26
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
configure | 18 +++++++++---------
man/mtaBin_next.Rd | 2 +-
src/dfmta.cpp | 7 +++----
5 files changed, 23 insertions(+), 24 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Diff between dfcomb versions 2.1 dated 2015-04-21 and 2.1-1 dated 2015-04-26
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 6 +++---
MD5 | 6 +++---
configure | 18 +++++++++---------
src/plateau.cpp | 1 +
4 files changed, 16 insertions(+), 15 deletions(-)
Title: Time-Frequency Analysis of 1-D Signals
Diff between Rwave versions 2.2 dated 2014-05-08 and 2.4 dated 2015-04-26
Description: A set of R functions which provide an
environment for the Time-Frequency analysis of 1-D signals (and
especially for the wavelet and Gabor transforms of noisy
signals). It was originally written for Splus by Rene Carmona,
Bruno Torresani, and Wen L. Hwang, first at the University of
California at Irvine and then at Princeton University. Credit
should also be given to Andrea Wang whose functions on the
dyadic wavelet transform are included. Rwave is based on the
book: "Practical Time-Frequency Analysis: Gabor and Wavelet
Transforms with an Implementation in S", by Rene Carmona, Wen
L. Hwang and Bruno Torresani, Academic Press, 1998.
Author: S original by Rene Carmona
Maintainer: Jonathan M. Lees
DESCRIPTION | 12 +++++-----
MD5 | 54 ++++++++++++++++++++++++-------------------------
src/choldc.c | 28 ++++++++++++-------------
src/compinteg.c | 12 +++++-----
src/crazy_family.c | 4 +--
src/cwt_maxima.c | 3 --
src/cwt_morlet.c | 6 ++---
src/cwt_thierry.c | 4 +--
src/dau.c | 5 ++--
src/dau_wave.c | 2 -
src/dualwavelet.c | 8 +++----
src/dwfilter.c | 10 ++++-----
src/dwkernel.c | 2 -
src/gabor.c | 8 +++----
src/gkernel.c | 8 +++----
src/hessian_climbers.c | 2 -
src/mreconst.c | 8 +++----
src/pca_climbers.c | 10 ++++-----
src/pca_family.c | 8 +++----
src/ridge_annealing.c | 2 -
src/ridge_coronoid.c | 2 -
src/ridge_snakenoid.c | 6 ++---
src/rwkernel.c | 18 ++++++++--------
src/snake_annealing.c | 4 +--
src/splridge.c | 2 -
src/splsnake.c | 2 -
src/svd.c | 2 -
src/wv.c | 4 +--
28 files changed, 118 insertions(+), 118 deletions(-)
Title: Graphical User Interface (GUI) for Interactive R Analysis
Sessions
Diff between RPMG versions 2.1-5 dated 2014-01-03 and 2.1-7 dated 2015-04-26
Description: Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 16 ++++----
MD5 | 15 ++++----
R/jpng.R | 96 +++++++++++++++++++++++++++++++++++++++-------------
man/SELOPT.Rd | 2 -
man/SHOWPAL.Rd | 2 -
man/aGETXprofile.Rd | 3 +
man/chooser.Rd | 4 +-
man/jpng.Rd |only
man/jpostscript.Rd | 2 -
9 files changed, 95 insertions(+), 45 deletions(-)
Title: Various Programming Utilities
Diff between R.utils versions 2.0.0 dated 2015-03-01 and 2.0.1 dated 2015-04-26
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 -
MD5 | 18 +-
NEWS | 21 ++-
R/addFinalizerToLast.R | 5
R/compressFile.R | 2
R/toCamelCase.R | 2
R/withSeed.R | 144 ++++++++++-----------
R/withSink.R | 334 ++++++++++++++++++++++++-------------------------
tests/toCamelCase.R | 13 +
tests/withLocale.R | 118 ++++++++---------
10 files changed, 344 insertions(+), 321 deletions(-)
Title: Classes and Methods for Trajectory Data
Diff between trajectories versions 0.1-1 dated 2014-08-28 and 0.1-2 dated 2015-04-25
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut],
Benedikt Klus [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 10 ++++-----
MD5 | 10 ++++-----
R/Tracks-methods.R | 52 +++++++++++++++++++++++++++++--------------------
R/stplot.R | 4 +--
build/vignette.rds |binary
tests/tracks.Rout.save | 34 ++++++++++++++++----------------
6 files changed, 60 insertions(+), 50 deletions(-)
Title: Three L1-Norm PCA Methods
Diff between pcaL1 versions 1.2.1 dated 2013-12-23 and 1.3 dated 2015-04-25
Description: Three implementations of principal component analysis methods
using the L1 norm. The package depends on COIN-OR Clp version >=
1.12.0. The methods implemented are PCA-L1 (Kwak 2008), L1-PCA (Ke and
Kanade 2003, 2005), and L1-PCA* (Brooks, Dula, and Boone 2013).
Author: Sapan Jot
Maintainer: Paul Brooks
ChangeLog | 10 +
DESCRIPTION | 17 +-
INSTALL | 36 +++-
MD5 | 28 +--
NAMESPACE | 3
NEWS | 6
R/l1pca.R | 14 +
R/pcal1.R | 13 +
configure | 383 ++++++++++++++++++---------------------------------
configure.ac | 46 ++----
man/l1pcastar.Rd | 6
man/pcaL1-package.Rd | 8 -
src/pcal1.c | 21 +-
src/pcal1_R.c | 8 -
src/type.h | 1
15 files changed, 266 insertions(+), 334 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Diff between lifecontingencies versions 1.1.5 dated 2015-01-03 and 1.1.6 dated 2015-04-25
More information about lifecontingencies at CRAN
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb] and Kevin J. Owens [ctb]
Maintainer: Giorgio Alfredo Spedicato
lifecontingencies-1.1.5/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package-deathsIPS55Mfig.pdf |only
lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-003.pdf |only
lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-ktProjectionPlot.pdf |only
lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-leeCarterResults.pdf |only
lifecontingencies-1.1.6/lifecontingencies/ChangeLog | 8 +
lifecontingencies-1.1.6/lifecontingencies/DESCRIPTION | 25 ++--
lifecontingencies-1.1.6/lifecontingencies/MD5 | 58 +++++-----
lifecontingencies-1.1.6/lifecontingencies/NAMESPACE | 2
lifecontingencies-1.1.6/lifecontingencies/NEWS | 10 -
lifecontingencies-1.1.6/lifecontingencies/R/0_lifetableAndActuarialtableClassesAndMethods.R | 7 +
lifecontingencies-1.1.6/lifecontingencies/R/4_financialFunctions.R | 19 +--
lifecontingencies-1.1.6/lifecontingencies/R/6_randomGenerationFunctions.R | 2
lifecontingencies-1.1.6/lifecontingencies/R/RcppExports.R |only
lifecontingencies-1.1.6/lifecontingencies/R/zzz.R | 8 +
lifecontingencies-1.1.6/lifecontingencies/README.md |only
lifecontingencies-1.1.6/lifecontingencies/build/vignette.rds |binary
lifecontingencies-1.1.6/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 4
lifecontingencies-1.1.6/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary
lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.R |only
lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.Rmd |only
lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.pdf |only
lifecontingencies-1.1.6/lifecontingencies/inst/doc/mortality_projection.pdf |binary
lifecontingencies-1.1.6/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.pdf |binary
lifecontingencies-1.1.6/lifecontingencies/man/demoFrance.Rd | 6 -
lifecontingencies-1.1.6/lifecontingencies/man/demoIta.Rd | 1
lifecontingencies-1.1.6/lifecontingencies/man/lifecontingencies-package.Rd | 4
lifecontingencies-1.1.6/lifecontingencies/man/soa08.Rd | 3
lifecontingencies-1.1.6/lifecontingencies/man/soa08Act.Rd | 5
lifecontingencies-1.1.6/lifecontingencies/man/soaLt.Rd | 3
lifecontingencies-1.1.6/lifecontingencies/src |only
lifecontingencies-1.1.6/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.Rnw | 4
lifecontingencies-1.1.6/lifecontingencies/vignettes/introToLifecontingencies.Rmd |only
lifecontingencies-1.1.6/lifecontingencies/vignettes/introToLifecontingencies_files |only
lifecontingencies-1.1.6/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 40 +++++-
34 files changed, 122 insertions(+), 87 deletions(-)
Permanent link
Title: Code Examples to Accompany the Book "R for Dummies"
Diff between rfordummies versions 0.0-2 dated 2014-08-18 and 0.1.1 dated 2015-04-24
Description: Contains all the code examples in the book "R for
Dummies" (1st edition). You can view the table of contents as well as the sample code for each chapter.
Author: Andrie de Vries [aut, cre],
Joris Meys [aut]
Maintainer: Andrie de Vries
DESCRIPTION | 16 +++++++--------
MD5 | 54 ++++++++++++++++++++++++++--------------------------
NAMESPACE | 3 +-
R/chapters.R | 2 -
R/saveElements.R |only
man/ch01.Rd | 3 +-
man/ch02.Rd | 3 +-
man/ch03.Rd | 3 +-
man/ch04.Rd | 3 +-
man/ch05.Rd | 3 +-
man/ch06.Rd | 3 +-
man/ch07.Rd | 3 +-
man/ch08.Rd | 3 +-
man/ch09.Rd | 3 +-
man/ch10.Rd | 3 +-
man/ch11.Rd | 3 +-
man/ch12.Rd | 3 +-
man/ch13.Rd | 3 +-
man/ch14.Rd | 3 +-
man/ch15.Rd | 3 +-
man/ch16.Rd | 3 +-
man/ch17.Rd | 3 +-
man/ch18.Rd | 3 +-
man/ch19.Rd | 3 +-
man/ch20.Rd | 3 +-
man/elements.Rd | 3 +-
man/rfordummies.Rd | 3 +-
man/saveElements.Rd |only
man/toc.Rd | 3 +-
29 files changed, 85 insertions(+), 59 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Diff between spacetime versions 1.1-3 dated 2015-01-22 and 1.1-4 dated 2015-04-24
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut],
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma
DESCRIPTION | 12
MD5 | 66 +--
NAMESPACE | 4
R/Class-ST.R | 4
R/Class-STSDF.R | 2
R/STFDF-methods.R | 13
R/STSDF-methods.R | 7
R/stplot.R | 65 ++-
build/vignette.rds |binary
data/air.rda |binary
data/datalist | 2
data/fires.rda |binary
demo/CressieWikle.R | 2
demo/aggregate.R | 2
demo/edc.R | 4
demo/sos4R.R | 2
inst/ChangeLog | 258 ++++++++++++++
inst/doc/jss816.R | 91 ++---
inst/doc/jss816.Rnw | 7
inst/doc/jss816.pdf | 891 +++++++++++++++++++++++++-------------------------
inst/doc/stgvis.html | 217 ++++++------
inst/doc/sto.R | 33 -
inst/doc/sto.Rnw | 17
inst/doc/sto.pdf |binary
inst/doc/stpg.pdf |binary
inst/doc/stsubs.pdf |binary
man/air.Rd | 4
man/fires.Rd | 5
man/stconstruct.Rd | 3
man/stplot.Rd | 4
tests/basic.Rout.save | 70 +--
tests/rw.Rout.save | 4
vignettes/jss816.Rnw | 7
vignettes/sto.Rnw | 17
34 files changed, 1033 insertions(+), 780 deletions(-)
Title: Classes and Methods for Spatial Data
Diff between sp versions 1.0-17 dated 2015-01-08 and 1.1-0 dated 2015-04-24
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma
sp-1.0-17/sp/R/overlay.R |only
sp-1.1-0/sp/ChangeLog |only
sp-1.1-0/sp/DESCRIPTION | 46 +-
sp-1.1-0/sp/MD5 | 150 +++----
sp-1.1-0/sp/NAMESPACE | 4
sp-1.1-0/sp/R/CRS-methods.R | 15
sp-1.1-0/sp/R/Class-CRS.R | 14
sp-1.1-0/sp/R/Class-GridTopology.R | 9
sp-1.1-0/sp/R/Class-Spatial.R | 11
sp-1.1-0/sp/R/Class-SpatialGrid.R | 18
sp-1.1-0/sp/R/Class-SpatialGridDataFrame.R | 12
sp-1.1-0/sp/R/Class-SpatialLines.R | 16
sp-1.1-0/sp/R/Class-SpatialLinesDataFrame.R | 4
sp-1.1-0/sp/R/Class-SpatialPoints.R | 15
sp-1.1-0/sp/R/Class-SpatialPointsDataFrame.R | 17
sp-1.1-0/sp/R/Class-SpatialPolygons.R | 16
sp-1.1-0/sp/R/Class-SpatialPolygonsDataFrame.R | 9
sp-1.1-0/sp/R/Spatial-methods.R | 40 +-
sp-1.1-0/sp/R/SpatialGrid-methods.R | 118 +++++-
sp-1.1-0/sp/R/SpatialGridDataFrame-methods.R | 36 +
sp-1.1-0/sp/R/SpatialLines-methods.R | 23 -
sp-1.1-0/sp/R/SpatialPoints-methods.R | 30 -
sp-1.1-0/sp/R/SpatialPointsDataFrame-methods.R | 40 +-
sp-1.1-0/sp/R/SpatialPolygons-methods.R | 42 +-
sp-1.1-0/sp/R/SpatialPolygonsDataFrame-methods.R | 21 -
sp-1.1-0/sp/R/aggregate.R | 35 +
sp-1.1-0/sp/R/bubble.R | 3
sp-1.1-0/sp/R/over.R | 8
sp-1.1-0/sp/R/projected.R | 12
sp-1.1-0/sp/R/rbind.R | 9
sp-1.1-0/sp/R/spplot.R | 156 ++++----
sp-1.1-0/sp/R/spsample.R | 24 -
sp-1.1-0/sp/R/subset.R | 21 -
sp-1.1-0/sp/build/vignette.rds |binary
sp-1.1-0/sp/demo/depend.R | 12
sp-1.1-0/sp/demo/gallery.R | 2
sp-1.1-0/sp/inst/ChangeLog | 408 +++++++++++++++++++++
sp-1.1-0/sp/inst/doc/csdacm.pdf |binary
sp-1.1-0/sp/inst/doc/intro_sp.pdf |binary
sp-1.1-0/sp/inst/doc/over.R | 14
sp-1.1-0/sp/inst/doc/over.Rnw | 13
sp-1.1-0/sp/inst/doc/over.pdf |binary
sp-1.1-0/sp/inst/include/sp.h | 37 +
sp-1.1-0/sp/inst/include/sp_xports.c | 217 ++++++-----
sp-1.1-0/sp/man/CRS-class.Rd | 2
sp-1.1-0/sp/man/Spatial-class.Rd | 22 +
sp-1.1-0/sp/man/SpatialLines-class.Rd | 20 +
sp-1.1-0/sp/man/SpatialPixels-class.Rd | 4
sp-1.1-0/sp/man/SpatialPoints-class.Rd | 20 +
sp-1.1-0/sp/man/SpatialPoints.Rd | 34 +
sp-1.1-0/sp/man/SpatialPolygons-class.Rd | 2
sp-1.1-0/sp/man/addattr.Rd | 3
sp-1.1-0/sp/man/aggregate.Rd | 50 ++
sp-1.1-0/sp/man/as.SpatialPolygons.GridTopology.Rd | 3
sp-1.1-0/sp/man/degaxis.Rd | 2
sp-1.1-0/sp/man/is.projected.Rd | 7
sp-1.1-0/sp/man/meuse.Rd | 2
sp-1.1-0/sp/man/nowrapSpatialLines.Rd | 2
sp-1.1-0/sp/man/over.Rd | 13
sp-1.1-0/sp/man/panel.Rd | 2
sp-1.1-0/sp/man/recenter-methods.Rd | 10
sp-1.1-0/sp/man/sp-deprecated.Rd | 43 --
sp-1.1-0/sp/man/spDistsN1.Rd | 2
sp-1.1-0/sp/man/spTransform.Rd | 16
sp-1.1-0/sp/man/spplot.Rd | 97 +++-
sp-1.1-0/sp/man/spsample.Rd | 11
sp-1.1-0/sp/src/init.c | 1
sp-1.1-0/sp/src/pip.c | 16
sp-1.1-0/sp/src/pip2.c | 20 -
sp-1.1-0/sp/src/sp.h | 34 -
sp-1.1-0/sp/src/sp_xports.c | 217 ++++++-----
sp-1.1-0/sp/tests/fail1.R | 4
sp-1.1-0/sp/tests/fail1.Rout.save | 26 -
sp-1.1-0/sp/tests/grid.Rout.save | 27 -
sp-1.1-0/sp/tests/pass1.R | 89 ++++
sp-1.1-0/sp/tests/pass1.Rout.save | 343 +++++++++++++++++
sp-1.1-0/sp/vignettes/over.Rnw | 13
77 files changed, 2032 insertions(+), 802 deletions(-)
Title: General network (HTTP/FTP/...) client interface for R
Diff between RCurl versions 1.95-4.5 dated 2014-12-06 and 1.95-4.6 dated 2015-04-24
Description: The package allows one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
DESCRIPTION | 12 +++++-------
MD5 | 6 +++---
R/dynamic.R | 2 +-
data/mimeTypeExtensions.rda |binary
4 files changed, 9 insertions(+), 11 deletions(-)
Title: Tools for Reading and Handling Spatial Objects
Diff between maptools versions 0.8-34 dated 2015-02-03 and 0.8-36 dated 2015-04-24
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand
ChangeLog | 1680 ++++++++----------------------------------
DESCRIPTION | 14
MD5 | 28
R/checkHoles.R | 10
R/sp2pbs.R | 8
build/vignette.rds |binary
data/wrld_simpl.rda |binary
inst/ChangeLog | 1680 ++++++++----------------------------------
inst/doc/combine_maptools.pdf |binary
man/GE_SpatialGrid.Rd | 4
man/SpatialLines2PolySet.Rd | 4
man/kmlLine.Rd | 2
man/kmlLines.Rd | 2
man/kmlOverlay.Rd | 16
man/nowrapRecenter.Rd | 7
15 files changed, 717 insertions(+), 2738 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-29 2013.9-1
2012-10-02 2012.8-1
2012-05-03 2012.4-1
2012-03-29 2012.3-1
2011-11-02 2011.11-1
2011-09-14 2011.8-2
2011-08-14 2011.8-1
2011-07-25 2011.7-1
2011-03-23 2011.3-1
2010-12-22 2010.12-1
2010-05-31 2010.5-1
2010-04-11 2010.3-1
2009-12-16 2009.10-1
2009-10-27 2009.5-1
2009-03-25 2009.3-2
2009-03-22 2009.3-1
2008-11-03 2008.11-1
2008-08-06 2008.8-1
2008-05-08 2008.5-1
2007-11-05 2007.10-1
Title: Kriging Methods for Computer Experiments
Diff between DiceKriging versions 1.5.4 dated 2015-01-05 and 1.5.5 dated 2015-04-24
Description: Estimation, validation and prediction of kriging models.
Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant
CHANGELOG | 7 +-
DESCRIPTION | 10 +-
MD5 | 24 +++----
NAMESPACE | 10 ++
R/allGenerics.R | 11 +--
R/covStruct_Base_TensorProduct.R | 131 +++++++++++++++++++--------------------
R/covStruct_User.R | 4 -
R/kmEstimate.R | 10 +-
R/logLikGrad.R | 3
R/scalingFun.R | 2
man/DiceKriging-package.Rd | 6 -
man/coef.Rd | 8 +-
man/covTensorProduct-class.Rd | 4 -
13 files changed, 125 insertions(+), 105 deletions(-)
Title: Nonlinear Time Series Models with Regime Switching
Diff between tsDyn versions 0.9-41 dated 2014-08-26 and 0.9-43 dated 2015-04-24
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut],
Jose Luis Aznarte [ctb],
Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler
tsDyn-0.9-41/tsDyn/man/predict.Rd |only
tsDyn-0.9-41/tsDyn/tests/lstar.Rout.save |only
tsDyn-0.9-43/tsDyn/DESCRIPTION | 18 -
tsDyn-0.9-43/tsDyn/MD5 | 130 +++++-----
tsDyn-0.9-43/tsDyn/NAMESPACE | 1
tsDyn-0.9-43/tsDyn/R/TVAR.sim.R | 131 +++++------
tsDyn-0.9-43/tsDyn/R/TVECM.R | 2
tsDyn-0.9-43/tsDyn/R/TVECM.sim.R | 17 +
tsDyn-0.9-43/tsDyn/R/VAR.sim.R |only
tsDyn-0.9-43/tsDyn/R/predict.R | 78 ++++++
tsDyn-0.9-43/tsDyn/R/predict.VAR.R |only
tsDyn-0.9-43/tsDyn/R/selectLSTAR.R | 2
tsDyn-0.9-43/tsDyn/R/star.R | 2
tsDyn-0.9-43/tsDyn/R/vec2var.tsDyn.R | 40 ---
tsDyn-0.9-43/tsDyn/build/vignette.rds |binary
tsDyn-0.9-43/tsDyn/data/barry.rda |binary
tsDyn-0.9-43/tsDyn/data/zeroyld.rda |binary
tsDyn-0.9-43/tsDyn/inst/ChangeLog | 8
tsDyn-0.9-43/tsDyn/inst/doc/ThCointOverview.pdf |binary
tsDyn-0.9-43/tsDyn/inst/doc/tsDyn.pdf |binary
tsDyn-0.9-43/tsDyn/man/BBCTest.Rd | 3
tsDyn-0.9-43/tsDyn/man/MAPE.Rd | 3
tsDyn-0.9-43/tsDyn/man/MakeThSpec.Rd | 7
tsDyn-0.9-43/tsDyn/man/TVAR.LRtest.Rd | 3
tsDyn-0.9-43/tsDyn/man/TVAR.Rd | 3
tsDyn-0.9-43/tsDyn/man/TVAR.boot.Rd | 9
tsDyn-0.9-43/tsDyn/man/TVAR.sim.Rd | 8
tsDyn-0.9-43/tsDyn/man/TVECM.Rd | 3
tsDyn-0.9-43/tsDyn/man/TVECM.SeoTest.Rd | 3
tsDyn-0.9-43/tsDyn/man/TVECM.sim.Rd | 31 +-
tsDyn-0.9-43/tsDyn/man/VAR.boot.Rd |only
tsDyn-0.9-43/tsDyn/man/VARrep.Rd | 3
tsDyn-0.9-43/tsDyn/man/VECM.Rd | 9
tsDyn-0.9-43/tsDyn/man/VECM_symbolic.Rd | 3
tsDyn-0.9-43/tsDyn/man/accuracy_stat.Rd | 3
tsDyn-0.9-43/tsDyn/man/addRegime.Rd | 3
tsDyn-0.9-43/tsDyn/man/autopairs.Rd | 3
tsDyn-0.9-43/tsDyn/man/autotriples.Rd | 3
tsDyn-0.9-43/tsDyn/man/autotriples.rgl.Rd | 3
tsDyn-0.9-43/tsDyn/man/availableModels.Rd | 3
tsDyn-0.9-43/tsDyn/man/coefB.Rd | 7
tsDyn-0.9-43/tsDyn/man/computeGradient.Rd | 3
tsDyn-0.9-43/tsDyn/man/delta.Rd | 3
tsDyn-0.9-43/tsDyn/man/delta.lin.Rd | 3
tsDyn-0.9-43/tsDyn/man/fitted.nlVar.Rd | 3
tsDyn-0.9-43/tsDyn/man/getTh.Rd | 3
tsDyn-0.9-43/tsDyn/man/isLinear.Rd | 3
tsDyn-0.9-43/tsDyn/man/lags.select.Rd | 3
tsDyn-0.9-43/tsDyn/man/lineVar.Rd | 9
tsDyn-0.9-43/tsDyn/man/logLik.VECM.Rd | 3
tsDyn-0.9-43/tsDyn/man/logLik.nlVar.Rd | 3
tsDyn-0.9-43/tsDyn/man/mse.Rd | 3
tsDyn-0.9-43/tsDyn/man/nlar.Rd | 3
tsDyn-0.9-43/tsDyn/man/oneStep.Rd | 3
tsDyn-0.9-43/tsDyn/man/predict.VAR.Rd |only
tsDyn-0.9-43/tsDyn/man/predict.nlar.Rd |only
tsDyn-0.9-43/tsDyn/man/predict_rolling.Rd | 3
tsDyn-0.9-43/tsDyn/man/rank.select.Rd | 7
tsDyn-0.9-43/tsDyn/man/rank.test.Rd | 7
tsDyn-0.9-43/tsDyn/man/regime.Rd | 3
tsDyn-0.9-43/tsDyn/man/setar.sim.Rd | 15 -
tsDyn-0.9-43/tsDyn/man/sigmoid.Rd | 3
tsDyn-0.9-43/tsDyn/man/toLatex.setar.Rd | 3
tsDyn-0.9-43/tsDyn/tests/TVECM.sim.Rout.save | 38 +--
tsDyn-0.9-43/tsDyn/tests/VAR.R | 23 +
tsDyn-0.9-43/tsDyn/tests/VAR.Rout.save | 213 +++++++++++-------
tsDyn-0.9-43/tsDyn/tests/VECM.Rout.save | 162 ++++++-------
tsDyn-0.9-43/tsDyn/tests/compare_tsDyn_vars.R | 2
tsDyn-0.9-43/tsDyn/tests/compare_tsDyn_vars.Rout.save | 13 -
tsDyn-0.9-43/tsDyn/tests/lstar.Rout.save_bkp |only
70 files changed, 622 insertions(+), 457 deletions(-)
Title: Mapping Fisheries Data and Spatial Analysis Tools
Diff between PBSmapping versions 2.68.68 dated 2015-01-14 and 2.69.76 dated 2015-04-24
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in `Nanaimo', British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include `C++' code developed by Angus Johnson for the `Clipper'
library. Also included are data for a global shoreline and other
data sets in the public domain. The R directory `.../library/PBSmapping/doc'
offers a complete user's guide, which should be consulted to use package
functions effectively.
Author: Jon T. Schnute [aut], Nicholas Boers [aut], Rowan Haigh [aut, cre],
Alex Couture-Beil [ctb], Denis Chabot [ctb], Chris Grandin [ctb],
Angus Johnson [ctb], Paul Wessel [ctb], Franklin Antonio [ctb],
Nicholas J. Lewin-Koh [ctb], Roger Bivand [ctb]
Maintainer: Rowan Haigh
PBSmapping-2.68.68/PBSmapping/man/nepacLLhigh.Rd |only
PBSmapping-2.68.68/PBSmapping/man/worldLL.Rd |only
PBSmapping-2.68.68/PBSmapping/man/worldLLhigh.Rd |only
PBSmapping-2.69.76/PBSmapping/DESCRIPTION | 45
PBSmapping-2.69.76/PBSmapping/MD5 | 41
PBSmapping-2.69.76/PBSmapping/NAMESPACE | 9
PBSmapping-2.69.76/PBSmapping/R/PBSfigs.r | 4
PBSmapping-2.69.76/PBSmapping/R/PBSmapping.r | 273
PBSmapping-2.69.76/PBSmapping/data/nepacLL.rda |binary
PBSmapping-2.69.76/PBSmapping/data/surveyData.rda |binary
PBSmapping-2.69.76/PBSmapping/inst/doc/ChangeLog.txt | 181
PBSmapping-2.69.76/PBSmapping/inst/doc/PBSmapping-UG.pdf |binary
PBSmapping-2.69.76/PBSmapping/inst/doc/index.html | 2
PBSmapping-2.69.76/PBSmapping/man/EventData.Rd | 67
PBSmapping-2.69.76/PBSmapping/man/LocationSet.Rd | 34
PBSmapping-2.69.76/PBSmapping/man/PolyData.Rd | 33
PBSmapping-2.69.76/PBSmapping/man/PolySet.Rd | 31
PBSmapping-2.69.76/PBSmapping/man/importGSHHS.Rd | 143
PBSmapping-2.69.76/PBSmapping/man/joinPolys.Rd | 55
PBSmapping-2.69.76/PBSmapping/man/nepacLL.Rd | 63
PBSmapping-2.69.76/PBSmapping/src/clipper.cpp | 4772 ++++++++-------
PBSmapping-2.69.76/PBSmapping/src/clipper.h | 358 -
PBSmapping-2.69.76/PBSmapping/src/clipperWrapper.cpp | 198
23 files changed, 3767 insertions(+), 2542 deletions(-)
Title: Multiple Mediation Analysis
Diff between mma versions 1.0-1 dated 2015-04-10 and 2.0-0 dated 2015-04-24
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu
DESCRIPTION | 8 +-
MD5 | 14 ++---
R/mma.r | 135 ++++++++++++++++++++++++++++++++++++++++----------
man/boot.med.binx.Rd | 3 -
man/boot.med.contx.Rd | 1
man/mma.Rd | 1
man/plot.mma.Rd | 18 ++++--
man/summary.mma.Rd | 7 +-
8 files changed, 140 insertions(+), 47 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Diff between knitr versions 1.9 dated 2015-01-20 and 1.10 dated 2015-04-23
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 61 ++++--------
MD5 | 171 +++++++++++++++++-----------------
NAMESPACE | 9 -
R/block.R | 59 ++++++-----
R/cache.R | 7 -
R/citation.R | 64 +++++-------
R/defaults.R | 12 +-
R/engine.R | 83 +++++++++++-----
R/header.R | 31 ++----
R/highlight.R | 18 +--
R/hooks-asciidoc.R | 2
R/hooks-extra.R | 10 +
R/hooks-html.R | 26 ++---
R/hooks-latex.R | 12 +-
R/hooks-md.R | 24 +++-
R/hooks-textile.R | 2
R/output.R | 108 +++++++++++++--------
R/package.R | 8 -
R/pandoc.R | 2
R/params.R |only
R/parser.R | 106 ++++++++++++++++-----
R/pattern.R | 3
R/plot.R | 46 +++------
R/rocco.R | 2
R/spin.R | 8 -
R/table.R | 40 +++++--
R/template.R | 9 -
R/themes-eclipse.R | 4
R/themes.R | 8 -
R/utils-base64.R | 18 +--
R/utils-conversion.R | 3
R/utils-rd2html.R | 10 -
R/utils-sweave.R | 2
R/utils-vignettes.R | 45 +++++++-
R/utils.R | 67 ++++++++++---
build/knitr.pdf |binary
build/vignette.rds |binary
inst/doc/knit_expand.html | 4
inst/doc/knit_print.html | 9 -
inst/doc/knitr-html.html | 12 +-
inst/doc/knitr-intro.Rmd | 4
inst/doc/knitr-intro.html | 18 +--
inst/doc/knitr-markdown.Rmd | 4
inst/doc/knitr-markdown.html | 8 +
inst/doc/knitr-refcard.pdf |binary
inst/examples/knitr-beamer.Rnw | 6 -
inst/examples/knitr-graphics.Rnw | 27 +----
inst/examples/knitr-listings.Rnw | 2
inst/examples/knitr-manual.Rnw | 46 +++------
inst/examples/knitr-minimal.Rnw | 2
inst/examples/knitr-packages.bib | 33 +++---
inst/examples/knitr-spin.R | 6 -
inst/examples/knitr-spin.Rmd | 4
inst/examples/knitr-subfloats.Rnw | 2
inst/examples/knitr-themes.Rnw | 22 +---
inst/examples/knitr-twocolumn.Rnw | 2
inst/misc/knitr.css | 12 +-
inst/misc/stitch-test.R | 4
inst/misc/tweak_bib.csv |only
inst/misc/vignette.css | 17 +--
man/all_labels.Rd | 29 +++++
man/all_patterns.Rd | 4
man/current_input.Rd | 6 -
man/eclipse_theme.Rd | 4
man/knit.Rd | 44 ++++----
man/knit_child.Rd | 4
man/knit_params.Rd |only
man/knit_print.Rd | 4
man/knit_rd.Rd | 2
man/knit_theme.Rd | 6 -
man/knitr-package.Rd | 4
man/rand_seed.Rd | 2
man/read_rforge.Rd | 1
man/set_alias.Rd | 2
man/stitch.Rd | 5
man/vignette_engines.Rd | 21 +++-
man/write_bib.Rd | 6 -
tests/testit/test-cache.R | 6 -
tests/testit/test-citation.R |only
tests/testit/test-closure.R | 12 +-
tests/testit/test-hooks.R | 2
tests/testit/test-params.R |only
tests/testit/test-parser.R | 32 ++++--
tests/testit/test-plot.R | 34 ++++--
tests/testit/test-table.R | 20 ++-
tests/testit/test-utils.R | 11 +-
vignettes/assets/template-refcard.tex | 2
vignettes/knitr-intro.Rmd | 4
vignettes/knitr-markdown.Rmd | 4
89 files changed, 928 insertions(+), 667 deletions(-)
Title: Acoustic Template Detection in R
Diff between monitoR versions 1.0.2 dated 2014-05-14 and 1.0.3 dated 2015-04-23
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner
Maintainer: Sasha D. Hafner
ChangeLog | 159 +++++++++++++++++++++++++++++++++++
DESCRIPTION | 12 +-
MD5 | 132 ++++++++++++++---------------
NAMESPACE | 2
R/binMatch.R | 54 ++++++------
R/bindEvents.R | 6 -
R/corMatch.R | 55 +++++-------
R/dbDownloadCardRecorderID.R | 47 +++++++---
R/dbDownloadResult.R | 18 +---
R/dbDownloadSurvey.R | 81 ++++++++++++------
R/dbDownloadTemplate.R | 76 +++++++++-------
R/dbSchema.R | 19 ++--
R/dbUploadAnno.R | 13 +-
R/dbUploadResult.R | 17 +--
R/dbUploadSurvey.R | 15 +--
R/dbUploadTemplate.R | 17 +--
R/eventEval.R | 10 --
R/fileCopyRename.R | 5 -
R/findPeaks.R | 5 -
R/getClip.R | 19 ++--
R/makeBinTemplate.R | 75 ++++++----------
R/makeCorTemplate.R | 42 +++++----
R/readBinTemplates.R | 5 -
R/readCorTemplates.R | 5 -
R/showPeaks.R | 52 +++++++++--
R/stft.R | 13 +-
R/templatePath.R |only
R/viewSpec.R | 29 ++++--
R/writeBinTemplates.R | 5 -
R/writeCorTemplates.R | 5 -
build/vignette.rds |binary
data/btnw.rda |binary
data/oven.rda |binary
data/survey.rda |binary
data/survey_anno.rda |binary
inst/doc/monitoR_QuickStart.R | 175 ++++++++++++++-------------------------
inst/doc/monitoR_QuickStart.Rnw | 39 +++++---
inst/doc/monitoR_QuickStart.pdf |binary
man/changeSampRate.Rd | 2
man/collapseClips.Rd | 10 --
man/combineTemplates.Rd | 46 ++++++----
man/compareTemplates.Rd | 32 ++++---
man/dbDownload.Rd | 10 +-
man/dbDownloadTemplate.Rd | 22 ++--
man/dbUploadResult.Rd | 24 ++++-
man/dbUploadTemplate.Rd | 6 -
man/eventEval.Rd | 31 ++++--
man/fileCopyRename.Rd | 13 +-
man/findPeaks.Rd | 43 ++++++---
man/getDetections.Rd | 37 +++++---
man/makeTemplate.Rd | 71 +++++++++------
man/monitoR-package.Rd | 32 ++++---
man/mp3Subsamp.Rd | 2
man/plot-methods.Rd | 50 ++++++-----
man/readTemplates.Rd | 31 ++++--
man/show-methods.Rd | 26 ++++-
man/showPeaks.Rd | 51 ++++++++---
man/specCols.Rd | 20 ++--
man/survey_anno.Rd | 8 +
man/templateComment.Rd | 54 ++++++------
man/templateCutoff.Rd | 32 ++++---
man/templateMatching.Rd | 12 +-
man/templateNames.Rd | 31 ++++--
man/templatePath.Rd |only
man/timeAlign.Rd | 17 ++-
man/viewSpec.Rd | 25 +++--
man/writeTemplates.Rd | 29 ++++--
vignettes/monitoR_QuickStart.Rnw | 39 +++++---
68 files changed, 1209 insertions(+), 804 deletions(-)
Title: Analysis of Geostatistical Data
Diff between geoR versions 1.7-4.1 dated 2014-09-14 and 1.7-5.1 dated 2015-04-23
Description: Geostatistical analysis including traditional, likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr
Maintainer: Paulo J. Ribeiro Jr
geoR-1.7-4.1/geoR/R/likOLD.R |only
geoR-1.7-4.1/geoR/inst/CITATION |only
geoR-1.7-5.1/geoR/DESCRIPTION | 25 +++----
geoR-1.7-5.1/geoR/MD5 | 79 ++++++++++++-------------
geoR-1.7-5.1/geoR/NAMESPACE | 28 ++++++--
geoR-1.7-5.1/geoR/R/Cwrappers.R | 1
geoR-1.7-5.1/geoR/R/auxiliar.R | 11 +--
geoR-1.7-5.1/geoR/R/corcov.R | 2
geoR-1.7-5.1/geoR/R/eyefit.R | 2
geoR-1.7-5.1/geoR/R/geobayes.R | 6 -
geoR-1.7-5.1/geoR/R/geodata.R | 4 -
geoR-1.7-5.1/geoR/R/profiles.R | 69 +++++++++++++++++++++
geoR-1.7-5.1/geoR/R/simul.R | 3
geoR-1.7-5.1/geoR/data/Ksat.rda |binary
geoR-1.7-5.1/geoR/data/SIC.rda |binary
geoR-1.7-5.1/geoR/data/ca20.rda |binary
geoR-1.7-5.1/geoR/data/camg.rda |binary
geoR-1.7-5.1/geoR/data/elevation.rda |binary
geoR-1.7-5.1/geoR/data/gambia.rda |binary
geoR-1.7-5.1/geoR/data/head.rda |binary
geoR-1.7-5.1/geoR/data/hoef.rda |binary
geoR-1.7-5.1/geoR/data/isaaks.rda |binary
geoR-1.7-5.1/geoR/data/kattegat.rda |binary
geoR-1.7-5.1/geoR/data/landim1.rda |binary
geoR-1.7-5.1/geoR/data/parana.rda |binary
geoR-1.7-5.1/geoR/data/s100.rda |binary
geoR-1.7-5.1/geoR/data/s121.rda |binary
geoR-1.7-5.1/geoR/data/s256i.rda |binary
geoR-1.7-5.1/geoR/data/soil250.rda |binary
geoR-1.7-5.1/geoR/data/soja98.rda |binary
geoR-1.7-5.1/geoR/data/tce.rda |binary
geoR-1.7-5.1/geoR/data/wo.rda |binary
geoR-1.7-5.1/geoR/data/wolfcamp.rda |binary
geoR-1.7-5.1/geoR/data/wrc.rda |binary
geoR-1.7-5.1/geoR/inst/CHANGES | 13 +++-
geoR-1.7-5.1/geoR/inst/doc/CHANGES |only
geoR-1.7-5.1/geoR/man/SIC.Rd | 2
geoR-1.7-5.1/geoR/man/coords2coords.Rd | 6 +
geoR-1.7-5.1/geoR/man/grf.Rd | 3
geoR-1.7-5.1/geoR/man/sample.prior.Rd | 5 +
geoR-1.7-5.1/geoR/man/statistics.predictive.Rd | 2
geoR-1.7-5.1/geoR/man/subarea.Rd | 8 +-
42 files changed, 184 insertions(+), 85 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Diff between drgee versions 1.0.1 dated 2014-01-27 and 1.1.0 dated 2015-04-23
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist
Maintainer: Johan Zetterqvist
drgee-1.0.1/drgee/R/ebeFit.R |only
drgee-1.0.1/drgee/R/obeFit.R |only
drgee-1.0.1/drgee/man/drFit.Rd |only
drgee-1.0.1/drgee/man/ebeFit.Rd |only
drgee-1.0.1/drgee/man/geeFit.Rd |only
drgee-1.0.1/drgee/man/obeFit.Rd |only
drgee-1.1.0/drgee/DESCRIPTION | 29 -
drgee-1.1.0/drgee/MD5 | 42 +-
drgee-1.1.0/drgee/NAMESPACE | 12
drgee-1.1.0/drgee/NEWS | 27 +
drgee-1.1.0/drgee/R/clogitRes.R |only
drgee-1.1.0/drgee/R/drFit.R | 191 -----------
drgee-1.1.0/drgee/R/dreFit.R |only
drgee-1.1.0/drgee/R/dreFitCond.R |only
drgee-1.1.0/drgee/R/drgee.R | 199 +++++++-----
drgee-1.1.0/drgee/R/drgeeData.R | 538 +++++++++++++++++++++++++--------
drgee-1.1.0/drgee/R/eFit.R |only
drgee-1.1.0/drgee/R/findRoots.R | 23 -
drgee-1.1.0/drgee/R/gee.R |only
drgee-1.1.0/drgee/R/geeFit.R | 51 +--
drgee-1.1.0/drgee/R/geeFitCond.R |only
drgee-1.1.0/drgee/R/oFit.R |only
drgee-1.1.0/drgee/R/robVcov.R | 29 -
drgee-1.1.0/drgee/man/drgee-package.Rd | 38 +-
drgee-1.1.0/drgee/man/drgee.Rd | 335 +++++++++++---------
drgee-1.1.0/drgee/man/drgeeData.Rd | 112 ++++--
drgee-1.1.0/drgee/man/findRoots.Rd | 16
drgee-1.1.0/drgee/man/gee.Rd |only
drgee-1.1.0/drgee/man/robVcov.Rd | 16
29 files changed, 971 insertions(+), 687 deletions(-)
Title: Visualization of Spatial and Spatio-temporal Objects in Google
Earth
Diff between plotKML versions 0.5-0 dated 2015-01-28 and 0.5-1 dated 2015-04-23
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 10 ++++----
MD5 | 34 ++++++++++++++++--------------
R/AAA-md.R | 6 +++++
R/AAAA.R | 10 ++++----
R/aesthetics.R | 3 --
R/kml.tiles.R |only
R/legend.bar.R | 2 -
R/plot.SpatialPredictions.R | 25 +++++++++++++++-------
R/plotKML.GDALobj.R | 25 ++++++++++++----------
R/spMetadata.R | 14 ++++++++++++
build/vignette.rds |binary
inst/INSPIRE_ISO19139.xml | 23 +++++++++++++++++++-
inst/doc/jss1079.pdf |binary
man/baranja.Rd | 49 ++++++++++++++++++++++++++------------------
man/kml.Rd | 4 ++-
man/kml.tiles.Rd |only
man/plotKML.GDALobj.Rd | 12 ++++++----
man/plotKML.Rd | 9 ++++++++
man/plotKML.env.Rd | 12 +++++-----
19 files changed, 158 insertions(+), 80 deletions(-)
Title: Interactive Interpretation of Linear Regression Models
Diff between LinRegInteractive versions 0.3-0 dated 2014-11-12 and 0.3-1 dated 2015-04-23
More information about LinRegInteractive at CRAN
Description: Interactive visualization of effects, response functions
and marginal effects for different kinds of regression models. In this version
linear regression models, generalized linear models, generalized additive
models and linear mixed-effects models are supported.
Major features are the interactive approach and the handling of the effects of categorical covariates:
if two or more factors are used as covariates every combination of the levels of each
factor is treated separately. The automatic calculation of
marginal effects and a number of possibilities to customize the graphical output
are useful features as well.
Author: Martin Meermeyer
Maintainer: Martin Meermeyer
DESCRIPTION | 10
MD5 | 24
build/vignette.rds |binary
inst/doc/LinRegInteractive.Rnw | 1647 +++++++++++++++++++--------------------
inst/doc/LinRegInteractive.pdf |binary
man/LinRegInteractive-package.Rd | 6
man/fxInteractive.Rd | 2
man/fxInteractive.glm.Rd | 2
man/fxInteractive.lm.Rd | 2
man/fxInteractive.lme.Rd | 2
man/munichrent03.Rd | 2
vignettes/LinRegInteractive.Rnw | 1647 +++++++++++++++++++--------------------
vignettes/LinRegInteractive.tex | 11
13 files changed, 1670 insertions(+), 1685 deletions(-)
Permanent link
Title: Soil Database Interface
Diff between soilDB versions 1.5-2 dated 2015-02-25 and 1.5-4 dated 2015-04-23
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 11 -
MD5 | 34 +--
NEWS | 20 +-
R/AAAA.R | 2
R/fetchNASIS.R | 24 +-
R/getHzErrorsNASIS.R | 2
R/get_colors_from_NASIS_db.R | 1
R/get_extended_data_from_NASIS_db.R | 16 -
R/get_hz_data_from_NASIS_db.R | 14 -
R/get_site_data_from_NASIS_db.R | 10 -
R/nasis_component_data.R | 343 ++++++++++++++++++------------------
R/utils.R | 24 ++
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/fetchNASIS.Rd | 25 +-
18 files changed, 280 insertions(+), 246 deletions(-)
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 1.8 dated 2015-02-20 and 1.8-6 dated 2015-04-23
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 12 +--
MD5 | 25 ++++---
NAMESPACE | 4 +
NEWS | 13 +++
R/SoilProfileCollection-methods.R | 19 ++---
R/aggregateSoilDepth.R |only
R/evalGenHz.R | 121 ++++++++++++++++++++-----------------
R/profile_plot.R | 85 +++++++++++++++++++++----
R/setters.R | 5 -
man/SPC-plotting.Rd | 18 ++++-
man/SPC-slab-methods.Rd | 9 +-
man/SPC-unique-methods.Rd |only
man/SoilProfileCollection-class.Rd | 28 --------
man/aggregateSoilDepth.Rd |only
man/plotMultipleSPC.Rd |only
man/profileGroupLabels.Rd |only
16 files changed, 209 insertions(+), 130 deletions(-)
Title: Distance Sampling Analyses
Diff between Rdistance versions 1.2.1 dated 2015-04-01 and 1.2.2 dated 2015-04-22
Description: Analysis of distance sampling data collected on line transect surveys. Estimates distance-based detection functions and abundances.
Author: Trent McDonald [cre, aut],
Ryan Nielson [aut],
Jason Carlisle [aut],
Ben Augustine [ctb],
James Griswald [ctb],
Joel Reynolds [ctb],
Pham Quang [ctb],
Earl Becker [ctb],
Aaron Christ [ctb],
Brook Russelland [ctb],
Patrick McKann [ctb]
Maintainer: Trent McDonald
Rdistance-1.2.1/Rdistance/data/sparrow.covs.rda |only
Rdistance-1.2.1/Rdistance/data/sparrow.dists.rda |only
Rdistance-1.2.1/Rdistance/man/sparrow.covs.Rd |only
Rdistance-1.2.1/Rdistance/man/sparrow.dists.Rd |only
Rdistance-1.2.1/Rdistance/vignettes/vignette.sparrow.example.R |only
Rdistance-1.2.2/Rdistance/DESCRIPTION | 12 -
Rdistance-1.2.2/Rdistance/MD5 | 46 ++-
Rdistance-1.2.2/Rdistance/R/F.abund.estim.r | 118 +---------
Rdistance-1.2.2/Rdistance/R/F.automated.CDA.r | 15 -
Rdistance-1.2.2/Rdistance/R/F.dfunc.estim.R | 11
Rdistance-1.2.2/Rdistance/R/perp.dists.R | 4
Rdistance-1.2.2/Rdistance/R/zzz.R | 2
Rdistance-1.2.2/Rdistance/build |only
Rdistance-1.2.2/Rdistance/data/sparrow.detections.rda |only
Rdistance-1.2.2/Rdistance/data/sparrow.transects.rda |only
Rdistance-1.2.2/Rdistance/inst |only
Rdistance-1.2.2/Rdistance/man/AIC.dfunc.Rd | 10
Rdistance-1.2.2/Rdistance/man/ESW.Rd | 10
Rdistance-1.2.2/Rdistance/man/F.abund.estim.Rd | 32 +-
Rdistance-1.2.2/Rdistance/man/F.automated.CDA.Rd | 18 -
Rdistance-1.2.2/Rdistance/man/F.dfunc.estim.Rd | 63 +----
Rdistance-1.2.2/Rdistance/man/Rdistance-package.Rd | 23 -
Rdistance-1.2.2/Rdistance/man/coef.dfunc.Rd | 10
Rdistance-1.2.2/Rdistance/man/perp.dists.Rd | 12 -
Rdistance-1.2.2/Rdistance/man/sparrow.detections.Rd |only
Rdistance-1.2.2/Rdistance/man/sparrow.transects.Rd |only
Rdistance-1.2.2/Rdistance/vignettes/Rdistance_BeginnerTutorial.Rmd |only
Rdistance-1.2.2/Rdistance/vignettes/Rdistance_CustomDetectionFunction.Rmd |only
28 files changed, 148 insertions(+), 238 deletions(-)
Title: Nested Association Mapping Analysis
Diff between NAM versions 1.2 dated 2015-04-07 and 1.3 dated 2015-04-22
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 8
MD5 | 18 -
NAMESPACE | 3
R/gibbs.R | 16 -
R/gwas.R | 90 +++++
R/gwas2.R | 813 +++++++++++++++++++++++++++++------------------------
R/manhattan.R | 47 +--
man/NAM-package.Rd | 4
man/gibbs.Rd | 151 ++++-----
man/gwas.Rd | 7
10 files changed, 668 insertions(+), 489 deletions(-)
Title: Global Charcoal Database
Diff between GCD versions 3.0.4 dated 2014-05-22 and 3.0.5 dated 2015-04-22
Description: Contains the Global Charcoal database data. Data include charcoal
series (age, depth, charcoal quantity, associated units and methods) and
informations on sedimentary sites (localisation, depositional environment, biome, etc.).
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
GCD-3.0.4/GCD/R/potveg.R |only
GCD-3.0.4/GCD/man/plot.potveg.Rd |only
GCD-3.0.4/GCD/man/potveg.Rd |only
GCD-3.0.5/GCD/DESCRIPTION | 15 +--
GCD-3.0.5/GCD/MD5 | 18 +--
GCD-3.0.5/GCD/NAMESPACE | 5 -
GCD-3.0.5/GCD/NEWS | 9 +
GCD-3.0.5/GCD/R/GCD-package.R |only
GCD-3.0.5/GCD/man/GCD-internal.Rd | 10 +-
GCD-3.0.5/GCD/man/GCD-package.Rd | 49 +++++-----
GCD-3.0.5/GCD/man/paleofiredata.Rd | 30 +++---
GCD-3.0.5/GCD/man/paleofiresites.Rd | 168 +++++++++++++++++++++---------------
12 files changed, 169 insertions(+), 135 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero/One Inflated
Beta Regression
Diff between zoib versions 1.2.1 dated 2015-03-26 and 1.3.0 dated 2015-04-22
Description: Fits beta regression and zero/one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu
Maintainer: Fang Liu
DESCRIPTION | 8 +++----
MD5 | 50 +++++++++++++++++++++++------------------------
R/fixed01.R | 2 -
R/zoib.R | 40 +++++++++++++++++++++++++++----------
inst/bugs/fixed.bug | 5 +---
inst/bugs/fixed0.bug | 4 +--
inst/bugs/fixed01.bug | 19 ++++++++++-------
inst/bugs/fixed1.bug | 6 ++---
inst/bugs/joint_1z.bug | 6 ++---
inst/bugs/joint_1z0.bug | 6 ++---
inst/bugs/joint_1z01.bug | 5 ++--
inst/bugs/joint_1z1.bug | 5 ++--
inst/bugs/joint_2z.bug | 5 ++--
inst/bugs/joint_2z0.bug | 5 ++--
inst/bugs/joint_2z01.bug | 5 ++--
inst/bugs/joint_2z1.bug | 5 ++--
inst/bugs/sep_1z.bug | 4 +--
inst/bugs/sep_1z0.bug | 4 +--
inst/bugs/sep_1z01.bug | 4 +--
inst/bugs/sep_1z1.bug | 5 ++--
inst/bugs/sep_2z.bug | 5 ++--
inst/bugs/sep_2z0.bug | 5 ++--
inst/bugs/sep_2z01.bug | 5 ++--
inst/bugs/sep_2z1.bug | 5 ++--
man/zoib-package.Rd | 6 ++---
man/zoib.Rd | 10 +++++----
26 files changed, 131 insertions(+), 98 deletions(-)
More information about shinydashboard at CRAN
Permanent link
Title: Read and Analyze PLEXOS Solutions
Diff between rplexos versions 0.13 dated 2015-03-18 and 1.0 dated 2015-04-22
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
DESCRIPTION | 20 -
MD5 | 69 +++---
NAMESPACE | 4
R/debug.R | 25 ++
R/process_folder.R | 8
R/process_input.R | 2
R/process_solution.R | 6
R/query.R | 34 +--
build/vignette.rds |binary
inst/doc/rplexos.R | 77 ++++++
inst/doc/rplexos.Rmd | 172 +++++++++++++--
inst/doc/rplexos.html | 439 ++++++++++++++++++---------------------
inst/extdata |only
man/get_query.Rd | 2
man/is_sample_stats.Rd | 2
man/list_folders.Rd | 2
man/location_solution_rplexos.Rd |only
man/plexos_open.Rd | 2
man/process_folder.Rd | 2
man/query_class_member.Rd | 2
man/query_config.Rd | 2
man/query_log.Rd | 2
man/query_master.Rd | 7
man/query_master_each.Rd | 4
man/query_phase.Rd | 2
man/query_property.Rd | 2
man/query_sql.Rd | 2
man/query_time.Rd | 2
man/rplexos.Rd | 2
man/start_debug_rplexos.Rd | 2
man/start_parallel_rplexos.Rd | 2
man/valid_columns.Rd | 2
src/RcppExports.cpp | 28 --
tests |only
vignettes/rplexos.Rmd | 170 +++++++++++++--
35 files changed, 712 insertions(+), 385 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Diff between paleofire versions 1.1.5 dated 2014-12-01 and 1.1.6 dated 2015-04-22
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
paleofire-1.1.5/paleofire/man/1paleofiRe-package.Rd |only
paleofire-1.1.6/paleofire/DESCRIPTION | 17
paleofire-1.1.6/paleofire/MD5 | 126 +++----
paleofire-1.1.6/paleofire/NAMESPACE | 5
paleofire-1.1.6/paleofire/NEWS | 20 +
paleofire-1.1.6/paleofire/R/contiguous.R |only
paleofire-1.1.6/paleofire/R/kdffreq.R |only
paleofire-1.1.6/paleofire/R/paleofire-package.R |only
paleofire-1.1.6/paleofire/R/pfAddData.R | 56 +++
paleofire-1.1.6/paleofire/R/pfBoxCox.R | 35 +
paleofire-1.1.6/paleofire/R/pfCircular.R | 68 +++
paleofire-1.1.6/paleofire/R/pfComposite.R | 80 ++++
paleofire-1.1.6/paleofire/R/pfCompositeLF.R | 126 ++++++-
paleofire-1.1.6/paleofire/R/pfDiagnostic.R | 58 +++
paleofire-1.1.6/paleofire/R/pfDotMap.r | 282 ++++++++++++----
paleofire-1.1.6/paleofire/R/pfExtract.R | 28 +
paleofire-1.1.6/paleofire/R/pfGridding.R | 205 ++++++++++-
paleofire-1.1.6/paleofire/R/pfInteractive.R | 33 +
paleofire-1.1.6/paleofire/R/pfKruskal.R | 83 ++++
paleofire-1.1.6/paleofire/R/pfMinMax.R | 31 +
paleofire-1.1.6/paleofire/R/pfPublication.R | 3
paleofire-1.1.6/paleofire/R/pfResolution.R | 23 +
paleofire-1.1.6/paleofire/R/pfSimpleGrid.r |only
paleofire-1.1.6/paleofire/R/pfSiteSel.R | 133 +++++++
paleofire-1.1.6/paleofire/R/pfToKml.R | 20 +
paleofire-1.1.6/paleofire/R/pfTransform.R | 69 +++
paleofire-1.1.6/paleofire/R/potveg.R |only
paleofire-1.1.6/paleofire/R/pretreatment.R | 72 ++++
paleofire-1.1.6/paleofire/R/zzz.R | 48 ++
paleofire-1.1.6/paleofire/build/vignette.rds |binary
paleofire-1.1.6/paleofire/data/countries.rda |only
paleofire-1.1.6/paleofire/data/datalist | 1
paleofire-1.1.6/paleofire/inst/doc/paleofire-paper.Rnw | 1
paleofire-1.1.6/paleofire/inst/doc/paleofire-paper.pdf |binary
paleofire-1.1.6/paleofire/man/checkGCDversion.Rd | 28 -
paleofire-1.1.6/paleofire/man/contiguous.Rd |only
paleofire-1.1.6/paleofire/man/kdffreq.Rd |only
paleofire-1.1.6/paleofire/man/paleofire-internal.Rd | 14
paleofire-1.1.6/paleofire/man/paleofire-package.Rd |only
paleofire-1.1.6/paleofire/man/pfAddData.Rd | 75 ++--
paleofire-1.1.6/paleofire/man/pfBoxCox.Rd | 55 +--
paleofire-1.1.6/paleofire/man/pfCircular.Rd | 65 +--
paleofire-1.1.6/paleofire/man/pfComposite.Rd | 77 ++--
paleofire-1.1.6/paleofire/man/pfCompositeLF.Rd | 106 +++---
paleofire-1.1.6/paleofire/man/pfDiagnostic.Rd | 131 +++----
paleofire-1.1.6/paleofire/man/pfDotMap.Rd | 209 +++++++----
paleofire-1.1.6/paleofire/man/pfExtract.Rd | 32 -
paleofire-1.1.6/paleofire/man/pfGridding.Rd | 127 ++++---
paleofire-1.1.6/paleofire/man/pfInteractive.Rd | 34 -
paleofire-1.1.6/paleofire/man/pfKruskal.Rd | 51 +-
paleofire-1.1.6/paleofire/man/pfMinMax.Rd | 30 -
paleofire-1.1.6/paleofire/man/pfPublication.Rd | 2
paleofire-1.1.6/paleofire/man/pfResolution.Rd | 42 --
paleofire-1.1.6/paleofire/man/pfSimpleGrid.Rd |only
paleofire-1.1.6/paleofire/man/pfSiteSel.Rd | 56 +--
paleofire-1.1.6/paleofire/man/pfToKml.Rd | 33 -
paleofire-1.1.6/paleofire/man/pfTransform.Rd | 131 +++----
paleofire-1.1.6/paleofire/man/plot.CHAR.Rd | 34 -
paleofire-1.1.6/paleofire/man/plot.contiguous.Rd |only
paleofire-1.1.6/paleofire/man/plot.kdffreq.Rd |only
paleofire-1.1.6/paleofire/man/plot.pfCircular.Rd | 52 +-
paleofire-1.1.6/paleofire/man/plot.pfComposite.Rd | 54 +--
paleofire-1.1.6/paleofire/man/plot.pfCompositeLF.Rd | 68 ++-
paleofire-1.1.6/paleofire/man/plot.pfGridding.Rd | 102 +++--
paleofire-1.1.6/paleofire/man/plot.pfKruskal.Rd | 62 +--
paleofire-1.1.6/paleofire/man/plot.pfSiteSel.Rd | 59 +--
paleofire-1.1.6/paleofire/man/plot.potveg.Rd |only
paleofire-1.1.6/paleofire/man/potveg.Rd |only
paleofire-1.1.6/paleofire/man/pretreatment.Rd | 67 +--
paleofire-1.1.6/paleofire/man/summary.pfSiteSel.Rd | 35 -
paleofire-1.1.6/paleofire/man/triCube.Rd |only
paleofire-1.1.6/paleofire/vignettes/paleofire-paper.Rnw | 1
72 files changed, 2421 insertions(+), 1034 deletions(-)
Title: Statistical Tools for Probing Moderation Effects
Diff between probemod versions 0.2 dated 2015-04-21 and 0.2.1 dated 2015-04-22
Description: Contains functions that are useful for probing moderation effects (or interactions) including techniques such as pick-a-point (also known as spotlight analysis) and Johnson-Neyman (also known as floodlight analysis). Plot function is also provided to facilitate visualization of results from each of these techniques.
Author: Jiat Chow Tan [aut, cre]
Maintainer: Jiat Chow Tan
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 11 +++++++----
R/jn.R | 20 +++++++++++---------
R/pickapoint.R | 19 +++++++++++--------
R/plot.jn.R | 4 ++--
man/plot.jn.Rd | 4 ++--
7 files changed, 43 insertions(+), 35 deletions(-)
Title: 'Markdown' Rendering for R
Diff between markdown versions 0.7.4 dated 2014-08-24 and 0.7.7 dated 2015-04-22
Description: Provides R bindings to the 'Sundown' 'Markdown' rendering library
(https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting
syntax that can be converted to 'XHTML' or other formats. See
http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie
DESCRIPTION | 19 +++++++------
MD5 | 44 ++++++++++++++++----------------
NEWS | 19 +++++++++++++
R/renderMarkdown.R | 55 +++++++++++++++++++++-------------------
R/rpubsUpload.R | 55 ++++++++++++++++++++++++++++++++--------
README.md | 2 +
build/vignette.rds |binary
inst/doc/markdown-examples.R | 4 +-
inst/doc/markdown-examples.html | 8 ++---
inst/doc/markdown-output.R | 4 +-
inst/doc/markdown-output.html | 8 ++---
inst/examples/HTMLOptions.R | 4 +-
man/markdown.Rd | 1
man/markdownExtensions.Rd | 1
man/markdownHTMLOptions.Rd | 1
man/markdownToHTML.Rd | 1
man/registeredRenderers.Rd | 1
man/renderMarkdown.Rd | 29 ++++++++++++---------
man/rendererExists.Rd | 1
man/rendererOutputType.Rd | 1
man/rpubsUpload.Rd | 1
man/smartypants.Rd | 1
tests/tests.Rout.save | 12 ++++----
23 files changed, 172 insertions(+), 100 deletions(-)
Title: Geographic Display of Survey Data Statistics
Diff between mapStats versions 2.3 dated 2015-02-19 and 2.4 dated 2015-04-22
Description: Automated calculation and visualization of survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman
DESCRIPTION | 8 +++---
MD5 | 21 +++++++++--------
R/calcStats.R | 32 ++++++++++++++++++++++++++-
R/jiggleClass.R | 44 +++++++++++++++++++++++++------------
R/mapStats.R | 4 +--
R/nobsEach.R |only
R/plotStats.R | 55 +++++++++++++++++++++++++++++++++++------------
demo/map_examples.R | 32 +++++++++++++++------------
man/jiggleClass.Rd | 43 ++++++++++++++++++++++++++++++------
man/mapStats-internal.Rd | 9 ++++++-
man/mapStats-package.Rd | 2 -
man/mapStats.Rd | 4 ++-
12 files changed, 186 insertions(+), 68 deletions(-)
Title: Karl Broman's R Code
Diff between broman versions 0.48-2 dated 2014-05-07 and 0.55-2 dated 2015-04-22
Description: Miscellaneous R functions.
Author: Karl W Broman
Maintainer: Karl W Broman
broman-0.48-2/broman/R/get.R |only
broman-0.48-2/broman/R/loadwork.R |only
broman-0.48-2/broman/inst/tests |only
broman-0.48-2/broman/man/attachwork.Rd |only
broman-0.48-2/broman/man/get0.Rd |only
broman-0.48-2/broman/man/loadwork.Rd |only
broman-0.48-2/broman/tests/run-all.R |only
broman-0.55-2/broman/DESCRIPTION | 19 -
broman-0.55-2/broman/MD5 | 189 ++++++-----
broman-0.55-2/broman/NAMESPACE | 20 -
broman-0.55-2/broman/R/arrowlocator.R | 25 -
broman-0.55-2/broman/R/attrnames.R |only
broman-0.55-2/broman/R/brocolors.R | 433 +++++++++++++-------------
broman-0.55-2/broman/R/cf.R | 14
broman-0.55-2/broman/R/colwalpha.R |only
broman-0.55-2/broman/R/convert2hex.R | 55 ---
broman-0.55-2/broman/R/errors2pushbullet.R |only
broman-0.55-2/broman/R/exit.R |only
broman-0.55-2/broman/R/fisher.R | 46 +-
broman-0.55-2/broman/R/grayplot.R | 231 +++++++------
broman-0.55-2/broman/R/help.R | 7
broman-0.55-2/broman/R/histlines.R | 30 -
broman-0.55-2/broman/R/holmans_triangle.R | 272 +++++++---------
broman-0.55-2/broman/R/kbdate.R | 16
broman-0.55-2/broman/R/lenuniq.R |only
broman-0.55-2/broman/R/loadfile.R |only
broman-0.55-2/broman/R/make.R | 28 +
broman-0.55-2/broman/R/manyboxplot.R | 85 ++---
broman-0.55-2/broman/R/mypairs.R | 37 +-
broman-0.55-2/broman/R/myround.R | 29 -
broman-0.55-2/broman/R/normalize.R | 41 +-
broman-0.55-2/broman/R/note.R |only
broman-0.55-2/broman/R/objectsizes.R | 19 -
broman-0.55-2/broman/R/pastedot.R | 18 -
broman-0.55-2/broman/R/permtest.R | 124 +++----
broman-0.55-2/broman/R/qr.R | 23 -
broman-0.55-2/broman/R/quantileSE.R | 25 -
broman-0.55-2/broman/R/revrainbow.R | 9
broman-0.55-2/broman/R/rmvn.R | 15
broman-0.55-2/broman/R/runningmean.R | 160 ++++-----
broman-0.55-2/broman/R/simp.R | 53 +--
broman-0.55-2/broman/R/strwidth2lines.R | 6
broman-0.55-2/broman/R/strwidth2xlim.R | 22 -
broman-0.55-2/broman/R/theme_karl.R |only
broman-0.55-2/broman/R/util.R | 11
broman-0.55-2/broman/R/venn_diagram.R | 302 ++++++++----------
broman-0.55-2/broman/R/winsorize.R | 19 -
broman-0.55-2/broman/R/xlimlabel.R | 24 -
broman-0.55-2/broman/README.md |only
broman-0.55-2/broman/inst/README.md |only
broman-0.55-2/broman/inst/STATUS.txt | 86 ++++-
broman-0.55-2/broman/man/arrowlocator.Rd | 6
broman-0.55-2/broman/man/attachfile.Rd | 16
broman-0.55-2/broman/man/attrnames.Rd |only
broman-0.55-2/broman/man/brocolors.Rd | 6
broman-0.55-2/broman/man/bromanversion.Rd | 6
broman-0.55-2/broman/man/cf.Rd | 6
broman-0.55-2/broman/man/chisq.Rd | 6
broman-0.55-2/broman/man/colwalpha.Rd |only
broman-0.55-2/broman/man/convert2hex.Rd | 6
broman-0.55-2/broman/man/done.Rd |only
broman-0.55-2/broman/man/errors2pushbullet.Rd |only
broman-0.55-2/broman/man/exit.Rd |only
broman-0.55-2/broman/man/fisher.Rd | 6
broman-0.55-2/broman/man/grayplot.Rd | 16
broman-0.55-2/broman/man/h.Rd | 6
broman-0.55-2/broman/man/hex2dec.Rd | 3
broman-0.55-2/broman/man/histlines.Rd | 6
broman-0.55-2/broman/man/kbdate.Rd | 6
broman-0.55-2/broman/man/lenuniq.Rd |only
broman-0.55-2/broman/man/loadfile.Rd | 16
broman-0.55-2/broman/man/make.Rd | 16
broman-0.55-2/broman/man/manyboxplot.Rd | 6
broman-0.55-2/broman/man/mypairs.Rd | 6
broman-0.55-2/broman/man/myround.Rd | 6
broman-0.55-2/broman/man/normalize.Rd | 6
broman-0.55-2/broman/man/note.Rd |only
broman-0.55-2/broman/man/objectsizes.Rd | 6
broman-0.55-2/broman/man/paired.perm.test.Rd | 6
broman-0.55-2/broman/man/paste..Rd | 6
broman-0.55-2/broman/man/paste00.Rd | 6
broman-0.55-2/broman/man/perm.test.Rd | 6
broman-0.55-2/broman/man/plot_crayons.Rd | 21 -
broman-0.55-2/broman/man/qqline2.Rd | 3
broman-0.55-2/broman/man/qr2.Rd | 6
broman-0.55-2/broman/man/quantileSE.Rd | 6
broman-0.55-2/broman/man/revrainbow.Rd | 6
broman-0.55-2/broman/man/rmvn.Rd | 6
broman-0.55-2/broman/man/runningmean.Rd | 3
broman-0.55-2/broman/man/runningratio.Rd | 3
broman-0.55-2/broman/man/simp.Rd | 6
broman-0.55-2/broman/man/strwidth2lines.Rd | 3
broman-0.55-2/broman/man/strwidth2xlim.Rd | 3
broman-0.55-2/broman/man/theme_karl.Rd |only
broman-0.55-2/broman/man/triarrow.Rd | 6
broman-0.55-2/broman/man/trilines.Rd | 6
broman-0.55-2/broman/man/triplot.Rd | 6
broman-0.55-2/broman/man/tripoints.Rd | 6
broman-0.55-2/broman/man/venn.Rd | 6
broman-0.55-2/broman/man/winsorize.Rd | 6
broman-0.55-2/broman/man/xlimlabel.Rd | 3
broman-0.55-2/broman/src/normalize.c | 134 ++++----
broman-0.55-2/broman/src/runningmean.c | 148 ++++----
broman-0.55-2/broman/tests/testthat |only
broman-0.55-2/broman/tests/testthat.R |only
105 files changed, 1514 insertions(+), 1547 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.7 dated 2015-03-11 and 1.8 dated 2015-04-22
Description: Collection of several plotting and table output functions for visualizing data.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
sjPlot-1.7/sjPlot/R/efc.R |only
sjPlot-1.7/sjPlot/R/sjImportSPSS.R |only
sjPlot-1.7/sjPlot/R/sjRecode.R |only
sjPlot-1.7/sjPlot/R/sjStatistics.R |only
sjPlot-1.7/sjPlot/data |only
sjPlot-1.7/sjPlot/man/chisq_gof.Rd |only
sjPlot-1.7/sjPlot/man/cramer.Rd |only
sjPlot-1.7/sjPlot/man/cronb.Rd |only
sjPlot-1.7/sjPlot/man/dicho.Rd |only
sjPlot-1.7/sjPlot/man/efc.Rd |only
sjPlot-1.7/sjPlot/man/efc2.Rd |only
sjPlot-1.7/sjPlot/man/efc3.Rd |only
sjPlot-1.7/sjPlot/man/eta_sq.Rd |only
sjPlot-1.7/sjPlot/man/get_val_labels.Rd |only
sjPlot-1.7/sjPlot/man/get_var_labels.Rd |only
sjPlot-1.7/sjPlot/man/group_labels.Rd |only
sjPlot-1.7/sjPlot/man/group_str.Rd |only
sjPlot-1.7/sjPlot/man/group_var.Rd |only
sjPlot-1.7/sjPlot/man/levene_test.Rd |only
sjPlot-1.7/sjPlot/man/mean_n.Rd |only
sjPlot-1.7/sjPlot/man/mic.Rd |only
sjPlot-1.7/sjPlot/man/mwu.Rd |only
sjPlot-1.7/sjPlot/man/phi.Rd |only
sjPlot-1.7/sjPlot/man/read_sas.Rd |only
sjPlot-1.7/sjPlot/man/read_spss.Rd |only
sjPlot-1.7/sjPlot/man/read_stata.Rd |only
sjPlot-1.7/sjPlot/man/recode_to.Rd |only
sjPlot-1.7/sjPlot/man/reliab_test.Rd |only
sjPlot-1.7/sjPlot/man/set_na.Rd |only
sjPlot-1.7/sjPlot/man/set_val_labels.Rd |only
sjPlot-1.7/sjPlot/man/set_var_labels.Rd |only
sjPlot-1.7/sjPlot/man/std_beta.Rd |only
sjPlot-1.7/sjPlot/man/std_e.Rd |only
sjPlot-1.7/sjPlot/man/str_pos.Rd |only
sjPlot-1.7/sjPlot/man/table_values.Rd |only
sjPlot-1.7/sjPlot/man/to_fac.Rd |only
sjPlot-1.7/sjPlot/man/to_label.Rd |only
sjPlot-1.7/sjPlot/man/to_sjPlot.Rd |only
sjPlot-1.7/sjPlot/man/to_value.Rd |only
sjPlot-1.7/sjPlot/man/weight.Rd |only
sjPlot-1.7/sjPlot/man/weight2.Rd |only
sjPlot-1.7/sjPlot/man/word_wrap.Rd |only
sjPlot-1.7/sjPlot/man/write_spss.Rd |only
sjPlot-1.7/sjPlot/man/write_stata.Rd |only
sjPlot-1.8/sjPlot/DESCRIPTION | 20
sjPlot-1.8/sjPlot/MD5 | 214 -
sjPlot-1.8/sjPlot/NAMESPACE | 43
sjPlot-1.8/sjPlot/NEWS | 48
sjPlot-1.8/sjPlot/R/helpfunctions.R | 1373 +++++-----
sjPlot-1.8/sjPlot/R/sjPlotAncovaLSMeans.R | 1025 +++++---
sjPlot-1.8/sjPlot/R/sjPlotAnova.R | 1046 ++++----
sjPlot-1.8/sjPlot/R/sjPlotClusterAnalysis.R | 1786 ++++++--------
sjPlot-1.8/sjPlot/R/sjPlotCorr.R | 37
sjPlot-1.8/sjPlot/R/sjPlotDist.R | 1088 ++++----
sjPlot-1.8/sjPlot/R/sjPlotFrequencies.R | 465 +--
sjPlot-1.8/sjPlot/R/sjPlotGLME.R | 3393 ++++++++++++++-------------
sjPlot-1.8/sjPlot/R/sjPlotGroupFrequencies.R | 2449 +++++++++----------
sjPlot-1.8/sjPlot/R/sjPlotInteractions.R | 1261 +++++++---
sjPlot-1.8/sjPlot/R/sjPlotLikert.R | 169 -
sjPlot-1.8/sjPlot/R/sjPlotLinreg.R | 1836 +++++++-------
sjPlot-1.8/sjPlot/R/sjPlotLinregMultiple.R | 808 +++---
sjPlot-1.8/sjPlot/R/sjPlotOdds.R | 299 +-
sjPlot-1.8/sjPlot/R/sjPlotOddsMultiple.R | 190 -
sjPlot-1.8/sjPlot/R/sjPlotPCA.R | 206 +
sjPlot-1.8/sjPlot/R/sjPlotPearsonsChi2Test.R | 295 +-
sjPlot-1.8/sjPlot/R/sjPlotPropTable.R | 434 +--
sjPlot-1.8/sjPlot/R/sjPlotScatter.R | 660 ++---
sjPlot-1.8/sjPlot/R/sjPlotSetTheme.R | 1615 ++++++------
sjPlot-1.8/sjPlot/R/sjPlotStackFrequencies.R | 260 +-
sjPlot-1.8/sjPlot/R/sjTabCorr.R | 1069 ++++----
sjPlot-1.8/sjPlot/R/sjTabDataFrame.R | 179 -
sjPlot-1.8/sjPlot/R/sjTabFrequencies.R | 103
sjPlot-1.8/sjPlot/R/sjTabGrpmean.R | 42
sjPlot-1.8/sjPlot/R/sjTabItemAnalysis.R | 110
sjPlot-1.8/sjPlot/R/sjTabLinReg.R | 312 +-
sjPlot-1.8/sjPlot/R/sjTabMannWhitney.R |only
sjPlot-1.8/sjPlot/R/sjTabOdds.R | 155 -
sjPlot-1.8/sjPlot/R/sjTabPCA.R | 99
sjPlot-1.8/sjPlot/R/sjTabPropTable.R | 291 --
sjPlot-1.8/sjPlot/R/sjTabSPSS.R | 84
sjPlot-1.8/sjPlot/R/sjTabStackFrq.R | 237 +
sjPlot-1.8/sjPlot/R/zzz.R |only
sjPlot-1.8/sjPlot/README.md | 75
sjPlot-1.8/sjPlot/man/adjust_plot_range.Rd | 5
sjPlot-1.8/sjPlot/man/dist_chisq.Rd | 2
sjPlot-1.8/sjPlot/man/dist_f.Rd | 2
sjPlot-1.8/sjPlot/man/dist_norm.Rd | 2
sjPlot-1.8/sjPlot/man/dist_t.Rd | 2
sjPlot-1.8/sjPlot/man/sj.setGeomColors.Rd | 2
sjPlot-1.8/sjPlot/man/sjPlot-package.Rd | 26
sjPlot-1.8/sjPlot/man/sjc.cluster.Rd | 12
sjPlot-1.8/sjPlot/man/sjc.dend.Rd | 7
sjPlot-1.8/sjPlot/man/sjc.elbow.Rd | 8
sjPlot-1.8/sjPlot/man/sjc.grpdisc.Rd | 7
sjPlot-1.8/sjPlot/man/sjc.kgap.Rd | 2
sjPlot-1.8/sjPlot/man/sjc.qclus.Rd | 12
sjPlot-1.8/sjPlot/man/sjp.aov1.Rd | 14
sjPlot-1.8/sjPlot/man/sjp.chi2.Rd | 4
sjPlot-1.8/sjPlot/man/sjp.corr.Rd | 5
sjPlot-1.8/sjPlot/man/sjp.emm.int.Rd | 106
sjPlot-1.8/sjPlot/man/sjp.frq.Rd | 19
sjPlot-1.8/sjPlot/man/sjp.glm.Rd | 21
sjPlot-1.8/sjPlot/man/sjp.glmer.Rd | 428 +--
sjPlot-1.8/sjPlot/man/sjp.glmm.Rd | 54
sjPlot-1.8/sjPlot/man/sjp.grpfrq.Rd | 23
sjPlot-1.8/sjPlot/man/sjp.int.Rd | 268 +-
sjPlot-1.8/sjPlot/man/sjp.likert.Rd | 69
sjPlot-1.8/sjPlot/man/sjp.lm.Rd | 23
sjPlot-1.8/sjPlot/man/sjp.lmer.Rd | 395 +--
sjPlot-1.8/sjPlot/man/sjp.lmm.Rd | 53
sjPlot-1.8/sjPlot/man/sjp.pca.Rd | 82
sjPlot-1.8/sjPlot/man/sjp.scatter.Rd | 13
sjPlot-1.8/sjPlot/man/sjp.setTheme.Rd | 26
sjPlot-1.8/sjPlot/man/sjp.stackfrq.Rd | 77
sjPlot-1.8/sjPlot/man/sjp.xtab.Rd | 73
sjPlot-1.8/sjPlot/man/sjt.corr.Rd | 377 +--
sjPlot-1.8/sjPlot/man/sjt.df.Rd | 309 +-
sjPlot-1.8/sjPlot/man/sjt.frq.Rd | 453 +--
sjPlot-1.8/sjPlot/man/sjt.glm.Rd | 673 ++---
sjPlot-1.8/sjPlot/man/sjt.grpmean.Rd | 7
sjPlot-1.8/sjPlot/man/sjt.itemanalysis.Rd | 396 +--
sjPlot-1.8/sjPlot/man/sjt.lm.Rd | 827 +++---
sjPlot-1.8/sjPlot/man/sjt.mwu.Rd |only
sjPlot-1.8/sjPlot/man/sjt.pca.Rd | 396 +--
sjPlot-1.8/sjPlot/man/sjt.stackfrq.Rd | 430 +--
sjPlot-1.8/sjPlot/man/sjt.xtab.Rd | 461 +--
sjPlot-1.8/sjPlot/man/view_spss.Rd | 255 +-
sjPlot-1.8/sjPlot/tests |only
128 files changed, 15652 insertions(+), 14550 deletions(-)
Title: Analytical Tools for Radiation Oncology
Diff between RadOnc versions 1.0.9 dated 2014-11-21 and 1.1.0 dated 2015-04-22
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from Varian's 'Eclipse' platform and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson
Maintainer: Reid F. Thompson
RadOnc-1.0.9/RadOnc/R/getStructureList.R |only
RadOnc-1.0.9/RadOnc/build |only
RadOnc-1.0.9/RadOnc/inst/doc/RadOnc.R |only
RadOnc-1.0.9/RadOnc/inst/doc/RadOnc.Rnw |only
RadOnc-1.0.9/RadOnc/man/getStructureList.Rd |only
RadOnc-1.1.0/RadOnc/DESCRIPTION | 12 -
RadOnc-1.1.0/RadOnc/MD5 | 39 ++----
RadOnc-1.1.0/RadOnc/NAMESPACE | 2
RadOnc-1.1.0/RadOnc/R/CLASSES.R | 2
RadOnc-1.1.0/RadOnc/R/DVH.R | 40 +++++-
RadOnc-1.1.0/RadOnc/R/convert.DVH.R | 72 +++++++----
RadOnc-1.1.0/RadOnc/R/mean.DVH.R | 28 ----
RadOnc-1.1.0/RadOnc/R/plot.DVH.R | 18 +-
RadOnc-1.1.0/RadOnc/R/read.DICOM.RT.R | 3
RadOnc-1.1.0/RadOnc/R/read.DVH.R | 166 ++++++++++++++++++++-------
RadOnc-1.1.0/RadOnc/R/subset.R |only
RadOnc-1.1.0/RadOnc/inst/NEWS.Rd | 46 +++++++
RadOnc-1.1.0/RadOnc/inst/doc/RadOnc.pdf |binary
RadOnc-1.1.0/RadOnc/man/DVH-class.Rd | 2
RadOnc-1.1.0/RadOnc/man/DVH.list-class.Rd | 4
RadOnc-1.1.0/RadOnc/man/plot-methods.Rd | 5
RadOnc-1.1.0/RadOnc/man/structure3D-class.Rd | 7 -
RadOnc-1.1.0/RadOnc/man/subset.Rd |only
RadOnc-1.1.0/RadOnc/vignettes/RadOnc.Rnw | 35 +++--
24 files changed, 328 insertions(+), 153 deletions(-)
Title: Management, Display, and Processing of Medical Imaging Data
Diff between MRIaggr versions 1.0 dated 2015-03-10 and 1.1 dated 2015-04-22
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne
MRIaggr-1.0/MRIaggr/man/calcCriteriaGR.Rd |only
MRIaggr-1.0/MRIaggr/man/calcRegionalIntensity.Rd |only
MRIaggr-1.0/MRIaggr/man/calcSigmaGR.Rd |only
MRIaggr-1.0/MRIaggr/man/constSweave.Rd |only
MRIaggr-1.1/MRIaggr/DESCRIPTION | 13
MRIaggr-1.1/MRIaggr/MD5 | 141 +-
MRIaggr-1.1/MRIaggr/NAMESPACE | 14
MRIaggr-1.1/MRIaggr/R/Associated_functions.R | 1161 +++++++++--------
MRIaggr-1.1/MRIaggr/R/Class_Carto3D.R | 63
MRIaggr-1.1/MRIaggr/R/Class_MRIaggr.R | 963 ++++++++------
MRIaggr-1.1/MRIaggr/R/GR_functions.R | 440 +++---
MRIaggr-1.1/MRIaggr/R/Generic_functions.R | 23
MRIaggr-1.1/MRIaggr/R/RcppExports.R | 4
MRIaggr-1.1/MRIaggr/data/MRIaggr.Pat1_red.RData |binary
MRIaggr-1.1/MRIaggr/demo/Analysis.R | 6
MRIaggr-1.1/MRIaggr/demo/preProcessing.R | 13
MRIaggr-1.1/MRIaggr/inst/List_of_arguments.R | 804 ++++++-----
MRIaggr-1.1/MRIaggr/inst/NEWS |only
MRIaggr-1.1/MRIaggr/inst/TODO |only
MRIaggr-1.1/MRIaggr/inst/Tests/Test2-1_IRMaggr.R | 30
MRIaggr-1.1/MRIaggr/inst/Tests/Test2-3_fctsAssociees.R | 39
MRIaggr-1.1/MRIaggr/inst/Tests/Test2-4_fctsGR.R | 14
MRIaggr-1.1/MRIaggr/inst/calcCriteriaGR.Rd |only
MRIaggr-1.1/MRIaggr/inst/calcSigmaGR.Rd |only
MRIaggr-1.1/MRIaggr/man/Carto3D-class.Rd | 26
MRIaggr-1.1/MRIaggr/man/Carto3D2MRIaggr.Rd | 11
MRIaggr-1.1/MRIaggr/man/EDK.Rd | 6
MRIaggr-1.1/MRIaggr/man/MRIaggr-class.Rd | 61
MRIaggr-1.1/MRIaggr/man/affectContrast.Rd | 8
MRIaggr-1.1/MRIaggr/man/affectDescStats.Rd | 3
MRIaggr-1.1/MRIaggr/man/affectHemisphere.Rd | 6
MRIaggr-1.1/MRIaggr/man/array2df.Rd | 4
MRIaggr-1.1/MRIaggr/man/calcAUPRC.Rd | 3
MRIaggr-1.1/MRIaggr/man/calcBrainMask.Rd | 6
MRIaggr-1.1/MRIaggr/man/calcDistMask.Rd | 5
MRIaggr-1.1/MRIaggr/man/calcFilter.Rd | 19
MRIaggr-1.1/MRIaggr/man/calcGR.Rd | 5
MRIaggr-1.1/MRIaggr/man/calcGroupsMask.Rd | 13
MRIaggr-1.1/MRIaggr/man/calcGroupsW.Rd | 4
MRIaggr-1.1/MRIaggr/man/calcHemi_cpp.Rd | 17
MRIaggr-1.1/MRIaggr/man/calcHemisphere.Rd | 7
MRIaggr-1.1/MRIaggr/man/calcROCthreshold.Rd | 3
MRIaggr-1.1/MRIaggr/man/calcRegionaContrast.Rd |only
MRIaggr-1.1/MRIaggr/man/calcSmoothMask.Rd | 4
MRIaggr-1.1/MRIaggr/man/calcTableHypoReperf.Rd | 2
MRIaggr-1.1/MRIaggr/man/calcThresholdMRIaggr.Rd | 16
MRIaggr-1.1/MRIaggr/man/calcTissueType.Rd | 13
MRIaggr-1.1/MRIaggr/man/calcW.Rd | 18
MRIaggr-1.1/MRIaggr/man/constCarto3D.Rd | 7
MRIaggr-1.1/MRIaggr/man/constCompressMRIaggr.Rd | 2
MRIaggr-1.1/MRIaggr/man/constLatex.Rd |only
MRIaggr-1.1/MRIaggr/man/constMRIaggr.Rd | 51
MRIaggr-1.1/MRIaggr/man/constReduceMRIaggr.Rd | 4
MRIaggr-1.1/MRIaggr/man/df2array.Rd | 15
MRIaggr-1.1/MRIaggr/man/heatmapMRIaggr.Rd | 3
MRIaggr-1.1/MRIaggr/man/initConstLatex.Rd |only
MRIaggr-1.1/MRIaggr/man/initFilter.Rd | 2
MRIaggr-1.1/MRIaggr/man/initMask.Rd |only
MRIaggr-1.1/MRIaggr/man/initParameter.Rd | 2
MRIaggr-1.1/MRIaggr/man/multiplot.Rd | 10
MRIaggr-1.1/MRIaggr/man/outline.Rd | 2
MRIaggr-1.1/MRIaggr/man/outlineMRIaggr.Rd | 2
MRIaggr-1.1/MRIaggr/man/readMRI.Rd | 43
MRIaggr-1.1/MRIaggr/man/selectContrast.Rd | 15
MRIaggr-1.1/MRIaggr/man/selectCoords.Rd | 11
MRIaggr-1.1/MRIaggr/man/selectDefault_value.Rd | 4
MRIaggr-1.1/MRIaggr/man/selectDescStats.Rd | 5
MRIaggr-1.1/MRIaggr/man/selectHemispheres.Rd | 4
MRIaggr-1.1/MRIaggr/man/selectHistory.Rd | 2
MRIaggr-1.1/MRIaggr/man/selectIdentifier.Rd | 4
MRIaggr-1.1/MRIaggr/man/selectN.Rd | 3
MRIaggr-1.1/MRIaggr/man/selectParameter.Rd | 4
MRIaggr-1.1/MRIaggr/man/selectVoxelDim.Rd | 4
MRIaggr-1.1/MRIaggr/man/summary.MRIaggr.Rd | 8
MRIaggr-1.1/MRIaggr/man/writeMRI.Rd |only
MRIaggr-1.1/MRIaggr/man/writeMRIaggr.Rd |only
MRIaggr-1.1/MRIaggr/src/Associated_functions.cpp | 172 +-
MRIaggr-1.1/MRIaggr/src/RcppExports.cpp | 19
MRIaggr-1.1/MRIaggr/tests |only
79 files changed, 2444 insertions(+), 1942 deletions(-)
Title: Estimation of Conditional Quantiles using Optimal Quantization
Diff between QuantifQuantile versions 1.0 dated 2014-08-28 and 2.0 dated 2015-04-22
More information about QuantifQuantile at CRAN
Description: Estimation of conditional quantiles using optimal quantization.
Construction of an optimal grid of N quantizers, estimation of conditional
quantiles and data driven selection of the size N of the grid. Graphical
illustrations for the selection of N and of resulting estimated curves or
surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier
QuantifQuantile-1.0/QuantifQuantile/R/plot.select.N.QuantifQuantile.R |only
QuantifQuantile-1.0/QuantifQuantile/man/plot.select.N.QuantifQuantile.Rd |only
QuantifQuantile-2.0/QuantifQuantile/DESCRIPTION | 12
QuantifQuantile-2.0/QuantifQuantile/MD5 | 30 -
QuantifQuantile-2.0/QuantifQuantile/NAMESPACE | 5
QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.R | 43 +-
QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.d.R | 39 +-
QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.d2.R | 36 +-
QuantifQuantile-2.0/QuantifQuantile/R/plot.QuantifQuantile.R | 165 +++++++---
QuantifQuantile-2.0/QuantifQuantile/R/print.QuantifQuantile.R | 50 +--
QuantifQuantile-2.0/QuantifQuantile/R/summary.QuantifQuantile.R | 8
QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.Rd | 22 -
QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.d.Rd | 19 -
QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.d2.Rd | 19 -
QuantifQuantile-2.0/QuantifQuantile/man/plot.QuantifQuantile.Rd | 37 +-
QuantifQuantile-2.0/QuantifQuantile/man/print.QuantifQuantile.Rd | 4
QuantifQuantile-2.0/QuantifQuantile/man/summary.QuantifQuantile.Rd | 6
17 files changed, 306 insertions(+), 189 deletions(-)
Permanent link
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Diff between mclust versions 5.0.0 dated 2015-04-09 and 5.0.1 dated 2015-04-22
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca
DESCRIPTION | 10 +-
MD5 | 42 +++++-----
NAMESPACE | 7 +
R/clustCombi.R | 9 +-
R/init.R | 126 ++++++++++++++++----------------
R/mclust.R | 7 -
R/mclustda.R | 4 +
build/vignette.rds |binary
data/Baudry_etal_2010_JCGS_examples.rda |binary
data/GvHD.rda |binary
data/acidity.rda |binary
data/chevron.rda |binary
data/cross.rda |binary
data/diabetes.rda |binary
data/thyroid.rda |binary
data/wreath.rda |binary
inst/NEWS | 8 +-
man/entPlot.Rd | 4 -
man/hc.Rd | 7 +
man/mclustModelNames.Rd | 5 +
man/randomPairs.Rd | 4 -
src/mclust.f | 2
22 files changed, 124 insertions(+), 111 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Diff between logmult versions 0.6.1 dated 2015-01-13 and 0.6.2 dated 2015-04-22
Description: Functions to fit log-multiplicative models using gnm, with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
DESCRIPTION | 8 +++---
MD5 | 6 ++--
NEWS | 3 ++
R/yrcskew.R | 75 +++++++++++++++++++++++++++++++-----------------------------
4 files changed, 49 insertions(+), 43 deletions(-)
Title: Generalized Nonlinear Models
Diff between gnm versions 1.0-7 dated 2014-01-02 and 1.0-8 dated 2015-04-22
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre],
David Firth [aut],
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Martin Maechler [ctb]
Maintainer: Heather Turner
gnm-1.0-7/gnm/data/House2001.csv.gz |only
gnm-1.0-7/gnm/data/backPain.txt.gz |only
gnm-1.0-7/gnm/data/barley.csv.gz |only
gnm-1.0-7/gnm/data/barley.txt.gz |only
gnm-1.0-7/gnm/data/mentalHealth.txt.gz |only
gnm-1.0-7/gnm/data/voting.txt.gz |only
gnm-1.0-7/gnm/data/wheat.txt.gz |only
gnm-1.0-8/gnm/DESCRIPTION | 38 +-
gnm-1.0-8/gnm/MD5 | 374 +++++++++++++---------------
gnm-1.0-8/gnm/R/Const.R | 15 +
gnm-1.0-8/gnm/R/Diag.R | 15 +
gnm-1.0-8/gnm/R/Dref.R | 15 +
gnm-1.0-8/gnm/R/DrefWeights.R | 15 +
gnm-1.0-8/gnm/R/Exp.R | 15 +
gnm-1.0-8/gnm/R/Inv.R | 15 +
gnm-1.0-8/gnm/R/Log.R | 15 +
gnm-1.0-8/gnm/R/Logistic.R | 15 +
gnm-1.0-8/gnm/R/Logit.R | 15 +
gnm-1.0-8/gnm/R/MPinv.R | 15 +
gnm-1.0-8/gnm/R/Mult.R | 15 +
gnm-1.0-8/gnm/R/MultHomog.R | 15 +
gnm-1.0-8/gnm/R/Raise.R | 15 +
gnm-1.0-8/gnm/R/Symm.R | 15 +
gnm-1.0-8/gnm/R/Topo.R | 15 +
gnm-1.0-8/gnm/R/add1.gnm.R | 23 +
gnm-1.0-8/gnm/R/addterm.gnm.R | 15 +
gnm-1.0-8/gnm/R/alias.gnm.R | 15 +
gnm-1.0-8/gnm/R/anova.gnm.R | 21 +
gnm-1.0-8/gnm/R/asGnm.R | 15 +
gnm-1.0-8/gnm/R/asGnm.default.R | 15 +
gnm-1.0-8/gnm/R/asGnm.glm.R | 15 +
gnm-1.0-8/gnm/R/asGnm.lm.R | 15 +
gnm-1.0-8/gnm/R/boxcox.gnm.R | 15 +
gnm-1.0-8/gnm/R/checkCall.R | 15 +
gnm-1.0-8/gnm/R/checkEstimable.R | 21 +
gnm-1.0-8/gnm/R/cholInv.R | 15 +
gnm-1.0-8/gnm/R/coef.gnm.R | 15 +
gnm-1.0-8/gnm/R/confint.gnm.R | 24 +
gnm-1.0-8/gnm/R/confint.profile.gnm.R | 18 +
gnm-1.0-8/gnm/R/cooks.distance.gnm.R | 18 +
gnm-1.0-8/gnm/R/dfbeta.gnm.R | 15 +
gnm-1.0-8/gnm/R/dfbetas.gnm.R | 15 +
gnm-1.0-8/gnm/R/drop1.gnm.R | 23 +
gnm-1.0-8/gnm/R/dropterm.gnm.R | 15 +
gnm-1.0-8/gnm/R/dummy.coef.gnm.R | 17 +
gnm-1.0-8/gnm/R/effects.gnm.R | 15 +
gnm-1.0-8/gnm/R/exitInfo.R | 15 +
gnm-1.0-8/gnm/R/expandCategorical.R | 57 ++--
gnm-1.0-8/gnm/R/fitted.gnm.R | 15 +
gnm-1.0-8/gnm/R/getContrasts.R | 17 +
gnm-1.0-8/gnm/R/getData.R | 19 +
gnm-1.0-8/gnm/R/glm.fit.e.R | 64 ++--
gnm-1.0-8/gnm/R/gnm-defunct.R | 15 +
gnm-1.0-8/gnm/R/gnm.R | 43 ++-
gnm-1.0-8/gnm/R/gnmFit.R | 21 +
gnm-1.0-8/gnm/R/gnmStart.R | 15 +
gnm-1.0-8/gnm/R/gnmTerms.R | 17 +
gnm-1.0-8/gnm/R/gnmTools.R | 27 +-
gnm-1.0-8/gnm/R/grp.sum.R | 15 +
gnm-1.0-8/gnm/R/hashSplit.R | 15 +
gnm-1.0-8/gnm/R/hatvalues.gnm.R | 20 +
gnm-1.0-8/gnm/R/influence.gnm.R | 17 +
gnm-1.0-8/gnm/R/instances.R | 15 +
gnm-1.0-8/gnm/R/kappa.gnm.R | 17 +
gnm-1.0-8/gnm/R/labels.gnm.R | 15 +
gnm-1.0-8/gnm/R/logtrans.gnm.R | 15 +
gnm-1.0-8/gnm/R/meanResiduals.R | 24 +
gnm-1.0-8/gnm/R/model.frame.gnm.R | 30 +-
gnm-1.0-8/gnm/R/model.matrix.gnm.R | 15 +
gnm-1.0-8/gnm/R/naToZero.R | 15 +
gnm-1.0-8/gnm/R/nonlinTerms.R | 15 +
gnm-1.0-8/gnm/R/ofInterest.R | 15 +
gnm-1.0-8/gnm/R/ofInterestReplacement.R | 17 +
gnm-1.0-8/gnm/R/parameters.R | 15 +
gnm-1.0-8/gnm/R/pickCoef.R | 17 +
gnm-1.0-8/gnm/R/plot.gnm.R | 18 +
gnm-1.0-8/gnm/R/plot.profile.gnm.R | 26 +
gnm-1.0-8/gnm/R/pprod.R | 15 +
gnm-1.0-8/gnm/R/prattle.R | 15 +
gnm-1.0-8/gnm/R/predict.gnm.R | 129 ++++++---
gnm-1.0-8/gnm/R/print.coef.gnm.R | 15 +
gnm-1.0-8/gnm/R/print.gnm.R | 15 +
gnm-1.0-8/gnm/R/print.meanResiduals.R | 16 +
gnm-1.0-8/gnm/R/print.profile.gnm.R | 15 +
gnm-1.0-8/gnm/R/print.summary.gnm.R | 27 +-
gnm-1.0-8/gnm/R/print.vcov.gnm.R | 15 +
gnm-1.0-8/gnm/R/profile.gnm.R | 24 +
gnm-1.0-8/gnm/R/proj.gnm.R | 17 +
gnm-1.0-8/gnm/R/psum.R | 15 +
gnm-1.0-8/gnm/R/quick.glm.fit.R | 17 +
gnm-1.0-8/gnm/R/quickRank.R | 21 +
gnm-1.0-8/gnm/R/residSVD.R | 15 +
gnm-1.0-8/gnm/R/residuals.gnm.R | 31 +-
gnm-1.0-8/gnm/R/rstandard.gnm.R | 15 +
gnm-1.0-8/gnm/R/rstudent.gnm.R | 17 +
gnm-1.0-8/gnm/R/se.R | 15 +
gnm-1.0-8/gnm/R/sumExpression.R | 15 +
gnm-1.0-8/gnm/R/summary.gnm.R | 34 ++
gnm-1.0-8/gnm/R/summary.meanResiduals.R | 15 +
gnm-1.0-8/gnm/R/termPredictors.R | 15 +
gnm-1.0-8/gnm/R/termPredictors.default.R | 15 +
gnm-1.0-8/gnm/R/termPredictors.gnm.R | 15 +
gnm-1.0-8/gnm/R/unlistOneLevel.R | 15 +
gnm-1.0-8/gnm/R/update.gnm.R | 18 +
gnm-1.0-8/gnm/R/updateLinear.R | 15 +
gnm-1.0-8/gnm/R/variable.names.gnm.R | 15 +
gnm-1.0-8/gnm/R/vcov.gnm.R | 18 +
gnm-1.0-8/gnm/R/wedderburn.R | 34 +-
gnm-1.0-8/gnm/R/weighted.MM.R | 15 +
gnm-1.0-8/gnm/R/weights.gnm.R | 15 +
gnm-1.0-8/gnm/build |only
gnm-1.0-8/gnm/data/House2001.rda |binary
gnm-1.0-8/gnm/data/backPain.rda |binary
gnm-1.0-8/gnm/data/barley.rda |binary
gnm-1.0-8/gnm/data/barleyHeights.rda |binary
gnm-1.0-8/gnm/data/cautres.rda |binary
gnm-1.0-8/gnm/data/erikson.rda |binary
gnm-1.0-8/gnm/data/friend.rda |binary
gnm-1.0-8/gnm/data/mentalHealth.rda |binary
gnm-1.0-8/gnm/data/voting.rda |binary
gnm-1.0-8/gnm/data/wheat.rda |binary
gnm-1.0-8/gnm/data/yaish.rda |binary
gnm-1.0-8/gnm/demo/gnm.R | 23 -
gnm-1.0-8/gnm/inst/NEWS | 37 ++
gnm-1.0-8/gnm/inst/doc/gnmOverview.R |only
gnm-1.0-8/gnm/inst/doc/gnmOverview.Rnw | 127 +++++----
gnm-1.0-8/gnm/inst/doc/gnmOverview.pdf |binary
gnm-1.0-8/gnm/man/Diag.Rd | 2
gnm-1.0-8/gnm/man/Dref.Rd | 2
gnm-1.0-8/gnm/man/Exp.Rd | 4
gnm-1.0-8/gnm/man/House2001.Rd | 3
gnm-1.0-8/gnm/man/MPinv.Rd | 2
gnm-1.0-8/gnm/man/Mult.Rd | 5
gnm-1.0-8/gnm/man/MultHomog.Rd | 1
gnm-1.0-8/gnm/man/Symm.Rd | 2
gnm-1.0-8/gnm/man/Topo.Rd | 1
gnm-1.0-8/gnm/man/anova.gnm.Rd | 4
gnm-1.0-8/gnm/man/asGnm.Rd | 1
gnm-1.0-8/gnm/man/backPain.Rd | 3
gnm-1.0-8/gnm/man/barley.Rd | 3
gnm-1.0-8/gnm/man/barleyHeights.Rd | 3
gnm-1.0-8/gnm/man/cautres.Rd | 3
gnm-1.0-8/gnm/man/checkEstimable.Rd | 3
gnm-1.0-8/gnm/man/confint.gnm.Rd | 5
gnm-1.0-8/gnm/man/erikson.Rd | 3
gnm-1.0-8/gnm/man/exitInfo.Rd | 1
gnm-1.0-8/gnm/man/expandCategorical.Rd | 2
gnm-1.0-8/gnm/man/friend.Rd | 3
gnm-1.0-8/gnm/man/getContrasts.Rd | 4
gnm-1.0-8/gnm/man/gnm.Rd | 3
gnm-1.0-8/gnm/man/instances.Rd | 1
gnm-1.0-8/gnm/man/meanResiduals.Rd | 2
gnm-1.0-8/gnm/man/mentalHealth.Rd | 3
gnm-1.0-8/gnm/man/nonlin.function.Rd | 1
gnm-1.0-8/gnm/man/ofInterest.Rd | 1
gnm-1.0-8/gnm/man/parameters.Rd | 1
gnm-1.0-8/gnm/man/pickCoef.Rd | 3
gnm-1.0-8/gnm/man/plot.gnm.Rd | 4
gnm-1.0-8/gnm/man/predict.gnm.Rd | 1
gnm-1.0-8/gnm/man/profile.gnm.Rd | 9
gnm-1.0-8/gnm/man/residSVD.Rd | 2
gnm-1.0-8/gnm/man/se.Rd | 3
gnm-1.0-8/gnm/man/summary.gnm.Rd | 4
gnm-1.0-8/gnm/man/vcov.gnm.Rd | 1
gnm-1.0-8/gnm/man/voting.Rd | 4
gnm-1.0-8/gnm/man/wedderburn.Rd | 5
gnm-1.0-8/gnm/man/wheat.Rd | 3
gnm-1.0-8/gnm/man/yaish.Rd | 4
gnm-1.0-8/gnm/src/gnm.c | 16 +
gnm-1.0-8/gnm/tests/RC.R | 1
gnm-1.0-8/gnm/tests/RC.Rout.save | 7
gnm-1.0-8/gnm/tests/RChomog.R | 2
gnm-1.0-8/gnm/tests/RChomog.Rout.save | 8
gnm-1.0-8/gnm/tests/biplot.R | 1
gnm-1.0-8/gnm/tests/biplot.Rout.save | 7
gnm-1.0-8/gnm/tests/bwt.R | 1
gnm-1.0-8/gnm/tests/bwt.Rout.save | 7
gnm-1.0-8/gnm/tests/diagonalRef.R | 1
gnm-1.0-8/gnm/tests/diagonalRef.Rout.save | 7
gnm-1.0-8/gnm/tests/doubleUnidiff.R | 1
gnm-1.0-8/gnm/tests/doubleUnidiff.Rout.save | 7
gnm-1.0-8/gnm/tests/gammi.R | 1
gnm-1.0-8/gnm/tests/gammi.Rout.save | 7
gnm-1.0-8/gnm/tests/logexcess.Rout.save | 6
gnm-1.0-8/gnm/tests/logistic.Rout.save | 6
gnm-1.0-8/gnm/tests/nls.Rout.save | 6
gnm-1.0-8/gnm/tests/stereotype.R | 1
gnm-1.0-8/gnm/tests/stereotype.Rout.save | 7
gnm-1.0-8/gnm/tests/unidiff.R | 1
gnm-1.0-8/gnm/tests/unidiff.Rout.save | 7
gnm-1.0-8/gnm/vignettes/gnmOverview.Rnw | 127 +++++----
gnm-1.0-8/gnm/vignettes/screenshot1.png |only
gnm-1.0-8/gnm/vignettes/screenshot2.png |only
gnm-1.0-8/gnm/vignettes/screenshot3.png |only
194 files changed, 2283 insertions(+), 630 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-23 1.1.1
2014-07-01 1.1
2014-06-21 1.0
Title: Visualization of Regression Models
Diff between visreg versions 2.1-1 dated 2015-02-25 and 2.2-0 dated 2015-04-22
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, randomForest, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
DESCRIPTION | 12 ++++++------
MD5 | 26 ++++++++++++++------------
NEWS | 5 +++++
R/Response.R | 28 ++++++++++++++++++++++++----
R/Terms.R | 1 +
R/makeYName.R |only
R/setupV.R | 6 ++++--
R/setupX.R | 2 +-
R/visreg.R | 12 +++++++++---
R/visreg2d.R | 13 +++++--------
R/visregLatticePlot.R | 7 ++-----
R/visregOverlayPlot.R | 5 +----
R/visregPlot.R | 13 ++++++++-----
inst/tests/mixed-models.R | 13 ++++++-------
tests/randomForest.R |only
15 files changed, 86 insertions(+), 57 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Diff between sspse versions 0.5 dated 2015-03-24 and 0.5-1 dated 2015-04-22
Description: An integrated set of tools to estimate the size of a networked population based on respondent-driven sampling data. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre, cph],
Krista J. Gile [aut, cph]
Maintainer: Mark S. Handcock
DESCRIPTION | 12 ++++++------
MD5 | 28 ++++++++++++++--------------
NAMESPACE | 2 +-
R/plot.sspse.R | 2 +-
R/print.summary.sspse.R | 2 +-
R/sspse.utilities.R | 26 +++++++++++++++++++++-----
R/summary.size.R | 2 +-
inst/CITATION | 6 +++---
man/beginparallel.Rd | 2 +-
man/dsizeprior.Rd | 2 +-
man/plot.sspse.Rd | 2 +-
man/posteriorsize.Rd | 2 +-
man/print.summary.sspse.Rd | 2 +-
man/sspse-package.Rd | 2 +-
man/summary.sspse.Rd | 2 +-
15 files changed, 55 insertions(+), 39 deletions(-)
Title: Simulation of Evolutionary and Epidemiological Dynamics
Diff between seedy versions 1.0 dated 2014-10-16 and 1.2 dated 2015-04-22
Description: Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.
Author: Colin Worby
Maintainer: Colin Worby
DESCRIPTION | 8 ++++----
MD5 | 26 ++++++++++++++++----------
R/diversity.range.R | 4 ++--
R/flat.r |only
R/hump.r |only
R/plotoutbreak.R | 6 +++++-
R/simfixoutbreak.r |only
R/simulateoutbreak.R | 14 ++++++++++----
R/simulatepopulation.R | 21 ++++++++++++---------
R/transroutes.r | 3 ++-
man/diversity.range.Rd | 10 +++++-----
man/flat.Rd |only
man/hump.Rd |only
man/seedy-package.Rd | 4 ++--
man/simfixoutbreak.Rd |only
man/simulateoutbreak.Rd | 13 +++++++++++--
man/simulatepopulation.Rd | 25 ++++++++++++++++---------
17 files changed, 85 insertions(+), 49 deletions(-)
Title: Global Soil Information Facilities
Diff between GSIF versions 0.4-4 dated 2015-01-30 and 0.4-5 dated 2015-04-22
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 12 ++--
MD5 | 58 ++++++++++-----------
NAMESPACE | 6 +-
R/AAAA.R | 2
R/AWCPTF.R | 2
R/LRI.R | 2
R/OCSKGM.R | 2
R/SoilGrid.validator.R |only
R/extract.list.R | 29 ++++++----
R/fit.gstatModel.R | 35 ++++++++----
R/fit.regModel.R | 107 ++++++++++++++++++++++++++-------------
R/fit.vgmModel.R | 36 ++++++-------
R/predict.gstatModel.R | 77 +++++++++++-----------------
R/spsample.prob.R | 6 +-
data/afsp.rda |binary
man/AWCPTF.Rd | 4 -
man/ERDICM.Rd | 2
man/FAO.SoilProfileCollection.Rd | 11 +---
man/LRI.Rd | 6 ++
man/OCSKGM.Rd | 2
man/SoilGrid.validator.Rd |only
man/afsp.Rd | 75 ++++++---------------------
man/cookfarm.Rd | 13 +++-
man/edgeroi.Rd | 4 -
man/extract.Rd | 5 +
man/fit.gstatModel.Rd | 63 +++++++++++-----------
man/fit.regModel.Rd | 26 ++++++++-
man/fit.vgmModel.Rd | 2
man/gstatModel.Rd | 2
man/mpspline.Rd | 5 -
man/spsample.prob.Rd | 14 ++---
31 files changed, 325 insertions(+), 283 deletions(-)
Title: Gender Prediction Based on First Names
Diff between genderizeR versions 1.0.0 dated 2015-02-08 and 1.1.0 dated 2015-04-22
Description: Utilizes the genderize.io API to predict gender from first
names extracted from a text vector. The accuracy of prediction could be
controlled by two parameters: counts of a first name in the database and
probability of prediction.
Author: Kamil Wais [aut, cre]
Maintainer: Kamil Wais
DESCRIPTION | 13 ++-
LICENSE | 2
MD5 | 48 +++++++-------
NAMESPACE | 2
NEWS | 52 +++++++++++----
R/findGivenNames.R | 87 +++++++++++++++++++++----
R/genderizeAPI.R | 136 +++++++++++++++++++++++++++++++---------
R/genderizeR.R | 2
R/numberOfNames.R | 8 +-
README.md | 43 +++++-------
man/authorships.Rd | 2
man/classificatonErrors.Rd | 2
man/findGivenNames.Rd | 9 ++
man/genderize.Rd | 2
man/genderizeAPI.Rd | 8 +-
man/genderizeBootstrapError.Rd | 2
man/genderizePredict.Rd | 2
man/genderizeR.Rd | 2
man/genderizeTrain.Rd | 2
man/givenNamesDB_authorships.Rd | 2
man/givenNamesDB_titles.Rd | 2
man/numberOfNames.Rd | 2
man/textPrepare.Rd | 2
man/titles.Rd | 2
tests |only
25 files changed, 299 insertions(+), 135 deletions(-)
Title: Fast, Exact Bootstrap Principal Component Analysis for High
Dimensional Data
Diff between bootSVD versions 0.1 dated 2014-07-21 and 0.2 dated 2015-04-22
Description: Implements fast, exact bootstrap Principal Component Analysis and
Singular Value Decompositions for high dimensional data, as described in
(arxiv.org/abs/1405.0922). For data matrices that are too large to operate
on in memory, users can input objects with class 'ff' (see the 'ff'
package), where the actual data is stored on disk. In response, this
package will implement a block matrix algebra procedure for calculating the
principal components (PCs) and bootstrap PCs. Depending on options set by
the user, the 'parallel' package can be used to parallelize the calculation of
the bootstrap PCs.
Author: Aaron Fisher
Maintainer: Aaron Fisher
bootSVD-0.1/bootSVD/man/reindexDsByK.Rd |only
bootSVD-0.1/bootSVD/man/reindexPCsByK.Rd |only
bootSVD-0.2/bootSVD/DESCRIPTION | 16
bootSVD-0.2/bootSVD/MD5 | 41 -
bootSVD-0.2/bootSVD/NAMESPACE | 8
bootSVD-0.2/bootSVD/R/bootstrap_functions.R | 746 ++++++++++++++++-------
bootSVD-0.2/bootSVD/README.md | 5
bootSVD-0.2/bootSVD/man/As2Vs.Rd | 50 -
bootSVD-0.2/bootSVD/man/EEG_leadingV.Rd | 27
bootSVD-0.2/bootSVD/man/EEG_mu.Rd | 27
bootSVD-0.2/bootSVD/man/EEG_score_var.Rd | 30
bootSVD-0.2/bootSVD/man/bootPCA.Rd | 14
bootSVD-0.2/bootSVD/man/bootSVD.Rd | 253 +++----
bootSVD-0.2/bootSVD/man/bootSVD_LD.Rd | 93 --
bootSVD-0.2/bootSVD/man/fastSVD.Rd | 44 -
bootSVD-0.2/bootSVD/man/ffmatrixmult.Rd |only
bootSVD-0.2/bootSVD/man/genBootIndeces.Rd | 22
bootSVD-0.2/bootSVD/man/genQ.Rd | 15
bootSVD-0.2/bootSVD/man/getMomentsAndMomentCI.Rd | 59 -
bootSVD-0.2/bootSVD/man/os.Rd | 6
bootSVD-0.2/bootSVD/man/qrSVD.Rd | 37 -
bootSVD-0.2/bootSVD/man/reindexMatricesByK.Rd |only
bootSVD-0.2/bootSVD/man/reindexVectorsByK.Rd |only
bootSVD-0.2/bootSVD/man/simEEG.Rd | 63 -
24 files changed, 848 insertions(+), 708 deletions(-)
Title: Ensure Values at Runtime
Diff between ensurer versions 1.0 dated 2014-11-18 and 1.1 dated 2015-04-21
Description: Add simple runtime contracts to R values. These ensure that values
fulfil certain conditions and will raise appropriate errors if they do not.
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache
DESCRIPTION | 14 ++--
LICENSE | 4 -
MD5 | 38 ++++++------
NAMESPACE | 4 +
NEWS |only
R/check_that.R |only
R/ensure_that.R | 20 ++++--
R/ensurer.R | 54 +++++++++---------
R/ensurer_env.R | 18 +++++-
R/ensures_that.R | 113 ++++++++++++++++++++++++++------------
R/utility_functions.R | 13 +++-
README.md | 63 ++++++++++++---------
build/vignette.rds |binary
inst/doc/ensurer.R | 18 +++---
inst/doc/ensurer.Rmd | 49 +++++++++-------
inst/doc/ensurer.html | 47 +++++++++------
man/ensurer.Rd | 57 +++++++++----------
man/ensures_that.Rd | 78 +++++++++++++++-----------
man/print.ensurer.Rd | 3 -
tests/testthat/test-ensure_that.r | 10 +++
vignettes/ensurer.Rmd | 37 +++++++-----
21 files changed, 387 insertions(+), 253 deletions(-)
Title: Efficient Effect Size Computation
Diff between effsize versions 0.5.2 dated 2014-08-28 and 0.5.4 dated 2015-04-21
Description: A collection of functions to compute the standardized
effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A).
The computation algorithms have been optimized to allow efficient computation even
with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano
DESCRIPTION | 23 +++++++++++++----------
MD5 | 18 +++++++++++-------
NAMESPACE | 7 +++++++
R/CliffDelta.R | 8 ++++----
R/CohenD.R | 14 +++++++++++++-
R/VD_A.R | 2 +-
man/cohen.d.Rd | 4 ++++
man/effsize-package.Rd | 17 +++++------------
tests |only
9 files changed, 58 insertions(+), 35 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions in
Causal Models
Diff between causaleffect versions 1.0 dated 2014-09-25 and 1.1 dated 2015-04-21
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka
causaleffect-1.0/causaleffect/R/anRpackage-internal.R |only
causaleffect-1.1/causaleffect/DESCRIPTION | 12 +++---
causaleffect-1.1/causaleffect/MD5 | 16 ++++----
causaleffect-1.1/causaleffect/NAMESPACE | 2 -
causaleffect-1.1/causaleffect/R/causal.effect.R | 22 +++++++++---
causaleffect-1.1/causaleffect/R/getExpression.probability.R | 6 +--
causaleffect-1.1/causaleffect/R/id.R | 16 ++++----
causaleffect-1.1/causaleffect/R/idc.R |only
causaleffect-1.1/causaleffect/man/causal.effect.Rd | 20 +++++++---
causaleffect-1.1/causaleffect/man/causaleffect-package.Rd | 22 +++++++-----
10 files changed, 70 insertions(+), 46 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.650.1.1 dated 2015-02-26 and 0.5.000.0 dated 2015-04-21
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 21 +
DESCRIPTION | 8
MD5 | 132 +++----
build/vignette.rds |binary
inst/NEWS.Rd | 28 +
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/armadillo | 32 +
inst/include/armadillo_bits/Col_bones.hpp | 10
inst/include/armadillo_bits/Col_meat.hpp | 60 ++-
inst/include/armadillo_bits/Cube_meat.hpp | 20 -
inst/include/armadillo_bits/Mat_bones.hpp | 8
inst/include/armadillo_bits/Mat_meat.hpp | 144 +++++++
inst/include/armadillo_bits/Op_bones.hpp | 3
inst/include/armadillo_bits/Proxy.hpp | 48 ++
inst/include/armadillo_bits/Row_bones.hpp | 10
inst/include/armadillo_bits/Row_meat.hpp | 60 ++-
inst/include/armadillo_bits/SpCol_bones.hpp | 41 --
inst/include/armadillo_bits/SpCol_meat.hpp | 157 --------
inst/include/armadillo_bits/SpMat_bones.hpp | 10
inst/include/armadillo_bits/SpMat_meat.hpp | 78 +++-
inst/include/armadillo_bits/SpProxy.hpp | 2
inst/include/armadillo_bits/SpRow_bones.hpp | 40 --
inst/include/armadillo_bits/SpRow_meat.hpp | 180 ---------
inst/include/armadillo_bits/arma_cmath.hpp | 6
inst/include/armadillo_bits/arma_config.hpp | 11
inst/include/armadillo_bits/arma_ostream_meat.hpp | 24 +
inst/include/armadillo_bits/arma_version.hpp | 12
inst/include/armadillo_bits/atlas_wrapper.hpp | 56 +-
inst/include/armadillo_bits/auxlib_meat.hpp | 94 ++++-
inst/include/armadillo_bits/compiler_setup.hpp | 28 +
inst/include/armadillo_bits/config.hpp | 52 +-
inst/include/armadillo_bits/debug.hpp | 119 +++++-
inst/include/armadillo_bits/diagview_meat.hpp | 10
inst/include/armadillo_bits/diskio_meat.hpp | 194 +++++++++-
inst/include/armadillo_bits/field_meat.hpp | 10
inst/include/armadillo_bits/fn_accu.hpp | 78 +++-
inst/include/armadillo_bits/fn_all.hpp | 11
inst/include/armadillo_bits/fn_any.hpp | 11
inst/include/armadillo_bits/fn_eigs_gen.hpp | 2
inst/include/armadillo_bits/fn_elem.hpp | 14
inst/include/armadillo_bits/fn_join.hpp | 55 ++
inst/include/armadillo_bits/fn_n_unique.hpp | 2
inst/include/armadillo_bits/fn_nonzeros.hpp |only
inst/include/armadillo_bits/fn_norm_sparse.hpp | 1
inst/include/armadillo_bits/fn_randg.hpp | 9
inst/include/armadillo_bits/fn_repmat.hpp | 18
inst/include/armadillo_bits/fn_sort_index.hpp | 271 --------------
inst/include/armadillo_bits/fn_spsolve.hpp |only
inst/include/armadillo_bits/fn_svds.hpp |only
inst/include/armadillo_bits/forward_bones.hpp | 54 ++
inst/include/armadillo_bits/gmm_diag_meat.hpp | 17
inst/include/armadillo_bits/include_superlu.hpp |only
inst/include/armadillo_bits/mtOp_bones.hpp | 13
inst/include/armadillo_bits/mul_gemm.hpp | 2
inst/include/armadillo_bits/mul_gemv.hpp | 2
inst/include/armadillo_bits/op_nonzeros_bones.hpp |only
inst/include/armadillo_bits/op_nonzeros_meat.hpp |only
inst/include/armadillo_bits/op_shuffle_meat.hpp | 2
inst/include/armadillo_bits/op_sort_index_bones.hpp |only
inst/include/armadillo_bits/op_sort_index_meat.hpp |only
inst/include/armadillo_bits/sp_auxlib_bones.hpp | 24 +
inst/include/armadillo_bits/sp_auxlib_meat.hpp | 374 +++++++++++++++++++-
inst/include/armadillo_bits/spdiagview_bones.hpp |only
inst/include/armadillo_bits/spdiagview_meat.hpp |only
inst/include/armadillo_bits/spglue_join_bones.hpp |only
inst/include/armadillo_bits/spglue_join_meat.hpp |only
inst/include/armadillo_bits/spop_misc_bones.hpp | 25 +
inst/include/armadillo_bits/spop_misc_meat.hpp | 80 ++++
inst/include/armadillo_bits/subview_meat.hpp | 8
inst/include/armadillo_bits/superlu_bones.hpp |only
inst/include/armadillo_bits/superlu_wrapper.hpp |only
inst/include/armadillo_bits/typedef_elem.hpp | 37 +
inst/include/armadillo_bits/unwrap.hpp | 4
74 files changed, 1874 insertions(+), 948 deletions(-)
Title: Calculate the NLTT Statistic
Diff between nLTT versions 1.0 dated 2015-01-19 and 1.1 dated 2015-04-21
Description: Provides functions to calculate the normalised Lineage-Through-Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
Author: Thijs Janzen
Maintainer: Thijs Janzen
nLTT-1.0/nLTT/man/normLTTdiffABS.Rd |only
nLTT-1.0/nLTT/man/normLTTdiffSQ.Rd |only
nLTT-1.1/nLTT/DESCRIPTION | 12 ++++++------
nLTT-1.1/nLTT/MD5 | 15 +++++++--------
nLTT-1.1/nLTT/R/nLTTDiff.R | 10 ++++++++++
nLTT-1.1/nLTT/man/ABC_SMC_nLTT.Rd | 2 +-
nLTT-1.1/nLTT/man/MCMC_nLTT.Rd | 2 +-
nLTT-1.1/nLTT/man/nLTT-internal.Rd | 4 +++-
nLTT-1.1/nLTT/man/nLTT-package.Rd | 25 ++++++++++++++++---------
nLTT-1.1/nLTT/man/nLTTstat.Rd |only
10 files changed, 44 insertions(+), 26 deletions(-)
Title: Implementation of Sampling Formulas for the Unified Neutral
Model of Biodiversity and Biogeography, with or without Guild
Structure
Diff between GUILDS versions 1.2 dated 2014-09-07 and 1.2.1 dated 2015-04-21
Description: The GUILDS package combines a range of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
Author: Thijs Janzen
Maintainer: Thijs Janzen
DESCRIPTION | 16 ++++++++--------
MD5 | 14 +++++++-------
man/GUILDS-package.Rd | 17 +++++++++--------
man/logLikelihood.ESF.Rd | 2 +-
man/logLikelihood.Guilds.Conditional.Rd | 4 ++--
man/logLikelihood.Guilds.Rd | 6 +++---
man/maxLikelihood.Guilds.Conditional.Rd | 2 +-
man/maxLikelihood.Guilds.Rd | 2 +-
8 files changed, 32 insertions(+), 31 deletions(-)
Title: Another Object Orientation System
Diff between aoos versions 0.1.0 dated 2014-12-19 and 0.2.0 dated 2015-04-21
Description: Another implementation of object-orientation in R. Has reference
semantics and is built around S4.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz
DESCRIPTION | 20 +--
MD5 | 61 +++++++----
NAMESPACE | 11 +-
NEWS | 31 +++++
R/Accessor.R |only
R/Binary.R |only
R/Class.R |only
R/Private.R |only
R/Show.R |only
R/aoos.R | 34 ++----
R/defineClass.R | 83 ++++++++++-----
R/public-interfaces.R | 30 +++++
build/vignette.rds |binary
inst/doc/Introduction.R | 108 --------------------
inst/doc/Introduction.Rmd | 162 +------------------------------
inst/doc/Introduction.html | 177 +---------------------------------
inst/doc/aoosClasses.R |only
inst/doc/aoosClasses.Rmd |only
inst/doc/aoosClasses.html |only
inst/doc/referenceClasses.R |only
inst/doc/referenceClasses.Rmd |only
inst/doc/referenceClasses.html |only
man/Accessor.Rd |only
man/Binary.Rd |only
man/Class.Rd |only
man/Private.Rd |only
man/Show.Rd |only
man/aoos.Rd | 2
man/defineClass.Rd | 31 ++++-
man/publicInterface.Rd | 8 +
tests/testthat.R | 2
tests/testthat/test-Accessor.R |only
tests/testthat/test-Binary.R |only
tests/testthat/test-Class.R |only
tests/testthat/test-basics.R | 82 +++++++++++++--
tests/testthat/test-inheritance.R | 46 ++++++--
tests/testthat/test-publicInterface.R | 68 ++++++++++++-
tests/testthat/test-self.R | 8 -
tests/testthat/test-summary.R | 10 -
vignettes/Introduction.Rmd | 162 +------------------------------
vignettes/aoosClasses.Rmd |only
vignettes/referenceClasses.Rmd |only
42 files changed, 426 insertions(+), 710 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Diff between sitar versions 1.0.1 dated 2014-06-27 and 1.0.2 dated 2015-04-21
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole
sitar-1.0.1/sitar/man/funcall.rd |only
sitar-1.0.1/sitar/man/makess.rd |only
sitar-1.0.1/sitar/man/mplot.rd |only
sitar-1.0.1/sitar/man/recalib.rd |only
sitar-1.0.1/sitar/man/xaxsd.rd |only
sitar-1.0.2/sitar/DESCRIPTION | 16 +-
sitar-1.0.2/sitar/MD5 | 61 ++++----
sitar-1.0.2/sitar/NAMESPACE | 8 -
sitar-1.0.2/sitar/NEWS | 34 ++++
sitar-1.0.2/sitar/R/LMSfit.R |only
sitar-1.0.2/sitar/R/lms2z.R | 10 -
sitar-1.0.2/sitar/R/mplot.R | 16 +-
sitar-1.0.2/sitar/R/plot.sitar.R | 60 +++++---
sitar-1.0.2/sitar/R/predict.R |only
sitar-1.0.2/sitar/R/sitar.R | 85 ++++++-----
sitar-1.0.2/sitar/R/sitarlib.R | 196 +++++----------------------
sitar-1.0.2/sitar/R/update.sitar.R |only
sitar-1.0.2/sitar/man/LMSfit.Rd |only
sitar-1.0.2/sitar/man/cLMS.Rd | 4
sitar-1.0.2/sitar/man/funcall.Rd |only
sitar-1.0.2/sitar/man/getData.sitar.Rd |only
sitar-1.0.2/sitar/man/getVarCov.sitar.Rd |only
sitar-1.0.2/sitar/man/heights.Rd | 25 +++
sitar-1.0.2/sitar/man/lms2z.Rd | 14 -
sitar-1.0.2/sitar/man/makess.Rd |only
sitar-1.0.2/sitar/man/mplot.Rd |only
sitar-1.0.2/sitar/man/plot.sitar.Rd | 10 -
sitar-1.0.2/sitar/man/plotclean.Rd | 10 -
sitar-1.0.2/sitar/man/predict.sitar.Rd |only
sitar-1.0.2/sitar/man/print.summary.sitar.Rd | 2
sitar-1.0.2/sitar/man/recalib.Rd |only
sitar-1.0.2/sitar/man/sitar-package.Rd | 40 +++--
sitar-1.0.2/sitar/man/sitar.Rd | 43 +++--
sitar-1.0.2/sitar/man/summary.sitar.Rd | 8 -
sitar-1.0.2/sitar/man/uk90.Rd | 12 +
sitar-1.0.2/sitar/man/ukwhopt.Rd | 17 +-
sitar-1.0.2/sitar/man/velout.Rd | 7
sitar-1.0.2/sitar/man/who06.Rd | 4
sitar-1.0.2/sitar/man/xaxsd.Rd |only
sitar-1.0.2/sitar/man/y2plot.Rd | 8 -
40 files changed, 348 insertions(+), 342 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Diff between RDML versions 0.8-3 dated 2015-04-08 and 0.8-4 dated 2015-04-21
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram
visualization for the structure of RDML object.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
CHANGELOG | 6
DESCRIPTION | 17 +-
MD5 | 30 +--
NAMESPACE | 24 +-
R/RDML.AsDendrogram.R | 2
R/RDML.Merge.R | 4
R/RDML.R | 10 -
R/RDML.init.R | 242 ++++++++++++++++------------
man/RDML.class.Rd | 378 ++++++++++++++++++++++-----------------------
man/asdendrogram-method.Rd | 60 +++----
man/astable-method.Rd | 156 +++++++++---------
man/getfdata-method.Rd | 114 ++++++-------
man/merge-method.Rd | 50 ++---
man/names.RDML.Rd | 48 ++---
man/new-method.Rd | 78 ++++-----
man/setfdata-method.Rd | 102 ++++++------
16 files changed, 678 insertions(+), 643 deletions(-)
Title: Running 'MLwiN' from Within R
Diff between R2MLwiN versions 0.8-0 dated 2015-03-04 and 0.8-1 dated 2015-04-21
Description: An R command interface to the 'MLwiN' multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang
DESCRIPTION | 18 -
MD5 | 38 +-
NEWS | 26 +
R/Formula.translate.R | 13
R/predLines.r | 47 +-
R/prior2macro.R | 24 -
R/runMLwiN.R | 785 +++++++++++++++++++++++++-------------------------
R/trajectories.R | 15
R/write.IGLS.R | 2
R/write.MCMC.R | 20 -
R/ws2foreign.R | 32 +-
demo/MCMCGuide07.R | 2
demo/MCMCGuide10.R | 2
demo/MCMCGuide17.R | 2
demo/MCMCGuide18.R | 4
demo/MCMCGuide23.R | 2
demo/MCMCGuide24.R | 2
demo/MCMCGuide25.R | 2
man/prior2macro.Rd | 11
man/runMLwiN.Rd | 42 +-
20 files changed, 578 insertions(+), 511 deletions(-)
Title: Advanced Tables for Markdown/HTML
Diff between htmlTable versions 1.2 dated 2015-03-03 and 1.3 dated 2015-04-21
Description: Tables with state-of-the-art layout elements such as
row spanners, column spanners, table spanners, zebra striping,
and more. While allowing advanced layout, the underlying CSS structure is
simple in order to maximize compatibility with word processors such as
MS Word or LibreOffice.
The package also contains a few text formatting functions that help outputting
text compatible with HTML/LaTeX.
Author: Max Gordon
Maintainer: Max Gordon
DESCRIPTION | 10 -
MD5 | 82 ++++-----
NAMESPACE | 2
NEWS | 6
R/htmlTable.R | 65 +++++--
R/htmlTable_helpers.R | 18 +-
R/txtFrmt.R | 75 +++++----
build/vignette.rds |binary
inst/doc/general.R | 38 +++-
inst/doc/general.Rmd | 72 ++++++--
inst/doc/general.html | 330 +++++++++++++++++++++++++++++-----------
inst/doc/tables.html | 24 +-
man/SCB.Rd | 2
man/htmlTable.Rd | 2
man/outputInt.Rd | 2
man/prAddCells.Rd | 2
man/prAddSemicolon2StrEnd.Rd | 2
man/prAttr4RgroupAdd.Rd | 2
man/prGetAlign.Rd | 2
man/prGetCgroupHeader.Rd | 2
man/prGetRgroupLine.Rd | 2
man/prGetRowlabelPos.Rd | 2
man/prGetStyle.Rd | 2
man/prGetThead.Rd | 2
man/prMergeClr.Rd | 2
man/prPrepareAlign.Rd | 2
man/prPrepareCgroup.Rd | 2
man/prPrepareColors.Rd | 2
man/prPrepareCss.Rd | 2
man/prSkipRownames.Rd | 2
man/prTblNo.Rd | 2
man/pvalueFormatter.Rd | 2
man/splitLines4Table.Rd | 2
man/tblNoLast.Rd | 2
man/tblNoNext.Rd | 2
man/txtInt.Rd | 2
man/txtMergeLines.Rd | 2
man/txtPval.Rd | 2
man/txtRound.Rd | 13 -
tests/testthat/test-htmlTable.R | 12 +
tests/testthat/test-txtFrmt.R | 12 +
vignettes/general.Rmd | 72 ++++++--
42 files changed, 609 insertions(+), 274 deletions(-)
Title: Tools for Sotkanet Open Data Portal
Diff between sotkanet versions 0.9.03 dated 2014-04-07 and 0.9.10 dated 2015-04-21
Description: Tools to download data from the Sotkanet open data portal.
Author: Leo Lahti, Einari Happonen, Juuso Parkkinen, Joona Lehtomaki
Maintainer: Leo Lahti
sotkanet-0.9.03/sotkanet/README.md |only
sotkanet-0.9.03/sotkanet/inst/NEWS |only
sotkanet-0.9.03/sotkanet/inst/blog |only
sotkanet-0.9.03/sotkanet/inst/extras |only
sotkanet-0.9.03/sotkanet/inst/vign |only
sotkanet-0.9.03/sotkanet/vignettes/figure |only
sotkanet-0.9.10/sotkanet/DESCRIPTION | 20
sotkanet-0.9.10/sotkanet/LICENSE | 4
sotkanet-0.9.10/sotkanet/MD5 | 57 -
sotkanet-0.9.10/sotkanet/NAMESPACE | 4
sotkanet-0.9.10/sotkanet/R/firstlib.R | 18
sotkanet-0.9.10/sotkanet/R/internal.R | 90 -
sotkanet-0.9.10/sotkanet/R/sotkanet-package.R | 4
sotkanet-0.9.10/sotkanet/R/sotkanet.R | 75 -
sotkanet-0.9.10/sotkanet/README |only
sotkanet-0.9.10/sotkanet/build/vignette.rds |binary
sotkanet-0.9.10/sotkanet/inst/CITATION | 5
sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.R | 70 -
sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.Rmd | 52 -
sotkanet-0.9.10/sotkanet/inst/doc/sotkanet_tutorial.html | 508 ++++++----
sotkanet-0.9.10/sotkanet/man/GetDataSotkanet.Rd | 30
sotkanet-0.9.10/sotkanet/man/GetDataSotkanetSingleIndicator.Rd | 27
sotkanet-0.9.10/sotkanet/man/SotkanetCollect.Rd | 13
sotkanet-0.9.10/sotkanet/man/SotkanetData.Rd | 17
sotkanet-0.9.10/sotkanet/man/SotkanetIndicators.Rd | 20
sotkanet-0.9.10/sotkanet/man/SotkanetRegions.Rd | 11
sotkanet-0.9.10/sotkanet/man/base_url.Rd |only
sotkanet-0.9.10/sotkanet/man/sotkanet-package.Rd | 19
sotkanet-0.9.10/sotkanet/man/sotkanet.csv_query.Rd | 9
sotkanet-0.9.10/sotkanet/man/sotkanet.json_query.Rd | 9
sotkanet-0.9.10/sotkanet/vignettes/sotkanet_tutorial.Rmd | 52 -
31 files changed, 659 insertions(+), 455 deletions(-)
Title: Manage a CRAN-Style Local Repository
Diff between managelocalrepo versions 0.1.4 dated 2014-10-25 and 0.1.5 dated 2015-04-21
More information about managelocalrepo at CRAN
Description: This will allow easier management of a CRAN-style repository on
local networks (i.e. not on CRAN). This might be necessary where hosted
packages contain intellectual property owned by a corporation.
Author: Imanuel Costigan
Maintainer: Imanuel Costigan
DESCRIPTION | 10 +--
MD5 | 20 +++----
NAMESPACE | 2
NEWS | 4 +
R/manage_local_repo.R | 108 +++++++++++++++++++++----------------------
README.md | 10 +--
man/create_terminal_dir.Rd | 3 -
man/full_repo_dir.Rd | 3 -
man/managelocalrepo.Rd | 3 -
man/quick_release_package.Rd | 3 -
man/release_package.Rd | 5 +
11 files changed, 90 insertions(+), 81 deletions(-)
Permanent link
Title: Tools for Splitting, Applying and Combining Data
Diff between plyr versions 1.8.1 dated 2014-02-26 and 1.8.2 dated 2015-04-21
Description: A set of tools that solves a common set of problems: you
need to break a big problem down into manageable pieces, operate on each
piece and then put all the pieces back together. For example, you might
want to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of 'plyr' has been generously supported
by 'Becton Dickinson'.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham
plyr-1.8.1/plyr/NEWS |only
plyr-1.8.1/plyr/R/utils-functional.r |only
plyr-1.8.1/plyr/inst/tests |only
plyr-1.8.1/plyr/tests/test-all.R |only
plyr-1.8.2/plyr/DESCRIPTION | 39 +--
plyr-1.8.2/plyr/MD5 | 334 +++++++++++++-------------
plyr-1.8.2/plyr/NAMESPACE | 3
plyr-1.8.2/plyr/R/RcppExports.R | 5
plyr-1.8.2/plyr/R/a_ply.r | 4
plyr-1.8.2/plyr/R/aaply.r | 3
plyr-1.8.2/plyr/R/adply.r | 17 +
plyr-1.8.2/plyr/R/d_ply.r | 4
plyr-1.8.2/plyr/R/daply.r | 2
plyr-1.8.2/plyr/R/data-frame.r | 6
plyr-1.8.2/plyr/R/ddply.r | 3
plyr-1.8.2/plyr/R/dimensions.r | 1
plyr-1.8.2/plyr/R/dlply.r | 2
plyr-1.8.2/plyr/R/each.r | 13 -
plyr-1.8.2/plyr/R/here.r | 2
plyr-1.8.2/plyr/R/id.r | 4
plyr-1.8.2/plyr/R/idataframe.r | 3
plyr-1.8.2/plyr/R/indexed.r | 2
plyr-1.8.2/plyr/R/join-all.r | 2
plyr-1.8.2/plyr/R/join.r | 2
plyr-1.8.2/plyr/R/l_ply.r | 57 +++-
plyr-1.8.2/plyr/R/ldply.r | 5
plyr-1.8.2/plyr/R/liply.r | 18 -
plyr-1.8.2/plyr/R/list-to-array.r | 3
plyr-1.8.2/plyr/R/llply.r | 4
plyr-1.8.2/plyr/R/mutate.r | 2
plyr-1.8.2/plyr/R/name-rows.r | 1
plyr-1.8.2/plyr/R/parallel.r | 15 -
plyr-1.8.2/plyr/R/plyr-deprecated.r |only
plyr-1.8.2/plyr/R/plyr.r | 2
plyr-1.8.2/plyr/R/progress-time.r | 2
plyr-1.8.2/plyr/R/progress.r | 20 -
plyr-1.8.2/plyr/R/quote.r | 7
plyr-1.8.2/plyr/R/rbind-fill-matrix.r | 2
plyr-1.8.2/plyr/R/rbind-fill.r | 10
plyr-1.8.2/plyr/R/rdply.r | 16 -
plyr-1.8.2/plyr/R/rename.r | 17 +
plyr-1.8.2/plyr/R/rlply.r | 8
plyr-1.8.2/plyr/R/splitter-a.r | 30 ++
plyr-1.8.2/plyr/R/summarise.r | 4
plyr-1.8.2/plyr/R/take.r | 2
plyr-1.8.2/plyr/R/try.r | 10
plyr-1.8.2/plyr/R/utils.r | 7
plyr-1.8.2/plyr/README.md | 2
plyr-1.8.2/plyr/man/a_ply.Rd | 72 ++---
plyr-1.8.2/plyr/man/aaply.Rd | 79 +++---
plyr-1.8.2/plyr/man/adply.Rd | 90 +++----
plyr-1.8.2/plyr/man/alply.Rd | 69 ++---
plyr-1.8.2/plyr/man/amv_dim.Rd | 5
plyr-1.8.2/plyr/man/amv_dimnames.Rd | 5
plyr-1.8.2/plyr/man/arrange.Rd | 9
plyr-1.8.2/plyr/man/as.data.frame.function.Rd | 18 -
plyr-1.8.2/plyr/man/as.list.split.Rd | 7
plyr-1.8.2/plyr/man/as.quoted.Rd | 11
plyr-1.8.2/plyr/man/baseball.Rd | 44 ++-
plyr-1.8.2/plyr/man/colwise.Rd | 12
plyr-1.8.2/plyr/man/compact.Rd | 5
plyr-1.8.2/plyr/man/count.Rd | 13 -
plyr-1.8.2/plyr/man/create_progress_bar.Rd | 8
plyr-1.8.2/plyr/man/d_ply.Rd | 62 ++--
plyr-1.8.2/plyr/man/daply.Rd | 59 ++--
plyr-1.8.2/plyr/man/ddply.Rd | 66 ++---
plyr-1.8.2/plyr/man/defaults.Rd | 7
plyr-1.8.2/plyr/man/desc.Rd | 5
plyr-1.8.2/plyr/man/dims.Rd | 5
plyr-1.8.2/plyr/man/dlply.Rd | 54 ++--
plyr-1.8.2/plyr/man/each.Rd | 7
plyr-1.8.2/plyr/man/empty.Rd | 5
plyr-1.8.2/plyr/man/eval.quoted.Rd | 8
plyr-1.8.2/plyr/man/failwith.Rd | 9
plyr-1.8.2/plyr/man/get-split.Rd | 9
plyr-1.8.2/plyr/man/here.Rd | 5
plyr-1.8.2/plyr/man/id.Rd | 7
plyr-1.8.2/plyr/man/id_var.Rd | 3
plyr-1.8.2/plyr/man/idata.frame.Rd | 5
plyr-1.8.2/plyr/man/indexed_array.Rd | 7
plyr-1.8.2/plyr/man/indexed_df.Rd | 10
plyr-1.8.2/plyr/man/is.discrete.Rd | 5
plyr-1.8.2/plyr/man/is.formula.Rd | 3
plyr-1.8.2/plyr/man/isplit2.Rd | 9
plyr-1.8.2/plyr/man/join.Rd | 24 -
plyr-1.8.2/plyr/man/join.keys.Rd | 9
plyr-1.8.2/plyr/man/join_all.Rd | 22 -
plyr-1.8.2/plyr/man/l_ply.Rd | 52 ++--
plyr-1.8.2/plyr/man/laply.Rd | 48 +--
plyr-1.8.2/plyr/man/ldply.Rd | 71 ++---
plyr-1.8.2/plyr/man/liply.Rd | 22 -
plyr-1.8.2/plyr/man/list_to_array.Rd | 11
plyr-1.8.2/plyr/man/list_to_dataframe.Rd | 12
plyr-1.8.2/plyr/man/list_to_vector.Rd | 5
plyr-1.8.2/plyr/man/llply.Rd | 42 +--
plyr-1.8.2/plyr/man/loop_apply.Rd | 9
plyr-1.8.2/plyr/man/m_ply.Rd | 54 ++--
plyr-1.8.2/plyr/man/maply.Rd | 64 ++--
plyr-1.8.2/plyr/man/mapvalues.Rd | 13 -
plyr-1.8.2/plyr/man/match_df.Rd | 11
plyr-1.8.2/plyr/man/mdply.Rd | 67 ++---
plyr-1.8.2/plyr/man/mlply.Rd | 56 ++--
plyr-1.8.2/plyr/man/mutate.Rd | 8
plyr-1.8.2/plyr/man/name_rows.Rd | 8
plyr-1.8.2/plyr/man/names.quoted.Rd | 3
plyr-1.8.2/plyr/man/nunique.Rd | 5
plyr-1.8.2/plyr/man/ozone.Rd | 3
plyr-1.8.2/plyr/man/plyr-deprecated.Rd |only
plyr-1.8.2/plyr/man/plyr.Rd | 70 ++---
plyr-1.8.2/plyr/man/print.quoted.Rd | 3
plyr-1.8.2/plyr/man/print.split.Rd | 7
plyr-1.8.2/plyr/man/progress_none.Rd | 3
plyr-1.8.2/plyr/man/progress_text.Rd | 9
plyr-1.8.2/plyr/man/progress_time.Rd | 3
plyr-1.8.2/plyr/man/progress_tk.Rd | 10
plyr-1.8.2/plyr/man/progress_win.Rd | 8
plyr-1.8.2/plyr/man/quickdf.Rd | 5
plyr-1.8.2/plyr/man/quoted.Rd | 13 -
plyr-1.8.2/plyr/man/r_ply.Rd | 13 -
plyr-1.8.2/plyr/man/raply.Rd | 14 -
plyr-1.8.2/plyr/man/rbind.fill.Rd | 12
plyr-1.8.2/plyr/man/rbind.fill.matrix.Rd | 8
plyr-1.8.2/plyr/man/rdply.Rd | 21 -
plyr-1.8.2/plyr/man/reduce_dim.Rd | 5
plyr-1.8.2/plyr/man/rename.Rd | 24 +
plyr-1.8.2/plyr/man/revalue.Rd | 13 -
plyr-1.8.2/plyr/man/rlply.Rd | 10
plyr-1.8.2/plyr/man/round_any.Rd | 12
plyr-1.8.2/plyr/man/splat.Rd | 5
plyr-1.8.2/plyr/man/split_indices.Rd | 14 -
plyr-1.8.2/plyr/man/split_labels.Rd | 8
plyr-1.8.2/plyr/man/splitter_a.Rd | 25 +
plyr-1.8.2/plyr/man/splitter_d.Rd | 9
plyr-1.8.2/plyr/man/strip_splits.Rd | 5
plyr-1.8.2/plyr/man/summarise.Rd | 7
plyr-1.8.2/plyr/man/take.Rd | 15 -
plyr-1.8.2/plyr/man/true.Rd | 5
plyr-1.8.2/plyr/man/try_default.Rd | 14 -
plyr-1.8.2/plyr/man/tryapply.Rd | 10
plyr-1.8.2/plyr/man/unrowname.Rd | 5
plyr-1.8.2/plyr/man/vaggregate.Rd | 18 -
plyr-1.8.2/plyr/src/RcppExports.cpp | 34 +-
plyr-1.8.2/plyr/src/split-numeric.cpp | 16 -
plyr-1.8.2/plyr/tests/testthat |only
plyr-1.8.2/plyr/tests/testthat.R |only
145 files changed, 1368 insertions(+), 1196 deletions(-)
Title: Using R to Run 'JAGS'
Diff between R2jags versions 0.05-03 dated 2015-03-05 and 0.5-6 dated 2015-04-21
Description: Providing wrapper functions to implement Bayesian analysis in JAGS. Some major features include monitoring convergence of a MCMC model using Rubin and Gelman Rhat statistics, automatically running a MCMC model till it converges, and implementing parallel processing of a MCMC model for multiple chains.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 5 +++++
DESCRIPTION | 14 +++++++-------
MD5 | 4 ++--
3 files changed, 14 insertions(+), 9 deletions(-)
Title: Relationship Between Species and Groups of Sites
Diff between indicspecies versions 1.7.4 dated 2014-11-24 and 1.7.5 dated 2015-04-21
Description: Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites. Also includes functions to measure species niche breadth using resource categories.
Author: Miquel De Caceres, Florian Jansen
Maintainer: Miquel De Caceres
indicspecies-1.7.4/indicspecies/R/nichearea.R |only
indicspecies-1.7.5/indicspecies/DESCRIPTION | 12 +-
indicspecies-1.7.5/indicspecies/MD5 | 28 ++---
indicspecies-1.7.5/indicspecies/NAMESPACE | 7 +
indicspecies-1.7.5/indicspecies/R/indicators.r | 2
indicspecies-1.7.5/indicspecies/R/plotcoverage.r | 56 +++++-----
indicspecies-1.7.5/indicspecies/R/summary.indicators.R |only
indicspecies-1.7.5/indicspecies/build/vignette.rds |binary
indicspecies-1.7.5/indicspecies/inst/doc/indicspeciesTutorial.R | 6 -
indicspecies-1.7.5/indicspecies/inst/doc/indicspeciesTutorial.Rnw | 6 -
indicspecies-1.7.5/indicspecies/man/coverage.Rd | 3
indicspecies-1.7.5/indicspecies/man/indicators.Rd | 9 +
indicspecies-1.7.5/indicspecies/man/indicspecies-package.Rd | 6 -
indicspecies-1.7.5/indicspecies/man/nichevar.Rd | 31 ++++-
indicspecies-1.7.5/indicspecies/vignettes/PigeonExample-005.pdf |binary
indicspecies-1.7.5/indicspecies/vignettes/indicspeciesTutorial.Rnw | 6 -
16 files changed, 100 insertions(+), 72 deletions(-)
Title: DNA Profiling Evidence Analysis
Diff between DNAprofiles versions 0.3 dated 2015-04-20 and 0.3.1 dated 2015-04-21
Description: Methods for studying forensic DNA profiling, in particular familial database searches.
Author: Maarten Kruijver
Maintainer: Maarten Kruijver
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
R/misc.R | 2 +-
build/vignette.rds |binary
inst/doc/exceedance-probabilities.Rmd | 2 +-
inst/doc/exceedance-probabilities.html | 12 ++++++------
man/normalize.freqs.Rd | 2 +-
vignettes/exceedance-probabilities.Rmd | 2 +-
9 files changed, 27 insertions(+), 22 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Diff between dfmta versions 1.1-2 dated 2015-01-24 and 1.2 dated 2015-04-21
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
configure | 18 +++++++++---------
src/dfmta.cpp | 33 ++++++++++++++-------------------
4 files changed, 32 insertions(+), 37 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Diff between dfcomb versions 2.0-2 dated 2015-01-24 and 2.1 dated 2015-04-21
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
configure | 18 +++++++++---------
src/plateau.cpp | 29 ++++++++++-------------------
4 files changed, 29 insertions(+), 38 deletions(-)
Title: Sensitivity Analysis for Causal Inference
Diff between treatSens versions 1.0 dated 2014-09-12 and 1.1 dated 2015-04-21
Description: Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.
Author: Nicole Bohme Carnegie, Masataka Harada, Jennifer Hill
Maintainer: "Nicole Bohme Carnegie"
DESCRIPTION | 10 -
MD5 | 28 ++--
NAMESPACE | 3
R/X_partials.R | 8 -
R/calc_range.R | 127 ++++++++-----------
R/grid_range.R | 2
R/housekeeping.R | 31 +++-
R/object_def.R | 9 +
R/sensPlot.R | 302 +++++++++++++++++++++++++++++++++++++----------
R/treatSens.R | 17 +-
R/warnings.R | 7 -
inst/CITATION | 7 -
man/sensPlot.Rd | 2
man/treatSens-package.Rd | 2
man/treatSens.Rd | 14 --
15 files changed, 373 insertions(+), 196 deletions(-)
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.10.2 dated 2015-02-24 and 0.10.3 dated 2015-04-21
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
RMySQL-0.10.2/RMySQL/R/zzz_compatibility.R |only
RMySQL-0.10.3/RMySQL/DESCRIPTION | 10 -
RMySQL-0.10.3/RMySQL/MD5 | 55 ++++------
RMySQL-0.10.3/RMySQL/NAMESPACE | 3
RMySQL-0.10.3/RMySQL/R/data-type.R | 3
RMySQL-0.10.3/RMySQL/man/MySQLConnection-class.Rd | 2
RMySQL-0.10.3/RMySQL/man/MySQLDriver-class.Rd | 2
RMySQL-0.10.3/RMySQL/man/MySQLResult-class.Rd | 2
RMySQL-0.10.3/RMySQL/man/constants.Rd | 2
RMySQL-0.10.3/RMySQL/man/db-meta.Rd | 5
RMySQL-0.10.3/RMySQL/man/dbApply.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbColumnInfo-MySQLConnection-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbConnect-MySQLDriver-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbDataType-MySQLDriver-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbEscapeStrings.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbGetInfo-MySQLDriver-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbNextResult.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbQuoteIdentifier-MySQLConnection-character-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbReadTable.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbUnloadDriver-MySQLDriver-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/dbWriteTable.Rd | 2
RMySQL-0.10.3/RMySQL/man/isIdCurrent.Rd | 2
RMySQL-0.10.3/RMySQL/man/make.db.names-MySQLConnection-character-method.Rd | 2
RMySQL-0.10.3/RMySQL/man/mysqlBuildTableDefinition.Rd | 2
RMySQL-0.10.3/RMySQL/man/mysqlClientLibraryVersions.Rd | 2
RMySQL-0.10.3/RMySQL/man/mysqlHasDefault.Rd | 2
RMySQL-0.10.3/RMySQL/man/query.Rd | 2
RMySQL-0.10.3/RMySQL/man/result-meta.Rd | 2
RMySQL-0.10.3/RMySQL/man/transactions.Rd | 2
29 files changed, 58 insertions(+), 64 deletions(-)
Title: Read, Write, Manipulate and Convert GenAlEx-Format Genotype
Files
Diff between readGenalex versions 0.4.1 dated 2015-01-12 and 1.0 dated 2015-04-21
Description: A collection of R functions to read, write, manipulate, and
convert genotype data in GenAlEx format. GenAlEx is a widely-used Excel
plugin for manipulating and analysing genotype data. This package reads
GenAlEx data from text or Excel files and creates an annotated data frame
of class 'genalex'. Several functions are provided for accessing,
manipulating, printing, writing and converting this data. GenAlEx and its
documentation are available at http://biology-assets.anu.edu.au/GenAlEx.
Author: Douglas G. Scofield [aut, cre]
Maintainer: Douglas G. Scofield
readGenalex-0.4.1/readGenalex/R/computeGenalexColumns.R |only
readGenalex-0.4.1/readGenalex/R/dropGenalexLoci.R |only
readGenalex-0.4.1/readGenalex/R/getGenalexLocus.R |only
readGenalex-0.4.1/readGenalex/R/is.genalex.R |only
readGenalex-0.4.1/readGenalex/R/printGenalexGenotype.R |only
readGenalex-0.4.1/readGenalex/R/putGenalexLocus.R |only
readGenalex-0.4.1/readGenalex/R/readGenalex-internal.R |only
readGenalex-0.4.1/readGenalex/R/reduceGenalexPloidy.R |only
readGenalex-0.4.1/readGenalex/R/reorderGenalexLoci.R |only
readGenalex-0.4.1/readGenalex/data/example_genotypes.RData |only
readGenalex-0.4.1/readGenalex/data/example_genotypes.txt.gz |only
readGenalex-0.4.1/readGenalex/man/computeGenalexColumns.Rd |only
readGenalex-0.4.1/readGenalex/man/dropGenalexLoci.Rd |only
readGenalex-0.4.1/readGenalex/man/example_genotypes.Rd |only
readGenalex-0.4.1/readGenalex/man/getGenalexLocus.Rd |only
readGenalex-0.4.1/readGenalex/man/printGenalexGenotype.Rd |only
readGenalex-0.4.1/readGenalex/man/putGenalexLocus.Rd |only
readGenalex-0.4.1/readGenalex/man/reduceGenalexPloidy.Rd |only
readGenalex-0.4.1/readGenalex/man/reorderGenalexLoci.Rd |only
readGenalex-1.0/readGenalex/DESCRIPTION | 33
readGenalex-1.0/readGenalex/MD5 | 85
readGenalex-1.0/readGenalex/NAMESPACE | 60
readGenalex-1.0/readGenalex/NEWS |only
readGenalex-1.0/readGenalex/R/checkNullAlleles.R |only
readGenalex-1.0/readGenalex/R/readGenalex-Genepop.R |only
readGenalex-1.0/readGenalex/R/readGenalex-data.R |only
readGenalex-1.0/readGenalex/R/readGenalex-deprecated.R |only
readGenalex-1.0/readGenalex/R/readGenalex-genetics.R |only
readGenalex-1.0/readGenalex/R/readGenalex-package.R |only
readGenalex-1.0/readGenalex/R/readGenalex-pegas.R |only
readGenalex-1.0/readGenalex/R/readGenalex-readwrite.R |only
readGenalex-1.0/readGenalex/R/readGenalex.R | 1624 +++++++++-
readGenalex-1.0/readGenalex/README.md |only
readGenalex-1.0/readGenalex/data/Qagr_adult_genotypes.RData |only
readGenalex-1.0/readGenalex/data/Qagr_pericarp_genotypes.RData |only
readGenalex-1.0/readGenalex/inst |only
readGenalex-1.0/readGenalex/man/Qagr_adult_genotypes.Rd |only
readGenalex-1.0/readGenalex/man/Qagr_pericarp_genotypes.Rd |only
readGenalex-1.0/readGenalex/man/addLocus.Rd |only
readGenalex-1.0/readGenalex/man/as.data.frame.genalex.Rd |only
readGenalex-1.0/readGenalex/man/as.genalex.Rd |only
readGenalex-1.0/readGenalex/man/as.genetics.Rd |only
readGenalex-1.0/readGenalex/man/as.loci.genalex.Rd |only
readGenalex-1.0/readGenalex/man/cbind.genalex.Rd |only
readGenalex-1.0/readGenalex/man/checkNullAlleles.Rd |only
readGenalex-1.0/readGenalex/man/dropLocus.Rd |only
readGenalex-1.0/readGenalex/man/extra.Rd |only
readGenalex-1.0/readGenalex/man/genalex.Rd |only
readGenalex-1.0/readGenalex/man/getLocus.Rd |only
readGenalex-1.0/readGenalex/man/getLocusColumns.Rd |only
readGenalex-1.0/readGenalex/man/getPopulation.Rd |only
readGenalex-1.0/readGenalex/man/is.genalex.Rd | 73
readGenalex-1.0/readGenalex/man/joinGenotypes.Rd |only
readGenalex-1.0/readGenalex/man/ploidy.Rd |only
readGenalex-1.0/readGenalex/man/printGenotype.Rd |only
readGenalex-1.0/readGenalex/man/rbind.genalex.Rd |only
readGenalex-1.0/readGenalex/man/readGenalex-deprecated.Rd |only
readGenalex-1.0/readGenalex/man/readGenalex-package.Rd | 67
readGenalex-1.0/readGenalex/man/readGenalex.Rd | 165 -
readGenalex-1.0/readGenalex/man/readGenalexExcel.Rd |only
readGenalex-1.0/readGenalex/man/reducePloidy.Rd |only
readGenalex-1.0/readGenalex/man/reorderLoci.Rd |only
readGenalex-1.0/readGenalex/man/replaceLocus.Rd |only
readGenalex-1.0/readGenalex/man/splitGenotypes.Rd |only
readGenalex-1.0/readGenalex/man/summary.genalex.Rd |only
readGenalex-1.0/readGenalex/man/writeGenalex.Rd |only
readGenalex-1.0/readGenalex/man/writeGenalexExcel.Rd |only
readGenalex-1.0/readGenalex/man/writeGenepop.Rd |only
readGenalex-1.0/readGenalex/tests |only
69 files changed, 1953 insertions(+), 154 deletions(-)
Title: Statistical Tools for Probing Moderation Effects
Diff between probemod versions 0.1 dated 2015-03-04 and 0.2 dated 2015-04-21
Description: Contains functions that are useful for probing moderation effects including techniques such as pick-a-point (also known as spotlight analysis), Johnson-Neyman (also known as floodlight analysis). Plot functions are also provided to facilitate visualization of results.
Author: Jiat Chow Tan [aut, cre]
Maintainer: Jiat Chow Tan
DESCRIPTION | 8 -
MD5 | 27 +++--
NAMESPACE | 1
NEWS |only
R/jn.R | 236 +++++++++++++++++++++++++++++++++---------------
R/pickapoint.R | 96 +++++++++++++++----
R/plot.jn.R | 48 ++++-----
R/plot.pickapoint.R |only
R/print.jn.R | 9 +
R/print.pickapoint.R | 2
man/jn.Rd | 17 ++-
man/pickapoint.Rd | 20 ++--
man/plot.jn.Rd | 19 ++-
man/plot.pickapoint.Rd |only
man/print.jn.Rd | 2
man/print.pickapoint.Rd | 2
16 files changed, 327 insertions(+), 160 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 2.1.3 dated 2015-01-31 and 2.1.4 dated 2015-04-21
Description: Extensive functions for the theory of L-moments (LMs) in addition to probability-weighted moments (PWMs), and parameter (p) estimation for numerous familiar and not-so-familiar distributions. Estimation of LMs for the same distributions is provided as are L-moment ratio diagrams. Estimation of LMs for right-tail and left-tail censoring by known or unknown threshold and also by indicator variable is available. Asymmetric trimmed LMs (TL-moments, TLMs) are supported as are numerical integrations to dynamically compute trajectories of select TLM ratios for TL-moment ratio diagram construction. LMs of residual (resid.) and reversed (rev.) resid. life are implemented along with 13 operators on quantile functions that are useful in reliability, lifetime, and survival analysis. Exact analytical bootstrap estimates of order statistics, LMs, and variances-covariances of LMs are provided. The Harri-Coble Tau34-squared Test for Normality is available. Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail censoring (RC) encompasses: Asymmetric (Asy.) Exponential (Exp.) Power [L], Asy. Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen.) Exp. Poisson [L], Gen. Extreme Value [L], Gen. Lambda [L,TL], Gen. Logistic [L), Gen. Normal [L], Gen. Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev. Gumbel [L+RC], Rice/Rician (L), Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L]. LMs have multivariate analogs; the sample L-comoments (LCMs) are implemented and might have considerable application with copulas because LCMs measure asymmetric association and higher comoments or comovements of variables.
Author: William Asquith
Maintainer: William Asquith
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 4 ++++
inst/CITATION | 1 -
4 files changed, 11 insertions(+), 8 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Diff between icd9 versions 1.1 dated 2015-03-12 and 1.2 dated 2015-04-21
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any
other mapping of codes, such as ICD-10, to comorbidities can be used.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb]
Maintainer: Jack O. Wasey
icd9-1.1/icd9/data/ahrqComorbidAll.RData |only
icd9-1.1/icd9/data/icd9Chapters.RData |only
icd9-1.1/icd9/inst/extdata/CMS32_DESC_LONG_DX.txt |only
icd9-1.1/icd9/inst/extdata/CMS32_DESC_SHORT_DX.txt |only
icd9-1.1/icd9/inst/extdata/ccs_multi_dx_tool_2013.csv |only
icd9-1.1/icd9/man/icd9GenerateSysData.Rd |only
icd9-1.1/icd9/man/icd9Is.Rd |only
icd9-1.1/icd9/man/icd9ParseAndSaveMappings.Rd |only
icd9-1.1/icd9/man/parseIcd9Descriptions.Rd |only
icd9-1.1/icd9/man/read.zip.url.Rd |only
icd9-1.1/icd9/src/Makevars |only
icd9-1.2/icd9/.Rinstignore |only
icd9-1.2/icd9/COPYING |only
icd9-1.2/icd9/DESCRIPTION | 28
icd9-1.2/icd9/MD5 | 292 +++---
icd9-1.2/icd9/NAMESPACE | 25
icd9-1.2/icd9/R/RcppExports.R | 114 --
icd9-1.2/icd9/R/RcppExportsShim.R |only
icd9-1.2/icd9/R/benchmark.R | 31
icd9-1.2/icd9/R/comorbid.R | 72 -
icd9-1.2/icd9/R/condense.R |only
icd9-1.2/icd9/R/convert.R | 124 +-
icd9-1.2/icd9/R/datadocs.R | 95 ++
icd9-1.2/icd9/R/explain.R | 244 +----
icd9-1.2/icd9/R/filter.R | 69 +
icd9-1.2/icd9/R/icd9-package.R | 17
icd9-1.2/icd9/R/manip.R | 40
icd9-1.2/icd9/R/parse-comorbid.R |only
icd9-1.2/icd9/R/parse-rtf.R |only
icd9-1.2/icd9/R/parse.R | 833 ++++++++----------
icd9-1.2/icd9/R/ranges.R | 314 +++---
icd9-1.2/icd9/R/real.R |only
icd9-1.2/icd9/R/sas.R | 58 -
icd9-1.2/icd9/R/score.R | 123 ++
icd9-1.2/icd9/R/sysdata.rda |binary
icd9-1.2/icd9/R/util.R | 167 ++-
icd9-1.2/icd9/R/valid.R | 112 +-
icd9-1.2/icd9/R/zzz.R | 43
icd9-1.2/icd9/README.md | 47 -
icd9-1.2/icd9/build/vignette.rds |binary
icd9-1.2/icd9/cleanup |only
icd9-1.2/icd9/configure |only
icd9-1.2/icd9/configure.ac |only
icd9-1.2/icd9/configure.win |only
icd9-1.2/icd9/data/ahrqComorbid.RData |binary
icd9-1.2/icd9/data/elixComorbid.RData |binary
icd9-1.2/icd9/data/icd9Billable.RData |only
icd9-1.2/icd9/data/icd9Chapters.rda |only
icd9-1.2/icd9/data/icd9Hierarchy.RData |binary
icd9-1.2/icd9/data/mappingNames.rda |binary
icd9-1.2/icd9/data/quanDeyoComorbid.RData |binary
icd9-1.2/icd9/data/quanElixComorbid.RData |binary
icd9-1.2/icd9/data/vermont_dx.RData |only
icd9-1.2/icd9/inst/doc/introduction.R | 45
icd9-1.2/icd9/inst/doc/introduction.Rmd | 50 -
icd9-1.2/icd9/inst/doc/introduction.html | 220 +++-
icd9-1.2/icd9/inst/extdata/all-covariates.xls |only
icd9-1.2/icd9/inst/include/icd9_RcppExports.h | 168 +--
icd9-1.2/icd9/man/ahrqComorbid.Rd | 2
icd9-1.2/icd9/man/ahrqComorbidAll.Rd | 2
icd9-1.2/icd9/man/convert.Rd | 58 -
icd9-1.2/icd9/man/cr.Rd | 2
icd9-1.2/icd9/man/elixComorbid.Rd | 2
icd9-1.2/icd9/man/elixComorbidNames.Rd | 2
icd9-1.2/icd9/man/generateSysData.Rd |only
icd9-1.2/icd9/man/icd9-package.Rd | 2
icd9-1.2/icd9/man/icd9AddLeadingZeroes.Rd | 23
icd9-1.2/icd9/man/icd9Benchmark.Rd | 2
icd9-1.2/icd9/man/icd9Billable.Rd |only
icd9-1.2/icd9/man/icd9Chapters.Rd | 5
icd9-1.2/icd9/man/icd9ChaptersToMap.Rd | 8
icd9-1.2/icd9/man/icd9Charlson.Rd | 12
icd9-1.2/icd9/man/icd9Children.Rd | 21
icd9-1.2/icd9/man/icd9Comorbid.Rd | 27
icd9-1.2/icd9/man/icd9ComorbidDfToMat.Rd | 20
icd9-1.2/icd9/man/icd9ComorbidMatToDf.Rd | 19
icd9-1.2/icd9/man/icd9Condense.Rd | 39
icd9-1.2/icd9/man/icd9Count.Rd | 13
icd9-1.2/icd9/man/icd9DiffComorbid.Rd | 2
icd9-1.2/icd9/man/icd9DropLeadingZeroes.Rd | 15
icd9-1.2/icd9/man/icd9ExpandMinor.Rd | 9
icd9-1.2/icd9/man/icd9ExpandRange.Rd | 36
icd9-1.2/icd9/man/icd9Explain.Rd | 27
icd9-1.2/icd9/man/icd9ExtractAlphaNumeric.Rd | 2
icd9-1.2/icd9/man/icd9FilterInvalid.Rd | 14
icd9-1.2/icd9/man/icd9FilterPoa.Rd | 28
icd9-1.2/icd9/man/icd9FilterValid.Rd | 13
icd9-1.2/icd9/man/icd9GetChapters.Rd | 9
icd9-1.2/icd9/man/icd9GetMajor.Rd |only
icd9-1.2/icd9/man/icd9GetValid.Rd | 12
icd9-1.2/icd9/man/icd9GuessIsShort.Rd | 2
icd9-1.2/icd9/man/icd9Hierarchy.Rd | 2
icd9-1.2/icd9/man/icd9InReferenceCode.Rd | 5
icd9-1.2/icd9/man/icd9IsA.Rd |only
icd9-1.2/icd9/man/icd9IsBillable.Rd |only
icd9-1.2/icd9/man/icd9IsN.Rd |only
icd9-1.2/icd9/man/icd9IsReal.Rd | 37
icd9-1.2/icd9/man/icd9IsValid.Rd | 21
icd9-1.2/icd9/man/icd9IsValidMapping.Rd | 2
icd9-1.2/icd9/man/icd9LongToWide.Rd | 35
icd9-1.2/icd9/man/icd9PoaChoices.Rd | 2
icd9-1.2/icd9/man/icd9ShortToDecimal.Rd |only
icd9-1.2/icd9/man/icd9Sort.Rd | 10
icd9-1.2/icd9/man/icd9VanWalraven.Rd |only
icd9-1.2/icd9/man/icd9WideToLong.Rd | 28
icd9-1.2/icd9/man/listTrimFlat.Rd |only
icd9-1.2/icd9/man/logicalToBinary.Rd | 8
icd9-1.2/icd9/man/parseAhrqSas.Rd | 19
icd9-1.2/icd9/man/parseAndSaveQuick.Rd |only
icd9-1.2/icd9/man/parseElix.Rd | 4
icd9-1.2/icd9/man/parseIcd9Chapters.Rd | 14
icd9-1.2/icd9/man/parseLeafDescriptionsAll.Rd |only
icd9-1.2/icd9/man/parseLeafDescriptionsVersion.Rd |only
icd9-1.2/icd9/man/parseQuanDeyoSas.Rd | 4
icd9-1.2/icd9/man/parseQuanElix.Rd | 4
icd9-1.2/icd9/man/parseRtfFifthDigitRanges.Rd |only
icd9-1.2/icd9/man/parseRtfLines.Rd |only
icd9-1.2/icd9/man/parseRtfYear.Rd |only
icd9-1.2/icd9/man/quanDeyoComorbid.Rd | 2
icd9-1.2/icd9/man/quanElixComorbid.Rd | 2
icd9-1.2/icd9/man/sasDropOtherAssignment.Rd | 2
icd9-1.2/icd9/man/sasExtractLetStrings.Rd | 2
icd9-1.2/icd9/man/sasFormatExtract.Rd | 10
icd9-1.2/icd9/man/sasParseAssignments.Rd | 2
icd9-1.2/icd9/man/strMultiMatch.Rd | 5
icd9-1.2/icd9/man/stripRtf.Rd |only
icd9-1.2/icd9/man/swapNamesWithVals.Rd |only
icd9-1.2/icd9/man/vermont_dx.Rd |only
icd9-1.2/icd9/src/Makevars.in |only
icd9-1.2/icd9/src/Makevars.win | 3
icd9-1.2/icd9/src/Makevars.win64 |only
icd9-1.2/icd9/src/RcppExports.cpp | 238 +----
icd9-1.2/icd9/src/comorbid.cpp | 36
icd9-1.2/icd9/src/comorbidCommon.cpp | 18
icd9-1.2/icd9/src/comorbidSetup.cpp | 189 ++--
icd9-1.2/icd9/src/config.h.in |only
icd9-1.2/icd9/src/config.h.win |only
icd9-1.2/icd9/src/convert.cpp | 238 ++---
icd9-1.2/icd9/src/convert.h | 37
icd9-1.2/icd9/src/is.cpp | 59 -
icd9-1.2/icd9/src/is.h | 22
icd9-1.2/icd9/src/local.h | 41
icd9-1.2/icd9/src/longToWide.cpp | 50 -
icd9-1.2/icd9/src/manip.cpp | 38
icd9-1.2/icd9/src/manip.h | 26
icd9-1.2/icd9/src/ranges.cpp | 280 +++---
icd9-1.2/icd9/src/ranges.h | 22
icd9-1.2/icd9/src/util.cpp | 25
icd9-1.2/icd9/src/util.h | 22
icd9-1.2/icd9/tests/test-all.R | 30
icd9-1.2/icd9/tests/testthat/helper-base.R | 31
icd9-1.2/icd9/tests/testthat/test-LongToWide.R | 24
icd9-1.2/icd9/tests/testthat/test-billable.R |only
icd9-1.2/icd9/tests/testthat/test-comorbid-calcs.R | 17
icd9-1.2/icd9/tests/testthat/test-comorbid.R | 602 +++++++++----
icd9-1.2/icd9/tests/testthat/test-condense.R |only
icd9-1.2/icd9/tests/testthat/test-convert.R | 76 -
icd9-1.2/icd9/tests/testthat/test-explain.R | 215 ----
icd9-1.2/icd9/tests/testthat/test-filter.R | 17
icd9-1.2/icd9/tests/testthat/test-hierarchy.R |only
icd9-1.2/icd9/tests/testthat/test-icd9.R | 69 +
icd9-1.2/icd9/tests/testthat/test-is.R | 53 -
icd9-1.2/icd9/tests/testthat/test-parse.R |only
icd9-1.2/icd9/tests/testthat/test-ranges.R | 374 ++++----
icd9-1.2/icd9/tests/testthat/test-reshape.R | 17
icd9-1.2/icd9/tests/testthat/test-sas.R | 30
icd9-1.2/icd9/tests/testthat/test-score.R | 61 +
icd9-1.2/icd9/tests/testthat/test-util.R | 17
icd9-1.2/icd9/tests/testthat/test-valid.R | 67 +
icd9-1.2/icd9/tools |only
icd9-1.2/icd9/vignettes/introduction.Rmd | 50 -
171 files changed, 4144 insertions(+), 2929 deletions(-)
Title: Syntax Highlighting for R Source Code
Diff between highr versions 0.4.1 dated 2015-03-29 and 0.5 dated 2015-04-21
Description: Provides syntax highlighting for R source code. Currently it
supports LaTeX and HTML output. Source code of other languages is supported
via Andre Simon's highlight package (http://www.andre-simon.de).
Author: Christopher Gandrud [ctb],
Qiang Li [ctb],
Yixuan Qiu [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
highr-0.4.1/highr/tests/test-R2 |only
highr-0.5/highr/DESCRIPTION | 11 +++++-----
highr-0.5/highr/MD5 | 15 ++++++--------
highr-0.5/highr/NEWS | 6 +++++
highr-0.5/highr/R/highlight.R | 30 +++++++---------------------
highr-0.5/highr/build/vignette.rds |binary
highr-0.5/highr/man/hilight.Rd | 19 ++++++-----------
highr-0.5/highr/tests/test-all.R | 2 -
highr-0.5/highr/tests/testit/test-hilight.R | 2 -
9 files changed, 36 insertions(+), 49 deletions(-)
Title: Generalized Waring Regression Model for Count Data
Diff between GWRM versions 1.1 dated 2010-02-03 and 2.0 dated 2015-04-21
Description: Statistical functions to fit, validate and describe a Generalized
Waring Regression Model (GWRM).
Author: Antonio Jose Saez-Castillo [aut, cre],
Silverio Vilchez-Lopez [aut],
Maria Jose Olmo-Jimenez [aut],
Jose Rodriguez-Avi [aut],
Antonio Conde-Sanchez [aut],
Ana Maria Martinez-Rodriguez [aut]
Maintainer: Antonio Jose Saez-Castillo
GWRM-1.1/GWRM/R/GWRM.add.R |only
GWRM-1.1/GWRM/R/GWRM.display.R |only
GWRM-1.1/GWRM/R/GWRM.fit.R |only
GWRM-1.1/GWRM/R/GWRM.stats.R |only
GWRM-1.1/GWRM/man/GWRM.add.Rd |only
GWRM-1.1/GWRM/man/GWRM.display.Rd |only
GWRM-1.1/GWRM/man/GWRM.fit.Rd |only
GWRM-1.1/GWRM/man/GWRM.stats.Rd |only
GWRM-1.1/GWRM/man/goals.rd |only
GWRM-2.0/GWRM/DESCRIPTION | 45 ++++++++++++++++++++++----------------
GWRM-2.0/GWRM/MD5 |only
GWRM-2.0/GWRM/NAMESPACE | 23 +++++++++++++++----
GWRM-2.0/GWRM/R/gw.r |only
GWRM-2.0/GWRM/build |only
GWRM-2.0/GWRM/inst/CITATION | 36 ++++++++++++------------------
GWRM-2.0/GWRM/inst/NEWS.Rd |only
GWRM-2.0/GWRM/man/GWRM-package.Rd |only
GWRM-2.0/GWRM/man/add1.gw.Rd |only
GWRM-2.0/GWRM/man/drop1.gw.Rd |only
GWRM-2.0/GWRM/man/goals.Rd |only
GWRM-2.0/GWRM/man/gw.Rd |only
GWRM-2.0/GWRM/man/partvar.Rd |only
GWRM-2.0/GWRM/man/predict.gw.Rd |only
GWRM-2.0/GWRM/man/residuals.gw.Rd |only
24 files changed, 60 insertions(+), 44 deletions(-)
Title: Genealogical Data Analysis
Diff between GENLIB versions 1.0.3 dated 2015-03-20 and 1.0.4 dated 2015-04-21
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon
DESCRIPTION | 7
MD5 | 66 +++----
NAMESPACE | 2
R/classes_methodes.R | 98 +++++------
R/fonctionsBase.R | 32 ++-
R/fonctionsPAR.R | 6
R/fonctionsPriv.R | 314 ++++++++++++++++++-------------------
R/fonctionsSimul.R | 4
R/fonctionsStat.R | 20 +-
man/GLCGMatrixGroupSingle-class.Rd | 26 +--
man/GLgen-class.Rd | 2
man/GLgroupe-class.Rd | 16 -
man/gen.completenessVar.Rd | 12 -
man/gen.f.Rd | 14 -
man/gen.find.Min.Distance.MRCA.Rd | 14 -
man/gen.findFounders.Rd | 12 -
man/gen.findMRCA.Rd | 4
man/gen.gc.Rd | 7
man/gen.half.founder.Rd | 2
man/gen.implex.Rd | 14 -
man/gen.implexVar.Rd | 14 -
man/gen.meangendepth.Rd | 4
man/gen.meangendepthVar.Rd | 10 -
man/gen.phi.Rd | 2
man/gen.phiCI.Rd | 14 -
man/gen.phiMean.Rd | 12 -
man/gen.phiOver.Rd | 14 -
man/gen.simuProb.Rd | 10 +
man/gen.simuSample.Rd | 5
man/gen.simuSampleFreq.Rd | 5
man/gen.simuSet.Rd | 16 +
man/genea140.Rd | 5
man/geneaJi.Rd | 4
src/congen.cpp | 4
34 files changed, 420 insertions(+), 371 deletions(-)
Title: Format R Code Automatically
Diff between formatR versions 1.1 dated 2015-03-29 and 1.2 dated 2015-04-21
Description: Provides a function tidy_source() to format R source code. Spaces
and indent will be added to the code automatically, and comments will be
preserved under certain conditions, so that R code will be more
human-readable and tidy. There is also a Shiny app as a user interface in
this package (see tidy_app()).
Author: Yihui Xie
Maintainer: Yihui Xie
DESCRIPTION | 11 ++++++-----
MD5 | 14 +++++++-------
NEWS | 6 ++++++
R/tidy.R | 20 +++++++++-----------
R/utils.R | 31 ++-----------------------------
build/vignette.rds |binary
inst/doc/formatR.html | 7 +++----
tests/testit/test-tidy.R | 12 ++++++------
8 files changed, 39 insertions(+), 62 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Diff between evaluate versions 0.6 dated 2015-04-13 and 0.7 dated 2015-04-21
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie
DESCRIPTION | 12 +++++-----
MD5 | 42 ++++++++++++++++++------------------
NEWS | 5 ++++
R/graphics.r | 19 +---------------
R/parse.r | 26 ++++++++++++++++------
R/replay.r | 1
R/watcher.r | 3 +-
man/line_prompt.Rd | 1
man/watchout.Rd | 1
tests/test-all.R | 3 --
tests/testthat/interleave-1.r | 2 -
tests/testthat/interleave-2.r | 2 -
tests/testthat/parse.r | 2 -
tests/testthat/plot-last-comment.r | 2 -
tests/testthat/plot-multi-layout.r | 2 -
tests/testthat/plot-multi-layout2.r | 2 -
tests/testthat/plot-par2.r | 4 +--
tests/testthat/plot-persp.r | 6 ++---
tests/testthat/plot-strwidth.r | 2 -
tests/testthat/test-evaluate.r | 8 ++++--
tests/testthat/test-graphics.r | 4 +--
tests/testthat/test-parse.r | 19 +++++++++++-----
22 files changed, 91 insertions(+), 77 deletions(-)
Title: Latent and Stochastic Block Model Estimation by a 'V-EM'
Algorithm
Diff between blockmodels versions 1.0.4 dated 2015-04-15 and 1.1.1 dated 2015-04-21
Description: Latent and Stochastic Block Model estimation by a Variational EM algorithm.
Various probability distribution are provided (Bernoulli,
Poisson...), with or without covariates.
Author: INRA, Jean-Benoist Leger
Maintainer: Jean-Benoist Leger
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++++----
NAMESPACE | 2 ++
R/zbernoulli_multiplex.R |only
man/BM_bernoulli_multiplex.Rd |only
src/dispatcher.h | 5 +++++
src/misc_functions.h | 4 ++--
src/models/bernoulli_multiplex.h |only
tests/BM_bernoulli_multiplex.R |only
9 files changed, 22 insertions(+), 11 deletions(-)
Title: Crunch.io Data Tools
Diff between crunch versions 1.1.0 dated 2015-04-16 and 1.1.1 dated 2015-04-20
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
tests/testthat.R | 2 +-
tests/testthat/test-encoding.R | 9 +++++++++
tests/testthat/test-subvariables.R | 4 ++--
5 files changed, 20 insertions(+), 11 deletions(-)
Title: A Hydraulics Package to Compute Open-Channel Flow over Weirs
Diff between weirs versions 0.23 dated 2013-12-03 and 0.24 dated 2015-04-20
Description: This hydraulics package provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Author: William Asquith
Maintainer: William Asquith
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/CITATION | 5 ++---
3 files changed, 8 insertions(+), 9 deletions(-)
Title: Radiation and Photovoltaic Systems
Diff between solaR versions 0.38 dated 2014-04-27 and 0.41 dated 2015-04-20
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpiñán Lamigueiro
Maintainer: Oscar Perpiñán Lamigueiro
solaR-0.38/solaR/LICENSE |only
solaR-0.38/solaR/man/TargetDiagram.Rd |only
solaR-0.38/solaR/man/readSIAR.Rd |only
solaR-0.41/solaR/DESCRIPTION | 18 ++--
solaR-0.41/solaR/MD5 | 76 ++++++++++----------
solaR-0.41/solaR/NAMESPACE | 6 +
solaR-0.41/solaR/R/AllClasses.R | 2
solaR-0.41/solaR/R/TargetDiagram.R | 88 ++++++++++--------------
solaR-0.41/solaR/R/analyzeData.R | 70 ++++---------------
solaR-0.41/solaR/R/calcG0.R | 58 ---------------
solaR-0.41/solaR/R/calcGef.R | 28 -------
solaR-0.41/solaR/R/calcShd.R | 16 ----
solaR-0.41/solaR/R/calcSol.R | 16 ----
solaR-0.41/solaR/R/fInclin.R | 106 +++++++++++++++--------------
solaR-0.41/solaR/R/markovG0.R | 13 +--
solaR-0.41/solaR/R/optimShd.R | 36 ---------
solaR-0.41/solaR/R/prodGCPV.R | 23 ------
solaR-0.41/solaR/R/prodPVPS.R | 24 ------
solaR-0.41/solaR/R/read.R | 36 ---------
solaR-0.41/solaR/R/zzz.R | 19 ++++-
solaR-0.41/solaR/README.md | 3
solaR-0.41/solaR/man/Meteo-class.Rd | 1
solaR-0.41/solaR/man/calcG0.Rd | 43 +----------
solaR-0.41/solaR/man/calcGef.Rd | 31 --------
solaR-0.41/solaR/man/calcShd.Rd | 11 ++-
solaR-0.41/solaR/man/calcSol.Rd | 2
solaR-0.41/solaR/man/compare-methods.Rd | 18 ----
solaR-0.41/solaR/man/defunct.Rd |only
solaR-0.41/solaR/man/deprecated.Rd |only
solaR-0.41/solaR/man/fCompD.Rd | 3
solaR-0.41/solaR/man/fSolD.Rd | 2
solaR-0.41/solaR/man/fSolI.Rd | 2
solaR-0.41/solaR/man/fTemp.Rd | 18 ----
solaR-0.41/solaR/man/getLat-methods.Rd | 2
solaR-0.41/solaR/man/mergesolaR-methods.Rd | 26 -------
solaR-0.41/solaR/man/optimShd.Rd | 7 -
solaR-0.41/solaR/man/prodExample.Rd | 4 -
solaR-0.41/solaR/man/prodGCPV.Rd | 69 ------------------
solaR-0.41/solaR/man/prodPVPS.Rd | 37 ----------
solaR-0.41/solaR/man/readBD.Rd | 1
solaR-0.41/solaR/man/readG0dm.Rd | 3
solaR-0.41/solaR/man/solaR-package.Rd |only
42 files changed, 218 insertions(+), 700 deletions(-)
Title: Tools for Prevalence Assessment Studies
Diff between prevalence versions 0.3.0 dated 2014-10-21 and 0.4.0 dated 2015-04-20
Description: The prevalence package provides Frequentist and Bayesian methods for prevalence assessment studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from http://mcmc-jags.sourceforge.net/.
Author: Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut],
Johannes Charlier [aut], Bruno Levecke [aut], Nicolas Praet [aut],
Sophie Roelandt [aut], Suzanne Smit [aut], Pierre Dorny [aut],
Dirk Berkvens [aut], Niko Speybroeck [aut]
Maintainer: Brecht Devleesschauwer
DESCRIPTION | 19 +++---
MD5 | 43 +++++++-------
NAMESPACE | 4 -
NEWS | 14 ++++
R/plot-methods-coda.R | 137 ++++++++++++++++++++++++++--------------------
R/truePrevBinom.R | 31 ++++++++--
R/truePrevMulti-helper.R | 6 +-
R/truePrevMulti-main.R | 2
R/truePrevPools.R | 33 ++++++++---
R/zzz.R | 94 ++++++++++++++++++++-----------
inst/CITATION | 8 +-
man/betaExpert.Rd | 4 -
man/betaPERT.Rd | 2
man/convert-methods.Rd |only
man/define.Rd | 2
man/plot-methods.Rd | 2
man/prev-class.Rd | 15 +++--
man/prevalence-package.Rd | 9 ++-
man/print-methods.Rd | 5 -
man/propCI.Rd | 2
man/truePrev.Rd | 2
man/truePrevMulti2.Rd | 4 -
man/truePrevPools.Rd | 6 +-
23 files changed, 274 insertions(+), 170 deletions(-)
Title: Estimation of the Number of Fatalities from Carcass Searches
Diff between carcass versions 1.3 dated 2014-10-02 and 1.4 dated 2015-04-20
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt, Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner, Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp
Maintainer: Fraenzi Korner-Nievergelt
DESCRIPTION | 12 ++++++------
MD5 | 11 ++++++-----
R/estimateN.r | 6 ++++++
R/pkorner.R | 19 ++++++++++++-------
R/posteriorN.R | 24 +++++++++++++++---------
inst |only
man/carcass-package.Rd | 2 +-
7 files changed, 46 insertions(+), 28 deletions(-)
Title: GUI for Entering Test Items and Obtaining Raw and Transformed
Scores
Diff between TestScorer versions 1.6 dated 2014-07-05 and 1.7 dated 2015-04-20
Description: GUI for entering test items and obtaining raw
and transformed scores. The results are shown on the
console and can be saved to a tabular text file for further
statistical analysis. The user can define his own tests and
scoring procedures through a GUI.
Author: Manel Salamero
Maintainer: Manel Salamero
TestScorer-1.6/TestScorer/inst/some.stuff/TestScorerHelp.pdf |only
TestScorer-1.7/TestScorer/DESCRIPTION | 14 +--
TestScorer-1.7/TestScorer/MD5 | 15 +--
TestScorer-1.7/TestScorer/NAMESPACE | 3
TestScorer-1.7/TestScorer/NEWS | 2
TestScorer-1.7/TestScorer/R/TestScorer.R | 42 +++++------
TestScorer-1.7/TestScorer/inst/some.stuff/TST_DASS.r | 6 -
TestScorer-1.7/TestScorer/inst/some.stuff/TST_MHLC.r | 4 -
TestScorer-1.7/TestScorer/inst/some.stuff/TST_RAAS.r | 32 ++++----
9 files changed, 60 insertions(+), 58 deletions(-)
Title: Sparklines and Graphical Tables for TeX and HTML
Diff between sparkTable versions 0.12.0 dated 2014-11-17 and 1.0.0 dated 2015-04-20
Description: Create sparklines and graphical tables for documents and websites.
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik
DESCRIPTION | 14 +-
MD5 | 24 ++--
R/classes.r | 20 ++--
R/exports.r | 39 +++++++-
R/methods.r | 180 ++++++++++++++++++++++++++-----------
R/showSparkTable.R | 8 -
inst/shinystuff/shinypara_server.R | 4
man/export.Rd | 6 -
man/newSparkBar.Rd | 9 +
man/newSparkTable.Rd | 2
man/setParameter.Rd | 2
man/sparkbar-class.Rd | 1
man/sparkbox-class.Rd | 1
13 files changed, 216 insertions(+), 94 deletions(-)
Title: Fast Nearest Neighbour Search (Wraps Arya and Mount's ANN
Library)
Diff between RANN versions 2.4.1 dated 2014-07-21 and 2.5 dated 2015-04-20
Description: Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is
support for approximate as well as exact searches, fixed radius searches
and bd as well as kd trees.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis
RANN-2.4.1/RANN/man/RANN-defunct.Rd |only
RANN-2.5/RANN/DESCRIPTION | 11 +++++------
RANN-2.5/RANN/MD5 | 17 ++++++++---------
RANN-2.5/RANN/NAMESPACE | 3 +--
RANN-2.5/RANN/NEWS | 8 ++++++++
RANN-2.5/RANN/R/nn.R | 14 --------------
RANN-2.5/RANN/README.md | 9 +++++----
RANN-2.5/RANN/man/RANN-package.Rd | 3 ++-
RANN-2.5/RANN/man/nn2.Rd | 3 ++-
RANN-2.5/RANN/src/NN.cc | 2 +-
10 files changed, 32 insertions(+), 38 deletions(-)
Title: Moment-Based Estimation for Hierarchical Models
Diff between mbest versions 0.1 dated 2014-06-05 and 0.3 dated 2015-04-20
Description:
Implements methods from the paper "Fast Moment-Based Estimation
for Hierarchical Models," by Perry (2015).
Author: Patrick O. Perry
Maintainer: Patrick O. Perry
DESCRIPTION | 10 +-
MD5 | 33 ++++---
R/backtrack.R |only
R/blindsearch.R |only
R/firthglm.fit.R | 169 +++++++++++++++++++++++++++++++---------
R/linesearch.R | 21 ++--
R/mhglm.R | 2
R/mhglm.fit.R | 25 +++--
R/moment.est.R | 41 ++++++++-
R/rdglm.fit.R | 20 ++--
README.md | 2
inst/CITATION | 2
inst/tests/firth-binomial10.rds |only
inst/tests/firth-binomial8.rds |only
inst/tests/firth-binomial9.rds |only
inst/tests/test-firthglm-fit.R | 51 +++++++++++-
inst/tests/test-mhglm.R | 2
man/firthglm.fit.Rd | 16 ++-
man/mbest-package.Rd | 6 -
man/mhglm.Rd | 2
20 files changed, 295 insertions(+), 107 deletions(-)
Title: Estimation of ICA Mixture Models
Diff between icamix versions 1.0.1 dated 2014-08-29 and 1.0.2 dated 2015-04-20
Description: The icamix package provides R functions as well as a C++ library which facilitate the estimation of ICA mixture models. We have developed and implemented the NSMM-ICA algorithm that currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture models. We will continue to build in algorithms that interweave the EM step with other types of ICA techniques.
Author: Xiaotian Zhu, David R. Hunter
Maintainer: Xiaotian Zhu
DESCRIPTION | 14 ++++----
MD5 | 8 ++---
NAMESPACE | 5 +++
man/icamix-package.Rd | 2 -
src/RcppExports.cpp | 78 +++++++++++++++++++++-----------------------------
5 files changed, 50 insertions(+), 57 deletions(-)
Title: Automated Feature Selection from 'caret'
Diff between fscaret versions 0.9.3 dated 2015-03-04 and 0.9.4 dated 2015-04-20
Description: Automated feature selection using variety of models
provided by 'caret' package.
This work was funded by Poland-Singapore bilateral cooperation
project no 2/3/POL-SIN/2012.
Author: Jakub Szlek [aut, cre],
Aleksander Mendyk [ctb]
Maintainer: Jakub Szlek
DESCRIPTION | 8 +--
MD5 | 40 +++++++--------
R/fscaret.R | 62 ++++++++++--------------
R/impCalc.R | 30 ++++++++++-
R/regVarImp.R | 6 +-
build/vignette.rds |binary
inst/NEWS.Rd | 12 ++++
inst/doc/fscaret.R | 110 +++++++++++++++++++++++++++++++++++-------
inst/doc/fscaret.Rnw | 126 ++++++++++++++++++++++++++++++++++++++-----------
inst/doc/fscaret.pdf |binary
man/MSE.Rd | 17 ------
man/RMSE.Rd | 15 -----
man/dataset.test.Rd | 11 ----
man/dataset.train.Rd | 10 ---
man/fscaret-package.Rd | 4 -
man/fscaret.Rd | 13 +++--
man/funcClass.all.Rd | 15 -----
man/funcReg.all.Rd | 13 -----
man/impCalc.Rd | 16 ++++--
man/timeout.Rd | 29 -----------
vignettes/fscaret.Rnw | 126 ++++++++++++++++++++++++++++++++++++++-----------
21 files changed, 409 insertions(+), 254 deletions(-)
Title: Estimation in Dual Frame Surveys
Diff between Frames2 versions 0.1.0 dated 2015-01-22 and 0.1.1 dated 2015-04-20
Description: Point and interval estimation in dual frame surveys. In contrast
to classic sampling theory, where only one sampling frame is considered,
dual frame methodology assumes that there are two frames available for
sampling and that, overall, they cover the entire target population. Then,
two probability samples (one from each frame) are drawn and information
collected is suitably combined to get estimators of the parameter of
interest.
Author: Antonio Arcos
Maintainer: David Molina
DESCRIPTION | 8 -
MD5 | 48 ++++++-----
NAMESPACE | 1
R/CalSF.R | 6 -
R/JackBKA.R | 204 ++++++++++++++++++++++------------------------
R/JackCalDF.R | 230 +++++++++++++++++++++++++---------------------------
R/JackCalSF.R | 231 +++++++++++++++++++++++++----------------------------
R/JackFB.R | 196 +++++++++++++++++++++-----------------------
R/JackHartley.R | 201 ++++++++++++++++++++++------------------------
R/JackPEL.R | 218 ++++++++++++++++++++++++--------------------------
R/JackPML.R | 197 ++++++++++++++++++++++-----------------------
R/JackSFRR.R | 202 ++++++++++++++++++++++------------------------
build |only
inst |only
man/JackBKA.Rd | 34 ++-----
man/JackCalDF.Rd | 44 +++-------
man/JackCalSF.Rd | 45 ++++------
man/JackFB.Rd | 30 ++----
man/JackHartley.Rd | 32 ++-----
man/JackPEL.Rd | 37 +++-----
man/JackPML.Rd | 28 ++----
man/JackSFRR.Rd | 34 ++-----
vignettes |only
23 files changed, 960 insertions(+), 1066 deletions(-)
Title: Computed ABC Analysis
Diff between ABCanalysis versions 1.0 dated 2015-02-13 and 1.0.1 dated 2015-04-20
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many").
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/ABCanalysis.R | 21 +++++++++------------
R/ABCanalysisPlot.R | 15 ---------------
R/ABCcurve.R | 5 +++++
R/ABCplot.R | 6 ++----
6 files changed, 26 insertions(+), 41 deletions(-)
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.2-2 dated 2015-04-07 and 0.3-0 dated 2015-04-20
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
userfriendlyscience-0.2-2/userfriendlyscience/R/scaleReliability.r |only
userfriendlyscience-0.2-2/userfriendlyscience/man/userfriendlyscience-scaleReliability.Rd |only
userfriendlyscience-0.3-0/userfriendlyscience/ChangeLog | 12 +
userfriendlyscience-0.3-0/userfriendlyscience/DESCRIPTION | 8
userfriendlyscience-0.3-0/userfriendlyscience/MD5 | 39 ++--
userfriendlyscience-0.3-0/userfriendlyscience/NAMESPACE | 8
userfriendlyscience-0.3-0/userfriendlyscience/NEWS | 11 +
userfriendlyscience-0.3-0/userfriendlyscience/R/confIntV.r | 2
userfriendlyscience-0.3-0/userfriendlyscience/R/crossTab.r |only
userfriendlyscience-0.3-0/userfriendlyscience/R/dlvPlot.r | 80 +++++++-
userfriendlyscience-0.3-0/userfriendlyscience/R/oneway.r | 41 +++-
userfriendlyscience-0.3-0/userfriendlyscience/R/powerHist.r | 50 +++--
userfriendlyscience-0.3-0/userfriendlyscience/R/rMatrix.r | 94 ++--------
userfriendlyscience-0.3-0/userfriendlyscience/R/regr.r | 26 ++
userfriendlyscience-0.3-0/userfriendlyscience/R/scaleStructure.r |only
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-confIntV.Rd | 29 ++-
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-dlvPlot.Rd | 15 +
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-package.Rd | 18 +
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-powerHist.Rd | 2
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-printMethods.Rd | 15 -
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-rMatrix.Rd | 6
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-regr.Rd | 12 -
userfriendlyscience-0.3-0/userfriendlyscience/man/userfriendlyscience-scaleStructure.Rd |only
23 files changed, 297 insertions(+), 171 deletions(-)
Permanent link
Title: Tests in Linear Mixed Effects Models
Diff between lmerTest versions 2.0-20 dated 2014-11-21 and 2.0-25 dated 2015-04-20
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova
lmerTest-2.0-20/lmerTest/R/devfuns.R |only
lmerTest-2.0-20/lmerTest/R/devfunsExtra.R |only
lmerTest-2.0-20/lmerTest/R/vcconv.R |only
lmerTest-2.0-25/lmerTest/DESCRIPTION | 30 -
lmerTest-2.0-25/lmerTest/MD5 | 59 +--
lmerTest-2.0-25/lmerTest/NAMESPACE | 5
lmerTest-2.0-25/lmerTest/R/deriv.R |only
lmerTest-2.0-25/lmerTest/R/devfunsLmerTest.R | 49 ++
lmerTest-2.0-25/lmerTest/R/generalFunctions.R | 30 +
lmerTest-2.0-25/lmerTest/R/lmerTestFunctions.R | 96 +----
lmerTest-2.0-25/lmerTest/R/lsmeans.R | 123 ++++---
lmerTest-2.0-25/lmerTest/R/utils.R | 171 ++++------
lmerTest-2.0-25/lmerTest/man/anova-methods.Rd | 3
lmerTest-2.0-25/lmerTest/man/difflsmeans.Rd | 1
lmerTest-2.0-25/lmerTest/man/lmer.Rd | 2
lmerTest-2.0-25/lmerTest/man/lmerTest-package.Rd | 23 +
lmerTest-2.0-25/lmerTest/man/lsmeans.Rd | 2
lmerTest-2.0-25/lmerTest/man/merModLmerTest-class.Rd | 2
lmerTest-2.0-25/lmerTest/tests/DamonData.R | 3
lmerTest-2.0-25/lmerTest/tests/Examples/lmerTest-Ex.Rout.save | 27 -
lmerTest-2.0-25/lmerTest/tests/MAMSatterthKR.R | 33 +
lmerTest-2.0-25/lmerTest/tests/bugRefit.R | 4
lmerTest-2.0-25/lmerTest/tests/bugUpdate.R | 2
lmerTest-2.0-25/lmerTest/tests/convergeTest.R | 2
lmerTest-2.0-25/lmerTest/tests/lmerMod.R | 14
lmerTest-2.0-25/lmerTest/tests/packageExamplesExtra.R | 13
lmerTest-2.0-25/lmerTest/tests/packageExamplesExtra.Rout.save | 29 +
lmerTest-2.0-25/lmerTest/tests/rankDeficiency.R | 5
lmerTest-2.0-25/lmerTest/tests/testANCOVA.R | 4
lmerTest-2.0-25/lmerTest/tests/testContrasts.R | 107 +++---
lmerTest-2.0-25/lmerTest/tests/testTVbo.Rout.save | 36 +-
lmerTest-2.0-25/lmerTest/tests/testType2.R |only
lmerTest-2.0-25/lmerTest/tests/zeroDenom.R | 3
33 files changed, 483 insertions(+), 395 deletions(-)
Title: DNA Profiling Evidence Analysis
Diff between DNAprofiles versions 0.2 dated 2014-06-23 and 0.3 dated 2015-04-20
Description: Methods for studying forensic DNA profiling, in particular familial database searches.
Author: Maarten Kruijver
Maintainer: Maarten Kruijver
DNAprofiles-0.2/DNAprofiles/man/ki.pairs.Rd |only
DNAprofiles-0.2/DNAprofiles/man/ki.pairs.precompute.Rd |only
DNAprofiles-0.3/DNAprofiles/ChangeLog | 14
DNAprofiles-0.3/DNAprofiles/DESCRIPTION | 15
DNAprofiles-0.3/DNAprofiles/MD5 | 170 ++++--
DNAprofiles-0.3/DNAprofiles/NAMESPACE | 37 +
DNAprofiles-0.3/DNAprofiles/R/RcppExports.R | 37 +
DNAprofiles-0.3/DNAprofiles/R/check.dist.R |only
DNAprofiles-0.3/DNAprofiles/R/est.freqs.R |only
DNAprofiles-0.3/DNAprofiles/R/exactq.R |only
DNAprofiles-0.3/DNAprofiles/R/findk.R | 1
DNAprofiles-0.3/DNAprofiles/R/freqs.R | 12
DNAprofiles-0.3/DNAprofiles/R/homozygous.R |only
DNAprofiles-0.3/DNAprofiles/R/ibdprobs.R | 3
DNAprofiles-0.3/DNAprofiles/R/ibs.R | 22
DNAprofiles-0.3/DNAprofiles/R/ibs.pairwise.db.R | 192 ++++++-
DNAprofiles-0.3/DNAprofiles/R/ki.R | 290 ++++-------
DNAprofiles-0.3/DNAprofiles/R/ki_ibs_dist.R | 293 ++++--------
DNAprofiles-0.3/DNAprofiles/R/ki_precomp.R | 38 -
DNAprofiles-0.3/DNAprofiles/R/kicdf.R | 5
DNAprofiles-0.3/DNAprofiles/R/lrdist.R | 33 +
DNAprofiles-0.3/DNAprofiles/R/lrdist_cdf.R | 1
DNAprofiles-0.3/DNAprofiles/R/misc.R | 18
DNAprofiles-0.3/DNAprofiles/R/pr_next_allele.R | 88 ++-
DNAprofiles-0.3/DNAprofiles/R/profiles.R | 101 +++-
DNAprofiles-0.3/DNAprofiles/R/profiles_extract.R | 5
DNAprofiles-0.3/DNAprofiles/R/rmp.R | 125 ++---
DNAprofiles-0.3/DNAprofiles/R/sample.R | 226 +++++----
DNAprofiles-0.3/DNAprofiles/R/simq.R | 18
DNAprofiles-0.3/DNAprofiles/R/write.genepop.R |only
DNAprofiles-0.3/DNAprofiles/build |only
DNAprofiles-0.3/DNAprofiles/inst |only
DNAprofiles-0.3/DNAprofiles/man/DNAprofiles-package.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/as.dbcompare.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/check.dist.Rd |only
DNAprofiles-0.3/DNAprofiles/man/dist.pair.cdf.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/dist.unique.events.Rd | 7
DNAprofiles-0.3/DNAprofiles/man/dists.product.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/dists.product.pair.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/enum.profiles.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/est.freqs.Rd |only
DNAprofiles-0.3/DNAprofiles/man/exact.q.Rd |only
DNAprofiles-0.3/DNAprofiles/man/find.kth.element.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/freqsNLngm.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/freqsNLsgmplus.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/freqsUScaucs.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/get.freqs.Rd |only
DNAprofiles-0.3/DNAprofiles/man/get.labels.Rd |only
DNAprofiles-0.3/DNAprofiles/man/get.markers.Rd |only
DNAprofiles-0.3/DNAprofiles/man/homozygous.Rd |only
DNAprofiles-0.3/DNAprofiles/man/ibdprobs.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/ibs.db.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/ibs.dist.Rd | 8
DNAprofiles-0.3/DNAprofiles/man/ibs.pairs.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/ibs.pairwise.db.Rd | 8
DNAprofiles-0.3/DNAprofiles/man/ibs.pairwise.db.exp.Rd | 38 +
DNAprofiles-0.3/DNAprofiles/man/ibs.pairwise.pr.Rd |only
DNAprofiles-0.3/DNAprofiles/man/ki.Rd |only
DNAprofiles-0.3/DNAprofiles/man/ki.cdf.Rd | 10
DNAprofiles-0.3/DNAprofiles/man/ki.db.Rd | 16
DNAprofiles-0.3/DNAprofiles/man/ki.dist.Rd | 13
DNAprofiles-0.3/DNAprofiles/man/ki.ibs.joint.dist.Rd | 8
DNAprofiles-0.3/DNAprofiles/man/ki.precompute.Rd |only
DNAprofiles-0.3/DNAprofiles/man/normalize.freqs.Rd |only
DNAprofiles-0.3/DNAprofiles/man/pr.next.allele.Rd | 39 -
DNAprofiles-0.3/DNAprofiles/man/pr.next.alleles.Rd | 32 -
DNAprofiles-0.3/DNAprofiles/man/print.profiles.Rd |only
DNAprofiles-0.3/DNAprofiles/man/profiles-extract.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/profiles.Rd | 24
DNAprofiles-0.3/DNAprofiles/man/profiles.to.chars.Rd | 3
DNAprofiles-0.3/DNAprofiles/man/recode.freqs.Rd | 5
DNAprofiles-0.3/DNAprofiles/man/rmp.Rd | 43 +
DNAprofiles-0.3/DNAprofiles/man/sample.pairs.Rd | 9
DNAprofiles-0.3/DNAprofiles/man/sample.profiles.Rd | 9
DNAprofiles-0.3/DNAprofiles/man/sample.relatives.Rd | 8
DNAprofiles-0.3/DNAprofiles/man/sim.q.Rd | 5
DNAprofiles-0.3/DNAprofiles/man/write.genepop.Rd |only
DNAprofiles-0.3/DNAprofiles/src/RcppExports.cpp | 366 +++++++++------
DNAprofiles-0.3/DNAprofiles/src/Zprnextallele.cpp |only
DNAprofiles-0.3/DNAprofiles/src/Zprnextalleles.cpp |only
DNAprofiles-0.3/DNAprofiles/src/allfinitepos.cpp |only
DNAprofiles-0.3/DNAprofiles/src/countalleles.cpp |only
DNAprofiles-0.3/DNAprofiles/src/dbcomparepairwise.cpp | 14
DNAprofiles-0.3/DNAprofiles/src/distproduct.cpp | 2
DNAprofiles-0.3/DNAprofiles/src/exactq.cpp |only
DNAprofiles-0.3/DNAprofiles/src/findInt.cpp | 2
DNAprofiles-0.3/DNAprofiles/src/ki.cpp |only
DNAprofiles-0.3/DNAprofiles/src/kipairswithtable.cpp | 7
DNAprofiles-0.3/DNAprofiles/src/kitargetsdbwithtable.cpp | 19
DNAprofiles-0.3/DNAprofiles/src/kiwithtable.cpp | 6
DNAprofiles-0.3/DNAprofiles/src/rmp.cpp |only
DNAprofiles-0.3/DNAprofiles/src/rmp_old.cpp |only
DNAprofiles-0.3/DNAprofiles/src/rmpmat.cpp |only
DNAprofiles-0.3/DNAprofiles/tests |only
DNAprofiles-0.3/DNAprofiles/vignettes |only
95 files changed, 1501 insertions(+), 986 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Diff between RandomFieldsUtils versions 0.0.1 dated 2015-04-09 and 0.0.2 dated 2015-04-20
More information about RandomFieldsUtils at CRAN
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 8 ++++----
MD5 | 37 ++++++++++++++++++++++---------------
R/RFutils.R | 2 +-
inst/CITATION | 4 ++--
inst/include |only
man/Struve.Rd | 4 ++--
man/solvePosDef.Rd | 10 ++++++----
src/Basic_utils.h | 18 +-----------------
src/Error_utils.h | 3 +++
src/RF.h | 18 +-----------------
src/RFutils.cc | 19 +++++++++++++++----
src/R_init.cc | 28 ++++++++++++++++++++++------
src/R_init.h |only
src/RandomFieldsUtils.h | 6 ++++++
src/Solve.h | 10 ----------
src/Struve.h | 1 -
src/solve.cc | 5 +++--
src/utils.h | 24 +++++++++++++++++++++---
18 files changed, 109 insertions(+), 88 deletions(-)
Permanent link
Title: Quick Wraps 2
Diff between qwraps2 versions 0.1 dated 2015-04-08 and 0.1.1 dated 2015-04-20
Description: A collection of (wrapper) functions the creator found useful for
quickly placing data summaries and formatted regression results into .Rnw or
.Rmd files. Functions for generating commonly used graphics, such as receiver
operating curves or Bland-Altman plots, are also provided by 'qwraps2'.
'qwraps2' is a updated version of a package 'qwraps'. The original version
'qwraps' was never submitted to CRAN but can be found at
https://github.com/dewittpe/qwraps. The implementation and limited scope of the
functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally
different from 'qwraps'.
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt
DESCRIPTION | 12 +++++------
MD5 | 38 ++++++++++++++++++-----------------
NAMESPACE | 4 +++
R/extract.R |only
R/frmt.R | 2 -
R/frmtp.R | 56 +++++++++++++++++++++++++---------------------------
R/mean_sd.R | 8 +++++--
R/qacf.R | 2 -
R/qblandaltman.R | 10 ++++++++-
R/qkmplot.R | 2 -
R/qroc.R | 10 ++++-----
R/qwraps2.R | 43 ++++++++++++++++++++++++++++++++++-----
README.md | 6 ++++-
man/extract.Rd |only
man/frmt.Rd | 2 -
man/frmtp.Rd | 24 ++++------------------
man/qacf.Rd | 2 -
man/qblandaltman.Rd | 13 ++++++++++--
man/qkmplot.Rd | 2 -
man/qroc.Rd | 13 ++++++------
man/qwraps2.Rd | 45 ++++++++++++++++++++++++++++++++++++-----
21 files changed, 187 insertions(+), 107 deletions(-)
Title: Rigorous - DICOM Input / Output
Diff between oro.dicom versions 0.4.3 dated 2015-01-17 and 0.5.0 dated 2015-04-20
Description: Data input/output functions for data that conform to the
Digital Imaging and Communications in Medicine (DICOM) standard, part
of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre]
Maintainer: Brandon Whitcher
oro.dicom-0.4.3/oro.dicom/man/create.Rd |only
oro.dicom-0.4.3/oro.dicom/man/dicom.Rd |only
oro.dicom-0.4.3/oro.dicom/man/parseData.Rd |only
oro.dicom-0.4.3/oro.dicom/man/planes.Rd |only
oro.dicom-0.5.0/oro.dicom/DESCRIPTION | 18
oro.dicom-0.5.0/oro.dicom/LICENSE | 2
oro.dicom-0.5.0/oro.dicom/MD5 | 74 +--
oro.dicom-0.5.0/oro.dicom/NAMESPACE | 28 +
oro.dicom-0.5.0/oro.dicom/R/convert.R | 58 ++
oro.dicom-0.5.0/oro.dicom/R/create.R | 98 +++-
oro.dicom-0.5.0/oro.dicom/R/dec2base.R | 24 -
oro.dicom-0.5.0/oro.dicom/R/dicom.R | 54 +-
oro.dicom-0.5.0/oro.dicom/R/dicom2nifti.R | 240 ++++++----
oro.dicom-0.5.0/oro.dicom/R/header.R | 140 +++++
oro.dicom-0.5.0/oro.dicom/R/orientation.R | 187 ++++++-
oro.dicom-0.5.0/oro.dicom/R/oro.dicom-package.R |only
oro.dicom-0.5.0/oro.dicom/R/recursive.R | 220 ++++++---
oro.dicom-0.5.0/oro.dicom/build/vignette.rds |binary
oro.dicom-0.5.0/oro.dicom/data/dicom.VR.rda |binary
oro.dicom-0.5.0/oro.dicom/data/dicom.dic.rda |binary
oro.dicom-0.5.0/oro.dicom/inst/doc/dicom.pdf |binary
oro.dicom-0.5.0/oro.dicom/man/create3D.Rd |only
oro.dicom-0.5.0/oro.dicom/man/dec2base.Rd | 45 -
oro.dicom-0.5.0/oro.dicom/man/dicom.dic.Rd |only
oro.dicom-0.5.0/oro.dicom/man/dicom2analyze.Rd | 70 +-
oro.dicom-0.5.0/oro.dicom/man/dicom2nifti.Rd | 98 ++--
oro.dicom-0.5.0/oro.dicom/man/dicomTable.Rd | 70 +-
oro.dicom-0.5.0/oro.dicom/man/extractHeader.Rd | 64 +-
oro.dicom-0.5.0/oro.dicom/man/getOrientation.Rd | 69 +-
oro.dicom-0.5.0/oro.dicom/man/header2matrix.Rd | 52 +-
oro.dicom-0.5.0/oro.dicom/man/is.axial.Rd |only
oro.dicom-0.5.0/oro.dicom/man/matchHeader.Rd | 44 -
oro.dicom-0.5.0/oro.dicom/man/nextHeader.Rd | 61 +-
oro.dicom-0.5.0/oro.dicom/man/parsePixelData.Rd |only
oro.dicom-0.5.0/oro.dicom/man/readDICOM.Rd | 81 +--
oro.dicom-0.5.0/oro.dicom/man/readDICOMFile.Rd | 137 +++--
oro.dicom-0.5.0/oro.dicom/man/str2time.Rd | 122 ++---
oro.dicom-0.5.0/oro.dicom/man/swapDimension.Rd | 55 --
oro.dicom-0.5.0/oro.dicom/man/writeHeader.Rd | 39 -
oro.dicom-0.5.0/oro.dicom/tests/Examples/oro.dicom-Ex.Rout.save | 116 ++--
oro.dicom-0.5.0/oro.dicom/tests/testthat |only
oro.dicom-0.5.0/oro.dicom/tests/testthat.R |only
42 files changed, 1459 insertions(+), 807 deletions(-)
Title: Rapid Digital Image Analysis of Leaf Area
Diff between LeafArea versions 0.0.6 dated 2015-03-08 and 0.1.0 dated 2015-04-20
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi
LeafArea-0.0.6/LeafArea/R/auto.run.R |only
LeafArea-0.0.6/LeafArea/R/file.manage.R |only
LeafArea-0.0.6/LeafArea/R/file.manage.list.R |only
LeafArea-0.0.6/LeafArea/R/findimagej.R |only
LeafArea-0.0.6/LeafArea/man/auto.run.Rd |only
LeafArea-0.0.6/LeafArea/man/file.manage.Rd |only
LeafArea-0.0.6/LeafArea/man/file.manage.list.Rd |only
LeafArea-0.0.6/LeafArea/man/findimagej.Rd |only
LeafArea-0.1.0/LeafArea/DESCRIPTION | 10 ++++-----
LeafArea-0.1.0/LeafArea/MD5 | 26 ++++++++++++------------
LeafArea-0.1.0/LeafArea/R/eximg.r | 14 ++++++------
LeafArea-0.1.0/LeafArea/R/find.ij.R |only
LeafArea-0.1.0/LeafArea/R/readtext.ij.R |only
LeafArea-0.1.0/LeafArea/R/resmerge.ij.R |only
LeafArea-0.1.0/LeafArea/R/run.ij.R |only
LeafArea-0.1.0/LeafArea/man/LeafArea-package.Rd | 14 +++++++++---
LeafArea-0.1.0/LeafArea/man/eximg.Rd | 4 +--
LeafArea-0.1.0/LeafArea/man/find.ij.Rd |only
LeafArea-0.1.0/LeafArea/man/leafdata.rd | 2 -
LeafArea-0.1.0/LeafArea/man/readtext.ij.Rd |only
LeafArea-0.1.0/LeafArea/man/resmerge.ij.Rd |only
LeafArea-0.1.0/LeafArea/man/run.ij.Rd |only
22 files changed, 38 insertions(+), 32 deletions(-)
Title: A Logging Utility for R
Diff between futile.logger versions 1.4 dated 2015-03-21 and 1.4.1 dated 2015-04-20
Description: Provides a simple yet powerful logging utility. Based loosely on
log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/futile.logger-package.R | 4 ++--
R/layout.R | 6 ++++--
man/futile.logger-package.Rd | 5 +++--
tests/testthat/test_json.R | 4 +++-
tests/testthat/test_layout.R | 27 ++++++++++++++++++++++-----
7 files changed, 44 insertions(+), 22 deletions(-)
Title: Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC
Diff between bayescount versions 0.9.99-4 dated 2015-03-02 and 0.9.99-5 dated 2015-04-20
Description: A set of functions to allow analysis of count data (such
as faecal egg count data) using Bayesian MCMC methods. Returns
information on the possible values for mean count, coefficient
of variation and zero inflation (true prevalence) present in
the data. A complete faecal egg count reduction test (FECRT)
model is implemented, which returns inference on the true
efficacy of the drug from the pre- and post-treatment data
provided, using non-parametric bootstrapping as well as using
Bayesian MCMC. Functions to perform power analyses for faecal
egg counts (including FECRT) are also provided.
Author: Matthew Denwood [aut, cre]
Maintainer: Matthew Denwood
bayescount-0.9.99-4/bayescount/inst |only
bayescount-0.9.99-5/bayescount/DESCRIPTION | 24 ++++++++++++------------
bayescount-0.9.99-5/bayescount/MD5 | 3 +--
3 files changed, 13 insertions(+), 14 deletions(-)
Title: Syntax Highlighter
Diff between highlight versions 0.4.5 dated 2015-04-15 and 0.4.7 dated 2015-04-20
Description: Syntax highlighter for R code based
on the results of the R parser. Rendering in HTML and latex
markup. Custom Sweave driver performing syntax highlighting
of R code chunks.
Author: Romain Francois [aut, cre],
Andre Simon [ctb]
Maintainer: Romain Francois
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NAMESPACE | 1 +
R/SweaveLatexDriver.R | 2 +-
R/css.R | 6 +++---
R/zzz.R | 1 +
6 files changed, 14 insertions(+), 12 deletions(-)
Title: Fast Estimation of Gaussian Mixture Copula Models
Diff between GMCM versions 1.2 dated 2015-04-13 and 1.2.1 dated 2015-04-20
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/is.theta.R | 4 ++--
inst/NEWS.Rd | 8 ++++++++
inst/doc/GMCM-JStatSoft.pdf |binary
inst/tests/test-is.theta.R | 4 +++-
6 files changed, 21 insertions(+), 11 deletions(-)
Title: Gaussian Copula Marginal Regression
Diff between gcmr versions 0.6.1 dated 2013-07-29 and 0.7.0 dated 2015-04-20
Description: Likelihood inference in Gaussian copula marginal
regression models.
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin
DESCRIPTION | 13 +--
MD5 | 52 +++++++-----
NAMESPACE | 12 ++
NEWS | 11 ++
R/cormat.R | 6 -
R/gcmr.R | 209 ++++++++++++++++++++++++++++++++++++++++----------
R/marginals.R | 105 +++++++++++++++----------
data/HUR.RData |only
data/epilepsy.RData |only
data/malaria.RData |only
man/HUR.Rd |only
man/arma.cormat.Rd | 2
man/cluster.cormat.Rd | 2
man/epilepsy.Rd |only
man/estfun.gcmr.Rd | 10 +-
man/gcmr-package.Rd | 9 +-
man/gcmr.Rd | 59 ++++----------
man/gcmr.options.Rd | 11 +-
man/gs.marg.Rd | 2
man/ind.cormat.Rd | 4
man/malaria.Rd |only
man/marginal.gcmr.Rd | 16 +--
man/matern.cormat.Rd | 4
man/plot.gcmr.Rd |only
man/profile.gcmr.Rd | 38 +++++----
man/residuals.gcmr.Rd | 34 ++++----
man/scotland.Rd | 3
man/se.Rd | 16 +--
man/summary.gcmr.Rd |only
man/vcov.gcmr.Rd | 21 ++---
src/gcmr.c | 6 -
31 files changed, 411 insertions(+), 234 deletions(-)
Title: Compressive Sampling: Sparse Signal Recovery Utilities
Diff between R1magic versions 0.2 dated 2013-04-09 and 0.3.2 dated 2015-04-19
Description: Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple sparse signal generator, mutual cumulative coherence between two matrices and examples, Lp complex norm, scaling back regression coefficients.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen
R1magic-0.2/R1magic/examples |only
R1magic-0.3.2/R1magic/DESCRIPTION | 20 ++++++------
R1magic-0.3.2/R1magic/MD5 | 21 ++++++++-----
R1magic-0.3.2/R1magic/NEWS |only
R1magic-0.3.2/R1magic/R/Lnorm.R |only
R1magic-0.3.2/R1magic/R/objectiveL1.R | 14 ++++++++
R1magic-0.3.2/R1magic/R/objectiveL2.R | 18 ++++++++---
R1magic-0.3.2/R1magic/R/scaleBack.lm.R |only
R1magic-0.3.2/R1magic/README.md | 6 +++
R1magic-0.3.2/R1magic/inst |only
R1magic-0.3.2/R1magic/man/Lnorm.Rd |only
R1magic-0.3.2/R1magic/man/R1magic-package.Rd | 6 +--
R1magic-0.3.2/R1magic/man/objectiveL1.Rd | 43 ++++++++++-----------------
R1magic-0.3.2/R1magic/man/objectiveL2.Rd | 43 ++++++++++-----------------
R1magic-0.3.2/R1magic/man/scaleBack.lm.Rd |only
15 files changed, 92 insertions(+), 79 deletions(-)
Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Diff between BNPTSclust versions 1.0 dated 2015-01-13 and 1.1 dated 2015-04-19
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez
BNPTSclust-1.0/BNPTSclust/R/readscaleperiods.R |only
BNPTSclust-1.0/BNPTSclust/inst/doc/BNPTSclust.pdf |only
BNPTSclust-1.0/BNPTSclust/man/readscaleperiods.Rd |only
BNPTSclust-1.0/BNPTSclust/vignettes/BNPTSclust.pdf |only
BNPTSclust-1.1/BNPTSclust/DESCRIPTION | 8
BNPTSclust-1.1/BNPTSclust/MD5 | 58 -
BNPTSclust-1.1/BNPTSclust/R/clusterplots.R |only
BNPTSclust-1.1/BNPTSclust/R/comp11.R | 3
BNPTSclust-1.1/BNPTSclust/R/designmatrices.R |only
BNPTSclust-1.1/BNPTSclust/R/diagplots.R |only
BNPTSclust-1.1/BNPTSclust/R/scaleandperiods.R |only
BNPTSclust-1.1/BNPTSclust/R/tseriesca.R | 800 +++++++++------
BNPTSclust-1.1/BNPTSclust/R/tseriescm.R | 925 ++++++++++-------
BNPTSclust-1.1/BNPTSclust/R/tseriescq.R | 929 ++++++++++--------
BNPTSclust-1.1/BNPTSclust/data/gdp.rda |binary
BNPTSclust-1.1/BNPTSclust/data/houses.rda |binary
BNPTSclust-1.1/BNPTSclust/data/stocks.rda |binary
BNPTSclust-1.1/BNPTSclust/data/tseriesca.out.rda |binary
BNPTSclust-1.1/BNPTSclust/data/tseriescm.out.rda |binary
BNPTSclust-1.1/BNPTSclust/data/tseriescq.out.rda |binary
BNPTSclust-1.1/BNPTSclust/inst/doc/BNPTSclust1.1.pdf |only
BNPTSclust-1.1/BNPTSclust/man/BNPTSclust-package.Rd | 17
BNPTSclust-1.1/BNPTSclust/man/clusterplots.Rd |only
BNPTSclust-1.1/BNPTSclust/man/comp11.Rd | 28
BNPTSclust-1.1/BNPTSclust/man/designmatrices.Rd |only
BNPTSclust-1.1/BNPTSclust/man/diagplots.Rd |only
BNPTSclust-1.1/BNPTSclust/man/gdp.Rd | 2
BNPTSclust-1.1/BNPTSclust/man/houses.Rd | 4
BNPTSclust-1.1/BNPTSclust/man/scaleandperiods.Rd |only
BNPTSclust-1.1/BNPTSclust/man/stocks.Rd | 2
BNPTSclust-1.1/BNPTSclust/man/tseriesca.Rd | 228 +---
BNPTSclust-1.1/BNPTSclust/man/tseriesca.out.Rd | 4
BNPTSclust-1.1/BNPTSclust/man/tseriescm.Rd | 222 +---
BNPTSclust-1.1/BNPTSclust/man/tseriescm.out.Rd | 4
BNPTSclust-1.1/BNPTSclust/man/tseriescq.Rd | 217 +---
BNPTSclust-1.1/BNPTSclust/man/tseriescq.out.Rd | 4
BNPTSclust-1.1/BNPTSclust/vignettes/BNPTSclust1.1.pdf |only
37 files changed, 1821 insertions(+), 1634 deletions(-)
Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly from
Convex Shapes
Diff between hitandrun versions 0.5 dated 2015-01-06 and 0.5-1 dated 2015-04-19
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NEWS | 11 +++++++++--
R/bound.R | 10 +++++++++-
4 files changed, 26 insertions(+), 11 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Diff between SKAT versions 1.0.1 dated 2014-11-04 and 1.0.7 dated 2015-04-19
Description: Functions for kernel regression based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee
SKAT-1.0.1/SKAT/R/KMTest_Linear.R |only
SKAT-1.0.1/SKAT/R/KMTest_Logistic.R |only
SKAT-1.0.1/SKAT/R/KMTest_Logistic_VarMatching.R |only
SKAT-1.0.1/SKAT/R/KMTest_Optimal.R |only
SKAT-1.0.1/SKAT/R/KMTest_Optimal_VarMatching.R |only
SKAT-1.0.1/SKAT/src/NPsort.cpp |only
SKAT-1.0.7/SKAT/DESCRIPTION | 12 -
SKAT-1.0.7/SKAT/MD5 | 59 +++---
SKAT-1.0.7/SKAT/NAMESPACE | 3
SKAT-1.0.7/SKAT/R/Binary_Function.R | 45 +++-
SKAT-1.0.7/SKAT/R/Binary_MAIN.R | 43 +++-
SKAT-1.0.7/SKAT/R/Binary_MAIN_ExactBin.R | 230 ++++++++++++++++++------
SKAT-1.0.7/SKAT/R/Function.R | 37 +++
SKAT-1.0.7/SKAT/R/Function_Power_Resampling.R | 2
SKAT-1.0.7/SKAT/R/Main.R | 142 ++++++++++----
SKAT-1.0.7/SKAT/R/Null_Model.R | 18 +
SKAT-1.0.7/SKAT/R/SKAT_Linear.R |only
SKAT-1.0.7/SKAT/R/SKAT_Logistic.R |only
SKAT-1.0.7/SKAT/R/SKAT_Logistic_VarMatching.R |only
SKAT-1.0.7/SKAT/R/SKAT_Optimal.R |only
SKAT-1.0.7/SKAT/R/SKAT_Optimal_VarMatching.R |only
SKAT-1.0.7/SKAT/R/X_Chrom.R |only
SKAT-1.0.7/SKAT/data/SKAT.example.ChrX.rda |only
SKAT-1.0.7/SKAT/data/datalist | 3
SKAT-1.0.7/SKAT/inst/doc/SKAT.pdf |binary
SKAT-1.0.7/SKAT/man/Get_EffectiveNumberTest.rd | 2
SKAT-1.0.7/SKAT/man/SKAT.example.ChrX.rd |only
SKAT-1.0.7/SKAT/man/SKAT_ChrX.rd |only
SKAT-1.0.7/SKAT/man/SKAT_Null_Model.rd | 7
SKAT-1.0.7/SKAT/src/Binary_global.cpp | 2
SKAT-1.0.7/SKAT/src/NPsort.h | 46 ++++
SKAT-1.0.7/SKAT/src/bed_reader.cpp | 70 +++----
SKAT-1.0.7/SKAT/src/bed_reader.h | 20 +-
SKAT-1.0.7/SKAT/src/interface_to_R.cpp | 6
SKAT-1.0.7/SKAT/src/mwo_reader.cpp | 67 +++---
SKAT-1.0.7/SKAT/src/mwo_reader.h | 27 +-
SKAT-1.0.7/SKAT/src/setid_bim_index.cpp | 40 ++--
SKAT-1.0.7/SKAT/src/setid_bim_index.h | 12 -
38 files changed, 625 insertions(+), 268 deletions(-)
More information about PortfolioAnalytics at CRAN
Permanent link
Title: Tools for Phoneticians and Phonologists
Diff between phonR versions 1.0-1 dated 2015-03-05 and 1.0-3 dated 2015-04-19
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/phonR.R | 21 +++++++++++----------
3 files changed, 17 insertions(+), 16 deletions(-)
Title: Tools for Analyzing Finite Mixture Models
Diff between mixtools versions 1.0.2 dated 2014-05-14 and 1.0.3 dated 2015-04-19
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre],
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young
DESCRIPTION | 16 -
MD5 | 51 ++--
NAMESPACE | 17 +
NEWS | 13 +
R/multmixEM.R | 9
R/npMSL.R | 486 ++++++++++++++++++++++++++++++---------------
build |only
inst/doc/mixtools.R | 10
inst/doc/mixtools.Rnw | 23 +-
inst/doc/mixtools.pdf |binary
man/ise.npEM.Rd | 221 ++++++++++----------
man/mixtools-internal.Rd | 41 +++
man/npEM.Rd | 24 +-
man/npMSL.Rd | 61 +++--
man/plot.npEM.Rd | 4
man/plotFDR.Rd | 4
man/print.npEM.Rd | 2
man/regmixEM.Rd | 3
man/regmixEM.mixed.Rd | 5
man/repnormmixEM.Rd | 2
man/repnormmixmodel.sel.Rd | 2
man/spEMsymlocN01.Rd | 9
man/summary.npEM.Rd | 4
man/wkde.Rd | 124 +++++------
src/npMSL.c | 54 ++---
vignettes/mixtools.Rnw | 23 +-
vignettes/mixtools.bib | 9
27 files changed, 761 insertions(+), 456 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Diff between gemtc versions 0.6-1 dated 2014-12-12 and 0.6-2 dated 2015-04-19
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian framework. You need either BUGS or JAGS to use this package, preferably JAGS (through the rjags package). Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
DESCRIPTION | 11 +-
MD5 | 18 +--
NAMESPACE | 3
NEWS | 20 +++
R/anohe.R | 6 -
R/blobbogram.R | 45 +++++---
R/inits.R | 7 +
R/mtc.network.R | 92 ++++++++++++------
man/blobbogram.Rd | 10 +
tests/testthat/test-unit-mtc.nr.comparisons.R |only
tests/testthat/test-unit-mtc.study.treatment.matrix.R |only
11 files changed, 145 insertions(+), 67 deletions(-)
Title: Models for Skewed Count Distributions Relevant to Networks
Diff between degreenet versions 1.3 dated 2015-04-06 and 1.3-1 dated 2015-04-19
Description: Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock
Maintainer: Mark S. Handcock
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/cmp.R | 39 +++++++++++++++++++++++++++++----------
R/degreenet.R | 2 +-
src/cmp.c | 48 +++++++++++++++++++++++++++++++++++++-----------
src/cmp.h | 2 +-
6 files changed, 77 insertions(+), 32 deletions(-)
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Diff between candisc versions 0.6-5 dated 2013-06-12 and 0.6-7 dated 2015-04-19
Description: Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly
DESCRIPTION | 44 ++++++-------
MD5 | 33 +++++-----
NAMESPACE | 5 +
NEWS | 157 ++++++++++++++++++++++++++-----------------------
R/can_lm.R |only
R/heplot.candisc.R | 42 ++++++-------
R/heplot3d.cancor.R | 9 +-
R/mlm2can.R |only
R/plot.candisc.R | 10 +--
R/vecscale.R |only
R/vectors3d.R | 4 -
data/Grass.rda |binary
data/HSB.rda |binary
data/Wolves.rda |binary
man/HSB.Rd | 4 -
man/can_lm.Rd |only
man/candisc-package.Rd | 4 -
man/candisc.Rd | 4 -
man/heplot.candisc.Rd | 6 -
man/vecscale.Rd |only
20 files changed, 173 insertions(+), 149 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.17 dated 2015-03-10 and 2.18 dated 2015-04-19
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.17/BDgraph/DESCRIPTION |only
BDgraph-2.17/BDgraph/MD5 |only
BDgraph-2.17/BDgraph/NAMESPACE |only
BDgraph-2.17/BDgraph/R |only
BDgraph-2.17/BDgraph/build |only
BDgraph-2.17/BDgraph/data |only
BDgraph-2.17/BDgraph/man |only
BDgraph-2.17/BDgraph/src |only
BDgraph-2.17/BDgraph/vignettes |only
BDgraph-2.18/BDgraph/inst/doc/BDgraph.pdf |binary
BDgraph-2.18/BDgraph/inst/doc/vignette.pdf |binary
11 files changed
Title: Access Vegetation Databases and Treat Taxonomy
Diff between vegdata versions 0.6-7 dated 2014-11-01 and 0.6.9 dated 2015-04-18
Description: Handling of vegetation data from Turboveg (http://www.synbiosys.alterra.nl/turboveg/) and other sources (http://www.vegetweb.de). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", http://www.botanik.uni-greifswald.de/GermanSL.html).
Author: Florian Jansen
Maintainer: Florian Jansen
vegdata-0.6-7/vegdata/vignettes/ecol_let.bst |only
vegdata-0.6.9/vegdata/DESCRIPTION | 17 +++----
vegdata-0.6.9/vegdata/MD5 | 57 +++++++++++-------------
vegdata-0.6.9/vegdata/NAMESPACE | 2
vegdata-0.6.9/vegdata/R/child.r | 12 ++---
vegdata-0.6.9/vegdata/R/internal.r | 13 ++++-
vegdata-0.6.9/vegdata/R/monotypic.r | 2
vegdata-0.6.9/vegdata/R/reflist.r | 11 ++--
vegdata-0.6.9/vegdata/R/syntab.r | 9 ++-
vegdata-0.6.9/vegdata/R/tax.r | 2
vegdata-0.6.9/vegdata/R/tax_add.r | 9 ++-
vegdata-0.6.9/vegdata/R/tv.biblio.r | 12 +++--
vegdata-0.6.9/vegdata/R/tv.coverperc.r | 15 +++---
vegdata-0.6.9/vegdata/R/tv.home.r | 11 ++--
vegdata-0.6.9/vegdata/R/tv.obs.r | 2
vegdata-0.6.9/vegdata/R/tv.site.r | 34 ++++++++------
vegdata-0.6.9/vegdata/R/tv.veg.r | 11 ++--
vegdata-0.6.9/vegdata/R/tv.write.r | 61 +++++++++++++++++++++++---
vegdata-0.6.9/vegdata/build/vignette.rds |binary
vegdata-0.6.9/vegdata/inst/ChangeLog | 5 ++
vegdata-0.6.9/vegdata/inst/doc/vegdata.R | 26 ++++++-----
vegdata-0.6.9/vegdata/inst/doc/vegdata.Rnw | 40 ++++++++++-------
vegdata-0.6.9/vegdata/inst/doc/vegdata.pdf |binary
vegdata-0.6.9/vegdata/man/tv.biblio.Rd | 4 +
vegdata-0.6.9/vegdata/man/tv.coverperc.Rd | 11 ++--
vegdata-0.6.9/vegdata/man/tv.site.Rd | 2
vegdata-0.6.9/vegdata/man/tv.veg.Rd | 2
vegdata-0.6.9/vegdata/man/tv.write.Rd | 4 +
vegdata-0.6.9/vegdata/man/vegdata-internal.Rd | 1
vegdata-0.6.9/vegdata/vignettes/vegdata.Rnw | 40 ++++++++++-------
30 files changed, 259 insertions(+), 156 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Diff between heplots versions 1.0-12 dated 2014-07-02 and 1.0-15 dated 2015-04-18
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly
DESCRIPTION | 12 +-
MD5 | 158 ++++++++++++++++----------------
NAMESPACE | 9 +
NEWS | 12 ++
R/arrow3d.R | 10 +-
R/cross3d.R | 6 -
R/ellipse3d.axes.R | 10 +-
R/heplot1d.R | 3
R/heplot3d.R | 48 +++++----
R/mark.H0.R | 4
build/vignette.rds |binary
data/Adopted.RData |binary
data/Bees.rda |binary
data/FootHead.rda |binary
data/Headache.RData |binary
data/Hernior.RData |binary
data/MockJury.RData |binary
data/NLSY.RData |binary
data/Oslo.RData |binary
data/Plastic.rda |binary
data/Pottery2.RData |binary
data/Probe1.RData |binary
data/Probe2.RData |binary
data/RatWeight.RData |binary
data/ReactTime.RData |binary
data/Rohwer.rda |binary
data/RootStock.rda |binary
data/Sake.RData |binary
data/Skulls.RData |binary
data/SocGrades.RData |binary
data/VocabGrowth.rda |binary
data/WeightLoss.RData |binary
data/schooldata.RData |binary
man/Oslo.Rd | 4
man/RatWeight.Rd | 2
man/Skulls.Rd | 3
man/heplot-package.Rd | 8 -
man/heplot.Rd | 4
man/robmlm.Rd | 7 -
vignettes/fig/plot-Ortho-fm1.pdf |binary
vignettes/fig/plot-Ortho-fm3.pdf |binary
vignettes/fig/plot-grades-can-class.pdf |binary
vignettes/fig/plot-grades-can-gpa.pdf |binary
vignettes/fig/plot-grades-can-sex.pdf |binary
vignettes/fig/plot-grades-pairs.pdf |binary
vignettes/fig/plot-hern-can-age.pdf |binary
vignettes/fig/plot-hern-can-build.pdf |binary
vignettes/fig/plot-hern-can-cardiac.pdf |binary
vignettes/fig/plot-hern-can-pstat.pdf |binary
vignettes/fig/plot-hern-pairs.pdf |binary
vignettes/fig/plot-jury-can1.pdf |binary
vignettes/fig/plot-jury-mod1-HE.pdf |binary
vignettes/fig/plot-jury-mod1-pairs.pdf |binary
vignettes/fig/plot-jury-mod2-HE.pdf |binary
vignettes/fig/plot-jury-mod3-eff.pdf |binary
vignettes/fig/plot-obk-HE1.pdf |binary
vignettes/fig/plot-obk-HE2.pdf |binary
vignettes/fig/plot-obk-HE3.pdf |binary
vignettes/fig/plot-obk2-HE1.pdf |binary
vignettes/fig/plot-obk2-HE2.pdf |binary
vignettes/fig/plot-ortho-HE.pdf |binary
vignettes/fig/plot-ortho-nonlin-HE.pdf |binary
vignettes/fig/plot-ortho-xyplot1.pdf |binary
vignettes/fig/plot-ortho-xyplot2.pdf |binary
vignettes/fig/plot-plastic2.pdf |binary
vignettes/fig/plot-rohwer-HE1.pdf |binary
vignettes/fig/plot-rohwer-HE2.pdf |binary
vignettes/fig/plot-rohwer-HE3.pdf |binary
vignettes/fig/plot-rohwer-HE4.pdf |binary
vignettes/fig/plot-skulls-HE-pairs.pdf |binary
vignettes/fig/plot-skulls-bwplot.pdf |binary
vignettes/fig/plot-skulls-can2.pdf |binary
vignettes/fig/plot-skulls4.pdf |binary
vignettes/fig/plot-voc1.pdf |binary
vignettes/fig/plot-voc4.pdf |binary
vignettes/fig/plot-voc8.pdf |binary
vignettes/fig/plot-wl-HE1.pdf |binary
vignettes/fig/plot-wl-HE2.pdf |binary
vignettes/fig/plot-wl-HE3.pdf |binary
vignettes/fig/plot-wl-means.pdf |binary
80 files changed, 163 insertions(+), 137 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Diff between eHOF versions 1.5.7 dated 2015-01-14 and 1.5.8 dated 2015-04-18
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen
eHOF-1.5.7/eHOF/vignettes/figure |only
eHOF-1.5.8/eHOF/DESCRIPTION | 15 ++++------
eHOF-1.5.8/eHOF/MD5 | 52 ++++++++++++++-----------------------
eHOF-1.5.8/eHOF/NAMESPACE | 5 +++
eHOF-1.5.8/eHOF/R/Para.deriv.r | 4 --
eHOF-1.5.8/eHOF/R/Para.opt.r | 15 ++++------
eHOF-1.5.8/eHOF/R/Para.r | 2 -
eHOF-1.5.8/eHOF/R/autolayout.r | 10 ++-----
eHOF-1.5.8/eHOF/R/coef.HOF.r | 18 +++++++-----
eHOF-1.5.8/eHOF/R/pick.model.r | 2 -
eHOF-1.5.8/eHOF/R/plot.HOF.list.r | 10 ++++---
eHOF-1.5.8/eHOF/R/plot.HOF.r | 42 ++++++++++++-----------------
eHOF-1.5.8/eHOF/R/print.HOF.list.r | 2 -
eHOF-1.5.8/eHOF/R/zzz.r | 4 --
eHOF-1.5.8/eHOF/build/vignette.rds |binary
eHOF-1.5.8/eHOF/inst/ChangeLog | 7 ++--
eHOF-1.5.8/eHOF/inst/doc/eHOF.R | 23 ++--------------
eHOF-1.5.8/eHOF/inst/doc/eHOF.Rnw | 46 ++++----------------------------
eHOF-1.5.8/eHOF/inst/doc/eHOF.pdf |binary
eHOF-1.5.8/eHOF/man/HOF.Rd | 7 ++--
eHOF-1.5.8/eHOF/man/autolayout.Rd | 6 +---
eHOF-1.5.8/eHOF/vignettes/eHOF.Rnw | 46 ++++----------------------------
22 files changed, 107 insertions(+), 209 deletions(-)
Title: Pairwise Distance Estimation with TKF91 and TKF92 Model
Diff between TKF versions 0.0.3 dated 2015-02-10 and 0.0.8 dated 2015-04-18
Description: Pairwise evolutionary distance estimation between protein sequences with the TKF91 and TKF92 model, which consider all the possible paths of transforming from one sequence to another.
Author: Ge Tan
Maintainer: Ge Tan
DESCRIPTION | 11 ++++++-----
MD5 | 25 ++++++++++++++++---------
NAMESPACE | 12 +++++++++++-
R/MinSqTree.R |only
R/TKF91.R | 21 ++++++++++++++++++---
R/TKF92.R | 22 +++++++++++++++++++---
R/TKF92HG.R |only
inst/makePackage/TKF.txt | 29 ++++++++++++++++++++++++-----
inst/unitTests/test_TKF92HG.R |only
man/TKF91.Rd | 1 +
man/TKF92.Rd | 25 ++++++++++++-------------
man/TKF92HG.Rd |only
man/optim.phylo.wls.Rd |only
src/R_init_TKF.c | 9 +++++++++
src/TKF92.h | 2 +-
src/TKF92HG.c |only
src/TKF92HG.h |only
17 files changed, 117 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-07 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-07 3.8.31-4
2014-07-04 3.8.31-3
2014-05-07 3.8.31-2
2013-03-29 3.8.31-1
2012-10-15 3.8.31-0
Title: Spatial Modeling on Stream Networks
Diff between SSN versions 1.1.4 dated 2014-11-03 and 1.1.5 dated 2015-04-18
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef
DESCRIPTION | 8 +-
MD5 | 58 ++++++++--------
NAMESPACE | 19 ++++-
R/SSN-methods.R | 12 +++
R/additive.function.jay.R | 54 +++++++++++----
R/copyLSN2temp.R |only
R/createDistMat.R | 28 ++++++--
R/createSSN.R | 2
R/split.predictions.R | 12 +--
R/writeSSN.r | 96 +++++++++++++++++++++-------
build/vignette.rds |binary
data/mf04.rda |binary
data/mf04p.rda |binary
data/modelFits.rda |binary
inst/doc/STARS.pdf |binary
man/AIC.glmssn.Rd | 8 +-
man/BLUP.Rd | 6 +
man/BlockPredict.Rd | 50 +++++++-------
man/CrossValidationSSN.Rd | 6 +
man/CrossValidationStatsSSN.Rd | 8 +-
man/additive.function.Rd | 6 +
man/as.SpatialLines.SpatialStreamNetwork.rd | 11 ++-
man/copyLSN2temp.Rd |only
man/covparms.Rd | 9 ++
man/createDistMat.Rd | 9 +-
man/getPreds.Rd | 9 ++
man/getStreamDistMat.rd | 6 +
man/importPredpts.Rd | 7 +-
man/plot.glmssn.predict.Rd | 11 ++-
man/splitPredictions.Rd | 15 +---
man/writeSSN.Rd | 5 +
31 files changed, 302 insertions(+), 153 deletions(-)
Title: Functions to Analyze Single System Data
Diff between SSDforR versions 1.4.8 dated 2014-12-07 and 1.4.9 dated 2015-04-18
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach
DESCRIPTION | 10 +--
MD5 | 138 +++++++++++++++++++++++++-------------------------
man/ABWilcox.Rd | 2
man/ABanova.Rd | 4 -
man/ABarrow.Rd | 2
man/ABautoacf.Rd | 2
man/ABbinomial.Rd | 2
man/ABdescrip.Rd | 2
man/ABiqr.Rd | 2
man/ABlineD.Rd | 2
man/ABlines.Rd | 2
man/ABma.Rd | 2
man/ABregres.Rd | 2
man/ABrf2.Rd | 2
man/ABrobust.Rd | 2
man/ABtext.Rd | 2
man/ABtsplot.Rd | 2
man/ABttest.Rd | 2
man/Append.Rd | 2
man/Aregres.Rd | 2
man/Arimadiff.Rd | 2
man/Arimama.Rd | 2
man/Arobust.Rd | 2
man/Cchart.Rd | 2
man/Effectsize.Rd | 2
man/GABrf2.Rd | 2
man/GABttest.Rd | 2
man/Getcsv.Rd | 2
man/Gindex.Rd | 2
man/Gline.Rd | 2
man/Gmedian.Rd | 2
man/IQRbandgraph.Rd | 2
man/IQRlegend.Rd | 2
man/IQRline.Rd | 2
man/PANDlegend.Rd | 2
man/PEMabove.Rd | 2
man/PEMbelow.Rd | 2
man/PNDbelow.Rd | 2
man/Pchart.Rd | 2
man/Rchart.Rd | 2
man/Rchartsd.Rd | 2
man/SD1legend.Rd | 2
man/SD2legend.Rd | 2
man/SDAband.Rd | 2
man/SN.Rd | 2
man/SPClegend.Rd | 2
man/SPCline.Rd | 2
man/SSDforR.Rd | 2
man/Savecsv.Rd | 2
man/Trimline.Rd | 2
man/XRchart.Rd | 2
man/Xmrchart.Rd | 2
man/cdcabove.rd | 2
man/cdcbelow.rd | 2
man/diffchart.Rd | 2
man/insert.rd | 2
man/ird.rd | 2
man/listnames.rd | 2
man/meanabove.rd | 2
man/meanbelow.rd | 2
man/pandabove.rd | 2
man/pandbelow.rd | 2
man/pemlegend.rd | 2
man/regabove.Rd | 2
man/regbelow.Rd | 2
man/robregabove.Rd | 2
man/robregbelow.Rd | 2
man/robustCDCabove.Rd | 2
man/robustCDCbelow.Rd | 2
man/trimabove.Rd | 2
70 files changed, 143 insertions(+), 143 deletions(-)
Title: Calculate Species Richness and Extrapolation Metrics
Diff between sprex versions 1.0 dated 2015-02-24 and 1.1 dated 2015-04-18
Description: Calculate species richness functions for rarefaction and
extrapolation.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 8 ++---
MD5 | 60 +++++++++++++++++++++---------------------
R/ACE.R | 1
R/Chao1.R | 5 ++-
R/Swor1.R | 21 ++++++++++----
R/bootstrap.assemblage.R | 10 ++++---
R/discovery.curve.R | 49 ++++++++++++++++++++--------------
R/expand.freqs.R | 14 ++++++---
R/expected.num.species.R | 26 ++++++++++--------
R/f.stats.R | 8 +++--
R/f0.R | 29 ++++++++++----------
R/iChao1.R | 4 ++
R/jack1.R | 1
R/jack2.R | 1
R/num.samples.required.R | 28 +++++++++++--------
R/plot.discovery.curve.R | 24 ++++++++++------
R/sample.to.species.freq.R | 17 +++++++----
R/species.to.sample.freq.R | 11 ++++---
R/sprex-package.R | 13 ++++-----
man/bootstrap.assemblage.Rd | 9 +++---
man/discovery.curve.Rd | 42 ++++++++++++++++-------------
man/expand.freqs.Rd | 13 +++++----
man/expected.num.species.Rd | 25 +++++++++--------
man/f.stats.Rd | 7 ++--
man/f0.Rd | 29 ++++++++++----------
man/num.samples.required.Rd | 22 ++++++++-------
man/osa.old.growth.Rd | 4 +-
man/plot.discovery.curve.Rd | 16 ++++++-----
man/sample.to.species.freq.Rd | 15 +++++++---
man/species.to.sample.freq.Rd | 10 ++++---
man/sprex-package.Rd | 9 +++---
31 files changed, 307 insertions(+), 224 deletions(-)
Title: Miscellaneous Data Management Tools
Diff between sjmisc versions 1.0.0 dated 2015-03-22 and 1.0.1 dated 2015-04-18
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
DESCRIPTION | 10
MD5 | 105 +-
NAMESPACE | 87 +
NEWS | 45 -
R/sjImportSPSS.R | 2191 +++++++++++++++++++++++++-------------------------
R/sjRecode.R | 212 ++--
R/sjStatistics.R | 240 ++++-
README.md | 96 +-
man/chisq_gof.Rd | 68 -
man/cramer.Rd | 52 -
man/cronb.Rd | 50 -
man/cv.Rd | 66 -
man/dicho.Rd | 87 +
man/efc.Rd | 84 -
man/efc2.Rd | 50 -
man/efc3.Rd | 50 -
man/eta_sq.Rd | 94 +-
man/get_val_labels.Rd | 146 +--
man/get_var_labels.Rd | 160 +--
man/group_labels.Rd | 164 +--
man/group_str.Rd | 98 +-
man/group_var.Rd | 146 +--
man/is_crossed.Rd |only
man/is_nested.Rd |only
man/is_num_fac.Rd |only
man/levene_test.Rd | 46 -
man/mean_n.Rd | 80 -
man/mic.Rd | 80 -
man/mwu.Rd | 104 +-
man/phi.Rd | 52 -
man/read_sas.Rd | 68 -
man/read_spss.Rd | 150 +--
man/read_stata.Rd | 64 -
man/rec.Rd | 120 +-
man/recode_to.Rd | 112 +-
man/reliab_test.Rd | 164 +--
man/rmse.Rd | 54 -
man/set_na.Rd | 93 +-
man/set_val_labels.Rd | 136 +--
man/set_var_labels.Rd | 174 +--
man/sjmisc-package.Rd | 60 -
man/std_beta.Rd | 92 +-
man/std_e.Rd | 42
man/str_pos.Rd | 138 +--
man/table_values.Rd | 72 -
man/to_fac.Rd | 91 +-
man/to_label.Rd | 101 +-
man/to_sjPlot.Rd | 68 -
man/to_value.Rd | 102 +-
man/weight.Rd | 78 -
man/weight2.Rd | 90 +-
man/word_wrap.Rd | 56 -
man/write_spss.Rd | 62 -
man/write_stata.Rd | 54 -
tests |only
55 files changed, 3619 insertions(+), 3285 deletions(-)
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Diff between MATA versions 0.2 dated 2015-01-08 and 0.3 dated 2015-04-18
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence
intervals, which are constructed using single-model estimators and model
weights.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek
DESCRIPTION | 14 +++++++-------
MD5 | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Diff between Luminescence versions 0.4.2 dated 2015-03-23 and 0.4.3 dated 2015-04-18
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer
DESCRIPTION | 10
MD5 | 78 -
NAMESPACE | 3
NEWS | 232 +++
R/Analyse_SAR.OSLdata.R | 415 +++---
R/RLum.Analysis-class.R | 801 ++++++-------
R/RisoeBINfileData-class.R | 198 +--
R/analyse_IRSAR.RF.R | 6
R/analyse_SAR.CWOSL.R | 20
R/calc_MinDose.R | 2
R/calc_OSLLxTxRatio.R | 282 ++--
R/calc_Statistics.R | 4
R/extract_IrradiationTimes.R | 186 ++-
R/fit_CWCurve.R | 744 ++++++------
R/plot_GrowthCurve.R | 2455 ++++++++++++++++++++--------------------
R/plot_Histogram.R | 1297 ++++++++++-----------
R/plot_RLum.Analysis.R | 309 +++--
R/plot_RLum.Data.Spectrum.R | 270 ++--
R/readBIN2R.R | 2013 ++++++++++++++++----------------
R/readXSYG2R.R | 13
R/writeR2BIN.R | 116 +
inst/CITATION | 6
inst/NEWS.Rd | 144 ++
man/Analyse_SAR.OSLdata.Rd | 93 -
man/Luminescence-package.Rd | 27
man/Risoe.BINfileData-class.Rd | 151 +-
man/analyse_IRSAR.RF.Rd | 2
man/analyse_SAR.CWOSL.Rd | 2
man/calc_MinDose.Rd | 2
man/calc_OSLLxTxRatio.Rd | 62 -
man/calc_Statistics.Rd | 2
man/extract_IrradiationTimes.Rd | 35
man/fit_CWCurve.Rd | 98 -
man/plot_GrowthCurve.Rd | 2
man/plot_Histogram.Rd | 9
man/plot_RLum.Analysis.Rd | 13
man/plot_RLum.Data.Spectrum.Rd | 55
man/readBIN2R.Rd | 7
man/readXSYG2R.Rd | 2
man/writeR2BIN.Rd | 14
40 files changed, 5543 insertions(+), 4637 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Diff between KFAS versions 1.0.4-1 dated 2014-06-06 and 1.1.0 dated 2015-04-18
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske
KFAS-1.0.4-1/KFAS/src/deviance.f95 |only
KFAS-1.0.4-1/KFAS/src/glogliku.f95 |only
KFAS-1.1.0/KFAS/ChangeLog | 50 -
KFAS-1.1.0/KFAS/DESCRIPTION | 19
KFAS-1.1.0/KFAS/MD5 | 202 ++--
KFAS-1.1.0/KFAS/NAMESPACE | 4
KFAS-1.1.0/KFAS/R/KFAS-package.R | 256 +++--
KFAS-1.1.0/KFAS/R/KFS.R | 985 ++++++++++-----------
KFAS-1.1.0/KFAS/R/SSMarima.R | 41
KFAS-1.1.0/KFAS/R/SSMcustom.R | 25
KFAS-1.1.0/KFAS/R/SSMcycle.R | 61 -
KFAS-1.1.0/KFAS/R/SSModel.R | 589 ++++++------
KFAS-1.1.0/KFAS/R/SSMregression.R | 360 +++----
KFAS-1.1.0/KFAS/R/SSMseasonal.R | 279 ++---
KFAS-1.1.0/KFAS/R/SSMtrend.R | 59 -
KFAS-1.1.0/KFAS/R/approxSSM.R | 160 ++-
KFAS-1.1.0/KFAS/R/artransform.R | 23
KFAS-1.1.0/KFAS/R/checkModel.R | 179 ++-
KFAS-1.1.0/KFAS/R/coef.KFS.R | 60 -
KFAS-1.1.0/KFAS/R/deviance.KFS.R | 19
KFAS-1.1.0/KFAS/R/extract.SSModel.R | 293 +++---
KFAS-1.1.0/KFAS/R/fitSSM.R | 189 ++--
KFAS-1.1.0/KFAS/R/fitted.KFS.R | 33
KFAS-1.1.0/KFAS/R/hatvalues.KFS.R | 60 -
KFAS-1.1.0/KFAS/R/importanceSSM.R | 259 ++---
KFAS-1.1.0/KFAS/R/initTheta.R |only
KFAS-1.1.0/KFAS/R/internalResids.R |only
KFAS-1.1.0/KFAS/R/interval.R | 159 +--
KFAS-1.1.0/KFAS/R/ldl.R | 9
KFAS-1.1.0/KFAS/R/logLik.SSModel.R | 294 +++---
KFAS-1.1.0/KFAS/R/mvInnovations.R |only
KFAS-1.1.0/KFAS/R/predict.SSModel.R | 368 +++----
KFAS-1.1.0/KFAS/R/print.objects.R | 144 +--
KFAS-1.1.0/KFAS/R/residuals.KFS.R | 209 ++--
KFAS-1.1.0/KFAS/R/rstandard.KFS.R | 238 +----
KFAS-1.1.0/KFAS/R/signals.R | 149 +--
KFAS-1.1.0/KFAS/R/simHelper.R |only
KFAS-1.1.0/KFAS/R/simulateSSM.R | 222 +---
KFAS-1.1.0/KFAS/R/subset.SSModel.R | 138 --
KFAS-1.1.0/KFAS/R/transformSSM.R | 279 +++--
KFAS-1.1.0/KFAS/README.md | 58 -
KFAS-1.1.0/KFAS/build |only
KFAS-1.1.0/KFAS/data/alcohol.rda |only
KFAS-1.1.0/KFAS/inst |only
KFAS-1.1.0/KFAS/man/Extract.SSModel.Rd | 79 -
KFAS-1.1.0/KFAS/man/GlobalTemp.Rd | 13
KFAS-1.1.0/KFAS/man/KFAS.Rd | 298 +++---
KFAS-1.1.0/KFAS/man/KFS.Rd | 347 +++----
KFAS-1.1.0/KFAS/man/SSModel.Rd | 303 +++---
KFAS-1.1.0/KFAS/man/alcohol.Rd |only
KFAS-1.1.0/KFAS/man/approxSSM.Rd | 105 +-
KFAS-1.1.0/KFAS/man/artransform.Rd | 22
KFAS-1.1.0/KFAS/man/boat.Rd | 8
KFAS-1.1.0/KFAS/man/checkModel.Rd | 40
KFAS-1.1.0/KFAS/man/coef.KFS.Rd | 38
KFAS-1.1.0/KFAS/man/deviance.KFS.Rd | 15
KFAS-1.1.0/KFAS/man/fitSSM.Rd | 90 +
KFAS-1.1.0/KFAS/man/fitted.KFS.Rd | 22
KFAS-1.1.0/KFAS/man/hatvalues.KFS.Rd | 30
KFAS-1.1.0/KFAS/man/importanceSSM.Rd | 96 +-
KFAS-1.1.0/KFAS/man/ldl.Rd | 16
KFAS-1.1.0/KFAS/man/logLik.SSModel.Rd | 108 +-
KFAS-1.1.0/KFAS/man/predict.SSModel.Rd | 129 +-
KFAS-1.1.0/KFAS/man/print.KFS.Rd | 14
KFAS-1.1.0/KFAS/man/print.SSModel.Rd | 6
KFAS-1.1.0/KFAS/man/residuals.KFS.Rd | 56 -
KFAS-1.1.0/KFAS/man/rstandard.KFS.Rd | 88 +
KFAS-1.1.0/KFAS/man/sexratio.Rd | 7
KFAS-1.1.0/KFAS/man/signal.Rd | 38
KFAS-1.1.0/KFAS/man/simulateSSM.Rd | 52 -
KFAS-1.1.0/KFAS/man/transformSSM.Rd | 48 -
KFAS-1.1.0/KFAS/src/Makevars | 2
KFAS-1.1.0/KFAS/src/Makevars.win |only
KFAS-1.1.0/KFAS/src/approx.f95 | 200 ++--
KFAS-1.1.0/KFAS/src/approxloop.f95 |only
KFAS-1.1.0/KFAS/src/artransform.f95 | 39
KFAS-1.1.0/KFAS/src/cdistwrap.c |only
KFAS-1.1.0/KFAS/src/covmeanw.f95 | 28
KFAS-1.1.0/KFAS/src/declarations.h | 12
KFAS-1.1.0/KFAS/src/filter1step.f95 |only
KFAS-1.1.0/KFAS/src/filter1stepnovar.f95 |only
KFAS-1.1.0/KFAS/src/filtersimfast.f95 | 111 --
KFAS-1.1.0/KFAS/src/gloglik.f95 | 179 +--
KFAS-1.1.0/KFAS/src/gsmoothall.f95 | 359 +++----
KFAS-1.1.0/KFAS/src/init.c | 11
KFAS-1.1.0/KFAS/src/isample.f95 | 57 -
KFAS-1.1.0/KFAS/src/isamplefilter.f95 | 95 +-
KFAS-1.1.0/KFAS/src/kfilter.f95 | 210 ----
KFAS-1.1.0/KFAS/src/kfstheta.f95 | 316 +-----
KFAS-1.1.0/KFAS/src/ldl.f95 | 5
KFAS-1.1.0/KFAS/src/ldlssm.f95 | 4
KFAS-1.1.0/KFAS/src/marginalxx.f95 |only
KFAS-1.1.0/KFAS/src/mvfilter.f95 |only
KFAS-1.1.0/KFAS/src/ngfilter.f95 | 27
KFAS-1.1.0/KFAS/src/ngloglik.f95 | 110 +-
KFAS-1.1.0/KFAS/src/ngsmooth.f95 | 26
KFAS-1.1.0/KFAS/src/predict.f95 | 5
KFAS-1.1.0/KFAS/src/ptheta.f95 |only
KFAS-1.1.0/KFAS/src/pytheta.f95 |only
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KFAS-1.1.0/KFAS/src/smoothsim.f95 | 306 +-----
KFAS-1.1.0/KFAS/src/smoothsimfast.f95 | 267 +----
KFAS-1.1.0/KFAS/tests/testthat/testBasics.R | 7
KFAS-1.1.0/KFAS/tests/testthat/testGLM.R | 113 --
KFAS-1.1.0/KFAS/tests/testthat/testImportanceSSM.R |only
KFAS-1.1.0/KFAS/tests/testthat/testNumerical.R |only
KFAS-1.1.0/KFAS/tests/testthat/testPredict.R |only
KFAS-1.1.0/KFAS/tests/testthat/testSSMarima.R | 26
KFAS-1.1.0/KFAS/tests/testthat/testSimulateSSM.R |only
KFAS-1.1.0/KFAS/tests/testthat/testStruct.R | 40
KFAS-1.1.0/KFAS/vignettes |only
113 files changed, 5332 insertions(+), 5890 deletions(-)
Title: Tools for Checking Data Consistency
Diff between datacheck versions 1.0.4 dated 2014-09-23 and 1.2.2 dated 2015-04-18
Description: Functions to check variables against a
set of data quality rules. A rule file can be accompanied by look-up tables. In
addition, there are some convenience functions that may
serve as an example for defining clearer 'data rules'. An
HTML based user interface facilitates initial exploration of the
functionality.
Author: "Simon, Reinhard (CIP)"
Maintainer: "Simon, Reinhard (CIP)"
datacheck-1.0.4/datacheck/build |only
datacheck-1.0.4/datacheck/inst/doc/index.R |only
datacheck-1.2.2/datacheck/DESCRIPTION | 35
datacheck-1.2.2/datacheck/LICENSE |only
datacheck-1.2.2/datacheck/MD5 | 106
datacheck-1.2.2/datacheck/NAMESPACE | 20
datacheck-1.2.2/datacheck/NEWS | 27
datacheck-1.2.2/datacheck/R/datacheck.R | 963 +++-
datacheck-1.2.2/datacheck/README.md | 18
datacheck-1.2.2/datacheck/inst/doc/RN_1.0.4.md |only
datacheck-1.2.2/datacheck/inst/doc/RN_1.0.4.pdf |only
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datacheck-1.2.2/datacheck/inst/doc/index.Rmd | 37
datacheck-1.2.2/datacheck/inst/doc/index.html | 2982 ++-----------
datacheck-1.2.2/datacheck/inst/examples/datadict_profile.R | 30
datacheck-1.2.2/datacheck/inst/examples/has_punct.R | 2
datacheck-1.2.2/datacheck/inst/examples/has_ruleErrors.R | 13
datacheck-1.2.2/datacheck/inst/examples/is_oneOf.R | 40
datacheck-1.2.2/datacheck/inst/examples/is_onlyLowers.R | 7
datacheck-1.2.2/datacheck/inst/examples/is_properName.R | 6
datacheck-1.2.2/datacheck/inst/examples/is_withinRange.R | 4
datacheck-1.2.2/datacheck/inst/examples/person_rules.R | 18
datacheck-1.2.2/datacheck/inst/examples/rules.R | 18
datacheck-1.2.2/datacheck/inst/examples/rules1.R | 12
datacheck-1.2.2/datacheck/inst/examples/rules2.R | 4
datacheck-1.2.2/datacheck/inst/examples/soil_rules.R | 59
datacheck-1.2.2/datacheck/inst/www/server.R | 22
datacheck-1.2.2/datacheck/inst/www/ui.R | 55
datacheck-1.2.2/datacheck/man/as.rules.Rd | 12
datacheck-1.2.2/datacheck/man/as_rules.Rd |only
datacheck-1.2.2/datacheck/man/datacheck-package.Rd | 9
datacheck-1.2.2/datacheck/man/datadict.profile.Rd | 39
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datacheck-1.2.2/datacheck/man/has.punct.Rd | 15
datacheck-1.2.2/datacheck/man/has.ruleErrors.Rd | 24
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datacheck-1.2.2/datacheck/man/heatmap.quality.Rd | 10
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datacheck-1.2.2/datacheck/man/is.datadict.profile.Rd | 43
datacheck-1.2.2/datacheck/man/is.oneOf.Rd | 53
datacheck-1.2.2/datacheck/man/is.onlyLowers.Rd | 18
datacheck-1.2.2/datacheck/man/is.properName.Rd | 19
datacheck-1.2.2/datacheck/man/is.withinRange.Rd | 14
datacheck-1.2.2/datacheck/man/is_datadict_profile.Rd |only
datacheck-1.2.2/datacheck/man/is_one_of.Rd |only
datacheck-1.2.2/datacheck/man/is_only_lowers.Rd |only
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datacheck-1.2.2/datacheck/man/pkg.version.Rd | 6
datacheck-1.2.2/datacheck/man/pkg_version.Rd |only
datacheck-1.2.2/datacheck/man/prep4rep.Rd | 10
datacheck-1.2.2/datacheck/man/read.rules.Rd | 11
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datacheck-1.2.2/datacheck/man/ruleCoverage.Rd | 7
datacheck-1.2.2/datacheck/man/rule_coverage.Rd |only
datacheck-1.2.2/datacheck/man/runDatacheck.Rd | 6
datacheck-1.2.2/datacheck/man/run_datacheck.Rd |only
datacheck-1.2.2/datacheck/man/scoreSum.Rd | 7
datacheck-1.2.2/datacheck/man/score_sum.Rd |only
datacheck-1.2.2/datacheck/man/shortSummary.Rd | 8
datacheck-1.2.2/datacheck/man/short_summary.Rd |only
datacheck-1.2.2/datacheck/vignettes/index.Rmd | 34
datacheck-1.2.2/datacheck/vignettes/index.html |only
67 files changed, 1754 insertions(+), 3069 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Diff between daff versions 0.1.2 dated 2015-02-24 and 0.1.4 dated 2015-04-18
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches.
Changes to data can be made visible by using render_diff. The V8 package is used to
wrap the 'daff.js' JavaScript library which is included in the package.
Author: Paul Fitzpatrick [aut] (JavaScript original,
http://paulfitz.github.io/daff/),
Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge
DESCRIPTION | 17 ++++++++---------
MD5 | 20 ++++++++++----------
NAMESPACE | 1 +
NEWS | 3 +++
R/TableView.R | 18 +++++++++---------
R/context.R | 2 +-
R/diff-data.R | 2 +-
R/merge-data.R | 6 +++---
R/patch-data.R | 2 +-
R/render-diff.R | 2 +-
README.md | 13 ++++++++-----
11 files changed, 46 insertions(+), 40 deletions(-)
Title: A Package for Coincidence Analysis (CNA)
Diff between cna versions 1.0-2 dated 2015-01-03 and 1.0-3 dated 2015-04-18
Description: Provides functions for performing Coincidence Analysis (CNA).
Author: Ambuehl, Mathias, Michael Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem
Maintainer: Alexis Kauffmann
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/cna_aux.r | 2 +-
inst/CITATION | 2 +-
inst/ChangeLog | 2 ++
man/cna.package.Rd | 4 ++--
6 files changed, 15 insertions(+), 13 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Diff between cheddar versions 0.1-626 dated 2014-08-28 and 0.1-629 dated 2015-04-18
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson
DESCRIPTION | 15 +--
LICENSE | 2
MD5 | 63 +++++++--------
NAMESPACE | 15 +++
R/community_MN.R | 6 -
R/community_trophic_links.R | 4
R/graph_nodes.R | 80 +++++++++++++++++++
build/vignette.rds |binary
inst/CITATION | 3
inst/doc/CheddarQuickstart.R | 18 ++--
inst/doc/CheddarQuickstart.Rnw | 6 +
inst/doc/CheddarQuickstart.pdf |binary
inst/doc/Collections.R | 104 ++++++++++++-------------
inst/doc/Collections.Rnw | 6 +
inst/doc/Collections.pdf |binary
inst/doc/Community.R | 166 ++++++++++++++++++++--------------------
inst/doc/Community.Rnw | 6 +
inst/doc/Community.pdf |binary
inst/doc/ImportExport.R | 36 ++++----
inst/doc/ImportExport.Rnw | 6 +
inst/doc/ImportExport.pdf |binary
inst/doc/PlotsAndStats.R | 138 ++++++++++++++++-----------------
inst/doc/PlotsAndStats.Rnw | 7 +
inst/doc/PlotsAndStats.pdf |binary
man/PlotCircularWeb.Rd | 3
man/PlotWagonWheel.Rd |only
man/TrophicLevels.Rd | 34 ++++----
man/cheddar.Rd | 4
vignettes/CheddarQuickstart.Rnw | 6 +
vignettes/Collections.Rnw | 6 +
vignettes/Community.Rnw | 6 +
vignettes/ImportExport.Rnw | 6 +
vignettes/PlotsAndStats.Rnw | 7 +
33 files changed, 448 insertions(+), 305 deletions(-)
Title: Interface to Bold Systems API
Diff between bold versions 0.2.0 dated 2014-08-20 and 0.2.6 dated 2015-04-18
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic barcode data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
DESCRIPTION | 10
MD5 | 50 ++--
NAMESPACE | 29 ++
NEWS | 16 +
R/bold_identify.R | 51 ++--
R/bold_seq.R | 24 --
R/bold_seqspec.R | 48 +---
R/bold_specimens.R | 39 +--
R/bold_tax_id.R | 49 ++--
R/bold_tax_name.R | 56 +----
R/bold_trace.R | 79 +++++--
R/zzz.R | 38 +++
README.md | 236 +++++++++-------------
build/vignette.rds |binary
inst/doc/bold_vignette.Rmd | 463 --------------------------------------------
inst/doc/bold_vignette.html | 268 +++++++++++++------------
man/bold-package.Rd | 3
man/bold_identify.Rd | 39 +--
man/bold_seq.Rd | 8
man/bold_seqspec.Rd | 11 -
man/bold_specimens.Rd | 7
man/bold_tax_id.Rd | 32 ++-
man/bold_tax_name.Rd | 16 +
man/bold_trace.Rd | 35 ++-
man/sequences.Rd | 3
vignettes/bold_vignette.Rmd | 463 --------------------------------------------
26 files changed, 629 insertions(+), 1444 deletions(-)
Title: Variable Length Markov Chains ('VLMC') Models
Diff between VLMC versions 1.4-0 dated 2014-10-06 and 1.4-1 dated 2015-04-17
Description: Functions, Classes & Methods for estimation, prediction, and
simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler
Maintainer: Martin Maechler
ChangeLog | 8 ++++++++
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
NAMESPACE | 4 +++-
R/dendrogram.R | 3 ++-
R/predict.R | 4 ++--
R/vlmc.R | 14 +++++++-------
src/predict.c | 15 +++++++++------
src/vlmc.h | 2 +-
tests/pred-vlmc.R | 6 ++++++
tests/pred-vlmc.Rout.save | 14 ++++++++++----
11 files changed, 64 insertions(+), 38 deletions(-)
Title: Tuned Data Mining in R
Diff between TDMR versions 1.2 dated 2014-08-30 and 1.3 dated 2015-04-17
Description: Tuned Data Mining in R (TDMR) performs a complete tuning of a data
mining task.
Author: Wolfgang Konen
Maintainer: Wolfgang Konen
DESCRIPTION | 15
MD5 | 193 +--
NAMESPACE | 43
R/tdmBigLoop.r | 3
R/tdmClassify.r | 29
R/tdmDispatchTuner.r | 10
R/tdmGeneralUtils.r | 6
R/tdmGraphicUtils.r | 2
R/tdmMetacostRf.r | 4
R/tdmModelingUtils.r | 8
R/tdmPlotResMeta.r | 4
R/tdmROCR.r | 13
R/tdmRegress.r | 6
R/tdmStartOther.r | 412 +++----
demo/demo06ROCR.r | 1
demo/demo07cma_j.r | 6
inst/demo02sonar/data/sonar.Rdata |binary
inst/demo02sonar/outcmaesdisp.dat |only
inst/demo02sonar/sonar_01.apd | 2
inst/demo02sonar/sonar_03.apd | 7
inst/demo02sonar/sonar_03.conf | 2
inst/doc/TDMR-docu.pdf |binary
inst/doc/TDMR-tutorial.pdf |binary
inst/doc/changes.html | 2141 +++++++++++++++++---------------------
inst/doc/index.html | 93 -
man/Opts.Rd | 40
man/TDMR-package.Rd | 52
man/bfgsTuner.Rd | 29
man/cat1.Rd | 14
man/cat2.Rd | 14
man/cma_jTuner.Rd | 40
man/cmaesTuner.Rd | 29
man/dsetTest.TDMdata.Rd | 18
man/dsetTrnVa.TDMdata.Rd | 19
man/lhdTuner.Rd | 28
man/makeTdmRandomSeed.Rd | 37
man/powellTuner.Rd | 26
man/predict.TDMenvir.Rd | 31
man/print.TDMclassifier.Rd | 40
man/print.TDMdata.Rd | 18
man/print.TDMregressor.Rd | 36
man/print1.Rd | 15
man/print2.Rd | 15
man/spotTuner.Rd | 24
man/tdmBigLoop.Rd | 257 +---
man/tdmBindResponse.Rd | 17
man/tdmClassify.Rd | 173 +--
man/tdmClassifyLoop.Rd | 117 --
man/tdmClassifySummary.Rd | 42
man/tdmDefaultsFill.Rd | 147 --
man/tdmDispatchTuner.Rd | 51
man/tdmEmbedDataFrame.Rd | 22
man/tdmEnvTAddBstRes.Rd | 18
man/tdmEnvTAddGetters.Rd | 11
man/tdmEnvTLoad.Rd | 12
man/tdmEnvTMakeNew.Rd | 39
man/tdmEnvTReadApd.Rd | 27
man/tdmEnvTSensi.Rd | 23
man/tdmExecSpotStep.Rd | 46
man/tdmGraAndLogFinalize.Rd | 19
man/tdmGraAndLogInitialize.Rd | 21
man/tdmGraphicCloseDev.Rd | 15
man/tdmGraphicCloseWin.Rd | 15
man/tdmGraphicInit.Rd | 28
man/tdmGraphicNewWin.Rd | 20
man/tdmGraphicToTop.Rd | 13
man/tdmMapDesApply.Rd | 32
man/tdmMapDesLoad.Rd | 27
man/tdmModConfmat.Rd | 93 -
man/tdmModCreateCVindex.Rd | 84 -
man/tdmModSortedRFimport.Rd | 88 -
man/tdmModVote2Target.Rd | 40
man/tdmOptsDefaultsFill.Rd | 63 -
man/tdmOptsDefaultsSet.Rd | 397 ++-----
man/tdmParaBootstrap.Rd | 56
man/tdmPlotResMeta.Rd | 113 --
man/tdmPreAddMonomials.Rd | 43
man/tdmPreFindConstVar.Rd | 13
man/tdmPreGroupLevels.Rd | 36
man/tdmPreLevel2Target.Rd | 24
man/tdmPreNAroughfix.Rd | 19
man/tdmPrePCA.apply.Rd | 51
man/tdmPrePCA.train.Rd | 64 -
man/tdmPreSFA.apply.Rd | 55
man/tdmPreSFA.train.Rd | 67 -
man/tdmROCR.Rd | 18
man/tdmROCR.TDMclassifier.Rd | 29
man/tdmROCRbase.Rd | 62 -
man/tdmRandomSeed.Rd | 23
man/tdmReadCmd.Rd | 43
man/tdmReadData.Rd | 69 -
man/tdmRegress.Rd | 125 --
man/tdmRegressLoop.Rd | 95 -
man/tdmRegressSummary.Rd | 40
man/tdmSplitTestData.Rd | 87 -
man/tdmStartSpot.Rd | 48
man/unbiasedBestRun_O.Rd | 69 -
man/unbiasedRun.Rd | 126 --
98 files changed, 3078 insertions(+), 3779 deletions(-)
Title: Functions to Explore L-Systems (Lindenmayer Systems)
Diff between LindenmayeR versions 0.1-0 dated 2014-08-12 and 0.1.4 dated 2015-04-16
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can
be used to simulate biological forms and certain kinds of fractals.
Briefly, in an L-system a series of symbols in a string are replaced
iteratively according to rules to give a more complex string. Eventually,
the symbols are translated into turtle graphics for plotting. Wikipedia has
a very good introduction: en.wikipedia.org/wiki/L-system This package
provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
NAMESPACE | 3 ++-
NEWS | 23 +++++++++++++++++++----
R/LindenmayeR-package.R | 2 ++
R/Lsys.R | 12 ++++++++++--
R/drawLsys.R | 24 +++++++++++++++++++++---
man/LindenmayeR-package.Rd | 4 +++-
man/Lsys.Rd | 3 ++-
man/drawLsys.Rd | 13 ++++++++++++-
10 files changed, 86 insertions(+), 28 deletions(-)
Title: Crunch.io Data Tools
Diff between crunch versions 1.0.2 dated 2015-04-04 and 1.1.0 dated 2015-04-16
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson
DESCRIPTION | 10 ++--
MD5 | 73 +++++++++++++++++++-----------------
NAMESPACE | 15 ++++++-
R/AllClasses.R | 2
R/AllGenerics.R | 25 ++++++++++++
R/api.R | 15 +------
R/append-dataset.R | 9 ++--
R/as-data-frame.R |only
R/auth.R | 2
R/categories.R | 21 ----------
R/crest.R |only
R/crunch.R | 3 +
R/dataset.R | 7 +--
R/get-datasets.R | 1
R/json.R |only
R/log.R |only
R/misc.R | 14 ++----
R/new-dataset.R | 9 +---
R/share.R | 2
R/shoji-catalog.R | 2
R/shoji.R | 1
R/tuple.R | 5 +-
R/variable-catalog.R | 4 -
R/variable-order.R | 25 ------------
R/variable-to-R.R | 24 -----------
R/variable-update.R | 8 ++-
R/variable.R | 25 +++++++++---
inst/doc/variables.html | 3 -
man/dataset-to-R.Rd | 25 ++++++++++--
man/tojson-crunch.Rd | 69 ++++++++++++++++------------------
tests/testthat/helper.R | 4 +
tests/testthat/test-api.R | 26 ++++++------
tests/testthat/test-as-data-frame.R | 33 +++++++++++++---
tests/testthat/test-encoding.R | 35 +----------------
tests/testthat/utftesting.R |only
vignettes/array-variables.RData |binary
vignettes/economist.RData |binary
vignettes/getting-started.RData |binary
vignettes/variable-order.RData |binary
vignettes/variables.RData |binary
40 files changed, 246 insertions(+), 251 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Diff between poweRlaw versions 0.30.1 dated 2015-03-13 and 0.30.2 dated 2015-04-16
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.R |only
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poweRlaw-0.30.2/poweRlaw/DESCRIPTION | 8 +-
poweRlaw-0.30.2/poweRlaw/MD5 | 39 +++++-----
poweRlaw-0.30.2/poweRlaw/NEWS | 6 +
poweRlaw-0.30.2/poweRlaw/R/plot_methods.R | 2
poweRlaw-0.30.2/poweRlaw/build/vignette.rds |binary
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36 files changed, 31 insertions(+), 24 deletions(-)
Title: Missing Data Imputation and Model Checking
Diff between mi versions 0.10-2 dated 2015-04-07 and 1.0 dated 2015-04-16
Description: The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.
Author: Andrew Gelman [ctb],
Jennifer Hill [ctb],
Yu-Sung Su [aut],
Masanao Yajima [ctb],
Maria Pittau [ctb],
Ben Goodrich [cre, aut],
Yajuan Si [ctb],
Jon Kropko [aut]
Maintainer: Ben Goodrich
mi-0.10-2/mi/CHANGELOG |only
mi-0.10-2/mi/R/AllInternal.R |only
mi-0.10-2/mi/R/bayesglm.mi.R |only
mi-0.10-2/mi/R/bayespolr.mi.R |only
mi-0.10-2/mi/R/coef.R |only
mi-0.10-2/mi/R/convergence.plot.R |only
mi-0.10-2/mi/R/display.R |only
mi-0.10-2/mi/R/fitted.R |only
mi-0.10-2/mi/R/glm.mi.R |only
mi-0.10-2/mi/R/imputation.models.R |only
mi-0.10-2/mi/R/imputed.R |only
mi-0.10-2/mi/R/lm.mi.R |only
mi-0.10-2/mi/R/lmer.mi.R |only
mi-0.10-2/mi/R/load.first.R |only
mi-0.10-2/mi/R/mi.binary.R |only
mi-0.10-2/mi/R/mi.categorical.R |only
mi-0.10-2/mi/R/mi.completed.R |only
mi-0.10-2/mi/R/mi.continuous.R |only
mi-0.10-2/mi/R/mi.count.R |only
mi-0.10-2/mi/R/mi.fixed.R |only
mi-0.10-2/mi/R/mi.hist.R |only
mi-0.10-2/mi/R/mi.info.R |only
mi-0.10-2/mi/R/mi.mean.R |only
mi-0.10-2/mi/R/mi.median.R |only
mi-0.10-2/mi/R/mi.misc.R |only
mi-0.10-2/mi/R/mi.pmm.R |only
mi-0.10-2/mi/R/mi.polr.R |only
mi-0.10-2/mi/R/mi.pooled.R |only
mi-0.10-2/mi/R/mi.preprocess.R |only
mi-0.10-2/mi/R/mi.scatterplot.R |only
mi-0.10-2/mi/R/missing.pattern.plot.R |only
mi-0.10-2/mi/R/plot.R |only
mi-0.10-2/mi/R/polr.mi.R |only
mi-0.10-2/mi/R/print.R |only
mi-0.10-2/mi/R/random.imp.R |only
mi-0.10-2/mi/R/resid.R |only
mi-0.10-2/mi/R/residual.plot.R |only
mi-0.10-2/mi/R/se.coef.R |only
mi-0.10-2/mi/R/show.R |only
mi-0.10-2/mi/R/sigma.hat.R |only
mi-0.10-2/mi/R/typecast.R |only
mi-0.10-2/mi/R/write.mi.R |only
mi-0.10-2/mi/TODO |only
mi-0.10-2/mi/data/CHAIN.rda |only
mi-0.10-2/mi/man/convergence.plot.Rd |only
mi-0.10-2/mi/man/mi.Rd |only
mi-0.10-2/mi/man/mi.binary.Rd |only
mi-0.10-2/mi/man/mi.categorical.Rd |only
mi-0.10-2/mi/man/mi.completed.Rd |only
mi-0.10-2/mi/man/mi.continuous.Rd |only
mi-0.10-2/mi/man/mi.count.Rd |only
mi-0.10-2/mi/man/mi.fixed.Rd |only
mi-0.10-2/mi/man/mi.hist.Rd |only
mi-0.10-2/mi/man/mi.info.Rd |only
mi-0.10-2/mi/man/mi.info.update.Rd |only
mi-0.10-2/mi/man/mi.method.Rd |only
mi-0.10-2/mi/man/mi.pmm.Rd |only
mi-0.10-2/mi/man/mi.polr.Rd |only
mi-0.10-2/mi/man/mi.pooled.Rd |only
mi-0.10-2/mi/man/mi.preprocess.Rd |only
mi-0.10-2/mi/man/mi.scatterplot.Rd |only
mi-0.10-2/mi/man/missing.pattern.plot.Rd |only
mi-0.10-2/mi/man/noise.control.Rd |only
mi-0.10-2/mi/man/plot.mi.Rd |only
mi-0.10-2/mi/man/random.imp.Rd |only
mi-0.10-2/mi/man/type.models.Rd |only
mi-0.10-2/mi/man/typecast.Rd |only
mi-0.10-2/mi/man/write.mi.Rd |only
mi-1.0/mi/DESCRIPTION | 44
mi-1.0/mi/MD5 | 143 -
mi-1.0/mi/NAMESPACE | 213 --
mi-1.0/mi/R/AllClass.R | 1380 ++++++++++++++--
mi-1.0/mi/R/AllGeneric.R | 244 --
mi-1.0/mi/R/change.R |only
mi-1.0/mi/R/change_family.R |only
mi-1.0/mi/R/change_imputation_method.R |only
mi-1.0/mi/R/change_link.R |only
mi-1.0/mi/R/change_model.R |only
mi-1.0/mi/R/change_size.R |only
mi-1.0/mi/R/change_transformation.R |only
mi-1.0/mi/R/change_type.R |only
mi-1.0/mi/R/complete.R |only
mi-1.0/mi/R/convenience.R |only
mi-1.0/mi/R/debug.R |only
mi-1.0/mi/R/fit_model.R |only
mi-1.0/mi/R/get_parameters.R |only
mi-1.0/mi/R/hist_methods.R |only
mi-1.0/mi/R/mi.R | 1783 ++++++++++++---------
mi-1.0/mi/R/misc.R |only
mi-1.0/mi/R/missing_data.frame.R |only
mi-1.0/mi/R/missing_variable.R |only
mi-1.0/mi/R/plot_methods.R |only
mi-1.0/mi/R/pool.R |only
mi-1.0/mi/R/random_df.R |only
mi-1.0/mi/R/sysdata.rda |only
mi-1.0/mi/R/tobin5.R |only
mi-1.0/mi/R/zzz.R |only
mi-1.0/mi/build |only
mi-1.0/mi/data/CHAIN.RData |only
mi-1.0/mi/data/nlsyV.RData |only
mi-1.0/mi/inst/CITATION | 30
mi-1.0/mi/inst/doc |only
mi-1.0/mi/man/00mi-package.Rd |only
mi-1.0/mi/man/01missing_variable.Rd |only
mi-1.0/mi/man/02missing_data.frame.Rd |only
mi-1.0/mi/man/03change.Rd |only
mi-1.0/mi/man/04mi.Rd |only
mi-1.0/mi/man/05Rhats.Rd |only
mi-1.0/mi/man/06pool.Rd |only
mi-1.0/mi/man/07complete.Rd |only
mi-1.0/mi/man/CHAIN.Rd | 63
mi-1.0/mi/man/allcategorical_missing_data.frame.Rd |only
mi-1.0/mi/man/bounded.Rd |only
mi-1.0/mi/man/categorical.Rd |only
mi-1.0/mi/man/censored-continuous.Rd |only
mi-1.0/mi/man/continuous.Rd |only
mi-1.0/mi/man/count.Rd |only
mi-1.0/mi/man/experiment_missing_data.frame.Rd |only
mi-1.0/mi/man/fit_model.Rd |only
mi-1.0/mi/man/get_parameters.Rd |only
mi-1.0/mi/man/hist.Rd |only
mi-1.0/mi/man/irrelevant.Rd |only
mi-1.0/mi/man/mi-internal.Rd |only
mi-1.0/mi/man/mi2stata.Rd |only
mi-1.0/mi/man/mipply.Rd |only
mi-1.0/mi/man/multilevel_missing_data.frame.Rd |only
mi-1.0/mi/man/multinomial.Rd |only
mi-1.0/mi/man/nlsyV.Rd |only
mi-1.0/mi/man/positive.Rd |only
mi-1.0/mi/man/rdata.frame.Rd |only
mi-1.0/mi/man/semi-continuous.Rd |only
mi-1.0/mi/tests |only
mi-1.0/mi/vignettes |only
133 files changed, 2503 insertions(+), 1397 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.16 dated 2015-03-14 and 2.17 dated 2015-04-16
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
DESCRIPTION | 18 ++++++++---------
MD5 | 45 ++++++++++++++++++++++----------------------
NAMESPACE | 34 ++++++++++++++++++++++++++-------
R/MCMC-support.R |only
R/S4-classes.R | 4 ++-
R/helpers.R | 9 +++++++-
R/lsmeans.R | 11 ++++++----
R/nonlin-support.R | 2 +
R/ref.grid.R | 25 +++++++++++++++---------
R/summary.R | 1
inst/NEWS | 16 +++++++++++++++
inst/doc/extending.pdf |binary
inst/doc/extending.rnw | 3 ++
inst/doc/using-lsmeans.R | 23 ++++++++++++++++++++++
inst/doc/using-lsmeans.pdf |binary
inst/doc/using-lsmeans.rnw | 19 ++++++++++++++++++
man/extending.Rd | 4 +--
man/lsmeans.Rd | 3 +-
man/models.Rd | 10 +++++++++
man/ref.grid.Rd | 2 -
man/ref.grid.class.Rd | 1
man/summary.Rd | 12 +++++++++--
vignettes/extending.rnw | 3 ++
vignettes/using-lsmeans.rnw | 19 ++++++++++++++++++
24 files changed, 205 insertions(+), 59 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Diff between compendiumdb versions 0.1.0 dated 2014-08-29 and 1.0.0 dated 2015-04-16
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal
Maintainer: Umesh Nandal
compendiumdb-0.1.0/compendiumdb/inst/scripts/README.txt |only
compendiumdb-0.1.0/compendiumdb/inst/tests |only
compendiumdb-1.0.0/compendiumdb/DESCRIPTION | 25
compendiumdb-1.0.0/compendiumdb/INSTALL |only
compendiumdb-1.0.0/compendiumdb/MD5 | 93
compendiumdb-1.0.0/compendiumdb/NAMESPACE | 2
compendiumdb-1.0.0/compendiumdb/R/GDSforGSE.R | 20
compendiumdb-1.0.0/compendiumdb/R/GSEforGPL.R | 10
compendiumdb-1.0.0/compendiumdb/R/GSEinDB.R | 55
compendiumdb-1.0.0/compendiumdb/R/GSMdescriptions.R | 19
compendiumdb-1.0.0/compendiumdb/R/connectDatabase.R | 20
compendiumdb-1.0.0/compendiumdb/R/createESET.R | 225 -
compendiumdb-1.0.0/compendiumdb/R/downloadGEOdata.R | 12
compendiumdb-1.0.0/compendiumdb/R/loadDataToCompendium.R | 8
compendiumdb-1.0.0/compendiumdb/R/loadDatabaseSchema.R | 6
compendiumdb-1.0.0/compendiumdb/R/parseSampleAnnot.R | 96
compendiumdb-1.0.0/compendiumdb/R/removeGSE.R | 19
compendiumdb-1.0.0/compendiumdb/R/tagExperiment.R | 4
compendiumdb-1.0.0/compendiumdb/R/updatePhenoData.R | 99
compendiumdb-1.0.0/compendiumdb/inst/doc/compendiumdb.pdf |binary
compendiumdb-1.0.0/compendiumdb/inst/extdata/compendiumSchema.sql | 1174 +++++-----
compendiumdb-1.0.0/compendiumdb/inst/scripts/BigMac/COMPENDIUM/compendiumSUB.pm | 2
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/deleteAllforGPL.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/deleteAllforGSE.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/expDesign.pl | 236 +-
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/fetchESET.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/getAllForGSE.pl | 34
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadAllforGSEeset.pl | 38
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGDS.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGPL.pl | 23
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGSMeset.pl | 6
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/load_notGDS.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/parsingSoftFile_forESET.pl | 36
compendiumdb-1.0.0/compendiumdb/inst/scripts/R/downloadSoftFile.R | 20
compendiumdb-1.0.0/compendiumdb/inst/scripts/R/esetGeneration.R | 2
compendiumdb-1.0.0/compendiumdb/inst/scripts/README |only
compendiumdb-1.0.0/compendiumdb/man/GDSforGSE.Rd | 84
compendiumdb-1.0.0/compendiumdb/man/GSEforGPL.Rd | 73
compendiumdb-1.0.0/compendiumdb/man/GSEinDB.Rd | 108
compendiumdb-1.0.0/compendiumdb/man/GSMdescriptions.Rd | 92
compendiumdb-1.0.0/compendiumdb/man/compendiumdb-package.Rd | 62
compendiumdb-1.0.0/compendiumdb/man/connectDatabase.Rd | 117
compendiumdb-1.0.0/compendiumdb/man/createESET.Rd | 147 -
compendiumdb-1.0.0/compendiumdb/man/downloadGEOdata.Rd | 122 -
compendiumdb-1.0.0/compendiumdb/man/loadDataToCompendium.Rd | 129 -
compendiumdb-1.0.0/compendiumdb/man/loadDatabaseSchema.Rd | 98
compendiumdb-1.0.0/compendiumdb/man/removeGSE.Rd | 68
compendiumdb-1.0.0/compendiumdb/man/tagExperiment.Rd | 88
compendiumdb-1.0.0/compendiumdb/man/updatePhenoData.Rd | 83
compendiumdb-1.0.0/compendiumdb/tests |only
50 files changed, 1825 insertions(+), 1750 deletions(-)
Title: Soft Classification Performance Measures
Diff between softclassval versions 1.0-20130317 dated 2013-04-03 and 1.0-20150416 dated 2015-04-16
Description: An extension of sensitivity, specificity, positive and negative
predictive value to continuous predicted and reference memberships in
[0, 1].
Author: C. Beleites
Maintainer: C. Beleites
softclassval-1.0-20130317/softclassval/inst/NEWS.Rd |only
softclassval-1.0-20150416/softclassval/DESCRIPTION | 30 +-
softclassval-1.0-20150416/softclassval/MD5 | 37 +--
softclassval-1.0-20150416/softclassval/NAMESPACE | 12 -
softclassval-1.0-20150416/softclassval/R/make01.R | 1
softclassval-1.0-20150416/softclassval/R/operators.R | 24 +-
softclassval-1.0-20150416/softclassval/R/softclassval.R | 4
softclassval-1.0-20150416/softclassval/R/unittests.R | 3
softclassval-1.0-20150416/softclassval/inst/CITATION | 9
softclassval-1.0-20150416/softclassval/man/checkrp.Rd | 36 +--
softclassval-1.0-20150416/softclassval/man/dev.Rd | 23 +-
softclassval-1.0-20150416/softclassval/man/factor2matrix.Rd | 15 -
softclassval-1.0-20150416/softclassval/man/hard.Rd | 23 +-
softclassval-1.0-20150416/softclassval/man/hardclasses.Rd | 39 +--
softclassval-1.0-20150416/softclassval/man/nsamples.Rd | 32 +--
softclassval-1.0-20150416/softclassval/man/operators.Rd | 79 +++----
softclassval-1.0-20150416/softclassval/man/performance.Rd | 106 ++++------
softclassval-1.0-20150416/softclassval/man/postproc.Rd | 29 +-
softclassval-1.0-20150416/softclassval/man/softclassval-package.Rd | 9
softclassval-1.0-20150416/softclassval/man/softclassval.unittest.Rd | 16 -
20 files changed, 248 insertions(+), 279 deletions(-)
Title: Loading Google Adwords Data into R
Diff between RAdwords versions 0.1.3 dated 2015-04-07 and 0.1.4 dated 2015-04-16
Description: Aims at loading Google Adwords data into R. Adwords is an online
advertising service that enables advertisers to display advertising copy to web users.
Therefore the package implements three main features. First, the package provides an
authentication process for R with the Google Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt
Maintainer: Johannes Burkhardt
DESCRIPTION | 17 ++++++++++-------
MD5 | 6 +++---
NEWS | 7 +++++++
R/transformData.R | 18 +++++++++++++-----
4 files changed, 33 insertions(+), 15 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Diff between letsR versions 2.0 dated 2015-02-09 and 2.1 dated 2015-04-16
Description: R functions for handling, processing, and analyzing geographic data on
species' distributions and environmental variables as well as species' description
and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
letsR-2.0/letsR/R/Data_iucn.R |only
letsR-2.0/letsR/data/iucn.rda |only
letsR-2.0/letsR/man/iucn.Rd |only
letsR-2.1/letsR/DESCRIPTION | 25 -
letsR-2.1/letsR/MD5 | 205 +++++++----
letsR-2.1/letsR/R/Data_helps.R |only
letsR-2.1/letsR/R/PresenceAbsence-class.R |only
letsR-2.1/letsR/R/getcode.R |only
letsR-2.1/letsR/R/getnames.R |only
letsR-2.1/letsR/R/letsR-package.R | 43 +-
letsR-2.1/letsR/R/lets_addpoly.R | 84 +++-
letsR-2.1/letsR/R/lets_addvar.R | 90 +++-
letsR-2.1/letsR/R/lets_classvar.R | 60 +--
letsR-2.1/letsR/R/lets_correl.R | 334 +++++++++++-------
letsR-2.1/letsR/R/lets_distmat.R | 68 +--
letsR-2.1/letsR/R/lets_field.R | 194 ++++++----
letsR-2.1/letsR/R/lets_gridirizer.R | 23 -
letsR-2.1/letsR/R/lets_iucn.R | 306 ++++++++--------
letsR-2.1/letsR/R/lets_iucn_habitats.R | 152 ++++----
letsR-2.1/letsR/R/lets_iucn_historic.R | 282 +++++++++------
letsR-2.1/letsR/R/lets_iucncont.R | 47 +-
letsR-2.1/letsR/R/lets_maplizer.R | 103 +++--
letsR-2.1/letsR/R/lets_midpoint.R | 102 +++--
letsR-2.1/letsR/R/lets_overlap.R | 118 +++---
letsR-2.1/letsR/R/lets_pamcrop.R | 60 ++-
letsR-2.1/letsR/R/lets_presab.R | 287 +++++++++------
letsR-2.1/letsR/R/lets_presab_birds.R | 344 +++++++++++--------
letsR-2.1/letsR/R/lets_presab_points.R | 128 ++++---
letsR-2.1/letsR/R/lets_rangesize.R | 146 +++++---
letsR-2.1/letsR/R/lets_shpfilter.R | 85 ++--
letsR-2.1/letsR/R/lets_summaryze.R | 58 ++-
letsR-2.1/letsR/R/lets_transf.R | 24 -
letsR-2.1/letsR/R/plot_PresenceAbsence.R | 67 ++-
letsR-2.1/letsR/R/print_PresenceAbsence.R | 10
letsR-2.1/letsR/R/print_summary_PresenceAbsence.R | 9
letsR-2.1/letsR/R/removecells.R | 14
letsR-2.1/letsR/R/removesp.R | 25 -
letsR-2.1/letsR/R/summary_PresenceAbsence.R | 45 +-
letsR-2.1/letsR/R/unicas.R | 27 -
letsR-2.1/letsR/README.md | 22 -
letsR-2.1/letsR/data/IUCN.rda |only
letsR-2.1/letsR/data/PAM.rda |binary
letsR-2.1/letsR/data/temp.rda |binary
letsR-2.1/letsR/inst |only
letsR-2.1/letsR/man/IUCN.Rd |only
letsR-2.1/letsR/man/PAM.Rd | 5
letsR-2.1/letsR/man/Phyllomedusa.Rd | 6
letsR-2.1/letsR/man/PresenceAbsence.Rd |only
letsR-2.1/letsR/man/lets.addpoly.Rd | 10
letsR-2.1/letsR/man/lets.addvar.Rd | 26 +
letsR-2.1/letsR/man/lets.classvar.Rd | 27 -
letsR-2.1/letsR/man/lets.correl.Rd | 40 +-
letsR-2.1/letsR/man/lets.distmat.Rd | 26 +
letsR-2.1/letsR/man/lets.field.Rd | 32 +
letsR-2.1/letsR/man/lets.gridirizer.Rd | 13
letsR-2.1/letsR/man/lets.iucn.Rd | 16
letsR-2.1/letsR/man/lets.iucn.ha.Rd | 14
letsR-2.1/letsR/man/lets.iucn.his.Rd | 44 ++
letsR-2.1/letsR/man/lets.iucncont.Rd | 20 -
letsR-2.1/letsR/man/lets.maplizer.Rd | 34 +
letsR-2.1/letsR/man/lets.midpoint.Rd | 16
letsR-2.1/letsR/man/lets.overlap.Rd | 32 +
letsR-2.1/letsR/man/lets.pamcrop.Rd | 23 +
letsR-2.1/letsR/man/lets.presab.Rd | 33 +
letsR-2.1/letsR/man/lets.presab.birds.Rd | 84 +++-
letsR-2.1/letsR/man/lets.presab.points.Rd | 28 -
letsR-2.1/letsR/man/lets.rangesize.Rd | 38 +-
letsR-2.1/letsR/man/lets.shFilter.Rd | 7
letsR-2.1/letsR/man/lets.summarizer.Rd | 23 +
letsR-2.1/letsR/man/lets.transf.Rd | 2
letsR-2.1/letsR/man/letsR.Rd |only
letsR-2.1/letsR/man/plot.PresenceAbsence.Rd | 16
letsR-2.1/letsR/man/print.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/print.summary.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/summary.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/temp.Rd | 12
letsR-2.1/letsR/tests |only
77 files changed, 2543 insertions(+), 1677 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Diff between iterpc versions 0.2.6 dated 2014-11-14 and 0.2.7 dated 2015-04-16
Description: It helps in 1) generating permutations and combinations with or without replacement; 2) with distinct items or non-distinct items (multiset); 3) calculating number of combinations or permutations in various situations. All generated sequences are in lexicographical order (AKA, dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai
DESCRIPTION | 10 +--
MD5 | 28 +++++-----
NAMESPACE | 2
README.md | 2
man/getall.Rd | 3 -
man/getcurrent.Rd | 3 -
man/getlength.Rd | 3 -
man/getnext.Rd | 3 -
man/iterpc.Rd | 3 -
man/multichoose.Rd | 3 -
man/nc_multiset.Rd | 3 -
man/np_multiset.Rd | 3 -
src/RcppExports.cpp | 118 ++++++++++++++++++----------------------------
src/utils/k-permutation.c | 11 +---
src/utils/k-permutation.h | 2
15 files changed, 90 insertions(+), 107 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Diff between etasFLP versions 1.2.0 dated 2014-12-22 and 1.2.1 dated 2015-04-16
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present, together with some diagnostic tools. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class 'etasclass').
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi
ChangeLog | 8 ++++++++
DESCRIPTION | 13 +++++--------
MD5 | 32 ++++++++++++++++----------------
R/eqcat.R | 2 +-
R/etasclass.R | 1 +
R/kde2dnew.fortran.R | 3 +++
R/plot.etasclass.R | 2 +-
R/plot.profile.etasclass.R | 4 ++--
R/summary.etasclass.R | 6 ++++--
data/californiacatalog.RData |binary
data/italycatalog.RData |binary
man/etasFLP-package.Rd | 17 ++++++++++-------
man/etasclass.Rd | 37 ++++++++++++++++++++-----------------
man/plot.etasclass.Rd | 14 +++++++-------
man/plot.profile.etasclass.Rd | 4 ++--
man/profile.etasclass.Rd | 15 +++++++--------
man/summary.etasclass.Rd | 3 +--
17 files changed, 88 insertions(+), 73 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.2.1 dated 2015-03-05 and 1.3.0 dated 2015-04-16
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 10 -
MD5 | 35 ++-
NAMESPACE | 3
R/BAT.R | 428 +++++++++++++++++++++++++++++++++--------------
man/accuracy.Rd | 3
man/alpha.Rd | 2
man/alpha.accum.Rd | 8
man/alpha.estimate.Rd | 2
man/beta.Rd | 10 -
man/beta.accum.Rd | 9
man/beta.multi.Rd | 8
man/contribution.Rd |only
man/dispersion.Rd |only
man/optim.alpha.Rd | 8
man/optim.alpha.stats.Rd | 2
man/optim.beta.Rd | 10 -
man/optim.beta.stats.Rd | 2
man/sim.sample.Rd | 2
man/sim.tree.Rd | 2
man/uniqueness.Rd |only
20 files changed, 370 insertions(+), 174 deletions(-)
Title: 'vcd' Extensions and Additions
Diff between vcdExtra versions 0.6-5 dated 2015-01-02 and 0.6-8 dated 2015-04-16
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly
vcdExtra-0.6-5/vcdExtra/R/loddsratio.R |only
vcdExtra-0.6-5/vcdExtra/man/loddsratio.Rd |only
vcdExtra-0.6-8/vcdExtra/DESCRIPTION | 25 +-
vcdExtra-0.6-8/vcdExtra/MD5 | 110 +++++-----
vcdExtra-0.6-8/vcdExtra/NAMESPACE | 216 ++++++++++----------
vcdExtra-0.6-8/vcdExtra/NEWS | 17 +
vcdExtra-0.6-8/vcdExtra/R/CMHtest.R | 9
vcdExtra-0.6-8/vcdExtra/R/mosaic3d.R | 2
vcdExtra-0.6-8/vcdExtra/build/vignette.rds |binary
vcdExtra-0.6-8/vcdExtra/data/Abortion.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Accident.RData |binary
vcdExtra-0.6-8/vcdExtra/data/AirCrash.RData |only
vcdExtra-0.6-8/vcdExtra/data/Alligator.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Bartlett.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Caesar.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Cancer.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Cormorants.RData |binary
vcdExtra-0.6-8/vcdExtra/data/CyclingDeaths.RData |binary
vcdExtra-0.6-8/vcdExtra/data/DaytonSurvey.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Depends.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Detergent.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Donner.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Draft1970.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Draft1970table.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Dyke.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Fungicide.rda |binary
vcdExtra-0.6-8/vcdExtra/data/GSS.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Geissler.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Gilby.rda |binary
vcdExtra-0.6-8/vcdExtra/data/HairEyePlace.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Hauser79.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Heart.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Heckman.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Hoyt.rda |binary
vcdExtra-0.6-8/vcdExtra/data/ICU.RData |binary
vcdExtra-0.6-8/vcdExtra/data/JobSat.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Mammograms.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Mental.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Mobility.rda |binary
vcdExtra-0.6-8/vcdExtra/data/PhdPubs.RData |binary
vcdExtra-0.6-8/vcdExtra/data/ShakeWords.RData |binary
vcdExtra-0.6-8/vcdExtra/data/TV.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Titanicp.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Toxaemia.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Vietnam.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Vietnam.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Vote1980.RData |binary
vcdExtra-0.6-8/vcdExtra/data/WorkerSat.RData |only
vcdExtra-0.6-8/vcdExtra/data/Yamaguchi87.RData |binary
vcdExtra-0.6-8/vcdExtra/man/AirCrash.Rd |only
vcdExtra-0.6-8/vcdExtra/man/CMHtest.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Caesar.Rd | 168 +++++++--------
vcdExtra-0.6-8/vcdExtra/man/Fungicide.Rd | 8
vcdExtra-0.6-8/vcdExtra/man/HairEyePlace.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Toxaemia.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Vietnam.Rd | 8
vcdExtra-0.6-8/vcdExtra/man/WorkerSat.Rd |only
vcdExtra-0.6-8/vcdExtra/man/expand.dft.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/vcdExtra-package.Rd | 232 +++++++++++-----------
59 files changed, 416 insertions(+), 387 deletions(-)
Title: Functions Relating to the Smoothing of Numerical Data
Diff between smoother versions 1.0.0.0 dated 2014-09-16 and 1.1 dated 2015-04-16
Description: A collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton
DESCRIPTION | 16 ++++----
MD5 | 21 ++++++----
NAMESPACE | 7 +++
NEWS | 20 +++++++++-
R/functions.R | 44 ++++++++++++++++++++--
R/onLoad.R |only
R/smoother-package.R | 17 +++++---
R/smth-gaussian.R | 100 +++++++++++++++++++++++++++++++--------------------
R/smth.R | 71 +++++++++++++++---------------------
man/smoother.Rd | 18 +++++----
man/smth.Rd | 59 ++++++++++++++----------------
man/smth.gaussian.Rd |only
man/smth.options.Rd |only
13 files changed, 226 insertions(+), 147 deletions(-)
Title: Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
Diff between networksis versions 2.1-2 dated 2013-05-01 and 2.1-3 dated 2015-04-16
Description: Tools to simulate bipartite networks/graphs with the
degrees of the nodes fixed and specified. 'networksis' is part
of the 'statnet' suite of packages for network analysis.
Author: Ryan Admiraal
Maintainer: Ryan Admiraal
networksis-2.1-2/networksis/R/simulate.network.R |only
networksis-2.1-2/networksis/man/networksis-internal.Rd |only
networksis-2.1-3/networksis/DESCRIPTION | 17 ++++----
networksis-2.1-3/networksis/MD5 | 16 +++-----
networksis-2.1-3/networksis/NAMESPACE | 11 +++--
networksis-2.1-3/networksis/R/simulate.sisnetwork.R | 11 ++++-
networksis-2.1-3/networksis/R/zzz.R | 34 +++++++----------
networksis-2.1-3/networksis/inst/CITATION | 30 ++++++++-------
networksis-2.1-3/networksis/man/networksis-package.Rd | 8 ++--
networksis-2.1-3/networksis/man/simulate.sisnetwork.Rd | 10 ++---
10 files changed, 72 insertions(+), 65 deletions(-)
Title: Fitting the copCAR Regression Model for Discrete Areal Data
Diff between copCAR versions 1.0 dated 2014-09-07 and 1.0-1 dated 2015-04-16
Description: Provides tools for fitting the copCAR regression model for discrete areal data. Three types of estimation are supported: continuous extension, composite marginal likelihood, and distributional transform.
Author: Emily Goren
Maintainer: John Hughes
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/zzz.R | 2 +-
inst/CITATION | 5 ++---
man/rcopCAR.Rd | 4 ++--
5 files changed, 15 insertions(+), 16 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Diff between BiodiversityR versions 2.5-1 dated 2014-11-23 and 2.5-2 dated 2015-04-16
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt
BiodiversityR-2.5-1/BiodiversityR/R/bioenv.numeric.R |only
BiodiversityR-2.5-1/BiodiversityR/R/bioenv.test.R |only
BiodiversityR-2.5-1/BiodiversityR/R/ensemble.category.simplify.R |only
BiodiversityR-2.5-2/BiodiversityR/DESCRIPTION | 12
BiodiversityR-2.5-2/BiodiversityR/MD5 | 78 ++--
BiodiversityR-2.5-2/BiodiversityR/NAMESPACE | 6
BiodiversityR-2.5-2/BiodiversityR/R/CAPdiscrim.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/NMSrandom.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/balanced.specaccum.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/distdisplayed.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/diversityresult.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.accepted.categories.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.analogue.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.batch.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.drop1.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.dummy.variables.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.formulae.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.mean.R | 25 +
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.raster.R | 75 ++--
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.simplified.categories.R | 6
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.strategy.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.R | 169 +++++-----
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.gbm.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.nnet.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.splits.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/evaluation.strip.data.R | 59 +--
BiodiversityR-2.5-2/BiodiversityR/R/import.from.Access.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/import.from.Excel.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/importancevalue.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/nested.anova.dbrda.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/nested.npmanova.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ordicoeno.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/prepare.bioenv.R |only
BiodiversityR-2.5-2/BiodiversityR/R/removeNAcomm.R | 7
BiodiversityR-2.5-2/BiodiversityR/R/residualssurface.R | 6
BiodiversityR-2.5-2/BiodiversityR/R/spatialsample.R | 2
BiodiversityR-2.5-2/BiodiversityR/data/BCI.env.txt.gz |binary
BiodiversityR-2.5-2/BiodiversityR/inst/etc/BiodiversityGUI.R | 16
BiodiversityR-2.5-2/BiodiversityR/man/BCI.env.Rd | 35 --
BiodiversityR-2.5-2/BiodiversityR/man/dist.eval.Rd | 38 +-
BiodiversityR-2.5-2/BiodiversityR/man/diversityresult.Rd | 2
BiodiversityR-2.5-2/BiodiversityR/man/ensemble.raster.Rd | 2
42 files changed, 311 insertions(+), 295 deletions(-)
Title: Refined Moving Average Filter
Diff between rmaf versions 3.0 dated 2015-04-13 and 3.0.1 dated 2015-04-15
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/mafilter.R | 48 +++++++++++++++++++++++++-----------------------
R/ssfilter.R | 48 +++++++++++++++++++++++++-----------------------
man/rmaf-package.Rd | 4 ++--
5 files changed, 60 insertions(+), 56 deletions(-)
Title: Bayesian Graphical Models using MCMC
Diff between rjags versions 3-14 dated 2014-10-27 and 3-15 dated 2015-04-15
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer
DESCRIPTION | 21 +++++---
MD5 | 12 ++---
NAMESPACE | 3 -
R/jags.R | 10 ++--
R/jags.object.R | 2
R/windows/zzz.R | 133 ++++++++++++++++++++++++++++++++------------------------
README | 8 ++-
7 files changed, 109 insertions(+), 80 deletions(-)
Title: Rainbow Plots, Bagplots and Boxplots for Functional Data
Diff between rainbow versions 3.2 dated 2013-08-28 and 3.3 dated 2015-04-15
Description: Functions and data sets for functional data display and outlier detection.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang
ChangeLog | 371 ++++++++++++++++++++++++++++++++-----------------
DESCRIPTION | 16 +-
MD5 | 25 +--
R/plot.fds.R | 18 ++
build |only
man/SVDplot.Rd | 118 +++++++--------
man/fboxplot.Rd | 112 +++++++-------
man/fdepth.Rd | 138 +++++++++---------
man/fds.Rd | 82 +++++-----
man/foutliers.Rd | 122 ++++++++--------
man/plot.fdepth.Rd | 52 +++---
man/plot.fds.Rd | 124 +++++++---------
man/rainbow-package.Rd | 44 ++---
man/summaryfunction.Rd | 82 +++++-----
14 files changed, 719 insertions(+), 585 deletions(-)
Title: Local Correlation, Spatial Inequalities and Other Tools
Diff between lctools versions 0.2 dated 2015-04-05 and 0.2-2 dated 2015-04-15
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou
DESCRIPTION | 9 +++++----
MD5 | 21 ++++++++++++++-------
R/lcorrel.R | 3 +--
R/mc_correl.R | 18 ++++--------------
R/mc_spGini.R | 22 ++++++----------------
R/spGini.R | 13 ++-----------
build |only
inst |only
man/lctools-package.Rd | 6 +++---
vignettes/SpatialInequalities.Rmd | 12 ++++++------
10 files changed, 41 insertions(+), 63 deletions(-)
Title: Knockoff Filter for Controlling the False Discovery Rate
Diff between knockoff versions 0.2 dated 2015-02-05 and 0.2.1 dated 2015-04-15
Description: The knockoff filter is a procedure for controlling the false
discovery rate (FDR) when performing variable selection. For more information,
see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
DESCRIPTION | 10 +++++-----
MD5 | 15 ++++++++++-----
NEWS | 6 ++++++
build/vignette.rds |binary
inst/doc/hiv.R |only
inst/doc/hiv.Rmd |only
inst/doc/hiv.html |only
inst/doc/intro.html | 4 ++--
inst/doc/sdp.html | 4 ++--
vignettes/hiv.Rmd |only
vignettes/references.bib |only
11 files changed, 25 insertions(+), 14 deletions(-)
Title: R Console Bindings for the 'Domino Command-Line Client'
Diff between domino versions 0.2-5 dated 2015-04-14 and 0.2-6 dated 2015-04-15
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite.
Author: Jacek Glodek
Maintainer: Nick Elprin
DESCRIPTION | 6 +++---
MD5 | 6 +++---
NAMESPACE | 3 ++-
man/domino-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 9 deletions(-)
Title: Copula Based Cluster Analysis
Diff between CoClust versions 0.3-0 dated 2014-07-07 and 0.3-1 dated 2015-04-15
Description: Copula Based Cluster Analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini
ChangeLog | 9 +++++++--
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
R/CoClust.R | 10 +++++-----
R/Internal_functions.R | 6 +++---
inst/CITATION | 8 ++++----
6 files changed, 30 insertions(+), 25 deletions(-)
Title: In-Source Documentation for R
Diff between roxygen2 versions 4.1.0 dated 2014-12-13 and 4.1.1 dated 2015-04-15
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham
roxygen2-4.1.0/roxygen2/vignettes/rd-keywords.html |only
roxygen2-4.1.0/roxygen2/vignettes/rd-keywords.md |only
roxygen2-4.1.1/roxygen2/DESCRIPTION | 18 +-
roxygen2-4.1.1/roxygen2/MD5 | 63 +++----
roxygen2-4.1.1/roxygen2/NAMESPACE | 7
roxygen2-4.1.1/roxygen2/R/description.R | 38 ++--
roxygen2-4.1.1/roxygen2/R/rd-file-api.R | 2
roxygen2-4.1.1/roxygen2/R/rd-tag-api.R | 2
roxygen2-4.1.1/roxygen2/R/roclet-rd.R | 6
roxygen2-4.1.1/roxygen2/R/roclet-vignette.R |only
roxygen2-4.1.1/roxygen2/build/vignette.rds |binary
roxygen2-4.1.1/roxygen2/inst/doc/rd.R | 4
roxygen2-4.1.1/roxygen2/inst/doc/rd.Rmd | 21 ++
roxygen2-4.1.1/roxygen2/inst/doc/rd.html | 19 ++
roxygen2-4.1.1/roxygen2/man/is_s3_generic.Rd | 2
roxygen2-4.1.1/roxygen2/man/namespace_roclet.Rd | 2
roxygen2-4.1.1/roxygen2/man/new_roclet.Rd | 2
roxygen2-4.1.1/roxygen2/man/object.Rd | 2
roxygen2-4.1.1/roxygen2/man/rd_roclet.Rd | 2
roxygen2-4.1.1/roxygen2/man/register-parser.Rd | 2
roxygen2-4.1.1/roxygen2/man/roc_proc_text.Rd | 2
roxygen2-4.1.1/roxygen2/man/roxygen.Rd | 2
roxygen2-4.1.1/roxygen2/man/roxygenize.Rd | 2
roxygen2-4.1.1/roxygen2/man/source_package.Rd | 2
roxygen2-4.1.1/roxygen2/man/update_collate.Rd | 2
roxygen2-4.1.1/roxygen2/man/vignette_roclet.Rd |only
roxygen2-4.1.1/roxygen2/src/RcppExports.cpp | 90 +++-------
roxygen2-4.1.1/roxygen2/src/parser.cpp | 40 ++--
roxygen2-4.1.1/roxygen2/tests/testthat/description-example_2.txt |only
roxygen2-4.1.1/roxygen2/tests/testthat/test-srcref-comment.R | 16 +
roxygen2-4.1.1/roxygen2/tests/testthat/test-wrapFieldIfNecessary.R | 28 ++-
roxygen2-4.1.1/roxygen2/vignettes/collate.md |only
roxygen2-4.1.1/roxygen2/vignettes/namespace.md |only
roxygen2-4.1.1/roxygen2/vignettes/rd.Rmd | 21 ++
roxygen2-4.1.1/roxygen2/vignettes/rd.md | 22 ++
roxygen2-4.1.1/roxygen2/vignettes/rdkeywords.md |only
roxygen2-4.1.1/roxygen2/vignettes/roxygen2.md |only
37 files changed, 269 insertions(+), 150 deletions(-)
Title: Count Longitudinal Data
Diff between cold versions 1.0-3 dated 2013-10-05 and 1.0-4 dated 2015-04-15
Description: Performs regression analysis for longitudinal count
data using a self-decomposable probability distribution,
a random intercept term is also allowed. Estimation is via maximization
of the exact likelihood of a suitably defined model. Missing values and
unbalanced data are allowed.
Author: M. Helena Gonçalves and M. Salomé Cabral,
apart from a set of Fortran-77 subroutines written by R. Piessens
and E. de Doncker, belonging to the suite "Quadpack".
Maintainer: M. Helena Gonçalves
cold-1.0-3/cold/INDEX |only
cold-1.0-3/cold/history.txt |only
cold-1.0-4/cold/DESCRIPTION | 20 +++---
cold-1.0-4/cold/MD5 | 37 +++++------
cold-1.0-4/cold/NEWS |only
cold-1.0-4/cold/inst/CITATION | 94 +++++++++++++++++++-----------
cold-1.0-4/cold/man/anova-methods.Rd | 6 -
cold-1.0-4/cold/man/cold-class.Rd | 2
cold-1.0-4/cold/man/cold-package.Rd | 4 -
cold-1.0-4/cold/man/cold.Rd | 26 ++++----
cold-1.0-4/cold/man/coldControl.Rd | 2
cold-1.0-4/cold/man/coldIntegrate.Rd | 16 ++---
cold-1.0-4/cold/man/datacold.rd | 16 ++---
cold-1.0-4/cold/man/fitted-methods.Rd | 18 ++---
cold-1.0-4/cold/man/plot-methods.Rd | 39 +++++++-----
cold-1.0-4/cold/man/predict-methods.Rd | 2
cold-1.0-4/cold/man/resid-methods.Rd | 14 ++--
cold-1.0-4/cold/man/seizure.rd | 18 ++---
cold-1.0-4/cold/man/show-methods.Rd | 2
cold-1.0-4/cold/man/summary-methods.Rd | 4 -
cold-1.0-4/cold/man/summary.cold-class.Rd | 2
21 files changed, 177 insertions(+), 145 deletions(-)
Title: Functions for Calculating Tolerance Intervals
Diff between tolerance versions 1.0.0 dated 2014-09-03 and 1.1.0 dated 2015-04-15
Description: Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits for various distributions. Plotting is also available for tolerance limits of continuous random variables.
Author: Derek S. Young [aut, cre]
Maintainer: Derek S. Young
DESCRIPTION | 12 ++++++------
MD5 | 12 +++++++++---
NEWS | 12 ++++++++++++
R/Kfactor.R | 2 +-
R/poislind.R |only
R/poislindll.R |only
R/poislindtolint.R |only
man/poislind.Rd |only
man/poislindll.Rd |only
man/poislindtolint.Rd |only
10 files changed, 28 insertions(+), 10 deletions(-)
Title: Miscellaneous Functions for Survival Data
Diff between survMisc versions 0.4.5 dated 2015-02-25 and 0.4.6 dated 2015-04-15
Description: A collection of functions for analysis of survival data. These
extend the methods available in the package survival.
Author: Chris Dardis
Maintainer: Chris Dardis
survMisc-0.4.5/survMisc/inst/doc/pbcDx.pdf |only
survMisc-0.4.6/survMisc/DESCRIPTION | 16 +--
survMisc-0.4.6/survMisc/MD5 | 109 ++++++++++++------------
survMisc-0.4.6/survMisc/NAMESPACE | 1
survMisc-0.4.6/survMisc/R/air.R | 2
survMisc-0.4.6/survMisc/R/autoplotRpart.R | 57 +++++-------
survMisc-0.4.6/survMisc/R/autoplotSurvfit.R | 105 +++++++++++------------
survMisc-0.4.6/survMisc/R/ci.R | 6 -
survMisc-0.4.6/survMisc/R/comp.R | 5 -
survMisc-0.4.6/survMisc/R/cutp.R | 44 ++++-----
survMisc-0.4.6/survMisc/R/dx.R | 12 +-
survMisc-0.4.6/survMisc/R/gamTerms.R | 2
survMisc-0.4.6/survMisc/R/gof.R | 13 +-
survMisc-0.4.6/survMisc/R/local.R | 53 +++++------
survMisc-0.4.6/survMisc/R/mpip.R | 8 -
survMisc-0.4.6/survMisc/R/multiCoxph.R | 28 ++----
survMisc-0.4.6/survMisc/R/plotMultiCoxph.R | 55 ++++++------
survMisc-0.4.6/survMisc/R/plotSurv.R | 67 +++++++-------
survMisc-0.4.6/survMisc/R/plotTerm.R | 2
survMisc-0.4.6/survMisc/R/profLik.R | 14 +--
survMisc-0.4.6/survMisc/R/quantile.R | 77 ++++++++--------
survMisc-0.4.6/survMisc/R/rsq.R | 3
survMisc-0.4.6/survMisc/R/sf.R | 25 ++---
survMisc-0.4.6/survMisc/R/sig.R | 21 ++--
survMisc-0.4.6/survMisc/R/survMisc_package.R | 38 +++++---
survMisc-0.4.6/survMisc/R/tne.R | 40 +++-----
survMisc-0.4.6/survMisc/R/tneBMT.R | 9 -
survMisc-0.4.6/survMisc/R/tneKidney.R | 4
survMisc-0.4.6/survMisc/R/whas100.R | 5 -
survMisc-0.4.6/survMisc/R/whas500.R | 5 -
survMisc-0.4.6/survMisc/man/air.Rd | 1
survMisc-0.4.6/survMisc/man/autoplotRpart.Rd | 46 ++++------
survMisc-0.4.6/survMisc/man/autoplotSurvfit.Rd | 92 +++++++++-----------
survMisc-0.4.6/survMisc/man/ci.Rd | 4
survMisc-0.4.6/survMisc/man/comp.Rd | 5 -
survMisc-0.4.6/survMisc/man/dx.Rd | 6 -
survMisc-0.4.6/survMisc/man/gamTerms.Rd | 2
survMisc-0.4.6/survMisc/man/gof.Rd | 7 -
survMisc-0.4.6/survMisc/man/local.Rd | 5 -
survMisc-0.4.6/survMisc/man/mpip.Rd | 8 -
survMisc-0.4.6/survMisc/man/plot.Surv.Rd | 3
survMisc-0.4.6/survMisc/man/plotMultiCoxph.Rd | 40 ++++----
survMisc-0.4.6/survMisc/man/plotTerm.Rd | 2
survMisc-0.4.6/survMisc/man/profLik.Rd | 2
survMisc-0.4.6/survMisc/man/quantile.Rd | 28 +++---
survMisc-0.4.6/survMisc/man/rsq.Rd | 3
survMisc-0.4.6/survMisc/man/sf.Rd | 23 ++---
survMisc-0.4.6/survMisc/man/sig.Rd | 6 -
survMisc-0.4.6/survMisc/man/survMisc-package.Rd | 22 +++-
survMisc-0.4.6/survMisc/man/tne.Rd | 5 -
survMisc-0.4.6/survMisc/man/tneBMT.Rd | 9 -
survMisc-0.4.6/survMisc/man/tneKidney.Rd | 4
survMisc-0.4.6/survMisc/man/whas100.Rd | 5 -
survMisc-0.4.6/survMisc/man/whas500.Rd | 5 -
survMisc-0.4.6/survMisc/vignettes |only
55 files changed, 575 insertions(+), 584 deletions(-)
Title: Sample Size Estimation
Diff between sse versions 0.5-1 dated 2014-05-19 and 0.5-4 dated 2015-04-15
Description: Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
Author: Thomas Fabbro
Maintainer: Thomas Fabbro
DESCRIPTION | 17 +++++++++--------
MD5 | 18 +++++++++---------
NAMESPACE | 2 +-
R/power.R | 35 ++++++++++++++++++++---------------
build/vignette.rds |binary
inst/doc/examples.Rnw | 30 +++++++++++++++---------------
inst/doc/examples.pdf |binary
man/n.Rd | 7 +++----
man/plot-methods.Rd | 16 ++++++++--------
vignettes/examples.Rnw | 30 +++++++++++++++---------------
10 files changed, 80 insertions(+), 75 deletions(-)
Title: Syntax Highlighter
Diff between highlight versions 0.4.4 dated 2013-12-16 and 0.4.5 dated 2015-04-15
Description: Syntax highlighter for R code based
on the results of the R parser. Rendering in HTML and latex
markup. Custom Sweave driver performing syntax highlighting
of R code chunks.
Author: Romain Francois [aut, cre],
Andre Simon [ctb]
Maintainer: Romain Francois
highlight-0.4.4/highlight/R/httpd.R |only
highlight-0.4.4/highlight/build |only
highlight-0.4.4/highlight/inst/rook |only
highlight-0.4.4/highlight/man/dummy_detective.Rd |only
highlight-0.4.4/highlight/man/highlight.httpd.handler.Rd |only
highlight-0.4.4/highlight/man/renderer_verbatim.Rd |only
highlight-0.4.5/highlight/DESCRIPTION | 26 -
highlight-0.4.5/highlight/MD5 | 72 +--
highlight-0.4.5/highlight/NAMESPACE | 63 +-
highlight-0.4.5/highlight/NEWS | 4
highlight-0.4.5/highlight/R/SweaveLatexDriver.R | 82 +++
highlight-0.4.5/highlight/R/css.R | 45 +-
highlight-0.4.5/highlight/R/detectives.R | 26 -
highlight-0.4.5/highlight/R/external_highlight.R | 34 +
highlight-0.4.5/highlight/R/highlight.R | 278 ++++++++----
highlight-0.4.5/highlight/R/renderer.R | 332 +++++++++++++--
highlight-0.4.5/highlight/R/zzz.R | 9
highlight-0.4.5/highlight/man/HighlightWeaveLatex.Rd | 74 +--
highlight-0.4.5/highlight/man/Hweave.Rd | 87 +--
highlight-0.4.5/highlight/man/boxes_latex.Rd | 30 -
highlight-0.4.5/highlight/man/css.parser.Rd | 69 +--
highlight-0.4.5/highlight/man/external_highlight.Rd | 63 +-
highlight-0.4.5/highlight/man/formatter_html.Rd | 39 -
highlight-0.4.5/highlight/man/formatter_latex.Rd | 35 -
highlight-0.4.5/highlight/man/getStyleFile.Rd | 44 -
highlight-0.4.5/highlight/man/header_html.Rd | 47 --
highlight-0.4.5/highlight/man/header_latex.Rd | 45 --
highlight-0.4.5/highlight/man/highlight-package.Rd | 65 +-
highlight-0.4.5/highlight/man/highlight.Rd | 162 ++-----
highlight-0.4.5/highlight/man/highlight_output_types.Rd | 18
highlight-0.4.5/highlight/man/highlight_themes.Rd | 14
highlight-0.4.5/highlight/man/renderer.Rd | 131 ++---
highlight-0.4.5/highlight/man/renderer_html.Rd | 129 ++---
highlight-0.4.5/highlight/man/renderer_latex.Rd | 138 ++----
highlight-0.4.5/highlight/man/simple_detective.Rd | 33 -
highlight-0.4.5/highlight/man/styler.Rd | 57 +-
highlight-0.4.5/highlight/man/styler_assistant_latex.Rd | 42 -
highlight-0.4.5/highlight/man/translator_latex.Rd | 33 -
38 files changed, 1253 insertions(+), 1073 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Diff between chillR versions 0.54 dated 2013-05-16 and 0.55 dated 2015-04-15
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat. 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records.
Author: Eike Luedeling
Maintainer: Eike Luedeling
DESCRIPTION | 20 +--
MD5 | 52 ++++---
NAMESPACE | 3
R/PLS_chill_force.R | 171 +++++--------------------
R/PLS_pheno.R | 264 +++++++++++++---------------------------
R/bloom_prediction.R | 17 ++
R/daily_chill.R | 20 ---
R/make_all_day_table.R |only
R/make_daily_chill_figures.R | 1
R/make_pheno_trend_plot.R | 7 -
R/plot_pheno_results.R |only
man/KA_bloom.Rd | 2
man/KA_weather.Rd | 2
man/PLS_chill_force.Rd | 41 +++---
man/PLS_pheno.Rd | 44 +++---
man/VIP.Rd | 79 +----------
man/bloom_prediction.Rd | 80 +++++-------
man/chillR-package.Rd | 36 ++---
man/chilling.Rd | 30 ++++
man/chilling_hourtable.Rd | 29 +++-
man/color_bar_maker.Rd | 17 --
man/daily_chill.Rd | 30 ++++
man/interpolate_gaps.Rd | 5
man/make_all_day_table.Rd |only
man/make_daily_chill_figures.Rd | 30 ++++
man/make_hourly_temps.Rd | 6
man/make_pheno_trend_plot.Rd | 28 +---
man/plot_PLS.Rd |only
man/stack_hourly_temps.Rd | 6
29 files changed, 418 insertions(+), 602 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Diff between runjags versions 2.0.1-2 dated 2015-04-12 and 2.0.1-4 dated 2015-04-14
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood
DESCRIPTION | 12 +--
MD5 | 14 +--
build/vignette.rds |binary
inst/doc/UserGuide.pdf |binary
inst/doc/quickjags.R | 9 --
inst/doc/quickjags.Rmd | 30 ++------
inst/doc/quickjags.html | 171 +++++++++++++++++++-----------------------------
vignettes/quickjags.Rmd | 30 ++------
8 files changed, 99 insertions(+), 167 deletions(-)
Title: BInary Longitudinal Data
Diff between bild versions 1.1-3 dated 2013-02-18 and 1.1-5 dated 2015-04-14
Description: Performs logistic regression for binary longitudinal
data, allowing for serial dependence among observations from a given
individual and a random intercept term. Estimation is via maximization
of the exact likelihood of a suitably defined model. Missing values and
unbalanced data are allowed, with some restrictions.
Author: M. Helena Gonçalves, M. Salomé Cabral and Adelchi Azzalini,
apart from a set of Fortran-77 subroutines written by R. Piessens
and E. de Doncker, belonging to the suite "Quadpack".
Maintainer: M. Helena Gonçalves
bild-1.1-3/bild/INDEX |only
bild-1.1-3/bild/history.txt |only
bild-1.1-5/bild/DESCRIPTION | 27 ++---
bild-1.1-5/bild/MD5 | 29 ++---
bild-1.1-5/bild/NEWS |only
bild-1.1-5/bild/inst/CITATION | 156 +++++++++++++++++++-----------
bild-1.1-5/bild/man/airpollution.rd | 9 -
bild-1.1-5/bild/man/anova-methods.Rd | 30 +++--
bild-1.1-5/bild/man/bild-class.Rd | 2
bild-1.1-5/bild/man/bild-package.Rd | 4
bild-1.1-5/bild/man/bild.Rd | 30 +++--
bild-1.1-5/bild/man/bildIntegrate.Rd | 12 +-
bild-1.1-5/bild/man/locust.rd | 7 -
bild-1.1-5/bild/man/muscatine.rd | 4
bild-1.1-5/bild/man/plot-methods.Rd | 23 ++--
bild-1.1-5/bild/man/summary-methods.Rd | 4
bild-1.1-5/bild/man/summary.bild-class.Rd | 4
17 files changed, 198 insertions(+), 143 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-5 dated 2015-02-09 and 1.5 dated 2015-04-14
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
DESCRIPTION | 16
MD5 | 185 +-
NAMESPACE | 170 +-
NEWS |only
R/GoogleMapsPlot.R | 1894 ++++++++++++++---------------
R/TaylorDiagram.R | 1278 ++++++++++---------
R/TheilSen.R | 1172 +++++++++---------
R/airbaseFindCode.R | 270 ++--
R/airbaseInfo.R | 88 -
R/airbaseSplice.R | 180 +-
R/airbaseStats.R | 674 +++++-----
R/aqStats.R | 48
R/calcFno2.R | 586 ++++-----
R/calendarPlot.R | 1020 +++++++--------
R/corPlot.R | 800 ++++++------
R/cutData.R | 16
R/getMeta.R | 14
R/import.R | 392 +++---
R/importADMS.R | 1974 +++++++++++++++---------------
R/importAirbase.R | 270 ++--
R/importKCL.R | 1191 +++++++++---------
R/linearRelation.R | 816 ++++++------
R/openair-package.R | 180 +-
R/percentileRose.R | 1112 ++++++++---------
R/polarAnnulus.R | 1470 +++++++++++-----------
R/polarCluster.R | 708 +++++-----
R/polarFreq.R | 922 +++++++-------
R/polarPlot.R | 1746 +++++++++++++-------------
R/scatterPlot.R | 2930 ++++++++++++++++++++++-----------------------
R/smoothTrend.R | 954 +++++++-------
R/timeAverage.R | 1012 +++++++--------
R/timePlot.R | 1242 +++++++++----------
R/timeVariation.R | 2067 ++++++++++++++++---------------
R/trajLevel.R | 889 ++++++-------
R/trajPlot.R | 624 ++++-----
R/trendLevel.R | 1202 +++++++++---------
R/utilities.R | 2030 +++++++++++++++----------------
R/windRose.R | 1482 +++++++++++-----------
README.md | 326 ++---
data/mydata.RData |binary
inst/CITATION | 27
man/GoogleMapsPlot.Rd | 438 +++---
man/TaylorDiagram.Rd | 550 ++++----
man/TheilSen.Rd | 546 ++++----
man/airbaseFindCode.Rd | 172 +-
man/airbaseInfo.Rd | 84 -
man/airbaseSplice.Rd | 122 -
man/airbaseStats.Rd | 536 ++++----
man/aqStats.Rd | 194 +-
man/calcFno2.Rd | 224 +--
man/calcPercentile.Rd | 130 -
man/calendarPlot.Rd | 404 +++---
man/conditionalEval.Rd | 398 +++---
man/conditionalQuantile.Rd | 330 ++---
man/corPlot.Rd | 306 ++--
man/cutData.Rd | 318 ++--
man/drawOpenKey.Rd | 366 ++---
man/import.Rd | 280 ++--
man/importADMS.Rd | 318 ++--
man/importAURN.Rd | 670 +++++-----
man/importAURNCsv.Rd | 356 ++---
man/importAirbase.Rd | 166 +-
man/importKCL.Rd | 972 +++++++-------
man/importMeta.Rd | 138 +-
man/importSAQN.Rd | 356 ++---
man/importTraj.Rd | 300 ++--
man/kernelExceed.Rd | 304 ++--
man/linearRelation.Rd | 292 ++--
man/modStats.Rd | 298 ++--
man/mydata.Rd | 100 -
man/openColours.Rd | 176 +-
man/openair.Rd | 190 +-
man/percentileRose.Rd | 386 ++---
man/polarAnnulus.Rd | 524 ++++----
man/polarCluster.Rd | 360 ++---
man/polarFreq.Rd | 432 +++---
man/polarPlot.Rd | 810 ++++++------
man/quickText.Rd | 90 -
man/rollingMean.Rd | 130 -
man/scatterPlot.Rd | 708 +++++-----
man/selectByDate.Rd | 166 +-
man/selectRunning.Rd | 114 -
man/smoothTrend.Rd | 448 +++---
man/splitByDate.Rd | 84 -
man/summaryPlot.Rd | 324 ++--
man/timeAverage.Rd | 392 +++---
man/timePlot.Rd | 582 ++++----
man/timeProp.Rd | 312 ++--
man/timeVariation.Rd | 615 ++++-----
man/trajCluster.Rd | 270 ++--
man/trajLevel.Rd | 522 ++++----
man/trajPlot.Rd | 318 ++--
man/trendLevel.Rd | 402 +++---
man/windRose.Rd | 585 ++++----
94 files changed, 26342 insertions(+), 26243 deletions(-)
Title: Invariant Causal Prediction
Diff between InvariantCausalPrediction versions 0.3 dated 2015-04-13 and 0.3-1 dated 2015-04-14
More information about InvariantCausalPrediction at CRAN
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen
InvariantCausalPrediction-0.3-1/InvariantCausalPrediction/DESCRIPTION | 8 ++++----
InvariantCausalPrediction-0.3-1/InvariantCausalPrediction/MD5 | 8 ++++----
InvariantCausalPrediction-0.3-1/InvariantCausalPrediction/NAMESPACE | 2 +-
InvariantCausalPrediction-0.3-1/InvariantCausalPrediction/R/hiddenICE.R |only
InvariantCausalPrediction-0.3-1/InvariantCausalPrediction/man/hiddenICE.Rd |only
InvariantCausalPrediction-0.3/InvariantCausalPrediction/R/feedbackNetwork.R |only
InvariantCausalPrediction-0.3/InvariantCausalPrediction/man/feedbackNetwork.Rd |only
7 files changed, 9 insertions(+), 9 deletions(-)
Permanent link
Title: Flexible Parametric Survival and Multi-State Models
Diff between flexsurv versions 0.5 dated 2014-09-22 and 0.6 dated 2015-04-14
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson
Maintainer: Christopher Jackson
DESCRIPTION | 16
MD5 | 65
NAMESPACE | 7
R/Gompertz.R | 1
R/Llogis.R |only
R/flexsurvreg.R | 1858 ++++++++++++-----------
R/mstate.R | 184 +-
R/utils.R | 17
build/vignette.rds |binary
inst/NEWS | 41
inst/doc/flexsurv-examples.R | 48
inst/doc/flexsurv-examples.pdf |binary
inst/doc/flexsurv.R | 489 ++----
inst/doc/flexsurv.pdf |binary
man/Llogis.Rd |only
man/flexsurvreg.Rd | 17
man/flexsurvspline.Rd | 10
man/msfit.flexsurvreg.Rd | 39
man/pars.fmsm.Rd |only
man/pmatrix.fs.Rd | 7
man/pmatrix.simfs.Rd | 9
man/sim.fmsm.Rd | 17
man/summary.flexsurvreg.Rd | 11
man/totlos.fs.Rd | 7
man/totlos.simfs.Rd | 9
tests/testthat/test_custom.R | 54
tests/testthat/test_deriv.R | 7
tests/testthat/test_flexsurvreg.R | 47
tests/testthat/test_mstate.R | 78
tests/testthat/test_outputs.R | 4
tests/testthat/test_spline.R | 7
tests/testthat/test_utils.R | 38
vignettes/flexsurv-examples.Rnw | 78
vignettes/flexsurv.Rnw | 3039 ++++++++++++++++++++------------------
vignettes/flexsurv.bib | 224 +-
35 files changed, 3575 insertions(+), 2853 deletions(-)
Title: Sample Size Estimation Functions for Cluster Randomized Trials
Diff between CRTSize versions 0.4 dated 2015-02-02 and 1.0 dated 2015-04-14
Description: Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
Author: Michael A Rotondi
Maintainer: Michael A Rotondi
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/n4incidence.R | 13 ++++++++-----
R/n4means.R | 4 ++--
R/n4props.R | 2 +-
man/n4meansMeta.Rd | 4 ++--
6 files changed, 23 insertions(+), 20 deletions(-)
Title: Manipulations of Triangular Meshes Based on the VCGLIB API
Diff between Rvcg versions 0.10.1 dated 2014-12-22 and 0.11 dated 2015-04-14
Description: Operations on triangular meshes based on VCGLIB. This package
integrates nicely with the R-package "rgl" to render the meshes processed
by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL
license, and it is the base of most of the software tools of the Visual
Computing Lab of the Italian National Research Council Institute ISTI
(http://vcg.isti.cnr.it), like metro and MeshLab.
The vcglib source is pulled from
trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work
with options determined by the configure script as well as
to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager
Rvcg-0.10.1/Rvcg/src/vcglib/vcg/space/index/index2D |only
Rvcg-0.10.1/Rvcg/src/vcglib/wrap/miq |only
Rvcg-0.11/Rvcg/DESCRIPTION | 8
Rvcg-0.11/Rvcg/MD5 | 342
Rvcg-0.11/Rvcg/NAMESPACE | 2
Rvcg-0.11/Rvcg/R/Rvcg-package.R | 4
Rvcg-0.11/Rvcg/R/vcgClost.r | 1
Rvcg-0.11/Rvcg/R/vcgKDtree.r | 11
Rvcg-0.11/Rvcg/inst/NEWS.Rd | 18
Rvcg-0.11/Rvcg/man/Rvcg-package.Rd | 7
Rvcg-0.11/Rvcg/man/dummyhead.Rd | 3
Rvcg-0.11/Rvcg/man/humface.Rd | 3
Rvcg-0.11/Rvcg/man/meshintegrity.Rd | 3
Rvcg-0.11/Rvcg/man/setRays.Rd | 3
Rvcg-0.11/Rvcg/man/vcgBary.Rd | 3
Rvcg-0.11/Rvcg/man/vcgBorder.Rd | 3
Rvcg-0.11/Rvcg/man/vcgClean.Rd | 3
Rvcg-0.11/Rvcg/man/vcgClost.Rd | 4
Rvcg-0.11/Rvcg/man/vcgClostKD.Rd | 3
Rvcg-0.11/Rvcg/man/vcgCurve.Rd | 3
Rvcg-0.11/Rvcg/man/vcgGetEdge.Rd | 3
Rvcg-0.11/Rvcg/man/vcgImport.Rd | 3
Rvcg-0.11/Rvcg/man/vcgIsolated.Rd | 3
Rvcg-0.11/Rvcg/man/vcgIsosurface.Rd | 3
Rvcg-0.11/Rvcg/man/vcgKDtree.Rd | 3
Rvcg-0.11/Rvcg/man/vcgMeshres.Rd | 3
Rvcg-0.11/Rvcg/man/vcgNonBorderEdge.Rd | 3
Rvcg-0.11/Rvcg/man/vcgPlyRead.Rd | 3
Rvcg-0.11/Rvcg/man/vcgPlyWrite.Rd | 3
Rvcg-0.11/Rvcg/man/vcgQEdecim.Rd | 3
Rvcg-0.11/Rvcg/man/vcgRaySearch.Rd | 3
Rvcg-0.11/Rvcg/man/vcgSample.Rd | 3
Rvcg-0.11/Rvcg/man/vcgSmooth.Rd | 3
Rvcg-0.11/Rvcg/man/vcgStlWrite.Rd | 3
Rvcg-0.11/Rvcg/man/vcgUniformRemesh.Rd | 3
Rvcg-0.11/Rvcg/man/vcgUpdateNormals.Rd | 3
Rvcg-0.11/Rvcg/man/vcgVFadj.Rd | 3
Rvcg-0.11/Rvcg/src/Rclean.cpp | 8
Rvcg-0.11/Rvcg/src/Rkdtree.cpp | 37
Rvcg-0.11/Rvcg/src/Runiform_resample.cpp | 2
Rvcg-0.11/Rvcg/src/RvcgKD.h | 11
Rvcg-0.11/Rvcg/src/Volume.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/autoalign_4pcs.h | 33
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/clean.h | 2039 ++---
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/closest.h | 64
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/clustering.h | 34
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/advancing_front.h | 47
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/ball_pivoting.h | 286
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/marching_cubes.h | 10
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/mc_trivial_walker.h | 101
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/platonic.h | 221
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/resampler.h | 1127 +--
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/geodesic.h | 20
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/harmonic.h | 490 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/hole.h | 8
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/implicit_smooth.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/inside.h | 43
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_collapse_quadric.h | 384 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_collapse_quadric_tex.h | 10
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/local_optimization/tri_edge_flip.h | 968 +-
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/mesh_assert.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/mesh_to_matrix.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/distortion.h | 463 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/poisson_solver.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/parametrization/tangent_field_operators.h | 1515 ++--
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/point_sampling.h | 265
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/pointcloud_normal.h | 49
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_polychord_collapse.h | 889 +-
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_support.h | 80
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/quadrangulator.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/refine.h | 1
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/refine_loop.h | 942 +-
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/smooth.h | 147
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/stat.h | 6
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/symmetry.h | 49
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/color.h | 115
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature.h | 36
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature_fitting.h | 464 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/flag.h | 80
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/normal.h | 41
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/quality.h | 20
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/selection.h | 3
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_processing.h | 113
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_volume_sampling.h | 244
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/allocate.h | 2475 +++---
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/append.h | 66
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/base.h | 82
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/complex.h | 1
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/exception.h | 17
Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/used_types.h | 1
Rvcg-0.11/Rvcg/src/vcglib/vcg/container/simple_temporary_data.h | 20
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/camera.h | 19
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/gen_normal.h | 103
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/matrix33.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/matrix44.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/quadric5.h | 1059 +-
Rvcg-0.11/Rvcg/src/vcglib/vcg/math/shot.h | 130
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/edge/component.h | 154
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/edge/pos.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/base.h | 306
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component.h | 50
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component_ocf.h | 83
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component_polygon.h | 123
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/pos.h | 677 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/topology.h | 4
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/tetrahedron/pos.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/vertex/component.h | 151
Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/vertex/component_ocf.h | 350
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/box2.h | 6
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/color4.h | 147
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/colorspace.h | 3664 +++++-----
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/deprecated_point3.h | 7
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/base2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/closest2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_closest2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_static_ptr2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_util.h | 20
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_util2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/kdtree.h | 623 +
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/kdtree.h.rej | 111
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/priorityqueue.h | 188
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/kdtree/priorityqueue.h.rej |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/octree.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/perfect_spatial_hashing.h | 3062 ++++----
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/space_iterators.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/space_iterators2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/spatial_hashing.h | 538 -
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/spatial_hashing2d.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/intersection2.h | 52
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/intersection3.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/polygon3.h |only
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/ray2.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/rect_packer.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/segment2.h | 25
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/tetra3.h | 2
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/texcoord2.h | 75
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/triangle2.h | 183
Rvcg-0.11/Rvcg/src/vcglib/vcg/space/triangle3.h | 171
Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/gl_field.h | 92
Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/glu_tessellator_cap.h | 7
Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/math.h | 33
Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/pick.h | 124
Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/trimesh.h | 320
Rvcg-0.11/Rvcg/src/vcglib/wrap/glw/program.h | 1062 +-
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/coordinateframe.cpp | 46
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/coordinateframe.h | 4
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/rubberband.cpp | 4
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackmode.cpp | 354
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackmode.h | 2
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackutils.h | 200
Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/view.h | 49
Rvcg-0.11/Rvcg/src/vcglib/wrap/igl |only
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_dxf.h | 5
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_field.h | 83
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_idtf.h | 4
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_obj.h | 19
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_off.h | 272
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_ply.h | 1214 +--
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_stl.h | 156
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_u3d.h | 423 -
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_asc.h | 4
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ctm.h | 3
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_field.h | 1
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_gts.h | 2
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_nvm.h | 89
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_obj.h | 58
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_off.h | 19
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_out.h | 102
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ply.h | 1842 ++---
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ptx.h | 782 +-
Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/precision.h |only
Rvcg-0.11/Rvcg/src/vcglib/wrap/qt/gl_label.h | 14
Rvcg-0.11/Rvcg/src/vcglib/wrap/system/qgetopt.cpp | 15
Rvcg-0.11/Rvcg/src/vcglib/wrap/system/qgetopt.h | 7
174 files changed, 17950 insertions(+), 16168 deletions(-)
Title: Analysis of Dose-Response Curves
Diff between drc versions 2.5-11 dated 2015-04-13 and 2.5-12 dated 2015-04-14
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz
Maintainer: Christian Ritz
DESCRIPTION | 8 -
MD5 | 8 -
R/plot.drc.R | 271 ++++++++++++++++++++++++++++++--------------------------
man/ED.drc.Rd | 3
man/plot.drc.Rd | 34 +++----
5 files changed, 175 insertions(+), 149 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Diff between ade4 versions 1.6-2 dated 2013-11-20 and 1.7-2 dated 2015-04-14
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray
Maintainer: Aurélie Siberchicot
ChangeLog | 353 ++++++++++++++++++++
DESCRIPTION | 21 -
MD5 | 781 +++++++++++++++++++++++----------------------
NAMESPACE | 56 ++-
R/add.scatter.R | 2
R/between.R | 26 +
R/betwitdpcoa.R |only
R/coinertia.R | 4
R/combine.4thcorner.R | 1
R/costatis.R | 33 +
R/dist.dudi.R | 4
R/dpcoa.R | 284 +++++++---------
R/dudi.R | 27 +
R/foucart.R | 4
R/fourthcorner.R | 4
R/fourthcorner.rlq.R | 16
R/kplot.foucart.R | 4
R/kplot.mcoa.R | 8
R/kplot.mfa.R | 4
R/kplot.pta.R | 16
R/kplot.sepan.R | 10
R/kplot.statis.R | 4
R/krandboot.R |only
R/krandxval.R |only
R/ktab.R | 93 +++--
R/ktab.data.frame.R | 5
R/ktab.list.df.R | 4
R/ktab.list.dudi.R | 7
R/ktab.match2ktabs.R | 4
R/ktab.within.R | 6
R/mbpcaiv.R |only
R/mbpls.R |only
R/mcoa.R | 29 -
R/mdpcoa.R | 10
R/mfa.R | 4
R/multiblock.R |only
R/multispati.R | 4
R/orthobasis.R | 104 ++---
R/plot.4thcorner.R | 36 +-
R/print.4thcorner.R | 2
R/procuste.R | 142 ++++----
R/pta.R | 27 -
R/randboot.R |only
R/randtest.between.R | 21 -
R/randtest.rlq.R | 2
R/randxval.R |only
R/rlq.R | 47 +-
R/s.image.R | 36 +-
R/s.kde2d.R | 1
R/s.logo.R | 1
R/scatterutil.R | 2
R/sepan.R | 1
R/statico.R | 43 ++
R/statis.R | 4
R/testdim.R | 16
R/utilities.R | 5
R/within.R | 18 +
data/abouheif.eg.rda |binary
data/acacia.rda |binary
data/aminoacyl.rda |binary
data/apis108.rda |binary
data/aravo.rda |binary
data/ardeche.rda |binary
data/arrival.rda |binary
data/atlas.rda |binary
data/atya.rda |binary
data/avijons.rda |binary
data/avimedi.rda |binary
data/aviurba.rda |binary
data/bacteria.rda |binary
data/banque.rda |binary
data/baran95.rda |binary
data/bf88.rda |binary
data/bordeaux.rda |binary
data/bsetal97.rda |binary
data/buech.rda |binary
data/butterfly.rda |binary
data/capitales.rda |binary
data/carni19.rda |binary
data/carni70.rda |binary
data/carniherbi49.rda |binary
data/casitas.rda |binary
data/chatcat.rda |binary
data/chats.rda |binary
data/chazeb.rda |binary
data/chevaine.rda |binary
data/chickenk.rda |only
data/clementines.rda |binary
data/cnc2003.rda |binary
data/coleo.rda |binary
data/corvus.rda |binary
data/datalist | 2
data/deug.rda |binary
data/doubs.rda |binary
data/dunedata.rda |binary
data/ecg.rda |binary
data/ecomor.rda |binary
data/elec88.rda |binary
data/escopage.rda |binary
data/euro123.rda |binary
data/fission.rda |binary
data/friday87.rda |binary
data/fruits.rda |binary
data/ggtortoises.rda |binary
data/granulo.rda |binary
data/hdpg.rda |binary
data/housetasks.rda |binary
data/humDNAm.rda |binary
data/ichtyo.rda |binary
data/irishdata.rda |binary
data/julliot.rda |binary
data/jv73.rda |binary
data/kcponds.rda |binary
data/lascaux.rda |binary
data/lizards.rda |binary
data/macaca.rda |binary
data/macon.rda |binary
data/macroloire.rda |binary
data/mafragh.rda |binary
data/maples.rda |binary
data/mariages.rda |binary
data/meau.rda |binary
data/meaudret.rda |binary
data/microsatt.rda |binary
data/mjrochet.rda |binary
data/mollusc.rda |binary
data/monde84.rda |binary
data/morphosport.rda |binary
data/newick.eg.rda |binary
data/njplot.rda |binary
data/olympic.rda |binary
data/oribatid.rda |binary
data/ours.rda |binary
data/palm.rda |binary
data/pap.rda |binary
data/pcw.rda |only
data/perthi02.rda |binary
data/piosphere.rda |binary
data/presid2002.rda |binary
data/procella.rda |binary
data/rankrock.rda |binary
data/rhizobium.rda |binary
data/rhone.rda |binary
data/rpjdl.rda |binary
data/santacatalina.rda |binary
data/sarcelles.rda |binary
data/seconde.rda |binary
data/skulls.rda |binary
data/steppe.rda |binary
data/syndicats.rda |binary
data/t3012.rda |binary
data/tarentaise.rda |binary
data/taxo.eg.rda |binary
data/tintoodiel.rda |binary
data/tithonia.rda |binary
data/tortues.rda |binary
data/toxicity.rda |binary
data/trichometeo.rda |binary
data/ungulates.rda |binary
data/vegtf.rda |binary
data/veuvage.rda |binary
data/westafrica.rda |binary
data/woangers.rda |binary
data/worksurv.rda |binary
data/yanomama.rda |binary
data/zealand.rda |binary
man/EH.Rd | 2
man/PI2newick.Rd | 2
man/abouheif.eg.Rd | 2
man/acacia.Rd | 19 -
man/add.scatter.Rd | 103 +++--
man/ade4.package.Rd | 2
man/adegraphicsLoaded.Rd |only
man/aminoacyl.Rd | 2
man/amova.Rd | 2
man/aravo.Rd | 25 -
man/ardeche.Rd | 6
man/area.plot.Rd | 172 +++++----
man/as.taxo.Rd | 2
man/atlas.Rd | 89 +++--
man/atya.Rd | 26 -
man/avijons.Rd | 104 +++--
man/avimedi.Rd | 40 +-
man/bacteria.Rd | 11
man/banque.Rd | 8
man/baran95.Rd | 64 ++-
man/between.Rd | 30 +
man/betweencoinertia.Rd | 4
man/bf88.Rd | 31 +
man/bsetal97.Rd | 2
man/buech.Rd | 25 -
man/butterfly.Rd | 29 +
man/bwca.dpcoa.Rd |only
man/cailliez.Rd | 2
man/capitales.Rd | 57 ++-
man/carni70.Rd | 9
man/cca.Rd | 99 +++--
man/chats.Rd | 40 +-
man/chazeb.Rd | 3
man/chevaine.Rd | 67 +--
man/chickenk.Rd |only
man/clementines.Rd | 41 +-
man/cnc2003.Rd | 1
man/coinertia.Rd | 21 -
man/coleo.Rd | 27 +
man/corkdist.Rd | 26 -
man/corvus.Rd | 14
man/costatis.Rd | 9
man/costatis.randtest.Rd |only
man/deug.Rd | 15
man/disc.Rd | 2
man/discrimin.Rd | 5
man/discrimin.coa.Rd | 2
man/dist.binary.Rd | 2
man/dist.dudi.Rd | 2
man/dist.genet.Rd | 2
man/dist.neig.Rd | 2
man/dist.prop.Rd | 24 -
man/dist.quant.Rd | 24 -
man/divc.Rd | 2
man/divcmax.Rd | 24 -
man/dotchart.phylog.Rd | 2
man/doubs.Rd | 50 +-
man/dpcoa.Rd | 58 ++-
man/dudi.Rd | 5
man/dudi.acm.Rd | 26 +
man/dudi.coa.Rd | 16
man/dudi.dec.Rd | 2
man/dudi.fca.Rd | 11
man/dudi.hillsmith.Rd | 18 -
man/dudi.mix.Rd | 16
man/dudi.nsc.Rd | 12
man/dudi.pca.Rd | 51 +-
man/dudi.pco.Rd | 2
man/ecg.Rd | 2
man/ecomor.Rd | 36 +-
man/elec88.Rd | 44 +-
man/euro123.Rd | 29 +
man/foucart.Rd | 12
man/friday87.Rd | 7
man/fruits.Rd | 31 +
man/gearymoran.Rd | 19 -
man/ggtortoises.Rd | 35 +-
man/granulo.Rd | 16
man/gridrowcol.Rd | 37 +-
man/hdpg.Rd | 24 -
man/housetasks.Rd | 11
man/humDNAm.Rd | 4
man/inertia.dudi.Rd | 2
man/irishdata.Rd | 45 ++
man/is.euclid.Rd | 2
man/julliot.Rd | 94 +++--
man/jv73.Rd | 33 +
man/kcponds.Rd | 50 +-
man/kdist.Rd | 2
man/kdist2ktab.Rd | 15
man/kdisteuclid.Rd | 39 +-
man/kplot.foucart.Rd | 8
man/kplot.mcoa.Rd | 12
man/kplot.mfa.Rd | 3
man/kplot.pta.Rd | 11
man/kplot.sepan.Rd | 38 +-
man/kplot.statis.Rd | 14
man/krandtest.Rd | 2
man/ktab.Rd | 18 -
man/ktab.data.frame.Rd | 2
man/ktab.list.df.Rd | 4
man/ktab.list.dudi.Rd | 18 -
man/ktab.within.Rd | 2
man/lascaux.Rd | 38 +-
man/lingoes.Rd | 2
man/lizards.Rd | 2
man/macaca.Rd | 22 -
man/macroloire.Rd | 4
man/mafragh.Rd | 86 +++-
man/mantel.randtest.Rd | 2
man/mantel.rtest.Rd | 2
man/maples.Rd | 5
man/mariages.Rd | 22 -
man/mbpcaiv.Rd |only
man/mbpls.Rd |only
man/mcoa.Rd | 2
man/mdpcoa.Rd | 316 +++++++++---------
man/meau.Rd | 25 +
man/meaudret.Rd | 25 +
man/mfa.Rd | 2
man/microsatt.Rd | 12
man/mjrochet.Rd | 22 -
man/mld.Rd | 2
man/mollusc.Rd | 26 +
man/mstree.Rd | 42 +-
man/multiblock.Rd |only
man/multispati.Rd | 71 ++--
man/multispati.randtest.Rd | 4
man/multispati.rtest.Rd | 4
man/neig.Rd | 91 ++---
man/newick.eg.Rd | 4
man/newick2phylog.Rd | 10
man/niche.Rd | 41 +-
man/nipals.Rd | 34 +
man/njplot.Rd | 2
man/olympic.Rd | 31 +
man/optimEH.Rd | 2
man/oribatid.Rd | 17
man/originality.Rd | 2
man/orisaved.Rd | 2
man/orthobasis.Rd | 119 ++++--
man/orthogram.Rd | 4
man/ours.Rd | 6
man/palm.Rd | 3
man/pap.Rd | 3
man/pcaiv.Rd | 2
man/pcaivortho.Rd | 43 +-
man/pcw.Rd |only
man/phylog.Rd | 16
man/plot.between.Rd | 37 +-
man/plot.phylog.Rd | 2
man/plot.within.Rd | 34 +
man/presid2002.Rd | 64 ++-
man/procella.Rd | 2
man/procuste.Rd | 78 ++--
man/procuste.randtest.Rd | 2
man/procuste.rtest.Rd | 2
man/pta.Rd | 7
man/quasieuclid.Rd | 2
man/randEH.Rd | 2
man/randboot.Rd |only
man/randboot.multiblock.Rd |only
man/randtest.amova.Rd | 2
man/randtest.between.Rd | 2
man/randtest.coinertia.Rd | 2
man/randtest.discrimin.Rd | 2
man/randtest.pcaiv.Rd | 2
man/randxval.Rd |only
man/rankrock.Rd | 7
man/reconst.Rd | 2
man/rhizobium.Rd | 156 ++++----
man/rlq.Rd | 2
man/rpjdl.Rd | 14
man/rtest.Rd | 7
man/s.chull.Rd | 11
man/s.class.Rd | 58 +--
man/s.corcircle.Rd | 20 -
man/s.distri.Rd | 47 +-
man/s.image.Rd | 62 +--
man/s.kde2d.Rd | 17
man/s.label.Rd | 43 +-
man/s.logo.Rd | 42 +-
man/s.match.Rd | 24 -
man/s.match.class.Rd | 37 +-
man/s.traject.Rd | 19 -
man/s.value.Rd | 42 +-
man/santacatalina.Rd | 22 -
man/sarcelles.Rd | 22 -
man/scatter.acm.Rd | 8
man/scatter.coa.Rd | 29 +
man/scatter.dudi.Rd | 8
man/scatter.fca.Rd | 9
man/scatterutil.Rd | 3
man/sco.class.Rd | 2
man/sco.distri.Rd | 66 +--
man/sco.gauss.Rd | 2
man/sco.label.Rd | 2
man/sco.match.Rd | 2
man/score.Rd | 6
man/score.acm.Rd | 4
man/score.coa.Rd | 6
man/score.pca.Rd | 2
man/seconde.Rd | 6
man/skulls.Rd | 3
man/statico.Rd | 4
man/statico.krandtest.Rd |only
man/statis.Rd | 11
man/supcol.Rd | 20 -
man/suprow.Rd | 47 +-
man/symbols.phylog.Rd | 2
man/t3012.Rd | 16
man/table.paint.Rd | 1
man/table.phylog.Rd | 2
man/table.value.Rd | 21 -
man/tarentaise.Rd | 2
man/testdim.Rd | 14
man/testdim.multiblock.Rd |only
man/tintoodiel.Rd | 40 +-
man/tortues.Rd | 18 -
man/toxicity.Rd | 15
man/triangle.class.Rd | 30 -
man/triangle.plot.Rd | 28 -
man/trichometeo.Rd | 18 -
man/variance.phylog.Rd | 2
man/vegtf.Rd | 36 +-
man/wca.rlq.Rd | 5
man/westafrica.Rd | 112 +++---
man/within.Rd | 27 +
man/withincoinertia.Rd | 6
man/withinpca.Rd | 8
man/witwit.coa.Rd | 16
man/worksurv.Rd | 16
man/zealand.Rd | 42 +-
src/adesub.c | 14
src/adesub.h | 1
src/fourthcorner.c | 2
src/tests.c | 4
403 files changed, 4569 insertions(+), 2887 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-21 0.5
2013-11-20 0.4
2012-08-01 0.2
2011-02-03 0.1
Title: Distance Measures for Time Series Data
Diff between TSdist versions 2.1 dated 2015-03-31 and 2.2 dated 2015-04-14
Description: A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series.
Author: Usue Mori, Alexander Mendiburu, J.A. Lozano
Maintainer: Usue Mori
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/TSdist-package.Rd | 5 ++---
man/lb.keoghDistance.Rd | 2 +-
4 files changed, 10 insertions(+), 11 deletions(-)
Title: Parallel Programming Tools for Rcpp
Diff between RcppParallel versions 4.3.6 dated 2015-03-10 and 4.3.8 dated 2015-04-14
Description: High level functions for doing parallel programming with Rcpp.
For example, the parallelFor() function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce()
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire
RcppParallel-4.3.6/RcppParallel/README.md |only
RcppParallel-4.3.8/RcppParallel/DESCRIPTION | 12 +--
RcppParallel-4.3.8/RcppParallel/MD5 | 34 +++++---
RcppParallel-4.3.8/RcppParallel/NEWS | 11 +-
RcppParallel-4.3.8/RcppParallel/R/build.R | 24 +++---
RcppParallel-4.3.8/RcppParallel/R/hooks.R | 15 +++
RcppParallel-4.3.8/RcppParallel/inst/include/RcppParallel.h | 2
RcppParallel-4.3.8/RcppParallel/inst/include/RcppParallel/TBB.h | 1
RcppParallel-4.3.8/RcppParallel/inst/include/tthread/tinythread.h | 1
RcppParallel-4.3.8/RcppParallel/man/RcppParallel-package.Rd | 4 -
RcppParallel-4.3.8/RcppParallel/src/Makevars | 39 ++++++----
RcppParallel-4.3.8/RcppParallel/src/tbb/build/SunOS.suncc.inc | 2
RcppParallel-4.3.8/RcppParallel/src/tbb/build/linux.clang.inc | 2
RcppParallel-4.3.8/RcppParallel/tests/testthat/cpp/malloc.cpp |only
RcppParallel-4.3.8/RcppParallel/tests/testthat/pkg |only
RcppParallel-4.3.8/RcppParallel/tests/testthat/test-malloc.R |only
RcppParallel-4.3.8/RcppParallel/tests/testthat/test-pkg.R |only
17 files changed, 93 insertions(+), 54 deletions(-)
Title: Testing Homoscedasticity, Multivariate Normality, and Missing
Completely at Random
Diff between MissMech versions 1.0.1 dated 2014-01-20 and 1.0.2 dated 2015-04-14
Description: To test whether the missing data mechanism, in a set of incompletely observed data, is one of missing completely at random (MCAR).
For detailed description see Jamshidian, M. Jalal, S., and Jansen, C. (2014). "MissMech: An R Package for Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random (MCAR)," Journal of Statistical Software, 56(6), 1-31. URL http://www.jstatsoft.org/v56/i06/.
Author: Mortaza Jamshidian, Siavash Jalal, and Camden Jansen
Maintainer: Mortaza Jamshidian
MissMech-1.0.1/MissMech/R/AndersonDarling.r |only
MissMech-1.0.2/MissMech/DESCRIPTION | 13 +++++++------
MissMech-1.0.2/MissMech/MD5 | 10 +++++-----
MissMech-1.0.2/MissMech/NAMESPACE | 7 +++++++
MissMech-1.0.2/MissMech/R/AndersonDarling.R |only
MissMech-1.0.2/MissMech/man/MissMech-package.Rd | 4 ++--
MissMech-1.0.2/MissMech/man/TestMCARNormality.Rd | 8 ++++----
7 files changed, 25 insertions(+), 17 deletions(-)
Title: Lucid Printing of Floating Point Numbers
Diff between lucid versions 1.1 dated 2015-02-10 and 1.2 dated 2015-04-14
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright
Maintainer: Kevin Wright
DESCRIPTION | 10 +--
MD5 | 26 +++++-----
NAMESPACE | 2
NEWS | 4 +
R/lucid.r | 13 +++--
R/vc.r | 35 ++++++++++++-
inst/doc/lucid_printing.R | 31 ++++++++++++
inst/doc/lucid_printing.Rnw | 78 +++++++++++++++++++------------
inst/doc/lucid_printing.pdf |binary
man/vc.Rd | 16 ++++--
vignettes/figure/unnamed-chunk-5-1.pdf |binary
vignettes/lucid.bib | 7 ++
vignettes/lucid_printing-concordance.tex | 4 -
vignettes/lucid_printing.Rnw | 78 +++++++++++++++++++------------
14 files changed, 215 insertions(+), 89 deletions(-)
Title: Gamma Lasso Regression
Diff between gamlr versions 1.13 dated 2015-04-01 and 1.13-1 dated 2015-04-14
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization, http://arxiv.org/abs/1308.5623.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/gamlr.c | 4 ----
3 files changed, 5 insertions(+), 9 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET)
Diff between EGRET versions 2.1.1 dated 2015-02-17 and 2.2.0 dated 2015-04-14
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
EGRET-2.1.1/EGRET/vignettes/EGRET-concordance.tex |only
EGRET-2.1.1/EGRET/vignettes/figure |only
EGRET-2.1.1/EGRET/vignettes/framed.sty |only
EGRET-2.2.0/EGRET/DESCRIPTION | 8
EGRET-2.2.0/EGRET/MD5 | 120 +--------
EGRET-2.2.0/EGRET/NEWS | 11
EGRET-2.2.0/EGRET/R/EGRET.R | 2
EGRET-2.2.0/EGRET/R/fluxUnit.R | 3
EGRET-2.2.0/EGRET/R/modelEstimation.R | 11
EGRET-2.2.0/EGRET/R/objectDefinitions.R | 281 +++++++++++-----------
EGRET-2.2.0/EGRET/R/plotFlowSingle.R | 9
EGRET-2.2.0/EGRET/R/sysdata.rda |binary
EGRET-2.2.0/EGRET/README.md | 2
EGRET-2.2.0/EGRET/build/vignette.rds |binary
EGRET-2.2.0/EGRET/inst/CITATION |only
EGRET-2.2.0/EGRET/inst/doc/EGRET.Rnw | 4
EGRET-2.2.0/EGRET/inst/doc/EGRET.pdf |binary
EGRET-2.2.0/EGRET/man/EGRET-package.Rd | 2
EGRET-2.2.0/EGRET/man/fluxUnit-class.Rd | 2
EGRET-2.2.0/EGRET/man/modelEstimation.Rd | 6
EGRET-2.2.0/EGRET/man/plotFlowSingle.Rd | 9
EGRET-2.2.0/EGRET/vignettes/EGRET.Rnw | 4
22 files changed, 222 insertions(+), 252 deletions(-)
Title: Automatic Creation of Dummies with Support for Predictive
Modeling
Diff between dummy versions 0.1.0 dated 2014-11-07 and 0.1.2 dated 2015-04-14
Description: Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set).
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings
DESCRIPTION | 6 +++---
MD5 | 10 +++++++---
R/categories.R | 4 +++-
R/dummy.R | 1 +
R/dummyNews.R |only
R/zzz.R |only
inst |only
man/dummyNews.Rd |only
8 files changed, 14 insertions(+), 7 deletions(-)
Title: R Console Bindings for the 'Domino Command-Line Client'
Diff between domino versions 0.2-1 dated 2014-09-09 and 0.2-5 dated 2015-04-14
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite.
Author: Jacek Glodek
Maintainer: Nick Elprin
DESCRIPTION | 12 +++----
MD5 | 9 +++--
R/domino.R | 78 +++++++++++++++++++++++++++++++++++++++++++++-----
man/domino-package.Rd | 8 ++---
man/domino.login.Rd | 13 ++++++--
man/domino.sync.Rd |only
6 files changed, 96 insertions(+), 24 deletions(-)
Title: Descriptive Statistics
Diff between descr versions 1.0.4 dated 2014-11-04 and 1.1 dated 2015-04-14
Description: Weighted frequency and contingency tables of categorical
variables and of the comparison of the mean value of a numerical
variable by the levels of a factor, and methods to produce xtable
objects of the tables and to plot them. There are also functions to
facilitate the character encoding conversion of objects, to quickly
convert fixed width files into csv ones, and to export a data.frame to
a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation
written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan
Kraft
Maintainer: Jakson Aquino
DESCRIPTION | 20 ++--
MD5 | 24 ++---
NEWS | 14 +++
R/CrossTable.R | 49 +++++------
R/crosstab.R | 75 +++++++++--------
inst/po/pt_BR/LC_MESSAGES/R-descr.mo |binary
inst/po/pt_BR/LC_MESSAGES/descr.mo |binary
man/crosstab.Rd | 21 ++--
man/plot.CrossTable.Rd | 2
po/R-descr.pot | 142 ++++++++++++++++-----------------
po/R-pt_BR.po | 150 +++++++++++++++++------------------
po/descr.pot | 16 +--
po/pt_BR.po | 22 ++---
13 files changed, 281 insertions(+), 254 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Diff between evaluate versions 0.5.5 dated 2014-04-29 and 0.6 dated 2015-04-13
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie
evaluate-0.5.5/evaluate/R/src-region.r |only
evaluate-0.5.5/evaluate/man/getSrcRegion.Rd |only
evaluate-0.6/evaluate/DESCRIPTION | 14 +-
evaluate-0.6/evaluate/MD5 | 34 ++--
evaluate-0.6/evaluate/NEWS | 9 +
evaluate-0.6/evaluate/R/eval.r | 3
evaluate-0.6/evaluate/R/graphics.r | 79 +++--------
evaluate-0.6/evaluate/R/parse.r | 167 ++++++++++--------------
evaluate-0.6/evaluate/man/create_traceback.Rd | 1
evaluate-0.6/evaluate/man/evaluate.Rd | 3
evaluate-0.6/evaluate/man/is.message.Rd | 1
evaluate-0.6/evaluate/man/line_prompt.Rd | 1
evaluate-0.6/evaluate/man/new_output_handler.Rd | 1
evaluate-0.6/evaluate/man/parse_all.Rd | 3
evaluate-0.6/evaluate/man/replay.Rd | 1
evaluate-0.6/evaluate/man/set_hooks.Rd | 1
evaluate-0.6/evaluate/man/try_capture_stack.Rd | 1
evaluate-0.6/evaluate/man/watchout.Rd | 1
evaluate-0.6/evaluate/tests/test-all.R | 2
19 files changed, 151 insertions(+), 171 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Diff between spartan versions 2.2 dated 2015-03-23 and 2.2.1 dated 2015-04-13
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden
spartan-2.2.1/spartan/DESCRIPTION | 6
spartan-2.2.1/spartan/MD5 | 65 +--
spartan-2.2.1/spartan/R/aa_getATestResults.R | 8
spartan-2.2.1/spartan/R/aa_graphATestsForSampleSize.R | 8
spartan-2.2.1/spartan/R/aa_graphSampleSizeSummary.R | 17
spartan-2.2.1/spartan/R/aa_sampleSizeSummary.R | 7
spartan-2.2.1/spartan/R/aa_summariseReplicateRuns.R | 3
spartan-2.2.1/spartan/R/efast_generate_medians_for_all_parameter_subsets.R | 2
spartan-2.2.1/spartan/R/efast_get_overall_medians.R | 7
spartan-2.2.1/spartan/R/efast_graph_Results.R | 2
spartan-2.2.1/spartan/R/efast_netlogo_get_overall_medians.R | 5
spartan-2.2.1/spartan/R/efast_netlogo_run_Analysis.R | 5
spartan-2.2.1/spartan/R/efast_process_netlogo_result.R | 15
spartan-2.2.1/spartan/R/efast_run_Analysis.R | 7
spartan-2.2.1/spartan/R/getMediansSubset.R | 10
spartan-2.2.1/spartan/R/lhc_generateLHCSummary.R | 5
spartan-2.2.1/spartan/R/lhc_generatePRCoEffs.R | 5
spartan-2.2.1/spartan/R/lhc_generate_netlogo_PRCoEffs.R | 5
spartan-2.2.1/spartan/R/lhc_graphMeasuresForParameterChange.R | 7
spartan-2.2.1/spartan/R/lhc_netlogo_graphMeasuresForParameterChange.R | 5
spartan-2.2.1/spartan/R/lhc_plotCoEfficients.R | 197 ++++++----
spartan-2.2.1/spartan/R/lhc_process_netlogo_result.R | 17
spartan-2.2.1/spartan/R/lhc_process_sample_run_subsets.R | 5
spartan-2.2.1/spartan/R/oat_countResponsesOfDesiredValue.R | 6
spartan-2.2.1/spartan/R/oat_csv_result_file_analysis.R | 105 ++---
spartan-2.2.1/spartan/R/oat_graphATestsForSampleSize.R | 14
spartan-2.2.1/spartan/R/oat_plotResultDistribution.R | 5
spartan-2.2.1/spartan/R/oat_processParamSubsets.R | 3
spartan-2.2.1/spartan/R/oat_process_netlogo_result.R | 13
spartan-2.2.1/spartan/R/pcor.mat.R | 12
spartan-2.2.1/spartan/R/pcor.rec.R | 12
spartan-2.2.1/spartan/R/pcor.test.R | 6
spartan-2.2.1/spartan/man/Technique3-lhc_perform_analysis.Rd | 6
spartan-2.2/spartan/R/eFAST_TestBed.R |only
34 files changed, 340 insertions(+), 255 deletions(-)
Title: Software Option Settings Manager for R
Diff between settings versions 0.1.1 dated 2014-10-28 and 0.2.1 dated 2015-04-13
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names and default values.
Settings can then be retrieved, altered and reset to defaults with ease.
For R programmers and package developers it offers cloning and merging
functionality which allows for conveniently defining global and local
options, possibly in a multilevel options hierarchy. See the package
vignette for some examples concerning functions, S4 classes, and reference
classes. There are convenience functions to reset par() and options() to
their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo
settings-0.1.1/settings/man/options-package.Rd |only
settings-0.2.1/settings/DESCRIPTION | 12 +++---
settings-0.2.1/settings/MD5 | 27 +++++++++------
settings-0.2.1/settings/NAMESPACE | 4 ++
settings-0.2.1/settings/NEWS |only
settings-0.2.1/settings/R/options.R | 10 -----
settings-0.2.1/settings/R/settings-package.R |only
settings-0.2.1/settings/R/utils.R |only
settings-0.2.1/settings/README.md | 10 ++++-
settings-0.2.1/settings/build/vignette.rds |binary
settings-0.2.1/settings/inst/doc/settings.R | 43 +++++++++++++++---------
settings-0.2.1/settings/inst/doc/settings.Rmd | 28 ++++++++++++++-
settings-0.2.1/settings/inst/doc/settings.html | 44 ++++++++++++++++++++++---
settings-0.2.1/settings/man/options_manager.Rd | 2 -
settings-0.2.1/settings/man/reset_options.Rd |only
settings-0.2.1/settings/man/reset_par.Rd |only
settings-0.2.1/settings/man/settings.Rd |only
settings-0.2.1/settings/vignettes/settings.Rmd | 28 ++++++++++++++-
18 files changed, 153 insertions(+), 55 deletions(-)
Title: Persistent Fast Amortized Stack and Queue Data Structures
Diff between rstackdeque versions 1.1 dated 2014-12-04 and 1.1.1 dated 2015-04-13
Description: Provides fast, persistent (side-effect-free) stack, queue and
deque (double-ended-queue) data structures. While deques include a superset
of functionality provided by queues, in these implementations queues are
more efficient in some specialized situations. See the documentation for
rstack, rdeque, and rpqueue for details.
Author: Shawn T. O'Neil
Maintainer: Shawn T. O'Neil
rstackdeque-1.1.1/rstackdeque/DESCRIPTION | 6 +--
rstackdeque-1.1.1/rstackdeque/LICENSE | 4 +-
rstackdeque-1.1.1/rstackdeque/MD5 | 27 +++++++---------
rstackdeque-1.1.1/rstackdeque/R/as.data.frame.rdeque.R | 1
rstackdeque-1.1.1/rstackdeque/R/rdeque.R | 3 -
rstackdeque-1.1.1/rstackdeque/R/rpqueue.R | 3 -
rstackdeque-1.1.1/rstackdeque/R/rstack.R | 4 +-
rstackdeque-1.1.1/rstackdeque/R/without_top.R | 3 -
rstackdeque-1.1.1/rstackdeque/R/without_top.rstack.R | 8 ++--
rstackdeque-1.1.1/rstackdeque/man/rdeque.Rd | 5 --
rstackdeque-1.1.1/rstackdeque/man/rpqueue.Rd | 5 --
rstackdeque-1.1.1/rstackdeque/man/rstack.Rd | 5 --
rstackdeque-1.1.1/rstackdeque/man/without_top.Rd | 3 -
rstackdeque-1.1.1/rstackdeque/man/without_top.rstack.Rd | 3 -
rstackdeque-1.1/rstackdeque/README.md |only
15 files changed, 30 insertions(+), 50 deletions(-)
Title: Refined Moving Average Filter
Diff between rmaf versions 2.0 dated 2014-03-10 and 3.0 dated 2015-04-13
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu
rmaf-2.0/rmaf/R/ma.filter.R |only
rmaf-3.0/rmaf/DESCRIPTION | 10 +-
rmaf-3.0/rmaf/MD5 | 18 ++-
rmaf-3.0/rmaf/R/mafilter.R |only
rmaf-3.0/rmaf/R/qn.R | 38 +++-----
rmaf-3.0/rmaf/R/ssfilter.R |only
rmaf-3.0/rmaf/data/globtemp.rda |binary
rmaf-3.0/rmaf/man/globtemp.Rd | 4
rmaf-3.0/rmaf/man/ma.filter.Rd | 176 ++++++++++++++++++++------------------
rmaf-3.0/rmaf/man/qn.Rd | 88 +++++++++----------
rmaf-3.0/rmaf/man/rmaf-package.Rd | 90 +++++++++----------
rmaf-3.0/rmaf/man/ss.filter.Rd |only
12 files changed, 224 insertions(+), 200 deletions(-)
Title: Import Professional Baseball Data from 'Retrosheet'
Diff between retrosheet versions 1.0.1 dated 2015-04-09 and 1.0.2 dated 2015-04-13
Description: A collection of tools to import and structure the (currently) single-season
event, game-log, roster, and schedule data available from http://www.retrosheet.org.
In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse.
This package does the parsing on those files, returning the requested data in the most
practical R structure to use for sabermetric or other analyses.
Author: Richard Scriven [aut, cre]
Maintainer: Richard Scriven
retrosheet-1.0.1/retrosheet/R/internals.R |only
retrosheet-1.0.2/retrosheet/DESCRIPTION | 18 +++++-----
retrosheet-1.0.2/retrosheet/MD5 | 13 ++++---
retrosheet-1.0.2/retrosheet/NAMESPACE | 1
retrosheet-1.0.2/retrosheet/R/getParkIDs.R |only
retrosheet-1.0.2/retrosheet/R/getPartialGamelog.R | 33 +++++++++++++++----
retrosheet-1.0.2/retrosheet/README.md | 14 +++++---
retrosheet-1.0.2/retrosheet/man/getParkIDs.Rd |only
retrosheet-1.0.2/retrosheet/man/getPartialGamelog.Rd | 7 ++--
9 files changed, 59 insertions(+), 27 deletions(-)
Title: Determining the Best Number of Clusters in a Data Set
Diff between NbClust versions 2.0.4 dated 2015-03-02 and 3.0 dated 2015-04-13
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad
DESCRIPTION | 8 +-
MD5 | 6 +-
R/NbClust.R | 165 ++++++++++++++++++++++++++++++++++-----------------------
man/NbClust.Rd | 28 ++++++++-
4 files changed, 131 insertions(+), 76 deletions(-)
Title: Estimation of Heritability in Linear Mixed Models
Diff between HiLMM versions 1.0 dated 2014-04-15 and 1.1 dated 2015-04-13
Description: Estimation of heritability with confidence intervals in linear mixed models.
Author: Anna Bonnet
Maintainer: Anna Bonnet
HiLMM-1.0/HiLMM/data/mat_W.rda |only
HiLMM-1.0/HiLMM/data/vec_Y.rda |only
HiLMM-1.0/HiLMM/man/mat_W.Rd |only
HiLMM-1.0/HiLMM/man/vec_Y.Rd |only
HiLMM-1.1/HiLMM/DESCRIPTION | 13 +++++-----
HiLMM-1.1/HiLMM/MD5 | 25 ++++++++++++++------
HiLMM-1.1/HiLMM/R/HiLMM-internal.R |only
HiLMM-1.1/HiLMM/R/data_simu.R |only
HiLMM-1.1/HiLMM/R/estim_herit.R | 42 +++++++++++++++++++++++++----------
HiLMM-1.1/HiLMM/build |only
HiLMM-1.1/HiLMM/data/W.rda |only
HiLMM-1.1/HiLMM/data/Y.rda |only
HiLMM-1.1/HiLMM/inst |only
HiLMM-1.1/HiLMM/man/HiLMM-package.Rd | 30 ++++++++++---------------
HiLMM-1.1/HiLMM/man/W.Rd |only
HiLMM-1.1/HiLMM/man/Y.Rd |only
HiLMM-1.1/HiLMM/man/data_simu.Rd |only
HiLMM-1.1/HiLMM/man/estim_herit.Rd | 38 +++++++++++++------------------
HiLMM-1.1/HiLMM/vignettes |only
19 files changed, 82 insertions(+), 66 deletions(-)
Title: Invariant Causal Prediction
Diff between InvariantCausalPrediction versions 0.1-4 dated 2014-12-12 and 0.3 dated 2015-04-13
More information about InvariantCausalPrediction at CRAN
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen
DESCRIPTION | 12 ++++++------
MD5 | 19 +++++++++++++------
NAMESPACE | 4 ++--
R/ICP.R | 17 ++++++++++++++---
R/computeDelta.R |only
R/edgeRetention.R |only
R/edgeSelection.R |only
R/feedbackNetwork.R |only
R/hiddenICP.R |only
man/ICP.Rd | 21 +++++++++++++++++----
man/feedbackNetwork.Rd |only
man/hiddenICP.Rd |only
man/plot.InvariantCausalPrediction.Rd | 6 +++++-
man/summary.InvariantCausalPrediction.Rd | 6 +++++-
14 files changed, 62 insertions(+), 23 deletions(-)
Permanent link
Title: Fast Estimation of Gaussian Mixture Copula Models
Diff between GMCM versions 1.1.1 dated 2014-10-06 and 1.2 dated 2015-04-13
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau
DESCRIPTION | 18 +--
MD5 | 104 ++++++++++----------
NAMESPACE | 2
R/EMAlgortihm.R | 4
R/GMCM-package.R | 59 +++++------
R/PseudoEMAlgorithm.R | 4
R/RcppExports.R | 8 -
R/Uhat.R | 2
R/colSds.R | 6 -
R/dgmcm.loglik.R | 6 -
R/fit.full.GMCM.R | 10 -
R/fit.meta.GMCM.R | 24 ++--
R/full2meta.R | 3
R/get.IDR2.R | 18 +--
R/is.theta.R | 17 ++-
R/pgmm.marginal.R | 22 ++--
R/rtheta.R | 162 +++++++++++++++++++++++--------
README.md | 68 ++++++++++++-
build |only
inst/CITATION | 39 ++++---
inst/NEWS.Rd | 15 ++
inst/doc |only
inst/tests/test-EMAlgorithm.R | 47 ++++-----
inst/tests/test-EStep.R | 24 ++--
inst/tests/test-full2meta-meta2full.R | 58 +++++------
inst/tests/test-is.theta.R | 25 ++++
man/EMAlgorithm.Rd | 7 -
man/EStep.Rd | 3
man/GMCM-package.Rd | 21 ++--
man/PseudoEMAlgorithm.Rd | 7 -
man/SimulateGMCMData.Rd | 3
man/Uhat.Rd | 5
man/choose.theta.Rd | 3
man/colSds.Rd | 8 -
man/cummean.Rd | 3
man/dgmcm.loglik.Rd | 9 -
man/dmvnormal.Rd | 11 +-
man/fit.full.GMCM.Rd | 13 +-
man/fit.meta.GMCM.Rd | 27 ++---
man/freshVsFrozen.Rd | 17 +--
man/full2meta.Rd | 3
man/get.IDR.Rd | 19 +--
man/is.theta.Rd | 7 +
man/logit.Rd | 3
man/rho.transform.Rd | 3
man/rtheta.Rd | 89 +++++++++++++++--
man/tt.Rd | 3
man/u133VsExon.Rd | 24 ++--
src/GMCM.cpp | 9 -
src/Makevars.win | 2
src/RcppExports.cpp | 174 +++++++++++++---------------------
vignettes |only
52 files changed, 734 insertions(+), 484 deletions(-)
Title: Estimation of Temporal Ordering of Cancer Abnormalities
Diff between cancerTiming versions 2.0.0 dated 2014-05-07 and 3.0.0 dated 2015-04-13
Description: This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom
DESCRIPTION | 14 +--
MD5 | 27 +++---
NAMESPACE | 3
R/eventTiming.R | 184 +++++++++++++++++++++++++++++---------------
R/eventTimingList.R |only
R/labelSeg.R | 24 ++---
R/plotPi0.R |only
inst/NEWS.Rd |only
man/alleleFreq.Rd | 3
man/eventTiming.Rd | 5 -
man/eventTimingOverList.Rd |only
man/makeEventHistory.Rd | 10 +-
man/mleAF.Rd | 2
man/mutData.Rd | 3
man/plotAlleleByPosition.Rd | 19 ++--
man/plotAlleleDensity.Rd | 11 +-
man/plotPi0.Rd |only
17 files changed, 192 insertions(+), 113 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Diff between ASMap versions 0.3-3 dated 2015-02-02 and 0.4 dated 2015-04-13
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor
Maintainer: Julian Taylor
ASMap-0.3-3/ASMap/data/mapDHu.RData |only
ASMap-0.3-3/ASMap/man/mapDHu.Rd |only
ASMap-0.4/ASMap/DESCRIPTION | 12 +++++----
ASMap-0.4/ASMap/MD5 | 45 +++++++++++++++++++++++++----------
ASMap-0.4/ASMap/R/mstmap9.R | 8 ++++--
ASMap-0.4/ASMap/build |only
ASMap-0.4/ASMap/data/mapBC.RData |only
ASMap-0.4/ASMap/data/mapBCu.RData |only
ASMap-0.4/ASMap/data/mapDH.RData |binary
ASMap-0.4/ASMap/data/mapDHf.RData |only
ASMap-0.4/ASMap/data/mapF2.RData |binary
ASMap-0.4/ASMap/inst |only
ASMap-0.4/ASMap/man/ASMap-package.Rd | 16 +++++++-----
ASMap-0.4/ASMap/man/genClones.Rd | 2 -
ASMap-0.4/ASMap/man/mapBC.Rd |only
ASMap-0.4/ASMap/man/mapBCu.Rd |only
ASMap-0.4/ASMap/man/mapDH.Rd | 13 +++++-----
ASMap-0.4/ASMap/man/mapDHf.Rd |only
ASMap-0.4/ASMap/man/mapF2.Rd | 10 ++++---
ASMap-0.4/ASMap/man/pullCross.Rd | 1
ASMap-0.4/ASMap/man/pushCross.Rd | 1
ASMap-0.4/ASMap/vignettes |only
22 files changed, 70 insertions(+), 38 deletions(-)
Title: Additional Matrix Functionality
Diff between ramify versions 0.1.0 dated 2015-03-23 and 0.2.0 dated 2015-04-13
Description: Additional matrix functionality for R including: (1) wrappers
for the base matrix function that allows matrices to be created from character
strings and lists (the former is especially useful for creating block
matrices), (ii) better default printing of large matrices, and (iii) a number
of convenience functions for users more familiar with other scientific
languages like Julia, Matlab/Octave, or Python.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell
ramify-0.1.0/ramify/man/falses.Rd |only
ramify-0.1.0/ramify/man/ones.Rd |only
ramify-0.2.0/ramify/DESCRIPTION | 23 +-
ramify-0.2.0/ramify/MD5 | 49 ++--
ramify-0.2.0/ramify/NAMESPACE | 14 +
ramify-0.2.0/ramify/NEWS | 14 -
ramify-0.2.0/ramify/R/bmat.R | 9
ramify-0.2.0/ramify/R/convenience.R | 279 +++++++++++++++++---------
ramify-0.2.0/ramify/R/dmat.R | 4
ramify-0.2.0/ramify/R/mat.R | 161 ++++++++++++++-
ramify-0.2.0/ramify/R/ramify.R | 43 ++--
ramify-0.2.0/ramify/R/utils.R |only
ramify-0.2.0/ramify/R/zzz.R |only
ramify-0.2.0/ramify/README.md | 70 ++++--
ramify-0.2.0/ramify/man/add_dots.Rd |only
ramify-0.2.0/ramify/man/argmax.Rd |only
ramify-0.2.0/ramify/man/as.mat.Rd |only
ramify-0.2.0/ramify/man/bmat.Rd | 5
ramify-0.2.0/ramify/man/desc_mat.Rd |only
ramify-0.2.0/ramify/man/dmat.Rd | 4
ramify-0.2.0/ramify/man/fill.Rd | 26 ++
ramify-0.2.0/ramify/man/flatten.Rd | 7
ramify-0.2.0/ramify/man/hcat.Rd | 2
ramify-0.2.0/ramify/man/print.mat.Rd |only
ramify-0.2.0/ramify/man/ramify.Rd | 43 ++--
ramify-0.2.0/ramify/man/rand.Rd | 30 +-
ramify-0.2.0/ramify/man/randi.Rd |only
ramify-0.2.0/ramify/man/randn.Rd |only
ramify-0.2.0/ramify/man/resize.Rd | 16 -
ramify-0.2.0/ramify/man/size.Rd | 8
ramify-0.2.0/ramify/tests/testthat/test-mat.R | 36 ++-
31 files changed, 597 insertions(+), 246 deletions(-)
Title: Analysis of the "Elements of Metacommunity Structure"
Diff between metacom versions 1.4.2 dated 2014-12-11 and 1.4.3 dated 2015-04-13
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas
DESCRIPTION | 15 ++++-----
MD5 | 40 +++++++++++++-----------
R/BoundaryClump.R | 4 +-
R/Coherence.R | 12 ++++---
R/IdentifyStructure.R | 78 ++++++++++++++++++-----------------------------
R/MetaImportance.R |only
R/Metacommunity.R | 27 ++++++++++------
R/Modularity.R |only
R/NullMaker.R | 12 +++----
R/Turnover.R | 8 ++--
data/TestMatrices.rda |binary
man/BoundaryClump.Rd | 16 +++++----
man/Coherence.Rd | 28 ++++++++--------
man/IdentifyStructure.Rd | 24 ++++++--------
man/Imagine.Rd | 6 +--
man/MetaImportance.Rd |only
man/Metacommunity.Rd | 39 +++++++++++++++--------
man/Modularity.Rd |only
man/NullMaker.Rd | 31 +++++++++---------
man/OrderMatrix.Rd | 11 +++---
man/TestMatrices.Rd | 26 +++++----------
man/Turnover.Rd | 18 +++++-----
man/metacom-package.Rd | 17 ++++------
23 files changed, 207 insertions(+), 205 deletions(-)
Title: Analysis of Dose-Response Curves
Diff between drc versions 2.3-96 dated 2013-11-29 and 2.5-11 dated 2015-04-13
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz
Maintainer: Christian Ritz
drc-2.3-96/drc/R/SI.R |only
drc-2.3-96/drc/R/actimL.R |only
drc-2.3-96/drc/R/genBliss.R |only
drc-2.3-96/drc/R/genBliss2.R |only
drc-2.3-96/drc/R/genLoewe.R |only
drc-2.3-96/drc/R/genLoewe2.r |only
drc-2.3-96/drc/R/genursa.R |only
drc-2.3-96/drc/R/genursa2.R |only
drc-2.3-96/drc/R/gompGrowth.R |only
drc-2.3-96/drc/R/iceLoewe.1.R |only
drc-2.3-96/drc/R/iceLoewe.1new.R |only
drc-2.3-96/drc/R/iceLoewe2.1.R |only
drc-2.3-96/drc/data/beetGrowth.rda |only
drc-2.3-96/drc/man/SI.Rd |only
drc-2.3-96/drc/man/beetGrowth.Rd |only
drc-2.3-96/drc/man/gompGrowth.Rd |only
drc-2.3-96/drc/man/mrdrm.Rd |only
drc-2.5-11/drc/DESCRIPTION | 19 +--
drc-2.5-11/drc/MD5 | 113 ++++++++----------
drc-2.5-11/drc/NAMESPACE | 40 +++---
drc-2.5-11/drc/NEWS | 35 +++++
drc-2.5-11/drc/R/ED.drc.R | 29 ++++
drc-2.5-11/drc/R/EDcomp.R |only
drc-2.5-11/drc/R/backfit.R | 2
drc-2.5-11/drc/R/compParm.R | 25 ++--
drc-2.5-11/drc/R/drm.R | 45 +++++--
drc-2.5-11/drc/R/gammadr.R |only
drc-2.5-11/drc/R/idrm.R | 6 -
drc-2.5-11/drc/R/isobole.R | 58 +++------
drc-2.5-11/drc/R/maED.R | 4
drc-2.5-11/drc/R/modelFunction.R | 17 ++
drc-2.5-11/drc/R/multi2.R |only
drc-2.5-11/drc/R/plot.drc.R | 49 ++++++--
drc-2.5-11/drc/R/predict.drc.R | 153 +++++++++++++++++--------
drc-2.5-11/drc/R/relpot.R | 6 -
drc-2.5-11/drc/R/resPrint.R | 2
drc-2.5-11/drc/R/sandwich.R | 110 ++++++++++++++++--
drc-2.5-11/drc/R/siInner.R | 13 +-
drc-2.5-11/drc/R/simDR.R | 2
drc-2.5-11/drc/R/summary.drc.R | 10 +
drc-2.5-11/drc/R/update.drc.R | 2
drc-2.5-11/drc/data/G.aparine.rda |binary
drc-2.5-11/drc/data/RScompetition.rda |binary
drc-2.5-11/drc/data/daphnids.rda |binary
drc-2.5-11/drc/data/earthworms.rda |binary
drc-2.5-11/drc/data/finney71.rda |binary
drc-2.5-11/drc/data/heartrate.rda |binary
drc-2.5-11/drc/data/leaflength.rda |binary
drc-2.5-11/drc/man/ED.drc.Rd | 64 ++++------
drc-2.5-11/drc/man/EDcomp.Rd |only
drc-2.5-11/drc/man/G.aparine.Rd | 38 +++---
drc-2.5-11/drc/man/H.virescens.Rd | 6 -
drc-2.5-11/drc/man/LL.2.Rd | 4
drc-2.5-11/drc/man/LL.3.Rd | 7 -
drc-2.5-11/drc/man/S.alba.Rd | 12 +-
drc-2.5-11/drc/man/bread.drc.Rd | 21 ++-
drc-2.5-11/drc/man/chickweed.Rd | 43 ++++---
drc-2.5-11/drc/man/compParm.Rd | 10 +
drc-2.5-11/drc/man/drm.Rd | 33 +++--
drc-2.5-11/drc/man/gammadr.Rd |only
drc-2.5-11/drc/man/germination.Rd | 39 +++---
drc-2.5-11/drc/man/gompertz.Rd | 8 -
drc-2.5-11/drc/man/isobole.Rd | 6 -
drc-2.5-11/drc/man/mixture.Rd | 8 -
drc-2.5-11/drc/man/multi2.Rd |only
drc-2.5-11/drc/man/plot.drc.Rd | 43 ++++---
drc-2.5-11/drc/man/predict.drc.Rd | 4
drc-2.5-11/drc/man/print.drc.Rd | 2
drc-2.5-11/drc/man/ursa.Rd | 203 +++++-----------------------------
69 files changed, 712 insertions(+), 579 deletions(-)
Title: Selecting Variable Subsets
Diff between subselect versions 0.12-4 dated 2014-10-08 and 0.12-5 dated 2015-04-13
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 21 +++++++++++++++------
R/trimmatrix.R | 11 +++++------
build/vignette.rds |binary
inst/CHANGELOG | 5 +++++
6 files changed, 35 insertions(+), 22 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 2.1-1640 dated 2015-03-11 and 2.2-1699 dated 2015-04-13
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 8 -
MD5 | 120 ++++++++--------
NAMESPACE | 15 +-
R/bccorr.R | 316 +++++++++++++++++++++++++++----------------
R/btrap.R | 12 +
R/cgsolve.R | 61 +++++---
R/chmethod.R | 27 +--
R/compfactor.R | 1
R/condfstat.R | 1
R/demeanlist.R | 24 +--
R/efactory.R | 1
R/felm.R | 118 +++++++++++-----
R/felm.old.R | 1
R/generics.R | 20 +-
R/getfe.R | 11 +
R/is.estimable.R | 2
R/kaczmarz.R | 10 -
R/oldfelm.R | 3
R/startup.R | 19 ++
R/trace.R | 26 +--
R/utils.R | 44 ++++-
R/waldtest.R | 1
build/vignette.rds |binary
exec/lfescript | 1
inst/NEWS.Rd | 15 ++
inst/TODO | 6
inst/doc/CHANGELOG | 23 ++-
inst/doc/identification.R | 5
inst/doc/identification.Rnw | 6
inst/doc/identification.pdf |binary
inst/doc/lfehow.Rnw | 1
inst/doc/lfehow.pdf |binary
inst/doc/speed.Rnw | 2
inst/doc/speed.pdf |binary
man/bccorr.Rd | 18 +-
man/cgsolve.Rd |only
man/demeanlist.Rd | 76 +++++-----
man/felm.Rd | 30 +++-
man/fevcov.Rd | 16 +-
man/getfe.Rd | 2
man/kaczmarz.Rd | 20 +-
man/lfe-package.Rd | 58 ++++---
man/makeDmatrix.Rd |only
man/mctrace.Rd |only
man/waldtest.Rd | 2
src/Makevars.in | 3
src/Makevars.win | 1
src/demean.c | 235 ++++++++++++++++++-------------
src/factor.c | 36 ++--
src/kaczmarz.c | 108 ++++----------
src/lfe-win.def |only
src/lfe.c | 36 ++--
src/lfe.h | 33 ++--
src/utils.c | 23 +--
tests/anomalies.Rout.save | 16 --
tests/bctest.Rout.save | 20 +-
tests/cgsolve.R |only
tests/cgsolve.Rout.save |only
tests/cluster.Rout.save | 7
tests/ivtest.Rout.save | 7
tests/weights.R |only
tests/weights.Rout.save |only
vignettes/identification.Rnw | 6
vignettes/lfehow.Rnw | 1
vignettes/speed.Rnw | 2
65 files changed, 987 insertions(+), 669 deletions(-)
Title: Fit Generalized Estimating Equations
Diff between geeM versions 0.7.2 dated 2014-12-03 and 0.7.3 dated 2015-04-13
Description: Allows generalized estimating equation fits with user-specified link and variance functions.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel
DESCRIPTION | 8
MD5 | 10
NAMESPACE | 4
R/geem.R | 922 ++++++++++++++++++++++++++++++------------------------------
R/print.R | 115 +++----
R/utility.R | 6
6 files changed, 537 insertions(+), 528 deletions(-)
Title: 'ADMB' to R Interface Functions
Diff between R2admb versions 0.7.10 dated 2013-09-22 and 0.7.13 dated 2015-04-13
Description: A series of functions to call AD Model Builder (i.e.,
compile and run models) from within R, read the results back
into R as 'admb' objects, and provide standard accessors (i.e.
coef(), vcov(), etc.)
Author: Ben Bolker, Hans Skaug, Jeff Laake
Maintainer: Ben Bolker
R2admb-0.7.10/R2admb/inst/doc/R2admb.R |only
R2admb-0.7.10/R2admb/inst/doc/R2admb.Rnw |only
R2admb-0.7.10/R2admb/vignettes/ADMB_runs.gz |only
R2admb-0.7.10/R2admb/vignettes/ReedfrogSizepred0.dat |only
R2admb-0.7.10/R2admb/vignettes/ReedfrogSizepred0.pin |only
R2admb-0.7.10/R2admb/vignettes/betamodel.txt |only
R2admb-0.7.10/R2admb/vignettes/cache |only
R2admb-0.7.10/R2admb/vignettes/figure |only
R2admb-0.7.10/R2admb/vignettes/gopherdat.RData |only
R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred.dat |only
R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred.pin |only
R2admb-0.7.10/R2admb/vignettes/reedfrogsizepred0.par |only
R2admb-0.7.10/R2admb/vignettes/rfjunk.tpl |only
R2admb-0.7.10/R2admb/vignettes/tadpole_bugs.txt |only
R2admb-0.7.10/R2admb/vignettes/toy1_gen.dat |only
R2admb-0.7.10/R2admb/vignettes/toy1_gen.par |only
R2admb-0.7.10/R2admb/vignettes/toy1_runs.RData |only
R2admb-0.7.13/R2admb/DESCRIPTION | 16
R2admb-0.7.13/R2admb/MD5 | 77 +---
R2admb-0.7.13/R2admb/NAMESPACE | 65 ++-
R2admb-0.7.13/R2admb/R/plot.admb_hist.r | 5
R2admb-0.7.13/R2admb/R/setup_admb.R | 169 +++++----
R2admb-0.7.13/R2admb/R/std_accessor.r | 33 -
R2admb-0.7.13/R2admb/R/utility-funs.R | 327 ++++++++-----------
R2admb-0.7.13/R2admb/build/vignette.rds |binary
R2admb-0.7.13/R2admb/inst/NEWS.Rd | 20 +
R2admb-0.7.13/R2admb/inst/admbtests/toy1.R | 10
R2admb-0.7.13/R2admb/inst/doc/R2admb.pdf |binary
R2admb-0.7.13/R2admb/inst/doc/toy1_runs.RData |binary
R2admb-0.7.13/R2admb/man/AIC.admb.Rd | 209 +++++-------
R2admb-0.7.13/R2admb/man/R2admb-package.Rd | 59 +--
R2admb-0.7.13/R2admb/man/admb_version.Rd | 43 +-
R2admb-0.7.13/R2admb/man/compile_admb.Rd | 76 ++--
R2admb-0.7.13/R2admb/man/do_admb.Rd | 268 +++++++--------
R2admb-0.7.13/R2admb/man/extract_gradient.Rd | 47 +-
R2admb-0.7.13/R2admb/man/find_large_cor.Rd | 54 +--
R2admb-0.7.13/R2admb/man/mcmc.control.Rd | 130 +++----
R2admb-0.7.13/R2admb/man/plot.admb_hist.Rd | 50 +-
R2admb-0.7.13/R2admb/man/read_pars.Rd | 119 +++---
R2admb-0.7.13/R2admb/man/read_plt.Rd | 50 +-
R2admb-0.7.13/R2admb/man/run.control.Rd | 101 ++---
R2admb-0.7.13/R2admb/man/setup_admb.Rd | 47 +-
R2admb-0.7.13/R2admb/man/write_pin.Rd | 79 ++--
R2admb-0.7.13/R2admb/vignettes/R2admb.Rnw | 113 +++---
R2admb-0.7.13/R2admb/vignettes/ReedfrogSizepred1.tpl |only
45 files changed, 1055 insertions(+), 1112 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Diff between inline versions 0.3.13 dated 2013-08-08 and 0.3.14 dated 2015-04-13
Description: Functionality to dynamically define R functions and S4 methods
with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel
DESCRIPTION | 20 +++++++++--------
MD5 | 17 ++++++++-------
NAMESPACE | 14 +++++++++---
R/cfunction.R | 47 ++++++++++++++++++++++++++++++++++-------
R/cxxfunction.R | 2 -
R/utilities.R |only
README.md |only
inst/NEWS.Rd | 14 ++++++++++++
man/cfunction.Rd | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
man/internals.Rd | 2 -
man/utilities.Rd |only
11 files changed, 147 insertions(+), 31 deletions(-)
Title: Basics of Certificates and Structured Products Valuation
Diff between fCertificates versions 0.5-3 dated 2014-03-02 and 0.5-4 dated 2015-04-13
Description: Collection of pricing by duplication methods for popular structured products ("Zertifikate").
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
DESCRIPTION | 14 +++++++-------
MD5 | 8 ++++----
NEWS | 5 +++++
inst/CITATION | 5 ++---
man/BonusProCertificate.Rd | 4 ++--
5 files changed, 20 insertions(+), 16 deletions(-)
Title: Age-Period-Cohort Analysis
Diff between apc versions 1.0 dated 2014-08-30 and 1.1 dated 2015-04-13
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen
apc-1.0/apc/COPYING |only
apc-1.0/apc/R/apc_data.r |only
apc-1.0/apc/R/apc_fit.r |only
apc-1.0/apc/R/apc_get_index.r |only
apc-1.0/apc/R/apc_identify.r |only
apc-1.0/apc/R/apc_plot_data.r |only
apc-1.0/apc/R/apc_plot_fit.r |only
apc-1.0/apc/man/apc-package.Rd |only
apc-1.1/apc/CHANGES |only
apc-1.1/apc/DESCRIPTION | 10 ++--
apc-1.1/apc/MD5 | 48 +++++++++++++------
apc-1.1/apc/NEWS |only
apc-1.1/apc/R/apc_data.R |only
apc-1.1/apc/R/apc_fit.R |only
apc-1.1/apc/R/apc_get_index.R |only
apc-1.1/apc/R/apc_identify.R |only
apc-1.1/apc/R/apc_plot_data.R |only
apc-1.1/apc/R/apc_plot_fit.R |only
apc-1.1/apc/build |only
apc-1.1/apc/inst/CHANGES |only
apc-1.1/apc/inst/CITATION | 11 ++++
apc-1.1/apc/inst/COPYING |only
apc-1.1/apc/inst/doc |only
apc-1.1/apc/man/apc.data.list.Rd | 14 ++++-
apc-1.1/apc/man/apc.get.design.Rd | 4 +
apc-1.1/apc/man/apc.get.index.Rd | 8 ++-
apc-1.1/apc/man/apc.identify.Rd | 77 ++++++++++++++++++++++++++++---
apc-1.1/apc/man/apc.plot.fit.Rd | 86 ++++++++++++++++++++++++++++-------
apc-1.1/apc/man/apc_1.1-package.Rd |only
apc-1.1/apc/man/data.asbestos.Rd | 15 ++----
apc-1.1/apc/man/data.loss.BZ.Rd |only
apc-1.1/apc/man/data.loss.TA.Rd |only
apc-1.1/apc/man/data.loss.VNJ.Rd |only
apc-1.1/apc/man/vector.2.triangle.Rd |only
apc-1.1/apc/vignettes |only
35 files changed, 213 insertions(+), 60 deletions(-)
Title: Time Dependent Point Process Modelling
Diff between PtProcess versions 3.3-7 dated 2014-10-16 and 3.3-9 dated 2015-04-12
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte
DESCRIPTION | 11 +++++------
MD5 | 14 +++++++-------
R/logLik.mpp.R | 2 +-
data/NthChina.rda |binary
data/Ogata.rda |binary
data/Phuket.rda |binary
data/Tangshan.rda |binary
man/Changes.Rd | 4 +++-
8 files changed, 16 insertions(+), 15 deletions(-)
Title: Hidden Markov Models
Diff between HiddenMarkov versions 1.8-1 dated 2014-09-25 and 1.8-3 dated 2015-04-12
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/CITATION | 11 +++++------
man/Changes.Rd | 2 ++
man/HiddenMarkov.Rd | 2 +-
5 files changed, 16 insertions(+), 15 deletions(-)
Title: Resampling Functions
Diff between resample versions 0.2 dated 2014-03-12 and 0.4 dated 2015-04-12
Description: Bootstrap, permutation tests, and other resampling functions,
featuring easy-to-use syntax.
Author: Tim Hesterberg
Maintainer: Tim Hesterberg
resample-0.2/resample/R/anyNA.R |only
resample-0.2/resample/R/cat.R |only
resample-0.2/resample/src |only
resample-0.4/resample/DESCRIPTION | 14 -
resample-0.4/resample/MD5 | 64 ++++----
resample-0.4/resample/NAMESPACE | 25 ++-
resample-0.4/resample/R/BootStats.R | 29 +++
resample-0.4/resample/R/MakeFunction.R | 12 -
resample-0.4/resample/R/SetSeed.R | 4
resample-0.4/resample/R/bootstrap.R | 40 ++---
resample-0.4/resample/R/bootstrap2.R | 137 ++++++++++-------
resample-0.4/resample/R/cat0.R |only
resample-0.4/resample/R/jackknife.R |only
resample-0.4/resample/R/limits.R | 160 +++++++++++++++++++-
resample-0.4/resample/R/permutationTest.R | 44 ++---
resample-0.4/resample/R/permutationTest2.R | 110 +++++++-------
resample-0.4/resample/R/resample.R | 140 ++++++++++++-----
resample-0.4/resample/R/samplers.R | 65 ++++++--
resample-0.4/resample/data |only
resample-0.4/resample/inst |only
resample-0.4/resample/man/ExpandProbs.Rd |only
resample-0.4/resample/man/IfElse.Rd |only
resample-0.4/resample/man/Quantile.Rd |only
resample-0.4/resample/man/bootstrap.Rd | 71 +++++----
resample-0.4/resample/man/cat0.Rd |only
resample-0.4/resample/man/colVars.Rd |only
resample-0.4/resample/man/deprecated.Rd |only
resample-0.4/resample/man/jackknife.Rd |only
resample-0.4/resample/man/limits.percentile.Rd | 60 ++++++-
resample-0.4/resample/man/print.resample.Rd | 99 ++++++++----
resample-0.4/resample/man/resample-data.Rd |only
resample-0.4/resample/man/resample-package.Rd | 195 +++++++++++++++++++++++--
resample-0.4/resample/man/resample.Rd | 40 +++--
resample-0.4/resample/man/samp.bootstrap.Rd | 13 -
resample-0.4/resample/tests/bootstrap.t | 37 ++--
resample-0.4/resample/tests/bootstrap2.t | 60 ++++---
resample-0.4/resample/tests/confidence.t |only
resample-0.4/resample/tests/jackknife.t |only
resample-0.4/resample/tests/permutationTest.t | 58 +++++--
resample-0.4/resample/tests/permutationTest2.t | 79 ++++++----
resample-0.4/resample/tests/samplers.t | 44 ++---
41 files changed, 1111 insertions(+), 489 deletions(-)
Title: Analysis of Queueing Networks and Models
Diff between queueing versions 0.2.3 dated 2014-12-07 and 0.2.4 dated 2015-04-12
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models
and Single and Multiclass Product-Form Queueing Networks.
It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K,
Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,
Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks
and Single Channel Multiple Class Mixed Networks.
Also it provides a B-Erlang, C-Erlang and Engset calculators.
This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla
ChangeLog | 3 +++
DESCRIPTION | 19 +++++++++++++------
MD5 | 6 +++---
inst/CITATION | 25 ++++++++-----------------
4 files changed, 27 insertions(+), 26 deletions(-)
Title: Data Sets from Montgomery, Peck and Vining's Book
Diff between MPV versions 1.35 dated 2014-09-03 and 1.38 dated 2015-04-12
Description: Most of this package consists of data sets from the
textbook Introduction
to Linear Regression Analysis (3rd ed), by Montgomery et al.
Some additional data sets and functions useful in an
undergraduate regression course are included.
Author: W.J. Braun
Maintainer: W.J. Braun
DESCRIPTION | 6 +++---
MD5 | 16 +++++++++++-----
R/GANOVA.R |only
R/Qyplot.R | 2 +-
R/Uplot.R | 4 ++--
data/Juliet.rda |only
data/oldwash.rda |only
data/pathoeg.rda |binary
man/GANOVA.Rd |only
man/Juliet.Rd |only
man/Uplot.Rd | 3 ++-
man/oldwash.Rd |only
12 files changed, 19 insertions(+), 12 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Diff between runjags versions 1.2.1-0 dated 2014-06-21 and 2.0.1-2 dated 2015-04-12
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood
runjags-1.2.1-0/runjags/R/autorun.run.jags.file.R |only
runjags-1.2.1-0/runjags/R/read.winbugs.R |only
runjags-1.2.1-0/runjags/inst/doc/module_distributions.pdf |only
runjags-1.2.1-0/runjags/inst/doc/runjags.Rtex |only
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runjags-1.2.1-0/runjags/src/distributions/DHCauchy.cc |only
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runjags-1.2.1-0/runjags/vignettes/runjags.Rtex |only
runjags-2.0.1-2/runjags/CHANGELOG | 83
runjags-2.0.1-2/runjags/DESCRIPTION | 49
runjags-2.0.1-2/runjags/MD5 | 130
runjags-2.0.1-2/runjags/NAMESPACE | 71
runjags-2.0.1-2/runjags/R/autoextend.jags.R | 942 +---
runjags-2.0.1-2/runjags/R/combine.mcmc.R | 155
runjags-2.0.1-2/runjags/R/dump.list.format.R | 42
runjags-2.0.1-2/runjags/R/extend.jags.R | 881 +++-
runjags-2.0.1-2/runjags/R/extract.runjags.R |only
runjags-2.0.1-2/runjags/R/load.module.runjags.R | 136
runjags-2.0.1-2/runjags/R/mutate.functions.R |only
runjags-2.0.1-2/runjags/R/print.methods.R | 487 --
runjags-2.0.1-2/runjags/R/read.jagsfile.R |only
runjags-2.0.1-2/runjags/R/results.jags.R |only
runjags-2.0.1-2/runjags/R/run.jags.study.R | 658 ++-
runjags-2.0.1-2/runjags/R/runjags.readin.R | 681 ++-
runjags-2.0.1-2/runjags/R/runjags.start.R | 2957 ++++++++------
runjags-2.0.1-2/runjags/R/runjags.summaries.R | 639 ++-
runjags-2.0.1-2/runjags/R/runjagsclass.R |only
runjags-2.0.1-2/runjags/R/setup.jags.jagsfile.R | 778 ++-
runjags-2.0.1-2/runjags/R/summary.R |only
runjags-2.0.1-2/runjags/R/template.jags.R |only
runjags-2.0.1-2/runjags/R/utilities.R | 1151 ++---
runjags-2.0.1-2/runjags/R/utilities.invisible.R | 1345 +++++-
runjags-2.0.1-2/runjags/R/xgrid.run.R | 2
runjags-2.0.1-2/runjags/R/xgrid.run.jags.R | 232 -
runjags-2.0.1-2/runjags/R/xgrid.utilities.R | 26
runjags-2.0.1-2/runjags/R/zzz.R | 21
runjags-2.0.1-2/runjags/build/vignette.rds |binary
runjags-2.0.1-2/runjags/inst/CITATION | 10
runjags-2.0.1-2/runjags/inst/doc/UserGuide.Rtex |only
runjags-2.0.1-2/runjags/inst/doc/UserGuide.pdf |only
runjags-2.0.1-2/runjags/inst/doc/quickjags.R |only
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runjags-2.0.1-2/runjags/man/add.summary.Rd |only
runjags-2.0.1-2/runjags/man/ask.Rd | 8
runjags-2.0.1-2/runjags/man/autorun.jags.Rd | 458 --
runjags-2.0.1-2/runjags/man/combine.mcmc.Rd | 96
runjags-2.0.1-2/runjags/man/extract.runjags.Rd |only
runjags-2.0.1-2/runjags/man/findjags.Rd | 2
runjags-2.0.1-2/runjags/man/list.dump.format.Rd | 11
runjags-2.0.1-2/runjags/man/load.runjagsmodule.Rd |only
runjags-2.0.1-2/runjags/man/mutate.functions.Rd |only
runjags-2.0.1-2/runjags/man/new_unique.Rd | 2
runjags-2.0.1-2/runjags/man/read.jagsfile.Rd |only
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runjags-2.0.1-2/runjags/man/run.jags.Rd | 516 --
runjags-2.0.1-2/runjags/man/run.jags.study.Rd | 208
runjags-2.0.1-2/runjags/man/runjags-class.Rd | 271 -
runjags-2.0.1-2/runjags/man/runjags.Rd | 98
runjags-2.0.1-2/runjags/man/runjags.options.Rd | 131
runjags-2.0.1-2/runjags/man/runjags.printmethods.Rd |only
runjags-2.0.1-2/runjags/man/template.jags.Rd |only
runjags-2.0.1-2/runjags/man/testjags.Rd | 11
runjags-2.0.1-2/runjags/man/timestring.Rd | 4
runjags-2.0.1-2/runjags/man/write.jagsfile.Rd |only
runjags-2.0.1-2/runjags/man/xgrid.run.Rd | 107
runjags-2.0.1-2/runjags/man/xgrid.run.jags.Rd | 97
runjags-2.0.1-2/runjags/src/Makevars.in | 4
runjags-2.0.1-2/runjags/src/Makevars.win | 2
runjags-2.0.1-2/runjags/src/distributions/DHalfCauchy.cc |only
runjags-2.0.1-2/runjags/src/distributions/DHalfCauchy.h |only
runjags-2.0.1-2/runjags/src/distributions/DPar4.cc | 2
runjags-2.0.1-2/runjags/src/runjags.cc | 4
runjags-2.0.1-2/runjags/src/testrunjags.cc | 4
runjags-2.0.1-2/runjags/tests/checkinputs.R | 65
runjags-2.0.1-2/runjags/tests/checkmethods.R | 97
runjags-2.0.1-2/runjags/tests/checkmodule.R | 143
runjags-2.0.1-2/runjags/tests/checkstudy.R |only
runjags-2.0.1-2/runjags/vignettes/UserGuide.Rtex |only
runjags-2.0.1-2/runjags/vignettes/quickjags.Rmd |only
runjags-2.0.1-2/runjags/vignettes/traceplots.pdf |binary
85 files changed, 8251 insertions(+), 5566 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Diff between GUTS versions 0.4.14 dated 2015-04-03 and 0.5.2 dated 2015-04-12
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert
Maintainer: Sören Vogel
GUTS-0.4.14/GUTS/cleanup |only
GUTS-0.4.14/GUTS/configure |only
GUTS-0.4.14/GUTS/src/GUTS.cpp |only
GUTS-0.4.14/GUTS/src/GUTS.h |only
GUTS-0.4.14/GUTS/src/GUTS_calcLoglikelihood.cpp |only
GUTS-0.4.14/GUTS/src/GUTS_calcSample.cpp |only
GUTS-0.4.14/GUTS/src/GUTS_calcSurvivalProbabilities.cpp |only
GUTS-0.4.14/GUTS/src/Makevars.in |only
GUTS-0.4.14/GUTS/src/Makevars.win |only
GUTS-0.5.2/GUTS/DESCRIPTION | 16
GUTS-0.5.2/GUTS/MD5 | 18
GUTS-0.5.2/GUTS/R/GUTS.R | 30
GUTS-0.5.2/GUTS/man/Rcpp_GUTS-class.Rd | 2
GUTS-0.5.2/GUTS/src/GUTS_Rcpp.cpp | 678 +++++++++++++++-
GUTS-0.5.2/GUTS/src/GUTS_Rcpp.h |only
15 files changed, 683 insertions(+), 61 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.1.3 dated 2015-01-18 and 1.1.4 dated 2015-04-12
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
EpiModel-1.1.3/EpiModel/R/conc.microsim.R |only
EpiModel-1.1.3/EpiModel/R/zzz.R |only
EpiModel-1.1.3/EpiModel/inst/shiny/dcm |only
EpiModel-1.1.3/EpiModel/inst/shiny/icm |only
EpiModel-1.1.3/EpiModel/man/conc_microsim.Rd |only
EpiModel-1.1.3/EpiModel/man/get_args.Rd |only
EpiModel-1.1.3/EpiModel/man/plot.conc_microsim.Rd |only
EpiModel-1.1.4/EpiModel/DESCRIPTION | 14 -
EpiModel-1.1.4/EpiModel/MD5 | 120 +++++-----
EpiModel-1.1.4/EpiModel/NAMESPACE | 3
EpiModel-1.1.4/EpiModel/NEWS | 29 ++
EpiModel-1.1.4/EpiModel/R/EpiModel-package.r | 4
EpiModel-1.1.4/EpiModel/R/control.R | 31 +-
EpiModel-1.1.4/EpiModel/R/crosscheck.R | 53 ++--
EpiModel-1.1.4/EpiModel/R/dcm.R | 8
EpiModel-1.1.4/EpiModel/R/dcm.mods.R | 153 ++++++++-----
EpiModel-1.1.4/EpiModel/R/get.R | 46 +--
EpiModel-1.1.4/EpiModel/R/icm.R | 7
EpiModel-1.1.4/EpiModel/R/icm.mod.status.R | 4
EpiModel-1.1.4/EpiModel/R/init.R | 11
EpiModel-1.1.4/EpiModel/R/net.mod.init.R | 21 -
EpiModel-1.1.4/EpiModel/R/net.mod.status.R | 5
EpiModel-1.1.4/EpiModel/R/net.mod.vital.R | 18 -
EpiModel-1.1.4/EpiModel/R/net.utils.R | 176 ++++++++++-----
EpiModel-1.1.4/EpiModel/R/netdx.R | 15 -
EpiModel-1.1.4/EpiModel/R/netest.R | 19 -
EpiModel-1.1.4/EpiModel/R/netsim.R | 28 --
EpiModel-1.1.4/EpiModel/R/param.R | 60 +++--
EpiModel-1.1.4/EpiModel/R/plot.R | 78 ++++--
EpiModel-1.1.4/EpiModel/R/print.r | 6
EpiModel-1.1.4/EpiModel/R/saveout.R | 1
EpiModel-1.1.4/EpiModel/R/shiny.R | 4
EpiModel-1.1.4/EpiModel/R/utils.R | 62 +----
EpiModel-1.1.4/EpiModel/build/vignette.rds |binary
EpiModel-1.1.4/EpiModel/inst/doc/Intro.Rmd | 2
EpiModel-1.1.4/EpiModel/inst/doc/Intro.html | 9
EpiModel-1.1.4/EpiModel/inst/shiny/epidcm |only
EpiModel-1.1.4/EpiModel/inst/shiny/epiicm |only
EpiModel-1.1.4/EpiModel/man/EpiModel-package.Rd | 4
EpiModel-1.1.4/EpiModel/man/check_bip_degdist.Rd | 2
EpiModel-1.1.4/EpiModel/man/control.dcm.Rd | 6
EpiModel-1.1.4/EpiModel/man/control.icm.Rd | 6
EpiModel-1.1.4/EpiModel/man/control.net.Rd | 32 +-
EpiModel-1.1.4/EpiModel/man/dcm.Rd | 8
EpiModel-1.1.4/EpiModel/man/dcm.mods.Rd | 25 +-
EpiModel-1.1.4/EpiModel/man/dissolution_coefs.Rd | 77 ++++--
EpiModel-1.1.4/EpiModel/man/get_nwstats.Rd | 2
EpiModel-1.1.4/EpiModel/man/get_transmat.Rd | 2
EpiModel-1.1.4/EpiModel/man/icm.Rd | 7
EpiModel-1.1.4/EpiModel/man/init.dcm.Rd | 5
EpiModel-1.1.4/EpiModel/man/init.icm.Rd | 2
EpiModel-1.1.4/EpiModel/man/init.net.Rd | 4
EpiModel-1.1.4/EpiModel/man/netdx.Rd | 6
EpiModel-1.1.4/EpiModel/man/netest.Rd | 5
EpiModel-1.1.4/EpiModel/man/netsim.Rd | 28 --
EpiModel-1.1.4/EpiModel/man/param.dcm.Rd | 26 +-
EpiModel-1.1.4/EpiModel/man/param.icm.Rd | 23 +
EpiModel-1.1.4/EpiModel/man/param.net.Rd | 24 +-
EpiModel-1.1.4/EpiModel/man/split_bip.Rd | 2
EpiModel-1.1.4/EpiModel/tests/testthat/test-get.R | 39 +++
EpiModel-1.1.4/EpiModel/tests/testthat/test-net-long.R | 11
EpiModel-1.1.4/EpiModel/tests/testthat/test-netest.R | 44 ++-
EpiModel-1.1.4/EpiModel/tests/testthat/test-netpids.R |only
EpiModel-1.1.4/EpiModel/tests/testthat/test-netrestart.R |only
EpiModel-1.1.4/EpiModel/tests/testthat/test-utils.R |only
EpiModel-1.1.4/EpiModel/vignettes/Intro.Rmd | 2
66 files changed, 854 insertions(+), 525 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Diff between glmnet versions 2.0-1 dated 2015-04-08 and 2.0-2 dated 2015-04-11
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie
DESCRIPTION | 10 +-
MD5 | 12 +-
inst/doc/Coxnet.pdf |binary
inst/doc/glmnet_beta.R | 27 ++++--
inst/doc/glmnet_beta.Rmd | 18 +++-
inst/doc/glmnet_beta.html | 192 ++++++++++++++++++++++------------------------
vignettes/glmnet_beta.Rmd | 18 +++-
7 files changed, 155 insertions(+), 122 deletions(-)
Title: Explorer of World Population Prospects
Diff between wppExplorer versions 1.5-0 dated 2015-02-07 and 1.6-1 dated 2015-04-11
Description: A shiny interface for exploring data in the 'wpp2012' (or 2010, 2008) package.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 6 ++++++
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
R/global.R | 10 ++++++----
R/wpp.R | 9 +++++++++
inst/explore/server.R | 25 ++++++++++++++-----------
inst/explore/ui.R | 12 ++++++++----
inst/explore/www/geochart.js | 34 ++++++++++++++++++++++++++++++++--
man/wpp.explore.Rd | 2 ++
man/wpp.indicator.Rd | 3 ++-
man/wppExplorer-package.Rd | 14 +++++++++-----
11 files changed, 103 insertions(+), 42 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Diff between scrm versions 1.3-3 dated 2014-11-18 and 1.5.0-1 dated 2015-04-11
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution. Different to
other coalescent based simulations, scrm has an optional approximation
parameter that allows for high accuracy while maintaining a linear run time
cost for long sequences. It is optimized for simulating massive data sets as
produced by Next-Generation Sequencing technologies for up to several thousand
sequences.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
DESCRIPTION | 15 -
MD5 | 115 +++----
NAMESPACE | 2
NEWS | 22 -
R/RcppExports.R | 26 -
R/scrm.R | 18 -
README.md | 11
build/vignette.rds |binary
inst/CITATION |only
inst/doc/scrm-Arguments.Rmd | 55 ++-
inst/doc/scrm-Arguments.html | 320 ++++++----------------
inst/doc/scrm-TreesForApe.Rmd | 2
inst/doc/scrm-TreesForApe.html | 261 +++--------------
man/scrm-package.Rd | 3
man/scrm.Rd | 3
src/Makevars | 2
src/Makevars.win | 2
src/RcppExports.cpp | 60 +---
src/r_random_generator.h | 18 -
src/scrm/contemporaries_container.h | 2
src/scrm/event.h | 2
src/scrm/forest.cc | 201 +++++++++----
src/scrm/forest.h | 12
src/scrm/macros.h | 21 +
src/scrm/model.cc | 111 ++++---
src/scrm/model.h | 34 +-
src/scrm/node.cc | 21 +
src/scrm/node.h | 32 +-
src/scrm/node_container.cc | 63 +++-
src/scrm/node_container.h | 45 ++-
src/scrm/param.cc | 111 +++++--
src/scrm/param.h | 39 ++
src/scrm/random/fastfunc.cc | 9
src/scrm/random/fastfunc.h | 28 -
src/scrm/random/random_generator.cc | 2
src/scrm/random/random_generator.h | 2
src/scrm/summary_statistics/frequency_spectrum.cc | 2
src/scrm/summary_statistics/frequency_spectrum.h | 2
src/scrm/summary_statistics/newick_tree.cc | 19 -
src/scrm/summary_statistics/newick_tree.h | 27 -
src/scrm/summary_statistics/oriented_forest.cc | 2
src/scrm/summary_statistics/oriented_forest.h | 2
src/scrm/summary_statistics/seg_sites.cc | 2
src/scrm/summary_statistics/seg_sites.h | 2
src/scrm/summary_statistics/summary_statistic.h | 2
src/scrm/summary_statistics/tmrca.cc | 2
src/scrm/summary_statistics/tmrca.h | 2
src/scrm/time_interval.cc | 2
src/scrm/time_interval.h | 2
src/scrm/tree_point.cc | 2
src/scrm/tree_point.h | 2
src/scrmr.cpp | 88 +++---
src/test_exports.cpp | 4
tests/testthat.R | 2
tests/testthat/test-r_random-generator.R | 8
tests/testthat/test-scrm.R | 86 ++++-
tests/testthat/test-summary-statistics.R | 54 +--
vignettes/scrm-Arguments.Rmd | 55 ++-
vignettes/scrm-TreesForApe.Rmd | 2
59 files changed, 1084 insertions(+), 957 deletions(-)
Title: Geographic Data Analysis and Modeling
Diff between raster versions 2.3-33 dated 2015-03-14 and 2.3-40 dated 2015-04-11
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 13
DESCRIPTION | 13
MD5 | 78 ++---
NAMESPACE | 2
R/GDALtransient.R | 30 +
R/area.R | 9
R/arith_sp.R | 12
R/as.data.frame.R | 40 +-
R/boxplot.R | 2
R/brick.R | 14
R/factor.R | 4
R/hdrPRJ.R | 2
R/hdrRaster.R | 83 ++---
R/intersect_sp.R | 39 ++
R/kml.R | 2
R/overlay.R | 8
R/rasterFromRasterFile.R | 86 ++---
R/rasterizeLines.R | 62 +++
R/rasterizePolygons.R | 4
R/shp.R | 2
R/speasy.R |only
R/spplot.R | 12
R/which.max.R | 2
R/writeAllGDAL.R | 3
R/writeRaster.R | 14
R/writeStartStopRaster.R | 11
build/vignette.rds |binary
inst/doc/Raster.R | 732 +++++++++++++++++++++++------------------------
inst/doc/Raster.pdf |binary
inst/doc/functions.R | 686 ++++++++++++++++++++++----------------------
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/Arith-methods.Rd | 4
man/as.data.frame.Rd | 6
man/autocor.Rd | 2
man/extract.Rd | 5
man/intersect.Rd | 5
man/rasterFromXYZ.Rd | 10
man/rasterize.Rd | 14
man/spEasy.Rd |only
man/spplot.Rd | 11
41 files changed, 1108 insertions(+), 914 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Diff between peptider versions 0.1.7 dated 2015-02-03 and 0.2 dated 2015-04-11
Description: Evaluation of diversity in peptide libraries, including NNN, NNB,
NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined.
Metrics for evaluation include expected coverage, relative efficiency, and
the functional diversity of the library. Peptide-level inclusion
probabilities are computable for both the native and custom encoding
schemes.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare
DESCRIPTION | 35 +++++++++++++++++++++++------------
MD5 | 4 ++--
R/peptider.r | 6 +++---
3 files changed, 28 insertions(+), 17 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.3-11 dated 2014-09-09 and 1.3-13 dated 2015-04-11
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/distRhumb.R | 2 +-
R/distVincentyEllipsoid.R | 2 +-
R/gcIntersectBearing.R | 2 +-
R/gcMaxLat.R | 2 +-
R/geomedian.R | 3 ++-
R/span.R | 18 +++++++++---------
build/vignette.rds |binary
inst/doc/geosphere.pdf |binary
man/centroid.Rd | 4 ----
11 files changed, 31 insertions(+), 34 deletions(-)
Title: Frequency Distribution Tables, Histograms and Polygons
Diff between fdth versions 1.1-8 dated 2013-11-22 and 1.2-1 dated 2015-04-11
Description: Perform frequency distribution tables, associated histograms
and polygons from vector, data.frame and matrix objects for
numerical and categorical variables.
Author: José Cláudio Faria, Enio G. Jelihovschi and Ivan B. Allaman
Maintainer: José Cláudio Faria
fdth-1.1-8/fdth/man/make.fdt.format.classes.Rd |only
fdth-1.1-8/fdth/man/make.fdt.multiple.Rd |only
fdth-1.1-8/fdth/man/make.fdt.simple.Rd |only
fdth-1.2-1/fdth/ChangeLog | 18 +
fdth-1.2-1/fdth/DESCRIPTION | 19 -
fdth-1.2-1/fdth/INDEX | 30 ++-
fdth-1.2-1/fdth/MD5 | 113 +++++++----
fdth-1.2-1/fdth/NAMESPACE | 40 ++++
fdth-1.2-1/fdth/R/fdt.R | 2
fdth-1.2-1/fdth/R/fdt.data.frame.R | 24 +-
fdth-1.2-1/fdth/R/fdt.default.R | 34 ++-
fdth-1.2-1/fdth/R/fdt.matrix.R | 10 -
fdth-1.2-1/fdth/R/fdt_cat.R |only
fdth-1.2-1/fdth/R/fdt_cat.data.frame.R |only
fdth-1.2-1/fdth/R/fdt_cat.default.R |only
fdth-1.2-1/fdth/R/fdt_cat.matrix.R |only
fdth-1.2-1/fdth/R/latex.fdt.R | 11 -
fdth-1.2-1/fdth/R/latex.fdt_cat.R |only
fdth-1.2-1/fdth/R/latex.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/make.fdt.R |only
fdth-1.2-1/fdth/R/make.fdt.format.classes.R | 1
fdth-1.2-1/fdth/R/make.fdt.multiple.R | 3
fdth-1.2-1/fdth/R/make.fdt.simple.R | 30 +--
fdth-1.2-1/fdth/R/make.fdt_cat.R |only
fdth-1.2-1/fdth/R/make.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/make.fdt_cat.simple.R |only
fdth-1.2-1/fdth/R/mean.fdt.R |only
fdth-1.2-1/fdth/R/mean.fdt.multiple.R |only
fdth-1.2-1/fdth/R/median.fdt.R |only
fdth-1.2-1/fdth/R/median.fdt.multiple.R |only
fdth-1.2-1/fdth/R/mfv.R |only
fdth-1.2-1/fdth/R/mfv.default.R |only
fdth-1.2-1/fdth/R/mfv.fdt.R |only
fdth-1.2-1/fdth/R/mfv.fdt.multiple.R |only
fdth-1.2-1/fdth/R/mfv.fdt_cat.R |only
fdth-1.2-1/fdth/R/mfv.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/plot.fdt.default.R | 247 ++++++++++++++++---------
fdth-1.2-1/fdth/R/plot.fdt.multiple.R | 27 +-
fdth-1.2-1/fdth/R/plot.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/plot.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/print.fdt.default.R | 5
fdth-1.2-1/fdth/R/print.fdt.multiple.R | 8
fdth-1.2-1/fdth/R/print.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/print.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/quantile.fdt.R |only
fdth-1.2-1/fdth/R/quantile.fdt.multiple.R |only
fdth-1.2-1/fdth/R/sd.R |only
fdth-1.2-1/fdth/R/sd.default.R |only
fdth-1.2-1/fdth/R/sd.fdt.R |only
fdth-1.2-1/fdth/R/sd.fdt.multiple.R |only
fdth-1.2-1/fdth/R/summary.fdt.default.R | 6
fdth-1.2-1/fdth/R/summary.fdt.multiple.R | 6
fdth-1.2-1/fdth/R/summary.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/summary.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/var.R |only
fdth-1.2-1/fdth/R/var.default.R |only
fdth-1.2-1/fdth/R/var.fdt.R |only
fdth-1.2-1/fdth/R/var.fdt.multiple.R |only
fdth-1.2-1/fdth/README.md |only
fdth-1.2-1/fdth/build/vignette.rds |binary
fdth-1.2-1/fdth/inst/CITATION | 10 -
fdth-1.2-1/fdth/inst/COPYRIGHTS | 2
fdth-1.2-1/fdth/inst/doc/latex_fdt.R | 32 +++
fdth-1.2-1/fdth/inst/doc/latex_fdt.Rnw | 36 +++
fdth-1.2-1/fdth/man/fdt.Rd | 184 ++++++++----------
fdth-1.2-1/fdth/man/fdt_cat.Rd |only
fdth-1.2-1/fdth/man/fdth-internal.Rd |only
fdth-1.2-1/fdth/man/fdth-package.Rd | 217 ++++++++++-----------
fdth-1.2-1/fdth/man/latex.fdt.Rd | 102 ++++++++--
fdth-1.2-1/fdth/man/make.fdt.Rd |only
fdth-1.2-1/fdth/man/mean.fdt.Rd |only
fdth-1.2-1/fdth/man/median.fdt.Rd |only
fdth-1.2-1/fdth/man/mfv.Rd |only
fdth-1.2-1/fdth/man/plot.Rd | 207 ++++++++++++++++----
fdth-1.2-1/fdth/man/print.Rd | 63 ++++--
fdth-1.2-1/fdth/man/print.latex.fdt.Rd | 19 +
fdth-1.2-1/fdth/man/quantile.fdt.Rd |only
fdth-1.2-1/fdth/man/sd.Rd |only
fdth-1.2-1/fdth/man/summary.Rd | 44 +++-
fdth-1.2-1/fdth/man/summary.latex.fdt.Rd | 24 +-
fdth-1.2-1/fdth/man/var.Rd |only
fdth-1.2-1/fdth/vignettes/latex_fdt.Rnw | 36 +++
82 files changed, 1083 insertions(+), 527 deletions(-)
Title: Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis
Diff between esaBcv versions 1.0.1 dated 2015-04-07 and 1.1.1 dated 2015-04-11
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Author: Art B. Owen [aut],
Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang
esaBcv-1.0.1/esaBcv/man/PseudoInv.Rd |only
esaBcv-1.1.1/esaBcv/DESCRIPTION | 8 -
esaBcv-1.1.1/esaBcv/MD5 | 17 +--
esaBcv-1.1.1/esaBcv/R/ESA_BCV.R | 158 ++++++++++++++++--------------
esaBcv-1.1.1/esaBcv/R/esaBcv-package.R | 2
esaBcv-1.1.1/esaBcv/R/simdat.R | 2
esaBcv-1.1.1/esaBcv/man/ESA.Rd | 18 +--
esaBcv-1.1.1/esaBcv/man/EsaBcv.Rd | 20 +--
esaBcv-1.1.1/esaBcv/man/esaBcv_package.Rd | 2
esaBcv-1.1.1/esaBcv/man/simdat.Rd | 2
10 files changed, 119 insertions(+), 110 deletions(-)
Title: Nonparametric Estimation for Multistate Models
Diff between msSurv versions 1.2-1 dated 2015-03-02 and 1.2-2 dated 2015-04-10
Description: Nonparametric estimation for right censored, left truncated time to event data in multistate models.
Author: Nicole Ferguson
Maintainer: Guy Brock
ChangeLog | 9 +++++++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/msSurv-Methods.R | 2 +-
R/msSurv-internal.R | 28 ++++++++++++++++------------
5 files changed, 34 insertions(+), 21 deletions(-)
Title: Multiple Mediation Analysis
Diff between mma versions 1.0-0 dated 2015-02-26 and 1.0-1 dated 2015-04-10
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/mma.r | 38 +++++++++++++++++++++++++++-----------
3 files changed, 34 insertions(+), 18 deletions(-)
Title: Soil Physical Analysis
Diff between soilphysics versions 2.1 dated 2015-03-11 and 2.2 dated 2015-04-10
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva
DESCRIPTION | 8 +-
MD5 | 18 ++---
NEWS | 8 ++
R/iwc.R | 156 ++++++++++++++++++++++++++++++---------------
R/sigmaP.r | 61 ++++++++++-------
man/hemc.Rd | 2
man/iwc.Rd | 19 ++++-
man/plotCIsigmaP.Rd | 2
man/simSigmaP.Rd | 2
man/soilphysics-package.Rd | 4 -
10 files changed, 183 insertions(+), 97 deletions(-)
Title: River Visualisation Tool
Diff between rivervis versions 0.39.4 dated 2014-06-18 and 0.45.0 dated 2015-04-10
Description: This R package is a flexible and efficient tool to
visualise both quantitative and qualitative data from river surveys.
It can be used to produce diagrams with the topological structure of
the river network.
Author: Feng Mao
Maintainer: Feng Mao
rivervis-0.39.4/rivervis/R/rivervis.R |only
rivervis-0.45.0/rivervis/DESCRIPTION | 14 -
rivervis-0.45.0/rivervis/MD5 | 58 +++-
rivervis-0.45.0/rivervis/NAMESPACE | 50 +---
rivervis-0.45.0/rivervis/R/ImplicitFunctions.R |only
rivervis-0.45.0/rivervis/R/RiverAxisLabel.R |only
rivervis-0.45.0/rivervis/R/RiverBar.R |only
rivervis-0.45.0/rivervis/R/RiverBlock.R |only
rivervis-0.45.0/rivervis/R/RiverBlockChart.R |only
rivervis-0.45.0/rivervis/R/RiverDirection.R |only
rivervis-0.45.0/rivervis/R/RiverDraw.R |only
rivervis-0.45.0/rivervis/R/RiverFrame.R |only
rivervis-0.45.0/rivervis/R/RiverLabel.R |only
rivervis-0.45.0/rivervis/R/RiverLayout.R |only
rivervis-0.45.0/rivervis/R/RiverMap.R |only
rivervis-0.45.0/rivervis/R/RiverPoint.R |only
rivervis-0.45.0/rivervis/R/RiverReach.R |only
rivervis-0.45.0/rivervis/R/RiverScale.R |only
rivervis-0.45.0/rivervis/R/RiverSite.R |only
rivervis-0.45.0/rivervis/R/RiverTM.R |only
rivervis-0.45.0/rivervis/R/rivervis-package.R |only
rivervis-0.45.0/rivervis/data/Ballinderry.RData |binary
rivervis-0.45.0/rivervis/man/Ballinderry.Rd | 184 ++++++++-------
rivervis-0.45.0/rivervis/man/RiverAxisLabel.Rd | 99 +++-----
rivervis-0.45.0/rivervis/man/RiverBar.Rd | 141 ++++-------
rivervis-0.45.0/rivervis/man/RiverBlock.Rd | 196 +++++++---------
rivervis-0.45.0/rivervis/man/RiverBlockChart.Rd | 278 ++++++++++-------------
rivervis-0.45.0/rivervis/man/RiverDirection.Rd | 105 +++-----
rivervis-0.45.0/rivervis/man/RiverDraw.Rd | 121 +++-------
rivervis-0.45.0/rivervis/man/RiverFrame.Rd | 110 +++------
rivervis-0.45.0/rivervis/man/RiverLabel.Rd | 84 ++----
rivervis-0.45.0/rivervis/man/RiverLayout.Rd | 120 ++++-----
rivervis-0.45.0/rivervis/man/RiverMap.Rd | 214 ++++++++---------
rivervis-0.45.0/rivervis/man/RiverPoint.Rd | 151 +++++-------
rivervis-0.45.0/rivervis/man/RiverReach.Rd | 176 +++++---------
rivervis-0.45.0/rivervis/man/RiverScale.Rd | 95 +++----
rivervis-0.45.0/rivervis/man/RiverSite.Rd | 135 ++++-------
rivervis-0.45.0/rivervis/man/RiverTM.Rd | 119 +++------
rivervis-0.45.0/rivervis/man/rivervis-package.Rd | 265 ++++++++++-----------
39 files changed, 1206 insertions(+), 1509 deletions(-)
Title: Latent Variable Models for Networks
Diff between lvm4net versions 0.1 dated 2014-07-04 and 0.2 dated 2015-04-10
Description: Latent variable models for network data using fast inferential
procedures.
Author: Isabella Gollini [aut, cre]
Maintainer: Isabella Gollini
DESCRIPTION | 15 +++---
MD5 | 79 +++++++++++++++++++---------------
NAMESPACE | 8 +++
R/Ell.R | 2
R/PPIgen.R | 5 --
R/PPInet.R | 3 -
R/PPIphy.R | 5 --
R/boxroc.R | 27 ++++++-----
R/degree2.R | 2
R/frEZ.R | 2
R/goflsm.R |only
R/indegree2.R | 2
R/is.adjacency.R | 4 -
R/lsjm.R | 54 ++++++++++++-----------
R/lsm.R | 113 ++++++++++++++++++++++++++++++++++++++++++-------
R/lvm4net-package.R | 5 +-
R/mainLSM.R | 2
R/outdegree2.R | 2
R/plot.gofobj.R |only
R/plot.lsjm.R | 15 ++++--
R/plot.lsm.R | 11 +++-
R/plotY.R | 16 ++++--
R/print.gofobj.R |only
R/restartlsm.R |only
R/simulateLSM.R |only
R/upPsi2T.R | 2
R/upSigmaT.R | 2
R/upXiT.R | 2
R/upZT.R | 2
README.md |only
inst |only
man/PPIgen.Rd | 8 +--
man/PPInet.Rd | 6 +-
man/PPIphy.Rd | 8 +--
man/boxroc.Rd | 18 +++----
man/goflsm.Rd |only
man/lsjm.Rd | 26 ++++++-----
man/lsm.Rd | 26 ++++++-----
man/lvm4net-package.Rd | 6 +-
man/plot.gofobj.Rd |only
man/plot.lsjm.Rd | 12 +++--
man/plot.lsm.Rd | 9 ++-
man/plotY.Rd | 12 +++--
man/print.gofobj.Rd |only
man/rotXtoY.Rd | 3 -
man/simulateLSM.Rd |only
46 files changed, 310 insertions(+), 204 deletions(-)
Title: A Robust, High Performance JSON Parser and Generator for R
Diff between jsonlite versions 0.9.15 dated 2015-03-25 and 0.9.16 dated 2015-04-10
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of RJSONIO, but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with web APIs. The implementation is
based on the mapping described in the vignette of the package (Ooms, 2014).
In addition to drop-in replacements for toJSON and fromJSON, jsonlite
contains functions to stream, validate, and prettify JSON data. The unit
tests included with the package verify that all edge cases are encoded and
decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms
jsonlite-0.9.15/jsonlite/vignettes/json-opencpu-concordance.tex |only
jsonlite-0.9.16/jsonlite/DESCRIPTION | 6
jsonlite-0.9.16/jsonlite/LICENSE | 2
jsonlite-0.9.16/jsonlite/MD5 | 70 -
jsonlite-0.9.16/jsonlite/NAMESPACE | 5
jsonlite-0.9.16/jsonlite/NEWS | 6
jsonlite-0.9.16/jsonlite/R/apply_by_pages.R | 4
jsonlite-0.9.16/jsonlite/R/asJSON.array.R | 7
jsonlite-0.9.16/jsonlite/R/asJSON.character.R | 4
jsonlite-0.9.16/jsonlite/R/asJSON.data.frame.R | 22
jsonlite-0.9.16/jsonlite/R/asJSON.json.R |only
jsonlite-0.9.16/jsonlite/R/asJSON.list.R | 12
jsonlite-0.9.16/jsonlite/R/asJSON.logical.R | 4
jsonlite-0.9.16/jsonlite/R/asJSON.numeric.R | 5
jsonlite-0.9.16/jsonlite/R/asJSON.raw.R | 2
jsonlite-0.9.16/jsonlite/R/collapse.R | 19
jsonlite-0.9.16/jsonlite/R/collapse_object.R | 19
jsonlite-0.9.16/jsonlite/R/pack.R | 2
jsonlite-0.9.16/jsonlite/R/serializeJSON.R | 2
jsonlite-0.9.16/jsonlite/R/stream.R | 2
jsonlite-0.9.16/jsonlite/R/toJSON.R | 10
jsonlite-0.9.16/jsonlite/build/vignette.rds |binary
jsonlite-0.9.16/jsonlite/inst/doc/json-aaquickstart.Rmd | 13
jsonlite-0.9.16/jsonlite/inst/doc/json-aaquickstart.html | 462 ++------
jsonlite-0.9.16/jsonlite/inst/doc/json-apis.Rmd | 129 +-
jsonlite-0.9.16/jsonlite/inst/doc/json-apis.html | 538 +++-------
jsonlite-0.9.16/jsonlite/inst/doc/json-mapping.pdf |binary
jsonlite-0.9.16/jsonlite/inst/doc/json-opencpu.pdf |binary
jsonlite-0.9.16/jsonlite/inst/doc/json-paging.Rmd | 9
jsonlite-0.9.16/jsonlite/inst/doc/json-paging.html | 317 +----
jsonlite-0.9.16/jsonlite/src/Makevars | 2
jsonlite-0.9.16/jsonlite/src/collapse_pretty.c |only
jsonlite-0.9.16/jsonlite/src/row_collapse.c |only
jsonlite-0.9.16/jsonlite/vignettes/json-aaquickstart.Rmd | 13
jsonlite-0.9.16/jsonlite/vignettes/json-apis.Rmd | 129 +-
jsonlite-0.9.16/jsonlite/vignettes/json-apis.Rmd.orig | 7
jsonlite-0.9.16/jsonlite/vignettes/json-paging.Rmd | 9
jsonlite-0.9.16/jsonlite/vignettes/json-paging.Rmd.orig | 7
38 files changed, 671 insertions(+), 1167 deletions(-)
Title: Create and Manipulate Discrete Random Variables
Diff between discreteRV versions 1.1.4 dated 2015-02-03 and 1.2 dated 2015-04-10
Description: Create, manipulate, transform, and simulate from discrete random
variables. The syntax is modeled after that which is used in mathematical
statistics and probability courses, but with powerful support more advanced
probability calculations. This includes the creation of joint random
variables, and the derivation and manipulation of their conditional and
marginal distributions.
Author: Andreas Buja [aut],
Eric Hare [aut, cre],
Heike Hofmann [aut]
Maintainer: Eric Hare
discreteRV-1.1.4/discreteRV/man/Conditional.Rd |only
discreteRV-1.1.4/discreteRV/man/make.RV.Rd |only
discreteRV-1.1.4/discreteRV/man/mult.Rd |only
discreteRV-1.1.4/discreteRV/man/multN.Rd |only
discreteRV-1.2/discreteRV/DESCRIPTION | 34 -
discreteRV-1.2/discreteRV/MD5 | 60 +-
discreteRV-1.2/discreteRV/NAMESPACE | 17
discreteRV-1.2/discreteRV/R/discreteRV-Probabilities.r | 433 +++++++++++------
discreteRV-1.2/discreteRV/R/discreteRV-Simulations.r | 38 -
discreteRV-1.2/discreteRV/man/E.Rd | 4
discreteRV-1.2/discreteRV/man/KURT.Rd | 2
discreteRV-1.2/discreteRV/man/P.Rd | 4
discreteRV-1.2/discreteRV/man/Prop.Rd | 4
discreteRV-1.2/discreteRV/man/RV.Rd |only
discreteRV-1.2/discreteRV/man/SD.Rd | 2
discreteRV-1.2/discreteRV/man/SKEW.Rd | 2
discreteRV-1.2/discreteRV/man/SofI.Rd | 4
discreteRV-1.2/discreteRV/man/SofIID.Rd | 2
discreteRV-1.2/discreteRV/man/V.Rd | 2
discreteRV-1.2/discreteRV/man/grapes-AND-grapes.Rd | 2
discreteRV-1.2/discreteRV/man/grapes-OR-grapes.Rd | 2
discreteRV-1.2/discreteRV/man/iid.Rd |only
discreteRV-1.2/discreteRV/man/independent.Rd |only
discreteRV-1.2/discreteRV/man/joint.Rd |only
discreteRV-1.2/discreteRV/man/jointRV.Rd |only
discreteRV-1.2/discreteRV/man/marginal.Rd |only
discreteRV-1.2/discreteRV/man/margins.Rd | 6
discreteRV-1.2/discreteRV/man/outcomes.Rd | 6
discreteRV-1.2/discreteRV/man/plot.RV.Rd | 2
discreteRV-1.2/discreteRV/man/plot.RVsim.Rd | 4
discreteRV-1.2/discreteRV/man/print.RV.Rd | 2
discreteRV-1.2/discreteRV/man/probs.Rd | 6
discreteRV-1.2/discreteRV/man/props.Rd | 8
discreteRV-1.2/discreteRV/man/qqnorm.RV.Rd | 2
discreteRV-1.2/discreteRV/man/rsim.Rd | 14
discreteRV-1.2/discreteRV/man/skewSim.Rd | 4
36 files changed, 418 insertions(+), 248 deletions(-)
Title: Probabilistic Population Projection
Diff between bayesPop versions 5.2-2 dated 2015-02-05 and 5.3-4 dated 2015-04-10
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
ChangeLog | 13 +
DESCRIPTION | 10
MD5 | 33 +-
R/aggregate.R | 91 +++++--
R/get_outputs.R | 12
R/plot_functions.R | 28 +-
R/predict.pop.R | 523 +++++++++++++++++++++++++++++--------------
data/MLTbx.R |only
data/MLTbx.txt |only
data/vwBaseYear2012.txt | 468 +++++++++++++++++++-------------------
man/MLTbx.Rd |only
man/bayesPop-package.Rd | 10
man/expressions.Rd | 9
man/pop.trajectories.plot.Rd | 6
man/predict.pop.Rd | 8
man/vwBaseYear.Rd | 11
src/projection_functions.c | 54 ++--
tests/run_tests.R | 8
tests/test_functions.R | 1
19 files changed, 778 insertions(+), 507 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Diff between sdcTable versions 0.17.1 dated 2014-06-23 and 0.18.0 dated 2015-04-10
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl
DESCRIPTION | 15 -
MD5 | 124 +++++-----
NAMESPACE | 2
R/export_functions.r | 24 +-
R/helper_functions.r | 1
R/methods_class_dataObj.r | 432 ++++++++++++++++++-------------------
R/methods_class_dimVar.r | 2
R/methods_class_sdcProblem.r | 6
R/methods_multiple_classes.r | 71 +++---
build/vignette.rds |binary
inst/doc/sdcTable.pdf |binary
man/attack.Rd | 25 --
man/calc.cutList-method.Rd | 47 ++--
man/calc.dimVar-method.Rd | 39 +--
man/calc.linProb-method.Rd | 47 +---
man/calc.multiple-method.Rd | 57 ++--
man/calc.problemInstance-method.Rd | 43 +--
man/calc.sdcProblem-method.Rd | 247 +++++++--------------
man/calc.simpleTriplet-method.Rd | 101 ++++----
man/cellInfo.Rd | 41 +--
man/changeCellStatus.Rd | 30 --
man/cutList-class.Rd | 39 +--
man/dataObj-class.Rd | 48 +---
man/dimInfo-class.Rd | 33 +-
man/dimVar-class.Rd | 59 +----
man/get.cutList-method.Rd | 30 +-
man/get.dataObj-method.Rd | 46 +--
man/get.dimInfo-method.Rd | 34 +-
man/get.dimVar-method.Rd | 58 ++--
man/get.linProb-method.Rd | 43 +--
man/get.problemInstance-method.Rd | 78 ++----
man/get.safeObj-method.Rd | 82 +++----
man/get.sdcProblem-method.Rd | 88 +++----
man/get.simpleTriplet-method.Rd | 58 ++--
man/getInfo.Rd | 99 ++------
man/init.cutList-method.Rd | 43 +--
man/init.dataObj-method.Rd | 24 --
man/init.dimVar-method.Rd | 13 -
man/init.simpleTriplet-method.Rd | 38 +--
man/linProb-class.Rd | 59 ++---
man/makeProblem.Rd | 75 ++----
man/microData1.Rd | 5
man/microData2.Rd | 2
man/primarySuppression.Rd | 77 ++----
man/print-method.Rd | 7
man/problem.Rd | 5
man/problemInstance-class.Rd | 52 +---
man/problemWithSupps.Rd | 5
man/protectLinkedTables.Rd | 69 ++---
man/protectTable.Rd | 135 +++--------
man/protectedData.Rd | 5
man/safeObj-class.Rd | 77 ++----
man/sdcProblem-class.Rd | 73 ++----
man/set.cutList-method.Rd | 32 +-
man/set.dataObj-method.Rd | 20 -
man/set.dimInfo-method.Rd | 19 -
man/set.linProb-method.Rd | 81 +++---
man/set.problemInstance-method.Rd | 33 +-
man/set.sdcProblem-method.Rd | 42 +--
man/setInfo.Rd | 63 +----
man/simpleTriplet-class.Rd | 34 +-
man/summary-method.Rd | 11
src/csp.cpp | 8
63 files changed, 1432 insertions(+), 1824 deletions(-)
Title: Various R Programming Tools
Diff between gtools versions 3.4.1 dated 2014-05-28 and 3.4.2 dated 2015-04-10
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binseach'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- Efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- Generate significance stars from p-values ('stars.pval').
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes
ChangeLog | 43 +++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 32 ++++++++++++++++++++++++++------
MD5 | 20 ++++++++++++--------
NAMESPACE | 2 ++
NEWS | 16 ++++++++++++++++
R/keywords.R | 6 +++++-
R/loadedPackages.R |only
R/na.replace.R |only
inst/ChangeLog | 43 +++++++++++++++++++++++++++++++++++++++++++
inst/NEWS | 16 ++++++++++++++++
man/dirichlet.Rd | 6 +++---
man/loadedPackages.Rd |only
man/na.replace.Rd |only
13 files changed, 166 insertions(+), 18 deletions(-)
Title: Comparing Correlations
Diff between cocor versions 1.1-0 dated 2015-01-07 and 1.1-1 dated 2015-04-10
Description: Statistical tests for the comparison between two correlations
based on either independent or dependent groups. Dependent correlations can
either be overlapping or nonoverlapping. A web interface is available at
http://comparingcorrelations.org. A plugin for 'RKWard' is included.
'RKWard' can be obtained freely from https://rkward.kde.org.
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen
ChangeLog | 10 ++++++++++
DESCRIPTION | 12 ++++++------
MD5 | 30 +++++++++++++++---------------
R/0helper.r | 5 +++++
R/cocor-package.R | 6 +++---
R/cocor.dep.groups.nonoverlap.r | 4 +++-
R/cocor.dep.groups.overlap.r | 4 +++-
R/cocor.indep.groups.r | 4 +++-
R/cocor.r | 14 ++++++++++++++
inst/CITATION | 22 ++++++++++------------
inst/rkward/cocor.pluginmap | 4 ++--
inst/tests/test.r | 5 +++++
man/cocor-package.Rd | 6 +++---
man/cocor.dep.groups.nonoverlap.Rd | 2 +-
man/cocor.dep.groups.overlap.Rd | 2 +-
man/cocor.indep.groups.Rd | 2 +-
16 files changed, 85 insertions(+), 47 deletions(-)
Title: Multi-States Semi-Markov Models
Diff between SemiMarkov versions 1.4 dated 2014-10-05 and 1.4.1 dated 2015-04-10
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol
DESCRIPTION | 11 -
MD5 | 10 -
R/SemiMarkov.r | 325 +++++++++++------------------------------------------
man/hazard.Rd | 45 +++----
man/plot.hazard.Rd | 31 ++---
man/semiMarkov.Rd | 57 ++++-----
6 files changed, 141 insertions(+), 338 deletions(-)
Title: Non-Negative Lasso and Elastic Net Penalized Generalized Linear
Models
Diff between nnlasso versions 0.1 dated 2015-03-16 and 0.2 dated 2015-04-10
Description: Estimates of coefficients of lasso penalized linear regression and generalized linear models subject to non-negativity constraints on the parameters using multiplicative iterative algorithm. Entire regularization path for a sequence of lambda values can be obtained. Functions are available for creating plots of regularization path, cross validation and estimating coefficients at a given lambda value. There is also provision for obtaining standard error of coefficient estimates.
Author: B N Mandal
Maintainer: B N Mandal
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
man/coef.nnlasso.Rd | 1 -
man/cv.nnlasso.Rd | 1 -
man/cv.nnlasso.binomial.Rd | 1 -
man/cv.nnlasso.normal.Rd | 1 -
man/cv.nnlasso.poisson.Rd | 1 -
man/nnlasso.Rd | 2 --
man/nnlasso.binomial.Rd | 2 --
man/nnlasso.normal.Rd | 1 -
man/nnlasso.poisson.Rd | 2 --
man/plot.nnlasso.Rd | 3 ---
man/predict.nnlasso.Rd | 3 ---
13 files changed, 16 insertions(+), 34 deletions(-)
Title: Drat R Archive Template
Diff between drat versions 0.0.2 dated 2015-03-01 and 0.0.3 dated 2015-04-10
Description: Creation and Use of R Repositories via two helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 11 +++++----
MD5 | 31 ++++++++++++++++++++-----
R/addRepo.R | 8 ++++++
R/insertPackage.R | 51 +++++++++++++++++++++++++++++-------------
README.md | 12 +++++++++-
build |only
inst/doc |only
inst/scripts |only
man/addRepo.Rd | 9 +++++++
man/insertPackage.Rd | 12 ++++++++--
vignettes |only
12 files changed, 164 insertions(+), 31 deletions(-)
Title: Estimation of Box-Cox Power Transformation Parameter
Diff between AID versions 1.4 dated 2014-01-21 and 1.5 dated 2015-04-10
Description: Power transformation parameter is estimated for different purposes.
Author: Osman Dag, Ozgur Asar, Ozlem Ilk
Maintainer: Osman Dag
DESCRIPTION | 17 +++++++++--------
MD5 | 14 +++++++++-----
NAMESPACE | 12 ++++++++++--
R/boxcoxfr.R |only
R/boxcoxnc.R | 9 ---------
data/AADT.rda |only
man/AADT.Rd |only
man/AID.Rd | 14 +++++++-------
man/boxcoxfr.Rd |only
man/boxcoxnc.Rd | 13 ++++++++-----
10 files changed, 43 insertions(+), 36 deletions(-)
Title: Functions for Handling Thermal Images
Diff between Thermimage versions 1.0 dated 2015-04-02 and 1.0.1 dated 2015-04-09
Description: A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature.
Author: Glenn J. Tattersall, PhD
Maintainer: Glenn J. Tattersall
DESCRIPTION | 9 +++++----
MD5 | 12 ++++++------
R/locate.fid.R | 33 ++++++++++++++++++++++++++++-----
R/meanEveryN.R | 14 +++++++++++---
man/locate.fid.Rd | 43 +++++++++++++++++++++++++++++++++----------
man/meanEveryN.Rd | 7 +++++--
man/samp.image.Rd | 1 -
7 files changed, 88 insertions(+), 31 deletions(-)
Title: Import Professional Baseball Data from 'Retrosheet'
Diff between retrosheet versions 1.0 dated 2015-04-08 and 1.0.1 dated 2015-04-09
Description: A collection of tools for importing the professional baseball data
available from http://www.retrosheet.org. In particular, the event (play-by-play)
files can be especially difficult to parse. This package does the parsing
on those files, returning the requested event as a structured R object.
It will also retrieve the game-log, roster, and schedule files if requested.
Author: Richard Scriven [aut, cre]
Maintainer: Richard Scriven
DESCRIPTION | 17 ++++++++---------
MD5 | 13 +++++++------
NAMESPACE | 1 +
R/getPartialGamelog.R | 8 ++++----
R/getRetrosheet.R | 44 ++++++++++++++++++++++++--------------------
README.md |only
man/getPartialGamelog.Rd | 6 +++---
man/getRetrosheet.Rd | 7 +------
8 files changed, 48 insertions(+), 48 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Dose Finding in Drug Combination Phase I Trials Using PO-CRM
Diff between pocrm versions 0.8 dated 2014-07-24 and 0.9 dated 2015-04-09
Description: Provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) for use in Phase I trials of combinations of agents. Provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Varhegyi, Nikole (nev4g)"
DESCRIPTION | 13 ++++++-------
MD5 | 2 +-
2 files changed, 7 insertions(+), 8 deletions(-)
Title: Interactive Web-Maps Based on the Leaflet JavaScript Library
Diff between leafletR versions 0.3-1 dated 2014-10-23 and 0.3-2 dated 2015-04-09
Description: Display your spatial data on interactive web-maps using the open-source JavaScript library Leaflet. leafletR provides basic web-mapping functionality to combine vector data and online map tiles from different sources. See
Author: Christian Graul, with contributions from Francois Guillem
Maintainer: Christian Graul
DESCRIPTION | 10 ++++----
MD5 | 38 +++++++++++++++----------------
R/fileToGeoJSON.R | 7 +----
R/spToGeoJSON.R | 2 -
R/styleCat.R | 2 +
R/styleGrad.R | 4 +++
R/styleSingle.R | 55 +++++++++++++++++++++++++++------------------
R/zzz.R | 34 +++++++++++++++++++++++++--
inst/CITATION | 17 ++++---------
inst/NEWS | 20 ++++++++++++++++
inst/templates/data.brew | 40 ++++++++++++++++++++++++++------
inst/templates/legend.brew | 18 +++++++++-----
inst/templates/popup.brew | 6 ++--
inst/templates/style.brew | 50 +++++++++++++++++++++++++++-------------
man/addBaseMap.Rd | 2 -
man/leaflet.Rd | 22 ++++++++++--------
man/leafletR-package.Rd | 4 +--
man/styleGrad.Rd | 2 -
man/styleSingle.Rd | 10 ++++++--
man/toGeoJSON.Rd | 2 +
20 files changed, 230 insertions(+), 115 deletions(-)
Title: An Import Mechanism for R
Diff between import versions 1.0.1 dated 2015-03-10 and 1.0.2 dated 2015-04-09
Description: This is an alternative mechanism for importing
objects from packages. The syntax allows for importing multiple objects
from a package with a single command in an expressive way. The import
package bridges some of the gap between using library (or require) and
direct (single-object) imports. Furthermore the imported objects are not
placed in the current environment.
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache
DESCRIPTION | 9 +--
MD5 | 16 +++---
NEWS |only
R/import.R | 122 +++++++++++++++++++++++++++++++++++-------------
R/make_import_call.R | 24 +++------
R/zzz.R |only
README | 45 +++++++++++++----
man/import.Rd | 21 ++++----
man/importfunctions.Rd | 30 +++++++----
man/make_import_call.Rd | 11 +---
10 files changed, 184 insertions(+), 94 deletions(-)
Title: The All-Configurations, Maximum-Interaction F-Test for Hidden
Additivity
Diff between hiddenf versions 1.2 dated 2015-03-25 and 1.3 dated 2015-04-09
Description: Computes the F-test and Bonferroni-adjusted p-value for a test of interaction in two-factor studies. Reports corresponding interaction plot and analysis of variance table and p-values from several other tests of non-additivity.
Author: Jason A. Osborne, Christopher T. Franck and Bongseog Choi
Maintainer: Jason A. Osborne
DESCRIPTION | 10 +++++-----
MD5 | 16 ++++++++--------
R/MalikPvalue.R | 3 ++-
R/Malikfunction.R | 3 ++-
R/anova.hiddenf.R | 4 ++--
R/print.hiddenf.R | 2 +-
man/MalikPvalue.Rd | 7 ++++---
man/anova.hiddenf.Rd | 3 ++-
man/hiddenf-package.Rd | 4 ++--
9 files changed, 28 insertions(+), 24 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Diff between dataRetrieval versions 2.1.2 dated 2015-02-20 and 2.2.0 dated 2015-04-09
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco
DESCRIPTION | 7 -
MD5 | 70 +++++-----
NAMESPACE | 3
NEWS | 13 +
R/importRDB1.r | 10 +
R/importWQP.R | 13 +
R/importWaterML1.r | 54 +++++--
R/readNWISdata.r | 176 +++++++++++++++++++++++---
R/readNWISdv.r | 4
R/readNWISqw.r | 32 ++--
R/readNWISunit.r | 40 ++++-
R/readWQPdata.R | 41 +++++-
R/readWQPqw.r | 12 +
R/sysdata.rda |binary
R/tabbedDataRetrievals.R | 45 ++++++
R/whatWQPsites.R | 4
README.md | 97 +++-----------
build/vignette.rds |binary
inst/CITATION |only
inst/doc/dataRetrieval.Rnw | 2
inst/doc/dataRetrieval.pdf |binary
man/countyCd.Rd |only
man/importRDB1.Rd | 2
man/importWaterML1.Rd | 3
man/readNWISdata.Rd | 37 ++++-
man/readNWISdv.Rd | 4
man/readNWISpeak.Rd | 9 +
man/readNWISqw.Rd | 32 ++--
man/readNWISuv.Rd | 14 +-
man/readWQPqw.Rd | 11 +
man/stateCd.Rd |only
man/stateCdLookup.Rd |only
tests/testthat/tests_general.R | 7 +
tests/testthat/tests_imports.R | 5
tests/testthat/tests_userFriendly_fxns.R | 6
vignettes/dataRetrieval-concordance.tex | 6
vignettes/dataRetrieval.Rnw | 2
vignettes/figure/getNWIStemperaturePlot-1.pdf |binary
38 files changed, 543 insertions(+), 218 deletions(-)
Title: Toolkit of Helper Functions to Pre-Process Amplification Data
Diff between chipPCR versions 0.0.8-8 dated 2015-03-12 and 0.0.8-10 dated 2015-04-09
Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.
Author: Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut],
Konstantin A. Blagodatskikh [ctb]
Maintainer: Stefan Roediger
chipPCR |only
1 file changed
Title: Suite of Functions to Flexibly Read Data from Files
Diff between reader versions 1.0.4 dated 2014-09-01 and 1.0.5 dated 2015-04-09
Description: A set of functions to simplify reading data from files. The main function, reader(), should read most common R datafile types without needing any parameters except the filename. Other functions provide simple ways of handling file paths and extensions, and automatically detecting file format and structure.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper
DESCRIPTION | 10 +++++-----
MD5 | 46 +++++++++++++++++++++++-----------------------
NAMESPACE | 2 +-
R/reader.R | 45 +++++++++++++++++++++++++++++++++++++++++----
man/cat.path.Rd | 3 ++-
man/classify.ext.Rd | 3 ++-
man/column.salvage.Rd | 3 ++-
man/conv.fixed.width.Rd | 5 ++++-
man/file.ncol.Rd | 5 ++++-
man/file.nrow.Rd | 5 ++++-
man/find.file.Rd | 5 ++++-
man/find.id.col.Rd | 3 ++-
man/force.frame.Rd | 5 ++++-
man/force.vec.Rd | 3 ++-
man/get.delim.Rd | 9 ++++++---
man/get.ext.Rd | 3 ++-
man/is.file.Rd | 5 ++++-
man/n.readLines.Rd | 5 ++++-
man/parse.args.Rd | 7 ++++---
man/reader-internal.Rd | 1 +
man/reader-package.Rd | 6 +++---
man/reader.Rd | 5 ++++-
man/rmv.ext.Rd | 3 ++-
man/shift.rownames.Rd | 3 ++-
24 files changed, 132 insertions(+), 58 deletions(-)
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Diff between mclust versions 4.4 dated 2014-09-16 and 5.0.0 dated 2015-04-09
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca
mclust-4.4/mclust/inst/doc/mclust.pdf |only
mclust-4.4/mclust/man/bicEMtrain.Rd |only
mclust-4.4/mclust/man/cv.MclustDA.Rd |only
mclust-4.4/mclust/man/cv1EMtrain.Rd |only
mclust-5.0.0/mclust/DESCRIPTION | 31
mclust-5.0.0/mclust/MD5 | 167
mclust-5.0.0/mclust/NAMESPACE | 175
mclust-5.0.0/mclust/R/bootstrap.R |only
mclust-5.0.0/mclust/R/densityMclust.R | 216
mclust-5.0.0/mclust/R/icl.R | 90
mclust-5.0.0/mclust/R/init.R | 103
mclust-5.0.0/mclust/R/mclust.R | 2904 ++++++------
mclust-5.0.0/mclust/R/mclustaddson.R |only
mclust-5.0.0/mclust/R/mclustda.R | 423 +
mclust-5.0.0/mclust/R/mclustdr.R | 114
mclust-5.0.0/mclust/R/options.R |only
mclust-5.0.0/mclust/R/weights.R | 52
mclust-5.0.0/mclust/R/zzz.R | 35
mclust-5.0.0/mclust/build |only
mclust-5.0.0/mclust/data/Baudry_etal_2010_JCGS_examples.rda |binary
mclust-5.0.0/mclust/data/GvHD.rda |binary
mclust-5.0.0/mclust/data/acidity.rda |only
mclust-5.0.0/mclust/data/chevron.rda |binary
mclust-5.0.0/mclust/data/cross.rda |binary
mclust-5.0.0/mclust/data/diabetes.rda |binary
mclust-5.0.0/mclust/data/thyroid.rda |only
mclust-5.0.0/mclust/data/wreath.rda |binary
mclust-5.0.0/mclust/inst/CITATION | 12
mclust-5.0.0/mclust/inst/NEWS | 26
mclust-5.0.0/mclust/inst/doc/index.html | 23
mclust-5.0.0/mclust/inst/doc/mclust.R |only
mclust-5.0.0/mclust/inst/doc/mclust.Rmd |only
mclust-5.0.0/mclust/inst/doc/mclust.html |only
mclust-5.0.0/mclust/inst/doc/mclust4.pdf |only
mclust-5.0.0/mclust/man/Mclust.Rd | 10
mclust-5.0.0/mclust/man/MclustBootstrap.Rd |only
mclust-5.0.0/mclust/man/MclustDA.Rd | 16
mclust-5.0.0/mclust/man/MclustDR.Rd | 7
mclust-5.0.0/mclust/man/acidity.Rd |only
mclust-5.0.0/mclust/man/banknote.Rd | 6
mclust-5.0.0/mclust/man/bic.Rd | 2
mclust-5.0.0/mclust/man/cdensE.Rd | 21
mclust-5.0.0/mclust/man/clPairs.Rd | 7
mclust-5.0.0/mclust/man/coordProj.Rd | 16
mclust-5.0.0/mclust/man/cross.Rd | 4
mclust-5.0.0/mclust/man/cvMclustDA.Rd |only
mclust-5.0.0/mclust/man/densityMclust.Rd | 15
mclust-5.0.0/mclust/man/densityMclust.diagnostic.Rd | 33
mclust-5.0.0/mclust/man/diabetes.Rd | 21
mclust-5.0.0/mclust/man/em.Rd | 18
mclust-5.0.0/mclust/man/emE.Rd | 44
mclust-5.0.0/mclust/man/estepE.Rd | 13
mclust-5.0.0/mclust/man/hc.Rd | 15
mclust-5.0.0/mclust/man/hcE.Rd | 1
mclust-5.0.0/mclust/man/icl.Rd | 2
mclust-5.0.0/mclust/man/imputePairs.Rd | 2
mclust-5.0.0/mclust/man/logLik.Mclust.Rd | 10
mclust-5.0.0/mclust/man/logLik.MclustDA.Rd | 6
mclust-5.0.0/mclust/man/map.Rd | 10
mclust-5.0.0/mclust/man/mclust-deprecated.Rd |only
mclust-5.0.0/mclust/man/mclust-package.Rd | 18
mclust-5.0.0/mclust/man/mclust.options.Rd | 2
mclust-5.0.0/mclust/man/mclust1Dplot.Rd | 16
mclust-5.0.0/mclust/man/mclust2Dplot.Rd | 12
mclust-5.0.0/mclust/man/mclustBIC.Rd | 29
mclust-5.0.0/mclust/man/mclustBootstrapLRT.Rd |only
mclust-5.0.0/mclust/man/mclustICL.Rd | 27
mclust-5.0.0/mclust/man/mclustModel.Rd | 2
mclust-5.0.0/mclust/man/me.Rd | 18
mclust-5.0.0/mclust/man/meE.Rd | 63
mclust-5.0.0/mclust/man/mstepE.Rd | 42
mclust-5.0.0/mclust/man/nMclustParams.Rd |only
mclust-5.0.0/mclust/man/nVarParams.Rd | 9
mclust-5.0.0/mclust/man/plot.Mclust.Rd | 18
mclust-5.0.0/mclust/man/plot.MclustDA.Rd | 4
mclust-5.0.0/mclust/man/plot.MclustDR.Rd | 8
mclust-5.0.0/mclust/man/plot.densityMclust.Rd | 52
mclust-5.0.0/mclust/man/plot.mclustBIC.Rd | 8
mclust-5.0.0/mclust/man/predict.Mclust.Rd | 2
mclust-5.0.0/mclust/man/predict.MclustDA.Rd | 2
mclust-5.0.0/mclust/man/predict.MclustDR.Rd | 2
mclust-5.0.0/mclust/man/predict.densityMclust.Rd | 2
mclust-5.0.0/mclust/man/print.clustCombi.Rd | 2
mclust-5.0.0/mclust/man/randProj.Rd | 14
mclust-5.0.0/mclust/man/randomPairs.Rd |only
mclust-5.0.0/mclust/man/sigma2decomp.Rd | 6
mclust-5.0.0/mclust/man/simE.Rd | 11
mclust-5.0.0/mclust/man/summary.Mclust.Rd | 4
mclust-5.0.0/mclust/man/summary.MclustBootstrap.Rd |only
mclust-5.0.0/mclust/man/summary.MclustDA.Rd | 4
mclust-5.0.0/mclust/man/summary.MclustDR.Rd | 4
mclust-5.0.0/mclust/man/summary.mclustBIC.Rd | 8
mclust-5.0.0/mclust/man/surfacePlot.Rd | 8
mclust-5.0.0/mclust/man/thyroid.Rd |only
mclust-5.0.0/mclust/man/wreath.Rd | 4
mclust-5.0.0/mclust/src/mclustaddson.f |only
mclust-5.0.0/mclust/vignettes |only
97 files changed, 2784 insertions(+), 2267 deletions(-)
Title: Digital PCR Analysis
Diff between dpcR versions 0.1.3.3 dated 2015-02-24 and 0.1.4.0 dated 2015-04-09
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut],
Bart Jacobs [aut],
Piotr Sobczyk [ctb]
Maintainer: Michal Burdukiewicz
CHANGELOG | 87 ++---
DESCRIPTION | 24 -
MD5 | 201 ++++++------
NAMESPACE | 98 +++---
R/AUCtest.R | 136 ++++----
R/adpcr-class.R | 144 ++++-----
R/adpcr2ppp.R | 154 ++++-----
R/binarize.R | 92 ++---
R/bind_dpcr.R | 284 ++++++++---------
R/bioamp.R | 151 ++++-----
R/calc_breaks.R | 24 -
R/calc_lambda.R | 39 +-
R/compare_dens.R | 122 +++----
R/count_test-class.R | 284 +++++++++--------
R/create_dpcr.R | 144 ++++-----
R/ddpcr-class.R | 118 +++----
R/dpcR-package.R | 130 ++++----
R/dpcr_calculator.R | 34 +-
R/dpcr_density.R | 309 +++++++++----------
R/dpcr_density_gui.R | 26 -
R/extract_dpcr.R | 112 +++----
R/fit_adpcr.R | 62 +--
R/fl.R | 2
R/get_k_n.R | 24 -
R/limit_cq.R | 332 ++++++++++----------
R/many_peaks.R | 38 +-
R/moments.R | 272 ++++++++---------
R/num2int.R | 40 +-
R/pds.R | 216 ++++++-------
R/pds_raw.R | 259 +++++++---------
R/plot_distr.R | 92 ++---
R/plot_panel.R | 318 +++++++++----------
R/plot_vf_circ.R | 6
R/plot_vic_fam.R | 260 ++++++++--------
R/print_summary.R | 45 +-
R/qpcr_analyser.R | 320 ++++++++++----------
R/qpcrpp.R | 427 +++++++++++++-------------
R/rtadpcr.R | 62 +--
R/safe_efficiency.R | 20 -
R/show_dpcr.R | 86 ++---
R/sim_adpcr.R | 198 ++++++------
R/sim_ddpcr.R | 182 +++++------
R/sim_ddpcr_bkm.R |only
R/simulations.R | 128 ++++----
R/summary_dpcr.R | 218 ++++++-------
R/test_counts.R | 309 ++++++++++++-------
R/test_counts_gui.R | 22 -
R/test_panel.R | 120 +++----
R/test_peaks.R | 210 ++++++-------
R/test_ratio.R | 306 +++++++++----------
R/valid_amp.R | 10
R/y_val_conf.R | 26 -
README.md | 52 +--
build/vignette.rds |binary
data/datalist | 6
data/many_peaks.rda |binary
data/pds.rda |binary
data/pds_raw.rda |binary
inst/doc/overview.R | 86 ++---
inst/doc/overview.Rmd | 162 +++++-----
inst/doc/overview.html | 652 ++++++++++++++++++++---------------------
inst/dpcr_density_gui/server.R | 146 ++++-----
inst/dpcr_density_gui/ui.R | 48 +--
inst/test_counts_gui/readme.md | 20 -
inst/test_counts_gui/server.R | 88 ++---
inst/test_counts_gui/ui.R | 54 +--
man/adpcr-class.Rd | 120 +++----
man/adpcr2ppp.Rd | 124 +++----
man/binarize.Rd | 70 ++--
man/bind_dpcr-methods.Rd | 130 ++++----
man/bioamp.Rd | 102 +++---
man/compare_dens.Rd | 72 ++--
man/count_test-class.Rd | 132 ++++----
man/create_dpcr.Rd | 133 ++++----
man/ddpcr-class.Rd | 108 +++---
man/dpcR-package.Rd | 120 +++----
man/dpcr_density.Rd | 262 ++++++++--------
man/dpcr_density_gui.Rd | 46 +-
man/extract_dpcr.Rd | 112 +++----
man/limit_cq.Rd | 190 +++++------
man/many_peaks.Rd | 42 +-
man/moments-methods.Rd | 146 ++++-----
man/num2int.Rd | 44 +-
man/pds.Rd | 234 +++++++-------
man/pds_raw.Rd | 277 ++++++++---------
man/plot.qpcrpp.Rd | 86 ++---
man/plot_panel.Rd | 224 +++++++-------
man/plot_vic_fam.Rd | 144 ++++-----
man/qpcr2pp.Rd | 178 +++++------
man/qpcr_analyser.Rd | 224 +++++++-------
man/qpcrpp-class.Rd | 80 ++---
man/rtadpcr-class.Rd | 72 ++--
man/show-methods.Rd | 80 ++---
man/sim_adpcr.Rd | 230 +++++++-------
man/sim_ddpcr.Rd | 172 +++++-----
man/summary-methods.Rd | 179 +++++------
man/test_counts.Rd | 150 ++++-----
man/test_counts_gui.Rd | 46 +-
man/test_panel.Rd | 170 +++++-----
man/test_peaks.Rd | 172 +++++-----
man/test_ratio.Rd | 200 ++++++------
vignettes/overview.Rmd | 162 +++++-----
102 files changed, 6890 insertions(+), 6780 deletions(-)
Title: Standard Processing Tools for Electromyogram Signals
Diff between biosignalEMG versions 1.0 dated 2015-03-20 and 1.0.2 dated 2015-04-09
Description: Data processing tools for electromyogram (EMG) signals to compute the rectified, integrated and averaged EMG. Tools to plot the ensemble average of the EMG.
Author: J.A. Guerrero, J.E. Macias-Diaz
Maintainer: Antonio Guerrero
biosignalEMG-1.0.2/biosignalEMG/DESCRIPTION | 12 -
biosignalEMG-1.0.2/biosignalEMG/MD5 | 69 +++---
biosignalEMG-1.0.2/biosignalEMG/NEWS |only
biosignalEMG-1.0.2/biosignalEMG/R/dcbiasremoval.R | 28 +-
biosignalEMG-1.0.2/biosignalEMG/R/eaemg.R | 101 ++++-----
biosignalEMG-1.0.2/biosignalEMG/R/emg.R | 28 +-
biosignalEMG-1.0.2/biosignalEMG/R/envelope.R | 53 ++---
biosignalEMG-1.0.2/biosignalEMG/R/iemg.R | 33 +--
biosignalEMG-1.0.2/biosignalEMG/R/integration.R | 123 +++++-------
biosignalEMG-1.0.2/biosignalEMG/R/movingaverage.R | 56 ++---
biosignalEMG-1.0.2/biosignalEMG/R/plot.eaemg.R | 39 ++-
biosignalEMG-1.0.2/biosignalEMG/R/plot.emg.R | 58 ++---
biosignalEMG-1.0.2/biosignalEMG/R/plot.iemg.R | 73 +++----
biosignalEMG-1.0.2/biosignalEMG/R/print.eaemg.R | 25 +-
biosignalEMG-1.0.2/biosignalEMG/R/print.emg.R | 33 +--
biosignalEMG-1.0.2/biosignalEMG/R/print.iemg.R | 42 +---
biosignalEMG-1.0.2/biosignalEMG/R/print.summary.eaemg.R | 21 --
biosignalEMG-1.0.2/biosignalEMG/R/print.summary.emg.R | 31 +--
biosignalEMG-1.0.2/biosignalEMG/R/print.summary.iemg.R | 44 +---
biosignalEMG-1.0.2/biosignalEMG/R/rectification.R | 36 +--
biosignalEMG-1.0.2/biosignalEMG/R/summary.eaemg.R | 12 -
biosignalEMG-1.0.2/biosignalEMG/R/summary.emg.R | 21 --
biosignalEMG-1.0.2/biosignalEMG/R/summary.iemg.R | 22 --
biosignalEMG-1.0.2/biosignalEMG/R/synthetic.emg.R | 82 ++++----
biosignalEMG-1.0.2/biosignalEMG/man/biosignalEMG-package.Rd | 10
biosignalEMG-1.0.2/biosignalEMG/man/dcbiasremoval.Rd |only
biosignalEMG-1.0.2/biosignalEMG/man/eaemg.Rd | 4
biosignalEMG-1.0.2/biosignalEMG/man/emg.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/envelope.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/iemg.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/integration.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/movingaverage.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/print.summary.eaemg.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/print.summary.emg.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/rectification.Rd | 2
biosignalEMG-1.0.2/biosignalEMG/man/synthetic.emg.Rd | 2
biosignalEMG-1.0/biosignalEMG/man/baselinecorrection.Rd |only
37 files changed, 518 insertions(+), 556 deletions(-)
Title: A Collection of Network Data Sets for the Igraph Package
Diff between igraphdata versions 0.2 dated 2014-02-04 and 0.2.2 dated 2015-04-09
Description: A small collection of various network data sets,
to use with the igraph package. They also work with the igraph0
package.
Author: Gabor Csardi
Maintainer: Gabor Csardi
igraphdata-0.2.2/igraphdata/DESCRIPTION | 13 ++++++-------
igraphdata-0.2.2/igraphdata/MD5 | 3 +--
igraphdata-0.2/igraphdata/inst/CITATION |only
3 files changed, 7 insertions(+), 9 deletions(-)
Title: Data Sets from "Forecasting with Exponential Smoothing"
Diff between expsmooth versions 2.02 dated 2012-10-30 and 2.3 dated 2015-04-09
Description: Data sets from the book "Forecasting with exponential smoothing: the state space approach" by
Hyndman, Koehler, Ord and Snyder (Springer, 2008).
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 9 +++++++--
DESCRIPTION | 20 ++++++++++----------
MD5 | 10 +++++-----
man/freight.Rd | 3 ---
man/gasprice.Rd | 10 ++++++----
man/ukcars.Rd | 2 +-
6 files changed, 29 insertions(+), 25 deletions(-)
Title: The Iterative Signature Algorithm
Diff between isa2 versions 0.3.3 dated 2013-09-24 and 0.3.4 dated 2015-04-08
Description: The ISA is a biclustering algorithm that finds modules
in an input matrix. A module or bicluster is a block of the
reordered input matrix.
Author: Gabor Csardi
Maintainer: Gabor Csardi
DESCRIPTION | 14 ++++++-----
MD5 | 16 ++++++------
NAMESPACE | 3 ++
R/biclust.R | 2 -
R/isa3.R | 52 ++++++++++++++++++++++-------------------
R/viz.R | 2 -
inst/doc/ISA_parallel.pdf |binary
inst/doc/ISA_tutorial.pdf |binary
inst/doc/ISA_tutorial.vignette | 1
9 files changed, 50 insertions(+), 40 deletions(-)
Title: Import SPSS, Stata and SAS Files
Diff between haven versions 0.1.1 dated 2015-03-03 and 0.2.0 dated 2015-04-08
Description: Import foreign statistical formats into R via the embedded
ReadStat C library (https://github.com/WizardMac/ReadStat). Package includes
preliminary support for writing Stata and SPSS formats.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph]
Maintainer: Hadley Wickham
haven-0.1.1/haven/src/DfBuilder.cpp |only
haven-0.2.0/haven/DESCRIPTION | 6
haven-0.2.0/haven/MD5 | 75 ++--
haven-0.2.0/haven/NAMESPACE | 1
haven-0.2.0/haven/R/RcppExports.R | 12
haven-0.2.0/haven/R/as_factor.R | 3
haven-0.2.0/haven/R/haven.R | 31 +
haven-0.2.0/haven/R/hhmm.R | 10
haven-0.2.0/haven/R/labelled.R | 17
haven-0.2.0/haven/README.md | 6
haven-0.2.0/haven/build/vignette.rds |binary
haven-0.2.0/haven/inst/doc/datetimes.html | 4
haven-0.2.0/haven/man/as_factor.Rd | 3
haven-0.2.0/haven/man/labelled.Rd | 2
haven-0.2.0/haven/man/read_dta.Rd | 18 -
haven-0.2.0/haven/man/read_spss.Rd | 12
haven-0.2.0/haven/src/DfReader.cpp |only
haven-0.2.0/haven/src/DfWriter.cpp | 19 -
haven-0.2.0/haven/src/RcppExports.cpp | 16
haven-0.2.0/haven/src/readstat.h | 5
haven-0.2.0/haven/src/readstat_dta.c | 2
haven-0.2.0/haven/src/readstat_dta.h | 4
haven-0.2.0/haven/src/readstat_dta_read.c | 37 ++
haven-0.2.0/haven/src/readstat_dta_write.c | 2
haven-0.2.0/haven/src/readstat_io.c | 14
haven-0.2.0/haven/src/readstat_io.h | 2
haven-0.2.0/haven/src/readstat_parser.c | 5
haven-0.2.0/haven/src/readstat_por.c | 71 ++-
haven-0.2.0/haven/src/readstat_por_parse.c | 97 ++---
haven-0.2.0/haven/src/readstat_por_parse.h | 2
haven-0.2.0/haven/src/readstat_sas.c | 54 ++-
haven-0.2.0/haven/src/readstat_sav.c | 2
haven-0.2.0/haven/src/readstat_sav.h | 4
haven-0.2.0/haven/src/readstat_sav_parse.c | 14
haven-0.2.0/haven/src/readstat_sav_read.c | 373 ++++++++++++++++-----
haven-0.2.0/haven/src/readstat_sav_write.c | 15
haven-0.2.0/haven/tests/testthat/test-labelled.R |only
haven-0.2.0/haven/tests/testthat/test-read-sas.R | 7
haven-0.2.0/haven/tests/testthat/test-read-sav.R | 11
haven-0.2.0/haven/tests/testthat/test-read-stata.R |only
haven-0.2.0/haven/tests/testthat/types.dta |only
41 files changed, 679 insertions(+), 277 deletions(-)
Title: Define Truthy and Falsy Values
Diff between falsy versions 1.0 dated 2014-08-27 and 1.0.1 dated 2015-04-08
Description: A value is falsy if it is NULL, FALSE, the empty string,
zero, or an empty vector or list. Other values are truthy. The new
%&&% and %||% operators work with falsy and truthy values and
can be used for concise conditional execution.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
DESCRIPTION | 14 +++++++-------
LICENSE | 2 +-
MD5 | 27 ++++++++++++++-------------
NAMESPACE | 2 +-
R/falsy-package.r | 14 --------------
man/FALSY.Rd | 3 ++-
man/Falsy-package.Rd | 3 ++-
man/TRUTHY.Rd | 3 ++-
man/and.Rd | 3 ++-
man/is_falsy.Rd | 3 ++-
man/is_truthy.Rd | 3 ++-
man/nay.Rd | 3 ++-
man/or.Rd | 12 ++----------
man/try_quietly.Rd | 8 ++------
vignettes |only
15 files changed, 41 insertions(+), 59 deletions(-)
Title: Colored Terminal Output
Diff between crayon versions 1.1.0 dated 2014-10-15 and 1.2.0 dated 2015-04-08
Description: Colored terminal output on
terminals that support ANSI color and highlight codes.
ANSI color support is automatically detected.
Colors and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by the chalk
JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
crayon-1.1.0/crayon/README.md |only
crayon-1.2.0/crayon/DESCRIPTION | 15 ++--
crayon-1.2.0/crayon/LICENSE | 2
crayon-1.2.0/crayon/MD5 | 43 ++++++-----
crayon-1.2.0/crayon/NAMESPACE | 6 +
crayon-1.2.0/crayon/R/machinery.r | 4 +
crayon-1.2.0/crayon/R/string_operations.r |only
crayon-1.2.0/crayon/R/utils.r | 70 +++++++++++++++++++
crayon-1.2.0/crayon/man/chr.Rd | 3
crayon-1.2.0/crayon/man/col_nchar.Rd |only
crayon-1.2.0/crayon/man/col_strsplit.Rd |only
crayon-1.2.0/crayon/man/col_substr.Rd |only
crayon-1.2.0/crayon/man/col_substring.Rd |only
crayon-1.2.0/crayon/man/combine_styles.Rd | 3
crayon-1.2.0/crayon/man/concat.Rd | 3
crayon-1.2.0/crayon/man/crayon.Rd | 3
crayon-1.2.0/crayon/man/drop_style.Rd | 3
crayon-1.2.0/crayon/man/has_color.Rd | 3
crayon-1.2.0/crayon/man/has_style.Rd | 3
crayon-1.2.0/crayon/man/make_style.Rd | 3
crayon-1.2.0/crayon/man/num_colors.Rd | 3
crayon-1.2.0/crayon/man/show_ansi_colors.Rd | 3
crayon-1.2.0/crayon/man/strip_style.Rd | 3
crayon-1.2.0/crayon/man/style.Rd | 3
crayon-1.2.0/crayon/man/styles.Rd | 3
crayon-1.2.0/crayon/tests/testthat/test-operations.R |only
26 files changed, 138 insertions(+), 41 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data in R
Diff between hsdar versions 0.1.1 dated 2015-03-25 and 0.1.2 dated 2015-04-08
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using PROSPECT and PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [ctb],
Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert
hsdar-0.1.1/hsdar/man/add2speclib.Rd |only
hsdar-0.1.2/hsdar/DESCRIPTION | 10 -
hsdar-0.1.2/hsdar/MD5 | 97 +++++++--------
hsdar-0.1.2/hsdar/R/AAAClasses.R | 6
hsdar-0.1.2/hsdar/R/HyperSpecRaster_methods.R | 28 ++--
hsdar-0.1.2/hsdar/R/rastermeta.R |only
hsdar-0.1.2/hsdar/R/speclib.R | 22 ++-
hsdar-0.1.2/hsdar/R/unmix.R | 8 -
hsdar-0.1.2/hsdar/R/vegindex.R | 18 +-
hsdar-0.1.2/hsdar/data/endmember_spectra.RData |binary
hsdar-0.1.2/hsdar/data/spectral_data.RData |binary
hsdar-0.1.2/hsdar/inst/doc/References.pdf |binary
hsdar-0.1.2/hsdar/man/Clman-class.Rd | 3
hsdar-0.1.2/hsdar/man/DistMat3D-class.Rd | 3
hsdar-0.1.2/hsdar/man/DistMat3D-methods.Rd | 2
hsdar-0.1.2/hsdar/man/HyperSpecRaster.Rd | 3
hsdar-0.1.2/hsdar/man/Nri-class.Rd | 9 -
hsdar-0.1.2/hsdar/man/Specfeat-class.Rd | 3
hsdar-0.1.2/hsdar/man/Speclib-class.Rd | 3
hsdar-0.1.2/hsdar/man/addcp.Rd | 8 -
hsdar-0.1.2/hsdar/man/applyDistMat3D.Rd | 6
hsdar-0.1.2/hsdar/man/applySpeclib.Rd | 2
hsdar-0.1.2/hsdar/man/bandnames.Rd | 4
hsdar-0.1.2/hsdar/man/bdri.Rd | 6
hsdar-0.1.2/hsdar/man/checkhull.Rd | 2
hsdar-0.1.2/hsdar/man/cor.test.normalized.ratio.index.Rd | 4
hsdar-0.1.2/hsdar/man/cut.specfeat.Rd | 2
hsdar-0.1.2/hsdar/man/define.features.Rd | 6
hsdar-0.1.2/hsdar/man/deletecp.Rd | 4
hsdar-0.1.2/hsdar/man/dist_speclib.Rd | 4
hsdar-0.1.2/hsdar/man/feature_properties.Rd | 22 ++-
hsdar-0.1.2/hsdar/man/figures |only
hsdar-0.1.2/hsdar/man/getNRI.Rd | 2
hsdar-0.1.2/hsdar/man/getcp.Rd | 2
hsdar-0.1.2/hsdar/man/glm.normalized.ratio.index.Rd | 23 +--
hsdar-0.1.2/hsdar/man/hsdar-package.Rd | 5
hsdar-0.1.2/hsdar/man/merge_speclib.Rd |only
hsdar-0.1.2/hsdar/man/plot.glm.normalized.ratio.index.Rd | 33 +----
hsdar-0.1.2/hsdar/man/plot.specfeat.Rd | 4
hsdar-0.1.2/hsdar/man/plot.speclib.Rd | 2
hsdar-0.1.2/hsdar/man/rastermeta.Rd |only
hsdar-0.1.2/hsdar/man/rededge.Rd | 6
hsdar-0.1.2/hsdar/man/response_functions.Rd | 6
hsdar-0.1.2/hsdar/man/smooth_speclib.Rd | 2
hsdar-0.1.2/hsdar/man/specfeat.Rd | 4
hsdar-0.1.2/hsdar/man/speclib.Rd | 7 -
hsdar-0.1.2/hsdar/man/spectra.Rd | 2
hsdar-0.1.2/hsdar/man/subset_speclib.Rd | 8 -
hsdar-0.1.2/hsdar/man/t.test.nri.Rd | 2
hsdar-0.1.2/hsdar/man/transform.Rd | 2
hsdar-0.1.2/hsdar/man/vegindex.Rd | 2
51 files changed, 218 insertions(+), 179 deletions(-)
Title: An Improved Heatmap Package
Diff between heatmap3 versions 1.0.7 dated 2014-08-29 and 1.1.1 dated 2015-04-08
Description: An improved heatmap package. Completely
compatible with the original R function heatmap,
and provides more powerful and convenient features.
Author: Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.RData |only
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.rdb |only
heatmap3-1.0.7/heatmap3/vignettes/cache/setting_3fb270dc41facb42653a4ae883076b21.rdx |only
heatmap3-1.1.1/heatmap3/DESCRIPTION | 16 -
heatmap3-1.1.1/heatmap3/MD5 | 32 +-
heatmap3-1.1.1/heatmap3/NAMESPACE | 2
heatmap3-1.1.1/heatmap3/NEWS | 12
heatmap3-1.1.1/heatmap3/R/heatmap3.R | 39 ++-
heatmap3-1.1.1/heatmap3/build/vignette.rds |binary
heatmap3-1.1.1/heatmap3/inst/doc/vignette.R | 16 -
heatmap3-1.1.1/heatmap3/inst/doc/vignette.Rnw | 4
heatmap3-1.1.1/heatmap3/inst/doc/vignette.pdf |binary
heatmap3-1.1.1/heatmap3/man/colByValue.Rd | 6
heatmap3-1.1.1/heatmap3/man/heatmap3.Rd | 122 +++++-----
heatmap3-1.1.1/heatmap3/man/showAnn.Rd | 2
heatmap3-1.1.1/heatmap3/man/showLegend.Rd | 10
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.RData |only
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.rdb |only
heatmap3-1.1.1/heatmap3/vignettes/cache/setting_6613d1170cc2b09af00f80888ca7726a.rdx |only
heatmap3-1.1.1/heatmap3/vignettes/vignette.Rnw | 4
20 files changed, 149 insertions(+), 116 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Diff between DVHmetrics versions 0.1 dated 2015-01-29 and 0.2 dated 2015-04-08
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files,
calculate DVH metrics, gEUD, NTCP, TCP, show DVH diagrams,
check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger
parseDVH.R | 118 +++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/R/dvhConvert.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/R/shine.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/man/harmoConstrDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.1/DVHmetrics/man/shine.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/DESCRIPTION | 12
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/MD5 | 115 ++--
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/NAMESPACE | 47 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/checkConstraint.R | 135 +++--
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/convertDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/dvhDistance.R | 59 +-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getBED.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getDMEAN.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getEUD.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getMetric.R | 257 ++++------
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/getNTCP.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/loessSelSpan.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseCadplan.R | 18
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseEclipse.R | 35 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseMasterplan.R | 41 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parseMetric.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/parsePinnacleDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/readConstraint.R | 7
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/readDVH.R | 73 ++
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/runGUI.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/showConstraint.R | 29 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/showDVH.R | 31 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/smoothDVH.R |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/R/unix/parseDVH.R | 88 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/build/vignette.rds |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/data/dataConstr.rda |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/data/dataMZ.rda |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/ChangeLog |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHnotebooks |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/ABOUT.md |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/helper.R | 16
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/server.R | 229 +++++++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/DVHshiny/ui.R | 202 ++++---
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.R | 19
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.Rnw | 80 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHmetrics.pdf |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.R | 2
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.Rnw | 6
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/inst/doc/DVHshiny.pdf |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/DVHmetrics-package.Rd | 9
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/checkConstraint.Rd | 30 -
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/convertDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/dataConstr.Rd | 2
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getBED.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getDMEAN.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getEQD2.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getEUD.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getIsoEffD.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getMetric.Rd | 51 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getNTCP.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/getTCP.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/mergeDVH.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/print.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/readDVH.Rd | 32 +
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/runGUI.Rd |only
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveConstraint.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveDVH.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/saveMetric.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/man/showDVH.Rd | 1
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/DVHmetrics.Rnw | 80 ++-
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/DVHshiny.Rnw | 6
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appCheckConstr.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appFileOpen.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appMetrics.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appShowConstr.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/appShowDVH.jpg |binary
tmp/cranberry2f5b6ecd196f/DVHmetrics-0.2/DVHmetrics/vignettes/lit.bib | 100 +++
72 files changed, 1380 insertions(+), 554 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Diff between wux versions 1.2-3 dated 2015-02-06 and 2.0-0 dated 2015-04-08
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik
wux-1.2-3/wux/man/AnnualCycleplotWux.Rd |only
wux-1.2-3/wux/man/AnovaBarplotWux.Rd |only
wux-1.2-3/wux/man/AnovaReconstructIterative.Rd |only
wux-1.2-3/wux/man/AnovaReconstructIterativeCC.Rd |only
wux-1.2-3/wux/man/AnovaReconstructLES.Rd |only
wux-1.2-3/wux/man/HistplotWux.Rd |only
wux-1.2-3/wux/man/ScatterplotWux.Rd |only
wux-1.2-3/wux/man/WuxAnova.Rd |only
wux-1.2-3/wux/man/summaryWux.Rd |only
wux-2.0-0/wux/DESCRIPTION | 12 -
wux-2.0-0/wux/MD5 | 79 +++++-----
wux-2.0-0/wux/NAMESPACE | 27 ++-
wux-2.0-0/wux/R/AnovaReconstruct.R | 32 +++-
wux-2.0-0/wux/R/CMIP5toModelinput.R |only
wux-2.0-0/wux/R/PlotFunctions.R | 44 +++--
wux-2.0-0/wux/R/models2wux.R | 36 ++--
wux-2.0-0/wux/R/models2wuxGetAggregatedSpatioTemporalData.R | 30 ++--
wux-2.0-0/wux/R/models2wuxSubregions.R | 28 +++
wux-2.0-0/wux/R/plotit.R | 89 ++++++++----
wux-2.0-0/wux/R/read.wux.table.R | 14 +
wux-2.0-0/wux/R/summaryWux.R | 22 +-
wux-2.0-0/wux/data/CMIP5_example_changesignal.rda |only
wux-2.0-0/wux/data/alpinesummer.csv.gz |only
wux-2.0-0/wux/data/cmip3_2050.rda |only
wux-2.0-0/wux/data/cmip3_2100.rda |only
wux-2.0-0/wux/data/cmip5_2050.rda |only
wux-2.0-0/wux/data/datalist | 1
wux-2.0-0/wux/data/ensembles.rda |only
wux-2.0-0/wux/data/ensembles_gcms.rda |only
wux-2.0-0/wux/data/modelinput_test.rda |binary
wux-2.0-0/wux/data/userinput_CMIP5_changesignal.rda |binary
wux-2.0-0/wux/data/userinput_CMIP5_timeseries.rda |binary
wux-2.0-0/wux/exec/CMIP5_downloader.py | 2
wux-2.0-0/wux/exec/cmip5_to_wux_modeldict.py |only
wux-2.0-0/wux/man/CMIP5toModelinput.Rd |only
wux-2.0-0/wux/man/alpinesummer.Rd |only
wux-2.0-0/wux/man/aovWux.Rd |only
wux-2.0-0/wux/man/cmip3_2050.Rd | 4
wux-2.0-0/wux/man/cmip3_2100.Rd | 4
wux-2.0-0/wux/man/cmip5_2050.Rd | 4
wux-2.0-0/wux/man/cmip5_2100.Rd | 4
wux-2.0-0/wux/man/ensembles.Rd | 8 -
wux-2.0-0/wux/man/ensembles_gcms.Rd | 4
wux-2.0-0/wux/man/hist.wux.df.Rd |only
wux-2.0-0/wux/man/models2wux.Rd | 66 ++++++--
wux-2.0-0/wux/man/plot.wux.aov.Rd |only
wux-2.0-0/wux/man/plot.wux.df.Rd |only
wux-2.0-0/wux/man/plotAnnualCycle.Rd |only
wux-2.0-0/wux/man/read.wux.table.Rd | 8 -
wux-2.0-0/wux/man/reconstruct.Rd |only
wux-2.0-0/wux/man/summary.wux.df.Rd |only
wux-2.0-0/wux/man/userinput_CMIP5_changesignal.Rd | 4
wux-2.0-0/wux/man/userinput_CMIP5_timeseries.Rd | 2
wux-2.0-0/wux/man/wux-package.Rd | 43 +++--
54 files changed, 373 insertions(+), 194 deletions(-)
Title: Functions to Compute Chemical Reaction Similarity
Diff between RxnSim versions 1.0 dated 2015-03-12 and 1.0.1 dated 2015-04-08
Description: Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality.
Author: Varun Giri [aut, cre]
Maintainer: Varun Giri
RxnSim-1.0.1/RxnSim/CHANGELOG |only
RxnSim-1.0.1/RxnSim/DESCRIPTION | 12 +-
RxnSim-1.0.1/RxnSim/MD5 | 20 ++--
RxnSim-1.0.1/RxnSim/NAMESPACE | 3
RxnSim-1.0.1/RxnSim/NEWS |only
RxnSim-1.0.1/RxnSim/R/RxnSim.R | 59 ++++++++-----
RxnSim-1.0.1/RxnSim/R/RxnSimHelper.R | 118 ++++++++++++++++++++-------
RxnSim-1.0.1/RxnSim/R/RxnSimMask.R | 18 ++--
RxnSim-1.0.1/RxnSim/inst/DB/RheaData_v60.txt |only
RxnSim-1.0.1/RxnSim/man/rs.compute.Rd | 2
RxnSim-1.0.1/RxnSim/man/rs.makeDB.Rd | 8 +
RxnSim-1.0.1/RxnSim/man/rs.mask.Rd | 8 +
RxnSim-1.0/RxnSim/inst/DB/RheaData_v59.txt |only
13 files changed, 168 insertions(+), 80 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Diff between RDML versions 0.8-2 dated 2015-04-07 and 0.8-3 dated 2015-04-08
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
CHANGELOG | 3 +++
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 1 -
R/RDML.AsDendrogram.R | 10 +++++++---
R/RDML.AsTable.R | 4 ++--
R/RDML.GetFData.R | 6 +++---
R/RDML.R | 2 +-
R/RDML.SetFData.R | 6 +++---
R/RDML.init.R | 3 +--
R/names.RDML.R | 4 ++--
man/RDML.class.Rd | 4 ++--
man/asdendrogram-method.Rd | 4 ++--
man/astable-method.Rd | 4 ++--
man/getfdata-method.Rd | 6 +++---
man/names.RDML.Rd | 4 ++--
man/setfdata-method.Rd | 6 +++---
17 files changed, 57 insertions(+), 52 deletions(-)
Title: Density Estimation with a Penalized Mixture Approach
Diff between pendensity versions 0.2.7 dated 2014-02-25 and 0.2.8 dated 2015-04-08
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase
DESCRIPTION | 10 +++++-----
MD5 | 13 +++++++------
NAMESPACE | 4 +++-
R/new.beta.val.R | 9 +--------
R/pendensity.R | 4 ++--
build |only
man/pendensity-package.Rd | 4 ++--
man/pendensity.Rd | 2 +-
8 files changed, 21 insertions(+), 25 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 1.0-0 dated 2015-02-21 and 1.0-1 dated 2015-04-08
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 15 ++++-----
MD5 | 50 +++++++++++++++---------------
R/as.party.R | 4 ++
R/glmtree.R | 23 +++++++++++--
R/lmtree.R | 23 +++++++++++--
R/plot.R | 24 +++++++++-----
build/vignette.rds |binary
data/HuntingSpiders.rda |only
inst/NEWS.Rd | 28 ++++++++++++++++
inst/doc/constparty.pdf |binary
inst/doc/ctree.R | 35 +++++++++------------
inst/doc/ctree.Rnw | 76 +++++++++++++++++++++++-----------------------
inst/doc/ctree.pdf |binary
inst/doc/mob.pdf |binary
inst/doc/partykit.pdf |binary
man/HuntingSpiders.Rd |only
man/WeatherPlay.Rd | 2 -
man/cforest.Rd | 69 +++++++++++++++++++++--------------------
man/ctree.Rd | 36 +++++++++++----------
man/glmtree.Rd | 11 +++---
man/lmtree.Rd | 11 +++---
man/mob.Rd | 6 +--
man/panelfunctions.Rd | 5 +--
man/party-plot.Rd | 4 +-
vignettes/ctree.Rnw | 76 +++++++++++++++++++++++-----------------------
vignettes/ctree.Rout.save | 60 +++++++++++++++++-------------------
vignettes/party.bib | 2 -
27 files changed, 316 insertions(+), 244 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Diff between glmnet versions 1.9-8 dated 2014-05-24 and 2.0-1 dated 2015-04-08
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie
ChangeLog | 5 +
DESCRIPTION | 17 ++--
MD5 | 43 +++++++-----
NAMESPACE | 8 ++
R/cv.coxnet.R | 96 +++++++++++++++------------
R/cv.elnet.R | 84 +++++++++++++----------
R/cv.fishnet.R | 105 ++++++++++++++++-------------
R/cv.glmnet.R | 144 +++++++++++++++++++++++++---------------
R/cv.lognet.R | 162 ++++++++++++++++++++++++----------------------
R/cv.mrelnet.R | 8 +-
R/cv.multnet.R | 133 +++++++++++++++++++------------------
R/lognet.R | 15 +++-
R/predict.multnet.R | 2
build/vignette.rds |binary
data |only
inst/doc/Coxnet.pdf |binary
inst/doc/glmnet_beta.R |only
inst/doc/glmnet_beta.Rmd |only
inst/doc/glmnet_beta.html |only
man/beta_CVX.Rd |only
man/glmnet.Rd | 7 +
vignettes/glmnet_beta.Rmd |only
22 files changed, 479 insertions(+), 350 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.1.0 dated 2015-02-28 and 1.1.1 dated 2015-04-08
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NAMESPACE | 2 ++
R/Create_Landscapes.r | 3 ++-
R/Test_Samples.r | 3 ++-
data/WolverineHabitat.rda |binary
6 files changed, 14 insertions(+), 10 deletions(-)
Title: Analysis of Binary Character Evolution
Diff between corHMM versions 1.15 dated 2014-09-18 and 1.16 dated 2015-04-08
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 14 +++---
MD5 | 10 ++--
NAMESPACE | 2
R/ancRECON.R | 4 -
R/corHMM.R | 117 ++++++++++++++++++++++++++++++----------------------------
man/corHMM.Rd | 7 +--
6 files changed, 79 insertions(+), 75 deletions(-)
Title: Model-Based Clustering of Categorical Sequences
Diff between ClickClust versions 1.1.3 dated 2014-11-24 and 1.1.4 dated 2015-04-08
Description: Clustering categorical sequences by means of finite mixtures with Markov model components is the main utility of ClickClust. The package also allows detecting blocks of equivalent states by forward and backward state selection procedures.
Author: Volodymyr Melnykov [aut, cre]
Maintainer: Volodymyr Melnykov
ClickClust-1.1.3/ClickClust/demo/sec3.1_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.2_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.2_ex2.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.3_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.4_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.4_ex2.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.5_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.6_ex1.R |only
ClickClust-1.1.3/ClickClust/demo/sec3.6_ex2.R |only
ClickClust-1.1.4/ClickClust/DESCRIPTION | 14
ClickClust-1.1.4/ClickClust/MD5 | 57 ++--
ClickClust-1.1.4/ClickClust/NEWS | 6
ClickClust-1.1.4/ClickClust/R/libClickClust.R | 93 +++---
ClickClust-1.1.4/ClickClust/R/libGraphics.R | 239 ++++++++++++-----
ClickClust-1.1.4/ClickClust/data |only
ClickClust-1.1.4/ClickClust/demo/00Index | 24 -
ClickClust-1.1.4/ClickClust/demo/BackwardSelection.R |only
ClickClust-1.1.4/ClickClust/demo/ClickPlot1.R |only
ClickClust-1.1.4/ClickClust/demo/ClickPlot2.R |only
ClickClust-1.1.4/ClickClust/demo/ConfidenceIntervals.R |only
ClickClust-1.1.4/ClickClust/demo/DataSimulation.R |only
ClickClust-1.1.4/ClickClust/demo/EMalgorithm1.R |only
ClickClust-1.1.4/ClickClust/demo/EMalgorithm2.R |only
ClickClust-1.1.4/ClickClust/demo/ForwardSelection.R |only
ClickClust-1.1.4/ClickClust/demo/ReadData.R |only
ClickClust-1.1.4/ClickClust/demo/StatePrediction.R |only
ClickClust-1.1.4/ClickClust/demo/demoClickClust.R | 2
ClickClust-1.1.4/ClickClust/demo/msnbc323.R |only
ClickClust-1.1.4/ClickClust/demo/utility.R | 7
ClickClust-1.1.4/ClickClust/man/B3.Rd |only
ClickClust-1.1.4/ClickClust/man/BackwardSearch.Rd | 5
ClickClust-1.1.4/ClickClust/man/C.Rd |only
ClickClust-1.1.4/ClickClust/man/ClickClust-package.Rd | 2
ClickClust-1.1.4/ClickClust/man/ClickClust.Rd | 2
ClickClust-1.1.4/ClickClust/man/ClickPlot.Rd | 22 +
ClickClust-1.1.4/ClickClust/man/ForwardSearch.Rd | 5
ClickClust-1.1.4/ClickClust/man/Predict.Rd | 2
ClickClust-1.1.4/ClickClust/man/ReadData.Rd | 11
ClickClust-1.1.4/ClickClust/man/VarEst.Rd | 2
ClickClust-1.1.4/ClickClust/man/msnbc323.Rd |only
ClickClust-1.1.4/ClickClust/man/synth.Rd |only
41 files changed, 318 insertions(+), 175 deletions(-)
Title: Generative Models for Complex Networks with Conditionally
Independent Dyadic Structure
Diff between CIDnetworks versions 0.8.0 dated 2015-03-11 and 0.8.1 dated 2015-04-08
Description: Generative models for complex networks with conditionally independent dyadic structure. Now supports directed arcs!
Author: Samrachana Adhikari [aut],
Beau Dabbs [cre, aut],
Brian Junker [aut],
Mauricio Sadinle [aut],
Tracy Sweet [aut],
A.C. Thomas [aut]
Maintainer: Beau Dabbs
DESCRIPTION | 8 +--
MD5 | 21 ++++----
NAMESPACE | 1
R/CID-external.R | 45 ++++++++++++++++-
R/CID-gibbs.R | 133 +++++++++++++++++++++++++++++++++++++++++-----------
R/COV-reference.R | 85 +++++++++++++++++++++++++--------
R/SBM-reference.R | 2
R/plotting-pieces.R | 8 +--
data/Advice.RData |only
man/CID-data.Rd | 13 ++++-
man/CID-gibbs.Rd | 4 -
man/CID-master.Rd | 3 -
12 files changed, 252 insertions(+), 71 deletions(-)
Title: Functions for Baseline-Based Time Series Prediction
Diff between TSPred versions 1.0 dated 2015-03-30 and 2.0 dated 2015-04-07
Description: Functions for time series prediction and accuracy assessment using automatic ARIMA modelling. The generated ARIMA models and its yielded prediction errors are intended to be used as baseline for evaluating the practical value of other time series prediction methods and creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ),
Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles
DESCRIPTION | 8 ++--
MD5 | 56 +++++++++++++++++++---------
R/arimainterp.R |only
R/arimapred.R | 7 ++-
R/marimapred.R | 88 +++++++++++++++++++++++++++++++++++++--------
data/CATS.cont.rda |only
data/CATS.rda |only
data/EUNITE.Loads.cont.rda |only
data/EUNITE.Loads.rda |only
data/EUNITE.Reg.cont.rda |only
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data/EUNITE.Temp.cont.rda |only
data/EUNITE.Temp.rda |only
data/NN3.A.cont.rda |binary
data/NN3.A.rda |binary
data/NN5.A.cont.rda |only
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data/SantaFe.A.cont.rda |binary
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data/SantaFe.D.cont.rda |binary
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man/EUNITE.Temp.Rd |only
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man/NN3.A.Rd | 4 +-
man/NN3.A.cont.Rd | 4 +-
man/NN5.A.Rd |only
man/NN5.A.cont.Rd |only
man/SantaFe.A.Rd | 2 -
man/SantaFe.A.cont.Rd | 6 +--
man/SantaFe.D.Rd | 2 -
man/SantaFe.D.cont.Rd | 6 +--
man/arimainterp.Rd |only
man/arimapred.Rd | 2 -
man/marimapred.Rd | 12 +++---
40 files changed, 141 insertions(+), 56 deletions(-)
Title: Propensity Score Matching of Non-Binary Treatments
Diff between TriMatch versions 0.9.1 dated 2013-09-20 and 0.9.4 dated 2015-04-07
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer
Maintainer: Jason Bryer
TriMatch-0.9.1/TriMatch/build |only
TriMatch-0.9.1/TriMatch/inst |only
TriMatch-0.9.1/TriMatch/vignettes |only
TriMatch-0.9.4/TriMatch/DESCRIPTION | 18 --
TriMatch-0.9.4/TriMatch/MD5 | 109 +++++++--------
TriMatch-0.9.4/TriMatch/NAMESPACE | 13 +
TriMatch-0.9.4/TriMatch/NEWS | 17 ++
TriMatch-0.9.4/TriMatch/R/TriMatch-package.R | 11 +
TriMatch-0.9.4/TriMatch/R/as.data.frame.list.R | 1
TriMatch-0.9.4/TriMatch/R/merge.triangle.matches.R | 1
TriMatch-0.9.4/TriMatch/R/merge.triangle.psa.R | 1
TriMatch-0.9.4/TriMatch/R/plot.balance.R | 4
TriMatch-0.9.4/TriMatch/R/plot.triangle.matches.R | 1
TriMatch-0.9.4/TriMatch/R/plot.triangle.psa.R | 4
TriMatch-0.9.4/TriMatch/R/summary.triangle.matches.R | 2
TriMatch-0.9.4/TriMatch/R/summary.triangle.psa.R | 1
TriMatch-0.9.4/TriMatch/R/triangle.match.R | 2
TriMatch-0.9.4/TriMatch/R/triangle.psa.R | 6
TriMatch-0.9.4/TriMatch/R/unmatched.R | 1
TriMatch-0.9.4/TriMatch/demo/00Index | 1
TriMatch-0.9.4/TriMatch/demo/one-to-one-to-one.R |only
TriMatch-0.9.4/TriMatch/demo/tutoring.R | 13 +
TriMatch-0.9.4/TriMatch/man/OneToN.Rd | 28 +---
TriMatch-0.9.4/TriMatch/man/TriMatch-package.Rd | 11 -
TriMatch-0.9.4/TriMatch/man/as.data.frame.list.Rd | 59 +++-----
TriMatch-0.9.4/TriMatch/man/balance.plot.Rd | 67 ++++-----
TriMatch-0.9.4/TriMatch/man/boxdiff.plot.Rd | 27 ++-
TriMatch-0.9.4/TriMatch/man/covariateBalance.Rd | 88 +++++-------
TriMatch-0.9.4/TriMatch/man/distance.euclid.Rd | 36 ++---
TriMatch-0.9.4/TriMatch/man/distances.plot.Rd | 20 +-
TriMatch-0.9.4/TriMatch/man/loess3.plot.Rd | 68 ++++-----
TriMatch-0.9.4/TriMatch/man/maximumTreat.Rd | 27 +--
TriMatch-0.9.4/TriMatch/man/merge.triangle.matches.Rd | 15 +-
TriMatch-0.9.4/TriMatch/man/merge.triangle.psa.Rd | 15 +-
TriMatch-0.9.4/TriMatch/man/multibalance.plot.Rd | 25 +--
TriMatch-0.9.4/TriMatch/man/nmes.Rd | 49 +++----
TriMatch-0.9.4/TriMatch/man/parallel.plot.Rd | 11 -
TriMatch-0.9.4/TriMatch/man/perpPt.Rd | 14 +-
TriMatch-0.9.4/TriMatch/man/plot.balance.plots.Rd | 28 +---
TriMatch-0.9.4/TriMatch/man/plot.triangle.matches.Rd | 59 +++-----
TriMatch-0.9.4/TriMatch/man/plot.triangle.psa.Rd | 57 +++-----
TriMatch-0.9.4/TriMatch/man/print.balance.plots.Rd | 15 +-
TriMatch-0.9.4/TriMatch/man/print.triangle.plot.Rd | 15 +-
TriMatch-0.9.4/TriMatch/man/print.trimatch.summary.Rd | 17 +-
TriMatch-0.9.4/TriMatch/man/segment1.Rd | 10 -
TriMatch-0.9.4/TriMatch/man/segment2.Rd | 10 -
TriMatch-0.9.4/TriMatch/man/star.Rd | 10 -
TriMatch-0.9.4/TriMatch/man/summary.balance.plots.Rd | 23 +--
TriMatch-0.9.4/TriMatch/man/summary.triangle.matches.Rd | 38 ++---
TriMatch-0.9.4/TriMatch/man/summary.triangle.psa.Rd | 15 +-
TriMatch-0.9.4/TriMatch/man/summary.unmatched.Rd | 16 +-
TriMatch-0.9.4/TriMatch/man/trimatch.Rd | 112 +++++++---------
TriMatch-0.9.4/TriMatch/man/trimatch.apply2.Rd | 55 +++----
TriMatch-0.9.4/TriMatch/man/trips.Rd | 46 +++---
TriMatch-0.9.4/TriMatch/man/tutoring.Rd | 50 +++----
TriMatch-0.9.4/TriMatch/man/unmatched.Rd | 16 +-
56 files changed, 666 insertions(+), 692 deletions(-)
Title: Matrix Completion via Iterative Soft-Thresholded SVD
Diff between softImpute versions 1.0 dated 2013-04-03 and 1.4 dated 2015-04-07
Description: Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an "EM" flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components)
Author: Trevor Hastie
Maintainer: Trevor Hastie
DESCRIPTION | 28 +++++++++------------------
MD5 | 42 +++++++++++++++++++++++++----------------
NAMESPACE | 5 ++--
R/Methods_splr.R | 2 +
R/Ssimpute.als.R | 4 +--
R/Ssimpute.svd.R | 4 +--
R/Ssvd.als.R | 4 +--
R/centerScale.R | 7 ++++--
R/clean.warm.start.R |only
R/deBias.R |only
R/onAttach.R |only
R/simpute.als.R | 4 +--
R/simpute.svd.R | 4 +--
R/softImpute.R | 5 ++++
R/svd.als.R | 4 +++
build |only
inst |only
man/SparseplusLowRank-class.Rd | 4 +++
man/biScale.Rd | 3 +-
man/deBias.Rd |only
man/softImpute-internal.Rd | 1
man/softImpute.Rd | 25 +++++++++++++-----------
man/svd.als.Rd | 9 +++++---
src/plusregC.f |only
vignettes |only
25 files changed, 92 insertions(+), 63 deletions(-)
Title: Tools for Custom Searches / Subsets / Slices of Named R Objects
Diff between searchable versions 0.1.2 dated 2015-03-24 and 0.3.3.1 dated 2015-04-07
Description: Provides functionality for searching / subsetting and slicing named
objects using 'stringr/i'-style modifiers by case (in)sensitivity,
regular expressions or fixed expressions; searches uses the standard '['
operator and allows specification of default search behavior to either the
search target (named object) and/or the search pattern.
Author: "DecisionPatterns [aut, cre]"
Maintainer: Christopher Brown
searchable-0.1.2/searchable/R/Class-searchable.R |only
searchable-0.1.2/searchable/R/match-modifiers.R |only
searchable-0.1.2/searchable/man/match.modifiers.Rd |only
searchable-0.1.2/searchable/tests/testthat/test-searchable.R |only
searchable-0.3.3.1/searchable/DESCRIPTION | 36
searchable-0.3.3.1/searchable/MD5 | 56 +
searchable-0.3.3.1/searchable/NAMESPACE | 54 +
searchable-0.3.3.1/searchable/NEWS |only
searchable-0.3.3.1/searchable/R/Class-Pattern.R |only
searchable-0.3.3.1/searchable/R/Class-PatternOrCharacter.R |only
searchable-0.3.3.1/searchable/R/Class-Searchable.R |only
searchable-0.3.3.1/searchable/R/Class-SearchableOrPattern.R |only
searchable-0.3.3.1/searchable/R/Class-Searchables.R |only
searchable-0.3.3.1/searchable/R/boundary.R |only
searchable-0.3.3.1/searchable/R/case.R |only
searchable-0.3.3.1/searchable/R/coll.R |only
searchable-0.3.3.1/searchable/R/detect.R |only
searchable-0.3.3.1/searchable/R/extract.R | 362 +++-------
searchable-0.3.3.1/searchable/R/fixed.R |only
searchable-0.3.3.1/searchable/R/invert.R | 2
searchable-0.3.3.1/searchable/R/regex.R |only
searchable-0.3.3.1/searchable/R/reverse.lookup.R | 23
searchable-0.3.3.1/searchable/R/searchable-package.R | 91 +-
searchable-0.3.3.1/searchable/R/std.R |only
searchable-0.3.3.1/searchable/R/stri_detect_std.R |only
searchable-0.3.3.1/searchable/README.md | 105 +-
searchable-0.3.3.1/searchable/man/boundary.Rd |only
searchable-0.3.3.1/searchable/man/case.Rd |only
searchable-0.3.3.1/searchable/man/coll.Rd |only
searchable-0.3.3.1/searchable/man/detect.Rd |only
searchable-0.3.3.1/searchable/man/extract.Rd | 137 +--
searchable-0.3.3.1/searchable/man/fixed.Rd |only
searchable-0.3.3.1/searchable/man/invert.Rd | 6
searchable-0.3.3.1/searchable/man/is.string.Rd | 2
searchable-0.3.3.1/searchable/man/pattern.Rd |only
searchable-0.3.3.1/searchable/man/regex.Rd |only
searchable-0.3.3.1/searchable/man/reverse.lookup.Rd | 10
searchable-0.3.3.1/searchable/man/searchable-package.Rd | 75 +-
searchable-0.3.3.1/searchable/man/searchable.Rd | 179 +++-
searchable-0.3.3.1/searchable/man/std.Rd |only
searchable-0.3.3.1/searchable/man/stri_std.Rd |only
searchable-0.3.3.1/searchable/tests/testthat/test-lists.r |only
searchable-0.3.3.1/searchable/tests/testthat/test-searchable.r |only
searchable-0.3.3.1/searchable/tests/testthat/test-vectors.r |only
44 files changed, 611 insertions(+), 527 deletions(-)
Title: Fast and Exact Algorithms for Computing Phylogenetic
Biodiversity Measures
Diff between PhyloMeasures versions 1.0 dated 2015-04-02 and 1.1 dated 2015-04-07
Description: Given a phylogenetic tree T and a sample S of species represented as
a subset of tips in T, we want to compute a measure of the diversity
of the species in S with respect to T. The current package offers the
implementations of efficient algorithms for several such measures.
Most importantly, the package includes algorithms for computing exactly and
efficiently the expectation and the variance of these measures, which are
essential for null model comparisons. Efficient computation of
richness-standardized versions of these metrics, such as the net
relatedness index (NRI), nearest taxon index (NTI), phylogenetic
diversity index (PDI), and the corresponding indices of two-sample measures
are also available in this package. The package also introduces a new
single-sample measure, the Core Ancestor Cost (CAC); the package provides
functions for computing the value and the standardised index of the CAC and,
more than that, there is an extra function available that can compute exactly
any statistical moment of the measure.
Author: Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Maintainer: Constantinos Tsirogiannis
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
man/PhyloMeasures-package.Rd | 4 ++--
src/Measures/Core_ancestor_cost_impl.h | 4 ----
src/Measures/Mean_nearest_taxon_distance_impl.h | 5 +----
src/Measures/Phylogenetic_diversity_impl.h | 2 --
src/Phylogenetic_tree_base.h | 24 ++++++++++++------------
7 files changed, 24 insertions(+), 33 deletions(-)
Title: Phylogenetic Analysis in R
Diff between phangorn versions 1.99-12 dated 2015-02-13 and 1.99-13 dated 2015-04-07
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
phangorn-1.99-12/phangorn/R/RcppExports.R |only
phangorn-1.99-12/phangorn/src/init.c |only
phangorn-1.99-13/phangorn/DESCRIPTION | 10
phangorn-1.99-13/phangorn/MD5 | 42 -
phangorn-1.99-13/phangorn/NAMESPACE | 6
phangorn-1.99-13/phangorn/NEWS | 10
phangorn-1.99-13/phangorn/R/distSeq.R | 3
phangorn-1.99-13/phangorn/R/fitch.R | 48 -
phangorn-1.99-13/phangorn/R/hadamard.R |only
phangorn-1.99-13/phangorn/R/parsimony.R | 51 +
phangorn-1.99-13/phangorn/R/phyDat.R | 222 +++++++-
phangorn-1.99-13/phangorn/R/phylo.R | 570 ++++++----------------
phangorn-1.99-13/phangorn/R/treedist.R | 2
phangorn-1.99-13/phangorn/R/zzz.R | 5
phangorn-1.99-13/phangorn/build/vignette.rds |binary
phangorn-1.99-13/phangorn/man/distanceHadamard.Rd | 74 +-
phangorn-1.99-13/phangorn/man/phyDat.Rd | 192 +++----
phangorn-1.99-13/phangorn/man/pmlCluster.Rd | 6
phangorn-1.99-13/phangorn/man/pmlPart.Rd | 8
phangorn-1.99-13/phangorn/src/dist.c | 2
phangorn-1.99-13/phangorn/src/ml.c | 426 +++++++++-------
phangorn-1.99-13/phangorn/src/phangorn.c | 40 -
phangorn-1.99-13/phangorn/src/read_aa.c |only
phangorn-1.99-13/phangorn/vignettes/phangorn.bib | 105 +++-
24 files changed, 952 insertions(+), 870 deletions(-)
Title: Miscellaneous Functions for Creating Adaptive Functions and
Scripts
Diff between NCmisc versions 1.1.3 dated 2014-09-03 and 1.1.4 dated 2015-04-07
Description: A set of handy functions. Includes a versatile one line progress bar, one
line function timer with detailed output, time delay function, text histogram, object
preview, CRAN package search, simpler package installer, Linux command install check,
a flexible Mode function, top function, simulation of correlated data, and more.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper
DESCRIPTION | 19 +
MD5 | 104 +++++-----
NAMESPACE | 11 -
R/NCmisc.R | 409 ++++++++++++++++++++++++++++++++++++++++--
man/Dim.Rd | 3
man/Header.Rd | 3
man/Mode.Rd | 3
man/NCmisc-internal.Rd | 1
man/NCmisc-package.Rd | 22 +-
man/Rfile.index.Rd | 6
man/Substitute.Rd | 3
man/Unlist.Rd | 3
man/Z.to.p.Rd |only
man/check.linux.install.Rd | 5
man/comify.Rd |only
man/cor.with.Rd | 3
man/dup.pairs.Rd |only
man/estimate.memory.Rd | 3
man/exists.not.function.Rd | 3
man/extend.pc.Rd | 9
man/fakeLines.Rd | 3
man/file.split.Rd | 12 +
man/force.percentage.Rd | 3
man/force.scalar.Rd | 3
man/get.distinct.cols.Rd | 3
man/getRepositories.Rd | 4
man/has.method.Rd |only
man/headl.Rd | 3
man/list.functions.in.file.Rd |only
man/list.to.env.Rd | 10 -
man/loess.scatter.Rd | 7
man/loop.tracker.Rd | 3
man/memory.summary.Rd | 3
man/must.use.package.Rd | 9
man/narm.Rd | 3
man/out.of.Rd | 3
man/p.to.Z.Rd |only
man/packages.loaded.Rd | 4
man/pad.left.Rd | 3
man/pctile.Rd | 3
man/ppa.Rd |only
man/preview.Rd | 3
man/prv.Rd | 3
man/prv.large.Rd | 3
man/rmv.spc.Rd | 3
man/search.cran.Rd | 4
man/sim.cor.Rd | 3
man/simple.date.Rd | 3
man/spc.Rd | 3
man/standardize.Rd | 3
man/summarise.r.datasets.Rd | 5
man/textogram.Rd | 3
man/timeit.Rd | 3
man/toheader.Rd | 3
man/top.Rd | 3
man/wait.Rd | 3
man/which.outlier.Rd |only
57 files changed, 600 insertions(+), 137 deletions(-)
Title: Tools for Nanoparticle Simulation and Calculation of PDF and
Total Scattering Structure Function
Diff between nanop versions 2.0-4 dated 2014-08-25 and 2.0-5 dated 2015-04-07
Description: This software package implements functions to simulate spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal structures and to calculate the associated pair-distribution function and X-ray/neutron total-scattering signals. It also provides a target function that can be used for simultaneous fitting of small- and wide-angle total scattering data in real and reciprocal spaces. The target function can be generated either as a sum of weighted residuals for individual datasets or as a vector of residuals suitable for optimization using multi-criteria algorithms (e.g. Pareto methods).
Author: Anton Gagin, Katharine Mullen, Igor Levin
Maintainer: Anton Gagin
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
NEWS | 2 ++
R/displacePart.R | 19 ++++++++++++-------
data |only
inst/CITATION | 2 +-
6 files changed, 24 insertions(+), 16 deletions(-)
Title: Nested Association Mapping Analysis
Diff between NAM versions 1.1.2 dated 2015-04-01 and 1.2 dated 2015-04-07
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
NAM-1.1.2/NAM/man/manhattan.Rd |only
NAM-1.2/NAM/DESCRIPTION | 12
NAM-1.2/NAM/MD5 | 25 -
NAM-1.2/NAM/NAMESPACE | 7
NAM-1.2/NAM/R/Fst.R | 85 ++-
NAM-1.2/NAM/R/gibbs.R | 392 ++++++++--------
NAM-1.2/NAM/R/gwas.R | 967 ++++++++++++++++++++---------------------
NAM-1.2/NAM/R/manhattan.R | 63 +-
NAM-1.2/NAM/R/snpH2.R | 15
NAM-1.2/NAM/man/Fst.Rd | 17
NAM-1.2/NAM/man/NAM-package.Rd | 66 +-
NAM-1.2/NAM/man/gibbs.Rd | 6
NAM-1.2/NAM/man/gwas.Rd | 136 +++--
NAM-1.2/NAM/man/snpH2.Rd | 67 +-
14 files changed, 955 insertions(+), 903 deletions(-)
Title: Running OpenBUGS from R
Diff between R2OpenBUGS versions 3.2-2.2 dated 2013-04-10 and 3.2-3.1 dated 2015-04-07
Description: Using this package,
it is possible to call a BUGS model, summarize inferences and
convergence in a table and graph, and save the simulations in arrays for easy access
in R.
Author: originally written as R2WinBUGS by Andrew Gelman
Maintainer: Neal Thomas
R2OpenBUGS-3.2-2.2/R2OpenBUGS/CreatevalidateOpenBUGS.R |only
R2OpenBUGS-3.2-2.2/R2OpenBUGS/inst/doc/R2OpenBUGS.R |only
R2OpenBUGS-3.2-2.2/R2OpenBUGS/tests |only
R2OpenBUGS-3.2-3.1/R2OpenBUGS/DESCRIPTION | 28 ++++++++---------
R2OpenBUGS-3.2-3.1/R2OpenBUGS/MD5 | 15 +++------
R2OpenBUGS-3.2-3.1/R2OpenBUGS/NAMESPACE | 1
R2OpenBUGS-3.2-3.1/R2OpenBUGS/R/findOpenBUGS.R | 6 +--
R2OpenBUGS-3.2-3.1/R2OpenBUGS/build |only
R2OpenBUGS-3.2-3.1/R2OpenBUGS/inst/NEWS | 3 +
R2OpenBUGS-3.2-3.1/R2OpenBUGS/man/bugs.Rd | 4 +-
10 files changed, 29 insertions(+), 28 deletions(-)
Title: Classes for Relational Data
Diff between network versions 1.11.3 dated 2014-12-06 and 1.12.0 dated 2015-04-07
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb]
Maintainer: Carter T. Butts
ChangeLog | 7
DESCRIPTION | 10
MD5 | 27 -
NAMESPACE | 35 +
R/coercion.R | 2
R/plot.R | 877 +++++++++++++++++++++++++------------------
inst/CITATION | 96 +++-
inst/doc/networkVignette.pdf |binary
man/network-package.Rd | 6
man/network.Rd | 6
man/network.edgelabel.Rd | 8
man/plot.network.Rd | 2
man/preparePlotArgs.Rd |only
tests/general.tests2.R | 23 +
tests/plot_tests.R | 12
15 files changed, 707 insertions(+), 404 deletions(-)
Title: Symbolic Differentiation
Diff between Deriv versions 3.0 dated 2015-03-06 and 3.2 dated 2015-04-07
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol
DESCRIPTION | 9 -
MD5 | 24 +--
NEWS | 16 ++
R/Deriv.R | 248 +++++++++++++++++++------------------
R/Simplify.R | 196 ++++++++++++++++++-----------
README.md | 2
inst/CITATION | 2
man/Deriv-package.Rd | 2
man/Deriv.Rd | 40 ++++-
tests/testthat/test_Deriv.R | 28 ++--
tests/testthat/test_Deriv.R.bck | 25 ++-
tests/testthat/test_Simplify.R | 3
tests/testthat/test_Simplify.R.bck | 4
13 files changed, 365 insertions(+), 234 deletions(-)
Title: Bayesian Generalized Linear Regression
Diff between BGLR versions 1.0.3 dated 2014-06-10 and 1.0.4 dated 2015-04-07
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez
BGLR-1.0.3/BGLR/man/effects.BGLR.Rd |only
BGLR-1.0.4/BGLR/CHANGELOG | 5
BGLR-1.0.4/BGLR/DESCRIPTION | 12 -
BGLR-1.0.4/BGLR/MD5 | 21 -
BGLR-1.0.4/BGLR/NAMESPACE | 11
BGLR-1.0.4/BGLR/R/BGLR.R | 413 +++++++++++++++++++++++++++--------
BGLR-1.0.4/BGLR/R/methods.R | 12 -
BGLR-1.0.4/BGLR/build/vignette.rds |binary
BGLR-1.0.4/BGLR/man/BGLR.Rd | 5
BGLR-1.0.4/BGLR/man/wheat.A.Rd | 7
BGLR-1.0.4/BGLR/man/wheat.Rd | 6
BGLR-1.0.4/BGLR/src/util_sample.c | 420 ++++++++++++++++++++++++++++++++++--
12 files changed, 771 insertions(+), 141 deletions(-)
Title: Extended Model Formulas
Diff between Formula versions 1.2-0 dated 2015-01-19 and 1.2-1 dated 2015-04-07
Description: Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
Author: Achim Zeileis [aut, cre],
Yves Croissant [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8 -
MD5 | 12 +-
NEWS | 10 ++
R/Formula.R | 145 ++++++++++++++++++++++--------------
inst/doc/Formula.pdf |binary
man/model.frame.Formula.Rd | 30 +++++--
tests/Examples/Formula-Ex.Rout.save | 22 +++--
7 files changed, 148 insertions(+), 79 deletions(-)
Title: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Diff between rehh versions 1.11 dated 2013-08-26 and 1.12 dated 2015-04-07
Description: Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.
Author: Mathieu Gautier and Renaud Vitalis
Maintainer: Mathieu Gautier
ChangeLog | 4 ++++
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 3 +++
R/data2haplohh.R | 4 ++--
inst/CITATION | 5 ++---
6 files changed, 21 insertions(+), 15 deletions(-)
Title: Loading Google Adwords Data into R
Diff between RAdwords versions 0.1.2 dated 2015-03-27 and 0.1.3 dated 2015-04-07
Description: The aim of RAdwords is loading Adwords data into R. Therefore the
package implements three main features. First, the package provides an
authentication process for R with the Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt
Maintainer: Johannes Burkhardt
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
NEWS | 7 +++++++
R/getAuth.R | 3 ++-
R/getData.R | 4 +++-
R/loadToken.R | 2 +-
R/refreshToken.R | 3 ++-
7 files changed, 24 insertions(+), 13 deletions(-)
Title: Missing Data Imputation and Model Checking
Diff between mi versions 0.10-1 dated 2015-04-06 and 0.10-2 dated 2015-04-07
Description: R functions for performing multiple imputation with several checks.
Author:
Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 2 -
DESCRIPTION | 12 +++++------
MD5 | 16 +++++++--------
NAMESPACE | 16 ++++++++-------
R/AllGeneric.R | 57 +++++++++++++++++++++++--------------------------------
R/coef.R | 36 +++++++++++++++++-----------------
R/fitted.R | 10 ++++-----
R/sigma.hat.R | 10 ++++-----
man/mi.method.Rd | 18 ++++++++---------
9 files changed, 85 insertions(+), 92 deletions(-)
Title: Interface to Dygraphs Interactive Time Series Charting Library
Diff between dygraphs versions 0.4.2 dated 2015-03-04 and 0.4.3 dated 2015-04-07
Description: An R interface to the dygraphs JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire
dygraphs-0.4.2/dygraphs/README.md |only
dygraphs-0.4.3/dygraphs/DESCRIPTION | 19 +-
dygraphs-0.4.3/dygraphs/MD5 | 17 +-
dygraphs-0.4.3/dygraphs/NEWS | 11 +
dygraphs-0.4.3/dygraphs/R/range-selector.R | 3
dygraphs-0.4.3/dygraphs/inst/examples/examples.html | 10 -
dygraphs-0.4.3/dygraphs/inst/htmlwidgets/dygraphs.js | 142 +++++++++++++----
dygraphs-0.4.3/dygraphs/inst/htmlwidgets/dygraphs.yaml | 4
dygraphs-0.4.3/dygraphs/inst/htmlwidgets/lib/jquery |only
dygraphs-0.4.3/dygraphs/man/dyRangeSelector.Rd | 3
10 files changed, 158 insertions(+), 51 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.8-03 dated 2015-04-03 and 1.8-4 dated 2015-04-07
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su
arm-1.8-03/arm/R/model.matrix.bayes.R |only
arm-1.8-03/arm/man/model.matrix.bayes.Rd |only
arm-1.8-4/arm/CHANGELOG | 7 ++
arm-1.8-4/arm/DESCRIPTION | 12 ++--
arm-1.8-4/arm/MD5 | 36 +++++++-------
arm-1.8-4/arm/NAMESPACE | 40 +++++++++------
arm-1.8-4/arm/R/AllGeneric.R | 42 +++-------------
arm-1.8-4/arm/R/balance.R | 28 +++++------
arm-1.8-4/arm/R/coef.R | 78 +++++++++++--------------------
arm-1.8-4/arm/R/corrplot.R | 18 +++----
arm-1.8-4/arm/R/fitted.R | 14 ++---
arm-1.8-4/arm/R/model.matrixBayes.R |only
arm-1.8-4/arm/R/sigma.hat.R | 78 ++++++-------------------------
arm-1.8-4/arm/R/traceplot.R | 48 +++++++++----------
arm-1.8-4/arm/R/triangleplot.R | 46 +++++++++---------
arm-1.8-4/arm/man/model.matrixBayes.Rd |only
arm-1.8-4/arm/man/multicomp.plot.Rd | 24 ++++-----
arm-1.8-4/arm/man/se.coef.Rd | 22 ++++----
arm-1.8-4/arm/man/sigma.hat.Rd | 32 ++++++------
arm-1.8-4/arm/man/sim.Rd | 38 +++++++--------
arm-1.8-4/arm/man/traceplot.Rd | 6 +-
21 files changed, 247 insertions(+), 322 deletions(-)
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.2-1 dated 2015-03-23 and 0.2-2 dated 2015-04-07
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
ChangeLog | 7 +++++++
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 5 +++++
R/basicSPSStranslationFunctions.r | 3 ++-
R/meanDiff.r | 24 +++++++++++++++++++-----
R/oneway.r | 2 +-
R/scaleReliability.r | 21 ++++++++-------------
man/userfriendlyscience-meanDiff.Rd | 5 ++++-
man/userfriendlyscience-package.Rd | 4 ++--
10 files changed, 61 insertions(+), 36 deletions(-)
Permanent link
Title: A Collection of Small Text Corpora of Interesting Data
Diff between rcorpora versions 1.0.0 dated 2015-04-07 and 1.0.1 dated 2015-04-07
Description: A collection of small text corpora of interesting data.
It contains all data sets from https://github.com/dariusk/corpora.
Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson,
Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup,
Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,
Ross Barclay, Ross Binden, Justin Alford, Cole Willsea,
Andrew Gorman, Javier Arce, Patrick Rodriguez,
Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody,
Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black,
Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,
Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi
DESCRIPTION | 14 +++++++-------
MD5 | 8 ++++----
R/corpora.R | 2 +-
build/rcorpora.pdf |binary
man/corpora.Rd | 2 +-
5 files changed, 13 insertions(+), 13 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Diff between StereoMorph versions 1.3 dated 2015-02-12 and 1.4 dated 2015-04-07
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen
StereoMorph-1.3/StereoMorph/inst/extdata/apps/initial_parameters.R |only
StereoMorph-1.4/StereoMorph/DESCRIPTION | 11
StereoMorph-1.4/StereoMorph/MD5 | 33
StereoMorph-1.4/StereoMorph/NAMESPACE | 3
StereoMorph-1.4/StereoMorph/R/digitizeImage.R | 262 ++
StereoMorph-1.4/StereoMorph/R/listToJSONStr.R |only
StereoMorph-1.4/StereoMorph/R/readShapes.R |only
StereoMorph-1.4/StereoMorph/R/readXML4R.R |only
StereoMorph-1.4/StereoMorph/inst/CITATION |only
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/digitize_image.html | 85
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/digitize_image_pre.html | 69
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/initial_parameters.R | 70
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/server.R | 352 +++
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/ui.R | 2
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/www/digitize_image.css | 129 +
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/www/digitize_image.js | 969 ++++++++--
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/www/help.html | 44
StereoMorph-1.4/StereoMorph/inst/extdata/apps/digitizeImage/www/preserve_directory.txt |only
StereoMorph-1.4/StereoMorph/man/StereoMorph-package.Rd | 11
StereoMorph-1.4/StereoMorph/man/digitizeImage.Rd | 19
StereoMorph-1.4/StereoMorph/man/readShapes.Rd |only
21 files changed, 1720 insertions(+), 339 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Diff between RDML versions 0.4-2 dated 2014-09-10 and 0.8-2 dated 2015-04-07
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) format files and transforms to the appropriate
formats of the 'qpcR' and 'chipPCR' packages.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
RDML-0.4-2/RDML/R/summary.RDML.R |only
RDML-0.4-2/RDML/inst/RDML_logo.png |only
RDML-0.4-2/RDML/man/RDML.Rd |only
RDML-0.4-2/RDML/man/summary-RDML_object.Rd |only
RDML-0.8-2/RDML/CHANGELOG | 63 +
RDML-0.8-2/RDML/DESCRIPTION | 37 -
RDML-0.8-2/RDML/MD5 | 30
RDML-0.8-2/RDML/NAMESPACE | 29
RDML-0.8-2/RDML/R/RDML.AsDendrogram.R |only
RDML-0.8-2/RDML/R/RDML.AsTable.R |only
RDML-0.8-2/RDML/R/RDML.GetFData.R |only
RDML-0.8-2/RDML/R/RDML.Merge.R |only
RDML-0.8-2/RDML/R/RDML.R | 1026 ++++++++++++++++++-----------
RDML-0.8-2/RDML/R/RDML.SetFData.R |only
RDML-0.8-2/RDML/R/RDML.asserts.R |only
RDML-0.8-2/RDML/R/RDML.init.R |only
RDML-0.8-2/RDML/R/names.RDML.R |only
RDML-0.8-2/RDML/README.md | 52 -
RDML-0.8-2/RDML/man/RDML.class.Rd |only
RDML-0.8-2/RDML/man/asdendrogram-method.Rd |only
RDML-0.8-2/RDML/man/astable-method.Rd |only
RDML-0.8-2/RDML/man/getfdata-method.Rd |only
RDML-0.8-2/RDML/man/merge-method.Rd |only
RDML-0.8-2/RDML/man/names.RDML.Rd |only
RDML-0.8-2/RDML/man/new-method.Rd |only
RDML-0.8-2/RDML/man/setfdata-method.Rd |only
26 files changed, 795 insertions(+), 442 deletions(-)
Title: Safely Access the RStudio API
Diff between rstudioapi versions 0.2 dated 2014-12-30 and 0.3.1 dated 2015-04-06
Description: Access the RStudio API (if available) and provide informative error messages
when it's not.
Author: Hadley Wickham [aut],
JJ Allaire [aut, cre],
RStudio [cph]
Maintainer: JJ Allaire
rstudioapi-0.2/rstudioapi/README.md |only
rstudioapi-0.3.1/rstudioapi/DESCRIPTION | 15 +++++++--------
rstudioapi-0.3.1/rstudioapi/LICENSE | 2 +-
rstudioapi-0.3.1/rstudioapi/MD5 | 12 ++++++------
rstudioapi-0.3.1/rstudioapi/NAMESPACE | 1 +
rstudioapi-0.3.1/rstudioapi/NEWS | 6 ++++++
rstudioapi-0.3.1/rstudioapi/R/stubs.R | 6 ++++++
rstudioapi-0.3.1/rstudioapi/man/sourceMarkers.Rd |only
8 files changed, 27 insertions(+), 15 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Diff between lpSolve versions 5.6.10 dated 2014-07-26 and 5.6.11 dated 2015-04-06
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
src/lp_rlp.h | 2 +-
src/lp_utils.c | 11 +++++++++--
4 files changed, 18 insertions(+), 11 deletions(-)
Title: Interface to the 'g:Profiler' Toolkit
Diff between gProfileR versions 0.5 dated 2013-10-09 and 0.5.3 dated 2015-04-06
Description: Functional enrichment analysis, gene identifier conversion
and mapping homologous genes across related organisms via the
'g:Profiler' toolkit (http://biit.cs.ut.ee/gprofiler/).
Author: Juri Reimand
Maintainer: Tambet Arak
gProfileR-0.5.3/gProfileR/ChangeLog | 14 +
gProfileR-0.5.3/gProfileR/DESCRIPTION | 13 -
gProfileR-0.5.3/gProfileR/MD5 | 22 +-
gProfileR-0.5.3/gProfileR/NAMESPACE | 8
gProfileR-0.5.3/gProfileR/R/gProfileR.R | 71 +++++++-
gProfileR-0.5.3/gProfileR/man/gconvert.Rd | 73 ++------
gProfileR-0.5.3/gProfileR/man/get-sub-base-sub-url.Rd |only
gProfileR-0.5.3/gProfileR/man/get-sub-user-sub-agent.Rd |only
gProfileR-0.5.3/gProfileR/man/gorth.Rd | 84 +++------
gProfileR-0.5.3/gProfileR/man/gprofiler.Rd | 138 ++++++----------
gProfileR-0.5.3/gProfileR/man/set-sub-base-sub-url.Rd |only
gProfileR-0.5.3/gProfileR/man/set-sub-user-sub-agent.Rd |only
gProfileR-0.5/gProfileR/man/get_base_url.Rd |only
gProfileR-0.5/gProfileR/man/get_user_agent.Rd |only
gProfileR-0.5/gProfileR/man/set_base_url.Rd |only
gProfileR-0.5/gProfileR/man/set_user_agent.Rd |only
16 files changed, 207 insertions(+), 216 deletions(-)
Title: Missing Data Imputation and Model Checking
Diff between mi versions 0.09-19 dated 2014-10-02 and 0.10-1 dated 2015-04-06
Description: R functions for performing multiple imputation with several checks.
Author:
Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 5
DESCRIPTION | 14 +-
MD5 | 44 ++++----
R/AllGeneric.R | 8 +
R/AllInternal.R | 2
R/coef.R | 1
R/mi.R | 266 +++++++++++++++++++++++++-------------------------
R/mi.binary.R | 8 -
R/mi.categorical.R | 36 +++---
R/mi.continuous.R | 36 +++---
R/mi.count.R | 40 +++----
R/mi.hist.R | 211 +++++++++++++++++++--------------------
R/mi.pmm.R | 28 ++---
R/mi.polr.R | 40 +++----
R/mi.scatterplot.R | 57 +++++-----
R/plot.R | 54 ++++------
R/resid.R | 4
man/mi.binary.Rd | 16 +--
man/mi.categorical.Rd | 16 +--
man/mi.continuous.Rd | 12 +-
man/mi.count.Rd | 22 ++--
man/mi.pmm.Rd | 14 +-
man/mi.polr.Rd | 20 +--
23 files changed, 482 insertions(+), 472 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Diff between BBEST versions 0.1-3 dated 2015-03-09 and 0.1-4 dated 2015-04-06
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin
ChangeLog | 11 +
DESCRIPTION | 10 -
MD5 | 18 +-
R/interface.R | 60 ++++----
R/plot.R | 8 -
README.md | 39 ++++-
inst/gui/help/help.html | 8 +
inst/gui/server.R | 321 ++++++++++++++++++++++++++++++++++++++++++++----
inst/gui/ui.R | 35 ++++-
man/set.sigma.Rd | 11 -
10 files changed, 434 insertions(+), 87 deletions(-)
Title: Replicability Analysis for Multiple Studies of High Dimension
Diff between repfdr versions 1.1 dated 2014-10-02 and 1.1-3 dated 2015-04-06
Description: Estimation of Bayes and local Bayes false discovery rates for
replicability analysis.
Author: Ruth Heller [cre, aut],
Shachar Kaufman [aut],
Shay Yaacoby [aut],
Daniel Yekutieli [aut]
Maintainer: Ruth Heller
DESCRIPTION | 22 ++++--
MD5 | 33 +++++----
R/ztobins.R | 152 +++++++++++++++++++++++++++------------------
README.md |only
data/Pi.RData |binary
data/SNPlocations.RData |binary
data/binned_zmat.RData |binary
data/binned_zmat_sim.RData |binary
data/hmat_sim.RData |binary
data/zmat_sim.RData |binary
man/SNPlocations.Rd | 4 -
man/hmat_sim.Rd | 2
man/piem.Rd | 2
man/repfdr.Rd | 7 +-
man/zmat_sim.Rd | 4 -
man/ztobins.Rd | 24 +++----
src/Makevars | 2
src/Makevars.win | 6 -
18 files changed, 153 insertions(+), 105 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Diff between qdapRegex versions 0.2.0 dated 2014-12-21 and 0.3.2 dated 2015-04-06
Description: A collection of regular expression tools associated with the
'qdap' package that may be useful outside of the context of discourse
analysis. Tools include removal/extraction/replacement of abbreviations,
dates, dollar amounts, email addresses, hash tags, numbers, percentages,
citations, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker
DESCRIPTION | 41 ++--
MD5 | 196 +++++++++++----------
NAMESPACE | 9
NEWS | 62 ++++++
R/case.R | 7
R/explain.R | 41 +++-
R/group_or.R |only
R/pastex.R | 15 +
R/print.regexr.R |only
R/qdapRegex-package.R | 16 +
R/rm_abbreviation.R | 3
R/rm_between.R | 4
R/rm_bracket.R | 14 +
R/rm_caps.R | 4
R/rm_caps_phrase.R | 7
R/rm_citation.R | 16 +
R/rm_citation_tex.R | 5
R/rm_city_state.R | 4
R/rm_city_state_zip.R | 5
R/rm_date.R | 4
R/rm_default.R | 4
R/rm_dollar.R | 5
R/rm_email.R | 4
R/rm_emoticon.R | 4
R/rm_endmark.R | 5
R/rm_hash.R | 4
R/rm_nchar_words.R | 4
R/rm_non_ascii.R | 4
R/rm_number.R | 4
R/rm_percent.R | 4
R/rm_phone.R | 4
R/rm_postal_code.R | 4
R/rm_repeated_characters.R |only
R/rm_repeated_phrases.R |only
R/rm_repeated_words.R |only
R/rm_tag.R | 4
R/rm_time.R | 4
R/rm_title_name.R | 4
R/rm_url.R | 5
R/rm_white.R | 13 +
R/rm_zip.R | 4
R/utils.R | 94 ++--------
README.md | 244 +++++++++++++++++++++++++--
data/regex_cheat.rda |binary
data/regex_supplement.rda |binary
data/regex_usa.rda |binary
inst/CITATION | 6
man/S.Rd | 3
man/bind.Rd | 3
man/case.Rd | 10 -
man/cheat.Rd | 3
man/escape.Rd | 3
man/explain.Rd | 8
man/grab.Rd | 3
man/group.Rd | 3
man/group_or.Rd |only
man/is.regex.Rd | 3
man/pastex.Rd | 16 +
man/print.explain.Rd |only
man/print.regexr.Rd |only
man/qdapRegex.Rd | 5
man/regex_cheat.Rd | 3
man/regex_supplement.Rd | 10 -
man/regex_usa.Rd | 13 +
man/rm_.Rd | 3
man/rm_abbreviation.Rd | 34 +++
man/rm_between.Rd | 33 +++
man/rm_bracket.Rd | 31 +++
man/rm_caps.Rd | 34 +++
man/rm_caps_phrase.Rd | 36 +++
man/rm_citation.Rd | 46 ++++-
man/rm_citation_tex.Rd | 34 +++
man/rm_city_state.Rd | 33 +++
man/rm_city_state_zip.Rd | 33 +++
man/rm_date.Rd | 34 +++
man/rm_default.Rd | 34 +++
man/rm_dollar.Rd | 34 +++
man/rm_email.Rd | 34 +++
man/rm_emoticon.Rd | 34 +++
man/rm_endmark.Rd | 34 +++
man/rm_hash.Rd | 34 +++
man/rm_nchar_words.Rd | 34 +++
man/rm_non_ascii.Rd | 34 +++
man/rm_number.Rd | 34 +++
man/rm_percent.Rd | 34 +++
man/rm_phone.Rd | 34 +++
man/rm_postal_code.Rd | 34 +++
man/rm_repeated_characters.Rd |only
man/rm_repeated_phrases.Rd |only
man/rm_repeated_words.Rd |only
man/rm_tag.Rd | 34 +++
man/rm_time.Rd | 34 +++
man/rm_title_name.Rd | 34 +++
man/rm_url.Rd | 33 +++
man/rm_white.Rd | 26 ++
man/rm_zip.Rd | 34 +++
man/validate.Rd | 3
tests/testthat/test-S.R |only
tests/testthat/test-cheat.R |only
tests/testthat/test-explain.R |only
tests/testthat/test-group_or.R |only
tests/testthat/test-hijack.R |only
tests/testthat/test-pastex.R | 1
tests/testthat/test-rm_bracket.R | 46 ++++-
tests/testthat/test-rm_caps_phrase.R | 16 +
tests/testthat/test-rm_non_ascii.R |only
tests/testthat/test-rm_repeated_characters.R |only
tests/testthat/test-rm_repeated_phrases.R |only
tests/testthat/test-rm_repeated_words.R |only
109 files changed, 1681 insertions(+), 306 deletions(-)
Title: Dictionaries and Word Lists for the 'qdap' Package
Diff between qdapDictionaries versions 1.0.2 dated 2014-08-01 and 1.0.5 dated 2015-04-06
More information about qdapDictionaries at CRAN
Description: A collection of dictionaries and word lists for use with the 'qdap' package.
Author: Tyler Rinker
Maintainer: Tyler Rinker
DESCRIPTION | 14 +--
MD5 | 164 ++++++++++++++++++-------------------
NAMESPACE | 2
NEWS | 31 +++++-
R/qdapDictionaries-package.R | 60 ++++++++++++-
README.md | 18 ++--
data/BuckleySaltonSWL.rda |binary
data/DICTIONARY.rda |binary
data/Dolch.rda |binary
data/Fry_1000.rda |binary
data/GradyAugmented.rda |binary
data/Leveled_Dolch.rda |binary
data/NAMES.rda |binary
data/NAMES_LIST.rda |binary
data/NAMES_SEX.rda |binary
data/OnixTxtRetToolkitSWL1.rda |binary
data/Top100Words.rda |binary
data/Top200Words.rda |binary
data/Top25Words.rda |binary
data/abbreviations.rda |binary
data/action.verbs.rda |binary
data/adverb.rda |binary
data/amplification.words.rda |binary
data/contractions.rda |binary
data/datalist | 2
data/deamplification.words.rda |binary
data/discourse.markers.alemany.rda |only
data/emoticon.rda |binary
data/function.words.rda |only
data/interjections.rda |binary
data/key.pol.rda |binary
data/key.power.rda |binary
data/key.strength.rda |binary
data/key.syl.rda |binary
data/key.syn.rda |binary
data/labMT.rda |binary
data/negation.words.rda |binary
data/negative.words.rda |binary
data/positive.words.rda |binary
data/power.words.rda |binary
data/preposition.rda |binary
data/strong.words.rda |binary
data/submit.words.rda |binary
data/weak.words.rda |binary
inst/CITATION | 6 -
man/BuckleySaltonSWL.Rd | 3
man/DICTIONARY.Rd | 3
man/Dolch.Rd | 3
man/Fry_1000.Rd | 3
man/GradyAugmented.Rd | 5 -
man/Leveled_Dolch.Rd | 3
man/NAMES.Rd | 5 -
man/NAMES_LIST.Rd | 5 -
man/NAMES_SEX.Rd | 5 -
man/OnixTxtRetToolkitSWL1.Rd | 3
man/Top100Words.Rd | 3
man/Top200Words.Rd | 3
man/Top25Words.Rd | 3
man/abbreviations.Rd | 3
man/action.verbs.Rd | 3
man/adverb.Rd | 3
man/amplification.words.Rd | 3
man/contractions.Rd | 5 -
man/deamplification.words.Rd | 3
man/discourse.markers.alemany.Rd |only
man/emoticon.Rd | 3
man/function.words.Rd |only
man/interjections.Rd | 3
man/key.pol.Rd | 3
man/key.power.Rd | 3
man/key.strength.Rd | 3
man/key.syl.Rd | 3
man/key.syn.Rd | 3
man/labMT.Rd | 3
man/negation.words.Rd | 3
man/negative.words.Rd | 3
man/positive.words.Rd | 3
man/power.words.Rd | 3
man/preposition.Rd | 3
man/print.view_data.Rd | 3
man/qdapDictionaries.Rd | 3
man/strong.words.Rd | 3
man/submit.words.Rd | 3
man/view_data.Rd | 3
man/weak.words.Rd | 3
85 files changed, 268 insertions(+), 153 deletions(-)
Permanent link
Title: Models for Skewed Count Distributions Relevant to Networks
Diff between degreenet versions 1.2 dated 2013-02-03 and 1.3 dated 2015-04-06
Description: Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock
Maintainer: Mark S. Handcock
degreenet-1.2/degreenet/R/simyule.R |only
degreenet-1.2/degreenet/src/f2c.h |only
degreenet-1.3/degreenet/DESCRIPTION | 15 -
degreenet-1.3/degreenet/MD5 | 62 ++---
degreenet-1.3/degreenet/NAMESPACE | 3
degreenet-1.3/degreenet/R/cmp.natural.R | 4
degreenet-1.3/degreenet/R/degreenet.R | 59 -----
degreenet-1.3/degreenet/R/degreenet.utils.R |only
degreenet-1.3/degreenet/R/reedmolloy.R | 78 ++----
degreenet-1.3/degreenet/R/ryule.R |only
degreenet-1.3/degreenet/R/zeta.R |only
degreenet-1.3/degreenet/R/zzz.R | 24 +-
degreenet-1.3/degreenet/data/sweden.RData |binary
degreenet-1.3/degreenet/inst/CITATION | 20 -
degreenet-1.3/degreenet/man/awarmle.Rd | 148 ++++++------
degreenet-1.3/degreenet/man/ayulemle.Rd | 130 +++++------
degreenet-1.3/degreenet/man/bsnb.Rd | 140 ++++++------
degreenet-1.3/degreenet/man/bspln.Rd | 144 ++++++------
degreenet-1.3/degreenet/man/bswar.Rd | 148 ++++++------
degreenet-1.3/degreenet/man/bsyule.Rd | 140 ++++++------
degreenet-1.3/degreenet/man/gyulemle.Rd | 166 +++++++-------
degreenet-1.3/degreenet/man/llgyule.Rd | 154 ++++++-------
degreenet-1.3/degreenet/man/llgyuleall.Rd | 152 ++++++-------
degreenet-1.3/degreenet/man/llyule.Rd | 165 +++++++-------
degreenet-1.3/degreenet/man/llyuleall.Rd | 148 ++++++------
degreenet-1.3/degreenet/man/reedmolloy.Rd | 6
degreenet-1.3/degreenet/man/ryule.Rd | 78 +++---
degreenet-1.3/degreenet/man/simnb.Rd | 66 ++---
degreenet-1.3/degreenet/man/simwar.Rd | 68 ++---
degreenet-1.3/degreenet/man/simyule.Rd | 66 ++---
degreenet-1.3/degreenet/src/cmp.c | 56 +++-
degreenet-1.3/degreenet/src/cmp.h | 2
degreenet-1.3/degreenet/src/dpoilog.c | 6
degreenet-1.3/degreenet/src/zeta.c | 320 +++-------------------------
degreenet-1.3/degreenet/src/zeta.h |only
35 files changed, 1140 insertions(+), 1428 deletions(-)
Title: Package for the Analysis of Lake Physics
Diff between rLakeAnalyzer versions 1.4 dated 2014-07-07 and 1.7.3 dated 2015-04-05
Description: Standardized methods for calculating common important derived
physical features of lakes including water density based based on
temperature, thermal layers, thermocline depth, lake number, Wedderburn
number, Schmidt stability and others.
Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor
Leach, Jake Zwart
Maintainer: Luke Winslow
DESCRIPTION | 16 ++-
MD5 | 51 ++++++-----
NAMESPACE | 21 ++--
R/buoyancy.freq.R | 11 +-
R/center.buoyancy.R |only
R/helper.functions.R | 62 ++++++++++++-
R/internal.energy.R |only
R/lake.number.R | 3
R/layer.temperature.R | 16 +--
R/meta.depths.R | 67 ++++++++++++--
R/schmidt.stability.R | 15 ---
R/thermo.depth.R | 68 ++++++++++++--
R/timeseries.functions.R | 72 ++++++++++++---
R/uStar.R | 24 -----
R/wedderburn.number.R | 3
R/wtr.lineseries.R | 200 +++++++++++++++++++++----------------------
R/wtr.plot.temp.R | 213 ++++++++++++++++++++++++++--------------------
README.md | 14 +--
man/center.buoyancy.Rd |only
man/internal.energy.Rd |only
man/lake.number.Rd | 7 +
man/meta.depths.Rd | 123 ++++++++++++--------------
man/schmidt.stability.Rd | 5 -
man/thermo.depth.Rd | 87 ++++++++----------
man/ts.center.buoyancy.Rd |only
man/ts.meta.depths.Rd | 14 +--
man/uStar.Rd | 5 -
man/wedderburn.number.Rd | 8 +
man/wtr.plot.temp.Rd | 40 ++++----
29 files changed, 676 insertions(+), 469 deletions(-)
Title: Local Correlation, Spatial Inequalities and Other Tools
Diff between lctools versions 0.1-3 dated 2014-07-29 and 0.2 dated 2015-04-05
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou
lctools-0.1-3/lctools/data/GreeceLAs.RData |only
lctools-0.1-3/lctools/data/GreeceNew.RData |only
lctools-0.1-3/lctools/man/GreeceLAs.Rd |only
lctools-0.1-3/lctools/man/GreeceNew.Rd |only
lctools-0.2/lctools/DESCRIPTION | 15 +++++-----
lctools-0.2/lctools/MD5 | 34 ++++++++++++-----------
lctools-0.2/lctools/R/l.moransI.R |only
lctools-0.2/lctools/R/moransI.R | 11 ++++---
lctools-0.2/lctools/data/GR.Municipalities.RData |only
lctools-0.2/lctools/data/VotesGR.RData |binary
lctools-0.2/lctools/data/datalist | 3 --
lctools-0.2/lctools/man/FLQ.Rd | 7 ----
lctools-0.2/lctools/man/GR.Municipalities.Rd |only
lctools-0.2/lctools/man/acc.Rd | 5 ++-
lctools-0.2/lctools/man/gw_variable.Rd | 6 ++--
lctools-0.2/lctools/man/l.moransI.Rd |only
lctools-0.2/lctools/man/lctools-package.Rd | 6 ++--
lctools-0.2/lctools/man/mc_correl.Rd | 2 -
lctools-0.2/lctools/man/mc_spGini.Rd | 6 ++--
lctools-0.2/lctools/man/moransI.Rd | 16 ++++------
lctools-0.2/lctools/man/spGini.Rd | 10 +++---
lctools-0.2/lctools/vignettes |only
22 files changed, 60 insertions(+), 61 deletions(-)
Title: Tools for the Analysis of Ecosystem Metabolism
Diff between LakeMetabolizer versions 1.1 dated 2014-08-11 and 1.3.1 dated 2015-04-05
More information about LakeMetabolizer at CRAN
Description: A collection of tools for the calculation of freewater metabolism.
Author: Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul
Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Maintainer: Luke Winslow
LakeMetabolizer-1.1/LakeMetabolizer/inst/argh.R |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/extdata/Mendota.doobs |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/extdata/Mendota.par |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/extdata/Mendota.rh |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/extdata/Mendota.wnd |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/extdata/Mendota.wtr |only
LakeMetabolizer-1.1/LakeMetabolizer/inst/fig.gen.code.R |only
LakeMetabolizer-1.3.1/LakeMetabolizer/DESCRIPTION | 10
LakeMetabolizer-1.3.1/LakeMetabolizer/MD5 | 109 ++--
LakeMetabolizer-1.3.1/LakeMetabolizer/NAMESPACE | 8
LakeMetabolizer-1.3.1/LakeMetabolizer/R/addNAs.R | 130 ++--
LakeMetabolizer-1.3.1/LakeMetabolizer/R/byeShort.R | 44 -
LakeMetabolizer-1.3.1/LakeMetabolizer/R/calc.lw.net.R | 16
LakeMetabolizer-1.3.1/LakeMetabolizer/R/calc.zeng.R | 17
LakeMetabolizer-1.3.1/LakeMetabolizer/R/date2doy.R | 16
LakeMetabolizer-1.3.1/LakeMetabolizer/R/helper.functions.R | 24
LakeMetabolizer-1.3.1/LakeMetabolizer/R/k.heiskanen.R |only
LakeMetabolizer-1.3.1/LakeMetabolizer/R/k.macIntyre.R | 23
LakeMetabolizer-1.3.1/LakeMetabolizer/R/k.read.R | 87 ++-
LakeMetabolizer-1.3.1/LakeMetabolizer/R/k.read.soloviev.R |only
LakeMetabolizer-1.3.1/LakeMetabolizer/R/k.vachon.R |only
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.R | 22
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.bayesian.R | 11
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.bookkeep.R | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.kalman.R | 261 +++++-----
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.mle.R | 6
LakeMetabolizer-1.3.1/LakeMetabolizer/R/metab.ols.R | 5
LakeMetabolizer-1.3.1/LakeMetabolizer/R/o2.at.sat.R | 6
LakeMetabolizer-1.3.1/LakeMetabolizer/R/par.to.sw.R | 17
LakeMetabolizer-1.3.1/LakeMetabolizer/R/sun.rise.set.R | 14
LakeMetabolizer-1.3.1/LakeMetabolizer/R/sw.to.par.R | 14
LakeMetabolizer-1.3.1/LakeMetabolizer/inst/extdata/mendota.doobs |only
LakeMetabolizer-1.3.1/LakeMetabolizer/inst/extdata/mendota.par |only
LakeMetabolizer-1.3.1/LakeMetabolizer/inst/extdata/mendota.rh |only
LakeMetabolizer-1.3.1/LakeMetabolizer/inst/extdata/mendota.wnd |only
LakeMetabolizer-1.3.1/LakeMetabolizer/inst/extdata/mendota.wtr |only
LakeMetabolizer-1.3.1/LakeMetabolizer/man/calc.lw.net.Rd | 11
LakeMetabolizer-1.3.1/LakeMetabolizer/man/calc.zeng.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/get.Ts.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/get.vars.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/getSchmidt.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/has.vars.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/is.day.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/is.night.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/k.read.Rd | 47 +
LakeMetabolizer-1.3.1/LakeMetabolizer/man/k.read.base.Rd | 56 +-
LakeMetabolizer-1.3.1/LakeMetabolizer/man/k600.2.kGAS.Rd | 7
LakeMetabolizer-1.3.1/LakeMetabolizer/man/load.all.data.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/load.meta.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.Rd | 5
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.bayesian.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.bookkeep.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.kalman.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.mle.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/metab.ols.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/o2.at.sat.Rd | 12
LakeMetabolizer-1.3.1/LakeMetabolizer/man/par.to.sw.Rd | 12
LakeMetabolizer-1.3.1/LakeMetabolizer/man/rmv.vars.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/sun.rise.set.Rd | 4
LakeMetabolizer-1.3.1/LakeMetabolizer/man/sw.to.par.Rd | 10
LakeMetabolizer-1.3.1/LakeMetabolizer/man/temp.kalman.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/var.indx.Rd | 3
LakeMetabolizer-1.3.1/LakeMetabolizer/man/wind.scale.Rd | 7
63 files changed, 652 insertions(+), 413 deletions(-)
Permanent link
Title: Efficient Rolling / Windowed Operations
Diff between RcppRoll versions 0.1.0 dated 2013-01-15 and 0.2.2 dated 2015-04-04
Description: Provides fast and efficient routines for
common rolling / windowed operations. Routines for the
efficient computation of windowed mean, median,
sum, product, minimum, maximum, standard deviation
and variance are provided.
Author: Kevin Ushey
Maintainer: Kevin Ushey
RcppRoll-0.1.0/RcppRoll/R/package_description.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_max.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_mean.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_median.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_min.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_prod.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_sd.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_sum.R |only
RcppRoll-0.1.0/RcppRoll/R/roll_var.R |only
RcppRoll-0.1.0/RcppRoll/man/roll_max.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_mean.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_median.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_min.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_prod.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_sd.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_sum.Rd |only
RcppRoll-0.1.0/RcppRoll/man/roll_var.Rd |only
RcppRoll-0.1.0/RcppRoll/src/Makevars |only
RcppRoll-0.1.0/RcppRoll/src/Makevars.win |only
RcppRoll-0.1.0/RcppRoll/src/source_files.cpp |only
RcppRoll-0.2.2/RcppRoll/DESCRIPTION | 32 -
RcppRoll-0.2.2/RcppRoll/MD5 | 47 -
RcppRoll-0.2.2/RcppRoll/NAMESPACE | 21
RcppRoll-0.2.2/RcppRoll/R/RcppExports.R | 64 --
RcppRoll-0.2.2/RcppRoll/R/RcppRoll-package.R |only
RcppRoll-0.2.2/RcppRoll/R/rollit.R | 702 +++++++++++------------
RcppRoll-0.2.2/RcppRoll/R/rollit_generated.R |only
RcppRoll-0.2.2/RcppRoll/R/rollit_raw.R | 223 +++----
RcppRoll-0.2.2/RcppRoll/README.md |only
RcppRoll-0.2.2/RcppRoll/man/RcppRoll-exports.Rd |only
RcppRoll-0.2.2/RcppRoll/man/RcppRoll.Rd | 53 -
RcppRoll-0.2.2/RcppRoll/man/get_rollit_source.Rd | 47 -
RcppRoll-0.2.2/RcppRoll/man/rollit.Rd | 268 ++++----
RcppRoll-0.2.2/RcppRoll/man/rollit_example.Rd | 79 +-
RcppRoll-0.2.2/RcppRoll/man/rollit_raw.Rd | 76 +-
RcppRoll-0.2.2/RcppRoll/src/RcppExports.cpp | 347 ++++-------
RcppRoll-0.2.2/RcppRoll/src/rollit.cpp |only
37 files changed, 944 insertions(+), 1015 deletions(-)
Title: Moving Grid Adjustment in Plant Breeding Field Trials
Diff between mvngGrAd versions 0.1.4 dated 2014-12-28 and 0.1.5 dated 2015-04-04
Description: Package for moving grid adjustment
in plant breeding field trials.
Author: Frank Technow
Maintainer: Frank Technow
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/CITATION | 6 +++---
man/mvngGrAd-package.Rd | 4 ++--
vignettes/mvngGrAd.Rnw | 2 +-
5 files changed, 14 insertions(+), 14 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Diff between pitchRx versions 1.6 dated 2014-10-27 and 1.7 dated 2015-04-04
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert
DESCRIPTION | 10 +++++-----
MD5 | 46 +++++++++++++++++++++++-----------------------
NAMESPACE | 2 +-
NEWS | 9 ++++++++-
R/data.R | 2 +-
data/fields.rda |binary
data/gids.rda |binary
inst/CITATION | 7 +++----
man/animateFX.Rd | 3 ++-
man/export.Rd | 7 ++++---
man/fields.Rd | 3 ++-
man/getSnapshots.Rd | 3 ++-
man/gids.Rd | 3 ++-
man/interactiveFX.Rd | 3 ++-
man/makeUrls.Rd | 3 ++-
man/nonMLBgids.Rd | 3 ++-
man/pitchRx.Rd | 3 ++-
man/pitches.Rd | 3 ++-
man/players.Rd | 6 +++---
man/scrape.Rd | 3 ++-
man/scrapeFX.Rd | 3 ++-
man/strikeFX.Rd | 3 ++-
man/update_db.Rd | 3 ++-
man/urlsToDataFrame.Rd | 3 ++-
24 files changed, 76 insertions(+), 55 deletions(-)
Title: Clustering using Mixture Models
Diff between MixAll versions 1.0 dated 2015-03-23 and 1.0.2 dated 2015-04-04
Description: Algorithms and methods for estimating parametric mixture models with missing data.
Author: Serge Iovleff [aut, cre]
Maintainer: Serge Iovleff
MixAll-1.0.2/MixAll/DESCRIPTION | 16 -
MixAll-1.0.2/MixAll/MD5 | 95 +++++-----
MixAll-1.0.2/MixAll/NAMESPACE | 1
MixAll-1.0.2/MixAll/R/ClusterAlgo.R | 21 +-
MixAll-1.0.2/MixAll/R/ClusterCategorical.R | 29 +--
MixAll-1.0.2/MixAll/R/ClusterDiagGaussian.R | 28 +-
MixAll-1.0.2/MixAll/R/ClusterGamma.R | 18 +
MixAll-1.0.2/MixAll/R/ClusterHeterogeneous.R | 16 -
MixAll-1.0.2/MixAll/R/ClusterInit.R | 36 +--
MixAll-1.0.2/MixAll/R/ClusterPlot.R | 9
MixAll-1.0.2/MixAll/R/ClusterPoisson.R | 11 -
MixAll-1.0.2/MixAll/R/ClusterStrategy.R | 68 ++++---
MixAll-1.0.2/MixAll/R/IClusterModel.R | 8
MixAll-1.0.2/MixAll/R/MixAll.R | 37 ++-
MixAll-1.0.2/MixAll/R/global.R | 36 +++
MixAll-1.0.2/MixAll/R/missingValues.R | 73 +++----
MixAll-1.0.2/MixAll/build |only
MixAll-1.0.2/MixAll/inst |only
MixAll-1.0.2/MixAll/man/ClusterAlgo-class.Rd | 5
MixAll-1.0.2/MixAll/man/ClusterCategorical-class.Rd | 2
MixAll-1.0.2/MixAll/man/ClusterCategoricalComponent-class.Rd |only
MixAll-1.0.2/MixAll/man/ClusterDiagGaussian-class.Rd | 2
MixAll-1.0.2/MixAll/man/ClusterDiagGaussianComponent-class.Rd |only
MixAll-1.0.2/MixAll/man/ClusterGamma-class.Rd | 2
MixAll-1.0.2/MixAll/man/ClusterGammaComponent-class.Rd |only
MixAll-1.0.2/MixAll/man/ClusterHeterogeneous-class.Rd | 10 -
MixAll-1.0.2/MixAll/man/ClusterInit-class.Rd | 7
MixAll-1.0.2/MixAll/man/ClusterStrategy-class.Rd | 15 -
MixAll-1.0.2/MixAll/man/IClusterComponent-class.Rd | 48 -----
MixAll-1.0.2/MixAll/man/MixAll-package.Rd |only
MixAll-1.0.2/MixAll/man/birds.Rd | 5
MixAll-1.0.2/MixAll/man/clusterAlgo.Rd | 8
MixAll-1.0.2/MixAll/man/clusterCategorical.Rd | 8
MixAll-1.0.2/MixAll/man/clusterDiagGaussian.Rd | 10 -
MixAll-1.0.2/MixAll/man/clusterInit.Rd | 21 +-
MixAll-1.0.2/MixAll/man/clusterStrategy.Rd | 29 +--
MixAll-1.0.2/MixAll/man/extract-methods.Rd | 4
MixAll-1.0.2/MixAll/man/initialize-methods.Rd | 30 +--
MixAll-1.0.2/MixAll/man/missingValues-methods.Rd | 2
MixAll-1.0.2/MixAll/man/print-methods.Rd | 6
MixAll-1.0.2/MixAll/man/show-methods.Rd | 6
MixAll-1.0.2/MixAll/man/summary-methods.Rd | 4
MixAll-1.0.2/MixAll/man/titanic.Rd | 4
MixAll-1.0.2/MixAll/src/ClusterFacade.cpp |only
MixAll-1.0.2/MixAll/src/ClusterFacade.h |only
MixAll-1.0.2/MixAll/src/ClusterLauncher.cpp |only
MixAll-1.0.2/MixAll/src/ClusterLauncher.h |only
MixAll-1.0.2/MixAll/src/RDataHandler.cpp |only
MixAll-1.0.2/MixAll/src/RDataHandler.h |only
MixAll-1.0.2/MixAll/src/clusterMixture.cpp | 18 +
MixAll-1.0.2/MixAll/tests/testPoissonExample.R |only
MixAll-1.0.2/MixAll/vignettes |only
MixAll-1.0/MixAll/man/rtkpp-package.Rd |only
MixAll-1.0/MixAll/src/STK_ClusterFacade.cpp |only
MixAll-1.0/MixAll/src/STK_ClusterLauncher.cpp |only
MixAll-1.0/MixAll/src/STK_RDataHandler.cpp |only
56 files changed, 413 insertions(+), 335 deletions(-)
Title: Density Estimation for Grouped Data
Diff between bda versions 3.2.0-3 dated 2014-05-07 and 5.1.3 dated 2015-04-04
Description: Functions for density estimation based on grouped (or pre-binned)
data.
Author: Bin Wang
Maintainer: Bin Wang
bda-3.2.0-3/bda/R/EDF.R |only
bda-3.2.0-3/bda/R/MediationTest.R |only
bda-3.2.0-3/bda/R/PermTest.R |only
bda-3.2.0-3/bda/R/Survival.R |only
bda-3.2.0-3/bda/R/histosmooth.R |only
bda-3.2.0-3/bda/R/old.R |only
bda-3.2.0-3/bda/R/wkde.R |only
bda-3.2.0-3/bda/man/BiasedSampling.Rd |only
bda-3.2.0-3/bda/man/MLE.Rd |only
bda-3.2.0-3/bda/man/Survival.Rd |only
bda-3.2.0-3/bda/man/bdfmm.Rd |only
bda-3.2.0-3/bda/man/edf.Rd |only
bda-3.2.0-3/bda/man/goftest.Rd |only
bda-3.2.0-3/bda/man/lprde.Rd |only
bda-3.2.0-3/bda/man/npr.Rd |only
bda-3.2.0-3/bda/man/pcb.Rd |only
bda-3.2.0-3/bda/man/permtest.Rd |only
bda-3.2.0-3/bda/man/weighting.Rd |only
bda-3.2.0-3/bda/man/wkde.Rd |only
bda-3.2.0-3/bda/src/DeconKernel.c |only
bda-3.2.0-3/bda/src/KernelWKDE.c |only
bda-3.2.0-3/bda/src/LLSKernel.c |only
bda-3.2.0-3/bda/src/bootkdec.c |only
bda-3.2.0-3/bda/src/bootkdef.f |only
bda-3.2.0-3/bda/src/cwkde.c |only
bda-3.2.0-3/bda/src/fmmc.c |only
bda-3.2.0-3/bda/src/fmmf.f |only
bda-5.1.3/bda/DESCRIPTION | 16
bda-5.1.3/bda/MD5 | 92 +-
bda-5.1.3/bda/NAMESPACE | 85 +-
bda-5.1.3/bda/PORTING | 32
bda-5.1.3/bda/R/EDA.R |only
bda-5.1.3/bda/R/EWD.R |only
bda-5.1.3/bda/R/GBdist.R |only
bda-5.1.3/bda/R/GBsmooth.R |only
bda-5.1.3/bda/R/GLDsmooth.R |only
bda-5.1.3/bda/R/GWD.R |only
bda-5.1.3/bda/R/Laplace.R |only
bda-5.1.3/bda/R/Weibull.R |only
bda-5.1.3/bda/R/bde.R |only
bda-5.1.3/bda/R/bemmix.R | 323 +++++----
bda-5.1.3/bda/R/binning.R |only
bda-5.1.3/bda/R/bootkde.R |only
bda-5.1.3/bda/R/fitDagum.R |only
bda-5.1.3/bda/R/gof.R |only
bda-5.1.3/bda/R/lpsmooth.R | 275 ++++++--
bda-5.1.3/bda/R/lt50.R |only
bda-5.1.3/bda/R/mediation.R |only
bda-5.1.3/bda/R/mixnorm.R | 2
bda-5.1.3/bda/R/oddsratio.R |only
bda-5.1.3/bda/R/ppower.R |only
bda-5.1.3/bda/R/zzz.R | 33
bda-5.1.3/bda/man/Dagum.Rd |only
bda-5.1.3/bda/man/EWD.Rd |only
bda-5.1.3/bda/man/FMKLGLD.Rd |only
bda-5.1.3/bda/man/GBSmooth.Rd |only
bda-5.1.3/bda/man/GBdist.Rd |only
bda-5.1.3/bda/man/GLDFitting.Rd |only
bda-5.1.3/bda/man/GWD.Rd |only
bda-5.1.3/bda/man/bda.Rd | 3
bda-5.1.3/bda/man/bde.Rd | 48 -
bda-5.1.3/bda/man/bemmix.Rd | 30
bda-5.1.3/bda/man/binning.Rd | 79 +-
bda-5.1.3/bda/man/eda.Rd |only
bda-5.1.3/bda/man/fitWeibull.Rd |only
bda-5.1.3/bda/man/gof.Rd |only
bda-5.1.3/bda/man/laplace.Rd |only
bda-5.1.3/bda/man/lpsmooth.Rd |only
bda-5.1.3/bda/man/lt50.logit.Rd |only
bda-5.1.3/bda/man/lt50.logitfit.Rd |only
bda-5.1.3/bda/man/medtest.Rd | 33
bda-5.1.3/bda/man/mixnorm.Rd | 3
bda-5.1.3/bda/man/oddsratio.Rd |only
bda-5.1.3/bda/man/ppower.Rd |only
bda-5.1.3/bda/src/Ckernel.c | 1140 ++++++++++++++++++----------------
bda-5.1.3/bda/src/Fkernel.f | 150 ++++
bda-5.1.3/bda/src/init.c | 127 ---
77 files changed, 1442 insertions(+), 1029 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 1.1-5 dated 2015-01-18 and 1.2-0 dated 2015-04-04
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates
Maintainer: Martin Maechler
Matrix-1.1-5/Matrix/R/associations.R |only
Matrix-1.1-5/Matrix/po/T |only
Matrix-1.2-0/Matrix/ChangeLog | 15
Matrix-1.2-0/Matrix/DESCRIPTION | 10
Matrix-1.2-0/Matrix/MD5 | 270 -
Matrix-1.2-0/Matrix/NAMESPACE | 9
Matrix-1.2-0/Matrix/R/AllClass.R | 33
Matrix-1.2-0/Matrix/R/AllGeneric.R | 13
Matrix-1.2-0/Matrix/R/Auxiliaries.R | 67
Matrix-1.2-0/Matrix/R/Csparse.R | 29
Matrix-1.2-0/Matrix/R/HBMM.R | 16
Matrix-1.2-0/Matrix/R/Math.R | 10
Matrix-1.2-0/Matrix/R/Matrix.R | 12
Matrix-1.2-0/Matrix/R/Ops.R | 30
Matrix-1.2-0/Matrix/R/Summary.R | 25
Matrix-1.2-0/Matrix/R/Tsparse.R | 16
Matrix-1.2-0/Matrix/R/abIndex.R | 20
Matrix-1.2-0/Matrix/R/bind2.R | 185
Matrix-1.2-0/Matrix/R/dMatrix.R | 28
Matrix-1.2-0/Matrix/R/ddenseMatrix.R | 32
Matrix-1.2-0/Matrix/R/denseMatrix.R | 27
Matrix-1.2-0/Matrix/R/dgCMatrix.R | 5
Matrix-1.2-0/Matrix/R/dgeMatrix.R | 3
Matrix-1.2-0/Matrix/R/diagMatrix.R | 308 +
Matrix-1.2-0/Matrix/R/dsCMatrix.R | 11
Matrix-1.2-0/Matrix/R/dsTMatrix.R | 2
Matrix-1.2-0/Matrix/R/dsyMatrix.R | 4
Matrix-1.2-0/Matrix/R/dtrMatrix.R | 8
Matrix-1.2-0/Matrix/R/indMatrix.R | 14
Matrix-1.2-0/Matrix/R/lMatrix.R | 42
Matrix-1.2-0/Matrix/R/ldenseMatrix.R | 6
Matrix-1.2-0/Matrix/R/lgTMatrix.R | 2
Matrix-1.2-0/Matrix/R/lsTMatrix.R | 2
Matrix-1.2-0/Matrix/R/lsparseMatrix.R | 5
Matrix-1.2-0/Matrix/R/ndenseMatrix.R | 11
Matrix-1.2-0/Matrix/R/ngCMatrix.R | 40
Matrix-1.2-0/Matrix/R/ngTMatrix.R | 4
Matrix-1.2-0/Matrix/R/nnzero.R | 2
Matrix-1.2-0/Matrix/R/not.R | 2
Matrix-1.2-0/Matrix/R/nsCMatrix.R | 25
Matrix-1.2-0/Matrix/R/nsTMatrix.R | 2
Matrix-1.2-0/Matrix/R/nsparseMatrix.R | 11
Matrix-1.2-0/Matrix/R/ntCMatrix.R | 29
Matrix-1.2-0/Matrix/R/pMatrix.R | 3
Matrix-1.2-0/Matrix/R/products.R | 752 ++-
Matrix-1.2-0/Matrix/R/rankMatrix.R | 2
Matrix-1.2-0/Matrix/R/spModels.R | 5
Matrix-1.2-0/Matrix/R/sparseMatrix.R | 17
Matrix-1.2-0/Matrix/R/sparseQR.R | 3
Matrix-1.2-0/Matrix/R/sparseVector.R | 4
Matrix-1.2-0/Matrix/R/symmetricMatrix.R | 28
Matrix-1.2-0/Matrix/R/zzz.R | 25
Matrix-1.2-0/Matrix/TODO | 38
Matrix-1.2-0/Matrix/build/vignette.rds |binary
Matrix-1.2-0/Matrix/inst/Doxyfile | 2357 +++++++-----
Matrix-1.2-0/Matrix/inst/NEWS.Rd |only
Matrix-1.2-0/Matrix/inst/doc/Comparisons.pdf |binary
Matrix-1.2-0/Matrix/inst/doc/Design-issues.pdf |binary
Matrix-1.2-0/Matrix/inst/doc/Intro2Matrix.pdf |binary
Matrix-1.2-0/Matrix/inst/doc/Introduction.pdf |binary
Matrix-1.2-0/Matrix/inst/doc/sparseModels.pdf |binary
Matrix-1.2-0/Matrix/inst/include/Matrix.h | 28
Matrix-1.2-0/Matrix/inst/include/Matrix_stubs.c | 74
Matrix-1.2-0/Matrix/inst/po/de/LC_MESSAGES/Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/fr/LC_MESSAGES/Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/fr/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/ko |only
Matrix-1.2-0/Matrix/inst/po/pl/LC_MESSAGES/Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/po/pl/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.2-0/Matrix/inst/test-tools-1.R | 17
Matrix-1.2-0/Matrix/inst/test-tools-Matrix.R | 91
Matrix-1.2-0/Matrix/man/CAex.Rd | 8
Matrix-1.2-0/Matrix/man/Cholesky.Rd | 4
Matrix-1.2-0/Matrix/man/Matrix-class.Rd | 6
Matrix-1.2-0/Matrix/man/TsparseMatrix-class.Rd | 3
Matrix-1.2-0/Matrix/man/USCounties.Rd | 4
Matrix-1.2-0/Matrix/man/boolean-matprod.Rd |only
Matrix-1.2-0/Matrix/man/cBind.Rd | 40
Matrix-1.2-0/Matrix/man/dgTMatrix-class.Rd | 24
Matrix-1.2-0/Matrix/man/dsCMatrix-class.Rd | 12
Matrix-1.2-0/Matrix/man/dtCMatrix-class.Rd | 10
Matrix-1.2-0/Matrix/man/graph2T.Rd | 2
Matrix-1.2-0/Matrix/man/indMatrix-class.Rd | 20
Matrix-1.2-0/Matrix/man/isTriangular.Rd | 3
Matrix-1.2-0/Matrix/man/lsparseMatrix-classes.Rd | 48
Matrix-1.2-0/Matrix/man/matrix-products.Rd | 82
Matrix-1.2-0/Matrix/man/nMatrix-class.Rd | 24
Matrix-1.2-0/Matrix/man/ndenseMatrix-class.Rd | 1
Matrix-1.2-0/Matrix/man/nsparseMatrix-classes.Rd | 21
Matrix-1.2-0/Matrix/man/rankMatrix.Rd | 3
Matrix-1.2-0/Matrix/man/rsparsematrix.Rd | 14
Matrix-1.2-0/Matrix/man/symmetricMatrix-class.Rd | 32
Matrix-1.2-0/Matrix/man/triangularMatrix-class.Rd | 12
Matrix-1.2-0/Matrix/man/uniqTsparse.Rd |only
Matrix-1.2-0/Matrix/po/Matrix.pot | 309 -
Matrix-1.2-0/Matrix/po/R-Matrix.pot | 13
Matrix-1.2-0/Matrix/po/R-de.po | 38
Matrix-1.2-0/Matrix/po/R-en@quot.po |only
Matrix-1.2-0/Matrix/po/R-fr.po | 15
Matrix-1.2-0/Matrix/po/R-ko.po |only
Matrix-1.2-0/Matrix/po/R-pl.po | 21
Matrix-1.2-0/Matrix/po/de.po | 406 +-
Matrix-1.2-0/Matrix/po/en@quot.po |only
Matrix-1.2-0/Matrix/po/fr.po | 307 -
Matrix-1.2-0/Matrix/po/pl.po | 327 -
Matrix-1.2-0/Matrix/po/update-me.sh | 5
Matrix-1.2-0/Matrix/src/CHMfactor.c | 2
Matrix-1.2-0/Matrix/src/Csparse.c | 570 ++
Matrix-1.2-0/Matrix/src/Csparse.h | 19
Matrix-1.2-0/Matrix/src/Mutils.c | 249 -
Matrix-1.2-0/Matrix/src/Mutils.h | 62
Matrix-1.2-0/Matrix/src/TMatrix_as.c | 31
Matrix-1.2-0/Matrix/src/abIndex.c | 3
Matrix-1.2-0/Matrix/src/chm_common.c | 128
Matrix-1.2-0/Matrix/src/chm_common.h | 5
Matrix-1.2-0/Matrix/src/dense.c | 22
Matrix-1.2-0/Matrix/src/dgCMatrix.c | 2
Matrix-1.2-0/Matrix/src/dgTMatrix.c | 16
Matrix-1.2-0/Matrix/src/dgeMatrix.c | 453 +-
Matrix-1.2-0/Matrix/src/dgeMatrix.h | 9
Matrix-1.2-0/Matrix/src/dsCMatrix.c | 2
Matrix-1.2-0/Matrix/src/dsyMatrix.c | 2
Matrix-1.2-0/Matrix/src/dtrMatrix.c | 17
Matrix-1.2-0/Matrix/src/init.c | 23
Matrix-1.2-0/Matrix/src/scripts/0get-SuiteSparse.sh | 48
Matrix-1.2-0/Matrix/tests/Simple.R | 163
Matrix-1.2-0/Matrix/tests/abIndex-tsts.R | 17
Matrix-1.2-0/Matrix/tests/bind.R | 150
Matrix-1.2-0/Matrix/tests/bind.Rout.save | 328 +
Matrix-1.2-0/Matrix/tests/dpo-test.R | 12
Matrix-1.2-0/Matrix/tests/factorizing.R | 10
Matrix-1.2-0/Matrix/tests/group-methods.R | 21
Matrix-1.2-0/Matrix/tests/indexing.R | 15
Matrix-1.2-0/Matrix/tests/indexing.Rout.save | 46
Matrix-1.2-0/Matrix/tests/matprod.R | 282 +
Matrix-1.2-0/Matrix/tests/other-pkgs.R | 2
Matrix-1.2-0/Matrix/tests/validObj.R | 13
140 files changed, 6088 insertions(+), 3277 deletions(-)
Title: Latent Variable Analysis
Diff between lavaan versions 0.5-17 dated 2014-09-30 and 0.5-18 dated 2015-04-04
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb]
Maintainer: Yves Rosseel
lavaan-0.5-17/lavaan/R/FIX_semTools.R |only
lavaan-0.5-17/lavaan/R/lav_deriv.R |only
lavaan-0.5-17/lavaan/R/lav_independence.R |only
lavaan-0.5-17/lavaan/R/lav_information.R |only
lavaan-0.5-17/lavaan/R/lav_vcov.R |only
lavaan-0.5-17/lavaan/man/pmlfit.Rd |only
lavaan-0.5-17/lavaan/man/utils-matrix.Rd |only
lavaan-0.5-18/lavaan/DESCRIPTION | 8
lavaan-0.5-18/lavaan/MD5 | 179 +--
lavaan-0.5-18/lavaan/NAMESPACE | 73 +
lavaan-0.5-18/lavaan/R/00class.R | 17
lavaan-0.5-18/lavaan/R/ctr_estfun.R | 6
lavaan-0.5-18/lavaan/R/ctr_informative_testing.R | 4
lavaan-0.5-18/lavaan/R/ctr_pairwise_fit.R | 2
lavaan-0.5-18/lavaan/R/ctr_pairwise_table.R | 394 +++---
lavaan-0.5-18/lavaan/R/ctr_pml_plrt.R |only
lavaan-0.5-18/lavaan/R/ctr_pml_plrt_nested.R |only
lavaan-0.5-18/lavaan/R/lav_binorm.R | 16
lavaan-0.5-18/lavaan/R/lav_bootstrap.R | 13
lavaan-0.5-18/lavaan/R/lav_bootstrap_lrt.R | 11
lavaan-0.5-18/lavaan/R/lav_constraints.R | 235 +++
lavaan-0.5-18/lavaan/R/lav_cor.R | 17
lavaan-0.5-18/lavaan/R/lav_data.R | 13
lavaan-0.5-18/lavaan/R/lav_export.R | 8
lavaan-0.5-18/lavaan/R/lav_export_mplus.R | 12
lavaan-0.5-18/lavaan/R/lav_fiml.R | 10
lavaan-0.5-18/lavaan/R/lav_fit.R | 20
lavaan-0.5-18/lavaan/R/lav_fit_measures.R | 70 -
lavaan-0.5-18/lavaan/R/lav_func_deriv.R |only
lavaan-0.5-18/lavaan/R/lav_gamma.R | 54
lavaan-0.5-18/lavaan/R/lav_integrate.R | 2
lavaan-0.5-18/lavaan/R/lav_matrix.R | 526 +++++++-
lavaan-0.5-18/lavaan/R/lav_missing.R | 46
lavaan-0.5-18/lavaan/R/lav_model.R | 170 +-
lavaan-0.5-18/lavaan/R/lav_model_compute.R | 13
lavaan-0.5-18/lavaan/R/lav_model_estimate.R | 59 -
lavaan-0.5-18/lavaan/R/lav_model_gradient.R | 100 -
lavaan-0.5-18/lavaan/R/lav_model_gradient_mml.R | 4
lavaan-0.5-18/lavaan/R/lav_model_gradient_pml.R | 38
lavaan-0.5-18/lavaan/R/lav_model_hessian.R |only
lavaan-0.5-18/lavaan/R/lav_model_information.R |only
lavaan-0.5-18/lavaan/R/lav_model_lik.R | 2
lavaan-0.5-18/lavaan/R/lav_model_objective.R | 59 -
lavaan-0.5-18/lavaan/R/lav_model_utils.R | 32
lavaan-0.5-18/lavaan/R/lav_model_vcov.R |only
lavaan-0.5-18/lavaan/R/lav_model_wls.R | 12
lavaan-0.5-18/lavaan/R/lav_modification.R | 519 ++++----
lavaan-0.5-18/lavaan/R/lav_mplus.R | 8
lavaan-0.5-18/lavaan/R/lav_muthen1984.R | 22
lavaan-0.5-18/lavaan/R/lav_norm.R | 34
lavaan-0.5-18/lavaan/R/lav_object_generate.R |only
lavaan-0.5-18/lavaan/R/lav_object_inspect.R | 308 ++++-
lavaan-0.5-18/lavaan/R/lav_object_methods.R | 218 ++-
lavaan-0.5-18/lavaan/R/lav_objective.R | 67 -
lavaan-0.5-18/lavaan/R/lav_ols.R | 10
lavaan-0.5-18/lavaan/R/lav_options.R | 21
lavaan-0.5-18/lavaan/R/lav_partable.R | 339 ++++-
lavaan-0.5-18/lavaan/R/lav_partable_check.R | 10
lavaan-0.5-18/lavaan/R/lav_partable_complete.R |only
lavaan-0.5-18/lavaan/R/lav_partable_constraints.R | 303 +++--
lavaan-0.5-18/lavaan/R/lav_partable_from_lm.R |only
lavaan-0.5-18/lavaan/R/lav_partable_independence.R | 109 +
lavaan-0.5-18/lavaan/R/lav_partable_merge.R |only
lavaan-0.5-18/lavaan/R/lav_partable_unrestricted.R | 96 -
lavaan-0.5-18/lavaan/R/lav_partable_vnames.R | 6
lavaan-0.5-18/lavaan/R/lav_pearson.R | 18
lavaan-0.5-18/lavaan/R/lav_polychor.R | 38
lavaan-0.5-18/lavaan/R/lav_polyserial.R | 14
lavaan-0.5-18/lavaan/R/lav_predict.R | 94 +
lavaan-0.5-18/lavaan/R/lav_prelis.R | 4
lavaan-0.5-18/lavaan/R/lav_representation_lisrel.R | 1238 +++++++++------------
lavaan-0.5-18/lavaan/R/lav_residuals.R | 25
lavaan-0.5-18/lavaan/R/lav_samplestats.R | 56
lavaan-0.5-18/lavaan/R/lav_samplestats_gamma.R |only
lavaan-0.5-18/lavaan/R/lav_simulate.R | 36
lavaan-0.5-18/lavaan/R/lav_standardize.R | 334 +++--
lavaan-0.5-18/lavaan/R/lav_start.R | 3
lavaan-0.5-18/lavaan/R/lav_syntax.R | 26
lavaan-0.5-18/lavaan/R/lav_syntax_independence.R | 6
lavaan-0.5-18/lavaan/R/lav_tables.R | 17
lavaan-0.5-18/lavaan/R/lav_test.R | 116 +
lavaan-0.5-18/lavaan/R/lav_test_LRT.R | 215 +--
lavaan-0.5-18/lavaan/R/lav_test_Wald.R | 8
lavaan-0.5-18/lavaan/R/lav_test_diff.R |only
lavaan-0.5-18/lavaan/R/lav_test_satorra_bentler.R |only
lavaan-0.5-18/lavaan/R/lav_test_score.R |only
lavaan-0.5-18/lavaan/R/lav_utils.R | 11
lavaan-0.5-18/lavaan/R/lavaan-deprecated.R |only
lavaan-0.5-18/lavaan/R/lavaan.R | 109 -
lavaan-0.5-18/lavaan/R/zzz_OLDNAMES.R | 3
lavaan-0.5-18/lavaan/man/lavInspect.Rd | 70 +
lavaan-0.5-18/lavaan/man/lavPredict.Rd |only
lavaan-0.5-18/lavaan/man/lavTablesFit.Rd |only
lavaan-0.5-18/lavaan/man/lavTestLRT.Rd | 31
lavaan-0.5-18/lavaan/man/lav_constraints.Rd |only
lavaan-0.5-18/lavaan/man/lav_matrix.Rd |only
lavaan-0.5-18/lavaan/man/lav_partable.Rd | 67 -
lavaan-0.5-18/lavaan/man/lavaan-class.Rd | 22
lavaan-0.5-18/lavaan/man/lavaan-deprecated.Rd |only
lavaan-0.5-18/lavaan/man/lavaan.Rd | 4
lavaan-0.5-18/lavaan/man/model.syntax.Rd | 20
lavaan-0.5-18/lavaan/man/modificationIndices.Rd | 18
lavaan-0.5-18/lavaan/man/parameterEstimates.Rd | 9
lavaan-0.5-18/lavaan/man/standardizedSolution.Rd | 11
104 files changed, 4351 insertions(+), 2567 deletions(-)
Title: Selected ISO Codes
Diff between ISOcodes versions 2015.01.24 dated 2015-01-24 and 2015.04.04 dated 2015-04-04
Description: ISO language, territory, currency, script and character codes.
Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
currency codes, ISO 15924 script codes, and the ISO 8859 character codes
as well as the UN M.49 area codes.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
data/ISO_639_3.rda |binary
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Wavelet-Based Enhanced FDR for Signal Detection in Noisy Images
Diff between EFDR versions 0.1.0 dated 2015-01-14 and 0.1.1 dated 2015-04-04
Description: Enhanced False Discovery Rate (EFDR) is a tool to detect anomalies
in an image. The image is first transformed into the wavelet domain in
order to decorrelate any noise components, following which the coefficients
at each resolution are standardised. Statistical tests (in a multiple
hypothesis testing setting) are then carried out to find the anomalies. The
power of EFDR exceeds that of standard FDR, which would carry out tests on
every wavelet coefficient: EFDR choose which wavelets to test based on a
criterion described in Shen et al. (2002). The package also provides
elementary tools to interpolate spatially irregular data onto a grid of the
required size. The work is based on Shen, X., Huang, H.-C., and Cressie, N.
'Nonparametric hypothesis testing for a spatial signal.' Journal of the
American Statistical Association 97.460 (2002): 1122-1140.
Author: Andrew Zammit-Mangion [aut, cre],
Hsin-Cheng Huang [aut]
Maintainer: Andrew Zammit-Mangion
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/EFDR_functions.R | 4 ++++
3 files changed, 10 insertions(+), 6 deletions(-)
Title: Manage Time Series with R and PostgreSQL
Diff between timeseriesdb versions 0.2 dated 2015-03-26 and 0.2.1 dated 2015-04-04
Description: Store and organize a large amount of low frequency time series data.
The package was designed to manage a large catalog of official statistics which are
typically published on monthly, quarterly or yearly basis. Thus timeseriesdb is
optimized to handle a large number of lower frequency time series as opposed to a
smaller amount of high frequency time series such as real time data from measuring devices.
Hence timeseriesdb provides the opportunity to store extensive multi-lingual
meta information. The package also provides a web GUI to explore the underlying
PostgreSQL database interactively.
Author: "Matthias Bannert
Maintainer: 'Matthias Bannert'
timeseriesdb-0.2.1/timeseriesdb/DESCRIPTION | 6 -
timeseriesdb-0.2.1/timeseriesdb/MD5 | 11 +-
timeseriesdb-0.2.1/timeseriesdb/NEWS | 7 +
timeseriesdb-0.2.1/timeseriesdb/R/exploreDb.R | 6 -
timeseriesdb-0.2.1/timeseriesdb/README.md | 60 ++++++------
timeseriesdb-0.2.1/timeseriesdb/inst/sql/setup.sql |only
timeseriesdb-0.2/timeseriesdb/inst/sql/ts_data_function.sql |only
timeseriesdb-0.2/timeseriesdb/inst/sql/upsert.sql |only
8 files changed, 51 insertions(+), 39 deletions(-)
Title: Rough - Enhanced - Bayesian Finite Mixture Modeling
Diff between rebmix versions 2.7.0 dated 2015-02-10 and 2.7.1 dated 2015-04-04
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode
DESCRIPTION | 10 ++++----
MD5 | 38 ++++++++++++++++----------------
R/RCLSMIX.R | 2 -
R/REBMIX.R | 2 -
R/RNGMIX.R | 2 -
build/vignette.rds |binary
data/adult.rda |binary
data/galaxy.rda |binary
data/truck.rda |binary
data/weibull.rda |binary
data/weibullnormal.rda |binary
data/wine.rda |binary
demo/rebmix.galaxy.R | 10 +++++---
demo/rebmix.mixed.continuous.discrete.R | 8 ++++--
demo/rebmix.multivariate.normal.R | 3 --
demo/rebmix.univariate.normal.R | 14 -----------
inst/NEWS.Rd | 8 +++++-
inst/doc/rebmix.pdf |binary
src/rebmixf.c | 2 -
src/rngmixf.c | 2 -
20 files changed, 49 insertions(+), 52 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Diff between GUTS versions 0.4.12 dated 2015-04-02 and 0.4.14 dated 2015-04-03
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert
Maintainer: Sören Vogel
DESCRIPTION | 14 +-
MD5 | 10 -
R/GUTS.R | 3
man/Rcpp_GUTS-class.Rd | 261 +++++++++++++++++++++++++++++++------------------
man/diazinon.Rd | 7 -
src/GUTS.cpp | 2
6 files changed, 188 insertions(+), 109 deletions(-)
Title: Exploring Water Quality Monitoring Data
Diff between wq versions 0.4-1 dated 2014-05-14 and 0.4.3 dated 2015-04-03
Description: Functions to assist in the processing and exploration of data from
environmental monitoring programs. The name "wq" stands for "water quality"
and reflects the original focus on time series data for physical and
chemical properties of water, as well as the plankton. Intended for programs
that sample approximately monthly at discrete stations, a feature of many
legacy data sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby
wq-0.4-1/wq/R/ammFrac.R |only
wq-0.4-1/wq/R/layOut.R |only
wq-0.4-1/wq/man/ammFrac.Rd |only
wq-0.4-1/wq/man/layOut.Rd |only
wq-0.4.3/wq/DESCRIPTION | 25 +++----
wq-0.4.3/wq/MD5 | 52 ++++++--------
wq-0.4.3/wq/NAMESPACE | 6 -
wq-0.4.3/wq/NEWS | 6 +
wq-0.4.3/wq/R/WqData-class.R | 1
wq-0.4.3/wq/R/eofNum.R | 2
wq-0.4.3/wq/R/eofPlot.R | 3
wq-0.4.3/wq/R/mannKen.R | 4 -
wq-0.4.3/wq/R/oxySol.R | 6 -
wq-0.4.3/wq/R/plotSeason.R | 5 -
wq-0.4.3/wq/R/plotTs.R | 3
wq-0.4.3/wq/R/plotTsAnom.R | 3
wq-0.4.3/wq/R/plotTsTile.R | 1
wq-0.4.3/wq/R/seaRoll.R | 1
wq-0.4.3/wq/R/seasonTrend.R | 1
wq-0.4.3/wq/R/tsMake.R | 1
wq-0.4.3/wq/R/wqData.R | 2
wq-0.4.3/wq/build/vignette.rds |binary
wq-0.4.3/wq/inst/doc/wq-package.R | 125 +++++++++++++----------------------
wq-0.4.3/wq/inst/doc/wq-package.Rnw | 31 --------
wq-0.4.3/wq/inst/doc/wq-package.pdf |binary
wq-0.4.3/wq/man/wq-package.Rd | 8 --
wq-0.4.3/wq/man/wqData.Rd | 2
wq-0.4.3/wq/vignettes/wq-package.Rnw | 31 --------
wq-0.4.3/wq/vignettes/wqFlow.pdf |binary
29 files changed, 103 insertions(+), 216 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.7-07 dated 2014-08-27 and 1.8-03 dated 2015-04-03
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su
CHANGELOG | 6
DESCRIPTION | 10
MD5 | 26 -
NAMESPACE | 5
R/bayesglm.R | 1239 +++++++++++++++++---------------------------------
R/bayespolr.R | 139 ++---
R/binnedplot.R | 24
R/sim.R | 8
man/bayesglm.Rd | 9
man/bayespolr.Rd | 136 ++---
man/extractDIC.mer.Rd | 2
man/lalonde.Rd | 4
man/mcsamp.Rd | 2
man/traceplot.Rd | 2
14 files changed, 631 insertions(+), 981 deletions(-)
Title: R/KEA Interface
Diff between RKEA versions 0.0-5 dated 2015-02-20 and 0.0-6 dated 2015-04-03
Description: An R interface to KEA (Version 5.0).
KEA (for Keyphrase Extraction Algorithm) allows for extracting
keyphrases from text documents. It can be either used for free
indexing or for indexing with a controlled vocabulary. For more
information see
Author: Ingo Feinerer [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
RKEA-0.0-5/RKEA/configure |only
RKEA-0.0-5/RKEA/inst/java |only
RKEA-0.0-5/RKEA/inst/stopwords |only
RKEA-0.0-5/RKEA/java |only
RKEA-0.0-5/RKEA/tools |only
RKEA-0.0-6/RKEA/DESCRIPTION | 37 +++-------------------
RKEA-0.0-6/RKEA/MD5 | 33 +++++--------------
RKEA-0.0-6/RKEA/NAMESPACE | 1
RKEA-0.0-6/RKEA/R/kea.R | 35 ++++++++++++++++++++
RKEA-0.0-6/RKEA/R/onLoad.R | 5 --
RKEA-0.0-6/RKEA/inst/doc/kea.R | 22 ++++++++++---
RKEA-0.0-6/RKEA/inst/doc/kea.Rnw | 62 ++++++++++++++++++++++++++++++++-----
RKEA-0.0-6/RKEA/inst/doc/kea.pdf |binary
RKEA-0.0-6/RKEA/man/createModel.Rd | 2 -
RKEA-0.0-6/RKEA/vignettes/kea.Rnw | 62 ++++++++++++++++++++++++++++++++-----
15 files changed, 178 insertions(+), 81 deletions(-)
Title: Test Analysis Modules
Diff between TAM versions 1.5-2 dated 2015-02-24 and 1.6-0 dated 2015-04-03
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 10
MD5 | 72 ++--
NAMESPACE | 4
R/IRT.drawPV.R |only
R/TAM.ic.R | 2
R/TAM.itempartable.R | 8
R/calc_posterior.v2.R | 8
R/designMatrices.mfr.R | 184 ++++++----
R/designMatrices.mfr2.R | 25 -
R/designMatrices.mfr_aux.R | 210 ++++++++----
R/designMatrices_aux.R | 100 ++++-
R/designMatrices_aux2.R | 4
R/lavaanify.sirt.v1.R | 4
R/mfr.dataprep.R |only
R/mml.3pl.TAM.ic.R | 4
R/plot.tam.R | 449 +++++++++++++++++---------
R/summary.tam.R | 5
R/tam.fa.R | 8
R/tam.mml.2pl.R | 4
R/tam.mml.3pl.R | 4
R/tam.mml.R | 8
R/tam.mml.mfr.R | 168 ++++++---
R/tam.parameterfix.defaults.R | 2
R/tam.wle.R | 26 +
R/tamaan.3pl.trait.R | 8
R/tamaan.R | 21 -
R/tamaanify.R | 4
R/tamaanify.modelprior.R | 5
R/tamaanify.proc.analysis.R | 4
R/tamaanify.tam.mml.3pl.designMatrices.OLCA.R | 2
R/tamcat.R |only
inst/NEWS | 41 ++
man/IRT.drawPV.Rd |only
man/TAM-package.Rd | 2
man/lavaanify.IRT.Rd | 2
man/plot.tam.Rd | 18 -
man/tam.mml.Rd | 103 +++++
man/tamaan.Rd | 22 +
src/tam_mml_mfr_helper.cpp | 98 +++++
39 files changed, 1181 insertions(+), 458 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.5 dated 2015-02-03 and 0.6 dated 2015-04-03
Description: An R interface to Google's open source, high performance JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition.
In addition, this package implements typed arrays as specified in ECMA 6 in order to
support high-performance computing and libraries compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
V8-0.5/V8/inst/include |only
V8-0.6/V8/DESCRIPTION | 21 ++---
V8-0.6/V8/MD5 | 38 +++++----
V8-0.6/V8/NAMESPACE | 2
V8-0.6/V8/NEWS |only
V8-0.6/V8/R/JS.R |only
V8-0.6/V8/R/V8.R | 39 ++++++---
V8-0.6/V8/R/tab_complete.R |only
V8-0.6/V8/build/vignette.rds |binary
V8-0.6/V8/inst/doc/npm.R | 4 -
V8-0.6/V8/inst/doc/npm.Rmd | 4 -
V8-0.6/V8/inst/doc/npm.html | 8 +-
V8-0.6/V8/inst/doc/v8_intro.R | 16 ++--
V8-0.6/V8/inst/doc/v8_intro.Rmd | 18 ++--
V8-0.6/V8/inst/doc/v8_intro.html | 29 +++----
V8-0.6/V8/man/JS.Rd |only
V8-0.6/V8/man/new_context.Rd | 8 +-
V8-0.6/V8/src/Makevars.win | 6 -
V8-0.6/V8/src/RcppExports.cpp | 154 ++++++++++++++-------------------------
V8-0.6/V8/src/V8_types.h |only
V8-0.6/V8/tools/winlibs.R | 4 -
V8-0.6/V8/vignettes/npm.Rmd | 4 -
V8-0.6/V8/vignettes/v8_intro.Rmd | 18 ++--
23 files changed, 174 insertions(+), 199 deletions(-)
Title: Relative Simulator
Diff between relSim versions 0.1-47 dated 2012-07-24 and 0.2-0 dated 2015-04-03
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran
relSim-0.1-47/relSim/R/randomProfiles.R |only
relSim-0.1-47/relSim/desktop.ini |only
relSim-0.2-0/relSim/DESCRIPTION | 17
relSim-0.2-0/relSim/MD5 | 51 -
relSim-0.2-0/relSim/NAMESPACE | 19
relSim-0.2-0/relSim/R/IBS.R | 47 -
relSim-0.2-0/relSim/R/RcppExports.R |only
relSim-0.2-0/relSim/R/blockSim.R | 206 +---
relSim-0.2-0/relSim/R/breedFst.R | 102 --
relSim-0.2-0/relSim/R/calcFst.R | 92 --
relSim-0.2-0/relSim/R/estimateQuantile.R | 449 ++++-----
relSim-0.2-0/relSim/R/fetchBMdata.R | 16
relSim-0.2-0/relSim/R/locusIBS.R | 66 -
relSim-0.2-0/relSim/R/lrMix.R | 33
relSim-0.2-0/relSim/R/lrPC.R | 97 --
relSim-0.2-0/relSim/R/lrSib.R | 92 --
relSim-0.2-0/relSim/R/print.population.R | 16
relSim-0.2-0/relSim/R/randomPCPairs.R | 118 --
relSim-0.2-0/relSim/R/randomProfilePairs.R | 98 --
relSim-0.2-0/relSim/R/randomSib.R | 57 -
relSim-0.2-0/relSim/R/randomSibPairs.R | 117 +-
relSim-0.2-0/relSim/README.md |only
relSim-0.2-0/relSim/data/USCaucs.rda |binary
relSim-0.2-0/relSim/data/fbiCaucs.rda |binary
relSim-0.2-0/relSim/man/blockSim.Rd | 180 +--
relSim-0.2-0/relSim/src/RcppExports.cpp |only
relSim-0.2-0/relSim/src/breed.cpp | 160 +--
relSim-0.2-0/relSim/src/calcFst.cpp | 356 +++----
relSim-0.2-0/relSim/src/relSim.cpp | 1313 +++++++++++++++--------------
29 files changed, 1662 insertions(+), 2040 deletions(-)
Title: The Multivariate Normal and t Distributions
Diff between mnormt versions 1.5-1 dated 2014-06-29 and 1.5-2 dated 2015-04-03
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via a non-Monte Carlo method. Different routines
are used for the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini
mnormt-1.5-1/mnormt/ChangeLog |only
mnormt-1.5-2/mnormt/DESCRIPTION | 16 +++++-----
mnormt-1.5-2/mnormt/MD5 | 10 +++---
mnormt-1.5-2/mnormt/NEWS |only
mnormt-1.5-2/mnormt/R/mnormt.R | 31 +++++++++++---------
mnormt-1.5-2/mnormt/man/dmnorm.Rd | 49 ++++++++++++++++++++++++++------
mnormt-1.5-2/mnormt/man/dmt.Rd | 58 ++++++++++++++++++++++++++++++--------
7 files changed, 117 insertions(+), 47 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-19 0.99.1
2014-11-15 0.99.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-04 1.5
2013-09-13 1.4
2013-08-23 1.3
Title: Tools to Convert ODM Files
Diff between ODMconverter versions 2.0 dated 2014-05-19 and 2.1 dated 2015-04-02
Description: Transformation of 'ODM' (see http://www.cdisc.org/odm) files into R format, Microsoft Office format, 'CDA' format and vice versa. 'ODM' format is commonly used in clinical trials. Semantic annotation (such as 'UMLS', 'SNOMED' or 'LOINC' codes) are transformed accordingly.
Author: Martin Dugas
Maintainer: Martin Dugas
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/ODM2CDA.R | 4 ++--
R/ODM2R.R | 2 +-
4 files changed, 12 insertions(+), 12 deletions(-)
Title: Solve Systems of Nonlinear Equations
Diff between nleqslv versions 2.6 dated 2015-03-04 and 2.7 dated 2015-04-02
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 13 +-
MD5 | 36 +++--
NEWS | 5
R/nleqslv.R | 1
man/nleqslv-package.Rd | 8 -
man/nleqslv.Rd | 293 ++++++++++++++++++++++++++++------------------
src/nleqslv.c | 9 -
src/nwbjac.f |only
src/nwbrdn.f | 80 ++++++++----
src/nwddlg.f | 6
src/nwnjac.f | 56 ++++++--
src/nwnleq.f | 2
src/nwnwtn.f | 2
src/nwout.c | 4
src/nwutil.f | 49 +++++++
tests/singular1.R |only
tests/singular1.Rout |only
tests/singular1.Rout.save |only
tests/singular2.R |only
tests/singular2.Rout |only
tests/singular2.Rout.save |only
tests/singular3.R |only
tests/singular3.Rout |only
tests/singular3.Rout.save |only
24 files changed, 388 insertions(+), 176 deletions(-)
Title: An R Package for the Analysis of Stable Matchings
Diff between matchingMarkets versions 0.1-2 dated 2014-11-23 and 0.1-3 dated 2015-04-02
More information about matchingMarkets at CRAN
Description: Implements a structural estimator to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein
DESCRIPTION | 21 +++++++++----------
MD5 | 44 ++++++++++++++++++++++-------------------
NAMESPACE | 3 +-
R/RcppExports.R | 4 +--
R/khb.R | 18 +++++++++-------
R/mce.R |only
R/mfx.R | 8 +++----
R/stabit.R | 30 ++++++++++++++++++---------
R/stabsim.R | 20 +++++++++++++-----
R/ttc.R | 2 -
data/baac00.RData |binary
data/datalist | 1
data/klein14.RData |only
man/daa.Rd | 2 -
man/khb.Rd | 20 ++++++++++--------
man/klein14.Rd |only
man/matchingMarkets-package.Rd | 4 +--
man/mce.Rd |only
man/mfx.Rd | 10 ++++-----
man/plp.Rd | 6 ++---
man/stabit.Rd | 13 ++++--------
man/stabsim.Rd | 6 ++---
man/ttc.Rd | 4 +--
src/RcppExports.cpp | 7 +++---
src/stabitCpp.cpp | 26 +++++++++++++++---------
25 files changed, 142 insertions(+), 107 deletions(-)
Permanent link
Title: Cost Constrained FLux Balance Analysis: MetabOlic Modeling with
ENzyme kineTics (MOMENT)
Diff between sybilccFBA versions 1.0.0 dated 2014-04-02 and 2.0.0 dated 2015-04-02
Description: An implementation of a cost constrained flux balance analysis technique (i.e. MetabOlic Modeling with ENzyme kineTics (MOMENT)).
MOMENT uses enzyme kinetic data and enzyme molecular weights to constrain flux balance analysis(FBA) and it is described in
Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass
Yield by a Metabolic Network with Kinetic Parameters, 8(7). doi:10.1371/journal.pcbi.1002575.
This package also implements an improvement of MOMENT that considers multi-functional enzymes.
FBA is a mathematical technique to find fluxes in metabolic models at steady state.
It is described in Orth, J.D., Thiele, I. and Palsson, B.O. What is flux balance analysis? Nat. Biotech. 28, 245-248(2010).
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 18 ++++++++++++------
MD5 | 26 +++++++++++++++++---------
R/calc_MW.R | 2 +-
R/cfba_moment.R | 8 +++++++-
R/cfba_moment_mr.R |only
R/cfba_moment_pw.R | 10 ++++++++--
data/iAF1260.RData |binary
data/iJO1366.RData |only
data/iMM904.RData |binary
data/kcat.RData |binary
data/mw.RData |binary
data/yst_kcat.RData |only
data/yst_mw.RData |only
man/cfba_moment.Rd | 17 +++++++++++------
man/cfba_moment_mr.Rd |only
man/iJO1366.Rd |only
man/yst_kcat.Rd |only
man/yst_mw.Rd |only
18 files changed, 56 insertions(+), 25 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Diff between sglasso versions 1.1-0 dated 2014-09-22 and 1.1-1 dated 2015-04-02
Description: RCON(V, E) models (Højsgaard, et al.,2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro
ChangeLog | 9 +++++++++
DESCRIPTION | 13 +++++++------
MD5 | 37 +++++++++++++++++++------------------
NAMESPACE | 1 +
R/fglasso_model2mask.R | 8 +++++++-
R/klcv.R | 4 +++-
R/loglik.R | 2 +-
R/mask2Te.R | 4 +++-
R/print.klcv.R |only
R/sglasso.fit.R | 4 ++--
man/Kh.Rd | 2 +-
man/fglasso.Rd | 16 ++++++++++------
man/klcv.Rd | 7 ++++---
man/sglasso-package.Rd | 6 +++---
man/sglasso.Rd | 2 +-
man/summary.sglasso.Rd | 4 ++--
src/sglasso_ccd_path.f90 | 15 +--------------
src/sglasso_ccd_single.f90 | 15 +--------------
src/sglasso_ccm_path.f90 | 19 +++----------------
src/sglasso_ccm_single.f90 | 13 -------------
20 files changed, 78 insertions(+), 103 deletions(-)
Title: Calculation of Rarity Indices for Species and Assemblages of
Species
Diff between Rarity versions 1.3-1 dated 2015-03-17 and 1.3-4 dated 2015-04-02
Description: Allows calculation of rarity weights for species and indices of rarity for assemblages of species according to different methods (Leroy et al. 2012, 2013).
Author: Boris Leroy
Maintainer: Boris Leroy
Rarity-1.3-1/Rarity/R/rarity_indices.R |only
Rarity-1.3-4/Rarity/DESCRIPTION | 8
Rarity-1.3-4/Rarity/MD5 | 21 -
Rarity-1.3-4/Rarity/R/correlation_plots.R | 10
Rarity-1.3-4/Rarity/R/rarity_weights.R | 69 ++--
Rarity-1.3-4/Rarity/R/relative_rarity.R |only
Rarity-1.3-4/Rarity/R/summed_rarity.R | 425 ++++++++++++++----------------
Rarity-1.3-4/Rarity/man/Irr.Rd | 14
Rarity-1.3-4/Rarity/man/Isr.Rd | 8
Rarity-1.3-4/Rarity/man/rWeights.Rd | 14
Rarity-1.3-4/Rarity/man/spid.occ.Rd | 7
Rarity-1.3-4/Rarity/tests |only
12 files changed, 298 insertions(+), 278 deletions(-)
Title: Unified Multiple Testing Procedures
Diff between mutoss versions 0.1-9 dated 2015-03-12 and 0.1-10 dated 2015-04-02
Description: The Mutoss package and accompanying mutossGUI package are
designed to ease the application and comparison of multiple
hypothesis testing procedures.
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/Hommel.R | 6 +++---
build/vignette.rds |binary
inst/doc/quickstart.pdf |binary
inst/doc/simToolManual.pdf |binary
6 files changed, 11 insertions(+), 11 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Diff between GUTS versions 0.3.5 dated 2014-05-05 and 0.4.12 dated 2015-04-02
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert
Maintainer: Sören Vogel
DESCRIPTION | 16
MD5 | 22
R/GUTS.R | 68 +-
configure | 20
data/diazinon.RData |binary
man/Rcpp_GUTS-class.Rd | 353 ++++++-------
src/GUTS.cpp | 840 ++++++++++++++++++++-------------
src/GUTS.h | 534 ++++++++++++++------
src/GUTS_Rcpp.cpp | 91 ++-
src/GUTS_calcLoglikelihood.cpp | 69 +-
src/GUTS_calcSample.cpp | 238 ++++++---
src/GUTS_calcSurvivalProbabilities.cpp | 512 +++++++++++---------
12 files changed, 1676 insertions(+), 1087 deletions(-)
Title: Gaussian Processes Modeling
Diff between GPfit versions 0.2-1 dated 2014-09-03 and 1.0-0 dated 2015-04-02
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld, Hugh Chipman, Pritam Ranjan
Maintainer: Hugh Chipman
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NAMESPACE | 7 ++++++-
NEWS |only
inst |only
man/GP_fit.Rd | 39 ++++++++++++++++++++++++---------------
man/GPfit-package.Rd | 9 ++++++---
man/corr_matrix.Rd | 21 ++++++++++++++-------
8 files changed, 61 insertions(+), 35 deletions(-)
Title: Geometric Morphometric Analyses of 2d/3D Landmark Data
Diff between geomorph versions 2.1.3 dated 2015-02-12 and 2.1.4 dated 2015-04-02
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.1.3/geomorph/R/define.links.R |only
geomorph-2.1.3/geomorph/R/define.modules.R |only
geomorph-2.1.3/geomorph/R/findMeanSpec.R |only
geomorph-2.1.3/geomorph/R/morphol.disparity.R |only
geomorph-2.1.3/geomorph/R/plotAllometry.R |only
geomorph-2.1.3/geomorph/R/plotOutliers.R |only
geomorph-2.1.3/geomorph/R/warpRefMesh.R |only
geomorph-2.1.3/geomorph/R/warpRefOutline.R |only
geomorph-2.1.4/geomorph/DESCRIPTION | 12
geomorph-2.1.4/geomorph/MD5 | 90 ++--
geomorph-2.1.4/geomorph/NEWS | 29 +
geomorph-2.1.4/geomorph/R/advanced.procD.lm.r | 34 -
geomorph-2.1.4/geomorph/R/bilat.symmetry.r | 2
geomorph-2.1.4/geomorph/R/build.template.r | 190 ++++----
geomorph-2.1.4/geomorph/R/define.links.r |only
geomorph-2.1.4/geomorph/R/define.modules.r |only
geomorph-2.1.4/geomorph/R/define.sliders.3d.r | 188 ++++----
geomorph-2.1.4/geomorph/R/digitsurface.r | 198 ++++----
geomorph-2.1.4/geomorph/R/editTemplate.r | 114 ++---
geomorph-2.1.4/geomorph/R/estimate.missing.r | 8
geomorph-2.1.4/geomorph/R/findMeanSpec.r |only
geomorph-2.1.4/geomorph/R/geomorph.support.code.r | 39 -
geomorph-2.1.4/geomorph/R/gpagen.r | 20
geomorph-2.1.4/geomorph/R/morphol.disparity.r |only
geomorph-2.1.4/geomorph/R/pairwise.slope.test.r | 24 -
geomorph-2.1.4/geomorph/R/pairwiseD.test.r | 23 -
geomorph-2.1.4/geomorph/R/plotAllometry.r |only
geomorph-2.1.4/geomorph/R/plotGMPhyloMorphoSpace.r | 152 +++---
geomorph-2.1.4/geomorph/R/plotOutliers.r |only
geomorph-2.1.4/geomorph/R/procD.lm.r | 45 --
geomorph-2.1.4/geomorph/R/procD.pgls.r | 19
geomorph-2.1.4/geomorph/R/read.morphologika.r | 8
geomorph-2.1.4/geomorph/R/readland.tps.r | 296 ++++++-------
geomorph-2.1.4/geomorph/R/trajectory.analysis.r | 468 ++++++++++-----------
geomorph-2.1.4/geomorph/R/warpRefMesh.r |only
geomorph-2.1.4/geomorph/R/warpRefOutline.r |only
geomorph-2.1.4/geomorph/man/advanced.procD.lm.Rd | 15
geomorph-2.1.4/geomorph/man/define.links.Rd | 2
geomorph-2.1.4/geomorph/man/define.modules.Rd | 2
geomorph-2.1.4/geomorph/man/estimate.missing.Rd | 6
geomorph-2.1.4/geomorph/man/findMeanSpec.Rd | 2
geomorph-2.1.4/geomorph/man/geomorph-package.Rd | 2
geomorph-2.1.4/geomorph/man/gpagen.Rd | 8
geomorph-2.1.4/geomorph/man/morphol.disparity.Rd | 6
geomorph-2.1.4/geomorph/man/pairwise.slope.test.Rd | 13
geomorph-2.1.4/geomorph/man/pairwiseD.test.Rd | 5
geomorph-2.1.4/geomorph/man/plotAllometry.Rd | 29 -
geomorph-2.1.4/geomorph/man/plotOutliers.Rd | 12
geomorph-2.1.4/geomorph/man/procD.lm.Rd | 19
geomorph-2.1.4/geomorph/man/procD.pgls.Rd | 8
geomorph-2.1.4/geomorph/man/read.morphologika.Rd | 2
geomorph-2.1.4/geomorph/man/trajectory.analysis.Rd | 2
geomorph-2.1.4/geomorph/man/warpRefMesh.Rd | 13
geomorph-2.1.4/geomorph/man/warpRefOutline.Rd | 2
54 files changed, 1064 insertions(+), 1043 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Diff between geoBayes versions 0.2.150308 dated 2015-03-08 and 0.2.150402 dated 2015-04-02
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou
Maintainer: Evangelos Evangelou
DESCRIPTION | 18 -
MD5 | 52 ++--
NAMESPACE | 2
NEWS | 4
R/calcbf.R | 4
man/bf1skel.Rd | 3
man/bf2new.Rd | 3
man/bf2optim.Rd | 3
man/bfse.Rd | 3
man/comparebinlinks.Rd | 3
man/ebsglmm.Rd | 3
man/ebstrga.Rd | 3
man/geoBayes.Rd | 3
man/linkfcn.Rd | 7
man/mcmcmake.Rd | 3
man/mcsglmm.Rd | 3
man/mcstrga.Rd | 3
man/mkpredgrid2d.Rd | 3
man/plotbf2.Rd | 3
man/rhizoctonia.Rd | 3
man/stackdata.Rd | 3
src/bfsp.f90 | 30 +-
src/calcb2.f90 | 40 +--
src/covfun.f90 | 12 -
src/llik.f90 | 32 +--
src/mcsp2.f90 | 510 +++++++++++++++++++++++++++++--------------------
src/mcspz0.f90 | 8
27 files changed, 448 insertions(+), 316 deletions(-)
Title: Inverse Regression for Text Analysis
Diff between textir versions 2.0-2 dated 2014-01-30 and 2.0-3 dated 2015-04-01
Description: Multinomial [inverse] regression inference for text documents and associated attributes. Provides fast sparse multinomial logistic regression for phrase counts. A minimalist partial least squares routine is also included. Note that the topic modeling capability of textir is now a separate package, maptpx.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 7 +++----
MD5 | 6 +++---
README.md | 6 ++++--
inst/CITATION | 4 ++--
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Distance Sampling Analyses
Diff between Rdistance versions 1.1 dated 2012-12-07 and 1.2.1 dated 2015-04-01
Description: Analysis of distance sampling data collected on line transect surveys. Estimates distance-based detection functions and abundances.
Author: Trent McDonald [cre, aut],
Ryan Nielson [aut],
Jason Carlisle [aut],
James Griswald [ctb],
Joel Reynolds [ctb],
Pham Quang [ctb],
Earl Becker [ctb],
Aaron Christ [ctb],
Brook Russelland [ctb],
Patrick McKann [ctb]
Maintainer: Trent McDonald
DESCRIPTION | 42 +++-
MD5 | 41 ++--
NAMESPACE | 1
R/AIC.dfunc.R | 12 -
R/F.abund.estim.r | 414 +++++++++++++++++++++++++++--------------------
R/F.automated.CDA.r | 274 ++++++++++++++-----------------
R/F.dfunc.estim.R | 113 +++++-------
R/perp.dists.R |only
R/zzz.R | 21 +-
data |only
man/AIC.dfunc.Rd | 43 ++--
man/ESW.Rd | 37 ++--
man/F.abund.estim.Rd | 126 ++++++--------
man/F.automated.CDA.Rd | 172 +++++++++----------
man/F.dfunc.estim.Rd | 94 +++-------
man/F.gx.estim.Rd | 3
man/Gamma.like.Rd | 3
man/Rdistance-package.Rd | 57 ++----
man/coef.dfunc.Rd | 33 ++-
man/perp.dists.Rd |only
man/sparrow.covs.Rd |only
man/sparrow.dists.Rd |only
man/uniform.like.Rd | 12 -
vignettes |only
24 files changed, 768 insertions(+), 730 deletions(-)
Title: Predicting Species Accumulation Curves
Diff between preseqR versions 1.1 dated 2015-03-11 and 1.1.1 dated 2015-04-01
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/continued_fraction.R | 28 ++++++++++++++++++----------
R/simulation.R | 4 ++--
R/ztnb.R | 12 +++++++++---
README.md | 5 +++++
man/preseqR.interpolate.distinct.Rd | 4 ++--
man/preseqR.nonreplace.sampling.Rd | 4 ++--
man/preseqR.rfa.curve.Rd | 4 ++--
man/preseqR.rfa.species.accum.curve.Rd | 8 ++++----
man/preseqR.simu.hist.Rd | 6 +++---
man/preseqR.ztnb.em.Rd | 4 ++--
man/preseqR.ztnb.estimate.Rd | 4 ++--
man/preseqR.ztnb.species.accum.curve.Rd | 4 ++--
14 files changed, 70 insertions(+), 51 deletions(-)
Title: Permutational Algorithm to Simulate Survival Data
Diff between PermAlgo versions 1.0 dated 2010-10-12 and 1.1 dated 2015-04-01
Description: This version of the permutational algorithm generates a
dataset in which event and censoring times are conditional on
an user-specified list of covariates, some or all of which are
time-dependent.
Author: Marie-Pierre Sylvestre, Thad Edens, Todd MacKenzie, Michal
Abrahamowicz
Maintainer: Marie-Pierre Sylvestre
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
inst/CITATION | 8 ++++----
3 files changed, 12 insertions(+), 12 deletions(-)
Title: MAP Estimation of Topic Models
Diff between maptpx versions 1.9-1 dated 2013-12-01 and 1.9-2 dated 2015-04-01
Description: Posterior maximization for topic models (LDA) in text analysis,
as described in Taddy (2012) `on estimation and selection for topic models'. Previous versions of this code were included as part of the textir package. If you want to take advantage of openmp parallelization, uncomment the relevant flags in src/MAKEVARS before compiling.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 9 ++++-----
MD5 | 16 ++++++++--------
NAMESPACE | 2 +-
R/count.R | 2 +-
R/tpx.R | 7 ++++---
inst/CITATION | 4 ++--
man/counts.Rd | 8 ++++----
man/topics.Rd | 4 ++--
src/Makevars | 2 +-
9 files changed, 27 insertions(+), 27 deletions(-)
Title: Gamma Lasso Regression
Diff between gamlr versions 1.12-1 dated 2014-10-01 and 1.13 dated 2015-04-01
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization, http://arxiv.org/abs/1308.5623.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 10 ++---
MD5 | 11 +++---
R/AICc.R | 1
R/gamlr.R | 31 ++++++++++++-----
inst |only
man/gamlr.Rd | 2 -
src/gamlr.c | 107 ++++++++++++++++++++++++++++++-----------------------------
7 files changed, 89 insertions(+), 73 deletions(-)
Title: Distributed Multinomial Regression
Diff between distrom versions 0.3-1 dated 2014-10-01 and 0.3-2 dated 2015-04-01
Description: Estimation for a multinomial logistic regression factorized into independent Poisson log regressions. See the textir package for applications in multinomial inverse regression analysis of text.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 9 +++------
MD5 | 6 +++---
R/dmr.R | 22 ++++++++++++++++++----
inst/CITATION | 4 ++--
4 files changed, 26 insertions(+), 15 deletions(-)
Title: Bayesian Sampling for Stick-Breaking Mixtures
Diff between Bmix versions 0.4 dated 2014-11-30 and 0.5 dated 2015-04-01
Description: This is a bare-bones implementation of sampling algorithms
for a variety of Bayesian stick-breaking (marginally DP)
mixture models, including particle learning and Gibbs sampling
for static DP mixtures, particle learning for dynamic BAR
stick-breaking, and DP mixture regression. The software is
designed to be easy to customize to suit different situations
and for experimentation with stick-breaking models. Since
particles are repeatedly copied, it is not an especially
efficient implementation.
Author: Matt Taddy
Maintainer: Matt Taddy
DESCRIPTION | 18 +++++++++---------
MD5 | 12 ++++++------
src/mix.cc | 4 ++--
src/particle.cc | 8 ++++----
src/rhelp.c | 38 +++++++++++++++++++-------------------
src/rhelp.h | 10 +++++-----
src/rvtools.c | 2 +-
7 files changed, 46 insertions(+), 46 deletions(-)
Title: An R Interface to SciDB
Diff between scidb versions 1.1-2 dated 2014-04-16 and 1.2-0 dated 2015-04-01
Description: An R interface to the SciDB array database (http://scidb.org).
Author: Paradigm4, B. W. Lewis
Maintainer: B. W. Lewis
scidb-1.1-2/scidb/inst/doc/scidb.R |only
scidb-1.1-2/scidb/inst/misc-documentation/SciDBR.list.functions |only
scidb-1.1-2/scidb/inst/misc-documentation/funs |only
scidb-1.1-2/scidb/inst/misc-documentation/scidb.pdf |only
scidb-1.1-2/scidb/man/substitute.Rd |only
scidb-1.2-0/scidb/DESCRIPTION | 14
scidb-1.2-0/scidb/MD5 | 135
scidb-1.2-0/scidb/NAMESPACE | 34
scidb-1.2-0/scidb/NEWS | 14
scidb-1.2-0/scidb/R/aggregate.R | 20
scidb-1.2-0/scidb/R/classes.R | 2
scidb-1.2-0/scidb/R/dbops.R | 210
scidb-1.2-0/scidb/R/distributions.R | 2
scidb-1.2-0/scidb/R/glm.R | 29
scidb-1.2-0/scidb/R/merge.R | 221
scidb-1.2-0/scidb/R/misc.R | 231
scidb-1.2-0/scidb/R/pkg.R | 50
scidb-1.2-0/scidb/R/redim.R |only
scidb-1.2-0/scidb/R/schema-utils.R | 127
scidb-1.2-0/scidb/R/scidb-arithmetic.R | 72
scidb-1.2-0/scidb/R/scidb-functions.R | 147
scidb-1.2-0/scidb/R/scidb-indexing-functions.R | 327
scidb-1.2-0/scidb/R/scidb-methods.R | 53
scidb-1.2-0/scidb/R/scidbdf-functions.R | 112
scidb-1.2-0/scidb/R/scidbdf-methods.R | 40
scidb-1.2-0/scidb/R/special_index.R |only
scidb-1.2-0/scidb/R/utility.R | 446 +
scidb-1.2-0/scidb/README.md | 9
scidb-1.2-0/scidb/build |only
scidb-1.2-0/scidb/inst/doc/scidb.Rnw | 679 +
scidb-1.2-0/scidb/inst/doc/scidb.pdf |binary
scidb-1.2-0/scidb/inst/misc-documentation/README | 5
scidb-1.2-0/scidb/inst/misc-documentation/Sweave.sty | 10
scidb-1.2-0/scidb/inst/misc-documentation/extra_ops |only
scidb-1.2-0/scidb/inst/misc-documentation/list.functions |only
scidb-1.2-0/scidb/inst/misc-documentation/scidb.Rnw | 427 -
scidb-1.2-0/scidb/inst/misc/image.jpg |binary
scidb-1.2-0/scidb/inst/misc/log | 3605 ----------
scidb-1.2-0/scidb/man/as.scidb.Rd | 15
scidb-1.2-0/scidb/man/bernoulli.Rd |only
scidb-1.2-0/scidb/man/bind.Rd | 2
scidb-1.2-0/scidb/man/build.Rd | 2
scidb-1.2-0/scidb/man/chunk_map.Rd |only
scidb-1.2-0/scidb/man/comparison-methods.Rd | 5
scidb-1.2-0/scidb/man/cumulate.Rd | 2
scidb-1.2-0/scidb/man/dist.Rd |only
scidb-1.2-0/scidb/man/factor_scidb.Rd |only
scidb-1.2-0/scidb/man/glm.fit.Rd | 36
scidb-1.2-0/scidb/man/index_lookup.Rd | 6
scidb-1.2-0/scidb/man/iquery.Rd | 62
scidb-1.2-0/scidb/man/is.temp.Rd |only
scidb-1.2-0/scidb/man/kmeans.Rd |only
scidb-1.2-0/scidb/man/levels_scidb.Rd |only
scidb-1.2-0/scidb/man/merge-methods.Rd | 63
scidb-1.2-0/scidb/man/na.locf-method.Rd | 7
scidb-1.2-0/scidb/man/order.Rd |only
scidb-1.2-0/scidb/man/peek.Rd |only
scidb-1.2-0/scidb/man/predict.glm_scidb.Rd | 7
scidb-1.2-0/scidb/man/project.Rd | 2
scidb-1.2-0/scidb/man/rank.Rd |only
scidb-1.2-0/scidb/man/redimension.Rd | 72
scidb-1.2-0/scidb/man/remove_old_versions.Rd |only
scidb-1.2-0/scidb/man/repart.Rd | 4
scidb-1.2-0/scidb/man/replaceNA.Rd |only
scidb-1.2-0/scidb/man/scidb-class.Rd | 10
scidb-1.2-0/scidb/man/scidb-package.Rd | 23
scidb-1.2-0/scidb/man/scidb.Rd | 1
scidb-1.2-0/scidb/man/scidb_attributes.Rd | 24
scidb-1.2-0/scidb/man/scidbconnect.Rd | 20
scidb-1.2-0/scidb/man/scidbdf-class.Rd | 23
scidb-1.2-0/scidb/man/scidbeval.Rd | 16
scidb-1.2-0/scidb/man/show_commit_log.Rd | 4
scidb-1.2-0/scidb/man/sort-methods.Rd | 13
scidb-1.2-0/scidb/man/subarray.Rd | 47
scidb-1.2-0/scidb/man/tsvd.Rd |only
scidb-1.2-0/scidb/man/unbound.Rd |only
scidb-1.2-0/scidb/src/parse.c |only
scidb-1.2-0/scidb/src/scidb.c | 142
scidb-1.2-0/scidb/tests/scidb.R | 179
scidb-1.2-0/scidb/tests/scidbdf.R | 41
scidb-1.2-0/scidb/vignettes/scidb.Rnw | 679 +
81 files changed, 3637 insertions(+), 4891 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Diff between rivr versions 0.9.1 dated 2015-02-22 and 0.9.2 dated 2015-04-01
Description: A tool for undergraduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan
rivr-0.9.1/rivr/README.md |only
rivr-0.9.2/rivr/DESCRIPTION | 11
rivr-0.9.2/rivr/MD5 | 35 +-
rivr-0.9.2/rivr/NAMESPACE | 1
rivr-0.9.2/rivr/R/RcppExports.R | 2
rivr-0.9.2/rivr/R/graduallyvariedflow_v2.r | 74 ++++--
rivr-0.9.2/rivr/R/route_wave_v4.r | 22 +
rivr-0.9.2/rivr/build/vignette.rds |binary
rivr-0.9.2/rivr/inst/doc/quickstart.R | 2
rivr-0.9.2/rivr/inst/doc/quickstart.Rmd | 2
rivr-0.9.2/rivr/inst/doc/quickstart.html | 3
rivr-0.9.2/rivr/man/compute_profile.Rd | 8
rivr-0.9.2/rivr/man/froude.Rd | 2
rivr-0.9.2/rivr/man/rivr-package.Rd | 8
rivr-0.9.2/rivr/man/route_wave.Rd | 2
rivr-0.9.2/rivr/man/waterolympics.Rd | 6
rivr-0.9.2/rivr/src/RcppExports.cpp | 264 +++++++++-------------
rivr-0.9.2/rivr/src/rivmech_characteristic_v7.cpp | 2
rivr-0.9.2/rivr/vignettes/quickstart.Rmd | 2
19 files changed, 226 insertions(+), 220 deletions(-)
Title: Nonparametric Boundary Regression
Diff between npbr versions 1.0 dated 2013-12-11 and 1.1 dated 2015-04-01
Description: A variety of functions for the best known and most innovative approaches to nonparametric boundary estimation. The selected methods are concerned with empirical, smoothed, unrestricted as well as constrained fits under both separate and multiple shape constraints. They cover robust approaches to outliers as well as data envelopment techniques based on piecewise polynomials, splines, local linear fitting, extreme values and kernel smoothing. The package also seamlessly allows for Monte Carlo comparisons among these different estimation methods. Its use is illustrated via a number of empirical applications and simulated examples.
Author: Abdelaati Daouia
Maintainer: Thibault Laurent
npbr-1.0/npbr/R/quad_spline_est_kn.R |only
npbr-1.0/npbr/man/quad_spline_est_kn.Rd |only
npbr-1.1/npbr/DESCRIPTION | 17
npbr-1.1/npbr/MD5 | 76
npbr-1.1/npbr/NAMESPACE | 3
npbr-1.1/npbr/R/cub_spline_est.r |only
npbr-1.1/npbr/R/cub_spline_kn.r |only
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npbr-1.1/npbr/R/kern_smooth_bw.R |only
npbr-1.1/npbr/R/kopt_momt_pick.r |only
npbr-1.1/npbr/R/loc_est.R | 13
npbr-1.1/npbr/R/loc_est_bw.R | 6
npbr-1.1/npbr/R/loc_max.r |only
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npbr-1.1/npbr/R/pick_est.r |only
npbr-1.1/npbr/R/poly_degree.r |only
npbr-1.1/npbr/R/quad_spline_est.R | 51
npbr-1.1/npbr/R/quad_spline_kn.R |only
npbr-1.1/npbr/R/rho_momt_pick.r |only
npbr-1.1/npbr/R/rho_pwm.r |only
npbr-1.1/npbr/R/zzz.r |only
npbr-1.1/npbr/build/vignette.rds |binary
npbr-1.1/npbr/data/air.rda |only
npbr-1.1/npbr/data/post.rda |only
npbr-1.1/npbr/data/records.rda |only
npbr-1.1/npbr/inst/doc/ex-npbr.R | 1205 +++++++++++++--
npbr-1.1/npbr/inst/doc/ex-npbr.pdf |binary
npbr-1.1/npbr/inst/doc/ex-npbr.rnw | 2496 +++++++++++++++++++++++++++-----
npbr-1.1/npbr/man/air.rd |only
npbr-1.1/npbr/man/cub_spline_est.rd |only
npbr-1.1/npbr/man/cub_spline_kn.rd |only
npbr-1.1/npbr/man/dea_est.Rd | 40
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npbr-1.1/npbr/man/dfs_pick.rd |only
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npbr-1.1/npbr/man/green.Rd | 12
npbr-1.1/npbr/man/kern_smooth.Rd |only
npbr-1.1/npbr/man/kern_smooth_bw.Rd |only
npbr-1.1/npbr/man/kopt_momt_pick.rd |only
npbr-1.1/npbr/man/loc_est.Rd | 75
npbr-1.1/npbr/man/loc_est_bw.Rd | 51
npbr-1.1/npbr/man/loc_max.rd |only
npbr-1.1/npbr/man/mopt_pwm.rd |only
npbr-1.1/npbr/man/npbr-package.Rd | 127 +
npbr-1.1/npbr/man/nuclear.Rd | 14
npbr-1.1/npbr/man/pick_est.rd |only
npbr-1.1/npbr/man/poly_degree.rd |only
npbr-1.1/npbr/man/poly_est.Rd | 40
npbr-1.1/npbr/man/post.Rd |only
npbr-1.1/npbr/man/quad_spline_est.Rd | 89 -
npbr-1.1/npbr/man/quad_spline_kn.Rd |only
npbr-1.1/npbr/man/records.Rd |only
npbr-1.1/npbr/man/rho_momt_pick.rd |only
npbr-1.1/npbr/man/rho_pwm.rd |only
npbr-1.1/npbr/src |only
npbr-1.1/npbr/vignettes/ex-npbr.rnw | 2496 +++++++++++++++++++++++++++-----
59 files changed, 5748 insertions(+), 1063 deletions(-)
Title: Nested Association Mapping Analysis
Diff between NAM versions 1.1 dated 2015-03-11 and 1.1.2 dated 2015-04-01
Description: Designed for association studies in nested association mapping (NAM) panels, but also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 8
MD5 | 28 -
R/gibbs.R | 382 ++++++++++----------
R/gwas.R | 973 ++++++++++++++++++++++++++---------------------------
R/gwas2.R | 722 +++++++++++++++++++--------------------
R/manhattan.R | 66 +--
R/reml.R | 2
man/NAM-package.Rd | 6
man/gibbs.Rd | 25 -
man/gwas.Rd | 126 +++---
man/manhattan.Rd | 79 ++--
man/reference.Rd | 66 +--
man/snpH2.Rd | 66 +--
man/snpQC.Rd | 82 ++--
man/tpod.Rd | 42 +-
15 files changed, 1339 insertions(+), 1334 deletions(-)
More information about HarmonicRegression at CRAN
Permanent link
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 2.1.0 dated 2015-02-03 and 3.0.0 dated 2015-04-01
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
decompr-2.1.0/decompr/R/vertical_specialisation.R |only
decompr-2.1.0/decompr/data/wiod.rda |only
decompr-2.1.0/decompr/man/final_demand.Rd |only
decompr-2.1.0/decompr/man/industry_names.Rd |only
decompr-2.1.0/decompr/man/intermediate_demand.Rd |only
decompr-2.1.0/decompr/man/kung_fu.Rd |only
decompr-2.1.0/decompr/man/output.Rd |only
decompr-2.1.0/decompr/man/region_names.Rd |only
decompr-2.1.0/decompr/man/vertical_specialisation.Rd |only
decompr-3.0.0/decompr/DESCRIPTION | 21
decompr-3.0.0/decompr/MD5 | 67 -
decompr-3.0.0/decompr/NAMESPACE | 18
decompr-3.0.0/decompr/NEWS | 262 +++----
decompr-3.0.0/decompr/R/decomp.R | 187 ++---
decompr-3.0.0/decompr/R/decompr.R | 119 +--
decompr-3.0.0/decompr/R/leontief.R | 188 ++---
decompr-3.0.0/decompr/R/leontief_output.R |only
decompr-3.0.0/decompr/R/load_tables.R | 94 +-
decompr-3.0.0/decompr/R/load_tables_vectors.R | 438 ++++++------
decompr-3.0.0/decompr/R/wwz.R | 675 +++++++++----------
decompr-3.0.0/decompr/README.md | 106 +-
decompr-3.0.0/decompr/build |only
decompr-3.0.0/decompr/data/leather.rda |binary
decompr-3.0.0/decompr/inst/CITATION | 34
decompr-3.0.0/decompr/inst/doc |only
decompr-3.0.0/decompr/man/countries.Rd | 20
decompr-3.0.0/decompr/man/decomp.Rd | 170 ++--
decompr-3.0.0/decompr/man/decompr.Rd | 43 -
decompr-3.0.0/decompr/man/final.Rd | 20
decompr-3.0.0/decompr/man/industries.Rd | 20
decompr-3.0.0/decompr/man/inter.Rd | 20
decompr-3.0.0/decompr/man/leontief.Rd | 82 +-
decompr-3.0.0/decompr/man/leontief_output.Rd | 82 +-
decompr-3.0.0/decompr/man/load_tables.Rd | 66 -
decompr-3.0.0/decompr/man/load_tables_vectors.Rd | 104 +-
decompr-3.0.0/decompr/man/out.Rd | 20
decompr-3.0.0/decompr/man/wwz.Rd | 87 +-
decompr-3.0.0/decompr/tests |only
decompr-3.0.0/decompr/vignettes |only
39 files changed, 1449 insertions(+), 1494 deletions(-)
Title: Simulation of Ordinal and Discrete Variables with Given
Correlation Matrix and Marginal Distributions
Diff between GenOrd versions 1.2.0 dated 2014-04-01 and 1.3.0 dated 2015-04-01
Description: A gaussian copula based procedure is implemented for generating samples from ordinal/discrete random variables with pre-specified correlation matrix and marginal distributions.
Author: Alessandro Barbiero, Pier Alda Ferrari
Maintainer: Alessandro Barbiero
DESCRIPTION | 16 ++++------
MD5 | 20 ++++++------
R/contord.R | 77 ++++++++++++++++++++++++--------------------------
R/corrcheck.R | 1
R/ordcont.R | 15 +++++----
R/ordsample.R | 24 ++++++++-------
man/GenOrd-package.Rd | 14 +++++----
man/contord.Rd | 19 ++++++------
man/corrcheck.Rd | 21 +++++++------
man/ordcont.Rd | 40 ++++++++++++-------------
man/ordsample.Rd | 45 ++++++++++++++---------------
11 files changed, 148 insertions(+), 144 deletions(-)
Title: Store Objects on Disk Automatically
Diff between track versions 1.1.7 dated 2015-03-14 and 1.1.8 dated 2015-04-01
Description: Automatically stores objects in files on disk
so that files are rewritten when objects are changed, and
so that objects are accessible but do not occupy memory
until they are accessed. Keeps track of times when objects
are created and modified, and caches some basic
characteristics of objects to allow for fast summaries of
objects. Also provides a command history mechanism that
saves the last command to a history file after each
command completes.
Author: Tony Plate
Maintainer: Tony Plate
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 4 ++++
tests/runtests.R | 4 +++-
tests/track.auto.rescan.Rt | 4 ++--
vignettes/track.Rnw | 6 ++++++
6 files changed, 24 insertions(+), 12 deletions(-)
Title: Date Calculations and Manipulation
Diff between TimeWarp versions 1.0.11 dated 2015-03-07 and 1.0.12 dated 2015-04-01
Description: Date sequence, relative date calculations, and date manipulation with business days
and holidays. Works with Date and POSIXt classes.
Author: Tony Plate, Jeffrey Horner, Lars Hansen
Maintainer: Tony Plate
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
tests/holidays.Rt | 3 ++-
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Functions to Calculate Common Laterality Statistics in
Primatology
Diff between Laterality versions 0.9.2 dated 2013-07-08 and 0.9.3 dated 2015-04-01
Description: Calculates and plots Handedness index (HI), absolute HI, mean HI and z-score which are commonly used indexes for the study of hand preference (laterality) in non-human primates.
Author: Borel A., Pouydebat E., Reghem E.
Maintainer: Antony Borel
DESCRIPTION | 19 +-
MD5 | 38 ++---
NAMESPACE | 33 +++--
R/HImeanindabs.R | 94 +++++++-------
R/HIndivabs.R | 116 ++++++++---------
R/laterAFCM.R | 79 +++++------
R/lvisAFCM.R | 131 ++++++++++---------
R/visAFCM.R | 75 +++++------
man/HImeanact.Rd | 242 ++++++++++++++++++------------------
man/HImeanactabs.Rd | 232 +++++++++++++++++------------------
man/HImeanind.Rd | 238 ++++++++++++++++++------------------
man/HImeanindabs.Rd | 232 +++++++++++++++++------------------
man/HIndiv.Rd | 234 +++++++++++++++++------------------
man/HIndivabs.Rd | 236 +++++++++++++++++------------------
man/Laterality-package.Rd | 182 +++++++++++++--------------
man/later.Rd | 164 ++++++++++++------------
man/laterAFCM.Rd | 175 ++++++++++++--------------
man/laterhist.Rd | 188 ++++++++++++++--------------
man/lvisAFCM.Rd | 303 +++++++++++++++++++++-------------------------
man/visAFCM.Rd | 208 +++++++++++++++----------------
20 files changed, 1597 insertions(+), 1622 deletions(-)
More information about FlexParamCurve at CRAN
Permanent link
Title: Spatial Areal Unit Modelling
Diff between CARBayes versions 4.0 dated 2014-12-16 and 4.1 dated 2015-04-01
Description: Implements a class of spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. A number of different CAR priors are available for the random effects, and full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee
CARBayes-4.0/CARBayes/data |only
CARBayes-4.0/CARBayes/man/spatialhousedata.Rd |only
CARBayes-4.0/CARBayes/man/spatialrespdata.Rd |only
CARBayes-4.1/CARBayes/DESCRIPTION | 14 -
CARBayes-4.1/CARBayes/MD5 | 105 +++----
CARBayes-4.1/CARBayes/NAMESPACE | 3
CARBayes-4.1/CARBayes/R/RcppExports.R | 1
CARBayes-4.1/CARBayes/R/S.CARbym.R | 2
CARBayes-4.1/CARBayes/R/S.CARcluster.R | 2
CARBayes-4.1/CARBayes/R/S.CARdissimilarity.R | 2
CARBayes-4.1/CARBayes/R/S.CARiar.R | 2
CARBayes-4.1/CARBayes/R/S.CARleroux.R | 2
CARBayes-4.1/CARBayes/R/S.independent.R | 2
CARBayes-4.1/CARBayes/R/binomial.bymCAR.R | 24 +
CARBayes-4.1/CARBayes/R/binomial.clusterCAR.R | 44 ++-
CARBayes-4.1/CARBayes/R/binomial.dissimilarityCAR.R | 22 +
CARBayes-4.1/CARBayes/R/binomial.iarCAR.R | 24 +
CARBayes-4.1/CARBayes/R/binomial.independent.R | 22 +
CARBayes-4.1/CARBayes/R/binomial.lerouxCAR.R | 24 +
CARBayes-4.1/CARBayes/R/combine.data.shapefile.R | 128 +++++----
CARBayes-4.1/CARBayes/R/gaussian.bymCAR.R | 24 +
CARBayes-4.1/CARBayes/R/gaussian.clusterCAR.R | 40 +-
CARBayes-4.1/CARBayes/R/gaussian.dissimilarityCAR.R | 22 +
CARBayes-4.1/CARBayes/R/gaussian.iarCAR.R | 24 +
CARBayes-4.1/CARBayes/R/gaussian.independent.R | 22 +
CARBayes-4.1/CARBayes/R/gaussian.lerouxCAR.R | 24 +
CARBayes-4.1/CARBayes/R/highlight.borders.R | 17 -
CARBayes-4.1/CARBayes/R/poisson.bymCAR.R | 24 +
CARBayes-4.1/CARBayes/R/poisson.clusterCAR.R | 46 ++-
CARBayes-4.1/CARBayes/R/poisson.clusterCARagg.R | 42 +--
CARBayes-4.1/CARBayes/R/poisson.dissimilarityCAR.R | 22 +
CARBayes-4.1/CARBayes/R/poisson.iarCAR.R | 24 +
CARBayes-4.1/CARBayes/R/poisson.independent.R | 22 +
CARBayes-4.1/CARBayes/R/poisson.lerouxCAR.R | 24 +
CARBayes-4.1/CARBayes/build/vignette.rds |binary
CARBayes-4.1/CARBayes/inst/doc/CARBayesvignette.R | 108 ++++---
CARBayes-4.1/CARBayes/inst/doc/CARBayesvignette.Rnw | 263 ++++++++++---------
CARBayes-4.1/CARBayes/inst/doc/CARBayesvignette.pdf |binary
CARBayes-4.1/CARBayes/man/CARBayes-package.Rd | 109 +++----
CARBayes-4.1/CARBayes/man/S.CARbym.Rd | 70 +++--
CARBayes-4.1/CARBayes/man/S.CARcluster.Rd | 84 +++---
CARBayes-4.1/CARBayes/man/S.CARdissimilarity.Rd | 78 +++--
CARBayes-4.1/CARBayes/man/S.CARiar.Rd | 70 +++--
CARBayes-4.1/CARBayes/man/S.CARleroux.Rd | 71 +++--
CARBayes-4.1/CARBayes/man/S.independent.Rd | 62 ++--
CARBayes-4.1/CARBayes/man/combine.data.shapefile.Rd | 26 +
CARBayes-4.1/CARBayes/man/highlight.borders.Rd | 34 +-
CARBayes-4.1/CARBayes/man/print.carbayes.Rd | 9
CARBayes-4.1/CARBayes/man/summarise.lincomb.Rd | 30 +-
CARBayes-4.1/CARBayes/man/summarise.samples.Rd | 28 +-
CARBayes-4.1/CARBayes/src/CARBayes.cpp | 1
CARBayes-4.1/CARBayes/src/RcppExports.cpp | 1
CARBayes-4.1/CARBayes/vignettes/CARBayesvignette.Rnw | 263 ++++++++++---------
CARBayes-4.1/CARBayes/vignettes/jss996.bib | 22 -
54 files changed, 1252 insertions(+), 877 deletions(-)
Title: Computation of the Balance - Sample Size Frontier in Matching
Methods for Causal Inference
Diff between MatchingFrontier versions 0.3.17 dated 2014-09-16 and 1.0.0 dated 2015-03-31
More information about MatchingFrontier at CRAN
Description: Returns the subset of the data with the minimum imbalance for
every possible subset size (N - 1, N - 2, ...), down to the data set with the
minimum possible imbalance. Also includes tools for the estimation
of causal effects for each subset size, functions for visualization
and data export, and functions for calculating
model dependence as proposed by Athey and Imbens.
Author: Gary King, Christopher Lucas, and Richard Nielsen
Maintainer: Christopher Lucas
DESCRIPTION | 21 +++++++-----
MD5 | 59 ++++++++++++++++++++++--------------
NAMESPACE | 5 ++-
R/L1FrontierSATT.R | 1
R/MahalFrontierFSATT.R | 1
R/checkDat.R | 8 ++--
R/distToFrontier.R | 28 +++++++++++++++--
R/estimateEffects.R | 50 ++++++++++++++++++++++++++----
R/generateDataset.R | 9 +++--
R/getCutpoint.R |only
R/getCutpointList.R |only
R/makeFrontier.R | 25 +++++++++++----
R/makeWeights.R | 10 ++++--
R/modelDependence.R |only
R/plotEstimates.R | 45 +++++++++++++++++++++++----
R/plotFrontier.R | 8 ++--
R/plotMeans.R |only
R/range01.R |only
R/trim.R |only
R/zzz.R | 4 +-
build |only
data/lalonde.RData |binary
inst/CITATION |only
inst/NEWS.Rd |only
inst/doc/Using_MatchingFrontier.R |only
inst/doc/Using_MatchingFrontier.Rnw |only
inst/doc/Using_MatchingFrontier.pdf |binary
man/estimateEffects.Rd | 49 ++++++++++++++++++++++++-----
man/generateDataset.Rd | 12 +++----
man/lalonde.Rd | 2 -
man/makeFrontier.Rd | 23 +++++++++-----
man/modelDependence.Rd |only
man/parallelPlot.Rd | 7 ----
man/plotEstimates.Rd | 56 +++++++++++++++++++++++++++-------
man/plotFrontier.Rd | 13 ++++---
man/plotMeans.Rd |only
vignettes |only
37 files changed, 318 insertions(+), 118 deletions(-)
Permanent link
Title: Fitting Mixed Models with Known Covariance Structures
Diff between EMMREML versions 2.0 dated 2014-05-24 and 3.0 dated 2015-03-31
Description: The main functions are 'emmreml', and 'emmremlMultiKernel'. 'emmreml' solves a mixed model with known covariance structure using the 'EMMA' algorithm. 'emmremlMultiKernel' is a wrapper for 'emmreml' to handle multiple random components with known covariance structures. The function 'emmremlMultivariate' solves a multivariate gaussian mixed model with known covariance structure using the 'ECM' algorithm.
Author: Deniz Akdemir, Okeke Uche Godfrey
Maintainer: Deniz Akdemir
DESCRIPTION | 12 ++++----
MD5 | 18 ++++++------
NAMESPACE | 2 -
R/emmreml.R | 43 ++++++++++++++++++++++++++++--
R/emmremlMultiKernel.R | 45 ++++++++++++++++++++++++++++++-
R/emmremlMultivariate.R | 64 ++++++++++++++++++++++++++++++++++++++++-----
man/EMMREML-package.Rd | 7 ++--
man/emmreml.Rd | 32 ++++++++++++++++++----
man/emmremlMultiKernel.Rd | 34 +++++++++++++++++++----
man/emmremlMultivariate.Rd | 41 +++++++++++++++++++++-------
10 files changed, 243 insertions(+), 55 deletions(-)
Title: Functions to Make Surveys Processing Easier
Diff between questionr versions 0.4.2 dated 2014-11-25 and 0.4.3 dated 2015-03-31
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps for data recoding, contingency
tables, dataset metadata handling, and several convenience functions.
Author: Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier
DESCRIPTION | 17 ++++---
MD5 | 100 +++++++++++++++++++++++-----------------------
NAMESPACE | 21 +++++----
NEWS | 9 +++-
R/describe.r | 2
R/icut.r | 54 +++++++++++-------------
R/iorder.R | 35 +++++++---------
R/irec.r | 53 ++++++++++++------------
R/lookfor.r | 2
R/odds.ratio.r | 11 ++---
R/table.multi.r | 17 ++++++-
R/tables.r | 4 -
R/tools.r | 14 ++++--
data/happy.rda |binary
data/hdv2003.rda |binary
data/rp99.rda |binary
inst/shiny/css/ifuncs.css | 34 ++++++++++++++-
inst/shiny/js/iorder.js | 2
man/addNAstr.Rd | 3 -
man/chisq.residuals.Rd | 3 -
man/clipcopy.Rd | 3 -
man/cprop.Rd | 3 -
man/cramer.v.Rd | 3 -
man/cross.multi.table.Rd | 12 ++++-
man/describe.Rd | 3 -
man/duplicated2.Rd | 3 -
man/format.proptab.Rd | 3 -
man/freq.Rd | 3 -
man/freq.na.Rd | 3 -
man/hdv2003.Rd | 3 -
man/icut.Rd | 3 -
man/iorder.Rd | 3 -
man/irec.Rd | 3 -
man/lookfor.Rd | 3 -
man/multi.split.Rd | 3 -
man/multi.table.Rd | 3 -
man/na.rm.Rd | 3 -
man/odds.ratio.Rd | 3 -
man/print.proptab.Rd | 3 -
man/prop.Rd | 3 -
man/qload.Rd | 3 -
man/qscan.Rd | 3 -
man/quant.cut.Rd | 3 -
man/questionr.Rd | 3 -
man/recode.na.Rd | 3 -
man/rename.variable.Rd | 3 -
man/rm.unused.levels.Rd | 3 -
man/rp99.Rd | 3 -
man/rprop.Rd | 3 -
man/wtd.mean.Rd | 3 -
man/wtd.table.Rd | 3 -
51 files changed, 287 insertions(+), 196 deletions(-)
Title: Data Augmentation and Multiple Imputation for Interval Censored
Data
Diff between MIICD versions 2.0 dated 2015-02-19 and 2.1 dated 2015-03-31
Description: Implements data augmentation schemes with multiple imputation steps for proportional hazards regression with interval censored data or proportional sub-distribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the 'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord
DESCRIPTION | 14 +++++++-------
MD5 | 33 +++++++++++++++++----------------
NAMESPACE | 2 +-
R/ANDA.coxph.R | 5 +++--
R/ANDA.crreg.R | 21 +++++++++++++--------
R/DA.ci.R | 4 ++--
R/DA.surv.R | 9 ++++-----
R/MI.ci.R | 17 ++++++++++-------
R/MI.surv.R | 2 +-
R/MIICD.crreg.R | 2 +-
R/PMDA.coxph.R | 16 ++++++++++------
R/PMDA.crreg.R | 34 +++++++++++++++++++++++-----------
R/get.est.FG.R | 2 +-
R/get.est.cr.cox.R |only
R/get_est_mi_surv.R | 2 +-
R/preproc.crreg.R | 5 +++--
man/DA.ci.Rd | 1 +
man/MIICD-package.Rd | 9 ++++-----
18 files changed, 102 insertions(+), 76 deletions(-)
Title: Functions for Analysis of Agreement in Method Comparison Studies
Diff between MethComp versions 1.22.1 dated 2015-03-08 and 1.22.2 dated 2015-03-31
Description: Methods (standard and advanced) for analysis of agreement
between measurement methods.
Author: Bendix Carstensen, Lyle Gurrin, Claus Ekstrom, Michal Figurski
Maintainer: Bendix Carstensen
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/MCmcmc.R | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Diff between mgcv versions 1.8-5 dated 2015-03-03 and 1.8-6 dated 2015-03-31
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood
Maintainer: Simon Wood
ChangeLog | 16 +
DESCRIPTION | 6
MD5 | 63 ++--
NAMESPACE | 2
R/bam.r | 187 ++++++------
R/efam.r | 15 -
R/gam.fit3.r | 12
R/gam.fit4.r | 15 -
R/gamlss.r | 140 +++++++++
R/mgcv.r | 240 +++++++++++++---
R/misc.r | 16 +
R/mvam.r | 131 +++++++-
R/plots.r | 33 --
inst/po/de/LC_MESSAGES/R-mgcv.mo |binary
inst/po/en@quot/LC_MESSAGES/R-mgcv.mo |binary
inst/po/en@quot/LC_MESSAGES/mgcv.mo |binary
inst/po/fr/LC_MESSAGES/R-mgcv.mo |binary
inst/po/ko/LC_MESSAGES/R-mgcv.mo |binary
inst/po/pl/LC_MESSAGES/R-mgcv.mo |binary
inst/po/po/LC_MESSAGES/R-mgcv.mo |binary
man/bam.Rd | 7
man/formula.gam.Rd | 19 +
man/gam.Rd | 17 -
man/mvn.Rd | 3
man/plot.gam.Rd | 3
man/rmvn.Rd |only
po/R-de.po | 506 +++++++++++++++++-----------------
po/R-fr.po | 20 +
po/R-ko.po | 19 +
po/R-mgcv.pot | 19 +
po/R-pl.po | 26 +
po/R-po.po | 26 +
po/mgcv.pot | 4
33 files changed, 1049 insertions(+), 496 deletions(-)
Title: Improved Access for Blind Users
Diff between BrailleR versions 0.16.1 dated 2015-02-02 and 0.18-1 dated 2015-03-31
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey
BrailleR-0.16.1/BrailleR/R/VIMethod.R |only
BrailleR-0.18-1/BrailleR/DESCRIPTION | 13 +--
BrailleR-0.18-1/BrailleR/MD5 | 41 ++++++---
BrailleR-0.18-1/BrailleR/NAMESPACE | 3
BrailleR-0.18-1/BrailleR/R/MakeRmdFiles.R |only
BrailleR-0.18-1/BrailleR/R/OneFactor.R | 21 +++-
BrailleR-0.18-1/BrailleR/R/Options.R | 40 +++++++++
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Title: Distance Measures for Time Series Data
Diff between TSdist versions 1.2 dated 2014-07-15 and 2.1 dated 2015-03-31
Description: A set of commonly used distance measures for time series data. The application of these distance measures is useful to perform clustering, classification or other data mining tasks.
Author: Usue Mori, Alexander Mendiburu, J.A. Lozano
Maintainer: Usue Mori
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TSdist-2.1/TSdist/R/database_distances.R | 195 +++++++++++++++-----
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Title: Functions for Generalized Simulated Annealing
Diff between GenSA versions 1.1.4 dated 2014-03-25 and 1.1.5 dated 2015-03-31
Description: Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian
DESCRIPTION | 12
MD5 | 16
NAMESPACE | 2
NEWS | 4
R/GenSA.R | 414 +--
man/GenSA-package.Rd | 6
man/GenSA.Rd | 230 +-
src/Engine.cpp | 1844 ++++++++---------
src/Utils.cpp | 5290 +++++++++++++++++++++++++--------------------------
9 files changed, 3911 insertions(+), 3907 deletions(-)
Title: Twitter Bootstrap Components for Shiny
Diff between shinyBS versions 0.20 dated 2014-03-19 and 0.61 dated 2015-03-31
Description: Adds additional Twitter Bootstrap components to Shiny.
Author: Eric Bailey
Maintainer: Eric Bailey
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More information about orthogonalsplinebasis at CRAN
Permanent link
Title: File-Based Access to Large Matrices Stored on HDD in Binary
Format
Diff between DatABEL versions 0.9-5 dated 2014-09-11 and 0.9-6 dated 2015-03-31
Description: Provides an interface to the C++ FILEVECTOR library
facilitating analysis using large (giga- to tera-bytes) matrices.
Matrix storage is organized in a way that either columns or rows
are quickly accessible. DatABEL is primarily aimed to support
genome-wide association analyses e.g. using GenABEL, MixABEL and
ProbABEL.
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim
Struchalin, Lennart C. Karssen
Maintainer: Lennart Karssen
DatABEL-0.9-5/DatABEL/R/checkPackageVersionOnCRAN.R |only
DatABEL-0.9-5/DatABEL/man/checkPackageVersionOnCRAN.Rd |only
DatABEL-0.9-6/DatABEL/ChangeLog | 16 +++-
DatABEL-0.9-6/DatABEL/DESCRIPTION | 27 +++---
DatABEL-0.9-6/DatABEL/MD5 | 44 +++++------
DatABEL-0.9-6/DatABEL/NAMESPACE | 2
DatABEL-0.9-6/DatABEL/R/databel_class.R | 5 +
DatABEL-0.9-6/DatABEL/R/zzz.R | 66 -----------------
DatABEL-0.9-6/DatABEL/build/vignette.rds |binary
DatABEL-0.9-6/DatABEL/inst/doc/intro_DatABEL.pdf |binary
DatABEL-0.9-6/DatABEL/inst/unitTests/Makefile | 31 +++----
DatABEL-0.9-6/DatABEL/man/DatABEL-package.Rd | 3
DatABEL-0.9-6/DatABEL/man/apply2dfo.Rd | 7 +
DatABEL-0.9-6/DatABEL/man/databel-class.Rd | 51 +++----------
DatABEL-0.9-6/DatABEL/man/databel.Rd | 3
DatABEL-0.9-6/DatABEL/man/databel2matrix.Rd | 3
DatABEL-0.9-6/DatABEL/man/databel2text.Rd | 3
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DatABEL-0.9-6/DatABEL/man/make_empty_fvf.Rd | 3
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DatABEL-0.9-6/DatABEL/man/process_lm_output.Rd | 3
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DatABEL-0.9-6/DatABEL/src/AbstractMatrix_R.cpp | 6 +
24 files changed, 113 insertions(+), 172 deletions(-)
Title: Scalable Rejection Sampling for Bayesian Hierarchical Models
Diff between bayesGDS versions 0.6.0 dated 2013-12-14 and 0.6.1 dated 2015-03-31
Description: Functions for implementing the Braun and Damien (2015) rejection sampling algorithm for Bayesian hierarchical models. The algorithm generates posterior samples in parallel, and is scalable when the individual units are conditionally independent.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
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bayesGDS-0.6.1/bayesGDS/NAMESPACE | 14 +
bayesGDS-0.6.1/bayesGDS/NEWS | 30 ++
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Title: Some Additional Distributions
Diff between sadists versions 0.1.0 dated 2015-03-05 and 0.2.0 dated 2015-03-30
Description: Provides the density, distribution, quantile and generation functions of some obscure probability
distributions, including the doubly non-central t, F, Beta, and Eta distributions;
Lecoutre's lambda-prime and K-prime; the upsilon distribution; the (weighted) sum of
non-central chi-squares to a power; the (weighted) sum of log non-central chi-squares;
the product of non-central chi-squares to powers; the product of doubly non-central
F variates.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav
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12 files changed, 126 insertions(+), 1 deletion(-)
Title: Technology Forecasting using DEA (Data Envelopment Analysis)
Diff between TFDEA versions 0.9.8 dated 2015-02-07 and 0.9.8.3 dated 2015-03-30
Description: The TFDEA algorithm for technology forecasts when future products
will be introduced based upon their features.
It also includes DEA (Data Envelopment Analysis) functions including extensions dealing with
with infeasibility.
In addition it includes some standard technology forecasting data sets.
Author: Tom Shott [aut, cre],
Dong-Joon Lim [aut]
Maintainer: Tom Shott
ChangeLog | 12 ++++++++----
DESCRIPTION | 20 ++++++++++----------
MD5 | 14 +++++++-------
R/dea_common.R | 2 +-
man/DEA.Rd | 6 ++++--
man/TFDEA.Rd | 4 ++--
man/fighter_jet.Rd | 8 +++++---
man/wireless_2012.Rd | 3 ++-
8 files changed, 39 insertions(+), 30 deletions(-)
Title: Small Area Estimation
Diff between sae versions 1.0-2 dated 2013-04-03 and 1.0-5 dated 2015-03-30
Description: Functions for small area estimation.
Author: Isabel Molina, Yolanda Marhuenda
Maintainer: Yolanda Marhuenda
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++++++----
R/pbmseSFH.R | 4 ++--
build |only
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8 files changed, 21 insertions(+), 12 deletions(-)
Title: Analysis of Subjective Perspectives Using Q Methodology
Diff between qmethod versions 1.2.4 dated 2014-12-03 and 1.3.0 dated 2015-03-30
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group. This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the webpages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala
DESCRIPTION | 29 +++++++----
MD5 | 72 ++++++++++++++++++++---------
NAMESPACE | 27 ++++++++--
R/build.q.set.R |only
R/import.q.concourse.R |only
R/import.q.feedback.R |only
R/import.q.sorts.R |only
R/make.cards.R |only
R/plot.QmethodRes.R | 7 +-
R/print.QmethodRes.R | 4 -
R/q.fnames.R |only
R/qdc.R | 4 -
R/qmethod.R | 76 ++++++++++++++++++------------
R/qzscores.R | 18 ++++---
data/importexample.RData |only
inst/CITATION | 22 ++++----
inst/cardtemplates |only
inst/extdata |only
man/build.q.set.Rd |only
man/export.qm.Rd | 6 +-
man/import.pqmethod.Rd | 11 ----
man/import.q.concourse.Rd |only
man/import.q.feedback.Rd |only
man/import.q.sorts.Rd |only
man/importexample.Rd |only
man/lipset.Rd | 5 +-
man/make.cards.Rd |only
man/plot.QmethodRes.Rd | 16 +++---
man/print.QmethodRes.Rd | 8 +--
man/q.fnames.Rd |only
man/qdc.Rd | 29 ++++++-----
man/qfcharact.Rd | 18 ++-----
man/qflag.Rd | 14 +++--
man/qmethod-package.Rd | 114 ++++++++++++++++++++++++++++++++++++----------
man/qmethod.Rd | 24 ++++-----
man/qzscores.Rd | 27 +++++-----
man/summary.QmethodRes.Rd | 8 +--
37 files changed, 341 insertions(+), 198 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.97 dated 2015-02-03 and 0.98 dated 2015-03-30
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++++-----
NAMESPACE | 4 +++-
NEWS | 9 +++++++++
R/predValues.R |only
R/ssizePCC.R |only
man/0MKmisc-package.Rd | 4 ++--
man/power.diagnostic.test.Rd | 10 +++++-----
man/predValues.Rd |only
man/ssize.pcc.Rd |only
10 files changed, 33 insertions(+), 18 deletions(-)
Title: Multidimensional Iterative Proportional Fitting and Alternative
Models
Diff between mipfp versions 1.5 dated 2015-02-10 and 2.0 dated 2015-03-30
Description: An implementation of the iterative proportional fitting (IPFP),
maximum likelihood, minimum chi-square and weighted least squares procedures
for updating a N-dimensional array with respect to given target marginal
distributions (which, in turn can be multi-dimensional). The package also
provides an application of the IPFP to simulate multivariate Bernoulli
distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy
mipfp-1.5/mipfp/R/ipfpMultiDim.R |only
mipfp-1.5/mipfp/man/IpfpCovar.Rd |only
mipfp-1.5/mipfp/man/array2vector.Rd |only
mipfp-1.5/mipfp/man/vector2array.Rd |only
mipfp-2.0/mipfp/DESCRIPTION | 25 +-
mipfp-2.0/mipfp/MD5 | 26 ++-
mipfp-2.0/mipfp/NAMESPACE | 2
mipfp-2.0/mipfp/R/binary.R |only
mipfp-2.0/mipfp/R/ipfp_multi_dim.R |only
mipfp-2.0/mipfp/R/models.R |only
mipfp-2.0/mipfp/R/utils.R |only
mipfp-2.0/mipfp/man/Array2Vector.Rd |only
mipfp-2.0/mipfp/man/Corr2Odds.Rd |only
mipfp-2.0/mipfp/man/Corr2PairProbs.Rd |only
mipfp-2.0/mipfp/man/Ipfp.Rd | 40 +++-
mipfp-2.0/mipfp/man/IpfpCov.Rd |only
mipfp-2.0/mipfp/man/ObtainModelEstimates.Rd |only
mipfp-2.0/mipfp/man/ObtainMultBinaryDist.Rd |only
mipfp-2.0/mipfp/man/Odds2Corr.Rd |only
mipfp-2.0/mipfp/man/Odds2PairProbs.Rd |only
mipfp-2.0/mipfp/man/RMultBinary.Rd |only
mipfp-2.0/mipfp/man/Vector2Array.Rd |only
mipfp-2.0/mipfp/man/mipfp-package.Rd | 242 ++++++++++++++++------------
23 files changed, 204 insertions(+), 131 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.20-30 dated 2015-02-22 and 0.20-31 dated 2015-03-30
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data, that is
sufficient for typical graphics needs, and is also flexible enough
to handle most nonstandard requirements. See ?Lattice for an
introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
DESCRIPTION | 8 +--
MD5 | 8 +--
inst/po/de/LC_MESSAGES/R-lattice.mo |binary
po/R-de.po | 85 +++++++++++++++++++++++++-----------
po/R-lattice.pot | 2
5 files changed, 69 insertions(+), 34 deletions(-)
Title: Functional Time Series Analysis
Diff between ftsa versions 4.2 dated 2015-03-12 and 4.3 dated 2015-03-30
Description: Functions for displaying and analyzing functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang
ChangeLog | 4 ++++
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
NAMESPACE | 1 -
R/MFDM.R | 12 +++++++++---
man/ftsa-package.Rd | 10 ++++++----
6 files changed, 30 insertions(+), 19 deletions(-)
Title: Plots of Scaled Prediction Variances for Response Surface
Designs
Diff between VdgRsm versions 1.4 dated 2015-02-01 and 1.5 dated 2015-03-30
Description: Functions for creating variance dispersion graphs, fraction of design space plots, and contour plots of scaled prediction variances for second-order response surface designs in spherical and cuboidal regions. Also, some standard response surface designs can be generated.
Author: Patchanok Srisuradetchai, John J. Borkowski
Maintainer: Patchanok Srisuradetchai
DESCRIPTION | 15 +-
MD5 | 26 ++--
R/VdgRsm.R | 303 ++++++++++++++++++++++++++++++---------------------
man/Borkowski2003.Rd | 2
man/VdgRsm.Rd | 9 -
man/cpv.Rd | 4
man/fds.cube.Rd | 4
man/fds.sphere.Rd | 16 +-
man/gen.BBD.Rd | 2
man/gen.HSCD.Rd | 2
man/gen.PBCD.Rd | 2
man/gen.Roquemore.Rd | 2
man/spv.Rd | 10 +
man/spvcontour.Rd | 4
14 files changed, 229 insertions(+), 172 deletions(-)
Title: Statistical Modeling
Diff between statmod versions 1.4.20 dated 2014-05-31 and 1.4.21 dated 2015-03-30
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth
DESCRIPTION | 10 +++---
MD5 | 24 +++++++-------
NAMESPACE | 3 +
R/elda.R | 33 +++++++++++++++++---
R/invgauss.R | 69 +++++++++++++++++++++++++++---------------
R/qres.R | 6 +--
inst/NEWS | 13 +++++++
man/elda.Rd | 16 ++++-----
man/gauss.quad.Rd | 2 -
man/gauss.quad.prob.Rd | 13 +------
man/invgauss.Rd | 11 ++++--
tests/statmod-Tests.R | 2 +
tests/statmod-Tests.Rout.save | 18 ++++++----
13 files changed, 140 insertions(+), 80 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Diff between servr versions 0.1 dated 2013-10-05 and 0.2 dated 2015-03-30
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Carson Sievert [ctb],
Jesse Anderson [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
servr-0.1/servr/R/serve.R |only
servr-0.2/servr/DESCRIPTION | 28 ++--
servr-0.2/servr/MD5 | 31 +++-
servr-0.2/servr/NAMESPACE | 14 ++
servr-0.2/servr/NEWS |only
servr-0.2/servr/R/dynamic.R |only
servr-0.2/servr/R/make.R |only
servr-0.2/servr/R/notebook.R |only
servr-0.2/servr/R/static.R |only
servr-0.2/servr/R/utils.R | 237 ++++++++++++++++++++++-------------
servr-0.2/servr/R/vignette.R |only
servr-0.2/servr/README.md | 61 +++++++--
servr-0.2/servr/inst/examples |only
servr-0.2/servr/inst/resources |only
servr-0.2/servr/man/daemon_stop.Rd |only
servr-0.2/servr/man/dynamic_site.Rd |only
servr-0.2/servr/man/httd.Rd | 28 +---
servr-0.2/servr/man/make.Rd |only
servr-0.2/servr/man/notebook.Rd |only
servr-0.2/servr/man/serve_example.Rd |only
servr-0.2/servr/man/server_config.Rd |only
servr-0.2/servr/man/vign.Rd |only
22 files changed, 266 insertions(+), 133 deletions(-)
Title: R Interactive Graphics via HTML
Diff between RIGHT versions 0.1.2 dated 2013-10-19 and 0.2.0 dated 2015-03-30
Description: Interactive data visualization supporting linked graphs can help users easily
explore data and gain valuable insights and enables such visualization and interactive
re-analysis using HTML5 canvas and JavaScript. Its R API is designed to create a seamless
analysis, visualization, and re-analysis workflow for interactive visualization and analysis.
Since HTML5 canvas and JavaScript is supported in virtually all modern web browsers, the
visualizations can be delivered to almost any device/platform for presentation purposes.
Author: ChungHa Sung, TaeJoon Song, JongHyun Bae, SangGi Hong, Jae W. Lee, and
Junghoon Lee
Maintainer: Jonghyun Bae
RIGHT-0.1.2/RIGHT/inst/JavaScript/Theoph-from-R.csv |only
RIGHT-0.1.2/RIGHT/inst/JavaScript/_sub.diamonds.csv |only
RIGHT-0.1.2/RIGHT/inst/JavaScript/button_event.js |only
RIGHT-0.1.2/RIGHT/inst/JavaScript/diamonds-from-R_100.csv |only
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RIGHT-0.1.2/RIGHT/inst/examples/example1 |only
RIGHT-0.1.2/RIGHT/inst/examples/example2 |only
RIGHT-0.1.2/RIGHT/inst/examples/example_box/example_box.html |only
RIGHT-0.2.0/RIGHT/DESCRIPTION | 41
RIGHT-0.2.0/RIGHT/MD5 | 214
RIGHT-0.2.0/RIGHT/NAMESPACE | 36
RIGHT-0.2.0/RIGHT/NEWS | 16
RIGHT-0.2.0/RIGHT/R/RIGHT.R | 676
RIGHT-0.2.0/RIGHT/R/body.R | 175
RIGHT-0.2.0/RIGHT/R/boxplot_RIGHT.R | 163
RIGHT-0.2.0/RIGHT/R/common.R | 17
RIGHT-0.2.0/RIGHT/R/ggplot_RIGHT.R |only
RIGHT-0.2.0/RIGHT/R/head.R | 239
RIGHT-0.2.0/RIGHT/R/hist_RIGHT.R | 168
RIGHT-0.2.0/RIGHT/R/lines_RIGHT.R | 219
RIGHT-0.2.0/RIGHT/R/pie_RIGHT.R | 160
RIGHT-0.2.0/RIGHT/R/plot_RIGHT.R | 265
RIGHT-0.2.0/RIGHT/R/points_RIGHT.R | 167
RIGHT-0.2.0/RIGHT/R/qplot_RIGHT.R |only
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RIGHT-0.2.0/RIGHT/inst/JavaScript/bar.js | 581
RIGHT-0.2.0/RIGHT/inst/JavaScript/box.js | 654
RIGHT-0.2.0/RIGHT/inst/JavaScript/callback.js | 107
RIGHT-0.2.0/RIGHT/inst/JavaScript/color.js | 108
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RIGHT-0.2.0/RIGHT/inst/JavaScript/dot.js | 484
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RIGHT-0.2.0/RIGHT/inst/JavaScript/menu.js | 106
RIGHT-0.2.0/RIGHT/inst/JavaScript/node_event.js | 460
RIGHT-0.2.0/RIGHT/inst/JavaScript/pie.js | 422
RIGHT-0.2.0/RIGHT/inst/JavaScript/search.js | 184
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/bootstrap/css/bootstrap-responsive.min.css | 8
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/bootstrap/css/bootstrap-theme.css |only
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RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/bootstrap/css/theme.css |only
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RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/bootstrap/js/bootstrap.js | 2996 +-
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/bootstrap/js/bootstrap.min.js | 10
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/jquery.js |14329 +++++-----
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/shiny-showcase.css |only
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RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/shiny.css | 20
RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/shiny.js | 1757 +
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RIGHT-0.2.0/RIGHT/inst/JavaScript/shared/slider/js/jquery.slider.min.js | 2
RIGHT-0.2.0/RIGHT/inst/JavaScript/shiny-right.js | 65
RIGHT-0.2.0/RIGHT/inst/JavaScript/structure.js | 1583 -
RIGHT-0.2.0/RIGHT/inst/JavaScript/table.js | 235
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RIGHT-0.2.0/RIGHT/inst/tests/testPlot_RIGHT.R | 101
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140 files changed, 21862 insertions(+), 17774 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Diff between glinternet versions 0.9.0 dated 2013-08-17 and 1.0.0 dated 2015-03-30
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2014).
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim
DESCRIPTION | 16 ++++++++--------
MD5 | 12 ++++++------
R/glinternet.cv.r | 11 ++++-------
R/glinternet.r | 8 ++++++++
R/plot.glinternet.cv.r | 42 ++++++++++++++++++++----------------------
R/predict.glinternet.r | 1 +
man/glinternet.Rd | 6 +++++-
7 files changed, 52 insertions(+), 44 deletions(-)
Title: Programmatic Interface to the API Serving UC Berkeley's Natural
History Data
Diff between ecoengine versions 1.9 dated 2015-03-14 and 1.9.1 dated 2015-03-30
Description: The ecoengine provides access to more than 5 million georeferenced specimen records from the University of California, Berkeley's Natural History Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
ecoengine-1.9.1/ecoengine/DESCRIPTION | 8
ecoengine-1.9.1/ecoengine/MD5 | 114
ecoengine-1.9.1/ecoengine/NAMESPACE | 4
ecoengine-1.9.1/ecoengine/NEWS | 9
ecoengine-1.9.1/ecoengine/R/ee_about.R | 2
ecoengine-1.9.1/ecoengine/R/ee_browse_photos.R | 1
ecoengine-1.9.1/ecoengine/R/ee_search.R | 16
ecoengine-1.9.1/ecoengine/R/ee_utils.R | 3
ecoengine-1.9.1/ecoengine/README.md | 7
ecoengine-1.9.1/ecoengine/inst/Using_ecoengine.Rmd | 75
ecoengine-1.9.1/ecoengine/inst/Using_ecoengine.md | 428 +--
ecoengine-1.9.1/ecoengine/inst/Using_ecoengine.pdf |binary
ecoengine-1.9.1/ecoengine/inst/cache/about_ad4112b8ea90d8283e271edaae557c9f.RData | 1248 +++++-----
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ecoengine-1.9.1/ecoengine/man/ee_pages.Rd | 4
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67 files changed, 868 insertions(+), 1083 deletions(-)
Title: Creates a Model Matrix via Feature Hashing with a Formula
Interface
Diff between FeatureHashing versions 0.8 dated 2015-01-01 and 0.9 dated 2015-03-29
More information about FeatureHashing at CRAN
Description: Feature hashing, also called as the hashing trick, is a method to transform
features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix.
Without looking up the indices in an associative array,
it applies a hash function to the features and uses their hash values as indices directly.
The method of feature hashing in this package was proposed in Weinberger et al. (2009).
The hashing algorithm is the murmurhash3 from the digest package.
Please see the README in https://github.com/wush978/FeatureHashing for more information.
Author: Wush Wu [aut, cre],
Michael Benesty [aut, ctb]
Maintainer: Wush Wu
FeatureHashing-0.8/FeatureHashing/R/tag.R |only
FeatureHashing-0.8/FeatureHashing/man/tag.Rd |only
FeatureHashing-0.8/FeatureHashing/src/tag.cpp |only
FeatureHashing-0.8/FeatureHashing/src/tag.h |only
FeatureHashing-0.9/FeatureHashing/Changelog | 23
FeatureHashing-0.9/FeatureHashing/DESCRIPTION | 36 -
FeatureHashing-0.9/FeatureHashing/LICENSE |only
FeatureHashing-0.9/FeatureHashing/MD5 | 72 +-
FeatureHashing-0.9/FeatureHashing/NAMESPACE | 12
FeatureHashing-0.9/FeatureHashing/R/RcppExports.R | 36 -
FeatureHashing-0.9/FeatureHashing/R/hash.mapping.R |only
FeatureHashing-0.9/FeatureHashing/R/hash.size.R |only
FeatureHashing-0.9/FeatureHashing/R/hashed.model.matrix.R | 240 ++++++--
FeatureHashing-0.9/FeatureHashing/R/simulate.split.R |only
FeatureHashing-0.9/FeatureHashing/R/zzz.R | 52 +
FeatureHashing-0.9/FeatureHashing/README.md | 231 +++-----
FeatureHashing-0.9/FeatureHashing/data/ipinyou.rda |only
FeatureHashing-0.9/FeatureHashing/inst/ftprl.R |only
FeatureHashing-0.9/FeatureHashing/man/CSCMatrix-class.Rd | 3
FeatureHashing-0.9/FeatureHashing/man/hash.mapping.Rd |only
FeatureHashing-0.9/FeatureHashing/man/hash.size.Rd |only
FeatureHashing-0.9/FeatureHashing/man/hashed.model.matrix.Rd | 197 +++++--
FeatureHashing-0.9/FeatureHashing/man/intToRaw.Rd |only
FeatureHashing-0.9/FeatureHashing/man/ipinyou.Rd |only
FeatureHashing-0.9/FeatureHashing/man/simulate.split.Rd |only
FeatureHashing-0.9/FeatureHashing/man/test.tag.Rd | 8
FeatureHashing-0.9/FeatureHashing/src/RcppExports.cpp | 266 ++++-----
FeatureHashing-0.9/FeatureHashing/src/as.cpp | 18
FeatureHashing-0.9/FeatureHashing/src/digest.c | 18
FeatureHashing-0.9/FeatureHashing/src/digestlocal.h | 10
FeatureHashing-0.9/FeatureHashing/src/hash_internal.cpp | 26
FeatureHashing-0.9/FeatureHashing/src/hashed_model_matrix.cpp | 72 ++
FeatureHashing-0.9/FeatureHashing/src/intToRaw.cpp |only
FeatureHashing-0.9/FeatureHashing/src/product.cpp | 18
FeatureHashing-0.9/FeatureHashing/src/split.cpp |only
FeatureHashing-0.9/FeatureHashing/src/split.h |only
FeatureHashing-0.9/FeatureHashing/src/subsetting.cpp | 18
FeatureHashing-0.9/FeatureHashing/tests/test-as-dgCMatrix.R | 135 ++--
FeatureHashing-0.9/FeatureHashing/tests/test-empty_array.R |only
FeatureHashing-0.9/FeatureHashing/tests/test-hash.mapping.R |only
FeatureHashing-0.9/FeatureHashing/tests/test-hashing.R | 278 +++++-----
FeatureHashing-0.9/FeatureHashing/tests/test-interpret.tag.R | 25
FeatureHashing-0.9/FeatureHashing/tests/test-memcheck.R | 44 +
FeatureHashing-0.9/FeatureHashing/tests/test-product.R | 73 +-
FeatureHashing-0.9/FeatureHashing/tests/test-signed.hash.R |only
FeatureHashing-0.9/FeatureHashing/tests/test-split.R |only
FeatureHashing-0.9/FeatureHashing/tests/test-subsetting.R | 195 +++----
FeatureHashing-0.9/FeatureHashing/tests/test-transpose.R | 19
48 files changed, 1291 insertions(+), 834 deletions(-)
Permanent link
Title: Connect MonetDB to R
Diff between MonetDB.R versions 0.9.6 dated 2015-03-20 and 0.9.7 dated 2015-03-29
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Thomas Lumley [ctb], Anthony Damico [ctb]
Maintainer: Hannes Muehleisen
DESCRIPTION | 6 +++---
MD5 | 6 +++---
NEWS | 3 +++
src/mapisplit-r.c | 12 +++++-------
4 files changed, 14 insertions(+), 13 deletions(-)
Title: Standard Normal Homogeneity Test
Diff between snht versions 1.0.1 dated 2015-01-25 and 1.0.2 dated 2015-03-29
Description: Robust and non-robust SNHT tests for changepoint detection.
Author: Josh Browning
Maintainer: Josh Browning
snht-1.0.1/snht/README.md |only
snht-1.0.2/snht/DESCRIPTION | 13 ++++++++-----
snht-1.0.2/snht/MD5 | 21 ++++++++++++++++++---
snht-1.0.2/snht/NAMESPACE | 4 ++++
snht-1.0.2/snht/R/plotSNHT.R |only
snht-1.0.2/snht/build |only
snht-1.0.2/snht/inst |only
snht-1.0.2/snht/man/plotSNHT.Rd |only
snht-1.0.2/snht/vignettes |only
9 files changed, 30 insertions(+), 8 deletions(-)
Title: Political Science Computational Laboratory, Stanford University
Diff between pscl versions 1.4.8 dated 2015-01-24 and 1.4.9 dated 2015-03-29
Description: Bayesian analysis of item-response theory (IRT) models,
roll call analysis; computing highest density regions; maximum
likelihood estimation of zero-inflated and hurdle models for count
data; goodness-of-fit measures for GLMs; data sets used
in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.
Author: Simon Jackman, with contributions from
Alex Tahk, Achim Zeileis, Christina Maimone and Jim Fearon
Maintainer: Simon Jackman
DESCRIPTION | 8 +++----
MD5 | 20 ++++++++---------
NEWS | 4 ++-
R/vuong.R | 54 +++++++++++++++++++++++++++++++-----------------
build/vignette.rds |binary
data/absentee.rda |binary
inst/doc/countreg.pdf |binary
man/UKHouseOfCommons.Rd | 2 -
man/nj07.Rd | 3 --
man/readKH.Rd | 2 -
man/summary.ideal.Rd | 17 +--------------
11 files changed, 57 insertions(+), 53 deletions(-)
Title: Convert Rd to Roxygen Documentation
Diff between Rd2roxygen versions 1.5 dated 2014-08-24 and 1.6 dated 2015-03-29
Description: Functions to convert Rd to roxygen documentation. It can parse an
Rd file to a list, create the roxygen documentation and update the original
R script (e.g. the one containing the definition of the function)
accordingly. This package also provides utilities which can help developers
build packages using roxygen more easily. The formatR package can be used
to reformat the R code in the examples sections so that the code will be
more readable.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
Rd2roxygen-1.5/Rd2roxygen/vignettes/Rd2roxygen.css |only
Rd2roxygen-1.6/Rd2roxygen/DESCRIPTION | 21 +-
Rd2roxygen-1.6/Rd2roxygen/MD5 | 37 ++--
Rd2roxygen-1.6/Rd2roxygen/NEWS | 23 +++
Rd2roxygen-1.6/Rd2roxygen/R/build.R | 145 ++++++++++++-------
Rd2roxygen-1.6/Rd2roxygen/R/rd2roxygen.R | 126 ++++++++--------
Rd2roxygen-1.6/Rd2roxygen/R/utils.R | 67 +++++++-
Rd2roxygen-1.6/Rd2roxygen/README.md | 2
Rd2roxygen-1.6/Rd2roxygen/build/vignette.rds |binary
Rd2roxygen-1.6/Rd2roxygen/inst/doc/Rd2roxygen.R | 6
Rd2roxygen-1.6/Rd2roxygen/inst/doc/Rd2roxygen.Rmd | 15 -
Rd2roxygen-1.6/Rd2roxygen/inst/doc/Rd2roxygen.html | 152 ++++++++++----------
Rd2roxygen-1.6/Rd2roxygen/man/Rd2roxygen-package.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/Rd2roxygen.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/create_roxygen.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/parse_and_save.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/parse_file.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/reformat_code.Rd | 1
Rd2roxygen-1.6/Rd2roxygen/man/roxygen_and_build.Rd | 16 +-
Rd2roxygen-1.6/Rd2roxygen/vignettes/Rd2roxygen.Rmd | 15 -
20 files changed, 383 insertions(+), 248 deletions(-)
Title: Multidimensional Item Response Theory
Diff between mirt versions 1.8 dated 2015-01-22 and 1.9 dated 2015-03-29
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers
DESCRIPTION | 10 -
MD5 | 150 ++++++++++++-------------
NAMESPACE | 1
R/01-itemtypes.R | 6 -
R/02-item_methods.R | 6 -
R/03-estimation.R | 26 ++--
R/04-derivatives.R | 37 +++++-
R/DIF.R | 7 +
R/DTF.R | 7 +
R/EMstep.group.R | 10 +
R/EMstep.utils.R | 56 ++++-----
R/LoadPars.R | 123 ++++++++++++--------
R/M2.R | 9 +
R/MHRM.group.R | 42 +++----
R/MultipleGroup-methods.R | 2
R/PLCI.mirt.R | 21 ++-
R/PrepData.R | 65 ++++++----
R/SE.methods.R | 4
R/SingleGroup-methods.R | 141 ++++++++++++++++++-----
R/averageMI.R | 2
R/bfactor.R | 1
R/boot.mirt.R | 1
R/calcLogLik.R | 2
R/createItem.R | 34 +++--
R/expand.table.R | 23 ++-
R/expected.item.R | 2
R/expected.test.R | 10 +
R/extract.group.R | 6 -
R/extract.item.R | 4
R/fixef.R |only
R/fscores.R | 7 -
R/fscores.internal.R | 80 ++++++++-----
R/imputeMissing.R | 4
R/itemfit.R | 9 -
R/itemplot.R | 9 +
R/itemplot.internal.R | 4
R/key2binary.R | 15 +-
R/mirt-package.R | 6 -
R/mirt.R | 34 ++++-
R/mirt.model.R | 21 +--
R/mixedmirt.R | 8 +
R/model.elements.R | 26 ++--
R/multipleGroup.R | 3
R/personfit.R | 6 -
R/probtrace.R | 4
R/randef.R | 3
R/simdata.R | 71 ++++++++---
R/testinfo.R | 2
R/utils.R | 66 ++++++++---
R/wald.R | 15 +-
README.md | 4
man/M2.Rd | 7 +
man/PLCI.mirt.Rd | 6 -
man/extract.group.Rd | 2
man/fixef.Rd |only
man/fscores.Rd | 6 -
man/itemplot.Rd | 5
man/mirt.Rd | 27 +++-
man/mirt.model.Rd | 21 +--
man/mixedmirt.Rd | 6 -
man/plot-method.Rd | 5
man/residuals-method.Rd | 7 +
man/simdata.Rd | 27 +++-
src/Estep.cpp | 74 +++---------
src/Estep.h | 5
src/Makevars | 3
src/Makevars.win | 3
src/Misc.cpp | 14 --
src/Misc.h | 4
src/dpars.cpp | 214 +++++++++++++++++++++++++++++++++++-
src/traceLinePts.cpp | 91 ++++++++++++++-
src/traceLinePts.h | 4
tests/tests/test-03-bfactor.R | 2
tests/tests/test-04-multipleGroup.R | 2
tests/tests/test-07-mixedmirt.R | 4
tests/tests/test-09-mirt.model.R | 6 +
tests/tests/test-10-extras.R | 23 +++
77 files changed, 1223 insertions(+), 550 deletions(-)
Title: Map Filenames to MIME Types
Diff between mime versions 0.2 dated 2014-09-26 and 0.3 dated 2015-03-29
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Jeffrey Horner [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 16 ++++++++--------
MD5 | 14 +++++++-------
NEWS | 8 +++++++-
R/mime.R | 4 +++-
R/mimemap.R | 14 +++++++++++---
man/guess_type.Rd | 1 +
man/mimemap.Rd | 1 +
man/parse_multipart.Rd | 1 +
8 files changed, 39 insertions(+), 20 deletions(-)
Title: Syntax Highlighting for R Source Code
Diff between highr versions 0.4 dated 2014-10-23 and 0.4.1 dated 2015-03-29
Description: Provides syntax highlighting for R source code. Currently it
supports LaTeX and HTML output. Source code of other languages is supported
via Andre Simon's highlight package (http://www.andre-simon.de).
Author: Christopher Gandrud [ctb],
Qiang Li [ctb],
Yixuan Qiu [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 16 ++++++++--------
MD5 | 16 ++++++++--------
R/highlight.R | 2 +-
README.md | 8 ++++----
build/vignette.rds |binary
inst/doc/highr-custom.html | 11 +++++++----
inst/doc/highr-internals.html | 11 +++++++----
man/hi_andre.Rd | 1 +
man/hilight.Rd | 1 +
9 files changed, 37 insertions(+), 29 deletions(-)
Title: Visually Exploring Random Forests
Diff between ggRandomForests versions 1.1.3 dated 2015-01-08 and 1.1.4 dated 2015-03-29
More information about ggRandomForests at CRAN
Description: Graphic elements for exploring Random Forests using the randomForestSRC package for survival, regression and
classification forests and ggplot2 package plotting.
Author: John Ehrlinger
Maintainer: John Ehrlinger
ggRandomForests-1.1.3/ggRandomForests/data/interaction_airq.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/interaction_mtcars.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/interaction_veteran.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_airq.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_coplot_Boston_surf.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_coplot_pbc_surf.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_coplot_pbc_surf2.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_mtcars.rda |only
ggRandomForests-1.1.3/ggRandomForests/data/partial_pbc_surf2.rda |only
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ggRandomForests-1.1.3/ggRandomForests/inst/doc/randomForestSRC-Regression.Rmd |only
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ggRandomForests-1.1.3/ggRandomForests/man/gg_interaction.rfsrc.Rd |only
ggRandomForests-1.1.3/ggRandomForests/man/gg_minimal_depth.rfsrc.Rd |only
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ggRandomForests-1.1.3/ggRandomForests/vignettes/randomForestSRC-Regression.Rmd |only
ggRandomForests-1.1.3/ggRandomForests/vignettes/randomForestSRC-Survival-concordance.tex |only
ggRandomForests-1.1.4/ggRandomForests/DESCRIPTION | 15
ggRandomForests-1.1.4/ggRandomForests/MD5 | 263 --
ggRandomForests-1.1.4/ggRandomForests/NAMESPACE | 46
ggRandomForests-1.1.4/ggRandomForests/NEWS | 21
ggRandomForests-1.1.4/ggRandomForests/R/calc_roc.R | 115 -
ggRandomForests-1.1.4/ggRandomForests/R/combine.gg_partial.R | 62
ggRandomForests-1.1.4/ggRandomForests/R/gg_error.R | 48
ggRandomForests-1.1.4/ggRandomForests/R/gg_interaction.R | 29
ggRandomForests-1.1.4/ggRandomForests/R/gg_minimal_depth.R | 37
ggRandomForests-1.1.4/ggRandomForests/R/gg_minimal_vimp.R | 46
ggRandomForests-1.1.4/ggRandomForests/R/gg_partial.R | 82
ggRandomForests-1.1.4/ggRandomForests/R/gg_partial_coplot.R | 65
ggRandomForests-1.1.4/ggRandomForests/R/gg_rfsrc.R | 98
ggRandomForests-1.1.4/ggRandomForests/R/gg_roc.R | 25
ggRandomForests-1.1.4/ggRandomForests/R/gg_survival.R | 3
ggRandomForests-1.1.4/ggRandomForests/R/gg_variable.R | 58
ggRandomForests-1.1.4/ggRandomForests/R/gg_vimp.R | 86
ggRandomForests-1.1.4/ggRandomForests/R/interaction_data.R | 79
ggRandomForests-1.1.4/ggRandomForests/R/kaplan.R | 62
ggRandomForests-1.1.4/ggRandomForests/R/nelson.R | 85
ggRandomForests-1.1.4/ggRandomForests/R/partial.rfsrc.R |only
ggRandomForests-1.1.4/ggRandomForests/R/partial_coplot_data.R | 16
ggRandomForests-1.1.4/ggRandomForests/R/partial_data.R | 102
ggRandomForests-1.1.4/ggRandomForests/R/partial_surface_data.R | 52
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_error.R | 5
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_interaction.R | 47
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_minimal_depth.R | 65
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_minimal_vimp.R | 15
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_partial.R | 83
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_partial_list.R | 16
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_rfsrc.R | 67
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_roc.R | 65
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_survival.R | 23
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_variable.R | 106
ggRandomForests-1.1.4/ggRandomForests/R/plot.gg_vimp.R | 83
ggRandomForests-1.1.4/ggRandomForests/R/print.gg_minimal_depth.R | 24
ggRandomForests-1.1.4/ggRandomForests/R/quantile_pts.R | 9
ggRandomForests-1.1.4/ggRandomForests/R/rfsrc_cache_datasets.R | 346 +--
ggRandomForests-1.1.4/ggRandomForests/R/rfsrc_data.R | 102
ggRandomForests-1.1.4/ggRandomForests/R/surface_matrix.gg_partial_coplot.R | 44
ggRandomForests-1.1.4/ggRandomForests/R/varsel_data.R | 92
ggRandomForests-1.1.4/ggRandomForests/README.md | 2
ggRandomForests-1.1.4/ggRandomForests/build/vignette.rds |binary
ggRandomForests-1.1.4/ggRandomForests/data/datalist | 16
ggRandomForests-1.1.4/ggRandomForests/data/interaction_Boston.rda |binary
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ggRandomForests-1.1.4/ggRandomForests/data/rfsrc_pbc_test.rda |binary
ggRandomForests-1.1.4/ggRandomForests/data/varsel_Boston.rda |binary
ggRandomForests-1.1.4/ggRandomForests/data/varsel_iris.rda |binary
ggRandomForests-1.1.4/ggRandomForests/data/varsel_pbc.rda |binary
ggRandomForests-1.1.4/ggRandomForests/inst/CITATION | 6
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Regression.R | 108
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Regression.Rnw |only
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Regression.pdf |only
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Survival.R | 735 +++---
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Survival.Rnw | 1132 +++++-----
ggRandomForests-1.1.4/ggRandomForests/inst/doc/randomForestSRC-Survival.pdf |binary
ggRandomForests-1.1.4/ggRandomForests/man/combine.gg_partial.Rd | 23
ggRandomForests-1.1.4/ggRandomForests/man/gg_error.Rd | 18
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ggRandomForests-1.1.4/ggRandomForests/man/gg_rfsrc.rfsrc.Rd | 20
ggRandomForests-1.1.4/ggRandomForests/man/gg_roc.rfsrc.Rd | 12
ggRandomForests-1.1.4/ggRandomForests/man/gg_variable.rfsrc.Rd | 15
ggRandomForests-1.1.4/ggRandomForests/man/gg_vimp.rfsrc.Rd |only
ggRandomForests-1.1.4/ggRandomForests/man/interaction_data.Rd | 77
ggRandomForests-1.1.4/ggRandomForests/man/partial.rfsrc.Rd |only
ggRandomForests-1.1.4/ggRandomForests/man/partial_coplot_data.Rd | 13
ggRandomForests-1.1.4/ggRandomForests/man/partial_data.Rd | 100
ggRandomForests-1.1.4/ggRandomForests/man/partial_surface_data.Rd |only
ggRandomForests-1.1.4/ggRandomForests/man/plot.gg_partial.Rd | 7
ggRandomForests-1.1.4/ggRandomForests/man/plot.gg_vimp.Rd | 6
ggRandomForests-1.1.4/ggRandomForests/man/print.gg_minimal_depth.Rd | 16
ggRandomForests-1.1.4/ggRandomForests/man/rfsrc_cache_datasets.Rd | 1
ggRandomForests-1.1.4/ggRandomForests/man/rfsrc_data.Rd | 97
ggRandomForests-1.1.4/ggRandomForests/man/shift.Rd |only
ggRandomForests-1.1.4/ggRandomForests/man/surface_matrix.Rd | 25
ggRandomForests-1.1.4/ggRandomForests/man/varsel_data.Rd | 88
ggRandomForests-1.1.4/ggRandomForests/vignettes/ggRandomForests.bib | 131 -
ggRandomForests-1.1.4/ggRandomForests/vignettes/randomForestSRC-Regression.Rnw |only
ggRandomForests-1.1.4/ggRandomForests/vignettes/randomForestSRC-Survival.Rnw | 1132 +++++-----
125 files changed, 3314 insertions(+), 3191 deletions(-)
Permanent link
Title: Format R Code Automatically
Diff between formatR versions 1.0 dated 2014-08-24 and 1.1 dated 2015-03-29
Description: Provides a function tidy_source() to format R source code. Spaces
and indent will be added to the code automatically, and comments will be
preserved under certain conditions, so that R code will be more
human-readable and tidy. There is also a Shiny app as a user interface in
this package (see tidy_app()).
Author: Yihui Xie
Maintainer: Yihui Xie
DESCRIPTION | 20 ++++++++++----------
MD5 | 28 ++++++++++++++--------------
NEWS | 11 +++++++++++
R/tidy.R | 2 +-
R/usage.R | 8 +++++---
R/utils.R | 1 +
build/vignette.rds |binary
inst/doc/formatR.html | 31 +++++++++++++++++--------------
inst/shiny/ui.R | 2 +-
man/deprecated.Rd | 1 +
man/tidy_app.Rd | 1 +
man/tidy_dir.Rd | 1 +
man/tidy_eval.Rd | 1 +
man/tidy_source.Rd | 3 ++-
man/usage.Rd | 8 ++++++--
15 files changed, 72 insertions(+), 46 deletions(-)
Title: Simulation-Based False Discovery Rate in RNA-Seq
Diff between empiricalFDR.DESeq2 versions 1.0 dated 2014-11-25 and 1.0.1 dated 2015-03-29
More information about empiricalFDR.DESeq2 at CRAN
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
DESCRIPTION | 10 +++++-----
MD5 | 12 +++++++-----
R/empiricalFDR.R | 4 ++--
R/fdrBiCurve_work.R |only
R/fdrTable_work.R |only
man/empiricalFDR.DESeq2-package.Rd | 6 +++---
man/empiricalFDR.Rd | 5 ++++-
man/fdrBiCurve.Rd | 2 +-
8 files changed, 22 insertions(+), 17 deletions(-)
Permanent link
Title: Analysis of Animal Movements
Diff between adehabitatLT versions 0.3.18 dated 2015-03-27 and 0.3.19 dated 2015-03-29
Description: A collection of tools for the analysis of animal movements.
Author: Clement Calenge, contributions from Stephane Dray and Manuela Royer
Maintainer: Clement Calenge
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/rasterize.r | 32 +++++++++++++++++++++-----------
inst/doc/adehabitatLT.pdf |binary
4 files changed, 28 insertions(+), 18 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Diff between DoE.base versions 0.26-3 dated 2014-09-29 and 0.27 dated 2015-03-28
Description: Package \pkg{DoE.base} creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class \code{design}, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 14 +++----
MD5 | 68 +++++++++++++++++++-------------------
NAMESPACE | 5 ++
R/DesignAccessors.r | 27 +++++++++++++--
R/GRind.R | 19 ++++++++--
R/fac.design.R | 71 +++++++++++++++++++++++++++++++---------
R/fastlengths.R | 10 +++--
R/halfnormal.R | 57 +++++++++++++++++++-------------
R/length2.R | 6 ---
R/lengths.R |only
R/oa.design.R | 13 ++++++-
R/planor2design.r | 2 +
R/plot.design.R | 23 +++++++++++-
R/printandsummary.design.R | 4 +-
R/rerandomize.R | 52 +++++++++++++++++++++++++++--
R/show.oas.R | 28 ++++++++++++---
R/sysdata.rda |binary
R/utilities.R | 59 +++++++++++++++++++++++++++++++++
inst/NEWS | 62 +++++++++++++++++++++++++++++++++-
man/GWLP.Rd | 8 ++--
man/VSGFS.Rd |only
man/class-design.Rd | 8 +++-
man/fac.design.Rd | 15 ++++++--
man/generalized.word.length.Rd | 50 +++++++++++++++++-----------
man/getblock.Rd | 16 +++++++--
man/halfnormal.Rd | 47 ++++++++++++++++----------
man/oa.design.Rd | 8 +++-
man/oacat.Rd | 22 ++++++++++--
man/planor2design.Rd | 4 +-
man/plot.design.Rd | 13 +++----
man/show.oas.Rd | 50 ++++++++++++++++++++++------
tests/test_aggregate.Rout.save | 12 ++++--
tests/test_colorder.Rout.save | 12 ++++--
tests/test_cross.Rout.save | 12 ++++--
tests/test_qua.design.Rout.save | 15 +++++---
tests/test_reshape.Rout.save | 15 +++++---
36 files changed, 624 insertions(+), 203 deletions(-)
Title: Weighted Correlation Network Analysis
Diff between WGCNA versions 1.43 dated 2015-01-15 and 1.46 dated 2015-03-28
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder
Maintainer: Peter Langfelder
WGCNA-1.43/WGCNA/R/smaFunctions-Rna.R |only
WGCNA-1.43/WGCNA/R/smaFunctions.R |only
WGCNA-1.43/WGCNA/man/na.Rd |only
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WGCNA-1.43/WGCNA/man/rgcolors.func.Rd |only
WGCNA-1.43/WGCNA/man/stat.diag.da.Rd |only
WGCNA-1.43/WGCNA/man/stats.bwss.Rd |only
WGCNA-1.46/WGCNA/Changelog | 33 ++++
WGCNA-1.46/WGCNA/DESCRIPTION | 10 -
WGCNA-1.46/WGCNA/MD5 | 41 ++---
WGCNA-1.46/WGCNA/NAMESPACE | 3
WGCNA-1.46/WGCNA/R/Functions.R | 50 ++++--
WGCNA-1.46/WGCNA/R/blockwiseModulesC.R | 6
WGCNA-1.46/WGCNA/R/consensusTOM.R | 8 -
WGCNA-1.46/WGCNA/R/empiricalBayesLM.R |only
WGCNA-1.46/WGCNA/R/exportFunctions.R | 15 +-
WGCNA-1.46/WGCNA/R/heatmapWithLegend.R | 6
WGCNA-1.46/WGCNA/man/WGCNA-package.Rd | 11 -
WGCNA-1.46/WGCNA/man/bicovWeights.Rd |only
WGCNA-1.46/WGCNA/man/empiricalBayesLM.Rd |only
WGCNA-1.46/WGCNA/man/labeledHeatmap.Rd | 15 +-
WGCNA-1.46/WGCNA/man/qvalue.Rd | 2
WGCNA-1.46/WGCNA/src/corFunctions-common.c | 76 +++++-----
WGCNA-1.46/WGCNA/src/corFunctions-common.h | 10 -
WGCNA-1.46/WGCNA/src/corFunctions-unified.c | 205 +++++++++++++++-------------
WGCNA-1.46/WGCNA/src/networkFunctions.c | 2
27 files changed, 293 insertions(+), 200 deletions(-)
Title: Unconditional Exact Test
Diff between Exact versions 1.4 dated 2013-07-22 and 1.5 dated 2015-03-28
Description: Performs unconditional exact tests and power calculations for 2x2 contingency
tables. Unconditional exact tests are often more powerful than conditional exact tests and asymptotic tests.
Author: Peter Calhoun
Maintainer: Peter Calhoun
DESCRIPTION | 11 -
MD5 | 16 -
R/binomialCode.R | 416 +++++++++++++++++++++++++--------------------------
R/exact.test.R | 134 ++++++++++++----
R/fisher.2x2.R | 37 ++--
R/multinomialCode.R | 209 ++++++++++++-------------
R/power.exact.test.R | 113 ++++++-------
man/Exact-package.Rd | 12 -
man/exact.test.Rd | 9 -
9 files changed, 514 insertions(+), 443 deletions(-)
Title: Create a Mini Version of CRAN Containing Only Selected Packages
Diff between miniCRAN versions 0.2.2 dated 2015-03-26 and 0.2.4 dated 2015-03-27
Description: Makes it possible to create an internally consistent
repository consisting of selected packages from CRAN-like repositories.
The user specifies a set of desired packages, and miniCRAN recursively
reads the dependency tree for these packages, then downloads only this
subset. The user can then install packages from this repository directly,
rather than from CRAN. This is useful in production settings, e.g. server
behind a firewall, or remote locations with slow broadband access.
Author: Revolution Analytics [aut],
Andrie de Vries [aut, cre],
Alex Chubaty [ctb]
Maintainer: Andrie de
Vries
miniCRAN-0.2.2/miniCRAN/vignettes/figure |only
miniCRAN-0.2.4/miniCRAN/DESCRIPTION | 6
miniCRAN-0.2.4/miniCRAN/MD5 | 32 +-
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-dependency-graph.R | 8
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-dependency-graph.html | 39 +--
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-dependency-graph.rmd | 8
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-introduction.R | 120 +++++-----
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-introduction.html | 115 ---------
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-introduction.rmd | 22 -
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.R | 50 ++--
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.html | 79 ------
miniCRAN-0.2.4/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.rmd | 8
miniCRAN-0.2.4/miniCRAN/inst/examples/example_addPackageListingGithub.R | 22 -
miniCRAN-0.2.4/miniCRAN/man/addPackageListingGithub.Rd | 22 -
miniCRAN-0.2.4/miniCRAN/vignettes/miniCRAN-dependency-graph.rmd | 8
miniCRAN-0.2.4/miniCRAN/vignettes/miniCRAN-introduction.rmd | 22 -
miniCRAN-0.2.4/miniCRAN/vignettes/miniCRAN-non-CRAN-repos.rmd | 8
17 files changed, 198 insertions(+), 371 deletions(-)
Title: High Dimensional Discriminant Analysis
Diff between HiDimDA versions 0.2-2 dated 2014-10-25 and 0.2-3 dated 2015-03-27
Description: Performs linear discriminant analysis in high dimensional
problems based on reliable covariance estimators for problems
with (many) more variables than observations. Includes routines
for classifier training, prediction, cross-validation and
variable selection.
Author: Antonio Pedro Duarte Silva
Maintainer: Antonio Pedro Duarte Silva
CHANGELOG | 7 +++-
DESCRIPTION | 8 ++--
MD5 | 8 ++--
NAMESPACE | 71 ++++++++++++++++++++++++++++++++++++++++++
R/RepLOptim.R | 97 ----------------------------------------------------------
5 files changed, 85 insertions(+), 106 deletions(-)
Title: General-to-Specific (GETS) Modelling
Diff between AutoSEARCH versions 1.4 dated 2014-12-22 and 1.5 dated 2015-03-27
Description: General-to-Specific (GETS) modelling of the mean and variance of a regression. NOTE: The package has been succeeded by gets, also available on the CRAN, which is more user-friendly, faster and easier to extend. Users are therefore encouraged to consider gets instead.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
DESCRIPTION | 14 +-
MD5 | 37 +++---
NAMESPACE | 4
NEWS | 7 +
R/AutoSEARCH-internal.R | 270 ++++++++++++++++++++++++----------------------
R/eqwma.R |only
R/gLag.R | 9 -
R/gets.mean.R | 18 ---
R/gets.vol.R | 70 -----------
R/info.criterion.R |only
R/jb.test.R |only
R/leqwma.R |only
R/ols.fit1.R | 1
R/ols.fit2.R | 1
R/skewness.test.R |only
man/AutoSEARCH-package.Rd | 12 +-
man/eqwma.Rd |only
man/gets.mean.Rd | 4
man/info.criterion.Rd |only
man/jb.test.Rd |only
man/regs.mean.sm.Rd | 2
man/regs.vol.sm.Rd | 2
man/skewness.test.Rd |only
man/sm.Rd | 6 -
24 files changed, 195 insertions(+), 262 deletions(-)
Title: Thematic Maps
Diff between tmap versions 0.6 dated 2014-07-30 and 0.7 dated 2015-03-27
Description: Thematic maps are geographical maps in which statistical data are visualized. This package offers a flexible, layer-based, way to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes
tmap-0.6/tmap/R/print_tm.R |only
tmap-0.6/tmap/R/split_lines.R |only
tmap-0.7/tmap/DESCRIPTION | 13 -
tmap-0.7/tmap/MD5 | 174 +++++++++++-----------
tmap-0.7/tmap/NAMESPACE | 9 +
tmap-0.7/tmap/NEWS | 15 +
tmap-0.7/tmap/R/animation_tmap.R | 25 +--
tmap-0.7/tmap/R/append_data.R | 72 ++++++---
tmap-0.7/tmap/R/approx_areas.R | 11 -
tmap-0.7/tmap/R/calc_densities.R | 20 +-
tmap-0.7/tmap/R/cellplot.R | 16 +-
tmap-0.7/tmap/R/convert_shape_data.R | 124 +++++++++++++--
tmap-0.7/tmap/R/crop_shape.R | 18 +-
tmap-0.7/tmap/R/double_line.R | 3
tmap-0.7/tmap/R/fit_polylines.R | 20 +-
tmap-0.7/tmap/R/get_IDs.R | 7
tmap-0.7/tmap/R/get_alpha_col.R |only
tmap-0.7/tmap/R/get_polygon_directions.R |only
tmap-0.7/tmap/R/get_polygon_ranges.R | 4
tmap-0.7/tmap/R/get_proj4_code.R | 25 +--
tmap-0.7/tmap/R/grid_shp.R | 26 +--
tmap-0.7/tmap/R/gridplot.R | 47 +++---
tmap-0.7/tmap/R/legend_plot.R | 129 ++++++++++------
tmap-0.7/tmap/R/legend_prepare.R | 9 +
tmap-0.7/tmap/R/map2scale.R |only
tmap-0.7/tmap/R/map_points_to_line.R | 16 +-
tmap-0.7/tmap/R/num2pal.R | 88 +++++------
tmap-0.7/tmap/R/pkg.R | 40 +++--
tmap-0.7/tmap/R/plot_map.R | 197 +++++++++++++++++--------
tmap-0.7/tmap/R/print_tmap.R |only
tmap-0.7/tmap/R/process_bubbles.R | 45 ++++-
tmap-0.7/tmap/R/process_fill.R | 13 +
tmap-0.7/tmap/R/process_layers.R | 35 +++-
tmap-0.7/tmap/R/process_lines.R | 8 -
tmap-0.7/tmap/R/process_meta.R | 53 +++++-
tmap-0.7/tmap/R/process_shapes.R | 218 ++++++++++++++++++++++------
tmap-0.7/tmap/R/process_text.R | 29 ++-
tmap-0.7/tmap/R/process_tm.R | 116 ++++++++++++--
tmap-0.7/tmap/R/qtm.R | 74 +++++----
tmap-0.7/tmap/R/read_shape.R | 56 +++++--
tmap-0.7/tmap/R/sbind.R |only
tmap-0.7/tmap/R/set_projection.R | 3
tmap-0.7/tmap/R/split_lines_equal.R |only
tmap-0.7/tmap/R/split_lines_poly.R | 9 -
tmap-0.7/tmap/R/split_shps.R |only
tmap-0.7/tmap/R/split_tm.R | 23 +-
tmap-0.7/tmap/R/tm_layers.R | 134 ++++++++++-------
tmap-0.7/tmap/R/tm_layout.R | 29 +--
tmap-0.7/tmap/build/vignette.rds |binary
tmap-0.7/tmap/data/Europe.rda |binary
tmap-0.7/tmap/data/NLD_muni.rda |binary
tmap-0.7/tmap/data/NLD_prov.rda |binary
tmap-0.7/tmap/data/World.rda |binary
tmap-0.7/tmap/data/cities.rda |binary
tmap-0.7/tmap/data/rivers.rda |binary
tmap-0.7/tmap/inst/doc/tmap-nutshell.R | 37 ++--
tmap-0.7/tmap/inst/doc/tmap-nutshell.Rmd | 125 +++++++++-------
tmap-0.7/tmap/inst/doc/tmap-nutshell.html | 174 +++++++++++++---------
tmap-0.7/tmap/man/Shapes.Rd | 27 ++-
tmap-0.7/tmap/man/Shapes2.Rd | 10 +
tmap-0.7/tmap/man/animation_tmap.Rd | 14 +
tmap-0.7/tmap/man/append_data.Rd | 46 ++++-
tmap-0.7/tmap/man/approx_areas.Rd | 24 ++-
tmap-0.7/tmap/man/calc_densities.Rd | 24 ++-
tmap-0.7/tmap/man/convert_shape_data.Rd | 34 +++-
tmap-0.7/tmap/man/crop_shape.Rd | 20 +-
tmap-0.7/tmap/man/double_line.Rd | 8 -
tmap-0.7/tmap/man/fit_polylines.Rd | 20 ++
tmap-0.7/tmap/man/get_IDs.Rd | 10 +
tmap-0.7/tmap/man/get_polygon_directions.Rd |only
tmap-0.7/tmap/man/get_polygon_ranges.Rd | 7
tmap-0.7/tmap/man/intersection_shapes.Rd |only
tmap-0.7/tmap/man/map_points_to_line.Rd |only
tmap-0.7/tmap/man/plus-.tmap.Rd | 3
tmap-0.7/tmap/man/print.tmap.Rd | 13 +
tmap-0.7/tmap/man/qtm.Rd | 22 +-
tmap-0.7/tmap/man/read_shape.Rd | 30 +++
tmap-0.7/tmap/man/sbind.Rd |only
tmap-0.7/tmap/man/set_projection.Rd | 6
tmap-0.7/tmap/man/split_lines_equal.Rd | 14 +
tmap-0.7/tmap/man/split_lines_poly.Rd | 14 +
tmap-0.7/tmap/man/split_shapes.Rd |only
tmap-0.7/tmap/man/tm_borders.Rd | 29 +--
tmap-0.7/tmap/man/tm_bubbles.Rd | 50 ++----
tmap-0.7/tmap/man/tm_facets.Rd | 73 ++++++---
tmap-0.7/tmap/man/tm_fill.Rd | 81 +++++-----
tmap-0.7/tmap/man/tm_grid.Rd | 5
tmap-0.7/tmap/man/tm_layout.Rd | 66 +++++---
tmap-0.7/tmap/man/tm_lines.Rd | 36 ++--
tmap-0.7/tmap/man/tm_shape.Rd | 59 ++++---
tmap-0.7/tmap/man/tm_text.Rd | 68 ++++----
tmap-0.7/tmap/man/tmap-element.Rd | 51 +++++-
tmap-0.7/tmap/man/tmap-package.Rd | 9 -
tmap-0.7/tmap/man/write_shape.Rd | 7
tmap-0.7/tmap/vignettes/tmap-nutshell.Rmd | 125 +++++++++-------
95 files changed, 2186 insertions(+), 1108 deletions(-)
Title: Hierarchical Climate Regionalization
Diff between HiClimR versions 1.1.6 dated 2015-03-01 and 1.2.0 dated 2015-03-27
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, hybrid hierarchical clustering, multi-variate clustering (MVC),
cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr
HiClimR-1.1.6/HiClimR/Changelog |only
HiClimR-1.2.0/HiClimR/DESCRIPTION | 20 -
HiClimR-1.2.0/HiClimR/MD5 | 41 +-
HiClimR-1.2.0/HiClimR/R/HiClimR.R | 557 ++++++++++++++++++--------------
HiClimR-1.2.0/HiClimR/R/coarseR.R | 87 ++--
HiClimR-1.2.0/HiClimR/R/fastCor.R | 158 ++++++---
HiClimR-1.2.0/HiClimR/R/geogMask.R | 85 ++--
HiClimR-1.2.0/HiClimR/R/grid2D.R | 78 ++--
HiClimR-1.2.0/HiClimR/R/minSigCor.R | 78 ++--
HiClimR-1.2.0/HiClimR/R/validClimR.R | 121 ++++--
HiClimR-1.2.0/HiClimR/README.md | 503 ++++++++++++++++++++++++++--
HiClimR-1.2.0/HiClimR/inst/CITATION | 27 +
HiClimR-1.2.0/HiClimR/man/HiClimR.Rd | 410 +++++++++++++++--------
HiClimR-1.2.0/HiClimR/man/TestCase.Rd | 20 -
HiClimR-1.2.0/HiClimR/man/WorldMask.Rd | 8
HiClimR-1.2.0/HiClimR/man/coarseR.Rd | 20 -
HiClimR-1.2.0/HiClimR/man/fastCor.Rd | 65 +++
HiClimR-1.2.0/HiClimR/man/geogMask.Rd | 17
HiClimR-1.2.0/HiClimR/man/grid2D.Rd | 8
HiClimR-1.2.0/HiClimR/man/minSigCor.Rd | 8
HiClimR-1.2.0/HiClimR/man/validClimR.Rd | 50 --
HiClimR-1.2.0/HiClimR/src/HiClimR.f90 | 266 ++++++---------
22 files changed, 1717 insertions(+), 910 deletions(-)
Title: Learned Pattern Similarity and Representation for Time Series
Diff between LPStimeSeries versions 1.0-4 dated 2015-01-09 and 1.0-5 dated 2015-03-27
Description: Learned Pattern Similarity (LPS) for time series.
Implements a novel approach to model the dependency structure
in time series that generalizes the concept of autoregression to local
auto-patterns. Generates a pattern-based representation of time series
along with a similarity measure called Learned Pattern Similarity (LPS).
Introduces a generalized autoregressive kernel.This package is based on the
'randomForest' package by Andy Liaw.
Author: Learned Pattern Similarity (LPS) for time series by Mustafa Gokce Baydogan
Maintainer: Mustafa Gokce Baydogan
DESCRIPTION | 21 ++++++++++++---------
MD5 | 4 ++--
man/learnPattern.Rd | 7 +++++--
3 files changed, 19 insertions(+), 13 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Diff between fanc versions 1.22 dated 2015-03-18 and 1.23 dated 2015-03-27
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto, Haruhisa Nagata
Maintainer: Kei Hirose
DESCRIPTION | 8
MD5 | 4
src/fanc.c | 2478 ++++++++++++++++++++++++++++++------------------------------
3 files changed, 1247 insertions(+), 1243 deletions(-)
Title: Analysis of Habitat Selection by Animals
Diff between adehabitat versions 1.8.15 dated 2014-12-17 and 1.8.17 dated 2015-03-27
Description: A collection of tools for the analysis of habitat selection by animals.
Author: Clement Calenge, contributions from Mathieu Basille, Stephane Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge
DESCRIPTION | 15 +++++++--------
MD5 | 20 ++++++++++----------
NAMESPACE | 17 ++++++++++++++++-
R/asc2im.r | 4 ----
R/biv.plot.r | 2 --
R/biv.test.r | 2 --
R/debut.r | 4 ++--
R/simm.crw.r | 2 --
man/kernelUD.Rd | 2 +-
man/modpartltraj.Rd | 2 +-
src/tests.c | 2 +-
11 files changed, 38 insertions(+), 34 deletions(-)
Title: Import Articles from 'Europresse' Using the 'tm' Text Mining
Framework
Diff between tm.plugin.europresse versions 1.1 dated 2014-06-11 and 1.2 dated 2015-03-27
More information about tm.plugin.europresse at CRAN
Description: Provides a 'tm' Source to create corpora from
articles exported from the 'Europresse' content provider as
HTML files. It is able to read both text content and meta-data
information (including source, date, title, author and pages).
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
NEWS | 3 +++
R/readEuropresseHTML.R | 4 ++--
4 files changed, 16 insertions(+), 13 deletions(-)
Permanent link
Title: Tools for Eurostat Open Data
Diff between eurostat versions 1.0.15 dated 2015-03-20 and 1.0.16 dated 2015-03-27
Description: Tools to download data from the Eurostat database
http://ec.europa.eu/eurostat/ together with search and manipulation
utilities.
Author: Lahti Leo [aut, cre],
Biecek Przemyslaw [aut],
Kainu Markus [aut],
Huovari Janne [aut]
Maintainer: Lahti Leo
DESCRIPTION | 8 -
MD5 | 12 +-
inst/doc/eurostat_tutorial.R | 10 +-
inst/doc/eurostat_tutorial.Rmd | 10 +-
inst/doc/eurostat_tutorial.html | 124 ++++++++++++++++++++---------
vignettes/eurostat_tutorial.Rmd | 10 +-
vignettes/eurostat_tutorial.md | 168 ++++++++++++++++++++--------------------
7 files changed, 196 insertions(+), 146 deletions(-)
Title: Tools to Deal with Raster Maps
Diff between adehabitatMA versions 0.3.8 dated 2013-09-23 and 0.3.9 dated 2015-03-27
Description: A collection of tools to deal with raster maps.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge
DESCRIPTION | 11 +++++------
MD5 | 10 +++++-----
R/explore.r | 52 ++++++++++++++++++++++++++++------------------------
build/vignette.rds |binary
man/explore.Rd | 2 +-
src/tests.c | 13 +++++++------
6 files changed, 46 insertions(+), 42 deletions(-)
Title: Analysis of Animal Movements
Diff between adehabitatLT versions 0.3.17 dated 2014-12-17 and 0.3.18 dated 2015-03-27
Description: A collection of tools for the analysis of animal movements.
Author: Clement Calenge, contributions from Stephane Dray and Manuela Royer
Maintainer: Clement Calenge
DESCRIPTION | 16 +++----
MD5 | 26 +++++------
NAMESPACE | 11 ++++
R/as.ltraj.r | 9 +---
R/rasterize.r | 2
R/testNM.r | 2
R/trajdyn.r | 3 -
build/vignette.rds |binary
inst/doc/adehabitatLT.R | 101 +++++++++++++++++++++------------------------
inst/doc/adehabitatLT.Rnw | 19 +++-----
inst/doc/adehabitatLT.pdf |binary
man/as.ltraj.Rd | 3 -
man/modpartltraj.Rd | 2
vignettes/adehabitatLT.Rnw | 19 +++-----
14 files changed, 104 insertions(+), 109 deletions(-)
Title: Analysis of Habitat Selection by Animals
Diff between adehabitatHS versions 0.3.10 dated 2014-12-17 and 0.3.11 dated 2015-03-27
Description: A collection of tools for the analysis of habitat selection.
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge
DESCRIPTION | 13 ++++++-------
MD5 | 12 ++++++------
NAMESPACE | 11 ++++++++++-
R/biv.plot.r | 4 ----
R/biv.test.r | 2 --
R/niche.test.r | 4 +++-
build/vignette.rds |binary
7 files changed, 25 insertions(+), 21 deletions(-)
Title: Home Range Estimation
Diff between adehabitatHR versions 0.4.12 dated 2014-12-17 and 0.4.13 dated 2015-03-27
Description: A collection of tools for the estimation of animals home range.
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge
DESCRIPTION | 13 -
MD5 | 18 +-
R/CharHull.r | 4
R/LoCoH.r | 8 -
build/vignette.rds |binary
inst/doc/adehabitatHR.R | 298 ++++++++++++++++++++++-----------------------
inst/doc/adehabitatHR.Rnw | 20 +--
inst/doc/adehabitatHR.pdf |binary
man/kernelUD.Rd | 2
vignettes/adehabitatHR.Rnw | 20 +--
10 files changed, 191 insertions(+), 192 deletions(-)
Title: Robust Data Envelopment Analysis (DEA) for R
Diff between rDEA versions 1.0-2 dated 2014-12-21 and 1.1-1 dated 2015-03-27
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre],
Galina Besstremyannaya [aut]
Maintainer: Jaak Simm
rDEA-1.0-2/rDEA/src/tags |only
rDEA-1.1-1/rDEA/DESCRIPTION | 6 ++--
rDEA-1.1-1/rDEA/MD5 | 17 ++++++-------
rDEA-1.1-1/rDEA/R/dea.env.robust.R | 1
rDEA-1.1-1/rDEA/R/dea.robust.R | 23 ++++++++++++------
rDEA-1.1-1/rDEA/README.md | 13 ++++++++--
rDEA-1.1-1/rDEA/inst/CHANGELOG | 5 +++
rDEA-1.1-1/rDEA/inst/tests/testthat/test-dea.robust.r | 14 ++++++++++
rDEA-1.1-1/rDEA/man/dea_env_robust.Rd | 8 +++---
rDEA-1.1-1/rDEA/man/dea_robust.Rd | 4 ++-
10 files changed, 65 insertions(+), 26 deletions(-)
Title: Loading Google Adwords Data into R
Diff between RAdwords versions 0.1.1 dated 2014-11-11 and 0.1.2 dated 2015-03-27
Description: The aim of RAdwords is loading Adwords data into R. Therefore the
package implements three main features. First, the package provides an
authentication process for R with the Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt
Maintainer: Johannes Burkhardt
RAdwords-0.1.1/RAdwords/inst/extdata/ACCOUNT_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/ACCOUNT_REACH_FREQUENCY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/ADGROUP_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/ADGROUP_REACH_FREQUENCY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/AD_EXTENSIONS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/AD_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/AGE_RANGE_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/AUDIENCE_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/AUTOMATIC_PLACEMENTS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/BID_GOAL_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/BUDGET_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CALL_METRICS_CALL_DETAILS_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_AD_SCHEDULE_TARGET_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_LOCATION_TARGET_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_NEGATIVE_KEYWORDS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_NEGATIVE_LOCATIONS_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_NEGATIVE_PLACEMENTS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_PLATFORM_TARGET_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_REACH_FREQUENCY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CAMPAIGN_SHARED_SET_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CLICK_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CREATIVE_CONVERSION_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/CRITERIA_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/DESTINATION_URL_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/DISPLAY_KEYWORD_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/DISPLAY_TOPICS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/GENDER_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/GEO_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/KEYWORDLESS_CATEGORY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/KEYWORDLESS_QUERY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/KEYWORDS_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/PAID_ORGANIC_QUERY_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/PLACEHOLDER_FEED_ITEM_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/PLACEHOLDER_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/PLACEMENT_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/PRODUCT_PARTITION_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/SEARCH_QUERY_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/SHARED_SET_CRITERIA_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/SHARED_SET_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/SHOPPING_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.1/RAdwords/inst/extdata/URL_PERFORMANCE_REPORT.csv |only
RAdwords-0.1.2/RAdwords/DESCRIPTION | 12
RAdwords-0.1.2/RAdwords/LICENSE | 2
RAdwords-0.1.2/RAdwords/MD5 | 170 ++++++----
RAdwords-0.1.2/RAdwords/NAMESPACE | 2
RAdwords-0.1.2/RAdwords/NEWS |only
RAdwords-0.1.2/RAdwords/R/getData.R | 6
RAdwords-0.1.2/RAdwords/R/metrics.R | 14
RAdwords-0.1.2/RAdwords/R/reports.R | 16
RAdwords-0.1.2/RAdwords/R/statement.R | 2
RAdwords-0.1.2/RAdwords/R/transformData.R | 35 +-
RAdwords-0.1.2/RAdwords/README.md | 10
RAdwords-0.1.2/RAdwords/inst/extdata/api201409 |only
RAdwords-0.1.2/RAdwords/inst/extdata/api201502 |only
RAdwords-0.1.2/RAdwords/man/RAdwords.Rd | 22 +
RAdwords-0.1.2/RAdwords/man/changeNames.Rd | 3
RAdwords-0.1.2/RAdwords/man/doAuth.Rd | 3
RAdwords-0.1.2/RAdwords/man/getAuth.Rd | 3
RAdwords-0.1.2/RAdwords/man/getData.Rd | 9
RAdwords-0.1.2/RAdwords/man/loadToken.Rd | 3
RAdwords-0.1.2/RAdwords/man/metrics.Rd | 7
RAdwords-0.1.2/RAdwords/man/refreshToken.Rd | 3
RAdwords-0.1.2/RAdwords/man/reports.Rd | 8
RAdwords-0.1.2/RAdwords/man/statement.Rd | 5
RAdwords-0.1.2/RAdwords/man/transformData.Rd | 7
66 files changed, 228 insertions(+), 114 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-27 1.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-03-09 1.0
2008-06-08 0.4
2007-05-10 0.3-4
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-12 dated 2015-02-13 and 3.1-15 dated 2015-03-27
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
DESCRIPTION | 8 +--
MD5 | 20 ++++-----
NAMESPACE | 1
R/layout20x.R | 5 --
R/normcheck.R | 16 ++++---
R/rowdistr.r | 11 ++--
R/summaryStats.R | 106 ++++++++++++++++++++++++++++++++++--------------
man/interactionPlots.Rd | 22 ++++-----
man/layout20x.Rd | 10 ++--
man/summary2way.Rd | 3 -
man/summaryStats.Rd | 75 ++++++++++++++++++++-------------
11 files changed, 174 insertions(+), 103 deletions(-)
Title: Tools for Creating Universal Numeric Fingerprints for Data
Diff between UNF versions 2.0 dated 2015-03-21 and 2.0.1 dated 2015-03-26
Description: Computes a universal numeric fingerprint (UNF) for an R data object. UNF is a cryptographic hash or signature that can be used to uniquely identify (a version of) a rectangular dataset, or a subset thereof. UNF can be used, in tandem with a DOI, to form a persistent citation to a versioned dataset.
Author: Thomas Leeper [aut, cre],
Micah Altman [aut]
Maintainer: Thomas Leeper
CHANGELOG | 105 ++++++++++++++++----------------
DESCRIPTION | 10 +--
MD5 | 16 ++--
R/unf5.R | 4 -
R/unf6.R | 4 -
inst/CITATION | 62 +++++++++---------
man/unf.Rd | 7 --
tests/testthat/test-unf6-common-tests.R | 4 -
tests/testthat/test-unf6-datetimes.R | 12 +--
9 files changed, 113 insertions(+), 111 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Diff between secrdesign versions 2.2.2 dated 2015-01-11 and 2.3.0 dated 2015-03-26
Description: Tools are provided for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'.
Author: Murray Efford
Maintainer: Murray Efford
secrdesign-2.2.2/secrdesign/vignettes/secrdesign-fig1.pdf |only
secrdesign-2.2.2/secrdesign/vignettes/secrdesign-fig2.pdf |only
secrdesign-2.3.0/secrdesign/DESCRIPTION | 12
secrdesign-2.3.0/secrdesign/MD5 | 34 -
secrdesign-2.3.0/secrdesign/NEWS | 18
secrdesign-2.3.0/secrdesign/R/make.scenarios.R | 3
secrdesign-2.3.0/secrdesign/R/methods.R | 22
secrdesign-2.3.0/secrdesign/R/run.scenarios.R | 295 +++++-----
secrdesign-2.3.0/secrdesign/R/select.stats.R | 9
secrdesign-2.3.0/secrdesign/build/vignette.rds |binary
secrdesign-2.3.0/secrdesign/inst/doc/secrdesign-manual.pdf |binary
secrdesign-2.3.0/secrdesign/inst/doc/secrdesign-vignette.R | 20
secrdesign-2.3.0/secrdesign/inst/doc/secrdesign-vignette.Rmd | 52 -
secrdesign-2.3.0/secrdesign/inst/doc/secrdesign-vignette.pdf |binary
secrdesign-2.3.0/secrdesign/man/run.scenarios.Rd | 8
secrdesign-2.3.0/secrdesign/man/secrdesign-package.Rd | 4
secrdesign-2.3.0/secrdesign/man/select.stats.Rd | 10
secrdesign-2.3.0/secrdesign/vignettes/secrdesign-fig1.png |only
secrdesign-2.3.0/secrdesign/vignettes/secrdesign-fig2.png |only
secrdesign-2.3.0/secrdesign/vignettes/secrdesign-vignette.Rmd | 52 -
20 files changed, 304 insertions(+), 235 deletions(-)
Title: Robust Covariance Matrix Estimators
Diff between sandwich versions 2.3-2 dated 2014-08-24 and 2.3-3 dated 2015-03-26
Description: Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.
Author: Thomas Lumley [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 8 ++++----
MD5 | 28 ++++++++++++++--------------
NAMESPACE | 4 +++-
NEWS | 10 ++++++++++
R/estfun.R | 2 --
R/vcovHAC.R | 2 +-
build/vignette.rds |binary
data/Investment.rda |binary
data/PublicSchools.rda |binary
inst/doc/sandwich-OOP.pdf |binary
inst/doc/sandwich.Rnw | 2 +-
inst/doc/sandwich.pdf |binary
man/vcovOPG.Rd | 2 +-
tests/Examples/sandwich-Ex.Rout.save | 12 ++++++------
vignettes/sandwich.Rnw | 2 +-
15 files changed, 41 insertions(+), 31 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero/One Inflated
Beta Regression
Diff between zoib versions 1.2 dated 2015-02-18 and 1.2.1 dated 2015-03-26
Description: Fits beta regression and zero/one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu
Maintainer: Fang Liu
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
man/fixed01.Rd | 2 +-
man/joint.1z01.Rd | 12 ++++++------
man/joint.2z01.Rd | 2 +-
man/sep.1z01.Rd | 2 +-
man/sep.2z01.Rd | 2 +-
man/zoib-package.Rd | 4 ++--
man/zoib.Rd | 8 ++++----
9 files changed, 28 insertions(+), 28 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Diff between Surrogate versions 0.1-4 dated 2014-12-12 and 0.1-5 dated 2015-03-26
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst
DESCRIPTION | 9 -
MD5 | 89 +++++++----
NAMESPACE | 35 ++++
NEWS | 5
R/CausalDiagramBinBin.R | 96 ++++++------
R/FixedContContIT.r | 2
R/ICA.BinBin.Grid.Full.R | 138 ++++++++++++-----
R/ICA.BinBin.Grid.Sample.R | 290 +++++++++++++++++++++++++++++--------
R/ICA.Sample.ContCont.R |only
R/ICABinBin.R | 223 ++++++++++++++++++++++++----
R/ICABinBinCounterAssum.R |only
R/ICAContCont.R | 4
R/MICA.Sample.ContCont.R |only
R/MICAContCont.R | 2
R/MarginalProbs.R | 2
R/MinSurrContCont.R | 3
R/RandVec.R | 2
R/SPP.BinBin.R |only
R/SimDataCounterfactualsBinBin.R | 12 +
R/SimDataSTSBinBin.R | 12 +
R/SummaryITContCont.R | 2
R/SummaryMetaAnalyticMTSContCont.R | 2
R/SummaryMetaAnalyticSTSContCont.R | 1
R/SummarySPPBinBin.R |only
R/plot.InfoTheoretic.R | 4
R/plot.MetaAnalyticMTS.R | 11 +
R/plot.MetaAnalyticSTS.R | 1
R/plot_ICABinBin.R | 94 ++++++++++-
R/plot_SPPBinBin.R |only
R/summ.ICA.By.Mon.R |only
R/summary_ICABinBin.R | 13 +
data/Schizo_Bin.rda |only
data/Schizo_Bin_ST.rda |only
data/Schizo_Bin_ST2.rda |only
data/Schizo_PANSS.rda |only
man/ICA.BinBin.Grid.Full.Rd | 4
man/ICA.BinBin.Grid.Sample.Rd | 14 +
man/ICA.Sample.ContCont.Rd |only
man/ICABinBin.Rd | 16 +-
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man/ICAContCont.Rd | 4
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man/MICAContCont.Rd | 2
man/MinSurrContCont.Rd | 3
man/RandVec.Rd | 4
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man/Schizo.Rd | 6
man/Schizo_Bin.Rd |only
man/Schizo_Bin_ST.Rd |only
man/Schizo_Bin_ST2.Rd |only
man/Schizo_PANSS.Rd |only
man/plot.ICABinBin.Rd | 7
man/plot.MetaAnalytic.Rd | 8 -
man/plot.SPPBinBin.Rd |only
man/summ.ICA.By.Mon.Rd |only
man/summary.gen.Rd | 4
56 files changed, 855 insertions(+), 269 deletions(-)
Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.2 dated 2015-03-21 and 1.3 dated 2015-03-26
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 3
DESCRIPTION | 8
MD5 | 18 +-
R/rr.R | 2
R/rrreg.predictor.R | 2
tests/testthat.R | 1
tests/testthat/test-bayes-mixed.R | 14 -
tests/testthat/test-bayes.R | 10 -
tests/testthat/test-power.R |only
tests/testthat/test-rrreg-predictor.R |only
tests/testthat/test-rrreg.R | 283 +---------------------------------
11 files changed, 41 insertions(+), 300 deletions(-)
Title: Visualizing the Performance of Scoring Classifiers
Diff between ROCR versions 1.0-6 dated 2015-03-22 and 1.0-7 dated 2015-03-26
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR is a
flexible tool for creating cutoff-parameterized 2D performance curves
by freely combining two from over 25 performance measures (new
performance measures can be added using a standard interface).
Curves from different cross-validation or bootstrapping runs can be
averaged by different methods, and standard deviations, standard
errors or box plots can be used to visualize the variability across
the runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with only
three commands and reasonable default values for all optional
parameters.
Author: Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
Maintainer: Tobias Sing
DESCRIPTION | 45 +++++++++++++++++++++------------------------
MD5 | 16 +++++++++++-----
NEWS | 3 +++
data/ROCR.hiv.rda |binary
data/ROCR.simple.rda |binary
data/ROCR.xval.rda |binary
tools |only
7 files changed, 35 insertions(+), 29 deletions(-)
Title: Quantile-Based Spectral Analysis of Time Series
Diff between quantspec versions 1.0-2 dated 2014-11-21 and 1.0-3 dated 2015-03-26
Description: Methods to determine, smooth and plot quantile (i. e., Laplace or
copula) periodograms for univariate time series.
Author: Tobias Kley [aut, cre]
Maintainer: Tobias Kley
DESCRIPTION | 11 -
MD5 | 200 +++++++++++-----------
NAMESPACE | 2
NEWS | 8
R/Class-ClippedFT.R | 7
R/Class-FreqRep.R | 4
R/Class-MovingBlocks.R | 6
R/Class-QSpecQuantity.R | 2
R/Class-QuantilePG.R | 8
R/Class-QuantileSD.R | 6
R/Class-SmoothedPG.R | 7
R/models.R | 1
R/quantspec-package.R | 26 +-
build/vignette.rds |binary
inst/doc/quantspec.R | 160 ++++++++----------
inst/doc/quantspec.Rnw | 301 ++++++++++++++++++++--------------
inst/doc/quantspec.pdf |binary
man/BootPos-class.Rd | 2
man/ClippedFT-class.Rd | 9 -
man/ClippedFT-constructor.Rd | 2
man/FreqRep-class.Rd | 2
man/IntegrQuantileSD-class.Rd | 2
man/IntegrQuantileSD-constructor.Rd | 2
man/KernelWeight-class.Rd | 2
man/KernelWeight-constructor.Rd | 2
man/MovingBlocks-class.Rd | 2
man/MovingBlocks-constructor.Rd | 2
man/QRegEstimator-class.Rd | 2
man/QRegEstimator-constructor.Rd | 2
man/QSpecQuantity-class.Rd | 2
man/QuantilePG-class.Rd | 10 -
man/QuantilePG-constructor.Rd | 2
man/QuantileSD-class.Rd | 8
man/QuantileSD-constructor.Rd | 2
man/SmoothedPG-class.Rd | 2
man/SmoothedPG-constructor.Rd | 2
man/SpecDistrWeight-class.Rd | 2
man/SpecDistrWeight-constructor.Rd | 2
man/Weight-class.Rd | 2
man/closest.pos.Rd | 2
man/data-sp500.Rd | 2
man/data-wheatprices.Rd | 2
man/frequenciesValidator.Rd | 2
man/generics-accessors.Rd | 2
man/generics-associations.Rd | 2
man/generics-functions.Rd | 2
man/getB-FreqRep.Rd | 2
man/getBootPos-FreqRep.Rd | 2
man/getBw-KernelWeight.Rd | 2
man/getDescr-Weight.Rd | 2
man/getFreqRep-QuantilePG.Rd | 2
man/getFrequencies-FreqRep.Rd | 2
man/getFrequencies-QSpecQuantity.Rd | 2
man/getIsRankBased-FreqRep.Rd | 2
man/getLevels-FreqRep.Rd | 2
man/getLevels-QSpecQuantity.Rd | 2
man/getMeanPG-QuantileSD.Rd | 2
man/getN-QuantileSD.Rd | 2
man/getParallel-QRegEstimator.Rd | 2
man/getPointwiseCIs-SmoothedPG.Rd | 2
man/getPositions-MovingBlocks.Rd | 2
man/getQuantilePG-QuantileSD.Rd | 2
man/getQuantilePG-SmoothedPG.Rd | 2
man/getQuantileSD-IntegrQuantileSD.Rd | 2
man/getR-QuantileSD.Rd | 2
man/getSdBoot-SmoothedPG.Rd | 2
man/getSdNaive-SmoothedPG.Rd | 9 -
man/getStdError-QuantileSD.Rd | 2
man/getTs-QuantileSD.Rd | 2
man/getType-QuantileSD.Rd | 2
man/getValues-FreqRep.Rd | 2
man/getValues-IntegrQuantileSD.Rd | 2
man/getValues-KernelWeight.Rd | 2
man/getValues-QuantilePG.Rd | 2
man/getValues-QuantileSD.Rd | 2
man/getValues-SmoothedPG.Rd | 2
man/getValues-SpecDistrWeight.Rd | 2
man/getW-KernelWeight.Rd | 2
man/getWeight-SmoothedPG.Rd | 2
man/getWnj-KernelWeight.Rd | 2
man/getY-FreqRep.Rd | 2
man/increasePrecision-QuantileSD.Rd | 2
man/is.wholenumber.Rd | 2
man/kernels.Rd | 2
man/plot-FreqRep.Rd | 2
man/plot-IntegrQuantileSD.Rd | 2
man/plot-KernelWeight.Rd | 2
man/plot-QuantilePG.Rd | 2
man/plot-QuantileSD.Rd | 2
man/plot-SmoothedPG.Rd | 2
man/plot-SpecDistrWeight.Rd | 2
man/quantspec-defunct.Rd | 2
man/quantspec-package.Rd | 28 +--
man/timeSeriesValidator.Rd | 2
man/ts-models-AR1.Rd | 2
man/ts-models-AR2.Rd | 2
man/ts-models-ARCH1.Rd | 2
man/ts-models-QAR1.Rd | 2
man/ts-models.Rd | 3
vignettes/quantspec-refs.bib | 52 +++--
vignettes/quantspec.Rnw | 301 ++++++++++++++++++++--------------
101 files changed, 740 insertions(+), 581 deletions(-)
Title: Create a Mini Version of CRAN Containing Only Selected Packages
Diff between miniCRAN versions 0.1-1 dated 2014-10-01 and 0.2.2 dated 2015-03-26
Description: Makes it possible to create an internally consistent
repository consisting of selected packages from CRAN-like repositories.
The user specifies a set of desired packages, and miniCRAN recursively
reads the dependency tree for these packages, then downloads only this
subset. The user can then install packages from this repository directly,
rather than from CRAN. This is useful in production settings, e.g. server
behind a firewall, or remote locations with slow broadband access.
Author: Revolution Analytics [aut],
Andrie de Vries [aut, cre],
Alex Chubaty [ctb]
Maintainer: Andrie de
Vries
miniCRAN-0.1-1/miniCRAN/inst/doc/miniCRAN.R |only
miniCRAN-0.1-1/miniCRAN/inst/doc/miniCRAN.html |only
miniCRAN-0.1-1/miniCRAN/inst/doc/miniCRAN.rmd |only
miniCRAN-0.1-1/miniCRAN/inst/examples/example_addPackage.R |only
miniCRAN-0.1-1/miniCRAN/man/addPackageGithub.Rd |only
miniCRAN-0.1-1/miniCRAN/vignettes/figure/makeDepGraph.png |only
miniCRAN-0.1-1/miniCRAN/vignettes/figure/so-tags.png |only
miniCRAN-0.1-1/miniCRAN/vignettes/miniCRAN.rmd |only
miniCRAN-0.2.2/miniCRAN/DESCRIPTION | 41 +-
miniCRAN-0.2.2/miniCRAN/MD5 | 88 ++--
miniCRAN-0.2.2/miniCRAN/NAMESPACE | 13
miniCRAN-0.2.2/miniCRAN/NEWS | 28 +
miniCRAN-0.2.2/miniCRAN/R/addPackages.R | 192 ++++++----
miniCRAN-0.2.2/miniCRAN/R/getCranDescription.R | 9
miniCRAN-0.2.2/miniCRAN/R/github-functions.R |only
miniCRAN-0.2.2/miniCRAN/R/helpers.R |only
miniCRAN-0.2.2/miniCRAN/R/makeDepGraph.R | 54 +-
miniCRAN-0.2.2/miniCRAN/R/makeRepo.R | 116 +++---
miniCRAN-0.2.2/miniCRAN/R/minicran-package.R | 45 +-
miniCRAN-0.2.2/miniCRAN/R/pkgDep.R | 112 ++++-
miniCRAN-0.2.2/miniCRAN/R/plot.pkgDepGraph.R | 58 +--
miniCRAN-0.2.2/miniCRAN/R/testSuiteFunctions.R |only
miniCRAN-0.2.2/miniCRAN/R/updatePackages.R |only
miniCRAN-0.2.2/miniCRAN/R/zzz.R | 4
miniCRAN-0.2.2/miniCRAN/build/vignette.rds |binary
miniCRAN-0.2.2/miniCRAN/inst/doc/miniCRAN-dependency-graph.R |only
miniCRAN-0.2.2/miniCRAN/inst/doc/miniCRAN-dependency-graph.html |only
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miniCRAN-0.2.2/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.R |only
miniCRAN-0.2.2/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.html |only
miniCRAN-0.2.2/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.rmd |only
miniCRAN-0.2.2/miniCRAN/inst/examples/example_addPackageListingGithub.R |only
miniCRAN-0.2.2/miniCRAN/inst/examples/example_checkVersions.R |only
miniCRAN-0.2.2/miniCRAN/inst/examples/example_updatePackages.R |only
miniCRAN-0.2.2/miniCRAN/man/addOldPackage.Rd |only
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miniCRAN-0.2.2/miniCRAN/man/addPackageListingGithub.Rd |only
miniCRAN-0.2.2/miniCRAN/man/basePkgs.Rd | 6
miniCRAN-0.2.2/miniCRAN/man/checkVersions.Rd |only
miniCRAN-0.2.2/miniCRAN/man/cranJuly2014.Rd | 3
miniCRAN-0.2.2/miniCRAN/man/getCranDescription.Rd | 5
miniCRAN-0.2.2/miniCRAN/man/makeDepGraph.Rd | 10
miniCRAN-0.2.2/miniCRAN/man/makeLibrary.Rd | 3
miniCRAN-0.2.2/miniCRAN/man/makeRepo.Rd | 71 ++-
miniCRAN-0.2.2/miniCRAN/man/miniCRAN-package.Rd | 45 +-
miniCRAN-0.2.2/miniCRAN/man/pkgAvail.Rd | 14
miniCRAN-0.2.2/miniCRAN/man/pkgDep.Rd | 20 -
miniCRAN-0.2.2/miniCRAN/man/pkgDepTools.Rd | 3
miniCRAN-0.2.2/miniCRAN/man/plot.pkgDepGraph.Rd | 10
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miniCRAN-0.2.2/miniCRAN/tests/testthat/test-2-makeDepGraph.R | 59 ++-
miniCRAN-0.2.2/miniCRAN/tests/testthat/test-3-makeRepo.R | 138 +------
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64 files changed, 673 insertions(+), 474 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Diff between MazamaSpatialUtils versions 0.2.2 dated 2015-03-01 and 0.2.3 dated 2015-03-26
More information about MazamaSpatialUtils at CRAN
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut]
Maintainer: Jonathan Callahan
DESCRIPTION | 6 ++--
MD5 | 60 ++++++++++++++++++++++-----------------------
R/MazamaSpatialUtils.R | 15 ++++++++---
R/getCountry.R | 4 +--
R/getCountryCode.R | 4 +--
R/getCountryName.R | 4 +--
R/getState.R | 4 +--
R/getStateCode.R | 4 +--
R/getStateName.R | 4 +--
R/getTimezone.R | 4 +--
R/getUSCounty.R | 4 +--
R/getVariable.R | 2 -
R/organizePolygons.R | 2 -
build/vignette.rds |binary
data/SimpleCountries.RData |binary
data/SimpleTimezones.RData |binary
inst/doc/introduction.html | 4 +--
man/MazamaSpatialUtils.Rd | 5 +++
man/codeToState.Rd | 2 -
man/getCountry.Rd | 4 +--
man/getCountryCode.Rd | 4 +--
man/getCountryName.Rd | 4 +--
man/getState.Rd | 4 +--
man/getStateCode.Rd | 4 +--
man/getStateName.Rd | 4 +--
man/getTimezone.Rd | 4 +--
man/getUSCounty.Rd | 4 +--
man/getVariable.Rd | 2 -
man/organizePolygons.Rd | 2 -
man/stateToCode.Rd | 2 -
tests/testthat/test1.R | 2 -
31 files changed, 89 insertions(+), 79 deletions(-)
Permanent link
Title: Binary Classifier Interpretation Functions
Diff between interpretR versions 0.2.0 dated 2014-12-19 and 0.2.1 dated 2015-03-26
Description: Compute permutation- based performance measures and create
partial dependence plots for (cross-validated) randomForest and ada models.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings
DESCRIPTION | 12 +--
MD5 | 14 +--
R/parDepPlot.R | 164 +++++++++++++++++++++++++++++++++++++++++++---
R/variableImportance.R | 3
inst/NEWS | 7 +
man/interpretR-package.Rd | 8 +-
man/parDepPlot.Rd | 14 ++-
man/variableImportance.Rd | 3
8 files changed, 188 insertions(+), 37 deletions(-)
Title: Seasonal Adjustment by Frequency Analysis
Diff between descomponer versions 1.1 dated 2014-11-12 and 1.2 dated 2015-03-26
Description: Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
Author: Francisco Parra
Maintainer: Francisco Parra
DESCRIPTION | 10 +-
MD5 | 36 ++++---
R/MW.R |only
R/cdf.R | 44 +--------
R/descomponer.R | 135 ++++++++++------------------
R/gdescomponer.R | 28 +----
R/gdf.R | 37 -------
R/gdt.R | 37 +------
R/gperiodograma.R | 2
build/vignette.rds |binary
inst/doc/descomponer_texto.R | 3
inst/doc/descomponer_texto.Rnw | 7 -
inst/doc/descomponer_texto.pdf |binary
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man/descomponer.rd | 18 +--
man/gdescomponer.rd | 6 -
vignettes/descomponer_texto-concordance.tex | 2
vignettes/descomponer_texto.Rnw | 7 -
vignettes/figure |only
19 files changed, 125 insertions(+), 247 deletions(-)
Title: Analysis and Search of Crossover Designs
Diff between Crossover versions 0.1-13 dated 2014-10-31 and 0.1-14 dated 2015-03-26
Description: Package Crossover provides different crossover designs from combinatorial or search algorithms as well as from literature and a GUI to access them.
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 8 -
MD5 | 67 ++++++-----
NAMESPACE | 2
R/buildSummary.R | 2
R/contrMat.R | 113 +++++++++++++++++--
R/doRUnitTests.R | 2
R/general.carryover.R | 31 -----
R/order.R |only
build/vignette.rds |binary
data/exampleSearchResults2t.rda |only
inst/doc/Crossover.R | 77 ++++++++++++
inst/doc/Crossover.pdf |binary
inst/java/crossover.jar |binary
inst/unitTests/runit.efficiency.R | 2
java/org/mutoss/gui/AlgorithmPanel.java | 7 +
java/org/mutoss/gui/CrossDes.java | 23 ++-
java/org/mutoss/gui/CrossoverGUI.java | 5
java/org/mutoss/gui/Design.java | 4
java/org/mutoss/gui/DesignSelectionPanel.java | 6 -
java/org/mutoss/gui/FillTableWorker.java | 82 +++++++------
java/org/mutoss/gui/RCallServicesREngineWrapper.java | 5
man/CrossoverDesign-class.Rd | 3
man/CrossoverGUI.Rd | 3
man/CrossoverSearchResult-class.Rd | 3
man/buildSummaryTable.Rd | 3
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man/design.efficiency.Rd | 3
man/general.carryover.Rd | 3
man/getDesign-methods.Rd | 3
man/getModelNr.Rd | 3
man/plot-methods.Rd | 3
man/rcd.Rd | 3
man/rcdMatrix.Rd | 3
man/resultL.Rd |only
man/searchCrossOverDesign.Rd | 3
vignettes/childs/Search.Rnw | 110 ++++++++++++++++++
37 files changed, 435 insertions(+), 147 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Diff between survsim versions 1.1.2 dated 2014-07-23 and 1.1.3 dated 2015-03-26
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler
DESCRIPTION | 12 +++---
MD5 | 42 ++++++++++-----------
NAMESPACE | 10 ++++-
R/crisk.ncens.sim.R | 59 +++++++++++++++++++++---------
R/crisk.sim.R | 29 ++++++++++++---
R/mult.ev.ncens.sim.R | 75 ++++++++++++++++++++++++++-------------
R/mult.ev.sim.R | 29 ++++++++++++---
R/print.summary.crisk.data.sim.R | 2 -
R/rec.ev.cens.sim.R | 47 +++++++++++++++++-------
R/rec.ev.ncens.sim.R | 43 ++++++++++++++++------
R/rec.ev.sim.R | 28 +++++++++++---
R/simple.ev.sim.R | 49 ++++++++++++++-----------
R/simple.surv.sim.R | 29 ++++++++++++---
R/summary.crisk.data.sim.R | 5 --
inst/CITATION | 4 +-
man/accum.Rd | 4 +-
man/crisk.sim.Rd | 16 ++++----
man/mult.ev.sim.Rd | 17 ++++----
man/rec.ev.sim.Rd | 20 +++++-----
man/simple.surv.sim.Rd | 14 +++----
man/survsim-internal.Rd | 10 ++---
man/survsim-package.Rd | 6 +--
22 files changed, 362 insertions(+), 188 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Diff between nodiv versions 1.0.2 dated 2015-03-05 and 1.0.3 dated 2015-03-26
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
DESCRIPTION | 14 +-
MD5 | 38 +++--
NAMESPACE | 11 +
R/Add_to_data_object.R |only
R/General_figure_functions.R | 61 +++++++--
R/Methods_for_data_objects.R | 262 ++++++++++++++++++++++++++++++++++-------
R/Methods_for_result_objects.R | 8 -
R/Node_based_analysis.R | 33 ++++-
R/Nodesig_function.R | 8 -
R/Prepare_data.R | 33 ++---
R/colors.R |only
data/coquettes.rda |binary
man/Nspecies.Rd | 11 +
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man/basal_node.Rd | 5
man/distrib_data.Rd | 7 -
man/nodiv-package.Rd | 4
man/occurrences.Rd |only
man/plotSOS.Rd | 6
man/plot_nodes_phylo.Rd | 2
man/plot_points.Rd | 12 -
man/update_object.Rd |only
23 files changed, 388 insertions(+), 127 deletions(-)
Title: Manage Time Series with R and PostgreSQL
Diff between timeseriesdb versions 0.1 dated 2014-11-26 and 0.2 dated 2015-03-26
Description: Store and organize a large amount of low frequency time series data.
The package was designed to manage a large catalog of official statistics which are
typically published on monthly, quarterly or yearly basis. Thus timeseriesdb is
optimized to handle a large number of lower frequency time series as opposed to a
smaller amount of high frequency time series such as real time data from measuring devices.
Hence timeseriesdb provides the opportunity to store extensive multi-lingual
meta information. The package also provides a web GUI to explore the underlying
PostgreSQL database interactively.
Author: "Matthias Bannert
Maintainer: 'Matthias Bannert'
timeseriesdb-0.1/timeseriesdb/man/depth.Rd |only
timeseriesdb-0.2/timeseriesdb/DESCRIPTION | 31 +-
timeseriesdb-0.2/timeseriesdb/MD5 | 83 +++++--
timeseriesdb-0.2/timeseriesdb/NAMESPACE | 37 +++
timeseriesdb-0.2/timeseriesdb/NEWS |only
timeseriesdb-0.2/timeseriesdb/R/addMetaInformation.R | 59 +++--
timeseriesdb-0.2/timeseriesdb/R/createConObj.R |only
timeseriesdb-0.2/timeseriesdb/R/createHstore.R | 61 ++---
timeseriesdb-0.2/timeseriesdb/R/dbExplorerUtils.R |only
timeseriesdb-0.2/timeseriesdb/R/deleteTimeSeries.R | 4
timeseriesdb-0.2/timeseriesdb/R/exploreDb.R |only
timeseriesdb-0.2/timeseriesdb/R/exportTsList.R |only
timeseriesdb-0.2/timeseriesdb/R/getMeta.R | 11 -
timeseriesdb-0.2/timeseriesdb/R/importTsList.R |only
timeseriesdb-0.2/timeseriesdb/R/plotMethod.R |only
timeseriesdb-0.2/timeseriesdb/R/print_methods.R | 3
timeseriesdb-0.2/timeseriesdb/R/quickHandleOps.R |only
timeseriesdb-0.2/timeseriesdb/R/readMetaInformation.R | 71 ++++--
timeseriesdb-0.2/timeseriesdb/R/readTimeseries.R | 99 ++++-----
timeseriesdb-0.2/timeseriesdb/R/resolveOverlap.R |only
timeseriesdb-0.2/timeseriesdb/R/searchHstore.R |only
timeseriesdb-0.2/timeseriesdb/R/setAttrListWise.R |only
timeseriesdb-0.2/timeseriesdb/R/storeMetaInformation.R | 64 ++++--
timeseriesdb-0.2/timeseriesdb/R/storeTimeseries.R | 126 +++++++-----
timeseriesdb-0.2/timeseriesdb/R/transactionUtils.R |only
timeseriesdb-0.2/timeseriesdb/R/tsSetFunctions.R |only
timeseriesdb-0.2/timeseriesdb/R/utils.R | 22 ++
timeseriesdb-0.2/timeseriesdb/README.md | 28 ++
timeseriesdb-0.2/timeseriesdb/inst/sql/createTable.sql | 24 +-
timeseriesdb-0.2/timeseriesdb/inst/sql/ts_data_function.sql |only
timeseriesdb-0.2/timeseriesdb/inst/sql/upsert.sql | 14 -
timeseriesdb-0.2/timeseriesdb/man/activateTsSet.Rd |only
timeseriesdb-0.2/timeseriesdb/man/addMetaInformation.Rd | 18 +
timeseriesdb-0.2/timeseriesdb/man/createChoices.Rd |only
timeseriesdb-0.2/timeseriesdb/man/createConObj.Rd |only
timeseriesdb-0.2/timeseriesdb/man/createHstore.Rd | 10
timeseriesdb-0.2/timeseriesdb/man/createUI.Rd |only
timeseriesdb-0.2/timeseriesdb/man/dbIsValid-methods.Rd |only
timeseriesdb-0.2/timeseriesdb/man/deactivateTsSet.Rd |only
timeseriesdb-0.2/timeseriesdb/man/deleteTimeSeries.Rd | 8
timeseriesdb-0.2/timeseriesdb/man/exploreDb.Rd |only
timeseriesdb-0.2/timeseriesdb/man/exportTsList.Rd |only
timeseriesdb-0.2/timeseriesdb/man/getListDepth.Rd |only
timeseriesdb-0.2/timeseriesdb/man/getMeta.Rd | 11 -
timeseriesdb-0.2/timeseriesdb/man/importTsList.Rd |only
timeseriesdb-0.2/timeseriesdb/man/listTsSets.Rd |only
timeseriesdb-0.2/timeseriesdb/man/loadTsSet.Rd |only
timeseriesdb-0.2/timeseriesdb/man/plotMethods.Rd |only
timeseriesdb-0.2/timeseriesdb/man/quickHandleOps.Rd |only
timeseriesdb-0.2/timeseriesdb/man/readMetaInformation.Rd | 27 +-
timeseriesdb-0.2/timeseriesdb/man/readTimeSeries.Rd | 19 -
timeseriesdb-0.2/timeseriesdb/man/resolveOverlap.Rd |only
timeseriesdb-0.2/timeseriesdb/man/searchHstore.Rd |only
timeseriesdb-0.2/timeseriesdb/man/searchKeys.Rd |only
timeseriesdb-0.2/timeseriesdb/man/setAttrListWise.Rd |only
timeseriesdb-0.2/timeseriesdb/man/storeMetaInformation.Rd | 18 +
timeseriesdb-0.2/timeseriesdb/man/storeTimeSeries.Rd | 23 +-
timeseriesdb-0.2/timeseriesdb/man/storeTsSet.Rd |only
timeseriesdb-0.2/timeseriesdb/man/transactionUtils.Rd |only
timeseriesdb-0.2/timeseriesdb/man/zooLikeDateConvert.Rd | 3
60 files changed, 562 insertions(+), 312 deletions(-)
Title: A Server-Side File System Viewer For Shiny
Diff between shinyFiles versions 0.5.0 dated 2015-01-30 and 0.6.0 dated 2015-03-26
Description: Provides functionality for client-side navigation of
the server side file system in shiny apps. In case the app is running
locally this gives the user direct access to the file system without the
need to "download" files to a temporary location. Both file and folder
selection as well as file saving is available.
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen
shinyFiles-0.5.0/shinyFiles/inst/www/bootstrap.min.css |only
shinyFiles-0.5.0/shinyFiles/man/parseFilePaths.Rd |only
shinyFiles-0.5.0/shinyFiles/man/shinyFileChoose.Rd |only
shinyFiles-0.5.0/shinyFiles/man/shinyFilesButton.Rd |only
shinyFiles-0.6.0/shinyFiles/DESCRIPTION | 17
shinyFiles-0.6.0/shinyFiles/MD5 | 39
shinyFiles-0.6.0/shinyFiles/NAMESPACE | 7
shinyFiles-0.6.0/shinyFiles/R/aaa.R | 78
shinyFiles-0.6.0/shinyFiles/R/dirchoose.R |only
shinyFiles-0.6.0/shinyFiles/R/filechoose.R | 286 -
shinyFiles-0.6.0/shinyFiles/R/filesave.R |only
shinyFiles-0.6.0/shinyFiles/README.md | 8
shinyFiles-0.6.0/shinyFiles/inst/example/server.R | 9
shinyFiles-0.6.0/shinyFiles/inst/example/ui.R | 70
shinyFiles-0.6.0/shinyFiles/inst/example/www |only
shinyFiles-0.6.0/shinyFiles/inst/www/icons/Icons16x16/drive.png |only
shinyFiles-0.6.0/shinyFiles/inst/www/icons/Icons32x32/drive.png |only
shinyFiles-0.6.0/shinyFiles/inst/www/shinyFiles.js | 1606 ++++++++--
shinyFiles-0.6.0/shinyFiles/inst/www/styles.css | 207 +
shinyFiles-0.6.0/shinyFiles/man/dirCreator.Rd |only
shinyFiles-0.6.0/shinyFiles/man/dirGetter.Rd |only
shinyFiles-0.6.0/shinyFiles/man/formatFiletype.Rd |only
shinyFiles-0.6.0/shinyFiles/man/getVolumes.Rd | 2
shinyFiles-0.6.0/shinyFiles/man/shinyFiles-buttons.Rd |only
shinyFiles-0.6.0/shinyFiles/man/shinyFiles-observers.Rd |only
shinyFiles-0.6.0/shinyFiles/man/shinyFiles-parsers.Rd |only
shinyFiles-0.6.0/shinyFiles/man/shinyFilesExample.Rd | 17
shinyFiles-0.6.0/shinyFiles/man/traverseDirs.Rd |only
shinyFiles-0.6.0/shinyFiles/man/updateChildren.Rd |only
29 files changed, 1866 insertions(+), 480 deletions(-)
Title: Miscellaneous Tools for Reproducible Research
Diff between repmis versions 0.4 dated 2015-01-23 and 0.4.2 dated 2015-03-26
Description: Tools to load R packages
and automatically generate BibTeX files citing them as well as load
plain-text and Excel formatted data stored on Dropbox, GitHub, and from
other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 15 ++++++++-------
MD5 | 18 +++++++++---------
NAMESPACE | 1 -
NEWS | 11 +++++++++++
R/source_DropboxData.R | 8 +++-----
R/source_XlsxData.R | 26 +++++++++++++++++---------
R/source_data.R | 6 ++----
README.md | 2 +-
man/source_DropboxData.Rd | 2 +-
man/source_XlsxData.Rd | 6 +++---
10 files changed, 55 insertions(+), 40 deletions(-)
Title: GUI for Cohen's and Fleiss' Kappa
Diff between KappaGUI versions 1.1 dated 2013-01-30 and 1.2 dated 2015-03-26
Description: Offers a complete and interactive GUI to work out Cohen's and Fleiss' Kappa.
Author: Frederic Santos
Maintainer: Frederic Santos
DESCRIPTION | 16 ++++++++--------
MD5 | 12 ++++++------
NAMESPACE | 4 +++-
R/Sel_procedure.R | 2 +-
R/StartKappa.R | 25 +++++++++++++++++--------
R/datafile_details.R | 2 +-
man/KappaGUI-package.Rd | 8 +++++---
7 files changed, 41 insertions(+), 28 deletions(-)
Title: A Robust, High Performance JSON Parser and Generator for R
Diff between jsonlite versions 0.9.14 dated 2014-12-01 and 0.9.15 dated 2015-03-25
Description: A fast JSON parser and generator optimized for statistical data
and the web. Started out as a fork of RJSONIO, but has been completely
rewritten in recent versions. The package offers flexible, robust, high
performance tools for working with JSON in R and is particularly powerful
for building pipelines and interacting with web APIs. The implementation is
based on the mapping described in the vignette of the package (Ooms, 2014).
In addition to drop-in replacements for toJSON and fromJSON, jsonlite
contains functions to stream, validate, and prettify JSON data. The unit
tests included with the package verify that all edge cases are encoded and
decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms
jsonlite-0.9.14/jsonlite/R/as.iso.R |only
jsonlite-0.9.14/jsonlite/R/download.R |only
jsonlite-0.9.14/jsonlite/R/toMongo.R |only
jsonlite-0.9.14/jsonlite/inst/doc/json-mapping.R |only
jsonlite-0.9.14/jsonlite/inst/doc/json-mapping.Rnw |only
jsonlite-0.9.14/jsonlite/man/toMongo.Rd |only
jsonlite-0.9.14/jsonlite/vignettes/json-mapping.Rnw |only
jsonlite-0.9.15/jsonlite/DESCRIPTION | 12
jsonlite-0.9.15/jsonlite/MD5 | 109 +-
jsonlite-0.9.15/jsonlite/NAMESPACE | 6
jsonlite-0.9.15/jsonlite/NEWS | 11
jsonlite-0.9.15/jsonlite/R/asJSON.AsIs.R |only
jsonlite-0.9.15/jsonlite/R/asJSON.Date.R | 2
jsonlite-0.9.15/jsonlite/R/asJSON.POSIXt.R | 28
jsonlite-0.9.15/jsonlite/R/asJSON.array.R | 2
jsonlite-0.9.15/jsonlite/R/asJSON.character.R | 10
jsonlite-0.9.15/jsonlite/R/asJSON.data.frame.R | 3
jsonlite-0.9.15/jsonlite/R/asJSON.factor.R | 8
jsonlite-0.9.15/jsonlite/R/asJSON.logical.R | 10
jsonlite-0.9.15/jsonlite/R/asJSON.numeric.R | 9
jsonlite-0.9.15/jsonlite/R/fromJSON.R | 23
jsonlite-0.9.15/jsonlite/R/onLoad.R |only
jsonlite-0.9.15/jsonlite/R/parseJSON.R | 15
jsonlite-0.9.15/jsonlite/R/push_parser.R |only
jsonlite-0.9.15/jsonlite/R/stream.R | 6
jsonlite-0.9.15/jsonlite/R/toJSON.R | 9
jsonlite-0.9.15/jsonlite/R/warn_keep_vec_names.R |only
jsonlite-0.9.15/jsonlite/build/vignette.rds |binary
jsonlite-0.9.15/jsonlite/inst/CITATION | 2
jsonlite-0.9.15/jsonlite/inst/doc/json-aaquickstart.Rmd | 2
jsonlite-0.9.15/jsonlite/inst/doc/json-aaquickstart.html | 416 ++++++----
jsonlite-0.9.15/jsonlite/inst/doc/json-apis.Rmd | 166 ++-
jsonlite-0.9.15/jsonlite/inst/doc/json-apis.html | 156 +--
jsonlite-0.9.15/jsonlite/inst/doc/json-mapping.pdf |binary
jsonlite-0.9.15/jsonlite/inst/doc/json-mapping.pdf.asis |only
jsonlite-0.9.15/jsonlite/inst/doc/json-opencpu.Rnw | 26
jsonlite-0.9.15/jsonlite/inst/doc/json-opencpu.pdf |binary
jsonlite-0.9.15/jsonlite/inst/doc/json-paging.Rmd | 38
jsonlite-0.9.15/jsonlite/inst/doc/json-paging.html | 27
jsonlite-0.9.15/jsonlite/inst/tests/helper-toJSON.R | 8
jsonlite-0.9.15/jsonlite/inst/tests/test-toJSON-AsIs.R |only
jsonlite-0.9.15/jsonlite/inst/tests/test-toJSON-keep-vec-names.R |only
jsonlite-0.9.15/jsonlite/man/flatten.Rd | 3
jsonlite-0.9.15/jsonlite/man/fromJSON.Rd | 6
jsonlite-0.9.15/jsonlite/man/prettify.Rd | 3
jsonlite-0.9.15/jsonlite/man/rbind.pages.Rd | 3
jsonlite-0.9.15/jsonlite/man/serializeJSON.Rd | 3
jsonlite-0.9.15/jsonlite/man/stream_in.Rd | 10
jsonlite-0.9.15/jsonlite/man/unbox.Rd | 3
jsonlite-0.9.15/jsonlite/man/validate.Rd | 3
jsonlite-0.9.15/jsonlite/src/Makevars | 3
jsonlite-0.9.15/jsonlite/src/parse.c | 43 -
jsonlite-0.9.15/jsonlite/src/push_parser.c |only
jsonlite-0.9.15/jsonlite/src/push_parser.h |only
jsonlite-0.9.15/jsonlite/src/yajl/readme.txt | 1
jsonlite-0.9.15/jsonlite/src/yajl/yajl_tree.c | 38
jsonlite-0.9.15/jsonlite/vignettes/json-aaquickstart.Rmd | 2
jsonlite-0.9.15/jsonlite/vignettes/json-apis.Rmd | 166 ++-
jsonlite-0.9.15/jsonlite/vignettes/json-apis.Rmd.orig | 16
jsonlite-0.9.15/jsonlite/vignettes/json-mapping.Rnw.orig |only
jsonlite-0.9.15/jsonlite/vignettes/json-mapping.pdf.asis |only
jsonlite-0.9.15/jsonlite/vignettes/json-opencpu-concordance.tex |only
jsonlite-0.9.15/jsonlite/vignettes/json-opencpu.Rnw | 26
jsonlite-0.9.15/jsonlite/vignettes/json-paging.Rmd | 38
jsonlite-0.9.15/jsonlite/vignettes/json-paging.Rmd.orig | 16
65 files changed, 918 insertions(+), 569 deletions(-)
Title: Scrapes Data from Fitbit.com
Diff between fitbitScraper versions 0.1.1 dated 2015-01-30 and 0.1.2 dated 2015-03-25
Description: Scrapes data from fitbit.com. This does not use the official API,
but instead uses the API that the web dashboard uses to generate the graphs
displayed on the dashboard after login at www.fitbit.com.
Author: Cory Nissen
Maintainer: Cory Nissen
DESCRIPTION | 8 ++--
MD5 | 26 +++++++++-----
NAMESPACE | 6 ++-
R/get_15_min_data.R | 47 +++++--------------------
R/get_daily_data.R | 85 ++++++++++++++++++++++++++++++++++++----------
R/get_intraday_data.R |only
R/get_premium_export.R |only
R/get_sleep_data.R |only
R/get_weight_data.R |only
R/login.R | 1
README.md | 14 +++++++
man/get_15_min_data.Rd | 20 +++++-----
man/get_daily_data.Rd | 14 +++++--
man/get_intraday_data.Rd |only
man/get_premium_export.Rd |only
man/get_sleep_data.Rd |only
man/get_weight_data.Rd |only
man/login.Rd | 6 ++-
18 files changed, 145 insertions(+), 82 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Diff between vines versions 1.1.1 dated 2015-01-20 and 1.1.3 dated 2015-03-25
Description: Implementation of the vine graphical model for building
high-dimensional distributions as a factorization of bivariate
copulas and marginal density functions. This package provides S4
classes for vines (C-vines and D-vines) and methods for inference,
goodness-of-fit tests, density/distribution function evaluation,
and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez
vines-1.1.1/vines/man/CVine-class.Rd |only
vines-1.1.1/vines/man/DVine-class.Rd |only
vines-1.1.1/vines/man/RVine-class.Rd |only
vines-1.1.3/vines/DESCRIPTION | 22 +++++++++++++++-------
vines-1.1.3/vines/MD5 | 22 ++++++++++------------
vines-1.1.3/vines/NEWS | 22 +++++++++++++++-------
vines-1.1.3/vines/R/dvine.R | 3 ++-
vines-1.1.3/vines/R/h.R | 1 -
vines-1.1.3/vines/R/rvine.R | 8 ++++----
vines-1.1.3/vines/R/vineFitML.R | 21 ++++++++++++++-------
vines-1.1.3/vines/inst/CITATION | 23 ++++++++++++-----------
vines-1.1.3/vines/man/RVine-classes.Rd |only
vines-1.1.3/vines/src/h.c | 10 +++++-----
vines-1.1.3/vines/src/register.c | 2 +-
14 files changed, 78 insertions(+), 56 deletions(-)
Title: Graph-Constrained Regularization for Sparse Generalized Linear
Models
Diff between glmgraph versions 1.0.0 dated 2015-03-15 and 1.0.1 dated 2015-03-25
Description: We propose to use sparse regression model to achieve variable selection while accounting for graph-constraints among coefficients. Different linear combination of a sparsity penalty(L1) and a smoothness(MCP) penalty has been used, which induces both sparsity of the solution and certain smoothness on the linear coefficients.
Author: Li Chen, Jun Chen
Maintainer: Li Chen
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
R/cv.glmgraph.R | 6 +++---
R/glmgraph.R | 14 ++++++++------
R/plot.cv.R | 2 +-
R/setcriteria.R | 8 ++++----
man/coef.cv.glmgraph.Rd | 2 +-
man/coef.glmgraph.Rd | 2 +-
man/cv.glmgraph.Rd | 4 ++--
man/glmgraph-package.Rd | 2 +-
man/glmgraph.Rd | 2 +-
man/plot.cv.glmgraph.Rd | 2 +-
man/plot.glmgraph.Rd | 2 +-
man/predict.cv.glmgraph.Rd | 2 +-
man/predict.glmgraph.Rd | 2 +-
man/print.cv.glmgraph.Rd | 2 +-
16 files changed, 46 insertions(+), 44 deletions(-)
Title: High-Throughput Generation of Genetic Markers and Maps from
Molecular Phenotypes for Crosses Between Inbred Strains
Diff between pheno2geno versions 1.2.1 dated 2014-07-29 and 1.3.1 dated 2015-03-25
Description: High-throughput generation of genetic markers from molecular phenotypes for crosses between inbred strains. These markers can be use to saturate existing genetic map or creating a new one.
Author: Konrad Zych
Maintainer: Konrad Zych
pheno2geno-1.2.1/pheno2geno/data/yeastCross.rda |only
pheno2geno-1.2.1/pheno2geno/data/yeastPopulation.rda |only
pheno2geno-1.2.1/pheno2geno/man/yeastCross.rd |only
pheno2geno-1.2.1/pheno2geno/man/yeastPopulation.rd |only
pheno2geno-1.3.1/pheno2geno/DESCRIPTION | 14 +-
pheno2geno-1.3.1/pheno2geno/MD5 | 62 ++++++-------
pheno2geno-1.3.1/pheno2geno/NAMESPACE | 4
pheno2geno-1.3.1/pheno2geno/R/findDiffExpressed.R | 9 +
pheno2geno-1.3.1/pheno2geno/README.md | 2
pheno2geno-1.3.1/pheno2geno/data/datalist | 4
pheno2geno-1.3.1/pheno2geno/data/testCross.rda |only
pheno2geno-1.3.1/pheno2geno/data/testPopulation.rda |only
pheno2geno-1.3.1/pheno2geno/man/RPpval.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/assignedChrToMarkers.rd | 10 +-
pheno2geno-1.3.1/pheno2geno/man/changeChromNumber.rd | 10 +-
pheno2geno-1.3.1/pheno2geno/man/cross.denovo.rd | 4
pheno2geno-1.3.1/pheno2geno/man/cross.saturate.rd | 4
pheno2geno-1.3.1/pheno2geno/man/find.mixups.rd | 4
pheno2geno-1.3.1/pheno2geno/man/findDiffExpressed.rd | 4
pheno2geno-1.3.1/pheno2geno/man/map.functions.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/markerPlacementPlot.rd | 8 -
pheno2geno-1.3.1/pheno2geno/man/markersCorPlot.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/plotChildrenExpression.rd | 4
pheno2geno-1.3.1/pheno2geno/man/plotMapComparison.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/plotMarkerDistribution.rd | 4
pheno2geno-1.3.1/pheno2geno/man/plotParentalExpression.rd | 4
pheno2geno-1.3.1/pheno2geno/man/power.plot.rd | 4
pheno2geno-1.3.1/pheno2geno/man/projectOldMarkers.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/pull.biomarkers.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/qtl.comparison.plot.rd | 4
pheno2geno-1.3.1/pheno2geno/man/reorganizeMarkersWithin.rd | 10 +-
pheno2geno-1.3.1/pheno2geno/man/save.gff.rd | 4
pheno2geno-1.3.1/pheno2geno/man/scan.qtls.rd | 4
pheno2geno-1.3.1/pheno2geno/man/set.geno.from.cross.rd | 6 -
pheno2geno-1.3.1/pheno2geno/man/testCross.rd |only
pheno2geno-1.3.1/pheno2geno/man/testPopulation.rd |only
36 files changed, 112 insertions(+), 107 deletions(-)
Title: Utilities for Producing Maps
Diff between mapmisc versions 1.2.0 dated 2015-03-23 and 1.2.1 dated 2015-03-25
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 12 ++++++------
MD5 | 12 ++++++------
R/openmapAttribution.R | 20 +++++++++++++++++++-
R/scaleBar.R | 2 +-
inst/doc/mapLayers.pdf |binary
inst/doc/mapmisc.pdf |binary
man/omerc.Rd | 3 ++-
7 files changed, 34 insertions(+), 15 deletions(-)
Title: Inverse Estimation/Calibration Functions
Diff between investr versions 1.2.1 dated 2015-01-06 and 1.3.0 dated 2015-03-25
Description: Functions to facilitate inverse estimation/calibration in linear,
generalized linear, nonlinear, and (linear) mixed models. A generic function
is also provided for plotting fitted regression models with or without
confidence/prediction bands that may be of use to the general user.
Author: Brandon M. Greenwell
Maintainer: Brandon M. Greenwell
investr-1.2.1/investr/R/predict2.R |only
investr-1.2.1/investr/man/investr-package.Rd |only
investr-1.2.1/investr/man/makeZ.Rd |only
investr-1.2.1/investr/man/predict2.Rd |only
investr-1.2.1/investr/tests/testthat/test-predict2.R |only
investr-1.3.0/investr/DESCRIPTION | 14
investr-1.3.0/investr/MD5 | 60 -
investr-1.3.0/investr/NAMESPACE | 7
investr-1.3.0/investr/NEWS | 19
investr-1.3.0/investr/R/calibrate.R | 237 ++--
investr-1.3.0/investr/R/data.R | 20
investr-1.3.0/investr/R/invest.R | 861 ++++++++++--------
investr-1.3.0/investr/R/investr.R |only
investr-1.3.0/investr/R/plotFit.R | 498 +++++++---
investr-1.3.0/investr/R/predFit.R |only
investr-1.3.0/investr/R/simulate.nls.R | 8
investr-1.3.0/investr/R/utilities.R | 81 -
investr-1.3.0/investr/README.md | 100 +-
investr-1.3.0/investr/data/beetle.rda |only
investr-1.3.0/investr/man/AnyNA.Rd | 3
investr-1.3.0/investr/man/Sigma.Rd | 3
investr-1.3.0/investr/man/arsenic.Rd | 3
investr-1.3.0/investr/man/beetle.Rd |only
investr-1.3.0/investr/man/calibrate.Rd | 23
investr-1.3.0/investr/man/crystal.Rd | 3
investr-1.3.0/investr/man/invest.Rd | 124 +-
investr-1.3.0/investr/man/investr.Rd |only
investr-1.3.0/investr/man/makeData.Rd | 3
investr-1.3.0/investr/man/makeX.Rd | 12
investr-1.3.0/investr/man/nasturtium.Rd | 3
investr-1.3.0/investr/man/plot.bootCal.Rd | 3
investr-1.3.0/investr/man/plotFit.Rd | 37
investr-1.3.0/investr/man/predFit.Rd |only
investr-1.3.0/investr/man/varY.Rd | 3
investr-1.3.0/investr/tests/testthat/test-calibrate.R | 6
investr-1.3.0/investr/tests/testthat/test-invest.R | 144 ++-
investr-1.3.0/investr/tests/testthat/test-predFit.R |only
37 files changed, 1466 insertions(+), 809 deletions(-)
Title: Flexible Cluster-Weighted Modeling
Diff between flexCWM versions 1.4 dated 2015-01-31 and 1.5 dated 2015-03-25
Description: Allows for maximum likelihood fitting of cluster-weighted models, a class of mixtures of regression models with random covariates.
Author: Mazza A., Punzo A., Ingrassia S.
Maintainer: Angelo Mazza
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/plot.R | 13 +++++++------
3 files changed, 13 insertions(+), 12 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Diff between sn versions 1.1-2 dated 2014-12-01 and 1.2-0 dated 2015-03-25
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini
sn-1.1-2/sn/ChangeLog |only
sn-1.2-0/sn/DESCRIPTION | 10 -
sn-1.2-0/sn/MD5 | 49 ++++----
sn-1.2-0/sn/NAMESPACE | 26 +++-
sn-1.2-0/sn/NEWS |only
sn-1.2-0/sn/R/sn-funct.R | 182 ++++++++++++++++++++++-----------
sn-1.2-0/sn/R/sn_S4.R | 5
sn-1.2-0/sn/R/zzz.R | 3
sn-1.2-0/sn/data/ais.rda |binary
sn-1.2-0/sn/data/barolo.rda |binary
sn-1.2-0/sn/data/frontier.rda |binary
sn-1.2-0/sn/data/wines.rda |binary
sn-1.2-0/sn/man/SECdistrMv-class.Rd | 26 +++-
sn-1.2-0/sn/man/SECdistrUv-class.Rd | 30 ++++-
sn-1.2-0/sn/man/affineTransSECdistr.Rd | 2
sn-1.2-0/sn/man/barolo.Rd | 14 +-
sn-1.2-0/sn/man/coef.selm.Rd | 1
sn-1.2-0/sn/man/dp2cp.Rd | 4
sn-1.2-0/sn/man/extractSECdistr.Rd |only
sn-1.2-0/sn/man/makeSECdistr.Rd | 16 +-
sn-1.2-0/sn/man/modeSECdistr.Rd |only
sn-1.2-0/sn/man/sd.Rd |only
sn-1.2-0/sn/man/selm-class.Rd | 5
sn-1.2-0/sn/man/selm.Rd | 22 ++-
sn-1.2-0/sn/man/sn-package.Rd | 17 +--
sn-1.2-0/sn/man/sn-st.info.Rd | 16 +-
sn-1.2-0/sn/man/summary.SECdistr.Rd | 29 +++--
sn-1.2-0/sn/man/wines.Rd | 69 ++++++------
28 files changed, 335 insertions(+), 191 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Diff between kohonen versions 2.0.15 dated 2014-08-04 and 2.0.18 dated 2015-03-25
Description: Functions to train supervised and self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens
Maintainer: Ron Wehrens
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NAMESPACE | 20 ++++++++++++--------
NEWS | 6 ++++++
R/bdk.R | 3 +++
R/xyf.R | 3 +++
man/plot.kohonen.Rd | 9 ---------
7 files changed, 35 insertions(+), 28 deletions(-)
Title: The all-Configurations, Maximum-Interaction F-Test for Hidden
Additivity
Diff between hiddenf versions 1.1 dated 2014-09-08 and 1.2 dated 2015-03-25
Description: Computes the F-test and Bonferroni-adjusted p-value for a test of interaction in two-factor studies. Reports corresponding interaction plot and analysis of variance table and p-values from several other tests of non-additivity.
Author: Jason A. Osborne, Christopher T. Franck and Bongseog Choi
Maintainer: Jason A. Osborne
hiddenf-1.1/hiddenf/data/graybill.mtx.rda |only
hiddenf-1.1/hiddenf/man/graybill.mtx.Rd |only
hiddenf-1.2/hiddenf/DESCRIPTION | 16 ++--
hiddenf-1.2/hiddenf/MD5 | 68 ++++++++++++-------
hiddenf-1.2/hiddenf/NAMESPACE | 6 +
hiddenf-1.2/hiddenf/R/KKSAPvalue.R |only
hiddenf-1.2/hiddenf/R/MalikPvalue.R |only
hiddenf-1.2/hiddenf/R/MalikTab.R |only
hiddenf-1.2/hiddenf/R/Malikfunction.R |only
hiddenf-1.2/hiddenf/R/MandelPvalue.R |only
hiddenf-1.2/hiddenf/R/TukeyPvalue.R |only
hiddenf-1.2/hiddenf/R/additivityPvalues.R |only
hiddenf-1.2/hiddenf/R/anova.hiddenf.R | 21 +++---
hiddenf-1.2/hiddenf/R/computePSS.R |only
hiddenf-1.2/hiddenf/R/hiddenf.R | 94 ++++++++++++++++++---------
hiddenf-1.2/hiddenf/R/makemtx.fcn.R | 10 +-
hiddenf-1.2/hiddenf/R/maketall.fcn.R | 40 +++++------
hiddenf-1.2/hiddenf/R/plot.hiddenf.R | 37 ++++++----
hiddenf-1.2/hiddenf/R/print.hiddenf.R | 26 +++----
hiddenf-1.2/hiddenf/R/rconfig.fcn.R | 94 +++++++++++++--------------
hiddenf-1.2/hiddenf/R/rkconfig.fcn.R |only
hiddenf-1.2/hiddenf/R/summary.hiddenf.R | 36 ++++++----
hiddenf-1.2/hiddenf/data/Boik.mtx.rda |binary
hiddenf-1.2/hiddenf/data/Graybill.mtx.rda |only
hiddenf-1.2/hiddenf/data/cjejuni.mtx.rda |binary
hiddenf-1.2/hiddenf/data/cnv1.mtx.rda |binary
hiddenf-1.2/hiddenf/data/cnvall.mtx.rda |binary
hiddenf-1.2/hiddenf/man/Boik.mtx.Rd | 5 -
hiddenf-1.2/hiddenf/man/Graybill.mtx.Rd |only
hiddenf-1.2/hiddenf/man/KKSAPvalue.Rd |only
hiddenf-1.2/hiddenf/man/MalikPvalue.Rd |only
hiddenf-1.2/hiddenf/man/MalikTab.Rd |only
hiddenf-1.2/hiddenf/man/Malikfunction.Rd |only
hiddenf-1.2/hiddenf/man/MandelPvalue.Rd |only
hiddenf-1.2/hiddenf/man/TukeyPvalue.Rd |only
hiddenf-1.2/hiddenf/man/additivityPvalues.Rd |only
hiddenf-1.2/hiddenf/man/anova.hiddenf.Rd | 15 +---
hiddenf-1.2/hiddenf/man/cjejuni.mtx.Rd | 12 +--
hiddenf-1.2/hiddenf/man/cnv1.mtx.Rd | 6 -
hiddenf-1.2/hiddenf/man/cnvall.mtx.Rd | 10 +-
hiddenf-1.2/hiddenf/man/hiddenf-package.Rd | 31 ++++++--
hiddenf-1.2/hiddenf/man/hiddenf.Rd | 25 ++-----
hiddenf-1.2/hiddenf/man/plot.hiddenf.Rd | 24 +++---
hiddenf-1.2/hiddenf/man/print.hiddenf.Rd | 13 +--
hiddenf-1.2/hiddenf/man/summary.hiddenf.Rd | 17 ++--
45 files changed, 335 insertions(+), 271 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Diff between diseasemapping versions 1.1.7 dated 2015-02-25 and 1.2.0 dated 2015-03-25
More information about diseasemapping at CRAN
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 12 ++++-----
MD5 | 28 ++++++++++-----------
R/bym.R | 1
R/getBreaks.R | 7 +++--
R/getSMR.R | 23 +++++++++++------
data/casedata.RData |binary
data/kentucky.RData |binary
data/popdata.RData |binary
data/referencepop.RData |binary
man/cancerRates.Rd | 7 -----
man/diseasemapping-package.Rd | 4 ---
man/kentucky.Rd | 1
man/popdata.Rd | 54 +++++++++++++++++++++++++++++++++++++++++-
tests/cancerRates.R | 1
tests/getSMR.R | 7 +++--
15 files changed, 98 insertions(+), 47 deletions(-)
Permanent link
Title: Access to Tumblr v2 API
Diff between tumblR versions 1.0 dated 2014-11-10 and 1.1 dated 2015-03-24
Description: Provides an R-interface to the Tumblr web API (see Tumblr v2 API on https://www.tumblr.com/docs/en/api/v2). Tumblr is a microblogging platform and social networking website (https://www.tumblr.com).
Author: Andrea Capozio
Maintainer: Andrea Capozio
DESCRIPTION | 16 ++++++++--------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 2 +-
R/dashboard.R | 2 +-
R/def.postParams.R | 4 ++--
R/follow.R | 2 +-
R/followers.R | 2 +-
R/like.post.R | 2 +-
R/post.R | 2 +-
R/post.delete.R | 2 +-
R/post.edit.R | 2 +-
R/post.reblog.R | 4 ++--
R/posts.draft.R | 2 +-
R/posts.queue.R | 2 +-
R/posts.submission.R | 2 +-
R/unfollow.R | 2 +-
R/unlike.post.R | 2 +-
R/user.following.R | 2 +-
R/user.info.R | 2 +-
R/user.likes.R | 2 +-
20 files changed, 47 insertions(+), 47 deletions(-)
Title: Time-Dependent ROC Curve and AUC for Censored Survival Data
Diff between timeROC versions 0.2 dated 2013-05-27 and 0.3 dated 2015-03-24
Description: Estimation of time-dependent ROC curve and area under time dependent ROC curve (AUC) in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator. Plot functions for time-dependent ROC curves and AUC curves are provided. Time-dependent Positive Predictive Values (PPV) and Negative Predictive Values (NPV) can also be computed.
Author: Paul Blanche
Maintainer: Paul Blanche
DESCRIPTION | 24 +++++++++---------------
MD5 | 31 ++++++++++++++++---------------
NEWS | 6 ++++++
R/SeSpPPVNPV.R | 6 +++---
R/confint_ipcwROC.R | 6 +++---
R/timeROC_3.R | 8 ++++----
THANKS | 1 -
inst |only
man/Paquid.Rd | 15 ++++++++++-----
man/SeSpPPVNPV.Rd | 9 +++++----
man/compare.Rd | 9 +++++----
man/confint.Rd | 9 +++++----
man/plot.Rd | 5 +++--
man/plotAUCcurve.Rd | 8 +++++---
man/plotAUCcurveDiff.Rd | 8 +++++---
man/print.Rd | 3 ++-
man/timeROC.Rd | 14 +++++++-------
17 files changed, 88 insertions(+), 74 deletions(-)
Title: Spatially Explicit Capture-Recapture
Diff between secr versions 2.9.3 dated 2015-01-11 and 2.9.4 dated 2015-03-24
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
secr-2.9.3/secr/inst/doc/secr-densitysurfaces.pdf |only
secr-2.9.3/secr/inst/doc/secr-finitemixtures.pdf |only
secr-2.9.3/secr/inst/doc/secr-noneuclidean.pdf |only
secr-2.9.3/secr/inst/doc/secr-parameterisations.pdf |only
secr-2.9.3/secr/inst/doc/secr-polygondetectors.pdf |only
secr-2.9.3/secr/inst/doc/secr-sound.pdf |only
secr-2.9.3/secr/inst/doc/secr-varyingeffort.pdf |only
secr-2.9.4/secr/DESCRIPTION | 11 -
secr-2.9.4/secr/MD5 | 115 +++++++------
secr-2.9.4/secr/NAMESPACE | 11 -
secr-2.9.4/secr/NEWS | 28 +++
secr-2.9.4/secr/R/esa.R | 7
secr-2.9.4/secr/R/fxi.R | 66 ++++++-
secr-2.9.4/secr/R/homerange.R | 3
secr-2.9.4/secr/R/join.R | 11 -
secr-2.9.4/secr/R/methods.R | 16 +
secr-2.9.4/secr/R/plot.mask.r | 15 +
secr-2.9.4/secr/R/rbind.capthist.R | 4
secr-2.9.4/secr/R/reduce.R | 4
secr-2.9.4/secr/R/regionN.R | 14 +
secr-2.9.4/secr/R/secr.fit.R | 31 ++-
secr-2.9.4/secr/R/secrloglik.R | 22 +-
secr-2.9.4/secr/R/sim.capthist.R | 3
secr-2.9.4/secr/R/sim.popn.R | 166 +++++++++++---------
secr-2.9.4/secr/R/sim.secr.R | 7
secr-2.9.4/secr/R/utility.R | 138 +++++++++++++++-
secr-2.9.4/secr/build |only
secr-2.9.4/secr/inst/doc/index.html | 107 +++++++++++-
secr-2.9.4/secr/inst/doc/secr-datainput.R |only
secr-2.9.4/secr/inst/doc/secr-datainput.Rmd |only
secr-2.9.4/secr/inst/doc/secr-datainput.pdf |binary
secr-2.9.4/secr/inst/doc/secr-manual.pdf |binary
secr-2.9.4/secr/inst/doc/secr-overview.R |only
secr-2.9.4/secr/inst/doc/secr-overview.Rmd |only
secr-2.9.4/secr/inst/doc/secr-overview.pdf |binary
secr-2.9.4/secr/man/DENSITY.Rd | 6
secr-2.9.4/secr/man/FAQ.Rd | 4
secr-2.9.4/secr/man/Parallel.Rd | 3
secr-2.9.4/secr/man/RMarkInput.Rd | 2
secr-2.9.4/secr/man/coulombe.Rd | 2
secr-2.9.4/secr/man/deletemaskpoints.Rd |only
secr-2.9.4/secr/man/details.Rd | 39 ++++
secr-2.9.4/secr/man/detector.Rd | 6
secr-2.9.4/secr/man/fx.total.Rd | 6
secr-2.9.4/secr/man/fxi.Rd | 49 +++++
secr-2.9.4/secr/man/hcov.Rd | 2
secr-2.9.4/secr/man/hornedlizard.Rd | 5
secr-2.9.4/secr/man/make.capthist.Rd | 19 +-
secr-2.9.4/secr/man/make.mask.Rd | 8
secr-2.9.4/secr/man/secr-package.Rd | 24 +-
secr-2.9.4/secr/man/secr.fit.Rd | 4
secr-2.9.4/secr/man/secr.model.density.Rd | 7
secr-2.9.4/secr/man/secr.model.detection.Rd | 2
secr-2.9.4/secr/man/secr.models.Rd | 4
secr-2.9.4/secr/man/sim.popn.Rd | 10 -
secr-2.9.4/secr/man/simpopndetails.Rd |only
secr-2.9.4/secr/man/smooths.Rd | 5
secr-2.9.4/secr/man/timevaryingcov.Rd | 4
secr-2.9.4/secr/man/troubleshooting.Rd | 10 -
secr-2.9.4/secr/man/usage.Rd | 4
secr-2.9.4/secr/man/userdist.Rd | 20 +-
secr-2.9.4/secr/man/utility.Rd | 68 ++++++--
secr-2.9.4/secr/src/secr.c | 32 +--
secr-2.9.4/secr/vignettes |only
64 files changed, 811 insertions(+), 313 deletions(-)
More information about internetarchive at CRAN
Permanent link
Title: Bayesian Analysis of Generalized Elliptical Semi-Parametric
Models and Flexible Measurement Error Models
Diff between BayesGESM versions 1.2 dated 2015-01-09 and 1.3 dated 2015-03-24
Description: It allows to perform the statistical inference based on the Bayesian approach for regression models under the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distributions, i.e., additive errors follow a scale mixtures of normal distributions. The regression models considered in this package are: (i) Generalized elliptical semi-parametric models, where both location and dispersion parameters of the response variable distribution include non-parametric additive components described by using B-splines; and (ii) Flexible measurement error models, which admit explanatory variables with and without measurement additive errors as well as the presence of nonlinear effects that are approximated by using B-splines.
Author: Luz Marina Rondon
Maintainer: Luz Marina Rondon
DESCRIPTION | 14 +-
MD5 | 22 +--
NAMESPACE | 8 -
R/bsp.R | 27 ++--
R/bsp.graph.fmem.R |only
R/fmem.R | 300 ++++++++++++++++++++++++++---------------------
R/mcmc.fmem.R | 231 ++++++++++++++++++++++--------------
R/summary.fmem.R | 60 +++++++--
man/BayesGESM-package.Rd | 27 ++--
man/bsp.graph.Rd | 2
man/bsp.graph.fmem.Rd |only
man/fmem.Rd | 29 +++-
man/summary.fmem.Rd | 2
13 files changed, 437 insertions(+), 285 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Diff between rscala versions 1.0.2 dated 2015-03-08 and 1.0.4 dated 2015-03-24
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl
rscala-1.0.2/rscala/inst/java/rscala_2.10-1.0.2.jar |only
rscala-1.0.2/rscala/inst/java/rscala_2.11-1.0.2.jar |only
rscala-1.0.2/rscala/java/rscala_2.10-1.0.2-sources.jar |only
rscala-1.0.2/rscala/java/rscala_2.11-1.0.2-sources.jar |only
rscala-1.0.4/rscala/DESCRIPTION | 8
rscala-1.0.4/rscala/MD5 | 28 +-
rscala-1.0.4/rscala/NAMESPACE | 8
rscala-1.0.4/rscala/NEWS | 32 ++
rscala-1.0.4/rscala/R/common.R | 5
rscala-1.0.4/rscala/R/protocol.R | 12
rscala-1.0.4/rscala/R/rServer.R | 32 ++
rscala-1.0.4/rscala/R/scalaInterpreter.R | 221 ++++++++++++++---
rscala-1.0.4/rscala/inst/java/rscala_2.10-1.0.4.jar |only
rscala-1.0.4/rscala/inst/java/rscala_2.11-1.0.4.jar |only
rscala-1.0.4/rscala/java/rscala_2.10-1.0.4-sources.jar |only
rscala-1.0.4/rscala/java/rscala_2.11-1.0.4-sources.jar |only
rscala-1.0.4/rscala/man/constructor.Rd | 29 ++
rscala-1.0.4/rscala/man/eval.Rd | 43 ++-
rscala-1.0.4/rscala/man/print.Rd | 4
19 files changed, 333 insertions(+), 89 deletions(-)
Title: Import Stata 13 Data Files
Diff between readstata13 versions 0.6 dated 2015-03-22 and 0.6.1 dated 2015-03-24
Description: Function to read and write the Stata 13 file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki
CHANGELOG | 3 +++
DESCRIPTION | 7 ++++---
MD5 | 8 ++++----
README.md | 8 +++++---
src/rcpp_readstata.cpp | 40 ++++++++++++++++++++--------------------
5 files changed, 36 insertions(+), 30 deletions(-)
Title: A Tool for PH/MAP Parameter Estimation
Diff between mapfit versions 0.9.6 dated 2015-03-19 and 0.9.7 dated 2015-03-24
Description: Estimation methods for phase-type
distribution (PH) and Markovian arrival process (MAP) from
empirical data (point and grouped data) and density function.
Author: Hiroyuki Okamura
Maintainer: Hiroyuki Okamura
DESCRIPTION | 12 ++++++------
MD5 | 30 +++++++++++++++---------------
man/cf1-class.Rd | 2 +-
man/cf1.Rd | 6 +++---
man/erhmm-class.Rd | 2 +-
man/erhmm.Rd | 2 +-
man/herlang.Rd | 9 +++++----
man/map.Rd | 4 ++--
man/map.mmoment.Rd | 10 +++++-----
man/mapfit-package.Rd | 13 +++++++------
man/ph.Rd | 6 +++---
man/ph.moment-method.Rd | 2 +-
man/phfit.3mom.Rd | 2 +-
src/mexp/include/mexp.hh | 2 ++
src/mexp/src/mexp_unif_thread.cc | 10 +++++++++-
src/mexp/src/mexpi_unif_thread.cc | 2 +-
16 files changed, 63 insertions(+), 51 deletions(-)
Title: Prediction of Fish Movement Parameters
Diff between fishmove versions 0.2-1 dated 2014-01-15 and 0.3-1 dated 2015-03-24
Description: Functions to predict fish movement parameters plotting leptokurtic fish dispersal kernels (see Radinger and Wolter, 2014: Patterns and predictors of fish dispersal in rivers. Fish and Fisheries. 15:456-473.)
Author: Johannes Radinger
Maintainer: Johannes Radinger
fishmove-0.2-1/fishmove/data |only
fishmove-0.3-1/fishmove/DESCRIPTION | 10 +++++-----
fishmove-0.3-1/fishmove/MD5 | 23 ++++++++++++-----------
fishmove-0.3-1/fishmove/NAMESPACE | 13 ++++++++-----
fishmove-0.3-1/fishmove/R/fishmove.R | 1 -
fishmove-0.3-1/fishmove/R/fishmove_estimate.R |only
fishmove-0.3-1/fishmove/R/sysdata.rda |only
fishmove-0.3-1/fishmove/inst/CITATION | 6 +++---
fishmove-0.3-1/fishmove/man/datafishmove.Rd | 4 ++--
fishmove-0.3-1/fishmove/man/fishmove-package.Rd | 12 ++++++------
fishmove-0.3-1/fishmove/man/fishmove.Rd | 4 ++--
fishmove-0.3-1/fishmove/man/fishmove.estimate.Rd |only
fishmove-0.3-1/fishmove/man/fishmove.query.Rd | 8 ++++----
fishmove-0.3-1/fishmove/man/pdk.Rd | 4 ++--
14 files changed, 44 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-18 0.1.75
2015-03-16 0.1.71
Title: Readable Check Functions to Ensure Code Integrity
Diff between assertive versions 0.2-1 dated 2015-02-04 and 0.2-4 dated 2015-03-24
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
assertive-0.2-1/assertive/man/is_S4.Rd |only
assertive-0.2-1/assertive/man/parenthesise.Rd |only
assertive-0.2-4/assertive/DESCRIPTION | 13
assertive-0.2-4/assertive/MD5 | 140 -
assertive-0.2-4/assertive/NAMESPACE | 23
assertive-0.2-4/assertive/NEWS | 5
assertive-0.2-4/assertive/R/assert-has.R | 24
assertive-0.2-4/assertive/R/assert-is-empty-scalar.R | 21
assertive-0.2-4/assertive/R/assert-is-file.R | 28
assertive-0.2-4/assertive/R/assert-is-in-range.R | 44
assertive-0.2-4/assertive/R/assert-is-na-nan-null.R | 28
assertive-0.2-4/assertive/R/assert-is-other.R | 26
assertive-0.2-4/assertive/R/assert-is-real-imaginary.R | 24
assertive-0.2-4/assertive/R/assert-is-reflection.R | 40
assertive-0.2-4/assertive/R/assert-is-set.R |only
assertive-0.2-4/assertive/R/assert-is-string-uk.R | 154 -
assertive-0.2-4/assertive/R/assert-is-string-us.R | 8
assertive-0.2-4/assertive/R/assert-is-string.R | 52
assertive-0.2-4/assertive/R/assert-is-time.R | 8
assertive-0.2-4/assertive/R/assert-is-true-false.R | 8
assertive-0.2-4/assertive/R/assert-is-type.R | 16
assertive-0.2-4/assertive/R/assert-r-has-capability.R | 271 +-
assertive-0.2-4/assertive/R/internal.R | 23
assertive-0.2-4/assertive/R/is-connection.R | 20
assertive-0.2-4/assertive/R/is-empty-scalar.R | 428 +--
assertive-0.2-4/assertive/R/is-file.R | 2
assertive-0.2-4/assertive/R/is-na-nan-null.R | 2
assertive-0.2-4/assertive/R/is-other.R | 577 ++--
assertive-0.2-4/assertive/R/is-real-imaginary.R | 17
assertive-0.2-4/assertive/R/is-reflection.R | 66
assertive-0.2-4/assertive/R/is-set.R |only
assertive-0.2-4/assertive/R/is-string-us.R | 284 +-
assertive-0.2-4/assertive/R/is-string.R | 1314 +++++-----
assertive-0.2-4/assertive/R/is-true-false.R | 194 -
assertive-0.2-4/assertive/R/is-type.R | 14
assertive-0.2-4/assertive/R/r-has-capability.R | 567 ++--
assertive-0.2-4/assertive/R/utils.R | 49
assertive-0.2-4/assertive/R/zzz.R | 2
assertive-0.2-4/assertive/README.md |only
assertive-0.2-4/assertive/build |only
assertive-0.2-4/assertive/inst/doc |only
assertive-0.2-4/assertive/inst/po |only
assertive-0.2-4/assertive/inst/tests/test-has.R | 6
assertive-0.2-4/assertive/inst/tests/test-is-reflection.R | 14
assertive-0.2-4/assertive/inst/tests/test-is-string.R | 4
assertive-0.2-4/assertive/inst/tests/test-is-type.R | 8
assertive-0.2-4/assertive/inst/tests/test-r-has-capabilities.R | 2
assertive-0.2-4/assertive/man/bapply.Rd | 2
assertive-0.2-4/assertive/man/cause.Rd | 2
assertive-0.2-4/assertive/man/false.Rd | 2
assertive-0.2-4/assertive/man/is_connection.Rd | 3
assertive-0.2-4/assertive/man/is_email_address.Rd | 10
assertive-0.2-4/assertive/man/is_empty.Rd | 12
assertive-0.2-4/assertive/man/is_existing.Rd | 2
assertive-0.2-4/assertive/man/is_hex_color.Rd | 10
assertive-0.2-4/assertive/man/is_null.Rd | 3
assertive-0.2-4/assertive/man/is_r.Rd | 26
assertive-0.2-4/assertive/man/is_real.Rd | 22
assertive-0.2-4/assertive/man/is_s4.Rd |only
assertive-0.2-4/assertive/man/is_set_equal.Rd |only
assertive-0.2-4/assertive/man/is_true.Rd | 4
assertive-0.2-4/assertive/man/is_valid_variable_name.Rd | 4
assertive-0.2-4/assertive/man/is_whole_number.Rd | 5
assertive-0.2-4/assertive/man/is_windows.Rd | 15
assertive-0.2-4/assertive/man/na.Rd | 2
assertive-0.2-4/assertive/man/parenthesize.Rd |only
assertive-0.2-4/assertive/man/r_can_build_translations.Rd |only
assertive-0.2-4/assertive/man/r_can_compile_code.Rd | 3
assertive-0.2-4/assertive/man/strip_invalid_chars.Rd | 2
assertive-0.2-4/assertive/po |only
assertive-0.2-4/assertive/vignettes |only
71 files changed, 2479 insertions(+), 2176 deletions(-)
Title: Data Analysis Using Rough Set and Fuzzy Rough Set Theories
Diff between RoughSets versions 1.2-0 dated 2015-03-19 and 1.2-1 dated 2015-03-24
Description: Implementations of algorithms for data analysis
based on the rough set theory (RST) and the fuzzy rough set theory (FRST). We
not only provide implementations for the basic concepts of RST and FRST but also
popular algorithms that derive from those theories. The methods included in the
package can be divided into several categories based on their functionality:
discretization, feature selection, instance selection, rule induction and classification
based on nearest neighbors. RST was introduced by Zdzisław Pawlak in 1982
as a sophisticated mathematical tool based on indiscernibility relations to
model and process imprecise or incomplete information. It works on
symbolic-valued datasets for tackling the data analysis problems. By using
the indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST. The
FRST combines concepts of vagueness and indiscernibility that are expressed
with fuzzy sets (as proposed by Zadeh, in 1965) and RST.
Author: Lala Septem Riza [aut],
Andrzej Janusz [aut],
Dominik Ślęzak [ctb],
Chris Cornelis [ctb],
Francisco Herrera [ctb],
Jose Manuel Benitez [ctb],
Christoph Bergmeir [ctb, cre],
Sebastian Stawicki [ctb]
Maintainer: Christoph Bergmeir
DESCRIPTION | 8
MD5 | 234 -
R/BasicFuzzyRoughSets.R | 3344 +++++++++++++--------------
R/BasicRoughSets.OtherFuncCollections.R | 2596 ++++++++++----------
R/BasicRoughSets.R | 804 +++---
R/Discretization.OtherFuncCollections.R | 582 ++--
R/Discretization.R | 2
R/FeatureSelection.OtherFuncCollections.R | 1872 +++++++--------
R/FeatureSelection.R | 3164 ++++++++++++-------------
R/FuzzyRoughSets-introduction.R | 274 +-
R/IOFunctions.R | 1660 ++++++-------
R/InstanceSelection.OtherFuncCollections.R | 126 -
R/InstanceSelection.R | 658 ++---
R/MissingValue.R | 804 +++---
R/NearestNeigbour.OtherFuncCollections.R | 480 +--
R/NearestNeigbour.R | 674 ++---
R/RcppExports.R | 22
R/RoughSets-introduction.R | 232 -
R/RoughSets-package.R | 1086 ++++----
R/RuleInduction.OtherFuncCollections.R | 950 +++----
R/RuleInduction.R | 2102 ++++++++--------
demo/BasicConcept.FRST.R | 94
demo/BasicConcept.RST.R | 50
demo/D.discretize.equal.intervals.RST.R | 28
demo/D.discretize.quantiles.RST.R | 28
demo/D.global.discernibility.heuristic.RST.R | 28
demo/D.local.discernibility.matrix.RST.R | 26
demo/D.max.discernibility.matrix.RST.R | 22
demo/DiscernibilityMatrix.FRST.R | 56
demo/DiscernibilityMatrix.RST.R | 22
demo/FRNN.O.iris.R | 66
demo/FRNN.iris.R | 76
demo/FS.QuickReduct.FRST.Ex1.R | 112
demo/FS.QuickReduct.FRST.Ex2.R | 102
demo/FS.QuickReduct.FRST.Ex3.R | 102
demo/FS.QuickReduct.FRST.Ex4.R | 108
demo/FS.QuickReduct.FRST.Ex5.R | 114
demo/FS.QuickReduct.RST.R | 20
demo/FS.greedy.heuristic.reduct.RST.R | 28
demo/FS.greedy.heuristic.superreduct.RST.R | 28
demo/FS.nearOpt.fvprs.FRST.R | 18
demo/FS.permutation.heuristic.reduct.RST.R | 28
demo/GettingStarted.A.R | 206 -
demo/GettingStarted.B.R | 272 +-
demo/IS.FRIS.FRST.R | 38
demo/IS.FRPS.FRST.R | 30
demo/MV.simpleData.R | 60
demo/POSNN.iris.R | 64
demo/RI.classification.FRST.R | 62
demo/RI.indiscernibilityBasedRules.RST.R | 38
demo/RI.regression.FRST.R | 38
demo/SimulationDataAnalysisWine.R | 296 +-
man/A.Introduction-RoughSets.Rd | 202 -
man/B.Introduction-FuzzyRoughSets.Rd | 246 -
man/BC.IND.relation.FRST.Rd | 634 ++---
man/BC.IND.relation.RST.Rd | 132 -
man/BC.LU.approximation.FRST.Rd | 796 +++---
man/BC.LU.approximation.RST.Rd | 116
man/BC.discernibility.mat.FRST.Rd | 434 +--
man/BC.discernibility.mat.RST.Rd | 132 -
man/BC.positive.reg.FRST.Rd | 224 -
man/BC.positive.reg.RST.Rd | 122
man/C.FRNN.FRST.Rd | 270 +-
man/C.FRNN.O.FRST.Rd | 166 -
man/C.POSNN.FRST.Rd | 162 -
man/D.discretization.RST.Rd | 164 -
man/D.discretize.equal.intervals.RST.Rd | 110
man/D.discretize.quantiles.RST.Rd | 112
man/D.global.discernibility.heuristic.RST.Rd | 160 -
man/D.local.discernibility.matrix.RST.Rd | 146 -
man/D.max.discernibility.matrix.RST.Rd | 150 -
man/FS.DAAR.heuristic.RST.Rd | 192 -
man/FS.all.reducts.computation.Rd | 132 -
man/FS.feature.subset.computation.Rd | 142 -
man/FS.greedy.heuristic.reduct.RST.Rd | 212 -
man/FS.greedy.heuristic.superreduct.RST.Rd | 148 -
man/FS.nearOpt.fvprs.FRST.Rd | 150 -
man/FS.one.reduct.computation.Rd | 132 -
man/FS.permutation.heuristic.reduct.RST.Rd | 158 -
man/FS.quickreduct.FRST.Rd | 582 ++--
man/FS.quickreduct.RST.Rd | 136 -
man/FS.reduct.computation.Rd | 140 -
man/IS.FRIS.FRST.Rd | 168 -
man/IS.FRPS.FRST.Rd | 152 -
man/MV.conceptClosestFit.Rd | 100
man/MV.deletionCases.Rd | 90
man/MV.globalClosestFit.Rd | 108
man/MV.missingValueCompletion.Rd | 120
man/MV.mostCommonVal.Rd | 90
man/MV.mostCommonValResConcept.Rd | 90
man/RI.AQRules.RST.Rd | 148 -
man/RI.CN2Rules.RST.Rd | 138 -
man/RI.GFRS.FRST.Rd | 174 -
man/RI.LEM2Rules.RST.Rd | 134 -
man/RI.hybridFS.FRST.Rd | 144 -
man/RI.indiscernibilityBasedRules.RST.Rd | 138 -
man/RoughSetData.Rd | 260 +-
man/RoughSets-package.Rd | 1054 ++++----
man/SF.applyDecTable.Rd | 222 -
man/SF.asDecisionTable.Rd | 140 -
man/SF.asFeatureSubset.Rd | 104
man/SF.read.DecisionTable.Rd | 98
man/X.entropy.Rd | 50
man/X.gini.Rd | 52
man/X.laplace.Rd | 48
man/X.nOfConflicts.Rd | 42
man/X.ruleStrength.Rd | 50
man/X.rulesCounting.Rd | 50
man/predict.RuleSetFRST.Rd | 136 -
man/predict.RuleSetRST.Rd | 182 -
man/print.FeatureSubset.Rd | 66
man/print.RuleSetRST.Rd | 68
man/summary.IndiscernibilityRelation.Rd | 92
man/summary.LowerUpperApproximation.Rd | 80
man/summary.PositiveRegion.Rd | 82
man/summary.RuleSetFRST.Rd | 120
man/summary.RuleSetRST.Rd | 88
src/discretization.cc | 160 -
118 files changed, 17787 insertions(+), 17787 deletions(-)
Title: Respondent-Driven Sampling
Diff between RDS versions 0.7 dated 2015-01-20 and 0.7-1 dated 2015-03-24
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock
DESCRIPTION | 14 -
MD5 | 36 +-
R/LRT.trend.R | 44 ++-
R/RDS.compare.proportions.R | 11
R/bgk_kde.R |only
R/bootstrap-intervals.R | 2
R/homophily.R | 2
R/llmeC.R | 530 ++++++++++++++---------------------------
R/me.impute.R | 193 ++++++--------
R/rds.data.frame-plots.R | 4
man/LRT.value.trend.Rd | 2
man/RDS.bootstrap.intervals.Rd | 2
man/RDS.compare.proportions.Rd | 2
man/homophily.estimates.Rd | 2
man/impute.degree.Rd | 45 ++-
man/plot.rds.data.frame.Rd | 2
man/reingold.tilford.plot.Rd | 2
src/dpoilog.c |only
src/llmeC.c | 114 ++++----
src/llmeC.h | 9
20 files changed, 450 insertions(+), 566 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Diff between rcbalance versions 1.3 dated 2015-03-13 and 1.4 dated 2015-03-24
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/rcbalance.R | 4 +++-
3 files changed, 8 insertions(+), 6 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Diff between jomo versions 0.1-2 dated 2015-01-07 and 0.2-0 dated 2015-03-24
Description: Building on Schafer's package pan and on the standalone program REALCOM, jomo is a package for multilevel joint modelling multiple imputation.
Binary and categorical variables are handled through latent normal variables and algorithms for cluster-specific covariance matrices are introduced.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno
jomo-0.1-2/jomo/src/rnglib.c |only
jomo-0.1-2/jomo/src/rnglib.h |only
jomo-0.2-0/jomo/DESCRIPTION | 8 +-
jomo-0.2-0/jomo/MD5 | 50 ++++++++----------
jomo-0.2-0/jomo/NAMESPACE | 2
jomo-0.2-0/jomo/R/jomo1rancathr.R | 2
jomo-0.2-0/jomo/inst/CITATION | 3 -
jomo-0.2-0/jomo/man/jomo1cat.Rd | 2
jomo-0.2-0/jomo/man/jomo1con.Rd | 4 -
jomo-0.2-0/jomo/man/jomo1mix.Rd | 12 ++--
jomo-0.2-0/jomo/man/jomo1rancat.Rd | 2
jomo-0.2-0/jomo/man/jomo1rancathr.Rd | 2
jomo-0.2-0/jomo/man/jomo1rancon.Rd | 4 -
jomo-0.2-0/jomo/man/jomo1ranconhr.Rd | 4 -
jomo-0.2-0/jomo/man/jomo1ranmix.Rd | 12 ++--
jomo-0.2-0/jomo/man/jomo1ranmixhr.Rd | 12 ++--
jomo-0.2-0/jomo/src/jomo1con.c | 1
jomo-0.2-0/jomo/src/jomo1mix.c | 95 +++++++++++++++++++++++-----------
jomo-0.2-0/jomo/src/jomo1mix2.c | 77 ++++++++++++++++++++--------
jomo-0.2-0/jomo/src/jomo1rancon.c | 1
jomo-0.2-0/jomo/src/jomo1ranconhf.c | 1
jomo-0.2-0/jomo/src/jomo1ranconhr.c | 5 -
jomo-0.2-0/jomo/src/jomo1ranmix.c | 96 ++++++++++++++++++++++++-----------
jomo-0.2-0/jomo/src/jomo1ranmix2.c | 88 +++++++++++++++++++++++---------
jomo-0.2-0/jomo/src/jomo1ranmixhr.c | 94 +++++++++++++++++++++-------------
jomo-0.2-0/jomo/src/pdflib.c | 9 ++-
jomo-0.2-0/jomo/src/wishart.c | 1
27 files changed, 379 insertions(+), 208 deletions(-)
Title: Tests of Fit for some Probability Distributions
Diff between goft versions 1.0 dated 2013-12-04 and 1.1 dated 2015-03-24
Description: Tests of fit for the gamma, normal, multivariate normal and generalized Pareto distributions.
Author: Elizabeth Gonzalez-Estrada, Jose A. Villasenor-Alva
Maintainer: Elizabeth Gonzalez-Estrada
goft-1.0/goft/R/gumbel.R |only
goft-1.0/goft/man/gumbel.Rd |only
goft-1.1/goft/DESCRIPTION | 15 +++----
goft-1.1/goft/MD5 | 19 +++++----
goft-1.1/goft/R/gamma.test.R |only
goft-1.1/goft/R/mvShapiro.Test.R | 74 ++++++++++++++++++------------------
goft-1.1/goft/R/normal.R | 70 +++++++++++++++++-----------------
goft-1.1/goft/data |only
goft-1.1/goft/inst |only
goft-1.1/goft/man/gamma.test.Rd |only
goft-1.1/goft/man/goats.Rd |only
goft-1.1/goft/man/gpd.test.Rd | 2
goft-1.1/goft/man/mvShapiro.Test.Rd | 12 +++--
goft-1.1/goft/man/normal.Rd | 11 ++---
14 files changed, 103 insertions(+), 100 deletions(-)
Title: Functions and Datasets for "Forest Analytics with R"
Diff between FAwR versions 1.0.1 dated 2011-05-15 and 1.1.0 dated 2015-03-24
Description: Provides functions and datasets from the book "Forest Analytics with R".
Author: Andrew Robinson and Jeff Hamann
Maintainer: Andrew Robinson
FAwR-1.0.1/FAwR/R/schedpack.r |only
FAwR-1.1.0/FAwR/ChangeLog |only
FAwR-1.1.0/FAwR/DESCRIPTION | 17
FAwR-1.1.0/FAwR/MD5 |only
FAwR-1.1.0/FAwR/NAMESPACE |only
FAwR-1.1.0/FAwR/R/from-weikko-jarros-schedpack.r |only
FAwR-1.1.0/FAwR/data/gutten.rda |binary
FAwR-1.1.0/FAwR/data/stage.rda |binary
FAwR-1.1.0/FAwR/data/sweetgum.rda |binary
FAwR-1.1.0/FAwR/data/ufc.rda |binary
FAwR-1.1.0/FAwR/inst/resources/data/final-plots.csv | 1832 +++++-----
FAwR-1.1.0/FAwR/inst/resources/errata.txt |only
FAwR-1.1.0/FAwR/inst/resources/scripts/book |only
FAwR-1.1.0/FAwR/inst/resources/scripts/chambers-1980.c |only
FAwR-1.1.0/FAwR/inst/resources/scripts/chambers-1980.h |only
FAwR-1.1.0/FAwR/inst/resources/scripts/chambers-1980.r |only
FAwR-1.1.0/FAwR/inst/resources/scripts/from-weikko-jarros-planning_glpkAPI-GenericPaths.R |only
FAwR-1.1.0/FAwR/inst/resources/scripts/from-weikko-jarros-schedpack.r |only
FAwR-1.1.0/FAwR/inst/resources/scripts/functions.R |only
FAwR-1.1.0/FAwR/inst/resources/scripts/interval_summary.R |only
FAwR-1.1.0/FAwR/inst/resources/scripts/interval_test.R |only
FAwR-1.1.0/FAwR/inst/resources/scripts/ratio_summary.R |only
FAwR-1.1.0/FAwR/inst/resources/scripts/ratio_test.R |only
23 files changed, 924 insertions(+), 925 deletions(-)
Title: Assertive Programming for R Analysis Pipelines
Diff between assertr versions 0.4 dated 2015-03-22 and 0.4.1 dated 2015-03-24
Description: Provides functionality to assert conditions
that have to be met so that errors in data used in
analysis pipelines can fail quickly. Similar to
'stopifnot()' but more powerful, friendly, and easier
for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
NEWS | 4 ++++
README.md | 9 ++++++---
inst/doc/assertr.html | 4 ++--
tests/testthat/test-assertions.R | 8 ++++----
tests/testthat/test-predicates.R | 14 +++++++-------
7 files changed, 32 insertions(+), 25 deletions(-)
Title: Basic Tools for the Analysis of Disease Outbreaks
Diff between OutbreakTools versions 0.1-12 dated 2015-02-06 and 0.1-13 dated 2015-03-23
Description: Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart
ChangeLog | 5 +++++
DESCRIPTION | 12 ++++++------
MD5 | 22 +++++++++++-----------
build/vignette.rds |binary
data/FluH1N1pdm2009.RData |binary
data/HorseFlu.RData |binary
data/HorseFluRaw.RData |binary
data/ToyOutbreak.RData |binary
data/ToyOutbreakRaw.RData |binary
inst/doc/OutbreakTools.pdf |binary
man/obkContacts.Rd | 1 +
man/obkDataPlot.Rd | 1 +
12 files changed, 24 insertions(+), 17 deletions(-)
Title: Utilities for Producing Maps
Diff between mapmisc versions 1.1.3 dated 2015-02-21 and 1.2.0 dated 2015-03-23
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 12 ++--
MD5 | 60 ++++++++++++---------
NAMESPACE | 5 +
R/col2html.R |only
R/colourScale.R | 132 +++++++++++++++++++++++++++++++++++++----------
R/geonames.R | 2
R/getTiles.R | 17 ++----
R/insetMap.R | 2
R/legendBreaks.R | 103 ++++++++++++++++++++++++++++++++----
R/legendTable.R |only
R/omerc.R |only
R/openmap.R | 30 +++++++---
R/openmapAttribution.R |only
R/scaleBar.R | 68 +++++++++++++++++-------
R/tpeqd.R |only
R/utils.R | 60 +++++----------------
build/vignette.rds |binary
inst/doc/mapLayers.R | 9 +--
inst/doc/mapLayers.pdf |binary
inst/doc/mapLayers.rnw | 11 ++-
inst/doc/mapmisc.R | 16 ++---
inst/doc/mapmisc.pdf |binary
inst/doc/mapmisc.rnw | 18 ++----
inst/extdata/tiles.RData |binary
man/col2html.Rd |only
man/geonames.Rd | 2
man/legendBreaks.Rd | 13 +++-
man/legendTable.Rd |only
man/omerc.Rd |only
man/openmap.Rd | 60 +++++----------------
man/scaleBar.Rd | 2
man/tpeqd.Rd |only
tests/omerc.R |only
tests/openmap.R | 7 +-
vignettes/mapLayers.rnw | 11 ++-
vignettes/mapmisc.rnw | 18 ++----
36 files changed, 406 insertions(+), 252 deletions(-)
Title: Create Waffle Chart Visualizations in R
Diff between waffle versions 0.3 dated 2015-03-22 and 0.3.1 dated 2015-03-23
Description: Square pie charts (a.k.a. waffle charts) can be used
to communicate parts of a whole for categorical quantities. To emulate the
percentage view of a pie chart, a 10x10 grid should be used with each square
representing 1% of the total. Modern uses of waffle charts do not
necessarily adhere to this rule and can be created with a grid of any
rectangular shape. Best practices suggest keeping the number of categories
small, just as should be done when creating pie charts.
Author: Bob Rudis
Maintainer: Bob Rudis
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.2-0 dated 2015-02-27 and 0.2-1 dated 2015-03-23
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
ChangeLog | 16 +++
DESCRIPTION | 8 -
MD5 | 36 ++++----
NAMESPACE | 1
NEWS | 11 +-
R/associationMatrix.r | 12 +-
R/basicSPSStranslationFunctions.r | 65 ++++++++++++++-
R/convert.r | 42 +++++++++
R/meanDiff.r | 13 ++-
R/oneway.r | 13 ++-
R/userfriendlyscienceBasics.r | 11 +-
man/userfriendlyscience-associationMatrix.Rd | 11 --
man/userfriendlyscience-basicSPSStranslationFunctions.Rd | 16 +++
man/userfriendlyscience-convert.Rd | 27 +++++-
man/userfriendlyscience-meanDiff.Rd | 19 ++++
man/userfriendlyscience-package.Rd | 6 -
man/userfriendlyscience-regr.Rd | 2
man/userfriendlyscience-scaleInspection.Rd | 2
man/userfriendlyscience-userfriendlyscienceBasics.Rd | 20 +++-
19 files changed, 264 insertions(+), 67 deletions(-)
Permanent link
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Diff between spartan versions 2.1 dated 2014-08-19 and 2.2 dated 2015-03-23
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden
DESCRIPTION | 10 ++++-----
MD5 | 35 ++++++++++++++++----------------
R/aa_getATestResults.R | 3 ++
R/aa_graphATestsForSampleSize.R | 11 ++++++----
R/aa_graphSampleSizeSummary.R | 14 +++++++++---
R/aa_sampleSizeSummary.R | 3 ++
R/aa_summariseReplicateRuns.R | 3 ++
R/efast_get_overall_medians.R | 3 ++
R/efast_run_Analysis.R | 3 ++
R/lhc_generateLHCSummary.R | 5 +++-
R/lhc_generatePRCoEffs.R | 3 ++
R/lhc_graphMeasuresForParameterChange.R | 3 ++
R/lhc_plotCoEfficients.R |only
R/lhc_process_sample_run_subsets.R | 3 ++
R/oat_csv_result_file_analysis.R | 3 ++
R/oat_graphATestsForSampleSize.R | 4 ++-
R/oat_plotResultDistribution.R | 3 ++
R/oat_processParamSubsets.R | 5 +++-
man/Technique3-lhc_perform_analysis.Rd | 18 +++++++++++++---
19 files changed, 96 insertions(+), 36 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Diff between PMCMR versions 1.0 dated 2014-06-25 and 1.1 dated 2015-03-23
Description: The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert
PMCMR-1.0/PMCMR/inst/CITATION |only
PMCMR-1.1/PMCMR/DESCRIPTION | 10 -
PMCMR-1.1/PMCMR/MD5 | 20 +--
PMCMR-1.1/PMCMR/NAMESPACE | 10 +
PMCMR-1.1/PMCMR/R/posthoc.friedman.nemenyi.test.R | 120 ++++++++++++-------
PMCMR-1.1/PMCMR/R/posthoc.kruskal.nemenyi.test.R | 63 +++++++++
PMCMR-1.1/PMCMR/build/vignette.rds |binary
PMCMR-1.1/PMCMR/inst/NEWS.Rd |only
PMCMR-1.1/PMCMR/inst/doc/PMCMR.pdf |binary
PMCMR-1.1/PMCMR/man/PMCMR-package.Rd | 6
PMCMR-1.1/PMCMR/man/posthoc.friedman.nemenyi.test.Rd | 32 ++++-
PMCMR-1.1/PMCMR/man/posthoc.kruskal.nemenyi.test.Rd | 51 ++++++--
12 files changed, 228 insertions(+), 84 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Diff between Luminescence versions 0.4.1 dated 2015-01-29 and 0.4.2 dated 2015-03-23
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Rachel K. Smedley [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer
DESCRIPTION | 18
MD5 | 211 -
NAMESPACE | 7
NEWS | 279 +
R/CW2pHMi.R | 280 -
R/CW2pLM.R | 132
R/CW2pLMi.R | 236 -
R/CW2pPMi.R | 214 -
R/RLum.Analysis-class.R | 788 ++-
R/RLum.Data.Image-class.R | 160
R/RLum.Results-class.R | 387 +
R/RcppExports.R |only
R/RisoeBINfileData-class.R | 194
R/Second2Gray.R | 280 -
R/analyse_IRSAR.RF.R | 1105 +++--
R/analyse_SAR.CWOSL.R | 679 +--
R/analyse_pIRIRSequence.R | 1476 +++----
R/apply_CosmicRayRemoval.R | 249 -
R/calc_CentralDose.R | 2
R/calc_CommonDose.R | 2
R/calc_FadingCorr.R | 158
R/calc_FiniteMixture.R | 14
R/calc_FuchsLang2001.R | 2
R/calc_HomogeneityTest.R | 2
R/calc_IEU.R |only
R/calc_MaxDose.R | 12
R/calc_MinDose.R | 968 ++--
R/calc_SourceDoseRate.R | 334 -
R/calc_Statistics.R | 104
R/extract_IrradiationTimes.R |only
R/fit_LMCurve.R | 728 +--
R/get_RLum.R | 188
R/merge_RLum.R | 220 -
R/merge_Risoe.BINfileData.R | 500 +-
R/plot_AbanicoPlot.R | 6184 +++++++++++++++----------------
R/plot_DRTResults.R | 1484 +++----
R/plot_GrowthCurve.R | 2382 ++++++-----
R/plot_Histogram.R | 1251 +++---
R/plot_KDE.R | 1704 ++++----
R/plot_RLum.Analysis.R | 407 +-
R/plot_RLum.Data.Spectrum.R | 671 +--
R/plot_RLum.Results.R | 39
R/plot_RadialPlot.R | 2971 +++++++-------
R/readBIN2R.R | 1961 ++++-----
R/readSPE2R.R | 878 ++--
R/readXSYG2R.R | 518 +-
R/writeR2BIN.R | 748 ++-
data/ExampleData.DeValues.RData |binary
inst/NEWS.Rd | 1137 +++--
inst/doc/S4classObjects.pdf |binary
man/Analyse_SAR.OSLdata.Rd | 2
man/CW2pHMi.Rd | 84
man/CW2pLM.Rd | 26
man/CW2pLMi.Rd | 74
man/CW2pPMi.Rd | 60
man/ExampleData.DeValues.Rd | 138
man/Luminescence-package.Rd | 11
man/Risoe.BINfileData-class.Rd | 62
man/Risoe.BINfileData2RLum.Analysis.Rd | 2
man/Risoe.BINfileData2RLum.Data.Curve.Rd | 2
man/Second2Gray.Rd | 6
man/analyse_IRSAR.RF.Rd | 150
man/analyse_SAR.CWOSL.Rd | 92
man/analyse_SAR.TL.Rd | 2
man/analyse_pIRIRSequence.Rd | 86
man/apply_CosmicRayRemoval.Rd | 47
man/apply_EfficiencyCorrection.Rd | 2
man/calc_AliquotSize.Rd | 2
man/calc_CentralDose.Rd | 4
man/calc_CommonDose.Rd | 2
man/calc_CosmicDoseRate.Rd | 2
man/calc_FadingCorr.Rd | 42
man/calc_FiniteMixture.Rd | 16
man/calc_FuchsLang2001.Rd | 4
man/calc_HomogeneityTest.Rd | 4
man/calc_IEU.Rd |only
man/calc_MaxDose.Rd | 11
man/calc_MinDose.Rd | 199
man/calc_OSLLxTxRatio.Rd | 2
man/calc_SourceDoseRate.Rd | 4
man/calc_Statistics.Rd | 16
man/calc_TLLxTxRatio.Rd | 2
man/extract_IrradiationTimes.Rd |only
man/fit_CWCurve.Rd | 2
man/fit_LMCurve.Rd | 132
man/get_Layout.Rd | 2
man/get_RLum.Rd | 4
man/merge_RLum.Analysis.Rd | 2
man/merge_RLum.Data.Curve.Rd | 2
man/merge_RLum.Rd | 6
man/merge_Risoe.BINfileData.Rd | 28
man/plot_AbanicoPlot.Rd | 116
man/plot_DRTResults.Rd | 16
man/plot_GrowthCurve.Rd | 106
man/plot_Histogram.Rd | 79
man/plot_KDE.Rd | 68
man/plot_RLum.Analysis.Rd | 44
man/plot_RLum.Data.Curve.Rd | 2
man/plot_RLum.Data.Image.Rd | 2
man/plot_RLum.Data.Spectrum.Rd | 80
man/plot_RLum.Rd | 2
man/plot_RLum.Results.Rd | 4
man/plot_RadialPlot.Rd | 104
man/plot_Risoe.BINfileData.Rd | 2
man/readBIN2R.Rd | 32
man/readSPE2R.Rd | 2
man/readXSYG2R.Rd | 38
man/writeR2BIN.Rd | 50
src |only
109 files changed, 18002 insertions(+), 16343 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Diff between BAMMtools versions 2.0.4 dated 2015-03-18 and 2.0.5 dated 2015-03-23
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang
Maintainer: Pascal Title
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
R/assignColorBreaks.R | 2 +-
R/plot.bammdata.R | 6 +++++-
R/plot.bammshifts.R | 7 +++++--
R/plot.credibleshiftset.R | 3 +++
R/speciesByRatesMatrix.R | 5 ++++-
man/assignColorBreaks.Rd | 8 ++++----
man/plot.bammdata.Rd | 4 ++--
man/plot.bammshifts.Rd | 2 +-
man/plot.credibleshiftset.Rd | 2 +-
man/speciesByRatesMatrix.Rd | 2 +-
src/jenksBrks.c | 20 ++++----------------
13 files changed, 47 insertions(+), 46 deletions(-)
Title: Response Surface Analysis
Diff between RSA versions 0.9.6 dated 2015-01-21 and 0.9.8 dated 2015-03-23
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full polynomial,
shifted and rotated squared differences, rising ridge surfaces, basic
squared differences). The package provides plotting functions for 3d
wireframe surfaces, interactive 3d plots, and contour plots. Calculates
many surface parameters (a1 to a4, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schönbrodt
Maintainer: Felix Schönbrodt
DESCRIPTION | 8 +--
MD5 | 38 ++++++++++--------
R/RSA.R | 30 ++++++++------
R/aictab.R | 100 +++++++++++++++++++++++++++++++++++++++++--------
R/compare.R | 22 +++++-----
R/confint.R | 25 +++++++++---
R/demoSRRR.R | 8 +--
R/getPar.R | 13 +++---
R/helpers.R | 2
R/motcon2-data.R |only
R/plot.RSA.R | 33 ++++++++--------
R/print.RSA.R | 28 ++-----------
data/motcon2.tab |only
inst/NEWS.Rd | 43 +++++++++++++++++++++
inst/RSA_modeltree.pdf |only
man/RSA.Rd | 9 ++--
man/aictab.Rd | 34 ++++++++++++++--
man/compare.Rd | 4 +
man/compare2.Rd | 4 +
man/getPar.Rd | 2
man/motcon2.Rd |only
man/plotRSA.Rd | 8 ++-
22 files changed, 284 insertions(+), 127 deletions(-)
Title: Detection and Control of Tree-Ring Widths on Scanned Image
Sections
Diff between measuRing versions 0.1 dated 2014-10-01 and 0.3 dated 2015-03-23
Description: Identification of ring borders on scanned image sections from dendrochronological samples. Processesing of image reflectances to produce gray matrices and a time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders, or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical device, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values.
Author: Wilson Lara, Carlos Sierra, Felipe Bravo
Maintainer: Wilson Lara
measuRing-0.1/measuRing/R/pixelTypes.R |only
measuRing-0.1/measuRing/man/pixelTypes.Rd |only
measuRing-0.3/measuRing/DESCRIPTION | 16 -
measuRing-0.3/measuRing/MD5 | 57 ++-
measuRing-0.3/measuRing/NAMESPACE | 16 -
measuRing-0.3/measuRing/NEWS |only
measuRing-0.3/measuRing/R/colNarrow.R |only
measuRing-0.3/measuRing/R/dataSegments.R |only
measuRing-0.3/measuRing/R/grayDarker.R | 61 ++-
measuRing-0.3/measuRing/R/graySmoothed.R | 79 +++-
measuRing-0.3/measuRing/R/imageTogray.R | 89 ++++-
measuRing-0.3/measuRing/R/lagIngray.R | 49 ++-
measuRing-0.3/measuRing/R/linearDetect.R | 80 +++--
measuRing-0.3/measuRing/R/multiDetect.R |only
measuRing-0.3/measuRing/R/plotSegments.R | 364 +++++++++++++++--------
measuRing-0.3/measuRing/R/ringBorders.R |only
measuRing-0.3/measuRing/R/ringDetect.R | 128 +++++---
measuRing-0.3/measuRing/R/ringSelect.R | 155 ++++-----
measuRing-0.3/measuRing/R/ringWidths.R | 80 +++--
measuRing-0.3/measuRing/inst/P105_a.png |only
measuRing-0.3/measuRing/inst/P105_b.tif |only
measuRing-0.3/measuRing/inst/P105_c.tif |only
measuRing-0.3/measuRing/inst/P105_d.tif |only
measuRing-0.3/measuRing/man/colNarrow.Rd |only
measuRing-0.3/measuRing/man/dataSegments.Rd |only
measuRing-0.3/measuRing/man/grayDarker.Rd | 38 +-
measuRing-0.3/measuRing/man/graySmoothed.Rd | 33 +-
measuRing-0.3/measuRing/man/imageTogray.Rd | 47 ++
measuRing-0.3/measuRing/man/lagIngray.Rd | 33 +-
measuRing-0.3/measuRing/man/linearDetect.Rd | 29 +
measuRing-0.3/measuRing/man/measuRing-package.Rd | 16 -
measuRing-0.3/measuRing/man/multiDetect.Rd |only
measuRing-0.3/measuRing/man/plotSegments.Rd | 66 ++--
measuRing-0.3/measuRing/man/ringBorders.Rd |only
measuRing-0.3/measuRing/man/ringDetect.Rd | 93 +++--
measuRing-0.3/measuRing/man/ringSelect.Rd | 86 ++---
measuRing-0.3/measuRing/man/ringWidths.Rd | 38 +-
37 files changed, 1095 insertions(+), 558 deletions(-)
Title: Multiple Hypothesis Testing for Variable Selection in
High-Dimensional Linear Models
Diff between mht versions 3.0.11 dated 2014-09-02 and 3.1.2 dated 2015-03-23
Description: Multiple Hypothesis Testing For Variable Selection in high dimensional linear models. This package performs variable selection with multiple hypothesis testing, either for ordered variable selection or non-ordered variable selection. In both cases, a sequential procedure is performed. It starts to test the null hypothesis "no variable is relevant"; if this hypothesis is rejected, it then tests "only the first variable is relevant", and so on until the null hypothesis is accepted.
Author: Florian Rohart
Maintainer: Florian Rohart
mht-3.0.11/mht/R/gaussrandom.R |only
mht-3.0.11/mht/R/predict.mht.R |only
mht-3.0.11/mht/R/predict.mht.order.R |only
mht-3.0.11/mht/R/print.mht.R |only
mht-3.0.11/mht/R/print.mht.order.R |only
mht-3.0.11/mht/man/predict.mht.Rd |only
mht-3.0.11/mht/man/predict.mht.order.Rd |only
mht-3.1.2/mht/DESCRIPTION | 18
mht-3.1.2/mht/MD5 | 69 +--
mht-3.1.2/mht/NAMESPACE | 8
mht-3.1.2/mht/NEWS | 12
mht-3.1.2/mht/R/bolassofunction.R | 229 +++++++-----
mht-3.1.2/mht/R/data.scale.R |only
mht-3.1.2/mht/R/decompbaseorthofunction.R | 110 ++++-
mht-3.1.2/mht/R/decoupdyadfunction.R | 349 +++++++++++-------
mht-3.1.2/mht/R/mht.R | 484 +++++++++++---------------
mht-3.1.2/mht/R/mht.order.R | 393 +++++++++++----------
mht-3.1.2/mht/R/order.variables.R |only
mht-3.1.2/mht/R/plot.R |only
mht-3.1.2/mht/R/predict.R |only
mht-3.1.2/mht/R/print.R |only
mht-3.1.2/mht/R/print.bolasso.R | 23 +
mht-3.1.2/mht/R/quantil_ord.R | 89 ++--
mht-3.1.2/mht/R/quantilemht.R | 256 +++++++------
mht-3.1.2/mht/R/quantiletest.R | 19 +
mht-3.1.2/mht/R/refit.R | 19 +
mht-3.1.2/mht/R/refit.mht.R | 553 ++++++++++++++----------------
mht-3.1.2/mht/R/refit.mht.order.R | 459 ++++++++++++++----------
mht-3.1.2/mht/R/zzz.R | 26 +
mht-3.1.2/mht/man/bolasso.Rd | 33 +
mht-3.1.2/mht/man/data.scale.Rd |only
mht-3.1.2/mht/man/decompbaseortho.Rd | 13
mht-3.1.2/mht/man/decoupdyad.Rd | 35 +
mht-3.1.2/mht/man/mht-package.Rd | 26 -
mht-3.1.2/mht/man/mht.Rd | 44 +-
mht-3.1.2/mht/man/mht.order.Rd | 47 +-
mht-3.1.2/mht/man/order.variables.Rd |only
mht-3.1.2/mht/man/plot.Rd |only
mht-3.1.2/mht/man/plot.bolasso.Rd |only
mht-3.1.2/mht/man/predict.Rd |only
mht-3.1.2/mht/man/quantilemht.Rd | 2
mht-3.1.2/mht/man/refit.mht.Rd | 31 +
mht-3.1.2/mht/man/refit.mht.order.Rd | 33 +
mht-3.1.2/mht/src/mhtquant.cpp | 54 ++
44 files changed, 1939 insertions(+), 1495 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Diff between MPTinR versions 1.6.3 dated 2014-10-21 and 1.7.5 dated 2015-03-22
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, MPTinR can fit a wide variety of other cognitive models such as SDT models (see fit.model). MPTinR supports multicore fitting and FIA calculation using the snowfall package. MPTinR can generate data from a model for e.g., simulation or parametric bootstrap and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann
DESCRIPTION | 14
MD5 | 28 -
NEWS | 65 ++-
R/bmpt.fia.R | 2
R/fit.mpt.old.R | 4
R/fit.mptinr.R | 31 +
R/select.mpt.R | 20 -
data/d.broeder.rda |binary
data/rb.fig1.data.rda |binary
data/rb.fig2.data.rda |binary
man/fit.mpt.Rd | 814 +++++++++++++++++++++++++-------------------------
man/fit.mptinr.Rd | 2
man/gen.data.Rd | 3
man/select.mpt.Rd | 15
src/RcppExports.cpp | 58 +--
15 files changed, 548 insertions(+), 508 deletions(-)
Title: Model Confidence Set Procedure
Diff between MCS versions 0.1.0 dated 2014-11-18 and 0.1.1 dated 2015-03-22
Description: Perform the model confidence set procedure of Hansen et al (2011).
Author: Leopoldo Catania & Mauro Bernardi
Maintainer: Leopoldo Catania
DESCRIPTION | 6 -
MD5 | 8 +-
R/MCS.R | 227 ++++++++++++++++++++++++++-------------------------------
man/LossVaR.Rd | 2
man/LossVol.Rd | 4 -
5 files changed, 115 insertions(+), 132 deletions(-)
Title: Import Stata 13 Data Files
Diff between readstata13 versions 0.5-3 dated 2015-02-11 and 0.6 dated 2015-03-22
Description: Function to read and write the Stata 13 file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki
CHANGELOG | 4 +
DESCRIPTION | 6 -
MD5 | 33 +++++----
NAMESPACE | 2
R/dbcal.R |only
R/save.R | 4 -
R/tools.R | 167 ++++++++++++++++++++++++++++------------------
README.md |only
inst/extdata/sp500.stbcal |only
inst/extdata/statacar.dta |binary
man/as.caldays.Rd |only
man/get.label.Rd | 4 -
man/get.origin.codes.Rd | 8 +-
man/set.label.Rd | 9 +-
man/set.lang.Rd | 10 ++
man/stbcal.Rd |only
src/RcppExports.cpp | 32 +++-----
src/rcpp_readstata.cpp | 3
src/rcpp_savestata.cpp | 5 -
src/statadefines.h | 10 +-
20 files changed, 177 insertions(+), 120 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density Estimation
Diff between psd versions 1.0-0 dated 2015-03-18 and 1.0-1 dated 2015-03-22
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability.
Author: Andrew J. Barbour and Robert L. Parker, with contributions from David
Myer
Maintainer: Andrew J. Barbour
psd-1.0-0/psd/vignettes/fftw.synctex.gz |only
psd-1.0-0/psd/vignettes/normalization.synctex.gz |only
psd-1.0-0/psd/vignettes/psd_overview.synctex.gz |only
psd-1.0-1/psd/DESCRIPTION | 13 +-
psd-1.0-1/psd/MD5 | 81 ++++++++----------
psd-1.0-1/psd/R/func_pspectrum.R | 12 +-
psd-1.0-1/psd/inst/Examples/rdex_confint.R | 12 ++
psd-1.0-1/psd/inst/Examples/rdex_constraintapers.R | 11 +-
psd-1.0-1/psd/inst/Examples/rdex_normalization.R | 25 +++--
psd-1.0-1/psd/inst/Examples/rdex_parabolicweights.R | 13 +-
psd-1.0-1/psd/inst/Examples/rdex_pilotspec.R | 11 +-
psd-1.0-1/psd/inst/Examples/rdex_prewhiten.R | 34 ++++---
psd-1.0-1/psd/inst/Examples/rdex_psdcore.R | 12 +-
psd-1.0-1/psd/inst/Examples/rdex_psdenv.R | 12 ++
psd-1.0-1/psd/inst/Examples/rdex_pspectrum.R | 64 ++------------
psd-1.0-1/psd/inst/Examples/rdex_riedsid.R | 14 ++-
psd-1.0-1/psd/inst/Examples/rdex_spec.R | 20 ++--
psd-1.0-1/psd/inst/Examples/rdex_spectralproperties.R | 26 +----
psd-1.0-1/psd/inst/Examples/rdex_splinegrad.R | 9 +-
psd-1.0-1/psd/inst/Examples/rdex_tapers.R | 4
psd-1.0-1/psd/inst/Examples/rdex_utilities.R | 3
psd-1.0-1/psd/inst/NEWS.Rd | 19 ++++
psd-1.0-1/psd/inst/doc/fftw.pdf |binary
psd-1.0-1/psd/inst/doc/normalization.pdf |binary
psd-1.0-1/psd/inst/doc/psd_overview.pdf |binary
psd-1.0-1/psd/man/as.tapers.Rd | 4
psd-1.0-1/psd/man/parabolic_weights.Rd | 13 +-
psd-1.0-1/psd/man/pilot_spec.Rd | 11 +-
psd-1.0-1/psd/man/prewhiten.Rd | 34 ++++---
psd-1.0-1/psd/man/psd-environment.Rd | 12 ++
psd-1.0-1/psd/man/psd-normalization.Rd | 25 +++--
psd-1.0-1/psd/man/psd-utilities.Rd | 3
psd-1.0-1/psd/man/psdcore.Rd | 12 +-
psd-1.0-1/psd/man/pspectrum.Rd | 76 +++-------------
psd-1.0-1/psd/man/riedsid.Rd | 14 ++-
psd-1.0-1/psd/man/spec-methods.Rd | 20 ++--
psd-1.0-1/psd/man/spec_confint.Rd | 12 ++
psd-1.0-1/psd/man/spectral_properties.Rd | 26 +----
psd-1.0-1/psd/man/splineGrad.Rd | 9 +-
psd-1.0-1/psd/man/tapers-constraints.Rd | 11 +-
psd-1.0-1/psd/src/RcppExports.cpp | 4
psd-1.0-1/psd/src/resample_fft.cpp | 23 +++--
psd-1.0-1/psd/tests/testthat/test-fft.R | 40 +++++---
43 files changed, 383 insertions(+), 361 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Diff between mvMORPH versions 1.0.3 dated 2015-03-17 and 1.0.4 dated 2015-03-22
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel
DESCRIPTION | 6 +++---
MD5 | 39 ++++++++++++++++++++-------------------
R/fun.r | 2 +-
R/mvBM.r | 4 ++--
R/mvEB.r | 4 ++--
R/mvSHIFT.r | 2 +-
R/testLRT.r | 2 +-
man/mv.Precalc.Rd | 4 ++--
man/mvBM.Rd | 2 +-
man/mvEB.Rd | 18 +++++++++++-------
man/mvSHIFT.Rd | 2 +-
man/mvSIM.Rd | 4 ++--
src/covar-matrix-simmap.c | 2 +-
src/covar.h |only
src/kronecker.c | 4 +++-
src/mvmorph-covar-mat.c | 2 +-
src/mvmorph-covar-ou-sparse.c | 2 +-
src/mvmorph.h | 14 --------------
src/pic_loglik_mvmorph.c | 8 ++++----
src/weight-matrix-mvmorph.c | 2 +-
src/weight-matrix-simmap.c | 2 +-
21 files changed, 59 insertions(+), 66 deletions(-)
Title: Visualizing the Performance of Scoring Classifiers
Diff between ROCR versions 1.0-5 dated 2013-05-16 and 1.0-6 dated 2015-03-22
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different
cross-validation or bootstrapping runs can be averaged by
different methods, and standard deviations, standard errors or
box plots can be used to visualize the variability across the
runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot
can be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.
Author: Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
Maintainer: Billy Aung Myint
ROCR-1.0-5/ROCR/README.unittests |only
ROCR-1.0-5/ROCR/unittests |only
ROCR-1.0-6/ROCR/DESCRIPTION | 16 +++++++++-------
ROCR-1.0-6/ROCR/MD5 | 14 ++++----------
ROCR-1.0-6/ROCR/data/ROCR.hiv.rda |binary
ROCR-1.0-6/ROCR/data/ROCR.simple.rda |binary
ROCR-1.0-6/ROCR/data/ROCR.xval.rda |binary
7 files changed, 13 insertions(+), 17 deletions(-)
Title: Latent Position and Cluster Models for Statistical Networks
Diff between latentnet versions 2.6.0 dated 2014-12-24 and 2.7.0 dated 2015-03-22
Description: Fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky
latentnet-2.6.0/latentnet/R/ergmm.midarrow.R |only
latentnet-2.6.0/latentnet/man/latentnet.Rd |only
latentnet-2.7.0/latentnet/ChangeLog | 57 +++-
latentnet-2.7.0/latentnet/DESCRIPTION | 18 -
latentnet-2.7.0/latentnet/LICENSE | 4
latentnet-2.7.0/latentnet/MD5 | 193 ++++++++--------
latentnet-2.7.0/latentnet/NAMESPACE | 30 ++
latentnet-2.7.0/latentnet/R/InitErgmm.fixed.R | 12
latentnet-2.7.0/latentnet/R/InitErgmm.latent.R | 9
latentnet-2.7.0/latentnet/R/InitErgmm.random.R | 9
latentnet-2.7.0/latentnet/R/P.alloc.R | 9
latentnet-2.7.0/latentnet/R/bayesmbc.MCMC.C.R | 9
latentnet-2.7.0/latentnet/R/bayesmbc.R | 9
latentnet-2.7.0/latentnet/R/ergmm.MCMC.C.R | 10
latentnet-2.7.0/latentnet/R/ergmm.R | 13 -
latentnet-2.7.0/latentnet/R/ergmm.defaults.R | 9
latentnet-2.7.0/latentnet/R/ergmm.draw.utils.R |only
latentnet-2.7.0/latentnet/R/ergmm.families.R | 9
latentnet-2.7.0/latentnet/R/ergmm.geodesicmatrix.R | 9
latentnet-2.7.0/latentnet/R/ergmm.get.model.R | 9
latentnet-2.7.0/latentnet/R/ergmm.initvals.R | 11
latentnet-2.7.0/latentnet/R/ergmm.latent.effects.R | 9
latentnet-2.7.0/latentnet/R/ergmm.par.R | 11
latentnet-2.7.0/latentnet/R/ergmm.permutation.R | 9
latentnet-2.7.0/latentnet/R/ergmm.probs.R | 53 +---
latentnet-2.7.0/latentnet/R/ergmm.statseval.R | 40 +--
latentnet-2.7.0/latentnet/R/ergmm.tuner.R | 9
latentnet-2.7.0/latentnet/R/gof.ergmm.R | 9
latentnet-2.7.0/latentnet/R/label.switching.R | 9
latentnet-2.7.0/latentnet/R/latent.R | 9
latentnet-2.7.0/latentnet/R/mcmc.diagnostics.ergmm.R | 15 -
latentnet-2.7.0/latentnet/R/merge.ergmm.R | 11
latentnet-2.7.0/latentnet/R/plot.ergmm.R | 23 -
latentnet-2.7.0/latentnet/R/predict.ergmm.R | 9
latentnet-2.7.0/latentnet/R/print.ergmm.R | 9
latentnet-2.7.0/latentnet/R/print.ergmm.model.R | 9
latentnet-2.7.0/latentnet/R/procrustes.R | 19 -
latentnet-2.7.0/latentnet/R/simulate.ergmm.R | 9
latentnet-2.7.0/latentnet/R/summary.ergmm.R | 37 +--
latentnet-2.7.0/latentnet/R/utilities.R | 9
latentnet-2.7.0/latentnet/R/zzz.R | 13 -
latentnet-2.7.0/latentnet/data/davis.RData |binary
latentnet-2.7.0/latentnet/inst/CITATION | 40 +++
latentnet-2.7.0/latentnet/man/as.mcmc.list.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/davis.Rd | 16 -
latentnet-2.7.0/latentnet/man/ergmm.Rd | 15 -
latentnet-2.7.0/latentnet/man/ergmm.control.Rd | 9
latentnet-2.7.0/latentnet/man/ergmm.drawpie.Rd |only
latentnet-2.7.0/latentnet/man/ergmm.object.Rd | 9
latentnet-2.7.0/latentnet/man/ergmm.par.list.object.Rd | 10
latentnet-2.7.0/latentnet/man/ergmm.prior.Rd | 9
latentnet-2.7.0/latentnet/man/families.ergmm.Rd | 10
latentnet-2.7.0/latentnet/man/gof.ergmm.Rd | 12
latentnet-2.7.0/latentnet/man/latentnet-internal.Rd | 128 ----------
latentnet-2.7.0/latentnet/man/latentnet-package.Rd |only
latentnet-2.7.0/latentnet/man/mcmc.diagnostics.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/merge.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/plot.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/predict.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/sampson.Rd | 9
latentnet-2.7.0/latentnet/man/simulate.ergmm.Rd | 9
latentnet-2.7.0/latentnet/man/summary.ergmm.Rd | 82 +++++-
latentnet-2.7.0/latentnet/man/terms.ergmm.Rd | 11
latentnet-2.7.0/latentnet/man/tribes.Rd | 9
latentnet-2.7.0/latentnet/src/P_alloc.c | 9
latentnet-2.7.0/latentnet/src/P_alloc.h | 9
latentnet-2.7.0/latentnet/src/ergmm_families.c | 9
latentnet-2.7.0/latentnet/src/ergmm_families.h | 9
latentnet-2.7.0/latentnet/src/ergmm_latent_effects.c | 9
latentnet-2.7.0/latentnet/src/ergmm_latent_effects.h | 9
latentnet-2.7.0/latentnet/src/ergmm_probs.c | 11
latentnet-2.7.0/latentnet/src/ergmm_probs.h | 9
latentnet-2.7.0/latentnet/src/ergmm_sampler.c | 11
latentnet-2.7.0/latentnet/src/ergmm_sampler.h | 9
latentnet-2.7.0/latentnet/src/ergmm_structs.h | 9
latentnet-2.7.0/latentnet/src/ergmm_updaters.c | 9
latentnet-2.7.0/latentnet/src/ergmm_updaters.h | 9
latentnet-2.7.0/latentnet/src/ergmm_utils.c | 9
latentnet-2.7.0/latentnet/src/ergmm_utils.h | 9
latentnet-2.7.0/latentnet/src/kl_switch.c | 9
latentnet-2.7.0/latentnet/src/kl_switch.h | 9
latentnet-2.7.0/latentnet/src/matrix_utils.c | 9
latentnet-2.7.0/latentnet/src/matrix_utils.h | 9
latentnet-2.7.0/latentnet/src/mbc_sampler.c | 9
latentnet-2.7.0/latentnet/src/mbc_sampler.h | 9
latentnet-2.7.0/latentnet/src/mvnorm.c | 9
latentnet-2.7.0/latentnet/src/mvnorm.h | 9
latentnet-2.7.0/latentnet/src/post_predict.c | 11
latentnet-2.7.0/latentnet/src/post_predict.h | 9
latentnet-2.7.0/latentnet/src/procrustes.c | 9
latentnet-2.7.0/latentnet/src/procrustes.h | 9
latentnet-2.7.0/latentnet/src/wishart.c | 9
latentnet-2.7.0/latentnet/src/wishart.h | 9
latentnet-2.7.0/latentnet/tests/examples.R | 9
latentnet-2.7.0/latentnet/tests/missing.R | 9
latentnet-2.7.0/latentnet/tests/nolatent.R | 9
latentnet-2.7.0/latentnet/tests/nomcmc.R | 9
latentnet-2.7.0/latentnet/tests/nomixing.R | 9
latentnet-2.7.0/latentnet/tests/normal.R | 15 -
latentnet-2.7.0/latentnet/tests/onlymcmc.R | 9
100 files changed, 378 insertions(+), 1131 deletions(-)
Title: A Tool for Downloading Functional Traits Data for Plant Species
Diff between TR8 versions 0.9.12 dated 2015-03-04 and 0.9.13 dated 2015-03-22
Description: Plant ecologists often need to collect "traits" data
about plant species which are often scattered among various
databases: TR8 contains a set of tools which take care of
automatically retrieving some of those functional traits data
for plant species from publicly available databases (Biolflor,
The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg
values for Italian Flora, Mycorrhizal intensity databases, Catminat).
The TR8 name, inspired by "car plates" jokes, was chosen since
it both reminds of the main object of the package and is
extremely short to type.
Author: Gionata Bocci
Maintainer: Gionata Bocci
DESCRIPTION | 11 +-
MD5 | 55 +++++++-------
NAMESPACE | 2
R/LEDA.R | 12 +--
R/biolflor.R | 5 +
R/catminat.R |only
R/catminat_download.R |only
R/ecoflora.R | 46 +++++++++++-
R/leda_download.R | 2
R/local_storage.R | 15 ++--
R/mycoflor.R | 15 ++--
R/results.R | 2
R/tr8.R | 96 ++++++++++++++++++++------
R/tr8_gui.R | 10 +-
data/available_tr8.rda |binary
data/column_list.rda |binary
data/traits_eco.rda |binary
inst/CITATION | 9 +-
inst/doc/Expanding_TR8.pdf |binary
inst/doc/TR8.R | 40 +++++++---
inst/doc/TR8.Rnw | 166 +++++++++++++++++++++++++++++++--------------
inst/doc/TR8.pdf |binary
inst/doc/TR8_workflow.pdf |binary
man/TR8-package.Rd | 19 ++++-
man/Tr8-class.Rd | 7 +
man/column_list.Rd | 126 +++++++++++++++++++++++-----------
man/tr8.Rd | 11 ++
vignettes/TR8.Rnw | 166 +++++++++++++++++++++++++++++++--------------
vignettes/temp.ps |only
vignettes/tr8.bib | 11 ++
30 files changed, 592 insertions(+), 234 deletions(-)
Title: Regularized Cox Model
Diff between Coxnet versions 0.1 dated 2015-03-17 and 0.1-1 dated 2015-03-22
Description: Cox model regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty. In addition, it can truncate the estimate by a hard threshold, which is selected simultaneously with other tuning parameters. Moreover, it can handle the adaptive version of these regularization forms, such as adaptive lasso and net adjusting for signs of linked coefficients. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
Author: Xiang Li, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
man/Coxnet-package.Rd | 6 +++---
man/Coxnet.Rd | 8 ++++----
man/coxsplit.Rd | 8 +++-----
man/print.Coxnet.Rd | 1 -
src/Coxnet.cpp | 2 +-
7 files changed, 22 insertions(+), 25 deletions(-)
Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.1 dated 2015-02-19 and 1.2 dated 2015-03-21
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 1 +
DESCRIPTION | 9 +++++----
MD5 | 22 ++++++++++++++--------
NAMESPACE | 16 +++++++++++++++-
R/onAttach.R | 8 --------
R/rr.R | 8 +++++---
R/rrBayes.R |only
R/rrreg.predictor.R | 2 +-
man/rr-package.Rd | 4 ++--
man/rrreg.bayes.Rd |only
src/R2models.c | 25 +++++++++++++++++--------
tests |only
12 files changed, 60 insertions(+), 35 deletions(-)
Title: Advanced Data Analysis of T-Cell Receptor Repertoires
Diff between tcR versions 1.1 dated 2015-01-10 and 1.3 dated 2015-03-21
Description: Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov, Mikhail Pogorelyy
Maintainer: Vadim Nazarov
tcR-1.1/tcR/data/human.alphabets.rda |only
tcR-1.1/tcR/data/mouse.alphabets.rda |only
tcR-1.1/tcR/data/segments.rda |only
tcR-1.1/tcR/man/parse.file.Rd |only
tcR-1.1/tcR/man/parse.file.list.Rd |only
tcR-1.3/tcR/DESCRIPTION | 16
tcR-1.3/tcR/MD5 | 119 +++----
tcR-1.3/tcR/NAMESPACE | 3
tcR-1.3/tcR/NEWS |only
tcR-1.3/tcR/R/crosses.R | 7
tcR-1.3/tcR/R/dataproc.R | 6
tcR-1.3/tcR/R/datatools.R | 63 +++
tcR-1.3/tcR/R/diversity.R | 55 ++-
tcR-1.3/tcR/R/docdata.R | 85 ++++-
tcR-1.3/tcR/R/filters.R | 2
tcR-1.3/tcR/R/graph.R |only
tcR-1.3/tcR/R/infoanalysis.R | 16
tcR-1.3/tcR/R/input.R | 449 ++++++++++++++++++----------
tcR-1.3/tcR/R/kmers.R | 32 +
tcR-1.3/tcR/R/measures.R | 15
tcR-1.3/tcR/R/plots.R | 207 +++++++++---
tcR-1.3/tcR/R/segments.R | 58 +--
tcR-1.3/tcR/R/shared.R | 10
tcR-1.3/tcR/R/spectrum.R | 8
tcR-1.3/tcR/R/stats.R | 137 ++++++--
tcR-1.3/tcR/R/strtools.R | 4
tcR-1.3/tcR/README.md | 9
tcR-1.3/tcR/data/datalist | 4
tcR-1.3/tcR/data/genesegments.rda |only
tcR-1.3/tcR/data/twa.rda |binary
tcR-1.3/tcR/data/twb.rda |binary
tcR-1.3/tcR/inst/crossanalysis.report.Rmd | 4
tcR-1.3/tcR/inst/doc/tcrvignette.R | 176 ++++++----
tcR-1.3/tcR/inst/doc/tcrvignette.Rnw | 218 ++++++++-----
tcR-1.3/tcR/inst/doc/tcrvignette.pdf |binary
tcR-1.3/tcR/inst/library.report.Rmd | 4
tcR-1.3/tcR/man/bootstrap.tcr.Rd | 6
tcR-1.3/tcR/man/clonal.space.homeostasis.Rd |only
tcR-1.3/tcR/man/column.summary.Rd | 4
tcR-1.3/tcR/man/entropy.Rd | 15
tcR-1.3/tcR/man/entropy.seg.Rd | 7
tcR-1.3/tcR/man/freq.segments.Rd | 28 -
tcR-1.3/tcR/man/generate.kmers.Rd | 2
tcR-1.3/tcR/man/generate.tcr.Rd | 9
tcR-1.3/tcR/man/get.inframes.Rd | 10
tcR-1.3/tcR/man/get.kmers.Rd | 2
tcR-1.3/tcR/man/group.clonotypes.Rd |only
tcR-1.3/tcR/man/intersect.Rd | 2
tcR-1.3/tcR/man/inverse.simpson.Rd | 19 -
tcR-1.3/tcR/man/kmer.profile.Rd | 9
tcR-1.3/tcR/man/kmer.table.Rd | 6
tcR-1.3/tcR/man/mitcr.stats.Rd | 13
tcR-1.3/tcR/man/mutated.neighbours.Rd |only
tcR-1.3/tcR/man/mutation.network.Rd |only
tcR-1.3/tcR/man/parse.cloneset.Rd |only
tcR-1.3/tcR/man/parse.folder.Rd | 83 ++++-
tcR-1.3/tcR/man/rarefaction.Rd | 4
tcR-1.3/tcR/man/segments.alphabets.Rd | 53 ++-
tcR-1.3/tcR/man/segments.list.Rd | 8
tcR-1.3/tcR/man/set.group.vector.Rd |only
tcR-1.3/tcR/man/set.people.vector.Rd |only
tcR-1.3/tcR/man/shared.repertoire.Rd | 4
tcR-1.3/tcR/man/vis.V.usage.Rd | 5
tcR-1.3/tcR/man/vis.clonal.space.Rd |only
tcR-1.3/tcR/man/vis.logo.Rd |only
tcR-1.3/tcR/man/vis.number.count.Rd | 3
tcR-1.3/tcR/src/RcppExports.cpp | 88 ++---
tcR-1.3/tcR/src/neighbour.search.cpp | 2
tcR-1.3/tcR/vignettes/tcrvignette.Rnw | 218 ++++++++-----
69 files changed, 1496 insertions(+), 811 deletions(-)
Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Diff between st versions 1.2.3 dated 2014-11-14 and 1.2.4 dated 2015-03-21
Description: Implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate
of the "correlation-adjusted t-score" (CAT score) described in
Zuber and Strimmer (2009). It also offers a convenient interface
to a number of other regularized t-statistics commonly
employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NEWS | 4 ++++
R/modt.R | 8 +++-----
R/sam.R | 6 ++----
man/choedata.Rd | 5 -----
man/regularizedt.Rd | 2 +-
man/shrinkcat.stat.Rd | 2 +-
man/shrinkt.stat.Rd | 2 +-
9 files changed, 26 insertions(+), 31 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Diff between sda versions 1.3.5 dated 2014-11-18 and 1.3.6 dated 2015-03-21
Description: Provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
NAMESPACE | 2 ++
NEWS | 5 +++++
man/khan2001.Rd | 6 ++----
man/singh2002.Rd | 2 +-
6 files changed, 21 insertions(+), 16 deletions(-)
Title: Tools for Descriptive Statistics
Diff between DescTools versions 0.99.9 dated 2015-01-20 and 0.99.10 dated 2015-03-21
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains as well functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Simon Urbanek, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell
DescTools-0.99.10/DescTools/DESCRIPTION | 12
DescTools-0.99.10/DescTools/MD5 | 205 +++++------
DescTools-0.99.10/DescTools/NAMESPACE | 121 ++++++
DescTools-0.99.10/DescTools/NEWS | 36 +
DescTools-0.99.10/DescTools/R/AscToChar.R | 2
DescTools-0.99.10/DescTools/R/CatTable.R | 2
DescTools-0.99.10/DescTools/R/CharToAsc.R | 5
DescTools-0.99.10/DescTools/R/ColorLegend.R | 2
DescTools-0.99.10/DescTools/R/Day.R | 2
DescTools-0.99.10/DescTools/R/Desc.Date.R | 40 +-
DescTools-0.99.10/DescTools/R/Desc.Lc.R | 2
DescTools-0.99.10/DescTools/R/Desc.data.frame.R | 2
DescTools-0.99.10/DescTools/R/Desc.factor.R | 2
DescTools-0.99.10/DescTools/R/Desc.integer.R | 2
DescTools-0.99.10/DescTools/R/Desc.list.R | 2
DescTools-0.99.10/DescTools/R/Desc.logical.R | 2
DescTools-0.99.10/DescTools/R/Desc.numeric.R | 11
DescTools-0.99.10/DescTools/R/Desc.table.R | 55 +--
DescTools-0.99.10/DescTools/R/DescNumFact.R | 8
DescTools-0.99.10/DescTools/R/DescNumNum.R | 12
DescTools-0.99.10/DescTools/R/DescTools-internal.R | 309 +++++++++--------
DescTools-0.99.10/DescTools/R/DescWrd.data.frame.R | 4
DescTools-0.99.10/DescTools/R/DescWrd.default.R | 11
DescTools-0.99.10/DescTools/R/DescWrd.formula.R | 8
DescTools-0.99.10/DescTools/R/DescWrd.list.R | 4
DescTools-0.99.10/DescTools/R/DrawBand.R | 18
DescTools-0.99.10/DescTools/R/DunnettTest.formula.R | 13
DescTools-0.99.10/DescTools/R/DurbinWatsonTest.R |only
DescTools-0.99.10/DescTools/R/Explore.R |only
DescTools-0.99.10/DescTools/R/FindColor.R | 2
DescTools-0.99.10/DescTools/R/Format.default.R | 30 +
DescTools-0.99.10/DescTools/R/GetPairs.R | 2
DescTools-0.99.10/DescTools/R/HighLow.R | 21 -
DescTools-0.99.10/DescTools/R/HuberM.R | 2
DescTools-0.99.10/DescTools/R/Impute.R | 2
DescTools-0.99.10/DescTools/R/Keywords.R | 25 -
DescTools-0.99.10/DescTools/R/Large.R | 36 +
DescTools-0.99.10/DescTools/R/MHChisqTest.R | 5
DescTools-0.99.10/DescTools/R/MeanCI.R | 10
DescTools-0.99.10/DescTools/R/MedianCI.R | 2
DescTools-0.99.10/DescTools/R/Month.R | 16
DescTools-0.99.10/DescTools/R/PalDescTools.R | 51 +-
DescTools-0.99.10/DescTools/R/PasswordDlg.R | 4
DescTools-0.99.10/DescTools/R/PlotACF.R | 2
DescTools-0.99.10/DescTools/R/PlotArea.R | 2
DescTools-0.99.10/DescTools/R/PlotDesc.Date.R | 2
DescTools-0.99.10/DescTools/R/PlotDesc.factor.R | 30 +
DescTools-0.99.10/DescTools/R/PlotDesc.table.R | 2
DescTools-0.99.10/DescTools/R/PlotGACF.R | 2
DescTools-0.99.10/DescTools/R/PlotMar.R | 2
DescTools-0.99.10/DescTools/R/PlotMonth.R | 2
DescTools-0.99.10/DescTools/R/PlotQQ.R | 31 +
DescTools-0.99.10/DescTools/R/PlotRCol.R | 4
DescTools-0.99.10/DescTools/R/PlotTernary.R | 3
DescTools-0.99.10/DescTools/R/PpPlot.R | 19 -
DescTools-0.99.10/DescTools/R/PpText.R | 2
DescTools-0.99.10/DescTools/R/SampleWord.R |only
DescTools-0.99.10/DescTools/R/SaveAs.R |only
DescTools-0.99.10/DescTools/R/ScheffeTest.aov.R | 4
DescTools-0.99.10/DescTools/R/SiegelTukeyRank.R | 23 -
DescTools-0.99.10/DescTools/R/Small.R | 36 +
DescTools-0.99.10/DescTools/R/SpreadOut.R | 5
DescTools-0.99.10/DescTools/R/Str.R | 2
DescTools-0.99.10/DescTools/R/StrTrunc.R | 2
DescTools-0.99.10/DescTools/R/StrVal.R | 4
DescTools-0.99.10/DescTools/R/ToLong.R | 17
DescTools-0.99.10/DescTools/R/Week.R | 56 ++-
DescTools-0.99.10/DescTools/R/Weekday.R | 16
DescTools-0.99.10/DescTools/R/WrdPlot.R | 5
DescTools-0.99.10/DescTools/R/WrdR.R | 2
DescTools-0.99.10/DescTools/R/WrdText.R | 2
DescTools-0.99.10/DescTools/R/XLGetRange.R | 3
DescTools-0.99.10/DescTools/R/Year.R | 2
DescTools-0.99.10/DescTools/R/YearDay.R | 3
DescTools-0.99.10/DescTools/R/YearMonth.R | 3
DescTools-0.99.10/DescTools/R/fastPOSIXct.R |only
DescTools-0.99.10/DescTools/inst/doc/DescTools.pdf |binary
DescTools-0.99.10/DescTools/man/AddMonths.Rd | 2
DescTools-0.99.10/DescTools/man/CochranArmitageTest.Rd | 2
DescTools-0.99.10/DescTools/man/CoefVar.Rd | 7
DescTools-0.99.10/DescTools/man/ConnLines.Rd | 2
DescTools-0.99.10/DescTools/man/CramerV.Rd | 5
DescTools-0.99.10/DescTools/man/DateFunctions.Rd | 28 -
DescTools-0.99.10/DescTools/man/Desc.Date.Rd | 7
DescTools-0.99.10/DescTools/man/Desc.Rd | 47 +-
DescTools-0.99.10/DescTools/man/DescTools-package.Rd | 7
DescTools-0.99.10/DescTools/man/DrawBand.Rd | 4
DescTools-0.99.10/DescTools/man/DurbinWatsonTest.Rd |only
DescTools-0.99.10/DescTools/man/Explore.Rd |only
DescTools-0.99.10/DescTools/man/Format.Rd | 3
DescTools-0.99.10/DescTools/man/GoodmanKruskalTauA.Rd | 2
DescTools-0.99.10/DescTools/man/KappaM.Rd |only
DescTools-0.99.10/DescTools/man/MeanCI.Rd | 7
DescTools-0.99.10/DescTools/man/MultinomCI.Rd | 9
DescTools-0.99.10/DescTools/man/OddsRatio.Rd | 10
DescTools-0.99.10/DescTools/man/PlotDesc.Rd | 4
DescTools-0.99.10/DescTools/man/PlotTernary.Rd | 6
DescTools-0.99.10/DescTools/man/RndPairs.Rd | 8
DescTools-0.99.10/DescTools/man/SaveAs.Rd |only
DescTools-0.99.10/DescTools/man/SiegelTukeyTest.Rd | 6
DescTools-0.99.10/DescTools/man/SpreadOut.Rd | 24 -
DescTools-0.99.10/DescTools/man/XLGetRange.Rd | 4
DescTools-0.99.10/DescTools/man/XLView.Rd | 6
DescTools-0.99.10/DescTools/man/ZeroIfNA.Rd | 2
DescTools-0.99.10/DescTools/man/fastPOSIXct.Rd |only
DescTools-0.99.10/DescTools/man/median.factor.Rd | 2
DescTools-0.99.10/DescTools/man/paste.Rd | 9
DescTools-0.99.10/DescTools/src/pan.f |only
DescTools-0.99.10/DescTools/src/tparse.c |only
DescTools-0.99.9/DescTools/man/Kappam.Rd |only
110 files changed, 1029 insertions(+), 572 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-39 dated 2015-02-20 and 7.3-40 dated 2015-03-21
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/lqs.R | 2 +-
tests/Examples/MASS-Ex.Rout.save | 18 +++++++-----------
4 files changed, 17 insertions(+), 21 deletions(-)
Title: Tools for Modeling Data with Functional Programming
Diff between lambda.tools versions 1.0.3 dated 2014-02-08 and 1.0.6 dated 2015-03-21
Description: Provides tools that manipulate and transform data using methods
and techniques consistent with functional programming. The idea is that
through the use of these tools, a program can be reasoned about insomuch
that the implementation can be proven to be equivalent to the mathematical
model.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
lambda.tools-1.0.3/lambda.tools/man/range.for.Rd |only
lambda.tools-1.0.6/lambda.tools/DESCRIPTION | 12 ++--
lambda.tools-1.0.6/lambda.tools/MD5 | 26 ++++-----
lambda.tools-1.0.6/lambda.tools/R/fold.R | 25 +++++---
lambda.tools-1.0.6/lambda.tools/R/lambda.tools-package.R | 4 -
lambda.tools-1.0.6/lambda.tools/R/map.R | 6 +-
lambda.tools-1.0.6/lambda.tools/R/ntry.R |only
lambda.tools-1.0.6/lambda.tools/R/transform.R | 8 +-
lambda.tools-1.0.6/lambda.tools/inst/tests/test_fold.R | 34 +++++++-----
lambda.tools-1.0.6/lambda.tools/inst/tests/test_rangefor.R | 8 +-
lambda.tools-1.0.6/lambda.tools/man/fold.Rd | 10 +--
lambda.tools-1.0.6/lambda.tools/man/foldblock.Rd | 2
lambda.tools-1.0.6/lambda.tools/man/lambda.tools-package.Rd | 4 -
lambda.tools-1.0.6/lambda.tools/man/mapblock.Rd | 2
lambda.tools-1.0.6/lambda.tools/man/ntry.Rd |only
lambda.tools-1.0.6/lambda.tools/man/range_for.Rd |only
16 files changed, 79 insertions(+), 62 deletions(-)
Title: A Logging Utility for R
Diff between futile.logger versions 1.3.7 dated 2014-01-23 and 1.4 dated 2015-03-21
Description: Provides a simple yet powerful logging utility. Based loosely on
log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
futile.logger-1.3.7/futile.logger/inst |only
futile.logger-1.3.7/futile.logger/tests/doRUnit.Rold |only
futile.logger-1.3.7/futile.logger/tests/run_tests.R |only
futile.logger-1.4/futile.logger/DESCRIPTION | 13 +--
futile.logger-1.4/futile.logger/MD5 | 27 +++----
futile.logger-1.4/futile.logger/R/appender.R | 15 +++
futile.logger-1.4/futile.logger/R/futile.logger-package.R | 9 +-
futile.logger-1.4/futile.logger/R/layout.R | 42 +++++++++--
futile.logger-1.4/futile.logger/R/logger.R | 27 +++++--
futile.logger-1.4/futile.logger/README.md |only
futile.logger-1.4/futile.logger/man/flog.appender.Rd | 6 +
futile.logger-1.4/futile.logger/man/flog.layout.Rd | 15 +++
futile.logger-1.4/futile.logger/man/futile.logger-package.Rd | 12 +--
futile.logger-1.4/futile.logger/tests/testthat |only
futile.logger-1.4/futile.logger/tests/testthat.R |only
15 files changed, 127 insertions(+), 39 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.11 dated 2015-03-16 and 0.9.11-1 dated 2015-03-21
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 10 -
MD5 | 24 +-
NEWS | 5
R/BayesFactorPCL-package.R | 2
build/vignette.rds |binary
inst/doc/compare_lme4.html | 72 +++----
inst/doc/manual.html | 261 ++++++++++++++--------------
inst/doc/odds_probs.html | 52 ++---
inst/doc/priors.html | 18 -
man/BayesFactor-package.Rd | 2
src/RcppExports.cpp | 418 +++++++++++++++++++--------------------------
src/jzs_marg_like.cpp | 2
src/logSummaryStats.cpp | 28 +--
13 files changed, 419 insertions(+), 475 deletions(-)
Title: Tools for Interacting with the Brazilian Flora Checklist
Diff between flora versions 0.2.3 dated 2014-07-17 and 0.2.4 dated 2015-03-20
Description: Tools to quickly compile taxonomic and distribution data from
the Brazilian Flora Checklist.
Author: Gustavo Carvalho
Maintainer: Gustavo Carvalho
DESCRIPTION | 14 ++++++------
MD5 | 54 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
NEWS | 7 ++++++
R/get.taxa.R | 17 ++++++--------
R/lower.taxa.R | 2 +
R/occurrence.R | 18 ++++++++++-----
R/remove.authors.R | 2 +
R/standardize.names.R | 2 +
R/suggest.names.R | 2 +
R/sysdata.rda |binary
R/trim.R | 2 +
R/vernacular.R | 2 +
data/plants.rda |binary
inst/plantminer/server.R | 17 ++++++++++----
inst/plantminer/ui.R | 4 +--
man/fixCase.Rd | 3 +-
man/flora.Rd | 3 +-
man/get.taxa.Rd | 9 ++++---
man/lower.taxa.Rd | 5 +++-
man/occurrence.Rd | 5 +++-
man/plants.Rd | 3 +-
man/remove.authors.Rd | 5 +++-
man/standardize.names.Rd | 5 +++-
man/suggest.names.Rd | 5 +++-
man/trim.Rd | 5 +++-
man/vernacular.Rd | 5 +++-
man/web.flora.Rd | 3 +-
28 files changed, 129 insertions(+), 72 deletions(-)
Title: Generalization of the Convex Hull of a Sample of Points in the
Plane
Diff between alphahull versions 1.0 dated 2013-11-28 and 2.0 dated 2015-03-20
Description: Computation of the alpha-shape and alpha-convex
hull of a given sample of points in the plane. The concepts of
alpha-shape and alpha-convex hull generalize the definition of
the convex hull of a finite set of points. The programming is
based on the duality between the Voronoi diagram and Delaunay
triangulation. The package also includes a function that
returns the Delaunay mesh of a given sample of points and its
dual Voronoi diagram in one single object.
Author: Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal.
Maintainer: Beatriz Pateiro-Lopez
DESCRIPTION | 16 +--
MD5 | 28 ++++--
NAMESPACE | 10 +-
R/ahull_track.R |only
R/dw.R |only
R/dw_track.R |only
build/vignette.rds |binary
inst/doc/alphahull.R | 192 ++++++++---------------------------------------
inst/doc/alphahull.pdf |binary
inst/doc/alphahull.rnw | 190 ++++------------------------------------------
man/ahull.Rd | 2
man/ahull_track.Rd |only
man/alphahull-package.Rd | 8 -
man/complement.Rd | 2
man/dw.Rd |only
man/dw_track.Rd |only
vignettes/alphahull.rnw | 190 ++++------------------------------------------
vignettes/biblioJSS.bib | 174 +++++++++++++++++++++---------------------
18 files changed, 202 insertions(+), 610 deletions(-)
Title: Bayesian Emulation, Calibration and Validation of Computer
Models
Diff between SAVE versions 0.9.3.9.2 dated 2014-05-28 and 1.0 dated 2015-03-20
Description: Implements Bayesian statistical methodology for the
analysis of complex computer models.
It allows for the emulation, calibration, and validation of computer models,
following methodology described in Bayarri et al 2007, Technometrics.
Author: Jesus Palomo [aut, cre],
Gonzalo Garcia-Donato [aut],
Rui Paulo [aut],
James Berger [ctb],
Maria Jesus Bayarri [ctb],
Jerome Sacks [ctb]
Maintainer: Jesus Palomo
SAVE-0.9.3.9.2/SAVE/build |only
SAVE-0.9.3.9.2/SAVE/inst/doc |only
SAVE-0.9.3.9.2/SAVE/vignettes |only
SAVE-1.0/SAVE/DESCRIPTION | 12 -
SAVE-1.0/SAVE/MD5 | 48 ++-----
SAVE-1.0/SAVE/NAMESPACE | 7 -
SAVE-1.0/SAVE/data/synthfield.rda |binary
SAVE-1.0/SAVE/data/synthmodel.rda |binary
SAVE-1.0/SAVE/inst/CITATION | 30 ++--
SAVE-1.0/SAVE/inst/extdata/SpotweldExample.r | 93 ++++++++-------
SAVE-1.0/SAVE/inst/extdata/SyntheticExample.r | 160 ++++++++++----------------
SAVE-1.0/SAVE/man/SAVE-package.Rd | 2
SAVE-1.0/SAVE/man/SAVE.Rd | 2
SAVE-1.0/SAVE/man/Spotweld.Rd | 2
SAVE-1.0/SAVE/man/bayesfit.SAVE.Rd | 2
SAVE-1.0/SAVE/man/validate.SAVE.Rd | 2
SAVE-1.0/SAVE/src/Makevars | 2
17 files changed, 166 insertions(+), 196 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Diff between PopED versions 0.1.2 dated 2014-11-19 and 0.2.0 dated 2015-03-20
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix (FIM). This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker
PopED-0.1.2/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only
PopED-0.1.2/PopED/inst/examples/test.csv |only
PopED-0.2.0/PopED/DESCRIPTION | 46
PopED-0.2.0/PopED/MD5 | 414 +++---
PopED-0.2.0/PopED/NEWS | 14
PopED-0.2.0/PopED/R/Doptim.R | 237 +--
PopED-0.2.0/PopED/R/Dtrace.R | 58
PopED-0.2.0/PopED/R/LEDoptim.R | 46
PopED-0.2.0/PopED/R/LinMatrixH.R | 34
PopED-0.2.0/PopED/R/LinMatrixL.R | 2
PopED-0.2.0/PopED/R/LinMatrixLH.R | 30
PopED-0.2.0/PopED/R/LinMatrixL_occ.R | 2
PopED-0.2.0/PopED/R/RS_opt.R | 134 +-
PopED-0.2.0/PopED/R/RS_opt_gen.R | 117 -
PopED-0.2.0/PopED/R/a_line_search.R | 258 ++--
PopED-0.2.0/PopED/R/blockexp.R | 72 -
PopED-0.2.0/PopED/R/blockfinal.R | 44
PopED-0.2.0/PopED/R/blockheader.R | 24
PopED-0.2.0/PopED/R/blockopt.R | 24
PopED-0.2.0/PopED/R/blockother.R | 114 -
PopED-0.2.0/PopED/R/calc_ofv_and_fim.R | 50
PopED-0.2.0/PopED/R/convert_variables.R | 179 +-
PopED-0.2.0/PopED/R/create.poped.database.R | 616 ++++------
PopED-0.2.0/PopED/R/create_design.R | 2
PopED-0.2.0/PopED/R/d2fimdalpha2.R | 10
PopED-0.2.0/PopED/R/dfimdalpha.R | 8
PopED-0.2.0/PopED/R/downsizing_general_design.R | 55
PopED-0.2.0/PopED/R/ed_laplace_ofv.R | 80 -
PopED-0.2.0/PopED/R/ed_mftot.R | 24
PopED-0.2.0/PopED/R/evaluate.e.ofv.fim.R | 34
PopED-0.2.0/PopED/R/evaluate.fim.R | 26
PopED-0.2.0/PopED/R/get_all_params.R | 18
PopED-0.2.0/PopED/R/get_cv.R | 20
PopED-0.2.0/PopED/R/get_fim_size.R | 16
PopED-0.2.0/PopED/R/get_unfixed_params.R | 52
PopED-0.2.0/PopED/R/graddetmfa.R | 32
PopED-0.2.0/PopED/R/graddetmfa_ext.R | 34
PopED-0.2.0/PopED/R/graddetmfxt.R | 30
PopED-0.2.0/PopED/R/graddetmfxt_ext.R | 34
PopED-0.2.0/PopED/R/gradff.R | 48
PopED-0.2.0/PopED/R/gradfg.R | 28
PopED-0.2.0/PopED/R/gradfg_occ.R | 26
PopED-0.2.0/PopED/R/gradlndetmfa.R | 32
PopED-0.2.0/PopED/R/gradlndetmfa_ext.R | 34
PopED-0.2.0/PopED/R/gradlndetmfxt.R | 30
PopED-0.2.0/PopED/R/gradlndetmfxt_ext.R | 34
PopED-0.2.0/PopED/R/gradofv_a.R | 98 -
PopED-0.2.0/PopED/R/gradofv_xt.R | 84 -
PopED-0.2.0/PopED/R/gradtrmfa.R | 30
PopED-0.2.0/PopED/R/gradtrmfxt.R | 28
PopED-0.2.0/PopED/R/hessian_eta_complex.R | 24
PopED-0.2.0/PopED/R/hesskalpha2.R | 8
PopED-0.2.0/PopED/R/ind_estimates.R | 14
PopED-0.2.0/PopED/R/ind_likelihood.R | 46
PopED-0.2.0/PopED/R/m1.R | 154 +-
PopED-0.2.0/PopED/R/m2.R | 54
PopED-0.2.0/PopED/R/m3.R | 224 +--
PopED-0.2.0/PopED/R/mf.R | 112 -
PopED-0.2.0/PopED/R/mf3.R | 37
PopED-0.2.0/PopED/R/mf5.R | 22
PopED-0.2.0/PopED/R/mf6.R | 38
PopED-0.2.0/PopED/R/mf7.R | 22
PopED-0.2.0/PopED/R/mf8.R | 22
PopED-0.2.0/PopED/R/mf_all.R | 20
PopED-0.2.0/PopED/R/mfea.R | 179 +-
PopED-0.2.0/PopED/R/mftot.R | 2
PopED-0.2.0/PopED/R/model_prediction.R | 26
PopED-0.2.0/PopED/R/models.R | 6
PopED-0.2.0/PopED/R/ofv_criterion.R | 4
PopED-0.2.0/PopED/R/ofv_fim.R | 10
PopED-0.2.0/PopED/R/pargen.R | 12
PopED-0.2.0/PopED/R/plot_efficiency_of_windows.R | 58
PopED-0.2.0/PopED/R/plot_model_prediction.R | 15
PopED-0.2.0/PopED/R/poped_optimize.R | 58
PopED-0.2.0/PopED/R/v.R | 40
PopED-0.2.0/PopED/R/write_iterationfile.R | 12
PopED-0.2.0/PopED/inst/examples/HCV_ode.c |only
PopED-0.2.0/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 2
PopED-0.2.0/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.R | 2
PopED-0.2.0/PopED/inst/examples/ex.10.PKPD.HCV.compiled.R |only
PopED-0.2.0/PopED/inst/examples/ex.2.a.warfarin.evaluate.R | 2
PopED-0.2.0/PopED/inst/examples/ex.2.b.warfarin.optimize.R | 2
PopED-0.2.0/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R | 2
PopED-0.2.0/PopED/inst/examples/ex.7.PK.1.comp.maturation.R | 2
PopED-0.2.0/PopED/inst/examples/ex.8.a.tmdd_qss_one_target.R | 2
PopED-0.2.0/PopED/inst/examples/ex.8.b.tmdd_qss_one_target_compiled.R | 2
PopED-0.2.0/PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R | 1
PopED-0.2.0/PopED/inst/shinyapp/server.R | 2
PopED-0.2.0/PopED/man/Doptim.Rd | 30
PopED-0.2.0/PopED/man/Dtrace.Rd | 82 -
PopED-0.2.0/PopED/man/LEDoptim.Rd | 9
PopED-0.2.0/PopED/man/LinMatrixH.Rd | 17
PopED-0.2.0/PopED/man/LinMatrixL.Rd | 15
PopED-0.2.0/PopED/man/LinMatrixLH.Rd | 19
PopED-0.2.0/PopED/man/LinMatrixL_occ.Rd | 15
PopED-0.2.0/PopED/man/PopED-package.Rd | 5
PopED-0.2.0/PopED/man/RS_opt.Rd | 15
PopED-0.2.0/PopED/man/RS_opt_gen.Rd | 22
PopED-0.2.0/PopED/man/a_line_search.Rd | 12
PopED-0.2.0/PopED/man/bfgsb_min.Rd | 26
PopED-0.2.0/PopED/man/blockexp.Rd | 10
PopED-0.2.0/PopED/man/blockfinal.Rd | 46
PopED-0.2.0/PopED/man/blockheader.Rd | 37
PopED-0.2.0/PopED/man/blockopt.Rd | 3
PopED-0.2.0/PopED/man/calc_autofocus.Rd | 5
PopED-0.2.0/PopED/man/calc_ofv_and_fim.Rd | 22
PopED-0.2.0/PopED/man/calc_ofv_and_grad.Rd | 29
PopED-0.2.0/PopED/man/cell.Rd | 3
PopED-0.2.0/PopED/man/convert_variables.Rd | 3
PopED-0.2.0/PopED/man/create.poped.database.Rd | 9
PopED-0.2.0/PopED/man/create_design.Rd | 3
PopED-0.2.0/PopED/man/create_design_space.Rd | 3
PopED-0.2.0/PopED/man/diag_matlab.Rd | 3
PopED-0.2.0/PopED/man/downsizing_general_design.Rd | 13
PopED-0.2.0/PopED/man/ed_laplace_ofv.Rd | 6
PopED-0.2.0/PopED/man/ed_mftot.Rd | 27
PopED-0.2.0/PopED/man/evaluate.e.ofv.fim.Rd | 21
PopED-0.2.0/PopED/man/evaluate.fim.Rd | 3
PopED-0.2.0/PopED/man/feps.add.Rd | 3
PopED-0.2.0/PopED/man/feps.add.prop.Rd | 3
PopED-0.2.0/PopED/man/feps.prop.Rd | 3
PopED-0.2.0/PopED/man/feval.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 3
PopED-0.2.0/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 5
PopED-0.2.0/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 5
PopED-0.2.0/PopED/man/fileparts.Rd | 3
PopED-0.2.0/PopED/man/getTruncatedNormal.Rd | 3
PopED-0.2.0/PopED/man/get_all_params.Rd | 3
PopED-0.2.0/PopED/man/get_rse.Rd | 11
PopED-0.2.0/PopED/man/getfulld.Rd | 3
PopED-0.2.0/PopED/man/gradf_eps.Rd | 17
PopED-0.2.0/PopED/man/isempty.Rd | 3
PopED-0.2.0/PopED/man/isfield.Rd | 3
PopED-0.2.0/PopED/man/log_prior_pdf.Rd | 9
PopED-0.2.0/PopED/man/mf.Rd | 17
PopED-0.2.0/PopED/man/mf3.Rd | 17
PopED-0.2.0/PopED/man/mf5.Rd | 17
PopED-0.2.0/PopED/man/mf6.Rd | 17
PopED-0.2.0/PopED/man/mf7.Rd | 17
PopED-0.2.0/PopED/man/mf8.Rd | 17
PopED-0.2.0/PopED/man/mfea.Rd | 10
PopED-0.2.0/PopED/man/mftot.Rd | 23
PopED-0.2.0/PopED/man/mftot0.Rd | 23
PopED-0.2.0/PopED/man/mftot1.Rd | 23
PopED-0.2.0/PopED/man/mftot2.Rd | 3
PopED-0.2.0/PopED/man/mftot3.Rd | 3
PopED-0.2.0/PopED/man/mftot4.Rd | 23
PopED-0.2.0/PopED/man/mftot5.Rd | 23
PopED-0.2.0/PopED/man/mftot6.Rd | 23
PopED-0.2.0/PopED/man/mftot7.Rd | 23
PopED-0.2.0/PopED/man/model_prediction.Rd | 27
PopED-0.2.0/PopED/man/ofv_criterion.Rd | 5
PopED-0.2.0/PopED/man/ofv_fim.Rd | 7
PopED-0.2.0/PopED/man/ones.Rd | 3
PopED-0.2.0/PopED/man/pargen.Rd | 8
PopED-0.2.0/PopED/man/plot_efficiency_of_windows.Rd | 11
PopED-0.2.0/PopED/man/plot_model_prediction.Rd | 3
PopED-0.2.0/PopED/man/poped.choose.Rd | 3
PopED-0.2.0/PopED/man/poped_optimize.Rd | 28
PopED-0.2.0/PopED/man/rand.Rd | 3
PopED-0.2.0/PopED/man/randn.Rd | 3
PopED-0.2.0/PopED/man/randperm.Rd | 3
PopED-0.2.0/PopED/man/size.Rd | 3
PopED-0.2.0/PopED/man/test_for_max.Rd | 3
PopED-0.2.0/PopED/man/test_for_min.Rd | 3
PopED-0.2.0/PopED/man/test_for_zeros.Rd | 3
PopED-0.2.0/PopED/man/test_mat_size.Rd | 3
PopED-0.2.0/PopED/man/tic.Rd | 3
PopED-0.2.0/PopED/man/toc.Rd | 3
PopED-0.2.0/PopED/man/zeros.Rd | 3
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 266 ++--
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt | 87 -
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 69 -
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 10
PopED-0.2.0/PopED/tests/testthat/Rplots.pdf |binary
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_Doptim.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_Dtrace.R | 70 -
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixH.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL.R | 12
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixLH.R | 16
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL_occ.R | 12
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_bfgsb_min.R | 23
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal.R | 34
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_blockheader.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_grad.R | 26
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_downsizing_general_design.R | 10
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ed_mftot.R | 24
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ff.PKPD.1.comp.oral.md.CL.imax.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ff.PKPD.1.comp.sd.CL.emax.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_gradf_eps.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_log_prior_pdf.R | 6
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf3.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf5.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf6.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf7.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf8.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot0.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot1.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot4.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot5.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot6.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot7.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 2
PopED-0.2.0/PopED/tests/testthat/test_distributions.R | 6
PopED-0.2.0/PopED/tests/testthat/test_examples.R | 8
210 files changed, 3403 insertions(+), 3265 deletions(-)
Title: Normalize NanoString miRNA and mRNA Data
Diff between NanoStringNorm versions 1.1.17 dated 2014-01-17 and 1.1.19 dated 2015-03-20
More information about NanoStringNorm at CRAN
Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
Author: Daryl M. Waggott
Maintainer: Paul Boutros
DESCRIPTION | 14 ++++++-------
MD5 | 24 +++++++++++-----------
R/Plot.NanoStringNorm.gvis.R | 8 +++----
R/norm.comp.R | 8 +++----
R/other.normalization.rank.normal.R | 33 +++++++++++++++++--------------
R/other.normalization.vsn.R | 6 ++---
R/read.markup.RCC.R | 22 +++++++++++++++++---
R/unit.testing.NanoStringNorm.R | 8 +++----
build/vignette.rds |binary
inst/doc/NanoStringNorm_Introduction.pdf |binary
man/Plot.NanoStringNorm.gvis.Rd | 16 +++++++++++++--
man/norm.comp.Rd | 2 -
man/read.markup.RCC.Rd | 4 ++-
13 files changed, 90 insertions(+), 55 deletions(-)
Permanent link
Title: Generalized Hermite Distribution
Diff between hermite versions 1.0.1 dated 2014-12-18 and 1.0.2 dated 2015-03-20
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and MarÃa Oliveira
Maintainer: David Moriña Soler
hermite-1.0.1/hermite/R/mle.hermite.R |only
hermite-1.0.1/hermite/man/mle.hermite.Rd |only
hermite-1.0.2/hermite/DESCRIPTION | 14 +++---
hermite-1.0.2/hermite/MD5 | 28 ++++++------
hermite-1.0.2/hermite/NAMESPACE | 5 ++
hermite-1.0.2/hermite/R/dhermite.R | 54 +++++++++++-------------
hermite-1.0.2/hermite/R/glm.hermite.R |only
hermite-1.0.2/hermite/R/int.hermite.R | 58 +++++++++++++-------------
hermite-1.0.2/hermite/R/rhermite.R | 4 +
hermite-1.0.2/hermite/data |only
hermite-1.0.2/hermite/man/dhermite.Rd | 44 +++++++++++++------
hermite-1.0.2/hermite/man/glm.hermite.Rd |only
hermite-1.0.2/hermite/man/hermite-internal.Rd | 3 -
hermite-1.0.2/hermite/man/hermite-package.Rd | 56 ++++++++++++++++++-------
hermite-1.0.2/hermite/man/hi_let.Rd |only
hermite-1.0.2/hermite/man/phermite.Rd | 46 ++++++++++++++------
hermite-1.0.2/hermite/man/qhermite.Rd | 49 +++++++++++++++------
hermite-1.0.2/hermite/man/rhermite.Rd | 41 ++++++++++++------
18 files changed, 255 insertions(+), 147 deletions(-)
Title: Genealogical Data Analysis
Diff between GENLIB versions 1.0.2 dated 2014-12-04 and 1.0.3 dated 2015-03-20
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon
GENLIB-1.0.2/GENLIB/man/gen.entropy.Rd |only
GENLIB-1.0.2/GENLIB/man/gen.entropyVar.Rd |only
GENLIB-1.0.2/GENLIB/man/gen.grimperPAR.Rd |only
GENLIB-1.0.3/GENLIB/DESCRIPTION | 9
GENLIB-1.0.3/GENLIB/MD5 | 142 +++++++-------
GENLIB-1.0.3/GENLIB/NAMESPACE | 2
GENLIB-1.0.3/GENLIB/R/classes_methodes.R | 6
GENLIB-1.0.3/GENLIB/R/fonctionsBase.R | 246 +++++++++++--------------
GENLIB-1.0.3/GENLIB/R/fonctionsGraph.R | 4
GENLIB-1.0.3/GENLIB/R/fonctionsPAR.R | 10 -
GENLIB-1.0.3/GENLIB/R/fonctionsPriv.R | 19 +
GENLIB-1.0.3/GENLIB/R/fonctionsSimul.R | 10 -
GENLIB-1.0.3/GENLIB/R/fonctionsStat.R | 14 -
GENLIB-1.0.3/GENLIB/man/gen.branching.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.children.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.climbPAR.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.completeness.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.completenessVar.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.depth.Rd | 2
GENLIB-1.0.3/GENLIB/man/gen.f.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.fCI.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.founder.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.gc.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.genealogy.Rd | 8
GENLIB-1.0.3/GENLIB/man/gen.genout.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.getAncestorsPAR.Rd | 2
GENLIB-1.0.3/GENLIB/man/gen.half.founder.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.implex.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.implexVar.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.lineages.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.max.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.mean.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.meangendepth.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.meangendepthVar.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.min.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.nochildren.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.noind.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.nomen.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.nowomen.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.occ.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.parent.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.phi.Rd | 4
GENLIB-1.0.3/GENLIB/man/gen.phiCI.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.phiMean.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.pro.Rd | 9
GENLIB-1.0.3/GENLIB/man/gen.rec.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.sibship.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.simuProb.Rd | 4
GENLIB-1.0.3/GENLIB/man/gen.simuSample.Rd | 8
GENLIB-1.0.3/GENLIB/man/gen.simuSet.Rd | 12 -
GENLIB-1.0.3/GENLIB/src/Makevars | 2
GENLIB-1.0.3/GENLIB/src/apparentement.cpp | 3
GENLIB-1.0.3/GENLIB/src/apparentement.h | 1
GENLIB-1.0.3/GENLIB/src/base.h | 18 +
GENLIB-1.0.3/GENLIB/src/cbignum.h | 1
GENLIB-1.0.3/GENLIB/src/congen.cpp | 1
GENLIB-1.0.3/GENLIB/src/congen.h | 1
GENLIB-1.0.3/GENLIB/src/consanguinite.cpp | 1
GENLIB-1.0.3/GENLIB/src/consanguinite.h | 1
GENLIB-1.0.3/GENLIB/src/fondateur.cpp | 178 ++++++++++++++----
GENLIB-1.0.3/GENLIB/src/fondateur.h | 1
GENLIB-1.0.3/GENLIB/src/genphi.cpp | 2
GENLIB-1.0.3/GENLIB/src/hal.cpp | 3
GENLIB-1.0.3/GENLIB/src/hal.h | 5
GENLIB-1.0.3/GENLIB/src/hashtable.h | 1
GENLIB-1.0.3/GENLIB/src/interface.cpp | 1
GENLIB-1.0.3/GENLIB/src/mpi-types.h | 2
GENLIB-1.0.3/GENLIB/src/mpi.c | 6
GENLIB-1.0.3/GENLIB/src/outils.cpp | 15 +
GENLIB-1.0.3/GENLIB/src/outils.h | 1
GENLIB-1.0.3/GENLIB/src/outilsalloc.h | 1
GENLIB-1.0.3/GENLIB/src/probsimul.cpp | 1
GENLIB-1.0.3/GENLIB/src/probsimul.h | 1
GENLIB-1.0.3/GENLIB/src/userInterface.cpp | 1
GENLIB-1.0.3/GENLIB/src/userInterface.h | 1
75 files changed, 493 insertions(+), 385 deletions(-)
Title: Database Preferences and Skyline Computation
Diff between rPref versions 0.4 dated 2015-01-15 and 0.5 dated 2015-03-20
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks
DESCRIPTION | 13 +-
MD5 | 61 +++++------
NAMESPACE | 10 +
NEWS | 14 +-
R/base-pref.r | 46 +++++++-
R/complex-pref.r | 59 ++++------
R/pred-succ.r | 42 +++++--
R/pref-classes.r | 256 ++++++++++++++++++++++++++++++++---------------
R/pref-eval.r | 29 ++---
R/rPref.r | 5
R/show-pref.r | 79 +++++++++++---
R/visualize.r | 5
inst/test/test-hasse.R | 48 ++++++++
inst/test/test-pref.r |only
inst/test/test-strings.R | 29 ++++-
man/base_pref.Rd | 42 ++++++-
man/base_pref_macros.Rd | 5
man/complex_pref.Rd | 24 +++-
man/get_btg.Rd | 5
man/get_hasse_diag.Rd | 7 -
man/plot_front.Rd | 8 -
man/pred_succ.Rd | 39 ++++---
man/psel.Rd | 34 +++---
man/rPref.Rd | 9 -
man/show.pref.Rd | 49 +++++++-
man/show.query.Rd | 20 ++-
src/Makevars |only
src/Makevars.win |only
src/RcppExports.cpp | 120 +++++++++-------------
src/psel-par-top.cpp | 48 +++++---
src/psel-par.cpp | 21 ++-
src/scalagon.cpp | 37 ++++--
src/scalagon.h | 19 ++-
33 files changed, 792 insertions(+), 391 deletions(-)
Title: Connect MonetDB to R
Diff between MonetDB.R versions 0.9.5 dated 2014-10-06 and 0.9.6 dated 2015-03-20
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Thomas Lumley [ctb], Anthony Damico [ctb]
Maintainer: Hannes Muehleisen
MonetDB.R-0.9.5/MonetDB.R/src/Makevars.win |only
MonetDB.R-0.9.5/MonetDB.R/src/mapi.c |only
MonetDB.R-0.9.6/MonetDB.R/DESCRIPTION | 6
MonetDB.R-0.9.6/MonetDB.R/MD5 | 30 +--
MonetDB.R-0.9.6/MonetDB.R/NAMESPACE | 6
MonetDB.R-0.9.6/MonetDB.R/NEWS | 7
MonetDB.R-0.9.6/MonetDB.R/R/control.R | 16 +
MonetDB.R-0.9.6/MonetDB.R/R/dbi.R | 174 ++++++++++---------
MonetDB.R-0.9.6/MonetDB.R/R/dplyr.R | 25 ++
MonetDB.R-0.9.6/MonetDB.R/R/mapi.R | 124 +++++--------
MonetDB.R-0.9.6/MonetDB.R/man/control.Rd | 3
MonetDB.R-0.9.6/MonetDB.R/man/mc.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/man/monetdb.read.csv.Rd | 3
MonetDB.R-0.9.6/MonetDB.R/man/monetdbRtype.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/man/src_monetdb.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit-r.c |only
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit.c | 195 ++++++----------------
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit.h |only
18 files changed, 267 insertions(+), 328 deletions(-)
Title: Latent Markov Models with and without Covariates
Diff between LMest versions 2.0 dated 2014-11-18 and 2.1 dated 2015-03-20
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT)
Maintainer: Francesco Bartolucci
LMest-2.0/LMest/R/deconding.R |only
LMest-2.0/LMest/data/data_SRHS.rda |only
LMest-2.0/LMest/man/data_SRHS.Rd |only
LMest-2.0/LMest/man/deconding.Rd |only
LMest-2.1/LMest/DESCRIPTION | 12 +--
LMest-2.1/LMest/MD5 | 86 ++++++++++++-------------
LMest-2.1/LMest/NAMESPACE | 15 ++++
LMest-2.1/LMest/R/bootstrap_lm_cov_latent.R | 34 ++++++++-
LMest-2.1/LMest/R/decoding.R |only
LMest-2.1/LMest/R/draw_lm_cov_latent.R | 9 +-
LMest-2.1/LMest/R/draw_lm_mixed.R | 2
LMest-2.1/LMest/R/est_lm_basic.R | 2
LMest-2.1/LMest/R/est_lm_cov_latent.R | 50 ++++++++------
LMest-2.1/LMest/R/est_lm_cov_manifest.R | 69 +++++++++++---------
LMest-2.1/LMest/R/est_lm_mixed.R | 6 -
LMest-2.1/LMest/R/lk_comp_latent.R | 19 +----
LMest-2.1/LMest/R/lk_obs_mixed.R | 2
LMest-2.1/LMest/R/long2matrices.R |only
LMest-2.1/LMest/R/sq.R | 15 +---
LMest-2.1/LMest/R/summary.LMbasic.R | 5 -
LMest-2.1/LMest/data/data_SRHS_long.rda |only
LMest-2.1/LMest/man/LMest-package.Rd | 10 +-
LMest-2.1/LMest/man/bootstrap_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/bootstrap_lm_cov_latent.Rd | 36 ++++------
LMest-2.1/LMest/man/complk.Rd | 10 +-
LMest-2.1/LMest/man/data_SRHS_long.Rd |only
LMest-2.1/LMest/man/decoding.Rd |only
LMest-2.1/LMest/man/draw_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/draw_lm_cov_latent.Rd | 12 +--
LMest-2.1/LMest/man/draw_lm_mixed.Rd | 2
LMest-2.1/LMest/man/est_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/est_lm_cov_latent.Rd | 44 ++++++------
LMest-2.1/LMest/man/est_lm_cov_manifest.Rd | 47 +++++--------
LMest-2.1/LMest/man/est_lm_mixed.Rd | 2
LMest-2.1/LMest/man/est_multilogit.Rd | 2
LMest-2.1/LMest/man/invglob.Rd | 2
LMest-2.1/LMest/man/lk_comp_latent.Rd | 10 +-
LMest-2.1/LMest/man/lk_obs.Rd | 6 -
LMest-2.1/LMest/man/lk_obs_manifest.Rd | 2
LMest-2.1/LMest/man/lk_sta.Rd | 2
LMest-2.1/LMest/man/long2matrices.Rd |only
LMest-2.1/LMest/man/long2wide.Rd | 4 -
LMest-2.1/LMest/man/marg_param.Rd | 2
LMest-2.1/LMest/man/prob_multilogit.Rd | 4 -
LMest-2.1/LMest/man/prob_post_cov.Rd | 6 -
LMest-2.1/LMest/man/prod_array.Rd | 4 -
LMest-2.1/LMest/man/rec1.Rd | 2
LMest-2.1/LMest/man/recursions.Rd | 6 -
LMest-2.1/LMest/man/sq.Rd | 2
49 files changed, 298 insertions(+), 263 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.3 dated 2015-02-22 and 0.2.4 dated 2015-03-20
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 26
MD5 | 189 -
NAMESPACE | 110
NEWS | 13
R/chordDiagram.R | 211 +
R/link.R | 199 +
R/plot.R | 3128 +++++++++++------------
R/utils.R | 704 ++---
R/zzz.R | 6
build/vignette.rds |binary
inst/CITATION | 38
inst/doc/circlize.R | 1532 +++++------
inst/doc/circlize.Rnw | 2835 ++++++++++----------
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.R | 242 -
inst/doc/circular_phylogenetic_tree.Rnw | 348 +-
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.R | 1244 ++++-----
inst/doc/circular_visualization_of_matrix.Rnw | 1727 ++++++------
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.R | 302 +-
inst/doc/draw_ideogram.Rnw | 508 +--
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.R | 2424 ++++++++---------
inst/doc/genomic_plot.Rnw | 3016 +++++++++++-----------
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.R | 200 -
inst/doc/interesting_graphics.Rnw | 356 +-
inst/doc/interesting_graphics.pdf |binary
inst/extdata/chromInfo.txt | 186 -
inst/extdata/cytoBand.txt | 1724 ++++++------
man/adjacencyList2Matrix.rd | 58
man/chordDiagram.rd | 132
man/circlize-package.rd | 132
man/circlize.rd | 68
man/circos.axis.rd | 110
man/circos.clear.rd | 50
man/circos.dendrogram.rd |only
man/circos.genomicDensity.rd | 90
man/circos.genomicInitialize.rd | 86
man/circos.genomicLines.rd | 108
man/circos.genomicLink.rd | 88
man/circos.genomicPoints.rd | 86
man/circos.genomicPosTransformLines.rd | 86
man/circos.genomicRainfall.rd | 82
man/circos.genomicRect.rd | 96
man/circos.genomicText.rd | 104
man/circos.genomicTrackPlotRegion.rd | 96
man/circos.info.rd | 70
man/circos.initialize.rd | 84
man/circos.initializeWithIdeogram.rd | 94
man/circos.lines.rd | 104
man/circos.link.rd | 117
man/circos.par.rd | 94
man/circos.points.rd | 84
man/circos.polygon.rd | 80
man/circos.rect.rd | 84
man/circos.text.rd | 94
man/circos.trackHist.rd | 102
man/circos.trackLines.rd | 96
man/circos.trackPlotRegion.rd | 122
man/circos.trackPoints.rd | 78
man/circos.trackText.rd | 88
man/circos.updatePlotRegion.rd | 74
man/colorRamp2.rd | 76
man/cytoband.col.rd | 62
man/draw.sector.rd | 84
man/generateRandomBed.rd | 70
man/genomicDensity.rd | 76
man/get.all.sector.index.rd | 52
man/get.all.track.index.rd | 46
man/get.cell.meta.data.rd | 116
man/get.current.chromosome.rd | 52
man/getI.rd | 64
man/highlight.chromosome.rd | 62
man/highlight.sector.rd | 86
man/posTransform.default.rd | 68
man/posTransform.text.rd | 76
man/rainfallTransform.rd | 64
man/rand_color.rd | 52
man/read.chromInfo.rd | 84
man/read.cytoband.rd | 96
man/reverse.circlize.rd | 74
man/show.index.rd | 46
vignettes/circlize.Rnw | 2835 ++++++++++----------
vignettes/circular_phylogenetic_tree.Rnw | 348 +-
vignettes/circular_visualization_of_matrix.Rnw | 1727 ++++++------
vignettes/draw_ideogram.Rnw | 508 +--
vignettes/genomic_plot.Rnw | 3016 +++++++++++-----------
vignettes/interesting_graphics.Rnw | 356 +-
vignettes/src/genomic-07-posTransformLinesText.R | 198 -
vignettes/src/intro-00-correspondence.R | 48
vignettes/src/intro-08-linescurve.R | 40
vignettes/src/intro-09-text-niceFacing.R | 338 +-
vignettes/src/intro-12-link.R | 19
vignettes/src/intro-15-heatmap.R | 43
96 files changed, 17723 insertions(+), 17364 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-10 4.0.4
2014-10-05 4.0
2014-08-25 3.72
2014-06-22 3.69
2014-04-07 3.63
2014-03-15 3.62
2014-02-26 3.58
2014-02-25 3.57
2013-11-21 3.55
2013-10-23 3.54
2013-07-11 3.51
2013-07-10 3.50
2013-06-23 3.49
2013-06-03 3.47
2013-01-29 3.44
2013-01-03 3.43
2012-11-26 3.41
2012-10-07 3.40
2012-05-15 3.31
2012-04-11 3.29
2012-04-08 3.28
2012-04-06 3.25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-25 1.6
2014-04-29 1.5
2014-03-26 1.4
2013-04-11 1.3
2013-02-22 1.2
2013-02-11 1.1
2012-02-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-12 0.13.0
2015-02-24 0.9.0
2015-02-23 0.7.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 5.1
2014-08-15 5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-13 0.5.0
Title: Easy to Use Tools for Common Forms of Random Assignment
Diff between randomizr versions 0.2.0 dated 2015-01-30 and 0.2.2 dated 2015-03-20
Description: Generates random assignments for common experimental
designs: simple, complete, blocked, and clustered.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock
DESCRIPTION | 10 ++++++----
MD5 | 13 +++++++++----
R/randomizr.r | 52 +++++++++++++++++++++++++++++++++++++++++++---------
README.md | 29 ++++++++++++++++++++++++++++-
build |only
inst |only
man/complete_ra.Rd | 4 +++-
vignettes |only
8 files changed, 89 insertions(+), 19 deletions(-)
Title: Methods for Patient-Centered Network Meta-Analysis
Diff between pcnetmeta versions 1.3 dated 2015-03-13 and 2.0 dated 2015-03-20
Description: Provides functions to conduct network meta-analysis using arm-based methods for different data types, which include binary and continuous outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin
pcnetmeta-1.3/pcnetmeta/R/create.tab.R |only
pcnetmeta-1.3/pcnetmeta/data/Middleton10.rda |only
pcnetmeta-1.3/pcnetmeta/man/Middleton10.Rd |only
pcnetmeta-1.3/pcnetmeta/man/create.tab.Rd |only
pcnetmeta-2.0/pcnetmeta/DESCRIPTION | 18
pcnetmeta-2.0/pcnetmeta/MD5 | 48 +-
pcnetmeta-2.0/pcnetmeta/NAMESPACE | 5
pcnetmeta-2.0/pcnetmeta/R/ci.plot.R | 68 +-
pcnetmeta-2.0/pcnetmeta/R/model.binary.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.binary.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.binary.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.R | 489 ++++++++++++++-------
pcnetmeta-2.0/pcnetmeta/R/nma.ab.cont.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.followup.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.py.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.networkplot.R | 214 ++++-----
pcnetmeta-2.0/pcnetmeta/data/diabetes.rda |only
pcnetmeta-2.0/pcnetmeta/data/dietaryfat.rda |only
pcnetmeta-2.0/pcnetmeta/data/parkinson.rda |only
pcnetmeta-2.0/pcnetmeta/data/smoke.rda |only
pcnetmeta-2.0/pcnetmeta/man/ci.plot.Rd | 46 -
pcnetmeta-2.0/pcnetmeta/man/diabetes.Rd |only
pcnetmeta-2.0/pcnetmeta/man/dietaryfat.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.Rd | 221 +++------
pcnetmeta-2.0/pcnetmeta/man/nma.ab.cont.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.followup.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.py.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.networkplot.Rd | 88 +--
pcnetmeta-2.0/pcnetmeta/man/parkinson.Rd |only
pcnetmeta-2.0/pcnetmeta/man/pcnetmeta-package.Rd | 29 -
pcnetmeta-2.0/pcnetmeta/man/smoke.Rd |only
40 files changed, 685 insertions(+), 541 deletions(-)
Title: Modeling Data with Functional Programming
Diff between lambda.r versions 1.1.6 dated 2014-01-23 and 1.1.7 dated 2015-03-20
Description: A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/framework.R | 2 +-
man/lambda.r-package.Rd | 17 +++++++++++++----
4 files changed, 21 insertions(+), 12 deletions(-)
Title: Diversity-Dependent Diversification
Diff between DDD versions 2.6 dated 2014-12-18 and 2.7 dated 2015-03-20
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DDD-2.6/DDD/R/dd_KI_loglikold.R |only
DDD-2.7/DDD/DESCRIPTION | 12 ++--
DDD-2.7/DDD/MD5 | 39 +++++++--------
DDD-2.7/DDD/R/bd_ML.R | 4 +
DDD-2.7/DDD/R/dd_KI_ML.R | 7 +-
DDD-2.7/DDD/R/dd_KI_loglik.R | 71 ++++++++++++++-------------
DDD-2.7/DDD/R/dd_ML.R | 6 +-
DDD-2.7/DDD/R/dd_SR_ML.R | 10 ++-
DDD-2.7/DDD/R/dd_SR_loglik.R | 26 +++++-----
DDD-2.7/DDD/R/dd_SR_loglik_choosepar.R | 2
DDD-2.7/DDD/R/dd_loglik.R | 11 +---
DDD-2.7/DDD/R/dd_loglik_rhs.R | 6 +-
DDD-2.7/DDD/R/dd_logliknorm_rhs2.R | 21 --------
DDD-2.7/DDD/R/flavec.R | 13 +++--
DDD-2.7/DDD/man/DDD-package.Rd | 84 +++++++++++++++++----------------
DDD-2.7/DDD/man/bd_ML.Rd | 5 +
DDD-2.7/DDD/man/dd_KI_ML.Rd | 21 ++++----
DDD-2.7/DDD/man/dd_KI_loglik.Rd | 3 -
DDD-2.7/DDD/man/dd_ML.Rd | 15 ++---
DDD-2.7/DDD/man/dd_SR_ML.Rd | 20 ++++---
DDD-2.7/DDD/man/dd_loglik.Rd | 2
21 files changed, 191 insertions(+), 187 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Diff between glmm versions 1.0.1 dated 2015-02-12 and 1.0.2 dated 2015-03-19
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson
glmm-1.0.1/glmm/src/fixelGH.c |only
glmm-1.0.2/glmm/DESCRIPTION | 8 +++++---
glmm-1.0.2/glmm/MD5 | 21 ++++++++++++++-------
glmm-1.0.2/glmm/R/glmm.R | 10 ++++++++--
glmm-1.0.2/glmm/R/summary.mcla.R | 11 +++++++++--
glmm-1.0.2/glmm/build |only
glmm-1.0.2/glmm/inst |only
glmm-1.0.2/glmm/man/glmm.Rd | 2 +-
glmm-1.0.2/glmm/man/summary.glmm.Rd | 1 +
glmm-1.0.2/glmm/tests/basicBHtest.Rout.save | 5 ++++-
glmm-1.0.2/glmm/tests/salamFiniteDiffs.R |only
glmm-1.0.2/glmm/tests/salamFiniteDiffs.Rout.save |only
glmm-1.0.2/glmm/vignettes |only
13 files changed, 42 insertions(+), 16 deletions(-)
Title: Direction Analysis for Pathways and Kinases
Diff between directPA versions 1.0 dated 2013-10-22 and 1.1 dated 2015-03-19
Description: Direction analysis is a set of tools designed to integrate multiple experimental treatments for analyzing pathways and kinases from microarray, RNA-seq, proteomics, or phosphoproteomics data.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang
directPA-1.0/directPA/R/rotate2Sphere.R |only
directPA-1.0/directPA/R/rotate3Sphere.R |only
directPA-1.0/directPA/data/PM.RData |only
directPA-1.0/directPA/data/reactome.RData |only
directPA-1.0/directPA/man/Ins.Rd |only
directPA-1.0/directPA/man/MK.Rd |only
directPA-1.0/directPA/man/Wmn.Rd |only
directPA-1.0/directPA/man/reactome.list.Rd |only
directPA-1.0/directPA/man/rotate2Sphere.Rd |only
directPA-1.0/directPA/man/rotate3Sphere.Rd |only
directPA-1.1/directPA/DESCRIPTION | 14 -
directPA-1.1/directPA/MD5 | 46 +++---
directPA-1.1/directPA/NAMESPACE | 16 +-
directPA-1.1/directPA/R/directEnrichPlot2d.R |only
directPA-1.1/directPA/R/directExplorer2d.R |only
directPA-1.1/directPA/R/directPA.R | 166 ++++++++++++++++-----
directPA-1.1/directPA/R/geneStats.R | 63 +++++---
directPA-1.1/directPA/R/pathwayStats.R | 91 ++++++++---
directPA-1.1/directPA/R/rotate2d.R |only
directPA-1.1/directPA/R/rotate3d.R |only
directPA-1.1/directPA/data/HEK.rda |only
directPA-1.1/directPA/data/PM.rda |only
directPA-1.1/directPA/data/Pathways.rda |only
directPA-1.1/directPA/data/PhosphoSite.rda |only
directPA-1.1/directPA/man/HEK.Rd |only
directPA-1.1/directPA/man/PM.Rd |only
directPA-1.1/directPA/man/Pathways.KEGG.Rd |only
directPA-1.1/directPA/man/Pathways.reactome.Rd |only
directPA-1.1/directPA/man/PhosphoSite.human.Rd |only
directPA-1.1/directPA/man/PhosphoSite.mouse.Rd |only
directPA-1.1/directPA/man/directEnrichPlot2d.Rd |only
directPA-1.1/directPA/man/directExplorer2d.Rd |only
directPA-1.1/directPA/man/directPA-package.Rd | 58 +++----
directPA-1.1/directPA/man/directPA.Rd | 183 ++++++++++++------------
directPA-1.1/directPA/man/geneStats.Rd | 100 ++++---------
directPA-1.1/directPA/man/pathwayStats.Rd | 106 ++++++-------
directPA-1.1/directPA/man/rotate2d.Rd |only
directPA-1.1/directPA/man/rotate3d.Rd |only
38 files changed, 488 insertions(+), 355 deletions(-)
Title: Fast and Versatile Argument Checks
Diff between checkmate versions 1.5.1 dated 2014-12-13 and 1.5.2 dated 2015-03-19
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang
Maintainer: Michel Lang
checkmate-1.5.1/checkmate/src/as_type.c |only
checkmate-1.5.1/checkmate/src/as_type.h |only
checkmate-1.5.1/checkmate/src/bounds.c |only
checkmate-1.5.1/checkmate/src/bounds.h |only
checkmate-1.5.1/checkmate/src/comps.c |only
checkmate-1.5.1/checkmate/src/comps.h |only
checkmate-1.5.1/checkmate/src/qtest.c |only
checkmate-1.5.1/checkmate/src/qtest.h |only
checkmate-1.5.1/checkmate/src/rules.c |only
checkmate-1.5.1/checkmate/src/rules.h |only
checkmate-1.5.2/checkmate/DESCRIPTION | 6
checkmate-1.5.2/checkmate/MD5 | 198 ++--
checkmate-1.5.2/checkmate/NAMESPACE | 2
checkmate-1.5.2/checkmate/NEWS | 10
checkmate-1.5.2/checkmate/R/checkAccess.r | 3
checkmate-1.5.2/checkmate/R/checkArray.r | 3
checkmate-1.5.2/checkmate/R/checkAtomic.r | 3
checkmate-1.5.2/checkmate/R/checkAtomicVector.r | 3
checkmate-1.5.2/checkmate/R/checkCharacter.r | 4
checkmate-1.5.2/checkmate/R/checkClass.r | 15
checkmate-1.5.2/checkmate/R/checkComplex.r | 3
checkmate-1.5.2/checkmate/R/checkCount.r | 3
checkmate-1.5.2/checkmate/R/checkDataFrame.r | 4
checkmate-1.5.2/checkmate/R/checkFactor.r | 40
checkmate-1.5.2/checkmate/R/checkFlag.r | 3
checkmate-1.5.2/checkmate/R/checkInt.r | 3
checkmate-1.5.2/checkmate/R/checkInteger.r | 3
checkmate-1.5.2/checkmate/R/checkIntegerish.r | 3
checkmate-1.5.2/checkmate/R/checkList.r | 4
checkmate-1.5.2/checkmate/R/checkLogical.r | 3
checkmate-1.5.2/checkmate/R/checkMatrix.r | 3
checkmate-1.5.2/checkmate/R/checkNamed.r | 3
checkmate-1.5.2/checkmate/R/checkNames.r | 3
checkmate-1.5.2/checkmate/R/checkNull.r | 2
checkmate-1.5.2/checkmate/R/checkNumber.r | 3
checkmate-1.5.2/checkmate/R/checkNumeric.r | 3
checkmate-1.5.2/checkmate/R/checkPercentage.r | 3
checkmate-1.5.2/checkmate/R/checkScalar.r | 3
checkmate-1.5.2/checkmate/R/checkVector.r | 3
checkmate-1.5.2/checkmate/R/qassert.r | 4
checkmate-1.5.2/checkmate/R/qassertr.r | 1
checkmate-1.5.2/checkmate/man/anyInfinite.Rd | 3
checkmate-1.5.2/checkmate/man/anyMissing.Rd | 3
checkmate-1.5.2/checkmate/man/asInteger.Rd | 3
checkmate-1.5.2/checkmate/man/assert.Rd | 3
checkmate-1.5.2/checkmate/man/checkAccess.Rd | 3
checkmate-1.5.2/checkmate/man/checkArray.Rd | 3
checkmate-1.5.2/checkmate/man/checkAtomic.Rd | 3
checkmate-1.5.2/checkmate/man/checkAtomicVector.Rd | 3
checkmate-1.5.2/checkmate/man/checkCharacter.Rd | 3
checkmate-1.5.2/checkmate/man/checkChoice.Rd | 3
checkmate-1.5.2/checkmate/man/checkClass.Rd | 3
checkmate-1.5.2/checkmate/man/checkComplex.Rd | 3
checkmate-1.5.2/checkmate/man/checkCount.Rd | 3
checkmate-1.5.2/checkmate/man/checkDataFrame.Rd | 3
checkmate-1.5.2/checkmate/man/checkDirectory.Rd | 3
checkmate-1.5.2/checkmate/man/checkEnvironment.Rd | 3
checkmate-1.5.2/checkmate/man/checkFactor.Rd | 24
checkmate-1.5.2/checkmate/man/checkFile.Rd | 3
checkmate-1.5.2/checkmate/man/checkFlag.Rd | 3
checkmate-1.5.2/checkmate/man/checkFunction.Rd | 3
checkmate-1.5.2/checkmate/man/checkInt.Rd | 3
checkmate-1.5.2/checkmate/man/checkInteger.Rd | 3
checkmate-1.5.2/checkmate/man/checkIntegerish.Rd | 3
checkmate-1.5.2/checkmate/man/checkList.Rd | 3
checkmate-1.5.2/checkmate/man/checkLogical.Rd | 3
checkmate-1.5.2/checkmate/man/checkMatrix.Rd | 3
checkmate-1.5.2/checkmate/man/checkNamed.Rd | 3
checkmate-1.5.2/checkmate/man/checkNames.Rd | 3
checkmate-1.5.2/checkmate/man/checkNull.Rd | 3
checkmate-1.5.2/checkmate/man/checkNumber.Rd | 3
checkmate-1.5.2/checkmate/man/checkNumeric.Rd | 3
checkmate-1.5.2/checkmate/man/checkPathForOutput.Rd | 3
checkmate-1.5.2/checkmate/man/checkPercentage.Rd | 3
checkmate-1.5.2/checkmate/man/checkScalar.Rd | 3
checkmate-1.5.2/checkmate/man/checkScalarNA.Rd | 3
checkmate-1.5.2/checkmate/man/checkSetEqual.Rd | 3
checkmate-1.5.2/checkmate/man/checkString.Rd | 3
checkmate-1.5.2/checkmate/man/checkSubset.Rd | 3
checkmate-1.5.2/checkmate/man/checkVector.Rd | 3
checkmate-1.5.2/checkmate/man/checkmate.Rd | 3
checkmate-1.5.2/checkmate/man/qassert.Rd | 5
checkmate-1.5.2/checkmate/man/qassertr.Rd | 3
checkmate-1.5.2/checkmate/src/all_nchar.c | 2
checkmate-1.5.2/checkmate/src/checks.c | 273 +++---
checkmate-1.5.2/checkmate/src/cmessages.c | 34
checkmate-1.5.2/checkmate/src/cmessages.h | 8
checkmate-1.5.2/checkmate/src/helper.c | 41
checkmate-1.5.2/checkmate/src/helper.h | 4
checkmate-1.5.2/checkmate/src/qassert.c | 415 +++++++++-
checkmate-1.5.2/checkmate/src/qassert.h | 1
checkmate-1.5.2/checkmate/tests/testthat/test_anyMissing.r | 50 -
checkmate-1.5.2/checkmate/tests/testthat/test_checkCharacter.r | 6
checkmate-1.5.2/checkmate/tests/testthat/test_checkClass.r | 8
checkmate-1.5.2/checkmate/tests/testthat/test_checkDataFrame.r | 2
checkmate-1.5.2/checkmate/tests/testthat/test_checkFactor.r | 12
checkmate-1.5.2/checkmate/tests/testthat/test_checkInteger.r | 4
checkmate-1.5.2/checkmate/tests/testthat/test_checkIntegerish.r | 3
checkmate-1.5.2/checkmate/tests/testthat/test_checkMatrix.r | 35
checkmate-1.5.2/checkmate/tests/testthat/test_checkNames.r | 5
checkmate-1.5.2/checkmate/tests/testthat/test_checkNumeric.r | 9
checkmate-1.5.2/checkmate/tests/testthat/test_checkVector.r | 18
checkmate-1.5.2/checkmate/tests/testthat/test_guessType.r |only
checkmate-1.5.2/checkmate/tests/testthat/test_qtest.r | 8
checkmate-1.5.2/checkmate/tests/testthat/test_qtestr.r | 5
checkmate-1.5.2/checkmate/tests/testthat/test_wfwl.r |only
106 files changed, 1066 insertions(+), 373 deletions(-)
Title: A Computational Tool for Astrochronology
Diff between astrochron versions 0.4.1 dated 2015-03-17 and 0.4.2 dated 2015-03-19
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers
astrochron-0.4.1/astrochron/R/FUNCTION-integratePower_v7.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-xplot_v3.R |only
astrochron-0.4.2/astrochron/DESCRIPTION | 8 ++---
astrochron-0.4.2/astrochron/MD5 | 20 ++++++-------
astrochron-0.4.2/astrochron/R/FUNCTION-integratePower_v8.R |only
astrochron-0.4.2/astrochron/R/FUNCTION-xplot_v4.R |only
astrochron-0.4.2/astrochron/data/modelA.rda |binary
astrochron-0.4.2/astrochron/man/ar1etp.Rd | 2 -
astrochron-0.4.2/astrochron/man/astrochron-package.Rd | 4 +-
astrochron-0.4.2/astrochron/man/cb.Rd | 2 -
astrochron-0.4.2/astrochron/man/integratePower.Rd | 3 -
astrochron-0.4.2/astrochron/man/stepHeat.Rd | 4 +-
astrochron-0.4.2/astrochron/man/surrogates.Rd | 4 +-
13 files changed, 24 insertions(+), 23 deletions(-)
Title: Simulation of Ecological (and Other) Dynamic Systems
Diff between simecol versions 0.8-4 dated 2013-09-26 and 0.8-6 dated 2015-03-19
Description: An object oriented framework to simulate
ecological (and other) dynamic systems. It can be used for
differential equations, individual-based (or agent-based) and other
models as well. The package helps to organize scenarios (to avoid copy
and paste) and aims to improve readability and usability of code.
Author: Thomas Petzoldt
Maintainer: Thomas Petzoldt
simecol-0.8-4/simecol/inst/doc/index.html |only
simecol-0.8-4/simecol/vignettes/index.html |only
simecol-0.8-6/simecol/DESCRIPTION | 21
simecol-0.8-6/simecol/MD5 | 50
simecol-0.8-6/simecol/R/approxTime1.R | 66
simecol-0.8-6/simecol/R/sEdit.R | 34
simecol-0.8-6/simecol/build/vignette.rds |binary
simecol-0.8-6/simecol/data/CA.rda |binary
simecol-0.8-6/simecol/data/chemostat.rda |binary
simecol-0.8-6/simecol/data/conway.rda |binary
simecol-0.8-6/simecol/data/diffusion.rda |binary
simecol-0.8-6/simecol/data/lv.rda |binary
simecol-0.8-6/simecol/data/lv3.rda |binary
simecol-0.8-6/simecol/data/upca.rda |binary
simecol-0.8-6/simecol/inst/NEWS | 9
simecol-0.8-6/simecol/inst/doc/a-simecol-introduction.R | 621 +++----
simecol-0.8-6/simecol/inst/doc/a-simecol-introduction.Rnw | 8
simecol-0.8-6/simecol/inst/doc/a-simecol-introduction.pdf |binary
simecol-0.8-6/simecol/inst/doc/b-simecol-howtos.R | 986 ++++++------
simecol-0.8-6/simecol/inst/doc/b-simecol-howtos.pdf |binary
simecol-0.8-6/simecol/inst/doc/examples/competition.R |only
simecol-0.8-6/simecol/inst/doc/examples/diffusion_barrier.R |only
simecol-0.8-6/simecol/man/conway.Rd | 1
simecol-0.8-6/simecol/man/fixParms.Rd | 1
simecol-0.8-6/simecol/man/sEdit.Rd | 3
simecol-0.8-6/simecol/man/simecol-package.Rd | 23
simecol-0.8-6/simecol/vignettes/a-simecol-introduction.Rnw | 8
simecol-0.8-6/simecol/vignettes/simecol.bib | 1
28 files changed, 924 insertions(+), 908 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Diff between rdrobust versions 0.70 dated 2014-10-26 and 0.80 dated 2015-03-19
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform bandwidth selection for the different procedures implemented, and rdplot to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico
Maintainer: Sebastian Calonico
DESCRIPTION | 26 ++++++---------------
MD5 | 28 +++++++++++-----------
NAMESPACE | 9 +++++++
R/functions.R | 14 +++++++----
R/rdbinselect.R | 26 ++++++++++-----------
R/rdbwselect.R | 46 +++++++++++++++++++------------------
R/rdplot.R | 45 +++++++++++++++++++-----------------
R/rdrobust.R | 58 ++++++++++++++++++++++++-----------------------
man/rdbinselect.Rd | 35 +++++++++-------------------
man/rdbwselect.Rd | 31 +++++++++----------------
man/rdplot.Rd | 29 +++++++++--------------
man/rdrobust-internal.Rd | 6 ++--
man/rdrobust-package.Rd | 6 ++--
man/rdrobust.Rd | 31 +++++++++----------------
man/rdrobust_RDsenate.Rd | 6 ++--
15 files changed, 188 insertions(+), 208 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 3.2 dated 2015-02-25 and 3.3 dated 2015-03-19
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing
lessR-3.2/lessR/R/reg.explain.R |only
lessR-3.2/lessR/R/reg.z1Basic.R |only
lessR-3.2/lessR/R/reg.z3Residual.R |only
lessR-3.3/lessR/DESCRIPTION | 10
lessR-3.3/lessR/MD5 | 113 -
lessR-3.3/lessR/NAMESPACE | 6
lessR-3.3/lessR/NEWS | 67 -
lessR-3.3/lessR/R/ANOVAz1.R | 10
lessR-3.3/lessR/R/ANOVAz2.R | 5
lessR-3.3/lessR/R/BarChart.R | 1
lessR-3.3/lessR/R/Help.R | 2077 +++++++++++++++----------------
lessR-3.3/lessR/R/Histogram.R | 23
lessR-3.3/lessR/R/Logit.R | 10
lessR-3.3/lessR/R/Nest.R | 3
lessR-3.3/lessR/R/Read.R | 36
lessR-3.3/lessR/R/Regression.R | 285 +++-
lessR-3.3/lessR/R/ScatterPlot.R | 8
lessR-3.3/lessR/R/Sort.R | 2
lessR-3.3/lessR/R/Subset.R | 2
lessR-3.3/lessR/R/SummaryStats.R | 118 +
lessR-3.3/lessR/R/bc.zmain.R | 10
lessR-3.3/lessR/R/corScree.R | 13
lessR-3.3/lessR/R/cr.data.frame.R | 20
lessR-3.3/lessR/R/details.R | 6
lessR-3.3/lessR/R/dn.zmain.R | 4
lessR-3.3/lessR/R/dp.zmain.R | 12
lessR-3.3/lessR/R/hst.zmain.R | 45
lessR-3.3/lessR/R/logit.z4Pred.R | 12
lessR-3.3/lessR/R/pc.zmain.R | 2
lessR-3.3/lessR/R/plt.zmain.R | 16
lessR-3.3/lessR/R/print.outall.r |only
lessR-3.3/lessR/R/print.outpiece.r |only
lessR-3.3/lessR/R/reg.z1anvBasic.R |only
lessR-3.3/lessR/R/reg.z1bckBasic.R |only
lessR-3.3/lessR/R/reg.z1fitBasic.R |only
lessR-3.3/lessR/R/reg.z1modelBasic.R |only
lessR-3.3/lessR/R/reg.z2Relations.R | 212 +--
lessR-3.3/lessR/R/reg.z3dnResidual.R |only
lessR-3.3/lessR/R/reg.z3resfitResidual.R |only
lessR-3.3/lessR/R/reg.z3txtResidual.R |only
lessR-3.3/lessR/R/reg.z4Pred.R | 90 -
lessR-3.3/lessR/R/reg.z5Plot.R | 67 -
lessR-3.3/lessR/R/reg.zknitr.R |only
lessR-3.3/lessR/R/regPlot.R |only
lessR-3.3/lessR/R/ss.zfactor.R | 200 ++
lessR-3.3/lessR/R/ss.znumeric.R | 159 +-
lessR-3.3/lessR/R/tt.z1graph.R | 2
lessR-3.3/lessR/R/tt.z1group.R | 9
lessR-3.3/lessR/R/tt.z2group.R | 9
lessR-3.3/lessR/R/ttest.R | 21
lessR-3.3/lessR/R/zzz.R | 251 +++
lessR-3.3/lessR/man/BoxPlot.Rd | 2
lessR-3.3/lessR/man/Histogram.Rd | 33
lessR-3.3/lessR/man/LineChart.Rd | 2
lessR-3.3/lessR/man/Logit.Rd | 2
lessR-3.3/lessR/man/Recode.Rd | 27
lessR-3.3/lessR/man/Regression.Rd | 165 +-
lessR-3.3/lessR/man/ScatterPlot.Rd | 2
lessR-3.3/lessR/man/SummaryStats.Rd | 22
lessR-3.3/lessR/man/Transform.Rd | 32
lessR-3.3/lessR/man/corCFA.Rd | 2
lessR-3.3/lessR/man/corProp.Rd | 2
lessR-3.3/lessR/man/print_outall.Rd |only
lessR-3.3/lessR/man/print_outpiece.Rd |only
lessR-3.3/lessR/man/regPlot.Rd |only
lessR-3.3/lessR/man/set.Rd | 2
66 files changed, 2549 insertions(+), 1680 deletions(-)
More information about james.analysis at CRAN
Permanent link
Title: Visualizing and Analyzing Animal Track Data
Diff between move versions 1.2.475 dated 2014-04-25 and 1.4.496 dated 2015-03-19
Description: Contains functions to access movement data stored in movebank.org as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Author: Bart Kranstauber
Maintainer: Bart Kranstauber
move-1.2.475/move/inst/unitTests/report.html |only
move-1.2.475/move/inst/unitTests/report.txt |only
move-1.2.475/move/inst/unitTests/reportSummary.txt |only
move-1.2.475/move/inst/unitTests/runit.seglength.R |only
move-1.4.496/move/ChangeLog | 67 ++
move-1.4.496/move/DESCRIPTION | 12
move-1.4.496/move/MD5 | 98 +--
move-1.4.496/move/NAMESPACE | 3
move-1.4.496/move/R/AAClass.R | 4
move-1.4.496/move/R/Summary.R | 2
move-1.4.496/move/R/WebImport.R | 30 -
move-1.4.496/move/R/angle.R | 6
move-1.4.496/move/R/brownianbridgedyn.R | 335 ++++++------
move-1.4.496/move/R/brownianmotionvariancedyn.R | 9
move-1.4.496/move/R/contour.R | 2
move-1.4.496/move/R/corridor.R | 14
move-1.4.496/move/R/dBGB.R | 6
move-1.4.496/move/R/hrBootstrap.R | 66 +-
move-1.4.496/move/R/interpolateTime.R | 4
move-1.4.496/move/R/move.R | 31 -
move-1.4.496/move/R/move2ade.R | 2
move-1.4.496/move/R/moveStack.R | 2
move-1.4.496/move/R/nindiv.R |only
move-1.4.496/move/R/sensor.R |only
move-1.4.496/move/R/speed.R | 2
move-1.4.496/move/R/split.R | 7
move-1.4.496/move/R/time.R | 2
move-1.4.496/move/R/timelag.R | 47 +
move-1.4.496/move/R/timestamps.R | 6
move-1.4.496/move/R/trackId.R | 5
move-1.4.496/move/build/vignette.rds |binary
move-1.4.496/move/inst/doc/browseMovebank.pdf |binary
move-1.4.496/move/inst/doc/move.R | 2
move-1.4.496/move/inst/doc/move.Rnw | 4
move-1.4.496/move/inst/doc/move.pdf |binary
move-1.4.496/move/inst/extdata/createsRDataFile.R | 2
move-1.4.496/move/inst/extdata/move.RData |binary
move-1.4.496/move/inst/unitTests/runit.interpolateTime.R | 3
move-1.4.496/move/inst/unitTests/runit.measures.R | 8
move-1.4.496/move/inst/unitTests/runit.move.R | 88 +--
move-1.4.496/move/inst/unitTests/runit.spTransform.R | 2
move-1.4.496/move/man/brownian.bridge.dyn.Rd | 2
move-1.4.496/move/man/move-package.Rd | 2
move-1.4.496/move/man/n.indiv.Rd |only
move-1.4.496/move/man/searchMovebankStudies.Rd | 2
move-1.4.496/move/man/sensor.Rd |only
move-1.4.496/move/man/split.Rd | 1
move-1.4.496/move/man/time.Rd | 6
move-1.4.496/move/man/time.lag.Rd | 13
move-1.4.496/move/man/timeLag.Rd |only
move-1.4.496/move/man/timestamps.Rd | 3
move-1.4.496/move/man/trackId.Rd | 1
move-1.4.496/move/tests/testthat/test.brownian.bridge.dyn.R | 148 +++--
move-1.4.496/move/tests/testthat/test.seglength.R |only
move-1.4.496/move/vignettes/move.Rnw | 4
55 files changed, 634 insertions(+), 419 deletions(-)
Title: Create Diagrams and Flowcharts Using R
Diff between DiagrammeR versions 0.4 dated 2015-01-30 and 0.5 dated 2015-03-19
Description: With the DiagrammeR package, you can create diagrams and flowcharts using R.
Markdown-like text is used to describe a diagram and, by doing this in R, we can also
add some R code into the mix and integrate these diagrams in the R console, through R
Markdown, and in shiny apps.
Author: knsv [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone
DiagrammeR-0.4/DiagrammeR/inst/DiagrammeR.png |only
DiagrammeR-0.4/DiagrammeR/inst/DiagrammeR_flow_diagram.png |only
DiagrammeR-0.4/DiagrammeR/inst/DiagrammeR_video_link.png |only
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DiagrammeR-0.4/DiagrammeR/inst/htmlwidgets/lib/mermaid/README.md |only
DiagrammeR-0.5/DiagrammeR/DESCRIPTION | 16
DiagrammeR-0.5/DiagrammeR/MD5 | 60 --
DiagrammeR-0.5/DiagrammeR/NAMESPACE | 5
DiagrammeR-0.5/DiagrammeR/R/grViz.R | 91 +--
DiagrammeR-0.5/DiagrammeR/R/graphviz_export.R |only
DiagrammeR-0.5/DiagrammeR/R/graphviz_nodes_edges_df.R |only
DiagrammeR-0.5/DiagrammeR/R/graphviz_single_df.R |only
DiagrammeR-0.5/DiagrammeR/R/mermaid.R | 4
DiagrammeR-0.5/DiagrammeR/R/spectools.R | 109 ++-
DiagrammeR-0.5/DiagrammeR/R/x11_hex.R |only
DiagrammeR-0.5/DiagrammeR/README.md | 300 +++++++---
DiagrammeR-0.5/DiagrammeR/inst/doc/DiagrammeR.html | 36 -
DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/DiagrammeR.js | 144 ++--
DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/DiagrammeR.yaml | 5
DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/grViz.js | 16
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DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.css |only
DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 24
DiagrammeR-0.5/DiagrammeR/inst/htmlwidgets/lib/styles/styles.css | 4
DiagrammeR-0.5/DiagrammeR/man/exportSVG.Rd |only
DiagrammeR-0.5/DiagrammeR/man/grViz.Rd | 22
DiagrammeR-0.5/DiagrammeR/man/graphviz_nodes_edges_df.Rd |only
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DiagrammeR-0.5/DiagrammeR/man/x11_hex.Rd |only
47 files changed, 512 insertions(+), 324 deletions(-)
Title: BiCluster Algorithms
Diff between biclust versions 1.0.2 dated 2013-03-10 and 1.1.0 dated 2015-03-19
Description: The main function biclust provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church,
Spectral, Plaid Model, Xmotifs and Bimax. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova,
Martin Sill, Roberto Theron, Luis Quintales, Friedrich
Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser
DESCRIPTION | 23 +++---
MD5 | 46 ++++++-------
NAMESPACE | 5 -
R/bicluster.r | 7 +-
R/clustmember.r | 2
R/drawHeatmap2.r | 5 -
R/jaccard.r | 142 ++++++++++++++++++++++++-------------------
R/plaid.r | 55 +++++++++-------
data/BicatYeast.rda |binary
data/EisenYeast.rda |binary
data/SyntrenEcoli.rda |binary
man/BCPlaid.Rd | 6 -
man/BCQuest.rd | 3
man/BCXmotifs.rd | 2
man/bubbleplot.Rd | 3
man/clustmember.rd | 8 +-
man/diagnoseColRow.Rd | 3
man/diagnosticPlot.Rd | 3
man/ensemble.Rd | 3
man/jaccard.rd | 3
man/parallelCoordinates.Rd | 3
man/plaid.grid.Rd | 6 +
man/writeBiclusterResults.Rd | 6 +
src/rbimax.c | 14 +++-
24 files changed, 204 insertions(+), 144 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Diff between pcalg versions 2.0-3 dated 2014-07-01 and 2.0-10 dated 2015-03-19
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm and the generalized
backdoor criterion is implemented.
Author: Diego Colombo, Alain Hauser, Markus Kalisch, Martin Maechler
Maintainer: Markus Kalisch
DESCRIPTION | 24
MD5 | 70 -
NAMESPACE | 19
R/Aaux.R | 2
R/AllClasses.R | 6
R/pcalg.R | 2166 ++++++++++++++++++++++++++--------------
TODO | 3
build/vignette.rds |binary
data/gmB.rda |binary
data/gmD.rda |binary
data/gmG.rda |binary
data/gmI.rda |binary
data/gmInt.rda |binary
data/gmL.rda |binary
man/EssGraph-class.Rd | 2
man/GaussL0penIntScore-class.Rd | 2
man/GaussL0penObsScore-class.Rd | 2
man/GaussParDAG-class.Rd | 2
man/ParDAG-class.Rd | 2
man/Score-class.Rd | 2
man/condIndFisherZ.Rd | 9
man/dag2essgraph.Rd | 2
man/fciPlus.Rd |only
man/gds.Rd | 2
man/ges.Rd | 2
man/gies.Rd | 2
man/jointIda.Rd |only
man/mat2targets.Rd | 2
man/r.gauss.pardag.Rd | 2
man/rmvnorm.ivent.Rd | 2
man/simy.Rd | 2
man/udag2pag.Rd | 4
man/udag2pdag.Rd | 7
src/Makevars.win | 12
src/greedy.cpp | 16
tests/test_dag2cpdag.R | 50
tests/test_fciPlus.R |only
tests/test_jointIda.R |only
38 files changed, 1590 insertions(+), 826 deletions(-)
Title: Mann-Kendall Test, Seasonal and Regional Kendall Tests
Diff between rkt versions 1.3 dated 2014-01-22 and 1.4 dated 2015-03-19
Description: Contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.
Author: Aldo Marchetto
Maintainer: Aldo Marchetto
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NAMESPACE | 1 +
R/rkt.R | 34 +++++++++++++++++++++++++++++-----
man/print.rkt.Rd | 3 ++-
man/rkt-package.Rd | 16 +++++++++++-----
man/rkt.Rd | 16 +++++++++++-----
7 files changed, 65 insertions(+), 27 deletions(-)
Title: Cluster Distances Through Trees
Diff between treeClust versions 0.2-2 dated 2015-02-20 and 1.0-0 dated 2015-03-19
Description: Create a measure of inter-point dissimilarity useful
for clustering mixed data, and, optionally, perform the clustering.
Author: Sam Buttrey
Maintainer: Sam Buttrey
DESCRIPTION | 8 ++++----
MD5 | 18 ++++++++++++------
NAMESPACE | 6 ++++--
R/plot.treeClust.R |only
R/summary.treeClust.R |only
R/tcdist.R | 9 ++++++---
R/tcnewdata.R |only
R/treeClust.R | 40 ++++++++++++++++++++--------------------
man/plot.treeClust.Rd |only
man/summary.treeClust.Rd |only
man/tcdist.Rd | 5 ++++-
man/tcnewdata.Rd |only
man/treeClust.Rd | 3 ++-
13 files changed, 52 insertions(+), 37 deletions(-)
Title: Data Analysis Using Rough Set and Fuzzy Rough Set Theories
Diff between RoughSets versions 1.1-0 dated 2014-06-19 and 1.2-0 dated 2015-03-19
Description: Implementations of algorithms for data analysis
based on the rough set theory (RST) and the fuzzy rough set theory (FRST). We
not only provide implementations for the basic concepts of RST and FRST but also
popular algorithms that derive from those theories. The methods included in the
package can be divided into several categories based on their functionality:
discretization, feature selection, instance selection, rule induction and classification
based on nearest neighbors. RST was introduced by Zdzisław Pawlak in 1982
as a sophisticated mathematical tool based on indiscernibility relations to
model and process imprecise or incomplete information. It works on
symbolic-valued datasets for tackling the data analysis problems. By using
the indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST. The
FRST combines concepts of vagueness and indiscernibility that are expressed
with fuzzy sets (as proposed by Zadeh, in 1965) and RST.
Author: Lala Septem Riza [aut],
Andrzej Janusz [aut],
Dominik Ślęzak [ctb],
Chris Cornelis [ctb],
Francisco Herrera [ctb],
Jose Manuel Benitez [ctb],
Christoph Bergmeir [ctb, cre],
Sebastian Stawicki [ctb]
Maintainer: Christoph Bergmeir
RoughSets-1.1-0/RoughSets/man/X.bestFirst.Rd |only
RoughSets-1.1-0/RoughSets/man/X.nOfConflictsLog.Rd |only
RoughSets-1.1-0/RoughSets/man/X.nOfConflictsSqrt.Rd |only
RoughSets-1.2-0/RoughSets/DESCRIPTION | 56
RoughSets-1.2-0/RoughSets/MD5 | 164 -
RoughSets-1.2-0/RoughSets/NAMESPACE | 16
RoughSets-1.2-0/RoughSets/R/BasicFuzzyRoughSets.R | 26
RoughSets-1.2-0/RoughSets/R/BasicRoughSets.OtherFuncCollections.R | 33
RoughSets-1.2-0/RoughSets/R/BasicRoughSets.R | 309 +-
RoughSets-1.2-0/RoughSets/R/Discretization.R | 363 +--
RoughSets-1.2-0/RoughSets/R/FeatureSelection.OtherFuncCollections.R | 123 -
RoughSets-1.2-0/RoughSets/R/FeatureSelection.R | 973 ++++++--
RoughSets-1.2-0/RoughSets/R/IOFunctions.R | 300 ++
RoughSets-1.2-0/RoughSets/R/InstanceSelection.OtherFuncCollections.R | 2
RoughSets-1.2-0/RoughSets/R/InstanceSelection.R | 14
RoughSets-1.2-0/RoughSets/R/MissingValue.R | 6
RoughSets-1.2-0/RoughSets/R/NearestNeigbour.OtherFuncCollections.R | 4
RoughSets-1.2-0/RoughSets/R/NearestNeigbour.R | 3
RoughSets-1.2-0/RoughSets/R/RcppExports.R |only
RoughSets-1.2-0/RoughSets/R/RoughSets-package.R | 1083 +++++-----
RoughSets-1.2-0/RoughSets/R/RuleInduction.OtherFuncCollections.R | 305 ++
RoughSets-1.2-0/RoughSets/R/RuleInduction.R | 588 ++++-
RoughSets-1.2-0/RoughSets/demo/BasicConcept.RST.R | 5
RoughSets-1.2-0/RoughSets/demo/GettingStarted.A.R | 6
RoughSets-1.2-0/RoughSets/man/A.Introduction-RoughSets.Rd | 188 -
RoughSets-1.2-0/RoughSets/man/B.Introduction-FuzzyRoughSets.Rd | 225 --
RoughSets-1.2-0/RoughSets/man/BC.IND.relation.FRST.Rd | 388 +--
RoughSets-1.2-0/RoughSets/man/BC.IND.relation.RST.Rd | 93
RoughSets-1.2-0/RoughSets/man/BC.LU.approximation.FRST.Rd | 521 +---
RoughSets-1.2-0/RoughSets/man/BC.LU.approximation.RST.Rd | 92
RoughSets-1.2-0/RoughSets/man/BC.discernibility.mat.FRST.Rd | 334 +--
RoughSets-1.2-0/RoughSets/man/BC.discernibility.mat.RST.Rd | 83
RoughSets-1.2-0/RoughSets/man/BC.positive.reg.FRST.Rd | 58
RoughSets-1.2-0/RoughSets/man/BC.positive.reg.RST.Rd | 84
RoughSets-1.2-0/RoughSets/man/C.FRNN.FRST.Rd | 136 -
RoughSets-1.2-0/RoughSets/man/C.FRNN.O.FRST.Rd | 62
RoughSets-1.2-0/RoughSets/man/C.POSNN.FRST.Rd | 53
RoughSets-1.2-0/RoughSets/man/D.discretization.RST.Rd | 109 -
RoughSets-1.2-0/RoughSets/man/D.discretize.equal.intervals.RST.Rd | 91
RoughSets-1.2-0/RoughSets/man/D.discretize.quantiles.RST.Rd | 85
RoughSets-1.2-0/RoughSets/man/D.global.discernibility.heuristic.RST.Rd | 125 -
RoughSets-1.2-0/RoughSets/man/D.local.discernibility.matrix.RST.Rd | 100
RoughSets-1.2-0/RoughSets/man/D.max.discernibility.matrix.RST.Rd | 92
RoughSets-1.2-0/RoughSets/man/FS.DAAR.heuristic.RST.Rd |only
RoughSets-1.2-0/RoughSets/man/FS.all.reducts.computation.Rd | 35
RoughSets-1.2-0/RoughSets/man/FS.feature.subset.computation.Rd | 55
RoughSets-1.2-0/RoughSets/man/FS.greedy.heuristic.reduct.RST.Rd | 150 -
RoughSets-1.2-0/RoughSets/man/FS.greedy.heuristic.superreduct.RST.Rd | 79
RoughSets-1.2-0/RoughSets/man/FS.nearOpt.fvprs.FRST.Rd | 73
RoughSets-1.2-0/RoughSets/man/FS.one.reduct.computation.Rd | 30
RoughSets-1.2-0/RoughSets/man/FS.permutation.heuristic.reduct.RST.Rd | 92
RoughSets-1.2-0/RoughSets/man/FS.quickreduct.FRST.Rd | 381 +--
RoughSets-1.2-0/RoughSets/man/FS.quickreduct.RST.Rd | 81
RoughSets-1.2-0/RoughSets/man/FS.reduct.computation.Rd | 76
RoughSets-1.2-0/RoughSets/man/IS.FRIS.FRST.Rd | 111 -
RoughSets-1.2-0/RoughSets/man/IS.FRPS.FRST.Rd | 95
RoughSets-1.2-0/RoughSets/man/MV.conceptClosestFit.Rd | 35
RoughSets-1.2-0/RoughSets/man/MV.deletionCases.Rd | 29
RoughSets-1.2-0/RoughSets/man/MV.globalClosestFit.Rd | 43
RoughSets-1.2-0/RoughSets/man/MV.missingValueCompletion.Rd | 53
RoughSets-1.2-0/RoughSets/man/MV.mostCommonVal.Rd | 28
RoughSets-1.2-0/RoughSets/man/MV.mostCommonValResConcept.Rd | 30
RoughSets-1.2-0/RoughSets/man/RI.AQRules.RST.Rd |only
RoughSets-1.2-0/RoughSets/man/RI.CN2Rules.RST.Rd |only
RoughSets-1.2-0/RoughSets/man/RI.GFRS.FRST.Rd | 137 -
RoughSets-1.2-0/RoughSets/man/RI.LEM2Rules.RST.Rd |only
RoughSets-1.2-0/RoughSets/man/RI.hybridFS.FRST.Rd | 75
RoughSets-1.2-0/RoughSets/man/RI.indiscernibilityBasedRules.RST.Rd | 91
RoughSets-1.2-0/RoughSets/man/RoughSetData.Rd | 216 -
RoughSets-1.2-0/RoughSets/man/RoughSets-package.Rd | 666 ++----
RoughSets-1.2-0/RoughSets/man/SF.applyDecTable.Rd | 47
RoughSets-1.2-0/RoughSets/man/SF.asDecisionTable.Rd | 109 -
RoughSets-1.2-0/RoughSets/man/SF.asFeatureSubset.Rd |only
RoughSets-1.2-0/RoughSets/man/SF.read.DecisionTable.Rd | 44
RoughSets-1.2-0/RoughSets/man/X.entropy.Rd | 23
RoughSets-1.2-0/RoughSets/man/X.gini.Rd | 26
RoughSets-1.2-0/RoughSets/man/X.laplace.Rd |only
RoughSets-1.2-0/RoughSets/man/X.nOfConflicts.Rd | 18
RoughSets-1.2-0/RoughSets/man/X.ruleStrength.Rd |only
RoughSets-1.2-0/RoughSets/man/X.rulesCounting.Rd |only
RoughSets-1.2-0/RoughSets/man/predict.RuleSetFRST.Rd | 37
RoughSets-1.2-0/RoughSets/man/predict.RuleSetRST.Rd | 106
RoughSets-1.2-0/RoughSets/man/print.FeatureSubset.Rd |only
RoughSets-1.2-0/RoughSets/man/print.RuleSetRST.Rd |only
RoughSets-1.2-0/RoughSets/man/summary.IndiscernibilityRelation.Rd | 20
RoughSets-1.2-0/RoughSets/man/summary.LowerUpperApproximation.Rd | 19
RoughSets-1.2-0/RoughSets/man/summary.PositiveRegion.Rd | 19
RoughSets-1.2-0/RoughSets/man/summary.RuleSetFRST.Rd | 37
RoughSets-1.2-0/RoughSets/man/summary.RuleSetRST.Rd | 26
RoughSets-1.2-0/RoughSets/src/RcppExports.cpp |only
RoughSets-1.2-0/RoughSets/src/indiscernibility.cpp |only
91 files changed, 5494 insertions(+), 4996 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Diff between NSM3 versions 1.2 dated 2015-03-17 and 1.3 dated 2015-03-19
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/pFrd.R | 3 ++-
data/goose.rda |binary
man/rhythmicity.Rd | 2 +-
5 files changed, 10 insertions(+), 9 deletions(-)
Title: Create Plots from MCMC Output
Diff between mcmcplots versions 0.4.1 dated 2012-11-03 and 0.4.2 dated 2015-03-19
Description: Functions for convenient plotting and viewing of MCMC output.
Author: S. McKay Curtis [aut, cre],
Ilya Goldin [ctb],
Evangelos Evangelou [ctb],
'sumtxt' from GitHub [ctb]
Maintainer: S. McKay Curtis
DESCRIPTION | 28 ++++++++++++++++-----------
MD5 | 48 +++++++++++++++++++++++++----------------------
NAMESPACE | 3 ++
NEWS | 8 +++++++
R/as.mcmc.bugs.R | 4 +--
R/as.mcmc.rjags.R | 2 -
R/caterplot.R | 43 ++++++++++++++++++++++++++----------------
R/mcmcplot1.R | 3 +-
R/rmeanplot.R |only
R/rmeanplot1.R |only
man/as.mcmc.bugs.Rd | 7 +++---
man/as.mcmc.rjags.Rd | 5 ++--
man/autplot1.Rd | 13 +++++++++---
man/caterplot.Rd | 22 +++++++++++++++------
man/caterpoints.Rd | 5 +++-
man/denoverplot.Rd | 26 +++++++++++++++++--------
man/denoverplot1.Rd | 4 ++-
man/denplot.Rd | 10 ++++++---
man/graypr.Rd | 6 ++++-
man/mcmcplot.Rd | 14 ++++++++-----
man/mcmcplot1.Rd | 4 +--
man/mcmcplots-package.Rd | 29 +++++++++++++++++++---------
man/mcmcplotsPalette.Rd | 5 +++-
man/rmeanplot.Rd |only
man/rmeanplot1.Rd |only
man/traplot.Rd | 7 ++++--
man/traplot1.Rd | 5 +++-
27 files changed, 200 insertions(+), 101 deletions(-)
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Diff between ensembleBMA versions 5.1 dated 2015-02-18 and 5.1.1 dated 2015-03-19
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley
CHANGELOG | 9 ++++++---
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/quantileForecast.ensembleBMAgamma.R | 2 +-
R/quantileForecast.ensembleBMAgamma0.R | 2 +-
5 files changed, 16 insertions(+), 13 deletions(-)
Title: Bayesian Isotonic Regression with Bernstein Polynomials
Diff between bisoreg versions 1.1 dated 2012-12-27 and 1.4 dated 2015-03-19
Description: Provides functions for fitting Bayesian monotonic regression models to data.
Author: S. McKay Curtis
Maintainer: S. McKay Curtis
DESCRIPTION | 13 +++++++------
MD5 | 17 +++++++++--------
NAMESPACE | 15 +++++++++++----
NEWS |only
R/bisoreg.R | 2 +-
R/nd2004.R | 45 +++++++++++++++++++++------------------------
man/as.mcmc.biso.Rd | 23 +++--------------------
man/aveslope.Rd | 33 ++++++++++++++++++++++++++-------
man/bisoreg.Rd | 37 ++++++++++++++++++++++++-------------
man/nd2004.Rd | 4 +---
10 files changed, 103 insertions(+), 86 deletions(-)
Title: Read and Analyze PLEXOS Solutions
Diff between rplexos versions 0.12.1 dated 2015-02-04 and 0.13 dated 2015-03-18
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
rplexos-0.12.1/rplexos/inst/web |only
rplexos-0.12.1/rplexos/man/plexos_close.Rd |only
rplexos-0.13/rplexos/DESCRIPTION | 15
rplexos-0.13/rplexos/LICENSE | 4
rplexos-0.13/rplexos/MD5 | 99 -
rplexos-0.13/rplexos/NAMESPACE | 91 -
rplexos-0.13/rplexos/R/RcppExports.R | 22
rplexos-0.13/rplexos/R/auxiliary.R | 261 ++--
rplexos-0.13/rplexos/R/debug.R |only
rplexos-0.13/rplexos/R/globalVariables.R | 18
rplexos-0.13/rplexos/R/help.R | 45
rplexos-0.13/rplexos/R/log_parser.R | 173 +-
rplexos-0.13/rplexos/R/parallel.R |only
rplexos-0.13/rplexos/R/plexos_open.R | 300 +---
rplexos-0.13/rplexos/R/process_folder.R | 203 ++-
rplexos-0.13/rplexos/R/process_input.R | 636 +++++-----
rplexos-0.13/rplexos/R/process_solution.R | 1288 ++++++++++-----------
rplexos-0.13/rplexos/R/query.R | 1198 ++++++++++---------
rplexos-0.13/rplexos/R/query_summary.R |only
rplexos-0.13/rplexos/R/zzz.R | 29
rplexos-0.13/rplexos/README.md | 36
rplexos-0.13/rplexos/build/vignette.rds |binary
rplexos-0.13/rplexos/inst/doc/rplexos.R | 6
rplexos-0.13/rplexos/inst/doc/rplexos.Rmd | 19
rplexos-0.13/rplexos/inst/doc/rplexos.html | 514 ++++----
rplexos-0.13/rplexos/man/get_query.Rd |only
rplexos-0.13/rplexos/man/is_sample_stats.Rd | 44
rplexos-0.13/rplexos/man/list_folders.Rd | 32
rplexos-0.13/rplexos/man/plexos_open.Rd | 56
rplexos-0.13/rplexos/man/process_folder.Rd | 104 -
rplexos-0.13/rplexos/man/query_class_member.Rd |only
rplexos-0.13/rplexos/man/query_config.Rd | 50
rplexos-0.13/rplexos/man/query_log.Rd | 53
rplexos-0.13/rplexos/man/query_master.Rd | 242 +--
rplexos-0.13/rplexos/man/query_master_each.Rd |only
rplexos-0.13/rplexos/man/query_phase.Rd |only
rplexos-0.13/rplexos/man/query_property.Rd | 50
rplexos-0.13/rplexos/man/query_sql.Rd |only
rplexos-0.13/rplexos/man/query_time.Rd |only
rplexos-0.13/rplexos/man/rplexos.Rd | 51
rplexos-0.13/rplexos/man/start_debug_rplexos.Rd |only
rplexos-0.13/rplexos/man/start_parallel_rplexos.Rd |only
rplexos-0.13/rplexos/man/valid_columns.Rd | 30
rplexos-0.13/rplexos/src/RcppExports.cpp | 4
rplexos-0.13/rplexos/src/process_xml.cpp | 22
rplexos-0.13/rplexos/vignettes/rplexos.Rmd | 131 --
46 files changed, 2969 insertions(+), 2857 deletions(-)
Title: Robust Variance Meta-Regression
Diff between robumeta versions 1.5 dated 2015-01-12 and 1.6 dated 2015-03-18
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +++-
R/robumeta.R | 4 +++-
4 files changed, 14 insertions(+), 10 deletions(-)
Title: Statistical Experiments on Batch Computing Clusters
Diff between BatchExperiments versions 1.4 dated 2014-10-31 and 1.4.1 dated 2015-03-18
More information about BatchExperiments at CRAN
Description: Extends the BatchJobs package to run statistical experiments on
batch computing clusters. For further details see the project web page.
Author: Bernd Bischl
Maintainer: Michel Lang
DESCRIPTION | 10 +-
MD5 | 79 ++++++++---------
NAMESPACE | 3
NEWS | 14 ++-
R/Algorithm.R | 2
R/Problem.R | 4
R/database.R | 33 ++++---
R/findExperiments.R | 12 ++
R/generateProblemInstance.R | 9 +
R/getExperimentParts.R |only
R/helpers.R | 13 ++
R/reduceResultsExperiments.R | 27 +++--
R/reduceResultsExperimentsParallel.R | 38 ++------
inst |only
man/BatchExperiments.Rd | 3
man/ExperimentJob.Rd | 3
man/addAlgorithm.Rd | 3
man/addExperiments.Rd | 3
man/addProblem.Rd | 3
man/findExperiments.Rd | 11 +-
man/generateProblemInstance.Rd | 8 +
man/getAlgorithm.Rd | 4
man/getAlgorithmIds.Rd | 4
man/getExperimentParts.Rd |only
man/getIndex.Rd | 3
man/getJobs.ExperimentRegistry.Rd | 8 +
man/getProblem.Rd | 4
man/getProblemIds.Rd | 4
man/getResultVars.Rd | 3
man/makeDesign.Rd | 3
man/makeExperimentRegistry.Rd | 3
man/reduceResultsExperiments.Rd | 13 ++
man/reduceResultsExperimentsParallel.Rd | 20 +++-
man/removeAlgorithm.Rd | 3
man/removeExperiments.Rd | 3
man/removeProblem.Rd | 3
man/summarizeExperiments.Rd | 3
tests/testthat/helpers.R | 1
tests/testthat/test_findExperiments.R | 23 ++++
tests/testthat/test_reduceResults.R | 12 ++
tests/testthat/test_reduceResultsExperimentsParallel.R | 12 ++
tests/testthat/test_summarizeExperiments.R | 7 +
42 files changed, 283 insertions(+), 131 deletions(-)
Permanent link
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Diff between ncvreg versions 3.2-0 dated 2014-07-12 and 3.3-0 dated 2015-03-18
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny
ncvreg-3.2-0/ncvreg/R/coxCVL.R |only
ncvreg-3.2-0/ncvreg/man/ncvreg_fit.Rd |only
ncvreg-3.3-0/ncvreg/DESCRIPTION | 17
ncvreg-3.3-0/ncvreg/MD5 | 61 +--
ncvreg-3.3-0/ncvreg/NAMESPACE | 31 -
ncvreg-3.3-0/ncvreg/NEWS | 11
ncvreg-3.3-0/ncvreg/R/cv.ncvreg.R | 89 +++-
ncvreg-3.3-0/ncvreg/R/cv.ncvsurv.R | 31 +
ncvreg-3.3-0/ncvreg/R/logLik.R | 11
ncvreg-3.3-0/ncvreg/R/loss.R | 23 +
ncvreg-3.3-0/ncvreg/R/ncvreg.R | 53 +-
ncvreg-3.3-0/ncvreg/R/ncvreg_fit.R | 69 ---
ncvreg-3.3-0/ncvreg/R/ncvsurv.R | 19 -
ncvreg-3.3-0/ncvreg/R/perm.ncvreg.R | 8
ncvreg-3.3-0/ncvreg/R/plot.cv.ncvreg.R | 6
ncvreg-3.3-0/ncvreg/R/predict.R | 16
ncvreg-3.3-0/ncvreg/R/predict.surv.R |only
ncvreg-3.3-0/ncvreg/R/setupLambdaCox.R | 12
ncvreg-3.3-0/ncvreg/R/summary.cv.ncvsurv.R |only
ncvreg-3.3-0/ncvreg/data/Lung.RData |only
ncvreg-3.3-0/ncvreg/inst/tests/par.R |only
ncvreg-3.3-0/ncvreg/inst/tests/surv.R | 322 +++++++++--------
ncvreg-3.3-0/ncvreg/inst/tests/test.R | 521 +++++++++++++++--------------
ncvreg-3.3-0/ncvreg/man/Lung.Rd |only
ncvreg-3.3-0/ncvreg/man/cv.ncvreg.Rd | 27 +
ncvreg-3.3-0/ncvreg/man/cv.ncvsurv.Rd |only
ncvreg-3.3-0/ncvreg/man/heart.Rd | 20 -
ncvreg-3.3-0/ncvreg/man/ncvreg-package.Rd | 11
ncvreg-3.3-0/ncvreg/man/ncvreg.Rd | 4
ncvreg-3.3-0/ncvreg/man/ncvsurv.Rd |only
ncvreg-3.3-0/ncvreg/man/perm.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/plot.cv.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/plot.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/predict.Rd | 2
ncvreg-3.3-0/ncvreg/man/prostate.Rd | 18 -
ncvreg-3.3-0/ncvreg/src/cox-dh.c | 84 +---
36 files changed, 783 insertions(+), 689 deletions(-)
Title: Multivariate Normality Tests
Diff between MVN versions 3.8 dated 2015-01-28 and 3.9 dated 2015-03-18
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
R/hzTest.R | 4 ++++
R/mardiaTest.R | 4 ++++
R/mvOutlier.R | 8 ++++++--
R/roystonTest.R | 6 +++++-
inst/CITATION | 4 ++--
inst/doc/MVN.pdf |binary
man/mvOutlier.Rd | 6 +++++-
9 files changed, 38 insertions(+), 18 deletions(-)
Title: Batch Computing with R
Diff between BatchJobs versions 1.5 dated 2014-10-30 and 1.6 dated 2015-03-18
Description: Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Author: Bernd Bischl
Maintainer: Bernd Bischl
DESCRIPTION | 17 +-
MD5 | 221 ++++++++++++++++-----------------
NAMESPACE | 6
NEWS | 14 ++
R/Exports.R | 13 +
R/Registry.R | 73 +++++++++-
R/Resources.R | 4
R/Worker.R | 8 -
R/addJob.R | 12 -
R/batchApply.R | 70 ++++++----
R/batchMapResults.R | 2
R/batchReduceResults.R | 2
R/clusterFunctionsMulticore.R | 8 -
R/clusterFunctionsSLURM.R | 4
R/conf.R | 22 +--
R/database.R | 131 ++++++++++---------
R/filenames.R | 55 +++++++-
R/findStatus.R | 86 +++++++-----
R/grepLogs.R | 2
R/helpers.R | 17 ++
R/installPackagesOnSSHWorkers.R | 2
R/killJobs.R | 2
R/resetJobs.R | 2
R/showLog.R | 4
R/showStatus.R | 28 ++--
R/submitJobs.R | 2
R/sweepRegistry.R | 2
R/testJob.R | 3
R/waitForJobs.R | 10 -
R/zzz.R | 2
inst/CITATION | 38 +++--
man/BatchJobs.Rd | 3
man/addRegistryPackages.Rd | 3
man/addRegistrySourceDirs.Rd | 3
man/addRegistrySourceFiles.Rd | 3
man/applyJobFunction.Rd | 3
man/batchExpandGrid.Rd | 3
man/batchExport.Rd | 3
man/batchMap.Rd | 3
man/batchMapQuick.Rd | 3
man/batchMapResults.Rd | 3
man/batchReduce.Rd | 3
man/batchReduceResults.Rd | 3
man/batchUnexport.Rd | 3
man/callFunctionOnSSHWorkers.Rd | 3
man/cfBrewTemplate.Rd | 3
man/cfHandleUnknownSubmitError.Rd | 3
man/cfKillBatchJob.Rd | 3
man/cfReadBrewTemplate.Rd | 3
man/configuration.Rd | 3
man/copyRequiredJobFiles.Rd | 3
man/dbCreateJobDefTable.Rd | 3
man/dbGetJobs.Rd | 3
man/debugMulticore.Rd | 3
man/debugSSH.Rd | 3
man/filterResults.Rd | 3
man/findJobs.Rd | 3
man/findState.Rd | 49 ++++---
man/getConfig.Rd | 3
man/getErrorMessages.Rd | 3
man/getJob.Rd | 3
man/getJobIds.Rd | 3
man/getJobInfo.Rd | 3
man/getJobNr.Rd | 3
man/getJobParamDf.Rd | 3
man/getJobResources.Rd | 3
man/getJobs.Rd | 3
man/getLogFiles.Rd | 3
man/getResources.Rd | 3
man/getSSHWorkersInfo.Rd | 3
man/grepLogs.Rd | 3
man/installPackagesOnSSHWorkers.Rd | 3
man/killJobs.Rd | 5
man/loadConfig.Rd | 3
man/loadExports.Rd | 11 +
man/loadRegistry.Rd | 9 +
man/loadResult.Rd | 3
man/loadResults.Rd | 3
man/makeClusterFunctions.Rd | 3
man/makeClusterFunctionsInteractive.Rd | 3
man/makeClusterFunctionsLSF.Rd | 3
man/makeClusterFunctionsLocal.Rd | 3
man/makeClusterFunctionsMulticore.Rd | 14 +-
man/makeClusterFunctionsSGE.Rd | 3
man/makeClusterFunctionsSLURM.Rd | 3
man/makeClusterFunctionsSSH.Rd | 3
man/makeClusterFunctionsTorque.Rd | 3
man/makeJob.Rd | 3
man/makeRegistry.Rd | 3
man/makeSSHWorker.Rd | 3
man/makeSubmitJobResult.Rd | 3
man/reduceResults.Rd | 3
man/removeRegistry.Rd |only
man/removeRegistryPackages.Rd | 3
man/removeRegistrySourceDirs.Rd | 3
man/removeRegistrySourceFiles.Rd | 3
man/resetJobs.Rd | 3
man/sanitizePath.Rd | 3
man/setConfig.Rd | 3
man/setJobFunction.Rd | 3
man/setJobNames.Rd | 3
man/showClusterStatus.Rd | 3
man/showLog.Rd | 3
man/showStatus.Rd | 14 +-
man/sourceRegistryFiles.Rd | 3
man/submitJobs.Rd | 3
man/sweepRegistry.Rd | 3
man/testJob.Rd | 3
man/updateRegistry.Rd | 3
man/waitForJobs.Rd | 3
tests/testthat/test_export.R | 11 +
tests/testthat/test_makeRegistry.R | 11 +
112 files changed, 769 insertions(+), 433 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Diff between BAMMtools versions 2.0.2 dated 2014-07-10 and 2.0.4 dated 2015-03-18
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang
Maintainer: Pascal Title
DESCRIPTION | 17 ++---
MD5 | 89 ++++++++++++++++-------------
R/NU.branching.times.R |only
R/addBAMMlegend.R |only
R/addBAMMshifts.R | 12 ++-
R/assignColorBreaks.R | 121 ++++++++++++++++++++++++++++++++++++----
R/barLegend.R | 29 ++++++++-
R/cohorts.R | 27 ++++++--
R/colorMap.R | 61 +++++++++++++++-----
R/credibleShiftSet.R | 4 +
R/distinctShiftConfigurations.R | 4 +
R/dtRates.R | 11 ++-
R/getBestShiftConfiguration.R | 6 -
R/getCladeRates.R | 4 +
R/getEventData.R | 25 ++++++--
R/getJenksBreaks.R |only
R/getRateThroughTimeMatrix.R | 14 +++-
R/getStartStopTimes.R | 17 +++--
R/plot.bammdata.R | 110 ++++++++++++++++++++++++++++--------
R/plot.bammshifts.R | 4 -
R/plot.credibleshiftset.R | 72 ++++++++++++-----------
R/plotRateThroughTime.R | 12 +++
R/segMap.R | 43 +++++++-------
R/setBAMMpriors.R | 37 +++++++++---
R/setPhyloTreeCoords.R | 40 ++++++-------
R/setPolarTreeCoords.R | 47 +++++++--------
R/speciesByRatesMatrix.R | 42 +++++++------
R/traitDependentBAMM.R |only
R/transparentColor.R | 6 -
R/writeEventData.R |only
data/events.fishes.rda |only
data/fishes.rda |only
data/traits.fishes.rda |only
man/BAMMtools-data.Rd | 14 +++-
man/BAMMtools-internal.Rd | 2
man/BAMMtools-package.Rd | 4 -
man/addBAMMlegend.Rd |only
man/addBAMMshifts.Rd | 6 -
man/assignColorBreaks.Rd | 27 ++++++--
man/cohorts.Rd | 10 ++-
man/getBranchShiftPriors.Rd | 2
man/getJenksBreaks.Rd |only
man/plot.bammdata.Rd | 61 ++++++++++++++------
man/plot.bammshifts.Rd | 15 ++++
man/plot.credibleshiftset.Rd | 24 ++++++-
man/plotRateThroughTime.Rd | 4 -
man/setBAMMpriors.Rd | 2
man/speciesByRatesMatrix.Rd | 36 +++++------
man/traitDependentBAMM.Rd |only
man/writeEventData.Rd |only
src/jenksBrks.c |only
src/treetraverse.c | 23 ++++---
52 files changed, 756 insertions(+), 328 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-09 1.1
2011-05-22 1.0
Title: Spatial and Space-Time Point Pattern Analysis
Diff between splancs versions 2.01-36 dated 2014-10-03 and 2.01-37 dated 2015-03-18
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre],
Barry Rowlingson [aut],
Peter Diggle [aut],
Giovanni Petris [ctb],
Stephen Eglen [ctb]
Maintainer: Roger Bivand
ChangeLog | 20 ++++++++++++++++++++
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 4 ++++
inst/ChangeLog | 20 ++++++++++++++++++++
src/ptinpoly.c | 2 +-
6 files changed, 55 insertions(+), 11 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Diff between fanc versions 1.13 dated 2013-08-06 and 1.22 dated 2015-03-18
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto
Maintainer: Kei Hirose
fanc-1.13/fanc/src/fancC_v1.12.c |only
fanc-1.13/fanc/src/profiling.h |only
fanc-1.22/fanc/DESCRIPTION | 15
fanc-1.22/fanc/MD5 | 25
fanc-1.22/fanc/NAMESPACE | 6
fanc-1.22/fanc/R/fanc.R | 431 +++++------
fanc-1.22/fanc/R/out.fanc.R | 274 +------
fanc-1.22/fanc/R/plot.fanc.R | 1391 ++++++++++++++++++++++----------------
fanc-1.22/fanc/R/select.fanc.R |only
fanc-1.22/fanc/man/fanc.Rd | 16
fanc-1.22/fanc/man/out.fanc.Rd | 18
fanc-1.22/fanc/man/plot.fanc.Rd | 16
fanc-1.22/fanc/man/select.fanc.Rd |only
fanc-1.22/fanc/src/ezprof.c |only
fanc-1.22/fanc/src/ezprof.h |only
fanc-1.22/fanc/src/fanc.c |only
fanc-1.22/fanc/src/zeroin.c |only
fanc-1.22/fanc/src/zeroin.h |only
18 files changed, 1105 insertions(+), 1087 deletions(-)
Title: Business Analytics using R and Shiny
Diff between radiant versions 0.1.71 dated 2015-03-16 and 0.1.75 dated 2015-03-18
Description:
A platform-independent browser-based interface for business analytics in R, based on the Shiny package.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs
radiant-0.1.71/radiant/inst/base/tools/help/LICENSE |only
radiant-0.1.71/radiant/inst/quant/tools/help/LICENSE |only
radiant-0.1.75/radiant/DESCRIPTION | 10
radiant-0.1.75/radiant/LICENSE |only
radiant-0.1.75/radiant/MD5 | 185 +++++-----
radiant-0.1.75/radiant/R/aaa.R | 49 --
radiant-0.1.75/radiant/R/compare_means.R | 4
radiant-0.1.75/radiant/R/compare_props.R | 4
radiant-0.1.75/radiant/R/conjoint.R | 4
radiant-0.1.75/radiant/R/conjoint_profiles.R | 8
radiant-0.1.75/radiant/R/correlation.R | 2
radiant-0.1.75/radiant/R/full_factor.R | 2
radiant-0.1.75/radiant/R/glm_reg.R | 17
radiant-0.1.75/radiant/R/hier_clus.R | 7
radiant-0.1.75/radiant/R/kmeans_clus.R | 2
radiant-0.1.75/radiant/R/mds.R | 4
radiant-0.1.75/radiant/R/merge.R | 28 -
radiant-0.1.75/radiant/R/pmap.R | 8
radiant-0.1.75/radiant/R/pre_factor.R | 2
radiant-0.1.75/radiant/R/radiant.R | 87 +++-
radiant-0.1.75/radiant/R/regression.R | 9
radiant-0.1.75/radiant/R/sample_size.R | 6
radiant-0.1.75/radiant/R/sampling.R | 3
radiant-0.1.75/radiant/R/single_mean.R | 4
radiant-0.1.75/radiant/R/single_prop.R | 4
radiant-0.1.75/radiant/README.md | 47 +-
radiant-0.1.75/radiant/inst/base/global.R | 21 -
radiant-0.1.75/radiant/inst/base/tools/app/about.md | 47 +-
radiant-0.1.75/radiant/inst/base/tools/app/quit.R | 2
radiant-0.1.75/radiant/inst/base/tools/app/report.R | 8
radiant-0.1.75/radiant/inst/base/tools/data/pivot.R | 31 -
radiant-0.1.75/radiant/inst/base/tools/help/figures/pivot.png |binary
radiant-0.1.75/radiant/inst/examples/radiant_rcode.R | 68 ++-
radiant-0.1.75/radiant/inst/examples/single_mean.Rmd | 2
radiant-0.1.75/radiant/inst/marketing/server.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/conjoint_profiles_ui.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/full_factor_ui.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/kmeans_clus_ui.R | 9
radiant-0.1.75/radiant/inst/marketing/tools/analysis/pmap_ui.R | 8
radiant-0.1.75/radiant/inst/marketing/tools/help/figures |only
radiant-0.1.75/radiant/inst/quant/tools/help/figures |only
radiant-0.1.75/radiant/inst/quant/ui.R | 2
radiant-0.1.75/radiant/man/changedata.Rd | 12
radiant-0.1.75/radiant/man/city.Rd | 17
radiant-0.1.75/radiant/man/computer.Rd | 9
radiant-0.1.75/radiant/man/diamonds.Rd | 9
radiant-0.1.75/radiant/man/getdata.Rd | 9
radiant-0.1.75/radiant/man/glm_reg.Rd | 2
radiant-0.1.75/radiant/man/hier_clus.Rd | 4
radiant-0.1.75/radiant/man/mac_launcher.Rd | 20 -
radiant-0.1.75/radiant/man/mergedata.Rd | 2
radiant-0.1.75/radiant/man/mp3.Rd | 7
radiant-0.1.75/radiant/man/newspaper.Rd | 9
radiant-0.1.75/radiant/man/plot.compare_means.Rd | 4
radiant-0.1.75/radiant/man/plot.compare_props.Rd | 4
radiant-0.1.75/radiant/man/plot.conjoint.Rd | 4
radiant-0.1.75/radiant/man/plot.glm_predict.Rd | 6
radiant-0.1.75/radiant/man/plot.glm_reg.Rd | 6
radiant-0.1.75/radiant/man/plot.hier_clus.Rd | 4
radiant-0.1.75/radiant/man/plot.pmap.Rd | 4
radiant-0.1.75/radiant/man/plot.regression.Rd | 4
radiant-0.1.75/radiant/man/plot.single_mean.Rd | 4
radiant-0.1.75/radiant/man/plot.single_prop.Rd | 4
radiant-0.1.75/radiant/man/predict.glm_reg.Rd | 8
radiant-0.1.75/radiant/man/predict.regression.Rd | 7
radiant-0.1.75/radiant/man/radiant.Rd | 5
radiant-0.1.75/radiant/man/rndnames.Rd | 9
radiant-0.1.75/radiant/man/sample_size.Rd | 2
radiant-0.1.75/radiant/man/save_glm_resid.Rd | 4
radiant-0.1.75/radiant/man/save_membership.Rd | 4
radiant-0.1.75/radiant/man/set_class.Rd | 4
radiant-0.1.75/radiant/man/shopping.Rd | 9
radiant-0.1.75/radiant/man/sig_stars.Rd | 3
radiant-0.1.75/radiant/man/sshh.Rd | 7
radiant-0.1.75/radiant/man/sshhr.Rd | 7
radiant-0.1.75/radiant/man/summary.compare_means.Rd | 4
radiant-0.1.75/radiant/man/summary.compare_props.Rd | 4
radiant-0.1.75/radiant/man/summary.conjoint.Rd | 4
radiant-0.1.75/radiant/man/summary.conjoint_profiles.Rd | 4
radiant-0.1.75/radiant/man/summary.correlation.Rd | 4
radiant-0.1.75/radiant/man/summary.full_factor.Rd | 4
radiant-0.1.75/radiant/man/summary.glm_reg.Rd | 6
radiant-0.1.75/radiant/man/summary.hier_clus.Rd | 4
radiant-0.1.75/radiant/man/summary.mds.Rd | 4
radiant-0.1.75/radiant/man/summary.pmap.Rd | 4
radiant-0.1.75/radiant/man/summary.pre_factor.Rd | 4
radiant-0.1.75/radiant/man/summary.regression.Rd | 4
radiant-0.1.75/radiant/man/summary.sample_size.Rd | 6
radiant-0.1.75/radiant/man/summary.sampling.Rd | 4
radiant-0.1.75/radiant/man/summary.single_mean.Rd | 4
radiant-0.1.75/radiant/man/summary.single_prop.Rd | 4
radiant-0.1.75/radiant/man/titanic.Rd | 7
radiant-0.1.75/radiant/man/titanic_pred.Rd | 7
radiant-0.1.75/radiant/man/toothpaste.Rd | 9
radiant-0.1.75/radiant/man/win_launcher.Rd | 18
radiant-0.1.75/radiant/tests/run-all.R | 4
96 files changed, 550 insertions(+), 482 deletions(-)
Title: Person Fit
Diff between PerFit versions 1.3 dated 2015-03-13 and 1.3.1 dated 2015-03-18
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
R/PrintPerFit.R | 44 ++++----------------------------------------
man/PerFit-package.Rd | 4 ++--
man/lz.Rd | 8 +++-----
man/print.PerFit.Rd | 26 ++------------------------
6 files changed, 22 insertions(+), 82 deletions(-)
Title: Johnson Transformation for Normality
Diff between jtrans versions 0.1 dated 2013-07-24 and 0.2.1 dated 2015-03-18
Description: Transforming univariate non-normal data to normality using Johnson
families of distributions. Johnson family is a comprehensive distribution
family that accommodates many kinds of non-normal distributions. A bunch of
distributions with various parameters will be fit and the corresponding
p-values under a user-specified normality test will be given. The final
transformation will be the one with the largest p-value under the given
normality test.
Author: Yuchen Wang [aut, cre]
Maintainer: Yuchen Wang
jtrans-0.1/jtrans/R/fit_sb.R |only
jtrans-0.1/jtrans/R/fit_sl.R |only
jtrans-0.1/jtrans/R/fit_su.R |only
jtrans-0.2.1/jtrans/DESCRIPTION | 29 ++++---
jtrans-0.2.1/jtrans/MD5 | 20 ++--
jtrans-0.2.1/jtrans/NAMESPACE | 11 ++
jtrans-0.2.1/jtrans/R/fit_functions.R |only
jtrans-0.2.1/jtrans/R/jtrans.R | 109 +++++++++++++++------------
jtrans-0.2.1/jtrans/R/predict.R |only
jtrans-0.2.1/jtrans/R/qtls.R | 3
jtrans-0.2.1/jtrans/R/transeq.R |only
jtrans-0.2.1/jtrans/man/fit_functions.Rd | 67 +++++++++-------
jtrans-0.2.1/jtrans/man/jtrans.Rd | 96 +++++++++++++----------
jtrans-0.2.1/jtrans/man/predict_functions.Rd |only
jtrans-0.2.1/jtrans/man/transeq.Rd |only
15 files changed, 198 insertions(+), 137 deletions(-)
Title: Detection of Fixations in Eye-Tracking Data
Diff between saccades versions 0.1 dated 2014-10-04 and 0.1-1 dated 2015-03-18
Description: Functions for detecting eye fixations in raw eye-tracking
data. The detection is done using a velocity-based algorithm for
saccade detection proposed by Ralf Engbert and Reinhold Kliegl in
2003. The algorithm labels segments as saccades when the velocity of
the eye movement exceeds a certain threshold. Anything between two
saccades is considered a fixation. Thus the algorithm is not
appropriate for data containing episodes of smooth pursuit eye
movements.
Author: Titus von der Malsburg [aut, cph, cre]
Maintainer: Titus von der Malsburg
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/saccade_recognition.R | 12 ++++++------
man/detect.fixations.Rd | 2 +-
4 files changed, 14 insertions(+), 14 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density Estimation
Diff between psd versions 0.4-1 dated 2014-04-16 and 1.0-0 dated 2015-03-18
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability.
Author: Andrew J. Barbour and Robert L. Parker, with contributions from David
Myer
Maintainer: Andrew J. Barbour
psd-0.4-1/psd/inst/Examples/benchmarking.R |only
psd-0.4-1/psd/inst/Examples/profiling.R |only
psd-0.4-1/psd/vignettes/framed.sty |only
psd-0.4-1/psd/vignettes/mathsyms.tex |only
psd-0.4-1/psd/vignettes/tbl_norms.tex |only
psd-0.4-1/psd/vignettes/tbl_specprogs.tex |only
psd-1.0-0/psd/DESCRIPTION | 42
psd-1.0-0/psd/MD5 | 181 ++-
psd-1.0-0/psd/NAMESPACE | 54 -
psd-1.0-0/psd/R/RcppExports.R |only
psd-1.0-0/psd/R/func_envir.R | 154 +--
psd-1.0-0/psd/R/func_norm.R | 73 -
psd-1.0-0/psd/R/func_pilot.R |only
psd-1.0-0/psd/R/func_psdcore.R | 648 +++++++------
psd-1.0-0/psd/R/func_pspectrum.R | 317 ++----
psd-1.0-0/psd/R/func_riedsid.R | 248 ++---
psd-1.0-0/psd/R/func_spec.R | 93 +
psd-1.0-0/psd/R/func_specprops.R | 75 -
psd-1.0-0/psd/R/func_tapers.R | 545 ++++++-----
psd-1.0-0/psd/R/func_utils.R | 302 ++----
psd-1.0-0/psd/R/func_whiten.R | 136 +-
psd-1.0-0/psd/R/psd-package.R | 60 -
psd-1.0-0/psd/R/zzz.R | 23
psd-1.0-0/psd/README.md |only
psd-1.0-0/psd/build/vignette.rds |binary
psd-1.0-0/psd/demo/ctap.R | 15
psd-1.0-0/psd/inst/CITATION | 2
psd-1.0-0/psd/inst/Examples/_benchmarking.R |only
psd-1.0-0/psd/inst/Examples/_profiling.R |only
psd-1.0-0/psd/inst/Examples/_resample.R |only
psd-1.0-0/psd/inst/Examples/benchmarking_data.rda |only
psd-1.0-0/psd/inst/Examples/current_benchmarking_data.rda |only
psd-1.0-0/psd/inst/Examples/fix_R |only
psd-1.0-0/psd/inst/Examples/rdex_confint.R | 6
psd-1.0-0/psd/inst/Examples/rdex_constraintapers.R | 14
psd-1.0-0/psd/inst/Examples/rdex_normalization.R | 6
psd-1.0-0/psd/inst/Examples/rdex_parabolicweights.R | 57 -
psd-1.0-0/psd/inst/Examples/rdex_pilotspec.R | 7
psd-1.0-0/psd/inst/Examples/rdex_prewhiten.R | 6
psd-1.0-0/psd/inst/Examples/rdex_psdcore.R | 10
psd-1.0-0/psd/inst/Examples/rdex_psdenv.R | 6
psd-1.0-0/psd/inst/Examples/rdex_pspectrum.R | 14
psd-1.0-0/psd/inst/Examples/rdex_riedsid.R | 13
psd-1.0-0/psd/inst/Examples/rdex_spec.R | 6
psd-1.0-0/psd/inst/Examples/rdex_spectralproperties.R | 6
psd-1.0-0/psd/inst/Examples/rdex_splinegrad.R | 6
psd-1.0-0/psd/inst/Examples/rdex_tapers.R | 17
psd-1.0-0/psd/inst/Examples/rdex_utilities.R | 70 -
psd-1.0-0/psd/inst/Examples/run.rdev |only
psd-1.0-0/psd/inst/NEWS.Rd | 73 +
psd-1.0-0/psd/inst/WISHLIST | 25
psd-1.0-0/psd/inst/doc/REFS.bib | 40
psd-1.0-0/psd/inst/doc/fftw.R | 164 +--
psd-1.0-0/psd/inst/doc/fftw.Rnw | 64 -
psd-1.0-0/psd/inst/doc/fftw.pdf |binary
psd-1.0-0/psd/inst/doc/normalization.R | 22
psd-1.0-0/psd/inst/doc/normalization.Rnw | 47
psd-1.0-0/psd/inst/doc/normalization.pdf |binary
psd-1.0-0/psd/inst/doc/psd_overview.R | 329 +++---
psd-1.0-0/psd/inst/doc/psd_overview.Rnw | 671 ++++++--------
psd-1.0-0/psd/inst/doc/psd_overview.pdf |binary
psd-1.0-0/psd/man/Tohoku.Rd | 43
psd-1.0-0/psd/man/as.tapers.Rd | 104 +-
psd-1.0-0/psd/man/ctap_loess.Rd |only
psd-1.0-0/psd/man/ctap_simple_rcpp.Rd |only
psd-1.0-0/psd/man/hfsnm.Rd | 26
psd-1.0-0/psd/man/magnet.Rd | 44
psd-1.0-0/psd/man/modulo_floor.Rd |only
psd-1.0-0/psd/man/parabolic_weights.Rd | 116 +-
psd-1.0-0/psd/man/pgram_compare.Rd |only
psd-1.0-0/psd/man/pilot_spec.Rd | 119 +-
psd-1.0-0/psd/man/prewhiten.Rd | 195 +---
psd-1.0-0/psd/man/psd-environment.Rd | 189 ++-
psd-1.0-0/psd/man/psd-normalization.Rd | 101 +-
psd-1.0-0/psd/man/psd-package.Rd | 137 +-
psd-1.0-0/psd/man/psd-utilities.Rd | 295 ++----
psd-1.0-0/psd/man/psdcore.Rd | 144 +--
psd-1.0-0/psd/man/pspectrum.Rd | 99 +-
psd-1.0-0/psd/man/rcpp_ctap_simple.Rd |only
psd-1.0-0/psd/man/resample_fft_rcpp.Rd |only
psd-1.0-0/psd/man/riedsid.Rd | 132 +-
psd-1.0-0/psd/man/spec-methods.Rd | 49 -
psd-1.0-0/psd/man/spec_confint.Rd | 76 -
psd-1.0-0/psd/man/spectral_properties.Rd | 118 +-
psd-1.0-0/psd/man/splineGrad.Rd | 49 -
psd-1.0-0/psd/man/tapers-constraints.Rd | 198 +---
psd-1.0-0/psd/man/tapers-methods.Rd | 47
psd-1.0-0/psd/src/Makevars |only
psd-1.0-0/psd/src/Makevars.win |only
psd-1.0-0/psd/src/RcppExports.cpp |only
psd-1.0-0/psd/src/ctap_simple.c | 105 --
psd-1.0-0/psd/src/ctap_simple_r.cpp |only
psd-1.0-0/psd/src/resample_fft.cpp |only
psd-1.0-0/psd/tests |only
psd-1.0-0/psd/vignettes/Makefile | 9
psd-1.0-0/psd/vignettes/README | 52 -
psd-1.0-0/psd/vignettes/REFS.bib | 40
psd-1.0-0/psd/vignettes/fftw.Rnw | 64 -
psd-1.0-0/psd/vignettes/fftw.synctex.gz |only
psd-1.0-0/psd/vignettes/normalization.Rnw | 47
psd-1.0-0/psd/vignettes/normalization.synctex.gz |only
psd-1.0-0/psd/vignettes/psd_overview.Rnw | 671 ++++++--------
psd-1.0-0/psd/vignettes/psd_overview.synctex.gz |only
psd-1.0-0/psd/vignettes/supp_mathsyms.tex |only
psd-1.0-0/psd/vignettes/supp_norms.tex |only
psd-1.0-0/psd/vignettes/supp_specprogs.tex |only
106 files changed, 3941 insertions(+), 3975 deletions(-)
Title: Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Diff between FuzzyStatProb versions 1.0 dated 2013-03-11 and 2.0 dated 2015-03-18
Description: An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley
in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package FuzzyNumbers is used to represent the output probabilities.
Author: Author: Pablo J. Villacorta
Maintainer: Pablo J. Villacorta
FuzzyStatProb-1.0/FuzzyStatProb/man/FuzzyStatProb.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/DESCRIPTION | 35
FuzzyStatProb-2.0/FuzzyStatProb/MD5 | 22
FuzzyStatProb-2.0/FuzzyStatProb/NAMESPACE | 5
FuzzyStatProb-2.0/FuzzyStatProb/R/FuzzyStatProb-package.R | 2
FuzzyStatProb-2.0/FuzzyStatProb/R/initial-pop.R | 2
FuzzyStatProb-2.0/FuzzyStatProb/R/main.R | 859 ++++++++-----
FuzzyStatProb-2.0/FuzzyStatProb/R/memb-fn-reg.R | 24
FuzzyStatProb-2.0/FuzzyStatProb/R/objective-fn.R | 5
FuzzyStatProb-2.0/FuzzyStatProb/build |only
FuzzyStatProb-2.0/FuzzyStatProb/data |only
FuzzyStatProb-2.0/FuzzyStatProb/inst |only
FuzzyStatProb-2.0/FuzzyStatProb/man/fuzzyStationaryProb.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/man/robotMatrix.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/vignettes |only
15 files changed, 603 insertions(+), 351 deletions(-)
Title: Wrapper for FFTW3: Includes 1-D, Univariate and Multivariate,
and 2-D Transform
Diff between fftwtools versions 0.9-6 dated 2014-02-20 and 0.9-7 dated 2015-03-18
Description: Provides a wrapper for several FFTW functions. This package provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using FFTW3. The package includes the functions fftw and mvfftw which are designed to mimic the functionality of the R functions fft and mvfft. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 16 +++++++-------
MD5 | 8 +++----
R/fftwtools.R | 41 +++++++++++++++++++++++---------------
build/vignette.rds |binary
inst/doc/testTimeAndSimpleUse.pdf |binary
5 files changed, 37 insertions(+), 28 deletions(-)
Title: Differential Co-Expression and Differential Expression Analysis
Diff between decode versions 1.0 dated 2015-01-28 and 1.1 dated 2015-03-18
Description: Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.
Author: Thomas Lui [aut, cre]
Maintainer: Thomas Lui
DESCRIPTION | 12 +++++++-----
MD5 | 11 ++++++++---
R/Decode.r | 16 +++++++++-------
build |only
inst/doc |only
man/runDecode.Rd | 9 +++++++--
vignettes |only
7 files changed, 31 insertions(+), 17 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.5-1 dated 2015-02-09 and 1.5-2 dated 2015-03-17
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NEWS | 4 ++++
R/momentEstim.R | 14 ++++++++++++++
inst/doc/gmm_with_R.pdf |binary
5 files changed, 27 insertions(+), 9 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Diff between checkpoint versions 0.3.3 dated 2014-10-10 and 0.3.9 dated 2015-03-17
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install
packages as they existed on CRAN on a specific snapshot date as if you had
a CRAN time machine. To achieve reproducibility, the checkpoint() function
installs the packages required or called by your project and scripts to a
local library exactly as they existed at the specified point in time. Only
those packages are available to your project, thereby avoiding any package
updates that came later and may have altered your results. In this way,
anyone using checkpoint's checkpoint() can ensure the reproducibility of
your scripts or projects at any time. To create the snapshot archives, once
a day (at midnight UTC) we refresh the Austria CRAN mirror, on the "Managed
R Archived Network" server (http://mran.revolutionanalytics.com/).
Immediately after completion of the rsync mirror process, we take a
snapshot, thus creating the archive. Snapshot archives exist starting from
2014-09-17.
Author: Revolution Analytics
Maintainer: Andrie de Vries
checkpoint-0.3.3/checkpoint/tests/testthat/test-1-checkpoint.R |only
checkpoint-0.3.9/checkpoint/DESCRIPTION | 15
checkpoint-0.3.9/checkpoint/MD5 | 29 +
checkpoint-0.3.9/checkpoint/NAMESPACE | 4
checkpoint-0.3.9/checkpoint/R/checkpoint.R | 146 ++++++-
checkpoint-0.3.9/checkpoint/R/checkpoint_paths.R | 42 +-
checkpoint-0.3.9/checkpoint/R/detach.R |only
checkpoint-0.3.9/checkpoint/R/fixRstudioBug.R |only
checkpoint-0.3.9/checkpoint/R/installMissingBasePackages.R |only
checkpoint-0.3.9/checkpoint/R/scanRepoPackages.R | 183 ++++++----
checkpoint-0.3.9/checkpoint/R/test-common-functions.R | 2
checkpoint-0.3.9/checkpoint/build |only
checkpoint-0.3.9/checkpoint/inst/doc |only
checkpoint-0.3.9/checkpoint/man/checkpoint-package.Rd | 3
checkpoint-0.3.9/checkpoint/man/checkpoint.Rd | 21 -
checkpoint-0.3.9/checkpoint/tests/testthat/test-1-scan.R |only
checkpoint-0.3.9/checkpoint/tests/testthat/test-2-checkpoint.R |only
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18 files changed, 317 insertions(+), 128 deletions(-)
Title: R Interface to Global Biotic Interactions
Diff between rglobi versions 0.2.5 dated 2015-02-24 and 0.2.6 dated 2015-03-17
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
build/vignette.rds |binary
tests/testthat/test-globi.R | 2 +-
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Diff between NSM3 versions 1.1 dated 2013-11-12 and 1.2 dated 2015-03-17
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider
DESCRIPTION | 14 +--
MD5 | 8 -
R/theil.R | 274 ++++++++++++++++++++++++-----------------------------------
man/pKW.Rd | 2
man/theil.Rd | 4
5 files changed, 130 insertions(+), 172 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Diff between mvMORPH versions 1.0.2 dated 2014-04-24 and 1.0.3 dated 2015-03-17
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel
mvMORPH-1.0.2/mvMORPH/R/mvOUC.r |only
mvMORPH-1.0.2/mvMORPH/man/mvSHIFT.rd |only
mvMORPH-1.0.2/mvMORPH/src/ouch.h |only
mvMORPH-1.0.3/mvMORPH/DESCRIPTION | 12
mvMORPH-1.0.3/mvMORPH/MD5 | 55 -
mvMORPH-1.0.3/mvMORPH/NAMESPACE | 18
mvMORPH-1.0.3/mvMORPH/R/fun.r | 533 ++++++++-
mvMORPH-1.0.3/mvMORPH/R/mvBM.r | 1071 ++++++++++----------
mvMORPH-1.0.3/mvMORPH/R/mvEB.r | 455 ++++----
mvMORPH-1.0.3/mvMORPH/R/mvLLIK.r |only
mvMORPH-1.0.3/mvMORPH/R/mvOU.r |only
mvMORPH-1.0.3/mvMORPH/R/mvSHIFT.r | 637 ++++++++---
mvMORPH-1.0.3/mvMORPH/R/mvSIM.r |only
mvMORPH-1.0.3/mvMORPH/R/mvmorphPrecalc.r |only
mvMORPH-1.0.3/mvMORPH/R/testLRT.r |only
mvMORPH-1.0.3/mvMORPH/man/LRT.Rd |only
mvMORPH-1.0.3/mvMORPH/man/mv.Precalc.Rd |only
mvMORPH-1.0.3/mvMORPH/man/mvBM.Rd | 399 ++++---
mvMORPH-1.0.3/mvMORPH/man/mvEB.Rd | 303 +++--
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mvMORPH-1.0.3/mvMORPH/man/mvMORPH-package.Rd | 97 -
mvMORPH-1.0.3/mvMORPH/man/mvOU.Rd | 405 ++++---
mvMORPH-1.0.3/mvMORPH/man/mvSHIFT.Rd |only
mvMORPH-1.0.3/mvMORPH/man/mvSIM.Rd |only
mvMORPH-1.0.3/mvMORPH/src/Makevars |only
mvMORPH-1.0.3/mvMORPH/src/chol_rpf_row.c |only
mvMORPH-1.0.3/mvMORPH/src/chol_rpf_univ.c |only
mvMORPH-1.0.3/mvMORPH/src/covar-matrix-simmap.c | 2
mvMORPH-1.0.3/mvMORPH/src/givens.c |only
mvMORPH-1.0.3/mvMORPH/src/kronecker.c |only
mvMORPH-1.0.3/mvMORPH/src/mvmorph-covar-mat.c | 102 +
mvMORPH-1.0.3/mvMORPH/src/mvmorph-covar-ou-sparse.c |only
mvMORPH-1.0.3/mvMORPH/src/mvmorph-covar-ou.c | 17
mvMORPH-1.0.3/mvMORPH/src/mvmorph.h |only
mvMORPH-1.0.3/mvMORPH/src/mvmorph_ou_mat_rpf.c |only
mvMORPH-1.0.3/mvMORPH/src/pic_loglik_mvmorph.c |only
mvMORPH-1.0.3/mvMORPH/src/quadprod.c |only
mvMORPH-1.0.3/mvMORPH/src/root2tip.c | 3
mvMORPH-1.0.3/mvMORPH/src/time_root_mvmorph.c |only
mvMORPH-1.0.3/mvMORPH/src/weight-matrix-mvmorph.c |only
mvMORPH-1.0.3/mvMORPH/src/weight-matrix-simmap.c | 4
41 files changed, 2479 insertions(+), 1634 deletions(-)
Title: Histogram-Valued Data Analysis
Diff between HistDAWass versions 0.1.1 dated 2015-02-24 and 0.1.2 dated 2015-03-17
Description: In the framework of Symbolic Data Analysis, a relatively new approach
to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e.,
data described by univariate histograms. The methods and the basic statistics for
histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification techniques,
least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino
DESCRIPTION | 14 +--
MD5 | 55 +++++++----
NAMESPACE | 12 ++
R/HistDAWass-package.R | 1
R/Met_HTS.R | 106 +++++++++++++++++++++--
R/Met_MatH.R | 184 +++++++++++-----------------------------
R/Met_distributionH.R | 106 ++---------------------
R/Plotting_with_ggplot.R |only
R/Utility.R | 159 ++++++++++++++++++++++++++++++++++
R/principal_components.R | 1
R/regression.R | 75 ++++++++++++++--
R/unsuperv_classification.R | 5 +
README.md |only
man/Center.cell.MatH-methods.Rd |only
man/DouglasPeucker.Rd |only
man/ShortestDistance.Rd |only
man/WH.regression.GOF.Rd |only
man/WH_hclust.Rd | 7 +
man/crwtransform-methods.Rd | 4
man/data2hist.Rd |only
man/extract-methods.Rd | 9 +
man/get.distr-methods.Rd | 4
man/get.histo-methods.Rd | 4
man/get.m-methods.Rd | 4
man/get.s-methods.Rd | 4
man/kurtH-methods.Rd | 4
man/meanH-methods.Rd | 4
man/plot-HTS.Rd |only
man/plot-MatH.Rd | 9 -
man/plotPredVsObs.Rd |only
man/plot_errors.Rd |only
man/skewH-methods.Rd | 4
man/stdH-methods.Rd | 4
man/subsetHTS-methods.Rd |only
34 files changed, 479 insertions(+), 300 deletions(-)
Title: Bayesian Analysis of Contingency Tables
Diff between conting versions 1.4 dated 2014-12-03 and 1.5 dated 2015-03-17
Description: Bayesian analysis of complete and incomplete contingency tables.
Author: Antony M. Overstall
Maintainer: Antony M. Overstall
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
NAMESPACE | 15 +++++++++++++++
data/AOH.rda |binary
data/ScotPWID.rda |binary
data/heart.rda |binary
data/spina.rda |binary
man/conting-package.Rd | 8 ++++----
8 files changed, 31 insertions(+), 16 deletions(-)
More information about EntropyExplorer at CRAN
Permanent link
Title: Tree-Based Varying Coefficient Regression for Generalized Linear
and Ordinal Mixed Models
Diff between vcrpart versions 0.3-2 dated 2015-02-11 and 0.3-3 dated 2015-03-17
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph],
Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin
DESCRIPTION | 8 +--
MD5 | 22 ++++-----
NEWS | 21 ++++++++
R/fvcm.R | 76 ++++++++++++++++++++-----------
R/olmm-methods.R | 10 ++--
R/tvcm-cv.R | 11 ++--
R/tvcm-utils.R | 124 +++++++++++++++++++++++-----------------------------
R/tvcm.R | 53 +++++++++++++---------
man/fvcm.Rd | 56 +++++++++--------------
man/olmm-gefp.Rd | 7 ++
man/tvcm-control.Rd | 4 -
man/tvcm-cv.Rd | 2
12 files changed, 218 insertions(+), 176 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-87 dated 2015-03-16 and 0.5-88 dated 2015-03-17
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
spdep-0.5-87/spdep/inst/copyright.diff |only
spdep-0.5-88/spdep/DESCRIPTION | 8 ++--
spdep-0.5-88/spdep/MD5 | 25 +++++++--------
spdep-0.5-88/spdep/R/lextrW.R | 4 +-
spdep-0.5-88/spdep/inst/doc/CO69.pdf |binary
spdep-0.5-88/spdep/inst/doc/SpatialFiltering.pdf |binary
spdep-0.5-88/spdep/inst/doc/nb.pdf |binary
spdep-0.5-88/spdep/inst/doc/nb_igraph.R | 12 ++++---
spdep-0.5-88/spdep/inst/doc/nb_igraph.Rmd | 12 ++++---
spdep-0.5-88/spdep/inst/doc/nb_igraph.html | 32 ++++++++++++++++---
spdep-0.5-88/spdep/inst/doc/sids.pdf |binary
spdep-0.5-88/spdep/man/eigenw.Rd | 12 +++++--
spdep-0.5-88/spdep/man/lextrB.Rd | 37 +++++++++++++++++++----
spdep-0.5-88/spdep/vignettes/nb_igraph.Rmd | 12 ++++---
14 files changed, 109 insertions(+), 45 deletions(-)
Title: Tools, Classes, and Methods for Interfacing with SaTScan
Stand-Alone Software
Diff between rsatscan versions 0.3.9122 dated 2015-02-08 and 0.3.9200 dated 2015-03-17
Description: SaTScan(TM) (http://www.satscan.org) is software for finding regions in
Time, Space, or Time-Space that have excess risk, based on scan statistics, and
uses Monte Carlo hypothesis testing to generate P-values for these regions. The
rsatscan package provides functions for writing R data frames in
SaTScan-readable formats, for setting SaTScan parameters, for running SaTScan in
the OS, and for reading the files that SaTScan creates.
Author: Ken Kleinman [aut, cre]
Maintainer: Ken Kleinman
rsatscan-0.3.9122/rsatscan/R/methods.r |only
rsatscan-0.3.9200/rsatscan/DESCRIPTION | 8 +--
rsatscan-0.3.9200/rsatscan/MD5 | 34 ++++++-------
rsatscan-0.3.9200/rsatscan/NEWS | 10 +++-
rsatscan-0.3.9200/rsatscan/R/methods.R |only
rsatscan-0.3.9200/rsatscan/R/satscan.R | 4 -
rsatscan-0.3.9200/rsatscan/R/zzz.R | 3 -
rsatscan-0.3.9200/rsatscan/README.md | 13 ++---
rsatscan-0.3.9200/rsatscan/inst/doc/rsatscan.R | 44 ++++++++---------
rsatscan-0.3.9200/rsatscan/inst/doc/rsatscan.Rmd | 50 ++++++++++----------
rsatscan-0.3.9200/rsatscan/inst/doc/rsatscan.html | 35 +++++++-------
rsatscan-0.3.9200/rsatscan/inst/doc/simulation.R | 10 ++--
rsatscan-0.3.9200/rsatscan/inst/doc/simulation.Rmd | 12 ++--
rsatscan-0.3.9200/rsatscan/inst/doc/simulation.html | 6 +-
rsatscan-0.3.9200/rsatscan/man/print.satscan.Rd | 2
rsatscan-0.3.9200/rsatscan/man/satscan.Rd | 2
rsatscan-0.3.9200/rsatscan/man/summary.satscan.Rd | 2
rsatscan-0.3.9200/rsatscan/vignettes/rsatscan.Rmd | 50 ++++++++++----------
rsatscan-0.3.9200/rsatscan/vignettes/simulation.Rmd | 12 ++--
19 files changed, 154 insertions(+), 143 deletions(-)
Title: Calculation of Rarity Indices for Species and Assemblages of
Species
Diff between Rarity versions 1.2-1 dated 2013-08-12 and 1.3-1 dated 2015-03-17
Description: Allows calculation of rarity weights for species and indices of rarity for assemblages of species according to different methods (Leroy et al. 2012, 2013).
Author: Boris Leroy
Maintainer: Boris Leroy
DESCRIPTION | 14 +-
MD5 | 20 ++-
NAMESPACE | 9 -
R/Rarity.R |only
R/rarity_indices.R | 265 ++------------------------------------------------
R/rarity_weights.R | 40 ++++++-
R/summed_rarity.R |only
README.md |only
man/Irr.Rd | 35 +++---
man/Isr.Rd |only
man/Rarity-package.Rd | 7 -
man/rWeights.Rd | 29 +++--
man/spid.occ.Rd | 2
13 files changed, 113 insertions(+), 308 deletions(-)
Title: An Implementation of the Grammar of Graphics
Diff between ggplot2 versions 1.0.0 dated 2014-05-21 and 1.0.1 dated 2015-03-17
Description: An implementation of the grammar of graphics
in R. It combines the advantages of both base and
lattice graphics: conditioning and shared axes are
handled automatically, and you can still build up a
plot step by step from multiple data sources. It also
implements a sophisticated multidimensional
conditioning system and a consistent interface to map
data to aesthetic attributes. See http://ggplot2.org
for more information, documentation and examples.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut]
Maintainer: Hadley Wickham
DESCRIPTION | 19 +
MD5 | 442 ++++++++++++++++++++---------------------
NAMESPACE | 2
NEWS | 7
R/annotation-custom.r | 6
R/coord-map.r | 2
R/fortify-spatial.r | 2
R/geom-hex.r | 2
R/guide-colorbar.r | 4
R/guide-legend.r | 4
R/layer.r | 2
R/scale-.r | 14 -
R/scale-area.r | 2
R/stat-binhex.r | 4
R/stat-smooth.r | 2
R/stat-ydensity.r | 2
R/templates.r | 12 -
R/theme-elements.r | 10
R/theme.r | 10
R/translate-qplot-lattice.r | 2
build/partial.rdb |binary
build/vignette.rds |binary
inst/doc/development.R | 10
inst/doc/development.html | 19 +
inst/doc/release.R | 2
inst/doc/release.html | 16 +
man/absoluteGrob.Rd | 3
man/add_theme.Rd | 3
man/aes.Rd | 3
man/aes_all.Rd | 3
man/aes_auto.Rd | 3
man/aes_colour_fill_alpha.Rd | 3
man/aes_group_order.Rd | 3
man/aes_linetype_size_shape.Rd | 3
man/aes_position.Rd | 3
man/aes_string.Rd | 3
man/annotate.Rd | 3
man/annotation_custom.Rd | 9
man/annotation_logticks.Rd | 13 -
man/annotation_map.Rd | 3
man/annotation_raster.Rd | 3
man/autoplot.Rd | 3
man/benchplot.Rd | 3
man/borders.Rd | 3
man/calc_element.Rd | 3
man/continuous_scale.Rd | 27 +-
man/coord.Rd | 3
man/coord_cartesian.Rd | 3
man/coord_expand_defaults.Rd | 3
man/coord_fixed.Rd | 3
man/coord_flip.Rd | 3
man/coord_map.Rd | 3
man/coord_polar.Rd | 3
man/coord_quickmap.Rd | 3
man/coord_trans.Rd | 3
man/cut_interval.Rd | 3
man/cut_number.Rd | 3
man/cweave.Rd | 3
man/diamonds.Rd | 3
man/discrete_scale.Rd | 15 -
man/economics.Rd | 3
man/element_blank.Rd | 3
man/element_line.Rd | 3
man/element_rect.Rd | 3
man/element_text.Rd | 3
man/expand_limits.Rd | 3
man/facet.Rd | 3
man/facet_grid.Rd | 11 -
man/facet_null.Rd | 3
man/facet_wrap.Rd | 7
man/fortify-multcomp.Rd | 3
man/fortify.Rd | 3
man/fortify.lm.Rd | 3
man/fortify.map.Rd | 3
man/fortify.sp.Rd | 3
man/geom_abline.Rd | 7
man/geom_area.Rd | 3
man/geom_bar.Rd | 3
man/geom_bin2d.Rd | 3
man/geom_blank.Rd | 3
man/geom_boxplot.Rd | 29 +-
man/geom_contour.Rd | 15 -
man/geom_crossbar.Rd | 7
man/geom_density.Rd | 3
man/geom_density2d.Rd | 15 -
man/geom_dotplot.Rd | 41 +--
man/geom_errorbar.Rd | 3
man/geom_errorbarh.Rd | 3
man/geom_freqpoly.Rd | 3
man/geom_hex.Rd | 3
man/geom_histogram.Rd | 3
man/geom_hline.Rd | 7
man/geom_jitter.Rd | 3
man/geom_line.Rd | 3
man/geom_linerange.Rd | 3
man/geom_map.Rd | 13 -
man/geom_path.Rd | 19 -
man/geom_point.Rd | 3
man/geom_pointrange.Rd | 3
man/geom_polygon.Rd | 3
man/geom_quantile.Rd | 15 -
man/geom_raster.Rd | 17 -
man/geom_rect.Rd | 3
man/geom_ribbon.Rd | 3
man/geom_rug.Rd | 11 -
man/geom_segment.Rd | 11 -
man/geom_smooth.Rd | 3
man/geom_step.Rd | 9
man/geom_text.Rd | 9
man/geom_tile.Rd | 3
man/geom_violin.Rd | 17 -
man/geom_vline.Rd | 7
man/gg-add.Rd | 3
man/gg_dep.Rd | 3
man/ggplot.Rd | 3
man/ggplot.data.frame.Rd | 3
man/ggplot2.Rd | 3
man/ggplotGrob.Rd | 3
man/ggplot_build.Rd | 3
man/ggplot_gtable.Rd | 7
man/ggsave.Rd | 3
man/ggscale.Rd | 3
man/ggtheme.Rd | 3
man/guide_colourbar.Rd | 73 +++---
man/guide_legend.Rd | 3
man/guides.Rd | 3
man/hmisc.Rd | 3
man/interleave.Rd | 3
man/is.coord.Rd | 3
man/is.facet.Rd | 3
man/is.ggplot.Rd | 3
man/is.rel.Rd | 3
man/is.theme.Rd | 3
man/label_both.Rd | 3
man/label_bquote.Rd | 3
man/label_parsed.Rd | 3
man/label_value.Rd | 3
man/label_wrap_gen.Rd | 3
man/labeller.Rd | 3
man/labs.Rd | 7
man/last_plot.Rd | 3
man/layer.Rd | 3
man/limits.Rd | 7
man/map_data.Rd | 3
man/mean_se.Rd | 3
man/midwest.Rd | 3
man/movies.Rd | 3
man/mpg.Rd | 3
man/msleep.Rd | 3
man/opts.Rd | 3
man/plot-templates.Rd | 3
man/position_dodge.Rd | 3
man/position_fill.Rd | 3
man/position_identity.Rd | 3
man/position_jitter.Rd | 3
man/position_jitterdodge.Rd | 3
man/position_stack.Rd | 3
man/presidential.Rd | 3
man/print.ggplot.Rd | 3
man/qplot.Rd | 3
man/rel.Rd | 3
man/resolution.Rd | 3
man/rweave.Rd | 3
man/scale_alpha.Rd | 3
man/scale_area.Rd | 3
man/scale_brewer.Rd | 13 -
man/scale_continuous.Rd | 3
man/scale_date.Rd | 19 -
man/scale_datetime.Rd | 19 -
man/scale_discrete.Rd | 3
man/scale_gradient.Rd | 13 -
man/scale_gradient2.Rd | 19 -
man/scale_gradientn.Rd | 13 -
man/scale_grey.Rd | 9
man/scale_hue.Rd | 7
man/scale_identity.Rd | 3
man/scale_linetype.Rd | 7
man/scale_manual.Rd | 11 -
man/scale_shape.Rd | 7
man/scale_size.Rd | 9
man/scale_size_area.Rd | 3
man/seals.Rd | 3
man/should_stop.Rd | 3
man/stat_abline.Rd | 3
man/stat_bin.Rd | 31 +-
man/stat_bin2d.Rd | 13 -
man/stat_bindot.Rd | 45 ++--
man/stat_binhex.Rd | 15 -
man/stat_boxplot.Rd | 13 -
man/stat_contour.Rd | 9
man/stat_density.Rd | 27 +-
man/stat_density2d.Rd | 23 +-
man/stat_ecdf.Rd | 9
man/stat_ellipse.Rd | 31 +-
man/stat_function.Rd | 15 -
man/stat_hline.Rd | 3
man/stat_identity.Rd | 3
man/stat_qq.Rd | 21 +
man/stat_quantile.Rd | 23 +-
man/stat_smooth.Rd | 33 +--
man/stat_spoke.Rd | 3
man/stat_sum.Rd | 3
man/stat_summary.Rd | 3
man/stat_summary2d.Rd | 19 -
man/stat_summary_hex.Rd | 19 -
man/stat_unique.Rd | 3
man/stat_vline.Rd | 3
man/stat_ydensity.Rd | 23 +-
man/summary.ggplot.Rd | 3
man/theme.Rd | 5
man/theme_blank.Rd | 3
man/theme_update.Rd | 3
man/translate_qplot_base.Rd | 3
man/translate_qplot_ggplot.Rd | 3
man/translate_qplot_gpl.Rd | 3
man/translate_qplot_lattice.Rd | 5
man/update_defaults.Rd | 7
man/update_element.Rd | 3
man/update_labels.Rd | 3
man/waiver.Rd | 3
man/xylim.Rd | 3
man/zeroGrob.Rd | 3
222 files changed, 1102 insertions(+), 863 deletions(-)
Title: Functions for the Detection of Spatial Clusters of Diseases
Diff between DCluster versions 0.2-6 dated 2013-01-06 and 0.2-7 dated 2015-03-17
Description: A set of functions for the detection of spatial clusters
of disease using count data. Bootstrap is used to estimate
sampling distributions of statistics.
Author: Virgilio Gómez-Rubio, Juan Ferrándiz-Ferragud and Antonio
López-Quílez, with contributions by Roger Bivand.
Maintainer: Virgilio Gómez-Rubio
DCluster-0.2-6/DCluster/R/zzz.R |only
DCluster-0.2-7/DCluster/DESCRIPTION | 11 -
DCluster-0.2-7/DCluster/MD5 | 88 ++++++-------
DCluster-0.2-7/DCluster/NAMESPACE | 100 ++++++++++++++
DCluster-0.2-7/DCluster/R/empbaysmooth.R | 114 ++++++++---------
DCluster-0.2-7/DCluster/R/kn.gumbel.iscluster.R |only
DCluster-0.2-7/DCluster/R/kullnagar.stat.R | 4
DCluster-0.2-7/DCluster/man/DCluster.Rd | 4
DCluster-0.2-7/DCluster/man/achisq.Rd | 2
DCluster-0.2-7/DCluster/man/achisq.boot.Rd | 2
DCluster-0.2-7/DCluster/man/achisq.stat.Rd | 2
DCluster-0.2-7/DCluster/man/besagnewell.Rd | 2
DCluster-0.2-7/DCluster/man/besagnewell.boot.Rd | 2
DCluster-0.2-7/DCluster/man/besagnewell.stat.Rd | 2
DCluster-0.2-7/DCluster/man/bn.iscluster.Rd | 2
DCluster-0.2-7/DCluster/man/calculate.mle.Rd | 2
DCluster-0.2-7/DCluster/man/dcluster.test.Rd | 2
DCluster-0.2-7/DCluster/man/dean_test.Rd | 2
DCluster-0.2-7/DCluster/man/gearyc.Rd | 2
DCluster-0.2-7/DCluster/man/gearyc.boot.Rd | 4
DCluster-0.2-7/DCluster/man/gearyc.stat.Rd | 6
DCluster-0.2-7/DCluster/man/get.knclusters.Rd | 2
DCluster-0.2-7/DCluster/man/kn.iscluster.Rd | 25 ++-
DCluster-0.2-7/DCluster/man/kullnagar.Rd | 2
DCluster-0.2-7/DCluster/man/kullnagar.boot.Rd | 2
DCluster-0.2-7/DCluster/man/kullnagar.stat.Rd | 2
DCluster-0.2-7/DCluster/man/lognormalEB.Rd | 2
DCluster-0.2-7/DCluster/man/moranI.Rd | 2
DCluster-0.2-7/DCluster/man/moranI.boot.Rd | 2
DCluster-0.2-7/DCluster/man/moranI.stat.Rd | 2
DCluster-0.2-7/DCluster/man/observed.sim.Rd | 2
DCluster-0.2-7/DCluster/man/opgam.Rd | 3
DCluster-0.2-7/DCluster/man/opgam.iscluster.default.Rd | 2
DCluster-0.2-7/DCluster/man/pkg-internal.Rd | 2
DCluster-0.2-7/DCluster/man/pottwhitt.Rd | 2
DCluster-0.2-7/DCluster/man/pottwhitt.boot.Rd | 2
DCluster-0.2-7/DCluster/man/pottwhitt.stat.Rd | 2
DCluster-0.2-7/DCluster/man/rmultin.Rd | 2
DCluster-0.2-7/DCluster/man/stone.boot.Rd | 11 +
DCluster-0.2-7/DCluster/man/stone.stat.Rd | 2
DCluster-0.2-7/DCluster/man/tango.Rd | 2
DCluster-0.2-7/DCluster/man/tango.boot.Rd | 2
DCluster-0.2-7/DCluster/man/tango.stat.Rd | 2
DCluster-0.2-7/DCluster/man/whittermore.Rd | 2
DCluster-0.2-7/DCluster/man/whittermore.boot.Rd | 2
DCluster-0.2-7/DCluster/man/whittermore.stat.Rd | 2
46 files changed, 275 insertions(+), 161 deletions(-)
Title: Smoothing Splines for Large Samples
Diff between bigsplines versions 1.0-5 dated 2015-02-11 and 1.0-6 dated 2015-03-17
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Parametric predictors are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
ChangeLog | 28 ++
DESCRIPTION | 8
MD5 | 156 +++++++--------
R/bigspline.R | 209 +++++++++++---------
R/bigssa.R | 16 -
R/bigssg.R | 14 -
R/bigssp.R | 16 -
R/bigtps.R | 272 ++++++++++++++------------
R/binsamp.R | 26 +-
R/gcvcss.R | 8
R/gcvgss.R | 224 +++++++++++----------
R/gcvssa.R | 31 +-
R/gcvssg.R | 238 +++++++++++-----------
R/gcvssp.R | 22 +-
R/imagebar.R | 31 +-
R/lamcoef.R | 44 ++--
R/lamcoefg.R | 255 ++++++++++++------------
R/lamloop.R | 26 +-
R/lamloopg.R | 233 +++++++++++-----------
R/makeZtX.R | 36 +--
R/makeZtZ.R | 38 +--
R/makerkm.R | 69 +++---
R/makessa.R | 274 +++++++++++++-------------
R/makessg.R | 300 +++++++++++++++-------------
R/makessp.R | 286 ++++++++++++++-------------
R/nbmle.R | 8
R/pdsXty.R | 6
R/pinvsm.R | 6
R/postvar.R | 2
R/predict.bigspline.R | 106 +++++-----
R/predict.bigssa.R | 177 +++++++++--------
R/predict.bigssg.R | 196 ++++++++++--------
R/predict.bigssp.R | 165 ++++++++-------
R/predict.bigtps.R | 58 +++--
R/print.bigssa.R | 8
R/print.bigssg.R | 8
R/print.bigssp.R | 8
R/print.summary.bigspline.R | 6
R/print.summary.bigssa.R | 6
R/print.summary.bigssg.R | 6
R/print.summary.bigssp.R | 6
R/print.summary.bigtps.R | 6
R/remlri.R | 77 ++++---
R/remlvc.R | 86 ++++----
R/rkron.R | 15 -
R/smartssa.R | 173 ++++++++--------
R/smartssg.R | 191 +++++++++---------
R/smartssp.R | 20 -
R/ssadpm.R | 200 ++++++++++---------
R/ssawork.R | 399 +++++++++++++++++++++-----------------
R/ssblup.R | 12 -
R/ssgwork.R | 456 ++++++++++++++++++++++++--------------------
R/sspdpm.R | 215 ++++++++++----------
R/sspwork.R | 349 ++++++++++++++++++---------------
R/summary.bigspline.R | 40 ++-
R/summary.bigssa.R | 48 ++--
R/summary.bigssg.R | 119 ++++++-----
R/summary.bigssp.R | 48 ++--
R/summary.bigtps.R | 40 ++-
R/tcprod.R | 8
R/unifqsum.R | 5
R/unifqsumg.R | 2
man/bigspline.Rd | 34 +--
man/bigsplines-package.Rd | 4
man/bigssa.Rd | 87 ++++----
man/bigssg.Rd | 165 ++++++++-------
man/bigssp.Rd | 41 ++-
man/bigtps.Rd | 55 ++---
man/binsamp.Rd | 24 +-
man/imagebar.Rd | 36 ++-
man/makessa.Rd | 26 +-
man/makessg.Rd | 32 +--
man/makessp.Rd | 26 +-
man/predict.bigspline.Rd | 73 +++----
man/predict.bigssa.Rd | 60 +++--
man/predict.bigssg.Rd | 76 ++++---
man/predict.bigssp.Rd | 59 +++--
man/predict.bigtps.Rd | 75 ++++---
man/summary.Rd | 55 +++--
79 files changed, 3796 insertions(+), 3273 deletions(-)
Title: A Computational Tool for Astrochronology
Diff between astrochron versions 0.3.1 dated 2014-07-20 and 0.4.1 dated 2015-03-17
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers
astrochron-0.3.1/astrochron/R/FUNCTION-ar1_v4.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-ar1etp_v7.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-bandpass_v11.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-eAsmTrack.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-eAsm_v1a.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-eha_v12.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-etp_v5a.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-extract_v3.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-hilbert_v11.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-idPts_v7.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-iso_v6.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-lowpass_v9.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-lowspec_v12.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-mtm_v8.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-peak_v4.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-periodogram_v10.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-pl_v5.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-plotEha_v2.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-readMatrix.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-read_v22.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-strats_v4.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-traceFreq_v4.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-trackFreq_v6.R |only
astrochron-0.3.1/astrochron/R/FUNCTION-xplot.R |only
astrochron-0.4.1/astrochron/DESCRIPTION | 14
astrochron-0.4.1/astrochron/MD5 | 227 ++++++------
astrochron-0.4.1/astrochron/NAMESPACE | 12
astrochron-0.4.1/astrochron/R/FUNCTION-anchorTime_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-ar1_v6.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-ar1etp_v9.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-arcsinT_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-armaGen_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-asm_v10a.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-autoPlot_v7.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-bandpass_v13.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-bergerPeriods_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-cb_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-clipIt.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-constantSedrate_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-cosTaper_v8.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-cycles_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-delPts_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-demean_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-detrend_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-divTrend_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-dpssTaper_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-eAsmTrack_v2.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-eAsm_v2.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-eha_v15.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-etp_v6.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-extract_v5.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-flip.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-freq2sedrate_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-gausTaper_v7.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-getColor.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-getLaskar.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-hannTaper_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-headn_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-hilbert_v14.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-idPts_v9.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-integratePower_v7.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-iso_v8.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-linage.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-linterp_v7.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-logT_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-lowpass_v10.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-lowspec_v16.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-mtmAR_v6.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-mtmML96_v8.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-mtm_v12.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-noKernel_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-noLow_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-pad.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-peak_v5.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-periodogram_v12.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-plS.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-pl_v6.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-plotEha_v3.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-prewhiteAR1_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-prewhiteAR_v4.R | 4
astrochron-0.4.1/astrochron/R/FUNCTION-rankSeries.R | 4
astrochron-0.4.1/astrochron/R/FUNCTION-readMatrix_v3.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-read_v23.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-repl0_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-replEps_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-resample_v4.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-s.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-sedRamp_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-sedrate2time_v2.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-sortNave_v7.R | 6
astrochron-0.4.1/astrochron/R/FUNCTION-stepHeat_v3.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-strats_v9.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-surrogates.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-taner_v5.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-testPrecession.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-tones.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-traceFreq_v5.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-trackFreq_v7.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-trimAT_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-trim_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-trough.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-tune_v7a.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-writeCSV_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-writeT_v3.R | 2
astrochron-0.4.1/astrochron/R/FUNCTION-wtMean_v11.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-xplot_v3.R |only
astrochron-0.4.1/astrochron/R/FUNCTION-zoomIn_v2.R | 2
astrochron-0.4.1/astrochron/data/modelA.rda |binary
astrochron-0.4.1/astrochron/inst/CITATION | 6
astrochron-0.4.1/astrochron/man/ar1.Rd | 25 -
astrochron-0.4.1/astrochron/man/ar1etp.Rd | 44 +-
astrochron-0.4.1/astrochron/man/asm.Rd | 8
astrochron-0.4.1/astrochron/man/astrochron-package.Rd | 33 +
astrochron-0.4.1/astrochron/man/bandpass.Rd | 9
astrochron-0.4.1/astrochron/man/cb.Rd | 2
astrochron-0.4.1/astrochron/man/cycles.Rd | 5
astrochron-0.4.1/astrochron/man/eAsm.Rd | 7
astrochron-0.4.1/astrochron/man/eha.Rd | 2
astrochron-0.4.1/astrochron/man/etp.Rd | 40 +-
astrochron-0.4.1/astrochron/man/extract.Rd | 2
astrochron-0.4.1/astrochron/man/getLaskar.Rd |only
astrochron-0.4.1/astrochron/man/hilbert.Rd | 15
astrochron-0.4.1/astrochron/man/idPts.Rd | 8
astrochron-0.4.1/astrochron/man/integratePower.Rd |only
astrochron-0.4.1/astrochron/man/iso.Rd | 4
astrochron-0.4.1/astrochron/man/linage.Rd | 13
astrochron-0.4.1/astrochron/man/lowpass.Rd | 15
astrochron-0.4.1/astrochron/man/lowspec.Rd | 49 +-
astrochron-0.4.1/astrochron/man/mtm.Rd | 31 +
astrochron-0.4.1/astrochron/man/mtmAR.Rd |only
astrochron-0.4.1/astrochron/man/mtmML96.Rd |only
astrochron-0.4.1/astrochron/man/peak.Rd | 7
astrochron-0.4.1/astrochron/man/periodogram.Rd | 75 ++-
astrochron-0.4.1/astrochron/man/pl.Rd | 5
astrochron-0.4.1/astrochron/man/rankSeries.Rd | 3
astrochron-0.4.1/astrochron/man/read.Rd | 4
astrochron-0.4.1/astrochron/man/readMatrix.Rd | 6
astrochron-0.4.1/astrochron/man/sedRamp.Rd | 2
astrochron-0.4.1/astrochron/man/stepHeat.Rd |only
astrochron-0.4.1/astrochron/man/strats.Rd | 9
astrochron-0.4.1/astrochron/man/surrogates.Rd |only
astrochron-0.4.1/astrochron/man/taner.Rd |only
astrochron-0.4.1/astrochron/man/testPrecession.Rd |only
astrochron-0.4.1/astrochron/man/traceFreq.Rd | 10
astrochron-0.4.1/astrochron/man/trackFreq.Rd | 10
astrochron-0.4.1/astrochron/man/trough.Rd |only
astrochron-0.4.1/astrochron/man/wtMean.Rd |only
astrochron-0.4.1/astrochron/man/xplot.Rd | 14
astrochron-0.4.1/astrochron/src/trough_R.f |only
149 files changed, 524 insertions(+), 292 deletions(-)
Title: A Google Analytics API Client
Diff between RGA versions 0.2 dated 2015-02-02 and 0.2.1 dated 2015-03-17
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/shiny.R | 9 ++++++++-
R/url.R | 4 +++-
build/vignette.rds |binary
data/ga.rda |binary
inst/NEWS.Rd | 29 ++++++++++++++++++++---------
inst/doc/management-api.html | 4 ++--
inst/doc/metadata-api.Rmd | 20 ++++++++++----------
inst/doc/metadata-api.html | 24 ++++++++++++------------
inst/doc/reporting-api.html | 4 ++--
vignettes/metadata-api.Rmd | 20 ++++++++++----------
12 files changed, 82 insertions(+), 62 deletions(-)
Title: Clustering of Variables Around Latent Variables
Diff between ClustVarLV versions 1.3.1 dated 2014-09-04 and 1.3.2 dated 2015-03-17
Description: Functions for the clustering of variables around Latent Variables. Each cluster of variables, which may be defined as a local or directional cluster, is associated with a latent variable.
External variables measured on the same observations or/and additional information on the variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau
ClustVarLV-1.3.1/ClustVarLV/R/CLV-internal.R |only
ClustVarLV-1.3.1/ClustVarLV/src/Makevars |only
ClustVarLV-1.3.1/ClustVarLV/src/Makevars.win |only
ClustVarLV-1.3.2/ClustVarLV/DESCRIPTION | 21 +--
ClustVarLV-1.3.2/ClustVarLV/MD5 | 40 +++----
ClustVarLV-1.3.2/ClustVarLV/R/CLV.R | 49 +++++---
ClustVarLV-1.3.2/ClustVarLV/R/CLV_kmeans.R | 27 ++++
ClustVarLV-1.3.2/ClustVarLV/R/LCLV.R | 11 +-
ClustVarLV-1.3.2/ClustVarLV/R/consol_calcul.R | 25 ++--
ClustVarLV-1.3.2/ClustVarLV/R/consol_calcul_s.R | 8 -
ClustVarLV-1.3.2/ClustVarLV/R/gpmb_on_pc.R | 114 ++++++++++++++++++--
ClustVarLV-1.3.2/ClustVarLV/R/print.clv.r | 2
ClustVarLV-1.3.2/ClustVarLV/R/print.clvkmeans.r | 2
ClustVarLV-1.3.2/ClustVarLV/R/print.lclv.r | 2
ClustVarLV-1.3.2/ClustVarLV/man/CLV.Rd | 115 +++++++++------------
ClustVarLV-1.3.2/ClustVarLV/man/CLV_kmeans.Rd | 84 ++++++---------
ClustVarLV-1.3.2/ClustVarLV/man/LCLV.Rd | 104 +++++++-----------
ClustVarLV-1.3.2/ClustVarLV/man/descrip_gp.Rd | 13 +-
ClustVarLV-1.3.2/ClustVarLV/man/gpmb_on_pc.Rd | 30 ++---
ClustVarLV-1.3.2/ClustVarLV/man/print.clv.Rd | 7 -
ClustVarLV-1.3.2/ClustVarLV/man/print.clvkmeans.Rd | 7 -
ClustVarLV-1.3.2/ClustVarLV/man/print.lclv.Rd | 7 -
ClustVarLV-1.3.2/ClustVarLV/vignettes |only
23 files changed, 376 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-16 1.1
Title: Data Supporting the 'VGAM' Package
Diff between VGAMdata versions 0.9-5 dated 2014-11-04 and 0.9-7 dated 2015-03-17
Description: Data sets to accompany the VGAM package.
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology.
Author: Thomas W. Yee
Maintainer: Thomas Yee
DESCRIPTION | 10 +++---
MD5 | 74 ++++++++++++++++++++++++++-------------------------
NAMESPACE | 2 -
NEWS | 14 +++++++++
R/family.fishing.R | 2 -
data/bb.de.rda |binary
data/belcap.rda |binary
data/crashf.au.rda |binary
data/crime.us.rda |binary
data/datalist | 1
data/exam1.rda |binary
data/fibre15.rda |binary
data/fibre1dot5.rda |binary
data/gala.rda |binary
data/hued.rda |binary
data/huie.rda |binary
data/huse.rda |binary
data/oly12.rda |binary
data/prison.us.rda |binary
data/profs.nz.rda |binary
data/rainfall.rda |binary
data/rugby.rda |binary
data/rugby.ties.rda |binary
data/students.tw.rda |binary
data/trapO.rda |binary
data/tube10.rda |only
data/ugss.rda |binary
data/vtinpat.rda |binary
data/wffc.indiv.rda |binary
data/wffc.nc.rda |binary
data/wffc.rda |binary
data/wffc.teams.rda |binary
data/xs.nz.rda |binary
man/belcap.Rd | 10 ++++--
man/exam1.Rd | 3 +-
man/profs.nz.Rd | 17 +++++++++++
man/tube10.Rd |only
man/wffc.P2star.Rd | 4 ++
man/wffc.Rd | 5 ++-
39 files changed, 90 insertions(+), 52 deletions(-)
Title: Markov Beta and Gamma Processes for Modeling Hazard Rates
Diff between BGPhazard versions 1.1 dated 2014-09-09 and 1.2.2 dated 2015-03-17
Description: Computes the hazard rate estimate as described by Nieto-Barajas and Walker (2002) and Nieto-Barajas (2003).
Author: L. E. Nieto-Barajas and J. A. Garcia Bueno
Maintainer: Jose Antonio Garcia Bueno
BGPhazard-1.1/BGPhazard/R/CGaPrU.R |only
BGPhazard-1.1/BGPhazard/R/CGaTao.R |only
BGPhazard-1.1/BGPhazard/R/CGaUpdC.R |only
BGPhazard-1.1/BGPhazard/R/CGaUpdU.R |only
BGPhazard-1.1/BGPhazard/R/CUpdLambda.R |only
BGPhazard-1.1/BGPhazard/man/CGaPrU.Rd |only
BGPhazard-1.1/BGPhazard/man/CGaTao.Rd |only
BGPhazard-1.1/BGPhazard/man/CGaUpdC.Rd |only
BGPhazard-1.1/BGPhazard/man/CGaUpdU.Rd |only
BGPhazard-1.1/BGPhazard/man/CUpdLambda.Rd |only
BGPhazard-1.2.2/BGPhazard/DESCRIPTION | 18 --
BGPhazard-1.2.2/BGPhazard/MD5 | 76 ++++----
BGPhazard-1.2.2/BGPhazard/NAMESPACE | 2
BGPhazard-1.2.2/BGPhazard/R/BePloth.R | 22 +-
BGPhazard-1.2.2/BGPhazard/R/CGaM.R | 2
BGPhazard-1.2.2/BGPhazard/R/CGaMRes.R | 8
BGPhazard-1.2.2/BGPhazard/R/CGaN.R | 2
BGPhazard-1.2.2/BGPhazard/R/CGaPloth.R | 22 +-
BGPhazard-1.2.2/BGPhazard/R/GaPloth.R | 20 +-
BGPhazard-1.2.2/BGPhazard/R/GaTao.R | 1
BGPhazard-1.2.2/BGPhazard/R/PlotTheta.R | 27 ++-
BGPhazard-1.2.2/BGPhazard/build/vignette.rds |binary
BGPhazard-1.2.2/BGPhazard/data |only
BGPhazard-1.2.2/BGPhazard/inst/doc/BGPhazard.R | 58 ++----
BGPhazard-1.2.2/BGPhazard/inst/doc/BGPhazard.Rnw | 34 +---
BGPhazard-1.2.2/BGPhazard/inst/doc/BGPhazard.pdf |binary
BGPhazard-1.2.2/BGPhazard/man/BGPhazard-package.Rd | 85 ++++++++--
BGPhazard-1.2.2/BGPhazard/man/BeMRes.Rd | 29 ++-
BGPhazard-1.2.2/BGPhazard/man/BePlotDiag.Rd | 25 ++
BGPhazard-1.2.2/BGPhazard/man/BePloth.Rd | 24 +-
BGPhazard-1.2.2/BGPhazard/man/CGaM.Rd | 4
BGPhazard-1.2.2/BGPhazard/man/CGaMRes.Rd | 56 ++++--
BGPhazard-1.2.2/BGPhazard/man/CGaN.Rd | 4
BGPhazard-1.2.2/BGPhazard/man/CGaPlotDiag.Rd | 18 +-
BGPhazard-1.2.2/BGPhazard/man/CGaPloth.Rd | 42 +++-
BGPhazard-1.2.2/BGPhazard/man/CGaPred.Rd | 16 +
BGPhazard-1.2.2/BGPhazard/man/GaMRes.Rd | 31 ++-
BGPhazard-1.2.2/BGPhazard/man/GaPlotDiag.Rd | 25 ++
BGPhazard-1.2.2/BGPhazard/man/GaPloth.Rd | 24 +-
BGPhazard-1.2.2/BGPhazard/man/PlotTheta.Rd | 33 ++-
BGPhazard-1.2.2/BGPhazard/man/gehan.Rd |only
BGPhazard-1.2.2/BGPhazard/man/leukemiaFZ.Rd |only
BGPhazard-1.2.2/BGPhazard/man/psych.Rd |only
BGPhazard-1.2.2/BGPhazard/vignettes/BGPhazard-concordance.tex |only
BGPhazard-1.2.2/BGPhazard/vignettes/BGPhazard.Rnw | 34 +---
BGPhazard-1.2.2/BGPhazard/vignettes/BGPhazard.tex |only
46 files changed, 447 insertions(+), 295 deletions(-)
Title: A Most Informative Histogram-Like Model
Diff between histmdl versions 0.3-2 dated 2015-03-10 and 0.4-1 dated 2015-03-16
Description: Using the MDL principle, it is possible to estimate
parameters for a histogram-like model. The package contains
the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen
histmdl-0.3-2/histmdl/build |only
histmdl-0.3-2/histmdl/inst |only
histmdl-0.3-2/histmdl/vignettes |only
histmdl-0.4-1/histmdl/DESCRIPTION | 8 ++++----
histmdl-0.4-1/histmdl/MD5 | 12 +++---------
histmdl-0.4-1/histmdl/R/histmdl.R | 9 ++++++---
histmdl-0.4-1/histmdl/man/histmdl-package.Rd | 4 ++--
7 files changed, 15 insertions(+), 18 deletions(-)
Title: Comparing Restricted Mean Survival Time
Diff between survRM2 versions 1.0 dated 2015-02-05 and 1.0-1 dated 2015-03-16
Description: Performs two-sample comparisons using the restricted mean survival time (RMST) as a summary measure of the survival time distribution. Three kinds of between-group contrast metrics (i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It performs an ANCOVA-type covariate adjustment as well as unadjusted analyses for those measures.
Author: Hajime Uno, Lu Tian, Angel Cronin, Chakib Battioui
Maintainer: Hajime Uno
survRM2-1.0-1/survRM2/DESCRIPTION | 8 +++----
survRM2-1.0-1/survRM2/MD5 | 18 ++++++++--------
survRM2-1.0-1/survRM2/R/rmst2-ver002.R | 2 -
survRM2-1.0-1/survRM2/build/vignette.rds |binary
survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.R |only
survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.Rnw |only
survRM2-1.0-1/survRM2/inst/doc/survRM2-vignette3-1.pdf |only
survRM2-1.0-1/survRM2/man/rmst2.Rd | 2 -
survRM2-1.0-1/survRM2/man/survRM2-package.Rd | 4 +--
survRM2-1.0-1/survRM2/vignettes/survRM2-vignette3-1.Rnw |only
survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.R |only
survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.Rnw |only
survRM2-1.0/survRM2/inst/doc/survRM2-vignette3.pdf |only
survRM2-1.0/survRM2/vignettes/survRM2-vignette3.Rnw |only
14 files changed, 17 insertions(+), 17 deletions(-)
Title: Design and Analysis of Mixture Experiments
Diff between mixexp versions 1.1.9 dated 2014-12-13 and 1.2.1 dated 2015-03-16
Description: Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson [aut, cre],
Cameron Willden [aut],
Greg Piepel [ctb]
Maintainer: John Lawson
mixexp-1.1.9/mixexp/R/ModelPlot.R |only
mixexp-1.2.1/mixexp/DESCRIPTION | 27 -
mixexp-1.2.1/mixexp/MD5 | 62 +--
mixexp-1.2.1/mixexp/NAMESPACE | 20 -
mixexp-1.2.1/mixexp/R/DesignPoints.R | 30 -
mixexp-1.2.1/mixexp/R/EffPlot.R | 16
mixexp-1.2.1/mixexp/R/MixModel.R | 162 ++++++---
mixexp-1.2.1/mixexp/R/MixturePlot.R | 21 -
mixexp-1.2.1/mixexp/R/ModelEff.R | 518 ++++++++++++++++++++++--------
mixexp-1.2.1/mixexp/R/ModelPLot.R |only
mixexp-1.2.1/mixexp/R/SLD.R | 2
mixexp-1.2.1/mixexp/R/cubic.R | 6
mixexp-1.2.1/mixexp/data/Burn.rda |binary
mixexp-1.2.1/mixexp/data/SneeMq.rda |binary
mixexp-1.2.1/mixexp/data/conmx.rda |binary
mixexp-1.2.1/mixexp/data/etch.rda |only
mixexp-1.2.1/mixexp/data/fishp.rda |only
mixexp-1.2.1/mixexp/man/Burn.Rd | 11
mixexp-1.2.1/mixexp/man/DesignPoints.Rd | 23 -
mixexp-1.2.1/mixexp/man/EffPlot.Rd | 20 -
mixexp-1.2.1/mixexp/man/Eflags.Rd | 2
mixexp-1.2.1/mixexp/man/Fillv.Rd | 4
mixexp-1.2.1/mixexp/man/MixModel.Rd | 35 +-
mixexp-1.2.1/mixexp/man/MixturePlot.Rd | 22 -
mixexp-1.2.1/mixexp/man/ModelEff.Rd | 130 +++----
mixexp-1.2.1/mixexp/man/ModelPlot.Rd | 80 ++--
mixexp-1.2.1/mixexp/man/SLD.Rd | 2
mixexp-1.2.1/mixexp/man/SneeMq.Rd | 2
mixexp-1.2.1/mixexp/man/Vertcen.Rd | 2
mixexp-1.2.1/mixexp/man/Xvert.Rd | 4
mixexp-1.2.1/mixexp/man/crvtave.Rd | 2
mixexp-1.2.1/mixexp/man/cubic.Rd | 6
mixexp-1.2.1/mixexp/man/etch.Rd |only
mixexp-1.2.1/mixexp/man/fishp.Rd |only
mixexp-1.2.1/mixexp/man/mixexp-package.Rd | 15
35 files changed, 768 insertions(+), 456 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Diff between marked versions 1.1.6 dated 2014-06-17 and 1.1.8 dated 2015-03-16
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake
Maintainer: Jeff Laake
marked-1.1.6/marked/R/compute_matrices.r |only
marked-1.1.6/marked/man/cjs_dmat.Rd |only
marked-1.1.8/marked/DESCRIPTION | 25 -
marked-1.1.8/marked/MD5 | 200 ++++----
marked-1.1.8/marked/NAMESPACE | 14
marked-1.1.8/marked/NEWS | 51 ++
marked-1.1.8/marked/R/HMMLikelihood.r | 307 ++-----------
marked-1.1.8/marked/R/HMMutilities.r |only
marked-1.1.8/marked/R/Observation_functions.r | 46 +-
marked-1.1.8/marked/R/RHMMLikelihood.r |only
marked-1.1.8/marked/R/Transition_functions.r | 50 ++
marked-1.1.8/marked/R/cjs.R | 29 -
marked-1.1.8/marked/R/cjs.hessian.r | 2
marked-1.1.8/marked/R/cjs.lnl.r | 88 ++-
marked-1.1.8/marked/R/coef.r |only
marked-1.1.8/marked/R/compute.real.R | 24 -
marked-1.1.8/marked/R/create.dm.R | 5
marked-1.1.8/marked/R/create.dmdf.R | 148 +++---
marked-1.1.8/marked/R/crm.R | 140 +++---
marked-1.1.8/marked/R/crm.wrapper.R | 160 ++++++-
marked-1.1.8/marked/R/hmmDemo.r | 191 ++------
marked-1.1.8/marked/R/js.r | 5
marked-1.1.8/marked/R/make.design.data.R | 3
marked-1.1.8/marked/R/marked-package.R | 77 ++-
marked-1.1.8/marked/R/mscjs.r | 28 +
marked-1.1.8/marked/R/omega.r | 1
marked-1.1.8/marked/R/predict.crm.r | 7
marked-1.1.8/marked/R/print.crm.r | 66 --
marked-1.1.8/marked/R/probitCJS.R | 242 ++++++----
marked-1.1.8/marked/R/process.ch.R | 1
marked-1.1.8/marked/R/process.data.R | 43 +
marked-1.1.8/marked/R/set.initial.r | 8
marked-1.1.8/marked/R/set_mvms.r | 100 ++++
marked-1.1.8/marked/R/setup.model.R | 21
marked-1.1.8/marked/R/setup.parameters.R | 2
marked-1.1.8/marked/build/vignette.rds |binary
marked-1.1.8/marked/data/mstrata.rda |only
marked-1.1.8/marked/inst/CITATION |only
marked-1.1.8/marked/inst/cjs.tpl | 13
marked-1.1.8/marked/inst/cjs_reml.tpl | 15
marked-1.1.8/marked/inst/cjsre.tpl | 16
marked-1.1.8/marked/inst/doc/markedVignette.R | 2
marked-1.1.8/marked/inst/doc/markedVignette.pdf |binary
marked-1.1.8/marked/inst/models.txt | 2
marked-1.1.8/marked/inst/multistate.tpl | 2
marked-1.1.8/marked/inst/parameters.txt | 89 ++-
marked-1.1.8/marked/man/HMMLikelihood.Rd | 119 +----
marked-1.1.8/marked/man/Phi.mean.Rd | 25 -
marked-1.1.8/marked/man/R_HMMLikelihood.Rd | 69 ---
marked-1.1.8/marked/man/backward_prob.Rd |only
marked-1.1.8/marked/man/cjs.Rd | 133 ++---
marked-1.1.8/marked/man/cjs.accumulate.Rd | 31 -
marked-1.1.8/marked/man/cjs.hessian.Rd | 11
marked-1.1.8/marked/man/cjs.initial.Rd | 15
marked-1.1.8/marked/man/cjs.lnl.Rd | 76 +--
marked-1.1.8/marked/man/cjs_delta.Rd | 26 -
marked-1.1.8/marked/man/cjs_gamma.Rd | 22
marked-1.1.8/marked/man/coef.crm.Rd |only
marked-1.1.8/marked/man/compute.real.Rd | 77 +--
marked-1.1.8/marked/man/compute_matrices.Rd | 14
marked-1.1.8/marked/man/convert.link.to.real.Rd | 33 -
marked-1.1.8/marked/man/create.dm.Rd | 64 +-
marked-1.1.8/marked/man/create.dmdf.Rd | 429 +++++++++----------
marked-1.1.8/marked/man/create.fixed.matrix.Rd | 6
marked-1.1.8/marked/man/create.links.Rd | 17
marked-1.1.8/marked/man/crm.Rd | 469 +++++++++------------
marked-1.1.8/marked/man/crm.wrapper.Rd | 101 ++--
marked-1.1.8/marked/man/deriv_inverse.link.Rd | 32 -
marked-1.1.8/marked/man/dipper.Rd | 87 +--
marked-1.1.8/marked/man/fix.parameters.Rd | 22
marked-1.1.8/marked/man/function.wrapper.Rd | 25 -
marked-1.1.8/marked/man/global_decode.Rd |only
marked-1.1.8/marked/man/hmmDemo.Rd | 99 +---
marked-1.1.8/marked/man/inverse.link.Rd | 53 +-
marked-1.1.8/marked/man/js.Rd | 121 ++---
marked-1.1.8/marked/man/js.accumulate.Rd | 31 -
marked-1.1.8/marked/man/js.hessian.Rd | 11
marked-1.1.8/marked/man/js.lnl.Rd | 63 +-
marked-1.1.8/marked/man/local_decode.Rd |only
marked-1.1.8/marked/man/make.design.data.Rd | 104 +---
marked-1.1.8/marked/man/merge_design.covariates.Rd | 73 +--
marked-1.1.8/marked/man/mixed.model.admb.Rd | 70 +--
marked-1.1.8/marked/man/mscjs.Rd | 118 ++---
marked-1.1.8/marked/man/mstrata.Rd |only
marked-1.1.8/marked/man/mvms_design_data.Rd |only
marked-1.1.8/marked/man/mvms_dmat.Rd |only
marked-1.1.8/marked/man/omega.Rd | 15
marked-1.1.8/marked/man/predict.crm.Rd | 44 -
marked-1.1.8/marked/man/print.crm.Rd | 24 -
marked-1.1.8/marked/man/print.crmlist.Rd |only
marked-1.1.8/marked/man/probitCJS.Rd | 104 +++-
marked-1.1.8/marked/man/proc.form.Rd | 17
marked-1.1.8/marked/man/process.ch.Rd | 47 --
marked-1.1.8/marked/man/process.data.Rd | 331 ++++++--------
marked-1.1.8/marked/man/resight.matrix.Rd | 26 -
marked-1.1.8/marked/man/set.fixed.Rd | 12
marked-1.1.8/marked/man/set.initial.Rd | 11
marked-1.1.8/marked/man/set.scale.Rd | 17
marked-1.1.8/marked/man/set_mvms.Rd | 42 -
marked-1.1.8/marked/man/setup.model.Rd | 62 +-
marked-1.1.8/marked/man/setup.parameters.Rd | 98 +---
marked-1.1.8/marked/man/simHMM.Rd | 67 +--
marked-1.1.8/marked/man/splitCH.Rd | 35 -
marked-1.1.8/marked/man/tagloss.Rd | 75 +--
marked-1.1.8/marked/man/valid.parameters.Rd | 15
marked-1.1.8/marked/src/hmm_like.f | 8
marked-1.1.8/marked/src/msgamma.f | 7
marked-1.1.8/marked/src/mvmsdmat.f |only
marked-1.1.8/marked/src/umsdmat.f | 2
109 files changed, 2936 insertions(+), 2992 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10-2 dated 2015-02-09 and 0.9.11 dated 2015-03-16
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
BayesFactor-0.9.10-2/BayesFactor/R/debug.R |only
BayesFactor-0.9.10-2/BayesFactor/src/BFPCL.h |only
BayesFactor-0.9.10-2/BayesFactor/src/Makevars |only
BayesFactor-0.9.10-2/BayesFactor/src/common.c |only
BayesFactor-0.9.10-2/BayesFactor/src/debug.c |only
BayesFactor-0.9.10-2/BayesFactor/src/linearReg.c |only
BayesFactor-0.9.10-2/BayesFactor/src/matSums.cpp |only
BayesFactor-0.9.10-2/BayesFactor/src/matrix.c |only
BayesFactor-0.9.10-2/BayesFactor/src/nWayAOV.c |only
BayesFactor-0.9.10-2/BayesFactor/src/oneWayAOV.c |only
BayesFactor-0.9.11/BayesFactor/DESCRIPTION | 16
BayesFactor-0.9.11/BayesFactor/MD5 | 120 ++--
BayesFactor-0.9.11/BayesFactor/NAMESPACE | 41 +
BayesFactor-0.9.11/BayesFactor/NEWS | 13
BayesFactor-0.9.11/BayesFactor/R/BayesFactorPCL-package.R | 2
BayesFactor-0.9.11/BayesFactor/R/RcppExports.R | 32 +
BayesFactor-0.9.11/BayesFactor/R/aaClasses.R | 49 +
BayesFactor-0.9.11/BayesFactor/R/aaGenerics.R | 35 +
BayesFactor-0.9.11/BayesFactor/R/anovaBF.R | 4
BayesFactor-0.9.11/BayesFactor/R/checkCallback.R |only
BayesFactor-0.9.11/BayesFactor/R/checking.R | 6
BayesFactor-0.9.11/BayesFactor/R/common.R | 15
BayesFactor-0.9.11/BayesFactor/R/contingency.R | 4
BayesFactor-0.9.11/BayesFactor/R/gaussApproxAOV.R | 299 +---------
BayesFactor-0.9.11/BayesFactor/R/generalTestBF.R | 4
BayesFactor-0.9.11/BayesFactor/R/meta-ttest-utility.R | 64 +-
BayesFactor-0.9.11/BayesFactor/R/methods-BFBayesFactor.R | 12
BayesFactor-0.9.11/BayesFactor/R/methods-BFlinearModel-compare.R | 5
BayesFactor-0.9.11/BayesFactor/R/methods-BFmodelSample.R | 9
BayesFactor-0.9.11/BayesFactor/R/methods-BFodds.R |only
BayesFactor-0.9.11/BayesFactor/R/methods-BFprobability.R |only
BayesFactor-0.9.11/BayesFactor/R/model.matrix.R | 7
BayesFactor-0.9.11/BayesFactor/R/nWayAOV-utility.R | 131 ++--
BayesFactor-0.9.11/BayesFactor/R/nWayAOV.R | 225 ++-----
BayesFactor-0.9.11/BayesFactor/R/newPriorOdds.R |only
BayesFactor-0.9.11/BayesFactor/R/oneWayAOV-utility.R | 43 -
BayesFactor-0.9.11/BayesFactor/R/proportionBF.R | 4
BayesFactor-0.9.11/BayesFactor/R/regressionBF-utility.R | 48 -
BayesFactor-0.9.11/BayesFactor/R/regressionBF.R | 6
BayesFactor-0.9.11/BayesFactor/R/ttest-utility.R | 7
BayesFactor-0.9.11/BayesFactor/R/ttestBF.R | 2
BayesFactor-0.9.11/BayesFactor/build/vignette.rds |binary
BayesFactor-0.9.11/BayesFactor/inst/doc/compare_lme4.html | 74 +-
BayesFactor-0.9.11/BayesFactor/inst/doc/index.Rmd | 2
BayesFactor-0.9.11/BayesFactor/inst/doc/index.html | 1
BayesFactor-0.9.11/BayesFactor/inst/doc/manual.html | 246 ++++----
BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.R |only
BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.Rmd |only
BayesFactor-0.9.11/BayesFactor/inst/doc/odds_probs.html |only
BayesFactor-0.9.11/BayesFactor/inst/doc/priors.html | 18
BayesFactor-0.9.11/BayesFactor/man/BFBayesFactor-class.Rd | 3
BayesFactor-0.9.11/BayesFactor/man/BFodds-class.Rd |only
BayesFactor-0.9.11/BayesFactor/man/BFprobability-class.Rd |only
BayesFactor-0.9.11/BayesFactor/man/BayesFactor-package.Rd | 2
BayesFactor-0.9.11/BayesFactor/man/as.BFprobability.Rd |only
BayesFactor-0.9.11/BayesFactor/man/extractOdds-methods.Rd |only
BayesFactor-0.9.11/BayesFactor/man/extractProbabilities-methods.Rd |only
BayesFactor-0.9.11/BayesFactor/man/nWayAOV.Rd | 42 -
BayesFactor-0.9.11/BayesFactor/man/newPriorOdds.Rd |only
BayesFactor-0.9.11/BayesFactor/man/priorLogodds-method.Rd |only
BayesFactor-0.9.11/BayesFactor/man/priorOdds-method.Rd |only
BayesFactor-0.9.11/BayesFactor/man/recompute-methods.Rd | 6
BayesFactor-0.9.11/BayesFactor/src/RcppExports.cpp | 171 +++++
BayesFactor-0.9.11/BayesFactor/src/bfcommon.h | 21
BayesFactor-0.9.11/BayesFactor/src/dinvgamma.cpp |only
BayesFactor-0.9.11/BayesFactor/src/jzs_Gauss_approx_aov.cpp |only
BayesFactor-0.9.11/BayesFactor/src/jzs_Gibbs.cpp |only
BayesFactor-0.9.11/BayesFactor/src/jzs_bf_samplers.cpp |only
BayesFactor-0.9.11/BayesFactor/src/jzs_marg_like.cpp |only
BayesFactor-0.9.11/BayesFactor/src/linearRegGibbsRcpp.cpp |only
BayesFactor-0.9.11/BayesFactor/src/logDeterminant.cpp |only
BayesFactor-0.9.11/BayesFactor/src/metattest.cpp | 2
BayesFactor-0.9.11/BayesFactor/src/proportion.cpp | 2
BayesFactor-0.9.11/BayesFactor/src/rmvnorm.cpp |only
BayesFactor-0.9.11/BayesFactor/src/ttestIndepRcpp.cpp | 18
BayesFactor-0.9.11/BayesFactor/src/ttestRcpp.cpp | 19
BayesFactor-0.9.11/BayesFactor/vignettes/index.Rmd | 2
BayesFactor-0.9.11/BayesFactor/vignettes/odds_probs.Rmd |only
78 files changed, 990 insertions(+), 842 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Diff between zoo versions 1.7-11 dated 2014-02-27 and 1.7-12 dated 2015-03-16
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre],
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Felix Andrews [ctb]
Maintainer: Achim Zeileis
zoo-1.7-11/zoo/src/zoo.h |only
zoo-1.7-12/zoo/DESCRIPTION | 10 -
zoo-1.7-12/zoo/MD5 | 91 +++++++--------
zoo-1.7-12/zoo/NAMESPACE | 13 ++
zoo-1.7-12/zoo/NEWS | 22 +++
zoo-1.7-12/zoo/R/MATCH.R | 4
zoo-1.7-12/zoo/R/ORDER.R | 1
zoo-1.7-12/zoo/R/as.zoo.R | 27 +---
zoo-1.7-12/zoo/R/as.zoo.tis.R | 27 +---
zoo-1.7-12/zoo/R/coredata.R | 2
zoo-1.7-12/zoo/R/ggplot2.zoo.R | 22 +--
zoo-1.7-12/zoo/R/index.R | 4
zoo-1.7-12/zoo/R/na.StructTS.R | 2
zoo-1.7-12/zoo/R/na.fill.R | 6 -
zoo-1.7-12/zoo/R/plot.zoo.R | 14 +-
zoo-1.7-12/zoo/R/read.zoo.R | 38 ++++--
zoo-1.7-12/zoo/R/xyplot.zoo.R | 2
zoo-1.7-12/zoo/R/yearmon.R | 10 -
zoo-1.7-12/zoo/R/yearqtr.R | 10 -
zoo-1.7-12/zoo/R/zoo.R | 19 ++-
zoo-1.7-12/zoo/R/zooreg.R | 4
zoo-1.7-12/zoo/build/vignette.rds |binary
zoo-1.7-12/zoo/inst/doc/zoo-design.pdf |binary
zoo-1.7-12/zoo/inst/doc/zoo-faq.pdf |binary
zoo-1.7-12/zoo/inst/doc/zoo-quickref.R | 1
zoo-1.7-12/zoo/inst/doc/zoo-quickref.Rnw | 6 -
zoo-1.7-12/zoo/inst/doc/zoo-quickref.pdf |binary
zoo-1.7-12/zoo/inst/doc/zoo-read.Rnw | 2
zoo-1.7-12/zoo/inst/doc/zoo-read.pdf |binary
zoo-1.7-12/zoo/inst/doc/zoo.R |only
zoo-1.7-12/zoo/inst/doc/zoo.Rnw | 35 +++--
zoo-1.7-12/zoo/inst/doc/zoo.pdf |binary
zoo-1.7-12/zoo/inst/include |only
zoo-1.7-12/zoo/man/na.StructTS.Rd | 4
zoo-1.7-12/zoo/man/plot.zoo.Rd | 31 +++++
zoo-1.7-12/zoo/man/read.zoo.Rd | 75 ++++++++----
zoo-1.7-12/zoo/man/rollapply.Rd | 23 +++
zoo-1.7-12/zoo/man/zoo.Rd | 4
zoo-1.7-12/zoo/src/Makevars |only
zoo-1.7-12/zoo/src/Makevars.win |only
zoo-1.7-12/zoo/src/init.c | 2
zoo-1.7-12/zoo/src/lag.c | 9 +
zoo-1.7-12/zoo/tests/Examples/zoo-Ex.Rout.save | 148 +++++++++++++++++++------
zoo-1.7-12/zoo/tests/bugfixes.R | 4
zoo-1.7-12/zoo/tests/bugfixes.Rout.save | 12 +-
zoo-1.7-12/zoo/vignettes/zoo-quickref.Rnw | 6 -
zoo-1.7-12/zoo/vignettes/zoo-read.Rnw | 2
zoo-1.7-12/zoo/vignettes/zoo.Rnw | 35 +++--
zoo-1.7-12/zoo/vignettes/zoo.bib | 2
49 files changed, 492 insertions(+), 237 deletions(-)
Title: Sure Independence Screening
Diff between SIS versions 0.7-4 dated 2014-08-01 and 0.7-5 dated 2015-03-16
Description: Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) and all of its variants in generalized linear models and the Cox proportional hazards model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
R/partialfits.R | 2 +-
data/leukemia.RData |binary
data/leukemia.test.RData |binary
data/leukemia.train.RData |binary
data/prostate.test.RData |binary
data/prostate.train.RData |binary
8 files changed, 14 insertions(+), 14 deletions(-)
Title: Regularized Categorical Effects/Categorical Effect
Modifiers/Continuous/Smooth Effects in GLMs
Diff between gvcm.cat versions 1.8 dated 2015-03-04 and 1.9 dated 2015-03-16
Description: Generalized structured regression models with regularized categorical effects, categorical effect modifiers, continuous effects and smooth effects.
Author: Margret Oelker
Maintainer: Margret Oelker
DESCRIPTION | 10 +++++-----
MD5 | 13 ++++++++-----
NAMESPACE | 6 ++----
R/a.R |only
R/gvcm.cat.flex.R |only
R/optimierung.R | 2 +-
inst/CITATION | 27 ++++++++++-----------------
man/gvcm.cat-internal.Rd | 1 +
man/gvcm.cat.flex.Rd |only
9 files changed, 27 insertions(+), 32 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Diff between plotROC versions 1.3 dated 2015-01-27 and 1.3.3 dated 2015-03-16
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 10 -
MD5 | 34 ++--
NEWS | 21 ++
R/ggroc.R | 122 ++++++++++----
R/interactive_roc.R | 92 ++++++-----
R/plot_journal_roc.R | 83 ++++++++--
inst/doc/examples.R | 147 ++++++++++++-----
inst/doc/examples.Rmd | 202 ++++++++++++++++--------
inst/doc/examples.html | 231 ++++++++++++++++------------
inst/shinyApp/server.R | 20 --
inst/shinyApp/shinyapps/sachsmc/plotROC.dcf | 2
inst/shinyApp/ui.R | 1
man/export_interactive_roc.Rd | 15 +
man/ggroc.Rd | 14 +
man/multi_ggroc.Rd | 21 +-
man/plot_interactive_roc.Rd | 6
man/plot_journal_roc.Rd | 14 +
vignettes/examples.Rmd | 202 ++++++++++++++++--------
18 files changed, 819 insertions(+), 418 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Diff between ChemoSpec versions 4.0-0 dated 2015-03-10 and 4.0.1 dated 2015-03-16
Description: A collection of functions for plotting spectra (NMR, IR, Raman) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA, model-based clustering and STOCSY analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette illustrating typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
DESCRIPTION | 19 ++--
MD5 | 74 +++++++++---------
NAMESPACE | 18 ----
NEWS | 5 +
R/baselineSpectra.R | 20 ++++
R/clupaSpectra.R | 14 ++-
R/coordProjCS.R | 18 ++--
R/corSpectra.R | 18 +++-
R/cv_pcaSpectra.R | 8 +
R/evalClusters.R | 12 +-
R/files2SpectraObject.R | 10 +-
R/groupNcolor.R | 15 ++-
R/hmapSpectra.R | 17 +++-
R/makeEllipsoid.R | 5 -
R/mclust3D.R | 16 ++-
R/mclustSpectra.R | 6 +
R/plotLoadings.R | 12 +-
R/plotScores3D.R | 14 ++-
R/plotScoresCor.R | 6 +
R/plotSpectraJS.R | 189 +++++++++++++++++++++++++----------------------
R/r_pcaSpectra.R | 6 +
R/readJDX.R | 12 +-
R/rowDist.R | 7 +
R/sampleDistSpectra.R | 6 -
R/surveySpectra.R | 24 +++--
inst/doc/ChemoSpec.R | 1
inst/doc/ChemoSpec.Rnw | 1
inst/doc/ChemoSpec.pdf |binary
man/ChemoSpec-package.Rd | 4
man/clupaSpectra.Rd | 2
man/coordProjCS.Rd | 40 ++++-----
man/evalClusters.Rd | 6 -
man/hmapSpectra.Rd | 4
man/mclust3D.Rd | 1
man/mclust3dSpectra.Rd | 2
man/mclustSpectra.Rd | 5 -
man/rowDist.Rd | 4
vignettes/ChemoSpec.Rnw | 1
38 files changed, 371 insertions(+), 251 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-86 dated 2015-03-15 and 0.5-87 dated 2015-03-16
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 10 ++++++++++
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/lextrB.R | 17 +++++++++++++++--
R/lextrW.R | 18 ++++++++++++++++--
inst/ChangeLog | 10 ++++++++++
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/sids.pdf |binary
10 files changed, 64 insertions(+), 17 deletions(-)
Title: Protocol Inspection and State Machine Analysis
Diff between PRISMA versions 0.2-3 dated 2015-03-03 and 0.2-5 dated 2015-03-16
Description: The PRISMA package is capable of loading and processing huge text
corpora processed with the sally toolbox (http://www.mlsec.org/sally/).
sally acts as a very fast preprocessor which splits the text files into
tokens or n-grams. These output files can then be read with the PRISMA
package which applies testing-based token selection and has some
replicate-aware, highly tuned non-negative matrix factorization and
principal component analysis implementation which allows the processing of
very big data sets even on desktop machines.
Author: Tammo Krueger, Nicole Kraemer
Maintainer: Tammo Krueger
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/prisma.R | 4 ++--
inst/doc/PRISMA.pdf |binary
man/corpusToPrisma.Rd | 10 ++++++----
5 files changed, 16 insertions(+), 14 deletions(-)
Title: R Based Genetic Algorithm
Diff between genalg versions 0.1.1.1 dated 2014-01-10 and 0.2.0 dated 2015-03-16
Description: R based genetic algorithm for binary and floating point
chromosomes.
Author: Egon Willighagen and Michel Ballings
Maintainer: Michel Ballings
genalg-0.1.1.1/genalg/COPYING |only
genalg-0.1.1.1/genalg/TODO |only
genalg-0.2.0/genalg/ChangeLog | 5 +++++
genalg-0.2.0/genalg/DESCRIPTION | 12 ++++++------
genalg-0.2.0/genalg/MD5 | 14 ++++++--------
genalg-0.2.0/genalg/NAMESPACE | 9 ++++-----
genalg-0.2.0/genalg/R/rbga.R | 4 +++-
genalg-0.2.0/genalg/man/rbga.Rd | 3 ++-
genalg-0.2.0/genalg/man/rbga.bin.Rd | 5 +++--
9 files changed, 29 insertions(+), 23 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Diff between choroplethr versions 2.1.1 dated 2014-12-11 and 3.0.0 dated 2015-03-16
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. choroplethr simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein
Maintainer: Ari Lamstein
choroplethr-2.1.1/choroplethr/R/admin1_data.R |only
choroplethr-2.1.1/choroplethr/R/choroplethr.R |only
choroplethr-2.1.1/choroplethr/R/choroplethr_acs.R |only
choroplethr-2.1.1/choroplethr/R/country_data.R |only
choroplethr-2.1.1/choroplethr/R/county_data.R |only
choroplethr-2.1.1/choroplethr/R/state_data.R |only
choroplethr-2.1.1/choroplethr/R/zip.R |only
choroplethr-2.1.1/choroplethr/R/zip_data.R |only
choroplethr-2.1.1/choroplethr/data/df_pop_zip.rdata |only
choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.R |only
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choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.html |only
choroplethr-2.1.1/choroplethr/inst/doc/e-country-choropleth.R |only
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choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.R |only
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choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.R |only
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choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.html |only
choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.R |only
choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.Rmd |only
choroplethr-2.1.1/choroplethr/inst/doc/h-animated-choropleths.html |only
choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.R |only
choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.Rmd |only
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choroplethr-2.1.1/choroplethr/inst/doc/j-creating-admin1-maps.R |only
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choroplethr-2.1.1/choroplethr/inst/doc/j-creating-admin1-maps.html |only
choroplethr-2.1.1/choroplethr/inst/tests/test-num_buckets.R |only
choroplethr-2.1.1/choroplethr/inst/tests/test-zip.R |only
choroplethr-2.1.1/choroplethr/man/ZipMap.Rd |only
choroplethr-2.1.1/choroplethr/man/df_pop_zip.Rd |only
choroplethr-2.1.1/choroplethr/vignettes/d-zip-map.Rmd |only
choroplethr-2.1.1/choroplethr/vignettes/e-country-choropleth.Rmd |only
choroplethr-2.1.1/choroplethr/vignettes/f-mapping-us-census-data.Rmd |only
choroplethr-2.1.1/choroplethr/vignettes/g-world-bank-data.Rmd |only
choroplethr-2.1.1/choroplethr/vignettes/h-animated-choropleths.Rmd |only
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choroplethr-2.1.1/choroplethr/vignettes/j-creating-admin1-maps.Rmd |only
choroplethr-3.0.0/choroplethr/DESCRIPTION | 19 -
choroplethr-3.0.0/choroplethr/MD5 | 178 ++++------
choroplethr-3.0.0/choroplethr/NAMESPACE | 9
choroplethr-3.0.0/choroplethr/NEWS | 11
choroplethr-3.0.0/choroplethr/R/acs.R |only
choroplethr-3.0.0/choroplethr/R/admin1.R | 10
choroplethr-3.0.0/choroplethr/R/choropleth.R | 28 -
choroplethr-3.0.0/choroplethr/R/choroplethr_animate.R | 8
choroplethr-3.0.0/choroplethr/R/choroplethr_wdi.R | 16
choroplethr-3.0.0/choroplethr/R/country.R | 16
choroplethr-3.0.0/choroplethr/R/county.R | 81 ++--
choroplethr-3.0.0/choroplethr/R/county_zoom.R | 74 ----
choroplethr-3.0.0/choroplethr/R/data.R |only
choroplethr-3.0.0/choroplethr/R/deprecated.R |only
choroplethr-3.0.0/choroplethr/R/state.R | 25 -
choroplethr-3.0.0/choroplethr/R/usa.R | 8
choroplethr-3.0.0/choroplethr/README.md | 7
choroplethr-3.0.0/choroplethr/build/vignette.rds |binary
choroplethr-3.0.0/choroplethr/data/df_pop_country.rdata |binary
choroplethr-3.0.0/choroplethr/data/df_president.rdata |binary
choroplethr-3.0.0/choroplethr/inst/doc/a-introduction.html | 2
choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.R | 8
choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.Rmd | 14
choroplethr-3.0.0/choroplethr/inst/doc/b-state-choropleth.html | 20 -
choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.R | 18 -
choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.Rmd | 27 +
choroplethr-3.0.0/choroplethr/inst/doc/c-county-choropleth.html | 34 +
choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.R |only
choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.Rmd |only
choroplethr-3.0.0/choroplethr/inst/doc/d-country-choropleth.html |only
choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.R |only
choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.Rmd |only
choroplethr-3.0.0/choroplethr/inst/doc/e-mapping-us-census-data.html |only
choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.R |only
choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.Rmd |only
choroplethr-3.0.0/choroplethr/inst/doc/f-world-bank-data.html |only
choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.R |only
choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.Rmd |only
choroplethr-3.0.0/choroplethr/inst/doc/g-animated-choropleths.html |only
choroplethr-3.0.0/choroplethr/inst/doc/h-creating-your-own-maps.R |only
choroplethr-3.0.0/choroplethr/inst/doc/h-creating-your-own-maps.Rmd |only
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choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.R |only
choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.Rmd |only
choroplethr-3.0.0/choroplethr/inst/doc/i-creating-admin1-maps.html |only
choroplethr-3.0.0/choroplethr/inst/tests/test-acs.R |only
choroplethr-3.0.0/choroplethr/inst/tests/test-country.R | 11
choroplethr-3.0.0/choroplethr/inst/tests/test-county.R | 12
choroplethr-3.0.0/choroplethr/inst/tests/test-num_colors.R |only
choroplethr-3.0.0/choroplethr/inst/tests/test-state.R | 4
choroplethr-3.0.0/choroplethr/man/Admin1Choropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/Choropleth.Rd |only
choroplethr-3.0.0/choroplethr/man/CountryChoropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/CountyChoropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/CountyZoomChoropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/StateChoropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/USAChoropleth.Rd | 5
choroplethr-3.0.0/choroplethr/man/admin1_choropleth.Rd | 11
choroplethr-3.0.0/choroplethr/man/choroplethr.Rd | 7
choroplethr-3.0.0/choroplethr/man/choroplethr_acs.Rd | 53 --
choroplethr-3.0.0/choroplethr/man/choroplethr_animate.Rd | 11
choroplethr-3.0.0/choroplethr/man/choroplethr_wdi.Rd | 15
choroplethr-3.0.0/choroplethr/man/country_choropleth.Rd | 13
choroplethr-3.0.0/choroplethr/man/county_choropleth.Rd | 54 +--
choroplethr-3.0.0/choroplethr/man/county_choropleth_acs.Rd |only
choroplethr-3.0.0/choroplethr/man/county_zoom_choropleth.Rd | 65 ---
choroplethr-3.0.0/choroplethr/man/df_japan_census.Rd | 3
choroplethr-3.0.0/choroplethr/man/df_pop_country.Rd | 3
choroplethr-3.0.0/choroplethr/man/df_pop_county.Rd | 3
choroplethr-3.0.0/choroplethr/man/df_pop_state.Rd | 3
choroplethr-3.0.0/choroplethr/man/df_president.Rd | 3
choroplethr-3.0.0/choroplethr/man/df_president_ts.Rd | 3
choroplethr-3.0.0/choroplethr/man/get_acs_data.Rd |only
choroplethr-3.0.0/choroplethr/man/get_acs_df.Rd | 48 --
choroplethr-3.0.0/choroplethr/man/state_choropleth.Rd | 22 -
choroplethr-3.0.0/choroplethr/man/state_choropleth_acs.Rd |only
choroplethr-3.0.0/choroplethr/man/zip_map.Rd | 42 --
choroplethr-3.0.0/choroplethr/tests/test-all.R | 6
choroplethr-3.0.0/choroplethr/vignettes/b-state-choropleth.Rmd | 14
choroplethr-3.0.0/choroplethr/vignettes/c-county-choropleth.Rmd | 27 +
choroplethr-3.0.0/choroplethr/vignettes/d-country-choropleth.Rmd |only
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choroplethr-3.0.0/choroplethr/vignettes/f-world-bank-data.Rmd |only
choroplethr-3.0.0/choroplethr/vignettes/g-animated-choropleths.Rmd |only
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127 files changed, 494 insertions(+), 582 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-83 dated 2015-01-16 and 0.5-86 dated 2015-03-15
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 118 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 8 +-
MD5 | 84 +++++++++++++++--------------
NAMESPACE | 5 +
R/autocov.R | 3 -
R/error.spsarlm.R | 49 +++++++++++------
R/jacobian_setup.R | 7 +-
R/lag.spsarlm.R | 110 ++++++++++++++++++++++-----------------
R/lextrB.R |only
R/lextrW.R |only
R/localmoran.exact.R | 2
R/moran.exact.R | 2
R/sacsarlm.R | 31 +++++++----
R/utils.R | 20 +++++--
build/vignette.rds |binary
data/oldcol.rda |binary
inst/ChangeLog | 118 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/CO69.R | 2
inst/doc/CO69.Rnw | 2
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/nb_igraph.Rmd | 13 ++--
inst/doc/nb_igraph.html | 16 ++---
inst/doc/sids.R | 1
inst/doc/sids.pdf |binary
man/COL.OLD.Rd | 6 +-
man/NY_data.Rd | 2
man/autocov_dist.Rd | 21 ++++---
man/baltimore.Rd | 2
man/boston.Rd | 2
man/columbus.Rd | 2
man/eire.Rd | 2
man/graphneigh.Rd | 11 +++
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man/lm.morantest.Rd | 2
man/nc.sids.Rd | 2
man/read.gal.Rd | 4 -
man/read.gwt2nb.Rd | 2
man/wheat.Rd | 2
src/eminmaxC.c |only
src/init.c | 5 +
src/spdep.h | 5 +
vignettes/CO69.Rnw | 2
vignettes/nb_igraph.Rmd | 13 ++--
45 files changed, 500 insertions(+), 176 deletions(-)
Title: Penalized Quantile Regression
Diff between rqPen versions 1.0 dated 2014-10-29 and 1.1 dated 2015-03-15
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood
Maintainer: Ben Sherwood
rqPen-1.0/rqPen/man/scad_1_deriv.Rd |only
rqPen-1.0/rqPen/man/scad_2_deriv.Rd |only
rqPen-1.1/rqPen/DESCRIPTION | 10 ++--
rqPen-1.1/rqPen/LICENSE | 2
rqPen-1.1/rqPen/MD5 | 19 +++-----
rqPen-1.1/rqPen/NAMESPACE | 2
rqPen-1.1/rqPen/NEWS |only
rqPen-1.1/rqPen/R/rqPen.R | 82 +++++++++++++++++++++++-------------
rqPen-1.1/rqPen/man/beta_plots.Rd | 2
rqPen-1.1/rqPen/man/cv.rq.pen.Rd | 6 +-
rqPen-1.1/rqPen/man/rq.lasso.fit.Rd | 4 -
rqPen-1.1/rqPen/man/rq.nc.fit.Rd | 4 -
12 files changed, 76 insertions(+), 55 deletions(-)
Title: R Code for Mark Analysis
Diff between RMark versions 2.1.9 dated 2014-10-06 and 2.1.12 dated 2015-03-15
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at (http://www.phidot.org/software/mark/downloads/)
but is not open source.
Author: Jeff Laake
Maintainer: Jeff Laake
RMark-2.1.12/RMark/DESCRIPTION | 23 -
RMark-2.1.12/RMark/MD5 | 311 ++++++++--------
RMark-2.1.12/RMark/NAMESPACE | 14
RMark-2.1.12/RMark/NEWS | 36 +
RMark-2.1.12/RMark/R/PIMS.R | 1
RMark-2.1.12/RMark/R/RMark-package.R | 64 ++-
RMark-2.1.12/RMark/R/TransitionMatrix.R | 7
RMark-2.1.12/RMark/R/add.design.data.R | 1
RMark-2.1.12/RMark/R/adjust.chat.R | 11
RMark-2.1.12/RMark/R/adjust.parameter.count.R | 1
RMark-2.1.12/RMark/R/convert.inp.r | 17
RMark-2.1.12/RMark/R/covariate.predictions.r | 37 +
RMark-2.1.12/RMark/R/create.mark.mcmc.R | 6
RMark-2.1.12/RMark/R/create.model.list.R | 1
RMark-2.1.12/RMark/R/deltamethod.r | 1
RMark-2.1.12/RMark/R/export.MARK.r | 62 ---
RMark-2.1.12/RMark/R/export.model.r | 2
RMark-2.1.12/RMark/R/extract.mark.output.R | 55 ++
RMark-2.1.12/RMark/R/fill.covariates.R | 4
RMark-2.1.12/RMark/R/get.real.R | 2
RMark-2.1.12/RMark/R/import.chdata.R | 3
RMark-2.1.12/RMark/R/make.design.data.R | 36 +
RMark-2.1.12/RMark/R/make.mark.model.R | 35 +
RMark-2.1.12/RMark/R/mark.R | 17
RMark-2.1.12/RMark/R/mark.wrapper.R | 7
RMark-2.1.12/RMark/R/mark.wrapper.parallel.r | 10
RMark-2.1.12/RMark/R/merge.design.covariates.r | 1
RMark-2.1.12/RMark/R/merge.mark.r | 4
RMark-2.1.12/RMark/R/model.average.list.r | 3
RMark-2.1.12/RMark/R/model.average.marklist.R | 3
RMark-2.1.12/RMark/R/model.table.R | 3
RMark-2.1.12/RMark/R/popan.r | 87 +++-
RMark-2.1.12/RMark/R/print.mark.R | 48 +-
RMark-2.1.12/RMark/R/print.summary.mark.R | 23 -
RMark-2.1.12/RMark/R/process.data.R | 5
RMark-2.1.12/RMark/R/read.mark.binary.R | 63 +--
RMark-2.1.12/RMark/R/read.mark.binary.linux.R | 73 +--
RMark-2.1.12/RMark/R/release.gof.R | 6
RMark-2.1.12/RMark/R/rerun.mark.R | 1
RMark-2.1.12/RMark/R/run.mark.model.R | 22 -
RMark-2.1.12/RMark/R/setup.model.R | 9
RMark-2.1.12/RMark/R/splitCH.r | 1
RMark-2.1.12/RMark/R/summary.mark.R | 19
RMark-2.1.12/RMark/R/utility.r | 82 ++++
RMark-2.1.12/RMark/R/var.components.R | 1
RMark-2.1.12/RMark/R/var.components.reml.r | 1
RMark-2.1.12/RMark/inst/DerivedPar.txt |only
RMark-2.1.12/RMark/inst/extdata/blackduck.txt |only
RMark-2.1.12/RMark/inst/extdata/blckduck.inp |only
RMark-2.1.12/RMark/inst/extdata/brownadt.inp |only
RMark-2.1.12/RMark/inst/extdata/brownie.inp |only
RMark-2.1.12/RMark/inst/extdata/donovan.7.inp |only
RMark-2.1.12/RMark/inst/extdata/donovan.8.inp |only
RMark-2.1.12/RMark/inst/extdata/edwardsandeberhardt.inp |only
RMark-2.1.12/RMark/inst/extdata/f_age.inp |only
RMark-2.1.12/RMark/inst/extdata/ld1.inp |only
RMark-2.1.12/RMark/inst/extdata/linear.inp |only
RMark-2.1.12/RMark/inst/extdata/m_age.inp |only
RMark-2.1.12/RMark/inst/extdata/mallardnestexample.inp |only
RMark-2.1.12/RMark/inst/extdata/ms_rdsimple1.inp |only
RMark-2.1.12/RMark/inst/extdata/mssurv.inp |only
RMark-2.1.12/RMark/inst/extdata/nicholsmsoccupancy.inp |only
RMark-2.1.12/RMark/inst/extdata/pass3mstrata5.inp |only
RMark-2.1.12/RMark/inst/extdata/rdsalamander.inp |only
RMark-2.1.12/RMark/inst/extdata/robust.inp |only
RMark-2.1.12/RMark/inst/models.txt | 196 +++++-----
RMark-2.1.12/RMark/man/ABeginnersGuide.Rd | 3
RMark-2.1.12/RMark/man/Blackduck.Rd | 5
RMark-2.1.12/RMark/man/Donovan.7.Rd | 9
RMark-2.1.12/RMark/man/Donovan.8.Rd | 6
RMark-2.1.12/RMark/man/IELogitNormalMR.Rd | 10
RMark-2.1.12/RMark/man/LogitNormalMR.Rd | 5
RMark-2.1.12/RMark/man/MS_popan.Rd |only
RMark-2.1.12/RMark/man/NicholsMSOccupancy.Rd | 4
RMark-2.1.12/RMark/man/PIMS.Rd | 4
RMark-2.1.12/RMark/man/PoissonMR.Rd | 4
RMark-2.1.12/RMark/man/Poisson_twoMR.Rd | 4
RMark-2.1.12/RMark/man/RDOccupancy.Rd | 6
RMark-2.1.12/RMark/man/RDSalamander.Rd | 4
RMark-2.1.12/RMark/man/TransitionMatrix.Rd | 10
RMark-2.1.12/RMark/man/Whatsnew.Rd | 3
RMark-2.1.12/RMark/man/add.design.data.Rd | 4
RMark-2.1.12/RMark/man/adjust.parameter.count.Rd | 4
RMark-2.1.12/RMark/man/adjust.value.Rd | 14
RMark-2.1.12/RMark/man/brownie.Rd | 4
RMark-2.1.12/RMark/man/cleanup.Rd | 3
RMark-2.1.12/RMark/man/coef.mark.Rd |only
RMark-2.1.12/RMark/man/collect.model.names.Rd | 3
RMark-2.1.12/RMark/man/collect.models.Rd | 3
RMark-2.1.12/RMark/man/compute.design.data.Rd | 3
RMark-2.1.12/RMark/man/compute.link.Rd | 3
RMark-2.1.12/RMark/man/compute.links.from.reals.Rd | 3
RMark-2.1.12/RMark/man/compute.real.Rd | 3
RMark-2.1.12/RMark/man/convert.inp.Rd | 8
RMark-2.1.12/RMark/man/convert.link.to.real.Rd | 3
RMark-2.1.12/RMark/man/covariate.predictions.Rd | 4
RMark-2.1.12/RMark/man/crdms.Rd | 19
RMark-2.1.12/RMark/man/create.mark.mcmc.Rd | 3
RMark-2.1.12/RMark/man/create.model.list.Rd | 4
RMark-2.1.12/RMark/man/deer.Rd | 4
RMark-2.1.12/RMark/man/deltamethod.special.Rd | 4
RMark-2.1.12/RMark/man/deriv_inverse.link.Rd | 3
RMark-2.1.12/RMark/man/dipper.Rd | 4
RMark-2.1.12/RMark/man/edwards.eberhardt.Rd | 4
RMark-2.1.12/RMark/man/example.data.Rd | 4
RMark-2.1.12/RMark/man/export.MARK.Rd | 65 ---
RMark-2.1.12/RMark/man/export.chdata.Rd | 3
RMark-2.1.12/RMark/man/export.model.Rd | 5
RMark-2.1.12/RMark/man/extract.indices.Rd | 4
RMark-2.1.12/RMark/man/extract.mark.output.Rd | 3
RMark-2.1.12/RMark/man/fill.covariates.Rd | 5
RMark-2.1.12/RMark/man/find.covariates.Rd | 3
RMark-2.1.12/RMark/man/get.link.Rd | 3
RMark-2.1.12/RMark/man/get.real.Rd | 5
RMark-2.1.12/RMark/man/import.chdata.Rd | 6
RMark-2.1.12/RMark/man/inverse.link.Rd | 3
RMark-2.1.12/RMark/man/killdeer.Rd | 4
RMark-2.1.12/RMark/man/larksparrow.Rd | 4
RMark-2.1.12/RMark/man/load.model.Rd | 3
RMark-2.1.12/RMark/man/make.design.data.Rd | 36 +
RMark-2.1.12/RMark/man/make.mark.model.Rd | 8
RMark-2.1.12/RMark/man/make.time.factor.Rd | 3
RMark-2.1.12/RMark/man/mallard.Rd | 6
RMark-2.1.12/RMark/man/mark.Rd | 9
RMark-2.1.12/RMark/man/mark.wrapper.Rd | 3
RMark-2.1.12/RMark/man/mark.wrapper.parallel.Rd | 6
RMark-2.1.12/RMark/man/mata.wald.Rd | 3
RMark-2.1.12/RMark/man/merge.mark.Rd | 6
RMark-2.1.12/RMark/man/merge_design.covariates.Rd | 4
RMark-2.1.12/RMark/man/model.average.Rd | 3
RMark-2.1.12/RMark/man/model.average.list.Rd | 4
RMark-2.1.12/RMark/man/model.average.marklist.Rd | 4
RMark-2.1.12/RMark/man/model.table.Rd | 4
RMark-2.1.12/RMark/man/mstrata.Rd | 10
RMark-2.1.12/RMark/man/popan.derived.Rd | 4
RMark-2.1.12/RMark/man/print.mark.Rd | 14
RMark-2.1.12/RMark/man/print.marklist.Rd |only
RMark-2.1.12/RMark/man/print.summary.mark.Rd |only
RMark-2.1.12/RMark/man/process.data.Rd | 3
RMark-2.1.12/RMark/man/read.mark.binary.Rd | 7
RMark-2.1.12/RMark/man/release.gof.Rd | 4
RMark-2.1.12/RMark/man/remove.mark.Rd | 3
RMark-2.1.12/RMark/man/rerun.mark.Rd | 4
RMark-2.1.12/RMark/man/robust.Rd | 4
RMark-2.1.12/RMark/man/run.mark.model.Rd | 4
RMark-2.1.12/RMark/man/run.models.Rd | 3
RMark-2.1.12/RMark/man/salamander.Rd | 4
RMark-2.1.12/RMark/man/setup.model.Rd | 3
RMark-2.1.12/RMark/man/setup.parameters.Rd | 3
RMark-2.1.12/RMark/man/splitCH.Rd | 4
RMark-2.1.12/RMark/man/store.Rd | 3
RMark-2.1.12/RMark/man/strip.comments.Rd | 3
RMark-2.1.12/RMark/man/summary.mark.Rd | 9
RMark-2.1.12/RMark/man/summary_ch.Rd | 3
RMark-2.1.12/RMark/man/valid.parameters.Rd | 3
RMark-2.1.12/RMark/man/var.components.Rd | 4
RMark-2.1.12/RMark/man/var.components.reml.Rd | 4
RMark-2.1.12/RMark/man/weta.Rd | 4
RMark-2.1.12/RMark/man/wwdo.popan.Rd | 4
RMark-2.1.9/RMark/inst/extdata/BLCKDUCK.INP |only
RMark-2.1.9/RMark/inst/extdata/BROWNADT.INP |only
RMark-2.1.9/RMark/inst/extdata/Blackduck.txt |only
RMark-2.1.9/RMark/inst/extdata/Brownie.inp |only
RMark-2.1.9/RMark/inst/extdata/Donovan.7.inp |only
RMark-2.1.9/RMark/inst/extdata/Donovan.8.inp |only
RMark-2.1.9/RMark/inst/extdata/EDWARDSANDEBERHARDT.INP |only
RMark-2.1.9/RMark/inst/extdata/F_AGE.INP |only
RMark-2.1.9/RMark/inst/extdata/LD1.inp |only
RMark-2.1.9/RMark/inst/extdata/LINEAR.INP |only
RMark-2.1.9/RMark/inst/extdata/MSSURV.INP |only
RMark-2.1.9/RMark/inst/extdata/MS_rdsimple1.inp |only
RMark-2.1.9/RMark/inst/extdata/M_AGE.INP |only
RMark-2.1.9/RMark/inst/extdata/MallardNestExample.inp |only
RMark-2.1.9/RMark/inst/extdata/NicholsMSOccupancy.inp |only
RMark-2.1.9/RMark/inst/extdata/Pass3MStrata5.inp |only
RMark-2.1.9/RMark/inst/extdata/RDSalamander.inp |only
RMark-2.1.9/RMark/inst/extdata/ROBUST.INP |only
177 files changed, 1186 insertions(+), 743 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.9-1 dated 2014-09-18 and 0.9-2 dated 2015-03-15
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3, < 2) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand
ChangeLog | 44 +++++++++++++++++
DESCRIPTION | 8 +--
MD5 | 42 +++++++++-------
NAMESPACE | 1
R/ogr.R | 101 ++++++++++++++++++++++++++--------------
R/ogr_sp.R | 78 ++++++++++++++++++++++--------
build/vignette.rds |binary
configure | 95 +++++++++++++++++++++++++++++++++----
configure.ac | 28 ++++++++++-
inst/ChangeLog | 44 +++++++++++++++++
inst/README | 16 ++++++
inst/SVN_VERSION | 2
inst/doc/OGR_shape_encoding.pdf |binary
inst/vectors/PacoursIKA2.DAT |only
inst/vectors/PacoursIKA2.ID |only
inst/vectors/PacoursIKA2.MAP |only
inst/vectors/PacoursIKA2.TAB |only
inst/vectors/SOURCES | 2
man/make_EPSG.Rd | 2
man/project.Rd | 5 +
man/readOGR.Rd | 10 +++
man/spTransform-methods.Rd | 6 +-
tests/test_proj.R | 5 +
tests/test_proj.Rout.save | 12 ++--
24 files changed, 393 insertions(+), 108 deletions(-)
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Diff between metaMix versions 0.1 dated 2014-10-15 and 0.2 dated 2015-03-15
Description: Resolves complex metagenomic mixtures by analysing
deep sequencing data, using a mixture model based approach.
The use of parallel Monte Carlo Markov chains for the exploration
of the species space enables the identification of the set
of species more likely to contribute to the mixture.
Author: Sofia Morfopoulou
Maintainer: Sofia Morfopoulou
DESCRIPTION | 10 +++----
MD5 | 30 ++++++++++++-----------
R/Gibbs.R | 6 ++--
R/logmean.R |only
R/step1_preprocess.R | 12 ++++-----
R/step2_allInclusive_MM.R | 13 ++++++----
R/step3_parallelTemper.R | 8 +++---
R/step3_parallelTemper_nucl.R | 10 +++----
R/step4_bayesModelAver.R | 53 ++++++++++++++++++++++++++++++++++++------
data/step3.RData |binary
inst/doc/guide.Rnw | 2 +
inst/doc/guide.pdf |binary
man/generative.prob.Rd | 4 +--
man/parallel.temper.nucl.Rd | 6 ++--
man/reduce.space.Rd | 6 +++-
vignettes/guide.Rnw | 2 +
vignettes/guide.Rnw.bck |only
17 files changed, 106 insertions(+), 56 deletions(-)
Title: Modelling and Validation of Non Homogeneous Poisson Processes
Diff between NHPoisson versions 3.0 dated 2014-05-26 and 3.1 dated 2015-03-15
Description: Tools for modelling, ML estimation, validation analysis and simulation of non homogeneous Poisson processes in time.
Author: Ana C. Cebrian
Maintainer: Ana C. Cebrian
DESCRIPTION | 10 ++--
MD5 | 71 +++++++++++++++++-----------------
R/GenEnv.fun.r | 11 ++---
R/emplambda.fun.r | 1
R/emplambdaD.fun.r | 1
R/fitPP.fun.r | 4 -
R/funSim.fun.r | 4 -
R/globalval.fun.r | 25 +++++++-----
R/graphResCov.fun.r | 35 +++--------------
R/graphrate.fun.r | 8 ++-
R/graphres.fun.r | 98 ++++--------------------------------------------
R/graphresU.fun.r | 90 ++++++++------------------------------------
R/resQQplot.fun.r | 100 ++++++++++++++++++++++++++-----------------------
R/resSim.fun.r | 4 -
R/simNHP.fun.r | 34 +++++++++-------
inst |only
man/BarTxTn.Rd | 8 +++
man/CIdelta.fun.Rd | 5 ++
man/CItran.fun.Rd | 5 ++
man/CalcRes.fun.Rd | 5 ++
man/CalcResD.fun.Rd | 5 ++
man/GenEnv.fun.Rd | 26 ++++++++----
man/VARbeta.fun.Rd | 4 +
man/confintAsin.fun.Rd | 5 ++
man/dropAIC.fun.Rd | 5 ++
man/fitPP.fun.Rd | 5 ++
man/globalval.fun.Rd | 71 +++++++++++++++++++++++-----------
man/graphResCov.fun.Rd | 29 ++++++++++----
man/graphResX.fun.Rd | 5 ++
man/graphrate.fun.Rd | 6 ++
man/graphres.fun.Rd | 44 ++++++++++++++-------
man/graphresU.fun.Rd | 27 +++++++++++--
man/resQQplot.fun.Rd | 30 +++++++++++---
man/simNHP.fun.Rd | 31 ++++++++++-----
man/stepAICmle.fun.Rd | 4 +
man/transfH.fun.Rd | 8 +++
man/unifres.fun.Rd | 3 +
37 files changed, 440 insertions(+), 387 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Diff between TSP versions 1.0-10 dated 2015-02-03 and 1.1-0 dated 2015-03-15
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 20 +-
MD5 | 72 ++++----
NAMESPACE | 30 +++
R/ATSP.R | 36 ++--
R/ETSP.R |only
R/TOUR.R | 62 +++----
R/TSP.R | 44 ++---
R/insert_dummy.R | 15 -
R/read_TSPLIB.R | 181 +++++++++++----------
R/solve_TSP.R | 147 ++++++++++-------
R/tour_length.R | 52 ++++--
R/tsp_concorde.R | 343 +++++++++++++++++++----------------------
R/tsp_insertion.R | 202 +++++++++++++-----------
R/tsp_nn.R | 36 ++--
R/tsp_two_opt.R | 2
R/write_TSPLIB.R | 171 +++++++++++---------
build/vignette.rds |binary
data/USCA312.rda |binary
data/USCA312_map.rda |binary
data/USCA50.rda |binary
inst/NEWS | 15 +
inst/doc/TSP.R | 6
inst/doc/TSP.Rnw | 8
inst/doc/TSP.pdf |binary
inst/examples |only
inst/tests |only
man/ATSP.Rd | 10 -
man/ETSP.Rd |only
man/TOUR.Rd | 3
man/TSP.Rd | 2
man/TSPLIB.Rd | 52 +++++-
man/USCA312.Rd | 4
man/insert_dummy.Rd | 3
man/reformulate_ATSP_as_TSP.Rd | 10 -
man/solve_TSP.Rd | 107 +++++++++---
man/tour_length.Rd | 32 ++-
src/two_opt.c | 9 -
tests |only
vignettes/TSP.Rnw | 8
39 files changed, 967 insertions(+), 715 deletions(-)
Title: A Boosted Tweedie Compound Poisson Model
Diff between TDboost versions 1.0 dated 2014-10-22 and 1.1 dated 2015-03-15
Description: A boosted Tweedie compound Poisson model using the gradient boosting. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing interactions among predictors.
Author: Yi Yang
Maintainer: Yi Yang
DESCRIPTION | 12 +++---
MD5 | 20 +++++------
NAMESPACE | 6 ++-
R/TDboost.R | 6 +--
man/FHT.Rd | 2 -
man/TDboost.Rd | 17 ++++++++-
man/TDboost.perf.Rd | 2 -
man/plot.TDboost.Rd | 2 -
man/relative.influence.Rd | 4 --
man/summary.TDboost.Rd | 7 +--
src/EDM.cpp | 82 +++++++++++++++++++++++++++++-----------------
11 files changed, 98 insertions(+), 62 deletions(-)
Title: Functions for Creating Summary Tables for Statistical Reports
Diff between tab versions 2.1.3 dated 2014-09-16 and 3.1.1 dated 2015-03-15
Description: Contains functions for generating tables for statistical reports written in Microsoft Word or LaTeX. There are functions for I-by-J frequency tables, comparison of means or medians across levels of a categorical variable, and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards regression. Functions are available to handle data simple random samples or survey data. The package is intended to make it easier for researchers to translate results from statistical analyses in R to their reports or manuscripts.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen
DESCRIPTION | 12 -
MD5 | 52 +++----
R/tabcox.R | 132 ++++++++++++++----
R/tabfreq.R | 359 ++++++++++++++++++++++++++++++++++++++++++++------
R/tabfreq_svy.R | 73 +++++++---
R/tabgee.R | 67 ++++++++-
R/tabglm.R | 70 ++++++++-
R/tabglm_svy.R | 70 ++++++++-
R/tabmeans.R | 352 ++++++++++++++++++++++++++++++++++++++++---------
R/tabmeans_svy.R | 38 ++++-
R/tabmedians.R | 212 +++++++++++++++++++++--------
R/tabmedians_svy.R |only
R/tabmulti.R | 153 ++++++++++++++++-----
R/tabmulti_svy.R |only
data/d.rda |binary
man/d.Rd | 12 -
man/tab-package.Rd | 37 ++---
man/tabcox.Rd | 64 ++++++--
man/tabfreq.Rd | 114 ++++++++++-----
man/tabfreq_svy.Rd | 45 ++++--
man/tabgee.Rd | 34 +++-
man/tabglm.Rd | 36 ++++-
man/tabglm_svy.Rd | 26 +++
man/tabmeans.Rd | 118 +++++++++++-----
man/tabmeans_svy.Rd | 36 +++--
man/tabmedians.Rd | 97 ++++++++-----
man/tabmedians_svy.Rd |only
man/tabmulti.Rd | 138 ++++++++++++-------
man/tabmulti_svy.Rd |only
29 files changed, 1816 insertions(+), 531 deletions(-)
Title: Species Distribution Modeling
Diff between dismo versions 1.0-5 dated 2014-09-10 and 1.0-12 dated 2015-03-15
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans
dismo-1.0-12/dismo/ChangeLog | 3
dismo-1.0-12/dismo/DESCRIPTION | 14 -
dismo-1.0-12/dismo/MD5 | 71 +++---
dismo-1.0-12/dismo/R/biogeomancer.R | 2
dismo-1.0-12/dismo/R/biovars.R | 2
dismo-1.0-12/dismo/R/check.R | 10
dismo-1.0-12/dismo/R/circles.R | 20 +
dismo-1.0-12/dismo/R/circularArea.R | 2
dismo-1.0-12/dismo/R/domain.predict.R | 7
dismo-1.0-12/dismo/R/evaluate.R | 2
dismo-1.0-12/dismo/R/gbif.R | 331 ++++++++++----------------------
dismo-1.0-12/dismo/R/gbif_old.R |only
dismo-1.0-12/dismo/R/gbm.fixed.R | 7
dismo-1.0-12/dismo/R/gbm.holdout.R | 8
dismo-1.0-12/dismo/R/gbm.interactions.R | 5
dismo-1.0-12/dismo/R/gbm.perspec.R | 5
dismo-1.0-12/dismo/R/gbm.plot.R | 6
dismo-1.0-12/dismo/R/gbm.simplify.R | 6
dismo-1.0-12/dismo/R/gbm.step.R | 13 -
dismo-1.0-12/dismo/R/geoIDW.R | 2
dismo-1.0-12/dismo/R/geocode.R | 3
dismo-1.0-12/dismo/R/gmap.R | 8
dismo-1.0-12/dismo/R/gorilla.R | 2
dismo-1.0-12/dismo/R/maxent.R | 2
dismo-1.0-12/dismo/R/mess.R | 10
dismo-1.0-12/dismo/R/voronoi.R | 2
dismo-1.0-12/dismo/R/voronoiHull.R | 4
dismo-1.0-12/dismo/build/vignette.rds |binary
dismo-1.0-12/dismo/inst/doc/brt.R | 1
dismo-1.0-12/dismo/inst/doc/brt.Rnw | 1
dismo-1.0-12/dismo/inst/doc/brt.pdf |binary
dismo-1.0-12/dismo/inst/doc/sdm.pdf |binary
dismo-1.0-12/dismo/man/gbif.Rd | 52 +----
dismo-1.0-12/dismo/man/gmap.Rd | 3
dismo-1.0-12/dismo/man/randomPoints.Rd | 2
dismo-1.0-12/dismo/vignettes/brt.Rnw | 1
dismo-1.0-5/dismo/R/rowMinMax.R |only
dismo-1.0-5/dismo/man/lookUp.Rd |only
38 files changed, 243 insertions(+), 364 deletions(-)
Title: Store Objects on Disk Automatically
Diff between track versions 1.0-15 dated 2012-04-13 and 1.1.7 dated 2015-03-14
Description: Automatically stores objects in files on disk
so that files are rewritten when objects are changed, and
so that objects are accessible but do not occupy memory
until they are accessed. Keeps track of times when objects
are created and modified, and caches some basic
characteristics of objects to allow for fast summaries of
objects. Also provides a command history mechanism that
saves the last command to a history file after each
command completes.
Author: Tony Plate
Maintainer: Tony Plate
track-1.0-15/track/NOTES.txt |only
track-1.0-15/track/TODO.txt |only
track-1.0-15/track/doc |only
track-1.0-15/track/inst/performanceTrials/NOTES.txt |only
track-1.1.7/track/DESCRIPTION | 28 +-
track-1.1.7/track/MD5 | 101 +++++----
track-1.1.7/track/NAMESPACE | 4
track-1.1.7/track/NEWS | 63 +++++-
track-1.1.7/track/R/track.R | 20 -
track-1.1.7/track/R/track.attach.R | 38 +++
track-1.1.7/track/R/track.auto.R | 17 +
track-1.1.7/track/R/track.auto.monitor.R | 13 -
track-1.1.7/track/R/track.copy.R | 20 -
track-1.1.7/track/R/track.filename.R | 1
track-1.1.7/track/R/track.history.R | 45 ++--
track-1.1.7/track/R/track.info.R | 2
track-1.1.7/track/R/track.load.R | 9
track-1.1.7/track/R/track.manage.R | 16 -
track-1.1.7/track/R/track.mem.R |only
track-1.1.7/track/R/track.options.R | 10
track-1.1.7/track/R/track.rebuild.R | 19 -
track-1.1.7/track/R/track.rename.R | 85 +++-----
track-1.1.7/track/R/track.rescan.R | 95 ++++-----
track-1.1.7/track/R/track.start.R | 133 +++++++++----
track-1.1.7/track/R/track.summary.R | 3
track-1.1.7/track/R/track.sync.R | 59 +++--
track-1.1.7/track/R/utils.R | 204 +++++++++++++++-----
track-1.1.7/track/inst/sccversion.txt |only
track-1.1.7/track/inst/svnversion.txt |only
track-1.1.7/track/man/track-package.Rd | 151 +++++++++-----
track-1.1.7/track/man/track.attach.Rd | 9
track-1.1.7/track/man/track.copy.Rd | 27 ++
track-1.1.7/track/man/track.design.Rd | 9
track-1.1.7/track/man/track.info.Rd | 34 ++-
track-1.1.7/track/man/track.manage.Rd | 30 ++
track-1.1.7/track/man/track.options.Rd | 37 ++-
track-1.1.7/track/man/track.plugin.lru.Rd | 4
track-1.1.7/track/man/track.rebuild.Rd | 27 +-
track-1.1.7/track/man/track.rename.Rd | 21 +-
track-1.1.7/track/man/track.setup.Rd | 39 ++-
track-1.1.7/track/man/track.status.Rd | 37 ++-
track-1.1.7/track/man/track.summary.Rd | 18 +
track-1.1.7/track/man/track.sync.Rd | 10
track-1.1.7/track/tests/runtests.R | 9
track-1.1.7/track/tests/testBrokenFileSystem.Rt | 18 +
track-1.1.7/track/tests/testFollowObjs.Rt | 3
track-1.1.7/track/tests/testFollowObjsAutoFalse.Rt | 3
track-1.1.7/track/tests/testOptions.Rt | 3
track-1.1.7/track/tests/testSimpleTrack.Rt | 5
track-1.1.7/track/tests/track.attach.Rt | 1
track-1.1.7/track/tests/track.auto.rescan.Rt |only
track-1.1.7/track/tests/track.copy.Rt | 8
track-1.1.7/track/tests/track.rescan.Rt | 11 -
track-1.1.7/track/tests/track.start.Rt | 1
track-1.1.7/track/tests/track.sync.Rt | 4
track-1.1.7/track/vignettes |only
56 files changed, 990 insertions(+), 514 deletions(-)
Title: Transcript-Based Unit Tests that are Easy to Create and Maintain
Diff between scriptests versions 1.0-9 dated 2012-04-13 and 1.0-15 dated 2015-03-14
Description: Support for using .Rt (transcript) tests
in the tests directory of a package. Provides more
convenience and features than the standard .R/.Rout.save
tests. Tests can be run under R CMD check and also
interactively. Provides source.pkg() for quickly loading
code, DLLs, and data from a package for use in an
edit/compile/test development cycle.
Author: Tony Plate
Maintainer: Tony Plate
scriptests-1.0-15/scriptests/DESCRIPTION | 24
scriptests-1.0-15/scriptests/MD5 | 28 -
scriptests-1.0-15/scriptests/NEWS | 5
scriptests-1.0-15/scriptests/R/runPackageTests.R | 7
scriptests-1.0-15/scriptests/R/runScripTests.R | 5
scriptests-1.0-15/scriptests/R/runtests.R | 28 -
scriptests-1.0-15/scriptests/R/source.pkg.R | 617 ++++++++++++-----------
scriptests-1.0-15/scriptests/R/summarizeTests.R | 9
scriptests-1.0-15/scriptests/inst/sccversion.txt |only
scriptests-1.0-15/scriptests/inst/svnversion.txt |only
scriptests-1.0-15/scriptests/man/runtests.Rd | 3
scriptests-1.0-15/scriptests/man/setup.Rd | 6
scriptests-1.0-15/scriptests/man/source.pkg.Rd | 43 +
scriptests-1.0-15/scriptests/vignettes |only
scriptests-1.0-9/scriptests/DevNotes.txt |only
scriptests-1.0-9/scriptests/TODO.txt |only
scriptests-1.0-9/scriptests/doc |only
17 files changed, 443 insertions(+), 332 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.15 dated 2015-02-07 and 2.16 dated 2015-03-14
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
DESCRIPTION | 9 +++++----
MD5 | 35 ++++++++++++++++++-----------------
R/helpers.R | 12 ++++++++++--
R/lsmeans.R | 12 +++++++++---
R/lsmip.R | 2 +-
R/nonlin-support.R |only
R/summary.R | 2 +-
inst/NEWS | 12 ++++++++++++
inst/doc/extending.R | 14 +++++++-------
inst/doc/extending.pdf |binary
inst/doc/extending.rnw | 2 ++
inst/doc/using-lsmeans.R | 34 +++++++++++++++++++++++++++-------
inst/doc/using-lsmeans.pdf |binary
inst/doc/using-lsmeans.rnw | 26 +++++++++++++++++++++++---
man/contrast.Rd | 17 ++++++++---------
man/models.Rd | 17 +++++++++--------
tests/tests1.Rout.save | 8 ++++----
vignettes/extending.rnw | 2 ++
vignettes/using-lsmeans.rnw | 26 +++++++++++++++++++++++---
19 files changed, 161 insertions(+), 69 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Diff between gstat versions 1.0-21 dated 2015-01-19 and 1.0-22 dated 2015-03-14
Description: provides variogram modelling; simple, ordinary and universal point or block (co)kriging, spatio-temporal kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 13 +--
MD5 | 104 +++++++++++++-------------
NAMESPACE | 4 -
R/fit.variogram.reml.R | 2
R/gstat.R | 8 +-
R/krige0.R | 2
R/predict.gstat.R | 6 -
R/stVariogramModels.R | 176 ++++++++++++++++++++++++++++++++++++++++-----
R/variogram.default.R | 2
R/variogramLine.R | 11 +-
R/variogramST.R | 47 +++++++++---
build/vignette.rds |binary
data/coalash.rda |binary
data/fulmar.rda |binary
data/jura.rda |binary
data/meuse.all.rda |binary
data/meuse.alt.rda |binary
data/ncp.grid.rda |binary
data/oxford.rda |binary
data/pcb.rda |binary
data/sic2004.rda |binary
data/sic97.rda |binary
data/tull.rda |binary
data/vv.rda |binary
data/walker.rda |binary
data/wind.rda |binary
demo/a2p.R | 5 -
demo/stkrige.R | 52 +++++++++----
demo/wind.R | 8 +-
inst/ChangeLog | 77 +++++++++++++++++++
inst/doc/gstat.pdf |binary
inst/doc/prs.pdf |binary
inst/doc/st.pdf |binary
man/estiStAni.Rd |only
man/extractPar.Rd |only
man/fit.StVariogram.Rd | 35 +++++++-
man/gstat.Rd | 10 +-
man/meuse.all.Rd | 2
man/meuse.alt.Rd | 2
man/ossfim.Rd | 3
man/pcb.Rd | 2
man/plot.gstatVariogram.Rd | 8 +-
man/sic2004.Rd | 10 --
man/sic97.Rd | 4 -
man/variogram.Rd | 7 -
man/variogramST.Rd | 14 +--
man/vgmST.Rd | 2
man/wind.Rd | 5 -
src/defs.h | 2
src/s.c | 7 +
tests/unproj.R | 9 +-
tests/unproj.Rout.save | 15 ++-
tests/windst.R | 8 +-
tests/windst.Rout.save | 14 +--
54 files changed, 485 insertions(+), 191 deletions(-)
Title: Sparse Group Partial Least Square Methods
Diff between sgPLS versions 1.0 dated 2015-02-10 and 1.1 dated 2015-03-14
Description: The Sparse Group Partial Least Square package (sgPLS) provides sparse, group, and sparse group versions of partial least square regression models.
Author: Benoit Liquet and Pierre Lafaye de Micheaux
Maintainer: Benoit Liquet
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/per.variance.R | 2 +-
R/tuning.gPLS.X.R | 2 +-
R/tuning.sPLS.X.R | 2 +-
R/tuning.sgPLS.X.R | 2 +-
man/gPLS.Rd | 2 +-
man/predict.Rd | 2 +-
man/sPLS.Rd | 2 +-
man/sgPLS.Rd | 2 +-
10 files changed, 21 insertions(+), 21 deletions(-)
Title: Analysis of Symbolic Data
Diff between symbolicDA versions 0.4-1 dated 2013-10-12 and 0.4-2 dated 2015-03-14
Description: Symbolic data analysis methods: importing/ exporting data from ASSO XML Files, distance calculation for symbolic data (Ichino-Yaguchi, de Carvalho measure), zoom star plot, 3d interval plot, multidimensional scaling for symbolic interval data, dynamic clustering based on distance matrix, HINoV method for symbolic data, Ichino's feature selection method, principal component analysis for symbolic interval data, decision trees for symbolic data based on optimal split with bagging, boosting and random forest approach (+visualization), kernel discriminant analysis for symbolic data, Kohonen's self-organizing maps for symbolic, replication and profiling, artificial symbolic data generation.
Author: Andrzej Dudek, Marcin Pelka
Maintainer: Andrzej Dudek
symbolicDA-0.4-1/symbolicDA/R/Iscal.SDA.r |only
symbolicDA-0.4-1/symbolicDA/R/SO2Simple.r |only
symbolicDA-0.4-1/symbolicDA/R/interscal.SDA.r |only
symbolicDA-0.4-1/symbolicDA/R/simple2SO.r |only
symbolicDA-0.4-1/symbolicDA/R/symscal.SDA.r |only
symbolicDA-0.4-1/symbolicDA/man/summary.symbolic.rd |only
symbolicDA-0.4-1/symbolicDA/tests/DClust.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/HINoV.SDA.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/SClust.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/cars.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/cluster.Description.SDA.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/dist.SDA.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/index.G1d.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/plot3dInterval.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/replication.SDA.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/save.SO.Rout.save |only
symbolicDA-0.4-1/symbolicDA/tests/zoomStar.Rout.save |only
symbolicDA-0.4-2/symbolicDA/DESCRIPTION | 16 +-
symbolicDA-0.4-2/symbolicDA/MD5 | 54 +++++-----
symbolicDA-0.4-2/symbolicDA/NAMESPACE | 1
symbolicDA-0.4-2/symbolicDA/R/Interscal.SDA.r |only
symbolicDA-0.4-2/symbolicDA/R/Iscal.SDA.R |only
symbolicDA-0.4-2/symbolicDA/R/SO2Simple.R |only
symbolicDA-0.4-2/symbolicDA/R/Symscal.SDA.R |only
symbolicDA-0.4-2/symbolicDA/R/generate.SO.r | 2
symbolicDA-0.4-2/symbolicDA/R/replication.SDA.r | 3
symbolicDA-0.4-2/symbolicDA/R/simple2SO.R |only
symbolicDA-0.4-2/symbolicDA/data/data_symbolic.rda |only
symbolicDA-0.4-2/symbolicDA/inst/doc/SDA.pdf |only
symbolicDA-0.4-2/symbolicDA/inst/pdf |only
symbolicDA-0.4-2/symbolicDA/man/data_symbolic.rd |only
symbolicDA-0.4-2/symbolicDA/man/parse.SO.rd | 2
symbolicDA-0.4-2/symbolicDA/man/symbolic.object.rd | 2
symbolicDA-0.4-2/symbolicDA/src |only
symbolicDA-0.4-2/symbolicDA/tests/DClust.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/HINoV.SDA.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/SClust.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/cars.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/cluster.Description.SDA.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/dist.SDA.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/index.G1d.R | 2
symbolicDA-0.4-2/symbolicDA/tests/index.G1d.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/plot3dInterval.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/replication.SDA.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/save.SO.Rout |only
symbolicDA-0.4-2/symbolicDA/tests/zoomStar.Rout |only
46 files changed, 43 insertions(+), 39 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-41 dated 2014-11-15 and 0.9-45-2 dated 2015-03-14
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
RVAideMemoire-0.9-41/RVAideMemoire/man/friedman.rating.test.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/kruskal.rating.test.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/pairwise.manova.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/pairwise.wilcox.rating.test.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/wilcox.paired.rating.multcomp.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/wilcox.rating.signtest.Rd |only
RVAideMemoire-0.9-41/RVAideMemoire/man/wilcox.rating.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/DESCRIPTION | 16
RVAideMemoire-0.9-45-2/RVAideMemoire/MD5 | 243 +++++-----
RVAideMemoire-0.9-45-2/RVAideMemoire/NAMESPACE | 48 +
RVAideMemoire-0.9-45-2/RVAideMemoire/NEWS | 31 +
RVAideMemoire-0.9-45-2/RVAideMemoire/R/CvM.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/DA.confusion.R | 63 +-
RVAideMemoire-0.9-45-2/RVAideMemoire/R/DA.valid.R | 92 +++
RVAideMemoire-0.9-45-2/RVAideMemoire/R/G.bintest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/G.multcomp.R | 6
RVAideMemoire-0.9-45-2/RVAideMemoire/R/G.test.R | 5
RVAideMemoire-0.9-45-2/RVAideMemoire/R/MVA.synt.R | 7
RVAideMemoire-0.9-45-2/RVAideMemoire/R/PLSDA.ncomp.R | 9
RVAideMemoire-0.9-45-2/RVAideMemoire/R/PLSDA.test.R | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/R/adonis.II.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/back.lsmeans.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/chisq.bin.exp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/chisq.bintest.R | 35 -
RVAideMemoire-0.9-45-2/RVAideMemoire/R/chisq.theo.bintest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/cor.2comp.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/R/cramer.test.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/R/dendro.gp.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/R/dhist.R | 3
RVAideMemoire-0.9-45-2/RVAideMemoire/R/fisher.bintest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/fisher.multcomp.R | 37 +
RVAideMemoire-0.9-45-2/RVAideMemoire/R/fp.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/friedman.rating.test.R | 34 -
RVAideMemoire-0.9-45-2/RVAideMemoire/R/ind.contrib.R | 8
RVAideMemoire-0.9-45-2/RVAideMemoire/R/kruskal.rating.test.R | 33 -
RVAideMemoire-0.9-45-2/RVAideMemoire/R/mood.medtest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/multinomial.multcomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/multinomial.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/multinomial.theo.multcomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.manova.R | 20
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.mood.medtest.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.perm.manova.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.to.groups.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pairwise.wilcox.rating.test.R | 23
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pcor.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/pcor.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/perm.t.test.R | 19
RVAideMemoire-0.9-45-2/RVAideMemoire/R/perm.var.test.R | 18
RVAideMemoire-0.9-45-2/RVAideMemoire/R/plot1comp.var.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/R/plotresid.R | 6
RVAideMemoire-0.9-45-2/RVAideMemoire/R/predict.coadisc.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/print.RV.multcomp.R | 3
RVAideMemoire-0.9-45-2/RVAideMemoire/R/prop.bin.multcomp.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/prop.multinom.test.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/s.corcircle2.R | 35 +
RVAideMemoire-0.9-45-2/RVAideMemoire/R/scat.cr.R |only
RVAideMemoire-0.9-45-2/RVAideMemoire/R/scat.mix.categorical.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wald.ptheo.test.R | 9
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.paired.rating.multcomp.R | 32 -
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.rating.signtest.R | 53 --
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.rating.test.R | 69 --
RVAideMemoire-0.9-45-2/RVAideMemoire/R/wilcox.signtest.R | 96 ++-
RVAideMemoire-0.9-45-2/RVAideMemoire/R/zzz.R | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/CvM.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/DA.confusion.Rd | 22
RVAideMemoire-0.9-45-2/RVAideMemoire/man/DA.valid.Rd | 29 -
RVAideMemoire-0.9-45-2/RVAideMemoire/man/G.bintest.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/G.multcomp.Rd | 9
RVAideMemoire-0.9-45-2/RVAideMemoire/man/G.test.Rd | 14
RVAideMemoire-0.9-45-2/RVAideMemoire/man/G.theo.multcomp.Rd | 11
RVAideMemoire-0.9-45-2/RVAideMemoire/man/LDA.format.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/MVA.synt.Rd | 10
RVAideMemoire-0.9-45-2/RVAideMemoire/man/PLSDA.VIP.Rd | 3
RVAideMemoire-0.9-45-2/RVAideMemoire/man/PLSDA.ncomp.Rd | 3
RVAideMemoire-0.9-45-2/RVAideMemoire/man/PLSDA.test.Rd | 5
RVAideMemoire-0.9-45-2/RVAideMemoire/man/RVAideMemoire-package.Rd | 8
RVAideMemoire-0.9-45-2/RVAideMemoire/man/adonis.II.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/back.lsmeans.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/byf.hist.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/byf.mqqnorm.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/byf.mshapiro.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/byf.qqnorm.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/byf.shapiro.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.bin.exp.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.bintest.Rd | 20
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.exp.Rd | 8
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.multcomp.Rd | 9
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.theo.bintest.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/chisq.theo.multcomp.Rd | 11
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cochran.qtest.Rd | 5
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cor.2comp.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cor.conf.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cor.multcomp.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cor.sparse.Rd | 5
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cox.resid.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cramer.test.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/cv.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/dendro.gp.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/deprecated.Rd | 18
RVAideMemoire-0.9-45-2/RVAideMemoire/man/fisher.bintest.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/fisher.multcomp.Rd | 22
RVAideMemoire-0.9-45-2/RVAideMemoire/man/fp.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/ind.contrib.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/least.rect.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/logis.fit.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/logis.noise.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/mod.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/mood.medtest.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/mqqnorm.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/multinomial.multcomp.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/multinomial.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/multinomial.theo.multcomp.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/overdisp.glmer.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pairwise.G.test.Rd | 9
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pairwise.mood.medtest.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pairwise.perm.manova.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pairwise.perm.t.test.Rd | 5
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pairwise.to.groups.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pcor.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/pcor.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/perm.anova.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/perm.bartlett.test.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/perm.cor.test.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/perm.t.test.Rd | 30 -
RVAideMemoire-0.9-45-2/RVAideMemoire/man/perm.var.test.Rd | 29 -
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plot1comp.ind.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plot1comp.var.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plotresid.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/plotsurvivors.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/predict.coadisc.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/prop.bin.multcomp.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/prop.multcomp.Rd | 10
RVAideMemoire-0.9-45-2/RVAideMemoire/man/prop.multinom.test.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/rating.lsmeans.Rd | 8
RVAideMemoire-0.9-45-2/RVAideMemoire/man/rating.prob.Rd | 3
RVAideMemoire-0.9-45-2/RVAideMemoire/man/reg.ci.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/s.corcircle2.Rd | 19
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scat.cr.Rd |only
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scat.mix.categorical.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/scat.mix.numeric.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/se.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/seq2.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/spearman.ci.Rd | 4
RVAideMemoire-0.9-45-2/RVAideMemoire/man/user.cont.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/wald.ptheo.test.Rd | 10
RVAideMemoire-0.9-45-2/RVAideMemoire/man/wilcox.paired.multcomp.Rd | 2
RVAideMemoire-0.9-45-2/RVAideMemoire/man/wilcox.signtest.Rd | 44 +
147 files changed, 842 insertions(+), 694 deletions(-)
Title: R Interface to REDCap
Diff between redcapAPI versions 1.2 dated 2015-01-16 and 1.3 dated 2015-03-14
Description: Access data stored in REDCap databases using the Application
Programming Interface (API). REDCap (Research Electronic Data CAPture) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The redcapAPI package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with
contributions from Jeremy Stephens, and Will Beasley
Maintainer: Stephen Lane
DESCRIPTION | 12 +--
MD5 | 88 ++++++++++++-----------
NAMESPACE | 63 ++++++++---------
NEWS | 10 ++
R/allocationTable.R | 6 -
R/deleteFiles.R | 6 -
R/exportArms.R | 7 +
R/exportEvents.R | 7 +
R/exportFiles.R | 4 -
R/exportInstruments.R | 4 -
R/exportMappings.R | 8 +-
R/exportMetaData.R | 4 -
R/exportRecords.R | 13 ++-
R/exportReports.R | 4 -
R/exportUsers.R | 82 +++++++++++-----------
R/exportVersion.R | 30 ++++----
R/importFiles.R | 4 -
R/importRecords.R | 158 +++++++++++++++++++++----------------------
R/parseBranchingLogic.R |only
R/redcapProjectInfo.R | 4 -
README.md | 5 +
inst/CITATION | 2
man/allocationTable.Rd | 3
man/apiCall.Rd | 3
man/deleteFiles.Rd | 3
man/exportArms.Rd | 3
man/exportEvents.Rd | 3
man/exportFiles.Rd | 3
man/exportInstruments.Rd | 3
man/exportMappings.Rd | 3
man/exportMetaData.Rd | 3
man/exportRecords.Rd | 3
man/exportReports.Rd | 3
man/exportUsers.Rd | 5 -
man/exportVersion.Rd | 5 -
man/fieldToVar.Rd | 3
man/importFiles.Rd | 3
man/importRecords.Rd | 5 -
man/parseBranchingLogic.Rd |only
man/recodeCheck.Rd | 3
man/redcapAPI.Rd | 3
man/redcapConnection.Rd | 3
man/redcapFactorFlip.Rd | 3
man/redcapProjectInfo.Rd | 3
man/syncUnderscoreCodings.Rd | 3
man/validateImport.Rd | 3
46 files changed, 322 insertions(+), 274 deletions(-)
Title: Geographic Data Analysis and Modeling
Diff between raster versions 2.3-24 dated 2015-01-27 and 2.3-33 dated 2015-03-14
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 7 ++-
DESCRIPTION | 16 ++++----
MD5 | 89 ++++++++++++++++++++++++------------------------
R/aggregate_sp.R | 8 ++--
R/area.R | 10 ++---
R/as.data.frame.R | 2 -
R/as.spatial.R | 4 +-
R/bind.R | 12 ++++++
R/cellStats.R | 4 +-
R/clusterR.R | 24 ++++++------
R/distanceToEdge.R |only
R/extractLines.R | 8 ++--
R/extractPolygons.R | 22 +++++------
R/focalFun.R | 4 +-
R/getData.R | 2 -
R/hdrPRJ.R | 18 +++++----
R/imageplot2.R | 28 ++++++++++++---
R/multiCore.R | 17 +++++----
R/netCDFtoRasterCD.R | 14 +++++--
R/overlay.R | 5 ++
R/plot.R | 40 +++++++++++++--------
R/plotRaster2.R | 9 +++-
R/projectRaster.R | 14 +++----
R/rasterFromFile.R | 2 -
R/rasterFromGDAL.R | 20 ++++++++++
R/resample.R | 12 +++---
R/shift.R | 19 ++++++++--
R/shp.R | 2 -
R/terrain.R | 4 +-
R/union_sp.R | 5 +-
R/writeAllAscii.R | 13 +++++--
R/writeStartStop.R | 23 +++++++++++-
R/writeStartStopAscii.R | 2 +
R/xyValuesBuffer.R | 8 ++--
build/vignette.rds |binary
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/bind.Rd | 1
man/cluster.Rd | 2 +
man/plot.Rd | 4 +-
man/shapefile.Rd | 12 ++++++
man/terrain.Rd | 10 +----
man/writeRaster.Rd | 3 +
man/writeValues.Rd | 4 +-
src/terrain.c | 57 +++++++++++++++---------------
46 files changed, 351 insertions(+), 209 deletions(-)
Title: Analyzing Pointer Years and Components of Resilience
Diff between pointRes versions 1.0.1 dated 2015-03-06 and 1.0.2 dated 2015-03-14
Description: Functions to calculate and plot event and pointer years as well as components of resilience. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.
Author: Marieke van der Maaten-Theunissen and Ernst van der Maaten
Maintainer: Marieke van der Maaten-Theunissen
DESCRIPTION | 8 ++++----
MD5 | 28 ++++++++++++++--------------
R/event.plot.R | 6 +++---
R/norm.plot.R | 8 ++++----
R/pointer.norm.R | 25 +++++++++++++------------
R/pointer.plot.R | 10 +++++-----
R/pointer.rgc.R | 2 +-
R/res.comp.R | 2 +-
inst/Changelog | 20 ++++++++++++--------
man/event.plot.Rd | 6 +++---
man/norm.plot.Rd | 8 ++++----
man/pointer.norm.Rd | 19 +++++++++----------
man/pointer.plot.Rd | 10 +++++-----
man/pointer.rgc.Rd | 2 +-
man/res.comp.Rd | 2 +-
15 files changed, 80 insertions(+), 76 deletions(-)
Title: Number-Theoretic Functions
Diff between numbers versions 0.5-2 dated 2015-01-28 and 0.5-6 dated 2015-03-14
Description:
Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers
DESCRIPTION | 14 +++++++-------
MD5 | 16 ++++++++--------
NAMESPACE | 4 ++--
NEWS | 11 +++++++++++
R/droplet.R | 47 ++++++++++++++++++++++++++++++++++++++++++++++-
R/factorize.R | 6 ++++++
man/droplet_e.Rd | 35 ++++++++++++++++++++++++++---------
man/factorize.Rd | 35 ++++++++++++++++++++++++++++++++---
man/numbers-package.Rd | 2 +-
9 files changed, 139 insertions(+), 31 deletions(-)
Title: Programmatic Interface to the API Serving UC Berkeley's Natural
History Data
Diff between ecoengine versions 1.6 dated 2014-08-26 and 1.9 dated 2015-03-14
Description: The ecoengine provides access to more than 5 million georeferenced specimen records from the University of California, Berkeley's Natural History Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
ecoengine-1.6/ecoengine/inst/cache/fields_238cc4997a161669b1d7717ac8efc701.RData |only
ecoengine-1.6/ecoengine/inst/cache/fields_238cc4997a161669b1d7717ac8efc701.rdb |only
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ecoengine-1.6/ecoengine/inst/cache/version_c54e79368c8b2944c7d408eff6517323.rdb |only
ecoengine-1.6/ecoengine/inst/cache/version_c54e79368c8b2944c7d408eff6517323.rdx |only
ecoengine-1.9/ecoengine/DESCRIPTION | 16
ecoengine-1.9/ecoengine/MD5 | 323 +-
ecoengine-1.9/ecoengine/NAMESPACE | 2
ecoengine-1.9/ecoengine/NEWS | 6
ecoengine-1.9/ecoengine/R/ee_about.R | 2
ecoengine-1.9/ecoengine/R/ee_observations.R | 8
ecoengine-1.9/ecoengine/README.md | 10
ecoengine-1.9/ecoengine/inst/Using_ecoengine.Rmd | 25
ecoengine-1.9/ecoengine/inst/Using_ecoengine.md | 290 +-
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ecoengine-1.9/ecoengine/inst/Using_ecoengine_cache |only
ecoengine-1.9/ecoengine/inst/cache/__packages | 10
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ecoengine-1.9/ecoengine/man/california_counties.Rd | 3
ecoengine-1.9/ecoengine/man/checklist_details.Rd | 3
ecoengine-1.9/ecoengine/man/ecoengine.Rd | 3
ecoengine-1.9/ecoengine/man/ee_about.Rd | 3
ecoengine-1.9/ecoengine/man/ee_cbind.Rd | 3
ecoengine-1.9/ecoengine/man/ee_checklists.Rd | 3
ecoengine-1.9/ecoengine/man/ee_footprints.Rd | 3
ecoengine-1.9/ecoengine/man/ee_list_sensors.Rd | 3
ecoengine-1.9/ecoengine/man/ee_map.Rd | 3
ecoengine-1.9/ecoengine/man/ee_observations.Rd | 9
ecoengine-1.9/ecoengine/man/ee_pages.Rd | 3
ecoengine-1.9/ecoengine/man/ee_paginator.Rd | 3
ecoengine-1.9/ecoengine/man/ee_photos.Rd | 13
ecoengine-1.9/ecoengine/man/ee_search.Rd | 3
ecoengine-1.9/ecoengine/man/ee_search_obs.Rd | 13
ecoengine-1.9/ecoengine/man/ee_sensor_agg.Rd | 17
ecoengine-1.9/ecoengine/man/ee_sensor_data.Rd | 5
ecoengine-1.9/ecoengine/man/ee_sensors.Rd | 5
ecoengine-1.9/ecoengine/man/ee_sources.Rd | 3
ecoengine-1.9/ecoengine/man/full_sensor_list.Rd | 3
ecoengine-1.9/ecoengine/man/print.ecoengine.Rd | 3
ecoengine-1.9/ecoengine/man/view_photos.Rd | 3
148 files changed, 19242 insertions(+), 19090 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Diff between clusterSim versions 0.44-1 dated 2014-12-09 and 0.44-2 dated 2015-03-14
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas, data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorial and symbolic interval-valued data).
Author: Marek Walesiak
Maintainer: Andrzej Dudek
DESCRIPTION | 34 +++++------------------------
MD5 | 50 +++++++++++++++++++++++++++++++-------------
inst/pdf |only
man/cluster.Gen.rd | 4 +--
man/comparing.Partitions.rd | 2 -
man/data.Normalization.rd | 2 -
man/dist.BC.rd | 2 -
man/dist.GDM.rd | 2 -
man/dist.SM.rd | 2 -
man/dist.Symbolic.rd | 2 -
man/index.G2.rd | 2 -
man/index.G3.rd | 2 -
man/index.H.rd | 2 -
man/index.KL.rd | 34 +++++++++++++++++++----------
man/index.S.rd | 2 -
man/ordinalToMetric.rd | 5 ++--
16 files changed, 79 insertions(+), 68 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Diff between netassoc versions 0.4.1 dated 2015-01-31 and 0.4.3 dated 2015-03-13
Description: Infers species associations from local and regional-scale co-occurrence data (species x site matrices).
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder
netassoc-0.4.1/netassoc/data |only
netassoc-0.4.1/netassoc/man/fia.Rd |only
netassoc-0.4.3/netassoc/DESCRIPTION | 12
netassoc-0.4.3/netassoc/MD5 | 12
netassoc-0.4.3/netassoc/R/netassoc.R | 297 ++++++++++---------
netassoc-0.4.3/netassoc/man/makenetwork.Rd | 29 -
netassoc-0.4.3/netassoc/man/netassoc-package.Rd | 9
netassoc-0.4.3/netassoc/man/plot_netassoc_network.Rd | 18 -
8 files changed, 195 insertions(+), 182 deletions(-)
Title: R Client for the Lagotto Altmetrics Platform
Diff between alm versions 0.3.1 dated 2014-10-29 and 0.4.0 dated 2015-03-13
Description: An R interface to the open source article level metrics platform
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut],
Fenner Martin [aut]
Maintainer: Scott Chamberlain
DESCRIPTION | 25
LICENSE | 4
MD5 | 110 ++-
NAMESPACE | 3
NEWS | 32 +
R/alerts.R | 33 -
R/alm-package.R | 18
R/alm_datepub.R | 14
R/alm_events.R | 249 ++++----
R/alm_ids.R | 82 +-
R/alm_plot.R | 80 --
R/alm_requests.R |only
R/alm_signposts.R | 39 -
R/alm_sources.R | 27
R/alm_status.R | 10
R/alm_title.R | 14
R/globals.R | 2
R/plot_density.R | 32 -
R/plot_signposts.R | 78 --
R/zzz.R | 12
README.md | 691 +++++++++++-----------
build/vignette.rds |binary
inst/doc/alm_vignette.Rmd | 996 ++++++++++++++++----------------
inst/doc/alm_vignette.html | 990 ++++++++++++++++---------------
inst/vign/alm_vignette.Rmd | 227 ++++---
inst/vign/alm_vignette.md | 996 ++++++++++++++++----------------
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man/addmissing.Rd | 3
man/alert_classes.Rd | 3
man/alm-defunct.Rd | 3
man/alm-package.Rd | 21
man/alm_alerts.Rd | 28
man/alm_capwords.Rd | 3
man/alm_datepub.Rd | 17
man/alm_events.Rd | 61 +
man/alm_ids.Rd | 99 ++-
man/alm_plot.Rd | 23
man/alm_requests.Rd |only
man/alm_signposts.Rd | 24
man/alm_sources.Rd | 22
man/alm_status.Rd | 6
man/alm_title.Rd | 16
man/almcompact.Rd | 3
man/concat_todf.Rd | 3
man/getkey.Rd | 3
man/plot_density.Rd | 31
man/plot_signposts.Rd | 48 -
tests/testthat/test-alm_events.R | 6
tests/testthat/test-alm_signposts.R | 2
tests/testthat/test-alm_title.R | 12
vignettes/alm_vignette.Rmd | 996 ++++++++++++++++----------------
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64 files changed, 3250 insertions(+), 2947 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Diff between PReMiuM versions 3.0.32 dated 2014-12-29 and 3.1.0 dated 2015-03-13
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
Author: David I. Hastie
Maintainer: Silvia Liverani
PReMiuM-3.0.32/PReMiuM/inst/CITATION |only
PReMiuM-3.1.0/PReMiuM/ChangeLog | 10 ++
PReMiuM-3.1.0/PReMiuM/DESCRIPTION | 8 +-
PReMiuM-3.1.0/PReMiuM/MD5 | 48 ++++++------
PReMiuM-3.1.0/PReMiuM/R/postProcess.R | 54 ++++++++------
PReMiuM-3.1.0/PReMiuM/inst/citation |only
PReMiuM-3.1.0/PReMiuM/man/PReMiuM-package.Rd | 11 +-
PReMiuM-3.1.0/PReMiuM/man/calcAvgRiskAndProfile.Rd | 6 +
PReMiuM-3.1.0/PReMiuM/man/calcOptimalClustering.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/calcPredictions.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/clusSummaryBernoulliDiscrete.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/computeRatioOfVariance.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/generateSampleDataFile.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/globalParsTrace.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/heatDissMat.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/is.wholenumber.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/mapforGeneratedData.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/margModelPosterior.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/plotPredictions.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/plotRiskProfile.Rd | 4 -
PReMiuM-3.1.0/PReMiuM/man/profRegr.Rd | 4 -
PReMiuM-3.1.0/PReMiuM/man/setHyperparams.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/summariseVarSelectRho.Rd | 2
PReMiuM-3.1.0/PReMiuM/man/vec2mat.Rd | 2
PReMiuM-3.1.0/PReMiuM/src/include/PReMiuMModel.h | 1
PReMiuM-3.1.0/PReMiuM/src/include/PReMiuMProposals.h | 8 --
26 files changed, 101 insertions(+), 81 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Diff between JMbayes versions 0.6-1 dated 2014-06-11 and 0.7-0 dated 2015-03-13
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 12
MD5 | 83 ++--
NAMESPACE | 14
R/MCMCfit.R | 820 +++++++++++++++++++++++++++++++----------------
R/NextVisit.R | 18 -
R/adjustScaleRW.R | 6
R/bdiag.R | 1
R/check_td.R |only
R/cvDCL.R |only
R/dmvnorm.R | 11
R/dropAttr.R | 9
R/dynInfo.R |only
R/find_positions.R |only
R/ibs.R | 6
R/initSurvival.R | 7
R/ins.R | 6
R/jointModelBayes.R | 170 +++++++--
R/log.posterior.b.R | 2
R/logLik.JMbayes.R | 4
R/logh.b.R | 4
R/marglogLik.R | 11
R/plot.rocJM.R |only
R/plot.survfit.JMbayes.R | 10
R/predict.JMbayes.R | 17
R/print.rocJM.R |only
R/rocJM.JMbayes.R |only
R/rocJM.R |only
R/rowMedians.R |only
R/runDynPred.R |only
R/slice.shape.R | 22 -
R/survfitJM.JMbayes.R | 25 -
R/xtable.JMbayes.R | 2
data/aids.id.rda |binary
data/aids.rda |binary
data/pbc2.id.rda |binary
data/pbc2.rda |binary
data/prothro.rda |binary
data/prothros.rda |binary
demo/server.R | 115 ++++++
demo/ui.R | 5
inst/NEWS | 11
man/JMbayes.Rd | 4
man/aucJM.Rd | 14
man/bma.combine.Rd | 5
man/cvDCL.Rd |only
man/dynInfo.Rd |only
man/runDynPred.Rd |only
man/survfitJM.Rd | 9
man/xtable.Rd | 7
49 files changed, 1009 insertions(+), 421 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-03 0.3-3
2014-09-07 0.3-1
2014-09-07 0.3-2
2014-09-01 0.3-0
Title: Analysis of Heavy Tailed Distributions
Diff between poweRlaw versions 0.30.0 dated 2015-02-20 and 0.30.1 dated 2015-03-13
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.Rnw |only
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/blackouts.txt |only
poweRlaw-0.30.0/poweRlaw/vignettes/v61i10.Rnw |only
poweRlaw-0.30.0/poweRlaw/vignettes/v61i10.bib |only
poweRlaw-0.30.1/poweRlaw/DESCRIPTION | 8 -
poweRlaw-0.30.1/poweRlaw/MD5 | 65 +++++------
poweRlaw-0.30.1/poweRlaw/NEWS | 5
poweRlaw-0.30.1/poweRlaw/R/def_conexp.R | 34 ++---
poweRlaw-0.30.1/poweRlaw/R/def_conlorm.R | 29 ++--
poweRlaw-0.30.1/poweRlaw/R/def_conpl.R | 19 +--
poweRlaw-0.30.1/poweRlaw/R/def_disexp.R | 23 ++-
poweRlaw-0.30.1/poweRlaw/R/def_dislnorm.R | 23 ++-
poweRlaw-0.30.1/poweRlaw/R/def_dispois.R | 25 ++--
poweRlaw-0.30.1/poweRlaw/R/plcon.R | 20 ++-
poweRlaw-0.30.1/poweRlaw/R/pldis.R | 47 ++++---
poweRlaw-0.30.1/poweRlaw/build/vignette.rds |binary
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.R | 2
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.Rnw | 18 ---
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.pdf |binary
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.R | 4
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.Rnw | 27 ----
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.30.1/poweRlaw/inst/doc/poweRlaw.R | 3
poweRlaw-0.30.1/poweRlaw/inst/doc/poweRlaw.Rnw | 41 ------
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poweRlaw-0.30.1/poweRlaw/inst/doc/v64i02.pdf |only
poweRlaw-0.30.1/poweRlaw/vignettes/compare_distributions.Rnw | 18 ---
poweRlaw-0.30.1/poweRlaw/vignettes/examples.Rnw | 27 ----
poweRlaw-0.30.1/poweRlaw/vignettes/figure1.pdf |binary
poweRlaw-0.30.1/poweRlaw/vignettes/figure2.pdf |binary
poweRlaw-0.30.1/poweRlaw/vignettes/figure3.pdf |binary
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poweRlaw-0.30.1/poweRlaw/vignettes/figure5.pdf |binary
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poweRlaw-0.30.1/poweRlaw/vignettes/v64i02.Rnw |only
poweRlaw-0.30.1/poweRlaw/vignettes/v64i02.bib |only
38 files changed, 176 insertions(+), 303 deletions(-)
Title: Person Fit
Diff between PerFit versions 1.2 dated 2014-10-07 and 1.3 dated 2015-03-13
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro
PerFit-1.2/PerFit/R/Code.R |only
PerFit-1.3/PerFit/DESCRIPTION | 24 ++-
PerFit-1.3/PerFit/MD5 | 80 ++++++++----
PerFit-1.3/PerFit/NAMESPACE | 56 +++++---
PerFit-1.3/PerFit/R/ADE.R |only
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PerFit-1.3/PerFit/R/PRF.R | 165 +++++++++++++++++++-------
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PerFit-1.3/PerFit/data/IntelligenceData.RData |binary
PerFit-1.3/PerFit/data/PhysFuncData.RData |binary
PerFit-1.3/PerFit/man/ADE.KB.Rd | 74 +++++++++--
PerFit-1.3/PerFit/man/C.index.Rd | 141 ++++++++++++++--------
PerFit-1.3/PerFit/man/G.Rd | 144 ++++++++++++++--------
PerFit-1.3/PerFit/man/Gpoly.Rd | 142 ++++++++++++++--------
PerFit-1.3/PerFit/man/Ht.Rd | 135 +++++++++++++--------
PerFit-1.3/PerFit/man/NCI.Rd | 119 ++++++++++++------
PerFit-1.3/PerFit/man/PRFplot.Rd | 87 ++++++++++---
PerFit-1.3/PerFit/man/PerFit-package.Rd | 55 ++++----
PerFit-1.3/PerFit/man/PerFitPFS.Rd |only
PerFit-1.3/PerFit/man/PerFitSE.Rd |only
PerFit-1.3/PerFit/man/U3.Rd | 146 ++++++++++++++---------
PerFit-1.3/PerFit/man/U3poly.Rd | 52 +++++++-
PerFit-1.3/PerFit/man/cutoff.Rd | 53 +++++---
PerFit-1.3/PerFit/man/flagged.resp.Rd | 65 ++++++----
PerFit-1.3/PerFit/man/lz.Rd | 74 ++++++++---
PerFit-1.3/PerFit/man/lzpoly.Rd | 137 ++++++++++++---------
PerFit-1.3/PerFit/man/plot.PerFit.Rd | 69 +++++++---
PerFit-1.3/PerFit/man/print.PerFit.Rd |only
PerFit-1.3/PerFit/man/r.pbis.Rd | 107 +++++++++++-----
PerFit-1.3/PerFit/man/summary.PerFit.Rd |only
59 files changed, 1296 insertions(+), 629 deletions(-)
Title: Methods for Patient-Centered Network Meta-Analysis
Diff between pcnetmeta versions 1.2 dated 2014-07-19 and 1.3 dated 2015-03-13
Description: Provides functions to conduct network meta-analysis using arm-based method, which was proposed by Zhang et al (2014); contains functions to generate summary table for effect sizes (e.g., odds ratio, population-averaged event rate), plot network comparisons, and plot credible interval for population-averaged event rate.
Author: Lifeng Lin, Jing Zhang
Maintainer: Lifeng Lin
DESCRIPTION | 15 ++++++++-------
MD5 | 8 ++++----
NAMESPACE | 3 ++-
man/nma.ab.Rd | 1 +
man/pcnetmeta-package.Rd | 2 +-
5 files changed, 16 insertions(+), 13 deletions(-)
Title: Clustering in the Discriminative Functional Subspace
Diff between funFEM versions 1.0 dated 2014-09-11 and 1.1 dated 2015-03-13
Description: The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace.
Author: Charles Bouveyron
Maintainer: Charles Bouveyron
DESCRIPTION | 8 ++++----
MD5 | 8 +++++---
data/velib.rda |binary
data/velov.rda |only
man/velib.Rd | 4 ++--
man/velov.Rd |only
6 files changed, 11 insertions(+), 9 deletions(-)
Title: Business Days Calculations and Utilities
Diff between bizdays versions 0.2.1 dated 2015-02-01 and 0.2.2 dated 2015-03-13
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas
Maintainer: Wilson Freitas
DESCRIPTION | 8 ++-
MD5 | 47 ++++++++++++---------
NAMESPACE | 2
NEWS | 9 ++++
R/calendar.R | 28 +++++++-----
README.md | 4 -
build |only
inst/doc |only
inst/tests/test-calendar.R | 14 +++++-
man/Calendar.Rd | 15 +++---
man/adjust.date.Rd | 3 -
man/bizdays-package.Rd | 3 -
man/bizdays.Rd | 3 -
man/bizdays.options.Rd | 3 -
man/bizdayse.Rd | 3 -
man/bizseq.Rd | 3 -
man/bizyears.Rd | 3 -
man/bizyearse.Rd | 3 -
man/holidaysANBIMA.Rd | 3 -
man/is.bizday.Rd | 3 -
man/offset.Rd | 3 -
vignettes/Setting_default_calendar_in_Rprofile.Rmd | 4 +
vignettes/Using_bizdays.Rmd | 8 ++-
23 files changed, 111 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-10 1.4.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-21 1.1
2013-02-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-20 0.2.3
2010-09-16 0.2.2
2009-06-19 0.2.1
2009-06-18 0.2
2008-05-16 0.1.2
2008-05-04 0.1.1
2008-04-29 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-01 1.1
2014-11-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-04-09 0.9-8
2007-03-23 0.9-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-27 0.60-2
2014-06-01 0.60-0
2014-01-01 0.50-1.1
2013-03-14 0.50-1
2012-03-06 0.40-13
2011-11-25 0.40-12
2011-10-25 0.40-11
2011-10-24 0.40-10
2011-07-30 0.40-9
2011-06-09 0.40-7
2011-06-02 0.40-6
2011-04-26 0.40-5
2011-01-21 0.40-4
2010-07-25 0.40-3
2010-06-10 0.40-2
2010-05-26 0.40-0
2010-05-18 0.30-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-13 0.5-0
2013-09-13 0.4-0
2013-08-07 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-20 1.2
2013-02-24 1.1
2012-05-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-07 2.0
2012-09-26 1.8
2012-06-06 1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-13 0.4
2014-09-30 0.3
2014-09-04 0.2
2014-08-28 0.1
Title: Separation Plots
Description: Functions to generate separation plots for evaluation of
model fit.
Author: Brian D. Greenhill, Michael D. Ward and Audrey Sacks
Maintainer: ORPHANED
Diff between separationplot versions 1.0 dated 2011-06-15 and 1.1 dated 2015-03-13
DESCRIPTION | 19 ++++++++++++------- MD5 |only NAMESPACE |only R/separationplot.R | 8 ++------ R/sp.categorical.R | 5 +---- man/separationplot-package.Rd | 4 +++- man/separationplot.Rd | 9 +++++++-- man/sp.categorical.Rd | 28 +++++++++++++++++++--------- 8 files changed, 44 insertions(+), 29 deletions(-)
More information about separationplot at CRAN
Permanent link
Title: PCIC Implementation of Climdex Routines
Diff between climdex.pcic versions 1.1-5 dated 2015-01-30 and 1.1-5.1 dated 2015-03-13
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh
Maintainer: James Hiebert
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/climdexInput.csv.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Standardized Beta Coefficients
Diff between betas versions 0.1.0 dated 2015-01-14 and 0.1.1 dated 2015-03-13
Description: Computes standardized beta coefficients and corresponding
standard errors for the following models:
linear regression models with numerical covariates only,
linear regression models with numerical and factorial covariates,
weighted linear regression models,
all these linear regression models with interaction terms, and
robust linear regression models with numerical covariates only.
Author: Andrea Cantieni [aut, cre]
Maintainer: Andrea Cantieni
DESCRIPTION | 15 ++++++++-------
MD5 | 8 ++++----
R/betas.R | 42 +++++++++++++++++++++++++++---------------
README.md | 4 ++--
man/betas.lm.Rd | 15 +++++++++++++++
5 files changed, 56 insertions(+), 28 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Diff between rcbalance versions 1.2 dated 2014-11-12 and 1.3 dated 2015-03-13
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel
DESCRIPTION | 8 -
LICENSE | 2
MD5 | 14 +-
R/rcbalance-internal.R | 236 +++++++++++++++++------------------------------
R/rcbalance.R | 62 +++++++-----
man/dist2net.Rd | 15 +-
man/rcbalance-package.Rd | 4
man/rcbalance.Rd | 6 -
8 files changed, 154 insertions(+), 193 deletions(-)
Title: Holiday and Half-Day Data, for Use with the 'TimeWarp' Package
Diff between Holidays versions 1.0-0 dated 2011-12-19 and 1.0-6 dated 2015-03-13
Description: Contains trading holiday and half-day data that is automatically registered when loaded.
Author: Jeffery Horner, Lars Hansen, Tony Plate
Maintainer: Tony Plate
DESCRIPTION | 15 -
MD5 | 13 -
NEWS |only
R/holidays.R | 397 ++++++++++++++++++++++++++++++++++++++++++++++--
inst |only
man/Holidays-package.Rd | 4
tests/Makefile | 22 +-
tests/holidays.Rt | 9 -
8 files changed, 419 insertions(+), 41 deletions(-)
Title: Combine Multidimensional Arrays
Diff between abind versions 1.4-0 dated 2011-11-27 and 1.4-3 dated 2015-03-13
Description: Combine multidimensional arrays into a single array.
This is a generalization of 'cbind' and 'rbind'. Works with
vectors, matrices, and higher-dimensional arrays. Also
provides functions 'adrop', 'asub', and 'afill' for manipulating,
extracting and replacing data in arrays.
Author: Tony Plate
Maintainer: Tony Plate
abind-1.4-0/abind/DevNotes.txt |only
abind-1.4-3/abind/ChangeLog | 7 ++--
abind-1.4-3/abind/DESCRIPTION | 17 ++++++-----
abind-1.4-3/abind/MD5 | 21 ++++++++------
abind-1.4-3/abind/NAMESPACE | 3 +-
abind-1.4-3/abind/R/abind.R | 47 ++++++++++++++++++++++++++------
abind-1.4-3/abind/R/acorn.R |only
abind-1.4-3/abind/inst |only
abind-1.4-3/abind/man/abind.Rd | 13 ++++++--
abind-1.4-3/abind/man/acorn.Rd |only
abind-1.4-3/abind/tests/abind.R | 3 ++
abind-1.4-3/abind/tests/abind.Rout.save | 15 ++++++++++
abind-1.4-3/abind/tests/dnns.R |only
abind-1.4-3/abind/tests/dnns.Rout.save |only
14 files changed, 94 insertions(+), 32 deletions(-)
Title: Maximum Likelihood and Bayesian Estimation of Univariate
Probability Distributions
Diff between FAmle versions 1.3.2 dated 2015-01-04 and 1.3.3 dated 2015-03-12
Description: Estimate parameters of univariate probability distributions
with maximum likelihood and Bayesian methods.
Author: Francois Aucoin
Maintainer: Thomas Petzoldt
DESCRIPTION | 12 +-
MD5 | 14 +--
NAMESPACE | 7 +
build/vignette.rds |binary
inst/doc/FAmle.R | 210 ++++++++++++++++++++++++++++++----------------------
inst/doc/FAmle.pdf |binary
inst/doc/FAmle.rnw | 145 ++++++++++++++++++++++-------------
vignettes/FAmle.rnw | 145 ++++++++++++++++++++++-------------
8 files changed, 322 insertions(+), 211 deletions(-)
Title: Bootstrap Tolerance Levels for Credit Scoring Validation
Statistics
Diff between boottol versions 1.0 dated 2015-02-20 and 2.0 dated 2015-03-12
Description: Used to create bootstrap tolerance levels for the Kolmogorov-Smirnov (KS) statistic, the area under receiver operator characteristic curve (AUROC) statistic, and the Gini coefficient for each score cutoff. Also provides a bootstrap alternative to the Vasicek test.
Author: Garrett Schiltgen
Maintainer: Garrett Schiltgen
DESCRIPTION | 12 +-
MD5 | 14 +-
NAMESPACE | 3
R/boottol.R | 297 +++++++++++++++++++++++++++----------------------------
R/vastol.R |only
data/vasdata.rda |only
man/boottol.Rd | 16 ++
man/data.Rd | 2
man/vasdata.Rd |only
man/vastol.Rd |only
10 files changed, 174 insertions(+), 170 deletions(-)
Title: Qualitative Validation Methods
Diff between qualV versions 0.3 dated 2011-03-26 and 0.3-1 dated 2015-03-12
Description: Qualitative methods for the validation of models.
Author: K. Gerald van den Boogaart [aut, ths],
Stefanie Rost [aut],
Thomas Petzoldt [aut, ths, cre]
Maintainer: Thomas Petzoldt
DESCRIPTION | 15 +++++++++++----
MD5 |only
NAMESPACE | 9 +++++++++
data/phyto.rda |binary
inst/NEWS | 37 ++++++++++++++++++++-----------------
5 files changed, 40 insertions(+), 21 deletions(-)
Title: Interactive Grammar of Graphics
Diff between ggvis versions 0.4 dated 2014-10-04 and 0.4.1 dated 2015-03-12
Description: An implementation of an interactive grammar of graphics, taking the
best parts of ggplot2, combining them with shiny's reactive framework and
drawing web graphics using vega.
Author: Winston Chang [aut, cre],
Hadley Wickham [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/lib/jquery/AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/lib/jquery-ui/AUTHORS.txt),
Mike Bostock [ctb, cph] (D3 library),
D3 contributors [ctb] (D3 library; authors listed at
https://github.com/mbostock/d3/graphs/contributors),
Trifacta Inc. [cph] (Vega library),
Vega contributors [ctb] (Vega library; authors listed at
https://github.com/trifacta/vega/graphs/contributors)
Maintainer: Winston Chang
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/DESCRIPTION | 49
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/LICENSE |only
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/MD5 | 313
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/NAMESPACE | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/dplyr.R | 67
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/ggvis_html.R | 4
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/inputs.R | 19
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/interact_tooltip.R | 5
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/options.R | 4
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/print.R | 22
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/prop.R | 5
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/shiny.R | 14
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/shiny_layout.R | 2
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/R/zzz.r | 2
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/build/vignette.rds |binary
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/demo/apps/basic/ui.r | 2
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/demo/apps/brush-linked/server.r | 4
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/demo/apps/brush-linked/ui.r | 2
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/demo/rmarkdown/linked_brush.Rmd | 4
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/axes-legends.html | 2665 +--
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/cookbook.html | 4644 +++---
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/ggvis-basics.html | 7301 +++++-----
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/interactivity.html | 1221 -
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/layers.html | 2767 +--
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/overview.html | 476
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/doc/properties-scales.html | 1868 +-
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/ggvis/css/ggvis.css | 1
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/ggvis/js/ggvis.js | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/ggvis/js/shiny-ggvis.js | 20
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/d3/d3.js | 999 -
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/d3/d3.min.js | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/jquery-ui/AUTHORS.txt |only
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/jquery/AUTHORS.txt |only
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/vega/vega.js | 452
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/inst/www/lib/vega/vega.min.js | 9
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_axis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_data.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_guide_axis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_guide_legend.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_legend.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_relative_scales.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_scale.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/add_tooltip.Rd | 8
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/as.vega.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/auto_group.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/axis_props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/band.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/bin_vector.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/cocaine.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_align.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_bin.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_boxplot.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_count.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_density.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_model_prediction.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_stack.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/compute_tabulate.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/create_broker.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/create_input.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/default_options.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/dplyr-ggvis.Rd | 27
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/explain.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/explain.ggvis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/export_png.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/fullseq.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/get_data.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/ggvis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/ggvisControlOutput.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/ggvisOutputElements.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/ggvis_message.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/ggvis_scale.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/group_by.Rd | 5
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/handle_brush.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/handle_click.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/handle_resize.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/input_checkbox.Rd | 5
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/input_select.Rd | 5
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/input_slider.Rd | 27
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/input_text.Rd | 7
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.axis_props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.broker.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.dynamic.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.ggvis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.legend_props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/is.scaled_value.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/knit_print.ggvis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_bars.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_boxplots.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_densities.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_f.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_guess.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_histograms.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_lines.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/layer_model_predictions.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/left_right.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/legend_props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/linked_brush.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/mark.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/marks.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/new_prop.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/padding.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/pipe.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/print.ggvis.Rd | 22
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/prop.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/prop_domain.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/propname_to_scale.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/props.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/resolution.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/save_spec.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scale_datetime.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scale_numeric.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scale_ordinal.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scaled_value.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scales.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/scaletype_to_vega_scaletype.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/set_options.Rd | 7
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/set_scale_label.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/shiny-ggvis.Rd | 8
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/show_spec.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/show_tooltip.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/sidebarBottomPage.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/singular.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/subvis.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/vector_type.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/vega_data_parser.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/waggle.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/man/zero_range.Rd | 3
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/bar/categorical-x.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/bar/continuous-x.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/boxplot/boxplot-categorical.json | 28
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/boxplot/boxplot-continuous.json | 28
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/boxplot/boxplot-no-outliers.json | 28
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/data/dots.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/layer/freqpoly-grouped.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/layer/histogram.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/layer/smooth-grouped.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/layer/smooth.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/line/basic.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/line/layer-line-nominal-x.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/line/layer-line.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/line/sort.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/bars.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/combined_legend.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/custom.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/datetime.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/datetime_hist.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/domain_numeric.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/dual.json | 10
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/hide_guides.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scales/log.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scatter/basic.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scatter/fill-continuous.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scatter/fill-discrete.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/specs/scatter/transform.json | 6
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/testthat/test-props.r | 2
tmp/cranberry296a57ce7d6d/ggvis-0.4.1/ggvis/tests/testthat/test-utils-data.r | 14
ui.r | 4
158 files changed, 12559 insertions(+), 11047 deletions(-)
Title: Distributions that are Sometimes Used in Hydrology
Diff between FAdist versions 2.0 dated 2011-09-23 and 2.1 dated 2015-03-12
Description: Probability distributions that are sometimes useful in hydrology.
Author: Francois Aucoin
Maintainer: Thomas Petzoldt
DESCRIPTION | 18 +++----
INDEX | 52 +++++++++++-----------
MD5 | 117 +++++++++++++++++++++++++-------------------------
NAMESPACE |only
R/dgamma3.R | 16 +++---
R/dgev.R | 16 +++---
R/dgp.R | 16 +++---
R/dgumbel.R | 16 +++---
R/dkappa.R | 16 +++---
R/dkappa4.R | 16 +++---
R/dlgamma3.R | 16 +++---
R/dllog.R | 16 +++---
R/dllog3.R | 16 +++---
R/dlnorm3.R | 16 +++---
R/dweibull3.R | 8 +--
R/pgamma3.R | 18 +++----
R/pgev.R | 18 +++----
R/pgp.R | 18 +++----
R/pgumbel.R | 18 +++----
R/pkappa.R | 18 +++----
R/pkappa4.R | 18 +++----
R/plgamma3.R | 18 +++----
R/pllog.R | 18 +++----
R/pllog3.R | 18 +++----
R/plnorm3.R | 18 +++----
R/pweibull3.R | 8 +--
R/qgamma3.R | 18 +++----
R/qgev.R | 18 +++----
R/qgp.R | 18 +++----
R/qgumbel.R | 18 +++----
R/qkappa.R | 18 +++----
R/qkappa4.R | 20 ++++----
R/qlgamma3.R | 18 +++----
R/qllog.R | 18 +++----
R/qllog3.R | 18 +++----
R/qlnorm3.R | 18 +++----
R/qweibull3.R | 18 +++----
R/rgamma3.R | 8 +--
R/rgev.R | 8 +--
R/rgp.R | 8 +--
R/rgumbel.R | 8 +--
R/rkappa.R | 8 +--
R/rkappa4.R | 6 +-
R/rlgamma3.R | 8 +--
R/rllog.R | 8 +--
R/rllog3.R | 8 +--
R/rlnorm3.R | 8 +--
R/rweibull3.R | 8 +--
man/FAdist-package.Rd | 30 ++++++------
man/GAMMA3.Rd | 116 +++++++++++++++++++++++--------------------------
man/GEV.Rd | 111 ++++++++++++++++++++++-------------------------
man/GUMBEL.Rd | 108 ++++++++++++++++++++++------------------------
man/GenPARETO.Rd | 110 +++++++++++++++++++++--------------------------
man/KAPPA.Rd | 106 ++++++++++++++++++++-------------------------
man/KAPPA4.Rd | 114 ++++++++++++++++++++++++------------------------
man/LGAMMA3.Rd | 116 ++++++++++++++++++++++++-------------------------
man/LLOGIS.Rd | 107 +++++++++++++++++++++------------------------
man/LLOGIS3.Rd | 114 ++++++++++++++++++++++++------------------------
man/LNORM3.Rd | 114 +++++++++++++++++++++++-------------------------
man/WEIBULL3.Rd | 112 ++++++++++++++++++++++-------------------------
60 files changed, 1019 insertions(+), 1068 deletions(-)
Title: Identification of Cardinal Dates in Ecological Time Series
Diff between cardidates versions 0.4.5 dated 2013-12-18 and 0.4.6 dated 2015-03-12
Description: Identification of cardinal dates
(begin, time of maximum, end of mass developments)
in ecological time series using fitted Weibull functions.
Author: Susanne Rolinski [aut], René Sachse [aut], Thomas Petzoldt [aut, cre]
Maintainer: Thomas Petzoldt
cardidates-0.4.5/cardidates/vignettes/Z.cls |only
cardidates-0.4.6/cardidates/DESCRIPTION | 11 ++--
cardidates-0.4.6/cardidates/MD5 | 20 ++++----
cardidates-0.4.6/cardidates/NAMESPACE | 2
cardidates-0.4.6/cardidates/R/plot.cardiMetacdw.R | 1
cardidates-0.4.6/cardidates/build |only
cardidates-0.4.6/cardidates/inst/doc/vignette.R | 35 +++++++--------
cardidates-0.4.6/cardidates/inst/doc/vignette.Rnw | 41 ++++++++++++------
cardidates-0.4.6/cardidates/inst/doc/vignette.pdf |binary
cardidates-0.4.6/cardidates/man/cardidates-package.Rd | 4 -
cardidates-0.4.6/cardidates/vignettes/cardidates.bib | 19 ++++++--
cardidates-0.4.6/cardidates/vignettes/vignette.Rnw | 41 ++++++++++++------
12 files changed, 107 insertions(+), 67 deletions(-)
Title: Unified Multiple Testing Procedures
Diff between mutoss versions 0.1-8 dated 2014-02-17 and 0.1-9 dated 2015-03-12
Description: The Mutoss package and accompanying mutossGUI package are
designed to ease the application and comparison of multiple
hypothesis testing procedures.
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 8 +-
MD5 | 14 +--
NEWS | 42 +++++++----
R/Hommel.R | 3
R/localfdr.R | 166 ++++++++++++++++++++++-----------------------
build/vignette.rds |binary
inst/doc/quickstart.pdf |binary
inst/doc/simToolManual.pdf |binary
8 files changed, 123 insertions(+), 110 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Diff between icd9 versions 1.0 dated 2015-01-27 and 1.1 dated 2015-03-12
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey
icd9-1.0/icd9/R/RcppExportsShim.R |only
icd9-1.0/icd9/R/old.R |only
icd9-1.0/icd9/inst/doc/icd9.R |only
icd9-1.0/icd9/inst/doc/icd9.pdf |only
icd9-1.0/icd9/src/slow.cpp |only
icd9-1.0/icd9/tests/testthat/test-fast-convert.R |only
icd9-1.0/icd9/tests/testthat/test-fast-explain.R |only
icd9-1.0/icd9/tests/testthat/test-fast-icd9.R |only
icd9-1.0/icd9/tests/testthat/test-fast-ranges.R |only
icd9-1.0/icd9/tests/testthat/test-fast-reshape.R |only
icd9-1.0/icd9/tests/testthat/test-fast-sas.R |only
icd9-1.0/icd9/tests/testthat/test-fast-score.R |only
icd9-1.0/icd9/tests/testthat/test-fast-valid.R |only
icd9-1.0/icd9/tests/testthat/test-slow-comorbid.R |only
icd9-1.0/icd9/tests/testthat/test-slow-score.R |only
icd9-1.1/icd9/DESCRIPTION | 14
icd9-1.1/icd9/MD5 | 150 +--
icd9-1.1/icd9/NAMESPACE | 5
icd9-1.1/icd9/R/RcppExports.R | 113 --
icd9-1.1/icd9/R/benchmark.R | 254 ++++-
icd9-1.1/icd9/R/comorbid.R | 241 +++--
icd9-1.1/icd9/R/convert.R | 192 ++--
icd9-1.1/icd9/R/explain.R | 123 +-
icd9-1.1/icd9/R/filter.R | 19
icd9-1.1/icd9/R/manip.R | 11
icd9-1.1/icd9/R/parse.R | 13
icd9-1.1/icd9/R/ranges.R | 91 +-
icd9-1.1/icd9/R/sas.R | 6
icd9-1.1/icd9/R/score.R | 121 +-
icd9-1.1/icd9/R/sysdata.rda |binary
icd9-1.1/icd9/R/util.R | 37
icd9-1.1/icd9/R/valid.R | 80 +
icd9-1.1/icd9/R/zzz.R | 3
icd9-1.1/icd9/README.md | 98 --
icd9-1.1/icd9/build/vignette.rds |binary
icd9-1.1/icd9/data/mappingNames.rda |binary
icd9-1.1/icd9/inst/doc/introduction.R | 15
icd9-1.1/icd9/inst/doc/introduction.Rmd | 27
icd9-1.1/icd9/inst/doc/introduction.html | 675 +++++----------
icd9-1.1/icd9/inst/include/icd9_RcppExports.h | 388 ++------
icd9-1.1/icd9/man/convert.Rd | 7
icd9-1.1/icd9/man/cr.Rd |only
icd9-1.1/icd9/man/icd9AddLeadingZeroes.Rd | 23
icd9-1.1/icd9/man/icd9Charlson.Rd | 10
icd9-1.1/icd9/man/icd9Children.Rd | 33
icd9-1.1/icd9/man/icd9Comorbid.Rd | 48 -
icd9-1.1/icd9/man/icd9ComorbidDfToMat.Rd |only
icd9-1.1/icd9/man/icd9ComorbidMatToDf.Rd |only
icd9-1.1/icd9/man/icd9Condense.Rd | 13
icd9-1.1/icd9/man/icd9Count.Rd | 6
icd9-1.1/icd9/man/icd9DropLeadingZeroes.Rd | 7
icd9-1.1/icd9/man/icd9Explain.Rd | 46 -
icd9-1.1/icd9/man/icd9ExtractAlphaNumeric.Rd | 7
icd9-1.1/icd9/man/icd9GetValid.Rd | 7
icd9-1.1/icd9/man/icd9InReferenceCode.Rd | 7
icd9-1.1/icd9/man/icd9Is.Rd | 10
icd9-1.1/icd9/man/icd9IsReal.Rd | 7
icd9-1.1/icd9/man/icd9IsValid.Rd | 7
icd9-1.1/icd9/man/icd9LongToWide.Rd | 34
icd9-1.1/icd9/man/icd9Sort.Rd | 7
icd9-1.1/icd9/man/icd9WideToLong.Rd | 8
icd9-1.1/icd9/src/Makevars | 9
icd9-1.1/icd9/src/Makevars.win |only
icd9-1.1/icd9/src/RcppExports.cpp | 929 +++++----------------
icd9-1.1/icd9/src/comorbid.cpp | 229 ++---
icd9-1.1/icd9/src/comorbidCommon.cpp |only
icd9-1.1/icd9/src/comorbidSetup.cpp |only
icd9-1.1/icd9/src/convert.cpp | 342 ++++---
icd9-1.1/icd9/src/convert.h |only
icd9-1.1/icd9/src/cutil.c |only
icd9-1.1/icd9/src/cutil.h |only
icd9-1.1/icd9/src/is.cpp | 74 +
icd9-1.1/icd9/src/is.h |only
icd9-1.1/icd9/src/local.h |only
icd9-1.1/icd9/src/longToWide.cpp |only
icd9-1.1/icd9/src/manip.cpp | 119 +-
icd9-1.1/icd9/src/manip.h |only
icd9-1.1/icd9/src/ranges.cpp | 54 -
icd9-1.1/icd9/src/ranges.h |only
icd9-1.1/icd9/src/util.cpp | 73 +
icd9-1.1/icd9/src/util.h |only
icd9-1.1/icd9/tests/testthat/helper-base.R | 8
icd9-1.1/icd9/tests/testthat/test-LongToWide.R |only
icd9-1.1/icd9/tests/testthat/test-comorbid-calcs.R |only
icd9-1.1/icd9/tests/testthat/test-comorbid.R |only
icd9-1.1/icd9/tests/testthat/test-convert.R |only
icd9-1.1/icd9/tests/testthat/test-explain.R |only
icd9-1.1/icd9/tests/testthat/test-filter.R |only
icd9-1.1/icd9/tests/testthat/test-icd9.R |only
icd9-1.1/icd9/tests/testthat/test-is.R | 26
icd9-1.1/icd9/tests/testthat/test-ranges.R |only
icd9-1.1/icd9/tests/testthat/test-reshape.R |only
icd9-1.1/icd9/tests/testthat/test-sas.R |only
icd9-1.1/icd9/tests/testthat/test-score.R |only
icd9-1.1/icd9/tests/testthat/test-util.R | 15
icd9-1.1/icd9/tests/testthat/test-valid.R |only
icd9-1.1/icd9/vignettes/introduction.Rmd | 27
97 files changed, 2292 insertions(+), 2576 deletions(-)
Title: Genome-Wide Association/Interaction Analysis and Rare Variant
Analysis with Family Data
Diff between GWAF versions 2.1 dated 2013-06-07 and 2.2 dated 2015-03-12
Description: Functions for genome-wide association/interaction analysis and rare variant analysis on a continuous/dichotomous trait using family data, and for making genome-wide p-value plot and QQ plot.
Author: Ming-Huei Chen
Maintainer: Ming-Huei Chen
DESCRIPTION | 17 +++++++----------
MD5 | 4 ++--
NAMESPACE | 4 +++-
3 files changed, 12 insertions(+), 13 deletions(-)
Title: Bayesian Projection of Life Expectancy
Diff between bayesLife versions 2.1-3 dated 2014-11-20 and 2.2-0 dated 2015-03-12
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova, Adrian Raftery; original WinBugs code written by Jennifer Chunn
Maintainer: Hana Sevcikova
ChangeLog | 11 +++++++++++
DESCRIPTION | 10 +++++-----
MD5 | 18 +++++++++---------
R/projection_fcns.R | 27 +++++++++++++++++++--------
R/run_mcmc.R | 20 ++++++++++++--------
R/wpp_data.R | 15 +++++++++------
man/joint.male.estimate.Rd | 4 +++-
man/joint.male.predict.Rd | 3 ++-
man/run.e0.mcmc.Rd | 10 +++++++---
man/run.e0.mcmc.extra.Rd | 7 +++++--
10 files changed, 82 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-10 0.3
2012-11-15 0.2-18
2012-04-20 0.2-17
2011-09-29 0.2-16
2010-01-27 0.2-15
2009-08-25 0.2-14
2009-08-13 0.2-13
2009-07-01 0.2-11
2009-06-09 0.2-10
2009-04-14 0.2-9
2009-03-04 0.2-8
2009-02-25 0.2-6
Title: Tools to Determine DNA Profile Evidence
Diff between likeLTD versions 5.4.0 dated 2014-07-10 and 5.5.0 dated 2015-03-12
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide at the URL provided,
or the paper under citation.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele
likeLTD-5.4.0/likeLTD/data/lgc-allele-freqs-wbp.txt.gz |only
likeLTD-5.4.0/likeLTD/man/lgc-allele-freqs-wbp.Rd |only
likeLTD-5.5.0/likeLTD/DESCRIPTION | 10
likeLTD-5.5.0/likeLTD/MD5 | 103 -
likeLTD-5.5.0/likeLTD/NAMESPACE | 5
likeLTD-5.5.0/likeLTD/R/genetics.R | 177 ++
likeLTD-5.5.0/likeLTD/R/hypothesis.R | 95 +
likeLTD-5.5.0/likeLTD/R/maximize.R | 665 +++-------
likeLTD-5.5.0/likeLTD/R/plotter.R | 2
likeLTD-5.5.0/likeLTD/R/reports.R | 52
likeLTD-5.5.0/likeLTD/data/DNA17-db.txt.gz |only
likeLTD-5.5.0/likeLTD/data/Identifiler-db.txt.gz |only
likeLTD-5.5.0/likeLTD/data/SGMplus-db.txt.gz |only
likeLTD-5.5.0/likeLTD/data/linkage.txt.gz |only
likeLTD-5.5.0/likeLTD/demo/hammer.R | 2
likeLTD-5.5.0/likeLTD/demo/plotter.R | 2
likeLTD-5.5.0/likeLTD/demo/timings.R | 2
likeLTD-5.5.0/likeLTD/inst/doc/likeLTDguide.pdf |binary
likeLTD-5.5.0/likeLTD/inst/doc/usage.R | 14
likeLTD-5.5.0/likeLTD/inst/doc/usage.Rnw | 3
likeLTD-5.5.0/likeLTD/inst/doc/usage.pdf |binary
likeLTD-5.5.0/likeLTD/inst/extdata/hammer/hammer-CSP.csv | 10
likeLTD-5.5.0/likeLTD/inst/extdata/hammer/hammer-reference.csv | 8
likeLTD-5.5.0/likeLTD/inst/extdata/hammer/space-CSP.csv | 10
likeLTD-5.5.0/likeLTD/inst/extdata/hammer/space-reference.csv | 8
likeLTD-5.5.0/likeLTD/inst/extdata/nodropin/hammer-CSP.csv | 10
likeLTD-5.5.0/likeLTD/inst/extdata/nodropin/hammer-reference.csv | 8
likeLTD-5.5.0/likeLTD/inst/extdata/nodropout/CSP.csv | 10
likeLTD-5.5.0/likeLTD/inst/extdata/nodropout/reference.csv | 4
likeLTD-5.5.0/likeLTD/inst/extdata/novictim/hammer-CSP.csv | 10
likeLTD-5.5.0/likeLTD/inst/extdata/novictim/hammer-reference.csv | 4
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_genetics.R | 98 -
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_hypothesis.R | 28
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_nodropin.R | 34
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_nodropout.R | 16
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_novictims.R | 16
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_objective.R | 58
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_objectivePerLocus.R | 12
likeLTD-5.5.0/likeLTD/inst/unitTests/runit_reports.R | 4
likeLTD-5.5.0/likeLTD/man/DNA17-db.Rd |only
likeLTD-5.5.0/likeLTD/man/Identifiler-db.Rd |only
likeLTD-5.5.0/likeLTD/man/SGMplus-db.Rd |only
likeLTD-5.5.0/likeLTD/man/create.likelihood.log.Rd | 2
likeLTD-5.5.0/likeLTD/man/defence.hypothesis.Rd | 29
likeLTD-5.5.0/likeLTD/man/evaluate.Rd | 16
likeLTD-5.5.0/likeLTD/man/evaluate.from.interim.Rd |only
likeLTD-5.5.0/likeLTD/man/get.likely.genotypes.Rd | 6
likeLTD-5.5.0/likeLTD/man/initial.arguments.Rd | 4
likeLTD-5.5.0/likeLTD/man/linkage.Rd |only
likeLTD-5.5.0/likeLTD/man/load.allele.database.Rd | 9
likeLTD-5.5.0/likeLTD/man/locus.likes.Rd | 15
likeLTD-5.5.0/likeLTD/man/objective.functions.Rd | 8
likeLTD-5.5.0/likeLTD/man/optimisation.params.Rd | 20
likeLTD-5.5.0/likeLTD/man/output.report.Rd | 9
likeLTD-5.5.0/likeLTD/man/pack.admin.input.Rd | 7
likeLTD-5.5.0/likeLTD/man/penalties.Rd | 2
likeLTD-5.5.0/likeLTD/man/prosecution.hypothesis.Rd | 33
likeLTD-5.5.0/likeLTD/vignettes/usage.Rnw | 3
58 files changed, 906 insertions(+), 737 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Diff between hypervolume versions 1.2 dated 2015-02-28 and 1.2.2 dated 2015-03-12
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 8 +--
MD5 | 17 ++++----
NAMESPACE | 4 +
R/ZZZ.R |only
R/hypervolume_plot.R | 75 ++++++++++++++++++++++++++++--------
R/hypervolume_set.R | 20 +++++++--
R/hypervolume_sorensen_overlap.R | 3 -
man/hypervolume_set.Rd | 16 ++++---
man/hypervolume_sorensen_overlap.Rd | 2
man/plot.Hypervolume.Rd | 9 +++-
10 files changed, 112 insertions(+), 42 deletions(-)
Title: Graphical VAR for Experience Sampling Data
Diff between graphicalVAR versions 0.1.1 dated 2015-03-11 and 0.1.2 dated 2015-03-12
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical VAR model in combination with LASSO and EBIC.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/methods.R | 2 +-
src/Rothmana.cpp | 2 +-
4 files changed, 9 insertions(+), 9 deletions(-)
Title: Multiple Comparisons and Simultaneous Confidence Intervals
Diff between nparcomp versions 2.5 dated 2014-11-12 and 2.6 dated 2015-03-12
Description: With this package, it is possible to compute nonparametric simultaneous confidence intervals for relative contrast effects in the unbalanced one way layout. Moreover, it computes simultaneous p-values. The simultaneous confidence intervals can be computed using multivariate normal distribution, multivariate t-distribution with a Satterthwaite Approximation of the degree of freedom or using multivariate range preserving transformations with Logit or Probit as transformation function. 2 sample comparisons can be performed with the same methods described above. There is no assumption on the underlying distribution function, only that the data have to be at least ordinal numbers.
Author: Frank Konietschke
Maintainer: Frank Konietschke
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/mctp.rm.R | 2 +-
R/npar.t.test.R | 2 +-
inst/CITATION | 14 +++++++-------
5 files changed, 17 insertions(+), 17 deletions(-)
Title: Grain-Size Statistics and Description of Sediment
Diff between G2Sd versions 2.1.2 dated 2014-10-09 and 2.1.3 dated 2015-03-12
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves.
Author: Regis K. Gallon (MNHN), Jerome Fournier (CNRS|MNHN)
Maintainer: Regis K. Gallon
G2Sd |only
1 file changed
Title: Functional Data Analysis: K-Mean Alignment
Diff between fdakma versions 1.1.1 dated 2014-06-24 and 1.2 dated 2015-03-12
Description: It jointly performs clustering and alignment of a multidimensional or unidimensional functional dataset by means of k-mean alignment.
Author: Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi, Simone Vantini, Valeria Vitelli
Maintainer: Alice Parodi
DESCRIPTION | 10
MD5 | 22
R/kma.R | 1211 +++++++++++++++++++++++++-----------------------
R/kma.compare.R | 4
R/kma.similarity.R | 4
data/kma.data.rda |binary
man/fdakma-package.Rd | 12
man/kma.Rd | 23
man/kma.compare.Rd | 10
man/kma.data.Rd | 9
man/kma.show.results.Rd | 8
man/kma.similarity.Rd | 11
12 files changed, 700 insertions(+), 624 deletions(-)
Title: Toolkit of Helper Functions to Pre-Process Amplification Data
Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experiment
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-19 0.3-2
2008-12-19 0.3-1
2006-12-21 0.2-1
Title: Pull Data from 'trakt.tv'
Diff between tRakt versions 0.9.0 dated 2015-02-24 and 0.13.0 dated 2015-03-12
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk
tRakt |only
1 file changed
Title: R Commander Plug-in for University Level Applied Statistics
Diff between RcmdrPlugin.NMBU versions 1.8.0.1 dated 2015-02-23 and 1.8.0.4 dated 2015-03-12
More information about RcmdrPlugin.NMBU at CRAN
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 16 ++++----
MD5 | 8 ++--
R/NMBU.GUI.Data.R | 2 -
R/NMBU.GUI.Statistics.R | 78 ++++++++++++++++++++--------------------
man/RcmdrPlugin.NMBU-package.Rd | 2 -
5 files changed, 53 insertions(+), 53 deletions(-)
Permanent link
Title: Functional Time Series Analysis
Diff between ftsa versions 4.1 dated 2014-12-10 and 4.2 dated 2015-03-12
Description: Functions for displaying and analyzing functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang
ftsa-4.1/ftsa/R/plsPI.r |only
ftsa-4.2/ftsa/ChangeLog | 8 +
ftsa-4.2/ftsa/DESCRIPTION | 16 +--
ftsa-4.2/ftsa/MD5 | 24 ++---
ftsa-4.2/ftsa/NAMESPACE | 11 +-
ftsa-4.2/ftsa/R/MFDM.R |only
ftsa-4.2/ftsa/R/dynupdate.R | 175 +++++++++++++++++++++++---------------
ftsa-4.2/ftsa/R/fdpca.R | 17 ++-
ftsa-4.2/ftsa/R/ftsm.R | 12 ++
ftsa-4.2/ftsa/R/plsPI.R |only
ftsa-4.2/ftsa/R/wpcr.R | 23 +++-
ftsa-4.2/ftsa/build/vignette.rds |binary
ftsa-4.2/ftsa/man/MFDM.Rd |only
ftsa-4.2/ftsa/man/dynupdate.Rd | 2
ftsa-4.2/ftsa/man/ftsa-package.Rd | 70 +++++++--------
15 files changed, 216 insertions(+), 142 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Diff between LLSR versions 0.0.1.9000 dated 2015-02-24 and 0.0.1.9015 dated 2015-03-12
Description: The methods implemented here were based in the protocol proposed by Merchuk et al. (1998) and Murugesan & Perumalsamy (2005) to analyse Aqueous Two-Phases Systems. Each function brings in its description the reference for the original article which described it. These methods defines nonlinear equations that can be used to fit experimental data through regression methods and also allow us calculate other important system parameters (such as its critical composition, equivolume concentration and phase's composition). The package will include (every other update) new functions in order to comprise useful functions in liquid-liquid analysis.
Author: Diego F Coelho
Maintainer: Diego F Coelho
DESCRIPTION | 8 ++---
MD5 | 25 +++++++++-------
NAMESPACE | 6 +++
R/datasets.R |only
R/gsnchk.R | 84 ------------------------------------------------------
R/mrchk.R | 50 +++++++++++++++++++++++---------
R/mrgsn.R | 55 +++++++++++++++++++++++++----------
R/plotll.R |only
R/xyJn.R |only
man/mrchk.Rd | 2 -
man/mrchk.plot.Rd | 15 +++++++--
man/mrgsn.plot.Rd | 14 +++++----
man/peg4kslt.Rd | 2 -
man/plotll.Rd | 16 ++++++----
man/xyJn.Rd | 4 --
15 files changed, 134 insertions(+), 147 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Diff between lsbclust versions 1.0.1 dated 2015-02-16 and 1.0.2 dated 2015-03-11
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees
DESCRIPTION | 8 +++----
MD5 | 25 +++++++++++----------
R/int.lsbclust.R | 9 ++++---
R/lov.R | 33 ++++++++++++++++++-----------
R/lsbclust.R | 58 ++++++++++++++++++++++++++++++++++++++++++---------
R/orc.lsbclust.R | 32 +++++++++++++++++++++-------
R/plot.lsbclust.R | 2 +
inst |only
man/int.lsbclust.Rd | 4 ++-
man/lov.Rd | 35 ++++++++++++++++++++----------
man/lsbclust.Rd | 21 ++++++++++++++++--
man/orc.lsbclust.Rd | 18 ++++++++++++---
man/plot.lsbclust.Rd | 4 +++
src/RcppExports.cpp | 34 +++++++++++------------------
14 files changed, 194 insertions(+), 89 deletions(-)
Title: Predicting Species Accumulation Curves
Diff between preseqR versions 1.0.1 dated 2014-09-04 and 1.1 dated 2015-03-11
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng
DESCRIPTION | 10 -
MD5 | 38 ++-
NAMESPACE | 3
R/continued_fraction.R | 320 +++++++++++++++-----------------
R/simulation.R |only
R/ztnb.R | 83 +++-----
README.md | 2
data/FisherButterflyHist.txt.gz |binary
man/FisherButterflyHist.Rd | 2
man/preseqR.interpolate.distinct.Rd |only
man/preseqR.nonreplace.sampling.Rd |only
man/preseqR.package.Rd | 13 +
man/preseqR.rfa.curve.Rd | 33 ---
man/preseqR.rfa.estimate.Rd | 16 -
man/preseqR.rfa.species.accum.curve.Rd | 36 ---
man/preseqR.simu.hist.Rd |only
man/preseqR.ztnb.em.Rd | 11 -
man/preseqR.ztnb.estimate.Rd | 17 -
man/preseqR.ztnb.species.accum.curve.Rd | 12 -
src/continued_fraction.cpp | 72 +++++--
src/continued_fraction.h | 9
src/continued_fraction_c_interface.cpp | 72 ++++++-
22 files changed, 386 insertions(+), 363 deletions(-)
Title: Generative Models for Complex Networks with Conditionally
Independent Dyadic Structure
Diff between CIDnetworks versions 0.6.0 dated 2014-06-18 and 0.8.0 dated 2015-03-11
Description: Generative models for complex networks with conditionally independent dyadic structure. Now supports directed arcs!
Author: Samrachana Adhikari [aut],
Beau Dabbs [cre, aut],
Brian Junker [aut],
Mauricio Sadinle [aut],
Tracy Sweet [aut],
A.C. Thomas [aut]
Maintainer: Beau Dabbs
CIDnetworks-0.6.0/CIDnetworks/src/Makevars.win |only
CIDnetworks-0.8.0/CIDnetworks/DESCRIPTION | 27
CIDnetworks-0.8.0/CIDnetworks/MD5 | 42
CIDnetworks-0.8.0/CIDnetworks/NAMESPACE | 8
CIDnetworks-0.8.0/CIDnetworks/R/BETA-SR-reference.R | 66 -
CIDnetworks-0.8.0/CIDnetworks/R/CID-basefunctions.R | 413 ++++----
CIDnetworks-0.8.0/CIDnetworks/R/CID-external.R | 491 +++++----
CIDnetworks-0.8.0/CIDnetworks/R/CID-gibbs.R | 755 +++++++++------
CIDnetworks-0.8.0/CIDnetworks/R/COV-reference.R | 160 ++-
CIDnetworks-0.8.0/CIDnetworks/R/HBM-reference.R | 115 +-
CIDnetworks-0.8.0/CIDnetworks/R/LSM-reference.R | 25
CIDnetworks-0.8.0/CIDnetworks/R/LVM-reference.R | 83 -
CIDnetworks-0.8.0/CIDnetworks/R/MMSBM-reference.R | 200 ++-
CIDnetworks-0.8.0/CIDnetworks/R/SBM-reference.R | 68 +
CIDnetworks-0.8.0/CIDnetworks/R/SRa-reference.R | 15
CIDnetworks-0.8.0/CIDnetworks/R/plotting-pieces.R | 24
CIDnetworks-0.8.0/CIDnetworks/TODO | 66 +
CIDnetworks-0.8.0/CIDnetworks/man/CID-classes.Rd | 32
CIDnetworks-0.8.0/CIDnetworks/man/CID-gibbs.Rd | 32
CIDnetworks-0.8.0/CIDnetworks/man/CID-helpers.Rd | 9
CIDnetworks-0.8.0/CIDnetworks/man/CID-master.Rd | 42
CIDnetworks-0.8.0/CIDnetworks/man/CIDnetworks-package.Rd | 6
CIDnetworks-0.8.0/CIDnetworks/tests/input-test.R |only
23 files changed, 1757 insertions(+), 922 deletions(-)
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Diff between clusterSEs versions 1.1 dated 2015-03-05 and 1.2 dated 2015-03-11
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics for the GLM and mlogit models (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)).
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey
DESCRIPTION | 8 +++---
MD5 | 14 +++++-----
R/clusterBSmlogit.R | 3 +-
R/clusterIM.R | 56 +++++++++++++++++++++----------------------
R/clusterIMmlogit.R | 60 +++++++++++++++++++++++++----------------------
man/cluster.bs.mlogit.Rd | 3 +-
man/cluster.im.Rd | 25 ++++++++-----------
man/cluster.im.mlogit.Rd | 30 ++++++++++++-----------
8 files changed, 103 insertions(+), 96 deletions(-)
Title: Soil Physical Analysis
Diff between soilphysics versions 2.0 dated 2015-01-11 and 2.1 dated 2015-03-11
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva
DESCRIPTION | 10 +++---
MD5 | 26 ++++++++++-------
NAMESPACE | 4 ++
NEWS | 25 +++++++++++++----
R/iwc.R | 18 ++++++------
R/maxcurv.R | 49 +++++++++++++++------------------
R/onload.R | 2 -
R/plotCIsigmaP.R |only
R/sigmaP.r | 66 +++++++++++++++++++++------------------------
R/simSigmaP.R |only
man/llwr.Rd | 6 ++--
man/maxcurv.Rd | 10 +-----
man/plotCIsigmaP.Rd |only
man/sigmaP.Rd | 36 +++++++++++++++---------
man/simSigmaP.Rd |only
man/soilphysics-package.Rd | 4 +-
16 files changed, 138 insertions(+), 118 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Diff between multgee versions 1.5.0 dated 2014-11-02 and 1.5.1 dated 2015-03-11
Description: GEE solver for correlated nominal or ordinal multinomial responses using a local odds ratios parameterization.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
multgee-1.5.0/multgee/man/LORgee.Rd |only
multgee-1.5.0/multgee/man/LORgee.default.Rd |only
multgee-1.5.0/multgee/man/RCconstrains.Rd |only
multgee-1.5.0/multgee/man/RRCheter.Rd |only
multgee-1.5.0/multgee/man/RRChomog.Rd |only
multgee-1.5.0/multgee/man/combns.Rd |only
multgee-1.5.0/multgee/man/datacounts.Rd |only
multgee-1.5.0/multgee/man/derivacl.Rd |only
multgee-1.5.0/multgee/man/derivbcl.Rd |only
multgee-1.5.0/multgee/man/derivmclm.Rd |only
multgee-1.5.0/multgee/man/diagmod.Rd |only
multgee-1.5.0/multgee/man/fitLORgee.Rd |only
multgee-1.5.0/multgee/man/fitmm.Rd |only
multgee-1.5.0/multgee/man/inversemat.Rd |only
multgee-1.5.0/multgee/man/ipfp.Rd |only
multgee-1.5.0/multgee/man/mmpar.Rd |only
multgee-1.5.0/multgee/man/muprob.Rd |only
multgee-1.5.0/multgee/man/normscores.Rd |only
multgee-1.5.0/multgee/man/odds.ratio.Rd |only
multgee-1.5.0/multgee/man/print.LORgee.Rd |only
multgee-1.5.0/multgee/man/print.summary.LORgee.Rd |only
multgee-1.5.0/multgee/man/print.waldts.Rd |only
multgee-1.5.0/multgee/man/summary.LORgee.Rd |only
multgee-1.5.1/multgee/DESCRIPTION | 8 +--
multgee-1.5.1/multgee/MD5 | 47 +++++-------------
multgee-1.5.1/multgee/R/intrinsic.pars.R | 3 -
multgee-1.5.1/multgee/R/nomLORgee.R | 39 +++++++--------
multgee-1.5.1/multgee/R/ordLORgee.R | 5 +
multgee-1.5.1/multgee/build |only
multgee-1.5.1/multgee/inst/CITATION | 56 ++++++++++++----------
multgee-1.5.1/multgee/inst/NEWS | 6 ++
multgee-1.5.1/multgee/inst/doc |only
multgee-1.5.1/multgee/man/multgee-package.Rd | 2
multgee-1.5.1/multgee/man/nomLORgee.Rd | 4 +
multgee-1.5.1/multgee/man/ordLORgee.Rd | 2
multgee-1.5.1/multgee/vignettes |only
36 files changed, 88 insertions(+), 84 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Diff between mixlm versions 1.0.8.3 dated 2015-02-23 and 1.0.8.5 dated 2015-03-11
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/statistics.R | 3 ++-
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Distances and Routes on Geographical Grids
Diff between gdistance versions 1.1-6 dated 2015-01-07 and 1.1-7 dated 2015-03-11
Description: Calculate distances and routes on geographic grids.
Author: Jacob van Etten
Maintainer: Jacob van Etten
ChangeLog | 6 ++
DESCRIPTION | 8 +--
MD5 | 14 +++---
inst/doc/gdistance1.R | 100 ++++++++++++++++++++++++-----------------------
inst/doc/gdistance1.Rnw | 82 ++++++++++++++++++++------------------
inst/doc/gdistance1.pdf |binary
vignettes/gdistance1.Rnw | 82 ++++++++++++++++++++------------------
vignettes/gdistance1.bib | 10 ++--
8 files changed, 160 insertions(+), 142 deletions(-)
Title: Send Emails Using 'Blat' for Windows
Diff between blatr versions 1.0 dated 2015-03-10 and 1.0.1 dated 2015-03-11
Description: A wrapper around the 'Blat' command line SMTP mailer for Windows.
'Blat' is public domain software, but be sure to read the license before use.
It can be found at the Blat website http://www.blat.net.
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache
DESCRIPTION | 14 +++++++-------
MD5 | 8 ++++----
R/blatr.R | 56 ++++++++++++++++++++++++++++----------------------------
man/blat.Rd | 18 +++++++++---------
man/blatr.Rd | 32 ++++++++++++++++----------------
5 files changed, 64 insertions(+), 64 deletions(-)
Title: Baseline Correction of Spectra
Diff between baseline versions 1.1-4 dated 2015-01-20 and 1.2-0 dated 2015-03-11
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 13 +++++++------
MD5 | 23 ++++++++++++++---------
NEWS | 4 ++++
R/baseline.modpolyfit.R | 2 +-
R/baseline.shirley.R |only
R/baselineGUI.R | 4 ++++
R/optimisation.R | 15 ++++++++++++++-
data/C1s.RData |only
data/O1s.rda |only
data/datalist | 2 ++
man/XPSdata.Rd |only
man/baseline-package.Rd | 6 +++---
man/baseline.Rd | 3 ++-
man/baseline.shirley.Rd |only
man/baselineGUI.Rd | 5 ++++-
15 files changed, 55 insertions(+), 22 deletions(-)
Title: STK++ Integration to R Using Rcpp
Diff between rtkpp versions 0.8.5 dated 2015-02-20 and 0.8.6 dated 2015-03-11
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp.
The rtkpp package includes the header files from the STK++
library (currently version 0.8.6). Thus users do not need to
install STK++ itself in order to use it.
STK++ is licensed under the GNU LGPL version 2 or later. rtkpp
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre],
Vincent Kubicki [ctb],
Quentin Grimonprez [ctb],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff
rtkpp-0.8.5/rtkpp/R/ClusterAlgo.R |only
rtkpp-0.8.5/rtkpp/R/ClusterCategorical.R |only
rtkpp-0.8.5/rtkpp/R/ClusterDiagGaussian.R |only
rtkpp-0.8.5/rtkpp/R/ClusterGamma.R |only
rtkpp-0.8.5/rtkpp/R/ClusterHeterogeneous.R |only
rtkpp-0.8.5/rtkpp/R/ClusterInit.R |only
rtkpp-0.8.5/rtkpp/R/ClusterModelNames.R |only
rtkpp-0.8.5/rtkpp/R/ClusterPlot.R |only
rtkpp-0.8.5/rtkpp/R/ClusterPoisson.R |only
rtkpp-0.8.5/rtkpp/R/ClusterStrategy.R |only
rtkpp-0.8.5/rtkpp/R/IClusterModel.R |only
rtkpp-0.8.5/rtkpp/R/global.R |only
rtkpp-0.8.5/rtkpp/data |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ICAllocator.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_DiagOperator.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/MixturesBridges |only
rtkpp-0.8.5/rtkpp/man/ClusterAlgo-class.Rd |only
rtkpp-0.8.5/rtkpp/man/ClusterCategorical-class.Rd |only
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rtkpp-0.8.5/rtkpp/man/ClusterModels-class.Rd |only
rtkpp-0.8.5/rtkpp/man/ClusterPoisson-class.Rd |only
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rtkpp-0.8.5/rtkpp/man/HeartDisease.Rd |only
rtkpp-0.8.5/rtkpp/man/IClusterComponent-class.Rd |only
rtkpp-0.8.5/rtkpp/man/birds.Rd |only
rtkpp-0.8.5/rtkpp/man/car.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterAlgo.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterCategorical.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterCategoricalNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterDiagGaussian.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterDiagGaussianNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterGamma.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterGammaNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterHeterogeneous.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterInit.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterPoisson.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterPoissonNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterStrategy.Rd |only
rtkpp-0.8.5/rtkpp/man/extract-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/geyser.Rd |only
rtkpp-0.8.5/rtkpp/man/initialize-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/missingValues-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/plot-ClusterCategorical-method.Rd |only
rtkpp-0.8.5/rtkpp/man/plot-ClusterDiagGaussian-method.Rd |only
rtkpp-0.8.5/rtkpp/man/plot-ClusterGamma-method.Rd |only
rtkpp-0.8.5/rtkpp/man/plot-ClusterHeterogeneous-method.Rd |only
rtkpp-0.8.5/rtkpp/man/plot-ClusterPoisson-method.Rd |only
rtkpp-0.8.5/rtkpp/man/print-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/show-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/summary-methods.Rd |only
rtkpp-0.8.5/rtkpp/man/titanic.Rd |only
rtkpp-0.8.5/rtkpp/src/STK_ClusterFacade.cpp |only
rtkpp-0.8.5/rtkpp/src/STK_ClusterLauncher.cpp |only
rtkpp-0.8.5/rtkpp/src/STK_RDataHandler.cpp |only
rtkpp-0.8.5/rtkpp/src/clusterMixture.cpp |only
rtkpp-0.8.5/rtkpp/tests |only
rtkpp-0.8.6/rtkpp/DESCRIPTION | 19
rtkpp-0.8.6/rtkpp/MD5 | 275 +-
rtkpp-0.8.6/rtkpp/NAMESPACE | 48
rtkpp-0.8.6/rtkpp/R/rtkpp.R | 327 ---
rtkpp-0.8.6/rtkpp/build/vignette.rds |binary
rtkpp-0.8.6/rtkpp/cleanup | 1
rtkpp-0.8.6/rtkpp/inst/doc/rtkpp-introduction.R |only
rtkpp-0.8.6/rtkpp/inst/doc/rtkpp-introduction.Rnw | 38
rtkpp-0.8.6/rtkpp/inst/doc/rtkpp-introduction.pdf |binary
rtkpp-0.8.6/rtkpp/inst/include/Arrays.h | 1
rtkpp-0.8.6/rtkpp/inst/include/Clustering.h | 8
rtkpp-0.8.6/rtkpp/inst/projects/Algebra/include/STK_lapack_SymEigen.h | 2
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array1D.h | 21
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2D.h | 44
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DDiagonal.h | 46
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DLowerTriangular.h | 44
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DNumber.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DPoint.h | 48
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DSquare.h | 45
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DUpperTriangular.h | 45
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2DVector.h | 46
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Array2D_Functors.h | 69
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_ArrayBase.h | 57
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CAllocator.h | 280 +-
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CArray.h | 29
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CArrayNumber.h | 18
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CArrayPoint.h | 24
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CArraySquare.h | 7
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_CArrayVector.h | 24
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_Const_Arrays.h | 231 +-
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_ExprBase.h | 18
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_ExprBaseProduct.h | 67
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_ExprBaseVisitor.h | 4
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_IArray2DBase.h | 11
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_IArrayBase.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/STK_ITContainer.h | 307 +-
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_BinaryOperators.h | 159 -
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_DiagonalOperator.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_DotOperators.h | 20
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_SlicingOperators.h | 153 -
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_TransposeOperator.h | 33
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/operators/STK_UnaryOperators.h | 34
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByArrayProduct.h | 11
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/products/STK_ProductImpl.h | 31
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/products/STK_ProductOperators.h | 1043 +++-------
rtkpp-0.8.6/rtkpp/inst/projects/Arrays/include/visitors/STK_SlicingVisitors.h | 32
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBase.h | 22
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBridge.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalParameters.h | 18
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pjk.h | 16
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/DiagGaussianMixtureModels |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBase.h | 42
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBridge.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaParameters.h | 147 +
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bjk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bjk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_b.h | 20
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bj.h | 20
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bjk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bk.h | 16
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_b.h | 22
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bj.h | 22
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bjk.h | 16
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bk.h | 14
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/KernelMixtureModels |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonBase.h | 12
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonBridge.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_PoissonParameters.h | 36
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_ljk.h | 6
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_ljlk.h | 8
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels/STK_Poisson_lk.h | 6
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_IMixtureBridge.h |only
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_IMixtureComposer.h | 4
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_IMixtureManager.h | 29
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_IMixtureModel.h | 60
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_MixtureComposer.h | 18
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_MixtureData.h | 16
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_MixtureManager.h | 206 -
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/include/STK_MixtureParamStat.h | 18
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/src/STK_IMixtureManager.cpp | 38
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp | 6
rtkpp-0.8.6/rtkpp/inst/projects/Clustering/src/STK_MixtureFacade.cpp | 14
rtkpp-0.8.6/rtkpp/inst/projects/DManager/include/STK_DataFrame.h | 9
rtkpp-0.8.6/rtkpp/inst/projects/DManager/include/STK_IDataHandler.h | 2
rtkpp-0.8.6/rtkpp/inst/projects/DManager/include/STK_IVariable.h | 2
rtkpp-0.8.6/rtkpp/inst/projects/DManager/include/STK_Variable.h | 1
rtkpp-0.8.6/rtkpp/inst/projects/DManager/src/STK_DataFrame.cpp | 8
rtkpp-0.8.6/rtkpp/inst/projects/DManager/src/STK_IDataHandler.cpp | 2
rtkpp-0.8.6/rtkpp/inst/projects/Rtkpp/include/STK_RMatrix.h | 48
rtkpp-0.8.6/rtkpp/inst/projects/Rtkpp/include/STK_RVector.h | 52
rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Law_MultiNormal.h | 2
rtkpp-0.8.6/rtkpp/inst/projects/STatistiK/include/STK_Stat_Functors.h | 4
rtkpp-0.8.6/rtkpp/inst/projects/Sdk/include/STK_Macros.h | 15
rtkpp-0.8.6/rtkpp/inst/projects/Sdk/include/STK_MetaTemplate.h | 10
rtkpp-0.8.6/rtkpp/man/rtkpp-package.Rd | 11
rtkpp-0.8.6/rtkpp/src/rtkpp.cpp |only
rtkpp-0.8.6/rtkpp/vignettes/rtkpp-introduction.Rnw | 38
162 files changed, 2367 insertions(+), 2493 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.6.9 dated 2015-02-15 and 1.7 dated 2015-03-11
Description: Collection of several plotting and table output functions for
visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
sjPlot-1.6.9/sjPlot/man/sjd.chisq.Rd |only
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sjPlot-1.7/sjPlot/DESCRIPTION | 14
sjPlot-1.7/sjPlot/MD5 | 227 -
sjPlot-1.7/sjPlot/NAMESPACE | 84
sjPlot-1.7/sjPlot/NEWS | 966 +++---
sjPlot-1.7/sjPlot/R/efc.R | 146 -
sjPlot-1.7/sjPlot/R/helpfunctions.R | 296 +-
sjPlot-1.7/sjPlot/R/sjImportSPSS.R | 956 +++++-
sjPlot-1.7/sjPlot/R/sjPlotAncovaLSMeans.R | 719 ++---
sjPlot-1.7/sjPlot/R/sjPlotAnova.R | 38
sjPlot-1.7/sjPlot/R/sjPlotClusterAnalysis.R | 26
sjPlot-1.7/sjPlot/R/sjPlotCorr.R | 36
sjPlot-1.7/sjPlot/R/sjPlotDist.R | 43
sjPlot-1.7/sjPlot/R/sjPlotFrequencies.R | 1764 ++++++------
sjPlot-1.7/sjPlot/R/sjPlotGLME.R | 3223 +++++++++++------------
sjPlot-1.7/sjPlot/R/sjPlotGroupFrequencies.R | 2507 ++++++++---------
sjPlot-1.7/sjPlot/R/sjPlotInteractions.R | 10
sjPlot-1.7/sjPlot/R/sjPlotLikert.R | 1250 ++++----
sjPlot-1.7/sjPlot/R/sjPlotLinreg.R | 1842 ++++++-------
sjPlot-1.7/sjPlot/R/sjPlotLinregMultiple.R | 14
sjPlot-1.7/sjPlot/R/sjPlotOdds.R | 33
sjPlot-1.7/sjPlot/R/sjPlotOddsMultiple.R | 846 +++---
sjPlot-1.7/sjPlot/R/sjPlotPCA.R | 24
sjPlot-1.7/sjPlot/R/sjPlotPearsonsChi2Test.R | 53
sjPlot-1.7/sjPlot/R/sjPlotPropTable.R | 28
sjPlot-1.7/sjPlot/R/sjPlotScatter.R | 47
sjPlot-1.7/sjPlot/R/sjPlotSetTheme.R | 160 +
sjPlot-1.7/sjPlot/R/sjPlotStackFrequencies.R | 22
sjPlot-1.7/sjPlot/R/sjRecode.R | 254 -
sjPlot-1.7/sjPlot/R/sjStatistics.R | 1328 ++++-----
sjPlot-1.7/sjPlot/R/sjTabCorr.R | 1062 +++----
sjPlot-1.7/sjPlot/R/sjTabDataFrame.R | 4
sjPlot-1.7/sjPlot/R/sjTabFrequencies.R | 34
sjPlot-1.7/sjPlot/R/sjTabGrpmean.R | 373 +-
sjPlot-1.7/sjPlot/R/sjTabItemAnalysis.R | 59
sjPlot-1.7/sjPlot/R/sjTabLinReg.R | 698 +++-
sjPlot-1.7/sjPlot/R/sjTabOdds.R | 541 ++-
sjPlot-1.7/sjPlot/R/sjTabPCA.R | 66
sjPlot-1.7/sjPlot/R/sjTabPropTable.R | 46
sjPlot-1.7/sjPlot/R/sjTabSPSS.R | 98
sjPlot-1.7/sjPlot/R/sjTabStackFrq.R | 13
sjPlot-1.7/sjPlot/README.md | 59
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sjPlot-1.7/sjPlot/data/efc3.RData |only
sjPlot-1.7/sjPlot/man/adjust_plot_range.Rd |only
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sjPlot-1.7/sjPlot/man/set_var_labels.Rd |only
sjPlot-1.7/sjPlot/man/sjPlot-package.Rd | 46
sjPlot-1.7/sjPlot/man/sjc.qclus.Rd | 6
sjPlot-1.7/sjPlot/man/sjp.aov1.Rd | 18
sjPlot-1.7/sjPlot/man/sjp.chi2.Rd | 16
sjPlot-1.7/sjPlot/man/sjp.corr.Rd | 6
sjPlot-1.7/sjPlot/man/sjp.emm.int.Rd | 2
sjPlot-1.7/sjPlot/man/sjp.frq.Rd | 34
sjPlot-1.7/sjPlot/man/sjp.glm.Rd | 8
sjPlot-1.7/sjPlot/man/sjp.glmer.Rd | 6
sjPlot-1.7/sjPlot/man/sjp.glmm.Rd | 6
sjPlot-1.7/sjPlot/man/sjp.grpfrq.Rd | 29
sjPlot-1.7/sjPlot/man/sjp.int.Rd | 4
sjPlot-1.7/sjPlot/man/sjp.likert.Rd | 5
sjPlot-1.7/sjPlot/man/sjp.lm.Rd | 12
sjPlot-1.7/sjPlot/man/sjp.lmer.Rd | 2
sjPlot-1.7/sjPlot/man/sjp.lmm.Rd | 6
sjPlot-1.7/sjPlot/man/sjp.pca.Rd | 8
sjPlot-1.7/sjPlot/man/sjp.scatter.Rd | 33
sjPlot-1.7/sjPlot/man/sjp.setTheme.Rd | 499 +--
sjPlot-1.7/sjPlot/man/sjp.stackfrq.Rd | 11
sjPlot-1.7/sjPlot/man/sjp.xtab.Rd | 15
sjPlot-1.7/sjPlot/man/sjt.corr.Rd | 46
sjPlot-1.7/sjPlot/man/sjt.df.Rd | 4
sjPlot-1.7/sjPlot/man/sjt.frq.Rd | 12
sjPlot-1.7/sjPlot/man/sjt.glm.Rd | 161 -
sjPlot-1.7/sjPlot/man/sjt.grpmean.Rd | 2
sjPlot-1.7/sjPlot/man/sjt.itemanalysis.Rd | 26
sjPlot-1.7/sjPlot/man/sjt.lm.Rd | 180 +
sjPlot-1.7/sjPlot/man/sjt.pca.Rd | 60
sjPlot-1.7/sjPlot/man/sjt.stackfrq.Rd | 9
sjPlot-1.7/sjPlot/man/sjt.xtab.Rd | 12
sjPlot-1.7/sjPlot/man/std_beta.Rd |only
sjPlot-1.7/sjPlot/man/std_e.Rd |only
sjPlot-1.7/sjPlot/man/str_pos.Rd |only
sjPlot-1.7/sjPlot/man/table_values.Rd |only
sjPlot-1.7/sjPlot/man/to_fac.Rd |only
sjPlot-1.7/sjPlot/man/to_label.Rd |only
sjPlot-1.7/sjPlot/man/to_sjPlot.Rd |only
sjPlot-1.7/sjPlot/man/to_value.Rd |only
sjPlot-1.7/sjPlot/man/view_spss.Rd |only
sjPlot-1.7/sjPlot/man/weight.Rd |only
sjPlot-1.7/sjPlot/man/weight2.Rd |only
sjPlot-1.7/sjPlot/man/word_wrap.Rd |only
sjPlot-1.7/sjPlot/man/write_spss.Rd |only
sjPlot-1.7/sjPlot/man/write_stata.Rd |only
156 files changed, 11693 insertions(+), 9699 deletions(-)
Title: Fitting Structural Equation Mixture Models
Diff between nlsem versions 0.2 dated 2015-02-10 and 0.3 dated 2015-03-11
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach
ChangeLog |only
DESCRIPTION | 8 +--
MD5 | 37 ++++++++-------
NAMESPACE | 13 ++++-
R/em.R | 72 +++++++++++++++++------------
R/lms.R | 18 ++++---
R/model.R | 34 ++++++-------
R/nsemm.R | 38 +++++++++------
R/qml.R |only
R/s3generics.R | 106 ++++++++++++++++++++++++++++++++-----------
R/semm.R | 2
data |only
man/as.data.frame.Rd | 8 +--
man/count_free_parameters.Rd | 4 -
man/create_sem.Rd | 4 -
man/em.Rd | 20 +++++---
man/fill_model.Rd | 2
man/jordan.Rd |only
man/nlsem-package.Rd | 6 +-
man/qml.Rd |only
man/simulate.Rd | 8 +--
man/specify_sem.Rd | 8 +--
22 files changed, 245 insertions(+), 143 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 2.1-1629 dated 2015-03-05 and 2.1-1640 dated 2015-03-11
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
lfe-2.1-1629/lfe/NEWS |only
lfe-2.1-1640/lfe/DESCRIPTION | 10 +-
lfe-2.1-1640/lfe/MD5 | 46 +++++-----
lfe-2.1-1640/lfe/R/btrap.R | 3
lfe-2.1-1640/lfe/R/cgsolve.R | 14 +--
lfe-2.1-1640/lfe/R/demeanlist.R | 27 ------
lfe-2.1-1640/lfe/R/felm.R | 12 +-
lfe-2.1-1640/lfe/R/kaczmarz.R | 26 +-----
lfe-2.1-1640/lfe/R/oldfelm.R | 3
lfe-2.1-1640/lfe/R/startup.R | 41 +++++----
lfe-2.1-1640/lfe/cleanup | 3
lfe-2.1-1640/lfe/configure | 20 ++--
lfe-2.1-1640/lfe/configure.ac | 2
lfe-2.1-1640/lfe/inst/NEWS.Rd |only
lfe-2.1-1640/lfe/inst/doc/CHANGELOG | 4
lfe-2.1-1640/lfe/inst/doc/identification.pdf |binary
lfe-2.1-1640/lfe/inst/doc/lfehow.pdf |binary
lfe-2.1-1640/lfe/inst/doc/speed.pdf |binary
lfe-2.1-1640/lfe/man/lfe-package.Rd | 4
lfe-2.1-1640/lfe/src/demean.c | 116 +++++++++------------------
lfe-2.1-1640/lfe/src/lfe.c | 13 +--
lfe-2.1-1640/lfe/src/lfe.h | 6 -
lfe-2.1-1640/lfe/src/utils.c | 32 ++++---
lfe-2.1-1640/lfe/tests/ivtest.R | 1
lfe-2.1-1640/lfe/tests/ivtest.Rout.save | 7 +
25 files changed, 170 insertions(+), 220 deletions(-)
Title: Generalized Multistate Simulation Model
Diff between gems versions 0.9.5 dated 2014-05-27 and 1.0.0 dated 2015-03-11
Description: Simulate and analyze multistate models with general hazard functions. gems provides functionality for the preparation of hazard functions and parameters, simulation from a general multistate model and predicting future events. The multistate model is not required to be a Markov model and may take the history of previous events into account. In the basic version, it allows to simulate from transition-specific hazard function, whose parameters are multivariable normally distributed.
Author: Luisa Salazar Vizcaya, Nello Blaser, Thomas Gsponer
Maintainer: Luisa Salazar Vizcaya
gems-0.9.5/gems/man/ArtCohort-class.Rd |only
gems-0.9.5/gems/man/PosteriorProbabilities-class.Rd |only
gems-0.9.5/gems/man/transition.structure-class.Rd |only
gems-1.0.0/gems/ChangeLog | 15
gems-1.0.0/gems/DESCRIPTION | 18
gems-1.0.0/gems/MD5 | 54 +
gems-1.0.0/gems/NAMESPACE | 90 --
gems-1.0.0/gems/R/gems-package.R |only
gems-1.0.0/gems/R/gems.r | 453 +++++++++++++--
gems-1.0.0/gems/build |only
gems-1.0.0/gems/inst |only
gems-1.0.0/gems/man/ArtCohort.Rd |only
gems-1.0.0/gems/man/PosteriorProbabilities.Rd |only
gems-1.0.0/gems/man/cumulativeIncidence.Rd | 61 --
gems-1.0.0/gems/man/gems.Rd |only
gems-1.0.0/gems/man/generateHazardMatrix.Rd | 40 -
gems-1.0.0/gems/man/generateParameterCovarianceMatrix.Rd | 45 -
gems-1.0.0/gems/man/generateParameterMatrix.Rd | 43 -
gems-1.0.0/gems/man/simulateCohort.Rd | 178 +++--
gems-1.0.0/gems/man/tavi.Rd | 50 +
gems-1.0.0/gems/man/transition.structure.Rd |only
gems-1.0.0/gems/man/transitionProbabilities.Rd | 60 -
gems-1.0.0/gems/vignettes |only
23 files changed, 766 insertions(+), 341 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Diff between dbmss versions 2.1.2 dated 2014-11-01 and 2.2.0 dated 2015-03-11
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon
dbmss-2.1.2/dbmss/R/FillEnveloppe.R |only
dbmss-2.1.2/dbmss/man/FillEnveloppe.Rd |only
dbmss-2.2.0/dbmss/DESCRIPTION | 12 --
dbmss-2.2.0/dbmss/MD5 | 86 ++++++++--------
dbmss-2.2.0/dbmss/NAMESPACE | 8 +
dbmss-2.2.0/dbmss/NEWS | 17 +++
dbmss-2.2.0/dbmss/R/CheckdbmssArguments.R | 24 ++++
dbmss-2.2.0/dbmss/R/DEnvelope.R | 2
dbmss-2.2.0/dbmss/R/Dhat.R | 16 ++-
dbmss-2.2.0/dbmss/R/FillEnvelope.R |only
dbmss-2.2.0/dbmss/R/KEnvelope.R | 2
dbmss-2.2.0/dbmss/R/KdEnvelope.R | 10 +
dbmss-2.2.0/dbmss/R/Kdhat.R | 64 +++++++-----
dbmss-2.2.0/dbmss/R/KinhomEnvelope.R | 2
dbmss-2.2.0/dbmss/R/KmmEnvelope.R | 2
dbmss-2.2.0/dbmss/R/MEnvelope.R | 2
dbmss-2.2.0/dbmss/R/gEnvelope.R | 2
dbmss-2.2.0/dbmss/R/m_Envelope.R | 16 +--
dbmss-2.2.0/dbmss/R/m_hat.R | 110 ++++++++++++++++-----
dbmss-2.2.0/dbmss/build/vignette.rds |binary
dbmss-2.2.0/dbmss/inst/CITATION |only
dbmss-2.2.0/dbmss/inst/doc/dbmss.R | 128 ++++++++++++++++---------
dbmss-2.2.0/dbmss/inst/doc/dbmss.Rnw | 66 ++++++------
dbmss-2.2.0/dbmss/inst/doc/dbmss.pdf |binary
dbmss-2.2.0/dbmss/man/DEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/Dhat.Rd | 4
dbmss-2.2.0/dbmss/man/FillEnvelope.Rd |only
dbmss-2.2.0/dbmss/man/GlobalEnvelope.Rd | 2
dbmss-2.2.0/dbmss/man/KEnvelope.Rd | 6 -
dbmss-2.2.0/dbmss/man/KdEnvelope.Rd | 14 ++
dbmss-2.2.0/dbmss/man/Kdhat.Rd | 17 ++-
dbmss-2.2.0/dbmss/man/KinhomEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/KmmEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/LEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/LmmEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/MEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/dbmss-package.Rd | 10 -
dbmss-2.2.0/dbmss/man/gEnvelope.Rd | 4
dbmss-2.2.0/dbmss/man/m_Envelope.Rd | 30 ++++-
dbmss-2.2.0/dbmss/man/m_hat.Rd | 31 ++++--
dbmss-2.2.0/dbmss/man/print.dbmssEnvelope.Rd | 2
dbmss-2.2.0/dbmss/man/rRandomLabelingM.Rd | 4
dbmss-2.2.0/dbmss/man/summary.dbmssEnvelope.Rd | 2
dbmss-2.2.0/dbmss/src/RcppExports.cpp | 80 +++++++--------
dbmss-2.2.0/dbmss/vignettes/KdFig.pdf |only
dbmss-2.2.0/dbmss/vignettes/dbmss.Rnw | 66 ++++++------
dbmss-2.2.0/dbmss/vignettes/dbmss.bib | 23 ++--
47 files changed, 560 insertions(+), 328 deletions(-)
Title: Generalized Boosted Regression Models
Diff between gbm versions 2.1 dated 2013-05-10 and 2.1.1 dated 2015-03-11
Description: An implementation of extensions to Freund and
Schapire's AdaBoost algorithm and Friedman's gradient boosting
machine. Includes regression methods for least squares,
absolute loss, t-distribution loss, quantile regression,
logistic, multinomial logistic, Poisson, Cox proportional
hazards partial likelihood, AdaBoost exponential loss,
Huberized hinge loss, and Learning to Rank measures
(LambdaMart).
Author: Greg Ridgeway
Maintainer: Harry Southworth
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 7 +++++++
R/test.gbm.R | 23 +++++++++--------------
4 files changed, 24 insertions(+), 22 deletions(-)
Title: Dataframe Summaries, Frequency Tables and Numerical Summaries
with Customizable Output
Diff between summarytools versions 0.2 dated 2014-11-25 and 0.3 dated 2015-03-11
Description: Generates formatted summary tables for vectors and dataframes.
Three summarizing functions: 1) 'freq' generates frequency tables
reporting counts and proportions (including cumulative); 2) 'descr'
gives common central tendency statistics and measures of dispersion
for numerical data; 3) 'dfSummary' which attempts to give as much
information as possible about a dataframe and its components in a clear,
legible table. All three functions can either display plain text tables
in the console or write markdown, text or html files to disk. An
additional misc function, 'what.is', extends base 'is' function,
checking the object against all 'is' functions.
Author: Dominic Comtois
Maintainer: Dominic Comtois
summarytools-0.2/summarytools/R/summarytools.R |only
summarytools-0.3/summarytools/DESCRIPTION | 30 ++++---
summarytools-0.3/summarytools/MD5 | 27 +++++-
summarytools-0.3/summarytools/NAMESPACE | 18 ++++
summarytools-0.3/summarytools/NEWS | 17 ++++
summarytools-0.3/summarytools/R/descr.R |only
summarytools-0.3/summarytools/R/dfSummary.R |only
summarytools-0.3/summarytools/R/freq.R |only
summarytools-0.3/summarytools/R/misc.R |only
summarytools-0.3/summarytools/R/print.summarytools.R |only
summarytools-0.3/summarytools/R/what.is.R |only
summarytools-0.3/summarytools/inst |only
summarytools-0.3/summarytools/man/desc.Rd | 62 +++++++---------
summarytools-0.3/summarytools/man/dfSummary.Rd | 32 ++++----
summarytools-0.3/summarytools/man/freq.Rd | 59 +++++++--------
summarytools-0.3/summarytools/man/print.summarytools.Rd |only
summarytools-0.3/summarytools/man/view.Rd |only
summarytools-0.3/summarytools/man/what.is.Rd |only
18 files changed, 145 insertions(+), 100 deletions(-)
Title: Using Fonts More Easily in R Graphs
Diff between showtext versions 0.2 dated 2014-01-01 and 0.3 dated 2015-03-11
Description: Making it easy to use various types of fonts
(TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and
supporting most output formats of R graphics including PNG, PDF and
SVG. Fonts will be embedded in the graph file, hence after the plot
has been created, it no longer relies on the font files.
No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
showtext-0.2/showtext/NEWS |only
showtext-0.2/showtext/inst/fonts |only
showtext-0.3/showtext/DESCRIPTION | 27 ++---
showtext-0.3/showtext/MD5 | 43 ++++-----
showtext-0.3/showtext/NAMESPACE | 7 -
showtext-0.3/showtext/R/font.R | 22 +---
showtext-0.3/showtext/R/showtext.R | 33 +++---
showtext-0.3/showtext/R/zzz.R | 33 ++++--
showtext-0.3/showtext/README.md | 133 +++++++++++-----------------
showtext-0.3/showtext/configure | 18 +--
showtext-0.3/showtext/configure.ac | 2
showtext-0.3/showtext/inst/AUTHORS | 4
showtext-0.3/showtext/inst/COPYRIGHTS | 13 --
showtext-0.3/showtext/inst/NEWS.Rd |only
showtext-0.3/showtext/man/showtext.begin.Rd | 95 ++++++++++----------
showtext-0.3/showtext/man/showtext.end.Rd | 15 +--
showtext-0.3/showtext/src/devfuns.c | 2
showtext-0.3/showtext/src/outline.c | 11 +-
showtext-0.3/showtext/src/outline.h | 3
showtext-0.3/showtext/src/showtext-win.def | 10 +-
showtext-0.3/showtext/src/showtext.c | 57 ++++++++----
showtext-0.3/showtext/src/util.c | 21 ++--
showtext-0.3/showtext/src/util.h | 4
23 files changed, 262 insertions(+), 291 deletions(-)
Title: Nested Association Mapping Analysis
Diff between NAM versions 1.0.2.2 dated 2015-02-03 and 1.1 dated 2015-03-11
Description: Designed for association studies in nested association mapping (NAM) panels, but also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
NAM-1.0.2.2/NAM/R/blup.R |only
NAM-1.0.2.2/NAM/data/datalist |only
NAM-1.0.2.2/NAM/man/blup.Rd |only
NAM-1.1/NAM/DESCRIPTION | 12 +++----
NAM-1.1/NAM/MD5 | 38 ++++++++++++-----------
NAM-1.1/NAM/R/MCreml.R | 13 +++-----
NAM-1.1/NAM/R/RcppExports.R | 58 +++++++++++++++++++----------------
NAM-1.1/NAM/R/gibbs.R |only
NAM-1.1/NAM/R/gwas.R | 14 ++++----
NAM-1.1/NAM/R/gwas2.R | 16 ++++++---
NAM-1.1/NAM/R/manhattan.R | 25 ++++++++++++---
NAM-1.1/NAM/R/reference.R | 52 ++++++++++++++++----------------
NAM-1.1/NAM/R/reml.R | 2 -
NAM-1.1/NAM/R/snpH2.R |only
NAM-1.1/NAM/R/snpQC.R | 2 -
NAM-1.1/NAM/man/Internals.Rd | 4 +-
NAM-1.1/NAM/man/NAM-package.Rd | 65 ++++++++++++++++++++--------------------
NAM-1.1/NAM/man/gibbs.Rd |only
NAM-1.1/NAM/man/gwas.Rd | 6 +--
NAM-1.1/NAM/man/manhattan.Rd | 5 ++-
NAM-1.1/NAM/man/reml.Rd | 4 +-
NAM-1.1/NAM/man/snpH2.Rd |only
NAM-1.1/NAM/src/RcppExports.cpp | 16 +++++++++
NAM-1.1/NAM/src/SAMP.cpp |only
24 files changed, 190 insertions(+), 142 deletions(-)
Title: Multigroup Data Analysis
Diff between multigroup versions 0.4.3 dated 2015-01-04 and 0.4.4 dated 2015-03-11
Description: Several functions are presented in order to study data in a group structure,
where the same set of variables are measured on different groups of
individuals.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez
Questions and comments go to Aida Eslami
Maintainer: Aida Eslami
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/mgPLS.R | 37 +++++++++++++++++++++++++++++++++++--
man/mgPLS.Rd | 6 +++++-
4 files changed, 49 insertions(+), 12 deletions(-)
Title: Spatial Interpolation by Inverse Path Distance Weighting
Diff between ipdw versions 0.2-1 dated 2014-06-16 and 0.2-2 dated 2015-03-11
Description: Functions are provided to interpolate georeferenced point data via Inverse Path Distance Weighting. Useful for coastal marine applications where barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek
Maintainer: Joseph Stachelek
DESCRIPTION | 14 +++++++-------
MD5 | 37 ++++++++++++++++++++-----------------
NAMESPACE | 3 ++-
R/costrasterGen.R | 24 ++++++++++++++++++++----
R/errorGen.R | 7 ++++---
R/ipdw.R | 21 ++++++++++++++++-----
R/ipdwInterp.R | 4 +++-
R/pathdistGen.R | 5 ++---
R/pathdistGen_parallel.R |only
TODO |only
build/vignette.rds |binary
inst/CITATION |only
inst/doc/ipdw.R | 1 +
inst/doc/ipdw.Rnw | 4 +++-
inst/doc/ipdw.pdf |binary
man/costrasterGen.Rd | 29 +++++++++++++++++++++++------
man/errorGen.Rd | 3 ++-
man/ipdw.Rd | 17 ++++++++++++++---
man/ipdwInterp.Rd | 3 ++-
man/pathdistGen.Rd | 8 +++-----
vignettes/ipdw.Rnw | 4 +++-
21 files changed, 125 insertions(+), 59 deletions(-)
Title: Color Space Manipulation
Diff between colorspace versions 1.2-5 dated 2015-03-03 and 1.2-6 dated 2015-03-10
Description: Carries out mapping between assorted color spaces including
RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),
CIELAB and polar CIELAB. Qualitative, sequential, and
diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut],
Paul Murrell [aut],
Kurt Hornik [aut],
Jason C. Fisher [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 12 -
MD5 | 10 -
NAMESPACE | 1
NEWS | 6
R/choose_palette.R | 460 ++++++++++++++++++++++++------------------------
inst/doc/hcl-colors.pdf |binary
6 files changed, 247 insertions(+), 242 deletions(-)
Title: Rare Variants Association Analyses with Family Data
Diff between RVFam versions 1.0 dated 2015-02-19 and 1.1 dated 2015-03-10
Description: The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.
Author: Ming-Huei Chen
Maintainer: Ming-Huei Chen
DESCRIPTION | 6 +++---
MD5 | 4 ++--
NAMESPACE | 6 ++++--
3 files changed, 9 insertions(+), 7 deletions(-)
Title: Mixture Models for Clustering and Classification
Diff between mixture versions 1.3 dated 2015-01-02 and 1.4 dated 2015-03-10
Description: An implementation of all 14 Gaussian parsimonious
clustering models (GPCMs) for model-based clustering and
model-based classification.
Author: Ryan P. Browne, Aisha ElSherbiny and Paul D. McNicholas
Maintainer: Ryan Browne
DESCRIPTION | 9 ++-
MD5 | 14 +++---
R/mixture.R | 68 ++++++++++++++++++++---------
man/gpcm.Rd | 2
man/mixture.Rd | 4 -
src/Makevars | 2
src/functions.h | 2
src/mixture.c | 129 +++++++++++++++++++++++++++++++++++++-------------------
8 files changed, 152 insertions(+), 78 deletions(-)
Title: Mixed Data Sampling Regression
Diff between midasr versions 0.3 dated 2014-04-30 and 0.4 dated 2015-03-10
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras
Maintainer: Vaidotas Zemlys
midasr-0.3/midasr/man/AICc.Rd |only
midasr-0.3/midasr/man/almonp.gradient.Rd |only
midasr-0.3/midasr/man/checkARstar.Rd |only
midasr-0.3/midasr/man/gompertzp.gradient.Rd |only
midasr-0.3/midasr/man/hAh.test.Rd |only
midasr-0.3/midasr/man/hAhr.test.Rd |only
midasr-0.3/midasr/man/harstep.gradient.Rd |only
midasr-0.3/midasr/man/imidas_r.imidas_r.Rd |only
midasr-0.3/midasr/man/lcauchyp.gradient.Rd |only
midasr-0.3/midasr/man/midas.auto.sim.Rd |only
midasr-0.3/midasr/man/midas.sim.Rd |only
midasr-0.3/midasr/man/midas_coef.Rd |only
midasr-0.3/midasr/man/midas_r.midas_r.Rd |only
midasr-0.3/midasr/man/mls_coef.Rd |only
midasr-0.3/midasr/man/nakagamip.gradient.Rd |only
midasr-0.3/midasr/man/nbeta.gradient.Rd |only
midasr-0.3/midasr/man/nbetaMT.gradient.Rd |only
midasr-0.3/midasr/man/nealmon.gradient.Rd |only
midasr-0.3/midasr/man/polystep.gradient.Rd |only
midasr-0.3/midasr/man/prepmidas_r.Rd |only
midasr-0.3/midasr/man/simplearma.sim.Rd |only
midasr-0.3/midasr/man/weight_coef.Rd |only
midasr-0.3/midasr/man/weight_names.Rd |only
midasr-0.3/midasr/man/weight_param.Rd |only
midasr-0.4/midasr/DESCRIPTION | 10
midasr-0.4/midasr/LICENCE | 4
midasr-0.4/midasr/MD5 | 169 +++-----
midasr-0.4/midasr/NAMESPACE | 51 +-
midasr-0.4/midasr/NEWS | 22 +
midasr-0.4/midasr/R/imidasreg.R | 76 +--
midasr-0.4/midasr/R/lagspec.R | 28 -
midasr-0.4/midasr/R/midas_r_methods.R | 420 +++++++++++++-------
midasr-0.4/midasr/R/midasr-package.R | 9
midasr-0.4/midasr/R/midasreg.R | 512 +++++++++++++++----------
midasr-0.4/midasr/R/modsel.R | 150 +++----
midasr-0.4/midasr/R/nonparametric.R | 93 +++-
midasr-0.4/midasr/R/simulate.R | 252 ++++++++----
midasr-0.4/midasr/R/tests.R | 96 ++--
midasr-0.4/midasr/demo/RV.R | 26 -
midasr-0.4/midasr/demo/autoreg.R | 19
midasr-0.4/midasr/demo/imidasr.R | 17
midasr-0.4/midasr/demo/logRV.R | 28 -
midasr-0.4/midasr/demo/okun.R | 24 -
midasr-0.4/midasr/man/USpayems.Rd | 10
midasr-0.4/midasr/man/USqgdp.Rd | 10
midasr-0.4/midasr/man/USrealgdp.Rd | 8
midasr-0.4/midasr/man/USunempr.Rd | 8
midasr-0.4/midasr/man/agk.test.Rd | 12
midasr-0.4/midasr/man/almonp.Rd | 8
midasr-0.4/midasr/man/almonp_gradient.Rd |only
midasr-0.4/midasr/man/amidas_table.Rd | 75 +--
midasr-0.4/midasr/man/amweights.Rd | 26 -
midasr-0.4/midasr/man/average_forecast.Rd | 47 --
midasr-0.4/midasr/man/check_mixfreq.Rd | 15
midasr-0.4/midasr/man/coef.midas_r.Rd |only
midasr-0.4/midasr/man/deriv_tests.Rd | 15
midasr-0.4/midasr/man/deviance.midas_r.Rd | 6
midasr-0.4/midasr/man/dmls.Rd | 11
midasr-0.4/midasr/man/expand_amidas.Rd | 29 -
midasr-0.4/midasr/man/expand_weights_lags.Rd | 24 -
midasr-0.4/midasr/man/fmls.Rd | 16
midasr-0.4/midasr/man/forecast.midas_r.Rd | 66 ++-
midasr-0.4/midasr/man/get_estimation_sample.Rd | 4
midasr-0.4/midasr/man/gompertzp.Rd | 15
midasr-0.4/midasr/man/gompertzp_gradient.Rd |only
midasr-0.4/midasr/man/hAh_test.Rd |only
midasr-0.4/midasr/man/hAhr_test.Rd |only
midasr-0.4/midasr/man/harstep.Rd | 16
midasr-0.4/midasr/man/harstep_gradient.Rd |only
midasr-0.4/midasr/man/hf_lags_table.Rd | 58 --
midasr-0.4/midasr/man/imidas_r.Rd | 130 ++----
midasr-0.4/midasr/man/lcauchyp.Rd | 15
midasr-0.4/midasr/man/lcauchyp_gradient.Rd |only
midasr-0.4/midasr/man/lf_lags_table.Rd | 54 --
midasr-0.4/midasr/man/lws_table-add.Rd | 14
midasr-0.4/midasr/man/midas_auto_sim.Rd |only
midasr-0.4/midasr/man/midas_r.Rd | 151 +++----
midasr-0.4/midasr/man/midas_r.fit.Rd | 6
midasr-0.4/midasr/man/midas_r_ic_table.Rd | 56 --
midasr-0.4/midasr/man/midas_r_np.Rd | 21 -
midasr-0.4/midasr/man/midas_r_simple.Rd | 24 -
midasr-0.4/midasr/man/midas_sim.Rd |only
midasr-0.4/midasr/man/midas_u.Rd | 50 --
midasr-0.4/midasr/man/midasr-package.Rd | 14
midasr-0.4/midasr/man/mls.Rd | 15
midasr-0.4/midasr/man/modsel.Rd | 29 -
midasr-0.4/midasr/man/nakagamip.Rd | 15
midasr-0.4/midasr/man/nakagamip_gradient.Rd |only
midasr-0.4/midasr/man/nbeta.Rd | 14
midasr-0.4/midasr/man/nbetaMT.Rd | 16
midasr-0.4/midasr/man/nbetaMT_gradient.Rd |only
midasr-0.4/midasr/man/nbeta_gradient.Rd |only
midasr-0.4/midasr/man/nealmon.Rd | 18
midasr-0.4/midasr/man/nealmon_gradient.Rd |only
midasr-0.4/midasr/man/oos_prec.Rd | 9
midasr-0.4/midasr/man/plot_midas_coef.Rd |only
midasr-0.4/midasr/man/polystep.Rd | 11
midasr-0.4/midasr/man/polystep_gradient.Rd |only
midasr-0.4/midasr/man/predict.midas_r.Rd | 26 -
midasr-0.4/midasr/man/prep_hAh.Rd | 12
midasr-0.4/midasr/man/rvsp500.Rd | 9
midasr-0.4/midasr/man/select_and_forecast.Rd | 54 +-
midasr-0.4/midasr/man/simulate.midas_r.Rd |only
midasr-0.4/midasr/man/split_data.Rd | 22 -
midasr-0.4/midasr/man/update_weights.Rd |only
midasr-0.4/midasr/man/weights_table.Rd | 41 --
106 files changed, 1759 insertions(+), 1552 deletions(-)
Title: Kriging-Based Optimization for Computer Experiments
Diff between DiceOptim versions 1.4 dated 2013-04-04 and 1.5 dated 2015-03-10
Description: Expected Improvement. EGO algorithm. Multipoint EI and parallelized versions of EGO. Criteria and algorithms for Noisy Kriging-based Optimization , including AEI, AKG, EQI, and EI with plugin.
Author: D. Ginsbourger, V. Picheny, O. Roustant, with contributions by
C. Chevalier, S. Marmin, and T. Wagner
Maintainer: D. Ginsbourger
DiceOptim-1.4/DiceOptim/R/max_qEI.CL.R |only
DiceOptim-1.4/DiceOptim/man/CL.nsteps.Rd |only
DiceOptim-1.4/DiceOptim/man/max_qEI.CL.Rd |only
DiceOptim-1.5/DiceOptim/DESCRIPTION | 19
DiceOptim-1.5/DiceOptim/MD5 | 73 +--
DiceOptim-1.5/DiceOptim/NAMESPACE | 4
DiceOptim-1.5/DiceOptim/R/EI.R | 13
DiceOptim-1.5/DiceOptim/R/EI.grad.R | 13
DiceOptim-1.5/DiceOptim/R/max_EI.R | 4
DiceOptim-1.5/DiceOptim/R/max_qEI.R |only
DiceOptim-1.5/DiceOptim/R/qEGO.nsteps.R |only
DiceOptim-1.5/DiceOptim/R/qEI.R | 176 ++++++-
DiceOptim-1.5/DiceOptim/R/qEI.grad.R |only
DiceOptim-1.5/DiceOptim/R/sampleFromEI.R |only
DiceOptim-1.5/DiceOptim/man/AEI.Rd | 3
DiceOptim-1.5/DiceOptim/man/AEI.grad.Rd | 1
DiceOptim-1.5/DiceOptim/man/AKG.Rd | 1
DiceOptim-1.5/DiceOptim/man/AKG.grad.Rd | 4
DiceOptim-1.5/DiceOptim/man/DiceOptim-package.Rd | 33 -
DiceOptim-1.5/DiceOptim/man/EGO.nsteps.Rd | 446 +++++++++----------
DiceOptim-1.5/DiceOptim/man/EI.Rd | 10
DiceOptim-1.5/DiceOptim/man/EI.grad.Rd | 6
DiceOptim-1.5/DiceOptim/man/EQI.Rd | 1
DiceOptim-1.5/DiceOptim/man/EQI.grad.Rd | 7
DiceOptim-1.5/DiceOptim/man/branin2.Rd | 2
DiceOptim-1.5/DiceOptim/man/goldsteinprice.Rd | 1
DiceOptim-1.5/DiceOptim/man/hartman4.Rd | 2
DiceOptim-1.5/DiceOptim/man/kriging.quantile.Rd | 1
DiceOptim-1.5/DiceOptim/man/kriging.quantile.grad.Rd | 5
DiceOptim-1.5/DiceOptim/man/max_AEI.Rd | 4
DiceOptim-1.5/DiceOptim/man/max_AKG.Rd | 1
DiceOptim-1.5/DiceOptim/man/max_EI.Rd | 5
DiceOptim-1.5/DiceOptim/man/max_EQI.Rd | 4
DiceOptim-1.5/DiceOptim/man/max_qEI.Rd |only
DiceOptim-1.5/DiceOptim/man/min_quantile.Rd | 1
DiceOptim-1.5/DiceOptim/man/noisy.optimizer.Rd | 5
DiceOptim-1.5/DiceOptim/man/qEGO.nsteps.Rd |only
DiceOptim-1.5/DiceOptim/man/qEI.Rd | 164 +++---
DiceOptim-1.5/DiceOptim/man/qEI.grad.Rd |only
DiceOptim-1.5/DiceOptim/man/rosenbrock4.Rd | 2
DiceOptim-1.5/DiceOptim/man/sampleFromEI.Rd |only
DiceOptim-1.5/DiceOptim/man/sphere6.Rd | 2
DiceOptim-1.5/DiceOptim/man/update_km_noisyEGO.Rd | 4
43 files changed, 593 insertions(+), 424 deletions(-)
Title: Causal Inference Test
Diff between cit versions 1.3 dated 2014-12-10 and 1.4 dated 2015-03-10
Description: A formal statistical hypothesis test, resulting in a p-value, is provided to quantify uncertainty in a causal inference pertaining to a measured factor, e.g. a molecular species, which potentially mediates a known causal association between a locus and a quantitative trait. The test is applicable to data that includes genotype (discrete), possible causal mediator such as gene expression (continuous) and an outcome of interest (continuous).
Author: Joshua Millstein
Maintainer: Joshua Millstein
cit-1.3/cit/src/cit_v6.cpp |only
cit-1.4/cit/DESCRIPTION | 10 +++++-----
cit-1.4/cit/MD5 | 8 ++++----
cit-1.4/cit/man/cit-package.Rd | 2 +-
cit-1.4/cit/src/Makevars | 2 +-
cit-1.4/cit/src/cit_v7.cpp |only
6 files changed, 11 insertions(+), 11 deletions(-)
Title: Cut Numeric Values into Evenly Distributed Groups
Diff between binr versions 1.0 dated 2014-07-03 and 1.1 dated 2015-03-10
Description: Implementation of algorithms for cutting numerical values
exhibiting a potentially highly skewed distribution into evenly distributed
groups (bins). This functionality can be applied for binning discrete
values, such as counts, as well as for discretization of continuous values,
for example, during generation of features used in machine learning
algorithms.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev
DESCRIPTION | 16 ++++++++--------
MD5 | 25 +++++++++++++------------
NAMESPACE | 2 +-
NEWS | 8 ++++++++
R/binr-package.R | 6 +++---
R/bins.R | 17 +++++++++++++----
README.md | 2 ++
inst/COPYRIGHTS | 1 +
inst/binr_1.1.pdf |only
man/binr.Rd | 9 +++++----
man/bins.Rd | 3 ++-
man/bins.greedy.Rd | 15 ++++++++-------
man/bins.optimize.Rd | 7 ++++---
man/bins.quantiles.Rd | 3 ++-
14 files changed, 70 insertions(+), 44 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Diff between qgraph versions 1.3 dated 2014-12-02 and 1.3.1 dated 2015-03-10
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp
qgraph-1.3.1/qgraph/DESCRIPTION | 15
qgraph-1.3.1/qgraph/MD5 | 48
qgraph-1.3.1/qgraph/NAMESPACE | 4
qgraph-1.3.1/qgraph/NEWS | 815 +++++-----
qgraph-1.3.1/qgraph/R/PLOT.R | 2376 +++++++++++++++----------------
qgraph-1.3.1/qgraph/R/addTitle.R | 2
qgraph-1.3.1/qgraph/R/averageLayout.R | 6
qgraph-1.3.1/qgraph/R/centrality.R | 2
qgraph-1.3.1/qgraph/R/centralityTable.R | 2
qgraph-1.3.1/qgraph/R/clusteringPlot.R | 3
qgraph-1.3.1/qgraph/R/clusteringTable.R | 2
qgraph-1.3.1/qgraph/R/cor_auto.R | 12
qgraph-1.3.1/qgraph/R/glasso_methods.R | 19
qgraph-1.3.1/qgraph/R/qgraph.R | 18
qgraph-1.3.1/qgraph/R/qgraph.panel.R | 118 -
qgraph-1.3.1/qgraph/R/qgraphAnnotate.R | 6
qgraph-1.3.1/qgraph/R/qgraph_loadings.R | 640 ++++----
qgraph-1.3.1/qgraph/R/qgraph_mixed.R |only
qgraph-1.3.1/qgraph/R/qgraph_svg.R | 358 ++--
qgraph-1.3.1/qgraph/R/scale2.R |only
qgraph-1.3.1/qgraph/README | 8
qgraph-1.3.1/qgraph/man/EBICglasso.Rd | 6
qgraph-1.3.1/qgraph/man/averageLayout.Rd | 5
qgraph-1.3.1/qgraph/man/cor_auto.Rd | 3
qgraph-1.3.1/qgraph/man/qgraph.Rd | 1
qgraph-1.3.1/qgraph/man/qgraphMixed.Rd |only
qgraph-1.3/qgraph/man/qgraph-package.Rd |only
27 files changed, 2266 insertions(+), 2203 deletions(-)
Title: Pretty Heatmaps
Diff between pheatmap versions 0.7.7 dated 2013-09-19 and 1.0.2 dated 2015-03-10
Description: A grid based implementation of heatmaps that offers more control
over heatmap dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde
DESCRIPTION | 19
MD5 | 14
NAMESPACE | 4
NEWS | 38 +
R/pheatmap-package.r | 10
R/pheatmap.r | 1390 ++++++++++++++++++++++++++++--------------------
man/pheatmap-package.Rd | 10
man/pheatmap.Rd | 315 +++++-----
8 files changed, 1049 insertions(+), 751 deletions(-)
Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Diff between orca versions 1.0 dated 2014-03-29 and 1.1 dated 2015-03-10
Description: Implements orbit counting using a fast combinatorial approach.
Counts orbits of nodes and edges from edge matrix or data frame, or a
graph object from the graph package.
Author: Tomaz Hocevar, Janez Demsar
Maintainer: Janez Demsar
DESCRIPTION | 16
MD5 | 24
R/orca.R | 26
data/petersen.txt.gz |only
data/usastates.txt.gz |only
data/yeast.txt.gz |only
man/karate.Rd | 2
man/orca.Rd | 31
man/petersen.Rd |only
man/usastates.Rd |only
man/yeast.Rd |only
src/count.cpp | 410 +++++------
tests/karate-as-matrix.Rout.save | 113 +--
tests/karate.Rout.save | 1411 +++++++++++++++------------------------
tests/permutation.R |only
tests/permutation.Rout.save |only
tests/symmetry.R |only
tests/symmetry.Rout.save |only
18 files changed, 892 insertions(+), 1141 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Diff between ChemoSpec versions 3.0-1 dated 2015-01-21 and 4.0-0 dated 2015-03-10
Description: A collection of functions for plotting spectra (NMR, IR, Raman) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA, model-based clustering and STOCSY analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette illustrating typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
ChemoSpec-3.0-1/ChemoSpec/R/LoopThruSpectra.R |only
ChemoSpec-3.0-1/ChemoSpec/R/aovPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/baselineSpec.R |only
ChemoSpec-3.0-1/ChemoSpec/R/binBuck.R |only
ChemoSpec-3.0-1/ChemoSpec/R/calcSN.R |only
ChemoSpec-3.0-1/ChemoSpec/R/classPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/findTMS.R |only
ChemoSpec-3.0-1/ChemoSpec/R/pcaBoot.R |only
ChemoSpec-3.0-1/ChemoSpec/R/readBrukerAscii.R |only
ChemoSpec-3.0-1/ChemoSpec/R/readBrukerTxt.R |only
ChemoSpec-3.0-1/ChemoSpec/R/robPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/specSurvey.R |only
ChemoSpec-3.0-1/ChemoSpec/data/CuticleIR.RData |only
ChemoSpec-3.0-1/ChemoSpec/man/CuticleIR.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/LoopThruSpectra.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/aovPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/baselineSpec.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/binBuck.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/calcSN.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/classPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/findTMS.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/pcaBoot.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/readBrukerTxt.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/robPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/specSurvey.Rd |only
ChemoSpec-4.0-0/ChemoSpec/DESCRIPTION | 19
ChemoSpec-4.0-0/ChemoSpec/MD5 | 210 ++---
ChemoSpec-4.0-0/ChemoSpec/NAMESPACE | 136 ++-
ChemoSpec-4.0-0/ChemoSpec/NEWS | 639 +++++++---------
ChemoSpec-4.0-0/ChemoSpec/R/aovPCAloadings.R | 4
ChemoSpec-4.0-0/ChemoSpec/R/aovPCAscores.R | 8
ChemoSpec-4.0-0/ChemoSpec/R/aov_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/avgFacLvls.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/baselineSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/binSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/c_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/chooseLvls.R |only
ChemoSpec-4.0-0/ChemoSpec/R/clupaSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/corSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/covSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/cv_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/evalClusters.R | 20
ChemoSpec-4.0-0/ChemoSpec/R/files2SpectraObject.R | 238 ++---
ChemoSpec-4.0-0/ChemoSpec/R/getMaxCovByFreq.R |only
ChemoSpec-4.0-0/ChemoSpec/R/hcaSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/hmapSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/loopThruSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/mclust3D.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/mclust3dSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/mclustSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/plotSpectraJS.R |only
ChemoSpec-4.0-0/ChemoSpec/R/r_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/rowDist.R | 25
ChemoSpec-4.0-0/ChemoSpec/R/sampleDistSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/splitSpectraGroups.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/surveySpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/build/vignette.rds |binary
ChemoSpec-4.0-0/ChemoSpec/data/alignMUD.RData |only
ChemoSpec-4.0-0/ChemoSpec/data/datalist | 4
ChemoSpec-4.0-0/ChemoSpec/data/metMUD1.RData |only
ChemoSpec-4.0-0/ChemoSpec/data/metMUD2.RData |only
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.R | 19
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.Rnw | 61 -
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.pdf |binary
ChemoSpec-4.0-0/ChemoSpec/inst/extdata |only
ChemoSpec-4.0-0/ChemoSpec/man/ChemoSpec-package.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/MUD.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/Spectra.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/SrE.IR.Rd | 13
ChemoSpec-4.0-0/ChemoSpec/man/aovPCAloadings.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/aovPCAscores.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/aov_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/avgFacLvls.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/baselineSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/binData.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/binSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/c_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/check4Gaps.Rd | 9
ChemoSpec-4.0-0/ChemoSpec/man/chkSpectra.Rd | 20
ChemoSpec-4.0-0/ChemoSpec/man/chooseLvls.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/clupaSpectra.Rd | 26
ChemoSpec-4.0-0/ChemoSpec/man/colLeaf.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/colorSymbol.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/conColScheme.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/coordProjCS.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/corSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/cv_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/evalClusters.Rd | 56 -
ChemoSpec-4.0-0/ChemoSpec/man/files2SpectraObject.Rd | 24
ChemoSpec-4.0-0/ChemoSpec/man/getMaxCovByFreq.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/groupNcolor.Rd | 7
ChemoSpec-4.0-0/ChemoSpec/man/hcaScores.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/hcaSpectra.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/hmapSpectra.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/hypTestScores.Rd | 22
ChemoSpec-4.0-0/ChemoSpec/man/isWholeNo.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/labelExtremes.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/labelExtremes3d.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/loopThruSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/makeEllipsoid.Rd | 5
ChemoSpec-4.0-0/ChemoSpec/man/mclust3D.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/mclust3dSpectra.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/mclustSpectra.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/normSpectra.Rd | 13
ChemoSpec-4.0-0/ChemoSpec/man/normVec.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/pcaDiag.Rd | 9
ChemoSpec-4.0-0/ChemoSpec/man/plot2Loadings.Rd | 8
ChemoSpec-4.0-0/ChemoSpec/man/plotHCA.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/plotLoadings.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/plotScores.Rd | 19
ChemoSpec-4.0-0/ChemoSpec/man/plotScores3D.Rd | 12
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresCor.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresDecoration.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresRGL.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/plotScree.Rd | 17
ChemoSpec-4.0-0/ChemoSpec/man/plotSpectra.Rd | 18
ChemoSpec-4.0-0/ChemoSpec/man/plotSpectraJS.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/q2rPCA.Rd | 3
ChemoSpec-4.0-0/ChemoSpec/man/r_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/readJDX.Rd | 5
ChemoSpec-4.0-0/ChemoSpec/man/removeFreq.Rd | 20
ChemoSpec-4.0-0/ChemoSpec/man/removeSample.Rd | 18
ChemoSpec-4.0-0/ChemoSpec/man/rowDist.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/sPlotSpectra.Rd | 7
ChemoSpec-4.0-0/ChemoSpec/man/sampleDistSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/shrinkLeaf.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/splitSpectraGroups.Rd | 38
ChemoSpec-4.0-0/ChemoSpec/man/sumGroups.Rd | 8
ChemoSpec-4.0-0/ChemoSpec/man/sumSpectra.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/surveySpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/vignettes/ChemoSpec.Rnw | 61 -
ChemoSpec-4.0-0/ChemoSpec/vignettes/MetabPreProcess.pdf |only
132 files changed, 1025 insertions(+), 982 deletions(-)
Title: Code Analysis Tools for R
Diff between codetools versions 0.2-10 dated 2015-01-17 and 0.2-11 dated 2015-03-10
Description: Code analysis tools for R.
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Diff between forestplot versions 1.0 dated 2014-12-29 and 1.1 dated 2015-03-10
Description: The plot allows for multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-10-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-2-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-3-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-4-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-5-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-6-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-7-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-8-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-9-1.svg |only
forestplot-1.1/forestplot/DESCRIPTION | 8
forestplot-1.1/forestplot/MD5 | 59 +-
forestplot-1.1/forestplot/NEWS | 10
forestplot-1.1/forestplot/R/forestplot-package.R | 22
forestplot-1.1/forestplot/R/forestplot.R | 138 ++++--
forestplot-1.1/forestplot/R/forestplot_helpers.R | 56 +-
forestplot-1.1/forestplot/R/private.R | 227 +++++++++-
forestplot-1.1/forestplot/inst/doc/forestplot.R | 58 +-
forestplot-1.1/forestplot/inst/doc/forestplot.Rmd | 92 +++-
forestplot-1.1/forestplot/inst/doc/forestplot.html | 103 +++-
forestplot-1.1/forestplot/man/forestplot-package.Rd | 21
forestplot-1.1/forestplot/man/forestplot.Rd | 58 ++
forestplot-1.1/forestplot/man/fpColors.Rd | 5
forestplot-1.1/forestplot/man/prFpDrawLines.Rd |only
forestplot-1.1/forestplot/man/prFpGetGraphTicksAndClips.Rd | 9
forestplot-1.1/forestplot/man/prFpGetLabels.Rd | 6
forestplot-1.1/forestplot/man/prFpGetLines.Rd |only
forestplot-1.1/forestplot/man/prFpPrintLabels.Rd | 7
forestplot-1.1/forestplot/man/prGparMerge.Rd |only
forestplot-1.1/forestplot/tests/testthat/test-prFpGetLines.R |only
forestplot-1.1/forestplot/tests/testthat/test-prGparMerge.R |only
forestplot-1.1/forestplot/vignettes/forestplot.Rmd | 92 +++-
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/Thumbs.db |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-10-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-11-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-12-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-13-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-2-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-3-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-4-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-5-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-6-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-7-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-8-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-9-1.png |only
44 files changed, 748 insertions(+), 223 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Diff between eVenn versions 2.1.6 dated 2012-07-12 and 2.2 dated 2015-03-10
Description: Compute a matrix comparison of lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard
eVenn-2.1.6/eVenn/R/evenn.r |only
eVenn-2.1.6/eVenn/data/res2.rda |only
eVenn-2.1.6/eVenn/data/res3.rda |only
eVenn-2.1.6/eVenn/data/res4.rda |only
eVenn-2.1.6/eVenn/man/res2.Rd |only
eVenn-2.1.6/eVenn/man/res3.Rd |only
eVenn-2.1.6/eVenn/man/res4.Rd |only
eVenn-2.2/eVenn/DESCRIPTION | 23 +-
eVenn-2.2/eVenn/MD5 | 30 ++-
eVenn-2.2/eVenn/NAMESPACE | 6
eVenn-2.2/eVenn/R/autoevenn.R |only
eVenn-2.2/eVenn/R/evenn.R |only
eVenn-2.2/eVenn/R/man.evenn.R | 106 +++++++------
eVenn-2.2/eVenn/data/Data_Binary_Matrix.rda |only
eVenn-2.2/eVenn/data/Data_Lists.rda |only
eVenn-2.2/eVenn/data/Data_Matrix_Of_Folds.rda |only
eVenn-2.2/eVenn/data/Data_Matrix_Of_Ratios.rda |only
eVenn-2.2/eVenn/man/Data_Binary_Matrix.Rd |only
eVenn-2.2/eVenn/man/Data_Lists.Rd |only
eVenn-2.2/eVenn/man/Data_Matrix_Of_Folds.Rd |only
eVenn-2.2/eVenn/man/Data_Matrix_Of_Ratios.Rd |only
eVenn-2.2/eVenn/man/autoevenn.Rd |only
eVenn-2.2/eVenn/man/eVenn-package.Rd | 110 +++++++-------
eVenn-2.2/eVenn/man/evenn.Rd | 192 ++++++++++++++-----------
eVenn-2.2/eVenn/man/man.evenn.Rd | 36 ++--
25 files changed, 278 insertions(+), 225 deletions(-)
Title: Bayesian Additive Regression Trees
Diff between bartMachine versions 1.1.1 dated 2014-12-02 and 1.2.0 dated 2015-03-10
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package), see COPYRIGHTS file for the authors of the java libraries
Maintainer: Adam Kapelner
CHANGELOG | 14 ++++
DESCRIPTION | 10 +--
MD5 | 32 +++++------
R/bartMachine.R | 30 +++-------
R/bart_package_builders.R | 13 +++-
R/bart_package_inits.R | 6 +-
R/bart_package_plots.R | 23 ++++---
R/zzz.R | 3 -
inst/doc/bartMachine.pdf |binary
inst/java/bart_java.jar |binary
java/bartMachine/bartMachineClassification.java | 4 +
java/bartMachine/bartMachineRegression.java | 1
java/bartMachine/bartMachineRegressionMultThread.java | 8 ++
java/bartMachine/bartMachineTreeNode.java | 52 +++++++++---------
java/bartMachine/bartMachine_a_base.java | 2
java/bartMachine/bartMachine_g_mh.java | 7 --
man/bartMachine.Rd | 9 ++-
17 files changed, 120 insertions(+), 94 deletions(-)
Title: Relational Event Models
Diff between relevent versions 1.0-3 dated 2013-04-03 and 1.0-4 dated 2015-03-10
Description: Tools to fit relational event models.
Author: Carter T. Butts
Maintainer: Carter T. Butts
ChangeLog | 7 +++++++
DESCRIPTION | 11 +++++------
MD5 | 11 ++++++-----
NAMESPACE | 3 +++
R/rem.R | 11 +++++------
R/rem.dyad.R | 4 +---
inst |only
7 files changed, 27 insertions(+), 20 deletions(-)
Title: Parallel Programming Tools for Rcpp
Diff between RcppParallel versions 4.3.4 dated 2015-03-07 and 4.3.6 dated 2015-03-10
Description: High level functions for doing parallel programming with Rcpp.
For example, the parallelFor function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire
DESCRIPTION | 10 +++++-----
MD5 | 22 +++++++++++-----------
NEWS | 7 +++++++
R/build.R | 9 +++++++--
inst/include/tbb/concurrent_vector.h | 4 ++--
src/Makevars | 11 ++++++-----
src/options.cpp | 4 ++++
src/tbb/build/windows.inc | 18 ++++++++++++------
src/tbb/include/tbb/concurrent_vector.h | 4 ++--
tests/testthat/cpp/distance.cpp | 2 +-
tests/testthat/cpp/transform.cpp | 23 +++++++++++++----------
tests/testthat/test-transform.R | 2 +-
12 files changed, 71 insertions(+), 45 deletions(-)
Title: R Wrapper for the Energy Information Administration (EIA) API
Diff between EIAdata versions 0.0.2 dated 2014-12-16 and 0.0.3 dated 2015-03-10
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API.
Author: Matthew Brigida
Maintainer: Matthew Brigida
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/EIAdata-package.Rd | 9 ++++++---
man/getCatEIA.Rd | 44 +++++++++++++++++++++++++++++---------------
4 files changed, 42 insertions(+), 25 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.16 dated 2015-02-27 and 2.17 dated 2015-03-10
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.16/BDgraph/R/I.g.R |only
BDgraph-2.16/BDgraph/man/I.g.Rd |only
BDgraph-2.17/BDgraph/DESCRIPTION | 6 +++---
BDgraph-2.17/BDgraph/MD5 | 24 ++++++++++++++----------
BDgraph-2.17/BDgraph/NAMESPACE | 1 -
BDgraph-2.17/BDgraph/R/bdgraph.R | 14 ++++++++++----
BDgraph-2.17/BDgraph/R/phat.R | 15 ++++++++-------
BDgraph-2.17/BDgraph/R/plotcoda.R | 22 +++++++++++++++-------
BDgraph-2.17/BDgraph/R/select.R | 16 ++++++++--------
BDgraph-2.17/BDgraph/build |only
BDgraph-2.17/BDgraph/inst |only
BDgraph-2.17/BDgraph/man/plotcoda.Rd | 4 +++-
BDgraph-2.17/BDgraph/src/BDgraph.cpp | 19 +++++++++++++++++++
BDgraph-2.17/BDgraph/vignettes |only
14 files changed, 80 insertions(+), 41 deletions(-)
Title: Analysis of Multiple Time Course Data
Diff between longitudinal versions 1.1.10 dated 2014-11-14 and 1.1.11 dated 2015-03-09
Description: Contains general data structures and
functions for longitudinal data with multiple variables,
repeated measurements, and irregularly spaced time points.
Also implements a shrinkage estimator of dynamical correlation
and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 12 ++++++------
NAMESPACE | 3 +++
NEWS | 7 +++++++
man/dyn.cor.Rd | 2 +-
man/dyn.scale.Rd | 2 +-
man/tcell.Rd | 6 +-----
7 files changed, 25 insertions(+), 19 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Diff between EnvStats versions 1.0.3 dated 2014-10-21 and 2.0.0 dated 2015-03-09
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer).
Author: Steven P. Millard
Maintainer: Steven P. Millard
DESCRIPTION | 23 +
MD5 | 278 ++++++++++++------------
NAMESPACE | 11
NEWS | 34 ++
R/calibrate.R | 1
R/check.distribution.args.R | 9
R/check.distribution.args.simulate.R | 9
R/detectionLimitCalibrate.R | 6
R/elnorm3.R | 19 -
R/errorBar.R | 100 ++++----
R/gofGroupTest.formula.R | 2
R/gofTest.formula.R | 2
R/inversePredictCalibrate.R | 6
R/kendallSeasonalTrendTest.formula.R | 2
R/kendallTrendTest.formula.R | 2
R/pointwise.R | 4
R/predict.R |only
R/predict.default.R |only
R/predict.lm.R | 33 +-
R/print.R |only
R/print.default.R |only
R/simulateMvMatrix.R | 2
R/simulateVector.R | 2
R/stripChart.default.R | 24 +-
R/stripChart.formula.R | 2
R/summaryFull.formula.R | 2
R/summaryStats.character.R |only
R/summaryStats.formula.R | 2
R/summaryStats.logical.R |only
R/varGroupTest.formula.R | 2
data/Air.df.rda |binary
data/Benthic.df.rda |binary
data/Distribution.df.rda |binary
data/EPA.02d.Ex.2.ug.per.L.vec.rda |binary
data/EPA.02d.Ex.4.mg.per.kg.vec.rda |binary
data/EPA.02d.Ex.6.mg.per.kg.vec.rda |binary
data/EPA.02d.Ex.9.mg.per.L.vec.rda |binary
data/EPA.09.Ex.10.1.nickel.df.rda |binary
data/EPA.09.Ex.11.1.arsenic.df.rda |binary
data/EPA.09.Ex.12.1.ccl4.df.rda |binary
data/EPA.09.Ex.12.4.naphthalene.df.rda |binary
data/EPA.09.Ex.13.1.iron.df.rda |binary
data/EPA.09.Ex.14.1.manganese.df.rda |binary
data/EPA.09.Ex.14.3.alkalinity.df.rda |binary
data/EPA.09.Ex.14.4.arsenic.df.rda |binary
data/EPA.09.Ex.14.8.df.rda |binary
data/EPA.09.Ex.15.1.manganese.df.rda |binary
data/EPA.09.Ex.16.1.sulfate.df.rda |binary
data/EPA.09.Ex.16.2.benzene.df.rda |binary
data/EPA.09.Ex.16.4.copper.df.rda |binary
data/EPA.09.Ex.16.5.PCE.df.rda |binary
data/EPA.09.Ex.17.1.loglead.df.rda |binary
data/EPA.09.Ex.17.2.toluene.df.rda |binary
data/EPA.09.Ex.17.3.chrysene.df.rda |binary
data/EPA.09.Ex.17.3.log.chrysene.df.rda |binary
data/EPA.09.Ex.17.4.copper.df.rda |binary
data/EPA.09.Ex.17.5.chloride.df.rda |binary
data/EPA.09.Ex.17.6.sulfate.df.rda |binary
data/EPA.09.Ex.17.7.sodium.df.rda |binary
data/EPA.09.Ex.18.1.arsenic.df.rda |binary
data/EPA.09.Ex.18.2.chrysene.df.rda |binary
data/EPA.09.Ex.18.3.TCE.df.rda |binary
data/EPA.09.Ex.18.4.xylene.df.rda |binary
data/EPA.09.Ex.19.1.sulfate.df.rda |binary
data/EPA.09.Ex.19.2.chloride.df.rda |binary
data/EPA.09.Ex.19.5.mercury.df.rda |binary
data/EPA.09.Ex.20.1.nickel.df.rda |binary
data/EPA.09.Ex.21.1.aldicarb.df.rda |binary
data/EPA.09.Ex.21.2.benzene.df.rda |binary
data/EPA.09.Ex.21.5.beryllium.df.rda |binary
data/EPA.09.Ex.21.6.nitrate.df.rda |binary
data/EPA.09.Ex.21.7.TCE.df.rda |binary
data/EPA.09.Ex.22.1.VC.df.rda |binary
data/EPA.09.Ex.22.2.Specific.Conductance.df.rda |binary
data/EPA.09.Ex.6.3.sulfate.df.rda |binary
data/EPA.09.Ex.7.1.arsenic.df.rda |binary
data/EPA.09.Table.9.1.TCE.df.rda |binary
data/EPA.09.Table.9.3.df.rda |binary
data/EPA.09.Table.9.4.nickel.vec.rda |binary
data/EPA.89b.aldicarb1.df.rda |binary
data/EPA.89b.aldicarb2.df.rda |binary
data/EPA.89b.benzene.df.rda |binary
data/EPA.89b.cadmium.df.rda |binary
data/EPA.89b.chlordane1.df.rda |binary
data/EPA.89b.chlordane2.df.rda |binary
data/EPA.89b.edb.df.rda |binary
data/EPA.89b.lead.df.rda |binary
data/EPA.89b.loglead.df.rda |binary
data/EPA.89b.manganese.df.rda |binary
data/EPA.89b.sulfate.df.rda |binary
data/EPA.89b.t29.df.rda |binary
data/EPA.89b.toc.vec.rda |binary
data/EPA.92c.arsenic1.df.rda |binary
data/EPA.92c.arsenic2.df.rda |binary
data/EPA.92c.arsenic3.df.rda |binary
data/EPA.92c.benzene1.df.rda |binary
data/EPA.92c.benzene2.df.rda |binary
data/EPA.92c.ccl4.df.rda |binary
data/EPA.92c.chrysene.df.rda |binary
data/EPA.92c.copper1.df.rda |binary
data/EPA.92c.copper2.df.rda |binary
data/EPA.92c.lognickel1.df.rda |binary
data/EPA.92c.nickel1.df.rda |binary
data/EPA.92c.nickel2.df.rda |binary
data/EPA.92c.toluene.df.rda |binary
data/EPA.92c.zinc.df.rda |binary
data/EPA.92d.chromium.df.rda |binary
data/EPA.92d.chromium.vec.rda |binary
data/EPA.94b.lead.df.rda |binary
data/EPA.94b.tccb.df.rda |binary
data/EPA.97.cadmium.111.df.rda |binary
data/Environmental.df.rda |binary
data/Gibbons.et.al.09.Alkilinity.vec.rda |binary
data/Gibbons.et.al.09.Vinyl.Chloride.vec.rda |binary
data/Graham.et.al.75.etu.df.rda |binary
data/Helsel.Cohn.88.app.b.df.rda |binary
data/Helsel.Cohn.88.silver.df.rda |binary
data/Lin.Evans.80.df.rda |binary
data/Millard.Deverel.88.df.rda |binary
data/Modified.TcCB.df.rda |binary
data/NIOSH.89.air.lead.vec.rda |binary
data/Olympic.NH4.df.rda |binary
data/Ozone.NE.df.rda |binary
data/Refinery.CO.df.rda |binary
data/Skagit.NH3_N.df.rda |binary
data/Total.P.df.rda |binary
inst/doc/EnvStats-manual.pdf |binary
man/Distribution.df.Rd | 4
man/EnvStats-package.Rd | 46 ++-
man/calibrate.Rd | 9
man/calibrate.object.Rd |only
man/detectionLimitCalibrate.Rd | 3
man/elnorm3.Rd | 6
man/errorBar.Rd |only
man/inversePredictCalibrate.Rd | 26 +-
man/kendallSeasonalTrendTest.Rd | 2
man/kendallTrendTest.Rd | 2
man/pointwise.Rd | 26 +-
man/predict.Rd |only
man/predict.lm.Rd | 152 +++----------
man/print.Rd |only
man/print.htest.Rd | 14 -
man/simulateMvMatrix.Rd | 2
man/simulateVector.Rd | 2
man/stripChart.Rd | 21 +
145 files changed, 457 insertions(+), 435 deletions(-)
Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Diff between fdrtool versions 1.2.13 dated 2014-11-14 and 1.2.14 dated 2015-03-09
Description: Estimates both tail area-based false
discovery rates (Fdr) as well as local false discovery rates (fdr) for a
variety of null models (p-values, z-scores, correlation coefficients,
t-scores). The proportion of null values and the parameters of the null
distribution are adaptively estimated from the data. In addition, the package
contains functions for non-parametric density estimation (Grenander estimator),
for monotone regression (isotonic regression and antitonic regression with weights),
for computing the greatest convex minorant (GCM) and the least concave majorant (LCM),
for the half-normal and correlation distributions, and for computing
empirical higher criticism (HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NAMESPACE | 4 ++++
NEWS | 6 ++++++
man/pval.estimate.eta0.Rd | 3 +--
5 files changed, 20 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-09 0.3-1
Title: Interface to the Global Biodiversity Information Facility API
Diff between rgbif versions 0.7.7 dated 2014-11-06 and 0.8.0 dated 2015-03-09
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF).
GBIF is a database of species occurrence records from sources all
over the globe. rgbif includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain
DESCRIPTION | 14
LICENSE | 4
MD5 | 231 ++++++-------
NAMESPACE | 3
NEWS | 25 +
R/check_wkt.r | 14
R/count_facet.r | 37 +-
R/dataset_search.r | 10
R/dataset_suggest.r | 51 +-
R/datasets.r | 6
R/elevation.r | 18 -
R/gbif_names.R | 14
R/gbifmap.r | 2
R/installations.r | 31 -
R/name_backbone.r | 54 +--
R/name_lookup.r | 8
R/name_suggest.r | 37 +-
R/name_usage.r | 152 ++++----
R/networks.r | 19 -
R/nodes.r | 29 -
R/occ_count.r | 2
R/occ_get.r | 44 +-
R/occ_issues.r | 21 -
R/occ_issues_lookup.r | 3
R/occ_metadata.r | 39 --
R/occ_search.r | 230 +++----------
R/organizations.r | 67 +--
R/parsenames.R | 18 -
R/rgbif-package.r | 18 -
R/tbl_df_utils.R |only
R/zzz.r | 92 +++--
README.md | 298 +++++++++--------
inst/assets/img/unnamed-chunk-8-1.png |only
inst/doc/issues_vignette.Rmd | 182 ++++------
inst/doc/issues_vignette.html | 182 ++++------
inst/doc/rgbif_vignette.html | 579 +++++++++++++++++++++-------------
inst/vign/figure/gbifmap1-1.png |only
inst/vign/issues_vignette.Rmd | 4
inst/vign/issues_vignette.md | 182 ++++------
inst/vign/rgbif_vignette.Rmd | 2
inst/vign/rgbif_vignette.md | 579 +++++++++++++++++++++-------------
man/blanktheme.Rd | 3
man/check_wkt.Rd | 3
man/commas_to_periods.Rd | 3
man/count_facet.Rd | 9
man/create_gist.Rd | 3
man/dataset_metrics.Rd | 3
man/dataset_search.Rd | 11
man/dataset_suggest.Rd | 11
man/datasetparser.Rd | 3
man/datasets.Rd | 11
man/density_spplist.Rd | 3
man/densitylist.Rd | 3
man/elevation.Rd | 3
man/gbif_bbox2wkt.Rd | 5
man/gbif_capwords.Rd | 3
man/gbif_issues.Rd | 3
man/gbif_names.Rd | 7
man/gbif_photos.Rd | 3
man/gbifdata.Rd | 3
man/gbifmap.Rd | 5
man/gbifmap_dens.Rd | 3
man/gbifmap_list.Rd | 3
man/gbifparser.Rd | 3
man/gbifparser_verbatim.Rd | 3
man/get_credentials.Rd | 3
man/gist.Rd | 3
man/installations.Rd | 11
man/isocodes.Rd | 3
man/ldfast.Rd | 3
man/name_backbone.Rd | 11
man/name_lookup.Rd | 17
man/name_suggest.Rd | 11
man/name_usage.Rd | 44 +-
man/namelkupparser.Rd | 3
man/networks.Rd | 11
man/nodes.Rd | 11
man/occ_count.Rd | 3
man/occ_fields.Rd | 3
man/occ_get.Rd | 8
man/occ_issues.Rd | 17
man/occ_issues_lookup.Rd | 5
man/occ_metadata.Rd | 3
man/occ_search.Rd | 49 +-
man/occurrencecount.Rd | 3
man/occurrencedensity.Rd | 3
man/occurrenceget.Rd | 3
man/occurrencelist.Rd | 3
man/occurrencelist_all.Rd | 3
man/occurrencelist_many.Rd | 3
man/organizations.Rd | 11
man/parsenames.Rd | 3
man/parseresults.Rd | 3
man/pipe.Rd | 3
man/providers.Rd | 3
man/resources.Rd | 3
man/rgb_country_codes.Rd | 3
man/rgbif-defunct.Rd | 3
man/rgbif-package.Rd | 21 -
man/stylegeojson.Rd | 3
man/suggestfields.Rd | 3
man/taxoncount.Rd | 3
man/taxonget.Rd | 3
man/taxonsearch.Rd | 3
man/taxrank.Rd | 3
man/togeojson.Rd | 3
man/type_sum.Rd | 3
man/typestatus.Rd | 3
tests/testthat/test-count_facet.r |only
tests/testthat/test-name_backbone.r | 4
tests/testthat/test-name_lookup.r | 2
tests/testthat/test-name_usage.r | 31 +
tests/testthat/test-nodes.r | 2
tests/testthat/test-occ_get.r | 4
tests/testthat/test-occ_metadata.r | 8
tests/testthat/test-occ_search.r | 4
vignettes/figure/gbifmap1-1.png |only
vignettes/issues_vignette.Rmd | 182 ++++------
vignettes/rgbif_vignette.Rmd | 579 +++++++++++++++++++++-------------
119 files changed, 2508 insertions(+), 2036 deletions(-)
Title: Sequence Statistics for Relational Event Models
Diff between informR versions 1.0.04 dated 2012-04-07 and 1.0-5 dated 2015-03-09
Description: Aids in creating sequence statistics for Butts's 'relevent' software.
Author: Christopher Steven Marcum
Maintainer: Christopher Steven Marcum
ChangeLog | 9 +++++++++
DESCRIPTION | 20 +++++++++-----------
MD5 | 23 ++++++++++++-----------
NAMESPACE | 6 +++++-
R/slbind.R | 1 -
R/slbind.cov.R | 1 -
R/sldrop.R | 1 -
R/zzz.R | 29 ++++++++++++++++-------------
data/atus80int.rda |binary
data/atus80ord.rda |binary
inst |only
man/gen.sformlist.Rd | 2 --
man/glb.sformlist.Rd | 3 ++-
13 files changed, 53 insertions(+), 42 deletions(-)
Title: Probabilities for Pedigrees Given DNA Data
Diff between Familias versions 2.1 dated 2014-08-01 and 2.2 dated 2015-03-09
Description:
An interface to the core Familias functions (www.familias.name),
which are programmed in C++.
Author: Petter Mostad and Thore Egeland
Maintainer: Petter Mostad
DESCRIPTION | 17 -
MD5 | 22 +-
NAMESPACE | 4
R/FamiliasLocus.R | 452 ++++++++++++++++++++++++-----------------
R/FamiliasPosterior.R | 472 ++++++++++++++++++++-----------------------
R/plot.FamiliasPedigree.R |only
data |only
man/Familias-package.Rd | 14 -
man/FamiliasLocus.Rd | 166 ++++++++++-----
man/FamiliasPedigree.Rd | 14 -
man/FamiliasPosterior.Rd | 31 +-
man/FamiliasPrior.Rd | 13 -
man/NorwegianFrequencies.Rd |only
man/plot.FamiliasPedigree.Rd |only
14 files changed, 669 insertions(+), 536 deletions(-)
Title: A Dynamic Nomogram for Linear and Generalized Linear Models as
Shiny Applications
Diff between DynNom versions 1.0 dated 2014-10-04 and 1.0.1 dated 2015-03-09
Description: The DynNom function makes it possible to present the results of an
lm or glm model object as a dynamic nomogram that can be displayed in an R
Studio panel or web browser.
Author: Amirhossein Jalali, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali
DESCRIPTION | 6 +++---
MD5 | 6 +++---
man/DynNom-package.Rd | 12 ++++++++----
man/DynNom.Rd | 10 +++++++---
4 files changed, 21 insertions(+), 13 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.1.7 dated 2014-11-23 and 1.1.8 dated 2015-03-09
Description: The "care" package implements the regression approach
of Zuber and Strimmer (2011) "High-dimensional regression and variable
selection using CAR scores" SAGMB 10: 34.
CAR scores measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is a
natural measure of variable importance and provides a canonical
ordering of variables. This package provides functions for estimating
CAR scores, for variable selection using CAR scores, and for estimating
corresponding regression coefficients. Both shrinkage as well as
empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 1 +
NEWS | 6 ++++++
4 files changed, 14 insertions(+), 7 deletions(-)
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Diff between HSAUR3 versions 1.0-3 dated 2015-01-05 and 1.0-4 dated 2015-03-09
Description: Functions, data sets, analyses and examples from the
third edition of the book
`A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 -
MD5 | 138 ++++++++++++-------------
inst/NEWS | 4
inst/doc/Ch_analysing_longitudinal_dataI.Rnw | 19 ++-
inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
inst/doc/Ch_analysing_longitudinal_dataII.Rnw | 13 ++
inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
inst/doc/Ch_analysis_of_variance.Rnw | 13 ++
inst/doc/Ch_analysis_of_variance.pdf |binary
inst/doc/Ch_bayesian_inference.Rnw | 13 ++
inst/doc/Ch_bayesian_inference.pdf |binary
inst/doc/Ch_cluster_analysis.Rnw | 13 ++
inst/doc/Ch_cluster_analysis.pdf |binary
inst/doc/Ch_conditional_inference.Rnw | 13 ++
inst/doc/Ch_conditional_inference.pdf |binary
inst/doc/Ch_density_estimation.Rnw | 13 ++
inst/doc/Ch_density_estimation.pdf |binary
inst/doc/Ch_errata.Rnw | 13 ++
inst/doc/Ch_errata.pdf |binary
inst/doc/Ch_gam.Rnw | 13 ++
inst/doc/Ch_gam.pdf |binary
inst/doc/Ch_graphical_display.R | 2
inst/doc/Ch_graphical_display.Rnw | 15 ++
inst/doc/Ch_graphical_display.pdf |binary
inst/doc/Ch_introduction_to_R.Rnw | 13 ++
inst/doc/Ch_introduction_to_R.pdf |binary
inst/doc/Ch_logistic_regression_glm.Rnw | 13 ++
inst/doc/Ch_logistic_regression_glm.pdf |binary
inst/doc/Ch_meta_analysis.Rnw | 13 ++
inst/doc/Ch_meta_analysis.pdf |binary
inst/doc/Ch_missing_values.Rnw | 13 ++
inst/doc/Ch_missing_values.pdf |binary
inst/doc/Ch_multidimensional_scaling.Rnw | 13 ++
inst/doc/Ch_multidimensional_scaling.pdf |binary
inst/doc/Ch_multiple_linear_regression.Rnw | 13 ++
inst/doc/Ch_multiple_linear_regression.pdf |binary
inst/doc/Ch_principal_components_analysis.Rnw | 26 ++--
inst/doc/Ch_principal_components_analysis.pdf |binary
inst/doc/Ch_quantile_regression.Rnw | 15 ++
inst/doc/Ch_quantile_regression.pdf |binary
inst/doc/Ch_recursive_partitioning.Rnw | 13 ++
inst/doc/Ch_recursive_partitioning.pdf |binary
inst/doc/Ch_simple_inference.Rnw | 13 ++
inst/doc/Ch_simple_inference.pdf |binary
inst/doc/Ch_simultaneous_inference.Rnw | 13 ++
inst/doc/Ch_simultaneous_inference.pdf |binary
inst/doc/Ch_survival_analysis.Rnw | 13 ++
inst/doc/Ch_survival_analysis.pdf |binary
vignettes/Ch_analysing_longitudinal_dataI.Rnw | 19 ++-
vignettes/Ch_analysing_longitudinal_dataII.Rnw | 13 ++
vignettes/Ch_analysis_of_variance.Rnw | 13 ++
vignettes/Ch_bayesian_inference.Rnw | 13 ++
vignettes/Ch_cluster_analysis.Rnw | 13 ++
vignettes/Ch_conditional_inference.Rnw | 13 ++
vignettes/Ch_density_estimation.Rnw | 13 ++
vignettes/Ch_errata.Rnw | 13 ++
vignettes/Ch_gam.Rnw | 13 ++
vignettes/Ch_graphical_display.Rnw | 15 ++
vignettes/Ch_introduction_to_R.Rnw | 13 ++
vignettes/Ch_logistic_regression_glm.Rnw | 13 ++
vignettes/Ch_meta_analysis.Rnw | 13 ++
vignettes/Ch_missing_values.Rnw | 13 ++
vignettes/Ch_multidimensional_scaling.Rnw | 13 ++
vignettes/Ch_multiple_linear_regression.Rnw | 13 ++
vignettes/Ch_principal_components_analysis.Rnw | 26 ++--
vignettes/Ch_quantile_regression.Rnw | 15 ++
vignettes/Ch_recursive_partitioning.Rnw | 13 ++
vignettes/Ch_simple_inference.Rnw | 13 ++
vignettes/Ch_simultaneous_inference.Rnw | 13 ++
vignettes/Ch_survival_analysis.Rnw | 13 ++
70 files changed, 652 insertions(+), 118 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Diff between BBEST versions 0.1-2 dated 2015-02-06 and 0.1-3 dated 2015-03-09
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin
ChangeLog |only
DESCRIPTION | 6 +--
MD5 | 15 +++++----
NAMESPACE | 2 -
R/fits.R | 16 +++++-----
R/interface.R | 83 +++++++++++++++++++++++++++++++++++++++++++++++-------
inst/gui/server.R | 18 +++++++++--
inst/gui/ui.R | 1
man/merge.fix.Rd |only
man/split.sqa.Rd |only
10 files changed, 110 insertions(+), 31 deletions(-)
Title: Spatial Graph Based Clustering Summaries for Spatial Point
Patterns
Diff between SGCS versions 2.0 dated 2014-03-09 and 2.3 dated 2015-03-09
Description: Graph based clustering summaries for spatial point patterns. Includes Connectivity function,
Cumulative connectivity function and clustering function, plus the triangle/triplet intensity function T.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala
SGCS-2.0/SGCS/R/First.R |only
SGCS-2.0/SGCS/R/Kfun.R |only
SGCS-2.0/SGCS/R/Tfun.R |only
SGCS-2.0/SGCS/R/clustfun.R |only
SGCS-2.0/SGCS/R/confun.R |only
SGCS-2.0/SGCS/R/cumconfun.R |only
SGCS-2.0/SGCS/R/fclass.R |only
SGCS-2.0/SGCS/R/fun.R |only
SGCS-2.0/SGCS/R/fun_old.R |only
SGCS-2.0/SGCS/data |only
SGCS-2.0/SGCS/man/SGCS-funs.Rd |only
SGCS-2.0/SGCS/man/SGCS-package.Rd |only
SGCS-2.0/SGCS/src/Clustfun.cpp |only
SGCS-2.0/SGCS/src/Clustfun.h |only
SGCS-2.0/SGCS/src/Components.cpp |only
SGCS-2.0/SGCS/src/Components.h |only
SGCS-2.0/SGCS/src/Confun.cpp |only
SGCS-2.0/SGCS/src/Confun.h |only
SGCS-2.0/SGCS/src/Fun.cpp |only
SGCS-2.0/SGCS/src/Fun.h |only
SGCS-2.0/SGCS/src/Kfun.h |only
SGCS-2.0/SGCS/src/Tfun.h |only
SGCS-2.0/SGCS/src/dists.cpp |only
SGCS-2.0/SGCS/src/dists.h |only
SGCS-2.0/SGCS/src/rfun.cpp |only
SGCS-2.0/SGCS/src/weights.cpp |only
SGCS-2.0/SGCS/src/weights.h |only
SGCS-2.3/SGCS/DESCRIPTION | 15 -
SGCS-2.3/SGCS/MD5 | 88 +++++----
SGCS-2.3/SGCS/NAMESPACE | 19 +
SGCS-2.3/SGCS/R/K-function.R |only
SGCS-2.3/SGCS/R/R-function.R |only
SGCS-2.3/SGCS/R/T-function.R |only
SGCS-2.3/SGCS/R/bounding-box-xy.R |only
SGCS-2.3/SGCS/R/clustering-function.R |only
SGCS-2.3/SGCS/R/connectivity-function.R |only
SGCS-2.3/SGCS/R/defaults.R |only
SGCS-2.3/SGCS/R/edge-distance.R |only
SGCS-2.3/SGCS/R/internal-to-ppp.R |only
SGCS-2.3/SGCS/R/internalise_pp.R |only
SGCS-2.3/SGCS/R/morpho-Area.R |only
SGCS-2.3/SGCS/R/morpho-Euler.R |only
SGCS-2.3/SGCS/R/morpho-Length.R |only
SGCS-2.3/SGCS/R/package.R |only
SGCS-2.3/SGCS/R/pairwise-distances.R |only
SGCS-2.3/SGCS/R/translation-weights.R |only
SGCS-2.3/SGCS/README.md |only
SGCS-2.3/SGCS/man/Kfun.Rd |only
SGCS-2.3/SGCS/man/Rfun.Rd |only
SGCS-2.3/SGCS/man/SGCS.Rd |only
SGCS-2.3/SGCS/man/Tfun.Rd |only
SGCS-2.3/SGCS/man/bounding_box_xy.Rd |only
SGCS-2.3/SGCS/man/clustfun.Rd |only
SGCS-2.3/SGCS/man/confun.Rd |only
SGCS-2.3/SGCS/man/default_r.Rd |only
SGCS-2.3/SGCS/man/edge_distance.Rd |only
SGCS-2.3/SGCS/man/internal_to_ppp.Rd |only
SGCS-2.3/SGCS/man/internalise_pp.Rd |only
SGCS-2.3/SGCS/man/morphoArea.Rd |only
SGCS-2.3/SGCS/man/morphoEuler.Rd |only
SGCS-2.3/SGCS/man/morphoLength.Rd |only
SGCS-2.3/SGCS/man/pairwise_distances.Rd |only
SGCS-2.3/SGCS/man/translation_weights.Rd |only
SGCS-2.3/SGCS/src/Graph.cpp | 224 ++++++++--------------
SGCS-2.3/SGCS/src/Graph.h | 62 ++----
SGCS-2.3/SGCS/src/Kfun.cpp | 89 ++++-----
SGCS-2.3/SGCS/src/Pp.cpp | 293 +++++++++++++++++++++++-------
SGCS-2.3/SGCS/src/Pp.h | 92 +++++++--
SGCS-2.3/SGCS/src/Rextras.cpp | 47 +++-
SGCS-2.3/SGCS/src/Rextras.h | 6
SGCS-2.3/SGCS/src/Rfun.cpp |only
SGCS-2.3/SGCS/src/Tfun.cpp | 119 +++++-------
SGCS-2.3/SGCS/src/arcs.cpp |only
SGCS-2.3/SGCS/src/arcs.h |only
SGCS-2.3/SGCS/src/clustfun.cpp |only
SGCS-2.3/SGCS/src/pairwise-distances.cpp |only
SGCS-2.3/SGCS/src/translation-weights.cpp |only
77 files changed, 618 insertions(+), 436 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Diff between GetoptLong versions 0.0.9 dated 2015-01-29 and 0.1.0 dated 2015-03-09
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu
GetoptLong-0.0.9/GetoptLong/R/overview.R |only
GetoptLong-0.0.9/GetoptLong/man/GetoptLong-package.rd |only
GetoptLong-0.1.0/GetoptLong/DESCRIPTION | 17 -
GetoptLong-0.1.0/GetoptLong/MD5 | 27 +-
GetoptLong-0.1.0/GetoptLong/NAMESPACE | 19 -
GetoptLong-0.1.0/GetoptLong/NEWS | 8
GetoptLong-0.1.0/GetoptLong/R/GetoptLong.R | 37 +++
GetoptLong-0.1.0/GetoptLong/inst/doc/GetoptLong.pdf |binary
GetoptLong-0.1.0/GetoptLong/inst/doc/variable_interpolation.pdf |binary
GetoptLong-0.1.0/GetoptLong/man/GetOptions.rd |only
GetoptLong-0.1.0/GetoptLong/man/GetoptLong.options.rd | 64 +++---
GetoptLong-0.1.0/GetoptLong/man/GetoptLong.rd | 79 ++++---
GetoptLong-0.1.0/GetoptLong/man/get_scriptname.rd | 40 +--
GetoptLong-0.1.0/GetoptLong/man/qq.options.rd | 64 +++---
GetoptLong-0.1.0/GetoptLong/man/qq.rd | 63 +++---
GetoptLong-0.1.0/GetoptLong/man/qqcat.rd | 104 +++++-----
16 files changed, 297 insertions(+), 225 deletions(-)
Title: Client for the HuffPost Pollster API
Diff between pollstR versions 1.1.1 dated 2014-10-30 and 1.2.0 dated 2015-03-09
Description: Client for the HuffPost Pollster API, which provides
access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre],
Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold
pollstR-1.1.1/pollstR/inst/vign-src/children/introduction.md |only
pollstR-1.2.0/pollstR/DESCRIPTION | 14
pollstR-1.2.0/pollstR/MD5 | 43
pollstR-1.2.0/pollstR/NAMESPACE | 2
pollstR-1.2.0/pollstR/NEWS | 4
pollstR-1.2.0/pollstR/R/chart.R | 5
pollstR-1.2.0/pollstR/R/charts.R | 102 -
pollstR-1.2.0/pollstR/R/polls.R | 260 ++--
pollstR-1.2.0/pollstR/build/vignette.rds |binary
pollstR-1.2.0/pollstR/inst/doc/introduction.Rmd | 143 +-
pollstR-1.2.0/pollstR/inst/doc/introduction.html | 628 +++-------
pollstR-1.2.0/pollstR/inst/vign-src/children/intro.Rmd | 2
pollstR-1.2.0/pollstR/inst/vign-src/figures/obama-favorable-chart-1.png |binary
pollstR-1.2.0/pollstR/inst/vign-src/figures/obama-favorable-chart-2-1.png |binary
pollstR-1.2.0/pollstR/inst/vign-src/introduction.Rmd | 14
pollstR-1.2.0/pollstR/inst/vign-src/introduction.md | 143 +-
pollstR-1.2.0/pollstR/man/pollstR.Rd | 3
pollstR-1.2.0/pollstR/man/pollstr_chart.Rd | 8
pollstR-1.2.0/pollstR/man/pollstr_charts.Rd | 23
pollstR-1.2.0/pollstR/man/pollstr_polls.Rd | 18
pollstR-1.2.0/pollstR/vignettes/assets/obama-favorable-chart-1.png |binary
pollstR-1.2.0/pollstR/vignettes/assets/obama-favorable-chart-2-1.png |binary
pollstR-1.2.0/pollstR/vignettes/introduction.Rmd | 143 +-
23 files changed, 691 insertions(+), 864 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Diff between OUwie versions 1.44 dated 2015-02-19 and 1.45 dated 2015-03-09
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/OUwie.R | 2 +-
R/OUwie.slice.R | 2 +-
4 files changed, 9 insertions(+), 9 deletions(-)
Title: Desirability Function Optimization and Ranking
Diff between desirability versions 1.6 dated 2014-01-16 and 1.9 dated 2015-03-09
Description: S3 classes for multivariate optimization using the desirability function by Derringer and Suich (1980).
Author: Max Kuhn
Maintainer: Max Kuhn
desirability-1.6/desirability/inst/NEWS |only
desirability-1.9/desirability/DESCRIPTION | 13 -
desirability-1.9/desirability/MD5 | 10
desirability-1.9/desirability/R/predict.R | 193 +++++++---------
desirability-1.9/desirability/build/vignette.rds |binary
desirability-1.9/desirability/inst/NEWS.Rd |only
desirability-1.9/desirability/inst/doc/desirability.pdf |binary
7 files changed, 104 insertions(+), 112 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Diff between deldir versions 0.1-7 dated 2014-11-27 and 0.1-9 dated 2015-03-09
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations.
Author: Rolf Turner
Maintainer: Rolf Turner
ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++-----
DESCRIPTION | 12 ++++----
MD5 | 40 ++++++++++++++--------------
NAMESPACE | 4 ++
R/deldir.R | 6 ++--
R/plot.tile.list.R | 21 +++++++-------
R/plot.triang.list.R | 2 -
R/tile.list.R | 6 ++++
R/triMat.R | 4 +-
R/triang.list.R | 3 +-
man/deldir-internal.Rd | 2 +
man/deldir.Rd | 7 ++++
man/duplicatedxy.Rd | 2 -
man/plot.deldir.Rd | 2 -
man/plot.tile.list.Rd | 2 -
man/plot.triang.list.Rd | 2 -
man/tile.centroids.Rd | 2 -
man/tile.list.Rd | 2 -
man/tilePerim.Rd | 2 -
man/triMat.Rd | 2 -
man/triang.list.Rd | 2 -
21 files changed, 135 insertions(+), 58 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Diff between C50 versions 0.1.0-21 dated 2014-11-18 and 0.1.0-24 dated 2015-03-09
Description: C5.0 decision trees and rule-based models for pattern recognition.
Author: Max Kuhn, Steve Weston, Nathan Coulter, Mark Culp. C code for C5.0 by R. Quinlan
Maintainer: Max Kuhn
DESCRIPTION | 13 +++++++------
MD5 | 8 +++++---
NAMESPACE | 6 ++++++
R/C5.0.R | 2 +-
R/as.party.C5.0.R |only
man/plot.C5.0.Rd |only
6 files changed, 19 insertions(+), 10 deletions(-)
Title: Maxwell Bolzano Bose Einstein Fermi Dirac Distribution and
Exposure Curve
Diff between mbbefd versions 0.6 dated 2015-02-13 and 0.6.1 dated 2015-03-08
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi
Dirac (MBBEFD) distribution (distribution, density, quantile, random
generation functions) as well as MBBEFD exposure curve, used in actuarial
application to price reinsurance contracts. The vignette shows code
snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato
mbbefd-0.6.1/mbbefd/ChangeLog | 10 ++
mbbefd-0.6.1/mbbefd/DESCRIPTION | 17 ++--
mbbefd-0.6.1/mbbefd/MD5 | 22 ++---
mbbefd-0.6.1/mbbefd/NEWS | 8 +-
mbbefd-0.6.1/mbbefd/README.md |only
mbbefd-0.6.1/mbbefd/inst/CITATION | 4 -
mbbefd-0.6.1/mbbefd/inst/doc/mbbefd.Rnw | 71 ++++++++++++++----
mbbefd-0.6.1/mbbefd/man/mbbefd-package.Rd | 4 -
mbbefd-0.6.1/mbbefd/vignettes/mbbefd-distrPlot.pdf |binary
mbbefd-0.6.1/mbbefd/vignettes/mbbefd-drateplot.pdf |binary
mbbefd-0.6.1/mbbefd/vignettes/mbbefd-survivalPlot.pdf |binary
mbbefd-0.6.1/mbbefd/vignettes/mbbefd.Rnw | 71 ++++++++++++++----
mbbefd-0.6/mbbefd/vignettes/mbbefd.tex |only
13 files changed, 158 insertions(+), 49 deletions(-)
Title: Quantitative Financial Modelling Framework
Diff between quantmod versions 0.4-3 dated 2014-12-15 and 0.4-4 dated 2015-03-08
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, ctb],
Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich
DESCRIPTION | 28 +++--
MD5 | 16 +--
NAMESPACE | 1
R/getOptionChain.R | 129 +++++++++++++++----------
R/getSymbols.R | 240 +++++++++++++++++++++++++++++++++++++++--------
man/TA.Rd | 1
man/addCCI.Rd |only
man/getOptionChain.Rd | 19 ++-
man/getSymbols.yahooj.Rd |only
man/quantmod-package.Rd | 6 -
10 files changed, 324 insertions(+), 116 deletions(-)
Title: Tools for Management of Survey Data, Graphics, Programming,
Statistics, and Simulation
Diff between memisc versions 0.96-10 dated 2014-10-13 and 0.97 dated 2015-03-08
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates. Also some convenience tools for graphics,
programming, and simulation are provided.
Author: Martin Elff (with contributions by Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Deepayan Sarkar, Achim Zeileis)
Maintainer: Martin Elff
memisc-0.96-10/memisc/R/aggregateFormula.R |only
memisc-0.96-10/memisc/R/attch.R |only
memisc-0.96-10/memisc/inst/NEWS |only
memisc-0.96-10/memisc/man/aggregateFormula.Rd |only
memisc-0.96-10/memisc/man/include.Rd |only
memisc-0.97/memisc/DESCRIPTION | 21 -
memisc-0.97/memisc/MD5 | 79 ++--
memisc-0.97/memisc/NAMESPACE | 45 +-
memisc-0.97/memisc/R/AllGenerics.R | 10
memisc-0.97/memisc/R/Iconv.R |only
memisc-0.97/memisc/R/Termplot.R | 55 ---
memisc-0.97/memisc/R/codebook-methods.R | 28 +
memisc-0.97/memisc/R/contrasts.R | 349 ++++++++++----------
memisc-0.97/memisc/R/dataset-methods.R | 110 +++---
memisc-0.97/memisc/R/genTable.R |only
memisc-0.97/memisc/R/import-internal-spss-sysfile.R | 3
memisc-0.97/memisc/R/paste-and-draw.R |only
memisc-0.97/memisc/R/recode.R | 2
memisc-0.97/memisc/R/yy-mtable-ext-DaveAtkins.R | 4
memisc-0.97/memisc/build/vignette.rds |binary
memisc-0.97/memisc/demo/Termplot.R | 98 ++---
memisc-0.97/memisc/demo/anes48.R | 264 +++++++--------
memisc-0.97/memisc/demo/monte.carlo.R | 260 +++++++-------
memisc-0.97/memisc/inst/ChangeLog |only
memisc-0.97/memisc/inst/NEWS.Rd |only
memisc-0.97/memisc/inst/doc/anes48.R | 4
memisc-0.97/memisc/inst/doc/anes48.Rnw | 4
memisc-0.97/memisc/inst/doc/anes48.pdf |binary
memisc-0.97/memisc/man/00memisc.Rd | 4
memisc-0.97/memisc/man/By.Rd | 2
memisc-0.97/memisc/man/Iconv.Rd |only
memisc-0.97/memisc/man/Sapply.Rd | 2
memisc-0.97/memisc/man/Table.Rd | 4
memisc-0.97/memisc/man/Termplot.Rd | 2
memisc-0.97/memisc/man/Write.Rd |only
memisc-0.97/memisc/man/codebook.Rd | 11
memisc-0.97/memisc/man/contrasts.Rd | 4
memisc-0.97/memisc/man/errbars.Rd | 4
memisc-0.97/memisc/man/genTable.Rd |only
memisc-0.97/memisc/man/getSummary.Rd | 11
memisc-0.97/memisc/man/importers.Rd | 17
memisc-0.97/memisc/man/mtable.Rd | 2
memisc-0.97/memisc/man/percent.Rd | 4
memisc-0.97/memisc/man/predictionFrame.Rd | 2
memisc-0.97/memisc/man/toDataFrame.Rd | 2
memisc-0.97/memisc/src/pspp-portableStream-for-R.c | 6
memisc-0.97/memisc/vignettes/anes48.Rnw | 4
47 files changed, 737 insertions(+), 680 deletions(-)
Title: Fast Specialized CSV File Loader
Diff between csvread versions 1.1 dated 2014-11-11 and 1.2 dated 2015-03-08
Description: Functions for loading large (10M+ lines) CSV
and other delimited files, similar to read.csv, but typically faster and
using less memory than the standard R loader. While not entirely general,
it covers many common use cases when the types of columns in the CSV file
are known in advance. In addition, the package provides a class 'int64',
which represents 64-bit integers exactly when reading from a file. The
latter is useful when working with 64-bit integer identifiers exported from
databases. The CSV file loader supports common column types including
'integer', 'double', 'string', and 'int64', leaving further type
transformations to the user.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev
DESCRIPTION | 14 +++---
MD5 | 30 +++++++------
NAMESPACE | 2
NEWS | 8 +++
R/csvread-package.R | 9 ++--
R/csvread.R | 103 +++++++++++++++++++++++++++++++++++++++++++---
R/longint.R | 2
README.md | 2
inst/10rows_na.csv |only
inst/COPYRIGHTS | 1
inst/csvread_1.2.pdf |only
man/Ops.int64.Rd | 3 -
man/csvread.Rd | 108 ++++++++++++++++++++++++++++++++++++++++++++-----
man/int64.Rd | 7 +--
src/CMRDataCollector.h | 86 ++++++++++++++++++++++++++++++++++-----
src/csvread.cpp | 70 ++++++++-----------------------
src/int64.h | 18 +++++---
17 files changed, 346 insertions(+), 117 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Diff between blocksdesign versions 1.4 dated 2015-01-13 and 1.5 dated 2015-03-08
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each set of
nested blocks optimized within the levels of the preceding set of blocks. Block sizes
are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson
DESCRIPTION | 12 -
MD5 | 18 -
NAMESPACE | 2
R/blocks.r | 501 ++++++++++++++++++++++++--------------------
R/blocksdesign-package.r | 14 -
R/upper_bounds.r | 2
man/blocks.Rd | 96 ++++----
man/blocksdesign-package.Rd | 17 -
man/efficiencies.Rd | 3
man/upper_bounds.Rd | 5
10 files changed, 368 insertions(+), 302 deletions(-)
Title: Functions for Analysis of Agreement in Method Comparison Studies
Diff between MethComp versions 1.22 dated 2013-06-18 and 1.22.1 dated 2015-03-08
Description: Methods (standard and advanced) for analysis of agreement
between measurement methods.
Author: Bendix Carstensen, Lyle Gurrin, Claus Ekstrom, Michal Figurski
Maintainer: Bendix Carstensen
DESCRIPTION | 9 ++++-----
MD5 | 10 +++++-----
R/MCmcmc.R | 12 ++++++------
R/Meth.r | 4 ++--
R/check.MCmcmc.R | 16 ++++++++--------
R/subset.MCmcmc.R | 4 ++--
6 files changed, 27 insertions(+), 28 deletions(-)
Title: Scores Features for Feature Selection
Diff between FeaLect versions 1.7 dated 2014-12-31 and 1.8 dated 2015-03-08
Description: For each feature, a score is computed that can be useful
for feature selection. Several random subsets are sampled from
the input data and for each random subset, various linear
models are fitted using lars method. A score is assigned to
each feature based on the tendency of LASSO in including that
feature in the models.Finally, the average score and the models
are returned as the output. The features with relatively low
scores are recommended to be ignored because they can lead to
overfitting of the model to the training data. Moreover, for
each random subset, the best set of features in terms of global
error is returned. They are useful for applying Bolasso, the
alternative feature selection method that recommends the
intersection of features subsets.
Author: Habil Zare
Maintainer: Habil Zare
DESCRIPTION | 6 +++---
MD5 | 6 +++---
inst/doc/FeaLect_feature_scorer.Rnw | 4 ++--
vignettes/FeaLect_feature_scorer.Rnw | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Diff between geoBayes versions 0.1.3 dated 2014-09-01 and 0.2.150308 dated 2015-03-08
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou
Maintainer: Evangelos Evangelou
DESCRIPTION | 27 +-
MD5 | 67 ++---
NAMESPACE | 1
NEWS | 4
R/bf.R | 122 ++++++---
R/bfse.R |only
R/calcbf.R | 129 +++++++---
R/geoesteb.R | 573 +++++++++++++++++++++++++++------------------
R/linkfcn.R | 44 +++
R/mcsp2.R | 234 ++++++++++++------
R/util.R | 66 +++--
demo/00Index | 9
demo/rhizoctonia3.R | 4
demo/rhizoctonia5.R |only
man/bf1skel.Rd | 36 +-
man/bf2optim.Rd | 11
man/bfse.Rd |only
man/ebsglmm.Rd | 68 +++--
man/ebstrga.Rd | 55 ++--
man/linkfcn.Rd | 12
man/mcsglmm.Rd | 31 +-
man/mcstrga.Rd | 11
man/stackdata.Rd | 20 -
src/Makevars | 16 -
src/auxfcns.c | 17 -
src/bfsp.f90 | 382 ++++++++++++++++++++++--------
src/bmargin.f90 | 1
src/calcb2.f90 | 651 ++++++++++++++++++++++++++++++++++++++++++----------
src/covfun.f90 | 4
src/flogsumexp.f90 | 8
src/interfaces.f90 | 499 +++++----------------------------------
src/lbfgsbmod.f90 | 83 ------
src/linkfcn.f90 | 344 ++++++++++++++++++++++++++-
src/llik.f90 |only
src/mcsp2.f90 | 552 ++++++++++++++++++++++++++++++++++----------
src/mcspz0.f90 |only
src/pdfy.f90 |only
src/skelpnts.f90 |only
38 files changed, 2647 insertions(+), 1434 deletions(-)
Title: Predict Presence of Signal Peptides
Diff between signal.hsmm versions 1.2 dated 2015-03-05 and 1.2.1 dated 2015-03-08
Description: Predicts presence of signal peptides in eukaryotic protein using
hidden semi-Markov models. The implemented algorithm can be accessed both
from command line and GUI.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/signal.hsmm.Rd | 5 ++---
3 files changed, 8 insertions(+), 9 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Diff between rscala versions 1.0.1 dated 2015-03-06 and 1.0.2 dated 2015-03-08
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl
rscala-1.0.1/rscala/inst/java/rscala_2.10-1.0.1.jar |only
rscala-1.0.1/rscala/inst/java/rscala_2.11-1.0.1.jar |only
rscala-1.0.1/rscala/java/rscala_2.10-1.0.1-sources.jar |only
rscala-1.0.1/rscala/java/rscala_2.11-1.0.1-sources.jar |only
rscala-1.0.2/rscala/DESCRIPTION | 9 +++--
rscala-1.0.2/rscala/MD5 | 22 ++++++-------
rscala-1.0.2/rscala/NAMESPACE | 2 +
rscala-1.0.2/rscala/NEWS | 8 +++--
rscala-1.0.2/rscala/R/scalaInterpreter.R | 27 ++++++++++++++---
rscala-1.0.2/rscala/inst/java/rscala_2.10-1.0.2.jar |only
rscala-1.0.2/rscala/inst/java/rscala_2.11-1.0.2.jar |only
rscala-1.0.2/rscala/java/rscala_2.10-1.0.2-sources.jar |only
rscala-1.0.2/rscala/java/rscala_2.11-1.0.2-sources.jar |only
rscala-1.0.2/rscala/man/constructor.Rd | 4 +-
rscala-1.0.2/rscala/man/eval.Rd | 2 -
rscala-1.0.2/rscala/man/rscala-package.Rd | 4 +-
16 files changed, 52 insertions(+), 26 deletions(-)
Title: Network-Based Gene Set Analysis
Diff between netgsa versions 1.0 dated 2014-12-02 and 2.0 dated 2015-03-08
Description: The netgsa-package contains functions for carrying out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.
Author: Ali Shojaie and Jing Ma
Maintainer: Jing Ma
DESCRIPTION | 14 +---
MD5 | 8 +-
R/call.netGSA.R | 2
man/NetGSA.Rd | 157 ++++++++++++++++++++++++--------------------------
man/netgsa-package.Rd | 17 +----
5 files changed, 94 insertions(+), 104 deletions(-)
Title: A Rapid Digital Image Analysis for Leaf Area
Diff between LeafArea versions 0.0.5 dated 2015-02-02 and 0.0.6 dated 2015-03-08
Description: An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes. This package includes function to write an ImageJ macro which is optimized for a leaf area analysis by default.
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/auto.run.R | 17 ++++++++++++++++-
R/findimagej.R | 23 +++++++++++++----------
man/LeafArea-package.Rd | 4 ++--
man/auto.run.Rd | 6 ++----
6 files changed, 42 insertions(+), 26 deletions(-)
Title: IBM in-Database Analytics for R
Diff between ibmdbR versions 1.34.3 dated 2014-12-12 and 1.36.7 dated 2015-03-08
Description: Functionality required to efficiently use R with
IBM DB2(C) for Linux, Unix and Windows as well as IBM dashDB(C).
Many basic and complex R operations are pushed down into the database, which removes
the main memory boundary of R and allows to make full use of parallel processing in
the underlying database.
Author: IBM Corporation
Maintainer: Michael Wurst
DESCRIPTION | 12 ++++----
MD5 | 61 ++++++++++++++++++++++++------------------
NAMESPACE | 26 ++++++++++++++++-
R/connection.R | 26 +++++++++++++++++
R/kMeans.R |only
R/list.R | 17 ++++++++++-
R/model.management.R |only
R/nb.R |only
R/sql.R | 4 ++
README.md | 8 ++---
inst/doc/ibmdbR.pdf |binary
man/as.ida.data.frame.Rd | 19 +++++++------
man/createview.Rd | 8 ++---
man/ida.col.def.methods.Rd | 3 +-
man/ida.data.frame.Rd | 20 ++++++-------
man/ida.data.frame.methods.Rd | 1
man/ida.list.Rd | 15 ++--------
man/ida.list.methods.Rd | 2 +
man/idaConnect.Rd | 4 +-
man/idaDropModel.Rd |only
man/idaKMeans.Rd |only
man/idaListModels.Rd |only
man/idaLm.Rd | 8 ++---
man/idaMerge.Rd | 14 ++++-----
man/idaNb.Rd |only
man/idaQuery.Rd | 8 ++---
man/idaRetrieveModel.Rd |only
man/idaSample.Rd | 10 ++----
man/idaTable.Rd | 13 ++++++--
man/idadf.Rd | 9 ++++--
man/idatools.Rd | 15 +++++-----
man/init.Rd | 8 ++++-
man/overview.Rd | 39 --------------------------
man/showtables.Rd | 7 +++-
tests |only
35 files changed, 202 insertions(+), 155 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Diff between hergm versions 2.2-0 dated 2015-02-25 and 2.2-1 dated 2015-03-08
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/hergm.R | 2 +-
R/hergm.postprocess.R | 17 ++++++++++-------
R/hergm.preprocess.R | 2 +-
R/hergm.terms.R | 1 -
R/zzz.R | 2 +-
man/hergm.Rd | 2 +-
8 files changed, 25 insertions(+), 23 deletions(-)
Title: Date Calculations and Manipulation
Diff between TimeWarp versions 1.0-7 dated 2013-04-03 and 1.0.11 dated 2015-03-07
Description: Date sequence, relative date calculations, and date manipulation with business days
and holidays. Works with Date and POSIXt classes.
Author: Tony Plate, Jeffrey Horner, Lars Hansen
Maintainer: Tony Plate
TimeWarp-1.0-7/TimeWarp/TODO.txt |only
TimeWarp-1.0-7/TimeWarp/portingNotes.txt |only
TimeWarp-1.0.11/TimeWarp/DESCRIPTION | 15 -
TimeWarp-1.0.11/TimeWarp/MD5 | 46 ++--
TimeWarp-1.0.11/TimeWarp/NEWS | 12 +
TimeWarp-1.0.11/TimeWarp/R/dateMatch.R | 240 +++++++++++------------
TimeWarp-1.0.11/TimeWarp/R/dateParse.R | 70 ++++++
TimeWarp-1.0.11/TimeWarp/R/dateSeq.R | 37 +--
TimeWarp-1.0.11/TimeWarp/R/dateWarp.R | 135 ++++--------
TimeWarp-1.0.11/TimeWarp/R/holidays.R | 16 -
TimeWarp-1.0.11/TimeWarp/R/misc.R | 2
TimeWarp-1.0.11/TimeWarp/inst |only
TimeWarp-1.0.11/TimeWarp/man/TimeWarp-package.Rd | 3
TimeWarp-1.0.11/TimeWarp/man/dateAlign.Rd | 19 -
TimeWarp-1.0.11/TimeWarp/man/dateMatch.Rd | 3
TimeWarp-1.0.11/TimeWarp/man/dateParse.Rd | 12 -
TimeWarp-1.0.11/TimeWarp/man/dateSeq.Rd | 5
TimeWarp-1.0.11/TimeWarp/man/holidays.Rd | 3
TimeWarp-1.0.11/TimeWarp/man/pitfalls.Rd | 35 +++
TimeWarp-1.0.11/TimeWarp/tests/dateMatch.Rt | 5
TimeWarp-1.0.11/TimeWarp/tests/dateParse.Rt | 2
TimeWarp-1.0.11/TimeWarp/tests/dateSeq.Rt | 80 +++++++
TimeWarp-1.0.11/TimeWarp/tests/dateShift.Rt | 2
TimeWarp-1.0.11/TimeWarp/tests/dateWarp.Rt | 5
TimeWarp-1.0.11/TimeWarp/tests/holidays.Rt | 11 -
25 files changed, 463 insertions(+), 295 deletions(-)
Title: Read, Write and Edit XLSX Files
Diff between openxlsx versions 2.2.1 dated 2014-10-18 and 2.4.0 dated 2015-03-07
Description: Simplifies the creation of .xlsx files by providing a
high level interface to writing, styling and editing worksheets. Through
the use of Rcpp, read/write times are comparable to the xlsx and XLConnect
packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker
DESCRIPTION | 12
MD5 | 153 +++--
NAMESPACE | 8
NEWS | 43 +
R/RcppExports.R | 48 +
R/StyleClass.R | 133 ++++-
R/WorkbookClass.R | 921 ++++++++++++++++++++++++++++-------
R/baseXML.R | 81 ++-
R/borderFunctions.R | 267 +++++-----
R/helperFunctions.R | 151 +++--
R/loadWorkbook.R | 484 +++++++++++++-----
R/openxlsxCoerce.R |only
R/readWorkbook.R | 533 ++++++++++++++++++--
R/wrappers.R | 789 ++++++++++++++++++++++--------
R/writeData.R | 174 ------
R/writeDataTable.R | 28 -
R/writexlsx.R | 76 ++
build/vignette.rds |binary
inst/doc/Introduction.Rnw | 102 ++-
inst/doc/Introduction.pdf |binary
inst/doc/formatting.Rnw | 85 +--
inst/doc/formatting.pdf |binary
inst/loadExample.xlsx |binary
inst/readTest.xlsx |binary
man/addFilter.Rd | 7
man/addStyle.Rd | 10
man/addWorksheet.Rd | 7
man/conditionalFormat.Rd | 25
man/conditionalFormatting.Rd |only
man/convertFromExcelRef.Rd | 3
man/convertToDate.Rd | 14
man/convertToDateTime.Rd | 10
man/createStyle.Rd | 13
man/createWorkbook.Rd | 3
man/deleteData.Rd | 9
man/freezePane.Rd | 7
man/getBaseFont.Rd | 3
man/getCellRefs.Rd | 3
man/getDateOrigin.Rd |only
man/getStyles.Rd | 7
man/insertImage.Rd | 3
man/insertPlot.Rd | 11
man/loadWorkbook.Rd | 16
man/mergeCells.Rd | 3
man/modifyBaseFont.Rd | 3
man/names.Rd | 3
man/openXL.Rd | 3
man/openxlsx.Rd | 3
man/pageSetup.Rd | 7
man/read.xlsx.Rd | 54 +-
man/readWorkbook.Rd | 23
man/removeCellMerge.Rd | 3
man/removeColWidths.Rd | 9
man/removeFilter.Rd | 3
man/removeRowHeights.Rd | 5
man/removeWorksheet.Rd | 5
man/renameWorksheet.Rd | 3
man/replaceStyle.Rd | 7
man/saveWorkbook.Rd | 5
man/setColWidths.Rd | 7
man/setFooter.Rd | 5
man/setHeader.Rd | 7
man/setHeaderFooter.Rd | 3
man/setRowHeights.Rd | 3
man/sheets.Rd | 3
man/showGridLines.Rd | 9
man/worksheetOrder.Rd | 3
man/write.xlsx.Rd | 9
man/writeData.Rd | 15
man/writeDataTable.Rd | 17
src/RcppExports.cpp | 181 +++++--
src/cppFunctions.cpp | 1101 +++++++++++++++++++++++++++++--------------
tests |only
vignettes/Introduction.Rnw | 102 ++-
vignettes/formatting.Rnw | 85 +--
75 files changed, 4154 insertions(+), 1774 deletions(-)
Title: Import Articles from LexisNexis Using the tm Text Mining
Framework
Diff between tm.plugin.lexisnexis versions 1.1 dated 2014-06-11 and 1.2 dated 2015-03-07
More information about tm.plugin.lexisnexis at CRAN
Description: Provides a tm Source to create corpora from
articles exported from the LexisNexis content provider as
HTML files. It is able to read both text content and meta-data
information (including source, date, title, author and pages).
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
tm.plugin.lexisnexis-1.1/tm.plugin.lexisnexis/inst/texts/lexisnexis_test.html |only
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/DESCRIPTION | 14 -
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/MD5 | 14 -
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/NEWS | 3
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/R/readLexisNexisHTML.R | 92 ++++++----
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/inst/texts/lexisnexis_test_en.html |only
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/inst/texts/lexisnexis_test_fr.html |only
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/man/LexisNexisSource.Rd | 4
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/man/tm.plugin.lexisnexis-package.Rd | 2
tm.plugin.lexisnexis-1.2/tm.plugin.lexisnexis/tests |only
10 files changed, 83 insertions(+), 46 deletions(-)
Permanent link
Title: Nonparametric Simulation of RNA-Seq Data
Diff between SimSeq versions 1.2.0 dated 2014-12-10 and 1.3.0 dated 2015-03-07
Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.
Author: Samuel Benidt
Maintainer: Samuel Benidt
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NEWS | 6 ++++++
R/SimData.R | 7 +++++--
data/kidney.rda |binary
inst |only
man/SimData.Rd | 9 ++++++---
man/SimSeq-package.Rd | 4 ++--
man/kidney.Rd | 18 +++++++++++++++---
9 files changed, 46 insertions(+), 21 deletions(-)
Title: Parallel Programming Tools for Rcpp
Diff between RcppParallel versions 4.3.3 dated 2014-10-21 and 4.3.4 dated 2015-03-07
Description: High level functions for doing parallel programming with Rcpp.
For example, the parallelFor function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire
RcppParallel-4.3.3/RcppParallel/src/Makevars.win |only
RcppParallel-4.3.4/RcppParallel/DESCRIPTION | 37 ++++-
RcppParallel-4.3.4/RcppParallel/MD5 | 42 ++++--
RcppParallel-4.3.4/RcppParallel/NAMESPACE | 1
RcppParallel-4.3.4/RcppParallel/NEWS | 7 -
RcppParallel-4.3.4/RcppParallel/R/build.R |only
RcppParallel-4.3.4/RcppParallel/R/hooks.R |only
RcppParallel-4.3.4/RcppParallel/R/options.R | 35 -----
RcppParallel-4.3.4/RcppParallel/README.md | 48 -------
RcppParallel-4.3.4/RcppParallel/inst/include/RcppParallel.h | 13 +
RcppParallel-4.3.4/RcppParallel/inst/presentations |only
RcppParallel-4.3.4/RcppParallel/man/RcppParallel-package.Rd | 18 ++
RcppParallel-4.3.4/RcppParallel/man/RcppParallelLibs.Rd |only
RcppParallel-4.3.4/RcppParallel/man/setThreadOptions.Rd | 4
RcppParallel-4.3.4/RcppParallel/src/Makevars | 66 +++++++---
RcppParallel-4.3.4/RcppParallel/src/options.cpp | 4
RcppParallel-4.3.4/RcppParallel/src/tbb/build/common_rules.inc | 6
RcppParallel-4.3.4/RcppParallel/src/tbb/build/windows.inc | 25 ++-
RcppParallel-4.3.4/RcppParallel/tests |only
19 files changed, 171 insertions(+), 135 deletions(-)
Title: R Binder for the Yhat API
Diff between yhatr versions 0.13.2 dated 2014-12-17 and 0.13.4 dated 2015-03-06
Description: Deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp
Maintainer: Greg Lamp
DESCRIPTION | 8 +++---
MD5 | 44 ++++++++++++++++++-------------------
NAMESPACE | 2 -
NEWS | 10 ++++++++
R/yhatR.R | 31 +++++++++++++++++++-------
man/capture.src.Rd | 3 +-
man/check.dependencies.Rd | 3 +-
man/check.image.size.Rd | 3 +-
man/yhat.deploy.Rd | 3 +-
man/yhat.deploy.to.file.Rd | 3 +-
man/yhat.deploy.with.scp.Rd | 3 +-
man/yhat.get.Rd | 3 +-
man/yhat.ls.Rd | 3 +-
man/yhat.post.Rd | 3 +-
man/yhat.predict.Rd | 3 +-
man/yhat.predict_raw.Rd | 3 +-
man/yhat.scaffolding.Rd | 3 +-
man/yhat.show_models.Rd | 3 +-
man/yhat.spider.block.Rd | 3 +-
man/yhat.spider.func.Rd | 3 +-
man/yhat.test_predict.Rd | 7 ++++-
man/yhat.transform_from_example.Rd | 3 +-
man/yhat.verify.Rd | 3 +-
23 files changed, 99 insertions(+), 54 deletions(-)
Title: Kernel Smoothing
Diff between ks versions 1.9.3 dated 2014-08-26 and 1.9.4 dated 2015-03-06
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong
Maintainer: Tarn Duong
CHANGELOG | 6 ++
DESCRIPTION | 14 +++---
MD5 | 22 +++++-----
R/kda.R | 19 ++++++++
R/kdde.R | 13 +++---
R/kde.R | 2
R/normal.R | 98 +++++++++++++++++++++++----------------------
R/prelim.R | 10 ++--
R/selector.R | 113 ++++++++++++++++++++++++++++++++++++++++++++++++++++-
build/vignette.rds |binary
inst/doc/kde.pdf |binary
man/plot.kda.Rd | 2
12 files changed, 220 insertions(+), 79 deletions(-)
Title: Ordination Methods for the Analysis of Beta-Diversity Indices
Diff between recluster versions 2.7 dated 2014-12-17 and 2.8 dated 2015-03-06
Description: Beta-diversity indices provide dissimilarity matrices with particular distribution of data requiring specific treatment. For example the high frequency of ties and zero values in turnover indices produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, biogeographical regionalization can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to analyze pattern of similarity in species composition.
Author: Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger
Vila, Gerard Talavera, Roger H.L. Dennis
Maintainer: Leonardo Dapporto
DESCRIPTION | 8 +--
MD5 | 16 +++----
NAMESPACE | 2
R/recluster.col.R | 67 +++++++++++++++----------------
R/recluster.cons.R | 15 ++++--
R/recluster.region.R | 103 +++++++++++++++++++++++-------------------------
man/recluster.Rd | 7 +--
man/recluster.cons.Rd | 6 +-
man/recluster.region.Rd | 13 +++---
9 files changed, 120 insertions(+), 117 deletions(-)
Title: Symbolic Differentiation
Diff between Deriv versions 2.0 dated 2015-02-05 and 3.0 dated 2015-03-06
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol
DESCRIPTION | 13
MD5 | 24 -
NEWS | 16 +
R/Deriv.R | 273 ++++++++++++++----
R/Simplify.R | 550 +++++++++++++++++++++++--------------
README.md | 21 +
man/Deriv-package.Rd | 18 -
man/Deriv.Rd | 93 ++++--
man/Simplify.Rd | 6
tests/testthat/test_Deriv.R | 107 ++++++-
tests/testthat/test_Deriv.R.bck | 106 ++++++-
tests/testthat/test_Simplify.R | 6
tests/testthat/test_Simplify.R.bck | 10
13 files changed, 899 insertions(+), 344 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.6 dated 2015-02-09 and 0.2.8 dated 2015-03-06
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 8 ++++----
MD5 | 36 ++++++++++++++++++------------------
R/linqsr.R | 27 +++++++++++++--------------
R/vardom.R | 2 +-
R/vardomh.R | 43 +++++++++++++++++++++++--------------------
R/varpoord.R | 37 +++++++++++++++++++------------------
inst/CITATION | 4 ++--
inst/NEWS | 6 +++++-
man/linarpr.Rd | 18 +++++++++---------
man/linarpt.Rd | 12 ++++++------
man/lingini.Rd | 4 ++--
man/lingini2.Rd | 14 +++++++++-----
man/lingpg.Rd | 4 ++--
man/linpoormed.Rd | 8 ++++----
man/linqsr.Rd | 10 +++++-----
man/linrmpg.Rd | 6 +++---
man/var_srs.Rd | 2 +-
man/vardpoor-package.Rd | 14 +++++++-------
man/varpoord.Rd | 19 +++++++++++--------
19 files changed, 144 insertions(+), 130 deletions(-)
Title: Sensitivity Analysis
Diff between sensitivity versions 1.10.1 dated 2014-12-03 and 1.11 dated 2015-03-06
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis of model output.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Sebastien Da Veiga, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Bernardo Ramos, Taieb Touati
Maintainer: Bertrand Iooss
sensitivity-1.10.1/sensitivity/R/DMBRSI.R |only
sensitivity-1.10.1/sensitivity/man/DMBRSI.Rd |only
sensitivity-1.11/sensitivity/DESCRIPTION | 13 ++--
sensitivity-1.11/sensitivity/MD5 | 46 +++++++++-------
sensitivity-1.11/sensitivity/NAMESPACE | 17 +++++
sensitivity-1.11/sensitivity/R/PLI.R |only
sensitivity-1.11/sensitivity/R/delsa.R |only
sensitivity-1.11/sensitivity/R/parameterSets.R |only
sensitivity-1.11/sensitivity/R/sobolCert.R | 4 -
sensitivity-1.11/sensitivity/R/sobolMultOut.R |only
sensitivity-1.11/sensitivity/R/sobolTIIlo.R | 4 -
sensitivity-1.11/sensitivity/R/sobolTIIpf.R | 4 -
sensitivity-1.11/sensitivity/R/sobolmartinez.R |only
sensitivity-1.11/sensitivity/man/PLI.Rd |only
sensitivity-1.11/sensitivity/man/delsa.Rd |only
sensitivity-1.11/sensitivity/man/parameterSets.Rd |only
sensitivity-1.11/sensitivity/man/sensitivity-package.Rd | 23 +++++---
sensitivity-1.11/sensitivity/man/sobol.Rd | 2
sensitivity-1.11/sensitivity/man/sobol2002.Rd | 11 +++
sensitivity-1.11/sensitivity/man/sobol2007.Rd | 11 +++
sensitivity-1.11/sensitivity/man/sobolEff.Rd | 6 +-
sensitivity-1.11/sensitivity/man/sobolMultOut.Rd |only
sensitivity-1.11/sensitivity/man/sobolTIIlo.Rd | 2
sensitivity-1.11/sensitivity/man/soboljansen.Rd | 2
sensitivity-1.11/sensitivity/man/sobolmara.Rd | 2
sensitivity-1.11/sensitivity/man/sobolmartinez.Rd |only
sensitivity-1.11/sensitivity/man/sobolowen.Rd | 2
sensitivity-1.11/sensitivity/man/sobolroalhs.Rd | 3 +
sensitivity-1.11/sensitivity/src/Makevars | 5 +
sensitivity-1.11/sensitivity/src/as.cpp | 6 +-
30 files changed, 109 insertions(+), 54 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Diff between frailtypack versions 2.7.4 dated 2015-02-25 and 2.7.5 dated 2015-03-06
Description: Frailtypack fits several classes of frailty models using a penalized likelihood
estimation on the hazard function but also a parametric estimation.
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated
random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of
clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events
with terminal event for clustered data or not.
Prediction values are available. Left-truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional hazard
and shared frailty model) and strata are allowed. In each model,
the random effects have a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying covariates
effects in Cox, shared and joint models. The package includes concordance measures
for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 4 ++++
src/aresidusMartingale.f90 | 24 +++++++++++++++---------
4 files changed, 26 insertions(+), 16 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Diff between ecospat versions 1.0 dated 2014-07-23 and 1.1 dated 2015-03-06
Description: R package for the support of spatial analyses and modelling of species niches and distributions, written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann
Maintainer: Valeria Di Cola
ecospat-1.0/ecospat/inst/doc/Code-ecospat.pdf |only
ecospat-1.1/ecospat/DESCRIPTION | 24 +--
ecospat-1.1/ecospat/MD5 | 69 +++++-----
ecospat-1.1/ecospat/NAMESPACE | 2
ecospat-1.1/ecospat/R/ecospat.binary_models.R | 2
ecospat-1.1/ecospat/R/ecospat.boyce.R | 2
ecospat-1.1/ecospat/R/ecospat.constrainedCoOcc.R | 28 ++--
ecospat-1.1/ecospat/R/ecospat.cv.R | 21 +--
ecospat-1.1/ecospat/R/ecospat.makeDataFrame.R | 32 ++++
ecospat-1.1/ecospat/R/ecospat.migclim.R | 2
ecospat-1.1/ecospat/R/ecospat.nichedynamic.R | 76 ++++++-----
ecospat-1.1/ecospat/data/ecospat.testData.txt.gz |binary
ecospat-1.1/ecospat/inst/doc/ecospat.pdf |binary
ecospat-1.1/ecospat/man/ecospat-package.Rd | 22 +--
ecospat-1.1/ecospat/man/ecospat.Epred.Rd | 2
ecospat-1.1/ecospat/man/ecospat.SSDMeval.Rd | 8 -
ecospat-1.1/ecospat/man/ecospat.boyce.Rd | 4
ecospat-1.1/ecospat/man/ecospat.calculate.pd.Rd | 9 +
ecospat-1.1/ecospat/man/ecospat.caleval.Rd | 2
ecospat-1.1/ecospat/man/ecospat.co_occurrences.Rd | 1
ecospat-1.1/ecospat/man/ecospat.cons_Cscore.Rd | 8 -
ecospat-1.1/ecospat/man/ecospat.cv.example.Rd | 2
ecospat-1.1/ecospat/man/ecospat.cv.gam.Rd | 2
ecospat-1.1/ecospat/man/ecospat.cv.gbm.Rd | 2
ecospat-1.1/ecospat/man/ecospat.cv.glm.Rd | 2
ecospat-1.1/ecospat/man/ecospat.cv.me.Rd | 4
ecospat-1.1/ecospat/man/ecospat.cv.rf.Rd | 4
ecospat-1.1/ecospat/man/ecospat.grid.clim.dyn.Rd | 4
ecospat-1.1/ecospat/man/ecospat.makeDataFrame.Rd | 23 +--
ecospat-1.1/ecospat/man/ecospat.maxentvarimport.Rd | 2
ecospat-1.1/ecospat/man/ecospat.permut.glm.Rd | 2
ecospat-1.1/ecospat/man/ecospat.plot.niche.Rd | 2
ecospat-1.1/ecospat/man/ecospat.plot.niche.dyn.Rd | 2
ecospat-1.1/ecospat/man/ecospat.testData.Rd | 136 +++++++++++----------
ecospat-1.1/ecospat/man/ecospat.testNiche.Rd | 4
ecospat-1.1/ecospat/man/ecospat.varpart.Rd | 6
36 files changed, 276 insertions(+), 235 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.11.4 dated 2015-01-24 and 0.11.5 dated 2015-03-06
Description: The Rcpp package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about Rcpp is provided by several vignettes included in this package, via the
Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Douglas Bates, and John Chambers
Maintainer: Dirk Eddelbuettel
ChangeLog | 138 +++++++++
DESCRIPTION | 8
MD5 | 126 ++++----
R/Attributes.R | 43 ++
R/exceptions.R | 15
README.md | 13
TODO | 46 ---
build/Rcpp.pdf |binary
inst/NEWS.Rd | 496 ++++++++++++++++++---------------
inst/doc/Rcpp-FAQ.R | 36 +-
inst/doc/Rcpp-FAQ.Rnw | 2
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-attributes.R | 20 -
inst/doc/Rcpp-attributes.Rnw | 267 +++++++++++++++--
inst/doc/Rcpp-attributes.pdf |binary
inst/doc/Rcpp-extending.R | 10
inst/doc/Rcpp-extending.Rnw | 2
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.Rnw | 1
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.R | 46 +--
inst/doc/Rcpp-modules.Rnw | 1
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-package.Rnw | 13
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.R | 2
inst/doc/Rcpp-quickref.Rnw | 1
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.R | 4
inst/doc/Rcpp-sugar.Rnw | 1
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.R | 2
inst/doc/Rcpp-unitTests.Rnw | 1
inst/doc/Rcpp-unitTests.pdf |binary
inst/include/Rcpp/Environment.h | 9
inst/include/Rcpp/Function.h | 31 +-
inst/include/Rcpp/XPtr.h | 62 +++-
inst/include/Rcpp/api/meat/Rcpp_eval.h | 75 ++++
inst/include/Rcpp/config.h | 6
inst/include/Rcpp/exceptions.h | 55 +++
inst/include/Rcpp/print.h |only
inst/include/Rcpp/routines.h | 284 ++++++++++--------
inst/include/Rcpp/utils/tinyformat.h | 17 -
inst/include/Rcpp/vector/Subsetter.h | 17 -
inst/include/RcppCommon.h | 2
inst/unitTests/cpp/Environment.cpp | 8
inst/unitTests/cpp/Function.cpp | 11
inst/unitTests/cpp/XPtr.cpp | 21 +
inst/unitTests/cpp/attributes.cpp | 3
inst/unitTests/cpp/attributes.hpp |only
inst/unitTests/runit.Function.R | 21 +
inst/unitTests/runit.XPTr.R | 8
inst/unitTests/runit.environments.R | 5
src/Rcpp_init.cpp | 5
src/api.cpp | 14
src/attributes.cpp | 483 +++++++++++++++++++++++++++-----
vignettes/Rcpp-FAQ.Rnw | 2
vignettes/Rcpp-attributes.Rnw | 267 +++++++++++++++--
vignettes/Rcpp-extending.Rnw | 2
vignettes/Rcpp-introduction.Rnw | 1
vignettes/Rcpp-modules.Rnw | 1
vignettes/Rcpp-package.Rnw | 13
vignettes/Rcpp-quickref.Rnw | 1
vignettes/Rcpp-sugar.Rnw | 1
vignettes/Rcpp-unitTests.Rnw | 1
65 files changed, 1983 insertions(+), 737 deletions(-)
Title: Vector Generalized Linear and Additive Models
Diff between VGAM versions 0.9-6 dated 2014-12-08 and 0.9-7 dated 2015-03-06
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes. Many (150+) models and distributions are estimated
by maximum likelihood estimation (MLE) or penalized MLE, using
Fisher scoring. VGLMs can be loosely thought of as multivariate
GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The
other classes are RR-VGLMs (reduced-rank VGLMs), quadratic
RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction
models)---these classes perform constrained and unconstrained
quadratic ordination (CQO/UQO) models in ecology, as well
as constrained additive ordination (CAO). Note that these
functions are subject to change, especially before version
1.0.0 is released; see the NEWS file for latest changes.
Author: Thomas W. Yee
Maintainer: Thomas Yee
VGAM-0.9-6/VGAM/build |only
VGAM-0.9-6/VGAM/inst/doc |only
VGAM-0.9-6/VGAM/man/fsqrt.Rd |only
VGAM-0.9-6/VGAM/vignettes |only
VGAM-0.9-7/VGAM/DESCRIPTION | 8
VGAM-0.9-7/VGAM/MD5 | 415 ++++++-------
VGAM-0.9-7/VGAM/NAMESPACE | 43 +
VGAM-0.9-7/VGAM/NEWS | 52 +
VGAM-0.9-7/VGAM/R/Links.R | 2
VGAM-0.9-7/VGAM/R/aamethods.q | 2
VGAM-0.9-7/VGAM/R/add1.vglm.q | 2
VGAM-0.9-7/VGAM/R/attrassign.R | 2
VGAM-0.9-7/VGAM/R/bAIC.q | 233 +++++--
VGAM-0.9-7/VGAM/R/build.terms.vlm.q | 2
VGAM-0.9-7/VGAM/R/calibrate.q | 2
VGAM-0.9-7/VGAM/R/cao.R | 2
VGAM-0.9-7/VGAM/R/cao.fit.q | 4
VGAM-0.9-7/VGAM/R/coef.vlm.q | 2
VGAM-0.9-7/VGAM/R/cqo.R | 2
VGAM-0.9-7/VGAM/R/cqo.fit.q | 6
VGAM-0.9-7/VGAM/R/deviance.vlm.q | 2
VGAM-0.9-7/VGAM/R/effects.vglm.q | 2
VGAM-0.9-7/VGAM/R/family.actuary.R | 776 +++++++++++++++++++------
VGAM-0.9-7/VGAM/R/family.aunivariate.R | 336 +++++++++-
VGAM-0.9-7/VGAM/R/family.basics.R | 20
VGAM-0.9-7/VGAM/R/family.binomial.R | 119 ++-
VGAM-0.9-7/VGAM/R/family.bivariate.R | 26
VGAM-0.9-7/VGAM/R/family.categorical.R | 54 -
VGAM-0.9-7/VGAM/R/family.censored.R | 2
VGAM-0.9-7/VGAM/R/family.circular.R | 136 +++-
VGAM-0.9-7/VGAM/R/family.exp.R | 324 ++++++++--
VGAM-0.9-7/VGAM/R/family.extremes.R | 344 ++++++++---
VGAM-0.9-7/VGAM/R/family.functions.R | 2
VGAM-0.9-7/VGAM/R/family.genetic.R | 269 ++++----
VGAM-0.9-7/VGAM/R/family.glmgam.R | 118 ++-
VGAM-0.9-7/VGAM/R/family.loglin.R | 2
VGAM-0.9-7/VGAM/R/family.math.R | 2
VGAM-0.9-7/VGAM/R/family.mixture.R | 2
VGAM-0.9-7/VGAM/R/family.nonlinear.R | 14
VGAM-0.9-7/VGAM/R/family.normal.R | 315 ++++++----
VGAM-0.9-7/VGAM/R/family.others.R | 178 ++++-
VGAM-0.9-7/VGAM/R/family.positive.R | 66 +-
VGAM-0.9-7/VGAM/R/family.qreg.R | 505 ++++++++++++----
VGAM-0.9-7/VGAM/R/family.quantal.R | 4
VGAM-0.9-7/VGAM/R/family.rcim.R | 2
VGAM-0.9-7/VGAM/R/family.rcqo.R | 2
VGAM-0.9-7/VGAM/R/family.robust.R | 77 ++
VGAM-0.9-7/VGAM/R/family.rrr.R | 6
VGAM-0.9-7/VGAM/R/family.sur.R | 2
VGAM-0.9-7/VGAM/R/family.survival.R | 82 +-
VGAM-0.9-7/VGAM/R/family.ts.R | 10
VGAM-0.9-7/VGAM/R/family.univariate.R | 834 +++++++++++++++++----------
VGAM-0.9-7/VGAM/R/family.vglm.R | 2
VGAM-0.9-7/VGAM/R/family.zeroinf.R | 34 -
VGAM-0.9-7/VGAM/R/fittedvlm.R | 2
VGAM-0.9-7/VGAM/R/formula.vlm.q | 2
VGAM-0.9-7/VGAM/R/generic.q | 2
VGAM-0.9-7/VGAM/R/links.q | 73 ++
VGAM-0.9-7/VGAM/R/logLik.vlm.q | 2
VGAM-0.9-7/VGAM/R/lrwaldtest.R | 2
VGAM-0.9-7/VGAM/R/model.matrix.vglm.q | 6
VGAM-0.9-7/VGAM/R/mux.q | 2
VGAM-0.9-7/VGAM/R/nobs.R | 2
VGAM-0.9-7/VGAM/R/plot.vglm.q | 2
VGAM-0.9-7/VGAM/R/predict.vgam.q | 2
VGAM-0.9-7/VGAM/R/predict.vglm.q | 2
VGAM-0.9-7/VGAM/R/predict.vlm.q | 2
VGAM-0.9-7/VGAM/R/print.vglm.q | 2
VGAM-0.9-7/VGAM/R/print.vlm.q | 2
VGAM-0.9-7/VGAM/R/qrrvglm.control.q | 2
VGAM-0.9-7/VGAM/R/qtplot.q | 2
VGAM-0.9-7/VGAM/R/residuals.vlm.q | 2
VGAM-0.9-7/VGAM/R/rrvglm.R | 2
VGAM-0.9-7/VGAM/R/rrvglm.control.q | 2
VGAM-0.9-7/VGAM/R/rrvglm.fit.q | 6
VGAM-0.9-7/VGAM/R/s.q | 2
VGAM-0.9-7/VGAM/R/s.vam.q | 2
VGAM-0.9-7/VGAM/R/smart.R | 2
VGAM-0.9-7/VGAM/R/step.vglm.q | 2
VGAM-0.9-7/VGAM/R/summary.vgam.q | 2
VGAM-0.9-7/VGAM/R/summary.vglm.q | 2
VGAM-0.9-7/VGAM/R/summary.vlm.q | 2
VGAM-0.9-7/VGAM/R/vgam.R | 2
VGAM-0.9-7/VGAM/R/vgam.control.q | 2
VGAM-0.9-7/VGAM/R/vgam.fit.q | 6
VGAM-0.9-7/VGAM/R/vgam.match.q | 2
VGAM-0.9-7/VGAM/R/vglm.R | 2
VGAM-0.9-7/VGAM/R/vglm.control.q | 2
VGAM-0.9-7/VGAM/R/vglm.fit.q | 6
VGAM-0.9-7/VGAM/R/vlm.R | 4
VGAM-0.9-7/VGAM/R/vlm.wfit.q | 2
VGAM-0.9-7/VGAM/R/vsmooth.spline.q | 17
VGAM-0.9-7/VGAM/data/ducklings.rda |only
VGAM-0.9-7/VGAM/man/A1A2A3.Rd | 10
VGAM-0.9-7/VGAM/man/AA.Aa.aa.Rd | 11
VGAM-0.9-7/VGAM/man/ABO.Rd | 19
VGAM-0.9-7/VGAM/man/CommonVGAMffArguments.Rd | 25
VGAM-0.9-7/VGAM/man/Links.Rd | 5
VGAM-0.9-7/VGAM/man/ParetoUC.Rd | 12
VGAM-0.9-7/VGAM/man/QvarUC.Rd | 2
VGAM-0.9-7/VGAM/man/VGAM-package.Rd | 12
VGAM-0.9-7/VGAM/man/alaplaceUC.Rd | 14
VGAM-0.9-7/VGAM/man/benfUC.Rd | 11
VGAM-0.9-7/VGAM/man/beniniUC.Rd | 12
VGAM-0.9-7/VGAM/man/betabinomialff.Rd | 17
VGAM-0.9-7/VGAM/man/betaff.Rd | 10
VGAM-0.9-7/VGAM/man/betanormUC.Rd | 13
VGAM-0.9-7/VGAM/man/bilogistic.Rd | 5
VGAM-0.9-7/VGAM/man/binomialff.Rd | 23
VGAM-0.9-7/VGAM/man/bisa.Rd | 6
VGAM-0.9-7/VGAM/man/bisaUC.Rd | 12
VGAM-0.9-7/VGAM/man/cardUC.Rd | 13
VGAM-0.9-7/VGAM/man/cardioid.Rd | 6
VGAM-0.9-7/VGAM/man/cloglog.Rd | 6
VGAM-0.9-7/VGAM/man/cqo.Rd | 8
VGAM-0.9-7/VGAM/man/cumulative.Rd | 6
VGAM-0.9-7/VGAM/man/dagum.Rd | 16
VGAM-0.9-7/VGAM/man/dagumUC.Rd | 16
VGAM-0.9-7/VGAM/man/dirichlet.Rd | 5
VGAM-0.9-7/VGAM/man/dirmultinomial.Rd | 10
VGAM-0.9-7/VGAM/man/double.expbinomial.Rd | 8
VGAM-0.9-7/VGAM/man/ducklings.Rd |only
VGAM-0.9-7/VGAM/man/eexpUC.Rd | 13
VGAM-0.9-7/VGAM/man/enormUC.Rd | 15
VGAM-0.9-7/VGAM/man/eunifUC.Rd | 13
VGAM-0.9-7/VGAM/man/exppoissonUC.Rd | 42 -
VGAM-0.9-7/VGAM/man/felix.Rd | 2
VGAM-0.9-7/VGAM/man/fisk.Rd | 15
VGAM-0.9-7/VGAM/man/fiskUC.Rd | 20
VGAM-0.9-7/VGAM/man/foldnormUC.Rd | 18
VGAM-0.9-7/VGAM/man/foldsqrt.Rd |only
VGAM-0.9-7/VGAM/man/frechetUC.Rd | 14
VGAM-0.9-7/VGAM/man/genbetaII.Rd | 26
VGAM-0.9-7/VGAM/man/gengammaUC.Rd | 14
VGAM-0.9-7/VGAM/man/genpoisson.Rd | 2
VGAM-0.9-7/VGAM/man/genrayleighUC.Rd | 15
VGAM-0.9-7/VGAM/man/gev.Rd | 6
VGAM-0.9-7/VGAM/man/gevUC.Rd | 10
VGAM-0.9-7/VGAM/man/golf.Rd | 6
VGAM-0.9-7/VGAM/man/gompertz.Rd | 6
VGAM-0.9-7/VGAM/man/gompertzUC.Rd | 12
VGAM-0.9-7/VGAM/man/gpd.Rd | 4
VGAM-0.9-7/VGAM/man/gpdUC.Rd | 16
VGAM-0.9-7/VGAM/man/grc.Rd | 2
VGAM-0.9-7/VGAM/man/gumbelIIUC.Rd | 14
VGAM-0.9-7/VGAM/man/gumbelUC.Rd | 24
VGAM-0.9-7/VGAM/man/hormone.Rd | 3
VGAM-0.9-7/VGAM/man/hspider.Rd | 3
VGAM-0.9-7/VGAM/man/huberUC.Rd | 22
VGAM-0.9-7/VGAM/man/hypersecant.Rd | 6
VGAM-0.9-7/VGAM/man/hzetaUC.Rd | 10
VGAM-0.9-7/VGAM/man/inv.binomial.Rd | 2
VGAM-0.9-7/VGAM/man/inv.lomaxUC.Rd | 10
VGAM-0.9-7/VGAM/man/inv.paralogistic.Rd | 15
VGAM-0.9-7/VGAM/man/inv.paralogisticUC.Rd | 18
VGAM-0.9-7/VGAM/man/kumarUC.Rd | 11
VGAM-0.9-7/VGAM/man/laplaceUC.Rd | 12
VGAM-0.9-7/VGAM/man/lgammaUC.Rd | 16
VGAM-0.9-7/VGAM/man/lindUC.Rd | 10
VGAM-0.9-7/VGAM/man/linkfun.Rd |only
VGAM-0.9-7/VGAM/man/linkfun.vglm.Rd |only
VGAM-0.9-7/VGAM/man/linoUC.Rd | 12
VGAM-0.9-7/VGAM/man/logit.Rd | 20
VGAM-0.9-7/VGAM/man/loglapUC.Rd | 12
VGAM-0.9-7/VGAM/man/lomaxUC.Rd | 12
VGAM-0.9-7/VGAM/man/makeham.Rd | 6
VGAM-0.9-7/VGAM/man/makehamUC.Rd | 13
VGAM-0.9-7/VGAM/man/maxwellUC.Rd | 12
VGAM-0.9-7/VGAM/man/nakagamiUC.Rd | 10
VGAM-0.9-7/VGAM/man/nbcanlink.Rd | 3
VGAM-0.9-7/VGAM/man/nbolf.Rd | 2
VGAM-0.9-7/VGAM/man/negbinomial.Rd | 214 ++++--
VGAM-0.9-7/VGAM/man/notdocumentedyet.Rd | 11
VGAM-0.9-7/VGAM/man/nparamvglm.Rd |only
VGAM-0.9-7/VGAM/man/olym.Rd | 14
VGAM-0.9-7/VGAM/man/paralogistic.Rd | 15
VGAM-0.9-7/VGAM/man/paralogisticUC.Rd | 21
VGAM-0.9-7/VGAM/man/paretoIVUC.Rd | 32 -
VGAM-0.9-7/VGAM/man/perks.Rd | 6
VGAM-0.9-7/VGAM/man/perksUC.Rd | 13
VGAM-0.9-7/VGAM/man/polf.Rd | 2
VGAM-0.9-7/VGAM/man/posbernoulli.t.Rd | 7
VGAM-0.9-7/VGAM/man/posbinomUC.Rd | 2
VGAM-0.9-7/VGAM/man/posbinomial.Rd | 8
VGAM-0.9-7/VGAM/man/posnormUC.Rd | 17
VGAM-0.9-7/VGAM/man/quasibinomialff.Rd | 43 -
VGAM-0.9-7/VGAM/man/rayleighUC.Rd | 12
VGAM-0.9-7/VGAM/man/riceUC.Rd | 12
VGAM-0.9-7/VGAM/man/riceff.Rd | 6
VGAM-0.9-7/VGAM/man/rrvglm.Rd | 9
VGAM-0.9-7/VGAM/man/rrvglm.control.Rd | 2
VGAM-0.9-7/VGAM/man/sc.t2UC.Rd | 12
VGAM-0.9-7/VGAM/man/sinmad.Rd | 25
VGAM-0.9-7/VGAM/man/sinmadUC.Rd | 20
VGAM-0.9-7/VGAM/man/slashUC.Rd | 9
VGAM-0.9-7/VGAM/man/tikuvUC.Rd | 12
VGAM-0.9-7/VGAM/man/tobitUC.Rd | 54 +
VGAM-0.9-7/VGAM/man/triangle.Rd | 8
VGAM-0.9-7/VGAM/man/triangleUC.Rd | 12
VGAM-0.9-7/VGAM/man/truncparetoUC.Rd | 18
VGAM-0.9-7/VGAM/man/undocumented-methods.Rd | 18
VGAM-0.9-7/VGAM/man/vgam.Rd | 8
VGAM-0.9-7/VGAM/man/vglm.Rd | 1
VGAM-0.9-7/VGAM/man/vonmises.Rd | 2
VGAM-0.9-7/VGAM/man/vsmooth.spline.Rd | 20
VGAM-0.9-7/VGAM/man/weibullR.Rd | 4
VGAM-0.9-7/VGAM/man/yulesimonUC.Rd | 8
VGAM-0.9-7/VGAM/man/zanegbinomial.Rd | 3
VGAM-0.9-7/VGAM/man/zapoisson.Rd | 3
VGAM-0.9-7/VGAM/man/zibinomial.Rd | 17
VGAM-0.9-7/VGAM/man/zipfUC.Rd | 7
VGAM-0.9-7/VGAM/man/zipoisson.Rd | 3
212 files changed, 5000 insertions(+), 2200 deletions(-)
Title: Microsoft Word, Microsoft Powerpoint and HTML Documents
Generation
Diff between ReporteRs versions 0.7.7 dated 2015-03-05 and 0.7.8 dated 2015-03-06
Description: Create Microsoft Word document (>=2007),
Microsoft Powerpoint document (>=2007) and HTML documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document (*.docx and *.pptx). You can use the package as a tool
for fast reporting and as a tool for reporting automation. The package does
not require any installation of Microsoft product to be able to write
Microsoft files (docx and pptx).
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation),
Dmitry Baranovskiy [ctb, cph] (raphael javascript
libraries)
Maintainer: David Gohel
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/ReporteRs.R | 4 ++--
R/drawingML.R | 11 ++++++++---
R/textProperties.R | 8 +++-----
man/ReporteRs-package.Rd | 4 ++--
man/chprop.textProperties.Rd | 2 ++
man/textProperties.Rd | 3 +--
8 files changed, 29 insertions(+), 25 deletions(-)
Title: Statistical Inference for Parametric and Semiparametric Models
Based on Dependently Truncated Data
Diff between depend.truncation versions 2.1 dated 2014-03-08 and 2.2 dated 2015-03-06
More information about depend.truncation at CRAN
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (X_j, Y_j), subject to X_j<=Y_j, for all j=1,...,n, are called truncated data. Parametric approach (Emura & Konno 2012 Stat Papers), semiparametric approach (Chaieb et al. 2006 Biometrika; Emura et al. 2011 Sinica), and the nonparametric maximum likelihood approach (Emura & Wang 2012 JMVA) are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians (Emura and Murotani 2015).
Author: Takeshi EMURA
Maintainer: Takeshi EMURA
DESCRIPTION | 14 +++++++-------
MD5 | 24 +++++++++++++-----------
data |only
man/CHAIEB.Clayton.Rd | 19 +++++++++++++------
man/CHAIEB.Frank.Rd | 13 +++++++------
man/EMURA.Clayton.Rd | 13 +++++++------
man/EMURA.Frank.Rd | 13 +++++++------
man/NPMLE.Frank.Rd | 7 +++----
man/NPMLE.Indep.Rd | 7 +++----
man/NPMLE.Normal.Rd | 9 ++++-----
man/NPMLE.Plackett.Rd | 7 +++----
man/PMLE.Normal.Rd | 6 ++++--
man/centenarian.Rd |only
man/depend.truncation-package.Rd | 22 ++++++++++++++++++----
14 files changed, 89 insertions(+), 65 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-27 0.1
Title: Microsoft Word, Microsoft Powerpoint and HTML Documents
Generation
Diff between ReporteRs versions 0.7.2 dated 2014-12-09 and 0.7.7 dated 2015-03-05
Description: Create Microsoft Word document (>=2007),
Microsoft Powerpoint document (>=2007) and HTML documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document (*.docx and *.pptx). You can use the package as a tool
for fast reporting and as a tool for reporting automation. The package does
not require any installation of Microsoft product to be able to write
Microsoft files (docx and pptx).
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation),
Dmitry Baranovskiy [ctb, cph] (raphael javascript
libraries)
Maintainer: David Gohel
ReporteRs-0.7.2/ReporteRs/man/pot-add.Rd |only
ReporteRs-0.7.7/ReporteRs/DESCRIPTION | 8
ReporteRs-0.7.7/ReporteRs/MD5 | 489 +--
ReporteRs-0.7.7/ReporteRs/NAMESPACE | 317 +-
ReporteRs-0.7.7/ReporteRs/NEWS | 792 ++---
ReporteRs-0.7.7/ReporteRs/R/00_AllGeneric.R | 1097 +++---
ReporteRs-0.7.7/ReporteRs/R/01_tools.R | 496 +--
ReporteRs-0.7.7/ReporteRs/R/BootstrapMenu.R | 105
ReporteRs-0.7.7/ReporteRs/R/DropDownMenu.R | 44
ReporteRs-0.7.7/ReporteRs/R/FlexCell.R | 128
ReporteRs-0.7.7/ReporteRs/R/FlexRow.R | 185 -
ReporteRs-0.7.7/ReporteRs/R/FlexTable.R | 542 +--
ReporteRs-0.7.7/ReporteRs/R/FlexTableContentTools.R | 133
ReporteRs-0.7.7/ReporteRs/R/FlexTableFormatTools.R | 432 +-
ReporteRs-0.7.7/ReporteRs/R/FlexTablePublicAPI.R | 1573 ++++------
ReporteRs-0.7.7/ReporteRs/R/FlexTableUpdateTools.R | 156
ReporteRs-0.7.7/ReporteRs/R/FlexTable_theme.R | 139
ReporteRs-0.7.7/ReporteRs/R/FontMetric.R | 48
ReporteRs-0.7.7/ReporteRs/R/Footnote.R | 221 -
ReporteRs-0.7.7/ReporteRs/R/Lists.R | 209 -
ReporteRs-0.7.7/ReporteRs/R/RScript.R | 390 +-
ReporteRs-0.7.7/ReporteRs/R/ReporteRs.R | 233 -
ReporteRs-0.7.7/ReporteRs/R/Section.R | 110
ReporteRs-0.7.7/ReporteRs/R/add.plot.interactivity.R | 208 -
ReporteRs-0.7.7/ReporteRs/R/addBootstrapMenu.R | 56
ReporteRs-0.7.7/ReporteRs/R/addDate.pptx.R | 104
ReporteRs-0.7.7/ReporteRs/R/addDocument.docx.R | 73
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.bsdoc.R | 83
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.docx.R | 83
ReporteRs-0.7.7/ReporteRs/R/addFlexTable.pptx.R | 153
ReporteRs-0.7.7/ReporteRs/R/addFooter.bsdoc.R | 115
ReporteRs-0.7.7/ReporteRs/R/addFooter.pptx.R | 83
ReporteRs-0.7.7/ReporteRs/R/addIframe.bsdoc.R | 63
ReporteRs-0.7.7/ReporteRs/R/addImage.bsdoc.R | 88
ReporteRs-0.7.7/ReporteRs/R/addImage.docx.R | 96
ReporteRs-0.7.7/ReporteRs/R/addImage.pptx.R | 141
ReporteRs-0.7.7/ReporteRs/R/addLinkItem.R | 117
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.bsdoc.R | 209 -
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.docx.R | 201 -
ReporteRs-0.7.7/ReporteRs/R/addMarkdown.pptx.R | 207 -
ReporteRs-0.7.7/ReporteRs/R/addPageBreak.docx.R | 39
ReporteRs-0.7.7/ReporteRs/R/addPageNumber.pptx.R | 103
ReporteRs-0.7.7/ReporteRs/R/addParagraph.bsdoc.R | 134
ReporteRs-0.7.7/ReporteRs/R/addParagraph.docx.R | 179 -
ReporteRs-0.7.7/ReporteRs/R/addParagraph.pptx.R | 259 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.bsdoc.R | 187 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.docx.R | 249 -
ReporteRs-0.7.7/ReporteRs/R/addPlot.pptx.R | 437 +-
ReporteRs-0.7.7/ReporteRs/R/addRScript.bsdoc.R | 79
ReporteRs-0.7.7/ReporteRs/R/addRScript.docx.R | 106
ReporteRs-0.7.7/ReporteRs/R/addRScript.pptx.R | 94
ReporteRs-0.7.7/ReporteRs/R/addSlide.pptx.R | 227 -
ReporteRs-0.7.7/ReporteRs/R/addSubtitle.pptx.R | 71
ReporteRs-0.7.7/ReporteRs/R/addTOC.bsdoc.R | 66
ReporteRs-0.7.7/ReporteRs/R/addTOC.docx.R | 129
ReporteRs-0.7.7/ReporteRs/R/addTitle.bsdoc.R | 105
ReporteRs-0.7.7/ReporteRs/R/addTitle.docx.R | 112
ReporteRs-0.7.7/ReporteRs/R/addTitle.pptx.R | 67
ReporteRs-0.7.7/ReporteRs/R/as.FlexTable.sessionInfo.R |only
ReporteRs-0.7.7/ReporteRs/R/as.html.FlexTable.R | 40
ReporteRs-0.7.7/ReporteRs/R/bootstrap.copy.R | 44
ReporteRs-0.7.7/ReporteRs/R/borderProperties.R | 243 -
ReporteRs-0.7.7/ReporteRs/R/bsdoc.R | 237 -
ReporteRs-0.7.7/ReporteRs/R/cellProperties.R | 1064 +++---
ReporteRs-0.7.7/ReporteRs/R/deleteBookmark.R | 106
ReporteRs-0.7.7/ReporteRs/R/dim.docx.R | 41
ReporteRs-0.7.7/ReporteRs/R/dim.pptx.R | 53
ReporteRs-0.7.7/ReporteRs/R/docx.R | 160 -
ReporteRs-0.7.7/ReporteRs/R/drawingML.R | 198 -
ReporteRs-0.7.7/ReporteRs/R/format.properties.R | 532 +--
ReporteRs-0.7.7/ReporteRs/R/is.color.R | 38
ReporteRs-0.7.7/ReporteRs/R/java_description.R | 90
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ReporteRs-0.7.7/ReporteRs/R/pot.R | 330 +-
ReporteRs-0.7.7/ReporteRs/R/pptx.R | 192 -
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ReporteRs-0.7.7/ReporteRs/R/print.pptx.R | 66
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ReporteRs-0.7.7/ReporteRs/R/set_of_pot.R | 149
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ReporteRs-0.7.7/ReporteRs/R/styles.docx.R | 58
ReporteRs-0.7.7/ReporteRs/R/textProperties.R | 509 +--
ReporteRs-0.7.7/ReporteRs/R/text_extract.R |only
ReporteRs-0.7.7/ReporteRs/R/toc.options.R | 65
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ReporteRs-0.7.7/ReporteRs/R/writeDoc.pptx.R | 91
ReporteRs-0.7.7/ReporteRs/inst/COPYRIGHTS | 178 -
ReporteRs-0.7.7/ReporteRs/inst/Rmd/example.Rmd | 180 -
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/css/bootstrap.min.css | 10
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/css/docs.min.css | 444 +-
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/fonts/glyphicons-halflings-regular.svg | 456 +-
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/bootstrap.min.js | 10
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/docs.min.js | 46
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/html5shiv.min.js | 6
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie-emulation-modes-warning.js | 102
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie10-viewport-bug-workaround.js | 44
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/ie8-responsive-file-warning.js | 26
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/jquery.min.js | 6
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/raphael-min.js | 20
ReporteRs-0.7.7/ReporteRs/inst/bootstrap/js/respond.min.js | 8
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ReporteRs-0.7.7/ReporteRs/java/ReporteRs-0.7-src.jar |binary
ReporteRs-0.7.7/ReporteRs/man/BootstrapMenu.Rd | 107
ReporteRs-0.7.7/ReporteRs/man/DropDownMenu.Rd | 61
ReporteRs-0.7.7/ReporteRs/man/FlexCell.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/FlexRow-alter.Rd | 66
ReporteRs-0.7.7/ReporteRs/man/FlexRow.Rd | 88
ReporteRs-0.7.7/ReporteRs/man/FlexTable-alter.Rd | 261 -
ReporteRs-0.7.7/ReporteRs/man/FlexTable.Rd | 600 +--
ReporteRs-0.7.7/ReporteRs/man/FontMetric.Rd | 32
ReporteRs-0.7.7/ReporteRs/man/Footnote.Rd | 238 -
ReporteRs-0.7.7/ReporteRs/man/RScript.Rd | 149
ReporteRs-0.7.7/ReporteRs/man/ReporteRs-package.Rd | 206 -
ReporteRs-0.7.7/ReporteRs/man/add.plot.interactivity.Rd | 202 -
ReporteRs-0.7.7/ReporteRs/man/add.pot.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/addBootstrapMenu.Rd | 84
ReporteRs-0.7.7/ReporteRs/man/addColumnBreak.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addColumnBreak.docx.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addDate.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/addDate.pptx.Rd | 109
ReporteRs-0.7.7/ReporteRs/man/addDocument.Rd | 50
ReporteRs-0.7.7/ReporteRs/man/addDocument.docx.Rd | 106
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.Rd | 67
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.bsdoc.Rd | 367 +-
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.docx.Rd | 377 +-
ReporteRs-0.7.7/ReporteRs/man/addFlexTable.pptx.Rd | 421 +-
ReporteRs-0.7.7/ReporteRs/man/addFooter.Rd | 52
ReporteRs-0.7.7/ReporteRs/man/addFooter.bsdoc.Rd | 109
ReporteRs-0.7.7/ReporteRs/man/addFooter.pptx.Rd | 91
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ReporteRs-0.7.7/ReporteRs/man/addIframe.Rd | 44
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ReporteRs-0.7.7/ReporteRs/man/addImage.Rd | 63
ReporteRs-0.7.7/ReporteRs/man/addImage.bsdoc.Rd | 123
ReporteRs-0.7.7/ReporteRs/man/addImage.docx.Rd | 147
ReporteRs-0.7.7/ReporteRs/man/addImage.pptx.Rd | 168 -
ReporteRs-0.7.7/ReporteRs/man/addJavascript.Rd | 45
ReporteRs-0.7.7/ReporteRs/man/addLinkItem.Rd | 113
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addMarkdown.bsdoc.Rd | 311 -
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ReporteRs-0.7.7/ReporteRs/man/addMarkdown.pptx.Rd | 325 +-
ReporteRs-0.7.7/ReporteRs/man/addPageBreak.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addPageBreak.docx.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/addPageNumber.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/addPageNumber.pptx.Rd | 100
ReporteRs-0.7.7/ReporteRs/man/addParagraph.Footnote.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/addParagraph.Rd | 71
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ReporteRs-0.7.7/ReporteRs/man/addPostCommand.Rd | 36
ReporteRs-0.7.7/ReporteRs/man/addRScript.Rd | 72
ReporteRs-0.7.7/ReporteRs/man/addRScript.bsdoc.Rd | 100
ReporteRs-0.7.7/ReporteRs/man/addRScript.docx.Rd | 119
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ReporteRs-0.7.7/ReporteRs/man/addSection.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/addSection.docx.Rd | 144
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ReporteRs-0.7.7/ReporteRs/man/addTOC.Rd | 55
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ReporteRs-0.7.7/ReporteRs/man/addTitle.Rd | 62
ReporteRs-0.7.7/ReporteRs/man/addTitle.bsdoc.Rd | 98
ReporteRs-0.7.7/ReporteRs/man/addTitle.docx.Rd | 125
ReporteRs-0.7.7/ReporteRs/man/addTitle.pptx.Rd | 83
ReporteRs-0.7.7/ReporteRs/man/as.FlexTable.Rd |only
ReporteRs-0.7.7/ReporteRs/man/as.FlexTable.sessionInfo.Rd |only
ReporteRs-0.7.7/ReporteRs/man/as.html.FlexTable.Rd | 99
ReporteRs-0.7.7/ReporteRs/man/as.html.RScript.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/as.html.Rd | 51
ReporteRs-0.7.7/ReporteRs/man/as.html.pot.Rd | 56
ReporteRs-0.7.7/ReporteRs/man/borderDashed.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderDotted.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderNone.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/borderProperties.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/borderSolid.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/bsdoc.Rd | 366 +-
ReporteRs-0.7.7/ReporteRs/man/cellProperties.Rd | 282 -
ReporteRs-0.7.7/ReporteRs/man/chprop.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/chprop.borderProperties.Rd | 69
ReporteRs-0.7.7/ReporteRs/man/chprop.cellProperties.Rd | 265 -
ReporteRs-0.7.7/ReporteRs/man/chprop.parProperties.Rd | 148
ReporteRs-0.7.7/ReporteRs/man/chprop.textProperties.Rd | 127
ReporteRs-0.7.7/ReporteRs/man/declareTitlesStyles.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/declareTitlesStyles.docx.Rd | 104
ReporteRs-0.7.7/ReporteRs/man/deleteBookmark.Rd | 39
ReporteRs-0.7.7/ReporteRs/man/deleteBookmarkNextContent.Rd | 39
ReporteRs-0.7.7/ReporteRs/man/dim.docx.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/dim.pptx.Rd | 50
ReporteRs-0.7.7/ReporteRs/man/doc-list-settings.Rd | 149
ReporteRs-0.7.7/ReporteRs/man/docx-bookmark.Rd | 217 -
ReporteRs-0.7.7/ReporteRs/man/docx.Rd | 397 +-
ReporteRs-0.7.7/ReporteRs/man/is.color.Rd | 47
ReporteRs-0.7.7/ReporteRs/man/light.table.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/list_bookmarks.Rd |only
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ReporteRs-0.7.7/ReporteRs/man/print.pot.Rd |only
ReporteRs-0.7.7/ReporteRs/man/print.pptx.Rd | 53
ReporteRs-0.7.7/ReporteRs/man/print.textProperties.Rd | 45
ReporteRs-0.7.7/ReporteRs/man/raphael.html.Rd | 117
ReporteRs-0.7.7/ReporteRs/man/registerRaphaelGraph.Rd | 32
ReporteRs-0.7.7/ReporteRs/man/setColumnsColors.Rd | 64
ReporteRs-0.7.7/ReporteRs/man/setFlexTableBackgroundColors.Rd | 128
ReporteRs-0.7.7/ReporteRs/man/setFlexTableBorders.Rd | 112
ReporteRs-0.7.7/ReporteRs/man/setFlexTableWidths.Rd | 52
ReporteRs-0.7.7/ReporteRs/man/setRowsColors.Rd | 64
ReporteRs-0.7.7/ReporteRs/man/setZebraStyle.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/set_of_paragraphs.Rd | 67
ReporteRs-0.7.7/ReporteRs/man/slide.layouts.Rd | 46
ReporteRs-0.7.7/ReporteRs/man/slide.layouts.pptx.Rd | 96
ReporteRs-0.7.7/ReporteRs/man/spanFlexTableColumns.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/spanFlexTableRows.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/styles.Rd | 49
ReporteRs-0.7.7/ReporteRs/man/styles.docx.Rd | 63
ReporteRs-0.7.7/ReporteRs/man/textBold.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textBoldItalic.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textItalic.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textNormal.Rd | 55
ReporteRs-0.7.7/ReporteRs/man/textProperties.Rd | 144
ReporteRs-0.7.7/ReporteRs/man/text_extract.Rd |only
ReporteRs-0.7.7/ReporteRs/man/toc.options.Rd | 54
ReporteRs-0.7.7/ReporteRs/man/toc.options.docx.Rd | 73
ReporteRs-0.7.7/ReporteRs/man/triggerPostCommand.Rd | 28
ReporteRs-0.7.7/ReporteRs/man/vanilla.table.Rd | 48
ReporteRs-0.7.7/ReporteRs/man/writeDoc.Rd | 57
ReporteRs-0.7.7/ReporteRs/man/writeDoc.bsdoc.Rd | 93
ReporteRs-0.7.7/ReporteRs/man/writeDoc.docx.Rd | 68
ReporteRs-0.7.7/ReporteRs/man/writeDoc.pptx.Rd | 77
251 files changed, 18490 insertions(+), 18572 deletions(-)
Title: Tools for Analyzing QTL Experiments
Diff between qtl versions 1.35-3 dated 2014-12-15 and 1.36-6 dated 2015-03-05
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 14 +++----
MD5 | 70 ++++++++++++++++++++-----------------
NAMESPACE | 5 ++
R/phyloqtl_util.R | 56 +++++++++++++++++++++++-------
R/plot.R | 51 ++++++++++++++++++---------
R/read.cross.mq.R | 11 +++--
R/scanonevar.R | 2 -
R/scanonevar.meanperm.R |only
R/scanonevar.varperm.R |only
R/summary.scantwo.old.R | 2 -
R/util.R | 74 +++++++++++++++++++++++++++++++++++++---
R/write.cross.mq.R | 2 -
build/vignette.rds |binary
data/badorder.RData |binary
data/bristle3.RData |binary
data/bristleX.RData |binary
data/fake.4way.RData |binary
data/fake.bc.RData |binary
data/fake.f2.RData |binary
data/hyper.RData |binary
data/listeria.RData |binary
data/locations.RData |binary
data/map10.RData |binary
data/mapthis.RData |binary
data/multitrait.RData |binary
inst/INSTALL_ME.txt | 12 +++---
inst/README.md | 2 -
inst/STATUS.txt | 35 ++++++++++++++++++
inst/TODO.txt | 13 +++----
inst/doc/rqtltour.pdf |binary
man/flip.order.Rd |only
man/geno.image.Rd | 6 +--
man/hyper.Rd | 18 ++++-----
man/plot.pxg.Rd | 9 ++--
man/scanonevar.meanperm.Rd |only
man/scanonevar.varperm.Rd |only
man/summary.scantwo.old.Rd | 11 ++---
man/switch.order.Rd | 12 +++---
tests/testthat/test-fliporder.R |only
39 files changed, 281 insertions(+), 124 deletions(-)
Title: Constrained Nonlinear Optimization
Diff between alabama versions 2014.12-1 dated 2014-12-01 and 2015.3-1 dated 2015-03-05
Description: Augmented Lagrangian Adaptive Barrier Minimization
Algorithm for optimizing smooth nonlinear objective functions
with constraints. Linear or nonlinear equality and inequality
constraints are allowed.
Author: Ravi Varadhan (with contributions from Gabor Grothendieck)
Maintainer: Ravi Varadhan
DESCRIPTION | 8 +--
MD5 | 10 +--
NEWS | 8 +++
R/auglag.R | 126 +++++++++++++++++++++++++++++++++++--------------
man/alabama-package.Rd | 8 +--
man/auglag.Rd | 18 +++++--
6 files changed, 126 insertions(+), 52 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Diff between pegas versions 0.6 dated 2014-08-21 and 0.7 dated 2015-03-05
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis
DESCRIPTION | 15 -
MD5 | 36 +--
NAMESPACE | 17 -
NEWS | 38 +++
R/IO.R | 6
R/geo.R |only
R/haplotype.R | 532 ++++++++++++++++++++++++++-------------------
R/zzz.R |only
build/vignette.rds |binary
inst/doc/ReadingFiles.Rnw | 2
inst/doc/ReadingFiles.pdf |binary
man/diffHaplo.Rd |only
man/geoTrans.Rd |only
man/geod.Rd |only
man/haploNet.Rd | 35 ++
man/haplotype.Rd | 3
man/pegas-package.Rd | 2
man/read.loci.Rd | 2
man/read.vcf.Rd | 44 +++
man/replot.Rd |only
src |only
vignettes/ReadingFiles.Rnw | 2
22 files changed, 463 insertions(+), 271 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-9 dated 2015-02-18 and 1.4-0 dated 2015-03-05
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 16
MD5 | 16
NAMESPACE | 1
R/expressions.R | 468 +++++++++++++++++++++++++++--
inst/NEWS | 7
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
tests/regtest-interface-extended.R |only
tests/regtest-interface-extended.Rout.save |only
10 files changed, 465 insertions(+), 43 deletions(-)
Title: Performing Continuous-Time Microsimulation
Diff between MicSim versions 1.0.7 dated 2015-02-27 and 1.0.8 dated 2015-03-05
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NAMESPACE | 10 ++++++++--
inst/NEWS.Rd | 5 +++++
man/MicSim-package.Rd | 4 ++--
5 files changed, 24 insertions(+), 13 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-12 dated 2014-10-02 and 0.999-13 dated 2015-03-05
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 13 +++++----
MD5 | 57 +++++++++++++++++++++---------------------
NAMESPACE | 21 ++++++++++-----
R/aux-acopula.R | 2 -
R/empcop.R | 4 +--
R/estimation.R | 15 +++++------
R/gofTrafos.R | 14 ++++++----
R/pairsRosenblatt.R | 2 -
R/special-func.R | 43 ++++++++++++++++++++++++++------
TODO | 3 ++
build/vignette.rds |binary
demo/00Index | 38 ++++++++++++++--------------
demo/dDiag-plots.R | 4 +--
demo/qrng.R | 60 +++++++++++++++++++++++++++++++++++++++++++++
demo/tail_compatibility.R |only
inst/CITATION | 4 +--
inst/NEWS.Rd | 10 ++++++-
inst/doc/Frank-Rmpfr.R | 1
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.R | 1
inst/doc/nacopula-pkg.pdf |binary
inst/doc/rhoAMH-dilog.R | 1
inst/doc/rhoAMH-dilog.Rnw | 4 +--
inst/doc/rhoAMH-dilog.pdf |binary
man/cCopula.Rd | 10 +++----
man/device.Rd | 18 ++++++-------
man/emle.Rd | 10 +++----
man/evTestA.Rd | 9 +++---
tests/Stirling-etc.R | 28 +++++++++++++++++++++
vignettes/rhoAMH-dilog.Rnw | 4 +--
30 files changed, 256 insertions(+), 120 deletions(-)
Title: A Package for Running 'JAGS' from R
Diff between R2jags versions 0.05-01 dated 2015-01-09 and 0.05-03 dated 2015-03-05
Description: Using this package to call 'JAGS' from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 3 +++
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NAMESPACE | 4 ++--
R/as.mcmc.R | 2 +-
man/attach.jags.Rd | 14 +++++++-------
man/autojags.Rd | 18 +++++++++---------
man/jags.Rd | 14 ++++++++------
man/traceplot.Rd | 6 +++---
9 files changed, 47 insertions(+), 42 deletions(-)
Title: Dynamic Assembly Model of Colonization, Local Extinction and
Speciation
Diff between DAMOCLES versions 1.0 dated 2014-10-29 and 1.1 dated 2015-03-05
Description: Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Author: Rampal S. Etienne & Alex L. Pigot
Maintainer: Rampal S. Etienne
DESCRIPTION | 15 +--
MD5 | 24 ++---
NAMESPACE | 2
R/DAMOCLES_ML.R | 24 +++--
R/DAMOCLES_bootstrap.R |only
R/DAMOCLES_loglik.R | 1
R/DAMOCLES_sim.R | 197 ++++++++++++++++++++++++++++++---------------
data/NWPrimates_data.RData |binary
man/DAMOCLES-internal.Rd | 6 -
man/DAMOCLES-package.Rd | 17 ++-
man/DAMOCLES_ML.Rd | 5 -
man/DAMOCLES_bootstrap.Rd |only
man/DAMOCLES_loglik.Rd | 2
man/DAMOCLES_sim.Rd | 16 +--
14 files changed, 198 insertions(+), 111 deletions(-)
Title: Multi-Class Discriminant Analysis using Binary Predictors
Diff between binda versions 1.0.1 dated 2014-11-14 and 1.0.2 dated 2015-03-05
Description: The "binda" package implements functions for multi-class
discriminant analysis using binary predictors, for corresponding
variable selection, and for dichotomizing continuous data.
Author: Sebastian Gibb and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 +++---
MD5 | 24 ++++++++++----------
NAMESPACE | 2 +
NEWS | 11 ++++++++-
R/binda.R | 59 +++++++++++++++++++++++----------------------------
R/binda.ranking.R | 57 ++++++++++++++++++-------------------------------
R/dichotomize.R | 6 ++---
R/getClassMeans.R | 21 ++++--------------
R/is.binaryMatrix.R | 12 ++++++----
man/binda.Rd | 11 +++++++++
man/binda.package.Rd | 4 +++
man/binda.ranking.Rd | 7 +++++-
man/dichotomize.Rd | 8 ++++++
13 files changed, 119 insertions(+), 111 deletions(-)
Title: Predict Presence of Signal Peptides
Diff between signal.hsmm versions 1.1 dated 2014-09-29 and 1.2 dated 2015-03-05
Description: Predicts presence of signal peptides in eukaryotic protein using
hidden semi-Markov models. The implemented algorithm can be accessed both
from command line and GUI.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz
signal.hsmm-1.1/signal.hsmm/R/degenerate.R |only
signal.hsmm-1.1/signal.hsmm/man/degenerate.Rd |only
signal.hsmm-1.2/signal.hsmm/DESCRIPTION | 8 -
signal.hsmm-1.2/signal.hsmm/MD5 | 63 +++++++-------
signal.hsmm-1.2/signal.hsmm/NAMESPACE | 6 -
signal.hsmm-1.2/signal.hsmm/R/datasets.R | 15 +--
signal.hsmm-1.2/signal.hsmm/R/duration_viterbi.R | 37 ++++----
signal.hsmm-1.2/signal.hsmm/R/find_nhc.R | 8 -
signal.hsmm-1.2/signal.hsmm/R/hsmm_pred.R | 2
signal.hsmm-1.2/signal.hsmm/R/predict.seq_hsmm.R |only
signal.hsmm-1.2/signal.hsmm/R/read_txt.R | 2
signal.hsmm-1.2/signal.hsmm/R/read_uniprot.R | 6 -
signal.hsmm-1.2/signal.hsmm/R/run_signal.hsmm.R | 6 -
signal.hsmm-1.2/signal.hsmm/R/signal.hsmm.R | 1
signal.hsmm-1.2/signal.hsmm/R/train_hsmm.R |only
signal.hsmm-1.2/signal.hsmm/README.md | 6 -
signal.hsmm-1.2/signal.hsmm/data/aaaggregation.rda |binary
signal.hsmm-1.2/signal.hsmm/inst/CITATION |only
signal.hsmm-1.2/signal.hsmm/man/aaaggregation.Rd | 6 -
signal.hsmm-1.2/signal.hsmm/man/benchmark_dat.Rd | 7 -
signal.hsmm-1.2/signal.hsmm/man/duration_viterbi.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/find_nhc.Rd | 9 +-
signal.hsmm-1.2/signal.hsmm/man/gui_signal.hsmm.Rd | 8 -
signal.hsmm-1.2/signal.hsmm/man/hsmm_pred.Rd | 5 -
signal.hsmm-1.2/signal.hsmm/man/hsmm_pred_list.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/is_protein.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/plot.hsmm_pred.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/pred2df.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/predict.sighsmm_model.Rd |only
signal.hsmm-1.2/signal.hsmm/man/read_txt.Rd | 5 -
signal.hsmm-1.2/signal.hsmm/man/read_uniprot.Rd | 9 +-
signal.hsmm-1.2/signal.hsmm/man/run_signal.hsmm.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/signal.hsmm.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/summary.hsmm_pred.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/summary.hsmm_pred_list.Rd | 3
signal.hsmm-1.2/signal.hsmm/man/train_hsmm.Rd |only
36 files changed, 125 insertions(+), 111 deletions(-)
Title: Tools for Phoneticians and Phonologists
Diff between phonR versions 0.4-2 dated 2013-03-25 and 1.0-1 dated 2015-03-05
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy
phonR-0.4-2/phonR/R/ellipse.R |only
phonR-0.4-2/phonR/R/phonR.r |only
phonR-0.4-2/phonR/data/indoVowelData.rda |only
phonR-0.4-2/phonR/man/ellipse.Rd |only
phonR-0.4-2/phonR/man/normalizeVowels.Rd |only
phonR-1.0-1/phonR/DESCRIPTION | 16 -
phonR-1.0-1/phonR/MD5 | 20 +-
phonR-1.0-1/phonR/NAMESPACE | 22 +-
phonR-1.0-1/phonR/R/phonR.R |only
phonR-1.0-1/phonR/data/indoVowels.rda |only
phonR-1.0-1/phonR/inst/CITATION | 4
phonR-1.0-1/phonR/man/indo.Rd | 15 -
phonR-1.0-1/phonR/man/normVowels.Rd |only
phonR-1.0-1/phonR/man/plotVowels.Rd | 281 ++++++++++++++++++++++---------
phonR-1.0-1/phonR/man/repulsiveForce.Rd |only
phonR-1.0-1/phonR/man/vowelSpaceArea.Rd |only
16 files changed, 247 insertions(+), 111 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Diff between nodiv versions 1.0.1 dated 2015-01-06 and 1.0.2 dated 2015-03-05
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
DESCRIPTION | 8 +++---
MD5 | 12 +++++-----
R/Methods_for_data_objects.R | 50 +++++++++++++++++++++++++------------------
R/Node_based_analysis.R | 19 ++++++++++++----
R/Prepare_data.R | 38 ++++++++++++++++++++++++++++----
man/distrib_data.Rd | 2 -
man/nodiv-package.Rd | 4 +--
7 files changed, 91 insertions(+), 42 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 2.1-1620 dated 2015-03-02 and 2.1-1629 dated 2015-03-05
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 8 +-
MD5 | 24 +++----
R/felm.R | 138 +++++++++++++++++++++++++++++++++++---------
R/generics.R | 10 ++-
R/oldfelm.R | 45 +++++++-------
R/utils.R | 16 ++++-
inst/doc/identification.pdf |binary
inst/doc/lfehow.pdf |binary
inst/doc/speed.pdf |binary
man/felm.Rd | 48 ++++++++++-----
src/demean.c | 2
src/lfe.c | 1
src/lfe.h | 1
13 files changed, 208 insertions(+), 85 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.2 dated 2015-02-12 and 1.2.1 dated 2015-03-05
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/BAT.R | 15 ++++++++++++---
3 files changed, 18 insertions(+), 9 deletions(-)
Title: Flexible Regression Models for Survival Data
Diff between timereg versions 1.8.6 dated 2014-11-18 and 1.8.7 dated 2015-03-05
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike
timereg-1.8.6/timereg/R/Gprop-odds-subdist.r |only
timereg-1.8.6/timereg/R/faster.reshape.r |only
timereg-1.8.6/timereg/man/Gprop.odds.subdist.Rd |only
timereg-1.8.7/timereg/DESCRIPTION | 26 ++--
timereg-1.8.7/timereg/MD5 | 75 ++++++-------
timereg-1.8.7/timereg/NAMESPACE | 19 +++
timereg-1.8.7/timereg/R/base.r | 38 ++++++
timereg-1.8.7/timereg/R/comprisk.ipw.r |only
timereg-1.8.7/timereg/R/comprisk.r | 27 +++-
timereg-1.8.7/timereg/R/cox.ipw.r | 4
timereg-1.8.7/timereg/R/dynadd.r | 10 +
timereg-1.8.7/timereg/R/kmplot.r | 2
timereg-1.8.7/timereg/R/mgresid.r | 9 -
timereg-1.8.7/timereg/R/new.cox-aalen.r | 4
timereg-1.8.7/timereg/R/new.prop-excess.r | 2
timereg-1.8.7/timereg/R/new.timecox.r | 4
timereg-1.8.7/timereg/R/prop-excess.r | 12 +-
timereg-1.8.7/timereg/R/restricted.residual.mean.r | 14 +-
timereg-1.8.7/timereg/R/timecox.r | 20 +--
timereg-1.8.7/timereg/man/Gprop.odds.Rd | 2
timereg-1.8.7/timereg/man/dynreg.Rd | 1
timereg-1.8.7/timereg/man/internal-addreg.Rd | 4
timereg-1.8.7/timereg/man/krylow.pls.Rd | 3
timereg-1.8.7/timereg/man/plot.dynreg.Rd | 1
timereg-1.8.7/timereg/man/predict.timereg.Rd | 2
timereg-1.8.7/timereg/man/prop.excess.Rd | 23 +---
timereg-1.8.7/timereg/man/prop.odds.subdist.Rd | 3
timereg-1.8.7/timereg/man/restricted.residual.mean.Rd | 4
timereg-1.8.7/timereg/man/timecox.Rd | 3
timereg-1.8.7/timereg/man/wald.test.Rd |only
timereg-1.8.7/timereg/src/Makevars | 1
timereg-1.8.7/timereg/src/aalen.c | 1
timereg-1.8.7/timereg/src/aalenC.c | 31 +++--
timereg-1.8.7/timereg/src/comprisk.c | 35 ++++--
timereg-1.8.7/timereg/src/cox-aalen.c | 7 -
timereg-1.8.7/timereg/src/dynadd.c | 17 +--
timereg-1.8.7/timereg/src/matrix.h | 3
timereg-1.8.7/timereg/src/pe-sasieni.c | 2
timereg-1.8.7/timereg/src/prop-excess.c | 52 ++++-----
timereg-1.8.7/timereg/src/smooth.c | 12 +-
timereg-1.8.7/timereg/src/timecox.c | 100 ++++++++++--------
41 files changed, 328 insertions(+), 245 deletions(-)
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Diff between hyperSpec versions 0.98-20140523 dated 2014-05-23 and 0.98-20150304 dated 2015-03-05
Description: Comfortable ways to work with hyperspectral data sets.
I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f (wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites
Maintainer: Claudia Beleites
hyperSpec-0.98-20140523/hyperSpec/R/logbook.R |only
hyperSpec-0.98-20140523/hyperSpec/R/logentry.R |only
hyperSpec-0.98-20140523/hyperSpec/R/sel.poly.R |only
hyperSpec-0.98-20140523/hyperSpec/man/logbook.Rd |only
hyperSpec-0.98-20140523/hyperSpec/man/logentry.Rd |only
hyperSpec-0.98-20140523/hyperSpec/man/map.sel.poly.Rd |only
hyperSpec-0.98-20140523/hyperSpec/vignettes/Rplots.pdf |only
hyperSpec-0.98-20150304/hyperSpec/DESCRIPTION | 74 -
hyperSpec-0.98-20150304/hyperSpec/MD5 | 406 ++++------
hyperSpec-0.98-20150304/hyperSpec/NAMESPACE | 33
hyperSpec-0.98-20150304/hyperSpec/R/Arith.R | 87 +-
hyperSpec-0.98-20150304/hyperSpec/R/Compare.R | 3
hyperSpec-0.98-20150304/hyperSpec/R/DollarNames.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/Math.R | 41 -
hyperSpec-0.98-20150304/hyperSpec/R/Summary.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/aggregate.R | 19
hyperSpec-0.98-20150304/hyperSpec/R/all.equal.R | 110 +-
hyperSpec-0.98-20150304/hyperSpec/R/apply.R | 13
hyperSpec-0.98-20150304/hyperSpec/R/as.data.frame.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/barbiturates.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/bind.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/chondro.R | 24
hyperSpec-0.98-20150304/hyperSpec/R/colMeans.R | 57 -
hyperSpec-0.98-20150304/hyperSpec/R/collapse.R | 54 -
hyperSpec-0.98-20150304/hyperSpec/R/cov.R | 1
hyperSpec-0.98-20150304/hyperSpec/R/decomposition.R | 58 +
hyperSpec-0.98-20150304/hyperSpec/R/dimnames.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/empty.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/extract.R | 23
hyperSpec-0.98-20150304/hyperSpec/R/fileio.optional.R |only
hyperSpec-0.98-20150304/hyperSpec/R/flu.R | 15
hyperSpec-0.98-20150304/hyperSpec/R/hyperspec-class.R | 24
hyperSpec-0.98-20150304/hyperSpec/R/hyperspec-package.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/initialize.R | 40
hyperSpec-0.98-20150304/hyperSpec/R/labels.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/levelplot.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/map.identify.R | 6
hyperSpec-0.98-20150304/hyperSpec/R/map.sel.poly.R | 87 +-
hyperSpec-0.98-20150304/hyperSpec/R/mark.dendrogram.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/matlab.palette.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/mean_sd.R | 56 -
hyperSpec-0.98-20150304/hyperSpec/R/merge.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/mvtnorm.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/normalize01.R | 22
hyperSpec-0.98-20150304/hyperSpec/R/options.R | 21
hyperSpec-0.98-20150304/hyperSpec/R/orderwl.R | 10
hyperSpec-0.98-20150304/hyperSpec/R/plot.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/plotc.R | 3
hyperSpec-0.98-20150304/hyperSpec/R/plotmap.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/plotmat.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/plotspc.R | 15
hyperSpec-0.98-20150304/hyperSpec/R/plotvoronoi.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/qplot.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/qplotmixmap.R | 45 -
hyperSpec-0.98-20150304/hyperSpec/R/quantile.R |only
hyperSpec-0.98-20150304/hyperSpec/R/rbind.fill.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.ENVI.Nicolet.R | 46 -
hyperSpec-0.98-20150304/hyperSpec/R/read.ENVI.R | 47 -
hyperSpec-0.98-20150304/hyperSpec/R/read.cytomat.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/read.jdx.R | 16
hyperSpec-0.98-20150304/hyperSpec/R/read.jdx.Shimadzu.R | 46 -
hyperSpec-0.98-20150304/hyperSpec/R/read.spc.Kaiser.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/read.spc.R | 76 -
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.Horiba.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.long.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/read.txt.wide.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/replace.R | 32
hyperSpec-0.98-20150304/hyperSpec/R/sample.R | 25
hyperSpec-0.98-20150304/hyperSpec/R/scan.txt.Renishaw.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/scan.txt.Witec.R | 28
hyperSpec-0.98-20150304/hyperSpec/R/seq.R | 18
hyperSpec-0.98-20150304/hyperSpec/R/show.R | 60 -
hyperSpec-0.98-20150304/hyperSpec/R/spc.NA.approx.R | 11
hyperSpec-0.98-20150304/hyperSpec/R/spc.bin.R | 10
hyperSpec-0.98-20150304/hyperSpec/R/spc.fit.poly.R | 30
hyperSpec-0.98-20150304/hyperSpec/R/spc.identify.R | 9
hyperSpec-0.98-20150304/hyperSpec/R/spc.loess.R | 6
hyperSpec-0.98-20150304/hyperSpec/R/spc.rubberband.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/split.R | 31
hyperSpec-0.98-20150304/hyperSpec/R/subset.R | 12
hyperSpec-0.98-20150304/hyperSpec/R/sweep.R | 42 -
hyperSpec-0.98-20150304/hyperSpec/R/sysdata.rda |binary
hyperSpec-0.98-20150304/hyperSpec/R/trellis.factor.key.R | 1
hyperSpec-0.98-20150304/hyperSpec/R/unittest.R | 7
hyperSpec-0.98-20150304/hyperSpec/R/validate.R | 4
hyperSpec-0.98-20150304/hyperSpec/R/vandermonde.R | 5
hyperSpec-0.98-20150304/hyperSpec/R/wl.R | 8
hyperSpec-0.98-20150304/hyperSpec/R/wleval.R | 2
hyperSpec-0.98-20150304/hyperSpec/R/write.txt.long.R | 5
hyperSpec-0.98-20150304/hyperSpec/build/vignette.rds |binary
hyperSpec-0.98-20150304/hyperSpec/data/barbiturates.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/flu.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/laser.rda |binary
hyperSpec-0.98-20150304/hyperSpec/data/paracetamol.rda |binary
hyperSpec-0.98-20150304/hyperSpec/inst/CITATION | 36
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.R | 11
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.Rnw | 33
hyperSpec-0.98-20150304/hyperSpec/inst/doc/baseline.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/chondro.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/inst/doc/fileio.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/inst/doc/fileio.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/flu.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/inst/doc/flu.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.R | 272 ++----
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.Rnw | 75 -
hyperSpec-0.98-20150304/hyperSpec/inst/doc/introduction.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/laser.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/inst/doc/laser.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.R | 157 +--
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.Rnw | 139 +--
hyperSpec-0.98-20150304/hyperSpec/inst/doc/plotting.pdf |binary
hyperSpec-0.98-20150304/hyperSpec/inst/doc/vignettes.defs | 15
hyperSpec-0.98-20150304/hyperSpec/man/Arith.Rd | 154 ++-
hyperSpec-0.98-20150304/hyperSpec/man/Comparison.Rd | 146 +--
hyperSpec-0.98-20150304/hyperSpec/man/aggregate.Rd | 87 --
hyperSpec-0.98-20150304/hyperSpec/man/apply.Rd | 85 --
hyperSpec-0.98-20150304/hyperSpec/man/asdataframe.Rd | 111 +-
hyperSpec-0.98-20150304/hyperSpec/man/barbiturates.Rd | 11
hyperSpec-0.98-20150304/hyperSpec/man/baselines.Rd | 70 -
hyperSpec-0.98-20150304/hyperSpec/man/bind.Rd | 88 --
hyperSpec-0.98-20150304/hyperSpec/man/chk.hy.Rd | 17
hyperSpec-0.98-20150304/hyperSpec/man/chondro.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/colSums.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/collapse.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/cov.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/decomposition.Rd | 118 +-
hyperSpec-0.98-20150304/hyperSpec/man/dim.Rd | 67 -
hyperSpec-0.98-20150304/hyperSpec/man/dimnames.Rd | 49 -
hyperSpec-0.98-20150304/hyperSpec/man/dollarnames.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/empty.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/extractreplace.Rd | 191 ++--
hyperSpec-0.98-20150304/hyperSpec/man/flu.Rd | 8
hyperSpec-0.98-20150304/hyperSpec/man/hyperSpec-package.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/initialize.Rd | 93 --
hyperSpec-0.98-20150304/hyperSpec/man/labels.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/laser.Rd | 6
hyperSpec-0.98-20150304/hyperSpec/man/levelplot.Rd | 201 ++--
hyperSpec-0.98-20150304/hyperSpec/man/makeraster.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/map-sel-poly.Rd | 65 +
hyperSpec-0.98-20150304/hyperSpec/man/mark.dendrogram.Rd | 44 -
hyperSpec-0.98-20150304/hyperSpec/man/math.Rd | 85 --
hyperSpec-0.98-20150304/hyperSpec/man/mean_sd.Rd | 92 --
hyperSpec-0.98-20150304/hyperSpec/man/merge.Rd | 40
hyperSpec-0.98-20150304/hyperSpec/man/normalize01.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/options.Rd | 50 -
hyperSpec-0.98-20150304/hyperSpec/man/orderwl.Rd | 21
hyperSpec-0.98-20150304/hyperSpec/man/palettes.Rd | 30
hyperSpec-0.98-20150304/hyperSpec/man/paracetamol.Rd | 8
hyperSpec-0.98-20150304/hyperSpec/man/pearson.dist.Rd | 25
hyperSpec-0.98-20150304/hyperSpec/man/plot.Rd | 90 +-
hyperSpec-0.98-20150304/hyperSpec/man/plotc.Rd | 55 -
hyperSpec-0.98-20150304/hyperSpec/man/plotmat.Rd | 38
hyperSpec-0.98-20150304/hyperSpec/man/plotspc.Rd | 279 ++----
hyperSpec-0.98-20150304/hyperSpec/man/qplotc.Rd | 36
hyperSpec-0.98-20150304/hyperSpec/man/qplotmap.Rd | 39
hyperSpec-0.98-20150304/hyperSpec/man/qplotmix.Rd | 122 +--
hyperSpec-0.98-20150304/hyperSpec/man/qplotmixmap.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/qplotspc.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/quickdf.Rd | 14
hyperSpec-0.98-20150304/hyperSpec/man/rbind-fill.Rd | 71 -
hyperSpec-0.98-20150304/hyperSpec/man/read-cytomat.Rd | 34
hyperSpec-0.98-20150304/hyperSpec/man/read-ini.Rd | 27
hyperSpec-0.98-20150304/hyperSpec/man/read-spc-Kaiser.Rd | 64 -
hyperSpec-0.98-20150304/hyperSpec/man/read-spc.Rd | 100 +-
hyperSpec-0.98-20150304/hyperSpec/man/read.jdx.Rd | 75 -
hyperSpec-0.98-20150304/hyperSpec/man/read.txt.Horiba.Rd | 41 -
hyperSpec-0.98-20150304/hyperSpec/man/read.txt.Shimadzu.Rd | 24
hyperSpec-0.98-20150304/hyperSpec/man/readENVI.Rd | 190 ++--
hyperSpec-0.98-20150304/hyperSpec/man/rmmvnorm.Rd | 43 -
hyperSpec-0.98-20150304/hyperSpec/man/sample.Rd | 63 -
hyperSpec-0.98-20150304/hyperSpec/man/scale.Rd | 41 -
hyperSpec-0.98-20150304/hyperSpec/man/scan-txt-Renishaw.Rd | 89 +-
hyperSpec-0.98-20150304/hyperSpec/man/scan.dat.Witec.Rd | 57 -
hyperSpec-0.98-20150304/hyperSpec/man/seq.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/show.Rd | 71 -
hyperSpec-0.98-20150304/hyperSpec/man/spc-bin.Rd | 44 -
hyperSpec-0.98-20150304/hyperSpec/man/spc-identify.Rd | 202 ++--
hyperSpec-0.98-20150304/hyperSpec/man/spc-loess.Rd | 35
hyperSpec-0.98-20150304/hyperSpec/man/spc-rubberband.Rd | 36
hyperSpec-0.98-20150304/hyperSpec/man/spc-spline.Rd | 25
hyperSpec-0.98-20150304/hyperSpec/man/spc.NA.linapprox.Rd | 22
hyperSpec-0.98-20150304/hyperSpec/man/split.Rd | 28
hyperSpec-0.98-20150304/hyperSpec/man/subset.Rd | 22
hyperSpec-0.98-20150304/hyperSpec/man/summary.Rd | 43 -
hyperSpec-0.98-20150304/hyperSpec/man/sweep.Rd | 55 -
hyperSpec-0.98-20150304/hyperSpec/man/textio.Rd | 231 ++---
hyperSpec-0.98-20150304/hyperSpec/man/trellis.factor.key.Rd | 20
hyperSpec-0.98-20150304/hyperSpec/man/unittests.Rd | 20
hyperSpec-0.98-20150304/hyperSpec/man/vanderMonde.Rd | 47 -
hyperSpec-0.98-20150304/hyperSpec/man/wc.Rd | 18
hyperSpec-0.98-20150304/hyperSpec/man/wl.Rd | 72 -
hyperSpec-0.98-20150304/hyperSpec/man/wl.eval.Rd | 28
hyperSpec-0.98-20150304/hyperSpec/man/wl2i.Rd | 49 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/Makefile | 69 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/baseline-pkg.bib |only
hyperSpec-0.98-20150304/hyperSpec/vignettes/baseline.Rnw | 33
hyperSpec-0.98-20150304/hyperSpec/vignettes/chondro.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/chondro.tex | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/fig-3D.png |binary
hyperSpec-0.98-20150304/hyperSpec/vignettes/fileio.Rnw | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/fileio.tex | 2
hyperSpec-0.98-20150304/hyperSpec/vignettes/flu.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/introduction-pkg.bib | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/introduction.Rnw | 75 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/laser-pkg.bib | 75 -
hyperSpec-0.98-20150304/hyperSpec/vignettes/laser.Rnw | 4
hyperSpec-0.98-20150304/hyperSpec/vignettes/plotting-pkg.bib | 12
hyperSpec-0.98-20150304/hyperSpec/vignettes/plotting.Rnw | 139 +--
hyperSpec-0.98-20150304/hyperSpec/vignettes/vignettes.defs | 15
209 files changed, 3849 insertions(+), 4575 deletions(-)
Title: Spatial Visualization with Google Maps and OpenStreetMap
Diff between ggmap versions 2.3 dated 2013-04-13 and 2.4 dated 2015-03-05
Description: Easily visualize of spatial data and models on top of Google Maps,
OpenStreetMaps, Stamen Maps, or CloudMade Maps with ggplot2.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle
ggmap-2.3/ggmap/inst/PH.txt |only
ggmap-2.3/ggmap/man/geocodeQueryCheck.Rd |only
ggmap-2.4/ggmap/DESCRIPTION | 37 -
ggmap-2.4/ggmap/MD5 | 116 +++--
ggmap-2.4/ggmap/NAMESPACE | 9
ggmap-2.4/ggmap/NEWS | 57 ++
ggmap-2.4/ggmap/R/OSM_scale_lookup.R | 68 +--
ggmap-2.4/ggmap/R/bb2bbox.R |only
ggmap-2.4/ggmap/R/calc_zoom.r |only
ggmap-2.4/ggmap/R/file_drawer.R |only
ggmap-2.4/ggmap/R/geocode.R | 419 ++++++++++++++-------
ggmap-2.4/ggmap/R/get_cloudmademap.R | 268 ++++++-------
ggmap-2.4/ggmap/R/get_googlemap.R | 577 +++++++++++++++--------------
ggmap-2.4/ggmap/R/get_map.R | 367 +++++++++---------
ggmap-2.4/ggmap/R/get_navermap.R |only
ggmap-2.4/ggmap/R/get_openstreetmap.R | 183 +++++----
ggmap-2.4/ggmap/R/get_stamenmap.R | 601 +++++++++++++++++++++----------
ggmap-2.4/ggmap/R/ggimage.R | 52 +-
ggmap-2.4/ggmap/R/gglocator.R | 50 +-
ggmap-2.4/ggmap/R/ggmap.R | 448 ++++++++++++-----------
ggmap-2.4/ggmap/R/ggplot2.R |only
ggmap-2.4/ggmap/R/help.R | 2
ggmap-2.4/ggmap/R/mapdist.R | 156 ++++----
ggmap-2.4/ggmap/R/qmap.R | 275 +++++++-------
ggmap-2.4/ggmap/R/qmplot.R | 369 ++++++++++++-------
ggmap-2.4/ggmap/R/revgeocode.R | 83 ++--
ggmap-2.4/ggmap/R/route.R | 307 +++++++--------
ggmap-2.4/ggmap/R/zips.R | 6
ggmap-2.4/ggmap/R/zzz.R |only
ggmap-2.4/ggmap/README.md |only
ggmap-2.4/ggmap/inst/CITATION |only
ggmap-2.4/ggmap/man/LonLat2XY.Rd | 26 -
ggmap-2.4/ggmap/man/OSM_scale_lookup.Rd | 57 +-
ggmap-2.4/ggmap/man/XY2LonLat.Rd | 30 -
ggmap-2.4/ggmap/man/bb2bbox.Rd |only
ggmap-2.4/ggmap/man/calc_zoom.Rd |only
ggmap-2.4/ggmap/man/crime.Rd | 10
ggmap-2.4/ggmap/man/distQueryCheck.Rd | 12
ggmap-2.4/ggmap/man/file_drawer.Rd |only
ggmap-2.4/ggmap/man/geocode.Rd | 82 ++--
ggmap-2.4/ggmap/man/geom_leg.Rd | 27 -
ggmap-2.4/ggmap/man/get_cloudmademap.Rd | 92 +---
ggmap-2.4/ggmap/man/get_googlemap.Rd | 189 ++++-----
ggmap-2.4/ggmap/man/get_map.Rd | 127 ++----
ggmap-2.4/ggmap/man/get_navermap.Rd |only
ggmap-2.4/ggmap/man/get_openstreetmap.Rd | 96 ++--
ggmap-2.4/ggmap/man/get_stamenmap.Rd | 213 ++++++++--
ggmap-2.4/ggmap/man/ggimage.Rd | 26 -
ggmap-2.4/ggmap/man/gglocator.Rd | 31 -
ggmap-2.4/ggmap/man/ggmap.Rd | 124 +++---
ggmap-2.4/ggmap/man/ggmapplot.Rd | 32 -
ggmap-2.4/ggmap/man/hadley.Rd | 7
ggmap-2.4/ggmap/man/inset.Rd | 30 -
ggmap-2.4/ggmap/man/inset_raster.Rd | 19
ggmap-2.4/ggmap/man/legs2route.Rd | 12
ggmap-2.4/ggmap/man/make_bbox.Rd | 17
ggmap-2.4/ggmap/man/mapdist.Rd | 51 --
ggmap-2.4/ggmap/man/qmap.Rd | 50 +-
ggmap-2.4/ggmap/man/qmplot.Rd | 255 +++++++++----
ggmap-2.4/ggmap/man/revgeocode.Rd | 43 --
ggmap-2.4/ggmap/man/route.Rd | 86 +---
ggmap-2.4/ggmap/man/routeQueryCheck.Rd | 12
ggmap-2.4/ggmap/man/theme_inset.Rd | 13
ggmap-2.4/ggmap/man/theme_nothing.Rd | 15
ggmap-2.4/ggmap/man/wind.Rd | 16
ggmap-2.4/ggmap/man/zips.Rd | 11
66 files changed, 3548 insertions(+), 2713 deletions(-)
Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Diff between clusterSEs versions 1.0 dated 2015-03-03 and 1.1 dated 2015-03-05
Description: Calculate p-values and confidence intervals using cluster-adjusted standard errors (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics for the GLM and mlogit models (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)).
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey
DESCRIPTION | 10 +-
MD5 | 18 ++-
NAMESPACE | 1
R/clusterBS.R | 27 ++++-
R/clusterBSmlogit.R |only
R/clusterIMmlogit.R | 9 +
R/clusterwild.R | 226 +++++++++++++++++++++++++++++++++--------------
man/cluster.bs.Rd | 7 +
man/cluster.bs.mlogit.Rd |only
man/cluster.im.mlogit.Rd | 9 +
man/cluster.wild.Rd | 31 ++++--
11 files changed, 241 insertions(+), 97 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Diff between randomForestSRC versions 1.6.0 dated 2015-01-12 and 1.6.1 dated 2015-03-04
More information about randomForestSRC at CRAN
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran
Maintainer: Udaya B. Kogalur
DESCRIPTION | 10 +-
MD5 | 216 ++++++++++++++++++++++-----------------------
NAMESPACE | 8 +
R/data.utilities.R | 2
R/factor.utilities.R | 2
R/find.interaction.R | 2
R/generic.impute.rfsrc.R | 2
R/generic.predict.rfsrc.R | 4
R/impute.rfsrc.R | 2
R/max.subtree.R | 2
R/plot.competing.risk.R | 2
R/plot.rfsrc.R | 2
R/plot.survival.R | 2
R/plot.variable.R | 2
R/predict.rfsrc.R | 2
R/print.rfsrc.R | 2
R/rf2rfz.R | 2
R/rfsrc.R | 4
R/rfsrc.news.R | 2
R/rfsrcSyn.R | 2
R/stat.split.R | 2
R/utilities.R | 2
R/var.select.R | 2
R/vimp.R | 2
R/zzz.R | 2
configure.ac | 2
inst/NEWS | 13 +-
inst/doc/rsf-Rnews.pdf |binary
man/breast.Rd | 2
man/find.interaction.Rd | 6 -
man/follic.Rd | 2
man/impute.Rd | 5 -
man/max.subtree.Rd | 2
man/pbc.Rd | 2
man/plot.competing.risk.Rd | 2
man/plot.rfsrc.Rd | 2
man/plot.survival.Rd | 5 -
man/plot.variable.Rd | 2
man/predict.rfsrc.Rd | 10 +-
man/rf2rfz.Rd | 2
man/rfsrc.Rd | 15 ++-
man/rfsrcSyn.Rd | 2
man/stat.split.Rd | 2
man/var.select.Rd | 8 +
man/vimp.Rd | 8 +
man/wihs.Rd | 2
src/bootstrap.c | 2
src/bootstrap.h | 2
src/classification.c | 2
src/classification.h | 2
src/dataParser.c | 2
src/dataParser.h | 2
src/entry.c | 2
src/entry.h | 2
src/extern.h | 2
src/factor.h | 2
src/factorOps.c | 2
src/factorOps.h | 2
src/global.h | 2
src/importance.c | 2
src/importance.h | 2
src/impute.c | 2
src/impute.h | 2
src/node.h | 2
src/nodeOps.c | 2
src/nodeOps.h | 2
src/nrutil.c | 2
src/nrutil.h | 2
src/random.c | 2
src/random.h | 2
src/regression.c | 2
src/regression.h | 2
src/rfsrc.c | 2
src/rfsrc.h | 2
src/rfsrcUtil.c | 2
src/rfsrcUtil.h | 2
src/split.c | 2
src/split.h | 2
src/splitClas.c | 2
src/splitClas.h | 2
src/splitCustom.c | 2
src/splitCustom.h | 2
src/splitRegr.c | 2
src/splitRegr.h | 2
src/splitSurv.c | 2
src/splitSurv.h | 2
src/splitUspv.c | 2
src/splitUspv.h | 2
src/splitUtil.c | 2
src/splitUtil.h | 2
src/stack.c | 2
src/stack.h | 2
src/stackOutput.c | 2
src/stackOutput.h | 2
src/stackPreDefined.c | 2
src/stackPreDefined.h | 2
src/survival.c | 2
src/survival.h | 2
src/survivalE.c | 2
src/survivalE.h | 2
src/termOps.c | 2
src/termOps.h | 2
src/terminal.h | 2
src/trace.c | 2
src/trace.h | 2
src/tree.c | 2
src/tree.h | 2
src/treeUtil.c | 2
src/treeUtil.h | 2
109 files changed, 264 insertions(+), 238 deletions(-)
Permanent link
Title: Solve Systems of Nonlinear Equations
Diff between nleqslv versions 2.5 dated 2014-09-29 and 2.6 dated 2015-03-04
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian and
for specifying that a numerical Jacobian is banded.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 14 ++--
MD5 | 45 +++++++++------
NEWS | 17 ++++-
R/nleqslv.R | 2
inst |only
man/nleqslv-package.Rd | 2
man/nleqslv.Rd | 4 -
man/testnslv.Rd | 2
man/zznleqslv-iterationreport.Rd | 112 ++++++++++++++++++++++++++-------------
src/nwbrdn.f | 9 ++-
src/nwddlg.f | 2
src/nwmhlm.f | 2
src/nwnjac.f | 2
src/nwnleq.f | 3 +
src/nwnwtn.f | 9 ++-
src/nwout.c | 46 +++++++++-------
src/nwpdlg.f | 2
src/nwtrup.f | 6 ++
src/nwutil.f | 4 +
19 files changed, 185 insertions(+), 98 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Diff between MixGHD versions 1.3 dated 2014-12-22 and 1.4 dated 2015-03-04
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The cMSGHD is a MSGHD with convex contour plots. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora
DESCRIPTION | 8 -
MD5 | 34 ++---
R/DA.R | 30 ++--
R/GHD.R | 304 +++++++++++++++++++++++++++++++++++++++++---------
R/MCGHD.R | 6
R/MGHD.R | 14 +-
R/MGHFA.R | 12 -
R/MSGHD.R | 11 +
R/Selection.R | 22 +--
R/cMSGHD.R | 11 +
man/DA.Rd | 6
man/MCGHD.Rd | 8 -
man/MGHD.Rd | 11 +
man/MGHFA.Rd | 22 ---
man/MSGHD.Rd | 6
man/MixGHD-package.Rd | 4
man/Selection.Rd | 7 -
man/cMSGHD.Rd | 6
18 files changed, 370 insertions(+), 152 deletions(-)
Title: Nonparametric Monotone Regression
Diff between monreg versions 0.1.2 dated 2013-02-15 and 0.1.3 dated 2015-03-04
Description: Estimates monotone regression and variance functions in a
nonparametric model.
Author: This version Kay Pilz and Steffanie Titoff. Earlier
developements by Holger Dette and Kay Pilz.
Maintainer: Scott Kostyshak
DESCRIPTION | 15 ++++++---------
MD5 | 8 ++++----
man/monreg.rd | 8 +++++++-
man/monvardiff.rd | 5 +++--
man/monvarresid.rd | 5 +++--
5 files changed, 23 insertions(+), 18 deletions(-)
Title: Kernel Based Regression Models
Diff between krm versions 2014.12-1 dated 2014-12-02 and 2015.3-4 dated 2015-03-04
Description: Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence.
Author: Youyi Fong
Maintainer: Youyi Fong
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/krm.most.R | 10 +++++-----
R/sim.liu.R | 4 ++--
man/krm.most.Rd | 10 ++++++++++
5 files changed, 26 insertions(+), 16 deletions(-)
Title: Companion Animal Population Management
Diff between capm versions 0.6.0 dated 2015-03-02 and 0.7.0 dated 2015-03-04
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero
DESCRIPTION | 14 ++---
MD5 | 40 ++++++++--------
NEWS | 4 +
R/CalculateGlobalSens.R | 2
R/CalculateLocalSens.R | 2
R/PlotGlobalSens.R | 2
R/PlotLocalSens.R | 6 +-
R/PlotModels.R | 32 ++++++-------
R/SetRanges.R | 2
R/SolveIASA.R | 110 ++++++++++++++++++++++-----------------------
R/SolveTC.R | 52 ++++++++++-----------
R/capm-package.R | 8 +--
man/CalculateGlobalSens.Rd | 2
man/CalculateLocalSens.Rd | 2
man/PlotGlobalSens.Rd | 2
man/PlotLocalSens.Rd | 6 +-
man/PlotModels.Rd | 10 ++--
man/SetRanges.Rd | 2
man/SolveIASA.Rd | 22 ++++-----
man/SolveTC.Rd | 16 +++---
man/capm-package.Rd | 8 +--
21 files changed, 174 insertions(+), 170 deletions(-)
Title: Tools for Creating D3 JavaScript Network Graphs from R
Diff between networkD3 versions 0.1.1 dated 2014-12-16 and 0.1.2.1 dated 2015-03-04
Description: Creates D3 JavaScript network, tree, dendrogram, and Sankey graphs
from R.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb]
Maintainer: Christopher Gandrud
DESCRIPTION | 22 ++++++++++++++++------
MD5 | 22 +++++++++++-----------
NEWS | 9 +++++++++
R/forceNetwork.R | 4 ++--
R/sankeyNetwork.R | 4 ++--
R/treeNetwork.R | 10 ++++------
README.md | 2 +-
inst/htmlwidgets/forceNetwork.yaml | 2 +-
inst/htmlwidgets/sankeyNetwork.yaml | 2 +-
inst/htmlwidgets/simpleNetwork.yaml | 2 +-
inst/htmlwidgets/treeNetwork.yaml | 2 +-
man/treeNetwork.Rd | 10 ++++------
12 files changed, 53 insertions(+), 38 deletions(-)
Title: Load Gap-Free Axon ABF2 Files
Diff between abf2 versions 0.7-0 dated 2013-07-19 and 0.7-1 dated 2015-03-04
Description: Loads ABF2 files containing gap-free data from electrophysiological recordings, as created by Axon Instruments/Molecular Devices software such as pClamp 10.
Author: Matthew Caldwell
Maintainer: Matthew Caldwell
DESCRIPTION | 12 +++---
MD5 | 6 +--
R/abf.R | 104 ++++++++++++++++++++++++++--------------------------
man/abf2-package.Rd | 2 -
4 files changed, 62 insertions(+), 62 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Diff between rNOMADS versions 2.1.2 dated 2015-01-16 and 2.1.3 dated 2015-03-04
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman
DESCRIPTION | 8 ++++----
MD5 | 5 +++--
R/GetDODS.R | 2 +-
inst |only
4 files changed, 8 insertions(+), 7 deletions(-)
Title: Download Aggregate Trial Information and Results from
ClinicalTrials.gov
Diff between rclinicaltrials versions 1.4 dated 2014-11-26 and 1.4.1 dated 2015-03-04
More information about rclinicaltrials at CRAN
Description: ClinicalTrials.gov is a registry and results database of publicly
and privately supported clinical studies of human participants conducted
around the world. Users can search for information about and results from
those trials. This provides a set of functions to interact with the search
and download features. Results are downloaded to temporary directories and
returned as R objects.
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
NAMESPACE | 2 +-
NEWS | 6 ++++++
R/clinicaltrials_download.R | 29 +++++++++++++++++++----------
build/vignette.rds |binary
man/advanced_search_terms.Rd | 3 ++-
man/clinicaltrials_count.Rd | 3 ++-
man/clinicaltrials_download.Rd | 3 ++-
man/clinicaltrials_search.Rd | 3 ++-
man/gather_results.Rd | 3 ++-
man/parse_study_xml.Rd | 3 ++-
tests/testthat/test-download.R | 2 +-
13 files changed, 55 insertions(+), 34 deletions(-)
Permanent link
Title: Automated Feature Selection from 'caret'
Diff between fscaret versions 0.9 dated 2015-01-11 and 0.9.3 dated 2015-03-04
Description: Automated feature selection using variety of models
provided by 'caret' package.
This work was funded by Poland-Singapore bilateral cooperation
project no 2/3/POL-SIN/2012.
Author: Jakub Szlek [aut, cre],
Aleksander Mendyk [ctb]
Maintainer: Jakub Szlek
DESCRIPTION | 26 +++++++------
MD5 | 32 ++++++++--------
R/classVarImp.R | 33 +++++++++++++++--
R/fscaret.R | 3 +
R/regVarImp.R | 37 ++++++++++++++++---
R/timeout.R | 39 ++++++++++++++------
data/funcClassPred.RData |binary
data/funcRegPred.RData |binary
inst/NEWS.Rd | 10 +++++
inst/doc/fscaret.R | 4 +-
inst/doc/fscaret.Rnw | 6 ++-
inst/doc/fscaret.pdf |binary
man/fscaret-package.Rd | 13 +++---
man/fscaret.Rd | 4 +-
man/regVarImp.Rd | 89 -----------------------------------------------
man/timeout.Rd | 50 ++++++++++++++++----------
vignettes/fscaret.Rnw | 6 ++-
17 files changed, 184 insertions(+), 168 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 2.0.1 dated 2015-02-24 and 2.0.2 dated 2015-03-04
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
DESCRIPTION | 8 +-
MD5 | 14 ++--
NEWS | 61 +++++++++++----------
inst/CITATION | 62 ++++++++++-----------
man/FunChisq-package.Rd | 11 +--
man/cp.fun.chisq.test.Rd | 14 ++--
man/fun.chisq.test.Rd | 27 +++++----
tests/testthat/test_FunChisq.R | 117 ++++++++++++++++++++---------------------
8 files changed, 161 insertions(+), 153 deletions(-)
Title: Visualisation of Oceanographic Data and Model Output
Diff between OceanView versions 1.0.2 dated 2014-12-29 and 1.0.3 dated 2015-03-04
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert
Maintainer: Karline Soetaert
OceanView |only
1 file changed
Title: Descriptive Statistics, Transition Plots, and More
Diff between Gmisc versions 1.0 dated 2015-01-04 and 1.1 dated 2015-03-04
Description:
Tools for making the descriptive "Table 1" used in medical articles,
a transition plot for showing changes between categories,
a method for variable selection based on the SVD,
Bézier lines with arrows complementing the ones in the 'grid' package,
and more.
Author: Max Gordon
Maintainer: Max Gordon
Gmisc-1.0/Gmisc/inst/doc/descriptives.R |only
Gmisc-1.0/Gmisc/inst/doc/descriptives.Rmd |only
Gmisc-1.0/Gmisc/inst/doc/descriptives.html |only
Gmisc-1.0/Gmisc/inst/examples/htmlTable_example.R |only
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Gmisc-1.1/Gmisc/DESCRIPTION | 16
Gmisc-1.1/Gmisc/MD5 | 111 +
Gmisc-1.1/Gmisc/NAMESPACE | 17
Gmisc-1.1/Gmisc/NEWS | 14
Gmisc-1.1/Gmisc/R/RcppExports.R |only
Gmisc-1.1/Gmisc/R/bezierArrowGradient.R | 516 +++----
Gmisc-1.1/Gmisc/R/bezierArrowSmpl.R | 264 +--
Gmisc-1.1/Gmisc/R/bezier_private_functions.R | 691 +++-------
Gmisc-1.1/Gmisc/R/descriptionStats.R | 8
Gmisc-1.1/Gmisc/R/getDescriptionStatsBy.R | 108 +
Gmisc-1.1/Gmisc/R/getPval.R |only
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Gmisc-1.1/Gmisc/R/transitionPlot.R | 57
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Gmisc-1.1/Gmisc/man/describeMean.Rd | 8
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Gmisc-1.1/Gmisc/tests/visual_tests/bezierArrowRcpp_vtests.R |only
Gmisc-1.1/Gmisc/tests/visual_tests/bezierArrowSmpl_vtests.R | 107 +
Gmisc-1.1/Gmisc/tests/visual_tests/tansitionPlot_vtests.R | 9
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76 files changed, 1310 insertions(+), 1147 deletions(-)
Title: Fitting Step-Functions
Diff between stepR versions 1.0 dated 2015-02-16 and 1.0-1 dated 2015-03-04
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Thomas Hotz [aut, cre],
Hannes Sieling [aut]
Maintainer: Thomas Hotz
ChangeLog |only
DESCRIPTION | 6 +++---
MD5 | 7 ++++---
src/StepBinom.cpp | 4 ++--
src/StepPoisson.cpp | 4 ++--
5 files changed, 11 insertions(+), 10 deletions(-)
Title: Safe Implementation of Monte Carlo Tests
Diff between simctest versions 2.4 dated 2013-12-13 and 2.4.1 dated 2015-03-04
Description: Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
Author: Axel Gandy
Maintainer: Axel Gandy
DESCRIPTION | 8 +--
MD5 | 31 ++++++------
NAMESPACE | 3 -
R/mmctest.R | 85 ++++++++++++++++++++++++++++-----
build/vignette.rds |binary
inst/doc/simctest-intro.R | 26 +++++-----
inst/doc/simctest-intro.Rnw | 6 --
inst/doc/simctest-intro.pdf |binary
inst/doc/simctest-mmctest-intro.R | 53 +++++++++++---------
inst/doc/simctest-mmctest-intro.Rnw | 89 ++++++++++++++++++++++++++++++-----
inst/doc/simctest-mmctest-intro.pdf |binary
man/mmctest-methods.Rd | 6 +-
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vignettes/simctest-intro.Rnw | 6 --
vignettes/simctest-mmctest-intro.Rnw | 89 ++++++++++++++++++++++++++++++-----
17 files changed, 339 insertions(+), 132 deletions(-)
Title: Running MLwiN from Within R
Diff between R2MLwiN versions 0.2-1 dated 2014-04-22 and 0.8-0 dated 2015-03-04
Description: An R command interface to the MLwiN multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang
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R2MLwiN-0.8-0/R2MLwiN/NAMESPACE | 78
R2MLwiN-0.8-0/R2MLwiN/NEWS | 199
R2MLwiN-0.8-0/R2MLwiN/R/BD.R | 35
R2MLwiN-0.8-0/R2MLwiN/R/Formula.translate.R | 2678 +++++---
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R2MLwiN-0.8-0/R2MLwiN/R/MCSE.R | 84
R2MLwiN-0.8-0/R2MLwiN/R/Untoggle.R | 64
R2MLwiN-0.8-0/R2MLwiN/R/caterpillar.R | 71
R2MLwiN-0.8-0/R2MLwiN/R/caterpillarR.R | 218
R2MLwiN-0.8-0/R2MLwiN/R/df2matrix.R |only
R2MLwiN-0.8-0/R2MLwiN/R/double2singlePrecision.R | 56
R2MLwiN-0.8-0/R2MLwiN/R/init.R |only
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R2MLwiN-0.8-0/R2MLwiN/R/mlwin2bugs.R | 318 -
R2MLwiN-0.8-0/R2MLwiN/R/mlwinfitIGLS.R | 1101 ++-
R2MLwiN-0.8-0/R2MLwiN/R/mlwinfitMCMC.R | 1329 ++--
R2MLwiN-0.8-0/R2MLwiN/R/pkgname.R |only
R2MLwiN-0.8-0/R2MLwiN/R/predCurves.r | 153
R2MLwiN-0.8-0/R2MLwiN/R/predLines.r | 346 -
R2MLwiN-0.8-0/R2MLwiN/R/prior2macro.R | 1218 ++-
R2MLwiN-0.8-0/R2MLwiN/R/runMLwiN.R | 3441 +++++++++--
R2MLwiN-0.8-0/R2MLwiN/R/sixway.R | 260
R2MLwiN-0.8-0/R2MLwiN/R/trajectories.R | 119
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184 files changed, 10103 insertions(+), 4217 deletions(-)
Title: Computes Pdf, Cdf, Quantile and Random Numbers, Measures of
Inference for 19 General Families of Distributions
Diff between Newdistns versions 1.0 dated 2013-08-19 and 2.0 dated 2015-03-04
Description: Computes the probability density function, cumulative distribution function, quantile function, random numbers and measures of inference for the following general families of distributions (each family defined in terms of an arbitrary cdf G): Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, and exponentiated exponential Poisson G distributions.
Author: Saralees Nadarajah, Ricardo Rocha
Maintainer: Saralees Nadarajah
DESCRIPTION | 18
MD5 | 46
NAMESPACE | 1
R/newdistns.R | 2381 ++++++++++++++++++++++++++++++++++++++++++++---
man/Newdistns-package.Rd | 13
man/beg.Rd | 23
man/betaexpg.Rd | 24
man/betag.Rd | 22
man/eepg.Rd | 22
man/eg.Rd | 22
man/expg.Rd | 23
man/expkumg.Rd | 22
man/gammag.Rd | 22
man/gammag1.Rd | 22
man/gammag2.Rd | 22
man/gbg.Rd | 22
man/gepg.Rd | 22
man/kumg.Rd | 22
man/loggammag1.Rd | 22
man/loggammag2.Rd | 22
man/mbetag.Rd | 22
man/mog.Rd | 24
man/tessg.Rd | 22
man/weibullg.Rd | 22
24 files changed, 2554 insertions(+), 329 deletions(-)
Title: Interface to Dygraphs Interactive Time Series Charting Library
Diff between dygraphs versions 0.4.1 dated 2015-01-26 and 0.4.2 dated 2015-03-04
Description: An R interface to the dygraphs JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph]
Maintainer: JJ Allaire
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 6 ++++++
R/options.R | 3 ++-
R/series.R | 7 ++-----
5 files changed, 18 insertions(+), 14 deletions(-)
Title: Interface to Colombos Compendia using the Exposed REST API
Diff between Rcolombos versions 1.5.0 dated 2014-03-26 and 1.5.2 dated 2015-03-04
Description: Provides programmatic access to Colombos, a web based
interface for exploring and analyzing comprehensive organism-specific
cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego
Maintainer: Paolo Sonego
DESCRIPTION | 10 ++---
MD5 | 30 +++++++--------
R/Rcolombos.R | 8 ++--
R/utilities.R | 12 +++---
man/advanced_search.Rd | 68 ++++++++++++++----------------------
man/advanced_search_by_both.Rd | 57 +++++++++++-------------------
man/advanced_search_by_contrasts.Rd | 36 ++++++-------------
man/advanced_search_by_genes.Rd | 33 +++++++----------
man/getCompendium.Rd | 27 ++++++--------
man/listAnnotationTypes.Rd | 21 +++++------
man/listContrasts.Rd | 20 +++++-----
man/listEntities.Rd | 24 +++++-------
man/listGenes.Rd | 20 +++++-----
man/listOrganisms.Rd | 11 +++--
man/parseCompendium.Rd | 21 +++++------
man/quick_search.Rd | 33 +++++++----------
16 files changed, 189 insertions(+), 242 deletions(-)
Title: Generation of Regular Factorial Designs
Diff between planor versions 0.2-0 dated 2014-07-10 and 0.2-3 dated 2015-03-04
Description: Automatic generation of regular factorial designs, including fractional designs, orthogonal block designs, row-column designs and split-plots.
Author: Hervé Monod, Annie Bouvier, André Kobilinsky
Maintainer: Annie Bouvier
planor-0.2-0/planor/tests/testSummary.R |only
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planor-0.2-3/planor/DESCRIPTION | 16
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planor-0.2-3/planor/R/designkey.R | 7
planor-0.2-3/planor/R/generic.R | 4
planor-0.2-3/planor/R/keymatrix.R | 11
planor-0.2-3/planor/R/keyring.R | 6
planor-0.2-3/planor/R/listofdesignkeys.R | 10
planor-0.2-3/planor/R/listofkeyrings.R | 9
planor-0.2-3/planor/R/planor.R | 1079 +++++++++++-----------
planor-0.2-3/planor/inst/doc/index.html | 12
planor-0.2-3/planor/inst/doc/planor-manual.pdf |binary
planor-0.2-3/planor/inst/doc/planorVignette.pdf |binary
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planor-0.2-3/planor/tests/Kobi1.Rout.save | 8
planor-0.2-3/planor/tests/Kobi2.Rout.save | 8
planor-0.2-3/planor/tests/Kobi3.Rout.save | 8
planor-0.2-3/planor/tests/KobiRecursive.Rout.save | 8
planor-0.2-3/planor/tests/NewKobi1.Rout.save | 8
planor-0.2-3/planor/tests/Touzeau2.Rout.save | 8
planor-0.2-3/planor/tests/exsimple.Rout.save | 8
planor-0.2-3/planor/tests/generate.Rout.save | 16
planor-0.2-3/planor/tests/haies.Rout.save | 8
planor-0.2-3/planor/tests/mixkey.Rout.save | 8
planor-0.2-3/planor/tests/noineligible.Rout.save | 8
32 files changed, 667 insertions(+), 678 deletions(-)
Title: Nonlinear Calibration
Diff between nCal versions 14.11-8 dated 2014-11-08 and 2015.3-3 dated 2015-03-04
Description: Performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong
Maintainer: Youyi Fong
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nCal-2015.3-3/nCal/NAMESPACE | 14 ++++
nCal-2015.3-3/nCal/R/bcrm.R | 7 +-
nCal-2015.3-3/nCal/R/ncalGUI.R | 2
nCal-2015.3-3/nCal/build/vignette.rds |binary
nCal-2015.3-3/nCal/inst/doc/nCal-vignette.R | 33 ++-------
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Title: Utility Functions by Youyi, Krisz and Others
Diff between kyotil versions 2014.10-5 dated 2014-10-01 and 2015.2-27 dated 2015-03-04
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong
Maintainer: Youyi Fong
kyotil-2014.10-5/kyotil/R/string.math.matrix.R |only
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kyotil-2015.2-27/kyotil/R/kernel.R | 312 +++++-----
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kyotil-2015.2-27/kyotil/R/print.R | 135 +++-
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kyotil-2015.2-27/kyotil/man/regression.model.functions.Rd | 4
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21 files changed, 424 insertions(+), 237 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Diff between ChainLadder versions 0.1.9 dated 2014-12-20 and 0.2.0 dated 2015-03-04
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Wayne Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [aut],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut]
Maintainer: Markus Gesmann
ChainLadder-0.1.9/ChainLadder/inst/CITATION |only
ChainLadder-0.2.0/ChainLadder/DESCRIPTION | 46
ChainLadder-0.2.0/ChainLadder/MD5 | 61
ChainLadder-0.2.0/ChainLadder/NAMESPACE | 22
ChainLadder-0.2.0/ChainLadder/NEWS | 49
ChainLadder-0.2.0/ChainLadder/R/BootstrapReserve.R | 818 +++++-----
ChainLadder-0.2.0/ChainLadder/R/CDRMethods.R |only
ChainLadder-0.2.0/ChainLadder/R/ChainLadder.R | 1
ChainLadder-0.2.0/ChainLadder/R/MWChainLadder.R |only
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ChainLadder-0.2.0/ChainLadder/R/Triangles.R | 219 +-
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ChainLadder-0.2.0/ChainLadder/R/zzz.R | 5
ChainLadder-0.2.0/ChainLadder/README.md | 27
ChainLadder-0.2.0/ChainLadder/THANKS | 34
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ChainLadder-0.2.0/ChainLadder/inst/doc/ChainLadder.R | 196 +-
ChainLadder-0.2.0/ChainLadder/inst/doc/ChainLadder.Rnw | 438 +++--
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Title: Download Content from NCBI Databases
Diff between RISmed versions 2.1.4 dated 2015-01-26 and 2.1.5 dated 2015-03-04
Description: A set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.
Author: Stephanie Kovalchik
Maintainer: S. A. Kovalchik
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RISmed-2.1.5/RISmed/NEWS | 10 -
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RISmed-2.1.5/RISmed/R/EUtilsSummary.R | 19 +
RISmed-2.1.5/RISmed/R/Medline.R | 217 ++++++++++++++++++----
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Title: Probability-Scale Residuals and Residual Correlations
Diff between PResiduals versions 0.2-0 dated 2014-08-22 and 0.2-1 dated 2015-03-03
Description: Computes probability-scale residuals and residual correlations
for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont
DESCRIPTION | 25 ++++-----
MD5 | 42 ++++++++-------
NAMESPACE | 7 ++
R/GKGamma.R | 1
R/PResiduals-package.R | 14 ++---
R/cobot.R | 11 ++--
R/cocobot.R | 6 +-
R/countbot.R |only
R/diagn.R | 1
R/presid.R | 123 +++++++++++++++++++++++++++++++++++++++++-----
R/print.cobot.R | 1
R/print.cocobot.R | 1
data/PResidData.rda |binary
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man/print.cobot.Rd | 3 -
man/print.cocobot.Rd | 3 -
23 files changed, 196 insertions(+), 107 deletions(-)
Title: Advanced Tables for Markdown/HTML
Diff between htmlTable versions 1.1 dated 2015-02-07 and 1.2 dated 2015-03-03
Description: Tables with state-of-the-art layout elements such as
row spanners, column spanners, table spanners, zebra striping,
and more. While allowing advanced layout, the underlying CSS structure is
simple in order to maximize compatibility with wordprocessors such as
MS Word or LibreOffice.
The package also contains a few text formatting functions that help outputting
text compatible with HTML/LaTeX.
Author: Max Gordon
Maintainer: Max Gordon
DESCRIPTION | 19
MD5 | 28
NAMESPACE | 1
NEWS | 6
R/htmlTable.R | 16
R/htmlTable_helpers.R | 7
build/vignette.rds |binary
inst/doc/general.Rmd | 2
inst/doc/general.html | 46
inst/doc/tables.R | 27
inst/doc/tables.Rmd | 40
inst/doc/tables.html | 1273 +++++++++++++++++++++++-
tests/testthat/test-htmlTable_rgroup_tspanner.R | 11
vignettes/general.Rmd | 2
vignettes/tables.Rmd | 40
15 files changed, 1426 insertions(+), 92 deletions(-)
Title: Performs the Processing and Normalisation of Nanostring miRNA
and mRNA Data
Diff between NAPPA versions 2.0 dated 2014-07-16 and 2.0.1 dated 2015-03-03
Description: Enables the processing and normalisation of the standard mRNA data output from the Nanostring nCounter software.
Author: Chris Harbron, Mark Wappett
Maintainer: Mark Wappett
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
build/vignette.rds |binary
inst/doc/NAPPA.pdf |binary
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Mixed Effects Cox Models
Diff between coxme versions 2.2-3 dated 2012-05-15 and 2.2-4 dated 2015-03-03
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau
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coxme-2.2-3/coxme/noweb/noweb.R |only
coxme-2.2-3/coxme/noweb/noweb.sty |only
coxme-2.2-3/coxme/noweb/nwmac.tex |only
coxme-2.2-4/coxme/DESCRIPTION | 25 +-
coxme-2.2-4/coxme/MD5 | 186 +++++++++--------
coxme-2.2-4/coxme/NAMESPACE | 18 -
coxme-2.2-4/coxme/R/anova.coxme.R | 5
coxme-2.2-4/coxme/R/bdsmatrix.R | 2
coxme-2.2-4/coxme/R/coxme.R | 18 +
coxme-2.2-4/coxme/R/coxme.control.R | 17 +
coxme-2.2-4/coxme/R/coxme.fit.R | 83 +++++--
coxme-2.2-4/coxme/R/coxme.varcheck.R | 9
coxme-2.2-4/coxme/R/coxmeFull.R | 23 --
coxme-2.2-4/coxme/R/coxmeMlist.R | 19 -
coxme-2.2-4/coxme/R/lmekin.R | 19 +
coxme-2.2-4/coxme/R/lmekin.control.R | 20 +
coxme-2.2-4/coxme/R/predict.coxme.R |only
coxme-2.2-4/coxme/R/print.coxme.R | 4
coxme-2.2-4/coxme/R/print.lmekin.R | 5
coxme-2.2-4/coxme/R/ranef.R | 23 ++
coxme-2.2-4/coxme/build |only
coxme-2.2-4/coxme/cleanup |only
coxme-2.2-4/coxme/cleanup.win |only
coxme-2.2-4/coxme/inst/COPYRIGHTS |only
coxme-2.2-4/coxme/inst/NEWS.Rd | 43 +++
coxme-2.2-4/coxme/inst/doc/coxme.R |only
coxme-2.2-4/coxme/inst/doc/coxme.pdf |binary
coxme-2.2-4/coxme/inst/doc/laplace.R |only
coxme-2.2-4/coxme/inst/doc/laplace.Rnw | 6
coxme-2.2-4/coxme/inst/doc/laplace.pdf |binary
coxme-2.2-4/coxme/inst/doc/lmekin.R |only
coxme-2.2-4/coxme/inst/doc/lmekin.Rnw | 10
coxme-2.2-4/coxme/inst/doc/lmekin.pdf |binary
coxme-2.2-4/coxme/inst/doc/variance.R |only
coxme-2.2-4/coxme/inst/doc/variance.Rnw | 12 -
coxme-2.2-4/coxme/inst/doc/variance.pdf |binary
coxme-2.2-4/coxme/man/VarCorr.Rd |only
coxme-2.2-4/coxme/man/coxme.Rd | 11 -
coxme-2.2-4/coxme/man/coxme.control.Rd | 51 ++++
coxme-2.2-4/coxme/man/coxme.object.Rd |only
coxme-2.2-4/coxme/man/fixed.effects.Rd |only
coxme-2.2-4/coxme/man/fixef.lmekin.Rd | 32 ++
coxme-2.2-4/coxme/man/lmekin.Rd | 39 ++-
coxme-2.2-4/coxme/man/lmekin.control.Rd |only
coxme-2.2-4/coxme/man/lmekin.object.Rd | 12 -
coxme-2.2-4/coxme/man/logLik.coxme.Rd |only
coxme-2.2-4/coxme/man/predict.coxme.Rd |only
coxme-2.2-4/coxme/man/print.coxme.Rd | 14 +
coxme-2.2-4/coxme/man/ranef.Rd |only
coxme-2.2-4/coxme/noweb/Makefile | 19 -
coxme-2.2-4/coxme/noweb/Readme | 13 -
coxme-2.2-4/coxme/noweb/all.nw | 323 +++++++++++++++++-------------
coxme-2.2-4/coxme/noweb/basic.Rnw | 6
coxme-2.2-4/coxme/noweb/bdsmatrix.Rnw | 4
coxme-2.2-4/coxme/noweb/build.Rnw | 19 -
coxme-2.2-4/coxme/noweb/fit.Rnw | 89 +++++---
coxme-2.2-4/coxme/noweb/formula.Rnw | 17 -
coxme-2.2-4/coxme/noweb/lmekin.Rnw | 29 +-
coxme-2.2-4/coxme/noweb/main.Rnw | 54 +----
coxme-2.2-4/coxme/noweb/ranef.Rnw | 28 ++
coxme-2.2-4/coxme/noweb/varfun.Rnw | 32 +-
coxme-2.2-4/coxme/noweb/varfun2.Rnw | 43 ++-
coxme-2.2-4/coxme/src/agfit6b.c | 1
coxme-2.2-4/coxme/src/bdsmatrix.h |only
coxme-2.2-4/coxme/src/bdsmatrix_stub.h |only
coxme-2.2-4/coxme/src/coxfit6a.c | 1
coxme-2.2-4/coxme/src/coxfit6c.c | 2
coxme-2.2-4/coxme/src/coxmeS.h | 17 -
coxme-2.2-4/coxme/tests/bdstest.R | 10
coxme-2.2-4/coxme/tests/bdstest.Rout.save | 23 +-
coxme-2.2-4/coxme/tests/brdat.rda |only
coxme-2.2-4/coxme/tests/brfit.R |only
coxme-2.2-4/coxme/tests/lmekin1.R | 16 +
coxme-2.2-4/coxme/tests/lmekin1.Rout.save | 30 +-
coxme-2.2-4/coxme/tests/lmekin2.R | 8
coxme-2.2-4/coxme/tests/lmekin2.Rout.save | 21 +
coxme-2.2-4/coxme/tests/nest1.Rout.save | 2
coxme-2.2-4/coxme/tests/nest2.Rout.save | 2
coxme-2.2-4/coxme/tests/refine.Rout.save | 2
coxme-2.2-4/coxme/tests/refine1.R | 2
coxme-2.2-4/coxme/tests/refine1.Rout.save | 15 -
coxme-2.2-4/coxme/tests/refine2.R | 2
coxme-2.2-4/coxme/tests/refine2.Rout.save | 15 -
coxme-2.2-4/coxme/tests/refine3.Rout.save | 2
coxme-2.2-4/coxme/tests/shrink.Rout.save | 2
coxme-2.2-4/coxme/tests/slope1.Rout.save | 2
coxme-2.2-4/coxme/tests/slope2.R | 6
coxme-2.2-4/coxme/tests/slope2.Rout.save | 19 -
coxme-2.2-4/coxme/tests/slope3.Rout.save | 2
coxme-2.2-4/coxme/tests/slope4.R | 2
coxme-2.2-4/coxme/tests/slope4.Rout.save | 15 -
coxme-2.2-4/coxme/tests/strata1.Rout.save | 2
coxme-2.2-4/coxme/tests/test0.R | 7
coxme-2.2-4/coxme/tests/test0.Rout.save | 22 +-
coxme-2.2-4/coxme/tests/test1.Rout.save | 2
coxme-2.2-4/coxme/tests/test2.R | 17 -
coxme-2.2-4/coxme/tests/test2.Rout.save | 30 +-
coxme-2.2-4/coxme/tests/test3.Rout.save | 2
coxme-2.2-4/coxme/tests/test4.Rout.save | 2
coxme-2.2-4/coxme/tests/twoterm.R | 2
coxme-2.2-4/coxme/tests/twoterm.Rout.save | 17 -
coxme-2.2-4/coxme/vignettes/figures |only
coxme-2.2-4/coxme/vignettes/laplace.Rnw | 6
coxme-2.2-4/coxme/vignettes/lmekin.Rnw | 10
coxme-2.2-4/coxme/vignettes/variance.Rnw | 12 -
107 files changed, 1028 insertions(+), 704 deletions(-)
Title: MCMC Algorithms for the Coalescent
Diff between coalescentMCMC versions 0.4 dated 2013-12-04 and 0.4-1 dated 2015-03-03
More information about coalescentMCMC at CRAN
Description: Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters.
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis
DESCRIPTION | 15 ++++++---------
MD5 | 26 ++++++++++++++------------
NAMESPACE | 6 ++++--
NEWS | 16 ++++++++++++++++
R/coalescentMCMC.R | 31 +++++++++++++++++++++----------
R/sim.coalescent.R |only
R/treeOperators.R | 8 ++++----
build/vignette.rds |binary
inst/doc/CoalescentModels.pdf |binary
inst/doc/Running_coalescentMCMC.R | 29 +++++++++++++++--------------
inst/doc/Running_coalescentMCMC.Rnw | 10 +++++-----
inst/doc/Running_coalescentMCMC.pdf |binary
man/coalesceMCMC.Rd | 7 ++++---
man/sim.coalescent.Rd |only
vignettes/Running_coalescentMCMC.Rnw | 10 +++++-----
15 files changed, 94 insertions(+), 64 deletions(-)
Permanent link
Title: Companion to Applied Regression
Diff between car versions 2.0-24 dated 2015-02-01 and 2.0-25 dated 2015-03-03
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 16
MD5 | 19
NAMESPACE | 540 ++++++++++----------
NEWS | 1288 ++++++++++++++++++++++++-------------------------
R/Anova.R | 6
R/Boot.R | 601 +++++++++++-----------
R/linearHypothesis.R | 3
inst/doc/embedding.pdf |binary
man/Anova.Rd | 653 ++++++++++++------------
man/car-internal.Rd |only
man/car-package.Rd | 72 +-
11 files changed, 1611 insertions(+), 1587 deletions(-)
Title: Agricultural Datasets
Diff between agridat versions 1.10 dated 2014-11-26 and 1.11 dated 2015-03-03
Description: Datasets from books, papers, and websites related to agriculture.
Example analyses are included. Includes functions for plotting field
designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright
agridat-1.10/agridat/data/piepho.cooksfoot.txt.gz |only
agridat-1.10/agridat/man/piepho.cooksfoot.Rd |only
agridat-1.11/agridat/DESCRIPTION | 23
agridat-1.11/agridat/MD5 | 407 +++++------
agridat-1.11/agridat/NAMESPACE | 4
agridat-1.11/agridat/NEWS | 153 ++--
agridat-1.11/agridat/R/gge.r | 565 ++++++++++------
agridat-1.11/agridat/build/vignette.rds |binary
agridat-1.11/agridat/data/besag.beans.txt.gz |only
agridat-1.11/agridat/data/besag.triticale.txt.gz |only
agridat-1.11/agridat/data/burgueno.alpha.txt.gz |only
agridat-1.11/agridat/data/burgueno.rowcol.txt.gz |only
agridat-1.11/agridat/data/burgueno.unreplicated.txt.gz |only
agridat-1.11/agridat/data/datalist | 9
agridat-1.11/agridat/data/piepho.cocksfoot.txt.gz |only
agridat-1.11/agridat/data/steptoe.morex.geno.rda |only
agridat-1.11/agridat/data/steptoe.morex.pheno.txt.gz |only
agridat-1.11/agridat/inst/doc/agridat_examples.Rnw | 6
agridat-1.11/agridat/inst/doc/agridat_examples.pdf |binary
agridat-1.11/agridat/man/aastveit.barley.Rd | 6
agridat-1.11/agridat/man/adugna.sorghum.Rd | 3
agridat-1.11/agridat/man/agridat.Rd | 60 +
agridat-1.11/agridat/man/allcroft.lodging.Rd | 22
agridat-1.11/agridat/man/archbold.apple.Rd | 5
agridat-1.11/agridat/man/ars.earlywhitecorn96.Rd | 11
agridat-1.11/agridat/man/australia.soybean.Rd | 2
agridat-1.11/agridat/man/baker.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/batchelor.uniformity.Rd | 26
agridat-1.11/agridat/man/beall.webworms.Rd | 1
agridat-1.11/agridat/man/beaven.barley.Rd | 1
agridat-1.11/agridat/man/besag.bayesian.Rd | 33
agridat-1.11/agridat/man/besag.beans.Rd |only
agridat-1.11/agridat/man/besag.elbatan.Rd | 63 +
agridat-1.11/agridat/man/besag.endive.Rd | 1
agridat-1.11/agridat/man/besag.met.Rd | 2
agridat-1.11/agridat/man/besag.triticale.Rd |only
agridat-1.11/agridat/man/blackman.wheat.Rd | 1
agridat-1.11/agridat/man/bliss.borers.Rd | 47 -
agridat-1.11/agridat/man/bond.diallel.Rd | 2
agridat-1.11/agridat/man/box.cork.Rd | 1
agridat-1.11/agridat/man/brandle.rape.Rd | 13
agridat-1.11/agridat/man/brandt.switchback.Rd | 2
agridat-1.11/agridat/man/bridges.cucmber.Rd | 1
agridat-1.11/agridat/man/broadbalk.wheat.Rd | 2
agridat-1.11/agridat/man/burgueno.alpha.Rd |only
agridat-1.11/agridat/man/burgueno.rowcol.Rd |only
agridat-1.11/agridat/man/burgueno.unreplicated.Rd |only
agridat-1.11/agridat/man/butron.maize.Rd | 1
agridat-1.11/agridat/man/byers.apple.Rd | 25
agridat-1.11/agridat/man/caribbean.maize.Rd | 2
agridat-1.11/agridat/man/carlson.germination.Rd | 35
agridat-1.11/agridat/man/carmer.density.Rd | 36 -
agridat-1.11/agridat/man/cate.potassium.Rd | 1
agridat-1.11/agridat/man/cleveland.soil.Rd | 2
agridat-1.11/agridat/man/cochran.bib.Rd | 7
agridat-1.11/agridat/man/cochran.crd.Rd | 1
agridat-1.11/agridat/man/cochran.eelworms.Rd | 2
agridat-1.11/agridat/man/cochran.factorial.Rd | 10
agridat-1.11/agridat/man/cochran.latin.Rd | 3
agridat-1.11/agridat/man/cochran.wireworms.Rd | 2
agridat-1.11/agridat/man/connolly.potato.Rd | 1
agridat-1.11/agridat/man/cornelius.maize.Rd | 2
agridat-1.11/agridat/man/corsten.interaction.Rd | 2
agridat-1.11/agridat/man/cox.stripsplit.Rd | 10
agridat-1.11/agridat/man/crossa.wheat.Rd | 33
agridat-1.11/agridat/man/crowder.seeds.Rd | 13
agridat-1.11/agridat/man/cullis.earlygen.Rd | 2
agridat-1.11/agridat/man/darwin.maize.Rd | 2
agridat-1.11/agridat/man/denis.missing.Rd | 3
agridat-1.11/agridat/man/denis.ryegrass.Rd | 2
agridat-1.11/agridat/man/desplot.Rd | 5
agridat-1.11/agridat/man/digby.jointregression.Rd | 3
agridat-1.11/agridat/man/diggle.cow.Rd | 9
agridat-1.11/agridat/man/durban.competition.Rd | 1
agridat-1.11/agridat/man/durban.rowcol.Rd | 3
agridat-1.11/agridat/man/durban.splitplot.Rd | 3
agridat-1.11/agridat/man/eden.potato.Rd | 4
agridat-1.11/agridat/man/engelstad.nitro.Rd | 8
agridat-1.11/agridat/man/fan.stability.Rd | 14
agridat-1.11/agridat/man/federer.diagcheck.Rd | 18
agridat-1.11/agridat/man/federer.tobacco.Rd | 3
agridat-1.11/agridat/man/fisher.latin.Rd | 1
agridat-1.11/agridat/man/foulley.calving.Rd | 4
agridat-1.11/agridat/man/fox.wheat.Rd | 1
agridat-1.11/agridat/man/garber.mulit.uniformity.Rd | 3
agridat-1.11/agridat/man/gathmann.bt.Rd | 3
agridat-1.11/agridat/man/gauch.soy.Rd | 28
agridat-1.11/agridat/man/gge.Rd | 17
agridat-1.11/agridat/man/gilmour.serpentine.Rd | 2
agridat-1.11/agridat/man/gilmour.slatehall.Rd | 1
agridat-1.11/agridat/man/gomez.fractionalfactorial.Rd | 14
agridat-1.11/agridat/man/gomez.groupsplit.Rd | 3
agridat-1.11/agridat/man/gomez.multilocsplitplot.Rd | 3
agridat-1.11/agridat/man/gomez.nitrogen.Rd | 2
agridat-1.11/agridat/man/gomez.rice.uniformity.Rd | 30
agridat-1.11/agridat/man/gomez.seedrate.Rd | 10
agridat-1.11/agridat/man/gomez.splitplot.subsample.Rd | 1
agridat-1.11/agridat/man/gomez.splitsplit.Rd | 2
agridat-1.11/agridat/man/gomez.stripplot.Rd | 1
agridat-1.11/agridat/man/gomez.stripsplitplot.Rd | 2
agridat-1.11/agridat/man/gotway.hessianfly.Rd | 2
agridat-1.11/agridat/man/goulden.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/goulden.latin.Rd | 1
agridat-1.11/agridat/man/graybill.heteroskedastic.Rd | 3
agridat-1.11/agridat/man/gumpertz.pepper.Rd | 1
agridat-1.11/agridat/man/hanks.sprinkler.Rd | 3
agridat-1.11/agridat/man/harris.multi.uniformity.Rd | 2
agridat-1.11/agridat/man/harris.wateruse.Rd | 11
agridat-1.11/agridat/man/harrison.priors.Rd | 20
agridat-1.11/agridat/man/hayman.tobacco.Rd | 1
agridat-1.11/agridat/man/hazell.vegetables.Rd | 2
agridat-1.11/agridat/man/heady.fertilizer.Rd | 1
agridat-1.11/agridat/man/henderson.milkfat.Rd | 2
agridat-1.11/agridat/man/hernandez.nitrogen.Rd | 6
agridat-1.11/agridat/man/hessling.argentina.Rd | 22
agridat-1.11/agridat/man/hildebrand.systems.Rd | 2
agridat-1.11/agridat/man/holland.arthropods.Rd | 2
agridat-1.11/agridat/man/holshouser.splitstrip.Rd | 8
agridat-1.11/agridat/man/hughes.grapes.Rd | 8
agridat-1.11/agridat/man/hunter.corn.Rd | 2
agridat-1.11/agridat/man/ilri.sheep.Rd | 3
agridat-1.11/agridat/man/immer.sugarbeet.uniformity.Rd | 3
agridat-1.11/agridat/man/ivins.herbs.Rd | 1
agridat-1.11/agridat/man/jansen.strawberry.Rd | 1
agridat-1.11/agridat/man/jenkyn.mildew.Rd | 2
agridat-1.11/agridat/man/john.alpha.Rd | 16
agridat-1.11/agridat/man/johnson.blight.Rd | 2
agridat-1.11/agridat/man/kalamkar.potato.uniformity.Rd | 1
agridat-1.11/agridat/man/kang.maize.Rd | 1
agridat-1.11/agridat/man/kang.peanut.Rd | 3
agridat-1.11/agridat/man/karcher.turfgrass.Rd | 1
agridat-1.11/agridat/man/keen.potatodamage.Rd | 23
agridat-1.11/agridat/man/kempton.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/kempton.competition.Rd | 3
agridat-1.11/agridat/man/kempton.rowcol.Rd | 2
agridat-1.11/agridat/man/kempton.slatehall.Rd | 8
agridat-1.11/agridat/man/lambert.soiltemp.Rd | 2
agridat-1.11/agridat/man/lasrosas.corn.Rd | 18
agridat-1.11/agridat/man/lavoranti.eucalyptus.Rd | 2
agridat-1.11/agridat/man/lee.potatoblight.Rd | 6
agridat-1.11/agridat/man/li.millet.uniformity.Rd | 2
agridat-1.11/agridat/man/lonnquist.maize.Rd | 4
agridat-1.11/agridat/man/lucas.switchback.Rd | 1
agridat-1.11/agridat/man/lyon.potato.uniformity.Rd | 2
agridat-1.11/agridat/man/lyons.wheat.Rd | 2
agridat-1.11/agridat/man/mcconway.turnip.Rd | 9
agridat-1.11/agridat/man/mcleod.barley.Rd | 2
agridat-1.11/agridat/man/mead.cauliflower.Rd | 5
agridat-1.11/agridat/man/mead.cowpeamaize.Rd | 13
agridat-1.11/agridat/man/mead.germination.Rd | 2
agridat-1.11/agridat/man/mead.strawberry.Rd | 2
agridat-1.11/agridat/man/mercer.mangold.uniformity.Rd | 2
agridat-1.11/agridat/man/mercer.wheat.uniformity.Rd | 3
agridat-1.11/agridat/man/minnesota.barley.weather.Rd | 25
agridat-1.11/agridat/man/minnesota.barley.yield.Rd | 3
agridat-1.11/agridat/man/nass.corn.Rd | 3
agridat-1.11/agridat/man/nebraska.farmincome.Rd | 58 -
agridat-1.11/agridat/man/odland.soy.uniformity.Rd | 2
agridat-1.11/agridat/man/ortiz.tomato.Rd | 8
agridat-1.11/agridat/man/pacheco.soybean.Rd | 23
agridat-1.11/agridat/man/patterson.switchback.Rd | 2
agridat-1.11/agridat/man/pearce.apple.Rd | 2
agridat-1.11/agridat/man/pearl.kernels.Rd | 1
agridat-1.11/agridat/man/perry.springwheat.Rd | 3
agridat-1.11/agridat/man/piepho.cocksfoot.Rd |only
agridat-1.11/agridat/man/ratkowsky.onions.Rd | 96 +-
agridat-1.11/agridat/man/ridout.appleshoots.Rd | 6
agridat-1.11/agridat/man/rothamsted.brussels.Rd | 2
agridat-1.11/agridat/man/ryder.groundnut.Rd | 3
agridat-1.11/agridat/man/salmon.bunt.Rd | 42 -
agridat-1.11/agridat/man/senshu.rice.Rd | 2
agridat-1.11/agridat/man/shafii.rapeseed.Rd | 2
agridat-1.11/agridat/man/sinclair.clover.Rd | 2
agridat-1.11/agridat/man/smith.corn.uniformity.Rd | 2
agridat-1.11/agridat/man/snedecor.asparagus.Rd | 5
agridat-1.11/agridat/man/snijders.fusarium.Rd | 2
agridat-1.11/agridat/man/steel.soybean.Rd | 2
agridat-1.11/agridat/man/stephens.sorghum.uniformity.Rd | 2
agridat-1.11/agridat/man/steptoe.morex.pheno.Rd |only
agridat-1.11/agridat/man/stirret.borers.Rd | 10
agridat-1.11/agridat/man/streibig.competition.Rd | 2
agridat-1.11/agridat/man/stroup.nin.Rd | 2
agridat-1.11/agridat/man/stroup.splitplot.Rd | 3
agridat-1.11/agridat/man/student.barley.Rd | 2
agridat-1.11/agridat/man/talbot.potato.Rd | 34
agridat-1.11/agridat/man/theobald.barley.Rd | 1
agridat-1.11/agridat/man/theobald.covariate.Rd | 1
agridat-1.11/agridat/man/thompson.cornsoy.Rd | 3
agridat-1.11/agridat/man/turner.herbicide.Rd | 15
agridat-1.11/agridat/man/vargas.txe.Rd | 2
agridat-1.11/agridat/man/vargas.wheat1.Rd | 79 +-
agridat-1.11/agridat/man/vargas.wheat2.Rd | 1
agridat-1.11/agridat/man/verbyla.lupin.Rd | 20
agridat-1.11/agridat/man/vold.longterm.Rd | 18
agridat-1.11/agridat/man/vsn.lupin3.Rd | 3
agridat-1.11/agridat/man/wallace.iowaland.Rd | 17
agridat-1.11/agridat/man/walsh.cottonprice.Rd | 2
agridat-1.11/agridat/man/wassom.brome1.uniformity.Rd | 1
agridat-1.11/agridat/man/waynick.soil.Rd | 2
agridat-1.11/agridat/man/wedderburn.barley.Rd | 1
agridat-1.11/agridat/man/weiss.incblock.Rd | 21
agridat-1.11/agridat/man/weiss.lattice.Rd | 1
agridat-1.11/agridat/man/welch.bermudagrass.Rd | 16
agridat-1.11/agridat/man/wiebe.wheat.uniformity.Rd | 2
agridat-1.11/agridat/man/williams.barley.uniformity.Rd | 3
agridat-1.11/agridat/man/williams.cotton.uniformity.Rd | 3
agridat-1.11/agridat/man/williams.trees.Rd | 3
agridat-1.11/agridat/man/yan.winterwheat.Rd | 1
agridat-1.11/agridat/man/yang.barley.Rd | 4
agridat-1.11/agridat/man/yates.missing.Rd | 4
agridat-1.11/agridat/man/yates.oats.Rd | 15
agridat-1.11/agridat/man/zuidhof.broiler.Rd | 3
agridat-1.11/agridat/vignettes/agridat_examples.Rnw | 6
213 files changed, 1659 insertions(+), 1060 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 1.3 dated 2015-01-06 and 1.5-0 dated 2015-03-03
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch
sirt-1.3/sirt/R/lllsa.R |only
sirt-1.3/sirt/R/rm.facets.IC.R |only
sirt-1.5-0/sirt/DESCRIPTION | 18 +-
sirt-1.5-0/sirt/MD5 | 209 ++++++++++++------------
sirt-1.5-0/sirt/NAMESPACE | 6
sirt-1.5-0/sirt/R/IRT.irfprob.sirt.R | 3
sirt-1.5-0/sirt/R/IRT.likelihood_sirt.R | 3
sirt-1.5-0/sirt/R/IRT.posterior_sirt.R | 4
sirt-1.5-0/sirt/R/anova_sirt.R | 4
sirt-1.5-0/sirt/R/detect.R | 4
sirt-1.5-0/sirt/R/dif.logisticregression.R | 3
sirt-1.5-0/sirt/R/dif.variance.R | 9 -
sirt-1.5-0/sirt/R/logLik_sirt.R | 3
sirt-1.5-0/sirt/R/pcm.fit.R | 5
sirt-1.5-0/sirt/R/plot.rm.sdt.R |only
sirt-1.5-0/sirt/R/prob.guttman.R | 20 --
sirt-1.5-0/sirt/R/rasch.conquest.R | 4
sirt-1.5-0/sirt/R/rasch.mml.raschtype.R | 53 ++----
sirt-1.5-0/sirt/R/rasch.mml2.R | 128 +++++++++++---
sirt-1.5-0/sirt/R/rasch.mml2.missing1.R | 28 ++-
sirt-1.5-0/sirt/R/rm.hrm.calcprobs.R |only
sirt-1.5-0/sirt/R/rm.hrm.est.tau.item.R |only
sirt-1.5-0/sirt/R/rm.sdt.R | 184 ++++++++++++++++-----
sirt-1.5-0/sirt/R/rm.sdt_alg.R | 130 ++------------
sirt-1.5-0/sirt/R/rm.smooth.distribution.R | 9 -
sirt-1.5-0/sirt/R/summary.rasch.mml2.R | 4
sirt-1.5-0/sirt/R/summary.rm.sdt.R | 19 +-
sirt-1.5-0/sirt/data/data.activity.itempars.rda |binary
sirt-1.5-0/sirt/data/data.big5.qgraph.rda |binary
sirt-1.5-0/sirt/data/data.big5.rda |binary
sirt-1.5-0/sirt/data/data.bs07a.rda |only
sirt-1.5-0/sirt/data/data.eid.rda |binary
sirt-1.5-0/sirt/data/data.ess2005.rda |binary
sirt-1.5-0/sirt/data/data.g308.rda |binary
sirt-1.5-0/sirt/data/data.inv4gr.rda |binary
sirt-1.5-0/sirt/data/data.liking.science.rda |binary
sirt-1.5-0/sirt/data/data.long.rda |binary
sirt-1.5-0/sirt/data/data.math.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.LSAT6.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.act15.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.rape.rda |binary
sirt-1.5-0/sirt/data/data.mixed1.rda |binary
sirt-1.5-0/sirt/data/data.ml1.rda |binary
sirt-1.5-0/sirt/data/data.ml2.rda |binary
sirt-1.5-0/sirt/data/data.noharm18.rda |binary
sirt-1.5-0/sirt/data/data.noharmExC.rda |binary
sirt-1.5-0/sirt/data/data.pars1.2pl.rda |binary
sirt-1.5-0/sirt/data/data.pars1.rasch.rda |binary
sirt-1.5-0/sirt/data/data.pirlsmissing.rda |binary
sirt-1.5-0/sirt/data/data.pisaMath.rda |binary
sirt-1.5-0/sirt/data/data.pisaPars.rda |binary
sirt-1.5-0/sirt/data/data.pisaRead.rda |binary
sirt-1.5-0/sirt/data/data.ratings1.rda |binary
sirt-1.5-0/sirt/data/data.ratings2.rda |binary
sirt-1.5-0/sirt/data/data.ratings3.rda |binary
sirt-1.5-0/sirt/data/data.raw1.rda |binary
sirt-1.5-0/sirt/data/data.read.rda |binary
sirt-1.5-0/sirt/data/data.reck21.rda |binary
sirt-1.5-0/sirt/data/data.reck61DAT1.rda |binary
sirt-1.5-0/sirt/data/data.reck61DAT2.rda |binary
sirt-1.5-0/sirt/data/data.reck73C1a.rda |binary
sirt-1.5-0/sirt/data/data.reck73C1b.rda |binary
sirt-1.5-0/sirt/data/data.reck75C2.rda |binary
sirt-1.5-0/sirt/data/data.reck78ExA.rda |binary
sirt-1.5-0/sirt/data/data.reck79ExB.rda |binary
sirt-1.5-0/sirt/data/data.si01.rda |binary
sirt-1.5-0/sirt/data/data.si02.rda |binary
sirt-1.5-0/sirt/data/data.si03.rda |binary
sirt-1.5-0/sirt/data/data.si04.rda |binary
sirt-1.5-0/sirt/data/data.si05.rda |binary
sirt-1.5-0/sirt/data/data.si06.rda |binary
sirt-1.5-0/sirt/data/data.timss.rda |binary
sirt-1.5-0/sirt/data/data.timss07.G8.RUS.rda |binary
sirt-1.5-0/sirt/inst/NEWS | 169 ++++++++++++-------
sirt-1.5-0/sirt/man/R2conquest.Rd | 32 ++-
sirt-1.5-0/sirt/man/R2noharm.Rd | 5
sirt-1.5-0/sirt/man/data.big5.Rd | 15 -
sirt-1.5-0/sirt/man/data.bs.Rd |only
sirt-1.5-0/sirt/man/data.eid.Rd | 28 ++-
sirt-1.5-0/sirt/man/data.ess2005.Rd | 8
sirt-1.5-0/sirt/man/data.g308.Rd | 3
sirt-1.5-0/sirt/man/data.inv4gr.Rd | 3
sirt-1.5-0/sirt/man/data.liking.science.Rd | 3
sirt-1.5-0/sirt/man/data.long.Rd | 5
sirt-1.5-0/sirt/man/data.math.Rd | 6
sirt-1.5-0/sirt/man/data.mixed1.Rd | 4
sirt-1.5-0/sirt/man/data.ml.Rd | 13 -
sirt-1.5-0/sirt/man/data.noharm.Rd | 13 -
sirt-1.5-0/sirt/man/data.pars1.rasch.Rd | 13 -
sirt-1.5-0/sirt/man/data.pirlsmissing.Rd | 5
sirt-1.5-0/sirt/man/data.pisaMath.Rd | 4
sirt-1.5-0/sirt/man/data.pisaPars.Rd | 5
sirt-1.5-0/sirt/man/data.pisaRead.Rd | 7
sirt-1.5-0/sirt/man/data.ratings1.Rd | 23 --
sirt-1.5-0/sirt/man/data.raw1.Rd | 3
sirt-1.5-0/sirt/man/data.read.Rd | 85 ++++-----
sirt-1.5-0/sirt/man/data.si.Rd | 36 ----
sirt-1.5-0/sirt/man/data.timss.Rd | 5
sirt-1.5-0/sirt/man/invariance.alignment.Rd | 2
sirt-1.5-0/sirt/man/linking.haberman.Rd | 2
sirt-1.5-0/sirt/man/mirt.wrapper.Rd | 3
sirt-1.5-0/sirt/man/noharm.sirt.Rd | 2
sirt-1.5-0/sirt/man/prob.guttman.Rd | 24 ++
sirt-1.5-0/sirt/man/rasch.copula.Rd | 2
sirt-1.5-0/sirt/man/rasch.mirtlc.Rd | 5
sirt-1.5-0/sirt/man/rasch.mml.Rd | 47 ++++-
sirt-1.5-0/sirt/man/rm.sdt.Rd | 90 ++++++++--
sirt-1.5-0/sirt/man/sirt-package.Rd | 186 ++++++++++-----------
sirt-1.5-0/sirt/src/rm_smirt_mml2_code.cpp | 8
109 files changed, 929 insertions(+), 785 deletions(-)
Title: Entrez in R
Diff between rentrez versions 0.4 dated 2015-02-08 and 0.4.1 dated 2015-03-03
Description: Rentrez provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NEWS | 6 ++++++
R/entrez_citmatch.r | 2 +-
inst/doc/rentrez_tutorial.html | 4 ++--
man/entrez_citmatch.Rd | 2 +-
6 files changed, 18 insertions(+), 12 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Diff between coda versions 0.16-1 dated 2012-11-06 and 0.17-1 dated 2015-03-03
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut]
Maintainer: Martyn Plummer
coda-0.16-1/coda/AUTHORS |only
coda-0.16-1/coda/misc |only
coda-0.17-1/coda/CHANGELOG | 23 ++++++++++++++++---
coda-0.17-1/coda/DESCRIPTION | 41 +++++++++++++++++++++-------------
coda-0.17-1/coda/MD5 | 26 +++++++++------------
coda-0.17-1/coda/NAMESPACE | 5 +++-
coda-0.17-1/coda/R/mcmc.R | 4 +--
coda-0.17-1/coda/R/mcmclist.R | 2 -
coda-0.17-1/coda/R/trellisplots.R | 2 -
coda-0.17-1/coda/R/util.R | 15 +++---------
coda-0.17-1/coda/data/line.rda |binary
coda-0.17-1/coda/inst/AUTHORS |only
coda-0.17-1/coda/man/effectiveSize.Rd | 7 +++--
coda-0.17-1/coda/man/mcmc.Rd | 3 +-
14 files changed, 75 insertions(+), 53 deletions(-)
Title: Plugin de R-Commander para el Manual 'EACSPIR'
Diff between RcmdrPlugin.EACSPIR versions 0.2-1 dated 2014-02-07 and 0.2-2 dated 2015-03-03
More information about RcmdrPlugin.EACSPIR at CRAN
Description: Este paquete proporciona una interfaz grafica de usuario (GUI) para algunos de los procedimientos estadisticos detallados en un curso de 'Estadistica aplicada a las Ciencias Sociales mediante el programa informatico R' (EACSPIR). LA GUI se ha desarrollado como un Plugin del programa R-Commander.
Author: Maribel Pero
Maintainer: David Leiva
DESCRIPTION | 12 +++++------
MD5 | 10 ++++-----
NAMESPACE | 2 -
R/RcmdrPlugin.EACSPIR.R | 31 ++++++++++++++++++++----------
inst/etc/menus.txt | 38 ++++++++++++++++++-------------------
man/RcmdrPlugin.EACSPIR-package.Rd | 4 +--
6 files changed, 54 insertions(+), 43 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-10 0.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-31 1.0.3.2
2014-01-31 1.0.3.1
2014-01-04 1.0.2.0
2013-12-18 1.0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-22 2.13
2012-01-05 2.10
2012-01-03 2.9
2010-07-30 2.7
2010-07-24 2.6
2010-02-05 2.4
2010-02-03 2.3
2008-10-09 2.2
2008-09-19 2.1
2008-06-27 1.3
2008-05-20 1.2
2007-11-20 1.1
2007-11-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-30 1.7
2013-11-14 1.6
2013-02-12 1.5
2012-06-14 1.4
2012-04-25 1.3
2012-03-30 1.2
2012-03-27 1.1
2012-03-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-30 0.5.3
2014-11-21 0.5.2
2014-09-04 0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-17 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-29 1.2
2012-11-03 1.1
2012-01-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-26 2.5.6
2013-05-18 2.5.3
2012-11-06 2.5.2
2012-10-29 2.5.1
2012-06-25 2.02
2012-06-04 2.00-3
2012-03-07 0.71
2012-02-16 0.66
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-21 0.1.0
2013-11-13 0.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-11 0.2.1
2014-11-29 0.2.0
Title: Color Space Manipulation
Diff between colorspace versions 1.2-4 dated 2013-09-30 and 1.2-5 dated 2015-03-03
Description: Carries out mapping between assorted color spaces including
RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),
CIELAB and polar CIELAB. Qualitative, sequential, and
diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut],
Paul Murrell [aut],
Kurt Hornik [aut],
Jason C. Fisher [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 11 ++++++-----
MD5 | 17 +++++++++--------
NAMESPACE | 1 +
NEWS | 5 +++++
R/choose_palette.R | 16 ++++++----------
build |only
data/USSouthPolygon.rda |binary
inst/doc/hcl-colors.pdf |binary
man/choose_palette.Rd | 6 ++++--
tests/Examples/colorspace-Ex.Rout.save | 11 ++++++++---
10 files changed, 39 insertions(+), 28 deletions(-)
Title: Toolkit to Identify Candidate Synthetic Lethality
Diff between BiSEp versions 2.0 dated 2014-10-25 and 2.0.1 dated 2015-03-03
Description: Enables the user to infer potential synthetic lethal relationships
by analysing relationships between bimodally distributed gene pairs in big
gene expression datasets. Enables the user to visualise these candidate
synthetic lethal relationships.
Author: Mark Wappett
Maintainer: Mark Wappett
DESCRIPTION | 20 ++++++++++++--------
MD5 | 20 ++++++++++----------
NAMESPACE | 3 +--
R/FURE.R | 6 +++---
build/vignette.rds |binary
data/BISEP_dat.RData |binary
data/BISEP_data.RData |binary
data/FURE_data.RData |binary
data/INPUT_data.RData |binary
data/MUT_data.RData |binary
inst/doc/BiSEp.pdf |binary
11 files changed, 26 insertions(+), 23 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-11 0.2-2
2013-12-10 0.2-1
2013-04-16 0.2-0
2012-10-08 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-11 1.4-3
2012-07-12 1.4-2
2012-06-27 1.4-1
2012-05-09 1.4
2012-02-04 1.3
2011-11-13 1.2
2011-09-21 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-09 1.0.1
2014-11-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-27 0.0.6
2014-04-25 0.0.5
2014-02-23 0.0.4
2014-01-05 0.0.3
2013-11-07 0.0.2
2013-09-25 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 0.1.1
2014-11-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-20 1.05
2013-08-02 1.04
2011-12-02 1.03
2010-11-29 1.02
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-31 0.9.11
2014-10-28 0.9
2014-08-26 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-17 0.3.7
2014-07-11 0.3.3
2014-05-17 0.3
Title: Simulation of Event Histories for Multi-State Models
Diff between simMSM versions 1.1.4 dated 2015-02-02 and 1.1.41 dated 2015-03-03
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
DESCRIPTION | 10 ++---
MD5 | 4 +-
R/tolongformat.R | 106 +++++++++++++++++++++++++++----------------------------
3 files changed, 60 insertions(+), 60 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-08 0.7.2.125
2014-04-07 0.7.2.124
Title: eXtreme Gradient Boosting
Diff between xgboost versions 0.3-2 dated 2014-09-07 and 0.3-3 dated 2015-03-03
Description: Xgboost is short for eXtreme Gradient Boosting, which is an
efficient and scalable implementation of gradient boosting framework.
This package is an R wrapper of xgboost. The package includes efficient
linear model solver and tree learning algorithms. The package can automatically
do parallel computation with OpenMP, and it can be more than 10 times faster
than existing gradient boosting packages such as gbm. It supports various
objective functions, including regression, classification and ranking. The
package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen
Maintainer: Tong He
DESCRIPTION | 26 +-
MD5 | 194 +++++++++++++-------
NAMESPACE | 40 ++++
R/getinfo.xgb.DMatrix.R | 9
R/predict.xgb.Booster.R | 45 ++++
R/predict.xgb.Booster.handle.R |only
R/slice.xgb.DMatrix.R | 14 +
R/utils.R | 70 +++++--
R/xgb.DMatrix.R | 2
R/xgb.cv.R | 78 ++++++--
R/xgb.dump.R | 58 +++++-
R/xgb.importance.R |only
R/xgb.load.R | 8
R/xgb.model.dt.tree.R |only
R/xgb.plot.importance.R |only
R/xgb.plot.tree.R |only
R/xgb.save.R | 5
R/xgb.save.raw.R |only
R/xgb.train.R | 89 +++++++--
R/xgboost.R | 42 ++--
README.md | 3
build |only
data/agaricus.test.rda |binary
data/agaricus.train.rda |binary
demo/00Index | 2
demo/basic_walkthrough.R | 34 ++-
demo/boost_from_prediction.R | 2
demo/create_sparse_matrix.R |only
demo/cross_validation.R | 8
demo/custom_objective.R | 25 ++
demo/generalized_linear_model.R | 2
demo/predict_first_ntree.R | 2
demo/predict_leaf_indices.R |only
inst |only
man/agaricus.test.Rd | 7
man/agaricus.train.Rd | 5
man/getinfo.Rd | 7
man/predict-xgb.Booster-method.Rd | 14 +
man/predict-xgb.Booster.handle-method.Rd |only
man/setinfo.Rd | 7
man/slice.Rd | 7
man/xgb.DMatrix.Rd | 6
man/xgb.DMatrix.save.Rd | 3
man/xgb.cv.Rd | 23 +-
man/xgb.dump.Rd | 33 ++-
man/xgb.importance.Rd |only
man/xgb.load.Rd | 5
man/xgb.model.dt.tree.Rd |only
man/xgb.plot.importance.Rd |only
man/xgb.plot.tree.Rd |only
man/xgb.save.Rd | 5
man/xgb.save.raw.Rd |only
man/xgb.train.Rd | 86 ++++++--
man/xgboost.Rd | 33 ++-
src/Makevars | 6
src/Makevars.win | 4
src/src/data.h | 3
src/src/gbm/gblinear-inl.hpp | 42 +++-
src/src/gbm/gbm.cpp | 1
src/src/gbm/gbm.h | 54 +++++
src/src/gbm/gbtree-inl.hpp | 162 +++++++++++++++-
src/src/io/io.cpp | 51 +++++
src/src/io/page_dmatrix-inl.hpp |only
src/src/io/page_fmatrix-inl.hpp |only
src/src/io/simple_dmatrix-inl.hpp | 15 +
src/src/io/simple_fmatrix-inl.hpp | 27 +-
src/src/learner/evaluation-inl.hpp | 51 ++++-
src/src/learner/evaluation.h | 11 -
src/src/learner/learner-inl.hpp | 241 +++++++++++++++++++++----
src/src/learner/objective-inl.hpp | 30 ++-
src/src/sync |only
src/src/tree/model.h | 31 ++-
src/src/tree/param.h | 32 +++
src/src/tree/updater.cpp | 13 +
src/src/tree/updater.h | 10 +
src/src/tree/updater_basemaker-inl.hpp |only
src/src/tree/updater_colmaker-inl.hpp | 297 +++++++++++++++++++++++++------
src/src/tree/updater_distcol-inl.hpp |only
src/src/tree/updater_histmaker-inl.hpp |only
src/src/tree/updater_prune-inl.hpp | 6
src/src/tree/updater_refresh-inl.hpp | 93 +++++----
src/src/tree/updater_skmaker-inl.hpp |only
src/src/tree/updater_sync-inl.hpp |only
src/src/utils/base64.h |only
src/src/utils/bitmap.h |only
src/src/utils/group_data.h |only
src/src/utils/io.h | 110 ++++++++++-
src/src/utils/matrix_csr.h | 137 ++++++++++++++
src/src/utils/quantile.h |only
src/src/utils/thread.h |only
src/src/utils/thread_buffer.h |only
src/src/xgboost_main.cpp | 125 ++++++++++---
src/subtree |only
src/wrapper/xgboost_wrapper.cpp | 56 ++++-
src/wrapper/xgboost_wrapper.h | 38 +++
src/xgboost_R.cpp | 54 +++--
src/xgboost_R.h | 21 +-
vignettes/discoverYourData.Rmd |only
vignettes/vignette.css |only
vignettes/xgboost.Rnw | 7
vignettes/xgboostPresentation.Rmd |only
101 files changed, 2196 insertions(+), 531 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Diff between Rssa versions 0.11 dated 2014-02-05 and 0.13 dated 2015-03-03
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov
DESCRIPTION | 14 -
MD5 | 91 +++++-----
NAMESPACE | 50 +++--
R/autossa.R |only
R/cadzow.R | 20 +-
R/chankel.R | 10 -
R/common.R | 38 ++--
R/forecast.R | 65 +++++--
R/gapfill.R |only
R/hankel.R | 165 ++++++++++++++++--
R/hbhankel.R | 119 ++++++++-----
R/igapfill.R | 190 ++++++++++++++++++---
R/mhankel.R | 28 +--
R/ossa.R | 193 +++++++++++++++-------
R/parest.R | 140 ++++++++++++++-
R/plot.R | 96 ++++++----
R/plot2.R | 71 +++++---
R/plotn.R |only
R/pssa.R | 62 +++++--
R/ssa.R | 207 ++++++++++++++++-------
R/toeplitz.R | 42 +++-
R/wcor.R | 138 +++++----------
data/Barbara.rda |only
inst/CITATION | 5
man/Barbara.rd |only
man/autossa.Rd |only
man/cadzow.Rd | 5
man/calcv.Rd | 4
man/clplot.Rd |only
man/clusterify.Rd | 37 +---
man/decompose.Rd | 4
man/fossa.Rd | 18 +-
man/gapfill.Rd |only
man/grouping.auto.Rd |only
man/hankel.Rd | 11 +
man/igapfill.Rd |only
man/iossa.Rd | 57 +++++-
man/lrr.Rd | 11 -
man/parest.Rd | 11 +
man/plot.Rd | 25 ++
man/plot.reconstruct.Rd | 35 +++
man/rforecast.Rd | 16 +
man/ssa-data.Rd | 11 +
man/ssa.Rd | 33 +++
man/summarize.gaps.Rd |only
man/vforecast.Rd | 3
man/wcor.Rd | 29 +--
man/wnorm.Rd | 6
src/fft_plan.h | 4
src/hankel.c | 224 +++++++++++++++++++------
src/hbhankel.c | 421 ++++++++++++++++++++++++++++++------------------
src/masks.c |only
src/masks.h |only
53 files changed, 1916 insertions(+), 793 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Diff between mgcv versions 1.8-4 dated 2014-11-27 and 1.8-5 dated 2015-03-03
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood
Maintainer: Simon Wood
ChangeLog | 42 +
DESCRIPTION | 17
MD5 | 109 ++--
NAMESPACE | 2
R/bam.r | 42 +
R/efam.r | 92 ++-
R/fast-REML.r | 2
R/gam.fit3.r | 13
R/gam.fit4.r | 26 -
R/gamlss.r | 16
R/gamm.r | 38 +
R/jagam.r | 14
R/mgcv.r | 43 +
R/misc.r | 7
R/mvam.r | 2
R/plots.r | 10
R/smooth.r | 26 -
R/soap.r | 4
R/sparse.r | 6
inst/po |only
man/Beta.Rd | 12
man/gam.Rd | 5
man/jagam.Rd | 4
man/mgcv-parallel.Rd | 17
man/plot.gam.Rd | 4
man/predict.bam.Rd | 3
man/single.index.Rd |only
man/vis.gam.Rd | 2
man/ziplss.Rd | 2
po/R-de.po | 1213 ++++++++++++++++++++++++++++++++++++++++----------
po/R-fr.po | 1223 ++++++++++++++++++++++++++++++++++++++++-----------
po/R-ko.po |only
po/R-mgcv.pot | 61 ++
po/R-pl.po | 688 ++++++++++++++++++++--------
po/R-po.po | 1150 ++++++++++++++++++++++++++++++++++++++---------
po/de.po | 128 -----
po/fr.po | 135 -----
po/ko.po |only
po/mgcv.pot | 116 ----
po/pl.po | 127 -----
po/po.po | 131 -----
src/coxph.c | 10
src/gdi.c | 54 +-
src/general.h | 21
src/init.c | 1
src/magic.c | 9
src/mat.c | 200 ++++++--
src/matrix.c | 35 -
src/mgcv.c | 8
src/mgcv.h | 20
src/qp.c | 5
src/tprs.c | 47 -
52 files changed, 4130 insertions(+), 1812 deletions(-)
Title: Random Fields (and Bridges) Simulations
Diff between FieldSim versions 3.1.3 dated 2010-07-30 and 3.2.1 dated 2015-03-03
Description: Tools for random fields and bridges simulations.
Author: Alexandre Brouste
Maintainer: Alexandre Brouste
FieldSim-3.1.3/FieldSim/R/AllClasses.R |only
FieldSim-3.1.3/FieldSim/R/constructcovf.R |only
FieldSim-3.1.3/FieldSim/R/constructgrid.R |only
FieldSim-3.1.3/FieldSim/inst |only
FieldSim-3.1.3/FieldSim/man/constructcovf.Rd |only
FieldSim-3.1.3/FieldSim/man/constructgrid.Rd |only
FieldSim-3.1.3/FieldSim/man/visualize.Rd |only
FieldSim-3.2.1/FieldSim/COPYING | 2
FieldSim-3.2.1/FieldSim/DESCRIPTION | 23 -
FieldSim-3.2.1/FieldSim/MD5 |only
FieldSim-3.2.1/FieldSim/NAMESPACE | 24 -
FieldSim-3.2.1/FieldSim/R/C2D.R | 30 --
FieldSim-3.2.1/FieldSim/R/fieldsim.R | 96 ++++---
FieldSim-3.2.1/FieldSim/R/global.R |only
FieldSim-3.2.1/FieldSim/R/locquadvar.R |only
FieldSim-3.2.1/FieldSim/R/manifold.R | 350 +++++++++++++++++---------
FieldSim-3.2.1/FieldSim/R/midpoint.R |only
FieldSim-3.2.1/FieldSim/R/process.R |only
FieldSim-3.2.1/FieldSim/R/quadvar.R | 98 ++++---
FieldSim-3.2.1/FieldSim/R/quadvaraux.R |only
FieldSim-3.2.1/FieldSim/R/setAtlas_under.R |only
FieldSim-3.2.1/FieldSim/R/setCovf_under.R |only
FieldSim-3.2.1/FieldSim/R/visualize.R | 63 ++--
FieldSim-3.2.1/FieldSim/man/fieldsim.Rd | 64 ++--
FieldSim-3.2.1/FieldSim/man/manifold-class.Rd | 13
FieldSim-3.2.1/FieldSim/man/midpoint.Rd |only
FieldSim-3.2.1/FieldSim/man/plot-methods.Rd |only
FieldSim-3.2.1/FieldSim/man/plot.Rd |only
FieldSim-3.2.1/FieldSim/man/process-class.Rd |only
FieldSim-3.2.1/FieldSim/man/process-method.Rd |only
FieldSim-3.2.1/FieldSim/man/quadvar.Rd | 31 +-
FieldSim-3.2.1/FieldSim/man/setAtlas.Rd |only
FieldSim-3.2.1/FieldSim/man/setManifold.Rd | 33 +-
FieldSim-3.2.1/FieldSim/man/setProcess.Rd |only
FieldSim-3.2.1/FieldSim/man/setValues.Rd |only
FieldSim-3.2.1/FieldSim/man/show-methods.Rd |only
36 files changed, 506 insertions(+), 321 deletions(-)
Title: Import SPSS, Stata and SAS Files
Diff between haven versions 0.1.0 dated 2015-03-01 and 0.1.1 dated 2015-03-03
Description: Import foreign statistical formats into R via the embedded
ReadStat C library (https://github.com/WizardMac/ReadStat). Package includes
preliminary support for writing Stata and SPSS formats.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 12 +++++------
MD5 | 10 ++++-----
inst/doc/datetimes.html | 4 +--
src/readstat.h | 2 -
src/readstat_dta_write.c | 16 +++++++--------
src/readstat_sav_write.c | 49 +++++++++++++++++++++++++++++++----------------
6 files changed, 55 insertions(+), 38 deletions(-)
Title: Biological Structure Analysis
Diff between bio3d versions 2.2-1 dated 2015-02-27 and 2.2-2 dated 2015-03-03
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/atom.select.pdb.R | 17 ++++++++++-------
man/bio3d.package.Rd | 4 ++--
tests/testthat/test-atom.select.R | 13 ++++++++++++-
5 files changed, 31 insertions(+), 17 deletions(-)
Title: MCMC Sampling of Bayesian Linear Models via Summary Statistics
Diff between BayesSummaryStatLM versions 1.0 dated 2015-02-25 and 1.0-1 dated 2015-03-02
More information about BayesSummaryStatLM at CRAN
Description: Methods for generating Markov Chain Monte Carlo (MCMC) posterior samples of Bayesian linear regression model parameters that require only summary statistics of data as input. Summary statistics are useful for systems with very limited amounts of physical memory. The package provides two functions: one function that computes summary statistics of data and one function that carries out the MCMC posterior sampling for Bayesian linear regression models where summary statistics are used as input. The function read.regress.data.ff utilizes the R package 'ff' to handle data sets that are too large to fit into a user's physical memory, by reading in data in chunks.
Author: Evgeny Savel'ev, Alexey Miroshnikov, Erin Conlon
Maintainer: Evgeny Savel'ev
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/bayes.regress.Rd | 38 ++++++++++++++++++++++----------------
3 files changed, 28 insertions(+), 22 deletions(-)
Permanent link
Title: Themes for Shiny
Diff between shinythemes versions 1.0 dated 2015-01-20 and 1.0.1 dated 2015-03-02
Description: Themes for use with Shiny. Includes several Bootstrap themes
from http://bootswatch.com/, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans font),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang
shinythemes-1.0.1/shinythemes/DESCRIPTION | 6 +-
shinythemes-1.0.1/shinythemes/MD5 | 23 ++++++----
shinythemes-1.0.1/shinythemes/NEWS |only
shinythemes-1.0.1/shinythemes/R/shinytheme.R | 6 +-
shinythemes-1.0.1/shinythemes/inst/shinythemes/css |only
shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.eot |only
shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.svg |only
shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.ttf |only
shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.woff |only
shinythemes-1.0/shinythemes/inst/shinythemes/cerulean.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/cosmo.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/flatly.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/journal.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/readable.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/spacelab.min.css |only
shinythemes-1.0/shinythemes/inst/shinythemes/united.min.css |only
16 files changed, 20 insertions(+), 15 deletions(-)
Title: Determining the Best Number of Clusters in a Data Set
Diff between NbClust versions 2.0.3 dated 2014-10-15 and 2.0.4 dated 2015-03-02
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad
DESCRIPTION | 19 +++++-----
MD5 | 6 +--
R/NbClust.R | 99 +++++++++++++++++++++++++++++----------------------------
man/NbClust.Rd | 54 ++-----------------------------
4 files changed, 68 insertions(+), 110 deletions(-)
Title: Causal Mediation Analysis
Diff between mediation versions 4.4.3 dated 2014-11-23 and 4.4.4 dated 2015-03-02
Description: We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley
Maintainer: Teppei Yamamoto
ChangeLog | 4
DESCRIPTION | 10 -
MD5 | 20 +-
R/mediate.R | 7
R/multimed.R | 331 +++++++++++++++++++++++++++++++++------------
build/vignette.rds |binary
inst/doc/mediation-old.pdf |binary
inst/doc/mediation.pdf |binary
man/multimed.Rd | 19 +-
man/plot.multimed.Rd | 8 -
man/summary.multimed.Rd | 6
11 files changed, 297 insertions(+), 108 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 2.0-1570 dated 2015-02-10 and 2.1-1620 dated 2015-03-02
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 10 -
MD5 | 76 +++++------
R/bccorr.R | 4
R/condfstat.R | 109 +++++++++++++++-
R/felm.R | 264 +++++++++++++++++++++++++--------------
R/generics.R | 146 ++++++++++++++-------
R/getfe.R | 2
R/startup.R | 2
R/utils.R | 86 ++++++++++++
exec/lfescript | 21 ++-
inst/doc/CHANGELOG | 4
inst/doc/identification.pdf |binary
inst/doc/lfeguide.txt | 34 ++++-
inst/doc/lfehow.pdf |binary
inst/doc/speed.pdf |binary
man/condfstat.Rd | 48 +++++--
man/lfe-package.Rd | 4
src/demean.c | 31 ++--
src/kaczmarz.c | 13 +
src/lfe.c | 1
src/lfe.h | 3
tests/anomalies.R | 12 +
tests/anomalies.Rout.save | 296 +++++++++++++++++++++++++++++++++++++++-----
tests/bctest.Rout.save | 4
tests/cluster.Rout.save | 25 ++-
tests/comparelm.Rout.save | 11 -
tests/degenerate.Rout.save | 11 -
tests/efcheck.Rout.save | 4
tests/fourfac.Rout.save | 4
tests/interact.Rout.save | 25 ++-
tests/ivtest.R | 2
tests/ivtest.Rout.save | 44 ++++--
tests/lfetest.Rout.save | 4
tests/mlhs.Rout.save | 51 ++++---
tests/multiway.Rout.save | 11 -
tests/naomit.Rout.save | 11 -
tests/nonest.Rout.save | 4
tests/onefac.Rout.save | 4
tests/verify.Rout.save | 11 -
39 files changed, 1031 insertions(+), 361 deletions(-)
Title: Joint Analysis of Genotype and Group-Specific Variability Using
a Novel Score Test Approach to Map eQTL
Diff between JAGUAR versions 1.1 dated 2014-09-07 and 2.0 dated 2015-03-02
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya
JAGUAR-1.1/JAGUAR/man/ComputeLinMax.Rd |only
JAGUAR-1.1/JAGUAR/man/getMAX.Rd |only
JAGUAR-1.1/JAGUAR/man/mc_scoreTest.Rd |only
JAGUAR-1.1/JAGUAR/man/sim.Rd |only
JAGUAR-1.1/JAGUAR/src/calc_lin_threshold.cpp |only
JAGUAR-1.1/JAGUAR/src/jag_simulations.cpp |only
JAGUAR-1.1/JAGUAR/src/scoreTest.cpp |only
JAGUAR-2.0/JAGUAR/DESCRIPTION | 12 -
JAGUAR-2.0/JAGUAR/MD5 | 43 ++--
JAGUAR-2.0/JAGUAR/R/JAGUAR.R | 231 ++++++++++++++++++--------
JAGUAR-2.0/JAGUAR/R/RcppExports.R | 24 +-
JAGUAR-2.0/JAGUAR/README.md | 2
JAGUAR-2.0/JAGUAR/man/GENEapply.Rd | 9 -
JAGUAR-2.0/JAGUAR/man/JAGUAR-package.Rd | 16 -
JAGUAR-2.0/JAGUAR/man/ProcessJaguarResults.Rd | 12 -
JAGUAR-2.0/JAGUAR/man/RowMin.Rd |only
JAGUAR-2.0/JAGUAR/man/RowSums.Rd |only
JAGUAR-2.0/JAGUAR/man/SliceGeneData.Rd | 10 -
JAGUAR-2.0/JAGUAR/man/calcThreshold.Rd | 23 +-
JAGUAR-2.0/JAGUAR/man/gamma_test.Rd |only
JAGUAR-2.0/JAGUAR/man/getMinP.Rd |only
JAGUAR-2.0/JAGUAR/man/jag_param.Rd |only
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JAGUAR-2.0/JAGUAR/man/jaguarSIM.Rd | 12 -
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JAGUAR-2.0/JAGUAR/man/plotqtl.Rd |only
JAGUAR-2.0/JAGUAR/man/scoreTest.Rd | 12 -
JAGUAR-2.0/JAGUAR/man/snpOUT.Rd | 10 -
JAGUAR-2.0/JAGUAR/src/RcppExports.cpp | 103 +++++++----
JAGUAR-2.0/JAGUAR/src/jaguar.cpp |only
30 files changed, 319 insertions(+), 221 deletions(-)
Title: Companion Animal Population Management
Diff between capm versions 0.5 dated 2014-05-27 and 0.6.0 dated 2015-03-02
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos
DESCRIPTION | 12 +-
MD5 | 72 ++++++++--------
NAMESPACE | 2
NEWS | 30 ++++++
R/Calculate2StageSampleSize.R | 7 -
R/GraphicInterface.R | 5 -
R/PlotPopPyramid.R | 25 +++--
R/SampleSystematic.R | 4
R/capm-package.R | 6 -
README.md | 14 +--
inst/shinyApps/CalculateSampleSize/server.R | 4
inst/shinyApps/CalculateSampleSize/ui.R | 12 +-
inst/shinyApps/SelectSamplingUnits/server.R | 18 ++--
inst/shinyApps/SelectSamplingUnits/ui.R | 17 ++-
inst/shinyApps/SurveyAnalysis/server.R | 23 ++---
inst/shinyApps/SurveyAnalysis/ui.R | 3
man/Calculate2StageSampleSize.Rd | 52 ++++-------
man/CalculateGlobalSens.Rd | 51 +++--------
man/CalculateLocalSens.Rd | 37 ++------
man/CalculatePopChange.Rd | 31 ++-----
man/CalculateSimpleSampleSize.Rd | 24 +----
man/CalculateStratifiedSampleSize.Rd | 31 +------
man/DesignSurvey.Rd | 73 ++++------------
man/GraphicInterface.Rd | 16 ---
man/MapkmlPSU.Rd | 27 ++----
man/PlotGlobalSens.Rd | 27 ++----
man/PlotLocalSens.Rd | 37 ++------
man/PlotModels.Rd | 122 ++++++++++------------------
man/PlotPopPyramid.Rd | 94 ++++++---------------
man/SamplePPS.Rd | 30 ++----
man/SampleSystematic.Rd | 60 +++----------
man/SetRanges.Rd | 27 +-----
man/SolveIASA.Rd | 106 ++++++------------------
man/SolveSI.Rd | 68 ++++-----------
man/SolveTC.Rd | 61 +++-----------
man/SummarySurvey.Rd | 25 ++---
man/capm-package.Rd | 31 +++----
37 files changed, 471 insertions(+), 813 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Diff between strum versions 0.5.1 dated 2015-02-02 and 0.6 dated 2015-03-02
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
ChangeLog | 13 ++
DESCRIPTION | 10 +-
MD5 | 18 ++--
R/03strumFittedModel.R | 8 +
R/estimateParameter.R | 4
R/fitModel.R | 186 ++++++++++++++++++++++++++++++++----------
inst/doc/strum-example.pdf |binary
inst/doc/strum-intro.pdf |binary
man/strum-package.Rd | 4
man/strumFittedModel-class.Rd | 1
10 files changed, 183 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-06 1.0.2
Title: Nonparametric Estimation for Multistate Models
Diff between msSurv versions 1.1-2 dated 2012-09-18 and 1.2-1 dated 2015-03-02
Description: Nonparametric estimation for right censored, left truncated time to event data in multistate models.
Author: Nicole Ferguson
Maintainer: Guy Brock
ChangeLog | 32
DESCRIPTION | 21
MD5 | 36
NAMESPACE | 2
R/msSurv-Classes.R | 8
R/msSurv-Methods.R | 382 ++++---
R/msSurv-internal.R | 559 ++++++++---
R/msSurv-user.R | 195 +--
build |only
inst/doc/msSurv.R |only
inst/doc/msSurv.Rnw | 493 +++++++--
inst/doc/msSurv.pdf |binary
man/EntryExit.rd | 4
man/LTRCdata.Rd | 33
man/RCdata.Rd | 22
vignettes/msSurv-EntryExitDepExStateModel.pdf |only
vignettes/msSurv-NormEntryDepExPlot.pdf |only
vignettes/msSurv-NormExitDepExPlot.pdf |only
vignettes/msSurv-StateDependentCensoringIllnessDeathPlot.pdf |only
vignettes/msSurv-entryplot1.pdf |only
vignettes/msSurv-ex3plot.pdf |only
vignettes/msSurv-ex3transplot.pdf |only
vignettes/msSurv-exitplot1.pdf |only
vignettes/msSurv.Rnw | 493 +++++++--
24 files changed, 1624 insertions(+), 656 deletions(-)
Title: Sampling Methods and Distribution Functions for the Ising Model
Diff between IsingSampler versions 0.1.1 dated 2014-01-09 and 0.2 dated 2015-03-02
Description: Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
DESCRIPTION | 16 -
MD5 | 38 ++-
NAMESPACE | 25 +-
NEWS |only
R/Distribution.R | 88 ++++----
R/EstimateIsing.R |only
R/IsingSampler.R | 118 +++++------
R/LinTransform.R | 44 ++--
R/PseudoLikelihood.R |only
R/RcppExports.R | 70 ++++--
R/logisticRegressionEstimation.R |only
R/positiveGraph.R |only
man/EstimateIsing.Rd |only
man/IsingLikelihood.Rd | 62 ++---
man/IsingPL.Rd |only
man/IsingSampler-package.Rd | 168 +++++++--------
man/IsingSampler.Rd | 125 +++++------
man/IsingStateProb.Rd | 68 +++---
man/IsingSumLikelihood.Rd | 62 ++---
man/LinTransform.Rd | 132 ++++++------
src/IsingCpp_CFTP.cpp | 410 +++++++++++++++++++++++++++------------
src/Makevars.win | 6
src/PseudoLikelihood.cpp |only
src/RcppExports.cpp | 93 +++++++-
24 files changed, 906 insertions(+), 619 deletions(-)
Title: Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC
Diff between bayescount versions 0.9.9-2 dated 2014-06-22 and 0.9.99-4 dated 2015-03-02
Description: A set of functions to allow analysis of count data (such
as faecal egg count data) using Bayesian MCMC methods. Returns
information on the possible values for mean count, coefficient
of variation and zero inflation (true prevalence) present in
the data. A complete faecal egg count reduction test (FECRT)
model is implemented, which returns inference on the true
efficacy of the drug from the pre- and post-treatment data
provided, using non-parametric bootstrapping as well as using
Bayesian MCMC. Functions to perform power analyses for faecal
egg counts (including FECRT) are also provided.
Author: Matthew Denwood
Maintainer: Matthew Denwood
bayescount-0.9.9-2/bayescount/R/fecrt.R |only
bayescount-0.9.9-2/bayescount/R/zzz.R |only
bayescount-0.9.9-2/bayescount/inst/version_history.txt |only
bayescount-0.9.9-2/bayescount/man/fecrt.Rd |only
bayescount-0.9.99-4/bayescount/CHANGELOG |only
bayescount-0.9.99-4/bayescount/DESCRIPTION | 24 +-
bayescount-0.9.99-4/bayescount/MD5 | 55 +++---
bayescount-0.9.99-4/bayescount/NAMESPACE | 60 ++++++-
bayescount-0.9.99-4/bayescount/R/bayescount.R | 11 -
bayescount-0.9.99-4/bayescount/R/bayescount.single.R | 108 +++++--------
bayescount-0.9.99-4/bayescount/R/fec.power.R | 4
bayescount-0.9.99-4/bayescount/R/fecrt.analysis.R |only
bayescount-0.9.99-4/bayescount/R/fecrt.model.R |only
bayescount-0.9.99-4/bayescount/R/fecrt.power.R | 2
bayescount-0.9.99-4/bayescount/R/invisible.R | 11 -
bayescount-0.9.99-4/bayescount/R/likelihood.R | 12 +
bayescount-0.9.99-4/bayescount/R/maximise.likelihood.R | 34 ++--
bayescount-0.9.99-4/bayescount/R/run.model.R | 16 +
bayescount-0.9.99-4/bayescount/inst/CITATION | 5
bayescount-0.9.99-4/bayescount/man/bayescount.Rd | 24 --
bayescount-0.9.99-4/bayescount/man/bayescount.single.Rd | 116 ++++++++++----
bayescount-0.9.99-4/bayescount/man/fec.power.Rd | 11 -
bayescount-0.9.99-4/bayescount/man/fec.power.limits.Rd | 15 -
bayescount-0.9.99-4/bayescount/man/fecrt.analysis.Rd |only
bayescount-0.9.99-4/bayescount/man/fecrt.model.Rd |only
bayescount-0.9.99-4/bayescount/man/fecrt.power.Rd | 4
bayescount-0.9.99-4/bayescount/man/fecrt.power.limits.Rd | 14 -
bayescount-0.9.99-4/bayescount/man/likelihood.Rd | 13 -
bayescount-0.9.99-4/bayescount/man/lnormal.params.Rd | 2
bayescount-0.9.99-4/bayescount/man/maximise.likelihood.Rd | 9 -
bayescount-0.9.99-4/bayescount/man/normal.params.Rd | 2
bayescount-0.9.99-4/bayescount/man/run.model.Rd | 39 ++--
bayescount-0.9.99-4/bayescount/src/power.c | 48 +++--
33 files changed, 380 insertions(+), 259 deletions(-)
Title: Predict Protein-Protein Interactions Based on Functional and
Topological Similarities
Diff between ppiPre versions 1.6 dated 2015-01-29 and 1.7 dated 2015-03-02
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng
DESCRIPTION | 16 ++++++++--------
MD5 | 8 ++++----
NAMESPACE | 1 -
R/GOKEGGSims.r | 2 +-
man/ppiPre-package.Rd | 11 +++++------
5 files changed, 18 insertions(+), 20 deletions(-)
Title: Robust Periodogram and Periodicity Detection Methods
Diff between RobPer versions 1.2 dated 2014-10-03 and 1.2.1 dated 2015-03-02
Description: Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit. Artificial light curves can be generated using the function tsgen. For more details see Thieler, Fried and Rathjens (2013).
Author: Anita M. Thieler, Jonathan Rathjens and Roland Fried, with contributions from Brenton R. Clarke, Uwe Ligges, Matias Salibian-Barrera, Gert Willems and Victor Yohai
Maintainer: Jonathan Rathjens
RobPer-1.2.1/RobPer/DESCRIPTION | 13 ++---
RobPer-1.2.1/RobPer/MD5 | 24 ++++------
RobPer-1.2.1/RobPer/build/vignette.rds |binary
RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.Rnw | 51 ++++++++++------------
RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.pdf |binary
RobPer-1.2.1/RobPer/man/RobPer-package.rd | 8 +--
RobPer-1.2.1/RobPer/vignettes/RobPer_Art.bib | 4 -
RobPer-1.2.1/RobPer/vignettes/RobPer_Vignette.Rnw | 51 ++++++++++------------
RobPer-1.2.1/RobPer/vignettes/chart/IRWLS.tex | 2
RobPer-1.2.1/RobPer/vignettes/chart/RobPer.tex | 2
RobPer-1.2.1/RobPer/vignettes/chart/boxenecht.tex | 2
RobPer-1.2.1/RobPer/vignettes/chart/singleFun.tex | 2
RobPer-1.2/RobPer/inst/CITATION |only
RobPer-1.2/RobPer/vignettes/chart/boxenzahlen.tex |only
14 files changed, 77 insertions(+), 82 deletions(-)
Title: Companion to "Learning Statistics with R"
Diff between lsr versions 0.3.2 dated 2014-01-31 and 0.5 dated 2015-03-02
Description: A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.5. [Lecture notes] School of Psychology, University of Adelaide, Adelaide, Australia. ISBN: 978-1-326-18972-3. URL: http://health.adelaide.edu.au/psychology/ccs/teaching/lsr/.
Author: Daniel Navarro
Maintainer: Daniel Navarro
DESCRIPTION | 13 +++++++------
MD5 | 14 +++++++-------
NEWS | 6 ++++++
R/correlate.R | 20 ++++++++++++++++++--
R/maxFreq.R | 6 ++++--
R/modeOf.R | 8 +++++---
inst/CITATION | 13 +++++++------
man/lsr-package.Rd | 16 +++++++++-------
8 files changed, 63 insertions(+), 33 deletions(-)
More information about PogromcyDanych at CRAN
Permanent link
Title: Mazama Science Spatial Data Download and Utility Functions
Diff between MazamaSpatialUtils versions 0.2.1 dated 2015-02-22 and 0.2.2 dated 2015-03-01
More information about MazamaSpatialUtils at CRAN
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut]
Maintainer: Jonathan Callahan
DESCRIPTION | 6 ++--
MD5 | 26 ++++++++---------
R/MazamaSpatialUtils.R | 58 +++++++++++++++++++++++++++++++++-------
R/convertGADM.R | 17 ++++++++---
R/convertNaturalEarthAdm1.R | 3 +-
R/convertTMWorldBorders.R | 1
R/convertTMWorldBordersSimple.R | 1
R/convertUSCensusCounties.R | 24 ++++++++++++++++
R/convertWorldTimezones.R | 11 +++++++
inst/doc/introduction.html | 4 +-
man/MazamaSpatialUtils.Rd | 33 ++++++++++++++++++++++
man/codeToState.Rd | 4 +-
man/convertWorldTimezones.Rd | 12 ++++++++
man/stateToCode.Rd | 4 +-
14 files changed, 166 insertions(+), 38 deletions(-)
Permanent link
Title: Hierarchical Climate Regionalization
Diff between HiClimR versions 1.1.5 dated 2014-11-13 and 1.1.6 dated 2015-03-01
Description: A tool for hierarchical climate regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, regional linkage) to hierarchical
clustering in R (`hclust` function in `stats` library): regridding, coarsening spatial resolution,
geographic masking, data filtering by thresholds, data preprocessing (detrending, standardization,
and PCA), faster correlation function, hybrid hierarchical clustering, and cluster validation.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr
Changelog | 20 +-
DESCRIPTION | 21 +-
MD5 | 41 ++--
R/HiClimR.R | 471 +++++++++++++++++++++++-------------------------------
R/coarseR.R | 61 +++---
R/fastCor.R | 15 -
R/geogMask.R | 135 ++++++++-------
R/grid2D.R | 17 +
R/minSigCor.R | 19 +-
R/validClimR.R | 257 +++++++++++++----------------
README.md |only
inst/CITATION | 4
man/HiClimR.Rd | 158 ++++++++----------
man/TestCase.Rd | 9 -
man/WorldMask.Rd | 11 -
man/coarseR.Rd | 14 -
man/fastCor.Rd | 10 -
man/geogMask.Rd | 8
man/grid2D.Rd | 12 -
man/minSigCor.Rd | 12 -
man/validClimR.Rd | 35 +---
src/HiClimR.f90 | 8
22 files changed, 632 insertions(+), 706 deletions(-)
Title: Extra Themes, Scales and Geoms for `ggplot2`
Diff between ggthemes versions 2.1.0 dated 2014-12-18 and 2.1.2 dated 2015-03-01
Description: Some extra themes, geoms, and scales for `ggplot2`.
Author: Jeffrey B. Arnold [aut, cre],
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Justin Talbot [ctb] (Some code from the labeling package)
Maintainer: Jeffrey B. Arnold
DESCRIPTION | 19 ++-
MD5 | 164 +++++++++++++++++-----------------
NAMESPACE | 2
NEWS | 22 +++-
R/colorblind.R | 8 -
R/few.R | 10 +-
R/pander.R | 155 ++++++++++++++++++++------------
R/shapes.R | 29 ------
build/partial.rdb |binary
inst/doc/ggthemes.html | 105 ++++++++++++++-------
man/bank_slopes.Rd | 3
man/calc_pal.Rd | 3
man/calc_shape_pal.Rd | 3
man/circlefill_shape_pal.Rd | 3
man/cleveland_shape_pal.Rd | 3
man/colorblind.Rd | 9 +
man/economist_pal.Rd | 3
man/excel_pal.Rd | 3
man/few_pal.Rd | 5 -
man/fivethirtyeight_pal.Rd | 3
man/gdocs_pal.Rd | 3
man/geom_rangeframe.Rd | 3
man/geom_tufteboxplot.Rd | 3
man/ggthemes.Rd | 3
man/ggthemes_data.Rd | 3
man/hc_pal.Rd | 3
man/palette_pander.Rd | 9 +
man/range_breaks.Rd | 3
man/scale_calc.Rd | 3
man/scale_color_tableau.Rd | 3
man/scale_colour_gradient2_tableau.Rd | 3
man/scale_colour_gradient_tableau.Rd | 3
man/scale_economist.Rd | 3
man/scale_excel.Rd | 3
man/scale_few.Rd | 5 -
man/scale_fivethirtyeight.Rd | 3
man/scale_gdocs.Rd | 3
man/scale_hc.Rd | 3
man/scale_linetype_stata.Rd | 3
man/scale_pander.Rd | 6 -
man/scale_shape_calc.Rd | 3
man/scale_shape_circlefill.Rd | 3
man/scale_shape_cleveland.Rd | 3
man/scale_shape_stata.Rd | 3
man/scale_shape_tableau.Rd | 3
man/scale_shape_tremmel.Rd | 3
man/scale_solarized.Rd | 3
man/scale_stata.Rd | 3
man/scale_tufte.Rd | 3
man/scale_wsj.Rd | 3
man/show_linetypes.Rd | 3
man/show_shapes.Rd | 3
man/smart_digits.Rd | 3
man/solarized_pal.Rd | 3
man/solarized_rebase.Rd | 3
man/stat_fivenumber.Rd | 3
man/stata_linetype_pal.Rd | 3
man/stata_pal.Rd | 3
man/stata_shape_pal.Rd | 3
man/tableau_color_pal.Rd | 3
man/tableau_div_gradient_pal.Rd | 3
man/tableau_seq_gradient_pal.Rd | 3
man/tableau_shape_pal.Rd | 3
man/theme_calc.Rd | 3
man/theme_economist.Rd | 3
man/theme_excel.Rd | 3
man/theme_few.Rd | 10 +-
man/theme_fivethirtyeight.Rd | 3
man/theme_foundation.Rd | 3
man/theme_gdocs.Rd | 3
man/theme_hc.Rd | 3
man/theme_igray.Rd | 3
man/theme_pander.Rd | 15 ++-
man/theme_solarized.Rd | 3
man/theme_solid.Rd | 3
man/theme_stata.Rd | 3
man/theme_tufte.Rd | 3
man/theme_wsj.Rd | 3
man/tremmel_shape_pal.Rd | 3
man/wsj_pal.Rd | 3
vignettes/children/examples.Rmd | 19 +++
vignettes/children/install.Rmd | 5 +
vignettes/children/intro.Rmd | 40 ++++++--
83 files changed, 510 insertions(+), 316 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Diff between archivist versions 1.2 dated 2014-11-29 and 1.3 dated 2015-03-01
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek
DESCRIPTION | 6 -
MD5 | 72 +++++++++++------------
NAMESPACE | 4 -
R/addTagsRepo.R | 7 +-
R/cache.R | 4 -
R/copyToRepo.R | 20 +++---
R/createEmptyRepo.R | 8 ++
R/extractData.R | 44 +++++++-------
R/getTags.R | 31 +++++----
R/loadFromRepo.R | 38 ++++++------
R/rmFromRepo.R | 140 ++++++++++++++++++++++++++++++++++++++++++---
R/saveToRepo.R | 20 +++---
R/searchInRepo.R | 39 +++++++-----
R/setRepo.R |only
R/shinySearchInLocalRepo.R | 5 -
R/showRepo.R | 27 ++++----
R/summaryRepo.R | 25 ++++----
R/zipRepo.R | 25 +++-----
R/zzz.R | 2
man/Repository.Rd | 6 +
man/Tags.Rd | 6 +
man/addTagsRepo.Rd | 11 ++-
man/archivist-package.Rd | 6 +
man/cache.Rd | 17 +++--
man/copyToRepo.Rd | 21 ++++--
man/createEmptyRepo.Rd | 6 +
man/deleteRepo.Rd | 6 +
man/getTags.Rd | 30 ++++++---
man/loadFromRepo.Rd | 24 +++++--
man/md5hash.Rd | 6 +
man/rmFromRepo.Rd | 93 ++++++++++++++++++++++++++++-
man/saveToRepo.Rd | 19 ++++--
man/searchInRepo.Rd | 36 ++++++++---
man/setRepo.Rd |only
man/shinySearchInRepo.Rd | 12 ++-
man/showRepo.Rd | 27 ++++++--
man/summaryRepo.Rd | 25 +++++---
man/zipRepo.Rd | 29 ++++++---
38 files changed, 625 insertions(+), 272 deletions(-)
Title: Excel Connector for R
Diff between XLConnect versions 0.2-10 dated 2015-01-25 and 0.2-11 dated 2015-03-01
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons
Codec),
Stephen Colebourne [ctb, cph] (Joda-Time Java library)
Maintainer: Martin Studer
XLConnect-0.2-10/XLConnect/inst/java/XLConnect-0.2-10.jar |only
XLConnect-0.2-10/XLConnect/inst/java/poi-3.11.jar |only
XLConnect-0.2-10/XLConnect/inst/java/poi-ooxml-3.11.jar |only
XLConnect-0.2-10/XLConnect/vignettes/img/AdvancedExample1a.png |only
XLConnect-0.2-10/XLConnect/vignettes/img/AdvancedExample1b.png |only
XLConnect-0.2-10/XLConnect/vignettes/img/AdvancedExample1c.png |only
XLConnect-0.2-11/XLConnect/DESCRIPTION | 13
XLConnect-0.2-11/XLConnect/MD5 | 37 -
XLConnect-0.2-11/XLConnect/NEWS | 6
XLConnect-0.2-11/XLConnect/README.md | 4
XLConnect-0.2-11/XLConnect/data |only
XLConnect-0.2-11/XLConnect/inst/XLConnect.R | 139 ++----
XLConnect-0.2-11/XLConnect/inst/doc/XLConnect.R | 137 ++----
XLConnect-0.2-11/XLConnect/inst/doc/XLConnect.Rnw | 209 +++-------
XLConnect-0.2-11/XLConnect/inst/doc/XLConnect.pdf |binary
XLConnect-0.2-11/XLConnect/inst/doc/XLConnectImpatient.Rnw | 2
XLConnect-0.2-11/XLConnect/inst/doc/XLConnectImpatient.pdf |binary
XLConnect-0.2-11/XLConnect/inst/java/XLConnect-0.2-11.jar |only
XLConnect-0.2-11/XLConnect/inst/java/poi-3.12-beta1.jar |only
XLConnect-0.2-11/XLConnect/inst/java/poi-ooxml-3.12-beta1.jar |only
XLConnect-0.2-11/XLConnect/java/README | 4
XLConnect-0.2-11/XLConnect/man/XLConnect-package.Rd | 8
XLConnect-0.2-11/XLConnect/man/swissfranc.Rd |only
XLConnect-0.2-11/XLConnect/vignettes/XLConnect.Rnw | 209 +++-------
XLConnect-0.2-11/XLConnect/vignettes/XLConnectImpatient.Rnw | 2
25 files changed, 295 insertions(+), 475 deletions(-)
Title: Data Generation with Binary and Continuous Non-Normal Components
Diff between BinNonNor versions 1.1 dated 2015-02-01 and 1.2 dated 2015-03-01
Description: Generation of multiple binary and continuous non-normal variables simultaneously
given the marginal characteristics and association structure based on the methodology
proposed by Demirtas et al. (2012).
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/gen.Bin.NonNor.R | 19 +++++++++++--------
man/BinNonNor-package.Rd | 10 ++++++----
man/gen.Bin.NonNor.Rd | 6 ++++--
man/validation.bin.Rd | 4 ++--
man/validation.skewness.kurtosis.Rd | 8 ++++----
7 files changed, 38 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-23 1.3.50
Title: Monte Carlo for Classical Ising Model
Diff between isingLenzMC versions 0.2.1 dated 2014-05-18 and 0.2.3 dated 2015-03-01
Description: Classical Ising Model is a land mark system in statistical physics. Model explains physics of spin glasses and magnetic materials, but used in many different context for example phase transitions and neural systems. This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions.
Author: Mehmet Suzen
Maintainer: Mehmet Suzen
isingLenzMC-0.2.1/isingLenzMC/inst/effectiveErgodicity |only
isingLenzMC-0.2.1/isingLenzMC/inst/vignettes |only
isingLenzMC-0.2.3/isingLenzMC/DESCRIPTION | 10 ++++----
isingLenzMC-0.2.3/isingLenzMC/GPL-3 |only
isingLenzMC-0.2.3/isingLenzMC/LICENCE.note |only
isingLenzMC-0.2.3/isingLenzMC/MD5 | 21 +++++++++++------
isingLenzMC-0.2.3/isingLenzMC/NEWS |only
isingLenzMC-0.2.3/isingLenzMC/build |only
isingLenzMC-0.2.3/isingLenzMC/inst/CITATION |only
isingLenzMC-0.2.3/isingLenzMC/inst/doc |only
isingLenzMC-0.2.3/isingLenzMC/inst/examples |only
isingLenzMC-0.2.3/isingLenzMC/vignettes |only
12 files changed, 19 insertions(+), 12 deletions(-)
Title: Various Programming Utilities
Diff between R.utils versions 1.34.0 dated 2014-10-08 and 2.0.0 dated 2015-03-01
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.utils-1.34.0/R.utils/R/bunzip2.R |only
R.utils-1.34.0/R.utils/R/gzip.R |only
R.utils-1.34.0/R.utils/man/bunzip2.Rd |only
R.utils-1.34.0/R.utils/man/gzip.Rd |only
R.utils-1.34.0/R.utils/tests/finalizer_crash.R |only
R.utils-1.34.0/R.utils/tests/symlinks.R |only
R.utils-2.0.0/R.utils/DESCRIPTION | 16
R.utils-2.0.0/R.utils/MD5 | 240 ++++++++-----
R.utils-2.0.0/R.utils/NAMESPACE | 11
R.utils-2.0.0/R.utils/NEWS | 47 ++
R.utils-2.0.0/R.utils/R/999.NonDocumentedObjects.R | 1
R.utils-2.0.0/R.utils/R/Arguments.R | 43 ++
R.utils-2.0.0/R.utils/R/CmdArgsFunction.R | 20 -
R.utils-2.0.0/R.utils/R/Java.R | 31 -
R.utils-2.0.0/R.utils/R/OperatorDelayedAssign.R | 79 ++++
R.utils-2.0.0/R.utils/R/ProgressBar.R | 59 +--
R.utils-2.0.0/R.utils/R/attachLocally.R | 45 +-
R.utils-2.0.0/R.utils/R/captureOutput.R | 8
R.utils-2.0.0/R.utils/R/cmdArgs.R | 2
R.utils-2.0.0/R.utils/R/commandArgs.R | 48 ++
R.utils-2.0.0/R.utils/R/compressFile.R |only
R.utils-2.0.0/R.utils/R/createLink.R | 9
R.utils-2.0.0/R.utils/R/displayCode.R | 7
R.utils-2.0.0/R.utils/R/downloadFile.R | 8
R.utils-2.0.0/R.utils/R/eget.R | 16
R.utils-2.0.0/R.utils/R/fileAccess.R | 2
R.utils-2.0.0/R.utils/R/findFiles.R | 19 -
R.utils-2.0.0/R.utils/R/getPathIfEmpty.R |only
R.utils-2.0.0/R.utils/R/insert.R | 14
R.utils-2.0.0/R.utils/R/isUrl.R | 10
R.utils-2.0.0/R.utils/R/listDirectory.R | 6
R.utils-2.0.0/R.utils/R/mout.R | 63 +++
R.utils-2.0.0/R.utils/R/mpager.R |only
R.utils-2.0.0/R.utils/R/readBinFragments.R | 10
R.utils-2.0.0/R.utils/R/readTableIndex.R | 9
R.utils-2.0.0/R.utils/R/readWindowsShortcut.R | 2
R.utils-2.0.0/R.utils/R/saveObject.R | 2
R.utils-2.0.0/R.utils/R/seqToIntervals.R | 23 -
R.utils-2.0.0/R.utils/R/toCamelCase.R | 61 +--
R.utils-2.0.0/R.utils/R/unwrap.array.R | 23 -
R.utils-2.0.0/R.utils/R/use.R | 98 +++--
R.utils-2.0.0/R.utils/R/withCapture.R | 14
R.utils-2.0.0/R.utils/R/withSeed.R | 14
R.utils-2.0.0/R.utils/R/withSink.R | 9
R.utils-2.0.0/R.utils/R/withTimeout.R | 16
R.utils-2.0.0/R.utils/R/writeBinFragments.R | 13
R.utils-2.0.0/R.utils/R/zzz.R | 29 -
R.utils-2.0.0/R.utils/man/Non-documented_objects.Rd | 1
R.utils-2.0.0/R.utils/man/PERCENTLT_-PERCENT.Rd | 1
R.utils-2.0.0/R.utils/man/ProgressBar.Rd | 36 -
R.utils-2.0.0/R.utils/man/R.utils-package.Rd | 2
R.utils-2.0.0/R.utils/man/as.character.ProgressBar.Rd | 38 +-
R.utils-2.0.0/R.utils/man/captureOutput.Rd | 8
R.utils-2.0.0/R.utils/man/compressFile.Rd |only
R.utils-2.0.0/R.utils/man/createLink.Rd | 1
R.utils-2.0.0/R.utils/man/eget.Rd | 3
R.utils-2.0.0/R.utils/man/findFiles.Rd | 11
R.utils-2.0.0/R.utils/man/getBarString.ProgressBar.Rd | 38 +-
R.utils-2.0.0/R.utils/man/getReadablePathname.Arguments.Rd | 10
R.utils-2.0.0/R.utils/man/increase.ProgressBar.Rd | 42 +-
R.utils-2.0.0/R.utils/man/isDone.ProgressBar.Rd | 38 +-
R.utils-2.0.0/R.utils/man/isUrl.Rd | 2
R.utils-2.0.0/R.utils/man/listDirectory.Rd | 6
R.utils-2.0.0/R.utils/man/mout.Rd | 7
R.utils-2.0.0/R.utils/man/mpager.Rd |only
R.utils-2.0.0/R.utils/man/readTableIndex.Rd | 78 ++--
R.utils-2.0.0/R.utils/man/reset.ProgressBar.Rd | 42 +-
R.utils-2.0.0/R.utils/man/seqToIntervals.Rd | 6
R.utils-2.0.0/R.utils/man/setMaxValue.ProgressBar.Rd | 40 +-
R.utils-2.0.0/R.utils/man/setProgress.ProgressBar.Rd | 48 +-
R.utils-2.0.0/R.utils/man/setStepLength.ProgressBar.Rd | 40 +-
R.utils-2.0.0/R.utils/man/setTicks.ProgressBar.Rd | 40 +-
R.utils-2.0.0/R.utils/man/setValue.ProgressBar.Rd | 48 +-
R.utils-2.0.0/R.utils/man/update.ProgressBar.Rd | 40 +-
R.utils-2.0.0/R.utils/man/use.Rd | 8
R.utils-2.0.0/R.utils/man/withSeed.Rd | 4
R.utils-2.0.0/R.utils/man/withTimeout.Rd | 7
R.utils-2.0.0/R.utils/tests/FileProgressBar.R |only
R.utils-2.0.0/R.utils/tests/GString.R |only
R.utils-2.0.0/R.utils/tests/Java.R |only
R.utils-2.0.0/R.utils/tests/MultiVerbose.R |only
R.utils-2.0.0/R.utils/tests/NullVerbose.R |only
R.utils-2.0.0/R.utils/tests/OperatorDelayedAssign.R |only
R.utils-2.0.0/R.utils/tests/Options.R |only
R.utils-2.0.0/R.utils/tests/ProgressBar.R |only
R.utils-2.0.0/R.utils/tests/Settings.R |only
R.utils-2.0.0/R.utils/tests/System.R |only
R.utils-2.0.0/R.utils/tests/TextStatusBar.R |only
R.utils-2.0.0/R.utils/tests/VComments.R |only
R.utils-2.0.0/R.utils/tests/Verbose.R |only
R.utils-2.0.0/R.utils/tests/absolute-relative-paths.R | 3
R.utils-2.0.0/R.utils/tests/arrayIndex.R |only
R.utils-2.0.0/R.utils/tests/attachLocally.R | 18
R.utils-2.0.0/R.utils/tests/callHooks.R |only
R.utils-2.0.0/R.utils/tests/capitalize.R |only
R.utils-2.0.0/R.utils/tests/captureOutput.R | 5
R.utils-2.0.0/R.utils/tests/cmdArgs.R | 14
R.utils-2.0.0/R.utils/tests/colClasses.R |only
R.utils-2.0.0/R.utils/tests/commandArgs.R | 44 ++
R.utils-2.0.0/R.utils/tests/compressFile.R |only
R.utils-2.0.0/R.utils/tests/copyRenameFile.R | 7
R.utils-2.0.0/R.utils/tests/cout.R |only
R.utils-2.0.0/R.utils/tests/createFileAtomically.R |only
R.utils-2.0.0/R.utils/tests/dataFrame.R |only
R.utils-2.0.0/R.utils/tests/dimNA.R |only
R.utils-2.0.0/R.utils/tests/displayCode.R |only
R.utils-2.0.0/R.utils/tests/eget.R |only
R.utils-2.0.0/R.utils/tests/egsub.R | 15
R.utils-2.0.0/R.utils/tests/env.R |only
R.utils-2.0.0/R.utils/tests/extract.array.R |only
R.utils-2.0.0/R.utils/tests/fileAccess.R |only
R.utils-2.0.0/R.utils/tests/findFiles.R |only
R.utils-2.0.0/R.utils/tests/findSourceTraceback.R |only
R.utils-2.0.0/R.utils/tests/gcat.R |only
R.utils-2.0.0/R.utils/tests/getParent.R |only
R.utils-2.0.0/R.utils/tests/hpaste.R |only
R.utils-2.0.0/R.utils/tests/insert.R |only
R.utils-2.0.0/R.utils/tests/intToHex.R |only
R.utils-2.0.0/R.utils/tests/isPackageLoaded.R |only
R.utils-2.0.0/R.utils/tests/isReplicated.R |only
R.utils-2.0.0/R.utils/tests/isUrl.R |only
R.utils-2.0.0/R.utils/tests/isZero.R |only
R.utils-2.0.0/R.utils/tests/listDirectory.R |only
R.utils-2.0.0/R.utils/tests/loadObject.R |only
R.utils-2.0.0/R.utils/tests/loadToEnv.R |only
R.utils-2.0.0/R.utils/tests/mkdirs.R | 53 +-
R.utils-2.0.0/R.utils/tests/mout.R | 160 ++++----
R.utils-2.0.0/R.utils/tests/mpager.R |only
R.utils-2.0.0/R.utils/tests/pushBackupFile.R |only
R.utils-2.0.0/R.utils/tests/pushTemporaryFile.R |only
R.utils-2.0.0/R.utils/tests/readBinFragments.R |only
R.utils-2.0.0/R.utils/tests/readWindowsShellLink.R |only
R.utils-2.0.0/R.utils/tests/readWindowsShortcut.R |only
R.utils-2.0.0/R.utils/tests/resample.R |only
R.utils-2.0.0/R.utils/tests/seqToHumanReadable.R |only
R.utils-2.0.0/R.utils/tests/seqToIntervals.R |only
R.utils-2.0.0/R.utils/tests/sourceTo.R |only
R.utils-2.0.0/R.utils/tests/splitByPattern.R |only
R.utils-2.0.0/R.utils/tests/subplots.R |only
R.utils-2.0.0/R.utils/tests/symlinks,dirs.R |only
R.utils-2.0.0/R.utils/tests/symlinks,files.R |only
R.utils-2.0.0/R.utils/tests/systemR.R |only
R.utils-2.0.0/R.utils/tests/tempvar.R |only
R.utils-2.0.0/R.utils/tests/toCamelCase.R | 8
R.utils-2.0.0/R.utils/tests/use.R | 3
R.utils-2.0.0/R.utils/tests/useRepos.R |only
R.utils-2.0.0/R.utils/tests/whichVector.R |only
R.utils-2.0.0/R.utils/tests/withCapture.R | 15
R.utils-2.0.0/R.utils/tests/withLocale.R | 20 +
R.utils-2.0.0/R.utils/tests/withOptions.R | 21 +
R.utils-2.0.0/R.utils/tests/withRepos.R | 21 +
R.utils-2.0.0/R.utils/tests/withSeed.R | 69 ++-
R.utils-2.0.0/R.utils/tests/withSink.R | 134 ++++---
R.utils-2.0.0/R.utils/tests/withTimeout.R | 80 +++-
R.utils-2.0.0/R.utils/tests/wrap.array.R |only
R.utils-2.0.0/R.utils/tests/writeDataFrame.R | 50 +-
R.utils-2.0.0/R.utils/tests/zzz_finalizer_crash.R |only
157 files changed, 1662 insertions(+), 850 deletions(-)
Title: Data Generation with Poisson, Binary and Ordinal Components
Diff between PoisBinOrd versions 1.0 dated 2015-02-03 and 1.1 dated 2015-03-01
Description: Generation of multiple count, binary and ordinal variables simultaneously
given the marginal characteristics and association structure. Throughout the package,
the word 'Poisson' is used to imply count data under the assumption of Poisson distribution.
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/gen.PoisBinOrd.R | 26 +++++++++++++++-----------
R/intermediate.corr.PP.R | 6 ++++--
man/PoisBinOrd-package.Rd | 9 +++++----
man/gen.PoisBinOrd.Rd | 10 ++++++----
man/intermediate.corr.P_BO.Rd | 4 ++--
man/validation.bin.Rd | 6 +++---
8 files changed, 46 insertions(+), 37 deletions(-)
Title: Generate and Modify Synthetic Datasets
Diff between gendata versions 1.0 dated 2014-05-08 and 1.1 dated 2015-03-01
Description: Set of functions to create datasets using a correlation matrix.
Author: Francis Huang
Maintainer: Francis Huang
DESCRIPTION | 11 +++----
MD5 | 14 ++++----
R/genmvnorm.R | 77 +++++++++++++++++++++++++++++--------------------
man/dtrans.Rd | 2 -
man/gendata-package.Rd | 8 ++---
man/genmvnorm.Rd | 4 +-
man/recalib.Rd | 2 -
man/revcode.Rd | 2 -
8 files changed, 67 insertions(+), 53 deletions(-)
More information about FinCovRegularization at CRAN
Permanent link
Title: Drat R Archive Template
Diff between drat versions 0.0.1 dated 2015-02-05 and 0.0.2 dated 2015-03-01
Description: Creation and Use of R Repositories via two helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 50 +++++++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 18 +++++++----------
MD5 | 19 +++++++++---------
R/addRepo.R | 3 --
R/insertPackage.R | 52 +++++++++++++++++++++++++++++++++++++++++++--------
R/pruneRepo.R |only
README.md | 47 +++++++++++++++++++++++++++++++++++++---------
inst/TODO.md | 9 +++++++-
man/addRepo.Rd | 3 --
man/drat-package.Rd | 2 -
man/insertPackage.Rd | 7 ++++--
11 files changed, 166 insertions(+), 44 deletions(-)
Title: Quantile, Composite Quantile Regression and Regularized Versions
Diff between cqrReg versions 1.0 dated 2014-11-27 and 1.1 dated 2015-03-01
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao
cqrReg-1.0/cqrReg/R/cqr.lasso.ip.R |only
cqrReg-1.0/cqrReg/man/cqr.lasso.ip.Rd |only
cqrReg-1.1/cqrReg/DESCRIPTION | 11 ++---
cqrReg-1.1/cqrReg/MD5 | 62 ++++++++++++++++++---------------
cqrReg-1.1/cqrReg/NAMESPACE | 3 -
cqrReg-1.1/cqrReg/R/QR.admm.R | 14 ++++---
cqrReg-1.1/cqrReg/R/QR.cd.R | 11 ++++-
cqrReg-1.1/cqrReg/R/QR.ip.R | 20 +---------
cqrReg-1.1/cqrReg/R/QR.lasso.admm.R | 10 ++---
cqrReg-1.1/cqrReg/R/QR.lasso.cd.R | 12 ++++--
cqrReg-1.1/cqrReg/R/QR.lasso.ip.R | 28 +-------------
cqrReg-1.1/cqrReg/R/QR.lasso.mm.R | 13 ++++--
cqrReg-1.1/cqrReg/R/QR.mm.R | 11 ++++-
cqrReg-1.1/cqrReg/R/cqr.admm.R | 13 ++++--
cqrReg-1.1/cqrReg/R/cqr.cd.R | 9 +++-
cqrReg-1.1/cqrReg/R/cqr.fit.R |only
cqrReg-1.1/cqrReg/R/cqr.fit.lasso.R |only
cqrReg-1.1/cqrReg/R/cqr.ip.R | 34 +++---------------
cqrReg-1.1/cqrReg/R/cqr.lasso.admm.R | 13 +++---
cqrReg-1.1/cqrReg/R/cqr.lasso.cd.R | 10 +++--
cqrReg-1.1/cqrReg/R/cqr.lasso.mm.R | 11 ++++-
cqrReg-1.1/cqrReg/R/cqr.mm.R | 9 +++-
cqrReg-1.1/cqrReg/R/qrfit.R |only
cqrReg-1.1/cqrReg/R/qrfit.lasso.R |only
cqrReg-1.1/cqrReg/man/QR.ip.Rd | 12 ++++--
cqrReg-1.1/cqrReg/man/QR.lasso.ip.Rd | 13 ++++--
cqrReg-1.1/cqrReg/man/cqr.fit.Rd |only
cqrReg-1.1/cqrReg/man/cqr.fit.lasso.Rd |only
cqrReg-1.1/cqrReg/man/cqr.ip.Rd | 12 ++++--
cqrReg-1.1/cqrReg/man/qrfit.Rd |only
cqrReg-1.1/cqrReg/man/qrfit.lasso.Rd |only
cqrReg-1.1/cqrReg/src/ADMM.cpp | 17 ++++-----
cqrReg-1.1/cqrReg/src/CQRMM.cpp | 2 -
cqrReg-1.1/cqrReg/src/CQRPMM.cpp | 2 -
cqrReg-1.1/cqrReg/src/QRMM.cpp | 2 -
cqrReg-1.1/cqrReg/src/QRPCD.cpp | 2 -
cqrReg-1.1/cqrReg/src/QRPMM.cpp | 2 -
37 files changed, 177 insertions(+), 181 deletions(-)
Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 1.2.0 dated 2015-01-11 and 1.2.1 dated 2015-02-28
Description: Prediction and ranking of drug combinations based on their drug-target interaction profiles and single-drug sensitivities in a given cancer cell line or patient-derived sample.
Author: Liye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Maintainer: Jing Tang
DESCRIPTION | 17 +++-----
MD5 | 70 +++++++++++++++++-----------------
NAMESPACE | 1
R/binarizeDrugTargets.R | 8 +--
R/drawGraph.R | 70 ++++++++++++++++++----------------
R/drugRank.R | 27 ++++++-------
R/normalizeSensitivity.R | 2
R/sffsBinary.R | 2
R/sffsCategory.R | 2
R/sffsCategory1.R | 2
R/sffsCategoryWeighted.R | 2
R/sffsCategoryWeighted1.R | 2
R/targetRank.R |only
R/timma.R | 44 +++++++++------------
build/vignette.rds |binary
data/ci.rda |binary
data/davis.rda |binary
data/kiba.rda |binary
data/miller_drug_response.rda |binary
data/miller_drugs.rda |binary
data/miller_interaction_binary.rda |binary
data/miller_sensitivity.rda |binary
data/tyner_interaction_binary.rda |binary
data/tyner_interaction_multiclass.rda |binary
data/tyner_sensitivity.rda |binary
inst/doc/timma.pdf |binary
man/binarizeDrugTargets.Rd | 2
man/drawGraph.Rd | 6 +-
man/drugRank.Rd | 2
man/normalizeSensitivity.Rd | 2
man/sffsBinary.Rd | 2
man/sffsCategory.Rd | 2
man/sffsCategory1.Rd | 2
man/sffsCategoryWeighted.Rd | 2
man/sffsCategoryWeighted1.Rd | 2
man/targetRank.Rd |only
man/timma.Rd | 12 -----
37 files changed, 139 insertions(+), 144 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.0.4 dated 2015-01-06 and 1.1.0 dated 2015-02-28
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 8 ++++----
MD5 | 34 +++++++++++++++++-----------------
R/ClickyBox.r | 6 ++----
R/Create_Landscapes.r | 8 ++++++--
R/Encounter_history.R | 12 +++++++-----
R/PlottingFunctions.r | 12 +++++++++---
R/Test_Samples.r | 29 +++++++----------------------
R/Test_file.r | 23 +++++++++++++++++------
R/checkParameters.R | 20 +++++++++++++++-----
R/createGrid.R | 47 ++++++++++++++++++++++++++++++++---------------
man/create.landscapes.Rd | 12 +++++++-----
man/encounter.history.Rd | 6 ++++--
man/enter.parameters.Rd | 6 ++++--
man/find.power.Rd | 8 +++++---
man/plot.results.Rd | 31 ++++++++++++++++++++++++++++++-
man/rSPACE-package.Rd | 16 ++++++++--------
man/test_file.Rd | 6 ++++--
man/test_samples.Rd | 35 ++++++++++++++++++++++++++++++-----
18 files changed, 208 insertions(+), 111 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Diff between hypervolume versions 1.1.2 dated 2015-01-16 and 1.2 dated 2015-02-28
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 10 +++----
MD5 | 10 +++----
NAMESPACE | 11 +++++++-
R/hypervolume_plot.R | 58 +++++++++++++++++++++++++++++++++++++++++++--
man/hypervolume-package.Rd | 38 -----------------------------
man/plot.Hypervolume.Rd | 43 +++++++++++++++++++++++----------
6 files changed, 107 insertions(+), 63 deletions(-)
Title: Tools for Spatial Data
Diff between fields versions 7.1 dated 2014-05-16 and 8.2-1 dated 2015-02-28
Description: Fields is for curve, surface and function
fitting with an emphasis on splines, spatial data and spatial
statistics. The major methods include cubic, and thin plate splines,
Kriging and compact covariances for large data sets. The splines and
Kriging methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross validation
and also by restricted maximum likelihood. For Kriging there is
an easy to function that also estimates the correlation scale (range).
A major feature is that
any covariance function implemented in R and following a simple fields
format can be used for spatial prediction. There are also many useful
functions for plotting and
working with spatial data as images. This package also contains an
implementation of sparse matrix methods for large spatial data sets and
currently requires the sparse matrix (spam) package.
Use help(fields) to get started and for an
overview. The fields source code is deliberately commented and
provides useful explanations of numerical details in addition to the
manual pages. The commented source code can be viewed by expanding the
source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka
fields-7.1/fields/R/Krig.R |only
fields-8.2-1/fields/DESCRIPTION | 29 -
fields-8.2-1/fields/MD5 | 137 ++++----
fields-8.2-1/fields/NAMESPACE | 46 ++
fields-8.2-1/fields/R/Krig.family.R | 110 ++-----
fields-8.2-1/fields/R/MLESpatialProcess.R |only
fields-8.2-1/fields/R/MLESpatialProcess.fast.R |only
fields-8.2-1/fields/R/Tps.R | 25 -
fields-8.2-1/fields/R/as.image.R | 4
fields-8.2-1/fields/R/discretize.image.R | 13
fields-8.2-1/fields/R/fastTps.family.R | 12
fields-8.2-1/fields/R/fitted.Krig.R | 2
fields-8.2-1/fields/R/gcv.Krig.R | 217 +++++++-------
fields-8.2-1/fields/R/gcv.sreg.R |only
fields-8.2-1/fields/R/image.family.R | 102 ++++++
fields-8.2-1/fields/R/image.plot.R | 114 +++----
fields-8.2-1/fields/R/plot.Krig.R | 16 -
fields-8.2-1/fields/R/plot.spatialProcess.R |only
fields-8.2-1/fields/R/predict.interp.surface.R | 25 -
fields-8.2-1/fields/R/print.Krig.R | 7
fields-8.2-1/fields/R/print.summary.spatialProcess.R |only
fields-8.2-1/fields/R/printGCVWarnings.R |only
fields-8.2-1/fields/R/quickPrint.R |only
fields-8.2-1/fields/R/quilt.plot.R | 6
fields-8.2-1/fields/R/sim.Krig.R | 6
fields-8.2-1/fields/R/sim.Krig.approx.R | 6
fields-8.2-1/fields/R/sim.mKrig.approx.R | 6
fields-8.2-1/fields/R/spatialProcess.R |only
fields-8.2-1/fields/R/sreg.family.R | 163 ----------
fields-8.2-1/fields/R/stationary.image.cov.R | 1
fields-8.2-1/fields/R/summary.spatialProcess.R |only
fields-8.2-1/fields/R/surface.family.R | 8
fields-8.2-1/fields/man/Krig.Rd | 19 -
fields-8.2-1/fields/man/Krig.replicates.Rd |only
fields-8.2-1/fields/man/MLESpatialProcess.Rd |only
fields-8.2-1/fields/man/QTps.Rd | 4
fields-8.2-1/fields/man/Tps.Rd | 20 -
fields-8.2-1/fields/man/fields-internal.Rd | 30 -
fields-8.2-1/fields/man/fields.Rd | 83 +++--
fields-8.2-1/fields/man/gcv.Krig.Rd | 40 +-
fields-8.2-1/fields/man/image.plot.Rd | 105 +++---
fields-8.2-1/fields/man/mKrig.MLE.Rd | 3
fields-8.2-1/fields/man/plot.Krig.Rd | 23 +
fields-8.2-1/fields/man/quilt.plot.Rd | 4
fields-8.2-1/fields/man/sim.Krig.Rd | 62 +++-
fields-8.2-1/fields/man/sim.rf.Rd | 26 -
fields-8.2-1/fields/man/spatialProcess.Rd |only
fields-8.2-1/fields/man/summary.Krig.Rd | 10
fields-8.2-1/fields/tests/Krig.Z.test.Rout.save | 8
fields-8.2-1/fields/tests/Krig.se.W.Rout.save | 8
fields-8.2-1/fields/tests/Krig.se.grid.test.Rout.save | 14
fields-8.2-1/fields/tests/Krig.se.test.Rout.save | 14
fields-8.2-1/fields/tests/Krig.test.R | 68 +---
fields-8.2-1/fields/tests/Krig.test.Rout.save | 40 +-
fields-8.2-1/fields/tests/Krig.test.W.Rout.save | 20 +
fields-8.2-1/fields/tests/KrigGCVREML.test.R |only
fields-8.2-1/fields/tests/KrigGCVREML.test.Rout.save |only
fields-8.2-1/fields/tests/Likelihood.test.Rout.save | 8
fields-8.2-1/fields/tests/REMLest.test.R | 28 +
fields-8.2-1/fields/tests/REMLest.test.Rout.save | 10
fields-8.2-1/fields/tests/Tps.test.R | 2
fields-8.2-1/fields/tests/Tps.test.Rout.save | 19 -
fields-8.2-1/fields/tests/Wend.test.Rout.save | 8
fields-8.2-1/fields/tests/cov.test.Rout.save | 8
fields-8.2-1/fields/tests/derivative.test.Rout.save | 30 -
fields-8.2-1/fields/tests/diag.multiply.test.Rout.save | 8
fields-8.2-1/fields/tests/diagonal2.test.Rout.save | 8
fields-8.2-1/fields/tests/evlpoly.test.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.Z.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.parameters.test.Rout.save | 15
fields-8.2-1/fields/tests/mKrig.se.test.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.test.Rout.save | 8
fields-8.2-1/fields/tests/misc.test.Rout.save | 8
fields-8.2-1/fields/tests/spam.test.Rout.save | 8
fields-8.2-1/fields/tests/sreg.test.R | 6
fields-8.2-1/fields/tests/sreg.test.Rout.save | 14
fields-8.2-1/fields/tests/vgram.test.Rout.save | 8
77 files changed, 961 insertions(+), 915 deletions(-)
Title: Extreme Bounds Analysis (EBA)
Diff between ExtremeBounds versions 0.1.4.2 dated 2014-11-18 and 0.1.5 dated 2015-02-28
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac
Maintainer: Marek Hlavac
DESCRIPTION | 8 ++--
MD5 | 32 ++++++++--------
NAMESPACE | 7 ++-
R/ExtremeBounds-internal.R | 4 +-
build/vignette.rds |binary
inst/CITATION | 6 +--
inst/ChangeLog | 4 ++
inst/doc/ExtremeBounds.Rtex | 86 +++++++++++++++++++++++--------------------
inst/doc/ExtremeBounds.pdf |binary
man/ExtremeBounds.Rd | 4 +-
man/eba.Rd | 6 +--
man/hist.eba.Rd | 4 +-
man/print.eba.Rd | 4 +-
vignettes/ExtremeBounds.Rtex | 86 +++++++++++++++++++++++--------------------
vignettes/ExtremeBounds.bib | 60 +++++++++++++++++++++++-------
vignettes/naive.pdf |binary
vignettes/sophisticated.pdf |binary
17 files changed, 184 insertions(+), 127 deletions(-)
Title: Substitution and Indel Distances to Infer Evolutionary
Relationships
Diff between sidier versions 3.0 dated 2014-11-18 and 3.0.1 dated 2015-02-27
Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares
DESCRIPTION | 12 +++++------
MD5 | 22 ++++++++++-----------
NEWS | 10 +++++++++
R/double.plot.R | 30 +++++++++++++++++-----------
R/mutation.network.R | 10 +++++----
R/perc.thr.R | 9 ++++----
R/pie.network.R | 8 ++++---
R/spatial.plot.R | 51 +++++++++++++++++++++++++++++++------------------
data/ex_alignment1.rda |binary
man/double.plot.Rd | 38 ++++++++++++++++++++++++------------
man/sidier-package.Rd | 6 ++---
man/spatial.plot.Rd | 14 +++++++------
12 files changed, 131 insertions(+), 79 deletions(-)
Title: R Object-Oriented Programming with or without References
Diff between R.oo versions 1.18.0 dated 2014-02-25 and 1.19.0 dated 2015-02-27
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.oo-1.18.0/R.oo/tests/Object.finalize,reentrant.R |only
R.oo-1.19.0/R.oo/DESCRIPTION | 14 -
R.oo-1.19.0/R.oo/MD5 | 75 +++++---
R.oo-1.19.0/R.oo/NAMESPACE | 7
R.oo-1.19.0/R.oo/NEWS | 44 ++++
R.oo-1.19.0/R.oo/R/050.Object.R | 58 +-----
R.oo-1.19.0/R.oo/R/060.Class.R | 22 +-
R.oo-1.19.0/R.oo/R/999.DEPRECATED.R | 86 +++++++++
R.oo-1.19.0/R.oo/R/ASCII.R | 8
R.oo-1.19.0/R.oo/R/Class.misc.R | 55 ++----
R.oo-1.19.0/R.oo/R/Package.R | 128 --------------
R.oo-1.19.0/R.oo/R/Rdoc.R | 46 ++++-
R.oo-1.19.0/R.oo/R/abort.R | 4
R.oo-1.19.0/R.oo/R/ll.default.R | 9
R.oo-1.19.0/R.oo/R/objectSize.default.R | 8
R.oo-1.19.0/R.oo/R/objectSize.environment.R | 40 +++-
R.oo-1.19.0/R.oo/R/zzz.R | 2
R.oo-1.19.0/R.oo/man/Class.Rd | 3
R.oo-1.19.0/R.oo/man/RccViolationException.Rd | 4
R.oo-1.19.0/R.oo/man/charToInt.Rd | 2
R.oo-1.19.0/R.oo/man/gc.Object.Rd | 16 +
R.oo-1.19.0/R.oo/man/intToChar.Rd | 2
R.oo-1.19.0/R.oo/man/ll.Rd | 5
R.oo-1.19.0/R.oo/man/registerFinalizer.Object.Rd | 8
R.oo-1.19.0/R.oo/man/update.Package.Rd | 16 -
R.oo-1.19.0/R.oo/tests/ASCII.R |only
R.oo-1.19.0/R.oo/tests/BasicObject.R |only
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R.oo-1.19.0/R.oo/tests/Exception.R |only
R.oo-1.19.0/R.oo/tests/InternalErrorException.reportBug.R |only
R.oo-1.19.0/R.oo/tests/Object.R |only
R.oo-1.19.0/R.oo/tests/Object.finalize,noattach.R | 17 +
R.oo-1.19.0/R.oo/tests/Object.finalize,onoff.R | 34 ++-
R.oo-1.19.0/R.oo/tests/Object.finalize.R |only
R.oo-1.19.0/R.oo/tests/Package.R |only
R.oo-1.19.0/R.oo/tests/Package.unload.R |only
R.oo-1.19.0/R.oo/tests/StaticMethodsAndNamespaces.R | 3
R.oo-1.19.0/R.oo/tests/abort.R |only
R.oo-1.19.0/R.oo/tests/attachLocally.Object.R |only
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R.oo-1.19.0/R.oo/tests/extend.default.R |only
R.oo-1.19.0/R.oo/tests/getConstructorS3.R |only
R.oo-1.19.0/R.oo/tests/isBeingCreated.Class.R |only
R.oo-1.19.0/R.oo/tests/ll.R |only
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R.oo-1.19.0/R.oo/tests/objectSize.R |only
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R.oo-1.19.0/R.oo/tests/trim.R |only
R.oo-1.19.0/R.oo/tests/typeOfClass.R |only
R.oo-1.19.0/R.oo/tests/zzz.Object.finalize,reentrant.R |only
50 files changed, 417 insertions(+), 299 deletions(-)
Title: Basic Functions for Power Analysis
Diff between pwr versions 1.1.1 dated 2009-10-26 and 1.1-2 dated 2015-02-27
Description: Power analysis functions along the lines of Cohen (1988).
Author: Stephane Champely [aut],
Claus Ekstrom [ctb],
Peter Dalgaard [ctb],
Jeffrey Gill [ctb],
Helios De Rosario [cre]
Maintainer: Helios De Rosario
ChangeLog |only
DESCRIPTION | 32 ++++++----
MD5 |only
NAMESPACE |only
R/ES.h.R | 10 +--
R/ES.w1.R | 10 +--
R/ES.w2.R | 16 ++---
R/cohen.ES.R | 58 +++++++++---------
R/pwr.2p.test.R | 128 ++++++++++++++++++++---------------------
R/pwr.2p2n.test.R | 140 ++++++++++++++++++++++-----------------------
R/pwr.anova.test.R | 88 ++++++++++++++--------------
R/pwr.chisq.test.R | 76 ++++++++++++------------
R/pwr.f2.test.R | 86 +++++++++++++--------------
R/pwr.norm.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.p.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.r.test.R | 142 +++++++++++++++++++++++-----------------------
R/pwr.t.test.R | 144 +++++++++++++++++++++++-----------------------
R/pwr.t2n.test.R | 154 +++++++++++++++++++++++++-------------------------
man/ES.h.Rd | 72 +++++++++++------------
man/ES.w1.Rd | 64 ++++++++++----------
man/ES.w2.Rd | 66 ++++++++++-----------
man/cohen.ES.Rd | 60 ++++++++++---------
man/pwr-package.Rd | 121 +++++++++++++++++++--------------------
man/pwr.2p.test.Rd | 100 ++++++++++++++++----------------
man/pwr.2p2n.test.Rd | 103 ++++++++++++++++-----------------
man/pwr.anova.test.Rd | 94 +++++++++++++++---------------
man/pwr.chisq.test.Rd | 102 ++++++++++++++++-----------------
man/pwr.f2.test.Rd | 82 +++++++++++++-------------
man/pwr.norm.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.p.test.Rd | 107 +++++++++++++++++-----------------
man/pwr.r.test.Rd | 112 ++++++++++++++++++------------------
man/pwr.t.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.t2n.test.Rd | 94 +++++++++++++++---------------
33 files changed, 1393 insertions(+), 1376 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Diff between MAMS versions 0.3 dated 2014-05-07 and 0.4 dated 2015-02-27
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki
Maintainer: Thomas Jaki
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NAMESPACE | 9 +++++++++
R/mams.R | 12 ++++++++++--
inst/NEWS | 6 +++++-
man/generic.Rd | 8 ++------
man/mams.Rd | 9 ++++-----
man/new.bounds.Rd | 3 ++-
man/step_down_mams.Rd | 6 +++---
9 files changed, 47 insertions(+), 30 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.15 dated 2015-01-23 and 2.16 dated 2015-02-27
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.15/BDgraph/src/bdmcmc.cpp |only
BDgraph-2.16/BDgraph/DESCRIPTION | 10 -
BDgraph-2.16/BDgraph/MD5 | 58 +++---
BDgraph-2.16/BDgraph/R/bdgraph.R | 258 ++++++++-------------------
BDgraph-2.16/BDgraph/R/bdgraph.npn.R | 24 +-
BDgraph-2.16/BDgraph/R/bdgraph.sim.R | 25 +-
BDgraph-2.16/BDgraph/R/compare.R | 60 ++++--
BDgraph-2.16/BDgraph/R/plotcoda.R | 2
BDgraph-2.16/BDgraph/R/select.R | 36 ++-
BDgraph-2.16/BDgraph/man/BDgraph-internal.Rd | 2
BDgraph-2.16/BDgraph/man/BDgraph-package.Rd | 8
BDgraph-2.16/BDgraph/man/I.g.Rd | 4
BDgraph-2.16/BDgraph/man/bdgraph.Rd | 10 -
BDgraph-2.16/BDgraph/man/bdgraph.npn.Rd | 6
BDgraph-2.16/BDgraph/man/bdgraph.sim.Rd | 6
BDgraph-2.16/BDgraph/man/compare.Rd | 33 +--
BDgraph-2.16/BDgraph/man/phat.Rd | 6
BDgraph-2.16/BDgraph/man/plot.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/plot.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/plotcoda.Rd | 6
BDgraph-2.16/BDgraph/man/plotroc.Rd | 8
BDgraph-2.16/BDgraph/man/print.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/print.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/prob.Rd | 6
BDgraph-2.16/BDgraph/man/rgwish.Rd | 8
BDgraph-2.16/BDgraph/man/rwish.Rd | 6
BDgraph-2.16/BDgraph/man/select.Rd | 6
BDgraph-2.16/BDgraph/man/summary.bdgraph.Rd | 11 -
BDgraph-2.16/BDgraph/man/surveyData.Rd | 8
BDgraph-2.16/BDgraph/man/traceplot.Rd | 6
BDgraph-2.16/BDgraph/src/BDgraph.cpp |only
31 files changed, 284 insertions(+), 353 deletions(-)
Title: Apache OpenNLP Tools Interface
Diff between openNLP versions 0.2-3 dated 2014-04-19 and 0.2-4 dated 2015-02-27
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 +++++---
MD5 | 14 +++++++-------
R/chunk.R | 4 +++-
R/ner.R | 5 ++++-
R/pos.R | 4 +++-
R/sentdetect.R | 4 +++-
R/tokenize.R | 4 +++-
R/utils.R | 3 ---
8 files changed, 28 insertions(+), 18 deletions(-)
Title: Performing Continuous-Time Microsimulation
Diff between MicSim versions 1.0.6 dated 2014-07-02 and 1.0.7 dated 2015-02-27
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn
DESCRIPTION | 14 +++++++-------
MD5 | 12 ++++++------
NAMESPACE | 6 +++---
R/micSim.r | 8 ++++----
inst/NEWS.Rd | 6 ++++++
man/MicSim-package.Rd | 12 +++---------
man/micSim.Rd | 7 -------
7 files changed, 29 insertions(+), 36 deletions(-)
Title: Data Mangement for Hydrology and Beyond Using the Observations
Data Model
Diff between RObsDat versions 14.12 dated 2014-12-29 and 15.02 dated 2015-02-27
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser
DESCRIPTION | 10 ++++-----
MD5 | 36 ++++++++++++++++-----------------
R/addCV.R | 2 -
R/addDataValues.R | 2 -
R/addISOMetadata.R | 2 -
R/addOffsetType.R | 2 -
R/addQualityControlLevel.R | 2 -
R/addSite.R | 2 -
R/addSource.R | 2 -
R/addSpatialReferences.R | 2 -
R/addUnits.R | 2 -
R/addVariable.R | 2 -
R/class_stfdf.R | 4 +--
R/createST.R | 6 ++---
R/getDataValues.R | 2 -
R/h.m.R | 2 -
inst/doc/RObsDat_Einstiegstutorial.pdf |binary
inst/tests/test_various.R | 23 ++++++++++++++++++++-
vignettes/RObsDat.bib | 30 +++++++++++----------------
19 files changed, 75 insertions(+), 58 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.7.1 dated 2015-02-26 and 1.7.2 dated 2015-02-27
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
DESCRIPTION | 8 +++---
MD5 | 20 +++++++--------
NEWS | 2 -
R/Jointlcmm.R | 12 ++++++++-
R/epoce.R | 66 +++++++++++++++++++++++++++++++++++++++++++++++-----
R/plot.predictY.R | 8 +++++-
THANKS | 4 ++-
man/epoce.Rd | 3 +-
man/lcmm-package.Rd | 4 +--
src/Makevars | 13 ++++------
src/predictCont.f90 | 6 ++--
11 files changed, 109 insertions(+), 37 deletions(-)
Title: Normalisation of Psychometric Tests
Diff between NormPsy versions 1.0.2 dated 2014-11-27 and 1.0.3 dated 2015-02-27
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
R/predictMMSE.R | 6 +++---
man/NormPsy-package.Rd | 4 ++--
4 files changed, 16 insertions(+), 16 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.4 dated 2015-02-07 and 0.5 dated 2015-02-27
Description: The heterogeneous treatment effect estimation procedure
proposed by Imai and Ratkovic (2013).
The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
The package also contains the function, INT, which estimates
the average marginal treatment effect, the average treatment
combination effect, and the average marginal treatment interaction
effect proposed by Egami and Imai (2015).
Author: Naoki Egami
Maintainer: Naoki Egami
FindIt-0.4/FindIt/data/GerberGreen.tab.gz |only
FindIt-0.4/FindIt/data/LaLonde.tab.gz |only
FindIt-0.4/FindIt/data/datalist |only
FindIt-0.5/FindIt/DESCRIPTION | 20
FindIt-0.5/FindIt/MD5 | 36
FindIt-0.5/FindIt/NAMESPACE | 2
FindIt-0.5/FindIt/R/INT.R |only
FindIt-0.5/FindIt/R/SVMHet.R | 1839 ----------------------------
FindIt-0.5/FindIt/R/full.FindIt.R |only
FindIt-0.5/FindIt/R/makeallway.R |only
FindIt-0.5/FindIt/R/maketwoway.R |only
FindIt-0.5/FindIt/R/plot.PredictEffect.R |only
FindIt-0.5/FindIt/R/predict.FindIt.R |only
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FindIt-0.5/FindIt/data/LaLonde.rdata |only
FindIt-0.5/FindIt/data/Unifdata.rdata |only
FindIt-0.5/FindIt/man/FindIt.Rd | 312 ++--
FindIt-0.5/FindIt/man/GerberGreen.Rd | 103 -
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FindIt-0.5/FindIt/man/Immigration.Rd |only
FindIt-0.5/FindIt/man/LaLonde.Rd | 25
FindIt-0.5/FindIt/man/MakeTwoWay.Rd | 5
FindIt-0.5/FindIt/man/Predict.FindIt.Rd | 12
FindIt-0.5/FindIt/man/full.FindIt.Rd |only
FindIt-0.5/FindIt/man/plot.PredictFindIt.Rd | 16
28 files changed, 282 insertions(+), 2088 deletions(-)
Title: Cox Models with Dynamic Ridge Penalties
Diff between CoxRidge versions 0.9.1 dated 2013-06-26 and 0.9.2 dated 2015-02-27
Description: A package for fitting Cox models with penalized ridge-type partial likelihood. The package includes functions for fitting simple Cox models with all covariates controlled by a ridge penalty. The weight of the penalty is optimised by using a REML type-algorithm. Models with time varying effects of the covariates can also be fitted. Some of the covariates may be allowed to be fixed and thus not controlled by the penalty. There are three different penalty functions, ridge, dynamic and weighted dynamic. Time varying effects can be fitted without the need of an expanded dataset.
Author: Aris Perperoglou
Maintainer: Aris Perperoglou
DESCRIPTION | 26 ++++++++------------------
MD5 | 4 ++--
NAMESPACE | 3 +++
3 files changed, 13 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-02 1.0.6
2014-08-20 0.0.4
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.1-2 dated 2014-04-22 and 0.2-0 dated 2015-02-27
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
userfriendlyscience-0.1-2/userfriendlyscience/R/basicSPSStranslationFunctions.R |only
userfriendlyscience-0.1-2/userfriendlyscience/R/simpleFunctions.r |only
userfriendlyscience-0.1-2/userfriendlyscience/R/sysrev.r |only
userfriendlyscience-0.1-2/userfriendlyscience/man/userfriendlyscience-sysrev.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/ChangeLog | 7
userfriendlyscience-0.2-0/userfriendlyscience/DESCRIPTION | 18
userfriendlyscience-0.2-0/userfriendlyscience/MD5 | 70 +--
userfriendlyscience-0.2-0/userfriendlyscience/NAMESPACE | 39 +
userfriendlyscience-0.2-0/userfriendlyscience/NEWS | 18
userfriendlyscience-0.2-0/userfriendlyscience/R/associationMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/basicSPSStranslationFunctions.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/confIntV.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/didacticPlot.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/dlvPlot.r | 8
userfriendlyscience-0.2-0/userfriendlyscience/R/freq.r | 22
userfriendlyscience-0.2-0/userfriendlyscience/R/meanDiff.multi.r | 3
userfriendlyscience-0.2-0/userfriendlyscience/R/normalityAssessment.r | 231 +++++++++-
userfriendlyscience-0.2-0/userfriendlyscience/R/oneway.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/posthocTGH.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/regr.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/rnwString.r | 2
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosis.r | 44 -
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosisToPDF.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleInspection.r | 20
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleReliability.r | 12
userfriendlyscience-0.2-0/userfriendlyscience/R/scatterMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/userfriendlyscienceBasics.r | 40 +
userfriendlyscience-0.2-0/userfriendlyscience/data/testRetestSimData.rda |binary
userfriendlyscience-0.2-0/userfriendlyscience/inst |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrixHelperFunctions.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-confIntV.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-didacticPlot.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-dlvPlot.Rd | 4
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-freq.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-normalityAssessment.Rd | 68 ++
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-oneway.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-package.Rd | 41 +
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-posthocTGH.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-printMethods.Rd | 47 +-
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-regr.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosis.Rd | 21
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosisToPDF.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleInspection.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scatterMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-userfriendlyscienceBasics.Rd | 32 +
userfriendlyscience-0.2-0/userfriendlyscience/tests/reliabilityTest.r | 50 +-
userfriendlyscience-0.2-0/userfriendlyscience/tests/sysRevExampleTemplate.r |only
48 files changed, 640 insertions(+), 167 deletions(-)
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Diff between spatstat versions 1.40-0 dated 2014-12-31 and 1.41-1 dated 2015-02-27
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
spatstat-1.40-0/spatstat/man/markcorrint.Rd |only
spatstat-1.40-0/spatstat/src/dppll.f |only
spatstat-1.40-0/spatstat/src/inxypOld.f |only
spatstat-1.41-1/spatstat/DESCRIPTION | 22
spatstat-1.41-1/spatstat/MD5 | 590 ++++++------
spatstat-1.41-1/spatstat/NAMESPACE | 145 +++
spatstat-1.41-1/spatstat/NEWS | 878 +++++++++++++++++++
spatstat-1.41-1/spatstat/R/Iest.R | 4
spatstat-1.41-1/spatstat/R/Kcom.R | 12
spatstat-1.41-1/spatstat/R/Kest.R | 13
spatstat-1.41-1/spatstat/R/Kinhom.R | 10
spatstat-1.41-1/spatstat/R/Kmeasure.R | 89 +
spatstat-1.41-1/spatstat/R/Kmulti.R | 10
spatstat-1.41-1/spatstat/R/Kmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/Kscaled.R | 5
spatstat-1.41-1/spatstat/R/Math.im.R | 6
spatstat-1.41-1/spatstat/R/Math.linim.R |only
spatstat-1.41-1/spatstat/R/Tstat.R | 4
spatstat-1.41-1/spatstat/R/anova.ppm.R | 492 +++++-----
spatstat-1.41-1/spatstat/R/cdf.test.mppm.R | 5
spatstat-1.41-1/spatstat/R/clickpoly.R | 13
spatstat-1.41-1/spatstat/R/clickppp.R | 152 +--
spatstat-1.41-1/spatstat/R/closepairs.R | 86 +
spatstat-1.41-1/spatstat/R/clusterfunctions.R |only
spatstat-1.41-1/spatstat/R/clusterinfo.R |only
spatstat-1.41-1/spatstat/R/colourtools.R | 4
spatstat-1.41-1/spatstat/R/concom.R | 4
spatstat-1.41-1/spatstat/R/crossdistlpp.R | 6
spatstat-1.41-1/spatstat/R/deldir.R | 30
spatstat-1.41-1/spatstat/R/density.ppp.R | 81 +
spatstat-1.41-1/spatstat/R/diagnoseppm.R | 25
spatstat-1.41-1/spatstat/R/diagram.R | 51 -
spatstat-1.41-1/spatstat/R/distances.psp.R | 8
spatstat-1.41-1/spatstat/R/distbdry.R | 5
spatstat-1.41-1/spatstat/R/dummy.R | 2
spatstat-1.41-1/spatstat/R/envelope.R | 7
spatstat-1.41-1/spatstat/R/fgk3.R | 36
spatstat-1.41-1/spatstat/R/fv.R | 8
spatstat-1.41-1/spatstat/R/hierstrauss.R | 21
spatstat-1.41-1/spatstat/R/hyperframe.R | 104 +-
spatstat-1.41-1/spatstat/R/hypersub.R | 13
spatstat-1.41-1/spatstat/R/images.R | 27
spatstat-1.41-1/spatstat/R/intensity.R | 4
spatstat-1.41-1/spatstat/R/interactions.R | 8
spatstat-1.41-1/spatstat/R/iplot.R | 6
spatstat-1.41-1/spatstat/R/iplotlayered.R | 30
spatstat-1.41-1/spatstat/R/istat.R | 4
spatstat-1.41-1/spatstat/R/kppm.R | 436 +++++----
spatstat-1.41-1/spatstat/R/layered.R | 64 -
spatstat-1.41-1/spatstat/R/levelset.R | 10
spatstat-1.41-1/spatstat/R/leverage.R | 19
spatstat-1.41-1/spatstat/R/linalg.R | 5
spatstat-1.41-1/spatstat/R/linearK.R | 24
spatstat-1.41-1/spatstat/R/linearKmulti.R | 11
spatstat-1.41-1/spatstat/R/lineardisc.R | 4
spatstat-1.41-1/spatstat/R/linearmrkcon.R | 13
spatstat-1.41-1/spatstat/R/linearpcf.R | 28
spatstat-1.41-1/spatstat/R/linearpcfmulti.R | 8
spatstat-1.41-1/spatstat/R/linfun.R | 45
spatstat-1.41-1/spatstat/R/linim.R | 81 +
spatstat-1.41-1/spatstat/R/linnet.R | 231 ++++
spatstat-1.41-1/spatstat/R/lpp.R | 203 +++-
spatstat-1.41-1/spatstat/R/lppm.R | 49 -
spatstat-1.41-1/spatstat/R/markcorr.R | 66 +
spatstat-1.41-1/spatstat/R/measures.R | 10
spatstat-1.41-1/spatstat/R/mincontrast.R | 524 ++---------
spatstat-1.41-1/spatstat/R/mpl.R | 46
spatstat-1.41-1/spatstat/R/multihard.R | 17
spatstat-1.41-1/spatstat/R/multistrauss.R | 3
spatstat-1.41-1/spatstat/R/multistrhard.R | 43
spatstat-1.41-1/spatstat/R/nncorr.R | 4
spatstat-1.41-1/spatstat/R/nndistlpp.R | 15
spatstat-1.41-1/spatstat/R/options.R | 16
spatstat-1.41-1/spatstat/R/pairdistlpp.R | 4
spatstat-1.41-1/spatstat/R/pairwise.family.R | 4
spatstat-1.41-1/spatstat/R/pcf.R | 6
spatstat-1.41-1/spatstat/R/pcfmulti.R | 18
spatstat-1.41-1/spatstat/R/pcfmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/pixellate.R | 57 -
spatstat-1.41-1/spatstat/R/plot.anylist.R | 5
spatstat-1.41-1/spatstat/R/plot.owin.R | 4
spatstat-1.41-1/spatstat/R/plot.plotppm.R | 8
spatstat-1.41-1/spatstat/R/plot.ppm.R | 4
spatstat-1.41-1/spatstat/R/plot3d.R |only
spatstat-1.41-1/spatstat/R/pool.R |only
spatstat-1.41-1/spatstat/R/pp3.R | 58 -
spatstat-1.41-1/spatstat/R/ppp.R | 110 --
spatstat-1.41-1/spatstat/R/predict.ppm.R | 2
spatstat-1.41-1/spatstat/R/profilepl.R | 7
spatstat-1.41-1/spatstat/R/psp2pix.R | 59 -
spatstat-1.41-1/spatstat/R/pspcross.R | 74 +
spatstat-1.41-1/spatstat/R/psst.R | 2
spatstat-1.41-1/spatstat/R/psstG.R | 8
spatstat-1.41-1/spatstat/R/quadratmtest.R | 3
spatstat-1.41-1/spatstat/R/quadrattest.R | 23
spatstat-1.41-1/spatstat/R/quantess.R |only
spatstat-1.41-1/spatstat/R/rLGCP.R | 139 +--
spatstat-1.41-1/spatstat/R/random.R | 131 +-
spatstat-1.41-1/spatstat/R/randomNS.R | 198 ++--
spatstat-1.41-1/spatstat/R/randomlpp.R | 8
spatstat-1.41-1/spatstat/R/randommk.R | 57 -
spatstat-1.41-1/spatstat/R/rat.R | 4
spatstat-1.41-1/spatstat/R/reduceformula.R | 2
spatstat-1.41-1/spatstat/R/relrisk.ppm.R | 4
spatstat-1.41-1/spatstat/R/resid4plot.R | 34
spatstat-1.41-1/spatstat/R/residuals.mppm.R | 4
spatstat-1.41-1/spatstat/R/rhohat.R | 10
spatstat-1.41-1/spatstat/R/rlabel.R | 4
spatstat-1.41-1/spatstat/R/rmh.ppm.R | 13
spatstat-1.41-1/spatstat/R/rose.R | 2
spatstat-1.41-1/spatstat/R/segtest.R |only
spatstat-1.41-1/spatstat/R/simulatelppm.R | 11
spatstat-1.41-1/spatstat/R/slrm.R | 13
spatstat-1.41-1/spatstat/R/solist.R | 39
spatstat-1.41-1/spatstat/R/split.ppp.R | 16
spatstat-1.41-1/spatstat/R/subfits.R | 28
spatstat-1.41-1/spatstat/R/summary.im.R | 80 -
spatstat-1.41-1/spatstat/R/summary.mppm.R | 78 -
spatstat-1.41-1/spatstat/R/summary.ppm.R | 2
spatstat-1.41-1/spatstat/R/terse.R | 47 -
spatstat-1.41-1/spatstat/R/tess.R | 198 +++-
spatstat-1.41-1/spatstat/R/units.R | 8
spatstat-1.41-1/spatstat/R/util.R | 56 +
spatstat-1.41-1/spatstat/R/vcov.kppm.R | 180 ++-
spatstat-1.41-1/spatstat/R/weights.R | 132 +-
spatstat-1.41-1/spatstat/R/window.R | 84 +
spatstat-1.41-1/spatstat/R/wingeom.R | 4
spatstat-1.41-1/spatstat/R/xypolygon.R | 31
spatstat-1.41-1/spatstat/R/xysegment.R | 68 -
spatstat-1.41-1/spatstat/data/Kovesi.rda |binary
spatstat-1.41-1/spatstat/data/bdspots.rda |binary
spatstat-1.41-1/spatstat/data/bei.rda |binary
spatstat-1.41-1/spatstat/data/chicago.rda |binary
spatstat-1.41-1/spatstat/data/clmfires.rda |binary
spatstat-1.41-1/spatstat/data/datalist | 2
spatstat-1.41-1/spatstat/data/demohyper.rda |binary
spatstat-1.41-1/spatstat/data/dendrite.rda |only
spatstat-1.41-1/spatstat/data/flu.rda |binary
spatstat-1.41-1/spatstat/data/gorillas.rda |binary
spatstat-1.41-1/spatstat/data/heather.rda |binary
spatstat-1.41-1/spatstat/data/murchison.rda |binary
spatstat-1.41-1/spatstat/data/osteo.rda |binary
spatstat-1.41-1/spatstat/data/pyramidal.rda |binary
spatstat-1.41-1/spatstat/data/spiders.rda |only
spatstat-1.41-1/spatstat/data/waterstriders.rda |binary
spatstat-1.41-1/spatstat/demo/data.R | 9
spatstat-1.41-1/spatstat/demo/spatstat.R | 4
spatstat-1.41-1/spatstat/inst/doc/datasets.R | 164 ++-
spatstat-1.41-1/spatstat/inst/doc/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/inst/doc/datasets.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/getstart.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/replicated.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/shapefiles.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/updates.R | 4
spatstat-1.41-1/spatstat/inst/doc/updates.Rnw | 250 +++++
spatstat-1.41-1/spatstat/inst/doc/updates.pdf |binary
spatstat-1.41-1/spatstat/inst/rawdata/osteo |only
spatstat-1.41-1/spatstat/inst/rawdata/sandholes |only
spatstat-1.41-1/spatstat/man/Emark.Rd | 10
spatstat-1.41-1/spatstat/man/K3est.Rd | 11
spatstat-1.41-1/spatstat/man/Kmark.Rd |only
spatstat-1.41-1/spatstat/man/Math.im.Rd | 4
spatstat-1.41-1/spatstat/man/Math.linim.Rd |only
spatstat-1.41-1/spatstat/man/anova.lppm.Rd | 29
spatstat-1.41-1/spatstat/man/anova.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/anova.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/anylist.Rd | 4
spatstat-1.41-1/spatstat/man/as.function.im.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.linim.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.psp.Rd |only
spatstat-1.41-1/spatstat/man/as.lpp.Rd | 7
spatstat-1.41-1/spatstat/man/as.solist.Rd | 4
spatstat-1.41-1/spatstat/man/cauchy.estK.Rd | 6
spatstat-1.41-1/spatstat/man/cauchy.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/cdf.test.Rd | 4
spatstat-1.41-1/spatstat/man/clickbox.Rd | 5
spatstat-1.41-1/spatstat/man/clickdist.Rd |only
spatstat-1.41-1/spatstat/man/clickpoly.Rd | 11
spatstat-1.41-1/spatstat/man/clickppp.Rd | 15
spatstat-1.41-1/spatstat/man/closepairs.Rd | 12
spatstat-1.41-1/spatstat/man/clusterfield.Rd |only
spatstat-1.41-1/spatstat/man/clusterfit.Rd |only
spatstat-1.41-1/spatstat/man/clusterkernel.Rd |only
spatstat-1.41-1/spatstat/man/clusterradius.Rd |only
spatstat-1.41-1/spatstat/man/coef.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/colourtools.Rd | 2
spatstat-1.41-1/spatstat/man/crossdist.psp.Rd | 10
spatstat-1.41-1/spatstat/man/delaunay.Rd | 4
spatstat-1.41-1/spatstat/man/delaunay.distance.Rd | 3
spatstat-1.41-1/spatstat/man/delaunay.network.Rd |only
spatstat-1.41-1/spatstat/man/dendrite.Rd |only
spatstat-1.41-1/spatstat/man/density.ppp.Rd | 9
spatstat-1.41-1/spatstat/man/diagnose.ppm.Rd | 23
spatstat-1.41-1/spatstat/man/dirichlet.vertices.Rd | 36
spatstat-1.41-1/spatstat/man/fitted.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/identify.ppp.Rd | 6
spatstat-1.41-1/spatstat/man/identify.psp.Rd | 4
spatstat-1.41-1/spatstat/man/improve.kppm.Rd | 2
spatstat-1.41-1/spatstat/man/integral.im.Rd | 33
spatstat-1.41-1/spatstat/man/integral.linim.Rd |only
spatstat-1.41-1/spatstat/man/integral.msr.Rd | 11
spatstat-1.41-1/spatstat/man/intersect.tess.Rd | 15
spatstat-1.41-1/spatstat/man/iplot.Rd | 14
spatstat-1.41-1/spatstat/man/is.marked.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppp.Rd | 8
spatstat-1.41-1/spatstat/man/kppm.Rd | 37
spatstat-1.41-1/spatstat/man/lgcp.estK.Rd | 9
spatstat-1.41-1/spatstat/man/lgcp.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/linearKcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKinhom.Rd | 6
spatstat-1.41-1/spatstat/man/linearpcfcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfinhom.Rd | 5
spatstat-1.41-1/spatstat/man/linfun.Rd | 30
spatstat-1.41-1/spatstat/man/linim.Rd | 3
spatstat-1.41-1/spatstat/man/linnet.Rd | 25
spatstat-1.41-1/spatstat/man/logLik.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/lpp.Rd | 5
spatstat-1.41-1/spatstat/man/markcorr.Rd | 6
spatstat-1.41-1/spatstat/man/marks.tess.Rd |only
spatstat-1.41-1/spatstat/man/matclust.estK.Rd | 11
spatstat-1.41-1/spatstat/man/matclust.estpcf.Rd | 9
spatstat-1.41-1/spatstat/man/methods.linfun.Rd | 5
spatstat-1.41-1/spatstat/man/methods.linnet.Rd | 50 -
spatstat-1.41-1/spatstat/man/methods.lppm.Rd | 4
spatstat-1.41-1/spatstat/man/mppm.Rd | 1
spatstat-1.41-1/spatstat/man/nestsplit.Rd |only
spatstat-1.41-1/spatstat/man/nndist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/osteo.Rd | 2
spatstat-1.41-1/spatstat/man/pairdist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/panel.contour.Rd | 2
spatstat-1.41-1/spatstat/man/paracou.Rd | 3
spatstat-1.41-1/spatstat/man/pixellate.Rd | 1
spatstat-1.41-1/spatstat/man/pixellate.psp.Rd | 18
spatstat-1.41-1/spatstat/man/plot.anylist.Rd | 12
spatstat-1.41-1/spatstat/man/plot.cdftest.Rd | 4
spatstat-1.41-1/spatstat/man/plot.fv.Rd | 4
spatstat-1.41-1/spatstat/man/plot.hyperframe.Rd | 11
spatstat-1.41-1/spatstat/man/plot.im.Rd | 11
spatstat-1.41-1/spatstat/man/plot.kppm.Rd | 39
spatstat-1.41-1/spatstat/man/plot.linim.Rd | 10
spatstat-1.41-1/spatstat/man/plot.linnet.Rd | 9
spatstat-1.41-1/spatstat/man/plot.listof.Rd | 12
spatstat-1.41-1/spatstat/man/plot.lpp.Rd | 11
spatstat-1.41-1/spatstat/man/plot.pp3.Rd | 68 -
spatstat-1.41-1/spatstat/man/plot.yardstick.Rd | 32
spatstat-1.41-1/spatstat/man/pool.Rd | 3
spatstat-1.41-1/spatstat/man/pool.anylist.Rd |only
spatstat-1.41-1/spatstat/man/pool.fv.Rd |only
spatstat-1.41-1/spatstat/man/pool.rat.Rd | 1
spatstat-1.41-1/spatstat/man/predict.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/print.owin.Rd | 3
spatstat-1.41-1/spatstat/man/quadrat.test.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/quantess.Rd |only
spatstat-1.41-1/spatstat/man/rCauchy.Rd | 68 +
spatstat-1.41-1/spatstat/man/rGaussPoisson.Rd | 8
spatstat-1.41-1/spatstat/man/rMatClust.Rd | 55 -
spatstat-1.41-1/spatstat/man/rMaternI.Rd | 8
spatstat-1.41-1/spatstat/man/rMaternII.Rd | 8
spatstat-1.41-1/spatstat/man/rNeymanScott.Rd | 33
spatstat-1.41-1/spatstat/man/rPoissonCluster.Rd | 41
spatstat-1.41-1/spatstat/man/rSSI.Rd | 8
spatstat-1.41-1/spatstat/man/rThomas.Rd | 47 -
spatstat-1.41-1/spatstat/man/rVarGamma.Rd | 69 -
spatstat-1.41-1/spatstat/man/rcell.Rd | 8
spatstat-1.41-1/spatstat/man/residuals.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/rjitter.Rd | 7
spatstat-1.41-1/spatstat/man/rmpoint.Rd | 24
spatstat-1.41-1/spatstat/man/rmpoispp.Rd | 22
spatstat-1.41-1/spatstat/man/rpoint.Rd | 7
spatstat-1.41-1/spatstat/man/rpoislpp.Rd | 5
spatstat-1.41-1/spatstat/man/rpoispp.Rd | 39
spatstat-1.41-1/spatstat/man/rpoisppOnLines.Rd | 2
spatstat-1.41-1/spatstat/man/rstrat.Rd | 7
spatstat-1.41-1/spatstat/man/rsyst.Rd | 8
spatstat-1.41-1/spatstat/man/rthin.Rd | 7
spatstat-1.41-1/spatstat/man/runifdisc.Rd | 7
spatstat-1.41-1/spatstat/man/runifpoint.Rd | 8
spatstat-1.41-1/spatstat/man/segregation.test.Rd |only
spatstat-1.41-1/spatstat/man/selfcut.psp.Rd |only
spatstat-1.41-1/spatstat/man/simulate.kppm.Rd | 8
spatstat-1.41-1/spatstat/man/simulate.lppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.slrm.Rd | 7
spatstat-1.41-1/spatstat/man/solapply.Rd |only
spatstat-1.41-1/spatstat/man/solist.Rd | 27
spatstat-1.41-1/spatstat/man/solutionset.Rd | 27
spatstat-1.41-1/spatstat/man/spatstat-internal.Rd | 99 +-
spatstat-1.41-1/spatstat/man/spatstat-package.Rd | 22
spatstat-1.41-1/spatstat/man/spatstat.options.Rd | 12
spatstat-1.41-1/spatstat/man/spiders.Rd |only
spatstat-1.41-1/spatstat/man/split.ppp.Rd | 13
spatstat-1.41-1/spatstat/man/spokes.Rd | 12
spatstat-1.41-1/spatstat/man/subfits.Rd | 1
spatstat-1.41-1/spatstat/man/subset.hyperframe.Rd |only
spatstat-1.41-1/spatstat/man/tess.Rd | 28
spatstat-1.41-1/spatstat/man/thomas.estK.Rd | 27
spatstat-1.41-1/spatstat/man/thomas.estpcf.Rd | 29
spatstat-1.41-1/spatstat/man/vargamma.estK.Rd | 19
spatstat-1.41-1/spatstat/man/vargamma.estpcf.Rd | 19
spatstat-1.41-1/spatstat/man/vcov.kppm.Rd | 7
spatstat-1.41-1/spatstat/man/vcov.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/vertices.Rd | 13
spatstat-1.41-1/spatstat/man/waka.Rd | 2
spatstat-1.41-1/spatstat/src/close3pair.c | 8
spatstat-1.41-1/spatstat/src/closefuns.h | 162 ++-
spatstat-1.41-1/spatstat/src/closepair.c | 19
spatstat-1.41-1/spatstat/src/seg2pix.c | 151 ---
spatstat-1.41-1/spatstat/src/seg2pix.h |only
spatstat-1.41-1/spatstat/tests/alltests.R | 59 -
spatstat-1.41-1/spatstat/vignettes/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/vignettes/packagesizes.txt | 2
spatstat-1.41-1/spatstat/vignettes/updates.Rnw | 250 +++++
315 files changed, 6877 insertions(+), 3297 deletions(-)
Title: Rcpp Integration for the Eigen Templated Linear Algebra Library
Diff between RcppEigen versions 0.3.2.3.0 dated 2014-12-23 and 0.3.2.4.0 dated 2015-02-27
Description: R and Eigen integration using Rcpp.
Eigen is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on Lapack and level-3 BLAS.
The RcppEigen package includes the header files from the Eigen C++
template library (currently version 3.2.3). Thus users do not need to
install Eigen itself in order to use RcppEigen.
Since version 3.1.1, Eigen is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/Core/Product.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/CoreIterators.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h |only
RcppEigen-0.3.2.4.0/RcppEigen/ChangeLog | 24 +++
RcppEigen-0.3.2.4.0/RcppEigen/DESCRIPTION | 12 -
RcppEigen-0.3.2.4.0/RcppEigen/MD5 | 36 ++---
RcppEigen-0.3.2.4.0/RcppEigen/R/RcppEigen.package.skeleton.R | 45 ++++--
RcppEigen-0.3.2.4.0/RcppEigen/README.md | 25 +--
RcppEigen-0.3.2.4.0/RcppEigen/inst/NEWS.Rd | 11 +
RcppEigen-0.3.2.4.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 70 ----------
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 11 -
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 5
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars.win | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/rcppeigen_hello_world.Rd |only
21 files changed, 118 insertions(+), 143 deletions(-)
Title: Multi-Analysis Distance Sampling
Diff between mads versions 0.1.1 dated 2014-12-23 and 0.1.2 dated 2015-02-27
Description: Performs distance sampling analyses on a number of species
accounting for unidentified sightings, model uncertainty and covariate
uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 11 +++++++++++
R/calculate.dht.R | 5 +++--
R/check.bootstrap.options.r | 6 +++---
R/check.ddf.models.R | 1 -
R/execute.multi.analysis.R | 9 +++++----
R/fit.ddf.models.R | 19 ++++++++++---------
R/mae.warning.R | 6 +++---
R/process.warnings.R | 5 ++++-
10 files changed, 52 insertions(+), 36 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Diff between geostatsp versions 1.1.9 dated 2015-01-23 and 1.2.1 dated 2015-02-27
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown
Maintainer: Patrick Brown
geostatsp-1.1.9/geostatsp/src/maternLogLgr.c |only
geostatsp-1.2.1/geostatsp/DESCRIPTION | 12
geostatsp-1.2.1/geostatsp/MD5 | 100 ++-
geostatsp-1.2.1/geostatsp/NAMESPACE | 9
geostatsp-1.2.1/geostatsp/R/RFsimulate.R | 45 -
geostatsp-1.2.1/geostatsp/R/excProb.R | 2
geostatsp-1.2.1/geostatsp/R/informationLgm.R | 72 +-
geostatsp-1.2.1/geostatsp/R/krige.R | 150 +++-
geostatsp-1.2.1/geostatsp/R/lgm.R | 55 -
geostatsp-1.2.1/geostatsp/R/lgm.Raster.R | 2
geostatsp-1.2.1/geostatsp/R/loglikGmrf.R | 321 ++++++++--
geostatsp-1.2.1/geostatsp/R/loglikLgm.R | 675 ++++++++++++----------
geostatsp-1.2.1/geostatsp/R/matern.R | 17
geostatsp-1.2.1/geostatsp/R/maternGmrfPrec.R | 17
geostatsp-1.2.1/geostatsp/R/param.R | 11
geostatsp-1.2.1/geostatsp/R/profLlgm.R | 150 ++--
geostatsp-1.2.1/geostatsp/R/spdfToBrick.R |only
geostatsp-1.2.1/geostatsp/R/variog.R | 8
geostatsp-1.2.1/geostatsp/data/datalist | 4
geostatsp-1.2.1/geostatsp/data/murder.RData |binary
geostatsp-1.2.1/geostatsp/data/torontoPop.RData |binary
geostatsp-1.2.1/geostatsp/inst/extdata |only
geostatsp-1.2.1/geostatsp/man/krige.Rd | 22
geostatsp-1.2.1/geostatsp/man/likfitLgm.Rd | 37 -
geostatsp-1.2.1/geostatsp/man/maternGmrfPrec.Rd | 10
geostatsp-1.2.1/geostatsp/man/murder.Rd | 199 ++++++
geostatsp-1.2.1/geostatsp/man/profLlgm.Rd | 2
geostatsp-1.2.1/geostatsp/man/stackRasterList.Rd | 19
geostatsp-1.2.1/geostatsp/man/variog.Rd | 12
geostatsp-1.2.1/geostatsp/src/geostatsp.h | 16
geostatsp-1.2.1/geostatsp/src/matern.c | 20
geostatsp-1.2.1/geostatsp/src/maternLogL.c | 203 +++---
geostatsp-1.2.1/geostatsp/src/maternLogLopt.c |only
geostatsp-1.2.1/geostatsp/src/sparseLogL.c |only
geostatsp-1.2.1/geostatsp/tests/RFsimulate.R | 39 -
geostatsp-1.2.1/geostatsp/tests/krige.R | 11
geostatsp-1.2.1/geostatsp/tests/lgm.R | 14
geostatsp-1.2.1/geostatsp/tests/lgmRaster.R | 76 --
geostatsp-1.2.1/geostatsp/tests/likfitLgm.R | 80 ++
geostatsp-1.2.1/geostatsp/tests/maternGmrfPrec.R | 4
geostatsp-1.2.1/geostatsp/tests/profLlgm.R | 111 ++-
geostatsp-1.2.1/geostatsp/tests/stackRasterList.R |only
42 files changed, 1635 insertions(+), 890 deletions(-)
Title: Distance Sampling Simulations
Diff between DSsim versions 1.0.2 dated 2014-12-23 and 1.0.3 dated 2015-02-27
Description: Performs distance sampling simulations. It repeatedly
generates instances of a user defined population within a given survey
region, generates realisations of a survey design (currently these must
be pre-generated using Distance software) and simulates the detection
process. The data are then analysed so that the results can be compared for
accuracy and precision across all replications. This will allow users to
select survey designs which will give them the best accuracy and precision
given their expectations about population distribution. Any uncertainty in
population distribution or population parameters can be included by running
the different survey designs for a number of different population
descriptions. An example simulation can be found in the help file
for make.simulation.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 +-
MD5 | 37 ++++-----
NEWS | 71 +++++++++++-------
R/Class.Constructors.R | 20 +++--
R/DDF.Analysis.R | 14 +--
R/Density.R | 156 +++++++++++++++++++++++++++++------------
R/LT.Design.R | 10 +-
R/Population.Description.R | 4 -
R/Region.R | 29 ++++---
R/Simulation.R | 2
R/add.dist.error.R | 2
R/check.intersection.R | 4 -
R/get.sampler.info.R | 4 -
R/is.gap.R | 2
R/single.simulation.loop.R | 10 --
inst/tests/test_Constructors.R |only
man/Density-class.Rd | 16 ++--
man/Region-class.Rd | 11 +-
man/make.density.Rd | 10 ++
man/make.simulation.Rd | 2
20 files changed, 256 insertions(+), 156 deletions(-)
Title: Biological Structure Analysis
Diff between bio3d versions 2.1-3 dated 2014-10-27 and 2.2-1 dated 2015-02-27
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant
bio3d-2.1-3/bio3d/R/cmap.filter.R |only
bio3d-2.1-3/bio3d/R/combine.sel.R |only
bio3d-2.1-3/bio3d/R/dssp.trj.R |only
bio3d-2.1-3/bio3d/R/ide.filter.R |only
bio3d-2.1-3/bio3d/R/pdbs.filter.R |only
bio3d-2.1-3/bio3d/R/plot.bio3d.R |only
bio3d-2.1-3/bio3d/R/plot.dccm2.R |only
bio3d-2.1-3/bio3d/R/rmsd.filter.R |only
bio3d-2.1-3/bio3d/data/aa.mass.rda |only
bio3d-2.1-3/bio3d/man/aa.mass.Rd |only
bio3d-2.1-3/bio3d/man/cmap.filter.Rd |only
bio3d-2.1-3/bio3d/man/combine.sel.Rd |only
bio3d-2.1-3/bio3d/man/dssp.pdbs.Rd |only
bio3d-2.1-3/bio3d/man/dssp.trj.Rd |only
bio3d-2.1-3/bio3d/man/ide.filter.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.enma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.nma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.pca.Rd |only
bio3d-2.1-3/bio3d/man/pdbs.filter.Rd |only
bio3d-2.1-3/bio3d/man/plot.blast.Rd |only
bio3d-2.1-3/bio3d/man/rmsd.filter.Rd |only
bio3d-2.1-3/bio3d/tests/test-all.R |only
bio3d-2.2-1/bio3d/DESCRIPTION | 6
bio3d-2.2-1/bio3d/MD5 | 453 ++++++++++----------
bio3d-2.2-1/bio3d/NAMESPACE | 100 ++++
bio3d-2.2-1/bio3d/NEWS | 78 ++-
bio3d-2.2-1/bio3d/R/aa2mass.R | 44 +
bio3d-2.2-1/bio3d/R/aa321.R | 43 +
bio3d-2.2-1/bio3d/R/amsm.xyz.R | 2
bio3d-2.2-1/bio3d/R/as.fasta.R |only
bio3d-2.2-1/bio3d/R/as.pdb.R |only
bio3d-2.2-1/bio3d/R/as.pdb.mol2.R |only
bio3d-2.2-1/bio3d/R/as.pdb.prmtop.R |only
bio3d-2.2-1/bio3d/R/as.select.R |only
bio3d-2.2-1/bio3d/R/as.xyz.R | 2
bio3d-2.2-1/bio3d/R/atom.select.R | 287 ------------
bio3d-2.2-1/bio3d/R/atom.select.pdb.R |only
bio3d-2.2-1/bio3d/R/atom.select.prmtop.R |only
bio3d-2.2-1/bio3d/R/basename.pdb.R |only
bio3d-2.2-1/bio3d/R/binding.site.R | 164 ++++---
bio3d-2.2-1/bio3d/R/biounit.R |only
bio3d-2.2-1/bio3d/R/bounds.sse.R |only
bio3d-2.2-1/bio3d/R/cat.pdb.R |only
bio3d-2.2-1/bio3d/R/chain.pdb.R | 15
bio3d-2.2-1/bio3d/R/clean.pdb.R |only
bio3d-2.2-1/bio3d/R/cmap.R | 12
bio3d-2.2-1/bio3d/R/cmap.pdb.R |only
bio3d-2.2-1/bio3d/R/cna.dccm.R | 10
bio3d-2.2-1/bio3d/R/cna.ensmb.R | 2
bio3d-2.2-1/bio3d/R/cnapath.R |only
bio3d-2.2-1/bio3d/R/com.R | 31 -
bio3d-2.2-1/bio3d/R/com.pdb.R |only
bio3d-2.2-1/bio3d/R/com.xyz.R | 23 -
bio3d-2.2-1/bio3d/R/combine.select.R |only
bio3d-2.2-1/bio3d/R/convert.pdb.R | 38 +
bio3d-2.2-1/bio3d/R/core.find.R | 114 +++--
bio3d-2.2-1/bio3d/R/dccm.pca.R | 38 +
bio3d-2.2-1/bio3d/R/dm.R | 36 -
bio3d-2.2-1/bio3d/R/dm.xyz.R | 77 +++
bio3d-2.2-1/bio3d/R/dssp.R | 274 ------------
bio3d-2.2-1/bio3d/R/dssp.pdb.R |only
bio3d-2.2-1/bio3d/R/dssp.pdbs.R | 47 +-
bio3d-2.2-1/bio3d/R/dssp.xyz.R |only
bio3d-2.2-1/bio3d/R/filter.cmap.R |only
bio3d-2.2-1/bio3d/R/filter.dccm.R | 7
bio3d-2.2-1/bio3d/R/filter.identity.R |only
bio3d-2.2-1/bio3d/R/filter.rmsd.R |only
bio3d-2.2-1/bio3d/R/fit.xyz.R | 36 -
bio3d-2.2-1/bio3d/R/geostas.R | 188 ++++++--
bio3d-2.2-1/bio3d/R/hmmer.R | 9
bio3d-2.2-1/bio3d/R/inspect.connectivity.R | 7
bio3d-2.2-1/bio3d/R/is.gap.R | 8
bio3d-2.2-1/bio3d/R/mktrj.R | 5
bio3d-2.2-1/bio3d/R/mktrj.enma.R | 30 -
bio3d-2.2-1/bio3d/R/mktrj.nma.R | 16
bio3d-2.2-1/bio3d/R/mktrj.pca.R | 14
bio3d-2.2-1/bio3d/R/mustang.R | 30 +
bio3d-2.2-1/bio3d/R/nma.pdbs.R | 40 -
bio3d-2.2-1/bio3d/R/pca.xyz.R | 37 +
bio3d-2.2-1/bio3d/R/pdb2aln.R | 37 -
bio3d-2.2-1/bio3d/R/pdb2aln.ind.R | 24 -
bio3d-2.2-1/bio3d/R/pdb2sse.R |only
bio3d-2.2-1/bio3d/R/pdbfit.R | 26 +
bio3d-2.2-1/bio3d/R/pdbsplit.R | 29 -
bio3d-2.2-1/bio3d/R/plot.cmap.R |only
bio3d-2.2-1/bio3d/R/plot.enma.R | 129 +++--
bio3d-2.2-1/bio3d/R/plot.fluct.R |only
bio3d-2.2-1/bio3d/R/plot.geostas.R |only
bio3d-2.2-1/bio3d/R/plot.pca.R | 49 +-
bio3d-2.2-1/bio3d/R/plotb3.R |only
bio3d-2.2-1/bio3d/R/print.fasta.R | 30 +
bio3d-2.2-1/bio3d/R/print.geostas.R |only
bio3d-2.2-1/bio3d/R/print.pdb.R | 4
bio3d-2.2-1/bio3d/R/print.prmtop.R |only
bio3d-2.2-1/bio3d/R/read.all.R | 2
bio3d-2.2-1/bio3d/R/read.crd.R | 56 --
bio3d-2.2-1/bio3d/R/read.crd.amber.R |only
bio3d-2.2-1/bio3d/R/read.crd.charmm.R |only
bio3d-2.2-1/bio3d/R/read.dcd.R | 6
bio3d-2.2-1/bio3d/R/read.fasta.pdb.R | 80 ++-
bio3d-2.2-1/bio3d/R/read.mol2.R | 100 +++-
bio3d-2.2-1/bio3d/R/read.pdb.R | 150 +++++-
bio3d-2.2-1/bio3d/R/read.prmtop.R |only
bio3d-2.2-1/bio3d/R/rmsf.R | 13
bio3d-2.2-1/bio3d/R/seq2aln.R | 45 -
bio3d-2.2-1/bio3d/R/seqaln.R | 15
bio3d-2.2-1/bio3d/R/seqaln.pair.R | 12
bio3d-2.2-1/bio3d/R/seqbind.R | 9
bio3d-2.2-1/bio3d/R/store.atom.R | 6
bio3d-2.2-1/bio3d/R/summary.cnapath.R |only
bio3d-2.2-1/bio3d/R/summary.pdb.R | 72 ++-
bio3d-2.2-1/bio3d/R/trim.pdb.R | 154 ++----
bio3d-2.2-1/bio3d/R/trim.pdbs.R |only
bio3d-2.2-1/bio3d/R/trim.xyz.R |only
bio3d-2.2-1/bio3d/R/unbound.R | 7
bio3d-2.2-1/bio3d/R/view.cnapath.R |only
bio3d-2.2-1/bio3d/R/wrap.tor.R | 9
bio3d-2.2-1/bio3d/R/write.pdb.R | 16
bio3d-2.2-1/bio3d/README.md | 8
bio3d-2.2-1/bio3d/build/vignette.rds |binary
bio3d-2.2-1/bio3d/data/aa.table.rda |only
bio3d-2.2-1/bio3d/data/kinesin.RData |binary
bio3d-2.2-1/bio3d/data/transducin.RData |binary
bio3d-2.2-1/bio3d/inst/CITATION | 2
bio3d-2.2-1/bio3d/inst/doc/bio3d_vignettes.Rmd | 18
bio3d-2.2-1/bio3d/inst/doc/bio3d_vignettes.html | 14
bio3d-2.2-1/bio3d/inst/examples/test.pdb |only
bio3d-2.2-1/bio3d/inst/staticdocs/index.r | 49 +-
bio3d-2.2-1/bio3d/man/aa.index.Rd | 4
bio3d-2.2-1/bio3d/man/aa.table.Rd |only
bio3d-2.2-1/bio3d/man/aa123.Rd | 18
bio3d-2.2-1/bio3d/man/aln2html.Rd | 2
bio3d-2.2-1/bio3d/man/angle.xyz.Rd | 8
bio3d-2.2-1/bio3d/man/as.fasta.Rd |only
bio3d-2.2-1/bio3d/man/as.pdb.Rd |only
bio3d-2.2-1/bio3d/man/as.select.Rd |only
bio3d-2.2-1/bio3d/man/atom.select.Rd | 180 ++++---
bio3d-2.2-1/bio3d/man/atom2ele.Rd | 2
bio3d-2.2-1/bio3d/man/atom2mass.Rd | 1
bio3d-2.2-1/bio3d/man/basename.pdb.Rd |only
bio3d-2.2-1/bio3d/man/bhattacharyya.Rd | 6
bio3d-2.2-1/bio3d/man/binding.site.Rd | 60 +-
bio3d-2.2-1/bio3d/man/bio3d.package.Rd | 232 ----------
bio3d-2.2-1/bio3d/man/biounit.Rd |only
bio3d-2.2-1/bio3d/man/blast.pdb.Rd | 86 +++
bio3d-2.2-1/bio3d/man/bounds.sse.Rd |only
bio3d-2.2-1/bio3d/man/bwr.colors.Rd | 4
bio3d-2.2-1/bio3d/man/cat.pdb.Rd |only
bio3d-2.2-1/bio3d/man/chain.pdb.Rd | 2
bio3d-2.2-1/bio3d/man/clean.pdb.Rd |only
bio3d-2.2-1/bio3d/man/cmap.Rd | 31 +
bio3d-2.2-1/bio3d/man/cna.Rd | 5
bio3d-2.2-1/bio3d/man/cnapath.Rd |only
bio3d-2.2-1/bio3d/man/com.Rd | 36 +
bio3d-2.2-1/bio3d/man/combine.select.Rd |only
bio3d-2.2-1/bio3d/man/community.tree.Rd | 1
bio3d-2.2-1/bio3d/man/conserv.Rd | 2
bio3d-2.2-1/bio3d/man/convert.pdb.Rd | 4
bio3d-2.2-1/bio3d/man/core.find.Rd | 32 +
bio3d-2.2-1/bio3d/man/covsoverlap.Rd | 5
bio3d-2.2-1/bio3d/man/dccm.enma.Rd | 2
bio3d-2.2-1/bio3d/man/dccm.nma.Rd | 2
bio3d-2.2-1/bio3d/man/dccm.pca.Rd | 21
bio3d-2.2-1/bio3d/man/dccm.xyz.Rd | 4
bio3d-2.2-1/bio3d/man/deformation.nma.Rd | 2
bio3d-2.2-1/bio3d/man/difference.vector.Rd | 3
bio3d-2.2-1/bio3d/man/dist.xyz.Rd | 2
bio3d-2.2-1/bio3d/man/dm.Rd | 28 -
bio3d-2.2-1/bio3d/man/dssp.Rd | 57 ++
bio3d-2.2-1/bio3d/man/filter.cmap.Rd |only
bio3d-2.2-1/bio3d/man/filter.dccm.Rd | 2
bio3d-2.2-1/bio3d/man/filter.identity.Rd |only
bio3d-2.2-1/bio3d/man/filter.rmsd.Rd |only
bio3d-2.2-1/bio3d/man/fit.xyz.Rd | 12
bio3d-2.2-1/bio3d/man/geostas.Rd | 134 ++++-
bio3d-2.2-1/bio3d/man/get.pdb.Rd | 1
bio3d-2.2-1/bio3d/man/get.seq.Rd | 12
bio3d-2.2-1/bio3d/man/hclustplot.Rd | 7
bio3d-2.2-1/bio3d/man/hmmer.Rd | 122 ++++-
bio3d-2.2-1/bio3d/man/identify.cna.Rd | 3
bio3d-2.2-1/bio3d/man/inspect.connectivity.Rd | 2
bio3d-2.2-1/bio3d/man/is.gap.Rd | 20
bio3d-2.2-1/bio3d/man/layout.cna.Rd | 4
bio3d-2.2-1/bio3d/man/lmi.Rd | 5
bio3d-2.2-1/bio3d/man/load.enmff.Rd | 1
bio3d-2.2-1/bio3d/man/mktrj.Rd | 93 ++--
bio3d-2.2-1/bio3d/man/motif.find.Rd | 2
bio3d-2.2-1/bio3d/man/mustang.Rd | 23 -
bio3d-2.2-1/bio3d/man/network.amendment.Rd | 1
bio3d-2.2-1/bio3d/man/nma.Rd | 80 ++-
bio3d-2.2-1/bio3d/man/nma.pdb.Rd | 55 +-
bio3d-2.2-1/bio3d/man/nma.pdbs.Rd | 27 -
bio3d-2.2-1/bio3d/man/orient.pdb.Rd | 4
bio3d-2.2-1/bio3d/man/overlap.Rd | 6
bio3d-2.2-1/bio3d/man/pca.Rd | 5
bio3d-2.2-1/bio3d/man/pca.pdbs.Rd | 2
bio3d-2.2-1/bio3d/man/pca.xyz.Rd | 53 +-
bio3d-2.2-1/bio3d/man/pdb.annotate.Rd | 1
bio3d-2.2-1/bio3d/man/pdb2aln.Rd | 83 +--
bio3d-2.2-1/bio3d/man/pdb2aln.ind.Rd | 90 ++-
bio3d-2.2-1/bio3d/man/pdb2sse.Rd |only
bio3d-2.2-1/bio3d/man/pdbfit.Rd | 28 -
bio3d-2.2-1/bio3d/man/pdbseq.Rd | 11
bio3d-2.2-1/bio3d/man/pdbsplit.Rd | 4
bio3d-2.2-1/bio3d/man/pfam.Rd | 2
bio3d-2.2-1/bio3d/man/plot.bio3d.Rd | 90 +++
bio3d-2.2-1/bio3d/man/plot.cmap.Rd |only
bio3d-2.2-1/bio3d/man/plot.cna.Rd | 4
bio3d-2.2-1/bio3d/man/plot.dccm.Rd | 9
bio3d-2.2-1/bio3d/man/plot.dmat.Rd | 14
bio3d-2.2-1/bio3d/man/plot.enma.Rd | 1
bio3d-2.2-1/bio3d/man/plot.fluct.Rd |only
bio3d-2.2-1/bio3d/man/plot.geostas.Rd |only
bio3d-2.2-1/bio3d/man/plot.hmmer.Rd | 1
bio3d-2.2-1/bio3d/man/plot.nma.Rd | 5
bio3d-2.2-1/bio3d/man/plot.pca.Rd | 28 -
bio3d-2.2-1/bio3d/man/print.cna.Rd | 2
bio3d-2.2-1/bio3d/man/print.fasta.Rd | 6
bio3d-2.2-1/bio3d/man/prune.cna.Rd | 3
bio3d-2.2-1/bio3d/man/read.all.Rd | 1
bio3d-2.2-1/bio3d/man/read.crd.Rd | 82 +--
bio3d-2.2-1/bio3d/man/read.crd.amber.Rd |only
bio3d-2.2-1/bio3d/man/read.crd.charmm.Rd |only
bio3d-2.2-1/bio3d/man/read.dcd.Rd | 6
bio3d-2.2-1/bio3d/man/read.fasta.pdb.Rd | 3
bio3d-2.2-1/bio3d/man/read.mol2.Rd | 36 +
bio3d-2.2-1/bio3d/man/read.ncdf.Rd | 2
bio3d-2.2-1/bio3d/man/read.pdb.Rd | 27 -
bio3d-2.2-1/bio3d/man/read.pdcBD.Rd | 2
bio3d-2.2-1/bio3d/man/read.pqr.Rd | 2
bio3d-2.2-1/bio3d/man/read.prmtop.Rd |only
bio3d-2.2-1/bio3d/man/rgyr.Rd | 2
bio3d-2.2-1/bio3d/man/rle2.Rd | 2
bio3d-2.2-1/bio3d/man/rmsd.Rd | 25 -
bio3d-2.2-1/bio3d/man/rmsf.Rd | 8
bio3d-2.2-1/bio3d/man/rmsip.Rd | 7
bio3d-2.2-1/bio3d/man/sdENM.Rd | 2
bio3d-2.2-1/bio3d/man/seq2aln.Rd | 5
bio3d-2.2-1/bio3d/man/seqaln.Rd | 12
bio3d-2.2-1/bio3d/man/seqaln.pair.Rd | 9
bio3d-2.2-1/bio3d/man/seqbind.Rd | 8
bio3d-2.2-1/bio3d/man/seqidentity.Rd | 5
bio3d-2.2-1/bio3d/man/sip.Rd | 4
bio3d-2.2-1/bio3d/man/struct.aln.Rd | 2
bio3d-2.2-1/bio3d/man/torsion.pdb.Rd | 8
bio3d-2.2-1/bio3d/man/torsion.xyz.Rd | 4
bio3d-2.2-1/bio3d/man/trim.pdb.Rd | 21
bio3d-2.2-1/bio3d/man/trim.pdbs.Rd |only
bio3d-2.2-1/bio3d/man/trim.xyz.Rd |only
bio3d-2.2-1/bio3d/man/unbound.Rd | 16
bio3d-2.2-1/bio3d/man/uniprot.Rd | 2
bio3d-2.2-1/bio3d/man/view.cna.Rd | 3
bio3d-2.2-1/bio3d/man/write.fasta.Rd | 2
bio3d-2.2-1/bio3d/man/write.ncdf.Rd | 2
bio3d-2.2-1/bio3d/man/write.pdb.Rd | 1
bio3d-2.2-1/bio3d/man/write.pir.Rd | 2
bio3d-2.2-1/bio3d/man/write.pqr.Rd | 1
bio3d-2.2-1/bio3d/tests/testthat.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-atom.select.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-atom2mass.R | 6
bio3d-2.2-1/bio3d/tests/testthat/test-clean.pdb.R |only
bio3d-2.2-1/bio3d/tests/testthat/test-core.find.R | 3
bio3d-2.2-1/bio3d/tests/testthat/test-fitting.R | 4
bio3d-2.2-1/bio3d/tests/testthat/test-nma.R | 6
bio3d-2.2-1/bio3d/tests/testthat/test-nma.pdbs.R | 10
bio3d-2.2-1/bio3d/tests/testthat/test-overlap.R | 8
bio3d-2.2-1/bio3d/tests/testthat/test-pca.R | 2
bio3d-2.2-1/bio3d/tests/testthat/test-read.pdb.R | 34 +
bio3d-2.2-1/bio3d/tests/testthat/test-rmsd.R | 3
bio3d-2.2-1/bio3d/vignettes/bio3d_vignettes.Rmd | 18
270 files changed, 3382 insertions(+), 2420 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-17 1.2-6
Title: Tests for Normality
Diff between nortest versions 1.0-2 dated 2012-05-30 and 1.0-3 dated 2015-02-26
Description: Five omnibus tests for testing the composite hypothesis of
normality.
Author: Juergen Gross [aut],
Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges
ChangeLog |only
DESCRIPTION | 21 ++++++++++++---------
MD5 | 7 ++++---
R/ad.test.R | 12 ++++++++----
man/cvm.test.Rd | 4 ++--
5 files changed, 26 insertions(+), 18 deletions(-)
Title: Generalized Turnbull's Estimator
Diff between gte versions 1.2-1 dated 2014-01-06 and 1.2-2 dated 2015-02-26
Description: Generalized Turnbull's estimator proposed by Dehghan and Duchesne
(2011).
Author: Mohammad Hossein Dehghan, Thierry Duchesne and Sophie Baillargeon
Maintainer: Thierry Duchesne
DESCRIPTION | 10 +-
MD5 | 16 +--
NAMESPACE | 3
NEWS | 5 +
R/gte-package.R | 4
R/gte.R | 54 ++++++-----
man/gte-package.Rd | 33 +++----
man/gte.Rd | 240 +++++++++++++++++++++--------------------------------
man/simul.Rd | 20 ++--
9 files changed, 175 insertions(+), 210 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Diff between amen versions 0.999 dated 2014-03-01 and 1.0 dated 2015-02-26
Description: Analysis of network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor
models (Hoff(2009)). Four different link functions accommodate different
relational data structures, including binary/network data (bin), normal
relational data (nrm), ordinal relational data (ord) and data from
fixed-rank nomination schemes (frn). Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this
software was supported in part by NICHD grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff
DESCRIPTION | 44 ++++++------
MD5 | 164 ++++++++++++++++++++++++++++--------------------
NAMESPACE | 33 +++++++++
R/Xbeta.R | 24 +++++++
R/ame.R | 81 +++++++++++++++++++++++
R/ame_rep.R |only
R/amen-package.R |only
R/design_array.R | 19 +++++
R/gofstats.R | 18 +++++
R/mhalf.R | 19 +++++
R/plot.ame.R | 48 ++++++++++++++
R/rUV_fc.R | 63 ++++++++++++++++++
R/rUV_rep_fc.R |only
R/rZ_bin_fc.R | 42 ++++++++++++
R/rZ_cbin_fc.R | 70 ++++++++++++++++++++
R/rZ_frn_fc.R | 80 +++++++++++++++++++++++
R/rZ_nrm_fc.R | 27 +++++++
R/rZ_ord_fc.R | 50 ++++++++++++++
R/rZ_rrl.R | 67 +++++++++++++++++++
R/raSab_bin_fc.R | 43 ++++++++++++
R/raSab_cbin_fc.R | 53 +++++++++++++++
R/raSab_frn_fc.R | 46 +++++++++++++
R/rbeta_ab_fc.R | 106 +++++++++++++++++++++++++++++++
R/rbeta_ab_rep_fc.R |only
R/rmvnorm.R | 23 ++++++
R/rrho_mh.R | 34 +++++++++
R/rrho_mh_rep.R |only
R/rs2_fc.R | 21 ++++++
R/rs2_rep.R |only
R/rwish.R | 25 +++++++
R/simY_bin.R | 26 +++++++
R/simY_frn.R | 46 +++++++++++++
R/simY_nrm.R | 26 +++++++
R/simY_ord.R | 33 +++++++++
R/simY_rrl.R | 40 +++++++++++
R/simZ.R | 24 +++++++
R/summary.ame.R | 32 +++++++++
R/zscores.R | 19 +++++
data/YX_bin_long.rda |only
data/addhealthc3.RData |only
data/addhealthc9.RData |only
data/coldwar.RData |only
data/comtrade.RData |only
data/conflict90s.RData |only
data/datalist |only
data/dutchcollege.RData |only
data/lazegalaw.RData |only
data/sampsonmonks.RData |only
man/Xbeta.Rd | 26 +++++--
man/YX_bin.Rd | 30 +++-----
man/YX_bin_long.Rd |only
man/YX_cbin.Rd | 32 ++++-----
man/YX_frn.Rd | 29 +++-----
man/YX_nrm.Rd | 29 +++-----
man/YX_ord.Rd | 28 +++-----
man/YX_rrl.Rd | 29 +++-----
man/addhealthc3.Rd |only
man/addhealthc9.Rd |only
man/ame.Rd | 142 +++++++++++++++++++++--------------------
man/ame_rep.Rd |only
man/amen-package.Rd | 45 ++++++-------
man/coldwar.Rd |only
man/comtrade.Rd |only
man/conflict90s.Rd |only
man/design_array.Rd | 36 +++++-----
man/dutchcollege.Rd |only
man/gofstats.Rd | 28 +++-----
man/lazegalaw.Rd |only
man/mhalf.Rd | 22 ++----
man/plot.ame.Rd | 27 +++----
man/rUV_fc.Rd | 52 ++++++---------
man/rUV_rep_fc.Rd |only
man/rZ_bin_fc.Rd | 43 +++++-------
man/rZ_cbin_fc.Rd | 80 +++++++++--------------
man/rZ_frn_fc.Rd | 80 +++++++++--------------
man/rZ_nrm_fc.Rd | 42 ++++--------
man/rZ_ord_fc.Rd | 42 ++++--------
man/rZ_rrl_fc.Rd | 52 ++++++---------
man/raSab_bin_fc.Rd | 62 +++++++-----------
man/raSab_cbin_fc.Rd | 70 ++++++++------------
man/raSab_frn_fc.Rd | 73 ++++++++-------------
man/rbeta_ab_fc.Rd | 77 ++++++++++------------
man/rbeta_ab_rep_fc.Rd |only
man/rmvnorm.Rd | 28 ++++----
man/rrho_mh.Rd | 40 +++++------
man/rrho_mh_rep.Rd |only
man/rs2_fc.Rd | 26 +++----
man/rs2_rep_fc.Rd |only
man/rwish.Rd | 33 +++++----
man/sampsonmonks.Rd |only
man/simY_bin.Rd | 27 +++----
man/simY_frn.Rd | 63 ++++++++----------
man/simY_nrm.Rd | 33 ++++-----
man/simY_ord.Rd | 34 ++++-----
man/simY_rrl.Rd | 41 +++++-------
man/simZ.Rd | 32 ++++-----
man/summary.ame.Rd | 45 ++++++-------
man/zscores.Rd | 27 +++----
98 files changed, 2087 insertions(+), 964 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.600.4.0 dated 2015-01-25 and 0.4.650.1.1 dated 2015-02-26
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 13
DESCRIPTION | 8
MD5 | 83
README.md | 6
inst/NEWS.Rd | 16
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/armadillo | 12
inst/include/armadillo_bits/Col_bones.hpp | 4
inst/include/armadillo_bits/Col_meat.hpp | 81
inst/include/armadillo_bits/Mat_bones.hpp | 20
inst/include/armadillo_bits/Mat_meat.hpp | 201 ++
inst/include/armadillo_bits/Row_bones.hpp | 4
inst/include/armadillo_bits/Row_meat.hpp | 81
inst/include/armadillo_bits/SpMat_bones.hpp | 57
inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 2
inst/include/armadillo_bits/SpMat_meat.hpp | 1308 +++++++--------
inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 4
inst/include/armadillo_bits/SpSubview_meat.hpp | 107 -
inst/include/armadillo_bits/arma_rng.hpp | 33
inst/include/armadillo_bits/arma_rng_cxx11.hpp | 30
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/arrayops_meat.hpp | 145 -
inst/include/armadillo_bits/compiler_setup.hpp | 17
inst/include/armadillo_bits/config.hpp | 14
inst/include/armadillo_bits/diskio_meat.hpp | 30
inst/include/armadillo_bits/eglue_core_bones.hpp | 6
inst/include/armadillo_bits/eglue_core_meat.hpp | 8
inst/include/armadillo_bits/eop_core_bones.hpp | 6
inst/include/armadillo_bits/eop_core_meat.hpp | 8
inst/include/armadillo_bits/fn_accu.hpp | 8
inst/include/armadillo_bits/fn_conv_to.hpp | 224 +-
inst/include/armadillo_bits/fn_misc.hpp | 47
inst/include/armadillo_bits/fn_randg.hpp |only
inst/include/armadillo_bits/op_pinv_meat.hpp | 14
inst/include/armadillo_bits/running_stat_vec_meat.hpp | 4
inst/include/armadillo_bits/sp_auxlib_bones.hpp | 2
inst/include/armadillo_bits/sp_auxlib_meat.hpp | 17
inst/include/armadillo_bits/subview_bones.hpp | 7
inst/include/armadillo_bits/subview_cube_bones.hpp | 6
inst/include/armadillo_bits/subview_cube_meat.hpp | 25
inst/include/armadillo_bits/subview_meat.hpp | 26
inst/include/armadillo_bits/unwrap.hpp | 24
43 files changed, 1641 insertions(+), 1073 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Diff between PDQutils versions 0.1.0 dated 2015-02-12 and 0.1.1 dated 2015-02-26
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav
PDQutils-0.1.0/PDQutils/R/appx.r |only
PDQutils-0.1.1/PDQutils/DESCRIPTION | 15 +-
PDQutils-0.1.1/PDQutils/MD5 | 37 +++---
PDQutils-0.1.1/PDQutils/NAMESPACE | 2
PDQutils-0.1.1/PDQutils/R/PDQutils.r | 10 +
PDQutils-0.1.1/PDQutils/R/cornish_fisher.r |only
PDQutils-0.1.1/PDQutils/R/edgeworth.r |only
PDQutils-0.1.1/PDQutils/R/gram_charlier.r |only
PDQutils-0.1.1/PDQutils/README.md | 151 ++++++++++++++++++++++---
PDQutils-0.1.1/PDQutils/inst/CITATION | 5
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.R | 73 +++++++++++-
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.pdf |binary
PDQutils-0.1.1/PDQutils/man/AS269.Rd | 2
PDQutils-0.1.1/PDQutils/man/NEWS.Rd | 7 +
PDQutils-0.1.1/PDQutils/man/PDQutils.Rd | 4
PDQutils-0.1.1/PDQutils/man/dapx_edgeworth.Rd |only
PDQutils-0.1.1/PDQutils/man/dapx_gca.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/qapx_cf.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/rapx_cf.Rd | 7 -
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.bib | 32 +++++
22 files changed, 540 insertions(+), 67 deletions(-)
Title: Association Analysis of CNV Data and Imputed SNPs
Diff between CNVassoc versions 2.0.1 dated 2013-09-19 and 2.1 dated 2015-02-26
Description: The CNVassoc package carries out analysis of common
Copy Number Variants (CNVs) and imputed Single Nucleotide
Polymorphisms (SNPs) in population-based studies.
It includes tools for estimating association under a series
of study designs (case-control, cohort, etc), using several
dependent variables (class status, censored data, counts)
as response, adjusting for covariates and considering
various inheritance models. Moreover, it is possible to
perform epistasis studies with pairs of CNVs or imputed SNPs.
It has been optimized in order to make feasible the analyses
of Genome Wide Association studies (GWAs) with hundreds of
thousands of genetic variants (CNVs / imputed SNPs). Also,
it incorporates functions for inferring copy number (CNV
genotype calling). Various classes and methods for generic
functions (print, summary, plot, anova, ...) have been
created to facilitate the analysis.
Author: Juan R González, Isaac Subirana
Maintainer: Isaac Subirana
DESCRIPTION | 38 ++++++++++++++++++++++----------------
MD5 | 31 ++++++++++++++++++++++---------
NAMESPACE | 10 +++++++++-
R/fastCNVassoc.R | 12 +++++++++---
R/fastCNVinter.R |only
R/getProbs.cghCall.R | 22 ++++++++++++----------
R/plapply.R | 2 +-
build |only
inst/doc/changelog.txt | 5 +++++
man/fastCNVassoc.Rd | 4 +++-
man/fastCNVinter.Rd |only
man/simCNVdataWeibull.Rd | 2 +-
src/CNVassoc.h | 10 ++++++++++
src/NRinterlogistic.c |only
src/NRinterlogisticcov.c |only
src/NRinterweibull.c |only
src/NRinterweibullcov.c |only
src/loglikinterlogistic.c |only
src/loglikinterlogisticcov.c |only
src/loglikinterweibull.c |only
src/loglikinterweibullcov.c |only
src/outerC.c |only
src/simcensrespC.c |only
23 files changed, 94 insertions(+), 42 deletions(-)
Title: Rcmdr Receiver Operator Characteristic Plug-In PACKAGE
Diff between RcmdrPlugin.ROC versions 1.0-17 dated 2014-12-20 and 1.0-18 dated 2015-02-26
More information about RcmdrPlugin.ROC at CRAN
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre],
Mihaela Hedesiu [ctb],
Andrei Achimas [ctb],
Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 6 +++---
inst/CHANGES | 2 ++
4 files changed, 13 insertions(+), 11 deletions(-)
Permanent link
Title: An R Interface to the Oniguruma Regular Expression Library
Diff between ore versions 1.0.6 dated 2015-01-01 and 1.1.0 dated 2015-02-26
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
ore-1.0.6/ore/src/main.c |only
ore-1.0.6/ore/src/main.h |only
ore-1.0.6/ore/src/onig/enc/big5.c |only
ore-1.0.6/ore/src/onig/enc/cp1251.c |only
ore-1.0.6/ore/src/onig/enc/cp932.c |only
ore-1.0.6/ore/src/onig/enc/euc_jp.c |only
ore-1.0.6/ore/src/onig/enc/euc_kr.c |only
ore-1.0.6/ore/src/onig/enc/euc_tw.c |only
ore-1.0.6/ore/src/onig/enc/gb18030.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_10.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_11.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_13.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_14.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_15.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_16.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_2.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_3.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_4.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_5.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_6.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_7.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_8.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_9.c |only
ore-1.0.6/ore/src/onig/enc/jis |only
ore-1.0.6/ore/src/onig/enc/koi8.c |only
ore-1.0.6/ore/src/onig/enc/koi8_r.c |only
ore-1.0.6/ore/src/onig/enc/sjis.c |only
ore-1.0.6/ore/src/onig/enc/utf16_be.c |only
ore-1.0.6/ore/src/onig/enc/utf16_le.c |only
ore-1.0.6/ore/src/onig/enc/utf32_be.c |only
ore-1.0.6/ore/src/onig/enc/utf32_le.c |only
ore-1.1.0/ore/DESCRIPTION | 9 +-
ore-1.1.0/ore/MD5 | 81 +++++++-----------
ore-1.1.0/ore/NAMESPACE | 5 -
ore-1.1.0/ore/NEWS | 25 +++++
ore-1.1.0/ore/R/dict.R |only
ore-1.1.0/ore/R/es.R |only
ore-1.1.0/ore/R/match.R | 92 ++++++++++++--------
ore-1.1.0/ore/R/ore.R | 23 +++--
ore-1.1.0/ore/R/workspace.R |only
ore-1.1.0/ore/README.md | 66 +++++++++++++-
ore-1.1.0/ore/man/es.Rd |only
ore-1.1.0/ore/man/matches.Rd | 6 +
ore-1.1.0/ore/man/ore.Rd | 23 +++--
ore-1.1.0/ore/man/ore.dict.Rd |only
ore-1.1.0/ore/man/ore.ismatch.Rd | 3
ore-1.1.0/ore/man/ore.lastmatch.Rd | 3
ore-1.1.0/ore/man/ore.search.Rd | 26 ++++-
ore-1.1.0/ore/man/ore.split.Rd | 3
ore-1.1.0/ore/man/ore.subst.Rd | 12 ++
ore-1.1.0/ore/src/Makevars | 4
ore-1.1.0/ore/src/compile.c |only
ore-1.1.0/ore/src/compile.h |only
ore-1.1.0/ore/src/match.c |only
ore-1.1.0/ore/src/match.h |only
ore-1.1.0/ore/src/onig/oniguruma.h | 125 +++++++++++++++-------------
ore-1.1.0/ore/src/print.c |only
ore-1.1.0/ore/src/print.h |only
ore-1.1.0/ore/src/split.c |only
ore-1.1.0/ore/src/split.h |only
ore-1.1.0/ore/src/subst.c |only
ore-1.1.0/ore/src/subst.h |only
ore-1.1.0/ore/src/zzz.c |only
ore-1.1.0/ore/src/zzz.h |only
ore-1.1.0/ore/tests/testthat/test-20-dict.R |only
ore-1.1.0/ore/tests/testthat/test-25-es.R |only
66 files changed, 324 insertions(+), 182 deletions(-)
Title: Tools for Nonlinear Regression Analysis
Diff between nlstools versions 1.0-0 dated 2014-06-25 and 1.0-1 dated 2015-02-26
Description: Several tools for assessing the quality of fit of a
gaussian nonlinear model are provided.
Author: Florent Baty
Maintainer: Florent Baty
ChangeLog | 7 ++++++-
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++++-----
NAMESPACE | 4 ++++
R/confint2.R |only
data/L.minor.rda |only
inst/CITATION | 8 ++++----
inst/NEWS | 10 +++++++++-
man/L.minor.Rd |only
man/confint2.Rd |only
10 files changed, 37 insertions(+), 16 deletions(-)
Title: Graphical Tests for Hardy-Weinberg Equilibrium
Diff between HardyWeinberg versions 1.5.4 dated 2014-08-11 and 1.5.5 dated 2015-02-26
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman
Maintainer: Jan Graffelman
HardyWeinberg-1.5.4/HardyWeinberg/R/combineC.R |only
HardyWeinberg-1.5.5/HardyWeinberg/DESCRIPTION | 25 +
HardyWeinberg-1.5.5/HardyWeinberg/MD5 | 62 +++-
HardyWeinberg-1.5.5/HardyWeinberg/NAMESPACE | 2
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineChisquare.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineExact.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/HWAlltests.R | 12
HardyWeinberg-1.5.5/HardyWeinberg/R/HWChisq.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/HWMissing.R | 137 +++++-----
HardyWeinberg-1.5.5/HardyWeinberg/R/HWPerm.R | 4
HardyWeinberg-1.5.5/HardyWeinberg/R/HWTernaryPlot.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/MakeFactor.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/mipvalue.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/missingentirerow.R |only
HardyWeinberg-1.5.5/HardyWeinberg/build |only
HardyWeinberg-1.5.5/HardyWeinberg/inst |only
HardyWeinberg-1.5.5/HardyWeinberg/man/HWAlltests.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWChisq.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWIlrPlot.Rd | 4
HardyWeinberg-1.5.5/HardyWeinberg/man/HWMissing.Rd | 32 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPerm.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPower.Rd | 9
HardyWeinberg-1.5.5/HardyWeinberg/man/HWQqplot.Rd | 2
HardyWeinberg-1.5.5/HardyWeinberg/man/HWTernaryPlot.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HardyWeinberg-package.Rd | 28 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/MakeFactor.Rd |only
HardyWeinberg-1.5.5/HardyWeinberg/man/Markers.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/vignettes |only
28 files changed, 233 insertions(+), 129 deletions(-)
Title: Tools to Deal with Fuzzy Numbers
Diff between FuzzyNumbers versions 0.3-5 dated 2014-10-01 and 0.4-1 dated 2015-02-26
Description: S4 classes and methods
to deal with fuzzy numbers. With them you can compute any arithmetic
operations (e.g. by using the Zadeh extension principle),
perform approximation of arbitrary FNs by trapezoidal and piecewise
linear FNs, prepare plots of FNs for publications, calculate
possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre],
Jan Caha [ctb]
Maintainer: Marek Gagolewski
DESCRIPTION | 19 +-
MD5 | 117 +++++++-----
NAMESPACE | 13 +
NEWS | 16 +
R/methods-Arithmetic.R | 6
R/methods-compare.R |only
R/methods-min_max.R |only
R/methods-special_functions.R |only
build/vignette.rds |binary
inst/CITATION | 6
inst/doc/FuzzyNumbersTutorial.R | 72 +++++++
inst/doc/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
inst/doc/FuzzyNumbersTutorial.pdf |binary
man/Arithmetic-methods.Rd | 31 +++
man/DiscontinuousFuzzyNumber-class.Rd | 3
man/DiscontinuousFuzzyNumber.Rd | 3
man/Extract-methods.Rd | 3
man/FuzzyNumber-class.Rd | 3
man/FuzzyNumber.Rd | 3
man/FuzzyNumbers-package.Rd | 3
man/PiecewiseLinearFuzzyNumber-class.Rd | 28 ++-
man/PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/PowerFuzzyNumber-class.Rd | 3
man/PowerFuzzyNumber.Rd | 3
man/TrapezoidalFuzzyNumber-class.Rd | 3
man/TrapezoidalFuzzyNumber.Rd | 3
man/TriangularFuzzyNumber.Rd | 3
man/alphaInterval-methods.Rd | 28 ++-
man/alphacut-methods.Rd | 3
man/ambiguity-methods.Rd | 3
man/approxInvert.Rd | 3
man/arctan2.Rd |only
man/as.FuzzyNumber.Rd | 3
man/as.PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/as.PowerFuzzyNumber.Rd | 28 ++-
man/as.TrapezoidalFuzzyNumber.Rd | 28 ++-
man/as.character-methods.Rd | 28 ++-
man/convertAlpha.Rd | 3
man/convertSide.Rd | 3
man/core-methods.Rd | 3
man/distance-methods.Rd | 3
man/evaluate-methods.Rd | 3
man/expectedInterval-methods.Rd | 28 ++-
man/expectedValue-methods.Rd | 3
man/fapply-methods.Rd | 31 +++
man/integrateAlpha-methods.Rd | 3
man/integrate_discont_val.Rd | 3
man/maximum.Rd |only
man/minimum.Rd |only
man/necessityExceedance.Rd |only
man/necessityStrictExceedance.Rd |only
man/necessityStrictUndervaluation.Rd |only
man/necessityUndervaluation.Rd |only
man/piecewiseLinearApproximation-methods.Rd | 3
man/plot-methods.Rd | 28 ++-
man/possibilityExceedance.Rd |only
man/possibilityStrictExceedance.Rd |only
man/possibilityStrictUndervaluation.Rd |only
man/possibilityUndervaluation.Rd |only
man/pow-PiecewiseLinearFuzzyNumber-numeric-method.Rd |only
man/show-methods.Rd | 3
man/supp-methods.Rd | 3
man/trapezoidalApproximation-methods.Rd | 3
man/value-methods.Rd | 3
man/weightedExpectedValue-methods.Rd | 3
man/width-methods.Rd | 3
vignettes/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
67 files changed, 866 insertions(+), 137 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Diff between forecast versions 5.8 dated 2015-01-06 and 5.9 dated 2015-02-26
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 8 +++
DESCRIPTION | 10 ++--
MD5 | 22 ++++-----
NAMESPACE | 3 -
R/arfima.R | 6 +-
R/arima.R | 135 ++++++++++++++++++++++++++++----------------------------
R/errors.R | 3 +
R/fpp.R | 31 ++++++++++--
R/getResponse.R | 4 -
R/newarima2.R | 21 ++++----
R/tbats.R | 4 -
man/accuracy.Rd | 24 ++++++++-
12 files changed, 162 insertions(+), 109 deletions(-)
Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Diff between exact2x2 versions 1.4.0 dated 2014-08-25 and 1.4.1 dated 2015-02-26
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals. Provides power and sample size calculations. Also gives melded confidence intervals for the binomial case.
Author: Michael P. Fay
Maintainer: Michael P. Fay
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/ss2x2.R | 29 +++++++++++++++++++++++++----
build/vignette.rds |binary
inst/doc/exact2x2.pdf |binary
inst/doc/exactMcNemar.R | 6 +++---
inst/doc/exactMcNemar.Rnw | 21 ++++++++++++++++-----
inst/doc/exactMcNemar.pdf |binary
man/exact2x2-package.Rd | 4 ++--
vignettes/exactMcNemar.Rnw | 21 ++++++++++++++++-----
11 files changed, 82 insertions(+), 33 deletions(-)
Title: ODBC Database Access
Diff between RODBC versions 1.3-10 dated 2013-11-25 and 1.3-11 dated 2015-02-26
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley
ChangeLog | 11 +++++
DESCRIPTION | 14 +++----
MD5 | 22 +++++------
R/RODBC.R | 4 +-
R/sql.R | 1
build/vignette.rds |binary
cleanup | 2 -
inst/doc/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
inst/doc/RODBC.pdf |binary
man/sqlColumns.Rd | 4 +-
man/sqlTypeInfo.Rd | 2 -
vignettes/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
12 files changed, 135 insertions(+), 121 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.6.6 dated 2014-09-11 and 1.7.1 dated 2015-02-26
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
lcmm-1.6.6/lcmm/R/VarCov.lcmm..R |only
lcmm-1.6.6/lcmm/R/link.confint.lcmm.R |only
lcmm-1.6.6/lcmm/R/link.confint.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.baselinerisk.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.predict.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.survival.Jointlcmm.R |only
lcmm-1.6.6/lcmm/man/link.confint.Rd |only
lcmm-1.6.6/lcmm/man/multlcmm.rd |only
lcmm-1.6.6/lcmm/man/plot.baselinerisk.Rd |only
lcmm-1.6.6/lcmm/man/plot.linkfunction.Rd |only
lcmm-1.6.6/lcmm/man/plot.postprob.Rd |only
lcmm-1.6.6/lcmm/man/plot.survival.Rd |only
lcmm-1.6.6/lcmm/src/predictDyn.f90 |only
lcmm-1.7.1/lcmm/DESCRIPTION | 17
lcmm-1.7.1/lcmm/MD5 | 187
lcmm-1.7.1/lcmm/NAMESPACE | 42
lcmm-1.7.1/lcmm/NEWS | 42
lcmm-1.7.1/lcmm/R/Contlcmm.R | 25
lcmm-1.7.1/lcmm/R/Jointlcmm.R | 2976 ++++++------
lcmm-1.7.1/lcmm/R/Ordlcmm.R | 18
lcmm-1.7.1/lcmm/R/VarCov.Jointlcmm.R | 53
lcmm-1.7.1/lcmm/R/VarCov.lcmm.R |only
lcmm-1.7.1/lcmm/R/VarCovRE.Jointlcmm.R | 314 -
lcmm-1.7.1/lcmm/R/VarCovRE.hlme.R | 39
lcmm-1.7.1/lcmm/R/VarCovRE.lcmm.R | 36
lcmm-1.7.1/lcmm/R/VarCovRE.multlcmm.R | 32
lcmm-1.7.1/lcmm/R/VarExpl.Jointlcmm.R | 251 -
lcmm-1.7.1/lcmm/R/VarExpl.hlme.R | 235
lcmm-1.7.1/lcmm/R/VarExpl.lcmm.R | 246 -
lcmm-1.7.1/lcmm/R/VarExpl.multlcmm.R | 261 -
lcmm-1.7.1/lcmm/R/WaldMult.R | 46
lcmm-1.7.1/lcmm/R/cuminc.R |only
lcmm-1.7.1/lcmm/R/dynpred.R | 1936 +++++--
lcmm-1.7.1/lcmm/R/epoce.R | 893 +--
lcmm-1.7.1/lcmm/R/estimates.Jointlcmm.R | 66
lcmm-1.7.1/lcmm/R/fitY.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.lcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.multlcmm.R |only
lcmm-1.7.1/lcmm/R/hlme.R | 21
lcmm-1.7.1/lcmm/R/lcmm.R | 42
lcmm-1.7.1/lcmm/R/multlcmm.R | 100
lcmm-1.7.1/lcmm/R/plot.Diffepoce.R | 71
lcmm-1.7.1/lcmm/R/plot.R |only
lcmm-1.7.1/lcmm/R/plot.cuminc.R |only
lcmm-1.7.1/lcmm/R/plot.dynpred.R | 632 +-
lcmm-1.7.1/lcmm/R/plot.epoce.R | 22
lcmm-1.7.1/lcmm/R/plot.predictL.R |only
lcmm-1.7.1/lcmm/R/plot.predictY.R |only
lcmm-1.7.1/lcmm/R/plot.predictlink.R |only
lcmm-1.7.1/lcmm/R/plotbaselinerisk.R |only
lcmm-1.7.1/lcmm/R/plotfit.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunction.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunctionmult.R |only
lcmm-1.7.1/lcmm/R/plotpostprob.R |only
lcmm-1.7.1/lcmm/R/plotresid.R |only
lcmm-1.7.1/lcmm/R/plotsurvival.R |only
lcmm-1.7.1/lcmm/R/postprob.Jointlcmm.R | 45
lcmm-1.7.1/lcmm/R/predictL.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictL.lcmm.R | 236
lcmm-1.7.1/lcmm/R/predictL.multlcmm.R | 173
lcmm-1.7.1/lcmm/R/predictY.Jointlcmm.R | 1238 +++--
lcmm-1.7.1/lcmm/R/predictY.hlme.R | 189
lcmm-1.7.1/lcmm/R/predictY.lcmm.R | 85
lcmm-1.7.1/lcmm/R/predictY.multlcmm.R | 59
lcmm-1.7.1/lcmm/R/predictlink.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.lcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.multlcmm.R |only
lcmm-1.7.1/lcmm/R/print.Diffepoce.R | 2
lcmm-1.7.1/lcmm/R/print.Jointlcmm.R | 187
lcmm-1.7.1/lcmm/R/risq_spl.R |only
lcmm-1.7.1/lcmm/R/risqcum_spl.R |only
lcmm-1.7.1/lcmm/R/summary.Jointlcmm.R | 565 +-
lcmm-1.7.1/lcmm/R/summarytable.R |only
lcmm-1.7.1/lcmm/man/Diffepoce.Rd | 6
lcmm-1.7.1/lcmm/man/ForInternalUse.Rd | 11
lcmm-1.7.1/lcmm/man/Jointlcmm.Rd | 119
lcmm-1.7.1/lcmm/man/VarExpl.Rd | 3
lcmm-1.7.1/lcmm/man/cuminc.Rd |only
lcmm-1.7.1/lcmm/man/data_hlme.Rd | 2
lcmm-1.7.1/lcmm/man/dynpred.Rd | 32
lcmm-1.7.1/lcmm/man/epoce.Rd | 6
lcmm-1.7.1/lcmm/man/fitY.Rd |only
lcmm-1.7.1/lcmm/man/hlme.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm-package.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm.Rd | 40
lcmm-1.7.1/lcmm/man/multlcmm.Rd |only
lcmm-1.7.1/lcmm/man/plot.cuminc.Rd |only
lcmm-1.7.1/lcmm/man/plot.dynpred.Rd | 19
lcmm-1.7.1/lcmm/man/plot.lcmm.Rd | 162
lcmm-1.7.1/lcmm/man/plot.pred.accuracy.Rd | 3
lcmm-1.7.1/lcmm/man/plot.predict.Rd | 81
lcmm-1.7.1/lcmm/man/postprob.Rd | 4
lcmm-1.7.1/lcmm/man/predictL.Rd | 41
lcmm-1.7.1/lcmm/man/predictY.Rd | 43
lcmm-1.7.1/lcmm/man/predictlink.Rd |only
lcmm-1.7.1/lcmm/man/print.lcmm.Rd | 2
lcmm-1.7.1/lcmm/man/summary.lcmm.Rd | 3
lcmm-1.7.1/lcmm/man/summarytable.Rd |only
lcmm-1.7.1/lcmm/src/AOptim.f90 | 26
lcmm-1.7.1/lcmm/src/Jointhet.f90 | 5841 +++++++++++++-----------
lcmm-1.7.1/lcmm/src/Makevars | 14
lcmm-1.7.1/lcmm/src/calculusTransfo.f90 | 6
lcmm-1.7.1/lcmm/src/cvpl.f90 | 3208 +++++++------
lcmm-1.7.1/lcmm/src/hetmixCont.f90 | 54
lcmm-1.7.1/lcmm/src/hetmixContMult.f90 | 71
lcmm-1.7.1/lcmm/src/hetmixOrd.f90 | 20
lcmm-1.7.1/lcmm/src/hetmixlin.f90 | 25
lcmm-1.7.1/lcmm/src/postprob2.f90 |only
lcmm-1.7.1/lcmm/src/predictCont.f90 | 7
lcmm-1.7.1/lcmm/src/predictMult.f90 | 4
123 files changed, 12217 insertions(+), 9042 deletions(-)
Title: Convert R Graphics to Flash Animations
Diff between R2SWF versions 0.8-2 dated 2014-12-19 and 0.9 dated 2015-02-26
Description: Using the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 12 +-
MD5 | 8 -
NEWS | 44 +++++---
R/svg2swf.R | 299 ++++++++++++++++++++++++++++----------------------------
src/image2swf.c | 2
5 files changed, 189 insertions(+), 176 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.5-1 dated 2014-10-24 and 0.5-2 dated 2015-02-26
Description: The following methods for cubature (numerical integration)
over polygonal domains are currently implemented:
the two-dimensional midpoint rule as a simple wrapper around
as.im.function() from package spatstat (Baddeley and Turner, 2005),
the product Gauss cubature by Sommariva and Vianello (2007),
an adaptive cubature for isotropic functions via line integrate()
along the boundary (Meyer and Held, 2014),
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains
(based on formulae from the Abramowitz and Stegun (1972) handbook).
For cubature over simple hypercubes, the packages "cubature" and
"R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
DESCRIPTION | 19 +++++----
MD5 | 64 ++++++++++++++++----------------
NAMESPACE | 8 +++-
R/coerce-gpc-methods.R | 22 ++++++++---
R/coerce-sp-methods.R | 63 ++++++++++++++++++++++----------
R/polyCub.exact.Gauss.R | 88 +++++++++++++++++++++++++++------------------
R/polyCub.iso.R | 41 +++++++++++++-------
R/polyCub.midpoint.R | 21 +++++-----
R/tools.R | 5 +-
R/xylist.R | 12 ++----
inst/CITATION | 10 -----
inst/NEWS.Rd | 24 ++++++++++++
man/checkintrfr.Rd | 3 +
man/circleCub.Gauss.Rd | 3 +
man/coerce-gpc-methods.Rd | 15 +++++--
man/coerce-sp-methods.Rd | 38 +++++++++++++++----
man/dotprod.Rd | 3 +
man/gpclibPermit.Rd | 3 +
man/isClosed.Rd | 3 +
man/isScalar.Rd | 3 +
man/makegrid.Rd | 3 +
man/plot_polyregion.Rd | 3 +
man/plotpolyf.Rd | 3 +
man/polyCub-package.Rd | 3 +
man/polyCub.Rd | 3 +
man/polyCub.SV.Rd | 3 +
man/polyCub.exact.Gauss.Rd | 9 ++--
man/polyCub.iso.Rd | 3 +
man/polyCub.midpoint.Rd | 10 ++++-
man/polygauss.Rd | 3 +
man/vecnorm.Rd | 3 +
man/xylist.Rd | 11 +++--
tests/test-all.R | 3 -
33 files changed, 324 insertions(+), 184 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Diff between multicool versions 0.1-2 dated 2013-07-10 and 0.1-5 dated 2015-02-26
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran
DESCRIPTION | 21 +-
MD5 | 25 ++
NAMESPACE | 20 +-
R/RcppExports.R |only
R/Stirling2.R |only
R/allPerm.R | 28 +--
R/genComp.R |only
R/initMC.r | 91 +++++-----
R/multinom.R | 11 -
R/nextPerm.R | 28 +--
README.md |only
man/Bell.Rd |only
man/Stirling2.Rd |only
man/genComp.Rd |only
src/RcppExports.cpp |only
src/compositions.cpp |only
src/multicool.cpp | 430 ++++++++++++++++++++++++++++-----------------------
src/multinomial.h | 2
18 files changed, 354 insertions(+), 302 deletions(-)
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Diff between PRROC versions 1.0 dated 2014-12-16 and 1.1 dated 2015-02-25
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau
DESCRIPTION | 9 ++-
MD5 | 21 +++++---
R/PRROC.R | 15 +-----
inst/doc/PRROC.R | 121 +++++++++++++++++++++++++++++++++++++--------------
inst/doc/PRROC.Rnw | 94 ++++++++++++++++++++++++++++++++++++++-
inst/doc/PRROC.pdf |binary
inst/tests |only
man/PRROC-package.Rd | 4 -
man/pr.curve.Rd | 7 +-
man/roc.curve.Rd | 6 --
tests |only
vignettes/PRROC.Rnw | 94 ++++++++++++++++++++++++++++++++++++++-
12 files changed, 300 insertions(+), 71 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Diff between hergm versions 2.1-1 dated 2015-01-11 and 2.2-0 dated 2015-02-25
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 11 +++++------
MD5 | 14 +++++++-------
R/hergm.gof.R | 2 +-
R/hergm.postprocess.R | 24 ++++++++++++++----------
R/hergm.preprocess.R | 9 +++------
R/zzz.R | 1 +
man/hergm.gof.Rd | 14 +++++++++++++-
src/h_ergm.c | 19 +++++++++----------
8 files changed, 53 insertions(+), 41 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Diff between frailtypack versions 2.7.2 dated 2014-10-16 and 2.7.4 dated 2015-02-25
Description: Frailtypack fits several classes of frailty models using a penalized likelihood
estimation on the hazard function but also a parametric estimation.
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated
random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of
clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events
with terminal event for clustered data or not.
Prediction values are available. Left-truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional hazard
and shared frailty model) and strata are allowed. In each model,
the random effects have a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying covariates
effects in Cox, shared and joint models. The package includes concordance measures
for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
DESCRIPTION | 8
MD5 | 39 -
NEWS | 10
R/epoce.R | 37 +
R/frailtyPenal.R | 4
R/multivPenal.R | 6
R/plot.predFrailty.R | 8
R/prediction.R | 1291 ++++++++++++++++++++++-------------------
R/print.jointPenal.R | 2
R/print.predFrailty.R | 2
man/SurvIC.Rd | 2
man/prediction.Rd | 15
src/Aparameters.f90 | 3
src/Makevars | 3
src/aaOptim.f90 | 5
src/distance.f90 | 43 -
src/epoce_log.f90 |only
src/frailtypack.f90 | 46 -
src/funcpassplines_intcens.f90 | 10
src/joint.f90 | 1
src/prediction_log.f90 |only
src/prediction_sha_logn.f90 |only
22 files changed, 881 insertions(+), 654 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Diff between diseasemapping versions 1.1.5 dated 2015-01-15 and 1.1.7 dated 2015-02-25
More information about diseasemapping at CRAN
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.SpatialPolygonsDataFrame.R |only
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.data.frame.R |only
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.list.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.SpatialPolygonsDataFrame.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.data.frame.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.list.r |only
diseasemapping-1.1.7/diseasemapping/DESCRIPTION | 14 -
diseasemapping-1.1.7/diseasemapping/MD5 | 27 +--
diseasemapping-1.1.7/diseasemapping/NAMESPACE | 19 --
diseasemapping-1.1.7/diseasemapping/R/formatPopulation.R |only
diseasemapping-1.1.7/diseasemapping/R/getBreaks.R | 2
diseasemapping-1.1.7/diseasemapping/R/getSMR.R |only
diseasemapping-1.1.7/diseasemapping/R/mergeBugsData.R | 23 +-
diseasemapping-1.1.7/diseasemapping/man/cancerRates.Rd | 2
diseasemapping-1.1.7/diseasemapping/man/formatPopulation.Rd | 41 ++--
diseasemapping-1.1.7/diseasemapping/man/getSMR.Rd | 87 +++++++---
diseasemapping-1.1.7/diseasemapping/man/kentucky.Rd | 17 +
diseasemapping-1.1.7/diseasemapping/man/mergeBugsData.Rd | 20 +-
diseasemapping-1.1.7/diseasemapping/tests/getSMR.R |only
19 files changed, 156 insertions(+), 96 deletions(-)
Permanent link
Title: Visualization of Regression Models
Diff between visreg versions 2.1-0 dated 2014-11-27 and 2.1-1 dated 2015-02-25
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
DESCRIPTION | 14 +++++++-------
MD5 | 21 +++++++++++----------
NEWS | 6 ++++++
R/Terms.R | 11 +++++++++--
R/plot.visreg.R | 3 ++-
R/setupX.R | 6 ++++++
R/visreg2d.R | 3 +--
R/visregLatticePlot.R | 1 +
README.md |only
inst/tests/formulas.R | 2 +-
inst/tests/mixed-models.R | 14 ++++++++++++++
tests/visreg-coxph.R | 1 +
12 files changed, 59 insertions(+), 23 deletions(-)
Title: Miscellaneous Functions for Survival Data
Diff between survMisc versions 0.4.4 dated 2015-01-06 and 0.4.5 dated 2015-02-25
Description: A collection of functions for analysis of survival data. These
extend the methods available in the survival package.
Author: Chris Dardis
Maintainer: Chris Dardis
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NAMESPACE | 1 +
R/survMisc_package.R | 3 ++-
man/gof.Rd | 4 ++--
man/survMisc-package.Rd | 2 +-
6 files changed, 14 insertions(+), 12 deletions(-)
Title: Multitaper Spectral Analysis Tools
Diff between multitaper versions 1.0-10 dated 2015-02-18 and 1.0-11 dated 2015-02-25
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim
Maintainer: Karim Rahim
multitaper-1.0-10/multitaper/man/multitaper-package.Rd |only
multitaper-1.0-11/multitaper/DESCRIPTION | 10 ++++----
multitaper-1.0-11/multitaper/MD5 | 11 ++++-----
multitaper-1.0-11/multitaper/R/demod.R | 1
multitaper-1.0-11/multitaper/R/multitaper.R | 9 +++----
multitaper-1.0-11/multitaper/R/plots.R | 20 ++++++++---------
multitaper-1.0-11/multitaper/R/plotsHelper.R | 6 ++---
7 files changed, 27 insertions(+), 30 deletions(-)
Title: Multi-Model Inference
Diff between MuMIn versions 1.12.1 dated 2014-12-17 and 1.13.4 dated 2015-02-25
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń
MuMIn-1.12.1/MuMIn/R/QAIC.R |only
MuMIn-1.12.1/MuMIn/R/oldR.R |only
MuMIn-1.13.4/MuMIn/DESCRIPTION | 12
MuMIn-1.13.4/MuMIn/MD5 | 107 +++----
MuMIn-1.13.4/MuMIn/NAMESPACE | 20 -
MuMIn-1.13.4/MuMIn/NEWS | 46 +++
MuMIn-1.13.4/MuMIn/R/AICc.R | 102 ++++---
MuMIn-1.13.4/MuMIn/R/Cp.R | 2
MuMIn-1.13.4/MuMIn/R/DIC.R | 2
MuMIn-1.13.4/MuMIn/R/Weights.R | 2
MuMIn-1.13.4/MuMIn/R/coefTable.R | 9
MuMIn-1.13.4/MuMIn/R/dredge.R | 308 ++++++++++++-----------
MuMIn-1.13.4/MuMIn/R/ext-gamm.R | 2
MuMIn-1.13.4/MuMIn/R/ext.R | 60 +++-
MuMIn-1.13.4/MuMIn/R/formulas.R | 32 ++
MuMIn-1.13.4/MuMIn/R/get.models.R | 30 +-
MuMIn-1.13.4/MuMIn/R/getAllTerms.R | 192 +++++++-------
MuMIn-1.13.4/MuMIn/R/makeArgs.R | 37 +-
MuMIn-1.13.4/MuMIn/R/methods-logLik.R | 8
MuMIn-1.13.4/MuMIn/R/model.avg.R | 194 +++++++-------
MuMIn-1.13.4/MuMIn/R/model.sel.R | 93 +++---
MuMIn-1.13.4/MuMIn/R/model.selection.R | 66 ++--
MuMIn-1.13.4/MuMIn/R/pdredge.R | 272 +++++++++++---------
MuMIn-1.13.4/MuMIn/R/predict.R |only
MuMIn-1.13.4/MuMIn/R/quasiLik.R | 4
MuMIn-1.13.4/MuMIn/R/r.squaredGLMM.R | 31 --
MuMIn-1.13.4/MuMIn/R/r.squaredLR.R | 4
MuMIn-1.13.4/MuMIn/R/stdize.R | 115 ++++++--
MuMIn-1.13.4/MuMIn/R/substitution.R | 84 ++----
MuMIn-1.13.4/MuMIn/R/termdeps.R | 2
MuMIn-1.13.4/MuMIn/R/updateable.R | 20 -
MuMIn-1.13.4/MuMIn/R/utils-misc.R | 36 +-
MuMIn-1.13.4/MuMIn/R/utils-models.R | 102 ++++++-
MuMIn-1.13.4/MuMIn/man/AICc.Rd | 31 +-
MuMIn-1.13.4/MuMIn/man/ICs.Rd | 4
MuMIn-1.13.4/MuMIn/man/MuMIn-package.Rd | 5
MuMIn-1.13.4/MuMIn/man/QAIC.Rd | 12
MuMIn-1.13.4/MuMIn/man/QIC.Rd | 7
MuMIn-1.13.4/MuMIn/man/dredge.Rd | 42 +--
MuMIn-1.13.4/MuMIn/man/get.models.Rd | 9
MuMIn-1.13.4/MuMIn/man/importance.Rd | 8
MuMIn-1.13.4/MuMIn/man/mod.sel.Rd | 33 +-
MuMIn-1.13.4/MuMIn/man/model-utils.Rd | 19 -
MuMIn-1.13.4/MuMIn/man/model.avg.Rd | 83 +++---
MuMIn-1.13.4/MuMIn/man/nested.Rd | 4
MuMIn-1.13.4/MuMIn/man/pdredge.Rd | 4
MuMIn-1.13.4/MuMIn/man/predict.averaging.Rd | 29 +-
MuMIn-1.13.4/MuMIn/man/r.squaredGLMM.Rd | 5
MuMIn-1.13.4/MuMIn/man/stdize.Rd | 152 +++++++----
MuMIn-1.13.4/MuMIn/man/subset.model.selection.Rd | 10
MuMIn-1.13.4/MuMIn/man/updateable.Rd | 33 +-
MuMIn-1.13.4/MuMIn/man/weights.Rd | 10
MuMIn-1.13.4/MuMIn/tests/_gam.R | 3
MuMIn-1.13.4/MuMIn/tests/classes.R | 12
MuMIn-1.13.4/MuMIn/tests/coxme.R | 11
MuMIn-1.13.4/MuMIn/tests/unmarked.R | 36 +-
56 files changed, 1515 insertions(+), 1041 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-14 0.9.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-30 2.11.2.1
2014-06-25 2.11.1.1
2013-07-16 1.0.4
2013-06-25 1.0.3
Title: Construction, Simulation and Analysis of Boolean Networks
Diff between BoolNet versions 2.1.0 dated 2015-02-23 and 2.1.1 dated 2015-02-25
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, probabilistic and temporal Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler
DESCRIPTION | 10
MD5 | 13
inst/NEWS.Rd | 6
inst/doc/BoolNet_package_vignette.pdf | 1555 +++++++++++++++++-----------------
man/BoolNet-package.Rd | 4
src/Makevars.win |only
src/picosat.c | 15
src/symbolic_simulator.c | 2
8 files changed, 809 insertions(+), 796 deletions(-)
Title: Serial Dependence Diagrams
Diff between SDD versions 1.1 dated 2014-02-27 and 1.2 dated 2015-02-25
Description: Allows for computing (and by default plotting) different types of serial dependence diagrams.
Author: Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
inst |only
man/ADF.Rd | 6 ++++--
man/SDD-package.Rd | 12 +++++++-----
man/SMI.Rd | 2 ++
6 files changed, 23 insertions(+), 16 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-8 dated 2015-02-04 and 1.3-9 dated 2015-02-25
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/doc/lgcp.pdf |binary
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Feature Grouping and Selection Over an Undirected Graph
Diff between FGSG versions 1.0 dated 2014-04-13 and 1.0.2 dated 2015-02-25
Description: Implement algorithms for feature grouping and selection over an undirected graph, solves problems like graph fused lasso, graph OSCAR and so on.
Author: Xiaotong Shen, Yiwen Sun, Julie Langou
Maintainer: Yiwen Sun
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NAMESPACE | 8 +++++++-
man/gflasso.Rd | 28 +++++++++++++++-------------
man/goscar.Rd | 27 ++++++++++++++-------------
man/ncFGS.Rd | 27 ++++++++++++++-------------
man/ncTF.Rd | 27 ++++++++++++++-------------
man/ncTFGS.Rd | 28 +++++++++++++++-------------
man/ncTL.Rd | 29 +++++++++++++++--------------
man/ncTLF.Rd | 29 +++++++++++++++--------------
src/lafunc.h | 22 +++++++++++-----------
11 files changed, 135 insertions(+), 120 deletions(-)
Title: Soil Database Interface
Diff between soilDB versions 1.5 dated 2015-02-20 and 1.5-2 dated 2015-02-25
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 15 -
MD5 | 44 ++--
NEWS | 3
R/SDA_query.R | 2
R/SSURGO_spatial_query.R | 2
R/fetchNASIS.R | 4
R/fetchPedonPC.R | 4
R/get_colors_from_NASIS_db.R | 4
R/get_extended_data_from_NASIS_db.R | 4
R/get_hz_data_from_NASIS_db.R | 4
R/get_lablayer_data_from_NASIS_db.R | 6
R/get_labpedon_data_from_NASIS_db.R | 4
R/get_site_data_from_NASIS_db.R | 4
R/get_text_notes_from_NASIS_db.R | 4
R/mapunit_geom_by_ll_bbox.R | 2
R/nasis_component_data.R | 338 ++++++++++++++++++------------------
R/seriesExtent.R | 4
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/SDA_query.Rd | 2
23 files changed, 224 insertions(+), 226 deletions(-)
Title: Skewed Generalized T Distribution
Diff between sgt versions 1.0 dated 2015-02-16 and 1.1 dated 2015-02-25
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis
Maintainer: Carter Davis
sgt-1.0/sgt/src |only
sgt-1.1/sgt/DESCRIPTION | 12 ++---
sgt-1.1/sgt/MD5 | 16 ++----
sgt-1.1/sgt/NAMESPACE | 2
sgt-1.1/sgt/R/SGT.R | 114 ++++++++++++++++++++++++------------------------
sgt-1.1/sgt/R/SGTMLE.R | 2
sgt-1.1/sgt/man/sgt.Rd | 24 ++--------
7 files changed, 77 insertions(+), 93 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Diff between R.matlab versions 3.1.1 dated 2014-10-10 and 3.2.0 dated 2015-02-25
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson
DESCRIPTION | 17 +--
MD5 | 25 ++--
NEWS | 25 ++++
R/999.package.R | 2
R/Matlab.R | 25 +++-
R/readMat.R | 142 +++++++++++++++++---------
R/zzz.R | 2
inst/externals/MatlabServer.m | 9 +
inst/mat-files/SparseMatrix,all_zeros.mat |only
man/1._The_MATLAB_server_running_in_MATLAB.Rd | 9 +
man/Matlab.Rd | 43 +++++++
man/R.matlab-package.Rd | 9 -
man/readMat.Rd | 16 ++
tests/readMat.R | 84 +++++++++++----
14 files changed, 291 insertions(+), 117 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Diff between npmv versions 2.1 dated 2013-12-04 and 2.2 dated 2015-02-25
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis
DESCRIPTION | 10 +++---
MD5 | 14 ++++-----
NAMESPACE | 1
R/basenonpartest.R | 17 ++++++++++-
R/nonpartest.R | 56 ++++++++++++++++++++++++++++++--------
R/ssnonpartest.R | 76 +++++++++++++++++++++++++++++++++++++++++-----------
man/nonpartest.Rd | 7 +++-
man/npmv-package.Rd | 4 +-
8 files changed, 141 insertions(+), 44 deletions(-)
Title: Variable Importance Analysis with Population Intervention Models
Diff between multiPIM versions 1.4-1 dated 2014-04-14 and 1.4-3 dated 2015-02-25
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter
Maintainer: Stephan Ritter
multiPIM-1.4-1/multiPIM/R/zzz.R |only
multiPIM-1.4-3/multiPIM/ChangeLog | 4 ++++
multiPIM-1.4-3/multiPIM/DESCRIPTION | 8 ++++----
multiPIM-1.4-3/multiPIM/MD5 | 7 +++----
multiPIM-1.4-3/multiPIM/R/multiPIMboot.R | 15 +++++++--------
5 files changed, 18 insertions(+), 16 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 3.1.1 dated 2014-09-23 and 3.2 dated 2015-02-25
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate descriptive statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function and color themes. The function Help provides a help system that suggests specific analyses and functions. Variable labels are available. A confirmatory factor analysis of multiple indicator measurement models is also available as is a pedagogical routines for data simulation such as for the Central Limit Theorem.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing
lessR-3.1.1/lessR/R/den.zmain.R |only
lessR-3.2/lessR/DESCRIPTION | 8
lessR-3.2/lessR/MD5 | 87 +++----
lessR-3.2/lessR/NEWS | 33 ++
lessR-3.2/lessR/R/ANOVA.R | 17 +
lessR-3.2/lessR/R/ANOVAz1.R | 46 ++-
lessR-3.2/lessR/R/ANOVAz2.R | 36 ++
lessR-3.2/lessR/R/BarChart.R | 6
lessR-3.2/lessR/R/BoxPlot.R | 4
lessR-3.2/lessR/R/Density.R | 4
lessR-3.2/lessR/R/Help.R | 272 +++++++++-------------
lessR-3.2/lessR/R/Histogram.R | 6
lessR-3.2/lessR/R/LineChart.R | 4
lessR-3.2/lessR/R/Logit.R | 2
lessR-3.2/lessR/R/Regression.R | 21 +
lessR-3.2/lessR/R/ScatterPlot.R | 27 +-
lessR-3.2/lessR/R/bc.data.frame.R | 4
lessR-3.2/lessR/R/bc.zmain.R | 6
lessR-3.2/lessR/R/bx.zmain.R | 8
lessR-3.2/lessR/R/corScree.R | 33 ++
lessR-3.2/lessR/R/dn.zmain.R | 6
lessR-3.2/lessR/R/dp.zmain.R | 4
lessR-3.2/lessR/R/hst.zmain.R | 6
lessR-3.2/lessR/R/lc.zmain.R | 6
lessR-3.2/lessR/R/logit.z4Pred.R | 7
lessR-3.2/lessR/R/pc.zmain.R | 31 ++
lessR-3.2/lessR/R/plt.zmain.R | 10
lessR-3.2/lessR/R/reg.z3Residual.R | 297 ++++++++++++------------
lessR-3.2/lessR/R/reg.z5Plot.R | 56 +++-
lessR-3.2/lessR/R/simCLT.R | 2
lessR-3.2/lessR/R/tt.z1graph.R | 2
lessR-3.2/lessR/R/tt.z1group.R | 86 ++++--
lessR-3.2/lessR/R/tt.z2graph.R | 2
lessR-3.2/lessR/R/tt.z2group.R | 75 +++---
lessR-3.2/lessR/R/ttest.R | 456 ++++++++++++++++++++++++++++++++-----
lessR-3.2/lessR/R/ttp2zgraph.R | 2
lessR-3.2/lessR/R/zzz.R | 67 +++--
lessR-3.2/lessR/man/BarChart.Rd | 5
lessR-3.2/lessR/man/BoxPlot.Rd | 7
lessR-3.2/lessR/man/Density.Rd | 9
lessR-3.2/lessR/man/Histogram.Rd | 14 -
lessR-3.2/lessR/man/LineChart.Rd | 21 +
lessR-3.2/lessR/man/PieChart.Rd | 4
lessR-3.2/lessR/man/ScatterPlot.Rd | 9
lessR-3.2/lessR/man/ttest.Rd | 2
45 files changed, 1179 insertions(+), 631 deletions(-)
Title: Interactive Q-Learning
Diff between iqLearn versions 1.2 dated 2014-03-04 and 1.3 dated 2015-02-25
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn
DESCRIPTION | 10 +++---
MD5 | 68 ++++++++++++++++++++++----------------------
NAMESPACE | 36 +++++++++++++++++++++++
README.md |only
build/vignette.rds |binary
inst/CITATION |only
inst/doc/iqLearn.Rnw | 2 -
inst/doc/iqLearn.pdf |binary
man/IQ1.Rd | 5 +--
man/IQ2.Rd | 5 +--
man/iqLearn-package.Rd | 5 +--
man/learnIQ1.Rd | 5 +--
man/learnIQ1cm.Rd | 5 +--
man/learnIQ1main.Rd | 5 +--
man/learnIQ1var.Rd | 5 +--
man/learnIQ2.Rd | 5 +--
man/plot.iqResids.Rd | 5 +--
man/plot.learnIQ1cm.Rd | 5 +--
man/plot.learnIQ1main.Rd | 5 +--
man/plot.learnIQ1var.Rd | 5 +--
man/plot.learnIQ2.Rd | 5 +--
man/plot.qLearnS1.Rd | 5 +--
man/plot.qLearnS2.Rd | 5 +--
man/qLearnQ1.Rd | 5 +--
man/qLearnQ2.Rd | 5 +--
man/qLearnS1.Rd | 5 +--
man/qLearnS2.Rd | 5 +--
man/summary.learnIQ1cm.Rd | 5 +--
man/summary.learnIQ1main.Rd | 5 +--
man/summary.learnIQ1var.Rd | 5 +--
man/summary.learnIQ2.Rd | 5 +--
man/summary.qLearnS1.Rd | 5 +--
man/summary.qLearnS2.Rd | 5 +--
man/summary.value.Rd | 5 +--
man/value.Rd | 5 +--
vignettes/iqLearn.Rnw | 2 -
36 files changed, 159 insertions(+), 94 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Diff between dunn.test versions 1.2.2 dated 2015-01-03 and 1.2.3 dated 2015-02-25
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/dunn.test.R | 18 ++++++++++++++----
man/dunn.test.Rd | 3 ++-
4 files changed, 24 insertions(+), 13 deletions(-)
More information about BayesSummaryStatLM at CRAN
Permanent link
Title: Pull Data from 'trakt.tv'
Diff between tRakt versions 0.7.4 dated 2015-02-23 and 0.9.0 dated 2015-02-24
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk
DESCRIPTION | 13 -
MD5 | 98 ++++----
NAMESPACE | 4
R/api.R | 25 +-
R/trakt.getEpisodeData.R | 63 ++---
R/trakt.getFullShowData.R | 32 +-
R/trakt.getSeasons.R | 11
R/trakt.search.R | 21 -
R/trakt.search.byid.R | 15 -
R/trakt.show.people.R | 20 +
R/trakt.show.related.R | 18 +
R/trakt.show.season.R | 41 ++-
R/trakt.show.stats.R | 13 -
R/trakt.show.summary.R | 19 -
R/trakt.shows.popular.R | 21 +
R/trakt.shows.trending.R | 25 +-
R/trakt.user.collection.R | 5
R/trakt.user.followers.R |only
R/trakt.user.following.R |only
R/trakt.user.friends.R |only
R/trakt.user.ratings.R |only
R/trakt.user.stats.R | 10
R/trakt.user.watched.R | 18 -
R/trakt.user.watchlist.R | 4
README.md | 39 ---
inst/doc/tRakt-Usage.R | 10
inst/doc/tRakt-Usage.Rmd | 10
inst/doc/tRakt-Usage.html | 180 +++++++--------
man/get_trakt_credentials.Rd | 7
man/trakt.api.call.Rd | 5
man/trakt.getEpisodeData.Rd | 19 +
man/trakt.getFullShowData.Rd | 11
man/trakt.getSeasons.Rd | 11
man/trakt.search.Rd | 9
man/trakt.search.byid.Rd | 7
man/trakt.show.people.Rd | 15 +
man/trakt.show.related.Rd | 15 +
man/trakt.show.season.Rd | 14 +
man/trakt.show.stats.Rd | 11
man/trakt.show.summary.Rd | 11
man/trakt.shows.popular.Rd | 16 +
man/trakt.shows.trending.Rd | 16 +
man/trakt.user.collection.Rd | 9
man/trakt.user.followers.Rd |only
man/trakt.user.following.Rd |only
man/trakt.user.friends.Rd |only
man/trakt.user.ratings.Rd |only
man/trakt.user.stats.Rd | 16 +
man/trakt.user.watched.Rd | 9
man/trakt.user.watchlist.Rd | 9
vignettes/tRakt-Usage.Rmd | 10
vignettes/tRakt-Usage_files/figure-html/Graphing_1-1.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-2.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-3.png |binary
54 files changed, 575 insertions(+), 360 deletions(-)
Title: A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]
Diff between aroma.apd versions 0.5.0 dated 2014-02-27 and 0.6.0 dated 2015-02-24
Description: DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 27 +++++++++++++++------------
MD5 | 30 ++++++++++++++++++------------
NEWS | 7 +++++++
R/cdfToApdMap.R | 8 ++++----
R/celToApd.R | 10 +++++-----
R/gtypeCelToPQ.R | 17 +++++++++--------
R/readApdRectangle.R | 6 +++---
R/readApdUnits.R | 24 ++++++++++--------------
R/updateApdUnits.R | 18 ++++++++++--------
R/zzz.R | 14 ++++++++------
man/aroma.apd-package.Rd | 2 +-
man/gtypeCelToPQ.Rd | 4 ++--
man/readApdUnits.Rd | 6 ------
tests |only
14 files changed, 92 insertions(+), 81 deletions(-)
Title: Tools for Nuclear Magnetic Resonance Spectrum Alignment and
Quantitative Analysis
Diff between speaq versions 1.2.0 dated 2015-01-14 and 1.2.1 dated 2015-02-24
Description: We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Related publication is available at http://www.biomedcentral.com/1471-2105/12/405/.
Author: Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Maintainer: Trung Nghia Vu
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
NEWS | 6 ++++++
man/speaq-package.Rd | 6 +++---
4 files changed, 19 insertions(+), 13 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Diff between rfUtilities versions 1.0 dated 2014-11-21 and 1.0-1 dated 2015-02-24
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans
rfUtilities-1.0-1/rfUtilities/DESCRIPTION | 26 +++++-----
rfUtilities-1.0-1/rfUtilities/MD5 | 34 ++++++++------
rfUtilities-1.0-1/rfUtilities/NAMESPACE | 3 -
rfUtilities-1.0-1/rfUtilities/R/multi.collinear.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.class.sensitivity.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.classBalance.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.crossValidation.R | 6 +-
rfUtilities-1.0-1/rfUtilities/R/rf.modelSel.R | 8 +--
rfUtilities-1.0-1/rfUtilities/R/rf.partial.ci.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.partial.prob.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.significance.R | 12 ++--
rfUtilities-1.0-1/rfUtilities/inst |only
rfUtilities-1.0-1/rfUtilities/man/multi.collinear.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.class.sensitivity.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.classBalance.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.crossValidation.Rd | 7 +-
rfUtilities-1.0-1/rfUtilities/man/rf.modelSel.Rd | 9 ++-
rfUtilities-1.0-1/rfUtilities/man/rf.partial.ci.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.partial.prob.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.significance.Rd | 13 ++---
rfUtilities-1.0/rfUtilities/R/MultiColinear.R |only
rfUtilities-1.0/rfUtilities/R/probPartialPlot.R |only
rfUtilities-1.0/rfUtilities/R/rf.ClassBalance.R |only
rfUtilities-1.0/rfUtilities/man/MultiColinear.Rd |only
rfUtilities-1.0/rfUtilities/man/probPartialPlot.Rd |only
rfUtilities-1.0/rfUtilities/man/rf.ClassBalance.Rd |only
26 files changed, 64 insertions(+), 54 deletions(-)
Title: R interface to Global Biotic Interactions
Diff between rglobi versions 0.2.4 dated 2015-01-28 and 0.2.5 dated 2015-02-24
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
source all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen
rglobi-0.2.4/rglobi/rglobi_0.2.4.tar.gz |only
rglobi-0.2.5/rglobi/DESCRIPTION | 8 ++--
rglobi-0.2.5/rglobi/MD5 | 7 +---
rglobi-0.2.5/rglobi/README.md | 41 +++++++++++++++---------
rglobi-0.2.5/rglobi/tests/testthat/test-globi.R | 2 -
5 files changed, 35 insertions(+), 23 deletions(-)
Title: Visualization Methods for Raster Data
Diff between rasterVis versions 0.32 dated 2014-10-25 and 0.35 dated 2015-02-24
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro
ChangeLog | 18 ++---
DESCRIPTION | 16 ++--
MD5 | 18 ++---
NAMESPACE | 2
R/grid.R | 26 +++++++
R/streamplot.R | 53 +++++++---------
R/vectorplot.R | 153 ++++++++++++++++++++++++++++++++---------------
README.md | 2
man/hovmoller-methods.Rd | 51 ++++++++++-----
man/vectorplot.Rd | 49 ++++++++++-----
10 files changed, 249 insertions(+), 139 deletions(-)
Title: Nonparametric Stability Analysis
Diff between phenability versions 1.0 dated 2014-04-23 and 2.0 dated 2015-02-24
Description: An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
Author: Leonardo Castelo Branco
Maintainer: Leonardo C. Branco
DESCRIPTION | 10 +-
MD5 | 21 ++--
R/fox.R | 62 ++++++++-----
R/kang.R | 54 ++++++++---
R/nahu.R | 212 +++++++++++++++++++++++---------------------
R/phenability-internal.R |only
R/thsu.R | 213 ++++++++++++++++++++++++---------------------
man/fox.Rd | 11 +-
man/kang.Rd | 9 +
man/nahu.Rd | 9 +
man/phenability-package.Rd | 15 ++-
man/thsu.Rd | 9 +
12 files changed, 357 insertions(+), 268 deletions(-)
Title: Methods for Maximum Likelihood Estimation
Diff between likelihood versions 1.6 dated 2014-06-27 and 1.7 dated 2015-02-24
Description: Tools for maximum likelihood estimation of parameters
of scientific models.
Author: Lora Murphy
Maintainer: Lora Murphy
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/anneal.R | 7 +++++--
man/anneal.Rd | 4 ++--
man/simulated_annealing_algorithm.Rd | 4 ++--
5 files changed, 18 insertions(+), 15 deletions(-)
Title: Freedom from Disease
Diff between FFD versions 1.0-2 dated 2013-04-22 and 1.0-6 dated 2015-02-24
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka
DESCRIPTION | 25 +++++------------
MD5 | 24 ++++++++--------
NAMESPACE | 1
R/FFD_GUI-internal.R | 6 ++--
R/FFD_GUI.R | 3 +-
R/computeAlphaLimitedSampling.R | 2 -
R/computeAposterioriError.R | 14 ++++-----
build |only
inst/doc/FFD-intro.R |only
inst/doc/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
inst/doc/FFD-intro.pdf |binary
man/lls.Rd | 6 ++--
vignettes/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
vignettes/FFD.bib | 9 ++++++
14 files changed, 106 insertions(+), 100 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Diff between clinfun versions 1.0.6 dated 2014-07-22 and 1.0.9 dated 2015-02-24
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan
CHANGES | 13 +++++++++
DESCRIPTION | 6 ++--
INDEX | 3 ++
MD5 | 18 ++++++-------
NAMESPACE | 2 -
R/calogrank.R | 3 +-
R/coxphQuantile.R | 32 +++++++++++------------
R/fedesign.R | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
R/permlogrank.R | 9 +++---
man/fedesign.Rd | 16 +++++++++--
10 files changed, 139 insertions(+), 37 deletions(-)
Title: Applied Econometrics with R
Diff between AER versions 1.2-2 dated 2014-01-28 and 1.2-3 dated 2015-02-24
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 13 -
MD5 | 282 +++++++++++++++++------------------
NAMESPACE | 4
NEWS | 9 +
R/dispersiontest.R | 9 -
R/tobit.R | 6
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data/ChinaIncome.rda |binary
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man/Baltagi2002.Rd | 1
man/BenderlyZwick.Rd | 4
man/CigarettesB.Rd | 4
man/DoctorVisits.Rd | 2
man/Equipment.Rd | 2
man/EuroEnergy.Rd | 4
man/GSOEP9402.Rd | 2
man/GSS7402.Rd | 2
man/GrowthDJ.Rd | 2
man/HousePrices.Rd | 2
man/MarkDollar.Rd | 2
man/MarkPound.Rd | 2
man/Mortgage.Rd | 4
man/Municipalities.Rd | 2
man/NMES1988.Rd | 2
man/NaturalGas.Rd | 4
man/OECDGas.Rd | 4
man/OrangeCounty.Rd | 4
man/PSID1982.Rd | 4
man/RecreationDemand.Rd | 2
man/TradeCredit.Rd | 4
man/USConsump1993.Rd | 4
man/USCrudes.Rd | 4
man/USGasB.Rd | 4
man/USMacroB.Rd | 4
man/tobit.Rd | 2
tests/Ch-Intro.Rout.save | 20 +-
tests/Ch-LinearRegression.R | 1
tests/Ch-LinearRegression.Rout.save | 11 -
tests/Ch-Microeconometrics.Rout.save | 12 -
142 files changed, 214 insertions(+), 230 deletions(-)
Title: Nomograms for Right-Censored Outcomes from Survey Designs
Diff between SvyNom versions 1.0 dated 2012-12-07 and 1.1 dated 2015-02-24
Description: Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
Author: Mithat Gonen, Marinela Capanu
Maintainer: Mithat Gonen
DESCRIPTION | 15 +++++++--------
MD5 | 17 ++++++++++-------
NAMESPACE | 7 +++++++
R/SvyNom.R |only
data/noNA.txt |only
inst |only
man/SvyNom-package.Rd | 17 +++++++++--------
man/noNA.Rd | 2 +-
man/svycox.calibrate.Rd | 10 +++++++---
man/svycox.nomogram.Rd | 17 ++++++++++-------
man/svycox.validate.Rd | 24 ++++++++++++++----------
11 files changed, 65 insertions(+), 44 deletions(-)
Title: Histogram-Valued Data Analysis
Diff between HistDAWass versions 0.1 dated 2015-02-18 and 0.1.1 dated 2015-02-24
Description: In the framework of Symbolic Data Analysis, a relatively new approach
to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e.,
data described by univariate histograms. The methods and the basic statistics for
histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification techniques,
least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/HistDAWass-package.R | 2 +-
R/unsuperv_classification.R | 2 +-
man/HistDAWass-package.Rd | 2 +-
man/WH_hclust.Rd | 2 +-
6 files changed, 13 insertions(+), 13 deletions(-)
Title: Construction Methods of some Series of PBIB Designs
Diff between CombinS versions 1.0 dated 2013-12-12 and 1.1 dated 2015-02-24
Description: The Combinatory Method (s) to Construct a series of PBIB designs and we give their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib
CombinS-1.0/CombinS/R/PBIB4.R |only
CombinS-1.0/CombinS/R/PBIB5.R |only
CombinS-1.0/CombinS/R/PBIB7.R |only
CombinS-1.0/CombinS/man/PBIB4.Rd |only
CombinS-1.0/CombinS/man/PBIB5.Rd |only
CombinS-1.0/CombinS/man/PBIB7.Rd |only
CombinS-1.1/CombinS/DESCRIPTION | 17 ++----
CombinS-1.1/CombinS/MD5 | 26 +++++----
CombinS-1.1/CombinS/R/CombS.R | 79 +++++++++++++++++++----------
CombinS-1.1/CombinS/R/GPBIB4A.R |only
CombinS-1.1/CombinS/R/GPBIB4B.R |only
CombinS-1.1/CombinS/R/GPBIB5.R |only
CombinS-1.1/CombinS/R/GPBIB7A.R |only
CombinS-1.1/CombinS/R/GPBIB7B.R |only
CombinS-1.1/CombinS/R/UType.R |only
CombinS-1.1/CombinS/man/CombS.Rd | 51 ++++++++++--------
CombinS-1.1/CombinS/man/CombinS-package.Rd | 52 +++++++++++++------
CombinS-1.1/CombinS/man/GPBIB4A.Rd |only
CombinS-1.1/CombinS/man/GPBIB4B.Rd |only
CombinS-1.1/CombinS/man/GPBIB5.Rd |only
CombinS-1.1/CombinS/man/GPBIB7A.Rd |only
CombinS-1.1/CombinS/man/GPBIB7B.Rd |only
CombinS-1.1/CombinS/man/UType.Rd |only
23 files changed, 143 insertions(+), 82 deletions(-)
Title: Partial Least Squares Regression with Backward Selection of
Predictors
Diff between autopls versions 1.2-7 dated 2013-08-13 and 1.3 dated 2015-02-24
Description: Some convenience functions for pls regression, including backward
variable selection and validation procedures, image based predictions
and plotting.
Author: Sebastian Schmidtlein, with contributions from C. Oldenburg and H. Feilhauer
and with a code snipped borrowed from Bjorn-Helge Mevik
Maintainer: Sebastian Schmidtlein
DESCRIPTION | 20 ++++++++++++--------
MD5 | 22 +++++++++++-----------
NAMESPACE | 1 +
R/autopls.R | 21 +++++----------------
R/autoplsVAL.R | 2 +-
R/postprocessing.R | 2 +-
R/predict.autopls.R | 14 +++++++-------
R/predict.slim.R | 14 +++++++-------
R/prepro.R | 2 +-
man/autopls.Rd | 36 ++++++++++++++++++++----------------
man/autoplsVAL.Rd | 12 +++++++++---
man/murnau.X.Rd | 2 +-
12 files changed, 76 insertions(+), 72 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Diff between daff versions 0.1.1 dated 2015-02-23 and 0.1.2 dated 2015-02-24
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches.
Changes to data can be made visible by using render_diff. Daff uses the V8 package to
wrap the 'daff.js' javascript library which is included in the package.
Daff exposes a subset of 'daff.js' functionality, tailored for usage within R.
Author: Paul Fitzpatrick [aut] (javascript original,
http://paulfitz.github.io/daff/),
Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge
DESCRIPTION | 9 ++++-----
MD5 | 11 ++++++-----
NEWS |only
R/TableView.R | 6 ++++--
README.md | 13 ++++++++++---
inst/js/util.js | 7 +++++--
tests/testthat/testdiff-data.R | 6 ++++++
7 files changed, 35 insertions(+), 17 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Diff between cds versions 1.0 dated 2015-02-16 and 1.0.1 dated 2015-02-24
Description: This is an implementation of constrained dual scaling for detecting response
styles in categorical data, including utility functions. The procedure involves adding
additional columns to the data matrix representing the boundaries between the rating categories.
The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are
sought which provide optimal scores for the rating categories. These optimal scores are
constrained to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can be diagnosed
from the optimal scores for said cluster, and this can be used to construct an
imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees
DESCRIPTION | 8 ++---
MD5 | 10 +++----
R/cds.sim.R | 4 +-
R/sensory.R | 79 +++------------------------------------------------------
man/cds.sim.Rd | 4 +-
man/sensory.Rd | 79 +++------------------------------------------------------
6 files changed, 23 insertions(+), 161 deletions(-)
Title: Test Analysis Modules
Diff between TAM versions 1.4-1 dated 2015-01-16 and 1.5-2 dated 2015-02-24
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 18 -
MD5 | 153 ++++++-----
NAMESPACE | 44 +++
R/IRT.WrightMap.R | 37 ++
R/IRT.data.tam.R |only
R/IRT.expectedCounts.tam.R |only
R/IRT.irfprob.tam.R | 6
R/IRT.likelihood.TAM.R | 6
R/IRT.linearCFA.R |only
R/IRT.modelfit.tam.R |only
R/IRT.threshold.R |only
R/calc_exp_TK.R | 2
R/calc_prob.v5.R | 9
R/doparse.R | 6
R/extend.label.group.R | 5
R/lavaanify.IRT.R | 5
R/msq.itemfit.R |only
R/mstep.regression.R | 4
R/plot.ctt.R | 50 +++
R/plot.tam.R | 2
R/plotDevianceTAM.R | 8
R/predict.tam.R |only
R/summary.msq.itemfit.R |only
R/tam.mml.2pl.R | 38 ++
R/tam.mml.3pl.R | 21 +
R/tam.mml.R | 18 +
R/tam.mml.mfr.R | 10
R/tam.modelfit.R | 321 ++++++++++++-------------
R/tam.modelfit.func.R |only
R/tam.parameterfix.defaults.R |only
R/tam.pv.R | 10
R/tamaan.3pl.trait.R | 1
R/tamaan.R | 6
R/tamaanify.R | 7
R/tamaanify.define.method.R | 12
R/tamaanify.modelconstraint.loadings.R | 28 ++
R/tamaanify.proc.lavaanmodel.R | 2
R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R | 4
data/data.cqc01.rda |binary
data/data.cqc02.rda |binary
data/data.cqc03.rda |binary
data/data.cqc04.rda |binary
data/data.cqc05.rda |binary
data/data.ctest1.rda |binary
data/data.ctest2.rda |binary
data/data.ex08.rda |binary
data/data.ex10.rda |binary
data/data.ex11.rda |binary
data/data.ex12.rda |binary
data/data.ex14.rda |binary
data/data.ex15.rda |binary
data/data.exJ03.rda |binary
data/data.fims.Aus.Jpn.raw.rda |binary
data/data.fims.Aus.Jpn.scored.rda |binary
data/data.geiser.rda |binary
data/data.gpcm.rda |binary
data/data.janssen.rda |binary
data/data.janssen2.rda |binary
data/data.mc.rda |binary
data/data.numeracy.rda |binary
data/data.timssAusTwn.rda |binary
data/data.timssAusTwn.scored.rda |binary
data/sim.facets.rda |binary
data/sim.mfr.rda |binary
data/sim.rasch.missing.rda |binary
data/sim.rasch.pweights.rda |binary
data/sim.rasch.rda |binary
inst/NEWS | 56 +++-
man/IRT.WrightMap.Rd | 5
man/IRT.data.tam.Rd |only
man/IRT.expectedCounts.tam.Rd |only
man/IRT.likelihood.tam.Rd | 8
man/IRT.linearCFA.Rd |only
man/IRT.threshold.Rd |only
man/TAM-package.Rd | 4
man/data.cqc.Rd | 2
man/msq.itemfit.Rd |only
man/plot.tam.Rd | 18 -
man/predict.Rd |only
man/tam.ctt.Rd | 13 -
man/tam.fit.Rd | 2
man/tam.jml.Rd | 2
man/tam.latreg.Rd | 8
man/tam.mml.Rd | 60 ++++
man/tam.modelfit.Rd | 72 ++++-
src/msq_itemfit.cpp |only
86 files changed, 724 insertions(+), 359 deletions(-)
Title: Survival Analysis
Diff between survival versions 2.37-7 dated 2014-01-22 and 2.38-1 dated 2015-02-24
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau
survival-2.37-7/survival/R/basehaz.S |only
survival-2.37-7/survival/inst/doc/sourcecode.pdf |only
survival-2.37-7/survival/src/msurv.c |only
survival-2.37-7/survival/vignettes/raheart.rda |only
survival-2.38-1/survival/.Rinstignore |only
survival-2.38-1/survival/DESCRIPTION | 21
survival-2.38-1/survival/MD5 | 306 ++++---
survival-2.38-1/survival/NAMESPACE | 20
survival-2.38-1/survival/R/agreg.fit.R | 37
survival-2.38-1/survival/R/agsurv.R | 1
survival-2.38-1/survival/R/anova.coxph.S | 52 -
survival-2.38-1/survival/R/anova.coxphlist.S | 5
survival-2.38-1/survival/R/basehaz.R |only
survival-2.38-1/survival/R/cch.R | 4
survival-2.38-1/survival/R/clogit.R | 21
survival-2.38-1/survival/R/coxexact.fit.R | 3
survival-2.38-1/survival/R/coxpenal.fit.R | 82 +
survival-2.38-1/survival/R/coxph.R | 58 -
survival-2.38-1/survival/R/coxph.detail.S | 1
survival-2.38-1/survival/R/frailty.controlaic.S | 2
survival-2.38-1/survival/R/frailty.controlgauss.S | 1
survival-2.38-1/survival/R/frailty.gamma.S | 11
survival-2.38-1/survival/R/frailty.gammacon.S | 1
survival-2.38-1/survival/R/frailty.gaussian.S | 11
survival-2.38-1/survival/R/frailty.t.S | 4
survival-2.38-1/survival/R/logLik.coxph.R | 13
survival-2.38-1/survival/R/model.matrix.coxph.R | 4
survival-2.38-1/survival/R/neardate.R |only
survival-2.38-1/survival/R/plot.survfit.R | 64 -
survival-2.38-1/survival/R/predict.coxph.penal.S | 9
survival-2.38-1/survival/R/predict.survreg.S | 5
survival-2.38-1/survival/R/print.coxph.S | 3
survival-2.38-1/survival/R/print.coxph.penal.S | 3
survival-2.38-1/survival/R/print.summary.coxph.S | 4
survival-2.38-1/survival/R/print.summary.coxph.penal.S | 4
survival-2.38-1/survival/R/print.summary.survexp.R | 13
survival-2.38-1/survival/R/print.summary.survfit.S | 11
survival-2.38-1/survival/R/print.summary.survfitms.S | 11
survival-2.38-1/survival/R/print.summary.survreg.S | 1
survival-2.38-1/survival/R/print.survexp.S | 12
survival-2.38-1/survival/R/print.survreg.penal.S | 3
survival-2.38-1/survival/R/pspline.S | 7
survival-2.38-1/survival/R/pyears.R | 20
survival-2.38-1/survival/R/strata.S | 24
survival-2.38-1/survival/R/summary.survreg.S | 2
survival-2.38-1/survival/R/survSplit.R | 4
survival-2.38-1/survival/R/survexp.R | 2
survival-2.38-1/survival/R/survfit.R | 2
survival-2.38-1/survival/R/survfitCI.R | 1
survival-2.38-1/survival/R/survfitTurnbull.S | 6
survival-2.38-1/survival/R/survfitms.R | 16
survival-2.38-1/survival/R/survreg.S | 5
survival-2.38-1/survival/R/survreg.distributions.S | 26
survival-2.38-1/survival/R/survreg.fit.S | 3
survival-2.38-1/survival/R/tmerge.R |only
survival-2.38-1/survival/R/xtras.R | 35
survival-2.38-1/survival/build/vignette.rds |binary
survival-2.38-1/survival/cleanup |only
survival-2.38-1/survival/cleanup.win |only
survival-2.38-1/survival/data/cgd.rda |binary
survival-2.38-1/survival/data/datalist | 6
survival-2.38-1/survival/data/kidney.rda |binary
survival-2.38-1/survival/data/mgus.rda |binary
survival-2.38-1/survival/data/mgus2.rda |only
survival-2.38-1/survival/data/ovarian.rda |binary
survival-2.38-1/survival/data/rats.rda |binary
survival-2.38-1/survival/data/transplant.rda |only
survival-2.38-1/survival/inst/CITATION | 12
survival-2.38-1/survival/inst/NEWS.Rd | 81 +
survival-2.38-1/survival/inst/NEWS.Rd.orig |only
survival-2.38-1/survival/inst/doc/adjcurve.R | 170 ++-
survival-2.38-1/survival/inst/doc/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/inst/doc/adjcurve.pdf |binary
survival-2.38-1/survival/inst/doc/compete.R |only
survival-2.38-1/survival/inst/doc/compete.Rnw |only
survival-2.38-1/survival/inst/doc/compete.pdf |only
survival-2.38-1/survival/inst/doc/splines.R |only
survival-2.38-1/survival/inst/doc/splines.Rnw |only
survival-2.38-1/survival/inst/doc/splines.pdf |only
survival-2.38-1/survival/inst/doc/tests.R | 25
survival-2.38-1/survival/inst/doc/tests.Rnw | 213 ++--
survival-2.38-1/survival/inst/doc/tests.pdf |binary
survival-2.38-1/survival/inst/doc/timedep.R | 130 ++-
survival-2.38-1/survival/inst/doc/timedep.Rnw | 735 ++++++++++++-----
survival-2.38-1/survival/inst/doc/timedep.pdf |binary
survival-2.38-1/survival/man/basehaz.Rd | 45 -
survival-2.38-1/survival/man/bladder.Rd | 8
survival-2.38-1/survival/man/cgd.Rd | 52 -
survival-2.38-1/survival/man/cgd0.Rd |only
survival-2.38-1/survival/man/cluster.Rd | 6
survival-2.38-1/survival/man/dsurvreg.Rd | 4
survival-2.38-1/survival/man/frailty.Rd | 6
survival-2.38-1/survival/man/mgus.Rd | 48 -
survival-2.38-1/survival/man/mgus2.Rd |only
survival-2.38-1/survival/man/neardate.Rd |only
survival-2.38-1/survival/man/ovarian.Rd | 3
survival-2.38-1/survival/man/pbcseq.Rd | 11
survival-2.38-1/survival/man/plot.survfit.Rd | 21
survival-2.38-1/survival/man/predict.coxph.Rd | 26
survival-2.38-1/survival/man/print.survfit.Rd | 4
survival-2.38-1/survival/man/rats.Rd | 7
survival-2.38-1/survival/man/strata.Rd | 11
survival-2.38-1/survival/man/summary.survfit.Rd | 3
survival-2.38-1/survival/man/survexp.Rd | 9
survival-2.38-1/survival/man/survfit.Rd | 3
survival-2.38-1/survival/man/survfit.coxph.Rd | 15
survival-2.38-1/survival/man/survfit.formula.Rd | 13
survival-2.38-1/survival/man/survreg.Rd | 2
survival-2.38-1/survival/man/survreg.object.Rd | 105 +-
survival-2.38-1/survival/man/tmerge.Rd |only
survival-2.38-1/survival/man/transplant.Rd |only
survival-2.38-1/survival/noweb |only
survival-2.38-1/survival/src/agexact.c | 1
survival-2.38-1/survival/src/agfit4.c | 4
survival-2.38-1/survival/src/agfit5.c | 151 ---
survival-2.38-1/survival/src/agmart.c | 6
survival-2.38-1/survival/src/agmart2.c | 2
survival-2.38-1/survival/src/agmart3.c |only
survival-2.38-1/survival/src/coxfit6.c | 37
survival-2.38-1/survival/src/init.c | 7
survival-2.38-1/survival/src/pyears2.c | 1
survival-2.38-1/survival/src/pyears3b.c | 1
survival-2.38-1/survival/src/survfitci.c | 2
survival-2.38-1/survival/src/survproto.h | 10
survival-2.38-1/survival/src/tmerge.c |only
survival-2.38-1/survival/tests/book1.R | 2
survival-2.38-1/survival/tests/book1.Rout.save | 12
survival-2.38-1/survival/tests/book2.R | 9
survival-2.38-1/survival/tests/book2.Rout.save | 20
survival-2.38-1/survival/tests/book3.R | 2
survival-2.38-1/survival/tests/book3.Rout.save | 13
survival-2.38-1/survival/tests/fr_rat1.R | 6
survival-2.38-1/survival/tests/fr_rat1.Rout.save | 24
survival-2.38-1/survival/tests/fr_resid.R | 10
survival-2.38-1/survival/tests/fr_resid.Rout.save | 23
survival-2.38-1/survival/tests/fr_simple.R | 2
survival-2.38-1/survival/tests/fr_simple.Rout.save | 11
survival-2.38-1/survival/tests/gray1.rda |binary
survival-2.38-1/survival/tests/model.matrix.R | 4
survival-2.38-1/survival/tests/model.matrix.Rout.save | 11
survival-2.38-1/survival/tests/plot.R |only
survival-2.38-1/survival/tests/plot1.pdf.save |only
survival-2.38-1/survival/tests/pspline.R | 21
survival-2.38-1/survival/tests/pspline.Rout.save | 36
survival-2.38-1/survival/tests/quantile.R | 6
survival-2.38-1/survival/tests/quantile.Rout.save | 14
survival-2.38-1/survival/tests/survreg2.R | 4
survival-2.38-1/survival/tests/survreg2.Rout.save | 13
survival-2.38-1/survival/tests/testci.R | 43
survival-2.38-1/survival/tests/testci.Rout.save | 51 -
survival-2.38-1/survival/tests/tt.R | 10
survival-2.38-1/survival/tests/tt.Rout.save | 18
survival-2.38-1/survival/vignettes/.install_extras |only
survival-2.38-1/survival/vignettes/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/vignettes/compete.Rnw |only
survival-2.38-1/survival/vignettes/figures |only
survival-2.38-1/survival/vignettes/splines.Rnw |only
survival-2.38-1/survival/vignettes/tests.Rnw | 213 ++--
survival-2.38-1/survival/vignettes/timedep.Rnw | 735 ++++++++++++-----
159 files changed, 3225 insertions(+), 2032 deletions(-)
Title: Causal Inference in Spatiotemporal Event Data
Diff between mwa versions 0.4 dated 2014-12-17 and 0.4.1 dated 2015-02-24
Description: Matched Wake Analysis (mwa) grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte
DESCRIPTION | 12 ++---
MD5 | 20 ++++----
R/mwa.R | 107 +++++++++++++++++++++++++++++++++++++--------
man/matchedwake.Rd | 8 +--
man/mwa-package.Rd | 6 +-
man/mwa_data.Rd | 6 +-
man/plot.matchedwake.Rd | 2
man/print.matchedwake.Rd | 2
man/slideWakeMatch.Rd | 2
man/slidingWake.Rd | 2
man/summary.matchedwake.Rd | 4 -
11 files changed, 122 insertions(+), 49 deletions(-)
Title: Digital PCR Analysis
Diff between dpcR versions 0.1.3.2 dated 2014-12-24 and 0.1.3.3 dated 2015-02-24
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut]
Maintainer: Michal Burdukiewicz
CHANGELOG | 3 +
DESCRIPTION | 8 ++--
MD5 | 80 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
R/count_test-class.R | 1
R/qpcrpp.R | 2 -
man/adpcr-class.Rd | 3 +
man/adpcr2ppp.Rd | 3 +
man/binarize.Rd | 3 +
man/bind_dpcr-methods.Rd | 3 +
man/bioamp.Rd | 3 +
man/compare_dens.Rd | 3 +
man/count_test-class.Rd | 7 ++--
man/create_dpcr.Rd | 3 +
man/ddpcr-class.Rd | 3 +
man/dpcR-package.Rd | 3 +
man/dpcr_density.Rd | 3 +
man/dpcr_density_gui.Rd | 3 +
man/extract_dpcr.Rd | 3 +
man/limit_cq.Rd | 3 +
man/many_peaks.Rd | 3 +
man/moments-methods.Rd | 3 +
man/num2int.Rd | 3 +
man/pds.Rd | 3 +
man/pds_raw.Rd | 3 +
man/plot.qpcrpp.Rd | 4 +-
man/plot_panel.Rd | 3 +
man/plot_vic_fam.Rd | 3 +
man/qpcr2pp.Rd | 3 +
man/qpcr_analyser.Rd | 3 +
man/qpcrpp-class.Rd | 3 +
man/rtadpcr-class.Rd | 3 +
man/show-methods.Rd | 3 +
man/sim_adpcr.Rd | 3 +
man/sim_ddpcr.Rd | 3 +
man/summary-methods.Rd | 3 +
man/test_counts.Rd | 3 +
man/test_counts_gui.Rd | 3 +
man/test_panel.Rd | 3 +
man/test_peaks.Rd | 3 +
man/test_ratio.Rd | 3 +
41 files changed, 124 insertions(+), 82 deletions(-)
Title: Spatial Analysis and Modeling
Diff between spatialEco versions 0.1-0 dated 2015-02-02 and 0.1-1 dated 2015-02-24
Description: Utilities to support spatial data manipulation, query, sampling and modeling.
Functions include models for species population density, download utilities for
climate and global deforestation spatial products, spatial smoothing,
multivariate separability, point process model for creating pseudo-absences
and subsampling, polygon and point-distance landscape metrics, auto-logistic
model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans
DESCRIPTION | 8 +-
MD5 | 81 +++++++++++++----------
NAMESPACE | 3
R/breeding.density.R | 6 -
R/correlogram.R | 4 -
R/csi.R |only
R/download.daymet.R | 6 -
R/download.prism.R | 4 -
R/idw.smoothing.R | 6 -
R/land.metrics.R | 2
R/local.min.max.R |only
R/logistic.regression.R | 58 ++++++++++-------
R/moments.R | 6 -
R/nni.R | 14 ++--
R/o.ring.R | 6 -
R/optimal.k.R | 2
R/outliers.R |only
R/parea.sample.R | 2
R/point.in.poly.R | 13 +--
R/pp.subsample.R | 2
R/pseudo.absence.R | 6 -
R/separability.R | 8 +-
R/stratified.random.R | 4 -
R/trend.line.R | 2
inst/NEWS |only
man/breeding.density.Rd | 130 +++++++++++++++++++-------------------
man/correlogram.Rd | 4 -
man/csi.Rd |only
man/download.daymet.Rd | 6 -
man/download.prism.Rd | 4 -
man/idw.smoothing.Rd | 90 +++++++++++++-------------
man/land.metrics.Rd | 118 +++++++++++++++++-----------------
man/local.min.max.Rd |only
man/logistic.regression.Rd | 36 ++++++----
man/moments.Rd | 6 -
man/nni.Rd | 88 +++++++++++++-------------
man/o.ring.Rd | 78 +++++++++++------------
man/optimal.k.Rd | 100 ++++++++++++++---------------
man/outliers.Rd |only
man/parea.sample.Rd | 108 +++++++++++++++----------------
man/pp.subsample.Rd | 2
man/pseudo.absence.Rd | 6 -
man/separability.Rd | 152 ++++++++++++++++++++++-----------------------
man/stratified.random.Rd | 150 ++++++++++++++++++++++----------------------
man/trend.line.Rd | 86 ++++++++++++-------------
45 files changed, 717 insertions(+), 690 deletions(-)
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.10.1 dated 2015-01-15 and 0.10.2 dated 2015-02-24
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
configure | 10 ++++++++++
src/Makevars.win | 4 ++--
tools/winlibs.R | 4 ++--
5 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools for Working with JavaScript in R
Diff between js versions 0.1 dated 2015-02-15 and 0.2 dated 2015-02-24
Description: A set of utility functions for working with JavaScript in R.
Currently includes functions to compile, validate, reformat, optimize
and analyze JavaScript code.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 12 ++--
MD5 | 17 ++++--
NAMESPACE | 1
NEWS |only
R/coffee.R |only
inst/doc/intro.R | 13 +++++
inst/doc/intro.Rmd | 35 +++++++++++--
inst/doc/intro.html | 126 ++++++++++++++++++++++++++++++++++++++++++++++----
inst/example |only
inst/js/coffee.min.js |only
man/coffee_compile.Rd |only
vignettes/intro.Rmd | 35 +++++++++++--
12 files changed, 208 insertions(+), 31 deletions(-)
Title: Integrative Bayesian Analysis of Transcriptomic and CGH Data
Diff between iBATCGH versions 1.1 dated 2014-09-13 and 1.2 dated 2015-02-24
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression.
Author: Alberto Cassese
Maintainer: Alberto Cassese
DESCRIPTION | 18 +++++++++---------
MD5 | 8 ++++----
src/Makevars | 2 +-
src/Makevars.win | 3 +--
src/ProbitMain.cpp | 8 +++++---
5 files changed, 20 insertions(+), 19 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 2.0.0 dated 2015-02-16 and 2.0.1 dated 2015-02-24
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
FunChisq-2.0.0/FunChisq/src/Makevars |only
FunChisq-2.0.0/FunChisq/src/Makevars.win |only
FunChisq-2.0.0/FunChisq/src/TransitionTableIO.cpp |only
FunChisq-2.0.0/FunChisq/tests/testthat/test_EFT.R |only
FunChisq-2.0.1/FunChisq/DESCRIPTION | 10 -
FunChisq-2.0.1/FunChisq/MD5 | 39 +++----
FunChisq-2.0.1/FunChisq/NAMESPACE | 3
FunChisq-2.0.1/FunChisq/NEWS | 58 +++++------
FunChisq-2.0.1/FunChisq/man/FunChisq-package.Rd | 10 -
FunChisq-2.0.1/FunChisq/man/cp.fun.chisq.test.Rd | 16 +--
FunChisq-2.0.1/FunChisq/man/fun.chisq.test.Rd | 48 ++++-----
FunChisq-2.0.1/FunChisq/src/AdjustPvalue.cpp | 88 ++++++++---------
FunChisq-2.0.1/FunChisq/src/ChisqDirTest.cpp | 2
FunChisq-2.0.1/FunChisq/src/ChisqTests.cpp | 66 ++++++------
FunChisq-2.0.1/FunChisq/src/ChisqTests.h | 2
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.cpp | 29 +----
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.h | 4
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.cpp | 20 +--
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.h | 10 +
FunChisq-2.0.1/FunChisq/src/StatDistributions.cpp | 4
FunChisq-2.0.1/FunChisq/src/TransitionTable.cpp | 26 ++---
FunChisq-2.0.1/FunChisq/src/TransitionTable.h | 6 -
FunChisq-2.0.1/FunChisq/tests/testthat/test_FunChisq.R |only
23 files changed, 214 insertions(+), 227 deletions(-)
Title: Cairo-based Graphics Device Driver
Diff between cairoDevice versions 2.21 dated 2015-01-20 and 2.22 dated 2015-02-24
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
src/cairoDevice.c | 3 ---
3 files changed, 8 insertions(+), 11 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Diff between aroma.cn versions 1.5.0 dated 2013-10-17 and 1.6.0 dated 2015-02-24
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson
aroma.cn-1.5.0/aroma.cn/R/PSCBS.flips.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.calibrateC1C2.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.deShearC1C2.R |only
aroma.cn-1.5.0/aroma.cn/inst/NEWS |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/ortho |only
aroma.cn-1.5.0/aroma.cn/man/calibrateC1C2.PairedPSCBS.Rd |only
aroma.cn-1.5.0/aroma.cn/man/deShearC1C2_20120922.PairedPSCBS.Rd |only
aroma.cn-1.6.0/aroma.cn/DESCRIPTION | 27
aroma.cn-1.6.0/aroma.cn/MD5 | 90
aroma.cn-1.6.0/aroma.cn/NAMESPACE | 47
aroma.cn-1.6.0/aroma.cn/NEWS |only
aroma.cn-1.6.0/aroma.cn/R/009.setup.R | 6
aroma.cn-1.6.0/aroma.cn/R/021.dynamic_imports.R |only
aroma.cn-1.6.0/aroma.cn/R/AbstractCurveNormalization.R | 11
aroma.cn-1.6.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R |only
aroma.cn-1.6.0/aroma.cn/R/C1C2.R | 72
aroma.cn-1.6.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R | 14
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.CALL2.R | 2
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.NORM.R | 4
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.PLOT3.R | 5
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.backgroundCorrect.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPscbsModel.R | 10
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurve.XTRAS.R | 2
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurveNormalization.R | 6
aroma.cn-1.6.0/aroma.cn/R/TotalFracBSnpData.R | 2
aroma.cn-1.6.0/aroma.cn/R/TumorBoostNormalization.R | 3
aroma.cn-1.6.0/aroma.cn/R/XYCurveNormalization.R | 4
aroma.cn-1.6.0/aroma.cn/R/callXXorXY.numeric.R | 6
aroma.cn-1.6.0/aroma.cn/R/normalizeMirroredBAFsByRegions.R | 7
aroma.cn-1.6.0/aroma.cn/R/normalizePrincipalCurve.matrix.R | 5
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex | 1020 +++++-----
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex | 414 ++--
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R | 54
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R | 34
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R | 204 +-
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R | 62
aroma.cn-1.6.0/aroma.cn/man/AbstractCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/Non-documented_objects.Rd | 36
aroma.cn-1.6.0/aroma.cn/man/PairedPscbsModel.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/PrincipalCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnKernelSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TumorBoostNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/XYCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd | 75
aroma.cn-1.6.0/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd | 61
aroma.cn-1.6.0/aroma.cn/tests |only
52 files changed, 1100 insertions(+), 1201 deletions(-)
Title: Stepwise Covariate Selection for the Fine & Gray Competing Risks
Regression Model
Diff between crrstep versions 2014-07.16 dated 2014-07-17 and 2015-2.1 dated 2015-02-23
Description: Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events.
Author: Ravi Varadhan & Deborah Kuk
Maintainer: Ravi Varadhan
DESCRIPTION | 14 ++++-----
MD5 | 8 ++---
R/crrstep.r | 88 ++++++++++++++++++++++++++++++++++-----------------------
inst/NEWS.Rd | 9 +++++
man/crrstep.Rd | 2 -
5 files changed, 74 insertions(+), 47 deletions(-)
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Diff between calmate versions 0.11.0 dated 2013-10-17 and 0.12.0 dated 2015-02-23
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson
calmate-0.11.0/calmate/inst/NEWS |only
calmate-0.11.0/calmate/inst/testScripts/publications/CalMaTe/R |only
calmate-0.11.0/calmate/inst/testScripts/publications/CalMaTe/dataSets |only
calmate-0.12.0/calmate/DESCRIPTION | 30 ++++-----
calmate-0.12.0/calmate/MD5 | 33 +++-------
calmate-0.12.0/calmate/NAMESPACE | 4 -
calmate-0.12.0/calmate/NEWS |only
calmate-0.12.0/calmate/R/000.R | 2
calmate-0.12.0/calmate/R/zzz.R | 11 +--
calmate-0.12.0/calmate/man/CalMaTeCalibration.Rd | 4 -
calmate-0.12.0/calmate/man/calmate-package.Rd | 4 -
calmate-0.12.0/calmate/man/calmateByThetaAB.array.Rd | 2
calmate-0.12.0/calmate/man/calmateByTotalAndFracB.array.Rd | 2
calmate-0.12.0/calmate/man/fitCalMaTe.matrix.Rd | 2
calmate-0.12.0/calmate/man/fitCalMaTeInternal.Rd | 2
calmate-0.12.0/calmate/tests/calmateByTotalAndFracB.R |only
calmate-0.12.0/calmate/tests/thetaAB2TotalAndFracB.R |only
17 files changed, 46 insertions(+), 50 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Diff between ACNE versions 0.7.0 dated 2013-10-18 and 0.8.0 dated 2015-02-23
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson
ACNE-0.7.0/ACNE/inst/NEWS |only
ACNE-0.8.0/ACNE/DESCRIPTION | 28 +++++++++--------
ACNE-0.8.0/ACNE/MD5 | 23 +++++++-------
ACNE-0.8.0/ACNE/NAMESPACE | 7 ++++
ACNE-0.8.0/ACNE/NEWS |only
ACNE-0.8.0/ACNE/R/000.R | 1
ACNE-0.8.0/ACNE/R/SnpNmfFit.plot.R | 2 -
ACNE-0.8.0/ACNE/R/pseudoinverse.R | 8 ++---
ACNE-0.8.0/ACNE/R/robustWInit.R | 53 +++++++++++++++++++++++++---------
ACNE-0.8.0/ACNE/R/zzz.R | 11 +++----
ACNE-0.8.0/ACNE/man/NmfPlm.Rd | 4 +-
ACNE-0.8.0/ACNE/man/NmfSnpPlm.Rd | 4 +-
ACNE-0.8.0/ACNE/man/fitSnpNmfArray.Rd | 18 +++++++----
ACNE-0.8.0/ACNE/tests |only
14 files changed, 102 insertions(+), 57 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Diff between miceadds versions 1.0 dated 2014-11-07 and 1.1-1 dated 2015-02-23
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch
DESCRIPTION | 28 +++++----
MD5 | 92 +++++++++++++++---------------
NAMESPACE | 3 -
R/datalist2mids.R | 56 +++++++++++++++---
R/load.data.R | 10 ++-
R/mice.impute.2l.plausible.values.R | 61 +++++++++++++-------
R/micombine.cor.R | 6 +-
R/mids2datlist.R | 4 +
R/save.data.R | 30 ++++++++--
R/write.mice.imputation.R | 15 -----
data/data.allison.gssexp.rda |binary
data/data.allison.hip.rda |binary
data/data.allison.usnews.rda |binary
data/data.enders.depression.rda |binary
data/data.enders.eatingattitudes.rda |binary
data/data.enders.employee.rda |binary
data/data.internet.rda |binary
data/data.largescale.rda |binary
data/data.ma01.rda |binary
data/data.ma02.rda |binary
data/data.ma03.rda |binary
data/data.ma04.rda |binary
data/data.ma05.rda |binary
data/data.smallscale.rda |binary
inst/NEWS | 19 +++++-
man/Reval.Rd | 4 -
man/Rhat.mice.Rd | 8 +-
man/Rsessinfo.Rd | 4 -
man/data.allison.Rd | 30 +++++-----
man/datalist2mids.Rd | 50 ++++++++--------
man/grep.vec.Rd | 16 ++---
man/index.dataframe.Rd | 20 +++---
man/ma.scale2.Rd | 12 ++--
man/mice.1chain.Rd | 71 +++++++++++------------
man/mice.impute.2l.plausible.values.Rd | 99 +++++++++++++++++++++++++++++++--
man/miceadds-package.Rd | 18 +++---
man/micombine.F.Rd | 8 +-
man/micombine.cor.Rd | 16 ++---
man/output.format1.Rd | 4 -
man/pca.covridge.Rd | 20 +++---
man/round2.Rd | 40 ++++++-------
man/save.data.Rd | 6 +-
man/scan.vector.Rd | 6 +-
man/str_C.expand.grid.Rd | 8 +-
man/sumpreserving.rounding.Rd | 24 ++++----
man/systime.Rd | 6 +-
man/tw.imputation.Rd | 20 +++---
47 files changed, 496 insertions(+), 318 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Diff between RRreg versions 0.2.0 dated 2014-11-18 and 0.3.0 dated 2015-02-23
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression and as
predictors in a linear regression. For simulation and bootstrap purposes,
RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck
DESCRIPTION | 10 -
MD5 | 70 ++++++-------
NAMESPACE | 4
NEWS | 9 +
R/RRcor.R | 4
R/RRgen.R | 4
R/RRlin.R | 49 ++++-----
R/RRlin.ll.R | 4
R/RRlog.CDM.R | 9 -
R/RRlog.FR.R | 4
R/RRlog.Kuk.R | 5
R/RRlog.Mangat.R | 4
R/RRlog.R | 246 +++++++++++++++++++++++++++++-----------------
R/RRlog.SLD.R | 4
R/RRlog.UQTknown.R | 6 -
R/RRlog.UQTunknown.R | 4
R/RRlog.Warner.R | 4
R/RRreg-package.R | 6 -
R/RRsimu.R | 267 +++++++++++++++++++++++++-------------------------
R/RRuni.R | 40 +++++--
R/RRuni.models.R | 2
R/powerplot.R | 15 +-
build/vignette.rds |binary
inst/doc/RRreg.R | 6 -
inst/doc/RRreg.Rmd | 6 -
inst/doc/RRreg.html | 144 +++++++++++++-------------
man/RRcor.Rd | 5
man/RRgen.Rd | 7 -
man/RRlin.Rd | 19 ++-
man/RRlog.Rd | 25 ++--
man/RRreg-package.Rd | 9 -
man/RRsimu.Rd | 21 ++-
man/RRuni.Rd | 36 +++++-
man/plot.powerplot.Rd |only
man/powerplot.Rd | 5
man/predict.RRlog.Rd |only
vignettes/RRreg.Rmd | 6 -
37 files changed, 601 insertions(+), 458 deletions(-)
Title: R Interface to SDMX Web Services
Diff between RJSDMX versions 1.2 dated 2014-11-07 and 1.3 dated 2015-02-23
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco
DESCRIPTION | 15 ++++---
MD5 | 17 ++++----
NAMESPACE | 1
R/SdmxClient.R | 32 ++++++++++-----
R/TSConverter.R | 88 +++++++++++++++++++++++++++++-------------
R/onLoad.R | 2
inst/configuration.properties | 3 -
inst/java/SDMX.jar |binary
man/addProvider.Rd | 6 ++
man/sdmxdf.Rd |only
10 files changed, 112 insertions(+), 52 deletions(-)
Title: Power/Sample Size Calculation for Mediation Analysis
Diff between powerMediation versions 0.1.7 dated 2013-11-09 and 0.2.3 dated 2015-02-23
More information about powerMediation at CRAN
Description: Functions to
calculate power and sample size for testing
(1) mediation effects;
(2) the slope in a simple linear regression;
(3) odds ratio in a simple logistic regression;
(4) mean change for longitudinal study with 2 time points;
and (5) interaction effect in 2-way ANOVA.
Author: Weiliang Qiu
Maintainer: Weiliang Qiu
DESCRIPTION | 28 +++++++++++++---------------
INDEX | 6 ++++++
MD5 | 20 ++++++++++++--------
NAMESPACE | 4 ++++
NEWS | 23 +++++++++++++++++++++++
R/powerLogisticsReg.R | 2 +-
R/powerLongitudinal.R | 41 +++++++++++++++++++++++++++++++++++++++--
R/power_interaction.R |only
man/SSizeLogisticCon.Rd | 1 +
man/powerInteract.Rd |only
man/powerLogisticCon.Rd | 4 ++--
man/powerLong.multiTime.Rd |only
man/ssLong.multiTime.Rd |only
13 files changed, 101 insertions(+), 28 deletions(-)
Permanent link
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Diff between fitdistrplus versions 1.0-3 dated 2014-12-12 and 1.0-4 dated 2015-02-23
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation method the package provides moment matching, quantile matching and maximum goodness-of-fit estimation methods (available only for non-censored data).
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller
DESCRIPTION | 12
MD5 | 44 +-
R/plotdistcens.R | 2
inst/CITATION | 35 -
inst/NEWS | 4
inst/doc/paper2JSS.Rnw | 2
inst/doc/paper2JSS.pdf |binary
man/bootdist.Rd | 6
man/bootdistcens.Rd | 6
man/cdfcompcens.Rd | 207 ++++-----
man/descdist.Rd | 268 ++++++------
man/fitdist.Rd | 1031 ++++++++++++++++++++++++------------------------
man/fitdistcens.Rd | 501 +++++++++++------------
man/gofstat.Rd | 373 ++++++++---------
man/graphcomp.Rd | 403 +++++++++---------
man/mgedist.Rd | 315 +++++++-------
man/mledist.Rd | 375 ++++++++---------
man/mmedist.Rd | 306 +++++++-------
man/plotdist.Rd | 245 +++++------
man/plotdistcens.Rd | 222 +++++-----
man/qmedist.Rd | 270 ++++++------
man/quantiles.Rd | 310 +++++++-------
vignettes/paper2JSS.Rnw | 2
23 files changed, 2516 insertions(+), 2423 deletions(-)
Title: Cognitive Diagnosis Modeling
Diff between CDM versions 4.1 dated 2014-12-17 and 4.2-12 dated 2015-02-23
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 13 -
MD5 | 125 ++++++++------
NAMESPACE | 57 ++++++
R/IRT.compareModels.R | 40 ++++
R/IRT.data.R |only
R/IRT.derivedParameters.R |only
R/IRT.expectedCounts.R |only
R/IRT.irfprob.R | 7
R/IRT.irfprobPlot.R |only
R/IRT.jackknife.R |only
R/IRT.jackknife.gdina.R |only
R/IRT.likelihood.R | 5
R/IRT.predict.R |only
R/IRT.repDesign.R |only
R/cdi.kli.R | 6
R/din.R | 23 +-
R/equivalent.skillclasses.R | 74 --------
R/gdina.R | 289 ++++++++++++++++++++++------------
R/gdina.partable.R |only
R/gdm.R | 53 +-----
R/gdm_algorithm.R | 10 -
R/jkestimates.R |only
R/logLik_CDM.R | 8
R/mcdina.R | 8
R/modelfit.cor.R | 10 -
R/modelfit.cor2.R | 21 +-
R/predict.CDM.R |only
R/print.summary.din.R | 6
R/skill.cor.R | 73 +++++++-
R/slca.R | 4
R/summary.din.R | 3
R/summary.gdina.R | 23 +-
data/data.Students.rda |binary
data/data.cdm01.rda |binary
data/data.cdm02.rda |binary
data/data.dcm.rda |binary
data/data.dtmr.rda |binary
data/data.ecpe.rda |binary
data/data.fraction1.rda |binary
data/data.fraction2.rda |binary
data/data.hr.rda |binary
data/data.jang.rda |binary
data/data.melab.rda |binary
data/data.mg.rda |binary
data/data.pgdina.rda |binary
data/data.sda6.rda |binary
data/data.timss03.G8.su.rda |binary
data/data.timss07.G4.lee.rda |binary
data/data.timss11.G4.AUT.part.rda |only
data/data.timss11.G4.AUT.rda |only
data/fraction.subtraction.data.rda |binary
data/fraction.subtraction.qmatrix.rda |binary
data/sim.dina.rda |binary
data/sim.dino.rda |binary
data/sim.qmatrix.rda |binary
inst/NEWS | 37 ++++
man/CDM-package.Rd | 131 ++++++++-------
man/IRT.compareModels.Rd | 10 +
man/IRT.data.Rd |only
man/IRT.expectedCounts.Rd |only
man/IRT.irfprob.Rd | 5
man/IRT.irfprobPlot.Rd |only
man/IRT.jackknife.Rd |only
man/IRT.modelfit.Rd | 3
man/IRT.repDesign.Rd |only
man/data.dcm.Rd | 2
man/data.timss11.G4.AUT.Rd |only
man/din.deterministic.Rd | 2
man/din.equivalent.class.Rd | 4
man/gdina.Rd | 53 ++++--
man/personfit.appropriateness.Rd | 2
man/predict.Rd |only
man/skill.cor.Rd | 24 +-
src/irt_predict_c.cpp |only
74 files changed, 702 insertions(+), 429 deletions(-)
Title: Construction, Simulation and Analysis of Boolean Networks
Diff between BoolNet versions 2.0.2 dated 2014-12-11 and 2.1.0 dated 2015-02-23
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler
BoolNet-2.0.2/BoolNet/src/boolean_network.c |only
BoolNet-2.1.0/BoolNet/DESCRIPTION | 28
BoolNet-2.1.0/BoolNet/MD5 | 91
BoolNet-2.1.0/BoolNet/R/attractorsToLaTeX.R | 38
BoolNet-2.1.0/BoolNet/R/fixGenes.R | 2
BoolNet-2.1.0/BoolNet/R/getAttractors.R | 66
BoolNet-2.1.0/BoolNet/R/helpers.R | 2
BoolNet-2.1.0/BoolNet/R/loadBioTapestry.R | 2
BoolNet-2.1.0/BoolNet/R/loadNetwork.R | 2
BoolNet-2.1.0/BoolNet/R/loadSBML.R | 2
BoolNet-2.1.0/BoolNet/R/parseBooleanFunction.R | 3
BoolNet-2.1.0/BoolNet/R/plotAttractors.R | 32
BoolNet-2.1.0/BoolNet/R/plotSequence.R | 12
BoolNet-2.1.0/BoolNet/R/sequenceToLaTeX.R | 10
BoolNet-2.1.0/BoolNet/R/simulateSymbolicModel.R | 90
BoolNet-2.1.0/BoolNet/R/stateTransition.R | 2
BoolNet-2.1.0/BoolNet/R/symbolicToTruthTable.R | 2
BoolNet-2.1.0/BoolNet/R/truthTableToSymbolic.R | 2
BoolNet-2.1.0/BoolNet/build/vignette.rds |binary
BoolNet-2.1.0/BoolNet/inst/NEWS.Rd | 13
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.R | 186
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.Snw | 106
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.pdf |binary
BoolNet-2.1.0/BoolNet/man/BoolNet-package.Rd | 15
BoolNet-2.1.0/BoolNet/man/attractorsToLaTeX.Rd | 8
BoolNet-2.1.0/BoolNet/man/getAttractors.Rd | 40
BoolNet-2.1.0/BoolNet/man/markovSimulation.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotAttractors.Rd | 8
BoolNet-2.1.0/BoolNet/man/plotNetworkWiring.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotPBNTransitions.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotSequence.Rd | 11
BoolNet-2.1.0/BoolNet/man/reconstructNetwork.Rd | 2
BoolNet-2.1.0/BoolNet/man/sequenceToLaTeX.Rd | 12
BoolNet-2.1.0/BoolNet/man/simulateSymbolicModel.Rd | 66
BoolNet-2.1.0/BoolNet/man/testNetworkProperties.Rd | 48
BoolNet-2.1.0/BoolNet/src/attractor_info.c |only
BoolNet-2.1.0/BoolNet/src/attractor_info.h |only
BoolNet-2.1.0/BoolNet/src/attractor_search_interface.c |only
BoolNet-2.1.0/BoolNet/src/boolean_network.h |only
BoolNet-2.1.0/BoolNet/src/common.c | 2
BoolNet-2.1.0/BoolNet/src/common.h | 50
BoolNet-2.1.0/BoolNet/src/picosat.c |only
BoolNet-2.1.0/BoolNet/src/picosat.h |only
BoolNet-2.1.0/BoolNet/src/probabilistic_boolean_network.c | 42
BoolNet-2.1.0/BoolNet/src/sat_search.c |only
BoolNet-2.1.0/BoolNet/src/sat_search.h |only
BoolNet-2.1.0/BoolNet/src/statespace_search.c |only
BoolNet-2.1.0/BoolNet/src/statespace_search.h |only
BoolNet-2.1.0/BoolNet/src/symbolic_network.c |only
BoolNet-2.1.0/BoolNet/src/symbolic_network.h |only
BoolNet-2.1.0/BoolNet/src/symbolic_simulator.c | 2628 +++++------
BoolNet-2.1.0/BoolNet/vignettes/BoolNet_package_vignette.Snw | 106
BoolNet-2.1.0/BoolNet/vignettes/BoolNet_package_vignette.bib | 18
53 files changed, 2004 insertions(+), 1749 deletions(-)
Title: SYMPHONY in R
Diff between Rsymphony versions 0.1-18 dated 2015-01-10 and 0.1-19 dated 2015-02-23
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut],
Kurt Hornik [aut, cre],
Stefan Theussl [aut],
Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/symphony.R | 27 ++++++++++++++++-----------
3 files changed, 21 insertions(+), 16 deletions(-)
Title: R Commander Plug-In for University Level Applied Statistics
Diff between RcmdrPlugin.NMBU versions 1.8.0 dated 2015-01-22 and 1.8.0.1 dated 2015-02-23
More information about RcmdrPlugin.NMBU at CRAN
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 17 -
MD5 | 14
NAMESPACE | 4
R/NMBU.GUI.Models.R | 2
R/NMBU.GUI.Statistics.R | 600 ++++++++++++++++++++--------------------
R/NMBU.Utilities.R | 1
inst/etc/menus.txt | 10
man/RcmdrPlugin.NMBU-package.Rd | 1
8 files changed, 333 insertions(+), 316 deletions(-)
Permanent link
Title: Biostatistics Utilities for Nephrology
Diff between nephro versions 1.0 dated 2013-01-30 and 1.1 dated 2015-02-23
Description: Set of functions to estimate the Glomerular Filtration Rate (GFR) using different biomarkers and other phenotypes of interest for nephrology.
Author: Cristian Pattaro
Maintainer: Cristian Pattaro
nephro-1.0/nephro/R/nephro.r |only
nephro-1.1/nephro/ChangeLog |only
nephro-1.1/nephro/DESCRIPTION | 15 +++-----
nephro-1.1/nephro/MD5 | 28 ++++++++-------
nephro-1.1/nephro/NAMESPACE | 2 -
nephro-1.1/nephro/R/nephro.R |only
nephro-1.1/nephro/man/CG.Rd |only
nephro-1.1/nephro/man/CKDEpi.creat.Rd | 17 +++------
nephro-1.1/nephro/man/CKDEpi.creat.cys.Rd | 13 ++----
nephro-1.1/nephro/man/CKDEpi.cys.Rd | 14 +++----
nephro-1.1/nephro/man/MDRD4.Rd | 22 ++++-------
nephro-1.1/nephro/man/MDRD6.Rd | 20 ++++------
nephro-1.1/nephro/man/Stevens.creat.cys.Rd | 16 +++-----
nephro-1.1/nephro/man/Stevens.cys1.Rd | 26 ++++---------
nephro-1.1/nephro/man/Stevens.cys2.Rd | 22 +++--------
nephro-1.1/nephro/man/Virga.Rd | 37 ++++++++++++-------
nephro-1.1/nephro/man/nephro-package.Rd | 54 +++++++++++++++++++----------
17 files changed, 137 insertions(+), 149 deletions(-)
Title: Provides Access to Git Repositories
Diff between git2r versions 0.6 dated 2015-02-18 and 0.7 dated 2015-02-23
Description: Interface to the libgit2 library, which is a pure C
implementation of the Git core methods. Provides access to Git
repositories to extract data and running some basic git commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren
filter.h | 38
tmp/cranberry50814e554202/git2r-0.7/git2r/DESCRIPTION | 8
tmp/cranberry50814e554202/git2r-0.7/git2r/MD5 | 42 -
tmp/cranberry50814e554202/git2r-0.7/git2r/NEWS | 10
tmp/cranberry50814e554202/git2r-0.7/git2r/configure | 17
tmp/cranberry50814e554202/git2r-0.7/git2r/src/Makevars.in | 7
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/attr.c | 5
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/blob.c | 14
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/buffer.c | 14
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/buffer.h | 6
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/checkout.c | 136 ++-
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/crlf.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff_driver.c | 9
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff_file.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/filter.c | 416 +++++++---
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/filter.h | 13
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/include/git2/types.h | 9
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/integer.h | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/pack.c | 11
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/repository.c | 2
21 files changed, 565 insertions(+), 200 deletions(-)
Title: An R Plug-in for the Distributed Hydrological Model GEOtop
Diff between geotopbricks versions 1.3.5.4 dated 2014-05-22 and 1.3.6 dated 2015-02-23
Description: It analyzes raster maps and other information as input/output
files from the Hydrological Distributed Model GEOtop. It contains functions
and methods to import maps and other keywords from geotop.inpts file. Some
examples with simulation cases of GEOtop 2.0 are presented in the package.
Any information about the GEOtop Distributed Hydrological Model source code
is available on http://code.google.com/p/geotop/ or
https://github.com/se27xx/GEOtop. Technical details about the model are
available in Endrizzi et al, 2014
(http://www.geosci-model-dev.net/7/2831/2014/gmd-7-2831-2014.html).
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano
geotopbricks-1.3.5.4/geotopbricks/R/geotopbricks-package.R |only
geotopbricks-1.3.5.4/geotopbricks/man/geotopbricks-package.Rd |only
geotopbricks-1.3.6/geotopbricks/DESCRIPTION | 34 +++---
geotopbricks-1.3.6/geotopbricks/MD5 | 41 +++----
geotopbricks-1.3.6/geotopbricks/NAMESPACE | 1
geotopbricks-1.3.6/geotopbricks/R/aggregate.brick.at.depth.R | 2
geotopbricks-1.3.6/geotopbricks/R/bar.color.raster.R | 55 +++++++++-
geotopbricks-1.3.6/geotopbricks/R/brickFromOutput3DTensor.R | 7 -
geotopbricks-1.3.6/geotopbricks/R/declared.geotop.inpts.keywords.R | 18 ++-
geotopbricks-1.3.6/geotopbricks/R/geotopbrick_S3.R | 10 -
geotopbricks-1.3.6/geotopbricks/R/get.keyword.value.R | 45 +++++++-
geotopbricks-1.3.6/geotopbricks/R/listFromOutput3DTensor.R | 4
geotopbricks-1.3.6/geotopbricks/R/writeRasterxgeotop.R | 40 +++++++
geotopbricks-1.3.6/geotopbricks/data/bondone.rda |binary
geotopbricks-1.3.6/geotopbricks/inst/doc/examples/example.brickFromOutput3DTensor.R | 2
geotopbricks-1.3.6/geotopbricks/inst/doc/examples/example.time.aggragation.R |only
geotopbricks-1.3.6/geotopbricks/inst/rendena100 |only
geotopbricks-1.3.6/geotopbricks/man/bondone.Rd | 2
geotopbricks-1.3.6/geotopbricks/man/brickFromOutputSoil3DTensor.Rd | 12 +-
geotopbricks-1.3.6/geotopbricks/man/color.bar.raster.Rd | 26 ++++
geotopbricks-1.3.6/geotopbricks/man/declared.geotop.inpts.keywords.Rd | 7 +
geotopbricks-1.3.6/geotopbricks/man/listFromOutputSoil3DTensor.Rd | 10 -
geotopbricks-1.3.6/geotopbricks/man/writeRasterxGEOtop.Rd | 15 ++
23 files changed, 254 insertions(+), 77 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Diff between rfPermute versions 1.6.1 dated 2014-08-12 and 1.6.2 dated 2015-02-23
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 16 ++++++++--------
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 13 +++++++------
R/plot.rfPermute.R | 4 ++--
R/plot.rp.importance.r | 17 ++++++++---------
R/rfPermute.R | 2 +-
R/rfPermute.default.R | 2 ++
R/rfPermute.formula.R | 3 +++
R/rp.importance.R | 7 +++++--
man/calc.imp.pval.Rd | 3 ++-
man/clean.rf.data.Rd | 3 ++-
man/plot.rfPermute.Rd | 5 +++--
man/plot.rp.importance.Rd | 5 +++--
man/proximity.plot.Rd | 3 ++-
man/rfPermute.Rd | 9 +++++----
man/rp.combine.Rd | 3 ++-
man/rp.importance.Rd | 9 ++++++---
17 files changed, 77 insertions(+), 59 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Diff between R.filesets versions 2.6.0 dated 2014-08-27 and 2.7.0 dated 2015-02-23
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 20 +--
MD5 | 64 +++++-----
NAMESPACE | 12 +
NEWS | 22 +++
R/ChecksumFile.R | 11 +
R/GenericDataFileSet.PARALLEL.R | 9 -
R/GenericDataFileSet.R | 33 +++--
R/RDataFile.R |only
R/RDataFileSet.R |only
R/RdsFile.R | 1
inst/exData/dataSetA,original/1.2(a).txt | 26 ++--
inst/exData/dataSetA,original/11.2(a).txt | 26 ++--
inst/exData/dataSetA,original/fileF.txt | 26 ++--
inst/exData/dataSetA,original/fileFF.txt | 26 ++--
inst/exData/dataSetB/fileG,EOL.txt | 22 +--
inst/exData/dataSetB/fileG,noEOL.txt | 20 +--
man/FullNameInterface.Rd | 2
man/GenericDataFile.Rd | 2
man/GenericDataFileSet.Rd | 36 ++---
man/GenericTabularFile.Rd | 12 -
man/RDataFile.Rd |only
man/RDataFileSet.Rd |only
man/RdsFile.Rd | 1
man/TabularTextFile.Rd | 10 -
man/TabularTextFileSet.Rd | 2
man/getFile.GenericDataFileSet.Rd | 5
man/loadToEnv.Rd |only
tests/GenericDataFile.R | 17 ++
tests/GenericDataFileSet,dsApply.R | 18 +-
tests/GenericDataFileSet,sortBy.R | 42 +++---
tests/GenericDataFileSet.R | 8 -
tests/RdsFileSet.R | 2
tests/TabularTextFile,huge.R |only
tests/TabularTextFile.R | 184 +++++++++++++++---------------
tests/TabularTextFileSet.R | 146 ++++++++++++-----------
tests/VectorAndListAPI.R | 14 +-
36 files changed, 458 insertions(+), 361 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Diff between mixlm versions 1.0.8.1 dated 2015-01-31 and 1.0.8.3 dated 2015-02-23
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/statistics.R | 25 ++++++++++++++++++++++---
3 files changed, 28 insertions(+), 9 deletions(-)
Title: Summaries and Population Structure Analyses of Haplotypic and
Genotypic Data
Diff between strataG versions 0.9.2 dated 2014-12-31 and 0.9.4 dated 2015-02-22
Description: A toolkit for analyzing stratified population genetic data.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 8 -
MD5 | 234 +++++++++++++++++-----------------
NAMESPACE | 2
R/gtypes.R | 20 +-
R/gtypes.default.R | 249 ++++++++++++++++++-------------------
R/is.gtypes.R | 2
R/jmodeltest.run.R | 39 +++--
R/merge.gtypes.R | 6
R/nucleotide.diversity.R | 13 +
R/pop.diff.test.R | 18 ++
man/align.clustal.Rd | 3
man/align.folder.Rd | 3
man/align.mafft.Rd | 3
man/allele.freq.format.Rd | 3
man/allele.freqs.Rd | 3
man/allele.split.Rd | 3
man/allelic.richness.Rd | 3
man/as.data.frame.gtypes.Rd | 3
man/as.dna.seq.Rd | 3
man/as.matrix.gtypes.Rd | 3
man/base.freqs.Rd | 3
man/bowhead.snp.position.Rd | 3
man/bowhead.snps.Rd | 3
man/check.genotypes.Rd | 3
man/check.seqs.Rd | 3
man/clumpp.run.Rd | 3
man/create.consensus.Rd | 3
man/decode.Rd | 3
man/diversity.Rd | 3
man/dolph.haps.Rd | 3
man/dolph.msats.Rd | 3
man/dolph.seqs.Rd | 3
man/dolph.strata.Rd | 3
man/dup.genotypes.Rd | 3
man/exptd.het.Rd | 3
man/fastsimcoal.run.Rd | 3
man/fisher.method.p.Rd | 3
man/fixed.differences.Rd | 3
man/fixed.sites.Rd | 3
man/fst.to.nm.Rd | 3
man/gelato.plot.Rd | 3
man/gelato.run.Rd | 3
man/gen.data.from.freq.Rd | 3
man/genepop.run.Rd | 3
man/gtype.struct.func.Rd | 3
man/gtypes.Rd | 21 +--
man/h.stats.Rd | 3
man/hap.freqs.Rd | 3
man/haplotype.likelihoods.Rd | 3
man/haplotypic.diversity.Rd | 3
man/hwe.genepop.Rd | 3
man/is.diploid.Rd | 3
man/is.gtype.struct.func.Rd | 3
man/iupac.code.Rd | 3
man/jack.hwe.Rd | 3
man/jmodeltest.run.Rd | 10 +
man/label.haplotypes.Rd | 3
man/linkage.genepop.Rd | 3
man/locus.names.Rd | 3
man/low.freq.subs.Rd | 3
man/merge.gtypes.Rd | 10 +
man/most.distant.sequences.Rd | 3
man/na.omit.gtypes.Rd | 3
man/nei.Da.Rd | 3
man/nucleotide.divergence.Rd | 3
man/nucleotide.diversity.Rd | 7 -
man/num.alleles.Rd | 3
man/num.alleles.shared.Rd | 3
man/num.gens.eq.Rd | 3
man/num.missing.Rd | 3
man/obsvd.het.Rd | 3
man/p.val.Rd | 3
man/pairwise.shared.loci.Rd | 3
man/pct.unique.haplotypes.Rd | 3
man/phase.run.Rd | 3
man/pop.diff.test.Rd | 19 ++
man/print.gtypeSummary.Rd | 3
man/read.arlequin.Rd | 3
man/read.fasta.Rd | 3
man/read.gen.data.Rd | 3
man/read.mega.Rd | 3
man/relabel.sequences.Rd | 3
man/restratify.Rd | 3
man/sequence.summary.Rd | 3
man/shared.haps.Rd | 3
man/sim.gamma.haps.Rd | 3
man/smry.by.locus.Rd | 3
man/smry.by.sample.Rd | 3
man/stat.chi2.Rd | 3
man/stat.d.jost.Rd | 3
man/stat.fst.Rd | 3
man/stat.fst.prime.Rd | 3
man/stat.gst.Rd | 3
man/stat.gst.dbl.prime.Rd | 3
man/stat.gst.prime.hedrick.Rd | 3
man/stat.gst.prime.nei.Rd | 3
man/stat.phist.Rd | 3
man/stopifnot.gtype.struct.func.Rd | 3
man/strata.pairs.Rd | 3
man/strata.split.Rd | 3
man/strataG-package.Rd | 3
man/structure.evanno.Rd | 3
man/structure.parse.q.mat.Rd | 3
man/structure.plot.Rd | 3
man/structure.run.Rd | 3
man/subset.gtypes.Rd | 3
man/summarize.loci.Rd | 3
man/summarize.sequences.Rd | 3
man/summary.gtypes.Rd | 3
man/tajimas.d.Rd | 3
man/theta.Rd | 3
man/ti.tv.ratio.Rd | 3
man/trim.ns.Rd | 3
man/valid.iupac.codes.Rd | 3
man/variable.sites.Rd | 3
man/wright.fst.Rd | 3
man/write.gtypes.Rd | 3
man/write.snapp.nexus.Rd | 3
118 files changed, 563 insertions(+), 404 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Diff between spaMM versions 1.4.1 dated 2014-11-08 and 1.5.1 dated 2015-02-22
Description: Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph]
Maintainer: François Rousset
spaMM-1.4.1/spaMM/R/blockDiag.R |only
spaMM-1.4.1/spaMM/R/ordinaryKrigingCoefs.R |only
spaMM-1.4.1/spaMM/man/spaMM-internal-blockDiag.Rd |only
spaMM-1.5.1/spaMM/DESCRIPTION | 8
spaMM-1.5.1/spaMM/MD5 | 126 +--
spaMM-1.5.1/spaMM/NAMESPACE | 17
spaMM-1.5.1/spaMM/R/HLCor.R | 31
spaMM-1.5.1/spaMM/R/HLFactorList.R | 65 -
spaMM-1.5.1/spaMM/R/HLfit.R | 789 ++++++++++++-------
spaMM-1.5.1/spaMM/R/HLframes.R | 63 +
spaMM-1.5.1/spaMM/R/LR.R | 12
spaMM-1.5.1/spaMM/R/MakeCovEst.R |only
spaMM-1.5.1/spaMM/R/RcppExports.R | 8
spaMM-1.5.1/spaMM/R/auglinmodfit.R | 156 ++-
spaMM-1.5.1/spaMM/R/calc.p_v.R | 20
spaMM-1.5.1/spaMM/R/confint.R | 6
spaMM-1.5.1/spaMM/R/corrHLfit.R | 66 -
spaMM-1.5.1/spaMM/R/corrMM.LRT.R | 16
spaMM-1.5.1/spaMM/R/correlationFns.R | 77 +
spaMM-1.5.1/spaMM/R/extractors.R | 42 -
spaMM-1.5.1/spaMM/R/is.diagonal.R | 15
spaMM-1.5.1/spaMM/R/locoptim.R | 2
spaMM-1.5.1/spaMM/R/locoptimthroughsmooth.R | 12
spaMM-1.5.1/spaMM/R/mapMM.R | 377 +++++----
spaMM-1.5.1/spaMM/R/migraineLike.R | 51 -
spaMM-1.5.1/spaMM/R/plot.HLfit.R | 15
spaMM-1.5.1/spaMM/R/predict.R | 223 +++--
spaMM-1.5.1/spaMM/R/preprocess.R | 11
spaMM-1.5.1/spaMM/R/profile.R | 2
spaMM-1.5.1/spaMM/R/simulate.HL.R | 31
spaMM-1.5.1/spaMM/R/spaMM.data.R | 15
spaMM-1.5.1/spaMM/R/summary.HL.R | 16
spaMM-1.5.1/spaMM/R/utils.R | 10
spaMM-1.5.1/spaMM/inst/CITATION | 8
spaMM-1.5.1/spaMM/inst/NEWS.Rd |only
spaMM-1.5.1/spaMM/man/HLCor.Rd | 21
spaMM-1.5.1/spaMM/man/HLfit.Rd | 2
spaMM-1.5.1/spaMM/man/Matern.corr.Rd | 4
spaMM-1.5.1/spaMM/man/Predictor.Rd | 2
spaMM-1.5.1/spaMM/man/arabidopsis.Rd | 2
spaMM-1.5.1/spaMM/man/confint.Rd | 8
spaMM-1.5.1/spaMM/man/corMatern.Rd | 14
spaMM-1.5.1/spaMM/man/corrHLfit.Rd | 37
spaMM-1.5.1/spaMM/man/extractors.Rd | 17
spaMM-1.5.1/spaMM/man/fixed.LRT.Rd | 16
spaMM-1.5.1/spaMM/man/make.scaled.dist.Rd | 25
spaMM-1.5.1/spaMM/man/mapMM.Rd | 96 +-
spaMM-1.5.1/spaMM/man/options.Rd | 13
spaMM-1.5.1/spaMM/man/predict.Rd | 52 -
spaMM-1.5.1/spaMM/man/salamander.Rd | 6
spaMM-1.5.1/spaMM/man/scotlip.Rd | 2
spaMM-1.5.1/spaMM/man/seaMask.Rd | 6
spaMM-1.5.1/spaMM/man/seeds.Rd | 2
spaMM-1.5.1/spaMM/man/simulate.HLCor.Rd | 6
spaMM-1.5.1/spaMM/man/spaMM-internal-Rcpp.Rd | 3
spaMM-1.5.1/spaMM/man/spaMM-internal-migraine.Rd | 1
spaMM-1.5.1/spaMM/man/spaMM-internal.Rd | 21
spaMM-1.5.1/spaMM/man/spaMM.Rd | 29
spaMM-1.5.1/spaMM/man/spaMM.filled.contour.Rd | 27
spaMM-1.5.1/spaMM/man/spaMMcolors.Rd | 4
spaMM-1.5.1/spaMM/src/RcppExports.cpp | 31
spaMM-1.5.1/spaMM/src/spaMM_linear.cpp | 99 +-
spaMM-1.5.1/spaMM/tests/test-all.R |only
spaMM-1.5.1/spaMM/tests/testthat/test-HLfit.R | 2
spaMM-1.5.1/spaMM/tests/testthat/test-filled.mapMM.R | 11
spaMM-1.5.1/spaMM/tests/testthat/test-sp-nsp.R | 2
spaMM-1.5.1/spaMM/tests/testthat/test-spaMM.R | 4
67 files changed, 1797 insertions(+), 1058 deletions(-)
Title: A Framework for Comparing the Performance of MCMC Samplers
Diff between SamplerCompare versions 1.2.5 dated 2013-12-22 and 1.2.6 dated 2015-02-22
More information about SamplerCompare at CRAN
Description: A framework for running sets of MCMC samplers on sets of
distributions with a variety of tuning parameters, along with plotting
functions to visualize the results of those simulations. See sc-intro.pdf
for an introduction.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by
G. W. Stewart.
Maintainer: Madeleine Thompson
DESCRIPTION | 21 ++++++++++-----------
MD5 | 42 +++++++++++++++++++++---------------------
NAMESPACE | 3 ++-
R/00dist-util.R | 10 +++++-----
R/act.R | 2 +-
R/compare-samplers.R | 2 +-
R/distributions.R | 4 +++-
build/vignette.rds |binary
inst/doc/glue.Rnw | 6 +++---
inst/doc/glue.pdf |binary
inst/doc/sc-intro.Rnw | 2 +-
inst/doc/sc-intro.pdf |binary
man/SamplerCompare-package.Rd | 16 ++++++++--------
man/compare.samplers.Rd | 4 ++--
man/dist-class.Rd | 4 ++--
man/make.c.dist.Rd | 2 +-
man/make.cone.dist.Rd | 2 +-
man/make.dist.Rd | 2 +-
man/make.multimodal.dist.Rd | 2 +-
man/make.mv.gamma.dist.Rd | 2 +-
vignettes/glue.Rnw | 6 +++---
vignettes/sc-intro.Rnw | 2 +-
22 files changed, 68 insertions(+), 66 deletions(-)
Permanent link
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.43.0 dated 2014-06-09 and 0.44.0 dated 2015-02-22
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson
PSCBS-0.43.0/PSCBS/R/PairedPSCBS.BOOT,DEPRECATED.R |only
PSCBS-0.44.0/PSCBS/DESCRIPTION | 20 +++++------
PSCBS-0.44.0/PSCBS/MD5 | 34 ++++++++++----------
PSCBS-0.44.0/PSCBS/NAMESPACE | 6 ++-
PSCBS-0.44.0/PSCBS/NEWS | 12 ++++++-
PSCBS-0.44.0/PSCBS/R/AbstractCBS.PRUNE.R | 2 -
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.BOOT,DEFUNCT.R |only
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.estimateDeltaLOH.R | 2 -
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.estimateKappa.R | 2 -
PSCBS-0.44.0/PSCBS/R/prememoize.R | 2 -
PSCBS-0.44.0/PSCBS/build/vignette.rds |binary
PSCBS-0.44.0/PSCBS/inst/doc/CBS.R | 5 +-
PSCBS-0.44.0/PSCBS/inst/doc/CBS.pdf |binary
PSCBS-0.44.0/PSCBS/inst/doc/CBS.tex.rsp | 14 ++++----
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.R | 5 +-
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.tex.rsp | 17 +++++-----
PSCBS-0.44.0/PSCBS/vignettes/CBS.tex.rsp | 14 ++++----
PSCBS-0.44.0/PSCBS/vignettes/PairedPSCBS.tex.rsp | 17 +++++-----
19 files changed, 89 insertions(+), 63 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Diff between MazamaSpatialUtils versions 0.1.2 dated 2015-02-11 and 0.2.1 dated 2015-02-22
More information about MazamaSpatialUtils at CRAN
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut]
Maintainer: Jonathan Callahan
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/CountryTable.Rd |only
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/StateTable.Rd |only
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/TimezoneTable.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/DESCRIPTION | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/MD5 | 116 ++++---
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/NAMESPACE | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/MazamaSpatialUtils.R | 151 +++-------
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertGADM.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertLayer.R | 9
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertNaturalEarthAdm1.R | 85 +++--
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertTMWorldBorders.R | 45 +-
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertTMWorldBordersSimple.R | 51 +--
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertUSCensusCounties.R | 43 +-
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertUSGSHUC8.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertWikipediaTimezoneTable.R | 20 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertWorldTimezones.R | 29 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountry.R | 16 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountryCode.R | 18 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountryName.R | 18 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getSpatialData.R | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getState.R | 13
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getStateCode.R | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getStateName.R | 13
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getTimezone.R | 10
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getUSCounty.R | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getVariable.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/installSpatialData.R | 14
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/loadSpatialData.R | 5
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/organizePolygons.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/data/SimpleCountries.RData |binary
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/data/SimpleTimezones.RData |binary
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/inst/doc/introduction.html | 19 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/MazamaSpatialUtils.Rd | 1
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/SpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToCode.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToCountry.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToState.Rd | 4
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertGADM.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertLayer.Rd | 9
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertNaturalEarthAdm1.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertTMWorldBorders.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertTMWorldBordersSimple.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertUSCensusCounties.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertUSGSHUC8.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertWikipediaTimezoneTable.Rd | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertWorldTimezones.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/countryToCode.Rd | 4
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountry.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountryCode.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountryName.Rd | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getSpatialData.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getSpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getState.Rd | 12
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getStateCode.Rd | 14
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getStateName.Rd | 12
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getTimezone.Rd | 10
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getUSCounty.Rd | 8
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getVariable.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/initializeSpatialData.Rd | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/installSpatialData.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/loadSpatialData.Rd | 2
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/organizePolygons.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/setSpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/stateToCode.Rd | 8
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/tests/testthat/test1.R | 4
65 files changed, 499 insertions(+), 487 deletions(-)
Permanent link
Title: Statistical Estimation of Game-Theoretic Models
Diff between games versions 1.1-1 dated 2014-01-17 and 1.1.2 dated 2015-02-22
Description: Provides estimation and analysis functions for
strategic statistical models.
Author: Curtis S. Signorino [aut],
Brenton Kenkel [aut, cre]
Maintainer: Brenton Kenkel
games-1.1-1/games/NEWS |only
games-1.1-1/games/R/helpers.r |only
games-1.1.2/games/DESCRIPTION | 14 +--
games-1.1.2/games/MD5 | 101 ++++++++++++++---------
games-1.1.2/games/NAMESPACE | 2
games-1.1.2/games/R/checkFormulas.r |only
games-1.1.2/games/R/checkLocalID.r |only
games-1.1.2/games/R/convergenceCriterion.r |only
games-1.1.2/games/R/doc.r | 17 ---
games-1.1.2/games/R/egame12.r | 48 -----------
games-1.1.2/games/R/egame122.r | 33 -------
games-1.1.2/games/R/egame123.r | 21 ----
games-1.1.2/games/R/finiteProbs.r |only
games-1.1.2/games/R/gameBoot.r |only
games-1.1.2/games/R/games.r | 26 +-----
games-1.1.2/games/R/getGameVcov.r |only
games-1.1.2/games/R/intersectAll.r |only
games-1.1.2/games/R/latexTable.r | 16 ---
games-1.1.2/games/R/makeFormulas.r | 86 -------------------
games-1.1.2/games/R/makeUtils.r |only
games-1.1.2/games/R/makeVarNames.r |only
games-1.1.2/games/R/nonnest.r | 38 --------
games-1.1.2/games/R/predProbs.r | 98 ++--------------------
games-1.1.2/games/R/profile.r | 25 -----
games-1.1.2/games/R/svalsFromProfile.r |only
games-1.1.2/games/R/ultimatum.r | 43 +++------
games-1.1.2/games/inst/examples |only
games-1.1.2/games/man/LW.Rd | 4
games-1.1.2/games/man/Mode.Rd | 14 +--
games-1.1.2/games/man/data_122.Rd | 2
games-1.1.2/games/man/data_123.Rd | 2
games-1.1.2/games/man/data_ult.Rd | 2
games-1.1.2/games/man/egame12.Rd | 121 ++++++++++++----------------
games-1.1.2/games/man/egame122.Rd | 118 +++++++++++----------------
games-1.1.2/games/man/egame123.Rd | 108 +++++++++++-------------
games-1.1.2/games/man/games-package.Rd | 6 -
games-1.1.2/games/man/latexTable.Rd | 47 +++++-----
games-1.1.2/games/man/leblang2003.Rd | 28 ++++--
games-1.1.2/games/man/makeFormulas.Rd | 31 +++----
games-1.1.2/games/man/plot.predProbs.Rd | 55 ++++++------
games-1.1.2/games/man/plot.profile.game.Rd | 13 +--
games-1.1.2/games/man/predProbs.Rd | 59 ++++++-------
games-1.1.2/games/man/predict.game.Rd | 24 ++---
games-1.1.2/games/man/print.game.Rd | 6 -
games-1.1.2/games/man/print.summary.game.Rd | 9 +-
games-1.1.2/games/man/profile.game.Rd | 55 ++++++------
games-1.1.2/games/man/student_offers.Rd | 2
games-1.1.2/games/man/summary.game.Rd | 10 +-
games-1.1.2/games/man/ultimatum.Rd | 84 ++++++++-----------
games-1.1.2/games/man/vuong.Rd | 50 +++++------
games-1.1.2/games/man/war1800.Rd | 2
games-1.1.2/games/tests |only
52 files changed, 539 insertions(+), 881 deletions(-)
Title: Toolkit of Helper Functions to Pre-Process Amplification Data
Diff between chipPCR versions 0.0.8-3 dated 2014-09-29 and 0.0.8-6 dated 2015-02-22
Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.
Author: Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut],
Konstantin A. Blagodatskikh [ctb]
Maintainer: Stefan Roediger
chipPCR-0.0.8-3/chipPCR/man/chipPCR.sp.Rd |only
chipPCR-0.0.8-6/chipPCR/CHANGELOG | 18
chipPCR-0.0.8-6/chipPCR/DESCRIPTION | 40
chipPCR-0.0.8-6/chipPCR/MD5 | 179
chipPCR-0.0.8-6/chipPCR/R/CPP.R | 8
chipPCR-0.0.8-6/chipPCR/R/MFIaggr.R | 5
chipPCR-0.0.8-6/chipPCR/R/classes.R | 217
chipPCR-0.0.8-6/chipPCR/R/effcalc.R | 28
chipPCR-0.0.8-6/chipPCR/R/linreg.R |only
chipPCR-0.0.8-6/chipPCR/R/smoother.R | 4
chipPCR-0.0.8-6/chipPCR/R/th.cyc.R | 66
chipPCR-0.0.8-6/chipPCR/README.md | 4
chipPCR-0.0.8-6/chipPCR/build/vignette.rds |binary
chipPCR-0.0.8-6/chipPCR/data/C126EG595.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C126EG685.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C127EGHP.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C17.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C54.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C60.amp.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C60.melt.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C67.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C81.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C85.rda |binary
chipPCR-0.0.8-6/chipPCR/data/CD74.rda |binary
chipPCR-0.0.8-6/chipPCR/data/CD75.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff1000.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff625.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff750.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff875.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_60.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_69.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_meltcurve.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_595.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_685.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_melt.rda |binary
chipPCR-0.0.8-6/chipPCR/data/capillaryPCR.rda |binary
chipPCR-0.0.8-6/chipPCR/inst/CITATION |only
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.R | 411 -
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.Rnw | 4813 +++++-------
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.pdf |binary
chipPCR-0.0.8-6/chipPCR/man/AmpSim.Rd | 20
chipPCR-0.0.8-6/chipPCR/man/AmpSim.gui.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/C126EG595.Rd | 22
chipPCR-0.0.8-6/chipPCR/man/C126EG685.Rd | 24
chipPCR-0.0.8-6/chipPCR/man/C127EGHP.Rd | 87
chipPCR-0.0.8-6/chipPCR/man/C17.Rd | 22
chipPCR-0.0.8-6/chipPCR/man/C54.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/C60.amp.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C60.melt.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C67.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C81.Rd | 12
chipPCR-0.0.8-6/chipPCR/man/C85.Rd | 175
chipPCR-0.0.8-6/chipPCR/man/CD74.Rd | 50
chipPCR-0.0.8-6/chipPCR/man/CD75.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/CPP.Rd | 62
chipPCR-0.0.8-6/chipPCR/man/Eff1000.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff625.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff750.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff875.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/MFIaggr.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/MFIaggr.gui.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_60.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_69.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_meltcurve.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_595.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_685.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_melt.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/amptest-class.Rd | 1
chipPCR-0.0.8-6/chipPCR/man/amptester.Rd | 9
chipPCR-0.0.8-6/chipPCR/man/amptester.gui.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/bg.max.Rd | 103
chipPCR-0.0.8-6/chipPCR/man/chipPCR-package.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/chipPCR.datasets.Rd | 49
chipPCR-0.0.8-6/chipPCR/man/effcalc.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/fixNA.Rd | 12
chipPCR-0.0.8-6/chipPCR/man/humanrater.Rd | 9
chipPCR-0.0.8-6/chipPCR/man/inder.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/lm.coefs.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/normalizer.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/plot-bg.Rd | 3
chipPCR-0.0.8-6/chipPCR/man/plot-der.Rd | 6
chipPCR-0.0.8-6/chipPCR/man/plot-eff.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/plot-refMFI.Rd | 17
chipPCR-0.0.8-6/chipPCR/man/plotCurves.Rd | 6
chipPCR-0.0.8-6/chipPCR/man/refMFI-class.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/rounder.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/smoother.Rd | 18
chipPCR-0.0.8-6/chipPCR/man/th.cyc.Rd | 8
chipPCR-0.0.8-6/chipPCR/vignettes/chipPCR.Rnw | 4813 +++++-------
chipPCR-0.0.8-6/chipPCR/vignettes/datdf.RData |binary
chipPCR-0.0.8-6/chipPCR/vignettes/natbib.bst |only
chipPCR-0.0.8-6/chipPCR/vignettes/natbib.sty |only
chipPCR-0.0.8-6/chipPCR/vignettes/roediger-burdukiewicz.bib | 4270 ++++------
93 files changed, 7421 insertions(+), 8416 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-6 dated 2015-02-03 and 2.1-7 dated 2015-02-22
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 8 ++--
MD5 | 12 +++---
NEWS | 6 +++
inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/zh_CN |only
man/Rcmdr-package.Rd | 5 +-
po/R-ca.po | 69 ++++++++++++++++++--------------------
po/R-zh_CN.po |only
8 files changed, 53 insertions(+), 47 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.20-29 dated 2014-04-04 and 0.20-30 dated 2015-02-22
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data, that is
sufficient for typical graphics needs, and is also flexible enough
to handle most nonstandard requirements. See ?Lattice for an
introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
DESCRIPTION | 8
MD5 | 72 ++--
R/bwplot.R | 16 -
R/cloud.R | 6
R/densityplot.R | 5
R/histogram.R | 3
R/interaction.R | 2
R/layout.R | 2
R/legend.R | 2
R/levelplot.R | 3
R/miscellaneous.R | 17 -
R/panels.R | 35 --
R/parallel.R | 4
R/print.trellis.R | 51 ---
R/qq.R | 4
R/qqmath.R | 4
R/scales.R | 2
R/settings.R | 496 +++++++++++++++----------------
R/splom.R | 4
R/xyplot.R | 3
data/barley.rda |binary
data/environmental.rda |binary
data/ethanol.rda |binary
data/melanoma.rda |binary
data/singer.rda |binary
inst/po/de/LC_MESSAGES/R-lattice.mo |binary
inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary
inst/po/fr/LC_MESSAGES/R-lattice.mo |binary
inst/po/ko/LC_MESSAGES/R-lattice.mo |binary
inst/po/pl/LC_MESSAGES/R-lattice.mo |binary
man/xyplot.Rd | 5
po/R-de.po | 11
po/R-en@quot.po | 11
po/R-fr.po | 11
po/R-ko.po | 274 ++++++++---------
po/R-lattice.pot | 9
po/R-pl.po | 15
37 files changed, 513 insertions(+), 562 deletions(-)
Title: Methods for Accessing Huge Amounts of Data [deprecated]
Diff between R.huge versions 0.8.0 dated 2014-02-26 and 0.9.0 dated 2015-02-22
Description: DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
.Rinstignore |only
DESCRIPTION | 18 +++++++------
MD5 | 20 +++++++-------
NAMESPACE | 4 ++
NEWS | 4 ++
man/AbstractFileArray.Rd | 2 -
man/FileMatrix.Rd | 2 -
man/FileVector.Rd | 2 -
man/R.huge-package.Rd | 2 -
tests/FileByteVector.R | 5 ++-
tests/FileMatrix,bug20070719.R | 41 ++++++++++++++++--------------
tests/FileMatrix,bug20070821.R | 55 +++++++++++++++++++++--------------------
12 files changed, 87 insertions(+), 68 deletions(-)
Title: Data Analysis Toolbox for Dota2
Diff between RDota versions 1.1 dated 2015-01-26 and 1.2 dated 2015-02-22
Description: Data analysis functions for Dota2. Dota2 is a popular online game (see, e.g.
Author: Xiao Lei
Maintainer: Xiao Lei
DESCRIPTION | 10 +++++-----
MD5 | 14 ++++++++------
NAMESPACE | 1 +
R/globalonline.R |only
R/quickpick.R | 6 +++---
data/antitable.rda |binary
data/matchtable.rda |binary
data/winrate.rda |binary
man/globalonline.Rd |only
9 files changed, 17 insertions(+), 14 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.2 dated 2015-01-30 and 0.2.3 dated 2015-02-22
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 21 +-
MD5 | 154 +++++++++++----------
NAMESPACE | 107 +++++++--------
NEWS | 11 +
R/chordDiagram.R | 28 +++
R/genomic.R | 133 ++++++------------
R/genomic_utils.R | 175 ++++++++++++++++++++++--
R/plot.R | 98 +++++++++++++
R/utils.R | 48 ++++++
inst/doc/circlize.R | 38 +++++
inst/doc/circlize.Rnw | 33 ++++
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.R | 47 ++++--
inst/doc/circular_visualization_of_matrix.Rnw | 56 ++++++-
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.R | 4
inst/doc/draw_ideogram.Rnw | 2
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.R | 28 +--
inst/doc/genomic_plot.Rnw | 45 +++---
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.pdf |binary
inst/extdata/chromInfo.txt |only
man/adjacencyList2Matrix.rd |only
man/chordDiagram.rd | 118 ++++++++--------
man/circlize-package.rd | 176 +++++++++++++------------
man/circlize.rd | 67 ++++-----
man/circos.axis.rd | 109 +++++++--------
man/circos.clear.rd | 50 +++----
man/circos.genomicDensity.rd | 89 ++++++------
man/circos.genomicInitialize.rd | 85 ++++++------
man/circos.genomicLines.rd | 107 +++++++--------
man/circos.genomicLink.rd | 87 ++++++------
man/circos.genomicPoints.rd | 85 ++++++------
man/circos.genomicPosTransformLines.rd | 85 ++++++------
man/circos.genomicRainfall.rd | 81 +++++------
man/circos.genomicRect.rd | 95 ++++++-------
man/circos.genomicText.rd | 103 +++++++-------
man/circos.genomicTrackPlotRegion.rd | 95 ++++++-------
man/circos.info.rd | 69 ++++-----
man/circos.initialize.rd | 83 +++++------
man/circos.initializeWithIdeogram.rd | 93 ++++++-------
man/circos.lines.rd | 103 +++++++-------
man/circos.link.rd | 107 +++++++--------
man/circos.par.rd | 92 ++++++-------
man/circos.points.rd | 83 +++++------
man/circos.polygon.rd | 79 +++++------
man/circos.rect.rd | 83 +++++------
man/circos.text.rd | 93 ++++++-------
man/circos.trackHist.rd | 101 +++++++-------
man/circos.trackLines.rd | 95 ++++++-------
man/circos.trackPlotRegion.rd | 121 ++++++++---------
man/circos.trackPoints.rd | 77 +++++-----
man/circos.trackText.rd | 87 ++++++------
man/circos.updatePlotRegion.rd | 73 +++++-----
man/colorRamp2.rd | 75 +++++-----
man/cytoband.col.rd | 61 ++++----
man/draw.sector.rd | 83 +++++------
man/generateRandomBed.rd | 69 ++++-----
man/genomicDensity.rd | 75 +++++-----
man/get.all.sector.index.rd | 52 +++----
man/get.all.track.index.rd | 46 +++---
man/get.cell.meta.data.rd | 114 ++++++++--------
man/get.current.chromosome.rd | 52 +++----
man/getI.rd | 63 ++++----
man/highlight.chromosome.rd | 71 ++++------
man/highlight.sector.rd |only
man/posTransform.default.rd | 67 ++++-----
man/posTransform.text.rd | 75 +++++-----
man/rainfallTransform.rd | 63 ++++----
man/rand_color.rd | 51 +++----
man/read.chromInfo.rd |only
man/read.cytoband.rd | 93 ++++++-------
man/reverse.circlize.rd | 73 +++++-----
man/show.index.rd | 46 +++---
vignettes/circlize.Rnw | 33 ++++
vignettes/circular_visualization_of_matrix.Rnw | 56 ++++++-
vignettes/draw_ideogram.Rnw | 2
vignettes/genomic_plot.Rnw | 45 +++---
80 files changed, 2894 insertions(+), 2370 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Diff between BIFIEsurvey versions 1.1 dated 2014-11-22 and 1.2-6 dated 2015-02-22
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply-imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre],
Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch
DESCRIPTION | 32
MD5 | 45 -
NAMESPACE | 24
R/BIFIE.correl.R | 2
R/BIFIE.data.R | 71 -
R/BIFIE.data.jack.R | 29
R/BIFIE.derivedParameters.R | 3
R/BIFIE.linreg.R | 2
R/BIFIE.pathmodel.R |only
R/BIFIE.twolevelreg.R |only
R/coef.BIFIEsurvey.R | 14
R/extract.replicated.pars.R | 14
R/summary.BIFIE.data.R |only
R/vcov.BIFIE.survey.R | 16
data/data.bifie01.rda |only
data/datalist | 1
inst/NEWS | 51 -
man/BIFIE.BIFIEdata2BIFIEcdata.Rd | 2
man/BIFIE.data.Rd | 52 +
man/BIFIE.data.jack.Rd | 5
man/BIFIE.pathmodel.Rd |only
man/BIFIE.twolevelreg.Rd |only
man/BIFIEsurvey-package.Rd | 43 -
man/data.bifie.Rd |only
man/data.timss1.Rd | 58 +
src/univar.cpp | 719 ++++++++++++++++++
src/univar_helpers.h | 1496 +++++++++++++++++++++++++++++++++++++-
27 files changed, 2490 insertions(+), 189 deletions(-)
Title: Unified Handling of Graphics Devices
Diff between R.devices versions 2.12.0 dated 2014-10-17 and 2.13.0 dated 2015-02-22
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 16 +++---
MD5 | 49 +++++++++----------
NAMESPACE | 1
NEWS | 22 ++++++++
R/devEval.R | 60 +++++++++++++++--------
R/devNew.R | 35 +++++++++++++
R/devOptions.R | 8 +--
R/deviceUtils.R | 5 -
R/eps.R | 6 +-
R/toNNN.R | 2
R/zzz.R | 2
build/vignette.rds |binary
inst/doc/R.devices-overview.R | 20 +++----
inst/doc/R.devices-overview.pdf |binary
inst/doc/R.devices-overview.tex.rsp | 42 ++++++++--------
man/R.devices-package.Rd | 7 +-
man/devEval.Rd | 4 -
man/eps.Rd | 4 +
man/toNNN.Rd | 6 +-
tests/DevEvalFileProduct.R | 7 ++
tests/devDump.R | 2
tests/devEval,error.R |only
tests/devEval.R | 90 ++++++++++++++++++++++++++++++++++-
tests/devList.R | 26 ++++++++--
tests/devTypeName.R | 37 ++++++++++++--
vignettes/R.devices-overview.tex.rsp | 42 ++++++++--------
26 files changed, 363 insertions(+), 130 deletions(-)
Title: Easy Interface to Advanced PostgreSQL Features
Diff between rpg versions 1.2 dated 2014-09-02 and 1.4 dated 2015-02-22
Description: Allows ad hoc queries and reading and
writing data frames to and from a database.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt
DESCRIPTION | 14 ++---
MD5 | 49 ++++++++++----------
NAMESPACE | 9 ++-
R/RcppExports.R | 80 ---------------------------------
R/rpg.R | 116 ++++++++++++++++++++++++++++++++++++++----------
R/utils.R | 71 +++++++++++++++++++++++------
man/async.Rd | 3 -
man/connection-utils.Rd | 3 -
man/connection.Rd | 3 -
man/copy.Rd | 3 -
man/cursor.Rd | 3 -
man/format_for_send.Rd |only
man/misc.Rd | 3 -
man/prepare.Rd | 53 +++++++--------------
man/psql.Rd | 3 -
man/query.Rd | 3 -
man/rpg-package.Rd | 9 ++-
man/stack.Rd | 3 -
man/stow.Rd | 3 -
man/table-info.Rd | 3 -
man/table-io.Rd | 3 -
man/tracing.Rd | 3 -
man/transactions.Rd | 3 -
src/RcppExports.cpp | 8 +--
src/rpg.cpp | 78 --------------------------------
src/rpg.h | 22 +++++++--
26 files changed, 264 insertions(+), 287 deletions(-)
Title: Hierarchical Clustering with Prototypes
Diff between protoclust versions 1.4 dated 2015-01-28 and 1.5 dated 2015-02-21
Description: Performs minimax linkage hierarchical clustering. Every cluster
has an associated prototype element that represents that cluster as
described in Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering
with Prototypes via Minimax Linkage," accepted for publication in The
Journal of the American Statistical Association, DOI:
10.1198/jasa.2011.tm10183.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/hier.c | 18 ++++++++++++------
3 files changed, 18 insertions(+), 12 deletions(-)
Title: Utilities for Producing Maps
Diff between mapmisc versions 1.1.1 dated 2015-01-05 and 1.1.3 dated 2015-02-21
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 14 ++++----
MD5 | 23 ++++++-------
R/colourScale.R | 11 +++++-
R/legendBreaks.R | 85 ++++++++++++++++++++++++++++++++++++++++++++++++-
R/openmap.R | 14 ++++----
R/utils.R | 76 +++++++++++++++++++++++++++++++++----------
inst/doc/mapLayers.pdf |binary
inst/doc/mapmisc.pdf |binary
man/colourScale.Rd | 16 ++-------
man/legendBreaks.Rd |only
man/netherlands.Rd | 2 -
man/openmap.Rd | 6 ++-
man/scaleBar.Rd | 2 -
13 files changed, 190 insertions(+), 59 deletions(-)
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Diff between highTtest versions 1.0 dated 2014-10-17 and 1.1 dated 2015-02-21
Description: Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.
Author: Hongyuan Cao [aut],
Michael Kosorok [aut],
Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
NAMESPACE | 1 -
R/methods-venn.R | 9 +++++++--
man/highTtest.Rd | 6 ++++--
5 files changed, 21 insertions(+), 14 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 0.8-4 dated 2015-01-07 and 1.0-0 dated 2015-02-21
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NAMESPACE | 12 ++++++++++++
R/cforest.R | 4 ++--
inst/CITATION | 15 +++++----------
inst/NEWS.Rd | 10 ++++++++++
inst/doc/constparty.pdf |binary
inst/doc/ctree.pdf |binary
inst/doc/mob.pdf |binary
inst/doc/partykit.pdf |binary
man/cforest.Rd | 2 +-
vignettes/ctree.Rout.save | 18 +++++++++---------
12 files changed, 54 insertions(+), 37 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Diff between markovchain versions 0.1.0 dated 2015-01-04 and 0.1.1 dated 2015-02-21
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato
Maintainer: Giorgio Alfredo Spedicato
ChangeLog | 4 +
DESCRIPTION | 12 ++---
MD5 | 28 ++++++------
NEWS | 8 +--
R/1_functions4Fitting.R | 44 ++++++++++++++-----
data/blanden.rda |binary
data/craigsendi.rda |binary
data/holson.rda |binary
data/preproglucacon.rda |binary
data/rain.rda |binary
inst/doc/an_introduction_to_markovchain_package.R | 3 -
inst/doc/an_introduction_to_markovchain_package.Rnw | 3 -
inst/doc/an_introduction_to_markovchain_package.pdf |binary
man/markovchain-package.Rd | 4 -
vignettes/an_introduction_to_markovchain_package.Rnw | 3 -
15 files changed, 69 insertions(+), 40 deletions(-)
Title: Improved Predictors
Diff between ipred versions 0.9-3 dated 2013-12-20 and 0.9-4 dated 2015-02-21
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems
as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut],
Torsten Hothorn [aut, cre],
Brian D. Ripley [ctb],
Terry Therneau [ctb],
Beth Atkinson [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NAMESPACE | 2 +-
build/vignette.rds |binary
inst/NEWS | 4 ++++
inst/doc/ipred-examples.pdf |binary
man/bagging.Rd | 2 +-
tests/Examples/ipred-Ex.Rout.save | 12 +++++-------
tests/ipred-bugs.Rout.save | 8 +++-----
tests/ipred-segfault.Rout.save | 8 +++-----
tests/ipred-smalltest.Rout.save | 8 +++-----
11 files changed, 34 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-19 2.0
2014-09-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-05 1.2
2013-03-19 1.1
2012-11-06 1.0
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Diff between synthpop versions 1.0-0 dated 2014-08-18 and 1.1-0 dated 2015-02-20
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
Author: Beata Nowok, Gillian M Raab and Chris Dibben
Maintainer: Beata Nowok
synthpop-1.0-0/synthpop/vignettes/Zcompare.pdf |only
synthpop-1.0-0/synthpop/vignettes/income.pdf |only
synthpop-1.0-0/synthpop/vignettes/incomeNA.pdf |only
synthpop-1.0-0/synthpop/vignettes/ls.pdf |only
synthpop-1.1-0/synthpop/DESCRIPTION | 18
synthpop-1.1-0/synthpop/MD5 | 72 +--
synthpop-1.1-0/synthpop/NAMESPACE | 20
synthpop-1.1-0/synthpop/NEWS |only
synthpop-1.1-0/synthpop/R/IO.r |only
synthpop-1.1-0/synthpop/R/compare.syn.r | 438 +++++++++-----------
synthpop-1.1-0/synthpop/R/functions.syn.r | 25 -
synthpop-1.1-0/synthpop/R/methods.syn.r | 78 ++-
synthpop-1.1-0/synthpop/R/padMis.syn.r | 47 +-
synthpop-1.1-0/synthpop/R/padModel.syn.r | 60 +-
synthpop-1.1-0/synthpop/R/sampler.syn.r | 30 -
synthpop-1.1-0/synthpop/R/syn.r | 296 +++++++------
synthpop-1.1-0/synthpop/build/vignette.rds |binary
synthpop-1.1-0/synthpop/inst/doc/synthpop.R | 157 +++----
synthpop-1.1-0/synthpop/inst/doc/synthpop.Rnw | 238 +++++-----
synthpop-1.1-0/synthpop/inst/doc/synthpop.pdf |binary
synthpop-1.1-0/synthpop/man/compare.fit.synds.Rd | 71 ++-
synthpop-1.1-0/synthpop/man/compare.synds.Rd | 34 +
synthpop-1.1-0/synthpop/man/glm.synds.Rd | 28 -
synthpop-1.1-0/synthpop/man/read.obs.Rd |only
synthpop-1.1-0/synthpop/man/replicated.uniques.Rd |only
synthpop-1.1-0/synthpop/man/sdc.Rd |only
synthpop-1.1-0/synthpop/man/summary.fit.synds.Rd | 62 +-
synthpop-1.1-0/synthpop/man/summary.synds.Rd | 4
synthpop-1.1-0/synthpop/man/syn.Rd | 183 ++++----
synthpop-1.1-0/synthpop/man/syn.cart.Rd | 1
synthpop-1.1-0/synthpop/man/syn.lognorm.Rd |only
synthpop-1.1-0/synthpop/man/syn.norm.Rd | 6
synthpop-1.1-0/synthpop/man/syn.normrank.Rd | 4
synthpop-1.1-0/synthpop/man/syn.pmm.Rd | 2
synthpop-1.1-0/synthpop/man/syn.polr.Rd | 4
synthpop-1.1-0/synthpop/man/syn.sample.Rd | 2
synthpop-1.1-0/synthpop/man/syn.surv.ctree.Rd | 2
synthpop-1.1-0/synthpop/man/synthpop-package.Rd | 20
synthpop-1.1-0/synthpop/man/write.syn.Rd |only
synthpop-1.1-0/synthpop/vignettes/Figure1ls.pdf |only
synthpop-1.1-0/synthpop/vignettes/Figure2income.pdf |only
synthpop-1.1-0/synthpop/vignettes/Figure3Z.pdf |only
synthpop-1.1-0/synthpop/vignettes/synthpop.Rnw | 238 +++++-----
synthpop-1.1-0/synthpop/vignettes/synthpop.bib | 435 +++++++++++++------
44 files changed, 1425 insertions(+), 1150 deletions(-)
Title: Soil Database Interface
Diff between soilDB versions 1.3-2 dated 2014-04-30 and 1.5 dated 2015-02-20
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 19 ++---
MD5 | 95 ++++++++++++++--------------
NAMESPACE | 28 ++++++--
NEWS | 28 +++++++-
R/MUKEYS_by_ll_bbox.R | 9 +-
R/SDA_query.R | 14 ++--
R/SSURGO_spatial_query.R |only
R/fetchHenry.R |only
R/fetchKSSL.R | 4 -
R/fetchNASIS.R | 85 +++++++++++++++++++------
R/fetchNASISLabData.R | 7 +-
R/fetchOSD.R | 3
R/fetchPedonPC.R | 11 +++
R/fetchRaCA.R | 14 ++--
R/fetchSCAN.R | 3
R/get_colors_from_NASIS_db.R | 44 ++++++++-----
R/get_colors_from_pedon_db.R | 10 ++-
R/get_extended_data_from_NASIS_db.R | 86 ++++++++++++++------------
R/get_extended_data_from_pedon_db.R | 20 +++---
R/get_hz_data_from_NASIS_db.R | 12 ++-
R/get_hz_data_from_pedon_db.R | 12 ++-
R/get_lablayer_data_from_NASIS_db.R | 11 ++-
R/get_labpedon_data_from_NASIS_db.R | 11 ++-
R/get_site_data_from_NASIS_db.R | 12 ++-
R/get_site_data_from_pedon_db.R | 11 ++-
R/get_text_notes_from_NASIS_db.R | 19 +++--
R/get_veg_from_AK_Site.R | 10 ++-
R/get_veg_from_MT_veg_db.R | 9 +-
R/get_veg_from_NPS_PLOTS_db.R | 11 ++-
R/get_veg_other_from_MT_veg_db.R | 10 ++-
R/get_veg_species_from_MT_veg_db.R | 11 ++-
R/mapunit_geom_by_ll_bbox.R | 11 +--
R/mix_and_clean_colors.R | 54 +++++++++-------
R/nasis_component_data.R | 37 +++++++----
R/seriesExtent.R | 61 +++++++++---------
R/utils.R | 109 ++++++++++++++++++++++++++++++++-
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/MUKEYS_by_ll_bbox.Rd | 6 -
man/SSURGO_spatial_query.Rd |only
man/fetchNASIS.Rd | 4 -
man/fetchOSD.Rd | 2
man/fetchRaCA.Rd | 7 +-
man/fetchSCAN.Rd | 1
man/gSSURGO.chunk.Rd | 2
man/get_extended_data_from_pedon_db.Rd | 2
man/seriesExtent.Rd | 6 -
50 files changed, 615 insertions(+), 306 deletions(-)
Title: Package Management Tool
Diff between pacman versions 0.2.0 dated 2015-02-15 and 0.3.0 dated 2015-02-20
Description: Tools to more conveniently perform tasks
associated with add-on packages. pacman conveniently wraps library and
package related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level functions which
can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut, ctb]
Maintainer: Tyler Rinker
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NEWS | 12 ++++++++++++
README.md | 2 +-
inst/CITATION | 4 ++--
inst/doc/Introduction_to_pacman.html | 16 ++++++++--------
6 files changed, 33 insertions(+), 21 deletions(-)
Title: Compute the Personalized Activity Index Based on a Flexible
Bayesian Negative Binomial Model
Diff between lmeNBBayes versions 1.3 dated 2015-01-20 and 1.3.1 dated 2015-02-20
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo, Y., Zhao, Y. and Petkau, A.J. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with the infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of a single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in the frequentist framework.
Author: Yumi Kondo
Maintainer: Yumi Kondo
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NAMESPACE | 7 +++++++
R/nbinDPmix_C.R | 2 +-
man/dqmix.Rd | 3 +--
man/getDIC.Rd | 5 ++---
man/getS.StatInMed.Rd | 3 +--
man/index_batch_Bayes.Rd | 3 +--
man/lmeNBBayes.Rd | 3 +--
9 files changed, 28 insertions(+), 26 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Diff between dataRetrieval versions 2.1.1 dated 2015-01-30 and 2.1.2 dated 2015-02-20
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco
dataRetrieval-2.1.1/dataRetrieval/inst/tests |only
dataRetrieval-2.1.2/dataRetrieval/DESCRIPTION | 13
dataRetrieval-2.1.2/dataRetrieval/MD5 | 75 +-
dataRetrieval-2.1.2/dataRetrieval/NAMESPACE | 2
dataRetrieval-2.1.2/dataRetrieval/NEWS | 1
dataRetrieval-2.1.2/dataRetrieval/R/getWebServiceData.R | 2
dataRetrieval-2.1.2/dataRetrieval/R/importWQP.R | 22
dataRetrieval-2.1.2/dataRetrieval/R/importWaterML1.r | 3
dataRetrieval-2.1.2/dataRetrieval/R/readNWISdata.r | 45 +
dataRetrieval-2.1.2/dataRetrieval/R/readNWISdv.r | 5
dataRetrieval-2.1.2/dataRetrieval/R/readNWISpCode.r | 4
dataRetrieval-2.1.2/dataRetrieval/R/readNWISqw.r | 103 ++-
dataRetrieval-2.1.2/dataRetrieval/R/readNWISunit.r | 10
dataRetrieval-2.1.2/dataRetrieval/R/readWQPdata.R | 3
dataRetrieval-2.1.2/dataRetrieval/R/renameColumns.R | 2
dataRetrieval-2.1.2/dataRetrieval/R/tabbedDataRetrievals.R | 58 ++
dataRetrieval-2.1.2/dataRetrieval/R/whatNWISsites.R | 5
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.R | 274 ++++------
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.Rnw | 110 +---
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.pdf |binary
dataRetrieval-2.1.2/dataRetrieval/inst/extdata/temperatureAndFlow.RData |only
dataRetrieval-2.1.2/dataRetrieval/man/dataRetrieval-package.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/pCodeToName.Rd |only
dataRetrieval-2.1.2/dataRetrieval/man/parameterCdFile.Rd |only
dataRetrieval-2.1.2/dataRetrieval/man/readNWISdata.Rd | 10
dataRetrieval-2.1.2/dataRetrieval/man/readNWISdv.Rd | 5
dataRetrieval-2.1.2/dataRetrieval/man/readNWISgwl.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISmeas.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISpCode.Rd | 4
dataRetrieval-2.1.2/dataRetrieval/man/readNWISpeak.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISqw.Rd | 36 +
dataRetrieval-2.1.2/dataRetrieval/man/readNWISrating.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISuv.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/renameNWISColumns.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/tests |only
dataRetrieval-2.1.2/dataRetrieval/vignettes/dataRetrieval-concordance.tex | 13
dataRetrieval-2.1.2/dataRetrieval/vignettes/dataRetrieval.Rnw | 110 +---
dataRetrieval-2.1.2/dataRetrieval/vignettes/figure/getNWIStemperaturePlot-1.pdf |binary
38 files changed, 526 insertions(+), 403 deletions(-)
Title: Analysis of Spatially Distributed Data
Diff between RSurvey versions 0.8-2 dated 2014-09-24 and 0.8-3 dated 2015-02-20
Description: A processing program for spatially distributed data.
It features graphing tools, query building, and polygon clipping.
A graphical user interface is provided.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
DESCRIPTION | 14 +++---
MD5 | 82 ++++++++++++++++++-------------------
NEWS | 7 +++
R/BuildPackage.R | 3 -
R/Data.R | 2
R/LoadPackages.R | 104 ++++++++++++++++++++++++++++++++---------------
R/ManageVariables.R | 5 +-
R/SetSortOrder.R | 4 -
README.md | 18 ++++----
data/ex.project.RData |binary
man/Autocrop.Rd | 2
man/AutocropRegion.Rd | 2
man/BuildHistogram.Rd | 2
man/ChooseColor.Rd | 2
man/ChoosePch.Rd | 2
man/EditData.Rd | 2
man/EditFunction.Rd | 2
man/EditText.Rd | 2
man/ExportData.Rd | 2
man/Format.Rd | 2
man/FormatDateTime.Rd | 2
man/GetBitmapImage.Rd | 2
man/GetFile.Rd | 2
man/ImportPackage.Rd | 2
man/ImportSpreadsheet.Rd | 2
man/ImportText.Rd | 2
man/LoadPackages.Rd | 2
man/ManagePolygons.Rd | 2
man/ManageVariables.Rd | 2
man/OpenRSurvey.Rd | 2
man/Plot3d.Rd | 2
man/ProgressBar.Rd | 2
man/RSurvey-package.Rd | 2
man/Rename.Rd | 2
man/Search.Rd | 2
man/SetAxesLimits.Rd | 2
man/SetConfiguration.Rd | 2
man/SetInterpolation.Rd | 2
man/SetPolygonLimits.Rd | 2
man/SetSortOrder.Rd | 2
man/ex.data.Rd | 2
man/ex.project.Rd | 2
42 files changed, 175 insertions(+), 128 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Diff between poweRlaw versions 0.20.5 dated 2014-06-12 and 0.30.0 dated 2015-02-20
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.20.5/poweRlaw/tests |only
poweRlaw-0.20.5/poweRlaw/vignettes/plpva.r |only
poweRlaw-0.30.0/poweRlaw/DESCRIPTION | 20 -
poweRlaw-0.30.0/poweRlaw/MD5 | 134 +++++------
poweRlaw-0.30.0/poweRlaw/NAMESPACE | 5
poweRlaw-0.30.0/poweRlaw/NEWS | 22 +
poweRlaw-0.30.0/poweRlaw/R/AllGenerics.R | 30 +-
poweRlaw-0.30.0/poweRlaw/R/bootstrap.R | 34 +-
poweRlaw-0.30.0/poweRlaw/R/bootstrap_p.R | 38 +--
poweRlaw-0.30.0/poweRlaw/R/checks.R | 6
poweRlaw-0.30.0/poweRlaw/R/data_help_files.R | 26 +-
poweRlaw-0.30.0/poweRlaw/R/def_conexp.R | 48 +++
poweRlaw-0.30.0/poweRlaw/R/def_conlorm.R | 49 +++-
poweRlaw-0.30.0/poweRlaw/R/def_conpl.R | 32 +-
poweRlaw-0.30.0/poweRlaw/R/def_disexp.R | 24 +
poweRlaw-0.30.0/poweRlaw/R/def_dislnorm.R | 32 +-
poweRlaw-0.30.0/poweRlaw/R/def_displ.R | 42 ++-
poweRlaw-0.30.0/poweRlaw/R/def_dispois.R | 29 +-
poweRlaw-0.30.0/poweRlaw/R/dist_data_cdf_methods.R | 65 ++---
poweRlaw-0.30.0/poweRlaw/R/estimate_xmin.R | 118 ++++++---
poweRlaw-0.30.0/poweRlaw/R/lines_methods.R | 2
poweRlaw-0.30.0/poweRlaw/build/vignette.rds |binary
poweRlaw-0.30.0/poweRlaw/data/bootstrap_moby.RData |binary
poweRlaw-0.30.0/poweRlaw/data/bootstrap_p_moby.RData |binary
poweRlaw-0.30.0/poweRlaw/demo/moby.R | 4
poweRlaw-0.30.0/poweRlaw/inst/CITATION | 29 +-
poweRlaw-0.30.0/poweRlaw/inst/doc/compare_distributions.Rnw | 2
poweRlaw-0.30.0/poweRlaw/inst/doc/compare_distributions.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.R | 92 ++++---
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.Rnw | 123 +++++-----
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.R | 36 +-
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.Rnw | 48 +--
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.Rnw |only
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.pdf |only
poweRlaw-0.30.0/poweRlaw/man/bootstrap_moby.Rd | 26 +-
poweRlaw-0.30.0/poweRlaw/man/compare_distributions.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/displ.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_cdf-methods.Rd | 53 ++--
poweRlaw-0.30.0/poweRlaw/man/dist_data_cdf-methods.Rd | 30 +-
poweRlaw-0.30.0/poweRlaw/man/dist_ll-methods.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_pdf-methods.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_rand-methods.Rd | 9
poweRlaw-0.30.0/poweRlaw/man/dplcon.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dpldis.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/estimate_pars.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/estimate_xmin.Rd | 54 ++--
poweRlaw-0.30.0/poweRlaw/man/moby.Rd | 6
poweRlaw-0.30.0/poweRlaw/man/native_american.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/plot-distribution-ANY-method.Rd | 17 -
poweRlaw-0.30.0/poweRlaw/man/plot.bs_xmin.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/population.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/poweRlaw-package.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/show-distribution-method.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/swiss_prot.Rd | 3
poweRlaw-0.30.0/poweRlaw/vignettes/compare_distributions.Rnw | 2
poweRlaw-0.30.0/poweRlaw/vignettes/examples.Rnw | 123 +++++-----
poweRlaw-0.30.0/poweRlaw/vignettes/examples1.rds |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure1.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure2.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure3.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure4.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure5.pdf |only
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poweRlaw-0.30.0/poweRlaw/vignettes/plfit_res.rds |only
poweRlaw-0.30.0/poweRlaw/vignettes/poweRlaw.Rnw | 48 +--
poweRlaw-0.30.0/poweRlaw/vignettes/poweRlaw.bib | 46 +--
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70 files changed, 917 insertions(+), 626 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Diff between outbreaker versions 1.1-4 dated 2014-12-05 and 1.1-5 dated 2015-02-20
Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 14 ++++++++++++--
DESCRIPTION | 14 +++++++-------
MD5 | 14 +++++++-------
NAMESPACE | 15 +++++++++++----
data/fakeOutbreak.RData |binary
src/likelihood.c | 19 ++++++++++++++++---
src/likelihood.h | 3 +++
src/outbreaker.c | 12 ++++++------
8 files changed, 62 insertions(+), 29 deletions(-)
Title: Maximally Selected Rank Statistics
Diff between maxstat versions 0.7-21 dated 2015-01-19 and 0.7-22 dated 2015-02-20
Description: Maximally selected rank statistics with
several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NAMESPACE | 2 ++
inst/NEWS | 4 ++++
inst/doc/maxstat.pdf |binary
5 files changed, 14 insertions(+), 8 deletions(-)
Title: Convert Spatial Grids to Polygons
Diff between Grid2Polygons versions 0.1-4 dated 2013-08-31 and 0.1-5 dated 2015-02-20
Description: Converts a spatial object from class SpatialGridDataFrame to
SpatialPolygonsDataFrame.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
Grid2Polygons-0.1-4/Grid2Polygons/README.md |only
Grid2Polygons-0.1-5/Grid2Polygons/DESCRIPTION | 12 ++++++------
Grid2Polygons-0.1-5/Grid2Polygons/MD5 | 9 ++++-----
Grid2Polygons-0.1-5/Grid2Polygons/NAMESPACE | 7 +++++++
Grid2Polygons-0.1-5/Grid2Polygons/NEWS | 4 ++++
Grid2Polygons-0.1-5/Grid2Polygons/R/Grid2Polygons.R | 2 +-
6 files changed, 22 insertions(+), 12 deletions(-)
Title: Regression Analysis of Fractional Responses Under Unobserved
Heterogeneity
Diff between frmhet versions 1.0 dated 2014-11-20 and 1.1.2 dated 2015-02-20
Description: Estimation and specification analysis of fractional regression models with neglected heterogeneity and/or endogenous covariates.
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
DESCRIPTION | 8 +--
MD5 | 12 ++---
R/frmhet.R | 119 +++++++++++++++++++++++++++++++-------------------
man/frmhet-package.Rd | 4 -
man/frmhet.Rd | 27 ++++++++++-
man/frmhet.pe.Rd | 22 ++++++++-
man/frmhet.reset.Rd | 19 +++++++
7 files changed, 149 insertions(+), 62 deletions(-)
Title: Regression Analysis of Fractional Responses
Diff between frm versions 1.2 dated 2014-05-27 and 1.2.2 dated 2015-02-20
Description: Estimation and specification analysis of one- and two-part fractional regression models and calculation of partial effects.
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
DESCRIPTION | 16 ++++++++--------
MD5 | 16 ++++++++--------
R/frm.R | 16 ++++++++++------
man/frm-package.Rd | 8 ++++----
man/frm.Rd | 35 ++++++++++++++++++++++++++++++++---
man/frm.ggoff.Rd | 25 +++++++++++++++++++++++--
man/frm.pe.Rd | 38 ++++++++++++++++++++++++++++++++------
man/frm.ptest.Rd | 22 ++++++++++++++++++++++
man/frm.reset.Rd | 24 +++++++++++++++++++++++-
9 files changed, 162 insertions(+), 38 deletions(-)
Title: Exact Distributions for Rank and Permutation Tests
Diff between exactRankTests versions 0.8-27 dated 2013-09-24 and 0.8-28 dated 2015-02-20
More information about exactRankTests at CRAN
Description: Computes exact conditional p-values and quantiles using an
implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
NAMESPACE | 9 +++++++++
data/ASAT.rda |binary
data/bloodp.rda |binary
data/ears.rda |binary
data/glioma.rda |binary
data/globulin.rda |binary
data/lungcancer.rda |binary
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data/ocarcinoma.rda |binary
data/rotarod.rda |binary
data/sal.rda |binary
inst/NEWS | 4 ++++
14 files changed, 31 insertions(+), 18 deletions(-)
Permanent link
Title: Conditional Density Estimation Network Construction and
Evaluation
Diff between CaDENCE versions 1.2.1 dated 2013-06-28 and 1.2.2 dated 2015-02-20
Description: Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, and the like.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon
DESCRIPTION | 11 +++++------
MD5 | 10 +++++-----
NAMESPACE | 4 +---
R/cadence.fit.R | 27 ++++++++++-----------------
man/CaDENCE-package.Rd | 8 ++++----
man/cadence.fit.Rd | 10 +++++++---
6 files changed, 32 insertions(+), 38 deletions(-)
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 1.7-7 dated 2014-11-13 and 1.8 dated 2015-02-20
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 13 +-
MD5 | 50 +++++-----
NEWS | 13 ++
R/SoilProfileCollection-methods.R | 43 ++++++++-
R/SoilProfileCollection-spatial.R | 4
R/evalGenHz.R | 106 +++++++++++-----------
R/get.ml.hz.R | 2
R/panel.depth_function.R | 17 +--
R/profile_plot.R | 38 ++++----
R/setters.R | 48 +++++++++-
R/texture-low-rv-high.R | 168 +++++++++++++++++++-----------------
data/amarillo.rda |binary
data/ca630.rda |binary
data/munsell.rda |binary
data/rruff.sample.rda |binary
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man/SPC-plotting.Rd | 1
man/SoilProfileCollection-class.Rd | 13 ++
man/addBracket.Rd | 7 +
man/hzDistinctnessCodeToOffset.Rd | 2
man/random_profile.Rd | 2
man/texture.triangle.low.rv.high.Rd | 31 ++++--
26 files changed, 341 insertions(+), 217 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-16 1.0.0
2013-06-11 0.0.1
Title: Time Series Analysis and Computational Finance
Diff between tseries versions 0.10-33 dated 2015-02-10 and 0.10-34 dated 2015-02-20
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik
ChangeLog | 7 +++++++
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/finance.R | 11 +++++++----
4 files changed, 20 insertions(+), 10 deletions(-)
Title: STK++ Integration to R Using Rcpp
Diff between rtkpp versions 0.8.4 dated 2014-11-18 and 0.8.5 dated 2015-02-20
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp. Some functionalities of the Clustering
project provided by the library are available in the R environment as R
functions.
The rtkpp package includes the header files from the STK++
library (currently version 0.8.5). Thus users do not need to
install STK++ itself in order to use it.
STK++ is licensed under the GNU LGPL version 2 or later. rtkpp
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre],
Vincent Kubicki [ctb],
Quentin Grimonprez [ctb],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff
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rtkpp-0.8.4/rtkpp/inst/projects/Analysis/include/STK_Funct_util.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/STK_ITContainer2D.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/STK_Wrappers.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/operators/STK_SliceOperators.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/products/STK_GeneralByGeneralProduct.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/products/STK_GeneralByVectorProduct.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureComponent.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IDataManager.cpp |only
rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_BSplineCoefficients.cpp |only
rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_RcppMatrix.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_RcppVector.h |only
rtkpp-0.8.5/rtkpp/DESCRIPTION | 19
rtkpp-0.8.5/rtkpp/MD5 | 533 ++--
rtkpp-0.8.5/rtkpp/NAMESPACE | 17
rtkpp-0.8.5/rtkpp/R/ClusterCategorical.R | 14
rtkpp-0.8.5/rtkpp/R/ClusterGamma.R | 7
rtkpp-0.8.5/rtkpp/R/ClusterInit.R | 90
rtkpp-0.8.5/rtkpp/R/ClusterModelNames.R | 86
rtkpp-0.8.5/rtkpp/R/ClusterPlot.R | 4
rtkpp-0.8.5/rtkpp/R/ClusterPoisson.R |only
rtkpp-0.8.5/rtkpp/R/ClusterStrategy.R | 8
rtkpp-0.8.5/rtkpp/R/rtkpp.R | 37
rtkpp-0.8.5/rtkpp/R/rtkppFlags.R | 14
rtkpp-0.8.5/rtkpp/build |only
rtkpp-0.8.5/rtkpp/cleanup | 2
rtkpp-0.8.5/rtkpp/data/DebTrivedi.rda |only
rtkpp-0.8.5/rtkpp/data/HeartDisease.cat.rda |binary
rtkpp-0.8.5/rtkpp/data/HeartDisease.cont.rda |binary
rtkpp-0.8.5/rtkpp/data/HeartDisease.target.rda |binary
rtkpp-0.8.5/rtkpp/data/birds.rda |binary
rtkpp-0.8.5/rtkpp/data/car.rda |binary
rtkpp-0.8.5/rtkpp/data/geyser.rda |binary
rtkpp-0.8.5/rtkpp/data/titanic.rda |binary
rtkpp-0.8.5/rtkpp/inst/NEWS.Rd | 8
rtkpp-0.8.5/rtkpp/inst/doc |only
rtkpp-0.8.5/rtkpp/inst/include/Algebra.h | 8
rtkpp-0.8.5/rtkpp/inst/include/Analysis.h | 2
rtkpp-0.8.5/rtkpp/inst/include/Arrays.h | 8
rtkpp-0.8.5/rtkpp/inst/include/Clustering.h | 3
rtkpp-0.8.5/rtkpp/inst/include/RTKpp.h | 7
rtkpp-0.8.5/rtkpp/inst/include/RTKppForward.h | 43
rtkpp-0.8.5/rtkpp/inst/include/STKpp.h | 130 -
rtkpp-0.8.5/rtkpp/inst/include/STatistiK.h | 1
rtkpp-0.8.5/rtkpp/inst/include/StatModels.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_GaussianAAModel.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_IAAModel.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_LinearAAModel.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_GaussianAAModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_IAAModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_LinearAAModel.cpp | 20
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/makevars.local |only
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Givens.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Householder.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_IQr.h | 27
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_ISymEigen.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Qr.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Svd.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_SymEigen.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_lapack_Qr.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_lapack_SymEigen.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_Qr.cpp | 3
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_Svd.cpp | 14
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_SymEigen.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_Funct_Util.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_Funct_raw.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_IFunction.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_betaRatio.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_dev0.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_expm1.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_g0.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_gamma.cpp | 10
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_gammaRatio.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_log1p.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_poisson_raw.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_psi_raw.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_AllocatorBase.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array1D.h | 6
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2D.h | 62
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DDiagonal.h | 28
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DLowerTriangular.h | 29
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DPoint.h | 31
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DSquare.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DUpperTriangular.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DVector.h | 27
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2D_Functors.h | 65
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBase.h | 143 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseApplier.h | 86
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseAssign.h | 68
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseInitializer.h | 25
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Arrays_Util.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CAllocator.h | 1153 ++++++----
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArray.h | 120 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayNumber.h | 49
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayPoint.h | 68
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArraySquare.h | 78
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayVector.h | 56
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Const_Arrays.h | 107
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBase.h | 174 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseFunctors.h | 213 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseProduct.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseVisitor.h | 246 +-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_IArray2D.h | 561 +++-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_IArray2DBase.h | 408 ++-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ICAllocator.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ICArray.h | 101
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ITContainer.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_BinaryOperators.h | 88
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_DiagOperator.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_DotOperators.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_SlicingOperators.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_TransposeOperator.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_UnaryOperators.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByArrayProduct.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByVectorProduct.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ProductImpl.h | 127 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ProductOperators.h | 245 +-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_SlicingVisitors.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorSelector.h | 246 --
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_Visitors.h | 210 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorsImpl.h | 469 ++--
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/STK_Arrays_Util.cpp | 8
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/makevars.local | 2
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBase.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalParameters.h | 102
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pjk.h | 26
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pk.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_ExponentialBase.h | 36
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_ExponentialParameters.h | 66
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bjk.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bk.h | 17
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBase.h | 59
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaParameters.h | 595 +++--
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bjk.h | 38
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bk.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bjk.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bk.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_b.h | 35
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bj.h | 39
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bjk.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bk.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_b.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bj.h | 39
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bjk.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bk.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_DiagGaussianBase.h | 78
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_DiagGaussianParameters.h | 153 -
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_s.h | 36
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sj.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sjk.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sk.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_IMixtureBridge.h | 33
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_MixtureBridge.h | 91
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_Clust_Util.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixture.h | 95
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureComposer.h | 61
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureManager.h | 5
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureModel.h | 113
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureModelBase.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureComposer.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureManager.h | 170 +
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureParamStat.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_Clust_Util.cpp | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixture.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureComposer.cpp | 111
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureData.cpp |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureModelBase.cpp | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureAlgo.cpp | 105
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureFacade.cpp | 8
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureInit.cpp | 60
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureStrategy.cpp | 62
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/makevars.local | 1
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_CsvToArray.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_DataFrame.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_ExportToCsv.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_IVariable.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_Variable.h | 44
rtkpp-0.8.5/rtkpp/inst/projects/DManager/src/STK_DataFrame.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/DManager/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_ILinearReduct.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_IReduct.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_LocalVariance.h | 20
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_ProjectedVariance.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_ILinearReduct.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_IReduct.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_LocalVariance.cpp | 21
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_ProjectedVariance.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineCoefficients.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegression.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_BSplineCoefficients.h | 364 +++
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_BSplineRegression.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_IRegression.h | 81
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_MultidimRegression.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegression.cpp | 27
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_BSplineRegression.cpp | 22
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_MultidimRegression.cpp | 27
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/Rcpp_as.h | 6
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/Rcpp_wrap.h | 54
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_ClusterLauncher.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RDataHandler.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RMatrix.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RVector.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_wrap.h |only
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Arithmetic.h | 25
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Constants.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Functors.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Range.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/src/STK_Real.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/MersenneTwister.h | 23
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Bernoulli.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Beta.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Categorical.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Cauchy.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Gamma.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_IUnivLaw.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_MultiNormal.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Normal.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Poisson.h |only
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_RandBase.h | 120 -
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_Functors.h | 400 +--
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_MultivariateReal.h | 35
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_UnivariateReal.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Beta.cpp | 26
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Categorical.cpp | 13
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Cauchy.cpp | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Exponential.cpp | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Gamma.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Normal.cpp | 98
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Poisson.cpp |only
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Uniform.cpp | 15
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/include/STK_MetaTemplate.h | 67
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/include/STK_StaticAssert.h | 7
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_Gaussian2BlocksModel.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_GaussianModel.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IGaussianModel.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IMultiParameters.h | 5
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IMultiStatModel.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IStatModelBase.h | 7
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointBernoulliModel.h | 9
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointGammaParameters.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointGaussianModel.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_Gaussian2BlocksModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_GaussianModel.cpp | 10
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_IGaussianModel.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/unitTests/runit.wrap.R | 6
rtkpp-0.8.5/rtkpp/man/ClusterInit-class.Rd | 4
rtkpp-0.8.5/rtkpp/man/ClusterPoisson-class.Rd |only
rtkpp-0.8.5/rtkpp/man/DebTrivedi.Rd |only
rtkpp-0.8.5/rtkpp/man/IClusterComponent-class.Rd | 11
rtkpp-0.8.5/rtkpp/man/clusterDiagGaussianNames.Rd | 7
rtkpp-0.8.5/rtkpp/man/clusterGamma.Rd | 2
rtkpp-0.8.5/rtkpp/man/clusterInit.Rd | 10
rtkpp-0.8.5/rtkpp/man/clusterPoisson.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterPoissonNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterStrategy.Rd | 4
rtkpp-0.8.5/rtkpp/man/extract-methods.Rd | 3
rtkpp-0.8.5/rtkpp/man/initialize-methods.Rd | 18
rtkpp-0.8.5/rtkpp/man/missingValues-methods.Rd | 6
rtkpp-0.8.5/rtkpp/man/plot-ClusterGamma-method.Rd | 3
rtkpp-0.8.5/rtkpp/man/plot-ClusterPoisson-method.Rd |only
rtkpp-0.8.5/rtkpp/man/print-methods.Rd | 6
rtkpp-0.8.5/rtkpp/man/rtkppFlags.Rd | 5
rtkpp-0.8.5/rtkpp/man/show-methods.Rd | 8
rtkpp-0.8.5/rtkpp/man/summary-methods.Rd | 3
rtkpp-0.8.5/rtkpp/src/Makevars | 12
rtkpp-0.8.5/rtkpp/src/STK_ClusterFacade.cpp | 4
rtkpp-0.8.5/rtkpp/src/STK_ClusterLauncher.cpp | 50
rtkpp-0.8.5/rtkpp/src/STK_RDataHandler.cpp | 4
rtkpp-0.8.5/rtkpp/tests/clusterGammaLikelihood.R | 4
rtkpp-0.8.5/rtkpp/vignettes |only
284 files changed, 6964 insertions(+), 4795 deletions(-)
Title: Forecastable Component Analysis
Diff between ForeCA versions 0.1 dated 2014-03-02 and 0.2.0 dated 2015-02-20
Description: Forecastable Component Analysis (ForeCA) is a novel dimension
reduction (DR) technique for temporally dependent signals. Contrary to
other popular DR methods, such as PCA or ICA, ForeCA takes time dependency
explicitly into account and searches for the most ''forecastable'' signal.
The measure of forecastability is based on the Shannon entropy of the
spectral density of the transformed signal. This R package provides the
main algorithms and auxiliary function (summary, plotting, etc.) to apply
ForeCA to multivariate time series data.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
ForeCA-0.1/ForeCA/R/foreca.EM.R |only
ForeCA-0.1/ForeCA/man/foreca.EM.Rd |only
ForeCA-0.2.0/ForeCA/DESCRIPTION | 28
ForeCA-0.2.0/ForeCA/MD5 | 94 +-
ForeCA-0.2.0/ForeCA/NAMESPACE | 27
ForeCA-0.2.0/ForeCA/NEWS | 82 ++
ForeCA-0.2.0/ForeCA/R/ForeCA-package.R | 66 +
ForeCA-0.2.0/ForeCA/R/Omega.R | 196 ++---
ForeCA-0.2.0/ForeCA/R/SDF2mvspectrum.R | 75 +-
ForeCA-0.2.0/ForeCA/R/common-arguments.R |only
ForeCA-0.2.0/ForeCA/R/complete_controls.R |only
ForeCA-0.2.0/ForeCA/R/continuous_entropy.R | 146 ++--
ForeCA-0.2.0/ForeCA/R/discrete_entropy.R | 158 ++--
ForeCA-0.2.0/ForeCA/R/foreca-utils.R | 240 +++----
ForeCA-0.2.0/ForeCA/R/foreca.EM-aux.R | 399 ++++++-----
ForeCA-0.2.0/ForeCA/R/foreca.EM.one_weightvector.R |only
ForeCA-0.2.0/ForeCA/R/foreca.R | 503 ++++++++++++++-
ForeCA-0.2.0/ForeCA/R/foreca.one_weightvector-utils.R |only
ForeCA-0.2.0/ForeCA/R/initialize_weightvector.R | 163 ++--
ForeCA-0.2.0/ForeCA/R/mvspec2mvspectrum.R | 56 -
ForeCA-0.2.0/ForeCA/R/mvspectrum.R | 383 ++++++++---
ForeCA-0.2.0/ForeCA/R/mvspectrum2wcov.R | 240 ++++---
ForeCA-0.2.0/ForeCA/R/quadratic_form.R | 86 +-
ForeCA-0.2.0/ForeCA/R/sfa.R |only
ForeCA-0.2.0/ForeCA/R/spectral_entropy.R | 254 +++----
ForeCA-0.2.0/ForeCA/R/univariate_spectrum-functions.R |only
ForeCA-0.2.0/ForeCA/R/whiten.R | 274 ++++++--
ForeCA-0.2.0/ForeCA/R/zzz.R |only
ForeCA-0.2.0/ForeCA/man/ForeCA-package.Rd | 43 -
ForeCA-0.2.0/ForeCA/man/Omega.Rd | 125 +--
ForeCA-0.2.0/ForeCA/man/common-arguments.Rd |only
ForeCA-0.2.0/ForeCA/man/complete-controls.Rd |only
ForeCA-0.2.0/ForeCA/man/continuous_entropy.Rd | 60 -
ForeCA-0.2.0/ForeCA/man/discrete_entropy.Rd | 95 +-
ForeCA-0.2.0/ForeCA/man/foreca-utils.Rd | 66 -
ForeCA-0.2.0/ForeCA/man/foreca.EM-aux.Rd | 160 ++--
ForeCA-0.2.0/ForeCA/man/foreca.EM.one_weightvector.Rd |only
ForeCA-0.2.0/ForeCA/man/foreca.Rd | 175 ++++-
ForeCA-0.2.0/ForeCA/man/foreca.one_weightvector-utils.Rd |only
ForeCA-0.2.0/ForeCA/man/initialize_weightvector.Rd | 116 +--
ForeCA-0.2.0/ForeCA/man/mvspectrum.Rd | 257 +++++--
ForeCA-0.2.0/ForeCA/man/mvspectrum2wcov.Rd | 98 ++
ForeCA-0.2.0/ForeCA/man/quadratic_form.Rd | 26
ForeCA-0.2.0/ForeCA/man/sfa.Rd |only
ForeCA-0.2.0/ForeCA/man/spectral_entropy.Rd | 118 +--
ForeCA-0.2.0/ForeCA/man/whiten.Rd | 99 ++
ForeCA-0.2.0/ForeCA/tests |only
47 files changed, 3116 insertions(+), 1792 deletions(-)
Title: High-Speed Processing of VCF, FASTA and Alignment Data
Diff between WhopGenome versions 0.9.1 dated 2015-02-19 and 0.9.2 dated 2015-02-20
Description: Provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Ulrich Wittelsbuerger
DESCRIPTION | 7 +
MD5 | 7 +
inst/CITATION |only
src/Makevars | 16 ----
src/Makevars.win | 212 +++++++++++++++++++++++++++----------------------------
5 files changed, 116 insertions(+), 126 deletions(-)
Title: S3 Methods Simplified
Diff between R.methodsS3 versions 1.6.1 dated 2014-01-05 and 1.7.0 dated 2015-02-20
Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.methodsS3-1.6.1/R.methodsS3/inst/NEWS |only
R.methodsS3-1.7.0/R.methodsS3/DESCRIPTION | 10 ++---
R.methodsS3-1.7.0/R.methodsS3/MD5 | 27 ++++++++++------
R.methodsS3-1.7.0/R.methodsS3/NEWS |only
R.methodsS3-1.7.0/R.methodsS3/R/000.R | 10 +++++
R.methodsS3-1.7.0/R.methodsS3/R/010.setGenericS3.R | 12 +++----
R.methodsS3-1.7.0/R.methodsS3/R/030.setMethodS3.R | 7 ++--
R.methodsS3-1.7.0/R.methodsS3/R/findDispatchMethodsS3.R | 27 ++++++++++++++++
R.methodsS3-1.7.0/R.methodsS3/R/isGenericS3.R | 15 +++++++-
R.methodsS3-1.7.0/R.methodsS3/R/pkgStartupMessage.R | 1
R.methodsS3-1.7.0/R.methodsS3/R/zzz.R | 22 +++++--------
R.methodsS3-1.7.0/R.methodsS3/tests |only
12 files changed, 91 insertions(+), 40 deletions(-)
Title: Multi-Class Sparse Discriminant Analysis
Diff between msda versions 1.0.1 dated 2014-10-02 and 1.0.2 dated 2015-02-20
Description: Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously.
Author: Qing Mai
Maintainer: Yi Yang
ChangeLog | 5 +
DESCRIPTION | 10 +--
MD5 | 28 +++++-----
NAMESPACE | 1
R/cv.msda.R | 19 +++---
R/msda.R | 6 +-
R/plot.msda.R |only
R/predict.msda.R | 11 ++--
R/utilities.R | 11 ++--
data/GDS1615.rda |binary
man/GDS1615.Rd | 56 ++++++++++----------
man/cv.msda.Rd | 142 ++++++++++++++++++++++++++--------------------------
man/msda.Rd | 16 +++--
man/plot.msda.Rd |only
man/predict.msda.Rd | 84 +++++++++++++++---------------
src/msda_new.f90 | 11 ++--
16 files changed, 216 insertions(+), 184 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-37 dated 2015-01-10 and 7.3-39 dated 2015-02-20
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 12 ++++++------
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 5 +++--
R/lda.R | 3 ++-
R/loglm.R | 2 +-
R/lqs.R | 2 +-
R/mvrnorm.R | 6 +++---
R/neg.bin.R | 2 +-
R/negbin.R | 2 +-
inst/NEWS | 3 ++-
man/OME.Rd | 2 +-
man/corresp.Rd | 2 +-
man/denumerate.Rd | 2 +-
man/geyser.Rd | 3 +++
man/mvrnorm.Rd | 9 ++++-----
man/npr1.Rd | 2 +-
man/summary.rlm.Rd | 2 +-
17 files changed, 48 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-17 0.3
2015-01-29 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-11 1.0
Title: R/KEA Interface
Diff between RKEA versions 0.0-4 dated 2014-06-12 and 0.0-5 dated 2015-02-20
Description: An R interface to KEA (Version 5.0).
KEA (for Keyphrase Extraction Algorithm) allows for extracting
keyphrases from text documents. It can be either used for free
indexing or for indexing with a controlled vocabulary. For more
information see
Author: Ingo Feinerer [aut],
Kurt Hornik [aut, cre],
Eibe Frank [ctb, cph] (KEA Java library),
Olena Medelyan [ctb, cph] (KEA Java library),
The Apache Software Foundation [ctb, cph] (Apache Commons Logging and
Apache Jena Java libraries),
International Business Machines Corporation and others [ctb, cph]
(International Components for Unicode for Java (ICU4J)),
Martin Porter [ctb, cph] (Snowball base),
Richard Boulton [ctb, cph] (Snowball Java library),
University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik
DESCRIPTION | 33 ++++++++++++++++++++++++++-------
MD5 | 11 ++++++-----
R/kea.R | 28 ++++++++++++++++++++++++++++
build/vignette.rds |binary
inst/doc/kea.pdf |binary
java |only
man/createModel.Rd | 23 +++++++++++++++++------
7 files changed, 77 insertions(+), 18 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-119 dated 2015-01-10 and 3.1-120 dated 2015-02-20
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
ChangeLog | 22 ++++++++-
DESCRIPTION | 10 ++--
MD5 | 80 +++++++++++++++++-----------------
NAMESPACE | 3 -
R/VarCorr.R | 4 -
R/corStruct.R | 1
R/groupedData.R | 6 --
R/lmList.R | 4 -
R/lme.R | 5 --
R/modelStruct.R | 5 --
R/newFunc.R | 5 --
R/newGenerics.R | 5 --
R/newMethods.R | 4 -
R/nlsList.R | 4 -
R/pdMat.R | 6 --
R/reStruct.R | 15 ------
inst/po/de/LC_MESSAGES/R-nlme.mo |binary
inst/po/de/LC_MESSAGES/nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/R-nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/nlme.mo |binary
inst/po/fr/LC_MESSAGES/nlme.mo |binary
inst/po/ko/LC_MESSAGES/nlme.mo |binary
inst/po/pl/LC_MESSAGES/nlme.mo |binary
inst/scripts/ch01.R | 2
inst/scripts/ch02.R | 2
inst/scripts/ch03.R | 2
inst/scripts/ch04.R | 2
inst/scripts/ch05.R | 2
inst/scripts/ch06.R | 2
inst/scripts/ch08.R | 2
man/bdf.Rd | 2
po/R-de.po | 27 ++++++++---
po/R-nlme.pot | 4 -
po/de.po | 22 ++++-----
po/fr.po | 22 ++++-----
po/ko.po | 22 ++++-----
po/nlme.pot | 24 +++++-----
po/pl.po | 22 ++++-----
tests/nlme.R | 1
tests/nlme.Rout.save | 2
tests/nlme2.R | 2
41 files changed, 157 insertions(+), 186 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Diff between foreign versions 0.8-62 dated 2015-01-07 and 0.8-63 dated 2015-02-20
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team
ChangeLog | 15 +++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/spss.R | 9 +++++----
R/writeForeignSAS.R | 5 +++--
man/lookup.xport.Rd | 2 +-
man/read.arff.Rd | 2 +-
man/read.dta.Rd | 2 ++
man/read.spss.Rd | 38 ++++++++++++++++++++------------------
man/read.xport.Rd | 2 +-
man/write.arff.Rd | 2 +-
src/stataread.c | 9 +++++----
12 files changed, 69 insertions(+), 47 deletions(-)
Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: plspm contains a set of functions for performing Partial Least
Squares Path Modeling (PLS-PM) analysis for both metric and non-metric
data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: ORPHANED
Diff between plspm versions 0.4.1 dated 2013-12-08 and 0.4.2 dated 2015-02-20
DESCRIPTION | 11 +++++++---- MD5 | 6 +++--- NAMESPACE | 1 + build/vignette.rds |binary 4 files changed, 11 insertions(+), 7 deletions(-)
More information about faisalconjoint at CRAN
Permanent link
Title: A Soil Survey Toolkit
Diff between sharpshootR versions 0.6-3 dated 2014-05-06 and 0.7-2 dated 2015-02-19
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: USDA-NRCS Soil Survey Staff
Maintainer: Dylan Beaudette
DESCRIPTION | 24 +++++----
MD5 | 41 +++++++++--------
NAMESPACE | 25 ++++++++--
R/SoilTaxonomyDendrogram.R | 6 +-
R/aspect.plot.R | 19 ++++---
R/component.adj.matrix.R | 26 ++++++----
R/diagnosticPropertyPlot.R | 16 +++++-
R/dueling.dendrograms.R | 12 ++++
R/hillslope.probability.R | 2
R/plotAvailWater.R |only
R/plotSoilRelationGraph.R | 101 +++++++++++++++++++++++++++++++++++-------
R/polygonAdjacency.R |only
R/transect-functions.R |only
data/CDEC.snow.courses.rda |binary
data/amador.rda |binary
man/CDECquery.Rd | 74 ++++++++++++++++++++++++++++--
man/SoilTaxonomyDendrogram.Rd | 6 ++
man/aspect.plot.Rd | 5 +-
man/component.adj.matrix.Rd | 3 -
man/diagnosticPropertyPlot.Rd | 2
man/dist.along.grad.Rd |only
man/plotAvailWater.Rd |only
man/plotSoilRelationGraph.Rd | 28 +++++++++++
man/plotTransect.Rd |only
man/polygonAdjacency.Rd |only
25 files changed, 307 insertions(+), 83 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Diff between OUwie versions 1.43 dated 2014-07-26 and 1.44 dated 2015-02-19
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 10 +-
MD5 | 23 +++---
R/OUwie.R | 153 ++++++++++++++++++++++++++++++++++--------
R/OUwie.boot.R | 4 -
R/OUwie.fixed.R | 1
R/OUwie.joint.R | 190 ++++++++++++++++++++++++++++-------------------------
R/OUwie.sim.R | 8 +-
R/OUwie.slice.R | 17 ++--
R/expect.trendy.R |only
man/OUwie.Rd | 8 --
man/OUwie.boot.Rd | 4 -
man/OUwie.joint.Rd | 7 -
man/OUwie.slice.Rd | 6 -
13 files changed, 267 insertions(+), 164 deletions(-)
Title: Earth Mover's Distance for Differential Analysis of Genomics
Data
Diff between EMDomics versions 0.99.0 dated 2014-11-15 and 0.99.1 dated 2015-02-19
Description: The EMDomics algorithm is used to perform a supervised two-class
analysis to measure the magnitude and statistical significance of observed
continuous genomics data between two groups. Usually the data will be gene
expression values from array-based or sequence-based experiments, but data
from other types of experiments can also be analyzed (e.g. copy number
variation). Traditional methods like Significance Analysis of Microarrays
(SAM) and Linear Models for Microarray Data (LIMMA) use significance tests
based on summary statistics (mean and standard deviation) of the two
distributions. This approach lacks power to identify expression differences
between groups that show high levels of intra-group heterogeneity. The Earth
Mover's Distance (EMD) algorithm instead computes the "work" needed to
transform one distribution into the other, thus providing a metric of the
overall difference in shape between two distributions. Permutation of sample
labels is used to generate q-values for the observed EMD scores.
Author: Daniel Schmolze [aut, cre],
Andrew Beck [aut],
Sheida Nabavi [aut]
Maintainer: Daniel Schmolze
DESCRIPTION | 8 -
MD5 | 28 +--
NAMESPACE | 2
NEWS | 6
R/main.R | 4
build/vignette.rds |binary
inst/doc/EMDomics.R | 128 ++++++++---------
inst/doc/EMDomics.html | 346 +++++++++++++++++++++++-----------------------
man/EMDomics.Rd | 3
man/calculate_emd.Rd | 3
man/calculate_emd_gene.Rd | 3
man/emdomics-package.Rd | 3
man/plot_density.Rd | 3
man/plot_emdnull.Rd | 3
man/plot_perms.Rd | 3
15 files changed, 278 insertions(+), 265 deletions(-)
Title: Error Grid Analysis
Diff between ega versions 1.0.0 dated 2014-11-13 and 1.0.1 dated 2015-02-19
Description: Functions for assigning Clarke or Parkes (Consensus) error grid
zones to blood glucose values, and for plotting both types of error grids.
Author: Daniel Schmolze [aut, cre]
Maintainer: Daniel Schmolze
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
NAMESPACE | 2 +-
NEWS |only
R/ega.R | 18 +++++++++++-------
R/plots.R | 11 ++++++-----
inst/doc/ega.html | 14 +++++++-------
man/ega-package.Rd | 3 ++-
man/getClarkeZones.Rd | 3 ++-
man/getParkesZones.Rd | 3 ++-
man/glucose_data.Rd | 3 ++-
man/plotClarkeGrid.Rd | 3 ++-
man/plotParkesGrid.Rd | 3 ++-
13 files changed, 52 insertions(+), 40 deletions(-)
More information about disparityfilter at CRAN
Permanent link
Title: Geographic Display of Survey Data Statistics
Diff between mapStats versions 1.17 dated 2014-04-14 and 2.3 dated 2015-02-19
Description: Automated calculation and visualization of survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman
DESCRIPTION | 15 -
INDEX | 4
MD5 | 22 +-
NAMESPACE | 3
R/calcQuantiles.R | 113 --------------
R/calcStats.R | 219 +++++++++++++++++----------
R/mapStats.R | 78 +++------
R/plotStats.R | 374 +++++++++++++++++++++++++++++++++--------------
demo/map_examples.R | 184 +++++++++++++----------
man/mapStats-internal.Rd | 30 ++-
man/mapStats-package.Rd | 15 -
man/mapStats.Rd | 139 +++++++----------
12 files changed, 646 insertions(+), 550 deletions(-)
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Diff between FRESA.CAD versions 1.0 dated 2014-09-11 and 2.0 dated 2015-02-19
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena
FRESA.CAD-1.0/FRESA.CAD/R/BootVarNeRIElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/R/boostrapVarElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/data/CancerVarNames.rda |only
FRESA.CAD-1.0/FRESA.CAD/man/bootVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/DESCRIPTION | 21
FRESA.CAD-2.0/FRESA.CAD/MD5 | 154 -
FRESA.CAD-2.0/FRESA.CAD/NAMESPACE | 11
FRESA.CAD-2.0/FRESA.CAD/NEWS |only
FRESA.CAD-2.0/FRESA.CAD/R/FRESA.Model.R | 494 ++--
FRESA.CAD-2.0/FRESA.CAD/R/NeRIBasedFRESA.Model.R | 377 +--
FRESA.CAD-2.0/FRESA.CAD/R/ReclassificationFRESA.Model.R | 617 +----
FRESA.CAD-2.0/FRESA.CAD/R/backVarElimination.r | 250 +-
FRESA.CAD-2.0/FRESA.CAD/R/backVarNeRIElimination.r | 32
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidation.R | 545 +----
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidationNeRI.R | 255 --
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarElimination.r | 284 +-
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarNeRIElimination.r |only
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationFeatureSelection.R | 1032 ++++------
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationNeRIFeatureSelection.R | 210 +-
FRESA.CAD-2.0/FRESA.CAD/R/featureAdjustment.R | 61
FRESA.CAD-2.0/FRESA.CAD/R/getKNNpredictionFromFormula.r | 22
FRESA.CAD-2.0/FRESA.CAD/R/getVarNeRI.R | 35
FRESA.CAD-2.0/FRESA.CAD/R/getVarReclassification.R | 39
FRESA.CAD-2.0/FRESA.CAD/R/heatMaps.R | 86
FRESA.CAD-2.0/FRESA.CAD/R/improvedResiduals.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/listTopCorrelatedVariables.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/medianPredict.r | 44
FRESA.CAD-2.0/FRESA.CAD/R/modelFitting.R | 96
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidation.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidationNeRI.R |only
FRESA.CAD-2.0/FRESA.CAD/R/plotModels.ROC.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/predictForFresa.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/rankInverseNormalDataFrame.R | 91
FRESA.CAD-2.0/FRESA.CAD/R/reportEquivalentVariables.R | 12
FRESA.CAD-2.0/FRESA.CAD/R/residualtForNeRIs.R | 33
FRESA.CAD-2.0/FRESA.CAD/R/summary.bootstrapValidation.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/summaryReport.r | 2
FRESA.CAD-2.0/FRESA.CAD/R/timeSerieAnalysis.R | 34
FRESA.CAD-2.0/FRESA.CAD/R/uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/univariateRankVariables.R | 731 -------
FRESA.CAD-2.0/FRESA.CAD/R/update.uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/updateModel.R | 512 ++--
FRESA.CAD-2.0/FRESA.CAD/R/updateNeRImodel.R | 128 -
FRESA.CAD-2.0/FRESA.CAD/data/cancerVarNames.rda |only
FRESA.CAD-2.0/FRESA.CAD/man/CancerVarNames.Rd | 44
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.CAD-package.Rd | 264 +-
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.Model.Rd | 396 +--
FRESA.CAD-2.0/FRESA.CAD/man/NeRIBasedFRESA.Model.Rd | 272 +-
FRESA.CAD-2.0/FRESA.CAD/man/ReclassificationFRESA.Model.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/backVarElimination.Rd | 181 +
FRESA.CAD-2.0/FRESA.CAD/man/backVarNeRIElimination.Rd | 187 +
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidation.Rd | 292 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidationNeRI.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarElimination.Rd | 226 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationFeatureSelection.Rd | 447 ++--
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationNeRIFeatureSelection.Rd | 433 ++--
FRESA.CAD-2.0/FRESA.CAD/man/featureAdjustment.Rd | 146 -
FRESA.CAD-2.0/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 145 -
FRESA.CAD-2.0/FRESA.CAD/man/getVarNeRI.Rd | 184 +
FRESA.CAD-2.0/FRESA.CAD/man/getVarReclassification.Rd | 176 -
FRESA.CAD-2.0/FRESA.CAD/man/heatMaps.Rd | 189 +
FRESA.CAD-2.0/FRESA.CAD/man/improvedResiduals.Rd | 177 +
FRESA.CAD-2.0/FRESA.CAD/man/listTopCorrelatedVariables.Rd | 128 -
FRESA.CAD-2.0/FRESA.CAD/man/medianPredict.Rd | 186 +
FRESA.CAD-2.0/FRESA.CAD/man/modelFitting.Rd | 120 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidation.Rd | 121 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidationNeRI.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/plotModels.ROC.Rd | 165 -
FRESA.CAD-2.0/FRESA.CAD/man/predictForFresa.Rd | 118 -
FRESA.CAD-2.0/FRESA.CAD/man/rankInverseNormalDataFrame.Rd | 111 -
FRESA.CAD-2.0/FRESA.CAD/man/reportEquivalentVariables.Rd | 159 -
FRESA.CAD-2.0/FRESA.CAD/man/residualForNeRIs.Rd | 123 -
FRESA.CAD-2.0/FRESA.CAD/man/summary.bootstrapValidation.Rd | 129 -
FRESA.CAD-2.0/FRESA.CAD/man/summaryReport.Rd | 162 -
FRESA.CAD-2.0/FRESA.CAD/man/timeSeriesAnalysis.Rd | 173 -
FRESA.CAD-2.0/FRESA.CAD/man/uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/univariateRankVariables.Rd | 461 ++--
FRESA.CAD-2.0/FRESA.CAD/man/update.uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/updateModel.Rd | 214 +-
FRESA.CAD-2.0/FRESA.CAD/man/updateNeRImodel.Rd | 236 +-
FRESA.CAD-2.0/FRESA.CAD/src |only
82 files changed, 6463 insertions(+), 6714 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Diff between EcoGenetics versions 1.0 dated 2015-01-30 and 1.1.0 dated 2015-02-19
Description: Analysis of phenotypic, genotypic and environmental data
with an object of class "ecogen", designed to make easy the
integration of the available information from multiple sources.
Also including geostatistical tools and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser
EcoGenetics-1.0/EcoGenetics/R/auxiliar.R |only
EcoGenetics-1.0/EcoGenetics/R/coordinates.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.sortalleles.R |only
EcoGenetics-1.0/EcoGenetics/R/environment.R |only
EcoGenetics-1.0/EcoGenetics/R/genotype.R |only
EcoGenetics-1.0/EcoGenetics/R/phenotype.R |only
EcoGenetics-1.0/EcoGenetics/R/structure.R |only
EcoGenetics-1.0/EcoGenetics/R/tab.R |only
EcoGenetics-1.0/EcoGenetics/man/auxiliar.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.lmtree-summary.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.sortalleles.Rd |only
EcoGenetics-1.1.0/EcoGenetics/DESCRIPTION | 46
EcoGenetics-1.1.0/EcoGenetics/MD5 | 158 +-
EcoGenetics-1.1.0/EcoGenetics/NAMESPACE | 23
EcoGenetics-1.1.0/EcoGenetics/NEWS |only
EcoGenetics-1.1.0/EcoGenetics/R/ZZZ.R | 2
EcoGenetics-1.1.0/EcoGenetics/R/eco.2columns.R | 109 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2geneland.R | 99 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2genepop.R | 186 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.2gstudio.R | 55
EcoGenetics-1.1.0/EcoGenetics/R/eco.2hierfstat.R | 89 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.R | 362 ++---
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.post.R | 300 +---
EcoGenetics-1.1.0/EcoGenetics/R/eco.alfreq.R | 104 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.append.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.association.R | 326 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.autocor.R | 629 ++++----
EcoGenetics-1.1.0/EcoGenetics/R/eco.boothet.R | 721 ++++------
EcoGenetics-1.1.0/EcoGenetics/R/eco.cbind.R | 232 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.char2num.R | 175 --
EcoGenetics-1.1.0/EcoGenetics/R/eco.clear.R | 32
EcoGenetics-1.1.0/EcoGenetics/R/eco.cormantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.forestplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.geary.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.getisord.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.joincount.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.laglistw.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.lmtree.R | 235 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.localmoran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.mantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.merge.R | 254 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.moran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.order.R | 191 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.pairtest.R | 30
EcoGenetics-1.1.0/EcoGenetics/R/eco.post.geneland.R | 113 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.rankplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.rarefact.R | 315 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.rbind.R | 93 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.remove.R | 42
EcoGenetics-1.1.0/EcoGenetics/R/eco.rescale.R | 21
EcoGenetics-1.1.0/EcoGenetics/R/eco.sort.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.subset.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.theilsen.R | 203 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.variogram.R | 119 -
EcoGenetics-1.1.0/EcoGenetics/R/ecogen.definition.R | 667 +++------
EcoGenetics-1.1.0/EcoGenetics/R/latlon2distm.R |only
EcoGenetics-1.1.0/EcoGenetics/R/other.classes.R | 577 ++++----
EcoGenetics-1.1.0/EcoGenetics/man/EcoGenetics-package.Rd | 152 +-
EcoGenetics-1.1.0/EcoGenetics/man/RelDist-methods.Rd | 51
EcoGenetics-1.1.0/EcoGenetics/man/eco.2columns.Rd | 8
EcoGenetics-1.1.0/EcoGenetics/man/eco.2geneland.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.2genepop.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2gstudio.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2hierfstat.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.post.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.alfreq.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.append.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.association.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.autocor.Rd | 110 -
EcoGenetics-1.1.0/EcoGenetics/man/eco.boothet.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.char2num.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.clear.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cormantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.geary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.getisord.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.joincount.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.laglistw.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.mctree-summary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.localmoran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.mantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.merge.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.moran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.order.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.pairtest.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.rarefact.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.rbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.remove.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.rescale.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.sort.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.subset.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.theilsen.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.variogram.Rd | 35
EcoGenetics-1.1.0/EcoGenetics/man/forestplot-methods.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/latlon2distm.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/rankplot-methods.Rd |only
99 files changed, 3261 insertions(+), 3737 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-25 2.55
2009-11-13 2.5
2009-09-23 2.4
2009-07-18 2.3
2009-06-26 2.1
2009-05-17 1.0
Title: Interact with Simile Models
Diff between Simile versions 1.3.2 dated 2015-02-14 and 1.3.3 dated 2015-02-19
Description: Allows a Simile model saved as a compiled binary to be
loaded, parameterized, executed and interrogated. This version works
with Simile v5.97 on.
Author: Simulistics Ltd
Maintainer: Jasper Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
exec/client5d.tcl | 20 +++++++++++++++-----
man/Simile-package.Rd | 7 +++++--
4 files changed, 27 insertions(+), 14 deletions(-)
Title: Data Augmentation and Multiple Imputation for Interval Censored
Data
Diff between MIICD versions 1.1 dated 2014-04-24 and 2.0 dated 2015-02-19
Description: Implements data augmentation schemes with multiple imputation steps for proportional hazards regression with interval censored data or proportional subdistribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. MIICD functions call Surv, survfit and coxph from survival package, FGR from riskRegression package, and mvrnorm from the MASS package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord
MIICD-1.1/MIICD/R/get.est.cr.cox.R |only
MIICD-1.1/MIICD/data/bcos.rda |only
MIICD-1.1/MIICD/man/ANDA.coxph.Rd |only
MIICD-1.1/MIICD/man/ANDA.crreg.Rd |only
MIICD-1.1/MIICD/man/PMDA.coxph.Rd |only
MIICD-1.1/MIICD/man/PMDA.crreg.Rd |only
MIICD-1.1/MIICD/man/get.est.FG.Rd |only
MIICD-1.1/MIICD/man/get.est.Rd |only
MIICD-1.1/MIICD/man/get.est.cr.cox.Rd |only
MIICD-1.1/MIICD/man/get.set.Rd |only
MIICD-1.1/MIICD/man/preproc.coxph.Rd |only
MIICD-1.1/MIICD/man/preproc.crreg.Rd |only
MIICD-2.0/MIICD/DESCRIPTION | 21 ++-
MIICD-2.0/MIICD/MD5 | 70 +++++++-----
MIICD-2.0/MIICD/NAMESPACE | 24 +++-
MIICD-2.0/MIICD/R/ANDA.coxph.R | 182 ++++++++++++++++----------------
MIICD-2.0/MIICD/R/ANDA.crreg.R | 164 ++++++++++++++--------------
MIICD-2.0/MIICD/R/DA.ci.R |only
MIICD-2.0/MIICD/R/DA.surv.R |only
MIICD-2.0/MIICD/R/ICCRD.R |only
MIICD-2.0/MIICD/R/MI.ci.R |only
MIICD-2.0/MIICD/R/MI.surv.R |only
MIICD-2.0/MIICD/R/MIICD.coxph.R | 138 ++++++++++++++++++++----
MIICD-2.0/MIICD/R/MIICD.crreg.R | 154 +++++++++++++++++++++------
MIICD-2.0/MIICD/R/PMDA.coxph.R | 143 ++++++++++++++-----------
MIICD-2.0/MIICD/R/PMDA.crreg.R | 145 ++++++++++++++-----------
MIICD-2.0/MIICD/R/bcos.R |only
MIICD-2.0/MIICD/R/get.est.FG.R | 26 +---
MIICD-2.0/MIICD/R/get.est.R | 12 --
MIICD-2.0/MIICD/R/get.set.R | 11 +
MIICD-2.0/MIICD/R/get_est_mi.R |only
MIICD-2.0/MIICD/R/get_est_mi_surv.R |only
MIICD-2.0/MIICD/R/get_values_at_time.R |only
MIICD-2.0/MIICD/R/get_z.R |only
MIICD-2.0/MIICD/R/post_point_est_CI.R |only
MIICD-2.0/MIICD/R/preproc.coxph.R | 10 -
MIICD-2.0/MIICD/R/preproc.crreg.R | 12 --
MIICD-2.0/MIICD/data/BCOS.rda |only
MIICD-2.0/MIICD/data/ICCRD.rda |only
MIICD-2.0/MIICD/man/DA.ci.Rd |only
MIICD-2.0/MIICD/man/DA.surv.Rd |only
MIICD-2.0/MIICD/man/ICCRD.Rd |only
MIICD-2.0/MIICD/man/MI.ci.Rd |only
MIICD-2.0/MIICD/man/MI.surv.Rd |only
MIICD-2.0/MIICD/man/MIICD-package.Rd | 52 +++++----
MIICD-2.0/MIICD/man/MIICD.coxph.Rd | 104 ++++++++++--------
MIICD-2.0/MIICD/man/MIICD.crreg.Rd | 127 ++++++++++++++--------
MIICD-2.0/MIICD/man/bcos.Rd | 39 +++---
MIICD-2.0/MIICD/man/plot.DA_ci.Rd |only
MIICD-2.0/MIICD/man/plot.DA_surv.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_coxph.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_crreg.Rd |only
MIICD-2.0/MIICD/man/plot.MI_ci.Rd |only
MIICD-2.0/MIICD/man/plot.MI_surv.Rd |only
54 files changed, 867 insertions(+), 567 deletions(-)
Title: Dynamic Generation of Scientific Reports
Diff between R.rsp versions 0.19.0 dated 2014-06-08 and 0.20.0 dated 2015-02-19
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.rsp-0.19.0/R.rsp/R/captureViaRaw.R |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.html |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.pdf |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.tex.rsp |only
R.rsp-0.19.0/R.rsp/man/getAttributes.RspObject.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspDocument.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspProduct.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspString.Rd |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/DESCRIPTION | 19
R.rsp-0.20.0/R.rsp/MD5 | 257 ++++---
R.rsp-0.20.0/R.rsp/NAMESPACE | 241 ++++++
R.rsp-0.20.0/R.rsp/NEWS | 85 ++
R.rsp-0.20.0/R.rsp/R/006.fixVarArgs.R | 7
R.rsp-0.20.0/R.rsp/R/999.NonDocumentedObjects.R | 1
R.rsp-0.20.0/R.rsp/R/999.RRspPackage.R | 6
R.rsp-0.20.0/R.rsp/R/999.package.R | 1
R.rsp-0.20.0/R.rsp/R/FileRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemon.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemonRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/RspDirective,COPY-PASTE.R |only
R.rsp-0.20.0/R.rsp/R/RspDirective,IF-THEN-ELSE.R | 25
R.rsp-0.20.0/R.rsp/R/RspDirective.R | 106 ++-
R.rsp-0.20.0/R.rsp/R/RspDocument.R | 346 ++++++----
R.rsp-0.20.0/R.rsp/R/RspException.R | 4
R.rsp-0.20.0/R.rsp/R/RspFileProduct.R | 40 +
R.rsp-0.20.0/R.rsp/R/RspObject.R | 95 --
R.rsp-0.20.0/R.rsp/R/RspParser.R | 13
R.rsp-0.20.0/R.rsp/R/RspProduct.R | 61 -
R.rsp-0.20.0/R.rsp/R/RspRSourceCode.R | 2
R.rsp-0.20.0/R.rsp/R/RspRSourceCodeFactory.R | 8
R.rsp-0.20.0/R.rsp/R/RspResponse.R | 2
R.rsp-0.20.0/R.rsp/R/RspString.R | 58 -
R.rsp-0.20.0/R.rsp/R/RspVoid.R |only
R.rsp-0.20.0/R.rsp/R/attributes.R |only
R.rsp-0.20.0/R.rsp/R/buildNonSweaveVignette.R | 2
R.rsp-0.20.0/R.rsp/R/compileAsciiDocNoweb.R | 2
R.rsp-0.20.0/R.rsp/R/compileKnitr.R | 2
R.rsp-0.20.0/R.rsp/R/compileLaTeX.R | 20
R.rsp-0.20.0/R.rsp/R/compileMarkdown.R | 37 -
R.rsp-0.20.0/R.rsp/R/epsDev.DEPRECATED.R | 36 -
R.rsp-0.20.0/R.rsp/R/indexOfNonQuoted.R | 12
R.rsp-0.20.0/R.rsp/R/parseInternetMediaType.R | 2
R.rsp-0.20.0/R.rsp/R/parseRVignetteMetadata.R | 53 -
R.rsp-0.20.0/R.rsp/R/rcat.R | 33
R.rsp-0.20.0/R.rsp/R/rfile.R | 10
R.rsp-0.20.0/R.rsp/R/rsptex.R | 2
R.rsp-0.20.0/R.rsp/R/translateRsp.R | 5
R.rsp-0.20.0/R.rsp/R/translateRspV1.R | 6
R.rsp-0.20.0/R.rsp/R/xweavetangle.R | 193 ++---
R.rsp-0.20.0/R.rsp/R/zzz.CmdArgsFunctions.R |only
R.rsp-0.20.0/R.rsp/R/zzz.R | 23
R.rsp-0.20.0/R.rsp/build/vignette.rds |binary
R.rsp-0.20.0/R.rsp/exec |only
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.html |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 35 -
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
R.rsp-0.20.0/R.rsp/inst/doc/templates/,install_extras | 2
R.rsp-0.20.0/R.rsp/inst/doc/templates/Makefile | 7
R.rsp-0.20.0/R.rsp/inst/doc/templates/enginesMap.R | 2
R.rsp-0.20.0/R.rsp/inst/rsp/src/simpleFooter.html.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.asciidoc.Rnw | 1
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.knitr.Rnw.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_encodings |only
R.rsp-0.20.0/R.rsp/inst/rsp_examples/LoremIpsum.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis.rsp | 3
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.tex.rsp | 7
R.rsp-0.20.0/R.rsp/inst/rsp_tests/R-vignette.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/cutnpaste.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R | 3
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt.rsp | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/trimming-4.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/tcl/r-httpd.tcl | 4
R.rsp-0.20.0/R.rsp/man/Non-documented_objects.Rd | 1
R.rsp-0.20.0/R.rsp/man/R.rsp-package.Rd | 7
R.rsp-0.20.0/R.rsp/man/RRspPackage.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCode.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCodeChunk.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspComment.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspConstruct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspCutDirective.Rd |only
R.rsp-0.20.0/R.rsp/man/RspDirective.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspDocument.Rd | 5
R.rsp-0.20.0/R.rsp/man/RspErrorDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspEvalDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspException.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspFileProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspIfDirective.Rd | 48 -
R.rsp-0.20.0/R.rsp/man/RspIncludeDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspMetaDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspObject.Rd | 7
R.rsp-0.20.0/R.rsp/man/RspPageDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspRSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspShSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspString.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspStringProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspText.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnknownDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVariableDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVoid.Rd |only
R.rsp-0.20.0/R.rsp/man/buildNonSweaveTexToPdf.Rd | 2
R.rsp-0.20.0/R.rsp/man/compileLaTeX.Rd | 11
R.rsp-0.20.0/R.rsp/man/compileMarkdown.Rd | 5
R.rsp-0.20.0/R.rsp/man/getAttributes.default.Rd |only
R.rsp-0.20.0/R.rsp/man/preprocess.RspDocument.Rd | 11
R.rsp-0.20.0/R.rsp/man/rargs.Rd | 2
R.rsp-0.20.0/R.rsp/man/rfile.Rd | 6
R.rsp-0.20.0/R.rsp/tests/000.session_information.R |only
R.rsp-0.20.0/R.rsp/tests/RspConstruct.R |only
R.rsp-0.20.0/R.rsp/tests/RspProduct.R |only
R.rsp-0.20.0/R.rsp/tests/RspString.R |only
R.rsp-0.20.0/R.rsp/tests/capabilities.R | 6
R.rsp-0.20.0/R.rsp/tests/deparse.R | 7
R.rsp-0.20.0/R.rsp/tests/rclean.R |only
R.rsp-0.20.0/R.rsp/tests/rcompile.R | 2
R.rsp-0.20.0/R.rsp/tests/rscript.R | 34
R.rsp-0.20.0/R.rsp/tests/wstring.R |only
R.rsp-0.20.0/R.rsp/vignettes/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/vignettes/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
146 files changed, 1629 insertions(+), 983 deletions(-)
Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.0 dated 2015-02-07 and 1.1 dated 2015-02-19
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 1
DESCRIPTION | 8
MD5 | 15
NAMESPACE | 2
R/power.R | 851 +++++++++++++++++++++++++++------------------------
inst/CITATION | 16
man/power.rr.plot.Rd |only
man/power.rr.test.Rd | 228 ++++++-------
man/rr-package.Rd | 6
9 files changed, 605 insertions(+), 522 deletions(-)
Title: Floating Grid Permutation Technique
Diff between fgpt versions 2.2 dated 2015-02-18 and 2.3 dated 2015-02-19
Description: A permutation technique to explore and control for spatial autocorrelation. This package contains low level functions for performing permutations and calculating statistics as well as higher level functions. Higher level functions are an easy to use function for performing spatially restricted permutation tests and summarize and plot results.
Author: Reinder Radersma & Ben Sheldon
Maintainer: Reinder Radersma
DESCRIPTION | 12
MD5 | 22 -
inst/doc/intro-fgpt.R | 3
inst/doc/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
inst/doc/intro-fgpt.pdf |binary
man/Gpulex.Rd | 2
man/Pmajor.Rd | 2
man/fgeasy.Rd | 2
man/fgperm.Rd | 2
man/fgpt-package.Rd | 2
man/fgstat.Rd | 2
vignettes/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
12 files changed, 1030 insertions(+), 1031 deletions(-)
Title: Functions for the Book "An Introduction to the Bootstrap"
Diff between bootstrap versions 2014.4 dated 2014-04-27 and 2015.2 dated 2015-02-19
Description: Software (bootstrap, cross-validation, jackknife) and data
for the book "An Introduction to the Bootstrap" by B. Efron and
R. Tibshirani, 1993, Chapman and Hall.
_____________________________________________________________
This package is primarily provided for projects already based
on it, and for support of the book. New projects should
preferentially use the recommended package "boot".
Author: S original, from StatLib, by Rob Tibshirani. R port by
Friedrich Leisch.
Maintainer: Scott Kostyshak
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
NEWS | 22 ++++++++++++++++++----
R/bcanon.R | 11 +++++++++--
man/bcanon.Rd | 2 +-
man/scor.Rd | 2 +-
tests |only
7 files changed, 39 insertions(+), 17 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero/One Inflated
Beta Regression
Diff between zoib versions 1.1 dated 2015-02-01 and 1.2 dated 2015-02-18
Description: Fits beta regression and zero/one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu
Maintainer: Fang Liu
DESCRIPTION | 15 +++----
MD5 | 90 +++++++++++++++++++++---------------------
NAMESPACE | 2
R/check.psrf.R | 37 ++++-------------
R/joint.1z.R | 6 +-
R/joint.1z0.R | 6 +-
R/joint.1z01.R | 6 +-
R/joint.1z1.R | 6 +-
R/joint.2z.R | 8 +--
R/joint.2z0.R | 8 +--
R/joint.2z01.R | 8 +--
R/joint.2z1.R | 8 +--
R/paraplot.R |only
R/sep.1z.R | 6 +-
R/sep.1z0.R | 6 +-
R/sep.1z01.R | 7 +--
R/sep.1z1.R | 6 +-
R/sep.2z.R | 10 ++--
R/sep.2z0.R | 8 +--
R/sep.2z01.R | 8 +--
R/sep.2z1.R | 9 +---
R/zoib.R | 32 ++-------------
data/AlcoholUse.rda |binary
data/BiRepeated.rda |binary
data/GasolineYield.rda |binary
inst/bugs/sep_2z.bug | 1
man/AlcoholUse.Rd | 52 ++++++++++++------------
man/BiRepeated.Rd | 53 ++++++++++--------------
man/GasolineYield.Rd | 45 +++++++++------------
man/check.psrf.Rd | 24 +++--------
man/joint.1z0.Rd | 2
man/joint.1z1.Rd | 6 +-
man/joint.2z01.Rd | 2
man/joint.2z1.Rd | 4 -
man/paraplot.Rd |only
man/sep.1z.Rd | 4 -
man/sep.1z0.Rd | 4 -
man/sep.1z01.Rd | 4 -
man/sep.1z1.Rd | 4 -
man/sep.2z.Rd | 4 -
man/sep.2z0.Rd | 4 -
man/sep.2z01.Rd | 4 -
man/sep.2z1.Rd | 4 -
man/zoib-package.Rd | 19 +++++---
man/zoib.Rd | 104 ++++++++++++++++++-------------------------------
tests/test1.R | 4 -
tests/test2.R | 14 +++---
47 files changed, 288 insertions(+), 366 deletions(-)
Title: Blinder-Oaxaca Decomposition
Diff between oaxaca versions 0.1 dated 2014-11-20 and 0.1.2 dated 2015-02-18
Description: An implementation of the Blinder-Oaxaca decomposition for linear regression models.
Author: Marek Hlavac
Maintainer: Marek Hlavac
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 6 ++++--
R/oaxaca-internal.R | 4 ++--
build/vignette.rds |binary
inst/CITATION | 6 +++---
inst/ChangeLog | 6 +++++-
inst/doc/oaxaca.Rtex | 43 +++++++++++++++++++------------------------
inst/doc/oaxaca.pdf |binary
man/oaxaca.Rd | 4 ++--
man/plot.oaxaca.Rd | 4 ++--
vignettes/figure1.pdf |binary
vignettes/figure2.pdf |binary
vignettes/figure3.pdf |binary
vignettes/figure4.pdf |binary
vignettes/oaxaca.Rtex | 43 +++++++++++++++++++------------------------
vignettes/oaxaca.bib | 10 +++++-----
17 files changed, 82 insertions(+), 86 deletions(-)
Title: Random Cluster Generation (with Specified Degree of Separation)
Diff between clusterGeneration versions 1.3.1 dated 2013-01-08 and 1.3.4 dated 2015-02-18
More information about clusterGeneration at CRAN
Description: We developed the clusterGeneration package to provide functions
for generating random clusters, generating random
covariance/correlation matrices,
calculating a separation index (data and population version)
for pairs of clusters or cluster distributions, and 1-D and 2-D
projection plots to visualize clusters. The package also
contains a function to generate random clusters based on
factorial designs with factors such as degree of separation,
number of clusters, number of variables, number of noisy
variables.
Author: Weiliang Qiu
Maintainer: Weiliang Qiu
DESCRIPTION | 16 +++++++++-------
MD5 | 6 +++---
NEWS | 7 +++++++
R/separation.R | 4 ++--
4 files changed, 21 insertions(+), 12 deletions(-)
Permanent link
Title: Clustering Method Based on Local Shrinking
Diff between clues versions 0.5-4 dated 2014-05-21 and 0.5.6 dated 2015-02-18
Description: We developed the clues R package to provide functions
for automatically estimating the number of clusters and
getting the final cluster partition without any input
parameter except the stopping rule for convergence.
The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Author: Fang Chang
Maintainer: Weiliang Qiu
DESCRIPTION | 17 +++++++++--------
MD5 | 11 ++++++-----
NEWS |only
R/clues.R | 17 ++++++++++++-----
R/clues_CH.R | 31 +++++++++++++++++++++++--------
R/clues_sil.R | 30 ++++++++++++++++++++++--------
man/clues.Rd | 2 +-
7 files changed, 73 insertions(+), 35 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Diff between broom versions 0.3.5 dated 2015-01-05 and 0.3.6 dated 2015-02-18
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like dplyr, tidyr and ggplot2. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson
DESCRIPTION | 24 ++++++++++++------------
MD5 | 24 +++++++++++++-----------
NAMESPACE | 3 +++
R/anova_tidiers.R | 40 +++++++++++++++++++++++++++++++++++++---
R/globals.R | 2 +-
R/lm_tidiers.R | 4 +++-
R/matrix_tidiers.R |only
R/stats_tidiers.R | 14 +++++++++-----
inst/doc/bootstrapping.html | 2 +-
inst/doc/broom_and_dplyr.html | 2 +-
inst/doc/kmeans.html | 6 +++---
man/anova_tidiers.Rd | 15 ++++++++++++++-
man/matrix_tidiers.Rd |only
man/tidy.pairwise.htest.Rd | 7 +++++--
14 files changed, 102 insertions(+), 41 deletions(-)
Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Diff between PST versions 0.84.1 dated 2013-12-20 and 0.86 dated 2015-02-18
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho
DESCRIPTION | 22 ++++++++++++----------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 2 +-
NEWS | 12 ++++++++++++
R/PSTf-functions.R | 11 +++++++++++
R/cprob.R | 12 +++++++-----
R/generate.R | 34 ++++++++++++++++++++++------------
R/plotNode.R | 28 +++++-----------------------
R/prune.R | 12 +++---------
R/pstree.R | 13 ++++---------
data/SRH.RData |binary
data/s1.rda |binary
man/PSTf-class.Rd | 2 +-
man/PSTr-class.Rd | 4 ++--
man/SRH-data.Rd | 2 +-
man/cprob.Rd | 2 +-
man/generate.Rd | 7 +++++--
man/nobs.Rd | 2 +-
man/prune.Rd | 3 ++-
man/pstree.Rd | 13 +++++++------
20 files changed, 116 insertions(+), 103 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-8 dated 2014-12-01 and 1.3-9 dated 2015-02-18
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/expressions.R | 2 +-
R/helpers.R | 9 ++++++---
inst/NEWS | 5 +++++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
8 files changed, 23 insertions(+), 15 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-19 dated 2014-12-18 and 1.0-20 dated 2015-02-18
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 11 ++++++-----
MD5 | 10 +++++-----
NAMESPACE | 2 +-
inst/NEWS | 5 +++++
inst/doc/MOB.pdf |binary
inst/doc/party.pdf |binary
6 files changed, 17 insertions(+), 11 deletions(-)
Title: Regression Models with Breakpoints/Changepoints Estimation
Diff between segmented versions 0.5-1.0 dated 2014-12-12 and 0.5-1.1 dated 2015-02-18
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo
segmented |only
1 file changed
Title: Medical Image Registration Using the NiftyReg Library
Diff between RNiftyReg versions 1.1.2 dated 2013-11-07 and 1.1.3 dated 2015-02-18
Description: Provides an R interface to the NiftyReg image registration tools
Author: Jon Clayden, based on original code by Marc Modat and Pankaj Daga
Maintainer: Jon Clayden
DESCRIPTION | 17 +++++++++--------
MD5 | 14 +++++++-------
NEWS | 7 +++++++
R/transform.R | 6 ++----
src/_reg_localTransformation_be.cpp | 4 ++++
src/_reg_localTransformation_jac.cpp | 4 ++++
src/_reg_tools.cpp | 12 ++++++++++++
src/niftyreg.cpp | 12 ++++++++----
8 files changed, 53 insertions(+), 23 deletions(-)
Title: Multitaper Spectral Analysis Tools
Diff between multitaper versions 1.0-9 dated 2014-12-13 and 1.0-10 dated 2015-02-18
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
NAMESPACE | 1 +
R/demod.R | 3 ++-
R/multitaper.R | 33 +++++++++++++++------------------
R/plots.R | 22 ++++++++++++----------
R/plotsHelper.R | 18 +++++++++++-------
man/mtm.coh.Rd | 3 ++-
man/plot.mtm.coh.Rd | 5 +++++
src/Makevars | 12 ++++++------
src/djt.f | 14 ++++++--------
src/dpss.f90 | 14 +++++++-------
src/sine.f | 19 ++++++++-----------
13 files changed, 91 insertions(+), 85 deletions(-)
More information about MortalitySmooth at CRAN
Permanent link
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Diff between ensembleBMA versions 5.0.8 dated 2014-04-14 and 5.1 dated 2015-02-18
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley
CHANGELOG | 5 +++
DESCRIPTION | 8 +++---
MD5 | 26 ++++++++++----------
NAMESPACE | 62 ++++++++++++++++++++++++++++++++++++++++++++++++
R/controlBMAgamma.R | 5 ++-
R/controlBMAgamma0.R | 5 ++-
R/controlBMAnormal.R | 2 -
R/dataNA.ensembleData.R | 2 -
R/ensembleBMAnormal.R | 3 +-
R/fitBMAgamma.R | 12 ++++++---
R/fitBMAgamma0.R | 8 +++++-
R/plotProbcast.R | 16 ++++++------
man/controlBMAgamma.Rd | 14 ++++++++--
man/controlBMAgamma0.Rd | 10 ++++++-
14 files changed, 137 insertions(+), 41 deletions(-)
Title: Finnish Open Government Data Toolkit
Diff between sorvi versions 0.6.23 dated 2014-06-03 and 0.7.20 dated 2015-02-17
Description: Algorithms for Finnish open government data.
Author: Leo Lahti, Juuso Parkkinen, Joona Lehtomaki, Juuso Haapanen, Jussi
Paananen, Einari Happonen
Maintainer: Leo Lahti
sorvi-0.6.23/sorvi/man/get_municipality_info_statfi.Rd |only
sorvi-0.7.20/sorvi/DESCRIPTION | 21
sorvi-0.7.20/sorvi/MD5 | 67 -
sorvi-0.7.20/sorvi/NAMESPACE | 5
sorvi-0.7.20/sorvi/R/firstlib.R | 15
sorvi-0.7.20/sorvi/R/provinceinfo.R | 76 -
sorvi-0.7.20/sorvi/R/visualization.R | 3
sorvi-0.7.20/sorvi/README.md | 5
sorvi-0.7.20/sorvi/build/vignette.rds |binary
sorvi-0.7.20/sorvi/inst/doc/sorvi.Rnw |only
sorvi-0.7.20/sorvi/inst/doc/sorvi.pdf |only
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.R | 107 +-
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.Rmd | 85 +-
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.html | 592 ++++++---------
sorvi-0.7.20/sorvi/man/convert_municipality_codes.Rd | 3
sorvi-0.7.20/sorvi/man/convert_municipality_names.Rd | 3
sorvi-0.7.20/sorvi/man/fi.en.maakunnat.Rd | 3
sorvi-0.7.20/sorvi/man/get_municipality_info_mml.Rd | 13
sorvi-0.7.20/sorvi/man/get_postal_code_info.Rd | 3
sorvi-0.7.20/sorvi/man/get_province_info_wikipedia.Rd | 3
sorvi-0.7.20/sorvi/man/hetu.Rd | 3
sorvi-0.7.20/sorvi/man/is_url.Rd | 3
sorvi-0.7.20/sorvi/man/korvaa_skandit.Rd | 3
sorvi-0.7.20/sorvi/man/load_sorvi_data.Rd | 3
sorvi-0.7.20/sorvi/man/municipality_to_province.Rd | 5
sorvi-0.7.20/sorvi/man/regression_plot.Rd | 5
sorvi-0.7.20/sorvi/man/ropengov_storage_path.Rd | 3
sorvi-0.7.20/sorvi/man/sorvi-package.Rd | 3
sorvi-0.7.20/sorvi/man/strip.Rd | 3
sorvi-0.7.20/sorvi/man/strstrip.Rd | 3
sorvi-0.7.20/sorvi/man/strstrip_single.Rd | 3
sorvi-0.7.20/sorvi/man/valid_hetu.Rd | 3
sorvi-0.7.20/sorvi/vignettes/TODO.Rmd |only
sorvi-0.7.20/sorvi/vignettes/figure/regressionline-1.png |only
sorvi-0.7.20/sorvi/vignettes/figure/regressionline.png |binary
sorvi-0.7.20/sorvi/vignettes/sorvi.Rnw |only
sorvi-0.7.20/sorvi/vignettes/sorvi_tutorial.Rmd | 85 +-
sorvi-0.7.20/sorvi/vignettes/sorvi_tutorial.md |only
38 files changed, 489 insertions(+), 640 deletions(-)
Title: Data Exchange Between R and LabKey Server
Diff between Rlabkey versions 2.1.126 dated 2014-12-17 and 2.1.127 dated 2015-02-17
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe
DESCRIPTION | 12 ++++++------
MD5 | 24 ++++++++++++------------
NEWS | 7 +++++++
R/labkey.executeSql.R | 14 +++++++++-----
R/labkey.getFolders.R | 15 ++++++++-------
R/labkey.selectRows.R | 6 ++++--
R/labkey.setCurlOptions.R | 4 ++--
inst/doc/RlabkeyExample.pdf |binary
inst/doc/usersguide.pdf |binary
man/Rlabkey-package.Rd | 4 ++--
man/labkey.executeSql.Rd | 8 ++++++--
man/labkey.getFolders.Rd | 4 +++-
man/labkey.selectRows.Rd | 8 ++++----
13 files changed, 63 insertions(+), 43 deletions(-)
Title: Latent Variable Models
Diff between lava versions 1.3 dated 2014-11-18 and 1.4.0 dated 2015-02-17
Description: Estimation and simulation of latent variable models.
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
DESCRIPTION | 16 -
INDEX | 13 -
MD5 | 433 +++++++++++++++++++++++------------------------
NAMESPACE | 14 -
NEWS | 15 +
R/By.R | 4
R/Expand.R | 22 +-
R/Missing.R | 22 +-
R/Objective.R | 64 +++---
R/addattr.R | 12 -
R/addhook.R | 20 +-
R/addvar.R | 19 --
R/assoc.R | 4
R/baptize.R | 16 -
R/bootstrap.R | 28 +--
R/cancel.R | 2
R/categorical.R | 12 -
R/cluster.hook.R | 12 -
R/coef.R | 144 +++++++--------
R/compare.R | 48 ++---
R/confint.R | 17 -
R/constrain.R | 76 ++++----
R/copy.R | 4
R/correlation.R | 6
R/covariance.R | 91 ++++-----
R/curereg.R | 61 +++---
R/deriv.R | 75 ++++----
R/describecoef.R | 15 -
R/diagtest.R |only
R/distribution.R | 123 +++++++++----
R/dsort.R | 17 +
R/effects.R | 61 +++---
R/endogenous.R | 2
R/equivalence.R | 44 ++--
R/estimate.default.R | 191 +++++++++++---------
R/estimate.lvm.R | 173 +++++++++---------
R/estimate.multigroup.R | 158 ++++++++---------
R/eventTime.R | 108 +++++------
R/exogenous.R | 12 -
R/finalize.R | 74 +++-----
R/fix.R | 128 +++++++------
R/fixsome.R | 28 +--
R/formula.R | 3
R/functional.R | 13 -
R/glmest.R | 69 +++----
R/gof.R | 84 ++++-----
R/graph.R | 15 -
R/graph2lvm.R | 5
R/heavytail.R | 8
R/iid.R | 16 -
R/index.sem.R | 49 ++---
R/information.R | 30 +--
R/iv.R | 85 ++++-----
R/kill.R | 12 -
R/labels.R | 111 +++++-------
R/latent.R | 11 -
R/lava-package.R | 32 +--
R/lisrel.R | 14 -
R/lmers.R | 2
R/logLik.R | 82 ++++----
R/logo.R | 10 -
R/lvm.R | 27 +-
R/makemissing.R | 5
R/manifest.R | 5
R/matrices.R | 110 +++++------
R/measurement.R | 9
R/merge.R | 22 +-
R/missingMLE.R | 52 ++---
R/model.R | 14 -
R/modelPar.R | 30 +--
R/modelsearch.R | 49 ++---
R/moments.R | 10 -
R/multigroup.R | 62 +++---
R/multinomial.R | 53 ++---
R/multipletesting.R | 12 -
R/nested.R | 3
R/nodecolor.R | 2
R/normal.R | 40 +++-
R/onload.R | 10 -
R/optims.R | 60 +++---
R/ordinal.R | 14 -
R/ordreg.R | 13 -
R/parameter.R | 2
R/parpos.R | 12 -
R/pars.R | 9
R/partialcor.R | 12 -
R/path.R | 47 ++---
R/pcor.R | 29 +--
R/plot.R | 66 +++----
R/predict.R | 40 ++--
R/print.R | 26 +-
R/profile.R | 4
R/randomslope.R | 11 -
R/regression.R | 118 ++++++------
R/reorder.R | 2
R/residuals.R | 12 -
R/scheffe.R | 3
R/score.R | 38 ++--
R/sim.R | 157 ++++++++---------
R/spaghetti.R |only
R/stack.R |only
R/startvalues.R | 64 +++---
R/subgraph.R | 3
R/subset.R | 14 -
R/summary.R | 18 -
R/survival.R | 3
R/transform.R | 22 +-
R/utils.R | 119 ++++++++----
R/variances.R | 5
R/vars.R | 28 +--
R/vcov.R | 1
R/zCol.R | 22 +-
R/zblockdiag.R | 1
R/zclick.R | 8
R/zcolorbar.R | 10 -
R/zcombine.R | 13 -
R/zcommutation.R | 10 -
R/zconfband.R | 45 ++--
R/zdevcoords.R | 9
R/zgetmplus.R | 56 +++---
R/zgetsas.R | 18 -
R/zimages.R | 14 -
R/zksmooth.R | 20 +-
R/zmypal.R | 1
R/zoperators.R | 23 +-
R/zorg.R | 23 +-
R/zpdfconvert.R | 8
R/zplotConf.R | 359 +++++++++++++++++++++++++++++++++++---
R/zrevdiag.R | 2
R/ztoformula.R | 18 -
R/ztr.R | 13 -
R/ztrim.R | 2
inst/doc/reference.pdf |binary
inst/gof1.png |only
inst/lava1.png |only
man/By.Rd | 2
man/Col.Rd | 2
man/Combine.Rd | 2
man/Expand.Rd | 6
man/Graph.Rd | 2
man/Missing.Rd | 4
man/Model.Rd | 2
man/PD.Rd | 2
man/Range.lvm.Rd | 2
man/addvar.Rd | 2
man/baptize.Rd | 2
man/blockdiag.Rd | 2
man/bmd.Rd | 2
man/bmidata.Rd | 2
man/bootstrap.Rd | 2
man/bootstrap.lvm.Rd | 2
man/brisa.Rd | 2
man/calcium.Rd | 2
man/cancel.Rd | 2
man/children.Rd | 2
man/click.Rd | 4
man/closed.testing.Rd | 2
man/colorbar.Rd | 2
man/compare.Rd | 3
man/confband.Rd | 9
man/confint.lvmfit.Rd | 2
man/constrain-set.Rd | 2
man/correlation.Rd | 2
man/covariance.Rd | 2
man/curereg.Rd | 2
man/devcoords.Rd | 2
man/diagtest.Rd |only
man/dsort.Rd | 8
man/equivalence.Rd | 2
man/estimate.default.Rd | 23 +-
man/estimate.lvm.Rd | 2
man/eventTime.Rd | 2
man/getMplus.Rd | 2
man/getSAS.Rd | 2
man/gof.Rd | 2
man/hubble.Rd | 2
man/hubble2.Rd | 2
man/iid.Rd | 2
man/images.Rd | 2
man/indoorenv.Rd | 2
man/intercept.Rd | 2
man/internal.Rd | 3
man/kill.Rd | 2
man/ksmooth2.Rd | 5
man/labels-set.Rd | 2
man/lava-package.Rd | 2
man/lava.options.Rd | 2
man/lvm.Rd | 2
man/makemissing.Rd | 4
man/measurement.error.Rd |only
man/missingdata.Rd | 2
man/modelsearch.Rd | 2
man/multinomial.Rd | 2
man/nldata.Rd | 2
man/nsem.Rd | 2
man/op_concat.Rd | 10 -
man/op_match.Rd | 2
man/ordreg.Rd | 2
man/org.Rd | 2
man/parpos.Rd | 2
man/partialcor.Rd | 2
man/path.Rd | 2
man/pdfconvert.Rd | 2
man/plot.lvm.Rd | 4
man/plotConf.Rd | 8
man/predict.lvm.Rd | 2
man/regression-set.Rd | 8
man/revdiag.Rd | 2
man/scheffe.Rd | 2
man/semdata.Rd | 2
man/serotonin.Rd | 2
man/serotonin2.Rd | 2
man/sim.Rd | 26 +-
man/spaghetti.Rd |only
man/stack.estimate.Rd |only
man/subset.lvm.Rd | 2
man/timedep.Rd | 2
man/toformula.Rd | 2
man/tr.Rd | 2
man/trim.Rd | 2
man/twindata.Rd | 2
man/vars.Rd | 2
222 files changed, 2939 insertions(+), 2499 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and Python
Diff between fastcluster versions 1.1.15 dated 2015-01-05 and 1.1.16 dated 2015-02-17
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: "linkage" in the SciPy package
"scipy.cluster.hierarchy", "hclust" in R's "stats" package, and the
"flashClust" package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner
DESCRIPTION | 18 +++++++++---------
MD5 | 22 +++++++++++-----------
NEWS | 7 ++++++-
inst/doc/fastcluster.Rtex | 4 ++--
inst/doc/fastcluster.pdf |binary
src/fastcluster.cpp | 5 ++++-
src/fastcluster_R.cpp | 37 +++++++++++++------------------------
src/python/fastcluster.py | 2 +-
src/python/test/nantest.py | 2 +-
src/python/test/test.py | 2 +-
src/python/test/vectortest.py | 2 +-
vignettes/fastcluster.Rtex | 4 ++--
12 files changed, 51 insertions(+), 54 deletions(-)
Title: High Performance Cluster Models Based on Kiefer-Wolfowitz
Recursion
Diff between hpcwld versions 0.4 dated 2014-07-16 and 0.5 dated 2015-02-17
Description: Probabilistic models describing the behavior
of workload and queue on a High Performance Cluster and computing GRID
under FIFO service discipline basing on modified Kiefer-Wolfowitz
recursion. Also sample data for inter-arrival times, service times,
number of cores per task and waiting times of HPC of Karelian
Research Centre are included, measurements took place from 06/03/2009 to 02/30/2011.
Functions provided to import/export workload traces in Standard Workload Format (swf).
Stability condition of the model may be verified either exactly, or approximately.
Author: Alexander Rumyantsev [aut, cre]
Maintainer: Alexander Rumyantsev
DESCRIPTION | 19 ++++++++++++-------
MD5 | 16 ++++++++++------
NAMESPACE | 4 +++-
R/ApproxC.R |only
R/StabC.R |only
data/HPC_KRC.rda |binary
data/HPC_KRC2.rda |binary
data/X.rda |binary
man/ApproxC.Rd |only
man/StabC.Rd |only
man/hpcwld-package.Rd | 13 +++++++++++--
11 files changed, 36 insertions(+), 16 deletions(-)
Title: Implementation of gWidgets2 for the RGtk2 Package
Diff between gWidgets2RGtk2 versions 1.0-2 dated 2013-10-29 and 1.0-3 dated 2015-02-17
More information about gWidgets2RGtk2 at CRAN
Description: Implements the gWidgets2 API for RGtk2.
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 28 -
MD5 | 62 +--
NAMESPACE | 3
NEWS | 8
R/GComponent.R | 52 ++
R/dialogs.R | 6
R/gbutton.R | 8
R/gcheckbox.R | 33 -
R/gcheckboxgroup.R | 4
R/gcombobox.R | 22 -
R/gdf.R | 50 ++
R/gedit.R | 16
R/gfile.R | 6
R/gformlayout.R | 16
R/ggraphics.R | 21 -
R/gimage.R | 56 +--
R/glabel.R | 47 +-
R/glayout.R | 9
R/gnotebook.R | 18
R/gprogressbar.R | 1
R/gtable.R | 57 +--
R/gtext.R | 44 +-
R/gtk-misc.R | 2
R/gtree.R | 33 +
R/gwindow.R | 3
man/add_editable_cell_renderer.Rd | 17
man/ensure_type.Rd | 12
man/gWidgets2RGtk2-package.Rd | 217 +++++++----
man/gWidgets2RGtk2-undocumented.Rd | 665 +++++++++++++++---------------------
man/guiWidgetsToolkitRGtk2-class.Rd | 4
man/isFirstMouseClick.Rd | 9
man/isRightMouseClick.Rd | 9
32 files changed, 862 insertions(+), 676 deletions(-)
Permanent link
Title: Exploration and Graphics for RivEr Trends (EGRET)
Diff between EGRET versions 2.1.0 dated 2014-12-18 and 2.1.1 dated 2015-02-17
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
EGRET-2.1.0/EGRET/man/readNWISInfo.Rd |only
EGRET-2.1.0/EGRET/man/readUserInfo.Rd |only
EGRET-2.1.0/EGRET/man/readWQPInfo.Rd |only
EGRET-2.1.0/EGRET/vignettes/cache |only
EGRET-2.1.1/EGRET/DESCRIPTION | 10
EGRET-2.1.1/EGRET/MD5 | 184 ++++------
EGRET-2.1.1/EGRET/NAMESPACE | 3
EGRET-2.1.1/EGRET/NEWS | 8
EGRET-2.1.1/EGRET/R/EGRET.R | 26 +
EGRET-2.1.1/EGRET/R/fluxBiasEight.R | 3
EGRET-2.1.1/EGRET/R/generalAxis.R | 10
EGRET-2.1.1/EGRET/R/logPretty3.R | 2
EGRET-2.1.1/EGRET/R/mergeReport.r | 11
EGRET-2.1.1/EGRET/R/objectDefinitions.R | 19 -
EGRET-2.1.1/EGRET/R/plotConcQ.R | 3
EGRET-2.1.1/EGRET/R/plotConcQSmooth.R | 3
EGRET-2.1.1/EGRET/R/plotConcTime.R | 5
EGRET-2.1.1/EGRET/R/plotConcTimeDaily.R | 5
EGRET-2.1.1/EGRET/R/plotConcTimeSmooth.R | 3
EGRET-2.1.1/EGRET/R/plotFluxTimeDaily.R | 6
EGRET-2.1.1/EGRET/R/plotQTimeDaily.R | 6
EGRET-2.1.1/EGRET/R/populateParameterINFO.r | 3
EGRET-2.1.1/EGRET/R/printFluxUnitCheatSheet.R | 1
EGRET-2.1.1/EGRET/R/readMetaData.r | 144 ++++---
EGRET-2.1.1/EGRET/R/readNWISDaily.r | 4
EGRET-2.1.1/EGRET/R/sysdata.rda |binary
EGRET-2.1.1/EGRET/README.md | 6
EGRET-2.1.1/EGRET/demo/checkData.R | 7
EGRET-2.1.1/EGRET/inst/doc/EGRET.R | 11
EGRET-2.1.1/EGRET/inst/doc/EGRET.Rnw | 16
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EGRET-2.1.1/EGRET/man/fluxBiasMulti.Rd | 3
EGRET-2.1.1/EGRET/man/generalAxis.Rd | 5
EGRET-2.1.1/EGRET/man/getDaily.Rd | 2
EGRET-2.1.1/EGRET/man/getInfo.Rd | 2
EGRET-2.1.1/EGRET/man/getSample.Rd | 2
EGRET-2.1.1/EGRET/man/getSurfaces.Rd | 2
EGRET-2.1.1/EGRET/man/plotConcQ.Rd | 3
EGRET-2.1.1/EGRET/man/plotConcQSmooth.Rd | 3
EGRET-2.1.1/EGRET/man/plotConcTime.Rd | 5
EGRET-2.1.1/EGRET/man/plotConcTimeDaily.Rd | 5
EGRET-2.1.1/EGRET/man/plotConcTimeSmooth.Rd | 3
EGRET-2.1.1/EGRET/man/plotFluxTimeDaily.Rd | 4
EGRET-2.1.1/EGRET/man/plotQTimeDaily.Rd | 5
EGRET-2.1.1/EGRET/man/populateParameterINFO.Rd | 3
EGRET-2.1.1/EGRET/man/printFluxUnitCheatSheet.Rd | 1
EGRET-2.1.1/EGRET/man/readNWISDaily.Rd | 3
EGRET-2.1.1/EGRET/tests |only
EGRET-2.1.1/EGRET/vignettes/EGRET-concordance.tex | 8
EGRET-2.1.1/EGRET/vignettes/EGRET.Rnw | 16
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93 files changed, 343 insertions(+), 235 deletions(-)
Title: Toolkit for Electroencephalography Data
Diff between eegkit versions 1.0-1 dated 2014-10-13 and 1.0-2 dated 2015-02-17
Description: Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for plotting (a) EEG caps, (b) single- and multi-channel EEG time courses, and (c) EEG spatial maps. Also includes smoothing and Independent Component Analysis functions for EEG data analysis, and a function for simulating event-related potential EEG data.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
ChangeLog | 42 +++++++++++++++++
DESCRIPTION | 8 +--
MD5 | 58 +++++++++++------------
R/colorbar3d.R | 20 ++++----
R/eegcap.R | 68 +++++++++++++++------------
R/eegcapdense.R | 76 +++++++++++++++++-------------
R/eegica.R | 20 ++++----
R/eegsim.R | 77 ++++++++++++++++---------------
R/eegsmooth.R | 40 ++++++++--------
R/eegspace.R | 123 +++++++++++++++++++++++++++-----------------------
R/eegtime.R | 64 +++++++++++++++-----------
R/eegtimemc.R | 70 +++++++++++++++++++---------
R/voltcol.R | 10 ++--
data/eegcoord.rda |binary
data/eegdense.rda |binary
data/eeghead.rda |binary
data/eegmesh.rda |binary
man/eegcap.Rd | 43 ++++++++---------
man/eegcapdense.Rd | 26 ++++++----
man/eegcoord.Rd | 6 +-
man/eegdense.Rd | 2
man/eeghead.Rd | 8 +--
man/eegica.Rd | 57 +++++++++++------------
man/eegkit-package.Rd | 6 +-
man/eegmesh.Rd | 8 +--
man/eegsim.Rd | 79 +++++++++++++++-----------------
man/eegsmooth.Rd | 83 +++++++++++++++++----------------
man/eegspace.Rd | 37 +++++++--------
man/eegtime.Rd | 31 ++++++------
man/eegtimemc.Rd | 34 ++++++++-----
30 files changed, 610 insertions(+), 486 deletions(-)
Title: Model Layer for Automatic Data Analysis via CSV File
Interpretation
Diff between analyz versions 1.3.21 dated 2015-02-07 and 1.4 dated 2015-02-17
Description: Class with methods to read and execute R commands described as steps in a CSV file.
Author: Rodrigo Buhler
Maintainer: Rodrigo Buhler
DESCRIPTION | 13 +++++++------
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/ClassAnalyz.R | 12 +++---------
man/Analyz-class.Rd | 4 ++--
man/Analyz.coerceType-methods.Rd | 10 +++++-----
man/Analyz.getNrColumns-methods.Rd | 8 ++++----
man/Analyz.getNrRows-methods.Rd | 8 ++++----
man/Analyz.getResult-methods.Rd | 10 +++++-----
man/Analyz.getStepCommand-methods.Rd | 8 ++++----
man/Analyz.getStepParameters-methods.Rd | 8 ++++----
man/Analyz.getStepTitle-methods.Rd | 8 ++++----
man/Analyz.loadSteps-methods.Rd | 10 +++++-----
man/Analyz.runAnalysis-methods.Rd | 12 ++++++------
man/Analyz.setResult-methods.Rd | 10 +++++-----
man/Analyz.setStepItems-methods.Rd | 10 +++++-----
16 files changed, 79 insertions(+), 84 deletions(-)
Title: Efficient Discrete Stochastic Simulation
Diff between StochKit2R versions 0.2 dated 2015-01-29 and 0.3 dated 2015-02-17
Description: Efficient discrete stochastic simulation using the Gillespie algorithm (aka the Stochastic Simulation Algorithm or SSA) and adaptive tau-leaping. It provides an R interface to simulation algorithms and it provides functions for visualizing (plotting) simulation output.
Author: Kevin R. Sanft
Maintainer: Kevin R. Sanft
DESCRIPTION | 8 -
MD5 | 12 +-
inst/doc/StochKit2R-UserGuide.R | 18 +--
inst/doc/StochKit2R-UserGuide.Rmd | 12 --
inst/doc/StochKit2R-UserGuide.html | 211 +++++++++++++++++++------------------
vignettes/StochKit2R-UserGuide.Rmd | 12 --
vignettes/ex_out |only
7 files changed, 139 insertions(+), 134 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Diff between Sleuth3 versions 0.1-6 dated 2013-03-10 and 0.1-8 dated 2015-02-17
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Statistical Sleuth: A Course in Methods of Data Analysis (3rd
ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer,
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach
Maintainer: Berwin A Turlach
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Sleuth3-0.1-8/Sleuth3/man/case1201.Rd | 5
Sleuth3-0.1-8/Sleuth3/man/case1202.Rd | 4
Sleuth3-0.1-8/Sleuth3/man/case1401.Rd | 3
Sleuth3-0.1-8/Sleuth3/man/ex0116.Rd | 2
Sleuth3-0.1-8/Sleuth3/man/ex0920.Rd | 3
Sleuth3-0.1-8/Sleuth3/man/ex1320.Rd | 2
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Sleuth3-0.1-8/Sleuth3/man/ex1519.Rd | 2
189 files changed, 211 insertions(+), 210 deletions(-)
Title: Significance Tests for Palaeoenvironmental Reconstructions
Diff between palaeoSig versions 1.1-2 dated 2013-04-18 and 1.1-3 dated 2015-02-17
Description: Tests if quantitative palaeoenvironmental reconstructions are statistically significant.
Author: Richard Telford, Mathias Trachsel
Maintainer: Richard Telford
palaeoSig-1.1-2/palaeoSig/R/rotate.R |only
palaeoSig-1.1-2/palaeoSig/R/simulateSpatial.R |only
palaeoSig-1.1-2/palaeoSig/man/rotate.Rd |only
palaeoSig-1.1-2/palaeoSig/man/simulateSpatial.Rd |only
palaeoSig-1.1-3/palaeoSig/DESCRIPTION | 19 ++++---
palaeoSig-1.1-3/palaeoSig/MD5 | 51 +++++++++++++--------
palaeoSig-1.1-3/palaeoSig/NAMESPACE | 32 +++++++++++--
palaeoSig-1.1-3/palaeoSig/R/Code1.r |only
palaeoSig-1.1-3/palaeoSig/R/agedepth.2015.r |only
palaeoSig-1.1-3/palaeoSig/R/centipede.plot.r |only
palaeoSig-1.1-3/palaeoSig/R/coverage.plot.r |only
palaeoSig-1.1-3/palaeoSig/R/make.dist.R | 6 +-
palaeoSig-1.1-3/palaeoSig/R/plot.fittedAgelme.R |only
palaeoSig-1.1-3/palaeoSig/R/randomTF.R | 1
palaeoSig-1.1-3/palaeoSig/R/randomTFmm.r | 1
palaeoSig-1.1-3/palaeoSig/data/STOR.rda |only
palaeoSig-1.1-3/palaeoSig/inst/CITATION | 24 ++++-----
palaeoSig-1.1-3/palaeoSig/inst/NEWS.Rd | 42 +++++++++++++++++
palaeoSig-1.1-3/palaeoSig/man/Hill.N2.core.Rd | 1
palaeoSig-1.1-3/palaeoSig/man/STOR.Rd |only
palaeoSig-1.1-3/palaeoSig/man/abundances.Rd |only
palaeoSig-1.1-3/palaeoSig/man/agelme.rd |only
palaeoSig-1.1-3/palaeoSig/man/centipede.plot.Rd |only
palaeoSig-1.1-3/palaeoSig/man/cor.mat.fun.Rd |only
palaeoSig-1.1-3/palaeoSig/man/coverage.plot.rd |only
palaeoSig-1.1-3/palaeoSig/man/jointsig.Rd | 8 ++-
palaeoSig-1.1-3/palaeoSig/man/make.env.Rd |only
palaeoSig-1.1-3/palaeoSig/man/make.set.Rd |only
palaeoSig-1.1-3/palaeoSig/man/mat.h.Rd | 41 ++++++----------
palaeoSig-1.1-3/palaeoSig/man/multi.mat.Rd | 24 +--------
palaeoSig-1.1-3/palaeoSig/man/obs.cor.Rd | 1
palaeoSig-1.1-3/palaeoSig/man/palaeoSig-package.Rd | 3 -
palaeoSig-1.1-3/palaeoSig/man/plot.fittedAgelme.Rd |only
palaeoSig-1.1-3/palaeoSig/man/predict.agelme.Rd |only
palaeoSig-1.1-3/palaeoSig/man/randomTF.Rd | 5 +-
palaeoSig-1.1-3/palaeoSig/man/rne.Rd | 14 +++--
palaeoSig-1.1-3/palaeoSig/man/species.Rd |only
37 files changed, 164 insertions(+), 109 deletions(-)
Title: Multivariate Sensitivity Analysis
Diff between multisensi versions 1.0-7 dated 2013-07-19 and 1.0-8 dated 2015-02-17
Description: Functions to perform sensitivity analysis on a model with multivariate output.
Author: Matieyendou LAMBONI
Maintainer: Herve MONOD
DESCRIPTION | 11 +++++------
MD5 | 22 +++++++++++-----------
NAMESPACE | 7 +++++++
NEWS | 9 +++++++++
R/anoasg.r | 28 ++++++++++++++++------------
R/graph.pc.r | 4 ++--
R/plot.gsi.r | 6 ++++--
R/summary.gsi.r | 2 +-
inst/CITATION | 8 +++-----
inst/doc/multisensi-manual.pdf |binary
man/graph.pc.Rd | 3 ++-
man/plot.gsi.Rd | 5 +++--
12 files changed, 63 insertions(+), 42 deletions(-)
Title: Functions for the Analysis of IBD Haplo Output
Diff between IBDhaploRtools versions 1.7 dated 2014-07-23 and 1.8 dated 2015-02-16
More information about IBDhaploRtools at CRAN
Description: Functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson
DESCRIPTION | 16 +++++++--------
MD5 | 30 ++++++++++++++---------------
R/ibdhap.make.calls.R | 4 +--
R/ibdhap.make.true.R | 25 ++++++++++++++++++++----
build/vignette.rds |binary
data/ids_phased.RData |binary
data/ids_unphased.RData |binary
data/posvec.RData |binary
data/qibd_phased.RData |binary
data/qibd_unphased.RData |binary
data/trueibd_phased.RData |binary
inst/doc/IBDhaploRtools_tutorial.R | 2 -
inst/doc/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++---------------
inst/doc/IBDhaploRtools_tutorial.pdf |binary
man/IBDhaploRtools-package.Rd | 4 +--
vignettes/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++---------------
16 files changed, 89 insertions(+), 62 deletions(-)
Permanent link
Title: Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Diff between randomUniformForest versions 1.1.2 dated 2015-01-06 and 1.1.5 dated 2015-02-16
More information about randomUniformForest at CRAN
Description: Ensemble model, for classification, regression
and unsupervised learning, based on a forest of unpruned
and randomized binary decision trees. Each tree is grown
by sampling, with replacement, a set of variables at each node.
Each cut-point is generated randomly, according to the continuous
Uniform distribution. For each tree, data are either bootstrapped
or subsampled. The unsupervised mode introduces clustering, dimension reduction
and variable importance, using a three-layer engine. Random Uniform Forests are mainly
aimed to lower correlation between trees (or trees residuals), to provide a deep analysis
of variable importance and to allow native distributed and incremental learning.
Author: Saip Ciss
Maintainer: Saip Ciss
randomUniformForest-1.1.2/randomUniformForest/man/combine.unsupervised.Rd |only
randomUniformForest-1.1.5/randomUniformForest/DESCRIPTION | 8
randomUniformForest-1.1.5/randomUniformForest/MD5 | 50
randomUniformForest-1.1.5/randomUniformForest/NAMESPACE | 6
randomUniformForest-1.1.5/randomUniformForest/NEWS | 57
randomUniformForest-1.1.5/randomUniformForest/R/DecisionTreesCPP.R | 23
randomUniformForest-1.1.5/randomUniformForest/R/OnliningRandomUniformForests.R | 44
randomUniformForest-1.1.5/randomUniformForest/R/RandomUniformForestsCPP.R | 1142 +++++++---
randomUniformForest-1.1.5/randomUniformForest/R/genericFunctions.R | 68
randomUniformForest-1.1.5/randomUniformForest/inst/doc/VariableImportanceInRandomUniformForests.pdf |binary
randomUniformForest-1.1.5/randomUniformForest/inst/doc/randomUniformForestsOverview.pdf |binary
randomUniformForest-1.1.5/randomUniformForest/man/clusterAnalysis.Rd |only
randomUniformForest-1.1.5/randomUniformForest/man/clusteringObservations.Rd | 39
randomUniformForest-1.1.5/randomUniformForest/man/combineUnsupervised.Rd |only
randomUniformForest-1.1.5/randomUniformForest/man/fillNA2.randomUniformForest.Rd | 97
randomUniformForest-1.1.5/randomUniformForest/man/generic.cv.Rd | 4
randomUniformForest-1.1.5/randomUniformForest/man/importance.randomUniformForest.Rd | 147 -
randomUniformForest-1.1.5/randomUniformForest/man/internalFunctions.Rd | 3
randomUniformForest-1.1.5/randomUniformForest/man/modifyClusters.Rd | 2
randomUniformForest-1.1.5/randomUniformForest/man/partialDependenceBetweenPredictors.Rd | 66
randomUniformForest-1.1.5/randomUniformForest/man/predict.randomUniformForest.Rd | 8
randomUniformForest-1.1.5/randomUniformForest/man/rUniformForest.big.Rd | 2
randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest-package.Rd | 153 +
randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest.Rd | 268 +-
randomUniformForest-1.1.5/randomUniformForest/man/reSMOTE.Rd | 147 -
randomUniformForest-1.1.5/randomUniformForest/man/splitClusters.Rd |only
randomUniformForest-1.1.5/randomUniformForest/man/unsupervised.randomUniformForest.Rd | 335 +-
randomUniformForest-1.1.5/randomUniformForest/man/update.unsupervised.Rd | 25
28 files changed, 1932 insertions(+), 762 deletions(-)
Permanent link
Title: Wild Binary Segmentation for Multiple Change-Point Detection
Diff between wbs versions 1.2 dated 2014-08-08 and 1.3 dated 2015-02-16
Description: Provides efficient implementation of the Wild Binary Segmentation and Binary
Segmentation algorithms for estimation of the number and locations of
multiple change-points in the piecewise constant function plus Gaussian
noise model.
Author: Rafal Baranowski and Piotr Fryzlewicz
Maintainer: Rafal Baranowski
wbs-1.2/wbs/R/mean.from.cpt.R |only
wbs-1.2/wbs/man/mean.from.cpt.Rd |only
wbs-1.3/wbs/DESCRIPTION | 12 -
wbs-1.3/wbs/MD5 | 45 ++---
wbs-1.3/wbs/NAMESPACE | 4
wbs-1.3/wbs/R/changepoints.R | 2
wbs-1.3/wbs/R/means.between.cpt.R |only
wbs-1.3/wbs/R/plot.R | 4
wbs-1.3/wbs/R/sbs.R | 7
wbs-1.3/wbs/R/wbs.R | 25 ++-
wbs-1.3/wbs/man/bic.penalty.Rd | 2
wbs-1.3/wbs/man/changepoints.Rd | 8 -
wbs-1.3/wbs/man/fixed.intervals.Rd | 2
wbs-1.3/wbs/man/mbic.penalty.Rd | 2
wbs-1.3/wbs/man/means.between.cpt.Rd |only
wbs-1.3/wbs/man/plot.sbs.Rd | 2
wbs-1.3/wbs/man/plot.wbs.Rd | 2
wbs-1.3/wbs/man/print.sbs.Rd | 2
wbs-1.3/wbs/man/print.wbs.Rd | 2
wbs-1.3/wbs/man/random.intervals.Rd | 2
wbs-1.3/wbs/man/sbs.Rd | 2
wbs-1.3/wbs/man/ssic.penalty.Rd | 2
wbs-1.3/wbs/man/wbs-package.Rd | 2
wbs-1.3/wbs/man/wbs.Rd | 6
wbs-1.3/wbs/src/wbs.c | 276 +++++++++++++++--------------------
wbs-1.3/wbs/src/wbs.h |only
26 files changed, 196 insertions(+), 215 deletions(-)
Title: An R Convenience Layer for CouchDB
Diff between R4CouchDB versions 0.6 dated 2014-08-12 and 0.7.1 dated 2015-02-16
Description: Provides a collection of functions for basic
database and document management operations such as add, get, list or
delete. Every cdbFunction() gets and returns a list() containing the
connection setup.
Such a list (in the documentation mostly called cdb) can be generated by
cdb <- cdbIni(). Then, the list cdb provides some functions respectively
functionality e.g cdb$baseUrl() or cdb$getDocRev().
Author: Thomas Bock
Maintainer: Thomas Bock
DESCRIPTION | 17 ++--
MD5 | 58 ++++++++--------
NAMESPACE | 3
R/cdbAddDocS.R |only
R/cdbDeleteDoc.R | 2
R/cdbGetConfig.R | 4 -
R/cdbGetDoc.R | 2
R/cdbGetList.R | 3
R/cdbGetUuid.R | 3
R/cdbGetUuidS.R | 4 -
R/cdbGetView.R | 4 -
R/cdbIni.R | 167 ++++++++++++++++++++++++++----------------------
R/cdbListDB.R | 6 -
R/cdbMakeDB.R | 1
R/cdbRemoveDB.R | 1
R/cdbUpdateDoc.R | 8 --
man/cdbAddAttachment.Rd | 3
man/cdbAddDoc.Rd | 3
man/cdbAddDocS.Rd |only
man/cdbDeleteDoc.Rd | 6 -
man/cdbGetConfig.Rd | 7 --
man/cdbGetDoc.Rd | 6 -
man/cdbGetList.Rd | 8 --
man/cdbGetUuid.Rd | 7 --
man/cdbGetUuidS.Rd | 7 --
man/cdbGetView.Rd | 8 --
man/cdbIni.Rd | 5 -
man/cdbListDB.Rd | 10 --
man/cdbMakeDB.Rd | 6 -
man/cdbRemoveDB.Rd | 6 -
man/cdbUpdateDoc.Rd | 7 --
31 files changed, 167 insertions(+), 205 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Diff between SIMMS versions 0.0.1 dated 2013-06-11 and 1.0.0 dated 2015-02-16
Description: Algorithms to create prognostic biomarkers using biological networks.
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider
mRNA_abundance.txt | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/DESCRIPTION | 15
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/MD5 | 116 ++-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/NAMESPACE | 26
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.meta.survival.R | 93 +--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.network.coefficients.R | 301 ++++++---
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.KM.plot.R | 12
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.multivariate.R |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.univariate.R |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.sensitivity.plot.R | 9
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survivalplots.R | 225 +++----
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survobj.R | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/derive.network.features.R | 307 +++++-----
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/dichotomize.meta.dataset.R | 11
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.coxmodel.R | 135 +++-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.interaction.model.R | 124 ++--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.survivalmodel.R | 34 -
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.adjacency.matrix.R | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.program.defaults.R | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/load.cancer.datasets.R | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/pred.survivalmodel.R | 80 --
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/prepare.training.validation.datasets.R | 241 +++++--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/build |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/doc |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.BRCA |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.COADREAD |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.GBM |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.KIRC |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.OV |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Mammaprint |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Oncotypedx |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/PI3K |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_networks_flattened.txt | 18
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks.txt | 19
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks_all.txt | 19
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/testdata/Breastdata1/mRNA_abundance.txt | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/SIMMS.Rd | 14
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.meta.survival.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.network.coefficients.Rd | 5
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.KM.plot.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.multivariate.Rd |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.univariate.Rd |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survivalplots.Rd | 14
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survobj.Rd | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/derive.network.features.Rd | 9
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/dichotomize.meta.dataset.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.coxmodel.Rd | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.interaction.model.Rd | 78 +-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.survivalmodel.Rd | 5
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/get.program.defaults.Rd | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/load.cancer.datasets.Rd | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/pred.survivalmodel.Rd | 10
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/prepare.training.validation.datasets.Rd | 10
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/vignettes |only
55 files changed, 1200 insertions(+), 793 deletions(-)
Title: Supervised Component Generalized Linear Regression
Diff between SCGLR versions 2.0.1 dated 2014-10-14 and 2.0.2 dated 2015-02-16
Description: The Fisher Scoring Algorithm is extended so as to combine Partial Least Squares
regression with Generalized Linear Model estimation in the multivariate context.
Author: Guillaume Cornu [cre, aut],
Frederic Mortier [aut],
Catherine Trottier [aut],
Xavier Bry [aut]
Maintainer: Guillaume Cornu
DESCRIPTION | 30 ++++++++-------
MD5 | 84 +++++++++++++++++++++---------------------
NAMESPACE | 4 +-
NEWS | 3 +
R/critConvergence.r | 2 -
R/customize.r | 2 -
R/data.r | 2 -
R/infoCriterion.r | 28 +++++++-------
R/ingUtils.r | 26 ++++++-------
R/methods.r | 2 -
R/metric.r | 2 -
R/multivariateFormula.r | 2 -
R/multivariateGlm.r | 8 ++--
R/multivariatePredictGlm.r | 4 +-
R/oneComponent.r | 10 +++--
R/package.r | 8 ++--
R/plot.r | 4 +-
R/print.r | 2 -
R/scglrCrossVal.r | 16 +++-----
R/summary.r | 6 +--
build/vignette.rds |binary
demo/scglrPrediction.r | 4 +-
inst/doc/scglrVignettes.R | 6 +--
inst/doc/scglrVignettes.pdf |binary
inst/doc/scglrVignettes.rnw | 8 ++--
inst/examples/exPrediction.r | 4 +-
man/barplot.SCGLR.Rd | 3 +
man/critConvergence.Rd | 3 +
man/customize.Rd | 3 +
man/genus.Rd | 5 +-
man/infoCriterion.Rd | 3 +
man/method.Rd | 3 +
man/multivariateFormula.Rd | 3 +
man/multivariateGlm.Rd | 5 +-
man/multivariatePredictGlm.Rd | 5 +-
man/pairs.SCGLR.Rd | 3 +
man/plot.SCGLR.Rd | 3 +
man/print.SCGLR.Rd | 3 +
man/scglr-package.Rd | 7 ++-
man/scglr.Rd | 3 +
man/scglrCrossVal.Rd | 3 +
man/summary.SCGLR.Rd | 3 +
vignettes/scglrVignettes.rnw | 8 ++--
43 files changed, 178 insertions(+), 155 deletions(-)
Title: Data Analysis Tool for Pharmacokinetics
Diff between PKfit versions 1.2.4 dated 2014-10-21 and 1.2.5 dated 2015-02-16
Description: A nonlinear regression program which is
designed to perform model/curve fitting and
model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
PKfit-1.2.4/PKfit/inst/CITATION |only
PKfit-1.2.4/PKfit/inst/UserDefinedModels/mymodel.R |only
PKfit-1.2.5/PKfit/DESCRIPTION | 18 ++++++++---------
PKfit-1.2.5/PKfit/MD5 | 21 +++++++++-----------
PKfit-1.2.5/PKfit/NEWS | 16 ++++++++++++++-
PKfit-1.2.5/PKfit/R/description_version.r | 7 +++++-
PKfit-1.2.5/PKfit/R/finfu2.R | 3 +-
PKfit-1.2.5/PKfit/R/fzero.nolag.R | 2 -
PKfit-1.2.5/PKfit/R/mmpk.demo.R | 2 -
PKfit-1.2.5/PKfit/R/sinfu1.R | 20 ++++---------------
PKfit-1.2.5/PKfit/R/sinfu2.R | 14 +++----------
PKfit-1.2.5/PKfit/R/zzz.R | 2 -
PKfit-1.2.5/PKfit/inst/UserDefinedModels/fitmodel.R |only
13 files changed, 54 insertions(+), 51 deletions(-)
Title: Partial Correlation Coefficient with Information Theory
Diff between PCIT versions 1.04-5 dated 2014-01-29 and 1.5-3 dated 2015-02-16
Description: Apply Partial Correlation coefficient with Information
Theory (PCIT) to a correlation matrix.
The PCIT algorithm identifies meaningful correlations to define
edges in a weighted network. The algorithm can be applied to
any correlation-based network including but not limited to gene
co-expression networks.
To reduce compute time by making use of multiple compute cores,
simply run PCIT on a computer with has multiple cores and also
has the Rmpi package installed. PCIT will then auto-detect the
multicore environment and run in parallel mode without the need
to rewrite your scripts. This makes scripts, using PCIT, portable
across single core (or no Rmpi package installed) computers
which will run in serial mode and multicore (with Rmpi package
installed) computers which will run in parallel mode.
Author: Nathan S. Watson-Haigh
Maintainer: Nathan S. Watson-Haigh
ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 24 +++++++++++++++---------
MD5 | 12 ++++++------
R/PCIT.R | 36 ++++++++++++++++++------------------
R/internal.R | 28 ++++++++++++++--------------
README.md | 20 ++++++++++++++++++++
inst/CITATION | 3 +--
7 files changed, 113 insertions(+), 49 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 1.0 dated 2014-03-07 and 2.0.0 dated 2015-02-16
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. It implements an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
FunChisq-1.0/FunChisq/INDEX |only
FunChisq-2.0.0/FunChisq/DESCRIPTION | 22 +-
FunChisq-2.0.0/FunChisq/MD5 | 32 +++
FunChisq-2.0.0/FunChisq/NAMESPACE | 6
FunChisq-2.0.0/FunChisq/NEWS |only
FunChisq-2.0.0/FunChisq/R/FunChisq.R | 145 ++++++++++++++---
FunChisq-2.0.0/FunChisq/inst |only
FunChisq-2.0.0/FunChisq/man/FunChisq-package.Rd | 76 ++++-----
FunChisq-2.0.0/FunChisq/man/cp.fun.chisq.test.Rd |only
FunChisq-2.0.0/FunChisq/man/fun.chisq.test.Rd | 188 ++++++++++++++++-------
FunChisq-2.0.0/FunChisq/src |only
FunChisq-2.0.0/FunChisq/tests |only
12 files changed, 333 insertions(+), 136 deletions(-)
Title: Boosting Functional Regression Models
Diff between FDboost versions 0.0-5 dated 2014-04-22 and 0.0-8 dated 2015-02-16
Description: Regression models for functional data, i.e. scalar-on-function,
function-on-scalar and function-on-function regression models are fitted
using a component-wise gradient boosting algorithm.
Author: Sarah Brockhaus
Maintainer: Sarah Brockhaus
FDboost-0.0-5/FDboost/R/bkroneckerTrafo.R |only
FDboost-0.0-5/FDboost/data/datalist |only
FDboost-0.0-5/FDboost/data/fuel.RData |only
FDboost-0.0-5/FDboost/inst/fuelAllModels |only
FDboost-0.0-5/FDboost/man/fuel.Rd |only
FDboost-0.0-5/FDboost/vignettes/mboostDevel-inference.R |only
FDboost-0.0-8/FDboost/DESCRIPTION | 20
FDboost-0.0-8/FDboost/MD5 | 103 -
FDboost-0.0-8/FDboost/NAMESPACE | 5
FDboost-0.0-8/FDboost/R/FDboost.R | 189 +
FDboost-0.0-8/FDboost/R/baselearners.R | 1645 +++++++++-------
FDboost-0.0-8/FDboost/R/crossvalidation.R | 48
FDboost-0.0-8/FDboost/R/internalsMboost.R |only
FDboost-0.0-8/FDboost/R/methods.R | 180 +
FDboost-0.0-8/FDboost/R/utilityFunctions.R | 155 +
FDboost-0.0-8/FDboost/build/vignette.rds |binary
FDboost-0.0-8/FDboost/data/fuelSubset.RData |only
FDboost-0.0-8/FDboost/inst/CITATION |only
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.R | 2
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.Rnw | 2
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.pdf |binary
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.R | 3
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.Rnw | 3
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.pdf |binary
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.R | 6
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.Rnw | 6
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.pdf |binary
FDboost-0.0-8/FDboost/inst/sim/analyze_results.R | 105 -
FDboost-0.0-8/FDboost/inst/sim/run_FDboost.R | 182 +
FDboost-0.0-8/FDboost/inst/sim/run_PlotModels.R | 150 -
FDboost-0.0-8/FDboost/inst/sim/run_pffr.R | 185 +
FDboost-0.0-8/FDboost/inst/sim/run_time.R |only
FDboost-0.0-8/FDboost/inst/sim/simfuns.R | 102
FDboost-0.0-8/FDboost/man/FDboost.Rd | 234 +-
FDboost-0.0-8/FDboost/man/bbsc.Rd | 168 -
FDboost-0.0-8/FDboost/man/bsignal.Rd | 242 +-
FDboost-0.0-8/FDboost/man/coef.FDboost.Rd | 81
FDboost-0.0-8/FDboost/man/extract.blg.Rd | 46
FDboost-0.0-8/FDboost/man/fitted.FDboost.Rd | 16
FDboost-0.0-8/FDboost/man/fuelSubset.Rd |only
FDboost-0.0-8/FDboost/man/funMRD.Rd | 52
FDboost-0.0-8/FDboost/man/funMSE.Rd | 70
FDboost-0.0-8/FDboost/man/funRsquared.Rd | 79
FDboost-0.0-8/FDboost/man/funplot.Rd | 29
FDboost-0.0-8/FDboost/man/integrationWeights.Rd | 72
FDboost-0.0-8/FDboost/man/o_control.Rd | 25
FDboost-0.0-8/FDboost/man/plot.FDboost.Rd | 111 -
FDboost-0.0-8/FDboost/man/plot.validateFDboost.Rd | 86
FDboost-0.0-8/FDboost/man/predict.FDboost.Rd | 56
FDboost-0.0-8/FDboost/man/print.FDboost.Rd | 15
FDboost-0.0-8/FDboost/man/residuals.FDboost.Rd | 18
FDboost-0.0-8/FDboost/man/summary.FDboost.Rd | 15
FDboost-0.0-8/FDboost/man/truncateTime.Rd | 25
FDboost-0.0-8/FDboost/man/validateFDboost.Rd | 222 --
FDboost-0.0-8/FDboost/man/viscosity.Rd | 28
FDboost-0.0-8/FDboost/vignettes/FLAM_canada.Rnw | 2
FDboost-0.0-8/FDboost/vignettes/FLAM_fuel.Rnw | 3
FDboost-0.0-8/FDboost/vignettes/FLAM_viscosity.Rnw | 6
58 files changed, 2749 insertions(+), 2043 deletions(-)
Title: Bayesian Network Feature Finder
Diff between BANFF versions 0.2 dated 2015-01-08 and 0.3 dated 2015-02-16
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan
DESCRIPTION | 10 ++--
MD5 | 16 ++++---
NAMESPACE | 13 ++++++
R/All_functions.R | 10 ----
R/main.R | 89 +++++++++++++++++++++++++++++++++++++++----
man/Networks.Fast.Rd | 5 +-
man/Networks.STD.Rd | 7 +--
man/plot.Networks.Fast.Rd |only
man/plot.Networks.STD.Rd |only
man/summary.Networks.Fast.Rd |only
man/summary.Networks.STD.Rd |only
11 files changed, 117 insertions(+), 33 deletions(-)
Title: Simulation Tools for Small Area Estimation
Diff between saeSim versions 0.6.0 dated 2014-10-22 and 0.7.0 dated 2015-02-16
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz
saeSim-0.6.0/saeSim/R/01-s_dplyr.R |only
saeSim-0.6.0/saeSim/R/02-mclapply.R |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.R |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.html |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.R |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.html |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.R |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.html |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.R |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.html |only
saeSim-0.6.0/saeSim/man/show-sim_setup-method.Rd |only
saeSim-0.6.0/saeSim/man/summary.sim_setup.Rd |only
saeSim-0.6.0/saeSim/vignettes/addingComputations.Rmd |only
saeSim-0.6.0/saeSim/vignettes/drawingSamples.Rmd |only
saeSim-0.6.0/saeSim/vignettes/generalOverview.Rmd |only
saeSim-0.6.0/saeSim/vignettes/generatingData.Rmd |only
saeSim-0.7.0/saeSim/DESCRIPTION | 19 -
saeSim-0.7.0/saeSim/MD5 | 131 ++++------
saeSim-0.7.0/saeSim/NAMESPACE | 13
saeSim-0.7.0/saeSim/NEWS | 27 ++
saeSim-0.7.0/saeSim/R/00-sim-lib.R | 17 -
saeSim-0.7.0/saeSim/R/01-as.data.frame.R | 2
saeSim-0.7.0/saeSim/R/01-helper-lib.R | 48 +++
saeSim-0.7.0/saeSim/R/01-plot.R | 1
saeSim-0.7.0/saeSim/R/01-show.R | 7
saeSim-0.7.0/saeSim/R/01-sim.R | 115 +++++---
saeSim-0.7.0/saeSim/R/01-summary.R | 64 ++--
saeSim-0.7.0/saeSim/R/03-agg.R | 12
saeSim-0.7.0/saeSim/R/03-base-lib.R | 2
saeSim-0.7.0/saeSim/R/03-comp_var.R | 24 -
saeSim-0.7.0/saeSim/R/03-generator.R | 19 -
saeSim-0.7.0/saeSim/R/03-sample.R | 44 +++
saeSim-0.7.0/saeSim/R/03-sim_agg.R | 2
saeSim-0.7.0/saeSim/R/03-sim_base.R | 4
saeSim-0.7.0/saeSim/R/03-sim_comp.R | 6
saeSim-0.7.0/saeSim/R/03-sim_comp_preconf.R | 8
saeSim-0.7.0/saeSim/R/03-sim_gen.R | 13
saeSim-0.7.0/saeSim/R/03-sim_gen_cont.R | 7
saeSim-0.7.0/saeSim/R/03-sim_resp.R | 4
saeSim-0.7.0/saeSim/R/03-sim_sample.R | 2
saeSim-0.7.0/saeSim/R/NAMESPACE.R |only
saeSim-0.7.0/saeSim/build/vignette.rds |binary
saeSim-0.7.0/saeSim/inst/doc/Introduction.R |only
saeSim-0.7.0/saeSim/inst/doc/Introduction.Rmd |only
saeSim-0.7.0/saeSim/inst/doc/Introduction.html |only
saeSim-0.7.0/saeSim/man/agg_all.Rd | 3
saeSim-0.7.0/saeSim/man/as.data.frame.sim_setup.Rd | 3
saeSim-0.7.0/saeSim/man/autoplot.Rd | 3
saeSim-0.7.0/saeSim/man/base_add_id.Rd | 3
saeSim-0.7.0/saeSim/man/base_id.Rd | 3
saeSim-0.7.0/saeSim/man/comp_var.Rd | 3
saeSim-0.7.0/saeSim/man/generators.Rd | 7
saeSim-0.7.0/saeSim/man/pipe.Rd | 3
saeSim-0.7.0/saeSim/man/plot.sim_setup.Rd | 3
saeSim-0.7.0/saeSim/man/sampling.Rd | 21 +
saeSim-0.7.0/saeSim/man/showMethods.Rd |only
saeSim-0.7.0/saeSim/man/sim.Rd | 48 ++-
saeSim-0.7.0/saeSim/man/sim_agg.Rd | 3
saeSim-0.7.0/saeSim/man/sim_base.Rd | 3
saeSim-0.7.0/saeSim/man/sim_comp.Rd | 3
saeSim-0.7.0/saeSim/man/sim_comp_preconf.Rd | 3
saeSim-0.7.0/saeSim/man/sim_gen.Rd | 13
saeSim-0.7.0/saeSim/man/sim_gen_cont.Rd | 3
saeSim-0.7.0/saeSim/man/sim_gen_preconf.Rd | 3
saeSim-0.7.0/saeSim/man/sim_read_data.Rd | 3
saeSim-0.7.0/saeSim/man/sim_resp.Rd | 3
saeSim-0.7.0/saeSim/man/sim_sample.Rd | 3
saeSim-0.7.0/saeSim/man/sim_setup_preconfigured.Rd | 3
saeSim-0.7.0/saeSim/man/sim_simName.Rd | 3
saeSim-0.7.0/saeSim/man/summary-sim_setup-method.Rd |only
saeSim-0.7.0/saeSim/tests/testthat/helper.R |only
saeSim-0.7.0/saeSim/tests/testthat/test-preserve_attributes.R |only
saeSim-0.7.0/saeSim/tests/testthat/test-sim.R | 2
saeSim-0.7.0/saeSim/tests/testthat/test-sim_comp.R | 7
saeSim-0.7.0/saeSim/tests/testthat/test-sim_generate.R | 12
saeSim-0.7.0/saeSim/tests/testthat/test-sim_sample.R | 26 +
saeSim-0.7.0/saeSim/vignettes/Introduction.Rmd |only
81 files changed, 505 insertions(+), 279 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Diff between Rlibeemd versions 1.3.1 dated 2015-02-09 and 1.3.2 dated 2015-02-16
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske
DESCRIPTION | 8
MD5 | 18
R/RcppExports.R | 4
R/Rlibeemd-package.R | 2
R/init.R |only
configure | 1529 ++++++++++++++++++++++-----------------------
configure.ac | 8
inst/CITATION | 5
man/Rlibeemd.Rd | 2
src/RcppExports.cpp | 11
src/gslErrorHandlerOff.cpp |only
11 files changed, 805 insertions(+), 782 deletions(-)
Title: Retinal Reconstruction Program
Diff between retistruct versions 0.5.9 dated 2014-12-02 and 0.5.10 dated 2015-02-16
Description: Reconstructs retinae by morphing a flat surface with
cuts (a dissected flat-mount retina) onto a curvilinear surface (the a
standard retinal shape). It can estimate the position of a point on the
intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis).
The coordinates in reconstructed retinae can be transformed to visuotopic
coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt
DESCRIPTION | 18 +++++++++++-------
MD5 | 15 ++++++++-------
NAMESPACE | 2 ++
NEWS |only
R/ReconstructedDataset.R | 2 +-
R/geometry.R | 2 ++
R/revision.R | 2 +-
inst/CITATION | 8 ++++++--
man/retistruct.global.revision.Rd | 2 +-
9 files changed, 32 insertions(+), 19 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Diff between lsbclust versions 1.0 dated 2015-02-10 and 1.0.1 dated 2015-02-16
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees
DESCRIPTION | 18 +++-
MD5 | 12 +-
R/plot.int.lsbclust.R | 5 -
R/supermarkets.R | 2
man/supermarkets.Rd | 2
tests/testthat/test_interactions.R | 159 +++++++++++++++++++++++++++++--------
tests/testthat/test_orc.R | 33 ++++++-
7 files changed, 178 insertions(+), 53 deletions(-)
Title: High-Dimensional Penalized Regression
Diff between HDPenReg versions 0.90 dated 2014-11-03 and 0.91 dated 2015-02-16
Description: Algorithms for lasso and fused-lasso
problems: implementation of the lars algorithm [1], for the
lasso and fusion penalization and EM-based algorithms for (logistic) lasso
and fused-lasso.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez
HDPenReg-0.90/HDPenReg/inst/doc/vignette.R |only
HDPenReg-0.90/HDPenReg/inst/doc/vignette.Rnw |only
HDPenReg-0.90/HDPenReg/inst/doc/vignette.pdf |only
HDPenReg-0.90/HDPenReg/man/predict.Rd |only
HDPenReg-0.90/HDPenReg/src/stkpp |only
HDPenReg-0.90/HDPenReg/vignettes/vignette.Rnw |only
HDPenReg-0.90/HDPenReg/vignettes/vignette.bib |only
HDPenReg-0.91/HDPenReg/DESCRIPTION | 28
HDPenReg-0.91/HDPenReg/MD5 | 434 +---------
HDPenReg-0.91/HDPenReg/NAMESPACE | 6
HDPenReg-0.91/HDPenReg/NEWS | 7
HDPenReg-0.91/HDPenReg/R/HDPenReg-package.R | 6
HDPenReg-0.91/HDPenReg/R/predict.R | 4
HDPenReg-0.91/HDPenReg/build/vignette.rds |binary
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.R |only
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.Rnw |only
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.pdf |only
HDPenReg-0.91/HDPenReg/man/EMcvfusedlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMcvlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMfusedlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDPenReg-package.Rd | 7
HDPenReg-0.91/HDPenReg/man/HDcvlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDfusion.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/LarsPath-class.Rd | 3
HDPenReg-0.91/HDPenReg/man/coef.LarsPath.Rd | 3
HDPenReg-0.91/HDPenReg/man/coeff.Rd | 3
HDPenReg-0.91/HDPenReg/man/computeCoefficients.Rd | 3
HDPenReg-0.91/HDPenReg/man/plot-methods.Rd | 3
HDPenReg-0.91/HDPenReg/man/plot.HDcvlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/plotCoefficient.Rd | 3
HDPenReg-0.91/HDPenReg/man/predict.LarsPath.Rd |only
HDPenReg-0.91/HDPenReg/man/simul.Rd | 3
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars.mk | 6
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Cvlars.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.cpp | 7
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/PathState.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/makefile | 34
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels.mk | 17
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/CV.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/EM.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/FusedLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IMeasure.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalizedSolver.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalty.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/Lasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoPenalty.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/PenalizedModels.h | 44 -
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/makefile | 2
HDPenReg-0.91/HDPenReg/src/Makevars | 45 -
HDPenReg-0.91/HDPenReg/src/emR.cpp | 3
HDPenReg-0.91/HDPenReg/src/emR.h | 5
HDPenReg-0.91/HDPenReg/src/larsR.cpp | 1
HDPenReg-0.91/HDPenReg/src/larsR.h | 5
HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.Rnw |only
HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.bib |only
60 files changed, 182 insertions(+), 537 deletions(-)
More information about fdrDiscreteNull at CRAN
Permanent link
Title: Bounded Density Estimation
Diff between bde versions 1.0 dated 2014-11-13 and 1.0.1 dated 2015-02-16
Description: A collection of S4 classes which implements different methods to estimate and deal with densities in bounded domains. That is, densities defined within the interval [lower.limit, upper.limit], where lower.limit and upper.limit are values that can be set by the user.
Author: Guzman Santafe, Borja Calvo, Aritz Perez and Jose A. Lozano
Maintainer: Guzman Santafe
DESCRIPTION | 12 ++++++------
MD5 | 5 +++--
NEWS |only
inst/App/server.R | 10 +++++-----
4 files changed, 14 insertions(+), 13 deletions(-)
Title: Using Gene Expression Data to Improve Flux Balance Analysis
Predictions
Diff between sybilEFBA versions 1.0.1 dated 2013-10-24 and 1.0.2 dated 2015-02-16
Description: Three different approaches to use gene expression data (or protein measurements) for improving FBA predictions.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 16 +-
MD5 | 28 ++--
NEWS | 10 +
R/FECorr.R | 27 +++-
R/eFBA_gene.R | 329 +++++++++++++++++++++++++++++++++++------------------
R/eFBA_rxn.R | 105 +++++++---------
R/findMDCFlux.R | 7 -
R/gene2Rule.R | 8 -
data/iAF1260.RData |binary
data/iMM904.RData |binary
data/iND750.RData |binary
man/eFBA_gene.Rd | 6
man/eFBA_rxn.Rd | 6
man/findMDCFlux.Rd | 7 -
man/gen2Rule.Rd | 2
15 files changed, 344 insertions(+), 207 deletions(-)
Title: Regression Modeling Strategies
Diff between rms versions 4.2-1 dated 2014-09-18 and 4.3-0 dated 2015-02-16
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. rms works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 11
INDEX | 2
MD5 | 113 ++++----
NAMESPACE | 12
NEWS | 30 ++
R/Function.rms.s | 10
R/Glm.s | 5
R/Predict.s | 433 ++++++++++++++++-----------------
R/Rq.s | 3
R/anova.rms.s | 14 -
R/bj.s | 7
R/bootcov.s | 11
R/calibrate.s | 190 +++++++-------
R/contrast.s | 110 +++++---
R/cph.s | 7
R/datadist.s | 295 ++++++++++------------
R/ggplot.Predict.s |only
R/latex.rms.s | 33 +-
R/lrm.s | 3
R/ols.s | 7
R/orm.s | 3
R/plot.Predict.s | 146 +++++++----
R/pphsm.s | 2
R/predictrms.s | 67 ++---
R/print.psm.s | 17 -
R/residuals.lrm.s | 30 +-
R/rmsMisc.s | 52 +++
R/robcov.s | 35 +-
R/summary.rms.s | 8
R/survplot.npsurv.s | 6
R/survplot.rms.s | 3
R/validate.cph.s | 25 -
man/Gls.Rd | 7
man/Predict.Rd | 10
man/anova.rms.Rd | 3
man/bootcov.Rd | 7
man/calibrate.Rd | 6
man/contrast.Rd | 52 ++-
man/cph.Rd | 8
man/datadist.Rd | 7
man/ggplot.Predict.Rd |only
man/lrm.Rd | 4
man/nomogram.Rd | 4
man/npsurv.Rd | 8
man/plot.Predict.Rd | 5
man/predictrms.Rd | 15 -
man/psm.Rd | 4
man/residuals.lrm.Rd | 20 +
man/rms-internal.Rd | 2
man/rms.Rd | 8
man/robcov.Rd | 6
man/sensuc.Rd | 3
man/survplot.Rd | 2
man/zzzrmsOverview.Rd | 9
tests/cph3.r |only
tests/ggplot2-without-ggplot.Predict.r |only
tests/ggplot2.r |only
tests/orm-bootcov.r |only
tests/orm-residuals.r |only
tests/robcov.r |only
tests/summary.r |only
tests/validate.cph.s | 2
62 files changed, 1068 insertions(+), 814 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Diff between ramps versions 0.6-12 dated 2013-11-12 and 0.6-13 dated 2015-02-16
Description: Bayesian geostatistical modeling of Gaussian processes using a reparameterized and marginalized posterior sampling (RAMPS) algorithm designed to lower autocorrelation in MCMC samples. Package performance is tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith
ramps-0.6-12/ramps/man/corClasses.Rd |only
ramps-0.6-13/ramps/DESCRIPTION | 8 +-
ramps-0.6-13/ramps/MD5 | 34 ++++----
ramps-0.6-13/ramps/NAMESPACE | 30 +++----
ramps-0.6-13/ramps/R/corStruct.R | 88 +++++++++++------------
ramps-0.6-13/ramps/man/corRCauchy.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRClasses.Rd |only
ramps-0.6-13/ramps/man/corRExp.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRExp2.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr2.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr2Dt.Rd | 6 -
ramps-0.6-13/ramps/man/corRGaus.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRGneit.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRLin.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRMatern.Rd | 6 -
ramps-0.6-13/ramps/man/corRSpher.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRWave.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/georamps.Rd | 6 -
19 files changed, 527 insertions(+), 551 deletions(-)
Title: Post-Hoc Interaction Analysis
Diff between phia versions 0.1-5 dated 2013-10-12 and 0.2-0 dated 2015-02-16
Description: Analysis of terms in linear, generalized and mixed linear models,
on the basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
Author: Helios De Rosario-Martinez [aut, cre],
John Fox [ctb],
R Core Team [ctb]
Maintainer: Helios De Rosario-Martinez
ChangeLog | 19 ++++
DESCRIPTION | 10 +-
MD5 | 34 ++++----
NAMESPACE | 4 -
R/contrastCoefficients.R | 2
R/getElements.R | 5 -
R/interactionMeans.R | 91 ++++++++++++++++++++--
R/testFactors.R | 187 +++++++++++++++++++----------------------------
build/vignette.rds |binary
data/Boik.rda |binary
data/Keselman.rda |binary
data/Rosnow.rda |binary
inst/doc/phia.Rnw | 97 ++++++++++++++----------
inst/doc/phia.pdf |binary
man/interactionMeans.Rd | 11 ++
man/phia-package.Rd | 6 -
man/testFactors.Rd | 5 -
vignettes/phia.Rnw | 97 ++++++++++++++----------
18 files changed, 334 insertions(+), 234 deletions(-)
Title: Analysis of Multivariate Event Times
Diff between mets versions 1.0 dated 2014-11-18 and 1.1.0 dated 2015-02-16
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
mets-1.0/mets/R/newbptwin.R |only
mets-1.1.0/mets/DESCRIPTION | 10 -
mets-1.1.0/mets/MD5 | 159 +++++++++++++-------------
mets-1.1.0/mets/NAMESPACE | 14 --
mets-1.1.0/mets/NEWS | 8 +
mets-1.1.0/mets/R/aalenfrailty.R | 8 -
mets-1.1.0/mets/R/bicomprisk.R | 2
mets-1.1.0/mets/R/biprobit.R | 20 +--
mets-1.1.0/mets/R/bptwin.R | 4
mets-1.1.0/mets/R/bptwin2.R | 2
mets-1.1.0/mets/R/cor.R | 14 --
mets-1.1.0/mets/R/divide.conquer.R | 6
mets-1.1.0/mets/R/event.R | 10 -
mets-1.1.0/mets/R/fastapprox.R | 33 +++--
mets-1.1.0/mets/R/fastreshape.R | 29 +++-
mets-1.1.0/mets/R/ipw.R | 1
mets-1.1.0/mets/R/lifetable.R | 120 ++++++++++++++++++-
mets-1.1.0/mets/R/mets-package.R | 2
mets-1.1.0/mets/R/normal0.R | 20 ++-
mets-1.1.0/mets/R/onload.R | 4
mets-1.1.0/mets/R/phreg.par.R | 6
mets-1.1.0/mets/R/tetrachor.R | 16 ++
mets-1.1.0/mets/R/twinlm.R | 6
mets-1.1.0/mets/R/twostage.R | 2
mets-1.1.0/mets/inst/mets1.png |only
mets-1.1.0/mets/man/ClaytonOakes.Rd | 3
mets-1.1.0/mets/man/Dbvn.Rd | 3
mets-1.1.0/mets/man/Event.Rd | 3
mets-1.1.0/mets/man/Grandom.cif.Rd | 19 +--
mets-1.1.0/mets/man/aalenfrailty.Rd | 11 +
mets-1.1.0/mets/man/back2timereg.Rd | 3
mets-1.1.0/mets/man/bicomprisk.Rd | 3
mets-1.1.0/mets/man/binomial.twostage.Rd | 3
mets-1.1.0/mets/man/biprobit.Rd | 23 +--
mets-1.1.0/mets/man/blocksample.Rd | 7 -
mets-1.1.0/mets/man/bptwin.Rd | 13 --
mets-1.1.0/mets/man/casewise.Rd | 3
mets-1.1.0/mets/man/casewise.test.Rd | 3
mets-1.1.0/mets/man/concordance.Rd | 3
mets-1.1.0/mets/man/cor.cif.Rd | 5
mets-1.1.0/mets/man/dermalridges.Rd | 3
mets-1.1.0/mets/man/dermalridgesMZ.Rd | 3
mets-1.1.0/mets/man/divide.conquer.Rd | 5
mets-1.1.0/mets/man/divide.conquer.timereg.Rd | 7 -
mets-1.1.0/mets/man/easy.binomial.twostage.Rd | 7 -
mets-1.1.0/mets/man/easy.twostage.Rd | 3
mets-1.1.0/mets/man/fast.approx.Rd | 13 +-
mets-1.1.0/mets/man/fast.pattern.Rd | 3
mets-1.1.0/mets/man/fast.reshape.Rd | 12 +
mets-1.1.0/mets/man/internal.Rd | 4
mets-1.1.0/mets/man/ipw.Rd | 3
mets-1.1.0/mets/man/lifetable.matrix.Rd | 11 -
mets-1.1.0/mets/man/mena.Rd | 3
mets-1.1.0/mets/man/mets-package.Rd | 3
mets-1.1.0/mets/man/migr.Rd | 3
mets-1.1.0/mets/man/multcif.Rd | 3
mets-1.1.0/mets/man/np.Rd | 3
mets-1.1.0/mets/man/phreg.Rd | 3
mets-1.1.0/mets/man/plack.cif.Rd | 3
mets-1.1.0/mets/man/printcasewisetest.Rd | 3
mets-1.1.0/mets/man/prt.Rd | 3
mets-1.1.0/mets/man/random.cif.Rd | 3
mets-1.1.0/mets/man/simAalenFrailty.Rd | 3
mets-1.1.0/mets/man/simClaytonOakes.Rd | 3
mets-1.1.0/mets/man/simClaytonOakesWei.Rd | 3
mets-1.1.0/mets/man/summary.cor.Rd | 3
mets-1.1.0/mets/man/survpois.Rd |only
mets-1.1.0/mets/man/test.conc.Rd | 3
mets-1.1.0/mets/man/tetrachoric.Rd |only
mets-1.1.0/mets/man/twin.clustertrunc.Rd | 3
mets-1.1.0/mets/man/twinbmi.Rd | 3
mets-1.1.0/mets/man/twinlm.Rd | 7 -
mets-1.1.0/mets/man/twinsim.Rd | 3
mets-1.1.0/mets/man/twinstut.Rd | 3
mets-1.1.0/mets/man/twostage.Rd | 3
mets-1.1.0/mets/src/fastcox.cpp | 2
mets-1.1.0/mets/src/mvn.cpp | 48 ++++++-
mets-1.1.0/mets/src/mvn.h | 5
mets-1.1.0/mets/src/mvt.f | 14 +-
mets-1.1.0/mets/src/tools.cpp | 35 +++--
mets-1.1.0/mets/src/tools.h | 2
mets-1.1.0/mets/src/tvpack.f | 8 -
mets-1.1.0/mets/tests/testthat/test_approx.R |only
83 files changed, 551 insertions(+), 305 deletions(-)
Title: Linear Predictor Score, for Binary Inference from Multiple
Continuous Variables
Diff between LPS versions 1.0.4 dated 2013-12-20 and 1.0.10 dated 2015-02-16
Description: An implementation of the Linear Predictor Score approach, as initiated by Radmacher et al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS 2003) for gene expression signatures. Several tools for unsupervised clustering of gene expression data are also provided.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal
DESCRIPTION | 17 +++++-----
MD5 | 31 +++++++++---------
R/LPS.coeff.r | 13 ++-----
R/LPS.r | 2 +
R/clusterize.r | 44 +++++++++++++++++++-------
R/heat.map.r | 89 ++++++++++++++++++++++++++++++++---------------------
R/heat.r | 2 -
R/heat.scale.r | 22 ++++++++++---
R/plot.LPS.r | 75 ++++++++++++++++++++++++++++++++++++++------
R/predict.LPS.r | 68 +++++++++++++++++++++++++---------------
README.md |only
inst/NEWS.Rd | 45 ++++++++++++++++++++++++++
man/clusterize.Rd | 22 ++++++++-----
man/heat.map.Rd | 24 ++++++++------
man/heat.scale.Rd | 9 ++++-
man/plot.LPS.Rd | 20 ++++++++++-
man/predict.LPS.Rd | 22 ++++++++-----
17 files changed, 359 insertions(+), 146 deletions(-)
Title: Harrell Miscellaneous
Diff between Hmisc versions 3.14-6 dated 2014-11-21 and 3.15-0 dated 2015-02-16
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 17 ++--
INDEX | 2
MD5 | 59 ++++++++-------
NAMESPACE | 190 ++++++++++++++++++++++++++++++++++++++++++++++++++
NEWS | 18 ++++
R/Misc.s | 16 +---
R/aregImpute.s | 47 ++++++------
R/histSpikeg.s |only
R/labcurve.s | 13 +--
R/latex.s | 58 +++++++++++----
R/rcspline.plot.s | 9 --
R/rcspline.restate.s | 12 +--
R/sas.get.s | 3
R/scat1d.s | 53 ++++++-------
R/stat-plsmo.r |only
R/summary.formula.s | 1
R/summaryM.s | 23 +++---
R/summaryP.s | 81 +++++++++++++++++++++
R/transace.s | 2
R/transcan.s | 54 +++++++++++++-
man/Hmisc-internal.Rd | 3
man/describe.Rd | 3
man/format.df.Rd | 9 +-
man/getHdata.Rd | 13 ---
man/labcurve.Rd | 12 +--
man/plsmo.Rd | 10 ++
man/scat1d.Rd | 86 +++++++++++++++++++---
man/stat_plsmo.Rd |only
man/summaryM.Rd | 10 +-
man/summaryP.Rd | 25 +++++-
man/transcan.Rd | 30 +++++--
tests/histSpike.r |only
tests/histSpikeg.r |only
33 files changed, 659 insertions(+), 200 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Diff between HH versions 3.1-14 dated 2015-01-09 and 3.1-15 dated 2015-02-16
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger
HH-3.1-14/HH/R/t.trellis.R |only
HH-3.1-14/HH/man/t.trellis.Rd |only
HH-3.1-15/HH/DESCRIPTION | 8
HH-3.1-15/HH/MD5 | 76 ++--
HH-3.1-15/HH/NAMESPACE | 7
HH-3.1-15/HH/NEWS | 47 ++-
HH-3.1-15/HH/R/ARIMA-trellis.R | 65 ----
HH-3.1-15/HH/R/extra.r | 5
HH-3.1-15/HH/R/interaction2wt.R | 2
HH-3.1-15/HH/R/intxplot.s | 24 -
HH-3.1-15/HH/R/matrix.trellis.r | 8
HH-3.1-15/HH/R/mmcplot.R | 22 +
HH-3.1-15/HH/R/normal.and.t.R | 27 -
HH-3.1-15/HH/R/normal.and.t.power.R | 30 +
HH-3.1-15/HH/R/normal.and.t.shiny.R | 80 ++---
HH-3.1-15/HH/R/normal.and.t.support.R | 2
HH-3.1-15/HH/R/panel.interaction2wt.R | 23 +
HH-3.1-15/HH/R/rbind.trellis.R | 111 +++++--
HH-3.1-15/HH/R/transpose.trellis.R | 20 -
HH-3.1-15/HH/inst/CITATION | 2
HH-3.1-15/HH/inst/scripts/hh2/conc.R | 196 ++++++++----
HH-3.1-15/HH/inst/scripts/hh2/grap.R | 48 +--
HH-3.1-15/HH/inst/scripts/hh2/iinf.R | 451 +++++++++++++++++++++++++++++
HH-3.1-15/HH/inst/scripts/hh2/logi.R | 30 -
HH-3.1-15/HH/inst/shiny/PopulationPyramid |only
HH-3.1-15/HH/man/NormalAndT.Rd | 8
HH-3.1-15/HH/man/NormalAndTplot.Rd | 10
HH-3.1-15/HH/man/ae.dotplot.Rd | 60 +--
HH-3.1-15/HH/man/as.vector.trellis.Rd | 37 +-
HH-3.1-15/HH/man/datasets.Rd | 3
HH-3.1-15/HH/man/extra.Rd | 3
HH-3.1-15/HH/man/intxplot.Rd | 5
HH-3.1-15/HH/man/mmc.Rd | 248 ++++++---------
HH-3.1-15/HH/man/normal.and.t.and.power.Rd | 4
HH-3.1-15/HH/man/normalApproxBinomial.Rd | 7
HH-3.1-15/HH/man/panel.confintMMC.Rd | 4
HH-3.1-15/HH/man/panel.interaction2wt.Rd | 2
HH-3.1-15/HH/man/rbind.trellis.Rd | 24 -
HH-3.1-15/HH/man/seqplot.Rd | 2
39 files changed, 1138 insertions(+), 563 deletions(-)
Title: High Dimensional Supervised Classification and Clustering
Diff between HDclassif versions 1.2.2 dated 2013-01-08 and 1.2.3 dated 2015-02-16
Description: Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.
Author: Laurent Berge, Charles Bouveyron and Stephane Girard
Maintainer: Laurent Berge
HDclassif-1.2.2/HDclassif/HDclassif-Ex.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc_acp.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc_crabs.R |only
HDclassif-1.2.2/HDclassif/R/hdda.R |only
HDclassif-1.2.2/HDclassif/R/hddc.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdclassif_dim_choice.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_bic.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_prms.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_prms_bis.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_tclass.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc_e_step.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc_m_step.R |only
HDclassif-1.2.2/HDclassif/R/plot.hdc.R |only
HDclassif-1.2.2/HDclassif/R/predict.hdc.R |only
HDclassif-1.2.2/HDclassif/R/print.hd.R |only
HDclassif-1.2.2/HDclassif/R/print.hdc.R |only
HDclassif-1.2.2/HDclassif/R/simuldata.R |only
HDclassif-1.2.3/HDclassif/ChangeLog | 4
HDclassif-1.2.3/HDclassif/DESCRIPTION | 20 +-
HDclassif-1.2.3/HDclassif/MD5 | 40 +----
HDclassif-1.2.3/HDclassif/R/hdclassif.R |only
HDclassif-1.2.3/HDclassif/man/Crabs.Rd | 2
HDclassif-1.2.3/HDclassif/man/HDclassif-package.Rd | 12 -
HDclassif-1.2.3/HDclassif/man/demo_hddc.Rd | 4
HDclassif-1.2.3/HDclassif/man/hdda.Rd | 130 ++++++++---------
HDclassif-1.2.3/HDclassif/man/hddc.Rd | 118 +++++++++++----
HDclassif-1.2.3/HDclassif/man/plot.hdc.Rd | 8 -
HDclassif-1.2.3/HDclassif/man/predict.hdc.Rd | 14 -
HDclassif-1.2.3/HDclassif/man/simuldata.Rd | 2
31 files changed, 196 insertions(+), 158 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.6.8 dated 2015-02-02 and 1.6.9 dated 2015-02-15
Description: Collection of several plotting and table output functions for
visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
DESCRIPTION | 8
MD5 | 199 ++---
NAMESPACE | 188 ++--
NEWS | 902 +++++++++++------------
R/helpfunctions.R | 978 ++++++++++++------------
R/sjImportSPSS.R | 859 +++++++++++----------
R/sjPlotAnova.R | 9
R/sjPlotDist.R |only
R/sjPlotFrequencies.R | 1684 ++++++++++++++++++++++---------------------
R/sjPlotGLME.R | 4
R/sjPlotInteractions.R | 19
R/sjPlotLinreg.R | 47 -
R/sjPlotScatter.R | 28
R/sjPlotSetTheme.R | 42 -
R/sjRecode.R | 8
R/sjStatistics.R | 29
R/sjTabCorr.R | 1036 +++++++++++++-------------
R/sjTabDataFrame.R | 14
R/sjTabFrequencies.R | 1324 +++++++++++++++++----------------
R/sjTabGrpmean.R | 340 ++++----
R/sjTabItemAnalysis.R | 842 ++++++++++-----------
R/sjTabLinReg.R | 1604 ++++++++++++++++++++--------------------
R/sjTabOdds.R | 1432 ++++++++++++++++++------------------
R/sjTabPCA.R | 14
R/sjTabPropTable.R | 1658 +++++++++++++++++++++---------------------
R/sjTabSPSS.R | 14
R/sjTabStackFrq.R | 28
README.md | 35
man/efc.Rd | 92 +-
man/sj.setGeomColors.Rd | 52 -
man/sjPlot-package.Rd | 4
man/sjc.cluster.Rd | 180 ++--
man/sjc.dend.Rd | 104 +-
man/sjc.elbow.Rd | 76 -
man/sjc.grpdisc.Rd | 110 +-
man/sjc.kgap.Rd | 134 +--
man/sjc.qclus.Rd | 386 ++++-----
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man/sjd.norm.Rd |only
man/sjd.t.Rd |only
man/sji.SPSS.Rd | 107 +-
man/sji.convertToLabel.Rd | 80 +-
man/sji.convertToValue.Rd | 78 -
man/sji.getValueLabels.Rd | 94 +-
man/sji.getVariableLabels.Rd | 92 +-
man/sji.setValueLabels.Rd | 98 +-
man/sji.setVariableLabels.Rd | 124 +--
man/sji.viewSPSS.Rd | 252 +++---
man/sjp.aov1.Rd | 311 ++++---
man/sjp.chi2.Rd | 122 +--
man/sjp.corr.Rd | 248 +++---
man/sjp.emm.int.Rd | 268 +++---
man/sjp.frq.Rd | 589 +++++++--------
man/sjp.glm.Rd | 394 +++++-----
man/sjp.glmer.Rd | 420 +++++-----
man/sjp.glmm.Rd | 324 ++++----
man/sjp.grpfrq.Rd | 562 +++++++-------
man/sjp.int.Rd | 450 +++++------
man/sjp.likert.Rd | 442 +++++------
man/sjp.lm.Rd | 486 ++++++------
man/sjp.lmer.Rd | 384 ++++-----
man/sjp.lmm.Rd | 310 +++----
man/sjp.pca.Rd | 288 +++----
man/sjp.scatter.Rd | 314 ++++----
man/sjp.setTheme.Rd | 22
man/sjp.stackfrq.Rd | 360 ++++-----
man/sjp.xtab.Rd | 470 ++++++------
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man/sjs.chi2.gof.Rd | 78 -
man/sjs.cramer.Rd | 54 -
man/sjs.cronbach.Rd | 60 -
man/sjs.etasq.Rd | 100 +-
man/sjs.mic.Rd | 98 +-
man/sjs.mwu.Rd | 114 +-
man/sjs.phi.Rd | 54 -
man/sjs.reliability.Rd | 178 ++--
man/sjs.se.Rd | 42 -
man/sjs.stdb.Rd | 94 +-
man/sjs.table.values.Rd | 80 +-
man/sjt.corr.Rd | 363 ++++-----
man/sjt.df.Rd | 295 +++----
man/sjt.frq.Rd | 450 +++++------
man/sjt.glm.Rd | 512 ++++++-------
man/sjt.grpmean.Rd | 162 ++--
man/sjt.itemanalysis.Rd | 397 +++++-----
man/sjt.lm.Rd | 557 +++++++-------
man/sjt.pca.Rd | 358 ++++-----
man/sjt.stackfrq.Rd | 397 +++++-----
man/sjt.xtab.Rd | 453 +++++------
man/sju.adjustPlotRange.y.Rd | 90 +-
man/sju.dicho.Rd | 78 -
man/sju.groupString.Rd | 98 +-
man/sju.groupVar.Rd | 132 +--
man/sju.groupVarLabels.Rd | 150 +--
man/sju.mean.n.Rd | 80 +-
man/sju.recode.Rd | 48 -
man/sju.recodeTo.Rd | 96 +-
man/sju.setNA.Rd | 62 -
man/sju.strpos.Rd | 138 +--
man/sju.weight.Rd | 78 -
man/sju.weight2.Rd | 90 +-
man/sju.wordwrap.Rd | 56 -
103 files changed, 14423 insertions(+), 13897 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.4 dated 2015-02-06 and 0.1.5 dated 2015-02-15
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
DESCRIPTION | 8
MD5 | 139
NAMESPACE | 2
NEWS | 11
R/print.ztable.html.R | 104
R/ztable.R | 5
R/ztable1.R | 44
R/zzz.R | 2
README.md | 9581 ++++++++++++++++++++++----------------------
inst/doc/ztable.R | 29
inst/doc/ztable.Rmd | 41
inst/doc/ztable.html | 3992 +++++++++++++-----
man/addCellColor.Rd | 3
man/addColColor.Rd | 3
man/addRowColor.Rd | 3
man/addSubColNames.Rd | 3
man/addcgroup.Rd | 3
man/addrgroup.Rd | 3
man/align2html.Rd | 3
man/align2lines.Rd | 3
man/align2nd.Rd | 3
man/alignCheck.Rd | 3
man/alignCount.Rd | 3
man/cGroupSpan.Rd | 3
man/caption2minipage.Rd | 3
man/colGroupCount.Rd | 3
man/data2table.Rd | 3
man/define_colors.Rd | 3
man/extractAlign.Rd | 3
man/getNewAlign.Rd | 3
man/getNewSpanCol.Rd | 3
man/getNewSpanRow.Rd | 3
man/getspanRowData.Rd | 3
man/getspanRowLength.Rd | 3
man/hlines.Rd |only
man/isGroupCol.Rd | 3
man/isspanCol.Rd | 3
man/isspanRow.Rd | 3
man/make.cell.color.Rd | 3
man/myhtmlStyle.Rd | 3
man/name2rgb.Rd | 3
man/parallelTables.Rd | 3
man/parallelTablesHTML.Rd | 3
man/parallelTablesLatex.Rd | 3
man/print.ztable.Rd | 3
man/printHTMLHead.Rd | 3
man/printLatexHead.Rd | 3
man/printRowGroup.Rd | 3
man/print_ztable.Rd | 3
man/repColor.Rd | 3
man/spanCol.Rd | 3
man/spanColWidth.Rd | 3
man/spanRow.Rd | 3
man/tableLength.Rd | 3
man/totalCol.Rd | 3
man/tr.Rd | 3
man/tr2.Rd | 3
man/update_ztable.Rd | 3
man/validColor.Rd | 3
man/validColor2.Rd | 3
man/vline2align.Rd | 3
man/vlines.Rd | 5
man/zcolors.Rd | 3
man/ztable.Rd | 13
man/ztable.cbind.mytable.Rd | 3
man/ztable.mytable.Rd | 3
man/ztable2html.Rd | 3
man/ztable2latex.Rd | 3
man/ztable2viewer.Rd | 3
man/ztable_sub.Rd | 3
vignettes/ztable.Rmd | 41
71 files changed, 8304 insertions(+), 5878 deletions(-)
Title: Sparse Biclustering of Transposable Data
Diff between sparseBC versions 1.0 dated 2013-10-02 and 1.1 dated 2015-02-15
Description: Implements the sparse biclustering proposal of Tan and Witten (2014), Sparse biclustering of transposable data. Journal of Computational and Graphical Statistics 23(4):985-1008.
Author: Kean Ming Tan
Maintainer: Kean Ming Tan
DESCRIPTION | 13 +++++++------
MD5 | 30 +++++++++++++++++++-----------
NAMESPACE | 12 +++++++++++-
R/image.matrixBC.R |only
R/image.sparseBC.R |only
R/matrixBC.R | 16 +++++++++++++++-
R/print.matrixBC.R |only
R/print.sparseBC.R |only
R/sparseBC.R | 29 ++++++++++++++++++++++++++---
R/summary.matrixBC.R |only
R/summary.sparseBC.R |only
man/image.sparseBC.Rd |only
man/lung.Rd | 2 +-
man/matrixBC.BIC.Rd | 8 ++++----
man/matrixBC.Rd | 31 ++++++++++++++++++++++---------
man/sparseBC-package.Rd | 42 +++++++++++++++++++++++-------------------
man/sparseBC.BIC.Rd | 6 +++---
man/sparseBC.Rd | 29 +++++++++++++++++++++--------
man/sparseBC.choosekr.Rd | 34 +++++++++++++++++-----------------
man/summary.sparseBC.Rd |only
20 files changed, 169 insertions(+), 83 deletions(-)
Title: Spectral Analysis for Physical Applications
Diff between sapa versions 2.0-0 dated 2013-12-30 and 2.0-1 dated 2015-02-15
Description: Software for the book Spectral Analysis for Physical
Applications, Donald B. Percival and Andrew T. Walden,
Cambridge University Press, 1993.
Author: William Constantine and Donald Percival (Applied Physics
Laboratory, University of Washington)
Maintainer: Don Percival
DESCRIPTION | 10
MD5 | 10
NAMESPACE | 3
man/ACVS.Rd | 82 ++++----
man/SDF.Rd | 596 +++++++++++++++++++++++++++++------------------------------
man/taper.Rd | 587 +++++++++++++++++++++++++++++-----------------------------
6 files changed, 646 insertions(+), 642 deletions(-)
Title: Bayesian Optimal Interval Design for Phase I Clinical Trials
Diff between BOIN versions 1.0 dated 2014-09-19 and 1.1 dated 2015-02-15
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields average performance comparable to the continual reassessment method (CRM, one of the best model-based design) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/get.boundary.R | 32 ++++++++++++++++++--------------
R/get.oc.R | 43 ++++++++++++++++++++++++-------------------
man/BOIN-package.Rd | 6 +++---
man/get.boundary.Rd | 18 +++++++++++++-----
man/get.oc.Rd | 19 ++++++++++++++-----
man/select.mtd.Rd | 2 +-
8 files changed, 84 insertions(+), 58 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Diff between SciencesPo versions 0.11.21 dated 2014-11-21 and 1.02.12 dated 2015-02-14
Description: A data analysis tool for the political science crowd
for ease analyzing random and nonrandom data.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino
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261 files changed, 974 insertions(+), 921 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Diff between rsdmx versions 0.4-4 dated 2015-01-16 and 0.4-5 dated 2015-02-14
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel
DESCRIPTION | 16 ++++++------
MD5 | 10 +++----
R/SDMXGenericData-methods.R | 56 +++++++++++++++++++++++++++++---------------
README.md | 8 +++---
man/readSDMX.Rd | 22 +++++++++++++++--
man/rsdmx-package.Rd | 4 +--
6 files changed, 77 insertions(+), 39 deletions(-)
Title: Multidimensional Latent Class Item Response Theory Models
Diff between MultiLCIRT versions 2.7 dated 2014-06-22 and 2.9 dated 2015-02-14
Description: Framework for the Item Response Theory analysis of dichotomous and ordinal polytomous outcomes under the assumption of multidimensionality and discreteness of the latent traits. The fitting algorithms allow for missing responses and for different item parameterizations and are based on the Expectation-Maximization paradigm. Individual covariates affecting the class weights may be included in the new version (since 2.1).
Author: Francesco Bartolucci, Silvia Bacci, Michela Gnaldi - University of Perugia (IT)
Maintainer: Francesco Bartolucci
DESCRIPTION | 12 +++---
MD5 | 22 +++++------
NAMESPACE | 10 +++++
R/est_multi_glob.R | 49 +++++++++----------------
R/est_multi_poly.R | 38 +++++++++++--------
R/est_multi_poly_clust.R | 89 +++++++++++++++++++++-------------------------
R/inv_glob.R | 9 ++--
R/lk_obs_score_clust.R | 22 ++++++++---
R/prob_multi_glob.R | 4 --
man/MultiLCIRT-package.Rd | 6 +--
man/est_multi_glob.Rd | 6 ++-
man/est_multi_poly.Rd | 8 ++--
12 files changed, 143 insertions(+), 132 deletions(-)
Title: Functions and Datasets for the Book by Keon-Woong Moon
Diff between moonBook versions 0.1.1 dated 2014-12-04 and 0.1.3 dated 2015-02-14
Description: Several analysis-related functions for the book entitled "R
statistics and graph for medical articles" (written in Korean), version 1,
by Keon-Woong Moon with Korean demographic data with several plot
functions.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
moonBook-0.1.1/moonBook/man/myhtml.cbind.mytable.Rd |only
moonBook-0.1.1/moonBook/man/myhtml.mytable.Rd |only
moonBook-0.1.1/moonBook/man/mylatex.cbind.mytable.Rd |only
moonBook-0.1.1/moonBook/man/mylatex.mytable.Rd |only
moonBook-0.1.3/moonBook/DESCRIPTION | 15
moonBook-0.1.3/moonBook/MD5 | 115 -
moonBook-0.1.3/moonBook/NAMESPACE | 15
moonBook-0.1.3/moonBook/NEWS | 18
moonBook-0.1.3/moonBook/R/ORplot.R | 69
moonBook-0.1.3/moonBook/R/myhtml.R | 57
moonBook-0.1.3/moonBook/R/mylatex.R | 109 -
moonBook-0.1.3/moonBook/R/mytable.R | 15
moonBook-0.1.3/moonBook/README.md | 472 +++---
moonBook-0.1.3/moonBook/build/vignette.rds |binary
moonBook-0.1.3/moonBook/inst/doc/moonBook.R | 61
moonBook-0.1.3/moonBook/inst/doc/moonBook.Rmd | 88 -
moonBook-0.1.3/moonBook/inst/doc/moonBook.html | 1492 ++++++++++++-------
moonBook-0.1.3/moonBook/man/HRplot.Rd | 3
moonBook-0.1.3/moonBook/man/ORplot.Rd | 3
moonBook-0.1.3/moonBook/man/ORplot.sub.Rd | 3
moonBook-0.1.3/moonBook/man/acs.Rd | 3
moonBook-0.1.3/moonBook/man/cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/centerprint.Rd | 3
moonBook-0.1.3/moonBook/man/densityplot.Rd | 3
moonBook-0.1.3/moonBook/man/extractHR.Rd | 3
moonBook-0.1.3/moonBook/man/extractOR.Rd | 3
moonBook-0.1.3/moonBook/man/my.chisq.test.Rd | 3
moonBook-0.1.3/moonBook/man/my.t.test.Rd | 3
moonBook-0.1.3/moonBook/man/mycph.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/myhtml.Rd | 34
moonBook-0.1.3/moonBook/man/myhtmlHead.Rd | 3
moonBook-0.1.3/moonBook/man/mylatex.Rd | 48
moonBook-0.1.3/moonBook/man/mytable.Rd | 3
moonBook-0.1.3/moonBook/man/mytable.sub.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2df.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2html.Rd | 3
moonBook-0.1.3/moonBook/man/num_summary.Rd | 3
moonBook-0.1.3/moonBook/man/obj2linecount.Rd | 3
moonBook-0.1.3/moonBook/man/p2sig.Rd | 3
moonBook-0.1.3/moonBook/man/print.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/print.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/printmytable2.Rd | 3
moonBook-0.1.3/moonBook/man/r.Rd | 3
moonBook-0.1.3/moonBook/man/radial.Rd | 3
moonBook-0.1.3/moonBook/man/rank2group.Rd | 3
moonBook-0.1.3/moonBook/man/reprint.Rd | 3
moonBook-0.1.3/moonBook/man/space.Rd | 3
moonBook-0.1.3/moonBook/man/summary.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/summary.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/validColname.Rd | 3
moonBook-0.1.3/moonBook/vignettes/figure |only
moonBook-0.1.3/moonBook/vignettes/moonBook.Rmd | 88 -
56 files changed, 1748 insertions(+), 1053 deletions(-)
Title: Methods that Apply to Rows and Columns of a Matrix
Diff between matrixStats versions 0.13.1 dated 2015-01-22 and 0.14.0 dated 2015-02-13
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson
matrixStats-0.13.1/matrixStats/R/anyMissing.S4.R |only
matrixStats-0.14.0/matrixStats/DESCRIPTION | 12
matrixStats-0.14.0/matrixStats/MD5 | 92 ++--
matrixStats-0.14.0/matrixStats/NAMESPACE | 2
matrixStats-0.14.0/matrixStats/NEWS | 39 +
matrixStats-0.14.0/matrixStats/R/anyMissing.R |only
matrixStats-0.14.0/matrixStats/R/benchmark.R | 2
matrixStats-0.14.0/matrixStats/R/pkgStartupMessage.R |only
matrixStats-0.14.0/matrixStats/R/rowCounts.R | 21
matrixStats-0.14.0/matrixStats/R/rowMads.R | 38 +
matrixStats-0.14.0/matrixStats/R/rowSds.R | 3
matrixStats-0.14.0/matrixStats/R/rowVars.R | 6
matrixStats-0.14.0/matrixStats/R/varDiff.R | 18
matrixStats-0.14.0/matrixStats/R/weightedMedian.R | 225 ----------
matrixStats-0.14.0/matrixStats/R/zzz.R | 1
matrixStats-0.14.0/matrixStats/build/vignette.rds |binary
matrixStats-0.14.0/matrixStats/inst/benchmarking/colRowMads.md.rsp | 23 +
matrixStats-0.14.0/matrixStats/inst/doc/matrixStats-methods.html | 80 ++-
matrixStats-0.14.0/matrixStats/inst/doc/matrixStats-methods.md.rsp | 90 ++--
matrixStats-0.14.0/matrixStats/man/anyMissing.Rd | 3
matrixStats-0.14.0/matrixStats/man/matrixStats-package.Rd | 2
matrixStats-0.14.0/matrixStats/man/rowSds.Rd | 7
matrixStats-0.14.0/matrixStats/man/rowVars.Rd | 4
matrixStats-0.14.0/matrixStats/src/allocMatrix2.c | 2
matrixStats-0.14.0/matrixStats/src/logSumExp_internal.c | 66 +-
matrixStats-0.14.0/matrixStats/src/psortKM.c | 2
matrixStats-0.14.0/matrixStats/src/rowCumMinMaxs_TYPE-template.h | 8
matrixStats-0.14.0/matrixStats/src/rowCumprods_TYPE-template.h | 10
matrixStats-0.14.0/matrixStats/src/rowCumsums_TYPE-template.h | 8
matrixStats-0.14.0/matrixStats/src/rowMads_TYPE-template.h | 9
matrixStats-0.14.0/matrixStats/src/rowMedians_TYPE-template.h | 13
matrixStats-0.14.0/matrixStats/src/rowVars_TYPE-template.h | 5
matrixStats-0.14.0/matrixStats/src/types.h | 4
matrixStats-0.14.0/matrixStats/tests/anyMissing.R | 2
matrixStats-0.14.0/matrixStats/tests/benchmark.R |only
matrixStats-0.14.0/matrixStats/tests/indexByRow.R | 7
matrixStats-0.14.0/matrixStats/tests/logSumExp.R | 64 ++
matrixStats-0.14.0/matrixStats/tests/rowAllAnys.R | 94 +++-
matrixStats-0.14.0/matrixStats/tests/rowCounts.R | 24 +
matrixStats-0.14.0/matrixStats/tests/rowIQRs.R | 57 ++
matrixStats-0.14.0/matrixStats/tests/rowLogSumExps.R | 99 ++++
matrixStats-0.14.0/matrixStats/tests/rowMads.R | 4
matrixStats-0.14.0/matrixStats/tests/rowRanges.R | 9
matrixStats-0.14.0/matrixStats/tests/rowTabulates.R | 5
matrixStats-0.14.0/matrixStats/tests/rowWeightedVars.R |only
matrixStats-0.14.0/matrixStats/tests/sumOver.R | 43 +
matrixStats-0.14.0/matrixStats/tests/varDiff_etal.R | 25 -
matrixStats-0.14.0/matrixStats/tests/weightedMedian.R | 42 -
matrixStats-0.14.0/matrixStats/tests/zzz.package-unload.R |only
matrixStats-0.14.0/matrixStats/vignettes/matrixStats-methods.md.rsp | 90 ++--
50 files changed, 841 insertions(+), 519 deletions(-)
Title: Phylogenetic Analysis in R
Diff between phangorn versions 1.99-11 dated 2014-11-11 and 1.99-12 dated 2015-02-13
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
DESCRIPTION | 21 +-
MD5 | 80 +++++----
NAMESPACE | 11 -
NEWS | 32 +++
R/RcppExports.R |only
R/fitch.R | 6
R/neighborNet.R |only
R/networx.R | 328 +++++++++++++++++++++++++++++++++-------
R/parsimony.R | 161 +++++++------------
R/phylo.R | 318 +++++++++++++-------------------------
R/treeManipulation.R | 43 ++++-
R/treedist.R | 19 --
build/vignette.rds |binary
inst/doc/Ancestral.R | 14 -
inst/doc/Ancestral.Rnw | 15 -
inst/doc/Networx.R |only
inst/doc/Networx.Rmd |only
inst/doc/Networx.html |only
inst/doc/Trees.R | 44 ++---
inst/doc/Trees.Rnw | 9 -
inst/doc/phangorn-specials.R | 18 +-
inst/doc/phangorn-specials.Rnw | 27 +--
man/SOWH.test.Rd | 2
man/ancestral.pml.Rd | 5
man/as.splits.Rd | 6
man/bootstrap.pml.Rd | 8
man/consensusNet.Rd | 4
man/densiTree.Rd | 4
man/designTree.Rd | 104 ++++++------
man/neighborNet.Rd |only
man/plot.networx.Rd | 10 -
man/read.aa.Rd | 87 +++++-----
man/splitsNetwork.Rd | 14 -
src/dist.c | 2
src/fitch.c | 34 +++-
src/init.c | 26 +--
src/ml.c | 2
src/phangorn.c | 2
src/sankoff.c | 135 +++-------------
vignettes/Ancestral.Rnw | 15 -
vignettes/Networx.Rmd |only
vignettes/Trees.Rnw | 9 -
vignettes/movie.gif |only
vignettes/phangorn-specials.Rnw | 27 +--
vignettes/phangorn.bib | 43 +++++
45 files changed, 919 insertions(+), 766 deletions(-)
Title: Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Diff between glmvsd versions 1.1 dated 2014-11-21 and 1.2 dated 2015-02-13
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan
Maintainer: Yi Yang
ChangeLog | 3 +++
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/lsARM.R | 2 +-
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Bridge Regression
Diff between BayesBridge versions 0.5 dated 2014-07-21 and 0.6 dated 2015-02-13
Description: Bayesian bridge regression.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/BridgeNMix.R | 2 +-
R/BridgeWrapper.R | 3 +--
4 files changed, 10 insertions(+), 11 deletions(-)
Title: Regression Estimation and Presentation
Diff between rockchalk versions 1.8.91 dated 2015-01-30 and 1.8.92 dated 2015-02-13
Description: A collection of functions for ease of
presentation and interpretation of regression analysis.
These functions are used to produce the statistics lectures
in http://pj.freefaculty.org/guides. There
are functions to explore the effect (or lack thereof) from
"mean centering," "residual centering", and standardization.
The vignette "rockchalk" offers a fairly comprehensive overview.
The vignette "Rstyle" has advice about coding in R.
See the outreg function for a convenient way to generate
regression models for reports. For nice, easy to use pictures,
see plotSlopes, plotCurves, plotPlane.
The package title "rockchalk" refers to our school motto,
"Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/genCorrelatedData.R | 7 ++-----
R/pctable.R | 8 ++++++--
R/plotCurves.R | 9 ++++++---
R/predictOMatic.R | 4 ++--
inst/ChangeLog | 5 +++++
inst/doc/Rchaeology.pdf |binary
inst/doc/Rstyle.pdf |binary
inst/doc/rockchalk.pdf |binary
man/mvrnorm.Rd | 6 +-----
11 files changed, 36 insertions(+), 31 deletions(-)
Title: Extraction of Business Financial Information from XBRL Documents
Diff between XBRL versions 0.99.14 dated 2015-01-08 and 0.99.15 dated 2015-02-13
Description:
Functions to extract business financial information from
an Extensible Business Reporting Language (XBRL) instance file and the
associated collection of files that defines its Discoverable Taxonomy
Set (DTS), usually disseminated across different remote locations.
XBRL documents employ many technologies defined by XML standards, such
as XML Schema, Namespaces, XLink, and XPath, which make the extraction
of information involved. The functions provided by this package
address this complexity, returning data frames containing the enclosed
information readily available to perform analyses.
XBRL has been successfully tested in analyzing 10-K and 10-Q
submissions from USA filing companies that are publicly available at
the EDGAR system of the Securities and Exchange Commission (SEC).
It has been reported to work with inline XBRL documents.
As published taxonomy files (such as
"http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd")
are immutable and are used by most filers, XBRL offers the option of
downloading them only the first time they are referred, keeping a
local cache copy that can be used from then on. This speeds-up the
process, specially on slow connections.
XBRL is not and does not aim to be (at least yet) a validating XBRL
processor.
XBRL is still a work in progress. As such, functions and produced data
frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
ChangeLog | 8 +++++
DESCRIPTION | 16 +++++-----
MD5 | 66 +++++++++++++++++++++----------------------
R/XBRL.R | 2 -
R/xbrlDoAll.R | 2 -
R/xbrlFree.R | 2 -
R/xbrlGetImportNames.R | 2 -
R/xbrlGetLinkbaseNames.R | 2 -
R/xbrlGetSchemaName.R | 2 -
R/xbrlParse.R | 2 -
R/xbrlProcessArcs.R | 2 -
R/xbrlProcessContexts.R | 2 -
R/xbrlProcessElements.R | 2 -
R/xbrlProcessFacts.R | 2 -
R/xbrlProcessFootnotes.R | 2 -
R/xbrlProcessLabels.R | 2 -
R/xbrlProcessRoles.R | 2 -
R/xbrlProcessUnits.R | 2 -
R/xbrlSECdev01.R | 2 -
man/XBRL-package.Rd | 8 ++---
src/XBRL.h | 2 -
src/xbrlFree.cpp | 2 -
src/xbrlGetImportNames.cpp | 2 -
src/xbrlGetLinkbaseNames.cpp | 2 -
src/xbrlGetSchemaName.cpp | 2 -
src/xbrlParse.cpp | 2 -
src/xbrlProcessArcs.cpp | 2 -
src/xbrlProcessContexts.cpp | 2 -
src/xbrlProcessElements.cpp | 2 -
src/xbrlProcessFacts.cpp | 7 +++-
src/xbrlProcessFootnotes.cpp | 2 -
src/xbrlProcessLabels.cpp | 2 -
src/xbrlProcessRoles.cpp | 2 -
src/xbrlProcessUnits.cpp | 2 -
34 files changed, 87 insertions(+), 76 deletions(-)
Title: Teitz and Bart's p-Median Algorithm
Diff between tbart versions 0.9.1 dated 2014-08-16 and 1.0 dated 2015-02-13
Description: Solves Teitz and Bart's p-median problem - given a set of
points attempts to find subset of size p such that summed distances of any
point in the set to the nearest point in p is minimised. Although
generally effective, this algorithm does not guarantee that a globally
optimal subset is found.
Author: Chris Brunsdon
Maintainer: Chris Brunsdon
DESCRIPTION | 13 +--
MD5 | 26 +++---
R/RcppExports.R | 8 +
R/tbart-describes.R | 7 -
R/tbmain.R | 218 ++++++++++++++++++++++++++++++++++++++++++---------
man/allocate.Rd | 12 +-
man/allocations.Rd |only
man/euc.dists.Rd | 2
man/mink.dists.Rd |only
man/star.diagram.Rd | 12 ++
man/tb.Rd | 10 +-
man/tb.raw.Rd | 2
man/tbart-package.Rd | 22 ++---
src/RcppExports.cpp | 37 ++++++++
src/tb.cpp | 54 ++++++++++++
15 files changed, 343 insertions(+), 80 deletions(-)
Title: R Interface For OAuth
Diff between ROAuth versions 0.9.5 dated 2014-12-03 and 0.9.6 dated 2015-02-13
Description: Provides an interface to the OAuth 1.0 specification
allowing users to authenticate via OAuth to the
server of their choice.
Author: Jeff Gentry
Maintainer: Pablo Barbera
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Differential Expression from Multiple Indicators
Diff between demi versions 1.1.1 dated 2013-11-05 and 1.1.2 dated 2015-02-13
Description: Implementation of the DEMI method for the analysis of high-density microarray data.
Author: Sten Ilmjarv [aut, cre],
Hendrik Luuk [aut]
Maintainer: Sten Ilmjarv
demi-1.1.1/demi/inst/doc/demi.R |only
demi-1.1.2/demi/DESCRIPTION | 16
demi-1.1.2/demi/MD5 | 232 +++++-----
demi-1.1.2/demi/NAMESPACE | 97 ++--
demi-1.1.2/demi/R/AllClasses.R | 6
demi-1.1.2/demi/R/AllGenerics.R | 54 ++
demi-1.1.2/demi/R/Constructors.R | 6
demi-1.1.2/demi/R/DEMICel-methods.R | 3
demi-1.1.2/demi/R/DEMIClust-methods.R | 12
demi-1.1.2/demi/R/DEMIDiff-methods.R | 27 -
demi-1.1.2/demi/R/DEMIExperiment-methods.R | 121 +++--
demi-1.1.2/demi/R/DEMIGroup-methods.R | 8
demi-1.1.2/demi/R/DEMIResult-methods.R | 5
demi-1.1.2/demi/R/custom-methods.R | 2
demi-1.1.2/demi/R/diffexp-methods.R | 6
demi-1.1.2/demi/R/messages.R | 2
demi-1.1.2/demi/R/normalization-methods.R | 4
demi-1.1.2/demi/R/zzz.R | 2
demi-1.1.2/demi/build |only
demi-1.1.2/demi/inst/doc/demi.Rnw | 6
demi-1.1.2/demi/inst/doc/demi.pdf |binary
demi-1.1.2/demi/man/DEMICel-class.Rd | 14
demi-1.1.2/demi/man/DEMICel-methods.Rd | 29 -
demi-1.1.2/demi/man/DEMIClust-class.Rd | 44 -
demi-1.1.2/demi/man/DEMIClust-methods.Rd | 152 ++----
demi-1.1.2/demi/man/DEMIDiff-class.Rd | 26 -
demi-1.1.2/demi/man/DEMIDiff-methods.Rd | 42 -
demi-1.1.2/demi/man/DEMIExperiment-class.Rd | 158 ++----
demi-1.1.2/demi/man/DEMIExperiment-methods.Rd | 218 +++------
demi-1.1.2/demi/man/DEMIGroup-class.Rd | 26 -
demi-1.1.2/demi/man/DEMIGroup-methods.Rd | 51 --
demi-1.1.2/demi/man/DEMIMessages.Rd | 191 +++++++-
demi-1.1.2/demi/man/DEMIPathway-methods.Rd | 31 -
demi-1.1.2/demi/man/DEMIResult-class.Rd | 16
demi-1.1.2/demi/man/DEMIWrap-methods.Rd | 341 +++++----------
demi-1.1.2/demi/man/addCustomTargets-methods.Rd | 75 +--
demi-1.1.2/demi/man/addCytoband-methods.Rd | 27 -
demi-1.1.2/demi/man/adjust4maxprobes-methods.Rd | 22
demi-1.1.2/demi/man/attachResult-methods.Rd | 62 +-
demi-1.1.2/demi/man/calcHypergeoExon-methods.Rd | 16
demi-1.1.2/demi/man/calcHypergeoProb-methods.Rd | 16
demi-1.1.2/demi/man/celMatrixNormalize-methods.Rd | 24 -
demi-1.1.2/demi/man/check4probe-methods.Rd | 29 -
demi-1.1.2/demi/man/check4target-methods.Rd | 28 -
demi-1.1.2/demi/man/checkDEMIExperiment_analysis.Rd | 16
demi-1.1.2/demi/man/checkDEMIExperiment_celpath.Rd | 16
demi-1.1.2/demi/man/checkDEMIExperiment_experiment.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_maxprobes.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_maxtargets.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_normalization.Rd | 20
demi-1.1.2/demi/man/checkDEMIExperiment_pmsize.Rd | 18
demi-1.1.2/demi/man/cleanorganismname-methods.Rd | 15
demi-1.1.2/demi/man/cluster-methods.Rd | 26 -
demi-1.1.2/demi/man/createGroup-methods.Rd | 26 -
demi-1.1.2/demi/man/customObject-methods.Rd | 25 -
demi-1.1.2/demi/man/demi.comp.test-methods.Rd | 30 -
demi-1.1.2/demi/man/demi.t.test-methods.Rd | 26 -
demi-1.1.2/demi/man/demi.wilcox.test-methods.Rd | 26 -
demi-1.1.2/demi/man/demi.wilcox.test.fast-methods.Rd | 30 -
demi-1.1.2/demi/man/demiequal-methods.Rd | 28 -
demi-1.1.2/demi/man/demisummary-methods.Rd | 60 +-
demi-1.1.2/demi/man/diffSpliceScore-methods.Rd | 16
demi-1.1.2/demi/man/diffexp-methods.Rd | 22
demi-1.1.2/demi/man/findCytoband-methods.Rd | 21
demi-1.1.2/demi/man/getAlignment-methods.Rd | 22
demi-1.1.2/demi/man/getAnalysis-methods.Rd | 22
demi-1.1.2/demi/man/getAnnotation-methods.Rd | 22
demi-1.1.2/demi/man/getArraytype-methods.Rd | 20
demi-1.1.2/demi/man/getCelMatrix-methods.Rd | 22
demi-1.1.2/demi/man/getCelpath-methods.Rd | 24 -
demi-1.1.2/demi/man/getClustMethod-methods.Rd | 21
demi-1.1.2/demi/man/getCluster-methods.Rd | 21
demi-1.1.2/demi/man/getCutoffPvalue-methods.Rd | 23 -
demi-1.1.2/demi/man/getCytoband-methods.Rd | 29 -
demi-1.1.2/demi/man/getDEMIClust-methods.Rd | 20
demi-1.1.2/demi/man/getExperiment-methods.Rd | 39 -
demi-1.1.2/demi/man/getGroup-methods.Rd | 24 -
demi-1.1.2/demi/man/getGroupA-methods.Rd | 21
demi-1.1.2/demi/man/getGroupB-methods.Rd | 21
demi-1.1.2/demi/man/getGroupNames-methods.Rd | 24 -
demi-1.1.2/demi/man/getIndexA-methods.Rd | 21
demi-1.1.2/demi/man/getIndexB-methods.Rd | 21
demi-1.1.2/demi/man/getMaxprobes-methods.Rd | 30 -
demi-1.1.2/demi/man/getMaxtargets-methods.Rd | 29 -
demi-1.1.2/demi/man/getName-methods.Rd | 24 -
demi-1.1.2/demi/man/getNormMatrix-methods.Rd | 22
demi-1.1.2/demi/man/getOrganism-methods.Rd | 21
demi-1.1.2/demi/man/getPathway-methods.Rd | 26 -
demi-1.1.2/demi/man/getProbeLevel-methods.Rd | 39 -
demi-1.1.2/demi/man/getResult-methods.Rd | 48 +-
demi-1.1.2/demi/man/getResultTable-methods.Rd | 27 -
demi-1.1.2/demi/man/getTargetAnnotation-methods.Rd | 39 -
demi-1.1.2/demi/man/getTargetProbes-methods.Rd | 45 +
demi-1.1.2/demi/man/initialize.DEMICel.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIClust.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIDiff.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIExperiment.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIGroup.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIResult.Rd | 14
demi-1.1.2/demi/man/loadAnnotation-methods.Rd | 23 -
demi-1.1.2/demi/man/loadBlat-methods.Rd | 23 -
demi-1.1.2/demi/man/loadCel-methods.Rd | 24 -
demi-1.1.2/demi/man/loadCytoband-methods.Rd | 23 -
demi-1.1.2/demi/man/loadDEMILibrary-methods.Rd | 33 -
demi-1.1.2/demi/man/loadPathway-methods.Rd | 23 -
demi-1.1.2/demi/man/makeDEMIResultsTable-methods.Rd | 21
demi-1.1.2/demi/man/makeUCSCLink-methods.Rd | 19
demi-1.1.2/demi/man/matchExonGene-methods.Rd | 23 -
demi-1.1.2/demi/man/norm.quantile-methods.Rd | 21
demi-1.1.2/demi/man/norm.rrank-methods.Rd | 22
demi-1.1.2/demi/man/probe.levels-methods.Rd | 31 -
demi-1.1.2/demi/man/probe.plot-methods.Rd | 31 -
demi-1.1.2/demi/man/totalMatches_all-methods.Rd | 17
demi-1.1.2/demi/man/totalMatches_cluster-methods.Rd | 20
demi-1.1.2/demi/man/validDEMIClust.Rd | 12
demi-1.1.2/demi/man/validDEMIExperiment.Rd | 10
demi-1.1.2/demi/man/wprob-methods.Rd | 22
demi-1.1.2/demi/vignettes/demi.Rnw | 6
118 files changed, 2107 insertions(+), 1861 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Diff between cati versions 0.8 dated 2014-06-24 and 0.96 dated 2015-02-13
Description: A package to detect and quantify community assembly processes
using trait values of individuals or populations, the T-statistics and
other metrics, and dedicated null models.
Author: Adrien Taudiere, Cyrille Violle with contribution of Francois Munoz
Maintainer: Adrien Taudiere
cati-0.8/cati/man/ab_to_ind.Rd |only
cati-0.8/cati/man/bar_partvar.Rd |only
cati-0.8/cati/man/com.index.Rd |only
cati-0.8/cati/man/com.index.multi.Rd |only
cati-0.8/cati/man/decomp_whithin.Rd |only
cati-0.8/cati/man/pie_partvar.Rd |only
cati-0.8/cati/man/plot_cor.Tstats.Rd |only
cati-0.8/cati/man/plot_dens.Rd |only
cati-0.8/cati/man/plot_randtest.Rd |only
cati-0.8/cati/man/plot_ses.var.Rd |only
cati-0.8/cati/man/plot_sp_pop.Rd |only
cati-0.8/cati/man/plot_sp_var.Rd |only
cati-0.8/cati/man/trait.flex.anova.Rd |only
cati-0.96/cati/DESCRIPTION | 16
cati-0.96/cati/MD5 | 61
cati-0.96/cati/NAMESPACE | 23
cati-0.96/cati/R/allfunctions_cati.r | 3140 ------------------------------
cati-0.96/cati/data/finch.ind.RData |binary
cati-0.96/cati/inst |only
cati-0.96/cati/man/AbToInd.Rd |only
cati-0.96/cati/man/Auxiliary.functions.rd |only
cati-0.96/cati/man/CVNND.Rd | 144 -
cati-0.96/cati/man/ComIndex.Rd |only
cati-0.96/cati/man/ComIndexMulti.Rd |only
cati-0.96/cati/man/Fred.Rd |only
cati-0.96/cati/man/IndexByGroups.Rd |only
cati-0.96/cati/man/MinMaxMST.Rd |only
cati-0.96/cati/man/Pval.Rd |only
cati-0.96/cati/man/RandCom.Rd |only
cati-0.96/cati/man/RaoRel.Rd | 348 +--
cati-0.96/cati/man/SumBL.Rd |only
cati-0.96/cati/man/Tstats.Rd | 490 ++--
cati-0.96/cati/man/as.listofindex.Rd | 166 -
cati-0.96/cati/man/cati-package.Rd | 60
cati-0.96/cati/man/decompCTRE.Rd |only
cati-0.96/cati/man/finch.ind.Rd | 74
cati-0.96/cati/man/partvar.Rd | 165 -
cati-0.96/cati/man/plot.listofindex.Rd | 388 +--
cati-0.96/cati/man/plotCorTstats.Rd |only
cati-0.96/cati/man/plotDistri.Rd |only
cati-0.96/cati/man/plotRandtest.Rd |only
cati-0.96/cati/man/plotSESvar.Rd |only
cati-0.96/cati/man/plotSpPop.Rd |only
cati-0.96/cati/man/plotSpVar.Rd |only
cati-0.96/cati/man/samplingSubsetData.Rd |only
cati-0.96/cati/man/ses.Rd | 124 -
cati-0.96/cati/man/ses.listofindex.Rd | 177 -
cati-0.96/cati/man/traitflex.anova.Rd |only
48 files changed, 1097 insertions(+), 4279 deletions(-)
Title: Hierarchical Modelling of Faecal Egg Counts
Diff between eggCounts versions 0.3 dated 2014-09-06 and 0.4-1 dated 2015-02-13
Description: An implementation of hierarchical models
for faecal egg count data to assess anthelmintic
efficacy. Bayesian inference is done via MCMC sampling.
Author: Michaela Paul [aut], Reinhard Furrer [cre, ctb]
Maintainer: Reinhard Furrer
eggCounts-0.3/eggCounts/tests/regtest-fecModelling.Rout.save |only
eggCounts-0.4-1/eggCounts/ChangeLog | 6
eggCounts-0.4-1/eggCounts/DESCRIPTION | 28 +-
eggCounts-0.4-1/eggCounts/MD5 | 132 +++++------
eggCounts-0.4-1/eggCounts/NAMESPACE | 2
eggCounts-0.4-1/eggCounts/R/FECR_PoGa.R | 67 ++++-
eggCounts-0.4-1/eggCounts/R/FEC_PoGa.R | 64 ++++-
eggCounts-0.4-1/eggCounts/R/MHsteps.R | 43 ++-
eggCounts-0.4-1/eggCounts/R/eggCounts-package.R | 8
eggCounts-0.4-1/eggCounts/R/printSummary.R | 21 +
eggCounts-0.4-1/eggCounts/R/profile.R | 6
eggCounts-0.4-1/eggCounts/R/updates.R | 68 ++++-
eggCounts-0.4-1/eggCounts/demo/fecm.R | 7
eggCounts-0.4-1/eggCounts/inst/NEWS | 13 +
eggCounts-0.4-1/eggCounts/man/MH_RW_unif.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/MH_RW_unif01.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/MHstep.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/checkAR.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/echinococcus.Rd | 11
eggCounts-0.4-1/eggCounts/man/eggCounts-package.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/epgs.Rd | 11
eggCounts-0.4-1/eggCounts/man/fc_approx_beta.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/fc_approx_gamma.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fc_approx_invgamma.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fc_approx_logNormal.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fec_mcmc.Rd | 90 +++----
eggCounts-0.4-1/eggCounts/man/fecr_mcmc.Rd | 116 ++++-----
eggCounts-0.4-1/eggCounts/man/fecrtCI.Rd | 59 ++--
eggCounts-0.4-1/eggCounts/man/logdgammaMixture.Rd | 21 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_delta.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_h.Rd | 15 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_phi.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_psi.Rd | 18 -
eggCounts-0.4-1/eggCounts/man/print.fecm.Rd | 18 +
eggCounts-0.4-1/eggCounts/man/print.fecrm.Rd | 18 +
eggCounts-0.4-1/eggCounts/man/samples2mcmc.Rd | 10
eggCounts-0.4-1/eggCounts/man/setDefaults1.Rd | 41 +--
eggCounts-0.4-1/eggCounts/man/setDefaults2.Rd | 82 +++---
eggCounts-0.4-1/eggCounts/man/setInitials1.Rd | 20 +
eggCounts-0.4-1/eggCounts/man/setInitials2.Rd | 30 +-
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa2.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_mu.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_p.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_u.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa2.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_mu.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_u.Rd | 21 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_u_pd.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/simData1s.Rd | 25 +-
eggCounts-0.4-1/eggCounts/man/simData2s.Rd | 37 +--
eggCounts-0.4-1/eggCounts/man/statusMsg.Rd | 10
eggCounts-0.4-1/eggCounts/man/tab1morgan.Rd | 56 ++--
eggCounts-0.4-1/eggCounts/man/update_Y.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/update_delta_beta.Rd | 20 -
eggCounts-0.4-1/eggCounts/man/update_h_gamma.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/update_h_invGamma.Rd | 20 -
eggCounts-0.4-1/eggCounts/man/update_h_kl.Rd | 25 --
eggCounts-0.4-1/eggCounts/man/update_h_logNormal.Rd | 19 -
eggCounts-0.4-1/eggCounts/man/update_phi_gamma.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/update_phi_unif.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/update_psi_beta.Rd | 29 +-
eggCounts-0.4-1/eggCounts/man/update_theta_beta.Rd | 17 -
eggCounts-0.4-1/eggCounts/man/update_theta_gamma.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/update_theta_gamma1.Rd | 19 -
eggCounts-0.4-1/eggCounts/man/update_theta_gammaAdd.Rd | 18 -
eggCounts-0.4-1/eggCounts/man/update_theta_gammaMix.Rd | 31 +-
eggCounts-0.4-1/eggCounts/tests/regtest-fecModelling.Rout |only
eggCounts-0.4-1/eggCounts/tests/special-cases.R |only
eggCounts-0.4-1/eggCounts/tests/special-cases.Rout |only
69 files changed, 978 insertions(+), 798 deletions(-)
Title: TAP-Compliant Unit Testing
Diff between unittest versions 1.1-1 dated 2014-12-14 and 1.2-0 dated 2015-02-13
Description:
Concise TAP (http://testanything.org/) compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre],
Anthony Hennessey [aut]
Maintainer: Jamie Lentin
ChangeLog | 8 +
DESCRIPTION | 8 -
MD5 | 24 ++---
NEWS | 3
R/non_interactive_summary.R | 18 +---
R/ok.R | 14 +--
README.md | 4
man/ok.Rd | 14 +--
man/ok_group.Rd | 14 +--
man/unittest-package.Rd | 175 ++++++++++++++++++++-----------------------
tests/test_non_interactive.R | 36 +++++++-
tests/test_ok.R | 34 ++++----
tests/test_ok_group.R | 4
13 files changed, 188 insertions(+), 168 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Diff between vdg versions 1.0 dated 2014-06-17 and 1.0.1 dated 2015-02-13
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph]
Maintainer: Pieter Schoonees
DESCRIPTION | 22 +-
MD5 | 64 +++----
NAMESPACE | 43 +++-
R/GJ54.R | 18 +-
R/LHS.R | 202 +++++++++++-----------
R/meanspv.R | 213 ++++++++++++-----------
R/plot.spv.R | 418 ++++++++++++++++++++++++-----------------------
R/plot.spvforlist.R | 282 +++++++++++++++----------------
R/plot.spvlist.R | 290 ++++++++++++++++----------------
R/plot.spvlistforlist.R | 310 +++++++++++++++++-----------------
R/print.spv.R | 46 ++---
R/print.spvforlist.R | 38 ++--
R/print.spvlist.R | 40 ++--
R/print.spvlistforlist.R | 36 ++--
R/runif_cube.R | 49 ++---
R/runif_sphere.R | 88 ++++-----
R/sampler.R | 62 +++---
R/spv.R | 72 ++++----
R/spv.data.frame.R | 156 ++++++++---------
R/spv.list.R | 140 +++++++--------
R/spv.matrix.R | 156 ++++++++---------
R/stdrange.R | 60 +++---
R/vdg-package.R | 26 +-
inst |only
man/GJ54.Rd | 33 +--
man/LHS.Rd | 119 ++++++-------
man/meanspv.Rd | 81 ++++-----
man/plot.spv.Rd | 272 +++++++++++++++---------------
man/print.spv.Rd | 61 +++---
man/runif_sphere.Rd | 85 ++++-----
man/sampler.Rd | 75 ++++----
man/spv.Rd | 133 +++++++-------
man/stdrange.Rd | 55 +++---
man/vdg-package.Rd |only
34 files changed, 1896 insertions(+), 1849 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-11 dated 2015-01-13 and 3.1-12 dated 2015-02-13
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
s20x-3.1-11/s20x/inst/rmarkdown/templates/STATS20x_Assignment/skeleton/styles.css |only
s20x-3.1-12/s20x/DESCRIPTION | 12
s20x-3.1-12/s20x/MD5 | 135 ++++----
s20x-3.1-12/s20x/inst/rmarkdown/templates/STATS20x_Assignment/skeleton/skeleton.Rmd | 48 +--
s20x-3.1-12/s20x/inst/rmarkdown/templates/STATS20x_Assignment/template.yaml | 7
s20x-3.1-12/s20x/man/airpass.df.Rd | 26 -
s20x-3.1-12/s20x/man/apples.df.Rd | 72 ++--
s20x-3.1-12/s20x/man/arousal.df.Rd | 36 +-
s20x-3.1-12/s20x/man/autocor.plot.Rd | 42 +-
s20x-3.1-12/s20x/man/beer.df.Rd | 26 -
s20x-3.1-12/s20x/man/body.df.Rd | 46 +-
s20x-3.1-12/s20x/man/books.df.Rd | 54 +--
s20x-3.1-12/s20x/man/boxqq.Rd | 60 +--
s20x-3.1-12/s20x/man/bursary.df.Rd | 34 +-
s20x-3.1-12/s20x/man/butterfat.df.Rd | 54 +--
s20x-3.1-12/s20x/man/camplake.df.Rd | 36 +-
s20x-3.1-12/s20x/man/chalk.df.Rd | 40 +-
s20x-3.1-12/s20x/man/ciReg.Rd | 52 +--
s20x-3.1-12/s20x/man/computer.df.Rd | 34 +-
s20x-3.1-12/s20x/man/cooks20x.Rd | 42 +-
s20x-3.1-12/s20x/man/course.df.Rd | 60 +--
s20x-3.1-12/s20x/man/course2way.df.Rd | 36 +-
s20x-3.1-12/s20x/man/crossFactors.Rd | 86 ++---
s20x-3.1-12/s20x/man/crosstabs.Rd | 54 +--
s20x-3.1-12/s20x/man/diamonds.df.Rd | 34 +-
s20x-3.1-12/s20x/man/eovcheck.Rd | 1
s20x-3.1-12/s20x/man/estimateContrasts.Rd | 74 ++--
s20x-3.1-12/s20x/man/fire.df.Rd | 34 +-
s20x-3.1-12/s20x/man/freq1way.Rd | 86 ++---
s20x-3.1-12/s20x/man/fruitfly.df.Rd | 50 +--
s20x-3.1-12/s20x/man/getVersion.Rd | 34 +-
s20x-3.1-12/s20x/man/house.df.Rd | 34 +-
s20x-3.1-12/s20x/man/incomes.df.Rd | 20 -
s20x-3.1-12/s20x/man/lakemary.df.Rd | 34 +-
s20x-3.1-12/s20x/man/larain.df.Rd | 26 -
s20x-3.1-12/s20x/man/layout20x.Rd | 46 +-
s20x-3.1-12/s20x/man/levene.test.Rd | 66 ++--
s20x-3.1-12/s20x/man/mazda.df.Rd | 34 +-
s20x-3.1-12/s20x/man/mening.df.Rd | 26 -
s20x-3.1-12/s20x/man/mergers.df.Rd | 20 -
s20x-3.1-12/s20x/man/mozart.df.Rd | 36 +-
s20x-3.1-12/s20x/man/multipleComp.Rd | 46 +-
s20x-3.1-12/s20x/man/nail.df.Rd | 38 +-
s20x-3.1-12/s20x/man/normcheck.Rd | 2
s20x-3.1-12/s20x/man/onewayPlot.Rd | 156 +++++-----
s20x-3.1-12/s20x/man/oysters.df.Rd | 34 +-
s20x-3.1-12/s20x/man/pairs20x.Rd | 56 +--
s20x-3.1-12/s20x/man/peru.df.Rd | 40 +-
s20x-3.1-12/s20x/man/predict20x.Rd | 108 +++---
s20x-3.1-12/s20x/man/propslsd.new.Rd | 32 +-
s20x-3.1-12/s20x/man/rain.df.Rd | 40 +-
s20x-3.1-12/s20x/man/residPlot.Rd | 60 +--
s20x-3.1-12/s20x/man/rowdistr.Rd | 1
s20x-3.1-12/s20x/man/rr.Rd | 14
s20x-3.1-12/s20x/man/seeds.df.Rd | 42 +-
s20x-3.1-12/s20x/man/sheep.df.Rd | 32 +-
s20x-3.1-12/s20x/man/skewness.Rd | 40 +-
s20x-3.1-12/s20x/man/skulls.df.Rd | 48 +--
s20x-3.1-12/s20x/man/soyabean.df.Rd | 38 +-
s20x-3.1-12/s20x/man/stripqq.Rd | 58 +--
s20x-3.1-12/s20x/man/summary1way.Rd | 106 +++---
s20x-3.1-12/s20x/man/summary2way.Rd | 94 +++---
s20x-3.1-12/s20x/man/summaryStats.Rd | 112 +++----
s20x-3.1-12/s20x/man/teach.df.Rd | 36 +-
s20x-3.1-12/s20x/man/technitron.df.Rd | 46 +-
s20x-3.1-12/s20x/man/thyroid.df.Rd | 36 +-
s20x-3.1-12/s20x/man/toothpaste.df.Rd | 34 +-
s20x-3.1-12/s20x/man/trendscatter.Rd | 1
s20x-3.1-12/s20x/man/zoo.df.Rd | 42 +-
69 files changed, 1566 insertions(+), 1573 deletions(-)
Title: Plot Spatial or Spatio-Temporal Data Over Google Maps
Diff between plotGoogleMaps versions 2.1 dated 2014-06-19 and 2.2 dated 2015-02-13
More information about plotGoogleMaps at CRAN
Description: Provides an interactive plot device for handling the geographic data for web browsers, designed for the automatic creation of web maps as a combination of users' data and Google Maps layers.
Author: Milan Kilibarda
Maintainer: Milan Kilibarda
plotGoogleMaps-2.1/plotGoogleMaps/build |only
plotGoogleMaps-2.1/plotGoogleMaps/inst/doc |only
plotGoogleMaps-2.1/plotGoogleMaps/vignettes |only
plotGoogleMaps-2.2/plotGoogleMaps/DESCRIPTION | 13
plotGoogleMaps-2.2/plotGoogleMaps/MD5 | 41 -
plotGoogleMaps-2.2/plotGoogleMaps/R/PolyCol.R | 195 +++---
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleGoogleMaps.R | 102 ++-
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleLegend.R | 124 ++--
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleSP.R | 147 +++--
plotGoogleMaps-2.2/plotGoogleMaps/R/createInfoWindowEvent.R | 15
plotGoogleMaps-2.2/plotGoogleMaps/R/createInfoWindowEventM.R | 9
plotGoogleMaps-2.2/plotGoogleMaps/R/ellipseGoogleMaps.R | 2
plotGoogleMaps-2.2/plotGoogleMaps/R/mcGoogleMaps.R | 10
plotGoogleMaps-2.2/plotGoogleMaps/R/pieSP.R | 308 +++++------
plotGoogleMaps-2.2/plotGoogleMaps/R/plotGoogleMaps.R | 19
plotGoogleMaps-2.2/plotGoogleMaps/R/segmentGoogleMaps.R | 2
plotGoogleMaps-2.2/plotGoogleMaps/man/bubbleGoogleMaps.Rd | 286 +++++-----
plotGoogleMaps-2.2/plotGoogleMaps/man/ellipseGoogleMaps.Rd | 268 ++++-----
plotGoogleMaps-2.2/plotGoogleMaps/man/mcGoogleMaps.Rd | 8
plotGoogleMaps-2.2/plotGoogleMaps/man/pieSP.Rd | 98 +--
plotGoogleMaps-2.2/plotGoogleMaps/man/plotGoogleMaps.Rd | 4
plotGoogleMaps-2.2/plotGoogleMaps/man/segmentGoogleMaps.Rd | 2
22 files changed, 862 insertions(+), 791 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-14 0.3
2005-12-13 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-15 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-26 1.5.1
2013-06-19 1.5.0
2008-08-27 1.3.3
2008-08-25 1.3.2
2008-03-21 1.2.0
2007-09-10 1.1.6.3
Title: Maxwell Bolzano Bose Einstein Fermi Dirac Distribution and
Exposure Curve
Diff between mbbefd versions 0.5.0.1 dated 2015-01-16 and 0.6 dated 2015-02-13
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi Dirac (MBBEFD) distribution (distribution, density, quantile, random generation functions) as well as MBBEFD exposure curve, used in actuarial application to price reinsurance contracts. The vignette shows code snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato
DESCRIPTION | 12 ++++++----
MD5 | 36 ++++++++++++++++++-------------
NAMESPACE | 6 ++++-
NEWS | 7 +++---
R/RcppExports.R |only
R/distributionDefinition.R | 44 +++++++++++++++++++++-----------------
R/zzz.R |only
inst/CITATION | 4 +--
inst/doc/mbbefd.R | 4 +--
inst/doc/mbbefd.Rnw | 12 +++++-----
inst/doc/mbbefd.pdf |binary
man/exposureCurve.Rd | 5 ----
man/g2a.Rd |only
man/mbbefd-package.Rd | 4 +--
src |only
vignettes/mbbefd-distrPlot.pdf |binary
vignettes/mbbefd-drateplot.pdf |binary
vignettes/mbbefd-survivalPlot.pdf |only
vignettes/mbbefd.Rnw | 12 +++++-----
vignettes/mbbefd.bib | 9 +++++++
vignettes/mbbefd.tex | 8 +++---
21 files changed, 93 insertions(+), 70 deletions(-)
Title: Plot a Correlogram
Diff between corrgram versions 1.6 dated 2014-08-28 and 1.7 dated 2015-02-13
Description: Calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals.
Author: Kevin Wright
Maintainer: Kevin Wright
corrgram-1.6/corrgram/inst/doc/corrgram_examples.rnw |only
corrgram-1.6/corrgram/vignettes/corrgram_examples.rnw |only
corrgram-1.7/corrgram/DESCRIPTION | 12 +++----
corrgram-1.7/corrgram/MD5 | 30 +++++++++---------
corrgram-1.7/corrgram/NEWS | 6 +++
corrgram-1.7/corrgram/R/corrgram.r | 10 ++++++
corrgram-1.7/corrgram/build/vignette.rds |binary
corrgram-1.7/corrgram/data/auto.rda |binary
corrgram-1.7/corrgram/data/baseball.rda |binary
corrgram-1.7/corrgram/data/vote.rda |binary
corrgram-1.7/corrgram/inst/doc/corrgram_examples.R | 3 -
corrgram-1.7/corrgram/inst/doc/corrgram_examples.Rnw |only
corrgram-1.7/corrgram/inst/doc/corrgram_examples.pdf |binary
corrgram-1.7/corrgram/man/baseball.Rd | 2 -
corrgram-1.7/corrgram/man/corrgram.Rd | 8 +++-
corrgram-1.7/corrgram/tests/misc.r | 7 +++-
corrgram-1.7/corrgram/tests/spearman.r | 29 -----------------
corrgram-1.7/corrgram/vignettes/corrgram_examples.Rnw |only
18 files changed, 49 insertions(+), 58 deletions(-)
Title: Voxelwise Semiparametrics
Diff between vows versions 0.3.1 dated 2015-01-08 and 0.4 dated 2015-02-12
Description: Parametric and semiparametric inference for massively parallel
models, i.e., a large number of models with common design matrix, as often
occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, Ruixin Tan, and Rong Jiao
Maintainer: Philip Reiss
vows-0.3.1/vows/R/vows_0.3-package.R |only
vows-0.4/vows/DESCRIPTION | 15 --
vows-0.4/vows/MD5 | 74 +++++-----
vows-0.4/vows/NAMESPACE | 9 +
vows-0.4/vows/R/R2nii.R | 62 ++++----
vows-0.4/vows/R/nii2R.R | 178 ++++++++++++------------
vows-0.4/vows/R/rlrt4d.R | 73 +++++-----
vows-0.4/vows/R/vows-internal.R | 135 +++++++++---------
vows-0.4/vows/R/vows-mgcv.R | 250 +++++++++++++++++------------------
vows-0.4/vows/R/vows_0.4-package.R |only
vows-0.4/vows/man/F.mp.Rd | 3
vows-0.4/vows/man/Fdr.rlrt.Rd | 3
vows-0.4/vows/man/R2nii.Rd | 7
vows-0.4/vows/man/extract.fd.Rd | 3
vows-0.4/vows/man/funkmeans.Rd | 3
vows-0.4/vows/man/funkmeans4d.Rd | 3
vows-0.4/vows/man/funkpanel.Rd | 3
vows-0.4/vows/man/lm.mp.Rd | 3
vows-0.4/vows/man/lm4d.Rd | 3
vows-0.4/vows/man/nii2R.Rd | 7
vows-0.4/vows/man/permF.mp.Rd | 3
vows-0.4/vows/man/plot.funkmeans.Rd | 3
vows-0.4/vows/man/plot.rlrt4d.Rd | 3
vows-0.4/vows/man/plot.semipar.mp.Rd | 3
vows-0.4/vows/man/qplsc.mp.Rd | 3
vows-0.4/vows/man/rlrt.mp.Rd | 9 -
vows-0.4/vows/man/rlrt.mp.fit.Rd | 3
vows-0.4/vows/man/rlrt4d.Rd | 5
vows-0.4/vows/man/rlrtpanel.Rd | 3
vows-0.4/vows/man/screen.vox.Rd | 3
vows-0.4/vows/man/semipar.mix.mp.Rd | 3
vows-0.4/vows/man/semipar.mp.Rd | 3
vows-0.4/vows/man/semipar4d.Rd | 3
vows-0.4/vows/man/sf.Rd | 3
vows-0.4/vows/man/summary.lm.mp.Rd | 3
vows-0.4/vows/man/test.Rd | 3
vows-0.4/vows/man/vows-internal.Rd | 10 +
vows-0.4/vows/man/vows-mgcv.Rd | 3
vows-0.4/vows/man/vows-package.Rd | 5
39 files changed, 478 insertions(+), 430 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Diff between StereoMorph versions 1.2.1 dated 2014-09-02 and 1.3 dated 2015-02-12
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen
DESCRIPTION | 13
MD5 | 42 +-
NAMESPACE | 22 +
R/digitizeImage.R | 40 +-
R/dltCalibrateCameras.R | 276 +++++++++++++---
R/dltMatchCurvePoints.R | 5
R/findCheckerboardCorners.R | 77 +++-
R/inverseGridTransform.R |only
inst/extdata/apps/digitizeImage/digitize_image.html | 2
inst/extdata/apps/digitizeImage/digitize_image_pre.html | 16
inst/extdata/apps/digitizeImage/initial_parameters.R | 45 +-
inst/extdata/apps/digitizeImage/server.R | 12
inst/extdata/apps/digitizeImage/www/digitize_image.css | 12
inst/extdata/apps/digitizeImage/www/digitize_image.js | 59 ++-
inst/extdata/apps/digitizeImage/www/help.html | 31 +
inst/extdata/apps/initial_parameters.R |only
man/StereoMorph-package.Rd | 6
man/digitizeImage.Rd | 2
man/dltCalibrateCameras.Rd | 41 +-
man/dltMatchCurvePoints.Rd | 3
man/dltReconstruct.Rd | 2
man/findCheckerboardCorners.Rd | 16
src/Makevars.win | 10
23 files changed, 552 insertions(+), 180 deletions(-)
Title: Spherical K-Function
Diff between SphericalK versions 1.0 dated 2014-11-26 and 1.1 dated 2015-02-12
Description: Spherical K-function for point-pattern analysis on the sphere.
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
R/SphericalK.R | 3 ++-
man/Hex272.Rd | 2 +-
man/Hex92.Rd | 2 +-
man/SphericalK-package.Rd | 4 ++--
man/sphere_grid.Rd | 2 +-
man/sphere_khat.Rd | 4 ++--
man/sphere_montekhat.Rd | 2 +-
man/sphere_random.Rd | 4 ++--
10 files changed, 27 insertions(+), 26 deletions(-)
Title: Tools for Simplifying the Population and Querying of SQLite
Databases
Diff between poplite versions 0.99.5 dated 2014-11-05 and 0.99.16 dated 2015-02-12
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
Author: Daniel Bottomly [cre, aut],
Shannon McWeeney [aut],
Beth Wilmot [aut]
Maintainer: Daniel Bottomly
DESCRIPTION | 22 +-
MD5 | 21 +-
NAMESPACE | 4
R/Database.R | 375 ++++++++++++++++++++++++++++++------------
R/external_funcs.R | 57 ++++--
R/tableSchemaList.R | 49 +++++
README.md |only
build/vignette.rds |binary
data/clinical.rda |binary
inst/doc/poplite.pdf |binary
tests/testthat.R | 92 ++++++++++
tests/testthat/test-poplite.R | 94 ++++++++++
12 files changed, 570 insertions(+), 144 deletions(-)
Title: Geometric Morphometric Analyses of 2d/3D Landmark Data
Diff between geomorph versions 2.1.2 dated 2014-11-04 and 2.1.3 dated 2015-02-12
Description: Geomorph allows users to read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.1.2/geomorph/R/plotAllometry.r |only
geomorph-2.1.3/geomorph/DESCRIPTION | 16
geomorph-2.1.3/geomorph/MD5 | 188 ++--
geomorph-2.1.3/geomorph/NAMESPACE | 5
geomorph-2.1.3/geomorph/NEWS | 29
geomorph-2.1.3/geomorph/R/advanced.procD.lm.r | 12
geomorph-2.1.3/geomorph/R/bilat.symmetry.r | 50 -
geomorph-2.1.3/geomorph/R/build.template.r | 190 ++--
geomorph-2.1.3/geomorph/R/compare.evol.rates.r | 8
geomorph-2.1.3/geomorph/R/compare.modular.partitions.r | 3
geomorph-2.1.3/geomorph/R/define.links.R |only
geomorph-2.1.3/geomorph/R/define.modules.R | 86 +
geomorph-2.1.3/geomorph/R/define.sliders.3d.r | 188 ++--
geomorph-2.1.3/geomorph/R/digit.fixed.r | 250 ++---
geomorph-2.1.3/geomorph/R/digitsurface.r | 198 ++--
geomorph-2.1.3/geomorph/R/editTemplate.r | 114 +-
geomorph-2.1.3/geomorph/R/geomorph.support.code.r | 621 +++++++-------
geomorph-2.1.3/geomorph/R/pairwise.slope.test.r | 40
geomorph-2.1.3/geomorph/R/pairwiseD.test.r | 41
geomorph-2.1.3/geomorph/R/phylo.pls.R | 33
geomorph-2.1.3/geomorph/R/physignal.r | 37
geomorph-2.1.3/geomorph/R/plotAllometry.R |only
geomorph-2.1.3/geomorph/R/plotOutliers.R |only
geomorph-2.1.3/geomorph/R/plotRefToTarget.r | 17
geomorph-2.1.3/geomorph/R/plotTangentSpace.r | 253 ++---
geomorph-2.1.3/geomorph/R/procD.lm.r | 7
geomorph-2.1.3/geomorph/R/procD.pgls.r | 11
geomorph-2.1.3/geomorph/R/read.ply.r | 7
geomorph-2.1.3/geomorph/R/readland.tps.r | 72 +
geomorph-2.1.3/geomorph/R/trajectory.analysis.r | 410 +++++----
geomorph-2.1.3/geomorph/data/hummingbirds.rda |binary
geomorph-2.1.3/geomorph/data/mosquito.rda |binary
geomorph-2.1.3/geomorph/data/motionpaths.rda |binary
geomorph-2.1.3/geomorph/data/plethShapeFood.rda |binary
geomorph-2.1.3/geomorph/data/plethodon.rda |binary
geomorph-2.1.3/geomorph/data/plethspecies.rda |binary
geomorph-2.1.3/geomorph/data/pupfish.rda |binary
geomorph-2.1.3/geomorph/data/ratland.rda |binary
geomorph-2.1.3/geomorph/data/scallopPLY.rda |binary
geomorph-2.1.3/geomorph/data/scallops.rda |binary
geomorph-2.1.3/geomorph/man/advanced.procD.lm.Rd | 5
geomorph-2.1.3/geomorph/man/arrayspecs.Rd | 3
geomorph-2.1.3/geomorph/man/bilat.symmetry.Rd | 3
geomorph-2.1.3/geomorph/man/buildtemplate.Rd | 7
geomorph-2.1.3/geomorph/man/compare.evol.rates.Rd | 3
geomorph-2.1.3/geomorph/man/compare.modular.partitions.Rd | 6
geomorph-2.1.3/geomorph/man/define.links.Rd |only
geomorph-2.1.3/geomorph/man/define.modules.Rd | 23
geomorph-2.1.3/geomorph/man/define.sliders.2d.Rd | 3
geomorph-2.1.3/geomorph/man/define.sliders.3d.Rd | 15
geomorph-2.1.3/geomorph/man/digit.fixed.Rd | 7
geomorph-2.1.3/geomorph/man/digitize2d.Rd | 3
geomorph-2.1.3/geomorph/man/digitsurface.Rd | 7
geomorph-2.1.3/geomorph/man/editTemplate.Rd | 7
geomorph-2.1.3/geomorph/man/estimate.missing.Rd | 3
geomorph-2.1.3/geomorph/man/findMeanSpec.Rd | 3
geomorph-2.1.3/geomorph/man/fixed.angle.Rd | 3
geomorph-2.1.3/geomorph/man/geomorph-package.Rd | 3
geomorph-2.1.3/geomorph/man/gpagen.Rd | 3
geomorph-2.1.3/geomorph/man/hummingbirds.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.disparity.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.integr.Rd | 3
geomorph-2.1.3/geomorph/man/mosquito.Rd | 3
geomorph-2.1.3/geomorph/man/motionpaths.Rd | 3
geomorph-2.1.3/geomorph/man/mshape.Rd | 3
geomorph-2.1.3/geomorph/man/pairwise.slope.test.Rd | 19
geomorph-2.1.3/geomorph/man/pairwiseD.test.Rd | 15
geomorph-2.1.3/geomorph/man/phylo.pls.Rd | 5
geomorph-2.1.3/geomorph/man/physignal.Rd | 5
geomorph-2.1.3/geomorph/man/plethShapeFood.Rd | 3
geomorph-2.1.3/geomorph/man/plethodon.Rd | 3
geomorph-2.1.3/geomorph/man/plethspecies.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllSpecimens.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllometry.Rd | 15
geomorph-2.1.3/geomorph/man/plotGMPhyloMorphoSpace.Rd | 3
geomorph-2.1.3/geomorph/man/plotOutliers.Rd |only
geomorph-2.1.3/geomorph/man/plotRefToTarget.Rd | 15
geomorph-2.1.3/geomorph/man/plotTangentSpace.Rd | 13
geomorph-2.1.3/geomorph/man/plotspec.Rd | 3
geomorph-2.1.3/geomorph/man/procD.lm.Rd | 7
geomorph-2.1.3/geomorph/man/procD.pgls.Rd | 9
geomorph-2.1.3/geomorph/man/pupfish.Rd | 13
geomorph-2.1.3/geomorph/man/ratland.Rd | 3
geomorph-2.1.3/geomorph/man/read.morphologika.Rd | 3
geomorph-2.1.3/geomorph/man/read.ply.Rd | 10
geomorph-2.1.3/geomorph/man/readland.nts.Rd | 3
geomorph-2.1.3/geomorph/man/readland.tps.Rd | 17
geomorph-2.1.3/geomorph/man/readmulti.nts.Rd | 3
geomorph-2.1.3/geomorph/man/scallopPLY.Rd | 3
geomorph-2.1.3/geomorph/man/scallops.Rd | 3
geomorph-2.1.3/geomorph/man/trajectory.analysis.Rd | 27
geomorph-2.1.3/geomorph/man/two.b.pls.Rd | 3
geomorph-2.1.3/geomorph/man/two.d.array.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefMesh.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefOutline.Rd | 3
geomorph-2.1.3/geomorph/man/writeland.tps.Rd | 3
geomorph-2.1.3/geomorph/src/Makevars | 2
geomorph-2.1.3/geomorph/src/Makevars.win | 2
98 files changed, 1790 insertions(+), 1446 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Diff between MXM versions 0.2.1 dated 2014-08-04 and 0.3 dated 2015-02-12
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou
MXM-0.2.1/MXM/man/SES-internal.Rd |only
MXM-0.3/MXM/DESCRIPTION | 11 ++--
MXM-0.3/MXM/MD5 | 28 +++++------
MXM-0.3/MXM/NAMESPACE | 18 ++++++-
MXM-0.3/MXM/R/SES.R | 14 ++---
MXM-0.3/MXM/R/censIndLR.R | 8 +--
MXM-0.3/MXM/R/gSquare.R | 8 +--
MXM-0.3/MXM/R/testIndFisher.R | 38 +++++++++------
MXM-0.3/MXM/R/testIndLogistic.R | 32 ++++++-------
MXM-0.3/MXM/man/MXM-internal.Rd |only
MXM-0.3/MXM/man/MXM-package.Rd | 2
MXM-0.3/MXM/man/SES.Rd | 6 ++
MXM-0.3/MXM/man/SESoutput-class.Rd | 5 ++
MXM-0.3/MXM/man/censIndLR.Rd | 36 +++++++-------
MXM-0.3/MXM/man/gSquare.Rd | 25 +++++-----
MXM-0.3/MXM/man/testIndLogistic.Rd | 89 ++++++++++++++++++++-----------------
16 files changed, 182 insertions(+), 138 deletions(-)
Title: All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS)
and Estimating Multivariate Volatility Models
Diff between MTS versions 0.32 dated 2014-03-01 and 0.33 dated 2015-02-12
Description: Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index, transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
Author: Ruey S. Tsay
Maintainer: Ruey S. Tsay
DESCRIPTION | 12
MD5 | 21 -
R/MTS.R | 777 +++++++++++++++++++++++++++++++++++++++++++++++++----
R/VARMACpp.R | 4
R/sVARMACpp.R | 8
man/BVAR.Rd | 2
man/Btfm2.Rd |only
man/GrangerTest.Rd |only
man/MTS-package.Rd | 4
man/tfm.Rd | 2
man/tfm1.Rd | 11
man/tfm2.Rd |only
src/varma.cpp | 361 +++++++++++++++---------
13 files changed, 982 insertions(+), 220 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.4-1 dated 2014-12-15 and 2.4-2 dated 2015-02-12
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++--
MD5 | 31 ++++++++---------
NAMESPACE | 4 +-
R/bl.R | 5 +-
R/bmono.R | 2 -
R/bmrf.R | 4 +-
R/brad.R | 5 --
R/btree.R | 2 -
inst/CITATION | 69 +++++++++++++++++++++++++-------------
inst/NEWS.Rd | 25 +++++++++++++
inst/doc/SurvivalEnsembles.pdf |binary
inst/doc/mboost.pdf |binary
inst/doc/mboost_illustrations.pdf |binary
inst/doc/mboost_tutorial.pdf |binary
man/blackboost.Rd | 18 +++++----
man/helper.Rd |only
man/mboost_package.Rd | 9 +++-
17 files changed, 117 insertions(+), 65 deletions(-)
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Diff between gaselect versions 1.0.4 dated 2015-02-10 and 1.0.5 dated 2015-02-12
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger
Maintainer: David Kepplinger
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
src/BICEvaluator.cpp | 4 ++--
src/LMEvaluator.cpp | 2 +-
src/PLSEvaluator.cpp | 2 +-
6 files changed, 16 insertions(+), 12 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.1 dated 2015-01-13 and 1.2 dated 2015-02-12
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 8 -
MD5 | 46 +++----
NAMESPACE | 6
R/BAT.R | 294 +++++++++++++++++++++++++++++++++++++++++++++--
man/accuracy.Rd | 3
man/alpha.Rd | 3
man/alpha.accum.Rd | 3
man/alpha.estimate.Rd | 3
man/arrabida.Rd | 3
man/beta.Rd | 3
man/beta.accum.Rd | 3
man/beta.multi.Rd | 3
man/functree.Rd | 3
man/geres.Rd | 3
man/guadiana.Rd | 3
man/optim.alpha.Rd |only
man/optim.alpha.stats.Rd |only
man/optim.beta.Rd |only
man/optim.beta.stats.Rd |only
man/phylotree.Rd | 3
man/sim.plot.Rd | 3
man/sim.sad.Rd | 3
man/sim.sample.Rd | 3
man/sim.spatial.Rd | 3
man/sim.tree.Rd | 13 +-
man/slope.Rd | 3
26 files changed, 359 insertions(+), 59 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Diff between glmm versions 1.0 dated 2015-02-11 and 1.0.1 dated 2015-02-12
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson
DESCRIPTION | 8 +-
MD5 | 4 -
src/objfunc.c | 187 ++++++++++++++++++++++++++++------------------------------
3 files changed, 98 insertions(+), 101 deletions(-)
Title: Calculate Generalized Eigenvalues of a Matrix Pair
Diff between geigen versions 1.4 dated 2014-08-18 and 1.5 dated 2015-02-12
Description: Compute generalized eigenvalues and eigenvectors of a pair of matrices,
using routines from Lapack (dggev and zggev). Compute the
generalized Schur decomposition of a pair of matrices using Lapack routines.
In the latter case options for ordering the generalized eigenvalues are provided.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
NEWS | 5 +++++
R/cmplxdiv.R | 14 +++++++-------
inst/CITATION | 8 ++++----
man/geigen-package.Rd | 10 +++++-----
man/geigen.Rd | 10 +++++-----
man/gevalues.Rd | 10 +++++-----
8 files changed, 44 insertions(+), 39 deletions(-)
Title: Estimability Tools for Linear Models
Diff between estimability versions 1.0-2 dated 2015-01-31 and 1.1 dated 2015-02-12
Description: Provides tools for determining estimability of linear functions of regression coefficients,
and 'epredict' methods that handle non-estimable cases correctly.
Author: Russell V. Lenth
Maintainer: Russell V. Lenth
DESCRIPTION | 12 +++----
MD5 | 13 ++++----
NAMESPACE | 14 ++++++---
R/epredict.lm.R | 79 ++++++++++++++++++++++++++++++++++------------------
R/estimability.R | 30 +++++++++++++++----
inst |only
man/epredict.lm.Rd | 66 ++++++++++++++++++++++++++++++++-----------
man/nonest.basis.Rd | 38 +++++++++++++++++--------
8 files changed, 174 insertions(+), 78 deletions(-)
Title: Multiple Hypothesis Testing
Diff between sgof versions 2.1.1 dated 2014-10-23 and 2.2 dated 2015-02-11
Description: seven different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez
Maintainer: Irene Castro Conde
DESCRIPTION | 17 +++++++++--------
MD5 | 41 ++++++++++++++++++++++-------------------
NAMESPACE | 2 ++
R/BBSGoF.R | 9 +++++++--
R/BH.R | 2 +-
R/BY.R | 2 +-
R/Bayesian.SGoF.R | 2 +-
R/Binomial.SGoF.R | 2 +-
R/Discrete.SGoF.R |only
R/SGoF.R | 2 +-
R/print.Discrete.SGoF.R |only
man/BBSGoF.Rd | 9 +++++----
man/BH.Rd | 2 +-
man/BY.Rd | 4 ++--
man/Bayesian.SGoF.Rd | 2 +-
man/Binomial.SGoF.Rd | 6 +++---
man/Discrete.SGoF.Rd |only
man/SGoF.Rd | 6 +++---
man/plot.Binomial.SGoF.Rd | 2 +-
man/plot.SGoF.Rd | 3 ++-
man/sgof-package.Rd | 37 +++++++++++++++++++++++++++++--------
man/summary.Binomial.SGoF.Rd | 2 +-
man/summary.SGoF.Rd | 2 +-
23 files changed, 94 insertions(+), 60 deletions(-)
Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Diff between RSNPset versions 0.3 dated 2014-12-16 and 0.4 dated 2015-02-11
Description: RSNPset is an implementation of the use of efficient score statistics
in genome-wide SNP set analysis with complex traits. The package provides three standard
score statistics (Cox, binomial, and Gaussian) but is easily extensible to include
others. Code implementing the inferential procedure is primarily written in C++ and
utilizes parallelization of the analysis to reduce runtime. A supporting function offers
simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
DESCRIPTION | 10 +-
MD5 | 31 +++----
NEWS |only
R/rsnpset.R | 184 ++++++++++++++++++++++++------------------
R/rsnpset.pvalue.R | 2
R/summary.RSNPset.R | 4
R/summary.RSNPset.pvalue.R | 4
inst/doc/rsnpset.R | 15 ++-
inst/doc/rsnpset.Rnw | 161 ++++++++++++++++++++++++++----------
inst/doc/rsnpset.pdf |binary
man/RSNPset-package.Rd | 16 +--
man/rsnpset.Rd | 44 +++++-----
man/rsnpset.pvalue.Rd | 30 +++---
man/summary.RSNPset.Rd | 33 +++----
man/summary.RSNPset.pvalue.Rd | 22 ++---
src/rsnpset.cpp | 60 ++++++++++---
vignettes/rsnpset.Rnw | 161 ++++++++++++++++++++++++++----------
17 files changed, 502 insertions(+), 275 deletions(-)
Title: Selection of K in K-Means Clustering
Diff between kselection versions 0.1.1 dated 2014-10-17 and 0.2.0 dated 2015-02-11
Description: Selection of k in k-means clustering based on Pham et al. paper
``Selection of k in k-means clustering''.
Author: Daniel Rodriguez
Maintainer: Daniel Rodriguez
kselection-0.1.1/kselection/inst |only
kselection-0.2.0/kselection/DESCRIPTION | 18 -
kselection-0.2.0/kselection/MD5 | 30 +--
kselection-0.2.0/kselection/NAMESPACE | 2
kselection-0.2.0/kselection/NEWS | 9
kselection-0.2.0/kselection/R/kselection.R | 6
kselection-0.2.0/kselection/R/pham.R | 173 +++++++++++-------
kselection-0.2.0/kselection/man/get_f_k.Rd | 5
kselection-0.2.0/kselection/man/get_k_threshold.Rd | 5
kselection-0.2.0/kselection/man/kselection-package.Rd | 9
kselection-0.2.0/kselection/man/kselection.Rd | 34 ++-
kselection-0.2.0/kselection/man/num_clusters.Rd | 5
kselection-0.2.0/kselection/man/num_clusters_all.Rd | 5
kselection-0.2.0/kselection/man/set_k_threshold.Rd | 5
kselection-0.2.0/kselection/tests |only
15 files changed, 190 insertions(+), 116 deletions(-)
Title: Bootstrap 2 Web Components for Use with Shiny
Diff between shinybootstrap2 versions 0.2 dated 2015-01-22 and 0.2.1 dated 2015-02-11
More information about shinybootstrap2 at CRAN
Description: Provides Bootstrap 2 web components for use with the Shiny
package. With versions of Shiny prior to 0.11, these Bootstrap 2 components
were included as part of the package. Later versions of Shiny include
Bootstrap 3, so the Bootstrap 2 components have been moved into this
package for those uses who rely on features specific to Bootstrap 2.
Author: Winston Chang [aut, cre],
RStudio [cph],
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library; authors listed at
https://github.com/twbs/bootstrap/graphs/contributors),
Twitter, Inc [cph] (Bootstrap library),
Brian Reavis [ctb, cph] (selectize.js library),
Egor Khmelev [ctb, cph] (jslider library),
SpryMedia Limited [ctb, cph] (DataTables library)
Maintainer: Winston Chang
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
NEWS |only
R/output-datatable.R | 28 +++++++++++++++-------------
README.md | 2 +-
5 files changed, 24 insertions(+), 21 deletions(-)
Permanent link
Title: Phylogenetics for the Environmental Sciences
Diff between pez versions 0.9-0 dated 2014-11-07 and 1.0-0 dated 2015-02-11
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('shape', 'evenness', 'dispersion',
and 'dissimilarity' metrics). Implementation of Cavender-Bares
(2004) correlation of phylogenetic and ecological matrices
('fingerprint.regression'). Phylogenetic Generalised Linear Mixed
Models (PGLMMs) following ('pglmm') following Ives & Helmus (2011)
and Rafferty & Ives (2013). Simulation of null assemblages,
traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse
pez-0.9-0/pez/inst/tests/vert.txt |only
pez-1.0-0/pez/DESCRIPTION | 19 +-
pez-1.0-0/pez/MD5 | 40 ++---
pez-1.0-0/pez/NAMESPACE | 29 +++-
pez-1.0-0/pez/NEWS |only
pez-1.0-0/pez/R/comparative.comm.R | 101 +++++++++++++-
pez-1.0-0/pez/R/dispersion.R | 8 -
pez-1.0-0/pez/R/dissimilarity.R | 8 -
pez-1.0-0/pez/R/evenness.R | 8 -
pez-1.0-0/pez/R/pglmm.R |only
pez-1.0-0/pez/R/phy.signal.R | 6
pez-1.0-0/pez/R/plotting.R | 8 -
pez-1.0-0/pez/R/shape.R | 23 +--
pez-1.0-0/pez/R/utility.R | 10 +
pez-1.0-0/pez/inst/doc/pez-intro.R | 61 ++++++++
pez-1.0-0/pez/inst/doc/pez-intro.Rnw | 163 +++++++++++++++++++++--
pez-1.0-0/pez/inst/doc/pez-intro.pdf |binary
pez-1.0-0/pez/inst/tests/test_comparative.comm.R | 57 +++++---
pez-1.0-0/pez/inst/tests/test_shape.R | 4
pez-1.0-0/pez/man/cc.manip.Rd | 49 ++++++
pez-1.0-0/pez/man/pglmm.Rd |only
pez-1.0-0/pez/man/plot.comparative.comm.Rd | 5
pez-1.0-0/pez/vignettes/pez-intro.Rnw | 163 +++++++++++++++++++++--
23 files changed, 629 insertions(+), 133 deletions(-)
Title: Smoothing Splines for Large Samples
Diff between bigsplines versions 1.0-4 dated 2014-10-03 and 1.0-5 dated 2015-02-11
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Parametric predictors are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
bigsplines-1.0-4/bigsplines/R/predict.css.R |only
bigsplines-1.0-4/bigsplines/R/predict.ssa.R |only
bigsplines-1.0-4/bigsplines/R/predict.ssg.R |only
bigsplines-1.0-4/bigsplines/R/predict.ssp.R |only
bigsplines-1.0-4/bigsplines/R/predict.tps.R |only
bigsplines-1.0-4/bigsplines/R/print.css.R |only
bigsplines-1.0-4/bigsplines/R/print.ssa.R |only
bigsplines-1.0-4/bigsplines/R/print.ssg.R |only
bigsplines-1.0-4/bigsplines/R/print.ssp.R |only
bigsplines-1.0-4/bigsplines/R/print.summary.css.R |only
bigsplines-1.0-4/bigsplines/R/print.summary.ssa.R |only
bigsplines-1.0-4/bigsplines/R/print.summary.ssg.R |only
bigsplines-1.0-4/bigsplines/R/print.summary.ssp.R |only
bigsplines-1.0-4/bigsplines/R/print.summary.tps.R |only
bigsplines-1.0-4/bigsplines/R/print.tps.R |only
bigsplines-1.0-4/bigsplines/R/summary.css.R |only
bigsplines-1.0-4/bigsplines/R/summary.ssa.R |only
bigsplines-1.0-4/bigsplines/R/summary.ssg.R |only
bigsplines-1.0-4/bigsplines/R/summary.ssp.R |only
bigsplines-1.0-4/bigsplines/R/summary.tps.R |only
bigsplines-1.0-4/bigsplines/man/predict.css.Rd |only
bigsplines-1.0-4/bigsplines/man/predict.ssa.Rd |only
bigsplines-1.0-4/bigsplines/man/predict.ssg.Rd |only
bigsplines-1.0-4/bigsplines/man/predict.ssp.Rd |only
bigsplines-1.0-4/bigsplines/man/predict.tps.Rd |only
bigsplines-1.0-5/bigsplines/ChangeLog | 32 ++++
bigsplines-1.0-5/bigsplines/DESCRIPTION | 8 -
bigsplines-1.0-5/bigsplines/MD5 | 117 ++++++++--------
bigsplines-1.0-5/bigsplines/NAMESPACE | 23 +++
bigsplines-1.0-5/bigsplines/R/bigspline.R | 4
bigsplines-1.0-5/bigsplines/R/bigssa.R | 10 -
bigsplines-1.0-5/bigsplines/R/bigssg.R | 9 -
bigsplines-1.0-5/bigsplines/R/bigssp.R | 10 -
bigsplines-1.0-5/bigsplines/R/bigtps.R | 4
bigsplines-1.0-5/bigsplines/R/gcvgss.R | 79 ++++++++--
bigsplines-1.0-5/bigsplines/R/gcvssg.R | 75 ++++++++--
bigsplines-1.0-5/bigsplines/R/imagebar.R | 1
bigsplines-1.0-5/bigsplines/R/lamcoefg.R | 77 ++++++++--
bigsplines-1.0-5/bigsplines/R/lamloopg.R | 75 ++++++++--
bigsplines-1.0-5/bigsplines/R/makeZtX.R |only
bigsplines-1.0-5/bigsplines/R/makeZtZ.R |only
bigsplines-1.0-5/bigsplines/R/makessa.R | 48 +++++-
bigsplines-1.0-5/bigsplines/R/makessg.R | 13 +
bigsplines-1.0-5/bigsplines/R/makessp.R | 49 +++++-
bigsplines-1.0-5/bigsplines/R/predict.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigssg.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigssp.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigtps.R |only
bigsplines-1.0-5/bigsplines/R/print.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/print.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/print.bigssg.R |only
bigsplines-1.0-5/bigsplines/R/print.bigssp.R |only
bigsplines-1.0-5/bigsplines/R/print.bigtps.R |only
bigsplines-1.0-5/bigsplines/R/print.summary.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/print.summary.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/print.summary.bigssg.R |only
bigsplines-1.0-5/bigsplines/R/print.summary.bigssp.R |only
bigsplines-1.0-5/bigsplines/R/print.summary.bigtps.R |only
bigsplines-1.0-5/bigsplines/R/remlri.R |only
bigsplines-1.0-5/bigsplines/R/remlvc.R |only
bigsplines-1.0-5/bigsplines/R/smartssg.R | 14 -
bigsplines-1.0-5/bigsplines/R/ssawork.R | 82 ++++++++++-
bigsplines-1.0-5/bigsplines/R/ssblup.R |only
bigsplines-1.0-5/bigsplines/R/ssgwork.R | 30 ++--
bigsplines-1.0-5/bigsplines/R/sspwork.R | 76 ++++++++++
bigsplines-1.0-5/bigsplines/R/summary.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssg.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssp.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigtps.R |only
bigsplines-1.0-5/bigsplines/man/bigspline.Rd | 4
bigsplines-1.0-5/bigsplines/man/bigsplines-internal.Rd | 5
bigsplines-1.0-5/bigsplines/man/bigssa.Rd | 25 +++
bigsplines-1.0-5/bigsplines/man/bigssg.Rd | 20 ++
bigsplines-1.0-5/bigsplines/man/bigssp.Rd | 25 +++
bigsplines-1.0-5/bigsplines/man/bigtps.Rd | 2
bigsplines-1.0-5/bigsplines/man/makessa.Rd | 14 +
bigsplines-1.0-5/bigsplines/man/makessg.Rd | 6
bigsplines-1.0-5/bigsplines/man/makessp.Rd | 14 +
bigsplines-1.0-5/bigsplines/man/predict.bigspline.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigssa.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigssg.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigssp.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigtps.Rd |only
bigsplines-1.0-5/bigsplines/man/print.Rd | 62 ++++----
bigsplines-1.0-5/bigsplines/man/summary.Rd | 39 ++---
87 files changed, 806 insertions(+), 246 deletions(-)
Title: Tree-Based Varying Coefficient Regression for Generalized Linear
and Ordinal Mixed Models
Diff between vcrpart versions 0.3-1 dated 2015-01-04 and 0.3-2 dated 2015-02-11
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph],
Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin
DESCRIPTION | 9 +-
MD5 | 50 +++++++-------
NEWS | 18 +++++
R/olmm-methods.R | 129 ++++++++++++++++++++++---------------
R/olmm.R | 10 +-
R/utils.R | 20 +++--
ToDo | 4 -
inst/CITATION | 15 ++--
man/PL.Rd | 2
man/fvcm-methods.Rd | 6 -
man/fvcm.Rd | 4 -
man/olmm-gefp.Rd | 5 -
man/olmm-methods.Rd | 6 -
man/olmm-predict.Rd | 118 ++++++++++++++++++++++++----------
man/olmm.Rd | 38 +++++++---
man/otsplot.Rd | 4 -
man/poverty.Rd | 2
man/schizo.Rd | 4 -
man/tvcglm.Rd | 11 +--
man/tvcm-cv.Rd | 9 +-
man/tvcm-plot.Rd | 4 -
man/tvcm.Rd | 7 +-
man/tvcolmm.Rd | 7 +-
src/init.c | 1
src/olmm.c | 180 +++++++++++++++++++++++++++++++++++++++++++++++++++-
src/olmm.h | 3
26 files changed, 478 insertions(+), 188 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Diff between spatial versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 8 +++++---
inst/po/en@quot/LC_MESSAGES/R-spatial.mo |binary
inst/po/ko |only
po/R-ko.po |only
po/R-spatial.pot | 4 ++--
6 files changed, 12 insertions(+), 10 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated From Cox Proportional Hazards Models
Diff between simPH versions 1.2.6.1 dated 2015-01-31 and 1.3 dated 2015-02-11
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 13 -
MD5 | 55 ++---
NAMESPACE | 2
NEWS | 24 ++
R/MinMaxLines.R | 4
R/SmoothSim.R | 42 ++--
R/coxsimInteract.R | 17 +
R/coxsimLinear.R | 238 +++++++++++------------
R/coxsimPoly.R | 194 +++++++++----------
R/coxsimSpline.R | 36 ++-
R/coxsimtvc.R | 299 ++++++++++++++---------------
R/simGG.siminteract.R | 418 +++++++++++++++++++++--------------------
R/simGG.simlinear.R | 288 +++++++++++++---------------
R/simGG.simpoly.R | 436 +++++++++++++++++++++----------------------
R/simGG.simspline.R | 316 +++++++++++++------------------
R/simGG.simtvc.R | 402 +++++++++++++++++----------------------
R/smallUtils.R | 51 +++++
README.md | 33 ++-
man/as.data.frame.coxsim.Rd |only
man/coxsimLinear.Rd | 12 -
man/coxsimPoly.Rd | 6
man/coxsimSpline.Rd | 9
man/coxsimtvc.Rd | 2
man/simGG.siminteract.Rd | 22 +-
man/simGG.simlinear.Rd | 21 +-
man/simGG.simpoly.Rd | 21 +-
man/simGG.simspline.Rd | 64 ++----
man/simGG.simtvc.Rd | 13 -
vignettes/simPH-overview.Rnw | 146 +++++++-------
29 files changed, 1630 insertions(+), 1554 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Diff between SeqFeatR versions 0.1.5 dated 2014-06-10 and 0.1.7 dated 2015-02-11
Description: SeqFeatR provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus
SeqFeatR-0.1.5/SeqFeatR/R/assocpointtuple.R |only
SeqFeatR-0.1.5/SeqFeatR/R/founderelim.R |only
SeqFeatR-0.1.5/SeqFeatR/R/hlaTree.R |only
SeqFeatR-0.1.5/SeqFeatR/R/vispair.R |only
SeqFeatR-0.1.5/SeqFeatR/R/vispairfeat.R |only
SeqFeatR-0.1.5/SeqFeatR/inst/extdata/co_mutation_results.csv |only
SeqFeatR-0.1.5/SeqFeatR/inst/extdata/co_mutation_results_wo_allels.csv |only
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SeqFeatR-0.1.5/SeqFeatR/inst/extdata/shared_mutations.csv |only
SeqFeatR-0.1.5/SeqFeatR/inst/extdata/shared_mutations_result.csv |only
SeqFeatR-0.1.5/SeqFeatR/man/assocpointtuple.Rd |only
SeqFeatR-0.1.5/SeqFeatR/man/founderelim.Rd |only
SeqFeatR-0.1.5/SeqFeatR/man/hlaTree.Rd |only
SeqFeatR-0.1.5/SeqFeatR/man/vispair.Rd |only
SeqFeatR-0.1.5/SeqFeatR/man/vispairfeat.Rd |only
SeqFeatR-0.1.7/SeqFeatR/DESCRIPTION | 16
SeqFeatR-0.1.7/SeqFeatR/INSTALL |only
SeqFeatR-0.1.7/SeqFeatR/MD5 | 104
SeqFeatR-0.1.7/SeqFeatR/NAMESPACE | 16
SeqFeatR-0.1.7/SeqFeatR/NEWS |only
SeqFeatR-0.1.7/SeqFeatR/R/SeqFeatR_GUI.R | 4713 +++++-----
SeqFeatR-0.1.7/SeqFeatR/R/assocpair.R | 12
SeqFeatR-0.1.7/SeqFeatR/R/assocpairfeat.R | 12
SeqFeatR-0.1.7/SeqFeatR/R/assocpoint.R | 413
SeqFeatR-0.1.7/SeqFeatR/R/assocpointpair.R |only
SeqFeatR-0.1.7/SeqFeatR/R/assoctuple.R | 43
SeqFeatR-0.1.7/SeqFeatR/R/comparewithancestral.R |only
SeqFeatR-0.1.7/SeqFeatR/R/foundereffectfinder.R |only
SeqFeatR-0.1.7/SeqFeatR/R/getfreqs.R |only
SeqFeatR-0.1.7/SeqFeatR/R/orPlot.R | 105
SeqFeatR-0.1.7/SeqFeatR/R/q-values.R | 6
SeqFeatR-0.1.7/SeqFeatR/R/rewritetuple.R | 10
SeqFeatR-0.1.7/SeqFeatR/R/tartan.R | 8
SeqFeatR-0.1.7/SeqFeatR/R/visualizepair.R |only
SeqFeatR-0.1.7/SeqFeatR/R/visualizepairfeat.R |only
SeqFeatR-0.1.7/SeqFeatR/R/volcanoplot.R |only
SeqFeatR-0.1.7/SeqFeatR/build |only
SeqFeatR-0.1.7/SeqFeatR/inst/doc |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_HLA_binding_motifs_aa.csv | 1
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_aa.fasta | 28
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_epitopes_aa.csv | 2
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/assocpair_results.csv |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/assocpairfeat_results.csv |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/assocpoint_results.csv |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/assocpoint_results_nt.csv |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/assoctuple_result.csv |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/config.cfg | 13
SeqFeatR-0.1.7/SeqFeatR/man/SeqFeatR-package.Rd | 19
SeqFeatR-0.1.7/SeqFeatR/man/SeqFeatR_GUI.Rd | 6
SeqFeatR-0.1.7/SeqFeatR/man/assocpair.Rd | 68
SeqFeatR-0.1.7/SeqFeatR/man/assocpairfeat.Rd | 103
SeqFeatR-0.1.7/SeqFeatR/man/assocpoint.Rd | 209
SeqFeatR-0.1.7/SeqFeatR/man/assocpointpair.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/assoctuple.Rd | 159
SeqFeatR-0.1.7/SeqFeatR/man/comparewithancestral.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/foundereffectfinder.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/getfreqs.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/orPlot.Rd | 99
SeqFeatR-0.1.7/SeqFeatR/man/q-values.Rd | 29
SeqFeatR-0.1.7/SeqFeatR/man/rewritetuple.Rd | 53
SeqFeatR-0.1.7/SeqFeatR/man/tartan.Rd | 124
SeqFeatR-0.1.7/SeqFeatR/man/visualizepair.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/visualizepairfeat.Rd |only
SeqFeatR-0.1.7/SeqFeatR/man/volcanoplot.Rd |only
SeqFeatR-0.1.7/SeqFeatR/vignettes |only
73 files changed, 3602 insertions(+), 2769 deletions(-)
Title: Recursive Partitioning and Regression Trees
Diff between rpart versions 4.1-8 dated 2014-03-28 and 4.1-9 dated 2015-02-11
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley
ChangeLog | 8 +
DESCRIPTION | 10 +-
MD5 | 28 ++---
R/rpart.R | 6 -
R/xpred.rpart.R | 2
inst/doc/longintro.pdf |binary
inst/doc/usercode.pdf |binary
inst/po/en@quot/LC_MESSAGES/R-rpart.mo |binary
inst/po/en@quot/LC_MESSAGES/rpart.mo |binary
inst/po/ko/LC_MESSAGES/R-rpart.mo |binary
inst/po/ko/LC_MESSAGES/rpart.mo |binary
po/R-ko.po | 159 +++++++++++++++------------------
po/R-rpart.pot | 4
po/ko.po | 47 ++++-----
po/rpart.pot | 4
15 files changed, 130 insertions(+), 138 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Diff between nnet versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 12 ++---
MD5 | 14 +++---
inst/po/en@quot/LC_MESSAGES/R-nnet.mo |binary
inst/po/ko/LC_MESSAGES/R-nnet.mo |binary
man/multinom.Rd | 15 ------
man/which.is.max.Rd | 6 +-
po/R-ko.po | 73 ++++++++++++++++------------------
po/R-nnet.pot | 4 -
8 files changed, 55 insertions(+), 69 deletions(-)
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Diff between KernSmooth versions 2.23-13 dated 2014-09-14 and 2.23-14 dated 2015-02-11
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley
DESCRIPTION | 14 ++++++------
MD5 | 14 ++++++------
PORTING | 7 ++++++
R/all.R | 4 +--
inst/po/en@quot/LC_MESSAGES/R-KernSmooth.mo |binary
inst/po/ko/LC_MESSAGES/R-KernSmooth.mo |binary
po/R-KernSmooth.pot | 4 +--
po/R-ko.po | 31 +++++++++++++---------------
8 files changed, 40 insertions(+), 34 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Diff between DataCombine versions 0.2.8.3 dated 2015-01-31 and 0.2.9 dated 2015-02-11
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NAMESPACE | 1 +
NEWS | 4 ++++
R/slide.R | 43 ++++++++++++++++++++++++-------------------
README.md | 2 +-
man/slideMA.Rd | 8 ++++----
7 files changed, 44 insertions(+), 34 deletions(-)
Title: Functions for Classification
Diff between class versions 7.3-11 dated 2014-07-21 and 7.3-12 dated 2015-02-11
Description: Various functions for classification.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++---
MD5 | 10 +++---
inst/po/en@quot/LC_MESSAGES/R-class.mo |binary
inst/po/ko/LC_MESSAGES/R-class.mo |binary
po/R-class.pot | 4 +-
po/R-ko.po | 51 ++++++++++++++++-----------------
6 files changed, 37 insertions(+), 38 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Diff between boot versions 1.3-14 dated 2015-01-10 and 1.3-15 dated 2015-02-11
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley
ChangeLog | 8 +
DESCRIPTION | 16 +--
MD5 | 14 +-
R/bootfuns.q | 5
inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
inst/po/ko/LC_MESSAGES/R-boot.mo |binary
po/R-boot.pot | 4
po/R-ko.po | 176 ++++++++++++++++------------------
8 files changed, 114 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-29 1.0-18
Title: Grammatical Evolution for R
Diff between gramEvol versions 1.2-1 dated 2014-10-22 and 2.0-2 dated 2015-02-11
Description: Context Free Grammar and Grammatical Evolution for R.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian
gramEvol-1.2-1/gramEvol/NEWS |only
gramEvol-1.2-1/gramEvol/R/ApplyGrammarRule.R |only
gramEvol-1.2-1/gramEvol/R/ChosenGrammarRule.R |only
gramEvol-1.2-1/gramEvol/R/GetFirstNonTerminalandRest.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarDepth.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarMaxRuleSize.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarMaxSequenceLen.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarNumOfExpressions.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarRuleIndex.R |only
gramEvol-1.2-1/gramEvol/R/GetPossibleRuleChoices.R |only
gramEvol-1.2-1/gramEvol/R/GrammarGenotypeToPhenotype.R |only
gramEvol-1.2-1/gramEvol/R/IsGrammarTerminal.R |only
gramEvol-1.2-1/gramEvol/R/TraverseCodon.R |only
gramEvol-1.2-1/gramEvol/man/GrammarGenotypeToPhenotype.Rd |only
gramEvol-1.2-1/gramEvol/tests/grammar.R |only
gramEvol-2.0-2/gramEvol/ChangeLog | 14
gramEvol-2.0-2/gramEvol/DESCRIPTION | 14
gramEvol-2.0-2/gramEvol/MD5 | 95 +-
gramEvol-2.0-2/gramEvol/NAMESPACE | 47 +
gramEvol-2.0-2/gramEvol/R/CreateGrammar.R | 59 +
gramEvol-2.0-2/gramEvol/R/EvalExpressions.R | 59 -
gramEvol-2.0-2/gramEvol/R/EvolutionStrategy.int.R |only
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gramEvol-2.0-2/gramEvol/R/GeneticAlg.int.R | 487 ++++++-------
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gramEvol-2.0-2/gramEvol/R/GrammarStartSymbol.R |only
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gramEvol-2.0-2/gramEvol/R/Grammar_helpers.R |only
gramEvol-2.0-2/gramEvol/R/GrammaticalEvolution.R | 146 ++-
gramEvol-2.0-2/gramEvol/R/GrammaticalExhaustiveSearch.R |only
gramEvol-2.0-2/gramEvol/R/GrammaticalRandomSearch.R |only
gramEvol-2.0-2/gramEvol/R/ReadBNFFile.R | 15
gramEvol-2.0-2/gramEvol/R/SymbolicRuleToListRule.R |only
gramEvol-2.0-2/gramEvol/R/print.GESearch.R |only
gramEvol-2.0-2/gramEvol/R/print.grammar.R | 29
gramEvol-2.0-2/gramEvol/R/summary.grammar.R |only
gramEvol-2.0-2/gramEvol/README.md | 6
gramEvol-2.0-2/gramEvol/build |only
gramEvol-2.0-2/gramEvol/inst |only
gramEvol-2.0-2/gramEvol/man/CreateGrammar.Rd | 110 +-
gramEvol-2.0-2/gramEvol/man/EvalExpressions.Rd | 24
gramEvol-2.0-2/gramEvol/man/EvolutionStrategy.int.Rd |only
gramEvol-2.0-2/gramEvol/man/GeneticAlg.int.Rd | 111 +-
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gramEvol-2.0-2/gramEvol/man/GrammaticalEvolution.Rd | 146 ++-
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gramEvol-2.0-2/gramEvol/man/summary.grammar.Rd |only
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gramEvol-2.0-2/gramEvol/tests/es.R |only
gramEvol-2.0-2/gramEvol/tests/exhaustive.R |only
gramEvol-2.0-2/gramEvol/tests/ga.R | 6
gramEvol-2.0-2/gramEvol/tests/ge.R | 16
gramEvol-2.0-2/gramEvol/tests/grammar_newstyle.R |only
gramEvol-2.0-2/gramEvol/tests/grammar_oldstyle.R |only
gramEvol-2.0-2/gramEvol/tests/grammar_sequence.R |only
gramEvol-2.0-2/gramEvol/tests/randomsearch.R |only
gramEvol-2.0-2/gramEvol/vignettes |only
76 files changed, 818 insertions(+), 574 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Tools for Simulating Direct Behavioral Observation Recording
Procedures Based on Alternating Renewal Processes
Diff between ARPobservation versions 1.0 dated 2014-05-29 and 1.1 dated 2015-02-11
More information about ARPobservation at CRAN
Description: Tools for simulating data generated by direct observation
recording. Behavior streams are simulated based on an alternating renewal
process, given specified distributions of event durations and interim
times. Different procedures for recording data can then be applied to the
simulated behavior streams. Functions are provided for the following
recording methods: continuous duration recording, event counting, momentary
time sampling, partial interval recording, and whole interval recording.
Author: James E. Pustejovsky, with contributions from Daniel M. Swan
Maintainer: James E. Pustejovsky
ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms-concordance.tex |only
ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms.tex |only
ARPobservation-1.1/ARPobservation/DESCRIPTION | 29
ARPobservation-1.1/ARPobservation/MD5 | 69 +-
ARPobservation-1.1/ARPobservation/NAMESPACE | 13
ARPobservation-1.1/ARPobservation/NEWS | 7
ARPobservation-1.1/ARPobservation/R/ARPobservation-package.r | 8
ARPobservation-1.1/ARPobservation/R/PIRapp.R |only
ARPobservation-1.1/ARPobservation/R/effect_size_estimators.R |only
ARPobservation-1.1/ARPobservation/R/simulate_behavior_stream.R | 308 ++++++++++
ARPobservation-1.1/ARPobservation/README.md | 3
ARPobservation-1.1/ARPobservation/build/vignette.rds |binary
ARPobservation-1.1/ARPobservation/data |only
ARPobservation-1.1/ARPobservation/demo/00Index | 1
ARPobservation-1.1/ARPobservation/demo/study_planning.R |only
ARPobservation-1.1/ARPobservation/inst/mc_est_test.R |only
ARPobservation-1.1/ARPobservation/man/ARPobservation.Rd | 9
ARPobservation-1.1/ARPobservation/man/Dunlap.Rd |only
ARPobservation-1.1/ARPobservation/man/F_const.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_exp.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_gam.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_gam_mix.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_unif.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_weib.Rd | 3
ARPobservation-1.1/ARPobservation/man/Moes.Rd |only
ARPobservation-1.1/ARPobservation/man/PIR_MOM.Rd |only
ARPobservation-1.1/ARPobservation/man/PIR_loglik.Rd |only
ARPobservation-1.1/ARPobservation/man/augmented_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/continuous_duration_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/eq_dist.Rd | 3
ARPobservation-1.1/ARPobservation/man/event_counting.Rd | 3
ARPobservation-1.1/ARPobservation/man/incidence_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/interim_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/interval_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/logRespRatio.Rd |only
ARPobservation-1.1/ARPobservation/man/momentary_time_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/prevalence_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/r_MTS.Rd |only
ARPobservation-1.1/ARPobservation/man/r_PIR.Rd |only
ARPobservation-1.1/ARPobservation/man/r_WIR.Rd |only
ARPobservation-1.1/ARPobservation/man/r_behavior_stream.Rd | 3
ARPobservation-1.1/ARPobservation/man/r_continuous_recording.Rd |only
ARPobservation-1.1/ARPobservation/man/r_event_counting.Rd |only
ARPobservation-1.1/ARPobservation/man/reported_observations.Rd | 3
ARPobservation-1.1/ARPobservation/tests |only
45 files changed, 431 insertions(+), 58 deletions(-)
Permanent link
Title: Extensions of Exponential Random Graph Models
Diff between xergm versions 1.3 dated 2014-11-01 and 1.4.1 dated 2015-02-10
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), and Temporal Network Autocorrelation Models (TNAM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld
xergm-1.3/xergm/vignettes/boxplots1.pdf |only
xergm-1.3/xergm/vignettes/boxplots2.pdf |only
xergm-1.3/xergm/vignettes/coefs.pdf |only
xergm-1.3/xergm/vignettes/nw.pdf |only
xergm-1.3/xergm/vignettes/rocpr.pdf |only
xergm-1.4.1/xergm/DESCRIPTION | 30 +-
xergm-1.4.1/xergm/MD5 | 50 ++--
xergm-1.4.1/xergm/NAMESPACE | 10
xergm-1.4.1/xergm/R/RcppExports.R |only
xergm-1.4.1/xergm/R/btergm.R | 42 ++-
xergm-1.4.1/xergm/R/gof.R | 245 ++++++++++++++++++++---
xergm-1.4.1/xergm/R/preprocess.R | 51 ++++
xergm-1.4.1/xergm/R/tnam.R | 77 +++----
xergm-1.4.1/xergm/build/vignette.rds |binary
xergm-1.4.1/xergm/data/knecht.rda |binary
xergm-1.4.1/xergm/inst/CITATION | 3
xergm-1.4.1/xergm/inst/doc/btergm.R | 54 ++---
xergm-1.4.1/xergm/inst/doc/btergm.Rnw | 20 +
xergm-1.4.1/xergm/inst/doc/btergm.pdf |binary
xergm-1.4.1/xergm/man/btergm.Rd | 75 +++++--
xergm-1.4.1/xergm/man/gof.Rd | 63 ++++-
xergm-1.4.1/xergm/man/preprocess.Rd | 6
xergm-1.4.1/xergm/man/timecov.Rd |only
xergm-1.4.1/xergm/man/tnam.Rd | 6
xergm-1.4.1/xergm/man/xergm-package.Rd | 12 -
xergm-1.4.1/xergm/src |only
xergm-1.4.1/xergm/vignettes/btergm-boxplots1.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-boxplots2.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-coefs.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-nw.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-rocpr.pdf |only
xergm-1.4.1/xergm/vignettes/btergm.Rnw | 20 +
32 files changed, 551 insertions(+), 213 deletions(-)
Title: Multidimensional Iterative Proportional Fitting
Diff between mipfp versions 1.0 dated 2014-12-01 and 1.5 dated 2015-02-10
Description: An implementation of the iterative proportional fitting procedure for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional).
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy
DESCRIPTION | 11 -
MD5 | 13 +
NAMESPACE | 1
R/ipfpMultiDim.R | 380 ++++++++++++++++++++++++++++++++++++---------------
man/Ipfp.Rd | 103 +++++++++----
man/IpfpCovar.Rd |only
man/array2vector.Rd |only
man/mipfp-package.Rd | 56 ++++---
man/vector2array.Rd |only
9 files changed, 392 insertions(+), 172 deletions(-)
Title: Lucid Printing of Floating Point Numbers
Diff between lucid versions 1.0 dated 2014-11-25 and 1.1 dated 2015-02-10
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright
Maintainer: Kevin Wright
lucid-1.0/lucid/inst/doc/lucid.R |only
lucid-1.0/lucid/inst/doc/lucid.Rnw |only
lucid-1.0/lucid/inst/doc/lucid.pdf |only
lucid-1.0/lucid/vignettes/figs |only
lucid-1.0/lucid/vignettes/lucid-concordance.tex |only
lucid-1.0/lucid/vignettes/lucid.Rnw |only
lucid-1.1/lucid/DESCRIPTION | 10 -
lucid-1.1/lucid/MD5 | 33 ++--
lucid-1.1/lucid/NEWS | 5
lucid-1.1/lucid/R/lucid.r | 105 +++++++++++----
lucid-1.1/lucid/R/vc.r | 29 ++--
lucid-1.1/lucid/README.md | 8 +
lucid-1.1/lucid/build/vignette.rds |binary
lucid-1.1/lucid/inst/doc/lucid_printing.R |only
lucid-1.1/lucid/inst/doc/lucid_printing.Rnw |only
lucid-1.1/lucid/inst/doc/lucid_printing.pdf |only
lucid-1.1/lucid/man/lucid.Rd | 38 +++--
lucid-1.1/lucid/man/vc.Rd | 3
lucid-1.1/lucid/vignettes/figure |only
lucid-1.1/lucid/vignettes/lucid.bib | 56 +++++++-
lucid-1.1/lucid/vignettes/lucid_printing-concordance.tex |only
lucid-1.1/lucid/vignettes/lucid_printing.Rnw |only
22 files changed, 212 insertions(+), 75 deletions(-)
Title: R Based Twitter Client
Diff between twitteR versions 1.1.7 dated 2013-07-09 and 1.1.8 dated 2015-02-10
Description: Provides an interface to the Twitter web API.
Author: Jeff Gentry
Maintainer: Jeff Gentry
twitteR-1.1.7/twitteR/inst/sweave |only
twitteR-1.1.7/twitteR/inst/vignette |only
twitteR-1.1.8/twitteR/DESCRIPTION | 20 +
twitteR-1.1.8/twitteR/MD5 | 66 +++---
twitteR-1.1.8/twitteR/NAMESPACE | 16 +
twitteR-1.1.8/twitteR/NEWS | 44 ++++
twitteR-1.1.8/twitteR/R/account.R | 28 ++
twitteR-1.1.8/twitteR/R/base.R | 5
twitteR-1.1.8/twitteR/R/comm.R | 191 ++++++++----------
twitteR-1.1.8/twitteR/R/convert.R | 22 ++
twitteR-1.1.8/twitteR/R/db.R |only
twitteR-1.1.8/twitteR/R/db_connections.R |only
twitteR-1.1.8/twitteR/R/db_search.R |only
twitteR-1.1.8/twitteR/R/db_utils.R |only
twitteR-1.1.8/twitteR/R/df_columns.R |only
twitteR-1.1.8/twitteR/R/dm.R | 6
twitteR-1.1.8/twitteR/R/followers.R | 20 +
twitteR-1.1.8/twitteR/R/oauth.R |only
twitteR-1.1.8/twitteR/R/search.R | 20 +
twitteR-1.1.8/twitteR/R/statuses.R | 132 ++++++++----
twitteR-1.1.8/twitteR/R/toys.R | 2
twitteR-1.1.8/twitteR/R/trends.R | 15 +
twitteR-1.1.8/twitteR/R/users.R | 51 +++-
twitteR-1.1.8/twitteR/R/utils.R | 84 ++++++-
twitteR-1.1.8/twitteR/R/zzz.R | 5
twitteR-1.1.8/twitteR/README.md | 14 +
twitteR-1.1.8/twitteR/inst/doc |only
twitteR-1.1.8/twitteR/inst/vignettes |only
twitteR-1.1.8/twitteR/man/getCurRateLimitInfo.Rd | 12 -
twitteR-1.1.8/twitteR/man/getUser.Rd | 2
twitteR-1.1.8/twitteR/man/get_latest_tweet_id.Rd |only
twitteR-1.1.8/twitteR/man/load_tweets_db.Rd |only
twitteR-1.1.8/twitteR/man/registerTwitterOAuth.Rd | 38 ---
twitteR-1.1.8/twitteR/man/register_db_backend.Rd |only
twitteR-1.1.8/twitteR/man/retweets.Rd |only
twitteR-1.1.8/twitteR/man/search.Rd | 45 +++-
twitteR-1.1.8/twitteR/man/search_twitter_and_store.Rd |only
twitteR-1.1.8/twitteR/man/setup_twitter_oauth.Rd |only
twitteR-1.1.8/twitteR/man/showStatus.Rd | 23 +-
twitteR-1.1.8/twitteR/man/strip_retweets.Rd |only
twitteR-1.1.8/twitteR/man/timelines.Rd | 9
twitteR-1.1.8/twitteR/man/updateStatus.Rd | 8
42 files changed, 577 insertions(+), 301 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.11 dated 2015-01-17 and 0.11.1 dated 2015-02-10
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang
DESCRIPTION | 16
MD5 | 114 +++---
NEWS | 36 ++
R/app.R | 45 +-
R/bootstrap.R | 180 +++++-----
R/jqueryui.R | 4
R/middleware.R | 2
R/reactives.R | 51 +-
R/run-url.R | 33 +
R/server.R | 95 +++--
R/shiny.R | 10
R/shinyui.R | 8
R/shinywrappers.R | 35 +
R/update-input.R | 49 +-
R/utils.R | 16
inst/examples/04_mpg/server.R | 2
inst/tests/test-bootstrap.r | 4
inst/tests/test-utils.R | 12
inst/www/shared/ionrangeslider/css/ion.rangeSlider.css | 11
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinFlat.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinHTML5.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinModern.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinNice.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinSimple.css | 4
inst/www/shared/ionrangeslider/js/ion.rangeSlider.js | 157 ++++----
inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 130 +++----
inst/www/shared/shiny.css | 12
inst/www/shared/shiny.js | 64 ++-
inst/www/shared/shiny.min.js | 6
inst/www/shared/shiny.min.js.map | 2
man/absolutePanel.Rd | 4
man/bootstrapPage.Rd | 10
man/checkboxGroupInput.Rd | 4
man/checkboxInput.Rd | 4
man/dateInput.Rd | 4
man/dateRangeInput.Rd | 4
man/fileInput.Rd | 4
man/htmlOutput.Rd | 20 -
man/navbarPage.Rd | 2
man/numericInput.Rd | 6
man/observeEvent.Rd | 51 +-
man/parseQueryString.Rd | 2
man/passwordInput.Rd | 6
man/plotOutput.Rd | 4
man/radioButtons.Rd | 4
man/renderDataTable.Rd | 35 +
man/runApp.Rd | 46 +-
man/runExample.Rd | 15
man/runUrl.Rd | 33 +
man/selectInput.Rd | 22 -
man/shinyApp.Rd | 45 +-
man/shinyServer.Rd | 21 +
man/shinyUI.Rd | 8
man/sliderInput.Rd | 6
man/tabPanel.Rd | 2
man/tableOutput.Rd | 51 +-
man/textInput.Rd | 6
man/updateSliderInput.Rd | 49 +-
58 files changed, 896 insertions(+), 686 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Diff between phenology versions 4.0 dated 2014-10-05 and 4.0.4 dated 2015-02-10
Description: Functions to fit and test the phenology of species based on counts. The package includes also several useful more general functions.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 11 +--
MD5 | 148 +++++++++++++++++++++----------------------
NAMESPACE | 3
NEWS | 8 ++
R/MHalgoGen.R | 34 ++++++++-
R/add_phenology.R | 14 +++-
R/barplot_errbar.R | 1
R/format_par.R | 53 ++++-----------
R/insidesearch.R |only
R/phenology-package.R | 6 -
R/plot.phenology.R | 1
R/plot.phenologymap.R | 25 +------
R/plot_errbar.R | 3
R/print.phenologyout.R | 6 +
R/read_phenology.R | 46 +++++++++----
man/BE_to_LBLE.Rd | 3
man/ChangeCoordinate.Rd | 3
man/Gratiot.Rd | 3
man/LBLE_to_BE.Rd | 3
man/LBLE_to_L.Rd | 3
man/L_to_LBLE.Rd | 3
man/MinBMinE_to_Min.Rd | 3
man/ScalePreviousPlot.Rd | 3
man/adapt_parameters.Rd | 3
man/add_SD.Rd | 3
man/add_phenology.Rd | 3
man/as.mcmc.mcmcComposite.Rd | 3
man/as.par.mcmcComposite.Rd | 3
man/asc.Rd | 3
man/barplot_errbar.Rd | 3
man/chr.Rd | 3
man/clean.knitr.Rd | 3
man/compare_AIC.Rd | 3
man/compassRose2.Rd | 3
man/convert.tz.Rd | 3
man/extract_result.Rd | 3
man/fit_phenology.Rd | 3
man/getTide.Rd | 3
man/growlnotify.Rd | 3
man/ind_long_lat.Rd | 3
man/insidesearch.Rd |only
man/likelihood_phenology.Rd | 3
man/local.search.Rd | 3
man/logLik.phenology.Rd | 3
man/map.scale2.Rd | 3
man/map_Gratiot.Rd | 3
man/map_phenology.Rd | 3
man/moon_phase.Rd | 3
man/par_init.Rd | 3
man/phenology-package.Rd | 9 +-
man/phenology.Rd | 3
man/phenology_MHmcmc.Rd | 3
man/phenology_MHmcmc_p.Rd | 3
man/plot.mcmcComposite.Rd | 3
man/plot.phenology.Rd | 3
man/plot.phenologymap.Rd | 7 --
man/plot_add.Rd | 3
man/plot_delta.Rd | 3
man/plot_errbar.Rd | 3
man/plot_phi.Rd | 3
man/print.phenology.Rd | 3
man/print.phenologymap.Rd | 3
man/print.phenologyout.Rd | 3
man/read_folder.Rd | 3
man/remove_site.Rd | 3
man/result_Gratiot.Rd | 3
man/result_Gratiot1.Rd | 3
man/result_Gratiot2.Rd | 3
man/result_Gratiot_Flat.Rd | 3
man/result_Gratiot_mcmc.Rd | 3
man/shift_sinusoid.Rd | 3
man/summary.mcmcComposite.Rd | 3
man/summary.phenology.Rd | 3
man/summary.phenologymap.Rd | 3
man/summary.phenologyout.Rd | 3
man/toggle_Min_PMin.Rd | 3
76 files changed, 317 insertions(+), 232 deletions(-)
Title: Multiple Imputation for Multivariate Panel or Clustered Data
Diff between pan versions 0.9 dated 2013-09-27 and 1.3 dated 2015-02-10
Description: Multiple imputation for multivariate panel or clustered data.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao
pan-0.9/pan/.Rinstignore |only
pan-0.9/pan/INDEX |only
pan-0.9/pan/LICENSE |only
pan-0.9/pan/inst/doc/pan-tr.R |only
pan-1.3/pan/ChangeLog | 14 ++++++++++++++
pan-1.3/pan/DESCRIPTION | 16 ++++++++--------
pan-1.3/pan/MD5 | 20 +++++++++-----------
pan-1.3/pan/build |only
pan-1.3/pan/inst/doc/pan-tr.Rnw | 6 +++---
pan-1.3/pan/inst/doc/pan-tr.pdf |binary
pan-1.3/pan/man/ecme.Rd | 9 ++++++---
pan-1.3/pan/man/pan.Rd | 9 ++++++---
pan-1.3/pan/src/pan.f | 4 ++--
pan-1.3/pan/vignettes/pan-tr.Rnw | 6 +++---
14 files changed, 51 insertions(+), 33 deletions(-)
Title: Optimal k-Means Clustering for One-Dimensional Data
Diff between Ckmeans.1d.dp versions 3.3.0 dated 2015-02-09 and 3.3.1 dated 2015-02-10
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 5 +++++
src/Ckmeans.1d.dp.cpp | 2 +-
4 files changed, 13 insertions(+), 8 deletions(-)
Title: Markov-Switching, Bayesian, Vector Autoregression Models
Diff between MSBVAR versions 0.9-1 dated 2014-07-25 and 0.9-2 dated 2015-02-10
Description: Provides methods for estimating frequentist and
Bayesian Vector Autoregression (VAR) models and Markov-switching
Bayesian VAR (MSBVAR). Functions for reduced
form and structural VAR models are also available. Includes
methods for the generating posterior inferences for these models,
forecasts, impulse responses (using likelihood-based error bands),
and forecast error decompositions. Also includes utility functions
for plotting forecasts and impulse responses, and generating draws
from Wishart and singular multivariate normal densities. Current
version includes functionality to build and evaluate models with
Markov switching.
Author: Patrick Brandt [aut, cre],
W. Ryan Davis [ctb]
Maintainer: Patrick Brandt
DESCRIPTION | 12 ++++++------
LICENSE | 4 ++--
MD5 | 25 +++++++++++++------------
NAMESPACE | 6 ++++++
R/zzz.R | 2 +-
README | 11 +++++++----
man/BCFdata.Rd | 12 ++++++------
man/IsraelPalestineConflict.Rd | 2 +-
man/hc.forecast.Rd | 2 +-
man/uc.forecast.Rd | 2 +-
src/FFBS.f | 8 ++++----
src/MSBVARfun.cpp | 3 ++-
src/utils.f | 38 ++++++++++++++++++++++++++++----------
src/wrapper.c |only
14 files changed, 78 insertions(+), 49 deletions(-)
Title: Marker-Based Estimation of Heritability Using Individual Plant
or Plot Data
Diff between heritability versions 1.0 dated 2014-11-07 and 1.1 dated 2015-02-10
Description: Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author: Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke.
Maintainer: Willem Kruijer
DESCRIPTION | 14 +++++++-------
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 1 +
R/AI_algorithm.R | 24 ++++++++++++------------
R/AI_algorithm_weights.r | 26 +++++++++++++-------------
R/marker_h2_means.r | 21 +++++++++++++++++++--
man/BT_LW_H.Rd | 4 ++--
man/K_arabidopsis.Rd | 3 ---
man/R_matrix.Rd | 4 ++--
man/floweringTime.Rd | 4 ++--
man/heritability-package.Rd | 6 +++---
man/leafArea.Rd | 4 ++--
man/marker_h2.Rd | 8 ++++----
man/marker_h2_means.Rd | 14 +++++++-------
man/means_floweringTime.Rd | 4 ++--
man/repeatability.Rd | 7 +++----
16 files changed, 94 insertions(+), 80 deletions(-)
Title: Time Series Analysis and Computational Finance
Diff between tseries versions 0.10-32 dated 2013-05-13 and 0.10-33 dated 2015-02-10
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik
ChangeLog | 7 ++++++
DESCRIPTION | 26 ++++++++++++----------
MD5 | 22 +++++++++----------
R/finance.R | 60 ++++++++++++++++++++--------------------------------
data/NelPlo.rda |binary
data/USeconomic.rda |binary
data/bev.rda |binary
data/camp.rda |binary
data/ice.river.rda |binary
data/nino.rda |binary
data/tcm.rda |binary
data/tcmd.rda |binary
12 files changed, 56 insertions(+), 59 deletions(-)
Title: Imperialist Competitive Algorithm
Diff between ICAFF versions 1.0 dated 2015-02-01 and 1.0.1 dated 2015-02-10
Description: Imperialist Competitive Algorithm (ICA)
Author: Farimah Houshmand, Farzad Eskandari Ph.D.
Maintainer: Farimah Houshmand
ICAFF-1.0.1/ICAFF/DESCRIPTION | 30 +
ICAFF-1.0.1/ICAFF/MD5 | 17 -
ICAFF-1.0.1/ICAFF/NAMESPACE | 6
ICAFF-1.0.1/ICAFF/R/ICA.R | 544 ++++++++++++++---------------------
ICAFF-1.0.1/ICAFF/R/ICAFF-internal.R | 251 ++++++++--------
ICAFF-1.0.1/ICAFF/R/coef.ICA.R |only
ICAFF-1.0.1/ICAFF/R/plot.ICA.R |only
ICAFF-1.0.1/ICAFF/R/print.ICA.R |only
ICAFF-1.0.1/ICAFF/R/summary.ICA.R |only
ICAFF-1.0.1/ICAFF/man/ICA.Rd | 184 +++++++----
ICAFF-1.0.1/ICAFF/man/plot.ICA.Rd |only
ICAFF-1.0/ICAFF/R/cost.R |only
ICAFF-1.0/ICAFF/man/ICAFF-package.Rd |only
13 files changed, 497 insertions(+), 535 deletions(-)
Title: Soft Clustering Algorithms
Diff between SoftClustering versions 0.14.02 dated 2014-02-17 and 1.1502 dated 2015-02-10
More information about SoftClustering at CRAN
Description: It contains soft clustering algorithms, in particular approaches derived from rough set theory: Lingras & West original rough k-means, Peters' refined rough k-means, and PI rough k-means. It also contains classic k-means and a corresponding illustrative demo.
Author: G. Peters (Ed.)
Maintainer: G. Peters
SoftClustering-0.14.02/SoftClustering/R/RoughClustering_01402.r |only
SoftClustering-0.14.02/SoftClustering/data/DemoDataC2D2a.txt.gz |only
SoftClustering-1.1502/SoftClustering/DESCRIPTION | 9 -
SoftClustering-1.1502/SoftClustering/MD5 | 39 +++--
SoftClustering-1.1502/SoftClustering/NAMESPACE | 4
SoftClustering-1.1502/SoftClustering/R/HardkMeansDemo.r |only
SoftClustering-1.1502/SoftClustering/R/RoughClustering.r |only
SoftClustering-1.1502/SoftClustering/data/DemoDataC2D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC2D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC3D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC4D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC5D2a.txt |only
SoftClustering-1.1502/SoftClustering/man/DemoDataC2D2a.Rd | 2
SoftClustering-1.1502/SoftClustering/man/HardKMeans.Rd | 36 +---
SoftClustering-1.1502/SoftClustering/man/HardKMeansDemo.Rd |only
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_LW.Rd | 72 +++------
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_PE.Rd | 57 ++-----
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_PI.Rd | 52 ++----
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_SHELL.Rd | 77 +++-------
SoftClustering-1.1502/SoftClustering/man/createLowerMShipMatrix.Rd | 7
SoftClustering-1.1502/SoftClustering/man/datatypeInteger.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC2D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC3D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC4D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC5D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initializeMeansMatrix.Rd | 14 -
SoftClustering-1.1502/SoftClustering/man/normalizeMatrix.Rd | 14 -
SoftClustering-1.1502/SoftClustering/man/plotRoughKMeans.Rd | 23 +-
28 files changed, 154 insertions(+), 252 deletions(-)
Permanent link
Title: R Individual Specialization (RInSp)
Diff between RInSp versions 1.1 dated 2015-02-04 and 1.2 dated 2015-02-10
Description: Functions to calculate several ecological indices of individual and population niche width
(Araujo's E, clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's
WIC/TNW) to assess individual specialization based on data of resource use. Resource use can be
quantified by counts of categories, measures of mass/lenght or proportions. Monte Carlo resampling
procedures are available for hypothesis testing against multinomial null models.
Author: Dr. Nicola Zaccarelli, Dr. Giorgio Mancinelli, and Prof. Dan Bolnick
Maintainer: Dr. Nicola Zaccarelli
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
man/RInSp-package.Rd | 6 +++---
src/Emc.c | 7 +++----
src/MCprocedure.c | 12 ++++++------
src/PSicalc.c | 14 +++++++-------
src/WTcMC.c | 17 +++++++++--------
src/WTdMC.c | 11 ++++++-----
8 files changed, 45 insertions(+), 44 deletions(-)
Title: Rough - Enhanced - Bayesian Finite Mixture Modeling
Diff between rebmix versions 2.6.2 dated 2014-09-05 and 2.7.0 dated 2015-02-10
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode
rebmix-2.6.2/rebmix/R/boot.R |only
rebmix-2.6.2/rebmix/R/predict.list.R |only
rebmix-2.6.2/rebmix/man/boot.Rd |only
rebmix-2.6.2/rebmix/man/predict.list.Rd |only
rebmix-2.7.0/rebmix/DESCRIPTION | 10
rebmix-2.7.0/rebmix/MD5 | 120 +++---
rebmix-2.7.0/rebmix/NAMESPACE | 56 ---
rebmix-2.7.0/rebmix/R/IC.R | 188 +---------
rebmix-2.7.0/rebmix/R/RCLSMIX.R |only
rebmix-2.7.0/rebmix/R/REBMIX.R | 108 +++---
rebmix-2.7.0/rebmix/R/RNGMIX.R | 2
rebmix-2.7.0/rebmix/R/boot.REBMIX.R |only
rebmix-2.7.0/rebmix/R/defaults.R | 2
rebmix-2.7.0/rebmix/R/densKNearestNeighbour.x.R | 17
rebmix-2.7.0/rebmix/R/densKNearestNeighbour.xy.R | 20 -
rebmix-2.7.0/rebmix/R/densParzenWindow.x.R | 19 -
rebmix-2.7.0/rebmix/R/densParzenWindow.xy.R | 18 -
rebmix-2.7.0/rebmix/R/dist.x.R | 20 -
rebmix-2.7.0/rebmix/R/dist.xy.R | 24 +
rebmix-2.7.0/rebmix/R/kseq.R | 8
rebmix-2.7.0/rebmix/R/plot.REBMIX.R | 123 ++++--
rebmix-2.7.0/rebmix/build/vignette.rds |binary
rebmix-2.7.0/rebmix/data/adult.rda |binary
rebmix-2.7.0/rebmix/data/galaxy.rda |binary
rebmix-2.7.0/rebmix/data/truck.rda |binary
rebmix-2.7.0/rebmix/data/weibull.rda |binary
rebmix-2.7.0/rebmix/data/weibullnormal.rda |binary
rebmix-2.7.0/rebmix/data/wine.rda |binary
rebmix-2.7.0/rebmix/demo/rebmix.truck.R | 2
rebmix-2.7.0/rebmix/demo/rebmix.weibullnormal.R | 2
rebmix-2.7.0/rebmix/inst/NEWS.Rd | 22 +
rebmix-2.7.0/rebmix/inst/doc/rebmix.Rnw | 16
rebmix-2.7.0/rebmix/inst/doc/rebmix.pdf |binary
rebmix-2.7.0/rebmix/man/AIC.Rd | 12
rebmix-2.7.0/rebmix/man/AWE.Rd | 4
rebmix-2.7.0/rebmix/man/BIC.Rd | 4
rebmix-2.7.0/rebmix/man/CLC.Rd | 4
rebmix-2.7.0/rebmix/man/HQC.Rd | 4
rebmix-2.7.0/rebmix/man/ICL.Rd | 4
rebmix-2.7.0/rebmix/man/ICLBIC.Rd | 4
rebmix-2.7.0/rebmix/man/MDL.Rd | 9
rebmix-2.7.0/rebmix/man/PC.Rd | 4
rebmix-2.7.0/rebmix/man/PRD.Rd | 4
rebmix-2.7.0/rebmix/man/RCLSMIX.Rd |only
rebmix-2.7.0/rebmix/man/REBMIX.Rd | 52 +-
rebmix-2.7.0/rebmix/man/SSE.Rd | 4
rebmix-2.7.0/rebmix/man/boot.REBMIX.Rd |only
rebmix-2.7.0/rebmix/man/coef.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/dfmix.Rd | 1
rebmix-2.7.0/rebmix/man/kseq.Rd | 2
rebmix-2.7.0/rebmix/man/logL.Rd | 4
rebmix-2.7.0/rebmix/man/pfmix.Rd | 1
rebmix-2.7.0/rebmix/man/plot.REBMIX.Rd | 9
rebmix-2.7.0/rebmix/man/print.REBMIX.Rd | 5
rebmix-2.7.0/rebmix/man/print.RNGMIX.Rd | 1
rebmix-2.7.0/rebmix/man/print.boot.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/summary.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/summary.boot.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/src/Makevars | 2
rebmix-2.7.0/rebmix/src/Rrebmix.c | 58 +--
rebmix-2.7.0/rebmix/src/rebmixf.c | 408 +++++++++++++++--------
rebmix-2.7.0/rebmix/src/rebmixf.h | 38 +-
rebmix-2.7.0/rebmix/src/rngmixf.c | 2
rebmix-2.7.0/rebmix/vignettes/algorithm.pdf |binary
rebmix-2.7.0/rebmix/vignettes/rebmix.Rnw | 16
65 files changed, 783 insertions(+), 662 deletions(-)
Title: Linear Mixed Models
Diff between lmm versions 0.9 dated 2013-12-10 and 1.0 dated 2015-02-10
Description: Some improved procedures for linear mixed models.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao
lmm-0.9/lmm/.Rinstignore |only
lmm-0.9/lmm/LICENSE |only
lmm-0.9/lmm/inst/doc/lmm-tr.R |only
lmm-1.0/lmm/ChangeLog | 8 +++++++-
lmm-1.0/lmm/DESCRIPTION | 16 ++++++++--------
lmm-1.0/lmm/MD5 | 11 +++++------
lmm-1.0/lmm/build |only
lmm-1.0/lmm/inst/doc/lmm-tr.pdf |binary
lmm-1.0/lmm/src/lmm.f | 6 +++---
9 files changed, 23 insertions(+), 18 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.8-1441 dated 2014-12-25 and 2.0-1570 dated 2015-02-10
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 14
MD5 | 130 +-
NAMESPACE | 12
NEWS |only
R/bccorr.R | 277 ++++--
R/btrap.R | 21
R/compfactor.R | 1
R/condfstat.R |only
R/felm.R | 1103 +++++++++++--------------
R/felm.old.R |only
R/generics.R |only
R/getfe.R | 4
R/kaczmarz.R | 40
R/oldfelm.R | 1027 ++++++++++++++++++++---
R/utils.R | 245 -----
R/waldtest.R |only
build/autoconf/install-sh | 668 ++++++++++-----
configure | 20
configure.ac | 2
exec/lfescript | 111 +-
inst/CITATION | 13
inst/doc/CHANGELOG | 33
inst/doc/identification.R | 54 -
inst/doc/identification.Rnw | 2
inst/doc/identification.pdf |binary
inst/doc/index.html | 60 -
inst/doc/lfeguide.txt | 40
inst/doc/lfehow.R | 20
inst/doc/lfehow.pdf |binary
inst/doc/speed.R | 10
inst/doc/speed.pdf |binary
man/bccorr.Rd | 4
man/btrap.Rd | 6
man/condfstat.Rd |only
man/demeanlist.Rd | 3
man/felm.Rd | 104 +-
man/fevcov.Rd | 58 -
man/getfe.Rd | 7
man/is.estimable.Rd | 7
man/kaczmarz.Rd | 3
man/lfe-package.Rd | 31
man/summary.felm.Rd | 43
man/varvars.Rd | 3
man/waldtest.Rd |only
src/Makevars.in | 2
src/Makevars.win | 3
src/demean.c |only
src/factor.c |only
src/kaczmarz.c |only
src/lfe.c | 1888 -------------------------------------------
src/lfe.h |only
src/utils.c |only
tests/anomalies.R |only
tests/anomalies.Rout.save |only
tests/bctest.Rout.save | 6
tests/cluster.R | 6
tests/cluster.Rout.save | 72 -
tests/comparelm.Rout.save | 13
tests/degenerate.Rout.save | 17
tests/efcheck.Rout.save | 10
tests/fourfac.Rout.save | 10
tests/interact.Rout.save | 821 +++++++++---------
tests/ivtest.R | 26
tests/ivtest.Rout.save | 144 +--
tests/lfetest.Rout.save | 6
tests/mlhs.R |only
tests/mlhs.Rout.save |only
tests/multiway.R | 14
tests/multiway.Rout.save | 92 --
tests/naomit.Rout.save | 9
tests/nonest.Rout.save | 10
tests/onefac.Rout.save | 6
tests/verify.Rout.save | 13
vignettes/identification.Rnw | 2
74 files changed, 3175 insertions(+), 4171 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Diff between treeclim versions 1.0.10 dated 2015-01-19 and 1.0.11 dated 2015-02-10
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang
DESCRIPTION | 8
MD5 | 37 +--
R/exclude_from.R | 94 ++++----
R/skills.R | 544 +++++++++++++++++++++++++-------------------------
R/zzz.R | 38 +--
README.md |only
inst/Changelog | 3
man/dcc.Rd | 478 +++++++++++++++++++++----------------------
man/g_test.Rd | 128 +++++------
man/init_boot_data.Rd | 52 ++--
man/norw015.Rd | 56 ++---
man/norway_prec.Rd | 48 ++--
man/norway_temp.Rd | 48 ++--
man/seascorr.Rd | 278 ++++++++++++-------------
man/skills.Rd | 212 +++++++++----------
man/spain_prec.Rd | 48 ++--
man/spain_temp.Rd | 48 ++--
man/tc_correlation.Rd | 52 ++--
man/tc_mfunc.Rd | 76 +++---
man/tc_response.Rd | 50 ++--
20 files changed, 1151 insertions(+), 1147 deletions(-)
Title: Fitting Structural Equation Mixture Models
Diff between nlsem versions 0.1 dated 2014-12-19 and 0.2 dated 2015-02-10
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach
DESCRIPTION | 9 +-
MD5 | 38 +++++------
NAMESPACE | 1
R/em.R | 50 ++++++++-------
R/lms.R | 4 -
R/model.R | 38 ++++++++---
R/s3generics.R | 65 ++++++++++++--------
R/semm.R | 15 ++--
man/anova.Rd | 2
man/as.data.frame.Rd | 4 -
man/count_free_parameters.Rd | 4 -
man/create_sem.Rd | 9 +-
man/em.Rd | 139 ++++++++-----------------------------------
man/fill_model.Rd | 8 +-
man/nlsem-package.Rd | 52 ++++++++--------
man/simulate.Rd | 17 ++---
man/specify_sem.Rd | 32 ++++-----
man/summary.Rd | 15 ----
tests/tests_for_model.R | 17 +----
tests/tests_for_semm.R | 42 ------------
20 files changed, 229 insertions(+), 332 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Diff between asbio versions 1.1-1 dated 2014-09-06 and 1.1-5 dated 2015-02-10
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.
Author: Ken Aho
Maintainer: Ken Aho
DESCRIPTION | 12 -
MD5 | 72 +++++------
NAMESPACE | 19 ++-
R/Bayes.disc.r | 5
R/Venn.R | 10 -
R/anm.ExpDesign.r | 6
R/bplot.r | 4
R/ci.prat.ak.R | 309 +++++++++++++++++++++++++++++--------------------
R/ci.prat.r | 4
R/huber.NR.R | 2
R/loess.surf.R | 3
R/loglik.norm.plot.r | 2
R/one.sample.t.R | 21 ++-
R/one.sample.z.R | 11 +
R/pairw.anova.R | 2
R/qq.Plot.R | 6
R/r.bw.R | 2
R/r.dist.r | 4
R/samp.dist.snap.tck.r | 2
R/samp.dist.tck.r | 2
R/see.regression.tck.r | 12 -
R/see.smooth.tck.r | 4
R/shade.r | 8 +
build/vignette.rds |binary
man/anm.loglik.rd | 2
man/bvn.plot.rd | 2
man/ci.prat.ak.Rd | 5
man/ci.prat.rd | 2
man/heart.rd | 4
man/huber.NR.Rd | 4
man/huber.mu.rd | 4
man/huber.one.step.rd | 4
man/one.sample.t.rd | 6
man/one.sample.z.Rd | 7 -
man/paik.rd | 2
man/r.dist.rd | 4
man/shade.norm.Rd | 5
37 files changed, 339 insertions(+), 234 deletions(-)
Title: Using V-algorithm and Newton-Raphson Method to Obtain
Multiple-objective Optimal Design
Diff between VNM versions 2.0 dated 2014-10-31 and 4.0 dated 2015-02-09
Description: Using V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang
DESCRIPTION | 14 +++---
MD5 | 34 +++++++++-----
NAMESPACE | 14 +++++-
R/AllClasses.R |only
R/Deff.R | 109 +++++++++++++++++++++++++++++++++-------------
R/MOPT.R | 113 +++++++++++++++++++++++++++++++++++++-----------
R/S.Weight.R | 95 ++++++++++++++++++++++++++++------------
R/ceff1.R | 104 ++++++++++++++++++++++++++++++++------------
R/ceff2.R | 114 ++++++++++++++++++++++++++++++++++++-------------
R/plot-methods.R |only
R/summary-methods.R |only
man/Deff.Rd | 8 +--
man/MOPT.Rd | 10 ++--
man/OPT-class.Rd |only
man/PAR-class.Rd |only
man/S.Weight.Rd | 2
man/SW-class.Rd |only
man/VNM-package.Rd | 12 ++---
man/ceff1.Rd | 11 ++--
man/ceff2.Rd | 8 +--
man/plot-methods.Rd |only
man/summary-methods.Rd |only
22 files changed, 464 insertions(+), 184 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and
Grouping Priors
Diff between psbcGroup versions 1.0 dated 2013-04-05 and 1.1 dated 2015-02-09
Description: The package provides algorithms for fitting penalized semiparametric Bayesian Cox (PSBC) models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee
DESCRIPTION | 17 ++++++++---------
MD5 | 18 +++++++++---------
NAMESPACE | 5 +++++
R/psbcEN.R | 1 -
R/psbcFL.R | 2 +-
R/psbcGL.R | 1 -
man/psbcEN.Rd | 22 +++++++++++++---------
man/psbcFL.Rd | 21 ++++++++++++---------
man/psbcGL.Rd | 25 +++++++++++++++----------
man/psbcGroup.Rd | 15 ++++++++-------
10 files changed, 71 insertions(+), 56 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Diff between nat versions 1.5.12 dated 2014-08-21 and 1.6.4 dated 2015-02-09
Description: NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite
(see https://github.com/jefferis/nat.as) bundle of R code that we have
been using for a number of years to analyse and visualise 3D biological
image data, especially traced neurons. The nat package is considerably
cleaner, properly documented and provides all of the core functionality of
nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira
formats and read surfaces in Amira's hxsurf format. Traced neurons can be
imported from and written to SWC and Amira LineSet and SkeletonGraph
formats. These data can then be visualised in 3D via rgl, manipulated
including applying calculated registrations, e.g. using the CMTK
registration suite, and analysed. The package also has a simple
representation for neurons that have been subjected to a 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the nat.nblast extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis
nat-1.5.12/nat/man/amiralandmark-io.Rd |only
nat-1.5.12/nat/man/cmtklandmarks.Rd |only
nat-1.5.12/nat/tests/testthat/test-amiralandmarks-io.R |only
nat-1.6.4/nat/DESCRIPTION | 46 -
nat-1.6.4/nat/MD5 | 346 +++++-----
nat-1.6.4/nat/NAMESPACE | 38 -
nat-1.6.4/nat/NEWS | 70 ++
nat-1.6.4/nat/R/amiralandmarks-io.R | 129 +++
nat-1.6.4/nat/R/amiramesh-io.R | 72 +-
nat-1.6.4/nat/R/cmtk-reformat.R | 58 +
nat-1.6.4/nat/R/cmtk.R | 17
nat-1.6.4/nat/R/cmtk_io.R | 91 +-
nat-1.6.4/nat/R/dotprops.R | 14
nat-1.6.4/nat/R/hxsurf.R | 5
nat-1.6.4/nat/R/im3d.R | 99 ++
nat-1.6.4/nat/R/nat-package.R | 4
nat-1.6.4/nat/R/ndigest.R | 12
nat-1.6.4/nat/R/neuron-io-amira.R | 28
nat-1.6.4/nat/R/neuron-io-fiji.R |only
nat-1.6.4/nat/R/neuron-io-neuroml.R |only
nat-1.6.4/nat/R/neuron-io.R | 284 ++++++--
nat-1.6.4/nat/R/neuron-plot.R | 21
nat-1.6.4/nat/R/neuron.R | 228 +++---
nat-1.6.4/nat/R/neuronlist.R | 225 +++++-
nat-1.6.4/nat/R/neuronlist_sets.R |only
nat-1.6.4/nat/R/ngraph.R | 85 +-
nat-1.6.4/nat/R/nrrd-io.R | 20
nat-1.6.4/nat/R/seglist.R | 46 -
nat-1.6.4/nat/R/vaa3draw-io.R | 40 -
nat-1.6.4/nat/R/xform.R | 53 +
nat-1.6.4/nat/R/xformimage.R |only
nat-1.6.4/nat/R/xformpoints.R | 8
nat-1.6.4/nat/R/zzz.R | 39 +
nat-1.6.4/nat/README.md | 5
nat-1.6.4/nat/man/Cell07PNs.Rd | 3
nat-1.6.4/nat/man/affmat2cmtkparams.Rd | 3
nat-1.6.4/nat/man/all.equal.dotprops.Rd | 3
nat-1.6.4/nat/man/all.equal.im3d.Rd | 21
nat-1.6.4/nat/man/all.equal.neuron.Rd | 31
nat-1.6.4/nat/man/amiramesh-io.Rd | 5
nat-1.6.4/nat/man/amiratype.Rd | 5
nat-1.6.4/nat/man/as.im3d.Rd | 36 -
nat-1.6.4/nat/man/as.mesh3d.Rd | 3
nat-1.6.4/nat/man/as.neuronlist.Rd | 5
nat-1.6.4/nat/man/as.neuronlist.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/boundingbox.Rd | 31
nat-1.6.4/nat/man/c.neuronlist.Rd | 3
nat-1.6.4/nat/man/clampmax.Rd | 3
nat-1.6.4/nat/man/cmtk.bindir.Rd | 5
nat-1.6.4/nat/man/cmtk.call.Rd | 5
nat-1.6.4/nat/man/cmtk.dof2mat.Rd | 3
nat-1.6.4/nat/man/cmtk.extract_affine.Rd |only
nat-1.6.4/nat/man/cmtk.mat2dof.Rd | 3
nat-1.6.4/nat/man/cmtk.reformatx.Rd | 42 -
nat-1.6.4/nat/man/cmtk.statistics.Rd | 3
nat-1.6.4/nat/man/cmtk.targetvolume.Rd | 18
nat-1.6.4/nat/man/cmtk.version.Rd | 3
nat-1.6.4/nat/man/cmtkparams2affmat.Rd | 11
nat-1.6.4/nat/man/cmtkreg.Rd | 3
nat-1.6.4/nat/man/cmtkreglist.Rd | 10
nat-1.6.4/nat/man/coord2ind.Rd | 3
nat-1.6.4/nat/man/dotprops-arithmetic.Rd | 3
nat-1.6.4/nat/man/dotprops.Rd | 21
nat-1.6.4/nat/man/fileformats.Rd | 71 +-
nat-1.6.4/nat/man/find.neuron.Rd | 8
nat-1.6.4/nat/man/find.soma.Rd |only
nat-1.6.4/nat/man/flip.Rd | 3
nat-1.6.4/nat/man/graph.nodes.Rd | 3
nat-1.6.4/nat/man/im3d-coords.Rd | 6
nat-1.6.4/nat/man/im3d-io.Rd | 15
nat-1.6.4/nat/man/im3d.Rd | 6
nat-1.6.4/nat/man/image.im3d.Rd | 27
nat-1.6.4/nat/man/imexpand.grid.Rd | 6
nat-1.6.4/nat/man/imscalebar.Rd | 3
nat-1.6.4/nat/man/imslice.Rd | 6
nat-1.6.4/nat/man/ind2coord.Rd | 3
nat-1.6.4/nat/man/intersect.Rd |only
nat-1.6.4/nat/man/is.amiramesh.Rd | 17
nat-1.6.4/nat/man/is.fijitraces.Rd |only
nat-1.6.4/nat/man/is.neuroml.Rd |only
nat-1.6.4/nat/man/is.neuronlist.Rd | 3
nat-1.6.4/nat/man/is.nrrd.Rd | 10
nat-1.6.4/nat/man/is.swc.Rd |only
nat-1.6.4/nat/man/is.vaa3draw.Rd | 11
nat-1.6.4/nat/man/kcs20.Rd | 3
nat-1.6.4/nat/man/materials.Rd | 3
nat-1.6.4/nat/man/mirror.Rd | 3
nat-1.6.4/nat/man/nat-internal.Rd | 3
nat-1.6.4/nat/man/nat-package.Rd | 10
nat-1.6.4/nat/man/ndigest.Rd | 16
nat-1.6.4/nat/man/neuron-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuron.Rd | 13
nat-1.6.4/nat/man/neuronlist-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuronlist-dataframe-methods.Rd | 15
nat-1.6.4/nat/man/neuronlist.Rd | 3
nat-1.6.4/nat/man/neuronlistfh.Rd | 9
nat-1.6.4/nat/man/ngraph.Rd | 81 +-
nat-1.6.4/nat/man/nlapply.Rd | 10
nat-1.6.4/nat/man/nlscan.Rd |only
nat-1.6.4/nat/man/nopen3d.Rd | 3
nat-1.6.4/nat/man/normalise_swc.Rd |only
nat-1.6.4/nat/man/npop3d.Rd | 3
nat-1.6.4/nat/man/nrrd.voxdims.Rd | 3
nat-1.6.4/nat/man/origin.Rd | 6
nat-1.6.4/nat/man/pan3d.Rd | 3
nat-1.6.4/nat/man/plot.neuron.Rd | 3
nat-1.6.4/nat/man/plot.neuronlist.Rd | 18
nat-1.6.4/nat/man/plot3d.boundingbox.Rd | 3
nat-1.6.4/nat/man/plot3d.dotprops.Rd | 3
nat-1.6.4/nat/man/plot3d.hxsurf.Rd | 3
nat-1.6.4/nat/man/plot3d.neuron.Rd | 10
nat-1.6.4/nat/man/plot3d.neuronlist.Rd | 18
nat-1.6.4/nat/man/pointsinside.Rd | 3
nat-1.6.4/nat/man/potential_synapses.Rd | 11
nat-1.6.4/nat/man/projection.Rd | 6
nat-1.6.4/nat/man/prune.Rd | 3
nat-1.6.4/nat/man/read.cmtk.Rd | 7
nat-1.6.4/nat/man/read.cmtkreg.Rd | 10
nat-1.6.4/nat/man/read.hxsurf.Rd | 10
nat-1.6.4/nat/man/read.landmarks.Rd |only
nat-1.6.4/nat/man/read.morphml.Rd |only
nat-1.6.4/nat/man/read.neuron.Rd | 39 +
nat-1.6.4/nat/man/read.neuron.fiji.Rd |only
nat-1.6.4/nat/man/read.neuron.neuroml.Rd |only
nat-1.6.4/nat/man/read.neuron.swc.Rd | 6
nat-1.6.4/nat/man/read.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/read.neurons.Rd | 26
nat-1.6.4/nat/man/read.nrrd.Rd | 7
nat-1.6.4/nat/man/read.vaa3draw.Rd | 3
nat-1.6.4/nat/man/remotesync.Rd | 7
nat-1.6.4/nat/man/resample.Rd | 20
nat-1.6.4/nat/man/rootpoints.Rd | 3
nat-1.6.4/nat/man/scale.dotprops.Rd | 3
nat-1.6.4/nat/man/scale.neuron.Rd | 3
nat-1.6.4/nat/man/seglengths.Rd | 3
nat-1.6.4/nat/man/seglist.Rd | 3
nat-1.6.4/nat/man/seglist2swc.Rd | 39 -
nat-1.6.4/nat/man/segmentgraph.Rd | 3
nat-1.6.4/nat/man/setdiff.Rd |only
nat-1.6.4/nat/man/spine.Rd | 16
nat-1.6.4/nat/man/sub-.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/sub2ind.Rd | 3
nat-1.6.4/nat/man/subset.dotprops.Rd | 3
nat-1.6.4/nat/man/subset.hxsurf.Rd | 3
nat-1.6.4/nat/man/subset.neuronlist.Rd | 3
nat-1.6.4/nat/man/threshold.Rd | 10
nat-1.6.4/nat/man/union.Rd |only
nat-1.6.4/nat/man/unmask.Rd | 12
nat-1.6.4/nat/man/voxdims.Rd | 6
nat-1.6.4/nat/man/write.amiramesh.Rd | 13
nat-1.6.4/nat/man/write.cmtk.Rd | 7
nat-1.6.4/nat/man/write.cmtkreg.Rd | 7
nat-1.6.4/nat/man/write.hxsurf.Rd | 5
nat-1.6.4/nat/man/write.neuron.Rd | 14
nat-1.6.4/nat/man/write.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/write.neurons.Rd | 41 -
nat-1.6.4/nat/man/write.nrrd.Rd | 3
nat-1.6.4/nat/man/xform.Rd | 29
nat-1.6.4/nat/man/xformimage.Rd |only
nat-1.6.4/nat/man/xformpoints.Rd | 3
nat-1.6.4/nat/man/xyzmatrix.Rd | 3
nat-1.6.4/nat/tests/testthat/test-.neuron-io-remote-nocran.R |only
nat-1.6.4/nat/tests/testthat/test-amiramesh-io.R | 23
nat-1.6.4/nat/tests/testthat/test-cmtk-reformat.R | 29
nat-1.6.4/nat/tests/testthat/test-cmtk.R | 1
nat-1.6.4/nat/tests/testthat/test-hxsurf.R | 7
nat-1.6.4/nat/tests/testthat/test-im3d.R | 16
nat-1.6.4/nat/tests/testthat/test-landmarks-io.R |only
nat-1.6.4/nat/tests/testthat/test-ndigest.R | 3
nat-1.6.4/nat/tests/testthat/test-neuroml-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-fiji-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-io.R | 63 +
nat-1.6.4/nat/tests/testthat/test-neuron.R | 33
nat-1.6.4/nat/tests/testthat/test-neuronlist.R | 34
nat-1.6.4/nat/tests/testthat/test-ngraph.R | 23
nat-1.6.4/nat/tests/testthat/test-nrrd-io.R | 10
nat-1.6.4/nat/tests/testthat/test-seglist.R | 7
nat-1.6.4/nat/tests/testthat/test-xform.R | 22
nat-1.6.4/nat/tests/testthat/test-xformimage.R |only
nat-1.6.4/nat/tests/testthat/testdata/amira/landmarks.am |only
nat-1.6.4/nat/tests/testthat/testdata/landmarks |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml2 |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/MultiplePathsJoinedToMainPath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SequentiallyBranchingTrace.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SinglePath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/fitted.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/unfitted.swc |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/FCWB_2um_mask.nrrd |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/JFRC2-444_mask.nrrd |only
190 files changed, 2452 insertions(+), 1044 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Diff between letsR versions 1.0 dated 2014-05-19 and 2.0 dated 2015-02-09
Description: Includes R functions for handling and analyzing geographic data, mainly
species' geographic distributions (in ESRI shapefile format) and
environmental variables (in raster format), as well as species' information
related to their description (e.g. taxonomy and year of description) and
conservation status (e.g. category of threat, population trend) as provided
by the IUCN's RedList database. The package includes functions to create
presence-absence matrices based on species distributions and user-defined
grid systems, from which several other functions could be applied to
generate, for example, species richness rasters and maps, and geographical
midpoints of species. In addition, it provides a function to create spatial
correlograms of variables, based on the Moran's I index, under the
equiprobable or equidistant criterion to define distance classes.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
letsR-1.0/letsR/R/Data_PAM.R |only
letsR-1.0/letsR/R/Data_Phyllomedusa.R |only
letsR-1.0/letsR/R/Data_temp.R |only
letsR-1.0/letsR/R/lets.correl.R |only
letsR-1.0/letsR/R/lets_cont.R |only
letsR-1.0/letsR/R/lets_iun_habitats.R |only
letsR-1.0/letsR/man/letsR.Rd |only
letsR-2.0/letsR/DESCRIPTION | 16 -
letsR-2.0/letsR/MD5 | 116 ++++++-----
letsR-2.0/letsR/NAMESPACE | 20 +-
letsR-2.0/letsR/R/Data_iucn.R | 32 +++
letsR-2.0/letsR/R/letsR-package.R | 12 -
letsR-2.0/letsR/R/lets_addpoly.R | 74 ++++---
letsR-2.0/letsR/R/lets_addvar.R | 8
letsR-2.0/letsR/R/lets_classvar.R |only
letsR-2.0/letsR/R/lets_correl.R |only
letsR-2.0/letsR/R/lets_distmat.R |only
letsR-2.0/letsR/R/lets_field.R | 19 +
letsR-2.0/letsR/R/lets_gridirizer.R |only
letsR-2.0/letsR/R/lets_iucn.R | 7
letsR-2.0/letsR/R/lets_iucn_habitats.R |only
letsR-2.0/letsR/R/lets_iucn_historic.R | 7
letsR-2.0/letsR/R/lets_iucncont.R |only
letsR-2.0/letsR/R/lets_maplizer.R | 8
letsR-2.0/letsR/R/lets_midpoint.R | 12 -
letsR-2.0/letsR/R/lets_overlap.R |only
letsR-2.0/letsR/R/lets_pamcrop.R |only
letsR-2.0/letsR/R/lets_presab.R | 188 +++++++++++++------
letsR-2.0/letsR/R/lets_presab_birds.R | 145 ++++++++++----
letsR-2.0/letsR/R/lets_presab_points.R |only
letsR-2.0/letsR/R/lets_rangesize.R |only
letsR-2.0/letsR/R/lets_shpfilter.R | 4
letsR-2.0/letsR/R/lets_summaryze.R |only
letsR-2.0/letsR/R/plot_PresenceAbsence.R | 14 -
letsR-2.0/letsR/R/print_PresenceAbsence.R | 2
letsR-2.0/letsR/R/print_summary_PresenceAbsence.R | 4
letsR-2.0/letsR/R/removecells.R | 2
letsR-2.0/letsR/R/removesp.R | 2
letsR-2.0/letsR/R/summary_PresenceAbsence.R | 2
letsR-2.0/letsR/R/unicas.R | 2
letsR-2.0/letsR/README.md | 41 ++--
letsR-2.0/letsR/data/temp.rda |binary
letsR-2.0/letsR/man/PAM.Rd | 8
letsR-2.0/letsR/man/Phyllomedusa.Rd | 9
letsR-2.0/letsR/man/iucn.Rd | 7
letsR-2.0/letsR/man/lets.addpoly.Rd | 23 +-
letsR-2.0/letsR/man/lets.addvar.Rd | 21 +-
letsR-2.0/letsR/man/lets.classvar.Rd |only
letsR-2.0/letsR/man/lets.correl.Rd | 39 +--
letsR-2.0/letsR/man/lets.distmat.Rd |only
letsR-2.0/letsR/man/lets.field.Rd | 37 +--
letsR-2.0/letsR/man/lets.gridirizer.Rd |only
letsR-2.0/letsR/man/lets.iucn.Rd | 26 +-
letsR-2.0/letsR/man/lets.iucn.ha.Rd | 23 +-
letsR-2.0/letsR/man/lets.iucn.his.Rd | 27 +-
letsR-2.0/letsR/man/lets.iucncont.Rd | 19 +
letsR-2.0/letsR/man/lets.maplizer.Rd | 22 +-
letsR-2.0/letsR/man/lets.midpoint.Rd | 19 -
letsR-2.0/letsR/man/lets.overlap.Rd |only
letsR-2.0/letsR/man/lets.pamcrop.Rd |only
letsR-2.0/letsR/man/lets.presab.Rd | 136 +++++--------
letsR-2.0/letsR/man/lets.presab.birds.Rd | 117 +++--------
letsR-2.0/letsR/man/lets.presab.points.Rd |only
letsR-2.0/letsR/man/lets.rangesize.Rd |only
letsR-2.0/letsR/man/lets.shFilter.Rd | 50 ++---
letsR-2.0/letsR/man/lets.summarizer.Rd |only
letsR-2.0/letsR/man/lets.transf.Rd | 12 -
letsR-2.0/letsR/man/plot.PresenceAbsence.Rd | 17 -
letsR-2.0/letsR/man/print.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/print.summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/temp.Rd | 11 -
72 files changed, 758 insertions(+), 623 deletions(-)
Title: K-Sample Rank Tests and their Combinations
Diff between kSamples versions 1.0 dated 2012-08-31 and 1.0.1 dated 2015-02-09
Description: Compares k samples using the Anderson-Darling test,
Kruskal-Wallis type tests with different rank score criteria,
and Steel's multiple comparison test. It computes asymptotic,
simulated or (limited) exact P-values, all valid under
randomization, with or without ties, or conditionally under
random sampling from populations, given the observed tie
pattern. Except for Steel's test it also combines these tests
across several blocks of samples. Also analyzed are 2 x t
contingency tables and their blocked combinations using the
Kruskal-Wallis criterion. Steel's test is inverted to provide
simultaneous confidence bounds for shift parameters. A
plotting function shows that asymptotic approximations for
small sample sizes provide only very limited utility when
comparing tail probabilities with those obtained via simulation
or exact calculations.
Author: Fritz Scholz [aut, cre],
Angie Zhu [aut]
Maintainer: Fritz Scholz
kSamples-1.0.1/kSamples/DESCRIPTION | 18 ++++++++++--------
kSamples-1.0.1/kSamples/MD5 | 9 ++++-----
kSamples-1.0.1/kSamples/NAMESPACE | 6 +++++-
kSamples-1.0.1/kSamples/R/qn.test.R | 2 +-
kSamples-1.0.1/kSamples/man/kSamples-package.Rd | 4 ++--
kSamples-1.0/kSamples/man/print.kSamples.Rd |only
6 files changed, 22 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Test Accuracy when Reference Test is
Imperfect
Diff between HSROC versions 2.1.7 dated 2013-08-22 and 2.1.8 dated 2015-02-09
Description: Implements a model for joint meta-analysis of sensitivity and specificity of the diagnostic test under evaluation, while taking into account the possibly imperfect sensitivity and specificity of the reference test. This hierarchical model accounts for both within and between study variability. Estimation is carried out using a Bayesian approach, implemented via a Gibbs sampler. The model can be applied in situations where more than one reference test is used in the selected studies.
Author: Ian Schiller and Nandini Dendukuri
Maintainer: Ian Schiller
HSROC-2.1.7/HSROC/inst/doc/Tutorial.R |only
HSROC-2.1.8/HSROC/DESCRIPTION | 16 ++++++++--------
HSROC-2.1.8/HSROC/MD5 | 16 ++++++++--------
HSROC-2.1.8/HSROC/NAMESPACE | 2 +-
HSROC-2.1.8/HSROC/NEWS | 9 ++++++++-
HSROC-2.1.8/HSROC/R/HSROC-internal.R | 2 +-
HSROC-2.1.8/HSROC/build |only
HSROC-2.1.8/HSROC/data/In.house.rda |binary
HSROC-2.1.8/HSROC/data/MRI.rda |binary
HSROC-2.1.8/HSROC/inst/doc/Tutorial.pdf |binary
10 files changed, 26 insertions(+), 19 deletions(-)
Title: Redraw Base Graphics Using grid Graphics
Diff between gridGraphics versions 0.1-2 dated 2014-11-26 and 0.1-3 dated 2015-02-09
Description: Functions to convert a page of plots drawn with the
graphics package into identical output drawn with the grid package.
The result looks like the original graphics-based plot, but consists
of grid grobs and viewports that can then be manipulated with
grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/par.R | 3 +++
inst/NEWS.Rd | 8 ++++++++
4 files changed, 18 insertions(+), 7 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Diff between cmvnorm versions 1.0 dated 2014-09-09 and 1.0-1 dated 2015-02-09
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 10 -
MD5 | 16 -
build/vignette.rds |binary
inst/doc/complicator.R | 59 ++++--
inst/doc/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
inst/doc/complicator.pdf |binary
man/corr_complex.Rd | 65 +++++--
vignettes/complex_gaussian.bib | 48 +++++
vignettes/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
9 files changed, 641 insertions(+), 305 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-13.2 dated 2015-01-15 and 3.3 dated 2015-02-09
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 6 +
DESCRIPTION | 8 -
MD5 | 82 +++++++++---------
NAMESPACE | 24 ++++-
R/AT.r | 119 +++++++++++++-------------
R/BCDF.r |only
R/BiCDF.r |only
R/LM.bpm.r | 22 ++--
R/S.m.r | 50 ++++-------
R/SemiParBIVProbit.fit.R | 8 -
R/SemiParBIVProbit.fit.post.r | 124 +++++++++++++++++----------
R/SemiParBIVProbit.fit1.R | 14 ++-
R/SemiParBIVProbit.r | 165 +++++++++++++++++++++++++++----------
R/adjCov.r | 10 +-
R/adjCovSD.r | 6 +
R/bprobgHs.r | 65 +++++++++++---
R/bprobgHsPL.r | 11 +-
R/bprobgHsPO.r | 60 ++++++++++---
R/bprobgHsSS.r | 95 ++++++++++++++-------
R/copgHs.r | 65 ++------------
R/est.prev.r | 6 +
R/gt.bpm.R | 2
R/pen.r | 90 ++++++++++++--------
R/penPL.r | 8 -
R/plot.SemiParBIVProbit.r | 11 +-
R/predict.SemiParBIVProbit.r | 14 ++-
R/print.SemiParBIVProbit.r | 47 ++++++----
R/print.summary.SemiParBIVProbit.r | 87 ++++++++++++-------
R/sem.checks.r | 2
R/startSS.r | 6 -
R/summary.SemiParBIVProbit.r | 150 +++++++++++++++++----------------
man/BCDF.Rd |only
man/BiCDF.Rd |only
man/LM.bpm.Rd | 5 -
man/S.m.Rd | 2
man/SemiParBIVProbit-package.Rd | 7 +
man/SemiParBIVProbit.Rd | 59 +++++++++----
man/SemiParBIVProbit.fit1.Rd | 2
man/SemiParBIVProbitObject.Rd | 11 +-
man/bprobgHs.Rd | 2
man/bprobgHsPL.Rd | 4
man/bprobgHsPO.Rd | 2
man/bprobgHsSS.Rd | 4
man/est.prev.Rd | 2
44 files changed, 880 insertions(+), 577 deletions(-)
Permanent link
Title: Optimal k-Means Clustering for One-Dimensional Data
Diff between Ckmeans.1d.dp versions 3.02 dated 2014-03-30 and 3.3.0 dated 2015-02-09
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song
DESCRIPTION | 13 +--
MD5 | 16 ++--
NAMESPACE | 3
NEWS |only
R/Ckmeans.1d.dp.R | 25 ++++--
inst/CITATION | 12 +--
man/Ckmeans.1d.dp.Rd | 29 ++++---
man/print.Ckmeans.1d.dp.Rd | 10 +-
src/Ckmeans.1d.dp.cpp | 178 +++++++++++++++------------------------------
tests |only
10 files changed, 124 insertions(+), 162 deletions(-)
Title: SNPs Enrichment Analysis
Diff between snpEnrichment versions 1.6.0 dated 2014-11-04 and 1.6.3 dated 2015-02-09
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil
ChangeLog | 15 +++++++++++++++
DESCRIPTION | 16 ++++++++--------
MD5 | 12 ++++++------
R/Global.R | 2 +-
R/chromosome.R | 2 +-
R/enrichment.R | 7 ++++---
data/toyEnrichment.RData |binary
7 files changed, 35 insertions(+), 19 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Diff between RPushbullet versions 0.1.1 dated 2014-11-04 and 0.2.0 dated 2015-02-09
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the site
http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 51 +++++++++++++++++++++
DESCRIPTION | 20 ++++----
MD5 | 19 ++++---
NAMESPACE | 4 +
R/init.R | 99 ++++++++++++++++++++++++++---------------
R/pushes.R | 82 ++++++++++++++++++++++------------
README.md | 43 +++++++++++++++--
inst |only
man/pbGetDevices.Rd | 3 -
man/pbPost.Rd | 14 ++++-
tests/simpleTests.R | 125 ++++++++++++++++++++++++++++++++++++++++++++++++----
11 files changed, 359 insertions(+), 101 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-3 dated 2015-01-27 and 1.1-5 dated 2015-02-09
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
DESCRIPTION | 14
MD5 | 83 ++--
NAMESPACE | 9
R/TaylorDiagram.R | 4
R/TheilSen.R | 10
R/aqStats.R | 303 ++++++--------
R/calcPercentile.R | 6
R/calendarPlot.R | 22 -
R/checkPrep.R | 27 -
R/conditionalEval.R | 14
R/conditionalQuantile.R | 6
R/cutData.R | 68 +--
R/importAURN.R | 2
R/importAURNCsv.R | 2
R/importAirbase.R | 2
R/importKCL.R | 14
R/importSAQN.R | 2
R/importTraj.R | 2
R/kernelExceed.R | 2
R/linearRelation.R | 20
R/modStats.R | 22 -
R/percentileRose.R | 20
R/polarAnnulus.R | 4
R/polarCluster.R | 2
R/polarFreq.R | 2
R/polarPlot.R | 977 +++++++++++++++++++++++------------------------
R/quickText.R | 9
R/scatterPlot.R | 104 ++---
R/smoothTrend.R | 8
R/summaryPlot.R | 33 +
R/timeAverage.R | 993 ++++++++++++++++++++++++------------------------
R/timePlot.R | 8
R/timeProp.R | 12
R/timeVariation.R | 56 +-
R/trajCluster.R | 4
R/trajLevel.R | 33 -
R/utilities.R | 113 +++--
R/windRose.R | 35 -
README.md | 12
man/aqStats.Rd | 5
man/scatterPlot.Rd | 4
src/Cquantile.cpp |only
src/rolling.cpp | 124 ++---
43 files changed, 1634 insertions(+), 1558 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.5-0 dated 2013-12-11 and 1.5-1 dated 2015-02-09
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 12 +++----
MD5 | 24 +++++++--------
NAMESPACE | 2 -
NEWS | 6 +++
R/Methods.gmm.R | 28 +++++++++++++----
R/getModel.R | 5 +--
R/gmm.R | 43 ++++++++++++++++++++-------
R/momentEstim.R | 21 ++++++-------
build/vignette.rds |binary
inst/doc/gmm_with_R.R | 74 ++++++++++++++++++++++++-----------------------
inst/doc/gmm_with_R.pdf |binary
inst/doc/gmm_with_R.rnw | 4 ++
vignettes/gmm_with_R.rnw | 4 ++
13 files changed, 138 insertions(+), 85 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.6-1 dated 2014-12-10 and 0.6-2 dated 2015-02-09
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DESCRIPTION | 15
MD5 | 32 -
NEWS | 9
R/plot_DRdata_3d.R | 2
R/sysdata.rda |binary
build/partial.rdb |binary
build/vignette.rds |binary
data/ArcticLake.RData |binary
data/BloodSamples.RData |binary
data/GlacialTills.RData |binary
data/ReadingSkills.RData |binary
data/Rocks.RData |binary
inst/CITATION | 5
inst/NEWS.Rd | 6
inst/NEWS.pdf |binary
inst/doc/DirichletReg-vig.R | 824 +++++++++++++++++++++---------------------
inst/doc/DirichletReg-vig.pdf |binary
17 files changed, 452 insertions(+), 441 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10-1 dated 2015-02-04 and 0.9.10-2 dated 2015-02-09
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/BayesFactorPCL-package.R | 3 +--
R/aaGenerics.R | 2 +-
build/vignette.rds |binary
inst/doc/compare_lme4.html | 14 +++++++-------
inst/doc/manual.html | 2 +-
inst/doc/priors.html | 2 +-
man/BayesFactor-package.Rd | 5 +----
man/grapes-termin-grapes.Rd | 4 ++--
11 files changed, 34 insertions(+), 33 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.4 dated 2015-01-04 and 0.2.6 dated 2015-02-09
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
R/vardcros.R | 2 +-
R/vardom.R | 6 +++---
R/vardomh.R | 18 ++++++++++++------
R/variance_est.R | 2 +-
R/varpoord.R | 44 +++++++++++++++++++++++++-------------------
inst/CITATION | 4 ++--
inst/NEWS | 11 ++++++++++-
man/vardchanges.Rd | 2 +-
man/vardcros.Rd | 3 ++-
man/vardom.Rd | 2 +-
man/vardomh.Rd | 2 +-
man/vardpoor-package.Rd | 4 ++--
14 files changed, 80 insertions(+), 58 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Diff between excursions versions 2.0.6 dated 2015-02-02 and 2.0.16 dated 2015-02-09
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin
Maintainer: David Bolin
DESCRIPTION | 12 ++--
MD5 | 41 +++++++-------
NAMESPACE | 7 ++
R/geometry.R | 12 ++--
R/utils.R | 68 ++++++++++++++++++-----
man/continuous.Rd | 12 ++--
man/contourmap.colors.Rd | 4 -
man/contourmap.inla.Rd | 4 -
man/excursions.inla.Rd | 4 -
man/excursions.variances.Rd | 4 -
man/require.nowarnings.Rd |only
man/simconf.inla.Rd | 4 -
man/tricontour.Rd | 2
man/tricontourmap.Rd | 10 +--
src/Makevars | 6 --
src/integration.cpp | 78 +++++++++++++++++++++++++++
tests/testthat/helper-data.R | 6 --
tests/testthat/test.contourmap.R | 6 +-
tests/testthat/test.contourmap.inla.R | 2
tests/testthat/test.excursions.R | 97 ++++++++++++++++------------------
tests/testthat/test.excursions.inla.R | 2
tests/testthat/test.integration.R | 37 ++++++++----
22 files changed, 275 insertions(+), 143 deletions(-)
Title: Transcription Factor Binding Site Identification Tool
Diff between rtfbs versions 0.3.3 dated 2015-01-13 and 0.3.4 dated 2015-02-09
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
DESCRIPTION | 10 -
MD5 | 20 +--
configure | 31 +++--
configure.ac | 8 -
inst/doc/vignette.pdf |binary
man/rtfbs-package.Rd | 8 -
src/Makevars.in | 108 +++++++++----------
src/Makevars.win | 108 +++++++++----------
src/fit_column.c | 14 ++
src/fit_feature.c | 4
src/maf.c | 274 +++++++++++++++++++++++++-------------------------
11 files changed, 302 insertions(+), 283 deletions(-)
Title: Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects
Diff between LARF versions 1.2 dated 2014-09-28 and 1.3 dated 2015-02-09
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An
DESCRIPTION | 8 +--
MD5 | 12 +++-
NAMESPACE | 7 ++
R/larf.R | 120 ++++++++++++++++++++++++++-----------------------
R/npse.R |only
man/Generate.Powers.Rd |only
man/cvlm.Rd |only
man/larf.Rd | 4 -
man/npse.Rd |only
9 files changed, 86 insertions(+), 65 deletions(-)
Title: Entrez in R
Diff between rentrez versions 0.3.1 dated 2014-09-24 and 0.4 dated 2015-02-08
Description: Rentrez provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter
rentrez-0.3.1/rentrez/R/make_entrez_query.r |only
rentrez-0.3.1/rentrez/R/set_globals.r |only
rentrez-0.3.1/rentrez/man/entrez_email.Rd |only
rentrez-0.4/rentrez/DESCRIPTION | 8
rentrez-0.4/rentrez/MD5 | 64 +++--
rentrez-0.4/rentrez/NAMESPACE | 16 +
rentrez-0.4/rentrez/NEWS | 47 ++-
rentrez-0.4/rentrez/R/base.r |only
rentrez-0.4/rentrez/R/entrez_citmatch.r |only
rentrez-0.4/rentrez/R/entrez_fetch.r | 6
rentrez-0.4/rentrez/R/entrez_global_query.r | 6
rentrez-0.4/rentrez/R/entrez_info.r |only
rentrez-0.4/rentrez/R/entrez_link.r | 25 +-
rentrez-0.4/rentrez/R/entrez_post.r | 2
rentrez-0.4/rentrez/R/entrez_search.r | 84 ++++---
rentrez-0.4/rentrez/R/entrez_summary.r | 196 ++++++++++++----
rentrez-0.4/rentrez/build/vignette.rds |binary
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.R | 21 +
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.Rmd | 57 +++-
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.html | 249 +++++++++++++--------
rentrez-0.4/rentrez/man/entrez_citmatch.Rd |only
rentrez-0.4/rentrez/man/entrez_db_links.Rd |only
rentrez-0.4/rentrez/man/entrez_db_searchable.Rd |only
rentrez-0.4/rentrez/man/entrez_db_summary.Rd |only
rentrez-0.4/rentrez/man/entrez_dbs.Rd |only
rentrez-0.4/rentrez/man/entrez_fetch.Rd | 13 -
rentrez-0.4/rentrez/man/entrez_global_query.Rd | 11
rentrez-0.4/rentrez/man/entrez_info.Rd |only
rentrez-0.4/rentrez/man/entrez_link.Rd | 29 +-
rentrez-0.4/rentrez/man/entrez_post.Rd | 9
rentrez-0.4/rentrez/man/entrez_search.Rd | 38 ++-
rentrez-0.4/rentrez/man/entrez_summary.Rd | 36 ++-
rentrez-0.4/rentrez/man/parse_pubmed_xml.Rd | 3
rentrez-0.4/rentrez/man/rentrez.Rd | 3
rentrez-0.4/rentrez/tests/testthat/test_citmatch.r |only
rentrez-0.4/rentrez/tests/testthat/test_fetch.r | 26 +-
rentrez-0.4/rentrez/tests/testthat/test_info.r |only
rentrez-0.4/rentrez/tests/testthat/test_search.r | 9
rentrez-0.4/rentrez/tests/testthat/test_webenv.r | 2
rentrez-0.4/rentrez/vignettes/rentrez_tutorial.Rmd | 57 +++-
40 files changed, 686 insertions(+), 331 deletions(-)
Title: Identifying Functional Polymorphisms
Diff between IFP versions 0.1.1 dated 2015-01-10 and 0.1.2 dated 2015-02-08
Description: A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
Author: Leeyoung Park
Maintainer: Leeyoung Park
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/drgen.gm.R | 4 ++--
R/drggn.gm.R | 2 +-
R/drgn.gm.R | 2 +-
man/iter.mcmc.Rd | 16 +++++++++++++++-
6 files changed, 27 insertions(+), 13 deletions(-)
Title: Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks
Diff between geospt versions 1.0-0 dated 2014-10-08 and 1.0-1 dated 2015-02-08
Description: Estimation of the variogram through trimmed mean, radial basis
functions (optimization, prediction and cross-validation), summary
statistics from cross-validation, pocket plot, and design of
optimal sampling networks through sequential and simultaneous
points methods.
Author: Carlos Melo
Maintainer: Alí Santacruz
DESCRIPTION | 23 ++----
MD5 | 26 +++---
NAMESPACE | 3
R/graph.rbf.R | 186 +++++++++++++++++++++++---------------------------
R/rbf.R | 74 ++++++++-----------
R/rbf.tcv.R | 5 +
man/RBF.phi.Rd | 2
man/criterio.cv.Rd | 2
man/est.variograms.Rd | 6 -
man/geospt-package.Rd | 7 -
man/graph.rbf.Rd | 30 ++++----
man/rbf.cv.Rd | 2
man/rbf.cv1.Rd | 6 -
man/rbf.tcv.Rd | 2
14 files changed, 180 insertions(+), 194 deletions(-)
Title: Bradley-Terry Models
Diff between BradleyTerry2 versions 1.0-5 dated 2014-06-16 and 1.0-6 dated 2015-02-08
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner and David Firth
Maintainer: Heather Turner
BradleyTerry2-1.0-5/BradleyTerry2/data/springall.txt.gz |only
BradleyTerry2-1.0-6/BradleyTerry2/DESCRIPTION | 10 -
BradleyTerry2-1.0-6/BradleyTerry2/MD5 | 52 +++++-----
BradleyTerry2-1.0-6/BradleyTerry2/NAMESPACE | 1
BradleyTerry2-1.0-6/BradleyTerry2/R/BTabilities.R | 46 +++++---
BradleyTerry2-1.0-6/BradleyTerry2/R/BTm.R | 5
BradleyTerry2-1.0-6/BradleyTerry2/R/BTm.setup.R | 4
BradleyTerry2-1.0-6/BradleyTerry2/R/Diff.R | 15 ++
BradleyTerry2-1.0-6/BradleyTerry2/R/model.matrix.BTm.R |only
BradleyTerry2-1.0-6/BradleyTerry2/build/vignette.rds |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/CEMS.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/chameleons.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/citations.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/icehockey.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/seeds.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/sound.fields.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/springall.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/inst/NEWS | 16 +++
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.R | 12 +-
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.Rnw | 29 +++--
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary
BradleyTerry2-1.0-6/BradleyTerry2/man/BTm.Rd | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/man/CEMS.Rd | 4
BradleyTerry2-1.0-6/BradleyTerry2/man/flatlizards.Rd | 4
BradleyTerry2-1.0-6/BradleyTerry2/man/football.Rd | 10 +
BradleyTerry2-1.0-6/BradleyTerry2/tests/flatlizards.Rout.save | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/tests/predict.Rout.save | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/vignettes/BradleyTerry.Rnw | 29 +++--
28 files changed, 168 insertions(+), 102 deletions(-)
More information about nestedRanksTest at CRAN
Permanent link
Title: Causal Effect Estimation and Diagnostics with Support Vector
Machines
Diff between SVMMatch versions 1.0 dated 2015-02-07 and 1.1 dated 2015-02-08
Description: Causal effect estimation in observational data often requires identifying a set of untreated observations that are comparable to some treated group of interest. This package provides a suite of functions for identifying such a set of observations and for implementing standard and new diagnostics tools. The primary function, svmmatch(), uses support vector machines to identify a region of common support between treatment and control groups. A sensitivity analysis, balance checking, and assessment of the region of overlap between treated and control groups is included. The Bayesian implementation allows for recovery of uncertainty estimates for the treatment effect and all other parameters.
Author: Marc Ratkovic
Maintainer: Marc Ratkovic
DESCRIPTION | 9 +++++----
MD5 | 8 +++++---
NEWS |only
man/LaLonde.Rd | 2 +-
src/Makevars | 2 +-
src/Makevars.win |only
6 files changed, 12 insertions(+), 9 deletions(-)
Title: Rcpp Integration for MLPACK Library
Diff between RcppMLPACK versions 1.0.10 dated 2014-12-21 and 1.0.10-2 dated 2015-02-08
Description: MLPACK is an intuitive, fast, scalable C++ machine learning
library, meant to be a machine learning analog to LAPACK. It
aims to implement a wide array of machine learning methods
and function as a Swiss army knife for machine learning
researchers: MLPACK is from http://www.mlpack.org/: sources are included in the package.
Author: Qiang Kou, Ryan Curtin
Maintainer: Qiang Kou
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
inst/doc/RcppMLPACK-intro.pdf |binary
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 2 +-
4 files changed, 9 insertions(+), 8 deletions(-)
Title: Practical Numerical Math Functions
Diff between pracma versions 1.7.9 dated 2014-11-15 and 1.8.3 dated 2015-02-08
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers
pracma-1.7.9/pracma/R/runstest.R |only
pracma-1.7.9/pracma/man/runstest.Rd |only
pracma-1.8.3/pracma/DESCRIPTION | 14 +++----
pracma-1.8.3/pracma/MD5 | 54 ++++++++++++++---------------
pracma-1.8.3/pracma/NEWS | 34 +++++++++++++-----
pracma-1.8.3/pracma/R/circlefit.R | 16 +++++---
pracma-1.8.3/pracma/R/hurst.R | 5 ++
pracma-1.8.3/pracma/R/sumalt.R |only
pracma-1.8.3/pracma/man/agmean.Rd | 16 ++++++++
pracma-1.8.3/pracma/man/cd.Rd | 1
pracma-1.8.3/pracma/man/circlefit.Rd | 13 ++++--
pracma-1.8.3/pracma/man/clear.Rd | 1
pracma-1.8.3/pracma/man/clenshaw_curtis.Rd | 4 +-
pracma-1.8.3/pracma/man/ellip.Rd | 2 -
pracma-1.8.3/pracma/man/eta.Rd | 2 -
pracma-1.8.3/pracma/man/fresnel.Rd | 2 -
pracma-1.8.3/pracma/man/gammainc.Rd | 2 -
pracma-1.8.3/pracma/man/gammaz.Rd | 2 -
pracma-1.8.3/pracma/man/hadamard.Rd | 2 -
pracma-1.8.3/pracma/man/hankel.Rd | 2 -
pracma-1.8.3/pracma/man/hilb.Rd | 2 -
pracma-1.8.3/pracma/man/lambertW.Rd | 2 -
pracma-1.8.3/pracma/man/moler.Rd | 2 -
pracma-1.8.3/pracma/man/nile.Rd | 5 --
pracma-1.8.3/pracma/man/pascal.Rd | 2 -
pracma-1.8.3/pracma/man/rosser.Rd | 2 -
pracma-1.8.3/pracma/man/sumalt.Rd |only
pracma-1.8.3/pracma/man/vander.Rd | 2 -
pracma-1.8.3/pracma/man/wilkinson.Rd | 2 -
pracma-1.8.3/pracma/man/zeta.Rd | 2 -
30 files changed, 119 insertions(+), 74 deletions(-)
Title: Benchmark for the CEC 2005 Special Session on Real-Parameter
Optimization
Diff between cec2005benchmark versions 1.0.3 dated 2013-03-20 and 1.0.4 dated 2015-02-08
More information about cec2005benchmark at CRAN
Description: This package is a wrapper for the C implementation of the 25 benchmark functions for the CEC 2005 Special Session on Real-Parameter Optimization. The original C code by Santosh Tiwari and related documentation are available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC-05/CEC05.htm.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez
DESCRIPTION | 25 ++++++++-----------
MD5 | 58 +++++++++++++++++++++++-----------------------
NEWS | 12 ++++++---
inst/CITATION | 27 ++++++++++-----------
man/cec2005benchmark.Rd | 9 +++----
man/cec2005benchmark1.Rd | 9 +++----
man/cec2005benchmark10.Rd | 9 +++----
man/cec2005benchmark11.Rd | 9 +++----
man/cec2005benchmark12.Rd | 9 +++----
man/cec2005benchmark13.Rd | 9 +++----
man/cec2005benchmark14.Rd | 9 +++----
man/cec2005benchmark15.Rd | 9 +++----
man/cec2005benchmark16.Rd | 9 +++----
man/cec2005benchmark17.Rd | 9 +++----
man/cec2005benchmark18.Rd | 9 +++----
man/cec2005benchmark19.Rd | 9 +++----
man/cec2005benchmark2.Rd | 9 +++----
man/cec2005benchmark20.Rd | 9 +++----
man/cec2005benchmark21.Rd | 9 +++----
man/cec2005benchmark22.Rd | 9 +++----
man/cec2005benchmark23.Rd | 9 +++----
man/cec2005benchmark24.Rd | 9 +++----
man/cec2005benchmark25.Rd | 9 +++----
man/cec2005benchmark3.Rd | 9 +++----
man/cec2005benchmark4.Rd | 9 +++----
man/cec2005benchmark5.Rd | 9 +++----
man/cec2005benchmark6.Rd | 9 +++----
man/cec2005benchmark7.Rd | 9 +++----
man/cec2005benchmark8.Rd | 11 ++++----
man/cec2005benchmark9.Rd | 9 +++----
30 files changed, 192 insertions(+), 166 deletions(-)
Permanent link
Title: Technology Forecasting using DEA
Diff between TFDEA versions 0.9.5 dated 2014-10-01 and 0.9.8 dated 2015-02-07
Description: The package implements the TFDEA algorithm for technology forecasting.
It enables to estimate the arrival and/or capabilities of future technologies.
It also implements DEA (Data Envelopment Analysis) that can employ not only basic models
but also alternate model(s) to deal with infeasibility.
In addition, the package includes some standard technology forecasting data sets.
Author: Tom Shott [aut, cre],
Dong-Joon Lim [aut]
Maintainer: Tom Shott
ChangeLog |only
DESCRIPTION | 25 +-
MD5 | 26 +-
R/DEA.R | 49 ++--
R/SDEA.R | 55 ++---
R/TFDEA.R | 17 -
R/dea_common.R |only
R/dea_internal.R | 483 ++++++++++++++++++-----------------------------
R/fast_internal.R |only
R/sdea_internal.R |only
R/utility.R | 230 ++++++++++++++++------
data/wireless_2012.RData |only
man/DEA.Rd | 2
man/SDEA.Rd | 45 ++--
man/TFDEA.Rd | 2
man/fighter_jet.Rd | 16 +
man/wireless_2012.Rd |only
17 files changed, 494 insertions(+), 456 deletions(-)
Title: Stochastic Newton Sampler (SNS)
Diff between sns versions 0.9.1 dated 2014-08-30 and 1.0.0 dated 2015-02-07
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability densities where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the pdf (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani
sns-0.9.1/sns/R/bayesGLM.R |only
sns-0.9.1/sns/R/expand.1par.R |only
sns-0.9.1/sns/man/bayesGLM.Rd |only
sns-1.0.0/sns/ChangeLog |only
sns-1.0.0/sns/DESCRIPTION | 15 +-
sns-1.0.0/sns/MD5 | 33 +++--
sns-1.0.0/sns/NAMESPACE | 13 +-
sns-1.0.0/sns/R/ess.R | 100 ++++-----------
sns-1.0.0/sns/R/sns.R | 219 +++++++++++++++-------------------
sns-1.0.0/sns/R/sns.methods.R | 249 ++++++++++++++++++++++++++++++++++-----
sns-1.0.0/sns/R/zzz.R | 3
sns-1.0.0/sns/build |only
sns-1.0.0/sns/inst |only
sns-1.0.0/sns/man/ess.Rd | 35 +----
sns-1.0.0/sns/man/plot.sns.Rd |only
sns-1.0.0/sns/man/predict.sns.Rd |only
sns-1.0.0/sns/man/sns.Rd | 73 +++++++----
sns-1.0.0/sns/man/sns.part.Rd |only
sns-1.0.0/sns/man/summary.sns.Rd |only
sns-1.0.0/sns/vignettes |only
20 files changed, 453 insertions(+), 287 deletions(-)
Title: Parametric and semi-parametric analysis of semi-competing risks
data
Diff between SemiCompRisks versions 1.0 dated 2013-12-21 and 2.0 dated 2015-02-07
Description: This package contains algorithms to perform various types of parametric and semi-parametric analyses of semi-competing risks data. We also provide functions to fit survival regression models to univariate time-to-event outcome.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee
DESCRIPTION | 12
MD5 | 101
NAMESPACE | 9
R/BayesID.R | 357 ++-
R/BayesIDcor.R |only
R/BayesSurv.R | 18
R/BayesSurvcor.R |only
R/ehr.R | 4
R/methods.R | 2003 ++++++++++++++++-
R/simSurv.R | 2
data/BMT.rda |binary
data/scrCorData.rda |only
data/scrData.rda |binary
data/survData.rda |binary
man/BayesID.Rd | 61
man/BayesIDcor.Rd |only
man/BayesSurv.Rd | 55
man/BayesSurvcor.Rd |only
man/SemiCompRisks-package.Rd | 29
man/ehr.Rd | 10
man/methods.Rd | 23
man/scrCorData.Rd |only
man/simID.Rd | 12
man/simSurv.Rd | 12
src/BpeDpCorScr.c |only
src/BpeDpCorScr.h |only
src/BpeDpCorScrSM.c |only
src/BpeDpCorScrSM.h |only
src/BpeDpCorScrSM_Updates.c |only
src/BpeDpCorScr_Updates.c |only
src/BpeDpCorSurv.c |only
src/BpeDpCorSurv.h |only
src/BpeDpCorSurv_Updates.c |only
src/BpeMvnCorScr.c |only
src/BpeMvnCorScr.h |only
src/BpeMvnCorScrSM.c |only
src/BpeMvnCorScrSM.h |only
src/BpeMvnCorScrSM_Updates.c |only
src/BpeMvnCorScr_Updates.c |only
src/BpeMvnCorSurv.c |only
src/BpeMvnCorSurv.h |only
src/BpeMvnCorSurv_Updates.c |only
src/BpeScr.c | 156 -
src/BpeScrSM.c | 201 -
src/BpeScrSM_Updates.c | 758 ------
src/BpeScr_Updates.c | 723 ------
src/BpeSurv.c | 302 --
src/BpeSurv_Updates.c | 348 ---
src/BweibCorSurv.c |only
src/BweibCorSurv.h |only
src/BweibCorSurv_Updates.c |only
src/BweibDpCorScr.c |only
src/BweibDpCorScr.h |only
src/BweibDpCorScrSM.c |only
src/BweibDpCorScrSM.h |only
src/BweibDpCorScrSM_Updates.c |only
src/BweibDpCorScr_Updates.c |only
src/BweibDpCorSurv.c |only
src/BweibDpCorSurv.h |only
src/BweibDpCorSurv_Updates.c |only
src/BweibMvnCorScr.c |only
src/BweibMvnCorScr.h |only
src/BweibMvnCorScrSM.c |only
src/BweibMvnCorScrSM.h |only
src/BweibMvnCorScrSM_Updates.c |only
src/BweibMvnCorScr_Updates.c |only
src/BweibScr.c | 19
src/BweibScrSM.c |only
src/BweibScrSM.h |only
src/BweibScrSM_Updates.c |only
src/BweibScr_Updates.c | 9
src/BweibSurv.c | 20
src/BweibSurv_Updates.c | 3
src/Utilities.c | 4597 ++++++++++++++++++++++++++++++++++++++++-
74 files changed, 7080 insertions(+), 2764 deletions(-)
Title: R Interface to FOAAS
Diff between rfoaas versions 0.1.1 dated 2015-01-11 and 0.1.3 dated 2015-02-07
Description: R access to the FOAAS (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 23 +++++++++++
DESCRIPTION | 12 +++---
MD5 | 12 +++---
R/foaas.R | 84 ++++++++++++++++++++++++-------------------
README.md | 2 -
man/rfoaas-package.Rd | 80 +++++++++++++++++++++++++---------------
tests/runTestsAgainstFOAAS.R | 1
7 files changed, 133 insertions(+), 81 deletions(-)
Title: Recommender System using Matrix Factorization
Diff between recosystem versions 0.2.4 dated 2014-09-13 and 0.2.5 dated 2015-02-07
Description: This package is an R wrapper of the libmf library
(http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender
system using matrix factorization. It is typically used to
approximate an incomplete matrix using the product of two
matrices in a latent space. Other common names for this task
include "collaborative filtering", "matrix completion",
"matrix recovery", etc.
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang,
Wei-Sheng Chin and other contributors. See file AUTHORS for
details.
Maintainer: Yixuan Qiu
DESCRIPTION | 8 -
MD5 | 25 ++-
R/RecoSys.R | 112 ++++++++++++++---
README.md |only
build/vignette.rds |binary
inst/NEWS.Rd | 6
inst/doc/introduction.Rmd | 11 -
inst/doc/introduction.html | 296 +++++++++++++++++++++++----------------------
man/Reco.Rd | 12 +
man/convert.Rd | 7 -
man/output.Rd |only
man/predict.Rd | 11 -
man/train.Rd | 7 -
src/output.cpp |only
vignettes/introduction.Rmd | 11 -
15 files changed, 305 insertions(+), 201 deletions(-)
Title: H2O R Interface
Diff between h2o versions 2.8.1.1 dated 2014-10-27 and 2.8.4.4 dated 2015-02-07
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Anqi Fu [aut], Spencer Aiello [aut], Ariel Rao [aut],
Amy Wang [aut], Tom Kraljevic [aut], and Petr Maj [ctb]
with contributions from the H2O team
Maintainer: Tom Kraljevic
h2o-2.8.1.1/h2o/man/ddply.H2OParsedData.Rd |only
h2o-2.8.4.4/h2o/DESCRIPTION | 28 -
h2o-2.8.4.4/h2o/MD5 | 89 ++--
h2o-2.8.4.4/h2o/NAMESPACE | 45 +-
h2o-2.8.4.4/h2o/R/Algorithms.R | 543 +++++++++++++++----------
h2o-2.8.4.4/h2o/R/Classes.R | 223 ++++++++--
h2o-2.8.4.4/h2o/R/Internal.R | 34 +
h2o-2.8.4.4/h2o/R/ParseImport.R | 171 +++++--
h2o-2.8.4.4/h2o/R/Wrapper.R | 38 +
h2o-2.8.4.4/h2o/R/models.R | 5
h2o-2.8.4.4/h2o/demo/h2o.kmeans.R | 3
h2o-2.8.4.4/h2o/inst/branch.txt | 2
h2o-2.8.4.4/h2o/inst/buildnum.txt | 2
h2o-2.8.4.4/h2o/man/H2OGapStatModel-class.Rd |only
h2o-2.8.4.4/h2o/man/H2OPerfModel-class.Rd | 1
h2o-2.8.4.4/h2o/man/H2ORawData-class.Rd | 2
h2o-2.8.4.4/h2o/man/data.frameORnull-class.Rd |only
h2o-2.8.4.4/h2o/man/h2o-package.Rd | 23 -
h2o-2.8.4.4/h2o/man/h2o.SpeeDRF.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.addFunction.Rd | 4
h2o-2.8.4.4/h2o/man/h2o.coxph.Rd | 24 -
h2o-2.8.4.4/h2o/man/h2o.createFrame.Rd | 99 ++--
h2o-2.8.4.4/h2o/man/h2o.ddply.Rd |only
h2o-2.8.4.4/h2o/man/h2o.deeplearning.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.gains.Rd |only
h2o-2.8.4.4/h2o/man/h2o.gapStatistic.Rd | 32 -
h2o-2.8.4.4/h2o/man/h2o.gbm.Rd | 23 -
h2o-2.8.4.4/h2o/man/h2o.getTimezone.Rd |only
h2o-2.8.4.4/h2o/man/h2o.glm.Rd | 324 +++++++-------
h2o-2.8.4.4/h2o/man/h2o.importFile.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importFolder.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importHDFS.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importURL.Rd | 9
h2o-2.8.4.4/h2o/man/h2o.init.Rd | 8
h2o-2.8.4.4/h2o/man/h2o.interaction.Rd |only
h2o-2.8.4.4/h2o/man/h2o.kmeans.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.listTimezones.Rd |only
h2o-2.8.4.4/h2o/man/h2o.makeGLMModel.Rd |only
h2o-2.8.4.4/h2o/man/h2o.naiveBayes.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.order.Rd |only
h2o-2.8.4.4/h2o/man/h2o.parseRaw.Rd | 6
h2o-2.8.4.4/h2o/man/h2o.pcr.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.performance.Rd | 4
h2o-2.8.4.4/h2o/man/h2o.predict.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.randomForest.Rd | 18
h2o-2.8.4.4/h2o/man/h2o.removeVecs.Rd |only
h2o-2.8.4.4/h2o/man/h2o.saveAll.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.saveModel.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.setTimezone.Rd |only
h2o-2.8.4.4/h2o/man/h2o.uploadFile.Rd | 5
h2o-2.8.4.4/h2o/man/plot.H2OGapStatModel.Rd |only
h2o-2.8.4.4/h2o/man/rbind.H2OParsedData.Rd |only
h2o-2.8.4.4/h2o/man/summary.H2OGapStatModel.Rd |only
53 files changed, 1187 insertions(+), 648 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.3 dated 2013-02-01 and 0.4 dated 2015-02-07
Description: FindIt implements the heterogeneous
treatment effect estimation procedure proposed by Imai and
Ratkovic (2013). The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
Author: Naoki Egami
Maintainer: Naoki Egami
FindIt-0.3/FindIt/ChangeLog |only
FindIt-0.4/FindIt/DESCRIPTION | 21
FindIt-0.4/FindIt/MD5 | 15
FindIt-0.4/FindIt/NAMESPACE | 6
FindIt-0.4/FindIt/R/SVMHet.R | 3275 ++++++++++++++++++++++++----
FindIt-0.4/FindIt/man/FindIt.Rd | 282 +-
FindIt-0.4/FindIt/man/MakeAllWay.Rd | 25
FindIt-0.4/FindIt/man/MakeTwoWay.Rd | 20
FindIt-0.4/FindIt/man/Predict.FindIt.Rd |only
FindIt-0.4/FindIt/man/plot.PredictFindIt.Rd |only
10 files changed, 3138 insertions(+), 506 deletions(-)
Title: Difference Metrics for Comparing Pairs of Maps
Diff between diffeR versions 0.0-1 dated 2014-11-29 and 0.0-2 dated 2015-02-07
Description: Difference metrics for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr.
Maintainer: Alí Santacruz
DESCRIPTION | 8 +++----
MD5 | 47 +++++++++++++++++++++++--------------------
NAMESPACE | 4 ++-
R/crosstabm.R | 27 +++++++++++++++---------
R/differenceMR.R | 4 +--
R/overallComponentsPlot.R |only
R/sample2pop.R |only
demo/00Index | 1
demo/diffMetrics.R |only
man/MAD.Rd | 2 -
man/composite.Rd | 6 ++---
man/crosstabm.Rd | 21 +++++++++++++++----
man/diffTablej.Rd | 9 ++++++--
man/diffeR-package.Rd | 4 +--
man/differenceMR.Rd | 12 ++++++++--
man/exchangeDij.Rd | 4 +--
man/exchangeDj.Rd | 4 +--
man/overallAllocD.Rd | 4 +--
man/overallComponentsPlot.Rd |only
man/overallDiff.Rd | 4 +--
man/overallDiffCatj.Rd | 4 +--
man/overallExchangeD.Rd | 4 +--
man/overallQtyD.Rd | 4 +--
man/overallShiftD.Rd | 4 +--
man/quantityDj.Rd | 4 +--
man/sample2pop.Rd |only
man/shiftDj.Rd | 4 +--
27 files changed, 112 insertions(+), 73 deletions(-)
Title: Multiple Choice Test Evaluation
Diff between klausuR versions 0.12-5 dated 2012-03-11 and 0.12-10 dated 2015-02-07
Description: A set of functions designed to quickly generate results of a
multiple choice test. Generates detailed global results, lists for
anonymous feedback and personalised result feedback (in LaTeX and/or PDF
format), as well as item statistics like Cronbach's alpha or disciminatory
power. klausuR also includes a plugin for the R GUI and IDE RKWard,
providing dialogs for its basic features. To use them, install RKWard from
http://rkward.sf.net (plugins are detected automatically). Due to some
restrictions on CRAN, the full package sources are only available from the
project homepage.
Author: m.eik michalke [aut, cre]
Maintainer: m.eik michalke
klausuR-0.12-10/klausuR/ChangeLog | 227 +-
klausuR-0.12-10/klausuR/DESCRIPTION | 48
klausuR-0.12-10/klausuR/MD5 | 102 -
klausuR-0.12-10/klausuR/NAMESPACE | 17
klausuR-0.12-10/klausuR/R/00_class_01_klausuR.test.R |only
klausuR-0.12-10/klausuR/R/00_class_02_klausuR.R |only
klausuR-0.12-10/klausuR/R/00_class_03_klausuR.answ.R |only
klausuR-0.12-10/klausuR/R/00_class_04_klausuR.mult.R |only
klausuR-0.12-10/klausuR/R/01_method_plot.klausuR.R |only
klausuR-0.12-10/klausuR/R/01_method_show.klausuR.R |only
klausuR-0.12-10/klausuR/R/01_method_sort.klausuR.R |only
klausuR-0.12-10/klausuR/R/compare.R | 548 +++---
klausuR-0.12-10/klausuR/R/grand.table.R | 158 +
klausuR-0.12-10/klausuR/R/klausuR-internal.R | 1150 ++++++++-----
klausuR-0.12-10/klausuR/R/klausuR-internal.roxy.all.R | 56
klausuR-0.12-10/klausuR/R/klausuR-package.R | 18
klausuR-0.12-10/klausuR/R/klausur.R | 637 ++++---
klausuR-0.12-10/klausuR/R/klausur.data.R | 276 +--
klausuR-0.12-10/klausuR/R/klausur.gen.R | 63
klausuR-0.12-10/klausuR/R/klausur.gen.corr.R | 64
klausuR-0.12-10/klausuR/R/klausur.gen.marks.R | 356 ++--
klausuR-0.12-10/klausuR/R/klausur.mufo.R | 265 +--
klausuR-0.12-10/klausuR/R/klausur.report.R | 1180 +++++++-------
klausuR-0.12-10/klausuR/R/nret.rescale.R | 106 -
klausuR-0.12-10/klausuR/R/nret.translator.R | 430 ++---
klausuR-0.12-10/klausuR/data/antworten.mufo.rda |binary
klausuR-0.12-10/klausuR/data/antworten.rda |binary
klausuR-0.12-10/klausuR/inst/CITATION | 22
klausuR-0.12-10/klausuR/inst/NEWS.Rd | 250 ++
klausuR-0.12-10/klausuR/inst/rkward/plugins/test_data.xml | 2
klausuR-0.12-10/klausuR/man/antworten.Rd | 9
klausuR-0.12-10/klausuR/man/antworten.mufo.Rd | 9
klausuR-0.12-10/klausuR/man/compare.Rd | 112 -
klausuR-0.12-10/klausuR/man/grand.table.Rd | 61
klausuR-0.12-10/klausuR/man/klausuR-class.Rd | 56
klausuR-0.12-10/klausuR/man/klausuR-package.Rd | 43
klausuR-0.12-10/klausuR/man/klausuR.answ-class.Rd | 70
klausuR-0.12-10/klausuR/man/klausuR.mult-class.Rd | 25
klausuR-0.12-10/klausuR/man/klausuR.test-class.Rd | 26
klausuR-0.12-10/klausuR/man/klausur.Rd | 415 ++--
klausuR-0.12-10/klausuR/man/klausur.data.Rd | 258 +--
klausuR-0.12-10/klausuR/man/klausur.gen.Rd | 29
klausuR-0.12-10/klausuR/man/klausur.gen.corr.Rd | 49
klausuR-0.12-10/klausuR/man/klausur.gen.marks.Rd | 149 -
klausuR-0.12-10/klausuR/man/klausur.mufo.Rd | 171 --
klausuR-0.12-10/klausuR/man/klausur.report.Rd | 237 +-
klausuR-0.12-10/klausuR/man/nret.rescale.Rd | 43
klausuR-0.12-10/klausuR/man/nret.translator.Rd | 160 -
klausuR-0.12-10/klausuR/man/plot-methods.Rd | 71
klausuR-0.12-10/klausuR/man/show-methods.Rd | 35
klausuR-0.12-10/klausuR/man/sort-methods.Rd | 41
klausuR-0.12-10/klausuR/man/spss.data.Rd | 6
klausuR-0.12-5/klausuR/R/klausuR-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.answ-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.mult-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.test-class.R |only
klausuR-0.12-5/klausuR/R/plot.klausuR.R |only
klausuR-0.12-5/klausuR/R/show.klausuR.R |only
klausuR-0.12-5/klausuR/R/sort.klausuR.R |only
59 files changed, 4387 insertions(+), 3663 deletions(-)
Title: Advanced Tables for Markdown/HTML
Diff between htmlTable versions 1.0 dated 2014-12-21 and 1.1 dated 2015-02-07
Description: Tables with state of the art layout containing
row spanners, column spanners, table spanners, zebra striping,
and more. While allowing advanced layout the underlying CSS structure is
simple in order to maximize compatibility with MS Word/LibreOffice.
The package also contains a few text formatting functions that help outputting
text compatible with HTML/LaTeX.
Author: Max Gordon
Maintainer: Max Gordon
DESCRIPTION | 20
MD5 | 89
NAMESPACE | 5
NEWS | 17
R/htmlTable.R | 297 -
R/htmlTable_helpers.R | 82
R/htmlTable_render.R |only
R/txtFrmt.R | 22
README.md |only
build/vignette.rds |binary
inst/doc/general.R |only
inst/doc/general.Rmd |only
inst/doc/general.html |only
inst/doc/tables.R | 16
inst/doc/tables.Rmd | 16
inst/doc/tables.html | 6350 ++++++++++++------------
man/SCB.Rd | 3
man/htmlTable.Rd | 111
man/outputInt.Rd | 3
man/prAddCells.Rd | 3
man/prAddSemicolon2StrEnd.Rd | 3
man/prAttr4RgroupAdd.Rd |only
man/prGetAlign.Rd | 3
man/prGetCgroupHeader.Rd | 7
man/prGetRgroupLine.Rd |only
man/prGetRowlabelPos.Rd | 3
man/prGetStyle.Rd | 3
man/prGetThead.Rd |only
man/prMergeClr.Rd | 3
man/prPrepareAlign.Rd | 7
man/prPrepareCgroup.Rd | 20
man/prPrepareColors.Rd | 9
man/prPrepareCss.Rd | 7
man/prSkipRownames.Rd | 3
man/prTblNo.Rd | 3
man/pvalueFormatter.Rd | 3
man/splitLines4Table.Rd | 3
man/tblNoLast.Rd | 4
man/tblNoNext.Rd | 4
man/txtInt.Rd | 3
man/txtMergeLines.Rd | 3
man/txtPval.Rd | 3
man/txtRound.Rd | 11
tests/testthat/test-htmlTable.R | 77
tests/testthat/test-htmlTable_rgroup_tspanner.R |only
tests/testthat/test-htmlTable_total.R |only
tests/testthat/test-txtFrmt.R | 48
tests/visual_tests/htmlTable_markdown.Rmd | 2
tests/visual_tests/pandoc_test.Rmd |only
tests/visual_tests/pandoc_v1.13_bug.md |only
vignettes/general.Rmd |only
vignettes/tables.Rmd | 16
52 files changed, 3872 insertions(+), 3410 deletions(-)
Title: Random name generating function and data set
Diff between randomNames versions 0.0-6 dated 2013-01-21 and 0.0-8 dated 2015-02-07
Description: Function to generate random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 14 ++++++--------
MD5 | 13 +++++++------
R/randomNames.R | 4 ++--
data/datalist |only
data/randomNamesData.rda |binary
inst/CITATION | 8 ++++----
inst/NEWS | 4 ++++
man/randomNames-package.Rd | 8 ++++----
8 files changed, 27 insertions(+), 24 deletions(-)
Title: Flexible Mediation Analysis using Natural Effect Models
Diff between medflex versions 0.4.0 dated 2014-12-11 and 0.5-0 dated 2015-02-07
Description: medflex allows to run flexible mediation analyses using natural
effect models as described in Lange, Vansteelandt and Bekaert (2012),
Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet,
Buysse, Steen and Vansteelandt (2013).
Author: Johan Steen [aut, cre],
Tom Loeys [aut],
Beatrijs Moerkerke [aut],
Stijn Vansteelandt [aut],
Joris Meys [ctb] (technical support),
Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen
DESCRIPTION | 17 -
MD5 | 63 +++--
NAMESPACE | 18 +
NEWS |only
R/UPBdata_descr.R | 21 +
R/neImpute.R | 88 +++++---
R/neLht.R | 403 +++++++++++++++++++++++++++----------
R/neModel.R | 510 ++++++++++++++++++++++++++++++++++++------------
R/neWeight.R | 125 +++++++----
R/terms-expand.R | 14 -
R/utils.R | 61 ++++-
R/zzz.R |only
data/UPBdata.rda |binary
inst/CITATION | 5
inst/doc |only
man/UPBdata.Rd | 22 +-
man/expData.Rd | 5
man/neImpute.Rd | 5
man/neImpute.default.Rd | 58 +++--
man/neImpute.formula.Rd | 23 +-
man/neLht-methods.Rd | 34 +--
man/neLht.Rd | 75 ++++++-
man/neModel-methods.Rd | 60 +++--
man/neModel.Rd | 147 +++++++++----
man/neWeight.Rd | 5
man/neWeight.default.Rd | 67 +++---
man/neWeight.formula.Rd | 23 +-
man/plot.neLht.Rd | 29 +-
man/plot.neModel.Rd | 30 +-
man/weights.expData.Rd |only
vignettes |only
31 files changed, 1339 insertions(+), 569 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.14 dated 2015-01-06 and 2.15 dated 2015-02-07
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
DESCRIPTION | 10 ++---
MD5 | 35 +++++++++---------
NAMESPACE | 5 +-
R/aovlist-support.R | 2 -
R/helpers.R | 84 +++++++++++++++++++++++++--------------------
R/lsmeans.R | 12 +++---
R/ordinal-support.R | 32 ++++++++++-------
R/ref.grid.R | 4 +-
R/rms-support.R |only
R/summary.R | 67 +++++++++++++++++++----------------
inst/NEWS | 8 ++++
inst/doc/extending.R | 6 +--
inst/doc/extending.pdf |binary
inst/doc/extending.rnw | 8 ++--
inst/doc/using-lsmeans.pdf |binary
man/extending.Rd | 40 ++++++++-------------
man/models.Rd | 26 ++++++++++++-
tests/tests1.Rout.save | 11 +++--
vignettes/extending.rnw | 8 ++--
19 files changed, 206 insertions(+), 152 deletions(-)
Title: Explorer of World Population Prospects
Diff between wppExplorer versions 1.4-0 dated 2014-08-22 and 1.5-0 dated 2015-02-07
Description: A shiny interface for exploring data in wpp2008-wpp2012 packages.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/global.R | 17 +++++++++--------
R/wpp.R | 17 ++++++++++++++++-
inst/explore/server.R | 6 +++---
inst/explore/ui.R | 2 +-
man/wpp.indicator.Rd | 4 +++-
man/wppExplorer-package.Rd | 4 ++--
tests/test_functions.R | 2 +-
10 files changed, 54 insertions(+), 30 deletions(-)
Title: Linked Micromap Plots
Diff between micromap versions 1.9.1 dated 2015-01-26 and 1.9.2 dated 2015-02-06
Description: This group of functions simplifies the creation of linked micromap
plots.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [cre, ctb]
Maintainer: Tom Kincaid
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
NAMESPACE | 6 +++---
inst/NEWS.Rd | 16 ++++++++++++++++
inst/doc/CHANGES.pdf |binary
5 files changed, 29 insertions(+), 13 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Diff between BBEST versions 0.1-1 dated 2014-12-05 and 0.1-2 dated 2015-02-06
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin
DESCRIPTION | 6 -
MD5 | 16 +-
R/fits.R | 23 ++++
R/plot.R | 6 -
R/uncertainty.R | 1
README.md | 272 +++++++++++++++++++++++++++++++++++++++++++++++-
inst/gui/help/help.html | 6 +
inst/gui/server.R | 3
inst/gui/ui.R | 9 +
9 files changed, 324 insertions(+), 18 deletions(-)
Title: Variance Component Models
Diff between varComp versions 0.1-317 dated 2013-08-31 and 0.1-360 dated 2015-02-06
Description: Variance component models: REML estimation, testing fixed effect contrasts through Satterthwaite or Kenward-Roger methods, testing the nullity of variance components through (linear or quadratic) score tests or likelihood ratio tests.
Author: Long Qu (long.qu@wright.edu)
Maintainer: Long Qu
varComp-0.1-317/varComp/man/char2list.Rd |only
varComp-0.1-360/varComp/DESCRIPTION | 10 ++---
varComp-0.1-360/varComp/MD5 | 37 +++++++++----------
varComp-0.1-360/varComp/NAMESPACE | 2 -
varComp-0.1-360/varComp/R/KR.varComp.R | 3 +
varComp-0.1-360/varComp/R/p.value.R | 2 -
varComp-0.1-360/varComp/R/print.varComp.test.R | 2 -
varComp-0.1-360/varComp/R/varComp-utilities.R | 2 +
varComp-0.1-360/varComp/R/varComp.LinScore.SSAS155.R | 6 +--
varComp-0.1-360/varComp/R/varComp.LinScore.test.R | 2 -
varComp-0.1-360/varComp/R/varComp.R | 21 +++++++---
varComp-0.1-360/varComp/R/varComp.RLRT.test.R | 2 -
varComp-0.1-360/varComp/R/varComp.VM03.test.R | 6 +--
varComp-0.1-360/varComp/R/varComp.test.R | 4 +-
varComp-0.1-360/varComp/man/logLik.varComp.Rd | 2 -
varComp-0.1-360/varComp/man/varComp-package.Rd | 6 +--
varComp-0.1-360/varComp/man/varComp.Rd | 4 +-
varComp-0.1-360/varComp/man/varComp.control.Rd | 2 -
varComp-0.1-360/varComp/man/varComp.test.Rd | 2 -
varComp-0.1-360/varComp/man/varComp.test.control.Rd | 10 ++---
20 files changed, 68 insertions(+), 57 deletions(-)
Title: Genetic Analysis of Populations With Mixed Reproduction
Diff between poppr versions 1.1.3 dated 2015-02-03 and 1.1.4 dated 2015-02-06
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar
DESCRIPTION | 6 ++--
MD5 | 38 +++++++++++++++---------------
NEWS | 11 ++++++--
inst/doc/algo.Rnw | 2 -
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.Rnw | 2 -
inst/doc/poppr_manual.pdf |binary
tests/testthat/test-values.R | 2 -
vignettes/algo.Rnw | 2 -
vignettes/figure/Aeut_MLG_Ahena-1.pdf |binary
vignettes/figure/Aeut_MLG_black-1.pdf |binary
vignettes/figure/Aeut_MLG_title-1.pdf |binary
vignettes/figure/bd_histogram-1.pdf |binary
vignettes/figure/ex_data_picture-1.pdf |binary
vignettes/figure/initializing_poppr-1.pdf |binary
vignettes/figure/mlgbarplot-1.pdf |binary
vignettes/figure/mlgrareplot-1.pdf |binary
vignettes/figure/subnor-1.pdf |binary
vignettes/figure/unnamed-chunk-3-1.pdf |binary
vignettes/poppr_manual.Rnw | 2 -
20 files changed, 35 insertions(+), 30 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Diff between wux versions 1.2-2 dated 2014-11-24 and 1.2-3 dated 2015-02-06
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary NetCDF format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global circulation models (GCMs), as the CMIP5 or CMIP3 simulations, can be read in the same way as Regional Climate Models (RCMs), as e.g. the CORDEX or ENSEMBLES simulations.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik
DESCRIPTION | 20 ++++++++++++++------
MD5 | 18 +++++++++---------
R/AnovaReconstruct.R | 14 +++++++-------
R/PlotFunctions.R | 12 ++++++------
R/models2wuxSubregions.R | 6 +++---
R/summaryWux.R | 6 +++---
data/modelinput_test.rda |binary
data/userinput_CMIP5_changesignal.rda |binary
data/userinput_CMIP5_timeseries.rda |binary
man/models2wux.Rd | 2 +-
10 files changed, 43 insertions(+), 35 deletions(-)
Title: n-gram Text Regression, aka Concise Comparative Summarization
Diff between textreg versions 0.1.1 dated 2015-02-02 and 0.1.2 dated 2015-02-06
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix
DESCRIPTION | 9
MD5 | 45 +
NAMESPACE | 3
R/cross_validation_code.R | 311 ++++++------
R/package_and_data_documentation.R | 11
R/textreg.R | 628 +++++++++++++++----------
R/vizualize_phrases.R | 3
build |only
inst/doc/bathtub_vignette.R |only
inst/doc/bathtub_vignette.Rnw |only
inst/doc/bathtub_vignette.pdf |binary
inst/testthat/test-Lq.R | 2
inst/testthat/test-build.corpus.R |only
inst/testthat/test-cross-validation.R | 8
inst/testthat/test-find-threshold-C.R | 2
inst/testthat/test-ngram-call-basics.R | 1
man/build.corpus.Rd |only
man/cpp_build.corpus.Rd |only
man/cpp_textreg.Rd | 7
man/is.textreg.corpus.Rd |only
man/print.textreg.corpus.Rd |only
man/textreg-package.Rd | 10
src/RcppExports.cpp |only
src/textreg.cpp | 808 ++++++++++++++++++++-------------
vignettes |only
25 files changed, 1094 insertions(+), 754 deletions(-)
Title: basic tools for the analysis of disease outbreaks.
Diff between OutbreakTools versions 0.1-11 dated 2014-08-11 and 0.1-12 dated 2015-02-06
Description: basic tools for the analysis of disease outbreaks.
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart
ChangeLog | 17 ++-
DESCRIPTION | 12 +-
MD5 | 36 +++---
NAMESPACE | 2
R/get.incidence.R | 4
R/importFromJSON.R | 126 +++++++++++++++++++++--
R/obkData_basics.R | 11 ++
R/plotggphy.R | 15 ++
R/utils.R | 33 +++++-
build/vignette.rds |binary
data/FluH1N1pdm2009.RData |binary
data/HorseFlu.RData |binary
data/HorseFluRaw.RData |binary
data/ToyOutbreak.RData |binary
data/ToyOutbreakRaw.RData |binary
inst/doc/OutbreakTools.R | 243 +++++++++++++++------------------------------
inst/doc/OutbreakTools.pdf |binary
man/ToyOutbreak.Rd | 9 -
man/ToyOutbreakRaw.Rd | 6 -
19 files changed, 298 insertions(+), 216 deletions(-)
Title: Engle-Granger Cointegration Models
Diff between egcm versions 1.0.2 dated 2014-03-28 and 1.0.6 dated 2015-02-06
Description: This package provides an easy-to-use implementation of the Engle-Granger
two-step procedure for identifying pairs of cointegrated series. It is geared towards
the analysis of pairs of securities. Summary and plot functions are provided,
and the package is able to fetch closing prices of securities from Yahoo.
A variety of unit root tests are supported, and an improved unit root test is included.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg
egcm-1.0.2/egcm/tests/tests.Rout.save |only
egcm-1.0.6/egcm/CHANGELOG |only
egcm-1.0.6/egcm/DESCRIPTION | 19 +++---
egcm-1.0.6/egcm/MD5 | 29 ++++-----
egcm-1.0.6/egcm/NAMESPACE | 5 -
egcm-1.0.6/egcm/R/egcm.R | 106 +++++++++++++++++++---------------
egcm-1.0.6/egcm/R/egcm_extras.R | 91 ++++++++++++++++++++++++++++-
egcm-1.0.6/egcm/R/init.R | 4 -
egcm-1.0.6/egcm/README.md | 2
egcm-1.0.6/egcm/TODO | 13 ++--
egcm-1.0.6/egcm/man/allpairs.egcm.Rd |only
egcm-1.0.6/egcm/man/egcm-package.Rd | 9 +-
egcm-1.0.6/egcm/man/egcm.Rd | 25 ++++----
egcm-1.0.6/egcm/man/rar1.Rd | 2
egcm-1.0.6/egcm/man/ur_power.Rd | 22 +++----
egcm-1.0.6/egcm/man/yegcm.Rd | 5 +
egcm-1.0.6/egcm/tests/tests.R | 9 ++
17 files changed, 232 insertions(+), 109 deletions(-)
Title: Robust estimation of the generalized log gamma model.
Diff between robustloggamma versions 0.4-28 dated 2013-12-19 and 0.4-31 dated 2015-02-06
More information about robustloggamma at CRAN
Description: Robust estimation of the generalized log gamma model is provided using Quantile Tau estimator and Weighted Likelihood estimator.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
DESCRIPTION | 11 ++--
MD5 | 44 +++++++++--------
NAMESPACE | 2
R/ScoresAndDerivatives.R | 35 ++++++++++----
R/WLfunctions.R | 8 ++-
R/loggammarob.R | 45 ++++++++++--------
README | 2
data/alcoa.rda |binary
data/drg2000.rda |binary
data/sqrtloggamma.rda |binary
man/LogGammaDist.Rd | 7 ++
src/ploggamma.f |only
src/regtau.f | 65 +++++++++++++-------------
src/wrapper.c |only
tests/QTau-savedvalues.R | 14 ++---
tests/WL-savedvalues.R | 72 ++++++++++++++---------------
tests/WQTau-savedvalues.R | 52 ++++++++++-----------
tests/loggammarob-QTau.R | 7 +-
tests/loggammarob-WL.R | 9 +--
tests/loggammarob-WQTau.R | 6 +-
tests/loggammarob-oneWL.R | 8 +--
tests/oneWL-savedvalues.R | 76 +++++++++++++++---------------
tests/sumWL-savedvalues.R | 102 ++++++++++++++++++++---------------------
tests/sumoneWL-savedvalues.R | 106 +++++++++++++++++++++----------------------
24 files changed, 351 insertions(+), 320 deletions(-)
Permanent link
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Diff between mixAK versions 3.8 dated 2014-09-03 and 3.10 dated 2015-02-06
Description: This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
mixAK-3.10/mixAK/DESCRIPTION | 12 ++--
mixAK-3.10/mixAK/MD5 | 18 +++---
mixAK-3.10/mixAK/NAMESPACE | 52 +++++++++++++++++-
mixAK-3.10/mixAK/NEWS | 6 ++
mixAK-3.10/mixAK/data/Acidity.rda |binary
mixAK-3.10/mixAK/data/Enzyme.rda |binary
mixAK-3.10/mixAK/data/Galaxy.rda |binary
mixAK-3.10/mixAK/inst/CITATION | 5 -
mixAK-3.10/mixAK/inst/doc/CITATION_includeMethodology |only
mixAK-3.10/mixAK/man/NMixRelabel.Rd | 4 -
mixAK-3.8/mixAK/inst/CITATION_includeMethodology |only
11 files changed, 76 insertions(+), 21 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Diff between FactoMineR versions 1.28 dated 2014-12-12 and 1.29 dated 2015-02-06
Description: Exploratory data analysis methods such as principal component methods and clustering
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
DESCRIPTION | 15 +-
MD5 | 38 ++---
NAMESPACE | 37 +++++
R/HCPC.R | 25 ++-
R/plot.HCPC.R | 2
R/plot.spMCA.R | 8 +
R/plotellipses.r | 4
R/spMCA.R | 108 +++++++++--------
R/summary.CA.r | 7 +
inst/doc/FactoMineR.pdf |binary
inst/doc/clustering_and_pricipal_component_methods.pdf |binary
man/CaGalt.Rd | 2
man/coord.ellipse.Rd | 2
man/health.Rd | 4
man/plot.HCPC.Rd | 2
man/plot.MCA.Rd | 6
man/plot.MFA.Rd | 27 ++++
man/plot.catdes.Rd | 2
man/spMCA.Rd | 14 +-
man/tea.Rd | 2
20 files changed, 205 insertions(+), 100 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-01 1.4.6
2014-01-07 1.4.5
2012-10-12 1.4.4
2012-09-29 1.4.3
2012-08-13 1.4.2
2012-07-17 1.4.1
2012-06-13 1.4.0
2012-01-23 1.3.5
2011-08-23 1.3.4
2011-04-13 1.3.3
2010-09-08 1.3.2
2010-09-06 1.3.1
2010-07-06 1.3
Title: Regularized Principal Component Analysis for Spatial Data
Diff between SpatPCA versions 1.0 dated 2015-01-23 and 1.0.0.1 dated 2015-02-06
Description: This package provides regularized principal component
analysis incorporating smoothness, sparseness and orthogonality of
eigenfunctions by using alternating direction method of multipliers (ADMM)
algorithm.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/SpatPCA-package.Rd | 4 ++--
src/RcppExports.cpp | 8 ++++----
src/rcpp_SpatPCA.cpp | 43 ++++++++++++++++++++++++++-----------------
5 files changed, 40 insertions(+), 31 deletions(-)
Title: Text mining of PubMed Abstracts
Diff between pubmed.mineR versions 1.0.3 dated 2014-12-26 and 1.0.3.1 dated 2015-02-06
Description: Text mining of PubMed Abstracts (text and XML) from http://www.ncbi.nlm.nih.gov/pubmed.
Author: Jyoti Sharma, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
NAMESPACE | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-16 1.2
2014-02-21 1.1
2011-08-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-22 1.1.0
2013-12-17 1.0.24
2013-11-18 1.0.6
2013-07-09 0.10.0
2013-04-18 0.9.1
2013-01-24 0.8-0
2012-10-26 0.7-0
2012-08-23 0.6-0
2012-05-20 0.5-0
2012-04-21 0.4-0
2012-03-31 0.3-3
2012-03-09 0.2-1
2012-02-14 0.1-24
2012-02-14 0.1-25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-31 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-18 0.7.0
2013-10-21 0.6.0
2013-04-14 0.5.0
2013-01-23 0.4-0
2012-12-17 0.3-0
2012-11-13 0.2-0
2012-10-13 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-10 0.6.0
2013-09-18 0.5.0
2013-04-15 0.4.1
2013-04-13 0.4.0
2012-12-18 0.3-0
2012-10-11 0.2-0
2012-09-23 0.1-56
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.3 dated 2015-01-18 and 0.1.4 dated 2015-02-06
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
DESCRIPTION | 17
MD5 | 45
NAMESPACE | 14
NEWS | 15
R/print.ztable.html.R | 533 +
R/ztable.R | 463 -
R/ztable.cbind.mytable.R |only
R/ztable.mytable.R |only
R/ztable2.R | 342
R/zzz.R | 5
README.md | 9199 +++++++++++++++-------
inst/doc/ztable.R | 141
inst/doc/ztable.Rmd | 210
inst/doc/ztable.html |18158 ++++++++++++++++++++++++++++++--------------
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-01 1.0
2010-10-01 0.92
2010-09-09 0.91
2010-07-24 0.90
2010-04-29 0.85
2010-04-06 0.80
2009-12-30 0.45
2009-12-28 0.4
2009-05-29 0.3
2009-03-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-19 1.1
2013-11-10 1.0
Title: R interface to X-13ARIMA-SEATS
Diff between seasonal versions 0.70.1 dated 2014-10-02 and 0.80.0 dated 2015-02-06
Description: seasonal is an easy-to-use R-interface to X-13ARIMA-SEATS, the
newest seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax
seasonal-0.70.1/seasonal/R/deprecated.R |only
seasonal-0.70.1/seasonal/data/chcpi.RData |only
seasonal-0.70.1/seasonal/man/seasonal-deprecated.Rd |only
seasonal-0.80.0/seasonal/DESCRIPTION | 20 -
seasonal-0.80.0/seasonal/MD5 | 89 ++---
seasonal-0.80.0/seasonal/NAMESPACE | 2
seasonal-0.80.0/seasonal/NEWS | 25 +
seasonal-0.80.0/seasonal/R/checkX13.R | 65 +++-
seasonal-0.80.0/seasonal/R/defunct.R |only
seasonal-0.80.0/seasonal/R/detect.R | 33 +-
seasonal-0.80.0/seasonal/R/diagnostics.R | 7
seasonal-0.80.0/seasonal/R/genhol.R | 49 ++-
seasonal-0.80.0/seasonal/R/outlier.R | 6
seasonal-0.80.0/seasonal/R/read_series.R | 4
seasonal-0.80.0/seasonal/R/seas.R | 130 ++++++--
seasonal-0.80.0/seasonal/R/seasonal-package.R | 57 +++
seasonal-0.80.0/seasonal/R/spclist.R | 36 +-
seasonal-0.80.0/seasonal/R/static.R | 4
seasonal-0.80.0/seasonal/R/summary.R | 33 +-
seasonal-0.80.0/seasonal/README.md | 320 +++++++++++++++++---
seasonal-0.80.0/seasonal/build/vignette.rds |binary
seasonal-0.80.0/seasonal/data/holiday.RData |binary
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seasonal-0.80.0/seasonal/demo/seas.R | 2
seasonal-0.80.0/seasonal/inst/doc/seas.Rnw | 4
seasonal-0.80.0/seasonal/inst/doc/seas.pdf |binary
seasonal-0.80.0/seasonal/man/SPECS.Rd | 5
seasonal-0.80.0/seasonal/man/checkX13.Rd | 3
seasonal-0.80.0/seasonal/man/cpi.Rd | 11
seasonal-0.80.0/seasonal/man/easter.Rd | 17 -
seasonal-0.80.0/seasonal/man/exp.Rd | 8
seasonal-0.80.0/seasonal/man/final.Rd | 3
seasonal-0.80.0/seasonal/man/genhol.Rd | 49 ++-
seasonal-0.80.0/seasonal/man/identify.seas.Rd | 3
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seasonal-0.80.0/seasonal/man/inspect.Rd | 7
seasonal-0.80.0/seasonal/man/na.x13.Rd | 3
seasonal-0.80.0/seasonal/man/out.Rd | 3
seasonal-0.80.0/seasonal/man/outlier.Rd | 3
seasonal-0.80.0/seasonal/man/plot.seas.Rd | 7
seasonal-0.80.0/seasonal/man/qs.Rd | 3
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seasonal-0.80.0/seasonal/man/seasonal-package.Rd | 3
seasonal-0.80.0/seasonal/man/series.Rd | 3
seasonal-0.80.0/seasonal/man/static.Rd | 3
seasonal-0.80.0/seasonal/man/summary.seas.Rd | 34 +-
seasonal-0.80.0/seasonal/vignettes/README.tex | 287 +++++++++++++----
seasonal-0.80.0/seasonal/vignettes/seas.Rnw | 4
49 files changed, 1035 insertions(+), 329 deletions(-)
More information about SimilarityMeasures at CRAN
Permanent link
Title: An interface to the Nexus Class Library
Diff between rncl versions 0.2.0 dated 2014-12-02 and 0.2.2 dated 2015-02-06
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's phylo or phylobase's phylo4(d).
Author: Francois Michonneau [aut, cre],
Ben Bolker [aut],
Mark Holder [aut],
Paul Lewis [aut],
Brian O'Meara [aut]
Maintainer: Francois Michonneau
DESCRIPTION | 18 +++++++++---------
MD5 | 10 +++++-----
NAMESPACE | 2 +-
R/rncl.R | 4 ++--
man/read_nexus_phylo.Rd | 3 ++-
man/rncl.Rd | 7 ++++---
6 files changed, 23 insertions(+), 21 deletions(-)
Title: Nearest-neighbor Classification with Categorical Variables
Diff between knncat versions 1.2.1 dated 2015-01-24 and 1.2.2 dated 2015-02-06
Description: Scale categorical variables in such a way as
to make NN classification as accurate as possible. The code also
handles continuous variables and prior probabilities, and does
intelligent variable selection and estimation of both error rates
and the right number of NN's.
Author: Sam Buttrey
Maintainer: Sam Buttrey
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/dsort.c | 3 ++-
src/ords.c | 3 ++-
4 files changed, 11 insertions(+), 9 deletions(-)
Title: Targeted Learning of a NP Importance of a Continuous Exposure
Diff between tmle.npvi versions 0.8.1 dated 2014-02-08 and 0.9.3 dated 2015-02-05
Description: Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.
Author: Antoine Chambaz, Pierre Neuvial
Maintainer: Pierre Neuvial
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tmle.npvi-0.9.3/tmle.npvi/DESCRIPTION | 18
tmle.npvi-0.9.3/tmle.npvi/MD5 | 77 ++-
tmle.npvi-0.9.3/tmle.npvi/NAMESPACE | 34 +
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.R | 112 +++++
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.update.R | 32 -
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.updatePsi.R | 6
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tmle.npvi-0.9.3/tmle.npvi/R/estimateDevG.R | 3
tmle.npvi-0.9.3/tmle.npvi/R/estimateDevMu.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateDevTheta.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateG.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateMuAux.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateTheta.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/getSample.R | 8
tmle.npvi-0.9.3/tmle.npvi/R/mu.R | 26 +
tmle.npvi-0.9.3/tmle.npvi/R/pcor.R | 3
tmle.npvi-0.9.3/tmle.npvi/R/simulateData.R | 33 +
tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyXgivenW.R | 214 ++++-------
tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyYgivenXW.R | 122 ++----
tmle.npvi-0.9.3/tmle.npvi/R/theta.R | 131 ++++--
tmle.npvi-0.9.3/tmle.npvi/R/tmle.npvi.R | 103 ++++-
tmle.npvi-0.9.3/tmle.npvi/R/validateArgumentObs.R | 2
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tmle.npvi-0.9.3/tmle.npvi/inst/NEWS | 93 +---
tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.R | 109 +++--
tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.Rnw | 110 +++++
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tmle.npvi-0.9.3/tmle.npvi/man/tmle.npvi..Rd |only
tmle.npvi-0.9.3/tmle.npvi/vignettes/tmle-npvi.Rnw | 110 +++++
42 files changed, 876 insertions(+), 488 deletions(-)
Title: Table Monster
Diff between TableMonster versions 1.1 dated 2014-07-21 and 1.2 dated 2015-02-05
Description: Provides a user friendly interface to generation of booktab style
tables using xtable.
Author: Grant Izmirlian Jr
Maintainer: Grant Izmirlian Jr
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/TableMonster.R | 31 ++++++++++++++++++++++++++++---
man/print.TableMonster.Rd | 8 +++++++-
4 files changed, 41 insertions(+), 10 deletions(-)
Title: Multivariate Normal Functions for Sparse Covariance and
Precision Matrices.
Diff between sparseMVN versions 0.1.0 dated 2013-11-05 and 0.2.0 dated 2015-02-05
Description: Computes multivariate normal (MVN) densities, and
samples from MVN distributions, when the covariance or
precision matrix is sparse.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
sparseMVN-0.1.0/sparseMVN/R/demo_funcs.R |only
sparseMVN-0.1.0/sparseMVN/R/mvnSparse.R |only
sparseMVN-0.1.0/sparseMVN/demo |only
sparseMVN-0.1.0/sparseMVN/inst/doc/sparseMVN-vignette.Rnw |only
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sparseMVN-0.2.0/sparseMVN/DESCRIPTION | 26 +
sparseMVN-0.2.0/sparseMVN/MD5 | 36 +-
sparseMVN-0.2.0/sparseMVN/NAMESPACE | 7
sparseMVN-0.2.0/sparseMVN/NEWS | 18 +
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sparseMVN-0.2.0/sparseMVN/man/sparseMVN-package.Rd | 33 +-
sparseMVN-0.2.0/sparseMVN/tests |only
sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN-demo.Rmd |only
sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN.bib | 171 +++++++++----
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29 files changed, 189 insertions(+), 102 deletions(-)
Title: R Interface to EPP-lab, a Java Program for Exploratory
Projection Pursuit
Diff between REPPlab versions 0.9 dated 2014-09-05 and 0.9.1 dated 2015-02-05
Description: An R Interface to EPP-lab v1.0. EPP-lab is a Java program for projection pursuit using genetic algorithms written by Alain Berro and S. Larabi Marie-Sainte and is included in the package.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
inst/ChangeLog | 4 ++++
man/REPPlab-package.Rd | 10 +++++-----
4 files changed, 20 insertions(+), 16 deletions(-)
Title: PANIC Tests of Nonstationarity
Diff between PANICr versions 0.0.0.2 dated 2014-10-24 and 0.0.0.5 dated 2015-02-05
Description: This package contains a methodology that makes use of the factor
structure of large dimensional panels to understand the nature of
nonstationarity inherent in data. This is referred to as PANIC - Panel
Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC
(2004) includes valid pooling methods that allow panel unit root tests
tests to be constructed. PANIC (2004) can detect whether the
nonstationarity in a series is pervasive, or variable specific, or both.
PANIC (2010) includes the Panel Modified Sargan-Bhargava test, three models
for a Moon and Perron style test, and a bias correction for the
idiosyncratic unit root test of PANIC (2004). The PANIC model approximates
the number of factors based on Bai and Ng (2002).
Author: Steve Bronder
Maintainer: Steve Bronder
PANICr-0.0.0.2/PANICr/inst/doc/PANICr.R |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg1.rda |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg2.rda |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg3.rda |only
PANICr-0.0.0.5/PANICr/DESCRIPTION | 19
PANICr-0.0.0.5/PANICr/MD5 | 106 +--
PANICr-0.0.0.5/PANICr/R/MCMCfacstuffzzz.R | 306 ++++-----
PANICr-0.0.0.5/PANICr/R/MCMCpanic10.R | 875 +++++++++++----------------
PANICr-0.0.0.5/PANICr/R/NIPAagg1.R | 26
PANICr-0.0.0.5/PANICr/R/NIPAagg2.R | 28
PANICr-0.0.0.5/PANICr/R/NIPAagg3.R | 26
PANICr-0.0.0.5/PANICr/R/adf04.r | 158 ++--
PANICr-0.0.0.5/PANICr/R/adf10.r | 166 ++---
PANICr-0.0.0.5/PANICr/R/adfc2.R | 22
PANICr-0.0.0.5/PANICr/R/adfnc.R | 22
PANICr-0.0.0.5/PANICr/R/adfp.r | 178 ++---
PANICr-0.0.0.5/PANICr/R/cPANIC.r | 412 ++++++------
PANICr-0.0.0.5/PANICr/R/coint0.R | 22
PANICr-0.0.0.5/PANICr/R/getnfac.r | 318 ++++-----
PANICr-0.0.0.5/PANICr/R/glsd.r | 116 +--
PANICr-0.0.0.5/PANICr/R/lagn.R | 78 +-
PANICr-0.0.0.5/PANICr/R/lm1.R | 22
PANICr-0.0.0.5/PANICr/R/minindc.r | 56 -
PANICr-0.0.0.5/PANICr/R/mydiff.r | 66 +-
PANICr-0.0.0.5/PANICr/R/myols.r | 30
PANICr-0.0.0.5/PANICr/R/nuisance.r | 114 +--
PANICr-0.0.0.5/PANICr/R/nw.r | 146 ++--
PANICr-0.0.0.5/PANICr/R/panic10b.r | 737 +++++++++++-----------
PANICr-0.0.0.5/PANICr/R/pc.R | 80 +-
PANICr-0.0.0.5/PANICr/R/pool10.r | 92 +-
PANICr-0.0.0.5/PANICr/R/poolcoint.R | 94 +-
PANICr-0.0.0.5/PANICr/R/s2ar.r | 174 ++---
PANICr-0.0.0.5/PANICr/R/trimr.r | 92 +-
PANICr-0.0.0.5/PANICr/README.md | 18
PANICr-0.0.0.5/PANICr/build/vignette.rds |binary
PANICr-0.0.0.5/PANICr/inst/doc/PANICr.Rmd | 127 ---
PANICr-0.0.0.5/PANICr/inst/doc/PANICr.html | 497 +--------------
PANICr-0.0.0.5/PANICr/man/MCMCpanic04.Rd | 17
PANICr-0.0.0.5/PANICr/man/MCMCpanic10.Rd | 148 ++--
PANICr-0.0.0.5/PANICr/man/NIPAagg1.Rd | 26
PANICr-0.0.0.5/PANICr/man/NIPAagg2.Rd | 26
PANICr-0.0.0.5/PANICr/man/NIPAagg3.Rd | 26
PANICr-0.0.0.5/PANICr/man/adf.Rd | 50 -
PANICr-0.0.0.5/PANICr/man/adfc2.Rd | 18
PANICr-0.0.0.5/PANICr/man/adfnc.Rd | 18
PANICr-0.0.0.5/PANICr/man/coint0.Rd | 18
PANICr-0.0.0.5/PANICr/man/getnfac.Rd | 94 +-
PANICr-0.0.0.5/PANICr/man/lm1.Rd | 18
PANICr-0.0.0.5/PANICr/man/mydiff.Rd | 40 -
PANICr-0.0.0.5/PANICr/man/nuisance.Rd | 50 -
PANICr-0.0.0.5/PANICr/man/panic04.Rd | 85 +-
PANICr-0.0.0.5/PANICr/man/panic10.Rd | 26
PANICr-0.0.0.5/PANICr/man/pool.Rd | 42 -
PANICr-0.0.0.5/PANICr/man/s2ar.Rd | 72 +-
PANICr-0.0.0.5/PANICr/man/trimr.Rd | 42 -
PANICr-0.0.0.5/PANICr/vignettes/PANICr.Rmd | 127 ---
56 files changed, 2671 insertions(+), 3495 deletions(-)
Title: Symbolic Differentiation
Diff between Deriv versions 1.0 dated 2014-12-23 and 2.0 dated 2015-02-05
Description: Compared to R functions deriv() and D(), Deriv() admits
user-defined function as well as function substitution
in arguments of functions to be differentiated.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol
DESCRIPTION | 23 +
MD5 | 24 +
NAMESPACE | 2
NEWS | 33 ++
R/Deriv.R | 495 ++++++++++++++++----------------------
R/Simplify.R | 660 +++++++++++++++++++++++++++++++++++++++++++--------
README.md | 23 +
inst |only
man/Deriv-package.Rd | 60 +---
man/Deriv.Rd | 102 ++++---
man/Simplify.Rd |only
man/format1.Rd |only
tests |only
13 files changed, 932 insertions(+), 490 deletions(-)
Title: Default Bayesian Hypothesis Tests for Correlation, Partial
Correlation, and Mediation
Diff between BayesMed versions 1.0 dated 2014-01-28 and 1.0.1 dated 2015-02-05
Description: Default Bayesian hypothesis tests for correlation, partial correlation, and mediation
Author: Michele B. Nuijten, Ruud Wetzels, Dora Matzke, Conor V. Dolan, and Eric-Jan Wagenmakers
Maintainer: Michele B. Nuijten
BayesMed-1.0.1/BayesMed/DESCRIPTION | 12 ++++-----
BayesMed-1.0.1/BayesMed/MD5 | 29 +++++++++++-------------
BayesMed-1.0.1/BayesMed/R/print.jzs_med.R |only
BayesMed-1.0.1/BayesMed/man/BayesMed-package.Rd | 25 ++++++++++++++------
BayesMed-1.0.1/BayesMed/man/Firefighters.Rd | 7 ++++-
BayesMed-1.0.1/BayesMed/man/jzs_cor.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_corSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_med.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_medSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_partcor.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_partcorSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/plot.CI.Rd | 6 ++--
BayesMed-1.0.1/BayesMed/man/plot.JZSMed.Rd | 4 +--
BayesMed-1.0.1/BayesMed/man/plot.rjags.Rd | 10 ++++----
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18 files changed, 58 insertions(+), 47 deletions(-)
Title: SciViews GUI API - Functions to interface with Komodo Edit/IDE
Diff between svKomodo versions 0.9-62 dated 2014-03-02 and 0.9-63 dated 2015-02-05
Description: Functions to manage the GUI client, like Komodo with the
SciViews-K extension
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 ++++++
R/svKomodo-internal.R | 20 +++++++++++++++-----
inst/NEWS.Rd | 8 +++++++-
man/svKomodo-package.Rd | 4 ++--
6 files changed, 39 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy
Diff between mada versions 0.5.6 dated 2014-07-23 and 0.5.7 dated 2015-02-05
Description: Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler
DESCRIPTION | 17 +++-----
MD5 | 30 +++++++--------
NAMESPACE | 8 ++++
R/reitsma.R | 56 ++++++++++++++++++++++++++++-
R/rsSROC.R | 2 -
build/vignette.rds |binary
data/AuditC.rda |binary
data/Dementia.rda |binary
data/IAQ.rda |binary
data/SAQ.rda |binary
data/smoking.rda |binary
inst/doc/mada.R | 97 +++++++++++++++++++++++++++++----------------------
inst/doc/mada.Rnw | 32 +++++++++++++---
inst/doc/mada.pdf |binary
man/reitsma-class.Rd | 5 ++
vignettes/mada.Rnw | 32 +++++++++++++---
16 files changed, 196 insertions(+), 83 deletions(-)
Title: Simulation of Longitudinal Data
Diff between mlxR versions 2.1.0 dated 2015-01-12 and 2.1.1 dated 2015-02-05
Description: Simulation and visualization of complex
models for longitudinal data. The models are encoded using the model coding
language Mlxtran, automatically converted into C++ codes, compiled on the
fly and linked to R using the Rcpp package. That allows one to implement
very easily complex ODE-based models and complex statistical models,
including mixed effects models, for continuous, count, categorical, and
time-to-event data.
Author: Marc Lavielle [aut, cre],
Romain Francois [aut],
Fazia Bellal [ctb]
Maintainer: Marc Lavielle
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/convertmlx.R | 10 ++++++++--
R/initMlxLibrary.R | 14 +++++++++-----
4 files changed, 24 insertions(+), 14 deletions(-)
Title: Interval Testing Procedure for Functional Data
Diff between fdatest versions 2.0 dated 2014-11-24 and 2.1 dated 2015-02-05
Description: Implementation of the Interval Testing Procedure for functional data in different frameworks (i.e., one or two-population frameworks, functional linear models) by means of different basis expansions (i.e., B-spline, Fourier, and phase-amplitude Fourier). The current version of the package requires functional data evaluated on a uniform grid; it automatically projects each function on a chosen functional basis; it performs the entire family of multivariate tests; and, finally, it provides the matrix of the p-values of the previous tests and the vector of the corrected p-values. The functional basis, the coupled or uncoupled scenario, and the kind of test can be chosen by the user. The package provides also a plotting function creating a graphical output of the procedure: the p-value heat-map, the plot of the corrected p-values, and the plot of the functional data.
Author: Alessia Pini, Simone Vantini
Maintainer: Alessia Pini
DESCRIPTION | 14 ++---
MD5 | 48 +++++++++---------
NAMESPACE | 8 +++
NEWS |only
R/ITPaovbspline.R | 115 ++++++++++++++++++++++---------------------
R/ITPimage.R | 23 +++++---
R/ITPlmbspline.R | 124 +++++++++++++++--------------------------------
R/fdatest_2.1-internal.R |only
R/plot.ITP1.R | 4 -
R/plot.ITP2.R | 8 +--
data/NASAtemp.rda |binary
man/ITP1bspline.Rd | 5 +
man/ITP1fourier.Rd | 6 +-
man/ITP2bspline.Rd | 14 ++---
man/ITP2fourier.Rd | 8 +--
man/ITP2pafourier.Rd | 7 +-
man/ITPaovbspline.Rd | 7 +-
man/ITPimage.Rd | 21 +------
man/ITPlmbspline.Rd | 8 +--
man/fdatest-package.Rd | 53 +++++++++++++++-----
man/plot.ITP1.Rd | 11 ----
man/plot.ITP2.Rd | 10 ---
man/plot.ITPaov.Rd | 8 +--
man/plot.ITPlm.Rd | 9 +--
man/summary.ITPaov.Rd | 13 ++--
man/summary.ITPlm.Rd | 13 ++--
26 files changed, 259 insertions(+), 278 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Diff between smoothSurv versions 1.3-2 dated 2013-06-12 and 1.5 dated 2015-02-05
Description: This package contains primarily a function to fit
a regression model with possibly right, left or interval
censored observations and with the error distribution
expressed as a mixture of G-splines. Core part
of the computation is done in compiled C++ written
using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
DESCRIPTION | 22 +++++++++---------
MD5 | 30 +++++++++++++-----------
NAMESPACE | 9 ++++---
NEWS | 10 ++++++++
R/confint.smoothSurvReg.R |only
R/estimTdiff.R | 50 ++++++++++++++++++++++++++++++-----------
R/fdensity.smoothSurvReg.R | 4 +--
R/hazard.smoothSurvReg.R | 4 +--
R/print.estimTdiff.R | 29 +++++++++++++----------
R/smoothSurvReg.R | 45 +++++++++++++++++++++++-------------
R/survfit.smoothSurvReg.R | 4 +--
inst/CITATION | 5 +---
man/confint.smoothSurvReg.Rd |only
man/fdensity.smoothSurvReg.Rd | 6 +++-
man/hazard.smoothSurvReg.Rd | 5 +++-
man/residuals.smoothSurvReg.Rd | 2 -
man/survfit.smoothSurvReg.Rd | 5 +++-
17 files changed, 145 insertions(+), 85 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Diff between HAC versions 1.0-1 dated 2014-08-13 and 1.0-2 dated 2015-02-05
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Alexander Ristig
DESCRIPTION | 16 ++++++++--------
MD5 | 14 +++++++-------
NAMESPACE | 4 +---
R/estimate.r | 36 +++++++++++++++++++++++++++++++-----
build/vignette.rds |binary
inst/ChangeLog | 8 ++++++++
inst/doc/HAC.pdf |binary
man/estimate.copula.Rd | 2 +-
8 files changed, 56 insertions(+), 24 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Diff between bayesSurv versions 2.3-1 dated 2014-08-09 and 2.4 dated 2015-02-05
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
CHANGES | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 5 ++---
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.4-31 dated 2014-08-26 and 0.4-45 dated 2015-02-05
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
phytools-0.4-31/phytools/man/repPhylo.Rd |only
phytools-0.4-45/phytools/DESCRIPTION | 10
phytools-0.4-45/phytools/MD5 | 294 +++++++++---------
phytools-0.4-45/phytools/NAMESPACE | 19 -
phytools-0.4-45/phytools/R/densityMap.R | 17 -
phytools-0.4-45/phytools/R/fancyTree.R | 9
phytools-0.4-45/phytools/R/fitPagel.R |only
phytools-0.4-45/phytools/R/locate.fossil.R |only
phytools-0.4-45/phytools/R/locate.yeti.R | 123 ++++++-
phytools-0.4-45/phytools/R/pbtree.R | 7
phytools-0.4-45/phytools/R/phenogram.R | 15
phytools-0.4-45/phytools/R/plotSimmap.R | 138 +++++---
phytools-0.4-45/phytools/R/read.newick.R | 48 +-
phytools-0.4-45/phytools/R/sim.history.R | 27 +
phytools-0.4-45/phytools/R/utilities.R | 85 ++++-
phytools-0.4-45/phytools/R/writeAncestors.R | 13
phytools-0.4-45/phytools/man/add.arrow.Rd |only
phytools-0.4-45/phytools/man/add.color.bar.Rd | 3
phytools-0.4-45/phytools/man/add.everywhere.Rd | 3
phytools-0.4-45/phytools/man/add.random.Rd | 3
phytools-0.4-45/phytools/man/add.simmap.legend.Rd | 3
phytools-0.4-45/phytools/man/add.species.to.genus.Rd | 3
phytools-0.4-45/phytools/man/allFurcTrees.Rd | 2
phytools-0.4-45/phytools/man/anc.Bayes.Rd | 3
phytools-0.4-45/phytools/man/anc.ML.Rd | 5
phytools-0.4-45/phytools/man/anc.trend.Rd | 3
phytools-0.4-45/phytools/man/ancThresh.Rd | 4
phytools-0.4-45/phytools/man/applyBranchLengths.Rd | 3
phytools-0.4-45/phytools/man/ave.rates.Rd | 3
phytools-0.4-45/phytools/man/bind.tip.Rd | 3
phytools-0.4-45/phytools/man/bmPlot.Rd | 4
phytools-0.4-45/phytools/man/branching.diffusion.Rd | 3
phytools-0.4-45/phytools/man/brownie.lite.Rd | 2
phytools-0.4-45/phytools/man/brownieREML.Rd | 6
phytools-0.4-45/phytools/man/cladelabels.Rd | 4
phytools-0.4-45/phytools/man/collapse.to.star.Rd | 3
phytools-0.4-45/phytools/man/contMap.Rd | 6
phytools-0.4-45/phytools/man/countSimmap.Rd | 3
phytools-0.4-45/phytools/man/densityMap.Rd | 6
phytools-0.4-45/phytools/man/describe.simmap.Rd | 3
phytools-0.4-45/phytools/man/di2multi.simmap.Rd | 3
phytools-0.4-45/phytools/man/drop.clade.Rd | 3
phytools-0.4-45/phytools/man/drop.leaves.Rd | 3
phytools-0.4-45/phytools/man/drop.tip.contMap.Rd | 3
phytools-0.4-45/phytools/man/drop.tip.simmap.Rd | 3
phytools-0.4-45/phytools/man/estDiversity.Rd | 2
phytools-0.4-45/phytools/man/evol.rate.mcmc.Rd | 2
phytools-0.4-45/phytools/man/evol.vcv.Rd | 2
phytools-0.4-45/phytools/man/evolvcv.lite.Rd | 2
phytools-0.4-45/phytools/man/exhaustiveMP.Rd | 2
phytools-0.4-45/phytools/man/expm.Rd | 3
phytools-0.4-45/phytools/man/export.as.xml.Rd | 4
phytools-0.4-45/phytools/man/fancyTree.Rd | 3
phytools-0.4-45/phytools/man/fastAnc.Rd | 3
phytools-0.4-45/phytools/man/fastBM.Rd | 3
phytools-0.4-45/phytools/man/fastMRCA.Rd | 3
phytools-0.4-45/phytools/man/findMRCA.Rd | 3
phytools-0.4-45/phytools/man/fitBayes.Rd | 2
phytools-0.4-45/phytools/man/fitDiversityModel.Rd | 2
phytools-0.4-45/phytools/man/fitPagel.Rd |only
phytools-0.4-45/phytools/man/gammatest.Rd | 2
phytools-0.4-45/phytools/man/genSeq.Rd | 3
phytools-0.4-45/phytools/man/getCladesofSize.Rd | 3
phytools-0.4-45/phytools/man/getDescendants.Rd | 3
phytools-0.4-45/phytools/man/getExtant.Rd | 3
phytools-0.4-45/phytools/man/getSisters.Rd | 3
phytools-0.4-45/phytools/man/getStates.Rd | 3
phytools-0.4-45/phytools/man/ladderize.simmap.Rd |only
phytools-0.4-45/phytools/man/lambda.transform.Rd | 3
phytools-0.4-45/phytools/man/likMlambda.Rd | 3
phytools-0.4-45/phytools/man/locate.fossil.Rd |only
phytools-0.4-45/phytools/man/locate.yeti.Rd | 8
phytools-0.4-45/phytools/man/ls.tree.Rd | 3
phytools-0.4-45/phytools/man/ltt.Rd | 2
phytools-0.4-45/phytools/man/ltt95.Rd | 3
phytools-0.4-45/phytools/man/make.era.map.Rd | 3
phytools-0.4-45/phytools/man/make.simmap.Rd | 6
phytools-0.4-45/phytools/man/map.overlap.Rd | 3
phytools-0.4-45/phytools/man/map.to.singleton.Rd | 3
phytools-0.4-45/phytools/man/matchNodes.Rd | 3
phytools-0.4-45/phytools/man/mergeMappedStates.Rd | 3
phytools-0.4-45/phytools/man/midpoint.root.Rd | 8
phytools-0.4-45/phytools/man/minRotate.Rd | 3
phytools-0.4-45/phytools/man/minSplit.Rd | 2
phytools-0.4-45/phytools/man/mrp.supertree.Rd | 10
phytools-0.4-45/phytools/man/multi.mantel.Rd | 2
phytools-0.4-45/phytools/man/multiC.Rd | 3
phytools-0.4-45/phytools/man/multiRF.Rd | 7
phytools-0.4-45/phytools/man/nodeHeights.Rd | 3
phytools-0.4-45/phytools/man/optim.phylo.ls.Rd | 4
phytools-0.4-45/phytools/man/orderMappedEdge.Rd | 3
phytools-0.4-45/phytools/man/paintSubTree.Rd | 3
phytools-0.4-45/phytools/man/paste.tree.Rd | 3
phytools-0.4-45/phytools/man/pbtree.Rd | 3
phytools-0.4-45/phytools/man/pgls.Ives.Rd | 4
phytools-0.4-45/phytools/man/phenogram.Rd | 11
phytools-0.4-45/phytools/man/phyl.RMA.Rd | 3
phytools-0.4-45/phytools/man/phyl.cca.Rd | 4
phytools-0.4-45/phytools/man/phyl.pairedttest.Rd | 4
phytools-0.4-45/phytools/man/phyl.pca.Rd | 4
phytools-0.4-45/phytools/man/phyl.resid.Rd | 6
phytools-0.4-45/phytools/man/phyl.vcv.Rd | 3
phytools-0.4-45/phytools/man/phylANOVA.Rd | 2
phytools-0.4-45/phytools/man/phylo.to.map.Rd | 3
phytools-0.4-45/phytools/man/phylo.toBackbone.Rd | 3
phytools-0.4-45/phytools/man/phyloDesign.Rd | 3
phytools-0.4-45/phytools/man/phylomorphospace.Rd | 6
phytools-0.4-45/phytools/man/phylomorphospace3d.Rd | 4
phytools-0.4-45/phytools/man/phylosig.Rd | 9
phytools-0.4-45/phytools/man/phytools-package.Rd | 2
phytools-0.4-45/phytools/man/plot.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/plotBranchbyTrait.Rd | 3
phytools-0.4-45/phytools/man/plotSimmap.Rd | 6
phytools-0.4-45/phytools/man/plotThresh.Rd | 5
phytools-0.4-45/phytools/man/plotTree.Rd | 5
phytools-0.4-45/phytools/man/plotTree.wBars.Rd | 3
phytools-0.4-45/phytools/man/print.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/ratebystate.Rd | 3
phytools-0.4-45/phytools/man/rateshift.Rd | 3
phytools-0.4-45/phytools/man/read.newick.Rd | 3
phytools-0.4-45/phytools/man/read.simmap.Rd | 6
phytools-0.4-45/phytools/man/reorder.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/reorderSimmap.Rd | 3
phytools-0.4-45/phytools/man/rep.phylo.Rd |only
phytools-0.4-45/phytools/man/reroot.Rd | 4
phytools-0.4-45/phytools/man/rerootingMethod.Rd | 7
phytools-0.4-45/phytools/man/rescaleSimmap.Rd | 3
phytools-0.4-45/phytools/man/rotateNodes.Rd | 3
phytools-0.4-45/phytools/man/roundBranches.Rd | 3
phytools-0.4-45/phytools/man/roundPhylogram.Rd | 3
phytools-0.4-45/phytools/man/rstate.Rd | 3
phytools-0.4-45/phytools/man/sampleFrom.Rd | 3
phytools-0.4-45/phytools/man/setMap.Rd | 5
phytools-0.4-45/phytools/man/sim.corrs.Rd | 5
phytools-0.4-45/phytools/man/sim.history.Rd | 8
phytools-0.4-45/phytools/man/sim.ratebystate.Rd | 3
phytools-0.4-45/phytools/man/sim.rates.Rd | 3
phytools-0.4-45/phytools/man/skewers.Rd | 2
phytools-0.4-45/phytools/man/splitTree.Rd | 3
phytools-0.4-45/phytools/man/splitplotTree.Rd | 3
phytools-0.4-45/phytools/man/starTree.Rd | 3
phytools-0.4-45/phytools/man/strahlerNumber.Rd | 3
phytools-0.4-45/phytools/man/threshBayes.Rd | 7
phytools-0.4-45/phytools/man/threshDIC.Rd | 5
phytools-0.4-45/phytools/man/threshState.Rd | 5
phytools-0.4-45/phytools/man/to.matrix.Rd | 3
phytools-0.4-45/phytools/man/treeSlice.Rd | 3
phytools-0.4-45/phytools/man/untangle.Rd | 3
phytools-0.4-45/phytools/man/vcvPhylo.Rd | 3
phytools-0.4-45/phytools/man/write.simmap.Rd | 4
phytools-0.4-45/phytools/man/writeAncestors.Rd | 3
phytools-0.4-45/phytools/man/writeNexus.Rd | 3
152 files changed, 941 insertions(+), 339 deletions(-)
Title: Knockoff Filter
Diff between knockoff versions 0.1.1 dated 2014-12-20 and 0.2 dated 2015-02-05
Description: The knockoff filter is a procedure for controlling the false
discovery rate (FDR) when performing variable selection. For more information,
see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
DESCRIPTION | 13 ++++---
MD5 | 52 +++++++++++++++-------------
NAMESPACE | 2 -
NEWS |only
R/create.R | 21 +++++------
R/knockoff.R | 12 ++++--
R/stats_lasso.R | 26 +++++++++-----
R/util.R | 15 ++++++++
build/vignette.rds |binary
inst/doc/intro.R | 5 ++
inst/doc/intro.Rmd | 10 +++++
inst/doc/intro.html | 10 ++++-
inst/doc/sdp.Rmd | 14 +++++--
inst/doc/sdp.html | 13 ++++---
man/fs.Rd | 3 +
man/knockoff.Rd | 3 +
man/knockoff.create.Rd | 7 ++-
man/knockoff.filter.Rd | 10 +++--
man/knockoff.stat.fs.Rd | 3 +
man/knockoff.stat.lasso.Rd | 24 +++++++++---
man/knockoff.threshold.Rd | 3 +
man/lasso_max_lambda.Rd | 3 +
tests/testthat/InputStreamByteWrapper.class |only
tests/testthat/MatlabServer.m |only
tests/testthat/matlab_compat.R | 4 +-
tests/testthat/test_create.R | 34 +++++++++++++++---
tests/testthat/test_util.R |only
vignettes/intro.Rmd | 10 +++++
vignettes/sdp.Rmd | 14 +++++--
29 files changed, 221 insertions(+), 90 deletions(-)
Title: Package to fit spatial data in gamlss
Diff between gamlss.spatial versions 0.1 dated 2014-02-21 and 0.2 dated 2015-02-05
More information about gamlss.spatial at CRAN
Description: Spatial models in gamlss
Author: Fernanda De Bastiani, Mikis Stasinopoulos,
Maintainer: Fernanda De Bastiani
DESCRIPTION | 10
MD5 | 8
NAMESPACE | 11 -
R/extraFunctions.R | 537 ++++++++++++++++++++++++++---------------------------
R/mrf-for-gamlss.R | 5
5 files changed, 287 insertions(+), 284 deletions(-)
Permanent link
Title: Probabilistic Population Projection
Diff between bayesPop versions 5.2-1 dated 2014-11-20 and 5.2-2 dated 2015-02-05
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/get_outputs.R | 4 ++--
man/bayesPop-package.Rd | 7 ++++---
5 files changed, 18 insertions(+), 13 deletions(-)
Title: Replication Interval Functions
Diff between replicationInterval versions 0.2 dated 2014-10-24 and 0.3 dated 2015-02-04
More information about replicationInterval at CRAN
Description: A common problem faced by journal reviewers and authors is the
question of whether the results of a replication study are consistent with
the original published study. One solution to this problem is to examine
the effect size from the published study and generate the range of effect
sizes that could reasonably be obtained (due to random sampling) in a
replication attempt (i.e., calculate a replication interval). If a
replication effect size falls outside the replication interval then that
value could not have occurred to due the effects of sampling error alone.
Alternatively, if a replication effect size falls within the replication
interval then the replication results could have reasonably occurred due to
the effects of sampling error alone. This package has functions that
calculate the replication interval for two different types of effect sizes,
namely correlation (i.e., r) and the standardized mean difference
(i.e., d-value).
Author: David Stanley
Maintainer: David Stanley
DESCRIPTION | 10 +--
MD5 | 10 +--
R/replicationInterval.R | 102 +++++++++++++++++++++++--------------
man/replicationInterval-package.Rd | 8 +-
man/ri.d.Rd | 8 ++
man/ri.r.Rd | 5 +
6 files changed, 91 insertions(+), 52 deletions(-)
Permanent link
Title: Mark-Recapture Distance Sampling
Diff between mrds versions 2.1.10 dated 2014-09-27 and 2.1.12 dated 2015-02-04
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake
Maintainer: David Miller
DESCRIPTION | 27 -
MD5 | 58 +--
NEWS | 569 ++++++++++++++++++-------------------
R/ddf.R | 125 +++-----
R/ddf.trial.R | 4
R/detfct.R | 24 -
R/detfct.fit.opt.R | 85 +++--
R/dht.R | 13
R/flpt.lnl.r | 4
R/gstdint.R | 129 ++++++--
R/integratepdf.r | 73 +++-
R/mrds-package.R | 335 ++++++++++++---------
R/pdot.dsr.integrate.logistic.R | 26 +
R/predict.ds.R | 22 -
R/setcov.R | 36 --
R/varn.R | 194 +++++-------
README.md | 2
data/book.tee.data.rda |binary
man/ddf.Rd | 125 +++-----
man/detfct.fit.opt.Rd | 9
man/dht.Rd | 2
man/distpdf.Rd | 24 -
man/gstdint.Rd | 4
man/integratepdf.Rd | 2
man/lfbcvi.Rd | 109 ++++---
man/lfgcwa.Rd | 215 ++++++++-----
man/pdot.dsr.integrate.logistic.Rd | 10
man/predict.ds.Rd | 21 -
man/stake77.Rd | 8
man/varn.Rd | 28 -
30 files changed, 1209 insertions(+), 1074 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Diff between Distance versions 0.9.2 dated 2014-09-15 and 0.9.3 dated 2015-02-04
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: David Lawrence Miller
Distance-0.9.2/Distance/tests |only
Distance-0.9.3/Distance/DESCRIPTION | 22 -
Distance-0.9.3/Distance/MD5 | 47 +-
Distance-0.9.3/Distance/NAMESPACE | 2
Distance-0.9.3/Distance/NEWS | 8
Distance-0.9.3/Distance/R/Distance-package.R | 2
Distance-0.9.3/Distance/R/checkdata.R | 13
Distance-0.9.3/Distance/R/create.bins.R | 5
Distance-0.9.3/Distance/R/ds.R | 4
Distance-0.9.3/Distance/R/plot.dsmodel.R | 2
Distance-0.9.3/Distance/R/print.dsmodel.R | 2
Distance-0.9.3/Distance/R/print.summary.dsmodel.R | 2
Distance-0.9.3/Distance/R/summary.dsmodel.R | 2
Distance-0.9.3/Distance/man/Distance-package.Rd | 24 -
Distance-0.9.3/Distance/man/checkdata.Rd | 17
Distance-0.9.3/Distance/man/create.bins.Rd | 13
Distance-0.9.3/Distance/man/ds.Rd | 374 +++++++------------
Distance-0.9.3/Distance/man/flatfile.Rd | 29 -
Distance-0.9.3/Distance/man/minke.Rd | 22 -
Distance-0.9.3/Distance/man/plot.dsmodel.Rd | 10
Distance-0.9.3/Distance/man/print.dsmodel.Rd | 12
Distance-0.9.3/Distance/man/print.summary.dsmodel.Rd | 13
Distance-0.9.3/Distance/man/summary.dsmodel.Rd | 13
23 files changed, 261 insertions(+), 377 deletions(-)
Title: Trust Region Optimization for Nonlinear Functions with Sparse
Hessians
Diff between trustOptim versions 0.8.4.1 dated 2014-09-27 and 0.8.5 dated 2015-02-04
Description: Trust region algorithm for nonlinear optimization. Efficient when the Hessian of the objective function is sparse (i.e., relatively few nonzero cross-partial derivatives).
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
trustOptim-0.8.4.1/trustOptim/R/hbc_funcs.R |only
trustOptim-0.8.4.1/trustOptim/R/logit.R |only
trustOptim-0.8.4.1/trustOptim/R/rosen_funcs.R |only
trustOptim-0.8.4.1/trustOptim/R/vech.R |only
trustOptim-0.8.4.1/trustOptim/demo |only
trustOptim-0.8.4.1/trustOptim/inst/doc/trustOptim.Rnw |only
trustOptim-0.8.4.1/trustOptim/inst/doc/trustOptim.pdf |only
trustOptim-0.8.4.1/trustOptim/man/demo_funcs_hbc.Rd |only
trustOptim-0.8.4.1/trustOptim/man/inv.vech.Rd |only
trustOptim-0.8.4.1/trustOptim/man/logit.Rd |only
trustOptim-0.8.4.1/trustOptim/man/rosen.Rd |only
trustOptim-0.8.4.1/trustOptim/man/vech.Rd |only
trustOptim-0.8.4.1/trustOptim/vignettes/trustOptim.Rnw |only
trustOptim-0.8.5/trustOptim/DESCRIPTION | 31 -
trustOptim-0.8.5/trustOptim/MD5 | 63 +-
trustOptim-0.8.5/trustOptim/NAMESPACE | 18
trustOptim-0.8.5/trustOptim/NEWS | 121 +++--
trustOptim-0.8.5/trustOptim/R/RcppExports.R |only
trustOptim-0.8.5/trustOptim/R/binary-data.R |only
trustOptim-0.8.5/trustOptim/R/binary.R |only
trustOptim-0.8.5/trustOptim/R/callTrust.R | 36 -
trustOptim-0.8.5/trustOptim/build/vignette.rds |binary
trustOptim-0.8.5/trustOptim/data |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.R |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.Rmd |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.html |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.R |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.Rmd |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.html |only
trustOptim-0.8.5/trustOptim/inst/include/CG-base.h | 7
trustOptim-0.8.5/trustOptim/inst/include/CG-quasi.h | 2
trustOptim-0.8.5/trustOptim/inst/include/CG-sparse.h | 2
trustOptim-0.8.5/trustOptim/inst/include/Rfunc.cpp | 2
trustOptim-0.8.5/trustOptim/inst/include/RfuncHess.cpp | 2
trustOptim-0.8.5/trustOptim/inst/include/common_R.hpp | 4
trustOptim-0.8.5/trustOptim/man/binary-data.Rd |only
trustOptim-0.8.5/trustOptim/man/binary.Rd |only
trustOptim-0.8.5/trustOptim/man/trust.optim.Rd | 24 -
trustOptim-0.8.5/trustOptim/man/trustOptim.Rd | 3
trustOptim-0.8.5/trustOptim/src/Makevars | 5
trustOptim-0.8.5/trustOptim/src/RcppExports.cpp |only
trustOptim-0.8.5/trustOptim/src/trustOptim.cpp | 245 +++++------
trustOptim-0.8.5/trustOptim/tests |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim-demo.Rmd |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim-quick.Rmd |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim.bib | 281 +++----------
46 files changed, 350 insertions(+), 496 deletions(-)
Title: Read and Analyze PLEXOS Solutions
Diff between rplexos versions 0.12 dated 2015-01-27 and 0.12.1 dated 2015-02-04
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
DESCRIPTION | 20 ++++++++++---------
MD5 | 40 +++++++++++++++++++--------------------
R/plexos_open.R | 18 ++++++++---------
R/process_folder.R | 3 ++
R/process_input.R | 26 ++++++++++++++++++++++++-
R/process_solution.R | 4 +--
R/query.R | 5 ++++
inst/web/index.html | 21 ++++++++++----------
inst/web/is_sample_stats.html | 19 ++++++------------
inst/web/list_folders.html | 13 +++---------
inst/web/plexos_close.html | 11 ++--------
inst/web/plexos_open.html | 19 ++++++++++--------
inst/web/process_folder.html | 43 +++++++++++++++++++++++-------------------
inst/web/query_config.html | 11 ++--------
inst/web/query_log.html | 11 ++--------
inst/web/query_master.html | 27 ++++++++++++++------------
inst/web/query_property.html | 11 ++--------
inst/web/rplexos.html | 13 +++---------
inst/web/valid_columns.html | 11 ++--------
man/plexos_open.Rd | 4 +++
man/process_folder.Rd | 3 ++
21 files changed, 173 insertions(+), 160 deletions(-)
Title: Distance and Similarity Measures
Diff between proxy versions 0.4-13 dated 2014-09-22 and 0.4-14 dated 2015-02-04
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre],
Christian Buchta [aut]
Maintainer: David Meyer
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/dissimilarities.R | 31 +++++++++++++++++++++++++++++++
R/dist.R | 4 ++++
R/similarities.R | 30 ------------------------------
build/vignette.rds |binary
inst/NEWS.Rd | 5 +++++
inst/doc/overview.pdf |binary
man/dist.Rd | 1 +
tests/apply.Rout.save | 10 +++++++---
tests/distance.Rout.save | 12 ++++++++----
tests/distcalls.R | 6 +++++-
tests/distcalls.Rout.save | 25 ++++++++++++++++---------
tests/registry.Rout.save | 14 ++++++++++----
tests/util.Rout.save | 14 ++++++++++----
16 files changed, 117 insertions(+), 75 deletions(-)
Title: General Package for Meta-Analysis
Diff between meta versions 4.0-3 dated 2015-01-07 and 4.1-0 dated 2015-02-04
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 12 ++++----
MD5 | 36 +++++++++++++-------------
NAMESPACE | 4 ++
NEWS | 47 ++++++++++++++++++++++++++++++++++
R/catmeth.R | 19 +++++++++++++
R/chklevel.R | 2 -
R/forest.meta.R | 3 +-
R/meta-internal.R | 4 ++
R/metacont.R | 67 ++++++++++++++++++++++++++++++++++++++++---------
R/metagen.R | 5 +--
R/paulemandel.R | 11 +++++++-
R/print.meta.R | 4 ++
R/print.summary.meta.R | 8 ++++-
R/setchar.R | 2 -
R/settings.meta.R | 16 +++++++++++
R/summary.meta.R | 2 +
R/update.meta.R | 3 ++
man/metacont.Rd | 67 ++++++++++++++++++++++++++++++++++++++++++++-----
man/update.meta.Rd | 15 ++++++++++
19 files changed, 271 insertions(+), 56 deletions(-)
Title: Numerical Estimation of Sparse Hessians
Diff between sparseHessianFD versions 0.1.1 dated 2013-11-06 and 0.2.0 dated 2015-02-04
More information about sparseHessianFD at CRAN
Description: Computes Hessian of a scalar-valued function, and returns it in
sparse Matrix format, using ACM TOMS Algorithm 636. The user must supply the objective function, the
gradient, and the row and column indices of the non-zero elements of the
lower triangle of the Hessian (i.e., the sparsity structure must be known
in advance). The algorithm exploits this sparsity, so Hessians can be
computed quickly even when the number of arguments to the objective
functions is large. This package is intended to be useful for numeric
optimization (e.g., with the trustOptim package) or in simulation (e.g.,
the sparseMVN package). The underlying algorithm is ACM TOMS Algorithm 636,
written by Coleman, Garbow and More (ACM Transactions on Mathematical
Software, 11:4, Dec. 1985).
Author: R interface code by Michael Braun
Original Fortran code by Thomas F. Coleman, Burton S. Garbow and
Jorge J. More.
Maintainer: Michael Braun
sparseHessianFD-0.1.1/sparseHessianFD/R/classes.R |only
sparseHessianFD-0.1.1/sparseHessianFD/R/wrappers.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/doc/sparseHessianFD.Rnw |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/doc/sparseHessianFD.pdf |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/examples/ex_funcs.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/examples/example.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/Rfunc.cpp |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/common_R.hpp |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/exceptions.hpp |only
sparseHessianFD-0.1.1/sparseHessianFD/man/Coord.to.Sym.Pattern.Matrix.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/Sym.CSC.to.Matrix.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/newSparseHessian.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/sparseHessianObj-class.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/wrappers.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/src/Rinterface.cpp |only
sparseHessianFD-0.1.1/sparseHessianFD/vignettes/sparseHessianFD.Rnw |only
sparseHessianFD-0.1.1/sparseHessianFD/vignettes/sparseHessianFD.bib |only
sparseHessianFD-0.2.0/sparseHessianFD/DESCRIPTION | 48 +++--
sparseHessianFD-0.2.0/sparseHessianFD/MD5 | 64 ++++---
sparseHessianFD-0.2.0/sparseHessianFD/NAMESPACE | 18 +-
sparseHessianFD-0.2.0/sparseHessianFD/NEWS | 39 ++++
sparseHessianFD-0.2.0/sparseHessianFD/R/binary-data.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/binary.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/deprecated.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/matrices.R | 84 +++++-----
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD-class.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD-new.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD.R |only
sparseHessianFD-0.2.0/sparseHessianFD/build/vignette.rds |binary
sparseHessianFD-0.2.0/sparseHessianFD/data |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/CITATION |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/Rfunc_old.cpp |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.R |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.Rmd |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.html |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/examples/ex2.R |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/include/except.h |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/include/func.h |only
sparseHessianFD-0.2.0/sparseHessianFD/man/Coord.to.Pattern.Matrix.Rd | 46 ++---
sparseHessianFD-0.2.0/sparseHessianFD/man/Matrix.to.Coord.Rd | 31 +--
sparseHessianFD-0.2.0/sparseHessianFD/man/binary-data.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/binary.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-class.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-deprecated.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-package.Rd | 69 +++-----
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD.new.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/src/FDHS-DSSM.c | 6
sparseHessianFD-0.2.0/sparseHessianFD/src/Makevars | 6
sparseHessianFD-0.2.0/sparseHessianFD/src/Makevars.win | 7
sparseHessianFD-0.2.0/sparseHessianFD/src/rcpp_module.cpp |only
sparseHessianFD-0.2.0/sparseHessianFD/tests |only
sparseHessianFD-0.2.0/sparseHessianFD/vignettes/sparseHessianFD.Rmd |only
52 files changed, 236 insertions(+), 182 deletions(-)
Permanent link
Title: Extract Statistics from Articles and Recompute P Values
Diff between statcheck versions 1.0.0 dated 2014-11-20 and 1.0.1 dated 2015-02-04
Description: Extract statistics from articles and recompute p values.
Author: Sacha Epskamp
Maintainer: Michele B. Nuijten
DESCRIPTION | 10 +--
MD5 | 8 +-
R/htmlImport.R | 2
R/statcheck.R | 32 +++++++++--
man/statcheck.Rd | 151 +++++++++++++++++++++++++++++++++++++------------------
5 files changed, 138 insertions(+), 65 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Diff between netmeta versions 0.6-0 dated 2014-07-29 and 0.7-0 dated 2015-02-04
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 14 +++---
MD5 | 47 ++++++++++++++--------
NAMESPACE | 6 ++
NEWS | 85 +++++++++++++++++++++++++++++++++++++++++
R/chklist.R |only
R/decomp.tau.R | 2
R/forest.netmeta.R | 29 +++++---------
R/netgraph.R | 73 +++++++++++++++--------------------
R/netheat.R | 19 +++++++--
R/netmeta.R | 88 ++++++++++++++++++-------------------------
R/nma.krahn.R | 14 +++---
R/nma.ruecker.R | 2
R/pairwise.R |only
R/print.decomp.design.R | 14 +++---
R/print.netmeta.R | 11 +++--
R/print.summary.netmeta.R | 48 +++++++++++++++++++----
R/setref.R |only
R/setseq.R |only
R/stress.R | 2
R/summary.netmeta.R | 3 +
R/tau.within.R | 7 ++-
data/dietaryfat.csv.gz |only
data/parkinson.csv.gz |only
data/smokingcessation.csv.gz |only
man/dietaryfat.Rd |only
man/netgraph.Rd | 14 +++---
man/netmeta.Rd | 2
man/pairwise.Rd |only
man/parkinson.Rd |only
man/smokingcessation.Rd |only
30 files changed, 306 insertions(+), 174 deletions(-)
Title: Plot rpart Models. An Enhanced Version of plot.rpart
Diff between rpart.plot versions 1.5.1 dated 2014-12-14 and 1.5.2 dated 2015-02-04
Description: Plot rpart models. Extends plot.rpart and text.rpart in
the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
NEWS | 4 ++++
R/layout.R | 4 ++--
R/lib.R | 26 +++++++++++---------------
inst/doc/prp.pdf |binary
inst/slowtests/test.prp.R | 11 +++++++++++
inst/slowtests/test.prp.Rout.save | 13 ++++++++++++-
8 files changed, 50 insertions(+), 28 deletions(-)
Title: R Individual Specialization (RInSp)
Diff between RInSp versions 1.0 dated 2013-07-26 and 1.1 dated 2015-02-04
Description: Functions to calculate several ecological indices of individual and population niche width
(Araujo's E, clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's
WIC/TNW) to assess individual specialization based on data of resource use. Resource use can be
quantified by counts of categories, measures of mass/lenght or proportions. Monte Carlo resampling
procedures are available for hypothesis testing against multinomial null models.
Author: Dr. Nicola Zaccarelli, Dr. Giorgio Mancinelli, and Prof. Dan Bolnick
Maintainer: Dr. Nicola Zaccarelli
DESCRIPTION | 21 +--
MD5 | 30 ++--
R/Eindex.R | 319 ++++++++++++++++++++++++++-------------------------
R/like.Wi.R | 8 -
inst/citation | 39 +++---
man/Eindex.Rd | 185 +++++++++++++++--------------
man/Emc.Rd | 2
man/RInSp-package.Rd | 18 ++
man/like.Wi.Rd | 107 ++++++++---------
man/overlap.Rd | 18 +-
man/sumMC.RInSp.Rd | 2
src/Emc.c | 61 +++++----
src/MCprocedure.c | 19 +--
src/PSicalc.c | 14 +-
src/WTcMC.c | 17 +-
src/WTdMC.c | 15 +-
16 files changed, 465 insertions(+), 410 deletions(-)
Title: Miscellaneous Useful Functions
Diff between miscFuncs versions 1.2-6 dated 2014-07-23 and 1.2-7 dated 2015-02-04
Description: LaTeX tables, Kalman filter, web scraping, development tools,
relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 +++----
MD5 | 48 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
build/vignette.rds |binary
inst/doc/miscFuncs.Rtex | 6 ++++-
inst/doc/miscFuncs.pdf |binary
man/EKFadvance.Rd | 3 +-
man/KFadvance.Rd | 3 +-
man/KFadvanceAR2.Rd | 3 +-
man/KFtemplates.Rd | 3 +-
man/bin.Rd | 3 +-
man/generic.Rd | 3 +-
man/getstrbetween.Rd | 3 +-
man/getwikicoords.Rd | 3 +-
man/latexformat.Rd | 3 +-
man/latextable.Rd | 3 +-
man/method.Rd | 3 +-
man/print22.Rd | 3 +-
man/roxbc.Rd | 3 +-
man/roxbuild.Rd | 3 +-
man/roxtext.Rd | 3 +-
man/timeop.Rd | 3 +-
man/twotwoinfo.Rd | 3 +-
man/vdc.Rd | 3 +-
vignettes/miscFuncs.Rtex | 6 ++++-
25 files changed, 75 insertions(+), 49 deletions(-)
Title: Multivariable Fractional Polynomials
Diff between mfp versions 1.5.0 dated 2014-10-02 and 1.5.1 dated 2015-02-04
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: original by Gareth Ambler
Maintainer: Stephan Luecke
mfp-1.5.0/mfp/Changelog |only
mfp-1.5.0/mfp/inst/doc/mfp.R |only
mfp-1.5.0/mfp/inst/doc/mfp.Rnw |only
mfp-1.5.0/mfp/inst/doc/mfp.pdf |only
mfp-1.5.0/mfp/vignettes/mfp.Rnw |only
mfp-1.5.0/mfp/vignettes/mfp.bib |only
mfp-1.5.1/mfp/ChangeLog |only
mfp-1.5.1/mfp/DESCRIPTION | 8
mfp-1.5.1/mfp/MD5 | 20 -
mfp-1.5.1/mfp/build/vignette.rds |binary
mfp-1.5.1/mfp/data/bodyfat.rda |binary
mfp-1.5.1/mfp/inst/doc/mfp_vignette.R |only
mfp-1.5.1/mfp/inst/doc/mfp_vignette.Rnw |only
mfp-1.5.1/mfp/inst/doc/mfp_vignette.pdf |only
mfp-1.5.1/mfp/man/mfp.Rd | 316 +++++++++++++++----------------
mfp-1.5.1/mfp/vignettes/mfp_vignette.Rnw |only
mfp-1.5.1/mfp/vignettes/mfp_vignette.bib |only
17 files changed, 172 insertions(+), 172 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-7 dated 2015-01-24 and 1.3-8 dated 2015-02-04
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
build/vignette.rds |binary
inst/doc/lgcp.Rnw | 8 ++++++--
inst/doc/lgcp.pdf |binary
vignettes/lgcp.Rnw | 8 ++++++--
6 files changed, 21 insertions(+), 13 deletions(-)
Title: Quasi-Periodic Time Series Characteristics
Diff between Tides versions 1.0 dated 2013-08-29 and 1.1 dated 2015-02-04
Description: Calculate Characteristics of Qasi-Periodic Time Series, e.g. Estuarine Water Levels.
Author: Tom Cox
Maintainer: Tom Cox
Tides-1.0/Tides/doc |only
Tides-1.1/Tides/ChangeLog |only
Tides-1.1/Tides/DESCRIPTION | 16 ++++-----
Tides-1.1/Tides/MD5 | 43 +++++++++---------------
Tides-1.1/Tides/R/Tides.R | 49 ++++++++++++++++++++++------
Tides-1.1/Tides/data/data.rda |binary
Tides-1.1/Tides/data/example.RData |binary
Tides-1.1/Tides/inst |only
Tides-1.1/Tides/man/IF.Rd | 2 -
Tides-1.1/Tides/man/IT.Rd | 2 -
Tides-1.1/Tides/man/TidalCharacteristics.Rd | 4 +-
Tides-1.1/Tides/man/Tides.Rd | 6 +--
Tides-1.1/Tides/man/extrema.Rd | 2 -
Tides-1.1/Tides/man/gapsts.Rd | 2 -
Tides-1.1/Tides/man/plot.Tides.Rd | 2 -
Tides-1.1/Tides/man/print.Tides.Rd | 2 -
Tides-1.1/Tides/vignettes |only
17 files changed, 74 insertions(+), 56 deletions(-)
Title: Build Regular Expressions in a Human Readable Way
Diff between rebus versions 0.0-4 dated 2015-01-21 and 0.0-5 dated 2015-02-04
Description: Build regular expressions piece by piece using human readable code.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
NEWS | 2 ++
R/number_range.R | 28 +++++++++++++++++++++++-----
inst/tests/test-number_range.R |only
man/number_range.Rd | 4 ++++
6 files changed, 38 insertions(+), 13 deletions(-)
Title: Collection of Genetic Data Analysis Tools
Diff between GeneticTools versions 0.3 dated 2014-08-06 and 0.3.1 dated 2015-02-04
Description: A loose collection of tools for the analysis of gene expression and genotype data, currently with main focus on eQTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer
GeneticTools |only
1 file changed
Title: Readable Check Functions to Ensure Code Integrity
Diff between assertive versions 0.1-8 dated 2013-10-13 and 0.2-1 dated 2015-02-04
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
assertive-0.1-8/assertive/man/is_R.Rd |only
assertive-0.1-8/assertive/man/is_ex_file.Rd |only
assertive-0.1-8/assertive/man/is_hex_colour.Rd |only
assertive-0.2-1/assertive/DESCRIPTION | 41
assertive-0.2-1/assertive/MD5 | 320 ++-
assertive-0.2-1/assertive/NAMESPACE | 145 +
assertive-0.2-1/assertive/NEWS | 7
assertive-0.2-1/assertive/R/are-same.R |only
assertive-0.2-1/assertive/R/assert-are-same.R |only
assertive-0.2-1/assertive/R/assert-is-a-type.R | 12
assertive-0.2-1/assertive/R/assert-is-connection.R | 117 +
assertive-0.2-1/assertive/R/assert-is-empty-scalar.R | 21
assertive-0.2-1/assertive/R/assert-is-file.R | 38
assertive-0.2-1/assertive/R/assert-is-in-range.R | 54
assertive-0.2-1/assertive/R/assert-is-na-nan-null.R | 32
assertive-0.2-1/assertive/R/assert-is-other.R | 92 +
assertive-0.2-1/assertive/R/assert-is-reflection.R | 63
assertive-0.2-1/assertive/R/assert-is-string-uk.R | 140 -
assertive-0.2-1/assertive/R/assert-is-string.R | 112 +
assertive-0.2-1/assertive/R/assert-is-type.R | 12
assertive-0.2-1/assertive/R/assert-r-has-capability.R |only
assertive-0.2-1/assertive/R/assertive-package.R | 17
assertive-0.2-1/assertive/R/has.R | 165 +
assertive-0.2-1/assertive/R/internal.R | 234 ++
assertive-0.2-1/assertive/R/is-a-type.R | 43
assertive-0.2-1/assertive/R/is-connection.R | 267 ++-
assertive-0.2-1/assertive/R/is-empty-scalar.R | 146 +
assertive-0.2-1/assertive/R/is-file.R | 157 +
assertive-0.2-1/assertive/R/is-in-range.R | 17
assertive-0.2-1/assertive/R/is-na-nan-null.R | 141 +
assertive-0.2-1/assertive/R/is-other.R | 112 -
assertive-0.2-1/assertive/R/is-real-imaginary.R | 23
assertive-0.2-1/assertive/R/is-reflection.R | 273 ++-
assertive-0.2-1/assertive/R/is-string-uk.R | 92 -
assertive-0.2-1/assertive/R/is-string-us.R | 85
assertive-0.2-1/assertive/R/is-string.R | 426 +++-
assertive-0.2-1/assertive/R/is-time.R | 30
assertive-0.2-1/assertive/R/is-true-false.R | 70
assertive-0.2-1/assertive/R/is-type.R | 102 -
assertive-0.2-1/assertive/R/r-has-capability.R |only
assertive-0.2-1/assertive/R/utils.R | 350 +++-
assertive-0.2-1/assertive/R/zzz.R | 2
assertive-0.2-1/assertive/inst/tests/test-has.R | 513 +++--
assertive-0.2-1/assertive/inst/tests/test-internal.R | 85
assertive-0.2-1/assertive/inst/tests/test-is-a-type.R | 401 ++--
assertive-0.2-1/assertive/inst/tests/test-is-atomic-recursive-vector.R | 226 +-
assertive-0.2-1/assertive/inst/tests/test-is-connection.R | 266 ++-
assertive-0.2-1/assertive/inst/tests/test-is-empty-scalar.R | 173 --
assertive-0.2-1/assertive/inst/tests/test-is-file.R | 131 -
assertive-0.2-1/assertive/inst/tests/test-is-in-range.R | 294 +--
assertive-0.2-1/assertive/inst/tests/test-is-na-nan-null.R | 64
assertive-0.2-1/assertive/inst/tests/test-is-other.R | 130 -
assertive-0.2-1/assertive/inst/tests/test-is-real-imaginary.R | 77
assertive-0.2-1/assertive/inst/tests/test-is-reflection.R | 313 ++-
assertive-0.2-1/assertive/inst/tests/test-is-string-uk.R | 862 +++-------
assertive-0.2-1/assertive/inst/tests/test-is-string-us.R | 114 -
assertive-0.2-1/assertive/inst/tests/test-is-string.R | 473 ++---
assertive-0.2-1/assertive/inst/tests/test-is-time.R | 38
assertive-0.2-1/assertive/inst/tests/test-is-true-false.R | 111 -
assertive-0.2-1/assertive/inst/tests/test-is-type.R | 735 +++-----
assertive-0.2-1/assertive/inst/tests/test-is-valid-variable-name.R | 174 --
assertive-0.2-1/assertive/inst/tests/test-r-has-capabilities.R |only
assertive-0.2-1/assertive/inst/tests/test-utils.R |only
assertive-0.2-1/assertive/man/DIM.Rd |only
assertive-0.2-1/assertive/man/are_identical.Rd |only
assertive-0.2-1/assertive/man/are_same_length.Rd |only
assertive-0.2-1/assertive/man/as.character.file.Rd |only
assertive-0.2-1/assertive/man/assert_engine.Rd | 32
assertive-0.2-1/assertive/man/assertive.Rd | 30
assertive-0.2-1/assertive/man/bapply.Rd | 22
assertive-0.2-1/assertive/man/call_and_name.Rd | 25
assertive-0.2-1/assertive/man/cause.Rd | 17
assertive-0.2-1/assertive/man/character_to_list_of_integer_vectors.Rd | 13
assertive-0.2-1/assertive/man/coerce_to.Rd | 34
assertive-0.2-1/assertive/man/create_regex.Rd | 31
assertive-0.2-1/assertive/man/d.Rd | 24
assertive-0.2-1/assertive/man/dont_stop.Rd |only
assertive-0.2-1/assertive/man/false.Rd | 16
assertive-0.2-1/assertive/man/get_name_in_parent.Rd | 11
assertive-0.2-1/assertive/man/has_any_attributes.Rd | 17
assertive-0.2-1/assertive/man/has_arg.Rd | 25
assertive-0.2-1/assertive/man/has_attributes.Rd | 27
assertive-0.2-1/assertive/man/has_cols.Rd | 28
assertive-0.2-1/assertive/man/has_dims.Rd | 20
assertive-0.2-1/assertive/man/has_duplicates.Rd | 28
assertive-0.2-1/assertive/man/has_names.Rd | 46
assertive-0.2-1/assertive/man/has_terms.Rd | 22
assertive-0.2-1/assertive/man/is2.Rd | 34
assertive-0.2-1/assertive/man/is_S4.Rd | 25
assertive-0.2-1/assertive/man/is_array.Rd | 31
assertive-0.2-1/assertive/man/is_atomic.Rd | 36
assertive-0.2-1/assertive/man/is_batch_mode.Rd | 21
assertive-0.2-1/assertive/man/is_cas_number.Rd | 42
assertive-0.2-1/assertive/man/is_character.Rd | 87 -
assertive-0.2-1/assertive/man/is_class.Rd | 24
assertive-0.2-1/assertive/man/is_complex.Rd | 38
assertive-0.2-1/assertive/man/is_connection.Rd | 177 +-
assertive-0.2-1/assertive/man/is_credit_card_number.Rd | 40
assertive-0.2-1/assertive/man/is_data.frame.Rd | 22
assertive-0.2-1/assertive/man/is_date_string.Rd | 31
assertive-0.2-1/assertive/man/is_debugged.Rd | 22
assertive-0.2-1/assertive/man/is_dir.Rd | 19
assertive-0.2-1/assertive/man/is_divisible_by.Rd |only
assertive-0.2-1/assertive/man/is_email_address.Rd | 61
assertive-0.2-1/assertive/man/is_empty.Rd | 111 +
assertive-0.2-1/assertive/man/is_empty_file.Rd |only
assertive-0.2-1/assertive/man/is_empty_model.Rd | 31
assertive-0.2-1/assertive/man/is_environment.Rd | 21
assertive-0.2-1/assertive/man/is_error_free.Rd | 15
assertive-0.2-1/assertive/man/is_executable_file.Rd |only
assertive-0.2-1/assertive/man/is_existing.Rd | 55
assertive-0.2-1/assertive/man/is_existing_file.Rd | 24
assertive-0.2-1/assertive/man/is_factor.Rd | 25
assertive-0.2-1/assertive/man/is_finite.Rd | 56
assertive-0.2-1/assertive/man/is_function.Rd | 34
assertive-0.2-1/assertive/man/is_hex_color.Rd |only
assertive-0.2-1/assertive/man/is_honorific.Rd | 35
assertive-0.2-1/assertive/man/is_in_past.Rd | 41
assertive-0.2-1/assertive/man/is_in_range.Rd | 126 -
assertive-0.2-1/assertive/man/is_inherited_from.Rd |only
assertive-0.2-1/assertive/man/is_integer.Rd | 40
assertive-0.2-1/assertive/man/is_ip_address.Rd | 31
assertive-0.2-1/assertive/man/is_isbn_code.Rd | 39
assertive-0.2-1/assertive/man/is_language.Rd | 53
assertive-0.2-1/assertive/man/is_leaf.Rd | 18
assertive-0.2-1/assertive/man/is_library.Rd | 23
assertive-0.2-1/assertive/man/is_list.Rd | 22
assertive-0.2-1/assertive/man/is_loaded.Rd | 27
assertive-0.2-1/assertive/man/is_logical.Rd | 38
assertive-0.2-1/assertive/man/is_na.Rd | 31
assertive-0.2-1/assertive/man/is_nan.Rd | 36
assertive-0.2-1/assertive/man/is_null.Rd | 26
assertive-0.2-1/assertive/man/is_numeric.Rd | 38
assertive-0.2-1/assertive/man/is_on_os_path.Rd | 23
assertive-0.2-1/assertive/man/is_qr.Rd | 22
assertive-0.2-1/assertive/man/is_r.Rd |only
assertive-0.2-1/assertive/man/is_raster.Rd | 25
assertive-0.2-1/assertive/man/is_raw.Rd | 39
assertive-0.2-1/assertive/man/is_real.Rd | 33
assertive-0.2-1/assertive/man/is_relistable.Rd | 26
assertive-0.2-1/assertive/man/is_single_character.Rd |only
assertive-0.2-1/assertive/man/is_symmetric_matrix.Rd | 28
assertive-0.2-1/assertive/man/is_table.Rd | 21
assertive-0.2-1/assertive/man/is_true.Rd | 79
assertive-0.2-1/assertive/man/is_ts.Rd | 29
assertive-0.2-1/assertive/man/is_uk_car_licence.Rd | 43
assertive-0.2-1/assertive/man/is_uk_national_insurance_number.Rd | 35
assertive-0.2-1/assertive/man/is_uk_postcode.Rd | 39
assertive-0.2-1/assertive/man/is_uk_telephone_number.Rd | 35
assertive-0.2-1/assertive/man/is_unsorted.Rd | 49
assertive-0.2-1/assertive/man/is_us_telephone_number.Rd | 41
assertive-0.2-1/assertive/man/is_us_zip_code.Rd | 56
assertive-0.2-1/assertive/man/is_valid_r_code.Rd | 14
assertive-0.2-1/assertive/man/is_valid_variable_name.Rd | 50
assertive-0.2-1/assertive/man/is_whole_number.Rd | 41
assertive-0.2-1/assertive/man/is_windows.Rd | 76
assertive-0.2-1/assertive/man/is_xxx_for_decimal_point.Rd | 49
assertive-0.2-1/assertive/man/locale_categories.Rd | 17
assertive-0.2-1/assertive/man/matches_regex.Rd | 25
assertive-0.2-1/assertive/man/merge.list.Rd |only
assertive-0.2-1/assertive/man/merge_dots_with_list.Rd | 28
assertive-0.2-1/assertive/man/modal_value.Rd | 12
assertive-0.2-1/assertive/man/n_elements.Rd |only
assertive-0.2-1/assertive/man/na.Rd | 16
assertive-0.2-1/assertive/man/parenthesise.Rd |only
assertive-0.2-1/assertive/man/print_and_capture.Rd |only
assertive-0.2-1/assertive/man/r_can_compile_code.Rd |only
assertive-0.2-1/assertive/man/r_has_jpeg_capability.Rd |only
assertive-0.2-1/assertive/man/recycle.Rd |only
assertive-0.2-1/assertive/man/set_cause.Rd |only
assertive-0.2-1/assertive/man/strip_attributes.Rd | 10
assertive-0.2-1/assertive/man/strip_invalid_chars.Rd | 37
assertive-0.2-1/assertive/man/sys_get_locale.Rd | 23
assertive-0.2-1/assertive/man/truncate.Rd |only
assertive-0.2-1/assertive/man/use_first.Rd | 18
assertive-0.2-1/assertive/man/warn_about_file.access_under_windows.Rd |only
assertive-0.2-1/assertive/tests |only
177 files changed, 7432 insertions(+), 4919 deletions(-)
Title: A GAMLSS Add-on Package For Fitting Mixture Distributions
Diff between gamlss.mx versions 4.2-7 dated 2014-01-18 and 4.3-1 dated 2015-02-04
Description: The main purpose of this package is to allow fitting of
mixture distributions with GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 13 +--
MD5 | 14 +--
NAMESPACE | 8 +-
R/gamlssMX-10-11-07.R | 189 ++++++++++++++++++++++++++++----------------------
R/gamlssNP.R | 132 ++++++++++++++++++----------------
data/brains.rda |binary
data/enzyme.rda |binary
man/dMX.Rd | 92 ++++++++++++------------
8 files changed, 240 insertions(+), 208 deletions(-)
Title: Demos for GAMLSS
Diff between gamlss.demo versions 4.2-7 dated 2014-01-11 and 4.3-1 dated 2015-02-04
Description: Demos for smoothing and gamlss.family distributions.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.demo-4.2-7/gamlss.demo/R/LocalSmother.r |only
gamlss.demo-4.3-1/gamlss.demo/DESCRIPTION | 14 -
gamlss.demo-4.3-1/gamlss.demo/MD5 | 31 +-
gamlss.demo-4.3-1/gamlss.demo/NAMESPACE | 19 -
gamlss.demo-4.3-1/gamlss.demo/R/DPO.R |only
gamlss.demo-4.3-1/gamlss.demo/R/Demo_All_Distibutions.r | 46 +--
gamlss.demo-4.3-1/gamlss.demo/R/LocalRegressionDemo.R |only
gamlss.demo-4.3-1/gamlss.demo/R/LocalSmother.R |only
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_bsplines.R | 2
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_discrete.r | 90 +++----
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_psplines.r | 162 +++++++-------
gamlss.demo-4.3-1/gamlss.demo/R/demoDist.R | 6
gamlss.demo-4.3-1/gamlss.demo/R/demoPsplines.R | 92 +++----
gamlss.demo-4.3-1/gamlss.demo/R/gamlss_demo.R | 155 ++++++-------
gamlss.demo-4.3-1/gamlss.demo/R/movMean.R |only
gamlss.demo-4.3-1/gamlss.demo/man/Locmean.Rd |only
gamlss.demo-4.3-1/gamlss.demo/man/demo.BetaSplines.Rd | 16 -
gamlss.demo-4.3-1/gamlss.demo/man/demo.LocalRegression.Rd |only
gamlss.demo-4.3-1/gamlss.demo/man/demo.Locmean.Rd | 2
gamlss.demo-4.3-1/gamlss.demo/man/demo.NO.Rd | 2
20 files changed, 324 insertions(+), 313 deletions(-)
Title: Partial Autoregression
Diff between partialAR versions 1.0.3 dated 2015-01-28 and 1.0.5 dated 2015-02-04
Description: Fits time series models which consist of a sum of a permanent and a transient component.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg
DESCRIPTION | 12 ++++++-----
MD5 | 20 +++++++++---------
R/RcppExports.R | 4 +++
R/lr.R | 39 +++++++++++++++++++----------------
R/lrdata.R | 4 +--
R/lrtables.R | 24 +++++++++++-----------
man/fit.par.Rd | 1
man/partialAR-package.Rd | 2 -
src/RcppExports.cpp | 17 +++++++++++++++
src/cfit.cc | 51 ++++++++++++++++++++++-------------------------
tests/tests.R | 6 +++++
11 files changed, 105 insertions(+), 75 deletions(-)
Title: Machine Learning in R
Diff between mlr versions 2.2 dated 2014-10-29 and 2.3 dated 2015-02-04
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut]
Maintainer: Bernd Bischl
mlr-2.2/mlr/R/RLearner_classif_plsDA.R |only
mlr-2.2/mlr/R/RLearner_cluster_DBScan.R |only
mlr-2.2/mlr/R/ResampleDescs.R |only
mlr-2.2/mlr/R/getBaggingModels.R |only
mlr-2.2/mlr/R/getFailuremodelMsg.R |only
mlr-2.2/mlr/man/getBaggingModels.Rd |only
mlr-2.2/mlr/man/getCostSensClassifModel.Rd |only
mlr-2.2/mlr/man/getCostSensRegrModels.Rd |only
mlr-2.2/mlr/man/getCostSensWeightedPairsModels.Rd |only
mlr-2.2/mlr/tests/run-imbal.R |only
mlr-2.2/mlr/tests/run-resample.R |only
mlr-2.2/mlr/tests/testthat/helper_fix_packages.R |only
mlr-2.2/mlr/tests/testthat/test_base_confMatrix.R |only
mlr-2.2/mlr/tests/testthat/test_base_convertColumnNames.R |only
mlr-2.2/mlr/tests/testthat/test_base_toString.R |only
mlr-2.2/mlr/tests/testthat/test_classif_hda.R |only
mlr-2.2/mlr/tests/testthat/test_classif_loclda.R |only
mlr-2.2/mlr/tests/testthat/test_classif_plsDA.R |only
mlr-2.2/mlr/tests/testthat/test_cluster_DBScan.R |only
mlr-2.2/mlr/tests/testthat/test_featsel_extra_FilterWrapper.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_OverBagging.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_overundersample.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_smote.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_weightedclasses.R |only
mlr-2.2/mlr/tests/testthat/test_regr_logicreg.R |only
mlr-2.2/mlr/tests/testthat/test_resample_b632.R |only
mlr-2.2/mlr/tests/testthat/test_resample_b632plus.R |only
mlr-2.2/mlr/tests/testthat/test_resample_bs.R |only
mlr-2.2/mlr/tests/testthat/test_resample_convenience.R |only
mlr-2.2/mlr/tests/testthat/test_resample_cv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_bs.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_cv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_repcv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_subsample.R |only
mlr-2.2/mlr/tests/testthat/test_resample_holdout.R |only
mlr-2.2/mlr/tests/testthat/test_resample_loo.R |only
mlr-2.2/mlr/tests/testthat/test_resample_makeResampleDesc.R |only
mlr-2.2/mlr/tests/testthat/test_resample_repcv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_stratify.R |only
mlr-2.2/mlr/tests/testthat/test_resample_subsample.R |only
mlr-2.2/mlr/tests/testthat/test_resample_weights.R |only
mlr-2.2/mlr/tests/testthat/test_tune_TuneWrapper.R |only
mlr-2.3/mlr/DESCRIPTION | 33
mlr-2.3/mlr/MD5 | 917 +++++-----
mlr-2.3/mlr/NAMESPACE | 150 +
mlr-2.3/mlr/NEWS | 63
mlr-2.3/mlr/R/Aggregation.R | 2
mlr-2.3/mlr/R/BaggingWrapper.R | 45
mlr-2.3/mlr/R/BaseEnsemble_operators.R | 7
mlr-2.3/mlr/R/BaseWrapper.R | 61
mlr-2.3/mlr/R/BaseWrapper_operators.R | 2
mlr-2.3/mlr/R/BenchmarkResult_operators.R | 25
mlr-2.3/mlr/R/ChainModel.R | 9
mlr-2.3/mlr/R/CostSensClassifWrapper.R | 36
mlr-2.3/mlr/R/CostSensRegrWrapper.R | 45
mlr-2.3/mlr/R/CostSensWeightedPairsLearner.R | 46
mlr-2.3/mlr/R/DownsampleWrapper.R | 6
mlr-2.3/mlr/R/FailureModel.R | 14
mlr-2.3/mlr/R/FeatSelControl.R | 29
mlr-2.3/mlr/R/FeatSelControlExhaustive.R | 7
mlr-2.3/mlr/R/FeatSelControlGA.R | 17
mlr-2.3/mlr/R/FeatSelControlRandom.R | 6
mlr-2.3/mlr/R/FeatSelControlSequential.R | 10
mlr-2.3/mlr/R/FeatSelResult.R | 21
mlr-2.3/mlr/R/FeatSelWrapper.R | 2
mlr-2.3/mlr/R/Filter.R | 27
mlr-2.3/mlr/R/FilterWrapper.R | 18
mlr-2.3/mlr/R/HomogeneousEnsemble.R |only
mlr-2.3/mlr/R/Impute.R | 4
mlr-2.3/mlr/R/ImputeWrapper.R | 5
mlr-2.3/mlr/R/Learner.R | 12
mlr-2.3/mlr/R/Learner_properties.R | 15
mlr-2.3/mlr/R/Measure.R | 40
mlr-2.3/mlr/R/Measure_custom_resampled.R | 8
mlr-2.3/mlr/R/Measure_make_cost.R | 5
mlr-2.3/mlr/R/ModelMultiplexer.R | 27
mlr-2.3/mlr/R/MulticlassWrapper.R | 22
mlr-2.3/mlr/R/NoFeaturesModel.R | 21
mlr-2.3/mlr/R/OptControl.R | 13
mlr-2.3/mlr/R/OptResult.R | 3
mlr-2.3/mlr/R/OptWrapper.R | 14
mlr-2.3/mlr/R/OverBaggingWrapper.R | 8
mlr-2.3/mlr/R/OverUndersampleWrapper.R | 6
mlr-2.3/mlr/R/Prediction.R | 26
mlr-2.3/mlr/R/PreprocWrapper.R | 3
mlr-2.3/mlr/R/PreprocWrapperCaret.R |only
mlr-2.3/mlr/R/RLearner.R | 4
mlr-2.3/mlr/R/RLearner_classif_LiblineaRBinary.R | 2
mlr-2.3/mlr/R/RLearner_classif_LiblineaRLogReg.R | 14
mlr-2.3/mlr/R/RLearner_classif_ada.R | 4
mlr-2.3/mlr/R/RLearner_classif_bartMachine.R | 20
mlr-2.3/mlr/R/RLearner_classif_bdk.R |only
mlr-2.3/mlr/R/RLearner_classif_binomial.R |only
mlr-2.3/mlr/R/RLearner_classif_blackboost.R | 6
mlr-2.3/mlr/R/RLearner_classif_extraTrees.R |only
mlr-2.3/mlr/R/RLearner_classif_gbm.R | 4
mlr-2.3/mlr/R/RLearner_classif_glmboost.R | 36
mlr-2.3/mlr/R/RLearner_classif_glmnet.R | 22
mlr-2.3/mlr/R/RLearner_classif_lda.R | 10
mlr-2.3/mlr/R/RLearner_classif_logreg.R | 9
mlr-2.3/mlr/R/RLearner_classif_lqa.R | 16
mlr-2.3/mlr/R/RLearner_classif_mda.R | 3
mlr-2.3/mlr/R/RLearner_classif_plr.R | 9
mlr-2.3/mlr/R/RLearner_classif_probit.R |only
mlr-2.3/mlr/R/RLearner_classif_qda.R | 10
mlr-2.3/mlr/R/RLearner_classif_randomForestSRC.R | 7
mlr-2.3/mlr/R/RLearner_classif_rrlda.R | 2
mlr-2.3/mlr/R/RLearner_classif_sda.R | 2
mlr-2.3/mlr/R/RLearner_classif_xgboost.R |only
mlr-2.3/mlr/R/RLearner_classif_xyf.R |only
mlr-2.3/mlr/R/RLearner_regr_bartMachine.R |only
mlr-2.3/mlr/R/RLearner_regr_bcart.R |only
mlr-2.3/mlr/R/RLearner_regr_bdk.R |only
mlr-2.3/mlr/R/RLearner_regr_bgp.R |only
mlr-2.3/mlr/R/RLearner_regr_bgpllm.R |only
mlr-2.3/mlr/R/RLearner_regr_blm.R |only
mlr-2.3/mlr/R/RLearner_regr_brnn.R |only
mlr-2.3/mlr/R/RLearner_regr_btgp.R |only
mlr-2.3/mlr/R/RLearner_regr_btgpllm.R |only
mlr-2.3/mlr/R/RLearner_regr_btlm.R |only
mlr-2.3/mlr/R/RLearner_regr_crs.R | 6
mlr-2.3/mlr/R/RLearner_regr_cubist.R |only
mlr-2.3/mlr/R/RLearner_regr_elmNN.R |only
mlr-2.3/mlr/R/RLearner_regr_extraTrees.R |only
mlr-2.3/mlr/R/RLearner_regr_gbm.R | 2
mlr-2.3/mlr/R/RLearner_regr_glmnet.R | 16
mlr-2.3/mlr/R/RLearner_regr_km.R | 8
mlr-2.3/mlr/R/RLearner_regr_laGP.R |only
mlr-2.3/mlr/R/RLearner_regr_mob.R | 8
mlr-2.3/mlr/R/RLearner_regr_randomForestSRC.R | 7
mlr-2.3/mlr/R/RLearner_regr_xgboost.R |only
mlr-2.3/mlr/R/RLearner_regr_xyf.R |only
mlr-2.3/mlr/R/RLearner_surv_CoxBoost.R | 24
mlr-2.3/mlr/R/RLearner_surv_cvglmnet.R | 18
mlr-2.3/mlr/R/RLearner_surv_glmboost.R | 58
mlr-2.3/mlr/R/RLearner_surv_glmnet.R | 18
mlr-2.3/mlr/R/RLearner_surv_optimCoxBoostPenalty.R | 50
mlr-2.3/mlr/R/RLearner_surv_penalized.R | 16
mlr-2.3/mlr/R/RLearner_surv_randomForestSRC.R | 17
mlr-2.3/mlr/R/RLearner_surv_rpart.R |only
mlr-2.3/mlr/R/ResampleDesc.R | 84
mlr-2.3/mlr/R/ResampleInstance.R | 30
mlr-2.3/mlr/R/ResampleResult.R |only
mlr-2.3/mlr/R/SMOTEWrapper.R | 3
mlr-2.3/mlr/R/Task_operators.R | 47
mlr-2.3/mlr/R/TuneControl.R | 37
mlr-2.3/mlr/R/TuneControlCMAES.R | 7
mlr-2.3/mlr/R/TuneControlGenSA.R | 7
mlr-2.3/mlr/R/TuneControlGrid.R | 8
mlr-2.3/mlr/R/TuneControlIrace.R | 7
mlr-2.3/mlr/R/TuneControlMBO.R | 14
mlr-2.3/mlr/R/TuneControlRandom.R | 7
mlr-2.3/mlr/R/TuneMultiCritControl.R | 8
mlr-2.3/mlr/R/TuneMultiCritControlGrid.R | 4
mlr-2.3/mlr/R/TuneMultiCritControlNSGA2.R | 4
mlr-2.3/mlr/R/TuneMultiCritControlRandom.R | 4
mlr-2.3/mlr/R/TuneMultiCritResult.R | 3
mlr-2.3/mlr/R/TuneResult.R | 12
mlr-2.3/mlr/R/TuneWrapper.R | 18
mlr-2.3/mlr/R/WeightedClassesWrapper.R | 4
mlr-2.3/mlr/R/WrappedModel.R | 64
mlr-2.3/mlr/R/aggregations.R | 62
mlr-2.3/mlr/R/asROCRPrediction.R | 9
mlr-2.3/mlr/R/benchmark.R | 5
mlr-2.3/mlr/R/checkPrediction.R |only
mlr-2.3/mlr/R/checkTunerParset.R | 4
mlr-2.3/mlr/R/configureMlr.R | 18
mlr-2.3/mlr/R/convertX.R | 1
mlr-2.3/mlr/R/evalOptimizationState.R | 47
mlr-2.3/mlr/R/filterFeatures.R | 14
mlr-2.3/mlr/R/fixDataForLearner.R |only
mlr-2.3/mlr/R/getConfMatrix.R | 45
mlr-2.3/mlr/R/getFilterValues.R | 2
mlr-2.3/mlr/R/getHyperPars.R | 1
mlr-2.3/mlr/R/helpers.R | 34
mlr-2.3/mlr/R/isFailureModel.R | 40
mlr-2.3/mlr/R/joinClassLevels.R | 4
mlr-2.3/mlr/R/listLearners.R | 5
mlr-2.3/mlr/R/logFunOpt.R |only
mlr-2.3/mlr/R/measures.R | 512 +++--
mlr-2.3/mlr/R/mergeSmallFactorLevels.R | 2
mlr-2.3/mlr/R/normalizeFeatures.R | 2
mlr-2.3/mlr/R/performance.R | 53
mlr-2.3/mlr/R/plotFilterValues.R | 1
mlr-2.3/mlr/R/plotLearnerPrediction.R | 29
mlr-2.3/mlr/R/plotROCRCurves.R |only
mlr-2.3/mlr/R/plotThreshVsPerf.R | 9
mlr-2.3/mlr/R/plotTuneMultiCritResult.R | 1
mlr-2.3/mlr/R/plotViperCharts.R |only
mlr-2.3/mlr/R/predict.R | 5
mlr-2.3/mlr/R/predictLearner.R | 1
mlr-2.3/mlr/R/removeConstantFeatures.R | 3
mlr-2.3/mlr/R/resample.R | 65
mlr-2.3/mlr/R/selectFeatures.R | 5
mlr-2.3/mlr/R/selectFeaturesExhaustive.R | 7
mlr-2.3/mlr/R/selectFeaturesGA.R | 4
mlr-2.3/mlr/R/selectFeaturesRandom.R | 11
mlr-2.3/mlr/R/selectFeaturesSequential.R | 4
mlr-2.3/mlr/R/setHyperPars.R | 23
mlr-2.3/mlr/R/setPredictThreshold.R |only
mlr-2.3/mlr/R/setThreshold.R | 3
mlr-2.3/mlr/R/smote.R | 6
mlr-2.3/mlr/R/summarizeColumns.R | 20
mlr-2.3/mlr/R/train.R | 5
mlr-2.3/mlr/R/tuneCMAES.R | 5
mlr-2.3/mlr/R/tuneGenSA.R | 6
mlr-2.3/mlr/R/tuneIrace.R | 9
mlr-2.3/mlr/R/tuneMBO.R | 23
mlr-2.3/mlr/R/tuneMultiCritNSGA2.R | 2
mlr-2.3/mlr/R/tuneParams.R | 2
mlr-2.3/mlr/R/tuneParamsMultiCrit.R | 2
mlr-2.3/mlr/R/tuneThreshold.R | 5
mlr-2.3/mlr/R/utils_opt.R | 32
mlr-2.3/mlr/R/zzz.R | 2
mlr-2.3/mlr/man/Aggregation.Rd | 14
mlr-2.3/mlr/man/BenchmarkResult.Rd | 3
mlr-2.3/mlr/man/FailureModel.Rd | 3
mlr-2.3/mlr/man/FeatSelControl.Rd | 33
mlr-2.3/mlr/man/FeatSelResult.Rd | 6
mlr-2.3/mlr/man/FilterValues.Rd | 3
mlr-2.3/mlr/man/LearnerProperties.Rd | 14
mlr-2.3/mlr/man/Prediction.Rd | 3
mlr-2.3/mlr/man/RLearner.Rd | 3
mlr-2.3/mlr/man/ResamplePrediction.Rd | 4
mlr-2.3/mlr/man/ResampleResult.Rd |only
mlr-2.3/mlr/man/Task.Rd | 3
mlr-2.3/mlr/man/TaskDesc.Rd | 3
mlr-2.3/mlr/man/TuneControl.Rd | 38
mlr-2.3/mlr/man/TuneMultiCritControl.Rd | 17
mlr-2.3/mlr/man/TuneMultiCritResult.Rd | 3
mlr-2.3/mlr/man/TuneResult.Rd | 6
mlr-2.3/mlr/man/aggregations.Rd | 45
mlr-2.3/mlr/man/agri.task.Rd | 3
mlr-2.3/mlr/man/analyzeFeatSelResult.Rd | 3
mlr-2.3/mlr/man/asROCRPrediction.Rd | 14
mlr-2.3/mlr/man/bc.task.Rd | 3
mlr-2.3/mlr/man/benchmark.Rd | 8
mlr-2.3/mlr/man/bh.task.Rd | 3
mlr-2.3/mlr/man/capLargeValues.Rd | 3
mlr-2.3/mlr/man/configureMlr.Rd | 12
mlr-2.3/mlr/man/costiris.task.Rd | 3
mlr-2.3/mlr/man/createDummyFeatures.Rd | 3
mlr-2.3/mlr/man/crossover.Rd | 3
mlr-2.3/mlr/man/downsample.Rd | 3
mlr-2.3/mlr/man/dropFeatures.Rd | 3
mlr-2.3/mlr/man/estimateResidualVariance.Rd | 3
mlr-2.3/mlr/man/filterFeatures.Rd | 8
mlr-2.3/mlr/man/getBMRAggrPerformances.Rd | 5
mlr-2.3/mlr/man/getBMRFeatSelResults.Rd | 5
mlr-2.3/mlr/man/getBMRFilteredFeatures.Rd | 5
mlr-2.3/mlr/man/getBMRLearnerIds.Rd | 10
mlr-2.3/mlr/man/getBMRPerformances.Rd | 3
mlr-2.3/mlr/man/getBMRPredictions.Rd | 5
mlr-2.3/mlr/man/getBMRTaskIds.Rd | 3
mlr-2.3/mlr/man/getBMRTuneResults.Rd | 5
mlr-2.3/mlr/man/getConfMatrix.Rd | 6
mlr-2.3/mlr/man/getFailureModelMsg.Rd | 3
mlr-2.3/mlr/man/getFeatSelResult.Rd | 3
mlr-2.3/mlr/man/getFilterValues.Rd | 3
mlr-2.3/mlr/man/getFilteredFeatures.Rd | 3
mlr-2.3/mlr/man/getHomogeneousEnsembleModels.Rd |only
mlr-2.3/mlr/man/getHyperPars.Rd | 10
mlr-2.3/mlr/man/getLearnerModel.Rd | 3
mlr-2.3/mlr/man/getMlrOptions.Rd | 3
mlr-2.3/mlr/man/getParamSet.Rd | 10
mlr-2.3/mlr/man/getProbabilities.Rd | 9
mlr-2.3/mlr/man/getStackedBaseLearnerPredictions.Rd | 3
mlr-2.3/mlr/man/getTaskCosts.Rd | 10
mlr-2.3/mlr/man/getTaskData.Rd | 10
mlr-2.3/mlr/man/getTaskDescription.Rd |only
mlr-2.3/mlr/man/getTaskFeatureNames.Rd | 13
mlr-2.3/mlr/man/getTaskFormula.Rd | 14
mlr-2.3/mlr/man/getTaskId.Rd |only
mlr-2.3/mlr/man/getTaskNFeats.Rd | 9
mlr-2.3/mlr/man/getTaskTargetNames.Rd |only
mlr-2.3/mlr/man/getTaskTargets.Rd | 8
mlr-2.3/mlr/man/getTaskType.Rd |only
mlr-2.3/mlr/man/getTuneResult.Rd | 3
mlr-2.3/mlr/man/imputations.Rd | 3
mlr-2.3/mlr/man/impute.Rd | 3
mlr-2.3/mlr/man/iris.task.Rd | 3
mlr-2.3/mlr/man/isFailureModel.Rd | 3
mlr-2.3/mlr/man/joinClassLevels.Rd | 3
mlr-2.3/mlr/man/learnerArgsToControl.Rd | 3
mlr-2.3/mlr/man/learners.Rd | 3
mlr-2.3/mlr/man/listFilterMethods.Rd | 3
mlr-2.3/mlr/man/listLearners.Rd | 3
mlr-2.3/mlr/man/listMeasures.Rd | 3
mlr-2.3/mlr/man/lung.task.Rd | 3
mlr-2.3/mlr/man/makeAggregation.Rd | 3
mlr-2.3/mlr/man/makeBaggingWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostMeasure.Rd | 35
mlr-2.3/mlr/man/makeCostSensClassifWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostSensRegrWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostSensWeightedPairsWrapper.Rd | 5
mlr-2.3/mlr/man/makeCustomResampledMeasure.Rd | 53
mlr-2.3/mlr/man/makeDownsampleWrapper.Rd | 4
mlr-2.3/mlr/man/makeFeatSelWrapper.Rd | 4
mlr-2.3/mlr/man/makeFilter.Rd | 3
mlr-2.3/mlr/man/makeFilterWrapper.Rd | 9
mlr-2.3/mlr/man/makeFixedHoldoutInstance.Rd | 3
mlr-2.3/mlr/man/makeImputeMethod.Rd | 3
mlr-2.3/mlr/man/makeImputeWrapper.Rd | 4
mlr-2.3/mlr/man/makeLearner.Rd | 23
mlr-2.3/mlr/man/makeMeasure.Rd | 65
mlr-2.3/mlr/man/makeModelMultiplexer.Rd | 3
mlr-2.3/mlr/man/makeModelMultiplexerParamSet.Rd | 3
mlr-2.3/mlr/man/makeMulticlassWrapper.Rd | 4
mlr-2.3/mlr/man/makeOverBaggingWrapper.Rd | 6
mlr-2.3/mlr/man/makePreprocWrapper.Rd | 4
mlr-2.3/mlr/man/makePreprocWrapperCaret.Rd |only
mlr-2.3/mlr/man/makeResampleDesc.Rd | 23
mlr-2.3/mlr/man/makeResampleInstance.Rd | 4
mlr-2.3/mlr/man/makeSMOTEWrapper.Rd | 4
mlr-2.3/mlr/man/makeStackedLearner.Rd | 3
mlr-2.3/mlr/man/makeTuneWrapper.Rd | 4
mlr-2.3/mlr/man/makeUndersampleWrapper.Rd | 4
mlr-2.3/mlr/man/makeWeightedClassesWrapper.Rd | 4
mlr-2.3/mlr/man/makeWrappedModel.Rd | 3
mlr-2.3/mlr/man/measures.Rd | 96 +
mlr-2.3/mlr/man/mergeSmallFactorLevels.Rd | 3
mlr-2.3/mlr/man/mtcars.task.Rd | 3
mlr-2.3/mlr/man/normalizeFeatures.Rd | 3
mlr-2.3/mlr/man/oversample.Rd | 3
mlr-2.3/mlr/man/performance.Rd | 36
mlr-2.3/mlr/man/pid.task.Rd | 3
mlr-2.3/mlr/man/plotFilterValues.Rd | 3
mlr-2.3/mlr/man/plotLearnerPrediction.Rd | 9
mlr-2.3/mlr/man/plotROCRCurves.Rd |only
mlr-2.3/mlr/man/plotThreshVsPerf.Rd | 3
mlr-2.3/mlr/man/plotTuneMultiCritResult.Rd | 3
mlr-2.3/mlr/man/plotViperCharts.Rd |only
mlr-2.3/mlr/man/predict.WrappedModel.Rd | 9
mlr-2.3/mlr/man/predictLearner.Rd | 3
mlr-2.3/mlr/man/reimpute.Rd | 3
mlr-2.3/mlr/man/removeConstantFeatures.Rd | 3
mlr-2.3/mlr/man/removeHyperPars.Rd | 13
mlr-2.3/mlr/man/resample.Rd | 91
mlr-2.3/mlr/man/selectFeatures.Rd | 3
mlr-2.3/mlr/man/setAggregation.Rd | 3
mlr-2.3/mlr/man/setHyperPars.Rd | 13
mlr-2.3/mlr/man/setHyperPars2.Rd | 3
mlr-2.3/mlr/man/setId.Rd | 14
mlr-2.3/mlr/man/setPredictThreshold.Rd |only
mlr-2.3/mlr/man/setPredictType.Rd | 18
mlr-2.3/mlr/man/setThreshold.Rd | 6
mlr-2.3/mlr/man/showHyperPars.Rd | 10
mlr-2.3/mlr/man/smote.Rd | 3
mlr-2.3/mlr/man/sonar.task.Rd | 3
mlr-2.3/mlr/man/subsetTask.Rd | 10
mlr-2.3/mlr/man/summarizeColumns.Rd | 3
mlr-2.3/mlr/man/summarizeLevels.Rd | 3
mlr-2.3/mlr/man/train.Rd | 3
mlr-2.3/mlr/man/trainLearner.Rd | 3
mlr-2.3/mlr/man/tuneParams.Rd | 3
mlr-2.3/mlr/man/tuneParamsMultiCrit.Rd | 3
mlr-2.3/mlr/man/tuneThreshold.Rd | 3
mlr-2.3/mlr/man/wpbc.task.Rd | 3
mlr-2.3/mlr/tests/run-classif.R | 2
mlr-2.3/mlr/tests/run-cluster.R | 2
mlr-2.3/mlr/tests/run-featsel.R | 2
mlr-2.3/mlr/tests/run-learners.R | 2
mlr-2.3/mlr/tests/run-parallel.R | 7
mlr-2.3/mlr/tests/run-regr.R | 2
mlr-2.3/mlr/tests/run-stack.R | 2
mlr-2.3/mlr/tests/run-surv.R | 2
mlr-2.3/mlr/tests/run-tune.R | 2
mlr-2.3/mlr/tests/testthat/Rplots.pdf |binary
mlr-2.3/mlr/tests/testthat/helper_helpers.R | 16
mlr-2.3/mlr/tests/testthat/helper_mock_learners.R | 25
mlr-2.3/mlr/tests/testthat/helper_objects.R | 10
mlr-2.3/mlr/tests/testthat/test_base_BaggingWrapper.R | 14
mlr-2.3/mlr/tests/testthat/test_base_BaseWrapper.R | 3
mlr-2.3/mlr/tests/testthat/test_base_MulticlassWrapper.R | 8
mlr-2.3/mlr/tests/testthat/test_base_PreprocWrapperCaret.R |only
mlr-2.3/mlr/tests/testthat/test_base_TuneWrapper.R |only
mlr-2.3/mlr/tests/testthat/test_base_aggregations.R | 8
mlr-2.3/mlr/tests/testthat/test_base_benchmark.R | 8
mlr-2.3/mlr/tests/testthat/test_base_blocking.R | 51
mlr-2.3/mlr/tests/testthat/test_base_clustering.R | 2
mlr-2.3/mlr/tests/testthat/test_base_configureMlr.R | 5
mlr-2.3/mlr/tests/testthat/test_base_costsens.R | 2
mlr-2.3/mlr/tests/testthat/test_base_dropFeatures.R | 4
mlr-2.3/mlr/tests/testthat/test_base_estimateResidualVariance.R | 2
mlr-2.3/mlr/tests/testthat/test_base_getConfMatrix.R |only
mlr-2.3/mlr/tests/testthat/test_base_getHyperPars.R |only
mlr-2.3/mlr/tests/testthat/test_base_getParamSet.R |only
mlr-2.3/mlr/tests/testthat/test_base_helpers.R | 9
mlr-2.3/mlr/tests/testthat/test_base_hyperpars.R | 67
mlr-2.3/mlr/tests/testthat/test_base_imbal_overbagging.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_overundersample.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_smote.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_weightedclasses.R |only
mlr-2.3/mlr/tests/testthat/test_base_impute.R | 24
mlr-2.3/mlr/tests/testthat/test_base_measures.R | 14
mlr-2.3/mlr/tests/testthat/test_base_performance.R | 22
mlr-2.3/mlr/tests/testthat/test_base_plotViperCharts.R |only
mlr-2.3/mlr/tests/testthat/test_base_predict.R | 27
mlr-2.3/mlr/tests/testthat/test_base_resample.R | 6
mlr-2.3/mlr/tests/testthat/test_base_resample_b632.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_b632plus.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_bs.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_convenience.R |only
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mlr-2.3/mlr/tests/testthat/test_base_resample_holdout.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_loo.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_makeResampleDesc.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_repcv.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_stratify.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_subsample.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_weights.R |only
mlr-2.3/mlr/tests/testthat/test_base_rocr.R | 17
mlr-2.3/mlr/tests/testthat/test_base_selectFeatures.R |only
mlr-2.3/mlr/tests/testthat/test_base_summarizeColumns.R | 14
mlr-2.3/mlr/tests/testthat/test_base_tuning.R | 53
mlr-2.3/mlr/tests/testthat/test_classif_IBk.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_J48.R | 67
mlr-2.3/mlr/tests/testthat/test_classif_JRip.R | 67
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRBinary.R | 4
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRLogReg.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRMultiClass.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_OneR.R | 62
mlr-2.3/mlr/tests/testthat/test_classif_PART.R | 7
mlr-2.3/mlr/tests/testthat/test_classif_ada.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_bartMachine.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_bdk.R |only
mlr-2.3/mlr/tests/testthat/test_classif_binomial.R |only
mlr-2.3/mlr/tests/testthat/test_classif_blackboost.R | 24
mlr-2.3/mlr/tests/testthat/test_classif_boost.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_cforest.R | 18
mlr-2.3/mlr/tests/testthat/test_classif_ctree.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_extraTrees.R |only
mlr-2.3/mlr/tests/testthat/test_classif_fnn.R | 15
mlr-2.3/mlr/tests/testthat/test_classif_gbm.R | 68
mlr-2.3/mlr/tests/testthat/test_classif_geoDA.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_glmboost.R | 56
mlr-2.3/mlr/tests/testthat/test_classif_glmnet.R | 19
mlr-2.3/mlr/tests/testthat/test_classif_kknn.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_knn.R | 14
mlr-2.3/mlr/tests/testthat/test_classif_ksvm.R | 60
mlr-2.3/mlr/tests/testthat/test_classif_lda.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_linDA.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_lqa.R | 14
mlr-2.3/mlr/tests/testthat/test_classif_lssvm.R | 50
mlr-2.3/mlr/tests/testthat/test_classif_mda.R | 72
mlr-2.3/mlr/tests/testthat/test_classif_multinom.R | 54
mlr-2.3/mlr/tests/testthat/test_classif_naiveBayes.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_nnet.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_plr.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_plsdaCaret.R | 4
mlr-2.3/mlr/tests/testthat/test_classif_probit.R |only
mlr-2.3/mlr/tests/testthat/test_classif_qda.R | 15
mlr-2.3/mlr/tests/testthat/test_classif_quaDA.R | 28
mlr-2.3/mlr/tests/testthat/test_classif_randomForest.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_randomForestSRC.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_rda.R | 76
mlr-2.3/mlr/tests/testthat/test_classif_rpart.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_rrlda.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_sda.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_svm.R | 34
mlr-2.3/mlr/tests/testthat/test_classif_xgboost.R |only
mlr-2.3/mlr/tests/testthat/test_classif_xyf.R |only
mlr-2.3/mlr/tests/testthat/test_cluster_EM.R | 36
mlr-2.3/mlr/tests/testthat/test_cluster_FarthestFirst.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_SimpleKMeans.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_XMeans.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_cmeans.R | 10
mlr-2.3/mlr/tests/testthat/test_cluster_kmeans.R | 6
mlr-2.3/mlr/tests/testthat/test_featsel_FilterWrapper.R | 4
mlr-2.3/mlr/tests/testthat/test_featsel_filterFeatures.R | 4
mlr-2.3/mlr/tests/testthat/test_featsel_selectFeatures.R | 77
mlr-2.3/mlr/tests/testthat/test_learners_all.R | 43
mlr-2.3/mlr/tests/testthat/test_learners_classiflabelswitch.R |only
mlr-2.3/mlr/tests/testthat/test_parallel_all.R | 48
mlr-2.3/mlr/tests/testthat/test_regr_IBk.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_bartMachine.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bcart.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bdk.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bgp.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bgpllm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_blackboost.R | 47
mlr-2.3/mlr/tests/testthat/test_regr_blm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_brnn.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btgp.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btgpllm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btlm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_cforest.R | 14
mlr-2.3/mlr/tests/testthat/test_regr_crs.R | 14
mlr-2.3/mlr/tests/testthat/test_regr_ctree.R | 8
mlr-2.3/mlr/tests/testthat/test_regr_cubist.R |only
mlr-2.3/mlr/tests/testthat/test_regr_earth.R | 40
mlr-2.3/mlr/tests/testthat/test_regr_elmNN.R |only
mlr-2.3/mlr/tests/testthat/test_regr_extraTrees.R |only
mlr-2.3/mlr/tests/testthat/test_regr_fnn.R | 16
mlr-2.3/mlr/tests/testthat/test_regr_gbm.R | 48
mlr-2.3/mlr/tests/testthat/test_regr_glmnet.R | 8
mlr-2.3/mlr/tests/testthat/test_regr_kknn.R | 63
mlr-2.3/mlr/tests/testthat/test_regr_km.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_ksvm.R | 4
mlr-2.3/mlr/tests/testthat/test_regr_laGP.R |only
mlr-2.3/mlr/tests/testthat/test_regr_lm.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_mob.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_penalized_lasso.R | 70
mlr-2.3/mlr/tests/testthat/test_regr_penalized_ridge.R | 66
mlr-2.3/mlr/tests/testthat/test_regr_plsr.R | 36
mlr-2.3/mlr/tests/testthat/test_regr_randomForest.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_randomForestSRC.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_rpart.R | 16
mlr-2.3/mlr/tests/testthat/test_regr_rsm.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_svm.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_xgboost.R |only
mlr-2.3/mlr/tests/testthat/test_regr_xyf.R |only
mlr-2.3/mlr/tests/testthat/test_stack.R | 6
mlr-2.3/mlr/tests/testthat/test_surv_CoxBoost.R |only
mlr-2.3/mlr/tests/testthat/test_surv_cforest.R | 17
mlr-2.3/mlr/tests/testthat/test_surv_coxph.R | 10
mlr-2.3/mlr/tests/testthat/test_surv_cvglmnet.R | 21
mlr-2.3/mlr/tests/testthat/test_surv_glmboost.R | 20
mlr-2.3/mlr/tests/testthat/test_surv_glmnet.R | 16
mlr-2.3/mlr/tests/testthat/test_surv_penalized.R | 8
mlr-2.3/mlr/tests/testthat/test_surv_randomForestSRC.R | 6
mlr-2.3/mlr/tests/testthat/test_tune_ModelMultiplexer.R | 18
mlr-2.3/mlr/tests/testthat/test_tune_tuneIraceR.R | 9
mlr-2.3/mlr/tests/testthat/test_tune_tuneMBO.R | 3
mlr-2.3/mlr/tests/testthat/test_tune_tuneParamsMultiCrit.R | 2
525 files changed, 4390 insertions(+), 2921 deletions(-)
Title: Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Diff between LiblineaR versions 1.80-10 dated 2014-09-16 and 1.94-2 dated 2015-02-04
Description: A wrapper around the LIBLINEAR C/C++ library for
machine learning (available at http://www.csie.ntu.edu.tw/~cjlin/liblinear).
LIBLINEAR is a simple library for solving large-scale regularized linear
classification and regression. It currently supports L2-regularized
classification (such as logistic regression, L2-loss linear SVM and L1-loss
linear SVM) as well as L1-regularized classification (such as L2-loss linear
SVM and logistic regression) and L2-regularized support vector regression
(with L1- or L2-loss). The main features of LiblineaR include multi-class
classification (one-vs-the rest, and Crammer & Singer method), cross
validation for model selection, probability estimates (logistic regression
only) or weights for unbalanced data. The estimation of the models is
particularly fast as compared to other libraries.
Author: Thibault Helleputte
Maintainer: Thibault Helleputte
LiblineaR-1.80-10/LiblineaR/man/LiblineaR-package.Rd |only
LiblineaR-1.94-2/LiblineaR/DESCRIPTION | 28
LiblineaR-1.94-2/LiblineaR/MD5 | 33
LiblineaR-1.94-2/LiblineaR/NEWS | 28
LiblineaR-1.94-2/LiblineaR/R/LiblineaR.R | 493 +++++++--
LiblineaR-1.94-2/LiblineaR/R/heuristicC.R | 76 +
LiblineaR-1.94-2/LiblineaR/R/predict.R | 132 +-
LiblineaR-1.94-2/LiblineaR/README | 50
LiblineaR-1.94-2/LiblineaR/inst/CITATION | 9
LiblineaR-1.94-2/LiblineaR/man/LiblineaR.Rd | 322 +++---
LiblineaR-1.94-2/LiblineaR/man/heuristicC.Rd | 71 -
LiblineaR-1.94-2/LiblineaR/man/predict.LiblineaR.Rd | 168 +--
LiblineaR-1.94-2/LiblineaR/src/linear.cpp | 960 ++++++++++++++-----
LiblineaR-1.94-2/LiblineaR/src/linear.h | 16
LiblineaR-1.94-2/LiblineaR/src/predictLinear.c | 136 +-
LiblineaR-1.94-2/LiblineaR/src/trainLinear.c | 304 +++---
LiblineaR-1.94-2/LiblineaR/src/tron.cpp | 11
LiblineaR-1.94-2/LiblineaR/tests |only
18 files changed, 1949 insertions(+), 888 deletions(-)
Title: A Genetic Algorithm for Fixed-Size Subset Selection
Diff between kofnGA versions 1.0 dated 2014-09-24 and 1.1 dated 2015-02-04
Description: Function kofnGA uses a genetic algorithm to choose a subset of a
fixed size k from the integers 1:n, such that a user-supplied objective function
is minimized at that subset. The selection step is done by tournament selection
based on ranks, and elitism may be used to retain a portion of the best solutions
from one generation to the next.
Author: Mark A. Wolters
Maintainer: Mark A. Wolters
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NAMESPACE | 6 +++++-
inst/CITATION | 4 ++--
man/kofnGA-package.Rd | 6 +++---
man/kofnGA.Rd | 4 +++-
6 files changed, 22 insertions(+), 16 deletions(-)
Title: Categorical Bayesian Network Inference
Diff between catnet versions 1.14.5 dated 2014-12-09 and 1.14.8 dated 2015-02-04
Description: Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov
DESCRIPTION | 8 +--
MD5 | 10 ++--
src/catnet_class.h | 122 ++++++++++++++++++++++++++++++---------------------
src/catnet_search2.h | 10 ++--
src/problist.h | 12 ++++-
src/rcatnet.cpp | 7 ++
6 files changed, 105 insertions(+), 64 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10 dated 2015-02-01 and 0.9.10-1 dated 2015-02-04
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NEWS | 5 +++++
R/BayesFactorPCL-package.R | 2 +-
inst/doc/compare_lme4.html | 10 +++++-----
inst/doc/manual.html | 2 +-
inst/doc/priors.html | 2 +-
src/logSummaryStats.cpp | 2 +-
8 files changed, 25 insertions(+), 20 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Diff between TSP versions 1.0-9 dated 2014-07-16 and 1.0-10 dated 2015-02-03
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to Concorde, the currently fastest TSP solver. Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 12 +++++------
MD5 | 44 ++++++++++++++++++++---------------------
R/ATSP.R | 2 -
R/TSP.R | 3 +-
R/cut_tour.R | 1
R/tsp_concorde.R | 26 +++++++++++++-----------
build/vignette.rds |binary
data/USCA312.rda |binary
data/USCA312_map.rda |binary
data/USCA50.rda |binary
inst/NEWS | 5 ++++
inst/doc/TSP.pdf |binary
man/ATSP.Rd | 1
man/Concorde.Rd | 10 +++++----
man/TOUR.Rd | 1
man/TSP.Rd | 1
man/TSPLIB.Rd | 3 +-
man/USCA312.Rd | 1
man/cut_tour.Rd | 1
man/insert_dummy.Rd | 1
man/reformulate_ATSP_as_TSP.Rd | 1
man/solve_TSP.Rd | 1
man/tour_length.Rd | 1
23 files changed, 68 insertions(+), 47 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Diff between qvcalc versions 0.8-8 dated 2012-06-05 and 0.8-9 dated 2015-02-03
Description: Functions to compute quasi variances and associated measures of approximation error
Author: David Firth
Maintainer: David Firth
qvcalc-0.8-8/qvcalc/INDEX |only
qvcalc-0.8-9/qvcalc/DESCRIPTION | 19 +++++++++----------
qvcalc-0.8-9/qvcalc/MD5 | 11 +++++------
qvcalc-0.8-9/qvcalc/R/qvcalc.R | 8 +++++++-
qvcalc-0.8-9/qvcalc/man/plot.qv.Rd | 5 ++++-
qvcalc-0.8-9/qvcalc/man/qvcalc.Rd | 17 +++++++++--------
qvcalc-0.8-9/qvcalc/man/worstErrors.Rd | 2 +-
7 files changed, 35 insertions(+), 27 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Diff between FactoClass versions 1.1.0 dated 2013-07-18 and 1.1.1 dated 2015-02-03
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo
Maintainer: Campo Elias Pardo
FactoClass-1.1.0/FactoClass/FactoClass-Ex.R |only
FactoClass-1.1.1/FactoClass/DESCRIPTION | 8
FactoClass-1.1.1/FactoClass/MD5 | 17 -
FactoClass-1.1.1/FactoClass/NAMESPACE | 25 +
FactoClass-1.1.1/FactoClass/R/plot.dudi.R | 351 ++++++++++++--------------
FactoClass-1.1.1/FactoClass/R/plotfp.R | 288 ++++++++++-----------
FactoClass-1.1.1/FactoClass/R/stableclus.R | 218 ++++++++--------
FactoClass-1.1.1/FactoClass/man/Bogota.Rd | 30 +-
FactoClass-1.1.1/FactoClass/man/plotfp.Rd | 115 ++++----
FactoClass-1.1.1/FactoClass/man/stableclus.Rd | 112 ++++----
10 files changed, 590 insertions(+), 574 deletions(-)
More information about AncestryMapper at CRAN
Permanent link
Title: R Commander Plug-in for the survival Package
Diff between RcmdrPlugin.survival versions 1.0-4 dated 2013-01-17 and 1.0-5 dated 2015-02-03
More information about RcmdrPlugin.survival at CRAN
Description: This package provides an R Commander plug-in for the survival
package, with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
diagnostics and graphs.
Author: John Fox
Maintainer: John Fox
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/anova.coxph.Rd |only
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/survQuantiles.Rd |only
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/DESCRIPTION | 20 +-
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/MD5 | 26 +--
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/NAMESPACE | 8 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/CoxModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survdiff.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survfit.R | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/misc.R | 12 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/quantile.survfit.R | 76 +++++-----
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/survregModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/unfold.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/CHANGES | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/etc/menus.txt | 5
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/man/RcmdrPlugin.survival-package.Rd | 4
15 files changed, 91 insertions(+), 84 deletions(-)
Permanent link
Title: Genetic Analysis of Populations With Mixed Reproduction
Diff between poppr versions 1.1.2 dated 2014-07-29 and 1.1.3 dated 2015-02-03
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar
DESCRIPTION | 29 ++-
MD5 | 222 +++++++++++++++--------------
NAMESPACE | 2
NEWS | 19 ++
R/Index_calculations.r | 8 -
R/amova.r | 14 -
R/bruvo.r | 99 +++++++-----
R/data_subset.r | 40 ++++-
R/distances.r | 29 ++-
R/file_handling.r | 5
R/internal.r | 38 +++-
R/methods.r | 3
R/mlg.r | 5
R/poppr.R | 2
R/sandbox.r | 24 +--
R/visualizations.r | 172 ++++++++++++++--------
R/zzz.r | 2
README.md | 16 --
build/vignette.rds |binary
data/Aeut.rda |binary
data/Pinf.rda |binary
data/monpop.rda |binary
data/partial_clone.rda |binary
inst/doc/algo.R | 4
inst/doc/algo.Rnw | 27 +++
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.R | 36 ++--
inst/doc/poppr_manual.Rnw | 48 +++---
inst/doc/poppr_manual.pdf |binary
man/Aeut.Rd | 3
man/Pinf.Rd | 3
man/aboot.Rd | 13 +
man/bootgen-class.Rd | 3
man/bootgen-methods.Rd | 10 -
man/bruvo.boot.Rd | 3
man/bruvo.dist.Rd | 95 ++++++------
man/bruvo.msn.Rd | 3
man/bruvomat-class.Rd | 3
man/bruvomat-methods.Rd | 3
man/clonecorrect.Rd | 3
man/coercion-methods.Rd | 3
man/diss.dist.Rd | 3
man/genclone-class.Rd | 3
man/genclone-method.Rd | 7
man/genetic_distance.Rd | 3
man/genind2genalex.Rd | 3
man/genotype_curve.Rd | 3
man/getfile.Rd | 3
man/greycurve.Rd | 3
man/hierarchy-methods.Rd | 3
man/ia.Rd | 9 -
man/info_table.Rd | 9 -
man/informloci.Rd | 3
man/is.genclone.Rd | 3
man/locus_table.Rd | 3
man/missingno.Rd | 3
man/mlg.Rd | 15 +
man/monpop.Rd | 3
man/partial_clone.Rd | 3
man/plot_poppr_msn.Rd | 127 +++++++++-------
man/poppr-package.Rd | 5
man/poppr.Rd | 3
man/poppr.all.Rd | 3
man/poppr.amova.Rd | 5
man/poppr.msn.Rd | 14 +
man/popsub.Rd | 3
man/population-methods.Rd | 3
man/private_alleles.Rd | 5
man/read.genalex.Rd | 3
man/recode_polyploids.Rd | 5
man/shufflepop.Rd | 3
man/splitcombine.Rd | 7
src/poppr_distance.c | 2
tests/testthat/test-amova.R | 19 ++
tests/testthat/test-colors.R |only
tests/testthat/test-distpop.R | 7
tests/testthat/test-import.R |only
tests/testthat/test-values.R | 30 +++
vignettes/algo-concordance.tex | 2
vignettes/algo.Rnw | 27 +++
vignettes/figure/Aeut_MLG_Ahena-1.pdf |only
vignettes/figure/Aeut_MLG_Ahena.pdf |binary
vignettes/figure/Aeut_MLG_Ahena1.pdf |only
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vignettes/figure/bruvo_msn.pdf |binary
vignettes/figure/bruvo_tree.pdf |binary
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vignettes/figure/ex_data_picture.pdf |binary
vignettes/figure/ggplotchart.pdf |binary
vignettes/figure/greycurve_normal.pdf |binary
vignettes/figure/greycurve_small_heavy.pdf |binary
vignettes/figure/greywidth_inverse.pdf |binary
vignettes/figure/greywidth_large_heavy.pdf |binary
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vignettes/figure/poppr_msn_fig.pdf |binary
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vignettes/poppr_manual-concordance.tex | 4
vignettes/poppr_manual.Rnw | 48 +++---
120 files changed, 862 insertions(+), 534 deletions(-)
Title: Confidence Intervals with Poisson Double Sampling
Diff between poisDoubleSamp versions 1.0 dated 2015-02-02 and 1.1 dated 2015-02-03
More information about poisDoubleSamp at CRAN
Description: Functions to create confidence intervals for ratios of Poisson
rates under misclassification using double sampling.
Author: David Kahle [aut, cre],
Phil Young [aut],
Dean Young [aut]
Maintainer: David Kahle
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/unNormedMargLogLikeCpp.cpp | 4 ++--
src/unNormedMargLogLikeMaxLogTermCpp.cpp | 8 ++++----
4 files changed, 13 insertions(+), 13 deletions(-)
Permanent link
Title: Tools for Reading and Handling Spatial Objects
Diff between maptools versions 0.8-30 dated 2014-06-05 and 0.8-34 dated 2015-02-03
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand
ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 12
MD5 | 54 +-
R/DP.R | 6
R/Rgshhs.R | 14
R/SP2owin.R | 14
R/checkHoles.R | 36 +
R/nowrapRecenter.R | 26 -
R/point_line_distance.R | 10
R/sp2pbs.R | 26 -
R/sp_spat1.R | 12
R/spatstat1.R | 95 ++--
R/spmaps.R | 16
R/union.R | 16
build/vignette.rds |binary
inst/ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/combine_maptools.pdf |binary
man/GE_SpatialGrid.Rd | 4
man/SpatialLines2PolySet.Rd | 5
man/dotsInPolys.Rd | 3
man/map2SpatialPolygons.Rd | 3
man/readGPS.Rd | 32 -
man/readSplus.Rd | 2
man/sp2WB.Rd | 4
man/sp2tmap.Rd | 2
man/symbolsInPolys.Rd | 3
src/Rgshhs.c | 10
src/shapefil.h | 14
28 files changed, 1983 insertions(+), 180 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Diff between llama versions 0.8 dated 2015-01-31 and 0.8.1 dated 2015-02-03
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff
DESCRIPTION | 8 +++----
MD5 | 38 +++++++++++++++++------------------
R/helpers.R | 6 +++++
inst/manual/llama.pdf |binary
man/analysis.Rd | 2 -
man/classify.Rd | 2 -
man/classifyPairs.Rd | 2 -
man/cluster.Rd | 2 -
man/imputeCensored.Rd | 2 -
man/llama-package.Rd | 2 -
man/misc.Rd | 2 -
man/misclassificationPenalties.Rd | 2 -
man/normalize.Rd | 2 -
man/parscores.Rd | 2 -
man/plot.Rd | 2 -
man/regression.Rd | 2 -
man/regressionPairs.Rd | 2 -
man/successes.Rd | 2 -
tests/testthat/helper_mockLearners.R | 6 ++---
tests/testthat/test.satsolvers.R | 14 ++++++------
20 files changed, 53 insertions(+), 47 deletions(-)
More information about RPPairwiseDesign at CRAN
Permanent link
Title: Relative Contribution of Effects in a Regression Model
Diff between relimp versions 1.0-3 dated 2011-10-17 and 1.0-4 dated 2015-02-03
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Author: David Firth with contributions from Heather Turner
Maintainer: David Firth
DESCRIPTION | 17 +--
MD5 | 13 +-
NAMESPACE | 2
R/Tcl-utilities.R |only
R/pickFrom.R | 165 ++++++++++++++++++-----------------
R/relimp.R | 40 ++++----
R/showData.R | 249 +++++++++++++++++++++++++++---------------------------
man/relimp.Rd | 5 -
8 files changed, 250 insertions(+), 241 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-5 dated 2014-12-10 and 2.1-6 dated 2015-02-03
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 13
MD5 | 14
NAMESPACE | 10
NEWS | 4
R/model-menu.R | 6
R/utilities.R | 5994 +++++++++++++++++++++++++--------------------------
man/Confint.Rd | 10
man/Rcmdr-package.Rd | 4
8 files changed, 3043 insertions(+), 3012 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning.
Diff between ParamHelpers versions 1.4 dated 2014-10-10 and 1.5 dated 2015-02-03
Description: Functions for parameter descriptions and operations in black-box optimization, tuning
and machine learning. Parameters can be described (type, constraints, defaults, etc.),
combined to parameter sets and can in general be programmed on.
A useful OptPath object (archive) to log function evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 19 +--
MD5 | 142 +++++++++++++--------------
NAMESPACE | 2
NEWS | 6 -
R/OptPath.R | 7 -
R/OptPath_getter.R | 2
R/OptPath_setter.R | 3
R/ParamSet.R | 8 -
R/aParam.R | 4
R/convertParamSetToIrace.R | 4
R/generateDesign.R | 2
R/getDefaults.R | 21 ++-
R/isMissingValue.R | 3
R/removeMissingValues.R | 4
man/LearnerParam.Rd | 3
man/OptPath.Rd | 5
man/Param.Rd | 3
man/addOptPathEl.Rd | 6 -
man/as.data.frame.OptPathDF.Rd | 3
man/convertParamSetToIrace.Rd | 3
man/dfRowsToList.Rd | 3
man/discreteNameToValue.Rd | 3
man/discreteValueToName.Rd | 3
man/dropParams.Rd | 3
man/extractParamSetFromSooFunction.Rd | 3
man/filterParams.Rd | 3
man/generateDesign.Rd | 3
man/generateGridDesign.Rd | 3
man/generateRandomDesign.Rd | 3
man/getDefaults.Rd | 11 +-
man/getLower.Rd | 3
man/getOptPathBestIndex.Rd | 3
man/getOptPathCol.Rd | 3
man/getOptPathCols.Rd | 3
man/getOptPathDOB.Rd | 3
man/getOptPathEOL.Rd | 3
man/getOptPathEl.Rd | 3
man/getOptPathErrorMessages.Rd | 3
man/getOptPathExecTimes.Rd | 3
man/getOptPathLength.Rd | 3
man/getOptPathParetoFront.Rd | 3
man/getOptPathX.Rd | 3
man/getOptPathY.Rd | 3
man/getParamIds.Rd | 3
man/getParamLengths.Rd | 3
man/getParamNr.Rd | 3
man/getParamTypeCounts.Rd | 3
man/getParamTypes.Rd | 3
man/hasFiniteBoxConstraints.Rd | 3
man/hasForbidden.Rd | 3
man/hasRequires.Rd | 3
man/hasTrafo.Rd | 3
man/hasType.Rd | 3
man/isEmpty.Rd | 3
man/isFeasible.Rd | 3
man/isForbidden.Rd | 3
man/isType.Rd | 3
man/makeParamSet.Rd | 3
man/paramValueToString.Rd | 3
man/removeMissingValues.Rd | 3
man/repairPoint.Rd | 3
man/sampleValue.Rd | 3
man/sampleValues.Rd | 3
man/setOptPathElDOB.Rd | 3
man/setOptPathElEOL.Rd | 3
man/setValueCNames.Rd | 3
man/trafoOptPath.Rd | 3
man/trafoValue.Rd | 3
tests/testthat/test_OptPath.R | 6 -
tests/testthat/test_convertParamSetToIrace.R | 16 ++-
tests/testthat/test_generateDesign.R | 11 +-
tests/testthat/test_getDefaults.R | 15 ++
72 files changed, 278 insertions(+), 172 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.34-0 dated 2014-11-05 and 0.34-1 dated 2015-02-03
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann
DESCRIPTION | 8
MD5 | 65 ++---
build/vignette.rds |binary
inst/NMOFex/NMOFman.R | 538 +++++++++++++++++++++++-----------------------
inst/doc/An_overview.R | 14 -
inst/doc/An_overview.Rnw | 3
inst/doc/An_overview.pdf |binary
inst/doc/DEnss.R | 60 ++---
inst/doc/DEnss.Rnw | 5
inst/doc/DEnss.pdf |binary
inst/doc/LSselect.R | 24 +-
inst/doc/LSselect.Rnw | 3
inst/doc/LSselect.pdf |binary
inst/doc/NMOF.bib |only
inst/doc/PSlms.R | 20 -
inst/doc/PSlms.Rnw | 2
inst/doc/PSlms.pdf |binary
inst/doc/TAportfolio.R | 40 +--
inst/doc/TAportfolio.Rnw | 5
inst/doc/TAportfolio.pdf |binary
inst/doc/qTableEx.Rnw | 2
inst/doc/qTableEx.pdf |binary
inst/doc/repair.R | 30 +-
inst/doc/repair.Rnw | 4
inst/doc/repair.pdf |binary
inst/doc/vectorise.pdf |binary
inst/unitTests/report.txt | 26 +-
vignettes/.install_extras |only
vignettes/An_overview.Rnw | 3
vignettes/DEnss.Rnw | 5
vignettes/LSselect.Rnw | 3
vignettes/PSlms.Rnw | 2
vignettes/TAportfolio.Rnw | 5
vignettes/qTableEx.Rnw | 2
vignettes/repair.Rnw | 4
35 files changed, 451 insertions(+), 422 deletions(-)
Title: Nested Association Mapping analysis
Diff between NAM versions 1.0.2.1 dated 2015-01-24 and 1.0.2.2 dated 2015-02-03
Description: Package designed for association studies in nested association mapping (NAM) panels, but it also can handle biparental and random populations. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
R/gwas.R | 9 +++++----
R/gwas2.R |only
man/NAM-package.Rd | 6 +++---
man/gwas.Rd | 3 +++
6 files changed, 21 insertions(+), 16 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.96 dated 2013-11-17 and 0.97 dated 2015-02-03
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl
DESCRIPTION | 15 ++--
MD5 | 18 ++--
NAMESPACE | 1
NEWS | 9 ++
R/or2rr.R |only
R/quantileCI.R | 11 ++
R/repMeans.R | 182 +++++++++++++++++++++++--------------------------
inst/CITATION | 16 +---
man/0MKmisc-package.Rd | 6 -
man/or2rr.Rd |only
man/quantileCI.Rd | 19 +++--
11 files changed, 146 insertions(+), 131 deletions(-)
Title: Distributions To Be Used For GAMLSS Modelling
Diff between gamlss.dist versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: This package contains the distributions for GAMLSS
modelling.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.dist-4.3-1/gamlss.dist/R/WA1.R |only
gamlss.dist-4.3-1/gamlss.dist/R/WARING.r |only
gamlss.dist-4.3-4/gamlss.dist/DESCRIPTION | 10
gamlss.dist-4.3-4/gamlss.dist/MD5 | 26
gamlss.dist-4.3-4/gamlss.dist/NAMESPACE | 3
gamlss.dist-4.3-4/gamlss.dist/R/BEOI.r | 550 +++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/BEZI.r | 544 ++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/DoublePoisson-30-12-14.R |only
gamlss.dist-4.3-4/gamlss.dist/R/NO.r | 280 +++----
gamlss.dist-4.3-4/gamlss.dist/R/WARING_BOB.r |only
gamlss.dist-4.3-4/gamlss.dist/R/ZAGA.R | 10
gamlss.dist-4.3-4/gamlss.dist/R/make-link-gamlss-4-4-13.R | 344 ++++----
gamlss.dist-4.3-4/gamlss.dist/man/DPO.Rd |only
gamlss.dist-4.3-4/gamlss.dist/man/WARING.Rd | 132 +--
gamlss.dist-4.3-4/gamlss.dist/man/ZAGA.Rd | 227 ++---
gamlss.dist-4.3-4/gamlss.dist/src/dDPOgetC5_C.c |only
gamlss.dist-4.3-4/gamlss.dist/src/tofyHead.h | 2
17 files changed, 1071 insertions(+), 1057 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Diff between divo versions 0.1 dated 2015-01-29 and 0.1.1 dated 2015-02-03
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak
DESCRIPTION | 8 ++---
MD5 | 15 +++++----
R/divo.R | 72 +++++++++++++++++++++++++++++++++-------------
inst/DivO_DP.py | 54 +++++++++++++++++++---------------
inst/DivO_EnvCheck.py |only
inst/DivO_Overlap.py | 13 +++-----
inst/doc/divo-Manual.Rnw | 2 -
inst/doc/divo-Manual.pdf |binary
vignettes/divo-Manual.Rnw | 2 -
9 files changed, 101 insertions(+), 65 deletions(-)
Title: Documentation for Packages distr, distrEx, distrSim, distrTEst,
distrTeach, distrMod, and distrEllipse
Diff between distrDoc versions 2.5 dated 2013-09-13 and 2.5.1 dated 2015-02-03
Description: provides documentation in form of a common vignette to packages distr, distrEx,
distrMod, distrSim, distrTEst, distrTeach, and distrEllipse
Author: Florian Camphausen [ctb] (contributed as student to the documented
packages in the initial phase --2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student to the documented packages
in the initial phase --2005)
Maintainer: Peter Ruckdeschel
DESCRIPTION | 31 ++++++++++++++++++++-----------
MD5 | 15 ++++++++-------
build |only
inst/CITATION | 22 +++++++++++++++++++++-
inst/NEWS | 9 +++++++++
inst/doc/distr.R | 3 ++-
inst/doc/distr.Rnw | 10 ++++++----
inst/doc/distr.pdf |binary
vignettes/distr.Rnw | 10 ++++++----
9 files changed, 72 insertions(+), 28 deletions(-)
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 2.0 dated 2015-01-27 and 2.1.0 dated 2015-02-03
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
DESCRIPTION | 8 +++----
MD5 | 19 +++++++++---------
NAMESPACE | 1
NEWS | 26 +++++++++++++++++-------
R/decomp.R | 10 ++++++++-
R/leontief.R | 51 ++++++++++++++++++++++++++++++++++++++++++++++---
README.md | 26 +++++++-----------------
man/decomp.Rd | 4 +--
man/kung_fu.Rd | 4 +--
man/leontief.Rd | 2 -
man/leontief_output.Rd |only
11 files changed, 103 insertions(+), 48 deletions(-)
Title: GAMLSS Utilities
Diff between gamlss.util versions 4.2-7 dated 2013-07-03 and 4.3-2 dated 2015-02-03
Description: Extra Functions For GAMLSS And Others Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.util-4.2-7/gamlss.util/R/createLags.R |only
gamlss.util-4.2-7/gamlss.util/R/flexDist.r |only
gamlss.util-4.2-7/gamlss.util/R/movMean.R |only
gamlss.util-4.2-7/gamlss.util/R/penLS.R |only
gamlss.util-4.2-7/gamlss.util/man/Locmean.Rd |only
gamlss.util-4.2-7/gamlss.util/man/flexDist.Rd |only
gamlss.util-4.2-7/gamlss.util/man/penLS.Rd |only
gamlss.util-4.3-2/gamlss.util/DESCRIPTION | 20
gamlss.util-4.3-2/gamlss.util/MD5 | 29 -
gamlss.util-4.3-2/gamlss.util/NAMESPACE | 56 +-
gamlss.util-4.3-2/gamlss.util/R/PenRegQ.R | 28 -
gamlss.util-4.3-2/gamlss.util/R/centiles-ts.R | 289 +++++++-------
gamlss.util-4.3-2/gamlss.util/R/garmaFit.R | 166 +++++---
gamlss.util-4.3-2/gamlss.util/R/plotSimpleGamlss-3-7-13.R | 7
gamlss.util-4.3-2/gamlss.util/R/scattersmooth.r | 257 ++++++------
gamlss.util-4.3-2/gamlss.util/man/garmaFit.Rd | 6
gamlss.util-4.3-2/gamlss.util/man/penReg.Rd | 26 -
gamlss.util-4.3-2/gamlss.util/man/plotSimpleGamlss.Rd | 2
gamlss.util-4.3-2/gamlss.util/man/scattersmooth.Rd | 28 +
19 files changed, 486 insertions(+), 428 deletions(-)
Title: Generating and fitting truncated (gamlss.family) distributions
Diff between gamlss.tr versions 4.2-7 dated 2014-01-18 and 4.3-1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +++-
man/fitTail.Rd | 3 ++-
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: The Library For Fitting GAMLSS Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.3-1/gamlss/R/SUMMARY-15-06-13.R |only
gamlss-4.3-1/gamlss/R/gamlss-01-05-13.R |only
gamlss-4.3-1/gamlss/R/vcoc-gamlss-03-10-13.R |only
gamlss-4.3-4/gamlss/DESCRIPTION | 10
gamlss-4.3-4/gamlss/MD5 | 47 +--
gamlss-4.3-4/gamlss/NAMESPACE | 1
gamlss-4.3-4/gamlss/R/SUMMARY.R |only
gamlss-4.3-4/gamlss/R/cubicSplines-10-08-12.R | 184 +++++------
gamlss-4.3-4/gamlss/R/extra.R | 119 ++++---
gamlss-4.3-4/gamlss/R/gamlss.R |only
gamlss-4.3-4/gamlss/R/lms.R | 6
gamlss-4.3-4/gamlss/R/lo_new.R | 18 -
gamlss-4.3-4/gamlss/R/lpred.R | 332 ++++++++++-----------
gamlss-4.3-4/gamlss/R/pb_03-02-2014.R | 14
gamlss-4.3-4/gamlss/R/pb_new.R |only
gamlss-4.3-4/gamlss/R/predict.gamlss.R | 2
gamlss-4.3-4/gamlss/R/pvc.R | 17 -
gamlss-4.3-4/gamlss/R/qstats-29-12-12.R | 13
gamlss-4.3-4/gamlss/R/quantSheets.R | 19 -
gamlss-4.3-4/gamlss/R/stepGAIC-03-10-13..R | 19 +
gamlss-4.3-4/gamlss/R/term-plot.R | 402 ++++++++++++++++++--------
gamlss-4.3-4/gamlss/R/vcov-gamlss.R |only
gamlss-4.3-4/gamlss/inst/doc/NEWS.txt | 44 ++
gamlss-4.3-4/gamlss/man/Q.stats.Rd | 102 +++---
gamlss-4.3-4/gamlss/man/gamlss.ps.Rd | 4
gamlss-4.3-4/gamlss/man/ps.Rd | 13
gamlss-4.3-4/gamlss/man/summary.gamlss.Rd | 6
gamlss-4.3-4/gamlss/man/term.plot.Rd | 66 ++--
28 files changed, 850 insertions(+), 588 deletions(-)
Title: Miscellaneous Helper Functions for B. Bischl
Diff between BBmisc versions 1.8 dated 2014-10-30 and 1.9 dated 2015-02-03
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Jakob Richter [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 10 -
MD5 | 215 +++++++++++++++++-----------------
NAMESPACE | 3
NEWS | 35 +++--
R/load2.R | 2
R/mapValues.R |only
R/messagef.R | 10 -
R/normalize.R | 11 +
R/optimizeSubInts.R | 21 ++-
R/pause.R | 2
R/requirePackages.R | 60 ++++++---
R/save2.R | 2
R/setClasses.R | 2
man/addClasses.Rd | 3
man/argsAsNamedList.Rd | 3
man/asMatrixCols.Rd | 3
man/asQuoted.Rd | 3
man/binPack.Rd | 3
man/btwn.Rd | 3
man/cFactor.Rd | 3
man/catf.Rd | 3
man/checkArg.Rd | 3
man/checkListElementClass.Rd | 3
man/chunk.Rd | 3
man/clipString.Rd | 3
man/coalesce.Rd | 3
man/collapse.Rd | 3
man/collapsef.Rd | 3
man/computeMode.Rd | 3
man/convertDataFrameCols.Rd | 3
man/convertInteger.Rd | 3
man/convertIntegers.Rd | 3
man/convertListOfRowsToDataFrame.Rd | 3
man/convertMatrixType.Rd | 3
man/convertRowsToList.Rd | 3
man/convertToShortString.Rd | 3
man/dapply.Rd | 3
man/deprecated.Rd | 3
man/do.call2.Rd | 3
man/dropNamed.Rd | 3
man/ensureVector.Rd | 3
man/explode.Rd | 3
man/extractSubList.Rd | 3
man/filterNull.Rd | 3
man/getAttributeNames.Rd | 3
man/getClass1.Rd | 3
man/getFirst.Rd | 3
man/getMaxIndex.Rd | 3
man/getMaxIndexOfRows.Rd | 3
man/getOperatingSystem.Rd | 3
man/getRelativePath.Rd | 3
man/getUnixTime.Rd | 3
man/getUsedFactorLevels.Rd | 3
man/hasAttributes.Rd | 3
man/insert.Rd | 3
man/is.error.Rd | 3
man/isDirectory.Rd | 3
man/isEmptyDirectory.Rd | 3
man/isExpensiveExampleOk.Rd | 3
man/isFALSE.Rd | 3
man/isProperlyNamed.Rd | 3
man/isScalarNA.Rd | 3
man/isScalarValue.Rd | 3
man/isSubset.Rd | 3
man/isSuperset.Rd | 3
man/isValidName.Rd | 3
man/itostr.Rd | 3
man/lib.Rd | 3
man/load2.Rd | 3
man/lsort.Rd | 3
man/makeDataFrame.Rd | 3
man/makeFileCache.Rd | 3
man/makeProgressBar.Rd | 3
man/makeS3Obj.Rd | 3
man/makeSimpleFileLogger.Rd | 3
man/mapValues.Rd |only
man/messagef.Rd | 8 -
man/namedList.Rd | 3
man/names2.Rd | 3
man/nin.Rd | 3
man/normalize.Rd | 5
man/optimizeSubInts.Rd | 6
man/pause.Rd | 3
man/printStrToChar.Rd | 3
man/printToChar.Rd | 3
man/rangeVal.Rd | 3
man/requirePackages.Rd | 26 ++--
man/rowLapply.Rd | 3
man/save2.Rd | 3
man/seq_row.Rd | 3
man/setAttribute.Rd | 3
man/setClasses.Rd | 3
man/setRowNames.Rd | 3
man/setValue.Rd | 3
man/sortByCol.Rd | 3
man/splitPath.Rd | 3
man/splitTime.Rd | 3
man/stopf.Rd | 3
man/strrepeat.Rd | 3
man/suppressAll.Rd | 3
man/symdiff.Rd | 3
man/system3.Rd | 3
man/toRangeStr.Rd | 3
man/vlapply.Rd | 3
man/warningf.Rd | 3
man/which.first.Rd | 3
tests/testthat/test_mapValues.R |only
tests/testthat/test_normalize.R | 14 ++
tests/testthat/test_optimizeSubInts.R | 6
tests/testthat/test_requirePackages.R | 25 ++-
110 files changed, 447 insertions(+), 280 deletions(-)
Title: Multinomial Processing Tree (MPT) Models
Diff between mpt versions 0.5-0 dated 2014-10-06 and 0.5-1 dated 2015-02-03
Description: Fitting and testing multinomial processing tree models, a class
of statistical models for categorical data. The parameters are the link
probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer &
Batchelder, 1988).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut]
Maintainer: Florian Wickelmaier
ChangeLog | 14 +++++++++-----
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++-----------
R/mpt.R | 13 +++++++------
R/mptspec.R | 47 +++++++++++++++++++++++++++++++++++++----------
data/proact.rda |binary
data/prospecMemory.rda |only
data/recogROC.rda |binary
data/retroact.rda |binary
man/mpt.Rd | 5 +++--
man/mptEM.Rd | 18 +++++++++---------
man/mptspec.Rd | 8 ++++++++
man/prospecMemory.Rd |only
man/simulate.mpt.Rd | 2 +-
14 files changed, 91 insertions(+), 48 deletions(-)
Title: Metapopulation and Landscape Simulation
Diff between MetaLandSim versions 0.1 dated 2014-11-09 and 0.2 dated 2015-02-03
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre
MetaLandSim-0.1/MetaLandSim/R/manage.simulations.R |only
MetaLandSim-0.1/MetaLandSim/man/manage.simulations.Rd |only
MetaLandSim-0.2/MetaLandSim/DESCRIPTION | 8 -
MetaLandSim-0.2/MetaLandSim/MD5 | 43 +++++-----
MetaLandSim-0.2/MetaLandSim/NAMESPACE | 4
MetaLandSim-0.2/MetaLandSim/R/manage_expansion_sim.R |only
MetaLandSim-0.2/MetaLandSim/R/manage_landscape_sim.R |only
MetaLandSim-0.2/MetaLandSim/build/vignette.rds |binary
MetaLandSim-0.2/MetaLandSim/data/cabrera.rda |binary
MetaLandSim-0.2/MetaLandSim/data/datalist | 1
MetaLandSim-0.2/MetaLandSim/data/landscape_change.rda |binary
MetaLandSim-0.2/MetaLandSim/data/mc_df.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape2.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param1.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param2.rda |only
MetaLandSim-0.2/MetaLandSim/data/rg_exp.rda |binary
MetaLandSim-0.2/MetaLandSim/data/rland.rda |binary
MetaLandSim-0.2/MetaLandSim/inst/CITATION |only
MetaLandSim-0.2/MetaLandSim/inst/doc/MetaLandSim.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/landscape_simulation.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/range_expansion.pdf |binary
MetaLandSim-0.2/MetaLandSim/man/MetaLandSim-package.Rd | 39 +++++++--
MetaLandSim-0.2/MetaLandSim/man/iterate.graph.Rd | 8 -
MetaLandSim-0.2/MetaLandSim/man/manage_expansion_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/manage_landscape_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/param2.Rd |only
27 files changed, 68 insertions(+), 35 deletions(-)
Title: Fitting an interval response variable using gamlss.family
distributions
Diff between gamlss.cens versions 4.2.7 dated 2014-01-11 and 4.3.1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 42 +++++++++++++++++++++---------------------
data/lip.rda |binary
4 files changed, 29 insertions(+), 29 deletions(-)
Title: GAMLSS Extra Additive terms
Diff between gamlss.add versions 4.3-0 dated 2014-06-03 and 4.3-3 dated 2015-02-03
Description: Extra additive terms for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 13 ++---
MD5 | 16 +++---
NAMESPACE | 13 +++--
R/freeKnots-18-06-13.R | 2
R/gam_gamlss.R | 13 +++--
R/nnet_gamlss.R | 28 +++++++----
R/plotNN.R |only
R/tree_gamlss.R | 23 ++++++---
man/gamlss.ga.Rd | 118 ++++++++++++++++++++++++-------------------------
man/plotNN.Rd |only
10 files changed, 128 insertions(+), 98 deletions(-)
Title: DetMCD Algorithm (Robust and Deterministic Estimation of
Location and Scatter)
Diff between DetMCD versions 0.0.1 dated 2014-10-21 and 0.0.2 dated 2015-02-03
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
Author: Vakili Kaveh [aut, cre],
Mia Hubert [ths]
Maintainer: Vakili Kaveh
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +---
R/DetMCD.R | 3 ++-
4 files changed, 11 insertions(+), 12 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Diff between biogram versions 1.0 dated 2014-12-19 and 1.1 dated 2015-02-03
Description: Tools for extraction and analysis of various
n-grams (sequences of n items) derived from biological sequences (proteins
or nucleic acids). To deal with the dimensionality of the n-gram data,
biogram uses QuiPT (quick permutation test) for fast feature-filtering.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut],
Chris Lauber [aut]
Maintainer: Michal Burdukiewicz
biogram-1.0/biogram/man/data_sample.Rd |only
biogram-1.0/biogram/man/prepare_data.Rd |only
biogram-1.0/biogram/tests/testthat/test_quit_consistency.R |only
biogram-1.1/biogram/CHANGELOG |only
biogram-1.1/biogram/DESCRIPTION | 7
biogram-1.1/biogram/MD5 | 80 ++++----
biogram-1.1/biogram/NAMESPACE | 10 -
biogram-1.1/biogram/R/biogram.R | 89 +++++----
biogram-1.1/biogram/R/check_criterion.R | 2
biogram-1.1/biogram/R/check_ngrams.R |only
biogram-1.1/biogram/R/count_multigrams.R | 36 ++-
biogram-1.1/biogram/R/count_ngrams.R | 61 ++++--
biogram-1.1/biogram/R/criterion_distribution.R | 32 +--
biogram-1.1/biogram/R/data_manipulation.R | 112 ++++++------
biogram-1.1/biogram/R/decode_ngrams.R |only
biogram-1.1/biogram/R/feature_test_class.R |only
biogram-1.1/biogram/R/information_gain.R | 24 +-
biogram-1.1/biogram/R/ngrams.R | 11 -
biogram-1.1/biogram/R/position_ngrams.R |only
biogram-1.1/biogram/R/test_features.R | 98 +++++++---
biogram-1.1/biogram/R/utilities.R | 1
biogram-1.1/biogram/README.md | 13 +
biogram-1.1/biogram/inst |only
biogram-1.1/biogram/man/biogram-package.Rd | 92 +++++----
biogram-1.1/biogram/man/calc_ig.Rd | 8
biogram-1.1/biogram/man/calc_ig_single.Rd | 5
biogram-1.1/biogram/man/count_multigrams.Rd | 43 ++--
biogram-1.1/biogram/man/count_ngrams.Rd | 61 ++++--
biogram-1.1/biogram/man/create_feature_target.Rd | 3
biogram-1.1/biogram/man/create_ngrams.Rd | 16 +
biogram-1.1/biogram/man/criterion_distribution.Rd | 9
biogram-1.1/biogram/man/criterions.Rd | 3
biogram-1.1/biogram/man/cut.feature_test.Rd |only
biogram-1.1/biogram/man/decode_ngrams.Rd |only
biogram-1.1/biogram/man/degenerate.Rd | 3
biogram-1.1/biogram/man/fast_crosstable.Rd | 3
biogram-1.1/biogram/man/feature_test.Rd |only
biogram-1.1/biogram/man/get_ngrams_ind.Rd | 3
biogram-1.1/biogram/man/human_cleave.Rd | 3
biogram-1.1/biogram/man/is_ngram.Rd |only
biogram-1.1/biogram/man/l2n.Rd | 3
biogram-1.1/biogram/man/n2l.Rd | 3
biogram-1.1/biogram/man/position_ngrams.Rd |only
biogram-1.1/biogram/man/print.feature_test.Rd |only
biogram-1.1/biogram/man/seq2ngrams.Rd | 6
biogram-1.1/biogram/man/summary.feature_test.Rd |only
biogram-1.1/biogram/man/test_features.Rd | 49 +++--
biogram-1.1/biogram/tests/testthat/test_count_ngrams.R | 76 ++++----
biogram-1.1/biogram/tests/testthat/test_position_ngrams.R |only
biogram-1.1/biogram/tests/testthat/test_quipt_consistency.R |only
50 files changed, 580 insertions(+), 385 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.4 dated 2015-01-12 and 0.5 dated 2015-02-03
Description: V8 is Google's open source, high performance JavaScript engine. It
is written in C++ and implements ECMAScript as specified in ECMA-262, 5th
edition. In addition, this package implements typed arrays as specified in
ECMA 6 in order to support high performance computing and libraries compiled
with emscripten.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 14
MD5 | 37 -
R/RcppExports.R | 12
R/V8.R | 7
configure | 6
inst/doc/npm.R | 2
inst/doc/npm.Rmd | 2
inst/doc/npm.html | 11
inst/doc/v8_intro.R | 22
inst/doc/v8_intro.Rmd | 20
inst/doc/v8_intro.html | 28
inst/js/crossfilter.js |only
inst/js/underscore.js | 1414 -------------------------------------------------
man/new_context.Rd | 5
src/RcppExports.cpp | 48 +
src/V8.cpp | 63 ++
src/v8_typed_array.cpp |only
src/v8_typed_array.h |only
tools/v8-3.14.5.rb | 5
vignettes/npm.Rmd | 2
vignettes/v8_intro.Rmd | 20
21 files changed, 238 insertions(+), 1480 deletions(-)
Title: Seawater Carbonate Chemistry
Diff between seacarb versions 3.0.5 dated 2015-01-12 and 3.0.6 dated 2015-02-03
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 6 ++-
DESCRIPTION | 8 ++--
MD5 | 26 ++++++-------
R/buffer.R | 19 ++++-----
R/carb.R | 112 ++++++++++++++++++++++++++++++++++++++-------------------
man/Om.Rd | 4 +-
man/buffer.Rd | 2 -
man/buffesm.Rd | 2 -
man/carb.Rd | 16 +++++---
man/oa.Rd | 2 -
man/pCa.Rd | 2 -
man/pTA.Rd | 2 -
man/pgas.Rd | 2 -
man/pmix.Rd | 2 -
14 files changed, 125 insertions(+), 80 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Diff between wgaim versions 1.4-5 dated 2015-01-31 and 1.4-6 dated 2015-02-03
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor
Maintainer: Julian Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/wgaim8.R | 9 +++++----
inst/doc/wgaim.pdf |binary
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.60 dated 2015-01-28 and 3.0.62 dated 2015-02-03
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 6
MD5 | 79 +++++-----
NAMESPACE | 8 +
R/Methods-RFsp.R | 18 ++
R/RC_GLOBALS.R | 3
R/RFempvario-Methods-plots.R | 2
R/RFgui.R | 4
R/RMmodels-Methods-plots.R | 11 -
R/RMmodelsSpecial.R | 4
R/convert.R | 21 +-
R/getNset.R | 37 +++++
R/rf-plots.R | 6
man/CoordinateSystems.Rd | 50 +++++-
man/RFgridDataFrame-class.Rd | 6
man/RFpar.Rd |only
man/RFpointsDataFrame-class.Rd | 6
man/RFspatialGridDataFrame-class.Rd | 6
man/RFspatialPointsDataFrame-class.Rd | 6
man/RandomFields.Rd | 1
man/plot-method.Rd | 4
src/Coordinate_systems.cc | 67 ++-------
src/Coordinate_systems.h | 13 -
src/Huetchen.cc | 2
src/InternalCov.cc | 17 +-
src/KeyInfo.cc | 245 ++++++++++++++++------------------
src/Makevars.in | 2
src/Primitive.cc | 97 ++++++++-----
src/RF.h | 150 ++++++++++++--------
src/auxiliary.cc | 2
src/basic.h | 3
src/circulant.cc | 2
src/extremes.cc | 4
src/families.cc | 7
src/getNset.cc | 7
src/initNerror.cc | 16 +-
src/operator.cc | 2
src/plusmalS.cc | 193 +++++++++++++++++++-------
src/primitive.h | 10 -
src/rf_interfaces.cc | 22 +--
src/startGetNset.cc | 16 +-
src/variogramAndCo.cc | 16 +-
41 files changed, 690 insertions(+), 481 deletions(-)
Title: Analyzing RNA Sequence Count Tables Using Quasi-likelihood
Diff between QuasiSeq versions 1.0-5 dated 2015-01-05 and 1.0-6 dated 2015-02-03
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund
Maintainer: Steve Lund
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/QL.results.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Diff between peptider versions 0.1.6 dated 2014-12-03 and 0.1.7 dated 2015-02-03
Description: Functions for evaluating diversity in peptide libraries, including
NNN, NNB, NNK/S, and 20/20 schemes. This includes expected coverage,
relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare
DESCRIPTION | 10 +++----
MD5 | 56 ++++++++++++++++++++++----------------------
NAMESPACE | 2 -
R/peptider.r | 45 +++++++++++++++++++----------------
R/tabulate.r | 8 +++---
data/schemes.rda |binary
man/BLOSUM80.Rd | 3 +-
man/codons.Rd | 3 +-
man/coverage.Rd | 5 ++-
man/detect.Rd | 3 +-
man/diversity.Rd | 3 +-
man/efficiency.Rd | 5 ++-
man/encodingReduce.Rd | 3 +-
man/genNeighbors.Rd | 5 ++-
man/genNeighbors_reduced.Rd | 5 ++-
man/generateCustom.Rd | 5 ++-
man/generateCustomLib.Rd | 5 ++-
man/generateCustomNei.Rd | 5 ++-
man/generateCustomProbs.Rd | 5 ++-
man/getChoices.Rd | 3 +-
man/getCounts.Rd | 3 +-
man/getNeighbors.Rd | 3 +-
man/getNofNeighbors.Rd | 3 +-
man/libBuild.Rd | 3 +-
man/libscheme.Rd | 5 ++-
man/makowski.Rd | 5 ++-
man/ppeptide.Rd | 3 +-
man/scheme.Rd | 3 +-
man/schemes.Rd | 11 ++++----
29 files changed, 123 insertions(+), 95 deletions(-)
Title: Unified interface to Some Popular Parallelization Back-ends for
Interactive Usage and Package Development
Diff between parallelMap versions 1.1 dated 2014-07-03 and 1.2 dated 2015-02-03
Description: Map over lists in parallel. Supports local, multicore, mpi
and BatchJobs mode. Allows "tagging" of the parallel operation
with a level name that can be later selected by the user to
switch on parallel execution for exactly this operation.
Author: Bernd Bischl
Maintainer: Bernd Bischl
parallelMap-1.1/parallelMap/man/parallelShowRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/DESCRIPTION | 16 -
parallelMap-1.2/parallelMap/MD5 | 71 ++++---
parallelMap-1.2/parallelMap/NAMESPACE | 6
parallelMap-1.2/parallelMap/NEWS | 8
parallelMap-1.2/parallelMap/R/autodetectCpus.R | 20 +-
parallelMap-1.2/parallelMap/R/batchjobs.R | 36 ----
parallelMap-1.2/parallelMap/R/displayErrorMessages.R | 15 -
parallelMap-1.2/parallelMap/R/getExtraPackages.R | 15 -
parallelMap-1.2/parallelMap/R/getOption.R | 4
parallelMap-1.2/parallelMap/R/logging.R | 2
parallelMap-1.2/parallelMap/R/makeMulticoreCluster.R |only
parallelMap-1.2/parallelMap/R/mclapply_fixed.R | 70 ++++---
parallelMap-1.2/parallelMap/R/parallelApply.R | 6
parallelMap-1.2/parallelMap/R/parallelExport.R | 15 -
parallelMap-1.2/parallelMap/R/parallelLibrary.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelMap.R | 89 ++++------
parallelMap-1.2/parallelMap/R/parallelRegisterLevels.R | 62 +++++-
parallelMap-1.2/parallelMap/R/parallelSource.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelStart.R | 59 ++++--
parallelMap-1.2/parallelMap/R/parallelStop.R | 13 -
parallelMap-1.2/parallelMap/R/utils.R | 10 -
parallelMap-1.2/parallelMap/R/zzz.R | 5
parallelMap-1.2/parallelMap/man/parallelExport.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelGetRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/man/parallelLapply.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelLibrary.Rd | 5
parallelMap-1.2/parallelMap/man/parallelMap.Rd | 5
parallelMap-1.2/parallelMap/man/parallelRegisterLevels.Rd | 27 ++-
parallelMap-1.2/parallelMap/man/parallelShowOptions.Rd | 3
parallelMap-1.2/parallelMap/man/parallelSource.Rd | 5
parallelMap-1.2/parallelMap/man/parallelStart.Rd | 11 -
parallelMap-1.2/parallelMap/man/parallelStop.Rd | 3
parallelMap-1.2/parallelMap/tests/testthat/helpers.R | 4
parallelMap-1.2/parallelMap/tests/testthat/test_autodetectCpus.R |only
parallelMap-1.2/parallelMap/tests/testthat/test_batchjobs.R | 20 --
parallelMap-1.2/parallelMap/tests/testthat/test_multicore.R | 2
parallelMap-1.2/parallelMap/tests/testthat/test_registerLevels.R | 32 ++-
parallelMap-1.2/parallelMap/tests/testthat/test_stopWithJobErrorMessages.R |only
39 files changed, 403 insertions(+), 336 deletions(-)
Title: Matrix eQTL: Ultra fast eQTL analysis via large matrix
operations
Diff between MatrixEQTL versions 2.1.0 dated 2014-02-25 and 2.1.1 dated 2015-02-03
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.
Author: Andrey Shabalin
Maintainer: Andrey Shabalin
MatrixEQTL-2.1.0/MatrixEQTL/demo/a.nocvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/b.cvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/c.weights.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA5.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/e.interaction.R |only
MatrixEQTL-2.1.1/MatrixEQTL/DESCRIPTION | 9
MatrixEQTL-2.1.1/MatrixEQTL/MD5 | 38 ++-
MatrixEQTL-2.1.1/MatrixEQTL/R/Matrix_eQTL_engine.R | 170 +++++++----------
MatrixEQTL-2.1.1/MatrixEQTL/demo/00Index | 6
MatrixEQTL-2.1.1/MatrixEQTL/demo/a.nocvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/b.cvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/c.weights.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA5.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/e.interaction.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/p.hist.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/q.qqplot.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/sample.cis.r | 6
MatrixEQTL-2.1.1/MatrixEQTL/inst/CITATION | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL-package.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL_cis_code.Rd | 4
MatrixEQTL-2.1.1/MatrixEQTL/man/Matrix_eQTL_main.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/modelANOVA.Rd | 15 +
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR.Rd | 6
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR_CROSS.Rd | 5
MatrixEQTL-2.1.1/MatrixEQTL/man/plot.MatrixEQTL.Rd | 5
27 files changed, 131 insertions(+), 139 deletions(-)
Title: Functions to Create and Manipulate Discrete Random Variables
Diff between discreteRV versions 1.1.3 dated 2014-12-03 and 1.1.4 dated 2015-02-03
Description: discreteRV implements a set of functions that allow computations
involving discrete random variables. It uses a syntax which is familiar to
that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare
DESCRIPTION | 12 ++++----
MD5 | 60 +++++++++++++++++++++----------------------
NAMESPACE | 3 +-
R/discreteRV-Probabilities.r | 31 ++++++++++++----------
man/Conditional.Rd | 3 +-
man/E.Rd | 3 +-
man/KURT.Rd | 3 +-
man/P.Rd | 3 +-
man/Prop.Rd | 3 +-
man/SD.Rd | 3 +-
man/SKEW.Rd | 3 +-
man/SofI.Rd | 3 +-
man/SofIID.Rd | 3 +-
man/V.Rd | 3 +-
man/as.RV.Rd | 3 +-
man/grapes-AND-grapes.Rd | 3 +-
man/grapes-OR-grapes.Rd | 3 +-
man/grapes-in-grapes.Rd | 3 +-
man/make.RV.Rd | 17 +++++++-----
man/margins.Rd | 3 +-
man/mult.Rd | 3 +-
man/multN.Rd | 3 +-
man/outcomes.Rd | 3 +-
man/plot.RV.Rd | 3 +-
man/plot.RVsim.Rd | 3 +-
man/print.RV.Rd | 3 +-
man/probs.Rd | 3 +-
man/props.Rd | 3 +-
man/qqnorm.RV.Rd | 3 +-
man/rsim.Rd | 3 +-
man/skewSim.Rd | 3 +-
31 files changed, 117 insertions(+), 84 deletions(-)
Title: Cross-Entropy Clustering
Diff between CEC versions 0.9.2 dated 2014-11-15 and 0.9.3 dated 2015-02-03
Description: Cross-Entropy Clustering (CEC) divides the data into Gaussian type clusters. It performs the automatic reduction of unnecessary clusters, while at the same time allows the simultaneous use of various type Gaussian mixture models.
Author: Konrad Kamieniecki [aut, cre], Przemyslaw Spurek [ctb]
Maintainer: Konrad Kamieniecki
CEC-0.9.2/CEC/R/initcenters.R |only
CEC-0.9.2/CEC/README.md |only
CEC-0.9.2/CEC/man/initcenters.Rd |only
CEC-0.9.3/CEC/DESCRIPTION | 8
CEC-0.9.3/CEC/MD5 | 31
CEC-0.9.3/CEC/NAMESPACE | 2
CEC-0.9.3/CEC/R/cec.R | 82
CEC-0.9.3/CEC/R/cec.plot.cost.function.R |only
CEC-0.9.3/CEC/R/init.centers.R |only
CEC-0.9.3/CEC/R/model.covariance.R |only
CEC-0.9.3/CEC/data/fourGaussians.rda |only
CEC-0.9.3/CEC/data/mixShapes.rda |only
CEC-0.9.3/CEC/inst/cec_tests/cec1.dp | 2481 --
CEC-0.9.3/CEC/inst/cec_tests/clustering.test.R | 9
CEC-0.9.3/CEC/inst/cec_tests/energy.calculation.test.mouseset3d.R | 22
CEC-0.9.3/CEC/inst/cec_tests/mouse3d.data |11330 +++-------
CEC-0.9.3/CEC/man/cec.Rd | 38
CEC-0.9.3/CEC/man/fourGaussians.Rd |only
CEC-0.9.3/CEC/man/init.centers.Rd |only
CEC-0.9.3/CEC/man/mixShapes.Rd |only
CEC-0.9.3/CEC/src/Makevars | 2
CEC-0.9.3/CEC/src/cec.c | 13
22 files changed, 4765 insertions(+), 9253 deletions(-)
More information about poisDoubleSamp at CRAN
Permanent link
Title: Compute the Personalized Activity Index Based on a Negative
Binomial Model
Diff between lmeNB versions 1.2 dated 2014-01-24 and 1.3 dated 2015-02-02
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "Detection of unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Zhao, Y., Li, D.K.B., Petkau, A.J., Riddehough, A., Traboulsee, A., published in Journal of the American Statistical Association in 2013. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which can be modelled with a gamma or log-normal distributions. One can also choose the semi-parametric option which does not assume any distribution for the random effect. These mixed-effect models could be useful beyond the application of the safety monitoring. The maximum likelihood methods are used to estimate the unknown fixed effect parameters of the model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNBBayes, which contains the functions to compute the Personalized Activity Index in Bayesian framework.
Author: Yinshan Zhao and Yumi Kondo (with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the integration subroutines)
Maintainer: Yumi Kondo
lmeNB-1.2/lmeNB/man/mle_a3_fun.Rd |only
lmeNB-1.2/lmeNB/man/mle_ar1_fun.Rd |only
lmeNB-1.2/lmeNB/man/mle_ar1_non3.Rd |only
lmeNB-1.2/lmeNB/man/mle_fun.Rd |only
lmeNB-1.3/lmeNB/DESCRIPTION | 29
lmeNB-1.3/lmeNB/MD5 | 36 -
lmeNB-1.3/lmeNB/NAMESPACE | 13
lmeNB-1.3/lmeNB/R/AR1models.R | 1016 ++++------------------------
lmeNB-1.3/lmeNB/R/CPI.R | 794 ++++++++--------------
lmeNB-1.3/lmeNB/R/INDmodels.R | 1269 +++++++++++++++++++++++-------------
lmeNB-1.3/lmeNB/R/Simulation.R | 20
lmeNB-1.3/lmeNB/R/oldCode.R |only
lmeNB-1.3/lmeNB/man/CP_se.Rd | 101 +-
lmeNB-1.3/lmeNB/man/RElmeNB.Rd |only
lmeNB-1.3/lmeNB/man/fitParaAR1.Rd |only
lmeNB-1.3/lmeNB/man/fitParaIND.Rd |only
lmeNB-1.3/lmeNB/man/fitSemiAR1.Rd |only
lmeNB-1.3/lmeNB/man/fitSemiIND.Rd |only
lmeNB-1.3/lmeNB/man/index_batch.Rd | 163 +++-
lmeNB-1.3/lmeNB/man/jCP_ar1.Rd | 111 +--
lmeNB-1.3/lmeNB/man/lmeNB.Rd | 474 +++++++++----
lmeNB-1.3/lmeNB/man/rNBME_R.Rd | 107 ---
lmeNB-1.3/lmeNB/src |only
23 files changed, 1882 insertions(+), 2251 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Diff between excursions versions 1.1-20140610 dated 2014-06-11 and 2.0.6 dated 2015-02-02
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin
Maintainer: David Bolin
excursions-1.1-20140610/excursions/R/excursions.int.R |only
excursions-1.1-20140610/excursions/R/excursions.simconf.R |only
excursions-1.1-20140610/excursions/inst/doc/copying/AMD.txt |only
excursions-1.1-20140610/excursions/inst/doc/copying/CHOLMOD.txt |only
excursions-1.1-20140610/excursions/inst/doc/copying/COLAMD.txt |only
excursions-1.1-20140610/excursions/man/excursions.int.Rd |only
excursions-1.1-20140610/excursions/man/excursions.simconf.Rd |only
excursions-1.1-20140610/excursions/src/AMD |only
excursions-1.1-20140610/excursions/src/CHOLMOD |only
excursions-1.1-20140610/excursions/src/COLAMD |only
excursions-1.1-20140610/excursions/src/Makefile |only
excursions-1.1-20140610/excursions/src/Makefile.win |only
excursions-1.1-20140610/excursions/src/excursions.cpp |only
excursions-1.1-20140610/excursions/src/gaussint.cpp |only
excursions-1.1-20140610/excursions/src/install.libs.R |only
excursions-1.1-20140610/excursions/src/utils.cpp |only
excursions-1.1-20140610/excursions/src/utils.h |only
excursions-1.1-20140610/excursions/src/xerbla.c |only
excursions-2.0.6/excursions/DESCRIPTION | 30
excursions-2.0.6/excursions/MD5 | 194 ----
excursions-2.0.6/excursions/NAMESPACE | 22
excursions-2.0.6/excursions/R/contourmap.R |only
excursions-2.0.6/excursions/R/contourmap.inla.R |only
excursions-2.0.6/excursions/R/contourutil.R |only
excursions-2.0.6/excursions/R/excursions.R | 406 +++-----
excursions-2.0.6/excursions/R/excursions.inla.R | 446 +++++----
excursions-2.0.6/excursions/R/gaussint.R |only
excursions-2.0.6/excursions/R/geometry.R |only
excursions-2.0.6/excursions/R/inlautils.R |only
excursions-2.0.6/excursions/R/simconf.R |only
excursions-2.0.6/excursions/R/simconf.inla.R |only
excursions-2.0.6/excursions/R/simconf.mixture.R |only
excursions-2.0.6/excursions/R/utils.R | 374 ++++++-
excursions-2.0.6/excursions/README.md |only
excursions-2.0.6/excursions/inst/CITATION |only
excursions-2.0.6/excursions/inst/COPYRIGHTS | 18
excursions-2.0.6/excursions/man/continuous.Rd |only
excursions-2.0.6/excursions/man/contourmap.Rd |only
excursions-2.0.6/excursions/man/contourmap.colors.Rd |only
excursions-2.0.6/excursions/man/contourmap.inla.Rd |only
excursions-2.0.6/excursions/man/excursions.Rd | 72 -
excursions-2.0.6/excursions/man/excursions.inla.Rd | 105 +-
excursions-2.0.6/excursions/man/excursions.variances.Rd |only
excursions-2.0.6/excursions/man/gaussint.Rd |only
excursions-2.0.6/excursions/man/simconf.Rd |only
excursions-2.0.6/excursions/man/simconf.inla.Rd |only
excursions-2.0.6/excursions/man/simconf.mixture.Rd |only
excursions-2.0.6/excursions/man/tricontour.Rd |only
excursions-2.0.6/excursions/man/tricontourmap.Rd |only
excursions-2.0.6/excursions/src/Makevars |only
excursions-2.0.6/excursions/src/RngStream.c | 120 +-
excursions-2.0.6/excursions/src/RngStream.h | 6
excursions-2.0.6/excursions/src/integration.cpp | 481 +++++-----
excursions-2.0.6/excursions/src/qinv.cpp |only
excursions-2.0.6/excursions/src/reordering.cpp |only
excursions-2.0.6/excursions/tests |only
56 files changed, 1264 insertions(+), 1010 deletions(-)
Title: Sample Size Estimation Functions for Cluster Randomized Trials
Diff between CRTSize versions 0.3 dated 2013-12-18 and 0.4 dated 2015-02-02
Description: This package contains basic tools for the purpose of sample size estimation in cluster (group) randomized trials. The package contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
Author: Michael A Rotondi
Maintainer: Michael A Rotondi
DESCRIPTION | 8
MD5 | 12
NAMESPACE | 22 +
R/n4incidence.R | 6
R/n4means.R | 4
R/n4meansMeta.R | 754 ++++++++++++++++++++++++++++----------------------------
R/n4props.R | 4
7 files changed, 415 insertions(+), 395 deletions(-)
Title: Simulation of Event Histories for Multi-state Models
Diff between simMSM versions 1.1.2 dated 2015-01-12 and 1.1.4 dated 2015-02-02
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
simMSM-1.1.2/simMSM/man/allcausehr.Rd |only
simMSM-1.1.2/simMSM/man/cumallcausehr.Rd |only
simMSM-1.1.2/simMSM/man/hr.Rd |only
simMSM-1.1.2/simMSM/man/meancentering.Rd |only
simMSM-1.1.2/simMSM/man/simCR.Rd |only
simMSM-1.1.2/simMSM/man/simEBMT.Rd |only
simMSM-1.1.2/simMSM/man/simMSM-package.Rd |only
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simMSM-1.1.2/simMSM/man/simexitinner.Rd |only
simMSM-1.1.2/simMSM/man/simsinglehistory.Rd |only
simMSM-1.1.2/simMSM/man/simto.Rd |only
simMSM-1.1.2/simMSM/man/unirootf.Rd |only
simMSM-1.1.4/simMSM/DESCRIPTION | 11 +-
simMSM-1.1.4/simMSM/MD5 | 51 ++++-----
simMSM-1.1.4/simMSM/NAMESPACE | 10 +
simMSM-1.1.4/simMSM/R/TraFromMpl.R |only
simMSM-1.1.4/simMSM/R/allcausehr.R | 5
simMSM-1.1.4/simMSM/R/cumallcausehr.R | 4
simMSM-1.1.4/simMSM/R/mplskeleton.R |only
simMSM-1.1.4/simMSM/R/plotbe.R |only
simMSM-1.1.4/simMSM/R/plotcph.R |only
simMSM-1.1.4/simMSM/R/plotnae.R |only
simMSM-1.1.4/simMSM/R/pmeskeleton.R |only
simMSM-1.1.4/simMSM/R/simCR.R | 4
simMSM-1.1.4/simMSM/R/simEBMT.R | 3
simMSM-1.1.4/simMSM/R/simeventhistories.R | 123 ++++++++++++++++++++---
simMSM-1.1.4/simMSM/R/simexit.R | 21 +--
simMSM-1.1.4/simMSM/R/simexitinner.R | 19 ---
simMSM-1.1.4/simMSM/R/simsinglehistory.R | 58 +++++++++-
simMSM-1.1.4/simMSM/R/simto.R | 10 -
simMSM-1.1.4/simMSM/R/tolongformat.R |only
simMSM-1.1.4/simMSM/R/unirootf.R | 4
simMSM-1.1.4/simMSM/man/mplskeleton.Rd |only
simMSM-1.1.4/simMSM/man/plotbe.Rd |only
simMSM-1.1.4/simMSM/man/plotcph.Rd |only
simMSM-1.1.4/simMSM/man/plotnae.Rd |only
simMSM-1.1.4/simMSM/man/pmeskeleton.Rd |only
simMSM-1.1.4/simMSM/man/simeventhistories.Rd | 144 ++++++++++++++++++---------
simMSM-1.1.4/simMSM/man/tolongformat.Rd |only
39 files changed, 323 insertions(+), 144 deletions(-)
Title: Data Structures and Algorithms for Relations
Diff between relations versions 0.6-3 dated 2014-04-02 and 0.6-4 dated 2015-02-02
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 ++--
MD5 | 28 ++++++++++-----------
build/vignette.rds |binary
data/Cetacea.rda |binary
data/Felines.rda |binary
data/SVM_Benchmarking_Classification.rda |binary
data/SVM_Benchmarking_Classification_Consensus.rda |binary
data/SVM_Benchmarking_Regression.rda |binary
data/SVM_Benchmarking_Regression_Consensus.rda |binary
inst/doc/relations.R | 1
inst/doc/relations.Rnw | 2 -
inst/doc/relations.pdf |binary
man/Felines.Rd | 2 -
man/algebra.Rd | 2 -
vignettes/relations.Rnw | 2 -
15 files changed, 22 insertions(+), 21 deletions(-)
Title: Cluster ensembles
Diff between clue versions 0.3-48 dated 2014-04-02 and 0.3-49 dated 2015-02-02
Description: CLUster Ensembles
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 32 ++++++++++++++++----------------
build/vignette.rds |binary
data/CKME.rda |binary
data/Cassini.rda |binary
data/GVME.rda |binary
data/GVME_Consensus.rda |binary
data/Kinship82.rda |binary
data/Kinship82_Consensus.rda |binary
data/Phonemes.rda |binary
inst/doc/clue.R | 1 +
inst/doc/clue.Rnw | 4 ++--
inst/doc/clue.pdf |binary
man/cl_bag.Rd | 2 +-
man/cl_dissimilarity.Rd | 7 +++----
vignettes/clue.Rnw | 4 ++--
vignettes/cluster.bib | 14 +++++++++++++-
17 files changed, 41 insertions(+), 29 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Diff between twang versions 1.4-0 dated 2014-03-18 and 1.4-9.3 dated 2015-02-02
Description: This package offers functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights. This package was originally developed by Drs.
Ridgeway, McCaffrey, and Morral. Burgette, Griffin and
McCaffrey updated the package during 2011-2015.
Author: Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann, Lane Burgette
Maintainer: Lane Burgette
twang-1.4-0/twang/R/ksStatTrueMN.R |only
twang-1.4-0/twang/R/plot.mnps.old.R |only
twang-1.4-9.3/twang/DESCRIPTION | 16
twang-1.4-9.3/twang/MD5 | 73
twang-1.4-9.3/twang/NAMESPACE | 2
twang-1.4-9.3/twang/R/bal.stat.R | 6
twang-1.4-9.3/twang/R/bal.table.R | 102
twang-1.4-9.3/twang/R/boxplot.mnps.R | 41
twang-1.4-9.3/twang/R/desc.wts.R | 4
twang-1.4-9.3/twang/R/diag.plot.color.R | 2
twang-1.4-9.3/twang/R/displayPlots.R |only
twang-1.4-9.3/twang/R/makeWeightsMNPS.R | 2
twang-1.4-9.3/twang/R/mnps2.R | 19
twang-1.4-9.3/twang/R/pairwiseComparison.R | 6
twang-1.4-9.3/twang/R/plot.mnps.2.R |only
twang-1.4-9.3/twang/R/plot.mnps.R | 384 ++-
twang-1.4-9.3/twang/R/plotTruePairs.R |only
twang-1.4-9.3/twang/R/print.summary.mnps.R | 28
twang-1.4-9.3/twang/R/ps.summary.new2.R | 6
twang-1.4-9.3/twang/R/summary.mnps.R | 54
twang-1.4-9.3/twang/R/summary.ps.R | 31
twang-1.4-9.3/twang/build/vignette.rds |binary
twang-1.4-9.3/twang/data/AOD.RData |binary
twang-1.4-9.3/twang/data/egsingle.RData |binary
twang-1.4-9.3/twang/data/lalonde.RData |binary
twang-1.4-9.3/twang/data/lindner.RData |binary
twang-1.4-9.3/twang/data/raceprofiling.RData |binary
twang-1.4-9.3/twang/inst/doc/mnps.R | 157 -
twang-1.4-9.3/twang/inst/doc/mnps.pdf |binary
twang-1.4-9.3/twang/inst/doc/mnps.rnw | 434 ++-
twang-1.4-9.3/twang/inst/doc/twang.R | 189 -
twang-1.4-9.3/twang/inst/doc/twang.pdf |binary
twang-1.4-9.3/twang/inst/doc/twang.rnw | 3418 +++++++++++++--------------
twang-1.4-9.3/twang/man/bal.stat.Rd | 5
twang-1.4-9.3/twang/man/bal.table.Rd | 14
twang-1.4-9.3/twang/man/boxplot.mnps.Rd | 7
twang-1.4-9.3/twang/man/desc.wts.Rd | 7
twang-1.4-9.3/twang/man/plot.mnps.Rd | 25
twang-1.4-9.3/twang/vignettes/mnps.rnw | 434 ++-
twang-1.4-9.3/twang/vignettes/twang.rnw | 3418 +++++++++++++--------------
40 files changed, 4874 insertions(+), 4010 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.6.5 dated 2014-12-15 and 1.6.8 dated 2015-02-02
Description: Collection of several plotting and table output functions for
visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
sjPlot-1.6.5/sjPlot/man/sjp.glm.ma.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.lm.ma.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.lm1.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.reglin.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.vif.Rd |only
sjPlot-1.6.8/sjPlot/DESCRIPTION | 10
sjPlot-1.6.8/sjPlot/MD5 | 189 -
sjPlot-1.6.8/sjPlot/NAMESPACE | 189 -
sjPlot-1.6.8/sjPlot/NEWS | 24
sjPlot-1.6.8/sjPlot/R/helpfunctions.R | 957 ++++----
sjPlot-1.6.8/sjPlot/R/sjImportSPSS.R | 802 +++----
sjPlot-1.6.8/sjPlot/R/sjPlotAncovaLSMeans.R | 714 +++---
sjPlot-1.6.8/sjPlot/R/sjPlotCorr.R | 697 +++---
sjPlot-1.6.8/sjPlot/R/sjPlotGLME.R | 292 ++
sjPlot-1.6.8/sjPlot/R/sjPlotGroupFrequencies.R | 2487 +++++++++++------------
sjPlot-1.6.8/sjPlot/R/sjPlotInteractions.R | 6
sjPlot-1.6.8/sjPlot/R/sjPlotLikert.R | 4
sjPlot-1.6.8/sjPlot/R/sjPlotLinreg.R | 535 ++--
sjPlot-1.6.8/sjPlot/R/sjPlotLinregMultiple.R | 831 +++----
sjPlot-1.6.8/sjPlot/R/sjPlotOdds.R | 1570 +++++++-------
sjPlot-1.6.8/sjPlot/R/sjPlotOddsMultiple.R | 1
sjPlot-1.6.8/sjPlot/R/sjPlotScatter.R | 2
sjPlot-1.6.8/sjPlot/R/sjPlotSetTheme.R | 7
sjPlot-1.6.8/sjPlot/R/sjRecode.R | 21
sjPlot-1.6.8/sjPlot/R/sjStatistics.R | 70
sjPlot-1.6.8/sjPlot/R/sjTabCorr.R | 5
sjPlot-1.6.8/sjPlot/R/sjTabFrequencies.R | 1287 ++++++-----
sjPlot-1.6.8/sjPlot/R/sjTabGrpmean.R | 6
sjPlot-1.6.8/sjPlot/R/sjTabLinReg.R | 75
sjPlot-1.6.8/sjPlot/R/sjTabOdds.R | 20
sjPlot-1.6.8/sjPlot/R/sjTabPropTable.R | 1642 +++++++--------
sjPlot-1.6.8/sjPlot/README.md | 39
sjPlot-1.6.8/sjPlot/man/efc.Rd | 92
sjPlot-1.6.8/sjPlot/man/sj.setGeomColors.Rd | 52
sjPlot-1.6.8/sjPlot/man/sjPlot-package.Rd | 4
sjPlot-1.6.8/sjPlot/man/sjc.cluster.Rd | 180 -
sjPlot-1.6.8/sjPlot/man/sjc.dend.Rd | 104
sjPlot-1.6.8/sjPlot/man/sjc.elbow.Rd | 76
sjPlot-1.6.8/sjPlot/man/sjc.grpdisc.Rd | 110 -
sjPlot-1.6.8/sjPlot/man/sjc.kgap.Rd | 134 -
sjPlot-1.6.8/sjPlot/man/sjc.qclus.Rd | 386 +--
sjPlot-1.6.8/sjPlot/man/sji.SPSS.Rd | 102
sjPlot-1.6.8/sjPlot/man/sji.convertToLabel.Rd | 80
sjPlot-1.6.8/sjPlot/man/sji.convertToValue.Rd | 78
sjPlot-1.6.8/sjPlot/man/sji.getValueLabels.Rd | 94
sjPlot-1.6.8/sjPlot/man/sji.getVariableLabels.Rd | 92
sjPlot-1.6.8/sjPlot/man/sji.setValueLabels.Rd | 96
sjPlot-1.6.8/sjPlot/man/sji.setVariableLabels.Rd | 124 -
sjPlot-1.6.8/sjPlot/man/sji.viewSPSS.Rd | 248 +-
sjPlot-1.6.8/sjPlot/man/sjp.chi2.Rd | 122 -
sjPlot-1.6.8/sjPlot/man/sjp.corr.Rd | 248 +-
sjPlot-1.6.8/sjPlot/man/sjp.emm.int.Rd | 270 +-
sjPlot-1.6.8/sjPlot/man/sjp.glm.Rd | 384 +--
sjPlot-1.6.8/sjPlot/man/sjp.glmer.Rd | 410 +--
sjPlot-1.6.8/sjPlot/man/sjp.glmm.Rd | 325 +--
sjPlot-1.6.8/sjPlot/man/sjp.int.Rd | 450 ++--
sjPlot-1.6.8/sjPlot/man/sjp.likert.Rd | 442 ++--
sjPlot-1.6.8/sjPlot/man/sjp.lm.Rd | 370 ++-
sjPlot-1.6.8/sjPlot/man/sjp.lmer.Rd | 369 +--
sjPlot-1.6.8/sjPlot/man/sjp.lmm.Rd | 311 +-
sjPlot-1.6.8/sjPlot/man/sjp.pca.Rd | 288 +-
sjPlot-1.6.8/sjPlot/man/sjp.scatter.Rd | 2
sjPlot-1.6.8/sjPlot/man/sjp.stackfrq.Rd | 360 +--
sjPlot-1.6.8/sjPlot/man/sjs.aov1.levene.Rd | 56
sjPlot-1.6.8/sjPlot/man/sjs.chi2.gof.Rd | 78
sjPlot-1.6.8/sjPlot/man/sjs.cramer.Rd | 54
sjPlot-1.6.8/sjPlot/man/sjs.cronbach.Rd | 60
sjPlot-1.6.8/sjPlot/man/sjs.etasq.Rd | 100
sjPlot-1.6.8/sjPlot/man/sjs.mic.Rd | 98
sjPlot-1.6.8/sjPlot/man/sjs.mwu.Rd | 114 -
sjPlot-1.6.8/sjPlot/man/sjs.phi.Rd | 54
sjPlot-1.6.8/sjPlot/man/sjs.reliability.Rd | 178 -
sjPlot-1.6.8/sjPlot/man/sjs.se.Rd | 42
sjPlot-1.6.8/sjPlot/man/sjs.stdb.Rd | 88
sjPlot-1.6.8/sjPlot/man/sjs.table.values.Rd | 80
sjPlot-1.6.8/sjPlot/man/sjt.corr.Rd | 358 +--
sjPlot-1.6.8/sjPlot/man/sjt.df.Rd | 290 +-
sjPlot-1.6.8/sjPlot/man/sjt.frq.Rd | 440 ++--
sjPlot-1.6.8/sjPlot/man/sjt.glm.Rd | 508 ++--
sjPlot-1.6.8/sjPlot/man/sjt.grpmean.Rd | 155 -
sjPlot-1.6.8/sjPlot/man/sjt.itemanalysis.Rd | 392 +--
sjPlot-1.6.8/sjPlot/man/sjt.lm.Rd | 552 ++---
sjPlot-1.6.8/sjPlot/man/sjt.pca.Rd | 354 +--
sjPlot-1.6.8/sjPlot/man/sjt.stackfrq.Rd | 386 +--
sjPlot-1.6.8/sjPlot/man/sjt.xtab.Rd | 446 ++--
sjPlot-1.6.8/sjPlot/man/sju.adjustPlotRange.y.Rd | 90
sjPlot-1.6.8/sjPlot/man/sju.dicho.Rd | 78
sjPlot-1.6.8/sjPlot/man/sju.groupString.Rd | 98
sjPlot-1.6.8/sjPlot/man/sju.groupVar.Rd | 132 -
sjPlot-1.6.8/sjPlot/man/sju.groupVarLabels.Rd | 150 -
sjPlot-1.6.8/sjPlot/man/sju.mean.n.Rd | 80
sjPlot-1.6.8/sjPlot/man/sju.recode.Rd | 48
sjPlot-1.6.8/sjPlot/man/sju.recodeTo.Rd | 96
sjPlot-1.6.8/sjPlot/man/sju.setNA.Rd | 62
sjPlot-1.6.8/sjPlot/man/sju.strpos.Rd | 138 -
sjPlot-1.6.8/sjPlot/man/sju.weight.Rd | 78
sjPlot-1.6.8/sjPlot/man/sju.weight2.Rd | 90
sjPlot-1.6.8/sjPlot/man/sju.wordwrap.Rd | 56
98 files changed, 12740 insertions(+), 12224 deletions(-)
Title: Improved Access for Blind Users
Diff between BrailleR versions 0.11 dated 2014-09-27 and 0.16.1 dated 2015-02-02
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], Paul Murrell [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey
DESCRIPTION | 12 -
MD5 | 58 +++++----
NAMESPACE | 9 +
R/DataViewer.R |only
R/MaskedFunctions.R | 9 -
R/OneFactor.R |only
R/Options.R |only
R/UniDesc.R | 125 ++++++++++++-------
R/VIMethod.R | 146 ++++++++++++++++++-----
R/WhereXY.R | 28 ++--
R/zzz.R |only
build/vignette.rds |binary
inst/CITATION | 4
inst/Sound |only
inst/doc/BrailleRManual.html | 44 ++++--
inst/doc/Ex1histograms.html | 110 ++++++++---------
inst/doc/Ex2BasicNumerical.html | 59 +++++----
inst/doc/Ex3UnivariateDescription.R | 4
inst/doc/Ex3UnivariateDescription.html | 24 ++-
inst/doc/Ex3UnivariateDescription.rmd | 10 -
inst/doc/Ex4SingleResponseOneGroupingFactor.R |only
inst/doc/Ex4SingleResponseOneGroupingFactor.html |only
inst/doc/Ex4SingleResponseOneGroupingFactor.rmd |only
man/BrailleR-package.Rd | 10 -
man/DataViewer.Rd |only
man/OneFactor.Rd |only
man/Options.Rd |only
man/R2txtJG.Rd | 12 -
man/UniDesc.Rd | 22 +--
man/VI.Rd | 23 ++-
man/WhereXY.Rd | 12 +
man/boxplot.Rd | 17 +-
man/hist.Rd | 15 +-
man/unfinished.Rd | 3
vignettes/Ex3UnivariateDescription.rmd | 10 -
vignettes/Ex4SingleResponseOneGroupingFactor.rmd |only
36 files changed, 480 insertions(+), 286 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-22 1.1
2014-08-09 1.0
Title: n-gram Text Regression, aka Concise Comparative Summarization
Diff between textreg versions 0.1 dated 2014-12-04 and 0.1.1 dated 2015-02-02
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/textreg.cpp | 15 +++++++++------
3 files changed, 14 insertions(+), 11 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Diff between strum versions 0.5 dated 2014-12-10 and 0.5.1 dated 2015-02-02
Description: This package implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/computeLLDeriv.cpp | 4 ++--
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Royston's H Test: Multivariate Normality Test
Diff between royston versions 1.1 dated 2015-01-16 and 1.2 dated 2015-02-02
Description: Performs a multivariate normality test based on Royston's H test
Author: Selcuk Korkmaz
Maintainer: Selcuk Korkmaz
royston-1.1/royston/data |only
royston-1.1/royston/man/a.Rd |only
royston-1.2/royston/DESCRIPTION | 11 ++++++-----
royston-1.2/royston/MD5 | 10 +++++-----
royston-1.2/royston/R/royston.test.R | 1 -
royston-1.2/royston/R/welcome.R |only
royston-1.2/royston/inst |only
royston-1.2/royston/man/royston-package.Rd | 2 --
8 files changed, 11 insertions(+), 13 deletions(-)
Title: A Google Analytics API client for R
Diff between RGA versions 0.1.4 dated 2014-12-19 and 0.2 dated 2015-02-02
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov
RGA-0.1.4/RGA/R/data.R |only
RGA-0.1.4/RGA/R/get-mgmt.R |only
RGA-0.1.4/RGA/R/get-pages.R |only
RGA-0.1.4/RGA/R/list-mgmt.R |only
RGA-0.1.4/RGA/R/onload.R |only
RGA-0.1.4/RGA/R/sysdata.rda |only
RGA-0.1.4/RGA/man/dims_mets.Rd |only
RGA-0.1.4/RGA/man/get_firstdate.Rd |only
RGA-0.2/RGA/DESCRIPTION | 24 +-
RGA-0.2/RGA/MD5 | 115 ++++++++----
RGA-0.2/RGA/NAMESPACE | 29 ++-
RGA-0.2/RGA/R/accounts.R |only
RGA-0.2/RGA/R/auth.R | 30 +--
RGA-0.2/RGA/R/convert.R | 110 ++++++------
RGA-0.2/RGA/R/custom.R |only
RGA-0.2/RGA/R/experiments.R |only
RGA-0.2/RGA/R/filters.R |only
RGA-0.2/RGA/R/first-date.R |only
RGA-0.2/RGA/R/ga.R |only
RGA-0.2/RGA/R/get-data.R | 23 ++
RGA-0.2/RGA/R/goals.R |only
RGA-0.2/RGA/R/mcf.R |only
RGA-0.2/RGA/R/metadata.R |only
RGA-0.2/RGA/R/mgmt.R |only
RGA-0.2/RGA/R/package.R | 33 ++-
RGA-0.2/RGA/R/profiles.R |only
RGA-0.2/RGA/R/query.R | 31 +--
RGA-0.2/RGA/R/report.R | 231 ++-----------------------
RGA-0.2/RGA/R/request.R | 93 +++-------
RGA-0.2/RGA/R/rt.R |only
RGA-0.2/RGA/R/segments.R |only
RGA-0.2/RGA/R/shiny.R | 41 ++--
RGA-0.2/RGA/R/unsampled.R |only
RGA-0.2/RGA/R/url.R | 72 ++------
RGA-0.2/RGA/R/utils.R | 61 +++++-
RGA-0.2/RGA/R/webproperties.R |only
RGA-0.2/RGA/R/zzz.R | 4
RGA-0.2/RGA/README.md | 268 +-----------------------------
RGA-0.2/RGA/build |only
RGA-0.2/RGA/data |only
RGA-0.2/RGA/inst |only
RGA-0.2/RGA/man/RGA.Rd | 37 +++-
RGA-0.2/RGA/man/authorize.Rd | 20 +-
RGA-0.2/RGA/man/dimsmets.Rd |only
RGA-0.2/RGA/man/firstdate.Rd |only
RGA-0.2/RGA/man/ga.Rd | 40 ++--
RGA-0.2/RGA/man/get_experiment.Rd |only
RGA-0.2/RGA/man/get_filter.Rd |only
RGA-0.2/RGA/man/get_ga.Rd | 22 +-
RGA-0.2/RGA/man/get_goal.Rd | 40 ++--
RGA-0.2/RGA/man/get_mcf.Rd | 19 +-
RGA-0.2/RGA/man/get_profile.Rd | 46 ++---
RGA-0.2/RGA/man/get_rt.Rd | 18 --
RGA-0.2/RGA/man/get_unsampled_report.Rd |only
RGA-0.2/RGA/man/get_webproperty.Rd | 44 ++--
RGA-0.2/RGA/man/list_accounts.Rd | 30 +--
RGA-0.2/RGA/man/list_custom_sources.Rd |only
RGA-0.2/RGA/man/list_experiments.Rd |only
RGA-0.2/RGA/man/list_filters.Rd |only
RGA-0.2/RGA/man/list_goals.Rd | 45 +----
RGA-0.2/RGA/man/list_metadata.Rd |only
RGA-0.2/RGA/man/list_profiles.Rd | 42 +---
RGA-0.2/RGA/man/list_segments.Rd | 31 +--
RGA-0.2/RGA/man/list_unsampled_reports.Rd |only
RGA-0.2/RGA/man/list_webproperties.Rd | 39 ++--
RGA-0.2/RGA/tests |only
RGA-0.2/RGA/vignettes |only
67 files changed, 640 insertions(+), 998 deletions(-)
Title: Metropolis Sampler and Supporting Functions for Estimating
Animal Movement from Archival Tags and Satellite Fixes
Diff between tripEstimation versions 0.0-41 dated 2013-07-10 and 0.0-42 dated 2015-02-02
More information about tripEstimation at CRAN
Description: Data handling and estimation functions for animal movement
estimation from archival or satellite tags. Helper functions are included
for making image summaries binned by time interval from MCMC simulations of
point data.
Author: Michael D. Sumner [aut, cre],
Simon Wotherspoon [ctb]
Maintainer: Michael D. Sumner
DESCRIPTION | 17 ++++++++++-------
MD5 | 10 +++++-----
NEWS | 4 ++++
README.md | 5 +----
TODO | 9 +++++++--
inst/CITATION | 16 +++++++++++-----
6 files changed, 38 insertions(+), 23 deletions(-)
Permanent link
Title: Linkage Map Construction using the MSTmap Algorithm
Diff between ASMap versions 0.3-2 dated 2014-10-13 and 0.3-3 dated 2015-02-02
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor
Maintainer: Julian Taylor
DESCRIPTION | 10 ++--
MD5 | 10 ++--
R/mstmap9.R | 106 +++++++++++++++++++++++++++++++++++++++++++----
man/ASMap-package.Rd | 2
man/mstmap.cross.Rd | 2
man/mstmap.data.frame.Rd | 4 -
6 files changed, 111 insertions(+), 23 deletions(-)
Title: The Analysis of Biological Data
Diff between abd versions 0.2-6 dated 2014-03-31 and 0.2-7 dated 2015-02-02
Description: The abd package contains data sets and sample code for The
Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009;
Roberts & Company Publishers).
Author: Kevin M. Middleton
Maintainer: Kevin M. Middleton
DESCRIPTION | 13 -
MD5 | 310 +++++++++++++++++++++----------------------
NAMESPACE | 3
R/abdData.R | 63 ++++----
R/datasets.R | 261 ++++++------------------------------
R/histochart.R | 7
R/themes.R | 2
man/AlgaeCO2.Rd | 18 +-
man/Antilles.Rd | 15 +-
man/Aspirin.Rd | 16 +-
man/BeeGenes.Rd | 16 +-
man/BeeLifespans.Rd | 10 -
man/Beetles.Rd | 14 -
man/BirdSexRatio.Rd | 10 -
man/Blackbirds.Rd | 16 +-
man/BodyFatHeatLoss.Rd | 13 -
man/BrainExpression.Rd | 17 +-
man/BrookTrout.Rd | 26 +--
man/Cavalry.Rd | 19 +-
man/Chickadees.Rd | 17 +-
man/ChimpBrains.Rd | 9 -
man/Cichlids.Rd | 19 +-
man/CichlidsGnRH.Rd | 17 +-
man/Clearcuts.Rd | 16 +-
man/CocaineDopamine.Rd | 20 +-
man/Convictions.Rd | 15 --
man/ConvictionsAndIncome.Rd | 15 +-
man/Crickets.Rd | 13 -
man/DEET.Rd | 15 --
man/DaphniaLongevity.Rd | 14 -
man/DaphniaResistance.Rd | 17 +-
man/DayOfBirth.Rd | 15 +-
man/DesertBirds.Rd | 16 +-
man/Dioecy.Rd | 11 -
man/Dolphins.Rd | 17 +-
man/DungBeetles.Rd | 18 +-
man/Earthworms.Rd | 16 +-
man/Earwigs.Rd | 19 +-
man/Eelgrass.Rd | 20 +-
man/ElVerde.Rd | 13 -
man/ElectricFish.Rd | 16 +-
man/EndangeredSpecies.Rd | 13 -
man/FingerRatio.Rd | 17 +-
man/Fireflies.Rd | 18 +-
man/FireflyFlash.Rd | 14 -
man/FlyTestes.Rd | 17 +-
man/FlycatcherPatch.Rd | 14 -
man/GeneRegulation.Rd | 14 -
man/GlidingSnakes.Rd | 16 +-
man/GodwitArrival.Rd | 15 +-
man/Grassland.Rd | 16 +-
man/GreatTitMalaria.Rd | 14 -
man/Greenspace.Rd | 15 --
man/Guppies.Rd | 18 +-
man/Hemoglobin.Rd | 18 +-
man/HippocampusLesions.Rd | 14 -
man/HornedLizards.Rd | 16 +-
man/HumanBodyTemp.Rd | 21 +-
man/HumanGeneLengths.Rd | 65 ++-------
man/Hurricanes.Rd | 18 +-
man/Iguanas.Rd | 16 +-
man/IntertidalAlgae.Rd | 14 -
man/JetLagKnees.Rd | 14 +
man/KenyaFinches.Rd | 17 +-
man/LanguageBrains.Rd | 16 +-
man/LarvalFish.Rd | 15 --
man/Lefthanded.Rd | 15 +-
man/LionCubs.Rd | 13 -
man/LionNoses.Rd | 14 -
man/LiverPreparation.Rd | 18 +-
man/LizardBite.Rd | 29 +---
man/LizardSprint.Rd | 24 +--
man/Lobsters.Rd | 16 +-
man/LodgepolePines.Rd | 21 +-
man/LupusMice.Rd | 14 -
man/Lynx.Rd | 12 -
man/MarineReserve.Rd | 15 --
man/MassExtinctions.Rd | 12 -
man/MoleRats.Rd | 20 +-
man/Mosquitoes.Rd | 17 +-
man/MouseEmpathy.Rd | 16 +-
man/NeanderthalBrains.Rd | 12 -
man/NematodeLifespan.Rd | 19 +-
man/NeotropicalTrees.Rd | 21 +-
man/Newts.Rd | 19 +-
man/NoSmokingDay.Rd | 17 +-
man/NorthSeaCod.Rd | 18 +-
man/OstrichTemp.Rd | 23 +--
man/Penguins.Rd | 16 +-
man/PlantPersistence.Rd | 14 -
man/Pollen.Rd | 14 -
man/Powerball.Rd | 12 -
man/PrimateMetabolism.Rd | 12 -
man/PrimateWBC.Rd | 11 -
man/ProgesteroneExercise.Rd | 18 +-
man/Pseudoscorpions.Rd | 20 +-
man/Pufferfish.Rd | 22 +--
man/Rattlesnakes.Rd | 16 +-
man/Rigormortis.Rd | 13 -
man/RopeTrick.Rd | 16 +-
man/SagebrushCrickets.Rd | 17 +-
man/SalmonColor.Rd | 20 +-
man/Seedlings.Rd | 6
man/Selection.Rd | 18 +-
man/SexualSelection.Rd | 21 +-
man/ShadParasites.Rd | 14 -
man/ShrinkingSeals.Rd | 16 +-
man/ShuttleDisaster.Rd | 22 +--
man/Silversword.Rd | 14 -
man/SleepAndPerformance.Rd | 15 +-
man/SockeyeFemales.Rd | 17 +-
man/Sparrows.Rd | 17 +-
man/SpiderColonies.Rd | 15 --
man/SpiderSpeed.Rd | 20 +-
man/Stalkies1.Rd | 9 -
man/Stalkies2.Rd | 16 +-
man/SticklebackPlates.Rd | 32 ++--
man/SticklebackPreference.Rd | 19 +-
man/Sumo.Rd | 11 -
man/SyrupSwimming.Rd | 17 +-
man/TeenDeaths.Rd | 15 --
man/Telomeres.Rd | 18 +-
man/TimeOfDeath.Rd | 14 -
man/Toads.Rd | 9 -
man/Tobacco.Rd | 16 +-
man/Tobacco2.Rd | 18 +-
man/ToothAge.Rd | 15 +-
man/TreeSeedlings.Rd | 16 +-
man/Trematodes.Rd | 15 +-
man/Trillium.Rd | 15 +-
man/Truffles.Rd | 20 +-
man/TsetseLearning.Rd | 16 +-
man/TwoKids.Rd | 13 -
man/VampireBites.Rd | 9 -
man/VasopressinVoles.Rd | 20 +-
man/Vines.Rd | 16 +-
man/VoleDispersal.Rd | 12 -
man/WalkingStickFemurs.Rd | 17 +-
man/WalkingStickHeads.Rd | 20 +-
man/WeddellSeals.Rd | 19 +-
man/WillsDebates.Rd | 9 -
man/WillsPresidents.Rd | 11 -
man/WolfTeeth.Rd | 18 +-
man/Wolves.Rd | 17 +-
man/WorldCup.Rd | 5
man/WrasseSexes.Rd | 6
man/YeastGenes.Rd | 12 -
man/ZebraFinchBeaks.Rd | 17 +-
man/ZebraFinches.Rd | 17 +-
man/ZooMortality.Rd | 13 -
man/Zooplankton.Rd | 19 +-
man/abd-package.Rd | 30 ++--
man/abdData.Rd | 45 ++----
man/dataInfo.Rd | 9 -
man/histochart.Rd | 32 +---
man/themes.Rd | 28 +--
156 files changed, 1455 insertions(+), 1693 deletions(-)
Title: Bayesian Inference for Zero/One Inflated Beta Regression
Diff between zoib versions 1.0 dated 2014-06-04 and 1.1 dated 2015-02-01
Description: zoib fits beta regression and zero or one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS
Author: Fang Liu
Maintainer: Fang Liu
zoib-1.0/zoib/tests/eg1-Gas.R |only
zoib-1.0/zoib/tests/eg2-Bivariate.R |only
zoib-1.1/zoib/DESCRIPTION | 10 -
zoib-1.1/zoib/MD5 | 74 ++++++-------
zoib-1.1/zoib/R/check.psrf.R | 42 ++++---
zoib-1.1/zoib/R/joint.2z.R | 2
zoib-1.1/zoib/R/sep.2z.R | 15 ++
zoib-1.1/zoib/R/sep.2z0.R | 17 ++-
zoib-1.1/zoib/R/sep.2z01.R | 16 ++
zoib-1.1/zoib/R/sep.2z1.R | 15 ++
zoib-1.1/zoib/R/zoib.R | 72 ++++++++++---
zoib-1.1/zoib/data/BiRepeated.rda |binary
zoib-1.1/zoib/inst/bugs/fixed.bug | 2
zoib-1.1/zoib/inst/bugs/fixed0.bug | 4
zoib-1.1/zoib/inst/bugs/fixed01.bug | 5
zoib-1.1/zoib/inst/bugs/fixed1.bug | 4
zoib-1.1/zoib/inst/bugs/joint_1z.bug | 21 ++-
zoib-1.1/zoib/inst/bugs/joint_1z0.bug | 7 -
zoib-1.1/zoib/inst/bugs/joint_1z01.bug | 4
zoib-1.1/zoib/inst/bugs/joint_1z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/joint_2z.bug | 2
zoib-1.1/zoib/inst/bugs/joint_2z0.bug | 2
zoib-1.1/zoib/inst/bugs/joint_2z01.bug | 4
zoib-1.1/zoib/inst/bugs/joint_2z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z0.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z01.bug | 4
zoib-1.1/zoib/inst/bugs/sep_1z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_2z.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z0.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z01.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z1.bug | 2
zoib-1.1/zoib/man/AlcoholUse.Rd | 31 +++--
zoib-1.1/zoib/man/BiRepeated.Rd | 50 ++++++---
zoib-1.1/zoib/man/GasolineYield.Rd | 67 +++++++++---
zoib-1.1/zoib/man/check.psrf.Rd | 4
zoib-1.1/zoib/man/zoib-package.Rd | 19 +--
zoib-1.1/zoib/man/zoib.Rd | 180 ++++++++++-----------------------
zoib-1.1/zoib/tests/test1.R |only
zoib-1.1/zoib/tests/test2.R |only
40 files changed, 427 insertions(+), 290 deletions(-)
Title: Multivariate Constructs
Diff between multicon versions 1.5 dated 2015-01-08 and 1.6 dated 2015-02-01
Description: Includes functions designed to examine relationships among multivariate constructs (e.g., personality). This includes functions for profile (within-person) analysis, dealing with large numbers of analyses, lens model analyses, and structural summary methods for data with circumplex structure. The package also includes functions for graphically comparing and displaying group means.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++++++-------
NAMESPACE | 8 ++++++++
R/diffPlot.formula.r | 2 +-
R/partwhole.R | 3 +--
R/tContrast.R |only
R/tContrast.default.R |only
R/tContrast.formula.R |only
R/winvar.r |only
R/yuenContrast.default.r |only
R/yuenContrast.formula.r |only
R/yuenContrast.r |only
man/diffPlot.Rd | 7 +++----
man/multicon-package.Rd | 4 ++--
man/partwhole.Rd | 4 ++--
man/tContrast.Rd |only
man/winvar.rd |only
man/yuenContrast.rd |only
18 files changed, 38 insertions(+), 22 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 2.0-22 dated 2014-11-18 and 2.0-24 dated 2015-02-01
Description:
This package accompanies J. Fox and S. Weisberg, An R Companion to Applied Regression,
Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 19
MD5 | 146 ++--
NAMESPACE | 6
NEWS | 22
R/Anova.R | 12
R/Boot.R | 31
R/bootCase.R | 7
R/linearHypothesis.R | 1429 ++++++++++++++++++++++----------------------
R/marginalModelPlot.R | 4
R/mcPlots.R | 4
R/scatterplotSmoothers.R | 72 +-
R/subsets.R | 14
R/utility-functions.R | 6
R/vif.R | 4
build/vignette.rds |binary
data/AMSsurvey.rda |binary
data/Adler.rda |binary
data/Angell.rda |binary
data/Anscombe.rda |binary
data/Baumann.rda |binary
data/Bfox.rda |binary
data/Blackmore.rda |binary
data/Burt.rda |binary
data/CanPop.rda |binary
data/Chile.rda |binary
data/Chirot.rda |binary
data/Cowles.rda |binary
data/Davis.rda |binary
data/DavisThin.rda |binary
data/Depredations.rda |binary
data/Duncan.rda |binary
data/Ericksen.rda |binary
data/Florida.rda |binary
data/Freedman.rda |binary
data/Friendly.rda |binary
data/Ginzberg.rda |binary
data/Greene.rda |binary
data/Guyer.rda |binary
data/Hartnagel.rda |binary
data/Highway1.rda |binary
data/KosteckiDillon.rda |binary
data/Leinhardt.rda |binary
data/Mandel.rda |binary
data/Migration.rda |binary
data/Moore.rda |binary
data/Mroz.rda |binary
data/OBrienKaiser.rda |binary
data/Ornstein.rda |binary
data/Pottery.rda |binary
data/Prestige.rda |binary
data/Quartet.rda |binary
data/Robey.rda |binary
data/SLID.rda |binary
data/Sahlins.rda |binary
data/Salaries.rda |binary
data/Soils.rda |binary
data/States.rda |binary
data/Transact.rda |binary
data/UN.rda |binary
data/USPop.rda |binary
data/Vocab.rda |binary
data/WeightLoss.rda |binary
data/Womenlf.rda |binary
data/Wong.rda |only
data/Wool.rda |binary
inst/doc/embedding.pdf |binary
man/AMSsurvey.Rd | 88 +-
man/Florida.Rd | 4
man/ScatterplotSmoothers.Rd | 17
man/Soils.Rd | 2
man/UN.Rd | 2
man/Wong.Rd |only
man/car-package.Rd | 8
man/marginalModelPlot.Rd | 40 -
man/subsets.Rd | 14
75 files changed, 1005 insertions(+), 946 deletions(-)
Title: Regional frequency analysis using L-moments
Diff between lmomRFA versions 3.0 dated 2014-01-15 and 3.0-1 dated 2015-02-01
Description: Functions for regional frequency analysis using the methods
of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis:
an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 10 ++--
MD5 | 48 ++++++++++-----------
NEWS | 7 ++-
R/lmomRFA.r | 8 ---
data/Appalach.rda |binary
data/Cascades.rda |binary
data/Maxwind.rda |binary
man/cluagg.Rd | 2
man/cluinf.Rd | 2
man/clukm.Rd | 2
man/evplot.rfd.Rd | 2
man/lmomRFA-package.Rd | 2
man/regavlmom.Rd | 2
man/regdata.Rd | 2
man/regfit.Rd | 2
man/reglmr.Rd | 2
man/regquant.Rd | 2
man/regquantbounds.Rd | 2
man/regsamlmu.Rd | 2
man/regsimh.Rd | 2
man/regsimq.Rd | 2
man/regtst.Rd | 2
man/sitequant.Rd | 2
man/summary.regtst.Rd | 2
src/lmomRFA.f | 108 ++++++++-----------------------------------------
25 files changed, 72 insertions(+), 143 deletions(-)
Title: L-moments
Diff between lmom versions 2.4 dated 2014-03-24 and 2.5 dated 2015-02-01
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples; parameter
estimation; L-moment ratio diagram; plot vs. quantiles of an
extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 10 +--
MD5 | 28 ++++----
NEWS | 21 ++++++
R/lmom.r | 53 +++++++++-------
man/evplot.Rd | 13 +--
man/lmom-package.Rd | 2
man/lmr-functions.Rd | 3
man/lmrd.Rd | 8 +-
man/lmrdpoints.Rd | 2
man/lmrp.Rd | 15 +---
man/pel-functions.Rd | 2
man/pelp.Rd | 2
man/samlmu.Rd | 2
src/lmoments.f | 166 ++++++++-------------------------------------------
src/samlm.f | 30 +++++----
15 files changed, 138 insertions(+), 219 deletions(-)
Title: Composite-Likelihood Based Analysis of Random Fields
Diff between CompRandFld versions 1.0.3-3 dated 2015-01-15 and 1.0.3-4 dated 2015-02-01
Description: A set of procedures for the analysis of Random Fields using likelihood and non-standard likelihood methods is provided. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood inference is emerging as a useful tool for mitigating such computational problems. This methodology shows satisfactory results when compared with other techniques such as the tapering method. Moreover, composite likelihood (and related quantities) have some useful properties similar to those of the standard likelihood.
Author: Simone Padoan[aut, cre]
Maintainer: Simone Padoan
DESCRIPTION | 20 ++---
MD5 | 57 ++++++++--------
NAMESPACE | 4 +
R/Covmatrix.r | 4 -
inst/CITATION |only
man/CheckCorrModel.Rd | 3
man/CheckInput.Rd | 3
man/CheckLikelihood.Rd | 2
man/CheckModel.Rd | 2
man/CheckType.Rd | 3
man/CheckVarType.Rd | 3
man/CompLikelihood.Rd | 2
man/CorrelationParam.Rd | 4 -
man/Covariogram.Rd | 5 +
man/Covmatrix.Rd | 60 +++++++++--------
man/Dist2Dist.Rd | 4 -
man/EVariogram.Rd | 6 +
man/FitComposite.Rd | 22 +++---
man/FitGev.Rd | 3
man/GevLogLik.Rd | 3
man/HypoTest.Rd | 9 +-
man/InitParam.Rd | 7 +-
man/Kri.Rd | 103 ++++++++++++++----------------
man/Likelihood.Rd | 2
man/MomEst.Rd | 2
man/NuisanceParam.Rd | 3
man/RFsim.Rd | 8 +-
man/WLeastSquare.Rd | 10 +-
man/WlsInit.Rd | 2
src/Utility.c | 164 ++++++++++++++++++++++++++----------------------
30 files changed, 274 insertions(+), 246 deletions(-)
Title: Variance Dispersion, Fraction of Design Space Plots, Designs,
and Contour Plots
Diff between VdgRsm versions 1.3 dated 2014-11-29 and 1.4 dated 2015-02-01
Description: This package creates variance dispersion graphs (VDGs), fraction of design space (FDS) plots, and contour of SPVs for second-order model designs in spherical or cuboidal regions. The package also generates some response surface designs.
Author: Patchanok Srisuradetchai, John J. Borkowski
Maintainer: Patchanok Srisuradetchai
VdgRsm-1.3/VdgRsm/man/VdgRsm-package.Rd |only
VdgRsm-1.4/VdgRsm/DESCRIPTION | 20
VdgRsm-1.4/VdgRsm/MD5 | 13
VdgRsm-1.4/VdgRsm/NAMESPACE | 10
VdgRsm-1.4/VdgRsm/R/VdgRsm.R | 757 ++++++++++++++++++++++++++++----
VdgRsm-1.4/VdgRsm/man/Borkowski2003.Rd | 10
VdgRsm-1.4/VdgRsm/man/VdgRsm.Rd |only
VdgRsm-1.4/VdgRsm/man/cpv.Rd | 16
VdgRsm-1.4/VdgRsm/man/spvcontour.Rd |only
9 files changed, 721 insertions(+), 105 deletions(-)
Title: Geographically-Weighted Models
Diff between GWmodel versions 1.2-3 dated 2014-05-12 and 1.2-5 dated 2015-02-01
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu
DESCRIPTION | 23 ++++----
MD5 | 116 +++++++++++++++++++++++----------------------
NAMESPACE | 3 -
R/LocalsummaryStatistics.r | 1
R/gw.weight.r | 90 +++++++++++++++++++++++++---------
R/gwr.basic.r | 83 --------------------------------
R/gwr.t.adjust.r | 12 +++-
R/minkovski.approach.r |only
R/zzz.r | 2
inst |only
man/EWHP.Rd | 4 -
man/EWOutline.rd | 2
man/GWmodel-package.Rd | 21 ++++----
man/LondonBorough.rd | 2
man/LondonHP.Rd | 11 +---
man/bw.ggwr.Rd | 2
man/bw.gwda.rd | 2
man/bw.gwpca.rd | 2
man/bw.gwr.Rd | 2
man/bw.gwr.lcr.rd | 2
man/check.components.rd | 2
man/ggwr.cv.Rd | 2
man/ggwr.cv.contrib.Rd | 2
man/glyph.plot.rd | 2
man/gw.dist.Rd | 2
man/gw.pcplot.rd | 9 +--
man/gwda.rd | 2
man/gwpca.cv.Rd | 2
man/gwpca.cv.contrib.Rd | 2
man/gwpca.rd | 20 +++----
man/gwr.basic.rd | 10 +--
man/gwr.collin.diagno.Rd | 2
man/gwr.cv.Rd | 2
man/gwr.cv.contrib.Rd | 2
man/gwr.generalised.Rd | 4 -
man/gwr.hetero.rd | 2
man/gwr.lcr.cv.Rd | 2
man/gwr.lcr.cv.contrib.Rd | 2
man/gwr.lcr.rd | 10 +--
man/gwr.mixed.rd | 2
man/gwr.predict.Rd | 2
man/gwr.robust.Rd | 2
man/gwr.t.adjust.rd | 2
man/gwss.rd | 2
man/mink.approach.rd |only
man/mink.matrixview.rd |only
man/model.selection.gwr.Rd | 8 +--
man/model.sort.gwr.Rd | 2
man/model.view.gwr.rd | 2
man/montecarlo.gwpca.1.rd | 2
man/montecarlo.gwpca.2.rd | 2
man/montecarlo.gwr.Rd | 2
man/montecarlo.gwss.Rd | 2
man/plot.mcsims.rd | 2
man/print.ggwrm.Rd | 2
man/print.gwrm.Rd | 3 -
man/print.gwrm.lcr.rd | 2
man/print.gwrm.pred.rd | 2
man/print.gwss.Rd | 2
man/writeGWR.Rd | 2
man/writeGWR.shp.Rd | 2
61 files changed, 236 insertions(+), 272 deletions(-)
Title: Differential Functioning of Items and Tests
Diff between DFIT versions 1.0-1 dated 2014-07-15 and 1.0-2 dated 2015-02-01
Description: A set of functions to perform Raju, van der Linden and Fleer's
(1995) Differential Functioning of Items and Tests (DFIT) analyses. It includes
functions to use the Monte Carlo Item Parameter Replication approach
(Oshima, Raju, & Nanda, 2006) for obtaining the associated statistical
significance tests cut-off points. They may also be used for a priori and
post-hoc power calculations.
Author: Victor H. Cervantes
Maintainer: Victor H. Cervantes
DESCRIPTION | 15 +++++++--------
MD5 | 6 +++---
NEWS | 3 +++
inst/CITATION | 2 +-
4 files changed, 14 insertions(+), 12 deletions(-)
Title: A Connection Interface to Libcurl
Diff between curl versions 0.4 dated 2015-01-08 and 0.5 dated 2015-02-01
Description: The curl() function provides a drop-in replacement for base url()
with better performance and support for http 2.0, ssl (https://, ftps://),
gzip, deflate and other libcurl goodies. This interface is implemented
using the RConnection API in order to support incremental processing of
both binary and text streams. If you are looking for a more-user-friendly
http client, try the RCurl or httr packages instead.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
NEWS | 3 +++
configure | 5 +++--
src/curl.c | 12 ++++++++++--
src/utils.c | 4 ++++
6 files changed, 32 insertions(+), 15 deletions(-)
Title: Business Days Calculations and Utilities
Diff between bizdays versions 0.1.5 dated 2014-06-16 and 0.2.1 dated 2015-02-01
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas
Maintainer: Wilson Freitas
bizdays-0.1.5/bizdays/man/add.bizdays.Rd |only
bizdays-0.2.1/bizdays/DESCRIPTION | 17
bizdays-0.2.1/bizdays/MD5 | 40 -
bizdays-0.2.1/bizdays/NAMESPACE | 41 -
bizdays-0.2.1/bizdays/NEWS | 28
bizdays-0.2.1/bizdays/R/R-bizdays-package.r | 35 -
bizdays-0.2.1/bizdays/R/calendar.R | 733 +++++++++++++----------
bizdays-0.2.1/bizdays/README.md | 56 +
bizdays-0.2.1/bizdays/inst/tests/test-bizdays.R | 7
bizdays-0.2.1/bizdays/inst/tests/test-calendar.R | 28
bizdays-0.2.1/bizdays/man/Calendar.Rd | 77 +-
bizdays-0.2.1/bizdays/man/adjust.date.Rd | 63 -
bizdays-0.2.1/bizdays/man/bizdays-package.Rd |only
bizdays-0.2.1/bizdays/man/bizdays.Rd | 82 +-
bizdays-0.2.1/bizdays/man/bizdays.options.Rd | 33 -
bizdays-0.2.1/bizdays/man/bizdayse.Rd | 87 +-
bizdays-0.2.1/bizdays/man/bizseq.Rd | 44 -
bizdays-0.2.1/bizdays/man/bizyears.Rd | 71 +-
bizdays-0.2.1/bizdays/man/bizyearse.Rd |only
bizdays-0.2.1/bizdays/man/holidaysANBIMA.Rd | 5
bizdays-0.2.1/bizdays/man/is.bizday.Rd | 47 -
bizdays-0.2.1/bizdays/man/offset.Rd |only
bizdays-0.2.1/bizdays/vignettes |only
23 files changed, 884 insertions(+), 610 deletions(-)
Title: Data Generation with Binary and Continuous Non-normal Components
Diff between BinNonNor versions 1.0 dated 2014-12-16 and 1.1 dated 2015-02-01
Description: Generation of multiple binary and continuous non-normal variables simultaneously
given the marginal characteristics and association structure based on the methodology
proposed by Demirtas et al. (2012).
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
DESCRIPTION | 8 +--
MD5 | 38 +++++++-------
R/Int.Corr.NN.R | 10 +--
R/Tetra.Corr.BB.R | 10 +--
R/correlation.bound.check.R | 3 -
R/fleishman.coef.R | 3 -
R/gen.Bin.NonNor.R | 14 ++---
R/overall.corr.mat.R | 1
man/BinNonNor-package.Rd | 4 -
man/Biserial.Corr.BN.Rd | 9 +++
man/Int.Corr.NN.Rd | 2
man/Tetra.Corr.BB.Rd | 2
man/correlation.bound.check.Rd | 21 ++++++-
man/correlation.limits.Rd | 14 +++--
man/fleishman.coef.Rd | 13 ++--
man/gen.Bin.NonNor.Rd | 95 +++++++++++++++++++++---------------
man/overall.corr.mat.Rd | 11 +++-
man/validation.bin.Rd | 22 +++++---
man/validation.corr.Rd | 27 ++++++----
man/validation.skewness.kurtosis.Rd | 26 ++++++---
20 files changed, 207 insertions(+), 126 deletions(-)
Title: MA Birk's Functions
Diff between birk versions 1.2 dated 2014-11-07 and 1.3.0 dated 2015-02-01
Description: This is a compilation of functions that I found useful to make. It currently includes a unit of measurement conversion function, a Q10 calculator for temperature dependence of chemical and biological rates, and some miscellaneous wrapper functions to make R code shorter and faster to write.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk
birk-1.2/birk/man/birk-package.Rd |only
birk-1.3.0/birk/DESCRIPTION | 19 ++---
birk-1.3.0/birk/MD5 | 26 ++++--
birk-1.3.0/birk/NAMESPACE | 9 ++
birk-1.3.0/birk/NEWS |only
birk-1.3.0/birk/R/Q10calc.R |only
birk-1.3.0/birk/R/birk.R |only
birk-1.3.0/birk/R/conv_unit.R | 117 +++++++++++++++++++++++++------
birk-1.3.0/birk/R/geom_mean.R | 23 +++++-
birk-1.3.0/birk/R/range_seq.R |only
birk-1.3.0/birk/R/se.R | 18 ++++
birk-1.3.0/birk/man/Q10calc.Rd |only
birk-1.3.0/birk/man/birk.Rd |only
birk-1.3.0/birk/man/conv_unit.Rd | 90 +++++++++++------------
birk-1.3.0/birk/man/conv_unit_options.Rd | 46 +++++++-----
birk-1.3.0/birk/man/geom_mean.Rd | 33 ++++++--
birk-1.3.0/birk/man/range_seq.Rd |only
birk-1.3.0/birk/man/se.Rd | 27 +++++--
18 files changed, 286 insertions(+), 122 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.9 dated 2014-10-22 and 0.9.10 dated 2015-02-01
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
BayesFactor-0.9.10/BayesFactor/DESCRIPTION | 12
BayesFactor-0.9.10/BayesFactor/MD5 | 127 +++++-----
BayesFactor-0.9.10/BayesFactor/NAMESPACE | 3
BayesFactor-0.9.10/BayesFactor/NEWS | 9
BayesFactor-0.9.10/BayesFactor/R/BayesFactorPCL-package.R | 4
BayesFactor-0.9.10/BayesFactor/R/RcppExports.R | 16 +
BayesFactor-0.9.10/BayesFactor/R/anovaBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/common.R | 24 -
BayesFactor-0.9.10/BayesFactor/R/contingency-utility.R | 2
BayesFactor-0.9.10/BayesFactor/R/generalTest-utility.R | 12
BayesFactor-0.9.10/BayesFactor/R/generalTestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/logMean.R | 16 -
BayesFactor-0.9.10/BayesFactor/R/meta-ttest-utility.R | 12
BayesFactor-0.9.10/BayesFactor/R/meta.ttestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/methods-BFBayesFactor.R | 2
BayesFactor-0.9.10/BayesFactor/R/methods-BFlinearModel-compare.R | 75 +++--
BayesFactor-0.9.10/BayesFactor/R/nWayAOV-utility.R | 8
BayesFactor-0.9.10/BayesFactor/R/nWayAOV.R | 2
BayesFactor-0.9.10/BayesFactor/R/oneWayAOV_Fstat.R | 18 -
BayesFactor-0.9.10/BayesFactor/R/proportion-utility.R | 6
BayesFactor-0.9.10/BayesFactor/R/ttestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/ttest_tstat.R | 7
BayesFactor-0.9.10/BayesFactor/build/vignette.rds |binary
BayesFactor-0.9.10/BayesFactor/inst/doc/compare_lme4.html | 76 ++---
BayesFactor-0.9.10/BayesFactor/inst/doc/manual.html | 88 +++---
BayesFactor-0.9.10/BayesFactor/inst/doc/priors.html | 42 +--
BayesFactor-0.9.10/BayesFactor/man/BFBayesFactor-class.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFBayesFactorList-class.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFInfo.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFManual.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BayesFactor-package.Rd | 7
BayesFactor-0.9.10/BayesFactor/man/anovaBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/as.BFBayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/compare-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/contingencyTableBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/enumerateGeneralModels.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/extractBF-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/generalTestBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/grapes-same-grapes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/grapes-termin-grapes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/linearReg.R2stat.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/lmBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/logMeanExpLogs.Rd | 12
BayesFactor-0.9.10/BayesFactor/man/meta.ttestBF.Rd | 5
BayesFactor-0.9.10/BayesFactor/man/model-classes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/model.matrix-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/nWayAOV.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/oneWayAOV.Fstat.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/options-BayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/plot.BFBayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/plot.BFBayesFactorTop.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/posterior-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/proportionBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/puzzles.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/raceDolls.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/recompute-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/regressionBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/ttest.tstat.Rd | 5
BayesFactor-0.9.10/BayesFactor/man/ttestBF.Rd | 5
BayesFactor-0.9.10/BayesFactor/src/BFPCL.h | 18 -
BayesFactor-0.9.10/BayesFactor/src/RcppExports.cpp | 62 ++++
BayesFactor-0.9.10/BayesFactor/src/bfcommon.h | 11
BayesFactor-0.9.10/BayesFactor/src/logRepresentedReal.cpp |only
BayesFactor-0.9.10/BayesFactor/src/logRepresentedReal.h |only
BayesFactor-0.9.10/BayesFactor/src/logSummaryStats.cpp |only
BayesFactor-0.9.10/BayesFactor/src/logUtility.cpp |only
BayesFactor-0.9.9/BayesFactor/src/logMean.c |only
67 files changed, 446 insertions(+), 332 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 2014.4-1
2013-09-29 2013.9-1
Title: Leveraging Learning to Automatically Manage Algorithms
Diff between llama versions 0.7.2 dated 2014-09-20 and 0.8 dated 2015-01-31
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff
llama-0.7.2/llama/R/featureFilter.R |only
llama-0.7.2/llama/man/featureFilter.Rd |only
llama-0.7.2/llama/tests/testthat/test.featureFilter.R |only
llama-0.8/llama/DESCRIPTION | 12
llama-0.8/llama/LICENSE | 2
llama-0.8/llama/MD5 | 124 ++---
llama-0.8/llama/NAMESPACE | 13
llama-0.8/llama/NEWS | 12
llama-0.8/llama/R/analysis.R | 2
llama-0.8/llama/R/bsFolds.R |only
llama-0.8/llama/R/classify.R | 102 +++-
llama-0.8/llama/R/classifyPairs.R | 120 +++--
llama-0.8/llama/R/cluster.R | 126 +++--
llama-0.8/llama/R/cvFolds.R | 31 -
llama-0.8/llama/R/helpers.R |only
llama-0.8/llama/R/imputeCensored.R | 22
llama-0.8/llama/R/input.R | 30 -
llama-0.8/llama/R/misc.R | 89 ++-
llama-0.8/llama/R/misclassificationPenalties.R | 49 --
llama-0.8/llama/R/parscores.R | 86 ++-
llama-0.8/llama/R/plot.R |only
llama-0.8/llama/R/regression.R | 116 +++-
llama-0.8/llama/R/regressionPairs.R | 146 ++++--
llama-0.8/llama/R/successes.R | 88 ++-
llama-0.8/llama/R/trainTest.R | 25 -
llama-0.8/llama/R/zzz.R | 5
llama-0.8/llama/data/satsolvers.rda |binary
llama-0.8/llama/inst/java/ShapleyValue.jar |binary
llama-0.8/llama/inst/manual/llama.pdf |binary
llama-0.8/llama/java/shapleyComputation/CoalitionValueCalculator.class |binary
llama-0.8/llama/java/shapleyComputation/Combinations.class |binary
llama-0.8/llama/java/shapleyComputation/ShapleyComputation.class |binary
llama-0.8/llama/man/analysis.Rd | 4
llama-0.8/llama/man/bsFolds.Rd |only
llama-0.8/llama/man/classify.Rd | 54 +-
llama-0.8/llama/man/classifyPairs.Rd | 60 +-
llama-0.8/llama/man/cluster.Rd | 57 +-
llama-0.8/llama/man/cvFolds.Rd | 23
llama-0.8/llama/man/helpers.Rd |only
llama-0.8/llama/man/imputeCensored.Rd | 4
llama-0.8/llama/man/input.Rd | 18
llama-0.8/llama/man/llama-package.Rd | 23
llama-0.8/llama/man/misc.Rd | 47 +-
llama-0.8/llama/man/misclassificationPenalties.Rd | 10
llama-0.8/llama/man/normalize.Rd | 4
llama-0.8/llama/man/parscores.Rd | 16
llama-0.8/llama/man/plot.Rd |only
llama-0.8/llama/man/regression.Rd | 58 +-
llama-0.8/llama/man/regressionPairs.Rd | 58 +-
llama-0.8/llama/man/successes.Rd | 20
llama-0.8/llama/man/trainTest.Rd | 25 -
llama-0.8/llama/tests/testthat/helper_mockLearners.R | 42 +
llama-0.8/llama/tests/testthat/helper_testData.R |only
llama-0.8/llama/tests/testthat/test.analysis.R | 2
llama-0.8/llama/tests/testthat/test.bsFolds.R |only
llama-0.8/llama/tests/testthat/test.classify.R | 138 ++++-
llama-0.8/llama/tests/testthat/test.classifyPairs.R | 97 +++-
llama-0.8/llama/tests/testthat/test.cluster.R | 149 +++++-
llama-0.8/llama/tests/testthat/test.cvFolds.R | 48 +-
llama-0.8/llama/tests/testthat/test.imputeCensored.R | 24 -
llama-0.8/llama/tests/testthat/test.input.R | 59 +-
llama-0.8/llama/tests/testthat/test.misc.R | 235 ++++++----
llama-0.8/llama/tests/testthat/test.misclassificationPenalties.R | 75 +--
llama-0.8/llama/tests/testthat/test.parscores.R | 163 +++---
llama-0.8/llama/tests/testthat/test.regression.R | 112 ++++
llama-0.8/llama/tests/testthat/test.regressionPairs.R | 112 ++++
llama-0.8/llama/tests/testthat/test.satsolvers.R |only
llama-0.8/llama/tests/testthat/test.successes.R | 136 +++--
llama-0.8/llama/tests/testthat/test.trainTest.R | 64 --
69 files changed, 2116 insertions(+), 1021 deletions(-)
Title: Fuzzy Clustering
Diff between fclust versions 1.0.1 dated 2014-03-26 and 1.1 dated 2015-01-31
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results
Author: Paolo Giordani, Maria Brigida Ferraro
Maintainer: Paolo Giordani
DESCRIPTION | 12 ++---
MD5 | 98 ++++++++++++++++++++++++++++++------------------
NAMESPACE | 5 +-
R/FKM.R | 12 ++++-
R/FKM.ent.R | 1
R/FKM.ent.noise.R |only
R/FKM.gk.R | 12 ++++-
R/FKM.gk.ent.R | 1
R/FKM.gk.ent.noise.R |only
R/FKM.gk.noise.R |only
R/FKM.med.R | 14 ++++--
R/FKM.med.noise.R |only
R/FKM.noise.R | 16 +++++--
R/FKM.pf.R |only
R/FKM.pf.noise.R |only
R/Fclust.R | 82 +++++++++++++++++++++++++++++++---------
R/Fclust.index.R | 2
R/Hraw.R | 4 -
R/VAT.R |only
R/VCV.R |only
R/VCV2.R |only
R/VIFCR.R |only
R/cl.memb.t.R | 14 +++---
R/plot.fclust.R |only
R/print.fclust.R |only
R/summary.fclust.R |only
man/FKM.Rd | 14 ++++--
man/FKM.ent.Rd | 17 ++++++--
man/FKM.ent.noise.Rd |only
man/FKM.gk.Rd | 11 +++--
man/FKM.gk.ent.Rd | 16 +++++--
man/FKM.gk.ent.noise.Rd |only
man/FKM.gk.noise.Rd |only
man/FKM.med.Rd | 16 +++++--
man/FKM.med.noise.Rd |only
man/FKM.noise.Rd | 10 +++-
man/FKM.pf.Rd |only
man/FKM.pf.noise.Rd |only
man/Fclust.Rd | 12 ++++-
man/Fclust.index.Rd | 15 +++++--
man/Hraw.Rd | 13 ++++--
man/MPC.Rd | 9 +++-
man/Mc.Rd | 36 ++++++++++++++---
man/PC.Rd | 9 +++-
man/PE.Rd | 13 ++++--
man/SIL.F.Rd | 11 ++++-
man/SIL.Rd | 11 ++++-
man/VAT.Rd |only
man/VCV.Rd |only
man/VCV2.Rd |only
man/VIFCR.Rd |only
man/XB.Rd | 11 ++++-
man/butterfly.Rd | 10 +++-
man/cl.memb.H.Rd | 7 ++-
man/cl.memb.Rd | 7 ++-
man/cl.memb.t.Rd | 9 +++-
man/cl.size.H.Rd | 6 +-
man/cl.size.Rd | 3 -
man/plot.fclust.Rd |only
man/print.fclust.Rd |only
man/summary.fclust.Rd |only
man/synt.data.Rd | 14 ++++--
man/unemployment.Rd | 10 ++--
63 files changed, 408 insertions(+), 155 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated From Cox Proportional Hazards Models
Diff between simPH versions 1.2.4 dated 2014-12-07 and 1.2.6.1 dated 2015-01-31
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 24 +--
MD5 | 60 +++----
NAMESPACE | 3
NEWS | 16 +-
R/SurvExpand.R | 3
R/coxsimPoly.R | 2
R/coxsimSpline.R | 8 -
R/simGG.simlinear.R | 68 ++++----
R/simGG.simspline.R | 358 +++++++++++++++++++++++------------------------
R/smallUtils.R | 153 +++++++++++++++-----
README.md | 4
build/vignette.rds |binary
man/CarpenterFdaData.Rd | 3
man/GolubEUPData.Rd | 3
man/MinMaxLines.Rd | 3
man/SurvExpand.Rd | 5
man/coxsimInteract.Rd | 3
man/coxsimLinear.Rd | 3
man/coxsimPoly.Rd | 3
man/coxsimSpline.Rd | 3
man/coxsimtvc.Rd | 3
man/ggfitStrata.Rd | 3
man/setXl.Rd | 3
man/simGG.Rd | 3
man/simGG.siminteract.Rd | 3
man/simGG.simlinear.Rd | 3
man/simGG.simpoly.Rd | 3
man/simGG.simspline.Rd | 11 -
man/simGG.simtvc.Rd | 3
man/simPH.Rd | 3
man/tvc.Rd | 3
31 files changed, 439 insertions(+), 327 deletions(-)
Title: Flexible Cluster-Weighted Modeling
Diff between flexCWM versions 1.3 dated 2014-12-16 and 1.4 dated 2015-01-31
Description: Allows for maximum likelihood fitting of cluster-weighted models, a class of mixtures of regression models with random covariates.
Author: Mazza A., Punzo A., Ingrassia S.
Maintainer: Angelo Mazza
flexCWM-1.3/flexCWM/data/tourism.RData |only
flexCWM-1.3/flexCWM/man/tourism.Rd |only
flexCWM-1.4/flexCWM/DESCRIPTION | 10 +-
flexCWM-1.4/flexCWM/MD5 | 35 +++----
flexCWM-1.4/flexCWM/NAMESPACE | 10 +-
flexCWM-1.4/flexCWM/R/Extractors.R | 129 ++++++++++++++++++++++----
flexCWM-1.4/flexCWM/R/Gamma.R | 4
flexCWM-1.4/flexCWM/R/PostInit.R | 2
flexCWM-1.4/flexCWM/R/PostProbs.R | 14 +-
flexCWM-1.4/flexCWM/R/code.R | 47 +++++----
flexCWM-1.4/flexCWM/R/cwm.R | 74 +++++----------
flexCWM-1.4/flexCWM/R/familyY2.R | 3
flexCWM-1.4/flexCWM/R/plot.R | 36 +++----
flexCWM-1.4/flexCWM/R/summary.R | 47 +++++----
flexCWM-1.4/flexCWM/data/ExCWM.RData |only
flexCWM-1.4/flexCWM/man/ExCWM.Rd |only
flexCWM-1.4/flexCWM/man/cwm.Rd | 143 ++++++++++++-----------------
flexCWM-1.4/flexCWM/man/extractors.Rd |only
flexCWM-1.4/flexCWM/man/flexCWM-package.Rd | 8 -
flexCWM-1.4/flexCWM/man/plot.Rd | 32 ++++--
flexCWM-1.4/flexCWM/man/students.Rd | 12 ++
21 files changed, 353 insertions(+), 253 deletions(-)
Title: Extending R's Dendrogram Functionality
Diff between dendextend versions 0.17.5 dated 2014-09-22 and 0.18.3 dated 2015-01-31
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a trees graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Yoav Benjamini [ths]
Maintainer: Tal Galili
dendextend-0.17.5/dendextend/R/imports_stats.R |only
dendextend-0.17.5/dendextend/man/get_branches_attr.Rd |only
dendextend-0.17.5/dendextend/tests/test-all.r |only
dendextend-0.18.3/dendextend/ChangeLog | 755 +++++++++-
dendextend-0.18.3/dendextend/DESCRIPTION | 24
dendextend-0.18.3/dendextend/MD5 | 294 ++-
dendextend-0.18.3/dendextend/NAMESPACE | 36
dendextend-0.18.3/dendextend/NEWS | 109 +
dendextend-0.18.3/dendextend/R/DendSer.R | 2
dendextend-0.18.3/dendextend/R/all.equal.R |only
dendextend-0.18.3/dendextend/R/ape.R |only
dendextend-0.18.3/dendextend/R/attr_access.R | 119 +
dendextend-0.18.3/dendextend/R/bk_method.R | 2
dendextend-0.18.3/dendextend/R/branches_attr_by.R | 1
dendextend-0.18.3/dendextend/R/cor.dendlist.R |only
dendextend-0.18.3/dendextend/R/cutree.dendrogram.R | 84 -
dendextend-0.18.3/dendextend/R/dist_long.R |only
dendextend-0.18.3/dendextend/R/distinct_edges.R |only
dendextend-0.18.3/dendextend/R/get_nodes_xy.R | 1
dendextend-0.18.3/dendextend/R/ggdend.R |only
dendextend-0.18.3/dendextend/R/ggdendro.R |only
dendextend-0.18.3/dendextend/R/labels.R | 41
dendextend-0.18.3/dendextend/R/nleaves.R | 623 ++++----
dendextend-0.18.3/dendextend/R/noded_with_condition.R | 48
dendextend-0.18.3/dendextend/R/prune.R | 2
dendextend-0.18.3/dendextend/R/rainbow_fun.R | 2
dendextend-0.18.3/dendextend/R/rotate.R | 138 +
dendextend-0.18.3/dendextend/R/set.dendrogram.R | 3
dendextend-0.18.3/dendextend/R/stats_imports.R |only
dendextend-0.18.3/dendextend/R/tanglegram.R | 7
dendextend-0.18.3/dendextend/R/unbranch.R | 596 ++++---
dendextend-0.18.3/dendextend/R/untangle.R | 358 ++--
dendextend-0.18.3/dendextend/R/zzz.R | 6
dendextend-0.18.3/dendextend/README.md | 3
dendextend-0.18.3/dendextend/TODO | 29
dendextend-0.18.3/dendextend/build/vignette.rds |binary
dendextend-0.18.3/dendextend/inst/doc/introduction.R | 194 ++
dendextend-0.18.3/dendextend/inst/doc/introduction.Rmd | 325 ++++
dendextend-0.18.3/dendextend/inst/doc/introduction.html | 630 +++++++-
dendextend-0.18.3/dendextend/inst/tests/test-attr_access.R | 27
dendextend-0.18.3/dendextend/inst/tests/test-cut_lower_fun.R | 199 +-
dendextend-0.18.3/dendextend/inst/tests/test-cutree.dendrogram.R | 53
dendextend-0.18.3/dendextend/inst/tests/test-distinct_edges.R |only
dendextend-0.18.3/dendextend/inst/tests/test-set.dendrogram.R | 5
dendextend-0.18.3/dendextend/inst/tests/test-unbranch.R | 8
dendextend-0.18.3/dendextend/man/Bk.Rd | 2
dendextend-0.18.3/dendextend/man/Bk_permutations.Rd | 2
dendextend-0.18.3/dendextend/man/Bk_plot.Rd | 2
dendextend-0.18.3/dendextend/man/DendSer.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/FM_index.Rd | 2
dendextend-0.18.3/dendextend/man/FM_index_R.Rd | 2
dendextend-0.18.3/dendextend/man/FM_index_permutation.Rd | 2
dendextend-0.18.3/dendextend/man/FM_index_profdpm.Rd | 2
dendextend-0.18.3/dendextend/man/all.equal.dendrogram.Rd |only
dendextend-0.18.3/dendextend/man/all_couple_rotations_at_k.Rd | 2
dendextend-0.18.3/dendextend/man/all_unique.Rd | 2
dendextend-0.18.3/dendextend/man/as.dendlist.Rd | 2
dendextend-0.18.3/dendextend/man/as.phylo.dendrogram.Rd |only
dendextend-0.18.3/dendextend/man/as_hclust_fixed.Rd | 2
dendextend-0.18.3/dendextend/man/assign_dendextend_options.Rd | 2
dendextend-0.18.3/dendextend/man/assign_values_to_branches_edgePar.Rd | 7
dendextend-0.18.3/dendextend/man/assign_values_to_leaves_edgePar.Rd | 2
dendextend-0.18.3/dendextend/man/assign_values_to_leaves_nodePar.Rd | 2
dendextend-0.18.3/dendextend/man/assign_values_to_nodes_nodePar.Rd | 2
dendextend-0.18.3/dendextend/man/bakers_gamma_for_2_k_matrix.Rd | 2
dendextend-0.18.3/dendextend/man/branches_attr_by_clusters.Rd | 2
dendextend-0.18.3/dendextend/man/branches_attr_by_labels.Rd | 3
dendextend-0.18.3/dendextend/man/click_rotate.Rd | 6
dendextend-0.18.3/dendextend/man/collapse_branch.Rd |only
dendextend-0.18.3/dendextend/man/color_branches.Rd | 2
dendextend-0.18.3/dendextend/man/color_labels.Rd | 8
dendextend-0.18.3/dendextend/man/colored_bars.Rd | 2
dendextend-0.18.3/dendextend/man/cor.dendlist.Rd |only
dendextend-0.18.3/dendextend/man/cor_bakers_gamma.Rd | 6
dendextend-0.18.3/dendextend/man/cor_cophenetic.Rd | 6
dendextend-0.18.3/dendextend/man/count_terminal_nodes.Rd | 2
dendextend-0.18.3/dendextend/man/cut_lower_fun.Rd | 2
dendextend-0.18.3/dendextend/man/cutree-methods.Rd | 13
dendextend-0.18.3/dendextend/man/cutree_1h.dendrogram.Rd | 10
dendextend-0.18.3/dendextend/man/cutree_1k.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/d3dendro_options.Rd | 2
dendextend-0.18.3/dendextend/man/d3dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/dend_diff.Rd |only
dendextend-0.18.3/dendextend/man/dendextend-package.Rd | 2
dendextend-0.18.3/dendextend/man/dendextend_options.Rd | 2
dendextend-0.18.3/dendextend/man/dendlist.Rd | 2
dendextend-0.18.3/dendextend/man/dist.dendlist.Rd |only
dendextend-0.18.3/dendextend/man/dist_long.Rd |only
dendextend-0.18.3/dendextend/man/distinct_edges.Rd |only
dendextend-0.18.3/dendextend/man/duplicate_leaf.Rd | 2
dendextend-0.18.3/dendextend/man/entanglement.Rd | 6
dendextend-0.18.3/dendextend/man/fac2num.Rd | 2
dendextend-0.18.3/dendextend/man/fix_members_attr.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/flatten.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/flip_leaves.Rd | 2
dendextend-0.18.3/dendextend/man/get_branches_heights.Rd | 2
dendextend-0.18.3/dendextend/man/get_childrens_heights.Rd | 2
dendextend-0.18.3/dendextend/man/get_leaves_attr.Rd | 2
dendextend-0.18.3/dendextend/man/get_leaves_nodePar.Rd |only
dendextend-0.18.3/dendextend/man/get_nodes_attr.Rd | 10
dendextend-0.18.3/dendextend/man/get_nodes_xy.Rd | 3
dendextend-0.18.3/dendextend/man/get_root_branches_attr.Rd |only
dendextend-0.18.3/dendextend/man/ggdend.Rd |only
dendextend-0.18.3/dendextend/man/hang.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/heights_per_k.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/highlight_distinct_edges.Rd |only
dendextend-0.18.3/dendextend/man/identify.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/intersect_trees.Rd | 2
dendextend-0.18.3/dendextend/man/is.dendlist.Rd | 2
dendextend-0.18.3/dendextend/man/is.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/is.hclust.Rd | 2
dendextend-0.18.3/dendextend/man/is.natural.number.Rd | 2
dendextend-0.18.3/dendextend/man/is.phylo.Rd | 2
dendextend-0.18.3/dendextend/man/is_null_list.Rd | 2
dendextend-0.18.3/dendextend/man/labels-assign.Rd | 12
dendextend-0.18.3/dendextend/man/labels_colors.Rd | 2
dendextend-0.18.3/dendextend/man/ladderize.Rd |only
dendextend-0.18.3/dendextend/man/leaf_Colors.Rd | 2
dendextend-0.18.3/dendextend/man/lowest_common_branch.Rd | 2
dendextend-0.18.3/dendextend/man/match_order_by_labels.Rd | 2
dendextend-0.18.3/dendextend/man/match_order_dendrogram_by_old_order.Rd | 2
dendextend-0.18.3/dendextend/man/na_locf.Rd | 2
dendextend-0.18.3/dendextend/man/nleaves.Rd | 6
dendextend-0.18.3/dendextend/man/nnodes.Rd | 2
dendextend-0.18.3/dendextend/man/noded_with_condition.Rd | 3
dendextend-0.18.3/dendextend/man/order.dendrogram-assign.Rd | 2
dendextend-0.18.3/dendextend/man/order.hclust.Rd | 2
dendextend-0.18.3/dendextend/man/partition_leaves.Rd |only
dendextend-0.18.3/dendextend/man/pipe.Rd | 2
dendextend-0.18.3/dendextend/man/plot_horiz.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/prune.Rd | 6
dendextend-0.18.3/dendextend/man/prune_leaf.Rd | 2
dendextend-0.18.3/dendextend/man/pvclust_show_signif.Rd | 2
dendextend-0.18.3/dendextend/man/pvclust_show_signif_gradient.Rd | 2
dendextend-0.18.3/dendextend/man/raise.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/rank_branches.Rd | 2
dendextend-0.18.3/dendextend/man/rank_order.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/rect.dendrogram.Rd | 6
dendextend-0.18.3/dendextend/man/remove_branches_edgePar.Rd | 4
dendextend-0.18.3/dendextend/man/remove_leaves_nodePar.Rd | 2
dendextend-0.18.3/dendextend/man/remove_nodes_nodePar.Rd |only
dendextend-0.18.3/dendextend/man/rllply.Rd | 2
dendextend-0.18.3/dendextend/man/rotate.Rd | 23
dendextend-0.18.3/dendextend/man/rotate_DendSer.Rd | 2
dendextend-0.18.3/dendextend/man/sample.dendrogram.Rd | 2
dendextend-0.18.3/dendextend/man/set.Rd | 7
dendextend-0.18.3/dendextend/man/shuffle.Rd | 6
dendextend-0.18.3/dendextend/man/sort_2_clusters_vectors.Rd | 2
dendextend-0.18.3/dendextend/man/sort_dist_mat.Rd | 2
dendextend-0.18.3/dendextend/man/sort_levels_values.Rd | 2
dendextend-0.18.3/dendextend/man/tanglegram.Rd | 7
dendextend-0.18.3/dendextend/man/theme_dendro.Rd |only
dendextend-0.18.3/dendextend/man/unbranch.Rd | 6
dendextend-0.18.3/dendextend/man/unclass_dend.Rd | 2
dendextend-0.18.3/dendextend/man/untangle.Rd | 6
dendextend-0.18.3/dendextend/man/untangle_DendSer.Rd | 2
dendextend-0.18.3/dendextend/man/untangle_random_search.Rd | 2
dendextend-0.18.3/dendextend/man/untangle_step_rotate_1side.Rd | 2
dendextend-0.18.3/dendextend/man/untangle_step_rotate_2side.Rd | 2
dendextend-0.18.3/dendextend/man/which_leaf.Rd | 3
dendextend-0.18.3/dendextend/man/which_node.Rd |only
dendextend-0.18.3/dendextend/tests/test-all.R |only
dendextend-0.18.3/dendextend/vignettes/introduction.Rmd | 325 ++++
163 files changed, 4069 insertions(+), 1303 deletions(-)
Title: Cluster Analysis Extended Rousseeuw et al.
Diff between cluster versions 2.0.0 dated 2015-01-29 and 2.0.1 dated 2015-01-31
Description: Cluster analysis methods. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990).
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb]
Maintainer: Martin Maechler
DESCRIPTION | 12 +++++------
MD5 | 14 ++++++-------
po/R-cluster.pot | 4 +--
po/cluster.pot | 10 ++++++---
po/update-me.sh | 5 ++--
src/pam.c | 19 +++++++++++------
tests/pam.R | 13 +++++++++---
tests/pam.Rout.save | 55 +++++++++++++++++++++++++++++-----------------------
8 files changed, 78 insertions(+), 54 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 2.1.1 dated 2014-06-02 and 2.1.3 dated 2015-01-31
Description: Extensive functions for the theory of L-moments (LMs) in addition to probability-weighted moments (PWMs), and parameter (p) estimation for numerous familiar and not-so-familiar distributions. Estimation of LMs for the same distributions is provided as are L-moment ratio diagrams. Estimation of LMs for right-tail and left-tail censoring by known or unknown threshold and also by indicator variable is available. Asymmetric trimmed LMs (TL-moments, TLMs) are supported as are numerical integrations to dynamically compute trajectories of select TLM ratios for TL-moment ratio diagram construction. LMs of residual (resid.) and reversed (rev.) resid. life are implemented along with 13 operators on quantile functions that are useful in reliability, lifetime, and survival analysis. Exact analytical bootstrap estimates of order statistics, LMs, and variances-covariances of LMs are provided. The Harri-Coble Tau34-squared Test for Normality is available. Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail censoring (RC) encompasses: Asymmetric (Asy.) Exponential (Exp.) Power [L], Asy. Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen.) Exp. Poisson [L], Gen. Extreme Value [L], Gen. Lambda [L,TL], Gen. Logistic [L), Gen. Normal [L], Gen. Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev. Gumbel [L+RC], Rice/Rician (L), Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L]. LMs have multivariate analogs; the sample L-comoments (LCMs) are implemented and might have considerable application with copulas because LCMs measure asymmetric association and higher comoments or comovements of variables.
Author: William Asquith
Maintainer: William Asquith
lmomco-2.1.1/lmomco/R/are.pargep.R |only
lmomco-2.1.3/lmomco/DESCRIPTION | 13
lmomco-2.1.3/lmomco/MD5 | 620 +++++++-------
lmomco-2.1.3/lmomco/NAMESPACE | 11
lmomco-2.1.3/lmomco/NEWS | 167 ++-
lmomco-2.1.3/lmomco/R/Lcomoment.Lk12.R | 24
lmomco-2.1.3/lmomco/R/Lcomoment.Wk.R | 21
lmomco-2.1.3/lmomco/R/add.lmomco.axis.R | 2
lmomco-2.1.3/lmomco/R/are.par.valid.R | 3
lmomco-2.1.3/lmomco/R/are.paraep4.valid.R | 7
lmomco-2.1.3/lmomco/R/are.parcau.valid.R | 4
lmomco-2.1.3/lmomco/R/are.paremu.valid.R | 8
lmomco-2.1.3/lmomco/R/are.parexp.valid.R | 4
lmomco-2.1.3/lmomco/R/are.pargam.valid.R | 10
lmomco-2.1.3/lmomco/R/are.pargep.valid.R |only
lmomco-2.1.3/lmomco/R/are.pargev.valid.R | 10
lmomco-2.1.3/lmomco/R/are.pargld.valid.R | 1
lmomco-2.1.3/lmomco/R/are.parglo.valid.R | 10
lmomco-2.1.3/lmomco/R/are.pargno.valid.R | 4
lmomco-2.1.3/lmomco/R/are.pargov.valid.R | 6
lmomco-2.1.3/lmomco/R/are.pargpa.valid.R | 10
lmomco-2.1.3/lmomco/R/are.pargum.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parkap.valid.R | 8
lmomco-2.1.3/lmomco/R/are.parkmu.valid.R | 6
lmomco-2.1.3/lmomco/R/are.parkur.valid.R | 15
lmomco-2.1.3/lmomco/R/are.parlap.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parlmrq.valid.R | 2
lmomco-2.1.3/lmomco/R/are.parln3.valid.R | 5
lmomco-2.1.3/lmomco/R/are.parnor.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parpe3.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parray.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parrevgum.valid.R | 2
lmomco-2.1.3/lmomco/R/are.parrice.valid.R | 6
lmomco-2.1.3/lmomco/R/are.parsla.valid.R | 4
lmomco-2.1.3/lmomco/R/are.parst3.valid.R | 6
lmomco-2.1.3/lmomco/R/are.partexp.valid.R | 2
lmomco-2.1.3/lmomco/R/are.partri.valid.R |only
lmomco-2.1.3/lmomco/R/are.parwak.valid.R | 1
lmomco-2.1.3/lmomco/R/are.parwei.valid.R | 9
lmomco-2.1.3/lmomco/R/cdfaep4.R | 4
lmomco-2.1.3/lmomco/R/cdfcau.R | 2
lmomco-2.1.3/lmomco/R/cdfemu.R | 2
lmomco-2.1.3/lmomco/R/cdfexp.R | 2
lmomco-2.1.3/lmomco/R/cdfgam.R | 2
lmomco-2.1.3/lmomco/R/cdfgev.R | 2
lmomco-2.1.3/lmomco/R/cdfgld.R | 2
lmomco-2.1.3/lmomco/R/cdfglo.R | 2
lmomco-2.1.3/lmomco/R/cdfgno.R | 2
lmomco-2.1.3/lmomco/R/cdfgov.R | 2
lmomco-2.1.3/lmomco/R/cdfgpa.R | 2
lmomco-2.1.3/lmomco/R/cdfgum.R | 2
lmomco-2.1.3/lmomco/R/cdfkap.R | 2
lmomco-2.1.3/lmomco/R/cdfkmu.R | 2
lmomco-2.1.3/lmomco/R/cdfkur.R | 6
lmomco-2.1.3/lmomco/R/cdflap.R | 2
lmomco-2.1.3/lmomco/R/cdfln3.R | 2
lmomco-2.1.3/lmomco/R/cdfnor.R | 2
lmomco-2.1.3/lmomco/R/cdfpe3.R | 2
lmomco-2.1.3/lmomco/R/cdfray.R | 2
lmomco-2.1.3/lmomco/R/cdfrevgum.R | 2
lmomco-2.1.3/lmomco/R/cdfrice.R | 2
lmomco-2.1.3/lmomco/R/cdfsla.R | 2
lmomco-2.1.3/lmomco/R/cdftri.R |only
lmomco-2.1.3/lmomco/R/cdfwak.R | 2
lmomco-2.1.3/lmomco/R/dat2bernquaf.R |only
lmomco-2.1.3/lmomco/R/dist.list.R | 4
lmomco-2.1.3/lmomco/R/freq.curve.all.R | 109 +-
lmomco-2.1.3/lmomco/R/genci.R | 24
lmomco-2.1.3/lmomco/R/headrick.sheng.lalpha.R |only
lmomco-2.1.3/lmomco/R/is.tri.R |only
lmomco-2.1.3/lmomco/R/lmom2par.R | 13
lmomco-2.1.3/lmomco/R/lmomgpaRC.R | 28
lmomco-2.1.3/lmomco/R/lmomtri.R |only
lmomco-2.1.3/lmomco/R/par2cdf.R | 3
lmomco-2.1.3/lmomco/R/par2cdf2.R | 4
lmomco-2.1.3/lmomco/R/par2pdf.R | 3
lmomco-2.1.3/lmomco/R/par2qua.R | 3
lmomco-2.1.3/lmomco/R/paremu.R | 24
lmomco-2.1.3/lmomco/R/partri.R |only
lmomco-2.1.3/lmomco/R/pdfaep4.R | 2
lmomco-2.1.3/lmomco/R/pdfcau.R | 2
lmomco-2.1.3/lmomco/R/pdfexp.R | 2
lmomco-2.1.3/lmomco/R/pdfgam.R | 2
lmomco-2.1.3/lmomco/R/pdfgev.R | 2
lmomco-2.1.3/lmomco/R/pdfgld.R | 2
lmomco-2.1.3/lmomco/R/pdfglo.R | 2
lmomco-2.1.3/lmomco/R/pdfgno.R | 2
lmomco-2.1.3/lmomco/R/pdfgov.R | 2
lmomco-2.1.3/lmomco/R/pdfgpa.R | 2
lmomco-2.1.3/lmomco/R/pdfgum.R | 2
lmomco-2.1.3/lmomco/R/pdfkap.R | 2
lmomco-2.1.3/lmomco/R/pdfkur.R | 12
lmomco-2.1.3/lmomco/R/pdflap.R | 2
lmomco-2.1.3/lmomco/R/pdflmrq.R | 2
lmomco-2.1.3/lmomco/R/pdfnor.R | 2
lmomco-2.1.3/lmomco/R/pdfpe3.R | 2
lmomco-2.1.3/lmomco/R/pdfray.R | 2
lmomco-2.1.3/lmomco/R/pdfrevgum.R | 2
lmomco-2.1.3/lmomco/R/pdfrice.R | 2
lmomco-2.1.3/lmomco/R/pdfsla.R | 2
lmomco-2.1.3/lmomco/R/pdftri.R |only
lmomco-2.1.3/lmomco/R/pdfwak.R | 16
lmomco-2.1.3/lmomco/R/pmoms.R | 4
lmomco-2.1.3/lmomco/R/prettydist.R | 2
lmomco-2.1.3/lmomco/R/pwmRC.R | 2
lmomco-2.1.3/lmomco/R/quacau.R | 5
lmomco-2.1.3/lmomco/R/quaemu.R | 2
lmomco-2.1.3/lmomco/R/quaexp.R | 5
lmomco-2.1.3/lmomco/R/quagam.R | 5
lmomco-2.1.3/lmomco/R/quagev.R | 5
lmomco-2.1.3/lmomco/R/quagld.R | 5
lmomco-2.1.3/lmomco/R/quaglo.R | 5
lmomco-2.1.3/lmomco/R/quagno.R | 5
lmomco-2.1.3/lmomco/R/quagov.R | 6
lmomco-2.1.3/lmomco/R/quagpa.R | 5
lmomco-2.1.3/lmomco/R/quagum.R | 5
lmomco-2.1.3/lmomco/R/quakap.R | 7
lmomco-2.1.3/lmomco/R/quakmu.R | 2
lmomco-2.1.3/lmomco/R/quakur.R | 5
lmomco-2.1.3/lmomco/R/qualap.R | 5
lmomco-2.1.3/lmomco/R/qualn3.R | 2
lmomco-2.1.3/lmomco/R/quanor.R | 2
lmomco-2.1.3/lmomco/R/quape3.R | 5
lmomco-2.1.3/lmomco/R/quaray.R | 5
lmomco-2.1.3/lmomco/R/quarevgum.R | 5
lmomco-2.1.3/lmomco/R/quarice.R | 2
lmomco-2.1.3/lmomco/R/quasla.R | 6
lmomco-2.1.3/lmomco/R/quatexp.R | 7
lmomco-2.1.3/lmomco/R/quatri.R |only
lmomco-2.1.3/lmomco/R/quawak.R | 18
lmomco-2.1.3/lmomco/R/supdist.R |only
lmomco-2.1.3/lmomco/R/theoLmoms.max.ostat.R | 24
lmomco-2.1.3/lmomco/R/theoTLmoms.R | 2
lmomco-2.1.3/lmomco/R/vec2par.R | 4
lmomco-2.1.3/lmomco/R/z.par2cdf.R | 2
lmomco-2.1.3/lmomco/R/z.par2qua.R | 2
lmomco-2.1.3/lmomco/README | 2
lmomco-2.1.3/lmomco/inst/ACKNOWLEDGEMENTS |only
lmomco-2.1.3/lmomco/inst/CITATION | 14
lmomco-2.1.3/lmomco/inst/ERRATA_FOR_ISBN9781463508418.txt | 9
lmomco-2.1.3/lmomco/man/Apwm2BpwmRC.Rd | 4
lmomco-2.1.3/lmomco/man/Bpwm2ApwmRC.Rd | 4
lmomco-2.1.3/lmomco/man/IRSrefunds.by.state.Rd | 3
lmomco-2.1.3/lmomco/man/Lcomoment.Lk12.Rd | 22
lmomco-2.1.3/lmomco/man/Lcomoment.Wk.Rd | 5
lmomco-2.1.3/lmomco/man/Lcomoment.coefficients.Rd | 7
lmomco-2.1.3/lmomco/man/Lcomoment.correlation.Rd | 41
lmomco-2.1.3/lmomco/man/Lcomoment.matrix.Rd | 10
lmomco-2.1.3/lmomco/man/TLmom.Rd | 2
lmomco-2.1.3/lmomco/man/TX38lgtrmFlow.Rd | 10
lmomco-2.1.3/lmomco/man/are.par.valid.Rd | 4
lmomco-2.1.3/lmomco/man/are.paraep4.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parcau.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.paremu.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parexp.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargam.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargep.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargev.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargld.valid.Rd | 10
lmomco-2.1.3/lmomco/man/are.parglo.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargno.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargov.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargpa.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.pargum.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parkap.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parkmu.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parkur.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parlap.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parlmrq.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parln3.valid.Rd | 4
lmomco-2.1.3/lmomco/man/are.parnor.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parpe3.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parray.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parrevgum.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parrice.valid.Rd | 4
lmomco-2.1.3/lmomco/man/are.parsla.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parst3.valid.Rd | 4
lmomco-2.1.3/lmomco/man/are.partexp.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.partri.valid.Rd |only
lmomco-2.1.3/lmomco/man/are.parwak.valid.Rd | 2
lmomco-2.1.3/lmomco/man/are.parwei.valid.Rd | 2
lmomco-2.1.3/lmomco/man/bfrlmomco.Rd | 2
lmomco-2.1.3/lmomco/man/cdf2lmom.Rd | 2
lmomco-2.1.3/lmomco/man/cdf2lmoms.Rd | 2
lmomco-2.1.3/lmomco/man/cdfemu.Rd | 3
lmomco-2.1.3/lmomco/man/cdfexp.Rd | 2
lmomco-2.1.3/lmomco/man/cdfgam.Rd | 2
lmomco-2.1.3/lmomco/man/cdfgno.Rd | 2
lmomco-2.1.3/lmomco/man/cdfkmu.Rd | 16
lmomco-2.1.3/lmomco/man/cdfln3.Rd | 4
lmomco-2.1.3/lmomco/man/cdfrevgum.Rd | 2
lmomco-2.1.3/lmomco/man/cdfrice.Rd | 2
lmomco-2.1.3/lmomco/man/cdfst3.Rd | 2
lmomco-2.1.3/lmomco/man/cdftri.Rd |only
lmomco-2.1.3/lmomco/man/cdfwei.Rd | 2
lmomco-2.1.3/lmomco/man/cmlmomco.Rd | 9
lmomco-2.1.3/lmomco/man/dat2bernqua.Rd | 8
lmomco-2.1.3/lmomco/man/dat2bernquaf.Rd |only
lmomco-2.1.3/lmomco/man/dist.list.Rd | 4
lmomco-2.1.3/lmomco/man/expect.max.ostat.Rd | 4
lmomco-2.1.3/lmomco/man/fliplmoms.Rd | 38
lmomco-2.1.3/lmomco/man/flo2f.Rd | 4
lmomco-2.1.3/lmomco/man/fpds2f.Rd | 6
lmomco-2.1.3/lmomco/man/freq.curve.all.Rd | 20
lmomco-2.1.3/lmomco/man/gen.freq.curves.Rd | 16
lmomco-2.1.3/lmomco/man/genci.Rd | 2
lmomco-2.1.3/lmomco/man/gini.mean.diff.Rd | 2
lmomco-2.1.3/lmomco/man/grv2prob.Rd | 2
lmomco-2.1.3/lmomco/man/headrick.sheng.lalpha.Rd |only
lmomco-2.1.3/lmomco/man/hlmomco.Rd | 4
lmomco-2.1.3/lmomco/man/is.ln3.Rd | 2
lmomco-2.1.3/lmomco/man/is.tri.Rd |only
lmomco-2.1.3/lmomco/man/lcomoms2.Rd | 4
lmomco-2.1.3/lmomco/man/lkhlmomco.Rd | 4
lmomco-2.1.3/lmomco/man/lmom.ub.Rd | 4
lmomco-2.1.3/lmomco/man/lmom2pwm.Rd | 2
lmomco-2.1.3/lmomco/man/lmom2vec.Rd | 2
lmomco-2.1.3/lmomco/man/lmomTLgld.Rd | 6
lmomco-2.1.3/lmomco/man/lmomcau.Rd | 2
lmomco-2.1.3/lmomco/man/lmomco-package.Rd |only
lmomco-2.1.3/lmomco/man/lmomcoBook.Rd | 4
lmomco-2.1.3/lmomco/man/lmomemu.Rd | 2
lmomco-2.1.3/lmomco/man/lmomexp.Rd | 2
lmomco-2.1.3/lmomco/man/lmomgep.Rd | 2
lmomco-2.1.3/lmomco/man/lmomgno.Rd | 4
lmomco-2.1.3/lmomco/man/lmomln3.Rd | 4
lmomco-2.1.3/lmomco/man/lmompe3.Rd | 2
lmomco-2.1.3/lmomco/man/lmomrevgum.Rd | 2
lmomco-2.1.3/lmomco/man/lmomrice.Rd | 4
lmomco-2.1.3/lmomco/man/lmoms.Rd | 4
lmomco-2.1.3/lmomco/man/lmoms.bernstein.Rd | 4
lmomco-2.1.3/lmomco/man/lmoms.bootbarvar.Rd | 2
lmomco-2.1.3/lmomco/man/lmomsRCmark.Rd | 6
lmomco-2.1.3/lmomco/man/lmomsla.Rd | 2
lmomco-2.1.3/lmomco/man/lmomst3.Rd | 2
lmomco-2.1.3/lmomco/man/lmomtri.Rd |only
lmomco-2.1.3/lmomco/man/lmrdia.Rd | 2
lmomco-2.1.3/lmomco/man/lmrdiscord.Rd | 2
lmomco-2.1.3/lmomco/man/lrv2prob.Rd | 4
lmomco-2.1.3/lmomco/man/lrzlmomco.Rd | 2
lmomco-2.1.3/lmomco/man/par2cdf2.Rd | 4
lmomco-2.1.3/lmomco/man/par2qua.Rd | 2
lmomco-2.1.3/lmomco/man/par2qua2.Rd | 2
lmomco-2.1.3/lmomco/man/parTLgld.Rd | 4
lmomco-2.1.3/lmomco/man/paraep4.Rd | 8
lmomco-2.1.3/lmomco/man/paremu.Rd | 2
lmomco-2.1.3/lmomco/man/pargep.Rd | 2
lmomco-2.1.3/lmomco/man/pargld.Rd | 6
lmomco-2.1.3/lmomco/man/pargno.Rd | 4
lmomco-2.1.3/lmomco/man/pargov.Rd | 2
lmomco-2.1.3/lmomco/man/pargpa.Rd | 2
lmomco-2.1.3/lmomco/man/parkmu.Rd | 2
lmomco-2.1.3/lmomco/man/parlap.Rd | 6
lmomco-2.1.3/lmomco/man/parln3.Rd | 4
lmomco-2.1.3/lmomco/man/parrevgum.Rd | 2
lmomco-2.1.3/lmomco/man/parrice.Rd | 2
lmomco-2.1.3/lmomco/man/parst3.Rd | 2
lmomco-2.1.3/lmomco/man/partri.Rd |only
lmomco-2.1.3/lmomco/man/pdfcau.Rd | 2
lmomco-2.1.3/lmomco/man/pdfexp.Rd | 2
lmomco-2.1.3/lmomco/man/pdfgep.Rd | 2
lmomco-2.1.3/lmomco/man/pdfgno.Rd | 2
lmomco-2.1.3/lmomco/man/pdfgpa.Rd | 2
lmomco-2.1.3/lmomco/man/pdfgum.Rd | 4
lmomco-2.1.3/lmomco/man/pdfln3.Rd | 4
lmomco-2.1.3/lmomco/man/pdfnor.Rd | 3
lmomco-2.1.3/lmomco/man/pdfpe3.Rd | 2
lmomco-2.1.3/lmomco/man/pdfrevgum.Rd | 2
lmomco-2.1.3/lmomco/man/pdfrice.Rd | 2
lmomco-2.1.3/lmomco/man/pdfst3.Rd | 2
lmomco-2.1.3/lmomco/man/pdftri.Rd |only
lmomco-2.1.3/lmomco/man/pfactor.bernstein.Rd | 2
lmomco-2.1.3/lmomco/man/plotlmrdia.Rd | 8
lmomco-2.1.3/lmomco/man/plotradarlmr.Rd | 2
lmomco-2.1.3/lmomco/man/pmoms.Rd | 6
lmomco-2.1.3/lmomco/man/pp.Rd | 2
lmomco-2.1.3/lmomco/man/prettydist.Rd | 3
lmomco-2.1.3/lmomco/man/prob2lrv.Rd | 4
lmomco-2.1.3/lmomco/man/pwm.Rd | 6
lmomco-2.1.3/lmomco/man/pwm.beta2alpha.Rd | 2
lmomco-2.1.3/lmomco/man/pwm.gev.Rd | 2
lmomco-2.1.3/lmomco/man/pwm.pp.Rd | 2
lmomco-2.1.3/lmomco/man/pwm.ub.Rd | 8
lmomco-2.1.3/lmomco/man/pwm2lmom.Rd | 39
lmomco-2.1.3/lmomco/man/pwmLC.Rd | 8
lmomco-2.1.3/lmomco/man/pwmRC.Rd | 4
lmomco-2.1.3/lmomco/man/qlmomco.Rd | 2
lmomco-2.1.3/lmomco/man/qua2ci.Rd | 4
lmomco-2.1.3/lmomco/man/quagam.Rd | 2
lmomco-2.1.3/lmomco/man/quagep.Rd | 5
lmomco-2.1.3/lmomco/man/quagld.Rd | 2
lmomco-2.1.3/lmomco/man/quagno.Rd | 4
lmomco-2.1.3/lmomco/man/quagov.Rd | 2
lmomco-2.1.3/lmomco/man/qualn3.Rd | 4
lmomco-2.1.3/lmomco/man/quarevgum.Rd | 2
lmomco-2.1.3/lmomco/man/quarice.Rd | 2
lmomco-2.1.3/lmomco/man/quast3.Rd | 2
lmomco-2.1.3/lmomco/man/quatri.Rd |only
lmomco-2.1.3/lmomco/man/ralmomco.Rd | 4
lmomco-2.1.3/lmomco/man/reslife.lmoms.Rd | 4
lmomco-2.1.3/lmomco/man/riglmomco.Rd | 6
lmomco-2.1.3/lmomco/man/rmlmomco.Rd | 10
lmomco-2.1.3/lmomco/man/rmvarlmomco.Rd | 4
lmomco-2.1.3/lmomco/man/rralmomco.Rd | 4
lmomco-2.1.3/lmomco/man/rreslife.lmoms.Rd | 2
lmomco-2.1.3/lmomco/man/rrmlmomco.Rd | 6
lmomco-2.1.3/lmomco/man/rrmvarlmomco.Rd | 2
lmomco-2.1.3/lmomco/man/sentiv.curve.Rd | 10
lmomco-2.1.3/lmomco/man/stttlmomco.Rd | 8
lmomco-2.1.3/lmomco/man/supdist.Rd |only
lmomco-2.1.3/lmomco/man/tau34sq.normtest.Rd | 4
lmomco-2.1.3/lmomco/man/theoLmoms.max.ostat.Rd | 14
lmomco-2.1.3/lmomco/man/theoTLmoms.Rd | 3
lmomco-2.1.3/lmomco/man/tlmrgev.Rd | 2
lmomco-2.1.3/lmomco/man/tlmrgno.Rd | 2
lmomco-2.1.3/lmomco/man/tlmrln3.Rd | 5
lmomco-2.1.3/lmomco/man/tttlmomco.Rd | 8
lmomco-2.1.3/lmomco/man/vec2lmom.Rd | 4
lmomco-2.1.3/lmomco/man/vec2par.Rd | 2
lmomco-2.1.3/lmomco/man/vec2pwm.Rd | 4
lmomco-2.1.3/lmomco/man/x2xlo.Rd | 6
lmomco-2.1.3/lmomco/man/z.par2cdf.Rd | 2
lmomco-2.1.3/lmomco/man/z.par2qua.Rd | 2
323 files changed, 1272 insertions(+), 1037 deletions(-)
Title: Model Selection and Post-hoc Analysis for (G)LMER Models
Diff between LMERConvenienceFunctions versions 2.5 dated 2013-12-14 and 2.10 dated 2015-01-31
More information about LMERConvenienceFunctions at CRAN
Description: The main function of the package is to perform backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. The data to run examples is contained in package LCF_data.
Author: Antoine Tremblay, Dalhousie University, and Johannes Ransijn, University of Copenhagen
Maintainer: "Antoine Tremblay, Dalhousie University"
DESCRIPTION | 16 ++++++---------
MD5 | 31 +++++++++++++++--------------
NAMESPACE | 8 ++++++-
NEWS | 7 ++++++
R/adjust.se.R |only
R/ffRanefLMER.fnc.R | 34 ++++++++++++++++----------------
R/mcposthoc.fnc.R | 3 --
R/plotDensity3d.fnc.R | 5 ----
R/plotLMER3d.fnc.R | 13 +-----------
R/plotRaw3d.fnc.R | 13 +-----------
man/LMERConvenienceFunctions-package.Rd | 22 ++++++++++----------
man/bfFixefLMER_F.fnc.Rd | 3 --
man/ffRanefLMER.fnc.Rd | 1
man/fitLMER.fnc.Rd | 3 +-
man/pamer.fnc.Rd | 3 --
man/plotLMER3d.fnc.Rd | 2 -
man/relLik.Rd | 5 ++++
17 files changed, 80 insertions(+), 89 deletions(-)
Permanent link
Title: Tools for creating D3 JavaScript network, tree, dendrogram, and
Sankey graphs from R
Diff between d3Network versions 0.5.1 dated 2014-07-13 and 0.5.2.1 dated 2015-01-31
Description: This packages is intended to make it easy to create D3 JavaScript
network, tree, dendrogram, and Sankey graphs from R using data frames.
!!! NOTE: Active development has moved to the networkD3 package. !!!
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
d3Network-0.5.1/d3Network/README.md |only
d3Network-0.5.1/d3Network/data/MisLinks.tab.gz |only
d3Network-0.5.1/d3Network/data/MisNodes.tab.gz |only
d3Network-0.5.2.1/d3Network/DESCRIPTION | 9 +++++----
d3Network-0.5.2.1/d3Network/MD5 | 11 +++++------
d3Network-0.5.2.1/d3Network/NEWS | 9 +++++++++
d3Network-0.5.2.1/d3Network/R/templates.R | 6 +++---
d3Network-0.5.2.1/d3Network/data/MisLinks.tab |only
d3Network-0.5.2.1/d3Network/data/MisNodes.tab |only
9 files changed, 22 insertions(+), 13 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Diff between DataCombine versions 0.2.7.1 dated 2014-12-08 and 0.2.8.3 dated 2015-01-31
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 24 ++++++----
MD5 | 65 +++++++++++++++-------------
NAMESPACE | 6 ++
NEWS | 32 +++++++++++++-
R/DropNA.R | 2
R/FillIn.R | 106 ++++++++++++++++++++++++++++++++++++++++++-----
R/PercChange.R | 55 +++++++++++++++---------
R/TimeFill.R | 42 +++++++++---------
R/internals.R | 6 +-
R/slide.R | 119 ++++++++++++++++++++++++++++-------------------------
R/utils.R | 73 ++++++++++++++++++++++----------
README.md | 7 ++-
man/CountSpell.Rd | 10 ++--
man/DropNA.Rd | 3 -
man/FillDown.Rd | 16 +++++--
man/FillIn.Rd | 3 -
man/FindReplace.Rd | 32 +++++++++-----
man/InsertRow.Rd | 3 -
man/MoveFront.Rd | 3 -
man/NaVar.Rd | 3 -
man/PercChange.Rd | 36 +++++++++++-----
man/SpreadDummy.Rd | 8 +--
man/StartEnd.Rd | 10 ++--
man/TimeExpand.Rd |only
man/TimeFill.Rd | 3 -
man/VarDrop.Rd | 3 -
man/dMerge.Rd | 31 +++++++++----
man/grepl.sub.Rd | 3 -
man/rmExcept.Rd | 3 -
man/shift.Rd | 3 -
man/shiftMA.Rd | 3 -
man/slide.Rd | 10 +++-
man/slideMA.Rd | 9 ++--
tests |only
34 files changed, 487 insertions(+), 245 deletions(-)
Title: Bayesian Analysis of Censored Regression Models Under Scale
Mixture of Skew Normal Distributions
Diff between BayesCR versions 1.0 dated 2013-11-02 and 2.0 dated 2015-01-31
Description: Propose a parametric fit for censored linear regression models based on SMSN distributions, from a Bayesian perspective. Also, generates SMSN random variables.
Author: Aldo M. Garay
Maintainer: Aldo M. Garay
BayesCR-1.0/BayesCR/R/GibbsTruncSMN.r |only
BayesCR-1.0/BayesCR/R/Utilitarios.r |only
BayesCR-1.0/BayesCR/data/wage.rate.txt.gz |only
BayesCR-1.0/BayesCR/man/wage.rate.Rd |only
BayesCR-2.0/BayesCR/DESCRIPTION | 24 -
BayesCR-2.0/BayesCR/MD5 | 22 -
BayesCR-2.0/BayesCR/NAMESPACE | 13
BayesCR-2.0/BayesCR/R/Bayes.CR.r | 467 ++++++++++++++++++++---------
BayesCR-2.0/BayesCR/R/Criterios.R |only
BayesCR-2.0/BayesCR/R/GibbsAssim.R |only
BayesCR-2.0/BayesCR/R/GibbsSim.r |only
BayesCR-2.0/BayesCR/R/SMSNloglik.r |only
BayesCR-2.0/BayesCR/R/UtilitariosAssim.R |only
BayesCR-2.0/BayesCR/R/UtilitariosSim.r |only
BayesCR-2.0/BayesCR/R/gerarSMSN.R |only
BayesCR-2.0/BayesCR/data/motorettes.txt.gz |only
BayesCR-2.0/BayesCR/man/Bayes.CR.Rd | 56 +--
BayesCR-2.0/BayesCR/man/motorettes.Rd |only
BayesCR-2.0/BayesCR/man/rSMSN.Rd |only
19 files changed, 394 insertions(+), 188 deletions(-)
Title: A System for Embedded Scientific Computing and Reproducible
Research with R
Diff between opencpu versions 1.4.5 dated 2014-11-08 and 1.4.6 dated 2015-01-31
Description: The OpenCPU system exposes an HTTP API for embedded scientific
computing with R. This provides scalable foundations for integrating R
based analysis and visualization modules into pipelines, web applications
or big data infrastructures. The OpenCPU server can run either as a
single-user development server within the interactive R session, or as a
high performance multi-user cloud server that builds on Linux, Nginx and
rApache. The current R package forms the core of the system. When loaded
in R, it automatically initiates the single-user server and displays the
web address in the console. Visit the OpenCPU website for detailed
information and documentation on the API.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 40 +++++++++----------
MD5 | 23 +++++------
NAMESPACE | 3 -
NEWS | 8 ++-
R/httpget_object.R | 92 ++++++++++++++++++++++----------------------
R/opencpu.R | 89 +++++++++++++++++++++---------------------
R/rhttpd.R | 56 +++++++++++++++-----------
inst/CITATION |only
inst/doc/opencpu-paper.pdf |binary
inst/doc/opencpu-server.pdf |binary
man/cleanup.Rd | 3 -
man/opencpu.Rd | 5 +-
man/rhttpd.Rd | 5 +-
13 files changed, 169 insertions(+), 155 deletions(-)
More information about multiAssetOptions at CRAN
Permanent link
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Diff between wgaim versions 1.4-3 dated 2014-09-03 and 1.4-5 dated 2015-01-31
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor
Maintainer: Julian Taylor
wgaim-1.4-3/wgaim/R/wgaim7.R |only
wgaim-1.4-5/wgaim/DESCRIPTION | 12 ++++++------
wgaim-1.4-5/wgaim/MD5 | 20 ++++++++++----------
wgaim-1.4-5/wgaim/NAMESPACE | 1 +
wgaim-1.4-5/wgaim/R/wgaim8.R |only
wgaim-1.4-5/wgaim/data/genoCxR.RData |binary
wgaim-1.4-5/wgaim/data/genoRxK.RData |binary
wgaim-1.4-5/wgaim/data/genoSxT.RData |binary
wgaim-1.4-5/wgaim/inst/NEWS.Rd | 9 +++++++--
wgaim-1.4-5/wgaim/inst/doc/wgaim.pdf |binary
wgaim-1.4-5/wgaim/man/cross2int.Rd | 14 ++++++--------
wgaim-1.4-5/wgaim/man/wgaim.asreml.Rd | 3 +--
12 files changed, 31 insertions(+), 28 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Diff between mixlm versions 1.0.8 dated 2015-01-21 and 1.0.8.1 dated 2015-01-31
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland
mixlm-1.0.8.1/mixlm/DESCRIPTION | 8
mixlm-1.0.8.1/mixlm/MD5 | 24
mixlm-1.0.8.1/mixlm/NAMESPACE | 42
mixlm-1.0.8.1/mixlm/R/borrowed.R | 480 ++---
mixlm-1.0.8.1/mixlm/R/glm.R | 270 +--
mixlm-1.0.8.1/mixlm/R/lm.R | 877 +++++-----
mixlm-1.0.8.1/mixlm/R/mixlm.R | 41
mixlm-1.0.8.1/mixlm/R/statistics.R | 2319 +++++++++++++--------------
mixlm-1.0.8.1/mixlm/R/utilities.R | 214 +-
mixlm-1.0.8.1/mixlm/man/Anova.Rd | 26
mixlm-1.0.8.1/mixlm/man/anova.lmm.Rd |only
mixlm-1.0.8.1/mixlm/man/lm.Rd | 10
mixlm-1.0.8.1/mixlm/man/print.summary.lmm.Rd |only
mixlm-1.0.8/mixlm/man/anova.lm.Rd |only
mixlm-1.0.8/mixlm/man/print.summary.lm.Rd |only
15 files changed, 2168 insertions(+), 2143 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Diff between stylo versions 0.5.8-2 dated 2014-10-19 and 0.5.9 dated 2015-01-30
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
NEWS | 9 +++++++++
R/assign.plot.colors.R | 2 +-
R/classify.R | 3 +--
R/define.plot.area.R | 2 +-
R/draw.polygons.R | 2 +-
R/gui.classify.R | 16 ++++++++--------
R/gui.oppose.R | 3 +--
R/gui.stylo.R | 16 ++++++++--------
R/load.corpus.and.parse.R | 10 ++++++----
R/make.samples.R | 2 +-
R/oppose.R | 3 +--
R/rolling.classify.r | 1 -
R/stylo.R | 3 +--
R/stylo.default.settings.R | 6 ++----
16 files changed, 60 insertions(+), 56 deletions(-)
Title: Global Soil Information Facilities
Diff between GSIF versions 0.4-3 dated 2014-12-09 and 0.4-4 dated 2015-01-30
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut],
Bas Kempen [ctb],
Gerard Heuvelink [ctb],
Brendan Malone [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 22 ++--
MD5 | 57 +++++-----
NAMESPACE | 11 --
R/AAAA.R | 14 +-
R/AWCPTF.R | 4
R/LRI.R |only
R/MaxEnt.R | 19 +--
R/RESTSoilGrids.R | 63 ++++++------
R/WPSworldgrids.R | 141 +++++++++++++--------------
R/as.data.frame.R | 47 ++++-----
R/as.geosamples.R | 225 +++++++++++++++++++++----------------------
R/extract.list.R | 139 ++++++++++++++------------
R/fit.regModel.R | 127 +++++++++++++-----------
R/fit.vgmModel.R | 12 +-
R/fkmeans.R | 19 +--
R/predict.gstatModel.R | 63 ++++++++----
R/spline.krige.R | 10 -
R/spmultinom.R | 24 ++--
R/spsample.prob.R | 65 +++++-------
R/tile.R | 10 -
R/validate.R | 3
R/warp.R | 254 ++++++++++++++++++++++++-------------------------
data/afsp.rda |binary
man/AWCPTF.Rd | 6 -
man/ERDICM.Rd |only
man/LRI.Rd |only
man/extract.Rd | 2
man/fit.gstatModel.Rd | 1
man/landmask.Rd | 8 -
man/spsample.prob.Rd | 79 ++++++++++-----
man/tile.Rd | 15 +-
31 files changed, 764 insertions(+), 676 deletions(-)
Title: General Copula Theory and Many Utility Functions
Diff between copBasic versions 1.7.0 dated 2015-01-03 and 1.7.1 dated 2015-01-30
Description: Extensive functions for copula computations and related mathematical operations are given that are oriented around the oft cited and fundamental copula theory described by Nelsen (2006), Joe (2015), and other selected works. The lower, upper, product, and select other copulas are implemented. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, co-copula, and numerical copula density. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses; functions for copula simulation thus are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) random variates of composited copulas. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma, tail dependency, and tail order. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. The Kullback-Leibler divergence and Vuong's Procedure to support inference are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 15 ++++++++-------
4 files changed, 19 insertions(+), 14 deletions(-)
Title: A server-side file system viewer for shiny
Diff between shinyFiles versions 0.4.0 dated 2014-09-23 and 0.5.0 dated 2015-01-30
Description: Provides functionality for client-side navigation of
the server side file system in shiny apps. In case the app is running
locally this gives the user direct access to the file system without the
need to "download" files to a temporary location.
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen
DESCRIPTION | 10 +++----
MD5 | 22 ++++++++--------
NAMESPACE | 2 -
inst/example/server.R | 4 +-
inst/www/shinyFiles.js | 63 ++++++++++++++++++++++++++++++++++++++++++-----
inst/www/styles.css | 14 +++++-----
man/fileGetter.Rd | 3 +-
man/getVolumes.Rd | 3 +-
man/parseFilePaths.Rd | 3 +-
man/shinyFileChoose.Rd | 3 +-
man/shinyFilesButton.Rd | 3 +-
man/shinyFilesExample.Rd | 3 +-
12 files changed, 95 insertions(+), 38 deletions(-)
Title: Multivariate outlier detection based on robust methods
Diff between mvoutlier versions 2.0.5 dated 2014-06-23 and 2.0.6 dated 2015-01-30
Description: various methods for multivariate outlier detection.
Author: Peter Filzmoser
Maintainer: Peter Filzmoser
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/pcout.R | 2 +-
data/X.rda |binary
data/Y.rda |binary
data/bhorizon.rda |binary
data/bss.background.rda |binary
data/bssbot.rda |binary
data/bsstop.rda |binary
data/chorizon.rda |binary
data/dat.rda |binary
data/humus.rda |binary
data/kola.background.rda |binary
data/moss.rda |binary
14 files changed, 18 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-21 0.0-1
Title: Tools for Accessing Various Datasets Developed by the Foundation
SmarterPoland.pl
Diff between SmarterPoland versions 1.2 dated 2013-03-18 and 1.5 dated 2015-01-30
Description: Tools for accessing and processing datasets presented on the blog SmarterPoland.pl. Among all: functions for downloading data from eurostat database, coordinates from Google Maps and data from GUS (Central Statistical Office of Poland).
Author: Przemyslaw Biecek (Foundation SmarterPoland.pl)
Maintainer: Przemyslaw Biecek
DESCRIPTION | 16 +++---
MD5 | 42 +++++++++++-------
NAMESPACE | 13 ++++-
R/BankDanychLokalnych.R |only
R/getEurostatDictionary.R | 8 +--
R/getEurostatRCV.R | 31 ++++++-------
R/getEurostatRaw.R | 42 ++++++++++--------
R/getEurostatTOC.R | 10 ++--
R/getGoogleMapsAddress.R | 78 ++++++++++++++++-----------------
R/getMillwardBrown.R |only
R/getWeatherForecast.R |only
R/gradeStat.R |only
R/grepEurostatTOC.R | 14 +++---
R/setEurostatTOC.R | 16 +++---
data |only
man/BankDanychLokalnych.Rd |only
man/SmarterPoland-package.Rd | 99 ++++++++++++++++++++++---------------------
man/cities_lon_lat.Rd |only
man/getEurostatDictionary.Rd | 70 +++++++++++++++---------------
man/getEurostatRCV.Rd | 92 ++++++++++++++++++++-------------------
man/getEurostatRaw.Rd | 80 +++++++++++++++++++---------------
man/getEurostatTOC.Rd | 66 +++++++++++++---------------
man/getGoogleMapsAddress.Rd | 70 ++++++++++++++++--------------
man/getMillwardBrown.Rd |only
man/grepEurostatTOC.Rd | 79 +++++++++++++++++-----------------
man/weatherForecast.Rd |only
26 files changed, 436 insertions(+), 390 deletions(-)
Title: Regression Estimation and Presentation
Diff between rockchalk versions 1.8.86 dated 2014-08-13 and 1.8.91 dated 2015-01-30
Description: A collection of functions for ease of
presentation and interpretation of regression analysis.
These functions are used to produce the statistics lectures
in http://pj.freefaculty.org/guides. There
are functions to explore the effect (or lack thereof) from
"mean centering," "residual centering", and standardization.
The vignette "rockchalk" offers a fairly comprehensive overview.
The vignette "Rstyle" has advice about coding in R.
See the outreg function for a convenient way to generate
regression models for reports. For nice, easy to use pictures,
see plotSlopes, plotCurves, plotPlane.
The package title "rockchalk" refers to our school motto,
"Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson
rockchalk-1.8.86/rockchalk/man/getFocal.default.Rd |only
rockchalk-1.8.86/rockchalk/man/getFocal.factor.Rd |only
rockchalk-1.8.86/rockchalk/man/mcGraph1.Rd |only
rockchalk-1.8.86/rockchalk/man/mcGraph2.Rd |only
rockchalk-1.8.86/rockchalk/man/mcGraph3.Rd |only
rockchalk-1.8.91/rockchalk/DESCRIPTION | 10
rockchalk-1.8.91/rockchalk/MD5 | 85
rockchalk-1.8.91/rockchalk/NAMESPACE | 8
rockchalk-1.8.91/rockchalk/R/mcGraph.R | 109
rockchalk-1.8.91/rockchalk/R/outreg.R | 2
rockchalk-1.8.91/rockchalk/R/pctable.R |only
rockchalk-1.8.91/rockchalk/R/plotCurves.R | 42
rockchalk-1.8.91/rockchalk/R/plotSlopes.R | 88
rockchalk-1.8.91/rockchalk/R/predictOMatic.R | 31
rockchalk-1.8.91/rockchalk/R/residualCenter.R | 1
rockchalk-1.8.91/rockchalk/R/summarize.R | 104
rockchalk-1.8.91/rockchalk/R/utils.R | 60
rockchalk-1.8.91/rockchalk/build/vignette.rds |binary
rockchalk-1.8.91/rockchalk/data/cheating.RData |binary
rockchalk-1.8.91/rockchalk/data/religioncrime.RData |binary
rockchalk-1.8.91/rockchalk/inst/ChangeLog | 39
rockchalk-1.8.91/rockchalk/inst/NEWS | 18
rockchalk-1.8.91/rockchalk/inst/doc/Rchaeology.R | 188
rockchalk-1.8.91/rockchalk/inst/doc/Rchaeology.Rnw | 876 ++++
rockchalk-1.8.91/rockchalk/inst/doc/Rchaeology.pdf |binary
rockchalk-1.8.91/rockchalk/inst/doc/Rstyle.R | 8
rockchalk-1.8.91/rockchalk/inst/doc/Rstyle.Rnw | 3
rockchalk-1.8.91/rockchalk/inst/doc/Rstyle.pdf |binary
rockchalk-1.8.91/rockchalk/inst/doc/rockchalk.R | 52
rockchalk-1.8.91/rockchalk/inst/doc/rockchalk.Rnw | 3
rockchalk-1.8.91/rockchalk/inst/doc/rockchalk.pdf |binary
rockchalk-1.8.91/rockchalk/man/getFocal.Rd | 55
rockchalk-1.8.91/rockchalk/man/mcGraph.Rd |only
rockchalk-1.8.91/rockchalk/man/outreg.Rd | 2
rockchalk-1.8.91/rockchalk/man/pctable.Rd |only
rockchalk-1.8.91/rockchalk/man/plotCurves.Rd | 41
rockchalk-1.8.91/rockchalk/man/plotSlopes.Rd | 51
rockchalk-1.8.91/rockchalk/man/predictCI.Rd | 3
rockchalk-1.8.91/rockchalk/man/print.pctable.Rd |only
rockchalk-1.8.91/rockchalk/man/print.summary.pctable.Rd |only
rockchalk-1.8.91/rockchalk/man/summarizeFactors.Rd | 3
rockchalk-1.8.91/rockchalk/man/summary.pctable.Rd |only
rockchalk-1.8.91/rockchalk/vignettes/Rchaeology.Rnw | 876 ++++
rockchalk-1.8.91/rockchalk/vignettes/Rchaeology.lyx | 3128 +++++++++++++++-
rockchalk-1.8.91/rockchalk/vignettes/Rstyle.Rnw | 3
rockchalk-1.8.91/rockchalk/vignettes/Rstyle.lyx | 3
rockchalk-1.8.91/rockchalk/vignettes/rockchalk.Rnw | 3
rockchalk-1.8.91/rockchalk/vignettes/rockchalk.bib | 572 +-
rockchalk-1.8.91/rockchalk/vignettes/rockchalk.lyx | 3
49 files changed, 5609 insertions(+), 861 deletions(-)
Title: Posterior Predictive Checks of Coalescent Models
Diff between P2C2M versions 0.5 dated 2014-10-24 and 0.6 dated 2015-01-30
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST or *BEAST. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, the installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is required.
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl
P2C2M-0.5/P2C2M/R/calc.gtp.R |only
P2C2M-0.5/P2C2M/R/calc.ray.R |only
P2C2M-0.6/P2C2M/DESCRIPTION | 14 +-
P2C2M-0.6/P2C2M/MD5 | 55 ++++-----
P2C2M-0.6/P2C2M/NAMESPACE | 4
P2C2M-0.6/P2C2M/R/calc.coal_liu.R |only
P2C2M-0.6/P2C2M/R/calc.coal_reid.R |only
P2C2M-0.6/P2C2M/R/corehelpers.metrics.R | 18 +--
P2C2M-0.6/P2C2M/R/p2c2M.statcalc.R | 2
P2C2M-0.6/P2C2M/R/p2c2m.analyze.R | 86 +++++++-------
P2C2M-0.6/P2C2M/R/p2c2m.complete.R | 4
P2C2M-0.6/P2C2M/R/p2c2m.init.R | 2
P2C2M-0.6/P2C2M/R/p2c2m.readstarb.R | 6 -
P2C2M-0.6/P2C2M/R/rmOutlrs.R |only
P2C2M-0.6/P2C2M/R/stats.main.R | 16 --
P2C2M-0.6/P2C2M/R/stats.perGene.R | 2
P2C2M-0.6/P2C2M/R/statshelpers.cv.R | 3
P2C2M-0.6/P2C2M/R/statshelpers.diffrnce.R | 14 +-
P2C2M-0.6/P2C2M/build/vignette.rds |binary
P2C2M-0.6/P2C2M/data/viz_example_1.rda |binary
P2C2M-0.6/P2C2M/inst/CITATION | 9 -
P2C2M-0.6/P2C2M/inst/doc/P2C2M_CmdList.pdf |binary
P2C2M-0.6/P2C2M/inst/doc/P2C2M_Vignette.R | 126 +++++++++++----------
P2C2M-0.6/P2C2M/inst/doc/P2C2M_Vignette.Rnw | 161 ++++++++++++++-------------
P2C2M-0.6/P2C2M/inst/doc/P2C2M_Vignette.pdf |binary
P2C2M-0.6/P2C2M/man/P2C2M-package.Rd | 108 +++++++++---------
P2C2M-0.6/P2C2M/man/p2c2m.complete.Rd | 126 +++++++++++----------
P2C2M-0.6/P2C2M/man/sim.E.003.small.Rd | 6 -
P2C2M-0.6/P2C2M/man/viz_example.1.Rd | 6 -
P2C2M-0.6/P2C2M/man/viz_example.2.Rd | 5
P2C2M-0.6/P2C2M/vignettes/P2C2M_Vignette.Rnw | 161 ++++++++++++++-------------
31 files changed, 489 insertions(+), 445 deletions(-)
Title: Create Diagrams and Flowcharts Using R
Diff between DiagrammeR versions 0.1 dated 2015-01-09 and 0.4 dated 2015-01-30
Description: With the DiagrammeR package, you can create diagrams and flowcharts using R.
Markdown-like text is used to describe a diagram and, by doing this in R, we can also
add some R code into the mix and integrate these diagrams in the R console, through R
Markdown, and in shiny apps.
Author: knsv [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
mdaines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone
DESCRIPTION | 39 -
MD5 | 64 +
NAMESPACE | 8
R/DiagrammeR.R | 104 +--
R/grViz.R |only
R/mermaid.R |only
R/spectools.R |only
README.md | 597 ++++++++++++++++--
build/vignette.rds |binary
inst/DiagrammeR.png |only
inst/DiagrammeR_flow_diagram.png |only
inst/DiagrammeR_video_link.png |only
inst/Example_3.png |binary
inst/Example_4.png |binary
inst/Example_6.png |only
inst/Example_7a.png |only
inst/Example_7b.png |only
inst/Example_7c_neato.png |only
inst/Example_7d_twopi.png |only
inst/Example_7e_circo.png |only
inst/Example_8a.png |only
inst/Example_8b.png |only
inst/Example_8c.png |only
inst/Example_8d.png |only
inst/Example_8e.png |only
inst/Example_8f.png |only
inst/Example_9.gif |only
inst/Graphviz_substitution.png |only
inst/doc/DiagrammeR.R | 32
inst/doc/DiagrammeR.Rmd | 39 -
inst/doc/DiagrammeR.html | 73 +-
inst/examples |only
inst/htmlwidgets/DiagrammeR.js | 101 ++-
inst/htmlwidgets/DiagrammeR.yaml | 4
inst/htmlwidgets/grViz.js |only
inst/htmlwidgets/grViz.yaml |only
inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 18
inst/htmlwidgets/lib/styles |only
inst/htmlwidgets/lib/viz |only
man/DiagrammeR.Rd | 77 +-
man/DiagrammeROutput.Rd | 3
man/grViz.Rd |only
man/grVizOutput.Rd |only
man/mermaid.Rd |only
man/renderDiagrammeR.Rd | 3
man/renderGrViz.Rd |only
man/replace_in_spec.Rd |only
vignettes/DiagrammeR.Rmd | 39 -
48 files changed, 991 insertions(+), 210 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Diff between dataRetrieval versions 2.1.0 dated 2014-12-17 and 2.1.1 dated 2015-01-30
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information Services (NWIS) tools found here:
http://waterservices.usgs.gov/ Both EPA and USGS water quality data are
obtained from the Water Quality Portal found here:
http://www.waterqualitydata.us/portal.jsp
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco
DESCRIPTION | 8 +-
MD5 | 94 +++++++++++++-------------
NAMESPACE | 3
NEWS | 7 +
R/checkWQPdates.r |only
R/constructNWISURL.r | 8 +-
R/getWebServiceData.R | 2
R/importRDB1.r | 11 +--
R/importWQP.R | 14 +++
R/importWaterML1.r | 14 ++-
R/importWaterML2.r | 3
R/readNWISdata.r | 11 ++-
R/readNWISqw.r | 37 ++++++++--
R/readNWISsite.r | 5 -
R/readNWISunit.r | 12 ++-
R/readWQPdata.R | 34 ++++++---
R/readWQPqw.r | 14 ++-
R/renameColumns.R | 2
R/tabbedDataRetrievals.R | 4 -
R/whatNWISsites.R | 2
R/whatWQPsites.R | 28 +++++--
inst/doc/dataRetrieval.pdf |binary
man/checkWQPdates.Rd |only
man/constructNWISURL.Rd | 3
man/constructWQPURL.Rd | 3
man/dataRetrieval-package.Rd | 7 +
man/getWebServiceData.Rd | 5 +
man/importRDB1.Rd | 6 +
man/importWQP.Rd | 3
man/importWaterML1.Rd | 16 ++--
man/importWaterML2.Rd | 6 +
man/readNWISdata.Rd | 5 -
man/readNWISdv.Rd | 3
man/readNWISgwl.Rd | 5 +
man/readNWISmeas.Rd | 5 +
man/readNWISpCode.Rd | 3
man/readNWISpeak.Rd | 5 +
man/readNWISqw.Rd | 8 +-
man/readNWISrating.Rd | 5 +
man/readNWISsite.Rd | 6 +
man/readNWISuv.Rd | 7 +
man/readWQPdata.Rd | 10 ++
man/readWQPqw.Rd | 5 -
man/renameNWISColumns.Rd | 5 +
man/whatNWISdata.Rd | 3
man/whatNWISsites.Rd | 5 +
man/whatWQPsites.Rd | 5 -
man/zeroPad.Rd | 3
vignettes/figure/getNWIStemperaturePlot-1.pdf |binary
49 files changed, 302 insertions(+), 148 deletions(-)
Title: PCIC Implementation of Climdex Routines
Diff between climdex.pcic versions 1.1-4 dated 2014-11-19 and 1.1-5 dated 2015-01-30
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh
Maintainer: James Hiebert
CHANGELOG | 2
DESCRIPTION | 10 +-
MD5 | 100 ++++++++++++++--------------
NAMESPACE | 2
man/climdex.cdd.Rd | 3
man/climdex.csdi.Rd | 3
man/climdex.cwd.Rd | 3
man/climdex.dtr.Rd | 3
man/climdex.fd.Rd | 3
man/climdex.get.available.indices.Rd | 3
man/climdex.gsl.Rd | 3
man/climdex.id.Rd | 3
man/climdex.pcic.Rd | 3
man/climdex.prcptot.Rd | 3
man/climdex.quantile.Rd | 3
man/climdex.r10mm.Rd | 3
man/climdex.r20mm.Rd | 3
man/climdex.r95ptot.Rd | 3
man/climdex.r99ptot.Rd | 3
man/climdex.rnnmm.Rd | 3
man/climdex.rx1day.Rd | 3
man/climdex.rx5day.Rd | 3
man/climdex.sdii.Rd | 3
man/climdex.su.Rd | 3
man/climdex.tn10p.Rd | 3
man/climdex.tn90p.Rd | 3
man/climdex.tnn.Rd | 3
man/climdex.tnx.Rd | 3
man/climdex.tr.Rd | 3
man/climdex.tx10p.Rd | 3
man/climdex.tx90p.Rd | 3
man/climdex.txn.Rd | 3
man/climdex.txx.Rd | 3
man/climdex.wsdi.Rd | 3
man/climdexInput.Rd | 3
man/climdexInput.csv.Rd | 3
man/climdexInput.raw.Rd | 3
man/ec.1018935.Rd | 3
man/get.last.monthday.of.year.Rd | 3
man/get.outofbase.quantiles.Rd | 3
man/get.series.lengths.at.ends.Rd | 3
man/growing.season.length.Rd | 3
man/nday.consec.prec.max.Rd | 3
man/number.days.op.threshold.Rd | 3
man/percent.days.op.threshold.Rd | 3
man/select.blocks.gt.length.Rd | 3
man/simple.precipitation.intensity.index.Rd | 3
man/spell.length.max.Rd | 3
man/threshold.exceedance.duration.index.Rd | 3
man/total.precip.op.threshold.Rd | 3
src/zhang_running_quantile.cc | 2
51 files changed, 150 insertions(+), 104 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.1 dated 2015-01-08 and 0.2.2 dated 2015-01-30
Description: This package implements circular visualization
(http://circos.ca/) in R. Due to the natural born feature of R to draw statistical
graphics, this package can provide a more general and flexible way to
visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 10 +++++-----
MD5 | 22 +++++++++++-----------
NAMESPACE | 2 +-
NEWS | 6 ++++++
R/global.R | 2 ++
R/zzz.R | 4 ++--
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.pdf |binary
12 files changed, 27 insertions(+), 19 deletions(-)
Title: Extracting Usable Data from the Grad Cafe Results Search
Diff between brewdata versions 0.3 dated 2015-01-28 and 0.4 dated 2015-01-30
Description: Retrieves and parses graduate admissions survey data from the Grad Cafe website (http://thegradcafe.com).
Author: Nathan Welch
Maintainer: Nathan Welch
DESCRIPTION | 8 +++----
MD5 | 20 +++++++++++--------
R/brewdata.R | 47 +--------------------------------------------
R/getGradCafeData.R |only
R/getMaxPages.R |only
man/brewdata-package.Rd | 4 +--
man/brewdata.Rd | 13 +++++++-----
man/findScorePercentile.Rd | 3 +-
man/getGradCafeData.Rd |only
man/getMaxPages.Rd |only
man/parseResults.Rd | 3 +-
man/parseSchools.Rd | 3 +-
man/translateScore.Rd | 3 +-
13 files changed, 36 insertions(+), 68 deletions(-)
Title: Analysing equity portfolios
Diff between portfolio versions 0.4-6 dated 2013-07-09 and 0.4-7 dated 2015-01-29
Description: Classes for analysing and implementing equity portfolios.
Author: Jeff Enos
Maintainer: Daniel Gerlanc
portfolio-0.4-6/portfolio/portfolio.Rproj |only
portfolio-0.4-7/portfolio/DESCRIPTION | 9 +++--
portfolio-0.4-7/portfolio/MD5 | 24 +++++++--------
portfolio-0.4-7/portfolio/NAMESPACE | 21 ++++++++++++-
portfolio-0.4-7/portfolio/R/AllClasses.R | 2 -
portfolio-0.4-7/portfolio/R/contribution.R | 2 -
portfolio-0.4-7/portfolio/R/exposure.R | 2 -
portfolio-0.4-7/portfolio/R/matchedPortfolioCollection.R | 2 -
portfolio-0.4-7/portfolio/R/portfolio.R | 2 -
portfolio-0.4-7/portfolio/R/tradelist.R | 14 ++++----
portfolio-0.4-7/portfolio/build |only
portfolio-0.4-7/portfolio/data/assay.RData |binary
portfolio-0.4-7/portfolio/data/dow.jan.2005.RData |binary
portfolio-0.4-7/portfolio/data/global.2004.RData |binary
14 files changed, 48 insertions(+), 30 deletions(-)
Title: Estimation in Adaptive Group Sequential Trials
Diff between AGSDest versions 2.1 dated 2013-11-06 and 2.2 dated 2015-01-29
Description: Calculation of repeated confidence intervals as well as confidence
intervals based on the stage-wise ordering in group sequential designs and
adaptive group sequential designs. For adaptive group sequential designs
the confidence intervals are based on the conditional rejection probability
principle. Currently the procedures do not support the use of futility
boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner
AGSDest-2.1/AGSDest/R/A.R |only
AGSDest-2.1/AGSDest/R/CO.R |only
AGSDest-2.1/AGSDest/R/P.r.ad.R |only
AGSDest-2.1/AGSDest/R/P.r.gsd.R |only
AGSDest-2.1/AGSDest/R/P.so.ad.R |only
AGSDest-2.1/AGSDest/R/P.so.gsd.R |only
AGSDest-2.1/AGSDest/R/as.AGST.R |only
AGSDest-2.1/AGSDest/R/as.GST.R |only
AGSDest-2.1/AGSDest/R/bh.R |only
AGSDest-2.1/AGSDest/R/cb.r.ad.R |only
AGSDest-2.1/AGSDest/R/cb.r.gsd.R |only
AGSDest-2.1/AGSDest/R/cb.so.ad.R |only
AGSDest-2.1/AGSDest/R/cb.so.gsd.R |only
AGSDest-2.1/AGSDest/R/cer.r.R |only
AGSDest-2.1/AGSDest/R/cerr.R |only
AGSDest-2.1/AGSDest/R/comp.alab.R |only
AGSDest-2.1/AGSDest/R/comp.als.R |only
AGSDest-2.1/AGSDest/R/comp.sT.R |only
AGSDest-2.1/AGSDest/R/comp.z1.R |only
AGSDest-2.1/AGSDest/R/comp.z2.R |only
AGSDest-2.1/AGSDest/R/compBounds.R |only
AGSDest-2.1/AGSDest/R/j.alab.R |only
AGSDest-2.1/AGSDest/R/j.als.R |only
AGSDest-2.1/AGSDest/R/plan.GST.R |only
AGSDest-2.1/AGSDest/R/plot.AGSTobj.R |only
AGSDest-2.1/AGSDest/R/plot.GSTobj.R |only
AGSDest-2.1/AGSDest/R/print.AGSTobj.R |only
AGSDest-2.1/AGSDest/R/print.GSTobj.R |only
AGSDest-2.1/AGSDest/R/print.summary.AGSTobj.R |only
AGSDest-2.1/AGSDest/R/print.summary.GSTobj.R |only
AGSDest-2.1/AGSDest/R/pvalue.r |only
AGSDest-2.1/AGSDest/R/rCER.R |only
AGSDest-2.1/AGSDest/R/rnorm..R |only
AGSDest-2.1/AGSDest/R/summary.AGSTobj.R |only
AGSDest-2.1/AGSDest/R/summary.GSTobj.R |only
AGSDest-2.1/AGSDest/R/tIerr.R |only
AGSDest-2.1/AGSDest/R/typeIerr.r |only
AGSDest-2.1/AGSDest/man/AGSDest-package.Rd |only
AGSDest-2.2/AGSDest/DESCRIPTION | 19
AGSDest-2.2/AGSDest/MD5 | 98 +---
AGSDest-2.2/AGSDest/NAMESPACE | 59 +-
AGSDest-2.2/AGSDest/R/AGSDest.R |only
AGSDest-2.2/AGSDest/R/AGSTobj.R | 427 +++++++++++++++++++++
AGSDest-2.2/AGSDest/R/GSTobj.R | 515 +++++++++++++++++++++++++-
AGSDest-2.2/AGSDest/R/adapt.R | 153 +++++--
AGSDest-2.2/AGSDest/R/cb.R |only
AGSDest-2.2/AGSDest/R/cer.R | 89 ++++
AGSDest-2.2/AGSDest/R/comp.R |only
AGSDest-2.2/AGSDest/R/cp.R | 23 +
AGSDest-2.2/AGSDest/R/pbounds.R | 21 -
AGSDest-2.2/AGSDest/R/pvalue.R |only
AGSDest-2.2/AGSDest/R/seqconfint.R | 231 ++++++++---
AGSDest-2.2/AGSDest/R/seqmon.R | 152 ++++++-
AGSDest-2.2/AGSDest/R/sword.R | 19
AGSDest-2.2/AGSDest/R/typeIerr.R |only
AGSDest-2.2/AGSDest/build/vignette.rds |binary
AGSDest-2.2/AGSDest/inst/doc/vignette.R | 28 -
AGSDest-2.2/AGSDest/inst/doc/vignette.Rnw | 228 +++++------
AGSDest-2.2/AGSDest/inst/doc/vignette.pdf |binary
AGSDest-2.2/AGSDest/man/AGSDest.Rd |only
AGSDest-2.2/AGSDest/man/AGSTobj.Rd | 285 ++++++--------
AGSDest-2.2/AGSDest/man/GSTobj.Rd | 231 +++++------
AGSDest-2.2/AGSDest/man/adapt.Rd | 117 +++--
AGSDest-2.2/AGSDest/man/as.AGST.Rd | 81 ++--
AGSDest-2.2/AGSDest/man/as.GST.Rd | 61 +--
AGSDest-2.2/AGSDest/man/cer.Rd | 69 +--
AGSDest-2.2/AGSDest/man/cp.Rd | 42 +-
AGSDest-2.2/AGSDest/man/plan.GST.Rd | 137 +++---
AGSDest-2.2/AGSDest/man/pvalue.Rd | 250 ++++++------
AGSDest-2.2/AGSDest/man/seqconfint.Rd | 162 ++++----
AGSDest-2.2/AGSDest/man/typeIerr.Rd | 73 +--
AGSDest-2.2/AGSDest/vignettes/vignette.Rnw | 228 +++++------
72 files changed, 2492 insertions(+), 1306 deletions(-)
Title: Statistical Matching
Diff between StatMatch versions 1.2.2 dated 2014-06-19 and 1.2.3 dated 2015-01-29
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio
DESCRIPTION | 16 +++---
MD5 | 38 +++++++-------
NAMESPACE | 5 +
NEWS | 2
R/Fbwidths.by.x.R | 14 +++--
R/Frechet.bounds.cat.R | 11 ++--
R/NND.hotdeck.R | 2
R/RANDwNND.hotdeck.r | 4 -
R/mixed.mtc.R | 2
R/rankNND_hotdeck.R | 2
build/vignette.rds |binary
inst/doc/Statistical_Matching_with_StatMatch.R | 56 +++++++++++-----------
inst/doc/Statistical_Matching_with_StatMatch.Rnw | 19 ++++---
inst/doc/Statistical_Matching_with_StatMatch.pdf |binary
man/Fbwidths.by.x.Rd | 21 +++-----
man/Frechet.bounds.cat.Rd | 6 +-
man/NND.hotdeck.Rd | 13 -----
man/StatMatch-package.Rd | 2
man/mixed.mtc.Rd | 1
vignettes/Statistical_Matching_with_StatMatch.Rnw | 19 ++++---
20 files changed, 114 insertions(+), 119 deletions(-)
Title: Tools for Biometry and Applied Statistics in Agricultural
Science
Diff between biotools versions 1.2 dated 2014-05-25 and 2.0 dated 2015-01-29
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm),
discriminant analysis and path analysis (standard and under collinearity), as well as some
useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva
DESCRIPTION | 14 +++++++-------
MD5 | 23 +++++++++++++----------
NAMESPACE | 2 ++
NEWS | 26 ++++++++++++++++++++------
R/D2.disc.R | 34 ++++++++++++++++++++++++++++++++++
R/boxM.R | 5 +++--
R/cov2pcov.R |only
R/samplesize.R | 2 +-
R/tocher.R | 10 ++++++++--
man/biotools-package.Rd | 10 +++++-----
man/cov2pcov.Rd |only
man/predict.D2.disc.Rd |only
man/samplesize.Rd | 4 ++--
man/tocher.Rd | 1 +
14 files changed, 96 insertions(+), 35 deletions(-)
Title: Parsing Command-line Arguments and Variable Interpolation
Diff between GetoptLong versions 0.0.8 dated 2014-11-05 and 0.0.9 dated 2015-01-29
Description: Parsing command-line arguments by Perl module Getopt::Long.
It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 10 ++++----
MD5 | 24 +++++++++----------
NEWS | 5 ++++
build/vignette.rds |binary
inst/doc/GetoptLong.R | 43 +++++++++++++++++++++++++++++++++++
inst/doc/GetoptLong.Rnw | 14 +++++------
inst/doc/GetoptLong.pdf |binary
inst/doc/variable_interpolation.R | 4 +--
inst/doc/variable_interpolation.Rnw | 4 +--
inst/doc/variable_interpolation.pdf |binary
inst/tests/test_qq.R | 1
vignettes/GetoptLong.Rnw | 14 +++++------
vignettes/variable_interpolation.Rnw | 4 +--
13 files changed, 85 insertions(+), 38 deletions(-)
Title: Cluster Analysis Extended Rousseeuw et al.
Diff between cluster versions 1.15.3 dated 2014-09-04 and 2.0.0 dated 2015-01-29
Description: Cluster Analysis Methods. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb]
Maintainer: Martin Maechler
cluster-1.15.3/cluster/man/pltree.twins.Rd |only
cluster-2.0.0/cluster/DESCRIPTION | 10
cluster-2.0.0/cluster/MD5 | 85 +-
cluster-2.0.0/cluster/NAMESPACE | 3
cluster-2.0.0/cluster/R/agnes.q | 17
cluster-2.0.0/cluster/R/clara.q | 33 -
cluster-2.0.0/cluster/R/daisy.q | 10
cluster-2.0.0/cluster/R/diana.q | 11
cluster-2.0.0/cluster/R/fanny.q | 5
cluster-2.0.0/cluster/R/internal.R | 22
cluster-2.0.0/cluster/R/pam.q | 95 ++-
cluster-2.0.0/cluster/R/silhouette.R | 3
cluster-2.0.0/cluster/inst/CITATION | 1
cluster-2.0.0/cluster/inst/po/de/LC_MESSAGES/R-cluster.mo |binary
cluster-2.0.0/cluster/inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary
cluster-2.0.0/cluster/inst/po/en@quot/LC_MESSAGES/cluster.mo |binary
cluster-2.0.0/cluster/inst/po/fr/LC_MESSAGES/R-cluster.mo |binary
cluster-2.0.0/cluster/inst/po/pl/LC_MESSAGES/R-cluster.mo |binary
cluster-2.0.0/cluster/man/agnes.Rd | 4
cluster-2.0.0/cluster/man/clusplot.default.Rd | 5
cluster-2.0.0/cluster/man/ellipsoidhull.Rd | 5
cluster-2.0.0/cluster/man/lower.to.upper.tri.inds.Rd | 4
cluster-2.0.0/cluster/man/pam.object.Rd | 8
cluster-2.0.0/cluster/man/pltree.Rd | 61 +-
cluster-2.0.0/cluster/man/pluton.Rd | 6
cluster-2.0.0/cluster/po/R-cluster.pot | 7
cluster-2.0.0/cluster/po/R-de.po | 16
cluster-2.0.0/cluster/po/R-fr.po | 5
cluster-2.0.0/cluster/po/R-pl.po | 5
cluster-2.0.0/cluster/po/cluster.pot | 14
cluster-2.0.0/cluster/src/clara.c | 6
cluster-2.0.0/cluster/src/cluster.h | 22
cluster-2.0.0/cluster/src/dysta.f | 4
cluster-2.0.0/cluster/src/fanny.c | 20
cluster-2.0.0/cluster/src/init.c | 13
cluster-2.0.0/cluster/src/pam.c | 293 ++++++++--
cluster-2.0.0/cluster/src/twins.c | 127 +---
cluster-2.0.0/cluster/tests/agnes-ex.R | 12
cluster-2.0.0/cluster/tests/agnes-ex.Rout.save | 107 ++-
cluster-2.0.0/cluster/tests/clara-NAs.Rout.save | 55 -
cluster-2.0.0/cluster/tests/clara-ex.R | 23
cluster-2.0.0/cluster/tests/clara.Rout.save | 11
cluster-2.0.0/cluster/tests/pam.R | 20
cluster-2.0.0/cluster/tests/pam.Rout.save | 93 +--
44 files changed, 790 insertions(+), 451 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Diff between Luminescence versions 0.4.0 dated 2014-12-18 and 0.4.1 dated 2015-01-29
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre],
Michael Dietze [aut],
Christoph Burow [aut],
Margret C. Fuchs [aut],
Christoph Schmidt [aut],
Manfred Fischer [aut, trl],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer
DESCRIPTION | 17
MD5 | 68 +--
NAMESPACE | 1
NEWS | 124 ++++++
R/RLum.Analysis-class.R | 64 ++-
R/RLum.Results-class.R | 4
R/RisoeBINfileData-class.R | 24 -
R/analyse_IRSAR.RF.R | 50 ++
R/analyse_SAR.CWOSL.R | 136 ++++---
R/analyse_pIRIRSequence.R | 33 -
R/calc_OSLLxTxRatio.R | 10
R/fit_CWCurve.R | 2
R/fit_LMCurve.R | 10
R/merge_RLum.Data.Curve.R |only
R/merge_RLum.R | 8
R/plot_AbanicoPlot.R | 627 +++++++++++++++++++++++++++------
R/plot_GrowthCurve.R | 90 +++-
R/readBIN2R.R | 728 +++++++++++++++++++++------------------
R/readSPE2R.R | 6
R/writeR2BIN.R | 16
inst/NEWS.Rd | 157 ++++++++
man/ExampleData.RLum.Analysis.Rd | 4
man/Luminescence-package.Rd | 21 -
man/analyse_IRSAR.RF.Rd | 9
man/analyse_SAR.CWOSL.Rd | 14
man/analyse_pIRIRSequence.Rd | 16
man/calc_OSLLxTxRatio.Rd | 12
man/fit_CWCurve.Rd | 2
man/fit_LMCurve.Rd | 4
man/merge_RLum.Data.Curve.Rd |only
man/merge_RLum.Rd | 2
man/plot_AbanicoPlot.Rd | 38 +-
man/plot_GrowthCurve.Rd | 16
man/readBIN2R.Rd | 2
man/readSPE2R.Rd | 2
man/writeR2BIN.Rd | 2
36 files changed, 1601 insertions(+), 718 deletions(-)
Title: Model-Based Clustering and Classification with the Multivariate
t Distribution
Diff between teigen versions 2.0.7 dated 2014-08-19 and 2.0.8 dated 2015-01-29
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews
ChangeLog | 10 +++++++---
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/teigen.R | 3 +++
inst/CITATION | 2 +-
man/plot.teigen.Rd | 2 +-
man/print.teigen.Rd | 2 +-
man/summary.teigen.Rd | 2 +-
man/teigen-package.Rd | 6 +++---
man/teigen.Rd | 6 ++++--
man/teigen.parallel.Rd | 2 +-
11 files changed, 38 insertions(+), 29 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Diff between packrat versions 0.4.2-1 dated 2014-12-16 and 0.4.3 dated 2015-01-28
Description: A tool for managing the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey
DESCRIPTION | 8 +--
MD5 | 70 ++++++++++++++---------------
NAMESPACE | 2
R/available-updates.R | 2
R/dependencies.R | 4 -
R/install.R | 4 -
R/migrate-library.R | 2
R/migrate-packrat.R | 4 -
R/options.R | 4 -
R/packrat.R | 17 ++++++-
R/snapshot.R | 23 ++++++++-
R/status.R | 98 +++++++++++++++++++++--------------------
README.md | 25 +++++++---
inst/resources/init-rprofile.R | 2
inst/resources/init.R | 12 ++++-
man/appDependencies.Rd | 3 -
man/bundle.Rd | 3 -
man/clean.Rd | 3 -
man/disable.Rd | 3 -
man/init.Rd | 3 -
man/install.Rd | 3 -
man/install_github.Rd | 3 -
man/install_local.Rd | 3 -
man/migrate.Rd | 3 -
man/packify.Rd | 3 -
man/packrat-external.Rd | 3 -
man/packrat-mode.Rd | 3 -
man/packrat-options.Rd | 7 +-
man/packrat.Rd | 3 -
man/restore.Rd | 3 -
man/search_path.Rd | 3 -
man/snapshot.Rd | 8 +--
man/snapshotImpl.Rd | 11 ++--
man/status.Rd | 3 -
man/unbundle.Rd | 3 -
man/unused_packages.Rd | 3 -
36 files changed, 216 insertions(+), 141 deletions(-)
Title: Meta-analysis for MicroArrays
Diff between metaMA versions 3.1.1 dated 2015-01-26 and 3.1.2 dated 2015-01-28
Description: Combines either p-values or modified effect sizes from different
studies to find differentially expressed genes
Author: Guillemette Marot
Maintainer: Guillemette Marot
DESCRIPTION | 10 +-
MD5 | 14 +--
inst/NEWS | 4
inst/doc/metaMA.R | 214 +++++++++++++++++++++++++-------------------------
inst/doc/metaMA.Rnw | 74 ++++++++---------
inst/doc/metaMA.pdf |binary
man/metaMA-package.Rd | 4
vignettes/metaMA.Rnw | 74 ++++++++---------
8 files changed, 198 insertions(+), 196 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Diff between marmap versions 0.9.1 dated 2014-12-16 and 0.9.2 dated 2015-01-28
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante
DESCRIPTION | 14 ++++++------
MD5 | 44 ++++++++++++++++++++++-----------------
NAMESPACE | 2 +
R/autoplot.bathy.R |only
R/fortify.bathy.R |only
R/palette.etopo.R |only
R/readGEBCO.bathy.R | 44 +++++++++++++++++++--------------------
R/scaleBathy.R | 4 +--
build/vignette.rds |binary
data/aleutians.rda |binary
data/celt.rda |binary
data/florida.rda |binary
data/hawaii.rda |binary
data/hawaii.sites.rda |binary
data/metallo.rda |binary
data/nw.atlantic.coast.rda |binary
data/nw.atlantic.rda |binary
inst/doc/marmap-ImportExport.pdf |binary
man/autoplot.bathy.Rd |only
man/etopo.Rd |only
man/fortify.bathy.Rd |only
man/marmap.Rd | 4 +--
man/nw.atlantic.coast.Rd | 4 +--
man/plot.bathy.Rd | 3 --
man/readGEBCO.bathy.Rd | 14 ++++--------
man/scaleBathy.Rd | 5 +++-
26 files changed, 72 insertions(+), 66 deletions(-)
Title: Generate Functions to Get or Set Global Options
Diff between GlobalOptions versions 0.0.5 dated 2014-12-24 and 0.0.6 dated 2015-01-28
Description: It provides more controls on the option values such as validation
and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu
GlobalOptions-0.0.5/GlobalOptions/inst/tests/package1 |only
GlobalOptions-0.0.5/GlobalOptions/inst/tests/package2 |only
GlobalOptions-0.0.6/GlobalOptions/DESCRIPTION | 9
GlobalOptions-0.0.6/GlobalOptions/MD5 | 23
GlobalOptions-0.0.6/GlobalOptions/NAMESPACE | 1
GlobalOptions-0.0.6/GlobalOptions/NEWS | 8
GlobalOptions-0.0.6/GlobalOptions/R/class.R |only
GlobalOptions-0.0.6/GlobalOptions/R/setGlobalOptions.R | 355 ++--------
GlobalOptions-0.0.6/GlobalOptions/inst/doc/GlobalOptions.R | 8
GlobalOptions-0.0.6/GlobalOptions/inst/doc/GlobalOptions.Rnw | 28
GlobalOptions-0.0.6/GlobalOptions/inst/doc/GlobalOptions.pdf |binary
GlobalOptions-0.0.6/GlobalOptions/inst/tests/test.R | 95 --
GlobalOptions-0.0.6/GlobalOptions/man/setGlobalOptions.rd | 3
GlobalOptions-0.0.6/GlobalOptions/vignettes/GlobalOptions.Rnw | 28
14 files changed, 170 insertions(+), 388 deletions(-)
Title: Statistical Methods for Visual Fields
Diff between visualFields versions 0.4 dated 2014-03-03 and 0.4.2 dated 2015-01-28
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch
Maintainer: Ivan Marin-Franch
DESCRIPTION | 12 ++---
MD5 | 106 +++++++++++++++++++++++------------------------
NAMESPACE | 9 ++-
R/ageLinearModel.R | 2
R/agecalc.R | 15 +++---
R/bebie.R | 7 +--
R/colormapgraph.R | 2
R/getnv.R | 2
R/ghpostd.R | 2
R/ghranktd.R | 4 -
R/gloperc.R | 2
R/lidLensArtifact.R | 2
R/loadvfcsv.R | 4 -
R/loadvfxml.R | 13 +++++
R/locperc.R | 2
R/pdpmap.R | 18 +++----
R/pdpmapghr.R | 18 +++----
R/pdval.R | 4 -
R/pdvalghr.R | 4 -
R/poplr.R | 2
R/poplr_pstat.R | 2
R/quad2Dfit.R | 4 -
R/sdnv.R | 2
R/sdnvghr.R | 2
R/setnv.R | 2
R/tdpmap.R | 18 +++----
R/tdrank.R | 6 +-
R/tdrankadjperc.R | 9 ++-
R/tdranknv.R | 2
R/tdrankperc.R | 2
R/tdval.R | 4 -
R/vfcolormap.R | 2
R/vfdemographics.R | 2
R/vfindex.R | 16 +++----
R/vfindexpmap.R | 20 ++++----
R/vfiperc.R | 2
R/vflayout.R | 22 ++++-----
R/vflayout_legoplot.R | 25 ++++-------
R/vflayout_poplr.R | 32 ++++++--------
R/vflayoutghr.R | 18 +++----
R/vfplot.R | 16 +++----
R/vfplot_poplr.R | 8 +--
R/vfstats.R | 10 ++--
R/vfstatspmap.R | 32 +++++++-------
inst/news.txt | 13 +++++
man/colormapgraph.Rd | 4 +
man/quad2Dfit.Rd | 4 -
man/tdrankadjperc.Rd | 5 +-
man/vfcolormap.Rd | 2
man/vfindex.Rd | 2
man/vflayout.Rd | 6 +-
man/vflayout_legoplot.Rd | 6 +-
man/vflayout_poplr.Rd | 6 +-
man/vfplot.Rd | 2
54 files changed, 284 insertions(+), 254 deletions(-)
Title: Fitting Univariate Censored Regression Model Under the Family of
Scale Mixture of Normal Distributions
Diff between SMNCensReg versions 2.4 dated 2014-07-17 and 3.0 dated 2015-01-28
Description: Fit univariate right, left or interval censored regression model under the scale mixture of normal distributions
Author: Aldo M. Garay
Maintainer: Aldo M. Garay
DESCRIPTION | 20 -
MD5 | 14
NAMESPACE | 3
R/CensRegSMN.r | 174 ++++-----
R/EM_SMN.r | 971 ++++++++++++++++++++++++++---------------------------
R/Utilitarios.r | 881 +++++++++++++++++++-----------------------------
man/CensReg.SMN.Rd | 47 +-
man/wage.rates.Rd | 14
8 files changed, 972 insertions(+), 1152 deletions(-)
Title: Visualization of Spatial and Spatio-temporal Objects in Google
Earth
Diff between plotKML versions 0.4-8 dated 2014-12-09 and 0.5-0 dated 2015-01-28
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 12 +--
MD5 | 66 +++++++++++----------
NAMESPACE | 1
R/AAAA.R | 20 +++---
R/geopath.R | 68 +++++++++++-----------
R/getWikiMedia.ImageInfo.R | 7 +-
R/grid2poly.R | 8 +-
R/layer.Raster.R | 9 ++
R/layer.SoilProfileCollection.R | 12 +--
R/layer.SpatialPixels.R | 7 +-
R/plotKML.GDALobj.R |only
R/reproject.R | 8 +-
R/spMetadata.R | 14 ++--
R/spPhoto.R | 17 ++---
R/vect2rast.R | 89 ++++++++++++++++-------------
build/vignette.rds |binary
inst/CITATION | 38 +++++++-----
inst/doc/jss1079.Rnw | 8 +-
inst/doc/jss1079.pdf |binary
man/LST.Rd | 4 -
man/geopath.rd | 1
man/layer.SoilProfileCollection.Rd | 1
man/plotKML-package.Rd | 1
man/plotKML.GDALobj.Rd |only
man/plotKML.env.Rd | 1
man/readKML.GBIFdensity.Rd | 2
man/reproject.Rd | 3
man/spMetadata.Rd | 5 +
man/vect2rast.Rd | 2
man/worldgrids_pal.Rd | 10 +--
vignettes/Fig_SpatialPredictions_meuse.jpg |binary
vignettes/Fig_bubble_plot.jpg |binary
vignettes/Fig_fmd_google_earth_2.jpg |binary
vignettes/Fig_fmd_google_earth_3.jpg |binary
vignettes/jss1079.Rnw | 8 +-
35 files changed, 235 insertions(+), 187 deletions(-)
Title: Statistical Significance of the Markowitz Portfolio
Diff between MarkowitzR versions 0.1402 dated 2014-02-12 and 0.1502 dated 2015-01-28
Description: a collection of tools for analyzing significance of
Markowitz portfolios.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav
MarkowitzR-0.1402/MarkowitzR/ChangeLog |only
MarkowitzR-0.1502/MarkowitzR/DESCRIPTION | 15 -
MarkowitzR-0.1502/MarkowitzR/MD5 | 35 +-
MarkowitzR-0.1502/MarkowitzR/NAMESPACE | 2
MarkowitzR-0.1502/MarkowitzR/R/MarkowitzR.r | 12
MarkowitzR-0.1502/MarkowitzR/R/portinf.r | 8
MarkowitzR-0.1502/MarkowitzR/README.md | 9
MarkowitzR-0.1502/MarkowitzR/build/vignette.rds |binary
MarkowitzR-0.1502/MarkowitzR/inst/doc/AsymptoticMarkowitz.R | 4
MarkowitzR-0.1502/MarkowitzR/inst/doc/AsymptoticMarkowitz.pdf |binary
MarkowitzR-0.1502/MarkowitzR/inst/doc/MarkowitzR.R | 56 +--
MarkowitzR-0.1502/MarkowitzR/inst/doc/MarkowitzR.pdf |binary
MarkowitzR-0.1502/MarkowitzR/inst/extdata/ff_data.rda |binary
MarkowitzR-0.1502/MarkowitzR/inst/tests |only
MarkowitzR-0.1502/MarkowitzR/man/MarkowitzR.Rd | 84 ++---
MarkowitzR-0.1502/MarkowitzR/man/NEWS.Rd | 20 +
MarkowitzR-0.1502/MarkowitzR/man/itheta_vcov.Rd | 79 ++---
MarkowitzR-0.1502/MarkowitzR/man/mp_vcov.Rd | 147 ++++------
MarkowitzR-0.1502/MarkowitzR/man/theta_vcov.Rd | 64 ++--
MarkowitzR-0.1502/MarkowitzR/tests |only
20 files changed, 268 insertions(+), 267 deletions(-)
Title: Fast access to large ASCII files
Diff between LaF versions 0.6.1 dated 2014-04-21 and 0.6.2 dated 2015-01-28
Description: Methods for fast access to large ASCII files. Currently the
following file formats are supported: comma separated format (csv) and fixed
width format. It is assumed that the files are too large to fit into memory,
although the package can also be used to efficiently access files that do
fit into memory. Methods are provided to access and process files blockwise.
Furthermore, an opened file can be accessed as one would an ordinary
data.frame. The LaF vignette gives an overview of the functionality
provided.
Author: Jan van der Laan
Maintainer: Jan van der Laan
DESCRIPTION | 10 +++++-----
MD5 | 18 +++++++++---------
NEWS | 4 ++++
R/meta.R | 8 ++++----
R/open.R | 2 +-
build/vignette.rds |binary
inst/doc/LaF-benchmark.pdf |binary
inst/doc/LaF-manual.pdf |binary
src/csvreader.cpp | 2 +-
src/fwfreader.cpp | 2 ++
10 files changed, 26 insertions(+), 20 deletions(-)
Title: Kalman Filter, Smoother and Disturbance Smoother
Diff between KFKSDS versions 1.5 dated 2014-07-27 and 1.6 dated 2015-01-28
Description: Naive implementation of the Kalman filter, smoother and disturbance
smoother for state space models.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
KFKSDS-1.5/KFKSDS/inst/NEWS |only
KFKSDS-1.6/KFKSDS/DESCRIPTION | 14 ++--
KFKSDS-1.6/KFKSDS/MD5 | 30 ++++-----
KFKSDS-1.6/KFKSDS/NEWS |only
KFKSDS-1.6/KFKSDS/R/KF-interfaces.R | 85 ++++++++++++++------------
KFKSDS-1.6/KFKSDS/R/KF.R | 1
KFKSDS-1.6/KFKSDS/inst/tests/DS-derivatives.R | 10 +--
KFKSDS-1.6/KFKSDS/inst/tests/KF-deriv-xreg.R | 10 +--
KFKSDS-1.6/KFKSDS/inst/tests/KF-derivatives.R | 10 +--
KFKSDS-1.6/KFKSDS/inst/tests/KS-derivatives.R | 10 +--
KFKSDS-1.6/KFKSDS/man/DS.Rd | 10 +--
KFKSDS-1.6/KFKSDS/man/KF-interfaces.Rd | 21 ++----
KFKSDS-1.6/KFKSDS/man/KF.Rd | 14 ++--
KFKSDS-1.6/KFKSDS/man/KFKSDS-package.Rd | 6 +
KFKSDS-1.6/KFKSDS/man/KFKSDS.Rd | 6 -
KFKSDS-1.6/KFKSDS/man/KS.Rd | 10 +--
KFKSDS-1.6/KFKSDS/man/predict-stsmSS.Rd | 13 ++-
17 files changed, 130 insertions(+), 120 deletions(-)
Title: Association Between Methylation and a Phenotype of Interest
Diff between CpGassoc versions 2.11 dated 2014-01-10 and 2.50 dated 2015-01-28
Description: Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest,
adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no
need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept.
Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots,
and scatterplots for individual CpG sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield
DESCRIPTION | 16 ++---
MD5 | 35 ++++++-----
NAMESPACE | 1
R/cpg.GC.R | 10 ++-
R/cpg.combine.R | 9 +-
R/cpg.perm.R | 4 -
R/cpg.qc.R | 144 ++++++++++++++++++++---------------------------
R/cpg.work.R | 9 +-
R/manhattan.R | 16 +++--
R/manhattan.reflect.R |only
R/plot.cpg.R | 9 +-
R/plot.cpg.perm.R | 9 +-
build |only
data/annotation.rda |binary
data/samplecpg.rda |binary
data/samplepheno.rda |binary
inst/doc/CpGassoc.pdf |binary
man/CpGassoc-package.Rd | 10 +--
man/manhattan.Rd | 6 +
man/manhattan.reflect.Rd |only
20 files changed, 147 insertions(+), 131 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Diff between stochvol versions 0.9-1 dated 2014-12-27 and 1.0.0 dated 2015-01-28
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner
DESCRIPTION | 8 -
MD5 | 28 +++---
NEWS | 11 ++
R/utilities_svdraws.R | 2
build/vignette.rds |binary
inst/CITATION | 19 +++-
inst/doc/article.R | 159 +++++++++++++++-------------------
inst/doc/article.Rnw | 220 ++++++++++++++++++++++++------------------------
inst/doc/article.pdf |binary
man/stochvol-package.Rd | 2
man/svsample.Rd | 4
man/svsample2.Rd | 6 -
man/svsim.Rd | 4
vignettes/article.Rnw | 220 ++++++++++++++++++++++++------------------------
vignettes/mybib.bib | 15 ++-
15 files changed, 361 insertions(+), 337 deletions(-)
Title: Kernel Estimator and Bandwidth Selection for Density and its
Derivatives
Diff between kedd versions 1.0.1 dated 2014-08-18 and 1.0.2 dated 2015-01-28
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum
DESCRIPTION | 10 ++---
MD5 | 44 ++++++++++++------------
NEWS | 2 +
R/AMISE.R | 4 +-
R/BCV.R | 4 +-
R/CCV.R | 4 +-
R/MCV.R | 4 +-
R/MLCV.R | 4 +-
R/TCV.R | 4 +-
R/UCV.R | 4 +-
R/dkde.R | 4 +-
R/kernel.R | 4 +-
R/utils.R | 4 +-
build/vignette.rds |binary
inst/CITATION | 11 ++----
inst/doc/intro.Rnw | 6 +--
inst/doc/intro.pdf |binary
inst/doc/kedd.R | 94 ++++++++++++++++++++++++++--------------------------
inst/doc/kedd.Rnw | 26 +++++++-------
inst/doc/kedd.pdf |binary
man/kedd-package.Rd | 4 +-
vignettes/intro.Rnw | 6 +--
vignettes/kedd.Rnw | 26 +++++++-------
23 files changed, 135 insertions(+), 134 deletions(-)
Title: Statistical Inference of Vine Copulas
Diff between VineCopula versions 1.3 dated 2014-04-22 and 1.4 dated 2015-01-28
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package CDVine are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler
Maintainer: Tobias Erhardt
DESCRIPTION | 16
MD5 | 162 +-
NAMESPACE | 6
R/BiCopCDF.r | 118 -
R/BiCopChiPlot.r | 14
R/BiCopEst.r | 1504 +++++++++----------
R/BiCopMetaContour.r | 93 -
R/BiCopPar2Tau.r | 449 +++--
R/BiCopSelect.r | 351 ++--
R/BiCopTau2Par.r | 56
R/RVineStructureSelect.r | 968 ++++++------
R/gof_PIT.r | 9
R/gof_White.r | 4
inst/ChangeLog | 38
man/BB1Copula-class.Rd | 150 -
man/BB1Copula.Rd | 10
man/BB6Copula.Rd | 12
man/BB7Copula.Rd | 12
man/BB8Copula.Rd | 12
man/BetaMatrix.Rd | 86 -
man/BiCopCDF.Rd | 16
man/BiCopChiPlot.Rd | 30
man/BiCopDeriv.Rd | 12
man/BiCopDeriv2.Rd | 12
man/BiCopEst.Rd | 45
man/BiCopGofTest.Rd | 27
man/BiCopHfunc.Rd | 11
man/BiCopHfuncDeriv.Rd | 14
man/BiCopHfuncDeriv2.Rd | 14
man/BiCopIndTest.Rd | 20
man/BiCopKPlot.Rd | 31
man/BiCopLambda.Rd | 52
man/BiCopMetaContour.Rd | 47
man/BiCopName.Rd | 8
man/BiCopPDF.Rd | 14
man/BiCopPar2Beta.Rd | 6
man/BiCopPar2TailDep.Rd | 8
man/BiCopPar2Tau.Rd | 141 +
man/BiCopSelect.Rd | 36
man/BiCopSim.Rd | 6
man/BiCopTau2Par.Rd | 74
man/BiCopVuongClarke.Rd | 15
man/C2RVine.Rd | 26
man/D2RVine.Rd | 26
man/RVineAICBIC.Rd | 44
man/RVineClarkeTest.Rd | 18
man/RVineCopSelect.Rd | 43
man/RVineCor2pcor.Rd | 49
man/RVineGofTest.Rd | 69
man/RVineGrad.Rd | 45
man/RVineHessian.Rd | 42
man/RVineLogLik.Rd | 69
man/RVineMLE.Rd | 50
man/RVineMatrix.Rd | 46
man/RVineMatrixNormalize.Rd | 30
man/RVinePIT.Rd | 19
man/RVinePar2Beta.Rd | 36
man/RVinePar2Tau.Rd | 114 -
man/RVineSeqEst.Rd | 49
man/RVineSim.Rd | 133 -
man/RVineStdError.rd | 42
man/RVineStructureSelect.Rd | 31
man/RVineTreePlot.Rd | 53
man/RVineVuongTest.Rd | 10
man/RvineMatrixCheck.Rd | 44
man/TauMatrix.Rd | 8
man/VineCopula-package.Rd | 27
man/copulaFromFamilyIndex.Rd | 6
man/dduCopula.Rd | 8
man/joeBiCopula.Rd | 8
man/pobs.Rd |only
man/surClaytonCopula.Rd | 11
man/surGumbelCopula.Rd | 11
man/tawnT1Copula.Rd | 10
man/tawnT2Copula.Rd | 10
man/vineCopula.Rd | 8
src/gof.c | 38
src/hfunc.c | 86 -
src/incompleteBeta.c | 8
tests/Examples/VineCopula-Ex.Rout.save | 2444 +++++++++++++++++++++----------
tests/TRUEadditonalExampleRuns.Rout.save |only
tests/additonalExampleRuns.R | 229 +-
tests/additonalExampleRuns.Rout.save | 235 +-
83 files changed, 5149 insertions(+), 3795 deletions(-)
Title: C++ Classes to Embed R in C++ Applications
Diff between RInside versions 0.2.11 dated 2014-02-12 and 0.2.12 dated 2015-01-28
Description: C++ classes to embed R in C++ applications
The RInside packages makes it easier to have 'R inside' your C++ application
by providing a C++ wrapper class providing the R interpreter.
As R itself is embedded into your application, a shared library build of R
is required. This works on Linux, OS X and even on Windows provided you use
the same tools used to build R itself.
Numerous examples are provided in the eight subdirectories of the examples/
directory of the installed package: standard, mpi (for parallel computing)
qt (showing how to embed RInside inside a Qt GUI application), wt (showing
how to build a 'web-application' using the Wt toolkit), armadillo (for
RInside use with RcppArmadillo) and eigen (for RInside use with RcppEigen).
The example use GNUmakefile(s) with GNU extensions, so a GNU make is required
(and will use the GNUmakefile automatically).
Doxygen-generated documentation of the C++ classes is available at the
RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel
RInside-0.2.11/RInside/inst/examples/armadillo/Makefile |only
RInside-0.2.11/RInside/inst/examples/eigen/Makefile |only
RInside-0.2.11/RInside/inst/examples/mpi/Makefile |only
RInside-0.2.11/RInside/inst/examples/standard/Makefile |only
RInside-0.2.11/RInside/inst/examples/threads/Makefile |only
RInside-0.2.11/RInside/inst/examples/wt/Makefile |only
RInside-0.2.12/RInside/ChangeLog | 58 ++++++++++
RInside-0.2.12/RInside/DESCRIPTION | 14 +-
RInside-0.2.12/RInside/MD5 | 54 ++++++---
RInside-0.2.12/RInside/inst/NEWS.Rd | 26 ++++
RInside-0.2.12/RInside/inst/examples/armadillo/GNUmakefile |only
RInside-0.2.12/RInside/inst/examples/eigen/GNUmakefile |only
RInside-0.2.12/RInside/inst/examples/mpi/GNUmakefile |only
RInside-0.2.12/RInside/inst/examples/sandboxed_server |only
RInside-0.2.12/RInside/inst/examples/standard/GNUmakefile |only
RInside-0.2.12/RInside/inst/examples/standard/rinside_callbacks1.cpp |only
RInside-0.2.12/RInside/inst/examples/standard/rinside_module_sample0.cpp | 10 -
RInside-0.2.12/RInside/inst/examples/standard/rinside_sample15.cpp |only
RInside-0.2.12/RInside/inst/examples/standard/rinside_sample16.cpp |only
RInside-0.2.12/RInside/inst/examples/standard/rinside_sample17.cpp |only
RInside-0.2.12/RInside/inst/examples/standard/rinside_sample9.cpp | 13 --
RInside-0.2.12/RInside/inst/examples/threads/GNUmakefile |only
RInside-0.2.12/RInside/inst/examples/wt/GNUmakefile |only
RInside-0.2.12/RInside/src/Makevars | 2
RInside-0.2.12/RInside/src/Makevars.win | 4
RInside-0.2.12/RInside/src/RInside.cpp | 4
26 files changed, 145 insertions(+), 40 deletions(-)
Title: Multivariate Normality Tests
Diff between MVN versions 3.7 dated 2014-11-16 and 3.8 dated 2015-01-28
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz
DESCRIPTION | 16 -
MD5 | 28 +-
NAMESPACE | 2
R/classes.R | 16 -
R/uniNorm.R | 70 ++++--
R/uniPlot.R | 10
build/vignette.rds |binary
inst/CITATION |only
inst/doc/MVN.R | 214 +++++++++----------
inst/doc/MVN.Rnw | 572 ++++++++++++++++++++++++++++++++++++-----------------
inst/doc/MVN.pdf |binary
man/MVN-package.Rd | 2
man/uniNorm.Rd | 6
man/uniPlot.Rd | 2
vignettes/MVN.Rnw | 572 ++++++++++++++++++++++++++++++++++++-----------------
vignettes/MVN.bib |only
16 files changed, 982 insertions(+), 528 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-29 1.0.5
2014-07-28 1.0.2
2013-12-10 1.0.1
2013-09-25 1.0.0
Title: Maximin-Distance (Sliced) Latin Hypercube Designs
Diff between SLHD versions 1.2-1 dated 2013-05-14 and 2.1-1 dated 2015-01-28
Description: Generate the optimal Latin Hypercube Designs (LHDs) for computer experiments with quantitative factors and the optimal Sliced Latin Hypercube Designs (SLHDs) for computer experiments with both quantitative and qualitative factors. Details of the algorithm can be found in Ba, S., Brenneman, W. A. and Myers, W. R. (2015), "Optimal Sliced Latin Hypercube Designs," Technometrics. Important function in this package is "maximinSLHD".
Author: Shan Ba
Maintainer: Shan Ba
DESCRIPTION | 16 ++-----
MD5 | 12 ++---
NAMESPACE | 2
R/maximinSLHD.R | 19 +++-----
man/SLHD-package.Rd | 8 +--
man/maximinSLHD.Rd | 24 +++++------
src/SLHD.cpp | 112 +++++++++++++++++++++++-----------------------------
7 files changed, 85 insertions(+), 108 deletions(-)
Title: R-values for Ranking in High-Dimensional Settings
Diff between rvalues versions 0.2 dated 2014-07-24 and 0.3 dated 2015-01-28
Description: A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
Author: Nicholas Henderson and Michael Newton
Maintainer: Nicholas Henderson
DESCRIPTION | 14 +++++-----
MD5 | 34 ++++++++++++++------------
NAMESPACE | 1
R/HyperEstimate.R | 42 ++++++++++++++++++++++++++++++--
R/ThetaQuantiles.R | 10 ++++---
R/TopList.R | 30 +++++++----------------
R/Vplot.R |only
R/agrid_fns.R | 63 ++++++++++++++++++++++++++++++++++++++++++++++--
R/mroot.R |only
R/rvalueGuts.R | 69 +++++++++++++++++++++++++++++++----------------------
R/rvalues.R | 8 ++++++
R/rvaluesMCMC.R | 2 -
man/MakeGrid.Rd | 4 +--
man/TopList.Rd | 4 +--
man/Valpha.Rd | 2 -
man/bcwest.Rd | 1
man/hiv.Rd | 3 --
man/mroot.Rd |only
man/npmixapply.Rd | 6 +++-
src/zeroin.c |only
20 files changed, 203 insertions(+), 90 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.59 dated 2015-01-27 and 3.0.60 dated 2015-01-28
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 6 +-
MD5 | 74 ++++++++++++-------------
R/Crossvalidation.R | 10 ++-
R/Methods-aux.R | 3 -
R/RMmodelsSpecial.R | 8 +-
R/basic.fctns.R | 6 +-
R/fitgauss.R | 2
R/kriging.R | 15 ++---
man/CoordinateSystems.Rd | 6 --
man/RFgetModelNames.Rd | 2
man/RMtrend.Rd | 23 ++++++-
src/Coordinate_systems.cc | 136 +++++++++++++++++++++++-----------------------
src/Coordinate_systems.h | 68 +++++++++++------------
src/Gneiting.cc | 10 +--
src/Huetchen.cc | 18 +++---
src/InternalCov.cc | 4 -
src/KeyInfo.cc | 6 +-
src/Operator.h | 16 ++---
src/Primitive.cc | 78 +++++++++++++-------------
src/RF.h | 12 ++--
src/auxiliary.cc | 14 ++--
src/auxiliary.h | 2
src/basic.h | 4 -
src/circulant.cc | 8 +-
src/extremes.cc | 18 +++---
src/families.cc | 4 -
src/fft.cc | 8 +-
src/getNset.cc | 44 ++++++++------
src/initNerror.cc | 12 ++--
src/kriging.cc | 97 ++++++++++++++++++--------------
src/operator.cc | 34 +++++------
src/plusmalS.cc | 86 +++++++++++++++--------------
src/primitive.h | 28 ++++-----
src/rf_interfaces.cc | 11 +--
src/shape_processes.h | 30 +++++-----
src/startGetNset.cc | 4 -
src/variogramAndCo.cc | 55 +++++++++++-------
src/variogramAndCo.h | 2
38 files changed, 506 insertions(+), 458 deletions(-)
Title: Number-theoretic Functions
Diff between numbers versions 0.4-5 dated 2014-01-08 and 0.5-2 dated 2015-01-28
Description:
Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers
DESCRIPTION | 12 ++++----
MD5 | 26 ++++++++++--------
NAMESPACE | 2 +
NEWS | 37 ++++++++++++++++++++------
R/agm.R | 21 ++++++++-------
R/egyptian.R | 19 +++++++++----
R/fibonacci.R | 41 +++++++++++++++++++----------
R/ordpn.R |only
R/qresidues.R | 2 -
R/rabin.R |only
man/agm.Rd | 18 +++++--------
man/egyptian_complete.Rd | 12 +++++---
man/fibonacci.Rd | 65 ++++++++++++++++++++++++++++-------------------
man/ordpn.Rd |only
man/rabin.Rd |only
man/zeck.Rd | 4 +-
16 files changed, 162 insertions(+), 97 deletions(-)
Title: Visualization and Analysis Tools for Neural Networks
Diff between NeuralNetTools versions 1.0.0 dated 2014-12-16 and 1.0.1 dated 2015-01-28
More information about NeuralNetTools at CRAN
Description: Visualization and analysis tools to aid in the interpretation of
neural network models. Functions are available for plotting,
quantifying variable importance, conducting a sensitivity analysis, and
obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
NAMESPACE | 38 +++++++++++++++++++-------------------
R/NeuralNetTools_gar.R | 22 +++++++++++-----------
R/NeuralNetTools_lek.R | 18 +++++++++++-------
R/NeuralNetTools_plot.R | 46 +++++++++++++++++++++++-----------------------
R/NeuralNetTools_utils.R | 18 ++++++++++--------
README.md | 2 +-
man/garson.Rd | 3 ++-
man/lekprofile.Rd | 3 ++-
man/neuraldat.Rd | 3 ++-
man/neuralweights.Rd | 3 ++-
man/plotnet.Rd | 3 ++-
man/pred_sens.Rd | 3 ++-
14 files changed, 105 insertions(+), 93 deletions(-)
Permanent link
Title: Visualisation of Sequential Probability Distributions Using Fan
Charts
Diff between fanplot versions 3.3 dated 2014-08-01 and 3.4.0 dated 2015-01-28
Description: Visualise sequential distributions using a range of plotting
styles. Sequential distribution data can be input as either simulations or
values corresponding to percentiles over time. Plots are added to
existing graphic devices using the fan function. Users can choose from four
different styles, including fan chart type plots, where a set of coloured
polygon, with shadings corresponding to the percentile values are layered
to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel"
fanplot-3.3/fanplot/R/fan.fill.R |only
fanplot-3.3/fanplot/R/fan.txt.R |only
fanplot-3.3/fanplot/R/fanplot-internal.R |only
fanplot-3.3/fanplot/R/head.pn.R |only
fanplot-3.3/fanplot/R/pn.R |only
fanplot-3.3/fanplot/data/boe.rda |only
fanplot-3.3/fanplot/data/cpi.rda |only
fanplot-3.3/fanplot/data/ips.rda |only
fanplot-3.3/fanplot/data/th.mcmc.rda |only
fanplot-3.3/fanplot/inst/model/my1.txt |only
fanplot-3.3/fanplot/man/fan.fill.Rd |only
fanplot-3.3/fanplot/man/fan.txt.Rd |only
fanplot-3.3/fanplot/man/fan0.Rd |only
fanplot-3.3/fanplot/man/fanplot-package.Rd |only
fanplot-3.3/fanplot/man/head.pn.Rd |only
fanplot-3.3/fanplot/man/pn.Rd |only
fanplot-3.4.0/fanplot/DESCRIPTION | 24 -
fanplot-3.4.0/fanplot/MD5 | 53 --
fanplot-3.4.0/fanplot/R/dsplitnorm.R | 16
fanplot-3.4.0/fanplot/R/fan.R | 550 ++++++++++++--------------
fanplot-3.4.0/fanplot/R/fan0.R | 68 +--
fanplot-3.4.0/fanplot/R/psplitnorm.R | 16
fanplot-3.4.0/fanplot/R/qsplitnorm.R | 14
fanplot-3.4.0/fanplot/R/rsplitnorm.R | 10
fanplot-3.4.0/fanplot/data/boe.RData |only
fanplot-3.4.0/fanplot/data/cpi.RData |only
fanplot-3.4.0/fanplot/data/datalist | 2
fanplot-3.4.0/fanplot/data/ips.RData |only
fanplot-3.4.0/fanplot/data/thmcmc.RData |only
fanplot-3.4.0/fanplot/demo/net_elicit.R | 6
fanplot-3.4.0/fanplot/demo/sv_fan.R | 2
fanplot-3.4.0/fanplot/inst/model/my1.R |only
fanplot-3.4.0/fanplot/inst/netelicit/server.R | 120 +----
fanplot-3.4.0/fanplot/inst/netelicit/ui.R | 25 -
fanplot-3.4.0/fanplot/man/boe.Rd | 8
fanplot-3.4.0/fanplot/man/dsplitnorm.Rd | 30 -
fanplot-3.4.0/fanplot/man/fan.Rd | 91 +++-
fanplot-3.4.0/fanplot/man/th.mcmc.Rd | 6
38 files changed, 496 insertions(+), 545 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Diff between plotROC versions 1.2 dated 2014-11-13 and 1.3 dated 2015-01-27
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 11 ++++---
LICENSE | 2 -
MD5 | 52 ++++++++++++++++++----------------
NAMESPACE | 2 -
NEWS | 8 +++++
R/calculate_roc.R | 63 ++++++++++++++++++++++++++++++------------
R/ggroc.R | 49 ++++++++++++++++++++------------
R/interactive_roc.R | 33 +++++++++++++---------
R/modCss.R | 2 -
R/modJs.R | 5 ++-
R/plot_journal_roc.R | 11 ++++---
build/vignette.rds |binary
inst/CITATION |only
inst/doc/examples.Rmd | 9 ++----
inst/doc/examples.html | 60 ++++++++++++++++++++--------------------
man/calculate_multi_roc.Rd | 15 +++++-----
man/calculate_roc.Rd | 17 ++++++-----
man/export_interactive_roc.Rd | 26 ++++++++++-------
man/ggroc.Rd | 22 +++++++++-----
man/modCss.Rd | 5 ++-
man/modJs.Rd | 10 ++++--
man/multi_ggroc.Rd | 23 ++++++++++-----
man/plot_interactive_roc.Rd | 7 ++--
man/plot_journal_roc.Rd | 10 +++---
man/shiny_plotROC.Rd | 3 +-
man/verify_d.Rd |only
tests |only
vignettes/examples.Rmd | 9 ++----
28 files changed, 272 insertions(+), 182 deletions(-)
Title: Tufte-style html document format for rmarkdown
Diff between tufterhandout versions 1.2 dated 2014-11-12 and 1.2.1 dated 2015-01-27
Description: Custom template and output formats for use with rmarkdown. Produce
Edward Tufte-style handouts in html formats with full support for rmarkdown
features
Author: Michael C Sachs
Maintainer: Michael C Sachs
DESCRIPTION | 17 +++++++++--------
LICENSE | 4 ++--
MD5 | 25 ++++++++++++++-----------
NAMESPACE | 2 +-
NEWS | 5 +++++
R/html_tufte_handout.R | 14 +++++++++++++-
README.md | 8 ++++++++
build/vignette.rds |binary
inst/CITATION |only
inst/doc/example.Rmd | 7 +++++--
inst/doc/example.html | 27 ++++++++++++++++++++-------
man/html_tufte_handout.Rd | 3 ++-
tests |only
vignettes/example.Rmd | 7 +++++--
14 files changed, 84 insertions(+), 35 deletions(-)
Title: Detection of Outliers in Time Series
Diff between tsoutliers versions 0.5 dated 2015-01-25 and 0.6 dated 2015-01-27
Description: Detection of outliers in time series following the
Chen and Liu (1993) procedure. Innovative outliers, additive outliers,
level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
tsoutliers-0.5/tsoutliers/inst/CHANGES |only
tsoutliers-0.6/tsoutliers/DESCRIPTION | 8 ++---
tsoutliers-0.6/tsoutliers/MD5 | 22 +++++++--------
tsoutliers-0.6/tsoutliers/NEWS |only
tsoutliers-0.6/tsoutliers/R/locate-outliers.R | 4 +-
tsoutliers-0.6/tsoutliers/R/tso.R | 3 --
tsoutliers-0.6/tsoutliers/inst/doc/index.html | 10 +++---
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.R | 10 +++---
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.Rnw | 18 ++++++------
tsoutliers-0.6/tsoutliers/inst/doc/tsoutliers-intro.pdf |binary
tsoutliers-0.6/tsoutliers/man/locate-outliers.Rd | 2 -
tsoutliers-0.6/tsoutliers/man/tsoutliers.Rd | 6 ++--
tsoutliers-0.6/tsoutliers/vignettes/tsoutliers-intro.Rnw | 18 ++++++------
13 files changed, 50 insertions(+), 51 deletions(-)
Title: Read and Analyze PLEXOS Solutions from R
Diff between rplexos versions 0.11 dated 2014-12-16 and 0.12 dated 2015-01-27
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
NAMESPACE | 1 +
R/process_folder.R | 32 ++++++++++++++++++++------------
R/process_input.R |only
R/process_solution.R | 36 +++++++++++++++++++-----------------
README.md | 2 +-
build/vignette.rds |binary
man/process_folder.Rd | 23 ++++++++++++++++-------
src/process_xml.cpp | 30 +++++++++++++++++++-----------
10 files changed, 89 insertions(+), 60 deletions(-)
Title: Bayesian analysis of qRT-PCR data
Diff between MCMC.qpcr versions 1.1.3 dated 2014-04-13 and 1.1.5 dated 2015-01-27
Description: This package implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. Tutorial: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
DESCRIPTION | 10 +++++-----
MD5 | 12 +++++++-----
NAMESPACE | 1 +
R/HPDplotBygeneBygroup.R | 7 +++++--
R/trellisByGene.R |only
man/MCMC.qpcr-package.Rd | 4 ++--
man/getNormalizedData.Rd | 32 ++++++++++++++++++++++----------
man/trellisByGene.Rd |only
8 files changed, 42 insertions(+), 24 deletions(-)
Title: Functions for Ecdat
Diff between Ecfun versions 0.1-3 dated 2014-11-27 and 0.1-4 dated 2015-01-27
Description: Functions to update datasets in Ecdat and to create,
manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves
DESCRIPTION | 13 -
MD5 | 40 ++---
NAMESPACE | 3
R/BoxCox.R |only
R/matchName.R | 46 ++++--
R/matchName1.R | 117 +++++++++------
R/parseName.R | 21 +-
R/pmatch2.R | 15 +-
R/readCookPVI.R | 6
R/readUShouse.R | 289 ++++++++++++++++++++-------------------
R/subNonStandardCharacters.R | 106 +++++++-------
R/subNonStandardNames.R | 39 ++++-
man/BoxCox.Rd |only
man/grepNonStandardCharacters.Rd | 143 +++++++++----------
man/matchName.Rd | 112 ++++++++++-----
man/mergeUShouse.senate.Rd | 11 -
man/parseName.Rd | 27 +++
man/pmatch2.Rd | 16 ++
man/readUShouse.Rd | 230 +++++++++++++++----------------
man/subNonStandardCharacters.Rd | 251 +++++++++++++++++++--------------
man/subNonStandardNames.Rd | 78 ++++++++--
man/truncdist.Rd | 10 +
22 files changed, 939 insertions(+), 634 deletions(-)
Title: Constrained Inference for Linear Mixed Effects Models
Diff between CLME versions 2.0-1 dated 2014-12-05 and 2.0-2 dated 2015-01-27
Description: Constrained inference for linear mixed effects models using residual bootstrap methodology
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema
DESCRIPTION | 8 -
MD5 | 31 +++---
NEWS | 27 ++++-
R/clme.r | 5 -
R/clme_resids.r | 3
R/minque.r | 2
R/resid_boot.r | 2
R/shiny_clme.r | 167 ++++++++++++++++++++++++++++------
R/summary.clme.r | 5 -
R/utilities.r | 14 +-
inst/doc/clme_intro.R | 218 +++++++++++++++++++++++----------------------
inst/doc/clme_intro.Rnw | 183 +++++++++++++++++++------------------
inst/doc/clme_intro.pdf |binary
inst/doc/clme_vignette.pdf |only
man/minque.Rd | 3
man/shiny.clme.Rd | 92 +++++++++---------
vignettes/clme_intro.Rnw | 183 +++++++++++++++++++------------------
17 files changed, 545 insertions(+), 398 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.10-5 dated 2015-01-23 and 0.10-6 dated 2015-01-27
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NEWS | 5 +++++
inst/doc/cap-recap.pdf |binary
inst/doc/colext.pdf |binary
inst/doc/distsamp.pdf |binary
inst/doc/spp-dist.pdf |binary
inst/doc/unmarked.pdf |binary
src/nll_pcountOpen.cpp | 2 +-
9 files changed, 18 insertions(+), 13 deletions(-)
Title: Maximum Projection Designs
Diff between MaxPro versions 3.1-1 dated 2015-01-27 and 3.1-2 dated 2015-01-27
Description: Generate a maximum projection (MaxPro) design, a MaxPro Latin hypercube design or improve an initial design based on the MaxPro criterion. Details of the MaxPro criterion can be found in: Joseph, V. R., Gul, E., and Ba, S. (2015) "Maximum Projection Designs for Computer Experiments", Biometrika.
Author: Shan Ba and V. Roshan Joseph
Maintainer: Shan Ba
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
man/MaxPro-package.Rd | 6 +++---
man/MaxPro.Rd | 2 +-
man/MaxProImproveLHD.Rd | 6 +++---
man/MaxProLHD.Rd | 2 +-
src/MaxPro.cpp | 8 ++++----
7 files changed, 22 insertions(+), 22 deletions(-)
Title: TraMineR Extension
Diff between TraMineRextras versions 0.2.2 dated 2013-10-29 and 0.2.3 dated 2015-01-27
More information about TraMineRextras at CRAN
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard
DESCRIPTION | 15 +++++++--------
MD5 | 21 ++++++++++++---------
NAMESPACE | 8 ++++++--
R/seqedplot.R | 12 +++++++-----
R/seqgranularity.R | 19 +++++++++++++++++--
R/seqtabstocc.R |only
inst/CITATION |only
inst/NEWS | 18 +++++++++++++++++-
inst/NEWS.Rd | 13 +++++++++++++
man/createdatadiscrete.Rd | 8 ++++----
man/seqemlt.Rd | 45 ++++++++++++++++++++++++++-------------------
man/seqgranularity.Rd | 10 +++-------
man/seqtabstocc.Rd |only
13 files changed, 112 insertions(+), 57 deletions(-)
Permanent link
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Diff between TraMineR versions 1.8-8 dated 2014-01-14 and 1.8-9 dated 2015-01-27
Description: This is a toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard
DESCRIPTION | 14 ++--
MD5 | 52 ++++++++---------
NAMESPACE | 5 +
NEWS | 33 ++++++++++-
R/STS_to_TSE.R | 16 +++--
R/TraMineRInternal.R | 8 ++
R/dissmfacw.R | 2
R/seqpcplot.R | 67 ++++++++++++++++++----
R/seqpm.R | 4 -
build/vignette.rds |binary
data/ex1.rda |binary
data/ex2.rda |binary
data/famform.rda |binary
inst/CITATION | 16 +++--
inst/doc/TraMineR-state-sequence.R | 1
inst/doc/TraMineR-state-sequence.pdf |binary
man/TraMineR-package.Rd | 10 +--
man/TraMineRInternal.Rd | 12 ++--
man/dissmfac.Rd | 5 +
man/seqdef.Rd | 12 ++--
man/seqformat.Rd | 81 +++++++++------------------
man/seqlegend.Rd | 4 -
man/seqlogp.Rd | 10 +--
man/seqpcplot.Rd | 102 ++++++++++++++++++++++++++---------
man/seqplot.Rd | 50 ++++++++---------
man/seqpm.Rd | 9 +--
man/seqtrate.Rd | 2
27 files changed, 319 insertions(+), 196 deletions(-)
Title: Copy Number Estimation from Tumor Genome Sequencing Data
Diff between sequenza versions 2.1.0 dated 2014-10-08 and 2.1.1 dated 2015-01-27
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero
DESCRIPTION | 12 +++---
MD5 | 18 ++++-----
NEWS | 5 ++
R/next.R | 18 ++++++---
exec/sequenza-utils.py | 97 +++++++++++--------------------------------------
inst/CITATION | 9 +++-
inst/doc/sequenza.Rnw | 4 +-
inst/doc/sequenza.pdf |binary
man/VarScan2seqz.Rd | 3 +
vignettes/sequenza.Rnw | 4 +-
10 files changed, 69 insertions(+), 101 deletions(-)
Title: Single-Case Visual Analysis
Diff between SCVA versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27
Description: A package to make graphical representations of single case data and to transform graphical displays back to raw data. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCVA-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Single-Case Randomization Tests
Diff between SCRT versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27
Description: A package for designing single-case phase, alternation and multiple-baseline experiments, as well as for conducting randomization tests on data gathered by means of such designs.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCRT-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Single-Case Meta-Analysis
Diff between SCMA versions 1.1 dated 2014-01-13 and 1.1.1 dated 2015-01-27
Description: An R package for single-case meta-analysis.
Author: Isis Bulte
Maintainer: Bart Michiels
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/SCMA-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Rcmdr Plugin for Designing and Analyzing Single-case Experiments
Diff between RcmdrPlugin.SCDA versions 1.0 dated 2014-03-19 and 1.1 dated 2015-01-27
More information about RcmdrPlugin.SCDA at CRAN
Description: Provides a GUI for the SCVA, SCRT and SCMA packages. The package is written as an Rcmdr plugin.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels
DESCRIPTION | 14
MD5 | 6
R/RcmdrPlugin.SCDA.R | 970 ++++++++++++++++------------------------
man/RcmdrPlugin.SCDA-package.Rd | 11
4 files changed, 420 insertions(+), 581 deletions(-)
Permanent link
Title: Quantile Regression for Linear Mixed-Effects Models
Diff between qrLMM versions 1.0-9 dated 2015-01-08 and 1.1 dated 2015-01-27
Description: Quantile regression (QR) for Linear
Mixed-Effects Models via the asymmetric Laplace distribution (ALD).
It uses the Stochastic Approximation of the EM (SAEM) algorithm for
deriving exact maximum likelihood estimates and full inference results
for the fixed-effects and variance components.
It also provides graphical summaries for assessing the algorithm
convergence and fitting results.
Author: Christian E. Galarza
Maintainer: Christian E. Galarza
DESCRIPTION | 8 ++++----
MD5 | 6 +++++-
data |only
man/Cholesterol.Rd |only
man/Orthodont.Rd |only
5 files changed, 9 insertions(+), 5 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-0 dated 2015-01-05 and 1.1-3 dated 2015-01-27
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
openair-1.1-0/openair/NEWS |only
openair-1.1-3/openair/DESCRIPTION | 14 ++--
openair-1.1-3/openair/MD5 | 75 +++++++++++++-------------
openair-1.1-3/openair/NAMESPACE | 1
openair-1.1-3/openair/R/GoogleMapsPlot.R | 3 +
openair-1.1-3/openair/R/TaylorDiagram.R | 28 ++++++---
openair-1.1-3/openair/R/TheilSen.R | 20 ++++--
openair-1.1-3/openair/R/calendarPlot.R | 18 +++++-
openair-1.1-3/openair/R/conditionalEval.R | 15 +++--
openair-1.1-3/openair/R/conditionalQuantile.R | 17 ++++-
openair-1.1-3/openair/R/corPlot.R | 13 +++-
openair-1.1-3/openair/R/kernelExceed.R | 9 ++-
openair-1.1-3/openair/R/linearRelation.R | 15 +++--
openair-1.1-3/openair/R/openair.generics.R | 3 -
openair-1.1-3/openair/R/percentileRose.R | 17 ++++-
openair-1.1-3/openair/R/polarAnnulus.R | 18 ++++--
openair-1.1-3/openair/R/polarCluster.R | 17 ++++-
openair-1.1-3/openair/R/polarFreq.R | 17 ++++-
openair-1.1-3/openair/R/polarPlot.R | 32 +++++++----
openair-1.1-3/openair/R/scatterPlot.R | 64 +++++++++++++---------
openair-1.1-3/openair/R/smoothTrend.R | 11 +++
openair-1.1-3/openair/R/summaryPlot.R | 18 ++++--
openair-1.1-3/openair/R/timePlot.R | 17 ++++-
openair-1.1-3/openair/R/timeProp.R | 11 +++
openair-1.1-3/openair/R/timeVariation.R | 18 ++++--
openair-1.1-3/openair/R/trajCluster.R | 11 +++
openair-1.1-3/openair/R/trajLevel.R | 27 +++++++--
openair-1.1-3/openair/R/trajPlot.R | 33 ++++++++++-
openair-1.1-3/openair/R/trendLevel.R | 35 +++++++-----
openair-1.1-3/openair/R/utilities.R | 7 ++
openair-1.1-3/openair/R/windRose.R | 12 +++-
openair-1.1-3/openair/README.md |only
openair-1.1-3/openair/inst/plume.png |only
openair-1.1-3/openair/inst/windRose.png |only
openair-1.1-3/openair/inst/windRosePM10.png |only
openair-1.1-3/openair/man/TaylorDiagram.Rd | 5 -
openair-1.1-3/openair/man/TheilSen.Rd | 2
openair-1.1-3/openair/man/scatterPlot.Rd | 9 ++-
openair-1.1-3/openair/man/trajLevel.Rd | 2
openair-1.1-3/openair/man/trajPlot.Rd | 2
openair-1.1-3/openair/src/rolling.cpp | 2
41 files changed, 434 insertions(+), 184 deletions(-)
Title: Draw Diagrams (mis)Representing the Results of Mass Spec
Experiments
Diff between msarc versions 1.4.3 dated 2014-12-04 and 1.4.5 dated 2015-01-27
Description: The output of an affinity-purification mass spectrometry
experiment is typically a list of proteins that were observed
in the experiment, identified by UniProt identifiers
(http://www.uniprot.org/). This package takes as input a list of
UniProt identifiers, and the associated Mascot scores from the
experiment (which indicate the likelihood that the protein has
been correctly identified), clusters them by gene ontology
category (http://geneontology.org/), then draws diagrams
showing the results in hierarchical clusters by category, with lines
for individual proteins representing the associated Mascot score.
The results are in general not publication-ready, but will rather
require editing via a graphics editor that can interpret SVG (scalable
vector graphics) format. As an alternative representation, the
package will also generate tag clouds based on the Mascot scores.
Author: Gord Brown, Hisham Mohammed
Maintainer: Gord Brown
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 6 +++---
R/cluster.R | 2 +-
R/plotter.R | 4 ++--
inst/doc/msarc.pdf |binary
6 files changed, 16 insertions(+), 16 deletions(-)
Title: Tools for Biostatistics, Public Policy, and Law
Diff between lawstat versions 2.4.1 dated 2013-12-16 and 2.5 dated 2015-01-27
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness,
measures of relative variability etc, the package contains new robust tests of symmetry,
omnibus and directional tests of normality, and their graphical counterparts such as
Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods
are illustrated by simulations and real-life examples from legal statistics, economics,
and biostatistics.
Author: (in alphabetical order)
Joseph L. Gastwirth
Maintainer: Vyacheslav Lyubchich
lawstat-2.4.1/lawstat/R/wavk.test.R |only
lawstat-2.4.1/lawstat/man/wavk.test.Rd |only
lawstat-2.5/lawstat/DESCRIPTION | 36 ++++++++++++++-------------------
lawstat-2.5/lawstat/MD5 | 6 +----
lawstat-2.5/lawstat/NAMESPACE | 4 ++-
5 files changed, 21 insertions(+), 25 deletions(-)
Title: Flux Estimation with Static Chamber Data
Diff between HMR versions 0.3.2 dated 2014-12-12 and 0.4.1 dated 2015-01-27
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen
Maintainer: Asger R. Pedersen
DESCRIPTION | 11 +++----
MD5 | 8 ++---
R/HMR.fit1.R | 67 +++++++++++++++++++++++++++++++++++-------
R/HMR.main.R | 92 ++++++++++++++++++++++++++++++++++++++++++++++-------------
man/HMR.Rd | 37 ++++++++++++++---------
5 files changed, 159 insertions(+), 56 deletions(-)
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 1.3.2 dated 2014-12-10 and 2.0 dated 2015-01-27
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
decompr-1.3.2/decompr/R/kung_fu.R |only
decompr-1.3.2/decompr/data/wiod2.rda |only
decompr-2.0/decompr/DESCRIPTION | 20
decompr-2.0/decompr/MD5 | 56 +
decompr-2.0/decompr/NAMESPACE | 16
decompr-2.0/decompr/NEWS | 198 +++---
decompr-2.0/decompr/R/decomp.R | 140 ++--
decompr-2.0/decompr/R/decompr.R | 130 ++--
decompr-2.0/decompr/R/leontief.R |only
decompr-2.0/decompr/R/load_tables.R | 97 +--
decompr-2.0/decompr/R/load_tables_vectors.R | 439 +++++++------
decompr-2.0/decompr/R/vertical_specialisation.R |only
decompr-2.0/decompr/R/wwz.R | 659 ++++++++++-----------
decompr-2.0/decompr/README.md | 134 ++--
decompr-2.0/decompr/data/leather.rda |only
decompr-2.0/decompr/data/wiod.rda |binary
decompr-2.0/decompr/inst/CITATION | 34 -
decompr-2.0/decompr/man/countries.Rd |only
decompr-2.0/decompr/man/decomp.Rd | 140 ++--
decompr-2.0/decompr/man/decompr.Rd | 41 -
decompr-2.0/decompr/man/final.Rd |only
decompr-2.0/decompr/man/final_demand.Rd | 27
decompr-2.0/decompr/man/industries.Rd |only
decompr-2.0/decompr/man/industry_names.Rd | 27
decompr-2.0/decompr/man/inter.Rd |only
decompr-2.0/decompr/man/intermediate_demand.Rd | 27
decompr-2.0/decompr/man/kung_fu.Rd | 79 +-
decompr-2.0/decompr/man/leontief.Rd |only
decompr-2.0/decompr/man/load_tables.Rd | 73 +-
decompr-2.0/decompr/man/load_tables_vectors.Rd | 101 +--
decompr-2.0/decompr/man/out.Rd |only
decompr-2.0/decompr/man/output.Rd | 27
decompr-2.0/decompr/man/region_names.Rd | 27
decompr-2.0/decompr/man/vertical_specialisation.Rd |only
decompr-2.0/decompr/man/wwz.Rd | 84 +-
35 files changed, 1351 insertions(+), 1225 deletions(-)
Title: Phenotypic Integration Index
Diff between PHENIX versions 1.0 dated 2014-10-24 and 1.1 dated 2015-01-27
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), a bootstrapping method to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
PHENIX-1.0/PHENIX/R/int.R |only
PHENIX-1.0/PHENIX/R/int.boot.R |only
PHENIX-1.0/PHENIX/R/intsc.R |only
PHENIX-1.0/PHENIX/R/intsc.boot.R |only
PHENIX-1.0/PHENIX/man/int.Rd |only
PHENIX-1.0/PHENIX/man/int.boot.Rd |only
PHENIX-1.0/PHENIX/man/intsc.Rd |only
PHENIX-1.0/PHENIX/man/intsc.boot.Rd |only
PHENIX-1.1/PHENIX/DESCRIPTION | 12 +++++-----
PHENIX-1.1/PHENIX/MD5 | 35 ++++++++++++++++++--------------
PHENIX-1.1/PHENIX/NAMESPACE | 3 +-
PHENIX-1.1/PHENIX/NEWS |only
PHENIX-1.1/PHENIX/R/cor.par.R | 12 ++++++----
PHENIX-1.1/PHENIX/R/pint.R |only
PHENIX-1.1/PHENIX/R/pint.boot.R |only
PHENIX-1.1/PHENIX/R/pint.p.R |only
PHENIX-1.1/PHENIX/R/pintsc.R |only
PHENIX-1.1/PHENIX/R/pintsc.boot.R |only
PHENIX-1.1/PHENIX/R/pintsc.p.R |only
PHENIX-1.1/PHENIX/man/PHENIX-package.Rd | 11 +++++-----
PHENIX-1.1/PHENIX/man/cor.par.Rd | 13 ++++++-----
PHENIX-1.1/PHENIX/man/paeonia.Rd | 8 +++----
PHENIX-1.1/PHENIX/man/pint.Rd |only
PHENIX-1.1/PHENIX/man/pint.boot.Rd |only
PHENIX-1.1/PHENIX/man/pint.p.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.boot.Rd |only
PHENIX-1.1/PHENIX/man/pintsc.p.Rd |only
PHENIX-1.1/PHENIX/man/tussilago.Rd | 6 ++---
29 files changed, 55 insertions(+), 45 deletions(-)
Title: Analysis of Feedback in Time Series
Diff between FeedbackTS versions 1.3 dated 2015-01-05 and 1.3.1 dated 2015-01-27
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NAMESPACE | 6 ++++--
man/FeedbackTS-package.Rd | 6 +++---
man/KDD-class.Rd | 27 +++++++++++++++------------
man/KDD.yearly.average-class.Rd | 11 ++++++-----
man/KT.output-class.Rd | 22 ++++++++++++++--------
man/feedback.test.Rd | 5 ++---
8 files changed, 55 insertions(+), 44 deletions(-)
Title: Geographic data analysis and modeling
Diff between raster versions 2.3-12 dated 2014-10-18 and 2.3-24 dated 2015-01-27
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 11 +
DESCRIPTION | 14 +-
MD5 | 121 ++++++++---------
R/AAAClasses.R | 1
R/aggregate_sp.R | 2
R/buffer.R | 2
R/canProcessInMemory.R | 4
R/clump.R | 2
R/connection.R | 6
R/coverPolygons.R | 2
R/cropSpatial.R | 4
R/erase.R | 2
R/extractPoints.R | 25 ---
R/extractPoints_sp.R |only
R/extractPolygons.R | 16 +-
R/factor.R | 7 -
R/freq.R | 12 -
R/gdal.R | 2
R/getData.R | 4
R/gridDistance.R | 2
R/hillShade.R | 2
R/imageplot.R | 30 ----
R/indexReplace.R | 2
R/indexReplaceBrick.R | 6
R/intersect.R | 12 -
R/intersect_sp.R | 101 +++++++++++++-
R/isLonLat.R | 10 +
R/kml_multiple.R | 6
R/mean.R | 101 ++------------
R/multiCore.R | 2
R/netCDFtoRasterCD.R | 4
R/netCDFutil.R | 4
R/netCDFwriteCD.R | 99 +++++++-------
R/nsidcICE.R | 114 ++++++++--------
R/overlay.R | 2
R/plotCT.R | 2
R/plotRGB.R | 2
R/progressBar.R | 2
R/rasterFromFile.R | 2
R/rasterFromRasterFile.R | 2
R/rasterToPolygons.R | 2
R/rowMinMax.R | 5
R/sampleStratified.R | 5
R/select.R | 4
R/symdif.R | 2
R/tmpFile.R | 4
R/trim.R | 10 -
R/union_sp.R | 4
R/writeRaster.R | 2
R/zApply.R | 2
build/vignette.rds |binary
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/Raster-classes.Rd | 1
man/extract.Rd | 25 ++-
man/getData.Rd | 17 ++
man/interpolate.Rd | 5
man/intersect.Rd | 10 -
man/raster.Rd | 326 ++++++++++++++++++++++++-----------------------
src/dist_util.c | 2
src/edge.c | 2
62 files changed, 594 insertions(+), 578 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.55 dated 2015-01-14 and 3.0.59 dated 2015-01-27
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
RandomFields-3.0.55/RandomFields/src/Covariance.h |only
RandomFields-3.0.59/RandomFields/DESCRIPTION | 8
RandomFields-3.0.59/RandomFields/MD5 | 253
RandomFields-3.0.59/RandomFields/NAMESPACE | 66
RandomFields-3.0.59/RandomFields/R/Class.R | 23
RandomFields-3.0.59/RandomFields/R/Crossvalidation.R | 2
RandomFields-3.0.59/RandomFields/R/Methods-aux.R | 144
RandomFields-3.0.59/RandomFields/R/QMath.R |only
RandomFields-3.0.59/RandomFields/R/RC_GLOBALS.R | 4
RandomFields-3.0.59/RandomFields/R/RCauto.R | 46
RandomFields-3.0.59/RandomFields/R/RFempvario-Methods-plots.R | 10
RandomFields-3.0.59/RandomFields/R/RFempvario.R | 104
RandomFields-3.0.59/RandomFields/R/RFgui.R | 32
RandomFields-3.0.59/RandomFields/R/RMmodels-Methods-plots.R | 176
RandomFields-3.0.59/RandomFields/R/RMmodels.R | 4333 +++++++---
RandomFields-3.0.59/RandomFields/R/RMmodelsConvenience.R | 17
RandomFields-3.0.59/RandomFields/R/RMmodelsSpecial.R | 2
RandomFields-3.0.59/RandomFields/R/auxiliary.R | 276
RandomFields-3.0.59/RandomFields/R/basic.fctns.R |only
RandomFields-3.0.59/RandomFields/R/convert.R | 377
RandomFields-3.0.59/RandomFields/R/convert_new.R | 291
RandomFields-3.0.59/RandomFields/R/fitgauss.R | 13
RandomFields-3.0.59/RandomFields/R/generatemodels.R | 319
RandomFields-3.0.59/RandomFields/R/getNset.R | 184
RandomFields-3.0.59/RandomFields/R/internal_use.R | 583 -
RandomFields-3.0.59/RandomFields/R/kriging.R | 753 -
RandomFields-3.0.59/RandomFields/R/obsolete.R | 17
RandomFields-3.0.59/RandomFields/R/rf.R | 291
RandomFields-3.0.59/RandomFields/R/zzz.R |only
RandomFields-3.0.59/RandomFields/inst/CITATION | 40
RandomFields-3.0.59/RandomFields/man/CoordinateSystems.Rd | 5
RandomFields-3.0.59/RandomFields/man/MajorRevisions.Rd | 14
RandomFields-3.0.59/RandomFields/man/QMath.Rd |only
RandomFields-3.0.59/RandomFields/man/RC.Rd | 4
RandomFields-3.0.59/RandomFields/man/RF.Rd | 17
RandomFields-3.0.59/RandomFields/man/RFcov.Rd | 3
RandomFields-3.0.59/RandomFields/man/RFcrossvalidate.Rd | 3
RandomFields-3.0.59/RandomFields/man/RFempVariog-class.Rd | 4
RandomFields-3.0.59/RandomFields/man/RFempiricalvariogram.Rd | 5
RandomFields-3.0.59/RandomFields/man/RFfit-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFfit.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFformula.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFgetModelNames.Rd | 8
RandomFields-3.0.59/RandomFields/man/RFgridDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFinterpolate.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFoptions.Rd | 15
RandomFields-3.0.59/RandomFields/man/RFpointsDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFratiotest.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulate.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulate.more.examples.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFsimulateAdvanced.Rd | 20
RandomFields-3.0.59/RandomFields/man/RFsp-class.Rd | 4
RandomFields-3.0.59/RandomFields/man/RFsp2conventional.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFspatialGridDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RFspatialPointsDataFrame-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMconstant.Rd | 35
RandomFields-3.0.59/RandomFields/man/RMcovariate.Rd |only
RandomFields-3.0.59/RandomFields/man/RMdelay.Rd | 9
RandomFields-3.0.59/RandomFields/man/RMfix.Rd |only
RandomFields-3.0.59/RandomFields/man/RMgennsst.Rd |only
RandomFields-3.0.59/RandomFields/man/RMgneiting.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMiaco.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmatrix.Rd | 9
RandomFields-3.0.59/RandomFields/man/RMmodel-class.Rd | 34
RandomFields-3.0.59/RandomFields/man/RMmodel.Rd | 6
RandomFields-3.0.59/RandomFields/man/RMmodelExt-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmodelgenerator-class.Rd | 2
RandomFields-3.0.59/RandomFields/man/RMmodelsAdvanced.Rd | 17
RandomFields-3.0.59/RandomFields/man/RMmodelsAuxiliary.Rd | 4
RandomFields-3.0.59/RandomFields/man/RMmodelsSphere.Rd | 7
RandomFields-3.0.59/RandomFields/man/RMmodelsTailcorrelation.Rd | 1
RandomFields-3.0.59/RandomFields/man/RMmult.Rd | 3
RandomFields-3.0.59/RandomFields/man/RMnsst.Rd | 3
RandomFields-3.0.59/RandomFields/man/RMplus.Rd | 1
RandomFields-3.0.59/RandomFields/man/RMprod.Rd |only
RandomFields-3.0.59/RandomFields/man/RMsum.Rd |only
RandomFields-3.0.59/RandomFields/man/RMtrafo.Rd | 16
RandomFields-3.0.59/RandomFields/man/RMtrend.Rd | 12
RandomFields-3.0.59/RandomFields/man/RP.Rd | 2
RandomFields-3.0.59/RandomFields/man/RR.Rd | 5
RandomFields-3.0.59/RandomFields/man/RandomFields.Rd | 17
RandomFields-3.0.59/RandomFields/man/conventional2RFspDataFrame.Rd | 3
RandomFields-3.0.59/RandomFields/man/internal.Rd | 5
RandomFields-3.0.59/RandomFields/man/papers.Rd | 12
RandomFields-3.0.59/RandomFields/man/papers.jss14.Rd | 15
RandomFields-3.0.59/RandomFields/man/soil.Rd | 4
RandomFields-3.0.59/RandomFields/src/AutoRandomFields.cc | 20
RandomFields-3.0.59/RandomFields/src/AutoRandomFields.h | 40
RandomFields-3.0.59/RandomFields/src/Brown.cc | 199
RandomFields-3.0.59/RandomFields/src/Coordinate_systems.cc | 248
RandomFields-3.0.59/RandomFields/src/Coordinate_systems.h |only
RandomFields-3.0.59/RandomFields/src/D.H.cc | 10
RandomFields-3.0.59/RandomFields/src/Gneiting.cc | 257
RandomFields-3.0.59/RandomFields/src/Huetchen.cc | 41
RandomFields-3.0.59/RandomFields/src/InternalCov.cc | 478 -
RandomFields-3.0.59/RandomFields/src/KeyInfo.cc | 151
RandomFields-3.0.59/RandomFields/src/MLE.cc | 126
RandomFields-3.0.59/RandomFields/src/Operator.h |only
RandomFields-3.0.59/RandomFields/src/PoissonPolygon.cc | 32
RandomFields-3.0.59/RandomFields/src/Primitive.cc | 945 +-
RandomFields-3.0.59/RandomFields/src/QMath.cc |only
RandomFields-3.0.59/RandomFields/src/RF.h | 176
RandomFields-3.0.59/RandomFields/src/RandomFields.h | 5
RandomFields-3.0.59/RandomFields/src/Specific.cc | 6
RandomFields-3.0.59/RandomFields/src/Xempvario.cc | 7
RandomFields-3.0.59/RandomFields/src/auxiliary.cc | 43
RandomFields-3.0.59/RandomFields/src/avltr_modified.cc | 2
RandomFields-3.0.59/RandomFields/src/basic.h | 3
RandomFields-3.0.59/RandomFields/src/circulant.cc | 88
RandomFields-3.0.59/RandomFields/src/direct.cc | 36
RandomFields-3.0.59/RandomFields/src/empvario.cc | 4
RandomFields-3.0.59/RandomFields/src/extremes.cc | 51
RandomFields-3.0.59/RandomFields/src/families.cc | 6
RandomFields-3.0.59/RandomFields/src/fftVario.cc | 5
RandomFields-3.0.59/RandomFields/src/gauss.cc | 71
RandomFields-3.0.59/RandomFields/src/getNset.cc | 565 -
RandomFields-3.0.59/RandomFields/src/hilfsdateien.cc | 2
RandomFields-3.0.59/RandomFields/src/hyperplan.cc | 26
RandomFields-3.0.59/RandomFields/src/initNerror.cc | 471 -
RandomFields-3.0.59/RandomFields/src/kriging.cc | 52
RandomFields-3.0.59/RandomFields/src/nugget.cc | 12
RandomFields-3.0.59/RandomFields/src/operator.cc | 220
RandomFields-3.0.59/RandomFields/src/plusmalS.cc | 523 -
RandomFields-3.0.59/RandomFields/src/primitive.h | 47
RandomFields-3.0.59/RandomFields/src/rf_interfaces.cc | 387
RandomFields-3.0.59/RandomFields/src/sequential.cc | 30
RandomFields-3.0.59/RandomFields/src/shape_processes.h | 2
RandomFields-3.0.59/RandomFields/src/spectral.cc | 7
RandomFields-3.0.59/RandomFields/src/startGetNset.cc | 125
RandomFields-3.0.59/RandomFields/src/tbm.cc | 28
RandomFields-3.0.59/RandomFields/src/trend.cc | 58
RandomFields-3.0.59/RandomFields/src/userinterfaces.cc | 90
RandomFields-3.0.59/RandomFields/src/variogramAndCo.cc | 388
RandomFields-3.0.59/RandomFields/src/variogramAndCo.h | 163
134 files changed, 8627 insertions(+), 6337 deletions(-)
Title: Permutations and Mallows Distributions
Diff between PerMallows versions 1.7 dated 2014-09-15 and 1.8 dated 2015-01-27
Description: Includes functions to work with the Mallows, Generalized Mallows and Weighted Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances and the random generation of permutations.
Author: Ekhine Irurozki
Maintainer: Ekhine Irurozki
DESCRIPTION | 10
MD5 | 129 ++++++------
R/PerMallows.R | 86 +++++---
man/compose.Rd | 3
man/count.derangements.Rd | 3
man/count.perms.cycles.Rd | 3
man/count.perms.distance.Rd | 3
man/count.perms.fixed.points.Rd | 3
man/count.perms.unfixed.points.gtet.Rd | 3
man/cycle2str.Rd | 3
man/cycles2permutation.Rd | 3
man/data.apa.Rd | 3
man/data.order.Rd | 3
man/decomposition2permutation.Rd | 3
man/dgmm.Rd | 3
man/distance.Rd | 3
man/dmm.Rd | 3
man/expectation.gmm.Rd | 3
man/expectation.mm.Rd | 3
man/freq.matrix.Rd | 3
man/generate.aux.files.Rd | 3
man/identity.permutation.Rd | 3
man/insert.at.Rd | 3
man/inverse.permutation.Rd | 3
man/inversion.at.Rd | 3
man/is.permutation.Rd | 7
man/lgmm.Rd | 3
man/lgmm.theta.Rd | 3
man/lmm.Rd | 3
man/lmm.theta.Rd | 3
man/marginal.Rd | 3
man/maxi.dist.Rd |only
man/order.ratings.Rd | 3
man/perm.sample.med.Rd | 3
man/perm.sample.small.Rd | 3
man/permutation2cycles.Rd | 3
man/permutation2decomposition.Rd | 3
man/permutations.of.Rd | 3
man/r.derangement.Rd | 3
man/r.dist.d.Rd | 3
man/r.perms.cycles.Rd | 3
man/read.permutation.file.Rd | 3
man/rgmm.Rd | 3
man/rmm.Rd | 3
man/runif.permutation.Rd | 3
man/swap.Rd | 3
src/Cayley.cpp | 345 ++++++++++++---------------------
src/Cayley.h | 50 +++-
src/Ferrers_diagram.cpp | 6
src/Ferrers_diagram.h | 7
src/Generic.cpp | 113 ++--------
src/Generic.h | 18 -
src/Hamming.cpp | 201 ++-----------------
src/Hamming.h | 48 ++--
src/Kendall.cpp | 71 +++---
src/Kendall.h | 2
src/Lap.h | 2
src/Newton_raphson.cpp | 45 +---
src/Newton_raphson.h | 3
src/Ulam.cpp | 145 ++-----------
src/Ulam.h | 51 +---
src/Ulam_disk.cpp | 270 ++++++++++++++++---------
src/Ulam_disk.h | 47 ++--
src/Wrapper.cpp | 9
src/main.cpp | 86 ++++++--
vignettes/PerMallows.tex | 204 +++++++++----------
66 files changed, 943 insertions(+), 1135 deletions(-)
Title: Classification, Regression and Feature Evaluation
Diff between CORElearn versions 0.9.44 dated 2014-12-24 and 0.9.45 dated 2015-01-27
Description: The package is a port of stand-alone C++ software to R.
It contains several machine learning model learning techniques in classification and regression,
for example classification and regression trees with optional constructive induction and models in the leafs,
random forests, kNN, naive Bayes, and locally weighted regression.
It is especially strong in feature evaluation where it contains several variants of Relief
algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM.
Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja"
ChangeLog | 1
DESCRIPTION | 18 -
MD5 | 139 +++----
NAMESPACE | 37 +-
R/Rinterface.R | 74 ++--
R/rfVisualize.R | 14
man/CORElearn-package.Rd | 6
man/CoreModel.Rd | 6
man/attrEval.Rd | 6
man/classPrototypes.Rd | 2
man/destroyModels.Rd | 2
man/display.CoreModel.Rd |only
man/getCoreModel.Rd | 2
man/getRpartModel.Rd | 26 -
man/modelEval.Rd | 16
man/ordDataGen.Rd | 2
man/ordEval.Rd | 2
man/plot.CoreModel.Rd | 41 +-
man/plot.ordEval.Rd | 7
man/predict.CoreModel.Rd | 2
man/rfOutliers.Rd | 2
man/saveRF.Rd | 10
src/Rconvert.cpp | 21 -
src/Rfront.cpp | 85 ++--
src/Rfront.h | 21 +
src/binarize.cpp | 26 -
src/binarizeReg.cpp | 28 -
src/binnode.h | 4
src/binnodeReg.h | 5
src/c45read.cpp | 2
src/c45read.h | 8
src/calibrate.cpp | 8
src/calibrate.h | 2
src/constrct.cpp | 8
src/constrct.h | 17
src/constrctReg.cpp | 6
src/constrctReg.h | 17
src/contain.h | 4
src/dataStore.cpp | 19 -
src/dataStore.h | 10
src/estCommon.cpp | 38 +-
src/estimator.cpp | 42 +-
src/estimatorReg.cpp | 22 -
src/expr.cpp | 12
src/expr.h | 6
src/exprReg.cpp | 8
src/exprReg.h | 10
src/frontend.cpp | 18 -
src/ftree.cpp | 44 --
src/ftree.h | 14
src/general.h | 2
src/kdtree.cpp | 26 -
src/kdtree.h | 7
src/modelReg.cpp | 2
src/mstring.cpp | 8
src/mstring.h | 1
src/printUtil.cpp | 4
src/regtree.cpp | 45 --
src/regtree.h | 159 ++++----
src/relieff.cpp | 2
src/rfUtil.cpp | 1
src/rfVisual.cpp | 8
src/rndforest.cpp | 10
src/rndforest.h | 2
src/rrelieff.cpp | 6
src/treenode.cpp | 18 -
src/treenodeReg.cpp | 18 -
src/trutil.cpp | 279 +++++++++------
src/trutilReg.cpp | 842 +++++++++++++++++++++++++----------------------
src/utils.cpp | 2
src/utils.h | 11
71 files changed, 1303 insertions(+), 1070 deletions(-)
Title: Univariate and Multivariate Spatial-temporal Modeling
Diff between spBayes versions 0.3-8 dated 2013-11-15 and 0.3-9 dated 2015-01-27
Description: Fits univariate and multivariate spatio-temporal
models with Markov chain Monte Carlo (MCMC).
Author: Andrew O. Finley
Maintainer: Andrew O. Finley
DESCRIPTION | 10 +++++-----
MD5 | 27 ++++++++++++++-------------
NAMESPACE | 2 ++
inst/CITATION |only
inst/ChangeLog | 6 ++++++
man/spDynLM.Rd | 4 ++++
man/spGLM.Rd | 8 +++++++-
man/spLM.Rd | 4 ++++
man/spMisalignGLM.Rd | 2 ++
man/spMisalignLM.Rd | 2 ++
man/spMvGLM.Rd | 4 ++++
man/spMvLM.Rd | 4 ++++
man/spPredict.Rd | 4 ++++
man/spRecover.Rd | 4 ++++
src/spMisalign.cpp | 2 +-
15 files changed, 63 insertions(+), 20 deletions(-)
Title: Multidimensional Scaling in R: SMACOF.
Diff between smacof versions 1.5-0 dated 2014-06-23 and 1.6-2 dated 2015-01-27
Description: This package provides the following approaches of multidimensional
scaling (MDS) based on stress minimization by means of majorization
(smacof): Simple smacof (basic MDS) on symmetric dissimilarity matrices,
smacof for rectangular matrices (unfolding models), smacof with constraints
on the configuration, three-way smacof for individual differences
(including constraints for idioscal, indscal, and identity), and spherical
smacof (primal and dual algorithm). The MDS type can be ratio, interval, ordinal manner
(including primary, secondary, and tertiary approaches for tie handling), and msplines.
Jackknife and permutation tests are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Ingwer Borg [ctb], Patrick
J. F. Groenen [aut]
Maintainer: Patrick Mair
smacof-1.5-0/smacof/inst/doc |only
smacof-1.6-2/smacof/DESCRIPTION | 19 +++++-----
smacof-1.6-2/smacof/MD5 | 54 ++++++++++---------------------
smacof-1.6-2/smacof/NAMESPACE | 4 ++
smacof-1.6-2/smacof/R/idioscal.R |only
smacof-1.6-2/smacof/R/indscal.R |only
smacof-1.6-2/smacof/R/mds.R |only
smacof-1.6-2/smacof/R/plot.smacof.R | 8 ++--
smacof-1.6-2/smacof/R/plot.smacofID.r | 8 ++--
smacof-1.6-2/smacof/R/plot.smacofJK.R | 4 +-
smacof-1.6-2/smacof/R/plot.smacofR.R | 4 +-
smacof-1.6-2/smacof/R/print.smacofB.R | 2 -
smacof-1.6-2/smacof/R/smacofIndDiff.R | 26 ++++----------
smacof-1.6-2/smacof/R/smacofRect.R | 17 +++++----
smacof-1.6-2/smacof/R/smacofSym.R | 2 -
smacof-1.6-2/smacof/R/unfolding.R |only
smacof-1.6-2/smacof/inst/NEWS.Rd | 7 ++++
smacof-1.6-2/smacof/man/smacofIndDiff.Rd | 29 ++++++++++++++--
smacof-1.6-2/smacof/man/smacofRect.Rd | 14 +++-----
smacof-1.6-2/smacof/man/smacofSym.Rd | 18 ++++++----
20 files changed, 114 insertions(+), 102 deletions(-)
Title: Relative Distribution Methods
Diff between reldist versions 1.6-3 dated 2014-08-20 and 1.6-4 dated 2015-01-27
Description: R functions for the comparison of distributions.
This includes nonparametric estimation of the relative distribution
PDF and CDF and numerical summaries as described in
"Relative Distribution Methods in the Social Sciences"
by Mark S. Handcock and Martina Morris,
Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789
Author: Mark S. Handcock
Maintainer: Mark S. Handcock
DESCRIPTION | 10 +++++-----
LICENSE | 2 +-
MD5 | 20 ++++++++++----------
R/bgk_kde.R | 7 +++++--
R/reldist.R | 33 +++++++++++++++++++++++++++------
R/wtd.quantile.R | 2 +-
inst/CITATION | 6 +++---
man/gini.Rd | 4 ++--
man/precipitation.Rd | 2 +-
man/reldist.Rd | 24 +++++++++++++++---------
tests/FigSM.R | 3 ++-
11 files changed, 72 insertions(+), 41 deletions(-)
More information about quantification at CRAN
Permanent link
Title: Metric Unfolding
Diff between munfold versions 0.3-1 dated 2013-01-05 and 0.3-3 dated 2015-01-27
Description: This package provides Schoeneman's algorithm for metric
multidimensional unfolding and Procrustes rotation of unfolding results.
Author: Martin Elff
Maintainer: Martin Elff
DESCRIPTION | 18 ++++++++++--------
MD5 | 9 +++++----
NAMESPACE | 30 +++++++++++++++---------------
R/Unfold.R | 4 ++--
R/schoenemann.R | 5 ++---
inst |only
6 files changed, 34 insertions(+), 32 deletions(-)
Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Diff between icd9 versions 0.5 dated 2014-07-21 and 1.0 dated 2015-01-27
Description: Calculate comorbidities, and perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9-CM
(clinical modification) codes. ICD-9 codes appear numeric but leading and
trailing zeroes, and both decimal and non-decimal "short" format codes
exist. The package enables a work flow from raw lists of ICD-9 codes from
hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey
icd9-0.5/icd9/NEWS |only
icd9-0.5/icd9/data/elixhauserComorbid.RData |only
icd9-0.5/icd9/data/quanElixhauserComorbid.RData |only
icd9-0.5/icd9/inst/doc/icd9.Rnw |only
icd9-0.5/icd9/inst/extdata/ICD9_E_Charlson.sas.txt |only
icd9-0.5/icd9/inst/extdata/ccs_multi_pr_tool_2014.csv |only
icd9-0.5/icd9/inst/extdata/comoanaly2012-2013.txt |only
icd9-0.5/icd9/man/allIsNumeric.Rd |only
icd9-0.5/icd9/man/appendZeroToNine.Rd |only
icd9-0.5/icd9/man/asCharacterNoWarn.Rd |only
icd9-0.5/icd9/man/asNumericNoWarn.Rd |only
icd9-0.5/icd9/man/elixhauserComorbid.Rd |only
icd9-0.5/icd9/man/elixhauserComorbidNames.Rd |only
icd9-0.5/icd9/man/grapes-nin-grapes.Rd |only
icd9-0.5/icd9/man/icd9ChildrenDecimal.Rd |only
icd9-0.5/icd9/man/icd9ChildrenShort.Rd |only
icd9-0.5/icd9/man/icd9Comorbidities.Rd |only
icd9-0.5/icd9/man/icd9CondenseToExplain.Rd |only
icd9-0.5/icd9/man/icd9CondenseToMajor.Rd |only
icd9-0.5/icd9/man/icd9DecimalToParts.Rd |only
icd9-0.5/icd9/man/icd9DecimalToShort.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeDecimal.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeMajor.Rd |only
icd9-0.5/icd9/man/icd9ExpandRangeShort.Rd |only
icd9-0.5/icd9/man/icd9GetMajor.Rd |only
icd9-0.5/icd9/man/icd9InvalidActions.Rd |only
icd9-0.5/icd9/man/icd9InvalidDecimal.Rd |only
icd9-0.5/icd9/man/icd9IsVE.Rd |only
icd9-0.5/icd9/man/icd9ParentMinor.Rd |only
icd9-0.5/icd9/man/icd9PartsRecompose.Rd |only
icd9-0.5/icd9/man/icd9Real.Rd |only
icd9-0.5/icd9/man/icd9ShortToDecimal.Rd |only
icd9-0.5/icd9/man/icd9ShortToParts.Rd |only
icd9-0.5/icd9/man/icd9SortShort.Rd |only
icd9-0.5/icd9/man/icd9SubsequentMinors.Rd |only
icd9-0.5/icd9/man/icd9Valid.Rd |only
icd9-0.5/icd9/man/icd9ValidDecimal.Rd |only
icd9-0.5/icd9/man/icd9ValidMajor.Rd |only
icd9-0.5/icd9/man/icd9ValidMapping.Rd |only
icd9-0.5/icd9/man/icd9ValidNaWarnStop.Rd |only
icd9-0.5/icd9/man/icd9ValidShort.Rd |only
icd9-0.5/icd9/man/icd9WarnStopMessage.Rd |only
icd9-0.5/icd9/man/parseElixhauser.Rd |only
icd9-0.5/icd9/man/parseQuanElixhauser.Rd |only
icd9-0.5/icd9/man/quanElixhauserComorbid.Rd |only
icd9-0.5/icd9/man/saveSourceTreeData.Rd |only
icd9-0.5/icd9/man/spawnReferenceChildren.Rd |only
icd9-0.5/icd9/man/stopIfInvalidIcd9.Rd |only
icd9-0.5/icd9/man/strip.Rd |only
icd9-0.5/icd9/man/trim.Rd |only
icd9-0.5/icd9/tests/testthat/test-comorbid.R |only
icd9-0.5/icd9/tests/testthat/test-convert.R |only
icd9-0.5/icd9/tests/testthat/test-explain.R |only
icd9-0.5/icd9/tests/testthat/test-icd9.R |only
icd9-0.5/icd9/tests/testthat/test-ranges.R |only
icd9-0.5/icd9/tests/testthat/test-sas.R |only
icd9-0.5/icd9/tests/testthat/test-validation.R |only
icd9-0.5/icd9/vignettes/icd9-concordance.tex |only
icd9-0.5/icd9/vignettes/icd9.Rnw |only
icd9-1.0/icd9/DESCRIPTION | 40 -
icd9-1.0/icd9/MD5 | 238 +++----
icd9-1.0/icd9/NAMESPACE | 85 +-
icd9-1.0/icd9/R/RcppExports.R |only
icd9-1.0/icd9/R/RcppExportsShim.R |only
icd9-1.0/icd9/R/benchmark.R | 166 ++++-
icd9-1.0/icd9/R/comorbid.R | 492 +++++++--------
icd9-1.0/icd9/R/convert.R | 374 ++++--------
icd9-1.0/icd9/R/datadocs.R | 66 +-
icd9-1.0/icd9/R/explain.R | 378 ++++++------
icd9-1.0/icd9/R/filter.R |only
icd9-1.0/icd9/R/icd9-package.R | 124 ++-
icd9-1.0/icd9/R/manip.R | 149 ----
icd9-1.0/icd9/R/old.R |only
icd9-1.0/icd9/R/parse.R | 468 +++++++++------
icd9-1.0/icd9/R/ranges.R | 561 ++++--------------
icd9-1.0/icd9/R/sas.R | 96 +--
icd9-1.0/icd9/R/score.R |only
icd9-1.0/icd9/R/sysdata.rda |only
icd9-1.0/icd9/R/util.R | 242 +++----
icd9-1.0/icd9/R/valid.R | 460 +++++---------
icd9-1.0/icd9/R/zzz.R | 19
icd9-1.0/icd9/README.md | 122 ++-
icd9-1.0/icd9/build/vignette.rds |binary
icd9-1.0/icd9/data/ahrqComorbid.RData |binary
icd9-1.0/icd9/data/ahrqComorbidAll.RData |binary
icd9-1.0/icd9/data/elixComorbid.RData |only
icd9-1.0/icd9/data/icd9Chapters.RData |binary
icd9-1.0/icd9/data/icd9ChaptersMajor.RData |binary
icd9-1.0/icd9/data/icd9ChaptersSub.RData |binary
icd9-1.0/icd9/data/icd9Hierarchy.RData |binary
icd9-1.0/icd9/data/mappingNames.rda |binary
icd9-1.0/icd9/data/quanDeyoComorbid.RData |binary
icd9-1.0/icd9/data/quanElixComorbid.RData |only
icd9-1.0/icd9/inst/COPYING |only
icd9-1.0/icd9/inst/COPYRIGHTS |only
icd9-1.0/icd9/inst/doc/icd9.R | 244 ++++---
icd9-1.0/icd9/inst/doc/icd9.pdf |binary
icd9-1.0/icd9/inst/doc/introduction.R |only
icd9-1.0/icd9/inst/doc/introduction.Rmd |only
icd9-1.0/icd9/inst/doc/introduction.html |only
icd9-1.0/icd9/inst/extdata/ICD9_E_Charlson.sas |only
icd9-1.0/icd9/inst/extdata/ICD9_E_Elixhauser.sas |only
icd9-1.0/icd9/inst/include |only
icd9-1.0/icd9/man/ahrqComorbid.Rd | 5
icd9-1.0/icd9/man/ahrqComorbidAll.Rd | 6
icd9-1.0/icd9/man/convert.Rd |only
icd9-1.0/icd9/man/elixComorbid.Rd |only
icd9-1.0/icd9/man/elixComorbidNames.Rd |only
icd9-1.0/icd9/man/icd9-package.Rd | 123 ++-
icd9-1.0/icd9/man/icd9AddLeadingZeroes.Rd | 70 --
icd9-1.0/icd9/man/icd9Benchmark.Rd | 4
icd9-1.0/icd9/man/icd9Chapters.Rd | 8
icd9-1.0/icd9/man/icd9ChaptersToMap.Rd | 23
icd9-1.0/icd9/man/icd9Charlson.Rd |only
icd9-1.0/icd9/man/icd9Children.Rd |only
icd9-1.0/icd9/man/icd9Comorbid.Rd |only
icd9-1.0/icd9/man/icd9Condense.Rd |only
icd9-1.0/icd9/man/icd9Count.Rd |only
icd9-1.0/icd9/man/icd9DiffComorbid.Rd |only
icd9-1.0/icd9/man/icd9DropLeadingZeroes.Rd | 71 --
icd9-1.0/icd9/man/icd9ExpandMinor.Rd | 44 -
icd9-1.0/icd9/man/icd9ExpandRange.Rd |only
icd9-1.0/icd9/man/icd9Explain.Rd | 61 +
icd9-1.0/icd9/man/icd9ExtractAlphaNumeric.Rd | 6
icd9-1.0/icd9/man/icd9FilterInvalid.Rd |only
icd9-1.0/icd9/man/icd9FilterPoa.Rd | 39 -
icd9-1.0/icd9/man/icd9FilterValid.Rd |only
icd9-1.0/icd9/man/icd9GenerateSysData.Rd |only
icd9-1.0/icd9/man/icd9GetChapters.Rd | 12
icd9-1.0/icd9/man/icd9GetValid.Rd |only
icd9-1.0/icd9/man/icd9GuessIsShort.Rd | 5
icd9-1.0/icd9/man/icd9Hierarchy.Rd | 3
icd9-1.0/icd9/man/icd9InReferenceCode.Rd | 45 -
icd9-1.0/icd9/man/icd9Is.Rd |only
icd9-1.0/icd9/man/icd9IsReal.Rd |only
icd9-1.0/icd9/man/icd9IsValid.Rd |only
icd9-1.0/icd9/man/icd9IsValidMapping.Rd |only
icd9-1.0/icd9/man/icd9LongToWide.Rd |only
icd9-1.0/icd9/man/icd9ParseAndSaveMappings.Rd | 7
icd9-1.0/icd9/man/icd9PoaChoices.Rd | 3
icd9-1.0/icd9/man/icd9Sort.Rd |only
icd9-1.0/icd9/man/icd9WideToLong.Rd |only
icd9-1.0/icd9/man/logicalToBinary.Rd | 16
icd9-1.0/icd9/man/parseAhrqSas.Rd | 8
icd9-1.0/icd9/man/parseElix.Rd |only
icd9-1.0/icd9/man/parseIcd9Chapters.Rd | 24
icd9-1.0/icd9/man/parseIcd9Descriptions.Rd | 6
icd9-1.0/icd9/man/parseQuanDeyoSas.Rd | 12
icd9-1.0/icd9/man/parseQuanElix.Rd |only
icd9-1.0/icd9/man/quanDeyoComorbid.Rd | 5
icd9-1.0/icd9/man/quanElixComorbid.Rd |only
icd9-1.0/icd9/man/read.zip.url.Rd | 3
icd9-1.0/icd9/man/sasDropOtherAssignment.Rd | 12
icd9-1.0/icd9/man/sasExtractLetStrings.Rd | 11
icd9-1.0/icd9/man/sasFormatExtract.Rd | 12
icd9-1.0/icd9/man/sasParseAssignments.Rd | 6
icd9-1.0/icd9/man/strMultiMatch.Rd | 15
icd9-1.0/icd9/src |only
icd9-1.0/icd9/tests/testthat/helper-base.R |only
icd9-1.0/icd9/tests/testthat/test-fast-convert.R |only
icd9-1.0/icd9/tests/testthat/test-fast-explain.R |only
icd9-1.0/icd9/tests/testthat/test-fast-icd9.R |only
icd9-1.0/icd9/tests/testthat/test-fast-ranges.R |only
icd9-1.0/icd9/tests/testthat/test-fast-reshape.R |only
icd9-1.0/icd9/tests/testthat/test-fast-sas.R |only
icd9-1.0/icd9/tests/testthat/test-fast-score.R |only
icd9-1.0/icd9/tests/testthat/test-fast-valid.R |only
icd9-1.0/icd9/tests/testthat/test-is.R |only
icd9-1.0/icd9/tests/testthat/test-slow-comorbid.R |only
icd9-1.0/icd9/tests/testthat/test-slow-score.R |only
icd9-1.0/icd9/tests/testthat/test-util.R | 55 +
icd9-1.0/icd9/vignettes/introduction.Rmd |only
172 files changed, 2489 insertions(+), 2555 deletions(-)
Title: Export grid Graphics as SVG
Diff between gridSVG versions 1.4-2 dated 2014-12-16 and 1.4-3 dated 2015-01-27
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/gridsvg.R | 38 ++++++++++++++++++++++++--------------
R/svg.R | 11 +++++++----
inst/NEWS.Rd | 14 ++++++++++++++
inst/doc/animation.pdf |binary
inst/doc/extensibility.pdf |binary
inst/doc/gridSVG.pdf |binary
8 files changed, 57 insertions(+), 30 deletions(-)
Title: Analysis and Modeling for Geostatistical Count Data
Diff between geoCount versions 1.131209 dated 2013-12-09 and 1.150120 dated 2015-01-27
Description: This package provides a variety of functions to analyze and model geostatistical count data with generalized linear spatial models, including
1) simulate and visualize the data;
2) posterior sampling with robust MCMC algorithms (in serial or parallel way);
3) perform prediction for unsampled locations;
4) conduct Bayesian model checking procedure to evaluate the goodness of fitting;
5) conduct transformed residual checking procedure.
In the package, seamlessly embedded C++ programs and parallel computing techniques are implemented to speed up the computing processes.
Author: Liang Jing
Maintainer: Liang Jing
DESCRIPTION | 13
MD5 | 13
NAMESPACE | 1
R/checkingTRC.R | 248 ++++++------
R/runMCMC.R | 822 +++++++++++++++++++++----------------------
inst/CITATION |only
inst/doc/geoCount_HowtoUse.R | 598 +++++++++++++++----------------
src/Makevars | 8
8 files changed, 868 insertions(+), 835 deletions(-)
Title: Structural Time Series Models
Diff between stsm versions 1.4 dated 2014-07-27 and 1.7 dated 2015-01-26
Description: Fit the basic structural time series model by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
stsm-1.4/stsm/inst/NEWS |only
stsm-1.4/stsm/inst/README |only
stsm-1.4/stsm/inst/doc/Rchunks.R |only
stsm-1.4/stsm/inst/doc/llm.pdf |only
stsm-1.4/stsm/inst/doc/llmseas.pdf |only
stsm-1.4/stsm/inst/doc/stsm.pdf |only
stsm-1.7/stsm/DESCRIPTION | 16 +--
stsm-1.7/stsm/MD5 | 83 +++++++++--------
stsm-1.7/stsm/NAMESPACE | 21 +++-
stsm-1.7/stsm/NEWS |only
stsm-1.7/stsm/R/datagen.R | 5 -
stsm-1.7/stsm/R/frequency-domain.R |only
stsm-1.7/stsm/R/maxlik-fd-optim.R | 8 +
stsm-1.7/stsm/R/maxlik-td-optim.R | 12 +-
stsm-1.7/stsm/R/stsm-class.R |only
stsm-1.7/stsm/R/stsm-methods.R |only
stsm-1.7/stsm/R/stsmFit.R | 29 +++++
stsm-1.7/stsm/R/transPars.R |only
stsm-1.7/stsm/build |only
stsm-1.7/stsm/inst/doc/index.html | 41 +++-----
stsm-1.7/stsm/inst/doc/stsm-intro.R |only
stsm-1.7/stsm/inst/doc/stsm-intro.Rnw |only
stsm-1.7/stsm/inst/doc/stsm-intro.pdf |only
stsm-1.7/stsm/inst/sims/datagen-llmseas.R | 4
stsm-1.7/stsm/inst/sims/sim-llm-mcl-fd.R | 1
stsm-1.7/stsm/inst/sims/sim-llm-ml-fd.R | 1
stsm-1.7/stsm/inst/sims/sim-llm-ml-td.R | 1
stsm-1.7/stsm/inst/sims/sim-llmseas-mcl-fd.R | 1
stsm-1.7/stsm/inst/sims/sim-llmseas-ml-fd.R | 1
stsm-1.7/stsm/inst/sims/sim-llmseas-ml-td.R | 1
stsm-1.7/stsm/inst/sims/test-derivatives-mcloglik-fd.R | 1
stsm-1.7/stsm/inst/sims/test-derivatives-mloglik-fd.R | 3
stsm-1.7/stsm/man/barrier-eval.Rd | 6 -
stsm-1.7/stsm/man/datagen-stsm.Rd | 14 +-
stsm-1.7/stsm/man/init-vars.Rd | 4
stsm-1.7/stsm/man/maxlik-em.Rd | 4
stsm-1.7/stsm/man/maxlik-fd.Rd | 14 +-
stsm-1.7/stsm/man/maxlik-td.Rd | 22 ++--
stsm-1.7/stsm/man/method-logLik.Rd | 6 -
stsm-1.7/stsm/man/methods-stsmFit.Rd | 18 +--
stsm-1.7/stsm/man/methods-vcov-confint.Rd | 8 -
stsm-1.7/stsm/man/mloglik-fd.Rd | 8 -
stsm-1.7/stsm/man/mloglik-td.Rd | 6 -
stsm-1.7/stsm/man/stsm-class.Rd |only
stsm-1.7/stsm/man/stsm-methods-char2numeric.Rd |only
stsm-1.7/stsm/man/stsm-methods-get.Rd |only
stsm-1.7/stsm/man/stsm-methods-set.Rd |only
stsm-1.7/stsm/man/stsm-methods-transPars.Rd |only
stsm-1.7/stsm/man/stsm-model.Rd |only
stsm-1.7/stsm/man/stsm-package.Rd | 4
stsm-1.7/stsm/man/stsm-sgf.Rd |only
stsm-1.7/stsm/man/stsm-show-methods.Rd |only
stsm-1.7/stsm/man/stsm-validObject.Rd |only
stsm-1.7/stsm/man/stsmFit.Rd | 12 ++
stsm-1.7/stsm/vignettes |only
55 files changed, 204 insertions(+), 151 deletions(-)
Title: Linked Micromap Plots
Diff between micromap versions 1.9 dated 2014-05-27 and 1.9.1 dated 2015-01-26
Description: This group of functions simplifies the creation of linked micromap
plots.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [cre, ctb]
Maintainer: Tom Kincaid
DESCRIPTION | 20 ++++++++++----------
MD5 | 26 +++++++++++++-------------
NAMESPACE | 17 +++++++++--------
data/OrEcoLevel3.rda |binary
data/USstates.rda |binary
data/WSA3.rda |binary
data/edPov.rda |binary
data/lungMort.rda |binary
data/statesFlatfile.rda |binary
data/vegCov.rda |binary
inst/CITATION | 31 ++++++++++++++++++++-----------
inst/NEWS.Rd | 16 ++++++++++++++++
inst/doc/CHANGES.pdf |binary
inst/doc/index.html | 5 +++--
14 files changed, 71 insertions(+), 44 deletions(-)
Title: Interface to Dygraphs Interactive Time Series Charting Library
Diff between dygraphs versions 0.3.3 dated 2014-12-23 and 0.4.1 dated 2015-01-26
Description: An R interface to the dygraphs JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph]
Maintainer: JJ Allaire
DESCRIPTION | 6 -
LICENSE | 2
MD5 | 29 ++--
NEWS |only
R/options.R | 19 ++-
R/range-selector.R | 6 +
R/series.R | 5
R/utils.R | 2
inst/examples/examples.html | 238 +++++++++++++++++++++--------------------
inst/examples/shiny/server.R | 9 +
inst/examples/shiny/ui.R | 7 +
inst/htmlwidgets/dygraphs.js | 197 +++++++++++++++++++++++++++++++++
inst/htmlwidgets/dygraphs.yaml | 8 +
inst/htmlwidgets/lib/timezone |only
man/dyOptions.Rd | 10 +
man/dyRangeSelector.Rd | 6 +
16 files changed, 404 insertions(+), 140 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Diff between simPop versions 0.2.6 dated 2014-11-18 and 0.2.9 dated 2015-01-26
Description: Simulate populations for surveys based on auxiliary data including model-based methods, calibration and combinatorial optimization tools. Developed with support of the International Household Survey Network, DFID Trust Fund TF011722
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik, and with contributions from Mathieu Ribatet
Maintainer: Matthias Templ
DESCRIPTION | 8 -
MD5 | 92 +++++++--------
NAMESPACE | 4
NEWS | 61 ++++++----
R/0classes.R | 2
R/addKnownMargins.R | 4
R/addWeights.r | 2
R/calibPop.R | 18 +-
R/calibSample.R | 8 -
R/calibVars.R | 2
R/ipu.r | 2
R/printFunctions.R | 2
R/simCategorical.R | 16 +-
R/simComponents.R | 12 -
R/simContinuous.R | 14 +-
R/simEUSILC.R | 36 ++---
R/simInitSpatial.R | 16 +-
R/simRelation.R | 18 +-
R/simStructure.R | 2
R/spBwplot.R | 4
R/spCdfplot.R | 4
R/spTable.R | 4
R/synthPop.R | 14 +-
R/utils.R | 6
inst/CITATION | 19 ++-
man/addKnownMargins.Rd | 6
man/addWeights-methods.Rd | 8 -
man/calibPop.Rd | 14 +-
man/calibSample-methods.Rd | 6
man/dataObj-class.Rd | 2
man/manageSynthPopObj.Rd | 22 +--
man/simCategorical.Rd | 14 +-
man/simComponents.Rd | 26 ++--
man/simContinuous.Rd | 12 -
man/simEUSILC.Rd | 2
man/simInitSpatial.Rd | 14 +-
man/simRelation.Rd | 8 -
man/simStructure.Rd | 2
man/spBwplot.Rd | 6
man/spCdfplot.Rd | 6
man/spTable.Rd | 2
man/synthPop-methods.Rd | 36 ++---
man/synthPopObj-class.Rd | 14 +-
src/calibPop.cpp | 24 +--
src/calibVars.cpp | 2
src/ipu.cpp | 2
tests/test_sprague.R | 274 +++++++++++++++++++++++++++++++++++++++++++++
47 files changed, 591 insertions(+), 281 deletions(-)
Title: Dynamic Documents for R
Diff between rmarkdown versions 0.4.2 dated 2014-12-22 and 0.5.1 dated 2015-01-26
Description: Convert R Markdown documents into a variety of formats
including HTML, MS Word, PDF, and Beamer.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire
DESCRIPTION | 72 +++++++++-
MD5 | 113 ++++++++--------
NAMESPACE | 2
NEWS | 10 +
R/beamer_presentation.R | 3
R/draft.R | 4
R/html_document.R | 8 -
R/html_document_base.R | 3
R/html_fragment.R | 3
R/html_vignette.R | 2
R/ioslides_presentation.R | 5
R/md_document.R | 3
R/output_format.R | 4
R/pandoc.R | 8 -
R/pdf_document.R | 6
R/relative_to.R | 7
R/render.R | 21 +-
R/shiny.R | 6
R/slidy_presentation.R | 3
R/tufte_handout.R | 4
R/util.R | 4
inst/NOTICE | 5
inst/rmd/h/jquery-AUTHORS.txt |only
inst/rmd/ioslides/ioslides-13.5.1/theme/css/default.css | 7
inst/rmd/latex/default.tex | 6
inst/rmd/slidy/Slidy2/styles/slidy.css | 5
man/beamer_presentation.Rd | 11 -
man/default_output_format.Rd | 3
man/draft.Rd | 3
man/html_document.Rd | 7
man/html_document_base.Rd | 3
man/html_fragment.Rd | 9 -
man/html_vignette.Rd | 8 -
man/includes.Rd | 3
man/ioslides_presentation.Rd | 8 -
man/knitr_options.Rd | 3
man/knitr_options_html.Rd | 7
man/knitr_options_pdf.Rd | 7
man/md_document.Rd | 7
man/metadata.Rd | 3
man/output_format.Rd | 3
man/pandoc_args.Rd | 3
man/pandoc_available.Rd | 3
man/pandoc_convert.Rd | 3
man/pandoc_options.Rd | 3
man/pandoc_path_arg.Rd | 3
man/pandoc_self_contained_html.Rd | 3
man/pandoc_template.Rd | 3
man/pdf_document.Rd | 13 +
man/relative_to.Rd | 3
man/render.Rd | 4
man/render_delayed.Rd | 3
man/render_supporting_files.Rd | 3
man/rmarkdown_format.Rd | 3
man/run.Rd | 3
man/slidy_presentation.Rd | 7
man/tufte_handout.Rd | 7
man/word_document.Rd | 3
58 files changed, 318 insertions(+), 151 deletions(-)
Title: Meta-analysis of RNA-seq data
Diff between metaRNASeq versions 0.4 dated 2014-03-14 and 1.0.2 dated 2015-01-26
Description: Implementation of two p-value combination techniques (inverse normal and Fisher methods). A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments.
Author: Guillemette Marot, Florence Jaffrezic, Andrea Rau
Maintainer: Guillemette Marot
DESCRIPTION | 17 ++---
MD5 | 42 ++++++------
NAMESPACE | 9 +-
R/IDD.IRR.R |only
build/vignette.rds |binary
data/dispFuncs.rda |binary
data/param.rda |binary
data/rawpval.rda |binary
inst/CITATION | 14 ++--
inst/NEWS | 4 +
inst/doc/metaRNASeq.R | 47 ++++++++++++-
inst/doc/metaRNASeq.Rnw | 74 ++++++++++++++++-----
inst/doc/metaRNASeq.pdf |binary
man/IDD.IRR.Rd |only
man/dispFuncs.Rd | 102 +++++++++++++++---------------
man/fishercomb.Rd | 112 ++++++++++++++++-----------------
man/invnorm.Rd | 156 +++++++++++++++++++++++-----------------------
man/metaRNASeq-package.Rd | 14 ++--
man/param.Rd | 68 ++++++++++----------
man/rawpval.Rd | 52 +++++++--------
man/sim.function.Rd | 138 ++++++++++++++++++++--------------------
vignettes/metaRNASeq.Rnw | 74 ++++++++++++++++-----
vignettes/metaRNASeq.bib | 56 ++++++++++------
23 files changed, 562 insertions(+), 417 deletions(-)
Title: Meta-analysis for MicroArrays
Diff between metaMA versions 2.1 dated 2011-08-29 and 3.1.1 dated 2015-01-26
Description: Combines either p-values or modified effect sizes from different
studies to find differentially expressed genes
Author: Guillemette Marot
Maintainer: Guillemette Marot
DESCRIPTION | 18 ++--
MD5 | 38 +++++----
NAMESPACE |only
R/EScombination.R | 168 ++++++++++++++++++++---------------------
R/EScombination.paired.R | 114 ++++++++++++++--------------
R/effectsize.R | 30 +++----
R/pvalcombination.R | 170 +++++++++++++++++++++---------------------
R/pvalcombination.paired.R | 128 +++++++++++++++----------------
build |only
data/datalist |only
inst |only
man/EScombination.Rd | 96 +++++++++++------------
man/EScombination.paired.Rd | 98 ++++++++++++------------
man/Singhdata.Rd | 48 +++++------
man/effectsize.Rd | 64 +++++++--------
man/metaMA-package.Rd | 80 ++++++++++---------
man/pvalcombination.Rd | 96 +++++++++++------------
man/pvalcombination.paired.Rd | 96 +++++++++++------------
man/row.ttest.stat.Rd | 2
vignettes |only
20 files changed, 633 insertions(+), 613 deletions(-)
Title: Bayes Factors, Model Choice And Variable Selection In Linear
Models
Diff between BayesVarSel versions 1.5.1 dated 2014-03-25 and 1.6.1 dated 2015-01-26
Description: Conceived to calculate Bayes factors in linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in the package is placed on the prior distributions and BayesVarSel allows using a wide range of them: Jeffreys-Zellner-Siow (Jeffreys, 1961; Zellner and Siow, 1980,1984) Zellner (1986); Fernandez et al. (2001), Liang et al. (2008) and Bayarri et al. (2012). The interaction with the package is through a friendly interface that syntactically mimics the well-known lm command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the true -data generating- model. Additionally, BayesVarSel incorporates abilities to handle problems with a large number of potential explanatory variables through parallel and heuristic versions (Garcia-Donato and Martinez-Beneito 2013) of the main commands.
Author: Gonzalo Garcia-Donato and Anabel Forte
Maintainer: Anabel Forte
BayesVarSel-1.5.1/BayesVarSel/R/predict.Bvs.R |only
BayesVarSel-1.5.1/BayesVarSel/R/print.Bvs.predict.R |only
BayesVarSel-1.5.1/BayesVarSel/man/predict.Bvs.Rd |only
BayesVarSel-1.6.1/BayesVarSel/DESCRIPTION | 17
BayesVarSel-1.6.1/BayesVarSel/MD5 | 50
BayesVarSel-1.6.1/BayesVarSel/NAMESPACE | 5
BayesVarSel-1.6.1/BayesVarSel/R/BayesFactor.R |only
BayesVarSel-1.6.1/BayesVarSel/R/Bvs.R | 436 +
BayesVarSel-1.6.1/BayesVarSel/R/GibbsBvs.R | 384 -
BayesVarSel-1.6.1/BayesVarSel/R/PBvs.R | 399 +
BayesVarSel-1.6.1/BayesVarSel/R/plotBvs.R | 43
BayesVarSel-1.6.1/BayesVarSel/R/print.BayesFactor.R |only
BayesVarSel-1.6.1/BayesVarSel/R/print.Bvs.R | 11
BayesVarSel-1.6.1/BayesVarSel/R/summary.Bvs.R | 20
BayesVarSel-1.6.1/BayesVarSel/man/BayesFactor.Rd |only
BayesVarSel-1.6.1/BayesVarSel/man/Bvs.Rd | 52
BayesVarSel-1.6.1/BayesVarSel/man/GibbsBvs.Rd | 40
BayesVarSel-1.6.1/BayesVarSel/man/PBvs.Rd | 28
BayesVarSel-1.6.1/BayesVarSel/man/bayesvarsel-package.rd | 17
BayesVarSel-1.6.1/BayesVarSel/man/plotbvs.rd | 2
BayesVarSel-1.6.1/BayesVarSel/src/Gibbsauxiliaryfuncs.c | 2
BayesVarSel-1.6.1/BayesVarSel/src/allBF.c | 23
BayesVarSel-1.6.1/BayesVarSel/src/allBF.h | 1
BayesVarSel-1.6.1/BayesVarSel/src/auxiliaryfuncs.c | 91
BayesVarSel-1.6.1/BayesVarSel/src/auxiliaryfuncs.h | 6
BayesVarSel-1.6.1/BayesVarSel/src/main.c | 4479 +++++++++++----
BayesVarSel-1.6.1/BayesVarSel/src/mainGibbs.c | 3925 +++++++++++--
BayesVarSel-1.6.1/BayesVarSel/src/mainSingle.c | 15
BayesVarSel-1.6.1/BayesVarSel/src/priorprob.c | 2
29 files changed, 8088 insertions(+), 1960 deletions(-)
More information about SocialPosition at CRAN
Permanent link
Title: Estimate Structured Additive Regression Models with BayesX
Diff between R2BayesX versions 0.3-1 dated 2013-08-19 and 1.0-0 dated 2015-01-26
Description: An R interface to estimate structured additive regression (STAR) models with BayesX.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf
R2BayesX-0.3-1/R2BayesX/R/SPDF2bnd.R |only
R2BayesX-1.0-0/R2BayesX/DESCRIPTION | 14 -
R2BayesX-1.0-0/R2BayesX/MD5 | 80 +++----
R2BayesX-1.0-0/R2BayesX/NAMESPACE | 3
R2BayesX-1.0-0/R2BayesX/R/GRstats.R | 3
R2BayesX-1.0-0/R2BayesX/R/bayesx.R | 9
R2BayesX-1.0-0/R2BayesX/R/bayesx.construct.mrf.smooth.spec.R | 11 -
R2BayesX-1.0-0/R2BayesX/R/bnd2gra.R | 4
R2BayesX-1.0-0/R2BayesX/R/centroids.R | 2
R2BayesX-1.0-0/R2BayesX/R/coeffun.R | 3
R2BayesX-1.0-0/R2BayesX/R/colorlegend.R | 19 +
R2BayesX-1.0-0/R2BayesX/R/compute.x.id.R | 27 +-
R2BayesX-1.0-0/R2BayesX/R/df2m.R | 2
R2BayesX-1.0-0/R2BayesX/R/dopos.R | 3
R2BayesX-1.0-0/R2BayesX/R/find.limits.R | 9
R2BayesX-1.0-0/R2BayesX/R/find.smooth.random.R | 4
R2BayesX-1.0-0/R2BayesX/R/geo.smooth.spec.R | 9
R2BayesX-1.0-0/R2BayesX/R/interp2.R | 11 -
R2BayesX-1.0-0/R2BayesX/R/make_pal.R | 3
R2BayesX-1.0-0/R2BayesX/R/parse.bayesx.input.R | 41 ++-
R2BayesX-1.0-0/R2BayesX/R/plot2d.R | 2
R2BayesX-1.0-0/R2BayesX/R/plot2d.default.R | 5
R2BayesX-1.0-0/R2BayesX/R/plotmap.R | 116 ++++++-----
R2BayesX-1.0-0/R2BayesX/R/plotsamples.R | 10
R2BayesX-1.0-0/R2BayesX/R/read.bnd.R | 18 -
R2BayesX-1.0-0/R2BayesX/R/s4class.R | 4
R2BayesX-1.0-0/R2BayesX/R/s4dim.R | 15 -
R2BayesX-1.0-0/R2BayesX/R/samples.R | 5
R2BayesX-1.0-0/R2BayesX/R/setmfrow.R | 6
R2BayesX-1.0-0/R2BayesX/R/shp2bnd.R | 5
R2BayesX-1.0-0/R2BayesX/R/sliceplot.R | 9
R2BayesX-1.0-0/R2BayesX/R/spAndBndConversion.R | 4
R2BayesX-1.0-0/R2BayesX/R/write.bayesx.input.R | 7
R2BayesX-1.0-0/R2BayesX/inst/CITATION |only
R2BayesX-1.0-0/R2BayesX/man/bayesx.Rd | 16 -
R2BayesX-1.0-0/R2BayesX/man/bayesx.control.Rd | 10
R2BayesX-1.0-0/R2BayesX/man/bnd2gra.Rd | 3
R2BayesX-1.0-0/R2BayesX/man/plot3d.Rd | 2
R2BayesX-1.0-0/R2BayesX/man/plotmap.Rd | 14 -
R2BayesX-1.0-0/R2BayesX/man/plotsamples.Rd | 8
R2BayesX-1.0-0/R2BayesX/man/shp2bnd.Rd | 2
R2BayesX-1.0-0/R2BayesX/man/sliceplot.Rd | 7
42 files changed, 302 insertions(+), 223 deletions(-)
Title: Discrete associated kernel estimators
Diff between Disake versions 1.0 dated 2014-01-20 and 1.5 dated 2015-01-26
Description: Discrete smoothing of probability mass function is performed using three discrete associated kernels: Dirac Discrete Uniform (DiracDU), Binomial and Discrete Triangular. Two automatic bandwidth selection procedures are implemented: the cross-validation method for the three kernels and the local Bayesian approach for Binomial kernel. Note that DiracDU is used for categorical data, Binomial kernel is appropriate for count data with small or moderate sample sizes, and Discrete Triangular kernel is recommended for count data with large sample sizes.
Author: W. E. Wansouwé, C. C. Kokonendji and D. T. Kolyang
Maintainer: W. E. Wansouwé
Disake-1.0/Disake/R/bwcv.R |only
Disake-1.0/Disake/R/dak.R |only
Disake-1.0/Disake/R/pmfe.R |only
Disake-1.0/Disake/man/bwcv.Rd |only
Disake-1.0/Disake/man/dak.Rd |only
Disake-1.0/Disake/man/pmfe.Rd |only
Disake-1.5/Disake/DESCRIPTION | 17 +++--
Disake-1.5/Disake/MD5 | 22 ++++---
Disake-1.5/Disake/NAMESPACE | 1
Disake-1.5/Disake/R/Baysbw.R |only
Disake-1.5/Disake/R/CVbw.R |only
Disake-1.5/Disake/R/kf.R |only
Disake-1.5/Disake/R/kpmfe.R |only
Disake-1.5/Disake/R/sumry.R |only
Disake-1.5/Disake/man/Baysbw.Rd |only
Disake-1.5/Disake/man/CVbw.Rd |only
Disake-1.5/Disake/man/Disake-package.Rd | 94 +++++++++++++++++++++++---------
Disake-1.5/Disake/man/kf.Rd |only
Disake-1.5/Disake/man/kpmfe.Rd |only
Disake-1.5/Disake/man/sumry.Rd |only
20 files changed, 90 insertions(+), 44 deletions(-)
Title: Download content from NCBI databases
Diff between RISmed versions 2.1.2 dated 2014-01-26 and 2.1.4 dated 2015-01-26
Description: Download content from NCBI databases. This package is intended to facilitate analyses of NCBI database content. This package is not intended for reference management.
Author: Stephanie Kovalchik
Maintainer: S. A. Kovalchik
DESCRIPTION | 8 ++++----
MD5 | 13 +++++++------
NEWS | 12 ++++++++++++
R/EUtils.R | 3 ++-
R/Medline.R | 26 ++++++++++++++++----------
inst |only
man/PublicationType.Rd | 2 +-
man/RISmed-package.Rd | 4 ++--
8 files changed, 44 insertions(+), 24 deletions(-)
Title: Local Time Space Kriging
Diff between ltsk versions 1.0.2 dated 2015-01-22 and 1.0.3 dated 2015-01-26
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/cmp_kriging.cpp | 4 ++--
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Detection of Outliers in Time Series
Diff between tsoutliers versions 0.4 dated 2014-06-27 and 0.5 dated 2015-01-25
Description: Detection of outliers in time series following the
Chen and Liu (1993) procedure. Innovative outliers, additive outliers,
level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
tsoutliers-0.4/tsoutliers/R/jarque-bera-test.R |only
tsoutliers-0.4/tsoutliers/R/tsoutliers.R |only
tsoutliers-0.4/tsoutliers/inst/doc/CHANGES.txt |only
tsoutliers-0.4/tsoutliers/inst/doc/tsoutliers.pdf |only
tsoutliers-0.5/tsoutliers/DESCRIPTION | 20 +--
tsoutliers-0.5/tsoutliers/MD5 | 40 +++---
tsoutliers-0.5/tsoutliers/NAMESPACE | 5
tsoutliers-0.5/tsoutliers/R/JarqueBera-test.R |only
tsoutliers-0.5/tsoutliers/R/locate-outliers.R | 40 ++++--
tsoutliers-0.5/tsoutliers/R/outliers-effects.R | 3
tsoutliers-0.5/tsoutliers/R/outliers-regressors-arima.R | 2
tsoutliers-0.5/tsoutliers/R/outliers-tstatistics.R | 28 +++-
tsoutliers-0.5/tsoutliers/R/remove-outliers.R | 92 +++-------------
tsoutliers-0.5/tsoutliers/R/tso.R |only
tsoutliers-0.5/tsoutliers/build |only
tsoutliers-0.5/tsoutliers/inst/CHANGES |only
tsoutliers-0.5/tsoutliers/inst/doc/index.html | 21 ++-
tsoutliers-0.5/tsoutliers/inst/doc/tsoutliers-intro.R |only
tsoutliers-0.5/tsoutliers/inst/doc/tsoutliers-intro.Rnw |only
tsoutliers-0.5/tsoutliers/inst/doc/tsoutliers-intro.pdf |only
tsoutliers-0.5/tsoutliers/man/locate-outliers-loops.Rd | 6 -
tsoutliers-0.5/tsoutliers/man/locate-outliers.Rd | 12 --
tsoutliers-0.5/tsoutliers/man/outliers-tstatistics.Rd | 2
tsoutliers-0.5/tsoutliers/man/remove-outliers.Rd | 25 ++--
tsoutliers-0.5/tsoutliers/man/tsoutliers-package.Rd | 2
tsoutliers-0.5/tsoutliers/man/tsoutliers.Rd | 17 +-
tsoutliers-0.5/tsoutliers/vignettes |only
27 files changed, 147 insertions(+), 168 deletions(-)
Title: Spatio-Temporal Modeling of Large Data Using a Spectral SPDE
Approach
Diff between spate versions 1.3 dated 2013-12-29 and 1.4 dated 2015-01-25
Description: This package provides functionality for spatio-temporal modeling of large data sets. A Gaussian process in space and time is defined through a stochastic partial differential equation (SPDE). The SPDE is solved in the spectral space, and after discretizing in time and space, a linear Gaussian state space model is obtained. When doing inference, the main computational difficulty consists in evaluating the likelihood and in sampling from the full conditional of the spectral coefficients, or equivalently, the latent space-time process. In comparison to the traditional approach of using a spatio-temporal covariance function, the spectral SPDE approach is computationally advantageous. This package aims at providing tools for two different modeling approaches. First, the SPDE based spatio-temporal model can be used as a component in a customized hierarchical Bayesian model (HBM). The functions of the package then provide parameterizations of the process part of the model as well as computationally efficient algorithms needed for doing inference with the HBM. Alternatively, the adaptive MCMC algorithm implemented in the package can be used as an algorithm for doing inference without any additional modeling. The MCMC algorithm supports data that follow a Gaussian or a censored distribution with point mass at zero. Covariates can be included in the model through a regression term.
Author: Fabio Sigrist, Hans R. Kuensch, Werner A. Stahel
Maintainer: Fabio Sigrist
spate-1.3/spate/src/Temp_Makevars |only
spate-1.3/spate/vignettes/auto |only
spate-1.3/spate/vignettes/spate.pdf |only
spate-1.4/spate/DESCRIPTION | 17 ++++++++---------
spate-1.4/spate/MD5 | 19 +++++++++----------
spate-1.4/spate/NAMESPACE | 5 +++++
spate-1.4/spate/build/vignette.rds |binary
spate-1.4/spate/data/spateMCMC.RData |binary
spate-1.4/spate/data/spateMLE.RData |binary
spate-1.4/spate/inst/CITATION |only
spate-1.4/spate/inst/doc/spate_tutorial.pdf |binary
spate-1.4/spate/man/spate-package.Rd | 7 ++++---
spate-1.4/spate/tools |only
13 files changed, 26 insertions(+), 22 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Diff between mirtCAT versions 0.4 dated 2015-01-22 and 0.4.2 dated 2015-01-25
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers
DESCRIPTION | 6 +++---
MD5 | 6 +++---
NEWS | 2 +-
src/CAT_functions.cpp | 2 +-
4 files changed, 8 insertions(+), 8 deletions(-)
Title: R/Weka interface jars
Diff between RWekajars versions 3.7.11-1 dated 2014-04-26 and 3.7.12-1 dated 2015-01-25
Description: External jars required for package RWeka.
Author: Kurt Hornik [aut, cre],
University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
configure | 14 +++++++-------
inst/java/weka.jar |binary
4 files changed, 16 insertions(+), 16 deletions(-)
Title: R/Weka interface
Diff between RWeka versions 0.4-23 dated 2014-04-26 and 0.4-24 dated 2015-01-25
Description: An R interface to Weka (Version 3.7.12).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package RWeka contains the interface code, the Weka
jar is in a separate package RWekajars. For more information on
Weka see
Author: Kurt Hornik [aut, cre],
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik
CHANGELOG | 6 ++++++
DESCRIPTION | 14 +++++++-------
MD5 | 20 ++++++++++----------
R/arff.R | 2 +-
R/readers.R | 2 +-
build/vignette.rds |binary
inst/doc/RWeka.pdf |binary
inst/java/RWeka.jar |binary
java/Makefile | 11 ++---------
java/RWekaInterfaces.class |binary
man/Weka_classifier_trees.Rd | 2 +-
11 files changed, 28 insertions(+), 29 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.600.0 dated 2014-12-27 and 0.4.600.4.0 dated 2015-01-25
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 25 +++
DESCRIPTION | 8 -
MD5 | 62 ++++-----
R/RcppArmadillo.package.skeleton.R | 2
R/unit.test.R | 4
cleanup | 2
inst/NEWS.Rd | 10 +
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/examples/fastLm.r | 3
inst/include/armadillo_bits/Op_bones.hpp | 17 +-
inst/include/armadillo_bits/Proxy.hpp | 47 ------
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/fn_elem.hpp | 22 +--
inst/include/armadillo_bits/fn_find.hpp | 12 -
inst/include/armadillo_bits/fn_flip.hpp | 16 +-
inst/include/armadillo_bits/fn_vectorise.hpp | 9 -
inst/include/armadillo_bits/forward_bones.hpp | 9 +
inst/include/armadillo_bits/glue_times_meat.hpp | 37 -----
inst/include/armadillo_bits/mtOp_bones.hpp | 14 +-
inst/include/armadillo_bits/op_cumsum_bones.hpp | 10 +
inst/include/armadillo_bits/op_cumsum_meat.hpp | 82 +++++++++--
inst/include/armadillo_bits/op_dot_meat.hpp | 8 +
inst/include/armadillo_bits/op_flip_meat.hpp | 52 +++++--
inst/include/armadillo_bits/op_htrans_meat.hpp | 88 +++++-------
inst/include/armadillo_bits/op_sort_bones.hpp | 7 -
inst/include/armadillo_bits/op_sort_meat.hpp | 56 +++++---
inst/include/armadillo_bits/op_strans_meat.hpp | 144 +++++++++------------
inst/include/armadillo_bits/op_sum_meat.hpp | 45 +++---
inst/include/armadillo_bits/op_vectorise_bones.hpp | 6
inst/include/armadillo_bits/op_vectorise_meat.hpp | 9 -
man/RcppArmadillo-package.Rd | 2
32 files changed, 436 insertions(+), 374 deletions(-)
Title: Excel Connector for R
Diff between XLConnect versions 0.2-9 dated 2014-08-14 and 0.2-10 dated 2015-01-25
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons
Codec),
Stephen Colebourne [ctb, cph] (Joda-Time Java library)
Maintainer: Martin Studer
XLConnect-0.2-10/XLConnect/DESCRIPTION | 21 +--
XLConnect-0.2-10/XLConnect/MD5 | 50 +++----
XLConnect-0.2-10/XLConnect/NAMESPACE | 13 -
XLConnect-0.2-10/XLConnect/NEWS | 8 +
XLConnect-0.2-10/XLConnect/R/workbook.createSheet.R | 77 +++++------
XLConnect-0.2-10/XLConnect/README.md | 4
XLConnect-0.2-10/XLConnect/build/vignette.rds |binary
XLConnect-0.2-10/XLConnect/inst/COPYRIGHTS | 18 --
XLConnect-0.2-10/XLConnect/inst/doc/XLConnect.Rnw | 12 +
XLConnect-0.2-10/XLConnect/inst/doc/XLConnect.pdf |binary
XLConnect-0.2-10/XLConnect/inst/doc/XLConnectImpatient.pdf |binary
XLConnect-0.2-10/XLConnect/inst/java/XLConnect-0.2-10.jar |only
XLConnect-0.2-10/XLConnect/inst/java/poi-3.11.jar |only
XLConnect-0.2-10/XLConnect/inst/java/poi-ooxml-3.11.jar |only
XLConnect-0.2-10/XLConnect/java/README | 13 -
XLConnect-0.2-10/XLConnect/man/XLConnect-package.Rd | 6
XLConnect-0.2-10/XLConnect/man/cellstyle-class.Rd | 4
XLConnect-0.2-10/XLConnect/man/readWorksheet-methods.Rd | 5
XLConnect-0.2-10/XLConnect/man/xlcFreeMemory.Rd | 4
XLConnect-0.2-10/XLConnect/man/xlcMemoryReport.Rd | 4
XLConnect-0.2-10/XLConnect/tests/run_tests.R | 74 ++++++++++
XLConnect-0.2-10/XLConnect/vignettes/XLConnect.Rnw | 12 +
XLConnect-0.2-9/XLConnect/R/checkNoException.R |only
XLConnect-0.2-9/XLConnect/R/rsrc.R |only
XLConnect-0.2-9/XLConnect/R/runUnitTests.R |only
XLConnect-0.2-9/XLConnect/inst/java/XLConnect-0.2-8.jar |only
XLConnect-0.2-9/XLConnect/inst/java/dom4j-1.6.1.jar |only
XLConnect-0.2-9/XLConnect/inst/java/poi-3.11-beta1.jar |only
XLConnect-0.2-9/XLConnect/inst/java/poi-ooxml-3.11-beta1.jar |only
XLConnect-0.2-9/XLConnect/inst/java/xml-apis-1.0.b2.jar |only
XLConnect-0.2-9/XLConnect/man/checkNoException.Rd |only
XLConnect-0.2-9/XLConnect/man/rsrc.Rd |only
XLConnect-0.2-9/XLConnect/man/runUnitTests.Rd |only
33 files changed, 184 insertions(+), 141 deletions(-)
Title: Standard Normal Homogeneity Test
Diff between snht versions 1.0 dated 2014-11-03 and 1.0.1 dated 2015-01-25
Description: Robust and non-robust SNHT tests for changepoint detection.
Author: Josh Browning
Maintainer: Josh Browning
DESCRIPTION | 10 -
MD5 | 32 ++--
NAMESPACE | 15 -
R/createCandidateMatrix.R |only
R/getPairs.R |only
R/getUniquePairs.R |only
R/pairwiseSNHT.R | 305 ++++++++++++++++-----------------------
R/removeSeasonalPeriod.R |only
R/robustSNHT.R | 201 +++++++++++++++++++------
R/robustSNHTunequal.R | 145 +++++++++++++-----
R/snht.R | 162 ++++++++++++++++----
R/unconfoundCandidateMatrix.R |only
README.md | 4
man/createCandidateMatrix.Rd |only
man/getPairs.Rd |only
man/getUniquePairs.Rd |only
man/pairwiseSNHT.Rd | 135 ++++++++++-------
man/removeSeasonalPeriod.Rd |only
man/robustSNHT.Rd |only
man/robustSNHTunequal.Rd |only
man/snht-package.Rd | 58 +++----
man/snht.Rd | 184 +++++++++++++----------
man/unconfoundCandidateMatrix.Rd |only
23 files changed, 757 insertions(+), 494 deletions(-)
Title: Expander Functions for Generating Full Gradient and Hessian from
Single- and Multi-Slot Base Distributions
Diff between RegressionFactory versions 0.7 dated 2014-12-01 and 0.7.1 dated 2015-01-25
More information about RegressionFactory at CRAN
Description: The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansion framework is of conceptual value by offering new opportunities to generate novel regression problems.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
RegressionFactory-0.7.1/RegressionFactory/ChangeLog |only
RegressionFactory-0.7.1/RegressionFactory/DESCRIPTION | 10 -
RegressionFactory-0.7.1/RegressionFactory/MD5 | 34 +++-
RegressionFactory-0.7.1/RegressionFactory/NAMESPACE | 6
RegressionFactory-0.7.1/RegressionFactory/R/expanders.R | 36 ++--
RegressionFactory-0.7.1/RegressionFactory/R/fbase.1par.R | 75 ++++++++--
RegressionFactory-0.7.1/RegressionFactory/R/fbase.2par.R |only
RegressionFactory-0.7.1/RegressionFactory/R/utils.R |only
RegressionFactory-0.7.1/RegressionFactory/build |only
RegressionFactory-0.7.1/RegressionFactory/inst |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase1.binomial.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase1.exponential.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase1.geometric.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase1.poisson.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase2.gamma.log.log.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase2.gaussian.identity.log.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/fbase2.inverse.gaussian.log.log.Rd |only
RegressionFactory-0.7.1/RegressionFactory/man/regfac.expand.1par.Rd | 8 -
RegressionFactory-0.7.1/RegressionFactory/man/regfac.expand.2par.Rd | 59 ++++++-
RegressionFactory-0.7.1/RegressionFactory/man/regfac.merge.Rd |only
RegressionFactory-0.7.1/RegressionFactory/vignettes |only
RegressionFactory-0.7/RegressionFactory/man/fbase.bern.ilogit.Rd |only
RegressionFactory-0.7/RegressionFactory/man/fbase.exp.exp.Rd |only
RegressionFactory-0.7/RegressionFactory/man/fbase.geo.ilogit.Rd |only
RegressionFactory-0.7/RegressionFactory/man/fbase.pois.exp.Rd |only
25 files changed, 171 insertions(+), 57 deletions(-)
Permanent link
Title: Fits Normal and Student-t Censored Regression Model
Diff between CensRegMod versions 0.0 dated 2012-07-12 and 1.0 dated 2015-01-24
Description: Fits univariate censored linear regression model under Normal or Student-t distribution
Author: Monique Bettio Massuia
Maintainer: Monique Bettio Massuia
CensRegMod-0.0/CensRegMod/data/motorettes.txt.gz |only
CensRegMod-0.0/CensRegMod/man/motorettes.Rd |only
CensRegMod-1.0/CensRegMod/DESCRIPTION | 22 -
CensRegMod-1.0/CensRegMod/MD5 | 12
CensRegMod-1.0/CensRegMod/R/Utillitarios.R | 331 +++++++++++----------
CensRegMod-1.0/CensRegMod/R/em.cens.R | 349 +++++++++++++----------
CensRegMod-1.0/CensRegMod/data/wage.rates.txt.gz |only
CensRegMod-1.0/CensRegMod/man/em.cens.Rd | 35 +-
CensRegMod-1.0/CensRegMod/man/wage.rates.Rd |only
9 files changed, 421 insertions(+), 328 deletions(-)
Title: Utility Functions for Web Applications
Diff between webutils versions 0.2 dated 2014-10-30 and 0.3 dated 2015-01-24
Description: Utility functions for developing web applications. Includes parsers
for application/x-www-form-urlencoded as well as multipart/form-data
and examples of using the parser with either httpuv or rhttpd.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 8 ++++----
LICENSE | 2 +-
MD5 | 6 +++---
R/demo_rhttpd.R | 11 ++++++++---
4 files changed, 16 insertions(+), 11 deletions(-)
Title: Natural Language Processing Infrastructure
Diff between NLP versions 0.1-5 dated 2014-08-23 and 0.1-6 dated 2015-01-24
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 6 ++---
MD5 | 32 ++++++++++++++---------------
R/sysdata.rda |binary
man/AnnotatedPlainTextDocument.Rd | 41 +++++++++++++++++++++-----------------
man/Annotation.Rd | 23 +++++++++++----------
man/Annotator.Rd | 10 ++++-----
man/CoNLLTextDocument.Rd | 16 +++++++++-----
man/Span.Rd | 11 +++++-----
man/String.Rd | 8 +++----
man/TaggedTextDocument.Rd | 17 ++++++++++-----
man/TextDocument.Rd | 6 ++---
man/Tree.Rd | 6 ++---
man/WordListDocument.Rd | 9 ++++----
man/annotators.Rd | 4 +--
man/datetime.Rd | 8 +++----
man/tokenizers.Rd | 6 ++---
man/viewers.Rd | 2 -
17 files changed, 111 insertions(+), 94 deletions(-)
Title: Selected ISO codes
Diff between ISOcodes versions 2014.03.24 dated 2014-03-24 and 2015.01.24 dated 2015-01-24
Description: ISO language, territory, currency, script and character codes.
Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
currency codes, ISO 15924 script codes, and the ISO 8859 character codes
as well as the UN M.49 area codes.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 30 +++++++++++++++---------------
data/ISO_15924.rda |binary
data/ISO_3166_1.rda |binary
data/ISO_3166_2.rda |binary
data/ISO_3166_3.rda |binary
data/ISO_4217.rda |binary
data/ISO_4217_Historic.rda |binary
data/ISO_639_2.rda |binary
data/ISO_639_3.rda |binary
data/ISO_639_3_Retirements.rda |binary
data/ISO_639_5.rda |binary
data/ISO_8859.rda |binary
data/UN_M.49_Countries.rda |binary
data/UN_M.49_Regions.rda |binary
man/ISO_639.Rd | 2 +-
16 files changed, 19 insertions(+), 19 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Diff between dfmta versions 1.1-0 dated 2015-01-12 and 1.1-2 dated 2015-01-24
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
DESCRIPTION | 8
MD5 | 27 -
NAMESPACE | 6
configure | 148 +++++++++-
configure.ac | 11
configure.win |only
src/CppBugs/cppbugs/cppbugs.hpp | 1
src/CppBugs/cppbugs/distributions/mcmc.discrete.hpp | 2
src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 10
src/CppBugs/cppbugs/distributions/mcmc.multivariate.normal.hpp | 4
src/CppBugs/cppbugs/mcmc.math.hpp | 4
src/CppBugs/cppbugs/mcmc.model.hpp | 8
src/CppBugs/cppbugs/mcmc.rng.hpp | 24 -
src/Makevars.in | 4
src/dfmta.cpp | 4
15 files changed, 203 insertions(+), 58 deletions(-)
Title: A Toolbox for Non-tabular Data Manipulation
Diff between rlist versions 0.3-2 dated 2014-08-22 and 0.4 dated 2015-01-24
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren
Maintainer: Kun Ren
rlist-0.3-2/rlist/R/equal.R |only
rlist-0.3-2/rlist/R/summary.list.R |only
rlist-0.3-2/rlist/build |only
rlist-0.3-2/rlist/inst |only
rlist-0.3-2/rlist/man/equal.Rd |only
rlist-0.3-2/rlist/man/rlist.Rd |only
rlist-0.3-2/rlist/man/summary.list.Rd |only
rlist-0.3-2/rlist/tests/testthat/test-summary.list.R |only
rlist-0.4/rlist/DESCRIPTION | 28 -
rlist-0.4/rlist/MD5 | 289 ++++++++-----------
rlist-0.4/rlist/NAMESPACE | 9
rlist-0.4/rlist/NEWS | 66 +++-
rlist-0.4/rlist/R/List.R | 97 ++----
rlist-0.4/rlist/R/data.R |only
rlist-0.4/rlist/R/functions.R | 109 ++++++-
rlist-0.4/rlist/R/internal.R | 176 +++++++----
rlist-0.4/rlist/R/lambda.R | 32 --
rlist-0.4/rlist/R/list.all.R | 27 +
rlist-0.4/rlist/R/list.any.R | 23 -
rlist-0.4/rlist/R/list.append.R | 2
rlist-0.4/rlist/R/list.apply.R | 4
rlist-0.4/rlist/R/list.cases.R | 25 -
rlist-0.4/rlist/R/list.cbind.R | 8
rlist-0.4/rlist/R/list.class.R | 24 -
rlist-0.4/rlist/R/list.clean.R | 5
rlist-0.4/rlist/R/list.common.R | 7
rlist-0.4/rlist/R/list.count.R | 12
rlist-0.4/rlist/R/list.do.R | 16 -
rlist-0.4/rlist/R/list.exclude.R | 11
rlist-0.4/rlist/R/list.extract.R | 9
rlist-0.4/rlist/R/list.filter.R | 20 -
rlist-0.4/rlist/R/list.find.R | 13
rlist-0.4/rlist/R/list.findi.R | 15
rlist-0.4/rlist/R/list.first.R |only
rlist-0.4/rlist/R/list.flatten.R | 11
rlist-0.4/rlist/R/list.group.R | 26 -
rlist-0.4/rlist/R/list.insert.R | 11
rlist-0.4/rlist/R/list.is.R | 9
rlist-0.4/rlist/R/list.iter.R | 8
rlist-0.4/rlist/R/list.join.R | 25 -
rlist-0.4/rlist/R/list.load.R | 98 ++++--
rlist-0.4/rlist/R/list.map.R | 43 +-
rlist-0.4/rlist/R/list.maps.R | 16 -
rlist-0.4/rlist/R/list.match.R | 9
rlist-0.4/rlist/R/list.merge.R | 16 -
rlist-0.4/rlist/R/list.names.R |only
rlist-0.4/rlist/R/list.order.R | 21 -
rlist-0.4/rlist/R/list.parse.R | 45 +-
rlist-0.4/rlist/R/list.prepend.R | 9
rlist-0.4/rlist/R/list.rbind.R | 8
rlist-0.4/rlist/R/list.remove.R | 15
rlist-0.4/rlist/R/list.reverse.R | 7
rlist-0.4/rlist/R/list.sample.R | 19 -
rlist-0.4/rlist/R/list.save.R | 41 +-
rlist-0.4/rlist/R/list.search.R | 76 ++--
rlist-0.4/rlist/R/list.select.R | 19 -
rlist-0.4/rlist/R/list.serialize.R | 14
rlist-0.4/rlist/R/list.skip.R | 13
rlist-0.4/rlist/R/list.skipWhile.R | 19 -
rlist-0.4/rlist/R/list.sort.R | 17 -
rlist-0.4/rlist/R/list.stack.R | 20 -
rlist-0.4/rlist/R/list.subset.R | 23 -
rlist-0.4/rlist/R/list.table.R | 22 -
rlist-0.4/rlist/R/list.take.R | 7
rlist-0.4/rlist/R/list.takeWhile.R | 17 -
rlist-0.4/rlist/R/list.ungroup.R | 8
rlist-0.4/rlist/R/list.unserialize.R | 14
rlist-0.4/rlist/R/list.update.R | 23 -
rlist-0.4/rlist/R/list.which.R | 9
rlist-0.4/rlist/R/list.zip.R | 75 ++++
rlist-0.4/rlist/R/rlist.R | 15
rlist-0.4/rlist/R/subset.list.R | 19 -
rlist-0.4/rlist/R/utils.R | 4
rlist-0.4/rlist/README.md | 102 ++----
rlist-0.4/rlist/data |only
rlist-0.4/rlist/man/List.Rd | 9
rlist-0.4/rlist/man/list.all.Rd | 25 +
rlist-0.4/rlist/man/list.any.Rd | 21 -
rlist-0.4/rlist/man/list.append.Rd | 5
rlist-0.4/rlist/man/list.apply.Rd | 9
rlist-0.4/rlist/man/list.cases.Rd | 15
rlist-0.4/rlist/man/list.cbind.Rd | 10
rlist-0.4/rlist/man/list.class.Rd | 20 -
rlist-0.4/rlist/man/list.clean.Rd | 7
rlist-0.4/rlist/man/list.common.Rd | 5
rlist-0.4/rlist/man/list.count.Rd | 9
rlist-0.4/rlist/man/list.do.Rd | 13
rlist-0.4/rlist/man/list.exclude.Rd | 11
rlist-0.4/rlist/man/list.extract.Rd | 11
rlist-0.4/rlist/man/list.filter.Rd | 16 -
rlist-0.4/rlist/man/list.find.Rd | 11
rlist-0.4/rlist/man/list.findi.Rd | 13
rlist-0.4/rlist/man/list.first.Rd |only
rlist-0.4/rlist/man/list.flatten.Rd | 5
rlist-0.4/rlist/man/list.group.Rd | 19 -
rlist-0.4/rlist/man/list.insert.Rd | 7
rlist-0.4/rlist/man/list.is.Rd | 5
rlist-0.4/rlist/man/list.iter.Rd | 9
rlist-0.4/rlist/man/list.join.Rd | 13
rlist-0.4/rlist/man/list.last.Rd |only
rlist-0.4/rlist/man/list.load.Rd | 38 ++
rlist-0.4/rlist/man/list.map.Rd | 19 -
rlist-0.4/rlist/man/list.maps.Rd | 8
rlist-0.4/rlist/man/list.mapv.Rd | 22 -
rlist-0.4/rlist/man/list.match.Rd | 7
rlist-0.4/rlist/man/list.merge.Rd | 9
rlist-0.4/rlist/man/list.names.Rd |only
rlist-0.4/rlist/man/list.order.Rd | 21 -
rlist-0.4/rlist/man/list.parse.Rd | 13
rlist-0.4/rlist/man/list.prepend.Rd | 11
rlist-0.4/rlist/man/list.rbind.Rd | 10
rlist-0.4/rlist/man/list.remove.Rd | 11
rlist-0.4/rlist/man/list.reverse.Rd | 7
rlist-0.4/rlist/man/list.sample.Rd | 13
rlist-0.4/rlist/man/list.save.Rd | 16 -
rlist-0.4/rlist/man/list.search.Rd | 57 +--
rlist-0.4/rlist/man/list.select.Rd | 15
rlist-0.4/rlist/man/list.serialize.Rd | 8
rlist-0.4/rlist/man/list.skip.Rd | 13
rlist-0.4/rlist/man/list.skipWhile.Rd | 11
rlist-0.4/rlist/man/list.sort.Rd | 17 -
rlist-0.4/rlist/man/list.stack.Rd | 19 -
rlist-0.4/rlist/man/list.subset.Rd | 24 -
rlist-0.4/rlist/man/list.table.Rd | 15
rlist-0.4/rlist/man/list.take.Rd | 5
rlist-0.4/rlist/man/list.takeWhile.Rd | 9
rlist-0.4/rlist/man/list.ungroup.Rd | 8
rlist-0.4/rlist/man/list.unserialize.Rd | 6
rlist-0.4/rlist/man/list.unzip.Rd |only
rlist-0.4/rlist/man/list.update.Rd | 17 -
rlist-0.4/rlist/man/list.which.Rd | 7
rlist-0.4/rlist/man/list.zip.Rd | 6
rlist-0.4/rlist/man/nyweather.Rd |only
rlist-0.4/rlist/man/rlist-package.Rd |only
rlist-0.4/rlist/man/subset.list.Rd | 16 -
rlist-0.4/rlist/man/tryEval.Rd | 5
rlist-0.4/rlist/man/tryGet.Rd | 5
rlist-0.4/rlist/tests/testthat/test-basic.R | 59 +++
rlist-0.4/rlist/tests/testthat/test-list.find.R | 8
rlist-0.4/rlist/tests/testthat/test-list.group.R | 8
rlist-0.4/rlist/tests/testthat/test-list.map.R | 3
rlist-0.4/rlist/tests/testthat/test-list.search.R | 82 ++---
rlist-0.4/rlist/tests/testthat/test-list.sort.R | 18 +
143 files changed, 1575 insertions(+), 1319 deletions(-)
Title: Rcpp Integration for GNU GSL Vectors and Matrices
Diff between RcppGSL versions 0.2.3 dated 2015-01-12 and 0.2.4 dated 2015-01-24
Description: Rcpp integration for GNU GSL vectors and matrices
The GNU Scientific Library (GSL) is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The RcppGSL package provides an easy-to-use interface between GSL data
structures and R using concepts from Rcpp which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses Rcpp to connect to another third-party library. The autoconf
script, inline plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 23 +++++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++++---------
R/RcppExports.R |only
R/init.R |only
README.md | 2 +-
inst/NEWS.Rd | 11 +++++++++++
inst/doc/RcppGSL-intro.R | 8 ++++----
inst/doc/RcppGSL-intro.Rnw | 32 ++++++++++++++++++++++++++++++++
inst/doc/RcppGSL-intro.pdf |binary
inst/doc/RcppGSL-unitTests.pdf |binary
src/RcppExports.cpp |only
src/setErrorHandler.cpp |only
vignettes/RcppGSL-intro.Rnw | 32 ++++++++++++++++++++++++++++++++
14 files changed, 120 insertions(+), 18 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.11.3 dated 2014-09-29 and 0.11.4 dated 2015-01-24
Description: The Rcpp package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about Rcpp is provided by several vignettes included in this package, via the
Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Douglas Bates, and John Chambers
Maintainer: Dirk Eddelbuettel
Rcpp-0.11.3/Rcpp/inst/examples/ConvolveBenchmarks/Makefile |only
Rcpp-0.11.3/Rcpp/inst/examples/OpenMP/Makefile |only
Rcpp-0.11.3/Rcpp/inst/unitTests/RcppTestA |only
Rcpp-0.11.4/Rcpp/.Rinstignore | 1
Rcpp-0.11.4/Rcpp/ChangeLog | 178 +++++
Rcpp-0.11.4/Rcpp/DESCRIPTION | 8
Rcpp-0.11.4/Rcpp/MD5 | 143 ++--
Rcpp-0.11.4/Rcpp/R/Attributes.R | 4
Rcpp-0.11.4/Rcpp/R/Rcpp.package.skeleton.R | 4
Rcpp-0.11.4/Rcpp/R/unit.tests.R | 4
Rcpp-0.11.4/Rcpp/README.md | 24
Rcpp-0.11.4/Rcpp/build/Rcpp.pdf |binary
Rcpp-0.11.4/Rcpp/build/vignette.rds |binary
Rcpp-0.11.4/Rcpp/inst/NEWS.Rd | 57 +
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-attributes.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-extending.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-introduction.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-modules.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-package.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-quickref.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-sugar.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary
Rcpp-0.11.4/Rcpp/inst/doc/Rcpp.bib | 32 -
Rcpp-0.11.4/Rcpp/inst/examples/ConvolveBenchmarks/GNUmakefile |only
Rcpp-0.11.4/Rcpp/inst/examples/OpenMP/GNUmakefile |only
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/Rmath.h | 10
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/String.h | 2
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/config.h | 8
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/exceptions.h | 50 +
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/grow.h | 6
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/internal/NAComparator.h | 25
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/internal/r_vector.h | 55 +
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/macros/macros.h | 33 -
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/r |only
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/sugar/functions/mean.h | 133 +++-
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/sugar/functions/setdiff.h | 10
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/sugar/functions/var.h | 59 +
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/sugar/matrix/as_vector.h | 4
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/sugar/nona/nona.h | 2
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/traits/enable_if.h |only
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/traits/is_bool.h |only
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/traits/traits.h | 2
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/utils |only
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/vector/ListOf.h | 6
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/vector/MatrixColumn.h | 2
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/vector/Vector.h | 21
Rcpp-0.11.4/Rcpp/inst/include/Rcpp/vector/proxy.h | 2
Rcpp-0.11.4/Rcpp/inst/include/RcppCommon.h | 12
Rcpp-0.11.4/Rcpp/inst/unitTests/bin |only
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/ListOf.cpp | 10
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/Matrix.cpp | 13
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/String.cpp | 5
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/Vector.cpp | 16
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/attributes.cpp | 7
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/misc.cpp | 5
Rcpp-0.11.4/Rcpp/inst/unitTests/cpp/sugar.cpp | 29
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.ListOf.R | 11
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.Matrix.R | 5
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.String.R | 6
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.Vector.R | 8
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.attributes.R | 4
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.binary.package.R |only
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.client.package.R | 38 -
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.misc.R | 7
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.sugar.R | 315 ++++------
Rcpp-0.11.4/Rcpp/inst/unitTests/runit.sugar.var.R |only
Rcpp-0.11.4/Rcpp/inst/unitTests/src |only
Rcpp-0.11.4/Rcpp/inst/unitTests/testRcppPackage |only
Rcpp-0.11.4/Rcpp/src/api.cpp | 17
Rcpp-0.11.4/Rcpp/src/attributes.cpp | 6
Rcpp-0.11.4/Rcpp/vignettes/Rcpp.bib | 32 -
72 files changed, 1036 insertions(+), 395 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Diff between dfcomb versions 1.0-1 dated 2014-11-07 and 2.0-2 dated 2015-01-24
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
dfcomb-1.0-1/dfcomb/man/logistic_next.Rd |only
dfcomb-1.0-1/dfcomb/man/logistic_sim.Rd |only
dfcomb-1.0-1/dfcomb/src/Makevars |only
dfcomb-2.0-2/dfcomb/DESCRIPTION | 11
dfcomb-2.0-2/dfcomb/MD5 | 53 +
dfcomb-2.0-2/dfcomb/NAMESPACE | 10
dfcomb-2.0-2/dfcomb/R/dfcomb.R | 690 ++++++++++++++--
dfcomb-2.0-2/dfcomb/cleanup |only
dfcomb-2.0-2/dfcomb/configure |only
dfcomb-2.0-2/dfcomb/configure.ac |only
dfcomb-2.0-2/dfcomb/configure.win |only
dfcomb-2.0-2/dfcomb/man/CombIncrease_next.Rd |only
dfcomb-2.0-2/dfcomb/man/CombIncrease_sim.Rd |only
dfcomb-2.0-2/dfcomb/man/CombPlateau_next.Rd |only
dfcomb-2.0-2/dfcomb/man/CombPlateau_sim.Rd |only
dfcomb-2.0-2/dfcomb/man/dfcomb-package.Rd | 25
dfcomb-2.0-2/dfcomb/src/CppBugs |only
dfcomb-2.0-2/dfcomb/src/Makevars.in |only
dfcomb-2.0-2/dfcomb/src/Makevars.win | 3
dfcomb-2.0-2/dfcomb/src/dfcomb.c | 6
dfcomb-2.0-2/dfcomb/src/dfcomb.h | 47 +
dfcomb-2.0-2/dfcomb/src/logistic.cpp | 1133 +++++++++++++--------------
dfcomb-2.0-2/dfcomb/src/plateau.cpp |only
dfcomb-2.0-2/dfcomb/tools |only
24 files changed, 1293 insertions(+), 685 deletions(-)
Title: Rcpp Bindings for Annoy, a Library for Approximate Nearest
Neighbors
Diff between RcppAnnoy versions 0.0.4 dated 2014-12-08 and 0.0.5 dated 2015-01-24
Description: Annoy is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the Rcpp and BH
packages, exposing the same interface as the original Python wrapper to
Annoy. See https://github.com/spotify/annoy for more on Annoy. Annoy is
released under Version 2.0 of the Apache License. Also included is a small
Windows port of mmap which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 21 ++++++++++++++++++++-
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
inst/include/annoylib.h | 33 ++++++++++++++++++++-------------
src/Makevars | 2 +-
5 files changed, 50 insertions(+), 24 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-6 dated 2014-05-09 and 1.3-7 dated 2015-01-24
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 19
MD5 | 794 +++++++--------
NAMESPACE | 136 ++
R/arealMethods.R | 4
R/getCounts.R | 1
R/lgcp.R | 30
R/lgcpMethods.R | 6
R/lgcpStructures.R | 4
R/mstpppClassDef.R | 2
R/parameterEstimation.R | 1
R/selectObsWindow.R | 1
R/spatialAtRiskClassDef.R | 4
R/stpppClassDef.R | 2
build/vignette.rds |binary
inst/CITATION | 83 -
inst/doc/lgcp.pdf |binary
man/BetaParameters.Rd | 7
man/C.diff.single.im.Rd | 56 -
man/CovFunction.Rd | 14
man/CovFunction.function.Rd | 12
man/CovParameters.Rd | 7
man/Cvb.Rd | 34
man/EvaluatePrior.Rd | 11
man/Extract.mstppp.Rd | 7
man/Extract.stppp.Rd | 7
man/GAfinalise.MonteCarloAverage.Rd | 13
man/GAfinalise.Rd | 16
man/GAfinalise.nullAverage.Rd | 9
man/GAinitialise.MonteCarloAverage.Rd | 10
man/GAinitialise.Rd | 16
man/GAinitialise.nullAverage.Rd | 9
man/GAreturnvalue.MonteCarloAverage.Rd | 10
man/GAreturnvalue.Rd | 16
man/GAreturnvalue.nullAverage.Rd | 9
man/GAupdate.MonteCarloAverage.Rd | 13
man/GAupdate.Rd | 16
man/GAupdate.nullAverage.Rd | 9
man/GFfinalise.Rd | 15
man/GFfinalise.dump2dir.Rd | 12
man/GFfinalise.nullFunction.Rd | 9
man/GFinitialise.Rd | 15
man/GFinitialise.dump2dir.Rd | 12
man/GFinitialise.nullFunction.Rd | 9
man/GFreturnvalue.Rd | 15
man/GFreturnvalue.dump2dir.Rd | 12
man/GFreturnvalue.nullFunction.Rd | 9
man/GFupdate.Rd | 15
man/GFupdate.dump2dir.Rd | 12
man/GFupdate.nullFunction.Rd | 9
man/GPdrv.Rd | 38
man/GPdrv2.Rd | 38
man/GPdrv2_Multitype.Rd | 44
man/GPlist2array.Rd | 11
man/GPrealisation.Rd | 25
man/GammafromY.Rd | 12
man/GaussianPrior.Rd | 9
man/K.diff.single.Rd | 51
man/K.u.Rd | 24
man/K.val.Rd | 24
man/KinhomAverage.Rd | 50
man/LogGaussianPrior.Rd | 11
man/MALAlgcp.Rd | 68 -
man/MALAlgcpAggregateSpatial.PlusPars.Rd | 68 -
man/MALAlgcpMultitypeSpatial.PlusPars.Rd | 68 -
man/MALAlgcpSpatial.PlusPars.Rd | 61 -
man/MALAlgcpSpatial.Rd | 57 -
man/MALAlgcpSpatioTemporal.PlusPars.Rd | 69 -
man/MonteCarloAverage.Rd | 49
man/PriorSpec.Rd | 10
man/PriorSpec.list.Rd | 11
man/RandomFieldsCovFct.Rd | 17
man/SpatialPolygonsDataFrame.stapp.Rd | 7
man/SpikedExponentialCovFct.Rd | 22
man/YfromGamma.Rd | 12
man/add.list.Rd | 11
man/addTemporalCovariates.Rd | 62 -
man/affine.SpatialPolygonsDataFrame.Rd | 11
man/affine.fromFunction.Rd | 11
man/affine.fromSPDF.Rd | 11
man/affine.fromXYZ.Rd | 11
man/affine.stppp.Rd | 8
man/aggCovInfo.ArealWeightedMean.Rd | 8
man/aggCovInfo.ArealWeightedSum.Rd | 11
man/aggCovInfo.Majority.Rd | 8
man/aggCovInfo.Rd | 6
man/aggregateCovariateInfo.Rd | 25
man/aggregateformulaList.Rd | 9
man/andrieuthomsh.Rd | 60 -
man/as.SpatialGridDataFrame.Rd | 9
man/as.SpatialGridDataFrame.fromXYZ.Rd | 9
man/as.SpatialPixelsDataFrame.Rd | 6
man/as.SpatialPixelsDataFrame.lgcpgrid.Rd | 13
man/as.array.lgcpgrid.Rd | 6
man/as.fromXYZ.Rd | 12
man/as.fromXYZ.fromFunction.Rd | 21
man/as.im.fromFunction.Rd | 18
man/as.im.fromSPDF.Rd | 15
man/as.im.fromXYZ.Rd | 12
man/as.list.lgcpgrid.Rd | 15
man/as.owin.stapp.Rd | 11
man/as.owinlist.Rd | 6
man/as.owinlist.SpatialPolygonsDataFrame.Rd | 23
man/as.owinlist.stapp.Rd | 16
man/as.ppp.mstppp.Rd | 12
man/as.ppp.stppp.Rd | 9
man/as.stppp.Rd | 6
man/as.stppp.stapp.Rd | 38
man/assigninterp.Rd | 52
man/at.Rd | 9
man/autocorr.Rd | 41
man/autocorrMultitype.Rd | 30
man/betavals.Rd | 20
man/blockcircbase.Rd | 27
man/blockcircbaseFunction.Rd | 39
man/bt.scalar.Rd | 6
man/checkObsWin.Rd | 11
man/chooseCellwidth.Rd | 33
man/circulant.Rd | 6
man/circulant.matrix.Rd | 15
man/circulant.numeric.Rd | 6
man/clearinterp.Rd | 7
man/computeGradtruncSpatial.Rd | 33
man/computeGradtruncSpatioTemporal.Rd | 35
man/condProbs.Rd | 55 -
man/constantInTime.Rd | 22
man/constantInTime.numeric.Rd | 30
man/constantInTime.stppp.Rd | 25
man/constanth.Rd | 11
man/cov.interp.fft.Rd | 30
man/covEffects.Rd | 26
man/d.func.Rd | 14
man/density.stppp.Rd | 14
man/discreteWindow.Rd | 6
man/discreteWindow.lgcpPredict.Rd | 15
man/dump2dir.Rd | 36
man/eigenfrombase.Rd | 7
man/etavals.Rd | 20
man/exceedProbs.Rd | 28
man/exceedProbsAggregated.Rd | 30
man/expectation.Rd | 9
man/expectation.lgcpPredict.Rd | 46
man/expectation.lgcpPredictSpatialOnlyPlusParameters.Rd | 24
man/exponentialCovFct.Rd | 13
man/extendspatialAtRisk.Rd | 14
man/extract.Rd | 9
man/extract.lgcpPredict.Rd | 34
man/fftgrid.Rd | 35
man/fftinterpolate.Rd | 9
man/fftinterpolate.fromFunction.Rd | 20
man/fftinterpolate.fromSPDF.Rd | 23
man/fftinterpolate.fromXYZ.Rd | 20
man/fftmultiply.Rd | 9
man/formulaList.Rd | 11
man/g.diff.single.Rd | 50
man/gOverlay.Rd | 13
man/genFFTgrid.Rd | 24
man/getCellCounts.Rd | 13
man/getCounts.Rd | 23
man/getCovParameters.GPrealisation.Rd | 9
man/getCovParameters.Rd | 9
man/getCovParameters.list.Rd | 9
man/getLHSformulaList.Rd | 7
man/getRotation.Rd | 6
man/getRotation.default.Rd | 9
man/getRotation.stppp.Rd | 14
man/getZmat.Rd | 93 -
man/getZmats.Rd | 10
man/getinterp.Rd | 35
man/getlgcpPredictSpatialINLA.Rd | 5
man/getpolyol.Rd | 48
man/getup.Rd | 8
man/ginhomAverage.Rd | 54 -
man/grid2spdf.Rd | 12
man/grid2spix.Rd | 12
man/grid2spoly.Rd | 12
man/grid2spts.Rd | 12
man/gridInWindow.Rd | 24
man/gridav.Rd | 6
man/gridav.lgcpPredict.Rd | 19
man/gridfun.Rd | 9
man/gridfun.lgcpPredict.Rd | 15
man/gu.Rd | 16
man/guessinterp.Rd | 56 -
man/hasNext.Rd | 4
man/hasNext.iter.Rd | 8
man/hvals.Rd | 9
man/hvals.lgcpPredict.Rd | 14
man/identify.lgcpPredict.Rd | 23
man/identifygrid.Rd | 13
man/image.lgcpgrid.Rd | 19
man/initialiseAMCMC.Rd | 17
man/initialiseAMCMC.andrieuthomsh.Rd | 18
man/initialiseAMCMC.constanth.Rd | 6
man/integerise.Rd | 9
man/integerise.mstppp.Rd | 9
man/integerise.stppp.Rd | 13
man/intens.Rd | 6
man/intens.lgcpPredict.Rd | 9
man/intens.lgcpSimMultitypeSpatialPlusParameters.Rd | 10
man/intens.lgcpSimSpatialPlusParameters.Rd | 10
man/interptypes.Rd | 33
man/inversebase.Rd | 7
man/is.SPD.Rd | 10
man/is.burnin.Rd | 7
man/is.pow2.Rd | 4
man/is.retain.Rd | 4
man/iteration.Rd | 7
man/lambdaEst.Rd | 9
man/lambdaEst.ppp.Rd | 79 -
man/lambdaEst.stppp.Rd | 79 -
man/lgcp-package.Rd | 77 -
man/lgcpForecast.Rd | 34
man/lgcpInits.Rd | 47
man/lgcpPredict.Rd | 255 +---
man/lgcpPredictAggregateSpatialPlusPars.Rd | 207 +--
man/lgcpPredictAggregated.Rd | 270 +----
man/lgcpPredictMultitypeSpatialPlusPars.Rd | 236 +---
man/lgcpPredictSpatial.Rd | 174 +--
man/lgcpPredictSpatialINLA.Rd | 164 +--
man/lgcpPredictSpatialPlusPars.Rd | 193 +--
man/lgcpPredictSpatioTemporalPlusPars.Rd | 239 +---
man/lgcpPrior.Rd | 29
man/lgcpSim.Rd | 133 --
man/lgcpSimMultitypeSpatialCovariates.Rd | 39
man/lgcpSimSpatial.Rd | 33
man/lgcpSimSpatialCovariates.Rd | 48
man/lgcpbayes.Rd | 2
man/lgcpgrid.Rd | 37
man/lgcpgrid.array.Rd | 24
man/lgcpgrid.list.Rd | 32
man/lgcpgrid.matrix.Rd | 20
man/lgcppars.Rd | 21
man/lgcpvignette.Rd | 2
man/loc2poly.Rd | 21
man/loop.mcmc.Rd | 6
man/ltar.Rd | 22
man/matchcovariance.Rd | 29
man/mcmcLoop.Rd | 14
man/mcmcProgressNone.Rd | 4
man/mcmcProgressPrint.Rd | 4
man/mcmcProgressTextBar.Rd | 4
man/mcmcProgressTk.Rd | 4
man/mcmcpars.Rd | 19
man/mcmctrace.Rd | 9
man/mcmctrace.lgcpPredict.Rd | 13
man/meanfield.Rd | 6
man/meanfield.lgcpPredict.Rd | 11
man/meanfield.lgcpPredictINLA.Rd | 9
man/minimum.contrast.Rd | 78 -
man/minimum.contrast.spatiotemporal.Rd | 95 -
man/mstppp.Rd | 15
man/mstppp.list.Rd | 15
man/mstppp.ppp.Rd | 17
man/mstppp.stppp.Rd | 12
man/muEst.Rd | 34
man/multiply.list.Rd | 11
man/my.KinhomAverage.Rd | 41
man/my.ginhomAverage.Rd | 44
man/neattable.Rd | 6
man/neigh2D.Rd | 15
man/nextStep.Rd | 4
man/nullAverage.Rd | 10
man/nullFunction.Rd | 5
man/numCases.Rd | 23
man/osppp2latlon.Rd | 8
man/osppp2merc.Rd | 8
man/paramprec.Rd | 18
man/paramprecbase.Rd | 22
man/parautocorr.Rd | 37
man/parsummary.Rd | 34
man/plot.fromSPDF.Rd | 6
man/plot.fromXYZ.Rd | 6
man/plot.lgcpAutocorr.Rd | 22
man/plot.lgcpPredict.Rd | 29
man/plot.lgcpQuantiles.Rd | 25
man/plot.lgcpZmat.Rd | 21
man/plot.lgcpgrid.Rd | 19
man/plot.mcmcdiag.Rd | 15
man/plot.mstppp.Rd | 9
man/plot.stppp.Rd | 6
man/plot.temporalAtRisk.Rd | 12
man/plotExceed.Rd | 6
man/plotExceed.array.Rd | 45
man/plotExceed.lgcpPredict.Rd | 34
man/plotit.Rd | 7
man/postcov.Rd | 24
man/postcov.lgcpPredictAggregateSpatialPlusParameters.Rd | 30
man/postcov.lgcpPredictMultitypeSpatialPlusParameters.Rd | 30
man/postcov.lgcpPredictSpatialOnlyPlusParameters.Rd | 30
man/postcov.lgcpPredictSpatioTemporalPlusParameters.Rd | 33
man/print.dump2dir.Rd | 6
man/print.fromFunction.Rd | 6
man/print.fromSPDF.Rd | 6
man/print.fromXYZ.Rd | 6
man/print.gridaverage.Rd | 6
man/print.lgcpPredict.Rd | 6
man/print.lgcpgrid.Rd | 12
man/print.mcmc.Rd | 9
man/print.mstppp.Rd | 6
man/print.stapp.Rd | 9
man/print.stppp.Rd | 6
man/print.temporalAtRisk.Rd | 12
man/priorpost.Rd | 37
man/quantile.lgcpPredict.Rd | 49
man/quantile.lgcpgrid.Rd | 16
man/raster.lgcpgrid.Rd | 15
man/rescale.mstppp.Rd | 9
man/rescale.stppp.Rd | 9
man/resetLoop.Rd | 4
man/rgauss.Rd | 28
man/roteffgain.Rd | 13
man/rotmat.Rd | 10
man/rr.Rd | 6
man/rr.lgcpPredict.Rd | 9
man/samplePosterior.Rd | 15
man/segProbs.Rd | 76 -
man/seintens.Rd | 9
man/seintens.lgcpPredict.Rd | 12
man/selectObsWindow.Rd | 15
man/selectObsWindow.default.Rd | 20
man/selectObsWindow.stppp.Rd | 28
man/serr.Rd | 6
man/serr.lgcpPredict.Rd | 9
man/setTxtProgressBar2.Rd | 13
man/setoutput.Rd | 19
man/showGrid.Rd | 12
man/showGrid.default.Rd | 11
man/showGrid.lgcpPredict.Rd | 19
man/showGrid.stppp.Rd | 18
man/smultiply.list.Rd | 13
man/sparsebase.Rd | 8
man/spatialAtRisk.Rd | 126 --
man/spatialAtRisk.SpatialGridDataFrame.Rd | 27
man/spatialAtRisk.SpatialPolygonsDataFrame.Rd | 29
man/spatialAtRisk.bivden.Rd | 24
man/spatialAtRisk.default.Rd | 31
man/spatialAtRisk.fromXYZ.Rd | 36
man/spatialAtRisk.function.Rd | 40
man/spatialAtRisk.im.Rd | 28
man/spatialAtRisk.lgcpgrid.Rd | 28
man/spatialIntensities.Rd | 9
man/spatialIntensities.fromSPDF.Rd | 16
man/spatialIntensities.fromXYZ.Rd | 16
man/spatialparsEst.Rd | 55 -
man/stGPrealisation.Rd | 27
man/stapp.Rd | 9
man/stapp.SpatialPolygonsDataFrame.Rd | 24
man/stapp.list.Rd | 20
man/stppp.Rd | 16
man/stppp.list.Rd | 13
man/stppp.ppp.Rd | 14
man/summary.lgcpgrid.Rd | 16
man/summary.mcmc.Rd | 12
man/target.and.grad.AggregateSpatialPlusPars.Rd | 26
man/target.and.grad.MultitypespatialPlusPars.Rd | 26
man/target.and.grad.SpatioTemporalPlusPars.Rd | 32
man/target.and.grad.spatial.Rd | 32
man/target.and.grad.spatialPlusPars.Rd | 25
man/target.and.grad.spatiotemporal.Rd | 38
man/tempRaster.Rd | 12
man/temporalAtRisk.Rd | 118 --
man/temporalAtRisk.function.Rd | 66 -
man/temporalAtRisk.numeric.Rd | 68 -
man/textsummary.Rd | 34
man/thetaEst.Rd | 55 -
man/toral.cov.mat.Rd | 18
man/touchingowin.Rd | 13
man/traceplots.Rd | 34
man/transblack.Rd | 4
man/transblue.Rd | 4
man/transgreen.Rd | 4
man/transred.Rd | 4
man/txtProgressBar2.Rd | 24
man/updateAMCMC.Rd | 17
man/updateAMCMC.andrieuthomsh.Rd | 18
man/updateAMCMC.constanth.Rd | 6
man/varfield.Rd | 9
man/varfield.lgcpPredict.Rd | 14
man/varfield.lgcpPredictINLA.Rd | 9
man/window.lgcpPredict.Rd | 15
man/xvals.Rd | 13
man/xvals.SpatialGridDataFrame.Rd | 16
man/xvals.default.Rd | 16
man/xvals.fromXYZ.Rd | 16
man/xvals.lgcpPredict.Rd | 9
man/yvals.Rd | 13
man/yvals.SpatialGridDataFrame.Rd | 16
man/yvals.default.Rd | 16
man/yvals.fromXYZ.Rd | 16
man/yvals.lgcpPredict.Rd | 9
man/zvals.Rd | 13
man/zvals.SpatialGridDataFrame.Rd | 16
man/zvals.default.Rd | 16
man/zvals.fromXYZ.Rd | 16
tests/fromSPDFTest.R | 2
tests/lgcpMethodsTest.R | 3
tests/mstpppClassTest.R | 1
tests/stpppClassTest.R | 1
398 files changed, 4464 insertions(+), 6115 deletions(-)
Title: Tools for Simulation Studies in Parallel with R
Diff between simsalapar versions 1.0-4 dated 2014-09-17 and 1.0-5 dated 2015-01-24
Description: Tools for setting up, conducting, and evaluating larger-scale
simulation studies, including parallel computations.
Author: Marius Hofert and Martin Maechler
Maintainer: Marius Hofert
DESCRIPTION | 17 +++---
MD5 | 35 ++++++------
NAMESPACE | 28 ++++++++--
R/array-stuff.R | 36 +++++--------
R/doApply.R | 4 -
R/graphics.R | 53 ++++++++++++-------
R/grid-stuff.R | 11 ++--
R/subjob.R | 17 ++----
demo/00Index | 1
demo/VaRsuperadd.R | 10 ++-
demo/rSeed-ex.R |only
demo/robcovMCD.R | 123 ++++++++++++++++++++++++++++++++++++---------
inst/xtraR/Sweave-prelim.R | 32 +++++++++--
man/array-stuff.Rd | 50 ++++++++++++------
man/doCallWE.Rd | 2
man/mayplot.Rd | 2
man/subjob.Rd | 94 +++++++++++++++++++---------------
man/varlist.Rd | 23 +++++---
tests/tstTGforecasts.R | 5 +
19 files changed, 354 insertions(+), 189 deletions(-)
Title: Political Science Computational Laboratory, Stanford University
Diff between pscl versions 1.4.6 dated 2014-08-27 and 1.4.8 dated 2015-01-24
Description: Bayesian analysis of item-response theory (IRT) models,
roll call analysis; computing highest density regions; maximum
likelihood estimation of zero-inflated and hurdle models for count
data; goodness-of-fit measures for GLMs; data sets used
in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.
Author: Simon Jackman, with contributions from
Alex Tahk, Achim Zeileis, Christina Maimone and Jim Fearon
Maintainer: Simon Jackman
pscl-1.4.6/pscl/inst/extdata/id1.RData |only
pscl-1.4.6/pscl/inst/extdata/id2.RData |only
pscl-1.4.8/pscl/DESCRIPTION | 13 ++-
pscl-1.4.8/pscl/MD5 | 74 +++++++++++-----------
pscl-1.4.8/pscl/NAMESPACE | 4 -
pscl-1.4.8/pscl/NEWS | 15 +++-
pscl-1.4.8/pscl/R/hurdle.R | 2
pscl-1.4.8/pscl/R/plot.ideal.r | 2
pscl-1.4.8/pscl/R/vuong.R | 76 +++++++++++++----------
pscl-1.4.8/pscl/inst/CITATION | 2
pscl-1.4.8/pscl/inst/doc/countreg.pdf |binary
pscl-1.4.8/pscl/inst/extdata/id1.rda |only
pscl-1.4.8/pscl/inst/extdata/id2.rda |only
pscl-1.4.8/pscl/man/AustralianElectionPolling.Rd | 5 -
pscl-1.4.8/pscl/man/admit.Rd | 2
pscl-1.4.8/pscl/man/bioChemists.Rd | 2
pscl-1.4.8/pscl/man/ca2006.Rd | 4 -
pscl-1.4.8/pscl/man/constrain.items.Rd | 2
pscl-1.4.8/pscl/man/extractRollCallObject.Rd | 2
pscl-1.4.8/pscl/man/hitmiss.Rd | 2
pscl-1.4.8/pscl/man/ideal.Rd | 69 ++++++++++----------
pscl-1.4.8/pscl/man/idealToMCMC.Rd | 2
pscl-1.4.8/pscl/man/odTest.Rd | 2
pscl-1.4.8/pscl/man/pR2.Rd | 2
pscl-1.4.8/pscl/man/partycodes.Rd | 2
pscl-1.4.8/pscl/man/plot.ideal.Rd | 3
pscl-1.4.8/pscl/man/plot.predict.ideal.Rd | 2
pscl-1.4.8/pscl/man/politicalInformation.Rd | 2
pscl-1.4.8/pscl/man/postProcess.Rd | 4 -
pscl-1.4.8/pscl/man/predict.ideal.Rd | 16 ----
pscl-1.4.8/pscl/man/predprob.ideal.Rd | 10 ---
pscl-1.4.8/pscl/man/presidentialElections.Rd | 2
pscl-1.4.8/pscl/man/readKH.Rd | 5 -
pscl-1.4.8/pscl/man/s109.Rd | 3
pscl-1.4.8/pscl/man/tracex.Rd | 19 +----
pscl-1.4.8/pscl/man/vuong.Rd | 8 ++
pscl-1.4.8/pscl/src/IDEAL.c | 50 +++++++++++++--
pscl-1.4.8/pscl/src/crossprod.c | 2
pscl-1.4.8/pscl/src/dtnorm.c | 10 +--
pscl-1.4.8/pscl/src/util.c | 45 ++++++-------
40 files changed, 250 insertions(+), 215 deletions(-)
Title: Nested Association Mapping analysis
Diff between NAM versions 1.0.2 dated 2015-01-15 and 1.0.2.1 dated 2015-01-24
Description: The NAM package was designed for association studies in nested association mapping (NAM) panels, but it also can handle biparental and random populations. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 14 ++++++-------
MD5 | 11 +++++-----
R/MCreml.R |only
R/reference.R | 57 ++++++++++++++++++++++++-----------------------------
R/reml.R | 4 +--
man/NAM-package.Rd | 13 ++----------
man/reml.Rd | 7 +++---
7 files changed, 48 insertions(+), 58 deletions(-)
Title: GUI Tools Made Easy: Interact with Models and Explore Data
Diff between PBSmodelling versions 2.66.264 dated 2014-04-07 and 2.67.266 dated 2015-01-23
Description: Provides software to facilitate the design, testing, and operation
of computer models. It focuses particularly on tools that make it easy to
construct and edit a customized graphical user interface (GUI). Although our
simplified GUI language depends heavily on the R interface to the Tcl/Tk
package, a user does not need to know Tcl/Tk. Examples illustrate models
built with other R packages, including PBSmapping, PBSddesolve, and BRugs.
A complete user's guide `PBSmodelling-UG.pdf' shows how to use this package
effectively.
Author: Jon T. Schnute
Maintainer: Rowan Haigh
DESCRIPTION | 37 ++++-------
MD5 | 30 ++++----
NAMESPACE | 2
R/listFuns.r | 151 ++++++++++++++++++++++++++++++++-------------
R/plotFuns.r | 12 ++-
R/presentTalk.r | 8 --
R/supportFuns.r | 40 ++++++++---
data/CCA.qbr.rda |binary
inst/PBStools/00ReadMe.txt | 18 ++---
inst/PBStools/RPaths.bat | 2
inst/PBStools/Rcopy.bat | 62 +++++++++---------
inst/doc/ChangeLog.txt | 8 ++
man/CCA.qbr.Rd | 2
man/readList.Rd | 21 +++---
man/showHelp.Rd | 3
man/viewCode.Rd | 5 +
16 files changed, 251 insertions(+), 150 deletions(-)
Title: Multi-paradigm Pipeline Implementation
Diff between pipeR versions 0.5 dated 2014-09-30 and 0.6 dated 2015-01-23
Description: Provides various styles of function chaining methods: Pipe
operator, Pipe object, and pipeline function, each representing a distinct
pipeline model yet sharing almost a common set of features: A value can be
piped to the first unnamed argument of a function and to dot symbol in an
enclosed expression. The syntax is designed to make the pipeline more
readable and friendly to a wide range of operations.
Author: Kun Ren
Maintainer: Kun Ren
pipeR-0.5/pipeR/inst |only
pipeR-0.6/pipeR/DESCRIPTION | 20
pipeR-0.6/pipeR/MD5 | 35 -
pipeR-0.6/pipeR/NAMESPACE | 3
pipeR-0.6/pipeR/NEWS | 41 +
pipeR-0.6/pipeR/R/functions.R | 197 ++++----
pipeR-0.6/pipeR/R/operator.R |only
pipeR-0.6/pipeR/R/pipe.R | 3
pipeR-0.6/pipeR/R/pipeR.R | 235 +---------
pipeR-0.6/pipeR/R/pipeline.R |only
pipeR-0.6/pipeR/R/utils.R | 21
pipeR-0.6/pipeR/README.md | 78 ++-
pipeR-0.6/pipeR/man/Pipe.Rd | 3
pipeR-0.6/pipeR/man/grapes-greater-than-greater-than-grapes.Rd | 50 +-
pipeR-0.6/pipeR/man/pipeR-package.Rd |only
pipeR-0.6/pipeR/man/pipeline.Rd |only
pipeR-0.6/pipeR/tests/testthat/test1-operator.R | 23
pipeR-0.6/pipeR/tests/testthat/test3-pipeline.R |only
18 files changed, 348 insertions(+), 361 deletions(-)
Title: Efficient authenticated interaction with the O*NET API
Diff between ONETr versions 1.0.1 dated 2014-11-04 and 1.0.2 dated 2015-01-23
Description: Provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API
Author: Eric Knudsen
Maintainer: Eric Knudsen
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/keySearch.R | 3 +++
R/setCreds.R | 1 +
4 files changed, 13 insertions(+), 9 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Diff between ExomeDepth versions 1.1.1 dated 2015-01-13 and 1.1.4 dated 2015-01-23
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
DESCRIPTION | 8 +-
MD5 | 16 ++--
NAMESPACE | 4 -
R/countBamInGranges.R | 139 +++++++++++++++++++-----------------
inst/doc/ExomeDepth-vignette.Rnw | 7 +
inst/doc/ExomeDepth-vignette.pdf |binary
man/countBamInGRanges.exomeDepth.Rd | 5 -
man/getBamCounts.Rd | 8 --
vignettes/ExomeDepth-vignette.Rnw | 7 +
9 files changed, 106 insertions(+), 88 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.10-4 dated 2014-04-28 and 0.10-5 dated 2015-01-23
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler
DESCRIPTION | 12 +--
MD5 | 42 ++++++------
NEWS | 22 ++++--
R/getDesign.R | 58 ++++++++++------
R/pcountOpen.R | 75 ++++++++++++++++-----
R/unmarkedFit.R | 137 ++++++++++++++++++++++++++++++++--------
R/utils.R | 2
build/vignette.rds |binary
inst/doc/cap-recap.pdf |binary
inst/doc/colext.pdf |binary
inst/doc/distsamp.pdf |binary
inst/doc/spp-dist.pdf |binary
inst/doc/unmarked.pdf |binary
inst/unitTests/sim.pcountOpen.r | 137 ++++++++++++++++++++++++++++++++++++++++
man/pcountOpen.Rd | 78 ++++++++++++++++------
man/unmarked-package.Rd | 4 -
man/unmarkedMultFrame.Rd | 3
man/unmarkedRanef-class.Rd | 6 -
src/Makevars.win | 3
src/nll_pcount.cpp | 2
src/nll_pcountOpen.cpp | 97 ++++++++++++++++++----------
src/nll_pcountOpen.h | 25 ++++++-
22 files changed, 540 insertions(+), 163 deletions(-)
Title: Interface to PLoS Journals Search API
Diff between rplos versions 0.4.1 dated 2014-07-22 and 0.4.6 dated 2015-01-23
Description: A programmatic interface to the SOLR based
search API provided by the Public Library
of Science journals to search their articles. Functions
are included for searching for articles, retrieving
articles, making plots, doing faceted searches, doing
highlight searches, and viewing results of highlighted
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain
rplos-0.4.1/rplos/R/help.R |only
rplos-0.4.1/rplos/man/crossref.Rd |only
rplos-0.4.1/rplos/man/formatcrossref.Rd |only
rplos-0.4.1/rplos/tests/testthat/test-crossref.R |only
rplos-0.4.6/rplos/DESCRIPTION | 30
rplos-0.4.6/rplos/LICENSE |only
rplos-0.4.6/rplos/MD5 | 157 +--
rplos-0.4.6/rplos/NAMESPACE | 17
rplos-0.4.6/rplos/NEWS | 27
rplos-0.4.6/rplos/R/crossref.R | 69 -
rplos-0.4.6/rplos/R/facetplos.r | 45
rplos-0.4.6/rplos/R/formatarticleurl.R | 21
rplos-0.4.6/rplos/R/fulltext.R | 19
rplos-0.4.6/rplos/R/highplos.r | 129 --
rplos-0.4.6/rplos/R/journalnamekey.R | 8
rplos-0.4.6/rplos/R/plosabstract.R | 10
rplos-0.4.6/rplos/R/plosauthor.R | 12
rplos-0.4.6/rplos/R/plosfields.R | 8
rplos-0.4.6/rplos/R/plosfigtabcaps.R | 11
rplos-0.4.6/rplos/R/plossubject.R | 12
rplos-0.4.6/rplos/R/plostitle.R | 12
rplos-0.4.6/rplos/R/plosviews.R | 28
rplos-0.4.6/rplos/R/plosword.R | 75 -
rplos-0.4.6/rplos/R/plot_throughtime.R | 126 --
rplos-0.4.6/rplos/R/rplos-package.R |only
rplos-0.4.6/rplos/R/searchplos.R | 166 +--
rplos-0.4.6/rplos/R/zzz.R | 16
rplos-0.4.6/rplos/README.md | 394 +++++++-
rplos-0.4.6/rplos/build/vignette.rds |binary
rplos-0.4.6/rplos/data/isocodes.rda |only
rplos-0.4.6/rplos/inst/doc/facethighlight.Rmd |only
rplos-0.4.6/rplos/inst/doc/facethighlight.html |only
rplos-0.4.6/rplos/inst/doc/fulltext.Rmd |only
rplos-0.4.6/rplos/inst/doc/fulltext.html |only
rplos-0.4.6/rplos/inst/doc/rplos_vignette.Rmd | 385 ++-----
rplos-0.4.6/rplos/inst/doc/rplos_vignette.html | 465 ++++-----
rplos-0.4.6/rplos/inst/schema.xml | 727 +++++++--------
rplos-0.4.6/rplos/inst/vign/facethighlight.Rmd |only
rplos-0.4.6/rplos/inst/vign/facethighlight.md |only
rplos-0.4.6/rplos/inst/vign/figure/highbrow.png |only
rplos-0.4.6/rplos/inst/vign/figure/highbrow_big.png |only
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rplos-0.4.6/rplos/inst/vign/figure/plosword1plot.png |binary
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rplos-0.4.6/rplos/inst/vign/figure/throughtime1.png |binary
rplos-0.4.6/rplos/inst/vign/fulltext.Rmd |only
rplos-0.4.6/rplos/inst/vign/fulltext.md |only
rplos-0.4.6/rplos/inst/vign/rplos_vignette.Rmd | 102 --
rplos-0.4.6/rplos/inst/vign/rplos_vignette.md |only
rplos-0.4.6/rplos/man/addmissing.Rd | 3
rplos-0.4.6/rplos/man/check_response.Rd | 3
rplos-0.4.6/rplos/man/concat_todf.Rd | 3
rplos-0.4.6/rplos/man/crossref-defunct.Rd |only
rplos-0.4.6/rplos/man/facetplos.Rd | 7
rplos-0.4.6/rplos/man/formatarticleurl.Rd | 5
rplos-0.4.6/rplos/man/full_text_urls.Rd | 5
rplos-0.4.6/rplos/man/highbrow.Rd | 3
rplos-0.4.6/rplos/man/highplos.Rd | 16
rplos-0.4.6/rplos/man/insertnones.Rd | 3
rplos-0.4.6/rplos/man/isocodes.Rd |only
rplos-0.4.6/rplos/man/journalnamekey.Rd | 3
rplos-0.4.6/rplos/man/plos_fulltext.Rd | 17
rplos-0.4.6/rplos/man/plosabstract.Rd | 59 -
rplos-0.4.6/rplos/man/plosauthor.Rd | 59 -
rplos-0.4.6/rplos/man/plosfields.Rd | 3
rplos-0.4.6/rplos/man/plosfigtabcaps.Rd | 59 -
rplos-0.4.6/rplos/man/plossubject.Rd | 59 -
rplos-0.4.6/rplos/man/plostitle.Rd | 59 -
rplos-0.4.6/rplos/man/plosviews.Rd | 14
rplos-0.4.6/rplos/man/plosword.Rd | 18
rplos-0.4.6/rplos/man/plot_throughtime.Rd | 18
rplos-0.4.6/rplos/man/rplos-defunct.Rd |only
rplos-0.4.6/rplos/man/rplos.Rd | 50 -
rplos-0.4.6/rplos/man/searchplos.Rd | 79 -
rplos-0.4.6/rplos/tests/testthat/test-check_response.R | 8
rplos-0.4.6/rplos/tests/testthat/test-journalnamekey.R | 9
rplos-0.4.6/rplos/tests/testthat/test-plosabstract.R | 10
rplos-0.4.6/rplos/tests/testthat/test-plosauthor.R | 10
rplos-0.4.6/rplos/tests/testthat/test-plosfigtabcaps.R | 16
rplos-0.4.6/rplos/tests/testthat/test-plossubject.R | 10
rplos-0.4.6/rplos/tests/testthat/test-plostitle.R | 12
rplos-0.4.6/rplos/tests/testthat/test-plosviews.R | 10
rplos-0.4.6/rplos/tests/testthat/test-plosword.R | 6
rplos-0.4.6/rplos/tests/testthat/test-plot_throughtime.R | 8
rplos-0.4.6/rplos/tests/testthat/test-searchplos.R | 28
rplos-0.4.6/rplos/vignettes/facethighlight.Rmd |only
rplos-0.4.6/rplos/vignettes/figure/highbrow.png |only
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rplos-0.4.6/rplos/vignettes/fulltext.Rmd |only
rplos-0.4.6/rplos/vignettes/rplos_vignette.Rmd | 385 ++-----
94 files changed, 1978 insertions(+), 2150 deletions(-)
Title: Miscellaneous Tools for Reproducible Research with R.
Diff between repmis versions 0.3.3 dated 2014-12-10 and 0.4 dated 2015-01-23
Description: The package includes tools to load R packages
and automatically generate BibTeX files citing them as well as load
plain-text and Excel formatted data stored on Dropbox, GitHub, and from
other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 21 ++++---
MD5 | 30 +++++-----
NAMESPACE | 3 -
NEWS | 7 ++
R/LoadandCite.R | 110 +++++++++++++++++++--------------------
R/source_DropboxData.R | 128 +++++++++++++++++++++++-----------------------
R/source_XlsxData.R | 9 +--
R/source_data.R | 28 +++++-----
README.md | 4 -
man/InstallOldPackages.Rd | 3 -
man/LoadandCite.Rd | 3 -
man/git_stamp.Rd | 3 -
man/scan_https.Rd | 3 -
man/source_DropboxData.Rd | 11 ++-
man/source_XlsxData.Rd | 3 -
man/source_data.Rd | 18 ++----
16 files changed, 202 insertions(+), 182 deletions(-)
Title: Reverse correlation image classification toolbox
Diff between rcicr versions 0.2.6 dated 2014-12-19 and 0.3.0 dated 2015-01-23
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch
ChangeLog | 5 +++++
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/rcicr.R | 19 +++++++++++++------
R/rcicr_2IFC.R | 13 +++++++------
man/generateCI.Rd | 2 +-
man/generateNoiseImage.Rd | 4 ++--
man/generateNoisePattern.Rd | 4 +++-
8 files changed, 43 insertions(+), 28 deletions(-)
Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for
(Bio)Equivalence Studies
Diff between PowerTOST versions 1.2-05 dated 2015-01-06 and 1.2-06 dated 2015-01-23
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes
PowerTOST-1.2-05/PowerTOST/inst/doc/BE_power_sample_size_excerpt_V07.pdf |only
PowerTOST-1.2-05/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.07.pdf |only
PowerTOST-1.2-05/PowerTOST/man/power2.TOST.Rd |only
PowerTOST-1.2-06/PowerTOST/DESCRIPTION | 8
PowerTOST-1.2-06/PowerTOST/MD5 | 67 +++-----
PowerTOST-1.2-06/PowerTOST/NEWS | 15 +
PowerTOST-1.2-06/PowerTOST/R/BE_CI.R | 1
PowerTOST-1.2-06/PowerTOST/R/OwensQ.R | 2
PowerTOST-1.2-06/PowerTOST/R/SampleSize.R | 63 +++----
PowerTOST-1.2-06/PowerTOST/R/SampleSize_doseprop.R | 1
PowerTOST-1.2-06/PowerTOST/R/SampleSize_noninf.R | 9 -
PowerTOST-1.2-06/PowerTOST/R/expSampleSize.R | 9 -
PowerTOST-1.2-06/PowerTOST/R/expSampleSize_noninf.R | 4
PowerTOST-1.2-06/PowerTOST/R/exppower.R | 12 -
PowerTOST-1.2-06/PowerTOST/R/exppower_noninf.R | 9 -
PowerTOST-1.2-06/PowerTOST/R/helper_dp.R | 1
PowerTOST-1.2-06/PowerTOST/R/pa.ABE.R | 15 -
PowerTOST-1.2-06/PowerTOST/R/pa.NTID.R | 6
PowerTOST-1.2-06/PowerTOST/R/pa.scABE.R | 2
PowerTOST-1.2-06/PowerTOST/R/power.R | 83 +++++-----
PowerTOST-1.2-06/PowerTOST/R/power2.R | 66 -------
PowerTOST-1.2-06/PowerTOST/R/power_RSABE.R | 1
PowerTOST-1.2-06/PowerTOST/R/power_doseprop.R | 7
PowerTOST-1.2-06/PowerTOST/R/power_noninf.R | 6
PowerTOST-1.2-06/PowerTOST/R/pwrA_S3methods.R | 3
PowerTOST-1.2-06/PowerTOST/inst/doc/BE_power_sample_size_excerpt.pdf |only
PowerTOST-1.2-06/PowerTOST/inst/doc/Implementation_scaledABE_sims.pdf |only
PowerTOST-1.2-06/PowerTOST/inst/tests/test_2x2.R | 2
PowerTOST-1.2-06/PowerTOST/inst/tests/test_2x2x3.R | 2
PowerTOST-1.2-06/PowerTOST/inst/tests/test_2x4x2.R | 2
PowerTOST-1.2-06/PowerTOST/inst/tests/test_2x4x4.R | 2
PowerTOST-1.2-06/PowerTOST/inst/tests/test_RatioF.R | 2
PowerTOST-1.2-06/PowerTOST/inst/tests/test_parallel.R | 6
PowerTOST-1.2-06/PowerTOST/man/exppower.TOST.Rd | 11 -
PowerTOST-1.2-06/PowerTOST/man/power.RatioF.Rd | 4
PowerTOST-1.2-06/PowerTOST/man/power.TOST.Rd | 53 ++++--
PowerTOST-1.2-06/PowerTOST/man/sampleN.TOST.Rd | 20 +-
37 files changed, 235 insertions(+), 259 deletions(-)
Title: Power and Sample-size Distribution of 2-stage Bioequivalence
Studies
Diff between Power2Stage versions 0.2-2 dated 2014-12-08 and 0.3-1 dated 2015-01-23
Description: - Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use PE and mse from stage 1 also for the
power monitoring steps.
- The third function power.2stage.fC() calculates power and sample
size distribution of 2-stage BE studies with a futility criterion
for the point estimator or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
All the functions use simulations to obtain their results.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes
DESCRIPTION | 8 -
MD5 | 35 ++++---
NAMESPACE | 1
NEWS | 13 ++
R/power.R | 87 +++++++++---------
R/power_2stage.R | 60 ++++++------
R/power_2stage_GS.R | 1
R/power_2stage_KM.R | 52 ++++++----
R/power_2stage_SSR.R | 44 ++++-----
R/power_2stage_fC.R | 62 +++++++------
R/power_2stage_parallel.R | 204 ++++++++++++++++++++++++++++---------------
R/power_2stage_parallel_AF.R |only
R/sampsiz.R | 140 +++--------------------------
R/sampsiz2.R |only
R/sampsiz_n0.R |only
man/power.2stage.KM.Rd | 6 -
man/power.2stage.Rd | 11 --
man/power.2stage.fC.Rd | 13 --
man/power.2stage.p.Rd | 55 +++++++----
man/power.2stage.ssr.Rd | 10 +-
20 files changed, 398 insertions(+), 404 deletions(-)
Title: Vectorized Bivariate Normal CDF
Diff between pbivnorm versions 0.5-1 dated 2012-10-31 and 0.6.0 dated 2015-01-23
Description: Provides a vectorized R function for calculating
probabilities from a standard bivariate normal CDF.
Author: Fortran code by Alan Genz. R code by Brenton Kenkel,
based on Adelchi Azzalini's 'mnormt' package.
Maintainer: Brenton Kenkel
DESCRIPTION | 17 ++++++------
MD5 | 9 +++---
NEWS | 8 +++++
R/pbivnorm.r | 32 +++++++++++++----------
README.md |only
man/pbivnorm.Rd | 77 ++++++++++++++++++++++++++++++++++----------------------
6 files changed, 88 insertions(+), 55 deletions(-)
Title: Fitting user specified models with Group Lasso penalty
Diff between grplasso versions 0.4-4 dated 2014-08-18 and 0.4-5 dated 2015-01-23
Description: Fits user specified (GLM-) models with Group Lasso penalty
Author: Lukas Meier
Maintainer: Lukas Meier
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/methods.R | 22 ++++++++++++++++++----
tests/test_grplasso.R | 7 ++++++-
4 files changed, 31 insertions(+), 12 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Diff between geostatsp versions 1.1.8 dated 2015-01-05 and 1.1.9 dated 2015-01-23
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 15 +-
MD5 | 93 +++++++-------
R/0gm.R | 122 +++---------------
R/RFsimulate.R | 273 ++++++++++++++++++++++++-----------------
R/glgm.R | 135 +++++++++++---------
R/informationLgm.R | 14 +-
R/krige.R | 22 +--
R/lgm.R | 147 +++++++++++++---------
R/lgm.Raster.R | 20 +--
R/loglikGmrf.R | 94 ++++++--------
R/loglikLgm.R | 205 +++++++++++++++++--------------
R/matern.R | 221 ++++++++++++++++++---------------
R/maternCholSolve.R |only
R/maternGmrfPrec.R | 31 ----
R/spatialRoc.R | 34 ++---
data/gambiaUTM.RData |binary
data/loaloa.RData |binary
data/murder.RData |binary
data/nn32.RData |binary
data/rongelapUTM.RData |binary
data/swissRain.RData |binary
data/swissRainR.RData |binary
data/torontoPop.RData |binary
data/wheat.RData |binary
inst |only
man/RFsimulate.Rd | 43 +-----
man/glgm.Rd | 38 ++---
man/krige.Rd | 15 +-
man/lgm.Rd | 38 ++---
man/likfitLgm.Rd | 35 +++--
man/matern.Rd | 95 +++++++++-----
man/maternGmrfPrec.Rd | 9 -
man/simLgcp.Rd | 4
man/swissRain.Rd | 15 +-
src/Makevars | 2
src/geostatsp.h |only
src/matern.c | 323 +++++++++++++++++++++++++++++++++----------------
src/maternLogL.c |only
src/maternLogLgr.c |only
tests/RFsimulate.R | 56 ++++----
tests/glgm.R | 8 -
tests/krige.R | 35 -----
tests/lgcp.R | 4
tests/lgm.R | 67 +++-------
tests/lgmRaster.R | 18 +-
tests/likfitLgm.R | 64 ++-------
tests/matern.R | 10 -
tests/maternGmrfPrec.R | 6
tests/profLlgm.R | 31 ++--
tests/simLgcp.R | 34 ++---
50 files changed, 1246 insertions(+), 1130 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.14 dated 2014-12-19 and 2.15 dated 2015-01-23
Description: This package provides a general framework to perform Bayesian structure learning in undirected graphical models. The package provides recent improvements in the Bayesian literature. The package consists of two main MCMC sampling algorithm efficiently implemented in C++ to maximize computational speed. The main target of the package is high-dimensional data analysis wherein either continuous or discrete variables and usually number of variables are less than number of observations. Acknowledgements: The help of the CRAN team to integrate C++ code with R is gratefully acknowledged.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
DESCRIPTION | 10 ++----
MD5 | 62 +++++++++++++++++++++---------------------
R/bdgraph.R | 12 ++++----
R/bdgraph.sim.R | 6 ++--
R/plotcoda.R | 12 ++++----
R/plotroc.R | 8 ++---
R/rgwish.R | 11 ++++++-
R/rwish.R | 2 -
R/select.R | 6 ++--
R/traceplot.R | 29 ++++++++++---------
man/BDgraph-package.Rd | 56 +++++++++++++++-----------------------
man/CellSignal.Rd | 2 -
man/I.g.Rd | 37 +++++++++++--------------
man/bdgraph.Rd | 52 ++++++++++++++++++-----------------
man/bdgraph.npn.Rd | 58 +++++++++++++++++----------------------
man/bdgraph.sim.Rd | 72 ++++++++++++++++++++++++++-----------------------
man/compare.Rd | 51 +++++++++++++++++-----------------
man/geneExpression.Rd | 4 +-
man/phat.Rd | 32 ++++++++++++---------
man/plot.bdgraph.Rd | 27 ++++++++++--------
man/plot.simulate.Rd | 22 ++++++++------
man/plotcoda.Rd | 18 ++++++++----
man/plotroc.Rd | 31 +++++++++++++--------
man/print.bdgraph.Rd | 26 +++++++++++------
man/print.simulate.Rd | 31 ++++++++++-----------
man/prob.Rd | 26 ++++++++++-------
man/rgwish.Rd | 27 ++++++++++--------
man/rwish.Rd | 19 ++++++++----
man/select.Rd | 24 ++++++++++------
man/summary.bdgraph.Rd | 27 +++++++++++++-----
man/surveyData.Rd | 22 +++++++++-----
man/traceplot.Rd | 22 ++++++++++----
32 files changed, 461 insertions(+), 383 deletions(-)
Title: Rmetrics - Financial Time Series Objects
Diff between timeSeries versions 3011.98 dated 2014-10-28 and 3012.99 dated 2015-01-23
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Managing financial time series objects.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz
DESCRIPTION | 9
MD5 | 16
R/methods-plot.R | 850 ++++++++++++++--------------
R/methods-plot2.R | 1186 +++++++++++++++++++---------------------
R/statistics-orderColnames.R | 5
build/vignette.rds |binary
inst/doc/timeSeriesPlot.pdf |binary
inst/unitTests/Makefile | 3
man/statistics-orderColnames.Rd | 260 ++++----
9 files changed, 1163 insertions(+), 1166 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Diff between timeDate versions 3011.99 dated 2014-10-27 and 3012.100 dated 2015-01-23
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Managing chronological and calendar objects.
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb],
Martin Maechler [ctb],
Joe W. Byers [ctb]
Maintainer: Tobias Setz
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
R/timeDate.R | 1 +
3 files changed, 8 insertions(+), 6 deletions(-)
Title: Graphical Integrated Text Mining Solution
Diff between RcmdrPlugin.temis versions 0.7.2 dated 2014-09-06 and 0.7.3 dated 2015-01-23
More information about RcmdrPlugin.temis at CRAN
Description: An R Commander plug-in providing an integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, vocabulary tables, terms
co-occurrences and documents similarity measures, time series analysis,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files, Twitter queries,
as well as from Dow Jones Factiva, LexisNexis, Europresse and Alceste files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NAMESPACE | 1 +
NEWS | 4 ++++
R/corpusCa.R | 2 +-
R/importCorpus.R | 18 ++++++++----------
R/output.R | 12 ++++++++++--
R/tablelist.R | 2 +-
man/importCorpusDlg.rd | 2 +-
9 files changed, 38 insertions(+), 27 deletions(-)
Permanent link
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Diff between evmix versions 2.3 dated 2014-09-07 and 2.4 dated 2015-01-23
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the evd package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott
DESCRIPTION | 10
MD5 | 296 +++++++++++++------------
NAMESPACE | 27 ++
R/checking.r | 577 +++++++++++++++++++++++++++++++++-----------------
R/dbckden.r | 105 ++-------
R/dbckdengpd.r | 165 +++++---------
R/dbckdengpdcon.r | 174 +++++----------
R/dbetagpd.r | 74 +++---
R/dbetagpdcon.r | 75 +++---
R/ddwm.r | 78 +++---
R/dgammagpd.r | 65 ++---
R/dgammagpdcon.r | 66 +++--
R/dgkg.r | 128 +++--------
R/dgkgcon.r | 112 +++------
R/dgng.r | 94 +++-----
R/dgngcon.r | 91 +++----
R/dgpd.r | 64 ++---
R/dhpd.r | 58 ++---
R/dhpdcon.r | 60 ++---
R/ditmgng.r | 113 ++++-----
R/ditmnormgpd.r | 78 +++---
R/ditmweibullgpd.r | 78 +++---
R/dkden.r | 55 +---
R/dkdengpd.r | 85 ++-----
R/dkdengpdcon.r | 83 ++-----
R/dlognormgpd.r | 65 ++---
R/dlognormgpdcon.r | 66 +++--
R/dmgamma.r | 105 ++++-----
R/dmgammagpd.r | 146 +++++-------
R/dmgammagpdcon.r | 142 +++++-------
R/dnormgpd.r | 65 ++---
R/dnormgpdcon.r | 65 +++--
R/dpsden.r |only
R/dpsdengpd.r |only
R/dweibullgpd.r | 65 ++---
R/dweibullgpdcon.r | 67 +++--
R/evmix-package.r | 3
R/evmixdiag.r | 137 +++--------
R/fbckden.r | 62 ++---
R/fbckdengpd.r | 176 ++++++++-------
R/fbckdengpdcon.r | 171 ++++++++------
R/fbetagpd.r | 144 +++++++-----
R/fbetagpdcon.r | 140 +++++++-----
R/fdwm.r | 77 +++---
R/fgammagpd.r | 116 +++++-----
R/fgammagpdcon.r | 113 +++++----
R/fgkg.r | 121 ++++++----
R/fgkgcon.r | 117 ++++++----
R/fgng.r | 130 +++++++----
R/fgngcon.r | 122 +++++++---
R/fgpd.r | 109 +++++----
R/fhpd.r | 75 +++---
R/fhpdcon.r | 79 ++++--
R/fitmgng.r | 119 +++++-----
R/fitmnormgpd.r | 135 ++++++-----
R/fitmweibullgpd.r | 134 +++++++----
R/fkden.r | 48 ++--
R/fkdengpd.r | 120 ++++++----
R/fkdengpdcon.r | 123 ++++++----
R/flognormgpd.r | 116 +++++-----
R/flognormgpdcon.r | 113 +++++----
R/fmgamma.r | 61 +++--
R/fmgammagpd.r | 98 ++++----
R/fmgammagpdcon.r | 113 +++++----
R/fnormgpd.r | 136 ++++++-----
R/fnormgpdcon.r | 121 ++++++----
R/fpsden.r |only
R/fpsdengpd.r |only
R/fweibullgpd.r | 116 +++++-----
R/fweibullgpdcon.r | 113 +++++----
R/hillplot.r | 61 ++---
R/kernels.r | 22 +
R/kfun.r | 18 -
R/mrlplot.r | 51 +---
R/pickandsplot.r | 35 +--
R/tcplot.r | 114 ++++-----
R/undocumented.r | 36 ++-
inst/CITATION | 2
inst/doc/Rd2.pdf |binary
man/bckden.Rd | 36 +--
man/bckdengpd.Rd | 33 +-
man/bckdengpdcon.Rd | 17 +
man/betagpd.Rd | 15 -
man/betagpdcon.Rd | 7
man/checking.Rd | 81 ++++---
man/dwm.Rd | 17 -
man/evmix-package.Rd | 3
man/evmix.diag.Rd | 14 -
man/fbckden.Rd | 45 ++-
man/fbckdengpd.Rd | 94 ++++----
man/fbckdengpdcon.Rd | 62 ++---
man/fbetagpd.Rd | 69 +++--
man/fbetagpdcon.Rd | 54 ++--
man/fdwm.Rd | 63 +++--
man/fgammagpd.Rd | 60 ++---
man/fgammagpdcon.Rd | 46 ++-
man/fgkg.Rd | 75 +++---
man/fgkgcon.Rd | 27 +-
man/fgng.Rd | 67 +++--
man/fgngcon.Rd | 27 +-
man/fgpd.Rd | 68 +++--
man/fhpd.Rd | 60 ++---
man/fhpdcon.Rd | 33 +-
man/fitmgng.Rd | 70 +++---
man/fitmnormgpd.Rd | 80 +++---
man/fitmweibullgpd.Rd | 62 +++--
man/fkden.Rd | 32 +-
man/fkdengpd.Rd | 78 +++---
man/fkdengpdcon.Rd | 56 ++--
man/flognormgpd.Rd | 60 ++---
man/flognormgpdcon.Rd | 46 ++-
man/fmgamma.Rd | 30 +-
man/fmgammagpd.Rd | 36 +--
man/fmgammagpdcon.Rd | 36 +--
man/fnormgpd.Rd | 79 +++---
man/fnormgpdcon.Rd | 46 ++-
man/fpsden.Rd |only
man/fpsdengpd.Rd |only
man/fweibullgpd.Rd | 54 ++--
man/fweibullgpdcon.Rd | 46 ++-
man/gammagpd.Rd | 15 -
man/gammagpdcon.Rd | 7
man/gkg.Rd | 28 +-
man/gkgcon.Rd | 16 -
man/gng.Rd | 19 -
man/gngcon.Rd | 7
man/gpd.Rd | 26 +-
man/hillplot.Rd | 11
man/hpd.Rd | 9
man/hpdcon.Rd | 9
man/internal.Rd | 19 +
man/itmgng.Rd | 22 +
man/itmnormgpd.Rd | 11
man/itmweibullgpd.Rd | 15 -
man/kden.Rd | 34 +-
man/kdengpd.Rd | 32 +-
man/kdengpdcon.Rd | 16 -
man/kernels.Rd | 9
man/kfun.Rd | 11
man/lognormgpd.Rd | 15 -
man/lognormgpdcon.Rd | 7
man/mgamma.Rd | 17 +
man/mgammagpd.Rd | 13 -
man/mgammagpdcon.Rd | 9
man/mrlplot.Rd | 17 -
man/normgpd.Rd | 15 -
man/normgpdcon.Rd | 7
man/pickandsplot.Rd | 5
man/psden.Rd |only
man/psdengpd.Rd |only
man/tcplot.Rd | 30 +-
man/weibullgpd.Rd | 11
man/weibullgpdcon.Rd | 15 -
153 files changed, 5415 insertions(+), 4440 deletions(-)
Title: Descriptive analysis by groups
Diff between compareGroups versions 2.0.5 dated 2014-08-28 and 3.0 dated 2015-01-23
Description: This package is designed to read, interpret, summarise, display and
analyse epidemiological data. Can be used to create data summaries for
quality control, extensive reports for exploring data, including
publication-ready univariate or bivariate tables in plain text HTML and
LaTeX, and a figures to quickly visualise the distribution of your data.
Depending on the nature of the variable, various statistics are
calculated (mean, median, frequencies, incidences) and appropriate
tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher,
log-rank, ...). The latest version includes functionality for summarising
genetic data, and for performing low-level quality control of your database
(see radiograph()) to help identify data-entry errors. This version has
also been implemented in a web-interface to make this package accessible
to non-R-users.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel
and David Giménez
Maintainer: Isaac Subirana
compareGroups-2.0.5/compareGroups/data/SNPs.rda |only
compareGroups-2.0.5/compareGroups/man/SNPs.Rd |only
compareGroups-3.0/compareGroups/DESCRIPTION | 14
compareGroups-3.0/compareGroups/MD5 | 106
compareGroups-3.0/compareGroups/NAMESPACE | 5
compareGroups-3.0/compareGroups/R/cGroupsGUI.R | 179
compareGroups-3.0/compareGroups/R/cGroupsWUI.R |only
compareGroups-3.0/compareGroups/R/compare.i.R | 2
compareGroups-3.0/compareGroups/R/createTable.R | 2
compareGroups-3.0/compareGroups/R/export2csv.R | 15
compareGroups-3.0/compareGroups/R/export2html.R | 38
compareGroups-3.0/compareGroups/R/export2latex.cbind.createTable.R | 26
compareGroups-3.0/compareGroups/R/export2latex.createTable.R | 24
compareGroups-3.0/compareGroups/R/export2pdf.R | 9
compareGroups-3.0/compareGroups/R/getResults.R |only
compareGroups-3.0/compareGroups/R/prepare.r | 40
compareGroups-3.0/compareGroups/R/print.cbind.createTable.R | 29
compareGroups-3.0/compareGroups/R/print.createTable.R | 16
compareGroups-3.0/compareGroups/R/printTable.R | 2
compareGroups-3.0/compareGroups/R/report.R | 7
compareGroups-3.0/compareGroups/R/table.i.R | 4
compareGroups-3.0/compareGroups/build/vignette.rds |binary
compareGroups-3.0/compareGroups/inst/app |only
compareGroups-3.0/compareGroups/inst/doc/changelog | 18
compareGroups-3.0/compareGroups/inst/doc/compareGroupsWUI_vignette.pdf |only
compareGroups-3.0/compareGroups/inst/doc/compareGroups_vignette.R | 219
compareGroups-3.0/compareGroups/inst/doc/compareGroups_vignette.pdf | 5363 +++++-----
compareGroups-3.0/compareGroups/inst/doc/compareGroups_vignette.rnw | 90
compareGroups-3.0/compareGroups/man/cGroupsGUI.Rd | 2
compareGroups-3.0/compareGroups/man/cGroupsWUI.Rd |only
compareGroups-3.0/compareGroups/man/compareGroups-internal.Rd | 3
compareGroups-3.0/compareGroups/man/compareGroups-package.Rd | 16
compareGroups-3.0/compareGroups/man/createTable.Rd | 11
compareGroups-3.0/compareGroups/man/export2csv.Rd | 8
compareGroups-3.0/compareGroups/man/export2html.Rd | 8
compareGroups-3.0/compareGroups/man/export2latex.Rd | 14
compareGroups-3.0/compareGroups/man/export2pdf.Rd | 130
compareGroups-3.0/compareGroups/man/getResults.Rd |only
compareGroups-3.0/compareGroups/man/missingTable.rd | 22
compareGroups-3.0/compareGroups/man/report.Rd | 8
compareGroups-3.0/compareGroups/vignettes/compareGroupsWUI_vignette.pdf |only
compareGroups-3.0/compareGroups/vignettes/compareGroupsWUI_vignette.tex |only
compareGroups-3.0/compareGroups/vignettes/compareGroups_vignette.bib | 36
compareGroups-3.0/compareGroups/vignettes/compareGroups_vignette.rnw | 90
compareGroups-3.0/compareGroups/vignettes/figures/WUI |only
compareGroups-3.0/compareGroups/vignettes/figures/bivar/age.pdf |binary
compareGroups-3.0/compareGroups/vignettes/figures/bivar/sex.pdf |binary
compareGroups-3.0/compareGroups/vignettes/figures/bivar/tmain.pdf |binary
compareGroups-3.0/compareGroups/vignettes/figures/univar/age.pdf |binary
compareGroups-3.0/compareGroups/vignettes/figures/univar/sex.pdf |binary
compareGroups-3.0/compareGroups/vignettes/figures/univar/tmain.pdf |binary
51 files changed, 3394 insertions(+), 3162 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Diff between bnlearn versions 3.7 dated 2015-01-13 and 3.7.1 dated 2015-01-23
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari
Changelog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
man/bnlearn-package.Rd | 4 ++--
src/graph.generation.c | 2 +-
src/loss.c | 2 +-
6 files changed, 17 insertions(+), 13 deletions(-)
Title: Coclustering package for binary, contingency, continuous and
categorical data-sets
Diff between blockcluster versions 3.0.1 dated 2014-01-16 and 3.0.2 dated 2015-01-23
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The blockcluster package provides a bridge between the C++
core library and the R statistical computing environment. This package
allows to co-cluster binary, contingency, continuous and categorical
data-sets. It also provides utility functions to visualize the results.
This package may be useful for various applications in fields of Data
mining,Information retrieval, Biology, computer vision and many more. More
information about the project and comprehensive tutorial can be found on
the link mentioned in URL.
Author: Parmeet Singh Bhatia
Maintainer: Vincent KUBICKI
DESCRIPTION | 16 +++++++---------
MD5 | 29 +++++++++++++++--------------
build/vignette.rds |binary
data/binarydata.rda |binary
data/categoricaldata.rda |binary
data/contingencydatalist.rda |binary
data/contingencydataunknown.rda |binary
data/gaussiandata.rda |binary
src/Makevars | 1 -
src/Makevars.win | 1 -
src/coclust/makefile | 1 +
src/coclust/src/Models/BinaryLBModel.cpp | 2 ++
src/coclust/src/Strategy/XStrategyAlgo.cpp | 23 +++++++++++++++++++++++
src/coclust/src/Strategy/XStrategyAlgo.h | 2 ++
src/test |only
vignettes/blockcluster_tutorial_V3.0.Rnw | 3 ++-
16 files changed, 52 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-02 1.1-0
2009-03-25 1.0-6
2009-01-07 1.0-5
2008-03-21 1.0
Title: Logic Regression
Diff between LogicReg versions 1.5.5 dated 2013-12-03 and 1.5.6 dated 2015-01-23
Description: Routines for Logic Regression
Author: Charles Kooperberg
Maintainer: Charles Kooperberg
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
src/slogic.f | 3 ++-
3 files changed, 10 insertions(+), 9 deletions(-)
Title: Tools for Modeling Rate-Dependent Hysteretic Processes and
Ellipses
Diff between hysteresis versions 2.0 dated 2013-11-19 and 2.5 dated 2015-01-23
Description: Fit, summarize and plot sinusoidal hysteretic processes using:
two-step simple harmonic least squares, ellipse-specific non-linear least
squares, the direct method, geometric least squares or linear least squares.
Author: Spencer Maynes, Fan Yang, and Anne Parkhurst
Maintainer: Anne Parkhurst
hysteresis-2.0/hysteresis/R/coef.splitloop.R |only
hysteresis-2.0/hysteresis/R/fitted.splitloop.R |only
hysteresis-2.0/hysteresis/R/floopSplit.R |only
hysteresis-2.0/hysteresis/R/plot.splitloop.R |only
hysteresis-2.0/hysteresis/R/print.splitloop.R |only
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hysteresis-2.5/hysteresis/DESCRIPTION | 10
hysteresis-2.5/hysteresis/MD5 | 174 ++-
hysteresis-2.5/hysteresis/NAMESPACE | 33
hysteresis-2.5/hysteresis/NEWS | 7
hysteresis-2.5/hysteresis/R/coef.fittedlooplist2r.R |only
hysteresis-2.5/hysteresis/R/coef.loop2r.R |only
hysteresis-2.5/hysteresis/R/coef.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/coef.loopsummarylist2r.R |only
hysteresis-2.5/hysteresis/R/delta.error.R | 13
hysteresis-2.5/hysteresis/R/delta.error.loop.R | 20
hysteresis-2.5/hysteresis/R/delta.error.loop2r.R |only
hysteresis-2.5/hysteresis/R/derived.2.r | 3
hysteresis-2.5/hysteresis/R/directsummary.R | 2
hysteresis-2.5/hysteresis/R/ellipsespot.R | 2
hysteresis-2.5/hysteresis/R/fel.R | 4
hysteresis-2.5/hysteresis/R/fel.geometric.R | 2
hysteresis-2.5/hysteresis/R/felReflect.R |only
hysteresis-2.5/hysteresis/R/fitted.fittedlooplist2r.R |only
hysteresis-2.5/hysteresis/R/fitted.loop2r.R |only
hysteresis-2.5/hysteresis/R/fitted.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/fitted.loopsummarylist.R | 14
hysteresis-2.5/hysteresis/R/floop.R | 74 +
hysteresis-2.5/hysteresis/R/floop.repeated.R | 2
hysteresis-2.5/hysteresis/R/floop2r.R |only
hysteresis-2.5/hysteresis/R/floop2r.repeated.R |only
hysteresis-2.5/hysteresis/R/floopCauchyLoss.R |only
hysteresis-2.5/hysteresis/R/floopCauchyLoss2r.R |only
hysteresis-2.5/hysteresis/R/floopReflect.R |only
hysteresis-2.5/hysteresis/R/geometric_distance.R | 20
hysteresis-2.5/hysteresis/R/geometricboot.R | 2
hysteresis-2.5/hysteresis/R/geometricsummary.R | 4
hysteresis-2.5/hysteresis/R/harmonic2summary.R | 16
hysteresis-2.5/hysteresis/R/harmonic2summaryEBS.r |only
hysteresis-2.5/hysteresis/R/lmsummary.R | 2
hysteresis-2.5/hysteresis/R/loopbootgeom.R |only
hysteresis-2.5/hysteresis/R/mel.r | 3
hysteresis-2.5/hysteresis/R/mloop.r | 3
hysteresis-2.5/hysteresis/R/mloop2r.R |only
hysteresis-2.5/hysteresis/R/nlssummary.R | 2
hysteresis-2.5/hysteresis/R/plot.ellipsefit.R | 31
hysteresis-2.5/hysteresis/R/plot.ellipsefitlist.R | 2
hysteresis-2.5/hysteresis/R/plot.ellipsesummary.R | 36
hysteresis-2.5/hysteresis/R/plot.fittedloop.R | 34
hysteresis-2.5/hysteresis/R/plot.fittedlooplist.R | 11
hysteresis-2.5/hysteresis/R/plot.loop2r.R |only
hysteresis-2.5/hysteresis/R/plot.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/plot.loopsummary.R | 41
hysteresis-2.5/hysteresis/R/plot.loopsummarylist.R | 11
hysteresis-2.5/hysteresis/R/print.fittedlooplist.R | 10
hysteresis-2.5/hysteresis/R/print.loop2r.R |only
hysteresis-2.5/hysteresis/R/print.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/print.loopsummary.R | 2
hysteresis-2.5/hysteresis/R/print.loopsummarylist.R | 31
hysteresis-2.5/hysteresis/R/residuals.fittedlooplist.R | 16
hysteresis-2.5/hysteresis/R/residuals.loop2r.R |only
hysteresis-2.5/hysteresis/R/residuals.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/residuals.loopsummarylist.R | 16
hysteresis-2.5/hysteresis/R/rstudent.fittedlooplist.R | 14
hysteresis-2.5/hysteresis/R/rstudent.loop2r.R |only
hysteresis-2.5/hysteresis/R/rstudent.loop2rsummary.R |only
hysteresis-2.5/hysteresis/R/rstudent.loopsummarylist.R | 15
hysteresis-2.5/hysteresis/R/splitloopboot.R |only
hysteresis-2.5/hysteresis/R/splitloopbootgeom.R |only
hysteresis-2.5/hysteresis/R/summary.ellipsefitlist.R | 4
hysteresis-2.5/hysteresis/R/summary.fittedloop.R | 17
hysteresis-2.5/hysteresis/R/summary.fittedlooplist2r.R |only
hysteresis-2.5/hysteresis/R/summary.loop2r.R |only
hysteresis-2.5/hysteresis/README.md |only
hysteresis-2.5/hysteresis/inst/doc/index.Rmd | 16
hysteresis-2.5/hysteresis/inst/doc/index.html | 548 +++++-----
hysteresis-2.5/hysteresis/man/EllipseData.Rd | 8
hysteresis-2.5/hysteresis/man/fel.Rd | 11
hysteresis-2.5/hysteresis/man/fel.repeated.Rd | 4
hysteresis-2.5/hysteresis/man/floop.Rd | 59 -
hysteresis-2.5/hysteresis/man/floop.repeated.Rd | 5
hysteresis-2.5/hysteresis/man/floopReflect.Rd |only
hysteresis-2.5/hysteresis/man/hysteresis-package.Rd | 7
hysteresis-2.5/hysteresis/man/loop.parameters.Rd | 8
hysteresis-2.5/hysteresis/man/mel.rd | 5
hysteresis-2.5/hysteresis/man/mloop.Rd | 18
hysteresis-2.5/hysteresis/man/plot.fittedloop.Rd |only
hysteresis-2.5/hysteresis/man/residuals.fittedloop.Rd |only
hysteresis-2.5/hysteresis/man/summary.fittedloop.Rd |only
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hysteresis-2.5/hysteresis/vignettes/index.Rmd | 16
121 files changed, 906 insertions(+), 502 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Diff between mirtCAT versions 0.3 dated 2014-12-15 and 0.4 dated 2015-01-22
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers
DESCRIPTION | 18 -
MD5 | 68 +++--
NAMESPACE | 6
NEWS | 41 +++
R/DesignClass.R | 352 +++++++++++++++++-------------
R/PersonClass.R | 36 +--
R/ShinyGUIClass.R | 46 ++-
R/TestClass.R | 143 ++++++------
R/findNextCATItem.R | 183 +++++++--------
R/generate.mirt_object.R |only
R/generate_pattern.R | 81 ++++--
R/mirtCAT-package.R | 3
R/mirtCAT.R | 419 ++++++++++++++++++++++--------------
R/run_pattern.R | 68 +++--
R/selection_criteria.R | 189 +++++-----------
R/server.R | 54 +++-
R/ui.R | 17 -
R/updateDesign.R | 3
R/util.R | 82 +++++--
R/zzz-methods.R | 32 +-
README.md | 5
inst/doc/mirtCAT-vignettes.Rmd | 2
inst/doc/mirtCAT-vignettes.html | 2
man/findNextItem.Rd | 9
man/generate.mirt_object.Rd |only
man/generate_pattern.Rd | 37 +--
man/mirtCAT-package.Rd | 3
man/mirtCAT.Rd | 265 ++++++++++++++--------
man/updateDesign.Rd | 6
src |only
tests/tests/test-mirtCAT_classify.R |only
tests/tests/test-mirtCAT_multi.R | 83 +------
tests/tests/test-mirtCAT_ordered.R | 80 ++++--
tests/tests/test-mirtCAT_uni.R | 117 +++++-----
vignettes/mirtCAT-vignettes.Rmd | 2
35 files changed, 1392 insertions(+), 1060 deletions(-)
Title: Multidimensional Item Response Theory
Diff between mirt versions 1.7 dated 2014-12-15 and 1.8 dated 2015-01-22
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers
DESCRIPTION | 9 +-
MD5 | 88 +++++++++++++-------------
NEWS | 29 ++++++++
R/03-estimation.R | 10 +-
R/DIF.R | 25 ++++---
R/DTF.R | 16 ++--
R/EMstep.utils.R | 6 +
R/MultipleGroup-methods.R | 10 --
R/PrepData.R | 2
R/SingleGroup-methods.R | 57 ++++++++++------
R/boot.mirt.R | 11 +--
R/extract.group.R | 4 -
R/fscores.R | 33 ++++++++-
R/fscores.internal.R | 132 +++++++++++++++++++++++----------------
R/imputeMissing.R | 20 +++++
R/itemfit.R | 2
R/iteminfo.R | 8 +-
R/itemplot.internal.R | 7 +-
R/mirt.R | 37 +++++-----
R/mirt.model.R | 19 ++++-
R/model.elements.R | 10 ++
R/multipleGroup.R | 10 +-
R/randef.R | 2
R/shinyItemplot.R | 3
R/utils.R | 29 ++++++--
README.md | 19 +----
inst/doc/mirt-vignettes.Rmd | 2
inst/doc/mirt-vignettes.html | 2
man/DIF.Rd | 9 +-
man/DTF.Rd | 17 +++--
man/extract.group.Rd | 2
man/fscores.Rd | 28 +++++++-
man/imputeMissing.Rd | 12 ++-
man/iteminfo.Rd | 5 +
man/mirt.Rd | 37 +++++-----
man/mirt.model.Rd | 15 +++-
man/multipleGroup.Rd | 9 +-
man/plot-method.Rd | 12 +--
src/Estep.cpp | 24 +++----
src/traceLinePts.cpp | 8 +-
tests/tests/test-01-mirtOne.R | 1
tests/tests/test-02-mirtTwo.R | 3
tests/tests/test-09-mirt.model.R | 22 ++++--
tests/tests/test-10-extras.R | 6 +
vignettes/mirt-vignettes.Rmd | 2
45 files changed, 515 insertions(+), 299 deletions(-)
Title: Methods that Apply to Rows and Columns of a Matrix
Diff between matrixStats versions 0.13.0 dated 2015-01-21 and 0.13.1 dated 2015-01-22
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 -
MD5 | 20 ++--
NEWS | 8 +
inst/doc/matrixStats-methods.html | 4
inst/doc/matrixStats-methods.md.rsp | 2
man/matrixStats-package.Rd | 2
src/diff2_TYPE-template.h | 6 +
src/rowDiffs_TYPE-template.h | 3
src/weightedMedian_TYPE-template.h | 2
tests/rowAvgsPerColSet.R | 168 +++++++++++++++++------------------
vignettes/matrixStats-methods.md.rsp | 2
11 files changed, 119 insertions(+), 106 deletions(-)
More information about shinybootstrap2 at CRAN
Permanent link
Title: Local Time Space Kriging
Diff between ltsk versions 1.0.1 dated 2014-02-06 and 1.0.2 dated 2015-01-22
Description: Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively.
Author: Naresh Kumar, Dong Liang, Jin Chen, Jun Chen
Maintainer: Dong Liang
DESCRIPTION | 16 ++---
MD5 | 92 +++++++++++++++++++++++---------
NAMESPACE | 3 +
R/cal.gamma.R | 2
R/check_input.R | 81 ++++++++++++++++------------
R/cltsk.R |only
R/dnb.R | 50 +++++++++--------
R/dsmooth.variogram.R | 66 +++++++++++------------
R/firstpeak.R | 41 +++++++++-----
R/lk.R | 76 ++++++++++++--------------
R/ltsk.R | 107 ++++++++++++++++++++------------------
R/ltsk.cv.R |only
R/partUtils.R |only
R/tsk.R |only
R/work.kriging.vec.R |only
R/working.cltsk.R |only
R/working.cltsk.par.R |only
R/working.fitvariog1.R | 28 +++++----
R/working.lk.par.R |only
R/working.ltsk.R | 87 ++++++++++++++----------------
R/working.ltsk.par.R | 52 ++----------------
R/working.tsk.R |only
man/cltsk.Rd |only
man/dnb.Rd | 36 ++++++------
man/lk.Rd | 52 ++++++++++--------
man/ltsk-internal.Rd | 8 ++
man/ltsk-package.Rd | 26 ++++++---
man/ltsk.Rd | 71 +++++++++++++------------
man/ltsk.cv.Rd |only
man/tsk.Rd |only
src/ANN.cpp | 6 +-
src/ConfigFile.cpp |only
src/ConfigFile.h |only
src/Makevars | 2
src/cmp_kriging.cpp | 62 ++++++++++++----------
src/include/ANN.cpp |only
src/include/Make-config |only
src/include/Makefile |only
src/include/bd_fix_rad_search.cpp |only
src/include/bd_pr_search.cpp |only
src/include/bd_search.cpp |only
src/include/bd_tree.cpp |only
src/include/bd_tree.h |only
src/include/brute.cpp |only
src/include/kd_dump.cpp |only
src/include/kd_fix_rad_search.cpp |only
src/include/kd_fix_rad_search.h |only
src/include/kd_pr_search.cpp |only
src/include/kd_pr_search.h |only
src/include/kd_search.cpp |only
src/include/kd_search.h |only
src/include/kd_split.cpp |only
src/include/kd_split.h |only
src/include/kd_tree.cpp |only
src/include/kd_tree.h |only
src/include/kd_util.cpp |only
src/include/kd_util.h |only
src/include/perf.cpp |only
src/include/pr_queue.h |only
src/include/pr_queue_k.h |only
src/io.cpp | 2
src/kd_dump.cpp | 2
src/kd_fix_rad_search.cpp | 10 +--
src/kd_pr_search.cpp | 12 ++--
src/kd_search.cpp | 12 ++--
src/kd_util.cpp | 10 +--
src/range_tree.h |only
67 files changed, 542 insertions(+), 470 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: Diagnostics plots for Bicluster Data
Diff between BcDiag versions 1.0.7 dated 2014-12-03 and 1.0.8 dated 2015-01-22
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/anomedOnlybic.R | 14 +++++++++-----
R/profileBic.R | 8 +++++---
R/support.R | 30 +++++++++++++++++++++++++-----
5 files changed, 49 insertions(+), 23 deletions(-)
Title: A Wes Anderson Palette Generator
Diff between wesanderson versions 0.3 dated 2014-03-27 and 0.3.2 dated 2015-01-22
Description: Palettes generated mostly from Wes Anderson movies
Author: Karthik Ram [aut, cre],
Hadley Wickham [aut],
Clark Richards [ctb]
Maintainer: Karthik Ram
wesanderson-0.3.2/wesanderson/DESCRIPTION | 18 +-
wesanderson-0.3.2/wesanderson/MD5 | 22 +-
wesanderson-0.3.2/wesanderson/NAMESPACE | 7
wesanderson-0.3.2/wesanderson/NEWS | 6
wesanderson-0.3.2/wesanderson/R/colors.R | 143 +++++++++--------
wesanderson-0.3.2/wesanderson/R/wesanderson.R | 13 -
wesanderson-0.3.2/wesanderson/man/heatmap.Rd | 13 +
wesanderson-0.3.2/wesanderson/man/wes_palette.Rd |only
wesanderson-0.3.2/wesanderson/man/wes_palettes.Rd |only
wesanderson-0.3.2/wesanderson/man/wesanderson.Rd | 5
wesanderson-0.3/wesanderson/README.md |only
wesanderson-0.3/wesanderson/data/namelist.rda |only
wesanderson-0.3/wesanderson/man/display.wes.palette.Rd |only
wesanderson-0.3/wesanderson/man/namelist.Rd |only
wesanderson-0.3/wesanderson/man/wes.palette.Rd |only
wesanderson-0.3/wesanderson/tests |only
16 files changed, 124 insertions(+), 103 deletions(-)
Title: Time-ordered and time-aggregated network analyses
Diff between timeordered versions 0.9.7 dated 2014-10-22 and 0.9.8 dated 2015-01-22
Description: Methods for incorporating time into network analysis. Construction of time-ordered networks (temporal graphs). Shortest-time and shortest-path-length analyses. Resource spread calculations. Data resampling and rarefaction for null model construction. Reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks. Vector clock latencies. Plotting functionalities.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 8 ++++----
MD5 | 7 ++++++-
R/null_models.R |only
R/randomization_procedures.R |only
man/randomize_edges_helper.Rd |only
man/randomly_permuted_times.Rd |only
man/swap.Rd |only
7 files changed, 10 insertions(+), 5 deletions(-)
Title: R Interface to Species Occurrence Data Sources
Diff between spocc versions 0.2.2 dated 2014-10-24 and 0.2.4 dated 2015-01-22
Description: A programmatic interface to many species occurrence data sources,
including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine
eBird, AntWeb, and more as sources become easily available. This package
includes functionality for retrieving species occurrence data, combining
that data, and creating various kinds of static and interactive maps.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain
spocc-0.2.2/spocc/R/startup.r |only
spocc-0.2.2/spocc/man/occ2sp.Rd |only
spocc-0.2.2/spocc/man/spocc_create_gist.Rd |only
spocc-0.2.2/spocc/man/spocc_gbifxmlToDataFrame.Rd |only
spocc-0.2.2/spocc/man/spocc_get_credentials.Rd |only
spocc-0.2.2/spocc/man/spocc_gist.Rd |only
spocc-0.2.4/spocc/DESCRIPTION | 23 +-
spocc-0.2.4/spocc/LICENSE | 4
spocc-0.2.4/spocc/MD5 | 105 ++++-----
spocc-0.2.4/spocc/NAMESPACE | 14 -
spocc-0.2.4/spocc/NEWS | 17 +
spocc-0.2.4/spocc/R/clean_spocc.r | 78 +++----
spocc-0.2.4/spocc/R/fixnames.r | 10
spocc-0.2.4/spocc/R/handle_sp.R | 9
spocc-0.2.4/spocc/R/mapggplot.R | 6
spocc-0.2.4/spocc/R/mapgist.r | 47 +---
spocc-0.2.4/spocc/R/mapleaflet.r | 38 +--
spocc-0.2.4/spocc/R/methods.r | 12 -
spocc-0.2.4/spocc/R/occ.r | 154 ++++++-------
spocc-0.2.4/spocc/R/occ_names_options.R | 30 +-
spocc-0.2.4/spocc/R/occ_options.r | 26 +-
spocc-0.2.4/spocc/R/plugins.r | 13 -
spocc-0.2.4/spocc/R/rbindfill.R |only
spocc-0.2.4/spocc/R/util_github.r | 136 ++----------
spocc-0.2.4/spocc/R/wkt_vis.r | 37 +--
spocc-0.2.4/spocc/R/zzz.r | 137 ++----------
spocc-0.2.4/spocc/README.md | 245 +++++++++++-----------
spocc-0.2.4/spocc/build/vignette.rds |binary
spocc-0.2.4/spocc/man/basemaps.Rd | 3
spocc-0.2.4/spocc/man/bbox2wkt.Rd | 3
spocc-0.2.4/spocc/man/clean_spocc.Rd | 7
spocc-0.2.4/spocc/man/fixnames.Rd | 7
spocc-0.2.4/spocc/man/get_colors.Rd | 3
spocc-0.2.4/spocc/man/get_palette.Rd | 3
spocc-0.2.4/spocc/man/handle_sp.Rd | 6
spocc-0.2.4/spocc/man/mapggplot.Rd | 9
spocc-0.2.4/spocc/man/mapgist.Rd | 31 --
spocc-0.2.4/spocc/man/mapleaflet.Rd | 23 +-
spocc-0.2.4/spocc/man/occ.Rd | 31 +-
spocc-0.2.4/spocc/man/occ2df.Rd | 7
spocc-0.2.4/spocc/man/occ_coverage.Rd | 3
spocc-0.2.4/spocc/man/occ_names.Rd | 3
spocc-0.2.4/spocc/man/occ_names_options.Rd | 5
spocc-0.2.4/spocc/man/occ_options.Rd | 5
spocc-0.2.4/spocc/man/occ_to_sp.Rd | 3
spocc-0.2.4/spocc/man/palettes.Rd | 3
spocc-0.2.4/spocc/man/spocc-package.Rd | 3
spocc-0.2.4/spocc/man/spocc_blanktheme.Rd | 3
spocc-0.2.4/spocc/man/spocc_capwords.Rd | 3
spocc-0.2.4/spocc/man/spocc_colClasses.Rd | 3
spocc-0.2.4/spocc/man/spocc_duplicates.Rd | 3
spocc-0.2.4/spocc/man/spocc_objects.Rd | 5
spocc-0.2.4/spocc/man/spocc_rcharts_togeojson.Rd | 3
spocc-0.2.4/spocc/man/spocc_stylegeojson.Rd | 3
spocc-0.2.4/spocc/man/spocc_togeojson.Rd | 3
spocc-0.2.4/spocc/man/spocc_type_sum.Rd | 3
spocc-0.2.4/spocc/man/wkt_vis.Rd | 5
57 files changed, 606 insertions(+), 727 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Diff between spacetime versions 1.1-2 dated 2015-01-15 and 1.1-3 dated 2015-01-22
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut],
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma
DESCRIPTION | 8 +-
MD5 | 22 ++---
R/STFDF-methods.R | 7 -
R/STSDF-methods.R | 7 +
inst/doc/jss816.pdf | 30 +++----
inst/doc/stgvis.html | 196 +++++++++++++++++++++++++--------------------------
inst/doc/sto.pdf |binary
inst/doc/stpg.pdf |binary
inst/doc/stsubs.pdf |binary
man/STTDF-class.Rd | 18 ++--
tests/rw.R | 17 ++--
tests/rw.Rout.save | 21 ++---
12 files changed, 165 insertions(+), 161 deletions(-)
Title: Data Sets, etc. for the Text "Using R for Introductory
Statistics", Second Edition
Diff between UsingR versions 2.0-3 dated 2015-01-21 and 2.0-4 dated 2015-01-22
Description: A collection of data sets to accompany the
textbook "Using R for Introductory Statistics," second
edition.
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NEWS | 5 +++++
R/getAnswer.R | 9 +++++++--
4 files changed, 20 insertions(+), 10 deletions(-)
Title: Estimation in dual frame surveys
Diff between Frames2 versions 0.0.3 dated 2014-09-02 and 0.1.0 dated 2015-01-22
Description: Point and interval estimation in dual frame surveys. In contrast
to classic sampling theory, where only one sampling frame is considered,
dual frame methodology assumes that there are two frames available for
sampling and that, overall, they cover the entire target population. Then,
two probability samples (one from each frame) are drawn and information
collected is suitably combined to get estimators of the parameter of
interest.
Author: Antonio Arcos
Maintainer: David Molina
Frames2-0.0.3/Frames2/R/HouseholdsA.R |only
Frames2-0.0.3/Frames2/R/HouseholdsB.R |only
Frames2-0.0.3/Frames2/data/HouseholdsA.txt.gz |only
Frames2-0.0.3/Frames2/data/HouseholdsB.txt.gz |only
Frames2-0.0.3/Frames2/man/HouseholdsA.Rd |only
Frames2-0.0.3/Frames2/man/HouseholdsB.Rd |only
Frames2-0.1.0/Frames2/DESCRIPTION | 8
Frames2-0.1.0/Frames2/MD5 | 119 +++---
Frames2-0.1.0/Frames2/NAMESPACE | 4
Frames2-0.1.0/Frames2/R/BKA.R | 173 +++++---
Frames2-0.1.0/Frames2/R/CalDF.R | 105 +++--
Frames2-0.1.0/Frames2/R/CalSF.R | 159 +++-----
Frames2-0.1.0/Frames2/R/Compare.R |only
Frames2-0.1.0/Frames2/R/CovHT.R | 10
Frames2-0.1.0/Frames2/R/Dat.R |only
Frames2-0.1.0/Frames2/R/DatA.R |only
Frames2-0.1.0/Frames2/R/DatB.R |only
Frames2-0.1.0/Frames2/R/Domains.R | 6
Frames2-0.1.0/Frames2/R/FB.R | 109 +++--
Frames2-0.1.0/Frames2/R/HT.R | 6
Frames2-0.1.0/Frames2/R/Hartley.R | 103 +++--
Frames2-0.1.0/Frames2/R/JackBKA.R | 285 +++++++++++---
Frames2-0.1.0/Frames2/R/JackCalDF.R | 296 +++++++++++----
Frames2-0.1.0/Frames2/R/JackCalSF.R | 294 +++++++++++----
Frames2-0.1.0/Frames2/R/JackFB.R | 290 +++++++++++---
Frames2-0.1.0/Frames2/R/JackHartley.R | 290 +++++++++++---
Frames2-0.1.0/Frames2/R/JackPEL.R | 273 ++++++++++----
Frames2-0.1.0/Frames2/R/JackPML.R | 290 +++++++++++---
Frames2-0.1.0/Frames2/R/JackSFRR.R | 298 +++++++++++----
Frames2-0.1.0/Frames2/R/PEL.R | 506 +++++++++++---------------
Frames2-0.1.0/Frames2/R/PML.R | 242 ++++++------
Frames2-0.1.0/Frames2/R/PiklA.R | 5
Frames2-0.1.0/Frames2/R/PiklB.R | 5
Frames2-0.1.0/Frames2/R/SFRR.R | 170 ++++----
Frames2-0.1.0/Frames2/R/VarHT.R | 8
Frames2-0.1.0/Frames2/R/WeightsCalDF.R | 22 -
Frames2-0.1.0/Frames2/R/WeightsCalSF.R | 38 -
Frames2-0.1.0/Frames2/R/internal.R | 38 +
Frames2-0.1.0/Frames2/data/Dat.txt.gz |only
Frames2-0.1.0/Frames2/data/DatA.txt.gz |only
Frames2-0.1.0/Frames2/data/DatB.txt.gz |only
Frames2-0.1.0/Frames2/man/BKA.Rd | 40 +-
Frames2-0.1.0/Frames2/man/CalDF.Rd | 39 +-
Frames2-0.1.0/Frames2/man/CalSF.Rd | 43 +-
Frames2-0.1.0/Frames2/man/Compare.Rd |only
Frames2-0.1.0/Frames2/man/CovHT.Rd | 10
Frames2-0.1.0/Frames2/man/Dat.Rd |only
Frames2-0.1.0/Frames2/man/DatA.Rd |only
Frames2-0.1.0/Frames2/man/DatB.Rd |only
Frames2-0.1.0/Frames2/man/Domains.Rd | 6
Frames2-0.1.0/Frames2/man/FB.Rd | 23 -
Frames2-0.1.0/Frames2/man/HT.Rd | 6
Frames2-0.1.0/Frames2/man/Hartley.Rd | 23 -
Frames2-0.1.0/Frames2/man/JackBKA.Rd | 51 +-
Frames2-0.1.0/Frames2/man/JackCalDF.Rd | 55 +-
Frames2-0.1.0/Frames2/man/JackCalSF.Rd | 51 +-
Frames2-0.1.0/Frames2/man/JackFB.Rd | 51 +-
Frames2-0.1.0/Frames2/man/JackHartley.Rd | 51 +-
Frames2-0.1.0/Frames2/man/JackPEL.Rd | 29 -
Frames2-0.1.0/Frames2/man/JackPML.Rd | 51 +-
Frames2-0.1.0/Frames2/man/JackSFRR.Rd | 59 +--
Frames2-0.1.0/Frames2/man/PEL.Rd | 27 -
Frames2-0.1.0/Frames2/man/PML.Rd | 33 +
Frames2-0.1.0/Frames2/man/PiklA.Rd | 6
Frames2-0.1.0/Frames2/man/PiklB.Rd | 6
Frames2-0.1.0/Frames2/man/SFRR.Rd | 39 +-
Frames2-0.1.0/Frames2/man/VarHT.Rd | 8
Frames2-0.1.0/Frames2/man/WeightsCalDF.Rd | 18
Frames2-0.1.0/Frames2/man/WeightsCalSF.Rd | 34 -
69 files changed, 3139 insertions(+), 1772 deletions(-)
Title: Print Function Signatures
Diff between sig versions 0.0-4 dated 2013-07-11 and 0.0-5 dated 2015-01-21
Description: Print function signatures and find overly complicated code.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
DESCRIPTION | 21 +++++++++-----
MD5 | 46 ++++++++++++++++----------------
NAMESPACE | 2 +
NEWS | 1
R/indexing.R | 2 -
R/sig.R | 11 +++++--
man/Extract.siglist.Rd | 28 ++++++++++---------
man/as.list.sig.Rd | 17 ++++++------
man/as.sig.Rd | 22 ++++++++-------
man/as.siglist.Rd | 20 +++++++-------
man/backquote.Rd | 15 +++++-----
man/exponential_cut.Rd | 16 ++++++-----
man/fix_fn_names.Rd | 16 ++++++-----
man/is.sig.Rd | 12 ++++----
man/is.siglist.Rd | 14 +++++----
man/list_sigs.Rd | 26 +++++++++---------
man/pkg2env.Rd | 14 +++++----
man/print.sig.Rd | 31 ++++++++++++----------
man/print.siglist.Rd | 23 +++++++---------
man/print_engine.Rd | 18 ++++++------
man/sig.Rd | 34 +++++++++++++-----------
man/sig_report.Rd | 66 +++++++++++++++++++++++------------------------
man/source_to_new_env.Rd | 14 +++++----
man/write_sigs.Rd | 42 ++++++++++++++---------------
24 files changed, 275 insertions(+), 236 deletions(-)
Title: Search VertNet, a Database of Vertebrate Specimen Records
Diff between rvertnet versions 0.0-5 dated 2012-11-23 and 0.2.2 dated 2015-01-21
Description: Retrieve, map and summarize data from the VertNet.org archives.
Functions allow searching by many parameters, including taxonomic names,
places, dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large datasets via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain
rvertnet-0.0-5/rvertnet/R/rvertnet.R |only
rvertnet-0.0-5/rvertnet/R/vertavailablemaps.R |only
rvertnet-0.0-5/rvertnet/R/vertlocations.R |only
rvertnet-0.0-5/rvertnet/R/vertoccurrence.R |only
rvertnet-0.0-5/rvertnet/R/vertoccurrencecount.R |only
rvertnet-0.0-5/rvertnet/R/vertproviders.R |only
rvertnet-0.0-5/rvertnet/R/verttaxa.R |only
rvertnet-0.0-5/rvertnet/data |only
rvertnet-0.0-5/rvertnet/inst/vertnetorg_ropensci2.png |only
rvertnet-0.0-5/rvertnet/man/dc.Rd |only
rvertnet-0.0-5/rvertnet/man/dcdatatypes.Rd |only
rvertnet-0.0-5/rvertnet/man/dcnames.Rd |only
rvertnet-0.0-5/rvertnet/man/vertavailablemaps.Rd |only
rvertnet-0.0-5/rvertnet/man/vertlocations.Rd |only
rvertnet-0.0-5/rvertnet/man/vertoccurrence.Rd |only
rvertnet-0.0-5/rvertnet/man/vertoccurrencecount.Rd |only
rvertnet-0.0-5/rvertnet/man/vertproviders.Rd |only
rvertnet-0.0-5/rvertnet/man/verttaxa.Rd |only
rvertnet-0.2.2/rvertnet/DESCRIPTION | 34 +--
rvertnet-0.2.2/rvertnet/LICENSE |only
rvertnet-0.2.2/rvertnet/MD5 | 68 +++---
rvertnet-0.2.2/rvertnet/NAMESPACE | 9
rvertnet-0.2.2/rvertnet/NEWS | 20 +
rvertnet-0.2.2/rvertnet/R/bigsearch.R |only
rvertnet-0.2.2/rvertnet/R/defunct.R |only
rvertnet-0.2.2/rvertnet/R/globals.R |only
rvertnet-0.2.2/rvertnet/R/rvertnet-package.R |only
rvertnet-0.2.2/rvertnet/R/searchbyterm.R |only
rvertnet-0.2.2/rvertnet/R/spatialsearch.R |only
rvertnet-0.2.2/rvertnet/R/vertmap.R | 119 +++++++---
rvertnet-0.2.2/rvertnet/R/vertsearch.R | 57 +++--
rvertnet-0.2.2/rvertnet/R/vertsummary.R |only
rvertnet-0.2.2/rvertnet/R/yyy.R |only
rvertnet-0.2.2/rvertnet/R/zzz.R | 112 +++++++---
rvertnet-0.2.2/rvertnet/README.md | 144 ++++++++++---
rvertnet-0.2.2/rvertnet/build |only
rvertnet-0.2.2/rvertnet/inst/doc |only
rvertnet-0.2.2/rvertnet/inst/vign |only
rvertnet-0.2.2/rvertnet/man/bigsearch.Rd |only
rvertnet-0.2.2/rvertnet/man/rvertnet-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/rvertnet-package.Rd |only
rvertnet-0.2.2/rvertnet/man/searchbyterm.Rd |only
rvertnet-0.2.2/rvertnet/man/spatialsearch.Rd |only
rvertnet-0.2.2/rvertnet/man/vertavailablemaps-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/vertlocations-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/vertmap.Rd | 64 ++++-
rvertnet-0.2.2/rvertnet/man/vertoccurrence-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/vertoccurrencecount-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/vertproviders-defunct.Rd |only
rvertnet-0.2.2/rvertnet/man/vertsearch.Rd | 54 +++-
rvertnet-0.2.2/rvertnet/man/vertsummary.Rd |only
rvertnet-0.2.2/rvertnet/man/verttaxa-defunct.Rd |only
rvertnet-0.2.2/rvertnet/tests |only
rvertnet-0.2.2/rvertnet/vignettes |only
54 files changed, 504 insertions(+), 177 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Diff between mvSLOUCH versions 1.1.4 dated 2014-11-02 and 1.1.5 dated 2015-01-21
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek
DESCRIPTION | 10 +++++-----
MD5 | 28 ++++++++++++++--------------
R/estimBM.R | 2 +-
R/simulVasicekprocphyl.R | 7 ++++---
man/BrownianMotionModel.Rd | 2 +-
man/SummarizeBM.Rd | 2 +-
man/SummarizeMVSLOUCH.Rd | 4 ++--
man/SummarizeOUCH.Rd | 2 +-
man/fitch.mvsl.Rd | 2 +-
man/mvSLOUCH-package.Rd | 2 +-
man/mvslouchModel.Rd | 4 ++--
man/ouchModel.Rd | 2 +-
man/simulBMProcPhylTree.Rd | 2 +-
man/simulMVSLOUCHProcPhylTree.Rd | 2 +-
man/simulOUCHProcPhylTree.Rd | 2 +-
15 files changed, 37 insertions(+), 36 deletions(-)
Title: Linked Micromap Plots for U. S. States
Diff between micromapST versions 1.0.3 dated 2014-03-09 and 1.0.5 dated 2015-01-21
Description: This package provides the user with the ability to quickly create Linked
Micromap plots of the 50 U.S. states and District of Columbia (51 areas).
Linked Micromap plots are visualizations of geo-referenced data that link statistical
graphics to an organized series of small maps.
The Help description contains examples of how to use the micromapST function.
This package contains the US and State boundary files and U. S. FIPS code to State conversion tables
used by the micromapST function and several data sets used in the micromapST examples.
Copyrighted 2013, 2014 and 2015 by Carr, Pearson and Pickle.
Author: Dan Carr
Maintainer: Jim Pearson
DESCRIPTION | 22 -
MD5 | 28 -
NEWS | 27 +
R/micromapST.r | 788 +++++++++++++++++++++++++---------------------
R/panelFunctions.r | 18 -
build |only
data/segBarData.rda |only
inst/CITATION | 35 +-
inst/doc |only
man/TSdata.Rd | 28 -
man/micromapST-package.Rd | 20 -
man/micromapST.Rd | 226 ++++++-------
man/micromapSTDefaults.Rd | 61 +--
man/panelDesc.Rd | 127 +++----
man/segBarData.Rd |only
man/wmlung5070US.Rd | 2
vignettes |only
17 files changed, 764 insertions(+), 618 deletions(-)
Title: R Interface to Google Charts
Diff between googleVis versions 0.5.7 dated 2014-12-20 and 0.5.8 dated 2015-01-21
Description: R interface to Google Charts API, allowing users
to create interactive charts based on data frames. Charts
are displayed locally via the R HTTP help server. A modern
browser with Internet connection is required and for some
charts a Flash player. The data remains local and is not
uploaded to Google.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann
DESCRIPTION | 14
MD5 | 32 -
NEWS | 6
R/gvisMethods.R | 10
README.md | 2
build/googleVis.pdf |binary
build/vignette.rds |binary
inst/doc/Using_Roles_via_googleVis.html | 220 +++----
inst/doc/Using_Trendlines_with_googleVis.html | 80 +-
inst/doc/Using_googleVis_with_knitr.html | 76 +-
inst/doc/googleVis.Rnw | 2
inst/doc/googleVis.pdf |binary
inst/doc/googleVis_examples.Rmd | 10
inst/doc/googleVis_examples.html | 740 +++++++++++++-------------
vignettes/googleVis.Rnw | 2
vignettes/googleVis.bib | 2
vignettes/googleVis_examples.Rmd | 10
17 files changed, 609 insertions(+), 597 deletions(-)
Title: Extreme Value Analysis
Diff between extRemes versions 2.0-4 dated 2014-12-17 and 2.0-5 dated 2015-01-21
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland
DESCRIPTION | 6 +--
MD5 | 16 ++++----
R/abba.R | 2 -
R/fitfuns.R | 107 ++++++++++++++++++++++++++++++++++++++++++++--------------
inst/CITATION | 11 +----
man/abba.Rd | 2 -
man/fevd.Rd | 6 ++-
man/hwmi.Rd | 8 ++++
src/Makevars | 2 -
9 files changed, 109 insertions(+), 51 deletions(-)
Title: Benchmark functions for the Special Session and Competition on
Real-Parameter Single Objective Optimization at CEC-2013
Diff between cec2013 versions 0.1-4 dated 2013-03-05 and 0.1-5 dated 2015-01-21
Description: This package provides R wrappers for the C implementation of 28 benchmark functions defined for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013. The focus of this package is to provide an open-source and multi-platform implementation of the CEC2013 benchmark functions, in order to make easier for researchers to test the performance of new optimization algorithms in a reproducible way. The original C code (Windows only) was provided by Jane Jing Liang, while GNU/Linux comments were made by Janez Brest. This package was gently authorised for publication on CRAN by Ponnuthurai Nagaratnam Suganthan. The official documentation is available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC2013/CEC2013.htm. Bugs reports/comments/questions are very welcomed (in English, Spanish or Italian).
Author: Mauricio Zambrano-Bigiarini [aut, cre], Yasser Gonzalez-Fernandez [aut]
Maintainer: Mauricio Zambrano-Bigiarini
cec2013-0.1-4/cec2013/COPYING |only
cec2013-0.1-5/cec2013/DESCRIPTION | 32 +++++++-------------------------
cec2013-0.1-5/cec2013/MD5 | 13 ++++++-------
cec2013-0.1-5/cec2013/NEWS | 5 +++++
cec2013-0.1-5/cec2013/R/cec2013.R | 2 +-
cec2013-0.1-5/cec2013/inst/CITATION | 11 +++++------
cec2013-0.1-5/cec2013/man/cec2013.Rd | 6 +++---
cec2013-0.1-5/cec2013/src/cec2013.c | 2 +-
8 files changed, 28 insertions(+), 43 deletions(-)
Title: Phonetic-Coding For Portuguese
Diff between SoundexBR versions 1.0 dated 2014-12-22 and 1.1 dated 2015-01-21
Description: The SoundexBR package provides an algorithm for decoding names
into phonetic codes, as pronounced in Portuguese. The goal is for
homophones to be encoded to the same representation so that they can be
matched despite minor differences in spelling. The algorithm mainly encodes
consonants; a vowel will not be encoded unless it is the first letter. The
soundex code resultant consists of a four digits long string composed by
one letter followed by three numerical digits: the letter is the first
letter of the name, and the digits encode the remaining consonants.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino
DESCRIPTION | 15 ++++++++---
MD5 | 19 +++++++-------
NAMESPACE | 19 ++++++--------
R/accent.R | 8 +++---
R/soundexBR.R | 52 ++++++++++++++++++++++++++++++++++++++-
R/utils.R | 1
README.md | 62 +++++++++++++++++++++++++++++++++++++++++++----
man/accent.Rd | 37 ++++++++++++++--------------
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man/soundexBR.Rd | 7 +++--
11 files changed, 168 insertions(+), 56 deletions(-)
Title: Tools for Designing and Weighting Survey Samples
Diff between PracTools versions 0.0-2 dated 2014-06-22 and 0.1 dated 2015-01-21
Description: PracTools contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example datasets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant
DESCRIPTION | 8 ++++----
MD5 | 48 +++++++++++++++++++++++++++++++-----------------
NAMESPACE | 9 +++++----
R/NRadjClass.R |only
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data/MDarea.pop.RData |binary
data/datalist | 1 +
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Title: Regression Models for Ordinal Data
Diff between ordinal versions 2014.12-22 dated 2014-12-23 and 2015.1-21 dated 2015-01-21
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen
DESCRIPTION | 10
MD5 | 71 +++---
NAMESPACE | 4
NEWS | 3
R/clm.R | 484 +++++++++---------------------------------
R/clm.Thetamat.R | 11
R/clm.fit.R | 215 +++++++++++-------
R/clm.fitter.R | 20 +
R/clm.frames.R | 304 ++++++++++----------------
R/clm.methods.R | 18 +
R/clm.predict.R | 3
R/clm.profile.R | 10
R/clm.simple.R | 8
R/clm.start.R | 20 -
R/clmm.R | 2
R/control.R | 2
R/convergence.R | 6
R/drop.coef.R | 19 -
R/utils.R | 103 +++++---
R/warning_functions.R |only
inst/CITATION | 9
inst/doc/clm_intro.pdf |binary
inst/doc/clm_tutorial.pdf |binary
inst/doc/clmm2_tutorial.pdf |binary
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man/clm.control.Rd | 9
man/clm.fit.Rd | 86 +++----
tests/clm.fit.R | 95 ++++----
tests/clm.formula.R | 11
tests/test-all.R |only
tests/test.clm.Theta.R | 15 +
tests/test.clm.model.matrix.R | 8
tests/test.clm.predict.R | 27 ++
tests/test0weights.R | 2
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35 files changed, 723 insertions(+), 854 deletions(-)
Title: Dual Empirical Likelihood Inference under Density Ratio Models
in the Presence of Multiple Samples
Diff between drmdel versions 1.3 dated 2014-04-09 and 1.3.1 dated 2015-01-21
Description: Dual empirical likelihood (DEL) inference under semiparametric density ratio models (DRM) in the presence of multiple samples, including population cumulative distribution function estimation, quantile estimation and comparison, density estimation, composite hypothesis testing for DRM parameters which encompasses testing for changes in population distribution functions as a special case, etc.
Author: Song Cai
Maintainer: Song Cai
ChangeLog | 8 +
DESCRIPTION | 16 +--
MD5 | 22 ++--
R/drmdel.R | 14 +-
man/cdfDRM.Rd | 48 +++++-----
man/densityDRM.Rd | 84 +++++++++--------
man/drmdel.Rd | 225 +++++++++++++++++++++++++-----------------------
man/meleCov.Rd | 10 +-
man/quantileCompWald.Rd | 125 ++++++++++++++------------
man/quantileDRM.Rd | 114 ++++++++++++------------
man/summaryDRM.Rd | 21 ++--
src/utilities.c | 3
12 files changed, 369 insertions(+), 321 deletions(-)
Title: Data sets, etc. for the text "Using R for Introductory
Statistics", second edition
Diff between UsingR versions 2.0-2 dated 2014-09-02 and 2.0-3 dated 2015-01-21
Description: A collection of data sets to accompany the
textbook "Using R for Introductory Statistics," second
edition.
Author: John Verzani
Maintainer: John Verzani
UsingR-2.0-2/UsingR/man/UsingR.Rd |only
UsingR-2.0-2/UsingR/man/sim.Rd |only
UsingR-2.0-3/UsingR/DESCRIPTION | 14 -
UsingR-2.0-3/UsingR/MD5 | 297 ++++++++++------------
UsingR-2.0-3/UsingR/NAMESPACE | 49 ++-
UsingR-2.0-3/UsingR/NEWS | 4
UsingR-2.0-3/UsingR/R/DOTplot.R | 32 ++
UsingR-2.0-3/UsingR/R/DensityPlot.R | 33 ++
UsingR-2.0-3/UsingR/R/QQplot.R | 17 +
UsingR-2.0-3/UsingR/R/Split.zoo.R | 8
UsingR-2.0-3/UsingR/R/aaa.R |only
UsingR-2.0-3/UsingR/R/datasets.R | 37 --
UsingR-2.0-3/UsingR/R/getAnswer.R | 27 +-
UsingR-2.0-3/UsingR/R/lorem.R | 3
UsingR-2.0-3/UsingR/R/scatter.with.hist.R | 11
UsingR-2.0-3/UsingR/R/simple.chutes.R | 7
UsingR-2.0-3/UsingR/R/simple.densityplot.R | 33 ++
UsingR-2.0-3/UsingR/R/simple.eda.R | 6
UsingR-2.0-3/UsingR/R/simple.eda.ts.R | 7
UsingR-2.0-3/UsingR/R/simple.fancy.stripchart.R | 6
UsingR-2.0-3/UsingR/R/simple.freqpoly.R | 9
UsingR-2.0-3/UsingR/R/simple.hist.and.boxplot.R | 9
UsingR-2.0-3/UsingR/R/simple.lag.R | 9
UsingR-2.0-3/UsingR/R/simple.lm.R | 11
UsingR-2.0-3/UsingR/R/simple.median.test.R | 6
UsingR-2.0-3/UsingR/R/simple.scatterplot.R | 8
UsingR-2.0-3/UsingR/R/simple.sim.R | 8
UsingR-2.0-3/UsingR/R/simple.violinplot.R | 36 ++
UsingR-2.0-3/UsingR/R/simple.z.test.R | 8
UsingR-2.0-3/UsingR/R/squareplot.R | 12
UsingR-2.0-3/UsingR/R/superbarplot.R | 9
UsingR-2.0-3/UsingR/R/utils.R | 22 -
UsingR-2.0-3/UsingR/R/violinplot.R | 33 ++
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Title: Thurstonian Models for Sensory Discrimination
Diff between sensR versions 1.4-4 dated 2014-12-23 and 1.4-5 dated 2015-01-21
Description: Provides methods for sensory discrimination methods;
duotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-different,
2-AC and degree-of-difference.
This enables the calculation of d-primes, standard errors of
d-primes, sample size and power computations, and
comparisons of different d-primes. Methods for profile likelihood
confidence intervals and plotting are included.
Author: Rune Haubo Bojesen Christensen [aut, cre],
Per Bruun Brockhoff [aut]
Maintainer: Rune Haubo Bojesen Christensen
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 8 ++++++--
inst/CITATION | 9 ++++-----
inst/doc/methodology.pdf |binary
inst/doc/twoACexamples.pdf |binary
6 files changed, 19 insertions(+), 16 deletions(-)
Title: Semiparametric Sample Selection Modelling with Continuous or
Discrete Response
Diff between SemiParSampleSel versions 1.1-1 dated 2014-08-27 and 1.2 dated 2015-01-21
More information about SemiParSampleSel at CRAN
Description: Routine for fitting continuous or discrete response copula sample selection models with semiparametric predictors, including linear and nonlinear effects.
Author: Giampiero Marra, Rosalba Radice, Malgorzata Wojtys and Karol Wyszynski
Maintainer: Giampiero Marra
SemiParSampleSel-1.1-1/SemiParSampleSel/R/ghss1.r |only
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SemiParSampleSel-1.2/SemiParSampleSel/DESCRIPTION | 18
SemiParSampleSel-1.2/SemiParSampleSel/MD5 | 78 +-
SemiParSampleSel-1.2/SemiParSampleSel/NAMESPACE | 11
SemiParSampleSel-1.2/SemiParSampleSel/R/S.m.r | 55 +-
SemiParSampleSel-1.2/SemiParSampleSel/R/SemiParSampleSel.r | 275 +++++++---
SemiParSampleSel-1.2/SemiParSampleSel/R/bitsgHs.r | 65 +-
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SemiParSampleSel-1.2/SemiParSampleSel/R/ghss.r | 211 +++----
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SemiParSampleSel-1.2/SemiParSampleSel/R/print.SemiParSampleSel.r | 97 ++-
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SemiParSampleSel-1.2/SemiParSampleSel/R/print.summary.SemiParSampleSel.r | 90 ++-
SemiParSampleSel-1.2/SemiParSampleSel/R/ss.checks.r | 25
SemiParSampleSel-1.2/SemiParSampleSel/R/st.theta.star.R | 23
SemiParSampleSel-1.2/SemiParSampleSel/R/summary.SemiParSampleSel.r | 83 +--
SemiParSampleSel-1.2/SemiParSampleSel/R/theta.tau.r | 24
SemiParSampleSel-1.2/SemiParSampleSel/R/working.comp.r | 79 ++
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SemiParSampleSel-1.2/SemiParSampleSel/inst/CITATION | 13
SemiParSampleSel-1.2/SemiParSampleSel/man/S.m.Rd | 2
SemiParSampleSel-1.2/SemiParSampleSel/man/SemiParSampleSel-package.Rd | 25
SemiParSampleSel-1.2/SemiParSampleSel/man/SemiParSampleSel.Rd | 132 ++--
SemiParSampleSel-1.2/SemiParSampleSel/man/SemiParSampleSelObject.Rd | 31 -
SemiParSampleSel-1.2/SemiParSampleSel/man/VuongClarke.bcm.Rd | 27
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SemiParSampleSel-1.2/SemiParSampleSel/man/theta.tau.Rd | 2
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48 files changed, 907 insertions(+), 573 deletions(-)
Permanent link
Title: Response Surface Analysis
Diff between RSA versions 0.9.3 dated 2014-06-27 and 0.9.6 dated 2015-01-21
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full polynomial,
shifted and rotated squared differences, rising ridge surfaces, basic
squared differences). The package provides plotting functions for 3d
wireframe surfaces, interactive 3d plots, and contour plots. Calculates
many surface parameters (a1 to a4, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schönbrodt
Maintainer: Felix Schönbrodt
DESCRIPTION | 17 +--
MD5 | 59 +++++------
NAMESPACE | 8 +
R/RSA.R | 271 +++++++++++++++++++++++++++++++++++----------------
R/RSA.ST.R | 51 ++++-----
R/aictab.R | 26 +++-
R/compare.R | 20 +--
R/confint.R | 4
R/demoRSA.R | 67 +++++++++++-
R/demoSRR.R |only
R/demoSRRR.R |only
R/getPar.R | 6 -
R/helpers.R | 74 ++++++-------
R/modeltree.R | 13 ++
R/outpro.R |only
R/plot.RSA.R | 257 +++++++++++++++++++++++++++++++++++-------------
R/print.RSA.R | 73 ++++++++++++-
inst/NEWS.Rd | 63 +++++++++++
man/RSA.Rd | 31 +++--
man/RSA.ST.Rd | 15 +-
man/aictab.Rd | 8 +
man/compare.Rd | 3
man/compare2.Rd | 5
man/confint.RSA.Rd | 13 +-
man/demoRSA.Rd | 35 ++++--
man/fitted.RSA.Rd | 3
man/getPar.Rd | 3
man/modeltree.Rd | 11 +-
man/motcon.Rd | 3
man/movieRSA.Rd | 3
man/plotRSA.Rd | 105 ++++++++++---------
man/residuals.RSA.Rd | 3
32 files changed, 863 insertions(+), 387 deletions(-)
Title: Overlays on Google map tiles in R
Diff between RgoogleMaps versions 1.2.0.6 dated 2014-04-30 and 1.2.0.7 dated 2015-01-21
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher
DESCRIPTION | 10 ++--
MD5 | 79 +++++++++++++++++++--------------------
NAMESPACE | 4 +
R/AddAlpha.R | 11 +++--
R/ColorMap.R | 6 +-
R/DF2SpatialPointsDataFrame.R | 25 +++++++-----
R/GetMap.R | 7 ++-
R/PlotOnStaticMap.R | 4 +
R/PlotPolysOnStaticMap.R | 12 ++---
R/SpatialToPBS.R | 5 --
R/bubbleMap.R | 15 +++----
R/degreeAxis.R | 1
R/getGeoCode.R | 2
inst/CITATION |only
man/AddAlpha.Rd | 13 ++++--
man/ColorMap.Rd | 2
man/DF2SpatialPointsDataFrame.Rd | 25 +++++++-----
man/GetMap.OSM.Rd | 2
man/GetMap.Rd | 5 +-
man/GetMap.bbox.Rd | 2
man/IdentifyPoints.Rd | 2
man/LatLon2XY.Rd | 2
man/LatLon2XY.centered.Rd | 2
man/MapBackground.Rd | 2
man/MaxZoom.Rd | 2
man/PlotArrowsOnStaticMap.Rd | 2
man/PlotOnStaticMap.Rd | 6 +-
man/PlotPolysOnStaticMap.Rd | 8 +--
man/RGB2GRAY.Rd | 2
man/ReadMapTile.Rd | 2
man/RgoogleMaps-package.Rd | 12 ++---
man/SpatialToPBS.Rd | 2
man/TextOnStaticMap.Rd | 2
man/Tile2R.Rd | 2
man/XY2LatLon.Rd | 2
man/bubbleMap.Rd | 16 +++----
man/degreeAxis.Rd | 2
man/getGeoCode.Rd | 2
man/mypolygon.Rd | 2
man/qbbox.Rd | 2
man/updateusr.Rd | 2
41 files changed, 170 insertions(+), 136 deletions(-)
Title: MODIS Subsetting Tools
Diff between MODISTools versions 0.94.5 dated 2014-12-23 and 0.94.6 dated 2015-01-21
Description: Provides several functions for downloading, storing and processing
subsets of MODIS Land Processes data as a batch process.
Author: Sean Tuck, Helen Phillips
Maintainer: Sean Tuck
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/CITATION | 2 +-
inst/doc/UsingMODISTools.pdf |binary
tests/Test.R | 40 +++++++++++++---------------------------
5 files changed, 22 insertions(+), 36 deletions(-)
Title: 2D and 3D Hive Plots for R
Diff between HiveR versions 0.2-27 dated 2014-06-02 and 0.2-28 dated 2015-01-21
Description: HiveR creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson
HiveR-0.2-27/HiveR/R/cart2sph.R |only
HiveR-0.2-27/HiveR/man/cart2sph.Rd |only
HiveR-0.2-28/HiveR/DESCRIPTION | 25 ++++++++--------
HiveR-0.2-28/HiveR/MD5 | 49 +++++++++++++++-----------------
HiveR-0.2-28/HiveR/NAMESPACE | 6 ++-
HiveR-0.2-28/HiveR/NEWS | 8 +++++
HiveR-0.2-28/HiveR/R/adj2HPD.R | 4 --
HiveR-0.2-28/HiveR/R/animateHive.R | 2 -
HiveR-0.2-28/HiveR/R/chkHPD.R | 3 -
HiveR-0.2-28/HiveR/R/dot2HPD.R | 2 -
HiveR-0.2-28/HiveR/R/drawHiveSpline.R | 2 -
HiveR-0.2-28/HiveR/R/edge2HPD.R | 2 -
HiveR-0.2-28/HiveR/R/manipAxis.R | 1
HiveR-0.2-28/HiveR/R/mineHPD.R | 2 -
HiveR-0.2-28/HiveR/R/plot3dHive.R | 2 -
HiveR-0.2-28/HiveR/R/plotHive.R | 6 +--
HiveR-0.2-28/HiveR/R/sph2cart.R | 2 -
HiveR-0.2-28/HiveR/R/sumHPD.R | 3 -
HiveR-0.2-28/HiveR/build/vignette.rds |binary
HiveR-0.2-28/HiveR/inst/CITATION | 5 +--
HiveR-0.2-28/HiveR/inst/doc/HiveR.R | 43 ++++++++++++++--------------
HiveR-0.2-28/HiveR/inst/doc/HiveR.Rnw | 5 +--
HiveR-0.2-28/HiveR/inst/doc/HiveR.pdf |binary
HiveR-0.2-28/HiveR/man/HiveR-package.Rd | 4 +-
HiveR-0.2-28/HiveR/man/plotHive.Rd | 1
HiveR-0.2-28/HiveR/man/sph2cart.Rd |only
HiveR-0.2-28/HiveR/vignettes/HiveR.Rnw | 5 +--
27 files changed, 95 insertions(+), 87 deletions(-)
Title: The Hilbert-Huang Transform: Tools and Methods
Diff between hht versions 2.1.1 dated 2014-10-28 and 2.1.2 dated 2015-01-21
Description: This package builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis. The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum. To see the version history and download the bleeding-edge version (at your own risk!), see the project website at code.google.com below. See the other links for PDF files describing numerical and exact analytical methods for determining instantaneous frequency, some examples of signals processed with this package, and some examples of the ensemble empirical mode decomposition method.
Author: Daniel C. Bowman [aut, cre],
Jonathan M. Lees [ctb]
Maintainer: Daniel C. Bowman
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NEWS | 3 +++
R/rendering_and_plotting.R | 2 +-
inst/CITATION | 22 ++++++++++------------
5 files changed, 21 insertions(+), 20 deletions(-)
Title: Cox regression with Firth's penalized likelihood
Diff between coxphf versions 1.10 dated 2013-07-08 and 1.11 dated 2015-01-21
Description: Cox regression with Firth's penalized likelihood
Author: R by Meinhard Ploner, Fortran by Georg Heinze
Maintainer: Georg Heinze
DESCRIPTION | 11 ++++++-----
MD5 | 10 +++++-----
NAMESPACE | 7 ++++++-
man/coxphf.rd | 17 +++++++++--------
man/coxphfplot.Rd | 12 ++++++------
man/coxphftest.Rd | 13 +++++++------
6 files changed, 39 insertions(+), 31 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Diff between ChemoSpec versions 2.0-2 dated 2014-05-31 and 3.0-1 dated 2015-01-21
Description: A collection of functions for plotting spectra (NMR, IR etc) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA and model-based clustering. The design allows comparison of data from samples which fall into groups such as treatment vs. control. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed to be very user friendly and suitable for people with limited background in R.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
DESCRIPTION | 13 +-
MD5 | 166 +++++++++++++++---------------
NAMESPACE | 13 +-
NEWS | 31 +++++
R/clupaSpectra.R |only
R/evalClusters.R |only
R/files2SpectraObject.R | 5
R/hcaScores.R | 12 +-
R/hcaSpectra.R | 9 +
R/normSpectra.R | 30 +++++
R/plotHCA.R | 4
R/plotScores.R | 5
R/removeGroup.R | 13 ++
R/sumSpectra.R | 9 +
build/vignette.rds |binary
data/SrE.IR.RData |binary
inst/CITATION | 7 -
inst/doc/ChemoSpec.R | 63 +++++------
inst/doc/ChemoSpec.Rnw | 242 ++++++++++++++++++++------------------------
inst/doc/ChemoSpec.pdf |binary
man/ChemoSpec-package.Rd | 6 -
man/CuticleIR.Rd | 2
man/LoopThruSpectra.Rd | 2
man/Spectra.Rd | 2
man/SrE.IR.Rd | 5
man/aovPCA.Rd | 3
man/aovPCAloadings.Rd | 3
man/aovPCAscores.Rd | 2
man/avgFacLvls.Rd | 4
man/baselineSpec.Rd | 2
man/binBuck.Rd | 2
man/binData.Rd | 2
man/calcSN.Rd | 2
man/check4Gaps.Rd | 2
man/chkSpectra.Rd | 2
man/classPCA.Rd | 2
man/clupaSpectra.Rd |only
man/colLeaf.Rd | 2
man/colorSymbol.Rd | 2
man/conColScheme.Rd | 2
man/coordProjCS.Rd | 2
man/evalClusters.Rd |only
man/files2SpectraObject.Rd | 2
man/findTMS.Rd | 2
man/groupNcolor.Rd | 2
man/hcaScores.Rd | 8 -
man/hcaSpectra.Rd | 8 -
man/hmapSpectra.Rd | 2
man/hypTestScores.Rd | 2
man/isWholeNo.Rd | 2
man/labelExtremes.Rd | 2
man/labelExtremes3d.Rd | 2
man/makeEllipsoid.Rd | 2
man/mclust3D.Rd | 2
man/mclust3dSpectra.Rd | 2
man/mclustSpectra.Rd | 2
man/normSpectra.Rd | 10 +
man/normVec.Rd | 2
man/pcaBoot.Rd | 2
man/pcaDiag.Rd | 2
man/plot2Loadings.Rd | 2
man/plotHCA.Rd | 16 +-
man/plotLoadings.Rd | 2
man/plotScores.Rd | 8 +
man/plotScores3D.Rd | 2
man/plotScoresCor.Rd | 2
man/plotScoresDecoration.Rd | 2
man/plotScoresRGL.Rd | 2
man/plotScree.Rd | 2
man/plotSpectra.Rd | 2
man/q2rPCA.Rd | 2
man/readBrukerTxt.Rd | 2
man/readJDX.Rd | 2
man/removeFreq.Rd | 4
man/removeSample.Rd | 4
man/robPCA.Rd | 2
man/rowDist.Rd | 2
man/sPlotSpectra.Rd | 8 +
man/seXy.Rd | 2
man/shrinkLeaf.Rd | 2
man/specSurvey.Rd | 2
man/splitSpectraGroups.Rd | 2
man/sumGroups.Rd | 2
man/sumSpectra.Rd | 4
vignettes/ChemoSpec.Rnw | 242 ++++++++++++++++++++------------------------
vignettes/chemometrics.bib | 71 +++++++-----
86 files changed, 606 insertions(+), 516 deletions(-)
Title: Collection of Configurable GTK+ Menus
Diff between MenuCollection versions 1.1 dated 2015-01-05 and 1.2 dated 2015-01-21
More information about MenuCollection at CRAN
Description: Set of configurable menus built with GTK+ to graphically interface new functions.
Author: Gianmarco Polotti
Maintainer: Gianmarco Polotti
DESCRIPTION | 6 +-
MD5 | 110 ++++++++++++++++++++++----------------------
R/menucollection.r | 24 ++++-----
man/dovc.Rd | 10 ++--
man/givedim.Rd | 6 +-
man/givemat.Rd | 13 ++---
man/inpboxc.Rd | 14 ++---
man/inpboxc2.Rd | 14 ++---
man/inpboxc2k.Rd | 16 +++---
man/inpboxck.Rd | 12 ++--
man/inpboxcke.Rd | 14 ++---
man/inpboxcr2.Rd | 12 ++--
man/inpboxcr3.Rd | 13 ++---
man/inpboxcr4.Rd | 14 +++--
man/inpboxe1.Rd | 12 ++--
man/inpboxe2.Rd | 10 ++--
man/inpboxe2c.Rd | 14 ++---
man/inpboxe2k.Rd | 12 ++--
man/inpboxe2k2.Rd | 12 ++--
man/inpboxe2r2.Rd | 12 ++--
man/inpboxe3.Rd | 12 ++--
man/inpboxe3c.Rd | 16 +++---
man/inpboxe3ce.Rd | 14 +++--
man/inpboxe3k.Rd | 12 ++--
man/inpboxe3k2.Rd | 12 ++--
man/inpboxe3k3.Rd | 12 ++--
man/inpboxe4.Rd | 12 ++--
man/inpboxe4c2.Rd | 18 ++++---
man/inpboxe4c2k.Rd | 20 ++++----
man/inpboxe4cek2.Rd | 14 +++--
man/inpboxe4ck.Rd | 18 ++++---
man/inpboxe4k.Rd | 14 +++--
man/inpboxe4k2.Rd | 14 +++--
man/inpboxe4k3.Rd | 14 +++--
man/inpboxe4r2.Rd | 12 ++--
man/inpboxe5.Rd | 12 ++--
man/inpboxe5k2.Rd | 14 +++--
man/inpboxe5k3.Rd | 12 ++--
man/inpboxe6k2.Rd | 14 +++--
man/inpboxe6k3.Rd | 14 +++--
man/inpboxe6r2.Rd | 14 +++--
man/inpboxe7k2.Rd | 12 ++--
man/inpboxe7r2.Rd | 12 ++--
man/inpboxe8r2.Rd | 12 ++--
man/inpboxec.Rd | 14 ++---
man/inpboxecece.Rd | 18 ++++---
man/inpboxek2.Rd | 14 ++---
man/inpboxer3.Rd | 10 ++--
man/inpboxk6.Rd | 12 ++--
man/inpboxk6k6e6.Rd | 18 ++++---
man/inpboxk7k7.Rd | 16 +++---
man/inpboxlist.Rd | 15 +++---
man/inpboxr2.Rd | 14 ++---
man/messabox.Rd | 6 +-
man/messayesno.Rd | 10 ++--
man/workspace_management.Rd | 13 ++---
56 files changed, 442 insertions(+), 398 deletions(-)
Permanent link
Title: Functions for graphical Markov models
Diff between ggm versions 2.2 dated 2014-12-04 and 2.3 dated 2015-01-21
Description: Functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
man/fitmlogit.Rd | 3 +--
3 files changed, 9 insertions(+), 10 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.4.8.11 dated 2014-08-12 and 1.5.1 dated 2015-01-21
Description: A general purpose toolbox for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
psych-1.4.8.11/psych/R/model.fit.R |only
psych-1.5.1/psych/DESCRIPTION | 18 -
psych-1.5.1/psych/MD5 | 196 +++++++--------
psych-1.5.1/psych/NAMESPACE | 23 +
psych-1.5.1/psych/R/ICLUST.R | 2
psych-1.5.1/psych/R/ICLUST.rgraph.R | 6
psych-1.5.1/psych/R/Promax.R | 16 -
psych-1.5.1/psych/R/VSS.R | 30 +-
psych-1.5.1/psych/R/Yule.R | 57 ++++
psych-1.5.1/psych/R/alpha.R | 16 -
psych-1.5.1/psych/R/bifactor.R | 17 -
psych-1.5.1/psych/R/cor.ci.R | 11
psych-1.5.1/psych/R/cor.plot.R | 17 -
psych-1.5.1/psych/R/cta.R | 2
psych-1.5.1/psych/R/cta.new.R |only
psych-1.5.1/psych/R/describe.R | 170 +++++++------
psych-1.5.1/psych/R/diagram.R | 25 +
psych-1.5.1/psych/R/draw.tetra.R | 14 -
psych-1.5.1/psych/R/errorCircles.r | 4
psych-1.5.1/psych/R/fa.R | 190 +++++++++++----
psych-1.5.1/psych/R/fa.parallel.R | 49 +++
psych-1.5.1/psych/R/fa.rgraph.R | 6
psych-1.5.1/psych/R/factor.congruence.R | 3
psych-1.5.1/psych/R/factor.minres.R | 2
psych-1.5.1/psych/R/factor.pa.R | 2
psych-1.5.1/psych/R/factor.stats.R | 5
psych-1.5.1/psych/R/factor.wls.R | 2
psych-1.5.1/psych/R/glb.algebraic.R | 5
psych-1.5.1/psych/R/kaiser.R | 5
psych-1.5.1/psych/R/make.hierarchical.R | 11
psych-1.5.1/psych/R/mediate.r |only
psych-1.5.1/psych/R/nearcor.r | 2
psych-1.5.1/psych/R/omega.R | 33 +-
psych-1.5.1/psych/R/omega.graph.R | 8
psych-1.5.1/psych/R/omegaSem.R | 9
psych-1.5.1/psych/R/parcels.R | 2
psych-1.5.1/psych/R/phi.demo.R | 28 +-
psych-1.5.1/psych/R/polychoric.R | 58 ++--
psych-1.5.1/psych/R/principal.R | 2
psych-1.5.1/psych/R/print.psych.R | 79 +++++-
psych-1.5.1/psych/R/print.psych.fa.R | 9
psych-1.5.1/psych/R/print.psych.omega.R | 8
psych-1.5.1/psych/R/print.psych.schmid.R | 13 -
psych-1.5.1/psych/R/r.test.R | 2
psych-1.5.1/psych/R/schmid.R | 85 ++++--
psych-1.5.1/psych/R/scoreOverlap.r | 3
psych-1.5.1/psych/R/set.cor.R | 109 ++++++--
psych-1.5.1/psych/R/sim.hierarchical.R | 12
psych-1.5.1/psych/R/sim.structural.R | 33 +-
psych-1.5.1/psych/R/stats.by.r | 326 +++++++++++++-------------
psych-1.5.1/psych/R/statsBy.r | 3
psych-1.5.1/psych/R/structure.graph.R | 7
psych-1.5.1/psych/R/summary.psych.R | 35 --
psych-1.5.1/psych/R/test.psych.r | 20 -
psych-1.5.1/psych/R/tetrachor.R | 58 ++--
psych-1.5.1/psych/R/toDotty.R | 7
psych-1.5.1/psych/inst/CITATION | 8
psych-1.5.1/psych/inst/NEWS.Rd | 53 +++-
psych-1.5.1/psych/inst/doc/overview.R | 205 ++++++++++------
psych-1.5.1/psych/inst/doc/overview.Rnw | 111 +++++++-
psych-1.5.1/psych/inst/doc/overview.pdf |binary
psych-1.5.1/psych/inst/doc/psych_for_sem.R | 87 +++---
psych-1.5.1/psych/inst/doc/psych_for_sem.Rnw | 4
psych-1.5.1/psych/inst/doc/psych_for_sem.pdf |binary
psych-1.5.1/psych/man/Harman.5.Rd | 3
psych-1.5.1/psych/man/VSS.Rd | 8
psych-1.5.1/psych/man/Yule.Rd | 30 ++
psych-1.5.1/psych/man/affect.Rd | 10
psych-1.5.1/psych/man/alpha.Rd | 11
psych-1.5.1/psych/man/bifactor.Rd | 3
psych-1.5.1/psych/man/bock.table.Rd | 3
psych-1.5.1/psych/man/burt.Rd | 5
psych-1.5.1/psych/man/cluster.cor.Rd | 45 +--
psych-1.5.1/psych/man/cor.ci.Rd | 14 -
psych-1.5.1/psych/man/cor.plot.Rd | 8
psych-1.5.1/psych/man/cor.smooth.Rd | 13 -
psych-1.5.1/psych/man/corr.test.Rd | 2
psych-1.5.1/psych/man/cortest.mat.Rd | 4
psych-1.5.1/psych/man/cosinor.Rd | 3
psych-1.5.1/psych/man/cta.Rd | 10
psych-1.5.1/psych/man/describe.Rd | 10
psych-1.5.1/psych/man/diagram.Rd | 2
psych-1.5.1/psych/man/draw.tetra.Rd | 10
psych-1.5.1/psych/man/error.circles.Rd | 6
psych-1.5.1/psych/man/fa.Rd | 31 +-
psych-1.5.1/psych/man/fa.parallel.Rd | 11
psych-1.5.1/psych/man/glb.algebraic.Rd | 19 -
psych-1.5.1/psych/man/mediate.Rd |only
psych-1.5.1/psych/man/omega.Rd | 10
psych-1.5.1/psych/man/pairs.panels.Rd | 5
psych-1.5.1/psych/man/phi.Rd | 2
psych-1.5.1/psych/man/phi2poly.Rd | 2
psych-1.5.1/psych/man/schmid.Rd | 3
psych-1.5.1/psych/man/set.cor.Rd | 33 +-
psych-1.5.1/psych/man/sim.item.Rd | 8
psych-1.5.1/psych/man/simulation.circ.Rd | 13 -
psych-1.5.1/psych/man/test.psych.Rd | 19 +
psych-1.5.1/psych/man/tetrachor.Rd | 10
psych-1.5.1/psych/man/withinBetween.Rd | 1
psych-1.5.1/psych/vignettes/overview.Rnw | 111 +++++++-
psych-1.5.1/psych/vignettes/psych_for_sem.Rnw | 4
101 files changed, 1806 insertions(+), 999 deletions(-)
Title: Online Principal Component Analysis
Diff between onlinePCA versions 1.0 dated 2014-12-26 and 1.0-1 dated 2015-01-21
Description: Online PCA for multivariate and functional data using perturbation, incremental, and stochastic gradient methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras
DESCRIPTION | 11 ++++++-----
MD5 | 25 +++++++++++++------------
NEWS |only
R/incRpca.R | 10 ++++------
R/perturbationRpca.R | 7 +++----
R/secularRpca.R | 8 ++++----
R/sgapca.R | 8 ++++----
R/snlpca.R | 8 ++++----
man/incRpca.Rd | 1 +
man/onlinePCA-package.Rd | 5 +++--
man/perturbationRpca.Rd | 6 ++++--
man/secularRpca.Rd | 5 ++++-
man/sgapca.Rd | 7 +++++--
man/snlpca.Rd | 5 ++++-
14 files changed, 59 insertions(+), 47 deletions(-)
Title: Methods that Apply to Rows and Columns of a Matrix
Diff between matrixStats versions 0.12.2 dated 2014-12-07 and 0.13.0 dated 2015-01-21
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson
matrixStats-0.12.2/matrixStats/R/anyMissing.R |only
matrixStats-0.12.2/matrixStats/R/madDiff.R |only
matrixStats-0.12.2/matrixStats/R/rowMedians.R |only
matrixStats-0.12.2/matrixStats/R/rowWeightedMeans.matrix.R |only
matrixStats-0.12.2/matrixStats/R/rowWeightedMedians.matrix.R |only
matrixStats-0.12.2/matrixStats/R/sdDiff.R |only
matrixStats-0.12.2/matrixStats/man/rowAvgsPerColSet.matrix.Rd |only
matrixStats-0.12.2/matrixStats/man/rowWeightedMeans.matrix.Rd |only
matrixStats-0.12.2/matrixStats/man/rowWeightedMedians.matrix.Rd |only
matrixStats-0.12.2/matrixStats/tests/sdDiff.R |only
matrixStats-0.13.0/matrixStats/DESCRIPTION | 15
matrixStats-0.13.0/matrixStats/MD5 | 193 ++++---
matrixStats-0.13.0/matrixStats/NAMESPACE | 58 --
matrixStats-0.13.0/matrixStats/NEWS | 67 ++
matrixStats-0.13.0/matrixStats/R/999.package.R | 21
matrixStats-0.13.0/matrixStats/R/anyMissing.S4.R |only
matrixStats-0.13.0/matrixStats/R/benchmark.R | 2
matrixStats-0.13.0/matrixStats/R/binCounts.R | 15
matrixStats-0.13.0/matrixStats/R/binMeans.R | 15
matrixStats-0.13.0/matrixStats/R/diff2.R |only
matrixStats-0.13.0/matrixStats/R/rowAvgsPerColSet.R | 15
matrixStats-0.13.0/matrixStats/R/rowCollapse.R | 16
matrixStats-0.13.0/matrixStats/R/rowCounts.R | 155 ++++--
matrixStats-0.13.0/matrixStats/R/rowDiffs.R | 25
matrixStats-0.13.0/matrixStats/R/rowIQRs.R | 49 +
matrixStats-0.13.0/matrixStats/R/rowMedians.S4.R |only
matrixStats-0.13.0/matrixStats/R/rowOrderStats.R | 20
matrixStats-0.13.0/matrixStats/R/rowQuantiles.R | 54 +-
matrixStats-0.13.0/matrixStats/R/rowRanges.R | 20
matrixStats-0.13.0/matrixStats/R/rowRanks.R | 20
matrixStats-0.13.0/matrixStats/R/rowTabulates.R | 28 -
matrixStats-0.13.0/matrixStats/R/rowVars.R | 10
matrixStats-0.13.0/matrixStats/R/rowWeightedMeans.R |only
matrixStats-0.13.0/matrixStats/R/rowWeightedMedians.R |only
matrixStats-0.13.0/matrixStats/R/varDiff.R | 257 +++++++++-
matrixStats-0.13.0/matrixStats/R/weightedMad.R | 22
matrixStats-0.13.0/matrixStats/R/weightedMean.R |only
matrixStats-0.13.0/matrixStats/R/weightedMedian.R | 81 ++-
matrixStats-0.13.0/matrixStats/R/weightedVar.R | 42 +
matrixStats-0.13.0/matrixStats/R/zzz.R | 4
matrixStats-0.13.0/matrixStats/build |only
matrixStats-0.13.0/matrixStats/inst/benchmarking/colRowAnyMissings.md.rsp | 32 -
matrixStats-0.13.0/matrixStats/inst/benchmarking/colRowDiffs.md.rsp | 17
matrixStats-0.13.0/matrixStats/inst/benchmarking/colRowOrderStats.md.rsp | 8
matrixStats-0.13.0/matrixStats/inst/benchmarking/colRowVars.md.rsp | 22
matrixStats-0.13.0/matrixStats/inst/benchmarking/count.md.rsp |only
matrixStats-0.13.0/matrixStats/inst/benchmarking/includes/setup.md.rsp | 20
matrixStats-0.13.0/matrixStats/inst/benchmarking/index.md.rsp | 2
matrixStats-0.13.0/matrixStats/inst/benchmarking/indexByRow.md.rsp | 64 +-
matrixStats-0.13.0/matrixStats/inst/benchmarking/weightedMean.md.rsp |only
matrixStats-0.13.0/matrixStats/inst/benchmarking/weightedMedian.md.rsp | 34 -
matrixStats-0.13.0/matrixStats/inst/doc |only
matrixStats-0.13.0/matrixStats/man/anyMissing.Rd | 16
matrixStats-0.13.0/matrixStats/man/binCounts.Rd | 4
matrixStats-0.13.0/matrixStats/man/binMeans.Rd | 4
matrixStats-0.13.0/matrixStats/man/diff2.Rd |only
matrixStats-0.13.0/matrixStats/man/matrixStats-package.Rd | 25
matrixStats-0.13.0/matrixStats/man/rowAvgsPerColSet.Rd |only
matrixStats-0.13.0/matrixStats/man/rowCollapse.Rd | 6
matrixStats-0.13.0/matrixStats/man/rowCounts.Rd | 22
matrixStats-0.13.0/matrixStats/man/rowDiffs.Rd | 8
matrixStats-0.13.0/matrixStats/man/rowIQRs.Rd | 13
matrixStats-0.13.0/matrixStats/man/rowMedians.Rd | 2
matrixStats-0.13.0/matrixStats/man/rowOrderStats.Rd | 2
matrixStats-0.13.0/matrixStats/man/rowRanges.Rd | 6
matrixStats-0.13.0/matrixStats/man/rowRanks.Rd | 2
matrixStats-0.13.0/matrixStats/man/rowTabulates.Rd | 6
matrixStats-0.13.0/matrixStats/man/rowWeightedMeans.Rd |only
matrixStats-0.13.0/matrixStats/man/rowWeightedMedians.Rd |only
matrixStats-0.13.0/matrixStats/man/varDiff.Rd | 59 +-
matrixStats-0.13.0/matrixStats/man/weightedMad.Rd | 6
matrixStats-0.13.0/matrixStats/man/weightedMean.Rd |only
matrixStats-0.13.0/matrixStats/man/weightedMedian.Rd | 49 -
matrixStats-0.13.0/matrixStats/man/weightedVar.Rd | 18
matrixStats-0.13.0/matrixStats/src/allocMatrix2.c | 10
matrixStats-0.13.0/matrixStats/src/anyMissing.c | 17
matrixStats-0.13.0/matrixStats/src/colCounts.c | 58 +-
matrixStats-0.13.0/matrixStats/src/colCounts_TYPE-template.h | 145 ++++-
matrixStats-0.13.0/matrixStats/src/diff2.c |only
matrixStats-0.13.0/matrixStats/src/diff2_TYPE-template.h |only
matrixStats-0.13.0/matrixStats/src/indexByRow.c | 2
matrixStats-0.13.0/matrixStats/src/meanOver.c | 2
matrixStats-0.13.0/matrixStats/src/meanOver_TYPE-template.h | 10
matrixStats-0.13.0/matrixStats/src/productExpSumLog_TYPE-template.h | 4
matrixStats-0.13.0/matrixStats/src/rowCounts.c | 13
matrixStats-0.13.0/matrixStats/src/rowCounts_TYPE-template.h | 147 ++++-
matrixStats-0.13.0/matrixStats/src/rowDiffs.c |only
matrixStats-0.13.0/matrixStats/src/rowDiffs_TYPE-template.h |only
matrixStats-0.13.0/matrixStats/src/sumOver.c | 2
matrixStats-0.13.0/matrixStats/src/sumOver_TYPE-template.h | 2
matrixStats-0.13.0/matrixStats/src/utils.h | 6
matrixStats-0.13.0/matrixStats/src/weightedMean.c |only
matrixStats-0.13.0/matrixStats/src/weightedMean_TYPE-template.h |only
matrixStats-0.13.0/matrixStats/src/weightedMedian.c |only
matrixStats-0.13.0/matrixStats/src/weightedMedian_TYPE-template.h |only
matrixStats-0.13.0/matrixStats/tests/anyMissing.R | 7
matrixStats-0.13.0/matrixStats/tests/binCounts.R | 16
matrixStats-0.13.0/matrixStats/tests/binMeans,binCounts.R | 35 +
matrixStats-0.13.0/matrixStats/tests/count.R |only
matrixStats-0.13.0/matrixStats/tests/diff2.R |only
matrixStats-0.13.0/matrixStats/tests/meanOver.R | 19
matrixStats-0.13.0/matrixStats/tests/rowAllAnys.R |only
matrixStats-0.13.0/matrixStats/tests/rowAvgsPerColSet.R |only
matrixStats-0.13.0/matrixStats/tests/rowCounts.R | 135 ++---
matrixStats-0.13.0/matrixStats/tests/rowDiffs.R | 72 +-
matrixStats-0.13.0/matrixStats/tests/rowIQRs.R |only
matrixStats-0.13.0/matrixStats/tests/rowMads.R | 19
matrixStats-0.13.0/matrixStats/tests/rowProds.R | 92 ++-
matrixStats-0.13.0/matrixStats/tests/rowQuantiles.R | 11
matrixStats-0.13.0/matrixStats/tests/rowSds.R | 36 +
matrixStats-0.13.0/matrixStats/tests/rowTabulates.R | 11
matrixStats-0.13.0/matrixStats/tests/rowVarDiffs.R |only
matrixStats-0.13.0/matrixStats/tests/rowVars.R | 29 +
matrixStats-0.13.0/matrixStats/tests/sumOver.R | 19
matrixStats-0.13.0/matrixStats/tests/varDiff_etal.R |only
matrixStats-0.13.0/matrixStats/tests/weightedMean.R |only
matrixStats-0.13.0/matrixStats/tests/weightedMedian.R |only
matrixStats-0.13.0/matrixStats/tests/weightedVar_etal.R |only
matrixStats-0.13.0/matrixStats/vignettes |only
119 files changed, 1774 insertions(+), 796 deletions(-)
Title: Distributed Gaussian Process Calculations
Diff between bigGP versions 0.1-4 dated 2014-12-06 and 0.1-5 dated 2015-01-21
Description: Distributes Gaussian process calculations across nodes
in a distributed memory setting, using Rmpi. The bigGP class
provides high-level methods for maximum likelihood with normal data,
prediction, calculation of uncertainty (i.e., posterior covariance
calculations), and simulation of realizations. In addition, bigGP
provides an API for basic matrix calculations with distributed
covariance matrices, including Cholesky decomposition, back/forwardsolve,
crossproduct, and matrix multiplication.
Author: Christopher Paciorek [aut, cre],
Benjamin Lipshitz [aut],
Prabhat [ctb],
Cari Kaufman [ctb],
Tina Zhuo [ctb],
Rollin Thomas [ctb]
Maintainer: Christopher Paciorek
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 4 ++++
data/SN2011fe.rda |binary
inst/CITATION | 39 +++++++++++++++++++++++----------------
man/bigGP.Rd | 3 +--
man/krigeProblem-class.Rd | 7 +++----
7 files changed, 41 insertions(+), 32 deletions(-)
Title: Various plotting functions
Diff between plotrix versions 3.5-10 dated 2014-11-09 and 3.5-11 dated 2015-01-20
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
NEWS | 4 ++++
3 files changed, 11 insertions(+), 7 deletions(-)
Title: Functions for Optimal Non-bipartite Matching
Diff between nbpMatching versions 1.4.0 dated 2013-04-17 and 1.4.4 dated 2015-01-20
Description: This package provides functions for performing nonbipartite
matching and matched randomization. A "bipartite" matching utilizes two
separate groups, e.g. smokers being matched to nonsmokers or cases being
matched to controls. A "nonbipartite" matching creates mates from one big
group, e.g. 100 hospitals being randomized for a two-arm cluster randomized
trial or 5000 children who have been exposed to various levels of
secondhand smoke and are being paired to form a greater exposure vs. lesser
exposure comparison. At the core of a nonbipartite matching is a NxN
distance matrix for N potential mates. The distance between two units
expresses a measure of similarity or quality as mates (the lower the
better). The 'gendistance()' and 'distancematrix()' functions assist in
creating this. The 'nonbimatch()' function creates the matching that
minimizes the total sum of distances between mates; hence, it is referred
to as an "optimal" matching. The 'assign.grp()' function aids in performing
a matched randomization. Note the package can also perform bipartite
matching using the prevent option in 'gendistance()'.
Author: Cole Beck [aut, cre], Bo Lu [aut], Robert Greevy [aut]
Maintainer: Cole Beck
DESCRIPTION | 39 +
MD5 | 55 +-
NAMESPACE | 24 -
R/assign.grp.R | 38 +
R/distancematrix.R | 69 ++-
R/fill.missing.R | 36 +
R/gendistance.R | 174 ++++++-
R/make.phantoms.R | 38 +
R/nbpmatching-package.R |only
R/nonbimatch.R | 75 ++-
R/qom.R | 70 ++-
R/quantile.R | 24 -
R/utils.R | 45 +
man/assign.grp.Rd | 49 --
man/distancematrix.Rd | 89 ++-
man/fill.missing.Rd | 66 +-
man/gendistance.Rd | 143 +++---
man/get.sets.Rd | 45 -
man/make.phantoms.Rd | 66 +-
man/nbpMatching-internal.Rd | 19
man/nbpMatching-package.Rd | 55 +-
man/nonbimatch.Rd | 67 +-
man/qom.Rd | 90 ++-
man/quantile.Rd | 43 -
man/scalar.dist.Rd | 36 -
src/fcorematch.f | 1003 +++++++++++++++++++++-----------------------
src/mwrap.f | 2
tests |only
28 files changed, 1462 insertions(+), 998 deletions(-)
Title: Various Options and Add-ins for Lattice
Diff between loa versions 0.2.21 dated 2015-01-13 and 0.2.22 dated 2015-01-20
Description: This package, Lattice Options and Add-ins (or loa), contains various plots and
functions that make use of the lattice/trellis plotting framework. The plots (which include
loaPlot, GoogleMap and trianglePlot) use panelPal, a function that extends lattice and hexbin
package methods to automate plot subscripting and panel-to-panel and panel-to key
synchronization/management. See ?loa for further details.
Author: Karl Ropkins
Maintainer: Karl Ropkins
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
inst/CITATION | 16 +++++++++-------
man/loa-package.Rd | 4 ++--
4 files changed, 21 insertions(+), 19 deletions(-)
Title: Modeling and Inferring Gene Networks
Diff between GeneNet versions 1.2.11 dated 2014-11-16 and 1.2.12 dated 2015-01-20
Description: GeneNet is a package for analyzing gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 6 ++++++
man/ggm.make.igraph.Rd | 2 +-
4 files changed, 14 insertions(+), 8 deletions(-)
Title: Sequential Event Interval Analysis
Diff between eventInterval versions 1.0-1 dated 2014-01-17 and 1.2 dated 2015-01-20
Description: Functions for analysis of rate changes in sequential events
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +++++++-------
MD5 | 10 +++++-----
NEWS | 4 ++++
R/EIglm.R | 12 +++++-------
man/EIglm.Rd | 23 ++++++++++++++++++++---
man/eventInterval-package.Rd | 7 ++++---
6 files changed, 45 insertions(+), 25 deletions(-)
Title: Predicting Causal Direction from Dependency Features
Diff between D2C versions 1.1 dated 2014-12-16 and 1.2.1 dated 2015-01-20
Description: The relationship between statistical dependency and causality lies
at the heart of all statistical approaches to causal inference. The D2C
package implements a supervised machine learning approach to infer the
existence of a directed causal link between two variables in multivariate
settings with n>2 variables. The approach relies on the asymmetry of some
conditional (in)dependence relations between the members of the Markov
blankets of two variables causally connected. The D2C algorithm predicts
the existence of a direct causal link between two variables in a
multivariate setting by (i) creating a set of of features of the
relationship based on asymmetric descriptors of the multivariate dependency
and (ii) using a classifier to learn a mapping between the features and the
presence of a causal link
Author: Gianluca Bontempi, Catharina Olsen, Maxime Flauder
Maintainer: Catharina Olsen
D2C-1.1/D2C/CHANGES |only
D2C-1.1/D2C/R/D2c.Data.R |only
D2C-1.1/D2C/R/D2c.network.R |only
D2C-1.1/D2C/man/D2C.descriptor-class.Rd |only
D2C-1.2.1/D2C/DESCRIPTION | 12 +--
D2C-1.2.1/D2C/MD5 | 39 ++++++----
D2C-1.2.1/D2C/NAMESPACE | 24 +++++-
D2C-1.2.1/D2C/R/classes.R |only
D2C-1.2.1/D2C/R/d2c.R | 45 ++---------
D2C-1.2.1/D2C/R/util.R | 68 +++++++++++++++++-
D2C-1.2.1/D2C/build |only
D2C-1.2.1/D2C/data/alarm.RData |only
D2C-1.2.1/D2C/data/datalist | 2
D2C-1.2.1/D2C/inst |only
D2C-1.2.1/D2C/man/BER.Rd |only
D2C-1.2.1/D2C/man/alarm.Rd |only
D2C-1.2.1/D2C/man/dataset.Rd |only
D2C-1.2.1/D2C/man/example.Rd | 6 +
D2C-1.2.1/D2C/man/initialize-D2C-method.Rd | 5 +
D2C-1.2.1/D2C/man/initialize-D2C.descriptor-method.Rd | 1
D2C-1.2.1/D2C/man/initialize-DAG.network-method.Rd | 2
D2C-1.2.1/D2C/man/initialize-simulatedDAG-method.Rd | 10 ++
D2C-1.2.1/D2C/man/predict-D2C-method.Rd | 1
D2C-1.2.1/D2C/man/true.net.Rd |only
D2C-1.2.1/D2C/man/update-simulatedDAG-method.Rd |only
D2C-1.2.1/D2C/man/updateD2C-D2C-method.Rd |only
D2C-1.2.1/D2C/vignettes |only
27 files changed, 148 insertions(+), 67 deletions(-)
Title: Completing Ranks
Diff between crank versions 1.0-6 dated 2014-11-09 and 1.0-7 dated 2015-01-20
Description: Functions for completing and recalculating rankings.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +++++++-------
MD5 | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
Title: Baseline Correction of Spectra
Diff between baseline versions 1.1-3 dated 2014-02-21 and 1.1-4 dated 2015-01-20
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 14
MD5 | 52 +-
R/baseline.fillPeaks.R | 162 +++-----
R/baseline.rfbaseline.R | 34 -
R/baselineGUI.R | 566 ++++++++++++++--------------
R/globals.R | 7
R/optimWizard.R | 796 ++++++++++++++++++++--------------------
R/optimisation.R | 826 ++++++++++++++++++++++--------------------
R/plotBaseline.R | 232 ++++++-----
R/plotOptim.R | 730 ++++++++++++++++++-------------------
man/baseline-package.Rd | 8
man/baseline.Rd | 4
man/baseline.als.Rd | 2
man/baseline.fillPeaks.Rd | 6
man/baseline.irls.Rd | 4
man/baseline.lowpass.Rd | 4
man/baseline.medianWindow.Rd | 4
man/baseline.modpolyfit.Rd | 4
man/baseline.peakDetection.Rd | 4
man/baseline.rfbaseline.Rd | 4
man/baseline.rollingBall.Rd | 4
man/baselineGUI.Rd | 8
man/custom.baseline.Rd | 2
man/doOptim.Rd | 1
man/milk.Rd | 2
man/optimWizard.Rd | 3
man/plotBaseline.Rd | 3
27 files changed, 1813 insertions(+), 1673 deletions(-)
Title: Random Forest for SNPs to Prevent X-chromosome SNP Importance
Bias
Diff between snpRF versions 0.3 dated 2014-12-31 and 0.4 dated 2015-01-20
Description: A modification of Breiman and Cutler's classification random forests modified for SNP (Single Nucleotide Polymorphism) data (based on randomForest v4.6-7) to prevent X-chromosome SNP variable importance bias compared to autosomal SNPs by simulating the process of X chromosome inactivation. Classification is based on a forest of trees using random subsets of SNPs and other variables as inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew
Wiener. Modifications of randomForest v 4.6-7 for SNPs by Greg Jenkins based on a
method developed by Stacey Winham, Greg Jenkins and Joanna Biernacka.
Maintainer: Greg Jenkins
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/MDSplot.R | 2 +-
R/margin.R | 7 ++++---
R/predict.snpRF.R | 2 +-
5 files changed, 14 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-09 1.0.7
2014-09-16 1.0.6
2014-06-29 1.0.5
2014-05-15 1.0.3
2014-03-20 1.0.2
2014-02-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 1.7.6
2014-09-19 1.7.5
2014-09-16 1.7.4
2014-06-30 1.7.3
2014-05-16 1.7.2
2014-03-20 1.7.1
2014-02-21 1.7.0
Title: Pretty Descriptive Stats
Diff between prettyR versions 2.0-8 dated 2014-05-25 and 2.1 dated 2015-01-20
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +--
MD5 | 25 +++--
NAMESPACE | 1
NEWS | 8 +
R/brkdn.R | 13 +--
R/describe.R | 203 +++++++++++++++++-------------------------------
R/print.xtab.R | 23 ++---
man/Mode.Rd | 15 +--
man/brkdn.Rd | 4
man/describe.Rd | 39 ++++-----
man/describe.factor.Rd | 15 ---
man/describe.logical.Rd | 8 -
man/describe.numeric.Rd | 8 -
man/print.desc.Rd |only
14 files changed, 157 insertions(+), 219 deletions(-)
Title: Tools for Descriptive Statistics
Diff between DescTools versions 0.99.8.1 dated 2014-09-22 and 0.99.9 dated 2015-01-20
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains as well functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Yongyi Min, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell
DescTools-0.99.8.1/DescTools/R/AreaIdent.R |only
DescTools-0.99.8.1/DescTools/R/DescFactFact.R |only
DescTools-0.99.8.1/DescTools/R/Explore.R |only
DescTools-0.99.8.1/DescTools/R/FormatFix.R |only
DescTools-0.99.8.1/DescTools/R/FormatSig.R |only
DescTools-0.99.8.1/DescTools/R/Kappam.R |only
DescTools-0.99.8.1/DescTools/R/Min.R |only
DescTools-0.99.8.1/DescTools/R/Mround.R |only
DescTools-0.99.8.1/DescTools/R/Sec.R |only
DescTools-0.99.8.1/DescTools/R/WhichCharacters.R |only
DescTools-0.99.8.1/DescTools/R/WhichFactors.R |only
DescTools-0.99.8.1/DescTools/R/WhichFlags.R |only
DescTools-0.99.8.1/DescTools/R/WhichNumerics.R |only
DescTools-0.99.8.1/DescTools/data/d.world.rda |only
DescTools-0.99.8.1/DescTools/man/Explore.Rd |only
DescTools-0.99.8.1/DescTools/man/FormatFix.Rd |only
DescTools-0.99.8.1/DescTools/man/FormatSig.Rd |only
DescTools-0.99.8.1/DescTools/man/Mround.Rd |only
DescTools-0.99.8.1/DescTools/man/PwApply.Rd |only
DescTools-0.99.8.1/DescTools/man/WhichFlags.Rd |only
DescTools-0.99.8.1/DescTools/man/XLGetWorkbook.Rd |only
DescTools-0.99.8.1/DescTools/man/d.world.Rd |only
DescTools-0.99.9/DescTools/DESCRIPTION | 19
DescTools-0.99.9/DescTools/MD5 | 544 +++++++------
DescTools-0.99.9/DescTools/NAMESPACE | 2
DescTools-0.99.9/DescTools/NEWS | 101 ++
DescTools-0.99.9/DescTools/R/AddMonths.R | 47 -
DescTools-0.99.9/DescTools/R/Agree.R |only
DescTools-0.99.9/DescTools/R/AscToChar.R | 1
DescTools-0.99.9/DescTools/R/Assocs.R | 53 -
DescTools-0.99.9/DescTools/R/BinomCI.R | 244 +++--
DescTools-0.99.9/DescTools/R/BinomDiffCI.R | 4
DescTools-0.99.9/DescTools/R/BinomRatioCI.R |only
DescTools-0.99.9/DescTools/R/BubbleLegend.R |only
DescTools-0.99.9/DescTools/R/CCC.R |only
DescTools-0.99.9/DescTools/R/CartToPol.R | 2
DescTools-0.99.9/DescTools/R/CartToSph.R |only
DescTools-0.99.9/DescTools/R/CharToAsc.R | 6
DescTools-0.99.9/DescTools/R/Closest.R | 28
DescTools-0.99.9/DescTools/R/CoefVar.R |only
DescTools-0.99.9/DescTools/R/CohenD.R |only
DescTools-0.99.9/DescTools/R/CohenKappa.R | 3
DescTools-0.99.9/DescTools/R/CollapseTable.R |only
DescTools-0.99.9/DescTools/R/ConDisPairs.R | 2
DescTools-0.99.9/DescTools/R/CorCI.R | 26
DescTools-0.99.9/DescTools/R/CramerV.R | 6
DescTools-0.99.9/DescTools/R/CronbachAlpha.R | 6
DescTools-0.99.9/DescTools/R/CutQ.R | 14
DescTools-0.99.9/DescTools/R/DenseRank.R |only
DescTools-0.99.9/DescTools/R/Desc.character.R | 3
DescTools-0.99.9/DescTools/R/Desc.data.frame.R | 23
DescTools-0.99.9/DescTools/R/Desc.factor.R | 10
DescTools-0.99.9/DescTools/R/Desc.flags.R | 5
DescTools-0.99.9/DescTools/R/Desc.formula.R | 15
DescTools-0.99.9/DescTools/R/Desc.integer.R | 5
DescTools-0.99.9/DescTools/R/Desc.list.R | 26
DescTools-0.99.9/DescTools/R/Desc.ordered.R | 8
DescTools-0.99.9/DescTools/R/Desc.table.R | 174 ++--
DescTools-0.99.9/DescTools/R/DescFactNum.R | 4
DescTools-0.99.9/DescTools/R/DescTools-internal.R | 424 +++++++---
DescTools-0.99.9/DescTools/R/DescToolsOptions.R | 40
DescTools-0.99.9/DescTools/R/DescWrd.data.frame.R | 15
DescTools-0.99.9/DescTools/R/DescWrd.default.R | 5
DescTools-0.99.9/DescTools/R/DescWrd.list.R |only
DescTools-0.99.9/DescTools/R/DunnTest.R |only
DescTools-0.99.9/DescTools/R/DunnTest.default.R |only
DescTools-0.99.9/DescTools/R/DunnTest.formula.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.default.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.formula.R |only
DescTools-0.99.9/DescTools/R/EtaSq.R | 123 --
DescTools-0.99.9/DescTools/R/EtaSq.aovlist.R |only
DescTools-0.99.9/DescTools/R/EtaSq.lm.R |only
DescTools-0.99.9/DescTools/R/Exec.R |only
DescTools-0.99.9/DescTools/R/FctArgs.R | 3
DescTools-0.99.9/DescTools/R/Fibonacci.R | 32
DescTools-0.99.9/DescTools/R/FindCorr.R |only
DescTools-0.99.9/DescTools/R/Flags.R | 2
DescTools-0.99.9/DescTools/R/Format.R |only
DescTools-0.99.9/DescTools/R/Format.default.R |only
DescTools-0.99.9/DescTools/R/Format.matrix.R |only
DescTools-0.99.9/DescTools/R/Freq.R | 11
DescTools-0.99.9/DescTools/R/GetCurrPP.R | 27
DescTools-0.99.9/DescTools/R/GetCurrWrd.R | 32
DescTools-0.99.9/DescTools/R/GetCurrXL.R | 17
DescTools-0.99.9/DescTools/R/GetNewPP.R | 33
DescTools-0.99.9/DescTools/R/GetNewWrd.R | 48 -
DescTools-0.99.9/DescTools/R/GetNewXL.R | 25
DescTools-0.99.9/DescTools/R/HmsToSec.R | 16
DescTools-0.99.9/DescTools/R/HodgesLehmann.R | 50 +
DescTools-0.99.9/DescTools/R/Hour.R | 3
DescTools-0.99.9/DescTools/R/HuberM.R | 33
DescTools-0.99.9/DescTools/R/ICC.R | 227 ++---
DescTools-0.99.9/DescTools/R/IdentifyA.R |only
DescTools-0.99.9/DescTools/R/ImportDlg.R | 4
DescTools-0.99.9/DescTools/R/Impute.R |only
DescTools-0.99.9/DescTools/R/Interval.R | 21
DescTools-0.99.9/DescTools/R/IsNumeric.R |only
DescTools-0.99.9/DescTools/R/IsPrime.R | 2
DescTools-0.99.9/DescTools/R/IsWhole.R | 2
DescTools-0.99.9/DescTools/R/IsZero.R |only
DescTools-0.99.9/DescTools/R/JarqueBeraTest.R | 10
DescTools-0.99.9/DescTools/R/KappaM.R |only
DescTools-0.99.9/DescTools/R/KendallW.R | 109 +-
DescTools-0.99.9/DescTools/R/Kurt.R | 38
DescTools-0.99.9/DescTools/R/LOCF.default.R | 2
DescTools-0.99.9/DescTools/R/Large.R | 2
DescTools-0.99.9/DescTools/R/LastDayOfMonth.R |only
DescTools-0.99.9/DescTools/R/Lc.R | 26
DescTools-0.99.9/DescTools/R/Lc.default.R |only
DescTools-0.99.9/DescTools/R/Lc.formula.R |only
DescTools-0.99.9/DescTools/R/MeanCI.R | 79 +
DescTools-0.99.9/DescTools/R/MeanSE.R | 5
DescTools-0.99.9/DescTools/R/Midx.R | 4
DescTools-0.99.9/DescTools/R/Minute.R |only
DescTools-0.99.9/DescTools/R/OddsRatio.R | 22
DescTools-0.99.9/DescTools/R/Outlier.R | 7
DescTools-0.99.9/DescTools/R/Overlap.R |only
DescTools-0.99.9/DescTools/R/PairApply.R | 2
DescTools-0.99.9/DescTools/R/PalDescTools.R | 36
DescTools-0.99.9/DescTools/R/PartitionBy.R |only
DescTools-0.99.9/DescTools/R/PasswordDlg.R | 2
DescTools-0.99.9/DescTools/R/PlotBubble.R | 15
DescTools-0.99.9/DescTools/R/PlotBubble.default.R |only
DescTools-0.99.9/DescTools/R/PlotBubble.formula.R |only
DescTools-0.99.9/DescTools/R/PlotCirc.R | 24
DescTools-0.99.9/DescTools/R/PlotCorr.R | 4
DescTools-0.99.9/DescTools/R/PlotDesc.default.R | 2
DescTools-0.99.9/DescTools/R/PlotDesc.factor.R | 15
DescTools-0.99.9/DescTools/R/PlotDesc.integer.R | 2
DescTools-0.99.9/DescTools/R/PlotDesc.ordered.R | 10
DescTools-0.99.9/DescTools/R/PlotDesc.table.R | 46 -
DescTools-0.99.9/DescTools/R/PlotDescFactNum.R | 4
DescTools-0.99.9/DescTools/R/PlotFct.R | 6
DescTools-0.99.9/DescTools/R/PlotPar.R | 5
DescTools-0.99.9/DescTools/R/PlotPyramid.R | 5
DescTools-0.99.9/DescTools/R/PlotRCol.R | 5
DescTools-0.99.9/DescTools/R/PlotTernary.R |only
DescTools-0.99.9/DescTools/R/PlotVenn.R | 122 +-
DescTools-0.99.9/DescTools/R/PlotWeb.R | 8
DescTools-0.99.9/DescTools/R/PolToCart.R | 2
DescTools-0.99.9/DescTools/R/PolarGrid.R | 2
DescTools-0.99.9/DescTools/R/PostHocTest.aov.R | 31
DescTools-0.99.9/DescTools/R/PostHocTest.matrix.R |only
DescTools-0.99.9/DescTools/R/PostHocTest.table.R |only
DescTools-0.99.9/DescTools/R/Prec.R |only
DescTools-0.99.9/DescTools/R/Quarter.R | 2
DescTools-0.99.9/DescTools/R/Ray.R | 42 -
DescTools-0.99.9/DescTools/R/RndPairs.R |only
DescTools-0.99.9/DescTools/R/RoundM.R |only
DescTools-0.99.9/DescTools/R/ScheffeTest.aov.R | 1
DescTools-0.99.9/DescTools/R/SecToHms.R | 24
DescTools-0.99.9/DescTools/R/Second.R |only
DescTools-0.99.9/DescTools/R/SelectVarDlg.data.frame.R | 4
DescTools-0.99.9/DescTools/R/SelectVarDlg.default.R | 3
DescTools-0.99.9/DescTools/R/Skew.R | 41
DescTools-0.99.9/DescTools/R/Small.R | 2
DescTools-0.99.9/DescTools/R/Sort.data.frame.R | 4
DescTools-0.99.9/DescTools/R/SphToCart.R |only
DescTools-0.99.9/DescTools/R/Stamp.R |only
DescTools-0.99.9/DescTools/R/Str.R | 2
DescTools-0.99.9/DescTools/R/StrLeft.R |only
DescTools-0.99.9/DescTools/R/StrPad.R | 17
DescTools-0.99.9/DescTools/R/StrRight.R |only
DescTools-0.99.9/DescTools/R/StrVal.R | 14
DescTools-0.99.9/DescTools/R/SysInfo.R | 1
DescTools-0.99.9/DescTools/R/TheilU.R | 4
DescTools-0.99.9/DescTools/R/Trim.R | 14
DescTools-0.99.9/DescTools/R/TukeyBiweight.R | 21
DescTools-0.99.9/DescTools/R/Untable.R | 41
DescTools-0.99.9/DescTools/R/Untable.data.frame.R |only
DescTools-0.99.9/DescTools/R/Untable.default.R |only
DescTools-0.99.9/DescTools/R/WrdInsTab.R | 10
DescTools-0.99.9/DescTools/R/WrdKill.R |only
DescTools-0.99.9/DescTools/R/WrdPlot.R | 13
DescTools-0.99.9/DescTools/R/WrdTable.Freq.R | 11
DescTools-0.99.9/DescTools/R/WrdTable.R | 2
DescTools-0.99.9/DescTools/R/WrdTable.default.R | 41
DescTools-0.99.9/DescTools/R/WrdText.R | 31
DescTools-0.99.9/DescTools/R/XLGetRange.R | 17
DescTools-0.99.9/DescTools/R/XLKill.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.default.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.formula.R |only
DescTools-0.99.9/DescTools/R/ZeroIfNA.R |only
DescTools-0.99.9/DescTools/R/Zodiac.R | 2
DescTools-0.99.9/DescTools/R/aovlDetails.R |only
DescTools-0.99.9/DescTools/R/aovlErrorTerms.R |only
DescTools-0.99.9/DescTools/R/createCOMReference.R |only
DescTools-0.99.9/DescTools/R/dBenf.R |only
DescTools-0.99.9/DescTools/R/dRevGumbel.R |only
DescTools-0.99.9/DescTools/R/identify.formula.R | 24
DescTools-0.99.9/DescTools/R/lines.smooth.spline.R |only
DescTools-0.99.9/DescTools/R/pBenf.R |only
DescTools-0.99.9/DescTools/R/pRevGumbel.R |only
DescTools-0.99.9/DescTools/R/plot.Lclist.R |only
DescTools-0.99.9/DescTools/R/print.Assocs.R | 3
DescTools-0.99.9/DescTools/R/print.DunnTest.R |only
DescTools-0.99.9/DescTools/R/print.ICC.R | 6
DescTools-0.99.9/DescTools/R/print.PostHocTest.R | 19
DescTools-0.99.9/DescTools/R/qBenf.R |only
DescTools-0.99.9/DescTools/R/qRevGumbel.R |only
DescTools-0.99.9/DescTools/R/qRevGumbelExp.R |only
DescTools-0.99.9/DescTools/R/rBenf.R |only
DescTools-0.99.9/DescTools/R/rRevGumbel.R |only
DescTools-0.99.9/DescTools/R/z%overlaps%.R | 8
DescTools-0.99.9/DescTools/data/d.countries.rda |only
DescTools-0.99.9/DescTools/data/d.prefix.rda |only
DescTools-0.99.9/DescTools/demo/plots.R | 2
DescTools-0.99.9/DescTools/inst/CITATION |only
DescTools-0.99.9/DescTools/inst/doc/DescTools.pdf |binary
DescTools-0.99.9/DescTools/inst/doc/DescToolsCompanion.pdf |binary
DescTools-0.99.9/DescTools/man/AddMonths.Rd | 8
DescTools-0.99.9/DescTools/man/Agree.Rd |only
DescTools-0.99.9/DescTools/man/AllDuplicated.Rd | 5
DescTools-0.99.9/DescTools/man/AndersonDarlingTest.Rd | 2
DescTools-0.99.9/DescTools/man/AreaIdent.Rd | 10
DescTools-0.99.9/DescTools/man/Assocs.Rd | 5
DescTools-0.99.9/DescTools/man/Benf.Rd |only
DescTools-0.99.9/DescTools/man/Between.Rd | 12
DescTools-0.99.9/DescTools/man/BinomCI.Rd | 24
DescTools-0.99.9/DescTools/man/BinomDiffCI.Rd | 2
DescTools-0.99.9/DescTools/man/BinomRatioCI.rd |only
DescTools-0.99.9/DescTools/man/BoxCoxLambda.Rd | 6
DescTools-0.99.9/DescTools/man/BubbleLegend.Rd |only
DescTools-0.99.9/DescTools/man/CCC.Rd |only
DescTools-0.99.9/DescTools/man/CartToPol.Rd | 23
DescTools-0.99.9/DescTools/man/Closest.Rd | 15
DescTools-0.99.9/DescTools/man/CochranArmitageTest.Rd | 5
DescTools-0.99.9/DescTools/man/CoefVar.Rd |only
DescTools-0.99.9/DescTools/man/CohenD.Rd |only
DescTools-0.99.9/DescTools/man/CohenKappa.Rd | 45 -
DescTools-0.99.9/DescTools/man/CollapseTable.Rd |only
DescTools-0.99.9/DescTools/man/ColorLegend.Rd | 7
DescTools-0.99.9/DescTools/man/ConnLines.Rd | 5
DescTools-0.99.9/DescTools/man/Contrasts.Rd | 17
DescTools-0.99.9/DescTools/man/CramerV.Rd | 20
DescTools-0.99.9/DescTools/man/CronbachAlpha.Rd | 11
DescTools-0.99.9/DescTools/man/CutQ.Rd | 11
DescTools-0.99.9/DescTools/man/DateFunctions.Rd | 27
DescTools-0.99.9/DescTools/man/DenseRank.Rd |only
DescTools-0.99.9/DescTools/man/Desc.Rd | 1
DescTools-0.99.9/DescTools/man/Desc.data.frame.Rd | 10
DescTools-0.99.9/DescTools/man/Desc.flags.Rd | 30
DescTools-0.99.9/DescTools/man/Desc.table.Rd | 10
DescTools-0.99.9/DescTools/man/DescTools-package.Rd | 227 +++--
DescTools-0.99.9/DescTools/man/DescWrd.Rd | 9
DescTools-0.99.9/DescTools/man/DunnTest.Rd |only
DescTools-0.99.9/DescTools/man/DunnettTest.Rd |only
DescTools-0.99.9/DescTools/man/Entropy.Rd | 2
DescTools-0.99.9/DescTools/man/EtaSq.Rd | 81 +
DescTools-0.99.9/DescTools/man/Exec.Rd |only
DescTools-0.99.9/DescTools/man/Fibonacci.Rd | 40
DescTools-0.99.9/DescTools/man/FindCorr.Rd |only
DescTools-0.99.9/DescTools/man/FisherZ.Rd | 48 -
DescTools-0.99.9/DescTools/man/Format.Rd |only
DescTools-0.99.9/DescTools/man/GetNewWrd.Rd | 56 +
DescTools-0.99.9/DescTools/man/GetNewXL.Rd | 12
DescTools-0.99.9/DescTools/man/GetPairs.Rd | 3
DescTools-0.99.9/DescTools/man/GoodmanKruskalTauA.Rd | 5
DescTools-0.99.9/DescTools/man/HmsToSec.Rd | 6
DescTools-0.99.9/DescTools/man/HoeffD.Rd | 9
DescTools-0.99.9/DescTools/man/HotellingsT.Rd | 11
DescTools-0.99.9/DescTools/man/HuberM.Rd | 25
DescTools-0.99.9/DescTools/man/ICC.Rd | 60 -
DescTools-0.99.9/DescTools/man/IsDichotomous.Rd | 2
DescTools-0.99.9/DescTools/man/IsOdd.Rd | 2
DescTools-0.99.9/DescTools/man/IsWhole.Rd | 35
DescTools-0.99.9/DescTools/man/JarqueBeraTest.Rd | 32
DescTools-0.99.9/DescTools/man/Kappam.Rd | 28
DescTools-0.99.9/DescTools/man/KendallW.Rd | 23
DescTools-0.99.9/DescTools/man/KrippAlpha.Rd | 38
DescTools-0.99.9/DescTools/man/Lambda.Rd | 33
DescTools-0.99.9/DescTools/man/Large.Rd | 14
DescTools-0.99.9/DescTools/man/Lc.Rd | 49 -
DescTools-0.99.9/DescTools/man/LogLin.Rd | 20
DescTools-0.99.9/DescTools/man/LogSt.Rd | 2
DescTools-0.99.9/DescTools/man/MHChisqTest.Rd | 4
DescTools-0.99.9/DescTools/man/MeanCI.Rd | 46 -
DescTools-0.99.9/DescTools/man/MeanDiffCI.Rd | 2
DescTools-0.99.9/DescTools/man/MeanSE.Rd | 11
DescTools-0.99.9/DescTools/man/Midx.Rd | 18
DescTools-0.99.9/DescTools/man/MultinomCI.Rd | 18
DescTools-0.99.9/DescTools/man/Ndec.Rd | 3
DescTools-0.99.9/DescTools/man/OddsRatio.Rd | 7
DescTools-0.99.9/DescTools/man/Outlier.Rd | 6
DescTools-0.99.9/DescTools/man/PairApply.Rd |only
DescTools-0.99.9/DescTools/man/PartCor.Rd | 2
DescTools-0.99.9/DescTools/man/PartitionBy.Rd |only
DescTools-0.99.9/DescTools/man/PasswordDlg.Rd | 8
DescTools-0.99.9/DescTools/man/Permn.Rd | 6
DescTools-0.99.9/DescTools/man/PlotBubble.Rd | 43 -
DescTools-0.99.9/DescTools/man/PlotCorr.Rd | 15
DescTools-0.99.9/DescTools/man/PlotDesc.Rd | 10
DescTools-0.99.9/DescTools/man/PlotFdist.Rd | 2
DescTools-0.99.9/DescTools/man/PlotPolar.Rd | 2
DescTools-0.99.9/DescTools/man/PlotTernary.Rd |only
DescTools-0.99.9/DescTools/man/PlotVenn.Rd | 12
DescTools-0.99.9/DescTools/man/PlotWeb.Rd | 24
DescTools-0.99.9/DescTools/man/PostHocTest.Rd | 16
DescTools-0.99.9/DescTools/man/RevGumbel.Rd |only
DescTools-0.99.9/DescTools/man/RndPairs.Rd |only
DescTools-0.99.9/DescTools/man/RoundM.Rd |only
DescTools-0.99.9/DescTools/man/ScheffeTest.Rd | 2
DescTools-0.99.9/DescTools/man/Skew.Rd | 44 -
DescTools-0.99.9/DescTools/man/SomersDelta.Rd | 8
DescTools-0.99.9/DescTools/man/Stamp.Rd |only
DescTools-0.99.9/DescTools/man/StrCountW.Rd | 4
DescTools-0.99.9/DescTools/man/StrPad.Rd | 6
DescTools-0.99.9/DescTools/man/StrRight.Rd |only
DescTools-0.99.9/DescTools/man/StrVal.Rd | 25
DescTools-0.99.9/DescTools/man/StuartTauC.Rd | 6
DescTools-0.99.9/DescTools/man/SysInfo.Rd | 10
DescTools-0.99.9/DescTools/man/TheilU.Rd | 18
DescTools-0.99.9/DescTools/man/Trim.Rd | 14
DescTools-0.99.9/DescTools/man/TukeyBiweight.Rd | 18
DescTools-0.99.9/DescTools/man/UncertCoef.Rd | 2
DescTools-0.99.9/DescTools/man/UnitConv.Rd | 110 +-
DescTools-0.99.9/DescTools/man/Untable.Rd | 19
DescTools-0.99.9/DescTools/man/Winsorize.Rd | 3
DescTools-0.99.9/DescTools/man/WrdInsTab.Rd | 7
DescTools-0.99.9/DescTools/man/WrdPlot.Rd | 5
DescTools-0.99.9/DescTools/man/WrdTable.Rd | 14
DescTools-0.99.9/DescTools/man/WrdText.Rd | 28
DescTools-0.99.9/DescTools/man/XLGetRange.Rd | 42 -
DescTools-0.99.9/DescTools/man/XLView.Rd | 9
DescTools-0.99.9/DescTools/man/YuenTTest.Rd |only
DescTools-0.99.9/DescTools/man/ZeroIfNA.Rd |only
DescTools-0.99.9/DescTools/man/d.countries.Rd |only
DescTools-0.99.9/DescTools/man/d.pizza.Rd | 15
DescTools-0.99.9/DescTools/man/identify.formula.Rd | 16
DescTools-0.99.9/DescTools/man/lines.loess.Rd | 19
DescTools-0.99.9/DescTools/man/overlaps.Rd | 31
333 files changed, 3478 insertions(+), 2089 deletions(-)
Title: Clinical Significance Functions
Diff between clinsig versions 1.0-4 dated 2013-04-14 and 1.0-5 dated 2015-01-20
Description: Functions for calculating clinical significance.
Author: Jim Lemon
Maintainer: Jim Lemon
clinsig-1.0-4/clinsig/INDEX |only
clinsig-1.0-5/clinsig/DESCRIPTION | 14 +++++++-------
clinsig-1.0-5/clinsig/MD5 | 5 ++---
clinsig-1.0-5/clinsig/man/clinsig.Rd | 4 ++--
4 files changed, 11 insertions(+), 12 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Diff between aroma.affymetrix versions 2.12.0 dated 2014-03-09 and 2.13.0 dated 2015-01-20
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the disk space that limits the number of arrays that can be analyzed.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson
31.doASCRMAv2,PairedPSCBS.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/Sc03b_MF_v04 |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/BatchJobs |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-addons.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-replication.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-system.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/DESCRIPTION | 36
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/MD5 | 556
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/NAMESPACE | 31
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/NEWS | 5641 +++++-----
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/021.dynamic_imports.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AdditiveCovariatesNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffinePlm.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 53
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.COUNTS.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 30
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 35
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 34
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.computeAffinities.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleCellPairs.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs2.R | 37
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getCellQuartets.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getProbeSequenceData.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R | 62
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.readDataFrame.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.writeCdfByExcludingCells.R | 32
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.BG.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.PLOT.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.R | 22
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.createFrom.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeAffine.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.BG.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.NORM.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.PLOT.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractAffyBatch.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractFeatureSet.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractMatrix.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.importFromDChip.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.justSNPRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.writeSgr.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSetTuple.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixFileSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixPgfFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AlleleSummation.R | 11
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.PLOT.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AromaCellMatchScoreFile.importFromBpmap.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AromaCellSequenceFile.importFromBpmap.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AvgPlm.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/BaseCountNormalization.R | 11
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/BasePositionNormalization.getFit.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.TOFULL.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.fromDataFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectGroupMerge.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.STATS.R | 50
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.TOFULL.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.extractExpressionSet.R | 48
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.extractTheta.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.xam.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChromosomalModel.getPositionChipTypeUnit.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectFile.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.writeWig.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnPlm.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnProbeAffinityFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnagCfhSet.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CopyNumberChromosomalModel.applyCCF.R | 68
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmModel.EXT.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmModel.R | 26
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmParametersSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipDcpSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipQuantileNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonChipEffectFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonChipEffectSet.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonProbeAffinityFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonRmaPlm.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R | 21
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaFile.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaModel.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaSet.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FragmentEquivalentClassNormalization.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/GcContentNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/GcContentNormalization2.plotCovariateEffects.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/HetLogAddPlm.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/LimmaBackgroundCorrection.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MatNormalization.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MatSmoothing.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MbeiPlm.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MultiArrayUnitModel.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/OpticalBackgroundCorrection.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ParameterCelFile.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ParameterCelSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/QualityAssessmentFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/QualityAssessmentModel.R | 27
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ReseqCrosstalkCalibration.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ResidualFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ResidualSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/RmaBackgroundCorrection.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/RmaPlm.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ScaleNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ScaleNormalization3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SingleArrayUnitModel.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SingleArrayUnitModel.fit.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SmoothMultiarrayModel.fit.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectFile.extractTotalAndFracB.R | 34
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.exportTotalAndFracB.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractAlleleSet.R | 37
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpCnvQSet.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpQSet.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractTotalAndFreqB.R | 36
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpCnvQSet.extractTheta.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpInformation.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpPlm.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpProbeAffinityFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpQSet.extractTheta.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SpatialReporter.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SpatialRowColumnNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/TransformReport.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/UnitModel.fitCnProbes.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/UnitTypeScaleNormalization.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/WeightsFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/WeightsSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/bpmapCluster2Cdf.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/createExonByTranscriptCdf.R | 66
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doCRMAv1.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doCRMAv2.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doFIRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doGCRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/env2Cdf.R | 38
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/fitPlasqUnit.R | 40
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/getPlasqTypes.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/justRMA.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/pdInfo2Cdf.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/profileCGH.writeRegions.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/readCdfGroupStrands.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/readCfnHeader.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/setupExampleData.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/buildScripts/chipTypes/HG-U133A |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R | 30
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,PSCBS.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R | 18
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R | 18
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/11.justSNPRMA_vs_oligo.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R | 107
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R | 120
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R | 99
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/21.MatSmoothing_vs_MAT.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/11.doASCRMAv1,CBS,invalid.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/setup/99a.cleanupRootDirectories.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,singleArray.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,PLM,withPriors.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/01c.installPackages.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,QC.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/12.doASCRMAv1.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,FLN,zero.R | 3
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,QA.R | 107
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ref.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,PSCN.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,extract.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots.R | 1
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,singleArray.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/41.ACC,expectile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/21.doASCRMAv1,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R | 182
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/11.RmaBackgroundCorrection.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/CRMA,Mapping50K_Hind240,BiasCorrectedChrXY.R | 72
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/CRMAv2,Mapping50K_Hind240.R | 167
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-CRLMM |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-GCRMA |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-MAT |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-RMA |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixPgfFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnagCfhFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnagCfhSet.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipDcpFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipDcpSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/FirmaFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/FirmaSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ParameterCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ParameterCelSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ResidualFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ResidualSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/WeightsFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/WeightsSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd | 3
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/justRMA.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/setupExampleData.AromaAffymetrix.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/setupExampleData.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/writeImage.AffymetrixCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/tests |only
282 files changed, 4882 insertions(+), 4572 deletions(-)
Permanent link
Title: A General-Purpose Package for Dynamic Report Generation in R
Diff between knitr versions 1.8 dated 2014-11-11 and 1.9 dated 2015-01-20
Description: This package provides a general-purpose tool for dynamic report
generation in R, which can be used to deal with any type of (plain text)
files, including Sweave, HTML, Markdown, reStructuredText, AsciiDoc, and
Textile. R code is evaluated as if it were copied and pasted in an R
terminal thanks to the evaluate package (e.g., we do not need to explicitly
print() plots from ggplot2 or lattice). R code can be reformatted by the
formatR package so that long lines are automatically wrapped, with indent
and spaces added, and comments preserved. A simple caching mechanism is
provided to cache results from computations for the first time and the
computations will be skipped the next time. Almost all common graphics
devices, including those in base R and add-on packages like Cairo,
cairoDevice and tikzDevice, are built-in with this package and it is
straightforward to switch between devices without writing any special
functions. The width and height as well as alignment of plots in the output
document can be specified in chunk options (the size of plots for graphics
devices is also supported). Multiple plots can be recorded in a single code
chunk, and it is also allowed to rearrange plots to the end of a chunk or
just keep the last plot. Warnings, messages and errors are written in the
output document by default (can be turned off). The large collection of
hooks in this package makes it possible for the user to control almost
everything in the R code input and output. Hooks can be used either to
format the output or to run R code fragments before or after a code chunk.
The language in code chunks is not restricted to R (there is simple support
to Python and shell scripts, etc). Many features are borrowed from or
inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
knitr-1.8/knitr/NEWS |only
knitr-1.9/knitr/DESCRIPTION | 138 +++++++-----
knitr-1.9/knitr/MD5 | 242 +++++++++++-----------
knitr-1.9/knitr/NAMESPACE | 2
knitr-1.9/knitr/R/block.R | 22 +-
knitr-1.9/knitr/R/cache.R | 94 ++++++++
knitr-1.9/knitr/R/citation.R | 5
knitr-1.9/knitr/R/defaults.R | 4
knitr-1.9/knitr/R/engine.R | 42 +++
knitr-1.9/knitr/R/hooks-extra.R | 18 -
knitr-1.9/knitr/R/hooks-html.R | 6
knitr-1.9/knitr/R/hooks-latex.R | 4
knitr-1.9/knitr/R/hooks-md.R | 3
knitr-1.9/knitr/R/hooks.R | 17 +
knitr-1.9/knitr/R/output.R | 21 +
knitr-1.9/knitr/R/package.R | 2
knitr-1.9/knitr/R/pandoc.R | 6
knitr-1.9/knitr/R/parser.R | 1
knitr-1.9/knitr/R/table.R | 42 ++-
knitr-1.9/knitr/R/template.R | 3
knitr-1.9/knitr/R/themes-eclipse.R | 1
knitr-1.9/knitr/R/themes.R | 8
knitr-1.9/knitr/R/utils-conversion.R | 40 ++-
knitr-1.9/knitr/R/utils-rd2html.R | 5
knitr-1.9/knitr/R/utils-sweave.R | 7
knitr-1.9/knitr/R/utils-vignettes.R | 16 -
knitr-1.9/knitr/R/utils.R | 7
knitr-1.9/knitr/README.md | 41 ---
knitr-1.9/knitr/build/knitr.pdf |binary
knitr-1.9/knitr/build/vignette.rds |binary
knitr-1.9/knitr/inst/NEWS.Rd |only
knitr-1.9/knitr/inst/doc/datatables.Rmd | 8
knitr-1.9/knitr/inst/doc/datatables.html | 8
knitr-1.9/knitr/inst/doc/docco-classic.html | 3
knitr-1.9/knitr/inst/doc/docco-linear.html | 2
knitr-1.9/knitr/inst/doc/knit_expand.html | 4
knitr-1.9/knitr/inst/doc/knit_print.html | 4
knitr-1.9/knitr/inst/doc/knitr-html.html | 4
knitr-1.9/knitr/inst/doc/knitr-intro.Rmd | 4
knitr-1.9/knitr/inst/doc/knitr-intro.html | 20 -
knitr-1.9/knitr/inst/doc/knitr-markdown.html | 4
knitr-1.9/knitr/inst/doc/knitr-refcard.Rmd | 2
knitr-1.9/knitr/inst/doc/knitr-refcard.pdf |binary
knitr-1.9/knitr/inst/examples/download_count.csv |only
knitr-1.9/knitr/inst/examples/knitr-beamer.Rnw | 59 ++---
knitr-1.9/knitr/inst/examples/knitr-beamer.lyx | 126 +++++------
knitr-1.9/knitr/inst/examples/knitr-graphics.Rnw | 26 +-
knitr-1.9/knitr/inst/examples/knitr-graphics.lyx | 47 ++--
knitr-1.9/knitr/inst/examples/knitr-listings.Rnw | 8
knitr-1.9/knitr/inst/examples/knitr-listings.lyx | 2
knitr-1.9/knitr/inst/examples/knitr-manual.Rnw | 4
knitr-1.9/knitr/inst/examples/knitr-minimal.Rnw | 4
knitr-1.9/knitr/inst/examples/knitr-minimal.lyx | 2
knitr-1.9/knitr/inst/examples/knitr-packages.bib | 32 +-
knitr-1.9/knitr/inst/examples/knitr-spin.html | 2
knitr-1.9/knitr/inst/examples/knitr-subfloats.Rnw | 4
knitr-1.9/knitr/inst/examples/knitr-themes.Rnw | 4
knitr-1.9/knitr/inst/examples/knitr-twocolumn.Rnw | 6
knitr-1.9/knitr/inst/examples/knitr-twocolumn.lyx | 2
knitr-1.9/knitr/inst/examples/upload-github.R |only
knitr-1.9/knitr/inst/misc/docco-classic.css | 1
knitr-1.9/knitr/man/Sweave2knitr.Rd | 3
knitr-1.9/knitr/man/all_labels.Rd | 1
knitr-1.9/knitr/man/all_patterns.Rd | 1
knitr-1.9/knitr/man/asis_output.Rd | 1
knitr-1.9/knitr/man/chunk_hook.Rd | 3
knitr-1.9/knitr/man/clean_cache.Rd |only
knitr-1.9/knitr/man/current_input.Rd | 1
knitr-1.9/knitr/man/dep_auto.Rd | 1
knitr-1.9/knitr/man/dep_prev.Rd | 1
knitr-1.9/knitr/man/eclipse_theme.Rd | 2
knitr-1.9/knitr/man/engine_output.Rd | 1
knitr-1.9/knitr/man/fig_chunk.Rd | 1
knitr-1.9/knitr/man/fig_path.Rd | 1
knitr-1.9/knitr/man/hook_animation.Rd | 1
knitr-1.9/knitr/man/hook_document.Rd | 1
knitr-1.9/knitr/man/hook_plot.Rd | 1
knitr-1.9/knitr/man/image_uri.Rd | 1
knitr-1.9/knitr/man/imgur_upload.Rd | 1
knitr-1.9/knitr/man/inline_expr.Rd | 1
knitr-1.9/knitr/man/kable.Rd | 4
knitr-1.9/knitr/man/knit.Rd | 11 -
knitr-1.9/knitr/man/knit2html.Rd | 1
knitr-1.9/knitr/man/knit2pdf.Rd | 1
knitr-1.9/knitr/man/knit2wp.Rd | 10
knitr-1.9/knitr/man/knit_child.Rd | 1
knitr-1.9/knitr/man/knit_engines.Rd | 1
knitr-1.9/knitr/man/knit_exit.Rd | 5
knitr-1.9/knitr/man/knit_expand.Rd | 1
knitr-1.9/knitr/man/knit_filter.Rd | 13 -
knitr-1.9/knitr/man/knit_global.Rd | 1
knitr-1.9/knitr/man/knit_hooks.Rd | 1
knitr-1.9/knitr/man/knit_meta.Rd | 1
knitr-1.9/knitr/man/knit_patterns.Rd | 1
knitr-1.9/knitr/man/knit_print.Rd | 1
knitr-1.9/knitr/man/knit_rd.Rd | 5
knitr-1.9/knitr/man/knit_theme.Rd | 11 -
knitr-1.9/knitr/man/knitr-package.Rd | 3
knitr-1.9/knitr/man/load_cache.Rd |only
knitr-1.9/knitr/man/opts_chunk.Rd | 1
knitr-1.9/knitr/man/opts_knit.Rd | 1
knitr-1.9/knitr/man/opts_template.Rd | 1
knitr-1.9/knitr/man/output_hooks.Rd | 3
knitr-1.9/knitr/man/pandoc.Rd | 7
knitr-1.9/knitr/man/pat_fun.Rd | 1
knitr-1.9/knitr/man/plot_crop.Rd | 1
knitr-1.9/knitr/man/rand_seed.Rd | 1
knitr-1.9/knitr/man/read_chunk.Rd | 7
knitr-1.9/knitr/man/read_rforge.Rd | 2
knitr-1.9/knitr/man/rocco.Rd | 1
knitr-1.9/knitr/man/rst2pdf.Rd | 1
knitr-1.9/knitr/man/set_alias.Rd | 1
knitr-1.9/knitr/man/set_header.Rd | 1
knitr-1.9/knitr/man/set_parent.Rd | 1
knitr-1.9/knitr/man/spin.Rd | 1
knitr-1.9/knitr/man/spin_child.Rd | 1
knitr-1.9/knitr/man/stitch.Rd | 1
knitr-1.9/knitr/man/vignette_engines.Rd | 1
knitr-1.9/knitr/man/wrap_rmd.Rd | 1
knitr-1.9/knitr/man/write_bib.Rd | 1
knitr-1.9/knitr/tests/testit/test-output.R | 11 +
knitr-1.9/knitr/tests/testit/test-table.R | 32 ++
knitr-1.9/knitr/vignettes/datatables.Rmd | 8
knitr-1.9/knitr/vignettes/knitr-intro.Rmd | 4
knitr-1.9/knitr/vignettes/knitr-refcard.Rmd | 2
125 files changed, 837 insertions(+), 540 deletions(-)
Title: Cairo-based cross-platform antialiased graphics device driver.
Diff between cairoDevice versions 2.20 dated 2014-02-22 and 2.21 dated 2015-01-20
Description: Cairo/GTK graphics device driver with output to screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/cairoDevice.R | 12 ++++++------
R/zzz.R | 3 +--
man/Cairo.Rd | 10 +++++-----
man/asCairoDevice.Rd | 2 +-
src/cairoDevice.c | 7 +++++--
7 files changed, 27 insertions(+), 25 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Diff between vines versions 1.1.0 dated 2014-05-11 and 1.1.1 dated 2015-01-20
Description: Vines are graphical models for pair-copula constructions that represent high-dimensional distributions as a factorization of bivariate copulas and marginal density functions. This package contains S4 classes for vines (C-vines and D-vines) and methods for inference, goodness-of-fit tests, density/distribution function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez
DESCRIPTION | 10 +++++-----
MD5 | 50 +++++++++++++++++++++++++-------------------------
NAMESPACE | 2 +-
NEWS | 12 ++++++++----
R/Vine.R | 6 +++---
R/dimnames.R | 6 +++---
R/dvine.R | 4 ++--
R/h.R | 6 +++---
R/hinverse.R | 6 +++---
R/pvine.R | 6 +++---
R/rvine.R | 28 ++++++++++++++--------------
R/show.R | 16 ++++++++--------
R/vineFit.R | 4 ++--
R/vineFitML.R | 12 ++++++------
R/vineGoF.R | 4 ++--
R/vineIter.R | 22 +++++++++++-----------
R/vineOrder.R | 8 ++++----
R/vinePIT.R | 8 ++++----
R/vineParameters.R | 4 ++--
inst/CITATION | 13 ++++++-------
src/h.c | 4 ++--
src/h.h | 4 ++--
src/hinverse.c | 4 ++--
src/hinverse.h | 4 ++--
src/register.c | 4 ++--
tests/hfunctions.R | 12 ++++++------
26 files changed, 131 insertions(+), 128 deletions(-)
Title: Compute the Personalized Activity Index via flexible Bayesian
Negative Binomial model.
Diff between lmeNBBayes versions 1.2 dated 2014-01-24 and 1.3 dated 2015-01-20
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo Y, Zhao Y and Petkau AJ. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in frequentist framework.
Author: Yumi Kondo
Maintainer: Yumi Kondo
DESCRIPTION | 13
MD5 | 15
NAMESPACE | 8
R/nbinDPmix_C.R | 5241 ++++++++++++++++++++++++-----------------------
man/getDIC.Rd | 88
man/getS.StatInMed.Rd |only
man/index_batch_Bayes.Rd | 97
man/lmeNBBayes.Rd | 160 +
src/nbinDPmix.c | 30
9 files changed, 3088 insertions(+), 2564 deletions(-)
Title: Recursive Partitioning Based on Psychometric Models
Diff between psychotree versions 0.14-0 dated 2014-08-28 and 0.15-0 dated 2015-01-19
Description: Recursive partitioning based on psychometric models,
employing the general MOB algorithm (from package partykit) to obtain
Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and
MPT trees.
Author: Achim Zeileis [aut, cre],
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Abou El-Komboz [aut],
Julia Kopf [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 17 ++--
MD5 | 33 ++++----
NAMESPACE | 21 +----
NEWS | 8 ++
R/bttree.R | 6 -
R/graphics.R | 125 +++++++++++++++++++++++++++++++--
R/mpttree.R |only
build/vignette.rds |binary
data/CEMSChoice.rda |binary
data/DIFSim.rda |binary
data/EuropeanValuesStudy.rda |binary
data/SPISA.rda |binary
data/Topmodel2007.rda |binary
inst/doc/raschtree.pdf |binary
man/bttree.Rd | 5 +
man/mpttree.Rd |only
man/node_mptplot.Rd |only
tests/Examples/psychotree-Ex.Rout.save | 100 ++++++++++++++++++++------
vignettes/raschtree.Rout.save | 10 --
19 files changed, 247 insertions(+), 78 deletions(-)
Title: Infrastructure for Psychometric Modeling
Diff between psychotools versions 0.3-0 dated 2014-08-28 and 0.4-0 dated 2015-01-19
Description: Infrastructure for psychometric modeling such as data classes
(for item response data and paired comparisons), basic model fitting
functions (for Bradley-Terry, Rasch, partial credit, rating scale,
multinomial processing tree models), extractor functions for different types
of parameters (item, person, threshold, discrimination), unified inference
and visualizations, and various datasets for illustration. Intended as a
common lightweight and efficient toolbox for psychometric modeling and a
common building block for fitting psychometric mixture models in package
"psychomix" and psychometric tree models in package "psychotree".
Author: Achim Zeileis [aut, cre],
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Abou El-Komboz [aut],
Julia Kopf [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 31 +++---
MD5 | 46 +++++----
NAMESPACE | 23 ++--
NEWS | 16 +++
R/itemresp.R | 50 ++++++++++
R/mptmodel.R |only
R/pcmodel.R | 2
R/raschmodel.R | 6 -
data/FirstNames.rda |binary
data/GermanParties2009.rda |binary
data/MemoryDeficits.rda |binary
data/SoundQuality.rda |binary
data/SourceMonitoring.rda |binary
data/StereotypeThreat.rda |binary
data/VerbalAggression.rda |binary
data/YouthGratitude.rda |binary
man/MemoryDeficits.Rd | 6 -
man/SourceMonitoring.Rd | 26 +++--
man/btmodel.Rd | 13 +-
man/itemresp.Rd | 40 ++++----
man/mptmodel.Rd |only
man/mscale.Rd | 14 ++
man/pcmodel.Rd | 4
man/summary.itemresp.Rd | 16 ++-
tests/Examples/psychotools-Ex.Rout.save | 150 ++++++++++++++++++++++++--------
25 files changed, 311 insertions(+), 132 deletions(-)
Title: Extended Model Formulas
Diff between Formula versions 1.1-2 dated 2014-07-13 and 1.2-0 dated 2015-01-19
Description: Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
Author: Achim Zeileis [aut, cre],
Yves Croissant [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8 -
MD5 | 14 +--
NEWS | 6 +
R/Formula.R | 152 ++++++++++++++++++++----------------
build/vignette.rds |binary
inst/doc/Formula.pdf |binary
man/model.frame.Formula.Rd | 24 ++++-
tests/Examples/Formula-Ex.Rout.save | 28 +++++-
8 files changed, 145 insertions(+), 87 deletions(-)
Title: Maximally Selected Rank Statistics
Diff between maxstat versions 0.7-20 dated 2014-02-07 and 0.7-21 dated 2015-01-19
Description: Maximally selected rank statistics with
several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/maxstat.R | 14 +++++++++-----
R/maxstat.test.R | 4 ++--
build/vignette.rds |binary
data/treepipit.rda |binary
inst/NEWS | 4 ++++
inst/doc/maxstat.pdf |binary
8 files changed, 26 insertions(+), 18 deletions(-)
Title: Bayesian Model Averaging with INLA
Diff between INLABMA versions 0.1-5 dated 2014-07-09 and 0.1-6 dated 2015-01-19
Description: Spatial Econometrics models using Bayesian Model Averaging
on models fitted with INLA. The INLA package can be obtained from
http://www.r-inla.org . We recommend the testing version, which can be
downloaded by running:
source("http://www.math.ntnu.no/inla/givemeINLA-testing.R")
Author: Virgilio Gómez-Rubio
Maintainer: Virgilio Gómez-Rubio
DESCRIPTION | 15 ++++++++-------
MD5 | 23 ++++++++++++-----------
NAMESPACE | 2 ++
R/BMArho.R | 5 ++++-
R/SE-utils.R | 48 ++++++++++++++++++++++++------------------------
R/leroux.R | 4 ++--
inst |only
man/BMA2.Rd | 11 +++++++++++
man/BMArho.Rd | 12 ++++++++++++
man/leroux.Rd | 18 +++++++++++++++---
man/rescalemarg.Rd | 4 +++-
man/sem.Rd | 31 +++++++++++++++++++++++--------
man/trIrhoWinv.Rd | 2 +-
13 files changed, 117 insertions(+), 58 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Diff between gstat versions 1.0-20 dated 2015-01-08 and 1.0-21 dated 2015-01-19
Description: variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
R/krige0.R | 15 +++++++++------
R/variogramST.R | 11 +++++++++--
inst/doc/gstat.pdf |binary
inst/doc/prs.pdf |binary
inst/doc/st.pdf |binary
man/krige.Rd | 9 +++++++++
man/krigeST.Rd | 3 ++-
9 files changed, 43 insertions(+), 23 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Diff between treeclim versions 1.0.9 dated 2015-01-12 and 1.0.10 dated 2015-01-19
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang
DESCRIPTION | 8
MD5 | 28 +-
R/dcc.R | 688 ++++++++++++++++++++++++++---------------------------
R/generics.R | 86 +++---
R/gershunov.R | 354 +++++++++++++--------------
R/init_boot_data.R | 5
R/ptest.R | 4
R/seascorr.R | 559 +++++++++++++++++++++----------------------
R/skills.R | 546 ++++++++++++++++++++----------------------
inst/Changelog | 7
man/dcc.Rd | 2
man/g_test.Rd | 130 ++++------
man/seascorr.Rd | 280 ++++++++++-----------
man/skills.Rd | 2
src/pcor.cpp | 16 +
15 files changed, 1370 insertions(+), 1345 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Diff between mdatools versions 0.5.3 dated 2014-04-26 and 0.6.0 dated 2015-01-19
Description: Package implements projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics.
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy
DESCRIPTION | 12
MD5 | 429 ++++++++++++++++-----------------
NEWS | 7
R/crossval.R | 71 ++++-
R/defaults.R | 29 ++
R/ldecomp.R | 3
R/mdaplots.R | 30 +-
R/pca.R | 39 +--
R/pls.R | 109 +++++---
R/prep.R | 3
R/randtest.R |only
R/simca.R | 61 ++--
README.md | 8
man/as.matrix.classres.Rd | 18 -
man/as.matrix.ldecomp.Rd | 10
man/as.matrix.plsdares.Rd | 16 -
man/as.matrix.plsres.Rd | 15 -
man/as.matrix.regcoeffs.Rd | 16 -
man/as.matrix.regres.Rd | 16 -
man/bars.Rd | 10
man/classify.plsda.Rd | 15 -
man/crossval.Rd | 16 -
man/erfinv.Rd | 4
man/errorbars.Rd | 14 -
man/getCalibrationData.Rd | 9
man/getCalibrationData.pca.Rd | 6
man/getCalibrationData.simcam.Rd | 6
man/getClassificationPerformance.Rd | 36 +-
man/getMainTitle.Rd | 9
man/getSelectedComponents.Rd | 15 -
man/getSelectedComponents.classres.Rd | 14 -
man/getSelectivityRatio.Rd | 9
man/getSelectivityRatio.pls.Rd | 20 -
man/getVIPScores.Rd | 9
man/getVIPScores.pls.Rd | 16 -
man/ldecomp.Rd | 56 +---
man/ldecomp.getDistances.Rd | 26 --
man/ldecomp.getResLimits.Rd | 13 -
man/ldecomp.getVariances.Rd | 11
man/mdaplot.areColors.Rd | 5
man/mdaplot.formatValues.Rd | 16 -
man/mdaplot.getAxesLim.Rd | 42 +--
man/mdaplot.getColors.Rd | 15 -
man/mdaplot.plotAxes.Rd | 18 -
man/mdaplot.showColorbar.Rd | 10
man/mdaplot.showGrid.Rd | 4
man/mdaplot.showLabels.Rd | 21 -
man/mdaplot.showLegend.Rd | 20 -
man/mdaplot.showLines.Rd | 14 -
man/mdaplot.showRegressionLine.Rd | 12
man/mdaplotg.Rd | 2
man/mdatools.Rd | 1
man/pca.cal.Rd | 16 -
man/pca.crossval.Rd | 16 -
man/pca.nipals.Rd | 17 -
man/pca.svd.Rd | 12
man/pinv.Rd | 5
man/plot.classres.Rd | 13 -
man/plot.pca.Rd | 18 -
man/plot.pcares.Rd | 15 -
man/plot.pls.Rd | 21 -
man/plot.plsda.Rd | 21 -
man/plot.plsdares.Rd | 21 -
man/plot.plsres.Rd | 15 -
man/plot.randtest.Rd |only
man/plot.regcoeffs.Rd | 32 +-
man/plot.regres.Rd | 14 -
man/plot.simca.Rd | 9
man/plot.simcam.Rd | 9
man/plot.simcamres.Rd | 7
man/plotCooman.Rd | 6
man/plotCooman.simcam.Rd | 11
man/plotCooman.simcamres.Rd | 24 -
man/plotCorr.Rd |only
man/plotCorr.randtest.Rd |only
man/plotCumVariance.Rd | 9
man/plotCumVariance.ldecomp.Rd | 21 -
man/plotCumVariance.pca.Rd | 16 -
man/plotDiscriminationPower.Rd | 9
man/plotDiscriminationPower.simcam.Rd | 22 -
man/plotHist.Rd |only
man/plotHist.randtest.Rd |only
man/plotLoadings.Rd | 9
man/plotLoadings.pca.Rd | 27 --
man/plotMisclassified.Rd | 9
man/plotMisclassified.classmodel.Rd | 17 -
man/plotMisclassified.classres.Rd | 19 -
man/plotModelDistance.Rd | 9
man/plotModelDistance.simcam.Rd | 24 -
man/plotModellingPower.Rd | 9
man/plotModellingPower.simca.Rd | 17 -
man/plotModellingPower.simcam.Rd | 16 -
man/plotPerformance.Rd | 9
man/plotPerformance.classmodel.Rd | 31 +-
man/plotPerformance.classres.Rd | 36 +-
man/plotPredictions.Rd | 9
man/plotPredictions.classmodel.Rd | 30 --
man/plotPredictions.classres.Rd | 37 +-
man/plotPredictions.pls.Rd | 39 +--
man/plotPredictions.plsres.Rd | 21 -
man/plotPredictions.regres.Rd | 33 +-
man/plotRMSE.Rd | 9
man/plotRMSE.pls.Rd | 27 --
man/plotRMSE.plsres.Rd | 12
man/plotRMSE.regres.Rd | 22 -
man/plotRegcoeffs.Rd | 9
man/plotRegcoeffs.pls.Rd | 20 -
man/plotResiduals.Rd | 9
man/plotResiduals.ldecomp.Rd | 22 -
man/plotResiduals.pca.Rd | 28 --
man/plotResiduals.simcam.Rd | 8
man/plotResiduals.simcamres.Rd | 23 -
man/plotResiduals.simcares.Rd | 24 -
man/plotScores.Rd | 6
man/plotScores.ldecomp.Rd | 18 -
man/plotScores.pca.Rd | 27 --
man/plotSelectivityRatio.Rd | 9
man/plotSelectivityRatio.pls.Rd | 28 +-
man/plotSensitivity.Rd | 9
man/plotSensitivity.classmodel.Rd | 17 -
man/plotSensitivity.classres.Rd | 18 -
man/plotSpecificity.Rd | 9
man/plotSpecificity.classmodel.Rd | 17 -
man/plotSpecificity.classres.Rd | 18 -
man/plotVIPScores.Rd | 9
man/plotVIPScores.pls.Rd | 25 -
man/plotVariance.Rd | 9
man/plotVariance.ldecomp.Rd | 21 -
man/plotVariance.pca.Rd | 27 --
man/plotVariance.pls.Rd | 27 --
man/plotXCumVariance.Rd | 9
man/plotXCumVariance.pls.Rd | 21 -
man/plotXCumVariance.plsres.Rd | 12
man/plotXLoadings.Rd | 9
man/plotXLoadings.pls.Rd | 21 -
man/plotXResiduals.Rd | 9
man/plotXResiduals.pls.Rd | 25 -
man/plotXResiduals.plsres.Rd | 15 -
man/plotXScores.Rd | 9
man/plotXScores.pls.Rd | 25 -
man/plotXScores.plsres.Rd | 15 -
man/plotXVariance.Rd | 9
man/plotXVariance.pls.Rd | 21 -
man/plotXVariance.plsres.Rd | 12
man/plotXYLoadings.Rd | 9
man/plotXYLoadings.pls.Rd | 22 -
man/plotXYScores.Rd | 9
man/plotXYScores.pls.Rd | 27 --
man/plotXYScores.plsres.Rd | 17 -
man/plotYCumVariance.Rd | 9
man/plotYCumVariance.pls.Rd | 21 -
man/plotYCumVariance.plsres.Rd | 12
man/plotYResiduals.Rd | 9
man/plotYResiduals.pls.Rd | 29 +-
man/plotYResiduals.regres.Rd | 29 +-
man/plotYVariance.Rd | 9
man/plotYVariance.pls.Rd | 21 -
man/plotYVariance.plsres.Rd | 12
man/pls.Rd | 2
man/pls.cal.Rd | 24 -
man/pls.calculateSelectivityRatio.Rd | 17 -
man/pls.calculateVIPScores.Rd | 11
man/pls.crossval.Rd | 22 -
man/pls.simpls.Rd | 21 -
man/plsda.crossval.Rd | 21 -
man/plsda.getReferenceValues.Rd | 6
man/predict.pca.Rd | 11
man/predict.pls.Rd | 14 -
man/predict.plsda.Rd | 14 -
man/predict.simca.Rd | 15 -
man/predict.simcam.Rd | 18 -
man/prep.autoscale.Rd | 13 -
man/prep.msc.Rd | 17 -
man/prep.savgol.Rd | 11
man/prep.snv.Rd | 12
man/print.classres.Rd | 14 -
man/print.ldecomp.Rd | 13 -
man/print.pca.Rd | 6
man/print.pcares.Rd | 6
man/print.pls.Rd | 6
man/print.plsda.Rd | 6
man/print.plsdares.Rd | 7
man/print.plsres.Rd | 6
man/print.randtest.Rd |only
man/print.regcoeffs.Rd | 18 -
man/print.regres.Rd | 7
man/print.simca.Rd | 6
man/print.simcam.Rd | 6
man/print.simcamres.Rd | 7
man/print.simcares.Rd | 6
man/randtest.Rd |only
man/regcoeffs.Rd | 32 +-
man/regcoeffs.getStat.Rd | 19 -
man/regres.Rd | 36 +-
man/regres.bias.Rd | 9
man/regres.r2.Rd | 9
man/regres.rmse.Rd | 9
man/regres.slope.Rd | 9
man/selectCompNum.Rd | 9
man/selectCompNum.pca.Rd | 9
man/selectCompNum.pls.Rd | 9
man/showPredictions.Rd | 9
man/showPredictions.classres.Rd | 19 -
man/simca.classify.Rd | 13 -
man/simca.crossval.Rd | 18 -
man/simcam.getPerformanceStatistics.Rd | 8
man/summary.classres.Rd | 20 -
man/summary.ldecomp.Rd | 12
man/summary.pca.Rd | 9
man/summary.pcares.Rd | 10
man/summary.pls.Rd | 12
man/summary.plsda.Rd | 13 -
man/summary.plsdares.Rd | 10
man/summary.plsres.Rd | 13 -
man/summary.randtest.Rd |only
man/summary.regres.Rd | 12
man/summary.simca.Rd | 7
man/summary.simcam.Rd | 7
man/summary.simcamres.Rd | 7
man/summary.simcares.Rd | 7
220 files changed, 1954 insertions(+), 1885 deletions(-)
Title: Spatio-Temporal Bayesian Modelling Using R
Diff between spTimer versions 1.0-3 dated 2014-10-02 and 2.0-0 dated 2015-01-19
Description: The package is able to fit, spatially predict and temporally forecast large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for big-n problem.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Shuvo Bakar
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
inst/CITATION | 23 +++++++++++------------
inst/ChangeLog | 40 +++-------------------------------------
man/spT.Gibbs.Rd | 8 +++++---
man/spTimer-package.Rd | 9 +--------
src/common.c | 27 ++++++++++++++-------------
7 files changed, 44 insertions(+), 83 deletions(-)
Title: A collection of methods for left-censored missing data
imputation
Diff between imputeLCMD versions 1.0 dated 2014-07-12 and 2.0 dated 2015-01-19
Description: The package contains a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random. * New functionality has been added: a hybrid method that allows the imputation of missing values in a more complex scenario where the missing data are both MAR and MNAR.
Author: Cosmin Lazar
Maintainer: Cosmin Lazar
imputeLCMD-1.0/imputeLCMD/man/imputeLCMD-package.Rd |only
imputeLCMD-2.0/imputeLCMD/DESCRIPTION | 10 +++++-----
imputeLCMD-2.0/imputeLCMD/MD5 | 9 +++++++--
imputeLCMD-2.0/imputeLCMD/R/imputeMAR-MNAR.R |only
imputeLCMD-2.0/imputeLCMD/R/imputeMAR.R |only
imputeLCMD-2.0/imputeLCMD/R/modelSelector.R |only
imputeLCMD-2.0/imputeLCMD/man/impute.MAR.MNAR.Rd |only
imputeLCMD-2.0/imputeLCMD/man/impute.MAR.Rd |only
imputeLCMD-2.0/imputeLCMD/man/model.Selector.Rd |only
9 files changed, 12 insertions(+), 7 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 1.1-4 dated 2014-06-15 and 1.1-5 dated 2015-01-18
Description: Classes and methods for dense and sparse matrices and
operations on them using LAPACK and SuiteSparse.
Author: Douglas Bates
Maintainer: Martin Maechler
Matrix-1.1-4/Matrix/po/R-en@quot.po |only
Matrix-1.1-4/Matrix/po/en@quot.po |only
Matrix-1.1-5/Matrix/ChangeLog | 13
Matrix-1.1-5/Matrix/DESCRIPTION | 8
Matrix-1.1-5/Matrix/MD5 | 209 ++++++------
Matrix-1.1-5/Matrix/NAMESPACE | 12
Matrix-1.1-5/Matrix/R/AllClass.R | 42 +-
Matrix-1.1-5/Matrix/R/AllGeneric.R | 2
Matrix-1.1-5/Matrix/R/Auxiliaries.R | 172 +++++++--
Matrix-1.1-5/Matrix/R/Csparse.R | 111 ++----
Matrix-1.1-5/Matrix/R/Math.R |only
Matrix-1.1-5/Matrix/R/Matrix.R | 105 ------
Matrix-1.1-5/Matrix/R/Ops.R | 29 -
Matrix-1.1-5/Matrix/R/Summary.R |only
Matrix-1.1-5/Matrix/R/associations.R |only
Matrix-1.1-5/Matrix/R/colSums.R | 28 +
Matrix-1.1-5/Matrix/R/dMatrix.R | 97 -----
Matrix-1.1-5/Matrix/R/ddenseMatrix.R | 15
Matrix-1.1-5/Matrix/R/denseMatrix.R | 10
Matrix-1.1-5/Matrix/R/dgCMatrix.R | 30 +
Matrix-1.1-5/Matrix/R/dgTMatrix.R | 2
Matrix-1.1-5/Matrix/R/dgeMatrix.R | 22 -
Matrix-1.1-5/Matrix/R/diagMatrix.R | 87 ++--
Matrix-1.1-5/Matrix/R/dspMatrix.R | 24 -
Matrix-1.1-5/Matrix/R/dsparseMatrix.R | 5
Matrix-1.1-5/Matrix/R/dsyMatrix.R | 70 ++--
Matrix-1.1-5/Matrix/R/dtpMatrix.R | 9
Matrix-1.1-5/Matrix/R/dtrMatrix.R | 4
Matrix-1.1-5/Matrix/R/lMatrix.R | 10
Matrix-1.1-5/Matrix/R/ldenseMatrix.R | 84 +---
Matrix-1.1-5/Matrix/R/lsparseMatrix.R | 17
Matrix-1.1-5/Matrix/R/ndenseMatrix.R | 69 +--
Matrix-1.1-5/Matrix/R/nsparseMatrix.R | 32 -
Matrix-1.1-5/Matrix/R/products.R | 59 ++-
Matrix-1.1-5/Matrix/R/sparseMatrix.R | 21 -
Matrix-1.1-5/Matrix/R/sparseVector.R | 52 --
Matrix-1.1-5/Matrix/R/symmetricMatrix.R | 24 -
Matrix-1.1-5/Matrix/R/triangularMatrix.R | 11
Matrix-1.1-5/Matrix/R/zzz.R | 7
Matrix-1.1-5/Matrix/TODO | 23 -
Matrix-1.1-5/Matrix/build |only
Matrix-1.1-5/Matrix/inst/doc/Comparisons.R |only
Matrix-1.1-5/Matrix/inst/doc/Comparisons.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Design-issues.R |only
Matrix-1.1-5/Matrix/inst/doc/Design-issues.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Intro2Matrix.R |only
Matrix-1.1-5/Matrix/inst/doc/Intro2Matrix.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Introduction.R |only
Matrix-1.1-5/Matrix/inst/doc/Introduction.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/sparseModels.R |only
Matrix-1.1-5/Matrix/inst/doc/sparseModels.Rnw |only
Matrix-1.1-5/Matrix/inst/po/de/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/fr/LC_MESSAGES/Matrix.mo |only
Matrix-1.1-5/Matrix/inst/po/fr/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/pl/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/pl/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/test-tools-1.R | 15
Matrix-1.1-5/Matrix/inst/test-tools-Matrix.R | 4
Matrix-1.1-5/Matrix/man/Matrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/band.Rd | 3
Matrix-1.1-5/Matrix/man/colSums.Rd | 6
Matrix-1.1-5/Matrix/man/diagonalMatrix-class.Rd | 7
Matrix-1.1-5/Matrix/man/dtCMatrix-class.Rd | 19 -
Matrix-1.1-5/Matrix/man/forceSymmetric.Rd | 26 -
Matrix-1.1-5/Matrix/man/invPerm.Rd | 4
Matrix-1.1-5/Matrix/man/isTriangular.Rd | 15
Matrix-1.1-5/Matrix/man/ldenseMatrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/matrix-products.Rd | 19 -
Matrix-1.1-5/Matrix/man/ndenseMatrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/sparseMatrix.Rd | 21 -
Matrix-1.1-5/Matrix/man/sparseVector-class.Rd | 9
Matrix-1.1-5/Matrix/man/symmpart.Rd | 21 -
Matrix-1.1-5/Matrix/man/triangularMatrix-class.Rd | 4
Matrix-1.1-5/Matrix/po/Matrix.pot | 194 +++++------
Matrix-1.1-5/Matrix/po/R-Matrix.pot | 42 +-
Matrix-1.1-5/Matrix/po/R-de.po | 57 ++-
Matrix-1.1-5/Matrix/po/R-fr.po | 59 ++-
Matrix-1.1-5/Matrix/po/R-pl.po | 76 +++-
Matrix-1.1-5/Matrix/po/T |only
Matrix-1.1-5/Matrix/po/de.po | 193 +++++------
Matrix-1.1-5/Matrix/po/fr.po | 193 +++++------
Matrix-1.1-5/Matrix/po/pl.po | 193 +++++------
Matrix-1.1-5/Matrix/src/CHMfactor.c | 10
Matrix-1.1-5/Matrix/src/Csparse.c | 99 ++++-
Matrix-1.1-5/Matrix/src/Csparse.h | 2
Matrix-1.1-5/Matrix/src/Mutils.c | 35 +-
Matrix-1.1-5/Matrix/src/Mutils.h | 21 -
Matrix-1.1-5/Matrix/src/chm_common.c | 10
Matrix-1.1-5/Matrix/src/chm_common.h | 2
Matrix-1.1-5/Matrix/src/cs.c | 14
Matrix-1.1-5/Matrix/src/cs.h | 3
Matrix-1.1-5/Matrix/src/cs_utils.c | 2
Matrix-1.1-5/Matrix/src/dense.c | 118 +++---
Matrix-1.1-5/Matrix/src/dgCMatrix.c | 36 +-
Matrix-1.1-5/Matrix/src/dgeMatrix.c | 171 +++++----
Matrix-1.1-5/Matrix/src/dpoMatrix.c | 10
Matrix-1.1-5/Matrix/src/dsCMatrix.c | 16
Matrix-1.1-5/Matrix/src/dsyMatrix.c | 6
Matrix-1.1-5/Matrix/src/dsyMatrix.h | 1
Matrix-1.1-5/Matrix/src/dtCMatrix.c | 37 +-
Matrix-1.1-5/Matrix/src/dtrMatrix.c | 11
Matrix-1.1-5/Matrix/src/dtrMatrix.h | 1
Matrix-1.1-5/Matrix/src/init.c | 4
Matrix-1.1-5/Matrix/src/t_Csparse_subassign.c | 8
Matrix-1.1-5/Matrix/tests/Simple.R | 64 +++
Matrix-1.1-5/Matrix/tests/factorizing.R | 6
Matrix-1.1-5/Matrix/tests/group-methods.R | 97 ++++-
Matrix-1.1-5/Matrix/tests/indexing.R | 27 +
Matrix-1.1-5/Matrix/tests/indexing.Rout.save | 57 ++-
Matrix-1.1-5/Matrix/tests/matprod.R | 97 +++++
Matrix-1.1-5/Matrix/tests/other-pkgs.R | 4
114 files changed, 2033 insertions(+), 1634 deletions(-)
Title: Rigorous - NIfTI+ANALYZE+AFNI Input / Output
Diff between oro.nifti versions 0.4.0 dated 2013-12-27 and 0.4.3 dated 2015-01-18
Description: Functions for the input/output and visualization of
medical imaging data that follow either the ANALYZE, NIfTI or AFNI
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher, Volker Schmid and Andrew Thornton, with
contributions by Karsten Tabelow and Jon Clayden
Maintainer: Brandon Whitcher
oro.nifti-0.4.0/oro.nifti/R/oro2fmri.R |only
oro.nifti-0.4.0/oro.nifti/man/oro2fmri.Rd |only
oro.nifti-0.4.3/oro.nifti/DESCRIPTION | 10
oro.nifti-0.4.3/oro.nifti/LICENSE | 2
oro.nifti-0.4.3/oro.nifti/MD5 | 36 +-
oro.nifti-0.4.3/oro.nifti/NAMESPACE | 6
oro.nifti-0.4.3/oro.nifti/R/afniS4.R | 130 ++++++----
oro.nifti-0.4.3/oro.nifti/R/auditTrail.R | 98 +++----
oro.nifti-0.4.3/oro.nifti/R/niftiS4.R | 24 +
oro.nifti-0.4.3/oro.nifti/R/readS4.R | 31 +-
oro.nifti-0.4.3/oro.nifti/R/tim_colors.R | 4
oro.nifti-0.4.3/oro.nifti/build/vignette.rds |binary
oro.nifti-0.4.3/oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.BRIK.gz |only
oro.nifti-0.4.3/oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.HEAD |only
oro.nifti-0.4.3/oro.nifti/inst/doc/nifti.Rnw | 13 -
oro.nifti-0.4.3/oro.nifti/inst/doc/nifti.pdf |binary
oro.nifti-0.4.3/oro.nifti/man/descrip-methods.Rd | 2
oro.nifti-0.4.3/oro.nifti/man/q2R.Rd | 2
oro.nifti-0.4.3/oro.nifti/man/read_afni.Rd | 7
oro.nifti-0.4.3/oro.nifti/tests/Examples/oro.nifti-Ex.Rout.save | 25 +
oro.nifti-0.4.3/oro.nifti/vignettes/nifti.Rnw | 13 -
21 files changed, 233 insertions(+), 170 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.2 dated 2015-01-03 and 0.1.3 dated 2015-01-18
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"
ztable-0.1.2/ztable/man/myhtmlHead.Rd |only
ztable-0.1.3/ztable/DESCRIPTION | 6
ztable-0.1.3/ztable/MD5 | 41
ztable-0.1.3/ztable/NEWS | 21
ztable-0.1.3/ztable/R/print.ztable.html.R | 285 -
ztable-0.1.3/ztable/R/ztable.R | 249
ztable-0.1.3/ztable/R/ztable2.R |only
ztable-0.1.3/ztable/R/zzz.R | 2
ztable-0.1.3/ztable/README.md | 3965 ++++++++++++--
ztable-0.1.3/ztable/inst/doc/ztable.R | 51
ztable-0.1.3/ztable/inst/doc/ztable.Rmd | 73
ztable-0.1.3/ztable/inst/doc/ztable.html | 7770 ++++++++++++++++++++--------
ztable-0.1.3/ztable/man/addCellColor.Rd |only
ztable-0.1.3/ztable/man/addColColor.Rd |only
ztable-0.1.3/ztable/man/addRowColor.Rd |only
ztable-0.1.3/ztable/man/addcgroup.Rd |only
ztable-0.1.3/ztable/man/addrgroup.Rd |only
ztable-0.1.3/ztable/man/cGroupSpan.Rd |only
ztable-0.1.3/ztable/man/caption2minipage.Rd |only
ztable-0.1.3/ztable/man/colGroupCount.Rd |only
ztable-0.1.3/ztable/man/getNewAlign.Rd |only
ztable-0.1.3/ztable/man/myhtmlStyle.Rd |only
ztable-0.1.3/ztable/man/printHTMLHead.Rd |only
ztable-0.1.3/ztable/man/printLatexHead.Rd |only
ztable-0.1.3/ztable/man/totalCol.Rd |only
ztable-0.1.3/ztable/man/update_ztable.Rd | 17
ztable-0.1.3/ztable/man/validColor2.Rd |only
ztable-0.1.3/ztable/man/ztable2viewer.Rd |only
ztable-0.1.3/ztable/man/ztable_sub.Rd | 21
ztable-0.1.3/ztable/vignettes/ztable.Rmd | 73
30 files changed, 9849 insertions(+), 2725 deletions(-)
Title: Fishery Stock Assessment by Generalized Depletion Models
Diff between CatDyn versions 1.0-5 dated 2014-04-10 and 1.0-6 dated 2015-01-18
Description: Using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean body weight by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 237 types of models of increasing complexity, and six likelihood models.
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta
DESCRIPTION | 12
MD5 | 48
NAMESPACE | 2
R/CatDyn-internal.R |77392 +++++++++++++++++++++++++++++++++++++++++++------
R/CatDynCor.R |only
R/CatDynFit.R |21588 ++++++++++++-
R/CatDynPred.R | 732
R/CatDynSum.R |only
R/as.CatDynData.R | 27
R/catdynexp_1.R | 2701 +
R/deltamethod.R | 6
R/plot.CatDynExp.R | 35
R/plot.CatDynMod.R | 33
data/gayhake.rda |only
data/lolgahi.rda |binary
data/twelver.rda |only
man/CatDyn-package.Rd | 34
man/CatDynCor.Rd |only
man/CatDynFit.Rd | 283
man/CatDynPred.Rd | 11
man/CatDynSum.Rd |only
man/as.CatDynData.Rd | 56
man/catdynexp_1.Rd | 30
man/gayhake.Rd |only
man/lolgahi.Rd | 11
man/plot.CatDynData.Rd | 2
man/plot.CatDynExp.Rd | 5
man/plot.CatDynMod.Rd | 5
man/twelver.Rd |only
29 files changed, 92131 insertions(+), 10882 deletions(-)
Title: Power Calculations for SNP Studies with Censored Outcomes
Diff between survSNP versions 0.21-7 dated 2013-12-12 and 0.23.2 dated 2015-01-18
Description: This package can be used to conduct asymptotic and empirical power and sample size calculations for SNP association studies with right censored time to event outcomes
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Kouros Owzar
survSNP-0.21-7/survSNP/configure.in |only
survSNP-0.23.2/survSNP/DESCRIPTION | 13
survSNP-0.23.2/survSNP/MD5 | 35 -
survSNP-0.23.2/survSNP/NAMESPACE | 1
survSNP-0.23.2/survSNP/R/sim.snp.expsurv.power.R | 83 +++-
survSNP-0.23.2/survSNP/R/sim.snp.expsurv.sctest.R | 22 -
survSNP-0.23.2/survSNP/R/surv.exp.gt.model.R | 18
survSNP-0.23.2/survSNP/R/survSNP.power.table.R | 8
survSNP-0.23.2/survSNP/build/vignette.rds |binary
survSNP-0.23.2/survSNP/cleanup | 6
survSNP-0.23.2/survSNP/configure | 369 ++++++++-----------
survSNP-0.23.2/survSNP/configure.ac |only
survSNP-0.23.2/survSNP/inst/CITATION |only
survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.R | 15
survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.pdf |binary
survSNP-0.23.2/survSNP/man/sim.snp.expsurv.sctest.Rd | 4
survSNP-0.23.2/survSNP/man/surv.exp.gt.model.Rd | 4
survSNP-0.23.2/survSNP/man/survSNP-package.Rd | 7
survSNP-0.23.2/survSNP/src/Makevars.in | 9
survSNP-0.23.2/survSNP/src/Makevars.win | 21 -
20 files changed, 304 insertions(+), 311 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.1.2 dated 2014-12-01 and 1.1.3 dated 2015-01-18
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
DESCRIPTION | 8 -
MD5 | 259 +++++++++++++++++++--------------------
NAMESPACE | 2
NEWS | 27 +++-
R/EpiModel-package.r | 4
R/as.data.frame.R | 22 +--
R/conc.microsim.R | 22 +--
R/control.R | 121 +++++++++---------
R/crosscheck.R | 59 +++-----
R/dcm.R | 6
R/dcm.mods.R | 8 -
R/get.R | 24 +--
R/icm.R | 6
R/icm.mod.init.R | 8 -
R/icm.mod.status.R | 8 -
R/icm.mod.vital.R | 8 -
R/icm.utils.R | 4
R/init.R | 44 +++---
R/merge.R | 15 +-
R/net.mod.init.R | 16 +-
R/net.mod.simnet.R | 18 +-
R/net.mod.status.R | 16 +-
R/net.mod.vital.R | 8 -
R/net.utils.R | 92 +++++++-------
R/netdx.R | 2
R/netest.R | 33 ++---
R/netsim.R | 63 ++-------
R/param.R | 60 ++++-----
R/plot.R | 88 ++++++-------
R/saveout.R | 22 +--
R/shiny.R | 2
R/summary.R | 30 ++--
R/test.R | 6
R/utils.R | 17 +-
R/verbose.R | 22 +--
inst/doc/Intro.R | 4
inst/doc/Intro.Rmd | 22 ++-
inst/doc/Intro.html | 269 ++++++++++-------------------------------
man/EpiModel-package.Rd | 7 -
man/as.data.frame.dcm.Rd | 13 +
man/as.data.frame.icm.Rd | 15 +-
man/bipvals.Rd | 3
man/births.icm.Rd | 7 -
man/births.net.Rd | 7 -
man/brewer_ramp.Rd | 7 -
man/check_bip_degdist.Rd | 3
man/color_tea.Rd | 23 +--
man/comp_plot.Rd | 13 +
man/conc_microsim.Rd | 25 +--
man/control.dcm.Rd | 3
man/control.icm.Rd | 35 ++---
man/control.net.Rd | 102 ++++++++-------
man/copy_toall_attr.Rd | 9 -
man/crosscheck.dcm.Rd | 9 -
man/crosscheck.icm.Rd | 9 -
man/crosscheck.net.Rd | 11 -
man/dcm.Rd | 9 -
man/dcm.mods.Rd | 11 -
man/deaths.icm.Rd | 7 -
man/deaths.net.Rd | 7 -
man/deleteAttr.Rd | 3
man/discord_edgelist.Rd | 11 -
man/dissolution_coefs.Rd | 9 -
man/edgelist_censor.Rd | 5
man/edgelist_meanage.Rd | 7 -
man/edges_correct.Rd | 7 -
man/epiweb.Rd | 5
man/get_args.Rd | 5
man/get_attr_prop.Rd | 9 -
man/get_formula_terms.Rd | 5
man/get_network.Rd | 13 +
man/get_nwparam.Rd | 7 -
man/get_nwstats.Rd | 9 -
man/get_prev.icm.Rd | 7 -
man/get_prev.net.Rd | 7 -
man/get_sims.Rd | 3
man/get_transmat.Rd | 7 -
man/icm.Rd | 9 -
man/idmode.Rd | 7 -
man/infection.icm.Rd | 7 -
man/infection.net.Rd | 7 -
man/init.dcm.Rd | 17 +-
man/init.icm.Rd | 19 +-
man/init.net.Rd | 17 +-
man/init_pids.Rd | 7 -
man/init_status.icm.Rd | 5
man/init_status.net.Rd | 5
man/initialize.icm.Rd | 9 -
man/initialize.net.Rd | 13 +
man/mcat.Rd | 5
man/merge.icm.Rd | 9 -
man/merge.netsim.Rd | 10 +
man/modeids.Rd | 7 -
man/modules.icm.Rd | 3
man/modules.net.Rd | 3
man/netdx.Rd | 3
man/netest.Rd | 27 ++--
man/netsim.Rd | 11 -
man/netsim_parallel.Rd | 5
man/node_active.Rd | 13 +
man/param.dcm.Rd | 35 ++---
man/param.icm.Rd | 35 ++---
man/param.net.Rd | 31 ++--
man/plot.conc_microsim.Rd | 3
man/plot.dcm.Rd | 31 ++--
man/plot.icm.Rd | 45 +++---
man/plot.netdx.Rd | 3
man/plot.netsim.Rd | 3
man/recovery.icm.Rd | 7 -
man/recovery.net.Rd | 7 -
man/resim_nets.Rd | 7 -
man/saveout.dcm.Rd | 13 +
man/saveout.icm.Rd | 9 -
man/saveout.net.Rd | 9 -
man/sim_nets.Rd | 13 +
man/split_bip.Rd | 17 +-
man/ssample.Rd | 7 -
man/summary.dcm.Rd | 13 +
man/summary.icm.Rd | 11 -
man/summary.netest.Rd | 7 -
man/summary.netsim.Rd | 11 -
man/test_icm.Rd | 5
man/test_net.Rd | 5
man/transco.Rd | 9 -
man/update_nwattr.Rd | 13 +
man/verbose.dcm.Rd | 9 -
man/verbose.icm.Rd | 11 -
man/verbose.net.Rd | 11 -
tests/testthat/test-newnet.R | 14 ++
tests/testthat/test-parallel.R |only
vignettes/Intro.Rmd | 22 ++-
131 files changed, 1269 insertions(+), 1264 deletions(-)
Title: Code Analysis Tools for R
Diff between codetools versions 0.2-9 dated 2014-08-21 and 0.2-10 dated 2015-01-17
Description: Code analysis tools for R
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/codetools.R | 16 +++++++++++++---
3 files changed, 18 insertions(+), 8 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.10.2.2 dated 2014-12-08 and 0.11 dated 2015-01-17
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang
shiny-0.10.2.2/shiny/inst/COPYING |only
shiny-0.10.2.2/shiny/inst/NOTICE |only
shiny-0.10.2.2/shiny/inst/tests-js |only
shiny-0.10.2.2/shiny/inst/www/shared/bootstrap/css/bootstrap-responsive.css |only
shiny-0.10.2.2/shiny/inst/www/shared/bootstrap/css/bootstrap-responsive.min.css |only
shiny-0.10.2.2/shiny/inst/www/shared/bootstrap/img |only
shiny-0.10.2.2/shiny/inst/www/shared/selectize/css/selectize.bootstrap2.css |only
shiny-0.10.2.2/shiny/inst/www/shared/slider |only
shiny-0.11/shiny/DESCRIPTION | 86
shiny-0.11/shiny/LICENSE |only
shiny-0.11/shiny/MD5 | 349
shiny-0.11/shiny/NAMESPACE | 5
shiny-0.11/shiny/NEWS | 45
shiny-0.11/shiny/R/app.R | 33
shiny-0.11/shiny/R/bootstrap-layout.R | 28
shiny-0.11/shiny/R/bootstrap.R | 580
shiny-0.11/shiny/R/middleware-shiny.R | 4
shiny-0.11/shiny/R/progress.R | 11
shiny-0.11/shiny/R/react.R | 8
shiny-0.11/shiny/R/reactives.R | 218
shiny-0.11/shiny/R/server.R | 27
shiny-0.11/shiny/R/shiny.R | 69
shiny-0.11/shiny/R/shinyui.R | 23
shiny-0.11/shiny/R/shinywrappers.R | 62
shiny-0.11/shiny/R/showcase.R | 35
shiny-0.11/shiny/R/slider.R | 116
shiny-0.11/shiny/R/update-input.R | 74
shiny-0.11/shiny/R/utils.R | 45
shiny-0.11/shiny/README.md | 18
shiny-0.11/shiny/inst/staticdocs/index.r | 5
shiny-0.11/shiny/inst/tests/test-bootstrap.r | 38
shiny-0.11/shiny/inst/tests/test-reactivity.r | 140
shiny-0.11/shiny/inst/www/shared/bootstrap/css/bootstrap-theme.css |only
shiny-0.11/shiny/inst/www/shared/bootstrap/css/bootstrap-theme.min.css |only
shiny-0.11/shiny/inst/www/shared/bootstrap/css/bootstrap.css |10113 +++++-----
shiny-0.11/shiny/inst/www/shared/bootstrap/css/bootstrap.min.css | 12
shiny-0.11/shiny/inst/www/shared/bootstrap/fonts |only
shiny-0.11/shiny/inst/www/shared/bootstrap/js/bootstrap.js | 3272 +--
shiny-0.11/shiny/inst/www/shared/bootstrap/js/bootstrap.min.js | 11
shiny-0.11/shiny/inst/www/shared/bootstrap/shim |only
shiny-0.11/shiny/inst/www/shared/datatables/css/dataTables.bootstrap.css | 166
shiny-0.11/shiny/inst/www/shared/datatables/css/dataTables.extra.css | 17
shiny-0.11/shiny/inst/www/shared/datatables/js/dataTables.bootstrap.js | 236
shiny-0.11/shiny/inst/www/shared/datatables/js/jquery.dataTables.min.js | 308
shiny-0.11/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.js | 6
shiny-0.11/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.min.js | 4
shiny-0.11/shiny/inst/www/shared/font-awesome/css/font-awesome.css | 454
shiny-0.11/shiny/inst/www/shared/font-awesome/css/font-awesome.min.css | 4
shiny-0.11/shiny/inst/www/shared/font-awesome/fonts/FontAwesome.otf |binary
shiny-0.11/shiny/inst/www/shared/font-awesome/fonts/fontawesome-webfont.eot |binary
shiny-0.11/shiny/inst/www/shared/font-awesome/fonts/fontawesome-webfont.svg | 174
shiny-0.11/shiny/inst/www/shared/font-awesome/fonts/fontawesome-webfont.ttf |binary
shiny-0.11/shiny/inst/www/shared/font-awesome/fonts/fontawesome-webfont.woff |binary
shiny-0.11/shiny/inst/www/shared/ionrangeslider |only
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shiny-0.11/shiny/inst/www/shared/jquery.min.js |only
shiny-0.11/shiny/inst/www/shared/jquery.min.map |only
shiny-0.11/shiny/inst/www/shared/selectize/css/selectize.bootstrap3.css |only
shiny-0.11/shiny/inst/www/shared/selectize/js/selectize.min.js | 6
shiny-0.11/shiny/inst/www/shared/shiny.css | 74
shiny-0.11/shiny/inst/www/shared/shiny.js | 195
shiny-0.11/shiny/inst/www/shared/shiny.min.js |only
shiny-0.11/shiny/inst/www/shared/shiny.min.js.map |only
shiny-0.11/shiny/man/Progress.Rd | 3
shiny-0.11/shiny/man/absolutePanel.Rd | 3
shiny-0.11/shiny/man/actionButton.Rd | 12
shiny-0.11/shiny/man/addResourcePath.Rd | 3
shiny-0.11/shiny/man/bootstrapPage.Rd | 11
shiny-0.11/shiny/man/checkboxGroupInput.Rd | 9
shiny-0.11/shiny/man/checkboxInput.Rd | 9
shiny-0.11/shiny/man/column.Rd | 3
shiny-0.11/shiny/man/conditionalPanel.Rd | 3
shiny-0.11/shiny/man/createWebDependency.Rd | 3
shiny-0.11/shiny/man/dateInput.Rd | 10
shiny-0.11/shiny/man/dateRangeInput.Rd | 9
shiny-0.11/shiny/man/domains.Rd | 3
shiny-0.11/shiny/man/downloadButton.Rd | 3
shiny-0.11/shiny/man/downloadHandler.Rd | 3
shiny-0.11/shiny/man/exprToFunction.Rd | 3
shiny-0.11/shiny/man/fileInput.Rd | 9
shiny-0.11/shiny/man/fixedPage.Rd | 12
shiny-0.11/shiny/man/flowLayout.Rd | 3
shiny-0.11/shiny/man/fluidPage.Rd | 14
shiny-0.11/shiny/man/headerPanel.Rd | 3
shiny-0.11/shiny/man/helpText.Rd | 3
shiny-0.11/shiny/man/htmlOutput.Rd | 3
shiny-0.11/shiny/man/icon.Rd | 32
shiny-0.11/shiny/man/imageOutput.Rd | 3
shiny-0.11/shiny/man/inputPanel.Rd | 3
shiny-0.11/shiny/man/installExprFunction.Rd | 3
shiny-0.11/shiny/man/invalidateLater.Rd | 3
shiny-0.11/shiny/man/is.reactivevalues.Rd | 3
shiny-0.11/shiny/man/isolate.Rd | 3
shiny-0.11/shiny/man/knitr_methods.Rd | 3
shiny-0.11/shiny/man/mainPanel.Rd | 3
shiny-0.11/shiny/man/makeReactiveBinding.Rd | 3
shiny-0.11/shiny/man/markRenderFunction.Rd | 3
shiny-0.11/shiny/man/maskReactiveContext.Rd | 3
shiny-0.11/shiny/man/navbarPage.Rd | 24
shiny-0.11/shiny/man/navlistPanel.Rd | 12
shiny-0.11/shiny/man/numericInput.Rd | 9
shiny-0.11/shiny/man/observe.Rd | 3
shiny-0.11/shiny/man/observeEvent.Rd |only
shiny-0.11/shiny/man/outputOptions.Rd | 3
shiny-0.11/shiny/man/pageWithSidebar.Rd | 3
shiny-0.11/shiny/man/parseQueryString.Rd | 3
shiny-0.11/shiny/man/passwordInput.Rd |only
shiny-0.11/shiny/man/plotOutput.Rd | 3
shiny-0.11/shiny/man/plotPNG.Rd | 3
shiny-0.11/shiny/man/radioButtons.Rd | 9
shiny-0.11/shiny/man/reactive.Rd | 3
shiny-0.11/shiny/man/reactiveFileReader.Rd | 3
shiny-0.11/shiny/man/reactivePlot.Rd | 3
shiny-0.11/shiny/man/reactivePoll.Rd | 3
shiny-0.11/shiny/man/reactivePrint.Rd | 3
shiny-0.11/shiny/man/reactiveTable.Rd | 3
shiny-0.11/shiny/man/reactiveText.Rd | 3
shiny-0.11/shiny/man/reactiveTimer.Rd | 3
shiny-0.11/shiny/man/reactiveUI.Rd | 3
shiny-0.11/shiny/man/reactiveValues.Rd | 14
shiny-0.11/shiny/man/reactiveValuesToList.Rd | 3
shiny-0.11/shiny/man/registerInputHandler.Rd | 3
shiny-0.11/shiny/man/removeInputHandler.Rd | 3
shiny-0.11/shiny/man/renderDataTable.Rd | 48
shiny-0.11/shiny/man/renderImage.Rd | 3
shiny-0.11/shiny/man/renderPlot.Rd | 3
shiny-0.11/shiny/man/renderPrint.Rd | 3
shiny-0.11/shiny/man/renderTable.Rd | 3
shiny-0.11/shiny/man/renderText.Rd | 3
shiny-0.11/shiny/man/renderUI.Rd | 3
shiny-0.11/shiny/man/repeatable.Rd | 3
shiny-0.11/shiny/man/runApp.Rd | 30
shiny-0.11/shiny/man/runExample.Rd | 3
shiny-0.11/shiny/man/runUrl.Rd | 3
shiny-0.11/shiny/man/selectInput.Rd | 8
shiny-0.11/shiny/man/serverInfo.Rd | 3
shiny-0.11/shiny/man/session.Rd | 3
shiny-0.11/shiny/man/shiny-options.Rd |only
shiny-0.11/shiny/man/shiny-package.Rd | 8
shiny-0.11/shiny/man/shinyApp.Rd | 37
shiny-0.11/shiny/man/shinyDeprecated.Rd | 8
shiny-0.11/shiny/man/shinyServer.Rd | 3
shiny-0.11/shiny/man/shinyUI.Rd | 3
shiny-0.11/shiny/man/showReactLog.Rd | 3
shiny-0.11/shiny/man/sidebarLayout.Rd | 3
shiny-0.11/shiny/man/sidebarPanel.Rd | 3
shiny-0.11/shiny/man/sliderInput.Rd | 41
shiny-0.11/shiny/man/splitLayout.Rd | 3
shiny-0.11/shiny/man/stopApp.Rd | 3
shiny-0.11/shiny/man/submitButton.Rd | 9
shiny-0.11/shiny/man/tabPanel.Rd | 3
shiny-0.11/shiny/man/tableOutput.Rd | 42
shiny-0.11/shiny/man/tabsetPanel.Rd | 3
shiny-0.11/shiny/man/textInput.Rd | 9
shiny-0.11/shiny/man/textOutput.Rd | 3
shiny-0.11/shiny/man/titlePanel.Rd | 3
shiny-0.11/shiny/man/updateCheckboxGroupInput.Rd | 3
shiny-0.11/shiny/man/updateCheckboxInput.Rd | 3
shiny-0.11/shiny/man/updateDateInput.Rd | 3
shiny-0.11/shiny/man/updateDateRangeInput.Rd | 3
shiny-0.11/shiny/man/updateNumericInput.Rd | 3
shiny-0.11/shiny/man/updateRadioButtons.Rd | 3
shiny-0.11/shiny/man/updateSelectInput.Rd | 3
shiny-0.11/shiny/man/updateSliderInput.Rd | 56
shiny-0.11/shiny/man/updateTabsetPanel.Rd | 3
shiny-0.11/shiny/man/updateTextInput.Rd | 3
shiny-0.11/shiny/man/validate.Rd | 5
shiny-0.11/shiny/man/verbatimTextOutput.Rd | 3
shiny-0.11/shiny/man/verticalLayout.Rd | 3
shiny-0.11/shiny/man/wellPanel.Rd | 3
shiny-0.11/shiny/man/withMathJax.Rd | 3
shiny-0.11/shiny/man/withProgress.Rd | 3
172 files changed, 9799 insertions(+), 8005 deletions(-)
Title: Rigorous - DICOM Input / Output
Diff between oro.dicom versions 0.4.1 dated 2014-01-26 and 0.4.3 dated 2015-01-17
Description: Data input/output functions for data that conform to the
Digital Imaging and Communications in Medicine (DICOM) standard, part
of the Rigorous Analytics bundle.
Author: Brandon Whitcher
Maintainer: Brandon Whitcher
DESCRIPTION | 11 ++---
MD5 | 20 ++++-----
R/dicom.R | 2
R/header.R | 4 -
R/recursive.R | 69 +++++++++++++++++++++-------------
build/vignette.rds |binary
data/dicom.VR.rda |binary
data/dicom.dic.rda |binary
inst/doc/dicom.pdf |binary
man/readDICOMFile.Rd | 10 ++--
tests/Examples/oro.dicom-Ex.Rout.save | 10 ++--
11 files changed, 73 insertions(+), 53 deletions(-)
Title: Flexible Mixture Modeling
Diff between flexmix versions 2.3-12 dated 2014-09-24 and 2.3-13 dated 2015-01-17
Description: FlexMix implements a general framework for finite
mixtures of regression models using the EM algorithm.
FlexMix provides the E-step and all data handling, while the M-step can be
supplied by the user to easily define new models. Existing drivers
implement mixtures of standard linear models, generalized linear
models and model-based clustering.
Author: Bettina Gruen [aut, cre],
Friedrich Leisch [aut],
Deepayan Sarkar [ctb],
Frederic Mortier [ctb],
Nicolas Picard [ctb]
Maintainer: Bettina Gruen
flexmix-2.3-12/flexmix/tests |only
flexmix-2.3-13/flexmix/DESCRIPTION | 19 +-
flexmix-2.3-13/flexmix/MD5 | 147 +++++++---------
flexmix-2.3-13/flexmix/NAMESPACE | 1
flexmix-2.3-13/flexmix/R/allClasses.R | 17 -
flexmix-2.3-13/flexmix/R/glmnet.R |only
flexmix-2.3-13/flexmix/build/vignette.rds |binary
flexmix-2.3-13/flexmix/data/Mehta.RData |binary
flexmix-2.3-13/flexmix/inst/NEWS.Rd | 9
flexmix-2.3-13/flexmix/inst/doc/bootstrapping.R | 32 +--
flexmix-2.3-13/flexmix/inst/doc/bootstrapping.Rnw | 27 +-
flexmix-2.3-13/flexmix/inst/doc/bootstrapping.pdf |binary
flexmix-2.3-13/flexmix/inst/doc/flexmix-intro.pdf |binary
flexmix-2.3-13/flexmix/inst/doc/mixture-regressions.pdf |binary
flexmix-2.3-13/flexmix/inst/doc/regression-examples.pdf |binary
flexmix-2.3-13/flexmix/man/AIC-methods.Rd | 4
flexmix-2.3-13/flexmix/man/BIC-methods.Rd | 4
flexmix-2.3-13/flexmix/man/BregFix.Rd | 6
flexmix-2.3-13/flexmix/man/EIC.Rd | 4
flexmix-2.3-13/flexmix/man/ExLinear.Rd | 35 +--
flexmix-2.3-13/flexmix/man/ExNPreg.Rd | 10 -
flexmix-2.3-13/flexmix/man/ExNclus.Rd | 6
flexmix-2.3-13/flexmix/man/FLXMCfactanal.Rd | 2
flexmix-2.3-13/flexmix/man/FLXMCmvcombi.Rd | 14 -
flexmix-2.3-13/flexmix/man/FLXMCmvpois.Rd | 4
flexmix-2.3-13/flexmix/man/FLXMRglmnet.Rd |only
flexmix-2.3-13/flexmix/man/FLXMRlmer.Rd | 6
flexmix-2.3-13/flexmix/man/FLXMRlmmc.Rd | 3
flexmix-2.3-13/flexmix/man/FLXMRrobglm.Rd | 40 ++--
flexmix-2.3-13/flexmix/man/FLXMRziglm.Rd | 8
flexmix-2.3-13/flexmix/man/FLXP-class.Rd | 4
flexmix-2.3-13/flexmix/man/FLXbclust.Rd | 4
flexmix-2.3-13/flexmix/man/FLXcomponent-class.Rd | 4
flexmix-2.3-13/flexmix/man/FLXconcomitant.Rd | 8
flexmix-2.3-13/flexmix/man/FLXcontrol-class.Rd | 6
flexmix-2.3-13/flexmix/man/FLXdist-class.Rd | 10 -
flexmix-2.3-13/flexmix/man/FLXdist.Rd | 2
flexmix-2.3-13/flexmix/man/FLXfit.Rd | 4
flexmix-2.3-13/flexmix/man/FLXglm.Rd | 8
flexmix-2.3-13/flexmix/man/FLXglmFix.Rd | 23 +-
flexmix-2.3-13/flexmix/man/FLXmclust.Rd | 20 --
flexmix-2.3-13/flexmix/man/FLXmodel-class.Rd | 4
flexmix-2.3-13/flexmix/man/FLXnested-class.Rd | 4
flexmix-2.3-13/flexmix/man/ICL.Rd | 8
flexmix-2.3-13/flexmix/man/KLdiv.Rd | 20 +-
flexmix-2.3-13/flexmix/man/Lapply-methods.Rd | 4
flexmix-2.3-13/flexmix/man/Mehta.Rd | 12 -
flexmix-2.3-13/flexmix/man/NregFix.Rd | 13 -
flexmix-2.3-13/flexmix/man/betablocker.Rd | 14 -
flexmix-2.3-13/flexmix/man/bioChemists.Rd | 6
flexmix-2.3-13/flexmix/man/boot.Rd | 2
flexmix-2.3-13/flexmix/man/candy.Rd | 6
flexmix-2.3-13/flexmix/man/dmft.Rd | 6
flexmix-2.3-13/flexmix/man/fabricfault.Rd | 12 -
flexmix-2.3-13/flexmix/man/fitted.Rd | 10 -
flexmix-2.3-13/flexmix/man/flexmix-class.Rd | 4
flexmix-2.3-13/flexmix/man/flexmix-internal.Rd | 6
flexmix-2.3-13/flexmix/man/flexmix.Rd | 37 ++--
flexmix-2.3-13/flexmix/man/group.Rd | 2
flexmix-2.3-13/flexmix/man/logLik-methods.Rd | 4
flexmix-2.3-13/flexmix/man/patent.Rd | 26 +-
flexmix-2.3-13/flexmix/man/plot-methods.Rd | 12 -
flexmix-2.3-13/flexmix/man/plotEll.Rd | 10 -
flexmix-2.3-13/flexmix/man/posterior.Rd | 6
flexmix-2.3-13/flexmix/man/refit.Rd | 23 +-
flexmix-2.3-13/flexmix/man/relabel.Rd | 12 -
flexmix-2.3-13/flexmix/man/rflexmix.Rd | 2
flexmix-2.3-13/flexmix/man/salmonellaTA98.Rd | 6
flexmix-2.3-13/flexmix/man/seizure.Rd | 25 +-
flexmix-2.3-13/flexmix/man/stepFlexmix.Rd | 47 ++---
flexmix-2.3-13/flexmix/man/tribolium.Rd | 8
flexmix-2.3-13/flexmix/man/trypanosome.Rd | 6
flexmix-2.3-13/flexmix/man/whiskey.Rd | 4
flexmix-2.3-13/flexmix/vignettes/bootstrapping.Rnw | 27 +-
74 files changed, 447 insertions(+), 432 deletions(-)
Title: Detecting, Combining and Filtering Isotope, Adduct and Homologue
Series Relations in High-Resolution Mass Spectrometry (HRMS)
Data
Diff between nontarget versions 1.6 dated 2014-12-10 and 1.7 dated 2015-01-17
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos
DESCRIPTION | 10 -
MD5 | 12 -
NEWS | 4
R/nontarget.R | 2
R/pattern.search.R | 37 ++++-
R/pattern.search2.R | 4
src/massCpp.cpp | 322 ++++++++++++++++++++++++----------------------------
7 files changed, 192 insertions(+), 199 deletions(-)
Title: Facilitates Automated HTML Report Creation
Diff between HTMLUtils versions 0.1.6 dated 2014-12-01 and 0.1.7 dated 2015-01-17
Description: Facilitates automated HTML report creation, in particular
framed HTML pages and dynamically sortable tables.
Author: "Markus Loecher, Berlin School of Economics and Law (BSEL)"
Maintainer: "Markus Loecher, Berlin School of Economics and Law (BSEL)"
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
NEWS |only
R/BasicHTML.R | 1 +
R/FramedHTML.R | 47 +++++++++++++++++++++++++++++++----------------
man/FramedHTML.Rd | 12 ++++++++++++
man/HTMLUtils-package.Rd | 4 ++--
7 files changed, 56 insertions(+), 27 deletions(-)
Title: Tools to Make Developing R Packages Easier
Diff between devtools versions 1.6.1 dated 2014-10-07 and 1.7.0 dated 2015-01-17
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham
devtools-1.6.1/devtools/R/reverse-dependencies.r |only
devtools-1.6.1/devtools/tests/testthat/test-checks.r |only
devtools-1.7.0/devtools/DESCRIPTION | 30 -
devtools-1.7.0/devtools/MD5 | 253 +++++----
devtools-1.7.0/devtools/NAMESPACE | 14
devtools-1.7.0/devtools/R/build.r | 14
devtools-1.7.0/devtools/R/check-cran.r | 254 +++-------
devtools-1.7.0/devtools/R/check-devtools.r | 90 +--
devtools-1.7.0/devtools/R/check.r | 18
devtools-1.7.0/devtools/R/compile-dll.r | 6
devtools-1.7.0/devtools/R/cran.r | 6
devtools-1.7.0/devtools/R/create.r | 48 +
devtools-1.7.0/devtools/R/decompress.r | 16
devtools-1.7.0/devtools/R/deps.R |only
devtools-1.7.0/devtools/R/dev-help.r | 22
devtools-1.7.0/devtools/R/dev-mode.r | 2
devtools-1.7.0/devtools/R/document.r | 5
devtools-1.7.0/devtools/R/git.R | 2
devtools-1.7.0/devtools/R/infrastructure.R | 140 +++++
devtools-1.7.0/devtools/R/install-git.r | 2
devtools-1.7.0/devtools/R/install-github.r | 4
devtools-1.7.0/devtools/R/install.r | 3
devtools-1.7.0/devtools/R/lint.r |only
devtools-1.7.0/devtools/R/load-data.r | 2
devtools-1.7.0/devtools/R/load-dll.r | 2
devtools-1.7.0/devtools/R/load.r | 11
devtools-1.7.0/devtools/R/missing-s3.r | 5
devtools-1.7.0/devtools/R/package.r | 26 +
devtools-1.7.0/devtools/R/release.r | 25
devtools-1.7.0/devtools/R/reload.r | 2
devtools-1.7.0/devtools/R/remove-s4-class.r | 2
devtools-1.7.0/devtools/R/revdep-summarise.R |only
devtools-1.7.0/devtools/R/revdep.R |only
devtools-1.7.0/devtools/R/run-examples.r | 2
devtools-1.7.0/devtools/R/session-info.r | 58 +-
devtools-1.7.0/devtools/R/unload.r | 2
devtools-1.7.0/devtools/R/utils.r | 15
devtools-1.7.0/devtools/R/vignettes.r | 2
devtools-1.7.0/devtools/R/with-debug.r | 37 -
devtools-1.7.0/devtools/R/zzz.r | 7
devtools-1.7.0/devtools/README.md | 21
devtools-1.7.0/devtools/inst/templates/README.Rmd |only
devtools-1.7.0/devtools/inst/templates/appveyor.yml |only
devtools-1.7.0/devtools/inst/templates/cran-comments.md |only
devtools-1.7.0/devtools/inst/templates/readme-rmd-pre-commit.sh |only
devtools-1.7.0/devtools/inst/templates/revdep.R |only
devtools-1.7.0/devtools/inst/templates/travis.yml | 5
devtools-1.7.0/devtools/man/as.package.Rd | 3
devtools-1.7.0/devtools/man/bash.Rd | 3
devtools-1.7.0/devtools/man/build.Rd | 9
devtools-1.7.0/devtools/man/build_github_devtools.Rd | 3
devtools-1.7.0/devtools/man/build_vignettes.Rd | 5
devtools-1.7.0/devtools/man/build_win.Rd | 3
devtools-1.7.0/devtools/man/check.Rd | 15
devtools-1.7.0/devtools/man/check_cran.Rd | 30 -
devtools-1.7.0/devtools/man/check_dep_version.Rd | 3
devtools-1.7.0/devtools/man/check_doc.Rd | 3
devtools-1.7.0/devtools/man/clean_dll.Rd | 3
devtools-1.7.0/devtools/man/clean_source.Rd | 3
devtools-1.7.0/devtools/man/clean_vignettes.Rd | 3
devtools-1.7.0/devtools/man/compile_dll.Rd | 5
devtools-1.7.0/devtools/man/compiler_flags.Rd | 7
devtools-1.7.0/devtools/man/cran_env_vars.Rd | 3
devtools-1.7.0/devtools/man/create.Rd | 16
devtools-1.7.0/devtools/man/create_description.Rd | 6
devtools-1.7.0/devtools/man/dev_example.Rd | 3
devtools-1.7.0/devtools/man/dev_help.Rd | 3
devtools-1.7.0/devtools/man/dev_meta.Rd | 3
devtools-1.7.0/devtools/man/dev_mode.Rd | 5
devtools-1.7.0/devtools/man/dev_packages.Rd | 3
devtools-1.7.0/devtools/man/devtest.Rd | 3
devtools-1.7.0/devtools/man/devtools.Rd | 5
devtools-1.7.0/devtools/man/document.Rd | 5
devtools-1.7.0/devtools/man/eval_clean.Rd | 3
devtools-1.7.0/devtools/man/find_rtools.Rd | 3
devtools-1.7.0/devtools/man/find_topic.Rd | 3
devtools-1.7.0/devtools/man/github_pat.Rd | 3
devtools-1.7.0/devtools/man/github_refs.Rd | 3
devtools-1.7.0/devtools/man/has_devel.Rd | 3
devtools-1.7.0/devtools/man/has_tests.Rd | 3
devtools-1.7.0/devtools/man/help.Rd | 25
devtools-1.7.0/devtools/man/imports_env.Rd | 3
devtools-1.7.0/devtools/man/infrastructure.Rd | 31 +
devtools-1.7.0/devtools/man/inst.Rd | 3
devtools-1.7.0/devtools/man/install.Rd | 5
devtools-1.7.0/devtools/man/install_bitbucket.Rd | 3
devtools-1.7.0/devtools/man/install_deps.Rd | 3
devtools-1.7.0/devtools/man/install_git.Rd | 5
devtools-1.7.0/devtools/man/install_github.Rd | 5
devtools-1.7.0/devtools/man/install_gitorious.Rd | 3
devtools-1.7.0/devtools/man/install_local.Rd | 3
devtools-1.7.0/devtools/man/install_svn.Rd | 3
devtools-1.7.0/devtools/man/install_url.Rd | 3
devtools-1.7.0/devtools/man/install_version.Rd | 26 -
devtools-1.7.0/devtools/man/is.package.Rd | 3
devtools-1.7.0/devtools/man/lint.Rd |only
devtools-1.7.0/devtools/man/load_all.Rd | 3
devtools-1.7.0/devtools/man/load_code.Rd | 3
devtools-1.7.0/devtools/man/load_data.Rd | 5
devtools-1.7.0/devtools/man/load_dll.Rd | 3
devtools-1.7.0/devtools/man/load_imports.Rd | 3
devtools-1.7.0/devtools/man/loaded_packages.Rd | 3
devtools-1.7.0/devtools/man/missing_s3.Rd | 3
devtools-1.7.0/devtools/man/ns_env.Rd | 3
devtools-1.7.0/devtools/man/on_path.Rd | 3
devtools-1.7.0/devtools/man/parse_deps.Rd | 3
devtools-1.7.0/devtools/man/parse_ns_file.Rd | 3
devtools-1.7.0/devtools/man/path.Rd | 3
devtools-1.7.0/devtools/man/pkg_env.Rd | 3
devtools-1.7.0/devtools/man/r_env_vars.Rd | 3
devtools-1.7.0/devtools/man/release.Rd | 3
devtools-1.7.0/devtools/man/release_checks.Rd |only
devtools-1.7.0/devtools/man/reload.Rd | 5
devtools-1.7.0/devtools/man/revdep.Rd | 40 -
devtools-1.7.0/devtools/man/revdep_check.Rd |only
devtools-1.7.0/devtools/man/run_examples.Rd | 5
devtools-1.7.0/devtools/man/run_pkg_hook.Rd | 3
devtools-1.7.0/devtools/man/session_info.Rd | 9
devtools-1.7.0/devtools/man/show_news.Rd | 3
devtools-1.7.0/devtools/man/source_gist.Rd | 3
devtools-1.7.0/devtools/man/source_url.Rd | 3
devtools-1.7.0/devtools/man/submit_cran.Rd | 5
devtools-1.7.0/devtools/man/system.file.Rd | 3
devtools-1.7.0/devtools/man/test.Rd | 3
devtools-1.7.0/devtools/man/unload.Rd | 5
devtools-1.7.0/devtools/man/use_build_ignore.Rd | 15
devtools-1.7.0/devtools/man/use_data.Rd | 14
devtools-1.7.0/devtools/man/use_data_raw.Rd | 14
devtools-1.7.0/devtools/man/use_git_hook.Rd |only
devtools-1.7.0/devtools/man/use_package.Rd | 14
devtools-1.7.0/devtools/man/use_readme_rmd.Rd |only
devtools-1.7.0/devtools/man/wd.Rd | 3
devtools-1.7.0/devtools/man/with_debug.Rd | 18
devtools-1.7.0/devtools/man/with_something.Rd | 3
devtools-1.7.0/devtools/tests/testthat/test-github.r | 3
devtools-1.7.0/devtools/tests/testthat/test-package.R |only
136 files changed, 967 insertions(+), 702 deletions(-)
Title: Coercion Routines for Network Data Objects
Diff between intergraph versions 2.0-0 dated 2013-05-08 and 2.0-1 dated 2015-01-17
Description: Functions implemented in this package allow to coerce (i.e.
convert) network data between classes provided by other R packages.
Currently supported classes are those defined in packages: network and
igraph.
Author: Michal Bojanowski
Maintainer: Michal Bojanowski
intergraph-2.0-0/intergraph/inst/LICENSE |only
intergraph-2.0-1/intergraph/DESCRIPTION | 29 +--
intergraph-2.0-1/intergraph/MD5 | 56 +++---
intergraph-2.0-1/intergraph/NAMESPACE | 3
intergraph-2.0-1/intergraph/R/asIgraph.R | 12 -
intergraph-2.0-1/intergraph/R/asNetwork.R | 10 -
intergraph-2.0-1/intergraph/R/attrmap.R | 3
intergraph-2.0-1/intergraph/R/intergraph-package.R | 5
intergraph-2.0-1/intergraph/R/netcompare.R | 56 +++---
intergraph-2.0-1/intergraph/README.md |only
intergraph-2.0-1/intergraph/build |only
intergraph-2.0-1/intergraph/data/exIgraph.rda |binary
intergraph-2.0-1/intergraph/data/exIgraph2.rda |binary
intergraph-2.0-1/intergraph/data/exNetwork.rda |binary
intergraph-2.0-1/intergraph/data/exNetwork2.rda |binary
intergraph-2.0-1/intergraph/inst/CITATION | 45 ++---
intergraph-2.0-1/intergraph/inst/doc |only
intergraph-2.0-1/intergraph/inst/tests/test-asIgraph.R | 13 -
intergraph-2.0-1/intergraph/inst/tests/test-asNetwork.R | 2
intergraph-2.0-1/intergraph/inst/tests/test-attrmap.R |only
intergraph-2.0-1/intergraph/inst/tests/test-github_issues.R |only
intergraph-2.0-1/intergraph/inst/tests/test-netcompare.R |only
intergraph-2.0-1/intergraph/man/as.matrix.igraph.Rd | 60 +++---
intergraph-2.0-1/intergraph/man/asDF.Rd | 107 +++++-------
intergraph-2.0-1/intergraph/man/asIgraph.Rd | 74 +++-----
intergraph-2.0-1/intergraph/man/asNetwork.Rd | 70 +++----
intergraph-2.0-1/intergraph/man/attrmap.Rd | 67 +++----
intergraph-2.0-1/intergraph/man/dumpAttr.Rd | 27 +--
intergraph-2.0-1/intergraph/man/exNetwork.Rd | 29 +--
intergraph-2.0-1/intergraph/man/intergraph-package.Rd | 62 +++---
intergraph-2.0-1/intergraph/man/netcompare.Rd | 79 ++++----
intergraph-2.0-1/intergraph/vignettes |only
32 files changed, 398 insertions(+), 411 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Diff between rsdmx versions 0.4-3 dated 2014-12-03 and 0.4-4 dated 2015-01-16
Description: rsdmx provides a set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework. The
package currently focuses on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel
DESCRIPTION | 31 ++++++------
MD5 | 25 +++++-----
NAMESPACE | 3 +
R/Class-SDMXHeader.R | 36 +++++++++++---
R/Class-SDMXType.R | 11 ++--
R/Class-SDMXUtilityData.R |only
R/SDMXCompactData-methods.R | 58 +++++++++++++++--------
R/SDMXHeader-methods.R | 105 +++++++++++++++++++++++++------------------
R/SDMXMessageGroup-methods.R | 8 ---
R/SDMXUtilityData-methods.R |only
R/readSDMX.R | 39 ++++++++-------
README.md | 8 ++-
man/SDMXType-class.Rd | 4 +
man/SDMXUtilityData-class.Rd |only
man/rsdmx-package.Rd | 4 -
15 files changed, 199 insertions(+), 133 deletions(-)
Title: Parameter estimation for the averaging model of Information
Integration Theory
Diff between rAverage versions 0.4-10 dated 2014-11-11 and 0.4-13 dated 2015-01-16
Description: Parameter estimation for averaging models of Anderson's Information Integration Theory
Author: Giulio Vidotto
Maintainer: Davide Massidda
DESCRIPTION | 12 +++++-----
MD5 | 18 +++++++--------
R/fun.rav.R | 57 +++++++++++++++---------------------------------
R/rAverage.R | 5 ++++
R/rav.R | 8 ------
man/outlier.replace.Rd | 6 +++--
man/rAverage-package.Rd | 6 ++---
man/rav.Rd | 6 ++---
src/combinations.c | 20 ++++++++--------
src/rAverage.h | 2 -
10 files changed, 60 insertions(+), 80 deletions(-)
Title: Bayesian Fertility Projection
Diff between bayesTFR versions 4.0-11 dated 2014-11-21 and 4.1-2 dated 2015-01-16
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova
ChangeLog | 13 +++++++++----
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/mcmc_ini.R | 13 ++++++-------
R/run_mcmc.R | 7 ++++---
R/wpp_data.R | 28 ++++++++++++++++++++++------
man/bayesTFR-package.Rd | 4 ++--
man/run-mcmc.Rd | 7 +++++--
man/run.tfr.mcmc.extra.Rd | 6 ++++--
tests/test_functions.R | 24 +++++++++++++++++++++---
10 files changed, 86 insertions(+), 42 deletions(-)
Title: Core Methods and Classes Used by aroma.* Packages Part of The
Aroma Framework
Diff between aroma.core versions 2.12.1 dated 2014-03-08 and 2.13.0 dated 2015-01-16
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API is mostly of interest
to developers and is rarely used by end users directly.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson
aroma.core-2.12.1/aroma.core/inst/annotationData/genomes/Human/Human,chromosomes,20100928.txt |only
aroma.core-2.12.1/aroma.core/inst/annotationData/genomes/Human/Human,chromosomes,max,20090503.txt |only
aroma.core-2.13.0/aroma.core/DESCRIPTION | 33 -
aroma.core-2.13.0/aroma.core/MD5 | 151 +++----
aroma.core-2.13.0/aroma.core/NAMESPACE | 28 -
aroma.core-2.13.0/aroma.core/NEWS | 58 ++
aroma.core-2.13.0/aroma.core/R/009.setup.R | 36 +
aroma.core-2.13.0/aroma.core/R/999.AromaCore.R | 10
aroma.core-2.13.0/aroma.core/R/AromaCellCpgFile.R | 50 --
aroma.core-2.13.0/aroma.core/R/AromaCellPositionFile.R | 64 ---
aroma.core-2.13.0/aroma.core/R/AromaCellTabularBinaryFile.R | 64 ++-
aroma.core-2.13.0/aroma.core/R/AromaMicroarrayDataFile.ATTRS.R | 14
aroma.core-2.13.0/aroma.core/R/AromaMicroarrayDataSet.ATTRS.R | 12
aroma.core-2.13.0/aroma.core/R/AromaMicroarrayDataSetTuple.R | 30 -
aroma.core-2.13.0/aroma.core/R/AromaMicroarrayTabularBinaryFile.R | 43 --
aroma.core-2.13.0/aroma.core/R/AromaPlatform.R | 38 +
aroma.core-2.13.0/aroma.core/R/AromaPlatformInterface.R | 213 +++++++++-
aroma.core-2.13.0/aroma.core/R/AromaTabularBinaryFile.R | 12
aroma.core-2.13.0/aroma.core/R/AromaTabularBinarySet.ATTRS.R | 16
aroma.core-2.13.0/aroma.core/R/AromaUnitCallSet.R | 12
aroma.core-2.13.0/aroma.core/R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 4
aroma.core-2.13.0/aroma.core/R/AromaUnitGenotypeCallSet.R | 18
aroma.core-2.13.0/aroma.core/R/AromaUnitPscnBinarySet.R | 4
aroma.core-2.13.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 18
aroma.core-2.13.0/aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R | 8
aroma.core-2.13.0/aroma.core/R/AromaUnitSignalBinarySet.R | 15
aroma.core-2.13.0/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 2
aroma.core-2.13.0/aroma.core/R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R | 8
aroma.core-2.13.0/aroma.core/R/AromaUnitTotalCnBinarySet.R | 4
aroma.core-2.13.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 4
aroma.core-2.13.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 4
aroma.core-2.13.0/aroma.core/R/CbsModel.R | 21
aroma.core-2.13.0/aroma.core/R/ChromosomeExplorer.R | 4
aroma.core-2.13.0/aroma.core/R/CopyNumberChromosomalModel.R | 11
aroma.core-2.13.0/aroma.core/R/CopyNumberRegions.R | 2
aroma.core-2.13.0/aroma.core/R/CopyNumberSegmentationModel.R | 2
aroma.core-2.13.0/aroma.core/R/Explorer.R | 32 +
aroma.core-2.13.0/aroma.core/R/HaarSegModel.R | 21
aroma.core-2.13.0/aroma.core/R/MPCBS.EXTS.R | 5
aroma.core-2.13.0/aroma.core/R/NonPairedPSCNData.R | 10
aroma.core-2.13.0/aroma.core/R/RasterImage.R | 4
aroma.core-2.13.0/aroma.core/R/SampleAnnotationFile.R | 2
aroma.core-2.13.0/aroma.core/R/SampleAnnotationSet.R | 18
aroma.core-2.13.0/aroma.core/R/SegmentationDataSet.R | 8
aroma.core-2.13.0/aroma.core/R/fitGenotypeCone.matrix.R | 6
aroma.core-2.13.0/aroma.core/R/fitMultiDimensionalCone.matrix.R | 8
aroma.core-2.13.0/aroma.core/R/fitWHRCModel.matrix.R | 13
aroma.core-2.13.0/aroma.core/R/getCommonListElements.R | 4
aroma.core-2.13.0/aroma.core/R/norm2d.matrix.R | 10
aroma.core-2.13.0/aroma.core/R/stringTree.R | 8
aroma.core-2.13.0/aroma.core/R/zzz.R | 2
aroma.core-2.13.0/aroma.core/inst/testScripts/fileFormats/acf/test20090107,AromaUnitGenotypeCallSet.R | 4
aroma.core-2.13.0/aroma.core/inst/testScripts/fileFormats/acf/test20090518,acf.R | 11
aroma.core-2.13.0/aroma.core/man/AromaCellTabularBinaryFile.Rd | 41 -
aroma.core-2.13.0/aroma.core/man/AromaMicroarrayDataSet.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaMicroarrayDataSetTuple.Rd | 28 -
aroma.core-2.13.0/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaPlatform.Rd | 39 +
aroma.core-2.13.0/aroma.core/man/AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/man/AromaTabularBinarySet.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaUnitCallFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/AromaUnitCallSet.Rd | 32 -
aroma.core-2.13.0/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/AromaUnitFracBCnBinarySet.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/AromaUnitGenotypeCallSet.Rd | 32 -
aroma.core-2.13.0/aroma.core/man/AromaUnitPscnBinaryFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/AromaUnitPscnBinarySet.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 3
aroma.core-2.13.0/aroma.core/man/AromaUnitSignalBinarySet.Rd | 32 -
aroma.core-2.13.0/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 2
aroma.core-2.13.0/aroma.core/man/AromaUnitTypesFile.Rd | 4
aroma.core-2.13.0/aroma.core/man/Non-documented_objects.Rd | 15
aroma.core-2.13.0/aroma.core/man/getAromaPlatform.AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/man/getChipType.AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/man/getPlatform.AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/man/getUnitAnnotationDataFile.AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/man/isCompatibleWith.AromaPlatformInterface.Rd |only
aroma.core-2.13.0/aroma.core/tests/aromaSettings.R |only
81 files changed, 849 insertions(+), 590 deletions(-)
Title: Biplot representations of ordinal variables
Diff between OrdinalLogisticBiplot versions 0.3 dated 2014-05-02 and 0.4 dated 2015-01-16
More information about OrdinalLogisticBiplot at CRAN
Description: Analysis of a matrix of polytomous items using Ordinal Logistic Biplots (OLB)
The OLB procedure extends the binary logistic biplot to ordinal (polytomous) data.
The individuals are represented as points on a plane and the variables are represented
as lines rather than vectors as in a classical or binary biplot, specifying the points
for each of the categories of the variable.
The set of prediction regions is established by stripes perpendicular to the line
between the category points, in such a way that the prediction for each individual is given
by its projection into the line of the variable.
Author: Julio Cesar Hernandez Sanchez, Jose Luis Vicente-Villardon
Maintainer: Julio Cesar Hernandez Sanchez
DESCRIPTION | 8 -
MD5 | 40 +++----
R/BiplotDensity.r | 5
R/CheckDataSet.r | 14 +-
R/OrdinalLogBiplotEM.r | 27 ++--
R/OrdinalLogisticBiplot.r | 190 ++++++++++++++++------------------
R/PlotClusters.r | 3
R/plotOrdinalFittedVariable.r | 4
R/plotOrdinalVariable.r | 1
R/pordlogist.r | 193 +++++++++++++++++++----------------
man/BiplotDensity.Rd | 7 -
man/CheckDataSet.Rd | 6 -
man/LevelSatPhd.Rd | 2
man/OrdinalLogBiplotEM.Rd | 8 -
man/OrdinalLogisticBiplot-package.Rd | 4
man/OrdinalLogisticBiplot.Rd | 10 -
man/plot.ordinal.logistic.biplot.Rd | 4
man/plotOrdinalFittedVariable.Rd | 2
man/plotOrdinalVariable.Rd | 2
man/pordlogist.Rd | 2
man/summary.pordlogist.Rd | 2
21 files changed, 277 insertions(+), 257 deletions(-)
Permanent link
Title: Bringing to light significant Columns correlated with Organism
Labels
Diff between bcool versions 1.1 dated 2014-02-21 and 1.2 dated 2015-01-16
Description: A set of analytical tools that helps searching for sites in an alignment, which might be associated with a phenotype label for the organism (e.g. changes in columns that can be associated with the pathogenicity character of an organism)
Author: Hugo Naya, Lucia Spangenberg
Maintainer: Hugo Naya
DESCRIPTION | 12
MD5 | 24 -
NAMESPACE | 2
R/bcool.R | 18 -
build/vignette.rds |binary
inst/doc/bcool.R | 678 ++++++++++++++++++++++++++++++++++--------
inst/doc/bcool.Snw | 20 -
inst/doc/bcool.pdf |binary
man/MCMCglmm.APPT.list.Rd | 3
man/RGBcolor.APPT.list.Rd | 3
man/bootMCMCglmm.APPT.list.Rd | 3
man/summaryAPPT.list.Rd | 1
vignettes/bcool.Snw | 20 -
13 files changed, 622 insertions(+), 162 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Diff between rNOMADS versions 2.1.1 dated 2015-01-03 and 2.1.2 dated 2015-01-16
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman
rNOMADS-2.1.1/rNOMADS/man/GetClosestGFSForecasts.Rd |only
rNOMADS-2.1.2/rNOMADS/DESCRIPTION | 8 ++--
rNOMADS-2.1.2/rNOMADS/MD5 | 38 ++++++++++----------
rNOMADS-2.1.2/rNOMADS/NEWS | 3 +
rNOMADS-2.1.2/rNOMADS/R/RNomadsTools.R | 11 +++--
rNOMADS-2.1.2/rNOMADS/man/BuildProfile.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/CrawlModels.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/DODSGrab.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/GetClosestForecasts.Rd |only
rNOMADS-2.1.2/rNOMADS/man/GetDODSDates.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/GetDODSModelRunInfo.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/GetDODSModelRuns.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/GribGrab.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/GribInfo.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/ModelGrid.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/ParseModelPage.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/PlotWindProfile.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/RTModelProfile.Rd | 4 +-
rNOMADS-2.1.2/rNOMADS/man/ReadGrib.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/WebCrawler.Rd | 2 -
rNOMADS-2.1.2/rNOMADS/man/rNOMADS-package.Rd | 2 -
21 files changed, 48 insertions(+), 44 deletions(-)
Title: Maximum Likelihood Inference for the Pearson VII Distribution
with Shape Parameter 3/2
Diff between pearson7 versions 1.0 dated 2013-02-14 and 1.0-1 dated 2015-01-16
Description: pearson7 supports maximum likelihood inference for the Pearson VII
distribution with shape parameter 3/2 and free location and scale
parameters. This distribution is relevant when estimating the velocity of
processive motor proteins with random detachment.
Author: John Hughes
Maintainer: John Hughes
DESCRIPTION | 18 +++++++++---------
MD5 | 6 +++---
R/zzz.R | 5 ++---
inst/CITATION | 5 ++---
4 files changed, 16 insertions(+), 18 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Diff between paleotree versions 2.2 dated 2014-09-18 and 2.3 dated 2015-01-16
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst
CHANGELOG | 10 +++
DESCRIPTION | 11 ++-
MD5 | 120 +++++++++++++++++++++--------------------
NAMESPACE | 4 +
R/cal3TimePaleoPhy.R | 8 ++
R/dateNodes.R | 2
R/degradeTree.R | 8 +-
R/durationFreq.R | 2
R/graptDisparity.R | 11 ++-
R/minBranchLength.R |only
R/modifyTerminalBranches.R | 121 +++++++++++++++++++++++++++++++++++++-----
R/perCapitaRates.R | 2
R/timePaleoPhy.R | 33 +++--------
R/timeSliceTree.R | 12 +++-
README | 25 ++++++++
man/DiversityCurves.Rd | 3 -
man/SamplingConv.Rd | 3 -
man/binTimeData.Rd | 3 -
man/branchClasses.Rd | 3 -
man/cal3TimePaleoPhy.Rd | 3 -
man/cladogeneticTraitCont.Rd | 3 -
man/compareTimescaling.Rd | 3 -
man/constrainParPaleo.Rd | 3 -
man/dateNodes.Rd | 3 -
man/degradeTree.Rd | 9 +--
man/depthRainbow.Rd | 3 -
man/durationFreq.Rd | 4 -
man/expandTaxonTree.Rd | 3 -
man/footeValues.Rd | 3 -
man/freqRat.Rd | 3 -
man/getSampProbDisc.Rd | 3 -
man/getSampRateCont.Rd | 3 -
man/graptDisparity.Rd | 14 ++--
man/horizonSampRate.Rd | 3 -
man/inverseSurv.Rd | 3 -
man/minBranchLength.Rd |only
man/modelMethods.Rd | 3 -
man/modifyTerminalBranches.Rd | 56 +++++++++++++++++--
man/multiDiv.Rd | 3 -
man/nearestNeighborDist.Rd | 3 -
man/optimPaleo.Rd | 3 -
man/paleotree-package.Rd | 3 -
man/perCapitaRates.Rd | 5 +
man/perfectParsCharTree.Rd | 3 -
man/plotTraitgram.Rd | 3 -
man/pqr2Ps.Rd | 3 -
man/probAnc.Rd | 3 -
man/retiolitinae.Rd | 3 -
man/reverseList.Rd | 3 -
man/rootSplit.Rd | 3 -
man/sampleRanges.Rd | 3 -
man/seqTimeList.Rd | 3 -
man/simFossilTaxa.Rd | 3 -
man/simFossilTaxa_SRCond.Rd | 3 -
man/simPaleoTrees.Rd | 3 -
man/taxa2cladogram.Rd | 3 -
man/taxa2phylo.Rd | 3 -
man/termTaxa.Rd | 3 -
man/timeLadderTree.Rd | 3 -
man/timePaleoPhy.Rd | 3 -
man/timeSliceTree.Rd | 5 +
man/unitLengthTree.Rd | 3 -
62 files changed, 401 insertions(+), 181 deletions(-)
Title: Fitting the centered autologistic and sparse spatial generalized
linear mixed models for areal data
Diff between ngspatial versions 1.0-4 dated 2014-09-09 and 1.0-5 dated 2015-01-16
Description: ngspatial provides tools for analyzing spatial data, especially
non-Gaussian areal data. The current version supports the sparse spatial
generalized linear mixed model of Hughes and Haran (2013) and the centered
autologistic model of Caragea and Kaiser (2009).
Author: John Hughes
Maintainer: John Hughes
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/zzz.R | 4 ++--
inst/CITATION | 5 ++---
4 files changed, 11 insertions(+), 12 deletions(-)
Title: Fisher-Wright Population Simulation
Diff between fwsim versions 0.3.2 dated 2014-08-27 and 0.3.3 dated 2015-01-16
Description: Simulates a population under the Fisher-Wright model (fixed or stochastic population size) with a one-step neutral mutation process (stepwise mutation model, logistic mutation model and exponential mutation model supported). The stochastic population sizes are random Poisson distributed and different kinds of population growth are supported. For the stepwise mutation model, it is possible to specify locus and direction specific mutation rate (in terms of upwards and downwards mutation rate). Intermediate generations can be saved in order to study e.g. drift.
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 3 +++
src/fwpopsim_fixed.cpp | 6 +++---
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Discrete Laplace mixture inference using the EM algorithm
Diff between disclapmix versions 1.5 dated 2014-06-14 and 1.6 dated 2015-01-16
Description: disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NEWS | 6 ++++++
R/helper.R | 32 +++++++++++++++++---------------
man/plot.disclapmixfit.Rd | 3 ++-
5 files changed, 34 insertions(+), 25 deletions(-)
Title: Consistent Batch Means Estimation of Monte Carlo Standard Errors
Diff between batchmeans versions 1.0-1 dated 2012-06-20 and 1.0-2 dated 2015-01-16
Description: batchmeans provides consistent batch means estimation of Monte
Carlo standard errors.
Author: Murali Haran
Maintainer: John Hughes
COPYING | 2 +-
DESCRIPTION | 18 +++++++++---------
MD5 | 16 ++++++++--------
R/batchmeans.R | 6 +++---
R/zzz.R | 10 +++++-----
inst/CITATION | 5 ++---
man/bm.Rd | 11 ++++++-----
man/bmmat.Rd | 6 +++---
man/estvssamp.Rd | 2 +-
9 files changed, 38 insertions(+), 38 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-82 dated 2015-01-07 and 0.5-83 dated 2015-01-16
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 14 ++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 39 ++++++++++++++++++++-------------------
R/AAA.R | 3 ++-
R/spChkOption.R | 13 ++++++++++++-
R/utils.R | 26 ++++++++++++++++++++------
inst/CITATION |only
inst/ChangeLog | 14 ++++++++++++++
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/sids.pdf |binary
man/GMerrorsar.Rd | 5 ++++-
man/do_ldet.Rd | 5 ++++-
man/errorsarlm.Rd | 7 ++++++-
man/gstsls.Rd | 5 ++++-
man/impacts.sarlm.Rd | 5 ++++-
man/lagsarlm.Rd | 8 +++++++-
man/sacsarlm.Rd | 7 ++++++-
man/set.spChkOption.Rd | 4 ++++
man/stsls.Rd | 5 ++++-
21 files changed, 129 insertions(+), 39 deletions(-)
Title: R interface to REDCap
Diff between redcapAPI versions 1.1 dated 2014-11-25 and 1.2 dated 2015-01-16
Description: Access data stored in REDCap databases using the Application
Programming Interface (API). REDCap (Research Electronic Data CAPture) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The redcapAPI package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with
contributions from Jeremy Stephens, and Will Beasley
Maintainer: Benjamin Nutter
redcapAPI-1.1/redcapAPI/man/queryRecords.Rd |only
redcapAPI-1.1/redcapAPI/man/redcapAPI-package.Rd |only
redcapAPI-1.2/redcapAPI/DESCRIPTION | 24 +
redcapAPI-1.2/redcapAPI/MD5 | 98 +++----
redcapAPI-1.2/redcapAPI/NAMESPACE | 104 +++----
redcapAPI-1.2/redcapAPI/NEWS | 12
redcapAPI-1.2/redcapAPI/R/allocationTable.R |only
redcapAPI-1.2/redcapAPI/R/allocationTable_offline.R |only
redcapAPI-1.2/redcapAPI/R/apiCall.R | 44 +++
redcapAPI-1.2/redcapAPI/R/deleteFiles.R | 58 ++++
redcapAPI-1.2/redcapAPI/R/exportArms.R | 55 ++++
redcapAPI-1.2/redcapAPI/R/exportEvents.R | 54 ++++
redcapAPI-1.2/redcapAPI/R/exportFiles.R | 82 ++++++
redcapAPI-1.2/redcapAPI/R/exportInstruments.R | 37 ++
redcapAPI-1.2/redcapAPI/R/exportMappings.R | 81 ++++++
redcapAPI-1.2/redcapAPI/R/exportMetaData.R | 49 +++
redcapAPI-1.2/redcapAPI/R/exportRecords.R | 223 ++++++++++++++++
redcapAPI-1.2/redcapAPI/R/exportRecords_offline.R |only
redcapAPI-1.2/redcapAPI/R/exportReports.R | 49 +++
redcapAPI-1.2/redcapAPI/R/exportUsers.R | 102 +++++++
redcapAPI-1.2/redcapAPI/R/exportVersion.R | 33 ++
redcapAPI-1.2/redcapAPI/R/fieldToVar.R | 27 ++
redcapAPI-1.2/redcapAPI/R/importFiles.R | 52 +++
redcapAPI-1.2/redcapAPI/R/importRecords.R | 122 +++++++++
redcapAPI-1.2/redcapAPI/R/recodeCheck.R | 181 +++++++++++++
redcapAPI-1.2/redcapAPI/R/redcapAPI-pkg.R |only
redcapAPI-1.2/redcapAPI/R/redcapConnection.R | 74 +++++
redcapAPI-1.2/redcapAPI/R/redcapFactorFlip.R | 20 +
redcapAPI-1.2/redcapAPI/R/redcapProjectInfo.R | 58 ++++
redcapAPI-1.2/redcapAPI/R/syncUnderscoreCodings.R | 45 +++
redcapAPI-1.2/redcapAPI/R/validateImport.R | 82 ++++++
redcapAPI-1.2/redcapAPI/man/allocationTable.Rd |only
redcapAPI-1.2/redcapAPI/man/apiCall.Rd | 59 ++--
redcapAPI-1.2/redcapAPI/man/deleteFiles.Rd | 77 +++--
redcapAPI-1.2/redcapAPI/man/exportArms.Rd | 76 +++--
redcapAPI-1.2/redcapAPI/man/exportEvents.Rd | 62 ++--
redcapAPI-1.2/redcapAPI/man/exportFiles.Rd | 140 +++++-----
redcapAPI-1.2/redcapAPI/man/exportInstruments.Rd | 44 +--
redcapAPI-1.2/redcapAPI/man/exportMappings.Rd | 62 ++--
redcapAPI-1.2/redcapAPI/man/exportMetaData.Rd | 57 ++--
redcapAPI-1.2/redcapAPI/man/exportRecords.Rd | 253 +++++++++++--------
redcapAPI-1.2/redcapAPI/man/exportReports.Rd | 65 +++-
redcapAPI-1.2/redcapAPI/man/exportUsers.Rd | 103 ++++---
redcapAPI-1.2/redcapAPI/man/exportVersion.Rd | 33 +-
redcapAPI-1.2/redcapAPI/man/fieldToVar.Rd | 54 ++--
redcapAPI-1.2/redcapAPI/man/importFiles.Rd | 75 +++--
redcapAPI-1.2/redcapAPI/man/importRecords.Rd | 165 ++++++------
redcapAPI-1.2/redcapAPI/man/recodeCheck.Rd | 136 +++++-----
redcapAPI-1.2/redcapAPI/man/redcapAPI.Rd |only
redcapAPI-1.2/redcapAPI/man/redcapConnection.Rd | 107 ++++----
redcapAPI-1.2/redcapAPI/man/redcapFactorFlip.Rd | 34 +-
redcapAPI-1.2/redcapAPI/man/redcapProjectInfo.Rd | 100 ++++---
redcapAPI-1.2/redcapAPI/man/syncUnderscoreCodings.Rd | 79 +++--
redcapAPI-1.2/redcapAPI/man/validateImport.Rd | 121 +++++----
54 files changed, 2726 insertions(+), 942 deletions(-)
Title: Draws diagrams useful for checking latent scales
Diff between latdiag versions 0.2 dated 2009-08-02 and 0.2-1 dated 2015-01-16
Description: Writes a file of commands for the dot program to draw a graph
proposed by Rosenbaum and useful for checking some properties of various
sorts of latent scale
Author: Michael Dewey
Maintainer: Michael Dewey
DESCRIPTION | 16 ++++++++--------
MD5 |only
NEWS |only
inst/CITATION | 5 ++---
man/draw.latent.Rd | 15 +++++++++++----
5 files changed, 21 insertions(+), 15 deletions(-)
Title: Royston's H Test: Multivariate Normality Test
Diff between royston versions 1.0 dated 2013-01-02 and 1.1 dated 2015-01-16
Description: Performs a multivariate normality test based on Royston's H test
Author: Selcuk Korkmaz
Maintainer: Selcuk Korkmaz
royston-1.0/royston/R/royston-internal.R |only
royston-1.1/royston/DESCRIPTION | 16 +-
royston-1.1/royston/MD5 | 7
royston-1.1/royston/NAMESPACE | 3
royston-1.1/royston/R/royston.test.R | 237 +++++++++++++++----------------
5 files changed, 133 insertions(+), 130 deletions(-)
Title: Multivariate Statistical Analysis in Chemometrics
Diff between chemometrics versions 1.3.8 dated 2012-02-16 and 1.3.9 dated 2015-01-16
Description: This package is the R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)
Author: Peter Filzmoser and Kurt Varmuza
Maintainer: P. Filzmoser
DESCRIPTION | 22 +-
MD5 | 169 ++++++++++-----------
NAMESPACE | 76 +++++----
R/Moutlier.R | 2
R/clvalidity.R | 4
R/delintercept.R |only
R/knnEval.R | 4
R/lassoCV.R | 6
R/lassocoef.R | 6
R/lmCV.R | 4
R/mvr_dcv.R | 4
R/nnetEval.R | 2
R/pcaCV.R | 2
R/plotRidge.R | 6
R/plotSEPmvr.R | 2
R/plotpredmvr.R | 2
R/plotresmvr.R | 2
R/prm.R | 2
R/prm_cv.R | 2
R/prm_dcv.R | 2
R/ridgeCV.R | 6
R/stepwise.R | 4
R/svmEval.R | 2
R/treeEval.R | 3
build |only
data/NIR.rda |binary
data/PAC.rda |binary
data/Phenyl.rda |binary
data/ash.rda |binary
data/cereal.rda |binary
data/glass.grp.rda |binary
data/glass.rda |binary
data/hyptis.rda |binary
inst/doc/chemometrics-vignette.R |only
inst/doc/chemometrics-vignette.pdf |binary
inst/doc/chemometrics-vignette.rnw | 10 -
man/Moutlier.Rd | 4
man/NIR.Rd | 6
man/RPvectors.Rd | 4
man/alr.Rd | 4
man/clr.Rd | 4
man/clvalidity.Rd | 4
man/delintercept.Rd |only
man/drawMahal.Rd | 7
man/hyptis.Rd | 3
man/ilr.Rd | 4
man/knnEval.Rd | 4
man/lassoCV.Rd | 27 +--
man/lassocoef.Rd | 4
man/lmCV.Rd | 10 -
man/mvr_dcv.Rd | 81 +++++-----
man/nipals.Rd | 4
man/nnetEval.Rd | 8
man/pcaCV.Rd | 11 -
man/pcaDiagplot.Rd | 7
man/pcaVarexpl.Rd | 4
man/plotRidge.Rd | 4
man/plotSEPmvr.Rd | 26 +--
man/plotSEPprm.Rd | 26 +--
man/plotcompmvr.Rd | 12 -
man/plotcompprm.Rd | 12 -
man/plotpredmvr.Rd | 17 +-
man/plotpredprm.Rd | 14 -
man/plotprm.Rd | 8
man/plotresmvr.Rd | 17 +-
man/plotresprm.Rd | 14 -
man/plotsom.Rd | 4
man/pls1_nipals.Rd | 4
man/pls2_nipals.Rd | 4
man/pls_eigen.Rd | 4
man/prm_cv.Rd | 44 +++--
man/prm_dcv.Rd | 47 +++--
man/ridgeCV.Rd | 17 +-
man/sd_trim.Rd | 4
man/stepwise.Rd | 29 ++-
man/svmEval.Rd | 15 -
man/treeEval.Rd | 4
vignettes/Figures/Fig-02-01-pcaCV.pdf |binary
vignettes/Figures/Fig-02-03-pcaDiagplot-nipals.pdf |binary
vignettes/Figures/Fig-02-04-pcaDiagplot-robust.pdf |binary
vignettes/Figures/Fig-03-01-BIC.pdf |binary
vignettes/Figures/Fig-03-02-lmCV.pdf |binary
vignettes/Figures/Fig-03-13-plotridge.pdf |binary
vignettes/Figures/Fig-04-01-knneval.pdf |binary
vignettes/Figures/Fig-04-03-treeeval.pdf |binary
vignettes/chemometrics-vignette.rnw | 10 -
vignettes/nicefrac.sty |only
vignettes/shadethm.sty |only
vignettes/zi4.sty |only
89 files changed, 488 insertions(+), 392 deletions(-)
Title: Test Analysis Modules
Diff between TAM versions 1.3 dated 2015-01-06 and 1.4-1 dated 2015-01-16
Description:
The package includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
TAM-1.3/TAM/R/taamanify.proc.lavaanmodel.R |only
TAM-1.4-1/TAM/DESCRIPTION | 15 -
TAM-1.4-1/TAM/MD5 | 100 ++++++-----
TAM-1.4-1/TAM/NAMESPACE | 20 +-
TAM-1.4-1/TAM/R/IRT.WrightMap.R |only
TAM-1.4-1/TAM/R/IRTLikelihood.cfa.R |only
TAM-1.4-1/TAM/R/TAM.ic.R | 1
TAM-1.4-1/TAM/R/TAM.itempartable.R | 5
TAM-1.4-1/TAM/R/cfa.extract.itempars.R |only
TAM-1.4-1/TAM/R/change.grep.lavpartable.R | 5
TAM-1.4-1/TAM/R/lavaanify.IRT.R | 25 ++
TAM-1.4-1/TAM/R/lavaanify.grep.MEASERR.R |only
TAM-1.4-1/TAM/R/lavaanify.sirt.v1.R | 28 +--
TAM-1.4-1/TAM/R/lavpartable.grep.underbrace.R | 11 +
TAM-1.4-1/TAM/R/lavpartable2lavsyntax.R | 22 ++
TAM-1.4-1/TAM/R/plot.ctt.R | 2
TAM-1.4-1/TAM/R/summary.tam.R | 1
TAM-1.4-1/TAM/R/summary.tam.fit.R |only
TAM-1.4-1/TAM/R/summary.tam.mml.3pl.R | 1
TAM-1.4-1/TAM/R/tam.fit.R | 15 -
TAM-1.4-1/TAM/R/tam.latreg.R | 26 ++
TAM-1.4-1/TAM/R/tam.mml.2pl.R | 9 -
TAM-1.4-1/TAM/R/tam.mml.3pl.R | 31 ++-
TAM-1.4-1/TAM/R/tam.mml.3pl.algorithm.R | 2
TAM-1.4-1/TAM/R/tam.mml.3pl.est.intercepts.R | 1
TAM-1.4-1/TAM/R/tam.mml.R | 16 +
TAM-1.4-1/TAM/R/tam.mml.mfr.R | 9 -
TAM-1.4-1/TAM/R/tam.pv.R | 12 -
TAM-1.4-1/TAM/R/tam.wle.R | 3
TAM-1.4-1/TAM/R/tam_thurstonian_threshold.R | 2
TAM-1.4-1/TAM/R/tamaan.3pl.mixture.R | 3
TAM-1.4-1/TAM/R/tamaanify.R | 4
TAM-1.4-1/TAM/R/tamaanify.create.A.R | 59 ++++++
TAM-1.4-1/TAM/R/tamaanify.define.method.R | 10 -
TAM-1.4-1/TAM/R/tamaanify.grep.linequations.R | 2
TAM-1.4-1/TAM/R/tamaanify.modelconstraint.loadings.R | 2
TAM-1.4-1/TAM/R/tamaanify.proc.lavaanmodel.R |only
TAM-1.4-1/TAM/R/tamaanify.proc.modelconstraint.R | 20 +-
TAM-1.4-1/TAM/data/data.ctest2.rda |only
TAM-1.4-1/TAM/inst/NEWS | 40 ++++
TAM-1.4-1/TAM/man/IRT.WrightMap.Rd |only
TAM-1.4-1/TAM/man/IRTLikelihood.cfa.Rd |only
TAM-1.4-1/TAM/man/TAM-package.Rd | 2
TAM-1.4-1/TAM/man/cfa.extract.itempars.Rd |only
TAM-1.4-1/TAM/man/data.cqc.Rd | 98 ++++++++++-
TAM-1.4-1/TAM/man/data.ctest.Rd | 34 +++
TAM-1.4-1/TAM/man/data.examples.Rd | 5
TAM-1.4-1/TAM/man/data.geiser.Rd | 70 +++++++
TAM-1.4-1/TAM/man/lavaanify.IRT.Rd | 39 ++++
TAM-1.4-1/TAM/man/tam.fit.Rd | 69 +++++--
TAM-1.4-1/TAM/man/tam.latreg.Rd | 91 +++++++++-
TAM-1.4-1/TAM/man/tam.mml.Rd | 15 -
TAM-1.4-1/TAM/man/tam.pv.Rd | 169 ++++++++++++++++++-
TAM-1.4-1/TAM/man/tamaan.Rd | 60 ++++--
TAM-1.4-1/TAM/man/tamaanify.Rd | 54 ++++--
TAM-1.4-1/TAM/man/tampv2datalist.Rd | 2
TAM-1.4-1/TAM/src/irt_likelihood_cfa2.cpp |only
57 files changed, 972 insertions(+), 238 deletions(-)
Title: Infrastructure for Data Stream Mining
Diff between stream versions 1.1-0 dated 2014-12-18 and 1.1-1 dated 2015-01-16
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 8 -
MD5 | 37 +++--
R/DSC_DStream.R | 94 ++++++++------
R/DSC_R.R | 2
R/DSC_TwoStage.R | 2
R/DSC_tNN.R | 43 +++++-
R/DSD_ReadCSV.R | 43 ++----
build/vignette.rds |binary
inst/NEWS | 5
inst/doc/stream.R | 158 +++++++++++++-----------
inst/doc/stream.Rnw | 328 +++++++++++++++++++++++++++++++++-----------------
inst/doc/stream.pdf |binary
man/DSC_DStream.Rd | 8 -
man/DSD_Memory.Rd | 3
man/evaluate.Rd | 2
man/update.Rd | 4
vignettes/classes.pdf |only
vignettes/mcs.pdf |only
vignettes/stream.Rnw | 328 +++++++++++++++++++++++++++++++++-----------------
vignettes/stream.bib | 19 ++
vignettes/time.pdf |only
21 files changed, 687 insertions(+), 397 deletions(-)
Title: Estimation of spatial autoregressive models with and without
heteroskedastic innovations
Diff between sphet versions 1.5 dated 2013-12-11 and 1.6 dated 2015-01-16
Description: Generalized Method of Moment estimation of Cliff-Ord-type
spatial autoregressive models with and without heteroskedastic
innovations
Author: Gianfranco Piras
Maintainer: Gianfranco Piras
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
R/spreg.R | 2 --
build |only
inst/CITATION | 18 ++++++++++++++++++
inst/doc/sphet.pdf |binary
man/spreg.Rd | 2 ++
7 files changed, 30 insertions(+), 11 deletions(-)
Title: Maxwell Bolzano Bose Einstein Fermi Dirac Distribution and
Exposure Curve
Diff between mbbefd versions 0.5 dated 2015-01-10 and 0.5.0.1 dated 2015-01-16
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi Dirac (MBBEFD) distribution (distribution, density, quantile, random generation functions) as well as MBBEFD exposure curve, used in actuarial application to price reinsurance contracts. The vignette shows code snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato
ChangeLog | 3 +++
DESCRIPTION | 14 +++++++-------
MD5 | 19 ++++++++++---------
NEWS | 8 +++-----
inst/CITATION | 6 +++---
inst/doc/mbbefd.Rnw | 6 +++---
man/mbbefd-package.Rd | 4 ++--
vignettes/mbbefd-distrPlot.pdf |binary
vignettes/mbbefd-drateplot.pdf |binary
vignettes/mbbefd.Rnw | 6 +++---
vignettes/mbbefd.tex |only
11 files changed, 34 insertions(+), 32 deletions(-)
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-10 dated 2013-09-14 and 1.0-11 dated 2015-01-16
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/lmmpower.R | 20 ++++++++++----------
build/vignette.rds |binary
inst/CITATION | 5 ++---
inst/doc/longpower.R | 25 ++++++++-----------------
inst/doc/longpower.pdf |binary
7 files changed, 31 insertions(+), 41 deletions(-)
Title: High-dimensional Kernel Density Estimation and Geometry
Operations
Diff between hypervolume versions 1.1.1 dated 2014-12-19 and 1.1.2 dated 2015-01-16
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++++----
NAMESPACE | 6 +++---
R/hypervolume_distance.R |only
R/hypervolume_sorensen_overlap.R |only
man/hypervolume_distance.Rd |only
man/hypervolume_set.Rd | 14 +++++++++++---
man/hypervolume_sorensen_overlap.Rd |only
src/RcppExports.cpp | 30 +++++++++++++++---------------
9 files changed, 42 insertions(+), 30 deletions(-)
Title: Fuzzy Rule-based Systems for Classification and Regression Tasks
Diff between frbs versions 2.2-0 dated 2014-02-03 and 3.0-0 dated 2015-01-16
Description: This package implements functionality and various algorithms to
build and use fuzzy rule-based systems (FRBSs). FRBSs are based on the
concept of fuzzy sets, proposed by Zadeh in 1965, which aims at
representing the reasoning of human experts in a set of IF-THEN rules, to
handle real-life problems in, e.g., control, prediction and inference, data
mining, bioinformatics data processing, and robotics. FRBSs are also known
as fuzzy inference systems and fuzzy models. During the modeling of an
FRBS, there are two important steps that need to be conducted: structure
identification and parameter estimation. Nowadays, there exists a wide
variety of algorithms to generate fuzzy IF-THEN rules automatically from
numerical data, covering both steps. Approaches that have been used in the
past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering
methods, genetic algorithms, squares methods, etc. Furthermore, in this
version we provide a universal framework named frbsPMML, which is adopted
from the Predictive Model Markup Language (PMML), for representing FRBS
models. PMML is an XML-based language to provide a standard for describing
models produced by data mining and machine learning algorithms. Therefore,
we are allowed to export and import an FRBS model to/from frbsPMML.
Finally, this package aims to implement the most widely used standard
procedures, thus offering a standard package for FRBS modeling to the R
community.
Author: Lala Septem Riza, Christoph Bergmeir, Francisco Herrera, and
Jose Manuel Benitez
Maintainer: Christoph Bergmeir
DESCRIPTION | 32 -
LICENSE |only
MD5 | 131 ++--
NAMESPACE | 11
R/FCluster.Methods.R | 6
R/FNN.Methods.R | 4
R/FRBS.MainFunction.R | 323 +++++-----
R/FRBS.pmml.R |only
R/FSpacePartition.FunctionCollection.R | 288 ++-------
R/FSpacePartition.Method.R | 6
R/FSpacePartition.Predict.R | 13
R/GFS.Methods.R | 4
R/docData.R | 4
R/frbs-package.R | 201 +++++-
R/pmml.R |only
R/pmml.frbs.R |only
demo/00Index | 26
demo/ANFIS.GasFur.PMML.R |only
demo/FRBS.Mamdani.Manual.R | 22
demo/FRBS.Manual.R | 6
demo/FRBS.TSK.Manual.R | 6
demo/GFS.GCCL.Iris.PMML.R |only
demo/GFS.GCCL.Iris.R | 2
demo/WM.GasFur.PMML.R | 18
man/ANFIS.Rd | 140 ++--
man/ANFIS.update.Rd | 67 +-
man/DENFIS.Rd | 123 +---
man/DENFIS.eng.Rd | 51 -
man/DM.update.Rd | 76 +-
man/ECM.Rd | 50 -
man/FH.GBML.Rd | 134 ++--
man/FIR.DM.Rd | 110 +--
man/FRBCS.CHI.Rd | 128 +---
man/FRBCS.W.Rd | 127 +---
man/FRBCS.eng.Rd | 43 -
man/FS.HGD.Rd | 123 +---
man/GFS.FR.MOGUL.Rd | 147 ++--
man/GFS.FR.MOGUL.test.Rd | 42 -
man/GFS.GCCL.Rd | 131 +---
man/GFS.GCCL.eng.Rd | 42 -
man/GFS.LT.RS.Rd | 163 ++---
man/GFS.LT.RS.test.Rd | 42 -
man/GFS.Thrift.Rd | 144 ++--
man/GFS.Thrift.test.Rd | 42 -
man/HGD.update.Rd | 72 +-
man/HyFIS.Rd | 132 +---
man/HyFIS.update.Rd | 94 +--
man/SBC.Rd | 119 +--
man/SBC.test.Rd | 42 -
man/SLAVE.Rd | 141 ++--
man/SLAVE.test.Rd | 42 -
man/WM.Rd | 175 ++---
man/data.gen3d.Rd | 53 -
man/defuzzifier.Rd | 134 ++--
man/denorm.data.Rd | 59 -
man/frbs-package.Rd | 769 ++++++++++++++-----------
man/frbs.eng.Rd | 91 +--
man/frbs.gen.Rd | 698 +++++++++++------------
man/frbs.learn.Rd | 998 +++++++++++++++------------------
man/frbsData.Rd | 97 +--
man/frbsObjectFactory.Rd | 145 ++--
man/frbsPMML.Rd |only
man/fuzzifier.Rd | 119 +--
man/inference.Rd | 154 ++---
man/norm.data.Rd | 59 -
man/plotMF.Rd | 153 ++---
man/predict.frbs.Rd | 160 ++---
man/read.frbsPMML.Rd |only
man/rulebase.Rd | 270 ++++----
man/summary.frbs.Rd | 244 +++-----
man/write.frbsPMML.Rd |only
71 files changed, 3858 insertions(+), 4190 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Diff between AICcmodavg versions 2.0-2 dated 2015-01-08 and 2.0-3 dated 2015-01-16
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). The package also features functions to conduct classic model averaging (multimodel inference) for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with Cox proportional hazards models and conditional logistic regression ('coxph' and 'coxme' classes), linear models ('lm' class), generalized linear models ('glm', 'vglm', 'hurdle', and 'zeroinfl' classes), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' and 'merMod' classes), multinomial and ordinal logistic regressions ('multinom'}, 'polr', 'clm', and 'clmm' classes), robust regression models ('rlm' class), beta regression models ('betareg' class), parametric survival models ('survreg' class), nonlinear models ('nls' and 'gnls' classes), and nonlinear mixed models ('nlme' and 'nlmer' classes). The package also supports various models of 'unmarkedFit' and 'maxLikeFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
data/newt.rda |only
inst/CITATION | 5 ++---
inst/NEWS | 9 ++++++++-
man/AICcmodavg-package.Rd | 4 ++--
man/newt.Rd |only
man/salamander.Rd | 8 ++++----
8 files changed, 27 insertions(+), 19 deletions(-)
Title: Weighted Correlation Network Analysis
Diff between WGCNA versions 1.42 dated 2014-12-04 and 1.43 dated 2015-01-15
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder
Maintainer: Peter Langfelder
Changelog | 15 +++
DESCRIPTION | 13 +-
MD5 | 18 ++--
NAMESPACE | 2
R/Functions.R | 206 ++++++++++++++++++++++++++++++++++++++++-------
R/GOenrichmentAnalysis.R | 12 +-
R/heatmapWithLegend.R | 26 -----
man/WGCNA-package.Rd | 4
man/blueWhiteRed.Rd | 8 +
man/labeledHeatmap.Rd | 40 ++++++++-
10 files changed, 262 insertions(+), 82 deletions(-)
Title: Random graph clustering
Diff between mixer versions 1.7 dated 2013-07-25 and 1.8 dated 2015-01-15
Description: Routines for the analysis (unsupervised clustering) of
networks using MIXtures of Erdos-Renyi random graphs
Author: Christophe Ambroise [aut],
Gilles Grasseau [aut],
Mark Hoebeke [aut],
Pierre Latouche [aut, cre],
Vincent Miele [aut],
Franck Picard [aut],
LAPACK authors [aut] (copyrights apply to src/*.f)
Maintainer: Pierre Latouche
mixer-1.7/mixer/mixer-Ex.R |only
mixer-1.8/mixer/DESCRIPTION | 16 ++++--
mixer-1.8/mixer/MD5 | 45 ++++++++----------
mixer-1.8/mixer/NAMESPACE | 1
mixer-1.8/mixer/NEWS | 7 ++
mixer-1.8/mixer/R/init.R | 8 ---
mixer-1.8/mixer/R/mixer.R | 7 +-
mixer-1.8/mixer/inst/CITATION | 72 ++++++++++++++---------------
mixer-1.8/mixer/man/a_mixer.Rd | 62 ++++++++++++++----------
mixer-1.8/mixer/man/b_graph.affiliation.Rd | 6 +-
mixer-1.8/mixer/man/c_plot.mixer.Rd | 3 -
mixer-1.8/mixer/man/d_getModel.Rd | 13 ++++-
mixer-1.8/mixer/man/d_getModel.mixer.Rd | 3 +
mixer-1.8/mixer/man/t_blog.Rd | 2
mixer-1.8/mixer/src/Ermg.cc | 11 +++-
mixer-1.8/mixer/src/Graph.cc | 4 -
mixer-1.8/mixer/src/ModelDesigner.cc | 6 ++
mixer-1.8/mixer/src/ModelImprover.cc | 7 ++
mixer-1.8/mixer/src/SOCEm.cc | 8 ++-
mixer-1.8/mixer/src/VEstep_R.cc | 5 +-
mixer-1.8/mixer/src/ermg_R.cc | 14 ++++-
mixer-1.8/mixer/src/ermgo_R.cc | 8 +++
mixer-1.8/mixer/src/init_ermg_R.cc | 8 +++
mixer-1.8/mixer/src/matrix.h | 6 +-
24 files changed, 199 insertions(+), 123 deletions(-)
Title: Expected Maximum Profit Classification Performance Measure
Diff between EMP versions 2.0.0 dated 2015-01-08 and 2.0.1 dated 2015-01-15
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014).
Author: Cristian Bravo, Seppe vanden Broucke and Thomas Verbraken
Maintainer: Cristian Bravo
EMP-2.0.0/EMP/man/empRocInfo.Rd |only
EMP-2.0.1/EMP/DESCRIPTION | 11 ++++++-----
EMP-2.0.1/EMP/MD5 | 19 +++++++++----------
EMP-2.0.1/EMP/NAMESPACE | 5 +++--
EMP-2.0.1/EMP/NEWS | 6 ++++++
EMP-2.0.1/EMP/R/empChurn.R | 14 +++++++++-----
EMP-2.0.1/EMP/R/empCreditScoring.R | 12 +++++++-----
EMP-2.0.1/EMP/R/empRocInfo.R | 21 +++++++++++++--------
EMP-2.0.1/EMP/man/EMP-package.Rd | 17 +++++------------
EMP-2.0.1/EMP/man/empChurn.Rd | 14 ++++++--------
EMP-2.0.1/EMP/man/empCreditScoring.Rd | 12 +++++-------
11 files changed, 69 insertions(+), 62 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Diff between spacetime versions 1.1-1 dated 2014-08-22 and 1.1-2 dated 2015-01-15
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut],
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma
spacetime-1.1-1/spacetime/vignettes/wind.pdf |only
spacetime-1.1-1/spacetime/vignettes/windts.pdf |only
spacetime-1.1-2/spacetime/DESCRIPTION | 14
spacetime-1.1-2/spacetime/MD5 | 92 +-
spacetime-1.1-2/spacetime/NAMESPACE | 3
spacetime-1.1-2/spacetime/R/Class-STFDF.R | 6
spacetime-1.1-2/spacetime/R/ST-methods.R | 6
spacetime-1.1-2/spacetime/R/STFDF-methods.R | 147 ++--
spacetime-1.1-2/spacetime/R/STIDF-methods.R | 45 -
spacetime-1.1-2/spacetime/R/STSDF-methods.R | 21
spacetime-1.1-2/spacetime/R/aggregate.R | 9
spacetime-1.1-2/spacetime/R/eof.R | 21
spacetime-1.1-2/spacetime/R/over.R | 73 +-
spacetime-1.1-2/spacetime/R/raster.R | 3
spacetime-1.1-2/spacetime/R/stconstruct.R | 4
spacetime-1.1-2/spacetime/R/stinteraction.R | 2
spacetime-1.1-2/spacetime/R/stplot.R | 1
spacetime-1.1-2/spacetime/R/timematch.R | 27
spacetime-1.1-2/spacetime/build/vignette.rds |binary
spacetime-1.1-2/spacetime/data/air.rda |binary
spacetime-1.1-2/spacetime/data/datalist |only
spacetime-1.1-2/spacetime/data/fires.rda |binary
spacetime-1.1-2/spacetime/demo/00Index | 1
spacetime-1.1-2/spacetime/demo/CressieWikle.R | 17
spacetime-1.1-2/spacetime/demo/aggregate.R |only
spacetime-1.1-2/spacetime/inst/ChangeLog | 66 ++
spacetime-1.1-2/spacetime/inst/doc/jss816.R | 99 +--
spacetime-1.1-2/spacetime/inst/doc/jss816.Rnw | 21
spacetime-1.1-2/spacetime/inst/doc/jss816.pdf |binary
spacetime-1.1-2/spacetime/inst/doc/stgvis.R | 113 ++-
spacetime-1.1-2/spacetime/inst/doc/stgvis.Rmd | 152 ++--
spacetime-1.1-2/spacetime/inst/doc/stgvis.html | 779 +++++++++++--------------
spacetime-1.1-2/spacetime/inst/doc/sto.pdf |binary
spacetime-1.1-2/spacetime/inst/doc/stpg.pdf |binary
spacetime-1.1-2/spacetime/inst/doc/stsubs.pdf |binary
spacetime-1.1-2/spacetime/man/STFDF-class.Rd | 3
spacetime-1.1-2/spacetime/man/STIDF-class.Rd | 22
spacetime-1.1-2/spacetime/man/STSDF-class.Rd | 3
spacetime-1.1-2/spacetime/man/STTDF-class.Rd | 1
spacetime-1.1-2/spacetime/man/air.Rd | 1
spacetime-1.1-2/spacetime/man/eof.Rd | 27
spacetime-1.1-2/spacetime/man/over.Rd | 5
spacetime-1.1-2/spacetime/man/stplot.Rd | 1
spacetime-1.1-2/spacetime/man/timematch.Rd | 1
spacetime-1.1-2/spacetime/tests/rw.R | 1
spacetime-1.1-2/spacetime/tests/rw.Rout.save | 11
spacetime-1.1-2/spacetime/tests/wind.Rout.save | 14
spacetime-1.1-2/spacetime/vignettes/jss816.Rnw | 21
spacetime-1.1-2/spacetime/vignettes/stgvis.Rmd | 152 ++--
49 files changed, 1083 insertions(+), 902 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Diff between diseasemapping versions 1.1.4 dated 2015-01-05 and 1.1.5 dated 2015-01-15
More information about diseasemapping at CRAN
Description: Formating of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 12 ++++++------
MD5 | 3 ++-
inst |only
3 files changed, 8 insertions(+), 7 deletions(-)
Permanent link
Title: Bundle Methods for Regularized Risk Minimization Package
Diff between bmrm versions 1.8 dated 2014-02-10 and 3.0 dated 2015-01-15
Description: Bundle methods for minimization of convex and non-convex risk
under L1 or L2 regularization. Implements the algorithm proposed by Teo et
al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR
2012). The package comes with lot of loss functions for machine learning
which make it powerful for big data analysis. The applications includes:
structured prediction, linear SVM, multi-class SVM, f-beta optimization,
ROC optimization, ordinal regression, quantile regression,
epsilon insensitive regression, least mean square, logistic regression,
least absolute deviation regression (see package examples), etc... all with
L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados
DESCRIPTION | 23 +-
MD5 | 54 +++---
NAMESPACE | 12 +
NEWS | 17 ++
R/bmrm.R | 185 ++++++++++-------------
R/cost.R | 16 +-
R/loss.R |only
R/nrbm.R |only
R/scalarClassificationLosses.R | 253 +++++++++++++-------------------
R/scalarRegressionLosses.R | 191 ++++++++----------------
R/vectorialLoss.R | 85 ++++------
build/vignette.rds |binary
inst/doc/bmrm.R | 10 -
inst/doc/bmrm.Rnw | 12 -
inst/doc/bmrm.pdf |binary
man/bmrm.Rd | 85 ++++------
man/costMatrix.Rd | 12 -
man/epsilonInsensitiveRegressionLoss.Rd | 31 +--
man/fbetaLoss.Rd | 28 +--
man/gradient.Rd |only
man/hingeLoss.Rd | 36 +---
man/ladRegressionLoss.Rd | 28 +--
man/lmsRegressionLoss.Rd | 25 +--
man/logisticRegressionLoss.Rd | 25 +--
man/nrbm.Rd |only
man/ordinalRegressionLoss.Rd | 37 +---
man/quantileRegressionLoss.Rd | 28 +--
man/rocLoss.Rd | 25 +--
man/softMarginVectorLoss.Rd | 47 ++---
vignettes/bmrm.Rnw | 12 -
30 files changed, 546 insertions(+), 731 deletions(-)
Title: Binary Generalized Extreme Value Additive Models
Diff between bgeva versions 0.2 dated 2013-07-05 and 0.3 dated 2015-01-15
Description: Routine for fitting regression models for binary rare events with linear and nonlinear covariate effects when using the quantile function of the Generalized Extreme Value random variable.
Author: Giampiero Marra, Raffaella Calabrese and Silvia Angela Osmetti
Maintainer: Giampiero Marra
ChangeLog | 3 +++
DESCRIPTION | 13 +++++--------
MD5 | 10 +++++-----
NAMESPACE | 4 +++-
inst/CITATION | 19 ++++++++-----------
man/bgeva.Rd | 3 ++-
6 files changed, 26 insertions(+), 26 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-13.1 dated 2015-01-08 and 3.2-13.2 dated 2015-01-15
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 3 +
DESCRIPTION | 6 +--
MD5 | 20 +++++------
R/LM.bpm.r | 6 +--
R/SemiParBIVProbit.r | 2 -
R/mb.r | 87 ++++++++++++++++++++++--------------------------
R/print.mb.r | 7 +++
inst/CITATION | 16 +-------
man/LM.bpm.Rd | 2 -
man/SemiParBIVProbit.Rd | 2 -
man/mb.Rd | 11 +++---
11 files changed, 77 insertions(+), 85 deletions(-)
Permanent link
Title: Database preferences and Skyline computation
Diff between rPref versions 0.3 dated 2014-11-18 and 0.4 dated 2015-01-15
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks
DESCRIPTION | 12 +-
MD5 | 57 +++++-----
NAMESPACE | 6 +
NEWS | 18 ---
R/base-pref-macros.R | 5
R/base-pref.r | 8 -
R/complex-pref.r | 8 -
R/pred-succ.r |only
R/pref-classes.r | 135 ++++++++++++++++++++++++--
R/pref-eval.r | 5
R/rPref.r | 9 +
R/show-pref.r | 84 ++++++++++++----
R/visualize.r | 4
inst/test/test-hasse.R | 28 +++++
inst/test/test-psel.R | 2
man/base_pref.Rd | 124 +++++++++++------------
man/base_pref_macros.Rd | 115 +++++++++++-----------
man/complex_pref.Rd | 220 +++++++++++++++++++++---------------------
man/get_btg.Rd | 122 +++++++++++------------
man/get_hasse_diag.Rd | 56 +++++-----
man/plot_front.Rd | 82 +++++++--------
man/pred_succ.Rd |only
man/psel.Rd | 249 ++++++++++++++++++++++++------------------------
man/rPref.Rd | 97 ++++++++++--------
man/show.pref.Rd |only
man/show.query.Rd | 86 ++++++++--------
src/bnl.cpp | 13 --
src/bnl.h | 9 +
src/hasse.cpp | 5
src/scalagon.cpp | 9 -
src/scalagon.h | 2
31 files changed, 893 insertions(+), 677 deletions(-)
Title: Record Linkage in R
Diff between RecordLinkage versions 0.4-6 dated 2014-12-11 and 0.4-7 dated 2015-01-15
Description: Provides functions for linking and de-duplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain.
Author: Andreas Borg
Maintainer: Andreas Borg
RecordLinkage-0.4-6/RecordLinkage/inst/unitTests |only
RecordLinkage-0.4-7/RecordLinkage/DESCRIPTION | 11 -
RecordLinkage-0.4-7/RecordLinkage/MD5 | 87 +------------
RecordLinkage-0.4-7/RecordLinkage/NEWS | 4
RecordLinkage-0.4-7/RecordLinkage/data/RLdata10000.rda |binary
RecordLinkage-0.4-7/RecordLinkage/data/RLdata500.rda |binary
RecordLinkage-0.4-7/RecordLinkage/inst/doc/BigData.pdf |binary
RecordLinkage-0.4-7/RecordLinkage/inst/doc/EVT.pdf |binary
RecordLinkage-0.4-7/RecordLinkage/inst/doc/Supervised.pdf |binary
RecordLinkage-0.4-7/RecordLinkage/inst/doc/WeightBased.pdf |binary
RecordLinkage-0.4-7/RecordLinkage/man/epiClassify.Rd | 2
RecordLinkage-0.4-7/RecordLinkage/man/epiWeights.Rd | 2
12 files changed, 20 insertions(+), 86 deletions(-)
Title: Estimating Potential and Actual Evapotranspiration with Multiple
Models
Diff between Evapotranspiration versions 1.4 dated 2014-06-12 and 1.5 dated 2015-01-15
More information about Evapotranspiration at CRAN
Description: Allows the use of user-defined data and constants to calculate potential evapotranspiration (PET i.e. the amount of evaporation from a surface if sufficient water is available) and actual evapotranspiration (AET i.e. the actual amount of water evaporated from a surface) from 17 different formulations including the Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo
Maintainer: Danlu Guo
Evapotranspiration-1.4/Evapotranspiration/man/ET.Truc.Rd |only
Evapotranspiration-1.5/Evapotranspiration/DESCRIPTION | 15
Evapotranspiration-1.5/Evapotranspiration/MD5 | 26 -
Evapotranspiration-1.5/Evapotranspiration/NAMESPACE | 2
Evapotranspiration-1.5/Evapotranspiration/NEWS | 30 -
Evapotranspiration-1.5/Evapotranspiration/R/Evapotranspiration.R | 162 +++++++---
Evapotranspiration-1.5/Evapotranspiration/R/Plotting.R | 68 +---
Evapotranspiration-1.5/Evapotranspiration/man/ET.BlaneyCriddle.Rd | 3
Evapotranspiration-1.5/Evapotranspiration/man/ET.BrutsaertStrickler.Rd | 9
Evapotranspiration-1.5/Evapotranspiration/man/ET.JensenHaise.Rd | 7
Evapotranspiration-1.5/Evapotranspiration/man/ET.MortonCRAE.Rd | 7
Evapotranspiration-1.5/Evapotranspiration/man/ET.MortonCRWE.Rd | 7
Evapotranspiration-1.5/Evapotranspiration/man/ET.Turc.Rd |only
Evapotranspiration-1.5/Evapotranspiration/man/ETComparison.Rd | 7
Evapotranspiration-1.5/Evapotranspiration/man/ETPlot.Rd | 3
15 files changed, 205 insertions(+), 141 deletions(-)
Permanent link
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.10 dated 2015-01-05 and 0.10.1 dated 2015-01-15
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
DESCRIPTION | 22 ++++++++++------------
MD5 | 6 +++---
R/table.R | 4 ++--
configure | 15 +++++++++++++--
4 files changed, 28 insertions(+), 19 deletions(-)
Title: Categorical Marginal Models
Diff between cmm versions 0.7 dated 2013-02-23 and 0.8 dated 2015-01-15
Description: Quite extensive package for the estimation of marginal models for categorical data.
Author: Wicher Bergsma and Andries van der Ark
Maintainer: L. A. van der Ark
DESCRIPTION | 13 ++++-----
MD5 | 36 +++++++++++++--------------
R/CMM.R | 2 -
inst/CITATION | 5 +--
man/Antisemitism.Rd | 24 +++++++++++-------
man/BodySatisfaction.Rd | 60 +++++++++++++++++++++++++++++-----------------
man/ConstraintMatrix.Rd | 26 +++++++++++++++----
man/DesignMatrix.Rd | 31 +++++++++++++++++------
man/DutchConcern.Rd | 19 ++++++++------
man/EVS.Rd | 41 ++++++++++++++++++-------------
man/GSS93.Rd | 53 +++++++++++++++++++++++++++++-----------
man/LaborParticipation.Rd | 27 +++++++++++---------
man/MarginalMatrix.Rd | 12 +++++----
man/MarginalModelFit.Rd | 13 +++++----
man/MarihuanaAlcohol.Rd | 12 ++++++---
man/ModelStatistics.Rd | 26 +++++++++++--------
man/NKPS.Rd | 19 ++++++++------
man/SampleStatistics.Rd | 37 ++++++++++++++++------------
man/Smoking.Rd | 12 +++++----
19 files changed, 290 insertions(+), 178 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-24 0.03
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-01-17 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-13 1.3-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-07-16 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-01-29 0.2
2008-10-29 0.1
2008-09-10 0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-11 1.1.1
2010-10-23 1.1
2010-10-13 1.0
Title: Nested Association Mapping
Diff between NAM versions 1.0.1 dated 2015-01-05 and 1.0.2 dated 2015-01-15
Description: NAM, biparental and random populations toolbox
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu
Maintainer: Alencar Xavier
DESCRIPTION | 8 ++++----
MD5 | 8 +++++---
R/reml.R |only
man/Internals.Rd | 2 +-
man/NAM-package.Rd | 8 ++++----
man/reml.Rd |only
6 files changed, 14 insertions(+), 12 deletions(-)
Title: Tools for processing COPAS large-particle flow cytometer data
Diff between COPASutils versions 0.1.5 dated 2014-12-10 and 0.1.6 dated 2015-01-15
Description: A logical workflow for the reading, processing, and visualization
of data obtained from the Union Biometrica Complex Object Parametric
Analyzer and Sorter (COPAS) platform large-particle flow cytometers and a
powerful suite of functions for the rapid processing and analysis of large
high-throughput screening data sets. It combines the speed of dplyr with
the elegance of ggplot2 to make analysis of COPAS data fast and painless.
Author: Tyler Shimko
Maintainer: Erik Andersen
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
R/COPASutils_functions.R | 2 +-
build/vignette.rds |binary
data/BioSorter.RData |binary
data/PresentationStyle.RData |binary
data/bubbleSVMmodel_noProfiler.RData |binary
data/doseData.RData |binary
data/plateData1.RData |binary
data/plateData2.RData |binary
inst/doc/Overview.html | 28 ++++++++++++++--------------
11 files changed, 28 insertions(+), 28 deletions(-)
Title: Composite-likelihood based Analysis of Random Fields
Diff between CompRandFld versions 1.0.3-1 dated 2014-08-23 and 1.0.3-3 dated 2015-01-15
Description: The aim of this package is to collect a set of procedures for the analysis of Random Fields by Composite Likelihood methods. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood based methods are emerging as useful tools for mitigating such computational problems and show satisfactory results when compared with other techniques such as, for example the tapering method. Moreover, composite likelihood (and related quantities) have some good properties similar to those of the standard likelihood.
Author: Simone Padoan
Maintainer: Simone Padoan
DESCRIPTION | 11 +++++----
MD5 | 14 +++++------
data/irishwinds.rda |binary
data/usrain.rda |binary
man/Covariogram.Rd | 56 +++++++++++++++++++++++-----------------------
man/Covmatrix.Rd | 19 +++++++--------
man/FitComposite.Rd | 58 ++++++++++++++++++++++++------------------------
man/Kri.Rd | 62 ++++++++++++++++++++++++++--------------------------
8 files changed, 111 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-05 0.9.5
2013-09-26 0.8.6
2013-02-06 0.8.5
2012-01-25 0.8.4
2010-04-27 0.7.1
2010-04-09 0.7.0
2009-12-30 0.6.0
2009-05-05 0.5.1
Title: Functions for Clustering of Presence-Absence, Abundance and
Multilocus Genetic Data
Diff between prabclus versions 2.2-5 dated 2015-01-13 and 2.2-6 dated 2015-01-14
Description: Distance-based parametric bootstrap tests for clustering with
spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus genetical data
for species delimitation, nearest neighbor
based noise detection. Try package?prabclus for on overview.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 30
MD5 | 59
R/abundfunctions.R | 31
R/geodist.R | 4
R/prabclust.R | 4
data/kykladspecreg.rda |binary
data/waterdist.rda |binary
man/alleleconvert.Rd | 9
man/autoconst.Rd | 1
man/coord2dist.Rd | 1
man/crmatrix.Rd | 4
man/dicedist.Rd | 1
man/distratio.Rd | 1
man/geco.Rd | 1
man/homogen.test.Rd | 1
man/jaccard.Rd | 1
man/kulczynski.Rd | 1
man/lociplots.Rd | 3
man/piecewiselin.Rd | 1
man/pop.sim.Rd | 1
man/prab.sarestimate.Rd | 1
man/prabclust.Rd | 2
man/prabtest.Rd | 1
man/qkulczynski.Rd | 1
man/regpop.sar.Rd | 1
man/specgroups.Rd | 1
man/stressvals.Rd | 1
tests/Examples/prabclus-Ex.Rout.save | 9289 ++++++++++++++---------------------
tests/donttestexamples.R |only
tests/prabclustests.R | 3
tests/prabclustests.Rout.save | 669 +-
31 files changed, 4119 insertions(+), 6004 deletions(-)
Title: Mapping Fisheries Data and Spatial Analysis Tools
Diff between PBSmapping versions 2.67.60 dated 2014-04-05 and 2.68.68 dated 2015-01-14
Description: This software has evolved from fisheries research conducted at the
Pacific Biological Station (PBS) in Nanaimo, British Columbia, Canada. It
extends the R language to include two-dimensional plotting features similar
to those commonly available in a Geographic Information System (GIS).
Embedded C code speeds algorithms from computational geometry, such as
finding polygons that contain specified point events or converting between
longitude-latitude and Universal Transverse Mercator (UTM) coordinates.
Additionally, we include C++ code developed by Angus Johnson for the Clipper
library. PBSmapping also includes data for a global shoreline and other
data sets in the public domain. The R directory `.../library/PBSmapping/doc'
offers a complete user's guide PBSmapping-UG.pdf, which should be consulted
to use all functions in the package effectively.
Author: Jon T. Schnute
Maintainer: Rowan Haigh
DESCRIPTION | 22
MD5 | 44 -
R/PBSmapping.r | 467 ++++++-----
R/zzz.r | 6
data/bcBathymetry.rda |binary
data/pythagoras.rda |binary
data/surveyData.rda |binary
data/towData.rda |binary
inst/Utils/00ReadMe.txt | 94 +-
inst/Utils/Makefile | 37
inst/Utils/clipPolys.cpp | 1774 +++++++++++++++++++++---------------------
inst/Utils/convUL.cpp | 914 ++++++++++-----------
inst/Utils/findPolys.cpp | 1624 +++++++++++++++++++-------------------
inst/Utils/makeUtils.bat | 1
inst/doc/ChangeLog.txt | 23
inst/doc/PBSmappingIntro.pdf |binary
inst/doc/index.html | 12
man/findCells.Rd | 23
man/findPolys.Rd | 18
src/clipper.cpp | 968 +++++++++++++---------
src/clipper.h | 38
src/clipperWrapper.cpp | 35
vignettes/PBSmappingIntro.Rnw | 4
23 files changed, 3192 insertions(+), 2912 deletions(-)
Title: Spatial Oblique Decision Tree
Diff between SPODT versions 0.9 dated 2014-04-24 and 0.9-1 dated 2015-01-14
Description: SPODT is a spatial partitioning method based on oblique decision trees, in order to classify study area into zones of different risks, determining their boundaries
Author: Jean Gaudart, Nathalie Graffeo, Guillaume Barbet, Bernard Fichet, Roch Giorgi (Aix-Marseille University)
Maintainer: Jean Gaudart
DESCRIPTION | 6 +++---
MD5 | 43 ++++++++++++++++++++++---------------------
inst |only
man/SPODT-package.Rd | 1 +
man/dataBALL0.Rd | 1 +
man/dataBALL0_5.Rd | 1 +
man/dataBALL1_5.Rd | 1 +
man/dataBALL2.Rd | 1 +
man/dataCOV.Rd | 1 +
man/dataMALARIA.Rd | 1 +
man/dataSQUARE0.Rd | 1 +
man/dataSQUARE0_5.Rd | 1 +
man/dataSQUARE1_5.Rd | 1 +
man/dataSQUARE2.Rd | 1 +
man/dataV0.Rd | 1 +
man/dataV0_5.Rd | 1 +
man/dataV1_5.Rd | 1 +
man/dataV2.Rd | 1 +
man/spodt-class.Rd | 1 +
man/spodt.Rd | 1 +
man/spodt.tree.Rd | 1 +
man/spodtSpatialLines.Rd | 1 +
man/test.spodt.Rd | 1 +
23 files changed, 45 insertions(+), 24 deletions(-)
Title: Plotting (social) networks on maps
Diff between spnet versions 0.9.0.1 dated 2014-07-31 and 0.9.0.6 dated 2015-01-14
Description: The package provides methods for dealing with spatial social
networks. It allows to plot networks for which actors have a specific
location on a map (cities, participants in a political debate, etc.).
SpatialPolygons objects from the sp package are supported.
Author: Emmanuel Rousseaux, Marion Deville, Gilbert Ritschard
Maintainer: Emmanuel Rousseaux
spnet-0.9.0.1/spnet/R/room.create.grid.r |only
spnet-0.9.0.1/spnet/man/room.create.grid.Rd |only
spnet-0.9.0.1/spnet/man/room.create.u.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.head.length-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.head.length.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.shortening-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.shortening.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.x-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.x.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.y-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.network.arrow.translate.y.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.x-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.x.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.y-set.Rd |only
spnet-0.9.0.1/spnet/man/spnet.symbol.translate.y.Rd |only
spnet-0.9.0.6/spnet/DESCRIPTION | 20
spnet-0.9.0.6/spnet/MD5 | 220 +-
spnet-0.9.0.6/spnet/NAMESPACE | 47
spnet-0.9.0.6/spnet/R/SpatialNetwork.r | 1028 +++++++---
spnet-0.9.0.6/spnet/R/plot.position.r | 20
spnet-0.9.0.6/spnet/R/spnet.example.basic.r | 81
spnet-0.9.0.6/spnet/R/world.map.simplified.r |only
spnet-0.9.0.6/spnet/R/zzz.r | 2
spnet-0.9.0.6/spnet/data |only
spnet-0.9.0.6/spnet/inst/CITATION | 43
spnet-0.9.0.6/spnet/inst/doc/spnet-overview.pdf |binary
spnet-0.9.0.6/spnet/man/SpatialNetwork.Rd | 8
spnet-0.9.0.6/spnet/man/extract-methods.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.bgcolor-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.bgcolor.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.lower-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.lower.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.upper-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.barplot.bound.upper.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.fgcolor-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.fgcolor.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.barplot.width-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.barplot.width.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.background-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.background.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.border-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.border.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.legend-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.legend.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.color.node-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.node.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.region-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.region.Rd |only
spnet-0.9.0.6/spnet/man/spnet.color.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.color.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.create.Rd | 37
spnet-0.9.0.6/spnet/man/spnet.example.basic.Rd | 8
spnet-0.9.0.6/spnet/man/spnet.get.local.user.manual.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.cex-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.cex.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.label.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.label.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.layout.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.layout.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.legend.cex-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.cex.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.horiz-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.horiz.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.line.width-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.line.width.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.legend.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.legend.ncol-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.ncol.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.print-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.legend.print.Rd |only
spnet-0.9.0.6/spnet/man/spnet.map-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.map.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.map.plot.position.Rd | 26
spnet-0.9.0.6/spnet/man/spnet.network.arrow.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.lth-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.lth.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.type-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.network.arrow.head.type.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.opacity-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.opacity.Rd | 9
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.x-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.x.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.y-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shift.y.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shorten-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.shorten.Rd |only
spnet-0.9.0.6/spnet/man/spnet.network.arrow.thickness-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.arrow.thickness.Rd | 9
spnet-0.9.0.6/spnet/man/spnet.network.data-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.data.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.exists.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.network.label-set.Rd | 7
spnet-0.9.0.6/spnet/man/spnet.network.label.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.network.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.add-set.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.networks.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.networks.remove-set.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.par.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.par.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.cex-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.cex.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.color-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.color.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.legend-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.legend.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.x-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.x.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.y-set.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.shift.y.Rd |only
spnet-0.9.0.6/spnet/man/spnet.symbol.variable-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.symbol.variable.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.list-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.list.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.main-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.main.Rd | 3
spnet-0.9.0.6/spnet/man/spnet.title.sub-set.Rd | 5
spnet-0.9.0.6/spnet/man/spnet.title.sub.Rd | 3
spnet-0.9.0.6/spnet/man/world.map.simplified.Rd |only
135 files changed, 1221 insertions(+), 637 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Diff between PrevMap versions 1.1.3 dated 2014-12-11 and 1.1.4 dated 2015-01-14
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is
also an extension of the 'geoR' package which should be installed first
together with the 'maxLik', 'raster' and 'pdist' packages.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/foo.R | 21 ++++++++++++---------
man/spatial.pred.binomial.MCML.Rd | 2 +-
4 files changed, 20 insertions(+), 17 deletions(-)
Title: Tools for Ecological Network Analysis (ena)
Diff between enaR versions 2.8 dated 2014-11-01 and 2.8.1 dated 2015-01-14
Description: Functions for the analysis of ecological networks
Author: M.K. Lau, S.R. Borrett, D.E. Hines, P. Singh
Maintainer: Matthew K. Lau
DESCRIPTION | 12 +--
MD5 | 92 ++++++++++++-------------
R/read.scor.R | 3
man/TES.Rd | 2
man/TET.Rd | 2
man/as.extended.Rd | 2
man/bal.Rd | 2
man/balance.Rd | 2
man/bcratio.Rd | 2
man/cycliv.Rd | 2
man/eigenCentrality.Rd | 2
man/enaAll.Rd | 2
man/enaAscendency.Rd | 156 +++++++++++++++++++++-----------------------
man/enaControl.Rd | 2
man/enaCycle.Rd | 2
man/enaEnviron.Rd | 2
man/enaFlow.Rd | 2
man/enaMTI.Rd | 2
man/enaModelInfo.Rd | 2
man/enaModels.Rd | 2
man/enaR-package.Rd | 6 +
man/enaStorage.Rd | 2
man/enaStructure.Rd | 2
man/enaTroAgg.Rd | 2
man/enaUtility.Rd | 2
man/environCentrality.Rd | 2
man/findPathLength.Rd | 2
man/force.balance.Rd | 2
man/get.ns.Rd | 2
man/get.orient.Rd | 2
man/m.list.Rd | 2
man/mExp.Rd | 2
man/netOrder.Rd | 2
man/oyster.Rd | 2
man/pack.Rd | 2
man/read.enam.Rd | 2
man/read.nea.Rd | 2
man/read.scor.Rd | 2
man/read.wand.Rd | 2
man/scc.Rd | 2
man/scifix.Rd | 2
man/set.orient.Rd | 2
man/ssCheck.Rd | 2
man/structure.statistics.Rd | 2
man/troModels.Rd | 2
man/unpack.Rd | 6 -
man/write.nea.Rd | 2
47 files changed, 176 insertions(+), 181 deletions(-)
Title: Extended hierarchical logistic regression (Huisman-Olff-Fresco)
models
Diff between eHOF versions 1.5.4 dated 2014-11-01 and 1.5.7 dated 2015-01-14
Description: Extended and enhanced hierarchical logistic regression models, so-called Huisman-Olff-Fresco models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen
DESCRIPTION | 18 ++++++------
MD5 | 54 +++++++++++++++++++++++---------------
R/HOF.fun.r | 9 +-----
R/HOF.model.r | 8 ++---
R/Para.deriv.r | 13 +++++----
R/Para.opt.r | 75 ++++++++++++++++++++++++++---------------------------
R/autolayout.r | 10 ++++---
R/coef.HOF.r | 27 +++++++------------
R/pick.model.r | 34 ++++++++++++++----------
R/plot.HOF.list.r | 10 ++-----
R/plot.HOF.r | 8 ++---
R/print.HOF.list.r | 2 -
R/print.HOF.r | 25 +++++++----------
R/zzz.r | 4 ++
build/vignette.rds |binary
inst/ChangeLog | 6 ++++
inst/doc/eHOF.R | 7 ++--
inst/doc/eHOF.Rnw | 11 ++++---
inst/doc/eHOF.pdf |binary
man/HOF.Rd | 7 ++--
man/autolayout.Rd | 6 ++--
vignettes/eHOF.Rnw | 11 ++++---
vignettes/figure |only
23 files changed, 184 insertions(+), 161 deletions(-)
Title: Bayesian Inference on Causal Genetic Variants using Affected
Sib-Pairs Data
Diff between ASPBay versions 1.1 dated 2014-12-09 and 1.2 dated 2015-01-14
Description: This package allows to make inference on the properties of causal genetic
variants in linkage disequilibrium with genotyped markers. In a first step,
we select a subset of variants using a score statistic for affected
sib-pairs. In a second step, on the selected subset, we make
inference on causal genetic variants in the considered region.
Author: Claire Dandine-Roulland
Maintainer: Claire Dandine-Roulland
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
R/ASP.Bayesian.R | 12 ++++++------
R/ASP.Score.R | 8 ++++----
R/Graphs.Bayesian.R | 14 +++++++-------
R/cred_int.R | 2 +-
R/graph_cred_int.R | 21 +++------------------
inst/doc/ASPBay.pdf |binary
man/ASP.Bayesian.Rd | 3 ++-
src/MH.cpp | 6 +++---
src/RcppExports.cpp | 7 ++++---
11 files changed, 43 insertions(+), 56 deletions(-)
Title: Automatic Generation of Exams in R
Diff between exams versions 2.0-1 dated 2014-12-26 and 2.0-2 dated 2015-01-14
Description: Sweave-based automatic generation of exams including multiple-choice
questions and arithmetic problems. Exams can be produced in various formats, including
PDF, HTML, Moodle XML, QTI 1.2 (for OLAT/OpenOLAT), QTI 2.1.
Author: Achim Zeileis [aut, cre],
Bettina Gruen [aut],
Friedrich Leisch [aut],
Nikolaus Umlauf [aut],
Dominik Ernst [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NEWS | 7 +++++++
R/exams2pdf.R | 6 +++---
R/exams2qti21.R | 1 -
R/exams_skeleton.R | 7 ++++++-
R/transformers.R | 9 ++++++---
build/vignette.rds |binary
inst/doc/exams.pdf |binary
inst/doc/exams2.pdf |binary
man/exams2pdf.Rd | 6 ++++--
11 files changed, 41 insertions(+), 25 deletions(-)
Title: Basic Robust Statistics
Diff between robustbase versions 0.92-2 dated 2014-11-22 and 0.92-3 dated 2015-01-14
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov
Maintainer: Martin Maechler
ChangeLog | 32 +++++++
DESCRIPTION | 13 +--
MD5 | 117 +++++++++++++++-------------
NAMESPACE | 7 +
R/AAA.R | 3
R/adjoutlyingness.R | 49 ++++++------
R/comedian.R |only
R/covMcd.R | 166 +++++++++++++++++++++++++++--------------
R/covPlot.R | 4
R/detmcd.R | 51 +++++-------
R/glmrob.R | 4
R/ltsPlot.R | 4
R/ltsReg.R | 5 -
R/mc.R | 15 ++-
R/nlrob.R | 2
R/rrcov.control.R | 19 ++--
R/tolEllipse.R | 4
TODO | 2
build/vignette.rds |binary
inst/doc/fastMcd-kmini.pdf |binary
inst/doc/lmrob_simulation.R | 24 +++--
inst/doc/lmrob_simulation.Rnw | 15 ++-
inst/doc/lmrob_simulation.pdf |binary
inst/doc/psi_functions.Rnw | 4
inst/doc/psi_functions.pdf |binary
inst/xtraR/ex-funs.R | 24 -----
inst/xtraR/plot-psiFun.R | 2
inst/xtraR/test_MCD.R | 3
man/M.psi.Rd | 15 +++
man/adjOutlyingness.Rd | 15 ++-
man/colMedians.Rd |only
man/covComed.Rd |only
man/covMcd.Rd | 29 +++++--
man/mc.Rd | 6 -
man/pkg-internal.Rd | 37 +++------
man/r6pack.Rd |only
man/radarImage.Rd | 2
man/rrcov.control.Rd | 19 +++-
man/smoothWgt.Rd |only
src/init.c | 4
src/mc.c | 26 +++---
src/rffastmcd.f | 21 ++---
src/rob-utils.c |only
src/robustbase.h | 6 +
src/rowMedians.c |only
src/rowMedians_TYPE-template.h |only
src/templates-types.h |only
src/templates-types_undef.h |only
tests/comedian-tst.R |only
tests/glmrob-1.R | 2
tests/lmrob-psifns.R | 1
tests/lmrob-psifns.Rout.save | 14 +--
tests/m-s-estimator.R | 1
tests/mc-strict.R | 106 +++++++++++++++++++++++---
tests/nlregrob-tst.R | 3
tests/nlrob-tst.R | 2
vignettes/lmrob_simulation.Rnw | 15 ++-
vignettes/psi-GGW.pdf |binary
vignettes/psi-Hampel.pdf |binary
vignettes/psi-Huber.pdf |binary
vignettes/psi-LQQ.pdf |binary
vignettes/psi-Welsh.pdf |binary
vignettes/psi-bisquare.pdf |binary
vignettes/psi-optimal.pdf |binary
vignettes/psi_functions.Rnw | 4
65 files changed, 580 insertions(+), 317 deletions(-)
Title: Inference on High Dimensional Max-Stable Distributions
Diff between HiDimMaxStable versions 0.1 dated 2014-10-08 and 0.1.1 dated 2015-01-14
More information about HiDimMaxStable at CRAN
Description: Inference of high dimensional max-stable
distributions, from the paper "Likelihood based inference for
high-dimensional extreme value distributions", by A. Bienvenüe
and C. Robert, arXiv:1403.0065 [stat.AP].
Author: Alexis Bienvenüe [aut, cre],
Christian Robert [aut]
Maintainer: Alexis Bienvenüe
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
man/dens.grid.Rd | 31 ++++++++++++++++++-------------
man/excess.censor.Rd | 2 +-
man/excess.l.Rd | 2 ++
man/maxgrid.Rd | 4 ++--
man/maxlik.Rd | 50 +++++++++++++++++++++++++++++---------------------
man/simultoccur.l.Rd | 4 +++-
8 files changed, 66 insertions(+), 49 deletions(-)
Permanent link
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.44 dated 2014-10-01 and 3.0.55 dated 2015-01-14
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [aut], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
RandomFields-3.0.44/RandomFields/R/Methods-RFestimation.R |only
RandomFields-3.0.44/RandomFields/R/Methods-RFmodel.R |only
RandomFields-3.0.44/RandomFields/R/RF_GLOBALS.R |only
RandomFields-3.0.44/RandomFields/R/RFsp-plots.R |only
RandomFields-3.0.44/RandomFields/R/RMConvenienceModels.R |only
RandomFields-3.0.44/RandomFields/R/SpecialRMmodel.R |only
RandomFields-3.0.44/RandomFields/R/empvario.R |only
RandomFields-3.0.44/RandomFields/R/evalpar.R |only
RandomFields-3.0.44/RandomFields/man/Circulant.Rd |only
RandomFields-3.0.44/RandomFields/man/Coin.Rd |only
RandomFields-3.0.44/RandomFields/man/Constants.Rd |only
RandomFields-3.0.44/RandomFields/man/Gaussian.Rd |only
RandomFields-3.0.44/RandomFields/man/Hyperplane.Rd |only
RandomFields-3.0.44/RandomFields/man/Maxstable.Rd |only
RandomFields-3.0.44/RandomFields/man/Nugget.Rd |only
RandomFields-3.0.44/RandomFields/man/Sequential.Rd |only
RandomFields-3.0.44/RandomFields/man/Specific.Rd |only
RandomFields-3.0.44/RandomFields/man/Spectral.Rd |only
RandomFields-3.0.44/RandomFields/man/Tbm.Rd |only
RandomFields-3.0.44/RandomFields/src/Families.cc |only
RandomFields-3.0.44/RandomFields/src/families.h |only
RandomFields-3.0.44/RandomFields/src/randomshape.h |only
RandomFields-3.0.44/RandomFields/src/simu.cc |only
RandomFields-3.0.55/RandomFields/DESCRIPTION | 13
RandomFields-3.0.55/RandomFields/MD5 | 250 +-
RandomFields-3.0.55/RandomFields/NAMESPACE | 38
RandomFields-3.0.55/RandomFields/R/Crossvalidation.R | 6
RandomFields-3.0.55/RandomFields/R/D.H.R | 33
RandomFields-3.0.55/RandomFields/R/Likelihoodratio.R | 37
RandomFields-3.0.55/RandomFields/R/Methods-RFsp.R | 187 -
RandomFields-3.0.55/RandomFields/R/Methods-aux.R | 8
RandomFields-3.0.55/RandomFields/R/RC_GLOBALS.R |only
RandomFields-3.0.55/RandomFields/R/RCauto.R |only
RandomFields-3.0.55/RandomFields/R/RFempvario-Methods-plots.R |only
RandomFields-3.0.55/RandomFields/R/RFempvario.R |only
RandomFields-3.0.55/RandomFields/R/RFfit.R | 23
RandomFields-3.0.55/RandomFields/R/RFgui.R | 16
RandomFields-3.0.55/RandomFields/R/RMmodels-Methods-plots.R |only
RandomFields-3.0.55/RandomFields/R/RMmodels.R | 605 +++---
RandomFields-3.0.55/RandomFields/R/RMmodelsConvenience.R |only
RandomFields-3.0.55/RandomFields/R/RMmodelsSpecial.R |only
RandomFields-3.0.55/RandomFields/R/auxiliary.R | 20
RandomFields-3.0.55/RandomFields/R/convert.R | 213 +-
RandomFields-3.0.55/RandomFields/R/fitgauss.R | 432 ++--
RandomFields-3.0.55/RandomFields/R/generatemodels.R | 263 ++
RandomFields-3.0.55/RandomFields/R/getNset.R | 144 -
RandomFields-3.0.55/RandomFields/R/internal_use.R | 168 -
RandomFields-3.0.55/RandomFields/R/kriging.R | 111 -
RandomFields-3.0.55/RandomFields/R/obsolete.R | 23
RandomFields-3.0.55/RandomFields/R/rf-plots.R |only
RandomFields-3.0.55/RandomFields/R/rf.R | 345 +--
RandomFields-3.0.55/RandomFields/data/weather.rda |binary
RandomFields-3.0.55/RandomFields/inst/CITATION | 34
RandomFields-3.0.55/RandomFields/inst/doc/version2.pdf |binary
RandomFields-3.0.55/RandomFields/man/CoordinateSystems.Rd |only
RandomFields-3.0.55/RandomFields/man/GaussianFields.Rd |only
RandomFields-3.0.55/RandomFields/man/MajorRevisions.Rd | 11
RandomFields-3.0.55/RandomFields/man/RC.Rd |only
RandomFields-3.0.55/RandomFields/man/RFcov.Rd | 18
RandomFields-3.0.55/RandomFields/man/RFcrossvalidate.Rd | 3
RandomFields-3.0.55/RandomFields/man/RFfit.Rd | 16
RandomFields-3.0.55/RandomFields/man/RFgetModelNames.Rd | 54
RandomFields-3.0.55/RandomFields/man/RFgridDataFrame-class.Rd | 8
RandomFields-3.0.55/RandomFields/man/RFinterpolate.Rd | 40
RandomFields-3.0.55/RandomFields/man/RFoptions.Rd | 798 ++++----
RandomFields-3.0.55/RandomFields/man/RFpointsDataFrame-class.Rd | 16
RandomFields-3.0.55/RandomFields/man/RFratiotest.Rd | 9
RandomFields-3.0.55/RandomFields/man/RFsimulate.Rd | 41
RandomFields-3.0.55/RandomFields/man/RFsimulate.more.examples.Rd | 2
RandomFields-3.0.55/RandomFields/man/RFsimulateAdvanced.Rd | 2
RandomFields-3.0.55/RandomFields/man/RFspatialGridDataFrame-class.Rd | 8
RandomFields-3.0.55/RandomFields/man/RFspatialPointsDataFrame-class.Rd | 16
RandomFields-3.0.55/RandomFields/man/RMS.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMbcw.Rd | 7
RandomFields-3.0.55/RandomFields/man/RMcutoff.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMgneiting.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMkolmogorov.Rd | 4
RandomFields-3.0.55/RandomFields/man/RMmodel.Rd | 4
RandomFields-3.0.55/RandomFields/man/RMmodelgenerator-class.Rd | 2
RandomFields-3.0.55/RandomFields/man/RMmodelsAuxiliary.Rd | 3
RandomFields-3.0.55/RandomFields/man/RMmodelsSphere.Rd |only
RandomFields-3.0.55/RandomFields/man/RMmodelsTailcorrelation.Rd |only
RandomFields-3.0.55/RandomFields/man/RMspheric.Rd | 8
RandomFields-3.0.55/RandomFields/man/RMtrafo.Rd | 49
RandomFields-3.0.55/RandomFields/man/RMuser.Rd | 2
RandomFields-3.0.55/RandomFields/man/RPcirculant.Rd |only
RandomFields-3.0.55/RandomFields/man/RPcoin.Rd |only
RandomFields-3.0.55/RandomFields/man/RPhyperplane.Rd |only
RandomFields-3.0.55/RandomFields/man/RPmaxstable.Rd |only
RandomFields-3.0.55/RandomFields/man/RPmaxstableAdvanced.Rd | 3
RandomFields-3.0.55/RandomFields/man/RPnugget.Rd |only
RandomFields-3.0.55/RandomFields/man/RPsequential.Rd |only
RandomFields-3.0.55/RandomFields/man/RPspecific.Rd |only
RandomFields-3.0.55/RandomFields/man/RPspectral.Rd |only
RandomFields-3.0.55/RandomFields/man/RPtbm.Rd |only
RandomFields-3.0.55/RandomFields/man/RRmcmc.Rd |only
RandomFields-3.0.55/RandomFields/man/RandomFields.Rd | 8
RandomFields-3.0.55/RandomFields/man/conventional2RFspDataFrame.Rd | 36
RandomFields-3.0.55/RandomFields/man/internal.Rd | 23
RandomFields-3.0.55/RandomFields/man/obsolete.Rd | 13
RandomFields-3.0.55/RandomFields/man/papers.SBS14.Rd | 25
RandomFields-3.0.55/RandomFields/man/papers.jss14.Rd | 39
RandomFields-3.0.55/RandomFields/man/plot-method.Rd | 25
RandomFields-3.0.55/RandomFields/man/soil.Rd | 12
RandomFields-3.0.55/RandomFields/man/weather.Rd | 1
RandomFields-3.0.55/RandomFields/src/AutoRandomFields.cc |only
RandomFields-3.0.55/RandomFields/src/AutoRandomFields.h |only
RandomFields-3.0.55/RandomFields/src/Brown.cc | 185 -
RandomFields-3.0.55/RandomFields/src/Coordinate_systems.cc |only
RandomFields-3.0.55/RandomFields/src/Covariance.h | 110 -
RandomFields-3.0.55/RandomFields/src/Families.h |only
RandomFields-3.0.55/RandomFields/src/Gneiting.cc | 36
RandomFields-3.0.55/RandomFields/src/Huetchen.cc | 352 ++-
RandomFields-3.0.55/RandomFields/src/InternalCov.cc | 791 ++------
RandomFields-3.0.55/RandomFields/src/KeyInfo.cc | 253 +-
RandomFields-3.0.55/RandomFields/src/MLE.cc | 115 -
RandomFields-3.0.55/RandomFields/src/Makevars.in | 2
RandomFields-3.0.55/RandomFields/src/Primitive.cc | 489 ++---
RandomFields-3.0.55/RandomFields/src/RF.h | 767 +++-----
RandomFields-3.0.55/RandomFields/src/RandomFields.h | 32
RandomFields-3.0.55/RandomFields/src/Specific.cc | 10
RandomFields-3.0.55/RandomFields/src/SpherModels.cc |only
RandomFields-3.0.55/RandomFields/src/SpherModels.h |only
RandomFields-3.0.55/RandomFields/src/auxiliary.cc | 392 ++++
RandomFields-3.0.55/RandomFields/src/auxiliary.h | 37
RandomFields-3.0.55/RandomFields/src/avltr_modified.cc | 2
RandomFields-3.0.55/RandomFields/src/basic.h | 42
RandomFields-3.0.55/RandomFields/src/circulant.cc | 151 -
RandomFields-3.0.55/RandomFields/src/direct.cc | 67
RandomFields-3.0.55/RandomFields/src/empvario.cc | 2
RandomFields-3.0.55/RandomFields/src/error.h | 10
RandomFields-3.0.55/RandomFields/src/extremes.cc | 945 ++++------
RandomFields-3.0.55/RandomFields/src/families.cc |only
RandomFields-3.0.55/RandomFields/src/fftVario.cc | 2
RandomFields-3.0.55/RandomFields/src/gauss.cc | 134 -
RandomFields-3.0.55/RandomFields/src/getNset.cc | 677 +++----
RandomFields-3.0.55/RandomFields/src/hilfsdateien.cc |only
RandomFields-3.0.55/RandomFields/src/hyperplan.cc | 114 -
RandomFields-3.0.55/RandomFields/src/initNerror.cc | 731 ++++---
RandomFields-3.0.55/RandomFields/src/initNerrorSpherModels.h |only
RandomFields-3.0.55/RandomFields/src/kriging.cc | 6
RandomFields-3.0.55/RandomFields/src/nugget.cc | 43
RandomFields-3.0.55/RandomFields/src/operator.cc | 511 ++++-
RandomFields-3.0.55/RandomFields/src/plusmalS.cc | 496 ++---
RandomFields-3.0.55/RandomFields/src/primitive.h | 38
RandomFields-3.0.55/RandomFields/src/rf_interfaces.cc |only
RandomFields-3.0.55/RandomFields/src/sequential.cc | 100 -
RandomFields-3.0.55/RandomFields/src/shape_processes.h |only
RandomFields-3.0.55/RandomFields/src/spectral.cc | 32
RandomFields-3.0.55/RandomFields/src/startGetNset.cc | 150 -
RandomFields-3.0.55/RandomFields/src/tbm.cc | 156 -
RandomFields-3.0.55/RandomFields/src/trend.cc | 103 -
RandomFields-3.0.55/RandomFields/src/userinterfaces.cc | 696 ++-----
RandomFields-3.0.55/RandomFields/src/variogramAndCo.cc | 233 --
RandomFields-3.0.55/RandomFields/src/variogramAndCo.h |only
155 files changed, 7147 insertions(+), 6146 deletions(-)
Title: A Grammar of Data Manipulation
Diff between dplyr versions 0.4.0 dated 2015-01-08 and 0.4.1 dated 2015-01-14
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 16 ++++-----
MD5 | 42 +++++++++++++-------------
R/funs.R | 4 +-
inst/doc/data_frames.html | 58 ++++++++++++++++++------------------
inst/doc/databases.html | 24 +++++++-------
inst/doc/hybrid-evaluation.html | 4 +-
inst/doc/introduction.html | 20 ++++++------
inst/doc/new-sql-backend.html | 4 +-
inst/doc/nse.html | 4 +-
inst/doc/two-table.html | 4 +-
inst/doc/window-functions.html | 16 ++++-----
man/funs.Rd | 4 +-
src/RcppExports.cpp | 1
src/group_indices.cpp | 2 +
tests/testthat/helper-data.r | 4 --
tests/testthat/test-filter.r | 2 -
tests/testthat/test-group-by.r | 6 +--
tests/testthat/test-group-indices.R | 11 ++++++
tests/testthat/test-joins.r | 16 ++++-----
tests/testthat/test-mutate.r | 2 -
tests/testthat/test-sample.R | 4 +-
tests/testthat/test-select.r | 2 -
22 files changed, 130 insertions(+), 120 deletions(-)
Title: Interface to PHAST Software for Comparative Genomics
Diff between rphast versions 1.5 dated 2013-12-13 and 1.6 dated 2015-01-14
Description: RPHAST is an R interface to the PHAST software
(Phylogenetic Analysis with Space/Time Models). It can be used for
many types of analysis in comparative and evolutionary genomics,
such as estimating models of evolution from sequence data, scoring
alignments for conservation or acceleration, and predicting
elements based on conservation or custom phylogenetic hidden Markov
models. It can also perform many basic operations on multiple
sequence alignments and phylogenetic trees.
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Maintainer: Melissa Hubisz
rphast-1.5/rphast/configure.win |only
rphast-1.5/rphast/inst/doc/vignette2.pdf |only
rphast-1.5/rphast/src/pcre |only
rphast-1.6/rphast/DESCRIPTION | 19
rphast-1.6/rphast/LICENSE | 4
rphast-1.6/rphast/MD5 | 403 +--
rphast-1.6/rphast/NAMESPACE | 82
rphast-1.6/rphast/build/vignette.rds |binary
rphast-1.6/rphast/cleanup | 2
rphast-1.6/rphast/configure | 2744 ++-------------------
rphast-1.6/rphast/configure.ac | 518 ---
rphast-1.6/rphast/inst/doc/vignette1.Rnw | 2
rphast-1.6/rphast/inst/doc/vignette1.pdf |binary
rphast-1.6/rphast/inst/doc/vignette3.R | 28
rphast-1.6/rphast/inst/doc/vignette3.Rnw | 30
rphast-1.6/rphast/inst/doc/vignette3.pdf |binary
rphast-1.6/rphast/inst/doc/vignette4.R | 3
rphast-1.6/rphast/inst/doc/vignette4.Rnw | 5
rphast-1.6/rphast/inst/doc/vignette4.pdf |binary
rphast-1.6/rphast/man/add.UTRs.feat.Rd | 21
rphast-1.6/rphast/man/add.introns.feat.Rd | 21
rphast-1.6/rphast/man/add.ls.mod.Rd | 194 -
rphast-1.6/rphast/man/add.signals.feat.Rd | 27
rphast-1.6/rphast/man/alphabet.msa.Rd | 12
rphast-1.6/rphast/man/apply.bgc.sel.Rd | 21
rphast-1.6/rphast/man/as.data.frame.feat.Rd | 30
rphast-1.6/rphast/man/as.list.tm.Rd | 15
rphast-1.6/rphast/man/as.pointer.feat.Rd | 20
rphast-1.6/rphast/man/as.pointer.msa.Rd | 17
rphast-1.6/rphast/man/as.track.feat.Rd | 38
rphast-1.6/rphast/man/as.track.msa.Rd | 69
rphast-1.6/rphast/man/as.track.wig.Rd | 60
rphast-1.6/rphast/man/base.freq.msa.Rd | 37
rphast-1.6/rphast/man/bgc.informative.Rd | 45
rphast-1.6/rphast/man/bgc.nucleotide.tests.Rd | 41
rphast-1.6/rphast/man/bgc.sel.factor.Rd | 20
rphast-1.6/rphast/man/branchlength.tree.Rd | 14
rphast-1.6/rphast/man/classify.muts.bgc.Rd | 22
rphast-1.6/rphast/man/codon.clean.msa.Rd | 50
rphast-1.6/rphast/man/col.expected.subs.msa.Rd | 18
rphast-1.6/rphast/man/complement.Rd | 15
rphast-1.6/rphast/man/composition.feat.Rd | 32
rphast-1.6/rphast/man/concat.msa.Rd | 32
rphast-1.6/rphast/man/convert.coords.feat.Rd | 71
rphast-1.6/rphast/man/coord.range.msa.Rd | 22
rphast-1.6/rphast/man/copy.feat.Rd | 21
rphast-1.6/rphast/man/copy.msa.Rd | 22
rphast-1.6/rphast/man/coverage.feat.Rd | 54
rphast-1.6/rphast/man/density.feat.Rd | 22
rphast-1.6/rphast/man/depth.tree.Rd | 20
rphast-1.6/rphast/man/dim.feat.Rd | 14
rphast-1.6/rphast/man/dim.msa.Rd | 15
rphast-1.6/rphast/man/enrichment.feat.Rd | 42
rphast-1.6/rphast/man/expected.subs.msa.Rd | 19
rphast-1.6/rphast/man/extract.feature.msa.Rd | 40
rphast-1.6/rphast/man/feat.Rd | 83
rphast-1.6/rphast/man/fix.semicolon.tree.Rd | 19
rphast-1.6/rphast/man/fix.start.stop.feat.Rd | 31
rphast-1.6/rphast/man/flatten.feat.Rd | 18
rphast-1.6/rphast/man/freq3x4.msa.Rd | 18
rphast-1.6/rphast/man/from.pointer.feat.Rd | 16
rphast-1.6/rphast/man/from.pointer.msa.Rd | 17
rphast-1.6/rphast/man/gc.content.msa.Rd | 26
rphast-1.6/rphast/man/get.rate.matrix.params.tm.Rd | 26
rphast-1.6/rphast/man/get4d.msa.Rd | 34
rphast-1.6/rphast/man/guess.format.msa.Rd | 28
rphast-1.6/rphast/man/hist.feat.Rd | 18
rphast-1.6/rphast/man/hmm.Rd | 32
rphast-1.6/rphast/man/informative.regions.msa.Rd | 67
rphast-1.6/rphast/man/inverse.feat.Rd | 28
rphast-1.6/rphast/man/is.format.msa.Rd | 24
rphast-1.6/rphast/man/is.msa.Rd | 12
rphast-1.6/rphast/man/is.ordered.msa.Rd | 13
rphast-1.6/rphast/man/is.subst.mod.tm.Rd | 16
rphast-1.6/rphast/man/is.tm.Rd | 12
rphast-1.6/rphast/man/is.track.Rd | 14
rphast-1.6/rphast/man/label.branches.Rd | 30
rphast-1.6/rphast/man/label.subtree.Rd | 31
rphast-1.6/rphast/man/leafnames.tree.Rd | 15
rphast-1.6/rphast/man/likelihood.msa.Rd | 40
rphast-1.6/rphast/man/mod.backgd.tm.Rd | 27
rphast-1.6/rphast/man/msa.Rd | 111
rphast-1.6/rphast/man/name.ancestors.Rd | 15
rphast-1.6/rphast/man/names.msa.Rd | 14
rphast-1.6/rphast/man/ncol.feat.Rd | 17
rphast-1.6/rphast/man/ncol.msa.Rd | 23
rphast-1.6/rphast/man/ninf.msa.Rd | 19
rphast-1.6/rphast/man/nothanks.rphast.Rd | 17
rphast-1.6/rphast/man/nrow.feat.Rd | 13
rphast-1.6/rphast/man/nrow.msa.Rd | 15
rphast-1.6/rphast/man/nstate.hmm.Rd | 12
rphast-1.6/rphast/man/numleaf.tree.Rd | 14
rphast-1.6/rphast/man/numnodes.tree.Rd | 14
rphast-1.6/rphast/man/offset.msa.Rd | 16
rphast-1.6/rphast/man/optim.rphast.Rd | 86
rphast-1.6/rphast/man/overlap.feat.Rd | 81
rphast-1.6/rphast/man/pairwise.diff.msa.Rd | 47
rphast-1.6/rphast/man/phastBias.Rd | 118
rphast-1.6/rphast/man/phastCons.Rd | 237 -
rphast-1.6/rphast/man/phyloFit.Rd | 283 --
rphast-1.6/rphast/man/phyloP.Rd | 135 -
rphast-1.6/rphast/man/phyloP.prior.Rd | 73
rphast-1.6/rphast/man/phyloP.sph.Rd | 156 -
rphast-1.6/rphast/man/plot.feat.Rd | 63
rphast-1.6/rphast/man/plot.gene.Rd | 42
rphast-1.6/rphast/man/plot.lsmodel.tm.Rd | 80
rphast-1.6/rphast/man/plot.msa.Rd | 64
rphast-1.6/rphast/man/plot.rate.matrix.Rd | 81
rphast-1.6/rphast/man/plot.tm.Rd | 74
rphast-1.6/rphast/man/plot.track.Rd | 77
rphast-1.6/rphast/man/postprob.msa.Rd | 25
rphast-1.6/rphast/man/print.feat.Rd | 15
rphast-1.6/rphast/man/print.msa.Rd | 50
rphast-1.6/rphast/man/print.phastBiasResult.Rd | 13
rphast-1.6/rphast/man/print.tm.Rd | 19
rphast-1.6/rphast/man/prune.tree.Rd | 21
rphast-1.6/rphast/man/range.feat.Rd | 17
rphast-1.6/rphast/man/range.track.Rd | 20
rphast-1.6/rphast/man/rbind.feat.Rd | 15
rphast-1.6/rphast/man/read.feat.Rd | 46
rphast-1.6/rphast/man/read.hmm.Rd | 16
rphast-1.6/rphast/man/read.msa.Rd | 140 -
rphast-1.6/rphast/man/read.newick.tree.Rd | 14
rphast-1.6/rphast/man/read.tm.Rd | 14
rphast-1.6/rphast/man/read.wig.Rd | 16
rphast-1.6/rphast/man/reflect.phylo.hmm.Rd | 34
rphast-1.6/rphast/man/register.rphast.Rd | 49
rphast-1.6/rphast/man/rename.tree.Rd | 23
rphast-1.6/rphast/man/rescale.tree.Rd | 28
rphast-1.6/rphast/man/reverse.complement.msa.Rd | 21
rphast-1.6/rphast/man/rphast-package.Rd | 17
rphast-1.6/rphast/man/sample.msa.Rd | 38
rphast-1.6/rphast/man/score.hmm.Rd | 114
rphast-1.6/rphast/man/set.rate.matrix.tm.Rd | 120
rphast-1.6/rphast/man/setup.branch.site.tm.Rd | 60
rphast-1.6/rphast/man/simulate.msa.Rd | 80
rphast-1.6/rphast/man/smooth.wig.Rd | 22
rphast-1.6/rphast/man/sort.feat.Rd | 23
rphast-1.6/rphast/man/split.by.feature.msa.Rd | 31
rphast-1.6/rphast/man/split.feat.Rd | 49
rphast-1.6/rphast/man/square-bracket-assign-msa.Rd | 54
rphast-1.6/rphast/man/square-bracket-msa.Rd | 60
rphast-1.6/rphast/man/state.freq.msa.Rd | 17
rphast-1.6/rphast/man/strip.gaps.msa.Rd | 44
rphast-1.6/rphast/man/sub.msa.Rd | 44
rphast-1.6/rphast/man/subst.mods.Rd | 12
rphast-1.6/rphast/man/subtree.Rd | 28
rphast-1.6/rphast/man/summary.feat.Rd | 13
rphast-1.6/rphast/man/summary.msa.Rd | 27
rphast-1.6/rphast/man/summary.tm.Rd | 15
rphast-1.6/rphast/man/summary.tree.Rd | 22
rphast-1.6/rphast/man/tagval.Rd | 34
rphast-1.6/rphast/man/tagval.feat.Rd | 38
rphast-1.6/rphast/man/tm.Rd | 101
rphast-1.6/rphast/man/total.expected.subs.msa.Rd | 17
rphast-1.6/rphast/man/translate.msa.Rd | 48
rphast-1.6/rphast/man/unapply.bgc.sel.Rd | 20
rphast-1.6/rphast/man/unique.feat.Rd | 60
rphast-1.6/rphast/man/write.feat.Rd | 15
rphast-1.6/rphast/man/write.hmm.Rd | 18
rphast-1.6/rphast/man/write.msa.Rd | 33
rphast-1.6/rphast/man/write.tm.Rd | 20
rphast-1.6/rphast/man/write.wig.Rd | 33
rphast-1.6/rphast/man/write.wig.feat.Rd | 32
rphast-1.6/rphast/src/Makevars.in | 126
rphast-1.6/rphast/src/Makevars.win | 126
rphast-1.6/rphast/src/complex_matrix.c | 34
rphast-1.6/rphast/src/eigen.c | 38
rphast-1.6/rphast/src/fit_column.c | 454 +--
rphast-1.6/rphast/src/fit_column.h | 74
rphast-1.6/rphast/src/fit_feature.c | 2
rphast-1.6/rphast/src/maf.c | 274 +-
rphast-1.6/rphast/src/markov_matrix.c | 98
rphast-1.6/rphast/src/matrix.c | 38
rphast-1.6/rphast/src/misc.c | 6
rphast-1.6/rphast/src/misc.h | 159 -
rphast-1.6/rphast/src/phast_cons.c | 298 +-
rphast-1.6/rphast/src/phylo_fit.c | 322 +-
rphast-1.6/rphast/src/phylo_p_print.c | 207 -
rphast-1.6/rphast/src/prob_matrix.c | 6
rphast-1.6/rphast/src/rph_trees.c | 38
rphast-1.6/rphast/src/subst_mods.c | 635 ++--
rphast-1.6/rphast/src/tree_likelihoods.c | 250 -
rphast-1.6/rphast/src/trees.c | 224 -
rphast-1.6/rphast/vignettes/vignette1.Rnw | 2
rphast-1.6/rphast/vignettes/vignette2-source.pdf |only
rphast-1.6/rphast/vignettes/vignette3.Rnw | 30
rphast-1.6/rphast/vignettes/vignette4.Rnw | 5
188 files changed, 5082 insertions(+), 8084 deletions(-)
Title: Process Rhea, KEGG, MetaCyc, Unipathway biochemical reaction
data
Diff between RbioRXN versions 1.3.1 dated 2014-07-30 and 1.5 dated 2015-01-14
Description: RbioRXN facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min
DESCRIPTION | 16 ++++++------
MD5 | 18 ++++++-------
NAMESPACE | 2 -
R/RbioRXN-internal.R | 2 -
R/get.metacyc.all.R | 16 +++++++++++-
R/get.metacyc.reaction.byId.R | 51 ++++++++++++++++++++++++---------------
R/instantiate.rhea.R | 15 ++++++++---
man/RbioRXN-package.Rd | 4 +--
man/get.metacyc.all.Rd | 2 +
man/get.metacyc.reaction.byId.Rd | 2 +
10 files changed, 83 insertions(+), 45 deletions(-)
Title: Modelling with Sparse And Dense Matrices
Diff between MatrixModels versions 0.3-1.1 dated 2014-02-12 and 0.4-0 dated 2015-01-14
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates
Maintainer: Martin Maechler
DESCRIPTION | 22 +++++++++++-----------
MD5 | 12 ++++++------
NAMESPACE | 45 ++++++++++++++++++++++++++-------------------
R/modelMatrix.R | 5 ++---
man/glm4.Rd | 8 ++++----
man/lm.fit.sparse.Rd | 19 ++++++++++---------
man/model.Matrix.Rd | 2 +-
7 files changed, 60 insertions(+), 53 deletions(-)
Title: Interactive Exploration of Contour Data
Diff between exCon versions 0.1-0 dated 2014-10-29 and 0.1-3 dated 2015-01-14
Description: exCon is an interactive tool to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. exCon creates an interactive web page
showing the contoured data set along with slices from the original matrix
parallel to each dimension. The page is written in d3/javascript.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson
DESCRIPTION | 10 +++---
MD5 | 15 ++++-----
NAMESPACE | 2 -
NEWS | 22 +++++++++++++
R/exCon.R | 66 ++++++++++++++++++++++++++--------------
inst/extdata/eC_brushNguides.js | 5 +--
inst/extdata/exCon.js |only
man/exCon-package.Rd | 3 +
man/exCon.Rd | 35 +++++++++++++++------
9 files changed, 109 insertions(+), 49 deletions(-)
Title: Toolkit for the plotting and analysis of stratigraphic and
palaeontological data
Diff between stratigraph versions 0.64 dated 2011-08-03 and 0.66 dated 2015-01-13
Description: A collection of tools for plotting and analyzing paleontological and geological data distributed through through time in stratigraphic cores or sections. Includes some miscellaneous functions for handling other kinds of palaeontological and paleoecological data.
Author: Walton A. Green
Maintainer: Walton A. Green
stratigraph-0.64/stratigraph/data/.Rapp.history |only
stratigraph-0.66/stratigraph/DESCRIPTION | 15 ++---
stratigraph-0.66/stratigraph/MD5 |only
stratigraph-0.66/stratigraph/NAMESPACE |only
stratigraph-0.66/stratigraph/R/plot.strat.column.R | 44 ++++++++--------
stratigraph-0.66/stratigraph/data/cerrejon.rda |binary
stratigraph-0.66/stratigraph/data/corneta.rda |binary
stratigraph-0.66/stratigraph/data/mohawk.rda |binary
stratigraph-0.66/stratigraph/data/plain.rda |binary
stratigraph-0.66/stratigraph/data/rogerslk.rda |binary
stratigraph-0.66/stratigraph/data/sI.rda |binary
stratigraph-0.66/stratigraph/data/sII.rda |binary
stratigraph-0.66/stratigraph/data/sIII.rda |binary
stratigraph-0.66/stratigraph/data/sIV.rda |binary
stratigraph-0.66/stratigraph/data/sV.rda |binary
stratigraph-0.66/stratigraph/data/sVI.rda |binary
stratigraph-0.66/stratigraph/data/stippled.rda |binary
stratigraph-0.66/stratigraph/data/striped.rda |binary
stratigraph-0.66/stratigraph/man/a.datums.Rd | 2
stratigraph-0.66/stratigraph/man/compress2matrix.Rd | 14 +----
stratigraph-0.66/stratigraph/man/corneta.Rd | 2
stratigraph-0.66/stratigraph/man/dloc.Rd | 7 +-
stratigraph-0.66/stratigraph/man/fill.ranges.Rd | 7 +-
stratigraph-0.66/stratigraph/man/gluesheets.Rd | 4 -
stratigraph-0.66/stratigraph/man/grid.prop.plot.Rd | 14 ++---
stratigraph-0.66/stratigraph/man/mohawk.Rd | 3 -
stratigraph-0.66/stratigraph/man/nonuser.Rd | 14 ++---
stratigraph-0.66/stratigraph/man/oe.rates.Rd | 3 -
stratigraph-0.66/stratigraph/man/plain.Rd | 6 +-
stratigraph-0.66/stratigraph/man/plot.strat.column.Rd | 3 -
stratigraph-0.66/stratigraph/man/rangechart.Rd | 6 +-
stratigraph-0.66/stratigraph/man/readGPDascii.Rd | 5 +
stratigraph-0.66/stratigraph/man/rogerslk.Rd | 3 -
stratigraph-0.66/stratigraph/man/sI.Rd | 4 -
stratigraph-0.66/stratigraph/man/strat.column.Rd | 10 +--
stratigraph-0.66/stratigraph/man/stratigraph.package.Rd | 6 +-
stratigraph-0.66/stratigraph/man/writeCONOP.Rd | 10 +--
stratigraph-0.66/stratigraph/man/writeGPDascii.Rd | 5 +
38 files changed, 93 insertions(+), 94 deletions(-)
Title: Robust Mixture Discriminant Analysis
Diff between robustDA versions 1.0 dated 2014-09-29 and 1.1 dated 2015-01-13
Description: Robust mixture discriminant analysis (RMDA, Bouveyron & Girard, 2009) allows to build a robust supervised classifier from learning data with label noise. The idea of the proposed method is to confront an unsupervised modeling of the data with the supervised information carried by the labels of the learning data in order to detect inconsistencies. The method is able afterward to build a robust classifier taking into account the detected inconsistencies into the labels.
Author: Charles Bouveyron & Stephane Girard
Maintainer: Charles Bouveyron
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/rmda.R | 26 +++++++++++++-------------
R/robustDA-internal.R | 2 +-
4 files changed, 20 insertions(+), 20 deletions(-)
Title: Multi-Resolution Estimation of the Hazard Rate
Diff between MRH versions 1.1 dated 2014-10-23 and 2.0 dated 2015-01-13
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times. Can accommodate covariates under the proportional and non-proportional hazards setting, and is ideal for analysis of survival data with long-term follow-up.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar
MRH-1.1/MRH/R/MRHCovNPHBA.r |only
MRH-1.1/MRH/R/MRHCovPH.r |only
MRH-2.0/MRH/DESCRIPTION | 10 -
MRH-2.0/MRH/MD5 | 52 +++--
MRH-2.0/MRH/R/FunctionsNotforUser_Assorted.r | 228 +++++++++++++-----------
MRH-2.0/MRH/R/FunctionsNotforUser_CheckChains.r |only
MRH-2.0/MRH/R/FunctionsNotforUser_Convergence.r | 7
MRH-2.0/MRH/R/FunctionsNotforUser_Posteriors.r | 27 ++
MRH-2.0/MRH/R/FunctionsforUser.r | 127 ++++++++-----
MRH-2.0/MRH/R/NPHBA_samplegamma.r |only
MRH-2.0/MRH/R/NPHBA_samplek.r |only
MRH-2.0/MRH/R/NPHBA_samplekandgamma.r |only
MRH-2.0/MRH/R/NPHBA_samplesimple.r |only
MRH-2.0/MRH/R/NPHBA_shell.r |only
MRH-2.0/MRH/R/PH_samplegamma.r |only
MRH-2.0/MRH/R/PH_samplek.r |only
MRH-2.0/MRH/R/PH_samplekandgamma.r |only
MRH-2.0/MRH/R/PH_samplesimple.r |only
MRH-2.0/MRH/R/PH_shell.r |only
MRH-2.0/MRH/R/S3functions.r | 103 ++++++++++
MRH-2.0/MRH/R/S3functions_BA.r | 62 ------
MRH-2.0/MRH/R/S3functions_PH.r | 106 +----------
MRH-2.0/MRH/R/estimateMRH.r | 187 +++++++++++++++++--
MRH-2.0/MRH/build/vignette.rds |binary
MRH-2.0/MRH/inst/doc/MRH.pdf |binary
MRH-2.0/MRH/man/AnalyzeMultiple.Rd | 23 +-
MRH-2.0/MRH/man/CalcFunction.Rd | 12 -
MRH-2.0/MRH/man/DIC.Rd | 17 +
MRH-2.0/MRH/man/MRH.Rd | 15 +
MRH-2.0/MRH/man/estimateMRH.Rd | 72 +++++--
MRH-2.0/MRH/man/nph.Rd | 3
MRH-2.0/MRH/man/plot.MRH.Rd | 23 +-
MRH-2.0/MRH/man/summary.MRH.Rd |only
MRH-2.0/MRH/src/arms-R.c | 4
34 files changed, 662 insertions(+), 416 deletions(-)
Title: A Utility to Send Emails from R
Diff between mailR versions 0.4 dated 2015-01-11 and 0.4.1 dated 2015-01-13
Description: Interface to Apache Commons Email to send emails
from R.
Author: Rahul Premraj
Maintainer: Rahul Premraj
mailR-0.4.1/mailR/DESCRIPTION | 8
mailR-0.4.1/mailR/MD5 | 577 ------------------------------------------
mailR-0.4.1/mailR/R/mailR.R | 2
mailR-0.4.1/mailR/java/README |only
mailR-0.4/mailR/java/email |only
mailR-0.4/mailR/java/javamail |only
6 files changed, 8 insertions(+), 579 deletions(-)
Title: Hive Plots of R Package Function Calls
Diff between FuncMap versions 1.0-2 dated 2013-03-29 and 1.0-3 dated 2015-01-13
Description: FuncMap analyzes the function calls in an R package and creates a hive plot of the calls, dividing them among functions that only make outgoing calls (sources), functions that have only incoming calls (sinks), and those that have both incoming calls and make outgoing calls (managers). Function calls can be mapped by their absolute numbers, their normalized absolute numbers, or their rank. FuncMap should be useful for comparing packages at a high level for their overall design. Plus, it's just plain fun. The hive plot concept was developed by Martin Krzywinski (www.hiveplot.com) and inspired this package.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
DESCRIPTION | 19 +++++--------------
MD5 | 8 ++++----
NEWS | 7 +++++++
inst/CITATION | 5 ++---
man/FuncMap-package.Rd | 4 ++--
5 files changed, 20 insertions(+), 23 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Diff between ExomeDepth versions 1.0.7 dated 2014-07-20 and 1.1.1 dated 2015-01-13
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
ExomeDepth-1.0.7/ExomeDepth/man/plot-methods.Rd |only
ExomeDepth-1.1.1/ExomeDepth/DESCRIPTION | 19
ExomeDepth-1.1.1/ExomeDepth/MD5 | 40 -
ExomeDepth-1.1.1/ExomeDepth/NAMESPACE | 12
ExomeDepth-1.1.1/ExomeDepth/R/class_definition.R | 18
ExomeDepth-1.1.1/ExomeDepth/R/countBamInGranges.R | 129 ++---
ExomeDepth-1.1.1/ExomeDepth/R/plot_CNVs_method.R | 22
ExomeDepth-1.1.1/ExomeDepth/R/tools.R | 8
ExomeDepth-1.1.1/ExomeDepth/build/vignette.rds |binary
ExomeDepth-1.1.1/ExomeDepth/data/Conrad.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/ExomeCount.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/exons.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/exons.hg19.X.RData |binary
ExomeDepth-1.1.1/ExomeDepth/data/genes.hg19.RData |binary
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.R | 249 +++-------
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.Rnw | 48 +
ExomeDepth-1.1.1/ExomeDepth/inst/doc/ExomeDepth-vignette.pdf |binary
ExomeDepth-1.1.1/ExomeDepth/man/plot.ExomeDepth.Rd |only
ExomeDepth-1.1.1/ExomeDepth/src/CNV_estimate.cpp | 2
ExomeDepth-1.1.1/ExomeDepth/src/VP_gamma.c | 2
ExomeDepth-1.1.1/ExomeDepth/src/hmm.cpp | 3
ExomeDepth-1.1.1/ExomeDepth/vignettes/ExomeDepth-vignette.Rnw | 48 +
22 files changed, 295 insertions(+), 305 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Diff between bnlearn versions 3.6 dated 2014-06-17 and 3.7 dated 2015-01-13
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari
bnlearn-3.6/bnlearn/src/gaussian.likelihood.c |only
bnlearn-3.6/bnlearn/src/mutual.information.c |only
bnlearn-3.7/bnlearn/Changelog | 29
bnlearn-3.7/bnlearn/DESCRIPTION | 16
bnlearn-3.7/bnlearn/MD5 | 213 +--
bnlearn-3.7/bnlearn/NAMESPACE | 11
bnlearn-3.7/bnlearn/R/arc.operations.R | 2
bnlearn-3.7/bnlearn/R/arc.strength.R | 2
bnlearn-3.7/bnlearn/R/backend-indep.R | 111 -
bnlearn-3.7/bnlearn/R/backend-s4.R | 6
bnlearn-3.7/bnlearn/R/backend-score.R | 2
bnlearn-3.7/bnlearn/R/bootstrap.R | 32
bnlearn-3.7/bnlearn/R/choose.direction.R | 437 ++----
bnlearn-3.7/bnlearn/R/ci.test.R | 192 --
bnlearn-3.7/bnlearn/R/cpq.R | 6
bnlearn-3.7/bnlearn/R/custom.fit.R |only
bnlearn-3.7/bnlearn/R/cv.R | 18
bnlearn-3.7/bnlearn/R/fast-iamb.R | 49
bnlearn-3.7/bnlearn/R/fit.R | 289 ++--
bnlearn-3.7/bnlearn/R/fitted.assignment.R |only
bnlearn-3.7/bnlearn/R/foreign-read.R | 60
bnlearn-3.7/bnlearn/R/frontend-bn.R | 16
bnlearn-3.7/bnlearn/R/frontend-bootstrap.R | 8
bnlearn-3.7/bnlearn/R/frontend-data.R | 16
bnlearn-3.7/bnlearn/R/frontend-fit.R | 207 --
bnlearn-3.7/bnlearn/R/frontend-foreign.R | 6
bnlearn-3.7/bnlearn/R/frontend-learning.R | 11
bnlearn-3.7/bnlearn/R/frontend-mvber.R | 2
bnlearn-3.7/bnlearn/R/frontend-nodes.R | 8
bnlearn-3.7/bnlearn/R/frontend-packages.R | 41
bnlearn-3.7/bnlearn/R/frontend-plot.R | 4
bnlearn-3.7/bnlearn/R/frontend-predict.R | 33
bnlearn-3.7/bnlearn/R/frontend-print.R | 31
bnlearn-3.7/bnlearn/R/frontend-score.R | 18
bnlearn-3.7/bnlearn/R/frontend-simulation.R | 18
bnlearn-3.7/bnlearn/R/globals.R | 54
bnlearn-3.7/bnlearn/R/graphviz.R | 60
bnlearn-3.7/bnlearn/R/grow-shrink.R | 41
bnlearn-3.7/bnlearn/R/hiton-pc.R | 48
bnlearn-3.7/bnlearn/R/incremental-association.R | 39
bnlearn-3.7/bnlearn/R/init.R | 4
bnlearn-3.7/bnlearn/R/inter-iamb.R | 43
bnlearn-3.7/bnlearn/R/lattice.R | 164 +-
bnlearn-3.7/bnlearn/R/learning-algorithms.R | 181 +-
bnlearn-3.7/bnlearn/R/loss.R | 4
bnlearn-3.7/bnlearn/R/maxmin-pc.R | 86 -
bnlearn-3.7/bnlearn/R/nparams.R |only
bnlearn-3.7/bnlearn/R/predict.R | 31
bnlearn-3.7/bnlearn/R/test.R | 11
bnlearn-3.7/bnlearn/R/utils-arcs.R | 14
bnlearn-3.7/bnlearn/R/utils-cluster.R | 21
bnlearn-3.7/bnlearn/R/utils-graph.R | 54
bnlearn-3.7/bnlearn/R/utils-misc.R | 96 -
bnlearn-3.7/bnlearn/R/utils-sanitization.R | 506 ++++---
bnlearn-3.7/bnlearn/data/clgaussian.test.rda |only
bnlearn-3.7/bnlearn/inst/network.scripts/clgaussian.test.R |only
bnlearn-3.7/bnlearn/man/arc.strength.Rd | 8
bnlearn-3.7/bnlearn/man/bn.cv.Rd | 2
bnlearn-3.7/bnlearn/man/bn.fit.Rd | 45
bnlearn-3.7/bnlearn/man/bn.fit.class.Rd | 83 -
bnlearn-3.7/bnlearn/man/bn.fit.methods.Rd | 8
bnlearn-3.7/bnlearn/man/bnlearn-package.Rd | 31
bnlearn-3.7/bnlearn/man/ci.test.Rd | 12
bnlearn-3.7/bnlearn/man/clgaussian-test.Rd |only
bnlearn-3.7/bnlearn/man/cpdag.Rd | 12
bnlearn-3.7/bnlearn/man/cpquery.Rd | 2
bnlearn-3.7/bnlearn/man/foreign.Rd | 4
bnlearn-3.7/bnlearn/man/gRain.Rd | 2
bnlearn-3.7/bnlearn/man/learn.Rd | 6
bnlearn-3.7/bnlearn/man/naive.bayes.Rd | 12
bnlearn-3.7/bnlearn/man/score.Rd | 13
bnlearn-3.7/bnlearn/src/allocations.c | 23
bnlearn-3.7/bnlearn/src/allsubs.test.c | 907 ++++++++-----
bnlearn-3.7/bnlearn/src/bayesian.network.c | 142 --
bnlearn-3.7/bnlearn/src/bind.c | 6
bnlearn-3.7/bnlearn/src/cache.structure.c | 2
bnlearn-3.7/bnlearn/src/cg.assumptions.c |only
bnlearn-3.7/bnlearn/src/cg.loglikelihood.c |only
bnlearn-3.7/bnlearn/src/cg.mutual.information.c |only
bnlearn-3.7/bnlearn/src/common.c | 21
bnlearn-3.7/bnlearn/src/common.h | 51
bnlearn-3.7/bnlearn/src/configurations.c | 93 -
bnlearn-3.7/bnlearn/src/ctest.c |only
bnlearn-3.7/bnlearn/src/data.frame.c | 3
bnlearn-3.7/bnlearn/src/dedup.c | 4
bnlearn-3.7/bnlearn/src/dirichlet.posterior.c | 7
bnlearn-3.7/bnlearn/src/discrete.loglikelihood.c | 10
bnlearn-3.7/bnlearn/src/discrete.monte.carlo.c | 2
bnlearn-3.7/bnlearn/src/discrete.mutual.information.c |only
bnlearn-3.7/bnlearn/src/filter.arcs.c | 2
bnlearn-3.7/bnlearn/src/fitted.c | 48
bnlearn-3.7/bnlearn/src/gaussian.loglikelihood.c |only
bnlearn-3.7/bnlearn/src/gaussian.monte.carlo.c | 5
bnlearn-3.7/bnlearn/src/gaussian.mutual.information.c |only
bnlearn-3.7/bnlearn/src/globals.c | 1
bnlearn-3.7/bnlearn/src/graph.generation.c | 2
bnlearn-3.7/bnlearn/src/graph.priors.c | 2
bnlearn-3.7/bnlearn/src/indep.test.c | 765 ----------
bnlearn-3.7/bnlearn/src/jonckheere.c | 2
bnlearn-3.7/bnlearn/src/likelihood.weighting.c | 4
bnlearn-3.7/bnlearn/src/linear.algebra.c | 36
bnlearn-3.7/bnlearn/src/linear.correlation.c | 2
bnlearn-3.7/bnlearn/src/loss.c | 224 ++-
bnlearn-3.7/bnlearn/src/map.lw.c | 5
bnlearn-3.7/bnlearn/src/nparams.c |only
bnlearn-3.7/bnlearn/src/pearson.x2.c | 1
bnlearn-3.7/bnlearn/src/per.node.score.c | 110 +
bnlearn-3.7/bnlearn/src/predict.c | 57
bnlearn-3.7/bnlearn/src/rbn.c | 176 +-
bnlearn-3.7/bnlearn/src/sanitization.c | 88 +
bnlearn-3.7/bnlearn/src/score.delta.c | 11
bnlearn-3.7/bnlearn/src/shrinkage.c | 16
bnlearn-3.7/bnlearn/src/subsets.c | 38
bnlearn-3.7/bnlearn/src/tiers.c | 15
bnlearn-3.7/bnlearn/src/utest.c |only
bnlearn-3.7/bnlearn/src/wishart.posterior.c | 7
116 files changed, 3068 insertions(+), 3411 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Diff between blocksdesign versions 1.3 dated 2014-12-01 and 1.4 dated 2015-01-13
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks strata are optimized hierarchically with each set of
nested blocks optimized within the levels of the preceding set. Block sizes
are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson
DESCRIPTION | 8
MD5 | 10
R/blocks.r | 689 +++++++++++++++++++++++++---------------------------
R/pairwise_effics.r | 6
R/upper_bounds.r | 7
man/blocks.Rd | 145 ++++++----
6 files changed, 431 insertions(+), 434 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Diff between BCEA versions 2.0-2 dated 2013-12-02 and 2.1-0 dated 2015-01-13
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, BCEA computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis
Author: Gianluca Baio, Andrea Berardi
Maintainer: Gianluca Baio
BCEA-2.0-2/BCEA/man/MCMCvaccine.Rd |only
BCEA-2.0-2/BCEA/man/N.Rd |only
BCEA-2.0-2/BCEA/man/N.outcomes.Rd |only
BCEA-2.0-2/BCEA/man/N.resources.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.adv.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.death.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.hosp.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.inf.Rd |only
BCEA-2.0-2/BCEA/man/QALYs.pne.Rd |only
BCEA-2.0-2/BCEA/man/c.Rd |only
BCEA-2.0-2/BCEA/man/cost.GP.Rd |only
BCEA-2.0-2/BCEA/man/cost.hosp.Rd |only
BCEA-2.0-2/BCEA/man/cost.otc.Rd |only
BCEA-2.0-2/BCEA/man/cost.time.off.Rd |only
BCEA-2.0-2/BCEA/man/cost.time.vac.Rd |only
BCEA-2.0-2/BCEA/man/cost.travel.Rd |only
BCEA-2.0-2/BCEA/man/cost.trt1.Rd |only
BCEA-2.0-2/BCEA/man/cost.trt2.Rd |only
BCEA-2.0-2/BCEA/man/cost.vac.Rd |only
BCEA-2.0-2/BCEA/man/e.Rd |only
BCEA-2.0-2/BCEA/man/treats.Rd |only
BCEA-2.1-0/BCEA/DESCRIPTION | 11
BCEA-2.1-0/BCEA/MD5 | 85 -
BCEA-2.1-0/BCEA/R/bcea.R | 2413 ++++++++++++++++++++-------------
BCEA-2.1-0/BCEA/data/Smoking.RData |only
BCEA-2.1-0/BCEA/data/Vaccine.RData |binary
BCEA-2.1-0/BCEA/data/datalist |only
BCEA-2.1-0/BCEA/man/BCEA-package.Rd | 4
BCEA-2.1-0/BCEA/man/CEriskav.Rd | 26
BCEA-2.1-0/BCEA/man/CreateInputs.Rd | 16
BCEA-2.1-0/BCEA/man/Smoking.Rd |only
BCEA-2.1-0/BCEA/man/Vaccine.Rd | 52
BCEA-2.1-0/BCEA/man/bcea.Rd | 52
BCEA-2.1-0/BCEA/man/ceac.plot.Rd | 14
BCEA-2.1-0/BCEA/man/ceaf.plot.Rd | 14
BCEA-2.1-0/BCEA/man/ceef.plot.Rd |only
BCEA-2.1-0/BCEA/man/ceplane.plot.Rd | 29
BCEA-2.1-0/BCEA/man/contour.bcea.Rd | 20
BCEA-2.1-0/BCEA/man/contour2.Rd | 32
BCEA-2.1-0/BCEA/man/diag.evppi.Rd | 45
BCEA-2.1-0/BCEA/man/eib.plot.Rd | 24
BCEA-2.1-0/BCEA/man/evi.plot.Rd | 15
BCEA-2.1-0/BCEA/man/evppi.Rd | 17
BCEA-2.1-0/BCEA/man/ib.plot.Rd | 22
BCEA-2.1-0/BCEA/man/mce.plot.Rd | 6
BCEA-2.1-0/BCEA/man/mixedAn.Rd | 11
BCEA-2.1-0/BCEA/man/multi.ce.Rd | 10
BCEA-2.1-0/BCEA/man/multi.evppi.Rd | 56
BCEA-2.1-0/BCEA/man/plot.CEriskav.Rd | 3
BCEA-2.1-0/BCEA/man/plot.bcea.Rd | 22
BCEA-2.1-0/BCEA/man/plot.evppi.Rd | 4
BCEA-2.1-0/BCEA/man/plot.mixedAn.Rd | 4
BCEA-2.1-0/BCEA/man/sim.table.Rd | 6
BCEA-2.1-0/BCEA/man/struct.psa.Rd | 87 -
BCEA-2.1-0/BCEA/man/summary.bcea.Rd | 10
BCEA-2.1-0/BCEA/man/summary.mixedAn.Rd | 10
56 files changed, 1808 insertions(+), 1312 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Diff between logmult versions 0.6 dated 2014-03-15 and 0.6.1 dated 2015-01-13
Description: Functions to fit log-multiplicative models using gnm, with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
DESCRIPTION | 12 +--
MD5 | 38 +++++-----
NEWS | 12 +++
R/jackboot.R | 7 -
R/jackknife.R | 2
R/maor.R | 83 ++++++++++++++++++-----
R/plot.assoc.R | 182 +++++++++++++++++++++++++++++++++++++++++----------
R/prepareTable.R | 2
R/survey.R | 2
R/unidiff.R | 7 +
man/HMSkew-nonlin.Rd | 2
man/hmskew.Rd | 2
man/hmskewL.Rd | 4 -
man/maor.Rd | 46 ++++++++----
man/plot.assoc.Rd | 34 +++++----
man/plot.unidiff.Rd | 5 -
man/rc.Rd | 4 -
man/rcL.Rd | 8 +-
man/rcL.trans.Rd | 4 -
tests/maor.R | 58 +++++++++++-----
20 files changed, 367 insertions(+), 147 deletions(-)
Title: Calculation of the Integrated Flow of Particles between Polygons
Diff between RCALI versions 0.2-6 dated 2013-01-22 and 0.2-15 dated 2015-01-13
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.
Author: Annie Bouvier, Kien Kieu, Kasia Adamczyk, and Herve Monod
Maintainer: Annie Bouvier
RCALI-0.2-15/RCALI/DESCRIPTION | 20 +++++-------
RCALI-0.2-15/RCALI/LICENSE |only
RCALI-0.2-15/RCALI/MD5 | 42 ++++++++++----------------
RCALI-0.2-15/RCALI/NAMESPACE | 14 ++++----
RCALI-0.2-15/RCALI/NEWS | 42 ++++++++++++++++++++++++++
RCALI-0.2-15/RCALI/R/califlopp.R | 6 +--
RCALI-0.2-15/RCALI/R/listpoly-methods.R | 1
RCALI-0.2-15/RCALI/R/poly-methods.R | 12 +++----
RCALI-0.2-15/RCALI/inst/CITATION | 7 +---
RCALI-0.2-15/RCALI/inst/doc/RCALIvignette.pdf |binary
RCALI-0.2-15/RCALI/src/caliconfig.h | 2 -
RCALI-0.2-15/RCALI/src/fluxsd.cc | 11 +++---
RCALI-0.2-15/RCALI/src/methodAdapt.cc | 1
RCALI-0.2-15/RCALI/src/read1Poly.cc | 3 +
RCALI-0.2-15/RCALI/src/readPoly.cc | 10 ++++--
RCALI-0.2-15/RCALI/tests/paysage.R | 2 -
RCALI-0.2-15/RCALI/tests/paysage.cubres | 9 +++--
RCALI-0.2-15/RCALI/tests/paysage.grid1.1res | 2 -
RCALI-0.2-6/RCALI/COPYING |only
RCALI-0.2-6/RCALI/Makevars |only
RCALI-0.2-6/RCALI/RCALI-Ex.R |only
RCALI-0.2-6/RCALI/tests/data |only
RCALI-0.2-6/RCALI/tests/data.R |only
RCALI-0.2-6/RCALI/tests/data.Rout.save |only
RCALI-0.2-6/RCALI/tests/data.txt |only
RCALI-0.2-6/RCALI/tests/data2 |only
RCALI-0.2-6/RCALI/tests/gridresult |only
27 files changed, 115 insertions(+), 69 deletions(-)
Title: Principal Coordinates of Phylogenetic Structure
Diff between PCPS versions 1.0.1 dated 2014-05-13 and 1.0.2 dated 2015-01-13
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/pcps.curve.R | 2 +-
R/pcps.sig.R | 53 ++++++++++++++++++++++++++++++-----------------------
R/plot.pcps.R | 16 +++++++++++++---
man/pcps.Rd | 6 +++---
man/pcps.sig.Rd | 9 ++++++---
7 files changed, 64 insertions(+), 44 deletions(-)
Title: Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R
Diff between MBmca versions 0.0.3-4 dated 2014-08-26 and 0.0.3-5 dated 2015-01-13
Description: The MBmca package provides data sets and lightweight utilities for
nucleic acid melting curve analysis and presentation on microbead surfaces
but also for reactions in solution (e.g., qPCR).
Author: Stefan Roediger [aut, cre],
Michal Burdukiewicz [ctb]
Maintainer: Stefan Roediger
CHANGELOG | 10
DESCRIPTION | 22 +-
MD5 | 46 ++--
NAMESPACE | 21 -
R/MBmca-package.R |only
R/MFIerror.R | 72 ++++++
R/datasets.R |only
R/diffQ.R | 529 +++++++++++++++++++++++++++++++++++++------------
R/diffQ2.R | 425 +++++++++++++++++++++++++++++++++------
R/mcaPeaks.R | 91 ++++++++
R/mcaSmoother.R | 238 +++++++++++++++++++++-
R/print.diffQ2object.R |only
R/print.diffQobject.R |only
README.md |only
data/DMP.rda |binary
data/DualHyb.rda |binary
data/MultiMelt.rda |binary
inst |only
man/DMP.Rd | 107 ++++-----
man/DualHyb.Rd | 109 ++++------
man/MBmca-package.Rd | 74 ++----
man/MFIerror.Rd | 123 +++++------
man/MultiMelt.Rd | 154 ++++++--------
man/diffQ.Rd | 375 ++++++++++++++++------------------
man/diffQ2.Rd | 413 +++++++++++++++++++-------------------
man/mcaPeaks.Rd | 88 +++-----
man/mcaSmoother.Rd | 266 ++++++++++++------------
27 files changed, 2047 insertions(+), 1116 deletions(-)
Title: A graphical user interface for calculating power and sample size
for hierarchical data
Diff between HierO versions 0.1 dated 2014-10-10 and 0.2 dated 2015-01-13
Description: HierO is a graphical user interface (GUI) tool for calculating optimal statistical power and sample size for hierarchical data structure. HierO constructs a user defined sample size optimization problem to GAMS (General Algebraic Modeling System)form and uses Rneos package to send the problem to NEOS server for solving.
Author: Kari Tokola
Maintainer: Kari Tokola
DESCRIPTION | 11 ++++++-----
MD5 | 4 ++--
NAMESPACE | 1 -
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Spatial point patterns analysis
Diff between ads versions 1.5-2.1 dated 2014-04-22 and 1.5-2.2 dated 2015-01-13
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function, for univariate,
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
statistical significance based on Monte Carlo simulations.
Author: R. Pelissier and F. Goreaud
Maintainer: Raphael Pelissier
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
inst |only
src/adssub.c | 4 ++--
src/adssub.h | 2 +-
src/triangulate.c | 24 +++++++++++++++++++++++-
6 files changed, 35 insertions(+), 12 deletions(-)
Title: Package for ttf2pt1 program
Description: This package contains the program ttf2pt1, for use with the
extrafont package. This product includes software developed by the TTF2PT1
Project and its contributors.
Author: Winston Chang,
Andrew Weeks,
Frank M. Siegert,
Mark Heath,
Thomas Henlick,
Sergey Babkin,
Turgut Uyar,
Rihardas Hepas,
Szalay Tamas,
Johan Vromans,
Petr Titera,
Lei Wang,
Chen Xiangyang,
Zvezdan Petkovic,
Rigel,
I. Lee Hetherington
Maintainer: ORPHANED
Diff between Rttf2pt1 versions 1.3.2 dated 2014-08-15 and 1.3.3 dated 2015-01-13
DESCRIPTION | 8 +++++--- MD5 | 6 +++--- src/ttf2pt1/bitmap.c | 10 +++++----- src/ttf2pt1/pt1.c | 4 ++-- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Reading Machine Learning Benchmark Data Sets in Different
Formats
Diff between readMLData versions 0.9-6 dated 2012-02-08 and 0.9-7 dated 2015-01-13
Description: Functions for reading data sets in different formats
for testing machine learning tools are provided. This allows to run
a loop over several data sets in their original form, for example
if they are downloaded from UCI Machine Learning Repository.
The data are not part of the package and have to be downloaded
separately.
Author: Petr Savicky
Maintainer: Petr Savicky
ChangeLog | 2 ++
DESCRIPTION | 30 +++++++++++++++---------------
MD5 | 8 ++++----
NAMESPACE | 2 ++
man/dsRead.Rd | 3 ++-
5 files changed, 25 insertions(+), 20 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.0.1 dated 2014-10-22 and 1.1 dated 2015-01-13
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 12 -
MD5 | 15 +-
NAMESPACE | 7 +
R/BAT.R | 354 +++++++++++++++++++++++++++++++++++++++++++++--------
man/alpha.accum.Rd | 11 +
man/beta.accum.Rd | 4
man/sim.plot.Rd |only
man/sim.sad.Rd |only
man/sim.sample.Rd |only
man/sim.spatial.Rd |only
man/sim.tree.Rd |only
11 files changed, 333 insertions(+), 70 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-04 1.0.4
2012-04-26 1.0
Title: Trajectory Analysis
Diff between traj versions 1.1 dated 2014-12-01 and 1.2 dated 2015-01-13
Description: Implements the three-step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
inst/CITATION | 5 ++---
inst/doc/Measurement_Equations.pdf |binary
man/traj-package.Rd | 2 +-
5 files changed, 10 insertions(+), 11 deletions(-)
Title: Quantification of the effect of geographic versus environmental
isolation on genetic differentiation
Diff between Sunder versions 0.0.3 dated 2014-08-26 and 0.0.4 dated 2015-01-13
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Casper Eriksen, Gilles Guillot
Maintainer: Filippo Botta
ChangeLog | 24 ++++++++----------------
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/MCMCCV.R | 6 +++---
inst/CITATION | 10 +++++++---
man/Sunder-package.Rd | 4 ++--
6 files changed, 29 insertions(+), 33 deletions(-)
Title: Functions for University of Auckland course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-10 dated 2013-01-14 and 3.1-11 dated 2015-01-13
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
s20x-3.1-10/s20x/data/airpass.df.txt.gz |only
s20x-3.1-10/s20x/data/apples.df.txt.gz |only
s20x-3.1-10/s20x/data/arousal.df.txt.gz |only
s20x-3.1-10/s20x/data/beer.df.txt.gz |only
s20x-3.1-10/s20x/data/body.df.txt.gz |only
s20x-3.1-10/s20x/data/books.df.txt.gz |only
s20x-3.1-10/s20x/data/bursary.df.txt.gz |only
s20x-3.1-10/s20x/data/butterfat.df.txt.gz |only
s20x-3.1-10/s20x/data/camplake.df.txt.gz |only
s20x-3.1-10/s20x/data/chalk.df.txt.gz |only
s20x-3.1-10/s20x/data/computer.df.txt.gz |only
s20x-3.1-10/s20x/data/course.df.txt.gz |only
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s20x-3.1-10/s20x/data/fruitfly.df.txt.gz |only
s20x-3.1-10/s20x/data/house.df.txt.gz |only
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s20x-3.1-10/s20x/data/mergers.df.txt.gz |only
s20x-3.1-10/s20x/data/mozart.df.txt.gz |only
s20x-3.1-10/s20x/data/nail.df.txt.gz |only
s20x-3.1-10/s20x/data/oysters.df.txt.gz |only
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s20x-3.1-10/s20x/data/rain.df.txt.gz |only
s20x-3.1-10/s20x/data/seeds.df.txt.gz |only
s20x-3.1-10/s20x/data/sheep.df.txt.gz |only
s20x-3.1-10/s20x/data/skulls.df.txt.gz |only
s20x-3.1-10/s20x/data/soyabean.df.txt.gz |only
s20x-3.1-10/s20x/data/teach.df.txt.gz |only
s20x-3.1-10/s20x/data/technitron.df.txt.gz |only
s20x-3.1-10/s20x/data/thyroid.df.txt.gz |only
s20x-3.1-10/s20x/data/toothpaste.df.txt.gz |only
s20x-3.1-10/s20x/data/zoo.df.txt.gz |only
s20x-3.1-10/s20x/tests |only
s20x-3.1-11/s20x/DESCRIPTION | 21 -
s20x-3.1-11/s20x/LICENSE |only
s20x-3.1-11/s20x/MD5 | 231 ++++++------
s20x-3.1-11/s20x/NAMESPACE | 94 ++--
s20x-3.1-11/s20x/R/boxqq.r | 106 ++---
s20x-3.1-11/s20x/R/ciReg.R | 46 +-
s20x-3.1-11/s20x/R/cooks20x.R | 22 -
s20x-3.1-11/s20x/R/crossFactors.R | 56 +-
s20x-3.1-11/s20x/R/crosstabs.R | 98 ++---
s20x-3.1-11/s20x/R/eovcheck.R | 290 +++++++--------
s20x-3.1-11/s20x/R/estimateContrasts.R | 18
s20x-3.1-11/s20x/R/estimateContrasts1.R | 90 ++--
s20x-3.1-11/s20x/R/estimateContrasts2.R | 104 ++---
s20x-3.1-11/s20x/R/interactionPlots.R | 306 +++++++--------
s20x-3.1-11/s20x/R/multipleComp.R | 58 +--
s20x-3.1-11/s20x/R/normcheck.R | 114 +++--
s20x-3.1-11/s20x/R/onewayPlot.R | 466 ++++++++++++------------
s20x-3.1-11/s20x/R/pairs20x.R | 54 +-
s20x-3.1-11/s20x/R/predict20x.R | 98 ++---
s20x-3.1-11/s20x/R/propslsd.new.R | 49 +-
s20x-3.1-11/s20x/R/residPlot.R | 84 ++--
s20x-3.1-11/s20x/R/rowdistr.r | 410 +++++++++++----------
s20x-3.1-11/s20x/R/rr.r | 12
s20x-3.1-11/s20x/R/stripqq.r | 106 ++---
s20x-3.1-11/s20x/R/summary1way.R | 150 +++----
s20x-3.1-11/s20x/R/summary2way.R | 558 ++++++++++++++---------------
s20x-3.1-11/s20x/R/summaryStats.R | 82 ++--
s20x-3.1-11/s20x/R/trendscatter.R | 100 +++--
s20x-3.1-11/s20x/README.md |only
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s20x-3.1-11/s20x/data/seeds.df.txt |only
s20x-3.1-11/s20x/data/sheep.df.txt |only
s20x-3.1-11/s20x/data/skulls.df.txt |only
s20x-3.1-11/s20x/data/soyabean.df.txt |only
s20x-3.1-11/s20x/data/teach.df.txt |only
s20x-3.1-11/s20x/data/technitron.df.txt |only
s20x-3.1-11/s20x/data/thyroid.df.txt |only
s20x-3.1-11/s20x/data/toothpaste.df.txt |only
s20x-3.1-11/s20x/data/zoo.df.txt |only
s20x-3.1-11/s20x/demo/00Index | 88 ++--
s20x-3.1-11/s20x/demo/cs1.r | 16
s20x-3.1-11/s20x/demo/cs10.r | 14
s20x-3.1-11/s20x/demo/cs11.r | 16
s20x-3.1-11/s20x/demo/cs12.r | 26 -
s20x-3.1-11/s20x/demo/cs13.r | 40 +-
s20x-3.1-11/s20x/demo/cs14.r | 24 -
s20x-3.1-11/s20x/demo/cs15.r | 30 -
s20x-3.1-11/s20x/demo/cs16.r | 44 +-
s20x-3.1-11/s20x/demo/cs17.r | 32 -
s20x-3.1-11/s20x/demo/cs18.r | 24 -
s20x-3.1-11/s20x/demo/cs19.r | 30 -
s20x-3.1-11/s20x/demo/cs2.r | 14
s20x-3.1-11/s20x/demo/cs20.r | 36 -
s20x-3.1-11/s20x/demo/cs21.r | 42 +-
s20x-3.1-11/s20x/demo/cs22.r | 22 -
s20x-3.1-11/s20x/demo/cs23.r | 66 +--
s20x-3.1-11/s20x/demo/cs24.r | 36 -
s20x-3.1-11/s20x/demo/cs25.r | 90 ++--
s20x-3.1-11/s20x/demo/cs26.r | 38 -
s20x-3.1-11/s20x/demo/cs27.r | 36 -
s20x-3.1-11/s20x/demo/cs28.r | 18
s20x-3.1-11/s20x/demo/cs29.r | 22 -
s20x-3.1-11/s20x/demo/cs3.r | 10
s20x-3.1-11/s20x/demo/cs30.r | 20 -
s20x-3.1-11/s20x/demo/cs31.r | 18
s20x-3.1-11/s20x/demo/cs32.r | 22 -
s20x-3.1-11/s20x/demo/cs33.r | 20 -
s20x-3.1-11/s20x/demo/cs34.r | 28 -
s20x-3.1-11/s20x/demo/cs35.r | 16
s20x-3.1-11/s20x/demo/cs36.r | 26 -
s20x-3.1-11/s20x/demo/cs37.r | 24 -
s20x-3.1-11/s20x/demo/cs38.r | 30 -
s20x-3.1-11/s20x/demo/cs39.r | 30 -
s20x-3.1-11/s20x/demo/cs4.r | 10
s20x-3.1-11/s20x/demo/cs40.r | 20 -
s20x-3.1-11/s20x/demo/cs41.r | 24 -
s20x-3.1-11/s20x/demo/cs42.r | 22 -
s20x-3.1-11/s20x/demo/cs43.r | 20 -
s20x-3.1-11/s20x/demo/cs5.r | 12
s20x-3.1-11/s20x/demo/cs6.r | 18
s20x-3.1-11/s20x/demo/cs7.r | 24 -
s20x-3.1-11/s20x/demo/cs8.r | 34 -
s20x-3.1-11/s20x/demo/cs9.r | 14
s20x-3.1-11/s20x/inst |only
s20x-3.1-11/s20x/man/eovcheck.Rd | 155 ++++----
s20x-3.1-11/s20x/man/interactionPlots.Rd | 145 ++++---
s20x-3.1-11/s20x/man/normcheck.Rd | 105 ++---
s20x-3.1-11/s20x/man/rowdistr.Rd | 79 ++--
s20x-3.1-11/s20x/man/trendscatter.Rd | 110 ++---
154 files changed, 2885 insertions(+), 2778 deletions(-)
Title: R Transcription Factor Binding Site identification tool
Diff between rtfbs versions 0.3.2 dated 2013-12-06 and 0.3.3 dated 2015-01-13
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
rtfbs-0.3.2/rtfbs/configure.win |only
rtfbs-0.3.2/rtfbs/src/pcre |only
rtfbs-0.3.2/rtfbs/tests/input.fas |only
rtfbs-0.3.2/rtfbs/tests/pwm.meme |only
rtfbs-0.3.3/rtfbs/ChangeLog | 1
rtfbs-0.3.3/rtfbs/DESCRIPTION | 15
rtfbs-0.3.3/rtfbs/LICENSE | 2
rtfbs-0.3.3/rtfbs/MD5 | 143 -
rtfbs-0.3.3/rtfbs/NAMESPACE | 16
rtfbs-0.3.3/rtfbs/build/vignette.rds |binary
rtfbs-0.3.3/rtfbs/configure | 2749 ++-----------------------------
rtfbs-0.3.3/rtfbs/configure.ac | 508 -----
rtfbs-0.3.3/rtfbs/inst/doc/vignette.pdf |binary
rtfbs-0.3.3/rtfbs/man/as.pointer.ms.Rd | 30
rtfbs-0.3.3/rtfbs/man/build.mm.Rd | 35
rtfbs-0.3.3/rtfbs/man/calc.fdr.Rd | 54
rtfbs-0.3.3/rtfbs/man/concat.ms.Rd | 10
rtfbs-0.3.3/rtfbs/man/from.pointer.ms.Rd | 35
rtfbs-0.3.3/rtfbs/man/gcContent.ms.Rd | 13
rtfbs-0.3.3/rtfbs/man/groupByGC.ms.Rd | 18
rtfbs-0.3.3/rtfbs/man/is.pointer.ms.Rd | 19
rtfbs-0.3.3/rtfbs/man/label.matrix.Rd | 28
rtfbs-0.3.3/rtfbs/man/length.ms.Rd | 11
rtfbs-0.3.3/rtfbs/man/lengths.ms.Rd | 13
rtfbs-0.3.3/rtfbs/man/makeFdrPlot.Rd | 39
rtfbs-0.3.3/rtfbs/man/ms.Rd | 89 -
rtfbs-0.3.3/rtfbs/man/names.ms.Rd | 15
rtfbs-0.3.3/rtfbs/man/offsets.ms.Rd | 14
rtfbs-0.3.3/rtfbs/man/open-brace.ms.Rd | 31
rtfbs-0.3.3/rtfbs/man/output.sites.Rd | 40
rtfbs-0.3.3/rtfbs/man/print.ms.Rd | 18
rtfbs-0.3.3/rtfbs/man/read.mm.Rd | 13
rtfbs-0.3.3/rtfbs/man/read.ms.Rd | 26
rtfbs-0.3.3/rtfbs/man/read.pwm.Rd | 29
rtfbs-0.3.3/rtfbs/man/rtfbs-package.Rd | 18
rtfbs-0.3.3/rtfbs/man/score.ms.Rd | 81
rtfbs-0.3.3/rtfbs/man/sequences.ms.Rd | 11
rtfbs-0.3.3/rtfbs/man/simulate.ms.Rd | 36
rtfbs-0.3.3/rtfbs/man/split.ms.Rd | 34
rtfbs-0.3.3/rtfbs/man/summary.ms.Rd | 25
rtfbs-0.3.3/rtfbs/man/write.mm.Rd | 15
rtfbs-0.3.3/rtfbs/man/write.ms.Rd | 14
rtfbs-0.3.3/rtfbs/src/Makevars.in | 125 -
rtfbs-0.3.3/rtfbs/src/Makevars.win | 125 -
rtfbs-0.3.3/rtfbs/src/complex_matrix.c | 34
rtfbs-0.3.3/rtfbs/src/fit_column.c | 454 ++---
rtfbs-0.3.3/rtfbs/src/fit_column.h | 74
rtfbs-0.3.3/rtfbs/src/fit_feature.c | 2
rtfbs-0.3.3/rtfbs/src/lists.h | 9
rtfbs-0.3.3/rtfbs/src/maf.c | 274 +--
rtfbs-0.3.3/rtfbs/src/markov_matrix.c | 98 -
rtfbs-0.3.3/rtfbs/src/matrix.c | 38
rtfbs-0.3.3/rtfbs/src/misc.c | 4
rtfbs-0.3.3/rtfbs/src/misc.h | 159 -
rtfbs-0.3.3/rtfbs/src/phylo_fit.c | 60
rtfbs-0.3.3/rtfbs/src/phylo_p_print.c | 207 +-
rtfbs-0.3.3/rtfbs/src/prob_matrix.c | 6
rtfbs-0.3.3/rtfbs/src/subst_mods.c | 635 +++----
58 files changed, 1838 insertions(+), 4714 deletions(-)
Title: Functions for clustering of presence-absence, abundance and
multilocus genetic data
Diff between prabclus versions 2.2-4 dated 2012-08-25 and 2.2-5 dated 2015-01-13
Description: Distance-based parametric bootstrap tests for clustering
with spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus
genetical data for species delimitation, nearest neighbor based
noise detection. Try package?prabclus for on overview.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 7 ++++---
MD5 | 4 ++--
R/abundfunctions.R | 1 +
3 files changed, 7 insertions(+), 5 deletions(-)
Title: Robust Meta-analysis and Meta-regression
Diff between metaplus versions 0.7-0 dated 2015-01-11 and 0.7-1 dated 2015-01-13
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Author: Ken Beath
Maintainer: Ken Beath
DESCRIPTION | 8
MD5 | 14
NAMESPACE | 2
R/makestart.profilemix.metaplus.R | 360 ++++++++++++------------
R/profilemix.metaplus.R | 298 ++++++++++----------
R/profilemix.profile.R | 556 +++++++++++++++++++-------------------
R/profilet.metaplus.R | 2
inst/NEWS | 44 +--
8 files changed, 671 insertions(+), 613 deletions(-)
Title: Various Options and Add-ins for Lattice
Diff between loa versions 0.2.15 dated 2014-01-15 and 0.2.21 dated 2015-01-13
Description: This package, Lattice Options and Add-ins (or loa), contains various plots and
functions that make use of the lattice/trellis plotting framework. The plots (which include
loaPlot, GoogleMap and trianglePlot) use panelPal, a function that extends lattice and hexbin
package methods to automate plot subscripting and panel-to-panel and panel-to key
synchronization. See ?loa for further details.
Author: Karl Ropkins
Maintainer: Karl Ropkins
DESCRIPTION | 20
MD5 | 32 -
NAMESPACE | 29 -
NEWS | 52 ++
R/formulaHandler.R | 467 +++++++++++-------
R/key.handlers.R | 22
R/lims.and.scales.handlers.R | 18
R/loaPlot.R | 24
R/panelPal.R | 26 -
R/trianglePlot.R | 941 ++++++++++++++++---------------------
data/lat.lon.meuse.RData |binary
data/roadmap.meuse.RData |binary
man/1.1.loaPlot.Rd | 3
man/1.2.googleMap.Rd | 2
man/1.3.trianglePlot.Rd | 359 ++++++--------
man/4.2.plot.structure.handlers.Rd | 18
man/loa-package.Rd | 4
17 files changed, 1077 insertions(+), 940 deletions(-)
Title: Linear regression based on linear structure between covariates
Diff between CorReg versions 0.15.8 dated 2014-11-04 and 1.0 dated 2015-01-13
Description: Linear regression based on a recursive structural equation model
(explicit correlations) found by a MCMC algorithm. It permits to face
highly correlated covariates. Variable selection is included (by lasso,
elasticnet, etc.). It also provides some graphical tools for basic
statistics.
Author: Clement THERY [aut, cre],
Christophe BIERNACKI [ctb],
Gaetan LORIDANT [ctb],
Florian WATRIN [ctb],
Quentin GRIMONPREZ [ctb],
Vincent KUBICKI [ctb],
Samuel BLANCK [ctb],
Jeremie KELLNER [ctb]
Maintainer: Clement THERY
DESCRIPTION | 25 +--
MD5 | 90 ++++++-------
NAMESPACE | 4
R/A_clere.R | 2
R/CorReg-package.R | 9 -
R/WhoIs.R | 2
R/correg.R | 311 +++++-----------------------------------------
R/density_estimation.R | 5
R/fillmiss.R | 26 +--
R/meilleur_lars.R | 6
man/BicZ.Rd | 3
man/BicZcurve.Rd | 3
man/CVMSE.Rd | 3
man/CorReg-package.Rd | 11 -
man/Estep.Rd | 3
man/MSEZ.Rd | 3
man/MSE_loc.Rd | 3
man/OLS.Rd | 3
man/ProbaZ.Rd | 3
man/R2Z.Rd | 3
man/Terminator.Rd | 3
man/WhoIs.Rd | 5
man/Winitial.Rd | 3
man/Y_generator.Rd | 3
man/cleanYtest.Rd | 3
man/cleanZ.Rd | 3
man/cleanZR2.Rd | 3
man/cleancolZ.Rd | 3
man/compare_beta.Rd | 3
man/compare_sign.Rd | 3
man/compare_struct.Rd | 3
man/compare_zero.Rd | 3
man/confint_coef.Rd | 3
man/correg.Rd | 28 +---
man/density_estimation.Rd | 3
man/fillmiss.Rd | 8 -
man/hatB.Rd | 3
man/matplot_zone.Rd | 3
man/mixture_generator.Rd | 3
man/readY.Rd | 3
man/readZ.Rd | 3
man/recursive_tree.Rd | 3
man/rforge.Rd | 3
man/searchZ_sparse.Rd | 3
man/showdata.Rd | 3
man/structureFinder.Rd | 3
46 files changed, 213 insertions(+), 415 deletions(-)
Title: Seawater Carbonate Chemistry
Diff between seacarb versions 3.0.4 dated 2015-01-05 and 3.0.5 dated 2015-01-12
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 7 +++++++
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/buffer.R | 53 ++++++++++++++++++++++++++++++++---------------------
R/carb.R | 2 +-
5 files changed, 49 insertions(+), 31 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Diff between randomForestSRC versions 1.5.5 dated 2014-08-26 and 1.6.0 dated 2015-01-12
More information about randomForestSRC at CRAN
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran
Maintainer: Udaya B. Kogalur
DESCRIPTION | 10
MD5 | 188 +++++++-------
R/data.utilities.R | 79 ++++--
R/factor.utilities.R | 2
R/find.interaction.R | 2
R/generic.impute.rfsrc.R | 15 -
R/generic.predict.rfsrc.R | 38 ++
R/impute.rfsrc.R | 63 +++-
R/max.subtree.R | 2
R/plot.competing.risk.R | 2
R/plot.rfsrc.R | 2
R/plot.survival.R | 2
R/plot.variable.R | 2
R/predict.rfsrc.R | 2
R/print.rfsrc.R | 10
R/rf2rfz.R | 2
R/rfsrc.R | 57 +++-
R/rfsrc.news.R | 2
R/rfsrcSyn.R | 2
R/stat.split.R | 2
R/utilities.R | 19 +
R/var.select.R | 6
R/vimp.R | 2
R/zzz.R | 2
configure.ac | 2
inst/NEWS | 19 +
inst/doc/rsf-Rnews.pdf |binary
man/find.interaction.Rd | 5
man/impute.Rd | 21 -
man/predict.rfsrc.Rd | 9
man/randomForestSRC_package.Rd | 5
man/rfsrc.Rd | 29 +-
man/var.select.Rd | 5
man/vimp.Rd | 5
src/bootstrap.c | 2
src/bootstrap.h | 2
src/classification.c | 64 +++-
src/classification.h | 13
src/dataParser.c | 2
src/dataParser.h | 2
src/entry.c | 29 +-
src/entry.h | 11
src/extern.h | 44 ++-
src/factor.h | 2
src/factorOps.c | 2
src/factorOps.h | 2
src/global.h | 19 +
src/importance.c | 133 +++++-----
src/importance.h | 32 +-
src/impute.c | 305 ++++++++++++-----------
src/impute.h | 2
src/node.h | 25 -
src/nodeOps.c | 463 -----------------------------------
src/nodeOps.h | 35 --
src/nrutil.c | 35 ++
src/nrutil.h | 37 +-
src/random.c | 2
src/random.h | 2
src/regression.c | 58 +++-
src/regression.h | 3
src/rfsrc.c | 293 +++++++++++-----------
src/rfsrc.h | 2
src/rfsrcUtil.c | 108 +++++++-
src/rfsrcUtil.h | 12
src/split.c | 18 +
src/split.h | 2
src/splitClas.c | 7
src/splitClas.h | 2
src/splitCustom.c |only
src/splitCustom.h |only
src/splitRegr.c | 7
src/splitRegr.h | 2
src/splitSurv.c | 12
src/splitSurv.h | 2
src/splitUspv.c | 535 +++++++++++++++++++++++++++++++++++------
src/splitUspv.h | 15 +
src/splitUtil.c | 17 -
src/splitUtil.h | 2
src/stack.c | 54 +++-
src/stack.h | 41 +--
src/stackOutput.c | 479 +++++++++++++++++++++++++++++++++++-
src/stackOutput.h | 29 ++
src/stackPreDefined.c | 30 +-
src/stackPreDefined.h | 2
src/survival.c | 473 +++++++++++++++++++-----------------
src/survival.h | 11
src/survivalE.c | 12
src/survivalE.h | 2
src/termOps.c |only
src/termOps.h |only
src/terminal.h | 28 +-
src/trace.c | 8
src/trace.h | 2
src/tree.c | 185 ++++++++------
src/tree.h | 18 -
src/treeUtil.c | 24 +
src/treeUtil.h | 11
97 files changed, 2686 insertions(+), 1698 deletions(-)
Permanent link
Title: Wraps libnabo, a fast K Nearest Neighbour library for low
dimensions
Diff between nabor versions 0.4.3 dated 2014-09-03 and 0.4.4 dated 2015-01-12
Description: An R wrapper for libnabo, an exact or approximate k nearest
neighbour library which is optimised for low dimensional spaces (e.g. 3D).
libnabo has speed and space advantages over the ANN library wrapped by
package RANN. nabor includes a knn function that is designed as a drop-in
replacement for RANN::nn2. In addition, objects which include the k-d tree
search structure can be returned to speed up repeated queries of the same
set of target points.
Author: Stephane Mangenat (for libnabo), Gregory Jefferis
Maintainer: Gregory Jefferis
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NAMESPACE | 2 +-
NEWS | 4 ++++
R/WKNNClasses.R | 14 ++++++++------
man/WKNN-class.Rd | 14 ++++++++------
man/kcpoints.Rd | 2 +-
man/knn.Rd | 2 +-
man/nabor-package.Rd | 2 +-
src/Makevars | 2 +-
10 files changed, 38 insertions(+), 30 deletions(-)
Title: Functions for Plotting HPO Terms
Diff between hpoPlot versions 1.0 dated 2014-05-10 and 2.0 dated 2015-01-12
Description: Collection of functions for manipulating sets of HPO terms and plotting them with a various options
Author: Daniel Greene
Maintainer: Daniel Greene
hpoPlot-1.0/hpoPlot/R/hpoPlotCode.R |only
hpoPlot-1.0/hpoPlot/data/hpo.rda |only
hpoPlot-1.0/hpoPlot/man/border.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/colouring.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/get.cohort.information.Rd |only
hpoPlot-1.0/hpoPlot/man/get.term.patient.matrix.Rd |only
hpoPlot-1.0/hpoPlot/man/hpo.graph.Rd |only
hpoPlot-1.0/hpoPlot/man/labelling.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/remove.duplicate.term.sets.Rd |only
hpoPlot-1.0/hpoPlot/man/size.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/suggest.aspect.ratio.width.to.height.Rd |only
hpoPlot-2.0/hpoPlot/DESCRIPTION | 17 +
hpoPlot-2.0/hpoPlot/MD5 | 91 +++++++---
hpoPlot-2.0/hpoPlot/NAMESPACE | 53 +++++
hpoPlot-2.0/hpoPlot/R/data.R |only
hpoPlot-2.0/hpoPlot/R/graphs.R |only
hpoPlot-2.0/hpoPlot/R/sets.R |only
hpoPlot-2.0/hpoPlot/R/utils.R |only
hpoPlot-2.0/hpoPlot/build |only
hpoPlot-2.0/hpoPlot/data/datalist |only
hpoPlot-2.0/hpoPlot/data/hpo.terms.RData |only
hpoPlot-2.0/hpoPlot/data/mpo.terms.RData |only
hpoPlot-2.0/hpoPlot/data/mpo.to.hpo.RData |only
hpoPlot-2.0/hpoPlot/inst |only
hpoPlot-2.0/hpoPlot/man/apply.term.filters.Rd |only
hpoPlot-2.0/hpoPlot/man/calibrate.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/clean.terms.Rd | 34 +--
hpoPlot-2.0/hpoPlot/man/exclude.branch.Rd |only
hpoPlot-2.0/hpoPlot/man/get.ancestors.Rd | 38 +---
hpoPlot-2.0/hpoPlot/man/get.case.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.case.based.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.case.term.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.code.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.descendants.Rd | 44 ++--
hpoPlot-2.0/hpoPlot/man/get.frequency.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.frequency.based.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.frequency.based.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.full.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.grey.borders.Rd |only
hpoPlot-2.0/hpoPlot/man/get.hpo.graph.Rd |only
hpoPlot-2.0/hpoPlot/man/get.hpo.terms.Rd | 35 ---
hpoPlot-2.0/hpoPlot/man/get.informative.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.mpo.to.hpo.Rd |only
hpoPlot-2.0/hpoPlot/man/get.no.borders.Rd |only
hpoPlot-2.0/hpoPlot/man/get.node.friendly.long.names.Rd | 42 +---
hpoPlot-2.0/hpoPlot/man/get.ontology.Rd |only
hpoPlot-2.0/hpoPlot/man/get.pop.frequency.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.shortened.names.Rd |only
hpoPlot-2.0/hpoPlot/man/get.significance.based.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.simple.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.standard.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.adjacency.matrix.Rd | 49 +----
hpoPlot-2.0/hpoPlot/man/get.term.descendancy.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.frequencies.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.info.content.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.pseudo.adjacency.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.white.nodes.Rd |only
hpoPlot-2.0/hpoPlot/man/hpo.plot.Rd |only
hpoPlot-2.0/hpoPlot/man/hpo.terms.Rd | 20 --
hpoPlot-2.0/hpoPlot/man/hpoPlot-package.Rd | 56 +-----
hpoPlot-2.0/hpoPlot/man/intersection.with.branches.Rd |only
hpoPlot-2.0/hpoPlot/man/mpo.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/mpo.to.hpo.Rd |only
hpoPlot-2.0/hpoPlot/man/n.most.frequent.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/p.values.for.occurrence.of.term.in.group.Rd |only
hpoPlot-2.0/hpoPlot/man/prune.branch.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.links.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.non.pa.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.terms.with.less.than.n.occurrences.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.uninformative.for.plot.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.uninformative.terms.Rd | 42 +---
hpoPlot-2.0/hpoPlot/man/setDimNames.Rd | 32 +--
hpoPlot-2.0/hpoPlot/man/simpleCap.Rd |only
hpoPlot-2.0/hpoPlot/man/swap.out.alt.ids.Rd | 36 +--
hpoPlot-2.0/hpoPlot/man/term.set.list.from.character.Rd | 41 +---
hpoPlot-2.0/hpoPlot/vignettes |only
76 files changed, 279 insertions(+), 351 deletions(-)
Title: Loading System Fonts into R
Diff between sysfonts versions 0.3 dated 2014-12-21 and 0.4 dated 2015-01-12
Description: This package uses FreeType to load system fonts
and Google Fonts (https://www.google.com/fonts) into R.
It is supposed to support other packages like R2SWF
and showtext.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 10 +++----
MD5 | 10 +++----
NEWS | 11 ++++++++
R/google.R | 56 +++++++++++++++++++++++---------------------
man/font.add.google.Rd | 11 +++++++-
man/font.families.google.Rd | 2 -
6 files changed, 61 insertions(+), 39 deletions(-)
Title: Stability Selection with Error Control
Diff between stabs versions 0.5-0 dated 2014-12-09 and 0.5-1 dated 2015-01-12
Description: Resampling procedures to assess the stability of selected variables
with additional finite sample error control for high-dimensional variable
selection procedures such as Lasso or boosting
Author: Benjamin Hofner [aut, cre],
Torsten Hothorn [aut]
Maintainer: Benjamin Hofner
ChangeLog | 37 ++++++++++++++++++++++++++++++++--
DESCRIPTION | 8 +++----
MD5 | 10 ++++-----
R/fitfuns.R | 8 +++----
inst/CITATION | 63 ++++++++++++++++++++++++++++------------------------------
inst/NEWS.Rd | 13 +++++++++++
6 files changed, 91 insertions(+), 48 deletions(-)
Title: Detection of structure from multilocus genetic data.
Diff between Geneland versions 4.0.4 dated 2014-03-24 and 4.0.5 dated 2015-01-12
Description: Stochastic simulation and MCMC inference of structure from genetic data.
Author: Gilles Guillot, Filipe Santos, Arnaud Estoup
Maintainer: Gilles Guillot
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/CITATION | 9 ++++++---
3 files changed, 12 insertions(+), 9 deletions(-)
Title: Boosting Methods for GAMLSS
Diff between gamboostLSS versions 1.1-2 dated 2014-06-26 and 1.1-3 dated 2015-01-12
Description: Boosting models for fitting generalized additive models for
location, shape and scale (GAMLSS) to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner
gamboostLSS-1.1-2/gamboostLSS/NEWS |only
gamboostLSS-1.1-2/gamboostLSS/inst/CHANGES |only
gamboostLSS-1.1-3/gamboostLSS/ChangeLog | 930 ++++++++++++---------
gamboostLSS-1.1-3/gamboostLSS/DESCRIPTION | 10
gamboostLSS-1.1-3/gamboostLSS/MD5 | 29
gamboostLSS-1.1-3/gamboostLSS/NAMESPACE | 1
gamboostLSS-1.1-3/gamboostLSS/R/as.families.R | 50 -
gamboostLSS-1.1-3/gamboostLSS/R/families.R | 12
gamboostLSS-1.1-3/gamboostLSS/R/helpers.R | 21
gamboostLSS-1.1-3/gamboostLSS/R/methods.R | 21
gamboostLSS-1.1-3/gamboostLSS/data/india.RData |binary
gamboostLSS-1.1-3/gamboostLSS/data/india.bnd.RData |binary
gamboostLSS-1.1-3/gamboostLSS/inst/CITATION | 7
gamboostLSS-1.1-3/gamboostLSS/inst/NEWS.Rd |only
gamboostLSS-1.1-3/gamboostLSS/man/as.families.Rd | 6
gamboostLSS-1.1-3/gamboostLSS/man/india.Rd | 7
gamboostLSS-1.1-3/gamboostLSS/man/methods.Rd | 10
17 files changed, 632 insertions(+), 472 deletions(-)
Title: Ecological models and data (book support)
Diff between emdbook versions 1.3.6 dated 2014-11-25 and 1.3.7 dated 2015-01-12
Description: Auxiliary functions and data sets for _Ecological Models and Data_, a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0)
Author: Ben Bolker
Maintainer: Ben Bolker
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 23 +++++++++++++++--------
inst/NEWS.Rd | 5 +++++
4 files changed, 27 insertions(+), 15 deletions(-)
Title: Multivariate Adaptive Regression Splines
Diff between earth versions 4.1.0 dated 2014-12-17 and 4.2.0 dated 2015-01-12
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow
earth-4.1.0/earth/man/print.evimp.Rd |only
earth-4.2.0/earth/DESCRIPTION | 8
earth-4.2.0/earth/MD5 | 122
earth-4.2.0/earth/NAMESPACE | 3
earth-4.2.0/earth/NEWS | 48
earth-4.2.0/earth/R/earth.R | 478
earth-4.2.0/earth/R/earth.cv.R | 23
earth-4.2.0/earth/R/earth.cv.lib.R | 2
earth-4.2.0/earth/R/earth.glm.R | 3
earth-4.2.0/earth/R/earth.methods.R |only
earth-4.2.0/earth/R/earth.regress.R | 14
earth-4.2.0/earth/R/earthlib.R | 172
earth-4.2.0/earth/R/evimp.R | 2
earth-4.2.0/earth/R/format.earth.R | 6
earth-4.2.0/earth/R/mars.to.earth.R | 14
earth-4.2.0/earth/R/model.matrix.earth.R | 4
earth-4.2.0/earth/R/plot.earth.R | 100
earth-4.2.0/earth/R/plot.model.selection.R | 33
earth-4.2.0/earth/R/plotd.R | 2
earth-4.2.0/earth/R/plotmor.R | 786 -
earth-4.2.0/earth/R/predict.earth.R | 10
earth-4.2.0/earth/R/print.earth.R | 39
earth-4.2.0/earth/R/residuals.earth.R |only
earth-4.2.0/earth/R/varmod.R | 621 -
earth-4.2.0/earth/inst/doc/earth-notes.pdf |binary
earth-4.2.0/earth/inst/doc/earth-varmod.pdf |binary
earth-4.2.0/earth/inst/slowtests/earth.times.R | 4
earth-4.2.0/earth/inst/slowtests/make.bat | 17
earth-4.2.0/earth/inst/slowtests/test.big.R | 6
earth-4.2.0/earth/inst/slowtests/test.big.Rout.save | 45
earth-4.2.0/earth/inst/slowtests/test.big.bat | 12
earth-4.2.0/earth/inst/slowtests/test.cv.R | 4
earth-4.2.0/earth/inst/slowtests/test.cv.Rout.save | 1438 +-
earth-4.2.0/earth/inst/slowtests/test.earthc.c | 129
earth-4.2.0/earth/inst/slowtests/test.earthc.out.save | 4408 +++++---
earth-4.2.0/earth/inst/slowtests/test.earthmain.out.save | 35
earth-4.2.0/earth/inst/slowtests/test.full.R | 449
earth-4.2.0/earth/inst/slowtests/test.full.Rout.save | 7654 ++++++---------
earth-4.2.0/earth/inst/slowtests/test.glm.R | 102
earth-4.2.0/earth/inst/slowtests/test.glm.Rout.save | 5808 ++++++-----
earth-4.2.0/earth/inst/slowtests/test.mods.R |only
earth-4.2.0/earth/inst/slowtests/test.mods.Rout.save |only
earth-4.2.0/earth/inst/slowtests/test.mods.bat |only
earth-4.2.0/earth/inst/slowtests/test.plotd.Rout.save | 16
earth-4.2.0/earth/inst/slowtests/test.varmod.R | 141
earth-4.2.0/earth/inst/slowtests/test.varmod.Rout.save | 2714 ++---
earth-4.2.0/earth/inst/slowtests/test.weights.R | 45
earth-4.2.0/earth/inst/slowtests/test.weights.Rout.save | 133
earth-4.2.0/earth/man/earth.Rd | 280
earth-4.2.0/earth/man/mars.to.earth.Rd | 23
earth-4.2.0/earth/man/model.matrix.earth.Rd | 35
earth-4.2.0/earth/man/plot.earth.Rd | 160
earth-4.2.0/earth/man/plot.earth.models.Rd | 8
earth-4.2.0/earth/man/plot.evimp.Rd | 2
earth-4.2.0/earth/man/plot.varmod.Rd | 6
earth-4.2.0/earth/man/predict.earth.Rd | 6
earth-4.2.0/earth/man/predict.varmod.Rd | 15
earth-4.2.0/earth/man/residuals.earth.Rd | 15
earth-4.2.0/earth/man/update.earth.Rd | 8
earth-4.2.0/earth/man/varmod.Rd | 47
earth-4.2.0/earth/src/allowed.c | 2
earth-4.2.0/earth/src/allowed.h | 2
earth-4.2.0/earth/src/earth.c | 554 -
earth-4.2.0/earth/src/earth.h | 6
earth-4.2.0/earth/tests/test.earth.Rout.save | 16
65 files changed, 14169 insertions(+), 12666 deletions(-)
Title: Copy Numbers of Genes in prokaryotes
Diff between CNOGpro versions 1.0 dated 2014-07-09 and 1.1 dated 2015-01-12
Description: Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.
Author: Ola Brynildsrud, Lars-Gustav Snipen
Maintainer: Ola Brynildsrud
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/CNOGpro.R | 3 +++
R/getreadcounts.R | 1 +
R/readGenBank.R | 1 +
man/CNOGpro-package.Rd | 4 ++--
6 files changed, 16 insertions(+), 11 deletions(-)
Title: Analysis of Factorial Experiments
Diff between afex versions 0.12-135 dated 2014-11-03 and 0.13-145 dated 2015-01-12
Description: Provides convenience functions for analyzing factorial experiments
using ANOVA or mixed models. ez.glm(), aov.car(), and aov4() allow
convenient specification of between, within (i.e., repeated-measures),
or mixed between-within (i.e., split-plot) ANOVAs for data in long
format (i.e., one observation per row), potentially aggregating multiple
observations per individual and cell of the design. mixed() fits a mixed
model using lme4::lmer() and computes p-values for all effects using either
Kenward-Roger approximation for degrees of freedom (LMM only), parametric
bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex
uses type 3 sums of squares as default (imitating commercial statistical
software). compare.2.vectors() compares two vectors using a variety of tests
(t, Wilcoxon, and permutation).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb]
Maintainer: Henrik Singmann
DESCRIPTION | 48 ++++++++++++++++---------------
MD5 | 32 ++++++++++----------
NAMESPACE | 1
NEWS | 30 +++++++++++++++++++
R/afex-package.R | 8 ++---
R/aov.car.R | 32 +++++++++-----------
R/ems.R |only
R/nice.anova.R | 5 +--
data/md_12.1.rda |binary
data/md_15.1.rda |binary
data/md_16.1.rda |binary
data/md_16.4.rda |binary
data/obk.long.rda |binary
man/afex-package.Rd | 8 ++---
man/aov.car.Rd | 24 +++++++--------
man/ems.Rd |only
tests/testthat/test-aov.car-bugs.R | 18 +++++++++++
tests/testthat/test-aov.car-structural.R | 16 ++++++++++
18 files changed, 144 insertions(+), 78 deletions(-)
Title: Rcpp Integration for GNU GSL Vectors and Matrices
Diff between RcppGSL versions 0.2.2 dated 2014-05-31 and 0.2.3 dated 2015-01-12
Description: Rcpp integration for GNU GSL vectors and matrices
The GNU Scientific Library (GSL) is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The RcppGSL package provides an easy-to-use interface between GSL data
structures and R using concepts from Rcpp which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses Rcpp to connect to another third-party library. The autoconf
script, inline plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 18 +++++++++++++++-
DESCRIPTION | 44 ++++++++++++++++++++---------------------
MD5 | 26 ++++++++++++------------
README.md | 10 +++------
build/vignette.rds |binary
configure | 22 ++++++++------------
configure.ac | 26 ++----------------------
inst/NEWS.Rd | 11 ++++++++++
inst/doc/RcppGSL-intro.R | 8 +++----
inst/doc/RcppGSL-intro.Rnw | 25 ++++++++++-------------
inst/doc/RcppGSL-intro.pdf |binary
inst/doc/RcppGSL-unitTests.pdf |binary
src/Makevars.in | 3 --
vignettes/RcppGSL-intro.Rnw | 25 ++++++++++-------------
14 files changed, 106 insertions(+), 112 deletions(-)
Title: Community Ecology Package
Diff between vegan versions 2.2-0 dated 2014-11-17 and 2.2-1 dated 2015-01-12
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen
vegan-2.2-0/vegan/README.md |only
vegan-2.2-1/vegan/DESCRIPTION | 8
vegan-2.2-1/vegan/MD5 | 137 +++++-----
vegan-2.2-1/vegan/NAMESPACE | 7
vegan-2.2-1/vegan/R/adonis.R | 2
vegan-2.2-1/vegan/R/alias.cca.R | 2
vegan-2.2-1/vegan/R/anosim.R | 9
vegan-2.2-1/vegan/R/as.hclust.spantree.R | 4
vegan-2.2-1/vegan/R/as.mlm.R | 7
vegan-2.2-1/vegan/R/bioenv.default.R | 3
vegan-2.2-1/vegan/R/biplot.rda.R | 11
vegan-2.2-1/vegan/R/coef.cca.R | 10
vegan-2.2-1/vegan/R/coef.rda.R | 6
vegan-2.2-1/vegan/R/cophenetic.spantree.R | 6
vegan-2.2-1/vegan/R/estaccumR.R | 38 ++
vegan-2.2-1/vegan/R/estimateR.default.R | 31 +-
vegan-2.2-1/vegan/R/fitted.capscale.R | 2
vegan-2.2-1/vegan/R/fitted.cca.R | 2
vegan-2.2-1/vegan/R/fitted.rda.R | 2
vegan-2.2-1/vegan/R/intersetcor.R | 2
vegan-2.2-1/vegan/R/lines.spantree.R | 7
vegan-2.2-1/vegan/R/linestack.R | 36 +-
vegan-2.2-1/vegan/R/mantel.R | 2
vegan-2.2-1/vegan/R/mantel.partial.R | 2
vegan-2.2-1/vegan/R/metaMDSiter.R | 2
vegan-2.2-1/vegan/R/mrpp.R | 2
vegan-2.2-1/vegan/R/oecosimu.R | 2
vegan-2.2-1/vegan/R/ordiareatest.R | 2
vegan-2.2-1/vegan/R/orditkplot.R | 275 ++++++++++----------
vegan-2.2-1/vegan/R/permutest.betadisper.R | 5
vegan-2.2-1/vegan/R/permutest.cca.R | 2
vegan-2.2-1/vegan/R/plot.spantree.R | 17 -
vegan-2.2-1/vegan/R/poolaccum.R | 14 -
vegan-2.2-1/vegan/R/print.mantel.correlog.R | 2
vegan-2.2-1/vegan/R/renyiaccum.R | 6
vegan-2.2-1/vegan/R/simper.R | 44 +--
vegan-2.2-1/vegan/R/spantree.R | 4
vegan-2.2-1/vegan/R/specaccum.R | 12
vegan-2.2-1/vegan/R/specpool.R | 2
vegan-2.2-1/vegan/R/tolerance.cca.R | 6
vegan-2.2-1/vegan/R/tsallisaccum.R | 10
vegan-2.2-1/vegan/R/vegandocs.R | 2
vegan-2.2-1/vegan/R/vif.cca.R | 2
vegan-2.2-1/vegan/inst/ChangeLog | 11
vegan-2.2-1/vegan/inst/NEWS.Rd | 66 ++++
vegan-2.2-1/vegan/inst/doc/FAQ-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/NEWS.html | 82 ++++++
vegan-2.2-1/vegan/inst/doc/decision-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/diversity-vegan.R | 50 +--
vegan-2.2-1/vegan/inst/doc/diversity-vegan.Rnw | 245 +++++++++++-------
vegan-2.2-1/vegan/inst/doc/diversity-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/intro-vegan.pdf |binary
vegan-2.2-1/vegan/man/betadisper.Rd | 8
vegan-2.2-1/vegan/man/isomap.Rd | 19 -
vegan-2.2-1/vegan/man/kendall.global.Rd | 2
vegan-2.2-1/vegan/man/linestack.Rd | 31 +-
vegan-2.2-1/vegan/man/monoMDS.Rd | 2
vegan-2.2-1/vegan/man/pcnm.Rd | 2
vegan-2.2-1/vegan/man/renyi.Rd | 6
vegan-2.2-1/vegan/man/specaccum.Rd | 7
vegan-2.2-1/vegan/man/specpool.Rd | 11
vegan-2.2-1/vegan/man/tsallis.Rd | 8
vegan-2.2-1/vegan/man/vegandocs.Rd | 5
vegan-2.2-1/vegan/vignettes/FAQ-vegan.pdf |binary
vegan-2.2-1/vegan/vignettes/NEWS.html | 82 ++++++
vegan-2.2-1/vegan/vignettes/decision-vegan.tex | 18 -
vegan-2.2-1/vegan/vignettes/diversity-vegan.Rnw | 245 +++++++++++-------
vegan-2.2-1/vegan/vignettes/diversity-vegan.tex | 321 ++++++++++++++----------
vegan-2.2-1/vegan/vignettes/intro-vegan.tex | 57 +---
vegan-2.2-1/vegan/vignettes/vegan.bib | 20 +
70 files changed, 1302 insertions(+), 743 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Diff between treeclim versions 1.0.7 dated 2014-08-08 and 1.0.9 dated 2015-01-12
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang
DESCRIPTION | 10 +++++-----
MD5 | 11 ++++++-----
R/dcc.R | 2 +-
R/init_boot_data.R | 4 ++++
inst/CITATION |only
inst/Changelog | 23 +++++++++++++++++++----
man/dcc.Rd | 2 +-
7 files changed, 36 insertions(+), 16 deletions(-)
Title: Simulation of Event Histories for Multi-state Models
Diff between simMSM versions 1.0.1 dated 2014-03-28 and 1.1.2 dated 2015-01-12
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
simMSM-1.0.1/simMSM/R/f.for.uniroot.R |only
simMSM-1.0.1/simMSM/R/sim.event.histories.R |only
simMSM-1.0.1/simMSM/R/sim.exit.R |only
simMSM-1.0.1/simMSM/R/sim.single.history.R |only
simMSM-1.0.1/simMSM/R/sim.to.R |only
simMSM-1.0.1/simMSM/inst |only
simMSM-1.0.1/simMSM/man/f.for.uniroot.Rd |only
simMSM-1.0.1/simMSM/man/sim.event.histories.Rd |only
simMSM-1.0.1/simMSM/man/sim.exit.Rd |only
simMSM-1.0.1/simMSM/man/sim.single.history.Rd |only
simMSM-1.0.1/simMSM/man/sim.to.Rd |only
simMSM-1.1.2/simMSM/DESCRIPTION | 13 +--
simMSM-1.1.2/simMSM/MD5 | 45 ++++++-----
simMSM-1.1.2/simMSM/R/allcausehr.R | 15 +--
simMSM-1.1.2/simMSM/R/cumallcausehr.R | 9 +-
simMSM-1.1.2/simMSM/R/hr.R | 6 -
simMSM-1.1.2/simMSM/R/meancentering.R |only
simMSM-1.1.2/simMSM/R/simCR.R |only
simMSM-1.1.2/simMSM/R/simEBMT.R |only
simMSM-1.1.2/simMSM/R/simeventhistories.R |only
simMSM-1.1.2/simMSM/R/simexit.R |only
simMSM-1.1.2/simMSM/R/simexitinner.R |only
simMSM-1.1.2/simMSM/R/simsinglehistory.R |only
simMSM-1.1.2/simMSM/R/simto.R |only
simMSM-1.1.2/simMSM/R/unirootf.R |only
simMSM-1.1.2/simMSM/man/allcausehr.Rd | 12 +--
simMSM-1.1.2/simMSM/man/cumallcausehr.Rd | 14 +--
simMSM-1.1.2/simMSM/man/hr.Rd | 13 ++-
simMSM-1.1.2/simMSM/man/meancentering.Rd |only
simMSM-1.1.2/simMSM/man/simCR.Rd |only
simMSM-1.1.2/simMSM/man/simEBMT.Rd |only
simMSM-1.1.2/simMSM/man/simMSM-package.Rd | 96 +------------------------
simMSM-1.1.2/simMSM/man/simeventhistories.Rd |only
simMSM-1.1.2/simMSM/man/simexit.Rd |only
simMSM-1.1.2/simMSM/man/simexitinner.Rd |only
simMSM-1.1.2/simMSM/man/simsinglehistory.Rd |only
simMSM-1.1.2/simMSM/man/simto.Rd |only
simMSM-1.1.2/simMSM/man/unirootf.Rd |only
38 files changed, 75 insertions(+), 148 deletions(-)
Title: Estimating Regularized Multi-state Models Using L1 Penalties
Diff between penMSM versions 0.97 dated 2014-07-02 and 0.99 dated 2015-01-12
Description: Structured fusion Lasso penalized estimation of multi-state models with the penalty applied to absolute effects and absolute effect differences (i.e., effects on transition-type specific hazard rates).
Author: Holger Reulen
Maintainer: Holger Reulen
DESCRIPTION | 17 ++++---
MD5 | 46 ++++++++++++-------
NAMESPACE | 4 +
R/RcppExports.R |only
R/buildrisksets.R | 40 ++++++++++------
R/dapproxpenalty.R | 7 +-
R/dpenaltyfunction.R | 4 -
R/fisherinfo.R | 19 ++++----
R/fisherinfoP.R |only
R/llP.R |only
R/lpl.R | 4 -
R/penMSM.R | 113 +++++++++++++++++++++++++++++++++++-------------
R/penaltymatrix.R | 14 ++---
R/plmatrix.R | 16 +++---
R/sF.R |only
R/scorevector.R | 16 ++----
R/scorevectorP.R |only
man/buildrisksets.Rd | 3 -
man/dapproxpenalty.Rd | 10 +---
man/dpenaltyfunction.Rd | 6 +-
man/fishercpp.Rd |only
man/fisherinfoP.Rd |only
man/llP.Rd |only
man/penMSM.Rd | 37 ++++++++++++---
man/penaltymatrix.Rd | 6 +-
man/plmatrix.Rd | 8 +--
man/sF.Rd |only
man/scorevectorP.Rd |only
src |only
29 files changed, 234 insertions(+), 136 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.3 dated 2014-12-21 and 0.4 dated 2015-01-12
Description: V8 is Google's open source, high performance JavaScript engine. It
is written in C++ and implements ECMAScript as specified in ECMA-262, 5th
edition.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 16 +++++++------
LICENSE | 4 +--
MD5 | 26 ++++++++++++++-------
NAMESPACE | 3 +-
R/RcppExports.R | 4 +--
R/V8.R | 64 +++++++++++++++++++++++++++++++++++++++-------------
build |only
inst/doc |only
man/new_context.Rd | 31 ++++++++++++++++++++-----
src/RcppExports.cpp | 7 +++--
src/V8.cpp | 42 ++++++++++++++++++++++++++++++++--
vignettes |only
12 files changed, 151 insertions(+), 46 deletions(-)
Title: Soundscape ecology
Diff between soundecology versions 1.1.1 dated 2014-04-14 and 1.2 dated 2015-01-12
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera
DESCRIPTION | 12 +--
MD5 | 22 +++---
NAMESPACE | 2
NEWS | 6 +
R/multiple_sounds.R | 63 +++++++++++++++++--
R/sound_raster.R | 2
build/vignette.rds |binary
inst/doc/changeADI.R | 2
inst/doc/changeADI.html | 142 +++++++++++++++++++++++++-------------------
inst/doc/intro.html | 122 ++++++++++++++++++++++---------------
man/multiple_sounds.Rd | 6 +
man/soundecology.package.Rd | 4 -
12 files changed, 240 insertions(+), 143 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Diff between dfmta versions 1.0-3 dated 2014-11-20 and 1.1-0 dated 2015-01-12
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
dfmta-1.0-3/dfmta/man/mta_next.Rd |only
dfmta-1.0-3/dfmta/man/mta_sim.Rd |only
dfmta-1.0-3/dfmta/src/Makevars |only
dfmta-1.1-0/dfmta/DESCRIPTION | 13
dfmta-1.1-0/dfmta/MD5 | 36
dfmta-1.1-0/dfmta/NAMESPACE | 4
dfmta-1.1-0/dfmta/R/dfmta.R | 238 ++--
dfmta-1.1-0/dfmta/cleanup |only
dfmta-1.1-0/dfmta/configure |only
dfmta-1.1-0/dfmta/configure.ac |only
dfmta-1.1-0/dfmta/man/dfmta-package.Rd | 6
dfmta-1.1-0/dfmta/man/mtaBin_next.Rd |only
dfmta-1.1-0/dfmta/man/mtaBin_sim.Rd |only
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.bernoulli.hpp | 10
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.discrete.hpp | 12
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 6
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 6
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.jump.hpp | 4
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.math.hpp | 176 +--
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.rng.hpp | 24
dfmta-1.1-0/dfmta/src/Makevars.in |only
dfmta-1.1-0/dfmta/src/Makevars.win | 2
dfmta-1.1-0/dfmta/src/dfmta.cpp | 533 ++++------
dfmta-1.1-0/dfmta/tools |only
24 files changed, 553 insertions(+), 517 deletions(-)
Title: Robust Variance Meta-regression
Diff between robumeta versions 1.4 dated 2014-12-09 and 1.5 dated 2015-01-12
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/robumeta.R | 37 ++++++++++++++++++++++++++-----------
3 files changed, 31 insertions(+), 16 deletions(-)
Title: Spatially Explicit Capture-Recapture for Linear Habitats
Diff between secrlinear versions 1.0.4 dated 2014-12-08 and 1.0.5 dated 2015-01-11
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 8 ++++----
MD5 | 28 ++++++++++++++--------------
NEWS | 5 +++++
R/clipmask.R | 4 ++--
R/networkdistance.R | 3 ++-
inst/CITATION | 5 ++---
inst/doc/secrlinear-manual.pdf |binary
inst/doc/secrlinear-vignette.Rmd | 19 +++++--------------
inst/doc/secrlinear-vignette.pdf |binary
man/clipmask.Rd | 2 +-
man/linearmask.object.Rd | 12 ++++++------
man/read.linearmask.Rd | 3 +--
man/secrlinear-package.Rd | 4 ++--
man/utility.Rd | 12 +++++++-----
vignettes/secrlinear-vignette.Rmd | 19 +++++--------------
15 files changed, 56 insertions(+), 68 deletions(-)
Title: R Interface to FOAAS
Diff between rfoaas versions 0.0.5 dated 2014-12-28 and 0.1.1 dated 2015-01-11
Description: R access to the FOAAS (F... Off As A Service) web service
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 24 ++++++++++++++++++++++++
DESCRIPTION | 9 +++++----
MD5 | 11 ++++++-----
NAMESPACE | 1 +
R/foaas.R | 24 +++++++++++++++++-------
README.md | 4 ++--
tests |only
7 files changed, 55 insertions(+), 18 deletions(-)
Title: R port of the Scilab neldermead module
Diff between neldermead versions 1.0-9 dated 2014-03-02 and 1.0-10 dated 2015-01-11
Description: Provides several direct search optimization algorithms based on the
simplex method. The provided algorithms are direct search algorithms, i.e.
algorithms which do not use the derivative of the cost function. They are
based on the update of a simplex. The following algorithms are available: the
fixed shape simplex method of Spendley, Hext and Himsworth (unconstrained
optimization with a fixed shape simplex), the variable shape simplex method of
Nelder and Mead (unconstrained optimization with a variable shape simplex
made), and Box's complex method (constrained optimization with a variable
shape simplex).
Author: Sebastien Bihorel, Michael Baudin (author of the original
module)
Maintainer: Sebastien Bihorel
Changelog | 5 +
DESCRIPTION | 8 +--
MD5 | 98 +++++++++++++++++++--------------------
R/boxlinesearch.R | 2
R/costf.transposex.R | 2
R/fmin.gridsearch.R | 2
R/fminbnd.R | 4 -
R/fminbnd.function.R | 2
R/fminbnd.outputfun.R | 2
R/fminsearch.R | 2
R/fminsearch.function.R | 2
R/fminsearch.outputfun.R | 2
R/is.R | 2
R/neldermead.R | 2
R/neldermead.algo.R | 2
R/neldermead.autorestart.R | 2
R/neldermead.box.R | 2
R/neldermead.costf.R | 2
R/neldermead.destroy.R | 2
R/neldermead.fixed.R | 2
R/neldermead.function.R | 2
R/neldermead.get.R | 2
R/neldermead.interpolate.R | 2
R/neldermead.isrkelley.R | 2
R/neldermead.isroneill.R | 8 +--
R/neldermead.istorestart.R | 2
R/neldermead.log.R | 2
R/neldermead.outputcmd.R | 2
R/neldermead.restart.R | 2
R/neldermead.scaletocenter.R | 2
R/neldermead.scaletox0.R | 2
R/neldermead.search.R | 2
R/neldermead.set.R | 2
R/neldermead.startup.R | 2
R/neldermead.storehistory.R | 4 -
R/neldermead.termination.R | 2
R/neldermead.termstartup.R | 2
R/neldermead.updatesimp.R | 6 +-
R/neldermead.variable.R | 2
R/optimget.R | 2
R/optimset.R | 2
R/optimset.method.R | 2
R/print.neldermead.R | 2
R/scaleinconstraints.R | 2
R/summary.neldermead.R | 2
inst/doc/neldermead_manual.Rnw | 2
inst/doc/neldermead_manual.pdf |binary
man/neldermead-package.Rd | 4 -
vignettes/neldermead-package.tex | 4 -
vignettes/neldermead_manual.Rnw | 2
50 files changed, 113 insertions(+), 108 deletions(-)
Title: A Utility to Send Emails from R
Diff between mailR versions 0.3 dated 2014-05-17 and 0.4 dated 2015-01-11
Description: Interface to Apache Commons Email to send emails
from R.
Author: Rahul Premraj
Maintainer: Rahul Premraj
mailR-0.3/mailR/NEWS |only
mailR-0.3/mailR/inst/java/commons-email-1.3.2.jar |only
mailR-0.3/mailR/inst/java/javax.mail-1.5.1.jar |only
mailR-0.4/mailR/DESCRIPTION | 14
mailR-0.4/mailR/MD5 | 587 +++++++++++++++++++++-
mailR-0.4/mailR/NAMESPACE | 3
mailR-0.4/mailR/R/mailR.R | 39 -
mailR-0.4/mailR/README.md | 131 +++-
mailR-0.4/mailR/inst/java/commons-email-1.3.3.jar |only
mailR-0.4/mailR/inst/java/javax.mail.jar |only
mailR-0.4/mailR/java |only
mailR-0.4/mailR/man/send.mail.Rd | 78 --
12 files changed, 721 insertions(+), 131 deletions(-)
Title: Robust multivariate classification using highly optimised SVM
ensembles
Diff between classyfire versions 0.1-1 dated 2014-11-22 and 0.1-2 dated 2015-01-11
Description: A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing.
Author: Eleni Chatzimichali
Maintainer: Eleni Chatzimichali
classyfire-0.1-1/classyfire/R/init.R |only
classyfire-0.1-2/classyfire/DESCRIPTION | 11 +++--
classyfire-0.1-2/classyfire/MD5 | 37 +++++++++++-------
classyfire-0.1-2/classyfire/NAMESPACE | 1
classyfire-0.1-2/classyfire/NEWS |only
classyfire-0.1-2/classyfire/R/attach.R |only
classyfire-0.1-2/classyfire/R/cfBuild.R | 35 +++++++++--------
classyfire-0.1-2/classyfire/R/cfPermute.R | 35 ++++++++---------
classyfire-0.1-2/classyfire/R/checks.R |only
classyfire-0.1-2/classyfire/R/complex.R | 13 +++---
classyfire-0.1-2/classyfire/R/parallel.R | 15 +++----
classyfire-0.1-2/classyfire/R/plots.R | 36 +++++++++++++++--
classyfire-0.1-2/classyfire/R/stats.R | 12 +++++
classyfire-0.1-2/classyfire/build |only
classyfire-0.1-2/classyfire/inst |only
classyfire-0.1-2/classyfire/man/cfBuild.Rd | 16 ++-----
classyfire-0.1-2/classyfire/man/cfPermute.Rd | 3 -
classyfire-0.1-2/classyfire/man/cfPredict.Rd | 14 ++++++
classyfire-0.1-2/classyfire/man/classyfire-package.Rd | 4 -
classyfire-0.1-2/classyfire/man/ggEnsHist.Rd | 2
classyfire-0.1-2/classyfire/man/ggFusedHist.Rd |only
classyfire-0.1-2/classyfire/tests |only
classyfire-0.1-2/classyfire/vignettes |only
23 files changed, 147 insertions(+), 87 deletions(-)
Title: Analysis of Growth Data
Diff between AGD versions 0.31 dated 2014-12-21 and 0.32 dated 2015-01-11
Description: Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23
2012, Rotterdam.
Author: Stef van Buuren
Maintainer: Stef van Buuren
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 32 ++++++++++++++++----------------
inst/NEWS | 3 +++
4 files changed, 26 insertions(+), 23 deletions(-)
Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 1.1.0 dated 2015-01-05 and 1.2.0 dated 2015-01-11
Description: Target Inhibition Interaction using Maximization/Minimization
Averaging
Author: Liye He
Maintainer: Liye He
DESCRIPTION | 8 +++++---
MD5 | 10 +++++++---
R/drugRank.R | 9 +++++++--
R/timma.R | 2 +-
build |only
inst |only
vignettes |only
7 files changed, 20 insertions(+), 9 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Diff between secrdesign versions 2.2.1 dated 2014-11-26 and 2.2.2 dated 2015-01-11
Description: Tools for designing spatially explicit capture--recapture studies of animal populations (primarily a simulation manager for package secr)
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 5 +++++
R/methods.R | 1 +
inst/CITATION | 5 ++---
inst/doc/secrdesign-manual.pdf |binary
inst/doc/secrdesign-vignette.pdf |binary
man/secrdesign-package.Rd | 4 ++--
vignettes/runsims1.RData |binary
vignettes/runsims2.RData |binary
10 files changed, 23 insertions(+), 18 deletions(-)
Title: Spatially Explicit Capture-Recapture
Diff between secr versions 2.9.2 dated 2014-11-26 and 2.9.3 dated 2015-01-11
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 10 ++--
MD5 | 60 ++++++++++++++---------------
NAMESPACE | 1
NEWS | 28 +++++++++++++
R/addCovariates.R | 8 ++-
R/autoini.R | 2
R/clone.R | 59 ++++++++++++++++++++++++++++
R/empirical.R | 2
R/homerange.R | 4 +
R/make.capthist.R | 4 -
R/make.grid.R | 2
R/methods.R | 26 +++++++-----
R/plot.mask.r | 1
R/rbind.capthist.R | 18 ++++++--
R/secr.fit.R | 75 ++++++++++++++++++------------------
R/secrloglik.R | 16 ++++---
R/sim.popn.R | 93 ++++++++++++++++++++++++++++++++++++++-------
R/telemetry.R | 4 -
R/trap.builder.R | 22 +++++++---
R/utility.R | 17 +++++---
R/verify.R | 7 ++-
R/writeGPS.R | 2
inst/CITATION | 5 --
inst/doc/index.html | 33 ++++++++++++---
inst/doc/secr-manual.pdf |binary
inst/doc/secr-overview.pdf |binary
man/clone.Rd | 23 ++++++++---
man/secr-package.Rd | 14 +++++-
man/signalmatrix.Rd | 4 -
man/sim.popn.Rd | 17 +++-----
man/subset.capthist.Rd | 3 -
31 files changed, 399 insertions(+), 161 deletions(-)
Title: Bivariate Linear Errors-In-Variables Estimation
Diff between leiv versions 2.0-6 dated 2014-03-04 and 2.0-7 dated 2015-01-11
Description: Estimate the slope and intercept of a bivariate
linear relationship by calculating a posterior density
that is invariant to interchange and scaling of the
coordinates.
Author: David Leonard [aut, cre]
Maintainer: David Leonard
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
build/vignette.rds |binary
inst/CITATION | 5 ++---
inst/NEWS | 10 ++++++++++
5 files changed, 21 insertions(+), 12 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.6.3 dated 2014-10-06 and 0.9 dated 2015-01-11
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 10 -
MD5 | 30 ++---
NAMESPACE | 2
R/classVarImp.R | 188 +++++++++++++++++++++++----------
R/fscaret.R | 61 +++++++++-
R/impCalc.R | 283 ++++++++++++++++++++++++++++++++++++++++++++------
R/regVarImp.R | 41 +++++--
build/vignette.rds |binary
inst/NEWS.Rd | 11 +
inst/doc/fscaret.R | 93 ++++++++++++++--
inst/doc/fscaret.Rnw | 90 +++++++++++++--
inst/doc/fscaret.pdf |binary
man/classVarImp.Rd | 14 --
man/fscaret.Rd | 2
man/impCalc.Rd | 15 +-
vignettes/fscaret.Rnw | 90 +++++++++++++--
16 files changed, 750 insertions(+), 180 deletions(-)
Title: Soil Physical Analysis
Diff between soilphysics versions 1.2 dated 2014-10-14 and 2.0 dated 2015-01-11
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva
DESCRIPTION | 8 -
MD5 | 49 ++++++---
NAMESPACE | 13 ++
NEWS | 14 ++
R/fitsoilwater.R | 127 ++++++++++++------------
R/fitsoilwater2.R |only
R/fitsoilwater3.R |only
R/fitsoilwater4.R |only
R/fitsoilwater5.R |only
R/hemc.R |only
R/hydraulicCutOff.R |only
R/iwc.R |only
R/llwr.R | 231 ++++++++++++++++++++++++++++----------------
R/sigmaP.r | 2
R/soilwater2.R |only
R/soilwater3.R |only
R/soilwater4.R |only
R/soilwater5.R |only
man/figures/Thumbs.db |binary
man/figures/sigmaPfluxo.jpg |only
man/fitsoilwater.Rd | 3
man/fitsoilwater2.Rd |only
man/fitsoilwater3.Rd |only
man/fitsoilwater4.Rd |only
man/fitsoilwater5.Rd |only
man/hemc.Rd |only
man/hydraulicCutOff.Rd |only
man/iwc.Rd |only
man/llwr.Rd | 55 ++++++----
man/sigmaP.Rd | 11 +-
man/soilphysics-package.Rd | 38 +++++--
man/soilwater.Rd | 2
man/soilwater2.Rd |only
man/soilwater3.Rd |only
man/soilwater4.Rd |only
man/soilwater5.Rd |only
man/voidratio.Rd | 4
37 files changed, 360 insertions(+), 197 deletions(-)
Title: Readable Regular Expressions
Diff between regexr versions 0.0.2 dated 2014-12-22 and 1.0.2 dated 2015-01-11
Description: An R framework for constructing and managing human readable regular
expressions. It aims to provide tools that enable the user to write
regular expressions in a way that is similar to the ways R code is written.
The tools allow the user to (1) write in smaller, modular, named,
sub-expressions, (2) write top to bottom, rather than a single string (3)
comment individual chunks, (4) indent expressions to clearly present regular
expression groups, (5) add vertical line spaces and R comments (i.e., #),
and (6) test the validity of the concatenated expression and the modular
sub-expressions.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker
regexr-0.0.2/regexr/R/regex.R |only
regexr-0.0.2/regexr/man/print.regex.Rd |only
regexr-0.0.2/regexr/man/regex-set-.regexr.Rd |only
regexr-0.0.2/regexr/man/regex.Rd |only
regexr-0.0.2/regexr/man/regex.regexr.Rd |only
regexr-0.0.2/regexr/tests/testthat/test-regex.R |only
regexr-1.0.2/regexr/DESCRIPTION | 21
regexr-1.0.2/regexr/MD5 | 86 +-
regexr-1.0.2/regexr/NAMESPACE | 19
regexr-1.0.2/regexr/NEWS | 64 +
regexr-1.0.2/regexr/R/add_comments.R | 4
regexr-1.0.2/regexr/R/as.regexr.R |only
regexr-1.0.2/regexr/R/comments.R | 19
regexr-1.0.2/regexr/R/construct.R | 125 +--
regexr-1.0.2/regexr/R/regex-class.R | 10
regexr-1.0.2/regexr/R/regexr-class.R | 81 +-
regexr-1.0.2/regexr/R/regexr-package.R | 20
regexr-1.0.2/regexr/R/set_names.R |only
regexr-1.0.2/regexr/R/subs.R |only
regexr-1.0.2/regexr/R/test.R | 8
regexr-1.0.2/regexr/R/unglue.R | 4
regexr-1.0.2/regexr/README.md | 351 +++++++---
regexr-1.0.2/regexr/inst/CITATION | 5
regexr-1.0.2/regexr/inst/functions_table/functions.R | 13
regexr-1.0.2/regexr/man/add_comments.Rd | 2
regexr-1.0.2/regexr/man/as.regexr.Rd |only
regexr-1.0.2/regexr/man/as.regexr.character.Rd |only
regexr-1.0.2/regexr/man/as.regexr.default.Rd |only
regexr-1.0.2/regexr/man/comments.Rd | 15
regexr-1.0.2/regexr/man/construct.Rd | 123 +--
regexr-1.0.2/regexr/man/get_construct.Rd |only
regexr-1.0.2/regexr/man/get_construct.reverse_construct.Rd |only
regexr-1.0.2/regexr/man/names-set-.regexr.Rd | 4
regexr-1.0.2/regexr/man/names.regexr.Rd | 2
regexr-1.0.2/regexr/man/print.reverse_construct.Rd |only
regexr-1.0.2/regexr/man/print.subcom.Rd |only
regexr-1.0.2/regexr/man/regexr.Rd | 20
regexr-1.0.2/regexr/man/set_names.Rd |only
regexr-1.0.2/regexr/man/subs-set-.regexr.Rd |only
regexr-1.0.2/regexr/man/subs.Rd |only
regexr-1.0.2/regexr/man/subs.regexr.Rd |only
regexr-1.0.2/regexr/man/test.Rd | 8
regexr-1.0.2/regexr/man/test.regexr.Rd | 4
regexr-1.0.2/regexr/man/unglue.Rd | 4
regexr-1.0.2/regexr/tests/testthat.R | 1
regexr-1.0.2/regexr/tests/testthat/test-as.regexr.R |only
regexr-1.0.2/regexr/tests/testthat/test-comment_binary_operator.R | 15
regexr-1.0.2/regexr/tests/testthat/test-comments.R | 29
regexr-1.0.2/regexr/tests/testthat/test-construct.R | 4
regexr-1.0.2/regexr/tests/testthat/test-get_construct.R |only
regexr-1.0.2/regexr/tests/testthat/test-names.R | 20
regexr-1.0.2/regexr/tests/testthat/test-print.subcom.R |only
regexr-1.0.2/regexr/tests/testthat/test-subs.R |only
regexr-1.0.2/regexr/tests/testthat/test-summary.R | 27
regexr-1.0.2/regexr/tests/testthat/test-test.R | 21
regexr-1.0.2/regexr/tests/testthat/test-unglue.R | 17
56 files changed, 750 insertions(+), 396 deletions(-)
Title: Quantile Regression
Diff between quantreg versions 5.08 dated 2015-01-09 and 5.11 dated 2015-01-11
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker with contributions from Stephen Portnoy, Pin Ng, Achim Zeileis, Philip Grosjean and Brian Ripley
Maintainer: Roger Koenker
DESCRIPTION | 18 +++++++++++-------
MD5 | 8 ++++----
R/quantreg.R | 2 +-
man/qrisk.Rd | 8 +++++---
man/rq.fit.hogg.Rd | 5 +++--
5 files changed, 24 insertions(+), 17 deletions(-)
Title: Robust Meta-analysis and Meta-regression
Diff between metaplus versions 0.6-1 dated 2014-10-14 and 0.7-0 dated 2015-01-11
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Author: Ken Beath
Maintainer: Ken Beath
DESCRIPTION | 12 +-
MD5 | 35 +++---
NAMESPACE | 8 -
R/aaaaa.R |only
R/confint.R |only
R/globals.R | 2
R/makestart.profilemix.metaplus.R | 6 -
R/makestart.profilenorm.metaplus.R | 24 ++--
R/mymle.R |only
R/myoptim.R |only
R/plot.metaplus.R | 72 ++++++------
R/profile.R |only
R/profilemix.metaplus.R | 56 ++++-----
R/profilemix.profile.R | 14 --
R/profilenorm.metaplus.R | 195 +++++++++++++++++-----------------
R/profilet.metaplus.R | 114 +++++++++++--------
R/profilet.profile.R | 23 +---
R/test.outliers.profilemix.metaplus.R | 83 +++++++-------
R/test.outliers.profilet.metaplus.R | 85 +++++++-------
inst/NEWS | 6 +
man/metaplus.Rd | 1
21 files changed, 381 insertions(+), 355 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models with Local
Dependence
Diff between hergm versions 2.1-0 dated 2015-01-04 and 2.1-1 dated 2015-01-11
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/hergm.preprocess.R | 12 ++++--------
inst/CITATION | 25 +++++++++----------------
4 files changed, 20 insertions(+), 31 deletions(-)
Title: Data Analysis of T-cell Receptor Repertoires
Diff between tcR versions 1.0 dated 2014-12-12 and 1.1 dated 2015-01-10
Description: Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov, Mikhail Pogorelyy
Maintainer: Vadim Nazarov
DESCRIPTION | 13 +--
MD5 | 161 +++++++++++++++++++++---------------------
R/crosses.R | 26 +++---
R/dataproc.R | 6 -
R/diversity.R | 133 +++++++++++++++++++++++++++++++---
R/measures.R | 34 +++++++-
R/plots.R | 12 ++-
R/shared.R | 6 +
R/stats.R | 18 ++--
README.md |only
inst/doc/tcrvignette.R | 22 +++--
inst/doc/tcrvignette.Rnw | 6 +
inst/doc/tcrvignette.pdf |binary
man/AA_TABLE.Rd | 3
man/apply.symm.Rd | 3
man/assymetry.Rd | 3
man/barcodes.to.reads.Rd | 3
man/beta.prob.Rd | 3
man/bootstrap.tcr.Rd | 3
man/check.distribution.Rd | 3
man/codon.variants.Rd | 3
man/column.summary.Rd | 3
man/contamination.stats.Rd | 3
man/convergence.index.Rd | 3
man/cosine.sharing.Rd | 3
man/cosine.similarity.Rd | 16 ++--
man/entropy.Rd | 3
man/entropy.seg.Rd | 3
man/find.clonotypes.Rd | 3
man/find.similar.sequences.Rd | 3
man/freq.segments.Rd | 3
man/gc.content.Rd | 3
man/generate.kmers.Rd | 3
man/generate.tcr.Rd | 3
man/get.all.substrings.Rd | 3
man/get.deletions.alpha.Rd | 3
man/get.inframes.Rd | 3
man/get.kmers.Rd | 3
man/get.n.barcodes.Rd | 3
man/gibbs.sampler.Rd | 3
man/has.class.Rd | 3
man/intersect.Rd | 29 +++----
man/inverse.simpson.Rd | 22 ++++-
man/kmer.profile.Rd | 3
man/kmer.table.Rd | 3
man/loglikelihood.Rd | 3
man/matrixdiagcopy.Rd | 3
man/mitcr.stats.Rd | 3
man/parse.file.Rd | 3
man/parse.file.list.Rd | 3
man/parse.folder.Rd | 3
man/pca.segments.Rd | 3
man/permutedf.Rd | 3
man/rarefaction.Rd | 11 +-
man/revcomp.Rd | 3
man/reverse.string.Rd | 3
man/sample.clones.Rd | 3
man/sample2D.Rd | 3
man/segments.alphabets.Rd | 3
man/segments.list.Rd | 3
man/set.pb.Rd | 3
man/set.rank.Rd | 3
man/shared.repertoire.Rd | 6 +
man/spectratyping.Rd | 3
man/startmitcr.Rd | 3
man/tailbound.proportion.Rd | 3
man/top.cross.Rd | 3
man/top.fun.Rd | 3
man/twinsdata.Rd | 3
man/vis.V.usage.Rd | 3
man/vis.clonal.dynamics.Rd | 3
man/vis.count.len.Rd | 3
man/vis.group.boxplot.Rd | 3
man/vis.heatmap.Rd | 3
man/vis.kmer.histogram.Rd | 3
man/vis.number.count.Rd | 3
man/vis.pca.Rd | 3
man/vis.radarlike.Rd | 3
man/vis.rarefaction.Rd | 5 +
man/vis.top.proportions.Rd | 3
src/Makevars | 2
vignettes/tcrvignette.Rnw | 6 +
82 files changed, 475 insertions(+), 242 deletions(-)
Title: Deprecated 'classic' Rcpp API
Diff between RcppClassic versions 0.9.5 dated 2014-01-25 and 0.9.6 dated 2015-01-10
Description: The RcppClassic package provides a deprecated C++ library which
facilitates the integration of R and C++.
New projects should use the new Rcpp API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss,
and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel
RcppClassic-0.9.5/RcppClassic/inst/examples/RcppClassicExample/R/foo.R |only
RcppClassic-0.9.5/RcppClassic/inst/examples/RcppClassicExample/src/foo.cpp |only
RcppClassic-0.9.5/RcppClassic/vignettes/Makefile |only
RcppClassic-0.9.5/RcppClassic/vignettes/unitTests-results |only
RcppClassic-0.9.6/RcppClassic/ChangeLog | 21 ++++
RcppClassic-0.9.6/RcppClassic/DESCRIPTION | 11 +-
RcppClassic-0.9.6/RcppClassic/MD5 | 37 +++----
RcppClassic-0.9.6/RcppClassic/README.md | 13 +-
RcppClassic-0.9.6/RcppClassic/build/vignette.rds |binary
RcppClassic-0.9.6/RcppClassic/cleanup | 3
RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.R | 9 +
RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.Rnw | 50 ++++++----
RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.pdf |binary
RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-unitTests.pdf |binary
RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/DESCRIPTION | 15 +--
RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/NAMESPACE | 6 -
RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/R/twoTimes.R |only
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RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/src/Makevars | 2
RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/src/twoTimesImpl.cpp |only
RcppClassic-0.9.6/RcppClassic/src/Makevars | 10 +-
RcppClassic-0.9.6/RcppClassic/vignettes/RcppClassic-intro.Rnw | 50 ++++++----
22 files changed, 140 insertions(+), 94 deletions(-)
Title: Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data
Diff between hsphase versions 2.0.0 dated 2014-06-27 and 2.0.1 dated 2015-01-10
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data
Author: Mohammad Ferdosi
Maintainer: Mohammad Ferdosi
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
build/vignette.rds |binary
inst/CITATION | 12 ++++++------
man/hsphase-package.Rd | 4 ++--
5 files changed, 18 insertions(+), 17 deletions(-)
Title: Extended Rasch Modeling
Diff between eRm versions 0.15-4 dated 2014-02-05 and 0.15-5 dated 2015-01-10
Description: eRm fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Löf-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices. An eRm platform is provided at R-forge (see URL).
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Thomas Rusch [ctb]
Maintainer: Patrick Mair
eRm-0.15-4/eRm/R/pifit.internal.r |only
eRm-0.15-4/eRm/inst/NEWSRd2txt.R |only
eRm-0.15-4/eRm/inst/doc/UCML.pdf |only
eRm-0.15-4/eRm/inst/doc/UCML.svg |only
eRm-0.15-4/eRm/inst/doc/eRm_object_tree.pdf |only
eRm-0.15-4/eRm/inst/doc/eRmvig.bib |only
eRm-0.15-4/eRm/inst/doc/modelhierarchy.pdf |only
eRm-0.15-4/eRm/vignettes/UCML.svg |only
eRm-0.15-5/eRm/.Rinstignore | 8
eRm-0.15-5/eRm/DESCRIPTION | 26
eRm-0.15-5/eRm/MD5 | 200 +--
eRm-0.15-5/eRm/NAMESPACE | 29
eRm-0.15-5/eRm/NEWS | 228 ++-
eRm-0.15-5/eRm/R/NPtest.R | 8
eRm-0.15-5/eRm/R/SepRel.R |only
eRm-0.15-5/eRm/R/anova.eRm.R |only
eRm-0.15-5/eRm/R/llra.internals.R | 201 +--
eRm-0.15-5/eRm/R/personfit.ppar.R | 45
eRm-0.15-5/eRm/R/pifit.internal.R |only
eRm-0.15-5/eRm/R/plotGOF.LR.R | 16
eRm-0.15-5/eRm/R/plotGR.R | 101 -
eRm-0.15-5/eRm/R/plotINFO.R | 46
eRm-0.15-5/eRm/R/plotPWmap.R | 58
eRm-0.15-5/eRm/R/plotTR.R | 60
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eRm-0.15-5/eRm/build/vignette.rds |binary
eRm-0.15-5/eRm/data/llraDat1.rda |binary
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eRm-0.15-5/eRm/data/llradat3.rda |binary
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eRm-0.15-5/eRm/data/lltmdat2.rda |binary
eRm-0.15-5/eRm/data/lpcmdat.rda |binary
eRm-0.15-5/eRm/data/lrsmdat.rda |binary
eRm-0.15-5/eRm/data/pcmdat.rda |binary
eRm-0.15-5/eRm/data/pcmdat2.rda |binary
eRm-0.15-5/eRm/data/raschdat1.rda |binary
eRm-0.15-5/eRm/data/raschdat1_RM_fitted.RData |binary
eRm-0.15-5/eRm/data/raschdat1_RM_lrres2.RData |binary
eRm-0.15-5/eRm/data/raschdat1_RM_plotDIF.RData |binary
eRm-0.15-5/eRm/data/raschdat2.rda |binary
eRm-0.15-5/eRm/data/raschdat3.rda |binary
eRm-0.15-5/eRm/data/raschdat4.rda |binary
eRm-0.15-5/eRm/data/rsmdat.rda |binary
eRm-0.15-5/eRm/data/xmpl.RData |binary
eRm-0.15-5/eRm/data/xmplbig.RData |binary
eRm-0.15-5/eRm/inst/CITATION | 182 +-
eRm-0.15-5/eRm/inst/NEWS.Rd | 12
eRm-0.15-5/eRm/inst/NEWS.pdf |binary
eRm-0.15-5/eRm/inst/doc/eRm.R | 216 +--
eRm-0.15-5/eRm/inst/doc/eRm.Rnw | 450 +++----
eRm-0.15-5/eRm/inst/doc/eRm.pdf |binary
eRm-0.15-5/eRm/man/IC.Rd | 1
eRm-0.15-5/eRm/man/LLRA.Rd | 8
eRm-0.15-5/eRm/man/LLTM.Rd | 1
eRm-0.15-5/eRm/man/LPCM.Rd | 7
eRm-0.15-5/eRm/man/LRSM.Rd | 7
eRm-0.15-5/eRm/man/LRtest.Rd | 5
eRm-0.15-5/eRm/man/MLoef.Rd | 52
eRm-0.15-5/eRm/man/NPtest.Rd | 203 +--
eRm-0.15-5/eRm/man/PCM.Rd | 5
eRm-0.15-5/eRm/man/RM.Rd | 5
eRm-0.15-5/eRm/man/RSM.Rd | 7
eRm-0.15-5/eRm/man/RSctr.Rd | 1
eRm-0.15-5/eRm/man/RSmpl.Rd | 1
eRm-0.15-5/eRm/man/RaschSampler.Rd | 7
eRm-0.15-5/eRm/man/SepRel.Rd |only
eRm-0.15-5/eRm/man/Waldtest.Rd | 1
eRm-0.15-5/eRm/man/anova.eRm.Rd |only
eRm-0.15-5/eRm/man/anova.llra.Rd | 1
eRm-0.15-5/eRm/man/build_W.Rd | 5
eRm-0.15-5/eRm/man/collapse_W.Rd | 5
eRm-0.15-5/eRm/man/eRm-package.Rd | 32
eRm-0.15-5/eRm/man/eRm.data.Rd | 1
eRm-0.15-5/eRm/man/gofIRT.Rd | 1
eRm-0.15-5/eRm/man/item_info.Rd | 5
eRm-0.15-5/eRm/man/itemfit.ppar.Rd | 1
eRm-0.15-5/eRm/man/llra.datprep.Rd | 5
eRm-0.15-5/eRm/man/llraDat1.Rd | 64 -
eRm-0.15-5/eRm/man/llraDat2.Rd | 56
eRm-0.15-5/eRm/man/llradat3.Rd | 20
eRm-0.15-5/eRm/man/person.parameter.Rd | 7
eRm-0.15-5/eRm/man/phi.range.Rd | 21
eRm-0.15-5/eRm/man/plotDIF.Rd | 5
eRm-0.15-5/eRm/man/plotGR.Rd | 5
eRm-0.15-5/eRm/man/plotICC.Rd | 1
eRm-0.15-5/eRm/man/plotINFO.Rd | 46
eRm-0.15-5/eRm/man/plotPImap.Rd | 3
eRm-0.15-5/eRm/man/plotPWmap.Rd | 27
eRm-0.15-5/eRm/man/plotTR.Rd | 5
eRm-0.15-5/eRm/man/predict.ppar.Rd | 1
eRm-0.15-5/eRm/man/print.eRm.Rd | 3
eRm-0.15-5/eRm/man/rsampler.Rd | 36
eRm-0.15-5/eRm/man/rsctrl.Rd | 12
eRm-0.15-5/eRm/man/rsextrmat.Rd | 1
eRm-0.15-5/eRm/man/rsextrobj.Rd | 1
eRm-0.15-5/eRm/man/rstats.Rd | 1
eRm-0.15-5/eRm/man/sim.2pl.Rd | 61
eRm-0.15-5/eRm/man/sim.locdep.Rd | 1
eRm-0.15-5/eRm/man/sim.rasch.Rd | 1
eRm-0.15-5/eRm/man/sim.xdim.Rd | 1
eRm-0.15-5/eRm/man/stepwiseIt.Rd | 1
eRm-0.15-5/eRm/man/summary.RSctr.Rd | 1
eRm-0.15-5/eRm/man/summary.RSmpl.Rd | 1
eRm-0.15-5/eRm/man/summary.llra.Rd | 5
eRm-0.15-5/eRm/man/test_info.Rd | 11
eRm-0.15-5/eRm/man/thresholds.Rd | 1
eRm-0.15-5/eRm/man/xmpl.Rd | 1
eRm-0.15-5/eRm/vignettes/eRm.Rnw | 450 +++----
eRm-0.15-5/eRm/vignettes/eRmvig.bib | 1534 +++++++++++++------------
109 files changed, 2443 insertions(+), 2194 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-118 dated 2014-10-07 and 3.1-119 dated 2015-01-10
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
ChangeLog | 12 +++++++++++-
DESCRIPTION | 8 ++++----
MD5 | 19 ++++++++++---------
R/gnls.R | 2 +-
R/lme.R | 2 +-
R/newMethods.R | 2 +-
R/nlme.R | 6 +++---
R/pdMat.R | 2 +-
R/reStruct.R | 2 +-
man/bdf.Rd | 3 ++-
tests/nlme2.R |only
11 files changed, 35 insertions(+), 23 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-35 dated 2014-09-30 and 7.3-37 dated 2015-01-10
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 24 ++++++++++++------------
R/glmmPQL.R | 7 ++++---
R/loglm.R | 2 +-
R/neg.bin.R | 2 +-
R/negbin.R | 3 +--
R/polr.R | 1 -
inst/NEWS | 2 +-
inst/scripts/ch10.R | 24 +++++++++++-------------
man/bacteria.Rd | 6 ++++--
man/corresp.Rd | 2 +-
man/denumerate.Rd | 2 +-
tests/Examples/MASS-Ex.Rout.save | 26 +++++++++-----------------
13 files changed, 51 insertions(+), 60 deletions(-)
Title: Bootstrap Functions (originally by Angelo Canty for S)
Diff between boot versions 1.3-13 dated 2014-09-30 and 1.3-14 dated 2015-01-10
Description: functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/bootfuns.q | 4 ----
R/bootpracs.q | 2 +-
man/EEF.profile.Rd | 2 +-
6 files changed, 16 insertions(+), 15 deletions(-)
Title: Maxwell Bolzano Bose Einstein Fermi Dirac distribution and
exposure curve
Diff between mbbefd versions 0.1 dated 2013-10-30 and 0.5 dated 2015-01-10
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi Dirac (MBBEFD) distribution (distribution function, density, quantile functions) as well as MBBEFD exposure curve, used in actuarial application to price reinsurance contracts. The vignette shows code snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato
ChangeLog | 5 +
DESCRIPTION | 14 +++--
MD5 | 29 ++++++----
NEWS | 7 +-
R/distributionDefinition.R | 51 ++++++++++++-------
build |only
inst/CITATION | 8 +--
inst/doc/mbbefd.R | 86 ++++++++++++++++++++++++++++----
inst/doc/mbbefd.Rnw | 109 ++++++++++++++++++++++++++++++++++++++---
inst/doc/mbbefd.pdf |binary
man/mbbefd-package.Rd | 9 +--
man/mbbefdDistribution.Rd | 16 +++---
tests |only
vignettes/mbbefd-distrPlot.pdf |only
vignettes/mbbefd-drateplot.pdf |only
vignettes/mbbefd.Rnw | 109 ++++++++++++++++++++++++++++++++++++++---
vignettes/mbbefd.bib | 43 ++++++++++------
17 files changed, 395 insertions(+), 91 deletions(-)
Title: CRAN Task Views
Diff between ctv versions 0.8-0 dated 2014-07-31 and 0.8-1 dated 2015-01-10
Description: Server-side and client-side tools for task views
to CRAN-style repositories
Author: Achim Zeileis [aut, cre],
Kurt Hornik [aut]
Maintainer: Achim Zeileis
ctv-0.8-0/ctv/inst/ctv/Bayesian.html |only
ctv-0.8-0/ctv/inst/ctv/ChemPhys.html |only
ctv-0.8-0/ctv/inst/ctv/ClinicalTrials.html |only
ctv-0.8-0/ctv/inst/ctv/Cluster.html |only
ctv-0.8-0/ctv/inst/ctv/DifferentialEquations.html |only
ctv-0.8-0/ctv/inst/ctv/Distributions.html |only
ctv-0.8-0/ctv/inst/ctv/Econometrics.html |only
ctv-0.8-0/ctv/inst/ctv/Environmetrics.html |only
ctv-0.8-0/ctv/inst/ctv/ExperimentalDesign.html |only
ctv-0.8-0/ctv/inst/ctv/Finance.html |only
ctv-0.8-0/ctv/inst/ctv/Genetics.html |only
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ctv-0.8-0/ctv/inst/ctv/gR.html |only
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ctv-0.8-1/ctv/MD5 | 113 -
ctv-0.8-1/ctv/NEWS | 6
ctv-0.8-1/ctv/R/ctv-server.R | 52
ctv-0.8-1/ctv/build/vignette.rds |binary
ctv-0.8-1/ctv/inst/ctv/Bayesian.ctv | 10
ctv-0.8-1/ctv/inst/ctv/ChemPhys.ctv | 13
ctv-0.8-1/ctv/inst/ctv/ClinicalTrials.ctv | 4
ctv-0.8-1/ctv/inst/ctv/Cluster.ctv | 55
ctv-0.8-1/ctv/inst/ctv/DifferentialEquations.ctv | 9
ctv-0.8-1/ctv/inst/ctv/Distributions.ctv | 22
ctv-0.8-1/ctv/inst/ctv/Econometrics.ctv | 26
ctv-0.8-1/ctv/inst/ctv/Environmetrics.ctv | 9
ctv-0.8-1/ctv/inst/ctv/ExperimentalDesign.ctv | 7
ctv-0.8-1/ctv/inst/ctv/Finance.ctv | 72 -
ctv-0.8-1/ctv/inst/ctv/Genetics.ctv | 19
ctv-0.8-1/ctv/inst/ctv/Graphics.ctv | 16
ctv-0.8-1/ctv/inst/ctv/HighPerformanceComputing.ctv | 58
ctv-0.8-1/ctv/inst/ctv/MachineLearning.ctv | 45
ctv-0.8-1/ctv/inst/ctv/MedicalImaging.ctv | 27
ctv-0.8-1/ctv/inst/ctv/MetaAnalysis.ctv | 61
ctv-0.8-1/ctv/inst/ctv/Multivariate.ctv | 11
ctv-0.8-1/ctv/inst/ctv/NaturalLanguageProcessing.ctv | 4
ctv-0.8-1/ctv/inst/ctv/NumericalMathematics.ctv | 70 -
ctv-0.8-1/ctv/inst/ctv/OfficialStatistics.ctv | 46
ctv-0.8-1/ctv/inst/ctv/Optimization.ctv | 79 -
ctv-0.8-1/ctv/inst/ctv/Pharmacokinetics.ctv | 21
ctv-0.8-1/ctv/inst/ctv/Phylogenetics.ctv | 17
ctv-0.8-1/ctv/inst/ctv/Psychometrics.ctv | 56
ctv-0.8-1/ctv/inst/ctv/ReproducibleResearch.ctv | 143 --
ctv-0.8-1/ctv/inst/ctv/Robust.ctv | 71 -
ctv-0.8-1/ctv/inst/ctv/SocialSciences.ctv | 2
ctv-0.8-1/ctv/inst/ctv/Spatial.ctv | 35
ctv-0.8-1/ctv/inst/ctv/SpatioTemporal.ctv | 1103 +++++++++---------
ctv-0.8-1/ctv/inst/ctv/Survival.ctv | 284 +++-
ctv-0.8-1/ctv/inst/ctv/TimeSeries.ctv | 27
ctv-0.8-1/ctv/inst/ctv/WebTechnologies.ctv | 980 ++++++++++-----
ctv-0.8-1/ctv/inst/doc/ctv-howto.R | 2
ctv-0.8-1/ctv/inst/doc/ctv-howto.Rnw | 11
ctv-0.8-1/ctv/inst/doc/ctv-howto.pdf |binary
ctv-0.8-1/ctv/vignettes/ctv-howto.Rnw | 11
74 files changed, 2044 insertions(+), 1561 deletions(-)
Title: aoristic analysis with spatial output (kml)
Diff between aoristic versions 0.5 dated 2014-07-31 and 0.6 dated 2015-01-10
Description: 'Aoristic' is one of the past tenses in Greek and represents an
uncertain occurrence time. Aoristic analysis suggested by Ratcliffe (2002)
is a method to analyze events that do not have exact times of occurrence
but have starting times and ending times. For example, a property crime
database (e.g., burglary) typically has a starting time and ending time of
the crime that could have occurred. Aoristic analysis allocates the
probability of a crime incident occurring at every hour over a 24-hour
period. The probability is aggregated over a study area to create an
aoristic graph.
Using crime incident data with lat/lon, DateTimeFrom, and
DateTimeTo, functions in this package create a total of three (3) kml
files and corresponding aoristic graphs: 1) density and contour; 2) grid
count; and 3) shapefile boundary. (see also:
https://sites.google.com/site/georgekick/software)
Author: George Kikuchi
Maintainer: George Kikuchi
DESCRIPTION | 11 ++++++-----
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 16 +++++++++++++++-
R/aoristic-package.R | 6 +++---
R/aoristic.all.graph.R | 12 ++++++++++--
R/aoristic.density.R | 5 ++++-
R/aoristic.grid.R | 3 ++-
R/aoristic.shp.R | 7 ++++++-
R/aoristic.spdf.R | 3 ++-
demo/aoristic.R | 6 ++++++
man/CouncilDistrict.Rd | 5 +++--
man/aoristic-package.Rd | 3 ++-
man/aoristic.Rd | 5 +++--
man/aoristic.all.graph.Rd | 13 +++++++++++--
man/aoristic.density.Rd | 3 ++-
man/aoristic.df.Rd | 3 ++-
man/aoristic.grid.Rd | 3 ++-
man/aoristic.shp.Rd | 3 ++-
man/aoristic.spdf.Rd | 5 +++--
man/arlington.Rd | 5 +++--
20 files changed, 106 insertions(+), 49 deletions(-)
Title: SYMPHONY in R
Diff between Rsymphony versions 0.1-17 dated 2013-11-13 and 0.1-18 dated 2015-01-10
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut],
Kurt Hornik [aut, cre],
Stefan Theussl [aut],
Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik
Rsymphony-0.1-17/Rsymphony/src/SYMPHONY |only
Rsymphony-0.1-18/Rsymphony/DESCRIPTION | 14
Rsymphony-0.1-18/Rsymphony/MD5 | 1351 ----------------------
Rsymphony-0.1-18/Rsymphony/cleanup | 7
Rsymphony-0.1-18/Rsymphony/configure | 44
Rsymphony-0.1-18/Rsymphony/man/Rsymphony_solve.Rd | 2
Rsymphony-0.1-18/Rsymphony/src/Makevars.in | 16
7 files changed, 30 insertions(+), 1404 deletions(-)
Title: Kernel-based Machine Learning Lab
Diff between kernlab versions 0.9-19 dated 2013-11-03 and 0.9-20 dated 2015-01-10
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods kernlab
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou
DESCRIPTION | 6 +++---
MD5 | 28 ++++++++++++++--------------
build/vignette.rds |binary
data/income.rda |binary
data/musk.rda |binary
data/promotergene.rda |binary
data/reuters.rda |binary
data/spam.rda |binary
data/spirals.rda |binary
data/ticdata.rda |binary
inst/COPYRIGHTS | 4 ++++
inst/doc/kernlab.pdf |binary
src/msufsort.cpp | 1 +
src/msufsort.h | 29 +++++++++++++++++++----------
src/svm.cpp | 7 ++++++-
15 files changed, 47 insertions(+), 28 deletions(-)
Title: Collection of common astronomical conversion routines
Diff between celestial versions 1.1 dated 2013-08-10 and 1.2 dated 2015-01-10
Description: This package includes a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former.
Author: Aaron Robotham
Maintainer: Aaron Robotham
DESCRIPTION | 10 +++++-----
MD5 | 12 +++++++++---
NEWS | 4 ++++
R/cosdist.R |only
R/cosvol.R |only
R/skyarea.R |only
man/celestial-package.Rd | 4 ++--
man/cosdist.Rd |only
man/cosvol.Rd |only
man/skyarea.Rd |only
10 files changed, 20 insertions(+), 10 deletions(-)
Title: Basic wavelet routines for one-, two- and three-dimensional
signal processing
Diff between waveslim versions 1.7.3 dated 2013-12-23 and 1.7.5 dated 2015-01-09
Description: Basic wavelet routines for time series (1D), image (2D)
and array (3D) analysis. The code provided here is based on
wavelet methodology developed in Percival and Walden (2000);
Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet
transform (DTCWT) from Kingsbury (1999, 2001) as implemented by
Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All
figures in chapters 4-7 of GSW (2001) are reproducible using this
package and R code available at the book website(s) below.
Author: Brandon Whitcher
Maintainer: Brandon Whitcher
DESCRIPTION | 12 ++--
LICENSE |only
MD5 | 56 ++++++++++----------
R/zzz.R | 2
data/acvs.andel10.rda |binary
data/acvs.andel11.rda |binary
data/acvs.andel8.rda |binary
data/acvs.andel9.rda |binary
data/ar1.rda |binary
data/barbara.rda |binary
data/blocks.rda |binary
data/cpi.rda |binary
data/dau.rda |binary
data/doppler.rda |binary
data/exchange.rda |binary
data/heavisine.rda |binary
data/ibm.rda |binary
data/japan.rda |binary
data/jumpsine.rda |binary
data/kobe.rda |binary
data/linchirp.rda |binary
data/mexm.rda |binary
data/nile.rda |binary
data/tourism.rda |binary
data/unemploy.rda |binary
data/xbox.rda |binary
man/basis.Rd | 2
man/hosking.sim.Rd | 2
src/dwt2.c | 140 ++++++++++++++++++++++++++++----------------------
tests |only
30 files changed, 120 insertions(+), 94 deletions(-)
Title: Approximate String Matching and String Distance Functions
Diff between stringdist versions 0.8.2 dated 2014-12-15 and 0.9.0 dated 2015-01-09
Description: Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams (q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler). An implementation of soundex is provided as well.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo
DESCRIPTION | 14 -
MD5 | 48 +++--
NEWS | 9 +
R/amatch.R | 69 ++++----
R/doc_encoding.R |only
R/doc_metrics.R |only
R/doc_parallel.R |only
R/phonetic.R | 14 -
R/stringdist.R | 321 +++++++++++---------------------------
R/utils.R | 22 +-
man/amatch.Rd | 33 ++-
man/phonetic.Rd | 11 -
man/printable_ascii.Rd | 13 -
man/stringdist-encoding.Rd |only
man/stringdist-metrics.Rd |only
man/stringdist-package.Rd | 118 ++-----------
man/stringdist-parallelization.Rd |only
man/stringdist.Rd | 133 +++------------
src/Makevars |only
src/dl.c | 236 ++++++++++++++-------------
src/hamming.c | 165 +++++++++++--------
src/jaro.c | 193 ++++++++++++----------
src/lcs.c | 187 ++++++++++++----------
src/lv.c | 196 +++++++++++++----------
src/osa.c | 202 +++++++++++++----------
src/qgram.c | 285 +++++++++++++++++++--------------
src/soundex.c | 255 +++++++++++++++++++-----------
src/utf8ToInt.c |only
src/utils.h | 60 +++++++
29 files changed, 1302 insertions(+), 1282 deletions(-)
More information about RFmarkerDetector at CRAN
Permanent link
Title: Quantile Regression
Diff between quantreg versions 5.05 dated 2013-09-23 and 5.08 dated 2015-01-09
Description: Quantile regression and related methods.
Author: Roger Koenker with contributions from Stephen Portnoy, Pin Ng, Achim Zeileis, Philip Grosjean and Brian Ripley
Maintainer: Roger Koenker
DESCRIPTION | 16 ++---------
MD5 | 21 ++++++++------
R/crq.R | 3 +-
R/qrisk.R |only
R/quantreg.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++-----
R/table.R | 7 ++--
demo/00Index | 1
demo/RB-r.R |only
inst/ChangeLog | 13 ++++++++
inst/FAQ | 17 +++++++++++
inst/doc/rq.Rnw | 6 ++--
man/qrisk.Rd |only
man/rq.fit.hogg.Rd |only
man/srisk.Rd |only
14 files changed, 128 insertions(+), 33 deletions(-)
Title: Access to Facebook API via R
Diff between Rfacebook versions 0.4 dated 2014-04-02 and 0.5 dated 2015-01-09
Description: Provides an interface to the Facebook API
Author: Pablo Barbera
Maintainer: Pablo Barbera
ChangeLog | 6 ++
DESCRIPTION | 11 ++---
MD5 | 60 +++++++++++++++--------------
NAMESPACE | 4 +
R/Rfacebook-package.R | 2
R/fbOAuth.R | 14 ++++++
R/getCheckins.R | 19 +++++++--
R/getFriends.R | 41 +++++++++++++++----
R/getInsights.R |only
R/getLikes.R | 7 ++-
R/getNetwork.R | 36 ++++++++++++++---
R/getPage.R | 55 +++++++++++++++++++++++---
R/getUsers.R | 75 +++++++++++++++++++++---------------
R/searchFacebook.R | 33 +++++++++++----
R/searchPages.R | 2
R/updateStatus.R | 88 +++++++++++++++++++++++-------------------
R/utils.R | 51 ++++++++++++++++++++++--
man/Rfacebook-package.Rd | 9 ++--
man/fbOAuth.Rd | 97 ++++++++++++++++++++---------------------------
man/getCheckins.Rd | 30 +++++++-------
man/getFQL.Rd | 17 ++++----
man/getFriends.Rd | 32 +++++++--------
man/getInsights.Rd |only
man/getLikes.Rd | 20 ++++-----
man/getNetwork.Rd | 39 ++++++++++--------
man/getNewsfeed.Rd | 14 +++---
man/getPage.Rd | 43 ++++++++++++--------
man/getPost.Rd | 49 +++++++++++------------
man/getUsers.Rd | 50 ++++++++++--------------
man/searchFacebook.Rd | 62 ++++++++++++++----------------
man/searchPages.Rd | 21 ++++------
man/updateStatus.Rd | 24 +++++------
32 files changed, 603 insertions(+), 408 deletions(-)
Title: Multivariate Nonparametric Methods. An Approach Based on Spatial
Signs and Ranks
Diff between MNM versions 1.0-0 dated 2011-07-18 and 1.0-1 dated 2015-01-09
Description: The package provides multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components.
Author: Klaus Nordhausen, Jyrki Mottonen, Hannu Oja
Maintainer: Klaus Nordhausen
DESCRIPTION | 22 ++++++++++------------
MD5 |only
NAMESPACE | 5 ++++-
R/affinetrans.R | 2 +-
R/internal_miscMNM.R |only
R/locEst.R | 8 ++++----
R/mv.2way.testInternal.R | 12 ++++++------
R/mv.ind.test.internal.R | 4 ++--
R/mv.l1lm.Internal.R | 10 +++++-----
R/mv.pca.R | 18 +++++++++---------
R/mv2sampleEstInternal.R | 16 ++++++++--------
R/spatial.sign2.R | 6 +++---
data/beans.rda |binary
inst/ChangeLog | 5 +++++
man/MNM-package.Rd | 8 ++++----
man/affine.trans.Rd | 2 +-
man/anova.mvl1lm.Rd | 2 +-
man/coef.mvl1lm.Rd | 2 +-
man/fitted.mvl1lm.Rd | 2 +-
man/mv.1sample.est.Rd | 2 +-
man/mv.1sample.test.Rd | 2 +-
man/mv.2sample.est.Rd | 2 +-
man/mv.Csample.test.Rd | 2 +-
man/mv.ind.test.Rd | 2 +-
man/mv.l1lm.Rd | 2 +-
man/mv.shape.est.Rd | 2 +-
man/mv.shape.test.Rd | 2 +-
man/mvPCA.Rd | 2 +-
man/pairs2.Rd | 2 +-
man/plot.mvl1lm.Rd | 2 +-
man/plot.mvloc.Rd | 2 +-
man/plotMvloc.Rd | 2 +-
man/plotShape.Rd | 2 +-
man/predict.mvPCA.Rd | 2 +-
man/predict.mvl1lm.Rd | 2 +-
man/print.anovamvl1lm.Rd | 2 +-
man/print.mvPCA.Rd | 2 +-
man/print.mvl1lm.Rd | 2 +-
man/print.mvloc.Rd | 2 +-
man/residuals.mvl1lm.Rd | 2 +-
man/rmvpowerexp.Rd | 2 +-
man/runifsphere.Rd | 2 +-
man/screeplot.mvPCA.Rd | 2 +-
man/spatial.sign2.Rd | 4 ++--
man/summary.mvPCA.Rd | 2 +-
man/summary.mvl1lm.Rd | 2 +-
man/summary.mvloc.Rd | 2 +-
man/vcov.mvl1lm.Rd | 2 +-
48 files changed, 95 insertions(+), 89 deletions(-)
Title: Textual Data Analysis Package used by the TXM Software
Diff between textometry versions 0.1.3 dated 2014-06-16 and 0.1.4 dated 2015-01-09
Description: Statistical exploration of textual corpora using several methods
from French 'Textometrie' (new name of 'Lexicometrie') and French 'Data Analysis' schools.
It includes methods for exploring irregularity of distribution of lexicon features across
text sets or parts of texts (Specificity analysis); multi-dimensional exploration (Factorial analysis), etc.
Those methods are used in the TXM software.
Author: Sylvain Loiseau, Lise Vaudor, Matthieu Decorde, Serge Heiden
Maintainer: Matthieu Decorde
textometry-0.1.3/textometry/man/specificities.lexicon.probabilities.Rd |only
textometry-0.1.3/textometry/tests/Rplots.pdf |only
textometry-0.1.3/textometry/tests/authors |only
textometry-0.1.3/textometry/tests/bfmprogression.Rout |only
textometry-0.1.3/textometry/tests/cgt75.R |only
textometry-0.1.3/textometry/tests/cgt75.Rout |only
textometry-0.1.3/textometry/tests/cgt75.splitted.txt |only
textometry-0.1.3/textometry/tests/cgt75.txt |only
textometry-0.1.3/textometry/tests/specificities.Rout |only
textometry-0.1.3/textometry/tests/specificities.lexicon.new.Rout |only
textometry-0.1.3/textometry/tests/specificities.probabilities.Rout |only
textometry-0.1.4/textometry/CHANGES | 7
textometry-0.1.4/textometry/DESCRIPTION | 10
textometry-0.1.4/textometry/MD5 | 21
textometry-0.1.4/textometry/NAMESPACE | 7
textometry-0.1.4/textometry/R/specificities.R | 360 +++++-----
textometry-0.1.4/textometry/man/specificities.distribution.plot.Rd |only
textometry-0.1.4/textometry/man/specificities.probabilities.vector.Rd |only
18 files changed, 230 insertions(+), 175 deletions(-)
Title: Random Effects Latent Class Analysis
Diff between randomLCA versions 1.0-1 dated 2014-11-17 and 1.0-2 dated 2015-01-09
Description: Fits random effects latent class models, as well as standard latent class models.
Author: Ken Beath
Maintainer: Ken Beath
DESCRIPTION | 8
MD5 | 12 -
R/randomLCA.R | 338 +++++++++++++++++------------------
build/vignette.rds |binary
inst/NEWS | 380 ++++++++++++++++++++--------------------
man/dentistry.Rd | 94 ++++-----
vignettes/randomLCA-example.tex | 40 ++--
7 files changed, 438 insertions(+), 434 deletions(-)
Title: Learned Pattern Similarity and Representation for Time Series
Diff between LPStimeSeries versions 1.0-3 dated 2014-07-31 and 1.0-4 dated 2015-01-09
Description: Learned Pattern Similarity (LPS) for time series. This package is based on the
'randomForest' package by Andy Liaw. LPS aims at finding time series patterns to
compute the similarity.
Author: Learned Pattern Similarity (LPS) for time series by Mustafa Gokce Baydogan,
Ensemble of regression trees by Andy Liaw and Matthew Wiener.
Maintainer: Mustafa Gokce Baydogan
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
NAMESPACE | 3 ++-
R/computeSimilarity.R | 23 +++++++++++++++++++++--
R/plotMDS.R | 4 ++--
inst/NEWS | 11 +++++++++++
man/computeSimilarity.Rd | 6 +++++-
man/learnPattern.Rd | 9 ++++++---
src/regTree.c | 12 ++++++------
src/regrf.c | 23 +++++++++++++++--------
src/rfutils.c | 13 +++++++++++--
11 files changed, 95 insertions(+), 41 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.04-03 dated 2014-06-19 and 0.05-01 dated 2015-01-09
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++
DESCRIPTION | 8 ++--
MD5 | 8 ++--
R/jagsParallel.R | 101 +++++++++++++++++++++++++------------------------------
man/jags.Rd | 3 +
5 files changed, 61 insertions(+), 63 deletions(-)
Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Diff between HSAUR2 versions 1.1-12 dated 2015-01-05 and 1.1-13 dated 2015-01-09
Description: Functions, data sets, analyses and examples from the
second edition of the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2008). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
the package contains Sweave code for producing slides for selected
chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 10 ++----
MD5 | 42 +++++++++++++-------------
inst/NEWS | 4 ++
inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
inst/doc/Ch_analysis_of_variance.pdf |binary
inst/doc/Ch_cluster_analysis.pdf |binary
inst/doc/Ch_conditional_inference.pdf |binary
inst/doc/Ch_density_estimation.pdf |binary
inst/doc/Ch_errata.pdf |binary
inst/doc/Ch_gam.pdf |binary
inst/doc/Ch_graphical_display.pdf |binary
inst/doc/Ch_introduction_to_R.pdf |binary
inst/doc/Ch_logistic_regression_glm.pdf |binary
inst/doc/Ch_meta_analysis.pdf |binary
inst/doc/Ch_multidimensional_scaling.pdf |binary
inst/doc/Ch_multiple_linear_regression.pdf |binary
inst/doc/Ch_principal_components_analysis.pdf |binary
inst/doc/Ch_recursive_partitioning.pdf |binary
inst/doc/Ch_simple_inference.pdf |binary
inst/doc/Ch_simultaneous_inference.pdf |binary
inst/doc/Ch_survival_analysis.pdf |binary
22 files changed, 29 insertions(+), 27 deletions(-)
Title: A Handbook of Statistical Analyses Using R (1st Edition)
Diff between HSAUR versions 1.3-5 dated 2015-01-05 and 1.3-6 dated 2015-01-09
Description: Functions, data sets, analyses and examples from the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2006). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available.
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 12 +++-----
MD5 | 38 +++++++++++++-------------
inst/NEWS | 6 ++++
inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
inst/doc/Ch_analysis_of_variance.pdf |binary
inst/doc/Ch_cluster_analysis.pdf |binary
inst/doc/Ch_conditional_inference.pdf |binary
inst/doc/Ch_density_estimation.pdf |binary
inst/doc/Ch_errata.pdf |binary
inst/doc/Ch_introduction_to_R.pdf |binary
inst/doc/Ch_logistic_regression_glm.pdf |binary
inst/doc/Ch_meta_analysis.pdf |binary
inst/doc/Ch_multidimensional_scaling.pdf |binary
inst/doc/Ch_multiple_linear_regression.pdf |binary
inst/doc/Ch_principal_components_analysis.pdf |binary
inst/doc/Ch_recursive_partitioning.pdf |binary
inst/doc/Ch_simple_inference.pdf |binary
inst/doc/Ch_survival_analysis.pdf |binary
inst/doc/preface.pdf |binary
20 files changed, 30 insertions(+), 26 deletions(-)
Title: Analyzes Clickstreams based on Markov Chains
Diff between clickstream versions 1.1.2 dated 2014-07-15 and 1.1.3 dated 2015-01-09
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e. clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz
DESCRIPTION | 12 ++++-----
MD5 | 48 ++++++++++++++++++-------------------
NEWS | 9 +++++-
R/Clickstream.r | 2 -
R/clickstream-package.R | 2 -
man/MarkovChain-class.Rd | 2 -
man/Pattern-class.Rd | 2 -
man/absorbingStates-methods.Rd | 2 -
man/clickstream-package.Rd | 4 +--
man/clusterClickstreams.Rd | 2 -
man/fitMarkovChain.Rd | 2 -
man/predict-methods.Rd | 2 -
man/predict.ClickstreamClusters.Rd | 2 -
man/print.ClickstreamClusters.Rd | 2 -
man/print.Clickstreams.Rd | 2 -
man/print.MarkovChainSummary.Rd | 2 -
man/randomClicks-methods.Rd | 2 -
man/randomClickstreams.Rd | 2 -
man/readClickstreams.Rd | 2 -
man/states-methods.Rd | 2 -
man/summary-methods.Rd | 2 -
man/summary.ClickstreamClusters.Rd | 2 -
man/summary.Clickstreams.Rd | 2 -
man/transientStates-methods.Rd | 2 -
man/writeClickstreams.Rd | 8 +++---
25 files changed, 63 insertions(+), 58 deletions(-)
Title: Calculation and Application of p-variation
Diff between pvar versions 2.1 dated 2014-12-23 and 2.2 dated 2015-01-09
Description: The calculation of p-variation of the finite sample data
Author: Vygantas Butkus
Maintainer: Vygantas Butkus
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/pvar-package.R | 4 ++--
build/vignette.rds |binary
inst/tests/test-Cinternal.R | 8 ++++----
man/pvar-package.Rd | 4 ++--
vignettes/pvar_intro.Rnw | 2 +-
7 files changed, 19 insertions(+), 19 deletions(-)
Title: Flexible Randomization-Based Inference
Diff between randomizationInference versions 1.0.2 dated 2014-09-20 and 1.0.3 dated 2015-01-09
More information about randomizationInference at CRAN
Description: Allows the user to conduct randomization-based inference for a wide variety of experimental scenarios. The package leverages a potential outcomes framework to output randomization-based p-values and null intervals for test statistics geared toward any estimands of interest, according to the specified null and alternative hypotheses. Users can define custom randomization schemes so that the randomization distributions are accurate for their experimental settings. The package also creates visualizations of randomization distributions and can test multiple test statistics simultaneously.
Author: Joseph J. Lee and Tirthankar Dasgupta
Maintainer: Joseph J. Lee
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/randPlot.R | 8 ++++----
man/randPlot.Rd | 7 +++++--
man/randomizationInference-package.Rd | 6 +++---
5 files changed, 22 insertions(+), 19 deletions(-)
Permanent link
Title: Lots of Superior Depictions
Diff between LSD versions 2.5 dated 2011-11-03 and 3.0 dated 2015-01-09
Description: Create lots of colorful plots in a plethora of variations (try the LSD demotour() )
Author: Bjoern Schwalb, Achim Tresch, Phillipp Torkler, Sebastian Duemcke, Carina Demel
Maintainer: Bjoern Schwalb
LSD-2.5/LSD/R/LSDdemotour.R |only
LSD-2.5/LSD/R/LSDpie.R |only
LSD-2.5/LSD/R/clusterplot.R |only
LSD-2.5/LSD/R/colorpalette.r |only
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LSD-2.5/LSD/R/heathistogram.r |only
LSD-2.5/LSD/R/heatscatterplot.R |only
LSD-2.5/LSD/R/linesplot.r |only
LSD-2.5/LSD/R/makemovie.R |only
LSD-2.5/LSD/R/msdplot.r |only
LSD-2.5/LSD/R/plotit.r |only
LSD-2.5/LSD/R/plotmatrix.r |only
LSD-2.5/LSD/R/utilities.R |only
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LSD-2.5/LSD/man/LSD.demo.tour.Rd |only
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LSD-2.5/LSD/man/heatmapoints.Rd |only
LSD-2.5/LSD/man/kde2dplot.Rd |only
LSD-3.0/LSD/DESCRIPTION | 16 +--
LSD-3.0/LSD/MD5 | 106 +++++++++++----------
LSD-3.0/LSD/NAMESPACE | 34 ++++++-
LSD-3.0/LSD/R/LSD.align.R |only
LSD-3.0/LSD/R/LSD.clusterplot.R |only
LSD-3.0/LSD/R/LSD.color.r |only
LSD-3.0/LSD/R/LSD.comparisonplot.r |only
LSD-3.0/LSD/R/LSD.demotour.R |only
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LSD-3.0/LSD/R/LSD.fusionplot.R |only
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LSD-3.0/LSD/man/LSD.pie.Rd |only
LSD-3.0/LSD/man/align.Rd |only
LSD-3.0/LSD/man/clusterplot.Rd | 125 ++++++++++++++++++-------
LSD-3.0/LSD/man/colorpalette.Rd | 50 ++++++++--
LSD-3.0/LSD/man/comparisonplot.Rd | 95 ++++++++++++++-----
LSD-3.0/LSD/man/complementarycolor.Rd |only
LSD-3.0/LSD/man/convertcolor.Rd | 33 ++++--
LSD-3.0/LSD/man/convertgrey.Rd | 34 +++++--
LSD-3.0/LSD/man/daltonize.Rd |only
LSD-3.0/LSD/man/demotour.Rd |only
LSD-3.0/LSD/man/densitylane.Rd | 56 ++++++++---
LSD-3.0/LSD/man/disco.Rd |only
LSD-3.0/LSD/man/distinctcolors.Rd | 44 ++++++---
LSD-3.0/LSD/man/ellipsescatter.Rd | 74 +++++++++++----
LSD-3.0/LSD/man/emptyplot.Rd |only
LSD-3.0/LSD/man/fusionplot.Rd |only
LSD-3.0/LSD/man/heatbarplot.Rd | 60 +++++++++---
LSD-3.0/LSD/man/heatboxplot.Rd | 136 ++++++++++++++++++++--------
LSD-3.0/LSD/man/heathist.Rd | 83 ++++++++++++-----
LSD-3.0/LSD/man/heatpairs.Rd | 117 +++++++++++++++++-------
LSD-3.0/LSD/man/heatscatter.Rd | 121 +++++++++++++++++++-----
LSD-3.0/LSD/man/heatscatterpoints.Rd | 106 ++++++++++++++++-----
LSD-3.0/LSD/man/homer.Rd |only
LSD-3.0/LSD/man/intersphere.Rd |only
LSD-3.0/LSD/man/linesplot.Rd | 92 ++++++++++++------
LSD-3.0/LSD/man/makemovie.Rd | 48 +++++++--
LSD-3.0/LSD/man/msdplot.Rd | 94 ++++++++++++++-----
LSD-3.0/LSD/man/plotit.Rd | 105 ++++++++++++++++-----
LSD-3.0/LSD/man/plotmatrix.Rd | 78 +++++++++++-----
LSD-3.0/LSD/man/seqs.Rd |only
LSD-3.0/LSD/man/singleclusterplot.Rd | 81 ++++++++++++----
LSD-3.0/LSD/man/singlefusionplot.Rd |only
LSD-3.0/LSD/man/singlemsdplot.Rd | 58 +++++++++--
LSD-3.0/LSD/man/webdesign.Rd |only
LSD-3.0/LSD/man/windowxy.Rd | 29 ++++-
82 files changed, 1369 insertions(+), 506 deletions(-)
Title: Straightforward BibTeX and BibLaTeX Bibliography Management
Diff between RefManageR versions 0.8.40 dated 2014-10-29 and 0.8.45 dated 2015-01-09
Description: RefManageR provides tools for importing and working with
bibliographic references. It greatly enhances the bibentry class by
providing a class BibEntry which stores BibTeX and BibLaTeX references,
supports UTF-8 encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. BibTeX and BibLaTeX .bib files
can be read into R and converted to BibEntry objects. Interfaces to NCBI's
Entrez, CrossRef, and Zotero are provided for importing references and
references can be created from locally stored PDFs using Poppler. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with RMarkdown or RHTML.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean
RefManageR-0.8.40/RefManageR/man/MatchDate.Rd |only
RefManageR-0.8.40/RefManageR/man/MatchName.Rd |only
RefManageR-0.8.40/RefManageR/man/format.BibEntry.Rd |only
RefManageR-0.8.40/RefManageR/man/format_author.Rd |only
RefManageR-0.8.40/RefManageR/man/toRd.BibEntry.Rd |only
RefManageR-0.8.45/RefManageR/DESCRIPTION | 8
RefManageR-0.8.45/RefManageR/MD5 | 106 +-
RefManageR-0.8.45/RefManageR/NAMESPACE | 3
RefManageR-0.8.45/RefManageR/R/04InternalFunctions.R | 127 ++
RefManageR-0.8.45/RefManageR/R/05makeBibLatex.R | 552 ++++++-------
RefManageR-0.8.45/RefManageR/R/BibEntryExtractOp.R | 88 +-
RefManageR-0.8.45/RefManageR/R/ReadBib.R | 24
RefManageR-0.8.45/RefManageR/R/ReadCrossRef.R | 24
RefManageR-0.8.45/RefManageR/R/ReadGS.R | 46 -
RefManageR-0.8.45/RefManageR/R/ReadZotero.R | 29
RefManageR-0.8.45/RefManageR/R/WriteBib.R | 1
RefManageR-0.8.45/RefManageR/R/format.R | 37
RefManageR-0.8.45/RefManageR/R/toBiblatex.R | 30
RefManageR-0.8.45/RefManageR/inst/NEWS | 15
RefManageR-0.8.45/RefManageR/inst/doc/manual.pdf |binary
RefManageR-0.8.45/RefManageR/man/BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/BibOptions.Rd | 3
RefManageR-0.8.45/RefManageR/man/Cite.Rd | 3
RefManageR-0.8.45/RefManageR/man/FindBibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/GetBibEntryWithDOI.Rd | 3
RefManageR-0.8.45/RefManageR/man/GetDOIs.Rd | 3
RefManageR-0.8.45/RefManageR/man/GetPubMedByID.Rd | 3
RefManageR-0.8.45/RefManageR/man/GetPubMedRelated.Rd | 3
RefManageR-0.8.45/RefManageR/man/LookupPubMedID.Rd | 3
RefManageR-0.8.45/RefManageR/man/ReadBib.Rd | 3
RefManageR-0.8.45/RefManageR/man/ReadCrossRef.Rd | 3
RefManageR-0.8.45/RefManageR/man/ReadGS.Rd | 23
RefManageR-0.8.45/RefManageR/man/ReadPDFs.Rd | 3
RefManageR-0.8.45/RefManageR/man/ReadPubMed.Rd | 3
RefManageR-0.8.45/RefManageR/man/ReadZotero.Rd | 15
RefManageR-0.8.45/RefManageR/man/RefManageR-package.Rd | 3
RefManageR-0.8.45/RefManageR/man/SearchBib.Rd | 3
RefManageR-0.8.45/RefManageR/man/UpdateFieldName.Rd | 3
RefManageR-0.8.45/RefManageR/man/WriteBib.Rd | 5
RefManageR-0.8.45/RefManageR/man/as.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/as.data.frame.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/c.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/cash-.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/cash-set-.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/format.Bibentry.Rd |only
RefManageR-0.8.45/RefManageR/man/head.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/levels.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/merge.BibEntry.Rd | 11
RefManageR-0.8.45/RefManageR/man/names.BibEntry.Rd | 13
RefManageR-0.8.45/RefManageR/man/open.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/print.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/sort.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/sub-sub-.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/sub-subset-.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/subset-.BibEntry.Rd | 3
RefManageR-0.8.45/RefManageR/man/toBiblatex.Rd | 7
RefManageR-0.8.45/RefManageR/man/unlist.BibEntry.Rd | 3
57 files changed, 716 insertions(+), 538 deletions(-)
Title: An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
Diff between RcppProgress versions 0.2 dated 2015-01-07 and 0.2.1 dated 2015-01-09
Description: This package allows to display a progress bar in the R
console for long running computations taking place in c++ code,
and support for interrupting those computations even in multithreaded
code, typically using OpenMP.
Author: Karl Forner
Maintainer: Karl Forner
DESCRIPTION | 6 +++---
MD5 | 6 +++---
inst/include/interruptable_progress_monitor.hpp | 3 +--
inst/include/progress.hpp | 2 +-
4 files changed, 8 insertions(+), 9 deletions(-)
Title: Rcmdr support for the HH package
Diff between RcmdrPlugin.HH versions 1.1-40 dated 2013-10-11 and 1.1-42 dated 2015-01-09
More information about RcmdrPlugin.HH at CRAN
Description: Rcmdr menu support for many of the functions in the HH package.
The focus is on menu items for functions we use in our introductory
courses.
Author: Richard M. Heiberger, with contributions from Burt Holland
Maintainer: Richard M. Heiberger
DESCRIPTION | 16 +++++++-------
MD5 | 10 ++++-----
NAMESPACE | 5 ++--
R/Scatter3DDialog.HH.R | 16 +++++++-------
man/Scatter3DDialog.HH.Rd | 16 +++++++-------
man/scatter3d.HH.Rd | 50 +++++++++++++++++++++++-----------------------
6 files changed, 57 insertions(+), 56 deletions(-)
Permanent link
Title: Statistical Analysis and Data Display: Heiberger and Holland
Diff between HH versions 3.1-8 dated 2014-12-16 and 3.1-14 dated 2015-01-09
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger
HH-3.1-14/HH/DESCRIPTION | 10
HH-3.1-14/HH/MD5 | 39 +-
HH-3.1-14/HH/NAMESPACE | 24 -
HH-3.1-14/HH/NEWS | 80 ++++
HH-3.1-14/HH/R/likert.formula.R | 20 -
HH-3.1-14/HH/R/normal.and.t.R | 527 ++++++++++++++++++++++-------
HH-3.1-14/HH/R/normal.and.t.htest.R | 209 +----------
HH-3.1-14/HH/R/normal.and.t.power.R | 233 +++++-------
HH-3.1-14/HH/R/normal.and.t.shiny.R |only
HH-3.1-14/HH/R/normal.and.t.support.R | 116 ++----
HH-3.1-14/HH/R/normalApproxBinomial.R |only
HH-3.1-14/HH/R/normalTable.R | 106 +----
HH-3.1-14/HH/demo/00Index | 7
HH-3.1-14/HH/demo/NTplot.R |only
HH-3.1-14/HH/inst/scripts/hh2/conc.R | 372 +++++++++-----------
HH-3.1-14/HH/inst/scripts/hh2/iinf.R |only
HH-3.1-14/HH/man/HH.package.Rd | 2
HH-3.1-14/HH/man/NormalAndT.Rd |only
HH-3.1-14/HH/man/NormalAndTplot.Rd |only
HH-3.1-14/HH/man/bivariateNormal.Rd | 2
HH-3.1-14/HH/man/likert.Rd | 14
HH-3.1-14/HH/man/normal.and.t.and.power.Rd | 94 ++---
HH-3.1-14/HH/man/normalApproxBinomial.Rd |only
HH-3.1-14/HH/man/print.NormalAndTplot.Rd |only
HH-3.1-8/HH/man/normal.and.t.Rd |only
25 files changed, 997 insertions(+), 858 deletions(-)
Title: FastRCS Robust Fit of Multivariable Linear Regression Model
Diff between FastRCS versions 0.0.5 dated 2014-11-13 and 0.0.6 dated 2015-01-09
Description: The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the multivariable linear regression model and outliers detection.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
FastRCS-0.0.5/FastRCS/data/DontGetKicked.txt.gz |only
FastRCS-0.0.5/FastRCS/data/Slump.txt.gz |only
FastRCS-0.0.5/FastRCS/man/DontGetKicked.Rd |only
FastRCS-0.0.5/FastRCS/man/Slump.Rd |only
FastRCS-0.0.5/FastRCS/man/numStarts.Rd |only
FastRCS-0.0.6/FastRCS/DESCRIPTION | 6 -
FastRCS-0.0.6/FastRCS/MD5 | 22 ++----
FastRCS-0.0.6/FastRCS/NAMESPACE | 4 -
FastRCS-0.0.6/FastRCS/R/FastRCS.R | 16 ++--
FastRCS-0.0.6/FastRCS/data/Lemons.txt.gz |only
FastRCS-0.0.6/FastRCS/man/FRCSnumStarts.Rd |only
FastRCS-0.0.6/FastRCS/man/FastRCS-package.Rd | 2
FastRCS-0.0.6/FastRCS/man/FastRCS.Rd | 25 +++++--
FastRCS-0.0.6/FastRCS/man/Lemons.Rd |only
FastRCS-0.0.6/FastRCS/man/plot.FastRCS.Rd | 2
FastRCS-0.0.6/FastRCS/src/FastRCS.cpp | 84 ++++++++++++++----------
16 files changed, 95 insertions(+), 66 deletions(-)
Title: Bayesian Analysis of Generalized Elliptical Semiparametric
Models and Flexible Measurement Error Models.
Diff between BayesGESM versions 1.1 dated 2014-12-10 and 1.2 dated 2015-01-09
Description: This package allows to perform the statistical inference based on the Bayesian approach for regression models under the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distributions, i.e., additive errors follow a scale mixtures of normal distributions. The regression models considered in this package are: (i) Generalized elliptical semiparametric models, where both location and dispersion parameters of the response variable distribution include nonparametric additive components described by using B-splines; and (ii) Flexible measurement error models, which admit explanatory variables with and without measurement additive errors as well as the presence of a nonparametric component approximated by using B-splines.
Author: Luz Marina Rondon
Maintainer: Luz Marina Rondon
BayesGESM-1.1/BayesGESM/R/BayesGESM.R |only
BayesGESM-1.1/BayesGESM/R/mcmc.R |only
BayesGESM-1.1/BayesGESM/R/summary.BayesGESM.R |only
BayesGESM-1.1/BayesGESM/man/BayesGESM.Rd |only
BayesGESM-1.1/BayesGESM/man/mcmc.Rd |only
BayesGESM-1.1/BayesGESM/man/summary.BayesGESM.Rd |only
BayesGESM-1.2/BayesGESM/DESCRIPTION | 14 +++---
BayesGESM-1.2/BayesGESM/MD5 | 34 ++++++++-------
BayesGESM-1.2/BayesGESM/NAMESPACE | 2
BayesGESM-1.2/BayesGESM/R/bsp.R | 16 +++++--
BayesGESM-1.2/BayesGESM/R/bsp.graph.R |only
BayesGESM-1.2/BayesGESM/R/fmem.R | 30 +++++++------
BayesGESM-1.2/BayesGESM/R/gesm.R |only
BayesGESM-1.2/BayesGESM/R/mcmc.gesm.R |only
BayesGESM-1.2/BayesGESM/R/summary.fmem.R | 2
BayesGESM-1.2/BayesGESM/R/summary.gesm.R |only
BayesGESM-1.2/BayesGESM/man/BayesGESM-package.Rd | 50 ++++++++++++++++-------
BayesGESM-1.2/BayesGESM/man/bsp.Rd | 12 ++++-
BayesGESM-1.2/BayesGESM/man/bsp.graph.Rd |only
BayesGESM-1.2/BayesGESM/man/fmem.Rd | 18 +++++++-
BayesGESM-1.2/BayesGESM/man/gesm.Rd |only
BayesGESM-1.2/BayesGESM/man/mcmc.fmem.Rd | 2
BayesGESM-1.2/BayesGESM/man/mcmc.gesm.Rd |only
BayesGESM-1.2/BayesGESM/man/summary.fmem.Rd | 2
BayesGESM-1.2/BayesGESM/man/summary.gesm.Rd |only
25 files changed, 121 insertions(+), 61 deletions(-)
Title: True Random Numbers using random.org
Diff between random versions 0.2.2 dated 2013-12-11 and 0.2.3 dated 2015-01-08
Description: The true random number service provided by the random.org
website created by Mads Haahr samples atmospheric noise via radio
tuned to an unused broadcasting frequency together with a skew
correction algorithm due to John von Neumann. More background is available
in the included vignette based on an essay by Mads Haahr. In its current
form, the package offers functions to retrieve random integers, randomized
sequences and random strings.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 17 ++++++++++++++
DESCRIPTION | 28 +++++++++++------------
MD5 | 15 ++++++------
NAMESPACE | 2 +
R/random.R | 54 +++++++++++++++++++++++++++++++---------------
README.md |only
build/vignette.rds |binary
inst/doc/random-essay.pdf |binary
inst/doc/random-intro.pdf |binary
9 files changed, 78 insertions(+), 38 deletions(-)
Title: Functions to support the Multicriteria Decision Aiding process
Diff between MCDA versions 0.0.7 dated 2014-12-09 and 0.0.8 dated 2015-01-08
Description: MCDA, which stands for Multicriteria Decision Aiding, implements functions which can be useful to support the analyst in the decision aiding process involving multiple, conflicting criteria. These functions include, but are not limited to, data pre-processing tools, preference elicitation procedures, aggregation functions, as well as post-processing techniques and data visualisation functions.
Author: Patrick Meyer, Sébastien Bigaret.
Maintainer: Patrick Meyer
DESCRIPTION | 10 +++++-----
MD5 | 7 +++++--
NAMESPACE | 1 +
R/normalizePerformanceTable.R |only
man/normalizePerformanceTable.Rd |only
tests/normalizePerformanceTable.R |only
6 files changed, 11 insertions(+), 7 deletions(-)
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Diff between MATA versions 0.1 dated 2014-11-22 and 0.2 dated 2015-01-08
Description: Provides a function for calculating the Model-Averaged Tail Area
Wald (MATA-Wald) confidence interval, which is generated from single-model
estimators and AIC model weights
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/MATA_package_source.R | 7 ++++---
man/mata.wald.Rd | 7 ++++---
4 files changed, 15 insertions(+), 13 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.0 dated 2014-12-08 and 0.2.1 dated 2015-01-08
Description: This package implements circular visualization
(http://circos.ca/) in R. Due to the natural born feature of R to draw statistical
graphics, this package can provide a more general and flexible way to
visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 8
MD5 | 80 ++++----
NEWS | 19 +
R/chordDiagram.R | 12 +
R/genomic.R | 49 +++-
R/global.R | 19 +
R/plot.R | 61 ++++--
R/utils.R | 13 +
R/zzz.R | 16 -
inst/doc/circlize.R | 8
inst/doc/circlize.Rnw | 15 -
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.R | 6
inst/doc/circular_phylogenetic_tree.Rnw | 5
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.R | 6
inst/doc/circular_visualization_of_matrix.Rnw | 4
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.R | 2
inst/doc/draw_ideogram.Rnw | 2
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.R | 176 +++++++++++++++++
inst/doc/genomic_plot.Rnw | 147 ++++++++++++++
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.R | 5
inst/doc/interesting_graphics.Rnw | 5
inst/doc/interesting_graphics.pdf |binary
man/circos.genomicText.rd | 2
man/circos.text.rd | 8
man/circos.trackText.rd | 4
man/draw.sector.rd | 66 +++---
man/posTransform.text.rd | 248 ++++++++++++-------------
vignettes/circlize.Rnw | 15 -
vignettes/circular_phylogenetic_tree.Rnw | 5
vignettes/circular_visualization_of_matrix.Rnw | 4
vignettes/draw_ideogram.Rnw | 2
vignettes/genomic_plot.Rnw | 147 ++++++++++++++
vignettes/interesting_graphics.Rnw | 5
vignettes/src/intro-07-direction.R | 8
vignettes/src/intro-09-text-niceFacing.R | 59 +++++
vignettes/src/intro-09-text.R | 7
41 files changed, 913 insertions(+), 325 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Diff between AICcmodavg versions 2.0-1 dated 2014-10-17 and 2.0-2 dated 2015-01-08
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). The package also features functions to conduct classic model averaging (multimodel inference) for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with Cox proportional hazards models and conditional logistic regression ('coxph' and 'coxme' classes), linear models ('lm' class), generalized linear models ('glm', 'vglm', 'hurdle', and 'zeroinfl' classes), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' and 'merMod' classes), multinomial and ordinal logistic regressions ('multinom'}, 'polr', 'clm', and 'clmm' classes), robust regression models ('rlm' class), beta regression models ('betareg' class), parametric survival models ('survreg' class), nonlinear models ('nls' and 'gnls' classes), and nonlinear mixed models ('nlme' and 'nlmer' classes). The package also supports various models of 'unmarkedFit' and 'maxLikeFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 12
MD5 | 36 +-
NAMESPACE | 70 ++++-
R/Nmix.gof.test.R | 430 ++++++++++++++++++++++++++++++-
R/aictab.R | 186 +++++++++++--
R/boot.wt.r | 123 ++++++++-
R/c_hat.R | 103 ++++---
R/evidence.R | 5
R/mb.gof.test.R | 627 ++++++++++++++++++++++++++++++++++++++++++++--
R/xtable.r |only
inst/NEWS | 20 +
man/AICcmodavg-package.Rd | 10
man/Nmix.gof.test.Rd | 132 +++++----
man/aictab.Rd | 18 -
man/boot.wt.Rd | 8
man/c_hat.Rd | 71 +++--
man/evidence.Rd | 7
man/mb.gof.test.Rd | 183 +++++++++----
man/modavg.Rd | 67 ++--
man/xtable.Rd |only
20 files changed, 1788 insertions(+), 320 deletions(-)
Title: Voxelwise semiparametrics
Diff between vows versions 0.3 dated 2014-08-29 and 0.3.1 dated 2015-01-08
Description: Parametric and semiparametric inference for massively parallel
models, i.e., a large number of models with common design matrix, as often
occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, and Ruixin Tan
Maintainer: Philip Reiss
DESCRIPTION | 9 +++++----
MD5 | 2 +-
2 files changed, 6 insertions(+), 5 deletions(-)
Title: Tools inspired by Stata to manipulate tabular data
Diff between statar versions 0.1.2 dated 2014-10-31 and 0.1.3 dated 2015-01-08
Description: statar makes it easier to work with tabular datasets. The package
includes a set of functions to clean and summarize variables, to join
datasets using an SQL-syntax, to manipulate datasets with a panel structure
(elapsed dates, lead/lag, rolling functions, fill in missing values based
on previous dates, add rows for missing dates). The package also includes
functions to emulate Stata and Julia string and expression interpolation.
statar is based on the data.table package and is inspired by Stata.
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez
statar-0.1.2/statar/R/duplicates.R |only
statar-0.1.2/statar/R/spread.R |only
statar-0.1.2/statar/man/duplicates.Rd |only
statar-0.1.3/statar/DESCRIPTION | 10
statar-0.1.3/statar/MD5 | 83 +++---
statar-0.1.3/statar/NAMESPACE | 10
statar-0.1.3/statar/R/elapsed_dates.R | 70 +++++
statar-0.1.3/statar/R/find_duplicates.R |only
statar-0.1.3/statar/R/spread_.R |only
statar-0.1.3/statar/R/statar.R | 1
statar-0.1.3/statar/R/sum_up.R | 298 ++++++++----------------
statar-0.1.3/statar/README.md | 2
statar-0.1.3/statar/build/vignette.rds |binary
statar-0.1.3/statar/inst/doc/macros.Rmd | 9
statar-0.1.3/statar/inst/doc/macros.html | 6
statar-0.1.3/statar/inst/doc/merge-records.Rmd |only
statar-0.1.3/statar/inst/doc/merge-records.html |only
statar-0.1.3/statar/inst/doc/panel-data.Rmd | 18 +
statar-0.1.3/statar/inst/doc/panel-data.html | 17 +
statar-0.1.3/statar/inst/doc/summary.Rmd | 64 +++--
statar-0.1.3/statar/inst/doc/summary.html | 64 +++--
statar-0.1.3/statar/man/bin.Rd | 3
statar-0.1.3/statar/man/demean.Rd | 3
statar-0.1.3/statar/man/elapsed.Rd | 3
statar-0.1.3/statar/man/fill_gap.Rd | 3
statar-0.1.3/statar/man/find_duplicates.Rd |only
statar-0.1.3/statar/man/floor_date.Rd | 3
statar-0.1.3/statar/man/graph.Rd | 3
statar-0.1.3/statar/man/join.Rd | 3
statar-0.1.3/statar/man/lead-lag.Rd | 3
statar-0.1.3/statar/man/pastem.Rd | 3
statar-0.1.3/statar/man/roll.Rd | 3
statar-0.1.3/statar/man/sample_mode.Rd | 3
statar-0.1.3/statar/man/setdrop.Rd | 3
statar-0.1.3/statar/man/setkeep.Rd | 3
statar-0.1.3/statar/man/setmutate.Rd | 3
statar-0.1.3/statar/man/setmutate_each.Rd | 3
statar-0.1.3/statar/man/setna.Rd | 3
statar-0.1.3/statar/man/statar.Rd | 3
statar-0.1.3/statar/man/sum_up.Rd | 11
statar-0.1.3/statar/man/tag.Rd | 3
statar-0.1.3/statar/man/tempname.Rd | 3
statar-0.1.3/statar/man/winsorize.Rd | 3
statar-0.1.3/statar/vignettes/macros.Rmd | 9
statar-0.1.3/statar/vignettes/merge-records.Rmd |only
statar-0.1.3/statar/vignettes/panel-data.Rmd | 18 +
statar-0.1.3/statar/vignettes/summary.Rmd | 64 +++--
47 files changed, 464 insertions(+), 350 deletions(-)
Title: brnn (Bayesian regularization for feed-forward neural networks)
Diff between brnn versions 0.4 dated 2014-12-05 and 0.5 dated 2015-01-08
Description: Bayesian regularization for feed-forward neural networks
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/brnn.R | 2 +-
inst/history.txt | 2 ++
src/Makevars | 4 ++--
src/Makevars.win | 6 +++---
6 files changed, 17 insertions(+), 15 deletions(-)
Title: Extraction of Business Financial Information from XBRL Documents
Diff between XBRL versions 0.99.13 dated 2014-11-18 and 0.99.14 dated 2015-01-08
Description:
XBRL is a package suited to extract business financial information from
an Extensible Business Reporting Language (XBRL) instance file and the
associated collection of files that defines its Discoverable Taxonomy
Set (DTS). These files are usually disseminated across different remote
locations.
XBRL documents employ many technologies defined by XML standards, such
as XML Schema, Namespaces, XLink, and XPath, which make the extraction
of information involved. The functions provided by this package
address this complexity, returning data frames containing the enclosed
information readily available to perform analyses.
XBRL has been successfully tested in analyzing 10-K and 10-Q
submissions from USA filing companies that are publicly available at
the EDGAR system of the Securities and Exchange Commission (SEC).
As published taxonomy files (such as
"http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd")
are immutable and are used by most filers, XBRL offers the option of
downloading them only the first time they are referred, keeping a
local cache copy that can be used from then on. This speeds-up the
process, specially on slow connections.
XBRL is not and does not aim to be (at least yet) a validating XBRL
processor.
XBRL is still a work in progress. As such, functions and produced data
frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/xbrlProcessElements.cpp | 8 ++++++++
4 files changed, 21 insertions(+), 7 deletions(-)
Title: Fitting Semi-parametric Log-symmetric Regression Models
Diff between ssym versions 1.5.1 dated 2014-10-07 and 1.5.2 dated 2015-01-08
Description: This package allows to to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, and asymmetric. In this setup, both median and skewness of the response variable distribution are explicitly modeled through semi-parametric functions, whose nonparametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas
Maintainer: Luis Hernando Vanegas
DESCRIPTION | 14 +--
MD5 | 82 ++++++++++++-----------
R/AIC.ssym.R |only
R/BIC.ssym.R |only
R/itpM.R | 4 -
R/itpM2.R | 8 +-
R/np.graph.R | 7 +
R/plot.ssym.R | 2
R/ssym.l.R | 50 +++++++-------
R/ssym.nl.R | 22 +++---
R/summary.ssym.R | 9 +-
data/Biaxial.rda |binary
data/Claims.rda |binary
data/Erabbits.rda |binary
data/Ovocytes.rda |binary
data/Snacks.rda |binary
data/gdp.rda |binary
man/AIC.ssym.Rd |only
man/BIC.ssym.Rd |only
man/Biaxial.Rd | 3
man/Claims.Rd | 2
man/Ovocytes.Rd | 9 +-
man/Snacks.Rd | 15 ++--
man/coef.ssym.Rd | 2
man/gdp.Rd | 8 +-
man/influence.ssym.Rd | 9 +-
man/itpE.Rd | 2
man/itpE2.Rd | 2
man/itpE3.Rd | 2
man/itpM.Rd | 2
man/itpM2.Rd | 2
man/itpM3.Rd | 2
man/lambda.hat.Rd | 19 +++--
man/logLik.ssym.Rd | 2
man/ncs.Rd | 9 +-
man/np.graph.Rd | 2
man/plot.ssym.Rd | 2
man/print.ssym.Rd | 2
man/psp.Rd | 12 +--
man/rvgs.Rd | 4 -
man/ssym-package.Rd | 14 ++-
man/ssym.l.Rd | 167 +++++++++++++++++++++++++++++++----------------
man/ssym.nl.Rd | 176 ++++++++++++++++++++++++++------------------------
man/vcov.ssym.Rd | 2
44 files changed, 382 insertions(+), 287 deletions(-)
Title: Simulates Correlated Multinomial Responses
Diff between SimCorMultRes versions 1.2 dated 2014-03-02 and 1.3.0 dated 2015-01-08
Description: Simulates correlated multinomial responses by utilizing threshold approaches under a cumulative link model, a continuation ratio model or a baseline-category logit marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
SimCorMultRes-1.2/SimCorMultRes/NEWS |only
SimCorMultRes-1.2/SimCorMultRes/inst/doc/Vignette.R |only
SimCorMultRes-1.2/SimCorMultRes/inst/doc/Vignette.Rnw |only
SimCorMultRes-1.2/SimCorMultRes/inst/doc/Vignette.pdf |only
SimCorMultRes-1.2/SimCorMultRes/vignettes/Vignette.Rnw |only
SimCorMultRes-1.3.0/SimCorMultRes/DESCRIPTION | 13 ++--
SimCorMultRes-1.3.0/SimCorMultRes/MD5 | 29 +++++-----
SimCorMultRes-1.3.0/SimCorMultRes/R/rmult.bcl.R | 1
SimCorMultRes-1.3.0/SimCorMultRes/R/rmult.clm.R | 2
SimCorMultRes-1.3.0/SimCorMultRes/R/rmult.crm.R | 2
SimCorMultRes-1.3.0/SimCorMultRes/build/vignette.rds |binary
SimCorMultRes-1.3.0/SimCorMultRes/inst/CITATION |only
SimCorMultRes-1.3.0/SimCorMultRes/inst/NEWS |only
SimCorMultRes-1.3.0/SimCorMultRes/inst/doc/SCMRvin.R |only
SimCorMultRes-1.3.0/SimCorMultRes/inst/doc/SCMRvin.Rnw |only
SimCorMultRes-1.3.0/SimCorMultRes/inst/doc/SCMRvin.pdf |only
SimCorMultRes-1.3.0/SimCorMultRes/man/SimCorMultRes-package.Rd | 4 -
SimCorMultRes-1.3.0/SimCorMultRes/man/rmult.bcl.Rd | 6 +-
SimCorMultRes-1.3.0/SimCorMultRes/man/rmult.clm.Rd | 4 +
SimCorMultRes-1.3.0/SimCorMultRes/man/rmult.crm.Rd | 2
SimCorMultRes-1.3.0/SimCorMultRes/vignettes/SCMRvin.Rnw |only
21 files changed, 36 insertions(+), 27 deletions(-)
Title: Shrinkage Covariance Matrix Estimators
Diff between ShrinkCovMat versions 1.0.3 dated 2014-11-02 and 1.1.0 dated 2015-01-08
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
DESCRIPTION | 10 +++++-----
MD5 | 16 ++++++++--------
inst/CITATION | 9 +++++----
inst/NEWS | 3 +++
man/ShrinkCovMat-package.Rd | 7 +++----
man/shrinkcovmat.equal.Rd | 2 +-
man/shrinkcovmat.identity.Rd | 2 +-
man/shrinkcovmat.unequal.Rd | 2 +-
man/targetselection.Rd | 6 +++---
9 files changed, 30 insertions(+), 27 deletions(-)
Title: Multivariate Constructs
Diff between multicon versions 1.3 dated 2014-10-30 and 1.5 dated 2015-01-08
Description: Includes functions designed to examine relationships among multivariate constructs (e.g., personality). This includes functions for profile (within-person) analysis, dealing with large numbers of analyses, lens model analyses, and structural summary methods for data with circumplex structure. The package also includes functions for graphically comparing and displaying group means.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman
DESCRIPTION | 12 +--
MD5 | 26 +++++---
R/diffPlot.default.r | 155 +++++++++++++++++++++++++++---------------------
R/diffPlot.formula.r | 140 ++++++++++++++++++++++++-------------------
R/lensDetect.r |only
R/lensModel.r |only
R/plotProfile.R |only
R/print.lensMod.r |only
R/scoreTest.R |only
data/lensData.rdata |only
man/diffPlot.Rd | 11 ++-
man/lensData.rd |only
man/lensDetect.rd |only
man/lensModel.rd |only
man/plotProfile.Rd |only
man/print.lensMod.rd |only
man/print.q.cor.rd | 2
man/scoreTest.Rd |only
man/vector.alpha.Rd | 4 -
man/vector.splithalf.Rd | 5 -
20 files changed, 204 insertions(+), 151 deletions(-)
Title: A Connection Interface to Libcurl
Diff between curl versions 0.3 dated 2014-12-01 and 0.4 dated 2015-01-08
Description: The curl() function provides a drop-in replacement for base url()
with better performance and support for http 2.0, ssl (https://, ftps://),
gzip, deflate and other libcurl goodies. This interface is implemented
using the RConnection API in order to support incremental processing of
both binary and text streams. If you are looking for a more-user-friendly
http client, try the RCurl or httr packages instead.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 8 ++++----
LICENSE | 2 +-
MD5 | 29 +++++++++++++++++++----------
NAMESPACE | 9 ++++++++-
NEWS | 5 +++++
R/curl.R | 8 ++++----
R/curl_escape.R |only
R/curl_version.R |only
configure | 15 +++++++++------
configure.win |only
man/curl.Rd | 11 ++++++-----
man/curl_download.Rd | 3 ++-
man/utilities.Rd |only
src/Makevars.win | 3 ++-
src/curl-symbols.h |only
src/curl.c | 2 +-
src/escape.c |only
src/options.c |only
src/options.h |only
src/version.c |only
20 files changed, 61 insertions(+), 34 deletions(-)
Title: spatial and spatio-temporal geostatistical modelling, prediction
and simulation
Diff between gstat versions 1.0-19 dated 2014-04-02 and 1.0-20 dated 2015-01-08
Description: variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 8 +--
MD5 | 91 +++++++++++++++++------------------
NAMESPACE | 2
R/hscat.R | 5 +
R/krige.R | 6 +-
R/krige0.R | 119 ++++++++++++++++++++++++++++++++--------------
R/variogramST.R | 42 ++++++++--------
build/vignette.rds |binary
configure.in | 4 +
data/coalash.rda |binary
data/fulmar.rda |binary
data/jura.rda |binary
data/meuse.all.rda |binary
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data/sic2004.rda |binary
data/sic97.rda |binary
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data/walker.rda |binary
data/wind.rda |binary
demo/00Index | 2
demo/a2p.R | 33 +-----------
demo/snow.R | 14 +++--
demo/stkrige.R | 10 +--
inst/ChangeLog | 111 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/gstat.R | 2
inst/doc/gstat.Rnw | 2
inst/doc/gstat.pdf |binary
inst/doc/prs.pdf |binary
inst/doc/st.pdf |binary
man/hscat.Rd | 3 -
man/jura.Rd | 98 ++++++++++++++++++++++++++++---------
man/krigeST.Rd | 6 +-
man/predict.gstat.Rd | 23 +++++---
man/vgmArea.Rd |only
man/wind.Rd | 10 +--
src/lex.c | 53 ++++++++++++--------
src/lex.l | 13 +++++
src/s.c | 2
tests/na.action.Rout.save | 22 ++++----
tests/unproj.Rout.save | 8 +--
tests/windst.Rout.save | 14 ++---
vignettes/gstat.Rnw | 2
vignettes/gstat.Rout.save | 2
47 files changed, 468 insertions(+), 239 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-13 dated 2014-12-18 and 3.2-13.1 dated 2015-01-08
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 7 -
DESCRIPTION | 6
MD5 | 110 ++++++++---------
NAMESPACE | 8 -
R/AT.r | 65 +++++-----
R/LM.bpm.r | 14 +-
R/SemiParBIVProbit.fit.R | 8 -
R/SemiParBIVProbit.fit.post.r | 33 +++--
R/SemiParBIVProbit.fit1.R | 15 +-
R/SemiParBIVProbit.r | 26 ++--
R/adjCov.r | 13 +-
R/bprobgHs.r | 73 +++++++----
R/bprobgHsPL.r | 107 +++++++++++-----
R/bprobgHsPO.r | 69 +++++++---
R/bprobgHsSS.r | 74 ++++++++---
R/mb.r | 217 ++++++++++++++++++++++++++++++++--
R/print.AT.r | 2
R/print.SemiParBIVProbit.r | 2
R/print.est.prev.r | 2
R/print.mb.r |only
R/print.summary.SemiParBIVProbit.r | 2
R/sem.checks.r | 9 -
R/startSS.r | 8 -
R/summary.SemiParBIVProbit.r | 61 +++++++--
R/working.comp.r | 6
R/working.comp1.r | 4
R/working.comp3.r | 6
man/AT.Rd | 33 ++---
man/LM.bpm.Rd | 30 ++--
man/S.m.Rd | 2
man/S.mPL.Rd | 3
man/SemiParBIVProbit-package.Rd | 43 ++++--
man/SemiParBIVProbit.Rd | 92 ++++++++------
man/SemiParBIVProbitObject.Rd | 58 +++------
man/VuongClarke.bcm.Rd | 4
man/adjCov.Rd | 2
man/adjCovSD.Rd | 2
man/bprobgHs.Rd | 4
man/bprobgHsPL.Rd | 4
man/bprobgHsPO.Rd | 12 -
man/bprobgHsSS.Rd | 6
man/est.prev.Rd | 12 +
man/gt.bpm.Rd | 17 ++
man/mb.Rd | 63 +++++++--
man/plot.SemiParBIVProbit.Rd | 8 -
man/predict.SemiParBIVProbit.Rd | 4
man/print.AT.Rd | 6
man/print.SemiParBIVProbit.Rd | 2
man/print.est.prev.Rd | 4
man/print.mb.Rd |only
man/print.summary.SemiParBIVProbit.Rd | 2
man/sem.checks.Rd | 2
man/startSS.Rd | 2
man/summary.SemiParBIVProbit.Rd | 40 +++---
man/working.comp.Rd | 2
man/working.comp1.Rd | 2
man/working.comp3.Rd | 2
57 files changed, 934 insertions(+), 476 deletions(-)
Permanent link
Title: Deconvolution of Tumour Profiles
Diff between ISOpureR versions 1.0.4 dated 2014-11-16 and 1.0.8 dated 2015-01-08
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using
the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires
mixed tumour profiles and a set of unmatched "basis" normal profiles.
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D
Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros
ISOpureR-1.0.4/ISOpureR/inst/extdata/Beer/beer.ISOpureS1model.2500.transcripts.43.patients.RData |only
ISOpureR-1.0.4/ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.2500.transcripts.43.patients.rounded.RData |only
ISOpureR-1.0.4/ISOpureR/inst/extdata/Beer/beer.normaldata.2500.transcripts.RData |only
ISOpureR-1.0.4/ISOpureR/inst/extdata/Beer/beer.tumordata.2500.transcripts.43.patients.RData |only
ISOpureR-1.0.8/ISOpureR/DESCRIPTION | 12 +--
ISOpureR-1.0.8/ISOpureR/MD5 | 40 +++++-----
ISOpureR-1.0.8/ISOpureR/NAMESPACE | 2
ISOpureR-1.0.8/ISOpureR/NEWS |only
ISOpureR-1.0.8/ISOpureR/R/ISOpure.util.logsum.R | 8 +-
ISOpureR-1.0.8/ISOpureR/R/RcppExports.R |only
ISOpureR-1.0.8/ISOpureR/inst/doc/ISOpureRGuide.Rnw | 36 ++++-----
ISOpureR-1.0.8/ISOpureR/inst/doc/ISOpureRGuide.pdf |binary
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ISOpureR-1.0.8/ISOpureR/tests/test.ISOpureS1.model_optimize.mm_functions.R | 4 -
ISOpureR-1.0.8/ISOpureR/tests/test.ISOpureS1.model_optimize.theta_functions.R | 4 -
ISOpureR-1.0.8/ISOpureR/tests/test.ISOpureS2.model_optimize.cc_functions.R | 4 -
ISOpureR-1.0.8/ISOpureR/tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R | 4 -
ISOpureR-1.0.8/ISOpureR/tests/test.ISOpureS2.model_optimize.theta_functions.R | 4 -
ISOpureR-1.0.8/ISOpureR/vignettes/ISOpureRGuide.Rnw | 36 ++++-----
26 files changed, 89 insertions(+), 79 deletions(-)
Title: A Unified Framework for Input-Output Operations in R
Diff between io versions 0.2.1 dated 2014-12-19 and 0.2.2 dated 2015-01-08
Description: One function to read files. One function to write files. One
function to direct plots to screen or file. Automatic file format inference
and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
R/hdf5.R | 8 +++++---
tests/testthat/helper.R | 19 ++++++++++++++++++-
4 files changed, 31 insertions(+), 11 deletions(-)
More information about interferenceCI at CRAN
Permanent link
Title: Visually Exploring Random Forests
Diff between ggRandomForests versions 1.1.2 dated 2014-12-25 and 1.1.3 dated 2015-01-08
More information about ggRandomForests at CRAN
Description: Graphics for Random Forests using the randomForestSRC package for survival, regression and
classification forests and ggplot2 package plotting.
Author: John Ehrlinger
Maintainer: John Ehrlinger
ggRandomForests-1.1.2/ggRandomForests/R/gg_error.ggRandomForests.R |only
ggRandomForests-1.1.2/ggRandomForests/R/gg_interaction.ggRandomForests.R |only
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ggRandomForests-1.1.3/ggRandomForests/R/calc_roc.R | 50 -
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ggRandomForests-1.1.3/ggRandomForests/R/partial_coplot_data.R | 12
ggRandomForests-1.1.3/ggRandomForests/R/partial_data.R | 11
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ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_interaction.R | 46 +
ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_minimal_depth.R | 52 +
ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_minimal_vimp.R | 56 +
ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_partial.R | 83 ++
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ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_rfsrc.R | 167 ++---
ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_roc.R | 16
ggRandomForests-1.1.3/ggRandomForests/R/plot.gg_survival.R | 16
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ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_interaction.Rd | 44 +
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_minimal_depth.Rd | 51 +
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_minimal_vimp.Rd | 56 +
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_partial.Rd | 83 ++
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_partial_list.Rd | 87 ++
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_rfsrc.Rd | 56 +
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_roc.Rd | 16
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_survival.Rd | 16
ggRandomForests-1.1.3/ggRandomForests/man/plot.gg_variable.Rd | 67 +-
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ggRandomForests-1.1.3/ggRandomForests/man/varsel_data.Rd | 8
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_error.R | 4
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_interaction.R | 72 ++
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_minimal_depth.R | 79 ++
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_minimal_vimp.R | 69 ++
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_partial.R | 85 ++
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_partial_coplot.R |only
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_rfsrc.R | 69 --
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_roc.R | 91 ++
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_survival.R | 119 ++-
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_variable.R | 78 +-
ggRandomForests-1.1.3/ggRandomForests/tests/testthat/test_gg_vimp.R | 49 +
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Permanent link
Title: FastHCS Robust Algortihm for Principal Component Analysis
Diff between FastHCS versions 0.0.3 dated 2014-11-13 and 0.0.4 dated 2015-01-08
Description: The FastHCS algorithm of Schmitt and Vakili (2014) for high-dimensional, robust PCA modelling and associated outlier detection and diagnostic tools.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
FastHCS-0.0.3/FastHCS/man/numStarts.Rd |only
FastHCS-0.0.4/FastHCS/DESCRIPTION | 8 +-
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FastHCS-0.0.4/FastHCS/R/FastHCS.R | 36 ++++++++----
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FastHCS-0.0.4/FastHCS/man/FastHCS-package.Rd | 2
FastHCS-0.0.4/FastHCS/man/FastHCS.Rd | 28 +++++++--
FastHCS-0.0.4/FastHCS/man/Ionosphere.Rd | 2
FastHCS-0.0.4/FastHCS/man/MultipleFeatures.Rd | 2
FastHCS-0.0.4/FastHCS/man/Tablets.Rd | 2
FastHCS-0.0.4/FastHCS/man/plot.FastHCS.Rd | 2
FastHCS-0.0.4/FastHCS/src/FastHCS.cpp | 73 ++++++++++++++------------
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Title: Tools for the Analysis of Epidemiological Data
Diff between epiR versions 0.9-61 dated 2014-12-17 and 0.9-62 dated 2015-01-08
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson
Maintainer: Mark Stevenson
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/epi.indirectadj.R | 2 +-
man/epi.indirectadj.Rd | 2 +-
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Expected Maximum Profit Classification Performance Measure
Diff between EMP versions 1.0.2 dated 2014-08-24 and 2.0.0 dated 2015-01-08
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014).
Author: Cristian Bravo, Seppe vanden Broucke and Thomas Verbraken
Maintainer: Cristian Bravo
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Title: A Grammar of Data Manipulation
Diff between dplyr versions 0.3.0.2 dated 2014-10-11 and 0.4.0 dated 2015-01-08
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham
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dplyr-0.4.0/dplyr/DESCRIPTION | 35
dplyr-0.4.0/dplyr/MD5 | 462 ++-
dplyr-0.4.0/dplyr/NAMESPACE | 51
dplyr-0.4.0/dplyr/R/RcppExports.R | 36
dplyr-0.4.0/dplyr/R/bench-compare.r | 6
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dplyr-0.4.0/dplyr/R/data-lahman.r | 6
dplyr-0.4.0/dplyr/R/dataframe.R | 286 ++
dplyr-0.4.0/dplyr/R/dbi-s3.r | 9
dplyr-0.4.0/dplyr/R/distinct.R | 56
dplyr-0.4.0/dplyr/R/do.r | 261 --
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dplyr-0.4.0/dplyr/R/src-postgres.r | 11
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dplyr-0.4.0/dplyr/R/tally.R | 6
dplyr-0.4.0/dplyr/R/tbl-cube.r | 138 +
dplyr-0.4.0/dplyr/R/tbl-df.r | 179 +
dplyr-0.4.0/dplyr/R/tbl-dt.r | 302 ++
dplyr-0.4.0/dplyr/R/tbl-sql.r | 440 +++
dplyr-0.4.0/dplyr/R/translate-sql.r | 4
dplyr-0.4.0/dplyr/R/type-sum.r | 7
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dplyr-0.4.0/dplyr/README.md | 147 -
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dplyr-0.4.0/dplyr/inst/doc/databases.Rmd | 28
dplyr-0.4.0/dplyr/inst/doc/databases.html | 823 ++-----
dplyr-0.4.0/dplyr/inst/doc/hybrid-evaluation.R | 4
dplyr-0.4.0/dplyr/inst/doc/hybrid-evaluation.Rmd | 19
dplyr-0.4.0/dplyr/inst/doc/hybrid-evaluation.html | 509 +---
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dplyr-0.4.0/dplyr/inst/doc/introduction.Rmd | 38
dplyr-0.4.0/dplyr/inst/doc/introduction.html | 1163 +++-------
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dplyr-0.4.0/dplyr/inst/doc/new-sql-backend.Rmd | 20
dplyr-0.4.0/dplyr/inst/doc/new-sql-backend.html | 368 ---
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dplyr-0.4.0/dplyr/inst/doc/window-functions.html | 927 +++----
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dplyr-0.4.0/dplyr/inst/include/dplyr/JoinVisitorImpl.h | 450 ++-
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dplyr-0.4.0/dplyr/inst/include/dplyr/NamedListAccumulator.h | 12
dplyr-0.4.0/dplyr/inst/include/dplyr/Order.h | 3
dplyr-0.4.0/dplyr/inst/include/dplyr/OrderVisitorImpl.h | 137 +
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dplyr-0.4.0/dplyr/inst/include/dplyr/Result/CallProxy.h | 76
dplyr-0.4.0/dplyr/inst/include/dplyr/Result/CallbackProcessor.h | 27
dplyr-0.4.0/dplyr/inst/include/dplyr/Result/DelayedProcessor.h | 124 -
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dplyr-0.4.0/dplyr/inst/include/dplyr/Result/In.h |only
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dplyr-0.4.0/dplyr/inst/include/dplyr/Result/LazyRowwiseSubsets.h | 6
dplyr-0.4.0/dplyr/inst/include/dplyr/Result/LazySubsets.h | 14
dplyr-0.4.0/dplyr/inst/include/dplyr/Result/Name.h |only
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dplyr-0.4.0/dplyr/inst/include/dplyr/Result/all.h | 3
dplyr-0.4.0/dplyr/inst/include/dplyr/VectorVisitor.h | 85
dplyr-0.4.0/dplyr/inst/include/dplyr/VectorVisitorImpl.h | 45
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dplyr-0.4.0/dplyr/inst/include/tools/Encoding.h | 37
dplyr-0.4.0/dplyr/inst/include/tools/ShrinkableVector.h | 14
dplyr-0.4.0/dplyr/inst/include/tools/StrictListOf.h | 38
dplyr-0.4.0/dplyr/inst/include/tools/all_na.h |only
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dplyr-0.4.0/dplyr/inst/include/tools/complex.h |only
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dplyr-0.4.0/dplyr/inst/include/tools/stop.h |only
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dplyr-0.4.0/dplyr/man/as_data_frame.Rd |only
dplyr-0.4.0/dplyr/man/backend_db.Rd | 3
dplyr-0.4.0/dplyr/man/backend_sql.Rd | 3
dplyr-0.4.0/dplyr/man/backend_src.Rd | 3
dplyr-0.4.0/dplyr/man/bench_compare.Rd | 5
dplyr-0.4.0/dplyr/man/between.Rd | 5
dplyr-0.4.0/dplyr/man/bind.Rd |only
dplyr-0.4.0/dplyr/man/build_sql.Rd | 3
dplyr-0.4.0/dplyr/man/chain.Rd | 3
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dplyr-0.4.0/dplyr/man/copy_to.src_sql.Rd | 7
dplyr-0.4.0/dplyr/man/cumall.Rd | 3
dplyr-0.4.0/dplyr/man/data_frame.Rd | 9
dplyr-0.4.0/dplyr/man/desc.Rd | 3
dplyr-0.4.0/dplyr/man/distinct.Rd | 3
dplyr-0.4.0/dplyr/man/do.Rd | 13
dplyr-0.4.0/dplyr/man/dplyr-cluster.Rd | 3
dplyr-0.4.0/dplyr/man/dplyr-formatting.Rd | 3
dplyr-0.4.0/dplyr/man/dplyr.Rd | 24
dplyr-0.4.0/dplyr/man/explain.Rd | 8
dplyr-0.4.0/dplyr/man/failwith.Rd | 3
dplyr-0.4.0/dplyr/man/filter.Rd | 3
dplyr-0.4.0/dplyr/man/funs.Rd | 3
dplyr-0.4.0/dplyr/man/glimpse.Rd | 3
dplyr-0.4.0/dplyr/man/group_by.Rd | 3
dplyr-0.4.0/dplyr/man/group_indices.Rd |only
dplyr-0.4.0/dplyr/man/group_size.Rd | 3
dplyr-0.4.0/dplyr/man/grouped_df.Rd | 3
dplyr-0.4.0/dplyr/man/grouped_dt.Rd | 3
dplyr-0.4.0/dplyr/man/groups.Rd | 3
dplyr-0.4.0/dplyr/man/id.Rd | 3
dplyr-0.4.0/dplyr/man/join.Rd | 14
dplyr-0.4.0/dplyr/man/join.tbl_df.Rd | 9
dplyr-0.4.0/dplyr/man/join.tbl_dt.Rd | 3
dplyr-0.4.0/dplyr/man/join.tbl_sql.Rd | 16
dplyr-0.4.0/dplyr/man/knit_print.trunc_mat.Rd |only
dplyr-0.4.0/dplyr/man/lahman.Rd | 3
dplyr-0.4.0/dplyr/man/lead-lag.Rd | 3
dplyr-0.4.0/dplyr/man/location.Rd | 3
dplyr-0.4.0/dplyr/man/make_tbl.Rd | 3
dplyr-0.4.0/dplyr/man/mutate.Rd | 3
dplyr-0.4.0/dplyr/man/n.Rd | 3
dplyr-0.4.0/dplyr/man/n_distinct.Rd | 3
dplyr-0.4.0/dplyr/man/nasa.Rd | 3
dplyr-0.4.0/dplyr/man/nth.Rd | 3
dplyr-0.4.0/dplyr/man/nycflights13.Rd | 3
dplyr-0.4.0/dplyr/man/order_by.Rd | 3
dplyr-0.4.0/dplyr/man/partial_eval.Rd | 3
dplyr-0.4.0/dplyr/man/progress_estimated.Rd | 3
dplyr-0.4.0/dplyr/man/query.Rd | 3
dplyr-0.4.0/dplyr/man/ranking.Rd | 9
dplyr-0.4.0/dplyr/man/rowwise.Rd | 5
dplyr-0.4.0/dplyr/man/same_src.Rd | 3
dplyr-0.4.0/dplyr/man/sample.Rd | 3
dplyr-0.4.0/dplyr/man/select.Rd | 8
dplyr-0.4.0/dplyr/man/select_vars.Rd | 3
dplyr-0.4.0/dplyr/man/setops.Rd | 3
dplyr-0.4.0/dplyr/man/slice.Rd | 14
dplyr-0.4.0/dplyr/man/sql.Rd | 3
dplyr-0.4.0/dplyr/man/sql_quote.Rd | 3
dplyr-0.4.0/dplyr/man/sql_variant.Rd | 3
dplyr-0.4.0/dplyr/man/src.Rd | 3
dplyr-0.4.0/dplyr/man/src_local.Rd | 3
dplyr-0.4.0/dplyr/man/src_mysql.Rd | 12
dplyr-0.4.0/dplyr/man/src_postgres.Rd | 12
dplyr-0.4.0/dplyr/man/src_sql.Rd | 5
dplyr-0.4.0/dplyr/man/src_sqlite.Rd | 16
dplyr-0.4.0/dplyr/man/src_tbls.Rd | 3
dplyr-0.4.0/dplyr/man/summarise.Rd | 25
dplyr-0.4.0/dplyr/man/summarise_each.Rd | 3
dplyr-0.4.0/dplyr/man/tally.Rd | 10
dplyr-0.4.0/dplyr/man/tbl.Rd | 3
dplyr-0.4.0/dplyr/man/tbl_cube.Rd | 3
dplyr-0.4.0/dplyr/man/tbl_df.Rd | 3
dplyr-0.4.0/dplyr/man/tbl_dt.Rd | 3
dplyr-0.4.0/dplyr/man/tbl_sql.Rd | 3
dplyr-0.4.0/dplyr/man/tbl_vars.Rd | 3
dplyr-0.4.0/dplyr/man/temp_srcs.Rd | 3
dplyr-0.4.0/dplyr/man/top_n.Rd | 3
dplyr-0.4.0/dplyr/man/translate_sql.Rd | 7
dplyr-0.4.0/dplyr/man/type_sum.Rd | 3
dplyr-0.4.0/dplyr/man/with_order.Rd | 3
dplyr-0.4.0/dplyr/src/RcppExports.cpp | 117 -
dplyr-0.4.0/dplyr/src/arrange.cpp | 31
dplyr-0.4.0/dplyr/src/between.cpp | 4
dplyr-0.4.0/dplyr/src/bind.cpp | 75
dplyr-0.4.0/dplyr/src/combine_variables.cpp |only
dplyr-0.4.0/dplyr/src/dplyr.cpp | 628 +++--
dplyr-0.4.0/dplyr/src/filter.cpp | 19
dplyr-0.4.0/dplyr/src/group_indices.cpp |only
dplyr-0.4.0/dplyr/src/join.cpp | 39
dplyr-0.4.0/dplyr/src/select.cpp | 10
dplyr-0.4.0/dplyr/src/strings_addresses.cpp |only
dplyr-0.4.0/dplyr/src/summarise.cpp | 5
dplyr-0.4.0/dplyr/tests/testthat/helper-data.r | 7
dplyr-0.4.0/dplyr/tests/testthat/test-arrange.r | 22
dplyr-0.4.0/dplyr/tests/testthat/test-cbind.R | 16
dplyr-0.4.0/dplyr/tests/testthat/test-data_frame.R |only
dplyr-0.4.0/dplyr/tests/testthat/test-do.R | 90
dplyr-0.4.0/dplyr/tests/testthat/test-filter.r | 44
dplyr-0.4.0/dplyr/tests/testthat/test-group-by.r | 61
dplyr-0.4.0/dplyr/tests/testthat/test-group-indices.R |only
dplyr-0.4.0/dplyr/tests/testthat/test-joins.r | 180 +
dplyr-0.4.0/dplyr/tests/testthat/test-mutate-windowed.R | 82
dplyr-0.4.0/dplyr/tests/testthat/test-mutate.r | 71
dplyr-0.4.0/dplyr/tests/testthat/test-rbind.r | 24
dplyr-0.4.0/dplyr/tests/testthat/test-select.r | 54
dplyr-0.4.0/dplyr/tests/testthat/test-slice.r | 38
dplyr-0.4.0/dplyr/tests/testthat/test-summarise.r | 99
dplyr-0.4.0/dplyr/tests/testthat/test-tbl-df.r | 16
dplyr-0.4.0/dplyr/tests/testthat/utf-8.R |only
dplyr-0.4.0/dplyr/vignettes/data_frames.Rmd |only
dplyr-0.4.0/dplyr/vignettes/databases.Rmd | 28
dplyr-0.4.0/dplyr/vignettes/databases.md |only
dplyr-0.4.0/dplyr/vignettes/figure |only
dplyr-0.4.0/dplyr/vignettes/hybrid-evaluation.Rmd | 19
dplyr-0.4.0/dplyr/vignettes/hybrid-evaluation.md |only
dplyr-0.4.0/dplyr/vignettes/introduction.Rmd | 38
dplyr-0.4.0/dplyr/vignettes/introduction.md |only
dplyr-0.4.0/dplyr/vignettes/memory.html |only
dplyr-0.4.0/dplyr/vignettes/new-sql-backend.Rmd | 20
dplyr-0.4.0/dplyr/vignettes/nse.Rmd | 1
dplyr-0.4.0/dplyr/vignettes/two-table.Rmd |only
dplyr-0.4.0/dplyr/vignettes/window-functions.Rmd | 18
258 files changed, 6402 insertions(+), 4689 deletions(-)
Title: Bayesian Network Feature Finder
Diff between BANFF versions 0.1 dated 2014-12-29 and 0.2 dated 2015-01-08
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/main.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Autoregressive Conditional Poisson
Diff between acp versions 1.0 dated 2014-07-23 and 1.1 dated 2015-01-08
Description: Time series analysis of count data
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/acp.R | 12 ++++--------
3 files changed, 11 insertions(+), 15 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 1.0-16 dated 2014-11-09 and 1.0-17 dated 2015-01-08
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb]
Maintainer: Edzer Pebesma
DESCRIPTION | 14 +++++-----
MD5 | 25 +++++++++---------
R/SpatialPoints-methods.R | 14 +++++++---
R/SpatialPointsDataFrame-methods.R | 2 -
R/merge.R | 51 +++++++++++++++++++++----------------
R/over.R | 2 -
data/meuse.area.rda |only
demo/meuse.R | 3 ++
inst/ChangeLog | 19 +++++++++++++
inst/doc/csdacm.pdf |binary
inst/doc/intro_sp.pdf |binary
inst/doc/over.pdf |binary
man/merge.Rd | 9 ++++--
man/meuse.riv.Rd | 21 +++++++++++++--
14 files changed, 108 insertions(+), 52 deletions(-)
Title: R Client for the MTurk Requester API
Diff between MTurkR versions 0.5.51 dated 2014-10-07 and 0.6 dated 2015-01-07
Description: Provides R access to the Amazon Mechanical Turk (MTurk) Requester API.
Author: Thomas J. Leeper [aut, cre],
Solomon Messing [ctb],
Sean Murphy [ctb]
Maintainer: Thomas J. Leeper
MTurkR-0.5.51/MTurkR/R/mturkr.wizard.R |only
MTurkR-0.5.51/MTurkR/R/wizard.simple.R |only
MTurkR-0.6/MTurkR/DESCRIPTION | 8 -
MTurkR-0.6/MTurkR/MD5 | 54 ++++-----
MTurkR-0.6/MTurkR/NEWS | 30 +++++
MTurkR-0.6/MTurkR/R/ContactWorker.R | 66 +++--------
MTurkR-0.6/MTurkR/R/CreateQualificationType.R | 5
MTurkR-0.6/MTurkR/R/GenerateAnswerKey.R | 3
MTurkR-0.6/MTurkR/R/GenerateQualificationRequirement.R | 2
MTurkR-0.6/MTurkR/R/GetReviewResultsForHIT.R | 83 +++++++++-----
MTurkR-0.6/MTurkR/R/SendTestEventNotification.R | 2
MTurkR-0.6/MTurkR/R/UpdateQualificationType.R | 3
MTurkR-0.6/MTurkR/R/asdataframe.R | 62 ++++------
MTurkR-0.6/MTurkR/R/onLoad.r | 5
MTurkR-0.6/MTurkR/R/wizard.R |only
MTurkR-0.6/MTurkR/R/wizardsimple.R |only
MTurkR-0.6/MTurkR/README.md | 2
MTurkR-0.6/MTurkR/inst/templates/htmlquestion1.xml | 6 -
MTurkR-0.6/MTurkR/man/CreateHIT.Rd | 62 +++++++---
MTurkR-0.6/MTurkR/man/CreateQualificationType.Rd | 33 ++---
MTurkR-0.6/MTurkR/man/GenerateHTMLQuestion.Rd | 10 +
MTurkR-0.6/MTurkR/man/GenerateNotification.Rd | 2
MTurkR-0.6/MTurkR/man/GenerateQualificationRequirement.Rd | 5
MTurkR-0.6/MTurkR/man/GenerateReviewPolicy.Rd | 14 +-
MTurkR-0.6/MTurkR/man/GetFileUpload.Rd | 4
MTurkR-0.6/MTurkR/man/GetReviewResultsForHIT.Rd | 4
MTurkR-0.6/MTurkR/man/GrantQualification.Rd | 6 -
MTurkR-0.6/MTurkR/man/RejectQualification.Rd | 4
MTurkR-0.6/MTurkR/man/SendTestEventNotification.Rd | 6 -
MTurkR-0.6/MTurkR/man/SetHITTypeNotification.Rd | 32 ++++-
30 files changed, 304 insertions(+), 209 deletions(-)
Title: Various R Programming Tools for Plotting Data
Diff between gplots versions 2.15.0 dated 2014-12-02 and 2.16.0 dated 2015-01-07
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes
ChangeLog | 23 +++++++++++++++++
DESCRIPTION | 12 ++++-----
MD5 | 18 ++++++-------
NEWS | 14 ++++++++++
R/plotmeans.R | 70 ++++++++++++++++++-----------------------------------
build/vignette.rds |binary
inst/ChangeLog | 23 +++++++++++++++++
inst/NEWS | 14 ++++++++++
inst/doc/venn.pdf |binary
man/plotmeans.Rd | 46 +++++++++++++++-------------------
10 files changed, 134 insertions(+), 86 deletions(-)
Title: Likelihood-ratio Tests for Two-Sample Comparisons
Diff between tsc versions 1.0-2 dated 2015-01-04 and 1.0-3 dated 2015-01-07
Description: Performs the two-sample comparisons using the following exact test procedures: the exact likelihood-ratio test (LRT) for equality of two normal populations proposed in Zhang et al. (2012); the combined test based on the LRT and Shapiro-Wilk test for normality via the Bonferroni correction technique; the newly proposed density-based empirical likelihood (DBEL) ratio test. To calculate p-values of the DBEL procedures, three procedures are used: (a) the traditional Monte Carlo (MC) method implemented in C++, (b) a new interpolation method based on regression techniques to operate with tabulated critical values of the test statistic; (c) a Bayesian type method that uses the tabulated critical values as the prior information and MC generated DBEL-test-statistic's values as data.
Author: Yang Zhao, Albert Vexler, Alan Hutson
Maintainer: Yang Zhao
DESCRIPTION | 6 +++---
MD5 | 4 ++--
man/tsc.test.Rd | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Generalized Diffusion Magnetic Resonance Imaging
Diff between gdimap versions 0.1-8 dated 2014-11-07 and 0.1-9 dated 2015-01-07
Description: Diffusion anisotropy has been used to characterize
white matter neuronal pathways in the human brain, and infer global
connectivity in the central nervous system. The package implements
algorithms to estimate and visualize the orientation of neuronal
pathways in model-free methods (q-space imaging methods).
For estimating fibre orientations two methods have been
implemented. One method implements fibre orientation detection
through local maxima extraction. A second more robust method
is based on directional statistical clustering of ODF voxel data.
Fibre orientations in multiple fibre voxels are estimated using
a mixture of von Mises-Fisher (vMF) distributions. This statistical
estimation procedure is used to resolve crossing fibre
configurations.
Reconstruction of orientation distribution function (ODF)
profiles may be performed using the standard generalized
q-sampling imaging (GQI) approach, Garyfallidis' GQI (GQI2)
approach, or Aganj's variant of the Q-ball imaging (CSA-QBI)
approach. Procedures for the visualization of RGB-maps,
line-maps and glyph-maps of real diffusion magnetic resonance
imaging (dMRI) data-sets are included in the package.
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
gdimap-0.1-8/gdimap/R/niisetup.R |only
gdimap-0.1-8/gdimap/man/niisetup.Rd |only
gdimap-0.1-9/gdimap/DESCRIPTION | 13 -
gdimap-0.1-9/gdimap/MD5 | 76 +++----
gdimap-0.1-9/gdimap/NAMESPACE | 8
gdimap-0.1-9/gdimap/NEWS | 12 +
gdimap-0.1-9/gdimap/R/gdiutils.R | 2
gdimap-0.1-9/gdimap/R/gqi.odfpeaklines.R | 189 +++++++++++--------
gdimap-0.1-9/gdimap/R/gqi.odfpeaks.R | 44 ++--
gdimap-0.1-9/gdimap/R/gqi.odfvmf.R | 80 +++-----
gdimap-0.1-9/gdimap/R/gqi.odfvmflines.R | 257 ++++++++++++++------------
gdimap-0.1-9/gdimap/R/gqi.odfvxgrid.R | 42 +---
gdimap-0.1-9/gdimap/R/niinorm.R | 22 +-
gdimap-0.1-9/gdimap/R/plotglyph.R | 2
gdimap-0.1-9/gdimap/R/readutils.R | 67 ++++++
gdimap-0.1-9/gdimap/R/rgbvolmap.R | 12 -
gdimap-0.1-9/gdimap/R/s2tessel.zorder.R | 2
gdimap-0.1-9/gdimap/R/simul.fandtasia.R | 35 +--
gdimap-0.1-9/gdimap/R/simul.fandtasiaSignal.R | 11 -
gdimap-0.1-9/gdimap/R/simul.simplefield.R | 33 +--
gdimap-0.1-9/gdimap/R/sph.odfpeaklines.R | 173 +++++++++--------
gdimap-0.1-9/gdimap/R/sph.odfpeaks.R | 44 +---
gdimap-0.1-9/gdimap/R/sph.odfvmf.R | 76 +++----
gdimap-0.1-9/gdimap/R/sph.odfvmflines.R | 234 ++++++++++++-----------
gdimap-0.1-9/gdimap/R/sph.odfvxgrid.R | 44 +---
gdimap-0.1-9/gdimap/R/synthfiberss2z.R | 2
gdimap-0.1-9/gdimap/man/data.Rd | 2
gdimap-0.1-9/gdimap/man/data_gfa.Rd | 2
gdimap-0.1-9/gdimap/man/gdimap-package.Rd | 12 -
gdimap-0.1-9/gdimap/man/gqi.odfpeaklines.Rd | 13 -
gdimap-0.1-9/gdimap/man/gqi.odfpeaks.Rd | 2
gdimap-0.1-9/gdimap/man/gqi.odfvmf.Rd | 6
gdimap-0.1-9/gdimap/man/gqi.odfvmflines.Rd | 38 +--
gdimap-0.1-9/gdimap/man/gqi.odfvxgrid.Rd | 2
gdimap-0.1-9/gdimap/man/niinorm.Rd | 2
gdimap-0.1-9/gdimap/man/simulglyph.vmf.Rd | 4
gdimap-0.1-9/gdimap/man/slfcst.Rd | 2
gdimap-0.1-9/gdimap/man/sph.odfpeaklines.Rd | 7
gdimap-0.1-9/gdimap/man/sph.odfvmf.Rd | 2
gdimap-0.1-9/gdimap/man/sph.odfvmflines.Rd | 18 +
40 files changed, 844 insertions(+), 748 deletions(-)
Title: R Graphics Output in LaTeX Format
Diff between tikzDevice versions 0.8 dated 2015-01-07 and 0.8.1 dated 2015-01-07
Description: The tikzDevice package provides a graphics output device for R
that records plots in a LaTeX-friendly format. The device transforms
plotting commands issued by R functions into LaTeX code blocks. When
included in a paper typeset by LaTeX, these blocks are interpreted with the
help of TikZ---a graphics package for TeX and friends written by Till
Tantau. Using the tikzDevice, the text of R plots can contain LaTeX
commands such as mathematical formula. The device also allows arbitrary
LaTeX code to be inserted into the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb, cre],
Yihui Xie [ctb]
Maintainer: Kirill Müller
tikzDevice-0.8.1/tikzDevice/DESCRIPTION | 6
tikzDevice-0.8.1/tikzDevice/MD5 | 234 ------------
tikzDevice-0.8.1/tikzDevice/inst/NEWS.Rd | 13
tikzDevice-0.8.1/tikzDevice/inst/doc/tikzDevice.pdf |binary
tikzDevice-0.8.1/tikzDevice/src/tikzDevice.c | 4
tikzDevice-0.8.1/tikzDevice/src/tikzDevice.h | 4
tikzDevice-0.8.1/tikzDevice/vignettes/figs/annotation.tex | 78 ++--
tikzDevice-0.8.1/tikzDevice/vignettes/figs/latexEx.tex | 84 ++--
tikzDevice-0.8.1/tikzDevice/vignettes/figs/pdf-example.pdf |binary
tikzDevice-0.8.1/tikzDevice/vignettes/figs/simpleEx.tex | 2
tikzDevice-0.8.1/tikzDevice/vignettes/figs/tikz-example.tex | 2
tikzDevice-0.8.1/tikzDevice/vignettes/figs/titlePlot.tex | 2
tikzDevice-0.8.1/tikzDevice/vignettes/figs/westCoast.tex | 2
tikzDevice-0.8/tikzDevice/tests/testthat/test_output |only
tikzDevice-0.8/tikzDevice/tests/testthat/test_work |only
15 files changed, 119 insertions(+), 312 deletions(-)
Title: An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
Diff between RcppProgress versions 0.1 dated 2013-05-10 and 0.2 dated 2015-01-07
Description: This package allows to display a progress bar in the R
console for long running computations taking place in c++ code,
and support for interrupting those computations even in multithreaded
code, typically using OpenMP.
Author: Karl Forner
Maintainer: Karl Forner
RcppProgress-0.1/RcppProgress/Makefile |only
RcppProgress-0.1/RcppProgress/README |only
RcppProgress-0.1/RcppProgress/cleanup |only
RcppProgress-0.2/RcppProgress/DESCRIPTION | 25 +++----
RcppProgress-0.2/RcppProgress/MD5 | 33 ++++++----
RcppProgress-0.2/RcppProgress/NAMESPACE | 1
RcppProgress-0.2/RcppProgress/README.md |only
RcppProgress-0.2/RcppProgress/inst/examples/RcppProgressArmadillo |only
RcppProgress-0.2/RcppProgress/inst/examples/RcppProgressExample/DESCRIPTION | 2
RcppProgress-0.2/RcppProgress/inst/examples/RcppProgressExample/src/example.cpp | 13 +--
RcppProgress-0.2/RcppProgress/inst/examples/dev.R |only
RcppProgress-0.2/RcppProgress/inst/include/interruptable_progress_monitor.hpp | 17 +++--
RcppProgress-0.2/RcppProgress/inst/include/interrupts.hpp | 6 +
RcppProgress-0.2/RcppProgress/inst/include/progress.hpp | 29 +++++---
RcppProgress-0.2/RcppProgress/man/RcppProgress-package.Rd | 27 ++++++--
RcppProgress-0.2/RcppProgress/src/Makevars | 2
RcppProgress-0.2/RcppProgress/src/tests.cpp | 7 --
17 files changed, 96 insertions(+), 66 deletions(-)
Title: Plot a Model's Response While Varying the Values of the
Predictors
Diff between plotmo versions 2.2.0 dated 2014-12-10 and 2.2.1 dated 2015-01-07
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 6
MD5 | 18 -
NEWS | 8
R/lib.R | 2
R/plotmo.R | 80 +++++---
inst/doc/plotmo-notes.pdf |binary
inst/slowtests/test.plotmo.R | 12 +
inst/slowtests/test.plotmo.Rout.save | 242 ++++++++++++-------------
inst/slowtests/test.plotmo.non.earth.Rout.save | 49 +----
man/plotmo.Rd | 3
10 files changed, 225 insertions(+), 195 deletions(-)
Title: CUDA Parallel Implementation of a Bayesian Multilevel Model for
fMRI Data Analysis
Diff between cudaBayesreg versions 0.3-15 dated 2014-03-03 and 0.3-16 dated 2015-01-07
Description: Compute Unified Device Architecture (CUDA) is a software
platform for massively parallel high-performance computing on
NVIDIA GPUs. This package provides a CUDA implementation of a
Bayesian multilevel model for the analysis of brain fMRI data.
A fMRI data set consists of time series of volume data in 4D
space. Typically, volumes are collected as slices of 64 x 64
voxels. Analysis of fMRI data often relies on fitting linear
regression models at each voxel of the brain. The volume of the
data to be processed, and the type of statistical analysis to
perform in fMRI analysis, call for high-performance computing
strategies. In this package, the CUDA programming model uses a
separate thread for fitting a linear regression model at each
voxel in parallel. The global statistical model implements a
Gibbs Sampler for hierarchical linear models with a normal
prior. This model has been proposed by Rossi, Allenby and
McCulloch in `Bayesian Statistics and Marketing', Chapter 3,
and is referred to as `rhierLinearModel' in the R-package
bayesm. A notebook equipped with a NVIDIA `GeForce 8400M GS'
card having Compute Capability 1.1 has been used in the tests.
The data sets used in the package's examples are available in
the separate package cudaBayesregData.
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
NEWS | 4 ++++
3 files changed, 12 insertions(+), 8 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-81 dated 2015-01-06 and 0.5-82 dated 2015-01-07
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 26 ++++++++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 32 ++++++++++++++++----------------
R/jacobian.R | 6 +++---
R/moran.R | 3 ++-
inst/ChangeLog | 26 ++++++++++++++++++++++++++
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/nb_igraph.R | 10 +++++-----
inst/doc/nb_igraph.Rmd | 12 ++++++------
inst/doc/nb_igraph.html | 23 ++++++-----------------
inst/doc/sids.pdf |binary
man/eigenw.Rd | 3 ++-
man/errorsarlm.Rd | 15 ++++++++++++++-
man/moran.mc.Rd | 3 ++-
vignettes/nb_igraph.Rmd | 12 ++++++------
17 files changed, 118 insertions(+), 61 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 0.8-3 dated 2014-12-15 and 0.8-4 dated 2015-01-07
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
partykit-0.8-3/partykit/inst/NEWS |only
partykit-0.8-3/partykit/src/party.h |only
partykit-0.8-3/partykit/src/partycall.c |only
partykit-0.8-3/partykit/src/partynode.c |only
partykit-0.8-3/partykit/src/partynode.h |only
partykit-0.8-3/partykit/src/partysplit.c |only
partykit-0.8-3/partykit/src/partysplit.h |only
partykit-0.8-3/partykit/src/partyutils.c |only
partykit-0.8-3/partykit/src/partyutils.h |only
partykit-0.8-4/partykit/DESCRIPTION | 10
partykit-0.8-4/partykit/MD5 | 66 +++---
partykit-0.8-4/partykit/NAMESPACE | 7
partykit-0.8-4/partykit/R/as.party.R | 2
partykit-0.8-4/partykit/R/cforest.R |only
partykit-0.8-4/partykit/R/ctree.R | 29 ++
partykit-0.8-4/partykit/R/glmtree.R | 4
partykit-0.8-4/partykit/R/lmtree.R | 4
partykit-0.8-4/partykit/R/modelparty.R | 177 +++++++++++------
partykit-0.8-4/partykit/R/plot.R | 2
partykit-0.8-4/partykit/inst/NEWS.Rd |only
partykit-0.8-4/partykit/inst/doc/constparty.pdf |binary
partykit-0.8-4/partykit/inst/doc/ctree.R | 2
partykit-0.8-4/partykit/inst/doc/ctree.Rnw | 2
partykit-0.8-4/partykit/inst/doc/ctree.pdf |binary
partykit-0.8-4/partykit/inst/doc/mob.Rnw | 6
partykit-0.8-4/partykit/inst/doc/mob.pdf |binary
partykit-0.8-4/partykit/inst/doc/partykit.pdf |binary
partykit-0.8-4/partykit/inst/tmp |only
partykit-0.8-4/partykit/man/cforest.Rd |only
partykit-0.8-4/partykit/man/ctree.Rd | 4
partykit-0.8-4/partykit/man/ctree_control.Rd | 10
partykit-0.8-4/partykit/man/glmtree.Rd | 7
partykit-0.8-4/partykit/man/lmtree.Rd | 7
partykit-0.8-4/partykit/man/mob.Rd | 7
partykit-0.8-4/partykit/man/mob_control.Rd | 14 +
partykit-0.8-4/partykit/man/panelfunctions.Rd | 2
partykit-0.8-4/partykit/man/party-plot.Rd | 2
partykit-0.8-4/partykit/vignettes/constparty.Rout.save |only
partykit-0.8-4/partykit/vignettes/ctree.Rnw | 2
partykit-0.8-4/partykit/vignettes/ctree.Rout.save |only
partykit-0.8-4/partykit/vignettes/mob.Rnw | 6
partykit-0.8-4/partykit/vignettes/partykit.Rout.save |only
42 files changed, 243 insertions(+), 129 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Diff between jomo versions 0.1-1 dated 2014-12-16 and 0.1-2 dated 2015-01-07
Description: Building on Schafer's package pan and on the standalone program REALCOM, jomo is a package for multilevel joint modelling multiple imputation.
Binary and categorical variables are handled through latent normal variables and algorithms for cluster-specific covariance matrices are introduced.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno
DESCRIPTION | 14 +++++++-------
MD5 | 44 ++++++++++++++++++++++----------------------
R/jomo1cat.R | 2 +-
R/jomo1mix.R | 2 +-
R/jomo1rancat.R | 4 ++--
R/jomo1rancathr.R | 4 ++--
R/jomo1rancon.R | 2 +-
R/jomo1ranconhr.R | 2 +-
R/jomo1ranmix.R | 4 ++--
R/jomo1ranmixhr.R | 4 ++--
man/jomo1rancat.Rd | 4 ++--
man/jomo1rancathr.Rd | 6 +++---
man/jomo1rancon.Rd | 4 ++--
man/jomo1ranconhr.Rd | 6 +++---
man/jomo1ranmix.Rd | 4 ++--
man/jomo1ranmixhr.Rd | 6 +++---
src/Makevars | 2 +-
src/jomo1rancon.c | 2 +-
src/jomo1ranconhf.c | 2 +-
src/jomo1ranconhr.c | 2 +-
src/jomo1ranmix.c | 2 +-
src/jomo1ranmix2.c | 2 +-
src/jomo1ranmixhr.c | 2 +-
23 files changed, 63 insertions(+), 63 deletions(-)
Title: Plots of the Empirical Attainment Function
Diff between eaf versions 1.06 dated 2014-10-01 and 1.07 dated 2015-01-07
Description: Plots of the empirical attainment function for two objectives.
Author: Carlos Fonseca, Luis Paquete, Thomas Stützle, Manuel López-Ibáñez and Marco Chiarandini.
Maintainer: Manuel López-Ibáñez
eaf-1.06/eaf/inst/scripts/eaf/Makefile |only
eaf-1.07/eaf/DESCRIPTION | 8 ++++----
eaf-1.07/eaf/MD5 | 10 +++++-----
eaf-1.07/eaf/NEWS | 6 ++++++
eaf-1.07/eaf/inst/scripts/eaf/GNUmakefile |only
eaf-1.07/eaf/inst/scripts/eaf/svn_version | 2 +-
eaf-1.07/eaf/man/eaf-package.Rd | 4 ++--
7 files changed, 18 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-09 0.0-32
2012-02-24 0.0-31
2010-08-11 0.0-29
2009-08-04 0.0-27
Title: Meta-Analysis with R
Diff between meta versions 4.0-2 dated 2014-12-06 and 4.0-3 dated 2015-01-07
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 8 ++++++++
R/metabin.R | 4 ++++
4 files changed, 19 insertions(+), 7 deletions(-)
Title: Comparing Correlations
Diff between cocor versions 1.0-0 dated 2013-09-21 and 1.1-0 dated 2015-01-07
Description: Statistical tests for the comparison between two correlations
based on either independent or dependent groups. Dependent correlations can
either be overlapping or nonoverlapping. A web interface is available at
http://comparingcorrelations.org. A plugin for RKWard is included. RKWard
can be obtained freely from http://rkward.sf.net.
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen
ChangeLog | 15
DESCRIPTION | 30 -
MD5 | 46 -
NAMESPACE | 6
R/0helper.r | 32 -
R/as.htest.r | 49 -
R/cocor-package.R | 14
R/cocor.dep.groups.nonoverlap.r | 17
R/cocor.dep.groups.overlap.r | 14
R/cocor.indep.groups.r | 22
R/cocor.r | 42 -
R/get.cocor.input.r |only
R/get.cocor.results.r |only
inst/CITATION | 22
inst/rkward/cocor.pluginmap | 6
inst/rkward/rkwarddev.cocor.plugin.script.R | 6
inst/tests/test.r | 80 ++
man/aptitude.Rd | 3
man/as.htest.Rd | 50 -
man/cocor-package.Rd | 27
man/cocor.Rd | 147 +----
man/cocor.dep.groups.nonoverlap.Rd | 503 +++++++----------
man/cocor.dep.groups.overlap.Rd | 788 +++++++++++-----------------
man/cocor.indep.groups.Rd | 247 +++-----
man/get.cocor.input.Rd |only
man/get.cocor.results.Rd |only
26 files changed, 976 insertions(+), 1190 deletions(-)
Title: Utilities from Seminar fuer Statistik ETH Zurich
Diff between sfsmisc versions 1.0-26 dated 2014-06-16 and 1.0-27 dated 2015-01-07
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, quite a few related to graphics; many ported from S-plus times.
Author: Martin Maechler et al.
Maintainer: Martin Maechler
sfsmisc-1.0-26/sfsmisc/NEWS |only
sfsmisc-1.0-26/sfsmisc/inst/NEWS |only
sfsmisc-1.0-26/sfsmisc/inst/doc |only
sfsmisc-1.0-27/sfsmisc/ChangeLog | 16 ++++++-
sfsmisc-1.0-27/sfsmisc/DESCRIPTION | 12 ++---
sfsmisc-1.0-27/sfsmisc/MD5 | 62 ++++++++++++++--------------
sfsmisc-1.0-27/sfsmisc/NAMESPACE | 6 +-
sfsmisc-1.0-27/sfsmisc/R/Ftest-rlm.R | 4 -
sfsmisc-1.0-27/sfsmisc/R/KS-confint.R | 2
sfsmisc-1.0-27/sfsmisc/R/TA.plot.R | 1
sfsmisc-1.0-27/sfsmisc/R/mat2tex.R | 6 +-
sfsmisc-1.0-27/sfsmisc/R/misc-goodies.R | 3 -
sfsmisc-1.0-27/sfsmisc/R/missingCh.R |only
sfsmisc-1.0-27/sfsmisc/R/p.goodies.R | 1
sfsmisc-1.0-27/sfsmisc/R/p.res.2x.formula.R | 40 +-----------------
sfsmisc-1.0-27/sfsmisc/R/prettylab.R | 30 +++++++++----
sfsmisc-1.0-27/sfsmisc/R/prime-numbers-fn.R | 4 -
sfsmisc-1.0-27/sfsmisc/R/ps.goodies.R |binary
sfsmisc-1.0-27/sfsmisc/R/rot13.R |only
sfsmisc-1.0-27/sfsmisc/R/sourceAttach.R | 2
sfsmisc-1.0-27/sfsmisc/R/tkdensity.R | 4 -
sfsmisc-1.0-27/sfsmisc/README.md |only
sfsmisc-1.0-27/sfsmisc/TODO |only
sfsmisc-1.0-27/sfsmisc/demo/prime-numbers.R | 2
sfsmisc-1.0-27/sfsmisc/inst/ChangeLog | 16 ++++++-
sfsmisc-1.0-27/sfsmisc/inst/NEWS.Rd |only
sfsmisc-1.0-27/sfsmisc/man/Deprecated.Rd | 10 +---
sfsmisc-1.0-27/sfsmisc/man/QUnif.Rd | 2
sfsmisc-1.0-27/sfsmisc/man/diagDA.Rd | 9 +++-
sfsmisc-1.0-27/sfsmisc/man/eaxis.Rd | 17 ++++++-
sfsmisc-1.0-27/sfsmisc/man/ecdf.ksCI.Rd | 2
sfsmisc-1.0-27/sfsmisc/man/mat2tex.Rd | 6 ++
sfsmisc-1.0-27/sfsmisc/man/missingCh.Rd |only
sfsmisc-1.0-27/sfsmisc/man/p.hboxp.Rd | 4 -
sfsmisc-1.0-27/sfsmisc/man/pretty10exp.Rd | 24 ++++++++--
sfsmisc-1.0-27/sfsmisc/man/rot13.Rd |only
sfsmisc-1.0-27/sfsmisc/man/u.assign0.Rd | 4 +
37 files changed, 167 insertions(+), 122 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Diff between foreign versions 0.8-61 dated 2014-03-28 and 0.8-62 dated 2015-01-07
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team
ChangeLog | 20 ++++++++++++++++++--
DESCRIPTION | 16 ++++++++--------
MD5 | 18 +++++++++---------
R/octave.R | 4 ++--
man/lookup.xport.Rd | 4 ++--
man/read.S.Rd | 2 +-
man/read.epiinfo.Rd | 2 +-
man/read.spss.Rd | 2 +-
man/read.ssd.Rd | 4 ++--
man/read.xport.Rd | 4 ++--
10 files changed, 46 insertions(+), 30 deletions(-)
Title: Bindings to OpenSSL
Diff between openssl versions 0.2 dated 2014-11-07 and 0.3 dated 2015-01-07
Description: Interfaces to the OpenSSL libraries libssl and libcrypto.
Currently implements bindings to the OpenSSL secure random number
generator and hashing functions.
Author: Jeroen Ooms, Oliver Keyes
Maintainer: Jeroen Ooms
openssl-0.2/openssl/R/random_num.R |only
openssl-0.2/openssl/man/rand_num.Rd |only
openssl-0.3/openssl/DESCRIPTION | 16 ++++++------
openssl-0.3/openssl/LICENSE | 4 +--
openssl-0.3/openssl/MD5 | 45 ++++++++++++++++++++++++----------
openssl-0.3/openssl/NAMESPACE | 17 +++++++++++-
openssl-0.3/openssl/R/hash.R |only
openssl-0.3/openssl/R/onload.R |only
openssl-0.3/openssl/R/openssl.R | 41 +++++++-----------------------
openssl-0.3/openssl/R/rand_bytes.R |only
openssl-0.3/openssl/R/stream.R |only
openssl-0.3/openssl/build |only
openssl-0.3/openssl/configure | 10 +++----
openssl-0.3/openssl/inst |only
openssl-0.3/openssl/man/hash.Rd |only
openssl-0.3/openssl/man/openssl.Rd |only
openssl-0.3/openssl/man/rand_bytes.Rd | 30 +++++++++++++++++-----
openssl-0.3/openssl/src/Makevars | 3 ++
openssl-0.3/openssl/src/Makevars.win | 2 -
openssl-0.3/openssl/src/digest.c |only
openssl-0.3/openssl/src/onload.c |only
openssl-0.3/openssl/src/rand_bytes.c | 4 ---
openssl-0.3/openssl/src/stream.c |only
openssl-0.3/openssl/tests |only
openssl-0.3/openssl/tools/winlibs.R | 11 +++++---
openssl-0.3/openssl/vignettes |only
26 files changed, 109 insertions(+), 74 deletions(-)
Title: Multichannel Wavelet Deconvolution with Additive Long Memory
Noise
Diff between mwaved versions 1.1.0 dated 2014-10-13 and 1.1.1 dated 2015-01-07
Description: Computes the Wavelet deconvolution estimate of a common signal
present in multiple channels that have possible different levels of blur
and long memory additive error.
Author: Justin Rory Wishart
Maintainer: Justin Rory Wishart
DESCRIPTION | 18 ++---
MD5 | 75 +++++++++++------------
NAMESPACE | 60 +++++++++---------
NEWS | 8 ++
R/functions.R | 9 +-
R/makeFunctions.R | 2
R/utility-mwaved.R | 141 +++++++++++++++++++++++---------------------
README.md | 2
build/vignette.rds |binary
inst/doc/mWaveD.R | 1
inst/doc/mWaveD.Rmd | 3
inst/doc/mWaveD.html | 109 ++++++++++++++++------------------
man/blurSignal.Rd | 3
man/boxcarBlur.Rd | 3
man/detectBlur.Rd | 3
man/directBlur.Rd | 3
man/gammaBlur.Rd | 3
man/mWaveDDemo.Rd | 3
man/makeSignals.Rd | 3
man/multiCoef.Rd | 5 -
man/multiEstimate.Rd | 5 -
man/multiNoise.Rd | 3
man/multiProj.Rd | 3
man/multiSigma.Rd | 3
man/multiThresh.Rd | 3
man/multiWaveD.Rd | 5 -
man/mwaved.Rd | 3
man/plot.mWaveD.Rd | 3
man/plot.waveletCoef.Rd | 3
man/resolutionMethod.Rd | 3
man/sigmaSNR.Rd | 3
man/summary.mWaveD.Rd | 3
man/theoreticalEta.Rd | 3
man/waveletThresh.Rd | 5 -
src/Makevars.in | 2
src/mwaved.cpp | 10 +--
tests/testthat/test-exact.R |only
tests/testthat/test-multi.R | 1
vignettes/mWaveD.Rmd | 3
39 files changed, 277 insertions(+), 241 deletions(-)
Title: R Graphics Output in LaTeX Format
Diff between tikzDevice versions 0.7.0 dated 2013-12-19 and 0.8 dated 2015-01-07
Description: The tikzDevice package provides a graphics output device for R
that records plots in a LaTeX-friendly format. The device transforms
plotting commands issued by R functions into LaTeX code blocks. When
included in a paper typeset by LaTeX, these blocks are interpreted with the
help of TikZ---a graphics package for TeX and friends written by Till
Tantau. Using the tikzDevice, the text of R plots can contain LaTeX
commands such as mathematical formula. The device also allows arbitrary
LaTeX code to be inserted into the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb, cre],
Yihui Xie [ctb]
Maintainer: Kirill Müller
tikzDevice-0.7.0/tikzDevice/NEWS |only
tikzDevice-0.7.0/tikzDevice/inst/tests |only
tikzDevice-0.8/tikzDevice/DESCRIPTION | 30
tikzDevice-0.8/tikzDevice/MD5 | 364 ++++++--
tikzDevice-0.8/tikzDevice/NAMESPACE | 2
tikzDevice-0.8/tikzDevice/R/cacheMetrics.R | 85 +
tikzDevice-0.8/tikzDevice/R/deviceUtils.R | 34
tikzDevice-0.8/tikzDevice/R/latexStrWidth.R | 454 +++++-----
tikzDevice-0.8/tikzDevice/R/sanitizeTexString.R | 34
tikzDevice-0.8/tikzDevice/R/tikz.R | 64 +
tikzDevice-0.8/tikzDevice/R/tikzAnnotate.R | 27
tikzDevice-0.8/tikzDevice/R/tikzDevice-package.R | 240 ++---
tikzDevice-0.8/tikzDevice/R/tikzInternal.R | 69 -
tikzDevice-0.8/tikzDevice/build/vignette.rds |binary
tikzDevice-0.8/tikzDevice/inst/NEWS.Rd |only
tikzDevice-0.8/tikzDevice/inst/doc/tikzDevice.R | 288 +++---
tikzDevice-0.8/tikzDevice/inst/doc/tikzDevice.Rnw | 327 ++++---
tikzDevice-0.8/tikzDevice/inst/doc/tikzDevice.pdf |binary
tikzDevice-0.8/tikzDevice/man/anyMultibyteUTF8Characters.Rd | 10
tikzDevice-0.8/tikzDevice/man/getLatexStrWidth.Rd | 48 -
tikzDevice-0.8/tikzDevice/man/gridToDevice.Rd | 15
tikzDevice-0.8/tikzDevice/man/sanitizeTexString.Rd | 12
tikzDevice-0.8/tikzDevice/man/setTikzDefaults.Rd | 12
tikzDevice-0.8/tikzDevice/man/tikz.Rd | 174 ++-
tikzDevice-0.8/tikzDevice/man/tikzAnnotate.Rd | 60 -
tikzDevice-0.8/tikzDevice/man/tikzCompilerInfo.Rd | 7
tikzDevice-0.8/tikzDevice/man/tikzDevice-package.Rd | 239 ++---
tikzDevice-0.8/tikzDevice/src/tikzDevice.c | 523 ++++++++----
tikzDevice-0.8/tikzDevice/src/tikzDevice.h | 82 +
tikzDevice-0.8/tikzDevice/tests/testthat |only
tikzDevice-0.8/tikzDevice/tests/unit_tests.R | 107 --
tikzDevice-0.8/tikzDevice/vignettes/consoleExample.tex |only
tikzDevice-0.8/tikzDevice/vignettes/figs |only
tikzDevice-0.8/tikzDevice/vignettes/refs.bib | 60 -
tikzDevice-0.8/tikzDevice/vignettes/tikzCodeBlock.sty | 152 +--
tikzDevice-0.8/tikzDevice/vignettes/tikzDevice.Rnw | 327 ++++---
tikzDevice-0.8/tikzDevice/vignettes/tikzDeviceVignette.sty | 12
37 files changed, 2180 insertions(+), 1678 deletions(-)
Title: Distances and Routes on Geographical Grids
Diff between gdistance versions 1.1-5 dated 2014-02-18 and 1.1-6 dated 2015-01-07
Description: Calculate distances and routes on geographic grids.
Author: Jacob van Etten
Maintainer: Jacob van Etten
gdistance-1.1-5/gdistance/inst/doc/gdistance.R |only
gdistance-1.1-5/gdistance/inst/doc/gdistance.Rnw |only
gdistance-1.1-5/gdistance/inst/doc/gdistance.pdf |only
gdistance-1.1-5/gdistance/vignettes/gdistance.Rnw |only
gdistance-1.1-5/gdistance/vignettes/gdistance2.bib |only
gdistance-1.1-6/gdistance/ChangeLog | 6 +++++
gdistance-1.1-6/gdistance/DESCRIPTION | 15 +++++++------
gdistance-1.1-6/gdistance/MD5 | 24 ++++++++++-----------
gdistance-1.1-6/gdistance/NAMESPACE | 11 +++++----
gdistance-1.1-6/gdistance/R/shortestPath.R | 5 ++--
gdistance-1.1-6/gdistance/build/vignette.rds |binary
gdistance-1.1-6/gdistance/inst/doc/gdistance1.R |only
gdistance-1.1-6/gdistance/inst/doc/gdistance1.Rnw |only
gdistance-1.1-6/gdistance/inst/doc/gdistance1.pdf |only
gdistance-1.1-6/gdistance/man/Transition-class.Rd | 10 +++++---
gdistance-1.1-6/gdistance/man/pathInc.Rd | 2 -
gdistance-1.1-6/gdistance/vignettes/gdistance1.Rnw |only
gdistance-1.1-6/gdistance/vignettes/gdistance1.bib |only
18 files changed, 42 insertions(+), 31 deletions(-)
Title: FastPCS Robust Fit of Multivariate Location and Scatter
Diff between FastPCS versions 0.1.1 dated 2014-11-13 and 0.1.2 dated 2015-01-07
Description: The FastPCS algorithm of Vakili and Schmitt (2014) for robust estimation of multivariate location and scatter and multivariate outliers detection.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
FastPCS-0.1.1/FastPCS/man/numStarts.Rd |only
FastPCS-0.1.2/FastPCS/DESCRIPTION | 6 +-
FastPCS-0.1.2/FastPCS/MD5 | 16 +++---
FastPCS-0.1.2/FastPCS/NAMESPACE | 4 -
FastPCS-0.1.2/FastPCS/R/FastPCS.R | 62 ++++++++++++--------------
FastPCS-0.1.2/FastPCS/man/FRCSnumStarts.Rd |only
FastPCS-0.1.2/FastPCS/man/FastPCS-package.Rd | 2
FastPCS-0.1.2/FastPCS/man/FastPCS.Rd | 19 ++++++--
FastPCS-0.1.2/FastPCS/man/plot.FastPCS.Rd | 2
FastPCS-0.1.2/FastPCS/src/FastPCS.cpp | 64 ++++++++++++++++-----------
10 files changed, 99 insertions(+), 76 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.0 dated 2014-12-16 and 1.0.4 dated 2015-01-06
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 8 +++++---
MD5 | 12 ++++++------
R/AddDropIndividuals.R | 2 +-
R/Create_Landscapes.r | 7 +------
R/Encounter_history.R | 3 ++-
R/Test_Samples.r | 2 +-
R/checkParameters.R | 27 ++++++++++++++++++++++-----
7 files changed, 38 insertions(+), 23 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.13 dated 2014-11-13 and 2.14 dated 2015-01-06
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
lsmeans-2.13/lsmeans/R/old-lsmeans.R |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.R |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.pdf |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.rnw |only
lsmeans-2.13/lsmeans/vignettes/lsmeans-changes.rnw |only
lsmeans-2.14/lsmeans/DESCRIPTION | 12
lsmeans-2.14/lsmeans/MD5 | 66 +--
lsmeans-2.14/lsmeans/NAMESPACE | 20 -
lsmeans-2.14/lsmeans/R/cld.lsm.R | 15
lsmeans-2.14/lsmeans/R/glht-support.R | 2
lsmeans-2.14/lsmeans/R/helpers.R | 11
lsmeans-2.14/lsmeans/R/lsm-contr.R | 21 -
lsmeans-2.14/lsmeans/R/lsmeans.R | 83 +++-
lsmeans-2.14/lsmeans/R/lsmip.R | 4
lsmeans-2.14/lsmeans/R/ordinal-support.R | 59 ++-
lsmeans-2.14/lsmeans/R/plot.lsm.R | 2
lsmeans-2.14/lsmeans/R/ref.grid.R | 413 ---------------------
lsmeans-2.14/lsmeans/R/summary.R |only
lsmeans-2.14/lsmeans/build/vignette.rds |binary
lsmeans-2.14/lsmeans/inst/NEWS | 28 +
lsmeans-2.14/lsmeans/inst/doc/extending.pdf |binary
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.R | 154 ++++---
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.pdf |binary
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.rnw | 60 +--
lsmeans-2.14/lsmeans/man/contrast.Rd | 5
lsmeans-2.14/lsmeans/man/glht.Rd | 2
lsmeans-2.14/lsmeans/man/lsmeans-package.Rd | 16
lsmeans-2.14/lsmeans/man/lsmeans.Rd | 22 -
lsmeans-2.14/lsmeans/man/models.Rd | 9
lsmeans-2.14/lsmeans/man/pairwise.lsmc.Rd | 11
lsmeans-2.14/lsmeans/man/ref.grid.Rd | 3
lsmeans-2.14/lsmeans/man/ref.grid.class.Rd | 2
lsmeans-2.14/lsmeans/man/summary.Rd | 26 -
lsmeans-2.14/lsmeans/man/update.Rd | 12
lsmeans-2.14/lsmeans/tests/tests1.Rout.save | 28 -
lsmeans-2.14/lsmeans/vignettes/lsmeans.bib | 34 +
lsmeans-2.14/lsmeans/vignettes/using-lsmeans.rnw | 60 +--
37 files changed, 512 insertions(+), 668 deletions(-)
Title: R Interface to C API of GLPK
Diff between glpkAPI versions 1.2.11 dated 2014-11-16 and 1.3.0 dated 2015-01-06
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Claus Jonathan Fritzemeier [cre],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Claus Jonathan Fritzemeier
DESCRIPTION | 16 +-
MD5 | 328 ++++++++++++++++++++---------------------
README.md |only
build/vignette.rds |binary
inst/NEWS.Rd | 10 +
inst/doc/glpk-gmpl-intro.R |only
inst/doc/glpk-gmpl-intro.Rnw |only
inst/doc/glpk-gmpl-intro.pdf |only
inst/doc/glpkAPI.pdf |binary
inst/extdata |only
man/addColsGLPK.Rd | 5
man/addRowsGLPK.Rd | 5
man/advBasisGLPK.Rd | 5
man/bfExistsGLPK.Rd | 5
man/bfUpdatedGLPK.Rd | 5
man/checkDupGLPK.Rd | 5
man/copyProbGLPK.Rd | 5
man/cpxBasisGLPK.Rd | 5
man/createIndexGLPK.Rd | 5
man/delColsGLPK.Rd | 5
man/delProbGLPK.Rd | 5
man/delRowsGLPK.Rd | 5
man/deleteIndexGLPK.Rd | 5
man/eraseProbGLPK.Rd | 5
man/factorizeGLPK.Rd | 5
man/findColGLPK.Rd | 5
man/findRowGLPK.Rd | 5
man/getBfcpGLPK.Rd | 5
man/getBheadGLPK.Rd | 5
man/getCbindGLPK.Rd | 5
man/getColDualGLPK.Rd | 5
man/getColDualIptGLPK.Rd | 5
man/getColKindGLPK.Rd | 5
man/getColLowBndGLPK.Rd | 5
man/getColNameGLPK.Rd | 5
man/getColPrimGLPK.Rd | 5
man/getColPrimIptGLPK.Rd | 5
man/getColStatGLPK.Rd | 5
man/getColTypeGLPK.Rd | 5
man/getColUppBndGLPK.Rd | 5
man/getColsDualGLPK.Rd | 5
man/getColsDualIptGLPK.Rd | 5
man/getColsKindGLPK.Rd | 5
man/getColsLowBndsGLPK.Rd | 5
man/getColsPrimGLPK.Rd | 5
man/getColsPrimIptGLPK.Rd | 5
man/getColsStatGLPK.Rd | 5
man/getColsUppBndsGLPK.Rd | 5
man/getDualStatGLPK.Rd | 5
man/getInteriorParmGLPK.Rd | 5
man/getMIPParmGLPK.Rd | 5
man/getMatColGLPK.Rd | 5
man/getMatRowGLPK.Rd | 5
man/getNumBinGLPK.Rd | 5
man/getNumColsGLPK.Rd | 5
man/getNumIntGLPK.Rd | 5
man/getNumNnzGLPK.Rd | 5
man/getNumRowsGLPK.Rd | 5
man/getObjCoefGLPK.Rd | 5
man/getObjCoefsGLPK.Rd | 5
man/getObjDirGLPK.Rd | 5
man/getObjNameGLPK.Rd | 5
man/getObjValGLPK.Rd | 5
man/getObjValIptGLPK.Rd | 5
man/getPrimStatGLPK.Rd | 5
man/getProbNameGLPK.Rd | 5
man/getRbindGLPK.Rd | 5
man/getRiiGLPK.Rd | 5
man/getRowDualGLPK.Rd | 5
man/getRowDualIptGLPK.Rd | 5
man/getRowLowBndGLPK.Rd | 5
man/getRowNameGLPK.Rd | 5
man/getRowPrimGLPK.Rd | 5
man/getRowPrimIptGLPK.Rd | 5
man/getRowStatGLPK.Rd | 5
man/getRowTypeGLPK.Rd | 5
man/getRowUppBndGLPK.Rd | 5
man/getRowsDualGLPK.Rd | 5
man/getRowsDualIptGLPK.Rd | 5
man/getRowsLowBndsGLPK.Rd | 5
man/getRowsPrimGLPK.Rd | 5
man/getRowsPrimIptGLPK.Rd | 5
man/getRowsStatGLPK.Rd | 5
man/getRowsTypesGLPK.Rd | 5
man/getRowsUppBndsGLPK.Rd | 5
man/getSimplexParmGLPK.Rd | 5
man/getSjjGLPK.Rd | 5
man/getSolStatGLPK.Rd | 5
man/getSolStatIptGLPK.Rd | 5
man/getUnbndRayGLPK.Rd | 5
man/glpkAPI-package.Rd | 5
man/glpkConstants.Rd | 5
man/glpkPtr-class.Rd | 5
man/initProbGLPK.Rd | 5
man/loadMatrixGLPK.Rd | 5
man/mipColValGLPK.Rd | 5
man/mipColsValGLPK.Rd | 5
man/mipObjValGLPK.Rd | 5
man/mipRowValGLPK.Rd | 5
man/mipRowsValGLPK.Rd | 5
man/mipStatusGLPK.Rd | 5
man/mplAllocWkspGLPK.Rd | 5
man/mplBuildProbGLPK.Rd | 5
man/mplFreeWkspGLPK.Rd | 5
man/mplGenerateGLPK.Rd | 5
man/mplPostsolveGLPK.Rd | 5
man/mplReadDataGLPK.Rd | 5
man/mplReadModelGLPK.Rd | 5
man/printIptGLPK.Rd | 5
man/printMIPGLPK.Rd | 5
man/printRangesGLPK.Rd | 5
man/printSolGLPK.Rd | 5
man/readIptGLPK.Rd | 5
man/readLPGLPK.Rd | 5
man/readMIPGLPK.Rd | 5
man/readMPSGLPK.Rd | 5
man/readProbGLPK.Rd | 5
man/readSolGLPK.Rd | 5
man/return_codeGLPK.Rd | 5
man/scaleProbGLPK.Rd | 5
man/setBfcpGLPK.Rd | 5
man/setColBndGLPK.Rd | 5
man/setColKindGLPK.Rd | 5
man/setColNameGLPK.Rd | 5
man/setColStatGLPK.Rd | 5
man/setColsBndsGLPK.Rd | 5
man/setColsBndsObjCoefsGLPK.Rd | 5
man/setColsKindGLPK.Rd | 5
man/setColsNamesGLPK.Rd | 5
man/setDefaultIptParmGLPK.Rd | 5
man/setDefaultMIPParmGLPK.Rd | 5
man/setDefaultSmpParmGLPK.Rd | 5
man/setInteriorParmGLPK.Rd | 5
man/setMIPParmGLPK.Rd | 5
man/setMatColGLPK.Rd | 5
man/setMatRowGLPK.Rd | 5
man/setObjCoefGLPK.Rd | 5
man/setObjCoefsGLPK.Rd | 5
man/setObjDirGLPK.Rd | 5
man/setObjNameGLPK.Rd | 5
man/setProbNameGLPK.Rd | 5
man/setRhsZeroGLPK.Rd | 5
man/setRiiGLPK.Rd | 5
man/setRowBndGLPK.Rd | 5
man/setRowNameGLPK.Rd | 5
man/setRowStatGLPK.Rd | 5
man/setRowsBndsGLPK.Rd | 5
man/setRowsNamesGLPK.Rd | 5
man/setSimplexParmGLPK.Rd | 5
man/setSjjGLPK.Rd | 5
man/solveInteriorGLPK.Rd | 5
man/solveMIPGLPK.Rd | 5
man/solveSimplexExactGLPK.Rd | 5
man/solveSimplexGLPK.Rd | 5
man/sortMatrixGLPK.Rd | 5
man/status_codeGLPK.Rd | 5
man/stdBasisGLPK.Rd | 5
man/termOutGLPK.Rd | 5
man/unscaleProbGLPK.Rd | 5
man/versionGLPK.Rd | 5
man/warmUpGLPK.Rd | 5
man/writeIptGLPK.Rd | 5
man/writeLPGLPK.Rd | 5
man/writeMIPGLPK.Rd | 5
man/writeMPSGLPK.Rd | 5
man/writeProbGLPK.Rd | 5
man/writeSolGLPK.Rd | 5
vignettes/glpk-gmpl-intro.Rnw |only
168 files changed, 657 insertions(+), 482 deletions(-)
Title: R Unit Test Framework
Diff between RUnit versions 0.4.27 dated 2014-09-19 and 0.4.28 dated 2015-01-06
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools
Author: Matthias Burger
Maintainer: ORPHANED
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/exportHTML.r | 6 +++---
build/RUnit.pdf |binary
inst/unitTests/Makefile | 13 +++++++------
5 files changed, 18 insertions(+), 17 deletions(-)
Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for
(Bio)Equivalence Studies
Diff between PowerTOST versions 1.2-04 dated 2014-12-19 and 1.2-05 dated 2015-01-06
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes
PowerTOST-1.2-04/PowerTOST/R/CVfromCI.R |only
PowerTOST-1.2-04/PowerTOST/inst/doc/BE_power_sample_size_excerpt_V06.pdf |only
PowerTOST-1.2-04/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.06.pdf |only
PowerTOST-1.2-05/PowerTOST/DESCRIPTION | 14 +++--
PowerTOST-1.2-05/PowerTOST/MD5 | 18 +++----
PowerTOST-1.2-05/PowerTOST/NEWS | 8 +++
PowerTOST-1.2-05/PowerTOST/R/CVfromCI_BL.R |only
PowerTOST-1.2-05/PowerTOST/R/OwensQOwen.R | 3 -
PowerTOST-1.2-05/PowerTOST/R/pvalue.TOST_Benjamin.R | 3 -
PowerTOST-1.2-05/PowerTOST/inst/doc/BE_power_sample_size_excerpt_V07.pdf |only
PowerTOST-1.2-05/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.07.pdf |only
PowerTOST-1.2-05/PowerTOST/man/CVfromCI.Rd | 25 ++++++----
PowerTOST-1.2-05/PowerTOST/man/pvalue.TOST.Rd | 6 +-
13 files changed, 48 insertions(+), 29 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Diff between nodiv versions 1.0.0 dated 2014-12-01 and 1.0.1 dated 2015-01-06
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
DESCRIPTION | 8 ++--
MD5 | 26 ++++++++-------
NAMESPACE | 6 +--
R/General_figure_functions.R | 8 +++-
R/Methods_for_data_objects.R | 69 ++++++++++++++++++++++++++++++++++-------
R/Methods_for_result_objects.R | 7 ++++
R/Node_based_analysis.R | 19 +++++++----
R/Prepare_data.R | 26 ++++++++++++++-
man/Node_size.Rd | 2 -
man/Nspecies.Rd | 10 +++--
man/nodiv-package.Rd | 2 -
man/plotSOS.Rd | 6 ++-
man/plot_points.Rd | 5 ++
tests |only
14 files changed, 145 insertions(+), 49 deletions(-)
Title: Project MOSAIC (mosaic-web.org) statistics and mathematics
teaching utilities
Diff between mosaic versions 0.9.1-3 dated 2014-08-23 and 0.9.2-2 dated 2015-01-06
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim
Maintainer: Randall Pruim
skeleton/skeleton.Rmd | 4
tmp/cranberry5dfb3a3c204e/mosaic-0.9.1-3/mosaic/R/MAD.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.1-3/mosaic/demo/example.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.1-3/mosaic/demo/phaseplane.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.1-3/mosaic/demo/regression.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/DESCRIPTION | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/MD5 | 357 +++++-----
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/NAMESPACE | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/CIsim.R | 66 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/Calculus.R | 28
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/aggregatingAux.R | 102 ++
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/aggregatingMeta.R | 71 +
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/binom.test.R | 5
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/chisq.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/collisions.R | 18
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/compareMean.R | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/compareProportion.R | 13
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/confint.R | 88 +-
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/diffmean.R | 19
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/do.R | 16
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/docFile.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/dpqrdist.R | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/factorize.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/fetchGoogle.R | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/fitModel.R | 4
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/mPlots.R | 101 +-
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/makeFun.R | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/maps2.R | 7
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/mplot.R | 9
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/msummary.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/plotCumfreq.R | 1
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/plotDist.R | 225 ++----
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/plotFun.R | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/prop.test.R | 5
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/read.file.R | 11
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/swap.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/tally.R | 51 +
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/themes.R | 125 ++-
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/utils.R | 38 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/xchisq.test.R | 36 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/xpnorm.R | 16
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/xqqmath.R | 1
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/00Index | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/funplots.R | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/histogram.R | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/leastsquares.R |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/NEWS.Rd | 22
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/GraphicsWithMosaic.html | 47 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/V2StartTeaching.pdf |binary
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/V3Commands.pdf |binary
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/mosaicresources.Rnw | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/mosaicresources.pdf |binary
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/rmarkdown/templates/mosaic-fancy/skeleton/skeleton.Rmd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/rmarkdown/templates/mosaic-plain-pdf |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/rmarkdown/templates/mosaic-plain/template.yaml | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/tests/test-groupwiseModels.R | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/tests/test-tabulation.R | 4
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/Broyden.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/CIAdata.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/CIsim.Rd | 53 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/Calculus.Rd | 28
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/FunctionsFromData.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/MAD.Rd | 31
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/MAD_.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/TukeyHSD.lm.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/adapt_seq.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregating.Rd | 20
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingAux.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingFunction1.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingFunction2.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/as-xtabs.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/bargraph.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/binom.test.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/cdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/chisq.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/clustering.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/coef.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/columns.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/compareMean.Rd | 11
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/compareProportion.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/confint.Rd | 52 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/cross.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/deg2rad.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/deltaMethod.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/derivedFactor.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/dfapply.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/diffmean.Rd | 13
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/do.Rd | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/docFile.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/dotPlot.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ediff.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/evalFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/evalSubFormula.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/expandFun.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/factorize.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fav_stats.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchData.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchGapminder.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchGoogle.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/findZeros.Rd | 18
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/findZerosMult.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitModel.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitSpline.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitdistr.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fortify.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fractions.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/freqpolygon.Rd | 22
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/getVarFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/googleMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/inferArgs.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/integrateODE.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/interval.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/is.wholenumber.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/joinFrames.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ladd.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/latlon2xyz.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/linear.algebra.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/logical2factor.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/logit.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mPlotting.Rd | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mUSMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mWorldMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeColorscheme.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeFun.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeMap.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mid.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mm.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/modelVars.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic-internal.Rd | 28
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic-package.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic.options.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaicformula.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mplot.Rd | 68 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/msummary.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/named.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/nicenames.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ntiles.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/numD.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/oddsRatio.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.levelcontourplot.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.lmbands.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.plotFun.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.plotFun1.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/parseFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/perctable.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotCumfreq.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotDist.Rd | 19
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotFun.Rd | 40 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotPoints.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pqrdata.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pqrdata2.Rd | 26
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/project-methods.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/prop.Rd | 17
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/prop.test.Rd | 16
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/qdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/r.squared.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rand.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/read.file.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/repeater-class.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/resample.Rd | 22
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rescale.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rflip.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rfun.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rgeo-internals.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rgeo.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rkintegrate.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rspin.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rsquared.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rstudio.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/simplify.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/sp2df.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/standardName.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/statTally.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/surround.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/swap.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/symbolicD.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/symbolicInt.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/tally.Rd | 46 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/theme_map.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/themes.Rd | 9
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ttest.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xchisq.test.Rd | 7
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xhistogram.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xpnorm.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xqqmath.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/zscore.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/vignettes/mosaicresources.Rnw | 2
188 files changed, 1602 insertions(+), 1104 deletions(-)
Title: Toolkit Implementation of gWidgets2 for tcltk
Diff between gWidgets2tcltk versions 1.0-3 dated 2014-12-06 and 1.0-4 dated 2015-01-06
More information about gWidgets2tcltk at CRAN
Description: Port of the gWidgets2 API for the tcltk
package.
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/gtable.R | 43 ++++++++++++++++++++++++-------------------
3 files changed, 29 insertions(+), 24 deletions(-)
Permanent link
Title: Test Analysis Modules
Diff between TAM versions 1.2 dated 2014-11-22 and 1.3 dated 2015-01-06
Description:
The package includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
TAM-1.2/TAM/R/TAM-internal_intermediate.R |only
TAM-1.2/TAM/R/TAM-internal_mstep.R |only
TAM-1.2/TAM/R/TAM-internal_postproc.R |only
TAM-1.2/TAM/R/tam.mml.3pl.postproc.R |only
TAM-1.3/TAM/DESCRIPTION | 25
TAM-1.3/TAM/MD5 | 163 +++--
TAM-1.3/TAM/NAMESPACE | 76 ++
TAM-1.3/TAM/R/IRT.factor.scores.tam.R | 18
TAM-1.3/TAM/R/IRT.irfprob.tam.R | 15
TAM-1.3/TAM/R/IRT.likelihood.TAM.R | 28
TAM-1.3/TAM/R/Mstep_slope.v2.R |only
TAM-1.3/TAM/R/TAM.ic.R |only
TAM-1.3/TAM/R/TAM.itempartable.R |only
TAM-1.3/TAM/R/add.colnames.resp.R |only
TAM-1.3/TAM/R/anova.tam.R | 7
TAM-1.3/TAM/R/calc_exp_TK.R |only
TAM-1.3/TAM/R/calc_posterior.v2.R |only
TAM-1.3/TAM/R/calc_prob.v5.R |only
TAM-1.3/TAM/R/change.grep.lavpartable.R |only
TAM-1.3/TAM/R/create.deltaDesign.R |only
TAM-1.3/TAM/R/designMatrices.R | 38 +
TAM-1.3/TAM/R/designMatrices.mfr2.R | 6
TAM-1.3/TAM/R/designMatrices_aux.R | 33 +
TAM-1.3/TAM/R/doparse.R |only
TAM-1.3/TAM/R/extend.label.group.R |only
TAM-1.3/TAM/R/latreg.mstep.regression.R |only
TAM-1.3/TAM/R/latreg_TAM.ic.R |only
TAM-1.3/TAM/R/lavaanify.IRT.R | 324 +----------
TAM-1.3/TAM/R/lavaanify.grep.nonlinear.R |only
TAM-1.3/TAM/R/lavaanify.sirt.v1.R |only
TAM-1.3/TAM/R/lavpartable.grep.underbrace.R |only
TAM-1.3/TAM/R/lavpartable2lavsyntax.R |only
TAM-1.3/TAM/R/logLik_tam.R | 3
TAM-1.3/TAM/R/mml.3pl.TAM.ic.R |only
TAM-1.3/TAM/R/mml.3pl.TAM.itempartable.R |only
TAM-1.3/TAM/R/mml.3pl.calc_prob.v5.R |only
TAM-1.3/TAM/R/mml.3pl.distrubutionmoments.R |only
TAM-1.3/TAM/R/mstep.regression.R |only
TAM-1.3/TAM/R/plot.tam.R | 210 +++++--
TAM-1.3/TAM/R/plotDevianceTAM.R | 2
TAM-1.3/TAM/R/rbind.twomatrices.R |only
TAM-1.3/TAM/R/remove.duplicated.variances.lavsyn.R |only
TAM-1.3/TAM/R/split.syn.string.R |only
TAM-1.3/TAM/R/stud_prior.R |only
TAM-1.3/TAM/R/summary.tam.R | 133 ++--
TAM-1.3/TAM/R/summary.tam.mml.3pl.R | 7
TAM-1.3/TAM/R/summary.tamaan.3pl.intro.R |only
TAM-1.3/TAM/R/summary.tamaan.R |only
TAM-1.3/TAM/R/summary.tamaan.aux.R |only
TAM-1.3/TAM/R/taamanify.proc.lavaanmodel.R |only
TAM-1.3/TAM/R/tam.calc.counts.R |only
TAM-1.3/TAM/R/tam.jml.R | 4
TAM-1.3/TAM/R/tam.jml2.R | 3
TAM-1.3/TAM/R/tam.latreg.R |only
TAM-1.3/TAM/R/tam.mml.2pl.R | 11
TAM-1.3/TAM/R/tam.mml.3pl.R | 150 +++--
TAM-1.3/TAM/R/tam.mml.3pl.algorithm.R | 84 --
TAM-1.3/TAM/R/tam.mml.3pl.est.intercepts.R | 18
TAM-1.3/TAM/R/tam.mml.3pl.est.slopes.R | 57 +
TAM-1.3/TAM/R/tam.mml.R | 27
TAM-1.3/TAM/R/tam.mml.mfr.R | 2
TAM-1.3/TAM/R/tam.modelfit.R | 12
TAM-1.3/TAM/R/tam.pv.R | 233 +++++--
TAM-1.3/TAM/R/tamaan.3pl.lca.R |only
TAM-1.3/TAM/R/tamaan.3pl.loclca.R |only
TAM-1.3/TAM/R/tamaan.3pl.mixture.R |only
TAM-1.3/TAM/R/tamaan.3pl.olca.R |only
TAM-1.3/TAM/R/tamaan.3pl.trait.R |only
TAM-1.3/TAM/R/tamaan.R |only
TAM-1.3/TAM/R/tamaanify.R |only
TAM-1.3/TAM/R/tamaanify.create.A.R |only
TAM-1.3/TAM/R/tamaanify.create.Q.R |only
TAM-1.3/TAM/R/tamaanify.define.method.R |only
TAM-1.3/TAM/R/tamaanify.grep.linequations.R |only
TAM-1.3/TAM/R/tamaanify.modelconstraint.loadings.R |only
TAM-1.3/TAM/R/tamaanify.modelprior.R |only
TAM-1.3/TAM/R/tamaanify.proc.analysis.R |only
TAM-1.3/TAM/R/tamaanify.proc.items.R |only
TAM-1.3/TAM/R/tamaanify.proc.itemtype.R |only
TAM-1.3/TAM/R/tamaanify.proc.loadings.B.fixed.R |only
TAM-1.3/TAM/R/tamaanify.proc.modelconstraint.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.deltadesign.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.LCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.LOCLCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.MIXTURE.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.OLCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pldesignMatrices.R |only
TAM-1.3/TAM/R/tamaanify.variance.fixed.R |only
TAM-1.3/TAM/R/tampv2datalist.R |only
TAM-1.3/TAM/data/data.geiser.rda |only
TAM-1.3/TAM/data/data.janssen.rda |only
TAM-1.3/TAM/data/data.janssen2.rda |only
TAM-1.3/TAM/inst/NEWS | 73 ++
TAM-1.3/TAM/man/IRT.factor.scores.tam.Rd | 10
TAM-1.3/TAM/man/IRT.irfprob.tam.Rd | 10
TAM-1.3/TAM/man/IRT.likelihood.tam.Rd | 17
TAM-1.3/TAM/man/TAM-internal.Rd | 2
TAM-1.3/TAM/man/TAM-package.Rd | 16
TAM-1.3/TAM/man/anova.tam.Rd | 39 -
TAM-1.3/TAM/man/data.examples.Rd | 1
TAM-1.3/TAM/man/data.geiser.Rd |only
TAM-1.3/TAM/man/data.janssen.Rd |only
TAM-1.3/TAM/man/designMatrices.Rd | 4
TAM-1.3/TAM/man/doparse.Rd |only
TAM-1.3/TAM/man/lavaanify.IRT.Rd | 116 +++
TAM-1.3/TAM/man/plot.tam.Rd | 34 +
TAM-1.3/TAM/man/tam.fit.Rd | 4
TAM-1.3/TAM/man/tam.latreg.Rd |only
TAM-1.3/TAM/man/tam.mml.3pl.Rd | 188 +++++-
TAM-1.3/TAM/man/tam.mml.Rd | 316 +++++++++-
TAM-1.3/TAM/man/tam.modelfit.Rd | 15
TAM-1.3/TAM/man/tam.pv.Rd | 134 ++++
TAM-1.3/TAM/man/tam.threshold.Rd | 41 +
TAM-1.3/TAM/man/tam.wle.Rd | 94 +++
TAM-1.3/TAM/man/tamaan.Rd |only
TAM-1.3/TAM/man/tamaanify.Rd |only
TAM-1.3/TAM/man/tampv2datalist.Rd |only
TAM-1.3/TAM/src/tam_caux.c | 50 +
119 files changed, 2014 insertions(+), 839 deletions(-)
Title: Inverse Estimation/Calibration Functions
Diff between investr versions 1.2.0 dated 2014-12-23 and 1.2.1 dated 2015-01-06
Description: Functions to facilitate inverse estimation/calibration in linear,
nonlinear, and (linear) mixed models. A generic function is also provided
for plotting fitted regression models with or without confidence/prediction
bands that may be of use to the general user.
Author: Brandon M. Greenwell
Maintainer: Brandon M. Greenwell
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
NEWS | 9 +++++++--
R/calibrate.R | 13 +++++++++++--
R/invest.R | 16 +++++++++-------
R/plotFit.R | 22 ++++++----------------
R/utilities.R | 15 +++++++++++++++
man/AnyNA.Rd |only
man/calibrate.Rd | 13 +++++++++++--
man/invest.Rd | 12 +++++++-----
man/investr-package.Rd | 10 ++++++----
man/plotFit.Rd | 4 ++--
tests/testthat/test-invest.R | 4 ++++
13 files changed, 93 insertions(+), 54 deletions(-)
Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly From
Convex Shapes
Diff between hitandrun versions 0.4-2 dated 2014-08-04 and 0.5 dated 2015-01-06
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef
DESCRIPTION | 13 +++++-----
MD5 | 31 ++++++++++++++----------
NAMESPACE | 8 +++---
NEWS | 9 +++++++
R/sample.R | 60 +++++++++++++++++++++++++++++++++++++++++++----
R/shakeandbake.R |only
R/transformSimplex.R | 4 ++-
man/findFace.Rd |only
man/har-constraint.Rd | 2 -
man/hitandrun-package.Rd | 5 ++-
man/sab.Rd |only
man/shakeandbake.Rd |only
src/Makevars | 3 +-
src/bbReject.c | 2 -
src/har.c | 2 -
src/har.h | 21 +++++++++++++++-
src/hit.c | 4 +--
src/intersect.c |only
src/rsabDir.c |only
src/sab.c |only
20 files changed, 128 insertions(+), 36 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 5.7 dated 2014-12-17 and 5.8 dated 2015-01-06
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/guerrero.R | 11 ++++++-----
R/season.R | 7 +++++++
README.md | 2 +-
6 files changed, 27 insertions(+), 15 deletions(-)
Title: Dave Armstrong's Miscellaneous Functions
Diff between DAMisc versions 1.2 dated 2013-04-09 and 1.3 dated 2015-01-06
Description: This package contains a miscellaneous set of functions I use in my teaching either at UWM or the ICPSR Summer Program. Broadly, the functions help with presentation and interpretation of GLMs.
Author: Dave Armstrong (UW-Milwaukee, Department of Political Science)
Maintainer: Dave Armstrong
DAMisc-1.2/DAMisc/man/multiChange.Rd |only
DAMisc-1.3/DAMisc/DESCRIPTION | 17
DAMisc-1.3/DAMisc/MD5 | 36
DAMisc-1.3/DAMisc/NAMESPACE | 74 +-
DAMisc-1.3/DAMisc/R/DAMisc_functions.R | 1118 ++++++++++++++++++++++++++++---
DAMisc-1.3/DAMisc/README.md |only
DAMisc-1.3/DAMisc/man/DAMisc-package.Rd | 10
DAMisc-1.3/DAMisc/man/aveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/combTest.Rd |only
DAMisc-1.3/DAMisc/man/crSpanTest.Rd | 3
DAMisc-1.3/DAMisc/man/glmChange.Rd | 6
DAMisc-1.3/DAMisc/man/glmChange2.Rd |only
DAMisc-1.3/DAMisc/man/intQualQuant.Rd | 32
DAMisc-1.3/DAMisc/man/mnlAveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/mnlChange.Rd |only
DAMisc-1.3/DAMisc/man/mnlChange2.Rd |only
DAMisc-1.3/DAMisc/man/mnlfit.Rd |only
DAMisc-1.3/DAMisc/man/ordAveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/ordChange.Rd | 8
DAMisc-1.3/DAMisc/man/ordChange2.Rd |only
DAMisc-1.3/DAMisc/man/ordFit.Rd |only
DAMisc-1.3/DAMisc/man/panel.ci.Rd | 2
DAMisc-1.3/DAMisc/man/panel.doublerug.Rd |only
DAMisc-1.3/DAMisc/man/panel.transci.Rd |only
DAMisc-1.3/DAMisc/man/prepanel.ci.Rd | 2
DAMisc-1.3/DAMisc/man/ziChange.Rd | 3
26 files changed, 1149 insertions(+), 162 deletions(-)
Title: Process Control And Internal Validation Of Forensic STR Kits
Diff between strvalidator versions 1.3.1 dated 2014-10-15 and 1.4.0 dated 2015-01-06
Description: strvalidator is an open source platform for validation and process
control. It provide tools to analyse data from internal validation of
forensic short tandem repeat (STR) kits. The tools are developed to provide
the necessary data to conform with the ENFSI guidelines for internal
validation. More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson
DESCRIPTION | 13
MD5 | 310 +++----
NAMESPACE | 9
NEWS | 37
R/addColor.r | 32
R/addData.r | 85 +-
R/addData_gui.r | 8
R/addMarker.r | 15
R/addMarker_gui.r | 2
R/addSize_gui.r | 11
R/calculateBalance.r | 45 -
R/calculateBalance_gui.r | 23
R/calculateCapillary.r | 51 -
R/calculateCapillary_gui.r | 4
R/calculateDropout.r | 9
R/calculateDropout_gui.r | 22
R/calculatePullup.r |only
R/calculatePullup_gui.r |only
R/calculateResultType.r | 107 +-
R/calculateResultType_gui.r | 10
R/calculateStutter.r | 15
R/calculateStutter_gui.r | 26
R/checkDataset.r | 2
R/combineBinsAndPanels.r | 2
R/combine_gui.r | 2
R/compact.r |only
R/detectKit.r | 2
R/editData_gui.r | 4
R/export.r | 17
R/export_gui.r | 2
R/filterProfile.r | 53 -
R/filterProfile_gui.r | 6
R/generateEPG.r |only
R/generateEPG_gui.r |only
R/getDb.r | 13
R/getKit.r | 20
R/heightToPeak.r |only
R/import.r | 49 -
R/import_gui.r | 4
R/makeKit_gui.r | 373 ++++-----
R/modelDropout_gui.r | 87 +-
R/plotBalance_gui.r | 37
R/plotDropout_gui.r | 2
R/plotPrecision_gui.r | 2
R/plotPullup_gui.r |only
R/plotStutter_gui.r | 61 -
R/readBinsFile.r | 9
R/readPanelsFile.r | 9
R/sortMarker.r | 11
R/strvalidator.r | 230 ++++-
R/tablePrecision_gui.r | 4
R/trim.r | 53 -
R/trim_gui.r | 4
README.md | 45 -
inst/extdata/kit.txt | 1363 ++++++++++++++++++++++-----------
man/addColor.Rd | 6
man/addData.Rd | 22
man/addData_gui.Rd | 2
man/addDye_gui.Rd | 2
man/addMarker.Rd | 6
man/addMarker_gui.Rd | 2
man/addSize.Rd | 2
man/addSize_gui.Rd | 2
man/calculateBalance.Rd | 10
man/calculateBalance_gui.Rd | 2
man/calculateCapillary.Rd | 10
man/calculateCapillary_gui.Rd | 2
man/calculateConcordance.Rd | 2
man/calculateConcordance_gui.Rd | 2
man/calculateDropout.Rd | 8
man/calculateDropout_gui.Rd | 2
man/calculateHeight.Rd | 8
man/calculateHeight_gui.Rd | 2
man/calculateHeterozygous.Rd | 2
man/calculateHeterozygous_gui.Rd | 2
man/calculateMixture.Rd | 2
man/calculateMixture_gui.Rd | 2
man/calculateOL.Rd | 2
man/calculateOL_gui.Rd | 2
man/calculateOverlap.Rd | 2
man/calculateOverlap_gui.Rd | 2
man/calculatePeaks.Rd | 6
man/calculatePeaks_gui.Rd | 2
man/calculatePullup.Rd |only
man/calculatePullup_gui.Rd |only
man/calculateResultType.Rd | 26
man/calculateResultType_gui.Rd | 2
man/calculateStutter.Rd | 8
man/calculateStutter_gui.Rd | 2
man/checkDataset.Rd | 2
man/checkSubset.Rd | 2
man/checkSubset_gui.Rd | 2
man/colNames.Rd | 2
man/combineBinsAndPanels.Rd | 4
man/combine_gui.Rd | 2
man/compact.Rd |only
man/cropData_gui.Rd | 2
man/detectKit.Rd | 2
man/editData_gui.Rd | 2
man/export.Rd | 6
man/export_gui.Rd | 2
man/filterProfile.Rd | 18
man/filterProfile_gui.Rd | 2
man/generateEPG.Rd |only
man/generateEPG_gui.Rd |only
man/getDb.Rd | 6
man/getKit.Rd | 4
man/ggsave_gui.Rd | 2
man/guessProfile.Rd | 2
man/guessProfile_gui.Rd | 2
man/heightToPeak.Rd |only
man/import.Rd | 12
man/import_gui.Rd | 2
man/listObjects.Rd | 2
man/loadPackage.Rd | 2
man/makeKit_gui.Rd | 2
man/modelDropout_gui.Rd | 2
man/plotBalance_gui.Rd | 4
man/plotCapillary_gui.Rd | 2
man/plotDistribution_gui.Rd | 2
man/plotDropout_gui.Rd | 2
man/plotKit_gui.Rd | 2
man/plotPeaks_gui.Rd | 2
man/plotPrecision_gui.Rd | 2
man/plotPullup_gui.Rd |only
man/plotResultType_gui.Rd | 2
man/plotStutter_gui.Rd | 2
man/readBinsFile.Rd | 6
man/readPanelsFile.Rd | 6
man/ref1.Rd | 2
man/ref11.Rd | 2
man/ref2.Rd | 2
man/ref3.Rd | 2
man/ref4.Rd | 2
man/ref51.Rd | 2
man/ref52.Rd | 2
man/saveObject.Rd | 2
man/set1.Rd | 2
man/set2.Rd | 2
man/set3.Rd | 2
man/set4.Rd | 2
man/set5.Rd | 2
man/slim.Rd | 2
man/slim_gui.Rd | 2
man/sortMarker.Rd | 6
man/strValidator-package.Rd | 2
man/strvalidator.Rd | 2
man/tableBalance.Rd | 2
man/tableBalance_gui.Rd | 2
man/tableCapillary.Rd | 2
man/tableCapillary_gui.Rd | 2
man/tablePrecision.Rd | 2
man/tablePrecision_gui.Rd | 2
man/tableStutter.Rd | 2
man/tableStutter_gui.Rd | 2
man/trim.Rd | 16
man/trim_gui.Rd | 2
tests/testthat/test-calculateBalance.r | 52 -
tests/testthat/test-calculateDropout.r | 16
tests/testthat/test-calculateStutter.r | 40
tests/testthat/test-filterProfile.r | 60 -
tests/testthat/test-tableBalance.r | 8
tests/testthat/test-trim.r | 44 -
163 files changed, 2370 insertions(+), 1496 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-77 dated 2014-09-19 and 0.5-81 dated 2015-01-06
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 174 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 22 ++---
MD5 | 134 ++++++++++++++++----------------
NAMESPACE | 4
R/ME.R | 5 -
R/SpatialFiltering.R | 1
R/aple.R | 3
R/aple.mc.R | 9 +-
R/edit.nb.R | 1
R/eigenw.R | 3
R/error.spsarlm.R | 5 -
R/globalG.R | 8 +
R/impacts.R | 16 ++-
R/jacobian.R | 22 ++---
R/jacobian_setup.R | 12 ++
R/kpgm_new.R | 6 -
R/lag.spsarlm.R | 1
R/lee.test.R | 2
R/listw2Matrix.R | 11 ++
R/listw2sn.R | 9 +-
R/mcmcsamp.R | 6 -
R/mess.R | 3
R/nb2blocknb.R | 3
R/nb2listw.R | 4
R/nb2mat.R | 2
R/nbcosts.R | 18 +++-
R/prunecost.R | 16 ++-
R/read.gal.R | 4
R/s2sls.R | 1
R/sacsarlm.R | 1
R/sarlm.R | 4
R/spautolm.R | 3
R/utils.R | 2
build/vignette.rds |binary
inst/ChangeLog | 174 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/nb_igraph.R |only
inst/doc/nb_igraph.Rmd |only
inst/doc/nb_igraph.html |only
inst/doc/sids.R | 43 +++++-----
inst/doc/sids.Rnw | 1
inst/doc/sids.pdf |binary
man/aple.mc.Rd | 2
man/as_dgRMatrix_listw.Rd | 22 ++---
man/boston.Rd | 68 ++++++++--------
man/compon.Rd | 14 +++
man/edit.nb.Rd | 3
man/eigenw.Rd | 19 ++++
man/errorsarlm.Rd | 3
man/globalG.test.Rd | 16 ++-
man/gstsls.Rd | 2
man/house.Rd | 48 +++++------
man/impacts.sarlm.Rd | 18 +---
man/invIrM.Rd | 4
man/lagsarlm.Rd | 4
man/mat2listw.Rd | 2
man/nblag.Rd | 14 +++
man/sacsarlm.Rd | 2
man/set.mcOption.Rd | 4
man/skater.Rd | 2
man/spautolm.Rd | 24 +----
man/trW.Rd | 6 -
src/card.c | 13 ++-
src/dnn.c | 4
src/insiders.c | 4
src/nbdists.c | 10 +-
vignettes/nb_igraph.Rmd |only
vignettes/sids.Rnw | 1
70 files changed, 758 insertions(+), 284 deletions(-)
Title: R Client for Adobe Analytics API v1.4
Diff between RSiteCatalyst versions 1.4.2 dated 2014-12-03 and 1.4.3 dated 2015-01-06
Description: Functions for interacting with the Adobe Analytics API v1.4
(https://api.omniture.com/admin/1.4/rest/)
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch
RSiteCatalyst-1.4.2/RSiteCatalyst/README.md |only
RSiteCatalyst-1.4.3/RSiteCatalyst/DESCRIPTION | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/MD5 | 251 ++++++----
RSiteCatalyst-1.4.3/RSiteCatalyst/NAMESPACE | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/NEWS | 13
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ApiRequest.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/BuildInnerBreakdownsRecursively.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetCalculatedMetrics.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetFeed.R |only
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetFeeds.R |only
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetPermanentTraffic.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetScheduledSpike.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetTimeZone.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetUniqueVisitorVariable.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/JsonQueueRealTimeReport.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseFallout.R | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseOvertime.R | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParsePathing.R | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseRanked.R | 11
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseTrended.R | 11
RSiteCatalyst-1.4.3/RSiteCatalyst/R/QueueOvertime.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/RSiteCatalyst.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/SCAuth.R | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/R/buildHeader.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ApiRequest.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildClassificationValueSegment.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildHeader.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildInnerBreakdownsRecursively.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildLineItemSegment.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildRealTimeReportStructure.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/CancelReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetActivation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetAxleStartDate.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBaseCurrency.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBaseURL.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBookmarks.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetCalculatedMetrics.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetClassifications.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetCustomCalendar.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDashboards.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDataWarehouseDisplay.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDefaultPage.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDiscoverEnabled.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEcommerce.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetElements.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEndpoint.Rd | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEvars.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetFeed.Rd |only
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetFeeds.Rd |only
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetGeoSegmentation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetGroups.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetIPAddressExclusions.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetIPObfuscation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetInternalURLFilters.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetKeyVisitors.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetListVariables.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLocalization.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLogin.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLogins.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannelExpiration.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannelRules.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannels.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMetrics.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMobileAppReporting.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetPaidSearchDetection.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetPermanentTraffic.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetProps.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetQueue.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetRealTimeReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetRealTimeSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetReportDescription.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetReportSuites.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetScheduledSpike.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSegments.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSiteTitle.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSuccessEvents.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTimeZone.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTrackingServer.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTransactionEnabled.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetUniqueVisitorVariable.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetUsageLog.Rd | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetVersionAccess.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetVideoSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/JsonQueueRealTimeReport.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseFallout.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseOvertime.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParsePathing.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseRanked.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseTrended.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueFallout.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueOvertime.Rd | 5
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueuePathing.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueRanked.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueTrended.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/RSiteCatalyst.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SCAuth.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SaveRealTimeSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SubmitJsonQueueReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ValidateReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/tests |only
100 files changed, 444 insertions(+), 291 deletions(-)
Title: Multi-state Markov and Hidden Markov Models in Continuous Time
Diff between msm versions 1.4 dated 2014-07-08 and 1.5 dated 2015-01-06
Description: Continuous-time Markov and hidden Markov multi-state
models for longitudinal data. Designed for processes observed at
arbitrary times in continuous time (panel data) but some other
observation schemes are supported. Both Markov transition rates and
the hidden Markov output process can be modelled in terms of
covariates, which may be constant or piecewise-constant in time.
Author: Christopher Jackson
Maintainer: Christopher Jackson
ChangeLog | 107 +++
DESCRIPTION | 31 -
MD5 | 79 +-
NAMESPACE | 8
R/boot.R | 64 +-
R/draic.R | 50 +
R/hmm.R | 18
R/msm.R | 146 +++--
R/optim.R | 32 -
R/outputs.R | 1096 +++++++++++++++++++-------------------
R/phase.R |only
R/utils.R | 8
TODO | 61 --
data/bos3.rda |only
data/bos4.rda |only
data/msmdata.rda |binary
inst/NEWS | 54 +
inst/NEWS.mine |only
inst/NEWS.r57 |only
inst/NEWS.r64 |only
inst/doc/msm-manual.R | 26
man/2phase.Rd |only
man/bos.Rd | 6
man/cav.Rd | 16
man/draic.msm.Rd | 6
man/efpt.msm.Rd | 4
man/logLik.msm.Rd | 5
man/lrtest.msm.Rd | 4
man/msm.Rd | 107 +++
man/msm2Surv.Rd | 13
man/paramdata.object.Rd | 3
man/phasemeans.msm.Rd |only
man/plot.survfit.msm.Rd | 13
man/pmatrix.msm.Rd | 9
man/pmatrix.piecewise.msm.Rd | 10
man/ppass.msm.Rd | 2
man/statetable.msm.Rd | 12
man/viterbi.msm.Rd | 14
src/analyticp.c | 2
src/doc/figures/fev_viterbi.pdf |only
src/doc/msm-manual.Rnw | 25
src/lik.c | 124 +++-
src/pijt.c | 5
tests/testthat/test_models.r | 30 -
tests/testthat/test_models_misc.r | 1
45 files changed, 1342 insertions(+), 849 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Diff between catR versions 3.3 dated 2014-11-26 and 3.4 dated 2015-01-06
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis
DESCRIPTION | 10 -
MD5 | 20 +-
NEWS | 47 +++++
R/genPattern.R | 29 +--
R/genPolyMatrix.R | 36 ++--
R/randomCAT.R | 63 ++++---
R/simulateRespondents.R | 396 +++++++++++++++++++++++----------------------
man/genPattern.Rd | 7
man/genPolyMatrix.Rd | 12 -
man/randomCAT.Rd | 28 +--
man/simulateRespondents.Rd | 24 +-
11 files changed, 381 insertions(+), 291 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 1.2 dated 2014-12-12 and 1.3 dated 2015-01-06
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch
DESCRIPTION | 29 +++--
MD5 | 87 +++++++++-------
NAMESPACE | 144 ++++++++++++++++++++-------
R/ARb_utils.R | 11 +-
R/IRT.factor.scores.sirt.R |only
R/IRT.irfprob.sirt.R |only
R/IRT.likelihood_sirt.R |only
R/IRT.mle.R |only
R/IRT.modelfit.sirt.R |only
R/IRT.posterior_sirt.R |only
R/anova_sirt.R |only
R/gom.em.R | 5
R/logLik_sirt.R |only
R/mirt.IRT.functions.R | 3
R/mle.reliability.R |only
R/modelfit.cor.R | 17 +++
R/modelfit.cor.poly.R |only
R/rasch.conquest.R | 75 ++++++++++----
R/rasch.copula2.R | 3
R/rasch.copula3.R | 3
R/rasch.copula3.covariance.R | 2
R/rasch.mirtlc.R | 17 +++
R/rasch.mml2.R | 18 ++-
R/rm.facets.IC.R |only
R/rm.facets.R | 92 +++++++++++------
R/rm.facets_IC.R |only
R/rm.facets_PP.R |only
R/rm.facets_alg.R | 78 +++++++++++---
R/rm.sdt.R | 22 +++-
R/rm.smooth.distribution.R |only
R/rm_proc.R | 2
R/smirt.R | 2
R/summary.rm.facets.R | 10 +
inst/NEWS | 35 ++++++
man/IRT.mle.Rd |only
man/R2conquest.Rd | 6 -
man/data.eid.Rd | 9 -
man/data.g308.Rd | 23 ++--
man/f1d.irt.Rd | 7 -
man/gom.em.Rd | 30 +++++
man/mirt.wrapper.Rd | 19 +--
man/modelfit.sirt.Rd | 20 +++
man/pcm.fit.Rd | 24 +++-
man/person.parameter.rasch.copula.Rd | 3
man/personfit.stat.Rd | 2
man/rasch.copula.Rd | 30 +++++
man/rasch.mirtlc.Rd | 56 ++++++++--
man/rasch.mml.Rd | 39 +++++++
man/rm.facets.Rd | 117 +++++++++++++++++++---
man/rm.sdt.Rd | 35 ++++++
man/sirt-package.Rd | 186 +++++++++++++++++++----------------
man/smirt.Rd | 22 ++++
52 files changed, 959 insertions(+), 324 deletions(-)
Title: COBS -- COnstrained B-Splines (Sparse matrix based)
Diff between cobs versions 1.2-2 dated 2011-04-26 and 1.3-0 dated 2015-01-06
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng
Maintainer: Martin Maechler
cobs-1.2-2/cobs/Notes-MM |only
cobs-1.2-2/cobs/Pin-notes_2009-02.txt |only
cobs-1.2-2/cobs/R_README |only
cobs-1.2-2/cobs/data/DublinWind.tab.gz |only
cobs-1.2-2/cobs/data/USArmyRoofs.tab.gz |only
cobs-1.2-2/cobs/data/exHe.tab.gz |only
cobs-1.2-2/cobs/data/globtemp.rda |only
cobs-1.2-2/cobs/no-NAMESPACE.R |only
cobs-1.2-2/cobs/scobs_02_09.txt |only
cobs-1.2-2/cobs/tests/ex1.Rout.save |only
cobs-1.2-2/cobs/tests/ex2-long.Rout.save |only
cobs-1.2-2/cobs/tests/pt-ex.R |only
cobs-1.2-2/cobs/tests/wind.Rout.save |only
cobs-1.3-0/cobs/ChangeLog | 10 ++++++
cobs-1.3-0/cobs/DESCRIPTION | 22 ++++++++------
cobs-1.3-0/cobs/MD5 |only
cobs-1.3-0/cobs/NAMESPACE | 5 ++-
cobs-1.3-0/cobs/R/concaveRegr.R | 2 -
cobs-1.3-0/cobs/R/scobs.R | 12 +++----
cobs-1.3-0/cobs/README | 42 +++++++++++++++++++++++++++
cobs-1.3-0/cobs/TODO | 22 +++++++++++---
cobs-1.3-0/cobs/data/DublinWind.tab |only
cobs-1.3-0/cobs/data/USArmyRoofs.tab |only
cobs-1.3-0/cobs/data/exHe.tab |only
cobs-1.3-0/cobs/data/globtemp.R |only
cobs-1.3-0/cobs/inst/CITATION |only
cobs-1.3-0/cobs/man/plot.cobs.Rd | 2 -
cobs-1.3-0/cobs/src/Makevars | 5 ---
cobs-1.3-0/cobs/tests/0_pt-ex.R |only
cobs-1.3-0/cobs/tests/README | 11 +++++--
cobs-1.3-0/cobs/tests/ex1.Rout-N-save |only
cobs-1.3-0/cobs/tests/ex1Old.Rout-N-save |only
cobs-1.3-0/cobs/tests/ex2-long.Rout-N-save |only
cobs-1.3-0/cobs/tests/multi-constr.Rout.save | 12 +++++--
cobs-1.3-0/cobs/tests/roof.Rout-N-save |only
cobs-1.3-0/cobs/tests/temp.Rout-N-save |only
cobs-1.3-0/cobs/tests/wind.Rout-N-save |only
37 files changed, 111 insertions(+), 34 deletions(-)
Title: Choose univariate class intervals
Diff between classInt versions 0.1-21 dated 2013-09-01 and 0.1-22 dated 2015-01-06
Description: A package for choosing univariate class intervals for mapping or other graphics purposes
Author: Roger Bivand [aut, cre],
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand
ChangeLog | 17 +++++++++++++++++
DESCRIPTION | 15 +++++++++------
MD5 | 8 ++++----
inst/ChangeLog | 17 +++++++++++++++++
man/classIntervals.Rd | 8 +++++---
5 files changed, 52 insertions(+), 13 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.8-2 dated 2014-12-20 and 1.8-3 dated 2015-01-06
Description: A package implementing statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g. discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for
surveillance data, or continuous-space point process data such as the
occurrence of disease or earthquakes. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of infectious diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently the package contains implementations of typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Hoehle and Paul (2008). Furthermore, inference
methods for the retrospective infectious disease model in Held
et al (2005), Held et al (2006), Paul et al (2008) and Paul
and Held (2011) are provided. A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ("twinSIR", discrete
space) and Meyer et al (2012) ("twinstim", continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: Using the 'boda' algorithm requires the the INLA
package, which should be installed automatically through the
specified Additional_repositories, if uninstalled dependencies
are also requested. As this might not work under Mac OS X it
might be necessary to manually install the INLA package as
specified at http://www.r-inla.org/download.
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
DESCRIPTION | 19 ++++---
MD5 | 38 +++++++--------
R/boda.R | 2
R/isoWeekYear.R | 72 +++++++++++++++-------------
R/linelist2sts.R | 35 +++++++-------
R/spatial_tools.R | 16 ++++--
R/sts_animate.R | 28 ++++++++---
build/partial.rdb |binary
inst/NEWS.Rd | 6 ++
inst/doc/glrnb.pdf |binary
inst/doc/hhh4.pdf |binary
inst/doc/surveillance.pdf |binary
man/algo.twins.Rd | 11 ++++
man/hepatitisA.Rd | 2
man/isoWeekYear.Rd | 5 +-
man/linelist2sts.Rd | 97 +++++++++++++++++++++++----------------
man/nowcast.Rd | 31 ++++++++----
man/sim.pointSource.Rd | 8 +--
man/sts_animate.Rd | 14 ++++-
tests/testthat/test-formatDate.R | 7 ++
20 files changed, 244 insertions(+), 147 deletions(-)
Title: Miscellaneous Functions for Survival Data
Diff between survMisc versions 0.4.2 dated 2014-05-13 and 0.4.4 dated 2015-01-06
Description: A collection of functions for analysis of survival data. These
extend the methods available in the survival package.
Author: Chris Dardis
Maintainer: Chris Dardis
survMisc-0.4.2/survMisc/R/autoplot.R |only
survMisc-0.4.2/survMisc/R/calcSurv.R |only
survMisc-0.4.2/survMisc/R/dxPlot.R |only
survMisc-0.4.2/survMisc/R/multiPlot.R |only
survMisc-0.4.2/survMisc/R/survEst.R |only
survMisc-0.4.2/survMisc/man/autoplot.rpart.Rd |only
survMisc-0.4.2/survMisc/man/autoplot.survfit.Rd |only
survMisc-0.4.2/survMisc/man/autoplot.tableAndPlot.Rd |only
survMisc-0.4.2/survMisc/man/calcSurv.Rd |only
survMisc-0.4.2/survMisc/man/dxPlot.Rd |only
survMisc-0.4.2/survMisc/man/mean.Surv.Rd |only
survMisc-0.4.2/survMisc/man/survEst.Rd |only
survMisc-0.4.4/survMisc/DESCRIPTION | 38
survMisc-0.4.4/survMisc/MD5 | 160 +-
survMisc-0.4.4/survMisc/NAMESPACE | 134 +-
survMisc-0.4.4/survMisc/R/air.R | 47
survMisc-0.4.4/survMisc/R/asSurv.R |only
survMisc-0.4.4/survMisc/R/autoplotRpart.R | 807 +++++++-------
survMisc-0.4.4/survMisc/R/autoplotSurvfit.R |only
survMisc-0.4.4/survMisc/R/autoplotTAP.R | 47
survMisc-0.4.4/survMisc/R/btumors.R | 53
survMisc-0.4.4/survMisc/R/ci.R |only
survMisc-0.4.4/survMisc/R/comp.R | 1068 +++++++++----------
survMisc-0.4.4/survMisc/R/covMatSurv.R | 143 +-
survMisc-0.4.4/survMisc/R/cutp.R | 120 +-
survMisc-0.4.4/survMisc/R/d1.R |only
survMisc-0.4.4/survMisc/R/dx.R |only
survMisc-0.4.4/survMisc/R/gamTerms.R | 104 +
survMisc-0.4.4/survMisc/R/gastric.R | 52
survMisc-0.4.4/survMisc/R/genSurv.R | 23
survMisc-0.4.4/survMisc/R/gof.R |only
survMisc-0.4.4/survMisc/R/ic.R | 186 +--
survMisc-0.4.4/survMisc/R/local.R | 788 +++++++-------
survMisc-0.4.4/survMisc/R/lrSS.R | 208 ++-
survMisc-0.4.4/survMisc/R/meanSurv.R | 198 +--
survMisc-0.4.4/survMisc/R/mpip.R |only
survMisc-0.4.4/survMisc/R/multiCoxph.R | 882 +++++++--------
survMisc-0.4.4/survMisc/R/plotMultiCoxph.R | 148 +-
survMisc-0.4.4/survMisc/R/plotSurv.R | 236 ++--
survMisc-0.4.4/survMisc/R/plotTerm.R |only
survMisc-0.4.4/survMisc/R/profLik.R | 238 ++--
survMisc-0.4.4/survMisc/R/quantile.R | 477 ++++----
survMisc-0.4.4/survMisc/R/rsq.R |only
survMisc-0.4.4/survMisc/R/sf.R |only
survMisc-0.4.4/survMisc/R/sig.R | 112 -
survMisc-0.4.4/survMisc/R/survMisc_package.R | 74 -
survMisc-0.4.4/survMisc/R/tableRhs.R | 85 +
survMisc-0.4.4/survMisc/R/tne.R | 707 ++++++------
survMisc-0.4.4/survMisc/R/tneBMT.R | 70 -
survMisc-0.4.4/survMisc/R/tneKidney.R | 38
survMisc-0.4.4/survMisc/R/whas100.R | 69 -
survMisc-0.4.4/survMisc/R/whas500.R |only
survMisc-0.4.4/survMisc/data/air.rda |binary
survMisc-0.4.4/survMisc/data/btumors.rda |binary
survMisc-0.4.4/survMisc/data/gastric.rda |binary
survMisc-0.4.4/survMisc/data/mpip.rda |only
survMisc-0.4.4/survMisc/data/tneBMT.rda |binary
survMisc-0.4.4/survMisc/data/tneKidney.rda |binary
survMisc-0.4.4/survMisc/data/whas100.rda |binary
survMisc-0.4.4/survMisc/data/whas500.rda |only
survMisc-0.4.4/survMisc/inst |only
survMisc-0.4.4/survMisc/man/air.Rd | 63 -
survMisc-0.4.4/survMisc/man/asSurv.Rd |only
survMisc-0.4.4/survMisc/man/autoplotRpart.Rd |only
survMisc-0.4.4/survMisc/man/autoplotSurvfit.Rd |only
survMisc-0.4.4/survMisc/man/autoplotTableAndPlot.Rd |only
survMisc-0.4.4/survMisc/man/btumors.Rd | 68 -
survMisc-0.4.4/survMisc/man/ci.Rd |only
survMisc-0.4.4/survMisc/man/comp.Rd | 432 +++----
survMisc-0.4.4/survMisc/man/covMatSurv.Rd | 114 +-
survMisc-0.4.4/survMisc/man/cutp.Rd | 172 +--
survMisc-0.4.4/survMisc/man/d1.Rd |only
survMisc-0.4.4/survMisc/man/dx.Rd |only
survMisc-0.4.4/survMisc/man/gamTerms.Rd | 138 +-
survMisc-0.4.4/survMisc/man/gastric.Rd | 82 -
survMisc-0.4.4/survMisc/man/genSurv.Rd | 186 +--
survMisc-0.4.4/survMisc/man/gof.Rd |only
survMisc-0.4.4/survMisc/man/ic.Rd | 138 +-
survMisc-0.4.4/survMisc/man/local.Rd | 249 ++--
survMisc-0.4.4/survMisc/man/lrSS.Rd | 190 +--
survMisc-0.4.4/survMisc/man/meanSurv.Rd |only
survMisc-0.4.4/survMisc/man/mpip.Rd |only
survMisc-0.4.4/survMisc/man/multi.Rd | 335 ++---
survMisc-0.4.4/survMisc/man/plot.Surv.Rd | 85 -
survMisc-0.4.4/survMisc/man/plotMultiCoxph.Rd | 99 -
survMisc-0.4.4/survMisc/man/plotTerm.Rd |only
survMisc-0.4.4/survMisc/man/profLik.Rd | 117 --
survMisc-0.4.4/survMisc/man/quantile.Rd | 266 ++--
survMisc-0.4.4/survMisc/man/rsq.Rd |only
survMisc-0.4.4/survMisc/man/sf.Rd |only
survMisc-0.4.4/survMisc/man/sig.Rd | 90 -
survMisc-0.4.4/survMisc/man/survMisc-package.Rd | 68 -
survMisc-0.4.4/survMisc/man/tableRhs.Rd | 161 +-
survMisc-0.4.4/survMisc/man/tne.Rd | 246 ++--
survMisc-0.4.4/survMisc/man/tneBMT.Rd | 93 -
survMisc-0.4.4/survMisc/man/tneKidney.Rd | 44
survMisc-0.4.4/survMisc/man/whas100.Rd | 86 -
survMisc-0.4.4/survMisc/man/whas500.Rd |only
survMisc-0.4.4/survMisc/src |only
99 files changed, 5666 insertions(+), 5168 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Diff between Rdsdp versions 1.0.1 dated 2015-01-01 and 1.0.2 dated 2015-01-06
Description: R interface to DSDP semidefinite programming library. Installs version 5.8 of DSDP from DSDP website. An existing installation of DSDP may be used by passing the proper configure arguments to the installation command.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu
DESCRIPTION | 8 ++---
MD5 | 12 ++++----
man/dsdp.Rd | 1
src/Rdsdp.c | 19 +++++--------
src/Rreadsdpa.c | 60 ++++++++++++++++++++-----------------------
src/dsdp/src/vecmat/dufull.c | 20 +++++++-------
tests/test2.R | 2 -
7 files changed, 56 insertions(+), 66 deletions(-)
Title: Read-Write Support for NumPy Files via Rcpp
Diff between RcppCNPy versions 0.2.3 dated 2014-04-10 and 0.2.4 dated 2015-01-06
Description: The cnpy library written by Carl Rogers provides read and write
facilities for files created with (or for) the NumPy extension for Python.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with -std=c++11 which is the default starting
with release 0.2.3 following the release of R 3.1.0.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel
ChangeLog | 78 +++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 24 ++++++-------
MD5 | 30 ++++++++--------
build/vignette.rds |binary
inst/NEWS.Rd | 14 +++++++
inst/doc/RcppCNPy-intro.R | 17 ++-------
inst/doc/RcppCNPy-intro.Rnw | 9 +---
inst/doc/RcppCNPy-intro.pdf |binary
src/cnpy.cpp | 8 ----
src/cnpy.h | 24 +++++++++++--
src/cnpyMod.cpp | 78 ++++++++++++++++++++++++++++++-------------
tests/loadFiles.R | 23 +++++-------
tests/loadFiles.Rout.save | 36 +++++++++----------
tests/saveAndLoad.R | 40 +++++++++++++++++++++-
tests/saveAndLoad.Rout.save | 54 +++++++++++++++++++++++++++--
vignettes/RcppCNPy-intro.Rnw | 9 +---
16 files changed, 322 insertions(+), 122 deletions(-)
Title: Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Diff between randomUniformForest versions 1.1.1 dated 2014-12-03 and 1.1.2 dated 2015-01-06
More information about randomUniformForest at CRAN
Description: Ensemble model, for classification, regression
and unsupervised learning, based on a forest of unpruned
and randomized binary decision trees. Each tree is grown
by sampling, with replacement, a set of variables at each node.
Each cut-point is generated randomly, according to the continuous
Uniform distribution. For each tree, data are either bootstrapped
or subsampled. The unsupervised mode introduces clustering, dimension reduction
and variable importance, using a three-layer engine. Random Uniform Forests are mainly
aimed to lower correlation between trees (or trees residuals), to provide a deep analysis
of variable importance and to allow native distributed and incremental learning.
Author: Saip Ciss
Maintainer: Saip Ciss
DESCRIPTION | 8
MD5 | 45
NAMESPACE | 6
NEWS | 62 -
R/DecisionTreesCPP.R | 252 +++-
R/OnliningRandomUniformForests.R | 107 +
R/RandomUniformForestsCPP.R | 712 +++++++++---
R/genericFunctions.R | 158 +-
build/vignette.rds |binary
inst/doc/VariableImportanceInRandomUniformForests.pdf |only
inst/doc/VariableImportanceInRandomUniformForests.pdf.asis |only
inst/doc/randomUniformForestsOverview.pdf |binary
man/clusteringObservations.Rd | 30
man/combine.unsupervised.Rd |only
man/generic.cv.Rd | 49
man/internalFunctions.Rd | 4
man/model.stats.Rd | 68 +
man/partialDependenceBetweenPredictors.Rd | 6
man/partialDependenceOverResponses.Rd | 6
man/predict.randomUniformForest.Rd | 6
man/rUniformForest.big.Rd | 8
man/randomUniformForest-package.Rd | 16
man/randomUniformForest.Rd | 82 -
man/unsupervised.randomUniformForest.Rd | 42
man/update.unsupervised.Rd |only
vignettes/VariableImportanceInRandomUniformForests.pdf.asis |only
26 files changed, 1229 insertions(+), 438 deletions(-)
Permanent link
Title: Boost C++ Header Files
Diff between BH versions 1.55.0-2 dated 2015-01-04 and 1.55.0-3 dated 2015-01-05
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel
ChangeLog | 7
DESCRIPTION | 8
MD5 | 400 +++++++++-
README.md | 24
inst/NEWS.Rd | 6
inst/include/boost/bimap |only
inst/include/boost/bimap.hpp |only
inst/include/boost/function_types/member_function_pointer.hpp |only
inst/include/boost/graph/adj_list_serialize.hpp |only
inst/include/boost/graph/adjacency_list_io.hpp |only
inst/include/boost/graph/adjacency_matrix.hpp |only
inst/include/boost/graph/astar_search.hpp |only
inst/include/boost/graph/bandwidth.hpp |only
inst/include/boost/graph/bc_clustering.hpp |only
inst/include/boost/graph/bellman_ford_shortest_paths.hpp |only
inst/include/boost/graph/betweenness_centrality.hpp |only
inst/include/boost/graph/biconnected_components.hpp |only
inst/include/boost/graph/bipartite.hpp |only
inst/include/boost/graph/boyer_myrvold_planar_test.hpp |only
inst/include/boost/graph/boykov_kolmogorov_max_flow.hpp |only
inst/include/boost/graph/bron_kerbosch_all_cliques.hpp |only
inst/include/boost/graph/chrobak_payne_drawing.hpp |only
inst/include/boost/graph/circle_layout.hpp |only
inst/include/boost/graph/closeness_centrality.hpp |only
inst/include/boost/graph/clustering_coefficient.hpp |only
inst/include/boost/graph/compressed_sparse_row_graph.hpp |only
inst/include/boost/graph/connected_components.hpp |only
inst/include/boost/graph/copy.hpp |only
inst/include/boost/graph/core_numbers.hpp |only
inst/include/boost/graph/create_condensation_graph.hpp |only
inst/include/boost/graph/cuthill_mckee_ordering.hpp |only
inst/include/boost/graph/cycle_canceling.hpp |only
inst/include/boost/graph/dag_shortest_paths.hpp |only
inst/include/boost/graph/degree_centrality.hpp |only
inst/include/boost/graph/depth_first_search.hpp |only
inst/include/boost/graph/detail/augment.hpp |only
inst/include/boost/graph/detail/compressed_sparse_row_struct.hpp |only
inst/include/boost/graph/detail/connected_components.hpp |only
inst/include/boost/graph/detail/geodesic.hpp |only
inst/include/boost/graph/detail/histogram_sort.hpp |only
inst/include/boost/graph/detail/incidence_iterator.hpp |only
inst/include/boost/graph/detail/incremental_components.hpp |only
inst/include/boost/graph/detail/index.hpp |only
inst/include/boost/graph/detail/indexed_properties.hpp |only
inst/include/boost/graph/detail/is_distributed_selector.hpp |only
inst/include/boost/graph/detail/labeled_graph_traits.hpp |only
inst/include/boost/graph/detail/list_base.hpp |only
inst/include/boost/graph/detail/permutation.hpp |only
inst/include/boost/graph/detail/read_graphviz_new.hpp |only
inst/include/boost/graph/detail/read_graphviz_spirit.hpp |only
inst/include/boost/graph/detail/self_avoiding_walk.hpp |only
inst/include/boost/graph/detail/set_adaptor.hpp |only
inst/include/boost/graph/detail/shadow_iterator.hpp |only
inst/include/boost/graph/detail/sparse_ordering.hpp |only
inst/include/boost/graph/dijkstra_shortest_paths_no_color_map.hpp |only
inst/include/boost/graph/dimacs.hpp |only
inst/include/boost/graph/directed_graph.hpp |only
inst/include/boost/graph/distributed/adjacency_list.hpp |only
inst/include/boost/graph/distributed/adjlist |only
inst/include/boost/graph/distributed/betweenness_centrality.hpp |only
inst/include/boost/graph/distributed/boman_et_al_graph_coloring.hpp |only
inst/include/boost/graph/distributed/compressed_sparse_row_graph.hpp |only
inst/include/boost/graph/distributed/connected_components.hpp |only
inst/include/boost/graph/distributed/connected_components_parallel_search.hpp |only
inst/include/boost/graph/distributed/dehne_gotz_min_spanning_tree.hpp |only
inst/include/boost/graph/distributed/delta_stepping_shortest_paths.hpp |only
inst/include/boost/graph/distributed/depth_first_search.hpp |only
inst/include/boost/graph/distributed/detail/mpi_process_group.ipp |only
inst/include/boost/graph/distributed/detail/tag_allocator.hpp |only
inst/include/boost/graph/distributed/distributed_graph_utility.hpp |only
inst/include/boost/graph/distributed/filtered_graph.hpp |only
inst/include/boost/graph/distributed/fruchterman_reingold.hpp |only
inst/include/boost/graph/distributed/graphviz.hpp |only
inst/include/boost/graph/distributed/hohberg_biconnected_components.hpp |only
inst/include/boost/graph/distributed/local_subgraph.hpp |only
inst/include/boost/graph/distributed/mpi_process_group.hpp |only
inst/include/boost/graph/distributed/named_graph.hpp |only
inst/include/boost/graph/distributed/one_bit_color_map.hpp |only
inst/include/boost/graph/distributed/page_rank.hpp |only
inst/include/boost/graph/distributed/reverse_graph.hpp |only
inst/include/boost/graph/distributed/rmat_graph_generator.hpp |only
inst/include/boost/graph/distributed/selector.hpp |only
inst/include/boost/graph/distributed/shuffled_distribution.hpp |only
inst/include/boost/graph/distributed/st_connected.hpp |only
inst/include/boost/graph/distributed/strong_components.hpp |only
inst/include/boost/graph/distributed/vertex_list_adaptor.hpp |only
inst/include/boost/graph/dll_import_export.hpp |only
inst/include/boost/graph/dominator_tree.hpp |only
inst/include/boost/graph/eccentricity.hpp |only
inst/include/boost/graph/edge_coloring.hpp |only
inst/include/boost/graph/edge_connectivity.hpp |only
inst/include/boost/graph/edge_list.hpp |only
inst/include/boost/graph/edmonds_karp_max_flow.hpp |only
inst/include/boost/graph/edmunds_karp_max_flow.hpp |only
inst/include/boost/graph/erdos_renyi_generator.hpp |only
inst/include/boost/graph/exterior_property.hpp |only
inst/include/boost/graph/filtered_graph.hpp |only
inst/include/boost/graph/find_flow_cost.hpp |only
inst/include/boost/graph/floyd_warshall_shortest.hpp |only
inst/include/boost/graph/fruchterman_reingold.hpp |only
inst/include/boost/graph/geodesic_distance.hpp |only
inst/include/boost/graph/graph_archetypes.hpp |only
inst/include/boost/graph/graph_as_tree.hpp |only
inst/include/boost/graph/graph_stats.hpp |only
inst/include/boost/graph/graph_test.hpp |only
inst/include/boost/graph/graph_utility.hpp |only
inst/include/boost/graph/graphml.hpp |only
inst/include/boost/graph/graphviz.hpp |only
inst/include/boost/graph/grid_graph.hpp |only
inst/include/boost/graph/gursoy_atun_layout.hpp |only
inst/include/boost/graph/hawick_circuits.hpp |only
inst/include/boost/graph/howard_cycle_ratio.hpp |only
inst/include/boost/graph/incremental_components.hpp |only
inst/include/boost/graph/is_kuratowski_subgraph.hpp |only
inst/include/boost/graph/is_straight_line_drawing.hpp |only
inst/include/boost/graph/isomorphism.hpp |only
inst/include/boost/graph/iteration_macros_undef.hpp |only
inst/include/boost/graph/johnson_all_pairs_shortest.hpp |only
inst/include/boost/graph/kamada_kawai_spring_layout.hpp |only
inst/include/boost/graph/king_ordering.hpp |only
inst/include/boost/graph/kruskal_min_spanning_tree.hpp |only
inst/include/boost/graph/labeled_graph.hpp |only
inst/include/boost/graph/leda_graph.hpp |only
inst/include/boost/graph/lookup_edge.hpp |only
inst/include/boost/graph/loop_erased_random_walk.hpp |only
inst/include/boost/graph/make_biconnected_planar.hpp |only
inst/include/boost/graph/make_connected.hpp |only
inst/include/boost/graph/make_maximal_planar.hpp |only
inst/include/boost/graph/matrix_as_graph.hpp |only
inst/include/boost/graph/max_cardinality_matching.hpp |only
inst/include/boost/graph/maximum_adjacency_search.hpp |only
inst/include/boost/graph/mcgregor_common_subgraphs.hpp |only
inst/include/boost/graph/mesh_graph_generator.hpp |only
inst/include/boost/graph/metis.hpp |only
inst/include/boost/graph/metric_tsp_approx.hpp |only
inst/include/boost/graph/minimum_degree_ordering.hpp |only
inst/include/boost/graph/neighbor_bfs.hpp |only
inst/include/boost/graph/one_bit_color_map.hpp |only
inst/include/boost/graph/page_rank.hpp |only
inst/include/boost/graph/parallel/detail/property_holders.hpp |only
inst/include/boost/graph/parallel/distribution.hpp |only
inst/include/boost/graph/planar_canonical_ordering.hpp |only
inst/include/boost/graph/planar_detail |only
inst/include/boost/graph/planar_face_traversal.hpp |only
inst/include/boost/graph/plod_generator.hpp |only
inst/include/boost/graph/point_traits.hpp |only
inst/include/boost/graph/prim_minimum_spanning_tree.hpp |only
inst/include/boost/graph/profile.hpp |only
inst/include/boost/graph/property_iter_range.hpp |only
inst/include/boost/graph/property_maps/container_property_map.hpp |only
inst/include/boost/graph/property_maps/matrix_property_map.hpp |only
inst/include/boost/graph/push_relabel_max_flow.hpp |only
inst/include/boost/graph/r_c_shortest_paths.hpp |only
inst/include/boost/graph/random.hpp |only
inst/include/boost/graph/random_layout.hpp |only
inst/include/boost/graph/random_spanning_tree.hpp |only
inst/include/boost/graph/read_dimacs.hpp |only
inst/include/boost/graph/rmat_graph_generator.hpp |only
inst/include/boost/graph/sequential_vertex_coloring.hpp |only
inst/include/boost/graph/simple_point.hpp |only
inst/include/boost/graph/sloan_ordering.hpp |only
inst/include/boost/graph/small_world_generator.hpp |only
inst/include/boost/graph/smallest_last_ordering.hpp |only
inst/include/boost/graph/ssca_graph_generator.hpp |only
inst/include/boost/graph/st_connected.hpp |only
inst/include/boost/graph/stanford_graph.hpp |only
inst/include/boost/graph/stoer_wagner_min_cut.hpp |only
inst/include/boost/graph/strong_components.hpp |only
inst/include/boost/graph/subgraph.hpp |only
inst/include/boost/graph/successive_shortest_path_nonnegative_weights.hpp |only
inst/include/boost/graph/tiernan_all_cycles.hpp |only
inst/include/boost/graph/topological_sort.hpp |only
inst/include/boost/graph/topology.hpp |only
inst/include/boost/graph/transitive_closure.hpp |only
inst/include/boost/graph/transitive_reduction.hpp |only
inst/include/boost/graph/transpose_graph.hpp |only
inst/include/boost/graph/tree_traits.hpp |only
inst/include/boost/graph/two_graphs_common_spanning_trees.hpp |only
inst/include/boost/graph/undirected_dfs.hpp |only
inst/include/boost/graph/undirected_graph.hpp |only
inst/include/boost/graph/use_mpi.hpp |only
inst/include/boost/graph/vector_as_graph.hpp |only
inst/include/boost/graph/vertex_and_edge_range.hpp |only
inst/include/boost/graph/vf2_sub_graph_iso.hpp |only
inst/include/boost/graph/wavefront.hpp |only
inst/include/boost/graph/write_dimacs.hpp |only
inst/include/boost/optional/optional_io.hpp |only
inst/include/boost/property_map/dynamic_property_map.hpp |only
inst/include/boost/property_map/function_property_map.hpp |only
inst/include/boost/property_map/parallel/global_index_map.hpp |only
inst/include/boost/property_map/transform_value_property_map.hpp |only
inst/include/boost/property_tree |only
inst/include/boost/tti |only
inst/include/boost/tuple/tuple_io.hpp |only
inst/include/boost/xpressive |only
man/BH-package.Rd | 4
196 files changed, 427 insertions(+), 22 deletions(-)
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.9-3 dated 2012-01-17 and 0.10 dated 2015-01-05
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David A. James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
RMySQL-0.10/RMySQL/DESCRIPTION | 48
RMySQL-0.10/RMySQL/MD5 | 123
RMySQL-0.10/RMySQL/NAMESPACE | 204
RMySQL-0.10/RMySQL/R/connection.R |only
RMySQL-0.10/RMySQL/R/data-type.R |only
RMySQL-0.10/RMySQL/R/default.R |only
RMySQL-0.10/RMySQL/R/driver.R |only
RMySQL-0.10/RMySQL/R/escaping.R |only
RMySQL-0.10/RMySQL/R/extension.R |only
RMySQL-0.10/RMySQL/R/is-valid.R |only
RMySQL-0.10/RMySQL/R/mysql.R |only
RMySQL-0.10/RMySQL/R/result.R |only
RMySQL-0.10/RMySQL/R/table.R |only
RMySQL-0.10/RMySQL/R/transaction.R |only
RMySQL-0.10/RMySQL/R/zzz_compatibility.R |only
RMySQL-0.10/RMySQL/README.md |only
RMySQL-0.10/RMySQL/configure | 4422 ----------
RMySQL-0.10/RMySQL/configure.win | 20
RMySQL-0.10/RMySQL/man/MySQLConnection-class.Rd | 73
RMySQL-0.10/RMySQL/man/MySQLDriver-class.Rd | 95
RMySQL-0.10/RMySQL/man/MySQLResult-class.Rd | 67
RMySQL-0.10/RMySQL/man/constants.Rd |only
RMySQL-0.10/RMySQL/man/db-meta.Rd |only
RMySQL-0.10/RMySQL/man/dbApply.Rd | 117
RMySQL-0.10/RMySQL/man/dbColumnInfo-MySQLConnection-method.Rd |only
RMySQL-0.10/RMySQL/man/dbConnect-MySQLDriver-method.Rd |only
RMySQL-0.10/RMySQL/man/dbDataType-MySQLDriver-method.Rd |only
RMySQL-0.10/RMySQL/man/dbEscapeStrings.Rd | 51
RMySQL-0.10/RMySQL/man/dbGetInfo-MySQLDriver-method.Rd |only
RMySQL-0.10/RMySQL/man/dbNextResult.Rd | 87
RMySQL-0.10/RMySQL/man/dbQuoteIdentifier-MySQLConnection-character-method.Rd |only
RMySQL-0.10/RMySQL/man/dbReadTable.Rd |only
RMySQL-0.10/RMySQL/man/dbUnloadDriver-MySQLDriver-method.Rd |only
RMySQL-0.10/RMySQL/man/dbWriteTable.Rd |only
RMySQL-0.10/RMySQL/man/isIdCurrent.Rd | 64
RMySQL-0.10/RMySQL/man/make.db.names-MySQLConnection-character-method.Rd |only
RMySQL-0.10/RMySQL/man/mysqlBuildTableDefinition.Rd |only
RMySQL-0.10/RMySQL/man/mysqlClientLibraryVersions.Rd | 21
RMySQL-0.10/RMySQL/man/mysqlHasDefault.Rd |only
RMySQL-0.10/RMySQL/man/query.Rd |only
RMySQL-0.10/RMySQL/man/result-meta.Rd |only
RMySQL-0.10/RMySQL/man/transactions.Rd |only
RMySQL-0.10/RMySQL/src/Makevars.win |only
RMySQL-0.10/RMySQL/src/RMySQL-init.c |only
RMySQL-0.10/RMySQL/src/RS-MySQL.h | 266
RMySQL-0.10/RMySQL/src/S4R.h | 169
RMySQL-0.10/RMySQL/src/connection.c |only
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96 files changed, 656 insertions(+), 5171 deletions(-)
Title: Collection of Configurable GTK+ Menus
Diff between MenuCollection versions 1.0 dated 2014-12-17 and 1.1 dated 2015-01-05
More information about MenuCollection at CRAN
Description: Set of configurable menus built with GTK+ to graphically interface new functions.
Author: Gianmarco Polotti
Maintainer: Gianmarco Polotti
DESCRIPTION | 6 -
MD5 | 206 +++++++++++++++++++++---------------------
R/menucollection.r | 18 +--
man/dovc.Rd | 2
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man/inpboxe2k2.Rd | 3
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man/inpboxe3k2.Rd | 3
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man/inpboxe4c2k.Rd | 3
man/inpboxe4cek2.Rd | 3
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man/inpboxe4k3.Rd | 3
man/inpboxe4r2.Rd | 3
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man/inpboxe5k2.Rd | 4
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man/inpboxe6k3.Rd | 3
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man/inpboxe7k2.Rd | 3
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man/inpboxek2.Rd | 3
man/inpboxer3.Rd | 3
man/inpboxk6.Rd | 3
man/inpboxk6k6e6.Rd | 11 +-
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man/inpboxlist.Rd | 3
man/inpboxr2.Rd | 3
man/menucollection-package.Rd | 8 -
man/messabox.Rd | 3
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104 files changed, 231 insertions(+), 181 deletions(-)
Permanent link
Title: Utilities for Producing Maps
Diff between mapmisc versions 1.0.0 dated 2014-09-17 and 1.1.1 dated 2015-01-05
Description: This package contains various utilities for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 14 -
MD5 | 50 ++---
NAMESPACE | 2
R/colourScale.R | 420 ++++++++++++++++++++++++++++-------------------
R/geonames.R | 7
R/getTiles.R | 32 ++-
R/insetMap.R | 34 +--
R/openmap.R | 36 ++--
build/vignette.rds |binary
data/netherlands.RData |binary
inst/doc/mapLayers.R | 6
inst/doc/mapLayers.pdf |binary
inst/doc/mapLayers.rnw | 6
inst/doc/mapmisc.R | 6
inst/doc/mapmisc.pdf |binary
inst/doc/mapmisc.rnw | 6
inst/extdata/tiles.RData |binary
man/colourScale.Rd | 3
man/geonames.Rd | 2
man/netherlands.Rd | 18 +-
man/openmap.Rd | 6
man/scaleBar.Rd | 11 -
tests/colourScale.R |only
vignettes/Makefile | 30 +--
vignettes/framed.sty |only
vignettes/mapLayers.rnw | 6
vignettes/mapmisc.rnw | 6
27 files changed, 405 insertions(+), 296 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Diff between geostatsp versions 1.1.5 dated 2014-11-13 and 1.1.8 dated 2015-01-05
Description: This package provides to geostatistical modelling facilities using Raster and SpatialPoints objects. Non-Gaussian models are fit using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
geostatsp-1.1.5/geostatsp/R/formulaLhs.R |only
geostatsp-1.1.8/geostatsp/DESCRIPTION | 13 ++---
geostatsp-1.1.8/geostatsp/MD5 | 30 ++++++-----
geostatsp-1.1.8/geostatsp/NAMESPACE | 2
geostatsp-1.1.8/geostatsp/R/0gm.R | 10 ++-
geostatsp-1.1.8/geostatsp/R/forInla.R |only
geostatsp-1.1.8/geostatsp/R/glgm.R | 2
geostatsp-1.1.8/geostatsp/R/krige.R | 67 +++++++++-----------------
geostatsp-1.1.8/geostatsp/R/loglikLgm.R | 55 ++++++++++-----------
geostatsp-1.1.8/geostatsp/R/resampleMethods.R |only
geostatsp-1.1.8/geostatsp/R/simLgcp.R | 23 ++++++--
geostatsp-1.1.8/geostatsp/R/stackRasterList.R | 2
geostatsp-1.1.8/geostatsp/man/inla.models.Rd |only
geostatsp-1.1.8/geostatsp/man/likfitLgm.Rd | 2
geostatsp-1.1.8/geostatsp/src/Makevars | 2
geostatsp-1.1.8/geostatsp/tests/glgm.R | 44 +++++++++++------
geostatsp-1.1.8/geostatsp/tests/lgcp.R | 10 +++
geostatsp-1.1.8/geostatsp/tests/simLgcp.R | 7 ++
18 files changed, 151 insertions(+), 118 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and Python
Diff between fastcluster versions 1.1.14 dated 2015-01-04 and 1.1.15 dated 2015-01-05
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: “linkage†in the SciPy package
“scipy.cluster.hierarchyâ€, “hclust†in R's “stats†package, and the
“flashClust†package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
inst/doc/fastcluster.Rtex | 4 ++--
inst/doc/fastcluster.pdf |binary
src/python/fastcluster.py | 2 +-
src/python/test/nantest.py | 2 +-
src/python/test/test.py | 2 +-
src/python/test/vectortest.py | 2 +-
tests/test_fastcluster.R | 17 ++++++++++++++---
vignettes/fastcluster.Rtex | 4 ++--
11 files changed, 41 insertions(+), 25 deletions(-)
Title: Time Frame Coding Kernel
Diff between tframe versions 2012.8-1 dated 2012-09-20 and 2015.1-1 dated 2015-01-05
Description: A kernel of functions for programming
time series methods in a way that is relatively independently of the
representation of time. Also provides plotting, time windowing,
and some
other utility functions which are specifically intended for time series.
See the Guide distributed as a vignette, or ?tframe.Intro for more
details. (User utilities are in package tfplot.)
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 29 ++++++++++++++---------------
MD5 | 5 +++--
NEWS | 4 ++++
build |only
4 files changed, 21 insertions(+), 17 deletions(-)
Title: Analyzing RNA Sequence Count Tables Using Quasi-likelihood
Diff between QuasiSeq versions 1.0-4 dated 2014-04-14 and 1.0-5 dated 2015-01-05
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund
Maintainer: Steve Lund
DESCRIPTION | 14 +-
MD5 | 18 +--
NAMESPACE | 2
R/NBDev.R | 42 -------
R/QL.fit.R | 314 +++++++++++++++++++++++++++---------------------------
R/QL.results.R | 8 +
R/negbin.br.R | 2
man/NBDev.Rd | 6 -
man/QL.fit.Rd | 29 +++-
man/QL.results.Rd | 21 ++-
10 files changed, 222 insertions(+), 234 deletions(-)
Title: Tools To Generate Vector Time Series
Diff between RGENERATE versions 1.1 dated 2014-08-07 and 1.3 dated 2015-01-05
Description: A method 'generate' is implemented in this package for the random
generation of vector time series according to models obtained by 'RMAWGEN',
'vars' or other packages. This package was created to generalize the
algorithms of the RMAWGEN package for the analysis and generation of any
environmental vector time series.
Author: Emanuele Cordano
Maintainer: Emanuele Cordano
RGENERATE-1.1/RGENERATE/inst/stuff |only
RGENERATE-1.3/RGENERATE/DESCRIPTION | 23 -
RGENERATE-1.3/RGENERATE/MD5 | 13
RGENERATE-1.3/RGENERATE/NAMESPACE | 5
RGENERATE-1.3/RGENERATE/R/gapFilling.R |only
RGENERATE-1.3/RGENERATE/R/generate.R | 391 ++++++++++++++++++++++--------
RGENERATE-1.3/RGENERATE/README.md |only
RGENERATE-1.3/RGENERATE/man/gapFilling.Rd |only
RGENERATE-1.3/RGENERATE/man/generate.Rd | 124 ++++++++-
9 files changed, 432 insertions(+), 124 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.0 dated 2014-06-10 and 1.1-0 dated 2015-01-05
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
DESCRIPTION | 17
MD5 | 164 ++++-----
NAMESPACE | 8
NEWS | 46 ++
R/GoogleMapsPlot.R | 9
R/airbaseStats.R | 412 +++++++++++------------
R/aqStats.R | 2
R/calendarPlot.R | 2
R/checkPrep.R | 12
R/corPlot.R | 178 ++++++----
R/cutData.R | 18 -
R/import.R | 4
R/importTraj.R | 27 -
R/linearRelation.R | 14
R/modStats.R | 2
R/openair.generics.R | 5
R/percentileRose.R | 246 +++++++------
R/polarPlot.R | 32 -
R/scatterPlot.R | 620 +++++++++++++++++++++++++---------
R/smoothTrend.R | 218 +++++++-----
R/summaryPlot.R | 183 +++++-----
R/timeAverage.R | 240 +++++++++----
R/timePlot.R | 21 -
R/timeVariation.R | 67 ++-
R/trajCluster.R | 28 +
R/trajLevel.R |only
R/trajPlot.R | 509 +++++++---------------------
R/trendLevel.R | 799 +++++++++++++++++++++++----------------------
R/utilities.R | 99 +++--
R/windRose.R | 174 ++++-----
data/mydata.RData |binary
man/GoogleMapsPlot.Rd | 3
man/TaylorDiagram.Rd | 3
man/TheilSen.Rd | 3
man/airbaseFindCode.Rd | 3
man/airbaseInfo.Rd | 3
man/airbaseSplice.Rd | 3
man/airbaseStats.Rd | 5
man/aqStats.Rd | 3
man/calcFno2.Rd | 3
man/calcPercentile.Rd | 3
man/calendarPlot.Rd | 3
man/conditionalEval.Rd | 3
man/conditionalQuantile.Rd | 3
man/corPlot.Rd | 108 +++---
man/cutData.Rd | 3
man/drawOpenKey.Rd | 3
man/import.Rd | 3
man/importADMS.Rd | 3
man/importAURN.Rd | 3
man/importAURNCsv.Rd | 3
man/importAirbase.Rd | 3
man/importKCL.Rd | 3
man/importMeta.Rd | 3
man/importSAQN.Rd | 3
man/importTraj.Rd | 30 -
man/kernelExceed.Rd | 3
man/linearRelation.Rd | 5
man/modStats.Rd | 3
man/mydata.Rd | 3
man/openColours.Rd | 3
man/openair.Rd | 3
man/percentileRose.Rd | 3
man/polarAnnulus.Rd | 3
man/polarCluster.Rd | 3
man/polarFreq.Rd | 3
man/polarPlot.Rd | 3
man/quickText.Rd | 3
man/rollingMean.Rd | 3
man/scatterPlot.Rd | 13
man/selectByDate.Rd | 3
man/selectRunning.Rd | 3
man/smoothTrend.Rd | 78 ++--
man/splitByDate.Rd | 3
man/summaryPlot.Rd | 194 +++++-----
man/timeAverage.Rd | 125 +++++--
man/timePlot.Rd | 17
man/timeProp.Rd | 3
man/timeVariation.Rd | 29 +
man/trajCluster.Rd | 27 +
man/trajLevel.Rd |only
man/trajPlot.Rd | 203 ++---------
man/trendLevel.Rd | 198 ++++++-----
man/windRose.Rd | 8
84 files changed, 2902 insertions(+), 2408 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Diff between diseasemapping versions 1.1.2 dated 2014-11-13 and 1.1.4 dated 2015-01-05
More information about diseasemapping at CRAN
Description: Formating of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
diseasemapping-1.1.2/diseasemapping/R/formulaLhs.R |only
diseasemapping-1.1.4/diseasemapping/DESCRIPTION | 18 +++---
diseasemapping-1.1.4/diseasemapping/MD5 | 19 +++----
diseasemapping-1.1.4/diseasemapping/NAMESPACE | 3 +
diseasemapping-1.1.4/diseasemapping/R/bym.R | 16 ++++--
diseasemapping-1.1.4/diseasemapping/R/forInla.R |only
diseasemapping-1.1.4/diseasemapping/data/casedata.RData |binary
diseasemapping-1.1.4/diseasemapping/data/kentucky.RData |binary
diseasemapping-1.1.4/diseasemapping/data/popdata.RData |binary
diseasemapping-1.1.4/diseasemapping/data/referencepop.RData |binary
diseasemapping-1.1.4/diseasemapping/man/inla.models.Rd |only
diseasemapping-1.1.4/diseasemapping/tests/bym.R | 31 ++++++++----
12 files changed, 55 insertions(+), 32 deletions(-)
Permanent link
Title: Convert Statistical Analysis Objects Into Tidy Data Frames
Diff between broom versions 0.3.4 dated 2014-11-23 and 0.3.5 dated 2015-01-05
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like dplyr, tidyr and ggplot2. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson
DESCRIPTION | 8 +-
MD5 | 134 +++++++++++++++++++++---------------------
NAMESPACE | 5 +
R/felm_tidiers.R | 4 -
R/gam_tidiers.R |only
R/glm_tidiers.R | 2
R/glmnet_tidiers.R | 2
R/globals.R | 2
R/lm_tidiers.R | 15 +++-
R/lme4_tidiers.R | 8 +-
R/rlm_tidiers.R |only
R/sp_tidiers.R | 1
R/utilities.R | 14 +++-
README.md | 7 +-
build/vignette.rds |binary
inst/doc/broom_and_dplyr.html | 45 +++-----------
inst/doc/kmeans.Rmd | 6 -
inst/doc/kmeans.html | 6 -
man/Arima_tidiers.Rd | 3
man/aareg_tidiers.Rd | 3
man/anova_tidiers.Rd | 3
man/augment.Rd | 3
man/augment_columns.Rd | 3
man/bootstrap.Rd | 3
man/cch_tidiers.Rd | 3
man/compact.Rd | 3
man/confint_tidy.Rd | 3
man/coxph_tidiers.Rd | 3
man/cv.glmnet_tidiers.Rd | 3
man/data.frame_tidiers.Rd | 3
man/felm_tidiers.Rd | 3
man/finish_glance.Rd | 3
man/fix_data_frame.Rd | 3
man/gam_tidiers.Rd |only
man/glance.Rd | 3
man/glm_tidiers.Rd | 5 -
man/glmnet_tidiers.Rd | 3
man/htest_tidiers.Rd | 3
man/inflate.Rd | 3
man/insert_NAs.Rd | 3
man/kmeans_tidiers.Rd | 3
man/lm_tidiers.Rd | 10 ++-
man/lme4_tidiers.Rd | 9 +-
man/multcomp_tidiers.Rd | 3
man/nls_tidiers.Rd | 3
man/pyears_tidiers.Rd | 3
man/ridgelm_tidiers.Rd | 3
man/rlm_tidiers.Rd |only
man/rowwise_df_tidiers.Rd | 3
man/sexpfit_tidiers.Rd | 3
man/smooth.spline_tidiers.Rd | 3
man/sp_tidiers.Rd | 3
man/survfit_tidiers.Rd | 3
man/survreg_tidiers.Rd | 3
man/tidy.NULL.Rd | 3
man/tidy.Rd | 3
man/tidy.TukeyHSD.Rd | 3
man/tidy.default.Rd | 3
man/tidy.density.Rd | 3
man/tidy.ftable.Rd | 3
man/tidy.manova.Rd | 3
man/tidy.map.Rd | 3
man/tidy.pairwise.htest.Rd | 3
man/tidy.spec.Rd | 3
man/tidy.table.Rd | 3
man/tidy.ts.Rd | 3
man/unrowname.Rd | 3
man/zoo_tidiers.Rd | 3
tests/testthat/test-lm.R | 6 +
vignettes/kmeans.Rmd | 6 -
70 files changed, 245 insertions(+), 185 deletions(-)
Title: TH's Data Archive
Diff between TH.data versions 1.0-5 dated 2014-11-24 and 1.0-6 dated 2015-01-05
Description: Contains data sets used in other packages Torsten Hothorn
maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn
DESCRIPTION | 8
MD5 | 6
demo/PROACT.R | 561 +++++++++++++++++++--------------------------
inst/PSGLMM_MEE/README.txt | 10
4 files changed, 259 insertions(+), 326 deletions(-)
Title: Sparse Linear Algebra
Diff between SparseM versions 1.05 dated 2014-07-14 and 1.6 dated 2015-01-05
Description: Basic linear algebra for sparse matrices
Author: Roger Koenker
Maintainer: Roger Koenker
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
NAMESPACE | 28 +++++++++++++++++++++++++---
3 files changed, 32 insertions(+), 9 deletions(-)
Title: Partial Orders and Relations
Diff between pooh versions 0.2-1 dated 2013-03-29 and 0.3 dated 2015-01-05
Description: functions for computing closures of relations
Author: Charles J. Geyer
Maintainer: Charles J. Geyer
DESCRIPTION | 10 +++++-----
LICENSE | 23 ++---------------------
MD5 | 13 +++++++++----
NAMESPACE | 1 +
R/tsort.R |only
man/tsort.Rd |only
man/weak.Rd | 2 +-
src/tsort.c |only
tests/heffalump.R |only
tests/heffalump.Rout.save |only
10 files changed, 18 insertions(+), 31 deletions(-)
Title: Nested Association Mapping
Diff between NAM versions 1.0 dated 2015-01-03 and 1.0.1 dated 2015-01-05
Description: NAM, biparental and random populations toolbox
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu
Maintainer: Alencar Xavier
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/blup.R | 4 +++-
man/NAM-package.Rd | 2 +-
man/blup.Rd | 4 ++--
5 files changed, 14 insertions(+), 12 deletions(-)
Title: Analysis of Feedback in Time Series
Diff between FeedbackTS versions 1.2 dated 2014-09-29 and 1.3 dated 2015-01-05
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand
DESCRIPTION | 8 ++++----
MD5 | 32 ++++++++++++++++----------------
man/FeedbackTS-package.Rd | 35 ++++++++++++++++-------------------
man/KDD-class.Rd | 2 +-
man/KDD.yearly.average-class.Rd | 2 +-
man/KT.output-class.Rd | 20 +++++++-------------
man/after.minus.before.Rd | 2 +-
man/feedback.stats.Rd | 2 +-
man/feedback.test.Rd | 3 ++-
man/kdd.Rd | 2 +-
man/kdd.from.raw.data.Rd | 5 ++---
man/kdd.yearly.average.Rd | 2 +-
man/krige.Rd | 8 ++++----
man/krige.test.Rd | 21 ++++++++-------------
man/map.statistic.Rd | 2 +-
man/rain.feedback.stats.Rd | 4 ++--
man/rain.site.6008.Rd | 4 ++--
17 files changed, 70 insertions(+), 84 deletions(-)
Title: docopt, command-line interface specification language
Diff between docopt versions 0.3 dated 2014-09-03 and 0.4.2 dated 2015-01-05
Description: docopt lets you define a command-line interface by just giving it
a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge
docopt-0.3/docopt/inst/paper/Makefile |only
docopt-0.3/docopt/inst/paper/beamer.tex |only
docopt-0.3/docopt/inst/paper/figures |only
docopt-0.3/docopt/inst/paper/test.R |only
docopt-0.3/docopt/inst/paper/user2014.Rmd |only
docopt-0.3/docopt/inst/paper/user2014.html |only
docopt-0.3/docopt/inst/paper/user2014.md |only
docopt-0.3/docopt/inst/paper/user2014.pdf |only
docopt-0.3/docopt/tests/testthat/test_quotedargs.R |only
docopt-0.4.2/docopt/DESCRIPTION | 11
docopt-0.4.2/docopt/LICENSE | 4
docopt-0.4.2/docopt/MD5 | 57
docopt-0.4.2/docopt/NAMESPACE | 10
docopt-0.4.2/docopt/NEWS | 5
docopt-0.4.2/docopt/R/Pattern.R | 941 +--
docopt-0.4.2/docopt/R/Tokens.R | 211
docopt-0.4.2/docopt/R/docopt.R | 7
docopt-0.4.2/docopt/R/parse.R | 544 +-
docopt-0.4.2/docopt/R/pkg.R | 20
docopt-0.4.2/docopt/README.md | 159
docopt-0.4.2/docopt/inst/paper/docopt.bib | 64
docopt-0.4.2/docopt/inst/paper/docopt.tex | 160
docopt-0.4.2/docopt/inst/spec/README.md | 14
docopt-0.4.2/docopt/inst/spec/docopt.py | 1162 ++--
docopt-0.4.2/docopt/inst/spec/generate_tests.R | 178
docopt-0.4.2/docopt/inst/spec/testcases.docopt | 1914 +++----
docopt-0.4.2/docopt/man/as.character-Pattern-method.Rd | 32
docopt-0.4.2/docopt/man/as.character-Tokens-method.Rd | 32
docopt-0.4.2/docopt/man/docopt-package.Rd | 27
docopt-0.4.2/docopt/man/docopt.Rd | 3
docopt-0.4.2/docopt/man/sub-Tokens-method.Rd | 61
docopt-0.4.2/docopt/man/subset-Tokens-method.Rd | 58
docopt-0.4.2/docopt/tests/testthat/test_specs.R | 4088 ++++++++---------
33 files changed, 4858 insertions(+), 4904 deletions(-)
Title: Stellar CharactEristics Pisa Estimation gRid
Diff between SCEPtER versions 0.2-0 dated 2014-12-16 and 0.2-1 dated 2015-01-05
Description: SCEPtER pipeline for estimating the stellar age, mass, and radius
given observational
effective temperature, [Fe/H], and astroseismic
parameters. The results are obtained adopting a maximum likelihood
technique over a grid of pre-computed stellar models.
Author: Matteo Dell'Omodarme [aut, cre],
Giada Valle [aut]
Maintainer: Matteo Dell'Omodarme
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Diff between HSAUR3 versions 1.0-2 dated 2014-08-19 and 1.0-3 dated 2015-01-05
Description: Functions, data sets, analyses and examples from the
third edition of the book
`A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
HSAUR3-1.0-2/HSAUR3/inst/slides/HSAUR_title.tex |only
HSAUR3-1.0-2/HSAUR3/inst/slides/Makefile |only
HSAUR3-1.0-2/HSAUR3/vignettes/LaTeXBibTeX/HSAUR.in |only
HSAUR3-1.0-2/HSAUR3/vignettes/LaTeXBibTeX/Makefile |only
HSAUR3-1.0-3/HSAUR3/DESCRIPTION | 8
HSAUR3-1.0-3/HSAUR3/MD5 | 112 ++++------
HSAUR3-1.0-3/HSAUR3/build/vignette.rds |binary
HSAUR3-1.0-3/HSAUR3/data/BCG.rda |binary
HSAUR3-1.0-3/HSAUR3/data/CYGOB1.rda |binary
HSAUR3-1.0-3/HSAUR3/data/Lanza.rda |binary
HSAUR3-1.0-3/HSAUR3/data/birthdeathrates.rda |binary
HSAUR3-1.0-3/HSAUR3/data/bladdercancer.rda |binary
HSAUR3-1.0-3/HSAUR3/data/epilepsy.rda |binary
HSAUR3-1.0-3/HSAUR3/data/foster.rda |binary
HSAUR3-1.0-3/HSAUR3/data/heptathlon.rda |binary
HSAUR3-1.0-3/HSAUR3/data/meteo.rda |binary
HSAUR3-1.0-3/HSAUR3/data/orallesions.rda |binary
HSAUR3-1.0-3/HSAUR3/data/phosphate.rda |binary
HSAUR3-1.0-3/HSAUR3/data/pistonrings.rda |binary
HSAUR3-1.0-3/HSAUR3/data/planets.rda |binary
HSAUR3-1.0-3/HSAUR3/data/plasma.rda |binary
HSAUR3-1.0-3/HSAUR3/data/polyps.rda |binary
HSAUR3-1.0-3/HSAUR3/data/rearrests.rda |binary
HSAUR3-1.0-3/HSAUR3/data/roomwidth.rda |binary
HSAUR3-1.0-3/HSAUR3/data/schizophrenia.rda |binary
HSAUR3-1.0-3/HSAUR3/data/schizophrenia2.rda |binary
HSAUR3-1.0-3/HSAUR3/data/smoking.rda |binary
HSAUR3-1.0-3/HSAUR3/data/students.rda |binary
HSAUR3-1.0-3/HSAUR3/data/suicides.rda |binary
HSAUR3-1.0-3/HSAUR3/data/toothpaste.rda |binary
HSAUR3-1.0-3/HSAUR3/data/voting.rda |binary
HSAUR3-1.0-3/HSAUR3/data/water.rda |binary
HSAUR3-1.0-3/HSAUR3/data/watervoles.rda |binary
HSAUR3-1.0-3/HSAUR3/data/waves.rda |binary
HSAUR3-1.0-3/HSAUR3/data/weightgain.rda |binary
HSAUR3-1.0-3/HSAUR3/inst/NEWS | 4
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_analysis_of_variance.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_bayesian_inference.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_cluster_analysis.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_conditional_inference.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_density_estimation.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_errata.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_gam.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_graphical_display.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_introduction_to_R.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_logistic_regression_glm.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_meta_analysis.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_missing_values.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_multidimensional_scaling.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_multiple_linear_regression.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_principal_components_analysis.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_quantile_regression.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_recursive_partitioning.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_simple_inference.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_simultaneous_inference.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/doc/Ch_survival_analysis.pdf |binary
HSAUR3-1.0-3/HSAUR3/inst/slides/title_UZH.tex | 2
59 files changed, 63 insertions(+), 63 deletions(-)
Title: A Handbook of Statistical Analyses Using R (2nd Edition)
Diff between HSAUR2 versions 1.1-11 dated 2014-08-19 and 1.1-12 dated 2015-01-05
Description: Functions, data sets, analyses and examples from the
second edition of the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2008). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
the package contains Sweave code for producing slides for selected
chapters (see HSAUR2/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
HSAUR2-1.1-11/HSAUR2/inst/slides/HSAUR_title.tex |only
HSAUR2-1.1-11/HSAUR2/inst/slides/Makefile |only
HSAUR2-1.1-11/HSAUR2/vignettes/LaTeXBibTeX/HSAUR.in |only
HSAUR2-1.1-11/HSAUR2/vignettes/LaTeXBibTeX/Makefile |only
HSAUR2-1.1-12/HSAUR2/DESCRIPTION | 8
HSAUR2-1.1-12/HSAUR2/MD5 | 104 ++++------
HSAUR2-1.1-12/HSAUR2/build/vignette.rds |binary
HSAUR2-1.1-12/HSAUR2/data/BCG.rda |binary
HSAUR2-1.1-12/HSAUR2/data/CYGOB1.rda |binary
HSAUR2-1.1-12/HSAUR2/data/Lanza.rda |binary
HSAUR2-1.1-12/HSAUR2/data/birthdeathrates.rda |binary
HSAUR2-1.1-12/HSAUR2/data/bladdercancer.rda |binary
HSAUR2-1.1-12/HSAUR2/data/epilepsy.rda |binary
HSAUR2-1.1-12/HSAUR2/data/foster.rda |binary
HSAUR2-1.1-12/HSAUR2/data/heptathlon.rda |binary
HSAUR2-1.1-12/HSAUR2/data/meteo.rda |binary
HSAUR2-1.1-12/HSAUR2/data/orallesions.rda |binary
HSAUR2-1.1-12/HSAUR2/data/phosphate.rda |binary
HSAUR2-1.1-12/HSAUR2/data/pistonrings.rda |binary
HSAUR2-1.1-12/HSAUR2/data/planets.rda |binary
HSAUR2-1.1-12/HSAUR2/data/plasma.rda |binary
HSAUR2-1.1-12/HSAUR2/data/polyps.rda |binary
HSAUR2-1.1-12/HSAUR2/data/rearrests.rda |binary
HSAUR2-1.1-12/HSAUR2/data/roomwidth.rda |binary
HSAUR2-1.1-12/HSAUR2/data/schizophrenia.rda |binary
HSAUR2-1.1-12/HSAUR2/data/schizophrenia2.rda |binary
HSAUR2-1.1-12/HSAUR2/data/smoking.rda |binary
HSAUR2-1.1-12/HSAUR2/data/students.rda |binary
HSAUR2-1.1-12/HSAUR2/data/suicides.rda |binary
HSAUR2-1.1-12/HSAUR2/data/toothpaste.rda |binary
HSAUR2-1.1-12/HSAUR2/data/voting.rda |binary
HSAUR2-1.1-12/HSAUR2/data/water.rda |binary
HSAUR2-1.1-12/HSAUR2/data/watervoles.rda |binary
HSAUR2-1.1-12/HSAUR2/data/waves.rda |binary
HSAUR2-1.1-12/HSAUR2/data/weightgain.rda |binary
HSAUR2-1.1-12/HSAUR2/inst/NEWS | 4
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_analysis_of_variance.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_cluster_analysis.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_conditional_inference.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_density_estimation.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_errata.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_gam.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_graphical_display.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_introduction_to_R.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_logistic_regression_glm.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_meta_analysis.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_multidimensional_scaling.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_multiple_linear_regression.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_principal_components_analysis.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_recursive_partitioning.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_simple_inference.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_simultaneous_inference.pdf |binary
HSAUR2-1.1-12/HSAUR2/inst/doc/Ch_survival_analysis.pdf |binary
55 files changed, 58 insertions(+), 58 deletions(-)
Title: A Handbook of Statistical Analyses Using R
Diff between HSAUR versions 1.3-4 dated 2014-08-19 and 1.3-5 dated 2015-01-05
Description: Functions, data sets, analyses and examples from the book
`A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten
Hothorn, Chapman & Hall/CRC, 2006). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available.
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
HSAUR-1.3-4/HSAUR/vignettes/LaTeXBibTeX/HSAUR.in |only
HSAUR-1.3-4/HSAUR/vignettes/LaTeXBibTeX/Makefile |only
HSAUR-1.3-5/HSAUR/DESCRIPTION | 8 -
HSAUR-1.3-5/HSAUR/MD5 | 42 ++++------
HSAUR-1.3-5/HSAUR/build/vignette.rds |binary
HSAUR-1.3-5/HSAUR/inst/NEWS | 4
HSAUR-1.3-5/HSAUR/inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_analysis_of_variance.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_cluster_analysis.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_conditional_inference.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_density_estimation.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_errata.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_introduction_to_R.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_logistic_regression_glm.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_meta_analysis.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_multidimensional_scaling.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_multiple_linear_regression.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_principal_components_analysis.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_recursive_partitioning.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_simple_inference.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/Ch_survival_analysis.pdf |binary
HSAUR-1.3-5/HSAUR/inst/doc/preface.pdf |binary
23 files changed, 28 insertions(+), 26 deletions(-)
Title: Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Diff between EnsembleBase versions 0.7 dated 2014-11-22 and 0.7.1 dated 2015-01-05
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, and K-Nearest Neighbors. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
NAMESPACE | 1 +
R/baselearners.R | 4 ++++
5 files changed, 13 insertions(+), 7 deletions(-)
Title: Kriging methods for computer experiments
Diff between DiceKriging versions 1.5.3 dated 2014-01-10 and 1.5.4 dated 2015-01-05
Description: Estimation, validation and prediction of kriging models.
Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant
DiceKriging-1.5.3/DiceKriging/R/covAdditive0.R |only
DiceKriging-1.5.4/DiceKriging/CHANGELOG | 14 -
DiceKriging-1.5.4/DiceKriging/DESCRIPTION | 10
DiceKriging-1.5.4/DiceKriging/MD5 | 33 +-
DiceKriging-1.5.4/DiceKriging/R/drop.reponse.R | 8
DiceKriging-1.5.4/DiceKriging/R/km.R | 8
DiceKriging-1.5.4/DiceKriging/R/km1Nugget.init.R | 41 +--
DiceKriging-1.5.4/DiceKriging/R/kmEstimate.R | 134 ++++++----
DiceKriging-1.5.4/DiceKriging/R/kmNoNugget.init.R | 32 +-
DiceKriging-1.5.4/DiceKriging/R/kmNuggets.init.R | 53 +--
DiceKriging-1.5.4/DiceKriging/R/kmStruct.R | 10
DiceKriging-1.5.4/DiceKriging/inst/tests/test-SK-OrnsteinUhlenbeck.R |only
DiceKriging-1.5.4/DiceKriging/inst/tests/test-interp.R |only
DiceKriging-1.5.4/DiceKriging/man/DiceKriging-package.Rd | 4
DiceKriging-1.5.4/DiceKriging/man/km.Rd | 23 +
DiceKriging-1.5.4/DiceKriging/man/km1Nugget.init.Rd | 9
DiceKriging-1.5.4/DiceKriging/man/kmNoNugget.init.Rd | 12
DiceKriging-1.5.4/DiceKriging/man/kmNuggets.init.Rd | 8
DiceKriging-1.5.4/DiceKriging/man/simulate.km.Rd | 6
19 files changed, 252 insertions(+), 153 deletions(-)
Title: Moments, cumulants, skewness, kurtosis and related tests
Diff between moments versions 0.13 dated 2012-01-24 and 0.14 dated 2015-01-05
Description: Functions to calculate: moments, Pearson's kurtosis,
Geary's kurtosis and skewness; tests related to them
(Anscombe-Glynn, D'Agostino, Bonett-Seier).
Author: Lukasz Komsta
Maintainer: Lukasz Komsta
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
R/agostino.test.R | 4 ++--
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 1.0.0 dated 2014-12-22 and 1.1.0 dated 2015-01-05
Description: Target Inhibition Interaction using Maximization/Minimization
Averaging
Author: Liye He
Maintainer: Liye He
DESCRIPTION | 8 +-
MD5 | 101 +++++++++++++++++++-----------------
R/binarizeDrugTargets.R |only
R/davis.R |only
R/drawGraph.R | 32 ++++-------
R/normalizeSensitivity.R |only
R/timma.R | 4 +
data/datalist | 1
data/davis.rda |only
man/binarizeDrugTargets.Rd |only
man/binarySet.Rd | 3 -
man/ci.Rd | 3 -
man/davis.Rd |only
man/dec2bin.Rd | 3 -
man/drawGraph.Rd | 3 -
man/drugRank.Rd | 3 -
man/findSameCol.Rd | 3 -
man/findSameSet.Rd | 3 -
man/floating2.Rd | 3 -
man/getBinary.Rd | 3 -
man/getBinary1.Rd | 3 -
man/graycode2.Rd | 3 -
man/graycode3.Rd | 3 -
man/graycodeNames.Rd | 3 -
man/grays.Rd | 3 -
man/kiba.Rd | 3 -
man/miller_drug_response.Rd | 3 -
man/miller_drugs.Rd | 3 -
man/miller_interaction_binary.Rd | 3 -
man/miller_sensitivity.Rd | 3 -
man/miller_targets.Rd | 3 -
man/normalizeSensitivity.Rd |only
man/searchSpace.Rd | 3 -
man/sffs.Rd | 3 -
man/sffsBinary.Rd | 3 -
man/sffsBinary1.Rd | 3 -
man/sffsBinary2.Rd | 3 -
man/sffsCategory.Rd | 3 -
man/sffsCategory1.Rd | 3 -
man/sffsCategoryWeighted.Rd | 3 -
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man/timma.Rd | 3 -
man/timmaBinary.Rd | 3 -
man/timmaBinary1.Rd | 3 -
man/timmaCategory.Rd | 3 -
man/timmaCategory1.Rd | 3 -
man/timmaCategoryWeighted.Rd | 3 -
man/timmaCategoryWeighted1.Rd | 3 -
man/timmaModel.Rd | 3 -
man/timmaModel1.Rd | 3 -
man/timmaSearchBinary.Rd | 3 -
man/timmaSearchBinary1.Rd | 3 -
man/tyner_interaction_binary.Rd | 27 ++++-----
man/tyner_interaction_multiclass.Rd | 27 ++++-----
man/tyner_sensitivity.Rd | 3 -
55 files changed, 184 insertions(+), 139 deletions(-)
Title: seawater carbonate chemistry with R
Diff between seacarb versions 3.0.3 dated 2014-12-10 and 3.0.4 dated 2015-01-05
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 16 ++++++++
DESCRIPTION | 11 +++--
MD5 | 38 ++++++++++----------
NAMESPACE | 1
R/K1.R | 21 ++++++-----
R/K2.R | 29 ++++++---------
R/Kb.R | 18 ++++-----
R/Kf.R | 29 +++++++--------
R/Ks.R | 12 ++----
R/Pcorrect.R | 12 +++---
R/at.R | 5 +-
R/buffer.R | 13 ++----
R/buffesm.R | 11 ++---
R/carb.R | 97 ++++++++++++++++++++++++++++++++++++----------------
R/kconv.R | 19 +++++++++-
R/pHconv.R | 5 +-
R/rho.R | 31 +++++++---------
R/theta.R |only
data/Pcoeffs.txt.gz |binary
man/carb.Rd | 3 +
man/theta.Rd |only
21 files changed, 217 insertions(+), 154 deletions(-)
Title: MRI Tissue Classification
Diff between mritc versions 0.4-0 dated 2012-04-20 and 0.5-0 dated 2015-01-05
Description: Various methods for MRI tissue classification.
Author: Dai Feng and Luke Tierney
Maintainer: Dai Feng
mritc-0.4-0/mritc/R/readNIfTI.R |only
mritc-0.4-0/mritc/R/writeNIfTI.R |only
mritc-0.5-0/mritc/ChangeLog | 16 +
mritc-0.5-0/mritc/DESCRIPTION | 13 -
mritc-0.5-0/mritc/MD5 | 36 ++-
mritc-0.5-0/mritc/NAMESPACE | 3
mritc-0.5-0/mritc/R/getWeightsMRI.R |only
mritc-0.5-0/mritc/R/mriio.R | 38 ++--
mritc-0.5-0/mritc/R/mrispatial.R | 23 +-
mritc-0.5-0/mritc/R/mritc.R | 19 +-
mritc-0.5-0/mritc/R/mritc.bayes.R | 237 +++++++++++++++++++++++--
mritc-0.5-0/mritc/man/makeMRIspatial.Rd | 26 ++
mritc-0.5-0/mritc/man/measureMRI.Rd | 2
mritc-0.5-0/mritc/man/mritc-package.Rd | 46 +++-
mritc-0.5-0/mritc/man/mritc.Rd | 100 +++++++---
mritc-0.5-0/mritc/man/readMRI.Rd | 23 --
mritc-0.5-0/mritc/man/writeMRI.Rd | 33 +--
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mritc-0.5-0/mritc/src/yIndicesSummariesBias.c |only
24 files changed, 473 insertions(+), 142 deletions(-)
Title: Dendrochronology Program Library in R
Diff between dplR versions 1.6.1 dated 2014-12-30 and 1.6.2 dated 2015-01-05
Description: This package contains functions for performing tree-ring
analyses such as detrending, chronology building, and cross dating.
The package reads and writes standard file formats used in
dendrochronology
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn
ChangeLog | 23 +++++++++++++++--------
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
inst/doc/intro-dplR.pdf |binary
inst/doc/timeseries-dplR.pdf |binary
inst/doc/xdate-dplR.pdf |binary
inst/unitTests/runit.dplR.R | 31 ++++++++++++++++++-------------
7 files changed, 43 insertions(+), 31 deletions(-)
Title: Nonparametrics with Clustered Binary and Multinomial Data
Diff between CorrBin versions 1.4 dated 2013-12-12 and 1.5 dated 2015-01-05
Description: This package implements non-parametric analyses for clustered
binary and multinomial data. The elements of the cluster are assumed
exchangeable, and identical joint distribution (also known as marginal
compatibility, or reproducibility) is assumed for clusters of different
sizes. A trend test based on stochastic ordering is implemented.
Author: Aniko Szabo [aut, cre]
Maintainer: Aniko Szabo
DESCRIPTION | 32 +++---
MD5 | 72 ++++++++-------
NAMESPACE | 16 +++
R/CBData.R | 61 +++++++------
R/CMData.R | 201 +++++++++++++++++++++++++++++++++++++++++--
R/CorrBin-package.R | 18 +--
R/ExchMultinomial.R | 174 ++++++++++++++++++++++++++++++++++---
R/Reprod.R | 87 ------------------
R/aaa-generics.R |only
R/aaa-generics1.R |only
build/vignette.rds |binary
data/dehp.rda |binary
data/egde.rda |binary
data/shelltox.rda |binary
inst/doc/CorrBinVignette.pdf |binary
man/CBData.Rd | 50 ++++------
man/CMData.Rd | 69 +++++---------
man/CorrBin-internal.Rd | 4
man/CorrBin-package.Rd | 62 ++++++-------
man/Extract.Rd |only
man/GEE.trend.test.Rd | 40 +++-----
man/NOSTASOT.Rd | 81 +++++++----------
man/RS.trend.test.Rd | 34 +++----
man/SO.LRT.Rd | 34 +++----
man/SO.mc.est.Rd | 71 ++++++---------
man/SO.trend.test.Rd | 58 +++++-------
man/dehp.Rd | 8 +
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man/mc.test.chisq.Rd | 64 ++++++-------
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man/pdf.Rd | 61 +++++--------
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man/ran.CMData.Rd |only
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man/read.CMData.Rd | 35 ++-----
man/soControl.Rd | 42 +++-----
man/trend.test.Rd | 64 +++++--------
man/uniprobs.Rd |only
man/unwrap.Rd | 45 +++------
41 files changed, 917 insertions(+), 706 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.2 dated 2014-12-22 and 0.2.4 dated 2015-01-04
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/vardchanges.R | 21 +++++++++++----------
inst/CITATION | 6 +++---
inst/COPYING | 2 +-
inst/NEWS | 5 +++++
man/vardpoor-package.Rd | 4 ++--
7 files changed, 33 insertions(+), 27 deletions(-)
More information about ThreeArmedTrials at CRAN
Permanent link
More information about rUnemploymentData at CRAN
Permanent link
Title: Companion Package to the Book “R: Einführung durch angewandte
Statistikâ€
Diff between REdaS versions 0.9.1 dated 2014-05-05 and 0.9.2 dated 2015-01-04
Description: This package provides functions used in the second edition of “R: Einführung durch angewandte Statistikâ€.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NAMESPACE | 28 +++++++++++++++-------------
R/bart_spher.R | 4 ++--
R/print.bart_spher.R | 9 ++-------
R/summary.REdaS_ORs.R | 3 ++-
R/zzz.R |only
build/partial.rdb |binary
man/densbox.Rd | 2 +-
9 files changed, 34 insertions(+), 35 deletions(-)
Title: Multigroup Data Analysis
Diff between multigroup versions 0.4.2 dated 2014-09-14 and 0.4.3 dated 2015-01-04
Description: This package includes several functions to study multigroup data,
where the same set of variables are measured on different groups of
individuals.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez
Questions and comments go to Aida Eslami
Maintainer: Aida Eslami
DESCRIPTION | 12
MD5 | 62 +--
NAMESPACE | 2
R/loadingsplotXY.R | 23 +
R/mbmgPCA.R | 830 ++++++++++++++++++++++-----------------------
R/mgPLS.R | 11
man/BGC.Rd | 3
man/DCCSWA.Rd | 3
man/DGPA.Rd | 3
man/DSTATIS.Rd | 3
man/FCPCA.Rd | 3
man/TBWvariance.Rd | 3
man/Trace.Rd | 3
man/deflation.Rd | 3
man/iteraite_fun_Iter.Rd | 3
man/loadingsplot.Rd | 3
man/loadingsplotXY.Rd | 5
man/mbmgPCA.Rd | 5
man/mgPCA.Rd | 3
man/mgPLS.Rd | 3
man/multigroup.Rd | 3
man/normM.Rd | 3
man/normv.Rd | 3
man/plot.mg.Rd | 3
man/prepare_data.Rd | 3
man/project.Rd | 3
man/scoreplot.Rd | 3
man/select_initial_Iter.Rd | 3
man/similarity_function.Rd | 3
man/similarity_noncum.Rd | 3
man/summarize.Rd | 3
man/transfer_Group.Rd | 3
32 files changed, 536 insertions(+), 486 deletions(-)
Title: Interval Regression
Diff between intReg versions 0.2-6 dated 2014-12-06 and 0.2-8 dated 2015-01-04
Description: Estimating interval regression models. Supports both common and observation-specific boundaries.
Author: Ott Toomet
Maintainer: Ott Toomet
DESCRIPTION | 6
MD5 | 14 +-
R/stdEr.intReg.R | 9 +
R/summary.intReg.R | 6
man/coef.intReg.Rd | 3
man/intReg.Rd | 2
tests/intReg.R | 12 +
tests/intReg.Rout.save | 296 ++++++++++++++++++++++++++++++++-----------------
8 files changed, 233 insertions(+), 115 deletions(-)
Title: Estimation of Entropy and Related Quantities
Diff between EntropyEstimation versions 1.1 dated 2014-11-08 and 1.2 dated 2015-01-04
More information about EntropyEstimation at CRAN
Description: Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Author: Lijuan Cao
Maintainer: Michael Grabchak
DESCRIPTION | 8 -
MD5 | 12 -
NAMESPACE | 1
R/EntropEst.r | 6
man/EntropyEstimation-package.Rd | 4
man/MI.sd.Rd | 2
src/EntropEst.c | 288 +++++++++++++++++++++++++++------------
7 files changed, 219 insertions(+), 102 deletions(-)
Permanent link
Title: Nonparametric Multiple Change-Point Analysis of Multivariate
Data
Diff between ecp versions 1.6.0 dated 2014-07-20 and 1.6.2 dated 2015-01-04
Description: Implements hierarchical procedures to find multiple change-points
through the use of U-statistics. The procedures do not make any
distributional assumptions other than the existence of certain
absolute moments. Both agglomerative and divisive procedures are
included. These methods return the set of estimated change-points
as well as other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James
DESCRIPTION | 25 +++++++++++++------------
MD5 | 40 ++++++++++++++++++++++------------------
NEWS | 13 +++++++++++++
R/e_agglomerative.R | 10 +++++-----
build |only
inst/CITATION | 36 ++++++++++++++++++++----------------
inst/doc |only
man/ACGH.RData.Rd | 4 +++-
man/DJIA.RData.Rd | 4 +++-
man/e.agglo.Rd | 8 +++++---
man/e.divisive.Rd | 4 +++-
man/e.split.Rd | 4 +++-
man/find.closest.Rd | 4 +++-
man/getBetween.Rd | 4 +++-
man/getWithin.Rd | 4 +++-
man/gof.update.Rd | 4 +++-
man/perm.cluster.Rd | 4 +++-
man/sig.test.Rd | 4 +++-
man/splitPoint.Rd | 4 +++-
man/splitPointC.Rd | 4 +++-
man/updateDistance.Rd | 4 +++-
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22 files changed, 117 insertions(+), 67 deletions(-)
Title: Datasets from Draper and Smith "Applied Regression Analysis"
(3rd ed., 1998)
Diff between aprean3 versions 0.5 dated 2014-12-26 and 1.0 dated 2015-01-04
Description: This package is an unofficial companion to the textbook
"Applied Regression Analysis" by N.R. Draper and H. Smith (3rd
ed., 1998). See ?aprean3 for more info.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia
aprean3-0.5/aprean3/R/ds01a.R |only
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aprean3-1.0/aprean3/man/dse03r.Rd | 3
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aprean3-1.0/aprean3/man/dse06l.Rd | 3
aprean3-1.0/aprean3/man/dse06z.Rd | 3
aprean3-1.0/aprean3/man/dse07b.Rd | 3
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aprean3-1.0/aprean3/man/dse08b.Rd | 3
aprean3-1.0/aprean3/man/dse09b.Rd | 3
aprean3-1.0/aprean3/man/dse12a.Rd | 3
aprean3-1.0/aprean3/man/dse12b.Rd | 3
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325 files changed, 509 insertions(+), 342 deletions(-)
Title: Tree-Based Varying Coefficient Regression for Generalized Linear
and Ordinal Mixed Models
Diff between vcrpart versions 0.2-3 dated 2014-11-25 and 0.3-1 dated 2015-01-04
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph],
Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin
DESCRIPTION | 11 ++-
MD5 | 57 +++++++++----------
NEWS | 35 +++++++++--
R/olmm-methods.R | 47 ++++++++-------
R/olmm-utils.R | 3 -
R/tvcm-methods.R | 1
R/tvcm-utils.R | 156 +++++++++++++++++++++++++++++++++++++---------------
R/tvcm.R | 31 ++++++----
ToDo |only
inst/CITATION | 14 ++--
man/PL.Rd | 7 +-
man/contr-wsum.Rd | 4 -
man/fvcm-methods.Rd | 12 ++--
man/fvcm.Rd | 18 +++---
man/movie.Rd | 7 +-
man/olmm-gefp.Rd | 14 ++--
man/olmm-methods.Rd | 14 ++--
man/olmm-predict.Rd | 6 ++
man/olmm.Rd | 36 +++++-------
man/otsplot.Rd | 10 +--
man/poverty.Rd | 10 +--
man/schizo.Rd | 2
man/tvcglm.Rd | 77 +++++++++++++++----------
man/tvcm-control.Rd | 9 ++-
man/tvcm-cv.Rd | 145 +++++++++++++++++++++++++++---------------------
man/tvcm-methods.Rd | 15 ++---
man/tvcm-plot.Rd | 4 -
man/tvcm.Rd | 23 +++----
man/tvcolmm.Rd | 89 +++++++++++++++++------------
src/Makevars | 3 -
30 files changed, 510 insertions(+), 350 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and Python
Diff between fastcluster versions 1.1.13 dated 2013-12-17 and 1.1.14 dated 2015-01-04
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: “linkage†in the SciPy package
“scipy.cluster.hierarchyâ€, “hclust†in R's “stats†package, and the
“flashClust†package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner
DESCRIPTION | 14 +++++------
MD5 | 36 +++++++++++++++---------------
NEWS | 9 ++++++-
R/fastcluster.R | 7 +++++
build/vignette.rds |binary
inst/doc/fastcluster.Rtex | 34 ++++++++++++++++------------
inst/doc/fastcluster.pdf |binary
man/fastcluster.Rd | 2 -
man/hclust.Rd | 6 ++---
man/hclust.vector.Rd | 10 +++++---
src/fastcluster.cpp | 50 +++++++++++++++++++++++++-----------------
src/fastcluster_R.cpp | 24 +++++++++++++++-----
src/fastcluster_python.cpp | 29 +++++++++++++-----------
src/python/fastcluster.py | 4 ++-
src/python/test/nantest.py | 4 +++
src/python/test/test.py | 10 +++++++-
src/python/test/vectortest.py | 4 +++
tests/test_fastcluster.R | 20 +++++++++++-----
vignettes/fastcluster.Rtex | 34 ++++++++++++++++------------
19 files changed, 187 insertions(+), 110 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models with Local
Dependence
Diff between hergm versions 2.0-0 dated 2014-12-15 and 2.1-0 dated 2015-01-04
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
hergm-2.0-0/hergm/R/hergm.dirichlet.R |only
hergm-2.1-0/hergm/DESCRIPTION | 14 +--
hergm-2.1-0/hergm/MD5 | 33 +++----
hergm-2.1-0/hergm/R/hergm.R | 15 +--
hergm-2.1-0/hergm/R/hergm.gof.R | 8 +
hergm-2.1-0/hergm/R/hergm.mcmc.R | 7 -
hergm-2.1-0/hergm/R/hergm.misc.R | 2
hergm-2.1-0/hergm/R/hergm.multiple.R | 2
hergm-2.1-0/hergm/R/hergm.postprocess.R | 12 --
hergm-2.1-0/hergm/R/hergm.preprocess.R | 14 ++-
hergm-2.1-0/hergm/R/hergm.set.mcmc.R | 10 +-
hergm-2.1-0/hergm/data/sampson.RData |binary
hergm-2.1-0/hergm/demo |only
hergm-2.1-0/hergm/man/hergm-internal.Rd | 4
hergm-2.1-0/hergm/man/hergm.Rd | 15 ++-
hergm-2.1-0/hergm/src/h_ergm.c | 141 ++++++++++++++++++++------------
hergm-2.1-0/hergm/src/h_ergm_mcmc.c | 5 -
hergm-2.1-0/hergm/src/h_ergm_utils.c | 6 -
18 files changed, 163 insertions(+), 125 deletions(-)
Title: Learn R, in R.
Diff between swirl versions 2.2.16 dated 2014-08-26 and 2.2.21 dated 2015-01-04
Description: swirl turns the R console into an interactive learning
environment. Users receive immediate feedback as they are guided through
self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre],
Bill Bauer [aut],
Gina Grdina [aut],
Sean Kross [aut]
Maintainer: Nick Carchedi
swirl-2.2.16/swirl/tests/testthat/test-play.R |only
swirl-2.2.21/swirl/DESCRIPTION | 6 -
swirl-2.2.21/swirl/MD5 | 89 +++++++++---------
swirl-2.2.21/swirl/NAMESPACE | 6 +
swirl-2.2.21/swirl/R/answerTests2.R | 45 +++++++--
swirl-2.2.21/swirl/R/courseraCheck.R | 10 +-
swirl-2.2.21/swirl/R/install_course.R | 60 +++++++++++-
swirl-2.2.21/swirl/R/lesson_constructor.R | 4
swirl-2.2.21/swirl/R/parse_content.R | 4
swirl-2.2.21/swirl/R/progress.R | 28 +++++
swirl-2.2.21/swirl/R/rmatch_calls.R |only
swirl-2.2.21/swirl/R/swirl.R | 3
swirl-2.2.21/swirl/R/utilities.R | 1
swirl-2.2.21/swirl/man/AnswerTests.Rd | 3
swirl-2.2.21/swirl/man/InstallCourses.Rd | 7 +
swirl-2.2.21/swirl/man/any_of_exprs.Rd | 3
swirl-2.2.21/swirl/man/bye.Rd | 3
swirl-2.2.21/swirl/man/delete_progress.Rd |only
swirl-2.2.21/swirl/man/email_admin.Rd | 3
swirl-2.2.21/swirl/man/expr_creates_var.Rd | 3
swirl-2.2.21/swirl/man/expr_identical_to.Rd | 3
swirl-2.2.21/swirl/man/expr_is_a.Rd | 3
swirl-2.2.21/swirl/man/expr_uses_func.Rd | 3
swirl-2.2.21/swirl/man/func_of_newvar_equals.Rd | 3
swirl-2.2.21/swirl/man/info.Rd | 3
swirl-2.2.21/swirl/man/install_course_directory.Rd | 4
swirl-2.2.21/swirl/man/install_course_dropbox.Rd | 4
swirl-2.2.21/swirl/man/install_course_github.Rd | 4
swirl-2.2.21/swirl/man/install_course_google_drive.Rd | 4
swirl-2.2.21/swirl/man/install_course_url.Rd | 4
swirl-2.2.21/swirl/man/install_course_zip.Rd | 4
swirl-2.2.21/swirl/man/install_from_swirl.Rd | 16 ++-
swirl-2.2.21/swirl/man/is_robust_match.Rd |only
swirl-2.2.21/swirl/man/main.Rd | 3
swirl-2.2.21/swirl/man/nxt.Rd | 3
swirl-2.2.21/swirl/man/omnitest.Rd | 8 +
swirl-2.2.21/swirl/man/play.Rd | 3
swirl-2.2.21/swirl/man/reset.Rd | 3
swirl-2.2.21/swirl/man/rmatch_calls.Rd |only
swirl-2.2.21/swirl/man/skip.Rd | 3
swirl-2.2.21/swirl/man/submit.Rd | 3
swirl-2.2.21/swirl/man/swirl.Rd | 3
swirl-2.2.21/swirl/man/uninstall_all_courses.Rd |only
swirl-2.2.21/swirl/man/uninstall_course.Rd | 4
swirl-2.2.21/swirl/man/val_has_length.Rd | 3
swirl-2.2.21/swirl/man/val_matches.Rd | 3
swirl-2.2.21/swirl/man/var_is_a.Rd | 3
swirl-2.2.21/swirl/man/zip_course.Rd | 4
swirl-2.2.21/swirl/tests/testthat/test-rmatch_calls.R |only
49 files changed, 285 insertions(+), 94 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Diff between markovchain versions 0.0.9.5 dated 2014-06-20 and 0.1.0 dated 2015-01-04
Description: The package contains classes and method to create and manage (plot, print, export for example) discrete time Markov chains (DTMC). In addition it provide functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis.
Author: Giorgio Alfredo Spedicato
Maintainer: Giorgio Alfredo Spedicato
markovchain-0.0.9.5/markovchain/R/classesAndMethods.R |only
markovchain-0.0.9.5/markovchain/R/functions4Fitting.R |only
markovchain-0.0.9.5/markovchain/R/probabilistic.R |only
markovchain-0.1.0/markovchain/ChangeLog | 6
markovchain-0.1.0/markovchain/DESCRIPTION | 13
markovchain-0.1.0/markovchain/MD5 | 41
markovchain-0.1.0/markovchain/NEWS | 7
markovchain-0.1.0/markovchain/R/0_classesAndMethods.R |only
markovchain-0.1.0/markovchain/R/1_functions4Fitting.R |only
markovchain-0.1.0/markovchain/R/2_probabilistic.R |only
markovchain-0.1.0/markovchain/build/vignette.rds |binary
markovchain-0.1.0/markovchain/data/blanden.rda |binary
markovchain-0.1.0/markovchain/data/craigsendi.rda |binary
markovchain-0.1.0/markovchain/data/holson.rda |only
markovchain-0.1.0/markovchain/data/preproglucacon.rda |binary
markovchain-0.1.0/markovchain/data/rain.rda |binary
markovchain-0.1.0/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 128 +-
markovchain-0.1.0/markovchain/inst/doc/an_introduction_to_markovchain_package.Rnw | 109 +-
markovchain-0.1.0/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary
markovchain-0.1.0/markovchain/man/holson.Rd |only
markovchain-0.1.0/markovchain/man/markovchain-package.Rd | 9
markovchain-0.1.0/markovchain/man/markovchainFit.Rd | 6
markovchain-0.1.0/markovchain/man/markovchainListFit.Rd |only
markovchain-0.1.0/markovchain/tests |only
markovchain-0.1.0/markovchain/vignettes/an_introduction_to_markovchain_package.Rnw | 109 +-
markovchain-0.1.0/markovchain/vignettes/markovchainBiblio.bib | 541 +++++-----
26 files changed, 530 insertions(+), 439 deletions(-)
Title: Chinese Text Segmentation
Diff between jiebaR versions 0.3 dated 2014-12-01 and 0.4 dated 2015-01-04
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng
jiebaR-0.3/jiebaR/inst/dict |only
jiebaR-0.3/jiebaR/inst/include/DictTrie.hpp |only
jiebaR-0.3/jiebaR/inst/include/FullSegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/HMMSegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/ISegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/KeywordExtractor.hpp |only
jiebaR-0.3/jiebaR/inst/include/Limonp |only
jiebaR-0.3/jiebaR/inst/include/MPSegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/MixSegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/PosTagger.hpp |only
jiebaR-0.3/jiebaR/inst/include/QuerySegment.hpp |only
jiebaR-0.3/jiebaR/inst/include/SegmentBase.hpp |only
jiebaR-0.3/jiebaR/inst/include/Simhasher.hpp |only
jiebaR-0.3/jiebaR/inst/include/TransCode.hpp |only
jiebaR-0.3/jiebaR/inst/include/Trie.hpp |only
jiebaR-0.3/jiebaR/inst/include/hashes |only
jiebaR-0.4/jiebaR/DESCRIPTION | 12
jiebaR-0.4/jiebaR/LICENSE | 4
jiebaR-0.4/jiebaR/MD5 | 130 ++---
jiebaR-0.4/jiebaR/NAMESPACE | 4
jiebaR-0.4/jiebaR/NEWS | 7
jiebaR-0.4/jiebaR/R/RcppExports.R | 68 +++
jiebaR-0.4/jiebaR/R/jiebaR-package.r | 4
jiebaR-0.4/jiebaR/R/jiebar.R | 20
jiebaR-0.4/jiebaR/R/keywords.R | 8
jiebaR-0.4/jiebaR/R/overload.R | 8
jiebaR-0.4/jiebaR/R/quick.R | 42 -
jiebaR-0.4/jiebaR/R/segment.R | 10
jiebaR-0.4/jiebaR/R/simhash.R | 15
jiebaR-0.4/jiebaR/R/tagger.R | 9
jiebaR-0.4/jiebaR/R/tools.R | 41 +
jiebaR-0.4/jiebaR/R/zzz.R | 34 -
jiebaR-0.4/jiebaR/README.md | 44 +
jiebaR-0.4/jiebaR/inst/doc/Quick_Start_Guide.html | 2
jiebaR-0.4/jiebaR/inst/include/jiebaR.h |only
jiebaR-0.4/jiebaR/inst/include/lib |only
jiebaR-0.4/jiebaR/inst/include/segtype.hpp |only
jiebaR-0.4/jiebaR/man/DICTPATH.Rd | 3
jiebaR-0.4/jiebaR/man/distance.Rd | 5
jiebaR-0.4/jiebaR/man/edit_dict.Rd | 21
jiebaR-0.4/jiebaR/man/filecoding.Rd | 3
jiebaR-0.4/jiebaR/man/jiebaR.Rd | 7
jiebaR-0.4/jiebaR/man/keywords.Rd | 5
jiebaR-0.4/jiebaR/man/less-than-equals-.keywords.Rd | 5
jiebaR-0.4/jiebaR/man/less-than-equals-.qseg.Rd | 5
jiebaR-0.4/jiebaR/man/less-than-equals-.segment.Rd | 5
jiebaR-0.4/jiebaR/man/less-than-equals-.simhash.Rd | 5
jiebaR-0.4/jiebaR/man/less-than-equals-.tagger.Rd | 5
jiebaR-0.4/jiebaR/man/print.hmmseg.Rd | 3
jiebaR-0.4/jiebaR/man/segment.Rd | 3
jiebaR-0.4/jiebaR/man/set_qsegmodel.Rd | 5
jiebaR-0.4/jiebaR/man/show_dictpath.Rd | 3
jiebaR-0.4/jiebaR/man/simhash.Rd | 5
jiebaR-0.4/jiebaR/man/tagging.Rd | 5
jiebaR-0.4/jiebaR/man/worker.Rd | 7
jiebaR-0.4/jiebaR/src/RcppExports.cpp | 283 ++++++++++++
jiebaR-0.4/jiebaR/src/segtype.cpp | 441 ++++----------------
jiebaR-0.4/jiebaR/vignettes/mystyle.css | 2
58 files changed, 740 insertions(+), 548 deletions(-)
Title: Boost C++ Header Files
Diff between BH versions 1.55.0-1 dated 2014-12-21 and 1.55.0-2 dated 2015-01-04
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel
ChangeLog | 7
DESCRIPTION | 11
MD5 | 188 +++++++++-
README.md | 5
inst/NEWS.Rd | 14
inst/include/boost/fusion/adapted.hpp |only
inst/include/boost/fusion/adapted/adt.hpp |only
inst/include/boost/fusion/adapted/adt/adapt_adt_named.hpp |only
inst/include/boost/fusion/adapted/adt/adapt_assoc_adt.hpp |only
inst/include/boost/fusion/adapted/adt/adapt_assoc_adt_named.hpp |only
inst/include/boost/fusion/adapted/boost_tuple |only
inst/include/boost/fusion/adapted/boost_tuple.hpp |only
inst/include/boost/fusion/adapted/std_tuple |only
inst/include/boost/fusion/adapted/std_tuple.hpp |only
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inst/include/boost/fusion/algorithm/auxiliary/move.hpp |only
inst/include/boost/fusion/container/map/detail/map_index.hpp |only
inst/include/boost/fusion/functional.hpp |only
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inst/include/boost/fusion/functional/adapter/fused_procedure.hpp |only
inst/include/boost/fusion/functional/adapter/limits.hpp |only
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inst/include/boost/fusion/functional/adapter/unfused_typed.hpp |only
inst/include/boost/fusion/functional/generation.hpp |only
inst/include/boost/fusion/functional/generation/make_fused_function_object.hpp |only
inst/include/boost/fusion/functional/generation/make_fused_procedure.hpp |only
inst/include/boost/fusion/functional/generation/make_unfused.hpp |only
inst/include/boost/fusion/functional/invocation.hpp |only
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inst/include/boost/fusion/include/accumulate.hpp |only
inst/include/boost/fusion/include/adapt_adt_named.cpp |only
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inst/include/boost/fusion/include/pair_tie.hpp |only
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inst/include/boost/fusion/sequence/intrinsic/swap.hpp |only
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inst/include/boost/tr1/memory.hpp |only
man/BH-package.Rd | 12
159 files changed, 226 insertions(+), 11 deletions(-)
More information about AnglerCreelSurveySimulation at CRAN
Permanent link
Title: Applied Geochemistry EDA
Diff between rgr versions 1.1.9 dated 2013-03-18 and 1.1.10 dated 2015-01-03
Description: Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot for concentration-area plots employs package akima, however, akima is only licensed for not-for-profit use. Therefore, not-for-profit users of rgr will have to independently make package akima available through library(akima); and use of function caplot by for-profit users will fail.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett
rgr-1.1.10/rgr/DESCRIPTION | 23 -
rgr-1.1.10/rgr/MD5 | 258 +++++++++++-----------
rgr-1.1.10/rgr/NAMESPACE | 4
rgr-1.1.10/rgr/R/ad.plot1.R | 25 +-
rgr-1.1.10/rgr/R/ad.plot3.R |only
rgr-1.1.10/rgr/R/ad.plot4.R |only
rgr-1.1.10/rgr/R/alts2dups.R |only
rgr-1.1.10/rgr/R/caplot.R | 2
rgr-1.1.10/rgr/R/crm.plot.new.R |only
rgr-1.1.10/rgr/R/df.test.R | 18 -
rgr-1.1.10/rgr/R/gx.2dproj.R | 80 ++++--
rgr-1.1.10/rgr/R/gx.2dproj.plot.R | 13 -
rgr-1.1.10/rgr/R/gx.hist.R | 3
rgr-1.1.10/rgr/R/gx.mva.R | 2
rgr-1.1.10/rgr/R/gx.mva.closed.R | 2
rgr-1.1.10/rgr/R/gx.robmva.R | 10
rgr-1.1.10/rgr/R/gx.robmva.closed.R | 8
rgr-1.1.10/rgr/R/gx.rqpca.plot.R | 19 +
rgr-1.1.10/rgr/R/gx.summary.mat.R | 15 +
rgr-1.1.10/rgr/R/inset.R | 6
rgr-1.1.10/rgr/R/inset.exporter.R | 2
rgr-1.1.10/rgr/R/ltdl.fix.R | 15 -
rgr-1.1.10/rgr/R/ltdl.fix.df.R | 13 -
rgr-1.1.10/rgr/R/thplot1.R | 8
rgr-1.1.10/rgr/data/ad.test.rda |binary
rgr-1.1.10/rgr/data/crm.test.new.rda |only
rgr-1.1.10/rgr/data/crm.test.rda |binary
rgr-1.1.10/rgr/data/fix.test.asis.rda |binary
rgr-1.1.10/rgr/data/fix.test.rda |binary
rgr-1.1.10/rgr/data/kola.c.rda |binary
rgr-1.1.10/rgr/data/kola.o.rda |binary
rgr-1.1.10/rgr/data/ms.data1.rda |binary
rgr-1.1.10/rgr/data/ms.data2.rda |binary
rgr-1.1.10/rgr/data/ms.data3.rda |binary
rgr-1.1.10/rgr/data/ogrady.mat2open.rda |binary
rgr-1.1.10/rgr/data/ogrady.rda |binary
rgr-1.1.10/rgr/data/sind.mat2open.rda |binary
rgr-1.1.10/rgr/data/sind.rda |binary
rgr-1.1.10/rgr/data/triples.test1.rda |binary
rgr-1.1.10/rgr/data/triples.test2.rda |binary
rgr-1.1.10/rgr/inst/doc/What_is_in_rgr_1-1-10.pdf |only
rgr-1.1.10/rgr/inst/doc/rgr_Overview_1-1-10.pdf |only
rgr-1.1.10/rgr/inst/doc/rgr_func_list_1-1-10.pdf |only
rgr-1.1.10/rgr/man/ad.plot1.Rd | 14 -
rgr-1.1.10/rgr/man/ad.plot2.Rd | 8
rgr-1.1.10/rgr/man/ad.plot3.Rd |only
rgr-1.1.10/rgr/man/ad.plot4.Rd |only
rgr-1.1.10/rgr/man/ad.test.Rd | 2
rgr-1.1.10/rgr/man/alr.Rd | 8
rgr-1.1.10/rgr/man/alts2dups.Rd |only
rgr-1.1.10/rgr/man/anova1.Rd | 2
rgr-1.1.10/rgr/man/anova2.Rd | 2
rgr-1.1.10/rgr/man/bwplots.Rd | 11
rgr-1.1.10/rgr/man/bwplots.by.var.Rd | 7
rgr-1.1.10/rgr/man/bxplot.Rd | 4
rgr-1.1.10/rgr/man/caplot.Rd | 10
rgr-1.1.10/rgr/man/cat2list.Rd | 2
rgr-1.1.10/rgr/man/clr.Rd | 8
rgr-1.1.10/rgr/man/cnpplt.Rd | 13 -
rgr-1.1.10/rgr/man/crm.plot.Rd | 2
rgr-1.1.10/rgr/man/crm.plot.new.Rd |only
rgr-1.1.10/rgr/man/crm.test.new.Rd |only
rgr-1.1.10/rgr/man/fences.summary.Rd | 2
rgr-1.1.10/rgr/man/fix.test.asis.Rd | 2
rgr-1.1.10/rgr/man/framework.summary.Rd | 6
rgr-1.1.10/rgr/man/gx.2dproj.Rd | 39 ++-
rgr-1.1.10/rgr/man/gx.2dproj.plot.Rd | 45 +++
rgr-1.1.10/rgr/man/gx.add.chisq.Rd | 4
rgr-1.1.10/rgr/man/gx.cnpplts.Rd | 11
rgr-1.1.10/rgr/man/gx.cnpplts.setup.Rd | 2
rgr-1.1.10/rgr/man/gx.ecdf.Rd | 15 +
rgr-1.1.10/rgr/man/gx.fractile.Rd | 2
rgr-1.1.10/rgr/man/gx.hist.Rd | 4
rgr-1.1.10/rgr/man/gx.md.gait.Rd | 30 +-
rgr-1.1.10/rgr/man/gx.md.gait.closed.Rd | 26 +-
rgr-1.1.10/rgr/man/gx.md.plot.Rd | 2
rgr-1.1.10/rgr/man/gx.md.print.Rd | 2
rgr-1.1.10/rgr/man/gx.mva.Rd | 46 +--
rgr-1.1.10/rgr/man/gx.mva.closed.Rd | 42 +--
rgr-1.1.10/rgr/man/gx.mvalloc.Rd | 4
rgr-1.1.10/rgr/man/gx.mvalloc.closed.Rd | 4
rgr-1.1.10/rgr/man/gx.pairs4parts.Rd | 2
rgr-1.1.10/rgr/man/gx.pearson.Rd | 2
rgr-1.1.10/rgr/man/gx.plot2parts.Rd | 2
rgr-1.1.10/rgr/man/gx.quantile.Rd | 2
rgr-1.1.10/rgr/man/gx.robmva.Rd | 50 ++--
rgr-1.1.10/rgr/man/gx.robmva.closed.Rd | 56 ++--
rgr-1.1.10/rgr/man/gx.rotate.Rd | 2
rgr-1.1.10/rgr/man/gx.rqpca.loadplot.Rd | 2
rgr-1.1.10/rgr/man/gx.rqpca.plot.Rd | 41 +--
rgr-1.1.10/rgr/man/gx.rqpca.print.Rd | 2
rgr-1.1.10/rgr/man/gx.rqpca.screeplot.Rd | 2
rgr-1.1.10/rgr/man/gx.scores.Rd | 9
rgr-1.1.10/rgr/man/gx.sm.Rd | 2
rgr-1.1.10/rgr/man/gx.spearman.Rd | 2
rgr-1.1.10/rgr/man/gx.stats.Rd | 2
rgr-1.1.10/rgr/man/gx.subset.Rd | 5
rgr-1.1.10/rgr/man/gx.summary1.Rd | 2
rgr-1.1.10/rgr/man/gx.triples.aov.Rd | 2
rgr-1.1.10/rgr/man/gx.triples.fgx.Rd | 2
rgr-1.1.10/rgr/man/gx.vm.Rd | 4
rgr-1.1.10/rgr/man/ilr.Rd | 6
rgr-1.1.10/rgr/man/ilr.stab.Rd | 6
rgr-1.1.10/rgr/man/inset.Rd | 5
rgr-1.1.10/rgr/man/inset.exporter.Rd | 12 -
rgr-1.1.10/rgr/man/ltdl.fix.Rd | 30 +-
rgr-1.1.10/rgr/man/ltdl.fix.df.Rd | 22 +
rgr-1.1.10/rgr/man/map.eda7.Rd | 2
rgr-1.1.10/rgr/man/map.eda8.Rd | 2
rgr-1.1.10/rgr/man/map.tags.Rd | 2
rgr-1.1.10/rgr/man/map.z.Rd | 8
rgr-1.1.10/rgr/man/ms.data1.Rd | 2
rgr-1.1.10/rgr/man/ms.data2.Rd | 2
rgr-1.1.10/rgr/man/ms.data3.Rd | 2
rgr-1.1.10/rgr/man/ogrady.Rd | 4
rgr-1.1.10/rgr/man/ogrady.mat2open.Rd | 6
rgr-1.1.10/rgr/man/orthonorm.Rd | 4
rgr-1.1.10/rgr/man/rgr_1.1.10-package.Rd |only
rgr-1.1.10/rgr/man/rng.Rd | 4
rgr-1.1.10/rgr/man/shape.Rd | 6
rgr-1.1.10/rgr/man/sind.Rd | 2
rgr-1.1.10/rgr/man/sind.mat2open.Rd | 2
rgr-1.1.10/rgr/man/syms.Rd | 10
rgr-1.1.10/rgr/man/tbplots.Rd | 4
rgr-1.1.10/rgr/man/tbplots.by.var.Rd | 4
rgr-1.1.10/rgr/man/thplot1.Rd | 4
rgr-1.1.10/rgr/man/thplot2.Rd | 4
rgr-1.1.10/rgr/man/triples.test1.Rd | 2
rgr-1.1.10/rgr/man/triples.test2.Rd | 2
rgr-1.1.10/rgr/man/var2fact.Rd | 6
rgr-1.1.10/rgr/man/wtd.sums.Rd | 12 -
rgr-1.1.10/rgr/man/xyplot.eda7.Rd | 2
rgr-1.1.10/rgr/man/xyplot.eda8.Rd | 2
rgr-1.1.10/rgr/man/xyplot.tags.Rd | 2
rgr-1.1.10/rgr/man/xyplot.z.Rd | 8
rgr-1.1.9/rgr/inst/doc/What_is_in_rgr_1-1-9.pdf |only
rgr-1.1.9/rgr/inst/doc/rgr_Overview_1-1-9.pdf |only
rgr-1.1.9/rgr/inst/doc/rgr_func_list_1-1-9.pdf |only
rgr-1.1.9/rgr/man/rgr_1.1.9-package.Rd |only
139 files changed, 732 insertions(+), 559 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Diff between lifecontingencies versions 1.1 dated 2014-05-01 and 1.1.5 dated 2015-01-03
More information about lifecontingencies at CRAN
Description: The package contains classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato with contributions from Reinhold Kainhofer and Kevin J. Owens
Maintainer: Giorgio Alfredo Spedicato
lifecontingencies-1.1.5/lifecontingencies/ChangeLog | 5
lifecontingencies-1.1.5/lifecontingencies/DESCRIPTION | 20
lifecontingencies-1.1.5/lifecontingencies/MD5 | 60 -
lifecontingencies-1.1.5/lifecontingencies/NAMESPACE | 7
lifecontingencies-1.1.5/lifecontingencies/NEWS | 8
lifecontingencies-1.1.5/lifecontingencies/R/0_lifetableAndActuarialtableClassesAndMethods.R |only
lifecontingencies-1.1.5/lifecontingencies/R/1_mdtClassesAndMethods.R |only
lifecontingencies-1.1.5/lifecontingencies/R/2_commonMethods.R |only
lifecontingencies-1.1.5/lifecontingencies/R/3_demographicFunctions.R |only
lifecontingencies-1.1.5/lifecontingencies/R/4_financialFunctions.R |only
lifecontingencies-1.1.5/lifecontingencies/R/5_actuarialFunctions.R |only
lifecontingencies-1.1.5/lifecontingencies/R/6_randomGenerationFunctions.R |only
lifecontingencies-1.1.5/lifecontingencies/R/7_tomarkovchain.R |only
lifecontingencies-1.1.5/lifecontingencies/R/8_mdtFunctions.R |only
lifecontingencies-1.1.5/lifecontingencies/build/vignette.rds |binary
lifecontingencies-1.1.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary
lifecontingencies-1.1.5/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.R | 13
lifecontingencies-1.1.5/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.Rnw | 48 -
lifecontingencies-1.1.5/lifecontingencies/man/actuarialtable-class.Rd | 16
lifecontingencies-1.1.5/lifecontingencies/man/lifecontingencies-package.Rd | 4
lifecontingencies-1.1.5/lifecontingencies/man/lifetable-class.Rd | 26
lifecontingencies-1.1.5/lifecontingencies/man/rmdt.Rd |only
lifecontingencies-1.1.5/lifecontingencies/tests |only
lifecontingencies-1.1.5/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 331 +++++-----
lifecontingencies-1.1.5/lifecontingencies/vignettes/multiple_decrements_with_lifecontingencies_package.Rnw | 48 -
lifecontingencies-1.1/lifecontingencies/R/actuarialFunctions.R |only
lifecontingencies-1.1/lifecontingencies/R/commonMethods.R |only
lifecontingencies-1.1/lifecontingencies/R/demographicFunctions.R |only
lifecontingencies-1.1/lifecontingencies/R/financialFunctions.R |only
lifecontingencies-1.1/lifecontingencies/R/lifetableAndActuarialtableClassesAndMethods.R |only
lifecontingencies-1.1/lifecontingencies/R/mdtClassesAndMethods.R |only
lifecontingencies-1.1/lifecontingencies/R/mdtFunctions.R |only
lifecontingencies-1.1/lifecontingencies/R/randomGenerationFunctions.R |only
lifecontingencies-1.1/lifecontingencies/R/tomarkovchain.R |only
lifecontingencies-1.1/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.R |only
lifecontingencies-1.1/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.Rnw |only
lifecontingencies-1.1/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.pdf |only
lifecontingencies-1.1/lifecontingencies/man/coerce-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/getOmega-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/head-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/plot-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/print-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/show-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/man/tail-methods.Rd |only
lifecontingencies-1.1/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package-figBalanceDue.pdf |only
lifecontingencies-1.1/lifecontingencies/vignettes/lifecontingencies_numerical_checks.Rnw |only
46 files changed, 325 insertions(+), 261 deletions(-)
Permanent link
Title: A Package for Coincidence Analysis (CNA)
Diff between cna versions 1.0-1 dated 2014-12-12 and 1.0-2 dated 2015-01-03
Description: Provides functions for performing Coincidence Analysis (CNA).
Author: Ambuehl, Mathias, Michael Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem
Maintainer: Alexis Kauffmann
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
inst/ChangeLog | 8 ++++++--
man/cna.Rd | 45 ++++++++++++++++++++++++---------------------
man/cna.package.Rd | 4 ++--
man/condition.Rd | 4 ++--
man/truthTab.Rd | 4 ++--
7 files changed, 46 insertions(+), 39 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.1 dated 2014-12-19 and 0.1.2 dated 2015-01-03
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"
DESCRIPTION | 6
MD5 | 31
NEWS | 12
R/print.ztable.html.R | 55
R/ztable.R | 525 +++++-
R/zzz.R | 8
inst/doc/ztable.R | 44
inst/doc/ztable.Rmd | 76
inst/doc/ztable.html | 4092 ++++++++++++++++++++++++++++++++++++-------------
man/data2table.Rd |only
man/make.cell.color.Rd |only
man/print_ztable.Rd | 5
man/repColor.Rd |only
man/tableLength.Rd |only
man/update_ztable.Rd |only
man/ztable2html.Rd | 4
man/ztable2latex.Rd | 4
man/ztable_sub.Rd | 54
vignettes/ztable.Rmd | 76
19 files changed, 3797 insertions(+), 1195 deletions(-)
Title: Dunn's Test Of Multiple Comparisons Using Rank Sums
Diff between dunn.test versions 1.2.1 dated 2014-12-10 and 1.2.2 dated 2015-01-03
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/dunn.test.R | 4 ++--
man/dunn.test.Rd | 3 ++-
4 files changed, 11 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-10 0.1.17.8
2014-09-16 0.1.17.3
2014-08-10 0.1.16.17
2014-06-11 0.1.16.12
2014-04-30 0.1.16.2
2014-03-11 0.1.15.1
2014-02-09 0.1.11.3
2014-01-08 0.1.9
2013-12-09 0.1.7
2013-12-09 0.1.8
2013-10-10 0.1.6
2013-09-10 0.1.5
2013-08-05 0.1.4
2013-07-02 0.1.2
2013-06-11 0.1.1
2013-06-07 0.1.0
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Diff between rNOMADS versions 2.1.0 dated 2015-01-01 and 2.1.1 dated 2015-01-03
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
NAMESPACE | 3 ++-
NEWS | 3 +++
R/GetDODS.R | 4 ++--
5 files changed, 17 insertions(+), 13 deletions(-)
Title: Calculate textures from grey-level co-occurrence matrices
(GLCMs) in R
Diff between glcm versions 1.0 dated 2014-09-26 and 1.2 dated 2015-01-03
Description: Enables calculation of image textures derived from grey-level
co-occurrence matrices (GLCMs) in R. Supports processing images that cannot
fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
NAMESPACE | 2 +-
NEWS | 4 ++++
man/L5TSR_1986.Rd | 3 ++-
man/calc_texture.Rd | 3 ++-
man/expected_textures_3x3_1x1.Rd | 3 ++-
man/expected_textures_5x3_n1xn2.Rd | 3 ++-
man/expected_textures_5x7_2x3.Rd | 3 ++-
man/glcm-package.Rd | 3 ++-
man/glcm.Rd | 3 ++-
man/test_raster.Rd | 3 ++-
src/calc_texture.cpp | 8 ++++----
tests/testthat/test-glcm.R | 3 +++
14 files changed, 46 insertions(+), 31 deletions(-)
Title: General Copula Theory and Many Utility Functions
Diff between copBasic versions 1.6.0 dated 2014-09-26 and 1.7.0 dated 2015-01-03
Description: Extensive functions for copula computations and related mathematical operations are given that are oriented around the oft cited and fundamental copula theory described by Nelsen (2006), Joe (2015), and other selected works. The lower, upper, product, and select other copulas are implemented. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, co-copula, and numerical copula density. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses; functions for copula simulation thus are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) random variates of composited copulas. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma, tail dependency, and tail order. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. The Kullback-Leibler divergence and Vuong's Procedure to support inference are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith
ChangeLog | 223 ++++++++++++++++++++++++--------------
DESCRIPTION | 13 +-
MD5 | 180 +++++++++++++++++-------------
NAMESPACE | 17 ++
R/EMPIRcop.R | 31 +++--
R/FRECHETcop.R |only
R/GHcop.R |only
R/PLACKETTcop.R | 10 -
R/PLACKETTpar.R | 40 ++++--
R/blomCOP.R | 24 +++-
R/densityCOP.R |only
R/densityCOPplot.R |only
R/derCOPinv.R | 20 ---
R/derCOPinv2.R | 17 --
R/diagCOPatf.R |only
R/hoefCOP.R | 104 ++++++++++++++++-
R/isCOP.PQD.R | 10 -
R/isCOP.permsym.R |only
R/kullCOP.R |only
R/lcomCOPpv.R |only
R/rhoCOP.R | 52 +++-----
R/semicorCOP.R |only
R/simCOP.R | 39 +++++-
R/taildepCOP.R | 19 +--
R/tailordCOP.R |only
R/tauCOP.R | 4
R/uvlmoms.R |only
R/vuongCOP.R |only
man/COP.Rd | 4
man/COPinv.Rd | 4
man/COPinv2.Rd | 4
man/EMPIRcop.Rd | 20 ++-
man/EMPIRcopdf.Rd | 5
man/EMPIRgrid.Rd | 9 -
man/EMPIRgridder.Rd | 1
man/EMPIRgridder2.Rd | 1
man/EMPIRgridderinv.Rd | 1
man/EMPIRgridderinv2.Rd | 1
man/EMPIRsim.Rd | 24 ++--
man/EMPIRsimv.Rd | 3
man/FRECHETcop.Rd |only
man/GHcop.Rd |only
man/M.Rd | 7 -
man/N4212cop.Rd | 6 -
man/P.Rd | 28 +++-
man/PLACKETTcop.Rd | 53 ++++++++-
man/PLACKETTpar.Rd | 66 ++++++++++-
man/PLACKETTsim.Rd | 4
man/PSP.Rd | 4
man/PlackettPlackettABKGtest.Rd | 6 -
man/PlackettPlackettNP.Rd | 6 -
man/W.Rd | 7 -
man/asCOP.Rd | 74 +++++++++++-
man/blomCOP.Rd | 48 +++++++-
man/coCOP.Rd | 12 --
man/composite1COP.Rd | 5
man/composite2COP.Rd | 9 -
man/composite3COP.Rd | 9 -
man/copBasic-package.Rd | 74 +++++++++---
man/densityCOP.Rd |only
man/densityCOPplot.Rd |only
man/derCOP.Rd | 7 -
man/derCOP2.Rd | 7 -
man/derCOPinv.Rd | 5
man/derCOPinv2.Rd | 5
man/diagCOP.Rd | 8 -
man/diagCOPatf.Rd |only
man/duCOP.Rd | 10 +
man/giniCOP.Rd | 16 +-
man/gridCOP.Rd | 7 +
man/hoefCOP.Rd | 75 +++++++++++-
man/isCOP.LTD.Rd | 23 +--
man/isCOP.PQD.Rd | 10 -
man/isCOP.RTI.Rd | 18 +--
man/isCOP.permsym.Rd |only
man/isCOP.radsym.Rd | 71 +++++++++++-
man/kullCOP.Rd |only
man/lcomCOPpv.Rd |only
man/lcomoms2.ABKGcop2parameter.Rd | 3
man/lcomoms2.ABcop2parameter.Rd | 12 +-
man/level.curvesCOP.Rd | 4
man/level.curvesCOP2.Rd | 4
man/level.setCOP.Rd | 8 -
man/level.setCOP2.Rd | 4
man/med.regressCOP.Rd | 6 -
man/med.regressCOP2.Rd | 7 -
man/qua.regressCOP.Rd | 8 -
man/qua.regressCOP.draw.Rd | 4
man/qua.regressCOP2.Rd | 4
man/rhoCOP.Rd | 53 +++++++--
man/sectionCOP.Rd | 9 -
man/semicorCOP.Rd |only
man/simCOP.Rd | 21 ++-
man/simCOPmicro.Rd | 4
man/simcompositeCOP.Rd | 4
man/surCOP.Rd | 8 -
man/surfuncCOP.Rd | 4
man/taildepCOP.Rd | 55 ++++++---
man/tailordCOP.Rd |only
man/tauCOP.Rd | 23 ++-
man/uvlmoms.Rd |only
man/vuongCOP.Rd |only
man/wolfCOP.Rd | 17 +-
103 files changed, 1266 insertions(+), 556 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 6.0-37 dated 2014-11-10 and 6.0-41 dated 2015-01-03
Description: Misc functions for training and plotting classification and
regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, and Luca Scrucca.
Maintainer: Max Kuhn
caret-6.0-37/caret/R/specificty.R |only
caret-6.0-41/caret/DESCRIPTION | 15
caret-6.0-41/caret/MD5 | 119 -
caret-6.0-41/caret/NAMESPACE | 40
caret-6.0-41/caret/R/BoxCoxTrans.R | 4
caret-6.0-41/caret/R/aaa.R | 37
caret-6.0-41/caret/R/avNNet.R | 18
caret-6.0-41/caret/R/bag.R | 10
caret-6.0-41/caret/R/bagEarth.R | 8
caret-6.0-41/caret/R/bagFDA.R | 8
caret-6.0-41/caret/R/common_code.R |only
caret-6.0-41/caret/R/confusionMatrix.R | 2
caret-6.0-41/caret/R/createModel.R | 48
caret-6.0-41/caret/R/expoTrans.R | 4
caret-6.0-41/caret/R/featurePlot.R | 2
caret-6.0-41/caret/R/findCorrelation.R | 90 -
caret-6.0-41/caret/R/gafs.R |only
caret-6.0-41/caret/R/getTrainPerf.R | 6
caret-6.0-41/caret/R/misc.R | 81
caret-6.0-41/caret/R/pcaNNet.R | 23
caret-6.0-41/caret/R/plsda.R | 16
caret-6.0-41/caret/R/postResample.R | 2
caret-6.0-41/caret/R/preProcess.R | 22
caret-6.0-41/caret/R/print.train.R | 3
caret-6.0-41/caret/R/reg_sims.R | 2
caret-6.0-41/caret/R/resamples.R | 1309 +++++++--------
caret-6.0-41/caret/R/safs.R |only
caret-6.0-41/caret/R/selectByFilter.R | 2
caret-6.0-41/caret/R/selection.R | 8
caret-6.0-41/caret/R/specificity.R |only
caret-6.0-41/caret/R/splsda.R | 20
caret-6.0-41/caret/R/train.default.R | 2
caret-6.0-41/caret/R/twoClassSim.R | 2
caret-6.0-41/caret/R/varImp.R | 4
caret-6.0-41/caret/inst/NEWS.Rd | 23
caret-6.0-41/caret/inst/doc/caret.Rnw | 30
caret-6.0-41/caret/inst/doc/caret.pdf |binary
caret-6.0-41/caret/inst/models/models.RData |binary
caret-6.0-41/caret/man/avNNet.Rd | 6
caret-6.0-41/caret/man/createDataPartition.Rd | 2
caret-6.0-41/caret/man/diff.resamples.Rd | 2
caret-6.0-41/caret/man/downSample.Rd | 2
caret-6.0-41/caret/man/dummyVars.Rd | 4
caret-6.0-41/caret/man/format.bagEarth.Rd | 4
caret-6.0-41/caret/man/ga_functions.Rd |only
caret-6.0-41/caret/man/gafs.default.Rd |only
caret-6.0-41/caret/man/index2vec.Rd |only
caret-6.0-41/caret/man/lattice.resamples.Rd | 2
caret-6.0-41/caret/man/mdrr.Rd | 2
caret-6.0-41/caret/man/models.Rd | 717 +++++---
caret-6.0-41/caret/man/plot.gafs.Rd |only
caret-6.0-41/caret/man/prcomp.resamples.Rd | 2
caret-6.0-41/caret/man/predict.bagEarth.Rd | 6
caret-6.0-41/caret/man/predict.gafs.Rd |only
caret-6.0-41/caret/man/print.train.Rd | 12
caret-6.0-41/caret/man/resamples.Rd | 2
caret-6.0-41/caret/man/sa_functions.Rd |only
caret-6.0-41/caret/man/safs.default.Rd |only
caret-6.0-41/caret/man/safsControl.Rd |only
caret-6.0-41/caret/man/sbf.Rd | 2
caret-6.0-41/caret/man/selection.Rd | 2
caret-6.0-41/caret/man/summary.bagEarth.Rd | 2
caret-6.0-41/caret/man/train.Rd | 6
caret-6.0-41/caret/man/twoClassSim.Rd | 6
caret-6.0-41/caret/man/update.safs.Rd |only
caret-6.0-41/caret/man/varImp.gafs.Rd |only
caret-6.0-41/caret/tests/testthat/test_models_bagEarth.R |only
caret-6.0-41/caret/vignettes/caret.Rnw | 30
caret-6.0-41/caret/vignettes/train_algo.pdf |only
69 files changed, 1523 insertions(+), 1248 deletions(-)
Title: vcd Extensions and Additions
Diff between vcdExtra versions 0.6-3 dated 2014-10-31 and 0.6-5 dated 2015-01-02
Description: Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data
and the gnm package for Generalized Nonlinear Models.
In particular, vcdExtra extends mosaic, assoc and sieve plots from vcd to handle glm() and gnm() models and
adds a 3D version in mosaic3d. Additionally, methods are provided for comparing and visualizing lists of
glm and loglm objects.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly
DESCRIPTION | 17
MD5 | 106 +--
NAMESPACE | 5
NEWS | 10
R/LRstats.R |only
R/collapse.table.R | 5
R/vcdExtra-deprecated.R |only
build/vignette.rds |binary
data/Abortion.rda |binary
data/Accident.RData |binary
data/Alligator.RData |binary
data/Bartlett.rda |binary
data/Caesar.rda |binary
data/Cancer.rda |binary
data/Cormorants.RData |only
data/CyclingDeaths.RData |binary
data/DaytonSurvey.RData |binary
data/Depends.RData |binary
data/Detergent.rda |binary
data/Donner.RData |binary
data/Draft1970.RData |binary
data/Draft1970table.RData |binary
data/Dyke.rda |binary
data/Fungicide.rda |binary
data/GSS.rda |binary
data/Geissler.RData |binary
data/Gilby.rda |binary
data/HairEyePlace.RData |binary
data/Hauser79.RData |binary
data/Heart.rda |binary
data/Heckman.rda |binary
data/Hoyt.rda |binary
data/ICU.RData |binary
data/JobSat.rda |binary
data/Mammograms.RData |binary
data/Mental.rda |binary
data/Mobility.rda |binary
data/PhdPubs.RData |binary
data/ShakeWords.RData |binary
data/TV.rda |binary
data/Titanicp.rda |binary
data/Toxaemia.RData |binary
data/Vietnam.RData |binary
data/Vietnam.rda |binary
data/Vote1980.RData |binary
data/Yamaguchi87.RData |binary
inst/doc/vcd-tutorial.R | 1524 ++++++++++++++++++++++-----------------------
inst/doc/vcd-tutorial.Rnw | 2
man/Cormorants.Rd |only
man/HairEyePlace.Rd | 2
man/LRstats.Rd |only
man/TV.Rd | 10
man/collapse.table.Rd | 8
man/cutfac.Rd | 39 -
man/vcdExtra-deprecated.Rd |only
man/vcdExtra-package.Rd | 4
vignettes/vcd-tutorial.Rnw | 2
57 files changed, 889 insertions(+), 845 deletions(-)
Title: Estimating birth and death rates based on phylogenies
Diff between TreePar versions 3.2 dated 2014-11-08 and 3.3 dated 2015-01-02
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
man/LikAge.Rd | 37 ++++++++++++++++++-------------------
man/LikShifts.Rd | 9 ++++++---
man/TreePar-package.Rd | 4 ++--
man/bd.age.optim.matlab.Rd | 41 ++++++++++++++++++++---------------------
man/bd.densdep.optim.Rd | 6 ++++--
man/create.mat.Rd | 20 ++++++++++----------
8 files changed, 71 insertions(+), 68 deletions(-)
Title: Lazy (Non-Standard) Evaluation
Diff between lazyeval versions 0.1.9 dated 2014-10-01 and 0.1.10 dated 2015-01-02
Description: A disciplined approach to non-standard evaluation.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 8 ++---
MD5 | 40 +++++++++++++------------
NAMESPACE | 3 +
R/as-lazy.R | 5 +++
R/names.R | 4 ++
build/vignette.rds |binary
inst/doc/benchmark.html | 8 ++---
inst/doc/chained-promises.html | 6 +--
inst/doc/lazyeval.html | 64 ++++++++++++++++++++---------------------
man/all_dots.Rd | 3 +
man/as.lazy.Rd | 3 +
man/auto_name.Rd | 3 +
man/common_env.Rd | 3 +
man/interp.Rd | 3 +
man/lazy_.Rd | 3 +
man/lazy_dots.Rd | 3 +
man/lazy_eval.Rd | 3 +
man/make_call.Rd | 3 +
man/missing_arg.Rd | 3 +
src/lazy.c | 4 +-
tests |only
21 files changed, 98 insertions(+), 74 deletions(-)
Title: Imputation of Missing Values Through a Forward Imputation
Algorithm
Diff between ForImp versions 1.0.2 dated 2013-01-31 and 1.0.3 dated 2015-01-02
Description: Imputation of missing values in datasets of ordinal variables through a forward imputation algorithm
Author: Alessandro Barbiero, Pier Alda Ferrari, Giancarlo Manzi
Maintainer: Alessandro Barbiero
ForImp-1.0.2/ForImp/doc |only
ForImp-1.0.3/ForImp/DESCRIPTION | 16 ++++++++--------
ForImp-1.0.3/ForImp/MD5 | 9 ++++-----
ForImp-1.0.3/ForImp/NAMESPACE | 1 +
ForImp-1.0.3/ForImp/man/ForImp.Rd | 2 --
ForImp-1.0.3/ForImp/man/missingmat2.Rd | 4 ++--
6 files changed, 15 insertions(+), 17 deletions(-)
Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server
(CGDS).
Diff between cgdsr versions 1.1.32 dated 2014-12-19 and 1.1.33 dated 2015-01-02
Description: Provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen Skanderup
Maintainer: Anders Jacobsen Skanderup
ChangeLog | 5 +++++
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/cgdsr.R | 2 +-
inst/doc/cgdsr.pdf |binary
5 files changed, 15 insertions(+), 10 deletions(-)
Title: Mixture Models for Clustering and Classification
Diff between mixture versions 1.2 dated 2014-12-27 and 1.3 dated 2015-01-02
Description: An implementation of all 14 Gaussian parsimonious
clustering models (GPCMs) for model-based clustering and
model-based classification.
Author: Ryan P. Browne, Aisha ElSherbiny and Paul D. McNicholas
Maintainer: Ryan Browne
DESCRIPTION | 6 -
MD5 | 12 +-
R/mixture.R | 262 +++++++++++++++++++++++++++++-----------------------------
man/e.step.Rd | 2
man/gpcm.Rd | 45 ++++-----
man/m.step.Rd | 7 -
src/Makevars | 2
7 files changed, 167 insertions(+), 169 deletions(-)
Title: Bayesian Non- and Semi-parametric Model Fitting
Diff between BNSP versions 1.0.1 dated 2014-11-03 and 1.0.2 dated 2015-01-02
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/BNSP-package.Rd | 2 +-
man/bnpglm.Rd | 2 +-
5 files changed, 13 insertions(+), 10 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Diff between rNOMADS versions 2.0.4 dated 2014-10-30 and 2.1.0 dated 2015-01-01
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman
DESCRIPTION | 16 +-
MD5 | 18 +--
NAMESPACE | 1
NEWS | 5
R/GetArchiveGrib.R | 4
R/Models.R | 228 +++++++++++++++---------------------------
man/DODSGrab.Rd | 2
man/GetClosestGFSForecasts.Rd | 5
man/NOMADSRealTimeList.Rd | 12 +-
man/ParseModelPage.Rd | 7 -
10 files changed, 129 insertions(+), 169 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Diff between rvest versions 0.1.0 dated 2014-11-21 and 0.2.0 dated 2015-01-01
Description: Wrappers around the XML and httr packages to make it easy to
download, then manipulate, both html and xml.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 18 ++++++----
MD5 | 66 +++++++++++++++++++++------------------
NAMESPACE | 26 +++++++++++----
R/form.R | 37 ++++++++++++++++++----
R/html.R | 67 +++++++++++++---------------------------
R/parse.R |only
R/selectors.R | 8 ++--
R/session.R | 57 ++++++++++++++++------------------
R/structure.R |only
R/table.R | 10 ++---
R/utils.R | 19 ++++-------
R/xml.R |only
README.md | 2 +
build/vignette.rds |binary
demo/zillow.R | 6 +--
inst/doc/selectorgadget.html | 18 +++++++---
man/encoding.Rd | 3 +
man/google_form.Rd | 3 +
man/html.Rd | 9 ++++-
man/html_form.Rd | 3 +
man/html_nodes.Rd | 5 +-
man/html_session.Rd | 6 +--
man/html_table.Rd | 11 +++---
man/html_text.Rd | 8 +++-
man/jump_to.Rd | 13 +++++--
man/minimal_html.Rd | 3 +
man/pipe.Rd | 3 +
man/pluck.Rd | 3 +
man/scrape.Rd | 3 +
man/session_history.Rd | 3 +
man/set_values.Rd | 3 +
man/submit_form.Rd | 3 +
man/xml.Rd |only
man/xml_structure.Rd |only
tests/testthat/test-forms.R | 9 +++++
tests/testthat/test-selectors.R | 7 ++++
tests/testthat/test-tables.R |only
37 files changed, 254 insertions(+), 178 deletions(-)
Title: Multiscale Bernstein Polynomials for Densities
Diff between msBP versions 1.0-2 dated 2014-12-23 and 1.0-2.1 dated 2015-01-01
Description: Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2014).
Author: Antonio Canale
Maintainer: Antonio Canale
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/auxGibbs.cpp | 6 +++---
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Write Storm Bolts in R using the Storm Multi-Language Protocol.
Diff between Storm versions 1.1 dated 2014-05-22 and 1.2 dated 2015-01-01
Description: Storm is a distributed real-time computation system. Similar to how
Hadoop provides a set of general primitives for doing batch processing, Storm
provides a set of general primitives for doing real-time computation.
Storm includes a "Multi-Language" (or "Multilang") Protocol to allow
implementation of Bolts and Spouts in languages other than Java. This R
extension provides implementations of utility functions to allow an application
developer to focus on application-specific functionality rather than Storm/R
communications plumbing.
Author: Allen Day
Maintainer: Allen Day
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
NAMESPACE | 3 ++-
R/Storm.R | 16 +++++-----------
man/Storm-package.Rd | 12 +++++-------
5 files changed, 22 insertions(+), 29 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Diff between ore versions 1.0.4 dated 2014-11-25 and 1.0.6 dated 2015-01-01
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
DESCRIPTION | 9
LICENCE | 2
MD5 | 22 -
NEWS | 19 +
R/match.R | 80 +-----
R/ore.R | 36 ---
README.md | 7
man/ore.ismatch.Rd | 4
man/ore.search.Rd | 2
man/ore.subst.Rd | 6
src/main.c | 621 ++++++++++++++++++++++++++++++++++++++++++++---------
src/main.h | 46 ++-
12 files changed, 613 insertions(+), 241 deletions(-)
Title: Tools for Working with URLs and HTTP
Diff between httr versions 0.6.0 dated 2014-12-13 and 0.6.1 dated 2015-01-01
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [cre, aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 6 ++--
MD5 | 18 +++++++-------
R/content.r | 2 -
R/perform.R | 2 -
R/timeout.r | 5 +++
demo/oauth2-linkedin.r | 14 ++++++++++-
inst/doc/api-packages.html | 8 +++---
inst/doc/quickstart.html | 54 +++++++++++++++++++++----------------------
man/timeout.Rd | 3 +-
tests/testthat/test-header.r | 10 +++++++
10 files changed, 75 insertions(+), 47 deletions(-)
Title: Graphical Analysis of Variance Using ggplot2
Diff between granovaGG versions 1.2 dated 2012-09-04 and 1.3 dated 2015-01-01
Description: This collection of functions in granovaGG
provides what we call elemental graphics for display of
anova results. The term elemental derives from the fact
that each function is aimed at construction of
graphical displays that afford direct visualizations of
data with respect to the fundamental questions that
drive the particular anova methods. This package
represents a modification of the original granova
package; the key change is to use ggplot2, Hadley
Wickham's package based on Grammar of Graphics concepts
(due to Wilkinson). The main function is granovagg.1w
(a graphic for one way anova); two other functions
(granovagg.ds and granovagg.contr) are to construct
graphics for dependent sample analyses and
contrast-based analyses respectively. (The function
granova.2w, which entails dynamic displays of data, is
not currently part of granovaGG.) The granovaGG
functions are to display data for any number of groups,
regardless of their sizes (however, very large data
sets or numbers of groups can be problematic). For
granovagg.1w a specialized approach is used to
construct data-based contrast vectors for which anova
data are displayed. The result is that the graphics use
a straight line to facilitate clear interpretations
while being faithful to the standard effect test in
anova. The graphic results are complementary to
standard summary tables; indeed, numerical summary
statistics are provided as side effects of the graphic
constructions. granovagg.ds and granovagg.contr provide
graphic displays and numerical outputs for a dependent
sample and contrast-based analyses. The graphics based
on these functions can be especially helpful for
learning how the respective methods work to answer the
basic question(s) that drive the analyses. This means
they can be particularly helpful for students and
non-statistician analysts. But these methods can be of
assistance for work-a-day applications of many kinds,
as they can help to identify outliers, clusters or
patterns, as well as highlight the role of non-linear
transformations of data. In the case of granovagg.1w
and granovagg.ds several arguments are provided to
facilitate flexibility in the construction of graphics
that accommodate diverse features of data, according to
their corresponding display requirements. See the help
files for individual functions.
Author: Brian A. Danielak
Maintainer: Brian A. Danielak
granovaGG-1.2/granovaGG/README.markdown |only
granovaGG-1.3/granovaGG/DESCRIPTION | 109 ++++---
granovaGG-1.3/granovaGG/MD5 | 37 +-
granovaGG-1.3/granovaGG/NAMESPACE | 2
granovaGG-1.3/granovaGG/R/granovagg.1w-helpers.R | 37 +-
granovaGG-1.3/granovaGG/R/granovagg.1w.R | 327 +++++++++++++----------
granovaGG-1.3/granovaGG/R/granovagg.contr.R | 111 ++++---
granovaGG-1.3/granovaGG/R/granovagg.ds.R | 193 +++++++------
granovaGG-1.3/granovaGG/demo/granovagg.ds.R | 13
granovaGG-1.3/granovaGG/inst/CITATION | 8
granovaGG-1.3/granovaGG/man/anorexia.sub.Rd | 18 -
granovaGG-1.3/granovaGG/man/arousal.Rd | 13
granovaGG-1.3/granovaGG/man/blood_lead.Rd | 25 -
granovaGG-1.3/granovaGG/man/granovaGG-package.Rd | 114 ++++----
granovaGG-1.3/granovaGG/man/granovagg.1w.Rd | 245 +++++++----------
granovaGG-1.3/granovaGG/man/granovagg.contr.Rd | 216 ++++++---------
granovaGG-1.3/granovaGG/man/granovagg.ds.Rd | 184 +++++-------
granovaGG-1.3/granovaGG/man/poison.Rd | 20 -
granovaGG-1.3/granovaGG/man/rat.Rd | 17 -
granovaGG-1.3/granovaGG/man/tobacco.Rd | 34 +-
20 files changed, 887 insertions(+), 836 deletions(-)
Title: Creates a Model Matrix via Feature Hashing With a Formula
Interface
Diff between FeatureHashing versions 0.7 dated 2014-12-21 and 0.8 dated 2015-01-01
More information about FeatureHashing at CRAN
Description: Feature hashing, also called as the hashing trick, is a method to
transform features to vector. Without looking up the indices in an
associative array, it applies a hash function to the features and uses their
hash values as indices directly. The method of feature hashing in this package
was proposed in Weinberger et. al. (2009). The hashing algorithm is the murmurhash3
from the digest package. Please see the README.md for more information.
Author: Wush Wu [aut, cre]
Maintainer: Wush Wu
FeatureHashing-0.7/FeatureHashing/src/MurmurHash3.cpp |only
FeatureHashing-0.7/FeatureHashing/src/MurmurHash3.h |only
FeatureHashing-0.7/FeatureHashing/tests/test-conver-to-dgCMatrix.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-hashed.model.matrix.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-hashing_result.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-interaction_name.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-merge.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-missing.R |only
FeatureHashing-0.7/FeatureHashing/tests/test-pair_sort.R |only
FeatureHashing-0.8/FeatureHashing/Changelog |only
FeatureHashing-0.8/FeatureHashing/DESCRIPTION | 32 +--
FeatureHashing-0.8/FeatureHashing/MD5 | 44 ++---
FeatureHashing-0.8/FeatureHashing/NAMESPACE | 3
FeatureHashing-0.8/FeatureHashing/R/zzz.R | 4
FeatureHashing-0.8/FeatureHashing/README.md | 88 +++++-----
FeatureHashing-0.8/FeatureHashing/inst |only
FeatureHashing-0.8/FeatureHashing/man/CSCMatrix-class.Rd | 2
FeatureHashing-0.8/FeatureHashing/man/hashed.model.matrix.Rd | 6
FeatureHashing-0.8/FeatureHashing/man/tag.Rd | 2
FeatureHashing-0.8/FeatureHashing/man/test.tag.Rd | 2
FeatureHashing-0.8/FeatureHashing/src/digest.c |only
FeatureHashing-0.8/FeatureHashing/src/digestlocal.h |only
FeatureHashing-0.8/FeatureHashing/src/hash_internal.cpp | 6
FeatureHashing-0.8/FeatureHashing/src/hashed_model_matrix.cpp | 39 +++-
FeatureHashing-0.8/FeatureHashing/tests/test-as-dgCMatrix.R |only
FeatureHashing-0.8/FeatureHashing/tests/test-hashing.R |only
FeatureHashing-0.8/FeatureHashing/tests/test-interpret.tag.R | 7
FeatureHashing-0.8/FeatureHashing/tests/test-memcheck.R |only
FeatureHashing-0.8/FeatureHashing/tests/test-product.R | 13 +
FeatureHashing-0.8/FeatureHashing/tests/test-subsetting.R | 58 +++---
FeatureHashing-0.8/FeatureHashing/tests/test-transpose.R | 4
31 files changed, 180 insertions(+), 130 deletions(-)
Permanent link
Title: Extensible Package for Cross-Validation-Based Integration of
Base Learners
Diff between EnsembleCV versions 0.7 dated 2014-11-25 and 0.7.1 dated 2015-01-01
Description: This package extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 5 +++--
man/ecv.save.Rd | 2 ++
4 files changed, 9 insertions(+), 6 deletions(-)